Multiple sequence alignment - TraesCS1B01G139200

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 TraesCS1B01G139200 chr1B 100.000 3442 0 0 1 3442 182200309 182196868 0.000000e+00 6357
1 TraesCS1B01G139200 chr1D 95.231 2076 51 16 1 2037 119406528 119404462 0.000000e+00 3241
2 TraesCS1B01G139200 chr1D 93.359 512 24 3 2330 2831 119404149 119403638 0.000000e+00 749
3 TraesCS1B01G139200 chr1D 89.417 463 27 9 2967 3423 119403385 119402939 6.450000e-157 564
4 TraesCS1B01G139200 chr1D 93.642 173 11 0 2830 3002 119403556 119403384 3.410000e-65 259
5 TraesCS1B01G139200 chr1D 95.946 74 3 0 2242 2315 119404207 119404134 1.680000e-23 121
6 TraesCS1B01G139200 chr1D 97.674 43 1 0 2036 2078 119404443 119404401 1.320000e-09 75
7 TraesCS1B01G139200 chr1A 93.929 2092 72 17 1 2037 132136433 132134342 0.000000e+00 3109
8 TraesCS1B01G139200 chr1A 92.773 512 27 4 2330 2831 132134029 132133518 0.000000e+00 732
9 TraesCS1B01G139200 chr1A 92.542 295 20 2 2830 3123 132133436 132133143 4.110000e-114 422
10 TraesCS1B01G139200 chr1A 88.927 289 19 7 3141 3423 132131716 132131435 9.150000e-91 344
11 TraesCS1B01G139200 chr1A 97.297 74 2 0 2242 2315 132134087 132134014 3.610000e-25 126
12 TraesCS1B01G139200 chr1A 97.674 43 1 0 2036 2078 132134323 132134281 1.320000e-09 75


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 TraesCS1B01G139200 chr1B 182196868 182200309 3441 True 6357.000000 6357 100.0000 1 3442 1 chr1B.!!$R1 3441
1 TraesCS1B01G139200 chr1D 119402939 119406528 3589 True 834.833333 3241 94.2115 1 3423 6 chr1D.!!$R1 3422
2 TraesCS1B01G139200 chr1A 132131435 132136433 4998 True 801.333333 3109 93.8570 1 3423 6 chr1A.!!$R1 3422

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
670 713 0.324460 GAGGGAGAAACGAGGAGGGA 60.324 60.0 0.00 0.0 0.0 4.20 F
1656 1718 0.534412 CAATGGAGGTCGAGCAGTCT 59.466 55.0 18.15 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2231 2500 0.319727 CGCTGCAAAAAGGGCATTCA 60.320 50.0 0.00 0.00 41.06 2.57 R
3002 3364 0.171903 ATGAACCTTGCATTGCGAGC 59.828 50.0 18.87 7.55 38.64 5.03 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
34 35 1.996292 TGACAATCTAGTGCTGCGTC 58.004 50.000 0.00 0.00 0.00 5.19
40 41 2.080286 TCTAGTGCTGCGTCTTTTCC 57.920 50.000 0.00 0.00 0.00 3.13
67 68 7.962964 TTGTGTGGTTTTAAAAATTGTGTGA 57.037 28.000 1.31 0.00 0.00 3.58
381 389 2.552591 GCATCCATGAATGAGAGGGGAG 60.553 54.545 0.00 0.00 0.00 4.30
437 463 4.527583 CTCCTGCTCCCGCTCTGC 62.528 72.222 0.00 0.00 36.97 4.26
572 608 1.004440 GCAGGCTCCGTTTGAGAGT 60.004 57.895 0.00 0.00 44.42 3.24
582 618 0.687354 GTTTGAGAGTGAGGGGCTCA 59.313 55.000 0.00 0.00 38.25 4.26
670 713 0.324460 GAGGGAGAAACGAGGAGGGA 60.324 60.000 0.00 0.00 0.00 4.20
746 790 2.429069 CTTGTTTTGGCCGCGAGC 60.429 61.111 8.23 9.71 42.60 5.03
1344 1394 4.424711 GGGTTCCAGATGCGCCCA 62.425 66.667 4.18 0.00 39.13 5.36
1470 1532 2.351276 GGTGGCATGTCCGTTCCT 59.649 61.111 0.00 0.00 37.80 3.36
1485 1547 3.118738 CCGTTCCTTGCACTAGGTTCTAT 60.119 47.826 4.36 0.00 36.63 1.98
1656 1718 0.534412 CAATGGAGGTCGAGCAGTCT 59.466 55.000 18.15 0.00 0.00 3.24
1905 1967 6.096705 TGAATGGCAACGAATCTTCCATTTAT 59.903 34.615 6.30 0.00 44.76 1.40
1937 1999 4.024556 CGATGCATTTACCCAGTCATCTTC 60.025 45.833 0.00 0.00 0.00 2.87
