Multiple sequence alignment - TraesCS4A01G226700

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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 TraesCS4A01G226700 chr4A 100.000 2930 0 0 1 2930 534810309 534813238 0.000000e+00 5411
1 TraesCS4A01G226700 chr4A 93.709 604 9 10 1 580 150662793 150662195 0.000000e+00 878
2 TraesCS4A01G226700 chr4A 85.156 256 33 5 2348 2599 534812533 534812787 1.040000e-64 257
3 TraesCS4A01G226700 chr4A 85.156 256 33 5 2225 2479 534812656 534812907 1.040000e-64 257
4 TraesCS4A01G226700 chr4D 92.650 1102 44 15 763 1847 61604755 61605836 0.000000e+00 1552
5 TraesCS4A01G226700 chr4B 93.110 1074 45 12 785 1847 91185239 91184184 0.000000e+00 1546
6 TraesCS4A01G226700 chr5D 89.733 1013 82 12 1868 2875 275404161 275403166 0.000000e+00 1275
7 TraesCS4A01G226700 chr5D 87.500 256 29 3 2225 2479 275403693 275403440 2.860000e-75 292
8 TraesCS4A01G226700 chr5D 87.500 232 26 3 2370 2598 275403793 275403562 6.230000e-67 265
9 TraesCS4A01G226700 chr3A 93.923 724 15 14 1 700 603918349 603919067 0.000000e+00 1066
10 TraesCS4A01G226700 chr5A 92.438 648 13 20 1 624 462874780 462874145 0.000000e+00 893
11 TraesCS4A01G226700 chr5A 93.805 565 30 4 1 562 536902490 536901928 0.000000e+00 845
12 TraesCS4A01G226700 chr5A 79.038 291 52 3 1870 2152 41709375 41709664 1.070000e-44 191
13 TraesCS4A01G226700 chrUn 93.607 610 13 7 1 588 465543103 465542498 0.000000e+00 887
14 TraesCS4A01G226700 chr7A 95.062 567 21 6 1 562 719998858 719999422 0.000000e+00 885
15 TraesCS4A01G226700 chr6B 92.283 635 14 20 1 609 457226688 457227313 0.000000e+00 869
16 TraesCS4A01G226700 chr3B 94.178 584 11 4 1 563 434649749 434649168 0.000000e+00 869
17 TraesCS4A01G226700 chr3B 90.608 543 39 8 1 533 812697655 812697115 0.000000e+00 710
18 TraesCS4A01G226700 chr1D 90.538 613 50 5 1869 2479 112623921 112624527 0.000000e+00 804
19 TraesCS4A01G226700 chr1D 87.127 536 54 9 2348 2874 112624279 112624808 6.990000e-166 593
20 TraesCS4A01G226700 chr2D 88.661 635 58 8 2251 2874 481146883 481147514 0.000000e+00 761
21 TraesCS4A01G226700 chr2D 84.649 228 32 3 2375 2599 481146885 481147112 1.060000e-54 224
22 TraesCS4A01G226700 chr5B 85.646 627 61 6 1869 2479 81188534 81187921 1.480000e-177 632
23 TraesCS4A01G226700 chr5B 86.415 530 55 11 2348 2873 81188164 81187648 5.480000e-157 564
24 TraesCS4A01G226700 chr5B 87.662 308 30 5 2572 2874 539024181 539024485 4.650000e-93 351
25 TraesCS4A01G226700 chr5B 85.197 304 36 6 2583 2878 106788897 106788595 1.320000e-78 303
26 TraesCS4A01G226700 chr7D 89.733 487 47 3 1872 2357 38661997 38662481 1.150000e-173 619
27 TraesCS4A01G226700 chr7D 87.019 416 45 7 2463 2874 38662345 38662755 7.400000e-126 460
28 TraesCS4A01G226700 chr7B 85.451 543 59 10 2342 2875 728813726 728814257 5.520000e-152 547
29 TraesCS4A01G226700 chr7B 82.630 616 76 8 1881 2479 728813374 728813975 1.560000e-142 516
30 TraesCS4A01G226700 chr7B 90.625 96 9 0 2291 2386 728813737 728813832 8.520000e-26 128
31 TraesCS4A01G226700 chr1A 85.915 284 36 3 2592 2871 94865388 94865671 1.710000e-77 300


