Multiple sequence alignment - TraesCS5B01G308700

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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 TraesCS5B01G308700 chr5B 100.000 2069 0 0 481 2549 491279526 491281594 0.000000e+00 3821.0
1 TraesCS5B01G308700 chr5B 92.562 484 30 2 993 1470 491272705 491273188 0.000000e+00 689.0
2 TraesCS5B01G308700 chr5B 90.514 506 36 4 972 1470 491370180 491370680 0.000000e+00 658.0
3 TraesCS5B01G308700 chr5B 96.970 198 6 0 1622 1819 491300304 491300501 1.460000e-87 333.0
4 TraesCS5B01G308700 chr5B 100.000 173 0 0 1 173 491279046 491279218 1.140000e-83 320.0
5 TraesCS5B01G308700 chr5B 98.837 172 2 0 1 172 544499363 544499534 8.860000e-80 307.0
6 TraesCS5B01G308700 chr5B 97.674 172 4 0 1 172 531857365 531857536 1.920000e-76 296.0
7 TraesCS5B01G308700 chr5B 95.930 172 6 1 492 662 531857875 531858046 6.950000e-71 278.0
8 TraesCS5B01G308700 chr5B 93.421 76 5 0 601 676 38017436 38017361 2.070000e-21 113.0
9 TraesCS5B01G308700 chr6D 89.869 918 82 8 1639 2549 154592497 154591584 0.000000e+00 1170.0
10 TraesCS5B01G308700 chr6D 89.531 917 86 7 1639 2549 136731503 136732415 0.000000e+00 1153.0
11 TraesCS5B01G308700 chr6D 97.093 172 5 0 1 172 32302496 32302667 8.920000e-75 291.0
12 TraesCS5B01G308700 chr6D 93.750 192 11 1 1658 1849 136737850 136738040 1.150000e-73 287.0
13 TraesCS5B01G308700 chr6D 83.333 162 21 5 501 662 32302735 32302890 7.350000e-31 145.0
14 TraesCS5B01G308700 chr7A 88.986 917 92 6 1639 2549 380884734 380883821 0.000000e+00 1125.0
15 TraesCS5B01G308700 chr7A 88.732 923 89 12 1626 2542 277486861 277487774 0.000000e+00 1114.0
16 TraesCS5B01G308700 chr7A 87.500 728 78 10 1830 2549 466507358 466506636 0.000000e+00 828.0
17 TraesCS5B01G308700 chr7A 90.076 262 22 4 1639 1898 102661162 102660903 1.130000e-88 337.0
18 TraesCS5B01G308700 chr7A 85.714 224 27 5 1626 1849 277492910 277493128 5.480000e-57 231.0
19 TraesCS5B01G308700 chr7A 83.140 172 27 2 1 172 151876421 151876590 3.400000e-34 156.0
20 TraesCS5B01G308700 chr5A 92.476 638 43 2 972 1608 520705889 520706522 0.000000e+00 907.0
21 TraesCS5B01G308700 chr5A 89.960 498 43 3 993 1484 520697466 520697962 9.950000e-179 636.0
22 TraesCS5B01G308700 chr5A 89.017 519 46 5 972 1484 520729522 520730035 1.290000e-177 632.0
23 TraesCS5B01G308700 chr5A 93.103 203 8 4 672 871 520703050 520703249 2.480000e-75 292.0
24 TraesCS5B01G308700 chr5A 82.624 282 23 14 679 950 520697118 520697383 2.550000e-55 226.0
25 TraesCS5B01G308700 chr5A 83.491 212 21 8 735 932 520729215 520729426 4.330000e-43 185.0
26 TraesCS5B01G308700 chr5A 98.113 53 1 0 902 954 520705783 520705835 2.700000e-15 93.5
27 TraesCS5B01G308700 chr6A 88.536 724 73 8 1831 2549 13749367 13750085 0.000000e+00 869.0
28 TraesCS5B01G308700 chr3A 88.627 721 66 12 1833 2549 603265117 603264409 0.000000e+00 863.0
29 TraesCS5B01G308700 chr3A 90.116 172 15 2 1 172 741361004 741361173 3.300000e-54 222.0
30 TraesCS5B01G308700 chr5D 91.200 625 51 2 983 1607 409542304 409542924 0.000000e+00 846.0
31 TraesCS5B01G308700 chr5D 87.709 716 79 8 1837 2548 340059906 340060616 0.000000e+00 826.0
32 TraesCS5B01G308700 chr5D 90.891 505 36 2 972 1470 409575585 409576085 0.000000e+00 669.0
33 TraesCS5B01G308700 chr5D 86.538 624 55 13 993 1608 409523263 409523865 0.000000e+00 660.0
34 TraesCS5B01G308700 chr5D 88.521 453 43 4 1039 1484 409454584 409455034 8.020000e-150 540.0
35 TraesCS5B01G308700 chr5D 97.093 172 5 0 1 172 490770796 490770967 8.920000e-75 291.0
