Multiple sequence alignment - TraesCS5A01G151600

Loading Multiple Alignment...

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 TraesCS5A01G151600 chr5A 100.000 2681 0 0 1 2681 328926065 328923385 0.000000e+00 4951.0
1 TraesCS5A01G151600 chr5A 97.297 37 1 0 604 640 95467493 95467457 2.230000e-06 63.9
2 TraesCS5A01G151600 chr5B 91.332 1269 63 15 730 1997 278044731 278043509 0.000000e+00 1690.0
3 TraesCS5A01G151600 chr5D 93.116 1104 25 8 642 1726 244641787 244640716 0.000000e+00 1570.0
4 TraesCS5A01G151600 chr5D 82.000 800 104 16 1727 2516 244640602 244639833 0.000000e+00 643.0
5 TraesCS5A01G151600 chr5D 73.438 576 107 31 2112 2680 495346088 495346624 9.870000e-40 174.0
6 TraesCS5A01G151600 chr5D 85.535 159 20 2 2524 2680 474701372 474701529 2.140000e-36 163.0
7 TraesCS5A01G151600 chr5D 87.313 134 14 3 2517 2650 244639790 244639660 1.660000e-32 150.0
8 TraesCS5A01G151600 chr5D 77.982 109 14 7 2111 2217 286160454 286160354 2.880000e-05 60.2
9 TraesCS5A01G151600 chr4A 99.367 632 4 0 1 632 739326868 739326237 0.000000e+00 1146.0
10 TraesCS5A01G151600 chr4A 78.261 115 22 3 2110 2223 544037193 544037305 1.330000e-08 71.3
11 TraesCS5A01G151600 chr6A 97.348 641 16 1 1 641 181488535 181487896 0.000000e+00 1088.0
12 TraesCS5A01G151600 chr3D 91.615 644 48 4 1 639 267662630 267661988 0.000000e+00 885.0
13 TraesCS5A01G151600 chr3D 91.420 641 37 6 2 639 1008538 1007913 0.000000e+00 863.0
14 TraesCS5A01G151600 chr3D 84.868 152 19 2 2533 2680 364524724 364524573 1.660000e-32 150.0
15 TraesCS5A01G151600 chr3A 91.969 635 44 6 1 631 291436560 291437191 0.000000e+00 883.0
16 TraesCS5A01G151600 chr1B 89.907 644 58 5 1 639 624835777 624835136 0.000000e+00 822.0
17 TraesCS5A01G151600 chr6D 89.799 647 54 6 1 638 304951259 304950616 0.000000e+00 819.0
18 TraesCS5A01G151600 chr6D 81.595 163 21 4 2527 2680 306202121 306201959 2.800000e-25 126.0
19 TraesCS5A01G151600 chr1D 87.920 654 56 10 1 639 81819710 81820355 0.000000e+00 749.0
20 TraesCS5A01G151600 chr1D 82.822 163 22 4 2522 2680 345273212 345273372 1.000000e-29 141.0
21 TraesCS5A01G151600 chr6B 88.869 557 46 9 91 641 132139825 132139279 0.000000e+00 671.0
22 TraesCS5A01G151600 chr2D 78.591 369 62 17 2103 2462 32966719 32966359 7.470000e-56 228.0
23 TraesCS5A01G151600 chr2D 79.310 145 25 4 2335 2476 52620778 52620636 2.200000e-16 97.1
24 TraesCS5A01G151600 chr7A 83.439 157 20 4 2528 2680 164669624 164669470 1.000000e-29 141.0
25 TraesCS5A01G151600 chr4D 81.988 161 23 4 2524 2680 67247636 67247478 6.020000e-27 132.0
26 TraesCS5A01G151600 chr4B 81.290 155 21 7 2532 2680 645308715 645308563 4.690000e-23 119.0
27 TraesCS5A01G151600 chrUn 81.890 127 21 2 2231 2357 31195650 31195774 3.650000e-19 106.0


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 TraesCS5A01G151600 chr5A 328923385 328926065 2680 True 4951.000000 4951 100.000000 1 2681 1 chr5A.!!$R2 2680
1 TraesCS5A01G151600 chr5B 278043509 278044731 1222 True 1690.000000 1690 91.332000 730 1997 1 chr5B.!!$R1 1267
2 TraesCS5A01G151600 chr5D 244639660 244641787 2127 True 787.666667 1570 87.476333 642 2650 3 chr5D.!!$R2 2008
3 TraesCS5A01G151600 chr4A 739326237 739326868 631 True 1146.000000 1146 99.367000 1 632 1 chr4A.!!$R1 631
