Multiple sequence alignment - TraesCS5D01G443500

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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 TraesCS5D01G443500 chr5D 100.000 3797 0 0 1 3797 494818676 494814880 0.000000e+00 7012.0
1 TraesCS5D01G443500 chr5B 92.113 2802 119 48 605 3349 611389233 611386477 0.000000e+00 3856.0
2 TraesCS5D01G443500 chr5B 87.805 410 32 12 3401 3797 611386367 611385963 7.430000e-127 464.0
3 TraesCS5D01G443500 chr5B 80.470 553 33 42 59 556 611389772 611389240 1.680000e-93 353.0
4 TraesCS5D01G443500 chr5A 90.163 2084 62 48 113 2122 618968909 618966895 0.000000e+00 2580.0
5 TraesCS5D01G443500 chr5A 94.177 1185 43 13 2186 3349 618966790 618965611 0.000000e+00 1783.0
6 TraesCS5D01G443500 chr5A 93.060 317 15 3 3401 3716 618965406 618965096 1.240000e-124 457.0
7 TraesCS5D01G443500 chr2B 85.149 101 13 2 3305 3405 144610144 144610046 6.710000e-18 102.0
8 TraesCS5D01G443500 chr2B 84.158 101 14 2 3305 3405 144610027 144610125 3.120000e-16 97.1
9 TraesCS5D01G443500 chr2B 83.036 112 11 6 3301 3405 93015988 93015878 1.120000e-15 95.3
10 TraesCS5D01G443500 chr3D 84.314 102 15 1 3305 3405 43024167 43024268 8.680000e-17 99.0
11 TraesCS5D01G443500 chr6A 81.600 125 14 7 3290 3406 924709 924586 1.120000e-15 95.3
12 TraesCS5D01G443500 chr3B 83.486 109 11 5 3304 3405 53573886 53573994 1.120000e-15 95.3
13 TraesCS5D01G443500 chr2A 83.636 110 9 7 3304 3405 700970212 700970104 1.120000e-15 95.3
14 TraesCS5D01G443500 chr7A 81.301 123 14 6 3290 3405 351612896 351612776 1.450000e-14 91.6
15 TraesCS5D01G443500 chr7A 81.897 116 13 6 3297 3405 409866211 409866097 1.450000e-14 91.6


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 TraesCS5D01G443500 chr5D 494814880 494818676 3796 True 7012.000000 7012 100.000000 1 3797 1 chr5D.!!$R1 3796
1 TraesCS5D01G443500 chr5B 611385963 611389772 3809 True 1557.666667 3856 86.796000 59 3797 3 chr5B.!!$R1 3738
2 TraesCS5D01G443500 chr5A 618965096 618968909 3813 True 1606.666667 2580 92.466667 113 3716 3 chr5A.!!$R1 3603

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
23 24 0.740737 GCGCACAAGGGAGCATAATT 59.259 50.0 0.3 0.0 0.00 1.40 F
695 769 0.742281 TTCAATCTGCTCCTGCTCGC 60.742 55.0 0.0 0.0 40.48 5.03 F
1629 1757 0.459899 GAATGAAACCATTCCCCGGC 59.540 55.0 0.0 0.0 42.40 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1243 1359 0.179073 CTCTTGGGTAGTGGCATCGG 60.179 60.0 0.00 0.0 0.0 4.18 R
1751 1883 0.878961 ACCGAGTCGTTCCAAGTTGC 60.879 55.0 12.31 0.0 0.0 4.17 R
2940 3166 0.099613 CACGACGGATCTGAGACTGG 59.900 60.0 9.00 0.0 0.0 4.00 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 2.511373 CGCGCACAAGGGAGCATA 60.511 61.111 8.75 0.00 0.00 3.14
21 22 2.106074 CGCGCACAAGGGAGCATAA 61.106 57.895 8.75 0.00 0.00 1.90
22 23 1.439353 CGCGCACAAGGGAGCATAAT 61.439 55.000 8.75 0.00 0.00 1.28
23 24 0.740737 GCGCACAAGGGAGCATAATT 59.259 50.000 0.30 0.00 0.00 1.40
24 25 1.534595 GCGCACAAGGGAGCATAATTG 60.535 52.381 0.30 0.00 0.00 2.32
25 26 1.745087 CGCACAAGGGAGCATAATTGT 59.255 47.619 0.00 0.00 36.34 2.71
26 27 2.942376 CGCACAAGGGAGCATAATTGTA 59.058 45.455 0.00 0.00 34.26 2.41
