Multiple sequence alignment - TraesCS5D01G331400

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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 TraesCS5D01G331400 chr5D 100.000 2609 0 0 1 2609 422435983 422438591 0.000000e+00 4819
1 TraesCS5D01G331400 chr5D 83.847 1201 90 41 661 1793 422419885 422421049 0.000000e+00 1048
2 TraesCS5D01G331400 chr5A 90.984 1331 67 19 663 1974 535674008 535675304 0.000000e+00 1744
3 TraesCS5D01G331400 chr5A 84.981 1072 117 32 898 1946 535653530 535654580 0.000000e+00 1048
4 TraesCS5D01G331400 chr5A 88.988 672 48 10 1 661 535673189 535673845 0.000000e+00 808
5 TraesCS5D01G331400 chr5A 78.396 449 77 15 61 494 589064253 589064696 9.200000e-70 274
6 TraesCS5D01G331400 chr5A 93.452 168 11 0 2442 2609 535676114 535676281 1.550000e-62 250
7 TraesCS5D01G331400 chr5A 92.727 110 6 2 2232 2341 535676006 535676113 9.670000e-35 158
8 TraesCS5D01G331400 chr5B 90.828 1232 69 15 681 1894 509190896 509192101 0.000000e+00 1609
9 TraesCS5D01G331400 chr5B 84.125 1052 91 33 779 1793 509171942 509172954 0.000000e+00 948
10 TraesCS5D01G331400 chr5B 92.328 378 26 2 1 376 509190431 509190807 3.820000e-148 534
11 TraesCS5D01G331400 chr5B 84.384 365 26 9 1977 2341 509192339 509192672 1.940000e-86 329
12 TraesCS5D01G331400 chr5B 90.058 171 14 2 2442 2609 509192673 509192843 4.370000e-53 219
13 TraesCS5D01G331400 chr5B 85.217 115 11 5 664 773 509171796 509171909 2.120000e-21 113
14 TraesCS5D01G331400 chr3D 100.000 101 0 0 2345 2445 326124612 326124512 1.230000e-43 187
15 TraesCS5D01G331400 chr3D 98.039 102 2 0 2345 2446 39898757 39898858 7.420000e-41 178
16 TraesCS5D01G331400 chr3D 94.643 112 4 2 2345 2454 565536685 565536796 3.450000e-39 172
17 TraesCS5D01G331400 chr6D 95.413 109 4 1 2345 2452 81674738 81674630 3.450000e-39 172
18 TraesCS5D01G331400 chr2B 95.413 109 4 1 2345 2453 171460075 171459968 3.450000e-39 172
19 TraesCS5D01G331400 chr1D 92.000 125 4 5 2332 2451 11672294 11672171 1.240000e-38 171
20 TraesCS5D01G331400 chr2A 93.805 113 6 1 2345 2457 179352274 179352163 4.470000e-38 169
21 TraesCS5D01G331400 chr1A 90.625 128 7 4 2345 2470 56105911 56105787 5.780000e-37 165
22 TraesCS5D01G331400 chr3B 90.400 125 8 1 2329 2449 112452088 112452212 7.470000e-36 161


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 TraesCS5D01G331400 chr5D 422435983 422438591 2608 False 4819.00 4819 100.00000 1 2609 1 chr5D.!!$F2 2608
1 TraesCS5D01G331400 chr5D 422419885 422421049 1164 False 1048.00 1048 83.84700 661 1793 1 chr5D.!!$F1 1132
2 TraesCS5D01G331400 chr5A 535653530 535654580 1050 False 1048.00 1048 84.98100 898 1946 1 chr5A.!!$F1 1048
3 TraesCS5D01G331400 chr5A 535673189 535676281 3092 False 740.00 1744 91.53775 1 2609 4 chr5A.!!$F3 2608
4 TraesCS5D01G331400 chr5B 509190431 509192843 2412 False 672.75 1609 89.39950 1 2609 4 chr5B.!!$F2 2608
5 TraesCS5D01G331400 chr5B 509171796 509172954 1158 False 530.50 948 84.67100 664 1793 2 chr5B.!!$F1 1129

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
732 948 0.039074 GGTAGGATGCGATGGAGACG 60.039 60.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2135 2626 0.031994 GCTTTTTGCGTCCCACATGT 59.968 50.0 0.0 0.0 0.0 3.21 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
27 28 7.869937 CGATTCTATTTGACCACATCTACATCT 59.130 37.037 0.00 0.00 0.00 2.90
74 75 4.633175 TCAATACCGTTGCAACAACTCTA 58.367 39.130 28.01 10.09 0.00 2.43
172 175 7.878127 AGAAAATTCTTGATCCGAAGTAAGTGA 59.122 33.333 0.00 0.00 32.55 3.41
210 213 3.002451 GCTATCTCTGATTTGCTGCACAG 59.998 47.826 0.00 7.14 0.00 3.66
