Multiple sequence alignment - TraesCS6B01G162100

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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 TraesCS6B01G162100 chr6B 100.000 3431 0 0 1 3431 166624314 166620884 0.000000e+00 6336.0
1 TraesCS6B01G162100 chr6B 96.774 62 2 0 3366 3427 716945210 716945149 1.680000e-18 104.0
2 TraesCS6B01G162100 chr6D 93.229 2437 102 30 849 3241 88103998 88101581 0.000000e+00 3528.0
3 TraesCS6B01G162100 chr6D 90.244 82 7 1 3351 3431 88101568 88101487 4.680000e-19 106.0
4 TraesCS6B01G162100 chr6A 94.158 1917 70 18 923 2803 106080953 106079043 0.000000e+00 2881.0
5 TraesCS6B01G162100 chr6A 82.692 312 21 10 2992 3276 106078961 106078656 2.640000e-61 246.0
6 TraesCS6B01G162100 chr6A 97.368 76 2 0 3031 3106 616825965 616825890 2.780000e-26 130.0
7 TraesCS6B01G162100 chr6A 98.113 53 1 0 2835 2887 106079043 106078991 3.650000e-15 93.5
8 TraesCS6B01G162100 chr4D 88.132 851 96 4 1 847 383771224 383772073 0.000000e+00 1007.0
9 TraesCS6B01G162100 chr4D 87.588 854 91 11 1 847 300245270 300244425 0.000000e+00 976.0
10 TraesCS6B01G162100 chr3A 87.059 850 104 3 1 847 74452923 74452077 0.000000e+00 955.0
11 TraesCS6B01G162100 chr3A 77.891 588 120 8 263 844 8926068 8925485 1.170000e-94 357.0
12 TraesCS6B01G162100 chr2B 84.698 843 116 8 11 847 366025308 366024473 0.000000e+00 830.0
13 TraesCS6B01G162100 chr2B 87.584 298 33 3 1 294 174303208 174302911 3.280000e-90 342.0
14 TraesCS6B01G162100 chr2B 87.342 79 8 2 3273 3350 202047369 202047446 4.720000e-14 89.8
15 TraesCS6B01G162100 chrUn 83.822 853 132 5 1 848 50868142 50868993 0.000000e+00 806.0
16 TraesCS6B01G162100 chrUn 97.368 76 2 0 3031 3106 341586028 341585953 2.780000e-26 130.0
17 TraesCS6B01G162100 chrUn 96.203 79 3 0 3028 3106 453615317 453615395 2.780000e-26 130.0
18 TraesCS6B01G162100 chr4A 83.529 850 134 5 4 848 714254959 714254111 0.000000e+00 789.0
19 TraesCS6B01G162100 chr4A 97.368 76 2 0 3031 3106 714759916 714759841 2.780000e-26 130.0
20 TraesCS6B01G162100 chr2A 75.639 587 135 8 248 829 687072823 687073406 5.600000e-73 285.0
21 TraesCS6B01G162100 chr4B 93.220 177 8 3 3037 3209 410810984 410811160 1.220000e-64 257.0
22 TraesCS6B01G162100 chr4B 98.571 70 1 0 3358 3427 410811209 410811278 1.290000e-24 124.0
23 TraesCS6B01G162100 chr7B 73.314 682 168 13 155 829 639868045 639868719 4.430000e-59 239.0
24 TraesCS6B01G162100 chr7B 90.667 75 5 2 3277 3350 526680090 526680017 7.840000e-17 99.0
25 TraesCS6B01G162100 chr3B 96.203 79 3 0 3028 3106 262586925 262587003 2.780000e-26 130.0
26 TraesCS6B01G162100 chr3B 87.179 78 10 0 3273 3350 98459903 98459980 4.720000e-14 89.8
27 TraesCS6B01G162100 chr1B 96.203 79 3 0 3028 3106 373693377 373693455 2.780000e-26 130.0
28 TraesCS6B01G162100 chr1A 97.368 76 2 0 3031 3106 574280302 574280227 2.780000e-26 130.0
29 TraesCS6B01G162100 chr5B 90.541 74 6 1 3277 3350 450577717 450577645 2.820000e-16 97.1
30 TraesCS6B01G162100 chr7D 89.474 76 7 1 3276 3350 142234368 142234293 1.010000e-15 95.3
31 TraesCS6B01G162100 chr7D 88.000 75 9 0 3276 3350 403810546 403810472 4.720000e-14 89.8
32 TraesCS6B01G162100 chr5D 89.474 76 6 2 3276 3350 388572311 388572237 1.010000e-15 95.3
33 TraesCS6B01G162100 chr7A 88.000 75 9 0 3276 3350 638827265 638827339 4.720000e-14 89.8
34 TraesCS6B01G162100 chr5A 87.838 74 9 0 3277 3350 596013154 596013227 1.700000e-13 87.9


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 TraesCS6B01G162100 chr6B 166620884 166624314 3430 True 6336.0 6336 100.000000 1 3431 1 chr6B.!!$R1 3430