27 28 3.242739 CGCACAAGGGAGCATAATTGTAC 60.243 47.826 0.00 0.00 34.26 2.90
28 29 3.242739 GCACAAGGGAGCATAATTGTACG 60.243 47.826 0.00 0.00 34.26 3.67
29 30 3.938963 CACAAGGGAGCATAATTGTACGT 59.061 43.478 0.00 0.00 34.26 3.57
30 31 4.034048 CACAAGGGAGCATAATTGTACGTC 59.966 45.833 0.00 0.00 34.26 4.34
31 32 4.081087 ACAAGGGAGCATAATTGTACGTCT 60.081 41.667 0.00 0.00 34.26 4.18
32 33 4.323553 AGGGAGCATAATTGTACGTCTC 57.676 45.455 0.00 0.00 0.00 3.36
33 34 3.961408 AGGGAGCATAATTGTACGTCTCT 59.039 43.478 0.00 0.00 0.00 3.10
34 35 4.406003 AGGGAGCATAATTGTACGTCTCTT 59.594 41.667 0.00 0.00 0.00 2.85
35 36 4.508124 GGGAGCATAATTGTACGTCTCTTG 59.492 45.833 0.00 0.00 0.00 3.02
36 37 4.508124 GGAGCATAATTGTACGTCTCTTGG 59.492 45.833 0.00 0.00 0.00 3.61
37 38 5.339008 AGCATAATTGTACGTCTCTTGGA 57.661 39.130 0.00 0.00 0.00 3.53
38 39 5.730550 AGCATAATTGTACGTCTCTTGGAA 58.269 37.500 0.00 0.00 0.00 3.53
39 40 5.812642 AGCATAATTGTACGTCTCTTGGAAG 59.187 40.000 0.00 0.00 0.00 3.46
40 41 5.810587 GCATAATTGTACGTCTCTTGGAAGA 59.189 40.000 0.00 0.00 0.00 2.87
41 42 6.237861 GCATAATTGTACGTCTCTTGGAAGAC 60.238 42.308 0.00 0.00 41.88 3.01
42 43 4.866508 ATTGTACGTCTCTTGGAAGACA 57.133 40.909 0.00 0.00 44.88 3.41
43 44 4.866508 TTGTACGTCTCTTGGAAGACAT 57.133 40.909 0.00 0.00 44.88 3.06
44 45 5.970317 TTGTACGTCTCTTGGAAGACATA 57.030 39.130 0.00 0.00 44.88 2.29
45 46 5.970317 TGTACGTCTCTTGGAAGACATAA 57.030 39.130 0.00 0.00 44.88 1.90
46 47 5.706916 TGTACGTCTCTTGGAAGACATAAC 58.293 41.667 0.00 0.75 44.88 1.89
47 48 4.189639 ACGTCTCTTGGAAGACATAACC 57.810 45.455 5.04 0.00 44.88 2.85
48 49 3.833070 ACGTCTCTTGGAAGACATAACCT 59.167 43.478 5.04 0.00 44.88 3.50
49 50 4.283722 ACGTCTCTTGGAAGACATAACCTT 59.716 41.667 5.04 0.00 44.88 3.50
50 51 4.865365 CGTCTCTTGGAAGACATAACCTTC 59.135 45.833 5.04 0.00 44.88 3.46
51 52 5.566826 CGTCTCTTGGAAGACATAACCTTCA 60.567 44.000 0.00 0.00 44.88 3.02
52 53 6.231211 GTCTCTTGGAAGACATAACCTTCAA 58.769 40.000 0.00 0.00 44.20 2.69
53 54 6.370166 GTCTCTTGGAAGACATAACCTTCAAG 59.630 42.308 0.00 0.00 44.20 3.02
54 55 6.270000 TCTCTTGGAAGACATAACCTTCAAGA 59.730 38.462 0.00 0.00 41.22 3.02
55 56 7.020827 TCTTGGAAGACATAACCTTCAAGAT 57.979 36.000 0.00 0.00 41.22 2.40
56 57 7.461749 TCTTGGAAGACATAACCTTCAAGATT 58.538 34.615 0.00 0.00 41.22 2.40
57 58 7.607991 TCTTGGAAGACATAACCTTCAAGATTC 59.392 37.037 0.00 0.00 41.22 2.52
61 62 5.665459 AGACATAACCTTCAAGATTCCGAG 58.335 41.667 0.00 0.00 0.00 4.63
67 68 5.041191 ACCTTCAAGATTCCGAGCATAAT 57.959 39.130 0.00 0.00 0.00 1.28
78 79 6.371809 TTCCGAGCATAATTTTGTGGATAC 57.628 37.500 7.21 0.00 0.00 2.24
91 92 3.580658 GGATACAAAAGACGCGCAC 57.419 52.632 5.73 0.00 0.00 5.34
92 93 0.793861 GGATACAAAAGACGCGCACA 59.206 50.000 5.73 0.00 0.00 4.57
94 95 2.159572 GGATACAAAAGACGCGCACATT 60.160 45.455 5.73 0.00 0.00 2.71
95 96 3.062909 GGATACAAAAGACGCGCACATTA 59.937 43.478 5.73 0.00 0.00 1.90
96 97 4.260620 GGATACAAAAGACGCGCACATTAT 60.261 41.667 5.73 0.00 0.00 1.28
97 98 3.552604 ACAAAAGACGCGCACATTATT 57.447 38.095 5.73 0.00 0.00 1.40
98 99 4.671880 ACAAAAGACGCGCACATTATTA 57.328 36.364 5.73 0.00 0.00 0.98