1986 2051 5.464389 TGATTGTGATGTATCTTGAGATGCG 59.536 40.000 3.79 0.00 39.56 4.73
2011 2076 4.931601 TGACCATCTTCATTCAGTTCTTCG 59.068 41.667 0.00 0.00 0.00 3.79
2045 2222 9.440773 TGCATCACCTACATTCATAGATAATTC 57.559 33.333 0.00 0.00 0.00 2.17
2078 2255 7.668886 AGATGGAATGATGGATAGAATGGAAAC 59.331 37.037 0.00 0.00 0.00 2.78
2095 2363 5.069318 TGGAAACATACATGAAGAGTTGCA 58.931 37.500 0.00 0.00 33.40 4.08
2096 2364 5.048782 TGGAAACATACATGAAGAGTTGCAC 60.049 40.000 0.00 0.00 33.40 4.57
2104 2372 4.276926 ACATGAAGAGTTGCACTTCTTTCC 59.723 41.667 14.51 4.78 42.63 3.13
2111 2379 6.827727 AGAGTTGCACTTCTTTCCTTAACTA 58.172 36.000 0.00 0.00 0.00 2.24
2155 2424 9.625747 TTTGGCATCACATCATTTATCTACTTA 57.374 29.630 0.00 0.00 0.00 2.24
2156 2425 8.837788 TGGCATCACATCATTTATCTACTTAG 57.162 34.615 0.00 0.00 0.00 2.18
2157 2426 7.388776 TGGCATCACATCATTTATCTACTTAGC 59.611 37.037 0.00 0.00 0.00 3.09
2158 2427 7.388776 GGCATCACATCATTTATCTACTTAGCA 59.611 37.037 0.00 0.00 0.00 3.49
2159 2428 8.441608 GCATCACATCATTTATCTACTTAGCAG 58.558 37.037 0.00 0.00 0.00 4.24
2160 2429 9.486497 CATCACATCATTTATCTACTTAGCAGT 57.514 33.333 0.00 0.00 36.99 4.40
2180 2449 3.627577 AGTTAGCACCAGTGAACAAGTTG 59.372 43.478 0.00 0.00 0.00 3.16
2181 2450 2.128771 AGCACCAGTGAACAAGTTGT 57.871 45.000 1.64 1.64 0.00 3.32
2183 2452 2.164219 AGCACCAGTGAACAAGTTGTTG 59.836 45.455 25.46 12.93 41.28 3.33
2184 2453 2.163412 GCACCAGTGAACAAGTTGTTGA 59.837 45.455 25.46 15.08 41.28 3.18
2185 2454 3.181487 GCACCAGTGAACAAGTTGTTGAT 60.181 43.478 25.46 8.37 41.28 2.57
2186 2455 4.677779 GCACCAGTGAACAAGTTGTTGATT 60.678 41.667 25.46 11.63 41.28 2.57
2187 2456 5.410067 CACCAGTGAACAAGTTGTTGATTT 58.590 37.500 25.46 7.57 41.28 2.17
2188 2457 5.868801 CACCAGTGAACAAGTTGTTGATTTT 59.131 36.000 25.46 0.04 41.28 1.82
2189 2458 6.368516 CACCAGTGAACAAGTTGTTGATTTTT 59.631 34.615 25.46 0.00 41.28 1.94
2190 2459 6.589907 ACCAGTGAACAAGTTGTTGATTTTTC 59.410 34.615 25.46 10.02 41.28 2.29
2191 2460 6.589523 CCAGTGAACAAGTTGTTGATTTTTCA 59.410 34.615 25.46 12.50 41.28 2.69
2192 2461 7.411804 CCAGTGAACAAGTTGTTGATTTTTCAC 60.412 37.037 25.46 22.14 41.28 3.18
2193 2462 6.307800 AGTGAACAAGTTGTTGATTTTTCACG 59.692 34.615 25.46 0.00 43.75 4.35
2194 2463 6.088883 GTGAACAAGTTGTTGATTTTTCACGT 59.911 34.615 25.46 0.00 41.28 4.49
2195 2464 6.088749 TGAACAAGTTGTTGATTTTTCACGTG 59.911 34.615 25.46 9.94 41.28 4.49
2196 2465 5.465935 ACAAGTTGTTGATTTTTCACGTGT 58.534 33.333 16.51 0.00 37.10 4.49
2197 2466 5.571357 ACAAGTTGTTGATTTTTCACGTGTC 59.429 36.000 16.51 5.77 37.10 3.67
2198 2467 5.303747 AGTTGTTGATTTTTCACGTGTCA 57.696 34.783 16.51 8.62 0.00 3.58
2199 2468 5.890334 AGTTGTTGATTTTTCACGTGTCAT 58.110 33.333 16.51 3.41 0.00 3.06
2200 2469 7.022055 AGTTGTTGATTTTTCACGTGTCATA 57.978 32.000 16.51 0.48 0.00 2.15
2201 2470 7.132213 AGTTGTTGATTTTTCACGTGTCATAG 58.868 34.615 16.51 0.00 0.00 2.23
2202 2471 5.996219 TGTTGATTTTTCACGTGTCATAGG 58.004 37.500 16.51 0.00 0.00 2.57
2203 2472 5.760743 TGTTGATTTTTCACGTGTCATAGGA 59.239 36.000 16.51 0.00 0.00 2.94
2204 2473 6.261158 TGTTGATTTTTCACGTGTCATAGGAA 59.739 34.615 16.51 0.00 0.00 3.36
2205 2474 6.480524 TGATTTTTCACGTGTCATAGGAAG 57.519 37.500 16.51 0.00 0.00 3.46
2206 2475 6.227522 TGATTTTTCACGTGTCATAGGAAGA 58.772 36.000 16.51 0.00 0.00 2.87
