Multiple sequence alignment - TraesCS3B01G190800

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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 TraesCS3B01G190800 chr3B 100.000 2663 0 0 1 2663 203641974 203644636 0.000000e+00 4918.0
1 TraesCS3B01G190800 chr3A 92.311 2055 113 22 181 2207 160073646 160075683 0.000000e+00 2878.0
2 TraesCS3B01G190800 chr3A 90.909 352 22 6 2316 2661 160075689 160076036 5.190000e-127 464.0
3 TraesCS3B01G190800 chr3A 90.226 133 12 1 1 132 160073517 160073649 3.520000e-39 172.0
4 TraesCS3B01G190800 chr3D 91.555 1788 90 17 164 1918 141657293 141659052 0.000000e+00 2409.0
5 TraesCS3B01G190800 chr3D 95.904 293 12 0 1907 2199 141659505 141659797 2.400000e-130 475.0
6 TraesCS3B01G190800 chr3D 90.055 362 19 11 2316 2663 141659810 141660168 1.120000e-123 453.0
7 TraesCS3B01G190800 chr3D 74.568 405 83 9 79 482 96672449 96672064 2.740000e-35 159.0
8 TraesCS3B01G190800 chr3D 97.403 77 1 1 2205 2281 392282167 392282092 2.150000e-26 130.0
9 TraesCS3B01G190800 chr3D 97.143 70 2 0 2212 2281 604683582 604683513 4.660000e-23 119.0
10 TraesCS3B01G190800 chr7D 82.057 457 74 5 20 471 138285758 138285305 1.500000e-102 383.0
11 TraesCS3B01G190800 chr7D 94.805 77 3 1 2205 2281 131620132 131620207 4.660000e-23 119.0
12 TraesCS3B01G190800 chr7D 83.065 124 20 1 36 159 99967007 99966885 7.790000e-21 111.0
13 TraesCS3B01G190800 chrUn 81.513 476 77 8 20 484 10264374 10263899 5.380000e-102 381.0
14 TraesCS3B01G190800 chr5A 80.425 424 80 3 36 458 356103572 356103151 1.190000e-83 320.0
15 TraesCS3B01G190800 chr2B 80.285 421 82 1 38 458 569979080 569978661 1.540000e-82 316.0
16 TraesCS3B01G190800 chr2D 77.731 476 87 16 20 484 49353838 49353371 9.390000e-70 274.0
17 TraesCS3B01G190800 chr2D 83.516 91 14 1 56 146 398308702 398308791 1.700000e-12 84.2
18 TraesCS3B01G190800 chr2A 80.059 341 64 3 135 474 749909370 749909033 1.580000e-62 250.0
19 TraesCS3B01G190800 chr6D 82.258 186 32 1 58 242 453964285 453964100 2.740000e-35 159.0
20 TraesCS3B01G190800 chr6D 98.571 70 1 0 2212 2281 24825486 24825555 1.000000e-24 124.0
21 TraesCS3B01G190800 chr1A 96.000 75 3 0 2207 2281 561611238 561611312 3.600000e-24 122.0
22 TraesCS3B01G190800 chr4D 94.805 77 3 1 2205 2281 497036281 497036356 4.660000e-23 119.0
23 TraesCS3B01G190800 chr1B 95.946 74 2 1 2208 2281 436383753 436383681 4.660000e-23 119.0
24 TraesCS3B01G190800 chr5D 89.888 89 7 2 2193 2281 455323432 455323346 2.170000e-21 113.0
25 TraesCS3B01G190800 chr6A 93.333 75 5 0 2207 2281 1090373 1090299 7.790000e-21 111.0


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 TraesCS3B01G190800 chr3B 203641974 203644636 2662 False 4918.000000 4918 100.000000 1 2663 1 chr3B.!!$F1 2662
1 TraesCS3B01G190800 chr3A 160073517 160076036 2519 False 1171.333333 2878 91.148667 1 2661 3 chr3A.!!$F1 2660
2 TraesCS3B01G190800 chr3D 141657293 141660168 2875 False 1112.333333 2409 92.504667 164 2663 3 chr3D.!!$F1 2499

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
353 356 0.846427 AGGAGGATTGGAAGCCCACA 60.846 55.0 0.0 0.0 43.41 4.17 F
1527 1549 0.322546 GGAAGAACGGGAACAGCCAT 60.323 55.0 0.0 0.0 38.95 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1617 1639 0.039437 GGAGAACGACGAGCAAGTGA 60.039 55.0 0.0 0.0 0.0 3.41 R
