Multiple sequence alignment - TraesCS2D01G561800

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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 TraesCS2D01G561800 chr2D 100.000 2628 0 0 1 2628 633876471 633879098 0.000000e+00 4854.0
1 TraesCS2D01G561800 chr2D 85.328 259 26 6 1314 1561 633785532 633785275 9.330000e-65 257.0
2 TraesCS2D01G561800 chr2A 84.102 1258 71 44 475 1634 779809997 779808771 0.000000e+00 1096.0
3 TraesCS2D01G561800 chr2A 82.422 1024 80 30 798 1739 779675435 779674430 0.000000e+00 802.0
4 TraesCS2D01G561800 chr2A 85.366 246 14 9 1760 1999 779807999 779807770 4.370000e-58 235.0
5 TraesCS2D01G561800 chr2A 83.846 260 20 14 450 690 779675792 779675536 7.320000e-56 228.0
6 TraesCS2D01G561800 chr2B 83.008 1230 93 52 1004 2192 776888881 776890035 0.000000e+00 1007.0
7 TraesCS2D01G561800 chr2B 85.214 257 29 3 1314 1561 776766129 776765873 3.360000e-64 255.0
8 TraesCS2D01G561800 chr2B 85.769 260 14 5 1 250 609148748 609148502 1.210000e-63 254.0
9 TraesCS2D01G561800 chr2B 90.000 170 17 0 280 449 609146660 609146491 1.220000e-53 220.0
10 TraesCS2D01G561800 chr2B 87.940 199 8 9 2234 2428 776890044 776890230 1.220000e-53 220.0
11 TraesCS2D01G561800 chr2B 86.124 209 14 6 2433 2627 776890305 776890512 7.370000e-51 211.0
12 TraesCS2D01G561800 chr2B 91.971 137 11 0 1367 1503 776841822 776841958 2.670000e-45 193.0
13 TraesCS2D01G561800 chr2B 81.746 252 17 9 1760 1999 776850339 776850573 1.610000e-42 183.0
14 TraesCS2D01G561800 chr2B 82.703 185 12 8 798 969 776888510 776888687 2.110000e-31 147.0
15 TraesCS2D01G561800 chr2B 91.026 78 7 0 373 450 682167044 682166967 3.580000e-19 106.0
16 TraesCS2D01G561800 chr2B 94.737 38 2 0 653 690 776888386 776888423 2.820000e-05 60.2
17 TraesCS2D01G561800 chr3A 85.385 260 15 5 1 250 690963034 690962788 5.620000e-62 248.0
18 TraesCS2D01G561800 chr3A 89.143 175 16 1 278 449 348997693 348997519 5.700000e-52 215.0
19 TraesCS2D01G561800 chr3A 78.000 100 22 0 348 447 716982531 716982432 2.180000e-06 63.9
20 TraesCS2D01G561800 chr3B 84.942 259 16 8 2 250 82851075 82850830 9.400000e-60 241.0
21 TraesCS2D01G561800 chr3B 88.889 117 13 0 328 444 239249975 239249859 7.580000e-31 145.0
22 TraesCS2D01G561800 chr4D 83.784 259 17 9 4 250 386481208 386480963 3.400000e-54 222.0
23 TraesCS2D01G561800 chr1B 83.459 266 14 9 2 250 635437383 635437635 1.220000e-53 220.0
24 TraesCS2D01G561800 chr5B 83.333 264 17 10 1 250 6826767 6827017 4.400000e-53 219.0
25 TraesCS2D01G561800 chr7A 82.895 76 13 0 374 449 105751230 105751155 4.690000e-08 69.4
26 TraesCS2D01G561800 chr7B 77.778 99 22 0 349 447 334795311 334795409 7.850000e-06 62.1


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 TraesCS2D01G561800 chr2D 633876471 633879098 2627 False 4854.00 4854 100.0000 1 2628 1 chr2D.!!$F1 2627
1 TraesCS2D01G561800 chr2A 779807770 779809997 2227 True 665.50 1096 84.7340 475 1999 2 chr2A.!!$R2 1524
2 TraesCS2D01G561800 chr2A 779674430 779675792 1362 True 515.00 802 83.1340 450 1739 2 chr2A.!!$R1 1289
3 TraesCS2D01G561800 chr2B 776888386 776890512 2126 False 329.04 1007 86.9024 653 2627 5 chr2B.!!$F3 1974
4 TraesCS2D01G561800 chr2B 609146491 609148748 2257 True 237.00 254 87.8845 1 449 2 chr2B.!!$R3 448

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
890 2841 0.179045 AGCAACCAGATACCGGCATC 60.179 55.0 6.55 6.55 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2485 5495 0.030773 TCCATCGATGCAGCTCGTAC 59.969 55.0 20.25 0.0 39.62 3.67 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
22 23 3.071479 TGATCCTAAACCTGTTTGTCGC 58.929 45.455 5.55 0.00 34.23 5.19
45 46 2.287915 CGAAAATAGGCAATCCTGACCG 59.712 50.000 0.00 0.00 44.08 4.79
54 55 3.646932 ATCCTGACCGGGATTACCA 57.353 52.632 6.32 0.00 42.89 3.25
