Multiple sequence alignment - TraesCS2A01G385800

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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 TraesCS2A01G385800 chr2A 100.000 2828 0 0 1 2828 631842897 631845724 0.000000e+00 5223.0
1 TraesCS2A01G385800 chr2B 91.565 1233 51 20 791 1979 571335823 571337046 0.000000e+00 1652.0
2 TraesCS2A01G385800 chr2B 86.707 835 74 11 2011 2828 571338588 571339402 0.000000e+00 893.0
3 TraesCS2A01G385800 chr2B 87.086 573 48 10 1 559 442567261 442567821 2.390000e-175 625.0
4 TraesCS2A01G385800 chr2B 81.583 695 121 6 2076 2767 224215476 224214786 4.090000e-158 568.0
5 TraesCS2A01G385800 chr2B 77.419 248 44 7 1480 1727 538957317 538957082 1.370000e-28 137.0
6 TraesCS2A01G385800 chr2B 95.000 40 2 0 522 561 442567820 442567859 2.350000e-06 63.9
7 TraesCS2A01G385800 chr2D 97.332 787 21 0 944 1730 486335704 486336490 0.000000e+00 1338.0
8 TraesCS2A01G385800 chr2D 89.290 803 70 1 2042 2828 486345540 486346342 0.000000e+00 992.0
9 TraesCS2A01G385800 chr2D 81.439 695 124 4 2076 2768 175758345 175757654 5.290000e-157 564.0
10 TraesCS2A01G385800 chr2D 89.443 341 23 7 1722 2050 486337681 486338020 4.360000e-113 418.0
11 TraesCS2A01G385800 chr5A 93.761 577 21 8 1 563 438335279 438335854 0.000000e+00 852.0
12 TraesCS2A01G385800 chr5A 88.485 165 7 5 584 736 438335835 438335999 3.720000e-44 189.0
13 TraesCS2A01G385800 chr5A 85.714 175 11 3 584 744 591743985 591744159 3.750000e-39 172.0
14 TraesCS2A01G385800 chr4B 93.565 575 25 6 1 563 334073392 334073966 0.000000e+00 846.0
15 TraesCS2A01G385800 chr4B 88.485 165 7 1 584 736 334073947 334074111 3.720000e-44 189.0
16 TraesCS2A01G385800 chr4B 85.802 162 10 6 584 733 471882220 471882380 2.920000e-35 159.0
17 TraesCS2A01G385800 chr4B 85.455 165 11 3 584 736 471910391 471910554 2.920000e-35 159.0
18 TraesCS2A01G385800 chr3B 92.870 575 29 6 1 563 171081685 171082259 0.000000e+00 824.0
19 TraesCS2A01G385800 chr3B 88.485 165 7 1 584 736 171082240 171082404 3.720000e-44 189.0
20 TraesCS2A01G385800 chr7B 92.857 574 24 4 1 563 79936388 79936955 0.000000e+00 817.0
21 TraesCS2A01G385800 chr7B 96.386 83 3 0 654 736 79937007 79937089 1.370000e-28 137.0
22 TraesCS2A01G385800 chr4D 91.812 574 29 8 5 563 209902838 209903408 0.000000e+00 784.0
23 TraesCS2A01G385800 chr4D 84.409 186 13 5 584 753 209903389 209903574 4.850000e-38 169.0
24 TraesCS2A01G385800 chr1B 88.927 587 36 13 1 563 13035279 13035860 0.000000e+00 697.0
25 TraesCS2A01G385800 chr1B 80.065 306 38 11 2541 2827 70239758 70239457 3.690000e-49 206.0
26 TraesCS2A01G385800 chr7A 89.043 575 39 6 1 563 640963068 640962506 0.000000e+00 691.0
27 TraesCS2A01G385800 chr7A 85.799 169 10 3 587 741 640962522 640962354 1.740000e-37 167.0
28 TraesCS2A01G385800 chr6B 87.413 572 55 7 5 561 452566995 452567564 2.380000e-180 641.0
29 TraesCS2A01G385800 chr1A 89.270 466 36 6 8 459 356315743 356315278 3.160000e-159 571.0
30 TraesCS2A01G385800 chr1A 94.737 57 3 0 507 563 356315257 356315201 3.880000e-14 89.8
31 TraesCS2A01G385800 chr5B 87.879 396 29 8 185 563 537771274 537771667 5.560000e-122 448.0
32 TraesCS2A01G385800 chr5B 90.533 169 13 3 2602 2767 590256776 590256944 1.320000e-53 220.0
33 TraesCS2A01G385800 chr7D 87.425 167 8 2 587 740 182826243 182826077 2.240000e-41 180.0
34 TraesCS2A01G385800 chr1D 92.647 68 5 0 496 563 451984942 451985009 6.450000e-17 99.0