36 TraesCS5B01G308700 chr5D 89.720 214 12 3 671 876 409541154 409541365 5.410000e-67 265.0
37 TraesCS5B01G308700 chr5D 88.525 183 17 4 481 662 490771031 490771210 4.270000e-53 219.0
38 TraesCS5B01G308700 chr2A 87.517 737 78 12 1821 2549 20813302 20814032 0.000000e+00 839.0
39 TraesCS5B01G308700 chr2B 97.826 184 3 1 481 663 641083624 641083807 1.470000e-82 316.0
40 TraesCS5B01G308700 chr2B 96.512 172 6 0 1 172 641083396 641083567 4.150000e-73 285.0
41 TraesCS5B01G308700 chr2B 92.228 193 13 2 1639 1830 734338694 734338503 3.230000e-69 272.0
42 TraesCS5B01G308700 chr2B 93.878 147 9 0 516 662 550730133 550729987 3.300000e-54 222.0
43 TraesCS5B01G308700 chr6B 97.674 172 4 0 1 172 681927067 681927238 1.920000e-76 296.0
44 TraesCS5B01G308700 chr6B 95.652 161 7 0 503 663 681927309 681927469 2.520000e-65 259.0
45 TraesCS5B01G308700 chr6B 94.595 74 3 1 601 674 134483646 134483574 2.070000e-21 113.0
46 TraesCS5B01G308700 chr1B 94.767 172 9 0 1 172 643451505 643451676 4.180000e-68 268.0
47 TraesCS5B01G308700 chr1B 95.000 100 3 2 506 603 643451751 643451850 3.400000e-34 156.0
48 TraesCS5B01G308700 chr4D 93.151 73 4 1 601 672 358453219 358453291 3.470000e-19 106.0


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 TraesCS5B01G308700 chr5B 491279046 491281594 2548 False 2070.500000 3821 100.000 1 2549 2 chr5B.!!$F5 2548
1 TraesCS5B01G308700 chr5B 491370180 491370680 500 False 658.000000 658 90.514 972 1470 1 chr5B.!!$F3 498
2 TraesCS5B01G308700 chr5B 531857365 531858046 681 False 287.000000 296 96.802 1 662 2 chr5B.!!$F6 661
3 TraesCS5B01G308700 chr6D 154591584 154592497 913 True 1170.000000 1170 89.869 1639 2549 1 chr6D.!!$R1 910
4 TraesCS5B01G308700 chr6D 136731503 136732415 912 False 1153.000000 1153 89.531 1639 2549 1 chr6D.!!$F1 910
5 TraesCS5B01G308700 chr7A 380883821 380884734 913 True 1125.000000 1125 88.986 1639 2549 1 chr7A.!!$R2 910
6 TraesCS5B01G308700 chr7A 277486861 277487774 913 False 1114.000000 1114 88.732 1626 2542 1 chr7A.!!$F2 916
7 TraesCS5B01G308700 chr7A 466506636 466507358 722 True 828.000000 828 87.500 1830 2549 1 chr7A.!!$R3 719
8 TraesCS5B01G308700 chr5A 520697118 520697962 844 False 431.000000 636 86.292 679 1484 2 chr5A.!!$F1 805
9 TraesCS5B01G308700 chr5A 520703050 520706522 3472 False 430.833333 907 94.564 672 1608 3 chr5A.!!$F2 936
10 TraesCS5B01G308700 chr5A 520729215 520730035 820 False 408.500000 632 86.254 735 1484 2 chr5A.!!$F3 749
11 TraesCS5B01G308700 chr6A 13749367 13750085 718 False 869.000000 869 88.536 1831 2549 1 chr6A.!!$F1 718
12 TraesCS5B01G308700 chr3A 603264409 603265117 708 True 863.000000 863 88.627 1833 2549 1 chr3A.!!$R1 716
13 TraesCS5B01G308700 chr5D 340059906 340060616 710 False 826.000000 826 87.709 1837 2548 1 chr5D.!!$F1 711
14 TraesCS5B01G308700 chr5D 409575585 409576085 500 False 669.000000 669 90.891 972 1470 1 chr5D.!!$F4 498
15 TraesCS5B01G308700 chr5D 409523263 409523865 602 False 660.000000 660 86.538 993 1608 1 chr5D.!!$F3 615
16 TraesCS5B01G308700 chr5D 409541154 409542924 1770 False 555.500000 846 90.460 671 1607 2 chr5D.!!$F5 936
17 TraesCS5B01G308700 chr2A 20813302 20814032 730 False 839.000000 839 87.517 1821 2549 1 chr2A.!!$F1 728

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
600 621 0.174617 GACGGGAGAAGAAGCAGGAG 59.825 60.0 0.00 0.0 0.0 3.69 F
957 3564 0.393077 ATCCAGTTCGAATAGCCGGG 59.607 55.0 2.18 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1542 4937 0.448197 TTGCGCGAAAAACTCACACA 59.552 45.0 12.1 0.0 0.0 3.72 R