404 407 9.434275 TTCCAAAGATCACTAATGATACTAGGA 57.566 33.333 0.00 0.00 46.01 2.94
468 471 5.801380 TCTCCCAATCTTTACACCAAGTAC 58.199 41.667 0.00 0.00 30.91 2.73
489 492 7.942990 AGTACTAGTCCATATGTAAGAGTTGC 58.057 38.462 0.00 0.00 0.00 4.17
491 494 5.900123 ACTAGTCCATATGTAAGAGTTGCCT 59.100 40.000 1.24 0.00 0.00 4.75
492 495 5.700402 AGTCCATATGTAAGAGTTGCCTT 57.300 39.130 1.24 0.00 0.00 4.35
493 496 6.067217 AGTCCATATGTAAGAGTTGCCTTT 57.933 37.500 1.24 0.00 0.00 3.11
494 497 7.195374 AGTCCATATGTAAGAGTTGCCTTTA 57.805 36.000 1.24 0.00 0.00 1.85
495 498 7.275920 AGTCCATATGTAAGAGTTGCCTTTAG 58.724 38.462 1.24 0.00 0.00 1.85
496 499 6.017852 GTCCATATGTAAGAGTTGCCTTTAGC 60.018 42.308 1.24 0.00 44.14 3.09
497 500 6.058183 CCATATGTAAGAGTTGCCTTTAGCT 58.942 40.000 1.24 0.00 44.23 3.32
498 501 6.017605 CCATATGTAAGAGTTGCCTTTAGCTG 60.018 42.308 0.00 0.00 44.23 4.24
522 525 6.072508 TGTTTAGCAATTTGAAGCTGACTAGG 60.073 38.462 0.00 0.00 41.97 3.02
523 526 4.026356 AGCAATTTGAAGCTGACTAGGT 57.974 40.909 0.00 0.00 40.13 3.08
535 553 9.251440 TGAAGCTGACTAGGTAGAACTTTTATA 57.749 33.333 0.00 0.00 33.49 0.98
559 577 5.133221 ACAGTTGTCCAAAAAGCTGACTAT 58.867 37.500 3.17 0.00 0.00 2.12
573 591 4.099266 AGCTGACTATGAGAGCTAGGTTTG 59.901 45.833 0.00 0.00 41.33 2.93
590 608 6.481954 AGGTTTGCAAATAGAAGAGTTACG 57.518 37.500 16.21 0.00 0.00 3.18
591 609 5.411669 AGGTTTGCAAATAGAAGAGTTACGG 59.588 40.000 16.21 0.00 0.00 4.02
605 623 7.927092 AGAAGAGTTACGGAAATATTTAGCTCC 59.073 37.037 0.00 0.00 0.00 4.70
608 626 7.711339 AGAGTTACGGAAATATTTAGCTCCAAG 59.289 37.037 0.00 0.00 0.00 3.61
612 630 7.881775 ACGGAAATATTTAGCTCCAAGAATT 57.118 32.000 0.00 0.00 0.00 2.17
732 948 0.039074 GGTAGGATGCGATGGAGACG 60.039 60.000 0.00 0.00 0.00 4.18
850 1095 0.670546 CCGATCTGCCGTTGTCAACT 60.671 55.000 13.67 0.00 0.00 3.16
856 1101 3.325870 TCTGCCGTTGTCAACTCTTATG 58.674 45.455 13.67 0.00 0.00 1.90
857 1102 3.006430 TCTGCCGTTGTCAACTCTTATGA 59.994 43.478 13.67 2.42 0.00 2.15
858 1103 3.325870 TGCCGTTGTCAACTCTTATGAG 58.674 45.455 13.67 4.14 45.43 2.90
859 1104 2.094417 GCCGTTGTCAACTCTTATGAGC 59.906 50.000 13.67 0.91 43.85 4.26
860 1105 3.589988 CCGTTGTCAACTCTTATGAGCT 58.410 45.455 13.67 0.00 43.85 4.09
861 1106 3.997021 CCGTTGTCAACTCTTATGAGCTT 59.003 43.478 13.67 0.00 43.85 3.74
862 1107 5.168569 CCGTTGTCAACTCTTATGAGCTTA 58.831 41.667 13.67 0.00 43.85 3.09
863 1108 5.812642 CCGTTGTCAACTCTTATGAGCTTAT 59.187 40.000 13.67 0.00 43.85 1.73
864 1109 6.019479 CCGTTGTCAACTCTTATGAGCTTATC 60.019 42.308 13.67 0.00 43.85 1.75
896 1144 1.182667 TACTATCTGCAGTGCACCGT 58.817 50.000 15.37 10.91 33.79 4.83
917 1165 2.791868 GCCGTGCACCAACCCTTTT 61.792 57.895 12.15 0.00 0.00 2.27
919 1167 0.249280 CCGTGCACCAACCCTTTTTC 60.249 55.000 12.15 0.00 0.00 2.29
931 1179 1.847088 CCCTTTTTCCCCTAGCTAGCT 59.153 52.381 23.12 23.12 0.00 3.32
932 1180 3.046374 CCCTTTTTCCCCTAGCTAGCTA 58.954 50.000 22.85 22.85 0.00 3.32
970 1218 7.299134 TCCCAAACCCAAAGTATTCTTTTCTA 58.701 34.615 0.00 0.00 41.31 2.10
1078 1328 0.247460 CCTGTCAGAATCCGAGCACA 59.753 55.000 0.00 0.00 0.00 4.57
1488 1744 3.382832 AAGGGCGTCGAGGTCCTG 61.383 66.667 30.26 0.00 0.00 3.86
1645 1909 0.655733 CCCGTACATCAATCGGTTGC 59.344 55.000 2.72 0.00 42.30 4.17
1669 1958 2.365635 GGCCAGGAGCTAGGTGGA 60.366 66.667 11.77 0.00 43.05 4.02
1728 2026 1.280421 AGAGATGGAGGGAAACTGTGC 59.720 52.381 0.00 0.00 0.00 4.57
1912 2223 8.280497 AGTACATCGTTTGATTTAAGTGTGTTC 58.720 33.333 0.00 0.00 30.49 3.18
1985 2472 5.623956 ATCCATATTAAGGACCAACGTCA 57.376 39.130 0.00 0.00 41.13 4.35
2000 2487 3.495434 ACGTCACCCCTTTCACAAATA 57.505 42.857 0.00 0.00 0.00 1.40
