Multiple sequence alignment - TraesCS3B01G456800

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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 TraesCS3B01G456800 chr3B 100.000 2736 0 0 1 2736 698193740 698196475 0.000000e+00 5053.0
1 TraesCS3B01G456800 chr3B 86.484 947 59 32 920 1834 698122035 698122944 0.000000e+00 976.0
2 TraesCS3B01G456800 chr3B 83.368 956 81 34 920 1834 697983028 697983946 0.000000e+00 813.0
3 TraesCS3B01G456800 chr3B 87.340 703 52 20 920 1602 697999979 698000664 0.000000e+00 771.0
4 TraesCS3B01G456800 chr2B 95.657 852 16 2 51 901 679905108 679905939 0.000000e+00 1349.0
5 TraesCS3B01G456800 chr2B 89.030 237 21 4 666 902 184364964 184364733 3.450000e-74 289.0
6 TraesCS3B01G456800 chr3D 95.300 851 37 2 51 900 445845418 445846266 0.000000e+00 1347.0
7 TraesCS3B01G456800 chr3D 90.455 880 63 7 48 908 200465004 200464127 0.000000e+00 1140.0
8 TraesCS3B01G456800 chr3D 89.749 878 65 13 49 906 114072958 114073830 0.000000e+00 1099.0
9 TraesCS3B01G456800 chr3D 87.671 949 64 24 901 1802 528094611 528095553 0.000000e+00 1055.0
10 TraesCS3B01G456800 chr3D 91.622 740 52 8 2002 2736 92379864 92380598 0.000000e+00 1014.0
11 TraesCS3B01G456800 chr3D 83.704 988 71 39 894 1834 527735442 527736386 0.000000e+00 850.0
12 TraesCS3B01G456800 chr3D 89.302 430 30 9 901 1314 528083538 528083967 2.410000e-145 525.0
13 TraesCS3B01G456800 chr3D 81.618 544 39 22 1310 1834 528084506 528085007 7.100000e-106 394.0
14 TraesCS3B01G456800 chr3D 93.750 96 6 0 467 562 445845937 445846032 7.900000e-31 145.0
15 TraesCS3B01G456800 chr3D 89.381 113 12 0 571 683 200464584 200464472 2.840000e-30 143.0
16 TraesCS3B01G456800 chr3D 95.455 88 4 0 467 554 200464463 200464376 1.020000e-29 141.0
17 TraesCS3B01G456800 chr7A 91.892 851 43 14 51 900 544293661 544292836 0.000000e+00 1166.0
18 TraesCS3B01G456800 chr7A 80.447 358 47 23 553 900 696015536 696015192 4.520000e-63 252.0
19 TraesCS3B01G456800 chr6B 92.318 742 48 8 2001 2736 648287467 648288205 0.000000e+00 1046.0
20 TraesCS3B01G456800 chr6B 92.318 742 45 12 2001 2736 54660435 54659700 0.000000e+00 1044.0
21 TraesCS3B01G456800 chr6B 91.746 739 53 7 2002 2736 252865433 252864699 0.000000e+00 1020.0
22 TraesCS3B01G456800 chr2D 92.173 741 51 7 2000 2736 527886467 527887204 0.000000e+00 1040.0
23 TraesCS3B01G456800 chr2D 91.848 736 49 8 2004 2736 446731218 446730491 0.000000e+00 1016.0
24 TraesCS3B01G456800 chr5D 91.903 741 52 8 2000 2736 545957499 545958235 0.000000e+00 1029.0
25 TraesCS3B01G456800 chr1D 91.521 743 55 8 1999 2736 458743039 458743778 0.000000e+00 1016.0
26 TraesCS3B01G456800 chr7D 91.386 743 57 7 1999 2736 158953408 158954148 0.000000e+00 1011.0
27 TraesCS3B01G456800 chr7D 97.436 39 1 0 467 505 127702243 127702281 1.760000e-07 67.6
28 TraesCS3B01G456800 chr3A 85.517 939 73 30 901 1802 662519949 662520861 0.000000e+00 922.0
29 TraesCS3B01G456800 chr2A 89.259 270 28 1 632 901 602695531 602695799 1.210000e-88 337.0
30 TraesCS3B01G456800 chr6A 90.244 246 18 5 658 901 115233429 115233670 1.580000e-82 316.0
31 TraesCS3B01G456800 chr1A 91.667 120 10 0 50 169 589673730 589673611 1.690000e-37 167.0
32 TraesCS3B01G456800 chr1A 91.379 116 10 0 229 344 589673602 589673487 2.820000e-35 159.0
33 TraesCS3B01G456800 chr1B 82.031 128 23 0 48 175 518169597 518169724 2.880000e-20 110.0


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 TraesCS3B01G456800 chr3B 698193740 698196475 2735 False 5053.000000 5053 100.000000 1 2736 1 chr3B.!!$F4 2735