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 TraesCS4A01G226700 chr4A 534810309 534813238 2929 False 1975.000000 5411 90.104000 1 2930 3 chr4A.!!$F1 2929
1 TraesCS4A01G226700 chr4A 150662195 150662793 598 True 878.000000 878 93.709000 1 580 1 chr4A.!!$R1 579
2 TraesCS4A01G226700 chr4D 61604755 61605836 1081 False 1552.000000 1552 92.650000 763 1847 1 chr4D.!!$F1 1084
3 TraesCS4A01G226700 chr4B 91184184 91185239 1055 True 1546.000000 1546 93.110000 785 1847 1 chr4B.!!$R1 1062
4 TraesCS4A01G226700 chr5D 275403166 275404161 995 True 610.666667 1275 88.244333 1868 2875 3 chr5D.!!$R1 1007
5 TraesCS4A01G226700 chr3A 603918349 603919067 718 False 1066.000000 1066 93.923000 1 700 1 chr3A.!!$F1 699
6 TraesCS4A01G226700 chr5A 462874145 462874780 635 True 893.000000 893 92.438000 1 624 1 chr5A.!!$R1 623
7 TraesCS4A01G226700 chr5A 536901928 536902490 562 True 845.000000 845 93.805000 1 562 1 chr5A.!!$R2 561
8 TraesCS4A01G226700 chrUn 465542498 465543103 605 True 887.000000 887 93.607000 1 588 1 chrUn.!!$R1 587
9 TraesCS4A01G226700 chr7A 719998858 719999422 564 False 885.000000 885 95.062000 1 562 1 chr7A.!!$F1 561
10 TraesCS4A01G226700 chr6B 457226688 457227313 625 False 869.000000 869 92.283000 1 609 1 chr6B.!!$F1 608
11 TraesCS4A01G226700 chr3B 434649168 434649749 581 True 869.000000 869 94.178000 1 563 1 chr3B.!!$R1 562
12 TraesCS4A01G226700 chr3B 812697115 812697655 540 True 710.000000 710 90.608000 1 533 1 chr3B.!!$R2 532
13 TraesCS4A01G226700 chr1D 112623921 112624808 887 False 698.500000 804 88.832500 1869 2874 2 chr1D.!!$F1 1005
14 TraesCS4A01G226700 chr2D 481146883 481147514 631 False 492.500000 761 86.655000 2251 2874 2 chr2D.!!$F1 623
15 TraesCS4A01G226700 chr5B 81187648 81188534 886 True 598.000000 632 86.030500 1869 2873 2 chr5B.!!$R2 1004
16 TraesCS4A01G226700 chr7D 38661997 38662755 758 False 539.500000 619 88.376000 1872 2874 2 chr7D.!!$F1 1002
17 TraesCS4A01G226700 chr7B 728813374 728814257 883 False 397.000000 547 86.235333 1881 2875 3 chr7B.!!$F1 994

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
811 865 0.179073 CTCCCTGATGACGCCGAATT 60.179 55.0 0.0 0.0 0.0 2.17 F
1038 1103 0.234884 GCGCGCAAACACTTTCTACT 59.765 50.0 29.1 0.0 0.0 2.57 F
1858 1929 0.307453 TGCGTGTGATGTTGTTGCTC 59.693 50.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1865 1936 0.696501 ACCAATCACGCCCTTAAGGT 59.303 50.0 20.22 0.0 38.26 3.50 R
1868 1939 0.885196 GCAACCAATCACGCCCTTAA 59.115 50.0 0.00 0.0 0.00 1.85 R
2858 2984 0.887387 GCACCTAAGGGCGTGTTTGA 60.887 55.0 0.00 0.0 35.63 2.69 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
127 128 6.741992 TCAGAACTCGCAATTGTTTGATAT 57.258 33.333 7.40 0.00 34.60 1.63
308 360 4.742438 TTACTGCGCTTGGTAAAAAGAG 57.258 40.909 9.73 0.00 0.00 2.85
489 542 1.468985 CCATTTACGGGTGGCATTGA 58.531 50.000 0.00 0.00 0.00 2.57
806 860 0.321653 ACAAACTCCCTGATGACGCC 60.322 55.000 0.00 0.00 0.00 5.68
808 862 1.541310 AAACTCCCTGATGACGCCGA 61.541 55.000 0.00 0.00 0.00 5.54
809 863 1.541310 AACTCCCTGATGACGCCGAA 61.541 55.000 0.00 0.00 0.00 4.30