2601 3121 1.665137 TTTTAGGGTGAGGGAGGGAC 58.335 55.0 0.0 0.0 0.0 4.46 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.285790 GTTGCTTTTGTGGTGAAAATAAGG 57.714 37.500 0.00 0.00 0.00 2.69
44 46 1.264288 GTTGCTTTTGGTGAGGAGTCG 59.736 52.381 0.00 0.00 0.00 4.18
59 61 5.419155 TGAGGAGTCGATTCAGTGTCTATTT 59.581 40.000 10.32 0.00 0.00 1.40
66 68 6.809196 GTCGATTCAGTGTCTATTTCTTCACT 59.191 38.462 0.00 0.00 41.02 3.41
98 100 2.656560 AGCTATTATGGCGATCGGTC 57.343 50.000 18.30 0.00 34.52 4.79
105 107 5.607939 ATTATGGCGATCGGTCCATATAA 57.392 39.130 25.55 18.06 42.85 0.98
106 108 2.736144 TGGCGATCGGTCCATATAAC 57.264 50.000 18.30 0.00 0.00 1.89
132 134 6.540438 TTAATCTACCTCTACCCACAAGTG 57.460 41.667 0.00 0.00 0.00 3.16
133 135 3.820195 TCTACCTCTACCCACAAGTGA 57.180 47.619 0.94 0.00 0.00 3.41
134 136 4.332683 TCTACCTCTACCCACAAGTGAT 57.667 45.455 0.94 0.00 0.00 3.06
135 137 5.461516 TCTACCTCTACCCACAAGTGATA 57.538 43.478 0.94 0.00 0.00 2.15
136 138 6.027025 TCTACCTCTACCCACAAGTGATAT 57.973 41.667 0.94 0.00 0.00 1.63
137 139 5.833667 TCTACCTCTACCCACAAGTGATATG 59.166 44.000 0.94 0.00 0.00 1.78
138 140 4.620723 ACCTCTACCCACAAGTGATATGA 58.379 43.478 0.94 0.00 0.00 2.15
139 141 5.030147 ACCTCTACCCACAAGTGATATGAA 58.970 41.667 0.94 0.00 0.00 2.57
140 142 5.667626 ACCTCTACCCACAAGTGATATGAAT 59.332 40.000 0.94 0.00 0.00 2.57
141 143 6.844388 ACCTCTACCCACAAGTGATATGAATA 59.156 38.462 0.94 0.00 0.00 1.75
142 144 7.514127 ACCTCTACCCACAAGTGATATGAATAT 59.486 37.037 0.94 0.00 0.00 1.28
143 145 7.821359 CCTCTACCCACAAGTGATATGAATATG 59.179 40.741 0.94 0.00 0.00 1.78
144 146 8.262601 TCTACCCACAAGTGATATGAATATGT 57.737 34.615 0.94 0.00 0.00 2.29
145 147 8.713971 TCTACCCACAAGTGATATGAATATGTT 58.286 33.333 0.94 0.00 0.00 2.71
146 148 7.807977 ACCCACAAGTGATATGAATATGTTC 57.192 36.000 0.94 0.00 34.85 3.18
147 149 6.483307 ACCCACAAGTGATATGAATATGTTCG 59.517 38.462 0.94 0.00 37.15 3.95
148 150 6.705825 CCCACAAGTGATATGAATATGTTCGA 59.294 38.462 0.94 0.00 37.15 3.71
149 151 7.226523 CCCACAAGTGATATGAATATGTTCGAA 59.773 37.037 0.94 0.00 37.15 3.71
150 152 8.611757 CCACAAGTGATATGAATATGTTCGAAA 58.388 33.333 0.00 0.00 37.15 3.46
151 153 9.986833 CACAAGTGATATGAATATGTTCGAAAA 57.013 29.630 0.00 0.00 37.15 2.29
152 154 9.988350 ACAAGTGATATGAATATGTTCGAAAAC 57.012 29.630 0.00 0.00 37.15 2.43
162 164 9.917129 TGAATATGTTCGAAAACTAGTTAGTGA 57.083 29.630 8.92 4.11 37.15 3.41
166 168 7.035840 TGTTCGAAAACTAGTTAGTGAGAGT 57.964 36.000 8.92 0.00 36.50 3.24
168 170 6.630444 TCGAAAACTAGTTAGTGAGAGTGT 57.370 37.500 8.92 0.00 36.50 3.55
192 194 3.261897 TCCCAAGTTGAAGTCTCAGATCC 59.738 47.826 3.87 0.00 31.69 3.36
217 219 8.030106 CCGTATGAAAATTTGGGCTTTACTTTA 58.970 33.333 0.00 0.00 0.00 1.85
218 220 9.413048 CGTATGAAAATTTGGGCTTTACTTTAA 57.587 29.630 0.00 0.00 0.00 1.52
242 244 6.215845 AGCCATTTCAAACACTTGTAATGAC 58.784 36.000 14.88 6.95 45.82 3.06
243 245 5.405269 GCCATTTCAAACACTTGTAATGACC 59.595 40.000 14.88 5.85 45.82 4.02
256 258 9.666626 CACTTGTAATGACCGTATTTTTAACAA 57.333 29.630 0.00 0.00 0.00 2.83
345 348 1.600058 ATGCAAGGAGGAGGATTGGA 58.400 50.000 0.00 0.00 0.00 3.53
353 356 0.846427 AGGAGGATTGGAAGCCCACA 60.846 55.000 0.00 0.00 43.41 4.17
433 436 6.618196 AGTTGGTGGGCTATTAGTAGGATTTA 59.382 38.462 0.00 0.00 0.00 1.40
487 494 4.615588 TTTTATTTCCCTTGGGCAACTG 57.384 40.909 0.00 0.00 0.00 3.16