2010 2497 4.403432 CCCTTTCACAAATATGTCAGCCAT 59.597 41.667 0.00 0.00 37.82 4.40
2048 2535 2.202810 GTCCTAGCAGCGCACTCC 60.203 66.667 11.47 0.00 0.00 3.85
2059 2546 1.064906 AGCGCACTCCTACCAGTACTA 60.065 52.381 11.47 0.00 0.00 1.82
2093 2584 4.107051 GAGCCACACATGCGCCAC 62.107 66.667 4.18 0.00 0.00 5.01
2096 2587 4.088762 CCACACATGCGCCACGAC 62.089 66.667 4.18 0.00 0.00 4.34
2105 2596 2.048222 CGCCACGACCACTGACAT 60.048 61.111 0.00 0.00 0.00 3.06
2106 2597 2.382746 CGCCACGACCACTGACATG 61.383 63.158 0.00 0.00 0.00 3.21
2107 2598 1.301716 GCCACGACCACTGACATGT 60.302 57.895 0.00 0.00 0.00 3.21
2108 2599 1.568612 GCCACGACCACTGACATGTG 61.569 60.000 1.15 0.00 37.66 3.21
2109 2600 0.033366 CCACGACCACTGACATGTGA 59.967 55.000 1.15 0.00 40.12 3.58
2110 2601 1.139989 CACGACCACTGACATGTGAC 58.860 55.000 1.15 0.00 40.12 3.67
2111 2602 0.750249 ACGACCACTGACATGTGACA 59.250 50.000 1.15 0.00 40.12 3.58
2112 2603 1.344438 ACGACCACTGACATGTGACAT 59.656 47.619 1.15 0.00 40.12 3.06
2113 2604 1.728425 CGACCACTGACATGTGACATG 59.272 52.381 22.97 22.97 40.12 3.21
2114 2605 2.771089 GACCACTGACATGTGACATGT 58.229 47.619 29.32 29.32 40.12 3.21
2115 2606 2.481568 GACCACTGACATGTGACATGTG 59.518 50.000 33.26 22.20 40.12 3.21
2116 2607 1.808343 CCACTGACATGTGACATGTGG 59.192 52.381 33.26 23.61 40.12 4.17
2117 2608 1.808343 CACTGACATGTGACATGTGGG 59.192 52.381 33.26 25.01 40.12 4.61
2118 2609 1.699083 ACTGACATGTGACATGTGGGA 59.301 47.619 33.26 16.56 31.52 4.37
2119 2610 2.079158 CTGACATGTGACATGTGGGAC 58.921 52.381 33.26 19.66 31.52 4.46
2120 2611 1.078709 GACATGTGACATGTGGGACG 58.921 55.000 33.26 5.61 31.52 4.79
2121 2612 0.321564 ACATGTGACATGTGGGACGG 60.322 55.000 28.51 2.08 0.00 4.79
2122 2613 1.377202 ATGTGACATGTGGGACGGC 60.377 57.895 1.15 0.00 0.00 5.68
2123 2614 2.746277 GTGACATGTGGGACGGCC 60.746 66.667 1.15 0.00 0.00 6.13
2124 2615 3.245346 TGACATGTGGGACGGCCA 61.245 61.111 11.00 0.00 35.15 5.36
2125 2616 2.746277 GACATGTGGGACGGCCAC 60.746 66.667 11.00 6.24 38.52 5.01
2126 2617 3.249189 ACATGTGGGACGGCCACT 61.249 61.111 11.00 0.00 38.79 4.00
2127 2618 2.747460 CATGTGGGACGGCCACTG 60.747 66.667 11.00 0.00 38.79 3.66
2128 2619 2.927856 ATGTGGGACGGCCACTGA 60.928 61.111 11.00 0.00 38.79 3.41
2129 2620 3.254024 ATGTGGGACGGCCACTGAC 62.254 63.158 11.00 0.00 38.79 3.51
2130 2621 3.936203 GTGGGACGGCCACTGACA 61.936 66.667 11.00 0.00 35.53 3.58
2131 2622 2.927856 TGGGACGGCCACTGACAT 60.928 61.111 11.00 0.00 35.15 3.06
2132 2623 2.436646 GGGACGGCCACTGACATG 60.437 66.667 11.00 0.00 35.15 3.21
2133 2624 2.347490 GGACGGCCACTGACATGT 59.653 61.111 0.00 0.00 0.00 3.21
2134 2625 2.034879 GGACGGCCACTGACATGTG 61.035 63.158 0.00 0.00 37.66 3.21
2135 2626 1.005037 GACGGCCACTGACATGTGA 60.005 57.895 1.15 0.00 40.12 3.58
2136 2627 1.291877 GACGGCCACTGACATGTGAC 61.292 60.000 1.15 0.00 40.12 3.67
2137 2628 1.301637 CGGCCACTGACATGTGACA 60.302 57.895 1.15 0.00 40.12 3.58
2138 2629 0.674581 CGGCCACTGACATGTGACAT 60.675 55.000 1.15 0.00 40.12 3.06
2142 2633 1.808343 CCACTGACATGTGACATGTGG 59.192 52.381 33.26 23.61 40.12 4.17
2174 2665 2.677836 GCCATACACACACCACACATAG 59.322 50.000 0.00 0.00 0.00 2.23
2188 2679 4.072131 CACACATAGGTAGGCACAAAAGT 58.928 43.478 0.00 0.00 0.00 2.66
2197 2688 3.508845 AGGCACAAAAGTCCTACACAT 57.491 42.857 0.00 0.00 0.00 3.21
2198 2689 3.412386 AGGCACAAAAGTCCTACACATC 58.588 45.455 0.00 0.00 0.00 3.06
2256 3055 5.068855 TCAACATTTGAGAATTGACTGGCAA 59.931 36.000 0.00 0.00 36.36 4.52
2263 3062 3.755378 GAGAATTGACTGGCAATGACTGT 59.245 43.478 9.96 0.00 46.25 3.55
2284 3083 9.349713 GACTGTTATGACAATAAAATATCCCCA 57.650 33.333 0.00 0.00 34.85 4.96