1 TraesCS3B01G456800 chr3B 698122035 698122944 909 False 976.000000 976 86.484000 920 1834 1 chr3B.!!$F3 914
2 TraesCS3B01G456800 chr3B 697983028 697983946 918 False 813.000000 813 83.368000 920 1834 1 chr3B.!!$F1 914
3 TraesCS3B01G456800 chr3B 697999979 698000664 685 False 771.000000 771 87.340000 920 1602 1 chr3B.!!$F2 682
4 TraesCS3B01G456800 chr2B 679905108 679905939 831 False 1349.000000 1349 95.657000 51 901 1 chr2B.!!$F1 850
5 TraesCS3B01G456800 chr3D 114072958 114073830 872 False 1099.000000 1099 89.749000 49 906 1 chr3D.!!$F2 857
6 TraesCS3B01G456800 chr3D 528094611 528095553 942 False 1055.000000 1055 87.671000 901 1802 1 chr3D.!!$F4 901
7 TraesCS3B01G456800 chr3D 92379864 92380598 734 False 1014.000000 1014 91.622000 2002 2736 1 chr3D.!!$F1 734
8 TraesCS3B01G456800 chr3D 527735442 527736386 944 False 850.000000 850 83.704000 894 1834 1 chr3D.!!$F3 940
9 TraesCS3B01G456800 chr3D 445845418 445846266 848 False 746.000000 1347 94.525000 51 900 2 chr3D.!!$F5 849
10 TraesCS3B01G456800 chr3D 200464127 200465004 877 True 474.666667 1140 91.763667 48 908 3 chr3D.!!$R1 860
11 TraesCS3B01G456800 chr3D 528083538 528085007 1469 False 459.500000 525 85.460000 901 1834 2 chr3D.!!$F6 933
12 TraesCS3B01G456800 chr7A 544292836 544293661 825 True 1166.000000 1166 91.892000 51 900 1 chr7A.!!$R1 849
13 TraesCS3B01G456800 chr6B 648287467 648288205 738 False 1046.000000 1046 92.318000 2001 2736 1 chr6B.!!$F1 735
14 TraesCS3B01G456800 chr6B 54659700 54660435 735 True 1044.000000 1044 92.318000 2001 2736 1 chr6B.!!$R1 735
15 TraesCS3B01G456800 chr6B 252864699 252865433 734 True 1020.000000 1020 91.746000 2002 2736 1 chr6B.!!$R2 734
16 TraesCS3B01G456800 chr2D 527886467 527887204 737 False 1040.000000 1040 92.173000 2000 2736 1 chr2D.!!$F1 736
17 TraesCS3B01G456800 chr2D 446730491 446731218 727 True 1016.000000 1016 91.848000 2004 2736 1 chr2D.!!$R1 732
18 TraesCS3B01G456800 chr5D 545957499 545958235 736 False 1029.000000 1029 91.903000 2000 2736 1 chr5D.!!$F1 736
19 TraesCS3B01G456800 chr1D 458743039 458743778 739 False 1016.000000 1016 91.521000 1999 2736 1 chr1D.!!$F1 737
20 TraesCS3B01G456800 chr7D 158953408 158954148 740 False 1011.000000 1011 91.386000 1999 2736 1 chr7D.!!$F2 737
21 TraesCS3B01G456800 chr3A 662519949 662520861 912 False 922.000000 922 85.517000 901 1802 1 chr3A.!!$F1 901

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
95 96 2.033141 AGGCTGCATTGCACGAGT 59.967 55.556 7.38 0.0 33.79 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1921 2634 0.035458 CCGTTGGCCTCTTCTTGAGT 59.965 55.0 3.32 0.0 41.11 3.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 2.033141 AGGCTGCATTGCACGAGT 59.967 55.556 7.38 0.00 33.79 4.18
313 315 2.557924 CCAGTGATAGCCAAAACTGCAA 59.442 45.455 0.00 0.00 38.95 4.08
361 363 2.506217 GGAATCGCGACGCACTCA 60.506 61.111 21.35 0.01 0.00 3.41
1121 1209 4.095036 TCAGTGATCTAGCTAAGACACACG 59.905 45.833 18.95 12.68 43.59 4.49
1148 1238 1.298157 CGTGAAATGGCTCGGCTGAA 61.298 55.000 0.00 0.00 0.00 3.02
1158 1248 2.046023 CGGCTGAATGGTGCCTCA 60.046 61.111 0.00 0.00 46.42 3.86
1161 1251 1.751927 GCTGAATGGTGCCTCAGGG 60.752 63.158 0.00 0.00 39.61 4.45
1188 1278 2.336478 ACTCCTCGTCGTCCTGCTG 61.336 63.158 0.00 0.00 0.00 4.41
1305 1395 3.319198 GTGGAGGGCGACAGGGAA 61.319 66.667 0.00 0.00 0.00 3.97
1634 2318 0.595567 TTTGCGCGTGAGAGTACGTT 60.596 50.000 8.43 0.00 45.36 3.99
1640 2324 3.278303 CGCGTGAGAGTACGTTATGTAG 58.722 50.000 0.00 0.00 45.36 2.74