2235 5640 0.537653 GCAAGAGTCAGGGGGAGTAC 59.462 60.0 0.0 0.0 0.0 2.73 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
43 44 3.682315 CGCCGTCGAAGCTATGCG 61.682 66.667 5.51 5.51 38.10 4.73
559 580 3.345808 GGCAGCTCGTTGTCGCAA 61.346 61.111 0.00 0.00 36.96 4.85
560 581 2.127609 GCAGCTCGTTGTCGCAAC 60.128 61.111 11.24 11.24 36.96 4.17
561 582 2.598632 GCAGCTCGTTGTCGCAACT 61.599 57.895 16.76 0.60 36.96 3.16
562 583 1.488957 CAGCTCGTTGTCGCAACTC 59.511 57.895 16.76 8.68 36.96 3.01
563 584 2.016704 AGCTCGTTGTCGCAACTCG 61.017 57.895 16.76 10.45 40.15 4.18
564 585 2.465920 CTCGTTGTCGCAACTCGC 59.534 61.111 16.76 0.00 38.27 5.03
565 586 3.000080 CTCGTTGTCGCAACTCGCC 62.000 63.158 16.76 0.00 37.30 5.54
566 587 4.409588 CGTTGTCGCAACTCGCCG 62.410 66.667 16.76 4.06 37.30 6.46
567 588 3.335534 GTTGTCGCAACTCGCCGT 61.336 61.111 13.26 0.00 37.30 5.68
568 589 2.017783 GTTGTCGCAACTCGCCGTA 61.018 57.895 13.26 0.00 37.30 4.02
569 590 1.731613 TTGTCGCAACTCGCCGTAG 60.732 57.895 0.00 0.00 37.30 3.51
570 591 3.542742 GTCGCAACTCGCCGTAGC 61.543 66.667 0.00 0.00 37.30 3.58
571 592 4.045771 TCGCAACTCGCCGTAGCA 62.046 61.111 0.00 0.00 39.83 3.49
572 593 3.545481 CGCAACTCGCCGTAGCAG 61.545 66.667 0.00 0.00 39.83 4.24
573 594 3.854459 GCAACTCGCCGTAGCAGC 61.854 66.667 0.00 0.00 39.83 5.25
583 604 4.468689 GTAGCAGCGGGGTGGGAC 62.469 72.222 0.00 0.00 0.00 4.46
591 612 3.400054 GGGGTGGGACGGGAGAAG 61.400 72.222 0.00 0.00 0.00 2.85
592 613 2.284405 GGGTGGGACGGGAGAAGA 60.284 66.667 0.00 0.00 0.00 2.87
593 614 1.916777 GGGTGGGACGGGAGAAGAA 60.917 63.158 0.00 0.00 0.00 2.52
594 615 1.597461 GGTGGGACGGGAGAAGAAG 59.403 63.158 0.00 0.00 0.00 2.85
595 616 1.079057 GTGGGACGGGAGAAGAAGC 60.079 63.158 0.00 0.00 0.00 3.86
596 617 1.535444 TGGGACGGGAGAAGAAGCA 60.535 57.895 0.00 0.00 0.00 3.91
597 618 1.219393 GGGACGGGAGAAGAAGCAG 59.781 63.158 0.00 0.00 0.00 4.24
598 619 1.219393 GGACGGGAGAAGAAGCAGG 59.781 63.158 0.00 0.00 0.00 4.85
599 620 1.258445 GGACGGGAGAAGAAGCAGGA 61.258 60.000 0.00 0.00 0.00 3.86
600 621 0.174617 GACGGGAGAAGAAGCAGGAG 59.825 60.000 0.00 0.00 0.00 3.69
601 622 1.153469 CGGGAGAAGAAGCAGGAGC 60.153 63.158 0.00 0.00 42.56 4.70
611 632 4.135153 GCAGGAGCGCGAGGAAGA 62.135 66.667 12.10 0.00 0.00 2.87
612 633 2.103934 CAGGAGCGCGAGGAAGAG 59.896 66.667 12.10 0.00 0.00 2.85
613 634 3.144193 AGGAGCGCGAGGAAGAGG 61.144 66.667 12.10 0.00 0.00 3.69
614 635 4.214327 GGAGCGCGAGGAAGAGGG 62.214 72.222 12.10 0.00 0.00 4.30
615 636 3.141488 GAGCGCGAGGAAGAGGGA 61.141 66.667 12.10 0.00 0.00 4.20
616 637 3.132481 GAGCGCGAGGAAGAGGGAG 62.132 68.421 12.10 0.00 0.00 4.30
617 638 3.141488 GCGCGAGGAAGAGGGAGA 61.141 66.667 12.10 0.00 0.00 3.71
618 639 2.802106 CGCGAGGAAGAGGGAGAC 59.198 66.667 0.00 0.00 0.00 3.36
629 650 4.587189 GGGAGACCGGCCGAATCG 62.587 72.222 30.73 12.89 43.64 3.34
630 651 3.834799 GGAGACCGGCCGAATCGT 61.835 66.667 30.73 16.76 0.00 3.73
631 652 2.183555 GAGACCGGCCGAATCGTT 59.816 61.111 30.73 8.83 0.00 3.85
632 653 1.877165 GAGACCGGCCGAATCGTTC 60.877 63.158 30.73 14.08 0.00 3.95
633 654 2.889018 GACCGGCCGAATCGTTCC 60.889 66.667 30.73 0.48 0.00 3.62
634 655 4.807039 ACCGGCCGAATCGTTCCG 62.807 66.667 30.73 20.95 39.46 4.30
639 660 4.807039 CCGAATCGTTCCGCCGGT 62.807 66.667 1.63 0.00 35.83 5.28
640 661 3.550992 CGAATCGTTCCGCCGGTG 61.551 66.667 8.42 8.42 0.00 4.94
641 662 3.861263 GAATCGTTCCGCCGGTGC 61.861 66.667 10.27 0.00 0.00 5.01
658 679 4.631740 CCCCGGCCCCAAAGGTTT 62.632 66.667 0.00 0.00 38.26 3.27