2293 3092 3.603965 AAAATATCCCCATAACCGGCA 57.396 42.857 0.00 0.00 0.00 5.69
2309 3109 1.407437 CGGCAAGTTTCCTAGCTCCAT 60.407 52.381 0.00 0.00 0.00 3.41
2342 3142 9.507329 TGATATTCTCTTTGTTGCTCTAAAAGT 57.493 29.630 0.00 0.00 33.56 2.66
2348 3148 5.694910 TCTTTGTTGCTCTAAAAGTACTCCG 59.305 40.000 0.00 0.00 33.56 4.63
2349 3149 4.595762 TGTTGCTCTAAAAGTACTCCGT 57.404 40.909 0.00 0.00 0.00 4.69
2350 3150 4.952460 TGTTGCTCTAAAAGTACTCCGTT 58.048 39.130 0.00 0.00 0.00 4.44
2351 3151 4.986659 TGTTGCTCTAAAAGTACTCCGTTC 59.013 41.667 0.00 0.00 0.00 3.95
2352 3152 3.829948 TGCTCTAAAAGTACTCCGTTCG 58.170 45.455 0.00 0.00 0.00 3.95
2353 3153 3.177487 GCTCTAAAAGTACTCCGTTCGG 58.823 50.000 4.74 4.74 0.00 4.30
2354 3154 3.119708 GCTCTAAAAGTACTCCGTTCGGA 60.120 47.826 13.34 13.34 0.00 4.55
2355 3155 4.616835 GCTCTAAAAGTACTCCGTTCGGAA 60.617 45.833 14.79 0.00 33.41 4.30
2356 3156 5.648572 CTCTAAAAGTACTCCGTTCGGAAT 58.351 41.667 14.79 7.89 33.41 3.01
2357 3157 6.029346 TCTAAAAGTACTCCGTTCGGAATT 57.971 37.500 14.79 7.65 33.41 2.17
2358 3158 7.156876 TCTAAAAGTACTCCGTTCGGAATTA 57.843 36.000 14.79 6.75 33.41 1.40
2359 3159 7.029563 TCTAAAAGTACTCCGTTCGGAATTAC 58.970 38.462 14.79 16.51 33.41 1.89
2360 3160 5.397142 AAAGTACTCCGTTCGGAATTACT 57.603 39.130 20.25 20.25 35.97 2.24
2361 3161 5.397142 AAGTACTCCGTTCGGAATTACTT 57.603 39.130 25.67 25.67 37.82 2.24
2362 3162 4.741342 AGTACTCCGTTCGGAATTACTTG 58.259 43.478 20.25 9.75 33.12 3.16
2363 3163 3.672767 ACTCCGTTCGGAATTACTTGT 57.327 42.857 14.79 5.03 33.41 3.16
2364 3164 3.582780 ACTCCGTTCGGAATTACTTGTC 58.417 45.455 14.79 0.00 33.41 3.18
2365 3165 3.257624 ACTCCGTTCGGAATTACTTGTCT 59.742 43.478 14.79 0.00 33.41 3.41
2366 3166 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
2367 3167 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
2368 3168 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
2369 3169 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
2370 3170 4.240096 GTTCGGAATTACTTGTCTCGGAA 58.760 43.478 0.00 0.00 0.00 4.30
2371 3171 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
2372 3172 5.080969 TCGGAATTACTTGTCTCGGAAAT 57.919 39.130 0.00 0.00 0.00 2.17
2373 3173 6.211587 TCGGAATTACTTGTCTCGGAAATA 57.788 37.500 0.00 0.00 0.00 1.40
2374 3174 6.270815 TCGGAATTACTTGTCTCGGAAATAG 58.729 40.000 0.00 0.00 0.00 1.73
2375 3175 6.095860 TCGGAATTACTTGTCTCGGAAATAGA 59.904 38.462 0.00 0.00 0.00 1.98
2376 3176 6.924060 CGGAATTACTTGTCTCGGAAATAGAT 59.076 38.462 0.00 0.00 0.00 1.98
2377 3177 7.096023 CGGAATTACTTGTCTCGGAAATAGATG 60.096 40.741 0.00 0.00 0.00 2.90
2378 3178 7.711339 GGAATTACTTGTCTCGGAAATAGATGT 59.289 37.037 0.00 0.00 0.00 3.06
2379 3179 9.745880 GAATTACTTGTCTCGGAAATAGATGTA 57.254 33.333 0.00 0.00 0.00 2.29
2381 3181 9.915629 ATTACTTGTCTCGGAAATAGATGTATC 57.084 33.333 0.00 0.00 0.00 2.24
2382 3182 7.589958 ACTTGTCTCGGAAATAGATGTATCT 57.410 36.000 0.00 0.00 40.86 1.98
2383 3183 8.693120 ACTTGTCTCGGAAATAGATGTATCTA 57.307 34.615 4.22 4.22 43.00 1.98
2384 3184 8.788806 ACTTGTCTCGGAAATAGATGTATCTAG 58.211 37.037 7.57 0.00 42.20 2.43
2385 3185 8.919777 TTGTCTCGGAAATAGATGTATCTAGA 57.080 34.615 7.57 0.00 42.20 2.43
2386 3186 8.919777 TGTCTCGGAAATAGATGTATCTAGAA 57.080 34.615 0.00 0.00 42.20 2.10
2387 3187 8.784994 TGTCTCGGAAATAGATGTATCTAGAAC 58.215 37.037 0.00 0.00 42.20 3.01
2388 3188 9.005777 GTCTCGGAAATAGATGTATCTAGAACT 57.994 37.037 0.00 0.00 42.20 3.01
2417 3217 9.915629 AATACGTCTAGATACATCCATTTCTTC 57.084 33.333 0.00 0.00 0.00 2.87
2418 3218 6.439599 ACGTCTAGATACATCCATTTCTTCG 58.560 40.000 0.00 0.00 0.00 3.79
2419 3219 6.262496 ACGTCTAGATACATCCATTTCTTCGA 59.738 38.462 0.00 0.00 0.00 3.71
