Multiple sequence alignment - TraesCS1B01G448900

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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 TraesCS1B01G448900 chr1B 100.000 3214 0 0 1 3214 667833748 667830535 0.000000e+00 5936.0
1 TraesCS1B01G448900 chr1B 100.000 187 0 0 3515 3701 667830234 667830048 2.740000e-91 346.0
2 TraesCS1B01G448900 chr1A 92.100 2557 147 25 672 3214 575966320 575968835 0.000000e+00 3552.0
3 TraesCS1B01G448900 chr1A 90.411 146 9 2 3555 3700 575969262 575969402 1.750000e-43 187.0
4 TraesCS1B01G448900 chr1A 80.420 143 14 6 677 805 575951432 575951574 3.040000e-16 97.1
5 TraesCS1B01G448900 chr1A 97.297 37 1 0 3518 3554 575969190 575969226 3.090000e-06 63.9
6 TraesCS1B01G448900 chr1A 97.222 36 1 0 768 803 575953603 575953638 1.110000e-05 62.1
7 TraesCS1B01G448900 chr1D 90.923 2545 152 34 672 3185 479610640 479613136 0.000000e+00 3347.0
8 TraesCS1B01G448900 chr1D 85.760 625 47 22 2549 3172 479614130 479614713 1.130000e-174 623.0
9 TraesCS1B01G448900 chr1D 88.356 146 10 3 3555 3700 479617608 479617746 6.360000e-38 169.0
10 TraesCS1B01G448900 chr1D 93.750 64 4 0 691 754 479608234 479608297 3.040000e-16 97.1
11 TraesCS1B01G448900 chr1D 100.000 36 0 0 3522 3557 479615098 479615133 2.390000e-07 67.6
12 TraesCS1B01G448900 chr7B 95.341 601 28 0 37 637 162332067 162332667 0.000000e+00 955.0
13 TraesCS1B01G448900 chr5D 94.176 601 35 0 37 637 87179477 87180077 0.000000e+00 917.0
14 TraesCS1B01G448900 chr6D 93.511 601 39 0 37 637 50570866 50570266 0.000000e+00 894.0
15 TraesCS1B01G448900 chr3B 93.344 601 40 0 37 637 17587201 17586601 0.000000e+00 889.0
16 TraesCS1B01G448900 chr2D 93.178 601 41 0 37 637 285896654 285897254 0.000000e+00 883.0
17 TraesCS1B01G448900 chr2D 93.035 603 40 1 37 637 306549187 306549789 0.000000e+00 880.0
18 TraesCS1B01G448900 chr4B 93.012 601 42 0 37 637 108958353 108958953 0.000000e+00 878.0
19 TraesCS1B01G448900 chr4B 91.639 598 50 0 38 635 472240089 472240686 0.000000e+00 828.0
20 TraesCS1B01G448900 chr6B 91.847 601 49 0 37 637 648797251 648797851 0.000000e+00 839.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G448900 chr1B 667830048 667833748 3700 True 3141.000000 5936 100.000000 1 3701 2 chr1B.!!$R1 3700
1 TraesCS1B01G448900 chr1A 575966320 575969402 3082 False 1267.633333 3552 93.269333 672 3700 3 chr1A.!!$F2 3028
2 TraesCS1B01G448900 chr1D 479608234 479617746 9512 False 860.740000 3347 91.757800 672 3700 5 chr1D.!!$F1 3028
3 TraesCS1B01G448900 chr7B 162332067 162332667 600 False 955.000000 955 95.341000 37 637 1 chr7B.!!$F1 600
4 TraesCS1B01G448900 chr5D 87179477 87180077 600 False 917.000000 917 94.176000 37 637 1 chr5D.!!$F1 600
5 TraesCS1B01G448900 chr6D 50570266 50570866 600 True 894.000000 894 93.511000 37 637 1 chr6D.!!$R1 600
6 TraesCS1B01G448900 chr3B 17586601 17587201 600 True 889.000000 889 93.344000 37 637 1 chr3B.!!$R1 600
7 TraesCS1B01G448900 chr2D 285896654 285897254 600 False 883.000000 883 93.178000 37 637 1 chr2D.!!$F1 600
8 TraesCS1B01G448900 chr2D 306549187 306549789 602 False 880.000000 880 93.035000 37 637 1 chr2D.!!$F2 600
9 TraesCS1B01G448900 chr4B 108958353 108958953 600 False 878.000000 878 93.012000 37 637 1 chr4B.!!$F1 600
10 TraesCS1B01G448900 chr4B 472240089 472240686 597 False 828.000000 828 91.639000 38 635 1 chr4B.!!$F2 597
11 TraesCS1B01G448900 chr6B 648797251 648797851 600 False 839.000000 839 91.847000 37 637 1 chr6B.!!$F1 600

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
170 171 0.321653 GGTTGGTCAAGCGATGGAGT 60.322 55.0 0.00 0.00 0.00 3.85 F