1 TraesCS6B01G162100 chr6D 88101487 88103998 2511 True 1817.0 3528 91.736500 849 3431 2 chr6D.!!$R1 2582
2 TraesCS6B01G162100 chr6A 106078656 106080953 2297 True 1073.5 2881 91.654333 923 3276 3 chr6A.!!$R2 2353
3 TraesCS6B01G162100 chr4D 383771224 383772073 849 False 1007.0 1007 88.132000 1 847 1 chr4D.!!$F1 846
4 TraesCS6B01G162100 chr4D 300244425 300245270 845 True 976.0 976 87.588000 1 847 1 chr4D.!!$R1 846
5 TraesCS6B01G162100 chr3A 74452077 74452923 846 True 955.0 955 87.059000 1 847 1 chr3A.!!$R2 846
6 TraesCS6B01G162100 chr3A 8925485 8926068 583 True 357.0 357 77.891000 263 844 1 chr3A.!!$R1 581
7 TraesCS6B01G162100 chr2B 366024473 366025308 835 True 830.0 830 84.698000 11 847 1 chr2B.!!$R2 836
8 TraesCS6B01G162100 chrUn 50868142 50868993 851 False 806.0 806 83.822000 1 848 1 chrUn.!!$F1 847
9 TraesCS6B01G162100 chr4A 714254111 714254959 848 True 789.0 789 83.529000 4 848 1 chr4A.!!$R1 844
10 TraesCS6B01G162100 chr2A 687072823 687073406 583 False 285.0 285 75.639000 248 829 1 chr2A.!!$F1 581
11 TraesCS6B01G162100 chr7B 639868045 639868719 674 False 239.0 239 73.314000 155 829 1 chr7B.!!$F1 674

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
690 699 0.336737 ATCCTCCGGTGAGTCCTCTT 59.663 55.0 4.76 0.0 36.86 2.85 F
915 926 0.673644 AAAGAGCCCGTGTGGAATCG 60.674 55.0 0.00 0.0 37.49 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2239 2269 1.178276 CAGCCAGAGTAGGAACGTCT 58.822 55.0 0.0 0.0 0.0 4.18 R
2582 2615 1.347062 TTGCCCCTTTCCAAACATCC 58.653 50.0 0.0 0.0 0.0 3.51 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
23 24 2.936498 GGCAGCGTAATATGTGTTCAGT 59.064 45.455 0.00 0.00 0.00 3.41
31 32 7.013369 AGCGTAATATGTGTTCAGTAGATCTCA 59.987 37.037 0.00 0.00 0.00 3.27
32 33 7.113684 GCGTAATATGTGTTCAGTAGATCTCAC 59.886 40.741 0.00 0.21 0.00 3.51
34 35 9.239002 GTAATATGTGTTCAGTAGATCTCACAC 57.761 37.037 13.17 12.53 38.34 3.82
39 40 3.458044 TCAGTAGATCTCACACCCTGT 57.542 47.619 0.00 0.00 0.00 4.00
46 47 0.760567 TCTCACACCCTGTCTGCACT 60.761 55.000 0.00 0.00 0.00 4.40
48 49 0.969149 TCACACCCTGTCTGCACTAG 59.031 55.000 0.00 0.00 0.00 2.57
75 80 9.173939 CACTTGTTGCTTTAAGAAATAAGACTG 57.826 33.333 23.20 11.80 34.85 3.51
78 83 8.677148 TGTTGCTTTAAGAAATAAGACTGTCT 57.323 30.769 4.06 4.06 0.00 3.41
105 110 4.142816 GCGAACAATAAGTGATTGACAGCT 60.143 41.667 7.25 0.00 46.94 4.24
106 111 5.063438 GCGAACAATAAGTGATTGACAGCTA 59.937 40.000 7.25 0.00 46.94 3.32
132 137 4.892433 CATTGGGTGCAATAAAAAGACCA 58.108 39.130 0.00 0.00 0.00 4.02
138 143 4.261447 GGTGCAATAAAAAGACCACGAACT 60.261 41.667 0.00 0.00 0.00 3.01
142 147 5.335661 GCAATAAAAAGACCACGAACTCCAT 60.336 40.000 0.00 0.00 0.00 3.41
177 182 1.563410 AGCAAGCAAGATAGCCCTTCT 59.437 47.619 0.00 0.00 34.23 2.85
201 206 5.390387 ACTGCCAACAAAAATAAGTAGGGA 58.610 37.500 0.00 0.00 0.00 4.20
231 236 3.143211 TCTCCCTAGCGTAATCCTCTC 57.857 52.381 0.00 0.00 0.00 3.20
241 246 1.107538 TAATCCTCTCGACGGCCTGG 61.108 60.000 0.00 0.00 0.00 4.45
260 265 3.141767 GGAAGTTTCCAAGCTACCACT 57.858 47.619 6.03 0.00 46.76 4.00
284 289 8.255206 ACTGTTAAAAAGGACCGAAAAAGAAAT 58.745 29.630 0.00 0.00 0.00 2.17
318 323 5.011329 ACACCTCATTACTGTCTCCGTAAAA 59.989 40.000 0.00 0.00 31.36 1.52
421 428 6.642131 CAGCTTAAGTGCACAAAATATGTTGT 59.358 34.615 21.04 5.37 41.46 3.32
433 440 8.783093 CACAAAATATGTTGTCCTTAACTCTCA 58.217 33.333 8.38 0.00 41.46 3.27
493 500 7.630242 ATGAAATTGTCCGTGATTAGACATT 57.370 32.000 0.00 0.00 42.32 2.71
508 515 0.958822 ACATTCAGGAACAAACGCCC 59.041 50.000 0.00 0.00 0.00 6.13
