Multiple sequence alignment - TraesCS5B01G448500

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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 TraesCS5B01G448500 chr5B 100.000 3155 0 0 1 3155 620825351 620828505 0.000000e+00 5827
1 TraesCS5B01G448500 chr5B 80.714 1960 232 79 3 1877 620668377 620670275 0.000000e+00 1391
2 TraesCS5B01G448500 chr5B 78.878 1818 263 65 15 1764 620305913 620307677 0.000000e+00 1118
3 TraesCS5B01G448500 chr5B 81.137 1214 175 36 3 1195 621399983 621398803 0.000000e+00 924
4 TraesCS5B01G448500 chr5B 81.761 636 64 30 1156 1747 621398809 621398182 4.730000e-133 484
5 TraesCS5B01G448500 chr5D 92.318 2161 134 23 16 2162 499652078 499654220 0.000000e+00 3042
6 TraesCS5B01G448500 chr5D 79.597 1838 252 63 1 1763 499446922 499448711 0.000000e+00 1203
7 TraesCS5B01G448500 chr5D 81.619 1186 178 28 15 1191 499957335 499956181 0.000000e+00 946
8 TraesCS5B01G448500 chr5D 90.237 676 44 10 2381 3035 499654434 499655108 0.000000e+00 863
9 TraesCS5B01G448500 chr5D 80.431 649 66 34 1165 1763 499956168 499955531 3.740000e-119 438
10 TraesCS5B01G448500 chr5A 90.295 1999 155 26 12 1994 623953973 623955948 0.000000e+00 2580
11 TraesCS5B01G448500 chr5A 78.571 1862 247 83 3 1764 623684094 623685903 0.000000e+00 1088
12 TraesCS5B01G448500 chr5A 81.524 1142 174 29 15 1149 624476355 624475244 0.000000e+00 905
13 TraesCS5B01G448500 chr5A 86.370 719 70 12 2340 3035 623956266 623956979 0.000000e+00 760
14 TraesCS5B01G448500 chr5A 84.310 478 43 14 1291 1747 624475031 624474565 3.740000e-119 438


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 TraesCS5B01G448500 chr5B 620825351 620828505 3154 False 5827.0 5827 100.0000 1 3155 1 chr5B.!!$F3 3154
1 TraesCS5B01G448500 chr5B 620668377 620670275 1898 False 1391.0 1391 80.7140 3 1877 1 chr5B.!!$F2 1874
2 TraesCS5B01G448500 chr5B 620305913 620307677 1764 False 1118.0 1118 78.8780 15 1764 1 chr5B.!!$F1 1749
3 TraesCS5B01G448500 chr5B 621398182 621399983 1801 True 704.0 924 81.4490 3 1747 2 chr5B.!!$R1 1744
4 TraesCS5B01G448500 chr5D 499652078 499655108 3030 False 1952.5 3042 91.2775 16 3035 2 chr5D.!!$F2 3019
5 TraesCS5B01G448500 chr5D 499446922 499448711 1789 False 1203.0 1203 79.5970 1 1763 1 chr5D.!!$F1 1762
6 TraesCS5B01G448500 chr5D 499955531 499957335 1804 True 692.0 946 81.0250 15 1763 2 chr5D.!!$R1 1748
7 TraesCS5B01G448500 chr5A 623953973 623956979 3006 False 1670.0 2580 88.3325 12 3035 2 chr5A.!!$F2 3023
8 TraesCS5B01G448500 chr5A 623684094 623685903 1809 False 1088.0 1088 78.5710 3 1764 1 chr5A.!!$F1 1761
9 TraesCS5B01G448500 chr5A 624474565 624476355 1790 True 671.5 905 82.9170 15 1747 2 chr5A.!!$R1 1732

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
404 411 0.033504 ACTTGCGTGACGTTCCATCT 59.966 50.0 6.91 0.0 0.0 2.90 F
697 704 0.173481 CTCGAATCGGTGCAGAGGAA 59.827 55.0 1.76 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1892 2154 0.105039 GGGCATCTAGGTCCGTCAAG 59.895 60.0 0.0 0.0 0.00 3.02 R
2442 2816 0.308993 GAAAGCAGGCATATCCACGC 59.691 55.0 0.0 0.0 37.29 5.34 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
54 55 1.531149 CAGTTCGTCGTTCCAGCAAAT 59.469 47.619 0.00 0.00 0.00 2.32
59 60 3.504863 TCGTCGTTCCAGCAAATACTAC 58.495 45.455 0.00 0.00 0.00 2.73
70 73 7.995289 TCCAGCAAATACTACATACAAATTGG 58.005 34.615 0.00 0.00 0.00 3.16
72 75 6.697019 CAGCAAATACTACATACAAATTGGGC 59.303 38.462 0.00 0.00 0.00 5.36
76 79 2.020720 CTACATACAAATTGGGCCGCA 58.979 47.619 0.00 0.00 0.00 5.69
91 94 1.258982 GCCGCACATCGAGAAGTTATG 59.741 52.381 0.00 0.00 41.67 1.90
134 139 1.266989 CTCACAGTCACGAGTAGCACA 59.733 52.381 0.00 0.00 0.00 4.57
211 216 5.503927 ACTGATCACTCCAGTGCAAATTAT 58.496 37.500 1.49 0.00 45.25 1.28
226 231 4.662145 CAAATTATTCCGGACTCAAGTGC 58.338 43.478 1.83 0.00 0.00 4.40
286 291 3.760035 CGCCTGCAGGAGTACGGT 61.760 66.667 37.21 0.00 37.39 4.83
327 332 4.758251 CACATCGCCGGTGCAGGA 62.758 66.667 11.05 0.00 37.32 3.86
404 411 0.033504 ACTTGCGTGACGTTCCATCT 59.966 50.000 6.91 0.00 0.00 2.90
408 415 0.389948 GCGTGACGTTCCATCTCCTT 60.390 55.000 6.91 0.00 0.00 3.36
443 450 2.582498 CGTCGGATCGGCCTGTTC 60.582 66.667 0.00 0.00 0.00 3.18
446 453 4.891727 CGGATCGGCCTGTTCCCG 62.892 72.222 14.93 10.43 46.88 5.14
554 561 3.864789 AATCTCCACCAAACTCACACT 57.135 42.857 0.00 0.00 0.00 3.55
604 611 1.803289 GGCGCATTTCTCCCAGAAC 59.197 57.895 10.83 0.00 33.26 3.01
608 615 2.086869 CGCATTTCTCCCAGAACACAT 58.913 47.619 0.00 0.00 33.26 3.21
667 674 2.218953 ATCCGTACCTACACAATGCG 57.781 50.000 0.00 0.00 0.00 4.73
697 704 0.173481 CTCGAATCGGTGCAGAGGAA 59.827 55.000 1.76 0.00 0.00 3.36
754 761 0.907230 ACTCTGGAAGTCTGGAGGCC 60.907 60.000 0.00 0.00 30.02 5.19
1035 1069 1.302192 CCTCACCTCCGGCGAAAAA 60.302 57.895 9.30 0.00 0.00 1.94