35 TraesCS2A01G385800 chr4A 93.023 43 3 0 2014 2056 572307101 572307143 2.350000e-06 63.9
36 TraesCS2A01G385800 chr6A 94.737 38 2 0 2014 2051 53925011 53924974 3.040000e-05 60.2


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 TraesCS2A01G385800 chr2A 631842897 631845724 2827 False 5223.00 5223 100.0000 1 2828 1 chr2A.!!$F1 2827
1 TraesCS2A01G385800 chr2B 571335823 571339402 3579 False 1272.50 1652 89.1360 791 2828 2 chr2B.!!$F2 2037
2 TraesCS2A01G385800 chr2B 224214786 224215476 690 True 568.00 568 81.5830 2076 2767 1 chr2B.!!$R1 691
3 TraesCS2A01G385800 chr2B 442567261 442567859 598 False 344.45 625 91.0430 1 561 2 chr2B.!!$F1 560
4 TraesCS2A01G385800 chr2D 486345540 486346342 802 False 992.00 992 89.2900 2042 2828 1 chr2D.!!$F1 786
5 TraesCS2A01G385800 chr2D 486335704 486338020 2316 False 878.00 1338 93.3875 944 2050 2 chr2D.!!$F2 1106
6 TraesCS2A01G385800 chr2D 175757654 175758345 691 True 564.00 564 81.4390 2076 2768 1 chr2D.!!$R1 692
7 TraesCS2A01G385800 chr5A 438335279 438335999 720 False 520.50 852 91.1230 1 736 2 chr5A.!!$F2 735
8 TraesCS2A01G385800 chr4B 334073392 334074111 719 False 517.50 846 91.0250 1 736 2 chr4B.!!$F3 735
9 TraesCS2A01G385800 chr3B 171081685 171082404 719 False 506.50 824 90.6775 1 736 2 chr3B.!!$F1 735
10 TraesCS2A01G385800 chr7B 79936388 79937089 701 False 477.00 817 94.6215 1 736 2 chr7B.!!$F1 735
11 TraesCS2A01G385800 chr4D 209902838 209903574 736 False 476.50 784 88.1105 5 753 2 chr4D.!!$F1 748
12 TraesCS2A01G385800 chr1B 13035279 13035860 581 False 697.00 697 88.9270 1 563 1 chr1B.!!$F1 562
13 TraesCS2A01G385800 chr7A 640962354 640963068 714 True 429.00 691 87.4210 1 741 2 chr7A.!!$R1 740
14 TraesCS2A01G385800 chr6B 452566995 452567564 569 False 641.00 641 87.4130 5 561 1 chr6B.!!$F1 556
15 TraesCS2A01G385800 chr1A 356315201 356315743 542 True 330.40 571 92.0035 8 563 2 chr1A.!!$R1 555

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
574 645 0.114364 ACTTCCCTTCCCCGCAAAAT 59.886 50.0 0.0 0.0 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2534 5372 0.187117 TTCCTGTTTGCCCATGGTCA 59.813 50.0 11.73 0.0 0.0 4.02 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
190 194 1.539827 GGGCGTTTGCTTGTAATCTGT 59.460 47.619 0.00 0.00 42.25 3.41
257 263 3.381333 CTCAGGCTCGGCTGATGCA 62.381 63.158 21.25 0.00 41.91 3.96
400 413 8.807948 TTCTTATTTCCTGGTTTATCCTTGAG 57.192 34.615 0.00 0.00 37.07 3.02
434 460 8.597662 ATTGTTCTGTCATTTCTGAATTTTGG 57.402 30.769 0.00 0.00 31.85 3.28
563 634 5.393866 TCTAAGAAATTTGGCACTTCCCTT 58.606 37.500 0.00 0.00 0.00 3.95
564 635 4.607293 AAGAAATTTGGCACTTCCCTTC 57.393 40.909 0.00 0.00 0.00 3.46
565 636 2.899900 AGAAATTTGGCACTTCCCTTCC 59.100 45.455 0.00 0.00 0.00 3.46
566 637 1.644509 AATTTGGCACTTCCCTTCCC 58.355 50.000 0.00 0.00 0.00 3.97
567 638 0.252239 ATTTGGCACTTCCCTTCCCC 60.252 55.000 0.00 0.00 0.00 4.81
568 639 2.706952 TTTGGCACTTCCCTTCCCCG 62.707 60.000 0.00 0.00 0.00 5.73
570 641 4.344865 GCACTTCCCTTCCCCGCA 62.345 66.667 0.00 0.00 0.00 5.69
571 642 2.434331 CACTTCCCTTCCCCGCAA 59.566 61.111 0.00 0.00 0.00 4.85
572 643 1.228429 CACTTCCCTTCCCCGCAAA 60.228 57.895 0.00 0.00 0.00 3.68
573 644 0.825840 CACTTCCCTTCCCCGCAAAA 60.826 55.000 0.00 0.00 0.00 2.44
574 645 0.114364 ACTTCCCTTCCCCGCAAAAT 59.886 50.000 0.00 0.00 0.00 1.82
