Multiple sequence alignment - TraesCS3A01G103100

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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 TraesCS3A01G103100 chr3A 100.000 2780 0 0 1 2780 66906856 66909635 0.000000e+00 5134.0
1 TraesCS3A01G103100 chr3A 71.522 460 118 10 1112 1564 464319833 464320286 8.140000e-21 111.0
2 TraesCS3A01G103100 chr3D 90.494 2472 136 45 96 2508 58079759 58082190 0.000000e+00 3171.0
3 TraesCS3A01G103100 chr3D 71.150 461 118 12 1112 1564 340415726 340415273 1.760000e-17 100.0
4 TraesCS3A01G103100 chr3B 91.402 1384 59 24 866 2214 90858107 90859465 0.000000e+00 1842.0
5 TraesCS3A01G103100 chr3B 88.047 686 62 13 1932 2614 90934066 90934734 0.000000e+00 795.0
6 TraesCS3A01G103100 chr3B 90.865 416 30 7 2200 2614 90860002 90860410 4.050000e-153 551.0
7 TraesCS3A01G103100 chr3B 90.146 274 7 9 530 788 90857593 90857861 3.430000e-89 339.0
8 TraesCS3A01G103100 chr3B 92.157 204 9 2 329 531 90857313 90857510 5.860000e-72 281.0
9 TraesCS3A01G103100 chr3B 86.264 182 9 6 2615 2780 90860455 90860636 1.700000e-42 183.0
10 TraesCS3A01G103100 chr3B 83.237 173 20 7 2615 2780 90934788 90934958 1.720000e-32 150.0
11 TraesCS3A01G103100 chr3B 71.304 460 119 10 1112 1564 439333732 439333279 3.790000e-19 106.0
12 TraesCS3A01G103100 chr5D 77.660 188 38 3 2056 2242 5567144 5566960 8.140000e-21 111.0
13 TraesCS3A01G103100 chrUn 74.627 268 55 10 2031 2291 103547392 103547131 3.790000e-19 106.0
14 TraesCS3A01G103100 chr7B 80.537 149 20 7 2116 2261 719159074 719158932 3.790000e-19 106.0
15 TraesCS3A01G103100 chr6A 75.845 207 38 10 2074 2275 607948633 607948434 8.200000e-16 95.3
16 TraesCS3A01G103100 chr5A 75.258 194 43 5 2070 2261 558239449 558239259 1.370000e-13 87.9
17 TraesCS3A01G103100 chr2D 74.634 205 41 9 2069 2269 13121617 13121814 2.300000e-11 80.5
18 TraesCS3A01G103100 chr6D 93.478 46 1 2 2230 2275 34538805 34538762 1.790000e-07 67.6
19 TraesCS3A01G103100 chr5B 100.000 31 0 0 2231 2261 563356870 563356840 1.080000e-04 58.4


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 TraesCS3A01G103100 chr3A 66906856 66909635 2779 False 5134.0 5134 100.0000 1 2780 1 chr3A.!!$F1 2779
1 TraesCS3A01G103100 chr3D 58079759 58082190 2431 False 3171.0 3171 90.4940 96 2508 1 chr3D.!!$F1 2412
2 TraesCS3A01G103100 chr3B 90857313 90860636 3323 False 639.2 1842 90.1668 329 2780 5 chr3B.!!$F1 2451
3 TraesCS3A01G103100 chr3B 90934066 90934958 892 False 472.5 795 85.6420 1932 2780 2 chr3B.!!$F2 848

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
63 64 0.102300 TCGTGGCGGTATGACATCAG 59.898 55.0 0.00 0.00 38.42 2.90 F
291 309 0.103572 ATGGATTTCCGCTTGCATGC 59.896 50.0 11.82 11.82 39.43 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1308 1627 0.734253 CGTTCTTCTGGCTGTCGGAG 60.734 60.0 0.00 0.0 31.44 4.63 R
2182 2515 0.597072 AGGAGACGTTCTTGTCGACC 59.403 55.0 14.12 0.0 43.70 4.79 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
25 26 7.874940 AGGTTACACTAAATTTTAACGAACCC 58.125 34.615 15.11 2.39 34.45 4.11
26 27 7.040478 AGGTTACACTAAATTTTAACGAACCCC 60.040 37.037 15.11 1.34 34.45 4.95
27 28 7.040478 GGTTACACTAAATTTTAACGAACCCCT 60.040 37.037 0.00 0.00 0.00 4.79
28 29 6.964807 ACACTAAATTTTAACGAACCCCTT 57.035 33.333 0.00 0.00 0.00 3.95
29 30 9.566432 TTACACTAAATTTTAACGAACCCCTTA 57.434 29.630 0.00 0.00 0.00 2.69
30 31 8.462589 ACACTAAATTTTAACGAACCCCTTAA 57.537 30.769 0.00 0.00 0.00 1.85
31 32 8.911965 ACACTAAATTTTAACGAACCCCTTAAA 58.088 29.630 0.00 0.00 0.00 1.52
