Multiple sequence alignment - TraesCS6D01G232700

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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 TraesCS6D01G232700 chr6D 100.000 3061 0 0 1 3061 326539035 326542095 0.000000e+00 5653
1 TraesCS6D01G232700 chr6D 85.547 256 37 0 1325 1580 326760710 326760965 5.030000e-68 268
2 TraesCS6D01G232700 chr6A 91.552 2320 123 30 1 2268 465230560 465232858 0.000000e+00 3131
3 TraesCS6D01G232700 chr6A 86.328 256 35 0 1325 1580 465389786 465390041 2.320000e-71 279
4 TraesCS6D01G232700 chr6B 92.257 1666 81 17 459 2096 495807584 495805939 0.000000e+00 2318
5 TraesCS6D01G232700 chr6B 90.105 475 17 6 1 450 495808179 495807710 9.450000e-165 590
6 TraesCS6D01G232700 chr6B 89.728 331 22 8 2540 2870 495803744 495803426 2.200000e-111 412
7 TraesCS6D01G232700 chr6B 85.938 256 36 0 1325 1580 495543774 495543519 1.080000e-69 274
8 TraesCS6D01G232700 chr2D 89.961 259 26 0 1326 1584 527293783 527293525 4.890000e-88 335
9 TraesCS6D01G232700 chr2B 89.575 259 27 0 1326 1584 624355484 624355226 2.280000e-86 329
10 TraesCS6D01G232700 chr2A 89.575 259 27 0 1326 1584 672292457 672292199 2.280000e-86 329
11 TraesCS6D01G232700 chr1B 85.283 265 31 6 1321 1580 418821467 418821728 1.810000e-67 267


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 TraesCS6D01G232700 chr6D 326539035 326542095 3060 False 5653.000000 5653 100.000000 1 3061 1 chr6D.!!$F1 3060
1 TraesCS6D01G232700 chr6A 465230560 465232858 2298 False 3131.000000 3131 91.552000 1 2268 1 chr6A.!!$F1 2267
2 TraesCS6D01G232700 chr6B 495803426 495808179 4753 True 1106.666667 2318 90.696667 1 2870 3 chr6B.!!$R2 2869

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
759 917 1.272147 ACTGGAGTTCTGAATTGGCCC 60.272 52.381 0.0 0.0 0.0 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2369 4417 0.323178 AATGTGAGGAGCAGGCTTGG 60.323 55.0 0.0 0.0 0.0 3.61 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
55 57 6.706270 AGGTTGTTAGCCATAAGTATCATTCG 59.294 38.462 0.00 0.00 0.00 3.34
179 182 4.822685 TGCTGGTGCATTTTCCATTATT 57.177 36.364 0.00 0.00 45.31 1.40
180 183 4.505808 TGCTGGTGCATTTTCCATTATTG 58.494 39.130 0.00 0.00 45.31 1.90
279 305 3.810941 TGACTGGAACGTGTTAATGGAAC 59.189 43.478 0.00 0.00 38.65 3.62
337 364 6.147164 CACCAATAGTAAAGCGAAGACTTTGA 59.853 38.462 6.62 0.00 40.08 2.69
373 400 2.737376 GACGCACCACCGTTCCTC 60.737 66.667 0.00 0.00 42.24 3.71
374 401 3.509137 GACGCACCACCGTTCCTCA 62.509 63.158 0.00 0.00 42.24 3.86
375 402 3.041940 CGCACCACCGTTCCTCAC 61.042 66.667 0.00 0.00 0.00 3.51
589 741 5.357032 TGCTCTCGATGACATCTACTTAACA 59.643 40.000 13.45 1.07 0.00 2.41
629 781 2.389386 CTCGTCTCTGAGGAGGACG 58.611 63.158 4.59 7.76 39.83 4.79
667 819 1.495509 CGTGGCCGTGTGTATGTTG 59.504 57.895 0.00 0.00 0.00 3.33
759 917 1.272147 ACTGGAGTTCTGAATTGGCCC 60.272 52.381 0.00 0.00 0.00 5.80
765 941 2.035626 CTGAATTGGCCCGGTGGT 59.964 61.111 0.00 0.00 0.00 4.16
796 972 3.617263 GGTCGCTGTTTGGTTATGTCTAG 59.383 47.826 0.00 0.00 0.00 2.43
805 981 7.198390 TGTTTGGTTATGTCTAGTATAGCGTC 58.802 38.462 0.00 0.00 38.99 5.19
879 1057 2.577911 GCTGCAGAATTTCGCGCC 60.578 61.111 20.43 0.00 0.00 6.53
925 1103 9.290988 TCCTAACAACAACATCAGCTTTATTTA 57.709 29.630 0.00 0.00 0.00 1.40
964 1142 4.638421 TGGTGGCGATATCTTTTGTTTAGG 59.362 41.667 0.34 0.00 0.00 2.69
993 1172 2.756840 AACGTAGGCTTCCACTAACC 57.243 50.000 0.00 0.00 0.00 2.85
1016 1195 3.293311 TCCACTATTTATAGTCGCGCC 57.707 47.619 0.00 0.00 41.44 6.53
1017 1196 2.624364 TCCACTATTTATAGTCGCGCCA 59.376 45.455 0.00 0.00 41.44 5.69
1028 1207 4.988598 CGCGCCACACCACCTTCT 62.989 66.667 0.00 0.00 0.00 2.85
1029 1208 2.594592 GCGCCACACCACCTTCTT 60.595 61.111 0.00 0.00 0.00 2.52
1089 1272 1.336440 CTAGAGCCATGGAGTCTGACG 59.664 57.143 18.40 6.02 0.00 4.35
1093 1276 1.517257 CCATGGAGTCTGACGCGAC 60.517 63.158 15.93 7.62 0.00 5.19
1130 1313 2.783510 CTCCTCTTCCTCCTCCTACTCT 59.216 54.545 0.00 0.00 0.00 3.24
1139 1322 1.914108 TCCTCCTACTCTTCCGACTCA 59.086 52.381 0.00 0.00 0.00 3.41
1142 1325 0.741915 CCTACTCTTCCGACTCAGCC 59.258 60.000 0.00 0.00 0.00 4.85
1222 1405 2.997897 GACCGCCACCTCTCCTGT 60.998 66.667 0.00 0.00 0.00 4.00
1248 1431 4.020617 CCACCGGCAGCCAAGAGA 62.021 66.667 13.30 0.00 0.00 3.10
1254 1437 2.125350 GCAGCCAAGAGACGGAGG 60.125 66.667 0.00 0.00 0.00 4.30
1255 1438 2.581354 CAGCCAAGAGACGGAGGG 59.419 66.667 0.00 0.00 0.00 4.30
1718 1904 2.125350 CTGCCCGACCTTCTGCTC 60.125 66.667 0.00 0.00 0.00 4.26
1846 2032 1.153686 GGACCTAGCCGTTCCGTTC 60.154 63.158 0.00 0.00 0.00 3.95
1847 2033 1.153686 GACCTAGCCGTTCCGTTCC 60.154 63.158 0.00 0.00 0.00 3.62
1981 2169 1.515521 CTTGGGGTGGCAAGTCGTTC 61.516 60.000 0.00 0.00 0.00 3.95
1991 2179 2.442424 GCAAGTCGTTCTAGCTAGACG 58.558 52.381 23.17 25.15 38.53 4.18
2004 2192 2.798847 AGCTAGACGTTTCACCGTTTTC 59.201 45.455 0.00 0.00 41.98 2.29
2121 4169 6.655078 AAGACGTTTTAGGTTACTACTCCA 57.345 37.500 0.00 0.00 0.00 3.86
2122 4170 6.655078 AGACGTTTTAGGTTACTACTCCAA 57.345 37.500 0.00 0.00 0.00 3.53