810 864 1.330655 ACTCCCTGATGACGCCGAAT 61.331 55.000 0.00 0.00 0.00 3.34
811 865 0.179073 CTCCCTGATGACGCCGAATT 60.179 55.000 0.00 0.00 0.00 2.17
812 866 0.461870 TCCCTGATGACGCCGAATTG 60.462 55.000 0.00 0.00 0.00 2.32
813 867 1.439353 CCCTGATGACGCCGAATTGG 61.439 60.000 0.00 0.00 42.50 3.16
822 887 3.142838 CCGAATTGGCCAGCCCAG 61.143 66.667 5.11 0.00 46.39 4.45
854 919 2.062519 GGCCGAAGATATTTCGAGAGC 58.937 52.381 16.51 12.57 43.97 4.09
859 924 3.986572 CGAAGATATTTCGAGAGCATGCT 59.013 43.478 22.92 22.92 43.97 3.79
860 925 4.143368 CGAAGATATTTCGAGAGCATGCTG 60.143 45.833 28.27 11.47 43.97 4.41
866 931 0.321346 TCGAGAGCATGCTGGAACAA 59.679 50.000 28.27 2.22 38.70 2.83
887 952 4.065281 CGTCACCCACCTCCGTCC 62.065 72.222 0.00 0.00 0.00 4.79
900 965 1.823041 CCGTCCCCGACTCCTACTC 60.823 68.421 0.00 0.00 35.63 2.59
939 1004 5.289595 TCCTAGAAATGAACGGAATGATCG 58.710 41.667 0.00 0.00 0.00 3.69
951 1016 2.527100 GAATGATCGACCGAACGAACT 58.473 47.619 7.81 0.00 45.16 3.01
982 1047 0.827925 TCGAGCTCACCTCACACCTT 60.828 55.000 15.40 0.00 40.78 3.50
1021 1086 5.237815 TCATGCCACCTTCTATAAATAGCG 58.762 41.667 0.00 0.00 0.00 4.26
1038 1103 0.234884 GCGCGCAAACACTTTCTACT 59.765 50.000 29.10 0.00 0.00 2.57
1039 1104 1.458064 GCGCGCAAACACTTTCTACTA 59.542 47.619 29.10 0.00 0.00 1.82
1040 1105 2.720891 GCGCGCAAACACTTTCTACTAC 60.721 50.000 29.10 0.00 0.00 2.73
1041 1106 2.473609 CGCGCAAACACTTTCTACTACA 59.526 45.455 8.75 0.00 0.00 2.74
1112 1183 4.023707 ACATTCGAGAAAGAAACAGCAAGG 60.024 41.667 0.00 0.00 33.43 3.61
1142 1213 7.509141 TCAAACAATTGAAGCTTCATACAGA 57.491 32.000 28.89 14.76 42.47 3.41
1143 1214 7.939782 TCAAACAATTGAAGCTTCATACAGAA 58.060 30.769 28.89 14.01 42.47 3.02
1144 1215 7.862372 TCAAACAATTGAAGCTTCATACAGAAC 59.138 33.333 28.89 0.00 42.47 3.01
1145 1216 6.882610 ACAATTGAAGCTTCATACAGAACA 57.117 33.333 28.89 12.52 37.00 3.18
1146 1217 6.906659 ACAATTGAAGCTTCATACAGAACAG 58.093 36.000 28.89 11.61 37.00 3.16
1149 1220 4.318332 TGAAGCTTCATACAGAACAGGTG 58.682 43.478 25.16 0.00 31.01 4.00
1182 1253 0.397941 TGTCCAAGAAGGCTCTGGTG 59.602 55.000 9.35 0.00 37.29 4.17
1395 1466 1.444553 GTGCGACTGGAAGGAGACG 60.445 63.158 0.00 0.00 39.30 4.18
1453 1524 3.195698 GGCGGGATGACGTGAAGC 61.196 66.667 0.00 0.00 35.98 3.86
1525 1596 1.076632 GAGGAGAAGGAGGGCGAGA 60.077 63.158 0.00 0.00 0.00 4.04
1662 1733 2.123428 GCCCAAGATTGCCGAGCAT 61.123 57.895 0.00 0.00 38.76 3.79
1696 1767 2.709475 GCGTCATCAACATCGCCC 59.291 61.111 0.00 0.00 42.33 6.13
1779 1850 3.258372 AGATGTGAGCTTTCGTGTAGGAA 59.742 43.478 0.00 0.00 0.00 3.36
1817 1888 1.919839 GCGTCACGTTTGGATGTGTTG 60.920 52.381 0.00 0.00 42.27 3.33
1847 1918 1.535028 CATGCTTACCTTTGCGTGTGA 59.465 47.619 0.00 0.00 40.24 3.58
1848 1919 1.890876 TGCTTACCTTTGCGTGTGAT 58.109 45.000 0.00 0.00 0.00 3.06
1849 1920 1.535028 TGCTTACCTTTGCGTGTGATG 59.465 47.619 0.00 0.00 0.00 3.07
1850 1921 1.535462 GCTTACCTTTGCGTGTGATGT 59.465 47.619 0.00 0.00 0.00 3.06
1851 1922 2.031157 GCTTACCTTTGCGTGTGATGTT 60.031 45.455 0.00 0.00 0.00 2.71
1852 1923 3.554524 CTTACCTTTGCGTGTGATGTTG 58.445 45.455 0.00 0.00 0.00 3.33