32 33 9.747293 CACTAAATTTTAACGAACCCCTTAAAA 57.253 29.630 0.00 0.00 36.65 1.52
33 34 9.970395 ACTAAATTTTAACGAACCCCTTAAAAG 57.030 29.630 0.00 0.00 36.03 2.27
34 35 7.718272 AAATTTTAACGAACCCCTTAAAAGC 57.282 32.000 0.00 0.00 36.03 3.51
35 36 6.659745 ATTTTAACGAACCCCTTAAAAGCT 57.340 33.333 0.00 0.00 36.03 3.74
36 37 6.468333 TTTTAACGAACCCCTTAAAAGCTT 57.532 33.333 0.00 0.00 31.35 3.74
37 38 5.441709 TTAACGAACCCCTTAAAAGCTTG 57.558 39.130 0.00 0.00 0.00 4.01
38 39 1.611977 ACGAACCCCTTAAAAGCTTGC 59.388 47.619 0.00 0.00 0.00 4.01
39 40 1.611491 CGAACCCCTTAAAAGCTTGCA 59.389 47.619 0.00 0.00 0.00 4.08
40 41 2.351738 CGAACCCCTTAAAAGCTTGCAG 60.352 50.000 0.00 0.00 0.00 4.41
41 42 2.381752 ACCCCTTAAAAGCTTGCAGT 57.618 45.000 0.00 0.00 0.00 4.40
42 43 2.677914 ACCCCTTAAAAGCTTGCAGTT 58.322 42.857 0.00 0.00 0.00 3.16
43 44 3.038280 ACCCCTTAAAAGCTTGCAGTTT 58.962 40.909 0.00 0.00 0.00 2.66
44 45 3.454447 ACCCCTTAAAAGCTTGCAGTTTT 59.546 39.130 0.00 8.15 29.65 2.43
45 46 4.058124 CCCCTTAAAAGCTTGCAGTTTTC 58.942 43.478 0.00 0.00 28.25 2.29
46 47 3.735746 CCCTTAAAAGCTTGCAGTTTTCG 59.264 43.478 0.00 2.04 28.25 3.46
47 48 4.359706 CCTTAAAAGCTTGCAGTTTTCGT 58.640 39.130 0.00 0.00 28.25 3.85
48 49 4.207019 CCTTAAAAGCTTGCAGTTTTCGTG 59.793 41.667 0.00 1.34 28.25 4.35
49 50 2.208326 AAAGCTTGCAGTTTTCGTGG 57.792 45.000 0.00 0.00 0.00 4.94
50 51 0.249031 AAGCTTGCAGTTTTCGTGGC 60.249 50.000 0.00 0.00 0.00 5.01
51 52 2.010817 GCTTGCAGTTTTCGTGGCG 61.011 57.895 0.00 0.00 0.00 5.69
52 53 1.370414 CTTGCAGTTTTCGTGGCGG 60.370 57.895 0.00 0.00 0.00 6.13
53 54 2.058829 CTTGCAGTTTTCGTGGCGGT 62.059 55.000 0.00 0.00 0.00 5.68
54 55 0.814410 TTGCAGTTTTCGTGGCGGTA 60.814 50.000 0.00 0.00 0.00 4.02
55 56 0.604243 TGCAGTTTTCGTGGCGGTAT 60.604 50.000 0.00 0.00 0.00 2.73
56 57 0.179200 GCAGTTTTCGTGGCGGTATG 60.179 55.000 0.00 0.00 0.00 2.39
57 58 1.434555 CAGTTTTCGTGGCGGTATGA 58.565 50.000 0.00 0.00 0.00 2.15
58 59 1.127951 CAGTTTTCGTGGCGGTATGAC 59.872 52.381 0.00 0.00 0.00 3.06
59 60 1.149987 GTTTTCGTGGCGGTATGACA 58.850 50.000 0.00 0.00 0.00 3.58
60 61 1.735571 GTTTTCGTGGCGGTATGACAT 59.264 47.619 0.00 0.00 38.42 3.06
61 62 1.647346 TTTCGTGGCGGTATGACATC 58.353 50.000 0.00 0.00 38.42 3.06
62 63 0.533032 TTCGTGGCGGTATGACATCA 59.467 50.000 0.00 0.00 38.42 3.07
63 64 0.102300 TCGTGGCGGTATGACATCAG 59.898 55.000 0.00 0.00 38.42 2.90
64 65 0.102300 CGTGGCGGTATGACATCAGA 59.898 55.000 0.00 0.00 38.42 3.27
65 66 1.858091 GTGGCGGTATGACATCAGAG 58.142 55.000 0.00 0.00 38.42 3.35
66 67 0.752658 TGGCGGTATGACATCAGAGG 59.247 55.000 0.00 0.00 0.00 3.69
67 68 1.040646 GGCGGTATGACATCAGAGGA 58.959 55.000 0.00 0.00 0.00 3.71
68 69 1.000283 GGCGGTATGACATCAGAGGAG 60.000 57.143 0.00 0.00 0.00 3.69
69 70 1.683917 GCGGTATGACATCAGAGGAGT 59.316 52.381 0.00 0.00 0.00 3.85
70 71 2.101582 GCGGTATGACATCAGAGGAGTT 59.898 50.000 0.00 0.00 0.00 3.01
71 72 3.430929 GCGGTATGACATCAGAGGAGTTT 60.431 47.826 0.00 0.00 0.00 2.66
72 73 4.759782 CGGTATGACATCAGAGGAGTTTT 58.240 43.478 0.00 0.00 0.00 2.43
73 74 4.806247 CGGTATGACATCAGAGGAGTTTTC 59.194 45.833 0.00 0.00 0.00 2.29
74 75 5.624509 CGGTATGACATCAGAGGAGTTTTCA 60.625 44.000 0.00 0.00 0.00 2.69
75 76 5.582665 GGTATGACATCAGAGGAGTTTTCAC 59.417 44.000 0.00 0.00 0.00 3.18
76 77 4.008074 TGACATCAGAGGAGTTTTCACC 57.992 45.455 0.00 0.00 0.00 4.02
77 78 2.996621 GACATCAGAGGAGTTTTCACCG 59.003 50.000 0.00 0.00 35.70 4.94
78 79 2.289694 ACATCAGAGGAGTTTTCACCGG 60.290 50.000 0.00 0.00 35.70 5.28