2123 4171 6.685657 AGACGTTTTAGGTTACTACTCCAAG 58.314 40.000 0.00 0.00 0.00 3.61
2124 4172 5.787380 ACGTTTTAGGTTACTACTCCAAGG 58.213 41.667 0.00 0.00 0.00 3.61
2125 4173 5.173664 CGTTTTAGGTTACTACTCCAAGGG 58.826 45.833 0.00 0.00 0.00 3.95
2126 4174 5.047092 CGTTTTAGGTTACTACTCCAAGGGA 60.047 44.000 0.00 0.00 0.00 4.20
2149 4197 7.177041 GGGAGTACAATCTATATCTTCGGTCTT 59.823 40.741 0.00 0.00 0.00 3.01
2153 4201 9.745880 GTACAATCTATATCTTCGGTCTTGAAA 57.254 33.333 0.00 0.00 0.00 2.69
2169 4217 6.073003 GGTCTTGAAATCTCAAACACTCGATT 60.073 38.462 0.00 0.00 41.05 3.34
2173 4221 9.483062 CTTGAAATCTCAAACACTCGATTAATC 57.517 33.333 5.30 5.30 41.05 1.75
2174 4222 8.546597 TGAAATCTCAAACACTCGATTAATCA 57.453 30.769 15.57 2.41 0.00 2.57
2175 4223 9.166173 TGAAATCTCAAACACTCGATTAATCAT 57.834 29.630 15.57 0.00 0.00 2.45
2176 4224 9.430838 GAAATCTCAAACACTCGATTAATCATG 57.569 33.333 15.57 11.84 0.00 3.07
2177 4225 8.722480 AATCTCAAACACTCGATTAATCATGA 57.278 30.769 15.57 0.00 0.00 3.07
2178 4226 8.722480 ATCTCAAACACTCGATTAATCATGAA 57.278 30.769 15.57 0.00 0.00 2.57
2179 4227 7.963981 TCTCAAACACTCGATTAATCATGAAC 58.036 34.615 15.57 0.00 0.00 3.18
2180 4228 6.761117 TCAAACACTCGATTAATCATGAACG 58.239 36.000 15.57 1.20 0.00 3.95
2184 4232 8.818141 AACACTCGATTAATCATGAACGATAT 57.182 30.769 15.57 0.00 0.00 1.63
2200 4248 5.296813 ACGATATTGTCCTTTTGTTCAGC 57.703 39.130 0.00 0.00 0.00 4.26
2228 4276 8.396272 AGGTATATTTGATATTTCCACACTGC 57.604 34.615 0.00 0.00 0.00 4.40
2284 4332 3.834799 GTAGACGTGGGCGGGGAG 61.835 72.222 0.00 0.00 43.45 4.30
2300 4348 2.678934 AGGTTGCCCTCGACGCTA 60.679 61.111 1.75 0.00 35.62 4.26
2301 4349 2.202756 GGTTGCCCTCGACGCTAG 60.203 66.667 1.75 0.00 0.00 3.42
2302 4350 2.572284 GTTGCCCTCGACGCTAGT 59.428 61.111 1.75 0.00 0.00 2.57
2303 4351 1.516603 GTTGCCCTCGACGCTAGTC 60.517 63.158 1.75 0.00 43.72 2.59
2341 4389 1.408266 GGTGTGTGGTCTTGTGGAGTT 60.408 52.381 0.00 0.00 0.00 3.01
2360 4408 2.860136 GTTTTTGCTTTGTCACCTCTGC 59.140 45.455 0.00 0.00 0.00 4.26
2363 4411 0.819259 TGCTTTGTCACCTCTGCACC 60.819 55.000 0.00 0.00 0.00 5.01
2369 4417 0.741221 GTCACCTCTGCACCGGATTC 60.741 60.000 9.46 0.00 0.00 2.52
2374 4422 1.372087 CTCTGCACCGGATTCCAAGC 61.372 60.000 9.46 3.94 0.00 4.01
2384 4432 0.254178 GATTCCAAGCCTGCTCCTCA 59.746 55.000 0.00 0.00 0.00 3.86
2388 4436 0.323178 CCAAGCCTGCTCCTCACATT 60.323 55.000 0.00 0.00 0.00 2.71
2411 4459 1.807742 AGTCTCGTCTTCTTCTGTCCG 59.192 52.381 0.00 0.00 0.00 4.79
2419 4467 2.430382 TTCTTCTGTCCGGCCGTGAC 62.430 60.000 28.99 28.99 0.00 3.67
2435 4483 2.018515 GTGACGAGAGGCTAGCTAGTT 58.981 52.381 21.62 10.76 42.42 2.24
2437 4485 3.090037 TGACGAGAGGCTAGCTAGTTTT 58.910 45.455 21.62 7.93 42.42 2.43
2449 4497 8.435982 AGGCTAGCTAGTTTTGATGAAATAGAT 58.564 33.333 21.62 0.00 0.00 1.98
2477 4525 5.231147 CCGTTTGTTTGTGTTTATGAGGTTG 59.769 40.000 0.00 0.00 0.00 3.77
2483 4531 2.621055 TGTGTTTATGAGGTTGGTGTGC 59.379 45.455 0.00 0.00 0.00 4.57
2489 4537 1.846007 TGAGGTTGGTGTGCTTTTGT 58.154 45.000 0.00 0.00 0.00 2.83
2507 4555 9.134734 TGCTTTTGTTGATTTTAATTCGGTATC 57.865 29.630 0.00 0.00 0.00 2.24
2508 4556 8.311120 GCTTTTGTTGATTTTAATTCGGTATCG 58.689 33.333 0.00 0.00 37.82 2.92
2509 4557 9.549509 CTTTTGTTGATTTTAATTCGGTATCGA 57.450 29.630 0.00 0.00 44.44 3.59
2510 4558 8.883789 TTTGTTGATTTTAATTCGGTATCGAC 57.116 30.769 0.00 0.00 45.92 4.20
2511 4559 6.698107 TGTTGATTTTAATTCGGTATCGACG 58.302 36.000 0.00 0.00 45.92 5.12
2512 4560 6.530887 TGTTGATTTTAATTCGGTATCGACGA 59.469 34.615 0.00 0.00 45.92 4.20
2513 4561 6.742999 TGATTTTAATTCGGTATCGACGAG 57.257 37.500 0.00 0.00 45.92 4.18
2514 4562 6.497437 TGATTTTAATTCGGTATCGACGAGA 58.503 36.000 0.00 0.00 45.92 4.04
2515 4563 6.635641 TGATTTTAATTCGGTATCGACGAGAG 59.364 38.462 0.00 0.00 45.92 3.20
2527 4575 1.581954 ACGAGAGTGAGCTTGACCG 59.418 57.895 0.00 0.00 46.97 4.79
2528 4576 0.889638 ACGAGAGTGAGCTTGACCGA 60.890 55.000 0.00 0.00 46.97 4.69
2529 4577 0.453793 CGAGAGTGAGCTTGACCGAT 59.546 55.000 0.00 0.00 0.00 4.18
2530 4578 1.796982 CGAGAGTGAGCTTGACCGATG 60.797 57.143 0.00 0.00 0.00 3.84
2531 4579 1.203523 GAGAGTGAGCTTGACCGATGT 59.796 52.381 0.00 0.00 0.00 3.06
2532 4580 2.423892 GAGAGTGAGCTTGACCGATGTA 59.576 50.000 0.00 0.00 0.00 2.29
2533 4581 3.027412 AGAGTGAGCTTGACCGATGTAT 58.973 45.455 0.00 0.00 0.00 2.29
2534 4582 4.207955 AGAGTGAGCTTGACCGATGTATA 58.792 43.478 0.00 0.00 0.00 1.47
2535 4583 4.645136 AGAGTGAGCTTGACCGATGTATAA 59.355 41.667 0.00 0.00 0.00 0.98
2536 4584 5.127194 AGAGTGAGCTTGACCGATGTATAAA 59.873 40.000 0.00 0.00 0.00 1.40
2537 4585 5.918608 AGTGAGCTTGACCGATGTATAAAT 58.081 37.500 0.00 0.00 0.00 1.40
2538 4586 5.755375 AGTGAGCTTGACCGATGTATAAATG 59.245 40.000 0.00 0.00 0.00 2.32
2539 4587 5.523916 GTGAGCTTGACCGATGTATAAATGT 59.476 40.000 0.00 0.00 0.00 2.71
2564 4612 3.191791 ACCCGATTTTCACAATTAACCGG 59.808 43.478 0.00 0.00 34.76 5.28
2565 4613 3.175929 CCGATTTTCACAATTAACCGGC 58.824 45.455 0.00 0.00 0.00 6.13