1288 1443 2.808321 GCCGTCGTTCCTCGTTCC 60.808 66.667 0.00 0.00 40.80 3.62
1298 1453 0.879765 TCCTCGTTCCGTCTGTTCTC 59.120 55.000 0.00 0.00 0.00 2.87
1331 1487 4.022849 CCCTGATCTGACTTTGGTTTTGTC 60.023 45.833 0.38 0.00 0.00 3.18
1426 1589 0.824109 TCGGCAAGTTCATCGAGGAT 59.176 50.000 0.00 0.00 0.00 3.24
1624 1799 3.793144 GCGCCAGCCAAGAAGACG 61.793 66.667 0.00 0.00 37.42 4.18
1777 2033 4.341783 AAGAAGGCGCCTGCTGCT 62.342 61.111 37.98 20.97 42.25 4.24
1795 2051 4.083862 GCGACCCCGAAGAAGCCT 62.084 66.667 0.00 0.00 38.22 4.58
1797 2053 2.943978 CGACCCCGAAGAAGCCTGT 61.944 63.158 0.00 0.00 38.22 4.00
1888 2150 3.604582 CAAGAAGGCCAAGAAGTAGAGG 58.395 50.000 5.01 0.00 0.00 3.69
1892 2154 1.815840 GCCAAGAAGTAGAGGCCGC 60.816 63.158 0.00 0.00 41.25 6.53
1893 2155 1.901085 CCAAGAAGTAGAGGCCGCT 59.099 57.895 15.29 15.29 0.00 5.52
2073 2346 6.098409 CCATGGGAATCAGTTGTACTAGTAGT 59.902 42.308 2.85 8.14 0.00 2.73
2081 2354 9.745018 AATCAGTTGTACTAGTAGTAGTAACCA 57.255 33.333 22.07 10.48 42.29 3.67
2123 2398 2.916702 TCGCAGCAATATCCATGAGT 57.083 45.000 0.00 0.00 0.00 3.41
2152 2427 7.687005 TGTCAAAATTACCGTGTTTCATTTC 57.313 32.000 0.00 0.00 0.00 2.17
2182 2524 8.378172 TCTGAAATTGAGTTCGTATCTTTTGT 57.622 30.769 0.00 0.00 0.00 2.83
2183 2525 9.483916 TCTGAAATTGAGTTCGTATCTTTTGTA 57.516 29.630 0.00 0.00 0.00 2.41
2184 2526 9.746711 CTGAAATTGAGTTCGTATCTTTTGTAG 57.253 33.333 0.00 0.00 0.00 2.74
2185 2527 9.268268 TGAAATTGAGTTCGTATCTTTTGTAGT 57.732 29.630 0.00 0.00 0.00 2.73
2192 2534 9.350357 GAGTTCGTATCTTTTGTAGTATTGTCA 57.650 33.333 0.00 0.00 0.00 3.58
2193 2535 9.701098 AGTTCGTATCTTTTGTAGTATTGTCAA 57.299 29.630 0.00 0.00 0.00 3.18
2196 2538 8.600625 TCGTATCTTTTGTAGTATTGTCAATGC 58.399 33.333 8.39 6.93 0.00 3.56
2197 2539 7.850982 CGTATCTTTTGTAGTATTGTCAATGCC 59.149 37.037 8.39 0.00 0.00 4.40
2199 2541 7.517614 TCTTTTGTAGTATTGTCAATGCCAA 57.482 32.000 8.39 5.04 0.00 4.52
2200 2542 8.121305 TCTTTTGTAGTATTGTCAATGCCAAT 57.879 30.769 8.39 0.00 36.53 3.16
2201 2543 8.243426 TCTTTTGTAGTATTGTCAATGCCAATC 58.757 33.333 8.39 0.00 34.51 2.67
2202 2544 7.701539 TTTGTAGTATTGTCAATGCCAATCT 57.298 32.000 8.39 0.00 34.51 2.40
2203 2545 6.925610 TGTAGTATTGTCAATGCCAATCTC 57.074 37.500 8.39 0.00 34.51 2.75
2204 2546 5.822519 TGTAGTATTGTCAATGCCAATCTCC 59.177 40.000 8.39 0.00 34.51 3.71
2205 2547 5.121380 AGTATTGTCAATGCCAATCTCCT 57.879 39.130 8.39 0.00 34.51 3.69
2207 2549 6.294473 AGTATTGTCAATGCCAATCTCCTAG 58.706 40.000 8.39 0.00 34.51 3.02
2209 2551 5.378230 TTGTCAATGCCAATCTCCTAGAT 57.622 39.130 0.00 0.00 36.28 1.98
2211 2553 5.759059 TGTCAATGCCAATCTCCTAGATTT 58.241 37.500 0.00 0.00 41.90 2.17
2212 2554 6.899089 TGTCAATGCCAATCTCCTAGATTTA 58.101 36.000 0.00 0.00 41.90 1.40
2213 2555 7.520798 TGTCAATGCCAATCTCCTAGATTTAT 58.479 34.615 0.00 0.00 41.90 1.40
2214 2556 8.000709 TGTCAATGCCAATCTCCTAGATTTATT 58.999 33.333 0.00 0.36 41.90 1.40
2216 2558 9.425248 TCAATGCCAATCTCCTAGATTTATTTT 57.575 29.630 0.00 0.00 41.90 1.82
2217 2559 9.472361 CAATGCCAATCTCCTAGATTTATTTTG 57.528 33.333 0.00 0.51 41.90 2.44
2218 2560 7.042797 TGCCAATCTCCTAGATTTATTTTGC 57.957 36.000 0.00 0.00 41.90 3.68
2220 2562 7.998383 TGCCAATCTCCTAGATTTATTTTGCTA 59.002 33.333 0.00 0.00 41.90 3.49
2238 2580 4.765273 TGCTAAGGATGATTCTGCGTTAA 58.235 39.130 0.00 0.00 0.00 2.01
2239 2581 5.368145 TGCTAAGGATGATTCTGCGTTAAT 58.632 37.500 0.00 0.00 0.00 1.40
2240 2582 5.237127 TGCTAAGGATGATTCTGCGTTAATG 59.763 40.000 0.00 0.00 0.00 1.90
2242 2584 2.880890 AGGATGATTCTGCGTTAATGGC 59.119 45.455 0.00 0.00 0.00 4.40
2243 2585 2.030805 GGATGATTCTGCGTTAATGGCC 60.031 50.000 0.00 0.00 0.00 5.36
2244 2586 2.121291 TGATTCTGCGTTAATGGCCA 57.879 45.000 8.56 8.56 0.00 5.36
2245 2587 1.742831 TGATTCTGCGTTAATGGCCAC 59.257 47.619 8.16 0.00 0.00 5.01
2246 2588 1.065551 GATTCTGCGTTAATGGCCACC 59.934 52.381 8.16 0.00 0.00 4.61
2247 2589 0.037590 TTCTGCGTTAATGGCCACCT 59.962 50.000 8.16 0.00 0.00 4.00
2248 2590 0.392461 TCTGCGTTAATGGCCACCTC 60.392 55.000 8.16 0.00 0.00 3.85
2249 2591 0.676466 CTGCGTTAATGGCCACCTCA 60.676 55.000 8.16 0.00 0.00 3.86
2250 2592 0.250945 TGCGTTAATGGCCACCTCAA 60.251 50.000 8.16 0.00 0.00 3.02
2253 2595 2.094234 GCGTTAATGGCCACCTCAATTT 60.094 45.455 8.16 0.00 0.00 1.82
2254 2596 3.129638 GCGTTAATGGCCACCTCAATTTA 59.870 43.478 8.16 0.00 0.00 1.40
2255 2597 4.668289 CGTTAATGGCCACCTCAATTTAC 58.332 43.478 8.16 0.00 0.00 2.01
2259 2601 1.824230 TGGCCACCTCAATTTACATGC 59.176 47.619 0.00 0.00 0.00 4.06
2260 2602 2.102578 GGCCACCTCAATTTACATGCT 58.897 47.619 0.00 0.00 0.00 3.79
2261 2603 3.287222 GGCCACCTCAATTTACATGCTA 58.713 45.455 0.00 0.00 0.00 3.49
2262 2604 3.316308 GGCCACCTCAATTTACATGCTAG 59.684 47.826 0.00 0.00 0.00 3.42