100 101 5.636837 ACAAAAGACGCGCACATTATTATT 58.363 33.333 5.73 0.00 0.00 1.40
101 102 6.777101 ACAAAAGACGCGCACATTATTATTA 58.223 32.000 5.73 0.00 0.00 0.98
102 103 7.414436 ACAAAAGACGCGCACATTATTATTAT 58.586 30.769 5.73 0.00 0.00 1.28
104 105 8.742188 CAAAAGACGCGCACATTATTATTATTT 58.258 29.630 5.73 0.00 0.00 1.40
105 106 8.850454 AAAGACGCGCACATTATTATTATTTT 57.150 26.923 5.73 0.00 0.00 1.82
106 107 8.850454 AAGACGCGCACATTATTATTATTTTT 57.150 26.923 5.73 0.00 0.00 1.94
132 134 8.587952 TGACGGTAATCATCAAATACATACAG 57.412 34.615 0.00 0.00 0.00 2.74
314 336 2.262915 CTCCACAGACCAGTCCGC 59.737 66.667 0.00 0.00 0.00 5.54
316 338 3.314331 CCACAGACCAGTCCGCCT 61.314 66.667 0.00 0.00 0.00 5.52
317 339 2.262915 CACAGACCAGTCCGCCTC 59.737 66.667 0.00 0.00 0.00 4.70
319 341 4.135153 CAGACCAGTCCGCCTCCG 62.135 72.222 0.00 0.00 0.00 4.63
320 342 4.680537 AGACCAGTCCGCCTCCGT 62.681 66.667 0.00 0.00 0.00 4.69
332 354 4.569023 CTCCGTCCGCATGCGCTA 62.569 66.667 34.00 21.06 38.24 4.26
333 355 4.569023 TCCGTCCGCATGCGCTAG 62.569 66.667 34.00 23.90 38.24 3.42
376 398 2.742372 AGCCGATTCACGCACACC 60.742 61.111 0.00 0.00 41.07 4.16
470 501 3.192466 GCAAGTTGGATGCATTTGATCC 58.808 45.455 11.37 4.43 43.29 3.36
471 502 3.788937 CAAGTTGGATGCATTTGATCCC 58.211 45.455 0.00 0.00 39.01 3.85
472 503 2.391678 AGTTGGATGCATTTGATCCCC 58.608 47.619 0.00 0.00 39.01 4.81
473 504 1.413812 GTTGGATGCATTTGATCCCCC 59.586 52.381 0.00 0.00 39.01 5.40
499 549 2.224769 CCTGTGGGGTAGCAAGAAGAAA 60.225 50.000 0.00 0.00 0.00 2.52
510 563 7.494298 GGGTAGCAAGAAGAAATAGAAGAAGAG 59.506 40.741 0.00 0.00 0.00 2.85
567 626 1.814634 GCTGGCTGGATTCCTCATCTG 60.815 57.143 3.95 0.00 31.67 2.90
570 629 1.133853 GGCTGGATTCCTCATCTGCTT 60.134 52.381 3.95 0.00 34.17 3.91
575 641 2.224499 GGATTCCTCATCTGCTTCTCCC 60.224 54.545 0.00 0.00 31.67 4.30
578 644 1.836166 TCCTCATCTGCTTCTCCCTTG 59.164 52.381 0.00 0.00 0.00 3.61
587 653 1.815613 GCTTCTCCCTTGCTTTCCTTC 59.184 52.381 0.00 0.00 0.00 3.46
633 699 3.707640 CTCGCGTCCTCCCTCCTCT 62.708 68.421 5.77 0.00 0.00 3.69
694 768 1.865970 GATTCAATCTGCTCCTGCTCG 59.134 52.381 0.00 0.00 40.48 5.03
695 769 0.742281 TTCAATCTGCTCCTGCTCGC 60.742 55.000 0.00 0.00 40.48 5.03
697 771 3.397613 AATCTGCTCCTGCTCGCCC 62.398 63.158 0.00 0.00 40.48 6.13
751 842 2.710826 GCCTCCCTCCTCCTCCTCT 61.711 68.421 0.00 0.00 0.00 3.69
753 844 1.541672 CTCCCTCCTCCTCCTCTCC 59.458 68.421 0.00 0.00 0.00 3.71
754 845 0.998945 CTCCCTCCTCCTCCTCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
755 846 0.996762 TCCCTCCTCCTCCTCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
756 847 1.150536 CCTCCTCCTCCTCTCCTCG 59.849 68.421 0.00 0.00 0.00 4.63
757 848 1.528309 CTCCTCCTCCTCTCCTCGC 60.528 68.421 0.00 0.00 0.00 5.03
758 849 2.904866 CCTCCTCCTCTCCTCGCG 60.905 72.222 0.00 0.00 0.00 5.87
759 850 3.591835 CTCCTCCTCTCCTCGCGC 61.592 72.222 0.00 0.00 0.00 6.86
785 876 1.218047 CGGTTCTTGATCCGCTCCA 59.782 57.895 7.12 0.00 40.28 3.86
1053 1163 2.511452 CCCCCTCTGCTACATCCCG 61.511 68.421 0.00 0.00 0.00 5.14
1143 1253 4.070552 GTCGAGGACAAGCCGCCT 62.071 66.667 0.00 0.00 43.43 5.52