79 80 0.685097 TCAGAGGAGTTTTCACCGGG 59.315 55.000 6.32 0.00 35.70 5.73
80 81 0.321653 CAGAGGAGTTTTCACCGGGG 60.322 60.000 6.32 0.00 35.70 5.73
81 82 1.002502 GAGGAGTTTTCACCGGGGG 60.003 63.158 2.42 0.00 35.70 5.40
82 83 1.462627 AGGAGTTTTCACCGGGGGA 60.463 57.895 2.42 0.00 35.70 4.81
83 84 1.002502 GGAGTTTTCACCGGGGGAG 60.003 63.158 2.42 0.00 0.00 4.30
84 85 1.002502 GAGTTTTCACCGGGGGAGG 60.003 63.158 2.42 0.00 37.30 4.30
85 86 2.035155 GTTTTCACCGGGGGAGGG 59.965 66.667 2.42 0.00 35.02 4.30
86 87 3.261677 TTTTCACCGGGGGAGGGG 61.262 66.667 2.42 0.00 35.56 4.79
110 111 4.317530 GGGGGTAGAAAGGTTCAGATTT 57.682 45.455 0.00 0.00 0.00 2.17
116 117 6.374613 GGGTAGAAAGGTTCAGATTTTCGATT 59.625 38.462 0.00 0.00 36.27 3.34
120 121 7.147976 AGAAAGGTTCAGATTTTCGATTTTGG 58.852 34.615 0.00 0.00 36.27 3.28
131 132 5.452078 TTTCGATTTTGGAGCACTGATTT 57.548 34.783 0.00 0.00 0.00 2.17
135 136 4.618489 CGATTTTGGAGCACTGATTTTGTC 59.382 41.667 0.00 0.00 0.00 3.18
139 140 4.572985 TGGAGCACTGATTTTGTCTTTG 57.427 40.909 0.00 0.00 0.00 2.77
144 145 1.330306 CTGATTTTGTCTTTGCCGCG 58.670 50.000 0.00 0.00 0.00 6.46
145 146 0.662970 TGATTTTGTCTTTGCCGCGC 60.663 50.000 0.00 0.00 0.00 6.86
169 170 2.158415 AGCTCCCCCAATGTCATATTGG 60.158 50.000 6.18 6.18 46.11 3.16
172 173 2.179645 TCCCCCAATGTCATATTGGCAT 59.820 45.455 7.66 0.00 45.92 4.40
183 184 5.804473 TGTCATATTGGCATTAAAGTTTGCG 59.196 36.000 0.00 0.00 39.78 4.85
184 185 4.803088 TCATATTGGCATTAAAGTTTGCGC 59.197 37.500 0.00 0.00 39.78 6.09
187 188 1.067669 TGGCATTAAAGTTTGCGCACA 59.932 42.857 11.12 0.00 39.78 4.57
190 191 2.730928 GCATTAAAGTTTGCGCACACAT 59.269 40.909 26.94 14.06 0.00 3.21
206 207 6.307800 GCGCACACATATAAAACTTGTTCATT 59.692 34.615 0.30 0.00 0.00 2.57
290 308 3.253921 TCATATGGATTTCCGCTTGCATG 59.746 43.478 2.13 0.00 39.43 4.06
291 309 0.103572 ATGGATTTCCGCTTGCATGC 59.896 50.000 11.82 11.82 39.43 4.06
297 315 1.024046 TTCCGCTTGCATGCACGTAT 61.024 50.000 22.58 0.00 0.00 3.06
300 318 1.208259 CGCTTGCATGCACGTATAGA 58.792 50.000 22.58 2.30 0.00 1.98
301 319 1.794701 CGCTTGCATGCACGTATAGAT 59.205 47.619 22.58 0.00 0.00 1.98
305 323 4.610007 GCTTGCATGCACGTATAGATTCAG 60.610 45.833 22.58 11.52 0.00 3.02
307 325 4.692228 TGCATGCACGTATAGATTCAGAA 58.308 39.130 18.46 0.00 0.00 3.02
317 335 6.763135 ACGTATAGATTCAGAATTGCATGTGT 59.237 34.615 0.00 0.00 0.00 3.72
326 344 2.592102 ATTGCATGTGTCTTGTCCCT 57.408 45.000 0.00 0.00 0.00 4.20
327 345 1.896220 TTGCATGTGTCTTGTCCCTC 58.104 50.000 0.00 0.00 0.00 4.30
457 478 2.972713 TCAGTTACCATGGCTAGGATCC 59.027 50.000 13.04 2.48 0.00 3.36
458 479 2.975489 CAGTTACCATGGCTAGGATCCT 59.025 50.000 20.48 20.48 0.00 3.24
459 480 3.007398 CAGTTACCATGGCTAGGATCCTC 59.993 52.174 20.22 4.44 0.00 3.71
460 481 2.303311 GTTACCATGGCTAGGATCCTCC 59.697 54.545 20.22 15.31 36.58 4.30
462 483 1.274712 CCATGGCTAGGATCCTCCTC 58.725 60.000 20.22 9.30 45.66 3.71
475 496 4.102367 GGATCCTCCTCTAACAATCAAGCT 59.898 45.833 3.84 0.00 32.53 3.74
576 681 3.065371 ACTGAAAGAACAAAACCAGCTCG 59.935 43.478 0.00 0.00 37.43 5.03
684 799 4.272018 CAGCTCCGATTGTCAAAAGGATAG 59.728 45.833 11.38 4.51 0.00 2.08
695 810 7.986085 TGTCAAAAGGATAGGAAAGAAGAAG 57.014 36.000 0.00 0.00 0.00 2.85
698 813 9.067986 GTCAAAAGGATAGGAAAGAAGAAGAAA 57.932 33.333 0.00 0.00 0.00 2.52
704 819 9.460019 AGGATAGGAAAGAAGAAGAAAAATCAG 57.540 33.333 0.00 0.00 0.00 2.90
705 820 9.454859 GGATAGGAAAGAAGAAGAAAAATCAGA 57.545 33.333 0.00 0.00 0.00 3.27
709 824 8.791675 AGGAAAGAAGAAGAAAAATCAGATCAC 58.208 33.333 0.00 0.00 0.00 3.06
