Multiple sequence alignment - TraesCS6B01G022200

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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 TraesCS6B01G022200 chr6B 100.000 3271 0 0 1 3271 13972145 13968875 0.000000e+00 6041
1 TraesCS6B01G022200 chr6B 93.917 1907 78 16 765 2657 14164531 14166413 0.000000e+00 2844
2 TraesCS6B01G022200 chr6B 93.972 647 29 3 803 1449 14207245 14207881 0.000000e+00 970
3 TraesCS6B01G022200 chr6B 93.972 647 29 3 803 1449 14223296 14223932 0.000000e+00 970
4 TraesCS6B01G022200 chr6B 93.818 647 30 3 803 1449 14198647 14199283 0.000000e+00 965
5 TraesCS6B01G022200 chr6B 93.663 647 31 3 803 1449 14215540 14216176 0.000000e+00 959
6 TraesCS6B01G022200 chr6B 95.238 84 3 1 708 791 14198584 14198666 7.360000e-27 132
7 TraesCS6B01G022200 chr6B 95.238 84 3 1 708 791 14207182 14207264 7.360000e-27 132
8 TraesCS6B01G022200 chr6B 95.238 84 3 1 708 791 14215477 14215559 7.360000e-27 132
9 TraesCS6B01G022200 chr6B 95.238 84 3 1 708 791 14223233 14223315 7.360000e-27 132
10 TraesCS6B01G022200 chr6D 91.867 2201 135 21 771 2955 7557602 7559774 0.000000e+00 3033
11 TraesCS6B01G022200 chr6D 85.484 186 22 5 2130 2311 7108583 7108399 4.310000e-44 189
12 TraesCS6B01G022200 chr6A 92.013 1590 100 11 741 2315 7723051 7724628 0.000000e+00 2207
13 TraesCS6B01G022200 chr6A 84.120 233 28 4 3024 3247 7725765 7725997 1.980000e-52 217
14 TraesCS6B01G022200 chr6A 89.404 151 14 2 2130 2279 6738495 6738346 4.310000e-44 189
15 TraesCS6B01G022200 chr6A 93.805 113 7 0 2843 2955 7725066 7725178 1.560000e-38 171
16 TraesCS6B01G022200 chrUn 93.972 647 29 3 803 1449 364883628 364884264 0.000000e+00 970
17 TraesCS6B01G022200 chrUn 93.972 647 29 3 803 1449 425466451 425467087 0.000000e+00 970
18 TraesCS6B01G022200 chrUn 95.238 84 3 1 708 791 364883565 364883647 7.360000e-27 132
19 TraesCS6B01G022200 chrUn 95.238 84 3 1 708 791 425466388 425466470 7.360000e-27 132
20 TraesCS6B01G022200 chr5B 90.247 728 50 6 1 709 402728792 402729517 0.000000e+00 931
21 TraesCS6B01G022200 chr5B 85.262 726 86 9 4 709 619917627 619918351 0.000000e+00 728
22 TraesCS6B01G022200 chr4A 89.197 722 59 5 7 709 19458550 19457829 0.000000e+00 883
23 TraesCS6B01G022200 chr1D 88.966 725 61 6 4 709 95787117 95787841 0.000000e+00 878
24 TraesCS6B01G022200 chr1D 88.690 725 62 7 4 709 75887048 75887771 0.000000e+00 867
25 TraesCS6B01G022200 chr3D 87.724 725 70 6 4 709 26081425 26082149 0.000000e+00 828
26 TraesCS6B01G022200 chr2B 86.878 724 77 6 4 709 654521333 654522056 0.000000e+00 795
27 TraesCS6B01G022200 chr2B 89.116 147 16 0 1915 2061 364320718 364320864 2.000000e-42 183
28 TraesCS6B01G022200 chr1B 85.615 723 83 9 7 709 679604659 679605380 0.000000e+00 739
29 TraesCS6B01G022200 chr3B 85.282 727 87 8 3 709 191134493 191133767 0.000000e+00 732
30 TraesCS6B01G022200 chr7B 81.250 304 57 0 1894 2197 504472517 504472820 2.520000e-61 246
31 TraesCS6B01G022200 chr2D 89.116 147 16 0 1915 2061 297296306 297296452 2.000000e-42 183


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 TraesCS6B01G022200 chr6B 13968875 13972145 3270 True 6041.0 6041 100.000000 1 3271 1 chr6B.!!$R1 3270
1 TraesCS6B01G022200 chr6B 14164531 14166413 1882 False 2844.0 2844 93.917000 765 2657 1 chr6B.!!$F1 1892
2 TraesCS6B01G022200 chr6B 14207182 14207881 699 False 551.0 970 94.605000 708 1449 2 chr6B.!!$F3 741