1853 1924 1.388547 ACCTTTGCGTGTGATGTTGT 58.611 45.000 0.00 0.00 0.00 3.32
1854 1925 1.748493 ACCTTTGCGTGTGATGTTGTT 59.252 42.857 0.00 0.00 0.00 2.83
1855 1926 2.118683 CCTTTGCGTGTGATGTTGTTG 58.881 47.619 0.00 0.00 0.00 3.33
1856 1927 1.518102 CTTTGCGTGTGATGTTGTTGC 59.482 47.619 0.00 0.00 0.00 4.17
1857 1928 0.737804 TTGCGTGTGATGTTGTTGCT 59.262 45.000 0.00 0.00 0.00 3.91
1858 1929 0.307453 TGCGTGTGATGTTGTTGCTC 59.693 50.000 0.00 0.00 0.00 4.26
1859 1930 0.588252 GCGTGTGATGTTGTTGCTCT 59.412 50.000 0.00 0.00 0.00 4.09
1860 1931 1.398960 GCGTGTGATGTTGTTGCTCTC 60.399 52.381 0.00 0.00 0.00 3.20
1861 1932 1.866601 CGTGTGATGTTGTTGCTCTCA 59.133 47.619 0.00 0.00 0.00 3.27
1862 1933 2.096565 CGTGTGATGTTGTTGCTCTCAG 60.097 50.000 0.00 0.00 0.00 3.35
1863 1934 2.225019 GTGTGATGTTGTTGCTCTCAGG 59.775 50.000 0.00 0.00 0.00 3.86
1864 1935 2.158769 TGTGATGTTGTTGCTCTCAGGT 60.159 45.455 0.00 0.00 0.00 4.00
1865 1936 3.070878 TGTGATGTTGTTGCTCTCAGGTA 59.929 43.478 0.00 0.00 0.00 3.08
1866 1937 3.433615 GTGATGTTGTTGCTCTCAGGTAC 59.566 47.826 0.00 0.00 0.00 3.34
1867 1938 2.543777 TGTTGTTGCTCTCAGGTACC 57.456 50.000 2.73 2.73 0.00 3.34
1868 1939 2.047061 TGTTGTTGCTCTCAGGTACCT 58.953 47.619 9.21 9.21 0.00 3.08
1869 1940 2.438021 TGTTGTTGCTCTCAGGTACCTT 59.562 45.455 13.15 0.00 0.00 3.50
1870 1941 3.644265 TGTTGTTGCTCTCAGGTACCTTA 59.356 43.478 13.15 3.01 0.00 2.69
1879 1950 0.899720 CAGGTACCTTAAGGGCGTGA 59.100 55.000 25.31 2.59 40.27 4.35
1913 1984 1.063166 GCTTTAGCCTGCATCGCAC 59.937 57.895 8.47 0.00 33.79 5.34
1968 2039 4.259356 CTGATGCAGAGATTGGTTGAGAA 58.741 43.478 0.00 0.00 32.44 2.87
2076 2147 9.801873 TTAATTTTGTGAACCTTTCTCTTTCAG 57.198 29.630 0.00 0.00 29.97 3.02
2083 2154 7.122650 TGTGAACCTTTCTCTTTCAGTTTCAAT 59.877 33.333 0.00 0.00 29.97 2.57
2160 2232 4.576330 AATCTGAACTAAACTCAGGGGG 57.424 45.455 0.31 0.00 40.65 5.40
2176 2248 0.271005 GGGGGAGAGGGGGAGAAATA 59.729 60.000 0.00 0.00 0.00 1.40
2178 2250 1.345112 GGGGAGAGGGGGAGAAATACA 60.345 57.143 0.00 0.00 0.00 2.29
2387 2485 2.599597 GTGGGCATGGAGGAGCAT 59.400 61.111 0.00 0.00 0.00 3.79
2391 2489 2.507944 GCATGGAGGAGCATCGGT 59.492 61.111 0.00 0.00 34.37 4.69
2580 2697 0.109723 AGGAGCGCCTACTAGAGAGG 59.890 60.000 7.45 10.16 44.74 3.69
2603 2720 1.229209 ACTGGTGTGGACGAGGGAT 60.229 57.895 0.00 0.00 32.39 3.85
2611 2728 1.758514 GGACGAGGGATCTCAGGCA 60.759 63.158 0.00 0.00 39.95 4.75
2612 2729 1.330655 GGACGAGGGATCTCAGGCAA 61.331 60.000 0.00 0.00 39.95 4.52
2617 2734 2.268920 GGATCTCAGGCAACGGCA 59.731 61.111 0.00 0.00 43.71 5.69
2633 2753 1.383456 GGCAGCGGCAATGGATTACA 61.383 55.000 11.88 0.00 43.71 2.41
2635 2755 1.093972 CAGCGGCAATGGATTACACA 58.906 50.000 1.45 0.00 0.00 3.72
2769 2894 3.641017 GCTGAGAGGCCTCTTTTGT 57.359 52.632 35.48 14.45 40.61 2.83
2772 2897 4.408182 GCTGAGAGGCCTCTTTTGTATA 57.592 45.455 35.48 14.82 40.61 1.47
2780 2905 4.017499 AGGCCTCTTTTGTATATGTTGGGT 60.017 41.667 0.00 0.00 0.00 4.51
2783 2908 5.417580 GCCTCTTTTGTATATGTTGGGTCAA 59.582 40.000 0.00 0.00 0.00 3.18