659 680 2.994995 CCCGGCCCCAAAGGTTTC 60.995 66.667 0.00 0.00 38.26 2.78
660 681 2.994995 CCGGCCCCAAAGGTTTCC 60.995 66.667 0.00 0.00 38.26 3.13
661 682 2.994995 CGGCCCCAAAGGTTTCCC 60.995 66.667 0.00 0.00 38.26 3.97
662 683 2.202899 GGCCCCAAAGGTTTCCCA 59.797 61.111 0.00 0.00 38.26 4.37
663 684 2.214216 GGCCCCAAAGGTTTCCCAC 61.214 63.158 0.00 0.00 38.26 4.61
664 685 1.458588 GCCCCAAAGGTTTCCCACA 60.459 57.895 0.00 0.00 38.26 4.17
665 686 0.835971 GCCCCAAAGGTTTCCCACAT 60.836 55.000 0.00 0.00 38.26 3.21
666 687 1.551329 GCCCCAAAGGTTTCCCACATA 60.551 52.381 0.00 0.00 38.26 2.29
667 688 2.892301 GCCCCAAAGGTTTCCCACATAT 60.892 50.000 0.00 0.00 38.26 1.78
668 689 3.628769 GCCCCAAAGGTTTCCCACATATA 60.629 47.826 0.00 0.00 38.26 0.86
669 690 4.814967 CCCCAAAGGTTTCCCACATATAT 58.185 43.478 0.00 0.00 0.00 0.86
670 691 5.694405 GCCCCAAAGGTTTCCCACATATATA 60.694 44.000 0.00 0.00 38.26 0.86
671 692 6.561294 CCCCAAAGGTTTCCCACATATATAT 58.439 40.000 0.00 0.00 0.00 0.86
672 693 6.437162 CCCCAAAGGTTTCCCACATATATATG 59.563 42.308 19.21 19.21 39.55 1.78
674 695 7.508977 CCCAAAGGTTTCCCACATATATATGTT 59.491 37.037 23.03 8.43 43.99 2.71
675 696 8.923270 CCAAAGGTTTCCCACATATATATGTTT 58.077 33.333 23.03 11.32 43.99 2.83
705 726 5.765576 TTTTATAACTGGCAGTAGGGACA 57.234 39.130 22.37 1.28 0.00 4.02
802 841 0.601558 GCCACTTGACAGTCGTAGGA 59.398 55.000 7.27 0.00 0.00 2.94
954 3561 3.058639 GCATCAATCCAGTTCGAATAGCC 60.059 47.826 0.00 0.00 0.00 3.93
955 3562 2.821546 TCAATCCAGTTCGAATAGCCG 58.178 47.619 0.00 0.00 0.00 5.52
957 3564 0.393077 ATCCAGTTCGAATAGCCGGG 59.607 55.000 2.18 0.00 0.00 5.73
958 3565 1.887707 CCAGTTCGAATAGCCGGGC 60.888 63.158 12.11 12.11 0.00 6.13
959 3566 2.106332 AGTTCGAATAGCCGGGCG 59.894 61.111 14.39 0.00 0.00 6.13
960 3567 2.105528 GTTCGAATAGCCGGGCGA 59.894 61.111 14.39 9.25 0.00 5.54
961 3568 1.949631 GTTCGAATAGCCGGGCGAG 60.950 63.158 14.39 4.71 34.01 5.03
962 3569 3.785189 TTCGAATAGCCGGGCGAGC 62.785 63.158 14.39 4.07 34.01 5.03
963 3570 4.286320 CGAATAGCCGGGCGAGCT 62.286 66.667 14.39 5.21 44.49 4.09
965 3572 3.447025 GAATAGCCGGGCGAGCTGT 62.447 63.158 14.39 0.00 41.71 4.40
966 3573 3.740128 AATAGCCGGGCGAGCTGTG 62.740 63.158 14.39 0.00 41.71 3.66
1095 4490 1.209640 GGCGGACTCGGATATCGAC 59.790 63.158 0.00 0.00 43.74 4.20
1131 4526 2.743928 CTGGCCGCGCTCTTCTTT 60.744 61.111 5.56 0.00 0.00 2.52
1536 4931 0.866061 CGGACACGATCATCACCGTC 60.866 60.000 0.00 0.00 44.60 4.79
1560 4955 4.987419 GTGTGAGTTTTTCGCGCA 57.013 50.000 8.75 0.00 44.33 6.09
1562 4957 1.112459 GTGTGAGTTTTTCGCGCAAG 58.888 50.000 8.75 0.00 44.33 4.01
1597 4994 1.914051 CTGACGATACAGCACAGTTCG 59.086 52.381 0.00 0.00 35.99 3.95
1598 4995 1.538075 TGACGATACAGCACAGTTCGA 59.462 47.619 0.00 0.00 34.15 3.71
1599 4996 2.030628 TGACGATACAGCACAGTTCGAA 60.031 45.455 0.00 0.00 34.15 3.71
1608 5005 1.967762 CACAGTTCGAAATGCGCAAT 58.032 45.000 24.26 1.49 40.61 3.56
1609 5006 1.906966 CACAGTTCGAAATGCGCAATC 59.093 47.619 24.26 15.54 40.61 2.67
1610 5007 1.174352 CAGTTCGAAATGCGCAATCG 58.826 50.000 31.25 31.25 40.61 3.34
1622 5019 1.757574 CGCAATCGCCCATGTAAATG 58.242 50.000 0.00 0.00 33.11 2.32
1623 5020 1.065401 CGCAATCGCCCATGTAAATGT 59.935 47.619 0.00 0.00 33.11 2.71
1624 5021 2.479389 CGCAATCGCCCATGTAAATGTT 60.479 45.455 0.00 0.00 33.11 2.71
1625 5022 2.859538 GCAATCGCCCATGTAAATGTTG 59.140 45.455 0.00 0.00 0.00 3.33
1626 5023 3.428725 GCAATCGCCCATGTAAATGTTGA 60.429 43.478 0.00 0.00 0.00 3.18
1627 5024 4.353737 CAATCGCCCATGTAAATGTTGAG 58.646 43.478 0.00 0.00 0.00 3.02