2207 2476 5.917541 TTTTTCACGTGTCATAGGAAGAC 57.082 39.130 16.51 0.00 36.55 3.01
2208 2477 4.866508 TTTCACGTGTCATAGGAAGACT 57.133 40.909 16.51 0.00 36.94 3.24
2209 2478 4.866508 TTCACGTGTCATAGGAAGACTT 57.133 40.909 16.51 0.00 36.94 3.01
2210 2479 5.970317 TTCACGTGTCATAGGAAGACTTA 57.030 39.130 16.51 0.00 36.94 2.24
2211 2480 5.970317 TCACGTGTCATAGGAAGACTTAA 57.030 39.130 16.51 0.00 36.94 1.85
2212 2481 5.950883 TCACGTGTCATAGGAAGACTTAAG 58.049 41.667 16.51 0.00 36.94 1.85
2213 2482 5.708697 TCACGTGTCATAGGAAGACTTAAGA 59.291 40.000 16.51 0.00 36.94 2.10
2214 2483 6.208007 TCACGTGTCATAGGAAGACTTAAGAA 59.792 38.462 16.51 0.00 36.94 2.52
2215 2484 6.866770 CACGTGTCATAGGAAGACTTAAGAAA 59.133 38.462 10.09 0.00 36.94 2.52
2216 2485 6.867293 ACGTGTCATAGGAAGACTTAAGAAAC 59.133 38.462 10.09 0.41 36.94 2.78
2217 2486 6.866770 CGTGTCATAGGAAGACTTAAGAAACA 59.133 38.462 10.09 0.00 36.94 2.83
2218 2487 7.148787 CGTGTCATAGGAAGACTTAAGAAACAC 60.149 40.741 10.09 3.86 36.94 3.32
2219 2488 7.873505 GTGTCATAGGAAGACTTAAGAAACACT 59.126 37.037 10.09 4.44 36.94 3.55
2220 2489 9.085645 TGTCATAGGAAGACTTAAGAAACACTA 57.914 33.333 10.09 6.47 36.94 2.74
2221 2490 9.924650 GTCATAGGAAGACTTAAGAAACACTAA 57.075 33.333 10.09 0.00 33.29 2.24
2226 2495 9.628500 AGGAAGACTTAAGAAACACTAAACAAT 57.372 29.630 10.09 0.00 0.00 2.71
2230 2499 9.516314 AGACTTAAGAAACACTAAACAATTTGC 57.484 29.630 10.09 0.00 0.00 3.68
2231 2500 9.516314 GACTTAAGAAACACTAAACAATTTGCT 57.484 29.630 10.09 0.00 0.00 3.91
2232 2501 9.301153 ACTTAAGAAACACTAAACAATTTGCTG 57.699 29.630 10.09 0.00 0.00 4.41
2233 2502 9.515020 CTTAAGAAACACTAAACAATTTGCTGA 57.485 29.630 0.00 0.00 0.00 4.26
2234 2503 9.862371 TTAAGAAACACTAAACAATTTGCTGAA 57.138 25.926 0.00 0.00 0.00 3.02
2235 2504 8.947055 AAGAAACACTAAACAATTTGCTGAAT 57.053 26.923 0.00 0.00 0.00 2.57
2236 2505 8.356533 AGAAACACTAAACAATTTGCTGAATG 57.643 30.769 0.00 0.00 0.00 2.67
2237 2506 6.529463 AACACTAAACAATTTGCTGAATGC 57.471 33.333 0.00 0.00 43.25 3.56
2238 2507 4.990426 ACACTAAACAATTTGCTGAATGCC 59.010 37.500 0.00 0.00 42.00 4.40
2239 2508 4.389687 CACTAAACAATTTGCTGAATGCCC 59.610 41.667 0.00 0.00 42.00 5.36
2240 2509 3.775261 AAACAATTTGCTGAATGCCCT 57.225 38.095 0.00 0.00 42.00 5.19
2306 2575 3.009916 ACCAAGCAGTCCTGAATGAAGAT 59.990 43.478 0.00 0.00 0.00 2.40
2307 2576 3.377485 CCAAGCAGTCCTGAATGAAGATG 59.623 47.826 0.00 0.00 0.00 2.90
2308 2577 4.259356 CAAGCAGTCCTGAATGAAGATGA 58.741 43.478 0.00 0.00 0.00 2.92
2309 2578 4.564782 AGCAGTCCTGAATGAAGATGAA 57.435 40.909 0.00 0.00 0.00 2.57
2310 2579 4.515361 AGCAGTCCTGAATGAAGATGAAG 58.485 43.478 0.00 0.00 0.00 3.02
2311 2580 4.224594 AGCAGTCCTGAATGAAGATGAAGA 59.775 41.667 0.00 0.00 0.00 2.87
2312 2581 5.104444 AGCAGTCCTGAATGAAGATGAAGAT 60.104 40.000 0.00 0.00 0.00 2.40
2313 2582 5.007823 GCAGTCCTGAATGAAGATGAAGATG 59.992 44.000 0.00 0.00 0.00 2.90
2314 2583 6.346896 CAGTCCTGAATGAAGATGAAGATGA 58.653 40.000 0.00 0.00 0.00 2.92
2315 2584 6.822170 CAGTCCTGAATGAAGATGAAGATGAA 59.178 38.462 0.00 0.00 0.00 2.57
2316 2585 7.011576 CAGTCCTGAATGAAGATGAAGATGAAG 59.988 40.741 0.00 0.00 0.00 3.02
2317 2586 7.046652 GTCCTGAATGAAGATGAAGATGAAGA 58.953 38.462 0.00 0.00 0.00 2.87
2318 2587 7.716123 GTCCTGAATGAAGATGAAGATGAAGAT 59.284 37.037 0.00 0.00 0.00 2.40
2319 2588 7.715686 TCCTGAATGAAGATGAAGATGAAGATG 59.284 37.037 0.00 0.00 0.00 2.90