488 495 1.555967 TATTTCCCTTGGGCAACTGC 58.444 50.000 0.00 0.00 41.14 4.40
571 578 1.332889 ACTCGATGATGCAGAGGCCA 61.333 55.000 5.01 0.00 40.13 5.36
649 661 7.710676 ATTAGTAGTGCTATTCCTCGATGAT 57.289 36.000 0.00 0.00 0.00 2.45
686 698 6.112058 CCTCACTCTTTCTTTAGATGGAAGG 58.888 44.000 0.00 0.00 0.00 3.46
690 702 7.235606 TCACTCTTTCTTTAGATGGAAGGAAGA 59.764 37.037 7.23 7.23 43.23 2.87
702 714 3.379057 TGGAAGGAAGAACGGTTTTTGTC 59.621 43.478 0.93 0.00 0.00 3.18
788 800 2.507886 TGAGTTCAAGTCCCAGGAAACA 59.492 45.455 0.00 0.00 0.00 2.83
842 854 6.963049 AATAACGACTACATTGACTGGAAC 57.037 37.500 0.00 0.00 0.00 3.62
843 855 2.942710 ACGACTACATTGACTGGAACG 58.057 47.619 0.00 0.00 0.00 3.95
844 856 2.295349 ACGACTACATTGACTGGAACGT 59.705 45.455 0.00 0.00 0.00 3.99
845 857 3.503363 ACGACTACATTGACTGGAACGTA 59.497 43.478 0.00 0.00 0.00 3.57
914 926 2.158943 CGTATTCAGTTCCCTCCCTTCC 60.159 54.545 0.00 0.00 0.00 3.46
964 976 2.429610 TCTACCGAACATACTTCAGCCC 59.570 50.000 0.00 0.00 0.00 5.19
967 979 1.737793 CCGAACATACTTCAGCCCAAC 59.262 52.381 0.00 0.00 0.00 3.77
1043 1055 4.637489 CCTCGCGCTCAGGATCGG 62.637 72.222 15.53 0.00 31.91 4.18
1047 1059 4.593864 GCGCTCAGGATCGGGACC 62.594 72.222 0.00 0.00 0.00 4.46
1190 1202 2.032528 TGCTCCCAGCTGTTTCCG 59.967 61.111 13.81 0.00 42.97 4.30
1432 1454 5.298276 TGATTAGGTCGTTTTTGCTGAACTT 59.702 36.000 0.00 0.00 30.94 2.66
1442 1464 3.713858 TTGCTGAACTTGTTGTCATGG 57.286 42.857 0.00 0.00 0.00 3.66
1451 1473 2.677524 TTGTCATGGGCTGCAGGC 60.678 61.111 30.97 30.97 40.90 4.85
1527 1549 0.322546 GGAAGAACGGGAACAGCCAT 60.323 55.000 0.00 0.00 38.95 4.40
1584 1606 3.295304 CTGCGACCATGTCACGGGA 62.295 63.158 0.00 0.00 32.09 5.14
1617 1639 3.606065 CTTCGTCGCGGTCGTCCTT 62.606 63.158 19.63 0.00 36.96 3.36
1623 1645 2.372690 CGCGGTCGTCCTTCACTTG 61.373 63.158 0.00 0.00 0.00 3.16
1726 1766 5.295152 TCGAATATACACGCTCTCTCAGTA 58.705 41.667 0.00 0.00 0.00 2.74
1825 1865 0.245539 TAAAGCTTCGTCGACCCAGG 59.754 55.000 10.58 0.00 0.00 4.45
1918 2422 5.065218 ACAATGTTTCTTGTCACTGTGAGTC 59.935 40.000 11.41 0.83 34.26 3.36
1937 2441 1.757118 TCGGCCAAGATCGATTCTTCT 59.243 47.619 2.24 0.00 42.98 2.85
1969 2473 6.877611 TGTATGAGTATGAGCGAGTAATGA 57.122 37.500 0.00 0.00 0.00 2.57
2190 2698 5.991328 AGCTATTGTCCGAACATGTATTG 57.009 39.130 0.00 0.00 34.73 1.90
2199 2707 3.353524 CGAACATGTATTGGAATGCACG 58.646 45.455 0.00 0.00 33.87 5.34
2202 2710 2.682856 ACATGTATTGGAATGCACGTCC 59.317 45.455 10.75 10.75 33.87 4.79
2203 2711 1.364721 TGTATTGGAATGCACGTCCG 58.635 50.000 12.46 0.00 38.06 4.79
2204 2712 1.066787 TGTATTGGAATGCACGTCCGA 60.067 47.619 10.05 10.05 38.06 4.55
2206 2714 1.750193 ATTGGAATGCACGTCCGATT 58.250 45.000 13.25 0.04 36.02 3.34
2207 2715 2.388310 TTGGAATGCACGTCCGATTA 57.612 45.000 12.46 0.00 38.06 1.75
2208 2716 2.613026 TGGAATGCACGTCCGATTAT 57.387 45.000 12.46 0.00 38.06 1.28
2209 2717 3.737032 TGGAATGCACGTCCGATTATA 57.263 42.857 12.46 0.00 38.06 0.98
2210 2718 3.649073 TGGAATGCACGTCCGATTATAG 58.351 45.455 12.46 0.00 38.06 1.31
2211 2719 3.069016 TGGAATGCACGTCCGATTATAGT 59.931 43.478 12.46 0.00 38.06 2.12
2212 2720 4.278919 TGGAATGCACGTCCGATTATAGTA 59.721 41.667 12.46 0.00 38.06 1.82
2213 2721 4.620184 GGAATGCACGTCCGATTATAGTAC 59.380 45.833 2.59 0.00 0.00 2.73
2214 2722 5.449107 AATGCACGTCCGATTATAGTACT 57.551 39.130 0.00 0.00 0.00 2.73