575 646 1.356398 ACTTCCCTTCCCCGCAAAATA 59.644 47.619 0.00 0.00 0.00 1.40
576 647 2.225167 ACTTCCCTTCCCCGCAAAATAA 60.225 45.455 0.00 0.00 0.00 1.40
577 648 2.606751 TCCCTTCCCCGCAAAATAAA 57.393 45.000 0.00 0.00 0.00 1.40
578 649 2.890814 TCCCTTCCCCGCAAAATAAAA 58.109 42.857 0.00 0.00 0.00 1.52
579 650 3.240302 TCCCTTCCCCGCAAAATAAAAA 58.760 40.909 0.00 0.00 0.00 1.94
580 651 3.841255 TCCCTTCCCCGCAAAATAAAAAT 59.159 39.130 0.00 0.00 0.00 1.82
581 652 5.024118 TCCCTTCCCCGCAAAATAAAAATA 58.976 37.500 0.00 0.00 0.00 1.40
582 653 5.484290 TCCCTTCCCCGCAAAATAAAAATAA 59.516 36.000 0.00 0.00 0.00 1.40
583 654 6.013639 TCCCTTCCCCGCAAAATAAAAATAAA 60.014 34.615 0.00 0.00 0.00 1.40
584 655 6.655425 CCCTTCCCCGCAAAATAAAAATAAAA 59.345 34.615 0.00 0.00 0.00 1.52
585 656 7.175119 CCCTTCCCCGCAAAATAAAAATAAAAA 59.825 33.333 0.00 0.00 0.00 1.94
644 715 2.036733 CCCTTGTCTCCAAACTCACGTA 59.963 50.000 0.00 0.00 0.00 3.57
685 768 1.686236 ATGACCATGGAAAGTCCCCT 58.314 50.000 21.47 0.00 35.03 4.79
736 819 0.396060 TTTGCAACCAAATGAGGCCC 59.604 50.000 0.00 0.00 36.09 5.80
737 820 0.762082 TTGCAACCAAATGAGGCCCA 60.762 50.000 0.00 0.00 0.00 5.36
741 824 1.693606 CAACCAAATGAGGCCCAAGTT 59.306 47.619 0.00 0.00 0.00 2.66
742 825 1.341080 ACCAAATGAGGCCCAAGTTG 58.659 50.000 0.00 3.51 0.00 3.16
743 826 1.341080 CCAAATGAGGCCCAAGTTGT 58.659 50.000 12.76 0.00 0.00 3.32
744 827 1.001181 CCAAATGAGGCCCAAGTTGTG 59.999 52.381 12.76 0.00 0.00 3.33
753 836 3.678921 CCAAGTTGTGGTCACTCGA 57.321 52.632 1.45 0.00 43.20 4.04
754 837 1.217882 CCAAGTTGTGGTCACTCGAC 58.782 55.000 1.45 0.00 43.20 4.20
755 838 1.472552 CCAAGTTGTGGTCACTCGACA 60.473 52.381 1.45 0.00 44.54 4.35
756 839 1.593006 CAAGTTGTGGTCACTCGACAC 59.407 52.381 2.66 0.00 44.54 3.67
757 840 0.248907 AGTTGTGGTCACTCGACACG 60.249 55.000 2.66 0.00 44.54 4.49
758 841 0.526954 GTTGTGGTCACTCGACACGT 60.527 55.000 2.66 0.00 44.54 4.49
759 842 0.248743 TTGTGGTCACTCGACACGTC 60.249 55.000 2.66 0.00 44.54 4.34
760 843 1.371389 GTGGTCACTCGACACGTCC 60.371 63.158 0.00 0.00 44.54 4.79
761 844 1.824760 TGGTCACTCGACACGTCCA 60.825 57.895 0.00 0.00 44.54 4.02
762 845 1.361271 GGTCACTCGACACGTCCAA 59.639 57.895 0.00 0.00 44.54 3.53
763 846 0.249155 GGTCACTCGACACGTCCAAA 60.249 55.000 0.00 0.00 44.54 3.28
764 847 1.563111 GTCACTCGACACGTCCAAAA 58.437 50.000 0.00 0.00 42.13 2.44
765 848 1.928503 GTCACTCGACACGTCCAAAAA 59.071 47.619 0.00 0.00 42.13 1.94
766 849 2.034001 GTCACTCGACACGTCCAAAAAG 60.034 50.000 0.00 0.00 42.13 2.27
767 850 0.935196 ACTCGACACGTCCAAAAAGC 59.065 50.000 0.00 0.00 0.00 3.51
768 851 0.934496 CTCGACACGTCCAAAAAGCA 59.066 50.000 0.00 0.00 0.00 3.91
769 852 1.329292 CTCGACACGTCCAAAAAGCAA 59.671 47.619 0.00 0.00 0.00 3.91
770 853 1.944024 TCGACACGTCCAAAAAGCAAT 59.056 42.857 0.00 0.00 0.00 3.56
771 854 2.032377 TCGACACGTCCAAAAAGCAATC 60.032 45.455 0.00 0.00 0.00 2.67
772 855 2.307049 GACACGTCCAAAAAGCAATCG 58.693 47.619 0.00 0.00 0.00 3.34
773 856 1.001815 ACACGTCCAAAAAGCAATCGG 60.002 47.619 0.00 0.00 0.00 4.18
774 857 1.265635 CACGTCCAAAAAGCAATCGGA 59.734 47.619 0.00 0.00 0.00 4.55
775 858 1.265905 ACGTCCAAAAAGCAATCGGAC 59.734 47.619 0.00 0.00 42.25 4.79
776 859 1.535462 CGTCCAAAAAGCAATCGGACT 59.465 47.619 0.00 0.00 43.27 3.85
777 860 2.665519 CGTCCAAAAAGCAATCGGACTG 60.666 50.000 0.00 0.00 43.27 3.51
778 861 1.269448 TCCAAAAAGCAATCGGACTGC 59.731 47.619 2.71 2.71 40.24 4.40