2420 3220 6.579292 CGTCTAGATACATCCATTTCTTCGAC 59.421 42.308 0.00 0.00 0.00 4.20
2421 3221 7.426410 GTCTAGATACATCCATTTCTTCGACA 58.574 38.462 0.00 0.00 0.00 4.35
2422 3222 7.921214 GTCTAGATACATCCATTTCTTCGACAA 59.079 37.037 0.00 0.00 0.00 3.18
2423 3223 6.910536 AGATACATCCATTTCTTCGACAAC 57.089 37.500 0.00 0.00 0.00 3.32
2424 3224 6.644347 AGATACATCCATTTCTTCGACAACT 58.356 36.000 0.00 0.00 0.00 3.16
2425 3225 7.782049 AGATACATCCATTTCTTCGACAACTA 58.218 34.615 0.00 0.00 0.00 2.24
2426 3226 8.258007 AGATACATCCATTTCTTCGACAACTAA 58.742 33.333 0.00 0.00 0.00 2.24
2427 3227 8.964476 ATACATCCATTTCTTCGACAACTAAT 57.036 30.769 0.00 0.00 0.00 1.73
2428 3228 7.687941 ACATCCATTTCTTCGACAACTAATT 57.312 32.000 0.00 0.00 0.00 1.40
2429 3229 7.752695 ACATCCATTTCTTCGACAACTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
2430 3230 6.737254 TCCATTTCTTCGACAACTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
2431 3231 5.350365 TCCATTTCTTCGACAACTAATTCCG 59.650 40.000 0.00 0.00 0.00 4.30
2432 3232 5.350365 CCATTTCTTCGACAACTAATTCCGA 59.650 40.000 0.00 0.00 0.00 4.55
2433 3233 6.128391 CCATTTCTTCGACAACTAATTCCGAA 60.128 38.462 0.00 0.00 37.61 4.30
2434 3234 5.834239 TTCTTCGACAACTAATTCCGAAC 57.166 39.130 0.00 0.00 35.71 3.95
2435 3235 3.916172 TCTTCGACAACTAATTCCGAACG 59.084 43.478 0.00 0.00 35.71 3.95
2436 3236 2.598589 TCGACAACTAATTCCGAACGG 58.401 47.619 6.94 6.94 0.00 4.44
2437 3237 2.228582 TCGACAACTAATTCCGAACGGA 59.771 45.455 12.04 12.04 43.52 4.69
2438 3238 2.597305 CGACAACTAATTCCGAACGGAG 59.403 50.000 15.34 7.27 46.06 4.63
2439 3239 2.928116 GACAACTAATTCCGAACGGAGG 59.072 50.000 15.34 10.00 46.06 4.30
2440 3240 2.277084 CAACTAATTCCGAACGGAGGG 58.723 52.381 15.34 9.70 46.06 4.30
2444 3244 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
2447 3247 0.038744 TCCGAACGGAGGGAGTAAGT 59.961 55.000 12.04 0.00 39.76 2.24
2533 3340 8.519526 CCATTATTTGCTTTAAGTGTGTTCCTA 58.480 33.333 0.00 0.00 0.00 2.94
2580 3387 8.978874 TCACCAAAATTGCAGTATATATGACT 57.021 30.769 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 7.341805 AGAGCTTCTAGGCATTCTGAAATAAA 58.658 34.615 0.00 0.00 34.17 1.40
30 31 5.104610 TGAGAGCTTCTAGGCATTCTGAAAT 60.105 40.000 0.00 0.00 34.17 2.17
34 35 3.815856 TGAGAGCTTCTAGGCATTCTG 57.184 47.619 0.00 0.00 34.17 3.02
172 175 3.964031 AGATAGCTCTTTGGGAAGACGAT 59.036 43.478 0.00 0.00 36.99 3.73
202 205 2.982470 GCATACAAAACTTCTGTGCAGC 59.018 45.455 0.00 0.00 0.00 5.25
242 245 2.540383 TGGACTCACACTCCTAATGCT 58.460 47.619 0.00 0.00 0.00 3.79
349 352 7.367285 CAAATCCAAACTTTCGGATAAAGACA 58.633 34.615 4.59 0.00 41.28 3.41
404 407 2.778270 GCCTAATTTAGAGGGACCCTGT 59.222 50.000 20.90 18.07 31.76 4.00
489 492 6.089954 GCTTCAAATTGCTAAACAGCTAAAGG 59.910 38.462 0.00 0.00 35.49 3.11
491 494 6.642131 CAGCTTCAAATTGCTAAACAGCTAAA 59.358 34.615 0.00 0.00 37.81 1.85
492 495 6.016360 TCAGCTTCAAATTGCTAAACAGCTAA 60.016 34.615 0.00 0.00 37.81 3.09
493 496 5.473162 TCAGCTTCAAATTGCTAAACAGCTA 59.527 36.000 0.00 0.00 37.81 3.32
494 497 4.279169 TCAGCTTCAAATTGCTAAACAGCT 59.721 37.500 0.00 0.00 37.81 4.24
495 498 4.383948 GTCAGCTTCAAATTGCTAAACAGC 59.616 41.667 0.00 0.00 37.81 4.40
496 499 5.766222 AGTCAGCTTCAAATTGCTAAACAG 58.234 37.500 0.00 0.00 37.81 3.16
497 500 5.772825 AGTCAGCTTCAAATTGCTAAACA 57.227 34.783 0.00 0.00 37.81 2.83
498 501 6.072452 ACCTAGTCAGCTTCAAATTGCTAAAC 60.072 38.462 0.00 0.00 37.81 2.01
535 553 3.763897 AGTCAGCTTTTTGGACAACTGTT 59.236 39.130 4.19 0.00 34.04 3.16
541 559 5.227569 TCTCATAGTCAGCTTTTTGGACA 57.772 39.130 4.19 0.00 34.04 4.02
559 577 5.420725 TCTATTTGCAAACCTAGCTCTCA 57.579 39.130 15.41 0.00 0.00 3.27