2215 2723 4.478843 TGCACGTCCGATTATAGTACTC 57.521 45.455 0.00 0.00 0.00 2.59
2216 2724 3.251729 TGCACGTCCGATTATAGTACTCC 59.748 47.826 0.00 0.00 0.00 3.85
2217 2725 3.365767 GCACGTCCGATTATAGTACTCCC 60.366 52.174 0.00 0.00 0.00 4.30
2218 2726 4.070716 CACGTCCGATTATAGTACTCCCT 58.929 47.826 0.00 0.00 0.00 4.20
2219 2727 4.153835 CACGTCCGATTATAGTACTCCCTC 59.846 50.000 0.00 0.00 0.00 4.30
2220 2728 3.688673 CGTCCGATTATAGTACTCCCTCC 59.311 52.174 0.00 0.00 0.00 4.30
2221 2729 3.688673 GTCCGATTATAGTACTCCCTCCG 59.311 52.174 0.00 0.00 0.00 4.63
2222 2730 3.328931 TCCGATTATAGTACTCCCTCCGT 59.671 47.826 0.00 0.00 0.00 4.69
2223 2731 3.688673 CCGATTATAGTACTCCCTCCGTC 59.311 52.174 0.00 0.00 0.00 4.79
2224 2732 3.688673 CGATTATAGTACTCCCTCCGTCC 59.311 52.174 0.00 0.00 0.00 4.79
2225 2733 3.515602 TTATAGTACTCCCTCCGTCCC 57.484 52.381 0.00 0.00 0.00 4.46
2226 2734 1.229131 ATAGTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
2227 2735 1.229131 TAGTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
2228 2736 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2229 2737 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2230 2738 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2231 2739 3.400322 AGTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
2232 2740 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2233 2741 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2234 2742 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2235 2743 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2236 2744 4.359105 TCCCTCCGTCCCATAATATAAGG 58.641 47.826 0.00 0.00 0.00 2.69
2237 2745 4.046231 TCCCTCCGTCCCATAATATAAGGA 59.954 45.833 0.00 0.00 0.00 3.36
2238 2746 4.161754 CCCTCCGTCCCATAATATAAGGAC 59.838 50.000 10.16 10.16 44.42 3.85
2246 2754 8.441312 GTCCCATAATATAAGGACGTTTTTGA 57.559 34.615 6.05 0.00 39.47 2.69
2247 2755 8.340443 GTCCCATAATATAAGGACGTTTTTGAC 58.660 37.037 6.05 0.00 39.47 3.18
2248 2756 8.047911 TCCCATAATATAAGGACGTTTTTGACA 58.952 33.333 0.00 0.00 0.00 3.58
2249 2757 8.846211 CCCATAATATAAGGACGTTTTTGACAT 58.154 33.333 0.00 0.00 0.00 3.06
2255 2763 7.739498 ATAAGGACGTTTTTGACATTAGTGT 57.261 32.000 0.00 0.00 42.49 3.55
2256 2764 8.836268 ATAAGGACGTTTTTGACATTAGTGTA 57.164 30.769 0.00 0.00 39.09 2.90
2257 2765 6.780706 AGGACGTTTTTGACATTAGTGTAG 57.219 37.500 0.00 0.00 39.09 2.74
2258 2766 6.285990 AGGACGTTTTTGACATTAGTGTAGT 58.714 36.000 0.00 0.00 39.09 2.73
2259 2767 6.202188 AGGACGTTTTTGACATTAGTGTAGTG 59.798 38.462 0.00 0.00 39.09 2.74
2260 2768 6.018507 GGACGTTTTTGACATTAGTGTAGTGT 60.019 38.462 0.00 0.00 39.09 3.55
2261 2769 6.940714 ACGTTTTTGACATTAGTGTAGTGTC 58.059 36.000 0.00 3.35 43.31 3.67
2269 2777 6.913873 ACATTAGTGTAGTGTCAAAAACGT 57.086 33.333 0.00 0.00 36.63 3.99
2270 2778 7.311364 ACATTAGTGTAGTGTCAAAAACGTT 57.689 32.000 0.00 0.00 36.63 3.99
2271 2779 7.404203 ACATTAGTGTAGTGTCAAAAACGTTC 58.596 34.615 0.00 0.00 36.63 3.95
2272 2780 7.279313 ACATTAGTGTAGTGTCAAAAACGTTCT 59.721 33.333 0.00 0.00 36.63 3.01
2273 2781 7.599630 TTAGTGTAGTGTCAAAAACGTTCTT 57.400 32.000 0.00 0.00 0.00 2.52
2274 2782 8.700722 TTAGTGTAGTGTCAAAAACGTTCTTA 57.299 30.769 0.00 0.00 0.00 2.10
2275 2783 7.781548 AGTGTAGTGTCAAAAACGTTCTTAT 57.218 32.000 0.00 0.00 0.00 1.73