1642 2333 3.310774 GCGTGAGAGTACGTTATGTAGGA 59.689 47.826 0.00 0.00 45.36 2.94
1664 2363 2.268298 CGAATAACGAAGGGTGTGAGG 58.732 52.381 0.00 0.00 45.77 3.86
1665 2364 2.353406 CGAATAACGAAGGGTGTGAGGT 60.353 50.000 0.00 0.00 45.77 3.85
1666 2365 3.119388 CGAATAACGAAGGGTGTGAGGTA 60.119 47.826 0.00 0.00 45.77 3.08
1667 2366 3.881937 ATAACGAAGGGTGTGAGGTAC 57.118 47.619 0.00 0.00 0.00 3.34
1684 2386 1.063764 GTACGTAGAGTTGAGCGGAGG 59.936 57.143 0.00 0.00 0.00 4.30
1687 2389 1.002251 CGTAGAGTTGAGCGGAGGATC 60.002 57.143 0.00 0.00 0.00 3.36
1688 2390 2.025155 GTAGAGTTGAGCGGAGGATCA 58.975 52.381 0.00 0.00 36.65 2.92
1702 2408 2.362397 GAGGATCAAGGCTGTACGATGA 59.638 50.000 0.00 0.00 33.17 2.92
1703 2409 2.363680 AGGATCAAGGCTGTACGATGAG 59.636 50.000 0.00 0.00 0.00 2.90
1704 2410 2.546795 GGATCAAGGCTGTACGATGAGG 60.547 54.545 0.00 0.00 0.00 3.86
1712 2418 4.221422 TACGATGAGGCAGGCGGC 62.221 66.667 0.00 0.00 43.74 6.53
1762 2473 7.761651 AAAAAGTTTTGCAAGAAGAGATGAC 57.238 32.000 0.61 0.00 0.00 3.06
1776 2487 6.809196 AGAAGAGATGACAGTGTCGAAATAAC 59.191 38.462 18.17 7.94 34.95 1.89
1823 2536 9.939802 ATTTTGTTTCTACTAGGTACTAACTGG 57.060 33.333 0.00 0.00 42.17 4.00
1834 2547 0.955428 ACTAACTGGTGCCATGTGCG 60.955 55.000 0.00 0.00 45.60 5.34
1835 2548 0.955428 CTAACTGGTGCCATGTGCGT 60.955 55.000 0.00 0.00 45.60 5.24
1836 2549 0.321996 TAACTGGTGCCATGTGCGTA 59.678 50.000 0.00 0.00 45.60 4.42
1837 2550 1.234615 AACTGGTGCCATGTGCGTAC 61.235 55.000 0.00 0.00 45.60 3.67
1838 2551 2.739704 CTGGTGCCATGTGCGTACG 61.740 63.158 11.84 11.84 45.60 3.67
1839 2552 2.433491 GGTGCCATGTGCGTACGA 60.433 61.111 21.65 0.00 45.60 3.43
1840 2553 2.736682 GGTGCCATGTGCGTACGAC 61.737 63.158 21.65 14.50 45.60 4.34
1841 2554 1.736645 GTGCCATGTGCGTACGACT 60.737 57.895 21.65 0.00 45.60 4.18
1842 2555 1.736282 TGCCATGTGCGTACGACTG 60.736 57.895 21.65 9.43 45.60 3.51
1843 2556 1.445410 GCCATGTGCGTACGACTGA 60.445 57.895 21.65 0.00 0.00 3.41
1844 2557 1.683790 GCCATGTGCGTACGACTGAC 61.684 60.000 21.65 9.64 0.00 3.51
1845 2558 0.109272 CCATGTGCGTACGACTGACT 60.109 55.000 21.65 0.00 0.00 3.41
1846 2559 0.984829 CATGTGCGTACGACTGACTG 59.015 55.000 21.65 4.09 0.00 3.51
1847 2560 0.596577 ATGTGCGTACGACTGACTGT 59.403 50.000 21.65 0.47 0.00 3.55
1848 2561 0.040692 TGTGCGTACGACTGACTGTC 60.041 55.000 21.65 0.00 42.06 3.51
1849 2562 0.728466 GTGCGTACGACTGACTGTCC 60.728 60.000 21.65 0.00 42.49 4.02
1850 2563 0.887836 TGCGTACGACTGACTGTCCT 60.888 55.000 21.65 0.00 42.49 3.85
1851 2564 0.454620 GCGTACGACTGACTGTCCTG 60.455 60.000 21.65 0.97 42.49 3.86
1852 2565 1.154197 CGTACGACTGACTGTCCTGA 58.846 55.000 10.44 0.00 42.49 3.86
1853 2566 1.738350 CGTACGACTGACTGTCCTGAT 59.262 52.381 10.44 0.00 42.49 2.90
1854 2567 2.223066 CGTACGACTGACTGTCCTGATC 60.223 54.545 10.44 0.00 42.49 2.92
1855 2568 1.911057 ACGACTGACTGTCCTGATCA 58.089 50.000 5.17 0.00 42.49 2.92
1856 2569 1.815613 ACGACTGACTGTCCTGATCAG 59.184 52.381 16.24 16.24 44.49 2.90
1872 2585 5.139435 TGATCAGGAGTAATAAGCCATCG 57.861 43.478 0.00 0.00 0.00 3.84
1873 2586 4.021104 TGATCAGGAGTAATAAGCCATCGG 60.021 45.833 0.00 0.00 0.00 4.18
1892 2605 4.927782 TGCACCGCACGCTTCCTT 62.928 61.111 0.00 0.00 31.71 3.36
1893 2606 4.090057 GCACCGCACGCTTCCTTC 62.090 66.667 0.00 0.00 0.00 3.46
1894 2607 2.357517 CACCGCACGCTTCCTTCT 60.358 61.111 0.00 0.00 0.00 2.85
1895 2608 2.048127 ACCGCACGCTTCCTTCTC 60.048 61.111 0.00 0.00 0.00 2.87
1896 2609 2.815647 CCGCACGCTTCCTTCTCC 60.816 66.667 0.00 0.00 0.00 3.71