732 948 1.488261 CCGACTATTTCCGCCGCTTC 61.488 60.000 0.00 0.00 0.00 3.86
850 1095 8.809468 ATATGTACTCCGATAAGCTCATAAGA 57.191 34.615 0.00 0.00 0.00 2.10
862 1107 9.278978 CTGCAGATAGTATATATGTACTCCGAT 57.721 37.037 14.69 4.56 36.39 4.18
863 1108 8.265764 ACTGCAGATAGTATATATGTACTCCGA 58.734 37.037 23.35 0.00 36.39 4.55
864 1109 8.338986 CACTGCAGATAGTATATATGTACTCCG 58.661 40.741 23.35 4.79 36.39 4.63
877 1125 1.134367 GACGGTGCACTGCAGATAGTA 59.866 52.381 25.67 6.49 40.08 1.82
878 1126 0.108615 GACGGTGCACTGCAGATAGT 60.109 55.000 25.67 10.91 40.08 2.12
879 1127 0.174389 AGACGGTGCACTGCAGATAG 59.826 55.000 25.67 10.90 40.08 2.08
896 1144 4.947147 GGGTTGGTGCACGGCAGA 62.947 66.667 11.45 0.00 40.08 4.26
917 1165 4.333690 CGAACTATAGCTAGCTAGGGGAA 58.666 47.826 27.42 7.85 31.45 3.97
919 1167 2.424246 GCGAACTATAGCTAGCTAGGGG 59.576 54.545 27.42 20.58 31.45 4.79
931 1179 4.510571 GGTTTGGGAGAAAGCGAACTATA 58.489 43.478 0.00 0.00 0.00 1.31
932 1180 3.344515 GGTTTGGGAGAAAGCGAACTAT 58.655 45.455 0.00 0.00 0.00 2.12
970 1218 4.735369 TCTCTTTCTCTCACTCTCTTGGT 58.265 43.478 0.00 0.00 0.00 3.67
1185 1435 4.753662 AGGGCGAGGCTCGTGGTA 62.754 66.667 34.41 0.00 42.81 3.25
1265 1521 4.193893 CATCCAGCCCCGCCATGA 62.194 66.667 0.00 0.00 0.00 3.07
1274 1530 3.628646 AAGTCCACGCCATCCAGCC 62.629 63.158 0.00 0.00 0.00 4.85
1536 1792 2.259818 CAGCGGCTCGACACTCTT 59.740 61.111 0.00 0.00 0.00 2.85
1645 1909 1.739338 CTAGCTCCTGGCCGGTACTG 61.739 65.000 11.58 0.39 43.05 2.74
1669 1958 0.110486 AAAGAAGCCGGACACCATGT 59.890 50.000 5.05 0.00 0.00 3.21
1761 2059 1.946745 GCTAGGAAGCTAGCCAGTTG 58.053 55.000 12.13 0.00 45.85 3.16
1881 2192 7.589587 CACTTAAATCAAACGATGTACTGCAAA 59.410 33.333 0.00 0.00 0.00 3.68
1912 2223 7.712264 TGATTTTGCTAATTTCAACACAAGG 57.288 32.000 0.00 0.00 0.00 3.61
1958 2269 7.215085 ACGTTGGTCCTTAATATGGATTAGAC 58.785 38.462 0.00 0.00 35.87 2.59
1962 2273 5.820947 GTGACGTTGGTCCTTAATATGGATT 59.179 40.000 0.00 0.00 42.73 3.01
1974 2285 0.887836 GAAAGGGGTGACGTTGGTCC 60.888 60.000 0.00 0.00 42.73 4.46
1985 2472 3.763897 GCTGACATATTTGTGAAAGGGGT 59.236 43.478 0.00 0.00 35.79 4.95
2000 2487 1.134280 GCCTCTGTGTATGGCTGACAT 60.134 52.381 0.00 0.00 43.05 3.06
2010 2497 2.826128 CCTAGTGAGTTGCCTCTGTGTA 59.174 50.000 0.00 0.00 38.61 2.90
2035 2522 1.667154 CTGGTAGGAGTGCGCTGCTA 61.667 60.000 22.85 22.85 41.78 3.49
2048 2535 6.072119 TGTGTCTCATGTGTTAGTACTGGTAG 60.072 42.308 5.39 0.00 0.00 3.18
2059 2546 2.880890 GGCTCTTTGTGTCTCATGTGTT 59.119 45.455 0.00 0.00 0.00 3.32
2093 2584 1.728425 CATGTCACATGTCAGTGGTCG 59.272 52.381 9.87 0.00 39.93 4.79
2096 2587 1.808343 CCACATGTCACATGTCAGTGG 59.192 52.381 21.04 14.87 39.93 4.00
2105 2596 2.031919 GCCGTCCCACATGTCACA 59.968 61.111 0.00 0.00 0.00 3.58
2106 2597 2.746277 GGCCGTCCCACATGTCAC 60.746 66.667 0.00 0.00 0.00 3.67
2107 2598 3.245346 TGGCCGTCCCACATGTCA 61.245 61.111 0.00 0.00 39.18 3.58
2114 2605 2.927856 ATGTCAGTGGCCGTCCCA 60.928 61.111 0.00 0.00 42.79 4.37
2115 2606 2.436646 CATGTCAGTGGCCGTCCC 60.437 66.667 0.00 0.00 0.00 4.46
2116 2607 2.034879 CACATGTCAGTGGCCGTCC 61.035 63.158 0.00 0.00 35.88 4.79
2117 2608 1.005037 TCACATGTCAGTGGCCGTC 60.005 57.895 0.00 0.00 39.93 4.79
2118 2609 1.301716 GTCACATGTCAGTGGCCGT 60.302 57.895 0.00 0.00 38.15 5.68
2119 2610 0.674581 ATGTCACATGTCAGTGGCCG 60.675 55.000 0.00 0.00 43.28 6.13
2120 2611 0.806868 CATGTCACATGTCAGTGGCC 59.193 55.000 9.87 0.00 43.28 5.36
2121 2612 1.198408 CACATGTCACATGTCAGTGGC 59.802 52.381 21.04 0.00 44.16 5.01
2122 2613 1.808343 CCACATGTCACATGTCAGTGG 59.192 52.381 21.04 14.87 39.93 4.00