2320 2589 7.715686 CCTGAATGAAGATGAAGATGAAGATGA 59.284 37.037 0.00 0.00 0.00 2.92
2321 2590 9.110502 CTGAATGAAGATGAAGATGAAGATGAA 57.889 33.333 0.00 0.00 0.00 2.57
2322 2591 9.110502 TGAATGAAGATGAAGATGAAGATGAAG 57.889 33.333 0.00 0.00 0.00 3.02
2323 2592 9.327628 GAATGAAGATGAAGATGAAGATGAAGA 57.672 33.333 0.00 0.00 0.00 2.87
2324 2593 9.854668 AATGAAGATGAAGATGAAGATGAAGAT 57.145 29.630 0.00 0.00 0.00 2.40
2325 2594 8.664211 TGAAGATGAAGATGAAGATGAAGATG 57.336 34.615 0.00 0.00 0.00 2.90
2326 2595 8.483758 TGAAGATGAAGATGAAGATGAAGATGA 58.516 33.333 0.00 0.00 0.00 2.92
2327 2596 9.327628 GAAGATGAAGATGAAGATGAAGATGAA 57.672 33.333 0.00 0.00 0.00 2.57
2328 2597 8.896320 AGATGAAGATGAAGATGAAGATGAAG 57.104 34.615 0.00 0.00 0.00 3.02
2329 2598 8.706521 AGATGAAGATGAAGATGAAGATGAAGA 58.293 33.333 0.00 0.00 0.00 2.87
2330 2599 9.496873 GATGAAGATGAAGATGAAGATGAAGAT 57.503 33.333 0.00 0.00 0.00 2.40
2331 2600 8.664211 TGAAGATGAAGATGAAGATGAAGATG 57.336 34.615 0.00 0.00 0.00 2.90
2332 2601 8.483758 TGAAGATGAAGATGAAGATGAAGATGA 58.516 33.333 0.00 0.00 0.00 2.92
2333 2602 9.327628 GAAGATGAAGATGAAGATGAAGATGAA 57.672 33.333 0.00 0.00 0.00 2.57
2334 2603 8.896320 AGATGAAGATGAAGATGAAGATGAAG 57.104 34.615 0.00 0.00 0.00 3.02
2335 2604 8.706521 AGATGAAGATGAAGATGAAGATGAAGA 58.293 33.333 0.00 0.00 0.00 2.87
2336 2605 9.496873 GATGAAGATGAAGATGAAGATGAAGAT 57.503 33.333 0.00 0.00 0.00 2.40
2348 2617 9.327628 GATGAAGATGAAGATGAAGATGAGAAA 57.672 33.333 0.00 0.00 0.00 2.52
2358 2627 5.633830 TGAAGATGAGAAAAATCCTGCAC 57.366 39.130 0.00 0.00 0.00 4.57
2459 2728 0.396695 GACCTCCGTGTCCCCTGATA 60.397 60.000 0.00 0.00 0.00 2.15
2480 2749 0.538057 CTGACCAATGCACCCTGTGT 60.538 55.000 0.00 0.00 35.75 3.72
2481 2750 0.537143 TGACCAATGCACCCTGTGTC 60.537 55.000 0.00 0.00 35.75 3.67
2535 2804 2.545526 GTGATCGTTCATCATCGCCATT 59.454 45.455 0.00 0.00 43.72 3.16
2587 2856 7.489757 TGGTTTTTGTAAGTTATGTTTCAGCAC 59.510 33.333 0.00 0.00 0.00 4.40
2695 2964 8.807948 TCCTTTTCTTTTTCTCTCTTCTTTGA 57.192 30.769 0.00 0.00 0.00 2.69
2723 2992 4.507879 GCAGCCATGGCAATGTTC 57.492 55.556 37.18 15.48 44.88 3.18
2770 3039 1.065926 TGAGATGACGGCATTGAGCTT 60.066 47.619 4.56 0.00 44.79 3.74
2822 3101 9.796062 CGTAGTTTGAAAAATCCAAAATTCATG 57.204 29.630 0.00 0.00 35.57 3.07
2955 3317 5.331098 CAAAAATTTGTGGCTTTCCAACAC 58.669 37.500 0.00 0.00 45.53 3.32
3002 3364 3.963665 TGGTTTCGATTTCTTTGTGCAG 58.036 40.909 0.00 0.00 0.00 4.41
3016 3412 2.202570 GCAGCTCGCAATGCAAGG 60.203 61.111 5.91 0.00 42.11 3.61
3030 3426 5.535333 CAATGCAAGGTTCATTCTCAAAGT 58.465 37.500 0.00 0.00 32.30 2.66
3041 3437 8.706035 GGTTCATTCTCAAAGTTCATGATTTTG 58.294 33.333 19.54 19.54 34.07 2.44
3078 3475 5.473504 AGTTCGCAAGTCAAGGTATTTCATT 59.526 36.000 0.00 0.00 39.48 2.57
3079 3476 5.295431 TCGCAAGTCAAGGTATTTCATTG 57.705 39.130 0.00 0.00 38.91 2.82
3197 5008 1.322538 ATTTCGGCCACCATTGAGCC 61.323 55.000 2.24 0.00 43.53 4.70
3210 5021 0.753479 TTGAGCCCGGTCTGCAAAAA 60.753 50.000 0.00 0.00 0.00 1.94
3233 5044 4.222145 AGCCTACTCGTTATTGGTTTCTCA 59.778 41.667 0.00 0.00 0.00 3.27
3265 5076 2.941720 CAGATAGAAGCTGGAGCAAACC 59.058 50.000 0.65 0.00 45.16 3.27
3266 5077 2.573462 AGATAGAAGCTGGAGCAAACCA 59.427 45.455 0.65 0.00 45.16 3.67