55 56 1.129058 ATCCTGACCGGGATTACCAC 58.871 55.000 6.32 0.00 42.89 4.16
59 60 1.411612 CTGACCGGGATTACCACTACC 59.588 57.143 6.32 0.00 40.22 3.18
77 78 0.969894 CCAGGTTCTCTCACCGACTT 59.030 55.000 0.00 0.00 42.33 3.01
79 80 2.164624 CCAGGTTCTCTCACCGACTTAG 59.835 54.545 0.00 0.00 42.33 2.18
91 92 0.680061 CGACTTAGGGGCCCTACATC 59.320 60.000 32.10 27.21 35.63 3.06
92 93 1.057471 GACTTAGGGGCCCTACATCC 58.943 60.000 32.10 16.77 35.63 3.51
93 94 0.648301 ACTTAGGGGCCCTACATCCT 59.352 55.000 32.10 11.79 35.63 3.24
94 95 1.871006 ACTTAGGGGCCCTACATCCTA 59.129 52.381 32.10 15.27 35.63 2.94
95 96 2.258109 CTTAGGGGCCCTACATCCTAC 58.742 57.143 32.10 0.26 35.63 3.18
96 97 1.247260 TAGGGGCCCTACATCCTACA 58.753 55.000 28.78 4.78 34.61 2.74
97 98 0.573279 AGGGGCCCTACATCCTACAT 59.427 55.000 27.62 0.00 28.47 2.29
143 152 2.250237 GCTTCGAGCTGCCTATGCC 61.250 63.158 0.00 0.00 38.45 4.40
144 153 1.596477 CTTCGAGCTGCCTATGCCC 60.596 63.158 0.00 0.00 36.33 5.36
156 165 0.676466 CTATGCCCACCTCGTTGCAA 60.676 55.000 0.00 0.00 37.27 4.08
161 170 1.893808 CCACCTCGTTGCAAGCACT 60.894 57.895 0.00 0.00 0.00 4.40
172 181 2.881441 CAAGCACTTGCAGCAGTTG 58.119 52.632 3.62 0.00 45.16 3.16
217 228 2.232108 TATGCCCCAACGTTCCCCA 61.232 57.895 0.00 0.00 0.00 4.96
311 2134 2.335681 TCCCGGGCAGGATTGATATA 57.664 50.000 18.49 0.00 45.00 0.86
317 2140 3.545703 GGGCAGGATTGATATATTCCCG 58.454 50.000 0.00 0.00 30.61 5.14
322 2145 3.587061 AGGATTGATATATTCCCGGTGCA 59.413 43.478 0.00 0.00 30.61 4.57
344 2167 2.497273 CCAAATTGGTCCAGGGTTGATC 59.503 50.000 3.34 0.00 31.35 2.92
350 2173 1.340114 GGTCCAGGGTTGATCTTGACC 60.340 57.143 0.00 0.00 39.03 4.02
358 2181 3.203716 GGTTGATCTTGACCGGGATTAC 58.796 50.000 6.32 1.71 0.00 1.89
360 2183 3.819564 TGATCTTGACCGGGATTACAG 57.180 47.619 6.32 0.00 0.00 2.74
369 2192 2.023695 ACCGGGATTACAGAGGTTAGGA 60.024 50.000 6.32 0.00 0.00 2.94
373 2196 4.220163 CGGGATTACAGAGGTTAGGATACC 59.780 50.000 0.00 0.00 38.53 2.73
385 2208 4.286291 GGTTAGGATACCGATTTCAGGGAT 59.714 45.833 0.00 0.00 34.31 3.85
387 2210 4.357918 AGGATACCGATTTCAGGGATTG 57.642 45.455 0.00 0.00 31.02 2.67
403 2226 3.496331 GGATTGAAAGGTGGAGGTTCAA 58.504 45.455 0.98 0.98 43.36 2.69
406 2229 5.336770 GGATTGAAAGGTGGAGGTTCAATTC 60.337 44.000 11.06 6.60 46.68 2.17
408 2231 3.117322 TGAAAGGTGGAGGTTCAATTCCA 60.117 43.478 0.00 0.00 41.06 3.53
420 2243 3.226346 TCAATTCCAACGAGGTCTACG 57.774 47.619 0.00 0.00 39.02 3.51
425 2248 1.808945 TCCAACGAGGTCTACGAGTTC 59.191 52.381 0.00 0.00 39.02 3.01
473 2296 1.383803 GGGCCACAGAGGAGGAGAT 60.384 63.158 4.39 0.00 41.22 2.75
502 2325 2.047443 AGGGGAGAAGAGCGTCGTC 61.047 63.158 0.00 0.00 0.00 4.20
506 2329 1.551145 GGAGAAGAGCGTCGTCAATC 58.449 55.000 0.00 0.00 0.00 2.67
507 2330 1.184349 GAGAAGAGCGTCGTCAATCG 58.816 55.000 0.00 0.00 41.41 3.34
509 2332 0.456312 GAAGAGCGTCGTCAATCGGT 60.456 55.000 0.00 0.00 40.32 4.69
531 2354 1.519751 CCATTTTCGGGTCGGCAACA 61.520 55.000 0.00 0.00 0.00 3.33
537 2360 0.828022 TCGGGTCGGCAACAAGATAT 59.172 50.000 0.00 0.00 0.00 1.63
546 2369 3.501062 CGGCAACAAGATATGAGCATGAT 59.499 43.478 0.00 0.00 36.02 2.45
608 2449 1.529865 CGCACGATGCTGATGATGATT 59.470 47.619 8.07 0.00 42.25 2.57
612 2453 4.563061 CACGATGCTGATGATGATTAGGA 58.437 43.478 0.00 0.00 0.00 2.94
618 2459 3.986572 GCTGATGATGATTAGGACACGAG 59.013 47.826 0.00 0.00 0.00 4.18
642 2483 1.573932 CAACGAATGGTGCGAGCAA 59.426 52.632 0.00 0.00 0.00 3.91
692 2550 2.835580 TGGAAATTGTTGGTGGCATG 57.164 45.000 0.00 0.00 0.00 4.06
699 2590 1.625511 TGTTGGTGGCATGCATAACA 58.374 45.000 21.36 19.38 0.00 2.41
760 2665 4.011698 GGAATGCCTGCCATTTTCAATTT 58.988 39.130 0.00 0.00 44.02 1.82
765 2670 5.071370 TGCCTGCCATTTTCAATTTTTCAT 58.929 33.333 0.00 0.00 0.00 2.57
810 2738 4.235372 TCTCTTTTCTTCCCAGTCTCCTT 58.765 43.478 0.00 0.00 0.00 3.36
