Multiple sequence alignment - TraesCS5A01G245600

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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 TraesCS5A01G245600 chr5A 100.000 3179 0 0 1 3179 458965764 458968942 0.000000e+00 5871.0
1 TraesCS5A01G245600 chr5A 92.784 97 7 0 1116 1212 373994061 373993965 1.190000e-29 141.0
2 TraesCS5A01G245600 chr5A 85.897 78 9 1 2163 2238 459334774 459334851 7.310000e-12 82.4
3 TraesCS5A01G245600 chr5D 88.267 1662 84 45 538 2145 358009764 358011368 0.000000e+00 1886.0
4 TraesCS5A01G245600 chr5D 95.106 940 43 3 2240 3179 358011435 358012371 0.000000e+00 1478.0
5 TraesCS5A01G245600 chr5D 87.887 388 21 9 1 366 358009129 358009512 1.750000e-117 433.0
6 TraesCS5A01G245600 chr5D 98.246 57 1 0 462 518 358009641 358009697 2.020000e-17 100.0
7 TraesCS5A01G245600 chr5D 88.312 77 7 1 2164 2238 389245501 389245425 1.210000e-14 91.6
8 TraesCS5A01G245600 chr5D 85.366 82 10 2 2159 2238 61045892 61045811 2.030000e-12 84.2
9 TraesCS5A01G245600 chr5B 92.703 1206 61 13 950 2145 423225195 423226383 0.000000e+00 1714.0
10 TraesCS5A01G245600 chr5B 92.447 940 60 5 2240 3173 423226450 423227384 0.000000e+00 1332.0
11 TraesCS5A01G245600 chr5B 85.678 398 18 17 1 366 423216118 423216508 1.790000e-102 383.0
12 TraesCS5A01G245600 chr5B 78.538 424 32 21 561 955 423224551 423224944 1.150000e-54 224.0
13 TraesCS5A01G245600 chr5B 81.437 167 7 7 364 520 423216561 423216713 7.210000e-22 115.0
14 TraesCS5A01G245600 chr2A 79.191 346 37 22 1287 1601 713936134 713935793 1.160000e-49 207.0
15 TraesCS5A01G245600 chr2A 90.000 70 5 1 2167 2234 75652801 75652870 4.370000e-14 89.8
16 TraesCS5A01G245600 chr2A 87.013 77 8 1 2167 2241 406769950 406770026 5.650000e-13 86.1
17 TraesCS5A01G245600 chr7A 97.030 101 3 0 1116 1216 12963742 12963642 1.520000e-38 171.0
18 TraesCS5A01G245600 chr7A 94.898 98 5 0 1116 1213 675516252 675516155 1.530000e-33 154.0
19 TraesCS5A01G245600 chr7B 95.918 98 4 0 1116 1213 65911345 65911248 3.280000e-35 159.0
20 TraesCS5A01G245600 chr3A 94.898 98 5 0 1116 1213 187385471 187385374 1.530000e-33 154.0
21 TraesCS5A01G245600 chr6B 91.837 98 8 0 1116 1213 89687216 89687119 1.540000e-28 137.0
22 TraesCS5A01G245600 chr2D 90.110 91 9 0 1116 1206 575770561 575770471 5.570000e-23 119.0
23 TraesCS5A01G245600 chr1D 90.541 74 6 1 2165 2238 442373861 442373789 2.610000e-16 97.1
24 TraesCS5A01G245600 chr1D 88.000 75 8 1 2165 2238 479730247 479730173 1.570000e-13 87.9
25 TraesCS5A01G245600 chr4B 88.889 72 8 0 2167 2238 172508806 172508735 4.370000e-14 89.8
26 TraesCS5A01G245600 chr3D 89.041 73 7 1 2166 2238 566551020 566550949 4.370000e-14 89.8


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 TraesCS5A01G245600 chr5A 458965764 458968942 3178 False 5871.00 5871 100.0000 1 3179 1 chr5A.!!$F1 3178
1 TraesCS5A01G245600 chr5D 358009129 358012371 3242 False 974.25 1886 92.3765 1 3179 4 chr5D.!!$F1 3178
2 TraesCS5A01G245600 chr5B 423224551 423227384 2833 False 1090.00 1714 87.8960 561 3173 3 chr5B.!!$F2 2612
3 TraesCS5A01G245600 chr5B 423216118 423216713 595 False 249.00 383 83.5575 1 520 2 chr5B.!!$F1 519

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