1897 2610 2.262915 CGCACGCTTCCTTCTCCT 59.737 61.111 0.00 0.00 0.00 3.69
1898 2611 1.807573 CGCACGCTTCCTTCTCCTC 60.808 63.158 0.00 0.00 0.00 3.71
1899 2612 1.293498 GCACGCTTCCTTCTCCTCA 59.707 57.895 0.00 0.00 0.00 3.86
1900 2613 1.016653 GCACGCTTCCTTCTCCTCAC 61.017 60.000 0.00 0.00 0.00 3.51
1901 2614 0.605589 CACGCTTCCTTCTCCTCACT 59.394 55.000 0.00 0.00 0.00 3.41
1902 2615 1.001406 CACGCTTCCTTCTCCTCACTT 59.999 52.381 0.00 0.00 0.00 3.16
1903 2616 1.001406 ACGCTTCCTTCTCCTCACTTG 59.999 52.381 0.00 0.00 0.00 3.16
1904 2617 1.447945 GCTTCCTTCTCCTCACTTGC 58.552 55.000 0.00 0.00 0.00 4.01
1905 2618 1.271054 GCTTCCTTCTCCTCACTTGCA 60.271 52.381 0.00 0.00 0.00 4.08
1906 2619 2.811873 GCTTCCTTCTCCTCACTTGCAA 60.812 50.000 0.00 0.00 0.00 4.08
1907 2620 3.683802 CTTCCTTCTCCTCACTTGCAAT 58.316 45.455 0.00 0.00 0.00 3.56
1908 2621 3.340814 TCCTTCTCCTCACTTGCAATC 57.659 47.619 0.00 0.00 0.00 2.67
1909 2622 2.026822 TCCTTCTCCTCACTTGCAATCC 60.027 50.000 0.00 0.00 0.00 3.01
1910 2623 2.026449 CCTTCTCCTCACTTGCAATCCT 60.026 50.000 0.00 0.00 0.00 3.24
1911 2624 3.269178 CTTCTCCTCACTTGCAATCCTC 58.731 50.000 0.00 0.00 0.00 3.71
1912 2625 2.544721 TCTCCTCACTTGCAATCCTCT 58.455 47.619 0.00 0.00 0.00 3.69
1913 2626 2.235650 TCTCCTCACTTGCAATCCTCTG 59.764 50.000 0.00 0.00 0.00 3.35
1914 2627 1.280133 TCCTCACTTGCAATCCTCTGG 59.720 52.381 0.00 0.00 0.00 3.86
1915 2628 1.093159 CTCACTTGCAATCCTCTGGC 58.907 55.000 0.00 0.00 0.00 4.85
1916 2629 0.694771 TCACTTGCAATCCTCTGGCT 59.305 50.000 0.00 0.00 0.00 4.75
1917 2630 1.093159 CACTTGCAATCCTCTGGCTC 58.907 55.000 0.00 0.00 0.00 4.70
1918 2631 0.990374 ACTTGCAATCCTCTGGCTCT 59.010 50.000 0.00 0.00 0.00 4.09
1919 2632 1.353694 ACTTGCAATCCTCTGGCTCTT 59.646 47.619 0.00 0.00 0.00 2.85
1920 2633 2.224967 ACTTGCAATCCTCTGGCTCTTT 60.225 45.455 0.00 0.00 0.00 2.52
1921 2634 3.009473 ACTTGCAATCCTCTGGCTCTTTA 59.991 43.478 0.00 0.00 0.00 1.85
1922 2635 2.991250 TGCAATCCTCTGGCTCTTTAC 58.009 47.619 0.00 0.00 0.00 2.01
1923 2636 2.573462 TGCAATCCTCTGGCTCTTTACT 59.427 45.455 0.00 0.00 0.00 2.24
1924 2637 3.202097 GCAATCCTCTGGCTCTTTACTC 58.798 50.000 0.00 0.00 0.00 2.59
1925 2638 3.369892 GCAATCCTCTGGCTCTTTACTCA 60.370 47.826 0.00 0.00 0.00 3.41
1926 2639 4.836825 CAATCCTCTGGCTCTTTACTCAA 58.163 43.478 0.00 0.00 0.00 3.02
1927 2640 4.751767 ATCCTCTGGCTCTTTACTCAAG 57.248 45.455 0.00 0.00 0.00 3.02
1928 2641 3.779444 TCCTCTGGCTCTTTACTCAAGA 58.221 45.455 0.00 0.00 39.39 3.02
1929 2642 4.160329 TCCTCTGGCTCTTTACTCAAGAA 58.840 43.478 0.00 0.00 41.25 2.52
1930 2643 4.221703 TCCTCTGGCTCTTTACTCAAGAAG 59.778 45.833 0.00 0.00 41.25 2.85
1931 2644 4.221703 CCTCTGGCTCTTTACTCAAGAAGA 59.778 45.833 0.00 0.00 41.25 2.87
1940 2653 2.846371 CTCAAGAAGAGGCCAACGG 58.154 57.895 5.01 0.00 40.84 4.44
1958 2671 4.388499 CCGGCCGGCACACTAGTT 62.388 66.667 34.96 0.00 0.00 2.24
1959 2672 2.358247 CGGCCGGCACACTAGTTT 60.358 61.111 30.85 0.00 0.00 2.66
1960 2673 2.388232 CGGCCGGCACACTAGTTTC 61.388 63.158 30.85 5.23 0.00 2.78
1961 2674 2.038837 GGCCGGCACACTAGTTTCC 61.039 63.158 30.85 1.22 0.00 3.13
1962 2675 1.003718 GCCGGCACACTAGTTTCCT 60.004 57.895 24.80 0.00 0.00 3.36
1963 2676 0.248289 GCCGGCACACTAGTTTCCTA 59.752 55.000 24.80 0.00 0.00 2.94
1964 2677 2.005560 GCCGGCACACTAGTTTCCTAC 61.006 57.143 24.80 0.00 0.00 3.18
1965 2678 1.274167 CCGGCACACTAGTTTCCTACA 59.726 52.381 0.00 0.00 0.00 2.74
1966 2679 2.334838 CGGCACACTAGTTTCCTACAC 58.665 52.381 0.00 0.00 0.00 2.90
1967 2680 2.334838 GGCACACTAGTTTCCTACACG 58.665 52.381 0.00 0.00 0.00 4.49