4 TraesCS5A01G151600 chr6A 181487896 181488535 639 True 1088.000000 1088 97.348000 1 641 1 chr6A.!!$R1 640
5 TraesCS5A01G151600 chr3D 267661988 267662630 642 True 885.000000 885 91.615000 1 639 1 chr3D.!!$R2 638
6 TraesCS5A01G151600 chr3D 1007913 1008538 625 True 863.000000 863 91.420000 2 639 1 chr3D.!!$R1 637
7 TraesCS5A01G151600 chr3A 291436560 291437191 631 False 883.000000 883 91.969000 1 631 1 chr3A.!!$F1 630
8 TraesCS5A01G151600 chr1B 624835136 624835777 641 True 822.000000 822 89.907000 1 639 1 chr1B.!!$R1 638
9 TraesCS5A01G151600 chr6D 304950616 304951259 643 True 819.000000 819 89.799000 1 638 1 chr6D.!!$R1 637
10 TraesCS5A01G151600 chr1D 81819710 81820355 645 False 749.000000 749 87.920000 1 639 1 chr1D.!!$F1 638
11 TraesCS5A01G151600 chr6B 132139279 132139825 546 True 671.000000 671 88.869000 91 641 1 chr6B.!!$R1 550

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
871 917 1.760613 TCGGAGAGAGAGAGAGAGACC 59.239 57.143 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 2177 0.03601 CAAGTGTCGCCCTTGGAGAT 60.036 55.0 0.0 0.0 36.5 2.75 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
391 409 6.828785 AGGCCATCGTCTAATTTTGATTACTT 59.171 34.615 5.01 0.00 0.00 2.24
614 648 3.009723 GAGAATGAGCGAACCCAATGAA 58.990 45.455 0.00 0.00 0.00 2.57
632 666 2.295909 TGAACAAATTTTCTGGCTCCGG 59.704 45.455 0.00 0.00 0.00 5.14
655 689 2.151202 CTGCACTTGTATGGACCGTTT 58.849 47.619 0.00 0.00 0.00 3.60
711 745 3.111741 ACCATCTTTACCTACCGGAGT 57.888 47.619 9.46 4.94 0.00 3.85
757 791 3.754850 TCACCAGCAATCTCAAACTGATG 59.245 43.478 0.00 0.00 31.67 3.07
761 795 3.943381 CAGCAATCTCAAACTGATGCCTA 59.057 43.478 0.00 0.00 31.67 3.93
806 840 5.630680 AGCGTTTACAAATTCAGCTTGAATG 59.369 36.000 10.78 5.50 45.57 2.67
810 844 9.767684 CGTTTACAAATTCAGCTTGAATGTATA 57.232 29.630 10.78 5.85 45.57 1.47
851 885 7.939039 TCAAATTAGGAGACAGAAATGTCAACT 59.061 33.333 10.72 9.72 41.02 3.16
871 917 1.760613 TCGGAGAGAGAGAGAGAGACC 59.239 57.143 0.00 0.00 0.00 3.85
1039 1092 1.077212 CTCCTCCCCGTCTCCGTTA 60.077 63.158 0.00 0.00 0.00 3.18
1082 1135 4.530857 CACCATCGTCCTCCCCGC 62.531 72.222 0.00 0.00 0.00 6.13
1656 1709 3.295228 CTTCTTCACCAACGCCGCG 62.295 63.158 12.14 12.14 0.00 6.46
1849 2015 8.437360 AGGAAATTTGGAGAAACAAAACATTC 57.563 30.769 0.00 0.00 42.91 2.67
1879 2045 7.865875 TTATTTGTTTGTGGATTGTTCGATG 57.134 32.000 0.00 0.00 0.00 3.84
1992 2159 7.592885 ATGAATTATTGGTTTCTCATCTGGG 57.407 36.000 0.00 0.00 0.00 4.45
2000 2167 2.844348 GTTTCTCATCTGGGGTAAGGGA 59.156 50.000 0.00 0.00 0.00 4.20
2002 2169 3.438131 TCTCATCTGGGGTAAGGGAAT 57.562 47.619 0.00 0.00 0.00 3.01
2003 2170 3.318313 TCTCATCTGGGGTAAGGGAATC 58.682 50.000 0.00 0.00 0.00 2.52
2004 2171 3.051032 TCTCATCTGGGGTAAGGGAATCT 60.051 47.826 0.00 0.00 0.00 2.40
2005 2172 3.318313 TCATCTGGGGTAAGGGAATCTC 58.682 50.000 0.00 0.00 0.00 2.75
2006 2173 1.789523 TCTGGGGTAAGGGAATCTCG 58.210 55.000 0.00 0.00 0.00 4.04
2007 2174 0.759346 CTGGGGTAAGGGAATCTCGG 59.241 60.000 0.00 0.00 0.00 4.63
2008 2175 0.693092 TGGGGTAAGGGAATCTCGGG 60.693 60.000 0.00 0.00 0.00 5.14
2009 2176 0.399519 GGGGTAAGGGAATCTCGGGA 60.400 60.000 0.00 0.00 0.00 5.14
2010 2177 1.503800 GGGTAAGGGAATCTCGGGAA 58.496 55.000 0.00 0.00 0.00 3.97
2011 2178 2.055579 GGGTAAGGGAATCTCGGGAAT 58.944 52.381 0.00 0.00 0.00 3.01