710 825 8.791675 GGAAAGAAGAAGAAAAATCAGATCACT 58.208 33.333 0.00 0.00 0.00 3.41
711 826 9.609950 GAAAGAAGAAGAAAAATCAGATCACTG 57.390 33.333 0.00 0.00 44.66 3.66
712 827 7.684937 AGAAGAAGAAAAATCAGATCACTGG 57.315 36.000 0.00 0.00 43.60 4.00
795 914 1.376942 CTTGGCAGCTCACCTCAGG 60.377 63.158 4.01 0.00 0.00 3.86
818 937 3.799432 TTGGTGCCCTGTAACTGTAAT 57.201 42.857 0.00 0.00 0.00 1.89
888 1176 0.833287 TGCTGGAGTAGATGCTTCCC 59.167 55.000 0.00 0.00 0.00 3.97
909 1197 1.658686 CTCACTCCTCTTCCCCGACG 61.659 65.000 0.00 0.00 0.00 5.12
910 1198 2.362632 ACTCCTCTTCCCCGACGG 60.363 66.667 6.99 6.99 0.00 4.79
911 1199 3.839432 CTCCTCTTCCCCGACGGC 61.839 72.222 8.86 0.00 0.00 5.68
983 1290 1.130561 CATCGAGTCTGCACGTCTACA 59.869 52.381 0.00 0.00 0.00 2.74
986 1305 2.608090 TCGAGTCTGCACGTCTACATAG 59.392 50.000 0.00 0.00 0.00 2.23
1308 1627 3.482783 GGCACGCTCAACTCGCTC 61.483 66.667 0.00 0.00 0.00 5.03
1745 2073 2.892334 CGGTGGTTCACGTGCTTGG 61.892 63.158 11.67 0.00 34.83 3.61
1749 2080 2.617274 GGTTCACGTGCTTGGCCTC 61.617 63.158 11.67 0.00 0.00 4.70
1750 2081 2.281484 TTCACGTGCTTGGCCTCC 60.281 61.111 11.67 0.00 0.00 4.30
1751 2082 2.818169 TTCACGTGCTTGGCCTCCT 61.818 57.895 11.67 0.00 0.00 3.69
1752 2083 1.476845 TTCACGTGCTTGGCCTCCTA 61.477 55.000 11.67 0.00 0.00 2.94
1783 2114 3.958860 GGGGGCTGCTGTGACAGT 61.959 66.667 14.82 0.00 39.96 3.55
1804 2135 2.279120 GCGCCCGATCAGAGAGTG 60.279 66.667 0.00 0.00 0.00 3.51
1805 2136 2.279120 CGCCCGATCAGAGAGTGC 60.279 66.667 0.00 0.00 0.00 4.40
1843 2174 3.188667 GTCTAGATCCATGCACGTCGATA 59.811 47.826 0.00 0.00 0.00 2.92
1844 2175 4.010349 TCTAGATCCATGCACGTCGATAT 58.990 43.478 0.00 0.00 0.00 1.63
1886 2217 6.793492 TTTCAAAAGGTGTTGGTCTTTTTG 57.207 33.333 6.83 6.83 40.08 2.44
1894 2225 4.808895 GGTGTTGGTCTTTTTGGTTTGATC 59.191 41.667 0.00 0.00 0.00 2.92
1901 2232 6.183360 TGGTCTTTTTGGTTTGATCTGTTCTC 60.183 38.462 0.00 0.00 0.00 2.87
1902 2233 6.183360 GGTCTTTTTGGTTTGATCTGTTCTCA 60.183 38.462 0.00 0.00 0.00 3.27
1918 2249 9.842775 ATCTGTTCTCATTATTTCAGCTCATTA 57.157 29.630 0.00 0.00 0.00 1.90
2107 2440 2.331893 GCATGCACGCACACCCTAA 61.332 57.895 14.21 0.00 0.00 2.69
2112 2445 4.011517 ACGCACACCCTAACCCCG 62.012 66.667 0.00 0.00 0.00 5.73
2130 2463 1.336440 CCGTGAGCATCTTCGAGAGAT 59.664 52.381 4.81 4.81 46.12 2.75
2136 2469 2.948979 AGCATCTTCGAGAGATCGAGTT 59.051 45.455 7.01 0.00 43.32 3.01
2208 2541 3.755378 GACAAGAACGTCTCCTACCACTA 59.245 47.826 0.00 0.00 32.92 2.74
2218 2551 6.039493 ACGTCTCCTACCACTAAATGAGTATG 59.961 42.308 0.00 0.00 35.64 2.39
2227 3109 5.299279 CCACTAAATGAGTATGGCCGAAAAT 59.701 40.000 0.00 0.00 35.64 1.82
2260 3142 8.958119 AATAAATCTAGAAAATACGAGCACCA 57.042 30.769 0.00 0.00 0.00 4.17
2263 3145 5.401531 TCTAGAAAATACGAGCACCAGTT 57.598 39.130 0.00 0.00 0.00 3.16
2264 3146 5.168569 TCTAGAAAATACGAGCACCAGTTG 58.831 41.667 0.00 0.00 0.00 3.16
2265 3147 3.740115 AGAAAATACGAGCACCAGTTGT 58.260 40.909 0.00 0.00 0.00 3.32
2266 3148 3.746492 AGAAAATACGAGCACCAGTTGTC 59.254 43.478 0.00 0.00 0.00 3.18
2267 3149 2.831685 AATACGAGCACCAGTTGTCA 57.168 45.000 0.00 0.00 0.00 3.58
2277 3159 5.133221 AGCACCAGTTGTCAAAGTCTAAAT 58.867 37.500 0.00 0.00 0.00 1.40
2287 3169 6.811954 TGTCAAAGTCTAAATTTTGAACCCC 58.188 36.000 3.84 0.00 41.16 4.95
2318 3200 9.457436 GGATTGTTCTACCATAAAAGACCTAAA 57.543 33.333 0.00 0.00 0.00 1.85
2401 3284 3.991999 TGCTTGACAGAGGCATGC 58.008 55.556 9.90 9.90 37.06 4.06
2494 3377 6.147492 GTGCATGCCATTTTCTTATGTCAAAA 59.853 34.615 16.68 0.00 0.00 2.44