2263 2605 4.199310 GCCACCTCAATTTACATGCTAGA 58.801 43.478 0.00 0.00 0.00 2.43
2266 2608 6.183360 GCCACCTCAATTTACATGCTAGATTT 60.183 38.462 0.00 0.00 0.00 2.17
2268 2610 7.917505 CCACCTCAATTTACATGCTAGATTTTC 59.082 37.037 0.00 0.00 0.00 2.29
2269 2611 8.461222 CACCTCAATTTACATGCTAGATTTTCA 58.539 33.333 0.00 0.00 0.00 2.69
2270 2612 8.680903 ACCTCAATTTACATGCTAGATTTTCAG 58.319 33.333 0.00 0.00 0.00 3.02
2277 2619 8.579850 TTACATGCTAGATTTTCAGGAAATGT 57.420 30.769 0.00 0.00 38.06 2.71
2278 2620 7.472334 ACATGCTAGATTTTCAGGAAATGTT 57.528 32.000 0.00 0.00 38.06 2.71
2279 2621 8.579850 ACATGCTAGATTTTCAGGAAATGTTA 57.420 30.769 0.00 0.00 38.06 2.41
2280 2622 8.462016 ACATGCTAGATTTTCAGGAAATGTTAC 58.538 33.333 0.00 0.00 38.06 2.50
2281 2623 8.680903 CATGCTAGATTTTCAGGAAATGTTACT 58.319 33.333 0.00 0.00 38.06 2.24
2282 2624 8.635765 TGCTAGATTTTCAGGAAATGTTACTT 57.364 30.769 0.00 0.00 38.06 2.24
2283 2625 9.733556 TGCTAGATTTTCAGGAAATGTTACTTA 57.266 29.630 0.00 0.00 38.06 2.24
2287 2629 9.023962 AGATTTTCAGGAAATGTTACTTATGCA 57.976 29.630 0.00 0.00 38.06 3.96
2288 2630 9.294030 GATTTTCAGGAAATGTTACTTATGCAG 57.706 33.333 0.00 0.00 38.06 4.41
2289 2631 6.757897 TTCAGGAAATGTTACTTATGCAGG 57.242 37.500 0.00 0.00 0.00 4.85
2290 2632 5.192927 TCAGGAAATGTTACTTATGCAGGG 58.807 41.667 0.00 0.00 0.00 4.45
2291 2633 5.045213 TCAGGAAATGTTACTTATGCAGGGA 60.045 40.000 0.00 0.00 0.00 4.20
2292 2634 5.297776 CAGGAAATGTTACTTATGCAGGGAG 59.702 44.000 0.00 0.00 0.00 4.30
2293 2635 5.191722 AGGAAATGTTACTTATGCAGGGAGA 59.808 40.000 0.00 0.00 0.00 3.71
2294 2636 6.064717 GGAAATGTTACTTATGCAGGGAGAT 58.935 40.000 0.00 0.00 0.00 2.75
2295 2637 6.016777 GGAAATGTTACTTATGCAGGGAGATG 60.017 42.308 0.00 0.00 0.00 2.90
2296 2638 5.894298 ATGTTACTTATGCAGGGAGATGA 57.106 39.130 0.00 0.00 0.00 2.92
2297 2639 5.692115 TGTTACTTATGCAGGGAGATGAA 57.308 39.130 0.00 0.00 0.00 2.57
2298 2640 6.252599 TGTTACTTATGCAGGGAGATGAAT 57.747 37.500 0.00 0.00 0.00 2.57
2299 2641 6.057533 TGTTACTTATGCAGGGAGATGAATG 58.942 40.000 0.00 0.00 0.00 2.67
2300 2642 4.096190 ACTTATGCAGGGAGATGAATGG 57.904 45.455 0.00 0.00 0.00 3.16
2301 2643 3.718434 ACTTATGCAGGGAGATGAATGGA 59.282 43.478 0.00 0.00 0.00 3.41
2302 2644 4.353191 ACTTATGCAGGGAGATGAATGGAT 59.647 41.667 0.00 0.00 0.00 3.41
2303 2645 2.651382 TGCAGGGAGATGAATGGATG 57.349 50.000 0.00 0.00 0.00 3.51
2304 2646 1.245732 GCAGGGAGATGAATGGATGC 58.754 55.000 0.00 0.00 0.00 3.91
2305 2647 1.906990 CAGGGAGATGAATGGATGCC 58.093 55.000 0.00 0.00 0.00 4.40
2306 2648 1.424302 CAGGGAGATGAATGGATGCCT 59.576 52.381 0.00 0.00 33.19 4.75
2311 2653 4.446889 GGGAGATGAATGGATGCCTACTTT 60.447 45.833 0.00 0.00 0.00 2.66
2313 2655 5.371526 GAGATGAATGGATGCCTACTTTCA 58.628 41.667 5.23 5.23 35.92 2.69
2314 2656 5.950023 AGATGAATGGATGCCTACTTTCAT 58.050 37.500 13.08 13.08 41.36 2.57
2315 2657 6.251655 GATGAATGGATGCCTACTTTCATC 57.748 41.667 19.89 19.89 44.03 2.92
2336 2678 8.882415 TCATCAAGAAAGTAAGAAACGTTAGT 57.118 30.769 0.00 0.00 29.28 2.24
2349 2720 3.802948 ACGTTAGTTATGCAGGGAGAG 57.197 47.619 0.00 0.00 0.00 3.20
2362 2733 1.765314 AGGGAGAGGAATGGAATCGTG 59.235 52.381 0.00 0.00 0.00 4.35
2363 2734 1.762957 GGGAGAGGAATGGAATCGTGA 59.237 52.381 0.00 0.00 0.00 4.35
2364 2735 2.170607 GGGAGAGGAATGGAATCGTGAA 59.829 50.000 0.00 0.00 0.00 3.18
2365 2736 3.198872 GGAGAGGAATGGAATCGTGAAC 58.801 50.000 0.00 0.00 0.00 3.18
2366 2737 3.369471 GGAGAGGAATGGAATCGTGAACA 60.369 47.826 0.00 0.00 0.00 3.18
2367 2738 3.600388 AGAGGAATGGAATCGTGAACAC 58.400 45.455 0.00 0.00 0.00 3.32
2368 2739 3.007940 AGAGGAATGGAATCGTGAACACA 59.992 43.478 5.80 0.00 0.00 3.72
2369 2740 3.338249 AGGAATGGAATCGTGAACACAG 58.662 45.455 5.80 0.00 0.00 3.66
2373 2744 3.303881 TGGAATCGTGAACACAGAGAG 57.696 47.619 5.80 0.00 0.00 3.20
2375 2746 3.057245 TGGAATCGTGAACACAGAGAGAG 60.057 47.826 5.80 0.00 0.00 3.20
2379 2750 3.070748 TCGTGAACACAGAGAGAGAGAG 58.929 50.000 5.80 0.00 0.00 3.20
2485 2867 1.893808 GATGTATGGTGGCTGCGGG 60.894 63.158 0.00 0.00 0.00 6.13
2630 3020 4.084888 CGCGCTTCCGAAACCCAC 62.085 66.667 5.56 0.00 36.29 4.61
2633 3023 3.733960 GCTTCCGAAACCCACGCC 61.734 66.667 0.00 0.00 0.00 5.68
2659 3049 0.443869 CAGCAAGCGTGTGGATGTAC 59.556 55.000 0.59 0.00 0.00 2.90
2677 3073 1.140589 CGCTCTACAGGAGTGGCTG 59.859 63.158 0.00 0.00 45.79 4.85
2702 3098 0.109132 GGGCCTGTTTGATTGAAGCG 60.109 55.000 0.84 0.00 0.00 4.68
2706 3102 2.414161 GCCTGTTTGATTGAAGCGTACC 60.414 50.000 0.00 0.00 0.00 3.34
2708 3104 4.250464 CCTGTTTGATTGAAGCGTACCTA 58.750 43.478 0.00 0.00 0.00 3.08
2709 3105 4.092968 CCTGTTTGATTGAAGCGTACCTAC 59.907 45.833 0.00 0.00 0.00 3.18
2718 3114 2.202518 CGTACCTACGCCACACCG 60.203 66.667 0.00 0.00 43.14 4.94
2722 3118 0.319727 TACCTACGCCACACCGTTTG 60.320 55.000 0.00 0.00 42.20 2.93