2123 2614 1.808343 CCCACATGTCACATGTCAGTG 59.192 52.381 21.04 9.63 40.85 3.66
2124 2615 1.699083 TCCCACATGTCACATGTCAGT 59.301 47.619 21.04 0.00 0.00 3.41
2125 2616 2.079158 GTCCCACATGTCACATGTCAG 58.921 52.381 21.04 14.52 0.00 3.51
2126 2617 1.607767 CGTCCCACATGTCACATGTCA 60.608 52.381 21.04 5.08 0.00 3.58
2127 2618 1.078709 CGTCCCACATGTCACATGTC 58.921 55.000 21.04 8.75 0.00 3.06
2128 2619 0.955428 GCGTCCCACATGTCACATGT 60.955 55.000 18.20 18.20 0.00 3.21
2129 2620 0.954938 TGCGTCCCACATGTCACATG 60.955 55.000 16.68 16.68 0.00 3.21
2130 2621 0.250684 TTGCGTCCCACATGTCACAT 60.251 50.000 0.00 0.00 0.00 3.21
2131 2622 0.464554 TTTGCGTCCCACATGTCACA 60.465 50.000 0.00 0.00 0.00 3.58
2132 2623 0.665835 TTTTGCGTCCCACATGTCAC 59.334 50.000 0.00 0.00 0.00 3.67
2133 2624 1.336440 CTTTTTGCGTCCCACATGTCA 59.664 47.619 0.00 0.00 0.00 3.58
2134 2625 1.930371 GCTTTTTGCGTCCCACATGTC 60.930 52.381 0.00 0.00 0.00 3.06
2135 2626 0.031994 GCTTTTTGCGTCCCACATGT 59.968 50.000 0.00 0.00 0.00 3.21
2136 2627 0.667184 GGCTTTTTGCGTCCCACATG 60.667 55.000 0.00 0.00 44.05 3.21
2137 2628 1.112315 TGGCTTTTTGCGTCCCACAT 61.112 50.000 0.00 0.00 44.05 3.21
2138 2629 1.112315 ATGGCTTTTTGCGTCCCACA 61.112 50.000 0.00 0.00 44.05 4.17
2142 2633 1.268352 TGTGTATGGCTTTTTGCGTCC 59.732 47.619 0.00 0.00 44.05 4.79
2174 2665 3.072211 GTGTAGGACTTTTGTGCCTACC 58.928 50.000 13.85 4.19 43.97 3.18
2188 2679 2.398754 ATGGATCCGGATGTGTAGGA 57.601 50.000 24.82 0.00 38.56 2.94
2197 2688 1.729586 CCCCTAGAAATGGATCCGGA 58.270 55.000 6.61 6.61 0.00 5.14
2198 2689 0.693049 CCCCCTAGAAATGGATCCGG 59.307 60.000 7.39 0.00 0.00 5.14
2230 2721 6.433716 TGCCAGTCAATTCTCAAATGTTGATA 59.566 34.615 0.00 0.00 39.30 2.15
2293 3092 4.640771 TCACAATGGAGCTAGGAAACTT 57.359 40.909 0.00 0.00 43.67 2.66
2309 3109 8.114331 AGCAACAAAGAGAATATCATTCACAA 57.886 30.769 2.03 0.00 0.00 3.33
2342 3142 4.460382 AGACAAGTAATTCCGAACGGAGTA 59.540 41.667 15.34 9.66 45.00 2.59
2344 3144 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
2348 3148 3.841643 TCCGAGACAAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
2349 3149 4.524316 TTCCGAGACAAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
2350 3150 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
2351 3151 6.270815 TCTATTTCCGAGACAAGTAATTCCG 58.729 40.000 0.00 0.00 0.00 4.30
2352 3152 7.711339 ACATCTATTTCCGAGACAAGTAATTCC 59.289 37.037 0.00 0.00 0.00 3.01
2353 3153 8.649973 ACATCTATTTCCGAGACAAGTAATTC 57.350 34.615 0.00 0.00 0.00 2.17
2355 3155 9.915629 GATACATCTATTTCCGAGACAAGTAAT 57.084 33.333 0.00 0.00 0.00 1.89
2356 3156 9.132923 AGATACATCTATTTCCGAGACAAGTAA 57.867 33.333 0.00 0.00 34.85 2.24
2357 3157 8.693120 AGATACATCTATTTCCGAGACAAGTA 57.307 34.615 0.00 0.00 34.85 2.24
2358 3158 7.589958 AGATACATCTATTTCCGAGACAAGT 57.410 36.000 0.00 0.00 34.85 3.16
2359 3159 9.004717 TCTAGATACATCTATTTCCGAGACAAG 57.995 37.037 0.00 0.00 38.60 3.16
2360 3160 8.919777 TCTAGATACATCTATTTCCGAGACAA 57.080 34.615 0.00 0.00 38.60 3.18
2361 3161 8.784994 GTTCTAGATACATCTATTTCCGAGACA 58.215 37.037 0.00 0.00 38.60 3.41
2362 3162 9.005777 AGTTCTAGATACATCTATTTCCGAGAC 57.994 37.037 0.00 0.00 38.60 3.36
2391 3191 9.915629 GAAGAAATGGATGTATCTAGACGTATT 57.084 33.333 0.00 0.00 0.00 1.89
2392 3192 8.237949 CGAAGAAATGGATGTATCTAGACGTAT 58.762 37.037 0.00 0.00 0.00 3.06
2393 3193 7.443272 TCGAAGAAATGGATGTATCTAGACGTA 59.557 37.037 0.00 0.00 0.00 3.57
2394 3194 6.262496 TCGAAGAAATGGATGTATCTAGACGT 59.738 38.462 0.00 0.00 0.00 4.34
2395 3195 6.579292 GTCGAAGAAATGGATGTATCTAGACG 59.421 42.308 0.00 0.00 39.69 4.18
2396 3196 7.426410 TGTCGAAGAAATGGATGTATCTAGAC 58.574 38.462 0.00 0.00 39.69 2.59