2574 3457 7.246674 TCTCAAGTTCTCAACACAAATACAC 57.753 36.000 0.00 0.00 0.00 2.90
2640 3576 6.040209 TGCTTCATAATGTTTTGGATGCTT 57.960 33.333 0.00 0.00 32.01 3.91
2724 3660 8.716674 ACCCTATTTGCAATAATTGAGATGAT 57.283 30.769 0.00 0.00 0.00 2.45
2725 3661 8.800332 ACCCTATTTGCAATAATTGAGATGATC 58.200 33.333 0.00 0.00 0.00 2.92
2726 3662 8.799367 CCCTATTTGCAATAATTGAGATGATCA 58.201 33.333 0.00 0.00 35.62 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.040478 GGGGTTCGTTAAAATTTAGTGTAACCT 60.040 37.037 17.31 0.00 37.80 3.50
1 2 7.040478 AGGGGTTCGTTAAAATTTAGTGTAACC 60.040 37.037 12.72 12.72 37.80 2.85
2 3 7.874940 AGGGGTTCGTTAAAATTTAGTGTAAC 58.125 34.615 0.00 0.00 0.00 2.50
3 4 8.462589 AAGGGGTTCGTTAAAATTTAGTGTAA 57.537 30.769 0.00 0.00 0.00 2.41
4 5 9.566432 TTAAGGGGTTCGTTAAAATTTAGTGTA 57.434 29.630 0.00 0.00 32.41 2.90
5 6 6.964807 AAGGGGTTCGTTAAAATTTAGTGT 57.035 33.333 0.00 0.00 0.00 3.55
6 7 9.747293 TTTTAAGGGGTTCGTTAAAATTTAGTG 57.253 29.630 10.64 0.00 42.86 2.74
7 8 9.970395 CTTTTAAGGGGTTCGTTAAAATTTAGT 57.030 29.630 13.43 0.00 44.72 2.24
8 9 8.918658 GCTTTTAAGGGGTTCGTTAAAATTTAG 58.081 33.333 13.43 6.72 44.72 1.85
9 10 8.640651 AGCTTTTAAGGGGTTCGTTAAAATTTA 58.359 29.630 13.43 0.00 44.72 1.40
10 11 7.502696 AGCTTTTAAGGGGTTCGTTAAAATTT 58.497 30.769 13.43 0.00 44.72 1.82
11 12 7.058023 AGCTTTTAAGGGGTTCGTTAAAATT 57.942 32.000 13.43 6.42 44.72 1.82
12 13 6.659745 AGCTTTTAAGGGGTTCGTTAAAAT 57.340 33.333 13.43 2.74 44.72 1.82
13 14 6.274579 CAAGCTTTTAAGGGGTTCGTTAAAA 58.725 36.000 0.00 12.80 44.18 1.52
14 15 5.736777 GCAAGCTTTTAAGGGGTTCGTTAAA 60.737 40.000 0.00 0.00 39.76 1.52
15 16 4.261698 GCAAGCTTTTAAGGGGTTCGTTAA 60.262 41.667 0.00 0.00 33.18 2.01
16 17 3.253921 GCAAGCTTTTAAGGGGTTCGTTA 59.746 43.478 0.00 0.00 0.00 3.18
17 18 2.035449 GCAAGCTTTTAAGGGGTTCGTT 59.965 45.455 0.00 0.00 0.00 3.85
18 19 1.611977 GCAAGCTTTTAAGGGGTTCGT 59.388 47.619 0.00 0.00 0.00 3.85
19 20 1.611491 TGCAAGCTTTTAAGGGGTTCG 59.389 47.619 0.00 0.00 0.00 3.95
20 21 2.628178 ACTGCAAGCTTTTAAGGGGTTC 59.372 45.455 0.00 0.00 37.60 3.62
21 22 2.677914 ACTGCAAGCTTTTAAGGGGTT 58.322 42.857 0.00 0.00 37.60 4.11
22 23 2.381752 ACTGCAAGCTTTTAAGGGGT 57.618 45.000 0.00 0.00 37.60 4.95
23 24 3.751479 AAACTGCAAGCTTTTAAGGGG 57.249 42.857 0.00 0.00 37.60 4.79
24 25 3.735746 CGAAAACTGCAAGCTTTTAAGGG 59.264 43.478 0.00 0.00 31.33 3.95
25 26 4.207019 CACGAAAACTGCAAGCTTTTAAGG 59.793 41.667 0.00 0.00 31.33 2.69
26 27 4.207019 CCACGAAAACTGCAAGCTTTTAAG 59.793 41.667 0.00 0.00 31.33 1.85
27 28 4.109050 CCACGAAAACTGCAAGCTTTTAA 58.891 39.130 0.00 0.00 31.33 1.52
28 29 3.701241 CCACGAAAACTGCAAGCTTTTA 58.299 40.909 0.00 0.00 31.33 1.52
29 30 2.539476 CCACGAAAACTGCAAGCTTTT 58.461 42.857 0.00 0.00 31.33 2.27
30 31 1.802508 GCCACGAAAACTGCAAGCTTT 60.803 47.619 0.00 0.00 34.42 3.51
31 32 0.249031 GCCACGAAAACTGCAAGCTT 60.249 50.000 0.00 0.00 37.60 3.74
32 33 1.360192 GCCACGAAAACTGCAAGCT 59.640 52.632 0.00 0.00 37.60 3.74
33 34 2.010817 CGCCACGAAAACTGCAAGC 61.011 57.895 0.00 0.00 37.60 4.01
34 35 1.370414 CCGCCACGAAAACTGCAAG 60.370 57.895 0.00 0.00 42.29 4.01
35 36 0.814410 TACCGCCACGAAAACTGCAA 60.814 50.000 0.00 0.00 0.00 4.08
36 37 0.604243 ATACCGCCACGAAAACTGCA 60.604 50.000 0.00 0.00 0.00 4.41
37 38 0.179200 CATACCGCCACGAAAACTGC 60.179 55.000 0.00 0.00 0.00 4.40
38 39 1.127951 GTCATACCGCCACGAAAACTG 59.872 52.381 0.00 0.00 0.00 3.16
39 40 1.270412 TGTCATACCGCCACGAAAACT 60.270 47.619 0.00 0.00 0.00 2.66
40 41 1.149987 TGTCATACCGCCACGAAAAC 58.850 50.000 0.00 0.00 0.00 2.43