1968 2681 2.288640 GGCACACTAGTTTCCTACACGT 60.289 50.000 0.00 0.00 0.00 4.49
1969 2682 2.985139 GCACACTAGTTTCCTACACGTC 59.015 50.000 0.00 0.00 0.00 4.34
1970 2683 3.551454 GCACACTAGTTTCCTACACGTCA 60.551 47.826 0.00 0.00 0.00 4.35
1971 2684 4.806330 CACACTAGTTTCCTACACGTCAT 58.194 43.478 0.00 0.00 0.00 3.06
1972 2685 4.621460 CACACTAGTTTCCTACACGTCATG 59.379 45.833 0.00 0.00 0.00 3.07
1973 2686 4.174009 CACTAGTTTCCTACACGTCATGG 58.826 47.826 0.00 0.00 0.00 3.66
1974 2687 2.762535 AGTTTCCTACACGTCATGGG 57.237 50.000 0.00 0.00 0.00 4.00
1975 2688 1.084289 GTTTCCTACACGTCATGGGC 58.916 55.000 0.00 0.00 0.00 5.36
1976 2689 0.981183 TTTCCTACACGTCATGGGCT 59.019 50.000 0.00 0.00 0.00 5.19
1977 2690 0.535335 TTCCTACACGTCATGGGCTC 59.465 55.000 0.00 0.00 0.00 4.70
1978 2691 0.613572 TCCTACACGTCATGGGCTCA 60.614 55.000 0.00 0.00 0.00 4.26
1979 2692 0.465705 CCTACACGTCATGGGCTCAT 59.534 55.000 0.00 0.00 0.00 2.90
1986 2699 3.455152 CATGGGCTCATGGCATGG 58.545 61.111 26.15 17.60 45.19 3.66
1987 2700 1.456892 CATGGGCTCATGGCATGGT 60.457 57.895 26.15 4.43 45.19 3.55
1988 2701 0.178984 CATGGGCTCATGGCATGGTA 60.179 55.000 26.15 8.13 45.19 3.25
1989 2702 0.111832 ATGGGCTCATGGCATGGTAG 59.888 55.000 26.15 18.05 44.01 3.18
1990 2703 0.987613 TGGGCTCATGGCATGGTAGA 60.988 55.000 26.15 7.02 44.01 2.59
1991 2704 0.536006 GGGCTCATGGCATGGTAGAC 60.536 60.000 26.15 18.99 44.01 2.59
1992 2705 0.181114 GGCTCATGGCATGGTAGACA 59.819 55.000 26.15 5.90 44.01 3.41
1993 2706 1.303309 GCTCATGGCATGGTAGACAC 58.697 55.000 26.15 5.72 41.35 3.67
1994 2707 1.959042 CTCATGGCATGGTAGACACC 58.041 55.000 26.15 0.00 46.00 4.16
2053 2768 1.403679 CGCATAAAAATCGCCCCTGAA 59.596 47.619 0.00 0.00 0.00 3.02
2083 2800 1.958579 CGATACATTCGGTACTGGGGA 59.041 52.381 0.85 0.00 44.28 4.81
2086 2803 0.612732 ACATTCGGTACTGGGGACGA 60.613 55.000 0.85 0.00 0.00 4.20
2089 2806 0.533491 TTCGGTACTGGGGACGATTG 59.467 55.000 0.85 0.00 35.10 2.67
2170 2890 1.539827 CCCATTTCGGCGAAAAGAGTT 59.460 47.619 34.99 18.23 35.11 3.01
2188 2908 5.080337 AGAGTTCATATGGGCGAGAATAGA 58.920 41.667 2.13 0.00 0.00 1.98
2209 2929 1.593196 CCATATTCGGCATGGTTCGT 58.407 50.000 0.00 0.00 38.53 3.85
2210 2930 1.946768 CCATATTCGGCATGGTTCGTT 59.053 47.619 0.00 0.00 38.53 3.85
2211 2931 3.135225 CCATATTCGGCATGGTTCGTTA 58.865 45.455 0.00 0.00 38.53 3.18
2435 3156 2.290197 TGCAGTTGATGATGCACCTGTA 60.290 45.455 0.00 0.00 46.97 2.74
2578 3299 4.053983 GCTCGCTCTCAATGATCATGTTA 58.946 43.478 9.46 0.00 0.00 2.41
2703 3425 0.179062 GCTCGACATCCTTCCTGCAT 60.179 55.000 0.00 0.00 0.00 3.96
2704 3426 1.069204 GCTCGACATCCTTCCTGCATA 59.931 52.381 0.00 0.00 0.00 3.14
2709 3431 2.435805 GACATCCTTCCTGCATACCTCA 59.564 50.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 3.675619 AACACGCCCATACCGGAGC 62.676 63.158 9.46 1.34 36.56 4.70
41 42 1.078708 AAACACGCCCATACCGGAG 60.079 57.895 9.46 0.00 36.56 4.63
42 43 1.376166 CAAACACGCCCATACCGGA 60.376 57.895 9.46 0.00 36.56 5.14
43 44 2.403378 CCAAACACGCCCATACCGG 61.403 63.158 0.00 0.00 0.00 5.28
44 45 1.238625 AACCAAACACGCCCATACCG 61.239 55.000 0.00 0.00 0.00 4.02
45 46 0.524414 GAACCAAACACGCCCATACC 59.476 55.000 0.00 0.00 0.00 2.73
46 47 0.524414 GGAACCAAACACGCCCATAC 59.476 55.000 0.00 0.00 0.00 2.39
95 96 2.997315 CGAGCTCACCCAGGACCA 60.997 66.667 15.40 0.00 0.00 4.02
313 315 2.959030 TGCGAGATAGTTACTGGAGCAT 59.041 45.455 0.00 0.00 0.00 3.79
361 363 3.884350 CCGCGCTGCTGCATCATT 61.884 61.111 16.29 0.00 39.64 2.57
962 997 2.736995 CTGCGAACGGAAAGGCGA 60.737 61.111 0.00 0.00 0.00 5.54