831 1017 0.107654 CAGGAGGAGGTAAAAGGCGG 60.108 60.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2492 2994 0.321564 AATCCAGCTGCTGTGCGTTA 60.322 50.0 26.41 6.69 38.13 3.18 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
65 66 3.849953 GTCGGTCGGCAATCGCAC 61.850 66.667 0.00 0.00 41.24 5.34
89 90 3.061848 CACGATGCCGCCCCTTTT 61.062 61.111 0.00 0.00 39.95 2.27
94 95 4.986708 TGCCGCCCCTTTTCCACC 62.987 66.667 0.00 0.00 0.00 4.61
218 236 2.101575 GCTACATCGACCGCACGA 59.898 61.111 4.84 4.84 46.04 4.35
228 246 1.503818 GACCGCACGAAGCAAAAGGA 61.504 55.000 0.00 0.00 46.13 3.36
312 339 2.322830 GGCGAAAACCACGAGTCCC 61.323 63.158 0.00 0.00 0.00 4.46
323 356 3.311110 GAGTCCCCACTGTGCCGA 61.311 66.667 1.29 0.00 30.63 5.54
399 488 4.454717 GGCACGGCGCGGTTAAAG 62.455 66.667 18.85 8.30 43.84 1.85
401 490 3.718097 CACGGCGCGGTTAAAGCA 61.718 61.111 18.85 0.00 34.19 3.91
402 491 2.973600 ACGGCGCGGTTAAAGCAA 60.974 55.556 15.60 0.00 34.19 3.91
403 492 2.202298 CGGCGCGGTTAAAGCAAG 60.202 61.111 8.83 0.00 34.19 4.01
404 493 2.504026 GGCGCGGTTAAAGCAAGC 60.504 61.111 8.83 1.57 34.19 4.01
405 494 2.254051 GCGCGGTTAAAGCAAGCA 59.746 55.556 8.83 0.00 34.13 3.91
406 495 1.797537 GCGCGGTTAAAGCAAGCAG 60.798 57.895 8.83 0.00 34.13 4.24
407 496 1.866237 CGCGGTTAAAGCAAGCAGA 59.134 52.632 0.00 0.00 34.13 4.26
408 497 0.452784 CGCGGTTAAAGCAAGCAGAC 60.453 55.000 0.00 0.00 34.13 3.51
409 498 0.591170 GCGGTTAAAGCAAGCAGACA 59.409 50.000 0.00 0.00 34.13 3.41
410 499 1.400242 GCGGTTAAAGCAAGCAGACAG 60.400 52.381 0.00 0.00 34.13 3.51
518 634 2.602267 TGTCCATCCCCGACACGT 60.602 61.111 0.00 0.00 35.35 4.49
520 636 1.140375 GTCCATCCCCGACACGTAC 59.860 63.158 0.00 0.00 0.00 3.67
521 637 2.103538 CCATCCCCGACACGTACG 59.896 66.667 15.01 15.01 0.00 3.67
562 724 1.065109 CGCACCGTGTATCCGATGA 59.935 57.895 0.00 0.00 0.00 2.92
563 725 0.318699 CGCACCGTGTATCCGATGAT 60.319 55.000 0.00 0.00 34.87 2.45
564 726 1.139989 GCACCGTGTATCCGATGATG 58.860 55.000 0.00 0.00 32.18 3.07
565 727 1.783284 CACCGTGTATCCGATGATGG 58.217 55.000 0.00 0.00 32.18 3.51
566 728 1.068588 CACCGTGTATCCGATGATGGT 59.931 52.381 0.00 0.00 32.18 3.55
569 731 2.295070 CCGTGTATCCGATGATGGTGTA 59.705 50.000 0.00 0.00 32.18 2.90
571 733 3.318017 GTGTATCCGATGATGGTGTAGC 58.682 50.000 0.00 0.00 32.18 3.58
594 756 3.078560 GCCGTCGTTAAAGGCGAG 58.921 61.111 16.98 8.06 42.82 5.03
595 757 2.450345 GCCGTCGTTAAAGGCGAGG 61.450 63.158 16.98 8.14 42.82 4.63
597 759 2.785105 CGTCGTTAAAGGCGAGGCG 61.785 63.158 9.91 0.00 39.14 5.52
625 792 1.768112 CGCCGACACTTTTTCACCGT 61.768 55.000 0.00 0.00 0.00 4.83
626 793 0.316689 GCCGACACTTTTTCACCGTG 60.317 55.000 0.00 0.00 34.92 4.94
627 794 1.292061 CCGACACTTTTTCACCGTGA 58.708 50.000 0.00 0.00 33.13 4.35
632 799 3.399330 ACACTTTTTCACCGTGATCGAT 58.601 40.909 1.09 0.00 39.71 3.59
635 802 2.018542 TTTTCACCGTGATCGATCCC 57.981 50.000 22.31 10.51 39.71 3.85
639 806 2.194212 ACCGTGATCGATCCCTCGG 61.194 63.158 32.18 32.18 45.10 4.63
640 807 2.194212 CCGTGATCGATCCCTCGGT 61.194 63.158 28.89 0.00 45.10 4.69
643 810 3.367725 GATCGATCCCTCGGTCCC 58.632 66.667 14.76 0.00 47.00 4.46
644 811 1.228613 GATCGATCCCTCGGTCCCT 60.229 63.158 14.76 0.00 47.00 4.20
645 812 1.228613 ATCGATCCCTCGGTCCCTC 60.229 63.158 0.00 0.00 45.10 4.30
646 813 2.716833 ATCGATCCCTCGGTCCCTCC 62.717 65.000 0.00 0.00 45.10 4.30
673 840 0.588737 TTACCACGCACGTACGTACA 59.411 50.000 22.34 0.00 46.34 2.90