41 42 2.004017 GATGTCATACCGCCACGAAAA 58.996 47.619 0.00 0.00 0.00 2.29
42 43 1.066787 TGATGTCATACCGCCACGAAA 60.067 47.619 0.00 0.00 0.00 3.46
43 44 0.533032 TGATGTCATACCGCCACGAA 59.467 50.000 0.00 0.00 0.00 3.85
44 45 0.102300 CTGATGTCATACCGCCACGA 59.898 55.000 0.00 0.00 0.00 4.35
45 46 0.102300 TCTGATGTCATACCGCCACG 59.898 55.000 0.00 0.00 0.00 4.94
46 47 1.539065 CCTCTGATGTCATACCGCCAC 60.539 57.143 0.00 0.00 0.00 5.01
47 48 0.752658 CCTCTGATGTCATACCGCCA 59.247 55.000 0.00 0.00 0.00 5.69
48 49 1.000283 CTCCTCTGATGTCATACCGCC 60.000 57.143 0.00 0.00 0.00 6.13
49 50 1.683917 ACTCCTCTGATGTCATACCGC 59.316 52.381 0.00 0.00 0.00 5.68
50 51 4.392921 AAACTCCTCTGATGTCATACCG 57.607 45.455 0.00 0.00 0.00 4.02
51 52 5.582665 GTGAAAACTCCTCTGATGTCATACC 59.417 44.000 0.00 0.00 0.00 2.73
52 53 5.582665 GGTGAAAACTCCTCTGATGTCATAC 59.417 44.000 0.00 0.00 0.00 2.39
53 54 5.624509 CGGTGAAAACTCCTCTGATGTCATA 60.625 44.000 0.00 0.00 0.00 2.15
54 55 4.583871 GGTGAAAACTCCTCTGATGTCAT 58.416 43.478 0.00 0.00 0.00 3.06
55 56 3.554960 CGGTGAAAACTCCTCTGATGTCA 60.555 47.826 0.00 0.00 0.00 3.58
56 57 2.996621 CGGTGAAAACTCCTCTGATGTC 59.003 50.000 0.00 0.00 0.00 3.06
57 58 2.289694 CCGGTGAAAACTCCTCTGATGT 60.290 50.000 0.00 0.00 0.00 3.06
58 59 2.350522 CCGGTGAAAACTCCTCTGATG 58.649 52.381 0.00 0.00 0.00 3.07
59 60 1.279271 CCCGGTGAAAACTCCTCTGAT 59.721 52.381 0.00 0.00 0.00 2.90
60 61 0.685097 CCCGGTGAAAACTCCTCTGA 59.315 55.000 0.00 0.00 0.00 3.27
61 62 0.321653 CCCCGGTGAAAACTCCTCTG 60.322 60.000 0.00 0.00 0.00 3.35
62 63 1.489560 CCCCCGGTGAAAACTCCTCT 61.490 60.000 0.00 0.00 0.00 3.69
63 64 1.002502 CCCCCGGTGAAAACTCCTC 60.003 63.158 0.00 0.00 0.00 3.71
64 65 1.462627 TCCCCCGGTGAAAACTCCT 60.463 57.895 0.00 0.00 0.00 3.69
65 66 1.002502 CTCCCCCGGTGAAAACTCC 60.003 63.158 0.00 0.00 0.00 3.85
66 67 1.002502 CCTCCCCCGGTGAAAACTC 60.003 63.158 0.00 0.00 0.00 3.01
67 68 2.535331 CCCTCCCCCGGTGAAAACT 61.535 63.158 0.00 0.00 0.00 2.66
68 69 2.035155 CCCTCCCCCGGTGAAAAC 59.965 66.667 0.00 0.00 0.00 2.43
69 70 3.261677 CCCCTCCCCCGGTGAAAA 61.262 66.667 0.00 0.00 0.00 2.29
89 90 4.317530 AAATCTGAACCTTTCTACCCCC 57.682 45.455 0.00 0.00 0.00 5.40
90 91 4.395231 CGAAAATCTGAACCTTTCTACCCC 59.605 45.833 7.96 0.00 0.00 4.95
91 92 5.243207 TCGAAAATCTGAACCTTTCTACCC 58.757 41.667 0.00 0.00 0.00 3.69
92 93 6.986904 ATCGAAAATCTGAACCTTTCTACC 57.013 37.500 0.00 0.00 0.00 3.18
93 94 9.118236 CAAAATCGAAAATCTGAACCTTTCTAC 57.882 33.333 0.00 0.00 0.00 2.59
94 95 8.296713 CCAAAATCGAAAATCTGAACCTTTCTA 58.703 33.333 0.00 0.54 0.00 2.10
104 105 4.855388 CAGTGCTCCAAAATCGAAAATCTG 59.145 41.667 0.00 0.00 0.00 2.90
106 107 5.046910 TCAGTGCTCCAAAATCGAAAATC 57.953 39.130 0.00 0.00 0.00 2.17
108 109 5.452078 AATCAGTGCTCCAAAATCGAAAA 57.548 34.783 0.00 0.00 0.00 2.29
110 111 5.221224 ACAAAATCAGTGCTCCAAAATCGAA 60.221 36.000 0.00 0.00 0.00 3.71
116 117 5.350633 CAAAGACAAAATCAGTGCTCCAAA 58.649 37.500 0.00 0.00 0.00 3.28
120 121 3.311966 GGCAAAGACAAAATCAGTGCTC 58.688 45.455 0.00 0.00 38.68 4.26
144 145 4.115199 ACATTGGGGGAGCTCGGC 62.115 66.667 7.83 0.00 0.00 5.54
145 146 1.987807 ATGACATTGGGGGAGCTCGG 61.988 60.000 7.83 0.00 0.00 4.63
158 159 6.476380 CGCAAACTTTAATGCCAATATGACAT 59.524 34.615 0.00 0.00 39.39 3.06
169 170 2.123342 TGTGTGCGCAAACTTTAATGC 58.877 42.857 29.77 6.32 39.17 3.56
172 173 7.863375 AGTTTTATATGTGTGCGCAAACTTTAA 59.137 29.630 29.77 20.20 30.61 1.52
173 174 7.364200 AGTTTTATATGTGTGCGCAAACTTTA 58.636 30.769 29.77 21.01 30.61 1.85