649 652 0.392863 CTGGGTCATTCATGGCGTGA 60.393 55.0 5.03 5.03 31.93 4.35 F
2310 4061 0.105593 ACGCGATCCAGCATCTCATT 59.894 50.0 15.93 0.00 36.85 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 3566 1.286880 GTGCTGCCATGTTGACACC 59.713 57.895 0.00 0.0 0.0 4.16 R
2547 4301 0.032017 AGAAGTACCTCTCGCCCCAT 60.032 55.000 0.00 0.0 0.0 4.00 R
3676 9583 0.248458 GTTGCCACGTTGGTGTGAAG 60.248 55.000 6.02 0.0 42.8 3.02 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
20 21 3.100658 TGGAAACACGATGTTCGAAGA 57.899 42.857 0.00 0.00 40.14 2.87
22 23 3.872182 TGGAAACACGATGTTCGAAGAAA 59.128 39.130 0.00 0.00 40.14 2.52
23 24 4.333095 TGGAAACACGATGTTCGAAGAAAA 59.667 37.500 0.00 0.00 40.14 2.29
24 25 4.904154 GGAAACACGATGTTCGAAGAAAAG 59.096 41.667 0.00 0.00 45.90 2.27
25 26 5.277154 GGAAACACGATGTTCGAAGAAAAGA 60.277 40.000 0.00 0.00 45.90 2.52
26 27 5.728351 AACACGATGTTCGAAGAAAAGAA 57.272 34.783 0.00 0.00 45.90 2.52
27 28 5.728351 ACACGATGTTCGAAGAAAAGAAA 57.272 34.783 0.00 0.00 45.90 2.52
28 29 6.114221 ACACGATGTTCGAAGAAAAGAAAA 57.886 33.333 0.00 0.00 45.90 2.29
29 30 6.192360 ACACGATGTTCGAAGAAAAGAAAAG 58.808 36.000 0.00 0.00 45.90 2.27
31 32 7.072030 CACGATGTTCGAAGAAAAGAAAAGAT 58.928 34.615 0.00 0.00 45.90 2.40
32 33 8.221100 CACGATGTTCGAAGAAAAGAAAAGATA 58.779 33.333 0.00 0.00 45.90 1.98
33 34 8.770828 ACGATGTTCGAAGAAAAGAAAAGATAA 58.229 29.630 0.00 0.00 45.90 1.75
95 96 1.674980 GAGGTCGTGAGAGTCCGGT 60.675 63.158 0.00 0.00 43.49 5.28
170 171 0.321653 GGTTGGTCAAGCGATGGAGT 60.322 55.000 0.00 0.00 0.00 3.85
179 180 0.687757 AGCGATGGAGTAGGCCAAGA 60.688 55.000 5.01 0.00 42.16 3.02
206 207 2.330372 ACGCAGCAGCATGGAGTTG 61.330 57.895 0.82 0.00 42.27 3.16
549 550 1.658686 AAACGCGCTTTGGTTGGTGA 61.659 50.000 5.73 0.00 0.00 4.02
630 633 3.491267 GGCGAAGATGTGTATAAGACTGC 59.509 47.826 0.00 0.00 0.00 4.40
637 640 3.169908 TGTGTATAAGACTGCTGGGTCA 58.830 45.455 0.00 0.00 38.57 4.02
638 641 3.774766 TGTGTATAAGACTGCTGGGTCAT 59.225 43.478 0.00 0.00 38.57 3.06
640 643 4.811557 GTGTATAAGACTGCTGGGTCATTC 59.188 45.833 0.00 0.00 38.57 2.67
641 644 4.469586 TGTATAAGACTGCTGGGTCATTCA 59.530 41.667 0.00 0.00 38.57 2.57
642 645 4.785346 ATAAGACTGCTGGGTCATTCAT 57.215 40.909 0.00 0.00 38.57 2.57
643 646 2.414994 AGACTGCTGGGTCATTCATG 57.585 50.000 0.00 0.00 38.57 3.07
644 647 1.064906 AGACTGCTGGGTCATTCATGG 60.065 52.381 0.00 0.00 38.57 3.66
645 648 0.682209 ACTGCTGGGTCATTCATGGC 60.682 55.000 0.00 0.00 0.00 4.40
646 649 1.721664 CTGCTGGGTCATTCATGGCG 61.722 60.000 0.00 0.00 31.93 5.69
647 650 1.750399 GCTGGGTCATTCATGGCGT 60.750 57.895 0.00 0.00 31.93 5.68
648 651 1.996786 GCTGGGTCATTCATGGCGTG 61.997 60.000 0.00 0.00 31.93 5.34
649 652 0.392863 CTGGGTCATTCATGGCGTGA 60.393 55.000 5.03 5.03 31.93 4.35
657 660 2.542020 TTCATGGCGTGAAACTGAGA 57.458 45.000 19.35 0.00 43.64 3.27
658 661 1.795768 TCATGGCGTGAAACTGAGAC 58.204 50.000 7.00 0.00 32.78 3.36
659 662 0.798776 CATGGCGTGAAACTGAGACC 59.201 55.000 0.00 0.00 31.75 3.85
660 663 0.687354 ATGGCGTGAAACTGAGACCT 59.313 50.000 0.00 0.00 31.75 3.85
661 664 1.334160 TGGCGTGAAACTGAGACCTA 58.666 50.000 0.00 0.00 31.75 3.08
662 665 1.272490 TGGCGTGAAACTGAGACCTAG 59.728 52.381 0.00 0.00 31.75 3.02
665 668 2.030185 GCGTGAAACTGAGACCTAGTCA 60.030 50.000 0.00 0.00 31.66 3.41
666 669 3.566523 CGTGAAACTGAGACCTAGTCAC 58.433 50.000 0.00 0.00 31.66 3.67
668 671 4.299978 GTGAAACTGAGACCTAGTCACAC 58.700 47.826 0.00 0.00 34.60 3.82
669 672 3.321111 TGAAACTGAGACCTAGTCACACC 59.679 47.826 0.00 0.00 34.60 4.16
670 673 1.926108 ACTGAGACCTAGTCACACCC 58.074 55.000 0.00 0.00 34.60 4.61