539 546 3.197116 TCAGAAATAACCTCGGGGAGAAC 59.803 47.826 9.33 0.00 36.25 3.01
551 558 1.961394 GGGGAGAACACTTTTCAACCC 59.039 52.381 0.00 0.00 36.93 4.11
584 591 6.149633 AGACCTTTGATGCGATTTTGTAAAC 58.850 36.000 0.00 0.00 0.00 2.01
592 599 4.302455 TGCGATTTTGTAAACCACATTGG 58.698 39.130 0.00 0.00 45.02 3.16
607 614 3.003689 CACATTGGAAAGGCTTATAGGCG 59.996 47.826 0.00 0.00 46.58 5.52
642 651 8.522830 CCTAAATTTTTGGACTTGCTATCTTGA 58.477 33.333 3.83 0.00 0.00 3.02
643 652 9.912634 CTAAATTTTTGGACTTGCTATCTTGAA 57.087 29.630 0.00 0.00 0.00 2.69
652 661 9.466497 TGGACTTGCTATCTTGAAAATAAGAAT 57.534 29.630 0.00 0.00 39.87 2.40
690 699 0.336737 ATCCTCCGGTGAGTCCTCTT 59.663 55.000 4.76 0.00 36.86 2.85
700 709 3.557898 GGTGAGTCCTCTTCATTGAGCAA 60.558 47.826 0.00 0.00 33.02 3.91
715 724 4.758773 TGAGCAACCTGATGATCATACA 57.241 40.909 8.54 7.80 40.52 2.29
740 749 2.630580 GACTTCCTCTCCACACAACTCT 59.369 50.000 0.00 0.00 0.00 3.24
762 773 4.206375 TCAATGCCTCTGAAAAAGTGTGA 58.794 39.130 0.00 0.00 0.00 3.58
832 843 4.228912 AGCGTTTTTGACTTCCTCATTG 57.771 40.909 0.00 0.00 0.00 2.82
833 844 3.882888 AGCGTTTTTGACTTCCTCATTGA 59.117 39.130 0.00 0.00 0.00 2.57
851 862 2.412870 TGATGTAAGGAGCGTTGTGTG 58.587 47.619 0.00 0.00 0.00 3.82
875 886 3.943691 CCGACCCACCAACCGGAA 61.944 66.667 9.46 0.00 44.29 4.30
876 887 2.349755 CGACCCACCAACCGGAAT 59.650 61.111 9.46 0.00 35.59 3.01
878 889 1.743995 GACCCACCAACCGGAATCG 60.744 63.158 9.46 0.00 35.59 3.34
879 890 3.131478 CCCACCAACCGGAATCGC 61.131 66.667 9.46 0.00 35.59 4.58
880 891 3.496131 CCACCAACCGGAATCGCG 61.496 66.667 9.46 0.00 35.59 5.87
884 895 4.499023 CAACCGGAATCGCGCGTG 62.499 66.667 30.98 14.79 34.56 5.34
889 900 3.554692 GGAATCGCGCGTGTGGAG 61.555 66.667 30.98 0.00 0.00 3.86
908 919 1.906824 TCGGAGAAAGAGCCCGTGT 60.907 57.895 0.00 0.00 43.40 4.49
915 926 0.673644 AAAGAGCCCGTGTGGAATCG 60.674 55.000 0.00 0.00 37.49 3.34
979 998 3.117794 GACGCGCCTTTATACATACACA 58.882 45.455 5.73 0.00 0.00 3.72
980 999 2.861935 ACGCGCCTTTATACATACACAC 59.138 45.455 5.73 0.00 0.00 3.82
981 1000 2.220133 CGCGCCTTTATACATACACACC 59.780 50.000 0.00 0.00 0.00 4.16
982 1001 2.546789 GCGCCTTTATACATACACACCC 59.453 50.000 0.00 0.00 0.00 4.61
983 1002 3.135994 CGCCTTTATACATACACACCCC 58.864 50.000 0.00 0.00 0.00 4.95
984 1003 3.432467 CGCCTTTATACATACACACCCCA 60.432 47.826 0.00 0.00 0.00 4.96
985 1004 3.881089 GCCTTTATACATACACACCCCAC 59.119 47.826 0.00 0.00 0.00 4.61
986 1005 4.384868 GCCTTTATACATACACACCCCACT 60.385 45.833 0.00 0.00 0.00 4.00
987 1006 5.123227 CCTTTATACATACACACCCCACTG 58.877 45.833 0.00 0.00 0.00 3.66
1026 1046 3.031013 CAAGAAGAACCCAACCCAAAGT 58.969 45.455 0.00 0.00 0.00 2.66
1334 1364 1.156645 CGTCTACCTCTCGTACCCGG 61.157 65.000 0.00 0.00 33.95 5.73
1861 1891 1.071471 CGTGGTGAAGCTGGAGGTT 59.929 57.895 0.00 0.00 38.61 3.50
2113 2143 2.526077 GGATTTCCGATTGAAAACCGC 58.474 47.619 0.00 0.00 45.67 5.68
2131 2161 2.272146 GGAATTCCTCTGCCGGCA 59.728 61.111 30.59 30.59 0.00 5.69
2161 2191 2.124570 AGCCACATGGATCGTGCC 60.125 61.111 0.87 0.00 37.39 5.01
2173 2203 1.913951 ATCGTGCCAAGCATCTCCCA 61.914 55.000 0.00 0.00 41.91 4.37
2233 2263 0.674581 TCGCTGCTTTCCTGGATGTG 60.675 55.000 0.00 0.00 0.00 3.21
2239 2269 1.887956 GCTTTCCTGGATGTGAAGGCA 60.888 52.381 0.00 0.00 41.59 4.75
2333 2363 2.497273 GCCTTGGCAGGTCAAACATAAT 59.503 45.455 6.79 0.00 43.18 1.28
2341 2371 5.181748 GCAGGTCAAACATAATCAGAGAGT 58.818 41.667 0.00 0.00 0.00 3.24
2342 2372 5.293079 GCAGGTCAAACATAATCAGAGAGTC 59.707 44.000 0.00 0.00 0.00 3.36