813 2741 4.284746 TCTTTTCTTCCCAGTCTCCTTCTC 59.715 45.833 0.00 0.00 0.00 2.87
822 2750 3.837731 CCAGTCTCCTTCTCCTTCTTCTT 59.162 47.826 0.00 0.00 0.00 2.52
840 2777 0.261991 TTCACGGATAGGAGGGAGCT 59.738 55.000 0.00 0.00 0.00 4.09
890 2841 0.179045 AGCAACCAGATACCGGCATC 60.179 55.000 6.55 6.55 0.00 3.91
955 2916 3.873883 GCAGCGAGCATGTGAGGC 61.874 66.667 0.00 0.00 44.79 4.70
956 2917 3.200593 CAGCGAGCATGTGAGGCC 61.201 66.667 0.00 0.00 0.00 5.19
973 2934 3.778955 CGTGAGGGTGAGGTCAGT 58.221 61.111 0.00 0.00 0.00 3.41
974 2935 2.957060 CGTGAGGGTGAGGTCAGTA 58.043 57.895 0.00 0.00 0.00 2.74
977 2938 1.819903 GTGAGGGTGAGGTCAGTAGAC 59.180 57.143 0.00 0.00 44.21 2.59
978 2939 1.427753 TGAGGGTGAGGTCAGTAGACA 59.572 52.381 0.00 0.00 46.80 3.41
1150 3310 2.330745 GCGACCCTCGACGGTATC 59.669 66.667 6.05 0.00 43.74 2.24
1167 3327 3.055819 GGTATCTGTTCTGCTCACCTTCA 60.056 47.826 0.00 0.00 0.00 3.02
1277 3445 2.578586 AATCTGCAGGCCATCCACCC 62.579 60.000 15.13 0.00 33.74 4.61
1280 3448 4.195334 GCAGGCCATCCACCCGAT 62.195 66.667 5.01 0.00 33.74 4.18
1312 3480 2.066999 GGAGGGAGAGGCCGTTGAT 61.067 63.158 0.00 0.00 37.63 2.57
1390 3558 1.338973 ACCGAGAGCAAGTACGTCAAA 59.661 47.619 0.00 0.00 0.00 2.69
1393 3561 2.657372 CGAGAGCAAGTACGTCAAAGTC 59.343 50.000 0.00 0.00 0.00 3.01
1600 3768 3.869140 GCAGGAGCATCAGGATAATGAGG 60.869 52.174 0.00 0.00 41.58 3.86
1665 3833 1.282248 CGCAACATCTCCGTGTCGTT 61.282 55.000 0.00 0.00 0.00 3.85
1679 3859 2.653766 CGTTGTTGCCGTTGGTGC 60.654 61.111 0.00 0.00 0.00 5.01
1699 3879 6.072175 TGGTGCTTTTCTTAGATGCGTTTATT 60.072 34.615 0.00 0.00 0.00 1.40
1700 3880 7.119992 TGGTGCTTTTCTTAGATGCGTTTATTA 59.880 33.333 0.00 0.00 0.00 0.98
1703 3883 8.673711 TGCTTTTCTTAGATGCGTTTATTATGT 58.326 29.630 0.00 0.00 0.00 2.29
1704 3884 9.503427 GCTTTTCTTAGATGCGTTTATTATGTT 57.497 29.630 0.00 0.00 0.00 2.71
1726 3912 6.539464 TGTTATTTCTACGTCTTGTTTGGTGT 59.461 34.615 0.00 0.00 0.00 4.16
1798 4719 1.405821 GGTCGGTCGATCACAGAGAAT 59.594 52.381 0.00 0.00 28.71 2.40
1808 4729 6.801377 GTCGATCACAGAGAATAAGCATCTAG 59.199 42.308 0.00 0.00 0.00 2.43
1809 4730 5.572511 CGATCACAGAGAATAAGCATCTAGC 59.427 44.000 0.00 0.00 46.19 3.42
1823 4744 5.449107 GCATCTAGCATTTGATTCACCAT 57.551 39.130 0.00 0.00 44.79 3.55
1868 4789 2.462456 AGCTCATGATTGTGTCACGT 57.538 45.000 0.00 0.00 40.28 4.49
1873 4794 1.799994 CATGATTGTGTCACGTCTGCA 59.200 47.619 0.00 0.00 40.28 4.41
1891 4812 2.910199 GCAGATGCATCTACAGGTGAA 58.090 47.619 28.27 0.00 41.59 3.18
1892 4813 3.273434 GCAGATGCATCTACAGGTGAAA 58.727 45.455 28.27 0.00 41.59 2.69
1893 4814 3.064545 GCAGATGCATCTACAGGTGAAAC 59.935 47.826 28.27 5.10 41.59 2.78
1894 4815 4.511527 CAGATGCATCTACAGGTGAAACT 58.488 43.478 28.27 0.00 34.85 2.66
1895 4816 4.569966 CAGATGCATCTACAGGTGAAACTC 59.430 45.833 28.27 0.00 34.85 3.01
1896 4817 4.469227 AGATGCATCTACAGGTGAAACTCT 59.531 41.667 27.73 0.00 34.85 3.24
1897 4818 3.930336 TGCATCTACAGGTGAAACTCTG 58.070 45.455 0.00 0.00 39.84 3.35
1898 4819 3.578282 TGCATCTACAGGTGAAACTCTGA 59.422 43.478 0.00 0.00 37.32 3.27
1958 4884 1.896660 GTTGGAGTCGGGCTTGCAA 60.897 57.895 0.00 0.00 0.00 4.08
1959 4885 1.600636 TTGGAGTCGGGCTTGCAAG 60.601 57.895 22.44 22.44 0.00 4.01
1960 4886 2.032681 GGAGTCGGGCTTGCAAGT 59.967 61.111 26.55 6.51 0.00 3.16
1961 4887 1.600916 GGAGTCGGGCTTGCAAGTT 60.601 57.895 26.55 6.84 0.00 2.66
1962 4888 1.578206 GGAGTCGGGCTTGCAAGTTC 61.578 60.000 26.55 18.42 0.00 3.01
1963 4889 0.884704 GAGTCGGGCTTGCAAGTTCA 60.885 55.000 26.55 6.85 0.00 3.18
1964 4890 0.886490 AGTCGGGCTTGCAAGTTCAG 60.886 55.000 26.55 18.71 0.00 3.02
2023 4949 2.450609 AACGTGTGTGACATAGGGAC 57.549 50.000 6.95 0.00 0.00 4.46
2053 4984 4.647564 AGGTGAATTGTGTGATCTCCTT 57.352 40.909 0.00 0.00 34.34 3.36