3 TraesCS6B01G022200 chr6B 14223233 14223932 699 False 551.0 970 94.605000 708 1449 2 chr6B.!!$F5 741
4 TraesCS6B01G022200 chr6B 14198584 14199283 699 False 548.5 965 94.528000 708 1449 2 chr6B.!!$F2 741
5 TraesCS6B01G022200 chr6B 14215477 14216176 699 False 545.5 959 94.450500 708 1449 2 chr6B.!!$F4 741
6 TraesCS6B01G022200 chr6D 7557602 7559774 2172 False 3033.0 3033 91.867000 771 2955 1 chr6D.!!$F1 2184
7 TraesCS6B01G022200 chr6A 7723051 7725997 2946 False 865.0 2207 89.979333 741 3247 3 chr6A.!!$F1 2506
8 TraesCS6B01G022200 chrUn 364883565 364884264 699 False 551.0 970 94.605000 708 1449 2 chrUn.!!$F1 741
9 TraesCS6B01G022200 chrUn 425466388 425467087 699 False 551.0 970 94.605000 708 1449 2 chrUn.!!$F2 741
10 TraesCS6B01G022200 chr5B 402728792 402729517 725 False 931.0 931 90.247000 1 709 1 chr5B.!!$F1 708
11 TraesCS6B01G022200 chr5B 619917627 619918351 724 False 728.0 728 85.262000 4 709 1 chr5B.!!$F2 705
12 TraesCS6B01G022200 chr4A 19457829 19458550 721 True 883.0 883 89.197000 7 709 1 chr4A.!!$R1 702
13 TraesCS6B01G022200 chr1D 95787117 95787841 724 False 878.0 878 88.966000 4 709 1 chr1D.!!$F2 705
14 TraesCS6B01G022200 chr1D 75887048 75887771 723 False 867.0 867 88.690000 4 709 1 chr1D.!!$F1 705
15 TraesCS6B01G022200 chr3D 26081425 26082149 724 False 828.0 828 87.724000 4 709 1 chr3D.!!$F1 705
16 TraesCS6B01G022200 chr2B 654521333 654522056 723 False 795.0 795 86.878000 4 709 1 chr2B.!!$F2 705
17 TraesCS6B01G022200 chr1B 679604659 679605380 721 False 739.0 739 85.615000 7 709 1 chr1B.!!$F1 702
18 TraesCS6B01G022200 chr3B 191133767 191134493 726 True 732.0 732 85.282000 3 709 1 chr3B.!!$R1 706

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
554 576 0.030369 ACGATCGTACGCCTTCATCC 59.970 55.0 21.32 0.0 36.70 3.51 F
1216 1240 0.038343 GCTTTGCATGGCCGAAAAGA 60.038 50.0 13.74 0.0 32.53 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1504 1528 0.306533 GCGAACCTTCTTTCACGCAA 59.693 50.0 0.0 0.0 44.29 4.85 R
2765 2861 0.321564 CCACCCGAGTGCAAGATCAA 60.322 55.0 0.0 0.0 43.09 2.57 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
33 34 0.544697 TTCTTCTGTTATCCGGCCCC 59.455 55.000 0.00 0.00 0.00 5.80
96 97 8.677148 TTCTCTGTAGATTTGCAAGTTACTTT 57.323 30.769 0.00 0.00 0.00 2.66
249 270 7.047891 ACTAGACAATCATCCGCAAATAAGAA 58.952 34.615 0.00 0.00 0.00 2.52
361 383 3.435671 CCCCGCAAAGTAGAAACAAGTAG 59.564 47.826 0.00 0.00 0.00 2.57
488 510 8.010697 TCATAACTAGAGATACCCATTCCTCAA 58.989 37.037 0.00 0.00 0.00 3.02
496 518 3.903530 ACCCATTCCTCAAAGAAACCT 57.096 42.857 0.00 0.00 0.00 3.50
512 534 4.768968 AGAAACCTAGCTGCAACATGATTT 59.231 37.500 0.00 0.00 0.00 2.17
554 576 0.030369 ACGATCGTACGCCTTCATCC 59.970 55.000 21.32 0.00 36.70 3.51
665 687 3.122727 AACCGCCCGGGAACAAAGA 62.123 57.895 29.31 0.00 39.97 2.52
725 747 7.181569 TCCCTCAAAGTTTGTCAAGAAAAAT 57.818 32.000 15.08 0.00 0.00 1.82
754 776 1.462616 TTTCCGTGGCAATCATCTGG 58.537 50.000 0.00 0.00 0.00 3.86
814 836 4.819966 CGTACGTACGTATCCGTCTTGGA 61.820 52.174 33.95 3.12 46.28 3.53
913 935 2.254703 AAGCCAGACGTACGAGAGCG 62.255 60.000 24.41 6.04 44.79 5.03
942 964 4.116328 CAACTCCGCGAGCTCCGA 62.116 66.667 21.43 8.91 41.76 4.55
966 988 2.351418 GCATCATTTTGACGTCGATCCA 59.649 45.455 11.62 0.00 0.00 3.41
1113 1137 1.987855 CCCCGACCTGGTGAAGCTA 60.988 63.158 2.82 0.00 35.15 3.32
1177 1201 0.323957 AGCATCTCAGCAGCTGAACA 59.676 50.000 25.35 15.40 40.18 3.18
1185 1209 3.808728 TCAGCAGCTGAACAAAACTAGT 58.191 40.909 23.41 0.00 37.57 2.57