683 2419 4.781934 AGTCACACCCTAGGAAAATATGC 58.218 43.478 11.48 0.00 0.00 3.14
744 2480 5.531287 ACCTAAAACGCAGAGAAGAACAAAT 59.469 36.000 0.00 0.00 0.00 2.32
745 2481 5.853282 CCTAAAACGCAGAGAAGAACAAATG 59.147 40.000 0.00 0.00 0.00 2.32
747 2483 5.695851 AAACGCAGAGAAGAACAAATGAT 57.304 34.783 0.00 0.00 0.00 2.45
826 2563 5.163663 CGGTATGTAGTACGGGTAGAAACAA 60.164 44.000 0.00 0.00 33.94 2.83
863 2604 9.301153 CCACATAAATTAGTGCTAATCAAAACC 57.699 33.333 5.08 0.00 34.90 3.27
907 2648 2.475685 GCGCATCGTTTTCTCCTTAACC 60.476 50.000 0.30 0.00 0.00 2.85
912 2653 5.676331 GCATCGTTTTCTCCTTAACCAATCC 60.676 44.000 0.00 0.00 0.00 3.01
932 2673 1.815866 GCCGGCCTGCATGTAAAAT 59.184 52.632 18.11 0.00 0.00 1.82
970 2715 2.099446 CATAAAACCCCACGCGCG 59.901 61.111 30.96 30.96 0.00 6.86
999 2750 1.448540 CTCCACAGTCCATGCGTCC 60.449 63.158 0.00 0.00 0.00 4.79
1096 2847 2.681666 GCAACGACGACGATGACG 59.318 61.111 20.02 4.49 43.20 4.35
1097 2848 1.794785 GCAACGACGACGATGACGA 60.795 57.895 20.02 0.00 43.20 4.20
1098 2849 1.971336 CAACGACGACGATGACGAC 59.029 57.895 15.32 0.00 43.20 4.34
1367 3118 1.654954 CTCTCCTACACCACGGACGG 61.655 65.000 0.00 0.00 0.00 4.79
1404 3155 2.827190 ATCGACCTCGTGGCGCTA 60.827 61.111 7.64 0.00 40.80 4.26
1512 3263 1.898574 CAGCAAGACCCTGGCGTTT 60.899 57.895 0.00 0.00 35.20 3.60
1779 3530 2.632547 CGTCACCGTGTTCGTCGTG 61.633 63.158 0.00 0.00 35.01 4.35
1788 3539 4.668118 TTCGTCGTGAACCGGCCC 62.668 66.667 0.00 0.00 38.13 5.80
1948 3699 3.073101 GGTTCTACCTCGGGCGGT 61.073 66.667 0.00 0.00 41.10 5.68
1995 3746 2.107141 CGGTTCCCAGAGATCGGC 59.893 66.667 0.00 0.00 0.00 5.54
1998 3749 1.443828 GTTCCCAGAGATCGGCCTC 59.556 63.158 0.00 0.00 0.00 4.70
1999 3750 2.127869 TTCCCAGAGATCGGCCTCG 61.128 63.158 0.00 0.00 38.19 4.63
2088 3839 2.987547 TCCACGTCGGACCTCACC 60.988 66.667 1.91 0.00 39.64 4.02
2106 3857 4.736896 GACCGGGTGCTCCACGAC 62.737 72.222 3.30 7.00 34.83 4.34
2217 3968 0.108329 CCAAGGCGTACGTCATCCTT 60.108 55.000 23.51 19.35 39.35 3.36
2294 4045 1.796796 GCAGAGGAAACATCCACGC 59.203 57.895 0.00 0.00 0.00 5.34
2310 4061 0.105593 ACGCGATCCAGCATCTCATT 59.894 50.000 15.93 0.00 36.85 2.57
2340 4091 3.429141 GACGACGACGGCCAGAGA 61.429 66.667 12.58 0.00 42.35 3.10
2341 4092 3.664223 GACGACGACGGCCAGAGAC 62.664 68.421 12.58 0.00 42.35 3.36
2377 4128 1.063166 CTACGCCGGTTCTACGACC 59.937 63.158 1.90 0.00 35.47 4.79
2458 4209 3.758023 TGATCTAGGCACCAACAACAATG 59.242 43.478 0.00 0.00 0.00 2.82
2459 4210 2.513753 TCTAGGCACCAACAACAATGG 58.486 47.619 0.00 0.00 43.84 3.16
2460 4211 0.965439 TAGGCACCAACAACAATGGC 59.035 50.000 0.00 0.00 41.89 4.40
2500 4254 3.761311 CTATAATAGGAGACGGCGACC 57.239 52.381 16.62 14.02 0.00 4.79
2501 4255 1.991121 ATAATAGGAGACGGCGACCA 58.009 50.000 16.62 5.64 0.00 4.02
2502 4256 1.766494 TAATAGGAGACGGCGACCAA 58.234 50.000 16.62 0.00 0.00 3.67
2503 4257 0.460311 AATAGGAGACGGCGACCAAG 59.540 55.000 16.62 0.00 0.00 3.61
2504 4258 0.395311 ATAGGAGACGGCGACCAAGA 60.395 55.000 16.62 4.32 0.00 3.02
2505 4259 0.395311 TAGGAGACGGCGACCAAGAT 60.395 55.000 16.62 0.86 0.00 2.40
2506 4260 1.519455 GGAGACGGCGACCAAGATG 60.519 63.158 16.62 0.00 0.00 2.90
2507 4261 1.519455 GAGACGGCGACCAAGATGG 60.519 63.158 16.62 0.00 45.02 3.51
2514 4268 2.045926 GACCAAGATGGCGGCAGT 60.046 61.111 19.29 9.39 42.67 4.40
2518 4272 1.817099 CAAGATGGCGGCAGTCCTC 60.817 63.158 19.29 10.17 0.00 3.71
2520 4274 1.965754 AAGATGGCGGCAGTCCTCTC 61.966 60.000 19.29 8.96 0.00 3.20
2566 4320 0.032017 ATGGGGCGAGAGGTACTTCT 60.032 55.000 7.31 7.31 41.55 2.85