2012 2179 2.038689 GGGTAAGGGAATCTCGGGAATC 59.961 54.545 0.00 0.00 0.00 2.52
2018 2185 2.224402 GGGAATCTCGGGAATCTCCAAG 60.224 54.545 12.14 0.00 38.64 3.61
2021 2188 1.147153 CTCGGGAATCTCCAAGGGC 59.853 63.158 0.00 0.00 38.64 5.19
2025 2192 1.602237 GGAATCTCCAAGGGCGACA 59.398 57.895 0.00 0.00 36.28 4.35
2028 2195 0.693049 AATCTCCAAGGGCGACACTT 59.307 50.000 0.00 0.00 0.00 3.16
2029 2196 0.036010 ATCTCCAAGGGCGACACTTG 60.036 55.000 12.97 12.97 43.73 3.16
2037 2204 2.665185 GCGACACTTGAACCGCCT 60.665 61.111 0.00 0.00 41.59 5.52
2043 2210 0.447801 CACTTGAACCGCCTGCATAC 59.552 55.000 0.00 0.00 0.00 2.39
2044 2211 0.036164 ACTTGAACCGCCTGCATACA 59.964 50.000 0.00 0.00 0.00 2.29
2045 2212 0.447801 CTTGAACCGCCTGCATACAC 59.552 55.000 0.00 0.00 0.00 2.90
2049 2216 1.296056 AACCGCCTGCATACACGTTC 61.296 55.000 0.00 0.00 0.00 3.95
2050 2217 2.695055 CGCCTGCATACACGTTCG 59.305 61.111 0.00 0.00 0.00 3.95
2053 2220 1.693083 GCCTGCATACACGTTCGGAC 61.693 60.000 0.00 0.00 0.00 4.79
2057 2224 1.988409 CATACACGTTCGGACTGCG 59.012 57.895 0.00 0.00 0.00 5.18
2058 2225 0.731514 CATACACGTTCGGACTGCGT 60.732 55.000 0.00 0.00 39.59 5.24
2064 2231 1.484227 CGTTCGGACTGCGTTGTTCA 61.484 55.000 0.00 0.00 0.00 3.18
2067 2234 0.596600 TCGGACTGCGTTGTTCAGAC 60.597 55.000 0.00 0.00 35.61 3.51
2070 2237 0.861837 GACTGCGTTGTTCAGACCAG 59.138 55.000 0.00 0.00 35.61 4.00
2075 2242 1.673920 GCGTTGTTCAGACCAGGAAAA 59.326 47.619 0.00 0.00 0.00 2.29
2076 2243 2.098443 GCGTTGTTCAGACCAGGAAAAA 59.902 45.455 0.00 0.00 0.00 1.94
2077 2244 3.691498 CGTTGTTCAGACCAGGAAAAAC 58.309 45.455 0.00 0.00 38.52 2.43
2078 2245 3.127895 CGTTGTTCAGACCAGGAAAAACA 59.872 43.478 0.00 0.00 40.78 2.83
2079 2246 4.202010 CGTTGTTCAGACCAGGAAAAACAT 60.202 41.667 0.00 0.00 40.78 2.71
2080 2247 5.008217 CGTTGTTCAGACCAGGAAAAACATA 59.992 40.000 0.00 0.00 40.78 2.29
2082 2249 6.817765 TGTTCAGACCAGGAAAAACATATC 57.182 37.500 0.00 0.00 0.00 1.63
2088 2255 6.153340 CAGACCAGGAAAAACATATCCAACAT 59.847 38.462 0.00 0.00 38.23 2.71
2093 2260 6.153340 CAGGAAAAACATATCCAACATGGTCT 59.847 38.462 0.00 0.00 39.03 3.85
2095 2262 6.813152 GGAAAAACATATCCAACATGGTCTTG 59.187 38.462 0.00 0.00 39.03 3.02
2099 2266 9.693739 AAAACATATCCAACATGGTCTTGTATA 57.306 29.630 0.00 0.00 39.03 1.47
2102 2269 8.370940 ACATATCCAACATGGTCTTGTATAGAG 58.629 37.037 0.00 0.00 39.03 2.43
2107 2274 3.590127 GGTCTTGTATAGAGCGGCC 57.410 57.895 0.00 0.00 41.17 6.13
2109 2276 0.318784 GTCTTGTATAGAGCGGCCGG 60.319 60.000 29.38 8.95 32.23 6.13
2129 2304 2.478200 GGGACGTGTTTTCTTTCGCAAA 60.478 45.455 0.00 0.00 0.00 3.68
2130 2305 3.368495 GGACGTGTTTTCTTTCGCAAAT 58.632 40.909 0.00 0.00 0.00 2.32
2136 2311 3.234386 GTTTTCTTTCGCAAATCGGAGG 58.766 45.455 0.00 0.00 39.05 4.30
2137 2312 0.802494 TTCTTTCGCAAATCGGAGGC 59.198 50.000 0.00 0.00 39.05 4.70
2141 2316 0.239879 TTCGCAAATCGGAGGCAAAC 59.760 50.000 0.00 0.00 39.05 2.93
2142 2317 0.886938 TCGCAAATCGGAGGCAAACA 60.887 50.000 0.00 0.00 39.05 2.83
2145 2320 1.067635 GCAAATCGGAGGCAAACATGT 60.068 47.619 0.00 0.00 0.00 3.21
2159 2334 0.611896 ACATGTAGGGCTTTGTGGGC 60.612 55.000 0.00 0.00 0.00 5.36
2161 2336 2.033602 GTAGGGCTTTGTGGGCGT 59.966 61.111 0.00 0.00 0.00 5.68
2162 2337 2.038837 GTAGGGCTTTGTGGGCGTC 61.039 63.158 0.00 0.00 0.00 5.19