2276 2784 8.876275 AGTGTAGTGTCAAAAACGTTCTTATA 57.124 30.769 0.00 0.00 0.00 0.98
2277 2785 9.485206 AGTGTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 0.00 0.00 0.00 0.86
2286 2794 9.919348 TCAAAAACGTTCTTATATTATAACCGC 57.081 29.630 0.00 0.00 0.00 5.68
2287 2795 9.705471 CAAAAACGTTCTTATATTATAACCGCA 57.295 29.630 0.00 0.00 0.00 5.69
2311 2819 4.632538 AAAGAAAACGTTGGACAGAAGG 57.367 40.909 0.00 0.00 0.00 3.46
2312 2820 3.553828 AGAAAACGTTGGACAGAAGGA 57.446 42.857 0.00 0.00 0.00 3.36
2313 2821 3.467803 AGAAAACGTTGGACAGAAGGAG 58.532 45.455 0.00 0.00 0.00 3.69
2314 2822 3.118371 AGAAAACGTTGGACAGAAGGAGT 60.118 43.478 0.00 0.00 0.00 3.85
2327 2835 8.204836 TGGACAGAAGGAGTAATATTTAAGAGC 58.795 37.037 0.00 0.00 0.00 4.09
2331 2839 7.169982 CAGAAGGAGTAATATTTAAGAGCCACG 59.830 40.741 0.00 0.00 0.00 4.94
2334 2842 5.701290 GGAGTAATATTTAAGAGCCACGCAT 59.299 40.000 0.00 0.00 0.00 4.73
2335 2843 6.128526 GGAGTAATATTTAAGAGCCACGCATC 60.129 42.308 0.00 0.00 0.00 3.91
2352 2860 5.565259 CACGCATCTCACAAGTGAATTTAAC 59.435 40.000 4.29 0.00 39.39 2.01
2400 2914 3.502123 AATCAAAAGGTGTCGAAGGGA 57.498 42.857 0.00 0.00 0.00 4.20
2447 2961 6.091076 AGACAATTATTTTGGGATGGAGGA 57.909 37.500 0.00 0.00 0.00 3.71
2452 2966 7.342026 ACAATTATTTTGGGATGGAGGAAGTAC 59.658 37.037 0.00 0.00 0.00 2.73
2461 2975 7.313731 TGGGATGGAGGAAGTACTTATTAGAT 58.686 38.462 8.42 0.00 0.00 1.98
2476 2990 8.494016 ACTTATTAGATTGAGTTAGGTGTTGC 57.506 34.615 0.00 0.00 0.00 4.17
2526 3042 3.529533 TGTTGATTTGCAGTTTGGTTGG 58.470 40.909 0.00 0.00 0.00 3.77
2601 3121 4.572985 TTCAGCTCACAAATCACTTTGG 57.427 40.909 3.42 0.00 44.97 3.28
2625 3145 3.621558 CCTCCCTCACCCTAAAATGAAC 58.378 50.000 0.00 0.00 0.00 3.18
2626 3146 3.010138 CCTCCCTCACCCTAAAATGAACA 59.990 47.826 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.165071 CCTCACCAAAAGCAACCCTTAT 58.835 45.455 0.00 0.00 32.20 1.73
23 24 1.609072 GACTCCTCACCAAAAGCAACC 59.391 52.381 0.00 0.00 0.00 3.77
59 61 1.228245 GGCAAGTGGGCAGTGAAGA 60.228 57.895 0.00 0.00 42.77 2.87
105 107 7.237055 ACTTGTGGGTAGAGGTAGATTAAAAGT 59.763 37.037 0.00 0.00 0.00 2.66
106 108 7.549488 CACTTGTGGGTAGAGGTAGATTAAAAG 59.451 40.741 0.00 0.00 0.00 2.27
121 123 7.655732 CGAACATATTCATATCACTTGTGGGTA 59.344 37.037 0.64 0.00 34.14 3.69
123 125 6.705825 TCGAACATATTCATATCACTTGTGGG 59.294 38.462 0.64 0.00 34.14 4.61
124 126 7.713764 TCGAACATATTCATATCACTTGTGG 57.286 36.000 0.64 0.00 34.14 4.17
136 138 9.917129 TCACTAACTAGTTTTCGAACATATTCA 57.083 29.630 14.49 0.00 33.46 2.57
139 141 9.790389 CTCTCACTAACTAGTTTTCGAACATAT 57.210 33.333 14.49 0.00 33.46 1.78
140 142 8.790718 ACTCTCACTAACTAGTTTTCGAACATA 58.209 33.333 14.49 0.00 33.46 2.29
141 143 7.595502 CACTCTCACTAACTAGTTTTCGAACAT 59.404 37.037 14.49 0.00 33.46 2.71
142 144 6.916387 CACTCTCACTAACTAGTTTTCGAACA 59.084 38.462 14.49 0.00 33.46 3.18
143 145 6.916932 ACACTCTCACTAACTAGTTTTCGAAC 59.083 38.462 14.49 0.00 33.46 3.95
144 146 7.035840 ACACTCTCACTAACTAGTTTTCGAA 57.964 36.000 14.49 0.00 33.46 3.71
145 147 6.630444 ACACTCTCACTAACTAGTTTTCGA 57.370 37.500 14.49 6.88 33.46 3.71
146 148 7.697291 GGATACACTCTCACTAACTAGTTTTCG 59.303 40.741 14.49 5.64 33.46 3.46
147 149 7.975058 GGGATACACTCTCACTAACTAGTTTTC 59.025 40.741 14.49 0.00 33.44 2.29
148 150 7.453752 TGGGATACACTCTCACTAACTAGTTTT 59.546 37.037 14.49 0.00 33.44 2.43