1202 1226 3.450457 ACTAGTCCAGAGGAGATGCTTTG 59.550 47.826 0.00 0.00 29.39 2.77
1216 1240 0.038343 GCTTTGCATGGCCGAAAAGA 60.038 50.000 13.74 0.00 32.53 2.52
1387 1411 2.315246 CTCGCCAAGGATAGCTTGC 58.685 57.895 0.00 0.00 0.00 4.01
1442 1466 0.097674 GTGCAGTGCAGCCTTAATCG 59.902 55.000 20.42 0.00 40.08 3.34
1479 1503 1.338136 AATCGGGCAGGTTCGAGGAT 61.338 55.000 0.00 0.00 38.83 3.24
1485 1509 1.970917 GCAGGTTCGAGGATTGCGTG 61.971 60.000 0.00 0.00 0.00 5.34
1488 1512 1.153353 GGTTCGAGGATTGCGTGAAA 58.847 50.000 0.00 0.00 0.00 2.69
1494 1518 2.427506 GAGGATTGCGTGAAAGAAGGT 58.572 47.619 0.00 0.00 0.00 3.50
1497 1521 2.412847 GGATTGCGTGAAAGAAGGTTCG 60.413 50.000 0.00 0.00 0.00 3.95
1499 1523 0.882927 TGCGTGAAAGAAGGTTCGGG 60.883 55.000 0.00 0.00 0.00 5.14
1500 1524 0.883370 GCGTGAAAGAAGGTTCGGGT 60.883 55.000 0.00 0.00 0.00 5.28
1501 1525 1.606224 GCGTGAAAGAAGGTTCGGGTA 60.606 52.381 0.00 0.00 0.00 3.69
1502 1526 2.334838 CGTGAAAGAAGGTTCGGGTAG 58.665 52.381 0.00 0.00 0.00 3.18
1503 1527 2.029649 CGTGAAAGAAGGTTCGGGTAGA 60.030 50.000 0.00 0.00 0.00 2.59
1504 1528 3.368116 CGTGAAAGAAGGTTCGGGTAGAT 60.368 47.826 0.00 0.00 0.00 1.98
1506 1530 4.392138 GTGAAAGAAGGTTCGGGTAGATTG 59.608 45.833 0.00 0.00 0.00 2.67
1508 1532 1.134788 AGAAGGTTCGGGTAGATTGCG 60.135 52.381 0.00 0.00 0.00 4.85
1509 1533 0.611714 AAGGTTCGGGTAGATTGCGT 59.388 50.000 0.00 0.00 0.00 5.24
1511 1535 0.108520 GGTTCGGGTAGATTGCGTGA 60.109 55.000 0.00 0.00 0.00 4.35
1512 1536 1.673626 GGTTCGGGTAGATTGCGTGAA 60.674 52.381 0.00 0.00 0.00 3.18
1513 1537 2.070783 GTTCGGGTAGATTGCGTGAAA 58.929 47.619 0.00 0.00 0.00 2.69
1515 1539 1.546923 TCGGGTAGATTGCGTGAAAGA 59.453 47.619 0.00 0.00 0.00 2.52
1516 1540 2.028839 TCGGGTAGATTGCGTGAAAGAA 60.029 45.455 0.00 0.00 0.00 2.52
1517 1541 2.348666 CGGGTAGATTGCGTGAAAGAAG 59.651 50.000 0.00 0.00 0.00 2.85
1518 1542 2.678336 GGGTAGATTGCGTGAAAGAAGG 59.322 50.000 0.00 0.00 0.00 3.46
1519 1543 3.335579 GGTAGATTGCGTGAAAGAAGGT 58.664 45.455 0.00 0.00 0.00 3.50
1520 1544 3.751698 GGTAGATTGCGTGAAAGAAGGTT 59.248 43.478 0.00 0.00 0.00 3.50
1521 1545 4.142881 GGTAGATTGCGTGAAAGAAGGTTC 60.143 45.833 0.00 0.00 0.00 3.62
1522 1546 2.480419 AGATTGCGTGAAAGAAGGTTCG 59.520 45.455 0.00 0.00 0.00 3.95
1562 1596 3.682292 GAGGGGCCAAGCGTACAGG 62.682 68.421 4.39 0.00 0.00 4.00
1607 1641 2.678324 GTCGCTGACTTGAGTAAAGCT 58.322 47.619 13.34 0.00 39.76 3.74
1746 1780 7.941919 AGAACTTCCAAAAGGAGTTGTTATTC 58.058 34.615 0.00 0.00 36.78 1.75
1844 1878 2.038557 AGTAAACAACCAGTCGCCATCT 59.961 45.455 0.00 0.00 0.00 2.90
1847 1881 1.267121 ACAACCAGTCGCCATCTAGT 58.733 50.000 0.00 0.00 0.00 2.57
1848 1882 1.623811 ACAACCAGTCGCCATCTAGTT 59.376 47.619 0.00 0.00 0.00 2.24
1849 1883 2.271800 CAACCAGTCGCCATCTAGTTC 58.728 52.381 0.00 0.00 0.00 3.01
1850 1884 0.824759 ACCAGTCGCCATCTAGTTCC 59.175 55.000 0.00 0.00 0.00 3.62
1851 1885 0.105039 CCAGTCGCCATCTAGTTCCC 59.895 60.000 0.00 0.00 0.00 3.97
1852 1886 0.105039 CAGTCGCCATCTAGTTCCCC 59.895 60.000 0.00 0.00 0.00 4.81
1853 1887 0.325296 AGTCGCCATCTAGTTCCCCA 60.325 55.000 0.00 0.00 0.00 4.96
1854 1888 0.179081 GTCGCCATCTAGTTCCCCAC 60.179 60.000 0.00 0.00 0.00 4.61
1855 1889 1.146263 CGCCATCTAGTTCCCCACC 59.854 63.158 0.00 0.00 0.00 4.61
1965 1999 0.543277 TCCTGATGTGATGGCAGACC 59.457 55.000 0.00 0.00 0.00 3.85
1989 2023 1.734465 GTCAGAAGTTCGGCATGAAGG 59.266 52.381 0.00 0.00 37.23 3.46