783 866 3.805267 GCAATCGGACTGCTCTGG 58.195 61.111 3.86 0.00 36.84 3.86
784 867 1.078848 GCAATCGGACTGCTCTGGT 60.079 57.895 3.86 0.00 36.84 4.00
785 868 0.175760 GCAATCGGACTGCTCTGGTA 59.824 55.000 3.86 0.00 36.84 3.25
786 869 1.405526 GCAATCGGACTGCTCTGGTAA 60.406 52.381 3.86 0.00 36.84 2.85
787 870 2.935238 GCAATCGGACTGCTCTGGTAAA 60.935 50.000 3.86 0.00 36.84 2.01
788 871 3.334691 CAATCGGACTGCTCTGGTAAAA 58.665 45.455 0.00 0.00 0.00 1.52
789 872 3.695830 ATCGGACTGCTCTGGTAAAAA 57.304 42.857 0.00 0.00 0.00 1.94
790 873 3.040147 TCGGACTGCTCTGGTAAAAAG 57.960 47.619 0.00 0.00 0.00 2.27
791 874 2.367567 TCGGACTGCTCTGGTAAAAAGT 59.632 45.455 0.00 0.00 0.00 2.66
792 875 2.737252 CGGACTGCTCTGGTAAAAAGTC 59.263 50.000 0.00 0.00 34.62 3.01
793 876 3.075148 GGACTGCTCTGGTAAAAAGTCC 58.925 50.000 4.06 4.06 44.90 3.85
794 877 3.740115 GACTGCTCTGGTAAAAAGTCCA 58.260 45.455 0.00 0.00 0.00 4.02
795 878 3.477530 ACTGCTCTGGTAAAAAGTCCAC 58.522 45.455 0.00 0.00 0.00 4.02
796 879 2.814336 CTGCTCTGGTAAAAAGTCCACC 59.186 50.000 0.00 0.00 0.00 4.61
797 880 1.804748 GCTCTGGTAAAAAGTCCACCG 59.195 52.381 0.00 0.00 34.94 4.94
798 881 2.549349 GCTCTGGTAAAAAGTCCACCGA 60.549 50.000 0.00 0.00 34.94 4.69
799 882 3.326747 CTCTGGTAAAAAGTCCACCGAG 58.673 50.000 0.00 0.00 34.94 4.63
800 883 2.701951 TCTGGTAAAAAGTCCACCGAGT 59.298 45.455 0.00 0.00 34.94 4.18
801 884 3.135167 TCTGGTAAAAAGTCCACCGAGTT 59.865 43.478 0.00 0.00 34.94 3.01
802 885 3.207778 TGGTAAAAAGTCCACCGAGTTG 58.792 45.455 0.00 0.00 34.94 3.16
827 910 2.020836 GAATCGGGCGCGTAACACAG 62.021 60.000 23.19 0.00 0.00 3.66
846 929 2.360350 CCACGGCCTGTCAGCAAT 60.360 61.111 0.00 0.00 0.00 3.56
851 934 0.813184 CGGCCTGTCAGCAATGAATT 59.187 50.000 0.00 0.00 0.00 2.17
852 935 1.202222 CGGCCTGTCAGCAATGAATTC 60.202 52.381 0.00 0.00 0.00 2.17
853 936 1.135721 GGCCTGTCAGCAATGAATTCC 59.864 52.381 2.27 0.00 0.00 3.01
862 945 6.183360 TGTCAGCAATGAATTCCTCTTGTTTT 60.183 34.615 2.27 0.00 0.00 2.43
879 962 5.123805 TGTTTTTAAATCAGGCGGGTAAC 57.876 39.130 0.00 0.00 0.00 2.50
884 967 0.398696 AATCAGGCGGGTAACACACA 59.601 50.000 0.00 0.00 39.74 3.72
890 973 1.067749 CGGGTAACACACACCACGA 59.932 57.895 0.00 0.00 37.84 4.35
891 974 1.216941 CGGGTAACACACACCACGAC 61.217 60.000 0.00 0.00 37.84 4.34
903 986 2.027192 ACACCACGACCTTATCTGCAAT 60.027 45.455 0.00 0.00 0.00 3.56
908 991 3.426859 CACGACCTTATCTGCAATCGATC 59.573 47.826 0.00 0.00 33.88 3.69
909 992 2.658802 CGACCTTATCTGCAATCGATCG 59.341 50.000 9.36 9.36 0.00 3.69
910 993 3.609409 CGACCTTATCTGCAATCGATCGA 60.609 47.826 21.86 21.86 0.00 3.59
911 994 4.489810 GACCTTATCTGCAATCGATCGAT 58.510 43.478 24.60 24.60 36.23 3.59
912 995 4.887748 ACCTTATCTGCAATCGATCGATT 58.112 39.130 32.29 32.29 44.73 3.34
913 996 6.025749 ACCTTATCTGCAATCGATCGATTA 57.974 37.500 35.65 23.94 42.30 1.75
914 997 6.634805 ACCTTATCTGCAATCGATCGATTAT 58.365 36.000 35.65 27.77 42.30 1.28
926 1009 8.523464 CAATCGATCGATTATTTGTTTCCAAAC 58.477 33.333 35.65 0.00 41.45 2.93
973 1080 0.309302 AAGACAGAGATCGATCCGCG 59.691 55.000 21.66 12.22 42.69 6.46
990 1097 0.938008 GCGCCTTTAGGATTTCGAGG 59.062 55.000 0.00 0.00 37.39 4.63
1071 1186 5.293569 GTCCATGGTAAACGAAGGAATAGTG 59.706 44.000 12.58 0.00 0.00 2.74
1084 1199 0.179045 AATAGTGGATCCGCACCTGC 60.179 55.000 26.71 1.66 37.78 4.85
1383 1498 1.065928 GTACCTGAGGACGATGCCG 59.934 63.158 4.99 0.00 42.50 5.69