2739 3137 3.265791 GTTTGTTTGCCAAATGTGTGGA 58.734 40.909 0.00 0.00 44.50 4.02
2741 3139 3.834489 TGTTTGCCAAATGTGTGGAAT 57.166 38.095 0.00 0.00 41.65 3.01
2777 3175 2.745281 GGCGAGTAAATTGTTAGCCACA 59.255 45.455 7.16 0.00 42.37 4.17
2781 3179 5.618561 CGAGTAAATTGTTAGCCACACTTC 58.381 41.667 0.00 0.00 33.98 3.01
2785 3183 2.270352 TTGTTAGCCACACTTCTGGG 57.730 50.000 0.00 0.00 33.98 4.45
2789 3187 0.909610 TAGCCACACTTCTGGGAGGG 60.910 60.000 0.00 0.00 0.00 4.30
2878 3278 1.466558 GGCAGAGAAACAAGCACTAGC 59.533 52.381 0.00 0.00 42.56 3.42
2930 3335 1.075536 GGACCCAAACCAAGGAGACAT 59.924 52.381 0.00 0.00 0.00 3.06
2966 3377 5.106712 GCCAGTGTCGAATTATTGAAGACAA 60.107 40.000 8.36 0.00 42.47 3.18
2974 3385 7.955324 GTCGAATTATTGAAGACAACGATTCAA 59.045 33.333 3.14 3.14 46.29 2.69
2992 3403 5.627499 TTCAATTAACTGATGGTGCAGAC 57.373 39.130 0.00 0.00 39.20 3.51
2996 3407 0.700564 AACTGATGGTGCAGACCCAT 59.299 50.000 7.02 7.02 45.37 4.00
3035 3446 3.458163 GGACGGCTCGGATGGACA 61.458 66.667 0.00 0.00 0.00 4.02
3036 3447 2.577059 GACGGCTCGGATGGACAA 59.423 61.111 0.00 0.00 0.00 3.18
3037 3448 1.519455 GACGGCTCGGATGGACAAG 60.519 63.158 0.00 0.00 0.00 3.16
3038 3449 2.202932 CGGCTCGGATGGACAAGG 60.203 66.667 0.00 0.00 0.00 3.61
3039 3450 2.190578 GGCTCGGATGGACAAGGG 59.809 66.667 0.00 0.00 0.00 3.95
3040 3451 2.190578 GCTCGGATGGACAAGGGG 59.809 66.667 0.00 0.00 0.00 4.79
3041 3452 2.190578 CTCGGATGGACAAGGGGC 59.809 66.667 0.00 0.00 0.00 5.80
3042 3453 2.285368 TCGGATGGACAAGGGGCT 60.285 61.111 0.00 0.00 0.00 5.19
3043 3454 2.124570 CGGATGGACAAGGGGCTG 60.125 66.667 0.00 0.00 0.00 4.85
3044 3455 2.276740 GGATGGACAAGGGGCTGG 59.723 66.667 0.00 0.00 0.00 4.85
3045 3456 2.276740 GATGGACAAGGGGCTGGG 59.723 66.667 0.00 0.00 0.00 4.45
3046 3457 4.066139 ATGGACAAGGGGCTGGGC 62.066 66.667 0.00 0.00 0.00 5.36
3048 3459 3.984732 GGACAAGGGGCTGGGCTT 61.985 66.667 0.00 0.00 0.00 4.35
3049 3460 2.677875 GACAAGGGGCTGGGCTTG 60.678 66.667 0.00 0.00 0.00 4.01
3050 3461 4.305956 ACAAGGGGCTGGGCTTGG 62.306 66.667 0.00 0.00 0.00 3.61
3057 3468 4.357279 GCTGGGCTTGGGCTCTGT 62.357 66.667 0.00 0.00 40.19 3.41
3058 3469 2.971598 GCTGGGCTTGGGCTCTGTA 61.972 63.158 0.00 0.00 40.19 2.74
3059 3470 1.078143 CTGGGCTTGGGCTCTGTAC 60.078 63.158 0.00 0.00 40.19 2.90
3060 3471 2.272471 GGGCTTGGGCTCTGTACC 59.728 66.667 0.00 0.00 35.73 3.34
3077 3488 4.508065 CCCCCATCCCTCTCTGTT 57.492 61.111 0.00 0.00 0.00 3.16
3078 3489 2.225792 CCCCCATCCCTCTCTGTTC 58.774 63.158 0.00 0.00 0.00 3.18
3079 3490 1.690219 CCCCCATCCCTCTCTGTTCG 61.690 65.000 0.00 0.00 0.00 3.95
3080 3491 1.144936 CCCATCCCTCTCTGTTCGC 59.855 63.158 0.00 0.00 0.00 4.70
3081 3492 1.227089 CCATCCCTCTCTGTTCGCG 60.227 63.158 0.00 0.00 0.00 5.87
3082 3493 1.227089 CATCCCTCTCTGTTCGCGG 60.227 63.158 6.13 0.00 0.00 6.46
3083 3494 3.082579 ATCCCTCTCTGTTCGCGGC 62.083 63.158 6.13 0.00 0.00 6.53
3097 3508 4.745751 CGGCGGCGGTGGAGTAAA 62.746 66.667 25.36 0.00 0.00 2.01
3098 3509 3.122971 GGCGGCGGTGGAGTAAAC 61.123 66.667 9.78 0.00 0.00 2.01
3099 3510 2.047560 GCGGCGGTGGAGTAAACT 60.048 61.111 9.78 0.00 0.00 2.66
3100 3511 2.388232 GCGGCGGTGGAGTAAACTG 61.388 63.158 9.78 0.00 0.00 3.16
3101 3512 1.005394 CGGCGGTGGAGTAAACTGT 60.005 57.895 0.00 0.00 0.00 3.55
3102 3513 1.289109 CGGCGGTGGAGTAAACTGTG 61.289 60.000 0.00 0.00 0.00 3.66
3103 3514 0.034337 GGCGGTGGAGTAAACTGTGA 59.966 55.000 0.00 0.00 0.00 3.58
3104 3515 1.145803 GCGGTGGAGTAAACTGTGAC 58.854 55.000 0.00 0.00 0.00 3.67
3105 3516 1.415374 CGGTGGAGTAAACTGTGACG 58.585 55.000 0.00 0.00 0.00 4.35
3106 3517 1.792006 GGTGGAGTAAACTGTGACGG 58.208 55.000 0.00 0.00 0.00 4.79
3107 3518 1.145803 GTGGAGTAAACTGTGACGGC 58.854 55.000 0.00 0.00 0.00 5.68
3108 3519 0.319211 TGGAGTAAACTGTGACGGCG 60.319 55.000 4.80 4.80 0.00 6.46
3109 3520 0.038892 GGAGTAAACTGTGACGGCGA 60.039 55.000 16.62 0.00 0.00 5.54
3110 3521 1.603678 GGAGTAAACTGTGACGGCGAA 60.604 52.381 16.62 0.00 0.00 4.70
3111 3522 2.129607 GAGTAAACTGTGACGGCGAAA 58.870 47.619 16.62 0.00 0.00 3.46
3112 3523 2.132762 AGTAAACTGTGACGGCGAAAG 58.867 47.619 16.62 7.63 0.00 2.62
3124 3535 4.336581 CGAAAGCAGTGACGGTGA 57.663 55.556 0.00 0.00 0.00 4.02
3125 3536 2.600388 CGAAAGCAGTGACGGTGAA 58.400 52.632 0.00 0.00 0.00 3.18
3126 3537 1.148310 CGAAAGCAGTGACGGTGAAT 58.852 50.000 0.00 0.00 0.00 2.57
3127 3538 1.126846 CGAAAGCAGTGACGGTGAATC 59.873 52.381 0.00 0.00 0.00 2.52
3128 3539 2.143122 GAAAGCAGTGACGGTGAATCA 58.857 47.619 0.00 0.00 0.00 2.57
3129 3540 2.479566 AAGCAGTGACGGTGAATCAT 57.520 45.000 0.00 0.00 0.00 2.45
3130 3541 2.479566 AGCAGTGACGGTGAATCATT 57.520 45.000 0.00 0.00 0.00 2.57
3131 3542 2.350522 AGCAGTGACGGTGAATCATTC 58.649 47.619 0.00 0.00 0.00 2.67
3132 3543 2.076100 GCAGTGACGGTGAATCATTCA 58.924 47.619 0.00 0.00 37.33 2.57