2568 4322 0.175989 GGGGCGAGAGGTACTTCTTG 59.824 60.000 16.18 16.18 41.55 3.02
2683 6061 1.812922 CTGCAGATGACCAGGCGTC 60.813 63.158 8.42 0.00 42.33 5.19
2684 6062 2.236223 CTGCAGATGACCAGGCGTCT 62.236 60.000 8.42 0.00 42.49 4.18
2706 6084 2.697229 TGCACATGACATCTAGCTAGCT 59.303 45.455 23.12 23.12 0.00 3.32
2707 6085 3.891366 TGCACATGACATCTAGCTAGCTA 59.109 43.478 22.85 22.85 0.00 3.32
2708 6086 4.022503 TGCACATGACATCTAGCTAGCTAG 60.023 45.833 36.20 36.20 45.38 3.42
2723 6101 0.099436 GCTAGCCCAAAGTTGCATCG 59.901 55.000 2.29 0.00 0.00 3.84
2729 6107 0.387622 CCAAAGTTGCATCGCACCAG 60.388 55.000 0.00 0.00 38.71 4.00
2740 6118 2.739704 CGCACCAGCACACCGTATG 61.740 63.158 0.00 0.00 42.27 2.39
2742 6120 1.635663 GCACCAGCACACCGTATGAC 61.636 60.000 0.00 0.00 41.58 3.06
2756 6134 5.005394 CACCGTATGACATTGTTGTAGCTAC 59.995 44.000 17.30 17.30 35.79 3.58
2772 6150 1.801178 GCTACAGAGCCAAACACACTC 59.199 52.381 0.00 0.00 43.49 3.51
2773 6151 2.548920 GCTACAGAGCCAAACACACTCT 60.549 50.000 0.00 0.00 43.49 3.24
2774 6152 2.717639 ACAGAGCCAAACACACTCTT 57.282 45.000 0.00 0.00 38.72 2.85
2777 6155 3.134804 ACAGAGCCAAACACACTCTTACT 59.865 43.478 0.00 0.00 38.72 2.24
2778 6156 4.130118 CAGAGCCAAACACACTCTTACTT 58.870 43.478 0.00 0.00 38.72 2.24
2779 6157 5.163343 ACAGAGCCAAACACACTCTTACTTA 60.163 40.000 0.00 0.00 38.72 2.24
2780 6158 5.177696 CAGAGCCAAACACACTCTTACTTAC 59.822 44.000 0.00 0.00 38.72 2.34
2781 6159 5.031066 AGCCAAACACACTCTTACTTACA 57.969 39.130 0.00 0.00 0.00 2.41
2782 6160 5.433526 AGCCAAACACACTCTTACTTACAA 58.566 37.500 0.00 0.00 0.00 2.41
2783 6161 5.883673 AGCCAAACACACTCTTACTTACAAA 59.116 36.000 0.00 0.00 0.00 2.83
2784 6162 6.038271 AGCCAAACACACTCTTACTTACAAAG 59.962 38.462 0.00 0.00 0.00 2.77
2785 6163 6.183360 GCCAAACACACTCTTACTTACAAAGT 60.183 38.462 0.00 0.00 45.40 2.66
2786 6164 7.407337 CCAAACACACTCTTACTTACAAAGTC 58.593 38.462 0.00 0.00 41.77 3.01
2787 6165 7.407337 CAAACACACTCTTACTTACAAAGTCC 58.593 38.462 0.00 0.00 41.77 3.85
2788 6166 6.229936 ACACACTCTTACTTACAAAGTCCA 57.770 37.500 0.00 0.00 41.77 4.02
2789 6167 6.047231 ACACACTCTTACTTACAAAGTCCAC 58.953 40.000 0.00 0.00 41.77 4.02
2790 6168 6.127140 ACACACTCTTACTTACAAAGTCCACT 60.127 38.462 0.00 0.00 41.77 4.00
2791 6169 7.069085 ACACACTCTTACTTACAAAGTCCACTA 59.931 37.037 0.00 0.00 41.77 2.74
2792 6170 8.088981 CACACTCTTACTTACAAAGTCCACTAT 58.911 37.037 0.00 0.00 41.77 2.12
2803 6181 7.435068 ACAAAGTCCACTATATGTTGAACAC 57.565 36.000 0.00 0.00 0.00 3.32
2884 6263 5.033589 TCAAAGTTGCATCCAAACCAAAT 57.966 34.783 0.00 0.00 31.68 2.32
2897 6276 6.310941 TCCAAACCAAATGGAAGAAGACATA 58.689 36.000 6.42 0.00 43.84 2.29
2898 6277 6.953520 TCCAAACCAAATGGAAGAAGACATAT 59.046 34.615 6.42 0.00 43.84 1.78
2920 6299 5.339008 TGTCATAGGAAGGACATACACAC 57.661 43.478 0.00 0.00 41.25 3.82
2935 6314 7.201609 GGACATACACACATATCGTCACATTTT 60.202 37.037 0.00 0.00 0.00 1.82
2991 6370 1.443872 CTGTCGTGGTGCCGTCTAC 60.444 63.158 0.00 0.00 0.00 2.59
3009 6388 5.471257 GTCTACAAGGACGATTTGTTCTCT 58.529 41.667 8.66 0.00 34.32 3.10
3079 6458 5.858581 AGCTGAAAACGAGATAATTGTTTGC 59.141 36.000 0.00 0.00 43.47 3.68
3115 6494 2.368439 CGCTCTTCCCCATTGAAATGA 58.632 47.619 4.58 0.00 38.70 2.57
3116 6495 2.954318 CGCTCTTCCCCATTGAAATGAT 59.046 45.455 4.58 0.00 38.70 2.45
3117 6496 4.136796 CGCTCTTCCCCATTGAAATGATA 58.863 43.478 4.58 0.00 38.70 2.15
3118 6497 4.763793 CGCTCTTCCCCATTGAAATGATAT 59.236 41.667 4.58 0.00 38.70 1.63
3137 6516 7.954666 TGATATATAGGAATCACGTCCATCA 57.045 36.000 0.00 0.00 40.48 3.07
3138 6517 8.539117 TGATATATAGGAATCACGTCCATCAT 57.461 34.615 0.00 0.00 40.48 2.45