1156 1266 2.286523 CCGCCTCAGGTCCAGAAGT 61.287 63.158 0.00 0.00 0.00 3.01
1163 1273 1.072331 TCAGGTCCAGAAGTTTGAGGC 59.928 52.381 0.00 0.00 0.00 4.70
1629 1757 0.459899 GAATGAAACCATTCCCCGGC 59.540 55.000 0.00 0.00 42.40 6.13
1695 1823 5.049167 TCTCACATTGCATTGTTTTGTTCC 58.951 37.500 11.43 0.00 0.00 3.62
1810 1942 7.340487 TCGGACACGTATAGATAGATAGGTCTA 59.660 40.741 0.00 0.00 40.09 2.59
1811 1943 8.143193 CGGACACGTATAGATAGATAGGTCTAT 58.857 40.741 0.00 0.00 41.40 1.98
1900 2032 2.896685 GGGGAGTAGATGACAGGATCAG 59.103 54.545 0.00 0.00 41.91 2.90
1928 2065 8.500753 TTATACATGTGTTGGACTTGGTATTC 57.499 34.615 9.11 0.00 34.66 1.75
1950 2087 4.512198 TCAAGCGAGTTTTGTTTATTCCGA 59.488 37.500 0.00 0.00 0.00 4.55
2083 2220 1.598701 GGGCATGCTTTCCACCTGTC 61.599 60.000 18.92 0.00 0.00 3.51
2098 2235 7.350744 TCCACCTGTCTATAATAGCGTAAAA 57.649 36.000 0.00 0.00 0.00 1.52
2125 2315 7.458397 TGTATGGTCAATAACTTTGGAGTCTT 58.542 34.615 0.00 0.00 34.21 3.01
2154 2352 4.157656 TGATCAAAAAGTAATTCTGGGGCG 59.842 41.667 0.00 0.00 0.00 6.13
2176 2374 9.322773 GGGCGATACCTATTTTATTTATACTCC 57.677 37.037 0.00 0.00 39.10 3.85
2233 2431 3.873952 GAGCCACATGATTTCAGTAGTCC 59.126 47.826 0.00 0.00 0.00 3.85
2262 2462 9.300681 TCTGTTTTAAGAGGATTGAAATGACAT 57.699 29.630 0.00 0.00 0.00 3.06
2272 2472 2.897436 TGAAATGACATCAGCTCTCCG 58.103 47.619 0.00 0.00 0.00 4.63
2279 2479 1.288350 CATCAGCTCTCCGCAGAAAG 58.712 55.000 0.00 0.00 42.61 2.62
2280 2480 0.177604 ATCAGCTCTCCGCAGAAAGG 59.822 55.000 0.00 0.00 42.61 3.11
2282 2482 0.321122 CAGCTCTCCGCAGAAAGGTT 60.321 55.000 0.00 0.00 42.61 3.50
2300 2500 6.500684 AAGGTTTAGTGTAGCATTGTCATG 57.499 37.500 0.00 0.00 0.00 3.07
2375 2580 6.260493 CACTGGTCATCACTACTACTACTACC 59.740 46.154 0.00 0.00 0.00 3.18
2483 2697 9.774742 CTAATAAAAAGTGCTTCATGGAACTAC 57.225 33.333 0.00 0.00 0.00 2.73
2498 2712 7.660208 TCATGGAACTACATCATGATGATTCAG 59.340 37.037 36.37 26.67 41.31 3.02
2501 2715 8.215736 TGGAACTACATCATGATGATTCAGAAT 58.784 33.333 36.37 17.34 41.20 2.40
2668 2884 9.703892 GTAGAGATATTATGCTTGTTCTCATGT 57.296 33.333 0.00 0.00 33.65 3.21
2676 2892 2.082231 CTTGTTCTCATGTCTGGCTGG 58.918 52.381 0.00 0.00 0.00 4.85
2678 2894 1.271001 TGTTCTCATGTCTGGCTGGTG 60.271 52.381 0.00 0.00 0.00 4.17
2679 2895 1.059098 TTCTCATGTCTGGCTGGTGT 58.941 50.000 0.00 0.00 0.00 4.16
2692 2908 1.338020 GCTGGTGTTTGACTTCCTTGG 59.662 52.381 0.00 0.00 0.00 3.61
2699 2915 2.884639 GTTTGACTTCCTTGGCTGCTTA 59.115 45.455 0.00 0.00 0.00 3.09
2940 3166 3.724374 GGGGGTTTTCTGCTGTTTTTAC 58.276 45.455 0.00 0.00 0.00 2.01
3019 3246 2.668457 CTGGAGTTGATACAGTGCGTTC 59.332 50.000 0.00 0.00 34.81 3.95
3072 3299 3.309296 TCAGGGTTGAGACTTGAGAGTT 58.691 45.455 0.00 0.00 35.88 3.01
3225 3459 2.505819 ACATGGGGATGTAGTGACCTTC 59.494 50.000 0.00 0.00 32.14 3.46
3319 3556 4.881019 AAATGATACTCCCTCTGATCCG 57.119 45.455 0.00 0.00 0.00 4.18
3349 3586 6.313905 ACTTGTTTCAGATTTGCCTAGATACG 59.686 38.462 0.00 0.00 0.00 3.06
3367 3710 9.723447 CTAGATACGGCTATATCTAAATGTGTG 57.277 37.037 14.48 3.18 41.48 3.82
3386 3729 7.586714 TGTGTGTATATACGTCCGTATCTAG 57.413 40.000 14.98 0.00 41.12 2.43