3133 3544 2.094894 GCAGTGACGGTGAATCATTCAG 59.905 50.000 0.00 0.00 41.01 3.02
3134 3545 2.674852 CAGTGACGGTGAATCATTCAGG 59.325 50.000 0.00 0.00 41.01 3.86
3135 3546 1.398390 GTGACGGTGAATCATTCAGGC 59.602 52.381 0.00 0.00 41.01 4.85
3136 3547 1.003003 TGACGGTGAATCATTCAGGCA 59.997 47.619 0.00 0.00 41.01 4.75
3137 3548 1.398390 GACGGTGAATCATTCAGGCAC 59.602 52.381 0.00 0.00 41.01 5.01
3138 3549 1.271325 ACGGTGAATCATTCAGGCACA 60.271 47.619 0.00 0.00 41.01 4.57
3139 3550 1.811965 CGGTGAATCATTCAGGCACAA 59.188 47.619 0.00 0.00 41.01 3.33
3140 3551 2.228582 CGGTGAATCATTCAGGCACAAA 59.771 45.455 0.00 0.00 41.01 2.83
3141 3552 3.578688 GGTGAATCATTCAGGCACAAAC 58.421 45.455 0.00 0.00 41.01 2.93
3142 3553 3.578688 GTGAATCATTCAGGCACAAACC 58.421 45.455 0.00 0.00 41.01 3.27
3143 3554 3.005684 GTGAATCATTCAGGCACAAACCA 59.994 43.478 0.00 0.00 41.01 3.67
3144 3555 3.640498 TGAATCATTCAGGCACAAACCAA 59.360 39.130 0.00 0.00 34.08 3.67
3145 3556 3.665745 ATCATTCAGGCACAAACCAAC 57.334 42.857 0.00 0.00 0.00 3.77
3146 3557 2.382882 TCATTCAGGCACAAACCAACA 58.617 42.857 0.00 0.00 0.00 3.33
3147 3558 2.762887 TCATTCAGGCACAAACCAACAA 59.237 40.909 0.00 0.00 0.00 2.83
3148 3559 2.957491 TTCAGGCACAAACCAACAAG 57.043 45.000 0.00 0.00 0.00 3.16
3149 3560 1.846007 TCAGGCACAAACCAACAAGT 58.154 45.000 0.00 0.00 0.00 3.16
3150 3561 1.748493 TCAGGCACAAACCAACAAGTC 59.252 47.619 0.00 0.00 0.00 3.01
3151 3562 1.111277 AGGCACAAACCAACAAGTCC 58.889 50.000 0.00 0.00 0.00 3.85
3152 3563 0.248866 GGCACAAACCAACAAGTCCG 60.249 55.000 0.00 0.00 0.00 4.79
3153 3564 0.736053 GCACAAACCAACAAGTCCGA 59.264 50.000 0.00 0.00 0.00 4.55
3154 3565 1.336755 GCACAAACCAACAAGTCCGAT 59.663 47.619 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.712205 ACTGGATTGGAAATTTTGAAAGTTCTG 59.288 33.333 14.01 0.00 41.31 3.02
54 55 3.207778 GCGGCCCAATTTGTATGTAGTA 58.792 45.455 0.00 0.00 0.00 1.82
59 60 0.529833 TGTGCGGCCCAATTTGTATG 59.470 50.000 0.00 0.00 0.00 2.39
70 73 0.459585 TAACTTCTCGATGTGCGGCC 60.460 55.000 0.00 0.00 41.33 6.13
72 75 2.540515 ACATAACTTCTCGATGTGCGG 58.459 47.619 0.00 0.00 41.33 5.69
134 139 3.445096 GGTGATCATACAAGCTGGCTTTT 59.555 43.478 4.98 2.19 33.42 2.27
211 216 1.006571 GTCGCACTTGAGTCCGGAA 60.007 57.895 5.23 0.00 28.67 4.30
226 231 1.593070 GCTACTGCATTTGCGATGTCG 60.593 52.381 0.00 0.00 45.83 4.35
262 267 4.314440 TCCTGCAGGCGTGGACAC 62.314 66.667 28.91 0.00 34.44 3.67
276 281 0.964358 CGGAGAACCACCGTACTCCT 60.964 60.000 0.00 0.00 44.47 3.69
329 334 1.338020 GTGAGTTCAACCCAGCTTTGG 59.662 52.381 0.00 0.00 0.00 3.28
340 345 2.016604 GCTGGTGGTGTGTGAGTTCAA 61.017 52.381 0.00 0.00 0.00 2.69
393 400 2.541556 GCTACAAGGAGATGGAACGTC 58.458 52.381 0.00 0.00 0.00 4.34
394 401 1.207329 GGCTACAAGGAGATGGAACGT 59.793 52.381 0.00 0.00 0.00 3.99
404 411 4.585879 GTGGTTTTGATAGGCTACAAGGA 58.414 43.478 0.00 0.00 0.00 3.36
408 415 3.592059 GACGTGGTTTTGATAGGCTACA 58.408 45.455 0.00 0.00 0.00 2.74
443 450 0.458669 AGCAACACGTAGATACCGGG 59.541 55.000 6.32 0.00 34.16 5.73
554 561 0.911769 CTGGTCAGGATGGTGCCTTA 59.088 55.000 0.00 0.00 35.66 2.69
604 611 5.125100 AGCTTGTGTGATTTGGTTATGTG 57.875 39.130 0.00 0.00 0.00 3.21
608 615 3.734463 TCGAGCTTGTGTGATTTGGTTA 58.266 40.909 0.00 0.00 0.00 2.85
667 674 4.726876 GCACCGATTCGAGTGTAATTTTCC 60.727 45.833 20.87 6.04 36.35 3.13
697 704 2.195741 TCCGATCGAATATCTCCGGT 57.804 50.000 18.66 0.00 38.25 5.28
754 761 3.997064 CTCGCTGGCTCAGGAACCG 62.997 68.421 4.65 0.57 31.21 4.44
949 967 3.196254 TGGTTAAATAGTGGGAGACGTCC 59.804 47.826 13.01 3.55 43.05 4.79
1035 1069 0.470833 AGAGGTGAGCTCTGGTGTGT 60.471 55.000 14.10 0.00 0.00 3.72
1288 1443 1.137513 GAAACACGGGAGAACAGACG 58.862 55.000 0.00 0.00 0.00 4.18
1298 1453 0.392998 CAGATCAGGGGAAACACGGG 60.393 60.000 0.00 0.00 40.46 5.28
1331 1487 3.767230 CTGAGCACGCACGAACGG 61.767 66.667 0.00 0.00 37.37 4.44
1426 1589 2.429930 AGGTGCGCCTTGTGCTTA 59.570 55.556 14.67 0.00 44.18 3.09
1774 2030 3.589654 CTTCTTCGGGGTCGCAGCA 62.590 63.158 0.00 0.00 36.13 4.41
1777 2033 4.388499 GGCTTCTTCGGGGTCGCA 62.388 66.667 0.00 0.00 36.13 5.10
1892 2154 0.105039 GGGCATCTAGGTCCGTCAAG 59.895 60.000 0.00 0.00 0.00 3.02
1893 2155 0.325296 AGGGCATCTAGGTCCGTCAA 60.325 55.000 0.00 0.00 37.71 3.18
2044 2314 5.930135 AGTACAACTGATTCCCATGGATAC 58.070 41.667 15.22 2.24 0.00 2.24
2073 2346 9.841295 AAAAAGACTCAATTACACTGGTTACTA 57.159 29.630 0.00 0.00 0.00 1.82
2090 2363 9.535270 GATATTGCTGCGATAATAAAAAGACTC 57.465 33.333 13.31 0.00 0.00 3.36
2105 2380 5.618056 AATAACTCATGGATATTGCTGCG 57.382 39.130 0.00 0.00 0.00 5.18
2123 2398 9.751542 ATGAAACACGGTAATTTTGACAAATAA 57.248 25.926 0.50 0.00 31.89 1.40
2152 2427 6.915300 AGATACGAACTCAATTTCAGATCTCG 59.085 38.462 0.00 0.00 0.00 4.04