1628 5025 3.342377 TCGCCCATGTAAATGTTGAGA 57.658 42.857 0.00 0.00 0.00 3.27
1629 5026 3.680490 TCGCCCATGTAAATGTTGAGAA 58.320 40.909 0.00 0.00 0.00 2.87
1630 5027 3.438781 TCGCCCATGTAAATGTTGAGAAC 59.561 43.478 0.00 0.00 0.00 3.01
1631 5028 3.427503 CGCCCATGTAAATGTTGAGAACC 60.428 47.826 0.00 0.00 0.00 3.62
1632 5029 3.509575 GCCCATGTAAATGTTGAGAACCA 59.490 43.478 0.00 0.00 0.00 3.67
1633 5030 4.021544 GCCCATGTAAATGTTGAGAACCAA 60.022 41.667 0.00 0.00 0.00 3.67
1634 5031 5.510520 GCCCATGTAAATGTTGAGAACCAAA 60.511 40.000 0.00 0.00 36.36 3.28
1635 5032 6.158598 CCCATGTAAATGTTGAGAACCAAAG 58.841 40.000 0.00 0.00 36.36 2.77
1636 5033 5.634859 CCATGTAAATGTTGAGAACCAAAGC 59.365 40.000 0.00 0.00 36.36 3.51
1637 5034 5.843673 TGTAAATGTTGAGAACCAAAGCA 57.156 34.783 0.00 0.00 36.36 3.91
1647 5044 5.540911 TGAGAACCAAAGCAAAATGAATCC 58.459 37.500 0.00 0.00 0.00 3.01
1649 5046 5.927819 AGAACCAAAGCAAAATGAATCCAA 58.072 33.333 0.00 0.00 0.00 3.53
1650 5047 5.759763 AGAACCAAAGCAAAATGAATCCAAC 59.240 36.000 0.00 0.00 0.00 3.77
1651 5048 4.388485 ACCAAAGCAAAATGAATCCAACC 58.612 39.130 0.00 0.00 0.00 3.77
1679 5076 6.267242 TCCTTTTCCATTGATGATTGAACACA 59.733 34.615 0.00 0.00 0.00 3.72
1698 5095 3.055385 CACATATATACAGGGGGAACGGG 60.055 52.174 0.00 0.00 0.00 5.28
1763 5160 0.249489 ACGCTCCAGGAACGATATGC 60.249 55.000 19.30 1.75 0.00 3.14
1797 5194 1.466025 GGGGATATCCACGTGCGGTA 61.466 60.000 23.27 4.70 37.91 4.02
1809 5206 2.490903 ACGTGCGGTAACAAGTAGAGAT 59.509 45.455 0.00 0.00 30.17 2.75
1899 5296 4.966366 GCGTGTTCATCATCTTGAAATAGC 59.034 41.667 0.00 0.00 37.36 2.97
1974 5376 6.361433 TGTAAAACTCCTTCAAATCCAGTGA 58.639 36.000 0.00 0.00 0.00 3.41
2098 5501 1.405872 ACTTTCCCAAAAACCCCGAC 58.594 50.000 0.00 0.00 0.00 4.79
2111 5516 2.266689 CCGACGGGGAAAACGGAT 59.733 61.111 5.81 0.00 46.94 4.18
2248 5653 0.042881 AGGAAGGTACTCCCCCTGAC 59.957 60.000 0.00 0.00 25.57 3.51
2310 5715 6.922957 TGAACATGTTTCTGGAATGTAAAAGC 59.077 34.615 13.36 0.00 33.48 3.51
2402 5807 7.835822 TGCTTATTATGTAACCTGTTTGCATT 58.164 30.769 0.00 0.00 40.62 3.56
2403 5808 8.310382 TGCTTATTATGTAACCTGTTTGCATTT 58.690 29.630 0.00 0.00 40.62 2.32
2448 5853 7.959658 TCATTGAGATAATGGTTGGTGAATT 57.040 32.000 0.00 0.00 0.00 2.17
2481 5886 4.991687 GGTCTGTTTCGAAGACTCTTCATT 59.008 41.667 17.23 0.00 43.03 2.57
2497 5902 1.754803 TCATTAGAGGGCTACCACACG 59.245 52.381 0.00 0.00 40.13 4.49
2523 5928 7.592885 AGTAGGAACACTAAACTTGTCTACA 57.407 36.000 0.00 0.00 31.39 2.74
2530 5935 9.209175 GAACACTAAACTTGTCTACAATCTGAT 57.791 33.333 0.00 0.00 35.02 2.90
2542 5947 7.179160 TGTCTACAATCTGATATAGTGGGGATG 59.821 40.741 8.10 0.00 0.00 3.51
2543 5948 7.397476 GTCTACAATCTGATATAGTGGGGATGA 59.603 40.741 8.10 0.00 0.00 2.92
2544 5949 8.125081 TCTACAATCTGATATAGTGGGGATGAT 58.875 37.037 8.10 0.00 0.00 2.45
2545 5950 7.192852 ACAATCTGATATAGTGGGGATGATC 57.807 40.000 0.00 0.00 0.00 2.92
2546 5951 6.127225 ACAATCTGATATAGTGGGGATGATCG 60.127 42.308 0.00 0.00 0.00 3.69
2547 5952 5.193099 TCTGATATAGTGGGGATGATCGA 57.807 43.478 0.00 0.00 0.00 3.59
2548 5953 5.770919 TCTGATATAGTGGGGATGATCGAT 58.229 41.667 0.00 0.00 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 3.444805 AGCTCCGACAGACGAGCC 61.445 66.667 5.48 0.00 45.77 4.70
151 152 1.229209 AGGTCGTCCTCCACACCAT 60.229 57.895 0.00 0.00 40.58 3.55
543 564 2.127609 GTTGCGACAACGAGCTGC 60.128 61.111 0.00 0.00 42.66 5.25
544 565 1.488957 GAGTTGCGACAACGAGCTG 59.511 57.895 6.90 0.00 42.66 4.24
545 566 2.016704 CGAGTTGCGACAACGAGCT 61.017 57.895 15.39 0.00 44.57 4.09