2813 2938 3.216292 GCACAGGCCACCAAACGT 61.216 61.111 5.01 0.00 0.00 3.99
2815 2940 1.852067 GCACAGGCCACCAAACGTAG 61.852 60.000 5.01 0.00 0.00 3.51
2858 2984 0.675633 GCAGGTGCCACACAAGAAAT 59.324 50.000 0.00 0.00 35.86 2.17
2875 3001 2.579410 AATCAAACACGCCCTTAGGT 57.421 45.000 0.00 0.00 34.57 3.08
2882 3008 2.668632 CGCCCTTAGGTGCCTTGA 59.331 61.111 0.00 0.00 36.70 3.02
2883 3009 1.224592 CGCCCTTAGGTGCCTTGAT 59.775 57.895 0.00 0.00 36.70 2.57
2884 3010 0.815615 CGCCCTTAGGTGCCTTGATC 60.816 60.000 0.00 0.00 36.70 2.92
2885 3011 0.255890 GCCCTTAGGTGCCTTGATCA 59.744 55.000 0.00 0.00 34.57 2.92
2886 3012 1.748591 GCCCTTAGGTGCCTTGATCAG 60.749 57.143 0.00 0.00 34.57 2.90
2887 3013 1.561542 CCCTTAGGTGCCTTGATCAGT 59.438 52.381 0.00 0.00 0.00 3.41
2888 3014 2.025887 CCCTTAGGTGCCTTGATCAGTT 60.026 50.000 0.00 0.00 0.00 3.16
2889 3015 3.012518 CCTTAGGTGCCTTGATCAGTTG 58.987 50.000 0.00 0.00 0.00 3.16
2890 3016 2.787473 TAGGTGCCTTGATCAGTTGG 57.213 50.000 0.00 1.32 0.00 3.77
2891 3017 1.067295 AGGTGCCTTGATCAGTTGGA 58.933 50.000 13.46 0.00 0.00 3.53
2892 3018 1.637553 AGGTGCCTTGATCAGTTGGAT 59.362 47.619 13.46 0.00 39.53 3.41
2893 3019 2.846206 AGGTGCCTTGATCAGTTGGATA 59.154 45.455 13.46 1.90 36.00 2.59
2894 3020 2.945668 GGTGCCTTGATCAGTTGGATAC 59.054 50.000 13.46 10.92 36.00 2.24
2895 3021 2.945668 GTGCCTTGATCAGTTGGATACC 59.054 50.000 13.46 0.00 36.00 2.73
2896 3022 2.092429 TGCCTTGATCAGTTGGATACCC 60.092 50.000 13.46 0.00 36.00 3.69
2897 3023 2.173569 GCCTTGATCAGTTGGATACCCT 59.826 50.000 13.46 0.00 36.00 4.34
2898 3024 3.813443 CCTTGATCAGTTGGATACCCTG 58.187 50.000 0.00 0.00 36.00 4.45
2899 3025 3.455910 CCTTGATCAGTTGGATACCCTGA 59.544 47.826 0.00 0.00 44.54 3.86
2903 3029 4.970860 ATCAGTTGGATACCCTGATCAG 57.029 45.455 16.24 16.24 45.77 2.90
2904 3030 3.724478 TCAGTTGGATACCCTGATCAGT 58.276 45.455 21.11 7.39 38.28 3.41
2905 3031 3.706594 TCAGTTGGATACCCTGATCAGTC 59.293 47.826 21.11 11.68 38.28 3.51
2906 3032 3.452264 CAGTTGGATACCCTGATCAGTCA 59.548 47.826 21.11 6.31 36.85 3.41
2907 3033 3.452627 AGTTGGATACCCTGATCAGTCAC 59.547 47.826 21.11 7.50 0.00 3.67
2908 3034 3.114643 TGGATACCCTGATCAGTCACA 57.885 47.619 21.11 9.31 0.00 3.58
2909 3035 3.657610 TGGATACCCTGATCAGTCACAT 58.342 45.455 21.11 8.71 0.00 3.21
2910 3036 4.040047 TGGATACCCTGATCAGTCACATT 58.960 43.478 21.11 1.26 0.00 2.71
2911 3037 4.474651 TGGATACCCTGATCAGTCACATTT 59.525 41.667 21.11 0.00 0.00 2.32
2912 3038 4.818546 GGATACCCTGATCAGTCACATTTG 59.181 45.833 21.11 3.37 0.00 2.32
2913 3039 2.440409 ACCCTGATCAGTCACATTTGC 58.560 47.619 21.11 0.00 0.00 3.68
2914 3040 2.224843 ACCCTGATCAGTCACATTTGCA 60.225 45.455 21.11 0.00 0.00 4.08
2915 3041 2.821378 CCCTGATCAGTCACATTTGCAA 59.179 45.455 21.11 0.00 0.00 4.08
2916 3042 3.119602 CCCTGATCAGTCACATTTGCAAG 60.120 47.826 21.11 1.25 0.00 4.01
2917 3043 3.754850 CCTGATCAGTCACATTTGCAAGA 59.245 43.478 21.11 0.00 0.00 3.02
2918 3044 4.216902 CCTGATCAGTCACATTTGCAAGAA 59.783 41.667 21.11 0.00 0.00 2.52
2919 3045 5.105877 CCTGATCAGTCACATTTGCAAGAAT 60.106 40.000 21.11 0.00 0.00 2.40
2920 3046 5.946298 TGATCAGTCACATTTGCAAGAATC 58.054 37.500 0.00 0.00 0.00 2.52