674 841 0.165727 TACCACGCACGTACGTACAG 59.834 55.000 22.34 16.79 46.34 2.74
675 842 1.081906 CCACGCACGTACGTACAGT 60.082 57.895 22.34 17.44 46.34 3.55
676 843 0.165727 CCACGCACGTACGTACAGTA 59.834 55.000 22.34 0.00 46.34 2.74
677 844 1.241744 CACGCACGTACGTACAGTAC 58.758 55.000 22.34 15.91 46.34 2.73
719 886 1.175983 GGCACCCGTCCATCACAAAA 61.176 55.000 0.00 0.00 0.00 2.44
732 899 3.513462 TCACAAAATAGTTGCACGTCG 57.487 42.857 0.00 0.00 0.00 5.12
751 918 3.119096 GCGGGAAAGAGGCGACAC 61.119 66.667 0.00 0.00 0.00 3.67
788 955 2.395690 CCGCTGTCGTTTGATCGC 59.604 61.111 0.00 0.00 0.00 4.58
789 956 2.395690 CGCTGTCGTTTGATCGCC 59.604 61.111 0.00 0.00 0.00 5.54
796 971 2.089936 CGTTTGATCGCCCGTTCGA 61.090 57.895 0.00 0.00 43.09 3.71
810 985 4.417506 CCCGTTCGATTTCAATTTTACCC 58.582 43.478 0.00 0.00 0.00 3.69
814 1000 5.407502 GTTCGATTTCAATTTTACCCCCAG 58.592 41.667 0.00 0.00 0.00 4.45
816 1002 4.020543 CGATTTCAATTTTACCCCCAGGA 58.979 43.478 0.00 0.00 36.73 3.86
819 1005 2.650013 TCAATTTTACCCCCAGGAGGA 58.350 47.619 0.00 0.00 38.24 3.71
821 1007 1.608425 ATTTTACCCCCAGGAGGAGG 58.392 55.000 0.00 0.00 38.24 4.30
822 1008 0.197661 TTTTACCCCCAGGAGGAGGT 59.802 55.000 0.00 0.00 40.91 3.85
831 1017 0.107654 CAGGAGGAGGTAAAAGGCGG 60.108 60.000 0.00 0.00 0.00 6.13
833 1019 1.298667 GAGGAGGTAAAAGGCGGCA 59.701 57.895 13.08 0.00 0.00 5.69
835 1021 0.111639 AGGAGGTAAAAGGCGGCAAA 59.888 50.000 13.08 0.00 0.00 3.68
839 1025 1.073284 AGGTAAAAGGCGGCAAAGAGA 59.927 47.619 13.08 0.00 0.00 3.10
840 1026 1.468914 GGTAAAAGGCGGCAAAGAGAG 59.531 52.381 13.08 0.00 0.00 3.20
841 1027 2.152016 GTAAAAGGCGGCAAAGAGAGT 58.848 47.619 13.08 0.00 0.00 3.24
842 1028 1.692411 AAAAGGCGGCAAAGAGAGTT 58.308 45.000 13.08 0.00 0.00 3.01
843 1029 0.954452 AAAGGCGGCAAAGAGAGTTG 59.046 50.000 13.08 0.00 0.00 3.16
844 1030 0.890996 AAGGCGGCAAAGAGAGTTGG 60.891 55.000 13.08 0.00 0.00 3.77
845 1031 1.600916 GGCGGCAAAGAGAGTTGGT 60.601 57.895 3.07 0.00 0.00 3.67
846 1032 1.576421 GCGGCAAAGAGAGTTGGTG 59.424 57.895 0.00 0.00 0.00 4.17
849 1035 1.692411 GGCAAAGAGAGTTGGTGGTT 58.308 50.000 0.00 0.00 0.00 3.67
866 1052 1.455402 TTGCAAGGTCAGCAAGGCA 60.455 52.632 0.00 0.00 46.13 4.75
1007 1483 2.119671 GTTTCAAACGGCTCCAAGTG 57.880 50.000 0.00 0.00 0.00 3.16
1008 1484 1.028905 TTTCAAACGGCTCCAAGTGG 58.971 50.000 0.00 0.00 0.00 4.00
1009 1485 1.452145 TTCAAACGGCTCCAAGTGGC 61.452 55.000 0.00 0.00 34.44 5.01
1087 1563 2.393989 GATGGACGATCAGCGCTCGA 62.394 60.000 22.23 16.56 46.04 4.04
1215 1691 3.368190 CTCCCAGGTGAGCTCGCTG 62.368 68.421 25.54 19.81 0.00 5.18
1236 1712 2.748605 CTTCCCATGCTCGTCATAGTC 58.251 52.381 0.00 0.00 33.19 2.59
1258 1734 1.430632 GTTGCGGTGATGATGCCAG 59.569 57.895 0.00 0.00 0.00 4.85
1265 1741 0.737219 GTGATGATGCCAGCTGAACC 59.263 55.000 17.39 3.53 0.00 3.62
1282 1758 2.355363 CGAGCCGGACACGTTTGA 60.355 61.111 5.05 0.00 38.78 2.69
1283 1759 2.654912 CGAGCCGGACACGTTTGAC 61.655 63.158 5.05 0.00 38.78 3.18
1418 1897 3.827898 GAGAGCGACGAGGTGGGG 61.828 72.222 0.00 0.00 0.00 4.96
1755 2234 2.347731 GTTTAGGCAGCTAGTGACACC 58.652 52.381 0.84 0.00 36.10 4.16
1810 2289 3.068307 AGCGTGTATCAACCTGTAGGATC 59.932 47.826 4.64 0.00 38.94 3.36
1860 2340 9.840427 AATATTTAGTTTGATCTGTGTTTTCCG 57.160 29.630 0.00 0.00 0.00 4.30