546 567 2.465920 CGAGTTGCGACAACGAGC 59.534 61.111 15.39 8.94 44.57 5.03
547 568 2.465920 GCGAGTTGCGACAACGAG 59.534 61.111 21.82 13.12 44.57 4.18
566 587 4.468689 GTCCCACCCCGCTGCTAC 62.469 72.222 0.00 0.00 0.00 3.58
574 595 3.400054 CTTCTCCCGTCCCACCCC 61.400 72.222 0.00 0.00 0.00 4.95
575 596 1.900545 CTTCTTCTCCCGTCCCACCC 61.901 65.000 0.00 0.00 0.00 4.61
576 597 1.597461 CTTCTTCTCCCGTCCCACC 59.403 63.158 0.00 0.00 0.00 4.61
577 598 1.079057 GCTTCTTCTCCCGTCCCAC 60.079 63.158 0.00 0.00 0.00 4.61
578 599 1.535444 TGCTTCTTCTCCCGTCCCA 60.535 57.895 0.00 0.00 0.00 4.37
579 600 1.219393 CTGCTTCTTCTCCCGTCCC 59.781 63.158 0.00 0.00 0.00 4.46
580 601 1.219393 CCTGCTTCTTCTCCCGTCC 59.781 63.158 0.00 0.00 0.00 4.79
581 602 0.174617 CTCCTGCTTCTTCTCCCGTC 59.825 60.000 0.00 0.00 0.00 4.79
582 603 1.893919 GCTCCTGCTTCTTCTCCCGT 61.894 60.000 0.00 0.00 36.03 5.28
583 604 1.153469 GCTCCTGCTTCTTCTCCCG 60.153 63.158 0.00 0.00 36.03 5.14
584 605 1.153469 CGCTCCTGCTTCTTCTCCC 60.153 63.158 0.00 0.00 36.97 4.30
585 606 1.813337 GCGCTCCTGCTTCTTCTCC 60.813 63.158 0.00 0.00 36.97 3.71
586 607 2.164026 CGCGCTCCTGCTTCTTCTC 61.164 63.158 5.56 0.00 36.97 2.87
587 608 2.125753 CGCGCTCCTGCTTCTTCT 60.126 61.111 5.56 0.00 36.97 2.85
588 609 2.125912 TCGCGCTCCTGCTTCTTC 60.126 61.111 5.56 0.00 36.97 2.87
589 610 2.125753 CTCGCGCTCCTGCTTCTT 60.126 61.111 5.56 0.00 36.97 2.52
590 611 4.140599 CCTCGCGCTCCTGCTTCT 62.141 66.667 5.56 0.00 36.97 2.85
591 612 3.649277 TTCCTCGCGCTCCTGCTTC 62.649 63.158 5.56 0.00 36.97 3.86
592 613 3.655810 CTTCCTCGCGCTCCTGCTT 62.656 63.158 5.56 0.00 36.97 3.91
593 614 4.140599 CTTCCTCGCGCTCCTGCT 62.141 66.667 5.56 0.00 36.97 4.24
594 615 4.135153 TCTTCCTCGCGCTCCTGC 62.135 66.667 5.56 0.00 0.00 4.85
595 616 2.103934 CTCTTCCTCGCGCTCCTG 59.896 66.667 5.56 0.00 0.00 3.86
596 617 3.144193 CCTCTTCCTCGCGCTCCT 61.144 66.667 5.56 0.00 0.00 3.69
597 618 4.214327 CCCTCTTCCTCGCGCTCC 62.214 72.222 5.56 0.00 0.00 4.70
598 619 3.132481 CTCCCTCTTCCTCGCGCTC 62.132 68.421 5.56 0.00 0.00 5.03
599 620 3.144193 CTCCCTCTTCCTCGCGCT 61.144 66.667 5.56 0.00 0.00 5.92
600 621 3.141488 TCTCCCTCTTCCTCGCGC 61.141 66.667 0.00 0.00 0.00 6.86
601 622 2.776913 GGTCTCCCTCTTCCTCGCG 61.777 68.421 0.00 0.00 0.00 5.87
602 623 2.776913 CGGTCTCCCTCTTCCTCGC 61.777 68.421 0.00 0.00 0.00 5.03
603 624 2.122167 CCGGTCTCCCTCTTCCTCG 61.122 68.421 0.00 0.00 0.00 4.63
604 625 2.428085 GCCGGTCTCCCTCTTCCTC 61.428 68.421 1.90 0.00 0.00 3.71
605 626 2.364448 GCCGGTCTCCCTCTTCCT 60.364 66.667 1.90 0.00 0.00 3.36
606 627 3.471806 GGCCGGTCTCCCTCTTCC 61.472 72.222 1.90 0.00 0.00 3.46
607 628 3.839432 CGGCCGGTCTCCCTCTTC 61.839 72.222 20.10 0.00 0.00 2.87
608 629 3.899545 TTCGGCCGGTCTCCCTCTT 62.900 63.158 27.83 0.00 0.00 2.85
609 630 3.680920 ATTCGGCCGGTCTCCCTCT 62.681 63.158 27.83 0.00 0.00 3.69
610 631 3.153270 GATTCGGCCGGTCTCCCTC 62.153 68.421 27.83 7.92 0.00 4.30
611 632 3.155167 GATTCGGCCGGTCTCCCT 61.155 66.667 27.83 1.75 0.00 4.20
612 633 4.587189 CGATTCGGCCGGTCTCCC 62.587 72.222 27.83 7.99 0.00 4.30
613 634 3.366739 AACGATTCGGCCGGTCTCC 62.367 63.158 27.83 9.47 0.00 3.71
614 635 1.877165 GAACGATTCGGCCGGTCTC 60.877 63.158 27.83 17.86 40.30 3.36
615 636 2.183555 GAACGATTCGGCCGGTCT 59.816 61.111 27.83 10.31 40.30 3.85
616 637 2.889018 GGAACGATTCGGCCGGTC 60.889 66.667 27.83 21.93 42.50 4.79
641 662 4.631740 AAACCTTTGGGGCCGGGG 62.632 66.667 2.18 0.00 39.10 5.73
642 663 2.994995 GAAACCTTTGGGGCCGGG 60.995 66.667 2.18 0.00 39.10 5.73