1419 1534 2.559840 GAACTCGTCGACTCGGCA 59.440 61.111 14.70 0.00 0.00 5.69
1731 3045 1.073199 GTCTGGGTGGTGGAGGTTG 59.927 63.158 0.00 0.00 0.00 3.77
1773 3090 1.422269 CGGCGGAATAACACCAACG 59.578 57.895 0.00 0.00 0.00 4.10
1822 3139 0.529773 GGCGACGCATCCACATCTTA 60.530 55.000 23.09 0.00 0.00 2.10
1920 3242 0.730265 TCAGTTGTTCGCGTTTTGCT 59.270 45.000 5.77 0.00 43.27 3.91
1928 3250 2.314561 TCGCGTTTTGCTGATTCAAG 57.685 45.000 5.77 0.00 43.27 3.02
1936 3258 6.405216 CGTTTTGCTGATTCAAGTGAAAAAG 58.595 36.000 0.00 0.62 37.61 2.27
1944 3266 9.122613 GCTGATTCAAGTGAAAAAGAATAGTTC 57.877 33.333 0.00 0.00 37.61 3.01
1946 3268 8.289618 TGATTCAAGTGAAAAAGAATAGTTCCG 58.710 33.333 0.00 0.00 37.61 4.30
1971 3958 1.344763 ACAACTGTGGAGTACCTCTGC 59.655 52.381 0.00 0.00 37.04 4.26
2003 3991 8.110970 TGTTTGTAGTGACATATCGTAAATCG 57.889 34.615 0.00 0.00 34.86 3.34
2012 4000 0.650512 ATCGTAAATCGTTGCTGCCG 59.349 50.000 0.00 0.00 40.80 5.69
2018 4854 3.357166 AAATCGTTGCTGCCGTAAAAA 57.643 38.095 0.00 0.00 0.00 1.94
2059 4895 7.075741 ACGTACTTTTGGAAAAAGAATCATCG 58.924 34.615 17.05 12.98 0.00 3.84
2134 4970 1.120530 CTCGCTTGGTACCTGGGTAT 58.879 55.000 14.36 0.00 32.82 2.73
2154 4990 5.221843 GGTATGAGACATTAGCCCCAACATA 60.222 44.000 0.00 0.00 0.00 2.29
2160 4996 4.289245 ACATTAGCCCCAACATAGCATTT 58.711 39.130 0.00 0.00 0.00 2.32
2182 5018 2.366533 CGGCTCTAGTGGAGTACTTGA 58.633 52.381 5.32 0.00 43.62 3.02
2185 5021 4.017808 GGCTCTAGTGGAGTACTTGAAGA 58.982 47.826 5.32 0.00 43.62 2.87
2226 5062 7.106439 AGATGTTCTGTTATAGGAGAGTGTG 57.894 40.000 0.00 0.00 0.00 3.82
2240 5076 1.209019 GAGTGTGGCTGACTCCATCAT 59.791 52.381 5.46 0.00 38.57 2.45
2246 5082 2.225091 TGGCTGACTCCATCATTTGGTT 60.225 45.455 0.00 0.00 46.52 3.67
2305 5141 4.383602 CCGTCAAGTTTGCCGGCG 62.384 66.667 23.90 6.13 43.00 6.46
2310 5146 4.589675 AAGTTTGCCGGCGGGGAA 62.590 61.111 29.48 13.37 42.51 3.97
2322 5158 2.520968 GGGGAAGTGGTGCCAACT 59.479 61.111 0.00 0.00 40.26 3.16
2333 5169 0.102300 GTGCCAACTGCGGACTTTTT 59.898 50.000 0.00 0.00 45.60 1.94
2343 5179 1.468914 GCGGACTTTTTGTGGAGATCC 59.531 52.381 0.00 0.00 0.00 3.36
2355 5191 0.105453 GGAGATCCAGAGCCCCACTA 60.105 60.000 0.00 0.00 35.64 2.74
2363 5199 0.916358 AGAGCCCCACTACAATGCCT 60.916 55.000 0.00 0.00 0.00 4.75
2365 5201 0.409484 AGCCCCACTACAATGCCTTT 59.591 50.000 0.00 0.00 0.00 3.11
2405 5241 1.675552 CGGAACAAGTGTTGGACCTT 58.324 50.000 0.42 0.00 38.56 3.50
2410 5246 1.485066 ACAAGTGTTGGACCTTCGACT 59.515 47.619 0.00 0.00 34.12 4.18
2415 5251 0.250338 GTTGGACCTTCGACTGCCTT 60.250 55.000 0.00 0.00 0.00 4.35
2491 5328 8.865090 AGGAAGAAACTATCGATCATATTCTGT 58.135 33.333 0.00 0.60 0.00 3.41
2506 5344 6.765512 TCATATTCTGTTGACTTGTGTGTTCA 59.234 34.615 0.00 0.00 0.00 3.18
2534 5372 2.080693 TGTGTGAAGAACGTTGTGCTT 58.919 42.857 5.00 2.39 33.50 3.91
2536 5374 2.095213 GTGTGAAGAACGTTGTGCTTGA 59.905 45.455 5.00 0.00 30.49 3.02
2683 5522 2.343101 CTTCGGAAACATAGGAACGCA 58.657 47.619 0.00 0.00 0.00 5.24
2684 5523 2.004583 TCGGAAACATAGGAACGCAG 57.995 50.000 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.558226 AGAACAATATCACACTGGCTCA 57.442 40.909 0.00 0.00 0.00 4.26
190 194 6.647334 TGAATTAACAAAGCCATCAACTGA 57.353 33.333 0.00 0.00 0.00 3.41
462 490 9.755804 TTTCTTACAGAATCATCATAGCAGTAG 57.244 33.333 0.00 0.00 33.67 2.57
585 656 2.035832 CGACAGGGAAGTGCCAATTTTT 59.964 45.455 0.00 0.00 38.95 1.94