1861 2341 6.928979 TTTAGTTTGATCTGTGTTTTCCGA 57.071 33.333 0.00 0.00 0.00 4.55
1868 2348 3.126001 TCTGTGTTTTCCGATTCAGCT 57.874 42.857 0.00 0.00 0.00 4.24
1949 2432 4.837972 AGGCACTGAGAGAAATTTAGACC 58.162 43.478 0.00 0.00 37.18 3.85
1965 2448 3.988976 AGACCAATGTCAGCACAGTAT 57.011 42.857 0.00 0.00 44.33 2.12
2003 2487 1.133407 TCAACCGGTTGCTGTTTGTTC 59.867 47.619 37.21 0.00 40.24 3.18
2013 2497 1.664016 GCTGTTTGTTCGCCAGTGATG 60.664 52.381 0.00 0.00 0.00 3.07
2014 2498 0.310543 TGTTTGTTCGCCAGTGATGC 59.689 50.000 0.00 0.00 0.00 3.91
2071 2555 0.175760 TGATAGCAGAACAGTCGCCC 59.824 55.000 0.00 0.00 0.00 6.13
2091 2575 4.777463 CCCAGTACCGTTTGGAATCTTAT 58.223 43.478 0.52 0.00 39.21 1.73
2126 2612 7.398332 AGTCATGAAAAGGAGGCAAGAAATATT 59.602 33.333 0.00 0.00 0.00 1.28
2164 2666 8.980596 ACAGAAATAAATAGGAATGGCAATGAA 58.019 29.630 0.00 0.00 0.00 2.57
2170 2672 7.573968 AAATAGGAATGGCAATGAACTACTC 57.426 36.000 0.00 0.00 0.00 2.59
2172 2674 2.952310 GGAATGGCAATGAACTACTCCC 59.048 50.000 0.00 0.00 0.00 4.30
2173 2675 3.372025 GGAATGGCAATGAACTACTCCCT 60.372 47.826 0.00 0.00 0.00 4.20
2174 2676 3.567478 ATGGCAATGAACTACTCCCTC 57.433 47.619 0.00 0.00 0.00 4.30
2175 2677 1.559682 TGGCAATGAACTACTCCCTCC 59.440 52.381 0.00 0.00 0.00 4.30
2178 2680 3.536570 GCAATGAACTACTCCCTCCTTC 58.463 50.000 0.00 0.00 0.00 3.46
2179 2681 3.682999 GCAATGAACTACTCCCTCCTTCC 60.683 52.174 0.00 0.00 0.00 3.46
2180 2682 2.249309 TGAACTACTCCCTCCTTCCC 57.751 55.000 0.00 0.00 0.00 3.97
2182 2684 0.412640 AACTACTCCCTCCTTCCCGT 59.587 55.000 0.00 0.00 0.00 5.28
2183 2685 1.302907 ACTACTCCCTCCTTCCCGTA 58.697 55.000 0.00 0.00 0.00 4.02
2184 2686 1.642762 ACTACTCCCTCCTTCCCGTAA 59.357 52.381 0.00 0.00 0.00 3.18
2186 2688 3.464833 ACTACTCCCTCCTTCCCGTAATA 59.535 47.826 0.00 0.00 0.00 0.98
2187 2689 3.632420 ACTCCCTCCTTCCCGTAATAT 57.368 47.619 0.00 0.00 0.00 1.28
2188 2690 4.754411 ACTCCCTCCTTCCCGTAATATA 57.246 45.455 0.00 0.00 0.00 0.86
2190 2692 4.024670 CTCCCTCCTTCCCGTAATATAGG 58.975 52.174 0.00 0.00 0.00 2.57
2191 2693 3.664127 TCCCTCCTTCCCGTAATATAGGA 59.336 47.826 0.00 0.00 34.07 2.94
2194 2696 3.087031 TCCTTCCCGTAATATAGGAGCG 58.913 50.000 0.00 0.00 31.60 5.03
2195 2697 2.416972 CCTTCCCGTAATATAGGAGCGC 60.417 54.545 0.00 0.00 0.00 5.92
2196 2698 2.211250 TCCCGTAATATAGGAGCGCT 57.789 50.000 11.27 11.27 0.00 5.92
2197 2699 2.522185 TCCCGTAATATAGGAGCGCTT 58.478 47.619 13.26 0.00 0.00 4.68
2198 2700 2.895404 TCCCGTAATATAGGAGCGCTTT 59.105 45.455 13.26 5.91 0.00 3.51
2199 2701 3.322828 TCCCGTAATATAGGAGCGCTTTT 59.677 43.478 13.26 5.48 0.00 2.27
2200 2702 3.432252 CCCGTAATATAGGAGCGCTTTTG 59.568 47.826 13.26 0.00 0.00 2.44
2201 2703 4.304110 CCGTAATATAGGAGCGCTTTTGA 58.696 43.478 13.26 0.00 0.00 2.69
2202 2704 4.150098 CCGTAATATAGGAGCGCTTTTGAC 59.850 45.833 13.26 0.00 0.00 3.18
2203 2705 4.743151 CGTAATATAGGAGCGCTTTTGACA 59.257 41.667 13.26 0.00 0.00 3.58
2204 2706 5.233476 CGTAATATAGGAGCGCTTTTGACAA 59.767 40.000 13.26 0.00 0.00 3.18
2205 2707 6.237996 CGTAATATAGGAGCGCTTTTGACAAA 60.238 38.462 13.26 0.00 0.00 2.83
2206 2708 6.699575 AATATAGGAGCGCTTTTGACAAAT 57.300 33.333 13.26 0.00 0.00 2.32
2207 2709 2.712057 AGGAGCGCTTTTGACAAATG 57.288 45.000 13.26 5.47 0.00 2.32
2208 2710 1.956477 AGGAGCGCTTTTGACAAATGT 59.044 42.857 13.26 0.00 0.00 2.71