2657 4705 6.823689 GGACAATAATAGCCTCTTCAACTCAA 59.176 38.462 0.00 0.00 0.00 3.02
2660 4708 8.515414 ACAATAATAGCCTCTTCAACTCAAAAC 58.485 33.333 0.00 0.00 0.00 2.43
2666 4714 6.796426 AGCCTCTTCAACTCAAAACTTTTAC 58.204 36.000 0.00 0.00 0.00 2.01
2667 4715 6.377146 AGCCTCTTCAACTCAAAACTTTTACA 59.623 34.615 0.00 0.00 0.00 2.41
2716 4764 4.847198 ACATATTCTTGCATCACACAGGA 58.153 39.130 0.00 0.00 0.00 3.86
2767 4815 7.585867 CAAAATTCATTGGAACATTGCATCAA 58.414 30.769 0.00 0.00 39.29 2.57
2768 4816 7.931578 AAATTCATTGGAACATTGCATCAAT 57.068 28.000 0.00 0.00 39.29 2.57
2770 4818 5.925506 TCATTGGAACATTGCATCAATCT 57.074 34.783 0.00 0.00 39.29 2.40
2819 4867 1.754226 TCCACCTCAACAACCTTTTGC 59.246 47.619 0.00 0.00 36.00 3.68
2823 4871 2.166254 ACCTCAACAACCTTTTGCACTG 59.834 45.455 0.00 0.00 36.00 3.66
2848 4896 6.585322 GCTAAGAGACAAACGAGCTAAACTTA 59.415 38.462 0.00 0.00 0.00 2.24
2909 4957 7.900782 TTGCTGTGTTTCTTATAACTCTACC 57.099 36.000 0.00 0.00 0.00 3.18
2910 4958 6.403878 TGCTGTGTTTCTTATAACTCTACCC 58.596 40.000 0.00 0.00 0.00 3.69
2911 4959 6.014070 TGCTGTGTTTCTTATAACTCTACCCA 60.014 38.462 0.00 0.00 0.00 4.51
2912 4960 7.048512 GCTGTGTTTCTTATAACTCTACCCAT 58.951 38.462 0.00 0.00 0.00 4.00
2913 4961 7.011482 GCTGTGTTTCTTATAACTCTACCCATG 59.989 40.741 0.00 0.00 0.00 3.66
2914 4962 8.141298 TGTGTTTCTTATAACTCTACCCATGA 57.859 34.615 0.00 0.00 0.00 3.07
2915 4963 8.598916 TGTGTTTCTTATAACTCTACCCATGAA 58.401 33.333 0.00 0.00 0.00 2.57
2916 4964 9.444600 GTGTTTCTTATAACTCTACCCATGAAA 57.555 33.333 0.00 0.00 0.00 2.69
2920 4968 8.732746 TCTTATAACTCTACCCATGAAAAAGC 57.267 34.615 0.00 0.00 0.00 3.51
2921 4969 8.548877 TCTTATAACTCTACCCATGAAAAAGCT 58.451 33.333 0.00 0.00 0.00 3.74
2922 4970 8.506168 TTATAACTCTACCCATGAAAAAGCTG 57.494 34.615 0.00 0.00 0.00 4.24
2923 4971 3.690460 ACTCTACCCATGAAAAAGCTGG 58.310 45.455 0.00 0.00 0.00 4.85
2924 4972 3.330701 ACTCTACCCATGAAAAAGCTGGA 59.669 43.478 0.00 0.00 31.38 3.86
2925 4973 3.686016 TCTACCCATGAAAAAGCTGGAC 58.314 45.455 0.00 0.00 31.38 4.02
2926 4974 2.380064 ACCCATGAAAAAGCTGGACA 57.620 45.000 0.00 0.00 31.38 4.02
2927 4975 1.963515 ACCCATGAAAAAGCTGGACAC 59.036 47.619 0.00 0.00 31.38 3.67
2928 4976 1.273327 CCCATGAAAAAGCTGGACACC 59.727 52.381 0.00 0.00 31.38 4.16
2929 4977 1.962807 CCATGAAAAAGCTGGACACCA 59.037 47.619 0.00 0.00 31.38 4.17
2930 4978 2.564062 CCATGAAAAAGCTGGACACCAT 59.436 45.455 0.00 0.00 30.82 3.55
2931 4979 3.367703 CCATGAAAAAGCTGGACACCATC 60.368 47.826 0.00 0.00 30.82 3.51
2932 4980 3.228188 TGAAAAAGCTGGACACCATCT 57.772 42.857 0.00 0.00 30.60 2.90
2933 4981 2.886523 TGAAAAAGCTGGACACCATCTG 59.113 45.455 0.00 0.00 29.79 2.90
2934 4982 2.664402 AAAAGCTGGACACCATCTGT 57.336 45.000 0.00 0.00 29.79 3.41
2935 4983 3.788227 AAAAGCTGGACACCATCTGTA 57.212 42.857 0.00 0.00 29.79 2.74
2936 4984 4.307032 AAAAGCTGGACACCATCTGTAT 57.693 40.909 0.00 0.00 29.79 2.29
2937 4985 3.550437 AAGCTGGACACCATCTGTATC 57.450 47.619 0.00 0.00 29.79 2.24
2938 4986 2.756907 AGCTGGACACCATCTGTATCT 58.243 47.619 0.00 0.00 28.01 1.98
2939 4987 3.110705 AGCTGGACACCATCTGTATCTT 58.889 45.455 0.00 0.00 28.01 2.40
2940 4988 3.118482 AGCTGGACACCATCTGTATCTTG 60.118 47.826 0.00 0.00 28.01 3.02
2941 4989 3.801698 CTGGACACCATCTGTATCTTGG 58.198 50.000 0.00 0.00 36.56 3.61
2942 4990 2.092968 TGGACACCATCTGTATCTTGGC 60.093 50.000 0.00 0.00 33.66 4.52
2943 4991 2.171448 GGACACCATCTGTATCTTGGCT 59.829 50.000 0.00 0.00 33.66 4.75
2944 4992 3.370953 GGACACCATCTGTATCTTGGCTT 60.371 47.826 0.00 0.00 33.66 4.35
2945 4993 4.265073 GACACCATCTGTATCTTGGCTTT 58.735 43.478 0.00 0.00 33.66 3.51
2946 4994 4.666512 ACACCATCTGTATCTTGGCTTTT 58.333 39.130 0.00 0.00 33.66 2.27
2947 4995 5.815581 ACACCATCTGTATCTTGGCTTTTA 58.184 37.500 0.00 0.00 33.66 1.52
2948 4996 5.882557 ACACCATCTGTATCTTGGCTTTTAG 59.117 40.000 0.00 0.00 33.66 1.85
2949 4997 4.884164 ACCATCTGTATCTTGGCTTTTAGC 59.116 41.667 0.00 0.00 41.46 3.09
2962 5010 3.454375 GCTTTTAGCCAGATACGCTACA 58.546 45.455 0.00 0.00 38.52 2.74
2963 5011 3.245519 GCTTTTAGCCAGATACGCTACAC 59.754 47.826 0.00 0.00 38.52 2.90
2964 5012 4.430007 CTTTTAGCCAGATACGCTACACA 58.570 43.478 0.00 0.00 38.52 3.72
2965 5013 4.459390 TTTAGCCAGATACGCTACACAA 57.541 40.909 0.00 0.00 38.52 3.33
2966 5014 4.459390 TTAGCCAGATACGCTACACAAA 57.541 40.909 0.00 0.00 38.52 2.83
2967 5015 2.618053 AGCCAGATACGCTACACAAAC 58.382 47.619 0.00 0.00 33.91 2.93
2968 5016 1.664151 GCCAGATACGCTACACAAACC 59.336 52.381 0.00 0.00 0.00 3.27
2969 5017 2.933492 GCCAGATACGCTACACAAACCA 60.933 50.000 0.00 0.00 0.00 3.67
2970 5018 3.531538 CCAGATACGCTACACAAACCAT 58.468 45.455 0.00 0.00 0.00 3.55
2971 5019 4.689071 CCAGATACGCTACACAAACCATA 58.311 43.478 0.00 0.00 0.00 2.74
2972 5020 5.297547 CCAGATACGCTACACAAACCATAT 58.702 41.667 0.00 0.00 0.00 1.78
2973 5021 6.452242 CCAGATACGCTACACAAACCATATA 58.548 40.000 0.00 0.00 0.00 0.86
2974 5022 6.365247 CCAGATACGCTACACAAACCATATAC 59.635 42.308 0.00 0.00 0.00 1.47
2975 5023 6.921307 CAGATACGCTACACAAACCATATACA 59.079 38.462 0.00 0.00 0.00 2.29