586 657 1.613437 CGACAGGGAAGTGCCAATTTT 59.387 47.619 0.00 0.00 38.95 1.82
587 658 1.247567 CGACAGGGAAGTGCCAATTT 58.752 50.000 0.00 0.00 38.95 1.82
588 659 0.110486 ACGACAGGGAAGTGCCAATT 59.890 50.000 0.00 0.00 38.95 2.32
589 660 0.606401 CACGACAGGGAAGTGCCAAT 60.606 55.000 0.00 0.00 38.95 3.16
590 661 1.227823 CACGACAGGGAAGTGCCAA 60.228 57.895 0.00 0.00 38.95 4.52
591 662 1.480212 ATCACGACAGGGAAGTGCCA 61.480 55.000 0.00 0.00 38.95 4.92
592 663 0.321653 AATCACGACAGGGAAGTGCC 60.322 55.000 0.00 0.00 35.97 5.01
593 664 1.079503 GAATCACGACAGGGAAGTGC 58.920 55.000 0.00 0.00 35.97 4.40
594 665 1.676014 GGGAATCACGACAGGGAAGTG 60.676 57.143 0.00 0.00 37.24 3.16
595 666 0.613777 GGGAATCACGACAGGGAAGT 59.386 55.000 0.00 0.00 30.96 3.01
596 667 0.905357 AGGGAATCACGACAGGGAAG 59.095 55.000 0.00 0.00 30.96 3.46
597 668 0.902531 GAGGGAATCACGACAGGGAA 59.097 55.000 0.00 0.00 30.96 3.97
598 669 0.976073 GGAGGGAATCACGACAGGGA 60.976 60.000 0.00 0.00 0.00 4.20
599 670 1.522569 GGAGGGAATCACGACAGGG 59.477 63.158 0.00 0.00 0.00 4.45
600 671 1.522569 GGGAGGGAATCACGACAGG 59.477 63.158 0.00 0.00 0.00 4.00
601 672 0.978146 AGGGGAGGGAATCACGACAG 60.978 60.000 0.00 0.00 28.88 3.51
602 673 0.976073 GAGGGGAGGGAATCACGACA 60.976 60.000 0.00 0.00 28.88 4.35
603 674 1.687297 GGAGGGGAGGGAATCACGAC 61.687 65.000 0.00 0.00 28.88 4.34
604 675 1.382695 GGAGGGGAGGGAATCACGA 60.383 63.158 0.00 0.00 28.88 4.35
644 715 2.178984 AGGAAATCCTCTCGAGATCCCT 59.821 50.000 22.62 15.95 44.77 4.20
685 768 2.112998 CCAGGGTAGTAATCCCACGAA 58.887 52.381 3.79 0.00 46.82 3.85
736 819 1.593006 GTGTCGAGTGACCACAACTTG 59.407 52.381 2.78 0.00 44.86 3.16
737 820 1.801395 CGTGTCGAGTGACCACAACTT 60.801 52.381 2.78 0.00 44.86 2.66
741 824 1.357690 GACGTGTCGAGTGACCACA 59.642 57.895 0.00 0.00 44.86 4.17
742 825 1.371389 GGACGTGTCGAGTGACCAC 60.371 63.158 0.00 0.00 44.86 4.16
743 826 1.385756 TTGGACGTGTCGAGTGACCA 61.386 55.000 0.00 0.00 44.86 4.02
744 827 0.249155 TTTGGACGTGTCGAGTGACC 60.249 55.000 0.00 0.00 44.86 4.02
745 828 1.563111 TTTTGGACGTGTCGAGTGAC 58.437 50.000 0.00 0.00 45.71 3.67
746 829 2.198406 CTTTTTGGACGTGTCGAGTGA 58.802 47.619 0.00 0.00 0.00 3.41
747 830 1.332904 GCTTTTTGGACGTGTCGAGTG 60.333 52.381 0.00 0.00 0.00 3.51
748 831 0.935196 GCTTTTTGGACGTGTCGAGT 59.065 50.000 0.00 0.00 0.00 4.18
749 832 0.934496 TGCTTTTTGGACGTGTCGAG 59.066 50.000 0.00 0.00 0.00 4.04
750 833 1.370609 TTGCTTTTTGGACGTGTCGA 58.629 45.000 0.00 0.00 0.00 4.20
751 834 2.307049 GATTGCTTTTTGGACGTGTCG 58.693 47.619 0.00 0.00 0.00 4.35
752 835 2.307049 CGATTGCTTTTTGGACGTGTC 58.693 47.619 0.00 0.00 0.00 3.67
753 836 1.001815 CCGATTGCTTTTTGGACGTGT 60.002 47.619 0.00 0.00 0.00 4.49
754 837 1.265635 TCCGATTGCTTTTTGGACGTG 59.734 47.619 0.00 0.00 0.00 4.49
755 838 1.265905 GTCCGATTGCTTTTTGGACGT 59.734 47.619 0.00 0.00 37.78 4.34
756 839 1.963747 GTCCGATTGCTTTTTGGACG 58.036 50.000 5.22 0.00 37.78 4.79
757 840 2.922335 GCAGTCCGATTGCTTTTTGGAC 60.922 50.000 8.55 10.75 44.81 4.02
758 841 1.269448 GCAGTCCGATTGCTTTTTGGA 59.731 47.619 8.55 0.00 38.51 3.53
759 842 1.701704 GCAGTCCGATTGCTTTTTGG 58.298 50.000 8.55 0.00 38.51 3.28
766 849 0.175760 TACCAGAGCAGTCCGATTGC 59.824 55.000 7.77 7.77 41.83 3.56
767 850 2.672961 TTACCAGAGCAGTCCGATTG 57.327 50.000 0.00 0.00 0.00 2.67
768 851 3.695830 TTTTACCAGAGCAGTCCGATT 57.304 42.857 0.00 0.00 0.00 3.34
769 852 3.008049 ACTTTTTACCAGAGCAGTCCGAT 59.992 43.478 0.00 0.00 0.00 4.18