2541 2571 2.577449 CGCAAGTCTTTTTGGTGGTT 57.423 45.000 0.00 0.00 0.00 3.67
2543 2573 2.857748 CGCAAGTCTTTTTGGTGGTTTC 59.142 45.455 0.00 0.00 0.00 2.78
2544 2574 3.674682 CGCAAGTCTTTTTGGTGGTTTCA 60.675 43.478 0.00 0.00 0.00 2.69
2589 2622 5.221682 TGACATTTTCATTGCCTGGATGTTT 60.222 36.000 0.00 0.00 0.00 2.83
2598 2631 1.560505 CCTGGATGTTTGGAAAGGGG 58.439 55.000 0.00 0.00 0.00 4.79
2621 2654 3.775261 AACATTGATTTTGCAAGGCCT 57.225 38.095 0.00 0.00 33.19 5.19
2625 2658 2.529780 TGATTTTGCAAGGCCTGTTG 57.470 45.000 5.69 2.04 0.00 3.33
2641 2690 4.623886 GCCTGTTGACTCAGATGGTAATCA 60.624 45.833 0.00 0.00 37.61 2.57
2651 2700 6.907853 TCAGATGGTAATCACTGAGATAGG 57.092 41.667 0.00 0.00 35.39 2.57
2736 2787 9.471702 AATGAAACTGAAGATATGACTTTGGAT 57.528 29.630 0.00 0.00 0.00 3.41
2778 2831 2.604046 AGTCTATGCCATCGGACAAC 57.396 50.000 11.50 0.00 0.00 3.32
2815 2868 0.250513 CAGACCTGGGTAGGACTTGC 59.749 60.000 0.00 0.00 44.98 4.01
2833 2886 3.342377 TGCGATGAACCACTTATCCAA 57.658 42.857 0.00 0.00 0.00 3.53
2873 2926 2.663852 GACCCAACCGACACACCG 60.664 66.667 0.00 0.00 0.00 4.94
2887 2940 2.237893 ACACACCGGGAATACCTTTAGG 59.762 50.000 6.32 0.00 42.17 2.69
2888 2941 2.502538 CACACCGGGAATACCTTTAGGA 59.497 50.000 6.32 0.00 38.94 2.94
2889 2942 2.502947 ACACCGGGAATACCTTTAGGAC 59.497 50.000 6.32 0.00 38.94 3.85
2890 2943 2.121948 ACCGGGAATACCTTTAGGACC 58.878 52.381 6.32 0.98 38.94 4.46
2891 2944 2.293385 ACCGGGAATACCTTTAGGACCT 60.293 50.000 6.32 0.00 38.94 3.85
2892 2945 2.775960 CCGGGAATACCTTTAGGACCTT 59.224 50.000 0.00 0.00 38.94 3.50
2893 2946 3.181457 CCGGGAATACCTTTAGGACCTTC 60.181 52.174 0.00 2.68 38.94 3.46
2894 2947 3.453353 CGGGAATACCTTTAGGACCTTCA 59.547 47.826 0.00 0.00 38.94 3.02
2918 2976 6.807708 ACGCATTTTACTCGTTATCTACAG 57.192 37.500 0.00 0.00 31.89 2.74
2919 2977 5.231568 ACGCATTTTACTCGTTATCTACAGC 59.768 40.000 0.00 0.00 31.89 4.40
2927 2985 9.865321 TTTACTCGTTATCTACAGCAAAGTTAT 57.135 29.630 0.00 0.00 0.00 1.89
2929 2987 6.255887 ACTCGTTATCTACAGCAAAGTTATGC 59.744 38.462 0.00 2.87 46.78 3.14
2963 3021 9.447157 CTGATCTTTTCTACTCAAATTTCCTCT 57.553 33.333 0.00 0.00 0.00 3.69
2981 3039 6.879276 TCCTCTACATATCCAAGTAGAACG 57.121 41.667 0.00 0.00 44.23 3.95
3019 3078 4.280677 CCATGTTTTAGGTTGCTCAAGGAA 59.719 41.667 0.00 0.00 0.00 3.36
3030 3089 2.846206 TGCTCAAGGAAGGGTGACATAT 59.154 45.455 0.00 0.00 0.00 1.78
3104 3172 6.092807 GGCTTGTGTTAAAATCAGAGGACTAG 59.907 42.308 0.00 0.00 0.00 2.57
3133 3204 0.962356 GGTGTGGATGGAGTGCCTTG 60.962 60.000 0.00 0.00 34.31 3.61
3172 3260 0.750850 TGGGCTCTTATAGACGTGGC 59.249 55.000 0.00 0.00 31.76 5.01
3212 3300 6.010850 TCCAGAATCGCTTCTATGTAGGTAT 58.989 40.000 0.39 0.00 39.78 2.73
3232 3320 5.363005 GGTATAGTGAAGGTGTGATGTAGGT 59.637 44.000 0.00 0.00 0.00 3.08
3272 3360 4.411540 ACATGAGAGACTATTTGGCCTCAT 59.588 41.667 3.32 0.00 40.17 2.90
3278 3366 4.781934 AGACTATTTGGCCTCATTGGTAC 58.218 43.478 3.32 0.00 38.35 3.34
3280 3368 4.781934 ACTATTTGGCCTCATTGGTACTC 58.218 43.478 3.32 0.00 38.35 2.59
3282 3370 0.623723 TTGGCCTCATTGGTACTCCC 59.376 55.000 3.32 0.00 38.35 4.30
3284 3372 0.470341 GGCCTCATTGGTACTCCCTC 59.530 60.000 0.00 0.00 38.35 4.30
3285 3373 0.470341 GCCTCATTGGTACTCCCTCC 59.530 60.000 0.00 0.00 38.35 4.30
3287 3375 1.486211 CTCATTGGTACTCCCTCCGT 58.514 55.000 0.00 0.00 0.00 4.69
3288 3376 1.409427 CTCATTGGTACTCCCTCCGTC 59.591 57.143 0.00 0.00 0.00 4.79
3289 3377 0.464452 CATTGGTACTCCCTCCGTCC 59.536 60.000 0.00 0.00 0.00 4.79
3290 3378 0.690077 ATTGGTACTCCCTCCGTCCC 60.690 60.000 0.00 0.00 0.00 4.46
3291 3379 2.096707 TTGGTACTCCCTCCGTCCCA 62.097 60.000 0.00 0.00 0.00 4.37