2209 2711 2.030805 AGGAGCGCTTTTGACAAATGTC 60.031 45.455 13.26 6.60 44.97 3.06
2232 2734 9.967451 TGTCAAAAACACTCTTATATTATGGGA 57.033 29.630 0.00 0.00 31.20 4.37
2250 2752 2.338500 GGACAGAGTACAAAGGAAGCG 58.662 52.381 0.00 0.00 0.00 4.68
2299 2801 6.728200 TCACAGTTTTGCTTATTTGAGTCAG 58.272 36.000 0.00 0.00 0.00 3.51
2300 2802 5.916883 CACAGTTTTGCTTATTTGAGTCAGG 59.083 40.000 0.00 0.00 0.00 3.86
2415 2917 2.361757 CAACACAAGGTCTGCCAAATGA 59.638 45.455 0.00 0.00 37.19 2.57
2430 2932 5.717078 CCAAATGAGGCAGCATTATACAT 57.283 39.130 6.11 0.00 37.50 2.29
2472 2974 2.265182 GCAGTTTTACTGGCCGCCA 61.265 57.895 12.67 12.67 46.01 5.69
2492 2994 5.053145 GCCATTTCACGATTCTAGACAGAT 58.947 41.667 0.00 0.00 0.00 2.90
2499 3001 4.438145 CACGATTCTAGACAGATAACGCAC 59.562 45.833 0.00 0.00 0.00 5.34
2504 3006 2.001812 AGACAGATAACGCACAGCAG 57.998 50.000 0.00 0.00 0.00 4.24
2554 3056 6.567891 GCAGTTTACAGGCTTTACTTTGGTAG 60.568 42.308 0.00 0.00 0.00 3.18
2576 3078 4.630069 AGTAATGTATTGTTCGCTGTGTCC 59.370 41.667 0.00 0.00 0.00 4.02
2591 3093 4.083271 GCTGTGTCCAACTTTACTCCATTC 60.083 45.833 0.00 0.00 0.00 2.67
2625 3127 4.578105 CCTCTGCAGTGAAAAGAGTTTCTT 59.422 41.667 17.19 0.00 43.13 2.52
2701 3203 1.923356 AACCATGCTTAACCACAGGG 58.077 50.000 0.00 0.00 43.28 4.45
2849 3351 8.523523 TCTCAAATGTGCAATCAATAAAGTTG 57.476 30.769 0.00 0.00 0.00 3.16
3035 3543 4.223700 AGGTTCAACTATCTCACATGCTCA 59.776 41.667 0.00 0.00 0.00 4.26
3067 3575 5.475220 TGGAACCGTACATTGATCAAACATT 59.525 36.000 13.09 3.89 0.00 2.71
3173 3681 5.953183 TGAATGCATATGAACTCAACCAAC 58.047 37.500 6.97 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 0.539669 GGTCTGTGGGTGGAAAAGGG 60.540 60.000 0.00 0.00 0.00 3.95
88 89 0.834261 TGATCGGTCTGTGGGTGGAA 60.834 55.000 0.00 0.00 0.00 3.53
89 90 0.617535 ATGATCGGTCTGTGGGTGGA 60.618 55.000 0.00 0.00 0.00 4.02
94 95 1.422388 CGCATATGATCGGTCTGTGG 58.578 55.000 6.97 0.00 0.00 4.17
130 135 1.080569 GAATGGCGTGCAGGGTTTG 60.081 57.895 8.72 0.00 0.00 2.93
131 136 0.899717 ATGAATGGCGTGCAGGGTTT 60.900 50.000 8.72 0.00 0.00 3.27
132 137 0.899717 AATGAATGGCGTGCAGGGTT 60.900 50.000 8.72 0.00 0.00 4.11
296 323 1.070105 TGGGGACTCGTGGTTTTCG 59.930 57.895 0.00 0.00 0.00 3.46
399 488 3.745803 GCCTGCCTGTCTGCTTGC 61.746 66.667 0.00 0.00 0.00 4.01
400 489 2.281970 TGCCTGCCTGTCTGCTTG 60.282 61.111 0.00 0.00 0.00 4.01
401 490 2.033757 CTGCCTGCCTGTCTGCTT 59.966 61.111 0.00 0.00 0.00 3.91
402 491 4.031129 CCTGCCTGCCTGTCTGCT 62.031 66.667 0.00 0.00 0.00 4.24
477 593 2.804368 AAGACGAGCGAGCGGTCAAG 62.804 60.000 20.02 8.72 42.17 3.02
526 642 1.431036 GCGTGACCCTACGGAGTAC 59.569 63.158 0.00 0.00 45.11 2.73
527 643 2.108514 CGCGTGACCCTACGGAGTA 61.109 63.158 0.00 0.00 45.11 2.59
529 645 4.849329 GCGCGTGACCCTACGGAG 62.849 72.222 8.43 0.00 43.87 4.63
538 654 2.785105 GATACACGGTGCGCGTGAC 61.785 63.158 22.67 4.75 40.22 3.67
552 714 2.030185 ACGCTACACCATCATCGGATAC 60.030 50.000 0.00 0.00 30.87 2.24
557 719 1.409412 GCTACGCTACACCATCATCG 58.591 55.000 0.00 0.00 0.00 3.84
571 733 1.622269 CTTTAACGACGGCGCTACG 59.378 57.895 12.58 13.50 42.48 3.51
581 743 2.125832 CCGCCTCGCCTTTAACGA 60.126 61.111 0.00 0.00 38.02 3.85
599 761 1.217882 AAAAGTGTCGGCGAACAGAG 58.782 50.000 12.92 0.00 0.00 3.35
600 762 1.595794 GAAAAAGTGTCGGCGAACAGA 59.404 47.619 12.92 0.00 0.00 3.41