2064 2098 5.526846 CCAGAAGGTCTAGAAAGAATGATGC 59.473 44.000 0.00 0.00 32.16 3.91
2395 2430 9.817809 TCATCTATATGTTTTTGTCCTAGACAC 57.182 33.333 0.00 0.00 37.05 3.67
2678 2771 3.863142 AAATTGAGAACATGAGCAGCC 57.137 42.857 0.00 0.00 0.00 4.85
2719 2815 8.807581 GGGCAAAATCAGAAACTTAATTAATCG 58.192 33.333 0.00 0.00 0.00 3.34
2733 2829 9.855021 ACTTAATTAATCGCTTGCTAAAATTGT 57.145 25.926 0.00 0.00 0.00 2.71
2798 2894 1.877258 CGGGTGGCATGCAAAAACATT 60.877 47.619 21.36 0.00 0.00 2.71
2820 2916 1.878953 ACGGTGACTGATTTGTGTCC 58.121 50.000 0.00 0.00 32.67 4.02
2821 2917 1.416401 ACGGTGACTGATTTGTGTCCT 59.584 47.619 0.00 0.00 32.67 3.85
2822 2918 2.631062 ACGGTGACTGATTTGTGTCCTA 59.369 45.455 0.00 0.00 32.67 2.94
2823 2919 3.070446 ACGGTGACTGATTTGTGTCCTAA 59.930 43.478 0.00 0.00 32.67 2.69
2906 3004 8.339344 ACACATGAAAATATCTGTGATTGACA 57.661 30.769 0.00 0.00 38.43 3.58
2955 3053 9.715121 AAATTTTAACAGCTGATGATTGACAAT 57.285 25.926 23.35 0.00 0.00 2.71
2956 3054 8.697846 ATTTTAACAGCTGATGATTGACAATG 57.302 30.769 23.35 0.00 0.00 2.82
2957 3055 4.713824 AACAGCTGATGATTGACAATGG 57.286 40.909 23.35 0.00 0.00 3.16
2959 3057 3.442625 ACAGCTGATGATTGACAATGGTG 59.557 43.478 23.35 8.95 33.98 4.17
2961 3059 4.157105 CAGCTGATGATTGACAATGGTGAA 59.843 41.667 8.42 0.00 31.63 3.18
2962 3060 4.398358 AGCTGATGATTGACAATGGTGAAG 59.602 41.667 5.14 0.00 0.00 3.02
2963 3061 4.439700 GCTGATGATTGACAATGGTGAAGG 60.440 45.833 5.14 0.00 0.00 3.46
2967 3065 6.891361 TGATGATTGACAATGGTGAAGGTATT 59.109 34.615 5.14 0.00 0.00 1.89
2968 3066 8.052141 TGATGATTGACAATGGTGAAGGTATTA 58.948 33.333 5.14 0.00 0.00 0.98
2969 3067 9.071276 GATGATTGACAATGGTGAAGGTATTAT 57.929 33.333 5.14 0.00 0.00 1.28
2971 3069 9.559732 TGATTGACAATGGTGAAGGTATTATAG 57.440 33.333 5.14 0.00 0.00 1.31
2972 3070 7.801716 TTGACAATGGTGAAGGTATTATAGC 57.198 36.000 0.00 0.00 0.00 2.97
2973 3071 6.894682 TGACAATGGTGAAGGTATTATAGCA 58.105 36.000 4.20 0.00 0.00 3.49
2975 3073 7.136822 ACAATGGTGAAGGTATTATAGCAGA 57.863 36.000 4.20 0.00 0.00 4.26
2976 3074 7.573710 ACAATGGTGAAGGTATTATAGCAGAA 58.426 34.615 4.20 0.00 0.00 3.02
2977 3075 8.220559 ACAATGGTGAAGGTATTATAGCAGAAT 58.779 33.333 4.20 0.00 0.00 2.40
2979 3077 7.373617 TGGTGAAGGTATTATAGCAGAATGA 57.626 36.000 4.20 0.00 39.69 2.57
2980 3078 7.977818 TGGTGAAGGTATTATAGCAGAATGAT 58.022 34.615 4.20 0.00 39.69 2.45
2981 3079 7.879677 TGGTGAAGGTATTATAGCAGAATGATG 59.120 37.037 4.20 0.00 39.69 3.07
2982 3080 8.097038 GGTGAAGGTATTATAGCAGAATGATGA 58.903 37.037 4.20 0.00 39.69 2.92
2983 3081 9.664332 GTGAAGGTATTATAGCAGAATGATGAT 57.336 33.333 4.20 0.00 39.69 2.45
2993 3091 6.879276 AGCAGAATGATGATAATGGTGAAG 57.121 37.500 0.00 0.00 39.69 3.02
2994 3092 5.768662 AGCAGAATGATGATAATGGTGAAGG 59.231 40.000 0.00 0.00 39.69 3.46
3010 3631 5.070685 GGTGAAGGTATTTTGTGGAGAAGT 58.929 41.667 0.00 0.00 0.00 3.01
3011 3632 5.535030 GGTGAAGGTATTTTGTGGAGAAGTT 59.465 40.000 0.00 0.00 0.00 2.66
3012 3633 6.294010 GGTGAAGGTATTTTGTGGAGAAGTTC 60.294 42.308 0.00 0.00 0.00 3.01
3014 3635 6.710744 TGAAGGTATTTTGTGGAGAAGTTCTC 59.289 38.462 22.47 22.47 42.66 2.87
3015 3636 6.187727 AGGTATTTTGTGGAGAAGTTCTCA 57.812 37.500 29.36 15.66 45.12 3.27
3016 3637 6.601332 AGGTATTTTGTGGAGAAGTTCTCAA 58.399 36.000 29.36 19.35 45.12 3.02
3018 3639 6.486993 GGTATTTTGTGGAGAAGTTCTCAAGT 59.513 38.462 29.36 16.24 45.12 3.16
3019 3640 7.013369 GGTATTTTGTGGAGAAGTTCTCAAGTT 59.987 37.037 29.36 12.58 45.12 2.66