3292 3380 1.075450 GGTACTCCCTCCGTCCCAT 60.075 63.158 0.00 0.00 0.00 4.00
3293 3381 0.186873 GGTACTCCCTCCGTCCCATA 59.813 60.000 0.00 0.00 0.00 2.74
3294 3382 1.412074 GGTACTCCCTCCGTCCCATAA 60.412 57.143 0.00 0.00 0.00 1.90
3295 3383 2.606378 GTACTCCCTCCGTCCCATAAT 58.394 52.381 0.00 0.00 0.00 1.28
3296 3384 3.501019 GGTACTCCCTCCGTCCCATAATA 60.501 52.174 0.00 0.00 0.00 0.98
3297 3385 3.339713 ACTCCCTCCGTCCCATAATAA 57.660 47.619 0.00 0.00 0.00 1.40
3298 3386 3.660959 ACTCCCTCCGTCCCATAATAAA 58.339 45.455 0.00 0.00 0.00 1.40
3299 3387 4.042174 ACTCCCTCCGTCCCATAATAAAA 58.958 43.478 0.00 0.00 0.00 1.52
3300 3388 4.102681 ACTCCCTCCGTCCCATAATAAAAG 59.897 45.833 0.00 0.00 0.00 2.27
3301 3389 4.300345 TCCCTCCGTCCCATAATAAAAGA 58.700 43.478 0.00 0.00 0.00 2.52
3302 3390 4.722781 TCCCTCCGTCCCATAATAAAAGAA 59.277 41.667 0.00 0.00 0.00 2.52
3303 3391 5.371472 TCCCTCCGTCCCATAATAAAAGAAT 59.629 40.000 0.00 0.00 0.00 2.40
3304 3392 5.473504 CCCTCCGTCCCATAATAAAAGAATG 59.526 44.000 0.00 0.00 0.00 2.67
3305 3393 6.062095 CCTCCGTCCCATAATAAAAGAATGT 58.938 40.000 0.00 0.00 0.00 2.71
3306 3394 6.546034 CCTCCGTCCCATAATAAAAGAATGTT 59.454 38.462 0.00 0.00 0.00 2.71
3307 3395 7.068226 CCTCCGTCCCATAATAAAAGAATGTTT 59.932 37.037 0.00 0.00 0.00 2.83
3308 3396 8.356000 TCCGTCCCATAATAAAAGAATGTTTT 57.644 30.769 0.00 0.00 0.00 2.43
3309 3397 8.808092 TCCGTCCCATAATAAAAGAATGTTTTT 58.192 29.630 0.00 0.00 0.00 1.94
3310 3398 8.868916 CCGTCCCATAATAAAAGAATGTTTTTG 58.131 33.333 0.00 0.00 0.00 2.44
3311 3399 9.632807 CGTCCCATAATAAAAGAATGTTTTTGA 57.367 29.630 0.00 0.00 0.00 2.69
3313 3401 9.632807 TCCCATAATAAAAGAATGTTTTTGACG 57.367 29.630 0.00 0.00 0.00 4.35
3314 3402 9.418045 CCCATAATAAAAGAATGTTTTTGACGT 57.582 29.630 0.00 0.00 0.00 4.34
3323 3411 8.502161 AAGAATGTTTTTGACGTTATGTTAGC 57.498 30.769 0.00 0.00 37.60 3.09
3324 3412 7.871853 AGAATGTTTTTGACGTTATGTTAGCT 58.128 30.769 0.00 0.00 37.60 3.32
3325 3413 8.349983 AGAATGTTTTTGACGTTATGTTAGCTT 58.650 29.630 0.00 0.00 37.60 3.74
3326 3414 8.502161 AATGTTTTTGACGTTATGTTAGCTTC 57.498 30.769 0.00 0.00 35.73 3.86
3327 3415 7.017498 TGTTTTTGACGTTATGTTAGCTTCA 57.983 32.000 0.00 0.00 0.00 3.02
3328 3416 7.473366 TGTTTTTGACGTTATGTTAGCTTCAA 58.527 30.769 0.00 0.00 0.00 2.69
3329 3417 7.968956 TGTTTTTGACGTTATGTTAGCTTCAAA 59.031 29.630 0.00 0.00 36.12 2.69
3330 3418 8.800031 GTTTTTGACGTTATGTTAGCTTCAAAA 58.200 29.630 11.28 11.28 41.59 2.44
3331 3419 8.912787 TTTTGACGTTATGTTAGCTTCAAAAA 57.087 26.923 12.42 4.04 40.95 1.94
3332 3420 7.901874 TTGACGTTATGTTAGCTTCAAAAAC 57.098 32.000 0.00 1.41 27.50 2.43
3333 3421 6.130723 TGACGTTATGTTAGCTTCAAAAACG 58.869 36.000 23.72 23.72 40.53 3.60
3334 3422 6.051646 ACGTTATGTTAGCTTCAAAAACGT 57.948 33.333 24.47 24.47 41.65 3.99
3335 3423 6.488817 ACGTTATGTTAGCTTCAAAAACGTT 58.511 32.000 24.47 0.00 42.65 3.99
3336 3424 6.630045 ACGTTATGTTAGCTTCAAAAACGTTC 59.370 34.615 24.47 10.22 42.65 3.95
3337 3425 6.849305 CGTTATGTTAGCTTCAAAAACGTTCT 59.151 34.615 20.67 0.00 35.54 3.01
3338 3426 7.375017 CGTTATGTTAGCTTCAAAAACGTTCTT 59.625 33.333 20.67 0.00 35.54 2.52
3339 3427 9.654417 GTTATGTTAGCTTCAAAAACGTTCTTA 57.346 29.630 0.00 0.00 0.00 2.10
3348 3436 9.233232 GCTTCAAAAACGTTCTTATATTATGGG 57.767 33.333 0.00 0.00 0.00 4.00
3351 3439 9.675464 TCAAAAACGTTCTTATATTATGGGAGT 57.325 29.630 0.00 0.00 0.00 3.85
3407 3495 0.991146 ACAAATGGGAAAATGGGGCC 59.009 50.000 0.00 0.00 0.00 5.80
3413 3501 1.080170 GGAAAATGGGGCCAAGGGA 59.920 57.895 4.39 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 8.414003 GGTGTGAGATCTACTGAACACATATTA 58.586 37.037 13.80 0.00 41.08 0.98