2976 5024 7.114953 CAGATACGCTACACAAACCATATACAG 59.885 40.741 0.00 0.00 0.00 2.74
2977 5025 5.333299 ACGCTACACAAACCATATACAGA 57.667 39.130 0.00 0.00 0.00 3.41
2978 5026 5.914033 ACGCTACACAAACCATATACAGAT 58.086 37.500 0.00 0.00 0.00 2.90
2979 5027 7.046292 ACGCTACACAAACCATATACAGATA 57.954 36.000 0.00 0.00 0.00 1.98
2980 5028 7.494211 ACGCTACACAAACCATATACAGATAA 58.506 34.615 0.00 0.00 0.00 1.75
2981 5029 7.982919 ACGCTACACAAACCATATACAGATAAA 59.017 33.333 0.00 0.00 0.00 1.40
2982 5030 8.988934 CGCTACACAAACCATATACAGATAAAT 58.011 33.333 0.00 0.00 0.00 1.40
2991 5039 9.621629 AACCATATACAGATAAATTTTCACGGA 57.378 29.630 0.00 0.00 0.00 4.69
2992 5040 9.793259 ACCATATACAGATAAATTTTCACGGAT 57.207 29.630 0.00 0.00 0.00 4.18
2994 5042 9.546909 CATATACAGATAAATTTTCACGGATGC 57.453 33.333 0.00 0.00 0.00 3.91
2995 5043 7.807977 ATACAGATAAATTTTCACGGATGCT 57.192 32.000 0.00 0.00 0.00 3.79
2996 5044 5.883661 ACAGATAAATTTTCACGGATGCTG 58.116 37.500 0.00 0.00 0.00 4.41
2997 5045 5.415701 ACAGATAAATTTTCACGGATGCTGT 59.584 36.000 0.00 0.00 0.00 4.40
2998 5046 6.597672 ACAGATAAATTTTCACGGATGCTGTA 59.402 34.615 0.00 0.00 30.79 2.74
2999 5047 7.120579 ACAGATAAATTTTCACGGATGCTGTAA 59.879 33.333 0.00 0.00 30.79 2.41
3000 5048 7.641411 CAGATAAATTTTCACGGATGCTGTAAG 59.359 37.037 0.00 0.00 0.00 2.34
3001 5049 5.957842 AAATTTTCACGGATGCTGTAAGA 57.042 34.783 0.00 0.00 34.07 2.10
3002 5050 5.551760 AATTTTCACGGATGCTGTAAGAG 57.448 39.130 0.00 0.00 34.07 2.85
3003 5051 3.953712 TTTCACGGATGCTGTAAGAGA 57.046 42.857 0.00 0.00 34.07 3.10
3004 5052 4.471904 TTTCACGGATGCTGTAAGAGAT 57.528 40.909 0.00 0.00 34.07 2.75
3005 5053 3.443099 TCACGGATGCTGTAAGAGATG 57.557 47.619 0.00 0.00 34.07 2.90
3006 5054 2.760650 TCACGGATGCTGTAAGAGATGT 59.239 45.455 0.00 0.00 34.07 3.06
3007 5055 2.862536 CACGGATGCTGTAAGAGATGTG 59.137 50.000 0.00 0.00 34.07 3.21
3008 5056 2.760650 ACGGATGCTGTAAGAGATGTGA 59.239 45.455 0.00 0.00 34.07 3.58
3009 5057 3.119291 CGGATGCTGTAAGAGATGTGAC 58.881 50.000 0.00 0.00 34.07 3.67
3010 5058 3.429410 CGGATGCTGTAAGAGATGTGACA 60.429 47.826 0.00 0.00 34.07 3.58
3011 5059 4.507710 GGATGCTGTAAGAGATGTGACAA 58.492 43.478 0.00 0.00 34.07 3.18
3012 5060 4.331168 GGATGCTGTAAGAGATGTGACAAC 59.669 45.833 0.00 0.00 34.07 3.32
3013 5061 4.607293 TGCTGTAAGAGATGTGACAACT 57.393 40.909 0.00 0.00 34.07 3.16
3014 5062 5.722021 TGCTGTAAGAGATGTGACAACTA 57.278 39.130 0.00 0.00 34.07 2.24
3015 5063 6.096673 TGCTGTAAGAGATGTGACAACTAA 57.903 37.500 0.00 0.00 34.07 2.24
3016 5064 6.159293 TGCTGTAAGAGATGTGACAACTAAG 58.841 40.000 0.00 0.00 34.07 2.18
3017 5065 6.159988 GCTGTAAGAGATGTGACAACTAAGT 58.840 40.000 0.00 0.00 34.07 2.24
3018 5066 7.039993 TGCTGTAAGAGATGTGACAACTAAGTA 60.040 37.037 0.00 0.00 34.07 2.24
3019 5067 7.273815 GCTGTAAGAGATGTGACAACTAAGTAC 59.726 40.741 0.00 0.14 34.07 2.73
3020 5068 8.405418 TGTAAGAGATGTGACAACTAAGTACT 57.595 34.615 0.00 0.00 0.00 2.73
3021 5069 9.511272 TGTAAGAGATGTGACAACTAAGTACTA 57.489 33.333 0.00 0.00 0.00 1.82
3022 5070 9.991388 GTAAGAGATGTGACAACTAAGTACTAG 57.009 37.037 0.00 0.00 0.00 2.57
3023 5071 8.638629 AAGAGATGTGACAACTAAGTACTAGT 57.361 34.615 0.00 0.00 43.06 2.57
3024 5072 9.736414 AAGAGATGTGACAACTAAGTACTAGTA 57.264 33.333 0.00 0.00 40.14 1.82
3025 5073 9.386010 AGAGATGTGACAACTAAGTACTAGTAG 57.614 37.037 1.87 0.00 40.14 2.57
3026 5074 9.165035 GAGATGTGACAACTAAGTACTAGTAGT 57.835 37.037 8.14 8.14 40.14 2.73
3037 5085 9.672673 ACTAAGTACTAGTAGTATTTGTTCCGA 57.327 33.333 21.96 6.03 39.20 4.55
3038 5086 9.928236 CTAAGTACTAGTAGTATTTGTTCCGAC 57.072 37.037 21.96 6.42 32.70 4.79
3039 5087 7.326968 AGTACTAGTAGTATTTGTTCCGACC 57.673 40.000 13.09 0.00 32.65 4.79
3040 5088 6.886459 AGTACTAGTAGTATTTGTTCCGACCA 59.114 38.462 13.09 0.00 32.65 4.02
3041 5089 6.786967 ACTAGTAGTATTTGTTCCGACCAT 57.213 37.500 0.00 0.00 0.00 3.55
3042 5090 6.803642 ACTAGTAGTATTTGTTCCGACCATC 58.196 40.000 0.00 0.00 0.00 3.51
3043 5091 5.934402 AGTAGTATTTGTTCCGACCATCT 57.066 39.130 0.00 0.00 0.00 2.90
3044 5092 6.295719 AGTAGTATTTGTTCCGACCATCTT 57.704 37.500 0.00 0.00 0.00 2.40
3045 5093 7.414222 AGTAGTATTTGTTCCGACCATCTTA 57.586 36.000 0.00 0.00 0.00 2.10
3046 5094 7.490000 AGTAGTATTTGTTCCGACCATCTTAG 58.510 38.462 0.00 0.00 0.00 2.18
3047 5095 5.116882 AGTATTTGTTCCGACCATCTTAGC 58.883 41.667 0.00 0.00 0.00 3.09
3048 5096 3.695830 TTTGTTCCGACCATCTTAGCT 57.304 42.857 0.00 0.00 0.00 3.32
3049 5097 4.811969 TTTGTTCCGACCATCTTAGCTA 57.188 40.909 0.00 0.00 0.00 3.32
3050 5098 4.386867 TTGTTCCGACCATCTTAGCTAG 57.613 45.455 0.00 0.00 0.00 3.42
3051 5099 2.100916 TGTTCCGACCATCTTAGCTAGC 59.899 50.000 6.62 6.62 0.00 3.42
3052 5100 0.952280 TCCGACCATCTTAGCTAGCG 59.048 55.000 9.55 0.00 0.00 4.26
3053 5101 0.952280 CCGACCATCTTAGCTAGCGA 59.048 55.000 9.55 0.00 0.00 4.93
3054 5102 1.337071 CCGACCATCTTAGCTAGCGAA 59.663 52.381 9.55 9.81 0.00 4.70
3055 5103 2.386249 CGACCATCTTAGCTAGCGAAC 58.614 52.381 9.55 0.00 0.00 3.95