2169 2344 3.818121 TTTGTGGGCGTCCGGACAG 62.818 63.158 32.80 24.88 35.24 3.51
2177 2352 3.041940 GTCCGGACAGTTGCCACG 61.042 66.667 29.75 0.00 0.00 4.94
2178 2353 4.980805 TCCGGACAGTTGCCACGC 62.981 66.667 0.00 0.00 0.00 5.34
2208 2383 4.621087 GCCCTGCCCACCCAAACT 62.621 66.667 0.00 0.00 0.00 2.66
2218 2393 1.841556 ACCCAAACTCGCTCCCTCA 60.842 57.895 0.00 0.00 0.00 3.86
2222 2397 0.390472 CAAACTCGCTCCCTCACCTC 60.390 60.000 0.00 0.00 0.00 3.85
2226 2401 0.682855 CTCGCTCCCTCACCTCTCTT 60.683 60.000 0.00 0.00 0.00 2.85
2229 2404 1.548357 GCTCCCTCACCTCTCTTGCA 61.548 60.000 0.00 0.00 0.00 4.08
2235 2410 2.421619 CTCACCTCTCTTGCACTTTCC 58.578 52.381 0.00 0.00 0.00 3.13
2246 2421 1.671054 CACTTTCCATCCCACGCGT 60.671 57.895 5.58 5.58 0.00 6.01
2247 2422 1.375523 ACTTTCCATCCCACGCGTC 60.376 57.895 9.86 0.00 0.00 5.19
2248 2423 1.375396 CTTTCCATCCCACGCGTCA 60.375 57.895 9.86 0.00 0.00 4.35
2321 2496 3.891422 TTGATGCCCATGATTTTGACC 57.109 42.857 0.00 0.00 0.00 4.02
2324 2499 1.916506 TGCCCATGATTTTGACCGAA 58.083 45.000 0.00 0.00 0.00 4.30
2325 2500 2.242926 TGCCCATGATTTTGACCGAAA 58.757 42.857 0.00 0.00 0.00 3.46
2354 2529 3.112709 GCAGACGGACGCAACCTC 61.113 66.667 0.00 0.00 0.00 3.85
2358 2533 1.215647 GACGGACGCAACCTCTCAT 59.784 57.895 0.00 0.00 0.00 2.90
2361 2536 1.361668 CGGACGCAACCTCTCATTGG 61.362 60.000 0.00 0.00 0.00 3.16
2363 2538 0.955428 GACGCAACCTCTCATTGGCA 60.955 55.000 0.00 0.00 0.00 4.92
2373 2548 1.469703 TCTCATTGGCAGCATTGAACG 59.530 47.619 0.00 0.00 0.00 3.95
2379 2554 4.817063 CAGCATTGAACGGGCGCG 62.817 66.667 22.69 22.69 0.00 6.86
2427 2604 1.597027 CGGTTGAACACGCCTCCTT 60.597 57.895 0.00 0.00 0.00 3.36
2430 2607 1.153066 TTGAACACGCCTCCTTGCA 60.153 52.632 0.00 0.00 0.00 4.08
2442 2619 2.253603 CTCCTTGCAGCATTTAAACGC 58.746 47.619 0.00 0.00 0.00 4.84
2443 2620 1.067915 TCCTTGCAGCATTTAAACGCC 60.068 47.619 2.03 0.00 0.00 5.68
2444 2621 1.349234 CTTGCAGCATTTAAACGCCC 58.651 50.000 2.03 0.00 0.00 6.13
2445 2622 0.387878 TTGCAGCATTTAAACGCCCG 60.388 50.000 2.03 0.00 0.00 6.13
2472 2649 0.819666 CCCGCCTTCCTCCATTAAGC 60.820 60.000 0.00 0.00 0.00 3.09
2475 2652 0.553333 GCCTTCCTCCATTAAGCCCT 59.447 55.000 0.00 0.00 0.00 5.19
2480 2657 0.753111 CCTCCATTAAGCCCTGCACC 60.753 60.000 0.00 0.00 0.00 5.01
2512 2689 0.886563 CCTACTCCGGACAAACGTCT 59.113 55.000 0.00 0.00 33.65 4.18
2521 2739 0.108019 GACAAACGTCTGTTCCCCCT 59.892 55.000 0.00 0.00 37.31 4.79
2522 2740 0.108019 ACAAACGTCTGTTCCCCCTC 59.892 55.000 0.00 0.00 37.31 4.30
2525 2743 2.606519 CGTCTGTTCCCCCTCCCA 60.607 66.667 0.00 0.00 0.00 4.37
2549 2767 4.023193 CCCGGTATTTAAATGATGGCAGAC 60.023 45.833 11.05 0.00 0.00 3.51
2557 2775 1.040893 ATGATGGCAGACGTCGGGTA 61.041 55.000 17.45 3.10 37.96 3.69
2564 2782 2.070783 GCAGACGTCGGGTAAAAATCA 58.929 47.619 17.45 0.00 0.00 2.57
2567 2785 3.062042 AGACGTCGGGTAAAAATCACAC 58.938 45.455 10.46 0.00 0.00 3.82
2574 2792 3.316868 CGGGTAAAAATCACACCACACTT 59.683 43.478 0.00 0.00 33.78 3.16
2586 2804 1.270358 ACCACACTTCGCTCTTCTTCC 60.270 52.381 0.00 0.00 0.00 3.46
2593 2811 0.681733 TCGCTCTTCTTCCTTGCACT 59.318 50.000 0.00 0.00 0.00 4.40
2595 2813 1.606480 CGCTCTTCTTCCTTGCACTCA 60.606 52.381 0.00 0.00 0.00 3.41
2624 2842 2.191513 CAAGCTCCATGGCATCCGG 61.192 63.158 6.96 0.00 34.17 5.14
2645 2863 2.853914 GCACGAAGCCGAGTTGTC 59.146 61.111 0.00 0.00 39.50 3.18