3388 3731 7.329471 TGTGTGTATATACGTCCGTATCTAGAC 59.671 40.741 14.98 16.70 41.12 2.59
3393 3736 9.913451 GTATATACGTCCGTATCTAGACAAATC 57.087 37.037 14.98 0.00 41.12 2.17
3397 3740 6.957150 ACGTCCGTATCTAGACAAATCTAAG 58.043 40.000 0.00 0.00 36.98 2.18
3398 3741 6.765036 ACGTCCGTATCTAGACAAATCTAAGA 59.235 38.462 0.00 0.00 36.98 2.10
3402 3745 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
3403 3746 8.407064 CCGTATCTAGACAAATCTAAGACAAGT 58.593 37.037 0.00 0.00 36.98 3.16
3442 3834 2.757868 TGTCCAAAACCAACCTTGACAG 59.242 45.455 0.00 0.00 0.00 3.51
3506 3899 8.840833 TTGGTTTATAGCCAAAATTTTCTTCC 57.159 30.769 0.00 0.00 42.39 3.46
3507 3900 8.201242 TGGTTTATAGCCAAAATTTTCTTCCT 57.799 30.769 0.00 0.00 32.29 3.36
3508 3901 8.655901 TGGTTTATAGCCAAAATTTTCTTCCTT 58.344 29.630 0.00 0.00 32.29 3.36
3527 3920 3.496515 CCTTGTTTGGATGGTTGGCAAAT 60.497 43.478 0.00 0.00 0.00 2.32
3584 3978 2.110967 CCTGCAGACATTGGCCGAG 61.111 63.158 17.39 0.00 0.00 4.63
3636 4030 1.493022 AGGCCAGCCGAATATTTGGTA 59.507 47.619 20.81 0.00 41.95 3.25
3651 4045 0.887387 TGGTAGTGCGAACTTTGGCC 60.887 55.000 0.00 0.00 0.00 5.36
3663 4057 3.092851 TTTGGCCCAAAGCAAAAGC 57.907 47.368 4.38 0.00 39.59 3.51
3707 4107 1.958288 ATCAGGCCAGGTACAAGAGT 58.042 50.000 5.01 0.00 0.00 3.24
3717 4117 2.904434 AGGTACAAGAGTAACCACCCAG 59.096 50.000 0.00 0.00 38.76 4.45
3718 4118 2.614734 GGTACAAGAGTAACCACCCAGC 60.615 54.545 0.00 0.00 31.53 4.85
3719 4119 1.136828 ACAAGAGTAACCACCCAGCA 58.863 50.000 0.00 0.00 0.00 4.41
3720 4120 1.202770 ACAAGAGTAACCACCCAGCAC 60.203 52.381 0.00 0.00 0.00 4.40
3721 4121 1.072331 CAAGAGTAACCACCCAGCACT 59.928 52.381 0.00 0.00 0.00 4.40
3722 4122 0.687354 AGAGTAACCACCCAGCACTG 59.313 55.000 0.00 0.00 0.00 3.66
3742 4144 8.850156 AGCACTGAAACAAAACTTATTACTCAT 58.150 29.630 0.00 0.00 0.00 2.90
3756 4160 7.512746 ACTTATTACTCATATTACAGCAGGGGA 59.487 37.037 0.00 0.00 0.00 4.81
3759 4163 4.781934 ACTCATATTACAGCAGGGGAAAC 58.218 43.478 0.00 0.00 0.00 2.78
3763 4167 1.975660 TTACAGCAGGGGAAACACAC 58.024 50.000 0.00 0.00 34.58 3.82
3768 4172 2.293399 CAGCAGGGGAAACACACTAAAC 59.707 50.000 0.00 0.00 34.58 2.01
3770 4174 2.751816 GCAGGGGAAACACACTAAACCT 60.752 50.000 0.00 0.00 34.58 3.50
3773 4177 1.611977 GGGAAACACACTAAACCTGCC 59.388 52.381 0.00 0.00 0.00 4.85
3793 4197 3.732892 CCGCACCGTTCGCCAATT 61.733 61.111 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.439353 ATTATGCTCCCTTGTGCGCG 61.439 55.000 0.00 0.00 33.71 6.86
4 5 0.740737 AATTATGCTCCCTTGTGCGC 59.259 50.000 0.00 0.00 33.71 6.09
5 6 1.745087 ACAATTATGCTCCCTTGTGCG 59.255 47.619 0.00 0.00 33.71 5.34
6 7 3.242739 CGTACAATTATGCTCCCTTGTGC 60.243 47.826 0.00 0.00 34.02 4.57
7 8 3.938963 ACGTACAATTATGCTCCCTTGTG 59.061 43.478 0.00 0.00 34.02 3.33
8 9 4.081087 AGACGTACAATTATGCTCCCTTGT 60.081 41.667 0.00 0.00 36.00 3.16
9 10 4.442706 AGACGTACAATTATGCTCCCTTG 58.557 43.478 0.00 0.00 0.00 3.61
10 11 4.406003 AGAGACGTACAATTATGCTCCCTT 59.594 41.667 0.00 0.00 0.00 3.95
11 12 3.961408 AGAGACGTACAATTATGCTCCCT 59.039 43.478 0.00 0.00 0.00 4.20
12 13 4.323553 AGAGACGTACAATTATGCTCCC 57.676 45.455 0.00 0.00 0.00 4.30