2077 5008 1.228894 TCTCCCACGTCAGCTCCTT 60.229 57.895 0.00 0.00 0.00 3.36
2081 5012 1.258445 CCCACGTCAGCTCCTTACCT 61.258 60.000 0.00 0.00 0.00 3.08
2083 5014 1.405821 CCACGTCAGCTCCTTACCTAG 59.594 57.143 0.00 0.00 0.00 3.02
2084 5015 1.104630 ACGTCAGCTCCTTACCTAGC 58.895 55.000 0.00 0.00 39.08 3.42
2108 5039 2.496817 CCCAGAGCTAGCACGACC 59.503 66.667 18.83 0.26 0.00 4.79
2138 5069 0.107703 CTACTTCATCAAGCCGCCCA 60.108 55.000 0.00 0.00 32.09 5.36
2141 5072 0.109132 CTTCATCAAGCCGCCCAAAC 60.109 55.000 0.00 0.00 0.00 2.93
2166 5102 0.116143 TTCCCATGGTTTGAAGGGGG 59.884 55.000 11.73 0.00 41.77 5.40
2186 5122 4.812476 TACGCCGCGCATCTTGCT 62.812 61.111 13.88 0.00 42.25 3.91
2193 5129 3.570638 CGCATCTTGCTGGAGCGG 61.571 66.667 0.00 0.00 45.83 5.52
2194 5130 2.437359 GCATCTTGCTGGAGCGGT 60.437 61.111 0.00 0.00 45.83 5.68
2195 5131 2.758089 GCATCTTGCTGGAGCGGTG 61.758 63.158 0.00 0.00 45.83 4.94
2196 5132 1.376424 CATCTTGCTGGAGCGGTGT 60.376 57.895 0.00 0.00 45.83 4.16
2197 5133 1.376424 ATCTTGCTGGAGCGGTGTG 60.376 57.895 0.00 0.00 45.83 3.82
2198 5134 2.116983 ATCTTGCTGGAGCGGTGTGT 62.117 55.000 0.00 0.00 45.83 3.72
2199 5135 2.280797 TTGCTGGAGCGGTGTGTC 60.281 61.111 0.00 0.00 45.83 3.67
2200 5136 2.721971 CTTGCTGGAGCGGTGTGTCT 62.722 60.000 0.00 0.00 45.83 3.41
2201 5137 2.433318 GCTGGAGCGGTGTGTCTC 60.433 66.667 0.00 0.00 0.00 3.36
2202 5138 2.126307 CTGGAGCGGTGTGTCTCG 60.126 66.667 0.00 0.00 0.00 4.04
2203 5139 2.910479 TGGAGCGGTGTGTCTCGT 60.910 61.111 0.00 0.00 0.00 4.18
2204 5140 1.583495 CTGGAGCGGTGTGTCTCGTA 61.583 60.000 0.00 0.00 0.00 3.43
2205 5141 1.154073 GGAGCGGTGTGTCTCGTAC 60.154 63.158 0.00 0.00 0.00 3.67
2206 5142 1.584380 GGAGCGGTGTGTCTCGTACT 61.584 60.000 0.00 0.00 0.00 2.73
2207 5143 0.240411 GAGCGGTGTGTCTCGTACTT 59.760 55.000 0.00 0.00 0.00 2.24
2208 5144 0.672342 AGCGGTGTGTCTCGTACTTT 59.328 50.000 0.00 0.00 0.00 2.66
2209 5145 0.782384 GCGGTGTGTCTCGTACTTTG 59.218 55.000 0.00 0.00 0.00 2.77
2210 5146 1.601162 GCGGTGTGTCTCGTACTTTGA 60.601 52.381 0.00 0.00 0.00 2.69
2211 5147 2.316792 CGGTGTGTCTCGTACTTTGAG 58.683 52.381 0.00 0.00 34.72 3.02
2212 5148 2.059541 GGTGTGTCTCGTACTTTGAGC 58.940 52.381 0.00 0.00 33.41 4.26
2213 5149 2.288273 GGTGTGTCTCGTACTTTGAGCT 60.288 50.000 0.00 0.00 33.41 4.09
2214 5150 2.981140 GTGTGTCTCGTACTTTGAGCTC 59.019 50.000 6.82 6.82 33.41 4.09
2215 5151 2.885266 TGTGTCTCGTACTTTGAGCTCT 59.115 45.455 16.19 0.00 33.41 4.09
2216 5152 4.070009 TGTGTCTCGTACTTTGAGCTCTA 58.930 43.478 16.19 4.09 33.41 2.43
2217 5153 4.083431 TGTGTCTCGTACTTTGAGCTCTAC 60.083 45.833 16.19 7.98 33.41 2.59
2218 5154 4.070009 TGTCTCGTACTTTGAGCTCTACA 58.930 43.478 16.19 0.00 33.41 2.74
2219 5155 4.700692 TGTCTCGTACTTTGAGCTCTACAT 59.299 41.667 16.19 0.37 33.41 2.29
2220 5156 5.031578 GTCTCGTACTTTGAGCTCTACATG 58.968 45.833 16.19 3.11 33.41 3.21
2221 5157 4.096532 TCTCGTACTTTGAGCTCTACATGG 59.903 45.833 16.19 2.11 33.41 3.66
2222 5158 3.762288 TCGTACTTTGAGCTCTACATGGT 59.238 43.478 16.19 7.74 0.00 3.55
2223 5159 3.859961 CGTACTTTGAGCTCTACATGGTG 59.140 47.826 16.19 0.00 0.00 4.17
2224 5160 2.704572 ACTTTGAGCTCTACATGGTGC 58.295 47.619 16.19 0.00 0.00 5.01
2225 5161 1.662629 CTTTGAGCTCTACATGGTGCG 59.337 52.381 16.19 0.00 0.00 5.34
2226 5162 0.108186 TTGAGCTCTACATGGTGCGG 60.108 55.000 16.19 0.00 0.00 5.69
2227 5163 1.884926 GAGCTCTACATGGTGCGGC 60.885 63.158 6.43 0.00 0.00 6.53
2228 5164 2.897350 GCTCTACATGGTGCGGCC 60.897 66.667 0.00 0.00 37.90 6.13
2229 5165 2.586079 CTCTACATGGTGCGGCCG 60.586 66.667 24.05 24.05 41.21 6.13
2230 5166 4.830765 TCTACATGGTGCGGCCGC 62.831 66.667 42.35 42.35 41.21 6.53
2269 5205 1.019278 GTGGCACTGTACATGGACGG 61.019 60.000 15.81 15.81 0.00 4.79
2270 5206 2.106683 GGCACTGTACATGGACGGC 61.107 63.158 17.33 13.18 0.00 5.68