2921 3047 5.708697 TGATCAGTCACATTTGCAAGAATCT 59.291 36.000 0.00 0.00 0.00 2.40
2922 3048 6.880529 TGATCAGTCACATTTGCAAGAATCTA 59.119 34.615 0.00 0.00 0.00 1.98
2923 3049 6.486253 TCAGTCACATTTGCAAGAATCTAC 57.514 37.500 0.00 0.00 0.00 2.59
2924 3050 5.997129 TCAGTCACATTTGCAAGAATCTACA 59.003 36.000 0.00 0.00 0.00 2.74
2925 3051 6.656270 TCAGTCACATTTGCAAGAATCTACAT 59.344 34.615 0.00 0.00 0.00 2.29
2926 3052 7.175467 TCAGTCACATTTGCAAGAATCTACATT 59.825 33.333 0.00 0.00 0.00 2.71
2927 3053 7.811236 CAGTCACATTTGCAAGAATCTACATTT 59.189 33.333 0.00 0.00 0.00 2.32
2928 3054 8.362639 AGTCACATTTGCAAGAATCTACATTTT 58.637 29.630 0.00 0.00 0.00 1.82
2929 3055 8.981647 GTCACATTTGCAAGAATCTACATTTTT 58.018 29.630 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
308 360 3.131396 TGGTTCTCACGCTTTTTCTCTC 58.869 45.455 0.00 0.00 0.00 3.20
473 526 1.468985 CCATCAATGCCACCCGTAAA 58.531 50.000 0.00 0.00 0.00 2.01
489 542 5.197451 TCGAAGTTGGCAATAATTACCCAT 58.803 37.500 1.92 0.00 0.00 4.00
736 790 9.886132 TCGCTTTATCTTTACCTCTTTATCTTT 57.114 29.630 0.00 0.00 0.00 2.52
737 791 9.886132 TTCGCTTTATCTTTACCTCTTTATCTT 57.114 29.630 0.00 0.00 0.00 2.40
738 792 9.886132 TTTCGCTTTATCTTTACCTCTTTATCT 57.114 29.630 0.00 0.00 0.00 1.98
806 860 1.978617 AACTGGGCTGGCCAATTCG 60.979 57.895 24.04 14.42 37.98 3.34
808 862 1.914764 CCAACTGGGCTGGCCAATT 60.915 57.895 24.04 18.00 37.98 2.32
809 863 2.284112 CCAACTGGGCTGGCCAAT 60.284 61.111 24.04 12.03 37.98 3.16
831 896 2.035961 TCTCGAAATATCTTCGGCCTGG 59.964 50.000 0.00 0.00 41.78 4.45
854 919 0.798776 GACGAGGTTGTTCCAGCATG 59.201 55.000 0.00 0.00 39.02 4.06
859 924 1.338890 TGGGTGACGAGGTTGTTCCA 61.339 55.000 0.00 0.00 39.02 3.53
860 925 0.883370 GTGGGTGACGAGGTTGTTCC 60.883 60.000 0.00 0.00 0.00 3.62
866 931 2.603776 GGAGGTGGGTGACGAGGT 60.604 66.667 0.00 0.00 0.00 3.85
887 952 1.546961 AGTGTTGAGTAGGAGTCGGG 58.453 55.000 0.00 0.00 0.00 5.14
890 955 2.475852 CGCGTAGTGTTGAGTAGGAGTC 60.476 54.545 0.00 0.00 0.00 3.36
892 957 1.736126 TCGCGTAGTGTTGAGTAGGAG 59.264 52.381 5.77 0.00 40.08 3.69
900 965 0.388649 AGGAGCTTCGCGTAGTGTTG 60.389 55.000 14.43 0.00 40.08 3.33
939 1004 1.977412 CTCGAGAAAGTTCGTTCGGTC 59.023 52.381 6.58 0.00 41.22 4.79
982 1047 2.687614 GCATGAGGGGTCAATTCCATGA 60.688 50.000 0.00 0.00 34.87 3.07
1021 1086 4.663636 ATGTAGTAGAAAGTGTTTGCGC 57.336 40.909 0.00 0.00 0.00 6.09
1112 1183 6.441274 TGAAGCTTCAATTGTTTGATGAGAC 58.559 36.000 26.61 0.00 41.38 3.36
1134 1205 3.346315 CATTGCCACCTGTTCTGTATGA 58.654 45.455 0.00 0.00 0.00 2.15
1135 1206 2.424601 CCATTGCCACCTGTTCTGTATG 59.575 50.000 0.00 0.00 0.00 2.39
1136 1207 2.726821 CCATTGCCACCTGTTCTGTAT 58.273 47.619 0.00 0.00 0.00 2.29
1137 1208 1.886222 GCCATTGCCACCTGTTCTGTA 60.886 52.381 0.00 0.00 0.00 2.74
1138 1209 1.181098 GCCATTGCCACCTGTTCTGT 61.181 55.000 0.00 0.00 0.00 3.41
1139 1210 1.588082 GCCATTGCCACCTGTTCTG 59.412 57.895 0.00 0.00 0.00 3.02
1140 1211 1.973281 CGCCATTGCCACCTGTTCT 60.973 57.895 0.00 0.00 0.00 3.01
1141 1212 2.568090 CGCCATTGCCACCTGTTC 59.432 61.111 0.00 0.00 0.00 3.18