23 24 2.103373 GCAGACAGGGTGTGAGATCTA 58.897 52.381 0.00 0.00 0.00 1.98
31 32 1.121407 TGCTAGTGCAGACAGGGTGT 61.121 55.000 0.00 0.00 45.31 4.16
32 33 1.673477 TGCTAGTGCAGACAGGGTG 59.327 57.895 0.00 0.00 45.31 4.61
61 62 5.100259 CGCCGAAGACAGTCTTATTTCTTA 58.900 41.667 16.14 0.00 36.73 2.10
64 65 3.508762 TCGCCGAAGACAGTCTTATTTC 58.491 45.455 16.14 2.90 36.73 2.17
75 80 2.991190 TCACTTATTGTTCGCCGAAGAC 59.009 45.455 0.00 0.00 0.00 3.01
78 83 3.997681 TCAATCACTTATTGTTCGCCGAA 59.002 39.130 0.00 0.00 44.58 4.30
122 127 5.127491 ACAATGGAGTTCGTGGTCTTTTTA 58.873 37.500 0.00 0.00 0.00 1.52
123 128 3.951680 ACAATGGAGTTCGTGGTCTTTTT 59.048 39.130 0.00 0.00 0.00 1.94
124 129 3.551846 ACAATGGAGTTCGTGGTCTTTT 58.448 40.909 0.00 0.00 0.00 2.27
126 131 2.104111 TGACAATGGAGTTCGTGGTCTT 59.896 45.455 0.00 0.00 36.50 3.01
132 137 1.806542 GCACATGACAATGGAGTTCGT 59.193 47.619 0.00 0.00 38.19 3.85
138 143 4.439305 GCTTAAAGCACATGACAATGGA 57.561 40.909 0.00 0.00 41.89 3.41
177 182 6.544650 TCCCTACTTATTTTTGTTGGCAGTA 58.455 36.000 0.00 0.00 0.00 2.74
201 206 2.240160 ACGCTAGGGAGATCCGATATCT 59.760 50.000 14.59 0.43 41.52 1.98
219 224 1.657794 GCCGTCGAGAGGATTACGC 60.658 63.158 10.77 0.00 34.13 4.42
231 236 2.033194 GGAAACTTCCAGGCCGTCG 61.033 63.158 0.00 0.00 46.76 5.12
241 246 3.477530 ACAGTGGTAGCTTGGAAACTTC 58.522 45.455 0.00 0.00 0.00 3.01
260 265 9.738832 CTATTTCTTTTTCGGTCCTTTTTAACA 57.261 29.630 0.00 0.00 0.00 2.41
433 440 8.959548 TGAGTGTCTGCATTACATGAAAATAAT 58.040 29.630 0.00 0.00 0.00 1.28
436 443 6.822667 TGAGTGTCTGCATTACATGAAAAT 57.177 33.333 0.00 0.00 0.00 1.82
468 475 7.630242 ATGTCTAATCACGGACAATTTCATT 57.370 32.000 0.00 0.00 44.10 2.57
493 500 0.817634 CAGTGGGCGTTTGTTCCTGA 60.818 55.000 0.00 0.00 0.00 3.86
508 515 4.187694 GAGGTTATTTCTGAGGAGCAGTG 58.812 47.826 0.00 0.00 45.14 3.66
539 546 2.577449 AGCAAACGGGTTGAAAAGTG 57.423 45.000 10.54 0.00 39.87 3.16
551 558 3.492313 GCATCAAAGGTCTTAGCAAACG 58.508 45.455 0.00 0.00 0.00 3.60
584 591 3.319122 GCCTATAAGCCTTTCCAATGTGG 59.681 47.826 0.00 0.00 39.43 4.17
592 599 4.338400 ACAATTTCCGCCTATAAGCCTTTC 59.662 41.667 0.00 0.00 0.00 2.62
652 661 6.483307 GGAGGATATCAATCAAACGTTCATCA 59.517 38.462 0.00 0.00 33.41 3.07
690 699 4.224991 TGATCATCAGGTTGCTCAATGA 57.775 40.909 0.00 0.00 0.00 2.57
700 709 5.883685 AGTCACATGTATGATCATCAGGT 57.116 39.130 12.53 14.25 0.00 4.00
715 724 2.329267 TGTGTGGAGAGGAAGTCACAT 58.671 47.619 0.00 0.00 41.33 3.21
740 749 4.036734 GTCACACTTTTTCAGAGGCATTGA 59.963 41.667 0.00 0.00 0.00 2.57
762 773 2.504367 CTGGTCTGGATGGTTTTTCGT 58.496 47.619 0.00 0.00 0.00 3.85
832 843 1.732259 CCACACAACGCTCCTTACATC 59.268 52.381 0.00 0.00 0.00 3.06
833 844 1.071699 ACCACACAACGCTCCTTACAT 59.928 47.619 0.00 0.00 0.00 2.29
873 884 2.789203 GACTCCACACGCGCGATTC 61.789 63.158 39.36 13.58 0.00 2.52
874 885 2.809601 GACTCCACACGCGCGATT 60.810 61.111 39.36 20.01 0.00 3.34
879 890 2.742710 TTTCTCCGACTCCACACGCG 62.743 60.000 3.53 3.53 0.00 6.01
880 891 1.006571 TTTCTCCGACTCCACACGC 60.007 57.895 0.00 0.00 0.00 5.34
882 893 1.670380 GCTCTTTCTCCGACTCCACAC 60.670 57.143 0.00 0.00 0.00 3.82
883 894 0.603569 GCTCTTTCTCCGACTCCACA 59.396 55.000 0.00 0.00 0.00 4.17
884 895 0.108567 GGCTCTTTCTCCGACTCCAC 60.109 60.000 0.00 0.00 0.00 4.02
885 896 1.258445 GGGCTCTTTCTCCGACTCCA 61.258 60.000 0.00 0.00 0.00 3.86
886 897 1.518302 GGGCTCTTTCTCCGACTCC 59.482 63.158 0.00 0.00 0.00 3.85
887 898 1.139947 CGGGCTCTTTCTCCGACTC 59.860 63.158 0.00 0.00 45.96 3.36