1121 1209 1.730547 GCCATTTCACGTGCACTGC 60.731 57.895 16.19 5.92 0.00 4.40
1158 1248 4.990910 AGGAGTGTGCAGGCCCCT 62.991 66.667 0.00 0.00 0.00 4.79
1161 1251 3.941657 GACGAGGAGTGTGCAGGCC 62.942 68.421 0.00 0.00 0.00 5.19
1246 1336 3.382832 CACCTTCCTCCCGTCGCT 61.383 66.667 0.00 0.00 0.00 4.93
1247 1337 4.452733 CCACCTTCCTCCCGTCGC 62.453 72.222 0.00 0.00 0.00 5.19
1623 2307 5.604565 TCGATCCTACATAACGTACTCTCA 58.395 41.667 0.00 0.00 0.00 3.27
1624 2308 6.536731 TTCGATCCTACATAACGTACTCTC 57.463 41.667 0.00 0.00 0.00 3.20
1660 2359 1.736126 CGCTCAACTCTACGTACCTCA 59.264 52.381 0.00 0.00 0.00 3.86
1662 2361 1.093159 CCGCTCAACTCTACGTACCT 58.907 55.000 0.00 0.00 0.00 3.08
1663 2362 1.063764 CTCCGCTCAACTCTACGTACC 59.936 57.143 0.00 0.00 0.00 3.34
1664 2363 1.063764 CCTCCGCTCAACTCTACGTAC 59.936 57.143 0.00 0.00 0.00 3.67
1665 2364 1.065926 TCCTCCGCTCAACTCTACGTA 60.066 52.381 0.00 0.00 0.00 3.57
1666 2365 0.322277 TCCTCCGCTCAACTCTACGT 60.322 55.000 0.00 0.00 0.00 3.57
1667 2366 1.002251 GATCCTCCGCTCAACTCTACG 60.002 57.143 0.00 0.00 0.00 3.51
1684 2386 2.748605 CCTCATCGTACAGCCTTGATC 58.251 52.381 0.00 0.00 0.00 2.92
1687 2389 0.108186 TGCCTCATCGTACAGCCTTG 60.108 55.000 0.00 0.00 0.00 3.61
1688 2390 0.176680 CTGCCTCATCGTACAGCCTT 59.823 55.000 0.00 0.00 0.00 4.35
1704 2410 3.615709 AAAACTTGGGCCGCCTGC 61.616 61.111 9.86 0.00 40.16 4.85
1797 2510 9.939802 CCAGTTAGTACCTAGTAGAAACAAAAT 57.060 33.333 0.00 0.00 0.00 1.82
1803 2516 5.420104 GGCACCAGTTAGTACCTAGTAGAAA 59.580 44.000 0.00 0.00 0.00 2.52
1808 2521 3.179902 TGGCACCAGTTAGTACCTAGT 57.820 47.619 0.00 0.00 0.00 2.57
1809 2522 3.451178 ACATGGCACCAGTTAGTACCTAG 59.549 47.826 0.00 0.00 0.00 3.02
1810 2523 3.196901 CACATGGCACCAGTTAGTACCTA 59.803 47.826 0.00 0.00 0.00 3.08
1811 2524 2.027192 CACATGGCACCAGTTAGTACCT 60.027 50.000 0.00 0.00 0.00 3.08
1823 2536 1.736645 AGTCGTACGCACATGGCAC 60.737 57.895 11.24 0.42 45.17 5.01
1849 2562 5.167121 CGATGGCTTATTACTCCTGATCAG 58.833 45.833 16.24 16.24 0.00 2.90
1850 2563 4.021104 CCGATGGCTTATTACTCCTGATCA 60.021 45.833 0.00 0.00 0.00 2.92
1851 2564 4.499183 CCGATGGCTTATTACTCCTGATC 58.501 47.826 0.00 0.00 0.00 2.92
1852 2565 3.307059 GCCGATGGCTTATTACTCCTGAT 60.307 47.826 0.00 0.00 46.69 2.90
1853 2566 2.037251 GCCGATGGCTTATTACTCCTGA 59.963 50.000 0.00 0.00 46.69 3.86
1854 2567 2.417719 GCCGATGGCTTATTACTCCTG 58.582 52.381 0.00 0.00 46.69 3.86
1855 2568 2.841442 GCCGATGGCTTATTACTCCT 57.159 50.000 0.00 0.00 46.69 3.69
1875 2588 4.927782 AAGGAAGCGTGCGGTGCA 62.928 61.111 4.11 0.00 35.60 4.57
1876 2589 4.090057 GAAGGAAGCGTGCGGTGC 62.090 66.667 0.00 0.00 0.00 5.01
1877 2590 2.357517 AGAAGGAAGCGTGCGGTG 60.358 61.111 0.00 0.00 0.00 4.94
1878 2591 2.048127 GAGAAGGAAGCGTGCGGT 60.048 61.111 0.00 0.00 0.00 5.68
1879 2592 2.815647 GGAGAAGGAAGCGTGCGG 60.816 66.667 0.00 0.00 0.00 5.69
1880 2593 1.807573 GAGGAGAAGGAAGCGTGCG 60.808 63.158 0.00 0.00 0.00 5.34
1881 2594 1.016653 GTGAGGAGAAGGAAGCGTGC 61.017 60.000 0.00 0.00 0.00 5.34
1882 2595 0.605589 AGTGAGGAGAAGGAAGCGTG 59.394 55.000 0.00 0.00 0.00 5.34
1883 2596 1.001406 CAAGTGAGGAGAAGGAAGCGT 59.999 52.381 0.00 0.00 0.00 5.07
1884 2597 1.719600 CAAGTGAGGAGAAGGAAGCG 58.280 55.000 0.00 0.00 0.00 4.68
1885 2598 1.271054 TGCAAGTGAGGAGAAGGAAGC 60.271 52.381 0.00 0.00 0.00 3.86
1886 2599 2.847327 TGCAAGTGAGGAGAAGGAAG 57.153 50.000 0.00 0.00 0.00 3.46
1887 2600 3.560025 GGATTGCAAGTGAGGAGAAGGAA 60.560 47.826 4.94 0.00 0.00 3.36
1888 2601 2.026822 GGATTGCAAGTGAGGAGAAGGA 60.027 50.000 4.94 0.00 0.00 3.36