13 14 4.508124 CCAAGAGACGTACAATTATGCTCC 59.492 45.833 0.00 0.00 0.00 4.70
14 15 5.348986 TCCAAGAGACGTACAATTATGCTC 58.651 41.667 0.00 0.00 0.00 4.26
15 16 5.339008 TCCAAGAGACGTACAATTATGCT 57.661 39.130 0.00 0.00 0.00 3.79
16 17 5.810587 TCTTCCAAGAGACGTACAATTATGC 59.189 40.000 0.00 0.00 0.00 3.14
17 18 7.223058 GTCTTCCAAGAGACGTACAATTATG 57.777 40.000 0.00 0.00 36.97 1.90
28 29 5.794894 TGAAGGTTATGTCTTCCAAGAGAC 58.205 41.667 0.00 0.00 44.97 3.36
29 30 6.270000 TCTTGAAGGTTATGTCTTCCAAGAGA 59.730 38.462 0.00 0.00 39.72 3.10
30 31 6.467677 TCTTGAAGGTTATGTCTTCCAAGAG 58.532 40.000 0.00 0.00 39.72 2.85
31 32 6.433847 TCTTGAAGGTTATGTCTTCCAAGA 57.566 37.500 0.00 0.00 39.72 3.02
32 33 7.148171 GGAATCTTGAAGGTTATGTCTTCCAAG 60.148 40.741 0.00 0.00 39.72 3.61
33 34 6.659242 GGAATCTTGAAGGTTATGTCTTCCAA 59.341 38.462 0.00 0.00 39.72 3.53
34 35 6.180472 GGAATCTTGAAGGTTATGTCTTCCA 58.820 40.000 0.00 0.00 39.72 3.53
35 36 5.294552 CGGAATCTTGAAGGTTATGTCTTCC 59.705 44.000 0.00 0.00 39.72 3.46
36 37 6.106673 TCGGAATCTTGAAGGTTATGTCTTC 58.893 40.000 0.00 0.00 40.57 2.87
37 38 6.049955 TCGGAATCTTGAAGGTTATGTCTT 57.950 37.500 0.00 0.00 0.00 3.01
38 39 5.665459 CTCGGAATCTTGAAGGTTATGTCT 58.335 41.667 0.00 0.00 0.00 3.41
39 40 4.271291 GCTCGGAATCTTGAAGGTTATGTC 59.729 45.833 0.00 0.00 0.00 3.06
40 41 4.192317 GCTCGGAATCTTGAAGGTTATGT 58.808 43.478 0.00 0.00 0.00 2.29
41 42 4.191544 TGCTCGGAATCTTGAAGGTTATG 58.808 43.478 0.00 0.00 0.00 1.90
42 43 4.487714 TGCTCGGAATCTTGAAGGTTAT 57.512 40.909 0.00 0.00 0.00 1.89
43 44 3.973206 TGCTCGGAATCTTGAAGGTTA 57.027 42.857 0.00 0.00 0.00 2.85
44 45 2.859165 TGCTCGGAATCTTGAAGGTT 57.141 45.000 0.00 0.00 0.00 3.50
45 46 4.487714 TTATGCTCGGAATCTTGAAGGT 57.512 40.909 0.00 0.00 0.00 3.50
46 47 6.382869 AAATTATGCTCGGAATCTTGAAGG 57.617 37.500 0.00 0.00 0.00 3.46
47 48 7.219535 CACAAAATTATGCTCGGAATCTTGAAG 59.780 37.037 0.00 0.00 0.00 3.02
48 49 7.028962 CACAAAATTATGCTCGGAATCTTGAA 58.971 34.615 0.00 0.00 0.00 2.69
49 50 6.404623 CCACAAAATTATGCTCGGAATCTTGA 60.405 38.462 0.00 0.00 0.00 3.02
50 51 5.745294 CCACAAAATTATGCTCGGAATCTTG 59.255 40.000 0.00 0.00 0.00 3.02
51 52 5.652014 TCCACAAAATTATGCTCGGAATCTT 59.348 36.000 0.00 0.00 0.00 2.40
52 53 5.192927 TCCACAAAATTATGCTCGGAATCT 58.807 37.500 0.00 0.00 0.00 2.40
53 54 5.499139 TCCACAAAATTATGCTCGGAATC 57.501 39.130 0.00 0.00 0.00 2.52
54 55 6.545666 TGTATCCACAAAATTATGCTCGGAAT 59.454 34.615 0.00 0.00 0.00 3.01
55 56 5.883115 TGTATCCACAAAATTATGCTCGGAA 59.117 36.000 0.00 0.00 0.00 4.30
56 57 5.432645 TGTATCCACAAAATTATGCTCGGA 58.567 37.500 0.00 0.00 0.00 4.55
57 58 5.749596 TGTATCCACAAAATTATGCTCGG 57.250 39.130 0.00 0.00 0.00 4.63
78 79 7.836358 ATAATAATAATGTGCGCGTCTTTTG 57.164 32.000 8.43 0.00 0.00 2.44
106 107 8.950208 TGTATGTATTTGATGATTACCGTCAA 57.050 30.769 0.00 0.00 46.07 3.18
107 108 8.201464 ACTGTATGTATTTGATGATTACCGTCA 58.799 33.333 0.00 0.00 38.94 4.35
111 112 9.935682 CAACACTGTATGTATTTGATGATTACC 57.064 33.333 0.00 0.00 42.31 2.85
125 126 6.910433 GTCATTTCGTTTTCAACACTGTATGT 59.090 34.615 0.00 0.00 46.42 2.29