3056 5104 2.386249 GACCATCTTAGCTAGCGAACG 58.614 52.381 9.55 5.04 0.00 3.95
3057 5105 1.749634 ACCATCTTAGCTAGCGAACGT 59.250 47.619 9.55 0.00 0.00 3.99
3058 5106 2.165845 ACCATCTTAGCTAGCGAACGTT 59.834 45.455 9.55 0.00 0.00 3.99
3059 5107 2.789893 CCATCTTAGCTAGCGAACGTTC 59.210 50.000 18.47 18.47 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 57 2.959516 GCAATAGGCCAACAAAAGGAC 58.040 47.619 5.01 0.00 36.11 3.85
178 181 8.784994 TGAGCGGTACAAAGATTAAATAAACAA 58.215 29.630 0.00 0.00 0.00 2.83
179 182 8.325421 TGAGCGGTACAAAGATTAAATAAACA 57.675 30.769 0.00 0.00 0.00 2.83
180 183 7.428472 GCTGAGCGGTACAAAGATTAAATAAAC 59.572 37.037 0.00 0.00 0.00 2.01
197 223 1.302033 CCTCAAGTTGCTGAGCGGT 60.302 57.895 0.00 0.00 41.36 5.68
199 225 1.303799 ATGCCTCAAGTTGCTGAGCG 61.304 55.000 0.00 0.00 41.36 5.03
279 305 5.235186 CCATCGAGCCATTAACAAGAGTAAG 59.765 44.000 0.00 0.00 0.00 2.34
373 400 3.121030 CGGAAGCAAGAGCCCGTG 61.121 66.667 0.00 0.00 43.56 4.94
374 401 4.394712 CCGGAAGCAAGAGCCCGT 62.395 66.667 0.00 0.00 41.96 5.28
376 403 3.978571 GACCCGGAAGCAAGAGCCC 62.979 68.421 0.73 0.00 43.56 5.19
429 463 4.777463 AGGATTTCGGGAACAACGATATT 58.223 39.130 0.00 0.00 40.38 1.28
532 683 0.962356 CAATCGGGCTGCTTGGTTCT 60.962 55.000 1.94 0.00 0.00 3.01
589 741 3.258622 GGACTACACCTCAACAACTAGCT 59.741 47.826 0.00 0.00 0.00 3.32
629 781 1.377856 GAGTTTGGAGGAGGCAGCC 60.378 63.158 1.84 1.84 0.00 4.85
759 917 1.079875 CGACCGTCCAAATACCACCG 61.080 60.000 0.00 0.00 0.00 4.94
765 941 1.801771 CAAACAGCGACCGTCCAAATA 59.198 47.619 0.00 0.00 0.00 1.40
796 972 2.286418 GCTTGCATTGGTGACGCTATAC 60.286 50.000 0.00 0.00 0.00 1.47
805 981 0.828022 ATGGATGGCTTGCATTGGTG 59.172 50.000 1.42 0.00 31.38 4.17
879 1057 5.057149 AGGATCTCCGGAATTAACAAATCG 58.943 41.667 5.23 0.00 42.08 3.34
964 1142 5.860182 GTGGAAGCCTACGTTTTATTTTTCC 59.140 40.000 0.00 0.00 33.81 3.13
993 1172 4.091509 GGCGCGACTATAAATAGTGGATTG 59.908 45.833 12.10 5.97 43.27 2.67
1016 1195 0.184933 TGGGGAAAGAAGGTGGTGTG 59.815 55.000 0.00 0.00 0.00 3.82
1017 1196 0.478507 CTGGGGAAAGAAGGTGGTGT 59.521 55.000 0.00 0.00 0.00 4.16
1028 1207 2.440599 GGCTCAAGGCTGGGGAAA 59.559 61.111 0.00 0.00 41.46 3.13
1130 1313 1.248101 TGATGACGGCTGAGTCGGAA 61.248 55.000 12.39 0.00 43.70 4.30
1139 1322 0.810031 GTACGCCATTGATGACGGCT 60.810 55.000 4.79 0.00 43.95 5.52
1142 1325 0.930310 CCTGTACGCCATTGATGACG 59.070 55.000 0.00 0.00 39.61 4.35
1580 1766 2.751436 GAAGGCTCGCATTGGGCA 60.751 61.111 0.00 0.00 45.17 5.36
1640 1826 2.892425 CTTGCGGCCGATGTCTCC 60.892 66.667 33.48 9.92 0.00 3.71
1672 1858 2.488355 CGTTCTCCTCGCCGCTAA 59.512 61.111 0.00 0.00 0.00 3.09
1673 1859 4.189188 GCGTTCTCCTCGCCGCTA 62.189 66.667 0.00 0.00 46.61 4.26
1958 2146 0.967380 GACTTGCCACCCCAAGATGG 60.967 60.000 8.71 0.00 43.79 3.51
1981 2169 2.915738 ACGGTGAAACGTCTAGCTAG 57.084 50.000 15.01 15.01 45.08 3.42
2004 2192 4.655607 GGGATACAACACACACCGTGAAG 61.656 52.174 5.28 0.00 44.43 3.02
2081 2271 6.864151 ACGTCTTATAAAGTTTAGAGGGGT 57.136 37.500 9.99 2.89 0.00 4.95
2100 4148 5.866092 CCTTGGAGTAGTAACCTAAAACGTC 59.134 44.000 0.00 0.00 0.00 4.34
2118 4166 7.176865 CGAAGATATAGATTGTACTCCCTTGGA 59.823 40.741 0.00 0.00 0.00 3.53
2119 4167 7.316640 CGAAGATATAGATTGTACTCCCTTGG 58.683 42.308 0.00 0.00 0.00 3.61
2120 4168 7.039644 ACCGAAGATATAGATTGTACTCCCTTG 60.040 40.741 0.00 0.00 0.00 3.61
2121 4169 7.011382 ACCGAAGATATAGATTGTACTCCCTT 58.989 38.462 0.00 0.00 0.00 3.95
2122 4170 6.553857 ACCGAAGATATAGATTGTACTCCCT 58.446 40.000 0.00 0.00 0.00 4.20
2123 4171 6.660094 AGACCGAAGATATAGATTGTACTCCC 59.340 42.308 0.00 0.00 0.00 4.30
2124 4172 7.690952 AGACCGAAGATATAGATTGTACTCC 57.309 40.000 0.00 0.00 0.00 3.85
2125 4173 8.784994 TCAAGACCGAAGATATAGATTGTACTC 58.215 37.037 0.00 0.00 0.00 2.59
2126 4174 8.693120 TCAAGACCGAAGATATAGATTGTACT 57.307 34.615 0.00 0.00 0.00 2.73
2127 4175 9.745880 TTTCAAGACCGAAGATATAGATTGTAC 57.254 33.333 0.00 0.00 0.00 2.90
2137 4185 7.117812 GTGTTTGAGATTTCAAGACCGAAGATA 59.882 37.037 0.00 0.00 43.76 1.98
2138 4186 5.997746 TGTTTGAGATTTCAAGACCGAAGAT 59.002 36.000 0.00 0.00 43.76 2.40
2141 4189 5.123227 AGTGTTTGAGATTTCAAGACCGAA 58.877 37.500 0.00 0.00 43.76 4.30
2149 4197 8.546597 TGATTAATCGAGTGTTTGAGATTTCA 57.453 30.769 10.80 0.00 35.30 2.69
2153 4201 8.607459 GTTCATGATTAATCGAGTGTTTGAGAT 58.393 33.333 10.80 0.00 0.00 2.75
2169 4217 9.173021 ACAAAAGGACAATATCGTTCATGATTA 57.827 29.630 0.00 0.00 34.29 1.75
2173 4221 7.304735 TGAACAAAAGGACAATATCGTTCATG 58.695 34.615 0.00 0.00 37.25 3.07
2174 4222 7.447374 TGAACAAAAGGACAATATCGTTCAT 57.553 32.000 0.00 0.00 37.25 2.57
2175 4223 6.567701 GCTGAACAAAAGGACAATATCGTTCA 60.568 38.462 0.00 0.00 39.18 3.18
2176 4224 5.795441 GCTGAACAAAAGGACAATATCGTTC 59.205 40.000 0.00 0.00 34.29 3.95
2177 4225 5.240623 TGCTGAACAAAAGGACAATATCGTT 59.759 36.000 0.00 0.00 36.99 3.85
2178 4226 4.759693 TGCTGAACAAAAGGACAATATCGT 59.240 37.500 0.00 0.00 0.00 3.73
2179 4227 5.295431 TGCTGAACAAAAGGACAATATCG 57.705 39.130 0.00 0.00 0.00 2.92