3267 5078 2.949177 TAGAAGCTGGAGCAAACCAA 57.051 45.000 0.65 0.00 45.16 3.67
3268 5079 2.071778 AGAAGCTGGAGCAAACCAAA 57.928 45.000 0.65 0.00 45.16 3.28
3269 5080 1.683385 AGAAGCTGGAGCAAACCAAAC 59.317 47.619 0.65 0.00 45.16 2.93
3270 5081 1.683385 GAAGCTGGAGCAAACCAAACT 59.317 47.619 0.65 0.00 45.16 2.66
3271 5082 1.780503 AGCTGGAGCAAACCAAACTT 58.219 45.000 0.65 0.00 45.16 2.66
3333 5144 2.294233 TGCCTGTGCAGACTGATTTTTC 59.706 45.455 6.65 0.00 44.23 2.29
3336 5147 4.500375 GCCTGTGCAGACTGATTTTTCTTT 60.500 41.667 6.65 0.00 37.47 2.52
3337 5148 5.594926 CCTGTGCAGACTGATTTTTCTTTT 58.405 37.500 6.65 0.00 0.00 2.27
3411 5222 4.971282 AGAGGGGTATGTGAGATCAATCAA 59.029 41.667 0.00 0.00 0.00 2.57
3423 5234 9.623000 TGTGAGATCAATCAACATTATTCAGAT 57.377 29.630 0.00 0.00 0.00 2.90
3424 5235 9.880064 GTGAGATCAATCAACATTATTCAGATG 57.120 33.333 0.00 0.00 0.00 2.90
3425 5236 9.841295 TGAGATCAATCAACATTATTCAGATGA 57.159 29.630 0.00 0.00 0.00 2.92
3432 5243 9.512588 AATCAACATTATTCAGATGATACTCCC 57.487 33.333 0.00 0.00 28.78 4.30
3433 5244 8.033178 TCAACATTATTCAGATGATACTCCCA 57.967 34.615 0.00 0.00 0.00 4.37
3434 5245 7.933577 TCAACATTATTCAGATGATACTCCCAC 59.066 37.037 0.00 0.00 0.00 4.61
3435 5246 6.773638 ACATTATTCAGATGATACTCCCACC 58.226 40.000 0.00 0.00 0.00 4.61
3436 5247 5.468540 TTATTCAGATGATACTCCCACCG 57.531 43.478 0.00 0.00 0.00 4.94
3437 5248 2.454336 TCAGATGATACTCCCACCGT 57.546 50.000 0.00 0.00 0.00 4.83
3438 5249 2.747177 TCAGATGATACTCCCACCGTT 58.253 47.619 0.00 0.00 0.00 4.44
3439 5250 2.693591 TCAGATGATACTCCCACCGTTC 59.306 50.000 0.00 0.00 0.00 3.95
3440 5251 2.040178 AGATGATACTCCCACCGTTCC 58.960 52.381 0.00 0.00 0.00 3.62
3441 5252 2.040178 GATGATACTCCCACCGTTCCT 58.960 52.381 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 9.059485 CACACAATTTTTAAAACCACACAAATG 57.941 29.630 0.00 0.00 0.00 2.32
67 68 2.868964 TCCTAGGCCTACTGGACATT 57.131 50.000 15.25 0.00 46.30 2.71
167 168 4.741676 GTGCAGACTCTTTTTCCACATTTG 59.258 41.667 0.00 0.00 0.00 2.32
381 389 2.685388 GGGCTTGCTTCTGAAATACTCC 59.315 50.000 0.00 0.00 0.00 3.85
437 463 1.510623 GCGTGCAGTGCATCGAAAG 60.511 57.895 30.73 16.96 41.91 2.62
515 541 1.433879 GTCACTCCATCCTCGACCG 59.566 63.158 0.00 0.00 0.00 4.79
582 618 2.439883 GCTAGGACCCGACGAGGT 60.440 66.667 7.61 7.61 45.12 3.85
633 676 4.335584 CTCGATCGCTCTCGCCCC 62.336 72.222 11.09 0.00 38.52 5.80
634 677 4.335584 CCTCGATCGCTCTCGCCC 62.336 72.222 11.09 0.00 38.52 6.13
635 678 3.248630 CTCCTCGATCGCTCTCGCC 62.249 68.421 11.09 0.00 38.52 5.54
670 713 5.340027 CCCTACCCACCTGATTAACTGAAAT 60.340 44.000 0.00 0.00 0.00 2.17
746 790 0.826715 TGAGGAGGAATCTCTTGCGG 59.173 55.000 0.00 0.00 39.86 5.69
751 795 1.501170 TCCGGATGAGGAGGAATCTCT 59.499 52.381 0.00 0.00 39.86 3.10
904 950 2.223044 GGCCGAGACTAAAAAGCAATCG 60.223 50.000 0.00 0.00 0.00 3.34
958 1004 4.127171 TCTCTGAAAACGAAACCAAGAGG 58.873 43.478 0.00 0.00 42.21 3.69
1344 1394 1.878775 GAGGCATTGCAGCTTCGTT 59.121 52.632 11.39 0.00 30.81 3.85
1455 1517 1.971167 GCAAGGAACGGACATGCCA 60.971 57.895 0.00 0.00 35.94 4.92
1464 1526 2.457366 AGAACCTAGTGCAAGGAACG 57.543 50.000 11.52 0.00 39.15 3.95
1470 1532 2.840511 TCCCCATAGAACCTAGTGCAA 58.159 47.619 0.00 0.00 0.00 4.08
1485 1547 0.984230 GACCAGACTTCACATCCCCA 59.016 55.000 0.00 0.00 0.00 4.96