770 853 2.367567 ACTTTTTACCAGAGCAGTCCGA 59.632 45.455 0.00 0.00 0.00 4.55
771 854 2.737252 GACTTTTTACCAGAGCAGTCCG 59.263 50.000 0.00 0.00 0.00 4.79
772 855 3.075148 GGACTTTTTACCAGAGCAGTCC 58.925 50.000 0.54 0.54 42.64 3.85
773 856 3.498777 GTGGACTTTTTACCAGAGCAGTC 59.501 47.826 0.00 0.00 36.82 3.51
774 857 3.477530 GTGGACTTTTTACCAGAGCAGT 58.522 45.455 0.00 0.00 36.82 4.40
775 858 2.814336 GGTGGACTTTTTACCAGAGCAG 59.186 50.000 0.00 0.00 36.82 4.24
776 859 2.808933 CGGTGGACTTTTTACCAGAGCA 60.809 50.000 0.00 0.00 36.82 4.26
777 860 1.804748 CGGTGGACTTTTTACCAGAGC 59.195 52.381 0.00 0.00 36.82 4.09
778 861 3.244112 ACTCGGTGGACTTTTTACCAGAG 60.244 47.826 0.00 0.00 39.14 3.35
779 862 2.701951 ACTCGGTGGACTTTTTACCAGA 59.298 45.455 0.00 0.00 36.82 3.86
780 863 3.121738 ACTCGGTGGACTTTTTACCAG 57.878 47.619 0.00 0.00 36.82 4.00
781 864 3.207778 CAACTCGGTGGACTTTTTACCA 58.792 45.455 0.00 0.00 34.10 3.25
782 865 3.208594 ACAACTCGGTGGACTTTTTACC 58.791 45.455 0.00 0.00 0.00 2.85
783 866 4.888038 AACAACTCGGTGGACTTTTTAC 57.112 40.909 0.00 0.00 0.00 2.01
784 867 5.447548 CGAAAACAACTCGGTGGACTTTTTA 60.448 40.000 0.00 0.00 32.62 1.52
785 868 4.673320 CGAAAACAACTCGGTGGACTTTTT 60.673 41.667 0.00 0.00 32.62 1.94
786 869 3.181504 CGAAAACAACTCGGTGGACTTTT 60.182 43.478 0.00 0.00 32.62 2.27
787 870 2.353579 CGAAAACAACTCGGTGGACTTT 59.646 45.455 0.00 0.00 32.62 2.66
788 871 1.937899 CGAAAACAACTCGGTGGACTT 59.062 47.619 0.00 0.00 32.62 3.01
789 872 1.137479 TCGAAAACAACTCGGTGGACT 59.863 47.619 0.00 0.00 36.93 3.85
790 873 1.574134 TCGAAAACAACTCGGTGGAC 58.426 50.000 0.00 0.00 36.93 4.02
791 874 2.312722 TTCGAAAACAACTCGGTGGA 57.687 45.000 0.00 0.00 36.93 4.02
792 875 2.411031 CGATTCGAAAACAACTCGGTGG 60.411 50.000 0.00 0.00 36.93 4.61
793 876 2.411031 CCGATTCGAAAACAACTCGGTG 60.411 50.000 21.69 3.76 40.47 4.94
794 877 1.796459 CCGATTCGAAAACAACTCGGT 59.204 47.619 21.69 0.00 40.47 4.69
795 878 1.127951 CCCGATTCGAAAACAACTCGG 59.872 52.381 22.60 22.60 43.93 4.63
796 879 1.463528 GCCCGATTCGAAAACAACTCG 60.464 52.381 7.83 5.73 37.66 4.18
797 880 1.463528 CGCCCGATTCGAAAACAACTC 60.464 52.381 7.83 0.00 0.00 3.01
798 881 0.515564 CGCCCGATTCGAAAACAACT 59.484 50.000 7.83 0.00 0.00 3.16
799 882 1.063412 GCGCCCGATTCGAAAACAAC 61.063 55.000 7.83 0.00 0.00 3.32
800 883 1.208103 GCGCCCGATTCGAAAACAA 59.792 52.632 7.83 0.00 0.00 2.83
801 884 2.864589 GCGCCCGATTCGAAAACA 59.135 55.556 7.83 0.00 0.00 2.83
802 885 1.685640 TACGCGCCCGATTCGAAAAC 61.686 55.000 5.73 0.00 38.29 2.43
846 929 7.872483 GCCTGATTTAAAAACAAGAGGAATTCA 59.128 33.333 7.93 0.00 0.00 2.57
851 934 4.217550 CCGCCTGATTTAAAAACAAGAGGA 59.782 41.667 9.69 0.00 0.00 3.71
852 935 4.485163 CCGCCTGATTTAAAAACAAGAGG 58.515 43.478 0.00 0.00 0.00 3.69
853 936 4.022329 ACCCGCCTGATTTAAAAACAAGAG 60.022 41.667 0.00 0.00 0.00 2.85
862 945 3.075884 GTGTGTTACCCGCCTGATTTAA 58.924 45.455 0.00 0.00 0.00 1.52
879 962 2.337583 CAGATAAGGTCGTGGTGTGTG 58.662 52.381 0.00 0.00 0.00 3.82
884 967 2.738643 CGATTGCAGATAAGGTCGTGGT 60.739 50.000 0.00 0.00 0.00 4.16
890 973 4.527509 ATCGATCGATTGCAGATAAGGT 57.472 40.909 24.60 0.00 0.00 3.50
891 974 7.531280 AATAATCGATCGATTGCAGATAAGG 57.469 36.000 40.08 1.11 43.75 2.69
1012 1127 2.044946 GCTCAAGGGCACGGGAAT 60.045 61.111 0.00 0.00 0.00 3.01
1084 1199 0.905357 ATGGTCCGGAAGAACTCCTG 59.095 55.000 5.23 0.00 42.85 3.86