2220 4268 1.915141 AAGGAAGGATTGCAGTGTGG 58.085 50.000 0.00 0.00 39.77 4.17
2226 4274 5.129485 TGTTAAAACCAAAGGAAGGATTGCA 59.871 36.000 0.00 0.00 39.77 4.08
2228 4276 7.224557 CAGTTGTTAAAACCAAAGGAAGGATTG 59.775 37.037 0.00 0.00 0.00 2.67
2298 4346 3.885521 GTCCGCCCCGACGACTAG 61.886 72.222 0.00 0.00 34.06 2.57
2303 4351 4.770874 AATTGGTCCGCCCCGACG 62.771 66.667 0.00 0.00 33.30 5.12
2323 4371 2.799126 AAACTCCACAAGACCACACA 57.201 45.000 0.00 0.00 0.00 3.72
2341 4389 2.098614 TGCAGAGGTGACAAAGCAAAA 58.901 42.857 0.00 0.00 31.11 2.44
2360 4408 2.409870 GCAGGCTTGGAATCCGGTG 61.410 63.158 0.00 0.00 0.00 4.94
2363 4411 1.821332 GGAGCAGGCTTGGAATCCG 60.821 63.158 0.00 0.00 0.00 4.18
2369 4417 0.323178 AATGTGAGGAGCAGGCTTGG 60.323 55.000 0.00 0.00 0.00 3.61
2374 4422 4.728409 TGCAATGTGAGGAGCAGG 57.272 55.556 0.00 0.00 32.48 4.85
2384 4432 3.006323 AGAAGAAGACGAGACTGCAATGT 59.994 43.478 0.00 0.00 0.00 2.71
2388 4436 1.957177 ACAGAAGAAGACGAGACTGCA 59.043 47.619 0.00 0.00 0.00 4.41
2411 4459 3.127352 CTAGCCTCTCGTCACGGCC 62.127 68.421 0.00 0.00 44.84 6.13
2419 4467 3.784701 TCAAAACTAGCTAGCCTCTCG 57.215 47.619 20.91 5.05 0.00 4.04
2435 4483 6.435904 ACAAACGGGGAATCTATTTCATCAAA 59.564 34.615 0.00 0.00 35.94 2.69
2437 4485 5.505780 ACAAACGGGGAATCTATTTCATCA 58.494 37.500 0.00 0.00 35.94 3.07
2449 4497 4.401519 TCATAAACACAAACAAACGGGGAA 59.598 37.500 0.00 0.00 0.00 3.97
2451 4499 4.295051 CTCATAAACACAAACAAACGGGG 58.705 43.478 0.00 0.00 0.00 5.73
2477 4525 7.062848 CGAATTAAAATCAACAAAAGCACACC 58.937 34.615 0.00 0.00 0.00 4.16
2483 4531 9.549509 TCGATACCGAATTAAAATCAACAAAAG 57.450 29.630 0.00 0.00 42.51 2.27
2507 4555 0.455295 GGTCAAGCTCACTCTCGTCG 60.455 60.000 0.00 0.00 0.00 5.12
2508 4556 0.455295 CGGTCAAGCTCACTCTCGTC 60.455 60.000 0.00 0.00 0.00 4.20
2509 4557 0.889638 TCGGTCAAGCTCACTCTCGT 60.890 55.000 0.00 0.00 0.00 4.18
2510 4558 0.453793 ATCGGTCAAGCTCACTCTCG 59.546 55.000 0.00 0.00 0.00 4.04
2511 4559 1.203523 ACATCGGTCAAGCTCACTCTC 59.796 52.381 0.00 0.00 0.00 3.20
2512 4560 1.261480 ACATCGGTCAAGCTCACTCT 58.739 50.000 0.00 0.00 0.00 3.24
2513 4561 2.941453 TACATCGGTCAAGCTCACTC 57.059 50.000 0.00 0.00 0.00 3.51
2514 4562 5.339008 TTTATACATCGGTCAAGCTCACT 57.661 39.130 0.00 0.00 0.00 3.41
2515 4563 5.523916 ACATTTATACATCGGTCAAGCTCAC 59.476 40.000 0.00 0.00 0.00 3.51
2516 4564 5.670485 ACATTTATACATCGGTCAAGCTCA 58.330 37.500 0.00 0.00 0.00 4.26
2517 4565 6.257849 TGAACATTTATACATCGGTCAAGCTC 59.742 38.462 0.00 0.00 0.00 4.09
2518 4566 6.037172 GTGAACATTTATACATCGGTCAAGCT 59.963 38.462 0.00 0.00 0.00 3.74
2519 4567 6.192360 GTGAACATTTATACATCGGTCAAGC 58.808 40.000 0.00 0.00 0.00 4.01
2520 4568 6.238374 GGGTGAACATTTATACATCGGTCAAG 60.238 42.308 0.00 0.00 0.00 3.02
2521 4569 5.587043 GGGTGAACATTTATACATCGGTCAA 59.413 40.000 0.00 0.00 0.00 3.18
2522 4570 5.120399 GGGTGAACATTTATACATCGGTCA 58.880 41.667 0.00 0.00 0.00 4.02
2523 4571 4.210537 CGGGTGAACATTTATACATCGGTC 59.789 45.833 0.00 0.00 0.00 4.79
2524 4572 4.124238 CGGGTGAACATTTATACATCGGT 58.876 43.478 0.00 0.00 0.00 4.69
2525 4573 4.373527 TCGGGTGAACATTTATACATCGG 58.626 43.478 0.00 0.00 0.00 4.18
2526 4574 6.539649 AATCGGGTGAACATTTATACATCG 57.460 37.500 0.00 0.00 0.00 3.84
2527 4575 8.402472 TGAAAATCGGGTGAACATTTATACATC 58.598 33.333 0.00 0.00 0.00 3.06
2528 4576 8.188139 GTGAAAATCGGGTGAACATTTATACAT 58.812 33.333 0.00 0.00 0.00 2.29
2529 4577 7.175119 TGTGAAAATCGGGTGAACATTTATACA 59.825 33.333 0.00 0.00 0.00 2.29
2530 4578 7.531716 TGTGAAAATCGGGTGAACATTTATAC 58.468 34.615 0.00 0.00 0.00 1.47
2531 4579 7.689446 TGTGAAAATCGGGTGAACATTTATA 57.311 32.000 0.00 0.00 0.00 0.98
2532 4580 6.582677 TGTGAAAATCGGGTGAACATTTAT 57.417 33.333 0.00 0.00 0.00 1.40
2533 4581 6.392625 TTGTGAAAATCGGGTGAACATTTA 57.607 33.333 0.00 0.00 0.00 1.40
2534 4582 4.927978 TGTGAAAATCGGGTGAACATTT 57.072 36.364 0.00 0.00 0.00 2.32
2535 4583 4.927978 TTGTGAAAATCGGGTGAACATT 57.072 36.364 0.00 0.00 0.00 2.71
2536 4584 5.467035 AATTGTGAAAATCGGGTGAACAT 57.533 34.783 0.00 0.00 0.00 2.71
2537 4585 4.927978 AATTGTGAAAATCGGGTGAACA 57.072 36.364 0.00 0.00 0.00 3.18
2538 4586 5.631929 GGTTAATTGTGAAAATCGGGTGAAC 59.368 40.000 0.00 0.00 0.00 3.18
2539 4587 5.563085 CGGTTAATTGTGAAAATCGGGTGAA 60.563 40.000 0.00 0.00 0.00 3.18
2583 4631 7.384932 GCAAAAGCTTTGTCTGTACCATTAATT 59.615 33.333 13.54 0.00 0.00 1.40
2584 4632 6.868339 GCAAAAGCTTTGTCTGTACCATTAAT 59.132 34.615 13.54 0.00 0.00 1.40
2585 4633 6.212955 GCAAAAGCTTTGTCTGTACCATTAA 58.787 36.000 13.54 0.00 0.00 1.40
2586 4634 5.278758 GGCAAAAGCTTTGTCTGTACCATTA 60.279 40.000 13.54 0.00 0.00 1.90
2587 4635 4.501400 GGCAAAAGCTTTGTCTGTACCATT 60.501 41.667 13.54 0.00 0.00 3.16
2588 4636 3.005791 GGCAAAAGCTTTGTCTGTACCAT 59.994 43.478 13.54 0.00 0.00 3.55
2589 4637 2.360801 GGCAAAAGCTTTGTCTGTACCA 59.639 45.455 13.54 0.00 0.00 3.25
2590 4638 2.623416 AGGCAAAAGCTTTGTCTGTACC 59.377 45.455 13.54 5.32 32.44 3.34
2591 4639 3.990318 AGGCAAAAGCTTTGTCTGTAC 57.010 42.857 13.54 5.44 32.44 2.90