3020 3641 6.436843 TTTTGTGGAGAAGTTCTCAAGTTC 57.563 37.500 29.36 15.08 45.12 3.01
3021 3642 4.753516 TGTGGAGAAGTTCTCAAGTTCA 57.246 40.909 29.36 17.20 45.12 3.18
3022 3643 5.296151 TGTGGAGAAGTTCTCAAGTTCAT 57.704 39.130 29.36 0.00 45.12 2.57
3028 3649 5.809001 AGAAGTTCTCAAGTTCATATGCCA 58.191 37.500 0.00 0.00 42.10 4.92
3030 3651 7.568349 AGAAGTTCTCAAGTTCATATGCCATA 58.432 34.615 0.00 0.00 42.10 2.74
3034 3655 6.925610 TCTCAAGTTCATATGCCATACAAC 57.074 37.500 0.00 0.00 0.00 3.32
3035 3656 6.413892 TCTCAAGTTCATATGCCATACAACA 58.586 36.000 9.79 0.00 0.00 3.33
3037 3658 7.066163 TCTCAAGTTCATATGCCATACAACAAG 59.934 37.037 9.79 5.67 0.00 3.16
3045 3666 0.107410 CCATACAACAAGGCCGCCTA 60.107 55.000 13.73 0.00 31.13 3.93
3050 3671 2.836187 AACAAGGCCGCCTAACCCA 61.836 57.895 13.73 0.00 31.13 4.51
3106 3732 6.054860 ACTGTGCACTAGAATTTACCTGAT 57.945 37.500 19.41 0.00 0.00 2.90
3139 3769 8.082242 ACAATGTACTAAATTTTGGAAGCAGTC 58.918 33.333 0.00 0.00 0.00 3.51
3140 3770 7.759489 ATGTACTAAATTTTGGAAGCAGTCA 57.241 32.000 0.00 0.00 0.00 3.41
3158 3788 3.070748 GTCAGTGAGCTCTTTTTCTCCC 58.929 50.000 16.19 0.00 0.00 4.30
3170 3800 7.664318 AGCTCTTTTTCTCCCGACTAAAATTTA 59.336 33.333 0.00 0.00 0.00 1.40
3179 3809 8.852135 TCTCCCGACTAAAATTTAATGTTTGTT 58.148 29.630 0.00 0.00 0.00 2.83
3190 3820 9.598517 AAATTTAATGTTTGTTTGAAGCTGAGA 57.401 25.926 0.00 0.00 0.00 3.27
3191 3821 8.807667 ATTTAATGTTTGTTTGAAGCTGAGAG 57.192 30.769 0.00 0.00 0.00 3.20
3194 3824 5.235305 TGTTTGTTTGAAGCTGAGAGTTC 57.765 39.130 0.00 0.00 0.00 3.01
3210 3840 8.695284 GCTGAGAGTTCATTTACATATAGAACG 58.305 37.037 0.00 0.00 42.39 3.95
3228 3858 4.712337 AGAACGTAAGGGATGTTGATCTCT 59.288 41.667 0.00 0.00 41.66 3.10
3238 3868 7.915930 AGGGATGTTGATCTCTTGGATATTAG 58.084 38.462 0.00 0.00 35.72 1.73
3247 3877 8.874156 TGATCTCTTGGATATTAGTTGCATAGT 58.126 33.333 0.00 0.00 34.33 2.12
3248 3878 9.717942 GATCTCTTGGATATTAGTTGCATAGTT 57.282 33.333 0.00 0.00 34.33 2.24
3250 3880 9.330063 TCTCTTGGATATTAGTTGCATAGTTTG 57.670 33.333 0.00 0.00 0.00 2.93
3251 3881 9.113838 CTCTTGGATATTAGTTGCATAGTTTGT 57.886 33.333 0.00 0.00 0.00 2.83
3252 3882 9.109393 TCTTGGATATTAGTTGCATAGTTTGTC 57.891 33.333 0.00 0.00 0.00 3.18
3253 3883 7.801716 TGGATATTAGTTGCATAGTTTGTCC 57.198 36.000 0.00 0.00 0.00 4.02
3254 3884 6.770785 TGGATATTAGTTGCATAGTTTGTCCC 59.229 38.462 0.00 0.00 0.00 4.46
3255 3885 6.770785 GGATATTAGTTGCATAGTTTGTCCCA 59.229 38.462 0.00 0.00 0.00 4.37
3256 3886 5.897377 ATTAGTTGCATAGTTTGTCCCAC 57.103 39.130 0.00 0.00 0.00 4.61
3257 3887 2.514803 AGTTGCATAGTTTGTCCCACC 58.485 47.619 0.00 0.00 0.00 4.61
3258 3888 2.108250 AGTTGCATAGTTTGTCCCACCT 59.892 45.455 0.00 0.00 0.00 4.00
3259 3889 2.890945 GTTGCATAGTTTGTCCCACCTT 59.109 45.455 0.00 0.00 0.00 3.50
3260 3890 2.513753 TGCATAGTTTGTCCCACCTTG 58.486 47.619 0.00 0.00 0.00 3.61
3261 3891 1.202348 GCATAGTTTGTCCCACCTTGC 59.798 52.381 0.00 0.00 0.00 4.01
3262 3892 1.818674 CATAGTTTGTCCCACCTTGCC 59.181 52.381 0.00 0.00 0.00 4.52
3263 3893 1.145571 TAGTTTGTCCCACCTTGCCT 58.854 50.000 0.00 0.00 0.00 4.75
3264 3894 0.178990 AGTTTGTCCCACCTTGCCTC 60.179 55.000 0.00 0.00 0.00 4.70
3265 3895 0.178990 GTTTGTCCCACCTTGCCTCT 60.179 55.000 0.00 0.00 0.00 3.69
3266 3896 0.178992 TTTGTCCCACCTTGCCTCTG 60.179 55.000 0.00 0.00 0.00 3.35
3267 3897 1.352622 TTGTCCCACCTTGCCTCTGT 61.353 55.000 0.00 0.00 0.00 3.41