3139 6518 8.633561 TGATATATAGGAATCACGTCCATCATC 58.366 37.037 0.00 0.00 40.48 2.92
3140 6519 2.515926 AGGAATCACGTCCATCATCG 57.484 50.000 0.00 0.00 40.48 3.84
3141 6520 2.031870 AGGAATCACGTCCATCATCGA 58.968 47.619 0.00 0.00 40.48 3.59
3142 6521 2.630098 AGGAATCACGTCCATCATCGAT 59.370 45.455 0.00 0.00 40.48 3.59
3143 6522 3.070159 AGGAATCACGTCCATCATCGATT 59.930 43.478 0.00 0.00 40.48 3.34
3144 6523 3.185188 GGAATCACGTCCATCATCGATTG 59.815 47.826 0.00 0.00 37.65 2.67
3145 6524 2.223537 TCACGTCCATCATCGATTGG 57.776 50.000 9.50 9.50 0.00 3.16
3146 6525 1.754226 TCACGTCCATCATCGATTGGA 59.246 47.619 13.71 13.71 0.00 3.53
3150 6529 3.383505 ACGTCCATCATCGATTGGAACTA 59.616 43.478 18.29 0.00 31.60 2.24
3153 6532 4.985409 GTCCATCATCGATTGGAACTACTC 59.015 45.833 18.29 3.97 31.60 2.59
3172 6551 3.809832 ACTCGTTGAGTTCTGTTTCATGG 59.190 43.478 0.00 0.00 40.28 3.66
3180 6559 8.946085 GTTGAGTTCTGTTTCATGGTGATAATA 58.054 33.333 0.00 0.00 0.00 0.98
3183 6562 9.167311 GAGTTCTGTTTCATGGTGATAATAACT 57.833 33.333 0.00 0.00 0.00 2.24
3188 6567 9.342308 CTGTTTCATGGTGATAATAACTATGGT 57.658 33.333 0.00 0.00 37.19 3.55
3566 9473 3.756434 TCTGCTGGCCTACAAATTAACAC 59.244 43.478 3.32 0.00 0.00 3.32
3568 9475 2.159435 GCTGGCCTACAAATTAACACGG 60.159 50.000 3.32 0.00 0.00 4.94
3571 9478 1.792632 GCCTACAAATTAACACGGCGC 60.793 52.381 6.90 0.00 0.00 6.53
3597 9504 3.791640 TGTCACGATGGACAGGCT 58.208 55.556 5.48 0.00 42.56 4.58
3618 9525 0.462759 GCTATATCCATCCGCTGCCC 60.463 60.000 0.00 0.00 0.00 5.36
3654 9561 1.226030 CTCCACCGTTTTGACCGACC 61.226 60.000 0.00 0.00 0.00 4.79
3658 9565 1.592131 CCGTTTTGACCGACCGACA 60.592 57.895 0.00 0.00 0.00 4.35
3665 9572 0.820482 TGACCGACCGACAACTCTCA 60.820 55.000 0.00 0.00 0.00 3.27
3675 9582 2.223157 CGACAACTCTCATCTCGTCCTC 60.223 54.545 0.00 0.00 0.00 3.71
3676 9583 2.096248 ACAACTCTCATCTCGTCCTCC 58.904 52.381 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.100658 TCTTCGAACATCGTGTTTCCA 57.899 42.857 0.00 0.00 41.28 3.53
1 2 4.461992 TTTCTTCGAACATCGTGTTTCC 57.538 40.909 0.00 0.00 41.28 3.13
2 3 5.734311 TCTTTTCTTCGAACATCGTGTTTC 58.266 37.500 0.00 0.00 41.28 2.78
4 5 5.728351 TTCTTTTCTTCGAACATCGTGTT 57.272 34.783 0.00 3.52 44.37 3.32
6 7 6.418956 TCTTTTCTTTTCTTCGAACATCGTG 58.581 36.000 0.00 0.00 41.35 4.35
8 9 9.594038 TTTATCTTTTCTTTTCTTCGAACATCG 57.406 29.630 0.00 0.00 42.10 3.84
10 11 9.899226 CCTTTATCTTTTCTTTTCTTCGAACAT 57.101 29.630 0.00 0.00 0.00 2.71
12 13 9.946165 TTCCTTTATCTTTTCTTTTCTTCGAAC 57.054 29.630 0.00 0.00 0.00 3.95
15 16 7.269297 CGCTTCCTTTATCTTTTCTTTTCTTCG 59.731 37.037 0.00 0.00 0.00 3.79
17 18 7.371159 CCGCTTCCTTTATCTTTTCTTTTCTT 58.629 34.615 0.00 0.00 0.00 2.52
18 19 6.071896 CCCGCTTCCTTTATCTTTTCTTTTCT 60.072 38.462 0.00 0.00 0.00 2.52
20 21 5.047306 CCCCGCTTCCTTTATCTTTTCTTTT 60.047 40.000 0.00 0.00 0.00 2.27
22 23 4.017126 CCCCGCTTCCTTTATCTTTTCTT 58.983 43.478 0.00 0.00 0.00 2.52
23 24 3.621558 CCCCGCTTCCTTTATCTTTTCT 58.378 45.455 0.00 0.00 0.00 2.52
24 25 2.099263 GCCCCGCTTCCTTTATCTTTTC 59.901 50.000 0.00 0.00 0.00 2.29
25 26 2.100197 GCCCCGCTTCCTTTATCTTTT 58.900 47.619 0.00 0.00 0.00 2.27
26 27 1.685180 GGCCCCGCTTCCTTTATCTTT 60.685 52.381 0.00 0.00 0.00 2.52
27 28 0.106669 GGCCCCGCTTCCTTTATCTT 60.107 55.000 0.00 0.00 0.00 2.40
28 29 1.279025 TGGCCCCGCTTCCTTTATCT 61.279 55.000 0.00 0.00 0.00 1.98
29 30 0.395173 TTGGCCCCGCTTCCTTTATC 60.395 55.000 0.00 0.00 0.00 1.75
31 32 0.610785 CTTTGGCCCCGCTTCCTTTA 60.611 55.000 0.00 0.00 0.00 1.85
32 33 1.908299 CTTTGGCCCCGCTTCCTTT 60.908 57.895 0.00 0.00 0.00 3.11
33 34 2.283173 CTTTGGCCCCGCTTCCTT 60.283 61.111 0.00 0.00 0.00 3.36