2592 4640 4.159506 ACAAAGGCAAAAGCTTTGTCTGTA 59.840 37.500 13.54 0.00 44.79 2.74
2593 4641 3.055891 ACAAAGGCAAAAGCTTTGTCTGT 60.056 39.130 13.54 6.30 44.79 3.41
2601 4649 7.622893 TTTTTATTGAACAAAGGCAAAAGCT 57.377 28.000 0.00 0.00 0.00 3.74
2746 4794 6.884832 AGATTGATGCAATGTTCCAATGAAT 58.115 32.000 0.00 0.00 33.90 2.57
2753 4801 4.813027 ACACAAGATTGATGCAATGTTCC 58.187 39.130 0.00 0.00 35.62 3.62
2819 4867 2.410053 GCTCGTTTGTCTCTTAGCAGTG 59.590 50.000 0.00 0.00 0.00 3.66
2823 4871 4.924462 AGTTTAGCTCGTTTGTCTCTTAGC 59.076 41.667 0.00 0.00 0.00 3.09
2883 4931 8.947115 GGTAGAGTTATAAGAAACACAGCAATT 58.053 33.333 0.00 0.00 0.00 2.32
2884 4932 7.553044 GGGTAGAGTTATAAGAAACACAGCAAT 59.447 37.037 0.00 0.00 0.00 3.56
2885 4933 6.877322 GGGTAGAGTTATAAGAAACACAGCAA 59.123 38.462 0.00 0.00 0.00 3.91
2886 4934 6.014070 TGGGTAGAGTTATAAGAAACACAGCA 60.014 38.462 0.00 0.00 0.00 4.41
2887 4935 6.403878 TGGGTAGAGTTATAAGAAACACAGC 58.596 40.000 0.00 0.00 0.00 4.40
2888 4936 8.258007 TCATGGGTAGAGTTATAAGAAACACAG 58.742 37.037 0.00 0.00 0.00 3.66
2889 4937 8.141298 TCATGGGTAGAGTTATAAGAAACACA 57.859 34.615 0.00 0.00 0.00 3.72
2890 4938 9.444600 TTTCATGGGTAGAGTTATAAGAAACAC 57.555 33.333 0.00 0.00 0.00 3.32
2894 4942 9.174166 GCTTTTTCATGGGTAGAGTTATAAGAA 57.826 33.333 0.00 0.00 0.00 2.52
2895 4943 8.548877 AGCTTTTTCATGGGTAGAGTTATAAGA 58.451 33.333 0.00 0.00 0.00 2.10
2896 4944 8.616076 CAGCTTTTTCATGGGTAGAGTTATAAG 58.384 37.037 0.00 0.00 0.00 1.73
2897 4945 7.556275 CCAGCTTTTTCATGGGTAGAGTTATAA 59.444 37.037 0.00 0.00 0.00 0.98
2898 4946 7.054124 CCAGCTTTTTCATGGGTAGAGTTATA 58.946 38.462 0.00 0.00 0.00 0.98
2899 4947 5.888161 CCAGCTTTTTCATGGGTAGAGTTAT 59.112 40.000 0.00 0.00 0.00 1.89
2900 4948 5.013704 TCCAGCTTTTTCATGGGTAGAGTTA 59.986 40.000 0.00 0.00 34.71 2.24
2901 4949 4.082125 CCAGCTTTTTCATGGGTAGAGTT 58.918 43.478 0.00 0.00 0.00 3.01
2902 4950 3.330701 TCCAGCTTTTTCATGGGTAGAGT 59.669 43.478 0.00 0.00 34.71 3.24
2903 4951 3.691609 GTCCAGCTTTTTCATGGGTAGAG 59.308 47.826 0.00 0.00 34.71 2.43
2904 4952 3.073798 TGTCCAGCTTTTTCATGGGTAGA 59.926 43.478 0.00 0.00 34.71 2.59
2905 4953 3.191371 GTGTCCAGCTTTTTCATGGGTAG 59.809 47.826 0.00 0.00 34.71 3.18
2906 4954 3.153919 GTGTCCAGCTTTTTCATGGGTA 58.846 45.455 0.00 0.00 34.71 3.69
2907 4955 1.963515 GTGTCCAGCTTTTTCATGGGT 59.036 47.619 0.00 0.00 34.71 4.51
2908 4956 1.273327 GGTGTCCAGCTTTTTCATGGG 59.727 52.381 0.00 0.00 34.71 4.00
2909 4957 1.962807 TGGTGTCCAGCTTTTTCATGG 59.037 47.619 0.00 0.00 35.30 3.66
2910 4958 3.841643 GATGGTGTCCAGCTTTTTCATG 58.158 45.455 0.00 0.00 36.92 3.07
2919 4967 3.201290 CAAGATACAGATGGTGTCCAGC 58.799 50.000 0.00 0.00 40.67 4.85
2920 4968 3.801698 CCAAGATACAGATGGTGTCCAG 58.198 50.000 0.00 0.00 40.94 3.86
2921 4969 2.092968 GCCAAGATACAGATGGTGTCCA 60.093 50.000 0.00 0.00 40.94 4.02
2922 4970 2.171448 AGCCAAGATACAGATGGTGTCC 59.829 50.000 0.00 0.00 40.94 4.02
2923 4971 3.550437 AGCCAAGATACAGATGGTGTC 57.450 47.619 0.00 0.00 40.94 3.67
2924 4972 4.307032 AAAGCCAAGATACAGATGGTGT 57.693 40.909 0.00 0.00 43.86 4.16
2925 4973 5.220931 GCTAAAAGCCAAGATACAGATGGTG 60.221 44.000 0.00 0.00 36.57 4.17
2926 4974 4.884164 GCTAAAAGCCAAGATACAGATGGT 59.116 41.667 0.00 0.00 36.57 3.55
2927 4975 5.429957 GCTAAAAGCCAAGATACAGATGG 57.570 43.478 0.00 0.00 34.48 3.51
2941 4989 3.245519 GTGTAGCGTATCTGGCTAAAAGC 59.754 47.826 0.00 0.00 43.98 3.51
2942 4990 4.430007 TGTGTAGCGTATCTGGCTAAAAG 58.570 43.478 0.00 0.00 43.98 2.27
2943 4991 4.459390 TGTGTAGCGTATCTGGCTAAAA 57.541 40.909 0.00 0.00 43.98 1.52
2944 4992 4.459390 TTGTGTAGCGTATCTGGCTAAA 57.541 40.909 0.00 0.00 43.98 1.85
2945 4993 4.178540 GTTTGTGTAGCGTATCTGGCTAA 58.821 43.478 0.00 0.00 43.98 3.09
2946 4994 3.429822 GGTTTGTGTAGCGTATCTGGCTA 60.430 47.826 0.00 0.00 41.80 3.93
2947 4995 2.618053 GTTTGTGTAGCGTATCTGGCT 58.382 47.619 0.00 0.00 44.35 4.75
2948 4996 1.664151 GGTTTGTGTAGCGTATCTGGC 59.336 52.381 0.00 0.00 0.00 4.85
2949 4997 2.967362 TGGTTTGTGTAGCGTATCTGG 58.033 47.619 0.00 0.00 0.00 3.86
2950 4998 6.921307 TGTATATGGTTTGTGTAGCGTATCTG 59.079 38.462 0.00 0.00 31.94 2.90
2951 4999 7.013942 TCTGTATATGGTTTGTGTAGCGTATCT 59.986 37.037 0.00 0.00 31.94 1.98
2952 5000 7.143340 TCTGTATATGGTTTGTGTAGCGTATC 58.857 38.462 0.00 0.00 31.94 2.24
2953 5001 7.046292 TCTGTATATGGTTTGTGTAGCGTAT 57.954 36.000 0.00 0.00 33.58 3.06
2954 5002 6.453926 TCTGTATATGGTTTGTGTAGCGTA 57.546 37.500 0.00 0.00 0.00 4.42
2955 5003 5.333299 TCTGTATATGGTTTGTGTAGCGT 57.667 39.130 0.00 0.00 0.00 5.07
2956 5004 7.940178 TTATCTGTATATGGTTTGTGTAGCG 57.060 36.000 0.00 0.00 0.00 4.26
2965 5013 9.621629 TCCGTGAAAATTTATCTGTATATGGTT 57.378 29.630 0.00 0.00 0.00 3.67
2966 5014 9.793259 ATCCGTGAAAATTTATCTGTATATGGT 57.207 29.630 0.00 0.00 0.00 3.55
2968 5016 9.546909 GCATCCGTGAAAATTTATCTGTATATG 57.453 33.333 0.00 0.00 0.00 1.78
2969 5017 9.507329 AGCATCCGTGAAAATTTATCTGTATAT 57.493 29.630 0.00 0.00 0.00 0.86
2970 5018 8.773645 CAGCATCCGTGAAAATTTATCTGTATA 58.226 33.333 0.00 0.00 0.00 1.47