149 151 6.952358 TGGGATACACTCTCACTAACTAGTTT 59.048 38.462 14.49 0.00 33.44 2.66
150 152 6.491383 TGGGATACACTCTCACTAACTAGTT 58.509 40.000 13.68 13.68 33.44 2.24
151 153 6.075949 TGGGATACACTCTCACTAACTAGT 57.924 41.667 0.00 0.00 35.65 2.57
152 154 6.603997 ACTTGGGATACACTCTCACTAACTAG 59.396 42.308 0.00 0.00 32.70 2.57
153 155 6.491383 ACTTGGGATACACTCTCACTAACTA 58.509 40.000 0.00 0.00 32.70 2.24
154 156 5.334421 ACTTGGGATACACTCTCACTAACT 58.666 41.667 0.00 0.00 32.70 2.24
155 157 5.662674 ACTTGGGATACACTCTCACTAAC 57.337 43.478 0.00 0.00 32.70 2.34
156 158 5.778241 TCAACTTGGGATACACTCTCACTAA 59.222 40.000 0.00 0.00 32.70 2.24
157 159 5.330233 TCAACTTGGGATACACTCTCACTA 58.670 41.667 0.00 0.00 32.70 2.74
158 160 4.160329 TCAACTTGGGATACACTCTCACT 58.840 43.478 0.00 0.00 32.70 3.41
159 161 4.537135 TCAACTTGGGATACACTCTCAC 57.463 45.455 0.00 0.00 32.70 3.51
160 162 4.593206 ACTTCAACTTGGGATACACTCTCA 59.407 41.667 0.00 0.00 39.74 3.27
161 163 5.046950 AGACTTCAACTTGGGATACACTCTC 60.047 44.000 0.00 0.00 39.74 3.20
162 164 4.841246 AGACTTCAACTTGGGATACACTCT 59.159 41.667 0.00 0.00 39.74 3.24
166 168 4.838423 TCTGAGACTTCAACTTGGGATACA 59.162 41.667 0.00 0.00 32.28 2.29
168 170 5.129485 GGATCTGAGACTTCAACTTGGGATA 59.871 44.000 0.00 0.00 31.69 2.59
192 194 7.883229 AAAGTAAAGCCCAAATTTTCATACG 57.117 32.000 0.00 0.00 0.00 3.06
217 219 6.701400 GTCATTACAAGTGTTTGAAATGGCTT 59.299 34.615 3.21 0.00 37.73 4.35
218 220 6.215845 GTCATTACAAGTGTTTGAAATGGCT 58.784 36.000 3.21 0.00 37.73 4.75
226 228 8.568732 AAAAATACGGTCATTACAAGTGTTTG 57.431 30.769 0.00 0.00 40.24 2.93
242 244 9.524106 AGAACTTTCCTTTTGTTAAAAATACGG 57.476 29.630 0.00 0.00 34.81 4.02
345 348 1.972872 CACTCAAAGACTGTGGGCTT 58.027 50.000 0.00 0.00 0.00 4.35
353 356 3.859961 CGTATCGATTGCACTCAAAGACT 59.140 43.478 1.71 0.00 35.56 3.24
433 436 9.911788 AGTAGAAAAATGAATCTCATACACCAT 57.088 29.630 0.00 0.00 35.76 3.55
487 494 3.499737 ACAATAGCTGCCGCACGC 61.500 61.111 2.05 6.68 39.10 5.34
488 495 1.431488 ATCACAATAGCTGCCGCACG 61.431 55.000 2.05 0.00 39.10 5.34
498 505 9.978044 TCAGAGTTCAATATCTGATCACAATAG 57.022 33.333 0.90 0.00 45.31 1.73
542 549 3.805971 TGCATCATCGAGTGATTCACATC 59.194 43.478 18.57 11.57 45.25 3.06
563 570 0.183731 GGAATACCCCTTGGCCTCTG 59.816 60.000 3.32 0.00 33.59 3.35
629 641 5.416326 ACCTATCATCGAGGAATAGCACTAC 59.584 44.000 2.91 0.00 37.53 2.73
686 698 2.034179 CCAGGGACAAAAACCGTTCTTC 59.966 50.000 0.00 0.00 0.00 2.87
690 702 1.478916 CAACCAGGGACAAAAACCGTT 59.521 47.619 0.00 0.00 0.00 4.44
702 714 2.231235 GTGCAAAGATAACCAACCAGGG 59.769 50.000 0.00 0.00 43.89 4.45
956 968 0.670162 CACTTGTGGTTGGGCTGAAG 59.330 55.000 0.00 0.00 0.00 3.02
964 976 1.518056 ATGCCGAGCACTTGTGGTTG 61.518 55.000 11.93 11.93 43.04 3.77
967 979 0.729116 CTTATGCCGAGCACTTGTGG 59.271 55.000 0.50 0.00 43.04 4.17
1116 1128 2.914097 AACTTGGCCTGCACCTGC 60.914 61.111 3.32 0.00 42.50 4.85
1432 1454 1.604308 CCTGCAGCCCATGACAACA 60.604 57.895 8.66 0.00 0.00 3.33
1617 1639 0.039437 GGAGAACGACGAGCAAGTGA 60.039 55.000 0.00 0.00 0.00 3.41
1623 1645 0.108804 TGGAATGGAGAACGACGAGC 60.109 55.000 0.00 0.00 0.00 5.03
1811 1851 0.249073 CATAGCCTGGGTCGACGAAG 60.249 60.000 9.92 9.21 0.00 3.79
1937 2441 9.196552 CTCGCTCATACTCATACATAATCAAAA 57.803 33.333 0.00 0.00 0.00 2.44