3268 3898 1.302832 GTCCCACCTTGCCTCTGTG 60.303 63.158 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 2.175931 TCCAGCCCAAACAAGGAGTAAA 59.824 45.455 0.00 0.00 0.00 2.01
101 102 2.166907 TTTTCCAGCCCAAACAAGGA 57.833 45.000 0.00 0.00 0.00 3.36
130 151 2.159170 GCAGTGTGTAAACAAGGCCAAA 60.159 45.455 5.01 0.00 0.00 3.28
249 270 1.152881 GCCCCTTGGATCTCGCATT 60.153 57.895 0.00 0.00 0.00 3.56
361 383 3.009714 GGTGACCCTGTCTCCCCC 61.010 72.222 4.39 0.00 39.46 5.40
454 476 7.785028 TGGGTATCTCTAGTTATGAGATGTGTT 59.215 37.037 14.29 0.00 46.84 3.32
488 510 3.754965 TCATGTTGCAGCTAGGTTTCTT 58.245 40.909 1.17 0.00 0.00 2.52
496 518 4.334552 TCCAAGAAATCATGTTGCAGCTA 58.665 39.130 1.17 0.00 31.11 3.32
512 534 1.112113 GAGTGGGCGTATCTCCAAGA 58.888 55.000 0.00 0.00 34.47 3.02
554 576 1.732259 GTGTGCGGTCAAGTTGGATAG 59.268 52.381 2.34 0.00 0.00 2.08
754 776 0.822164 ATAGGAGCACCGGTGTGTAC 59.178 55.000 33.92 22.67 44.65 2.90
814 836 0.252284 AGAGGTGACCCGAGTCCAAT 60.252 55.000 0.00 0.00 42.81 3.16
913 935 1.017387 CGGAGTTGGGAATTAGCTGC 58.983 55.000 0.00 0.00 0.00 5.25
942 964 2.412870 TCGACGTCAAAATGATGCACT 58.587 42.857 17.16 0.00 36.89 4.40
966 988 2.588877 CGCCGAGCAATCCCGATT 60.589 61.111 0.00 0.00 0.00 3.34
1113 1137 3.181462 TGTTTATCATGCTCTCGGATGCT 60.181 43.478 0.00 0.00 38.69 3.79
1141 1165 1.136085 TGCTATTTTGAAGTCGTGCGC 60.136 47.619 0.00 0.00 0.00 6.09
1143 1167 4.093408 TGAGATGCTATTTTGAAGTCGTGC 59.907 41.667 0.00 0.00 0.00 5.34
1177 1201 4.100373 AGCATCTCCTCTGGACTAGTTTT 58.900 43.478 0.00 0.00 0.00 2.43
1185 1209 0.986527 TGCAAAGCATCTCCTCTGGA 59.013 50.000 0.00 0.00 31.71 3.86
1216 1240 4.547367 GGGCTTAGCGGTGGCGAT 62.547 66.667 0.00 0.00 46.35 4.58
1407 1431 1.861542 GCACCCTTAATGTGTGCGCA 61.862 55.000 5.66 5.66 44.95 6.09
1442 1466 3.063997 CGATTTCAGGTAACAGGACATGC 59.936 47.826 0.00 0.00 41.41 4.06
1479 1503 0.941542 CCGAACCTTCTTTCACGCAA 59.058 50.000 0.00 0.00 0.00 4.85
1485 1509 3.374367 GCAATCTACCCGAACCTTCTTTC 59.626 47.826 0.00 0.00 0.00 2.62
1488 1512 1.134788 CGCAATCTACCCGAACCTTCT 60.135 52.381 0.00 0.00 0.00 2.85
1494 1518 2.028839 TCTTTCACGCAATCTACCCGAA 60.029 45.455 0.00 0.00 0.00 4.30
1497 1521 2.678336 CCTTCTTTCACGCAATCTACCC 59.322 50.000 0.00 0.00 0.00 3.69
1499 1523 4.434330 CGAACCTTCTTTCACGCAATCTAC 60.434 45.833 0.00 0.00 0.00 2.59
1500 1524 3.678072 CGAACCTTCTTTCACGCAATCTA 59.322 43.478 0.00 0.00 0.00 1.98
1501 1525 2.480419 CGAACCTTCTTTCACGCAATCT 59.520 45.455 0.00 0.00 0.00 2.40
1502 1526 2.839474 CGAACCTTCTTTCACGCAATC 58.161 47.619 0.00 0.00 0.00 2.67
1503 1527 1.069227 GCGAACCTTCTTTCACGCAAT 60.069 47.619 0.00 0.00 44.29 3.56
1504 1528 0.306533 GCGAACCTTCTTTCACGCAA 59.693 50.000 0.00 0.00 44.29 4.85
1506 1530 0.517316 ATGCGAACCTTCTTTCACGC 59.483 50.000 0.00 0.00 44.95 5.34
1508 1532 1.798813 ACGATGCGAACCTTCTTTCAC 59.201 47.619 0.00 0.00 0.00 3.18
1509 1533 2.066262 GACGATGCGAACCTTCTTTCA 58.934 47.619 0.00 0.00 0.00 2.69
1511 1535 2.163818 TGACGATGCGAACCTTCTTT 57.836 45.000 0.00 0.00 0.00 2.52
1512 1536 2.069273 CTTGACGATGCGAACCTTCTT 58.931 47.619 0.00 0.00 0.00 2.52
1513 1537 1.673033 CCTTGACGATGCGAACCTTCT 60.673 52.381 0.00 0.00 0.00 2.85
1515 1539 1.298859 GCCTTGACGATGCGAACCTT 61.299 55.000 0.00 0.00 0.00 3.50
1516 1540 1.741770 GCCTTGACGATGCGAACCT 60.742 57.895 0.00 0.00 0.00 3.50
1517 1541 2.785258 GCCTTGACGATGCGAACC 59.215 61.111 0.00 0.00 0.00 3.62
1522 1546 1.197910 GTAGTACGCCTTGACGATGC 58.802 55.000 0.00 0.00 36.70 3.91