2271 5207 1.079127 GCACTGTACATGGACGGCT 60.079 57.895 17.33 1.49 0.00 5.52
2355 5295 0.323908 AGCAGCGGTAGAAGAGGAGT 60.324 55.000 0.00 0.00 0.00 3.85
2359 5299 1.550976 AGCGGTAGAAGAGGAGTTTGG 59.449 52.381 0.00 0.00 0.00 3.28
2360 5300 1.405661 GCGGTAGAAGAGGAGTTTGGG 60.406 57.143 0.00 0.00 0.00 4.12
2361 5301 1.405661 CGGTAGAAGAGGAGTTTGGGC 60.406 57.143 0.00 0.00 0.00 5.36
2380 5320 1.888512 GCCTGAAGAATTTGAGGTGCA 59.111 47.619 0.00 0.00 32.25 4.57
2384 5324 4.142447 CCTGAAGAATTTGAGGTGCAGATG 60.142 45.833 0.00 0.00 0.00 2.90
2385 5325 4.401022 TGAAGAATTTGAGGTGCAGATGT 58.599 39.130 0.00 0.00 0.00 3.06
2386 5326 5.559770 TGAAGAATTTGAGGTGCAGATGTA 58.440 37.500 0.00 0.00 0.00 2.29
2387 5327 5.412594 TGAAGAATTTGAGGTGCAGATGTAC 59.587 40.000 0.00 0.00 0.00 2.90
2407 5347 3.313012 CCATCTGGTTCAGTTACGACA 57.687 47.619 0.00 0.00 32.61 4.35
2418 5358 1.080772 TTACGACAGACAGGCAGCG 60.081 57.895 0.00 0.00 0.00 5.18
2428 5368 0.391661 ACAGGCAGCGTACAGGAATG 60.392 55.000 0.00 0.00 0.00 2.67
2430 5370 1.078426 GGCAGCGTACAGGAATGGT 60.078 57.895 0.00 0.00 0.00 3.55
2431 5371 0.676782 GGCAGCGTACAGGAATGGTT 60.677 55.000 0.00 0.00 0.00 3.67
2451 5461 2.977914 TCAGCTACAAGGCATCAGAAC 58.022 47.619 0.00 0.00 34.17 3.01
2454 5464 3.077359 AGCTACAAGGCATCAGAACAAC 58.923 45.455 0.00 0.00 34.17 3.32
2460 5470 1.278985 AGGCATCAGAACAACGGATCA 59.721 47.619 0.00 0.00 31.53 2.92
2477 5487 2.315925 TCATCCACCGATTTCAGAGC 57.684 50.000 0.00 0.00 0.00 4.09
2481 5491 0.745845 CCACCGATTTCAGAGCTGGG 60.746 60.000 0.00 0.00 0.00 4.45
2485 5495 2.817423 GATTTCAGAGCTGGGCGCG 61.817 63.158 0.00 0.00 45.59 6.86
2488 5498 3.642778 TTCAGAGCTGGGCGCGTAC 62.643 63.158 8.43 0.80 45.59 3.67
2514 5525 1.599542 GCATCGATGGAGGTTGCTAAC 59.400 52.381 26.00 1.69 0.00 2.34
2516 5527 0.459585 TCGATGGAGGTTGCTAACGC 60.460 55.000 0.00 0.00 0.00 4.84
2520 5531 3.305131 CGATGGAGGTTGCTAACGCTATA 60.305 47.826 0.00 0.00 36.97 1.31
2523 5534 3.639561 TGGAGGTTGCTAACGCTATATGA 59.360 43.478 0.00 0.00 36.97 2.15
2566 5577 5.747197 GTCGAGCGATCTAACAAGGAAAATA 59.253 40.000 0.00 0.00 0.00 1.40
2623 5647 4.821589 GTTCGCCGAGCCCTCAGG 62.822 72.222 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.065371 GGTCAGGATTGCCTATTTTCGTG 59.935 47.826 0.00 0.00 44.80 4.35
45 46 3.113043 AGAACCTGGTAGTGGTAATCCC 58.887 50.000 0.00 0.00 36.69 3.85
50 51 3.428532 GTGAGAGAACCTGGTAGTGGTA 58.571 50.000 0.00 0.00 36.69 3.25
51 52 2.249139 GTGAGAGAACCTGGTAGTGGT 58.751 52.381 0.00 0.00 39.91 4.16
52 53 1.550976 GGTGAGAGAACCTGGTAGTGG 59.449 57.143 0.00 0.00 37.24 4.00
53 54 1.202582 CGGTGAGAGAACCTGGTAGTG 59.797 57.143 0.00 0.00 38.14 2.74
54 55 1.075050 TCGGTGAGAGAACCTGGTAGT 59.925 52.381 0.00 0.00 38.14 2.73
55 56 1.473278 GTCGGTGAGAGAACCTGGTAG 59.527 57.143 0.00 0.00 38.14 3.18
59 60 2.164624 CCTAAGTCGGTGAGAGAACCTG 59.835 54.545 0.00 0.00 38.14 4.00
77 78 1.247260 TGTAGGATGTAGGGCCCCTA 58.753 55.000 21.43 5.04 34.61 3.53
79 80 0.693049 CATGTAGGATGTAGGGCCCC 59.307 60.000 21.43 4.15 0.00 5.80
91 92 7.852945 GCGAGAAAGAAAAATATGACATGTAGG 59.147 37.037 0.00 0.00 0.00 3.18
92 93 8.607459 AGCGAGAAAGAAAAATATGACATGTAG 58.393 33.333 0.00 0.00 0.00 2.74
93 94 8.390354 CAGCGAGAAAGAAAAATATGACATGTA 58.610 33.333 0.00 0.00 0.00 2.29
94 95 7.094634 ACAGCGAGAAAGAAAAATATGACATGT 60.095 33.333 0.00 0.00 0.00 3.21
95 96 7.246311 ACAGCGAGAAAGAAAAATATGACATG 58.754 34.615 0.00 0.00 0.00 3.21
96 97 7.383102 ACAGCGAGAAAGAAAAATATGACAT 57.617 32.000 0.00 0.00 0.00 3.06
97 98 6.801539 ACAGCGAGAAAGAAAAATATGACA 57.198 33.333 0.00 0.00 0.00 3.58
115 116 1.439365 GCTCGAAGCAACAACAGCG 60.439 57.895 2.53 0.00 41.89 5.18
143 152 1.447317 AAGTGCTTGCAACGAGGTGG 61.447 55.000 0.00 0.00 0.00 4.61
144 153 0.317269 CAAGTGCTTGCAACGAGGTG 60.317 55.000 0.00 0.00 33.45 4.00
156 165 2.853290 GCCAACTGCTGCAAGTGCT 61.853 57.895 3.02 0.00 42.66 4.40