643 664 2.994995 GGAAACCTTTGGGGCCGG 60.995 66.667 0.00 0.00 39.10 6.13
647 668 7.916033 ACATATATATGTGGGAAACCTTTGGGG 60.916 40.741 24.39 0.00 44.66 4.96
648 669 7.010160 ACATATATATGTGGGAAACCTTTGGG 58.990 38.462 24.39 0.00 44.66 4.12
649 670 8.477419 AACATATATATGTGGGAAACCTTTGG 57.523 34.615 25.42 0.00 46.43 3.28
653 674 9.569122 GTGTAAACATATATATGTGGGAAACCT 57.431 33.333 25.42 7.68 46.43 3.50
654 675 9.569122 AGTGTAAACATATATATGTGGGAAACC 57.431 33.333 25.42 12.39 45.55 3.27
670 691 9.073475 TGCCAGTTATAAAAAGAGTGTAAACAT 57.927 29.630 0.00 0.00 0.00 2.71
671 692 8.453238 TGCCAGTTATAAAAAGAGTGTAAACA 57.547 30.769 0.00 0.00 0.00 2.83
672 693 8.565416 ACTGCCAGTTATAAAAAGAGTGTAAAC 58.435 33.333 0.00 0.00 0.00 2.01
673 694 8.685838 ACTGCCAGTTATAAAAAGAGTGTAAA 57.314 30.769 0.00 0.00 0.00 2.01
674 695 9.431887 CTACTGCCAGTTATAAAAAGAGTGTAA 57.568 33.333 1.02 0.00 0.00 2.41
675 696 8.038944 CCTACTGCCAGTTATAAAAAGAGTGTA 58.961 37.037 1.02 0.00 0.00 2.90
676 697 6.879458 CCTACTGCCAGTTATAAAAAGAGTGT 59.121 38.462 1.02 0.00 0.00 3.55
677 698 6.316390 CCCTACTGCCAGTTATAAAAAGAGTG 59.684 42.308 1.02 0.00 0.00 3.51
767 788 6.037172 GTCAAGTGGCACAAGTATAGGTATTG 59.963 42.308 21.41 10.57 44.16 1.90
955 3562 3.941657 GAGTCCACACAGCTCGCCC 62.942 68.421 0.00 0.00 0.00 6.13
957 3564 1.735920 CTGAGTCCACACAGCTCGC 60.736 63.158 0.00 0.00 32.32 5.03
958 3565 0.529833 ATCTGAGTCCACACAGCTCG 59.470 55.000 0.00 0.00 35.07 5.03
959 3566 2.758736 AATCTGAGTCCACACAGCTC 57.241 50.000 0.00 0.00 35.07 4.09
960 3567 2.899900 TGTAATCTGAGTCCACACAGCT 59.100 45.455 0.00 0.00 35.07 4.24
961 3568 3.319137 TGTAATCTGAGTCCACACAGC 57.681 47.619 0.00 0.00 35.07 4.40
962 3569 6.634805 AGTTATGTAATCTGAGTCCACACAG 58.365 40.000 0.00 0.00 36.17 3.66
963 3570 6.605471 AGTTATGTAATCTGAGTCCACACA 57.395 37.500 0.00 0.00 0.00 3.72
965 3572 7.239763 TGAAGTTATGTAATCTGAGTCCACA 57.760 36.000 0.00 0.00 0.00 4.17
966 3573 7.439655 GGATGAAGTTATGTAATCTGAGTCCAC 59.560 40.741 0.00 0.00 0.00 4.02
967 3574 7.125659 TGGATGAAGTTATGTAATCTGAGTCCA 59.874 37.037 0.00 0.00 0.00 4.02
970 3577 8.708378 TGATGGATGAAGTTATGTAATCTGAGT 58.292 33.333 0.00 0.00 0.00 3.41
1006 4395 2.107141 CGCCTCCGAATCAGGACC 59.893 66.667 0.00 0.00 36.14 4.46
1074 4463 2.989824 ATATCCGAGTCCGCCCCG 60.990 66.667 0.00 0.00 0.00 5.73
1131 4526 2.685017 ATGACGAGGAGCAGCCCA 60.685 61.111 0.00 0.00 37.37 5.36
1536 4931 2.713976 GCGAAAAACTCACACAATCACG 59.286 45.455 0.00 0.00 0.00 4.35
1542 4937 0.448197 TTGCGCGAAAAACTCACACA 59.552 45.000 12.10 0.00 0.00 3.72
1580 4977 2.717580 TTCGAACTGTGCTGTATCGT 57.282 45.000 0.00 0.00 35.20 3.73
1608 5005 3.342377 TCTCAACATTTACATGGGCGA 57.658 42.857 0.00 0.00 34.27 5.54
1609 5006 3.427503 GGTTCTCAACATTTACATGGGCG 60.428 47.826 0.00 0.00 34.27 6.13
1610 5007 3.509575 TGGTTCTCAACATTTACATGGGC 59.490 43.478 0.00 0.00 34.27 5.36
1611 5008 5.720371 TTGGTTCTCAACATTTACATGGG 57.280 39.130 0.00 0.00 34.27 4.00
1612 5009 5.634859 GCTTTGGTTCTCAACATTTACATGG 59.365 40.000 0.00 0.00 34.67 3.66
1613 5010 6.215121 TGCTTTGGTTCTCAACATTTACATG 58.785 36.000 0.00 0.00 34.67 3.21
1614 5011 6.403866 TGCTTTGGTTCTCAACATTTACAT 57.596 33.333 0.00 0.00 34.67 2.29
1615 5012 5.843673 TGCTTTGGTTCTCAACATTTACA 57.156 34.783 0.00 0.00 34.67 2.41
1616 5013 7.532682 TTTTGCTTTGGTTCTCAACATTTAC 57.467 32.000 0.00 0.00 34.67 2.01
1617 5014 7.984050 TCATTTTGCTTTGGTTCTCAACATTTA 59.016 29.630 0.00 0.00 34.67 1.40
1618 5015 6.822676 TCATTTTGCTTTGGTTCTCAACATTT 59.177 30.769 0.00 0.00 34.67 2.32