1550 1584 1.079127 CAGTCCCCTGTACGCTTGG 60.079 63.158 0.00 0.00 33.80 3.61
1553 1587 2.683933 CCCAGTCCCCTGTACGCT 60.684 66.667 0.00 0.00 36.95 5.07
1562 1596 1.272554 CCTGTAGGTTCCCCAGTCCC 61.273 65.000 5.73 0.00 0.00 4.46
1746 1780 7.095017 GGTTGGAAGTTCTTCTACAATCTCTTG 60.095 40.741 11.53 0.00 38.39 3.02
1802 1836 9.739276 TTTACTACAATTTCATCATGGTTCTCT 57.261 29.630 0.00 0.00 0.00 3.10
1844 1878 4.554553 AGCTATAGAAGGTGGGGAACTA 57.445 45.455 3.21 0.00 33.68 2.24
1853 1887 6.924913 TCTTGCATATCAGCTATAGAAGGT 57.075 37.500 3.21 0.00 35.94 3.50
1854 1888 6.313411 GCTTCTTGCATATCAGCTATAGAAGG 59.687 42.308 15.53 0.00 40.85 3.46
1855 1889 6.313411 GGCTTCTTGCATATCAGCTATAGAAG 59.687 42.308 3.21 11.38 45.15 2.85
1965 1999 1.998315 CATGCCGAACTTCTGACTCAG 59.002 52.381 0.00 0.00 0.00 3.35
2064 2098 1.890979 GTGCTCTGCCCATCCATCG 60.891 63.158 0.00 0.00 0.00 3.84
2142 2176 3.028130 TCAGCATGACAATGGCAATGAT 58.972 40.909 10.01 0.00 42.56 2.45
2384 2419 1.081481 TCAGAGGGGTGTCTAGGACA 58.919 55.000 0.00 0.00 40.50 4.02
2395 2430 3.083349 TGGTCGGCATCAGAGGGG 61.083 66.667 0.00 0.00 0.00 4.79
2678 2771 7.102346 TGATTTTGCCCTGTTATGTAATTTGG 58.898 34.615 0.00 0.00 0.00 3.28
2733 2829 7.550906 GGGGCAAAGCATTTTATGTTTACATTA 59.449 33.333 0.02 0.00 35.03 1.90
2737 2833 4.634004 GGGGGCAAAGCATTTTATGTTTAC 59.366 41.667 0.00 0.00 35.03 2.01
2740 2836 3.348647 GGGGGCAAAGCATTTTATGTT 57.651 42.857 0.00 0.00 35.03 2.71
2765 2861 0.321564 CCACCCGAGTGCAAGATCAA 60.322 55.000 0.00 0.00 43.09 2.57
2766 2862 1.296392 CCACCCGAGTGCAAGATCA 59.704 57.895 0.00 0.00 43.09 2.92
2768 2864 2.045926 GCCACCCGAGTGCAAGAT 60.046 61.111 0.00 0.00 43.09 2.40
2798 2894 3.810941 GGACACAAATCAGTCACCGTTTA 59.189 43.478 0.00 0.00 36.50 2.01
2820 2916 2.407361 CACGCTGTTGTAGTTCGGTTAG 59.593 50.000 0.00 0.00 0.00 2.34
2821 2917 2.396601 CACGCTGTTGTAGTTCGGTTA 58.603 47.619 0.00 0.00 0.00 2.85
2822 2918 1.214367 CACGCTGTTGTAGTTCGGTT 58.786 50.000 0.00 0.00 0.00 4.44
2823 2919 0.599204 CCACGCTGTTGTAGTTCGGT 60.599 55.000 0.00 0.00 0.00 4.69
2890 2988 7.984422 TCAACTGTTGTCAATCACAGATATT 57.016 32.000 19.12 0.00 35.97 1.28
2906 3004 4.945543 TGCAGCTATCAATCATCAACTGTT 59.054 37.500 0.00 0.00 0.00 3.16
2955 3053 7.373617 TCATTCTGCTATAATACCTTCACCA 57.626 36.000 0.00 0.00 0.00 4.17
2956 3054 8.097038 TCATCATTCTGCTATAATACCTTCACC 58.903 37.037 0.00 0.00 0.00 4.02
2957 3055 9.664332 ATCATCATTCTGCTATAATACCTTCAC 57.336 33.333 0.00 0.00 0.00 3.18
2967 3065 9.662947 CTTCACCATTATCATCATTCTGCTATA 57.337 33.333 0.00 0.00 0.00 1.31
2968 3066 7.610692 CCTTCACCATTATCATCATTCTGCTAT 59.389 37.037 0.00 0.00 0.00 2.97
2969 3067 6.938596 CCTTCACCATTATCATCATTCTGCTA 59.061 38.462 0.00 0.00 0.00 3.49
2971 3069 5.533903 ACCTTCACCATTATCATCATTCTGC 59.466 40.000 0.00 0.00 0.00 4.26
2972 3070 8.859236 ATACCTTCACCATTATCATCATTCTG 57.141 34.615 0.00 0.00 0.00 3.02
2973 3071 9.872684 AAATACCTTCACCATTATCATCATTCT 57.127 29.630 0.00 0.00 0.00 2.40
2976 3074 9.425248 ACAAAATACCTTCACCATTATCATCAT 57.575 29.630 0.00 0.00 0.00 2.45
2977 3075 8.685427 CACAAAATACCTTCACCATTATCATCA 58.315 33.333 0.00 0.00 0.00 3.07
2979 3077 7.838696 TCCACAAAATACCTTCACCATTATCAT 59.161 33.333 0.00 0.00 0.00 2.45
2980 3078 7.178573 TCCACAAAATACCTTCACCATTATCA 58.821 34.615 0.00 0.00 0.00 2.15
2981 3079 7.556275 TCTCCACAAAATACCTTCACCATTATC 59.444 37.037 0.00 0.00 0.00 1.75
2982 3080 7.410174 TCTCCACAAAATACCTTCACCATTAT 58.590 34.615 0.00 0.00 0.00 1.28