263 266 5.336213 GCAAGCGGAAATCCATATGATGAAT 60.336 40.000 3.65 0.00 32.68 2.57
270 273 2.029649 GCATGCAAGCGGAAATCCATAT 60.030 45.455 14.21 0.00 35.14 1.78
271 274 1.337703 GCATGCAAGCGGAAATCCATA 59.662 47.619 14.21 0.00 35.14 2.74
273 276 1.249469 TGCATGCAAGCGGAAATCCA 61.249 50.000 20.30 0.00 37.31 3.41
290 308 5.657470 TGCAATTCTGAATCTATACGTGC 57.343 39.130 11.91 11.91 0.00 5.34
291 309 7.067728 CACATGCAATTCTGAATCTATACGTG 58.932 38.462 2.92 6.17 0.00 4.49
297 315 6.656270 ACAAGACACATGCAATTCTGAATCTA 59.344 34.615 2.92 0.00 0.00 1.98
300 318 5.336213 GGACAAGACACATGCAATTCTGAAT 60.336 40.000 0.00 0.00 0.00 2.57
301 319 4.022935 GGACAAGACACATGCAATTCTGAA 60.023 41.667 0.00 0.00 0.00 3.02
305 323 2.821969 AGGGACAAGACACATGCAATTC 59.178 45.455 0.00 0.00 0.00 2.17
307 325 2.040813 AGAGGGACAAGACACATGCAAT 59.959 45.455 0.00 0.00 0.00 3.56
317 335 4.974645 TTTGCTTAAGAGAGGGACAAGA 57.025 40.909 6.67 0.00 0.00 3.02
410 428 4.035675 GCTTATGCTGTTAACTGGGTGATC 59.964 45.833 13.60 0.00 36.03 2.92
457 478 4.142513 GCCAAAGCTTGATTGTTAGAGGAG 60.143 45.833 0.00 0.00 35.50 3.69
458 479 3.758554 GCCAAAGCTTGATTGTTAGAGGA 59.241 43.478 0.00 0.00 35.50 3.71
459 480 3.119352 GGCCAAAGCTTGATTGTTAGAGG 60.119 47.826 0.00 0.00 39.73 3.69
460 481 3.119352 GGGCCAAAGCTTGATTGTTAGAG 60.119 47.826 4.39 0.00 39.73 2.43
461 482 2.825532 GGGCCAAAGCTTGATTGTTAGA 59.174 45.455 4.39 0.00 39.73 2.10
462 483 2.094026 GGGGCCAAAGCTTGATTGTTAG 60.094 50.000 4.39 0.00 39.73 2.34
500 521 3.986277 AGCTGAAAAGTGCATCCAAAAG 58.014 40.909 0.00 0.00 0.00 2.27
684 799 8.791675 AGTGATCTGATTTTTCTTCTTCTTTCC 58.208 33.333 0.00 0.00 0.00 3.13
695 810 4.593956 ACTCCCCAGTGATCTGATTTTTC 58.406 43.478 0.00 0.00 43.76 2.29
698 813 3.875369 GCAACTCCCCAGTGATCTGATTT 60.875 47.826 0.00 0.00 43.76 2.17
701 816 0.615331 GCAACTCCCCAGTGATCTGA 59.385 55.000 0.00 0.00 43.76 3.27
702 817 0.617413 AGCAACTCCCCAGTGATCTG 59.383 55.000 0.00 0.00 41.01 2.90
704 819 1.028868 GCAGCAACTCCCCAGTGATC 61.029 60.000 0.00 0.00 31.06 2.92
705 820 1.001641 GCAGCAACTCCCCAGTGAT 60.002 57.895 0.00 0.00 31.06 3.06
706 821 2.116983 GAGCAGCAACTCCCCAGTGA 62.117 60.000 0.00 0.00 31.06 3.41
707 822 1.673665 GAGCAGCAACTCCCCAGTG 60.674 63.158 0.00 0.00 31.06 3.66
746 865 2.482142 GCTAACCACCTACTAGCAGCTG 60.482 54.545 10.11 10.11 38.33 4.24
747 866 1.757699 GCTAACCACCTACTAGCAGCT 59.242 52.381 0.00 0.00 38.33 4.24
748 867 1.202545 GGCTAACCACCTACTAGCAGC 60.203 57.143 3.03 0.00 39.88 5.25
749 868 2.101582 CAGGCTAACCACCTACTAGCAG 59.898 54.545 3.03 0.00 39.88 4.24
755 874 1.626825 TGGAACAGGCTAACCACCTAC 59.373 52.381 3.02 0.00 39.06 3.18
818 937 1.758592 GGGGTAAGTGAGTGTGCCA 59.241 57.895 0.00 0.00 0.00 4.92
888 1176 2.060980 CGGGGAAGAGGAGTGAGGG 61.061 68.421 0.00 0.00 0.00 4.30
909 1197 1.053424 TATAACGAGATGGGTGGGCC 58.947 55.000 0.00 0.00 0.00 5.80
910 1198 2.767505 CTTATAACGAGATGGGTGGGC 58.232 52.381 0.00 0.00 0.00 5.36
911 1199 2.550208 GGCTTATAACGAGATGGGTGGG 60.550 54.545 0.00 0.00 0.00 4.61
912 1200 2.104111 TGGCTTATAACGAGATGGGTGG 59.896 50.000 0.00 0.00 0.00 4.61
914 1202 2.223971 CGTGGCTTATAACGAGATGGGT 60.224 50.000 0.00 0.00 42.32 4.51
915 1203 2.404215 CGTGGCTTATAACGAGATGGG 58.596 52.381 0.00 0.00 42.32 4.00
916 1204 1.792949 GCGTGGCTTATAACGAGATGG 59.207 52.381 0.00 0.00 42.32 3.51
918 1206 1.411246 TGGCGTGGCTTATAACGAGAT 59.589 47.619 0.00 0.00 42.32 2.75
919 1207 0.818938 TGGCGTGGCTTATAACGAGA 59.181 50.000 0.00 0.00 42.32 4.04