1969 2473 6.376018 GGTAGTGACATCTCAACTAACTCTCT 59.624 42.308 0.00 0.00 0.00 3.10
2053 2557 3.670898 AGGAGATCCTGCCATCCTT 57.329 52.632 0.00 0.00 46.55 3.36
2190 2698 3.650139 ACTATAATCGGACGTGCATTCC 58.350 45.455 8.11 7.17 0.00 3.01
2199 2707 3.688673 CGGAGGGAGTACTATAATCGGAC 59.311 52.174 0.00 0.00 0.00 4.79
2202 2710 3.688673 GGACGGAGGGAGTACTATAATCG 59.311 52.174 0.00 0.54 0.00 3.34
2203 2711 4.015764 GGGACGGAGGGAGTACTATAATC 58.984 52.174 0.00 0.00 0.00 1.75
2204 2712 3.400322 TGGGACGGAGGGAGTACTATAAT 59.600 47.826 0.00 0.00 0.00 1.28
2206 2714 2.421725 TGGGACGGAGGGAGTACTATA 58.578 52.381 0.00 0.00 0.00 1.31
2207 2715 1.229131 TGGGACGGAGGGAGTACTAT 58.771 55.000 0.00 0.00 0.00 2.12
2208 2716 1.229131 ATGGGACGGAGGGAGTACTA 58.771 55.000 0.00 0.00 0.00 1.82
2209 2717 1.229131 TATGGGACGGAGGGAGTACT 58.771 55.000 0.00 0.00 0.00 2.73
2210 2718 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
2211 2719 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
2212 2720 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2213 2721 4.406003 CCTTATATTATGGGACGGAGGGAG 59.594 50.000 0.00 0.00 0.00 4.30
2214 2722 4.046231 TCCTTATATTATGGGACGGAGGGA 59.954 45.833 0.00 0.00 0.00 4.20
2215 2723 4.161754 GTCCTTATATTATGGGACGGAGGG 59.838 50.000 11.96 0.00 38.77 4.30
2216 2724 5.340439 GTCCTTATATTATGGGACGGAGG 57.660 47.826 11.96 0.00 38.77 4.30
2221 2729 8.340443 GTCAAAAACGTCCTTATATTATGGGAC 58.660 37.037 15.08 15.08 43.22 4.46
2222 2730 8.047911 TGTCAAAAACGTCCTTATATTATGGGA 58.952 33.333 0.00 0.00 0.00 4.37
2223 2731 8.215926 TGTCAAAAACGTCCTTATATTATGGG 57.784 34.615 0.00 0.00 0.00 4.00
2229 2737 9.444600 ACACTAATGTCAAAAACGTCCTTATAT 57.555 29.630 0.00 0.00 31.55 0.86
2230 2738 8.836268 ACACTAATGTCAAAAACGTCCTTATA 57.164 30.769 0.00 0.00 31.55 0.98
2231 2739 7.739498 ACACTAATGTCAAAAACGTCCTTAT 57.261 32.000 0.00 0.00 31.55 1.73
2232 2740 7.927629 ACTACACTAATGTCAAAAACGTCCTTA 59.072 33.333 0.00 0.00 40.48 2.69
2233 2741 6.764560 ACTACACTAATGTCAAAAACGTCCTT 59.235 34.615 0.00 0.00 40.48 3.36
2234 2742 6.202188 CACTACACTAATGTCAAAAACGTCCT 59.798 38.462 0.00 0.00 40.48 3.85
2235 2743 6.018507 ACACTACACTAATGTCAAAAACGTCC 60.019 38.462 0.00 0.00 40.48 4.79
2236 2744 6.940714 ACACTACACTAATGTCAAAAACGTC 58.059 36.000 0.00 0.00 40.48 4.34
2237 2745 6.913873 ACACTACACTAATGTCAAAAACGT 57.086 33.333 0.00 0.00 40.48 3.99
2245 2753 6.940714 ACGTTTTTGACACTACACTAATGTC 58.059 36.000 0.00 0.00 42.54 3.06
2246 2754 6.913873 ACGTTTTTGACACTACACTAATGT 57.086 33.333 0.00 0.00 43.30 2.71
2247 2755 7.627340 AGAACGTTTTTGACACTACACTAATG 58.373 34.615 0.46 0.00 0.00 1.90
2248 2756 7.781548 AGAACGTTTTTGACACTACACTAAT 57.218 32.000 0.46 0.00 0.00 1.73
2249 2757 7.599630 AAGAACGTTTTTGACACTACACTAA 57.400 32.000 0.46 0.00 0.00 2.24
2250 2758 8.876275 ATAAGAACGTTTTTGACACTACACTA 57.124 30.769 13.87 0.00 0.00 2.74
2251 2759 7.781548 ATAAGAACGTTTTTGACACTACACT 57.218 32.000 13.87 0.00 0.00 3.55
2260 2768 9.919348 GCGGTTATAATATAAGAACGTTTTTGA 57.081 29.630 13.87 2.81 0.00 2.69
2261 2769 9.705471 TGCGGTTATAATATAAGAACGTTTTTG 57.295 29.630 13.87 0.00 0.00 2.44
2288 2796 5.184287 TCCTTCTGTCCAACGTTTTCTTTTT 59.816 36.000 0.00 0.00 0.00 1.94
2289 2797 4.703093 TCCTTCTGTCCAACGTTTTCTTTT 59.297 37.500 0.00 0.00 0.00 2.27
2290 2798 4.266714 TCCTTCTGTCCAACGTTTTCTTT 58.733 39.130 0.00 0.00 0.00 2.52