2983 3081 6.785076 TCTCCACAAAATACCTTCACCATTA 58.215 36.000 0.00 0.00 0.00 1.90
2984 3082 5.640147 TCTCCACAAAATACCTTCACCATT 58.360 37.500 0.00 0.00 0.00 3.16
2987 3085 5.070685 ACTTCTCCACAAAATACCTTCACC 58.929 41.667 0.00 0.00 0.00 4.02
2989 3087 6.601332 AGAACTTCTCCACAAAATACCTTCA 58.399 36.000 0.00 0.00 0.00 3.02
2990 3088 6.710744 TGAGAACTTCTCCACAAAATACCTTC 59.289 38.462 14.98 0.00 42.73 3.46
2991 3089 6.601332 TGAGAACTTCTCCACAAAATACCTT 58.399 36.000 14.98 0.00 42.73 3.50
2993 3091 6.486993 ACTTGAGAACTTCTCCACAAAATACC 59.513 38.462 14.98 0.00 42.73 2.73
2994 3092 7.497925 ACTTGAGAACTTCTCCACAAAATAC 57.502 36.000 14.98 0.00 42.73 1.89
3010 3631 6.883756 TGTTGTATGGCATATGAACTTGAGAA 59.116 34.615 22.55 8.00 0.00 2.87
3011 3632 6.413892 TGTTGTATGGCATATGAACTTGAGA 58.586 36.000 22.55 8.49 0.00 3.27
3012 3633 6.682423 TGTTGTATGGCATATGAACTTGAG 57.318 37.500 22.55 0.00 0.00 3.02
3014 3635 6.267817 CCTTGTTGTATGGCATATGAACTTG 58.732 40.000 22.55 17.18 0.00 3.16
3015 3636 5.163519 GCCTTGTTGTATGGCATATGAACTT 60.164 40.000 22.55 0.00 46.20 2.66
3016 3637 4.339247 GCCTTGTTGTATGGCATATGAACT 59.661 41.667 22.55 0.00 46.20 3.01
3018 3639 4.916983 GCCTTGTTGTATGGCATATGAA 57.083 40.909 10.92 4.28 46.20 2.57
3028 3649 1.680860 GGTTAGGCGGCCTTGTTGTAT 60.681 52.381 29.02 2.08 34.61 2.29
3030 3651 1.602605 GGTTAGGCGGCCTTGTTGT 60.603 57.895 29.02 3.79 34.61 3.32
3034 3655 2.438434 CTGGGTTAGGCGGCCTTG 60.438 66.667 29.02 7.10 34.61 3.61
3035 3656 3.728373 CCTGGGTTAGGCGGCCTT 61.728 66.667 29.02 11.52 40.38 4.35
3045 3666 3.891366 GCAGCATAATATTCACCTGGGTT 59.109 43.478 0.00 0.00 0.00 4.11
3050 3671 2.154462 GCGGCAGCATAATATTCACCT 58.846 47.619 3.18 0.00 44.35 4.00
3116 3742 7.448469 ACTGACTGCTTCCAAAATTTAGTACAT 59.552 33.333 0.00 0.00 0.00 2.29
3127 3757 1.141657 AGCTCACTGACTGCTTCCAAA 59.858 47.619 0.00 0.00 32.61 3.28
3130 3760 0.607620 AGAGCTCACTGACTGCTTCC 59.392 55.000 17.77 0.00 37.16 3.46
3131 3761 2.453983 AAGAGCTCACTGACTGCTTC 57.546 50.000 17.77 0.00 37.16 3.86
3139 3769 2.072298 CGGGAGAAAAAGAGCTCACTG 58.928 52.381 17.77 0.00 32.40 3.66
3140 3770 1.971357 TCGGGAGAAAAAGAGCTCACT 59.029 47.619 17.77 6.79 32.40 3.41
3170 3800 5.841957 ACTCTCAGCTTCAAACAAACATT 57.158 34.783 0.00 0.00 0.00 2.71
3190 3820 9.760077 CCCTTACGTTCTATATGTAAATGAACT 57.240 33.333 0.00 0.00 37.68 3.01
3191 3821 9.754382 TCCCTTACGTTCTATATGTAAATGAAC 57.246 33.333 0.00 0.00 37.68 3.18
3194 3824 9.706691 ACATCCCTTACGTTCTATATGTAAATG 57.293 33.333 0.00 0.00 37.68 2.32
3210 3840 5.359194 TCCAAGAGATCAACATCCCTTAC 57.641 43.478 0.00 0.00 26.48 2.34
3212 3842 6.776887 ATATCCAAGAGATCAACATCCCTT 57.223 37.500 0.00 0.00 36.33 3.95
3228 3858 7.284489 GGGACAAACTATGCAACTAATATCCAA 59.716 37.037 0.00 0.00 0.00 3.53
3233 3863 5.883673 GGTGGGACAAACTATGCAACTAATA 59.116 40.000 0.00 0.00 44.16 0.98
3238 3868 2.514803 AGGTGGGACAAACTATGCAAC 58.485 47.619 0.00 0.00 44.16 4.17
3247 3877 0.178992 CAGAGGCAAGGTGGGACAAA 60.179 55.000 0.00 0.00 44.16 2.83
3248 3878 1.352622 ACAGAGGCAAGGTGGGACAA 61.353 55.000 0.00 0.00 44.16 3.18
3249 3879 1.770110 ACAGAGGCAAGGTGGGACA 60.770 57.895 0.00 0.00 0.00 4.02
3250 3880 1.302832 CACAGAGGCAAGGTGGGAC 60.303 63.158 0.00 0.00 0.00 4.46
3251 3881 2.528818 CCACAGAGGCAAGGTGGGA 61.529 63.158 12.08 0.00 46.51 4.37
3252 3882 2.034687 CCACAGAGGCAAGGTGGG 59.965 66.667 12.08 0.00 46.51 4.61


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

AutoCloner maintained by Alex Coulton.