983 1290 1.540166 ATGGCTGCCATGGTGCTAT 59.460 52.632 32.12 21.66 43.39 2.97
1308 1627 0.734253 CGTTCTTCTGGCTGTCGGAG 60.734 60.000 0.00 0.00 31.44 4.63
1425 1744 3.712907 TTGAGCGGGTACTGGCCC 61.713 66.667 0.00 0.13 45.21 5.80
1745 2073 3.151022 AGACGCAGGCTAGGAGGC 61.151 66.667 0.00 0.00 41.73 4.70
1749 2080 2.185350 CACCAGACGCAGGCTAGG 59.815 66.667 0.00 0.00 0.00 3.02
1750 2081 2.185350 CCACCAGACGCAGGCTAG 59.815 66.667 0.00 0.00 0.00 3.42
1751 2082 3.390521 CCCACCAGACGCAGGCTA 61.391 66.667 0.00 0.00 0.00 3.93
1801 2132 4.335647 CAGGTTGGGGCTCGCACT 62.336 66.667 0.00 0.00 0.00 4.40
1804 2135 4.785453 CCTCAGGTTGGGGCTCGC 62.785 72.222 0.00 0.00 26.78 5.03
1805 2136 3.316573 GACCTCAGGTTGGGGCTCG 62.317 68.421 0.00 0.00 43.56 5.03
1870 2201 3.835395 TCAAACCAAAAAGACCAACACCT 59.165 39.130 0.00 0.00 0.00 4.00
1886 2217 7.699812 GCTGAAATAATGAGAACAGATCAAACC 59.300 37.037 0.00 0.00 0.00 3.27
1920 2251 7.954056 TGTCCCTAGCAATTACTACATAGGTAT 59.046 37.037 0.00 0.00 0.00 2.73
1921 2252 7.299896 TGTCCCTAGCAATTACTACATAGGTA 58.700 38.462 0.00 0.00 0.00 3.08
1922 2253 6.141083 TGTCCCTAGCAATTACTACATAGGT 58.859 40.000 0.00 0.00 0.00 3.08
1923 2254 6.665992 TGTCCCTAGCAATTACTACATAGG 57.334 41.667 0.00 0.00 0.00 2.57
1925 2256 7.612065 ACATGTCCCTAGCAATTACTACATA 57.388 36.000 0.00 0.00 0.00 2.29
1926 2257 6.500589 ACATGTCCCTAGCAATTACTACAT 57.499 37.500 0.00 0.00 0.00 2.29
1927 2258 5.950544 ACATGTCCCTAGCAATTACTACA 57.049 39.130 0.00 0.00 0.00 2.74
1928 2259 7.985752 ACTTTACATGTCCCTAGCAATTACTAC 59.014 37.037 0.00 0.00 0.00 2.73
1929 2260 7.985184 CACTTTACATGTCCCTAGCAATTACTA 59.015 37.037 0.00 0.00 0.00 1.82
1930 2261 6.823689 CACTTTACATGTCCCTAGCAATTACT 59.176 38.462 0.00 0.00 0.00 2.24
2040 2373 3.715495 TGTATGAACGTTTGTACCGTGT 58.285 40.909 16.50 0.00 38.77 4.49
2054 2387 6.583427 GGCGAATGTATGTACGTATGTATGAA 59.417 38.462 0.00 0.00 32.11 2.57
2055 2388 6.088173 GGCGAATGTATGTACGTATGTATGA 58.912 40.000 0.00 0.00 32.11 2.15
2074 2407 1.608055 CATGCATTCATAGGGGCGAA 58.392 50.000 0.00 0.00 0.00 4.70
2107 2440 1.949847 CTCGAAGATGCTCACGGGGT 61.950 60.000 0.00 0.00 33.89 4.95
2130 2463 2.744741 TCAAAATAATGCGCCAACTCGA 59.255 40.909 4.18 0.00 0.00 4.04
2136 2469 4.671377 GTCAATCTCAAAATAATGCGCCA 58.329 39.130 4.18 0.00 0.00 5.69
2182 2515 0.597072 AGGAGACGTTCTTGTCGACC 59.403 55.000 14.12 0.00 43.70 4.79
2189 2522 5.479375 TCATTTAGTGGTAGGAGACGTTCTT 59.521 40.000 0.00 0.00 0.00 2.52
2208 2541 7.502226 TCAGATTATTTTCGGCCATACTCATTT 59.498 33.333 2.24 0.00 0.00 2.32
2260 3142 7.979537 GGGTTCAAAATTTAGACTTTGACAACT 59.020 33.333 0.00 0.00 40.36 3.16
2263 3145 6.460399 CGGGGTTCAAAATTTAGACTTTGACA 60.460 38.462 0.00 0.00 40.36 3.58
2264 3146 5.918576 CGGGGTTCAAAATTTAGACTTTGAC 59.081 40.000 0.00 0.00 40.36 3.18
2265 3147 5.828859 TCGGGGTTCAAAATTTAGACTTTGA 59.171 36.000 0.00 0.00 39.24 2.69
2266 3148 6.079424 TCGGGGTTCAAAATTTAGACTTTG 57.921 37.500 0.00 0.00 34.49 2.77
2267 3149 6.911250 ATCGGGGTTCAAAATTTAGACTTT 57.089 33.333 0.00 0.00 0.00 2.66
2277 3159 4.310022 ACAATCCTATCGGGGTTCAAAA 57.690 40.909 0.00 0.00 35.99 2.44
2287 3169 8.979574 GTCTTTTATGGTAGAACAATCCTATCG 58.020 37.037 0.00 0.00 0.00 2.92
2294 3176 9.802039 TGTTTAGGTCTTTTATGGTAGAACAAT 57.198 29.630 0.00 0.00 30.36 2.71
2318 3200 8.473358 AGGCAAACTTAACCTAGTTTAAATGT 57.527 30.769 0.00 0.00 44.33 2.71
2574 3457 3.074412 ACATCTAAGGCGTTTGTCCAAG 58.926 45.455 0.00 0.00 0.00 3.61
2640 3576 1.127766 CGGCGATTCGATGTTTCACAA 59.872 47.619 10.88 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.