126 127 6.909895 TGTCATTTCGTTTTCAACACTGTATG 59.090 34.615 0.00 0.00 0.00 2.39
128 129 6.424176 TGTCATTTCGTTTTCAACACTGTA 57.576 33.333 0.00 0.00 0.00 2.74
132 134 5.895889 GCAATTGTCATTTCGTTTTCAACAC 59.104 36.000 7.40 0.00 0.00 3.32
335 357 2.224621 AGCCAATGATGGATTACCGGAG 60.225 50.000 9.46 0.00 44.90 4.63
499 549 5.598417 GCCTCTTCTTCTCCTCTTCTTCTAT 59.402 44.000 0.00 0.00 0.00 1.98
510 563 1.153469 CGGCAGCCTCTTCTTCTCC 60.153 63.158 10.54 0.00 0.00 3.71
567 626 1.815613 GAAGGAAAGCAAGGGAGAAGC 59.184 52.381 0.00 0.00 0.00 3.86
570 629 3.935993 CGAAGGAAAGCAAGGGAGA 57.064 52.632 0.00 0.00 0.00 3.71
603 669 3.827898 CGCGAGGTGGGTCTCTCC 61.828 72.222 0.00 0.00 0.00 3.71
697 771 4.222847 GGAGTAAGGGAGCGGCGG 62.223 72.222 9.78 0.00 0.00 6.13
760 851 3.083600 GATCAAGAACCGCCGCACG 62.084 63.158 0.00 0.00 43.15 5.34
761 852 2.750888 GGATCAAGAACCGCCGCAC 61.751 63.158 0.00 0.00 0.00 5.34
762 853 2.435938 GGATCAAGAACCGCCGCA 60.436 61.111 0.00 0.00 0.00 5.69
819 916 2.115266 CAACCTTTGGCCGGACCT 59.885 61.111 3.83 0.00 40.22 3.85
1053 1163 0.897621 CTTTGGATTTGGGGAGGCAC 59.102 55.000 0.00 0.00 0.00 5.01
1143 1253 1.072331 GCCTCAAACTTCTGGACCTGA 59.928 52.381 0.00 0.00 0.00 3.86
1240 1356 4.910585 GGGTAGTGGCATCGGCGG 62.911 72.222 7.21 0.00 42.47 6.13
1243 1359 0.179073 CTCTTGGGTAGTGGCATCGG 60.179 60.000 0.00 0.00 0.00 4.18
1245 1361 0.253044 TGCTCTTGGGTAGTGGCATC 59.747 55.000 0.00 0.00 32.24 3.91
1246 1362 0.698238 TTGCTCTTGGGTAGTGGCAT 59.302 50.000 0.00 0.00 35.19 4.40
1642 1770 9.334947 CATTGAAGATAGATTAAGGAAAGCAGA 57.665 33.333 0.00 0.00 0.00 4.26
1695 1823 6.640499 CGTATCAAGAAGCAGATTTCTAGGAG 59.360 42.308 0.00 0.00 36.42 3.69
1751 1883 0.878961 ACCGAGTCGTTCCAAGTTGC 60.879 55.000 12.31 0.00 0.00 4.17
1827 1959 3.304911 TCAGAAGGATGTCTCTCGGAT 57.695 47.619 0.00 0.00 0.00 4.18
1900 2032 5.183140 ACCAAGTCCAACACATGTATAAAGC 59.817 40.000 0.00 0.00 0.00 3.51
1928 2065 4.778904 TCGGAATAAACAAAACTCGCTTG 58.221 39.130 0.00 0.00 0.00 4.01
2098 2235 8.109634 AGACTCCAAAGTTATTGACCATACAAT 58.890 33.333 0.00 0.00 38.67 2.71
2125 2315 9.762933 CCCAGAATTACTTTTTGATCAGAAAAA 57.237 29.630 12.05 8.59 34.44 1.94
2205 2403 4.083110 ACTGAAATCATGTGGCTCGAAAAG 60.083 41.667 0.00 0.00 0.00 2.27
2272 2472 5.048713 ACAATGCTACACTAAACCTTTCTGC 60.049 40.000 0.00 0.00 0.00 4.26
2279 2479 4.700213 ACCATGACAATGCTACACTAAACC 59.300 41.667 0.00 0.00 31.93 3.27
2280 2480 5.643777 AGACCATGACAATGCTACACTAAAC 59.356 40.000 0.00 0.00 31.93 2.01
2282 2482 5.046663 TGAGACCATGACAATGCTACACTAA 60.047 40.000 0.00 0.00 31.93 2.24
2300 2500 4.220821 TGTTGACAAGGAGTCTATGAGACC 59.779 45.833 3.00 0.00 46.18 3.85
2347 2552 6.768861 AGTAGTAGTAGTGATGACCAGTGATC 59.231 42.308 0.00 0.00 0.00 2.92
2375 2580 4.488126 TGAGGAATTTTCTTGTTGCGAG 57.512 40.909 0.00 0.00 0.00 5.03
2467 2681 4.877823 TCATGATGTAGTTCCATGAAGCAC 59.122 41.667 0.00 0.00 42.33 4.40
2483 2697 7.862873 CCACTCAAATTCTGAATCATCATGATG 59.137 37.037 26.79 26.79 37.15 3.07
2498 2712 5.841957 ATAGGAACATGCCACTCAAATTC 57.158 39.130 0.00 0.00 0.00 2.17
2501 2715 5.048083 GTGAAATAGGAACATGCCACTCAAA 60.048 40.000 0.00 0.00 0.00 2.69