35 36 3.062466 GTCTTTGGCCCCGCTTCC 61.062 66.667 0.00 0.00 0.00 3.46
95 96 3.833650 ATGATGTGGTCATCTTTTGCCAA 59.166 39.130 9.15 0.00 44.23 4.52
170 171 0.392461 GTGCGGTTGATCTTGGCCTA 60.392 55.000 3.32 0.00 0.00 3.93
179 180 3.425713 CTGCTGCGTGCGGTTGAT 61.426 61.111 2.18 0.00 46.63 2.57
206 207 1.078759 CCTTGGTCATCGACGTGCTC 61.079 60.000 0.00 0.00 32.65 4.26
549 550 1.001641 GGCTGAGCACCATGGTCTT 60.002 57.895 16.53 5.79 44.58 3.01
561 562 4.567385 GCTCGCTCCTCGGCTGAG 62.567 72.222 16.14 16.14 42.18 3.35
630 633 0.392863 TCACGCCATGAATGACCCAG 60.393 55.000 0.00 0.00 33.02 4.45
637 640 2.744202 GTCTCAGTTTCACGCCATGAAT 59.256 45.455 0.00 0.00 46.80 2.57
638 641 2.143122 GTCTCAGTTTCACGCCATGAA 58.857 47.619 0.00 0.00 45.92 2.57
640 643 0.798776 GGTCTCAGTTTCACGCCATG 59.201 55.000 0.00 0.00 0.00 3.66
641 644 0.687354 AGGTCTCAGTTTCACGCCAT 59.313 50.000 0.00 0.00 0.00 4.40
642 645 1.272490 CTAGGTCTCAGTTTCACGCCA 59.728 52.381 0.00 0.00 0.00 5.69
643 646 1.272769 ACTAGGTCTCAGTTTCACGCC 59.727 52.381 0.00 0.00 0.00 5.68
644 647 2.030185 TGACTAGGTCTCAGTTTCACGC 60.030 50.000 0.00 0.00 33.15 5.34
645 648 3.004419 TGTGACTAGGTCTCAGTTTCACG 59.996 47.826 0.00 0.00 32.30 4.35
646 649 4.299978 GTGTGACTAGGTCTCAGTTTCAC 58.700 47.826 0.00 0.00 36.86 3.18
647 650 3.321111 GGTGTGACTAGGTCTCAGTTTCA 59.679 47.826 0.00 0.00 36.86 2.69
648 651 3.306156 GGGTGTGACTAGGTCTCAGTTTC 60.306 52.174 0.00 0.00 36.86 2.78
649 652 2.633481 GGGTGTGACTAGGTCTCAGTTT 59.367 50.000 0.00 0.00 36.86 2.66
650 653 2.158295 AGGGTGTGACTAGGTCTCAGTT 60.158 50.000 0.00 0.00 36.86 3.16
651 654 1.429687 AGGGTGTGACTAGGTCTCAGT 59.570 52.381 0.00 0.00 36.86 3.41
652 655 2.223803 AGGGTGTGACTAGGTCTCAG 57.776 55.000 0.00 0.00 36.86 3.35
653 656 3.367646 CTAGGGTGTGACTAGGTCTCA 57.632 52.381 0.00 0.00 35.42 3.27
659 662 5.992217 GCATATTTTCCTAGGGTGTGACTAG 59.008 44.000 9.46 0.00 38.09 2.57
660 663 5.427157 TGCATATTTTCCTAGGGTGTGACTA 59.573 40.000 9.46 0.00 0.00 2.59
661 664 4.227300 TGCATATTTTCCTAGGGTGTGACT 59.773 41.667 9.46 0.00 0.00 3.41
662 665 4.523083 TGCATATTTTCCTAGGGTGTGAC 58.477 43.478 9.46 0.00 0.00 3.67
665 668 4.536765 CCTTGCATATTTTCCTAGGGTGT 58.463 43.478 9.46 0.00 0.00 4.16
666 669 3.319122 GCCTTGCATATTTTCCTAGGGTG 59.681 47.826 9.46 0.34 0.00 4.61
668 671 2.554032 CGCCTTGCATATTTTCCTAGGG 59.446 50.000 9.46 0.00 0.00 3.53
669 672 3.476552 TCGCCTTGCATATTTTCCTAGG 58.523 45.455 0.82 0.82 0.00 3.02
670 673 4.335315 TGTTCGCCTTGCATATTTTCCTAG 59.665 41.667 0.00 0.00 0.00 3.02
682 2418 4.629527 CAAACTTATTTGTTCGCCTTGC 57.370 40.909 0.00 0.00 40.39 4.01
744 2480 1.001487 CCAGACGCACTTGCAAAATCA 60.001 47.619 0.00 0.00 42.21 2.57
745 2481 1.001378 ACCAGACGCACTTGCAAAATC 60.001 47.619 0.00 0.00 42.21 2.17
747 2483 1.601903 CTACCAGACGCACTTGCAAAA 59.398 47.619 0.00 0.00 42.21 2.44
863 2604 5.665217 GCAACGAGCGGTTAAAAATCATTTG 60.665 40.000 0.00 0.00 36.49 2.32
932 2673 1.944024 CAGGCCCGCGTGATTTTATTA 59.056 47.619 4.92 0.00 34.13 0.98
970 2715 0.319900 ACTGTGGAGTGTGACGATGC 60.320 55.000 0.00 0.00 0.00 3.91
1096 2847 2.887568 CGTCATCAGGGCGCTGTC 60.888 66.667 27.76 16.12 0.00 3.51
1097 2848 3.649277 GACGTCATCAGGGCGCTGT 62.649 63.158 27.76 14.15 0.00 4.40
1098 2849 2.887568 GACGTCATCAGGGCGCTG 60.888 66.667 23.98 23.98 0.00 5.18
1182 2933 1.446272 GTTCTGGACGGAGAAGGCG 60.446 63.158 0.00 0.00 32.53 5.52
1659 3410 3.746949 GACCTCCTCGCCCATGCTG 62.747 68.421 0.00 0.00 34.43 4.41
1660 3411 3.474570 GACCTCCTCGCCCATGCT 61.475 66.667 0.00 0.00 34.43 3.79
1815 3566 1.286880 GTGCTGCCATGTTGACACC 59.713 57.895 0.00 0.00 0.00 4.16