601 763 1.329292 TGAAAAAGTGTCGGCGAACAG 59.671 47.619 12.92 0.00 0.00 3.16
625 792 1.530891 GGGACCGAGGGATCGATCA 60.531 63.158 25.93 0.00 34.64 2.92
626 793 1.228613 AGGGACCGAGGGATCGATC 60.229 63.158 17.36 17.36 34.64 3.69
627 794 1.228613 GAGGGACCGAGGGATCGAT 60.229 63.158 0.00 0.00 34.64 3.59
639 806 1.829222 TGGTAATTCTGTCGGAGGGAC 59.171 52.381 0.00 0.00 46.27 4.46
640 807 1.829222 GTGGTAATTCTGTCGGAGGGA 59.171 52.381 0.00 0.00 0.00 4.20
641 808 1.470979 CGTGGTAATTCTGTCGGAGGG 60.471 57.143 0.00 0.00 0.00 4.30
642 809 1.922570 CGTGGTAATTCTGTCGGAGG 58.077 55.000 0.00 0.00 0.00 4.30
643 810 1.278238 GCGTGGTAATTCTGTCGGAG 58.722 55.000 0.00 0.00 0.00 4.63
644 811 0.604073 TGCGTGGTAATTCTGTCGGA 59.396 50.000 0.00 0.00 0.00 4.55
645 812 0.719465 GTGCGTGGTAATTCTGTCGG 59.281 55.000 0.00 0.00 0.00 4.79
646 813 0.365523 CGTGCGTGGTAATTCTGTCG 59.634 55.000 0.00 0.00 0.00 4.35
673 840 0.034477 CCGGGCCTTTGGAATGTACT 60.034 55.000 0.84 0.00 0.00 2.73
674 841 1.663379 GCCGGGCCTTTGGAATGTAC 61.663 60.000 8.12 0.00 0.00 2.90
675 842 1.379309 GCCGGGCCTTTGGAATGTA 60.379 57.895 8.12 0.00 0.00 2.29
676 843 2.679996 GCCGGGCCTTTGGAATGT 60.680 61.111 8.12 0.00 0.00 2.71
677 844 1.825281 TTTGCCGGGCCTTTGGAATG 61.825 55.000 17.97 0.00 0.00 2.67
678 845 1.124477 TTTTGCCGGGCCTTTGGAAT 61.124 50.000 17.97 0.00 0.00 3.01
719 886 3.541831 CGCGCGACGTGCAACTAT 61.542 61.111 30.36 0.00 46.97 2.12
751 918 2.202797 ACTGCAGCTCATACGCCG 60.203 61.111 15.27 0.00 0.00 6.46
754 921 2.233654 GGCGACTGCAGCTCATACG 61.234 63.158 15.27 11.07 45.35 3.06
755 922 2.233654 CGGCGACTGCAGCTCATAC 61.234 63.158 15.27 0.00 45.35 2.39
788 955 4.417506 GGGTAAAATTGAAATCGAACGGG 58.582 43.478 0.00 0.00 0.00 5.28
789 956 4.417506 GGGGTAAAATTGAAATCGAACGG 58.582 43.478 0.00 0.00 0.00 4.44
796 971 4.046618 TCCTCCTGGGGGTAAAATTGAAAT 59.953 41.667 13.53 0.00 35.33 2.17
810 985 0.256177 GCCTTTTACCTCCTCCTGGG 59.744 60.000 0.00 0.00 0.00 4.45
814 1000 1.451567 GCCGCCTTTTACCTCCTCC 60.452 63.158 0.00 0.00 0.00 4.30
816 1002 0.111639 TTTGCCGCCTTTTACCTCCT 59.888 50.000 0.00 0.00 0.00 3.69
819 1005 1.073284 TCTCTTTGCCGCCTTTTACCT 59.927 47.619 0.00 0.00 0.00 3.08
821 1007 2.152016 ACTCTCTTTGCCGCCTTTTAC 58.848 47.619 0.00 0.00 0.00 2.01
822 1008 2.552315 CAACTCTCTTTGCCGCCTTTTA 59.448 45.455 0.00 0.00 0.00 1.52
831 1017 1.269257 GCAACCACCAACTCTCTTTGC 60.269 52.381 0.00 0.00 0.00 3.68
833 1019 2.435372 TGCAACCACCAACTCTCTTT 57.565 45.000 0.00 0.00 0.00 2.52
835 1021 1.477558 CCTTGCAACCACCAACTCTCT 60.478 52.381 0.00 0.00 0.00 3.10
839 1025 0.033601 TGACCTTGCAACCACCAACT 60.034 50.000 0.00 0.00 0.00 3.16
840 1026 0.385390 CTGACCTTGCAACCACCAAC 59.615 55.000 0.00 0.00 0.00 3.77
841 1027 1.391157 GCTGACCTTGCAACCACCAA 61.391 55.000 0.00 0.00 0.00 3.67
842 1028 1.827789 GCTGACCTTGCAACCACCA 60.828 57.895 0.00 0.00 0.00 4.17
843 1029 1.391157 TTGCTGACCTTGCAACCACC 61.391 55.000 0.00 0.00 44.24 4.61
844 1030 0.031178 CTTGCTGACCTTGCAACCAC 59.969 55.000 0.00 0.00 44.24 4.16
845 1031 1.108727 CCTTGCTGACCTTGCAACCA 61.109 55.000 0.00 0.00 44.24 3.67
846 1032 1.662044 CCTTGCTGACCTTGCAACC 59.338 57.895 0.00 0.00 44.24 3.77
849 1035 1.228644 ATGCCTTGCTGACCTTGCA 60.229 52.632 0.00 0.00 38.80 4.08
1007 1483 3.455469 GCAGCACCATCTTGGGCC 61.455 66.667 0.00 0.00 43.37 5.80