888 899 1.606889 ACGGGCTCTTTCTCCGACT 60.607 57.895 8.02 0.00 45.96 4.18
889 900 1.446272 CACGGGCTCTTTCTCCGAC 60.446 63.158 8.02 0.00 45.96 4.79
1009 1029 3.302161 GGTTACTTTGGGTTGGGTTCTT 58.698 45.455 0.00 0.00 0.00 2.52
1026 1046 0.461339 GGAAGGAATCGCAGCGGTTA 60.461 55.000 14.68 0.00 27.16 2.85
1879 1909 2.792290 CGCCTCGAAGTGCACATCG 61.792 63.158 32.33 32.33 38.29 3.84
1882 1912 1.954146 GAACGCCTCGAAGTGCACA 60.954 57.895 21.04 0.00 0.00 4.57
2113 2143 2.897350 GCCGGCAGAGGAATTCCG 60.897 66.667 24.80 6.44 42.08 4.30
2161 2191 2.028420 TGACGAATGGGAGATGCTTG 57.972 50.000 0.00 0.00 0.00 4.01
2233 2263 1.819903 AGAGTAGGAACGTCTGCCTTC 59.180 52.381 9.48 5.49 35.73 3.46
2239 2269 1.178276 CAGCCAGAGTAGGAACGTCT 58.822 55.000 0.00 0.00 0.00 4.18
2287 2317 4.075793 AGGAGCCGGTAGCCCTCA 62.076 66.667 1.90 0.00 45.47 3.86
2333 2363 5.614324 TTGTTTCAGGAAAGACTCTCTGA 57.386 39.130 0.00 0.00 32.63 3.27
2341 2371 3.625764 CCGTGTCTTTGTTTCAGGAAAGA 59.374 43.478 0.00 0.00 36.15 2.52
2342 2372 3.377172 ACCGTGTCTTTGTTTCAGGAAAG 59.623 43.478 0.00 0.00 0.00 2.62
2534 2564 3.245229 ACATCTAGGCATTGAAACCACCA 60.245 43.478 0.00 0.00 0.00 4.17
2536 2566 5.391312 AAACATCTAGGCATTGAAACCAC 57.609 39.130 0.00 0.00 0.00 4.16
2537 2567 7.716799 AATAAACATCTAGGCATTGAAACCA 57.283 32.000 0.00 0.00 0.00 3.67
2573 2606 2.601240 TCCAAACATCCAGGCAATGA 57.399 45.000 0.00 0.00 0.00 2.57
2582 2615 1.347062 TTGCCCCTTTCCAAACATCC 58.653 50.000 0.00 0.00 0.00 3.51
2589 2622 2.094100 TCAATGTTTGCCCCTTTCCA 57.906 45.000 0.00 0.00 0.00 3.53
2621 2654 5.245977 TCAGTGATTACCATCTGAGTCAACA 59.754 40.000 0.00 0.00 32.82 3.33
2625 2658 5.843673 TCTCAGTGATTACCATCTGAGTC 57.156 43.478 16.82 0.00 43.52 3.36
2641 2690 4.974645 TTGTGTTGGTTCCTATCTCAGT 57.025 40.909 0.00 0.00 0.00 3.41
2651 2700 3.163616 TCCCCCTATTTGTGTTGGTTC 57.836 47.619 0.00 0.00 0.00 3.62
2756 2807 4.082949 CGTTGTCCGATGGCATAGACTATA 60.083 45.833 23.16 11.35 39.56 1.31
2783 2836 2.659610 GTCTGACTTGCCCTCGCT 59.340 61.111 0.00 0.00 35.36 4.93
2815 2868 7.282224 TCCTAAAATTGGATAAGTGGTTCATCG 59.718 37.037 0.00 0.00 0.00 3.84
2833 2886 9.091220 GGTCATACTAGTATCTGGTCCTAAAAT 57.909 37.037 12.62 0.00 0.00 1.82
2873 2926 5.191426 GTTGAAGGTCCTAAAGGTATTCCC 58.809 45.833 0.00 0.00 36.34 3.97
2887 2940 3.185797 ACGAGTAAAATGCGTTGAAGGTC 59.814 43.478 0.00 0.00 34.12 3.85
2888 2941 3.135994 ACGAGTAAAATGCGTTGAAGGT 58.864 40.909 0.00 0.00 34.12 3.50
2889 2942 3.806316 ACGAGTAAAATGCGTTGAAGG 57.194 42.857 0.00 0.00 34.12 3.46
2890 2943 6.762108 AGATAACGAGTAAAATGCGTTGAAG 58.238 36.000 9.73 0.00 46.28 3.02
2891 2944 6.715344 AGATAACGAGTAAAATGCGTTGAA 57.285 33.333 9.73 0.00 46.28 2.69
2892 2945 6.807720 TGTAGATAACGAGTAAAATGCGTTGA 59.192 34.615 9.73 0.00 46.28 3.18
2893 2946 6.985013 TGTAGATAACGAGTAAAATGCGTTG 58.015 36.000 9.73 0.00 46.28 4.10
2918 2976 4.858935 TCAGTTCAACAGCATAACTTTGC 58.141 39.130 0.00 0.00 43.09 3.68
2919 2977 6.906659 AGATCAGTTCAACAGCATAACTTTG 58.093 36.000 0.00 0.00 31.21 2.77
2927 2985 6.291377 AGTAGAAAAGATCAGTTCAACAGCA 58.709 36.000 10.10 0.00 0.00 4.41
2929 2987 7.953158 TGAGTAGAAAAGATCAGTTCAACAG 57.047 36.000 10.10 0.00 0.00 3.16
2963 3021 6.379133 ACCACTTCGTTCTACTTGGATATGTA 59.621 38.462 0.00 0.00 0.00 2.29
2966 3024 5.934402 ACCACTTCGTTCTACTTGGATAT 57.066 39.130 0.00 0.00 0.00 1.63
3005 3064 0.111253 CACCCTTCCTTGAGCAACCT 59.889 55.000 0.00 0.00 0.00 3.50
3007 3066 1.239347 GTCACCCTTCCTTGAGCAAC 58.761 55.000 0.00 0.00 0.00 4.17
3019 3078 8.522830 CAAACTTCAACATTAATATGTCACCCT 58.477 33.333 0.00 0.00 44.14 4.34