1889 2602 2.026449 AGGATTGCAAGTGAGGAGAAGG 60.026 50.000 4.94 0.00 0.00 3.46
1890 2603 3.055240 AGAGGATTGCAAGTGAGGAGAAG 60.055 47.826 4.94 0.00 0.00 2.85
1891 2604 2.909006 AGAGGATTGCAAGTGAGGAGAA 59.091 45.455 4.94 0.00 0.00 2.87
1892 2605 2.235650 CAGAGGATTGCAAGTGAGGAGA 59.764 50.000 4.94 0.00 0.00 3.71
1893 2606 2.630158 CAGAGGATTGCAAGTGAGGAG 58.370 52.381 4.94 0.00 0.00 3.69
1894 2607 1.280133 CCAGAGGATTGCAAGTGAGGA 59.720 52.381 4.94 0.00 0.00 3.71
1895 2608 1.747709 CCAGAGGATTGCAAGTGAGG 58.252 55.000 4.94 0.00 0.00 3.86
1896 2609 1.093159 GCCAGAGGATTGCAAGTGAG 58.907 55.000 4.94 0.00 0.00 3.51
1897 2610 0.694771 AGCCAGAGGATTGCAAGTGA 59.305 50.000 4.94 0.00 0.00 3.41
1898 2611 1.093159 GAGCCAGAGGATTGCAAGTG 58.907 55.000 4.94 0.00 0.00 3.16
1899 2612 0.990374 AGAGCCAGAGGATTGCAAGT 59.010 50.000 4.94 0.00 0.00 3.16
1900 2613 2.125773 AAGAGCCAGAGGATTGCAAG 57.874 50.000 4.94 0.00 0.00 4.01
1901 2614 2.592102 AAAGAGCCAGAGGATTGCAA 57.408 45.000 0.00 0.00 0.00 4.08
1902 2615 2.573462 AGTAAAGAGCCAGAGGATTGCA 59.427 45.455 0.00 0.00 0.00 4.08
1903 2616 3.202097 GAGTAAAGAGCCAGAGGATTGC 58.798 50.000 0.00 0.00 0.00 3.56
1904 2617 4.478206 TGAGTAAAGAGCCAGAGGATTG 57.522 45.455 0.00 0.00 0.00 2.67
1905 2618 4.780021 TCTTGAGTAAAGAGCCAGAGGATT 59.220 41.667 0.00 0.00 40.09 3.01
1906 2619 4.357325 TCTTGAGTAAAGAGCCAGAGGAT 58.643 43.478 0.00 0.00 40.09 3.24
1907 2620 3.779444 TCTTGAGTAAAGAGCCAGAGGA 58.221 45.455 0.00 0.00 40.09 3.71
1908 2621 4.221703 TCTTCTTGAGTAAAGAGCCAGAGG 59.778 45.833 0.00 0.00 45.64 3.69
1909 2622 5.398603 TCTTCTTGAGTAAAGAGCCAGAG 57.601 43.478 0.00 0.00 45.64 3.35
1910 2623 4.221703 CCTCTTCTTGAGTAAAGAGCCAGA 59.778 45.833 6.60 0.00 45.64 3.86
1911 2624 4.502962 CCTCTTCTTGAGTAAAGAGCCAG 58.497 47.826 6.60 0.00 45.64 4.85
1912 2625 3.307059 GCCTCTTCTTGAGTAAAGAGCCA 60.307 47.826 6.60 0.00 45.64 4.75
1913 2626 3.266636 GCCTCTTCTTGAGTAAAGAGCC 58.733 50.000 6.60 0.00 45.64 4.70
1914 2627 3.266636 GGCCTCTTCTTGAGTAAAGAGC 58.733 50.000 0.00 3.37 45.64 4.09
1915 2628 4.543590 TGGCCTCTTCTTGAGTAAAGAG 57.456 45.455 3.32 5.36 45.64 2.85
1916 2629 4.642429 GTTGGCCTCTTCTTGAGTAAAGA 58.358 43.478 3.32 0.00 43.37 2.52
1917 2630 3.433615 CGTTGGCCTCTTCTTGAGTAAAG 59.566 47.826 3.32 0.00 41.11 1.85
1918 2631 3.399330 CGTTGGCCTCTTCTTGAGTAAA 58.601 45.455 3.32 0.00 41.11 2.01
1919 2632 2.289444 CCGTTGGCCTCTTCTTGAGTAA 60.289 50.000 3.32 0.00 41.11 2.24
1920 2633 1.275291 CCGTTGGCCTCTTCTTGAGTA 59.725 52.381 3.32 0.00 41.11 2.59
1921 2634 0.035458 CCGTTGGCCTCTTCTTGAGT 59.965 55.000 3.32 0.00 41.11 3.41
1922 2635 1.301677 GCCGTTGGCCTCTTCTTGAG 61.302 60.000 3.32 0.00 44.06 3.02
1923 2636 1.302511 GCCGTTGGCCTCTTCTTGA 60.303 57.895 3.32 0.00 44.06 3.02
1924 2637 3.267974 GCCGTTGGCCTCTTCTTG 58.732 61.111 3.32 0.00 44.06 3.02
1941 2654 3.894547 AAACTAGTGTGCCGGCCGG 62.895 63.158 40.26 40.26 38.57 6.13
1942 2655 2.358247 AAACTAGTGTGCCGGCCG 60.358 61.111 26.77 21.04 0.00 6.13
1943 2656 2.038837 GGAAACTAGTGTGCCGGCC 61.039 63.158 26.77 16.24 0.00 6.13
1944 2657 0.248289 TAGGAAACTAGTGTGCCGGC 59.752 55.000 22.73 22.73 43.67 6.13
1945 2658 1.274167 TGTAGGAAACTAGTGTGCCGG 59.726 52.381 0.08 0.00 45.49 6.13
1946 2659 2.334838 GTGTAGGAAACTAGTGTGCCG 58.665 52.381 0.08 0.00 45.49 5.69
1947 2660 2.288640 ACGTGTAGGAAACTAGTGTGCC 60.289 50.000 0.08 1.00 45.49 5.01
1948 2661 2.985139 GACGTGTAGGAAACTAGTGTGC 59.015 50.000 0.00 0.00 45.49 4.57
1949 2662 4.233123 TGACGTGTAGGAAACTAGTGTG 57.767 45.455 0.00 0.00 45.49 3.82