161 170 3.121934 CAGTGCCAACTGCTGCAA 58.878 55.556 3.02 0.00 46.98 4.08
196 205 1.001887 GGAACGTTGGGGCATACCA 60.002 57.895 5.00 0.00 42.91 3.25
217 228 3.236003 GACCGGCGGAAAGACACCT 62.236 63.158 35.78 6.20 0.00 4.00
272 308 3.550561 GATCATAGTCTGCTCTCGAACG 58.449 50.000 0.00 0.00 0.00 3.95
276 312 1.198867 CGGGATCATAGTCTGCTCTCG 59.801 57.143 0.00 0.00 37.61 4.04
277 313 1.543802 CCGGGATCATAGTCTGCTCTC 59.456 57.143 0.00 0.00 0.00 3.20
311 2134 0.607620 CAATTTGGTGCACCGGGAAT 59.392 50.000 30.07 24.32 39.43 3.01
336 2159 0.546598 ATCCCGGTCAAGATCAACCC 59.453 55.000 0.00 0.00 31.49 4.11
344 2167 1.831736 ACCTCTGTAATCCCGGTCAAG 59.168 52.381 0.00 0.00 0.00 3.02
350 2173 4.220163 GGTATCCTAACCTCTGTAATCCCG 59.780 50.000 0.00 0.00 36.53 5.14
358 2181 5.509840 CCTGAAATCGGTATCCTAACCTCTG 60.510 48.000 0.00 0.00 37.39 3.35
360 2183 4.262506 CCCTGAAATCGGTATCCTAACCTC 60.263 50.000 0.00 0.00 37.39 3.85
385 2208 3.895041 GGAATTGAACCTCCACCTTTCAA 59.105 43.478 0.00 0.00 42.02 2.69
387 2210 3.496331 TGGAATTGAACCTCCACCTTTC 58.504 45.455 0.00 0.00 36.79 2.62
403 2226 2.444421 ACTCGTAGACCTCGTTGGAAT 58.556 47.619 4.38 0.00 39.71 3.01
406 2229 1.538512 TGAACTCGTAGACCTCGTTGG 59.461 52.381 0.00 0.00 42.93 3.77
408 2231 2.228343 CCTTGAACTCGTAGACCTCGTT 59.772 50.000 0.00 0.00 0.00 3.85
420 2243 9.499585 GTAAAGTCTGTTTTAAACCTTGAACTC 57.500 33.333 5.32 0.00 0.00 3.01
425 2248 6.631636 GCGAGTAAAGTCTGTTTTAAACCTTG 59.368 38.462 5.32 0.00 0.00 3.61
462 2285 1.428912 CCTGCCTCTATCTCCTCCTCT 59.571 57.143 0.00 0.00 0.00 3.69
473 2296 2.041508 CTCCCCTGCCTGCCTCTA 60.042 66.667 0.00 0.00 0.00 2.43
502 2325 1.627879 CCGAAAATGGCAACCGATTG 58.372 50.000 0.00 0.00 38.99 2.67
506 2329 1.211709 GACCCGAAAATGGCAACCG 59.788 57.895 0.00 0.00 0.00 4.44
507 2330 1.211709 CGACCCGAAAATGGCAACC 59.788 57.895 0.00 0.00 0.00 3.77
509 2332 2.631580 GCCGACCCGAAAATGGCAA 61.632 57.895 0.00 0.00 45.06 4.52
531 2354 5.047448 ACAGTCGCTATCATGCTCATATCTT 60.047 40.000 0.00 0.00 0.00 2.40
537 2360 1.067669 GGACAGTCGCTATCATGCTCA 59.932 52.381 0.00 0.00 0.00 4.26
546 2369 1.933500 GCTGAAAACGGACAGTCGCTA 60.934 52.381 0.00 0.00 36.62 4.26
608 2449 0.034337 GTTGGTTGGCTCGTGTCCTA 59.966 55.000 0.00 0.00 0.00 2.94
612 2453 0.534203 ATTCGTTGGTTGGCTCGTGT 60.534 50.000 0.00 0.00 0.00 4.49
692 2550 1.708822 CGTTTTGGCCCTTGTTATGC 58.291 50.000 0.00 0.00 0.00 3.14
760 2665 2.354729 CTGTGGGCCGGGATGAAA 59.645 61.111 2.18 0.00 0.00 2.69
779 2684 2.541556 GAAGAAAAGAGATCCGTCCGG 58.458 52.381 0.00 0.00 0.00 5.14
780 2685 2.541556 GGAAGAAAAGAGATCCGTCCG 58.458 52.381 0.00 0.00 0.00 4.79
810 2738 3.954904 CCTATCCGTGAAGAAGAAGGAGA 59.045 47.826 0.00 0.00 34.14 3.71
813 2741 3.068873 CCTCCTATCCGTGAAGAAGAAGG 59.931 52.174 0.00 0.00 0.00 3.46
822 2750 0.178987 GAGCTCCCTCCTATCCGTGA 60.179 60.000 0.87 0.00 31.68 4.35
890 2841 2.360350 AATGGCAGCCCTGTCGTG 60.360 61.111 9.64 0.00 38.19 4.35
928 2889 2.515523 CTCGCTGCAGGGAATGGG 60.516 66.667 30.43 17.27 36.54 4.00
955 2916 0.611062 TACTGACCTCACCCTCACGG 60.611 60.000 0.00 0.00 37.81 4.94
956 2917 0.811915 CTACTGACCTCACCCTCACG 59.188 60.000 0.00 0.00 0.00 4.35
969 2930 1.211969 GAACGCGGCTGTCTACTGA 59.788 57.895 12.47 0.00 0.00 3.41
970 2931 1.805945 GGAACGCGGCTGTCTACTG 60.806 63.158 12.47 0.00 0.00 2.74
971 2932 1.935327 GAGGAACGCGGCTGTCTACT 61.935 60.000 12.47 0.00 0.00 2.57
972 2933 1.516603 GAGGAACGCGGCTGTCTAC 60.517 63.158 12.47 0.00 0.00 2.59
973 2934 2.707849 GGAGGAACGCGGCTGTCTA 61.708 63.158 12.47 0.00 0.00 2.59
974 2935 4.070552 GGAGGAACGCGGCTGTCT 62.071 66.667 12.47 0.00 0.00 3.41
1059 3179 0.247736 GTAGCTGGGGATAGCCGATG 59.752 60.000 0.00 0.00 44.76 3.84
1150 3310 3.373439 GCTTATGAAGGTGAGCAGAACAG 59.627 47.826 0.00 0.00 35.29 3.16