2646 2864 2.668280 GCACGAAGCCGAGTTGTCC 61.668 63.158 0.00 0.00 39.50 4.02
2647 2865 1.006102 CACGAAGCCGAGTTGTCCT 60.006 57.895 0.00 0.00 39.50 3.85
2648 2866 1.006102 ACGAAGCCGAGTTGTCCTG 60.006 57.895 0.00 0.00 39.50 3.86
2649 2867 2.383527 CGAAGCCGAGTTGTCCTGC 61.384 63.158 0.00 0.00 38.22 4.85
2650 2868 1.301716 GAAGCCGAGTTGTCCTGCA 60.302 57.895 0.00 0.00 0.00 4.41
2651 2869 0.674895 GAAGCCGAGTTGTCCTGCAT 60.675 55.000 0.00 0.00 0.00 3.96
2652 2870 0.613260 AAGCCGAGTTGTCCTGCATA 59.387 50.000 0.00 0.00 0.00 3.14
2653 2871 0.108138 AGCCGAGTTGTCCTGCATAC 60.108 55.000 0.00 0.00 0.00 2.39
2654 2872 0.391130 GCCGAGTTGTCCTGCATACA 60.391 55.000 0.00 0.00 0.00 2.29
2655 2873 1.943968 GCCGAGTTGTCCTGCATACAA 60.944 52.381 9.94 9.94 34.56 2.41
2656 2874 2.002586 CCGAGTTGTCCTGCATACAAG 58.997 52.381 13.41 4.58 37.51 3.16
2657 2875 1.394917 CGAGTTGTCCTGCATACAAGC 59.605 52.381 13.41 8.94 37.51 4.01
2658 2876 2.704572 GAGTTGTCCTGCATACAAGCT 58.295 47.619 13.41 12.92 37.51 3.74
2659 2877 2.417933 GAGTTGTCCTGCATACAAGCTG 59.582 50.000 13.41 0.00 37.51 4.24
2660 2878 2.154462 GTTGTCCTGCATACAAGCTGT 58.846 47.619 13.41 0.00 37.51 4.40
2661 2879 2.099141 TGTCCTGCATACAAGCTGTC 57.901 50.000 0.00 0.00 34.99 3.51
2662 2880 1.625315 TGTCCTGCATACAAGCTGTCT 59.375 47.619 0.00 0.00 34.99 3.41
2663 2881 2.831526 TGTCCTGCATACAAGCTGTCTA 59.168 45.455 0.00 0.00 34.99 2.59
2664 2882 3.118992 TGTCCTGCATACAAGCTGTCTAG 60.119 47.826 0.00 0.00 34.99 2.43
2665 2883 2.432146 TCCTGCATACAAGCTGTCTAGG 59.568 50.000 0.00 0.00 34.99 3.02
2666 2884 2.169352 CCTGCATACAAGCTGTCTAGGT 59.831 50.000 0.00 0.00 35.86 3.08
2667 2885 3.193263 CTGCATACAAGCTGTCTAGGTG 58.807 50.000 0.00 0.00 34.27 4.00
2668 2886 2.093500 TGCATACAAGCTGTCTAGGTGG 60.093 50.000 0.00 0.00 34.27 4.61
2669 2887 2.555199 CATACAAGCTGTCTAGGTGGC 58.445 52.381 0.00 0.00 34.27 5.01
2670 2888 0.902531 TACAAGCTGTCTAGGTGGCC 59.097 55.000 0.00 0.00 34.27 5.36
2671 2889 1.078143 CAAGCTGTCTAGGTGGCCC 60.078 63.158 0.00 0.00 34.27 5.80
2672 2890 2.660064 AAGCTGTCTAGGTGGCCCG 61.660 63.158 0.00 0.00 34.27 6.13
2673 2891 3.391382 GCTGTCTAGGTGGCCCGT 61.391 66.667 0.00 0.00 35.12 5.28
2674 2892 2.893398 CTGTCTAGGTGGCCCGTC 59.107 66.667 0.00 0.00 35.12 4.79
2675 2893 3.064987 CTGTCTAGGTGGCCCGTCG 62.065 68.421 0.00 0.00 35.12 5.12
2676 2894 2.753043 GTCTAGGTGGCCCGTCGA 60.753 66.667 0.00 0.00 35.12 4.20
2677 2895 2.439701 TCTAGGTGGCCCGTCGAG 60.440 66.667 0.00 0.00 35.12 4.04
2678 2896 4.208686 CTAGGTGGCCCGTCGAGC 62.209 72.222 0.00 0.00 35.12 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
391 409 4.742012 AGTCTCTCCAACCTTTCTCTACA 58.258 43.478 0.00 0.00 0.00 2.74
398 416 2.434702 ACGTTGAGTCTCTCCAACCTTT 59.565 45.455 0.65 0.00 0.00 3.11
614 648 0.603065 GCCGGAGCCAGAAAATTTGT 59.397 50.000 5.05 0.00 0.00 2.83
632 666 1.032114 GGTCCATACAAGTGCAGGGC 61.032 60.000 0.00 0.00 0.00 5.19
681 715 9.603921 CGGTAGGTAAAGATGGTATTTTTCTTA 57.396 33.333 0.00 0.00 0.00 2.10
682 716 7.555195 CCGGTAGGTAAAGATGGTATTTTTCTT 59.445 37.037 0.00 0.00 0.00 2.52
683 717 7.052248 CCGGTAGGTAAAGATGGTATTTTTCT 58.948 38.462 0.00 0.00 0.00 2.52
684 718 7.049754 TCCGGTAGGTAAAGATGGTATTTTTC 58.950 38.462 0.00 0.00 39.05 2.29
689 723 4.587684 CACTCCGGTAGGTAAAGATGGTAT 59.412 45.833 0.00 0.00 39.05 2.73