2397 3197 7.582667 TGTCGAAGAAATGGATGTATCTAGA 57.417 36.000 0.00 0.00 39.69 2.43
2398 3198 7.923344 AGTTGTCGAAGAAATGGATGTATCTAG 59.077 37.037 0.00 0.00 39.69 2.43
2399 3199 7.782049 AGTTGTCGAAGAAATGGATGTATCTA 58.218 34.615 0.00 0.00 39.69 1.98
2400 3200 6.644347 AGTTGTCGAAGAAATGGATGTATCT 58.356 36.000 0.00 0.00 39.69 1.98
2401 3201 6.910536 AGTTGTCGAAGAAATGGATGTATC 57.089 37.500 0.00 0.00 39.69 2.24
2402 3202 8.964476 ATTAGTTGTCGAAGAAATGGATGTAT 57.036 30.769 0.00 0.00 39.69 2.29
2403 3203 8.786826 AATTAGTTGTCGAAGAAATGGATGTA 57.213 30.769 0.00 0.00 39.69 2.29
2404 3204 7.148239 GGAATTAGTTGTCGAAGAAATGGATGT 60.148 37.037 0.00 0.00 39.69 3.06
2405 3205 7.189512 GGAATTAGTTGTCGAAGAAATGGATG 58.810 38.462 0.00 0.00 39.69 3.51
2406 3206 6.037172 CGGAATTAGTTGTCGAAGAAATGGAT 59.963 38.462 0.00 0.00 39.69 3.41
2407 3207 5.350365 CGGAATTAGTTGTCGAAGAAATGGA 59.650 40.000 0.00 0.00 39.69 3.41
2408 3208 5.350365 TCGGAATTAGTTGTCGAAGAAATGG 59.650 40.000 0.00 0.00 39.69 3.16
2409 3209 6.403333 TCGGAATTAGTTGTCGAAGAAATG 57.597 37.500 0.00 0.00 39.69 2.32
2410 3210 6.400727 CGTTCGGAATTAGTTGTCGAAGAAAT 60.401 38.462 0.00 0.00 39.69 2.17
2411 3211 5.107760 CGTTCGGAATTAGTTGTCGAAGAAA 60.108 40.000 0.00 0.00 39.69 2.52
2412 3212 4.383649 CGTTCGGAATTAGTTGTCGAAGAA 59.616 41.667 0.00 0.00 39.69 2.52
2413 3213 3.916172 CGTTCGGAATTAGTTGTCGAAGA 59.084 43.478 0.00 0.00 39.89 2.87
2414 3214 3.060363 CCGTTCGGAATTAGTTGTCGAAG 59.940 47.826 5.19 0.00 39.89 3.79
2415 3215 2.988493 CCGTTCGGAATTAGTTGTCGAA 59.012 45.455 5.19 0.00 37.48 3.71
2416 3216 2.228582 TCCGTTCGGAATTAGTTGTCGA 59.771 45.455 11.66 0.00 0.00 4.20
2417 3217 2.597305 CTCCGTTCGGAATTAGTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
2418 3218 2.928116 CCTCCGTTCGGAATTAGTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2419 3219 2.354403 CCCTCCGTTCGGAATTAGTTGT 60.354 50.000 14.79 0.00 33.41 3.32
2420 3220 2.093869 TCCCTCCGTTCGGAATTAGTTG 60.094 50.000 14.79 1.97 33.41 3.16
2421 3221 2.167900 CTCCCTCCGTTCGGAATTAGTT 59.832 50.000 14.79 0.00 33.41 2.24
2422 3222 1.755380 CTCCCTCCGTTCGGAATTAGT 59.245 52.381 14.79 0.00 33.41 2.24
2423 3223 1.755380 ACTCCCTCCGTTCGGAATTAG 59.245 52.381 14.79 13.09 33.41 1.73
2424 3224 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2425 3225 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
2426 3226 1.755380 CTTACTCCCTCCGTTCGGAAT 59.245 52.381 14.79 2.09 33.41 3.01
2427 3227 1.180029 CTTACTCCCTCCGTTCGGAA 58.820 55.000 14.79 0.04 33.41 4.30
2428 3228 0.038744 ACTTACTCCCTCCGTTCGGA 59.961 55.000 13.34 13.34 0.00 4.55
2429 3229 0.172803 CACTTACTCCCTCCGTTCGG 59.827 60.000 4.74 4.74 0.00 4.30
2430 3230 0.886563 ACACTTACTCCCTCCGTTCG 59.113 55.000 0.00 0.00 0.00 3.95
2431 3231 4.732672 AATACACTTACTCCCTCCGTTC 57.267 45.455 0.00 0.00 0.00 3.95
2432 3232 4.529377 TCAAATACACTTACTCCCTCCGTT 59.471 41.667 0.00 0.00 0.00 4.44
2433 3233 4.091549 TCAAATACACTTACTCCCTCCGT 58.908 43.478 0.00 0.00 0.00 4.69
2434 3234 4.730949 TCAAATACACTTACTCCCTCCG 57.269 45.455 0.00 0.00 0.00 4.63
2435 3235 7.963532 TCATATCAAATACACTTACTCCCTCC 58.036 38.462 0.00 0.00 0.00 4.30
2436 3236 9.429359 CATCATATCAAATACACTTACTCCCTC 57.571 37.037 0.00 0.00 0.00 4.30
2437 3237 9.159254 TCATCATATCAAATACACTTACTCCCT 57.841 33.333 0.00 0.00 0.00 4.20
2438 3238 9.950496 ATCATCATATCAAATACACTTACTCCC 57.050 33.333 0.00 0.00 0.00 4.30
2557 3364 9.407380 TCAAGTCATATATACTGCAATTTTGGT 57.593 29.630 0.00 0.00 0.00 3.67
2580 3387 0.806102 GCGCGGCATCTTCTAGTCAA 60.806 55.000 8.83 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.