1167 3327 3.950395 GTGGCATCCTTCTTCTTGCTTAT 59.050 43.478 0.00 0.00 35.46 1.73
1253 3421 1.450531 GATGGCCTGCAGATTTCCGG 61.451 60.000 17.39 0.00 0.00 5.14
1254 3422 1.450531 GGATGGCCTGCAGATTTCCG 61.451 60.000 17.39 0.00 0.00 4.30
1277 3445 1.375140 CCATGGATGGGCTCGATCG 60.375 63.158 5.56 9.36 44.31 3.69
1278 3446 4.709840 CCATGGATGGGCTCGATC 57.290 61.111 5.56 0.00 44.31 3.69
1365 3533 0.790814 GTACTTGCTCTCGGTGCAAC 59.209 55.000 0.00 0.00 44.24 4.17
1366 3534 0.666274 CGTACTTGCTCTCGGTGCAA 60.666 55.000 11.17 11.17 46.48 4.08
1367 3535 1.080772 CGTACTTGCTCTCGGTGCA 60.081 57.895 0.00 0.00 38.80 4.57
1368 3536 1.071567 GACGTACTTGCTCTCGGTGC 61.072 60.000 0.00 0.00 0.00 5.01
1369 3537 0.240145 TGACGTACTTGCTCTCGGTG 59.760 55.000 0.00 0.00 0.00 4.94
1370 3538 0.956633 TTGACGTACTTGCTCTCGGT 59.043 50.000 0.00 0.00 0.00 4.69
1371 3539 1.986378 CTTTGACGTACTTGCTCTCGG 59.014 52.381 0.00 0.00 0.00 4.63
1372 3540 2.657372 GACTTTGACGTACTTGCTCTCG 59.343 50.000 0.00 0.00 0.00 4.04
1390 3558 2.659610 GCTCCTTCCACGCTGACT 59.340 61.111 0.00 0.00 0.00 3.41
1435 3603 4.530857 GCGTGCCCTCCGTATGCT 62.531 66.667 0.00 0.00 36.27 3.79
1489 3657 4.415150 ACGGCCAGGTCCAGCATG 62.415 66.667 2.24 0.00 0.00 4.06
1594 3762 1.298413 CGTCGTCGATCGCCTCATT 60.298 57.895 11.09 0.00 39.71 2.57
1600 3768 2.943034 GTCACCGTCGTCGATCGC 60.943 66.667 11.09 4.79 39.71 4.58
1634 3802 1.308069 ATGTTGCGTTGCTGCCCTAG 61.308 55.000 0.00 0.00 0.00 3.02
1635 3803 1.303236 ATGTTGCGTTGCTGCCCTA 60.303 52.632 0.00 0.00 0.00 3.53
1636 3804 2.598394 ATGTTGCGTTGCTGCCCT 60.598 55.556 0.00 0.00 0.00 5.19
1637 3805 2.126346 GATGTTGCGTTGCTGCCC 60.126 61.111 0.00 0.00 0.00 5.36
1665 3833 0.179124 GAAAAGCACCAACGGCAACA 60.179 50.000 0.00 0.00 0.00 3.33
1699 3879 8.714179 CACCAAACAAGACGTAGAAATAACATA 58.286 33.333 0.00 0.00 0.00 2.29
1700 3880 7.227910 ACACCAAACAAGACGTAGAAATAACAT 59.772 33.333 0.00 0.00 0.00 2.71
1703 3883 7.066043 ACAACACCAAACAAGACGTAGAAATAA 59.934 33.333 0.00 0.00 0.00 1.40
1704 3884 6.539464 ACAACACCAAACAAGACGTAGAAATA 59.461 34.615 0.00 0.00 0.00 1.40
1713 3899 2.666022 GTGCAACAACACCAAACAAGAC 59.334 45.455 0.00 0.00 36.32 3.01
1726 3912 3.057019 GACTGACACTATCGTGCAACAA 58.943 45.455 0.00 0.00 45.10 2.83
1798 4719 6.121590 TGGTGAATCAAATGCTAGATGCTTA 58.878 36.000 0.00 0.00 43.37 3.09
1808 4729 9.722056 CTAACTTAACTATGGTGAATCAAATGC 57.278 33.333 0.00 0.00 0.00 3.56
1860 4781 1.784062 GCATCTGCAGACGTGACAC 59.216 57.895 20.97 0.00 41.59 3.67
1873 4794 4.469227 AGAGTTTCACCTGTAGATGCATCT 59.531 41.667 30.85 30.85 40.86 2.90
1891 4812 1.141053 ACTTGCCCTCGTTTCAGAGTT 59.859 47.619 0.00 0.00 36.56 3.01
1892 4813 0.759346 ACTTGCCCTCGTTTCAGAGT 59.241 50.000 0.00 0.00 36.56 3.24
1893 4814 1.801178 GAACTTGCCCTCGTTTCAGAG 59.199 52.381 0.00 0.00 37.97 3.35
1894 4815 1.140052 TGAACTTGCCCTCGTTTCAGA 59.860 47.619 0.00 0.00 0.00 3.27
1895 4816 1.532868 CTGAACTTGCCCTCGTTTCAG 59.467 52.381 0.00 0.00 0.00 3.02
1896 4817 1.140052 TCTGAACTTGCCCTCGTTTCA 59.860 47.619 0.00 0.00 0.00 2.69
1897 4818 1.531578 GTCTGAACTTGCCCTCGTTTC 59.468 52.381 0.00 0.00 0.00 2.78
1898 4819 1.141053 AGTCTGAACTTGCCCTCGTTT 59.859 47.619 0.00 0.00 28.74 3.60
1958 4884 1.141019 ACACACACGCGTCTGAACT 59.859 52.632 21.59 0.00 0.00 3.01
1959 4885 1.272715 CACACACACGCGTCTGAAC 59.727 57.895 21.59 0.00 0.00 3.18
1960 4886 2.521771 GCACACACACGCGTCTGAA 61.522 57.895 21.59 0.00 0.00 3.02
1961 4887 2.959599 GCACACACACGCGTCTGA 60.960 61.111 21.59 0.00 0.00 3.27
1962 4888 4.000557 GGCACACACACGCGTCTG 62.001 66.667 9.86 11.84 0.00 3.51
2023 4949 2.286833 ACACAATTCACCTTCGTTGTCG 59.713 45.455 0.00 0.00 32.87 4.35
2053 4984 3.596799 TGACGTGGGAGAGGGGGA 61.597 66.667 0.00 0.00 0.00 4.81
2077 5008 1.142465 CTCTGGGGTCGTAGCTAGGTA 59.858 57.143 12.88 0.00 0.00 3.08