2182 2524 6.252599 AGGAGATTGGCATTGACAATACTA 57.747 37.500 17.63 0.00 41.86 1.82
2183 2525 5.121380 AGGAGATTGGCATTGACAATACT 57.879 39.130 17.63 15.25 41.86 2.12
2184 2526 6.291377 TCTAGGAGATTGGCATTGACAATAC 58.709 40.000 17.63 13.87 41.86 1.89
2185 2527 6.499106 TCTAGGAGATTGGCATTGACAATA 57.501 37.500 17.63 1.27 41.86 1.90
2186 2528 5.378230 TCTAGGAGATTGGCATTGACAAT 57.622 39.130 17.64 17.64 44.82 2.71
2187 2529 4.842531 TCTAGGAGATTGGCATTGACAA 57.157 40.909 7.53 7.53 33.93 3.18
2188 2530 5.378230 AATCTAGGAGATTGGCATTGACA 57.622 39.130 0.92 0.00 42.90 3.58
2189 2531 7.992754 ATAAATCTAGGAGATTGGCATTGAC 57.007 36.000 2.56 0.00 43.67 3.18
2192 2534 8.146412 GCAAAATAAATCTAGGAGATTGGCATT 58.854 33.333 2.56 1.73 43.67 3.56
2193 2535 7.508296 AGCAAAATAAATCTAGGAGATTGGCAT 59.492 33.333 2.56 0.00 43.67 4.40
2194 2536 6.835488 AGCAAAATAAATCTAGGAGATTGGCA 59.165 34.615 2.56 0.00 43.67 4.92
2195 2537 7.282332 AGCAAAATAAATCTAGGAGATTGGC 57.718 36.000 2.56 1.85 43.67 4.52
2200 2542 9.784531 CATCCTTAGCAAAATAAATCTAGGAGA 57.215 33.333 0.00 0.00 0.00 3.71
2201 2543 9.784531 TCATCCTTAGCAAAATAAATCTAGGAG 57.215 33.333 0.00 0.00 0.00 3.69
2207 2549 9.189723 GCAGAATCATCCTTAGCAAAATAAATC 57.810 33.333 0.00 0.00 0.00 2.17
2209 2551 7.148086 ACGCAGAATCATCCTTAGCAAAATAAA 60.148 33.333 0.00 0.00 0.00 1.40
2211 2553 5.822519 ACGCAGAATCATCCTTAGCAAAATA 59.177 36.000 0.00 0.00 0.00 1.40
2212 2554 4.641989 ACGCAGAATCATCCTTAGCAAAAT 59.358 37.500 0.00 0.00 0.00 1.82
2213 2555 4.009675 ACGCAGAATCATCCTTAGCAAAA 58.990 39.130 0.00 0.00 0.00 2.44
2214 2556 3.609853 ACGCAGAATCATCCTTAGCAAA 58.390 40.909 0.00 0.00 0.00 3.68
2216 2558 2.988010 ACGCAGAATCATCCTTAGCA 57.012 45.000 0.00 0.00 0.00 3.49
2217 2559 5.334414 CCATTAACGCAGAATCATCCTTAGC 60.334 44.000 0.00 0.00 0.00 3.09
2218 2560 5.334414 GCCATTAACGCAGAATCATCCTTAG 60.334 44.000 0.00 0.00 0.00 2.18
2220 2562 3.316308 GCCATTAACGCAGAATCATCCTT 59.684 43.478 0.00 0.00 0.00 3.36
2223 2565 2.618241 TGGCCATTAACGCAGAATCATC 59.382 45.455 0.00 0.00 0.00 2.92
2238 2580 2.431782 GCATGTAAATTGAGGTGGCCAT 59.568 45.455 9.72 0.00 0.00 4.40
2239 2581 1.824230 GCATGTAAATTGAGGTGGCCA 59.176 47.619 0.00 0.00 0.00 5.36
2240 2582 2.102578 AGCATGTAAATTGAGGTGGCC 58.897 47.619 0.00 0.00 0.00 5.36
2242 2584 6.949352 AATCTAGCATGTAAATTGAGGTGG 57.051 37.500 0.00 0.00 0.00 4.61
2243 2585 8.461222 TGAAAATCTAGCATGTAAATTGAGGTG 58.539 33.333 0.00 0.00 0.00 4.00
2244 2586 8.579850 TGAAAATCTAGCATGTAAATTGAGGT 57.420 30.769 0.00 0.00 0.00 3.85
2245 2587 8.133627 CCTGAAAATCTAGCATGTAAATTGAGG 58.866 37.037 0.00 0.00 0.00 3.86
2246 2588 8.896744 TCCTGAAAATCTAGCATGTAAATTGAG 58.103 33.333 0.00 0.00 0.00 3.02
2247 2589 8.806429 TCCTGAAAATCTAGCATGTAAATTGA 57.194 30.769 0.00 0.00 0.00 2.57
2248 2590 9.859427 TTTCCTGAAAATCTAGCATGTAAATTG 57.141 29.630 0.00 0.00 0.00 2.32
2253 2595 8.579850 AACATTTCCTGAAAATCTAGCATGTA 57.420 30.769 0.00 0.00 35.32 2.29
2254 2596 7.472334 AACATTTCCTGAAAATCTAGCATGT 57.528 32.000 0.00 0.00 35.32 3.21
2255 2597 8.680903 AGTAACATTTCCTGAAAATCTAGCATG 58.319 33.333 0.00 0.00 35.32 4.06
2261 2603 9.023962 TGCATAAGTAACATTTCCTGAAAATCT 57.976 29.630 0.00 0.00 35.32 2.40
2262 2604 9.294030 CTGCATAAGTAACATTTCCTGAAAATC 57.706 33.333 0.00 0.00 35.32 2.17
2263 2605 8.253113 CCTGCATAAGTAACATTTCCTGAAAAT 58.747 33.333 0.00 0.00 38.11 1.82
2266 2608 5.652014 CCCTGCATAAGTAACATTTCCTGAA 59.348 40.000 0.00 0.00 0.00 3.02
2268 2610 5.192927 TCCCTGCATAAGTAACATTTCCTG 58.807 41.667 0.00 0.00 0.00 3.86
2269 2611 5.191722 TCTCCCTGCATAAGTAACATTTCCT 59.808 40.000 0.00 0.00 0.00 3.36
2270 2612 5.437060 TCTCCCTGCATAAGTAACATTTCC 58.563 41.667 0.00 0.00 0.00 3.13
2275 2617 5.692115 TTCATCTCCCTGCATAAGTAACA 57.308 39.130 0.00 0.00 0.00 2.41
2276 2618 5.471456 CCATTCATCTCCCTGCATAAGTAAC 59.529 44.000 0.00 0.00 0.00 2.50
2277 2619 5.369404 TCCATTCATCTCCCTGCATAAGTAA 59.631 40.000 0.00 0.00 0.00 2.24
2278 2620 4.907269 TCCATTCATCTCCCTGCATAAGTA 59.093 41.667 0.00 0.00 0.00 2.24
2279 2621 3.718434 TCCATTCATCTCCCTGCATAAGT 59.282 43.478 0.00 0.00 0.00 2.24
2280 2622 4.362470 TCCATTCATCTCCCTGCATAAG 57.638 45.455 0.00 0.00 0.00 1.73
2281 2623 4.659115 CATCCATTCATCTCCCTGCATAA 58.341 43.478 0.00 0.00 0.00 1.90
2282 2624 3.560668 GCATCCATTCATCTCCCTGCATA 60.561 47.826 0.00 0.00 0.00 3.14
2283 2625 2.818216 GCATCCATTCATCTCCCTGCAT 60.818 50.000 0.00 0.00 0.00 3.96
2284 2626 1.478105 GCATCCATTCATCTCCCTGCA 60.478 52.381 0.00 0.00 0.00 4.41
2285 2627 1.245732 GCATCCATTCATCTCCCTGC 58.754 55.000 0.00 0.00 0.00 4.85
2286 2628 1.424302 AGGCATCCATTCATCTCCCTG 59.576 52.381 0.00 0.00 0.00 4.45
2287 2629 1.830486 AGGCATCCATTCATCTCCCT 58.170 50.000 0.00 0.00 0.00 4.20
2288 2630 2.641815 AGTAGGCATCCATTCATCTCCC 59.358 50.000 0.00 0.00 0.00 4.30