1593 1655 2.264794 GGTCCGCCAATCGACACT 59.735 61.111 0.00 0.00 41.67 3.55
1617 1679 1.731700 CGACACGGACCCGATGTAT 59.268 57.895 16.07 0.00 42.83 2.29
1656 1718 1.937191 TGATGCAGGTGTAGTCCTCA 58.063 50.000 0.00 0.00 35.37 3.86
1905 1967 3.386486 GGTAAATGCATCGACATACCGA 58.614 45.455 0.00 0.00 43.16 4.69
1937 1999 7.853377 TCGCTTATTCGAATCAATAGTACTG 57.147 36.000 15.25 0.00 35.31 2.74
1986 2051 6.238049 CGAAGAACTGAATGAAGATGGTCATC 60.238 42.308 2.92 2.92 37.25 2.92
2011 2076 2.733956 TGTAGGTGATGCAAATTCCCC 58.266 47.619 0.00 0.00 0.00 4.81
2045 2222 4.701651 TCCATCATTCCATCTGAAGAGG 57.298 45.455 0.00 0.00 36.14 3.69
2111 2379 9.949174 GATGCCAAATTCATTTTTAACTTGTTT 57.051 25.926 0.00 0.00 0.00 2.83
2129 2398 8.523915 AAGTAGATAAATGATGTGATGCCAAA 57.476 30.769 0.00 0.00 0.00 3.28
2131 2400 7.388776 GCTAAGTAGATAAATGATGTGATGCCA 59.611 37.037 0.00 0.00 0.00 4.92
2155 2424 1.140852 TGTTCACTGGTGCTAACTGCT 59.859 47.619 0.00 0.00 43.37 4.24
2156 2425 1.593196 TGTTCACTGGTGCTAACTGC 58.407 50.000 0.00 0.00 43.25 4.40
2157 2426 3.206150 ACTTGTTCACTGGTGCTAACTG 58.794 45.455 0.00 0.00 0.00 3.16
2158 2427 3.560636 ACTTGTTCACTGGTGCTAACT 57.439 42.857 0.00 0.00 0.00 2.24
2159 2428 3.377172 ACAACTTGTTCACTGGTGCTAAC 59.623 43.478 0.00 0.00 0.00 2.34
2160 2429 3.616219 ACAACTTGTTCACTGGTGCTAA 58.384 40.909 0.00 0.00 0.00 3.09
2161 2430 3.275617 ACAACTTGTTCACTGGTGCTA 57.724 42.857 0.00 0.00 0.00 3.49
2169 2438 6.088883 ACGTGAAAAATCAACAACTTGTTCAC 59.911 34.615 4.06 7.24 38.77 3.18
2180 2449 6.236017 TCCTATGACACGTGAAAAATCAAC 57.764 37.500 25.01 2.56 0.00 3.18
2181 2450 6.708502 TCTTCCTATGACACGTGAAAAATCAA 59.291 34.615 25.01 6.30 0.00 2.57
2183 2452 6.369065 AGTCTTCCTATGACACGTGAAAAATC 59.631 38.462 25.01 9.50 36.94 2.17
2184 2453 6.231211 AGTCTTCCTATGACACGTGAAAAAT 58.769 36.000 25.01 11.82 36.94 1.82
2185 2454 5.607477 AGTCTTCCTATGACACGTGAAAAA 58.393 37.500 25.01 4.57 36.94 1.94
2186 2455 5.209818 AGTCTTCCTATGACACGTGAAAA 57.790 39.130 25.01 7.33 36.94 2.29
2187 2456 4.866508 AGTCTTCCTATGACACGTGAAA 57.133 40.909 25.01 10.14 36.94 2.69
2188 2457 4.866508 AAGTCTTCCTATGACACGTGAA 57.133 40.909 25.01 10.55 36.94 3.18
2189 2458 5.708697 TCTTAAGTCTTCCTATGACACGTGA 59.291 40.000 25.01 0.00 36.94 4.35
2190 2459 5.950883 TCTTAAGTCTTCCTATGACACGTG 58.049 41.667 15.48 15.48 36.94 4.49
2191 2460 6.585695 TTCTTAAGTCTTCCTATGACACGT 57.414 37.500 1.63 0.00 36.94 4.49
2192 2461 6.866770 TGTTTCTTAAGTCTTCCTATGACACG 59.133 38.462 1.63 0.00 36.94 4.49
2193 2462 7.873505 AGTGTTTCTTAAGTCTTCCTATGACAC 59.126 37.037 1.63 0.00 36.94 3.67
2194 2463 7.963532 AGTGTTTCTTAAGTCTTCCTATGACA 58.036 34.615 1.63 0.00 36.94 3.58
2195 2464 9.924650 TTAGTGTTTCTTAAGTCTTCCTATGAC 57.075 33.333 1.63 0.00 34.88 3.06
2200 2469 9.628500 ATTGTTTAGTGTTTCTTAAGTCTTCCT 57.372 29.630 1.63 0.00 0.00 3.36
2204 2473 9.516314 GCAAATTGTTTAGTGTTTCTTAAGTCT 57.484 29.630 1.63 0.00 0.00 3.24
2205 2474 9.516314 AGCAAATTGTTTAGTGTTTCTTAAGTC 57.484 29.630 1.63 0.00 0.00 3.01
2206 2475 9.301153 CAGCAAATTGTTTAGTGTTTCTTAAGT 57.699 29.630 1.63 0.00 0.00 2.24
2207 2476 9.515020 TCAGCAAATTGTTTAGTGTTTCTTAAG 57.485 29.630 0.00 0.00 0.00 1.85
2208 2477 9.862371 TTCAGCAAATTGTTTAGTGTTTCTTAA 57.138 25.926 0.00 0.00 0.00 1.85
2210 2479 8.819974 CATTCAGCAAATTGTTTAGTGTTTCTT 58.180 29.630 0.00 0.00 0.00 2.52