3030 3089 7.430441 GCCTTACTTCCAAACTTCAACATTAA 58.570 34.615 0.00 0.00 0.00 1.40
3104 3172 2.955660 TCCATCCACACCACTTTTGTTC 59.044 45.455 0.00 0.00 0.00 3.18
3167 3255 1.156736 AAATTCCTTGTCGAGCCACG 58.843 50.000 0.00 0.00 44.09 4.94
3197 3285 7.014422 ACACCTTCACTATACCTACATAGAAGC 59.986 40.741 0.00 0.00 33.49 3.86
3201 3289 7.818997 TCACACCTTCACTATACCTACATAG 57.181 40.000 0.00 0.00 35.09 2.23
3204 3292 5.955959 ACATCACACCTTCACTATACCTACA 59.044 40.000 0.00 0.00 0.00 2.74
3212 3300 6.432581 AGATACCTACATCACACCTTCACTA 58.567 40.000 0.00 0.00 0.00 2.74
3232 3320 9.828691 TCTCTCATGTGGGATTTTAGATAGATA 57.171 33.333 0.00 0.00 0.00 1.98
3245 3333 3.118261 GCCAAATAGTCTCTCATGTGGGA 60.118 47.826 0.00 0.00 0.00 4.37
3272 3360 1.305549 GGGACGGAGGGAGTACCAA 60.306 63.158 0.00 0.00 42.20 3.67
3278 3366 4.347000 TCTTTTATTATGGGACGGAGGGAG 59.653 45.833 0.00 0.00 0.00 4.30
3280 3368 4.699925 TCTTTTATTATGGGACGGAGGG 57.300 45.455 0.00 0.00 0.00 4.30
3282 3370 7.568199 AACATTCTTTTATTATGGGACGGAG 57.432 36.000 0.00 0.00 0.00 4.63
3284 3372 8.868916 CAAAAACATTCTTTTATTATGGGACGG 58.131 33.333 0.00 0.00 0.00 4.79
3285 3373 9.632807 TCAAAAACATTCTTTTATTATGGGACG 57.367 29.630 0.00 0.00 0.00 4.79
3287 3375 9.632807 CGTCAAAAACATTCTTTTATTATGGGA 57.367 29.630 0.00 0.00 0.00 4.37
3288 3376 9.418045 ACGTCAAAAACATTCTTTTATTATGGG 57.582 29.630 0.00 0.00 0.00 4.00
3297 3385 8.964150 GCTAACATAACGTCAAAAACATTCTTT 58.036 29.630 0.00 0.00 0.00 2.52
3298 3386 8.349983 AGCTAACATAACGTCAAAAACATTCTT 58.650 29.630 0.00 0.00 0.00 2.52
3299 3387 7.871853 AGCTAACATAACGTCAAAAACATTCT 58.128 30.769 0.00 0.00 0.00 2.40
3300 3388 8.502161 AAGCTAACATAACGTCAAAAACATTC 57.498 30.769 0.00 0.00 0.00 2.67
3301 3389 8.132362 TGAAGCTAACATAACGTCAAAAACATT 58.868 29.630 0.00 0.00 0.00 2.71
3302 3390 7.644490 TGAAGCTAACATAACGTCAAAAACAT 58.356 30.769 0.00 0.00 0.00 2.71
3303 3391 7.017498 TGAAGCTAACATAACGTCAAAAACA 57.983 32.000 0.00 0.00 0.00 2.83
3304 3392 7.901874 TTGAAGCTAACATAACGTCAAAAAC 57.098 32.000 0.00 0.00 30.62 2.43
3305 3393 8.912787 TTTTGAAGCTAACATAACGTCAAAAA 57.087 26.923 12.42 1.05 43.62 1.94
3306 3394 8.800031 GTTTTTGAAGCTAACATAACGTCAAAA 58.200 29.630 11.28 11.28 44.31 2.44
3307 3395 7.164498 CGTTTTTGAAGCTAACATAACGTCAAA 59.836 33.333 20.24 13.14 39.09 2.69
3308 3396 6.629649 CGTTTTTGAAGCTAACATAACGTCAA 59.370 34.615 20.24 9.28 34.37 3.18
3309 3397 6.130723 CGTTTTTGAAGCTAACATAACGTCA 58.869 36.000 20.24 4.89 34.37 4.35
3310 3398 6.131389 ACGTTTTTGAAGCTAACATAACGTC 58.869 36.000 24.05 5.77 40.80 4.34
3311 3399 6.051646 ACGTTTTTGAAGCTAACATAACGT 57.948 33.333 24.05 24.05 40.41 3.99
3312 3400 6.849305 AGAACGTTTTTGAAGCTAACATAACG 59.151 34.615 23.30 23.30 39.31 3.18
3313 3401 8.556517 AAGAACGTTTTTGAAGCTAACATAAC 57.443 30.769 0.46 0.00 0.00 1.89
3322 3410 9.233232 CCCATAATATAAGAACGTTTTTGAAGC 57.767 33.333 13.87 0.00 0.00 3.86
3325 3413 9.675464 ACTCCCATAATATAAGAACGTTTTTGA 57.325 29.630 13.87 2.81 0.00 2.69
3355 3443 9.804758 GCTTGAGTAGTTAAGCTAATCTAAAGA 57.195 33.333 17.45 0.00 43.13 2.52
3367 3455 5.340803 TGTATCGCTGCTTGAGTAGTTAAG 58.659 41.667 0.00 0.00 0.00 1.85
3371 3459 3.868757 TTGTATCGCTGCTTGAGTAGT 57.131 42.857 0.00 0.00 0.00 2.73
3375 3463 2.032550 CCCATTTGTATCGCTGCTTGAG 59.967 50.000 0.00 0.00 0.00 3.02
3377 3465 2.016318 TCCCATTTGTATCGCTGCTTG 58.984 47.619 0.00 0.00 0.00 4.01
3407 3495 4.647853 ACATTCCATCATGTTCATCCCTTG 59.352 41.667 0.00 0.00 33.29 3.61


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

AutoCloner maintained by Alex Coulton.