761 795 5.450688 CGCTGATAAGTAGTTTGGCTAGACT 60.451 44.000 0.00 0.00 0.00 3.24
810 844 6.443849 TCCTAATTTGACCTGAACTGGTAGAT 59.556 38.462 3.50 0.00 41.00 1.98
811 845 5.783360 TCCTAATTTGACCTGAACTGGTAGA 59.217 40.000 3.50 0.00 41.00 2.59
812 846 6.049955 TCCTAATTTGACCTGAACTGGTAG 57.950 41.667 3.50 0.00 41.00 3.18
813 847 5.783360 TCTCCTAATTTGACCTGAACTGGTA 59.217 40.000 3.50 0.00 41.00 3.25
851 885 1.760613 GGTCTCTCTCTCTCTCTCCGA 59.239 57.143 0.00 0.00 0.00 4.55
871 917 0.535102 AAAGGTCAACGGTCAGCCTG 60.535 55.000 0.00 0.00 0.00 4.85
1105 1158 2.107141 GAGATAGGCGCGCTGGTT 59.893 61.111 32.29 16.31 0.00 3.67
1861 2027 2.228822 AGGCATCGAACAATCCACAAAC 59.771 45.455 0.00 0.00 0.00 2.93
1863 2029 2.198827 AGGCATCGAACAATCCACAA 57.801 45.000 0.00 0.00 0.00 3.33
1988 2155 0.759346 CCGAGATTCCCTTACCCCAG 59.241 60.000 0.00 0.00 0.00 4.45
1992 2159 2.973406 AGATTCCCGAGATTCCCTTACC 59.027 50.000 0.00 0.00 0.00 2.85
2000 2167 1.771255 CCCTTGGAGATTCCCGAGATT 59.229 52.381 9.04 0.00 39.60 2.40
2002 2169 1.338136 GCCCTTGGAGATTCCCGAGA 61.338 60.000 9.04 0.00 39.60 4.04
2003 2170 1.147153 GCCCTTGGAGATTCCCGAG 59.853 63.158 0.00 0.00 35.03 4.63
2004 2171 2.731571 CGCCCTTGGAGATTCCCGA 61.732 63.158 0.00 0.00 35.03 5.14
2005 2172 2.203070 CGCCCTTGGAGATTCCCG 60.203 66.667 0.00 0.00 35.03 5.14
2006 2173 1.153147 GTCGCCCTTGGAGATTCCC 60.153 63.158 0.00 0.00 35.03 3.97
2007 2174 0.744771 GTGTCGCCCTTGGAGATTCC 60.745 60.000 0.00 0.00 33.47 3.01
2008 2175 0.250513 AGTGTCGCCCTTGGAGATTC 59.749 55.000 0.00 0.00 33.47 2.52
2009 2176 0.693049 AAGTGTCGCCCTTGGAGATT 59.307 50.000 0.00 0.00 33.47 2.40
2010 2177 0.036010 CAAGTGTCGCCCTTGGAGAT 60.036 55.000 0.00 0.00 36.50 2.75
2011 2178 1.118965 TCAAGTGTCGCCCTTGGAGA 61.119 55.000 8.15 0.00 39.78 3.71
2012 2179 0.250295 TTCAAGTGTCGCCCTTGGAG 60.250 55.000 8.15 0.00 39.78 3.86
2018 2185 3.723348 GCGGTTCAAGTGTCGCCC 61.723 66.667 0.00 0.00 42.02 6.13
2021 2188 2.954753 GCAGGCGGTTCAAGTGTCG 61.955 63.158 0.00 0.00 0.00 4.35
2025 2192 0.036164 TGTATGCAGGCGGTTCAAGT 59.964 50.000 0.00 0.00 0.00 3.16
2028 2195 1.739929 CGTGTATGCAGGCGGTTCA 60.740 57.895 0.00 0.00 0.00 3.18
2029 2196 1.296056 AACGTGTATGCAGGCGGTTC 61.296 55.000 3.24 0.00 34.13 3.62
2037 2204 1.011968 GCAGTCCGAACGTGTATGCA 61.012 55.000 0.00 0.00 32.58 3.96
2043 2210 1.758319 AACAACGCAGTCCGAACGTG 61.758 55.000 0.00 0.00 45.00 4.49
2044 2211 1.485032 GAACAACGCAGTCCGAACGT 61.485 55.000 0.00 0.00 45.00 3.99
2045 2212 1.200839 GAACAACGCAGTCCGAACG 59.799 57.895 0.00 0.00 45.00 3.95
2049 2216 1.557443 GGTCTGAACAACGCAGTCCG 61.557 60.000 0.00 0.00 45.00 4.79
2050 2217 0.531974 TGGTCTGAACAACGCAGTCC 60.532 55.000 0.00 0.00 45.00 3.85
2053 2220 0.249868 TCCTGGTCTGAACAACGCAG 60.250 55.000 0.00 0.00 34.71 5.18
2057 2224 4.712122 TGTTTTTCCTGGTCTGAACAAC 57.288 40.909 0.00 0.00 34.54 3.32
2058 2225 6.208599 GGATATGTTTTTCCTGGTCTGAACAA 59.791 38.462 0.00 0.00 31.69 2.83
2064 2231 5.640147 TGTTGGATATGTTTTTCCTGGTCT 58.360 37.500 0.00 0.00 32.95 3.85
2067 2234 5.187576 ACCATGTTGGATATGTTTTTCCTGG 59.812 40.000 0.00 0.00 40.96 4.45
2070 2237 6.530019 AGACCATGTTGGATATGTTTTTCC 57.470 37.500 0.00 0.00 40.96 3.13
2075 2242 8.713971 TCTATACAAGACCATGTTGGATATGTT 58.286 33.333 0.00 0.00 40.96 2.71