1142 1213 2.990967 CCGCCATTGCCACCTGTT 60.991 61.111 0.00 0.00 0.00 3.16
1149 1220 4.120331 GACACTGCCGCCATTGCC 62.120 66.667 0.00 0.00 0.00 4.52
1182 1253 1.805945 CGCCAGAACAGCCGTAGTC 60.806 63.158 0.00 0.00 0.00 2.59
1453 1524 1.608717 CGGTTCTCCTCCACCTCCAG 61.609 65.000 0.00 0.00 0.00 3.86
1696 1767 2.825836 GCTGTTGGCATCCTCCCG 60.826 66.667 0.00 0.00 41.35 5.14
1779 1850 1.154016 CATCGCTCTCGTCGTGGTT 60.154 57.895 0.00 0.00 36.96 3.67
1817 1888 2.423577 AGGTAAGCATGAACCGACAAC 58.576 47.619 0.00 0.00 40.88 3.32
1847 1918 2.639839 AGGTACCTGAGAGCAACAACAT 59.360 45.455 15.42 0.00 0.00 2.71
1848 1919 2.047061 AGGTACCTGAGAGCAACAACA 58.953 47.619 15.42 0.00 0.00 3.33
1849 1920 2.841442 AGGTACCTGAGAGCAACAAC 57.159 50.000 15.42 0.00 0.00 3.32
1850 1921 4.262894 CCTTAAGGTACCTGAGAGCAACAA 60.263 45.833 17.14 0.00 0.00 2.83
1851 1922 3.260884 CCTTAAGGTACCTGAGAGCAACA 59.739 47.826 17.14 0.00 0.00 3.33
1852 1923 3.369576 CCCTTAAGGTACCTGAGAGCAAC 60.370 52.174 17.14 0.00 0.00 4.17
1853 1924 2.838202 CCCTTAAGGTACCTGAGAGCAA 59.162 50.000 17.14 2.49 0.00 3.91
1854 1925 2.467880 CCCTTAAGGTACCTGAGAGCA 58.532 52.381 17.14 0.00 0.00 4.26
1855 1926 1.139256 GCCCTTAAGGTACCTGAGAGC 59.861 57.143 17.14 15.08 38.26 4.09
1856 1927 1.409427 CGCCCTTAAGGTACCTGAGAG 59.591 57.143 17.14 13.22 38.26 3.20
1857 1928 1.272872 ACGCCCTTAAGGTACCTGAGA 60.273 52.381 17.14 0.63 38.26 3.27
1858 1929 1.134788 CACGCCCTTAAGGTACCTGAG 60.135 57.143 17.14 16.11 38.26 3.35
1859 1930 0.899720 CACGCCCTTAAGGTACCTGA 59.100 55.000 17.14 4.52 38.26 3.86
1860 1931 0.899720 TCACGCCCTTAAGGTACCTG 59.100 55.000 17.14 11.43 38.26 4.00
1861 1932 1.875488 ATCACGCCCTTAAGGTACCT 58.125 50.000 20.22 9.21 38.26 3.08
1862 1933 2.285977 CAATCACGCCCTTAAGGTACC 58.714 52.381 20.22 2.73 38.26 3.34
1863 1934 2.285977 CCAATCACGCCCTTAAGGTAC 58.714 52.381 20.22 10.83 38.26 3.34
1864 1935 1.910671 ACCAATCACGCCCTTAAGGTA 59.089 47.619 20.22 0.90 38.26 3.08
1865 1936 0.696501 ACCAATCACGCCCTTAAGGT 59.303 50.000 20.22 0.00 38.26 3.50
1866 1937 1.472480 CAACCAATCACGCCCTTAAGG 59.528 52.381 15.14 15.14 39.47 2.69
1867 1938 1.135402 GCAACCAATCACGCCCTTAAG 60.135 52.381 0.00 0.00 0.00 1.85
1868 1939 0.885196 GCAACCAATCACGCCCTTAA 59.115 50.000 0.00 0.00 0.00 1.85
1869 1940 0.963355 GGCAACCAATCACGCCCTTA 60.963 55.000 0.00 0.00 38.67 2.69
1870 1941 2.275380 GGCAACCAATCACGCCCTT 61.275 57.895 0.00 0.00 38.67 3.95
1913 1984 2.801631 GCTCACCCAGGATCCCTCG 61.802 68.421 8.55 0.00 0.00 4.63
1968 2039 2.411628 TACAGTGCACCAAACACACT 57.588 45.000 14.63 0.00 45.25 3.55
2025 2096 6.094603 AGCTCAAATGCAGTCTACCAAATAAG 59.905 38.462 0.00 0.00 34.99 1.73
2028 2099 4.338879 AGCTCAAATGCAGTCTACCAAAT 58.661 39.130 0.00 0.00 34.99 2.32
2160 2232 1.418264 GCTGTATTTCTCCCCCTCTCC 59.582 57.143 0.00 0.00 0.00 3.71
2203 2275 2.119495 GGATCCAGAGGAAAGCACCTA 58.881 52.381 6.95 0.00 40.73 3.08
2211 2283 1.264749 CCACCACGGATCCAGAGGAA 61.265 60.000 20.66 0.00 34.34 3.36
2212 2284 1.685765 CCACCACGGATCCAGAGGA 60.686 63.158 20.66 0.00 36.56 3.71
2368 2466 4.101448 GCTCCTCCATGCCCACGT 62.101 66.667 0.00 0.00 0.00 4.49