1196 1311 0.589223 CTCGACCTCCACTATCTCGC 59.411 60.000 0.00 0.00 0.00 5.03
1369 1484 2.121538 TCCTCGGCATCGTCCTCAG 61.122 63.158 0.00 0.00 37.69 3.35
1731 3045 1.595357 CCGGTTGAGGTACCTCCAC 59.405 63.158 34.05 31.74 42.09 4.02
1773 3090 2.890109 CGCGAGCATGGAGGATTGC 61.890 63.158 0.00 0.00 39.17 3.56
1841 3158 5.845985 TCGATCGATGCCTTGAATTAATC 57.154 39.130 15.15 0.00 0.00 1.75
1895 3212 2.732001 ACGCGAACAACTGAGAAAAC 57.268 45.000 15.93 0.00 0.00 2.43
1896 3213 3.750639 AAACGCGAACAACTGAGAAAA 57.249 38.095 15.93 0.00 0.00 2.29
1900 3217 1.112459 GCAAAACGCGAACAACTGAG 58.888 50.000 15.93 0.00 0.00 3.35
1920 3242 8.289618 CGGAACTATTCTTTTTCACTTGAATCA 58.710 33.333 0.00 0.00 33.54 2.57
1928 3250 9.887406 TTGTAATTCGGAACTATTCTTTTTCAC 57.113 29.630 0.00 0.00 0.00 3.18
1936 3258 6.592607 TCCACAGTTGTAATTCGGAACTATTC 59.407 38.462 0.00 0.00 0.00 1.75
1944 3266 3.930848 GGTACTCCACAGTTGTAATTCGG 59.069 47.826 0.00 0.00 33.62 4.30
1971 3958 6.401047 CGATATGTCACTACAAACAGTGTTGG 60.401 42.308 9.79 9.34 45.11 3.77
1993 3981 0.650512 CGGCAGCAACGATTTACGAT 59.349 50.000 0.00 0.00 45.77 3.73
1996 3984 3.458779 TTTACGGCAGCAACGATTTAC 57.541 42.857 0.00 0.00 34.93 2.01
2003 3991 4.168922 ACCTTATTTTTACGGCAGCAAC 57.831 40.909 0.00 0.00 0.00 4.17
2012 4000 5.961263 CGTCAATGGCGTACCTTATTTTTAC 59.039 40.000 0.00 0.00 36.63 2.01
2018 4854 2.973694 ACGTCAATGGCGTACCTTAT 57.026 45.000 12.48 0.00 41.06 1.73
2134 4970 3.433598 GCTATGTTGGGGCTAATGTCTCA 60.434 47.826 0.00 0.00 0.00 3.27
2154 4990 0.745845 CCACTAGAGCCGCAAATGCT 60.746 55.000 0.00 0.00 43.03 3.79
2169 5005 4.716784 TGCCATATCTTCAAGTACTCCACT 59.283 41.667 0.00 0.00 40.05 4.00
2210 5046 3.447586 GTCAGCCACACTCTCCTATAACA 59.552 47.826 0.00 0.00 0.00 2.41
2240 5076 1.132643 CGTTCGTTTCCCACAACCAAA 59.867 47.619 0.00 0.00 0.00 3.28
2246 5082 2.592287 GCCCGTTCGTTTCCCACA 60.592 61.111 0.00 0.00 0.00 4.17
2305 5141 1.903404 CAGTTGGCACCACTTCCCC 60.903 63.158 0.00 0.00 0.00 4.81
2310 5146 3.872603 TCCGCAGTTGGCACCACT 61.873 61.111 0.00 0.00 45.17 4.00
2322 5158 2.151202 GATCTCCACAAAAAGTCCGCA 58.849 47.619 0.00 0.00 0.00 5.69
2333 5169 1.690633 GGGGCTCTGGATCTCCACA 60.691 63.158 0.00 0.00 42.01 4.17
2343 5179 0.749454 GGCATTGTAGTGGGGCTCTG 60.749 60.000 0.00 0.00 0.00 3.35
2355 5191 2.629617 CCAGGTGAAGAAAAGGCATTGT 59.370 45.455 0.00 0.00 0.00 2.71
2363 5199 4.517285 CATAGCTAGCCAGGTGAAGAAAA 58.483 43.478 12.13 0.00 33.61 2.29
2365 5201 2.158900 GCATAGCTAGCCAGGTGAAGAA 60.159 50.000 12.13 0.00 33.61 2.52
2405 5241 2.258591 GTCGAGCAAGGCAGTCGA 59.741 61.111 0.00 0.00 40.29 4.20
2410 5246 3.611674 TCCACGTCGAGCAAGGCA 61.612 61.111 0.00 0.00 0.00 4.75
2415 5251 2.649034 GGAAGTCCACGTCGAGCA 59.351 61.111 0.00 0.00 35.64 4.26
2506 5344 3.596214 ACGTTCTTCACACAGTTCTTGT 58.404 40.909 0.00 0.00 41.94 3.16
2534 5372 0.187117 TTCCTGTTTGCCCATGGTCA 59.813 50.000 11.73 0.00 0.00 4.02
2536 5374 1.269012 CATTCCTGTTTGCCCATGGT 58.731 50.000 11.73 0.00 0.00 3.55
2666 5505 1.659098 GACTGCGTTCCTATGTTTCCG 59.341 52.381 0.00 0.00 0.00 4.30
2683 5522 2.037772 AGAAGCACCATCAAAGACGACT 59.962 45.455 0.00 0.00 0.00 4.18
2684 5523 2.413453 GAGAAGCACCATCAAAGACGAC 59.587 50.000 0.00 0.00 0.00 4.34
2761 5600 3.719173 GAACAGGCTATCTAGTTCGCT 57.281 47.619 0.00 0.00 32.17 4.93


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

AutoCloner maintained by Alex Coulton.