1619 5016 6.347696 TCATTTTGCTTTGGTTCTCAACATT 58.652 32.000 0.00 0.00 34.67 2.71
1620 5017 5.916318 TCATTTTGCTTTGGTTCTCAACAT 58.084 33.333 0.00 0.00 34.67 2.71
1621 5018 5.336150 TCATTTTGCTTTGGTTCTCAACA 57.664 34.783 0.00 0.00 34.67 3.33
1622 5019 6.073602 GGATTCATTTTGCTTTGGTTCTCAAC 60.074 38.462 0.00 0.00 34.67 3.18
1623 5020 5.990996 GGATTCATTTTGCTTTGGTTCTCAA 59.009 36.000 0.00 0.00 0.00 3.02
1624 5021 5.070180 TGGATTCATTTTGCTTTGGTTCTCA 59.930 36.000 0.00 0.00 0.00 3.27
1625 5022 5.540911 TGGATTCATTTTGCTTTGGTTCTC 58.459 37.500 0.00 0.00 0.00 2.87
1626 5023 5.549742 TGGATTCATTTTGCTTTGGTTCT 57.450 34.783 0.00 0.00 0.00 3.01
1627 5024 5.049474 GGTTGGATTCATTTTGCTTTGGTTC 60.049 40.000 0.00 0.00 0.00 3.62
1628 5025 4.821260 GGTTGGATTCATTTTGCTTTGGTT 59.179 37.500 0.00 0.00 0.00 3.67
1629 5026 4.388485 GGTTGGATTCATTTTGCTTTGGT 58.612 39.130 0.00 0.00 0.00 3.67
1630 5027 3.432933 CGGTTGGATTCATTTTGCTTTGG 59.567 43.478 0.00 0.00 0.00 3.28
1631 5028 4.305769 TCGGTTGGATTCATTTTGCTTTG 58.694 39.130 0.00 0.00 0.00 2.77
1632 5029 4.599047 TCGGTTGGATTCATTTTGCTTT 57.401 36.364 0.00 0.00 0.00 3.51
1633 5030 4.381932 GGATCGGTTGGATTCATTTTGCTT 60.382 41.667 0.00 0.00 34.82 3.91
1634 5031 3.131046 GGATCGGTTGGATTCATTTTGCT 59.869 43.478 0.00 0.00 34.82 3.91
1635 5032 3.131046 AGGATCGGTTGGATTCATTTTGC 59.869 43.478 0.00 0.00 34.82 3.68
1636 5033 4.989279 AGGATCGGTTGGATTCATTTTG 57.011 40.909 0.00 0.00 34.82 2.44
1637 5034 6.358974 AAAAGGATCGGTTGGATTCATTTT 57.641 33.333 0.00 0.00 29.37 1.82
1647 5044 4.398988 TCATCAATGGAAAAGGATCGGTTG 59.601 41.667 0.00 0.00 0.00 3.77
1649 5046 4.235079 TCATCAATGGAAAAGGATCGGT 57.765 40.909 0.00 0.00 0.00 4.69
1650 5047 5.300034 TCAATCATCAATGGAAAAGGATCGG 59.700 40.000 0.00 0.00 0.00 4.18
1651 5048 6.381481 TCAATCATCAATGGAAAAGGATCG 57.619 37.500 0.00 0.00 0.00 3.69
1679 5076 2.193993 GCCCGTTCCCCCTGTATATAT 58.806 52.381 0.00 0.00 0.00 0.86
1715 5112 0.883370 GAACCGCCTTCTGAACCGTT 60.883 55.000 5.39 0.00 0.00 4.44
1717 5114 2.033194 GGAACCGCCTTCTGAACCG 61.033 63.158 0.00 0.00 0.00 4.44
1899 5296 1.282157 CCCACAGGGTTTTAGAGGAGG 59.718 57.143 0.00 0.00 38.25 4.30
1949 5351 7.004086 TCACTGGATTTGAAGGAGTTTTACAT 58.996 34.615 0.00 0.00 0.00 2.29
1950 5352 6.361433 TCACTGGATTTGAAGGAGTTTTACA 58.639 36.000 0.00 0.00 0.00 2.41
1993 5395 7.998383 AGGCAATAATCACTATATGTTGGAACA 59.002 33.333 0.00 0.00 44.06 3.18
2007 5409 5.810587 TCGAGTTAACAGAGGCAATAATCAC 59.189 40.000 8.61 0.00 0.00 3.06
2046 5449 9.956720 GACATATTTATTGTCCTCCAAATTCTG 57.043 33.333 0.00 0.00 38.00 3.02
2098 5501 3.181473 TGTCATACTATCCGTTTTCCCCG 60.181 47.826 0.00 0.00 0.00 5.73
2184 5589 8.470002 GCATCATATTACACTCTTTTTCCCTTT 58.530 33.333 0.00 0.00 0.00 3.11
2225 5630 0.910338 GGGGGAGTACCTTCCTGAAC 59.090 60.000 0.00 0.00 40.03 3.18
2235 5640 0.537653 GCAAGAGTCAGGGGGAGTAC 59.462 60.000 0.00 0.00 0.00 2.73
2248 5653 2.288395 ACGGCTTTGGAATTTGCAAGAG 60.288 45.455 0.00 6.10 0.00 2.85
2310 5715 4.336889 TTGTTCACCAAGTCTCTACCAG 57.663 45.455 0.00 0.00 0.00 4.00
2402 5807 3.902881 AATGTTTCTTGTGTTGCCCAA 57.097 38.095 0.00 0.00 0.00 4.12
2403 5808 4.586421 TGATAATGTTTCTTGTGTTGCCCA 59.414 37.500 0.00 0.00 0.00 5.36
2448 5853 2.565391 TCGAAACAGACCTCATGGCTAA 59.435 45.455 0.00 0.00 36.63 3.09
2481 5886 2.048444 CTACGTGTGGTAGCCCTCTA 57.952 55.000 0.00 0.00 42.02 2.43
2497 5902 8.571336 TGTAGACAAGTTTAGTGTTCCTACTAC 58.429 37.037 0.00 0.00 33.14 2.73
2523 5928 6.197903 TCGATCATCCCCACTATATCAGATT 58.802 40.000 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.