2387 2485 3.749064 GCTGAGCTCCGTCACCGA 61.749 66.667 12.15 0.00 35.63 4.69
2487 2597 3.790437 CTCCTCCATGCCCACGCT 61.790 66.667 0.00 0.00 35.36 5.07
2548 2665 3.374402 CTCCTCCACGTCCACGCT 61.374 66.667 0.00 0.00 44.43 5.07
2612 2729 2.884997 TAATCCATTGCCGCTGCCGT 62.885 55.000 0.00 0.00 36.33 5.68
2617 2734 1.832883 TTGTGTAATCCATTGCCGCT 58.167 45.000 0.00 0.00 0.00 5.52
2633 2753 7.370905 TCTCTCACATATCAGATTGGATTGT 57.629 36.000 0.00 0.00 0.00 2.71
2635 2755 6.786461 TCCTCTCTCACATATCAGATTGGATT 59.214 38.462 0.00 0.00 0.00 3.01
2769 2894 4.037222 TCCTCAGCTTGACCCAACATATA 58.963 43.478 0.00 0.00 0.00 0.86
2772 2897 1.004044 CTCCTCAGCTTGACCCAACAT 59.996 52.381 0.00 0.00 0.00 2.71
2780 2905 4.087892 GCGGCCTCCTCAGCTTGA 62.088 66.667 0.00 0.00 0.00 3.02
2813 2938 2.942376 CACCCGCATGCAAAATCTACTA 59.058 45.455 19.57 0.00 0.00 1.82
2815 2940 1.798813 GCACCCGCATGCAAAATCTAC 60.799 52.381 19.57 0.00 45.39 2.59
2858 2984 0.887387 GCACCTAAGGGCGTGTTTGA 60.887 55.000 0.00 0.00 35.63 2.69
2875 3001 2.092429 GGGTATCCAACTGATCAAGGCA 60.092 50.000 0.00 0.00 34.76 4.75
2876 3002 2.173569 AGGGTATCCAACTGATCAAGGC 59.826 50.000 0.00 0.00 34.76 4.35
2877 3003 3.455910 TCAGGGTATCCAACTGATCAAGG 59.544 47.826 0.00 0.00 36.41 3.61
2878 3004 4.760530 TCAGGGTATCCAACTGATCAAG 57.239 45.455 0.00 0.00 36.41 3.02
2883 3009 3.706594 GACTGATCAGGGTATCCAACTGA 59.293 47.826 26.08 0.00 44.44 3.41
2884 3010 3.452264 TGACTGATCAGGGTATCCAACTG 59.548 47.826 26.08 0.00 34.83 3.16
2885 3011 3.452627 GTGACTGATCAGGGTATCCAACT 59.547 47.826 26.08 1.11 34.75 3.16
2886 3012 3.197766 TGTGACTGATCAGGGTATCCAAC 59.802 47.826 26.08 10.24 34.75 3.77
2887 3013 3.449918 TGTGACTGATCAGGGTATCCAA 58.550 45.455 26.08 3.64 34.75 3.53
2888 3014 3.114643 TGTGACTGATCAGGGTATCCA 57.885 47.619 26.08 11.50 34.75 3.41
2889 3015 4.696479 AATGTGACTGATCAGGGTATCC 57.304 45.455 26.08 9.37 34.75 2.59
2890 3016 4.274459 GCAAATGTGACTGATCAGGGTATC 59.726 45.833 26.08 14.79 34.75 2.24
2891 3017 4.202441 GCAAATGTGACTGATCAGGGTAT 58.798 43.478 26.08 11.95 34.75 2.73
2892 3018 3.008923 TGCAAATGTGACTGATCAGGGTA 59.991 43.478 26.08 9.45 34.75 3.69
2893 3019 2.224843 TGCAAATGTGACTGATCAGGGT 60.225 45.455 26.08 7.53 34.75 4.34
2894 3020 2.439409 TGCAAATGTGACTGATCAGGG 58.561 47.619 26.08 3.92 34.75 4.45
2895 3021 3.754850 TCTTGCAAATGTGACTGATCAGG 59.245 43.478 26.08 8.94 34.75 3.86
2896 3022 5.366829 TTCTTGCAAATGTGACTGATCAG 57.633 39.130 21.37 21.37 34.75 2.90
2897 3023 5.708697 AGATTCTTGCAAATGTGACTGATCA 59.291 36.000 0.00 0.00 0.00 2.92
2898 3024 6.192234 AGATTCTTGCAAATGTGACTGATC 57.808 37.500 0.00 0.00 0.00 2.92
2899 3025 6.656270 TGTAGATTCTTGCAAATGTGACTGAT 59.344 34.615 0.00 0.00 0.00 2.90
2900 3026 5.997129 TGTAGATTCTTGCAAATGTGACTGA 59.003 36.000 0.00 0.00 0.00 3.41
2901 3027 6.245115 TGTAGATTCTTGCAAATGTGACTG 57.755 37.500 0.00 0.00 0.00 3.51
2902 3028 7.458409 AATGTAGATTCTTGCAAATGTGACT 57.542 32.000 0.00 0.00 0.00 3.41
2903 3029 8.524870 AAAATGTAGATTCTTGCAAATGTGAC 57.475 30.769 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.