2971 5019 7.283127 ACAGCATCCGTGAAAATTTATCTGTAT 59.717 33.333 0.00 0.00 0.00 2.29
2972 5020 6.597672 ACAGCATCCGTGAAAATTTATCTGTA 59.402 34.615 0.00 0.00 0.00 2.74
2973 5021 5.415701 ACAGCATCCGTGAAAATTTATCTGT 59.584 36.000 0.00 0.00 0.00 3.41
2974 5022 5.883661 ACAGCATCCGTGAAAATTTATCTG 58.116 37.500 0.00 0.00 0.00 2.90
2975 5023 7.552687 TCTTACAGCATCCGTGAAAATTTATCT 59.447 33.333 0.00 0.00 0.00 1.98
2976 5024 7.693952 TCTTACAGCATCCGTGAAAATTTATC 58.306 34.615 0.00 0.00 0.00 1.75
2977 5025 7.552687 TCTCTTACAGCATCCGTGAAAATTTAT 59.447 33.333 0.00 0.00 0.00 1.40
2978 5026 6.876789 TCTCTTACAGCATCCGTGAAAATTTA 59.123 34.615 0.00 0.00 0.00 1.40
2979 5027 5.705441 TCTCTTACAGCATCCGTGAAAATTT 59.295 36.000 0.00 0.00 0.00 1.82
2980 5028 5.245531 TCTCTTACAGCATCCGTGAAAATT 58.754 37.500 0.00 0.00 0.00 1.82
2981 5029 4.832248 TCTCTTACAGCATCCGTGAAAAT 58.168 39.130 0.00 0.00 0.00 1.82
2982 5030 4.265904 TCTCTTACAGCATCCGTGAAAA 57.734 40.909 0.00 0.00 0.00 2.29
2983 5031 3.953712 TCTCTTACAGCATCCGTGAAA 57.046 42.857 0.00 0.00 0.00 2.69
2984 5032 3.195610 ACATCTCTTACAGCATCCGTGAA 59.804 43.478 0.00 0.00 0.00 3.18
2985 5033 2.760650 ACATCTCTTACAGCATCCGTGA 59.239 45.455 0.00 0.00 0.00 4.35
2986 5034 2.862536 CACATCTCTTACAGCATCCGTG 59.137 50.000 0.00 0.00 0.00 4.94
2987 5035 2.760650 TCACATCTCTTACAGCATCCGT 59.239 45.455 0.00 0.00 0.00 4.69
2988 5036 3.119291 GTCACATCTCTTACAGCATCCG 58.881 50.000 0.00 0.00 0.00 4.18
2989 5037 4.128925 TGTCACATCTCTTACAGCATCC 57.871 45.455 0.00 0.00 0.00 3.51
2990 5038 5.174395 AGTTGTCACATCTCTTACAGCATC 58.826 41.667 0.00 0.00 0.00 3.91
2991 5039 5.157940 AGTTGTCACATCTCTTACAGCAT 57.842 39.130 0.00 0.00 0.00 3.79
2992 5040 4.607293 AGTTGTCACATCTCTTACAGCA 57.393 40.909 0.00 0.00 0.00 4.41
2993 5041 6.159988 ACTTAGTTGTCACATCTCTTACAGC 58.840 40.000 0.00 0.00 0.00 4.40
2994 5042 8.516234 AGTACTTAGTTGTCACATCTCTTACAG 58.484 37.037 0.00 0.00 0.00 2.74
2995 5043 8.405418 AGTACTTAGTTGTCACATCTCTTACA 57.595 34.615 0.00 0.00 0.00 2.41
2996 5044 9.991388 CTAGTACTTAGTTGTCACATCTCTTAC 57.009 37.037 0.00 0.00 0.00 2.34
2997 5045 9.736414 ACTAGTACTTAGTTGTCACATCTCTTA 57.264 33.333 0.00 0.00 39.64 2.10
2998 5046 8.638629 ACTAGTACTTAGTTGTCACATCTCTT 57.361 34.615 0.00 0.00 39.64 2.85
2999 5047 9.386010 CTACTAGTACTTAGTTGTCACATCTCT 57.614 37.037 0.00 0.00 42.57 3.10
3000 5048 9.165035 ACTACTAGTACTTAGTTGTCACATCTC 57.835 37.037 0.00 0.00 42.23 2.75
3011 5059 9.672673 TCGGAACAAATACTACTAGTACTTAGT 57.327 33.333 0.00 6.59 44.71 2.24
3012 5060 9.928236 GTCGGAACAAATACTACTAGTACTTAG 57.072 37.037 0.00 0.00 32.84 2.18
3013 5061 8.893727 GGTCGGAACAAATACTACTAGTACTTA 58.106 37.037 0.00 0.00 32.84 2.24
3014 5062 7.394359 TGGTCGGAACAAATACTACTAGTACTT 59.606 37.037 0.00 0.00 32.84 2.24
3015 5063 6.886459 TGGTCGGAACAAATACTACTAGTACT 59.114 38.462 0.00 0.00 32.84 2.73
3016 5064 7.088589 TGGTCGGAACAAATACTACTAGTAC 57.911 40.000 0.00 0.00 32.84 2.73
3017 5065 7.776969 AGATGGTCGGAACAAATACTACTAGTA 59.223 37.037 0.00 1.89 34.82 1.82
3018 5066 6.606395 AGATGGTCGGAACAAATACTACTAGT 59.394 38.462 0.00 0.00 0.00 2.57
3019 5067 7.040473 AGATGGTCGGAACAAATACTACTAG 57.960 40.000 0.00 0.00 0.00 2.57
3020 5068 7.414222 AAGATGGTCGGAACAAATACTACTA 57.586 36.000 0.00 0.00 0.00 1.82
3021 5069 5.934402 AGATGGTCGGAACAAATACTACT 57.066 39.130 0.00 0.00 0.00 2.57
3022 5070 6.200475 GCTAAGATGGTCGGAACAAATACTAC 59.800 42.308 0.00 0.00 0.00 2.73
3023 5071 6.097839 AGCTAAGATGGTCGGAACAAATACTA 59.902 38.462 0.00 0.00 0.00 1.82
3024 5072 5.104900 AGCTAAGATGGTCGGAACAAATACT 60.105 40.000 0.00 0.00 0.00 2.12
3025 5073 5.116882 AGCTAAGATGGTCGGAACAAATAC 58.883 41.667 0.00 0.00 0.00 1.89
3026 5074 5.353394 AGCTAAGATGGTCGGAACAAATA 57.647 39.130 0.00 0.00 0.00 1.40
3027 5075 4.222124 AGCTAAGATGGTCGGAACAAAT 57.778 40.909 0.00 0.00 0.00 2.32
3028 5076 3.695830 AGCTAAGATGGTCGGAACAAA 57.304 42.857 0.00 0.00 0.00 2.83
3029 5077 3.430374 GCTAGCTAAGATGGTCGGAACAA 60.430 47.826 7.70 0.00 0.00 2.83
3030 5078 2.100916 GCTAGCTAAGATGGTCGGAACA 59.899 50.000 7.70 0.00 0.00 3.18
3031 5079 2.745102 GCTAGCTAAGATGGTCGGAAC 58.255 52.381 7.70 0.00 0.00 3.62
3032 5080 1.337071 CGCTAGCTAAGATGGTCGGAA 59.663 52.381 13.93 0.00 0.00 4.30
3033 5081 0.952280 CGCTAGCTAAGATGGTCGGA 59.048 55.000 13.93 0.00 0.00 4.55
3034 5082 0.952280 TCGCTAGCTAAGATGGTCGG 59.048 55.000 13.93 0.00 0.00 4.79
3035 5083 2.386249 GTTCGCTAGCTAAGATGGTCG 58.614 52.381 13.93 0.00 0.00 4.79
3036 5084 2.223525 ACGTTCGCTAGCTAAGATGGTC 60.224 50.000 13.93 0.00 0.00 4.02
3037 5085 1.749634 ACGTTCGCTAGCTAAGATGGT 59.250 47.619 13.93 1.58 0.00 3.55
3038 5086 2.493713 ACGTTCGCTAGCTAAGATGG 57.506 50.000 13.93 0.97 0.00 3.51
3039 5087 2.464380 CGAACGTTCGCTAGCTAAGATG 59.536 50.000 34.54 7.14 44.26 2.90
3040 5088 2.717530 CGAACGTTCGCTAGCTAAGAT 58.282 47.619 34.54 0.00 44.26 2.40
3041 5089 2.169663 CGAACGTTCGCTAGCTAAGA 57.830 50.000 34.54 0.00 44.26 2.10


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

AutoCloner maintained by Alex Coulton.