1953 3704 3.969995 GAGTATCTCCAACGCCTCC 57.030 57.895 0.00 0.00 0.00 4.30
1998 3749 4.796231 CTCGGGTTCAGGTCCGCG 62.796 72.222 0.00 0.00 45.31 6.46
1999 3750 3.358076 CTCTCGGGTTCAGGTCCGC 62.358 68.421 0.00 0.00 45.31 5.54
2061 3812 2.182030 GACGTGGAGCTCCCTTCG 59.818 66.667 29.95 28.79 38.30 3.79
2106 3857 4.137543 ACTTGGCCTTGAAGTAGTTCTTG 58.862 43.478 3.32 4.42 36.40 3.02
2279 4030 0.931005 GATCGCGTGGATGTTTCCTC 59.069 55.000 5.77 0.00 43.07 3.71
2294 4045 0.873054 GGCAATGAGATGCTGGATCG 59.127 55.000 3.41 0.00 45.68 3.69
2337 4088 2.428890 CCAGTCCATGTACTCCTGTCTC 59.571 54.545 0.00 0.00 0.00 3.36
2340 4091 0.905357 GCCAGTCCATGTACTCCTGT 59.095 55.000 0.00 0.00 0.00 4.00
2341 4092 1.198713 AGCCAGTCCATGTACTCCTG 58.801 55.000 0.00 0.00 0.00 3.86
2377 4128 0.103208 GACACGTAGGCTCCCATGAG 59.897 60.000 0.00 0.00 41.84 2.90
2458 4209 0.757512 TGATGATGAGCAGGAGAGCC 59.242 55.000 0.00 0.00 34.23 4.70
2459 4210 2.613474 GGATGATGATGAGCAGGAGAGC 60.613 54.545 0.00 0.00 0.00 4.09
2460 4211 2.901192 AGGATGATGATGAGCAGGAGAG 59.099 50.000 0.00 0.00 0.00 3.20
2496 4250 3.197790 CTGCCGCCATCTTGGTCG 61.198 66.667 0.00 0.14 40.46 4.79
2497 4251 2.045926 ACTGCCGCCATCTTGGTC 60.046 61.111 0.00 0.00 40.46 4.02
2498 4252 2.045926 GACTGCCGCCATCTTGGT 60.046 61.111 0.00 0.00 40.46 3.67
2499 4253 2.825836 GGACTGCCGCCATCTTGG 60.826 66.667 0.00 0.00 41.55 3.61
2500 4254 1.817099 GAGGACTGCCGCCATCTTG 60.817 63.158 0.00 0.00 39.96 3.02
2501 4255 1.965754 GAGAGGACTGCCGCCATCTT 61.966 60.000 0.00 0.00 39.96 2.40
2502 4256 2.364842 AGAGGACTGCCGCCATCT 60.365 61.111 0.00 0.00 39.96 2.90
2503 4257 2.107953 GAGAGGACTGCCGCCATC 59.892 66.667 0.00 0.00 39.96 3.51
2504 4258 2.293318 TTGAGAGGACTGCCGCCAT 61.293 57.895 0.00 0.00 39.96 4.40
2505 4259 2.922503 TTGAGAGGACTGCCGCCA 60.923 61.111 0.00 0.00 39.96 5.69
2506 4260 2.435059 GTTGAGAGGACTGCCGCC 60.435 66.667 0.00 0.00 39.96 6.13
2507 4261 1.446966 GAGTTGAGAGGACTGCCGC 60.447 63.158 0.00 0.00 39.96 6.53
2539 4293 4.899239 CTCGCCCCATGTCCTCGC 62.899 72.222 0.00 0.00 0.00 5.03
2547 4301 0.032017 AGAAGTACCTCTCGCCCCAT 60.032 55.000 0.00 0.00 0.00 4.00
2566 4320 0.956633 AGACGGTCGTAGTTGCTCAA 59.043 50.000 1.89 0.00 0.00 3.02
2568 4322 0.520827 CGAGACGGTCGTAGTTGCTC 60.521 60.000 1.89 0.00 44.20 4.26
2683 6061 3.493877 GCTAGCTAGATGTCATGTGCAAG 59.506 47.826 25.15 0.00 0.00 4.01
2684 6062 3.133542 AGCTAGCTAGATGTCATGTGCAA 59.866 43.478 25.15 0.00 0.00 4.08
2706 6084 0.607762 TGCGATGCAACTTTGGGCTA 60.608 50.000 0.00 0.00 34.76 3.93
2707 6085 1.902918 TGCGATGCAACTTTGGGCT 60.903 52.632 0.00 0.00 34.76 5.19
2708 6086 1.734117 GTGCGATGCAACTTTGGGC 60.734 57.895 0.00 0.00 41.47 5.36
2709 6087 1.080569 GGTGCGATGCAACTTTGGG 60.081 57.895 0.00 0.00 43.73 4.12
2723 6101 1.375396 TCATACGGTGTGCTGGTGC 60.375 57.895 0.00 0.00 40.20 5.01
2729 6107 2.225491 ACAACAATGTCATACGGTGTGC 59.775 45.455 5.31 0.00 33.41 4.57
2740 6118 4.849111 GCTCTGTAGCTACAACAATGTC 57.151 45.455 25.95 8.62 45.85 3.06
2756 6134 3.733337 AGTAAGAGTGTGTTTGGCTCTG 58.267 45.455 0.00 0.00 39.29 3.35
2777 6155 8.995220 GTGTTCAACATATAGTGGACTTTGTAA 58.005 33.333 0.00 0.00 27.00 2.41
2778 6156 7.329962 CGTGTTCAACATATAGTGGACTTTGTA 59.670 37.037 0.00 0.00 27.00 2.41
2779 6157 6.147164 CGTGTTCAACATATAGTGGACTTTGT 59.853 38.462 0.00 0.00 27.00 2.83
2780 6158 6.147164 ACGTGTTCAACATATAGTGGACTTTG 59.853 38.462 0.00 0.00 27.00 2.77
2781 6159 6.228258 ACGTGTTCAACATATAGTGGACTTT 58.772 36.000 0.00 0.00 27.00 2.66
2782 6160 5.790593 ACGTGTTCAACATATAGTGGACTT 58.209 37.500 0.00 0.00 27.00 3.01