1008 1484 3.455469 GGCAGCACCATCTTGGGC 61.455 66.667 0.00 0.00 43.37 5.36
1009 1485 3.136123 CGGCAGCACCATCTTGGG 61.136 66.667 0.00 0.00 43.37 4.12
1053 1529 2.444895 ATCTCCACCTCCGCCTCC 60.445 66.667 0.00 0.00 0.00 4.30
1054 1530 2.801631 CCATCTCCACCTCCGCCTC 61.802 68.421 0.00 0.00 0.00 4.70
1055 1531 2.765807 CCATCTCCACCTCCGCCT 60.766 66.667 0.00 0.00 0.00 5.52
1215 1691 1.202580 ACTATGACGAGCATGGGAAGC 60.203 52.381 10.02 0.00 39.57 3.86
1236 1712 0.316442 GCATCATCACCGCAACGATG 60.316 55.000 0.00 0.00 40.34 3.84
1265 1741 2.355363 TCAAACGTGTCCGGCTCG 60.355 61.111 15.42 15.42 38.78 5.03
1293 1772 4.214383 CTTGTCCATCTGCGCGCG 62.214 66.667 28.44 28.44 0.00 6.86
1418 1897 4.154347 CAGCGCTCCTCCTCCACC 62.154 72.222 7.13 0.00 0.00 4.61
1836 2316 8.610248 TCGGAAAACACAGATCAAACTAAATA 57.390 30.769 0.00 0.00 0.00 1.40
1837 2317 7.504924 TCGGAAAACACAGATCAAACTAAAT 57.495 32.000 0.00 0.00 0.00 1.40
1860 2340 2.443887 TTGCAAAGCCAAGCTGAATC 57.556 45.000 0.00 0.00 39.62 2.52
1861 2341 2.300723 TGATTGCAAAGCCAAGCTGAAT 59.699 40.909 1.71 0.00 39.62 2.57
1868 2348 2.224018 GGTTCAGTGATTGCAAAGCCAA 60.224 45.455 1.71 0.00 0.00 4.52
1965 2448 5.253330 GGTTGATGTGTTAAATCCAGAGGA 58.747 41.667 0.00 0.00 35.55 3.71
2013 2497 2.734079 GCAACTCTCTGTTCTACAGTGC 59.266 50.000 6.71 5.42 46.03 4.40
2014 2498 3.986572 CAGCAACTCTCTGTTCTACAGTG 59.013 47.826 6.71 4.89 46.03 3.66
2071 2555 6.106673 ACTGATAAGATTCCAAACGGTACTG 58.893 40.000 0.00 0.00 0.00 2.74
2091 2575 5.047021 CCTCCTTTTCATGACTCTGTACTGA 60.047 44.000 0.00 2.21 0.00 3.41
2126 2612 9.770097 CCTATTTATTTCTGTTATCTGAGAGCA 57.230 33.333 0.00 0.00 0.00 4.26
2158 2660 3.118223 GGGAAGGAGGGAGTAGTTCATTG 60.118 52.174 0.00 0.00 0.00 2.82
2164 2666 1.302907 TACGGGAAGGAGGGAGTAGT 58.697 55.000 0.00 0.00 0.00 2.73
2170 2672 4.024670 CTCCTATATTACGGGAAGGAGGG 58.975 52.174 8.52 0.00 46.37 4.30
2173 2675 3.087031 CGCTCCTATATTACGGGAAGGA 58.913 50.000 0.00 0.00 35.14 3.36
2174 2676 2.416972 GCGCTCCTATATTACGGGAAGG 60.417 54.545 0.00 0.00 0.00 3.46
2175 2677 2.492484 AGCGCTCCTATATTACGGGAAG 59.508 50.000 2.64 0.00 0.00 3.46
2178 2680 3.314541 AAAGCGCTCCTATATTACGGG 57.685 47.619 12.06 0.00 0.00 5.28
2179 2681 4.150098 GTCAAAAGCGCTCCTATATTACGG 59.850 45.833 12.06 0.00 0.00 4.02
2180 2682 4.743151 TGTCAAAAGCGCTCCTATATTACG 59.257 41.667 12.06 0.00 0.00 3.18
2182 2684 7.282224 ACATTTGTCAAAAGCGCTCCTATATTA 59.718 33.333 12.06 0.00 0.00 0.98
2183 2685 6.095440 ACATTTGTCAAAAGCGCTCCTATATT 59.905 34.615 12.06 0.00 0.00 1.28
2184 2686 5.590259 ACATTTGTCAAAAGCGCTCCTATAT 59.410 36.000 12.06 0.00 0.00 0.86
2186 2688 3.758554 ACATTTGTCAAAAGCGCTCCTAT 59.241 39.130 12.06 0.00 0.00 2.57
2187 2689 3.146066 ACATTTGTCAAAAGCGCTCCTA 58.854 40.909 12.06 0.00 0.00 2.94
2188 2690 1.956477 ACATTTGTCAAAAGCGCTCCT 59.044 42.857 12.06 0.00 0.00 3.69
2206 2708 9.967451 TCCCATAATATAAGAGTGTTTTTGACA 57.033 29.630 0.00 0.00 35.42 3.58
2208 2710 9.967451 TGTCCCATAATATAAGAGTGTTTTTGA 57.033 29.630 0.00 0.00 0.00 2.69
2211 2713 9.838339 CTCTGTCCCATAATATAAGAGTGTTTT 57.162 33.333 0.00 0.00 0.00 2.43
2212 2714 8.993424 ACTCTGTCCCATAATATAAGAGTGTTT 58.007 33.333 1.84 0.00 40.90 2.83
2213 2715 8.554490 ACTCTGTCCCATAATATAAGAGTGTT 57.446 34.615 1.84 0.00 40.90 3.32