2076 2243 8.262601 TCTATACAAGACCATGTTGGATATGT 57.737 34.615 0.00 4.70 40.96 2.29
2077 2244 7.332926 GCTCTATACAAGACCATGTTGGATATG 59.667 40.741 0.00 0.00 40.96 1.78
2078 2245 7.390027 GCTCTATACAAGACCATGTTGGATAT 58.610 38.462 0.00 0.00 40.96 1.63
2079 2246 6.516693 CGCTCTATACAAGACCATGTTGGATA 60.517 42.308 0.00 0.00 40.96 2.59
2080 2247 5.615289 GCTCTATACAAGACCATGTTGGAT 58.385 41.667 0.00 0.00 40.96 3.41
2082 2249 3.804325 CGCTCTATACAAGACCATGTTGG 59.196 47.826 0.00 0.00 45.02 3.77
2088 2255 0.750850 GGCCGCTCTATACAAGACCA 59.249 55.000 0.00 0.00 0.00 4.02
2093 2260 1.456145 TCCCGGCCGCTCTATACAA 60.456 57.895 22.85 0.00 0.00 2.41
2095 2262 2.649614 GTCCCGGCCGCTCTATAC 59.350 66.667 22.85 6.81 0.00 1.47
2104 2271 1.449726 AAAGAAAACACGTCCCGGCC 61.450 55.000 0.00 0.00 0.00 6.13
2107 2274 0.383860 GCGAAAGAAAACACGTCCCG 60.384 55.000 0.00 0.00 0.00 5.14
2109 2276 2.461897 TTGCGAAAGAAAACACGTCC 57.538 45.000 0.00 0.00 0.00 4.79
2129 2304 1.134098 CCCTACATGTTTGCCTCCGAT 60.134 52.381 2.30 0.00 0.00 4.18
2130 2305 0.251916 CCCTACATGTTTGCCTCCGA 59.748 55.000 2.30 0.00 0.00 4.55
2136 2311 2.610232 CCACAAAGCCCTACATGTTTGC 60.610 50.000 2.30 4.65 33.96 3.68
2137 2312 2.029110 CCCACAAAGCCCTACATGTTTG 60.029 50.000 2.30 3.71 36.24 2.93
2141 2316 1.656818 CGCCCACAAAGCCCTACATG 61.657 60.000 0.00 0.00 0.00 3.21
2142 2317 1.378514 CGCCCACAAAGCCCTACAT 60.379 57.895 0.00 0.00 0.00 2.29
2145 2320 2.349755 GACGCCCACAAAGCCCTA 59.650 61.111 0.00 0.00 0.00 3.53
2159 2334 3.041940 GTGGCAACTGTCCGGACG 61.042 66.667 28.70 23.92 37.61 4.79
2161 2336 4.980805 GCGTGGCAACTGTCCGGA 62.981 66.667 0.00 0.00 37.61 5.14
2182 2357 4.785453 GGGCAGGGCGGTCAGAAG 62.785 72.222 0.00 0.00 0.00 2.85
2191 2366 4.621087 AGTTTGGGTGGGCAGGGC 62.621 66.667 0.00 0.00 0.00 5.19
2208 2383 0.967887 CAAGAGAGGTGAGGGAGCGA 60.968 60.000 0.00 0.00 0.00 4.93
2218 2393 2.290577 GGATGGAAAGTGCAAGAGAGGT 60.291 50.000 0.00 0.00 0.00 3.85
2222 2397 1.815003 GTGGGATGGAAAGTGCAAGAG 59.185 52.381 0.00 0.00 0.00 2.85
2226 2401 1.971167 GCGTGGGATGGAAAGTGCA 60.971 57.895 0.00 0.00 0.00 4.57
2229 2404 1.375523 GACGCGTGGGATGGAAAGT 60.376 57.895 20.70 0.00 0.00 2.66
2265 2440 2.748166 GCTCTAGGCTGGCATGAATGC 61.748 57.143 6.73 6.73 44.52 3.56
2274 2449 1.892862 GCTGCATGCTCTAGGCTGG 60.893 63.158 20.33 0.00 42.39 4.85
2280 2455 1.153229 CTGGCTGCTGCATGCTCTA 60.153 57.895 20.33 3.72 43.37 2.43
2310 2485 3.356290 CCTCCCTTTCGGTCAAAATCAT 58.644 45.455 0.00 0.00 0.00 2.45
2311 2486 2.554344 CCCTCCCTTTCGGTCAAAATCA 60.554 50.000 0.00 0.00 0.00 2.57
2314 2489 0.538746 GCCCTCCCTTTCGGTCAAAA 60.539 55.000 0.00 0.00 0.00 2.44
2342 2517 1.361668 CCAATGAGAGGTTGCGTCCG 61.362 60.000 0.00 0.00 0.00 4.79
2349 2524 1.822990 CAATGCTGCCAATGAGAGGTT 59.177 47.619 0.00 0.00 0.00 3.50
2351 2526 1.758936 TCAATGCTGCCAATGAGAGG 58.241 50.000 0.00 0.00 0.00 3.69
2354 2529 1.468565 CCGTTCAATGCTGCCAATGAG 60.469 52.381 0.00 0.00 32.78 2.90
2358 2533 2.929903 GCCCGTTCAATGCTGCCAA 61.930 57.895 0.00 0.00 0.00 4.52
2412 2589 1.153066 TGCAAGGAGGCGTGTTCAA 60.153 52.632 0.00 0.00 36.28 2.69
2427 2604 1.211449 CGGGCGTTTAAATGCTGCA 59.789 52.632 26.96 4.13 40.71 4.41
2430 2607 0.958382 TCTGCGGGCGTTTAAATGCT 60.958 50.000 26.96 0.00 40.71 3.79
2456 2633 0.553333 AGGGCTTAATGGAGGAAGGC 59.447 55.000 0.00 0.00 45.06 4.35