2211 2480 7.042523 GCATTCAGCAAATTGTTTAGTGTTTCT 60.043 33.333 0.00 0.00 44.79 2.52
2212 2481 7.065283 GCATTCAGCAAATTGTTTAGTGTTTC 58.935 34.615 0.00 0.00 44.79 2.78
2213 2482 6.947258 GCATTCAGCAAATTGTTTAGTGTTT 58.053 32.000 0.00 0.00 44.79 2.83
2214 2483 6.529463 GCATTCAGCAAATTGTTTAGTGTT 57.471 33.333 0.00 0.00 44.79 3.32
2229 2498 1.435577 CTGCAAAAAGGGCATTCAGC 58.564 50.000 0.00 0.00 41.06 4.26
2230 2499 1.435577 GCTGCAAAAAGGGCATTCAG 58.564 50.000 0.00 0.00 41.06 3.02
2231 2500 0.319727 CGCTGCAAAAAGGGCATTCA 60.320 50.000 0.00 0.00 41.06 2.57
2232 2501 1.015607 CCGCTGCAAAAAGGGCATTC 61.016 55.000 0.00 0.00 41.06 2.67
2233 2502 1.004679 CCGCTGCAAAAAGGGCATT 60.005 52.632 0.00 0.00 41.06 3.56
2234 2503 2.209315 ACCGCTGCAAAAAGGGCAT 61.209 52.632 0.00 0.00 41.06 4.40
2235 2504 2.837291 ACCGCTGCAAAAAGGGCA 60.837 55.556 0.00 0.00 39.32 5.36
2236 2505 2.356194 CACCGCTGCAAAAAGGGC 60.356 61.111 0.00 0.00 0.00 5.19
2237 2506 1.172180 TCTCACCGCTGCAAAAAGGG 61.172 55.000 0.00 0.00 0.00 3.95
2238 2507 0.667993 TTCTCACCGCTGCAAAAAGG 59.332 50.000 0.00 0.00 0.00 3.11
2239 2508 2.322161 CATTCTCACCGCTGCAAAAAG 58.678 47.619 0.00 0.00 0.00 2.27
2240 2509 1.602668 GCATTCTCACCGCTGCAAAAA 60.603 47.619 0.00 0.00 34.77 1.94
2269 2538 0.746063 TTGGTTTCTGCAGTTGCCAG 59.254 50.000 14.67 0.06 41.18 4.85
2306 2575 8.483758 TCATCTTCATCTTCATCTTCATCTTCA 58.516 33.333 0.00 0.00 0.00 3.02
2307 2576 8.890124 TCATCTTCATCTTCATCTTCATCTTC 57.110 34.615 0.00 0.00 0.00 2.87
2308 2577 9.332502 CTTCATCTTCATCTTCATCTTCATCTT 57.667 33.333 0.00 0.00 0.00 2.40
2309 2578 8.706521 TCTTCATCTTCATCTTCATCTTCATCT 58.293 33.333 0.00 0.00 0.00 2.90
2310 2579 8.890124 TCTTCATCTTCATCTTCATCTTCATC 57.110 34.615 0.00 0.00 0.00 2.92
2311 2580 9.278978 CATCTTCATCTTCATCTTCATCTTCAT 57.721 33.333 0.00 0.00 0.00 2.57
2312 2581 8.483758 TCATCTTCATCTTCATCTTCATCTTCA 58.516 33.333 0.00 0.00 0.00 3.02
2313 2582 8.890124 TCATCTTCATCTTCATCTTCATCTTC 57.110 34.615 0.00 0.00 0.00 2.87
2314 2583 9.332502 CTTCATCTTCATCTTCATCTTCATCTT 57.667 33.333 0.00 0.00 0.00 2.40
2315 2584 8.706521 TCTTCATCTTCATCTTCATCTTCATCT 58.293 33.333 0.00 0.00 0.00 2.90
2316 2585 8.890124 TCTTCATCTTCATCTTCATCTTCATC 57.110 34.615 0.00 0.00 0.00 2.92
2317 2586 9.278978 CATCTTCATCTTCATCTTCATCTTCAT 57.721 33.333 0.00 0.00 0.00 2.57
2318 2587 8.483758 TCATCTTCATCTTCATCTTCATCTTCA 58.516 33.333 0.00 0.00 0.00 3.02
2319 2588 8.890124 TCATCTTCATCTTCATCTTCATCTTC 57.110 34.615 0.00 0.00 0.00 2.87
2320 2589 8.706521 TCTCATCTTCATCTTCATCTTCATCTT 58.293 33.333 0.00 0.00 0.00 2.40
2321 2590 8.252624 TCTCATCTTCATCTTCATCTTCATCT 57.747 34.615 0.00 0.00 0.00 2.90
2322 2591 8.890124 TTCTCATCTTCATCTTCATCTTCATC 57.110 34.615 0.00 0.00 0.00 2.92
2323 2592 9.682465 TTTTCTCATCTTCATCTTCATCTTCAT 57.318 29.630 0.00 0.00 0.00 2.57
2324 2593 9.511272 TTTTTCTCATCTTCATCTTCATCTTCA 57.489 29.630 0.00 0.00 0.00 3.02
2327 2596 9.122779 GGATTTTTCTCATCTTCATCTTCATCT 57.877 33.333 0.00 0.00 0.00 2.90
2328 2597 9.122779 AGGATTTTTCTCATCTTCATCTTCATC 57.877 33.333 0.00 0.00 0.00 2.92
2329 2598 8.904834 CAGGATTTTTCTCATCTTCATCTTCAT 58.095 33.333 0.00 0.00 0.00 2.57
2330 2599 7.148120 GCAGGATTTTTCTCATCTTCATCTTCA 60.148 37.037 0.00 0.00 0.00 3.02
2331 2600 7.148120 TGCAGGATTTTTCTCATCTTCATCTTC 60.148 37.037 0.00 0.00 0.00 2.87