2783 6161 5.401531 ACGTGTTCAACATATAGTGGACT 57.598 39.130 0.00 0.00 27.00 3.85
2784 6162 6.237384 CGTTACGTGTTCAACATATAGTGGAC 60.237 42.308 0.00 0.00 27.00 4.02
2785 6163 5.801444 CGTTACGTGTTCAACATATAGTGGA 59.199 40.000 0.00 0.00 0.00 4.02
2786 6164 5.499652 GCGTTACGTGTTCAACATATAGTGG 60.500 44.000 6.63 0.00 0.00 4.00
2787 6165 5.061187 TGCGTTACGTGTTCAACATATAGTG 59.939 40.000 6.63 0.00 0.00 2.74
2788 6166 5.162794 TGCGTTACGTGTTCAACATATAGT 58.837 37.500 6.63 0.00 0.00 2.12
2789 6167 5.689927 TGCGTTACGTGTTCAACATATAG 57.310 39.130 6.63 0.00 0.00 1.31
2790 6168 5.443040 CGTTGCGTTACGTGTTCAACATATA 60.443 40.000 19.66 0.00 37.47 0.86
2791 6169 4.664640 CGTTGCGTTACGTGTTCAACATAT 60.665 41.667 19.66 0.00 37.47 1.78
2792 6170 3.361820 CGTTGCGTTACGTGTTCAACATA 60.362 43.478 19.66 0.00 37.47 2.29
2795 6173 1.368886 CGTTGCGTTACGTGTTCAAC 58.631 50.000 6.63 10.73 36.80 3.18
2827 6206 2.017559 GAATCTGGTCGTCCCGAGGG 62.018 65.000 0.65 0.65 36.23 4.30
2836 6215 3.978687 GGTACCACATAGAATCTGGTCG 58.021 50.000 7.15 0.00 39.16 4.79
2856 6235 1.962807 TGGATGCAACTTTGAACAGGG 59.037 47.619 0.00 0.00 0.00 4.45
2884 6263 7.202038 CCTTCCTATGACATATGTCTTCTTCCA 60.202 40.741 30.67 14.11 44.99 3.53
2898 6277 4.775253 TGTGTGTATGTCCTTCCTATGACA 59.225 41.667 0.00 0.00 44.86 3.58
3047 6426 1.322936 CTCGTTTTCAGCTCATCTCGC 59.677 52.381 0.00 0.00 0.00 5.03
3079 6458 1.210155 GCGGCAAAGCACCAAGTAG 59.790 57.895 0.00 0.00 37.05 2.57
3115 6494 7.502561 TCGATGATGGACGTGATTCCTATATAT 59.497 37.037 0.00 0.00 36.51 0.86
3116 6495 6.826741 TCGATGATGGACGTGATTCCTATATA 59.173 38.462 0.00 0.00 36.51 0.86
3117 6496 5.652452 TCGATGATGGACGTGATTCCTATAT 59.348 40.000 0.00 0.00 36.51 0.86
3118 6497 5.007682 TCGATGATGGACGTGATTCCTATA 58.992 41.667 0.00 0.00 36.51 1.31
3137 6516 4.158025 ACTCAACGAGTAGTTCCAATCGAT 59.842 41.667 0.00 0.00 41.51 3.59
3138 6517 3.504906 ACTCAACGAGTAGTTCCAATCGA 59.495 43.478 0.00 0.00 41.51 3.59
3139 6518 3.834610 ACTCAACGAGTAGTTCCAATCG 58.165 45.455 0.00 0.00 41.51 3.34
3140 6519 5.765072 GAACTCAACGAGTAGTTCCAATC 57.235 43.478 13.74 0.00 42.59 2.67
3146 6525 5.657474 TGAAACAGAACTCAACGAGTAGTT 58.343 37.500 0.00 0.00 42.59 2.24
3150 6529 3.809832 CCATGAAACAGAACTCAACGAGT 59.190 43.478 0.00 0.00 45.64 4.18
3153 6532 3.559655 TCACCATGAAACAGAACTCAACG 59.440 43.478 0.00 0.00 0.00 4.10
3180 6559 7.787904 TCCTTGTGTGGATATAGTACCATAGTT 59.212 37.037 0.00 0.00 38.48 2.24
3514 6893 3.119245 TGAGCTAGAAACGTACCACCATC 60.119 47.826 0.00 0.00 0.00 3.51
3515 6894 2.829720 TGAGCTAGAAACGTACCACCAT 59.170 45.455 0.00 0.00 0.00 3.55
3568 9475 2.126346 GTGACAAAGGCCATGCGC 60.126 61.111 5.01 0.00 0.00 6.09
3571 9478 0.452987 CCATCGTGACAAAGGCCATG 59.547 55.000 5.01 6.21 0.00 3.66
3594 9501 2.035632 AGCGGATGGATATAGCTAGCC 58.964 52.381 12.13 0.00 36.28 3.93
3595 9502 2.801342 GCAGCGGATGGATATAGCTAGC 60.801 54.545 6.62 6.62 36.28 3.42
3596 9503 2.223923 GGCAGCGGATGGATATAGCTAG 60.224 54.545 0.00 0.00 36.28 3.42
3597 9504 1.757118 GGCAGCGGATGGATATAGCTA 59.243 52.381 0.00 0.00 36.28 3.32
3618 9525 3.068165 GTGGAGTTTTGGAGGGTTTTCAG 59.932 47.826 0.00 0.00 0.00 3.02
3654 9561 1.740585 AGGACGAGATGAGAGTTGTCG 59.259 52.381 0.00 0.00 36.71 4.35
3658 9565 2.818751 AGGAGGACGAGATGAGAGTT 57.181 50.000 0.00 0.00 0.00 3.01
3665 9572 1.187087 GGTGTGAAGGAGGACGAGAT 58.813 55.000 0.00 0.00 0.00 2.75
3675 9582 1.380403 TTGCCACGTTGGTGTGAAGG 61.380 55.000 6.02 0.00 42.80 3.46
3676 9583 0.248458 GTTGCCACGTTGGTGTGAAG 60.248 55.000 6.02 0.00 42.80 3.02


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

AutoCloner maintained by Alex Coulton.