2214 2716 9.080097 GTACTCTGTCCCATAATATAAGAGTGT 57.920 37.037 11.61 0.00 42.06 3.55
2215 2717 9.078990 TGTACTCTGTCCCATAATATAAGAGTG 57.921 37.037 11.61 0.00 42.06 3.51
2216 2718 9.656323 TTGTACTCTGTCCCATAATATAAGAGT 57.344 33.333 7.50 7.50 43.79 3.24
2219 2721 9.712305 CCTTTGTACTCTGTCCCATAATATAAG 57.288 37.037 0.00 0.00 0.00 1.73
2220 2722 9.442062 TCCTTTGTACTCTGTCCCATAATATAA 57.558 33.333 0.00 0.00 0.00 0.98
2221 2723 9.442062 TTCCTTTGTACTCTGTCCCATAATATA 57.558 33.333 0.00 0.00 0.00 0.86
2222 2724 7.931015 TCCTTTGTACTCTGTCCCATAATAT 57.069 36.000 0.00 0.00 0.00 1.28
2223 2725 7.635089 GCTTCCTTTGTACTCTGTCCCATAATA 60.635 40.741 0.00 0.00 0.00 0.98
2224 2726 6.636454 TTCCTTTGTACTCTGTCCCATAAT 57.364 37.500 0.00 0.00 0.00 1.28
2225 2727 5.570844 GCTTCCTTTGTACTCTGTCCCATAA 60.571 44.000 0.00 0.00 0.00 1.90
2226 2728 4.081087 GCTTCCTTTGTACTCTGTCCCATA 60.081 45.833 0.00 0.00 0.00 2.74
2227 2729 3.307762 GCTTCCTTTGTACTCTGTCCCAT 60.308 47.826 0.00 0.00 0.00 4.00
2228 2730 2.038557 GCTTCCTTTGTACTCTGTCCCA 59.961 50.000 0.00 0.00 0.00 4.37
2229 2731 2.701107 GCTTCCTTTGTACTCTGTCCC 58.299 52.381 0.00 0.00 0.00 4.46
2230 2732 2.338500 CGCTTCCTTTGTACTCTGTCC 58.662 52.381 0.00 0.00 0.00 4.02
2231 2733 2.288886 ACCGCTTCCTTTGTACTCTGTC 60.289 50.000 0.00 0.00 0.00 3.51
2232 2734 1.692519 ACCGCTTCCTTTGTACTCTGT 59.307 47.619 0.00 0.00 0.00 3.41
2233 2735 2.457366 ACCGCTTCCTTTGTACTCTG 57.543 50.000 0.00 0.00 0.00 3.35
2234 2736 2.094854 CGTACCGCTTCCTTTGTACTCT 60.095 50.000 0.00 0.00 33.17 3.24
2235 2737 2.257034 CGTACCGCTTCCTTTGTACTC 58.743 52.381 0.00 0.00 33.17 2.59
2236 2738 1.067354 CCGTACCGCTTCCTTTGTACT 60.067 52.381 0.00 0.00 33.17 2.73
2237 2739 1.067635 TCCGTACCGCTTCCTTTGTAC 60.068 52.381 0.00 0.00 0.00 2.90
2238 2740 1.255882 TCCGTACCGCTTCCTTTGTA 58.744 50.000 0.00 0.00 0.00 2.41
2250 2752 4.976116 GCAATGCTATTTTGAATCCGTACC 59.024 41.667 0.00 0.00 0.00 3.34
2255 2757 6.044046 TGTGATGCAATGCTATTTTGAATCC 58.956 36.000 6.82 0.00 38.05 3.01
2299 2801 9.480053 AGTGTATAATTATTTTGAATGCATGCC 57.520 29.630 16.68 0.00 0.00 4.40
2415 2917 5.658190 AGGAAACAAATGTATAATGCTGCCT 59.342 36.000 0.00 0.00 0.00 4.75
2430 2932 6.536941 GCAAAACCATAGTCAAAGGAAACAAA 59.463 34.615 0.00 0.00 0.00 2.83
2465 2967 1.064134 GAATCGTGAAATGGCGGCC 59.936 57.895 13.32 13.32 0.00 6.13
2472 2974 6.418226 GCGTTATCTGTCTAGAATCGTGAAAT 59.582 38.462 0.00 0.00 36.32 2.17
2492 2994 0.321564 AATCCAGCTGCTGTGCGTTA 60.322 50.000 26.41 6.69 38.13 3.18
2499 3001 1.533338 GCGAATTCAATCCAGCTGCTG 60.533 52.381 22.44 22.44 0.00 4.41
2504 3006 3.174375 GACAAAGCGAATTCAATCCAGC 58.826 45.455 6.22 0.00 0.00 4.85
2554 3056 4.390603 TGGACACAGCGAACAATACATTAC 59.609 41.667 0.00 0.00 0.00 1.89
2576 3078 5.447624 AAAACCGGAATGGAGTAAAGTTG 57.552 39.130 9.46 0.00 42.00 3.16
2591 3093 2.420022 CACTGCAGAGGAATAAAACCGG 59.580 50.000 23.35 0.00 0.00 5.28
2625 3127 3.500448 TGCTCCAGGTTGTATTGACAA 57.500 42.857 0.00 0.00 43.41 3.18
2701 3203 4.241681 CTCTGGTAAAGTTCACTCTGCTC 58.758 47.826 0.00 0.00 0.00 4.26
2736 3238 4.728772 ACCTGGTCTTGATCAATGAACAA 58.271 39.130 19.45 5.83 0.00 2.83
2849 3351 3.714798 TGAACCTTCATGGGGGATACTAC 59.285 47.826 10.95 0.00 41.11 2.73
3035 3543 6.582677 TCAATGTACGGTTCCATGAAATTT 57.417 33.333 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.