2668 2884 1.476833 GGAAGTCAAACACCAGCCAGA 60.477 52.381 0.00 0.00 0.00 3.86
2676 2892 1.269257 GCAGCCAAGGAAGTCAAACAC 60.269 52.381 0.00 0.00 0.00 3.32
2678 2894 1.322442 AGCAGCCAAGGAAGTCAAAC 58.678 50.000 0.00 0.00 0.00 2.93
2679 2895 2.071778 AAGCAGCCAAGGAAGTCAAA 57.928 45.000 0.00 0.00 0.00 2.69
2692 2908 5.853282 CACACTGTGAGTTTAATTAAGCAGC 59.147 40.000 15.86 6.45 35.23 5.25
2699 2915 5.930135 AGGAGACACACTGTGAGTTTAATT 58.070 37.500 16.30 0.00 36.96 1.40
2940 3166 0.099613 CACGACGGATCTGAGACTGG 59.900 60.000 9.00 0.00 0.00 4.00
3072 3299 6.547880 TGTATTGGGAACTTTACAGAAGCAAA 59.452 34.615 0.00 0.00 0.00 3.68
3313 3550 8.664798 CAAATCTGAAACAAGTAATACGGATCA 58.335 33.333 0.00 0.00 0.00 2.92
3319 3556 9.162764 TCTAGGCAAATCTGAAACAAGTAATAC 57.837 33.333 0.00 0.00 0.00 1.89
3353 3590 9.999009 CGGACGTATATACACACATTTAGATAT 57.001 33.333 13.22 0.00 0.00 1.63
3367 3710 9.913451 GATTTGTCTAGATACGGACGTATATAC 57.087 37.037 16.35 10.41 40.93 1.47
3370 3713 9.710900 TTAGATTTGTCTAGATACGGACGTATA 57.289 33.333 16.35 2.73 40.93 1.47
3371 3714 8.613060 TTAGATTTGTCTAGATACGGACGTAT 57.387 34.615 16.33 16.33 43.24 3.06
3375 3718 7.928103 TGTCTTAGATTTGTCTAGATACGGAC 58.072 38.462 0.00 0.00 0.00 4.79
3386 3729 8.258708 ACATACCCTACTTGTCTTAGATTTGTC 58.741 37.037 0.00 0.00 0.00 3.18
3388 3731 9.449719 AAACATACCCTACTTGTCTTAGATTTG 57.550 33.333 0.00 0.00 0.00 2.32
3393 3736 5.585047 GCCAAACATACCCTACTTGTCTTAG 59.415 44.000 0.00 0.00 0.00 2.18
3397 3740 3.951663 AGCCAAACATACCCTACTTGTC 58.048 45.455 0.00 0.00 0.00 3.18
3398 3741 4.079253 CAAGCCAAACATACCCTACTTGT 58.921 43.478 0.00 0.00 0.00 3.16
3402 3745 3.418047 ACACAAGCCAAACATACCCTAC 58.582 45.455 0.00 0.00 0.00 3.18
3403 3746 3.560453 GGACACAAGCCAAACATACCCTA 60.560 47.826 0.00 0.00 0.00 3.53
3442 3834 9.549078 TTCCCATACAAAATGGAACTTTTAAAC 57.451 29.630 5.59 0.00 41.64 2.01
3505 3898 1.047002 TGCCAACCATCCAAACAAGG 58.953 50.000 0.00 0.00 0.00 3.61
3506 3899 2.906691 TTGCCAACCATCCAAACAAG 57.093 45.000 0.00 0.00 0.00 3.16
3507 3900 3.853355 ATTTGCCAACCATCCAAACAA 57.147 38.095 0.00 0.00 32.02 2.83
3508 3901 3.853355 AATTTGCCAACCATCCAAACA 57.147 38.095 0.00 0.00 32.02 2.83
3527 3920 1.964552 CAAGGTTGGCATGGCAAAAA 58.035 45.000 33.36 12.26 0.00 1.94
3584 3978 5.106515 GGATAAGGTTCTGCTTTTCTGTCAC 60.107 44.000 0.00 0.00 0.00 3.67
3636 4030 1.040339 TTTGGGCCAAAGTTCGCACT 61.040 50.000 27.28 0.00 33.11 4.40
3707 4107 1.213182 TGTTTCAGTGCTGGGTGGTTA 59.787 47.619 0.00 0.00 0.00 2.85
3742 4144 3.329520 AGTGTGTTTCCCCTGCTGTAATA 59.670 43.478 0.00 0.00 0.00 0.98
3745 4147 1.136828 AGTGTGTTTCCCCTGCTGTA 58.863 50.000 0.00 0.00 0.00 2.74
3746 4148 1.136828 TAGTGTGTTTCCCCTGCTGT 58.863 50.000 0.00 0.00 0.00 4.40
3747 4149 2.270352 TTAGTGTGTTTCCCCTGCTG 57.730 50.000 0.00 0.00 0.00 4.41
3748 4150 2.583143 GTTTAGTGTGTTTCCCCTGCT 58.417 47.619 0.00 0.00 0.00 4.24
3749 4151 1.611977 GGTTTAGTGTGTTTCCCCTGC 59.388 52.381 0.00 0.00 0.00 4.85
3756 4160 1.681264 GCTGGCAGGTTTAGTGTGTTT 59.319 47.619 17.64 0.00 0.00 2.83
3759 4163 1.577328 CGGCTGGCAGGTTTAGTGTG 61.577 60.000 17.64 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.