1950 2663 4.321750 CCATGACGTGTAGGAAACTAGTGT 60.322 45.833 0.00 0.00 45.49 3.55
1951 2664 4.174009 CCATGACGTGTAGGAAACTAGTG 58.826 47.826 0.00 0.00 45.49 2.74
1952 2665 3.194968 CCCATGACGTGTAGGAAACTAGT 59.805 47.826 0.00 0.00 45.49 2.57
1953 2666 3.782046 CCCATGACGTGTAGGAAACTAG 58.218 50.000 0.00 0.00 45.49 2.57
1954 2667 2.093869 GCCCATGACGTGTAGGAAACTA 60.094 50.000 0.00 0.00 43.67 2.24
1956 2669 1.084289 GCCCATGACGTGTAGGAAAC 58.916 55.000 0.00 0.00 0.00 2.78
1957 2670 0.981183 AGCCCATGACGTGTAGGAAA 59.019 50.000 0.00 0.00 0.00 3.13
1958 2671 0.535335 GAGCCCATGACGTGTAGGAA 59.465 55.000 0.00 0.00 0.00 3.36
1959 2672 0.613572 TGAGCCCATGACGTGTAGGA 60.614 55.000 0.00 0.00 0.00 2.94
1960 2673 0.465705 ATGAGCCCATGACGTGTAGG 59.534 55.000 0.00 0.00 0.00 3.18
1970 2683 0.111832 CTACCATGCCATGAGCCCAT 59.888 55.000 6.18 0.00 42.71 4.00
1971 2684 0.987613 TCTACCATGCCATGAGCCCA 60.988 55.000 6.18 0.00 42.71 5.36
1972 2685 0.536006 GTCTACCATGCCATGAGCCC 60.536 60.000 6.18 0.00 42.71 5.19
1973 2686 0.181114 TGTCTACCATGCCATGAGCC 59.819 55.000 6.18 0.00 42.71 4.70
1974 2687 1.303309 GTGTCTACCATGCCATGAGC 58.697 55.000 6.18 0.00 44.14 4.26
1975 2688 1.959042 GGTGTCTACCATGCCATGAG 58.041 55.000 6.18 0.00 46.71 2.90
1985 2698 0.175073 CTAACCTGCCGGTGTCTACC 59.825 60.000 1.90 0.00 44.73 3.18
1986 2699 1.134560 CTCTAACCTGCCGGTGTCTAC 59.865 57.143 1.90 0.00 44.73 2.59
1987 2700 1.471119 CTCTAACCTGCCGGTGTCTA 58.529 55.000 1.90 0.00 44.73 2.59
1988 2701 1.889530 GCTCTAACCTGCCGGTGTCT 61.890 60.000 1.90 0.00 44.73 3.41
1989 2702 1.448013 GCTCTAACCTGCCGGTGTC 60.448 63.158 1.90 0.00 44.73 3.67
1990 2703 1.553690 ATGCTCTAACCTGCCGGTGT 61.554 55.000 1.90 0.00 44.73 4.16
1991 2704 0.811616 GATGCTCTAACCTGCCGGTG 60.812 60.000 1.90 0.00 44.73 4.94
1993 2706 0.179000 AAGATGCTCTAACCTGCCGG 59.821 55.000 0.00 0.00 0.00 6.13
1994 2707 1.576356 GAAGATGCTCTAACCTGCCG 58.424 55.000 0.00 0.00 0.00 5.69
1995 2708 1.576356 CGAAGATGCTCTAACCTGCC 58.424 55.000 0.00 0.00 0.00 4.85
1996 2709 1.576356 CCGAAGATGCTCTAACCTGC 58.424 55.000 0.00 0.00 0.00 4.85
1997 2710 1.576356 GCCGAAGATGCTCTAACCTG 58.424 55.000 0.00 0.00 0.00 4.00
2027 2742 1.400494 GGCGATTTTTATGCGTCCTGT 59.600 47.619 0.00 0.00 0.00 4.00
2053 2768 0.317938 GAATGTATCGCCGACTCGCT 60.318 55.000 0.00 0.00 0.00 4.93
2076 2793 2.047274 CGCACAATCGTCCCCAGT 60.047 61.111 0.00 0.00 0.00 4.00
2083 2800 2.742372 GACTGGGCGCACAATCGT 60.742 61.111 16.01 8.62 0.00 3.73
2086 2803 2.742372 GACGACTGGGCGCACAAT 60.742 61.111 16.01 1.79 33.86 2.71
2128 2845 1.962807 CTGAAAAGTGGGCCAACATCA 59.037 47.619 14.26 12.62 0.00 3.07
2170 2890 2.832129 GGGTCTATTCTCGCCCATATGA 59.168 50.000 3.65 0.00 40.76 2.15
2209 2929 5.069318 TGATAATTGAATGCCGAGCCATAA 58.931 37.500 0.00 0.00 0.00 1.90
2210 2930 4.650734 TGATAATTGAATGCCGAGCCATA 58.349 39.130 0.00 0.00 0.00 2.74
2211 2931 3.489355 TGATAATTGAATGCCGAGCCAT 58.511 40.909 0.00 0.00 0.00 4.40
2406 3127 2.502142 TCATCAACTGCAGCAGGATT 57.498 45.000 26.38 9.87 35.51 3.01
2410 3131 0.808755 TGCATCATCAACTGCAGCAG 59.191 50.000 21.54 21.54 43.11 4.24
2435 3156 0.464735 CGTCAGGAGATCCGAGACCT 60.465 60.000 16.67 0.00 40.44 3.85
2578 3299 1.271762 ACCTGCTGTGTCATCTTGCAT 60.272 47.619 0.00 0.00 33.02 3.96
2703 3425 3.938963 GGTTTGCGAAGATTCATGAGGTA 59.061 43.478 0.00 0.00 0.00 3.08
2704 3426 2.749621 GGTTTGCGAAGATTCATGAGGT 59.250 45.455 0.00 0.00 0.00 3.85
2709 3431 1.474077 GCCTGGTTTGCGAAGATTCAT 59.526 47.619 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.