2332 2601 6.662234 TGCAGGATTTTTCTCATCTTCATCTT 59.338 34.615 0.00 0.00 0.00 2.40
2333 2602 6.095160 GTGCAGGATTTTTCTCATCTTCATCT 59.905 38.462 0.00 0.00 0.00 2.90
2334 2603 6.095160 AGTGCAGGATTTTTCTCATCTTCATC 59.905 38.462 0.00 0.00 0.00 2.92
2335 2604 5.950549 AGTGCAGGATTTTTCTCATCTTCAT 59.049 36.000 0.00 0.00 0.00 2.57
2336 2605 5.319453 AGTGCAGGATTTTTCTCATCTTCA 58.681 37.500 0.00 0.00 0.00 3.02
2348 2617 1.836802 GGAGAGGAGAGTGCAGGATTT 59.163 52.381 0.00 0.00 0.00 2.17
2358 2627 1.394266 GCTGAGCTGGGAGAGGAGAG 61.394 65.000 0.00 0.00 0.00 3.20
2422 2691 2.034879 CATGTCAGCACGACCACCC 61.035 63.158 4.07 0.00 44.71 4.61
2459 2728 1.075482 CAGGGTGCATTGGTCAGGT 59.925 57.895 0.00 0.00 0.00 4.00
2480 2749 1.899437 GACCCATCTTCCTGGCACGA 61.899 60.000 0.00 0.00 34.77 4.35
2481 2750 1.450312 GACCCATCTTCCTGGCACG 60.450 63.158 0.00 0.00 34.77 5.34
2587 2856 6.015688 CCATCAATTCCACCCAATATCTCAAG 60.016 42.308 0.00 0.00 0.00 3.02
2695 2964 1.410648 CCATGGCTGCCAAGAGGTAAT 60.411 52.381 27.24 2.94 36.95 1.89
2723 2992 1.002659 TGTCCCAACTTACATCACGGG 59.997 52.381 0.00 0.00 34.81 5.28
2755 3024 1.603456 TTTCAAGCTCAATGCCGTCA 58.397 45.000 0.00 0.00 44.23 4.35
2756 3025 2.704725 TTTTCAAGCTCAATGCCGTC 57.295 45.000 0.00 0.00 44.23 4.79
2770 3039 2.230992 CGGTCTCCATTTGGCATTTTCA 59.769 45.455 0.00 0.00 34.44 2.69
2800 3079 9.518906 AAAGCATGAATTTTGGATTTTTCAAAC 57.481 25.926 0.00 0.00 34.34 2.93
2858 3220 7.118245 CGTGCACATTATGTCTCCAATATATGT 59.882 37.037 18.64 0.00 0.00 2.29
2866 3228 2.760634 ACGTGCACATTATGTCTCCA 57.239 45.000 18.64 0.00 0.00 3.86
2955 3317 3.753272 ACTTTGAGAATGAACCGTCCATG 59.247 43.478 0.00 0.00 0.00 3.66
3002 3364 0.171903 ATGAACCTTGCATTGCGAGC 59.828 50.000 18.87 7.55 38.64 5.03
3016 3412 9.252962 ACAAAATCATGAACTTTGAGAATGAAC 57.747 29.630 27.58 0.00 34.76 3.18
3030 3426 7.333921 ACTGCACAAAGAAAACAAAATCATGAA 59.666 29.630 0.00 0.00 0.00 2.57
3197 5008 0.521735 GTAGGCTTTTTGCAGACCGG 59.478 55.000 0.00 0.00 45.15 5.28
3210 5021 4.222145 TGAGAAACCAATAACGAGTAGGCT 59.778 41.667 0.00 0.00 0.00 4.58
3233 5044 5.124645 CAGCTTCTATCTGCCAGATCTTTT 58.875 41.667 11.20 0.00 36.20 2.27
3265 5076 7.225538 ACAATCTATCCGAATCTAGCAAGTTTG 59.774 37.037 0.00 0.00 0.00 2.93
3266 5077 7.275920 ACAATCTATCCGAATCTAGCAAGTTT 58.724 34.615 0.00 0.00 0.00 2.66
3267 5078 6.821388 ACAATCTATCCGAATCTAGCAAGTT 58.179 36.000 0.00 0.00 0.00 2.66
3268 5079 6.040955 TGACAATCTATCCGAATCTAGCAAGT 59.959 38.462 0.00 0.00 0.00 3.16
3269 5080 6.450545 TGACAATCTATCCGAATCTAGCAAG 58.549 40.000 0.00 0.00 0.00 4.01
3270 5081 6.040955 ACTGACAATCTATCCGAATCTAGCAA 59.959 38.462 0.00 0.00 0.00 3.91
3271 5082 5.536538 ACTGACAATCTATCCGAATCTAGCA 59.463 40.000 0.00 0.00 0.00 3.49
3333 5144 7.500992 TCCCTTATGATGCTACACTAGAAAAG 58.499 38.462 0.00 0.00 0.00 2.27
3336 5147 6.997655 CATCCCTTATGATGCTACACTAGAA 58.002 40.000 0.00 0.00 37.86 2.10
3337 5148 6.596309 CATCCCTTATGATGCTACACTAGA 57.404 41.667 0.00 0.00 37.86 2.43
3353 5164 0.962356 CCAGCTTTCGTGCATCCCTT 60.962 55.000 0.00 0.00 34.99 3.95
3411 5222 6.519043 CGGTGGGAGTATCATCTGAATAATGT 60.519 42.308 0.00 0.00 36.25 2.71
3423 5234 3.703804 AGGAACGGTGGGAGTATCA 57.296 52.632 0.00 0.00 36.25 2.15


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

AutoCloner maintained by Alex Coulton.