2480 2657 1.339151 GGAGTAGGTTTCCCAGCACAG 60.339 57.143 0.00 0.00 0.00 3.66
2488 2665 2.420642 GTTTGTCCGGAGTAGGTTTCC 58.579 52.381 3.06 0.00 0.00 3.13
2493 2670 0.886563 AGACGTTTGTCCGGAGTAGG 59.113 55.000 3.06 1.09 46.74 3.18
2494 2671 1.268899 ACAGACGTTTGTCCGGAGTAG 59.731 52.381 3.06 0.00 46.74 2.57
2503 2680 0.108019 GAGGGGGAACAGACGTTTGT 59.892 55.000 5.80 5.80 34.75 2.83
2506 2683 2.222013 GGGAGGGGGAACAGACGTT 61.222 63.158 0.00 0.00 38.33 3.99
2521 2739 4.465886 CATCATTTAAATACCGGGTGGGA 58.534 43.478 10.66 0.00 40.75 4.37
2522 2740 3.572255 CCATCATTTAAATACCGGGTGGG 59.428 47.826 10.66 0.00 40.75 4.61
2525 2743 3.888930 CTGCCATCATTTAAATACCGGGT 59.111 43.478 6.32 4.46 0.00 5.28
2530 2748 5.432157 CGACGTCTGCCATCATTTAAATAC 58.568 41.667 14.70 0.00 0.00 1.89
2549 2767 2.096119 GTGGTGTGATTTTTACCCGACG 60.096 50.000 0.00 0.00 33.51 5.12
2557 2775 2.687935 AGCGAAGTGTGGTGTGATTTTT 59.312 40.909 0.00 0.00 0.00 1.94
2564 2782 0.753262 AGAAGAGCGAAGTGTGGTGT 59.247 50.000 0.00 0.00 0.00 4.16
2567 2785 1.001406 AGGAAGAAGAGCGAAGTGTGG 59.999 52.381 0.00 0.00 0.00 4.17
2574 2792 0.681733 AGTGCAAGGAAGAAGAGCGA 59.318 50.000 0.00 0.00 0.00 4.93
2586 2804 4.572985 TGTGGAGAAAATTGAGTGCAAG 57.427 40.909 0.00 0.00 37.45 4.01
2593 2811 3.831323 TGGAGCTTGTGGAGAAAATTGA 58.169 40.909 0.00 0.00 0.00 2.57
2595 2813 3.512724 CCATGGAGCTTGTGGAGAAAATT 59.487 43.478 5.56 0.00 34.94 1.82
2626 2844 1.618640 GACAACTCGGCTTCGTGCTC 61.619 60.000 3.58 0.00 42.39 4.26
2631 2849 2.383527 GCAGGACAACTCGGCTTCG 61.384 63.158 0.00 0.00 0.00 3.79
2639 2857 2.224621 ACAGCTTGTATGCAGGACAACT 60.225 45.455 11.82 11.17 33.35 3.16
2640 2858 2.154462 ACAGCTTGTATGCAGGACAAC 58.846 47.619 11.82 9.55 33.35 3.32
2641 2859 2.038952 AGACAGCTTGTATGCAGGACAA 59.961 45.455 14.37 14.37 35.55 3.18
2643 2861 2.393271 AGACAGCTTGTATGCAGGAC 57.607 50.000 0.00 0.00 34.99 3.85
2645 2863 2.169352 ACCTAGACAGCTTGTATGCAGG 59.831 50.000 0.00 0.00 34.99 4.85
2646 2864 3.193263 CACCTAGACAGCTTGTATGCAG 58.807 50.000 0.00 0.00 34.99 4.41
2647 2865 2.093500 CCACCTAGACAGCTTGTATGCA 60.093 50.000 0.00 0.00 34.99 3.96
2648 2866 2.555199 CCACCTAGACAGCTTGTATGC 58.445 52.381 0.00 0.00 0.00 3.14
2649 2867 2.555199 GCCACCTAGACAGCTTGTATG 58.445 52.381 0.00 0.00 0.00 2.39
2650 2868 1.486726 GGCCACCTAGACAGCTTGTAT 59.513 52.381 0.00 0.00 0.00 2.29
2651 2869 0.902531 GGCCACCTAGACAGCTTGTA 59.097 55.000 0.00 0.00 0.00 2.41
2652 2870 1.679898 GGCCACCTAGACAGCTTGT 59.320 57.895 0.00 0.00 0.00 3.16
2653 2871 1.078143 GGGCCACCTAGACAGCTTG 60.078 63.158 4.39 0.00 0.00 4.01
2654 2872 2.660064 CGGGCCACCTAGACAGCTT 61.660 63.158 4.39 0.00 33.28 3.74
2655 2873 3.077556 CGGGCCACCTAGACAGCT 61.078 66.667 4.39 0.00 33.28 4.24
2656 2874 3.372554 GACGGGCCACCTAGACAGC 62.373 68.421 4.39 0.00 33.28 4.40
2657 2875 2.893398 GACGGGCCACCTAGACAG 59.107 66.667 4.39 0.00 33.28 3.51
2658 2876 3.066190 CGACGGGCCACCTAGACA 61.066 66.667 4.39 0.00 33.28 3.41
2659 2877 2.753043 TCGACGGGCCACCTAGAC 60.753 66.667 4.39 0.00 33.28 2.59
2660 2878 2.439701 CTCGACGGGCCACCTAGA 60.440 66.667 4.39 0.00 33.28 2.43
2661 2879 4.208686 GCTCGACGGGCCACCTAG 62.209 72.222 9.02 0.00 33.28 3.02


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

AutoCloner maintained by Alex Coulton.