2289 2631 4.363991 AAGTAGGCATCCATTCATCTCC 57.636 45.455 0.00 0.00 0.00 3.71
2290 2632 5.371526 TGAAAGTAGGCATCCATTCATCTC 58.628 41.667 0.00 0.00 0.00 2.75
2291 2633 5.378230 TGAAAGTAGGCATCCATTCATCT 57.622 39.130 0.00 0.00 0.00 2.90
2292 2634 5.766670 TGATGAAAGTAGGCATCCATTCATC 59.233 40.000 12.95 12.95 46.67 2.92
2293 2635 5.698104 TGATGAAAGTAGGCATCCATTCAT 58.302 37.500 0.00 0.00 40.05 2.57
2294 2636 5.114764 TGATGAAAGTAGGCATCCATTCA 57.885 39.130 0.00 0.00 40.05 2.57
2295 2637 5.824624 TCTTGATGAAAGTAGGCATCCATTC 59.175 40.000 0.00 0.00 40.05 2.67
2296 2638 5.759059 TCTTGATGAAAGTAGGCATCCATT 58.241 37.500 0.00 0.00 40.05 3.16
2297 2639 5.378230 TCTTGATGAAAGTAGGCATCCAT 57.622 39.130 0.00 0.00 40.05 3.41
2298 2640 4.842531 TCTTGATGAAAGTAGGCATCCA 57.157 40.909 0.00 0.00 40.05 3.41
2311 2653 8.882415 ACTAACGTTTCTTACTTTCTTGATGA 57.118 30.769 5.91 0.00 0.00 2.92
2315 2657 9.314501 GCATAACTAACGTTTCTTACTTTCTTG 57.685 33.333 5.91 0.00 34.59 3.02
2323 2665 6.040209 TCCCTGCATAACTAACGTTTCTTA 57.960 37.500 5.91 2.89 34.59 2.10
2329 2671 2.431057 CCTCTCCCTGCATAACTAACGT 59.569 50.000 0.00 0.00 0.00 3.99
2330 2672 2.693591 TCCTCTCCCTGCATAACTAACG 59.306 50.000 0.00 0.00 0.00 3.18
2333 2675 3.648067 CCATTCCTCTCCCTGCATAACTA 59.352 47.826 0.00 0.00 0.00 2.24
2334 2676 2.441001 CCATTCCTCTCCCTGCATAACT 59.559 50.000 0.00 0.00 0.00 2.24
2336 2678 2.775418 TCCATTCCTCTCCCTGCATAA 58.225 47.619 0.00 0.00 0.00 1.90
2349 2720 3.334691 TCTGTGTTCACGATTCCATTCC 58.665 45.455 0.00 0.00 0.00 3.01
2362 2733 3.375299 GCTCTCTCTCTCTCTCTGTGTTC 59.625 52.174 0.00 0.00 0.00 3.18
2363 2734 3.244875 TGCTCTCTCTCTCTCTCTGTGTT 60.245 47.826 0.00 0.00 0.00 3.32
2364 2735 2.305635 TGCTCTCTCTCTCTCTCTGTGT 59.694 50.000 0.00 0.00 0.00 3.72
2365 2736 2.679837 GTGCTCTCTCTCTCTCTCTGTG 59.320 54.545 0.00 0.00 0.00 3.66
2366 2737 2.305635 TGTGCTCTCTCTCTCTCTCTGT 59.694 50.000 0.00 0.00 0.00 3.41
2367 2738 2.941064 CTGTGCTCTCTCTCTCTCTCTG 59.059 54.545 0.00 0.00 0.00 3.35
2368 2739 2.573462 ACTGTGCTCTCTCTCTCTCTCT 59.427 50.000 0.00 0.00 0.00 3.10
2369 2740 2.991250 ACTGTGCTCTCTCTCTCTCTC 58.009 52.381 0.00 0.00 0.00 3.20
2373 2744 3.016736 AGCTTACTGTGCTCTCTCTCTC 58.983 50.000 0.00 0.00 35.67 3.20
2375 2746 4.398044 AGTTAGCTTACTGTGCTCTCTCTC 59.602 45.833 4.22 0.00 41.46 3.20
2379 2750 4.356289 GCTAGTTAGCTTACTGTGCTCTC 58.644 47.826 15.47 0.00 45.62 3.20
2442 2816 0.308993 GAAAGCAGGCATATCCACGC 59.691 55.000 0.00 0.00 37.29 5.34
2485 2867 2.476320 GGCTCCTGCGAATCTTGCC 61.476 63.158 0.00 0.00 40.82 4.52
2633 3023 4.034258 CACGCTTGCTGCCCACTG 62.034 66.667 0.00 0.00 38.78 3.66
2677 3073 0.958822 AATCAAACAGGCCCACGTTC 59.041 50.000 0.00 0.00 0.00 3.95
2702 3098 0.319813 AAACGGTGTGGCGTAGGTAC 60.320 55.000 0.00 0.00 0.00 3.34
2706 3102 0.658897 AAACAAACGGTGTGGCGTAG 59.341 50.000 2.91 0.00 40.60 3.51
2708 3104 1.137825 CAAACAAACGGTGTGGCGT 59.862 52.632 2.91 0.00 40.60 5.68
2709 3105 2.227568 GCAAACAAACGGTGTGGCG 61.228 57.895 2.91 0.00 40.60 5.69
2710 3106 3.699671 GCAAACAAACGGTGTGGC 58.300 55.556 2.91 0.00 40.60 5.01
2711 3107 0.108615 TTGGCAAACAAACGGTGTGG 60.109 50.000 0.00 0.00 40.60 4.17
2712 3108 1.714794 TTTGGCAAACAAACGGTGTG 58.285 45.000 8.93 0.00 43.81 3.82
2722 3118 2.223845 GCATTCCACACATTTGGCAAAC 59.776 45.455 16.00 0.00 36.48 2.93
2748 3146 1.583404 CAATTTACTCGCCGCAAATGC 59.417 47.619 0.00 0.00 37.78 3.56
2777 3175 0.768221 TGTCAAGCCCTCCCAGAAGT 60.768 55.000 0.00 0.00 0.00 3.01
2781 3179 0.178992 TTGTTGTCAAGCCCTCCCAG 60.179 55.000 0.00 0.00 0.00 4.45
2785 3183 2.031870 AGGTTTTGTTGTCAAGCCCTC 58.968 47.619 0.00 0.00 33.32 4.30
2808 3207 1.713647 ACCCAACCCCACATGTCATAA 59.286 47.619 0.00 0.00 0.00 1.90
2854 3254 1.265365 GTGCTTGTTTCTCTGCCTCAC 59.735 52.381 0.00 0.00 0.00 3.51
2855 3255 1.141657 AGTGCTTGTTTCTCTGCCTCA 59.858 47.619 0.00 0.00 0.00 3.86
2862 3262 4.822026 TCTTAGGCTAGTGCTTGTTTCTC 58.178 43.478 0.00 0.00 39.59 2.87
2878 3278 1.474077 GGCATGCCACACTTTCTTAGG 59.526 52.381 32.08 0.00 35.81 2.69
2908 3313 1.982958 GTCTCCTTGGTTTGGGTCCTA 59.017 52.381 0.00 0.00 0.00 2.94
2930 3335 2.297701 GACACTGGCTTGAACCTTCAA 58.702 47.619 0.68 0.68 44.31 2.69
2966 3377 4.699735 TGCACCATCAGTTAATTGAATCGT 59.300 37.500 4.64 0.00 0.00 3.73
2974 3385 2.308570 TGGGTCTGCACCATCAGTTAAT 59.691 45.455 0.00 0.00 45.94 1.40
2996 3407 2.655090 TTCCACTTGTGAGCCATTCA 57.345 45.000 1.89 0.00 0.00 2.57
3040 3451 2.971598 TACAGAGCCCAAGCCCAGC 61.972 63.158 0.00 0.00 41.25 4.85
3041 3452 1.078143 GTACAGAGCCCAAGCCCAG 60.078 63.158 0.00 0.00 41.25 4.45
3042 3453 2.602676 GGTACAGAGCCCAAGCCCA 61.603 63.158 0.00 0.00 41.25 5.36
3043 3454 2.272471 GGTACAGAGCCCAAGCCC 59.728 66.667 0.00 0.00 41.25 5.19
3044 3455 2.272471 GGGTACAGAGCCCAAGCC 59.728 66.667 0.00 0.00 45.40 4.35