2291 2799 3.877508 CTCCTTCTGTCCAACGTTTTCTT 59.122 43.478 0.00 0.00 0.00 2.52
2292 2800 3.118371 ACTCCTTCTGTCCAACGTTTTCT 60.118 43.478 0.00 0.00 0.00 2.52
2293 2801 3.203716 ACTCCTTCTGTCCAACGTTTTC 58.796 45.455 0.00 0.00 0.00 2.29
2294 2802 3.277142 ACTCCTTCTGTCCAACGTTTT 57.723 42.857 0.00 0.00 0.00 2.43
2295 2803 4.411256 TTACTCCTTCTGTCCAACGTTT 57.589 40.909 0.00 0.00 0.00 3.60
2296 2804 4.618920 ATTACTCCTTCTGTCCAACGTT 57.381 40.909 0.00 0.00 0.00 3.99
2297 2805 5.934402 ATATTACTCCTTCTGTCCAACGT 57.066 39.130 0.00 0.00 0.00 3.99
2298 2806 8.712285 TTAAATATTACTCCTTCTGTCCAACG 57.288 34.615 0.00 0.00 0.00 4.10
2299 2807 9.886132 TCTTAAATATTACTCCTTCTGTCCAAC 57.114 33.333 0.00 0.00 0.00 3.77
2301 2809 8.204836 GCTCTTAAATATTACTCCTTCTGTCCA 58.795 37.037 0.00 0.00 0.00 4.02
2302 2810 7.658167 GGCTCTTAAATATTACTCCTTCTGTCC 59.342 40.741 0.00 0.00 0.00 4.02
2303 2811 8.204836 TGGCTCTTAAATATTACTCCTTCTGTC 58.795 37.037 0.00 0.00 0.00 3.51
2304 2812 7.988028 GTGGCTCTTAAATATTACTCCTTCTGT 59.012 37.037 0.00 0.00 0.00 3.41
2305 2813 7.169982 CGTGGCTCTTAAATATTACTCCTTCTG 59.830 40.741 0.00 0.00 0.00 3.02
2306 2814 7.210873 CGTGGCTCTTAAATATTACTCCTTCT 58.789 38.462 0.00 0.00 0.00 2.85
2307 2815 6.073711 GCGTGGCTCTTAAATATTACTCCTTC 60.074 42.308 0.00 0.00 0.00 3.46
2308 2816 5.758784 GCGTGGCTCTTAAATATTACTCCTT 59.241 40.000 0.00 0.00 0.00 3.36
2309 2817 5.163343 TGCGTGGCTCTTAAATATTACTCCT 60.163 40.000 0.00 0.00 0.00 3.69
2310 2818 5.054477 TGCGTGGCTCTTAAATATTACTCC 58.946 41.667 0.00 0.00 0.00 3.85
2311 2819 6.647067 AGATGCGTGGCTCTTAAATATTACTC 59.353 38.462 0.00 0.00 0.00 2.59
2312 2820 6.525629 AGATGCGTGGCTCTTAAATATTACT 58.474 36.000 0.00 0.00 0.00 2.24
2313 2821 6.423905 TGAGATGCGTGGCTCTTAAATATTAC 59.576 38.462 0.00 0.00 32.44 1.89
2314 2822 6.423905 GTGAGATGCGTGGCTCTTAAATATTA 59.576 38.462 0.00 0.00 32.44 0.98
2327 2835 1.511850 TTCACTTGTGAGATGCGTGG 58.488 50.000 3.61 0.00 0.00 4.94
2331 2839 9.624697 TTATTGTTAAATTCACTTGTGAGATGC 57.375 29.630 3.61 0.00 0.00 3.91
2352 2860 9.626045 GGAACCTTCTGTTTTGTTATCTTATTG 57.374 33.333 0.00 0.00 37.29 1.90
2365 2879 6.070251 ACCTTTTGATTTGGAACCTTCTGTTT 60.070 34.615 0.00 0.00 37.29 2.83
2400 2914 2.661176 TTGGGATGGAGGGAGTACTT 57.339 50.000 0.00 0.00 0.00 2.24
2452 2966 8.723942 AGCAACACCTAACTCAATCTAATAAG 57.276 34.615 0.00 0.00 0.00 1.73
2461 2975 4.444536 ACGTTTAGCAACACCTAACTCAA 58.555 39.130 0.00 0.00 32.54 3.02
2476 2990 2.288458 TCCGCAAAAACTGGACGTTTAG 59.712 45.455 0.00 0.00 44.77 1.85
2535 3051 6.000219 CCACTACCTAAATATGCAGCTCAAT 59.000 40.000 0.00 0.00 0.00 2.57
2536 3052 5.368145 CCACTACCTAAATATGCAGCTCAA 58.632 41.667 0.00 0.00 0.00 3.02
2537 3053 4.202357 CCCACTACCTAAATATGCAGCTCA 60.202 45.833 0.00 0.00 0.00 4.26
2539 3055 3.973973 TCCCACTACCTAAATATGCAGCT 59.026 43.478 0.00 0.00 0.00 4.24
2540 3056 4.351874 TCCCACTACCTAAATATGCAGC 57.648 45.455 0.00 0.00 0.00 5.25
2541 3057 6.591935 TCTTTCCCACTACCTAAATATGCAG 58.408 40.000 0.00 0.00 0.00 4.41
2542 3058 6.569127 TCTTTCCCACTACCTAAATATGCA 57.431 37.500 0.00 0.00 0.00 3.96
2601 3121 1.665137 TTTTAGGGTGAGGGAGGGAC 58.335 55.000 0.00 0.00 0.00 4.46
2625 3145 4.122776 CCAAGAATAACGAGATCACCCTG 58.877 47.826 0.00 0.00 0.00 4.45
2626 3146 3.775316 ACCAAGAATAACGAGATCACCCT 59.225 43.478 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.