3060 3471 1.690219 CGAACAGAGAGGGATGGGGG 61.690 65.000 0.00 0.00 0.00 5.40
3061 3472 1.826024 CGAACAGAGAGGGATGGGG 59.174 63.158 0.00 0.00 0.00 4.96
3062 3473 1.144936 GCGAACAGAGAGGGATGGG 59.855 63.158 0.00 0.00 0.00 4.00
3063 3474 1.227089 CGCGAACAGAGAGGGATGG 60.227 63.158 0.00 0.00 0.00 3.51
3064 3475 1.227089 CCGCGAACAGAGAGGGATG 60.227 63.158 8.23 0.00 0.00 3.51
3065 3476 3.082579 GCCGCGAACAGAGAGGGAT 62.083 63.158 8.23 0.00 0.00 3.85
3066 3477 3.760035 GCCGCGAACAGAGAGGGA 61.760 66.667 8.23 0.00 0.00 4.20
3080 3491 4.745751 TTTACTCCACCGCCGCCG 62.746 66.667 0.00 0.00 0.00 6.46
3081 3492 3.122971 GTTTACTCCACCGCCGCC 61.123 66.667 0.00 0.00 0.00 6.13
3082 3493 2.047560 AGTTTACTCCACCGCCGC 60.048 61.111 0.00 0.00 0.00 6.53
3083 3494 1.005394 ACAGTTTACTCCACCGCCG 60.005 57.895 0.00 0.00 0.00 6.46
3084 3495 0.034337 TCACAGTTTACTCCACCGCC 59.966 55.000 0.00 0.00 0.00 6.13
3085 3496 1.145803 GTCACAGTTTACTCCACCGC 58.854 55.000 0.00 0.00 0.00 5.68
3086 3497 1.415374 CGTCACAGTTTACTCCACCG 58.585 55.000 0.00 0.00 0.00 4.94
3087 3498 1.792006 CCGTCACAGTTTACTCCACC 58.208 55.000 0.00 0.00 0.00 4.61
3088 3499 1.145803 GCCGTCACAGTTTACTCCAC 58.854 55.000 0.00 0.00 0.00 4.02
3089 3500 0.319211 CGCCGTCACAGTTTACTCCA 60.319 55.000 0.00 0.00 0.00 3.86
3090 3501 0.038892 TCGCCGTCACAGTTTACTCC 60.039 55.000 0.00 0.00 0.00 3.85
3091 3502 1.774639 TTCGCCGTCACAGTTTACTC 58.225 50.000 0.00 0.00 0.00 2.59
3092 3503 2.132762 CTTTCGCCGTCACAGTTTACT 58.867 47.619 0.00 0.00 0.00 2.24
3093 3504 1.398071 GCTTTCGCCGTCACAGTTTAC 60.398 52.381 0.00 0.00 0.00 2.01
3094 3505 0.863144 GCTTTCGCCGTCACAGTTTA 59.137 50.000 0.00 0.00 0.00 2.01
3095 3506 1.092921 TGCTTTCGCCGTCACAGTTT 61.093 50.000 0.00 0.00 34.43 2.66
3096 3507 1.498865 CTGCTTTCGCCGTCACAGTT 61.499 55.000 0.00 0.00 34.43 3.16
3097 3508 1.956170 CTGCTTTCGCCGTCACAGT 60.956 57.895 0.00 0.00 34.43 3.55
3098 3509 1.956170 ACTGCTTTCGCCGTCACAG 60.956 57.895 0.00 0.00 34.43 3.66
3099 3510 2.108157 ACTGCTTTCGCCGTCACA 59.892 55.556 0.00 0.00 34.43 3.58
3100 3511 1.954146 TCACTGCTTTCGCCGTCAC 60.954 57.895 0.00 0.00 30.75 3.67
3101 3512 1.954146 GTCACTGCTTTCGCCGTCA 60.954 57.895 0.00 0.00 30.75 4.35
3102 3513 2.853914 GTCACTGCTTTCGCCGTC 59.146 61.111 0.00 0.00 30.75 4.79
3103 3514 3.036084 CGTCACTGCTTTCGCCGT 61.036 61.111 0.00 0.00 33.62 5.68
3104 3515 3.777925 CCGTCACTGCTTTCGCCG 61.778 66.667 0.00 0.00 34.43 6.46
3105 3516 2.665185 ACCGTCACTGCTTTCGCC 60.665 61.111 0.00 0.00 34.43 5.54
3106 3517 1.495584 TTCACCGTCACTGCTTTCGC 61.496 55.000 0.00 0.00 0.00 4.70
3107 3518 1.126846 GATTCACCGTCACTGCTTTCG 59.873 52.381 0.00 0.00 0.00 3.46
3108 3519 2.143122 TGATTCACCGTCACTGCTTTC 58.857 47.619 0.00 0.00 0.00 2.62
3109 3520 2.254546 TGATTCACCGTCACTGCTTT 57.745 45.000 0.00 0.00 0.00 3.51
3110 3521 2.479566 ATGATTCACCGTCACTGCTT 57.520 45.000 0.00 0.00 0.00 3.91
3111 3522 2.289631 TGAATGATTCACCGTCACTGCT 60.290 45.455 3.29 0.00 34.08 4.24
3112 3523 2.076100 TGAATGATTCACCGTCACTGC 58.924 47.619 3.29 0.00 34.08 4.40
3113 3524 2.674852 CCTGAATGATTCACCGTCACTG 59.325 50.000 3.29 0.00 35.46 3.66
3114 3525 2.936993 GCCTGAATGATTCACCGTCACT 60.937 50.000 3.29 0.00 35.46 3.41
3115 3526 1.398390 GCCTGAATGATTCACCGTCAC 59.602 52.381 3.29 0.00 35.46 3.67
3116 3527 1.003003 TGCCTGAATGATTCACCGTCA 59.997 47.619 3.29 0.00 35.46 4.35
3117 3528 1.398390 GTGCCTGAATGATTCACCGTC 59.602 52.381 3.29 0.00 35.46 4.79
3118 3529 1.271325 TGTGCCTGAATGATTCACCGT 60.271 47.619 3.29 0.00 35.46 4.83
3119 3530 1.452110 TGTGCCTGAATGATTCACCG 58.548 50.000 3.29 0.00 35.46 4.94
3120 3531 3.578688 GTTTGTGCCTGAATGATTCACC 58.421 45.455 3.29 0.00 35.46 4.02
3121 3532 3.005684 TGGTTTGTGCCTGAATGATTCAC 59.994 43.478 3.29 0.00 35.46 3.18
3122 3533 3.229293 TGGTTTGTGCCTGAATGATTCA 58.771 40.909 7.73 7.73 38.17 2.57
3123 3534 3.940209 TGGTTTGTGCCTGAATGATTC 57.060 42.857 0.00 0.00 0.00 2.52
3124 3535 3.387374 TGTTGGTTTGTGCCTGAATGATT 59.613 39.130 0.00 0.00 0.00 2.57
3125 3536 2.964464 TGTTGGTTTGTGCCTGAATGAT 59.036 40.909 0.00 0.00 0.00 2.45
3126 3537 2.382882 TGTTGGTTTGTGCCTGAATGA 58.617 42.857 0.00 0.00 0.00 2.57
3127 3538 2.886862 TGTTGGTTTGTGCCTGAATG 57.113 45.000 0.00 0.00 0.00 2.67
3128 3539 2.765699 ACTTGTTGGTTTGTGCCTGAAT 59.234 40.909 0.00 0.00 0.00 2.57
3129 3540 2.165437 GACTTGTTGGTTTGTGCCTGAA 59.835 45.455 0.00 0.00 0.00 3.02
3130 3541 1.748493 GACTTGTTGGTTTGTGCCTGA 59.252 47.619 0.00 0.00 0.00 3.86
3131 3542 1.202405 GGACTTGTTGGTTTGTGCCTG 60.202 52.381 0.00 0.00 0.00 4.85
3132 3543 1.111277 GGACTTGTTGGTTTGTGCCT 58.889 50.000 0.00 0.00 0.00 4.75
3133 3544 0.248866 CGGACTTGTTGGTTTGTGCC 60.249 55.000 0.00 0.00 0.00 5.01
3134 3545 0.736053 TCGGACTTGTTGGTTTGTGC 59.264 50.000 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.