2081 5012 0.841961 TAGCTCTGGGGTCGTAGCTA 59.158 55.000 0.00 0.00 43.29 3.32
2083 5014 2.034607 CTAGCTCTGGGGTCGTAGC 58.965 63.158 0.00 0.00 35.16 3.58
2084 5015 0.752009 TGCTAGCTCTGGGGTCGTAG 60.752 60.000 17.23 0.00 0.00 3.51
2085 5016 1.035932 GTGCTAGCTCTGGGGTCGTA 61.036 60.000 17.23 0.00 0.00 3.43
2086 5017 2.037367 TGCTAGCTCTGGGGTCGT 59.963 61.111 17.23 0.00 0.00 4.34
2087 5018 2.496817 GTGCTAGCTCTGGGGTCG 59.503 66.667 17.23 0.00 0.00 4.79
2088 5019 2.052690 TCGTGCTAGCTCTGGGGTC 61.053 63.158 17.23 0.00 0.00 4.46
2089 5020 2.037367 TCGTGCTAGCTCTGGGGT 59.963 61.111 17.23 0.00 0.00 4.95
2090 5021 2.496817 GTCGTGCTAGCTCTGGGG 59.503 66.667 17.23 0.00 0.00 4.96
2108 5039 2.186076 GATGAAGTAGTCGCCTGAACG 58.814 52.381 0.00 0.00 0.00 3.95
2138 5069 0.469144 AACCATGGGAAGCCGTGTTT 60.469 50.000 18.09 0.00 0.00 2.83
2141 5072 0.893270 TCAAACCATGGGAAGCCGTG 60.893 55.000 18.09 3.15 0.00 4.94
2166 5102 2.661866 AAGATGCGCGGCGTATCC 60.662 61.111 37.44 24.64 46.87 2.59
2167 5103 2.546321 CAAGATGCGCGGCGTATC 59.454 61.111 35.53 35.53 46.25 2.24
2180 5116 2.031012 CACACCGCTCCAGCAAGA 59.969 61.111 0.00 0.00 42.21 3.02
2186 5122 1.601477 TACGAGACACACCGCTCCA 60.601 57.895 0.00 0.00 0.00 3.86
2192 5128 2.059541 GCTCAAAGTACGAGACACACC 58.940 52.381 0.00 0.00 31.84 4.16
2193 5129 2.981140 GAGCTCAAAGTACGAGACACAC 59.019 50.000 9.40 0.00 31.84 3.82
2194 5130 2.885266 AGAGCTCAAAGTACGAGACACA 59.115 45.455 17.77 0.00 31.84 3.72
2195 5131 3.562567 AGAGCTCAAAGTACGAGACAC 57.437 47.619 17.77 0.00 31.84 3.67
2196 5132 4.070009 TGTAGAGCTCAAAGTACGAGACA 58.930 43.478 17.77 1.32 31.84 3.41
2197 5133 4.681835 TGTAGAGCTCAAAGTACGAGAC 57.318 45.455 17.77 0.00 31.84 3.36
2198 5134 4.096532 CCATGTAGAGCTCAAAGTACGAGA 59.903 45.833 17.77 0.00 31.84 4.04
2199 5135 4.142359 ACCATGTAGAGCTCAAAGTACGAG 60.142 45.833 17.77 6.03 0.00 4.18
2200 5136 3.762288 ACCATGTAGAGCTCAAAGTACGA 59.238 43.478 17.77 1.66 0.00 3.43
2201 5137 3.859961 CACCATGTAGAGCTCAAAGTACG 59.140 47.826 17.77 0.00 0.00 3.67
2202 5138 3.619038 GCACCATGTAGAGCTCAAAGTAC 59.381 47.826 17.77 10.06 0.00 2.73
2203 5139 3.676049 CGCACCATGTAGAGCTCAAAGTA 60.676 47.826 17.77 0.00 0.00 2.24
2204 5140 2.704572 GCACCATGTAGAGCTCAAAGT 58.295 47.619 17.77 1.23 0.00 2.66
2205 5141 1.662629 CGCACCATGTAGAGCTCAAAG 59.337 52.381 17.77 0.55 0.00 2.77
2206 5142 1.675714 CCGCACCATGTAGAGCTCAAA 60.676 52.381 17.77 0.00 0.00 2.69
2207 5143 0.108186 CCGCACCATGTAGAGCTCAA 60.108 55.000 17.77 0.82 0.00 3.02
2208 5144 1.517361 CCGCACCATGTAGAGCTCA 59.483 57.895 17.77 0.00 0.00 4.26
2209 5145 1.884926 GCCGCACCATGTAGAGCTC 60.885 63.158 5.27 5.27 0.00 4.09
2210 5146 2.187946 GCCGCACCATGTAGAGCT 59.812 61.111 0.00 0.00 0.00 4.09
2211 5147 2.897350 GGCCGCACCATGTAGAGC 60.897 66.667 0.00 0.00 38.86 4.09
2212 5148 2.586079 CGGCCGCACCATGTAGAG 60.586 66.667 14.67 0.00 39.03 2.43
2213 5149 4.830765 GCGGCCGCACCATGTAGA 62.831 66.667 43.55 0.00 41.49 2.59
2228 5164 3.907260 ATGGTGACCCAGCTGTGCG 62.907 63.158 13.81 1.87 46.15 5.34
2229 5165 2.034687 ATGGTGACCCAGCTGTGC 59.965 61.111 13.81 1.74 46.15 4.57
2230 5166 1.742880 CGATGGTGACCCAGCTGTG 60.743 63.158 13.81 3.15 45.24 3.66
2231 5167 2.217038 ACGATGGTGACCCAGCTGT 61.217 57.895 13.81 0.00 45.24 4.40
2232 5168 1.742880 CACGATGGTGACCCAGCTG 60.743 63.158 6.78 6.78 45.24 4.24
2248 5184 1.156736 GTCCATGTACAGTGCCACAC 58.843 55.000 0.33 0.00 34.10 3.82
2249 5185 0.320334 CGTCCATGTACAGTGCCACA 60.320 55.000 0.33 1.01 0.00 4.17
2269 5205 2.037136 AGCCACATCGCAGTGAAGC 61.037 57.895 8.39 4.87 42.05 3.86
2270 5206 1.792301 CAGCCACATCGCAGTGAAG 59.208 57.895 8.39 0.00 42.05 3.02
2271 5207 2.327343 GCAGCCACATCGCAGTGAA 61.327 57.895 8.39 0.00 42.05 3.18
2329 5269 3.288092 TCTTCTACCGCTGCTCTGAATA 58.712 45.455 0.00 0.00 0.00 1.75
2355 5295 2.899256 CCTCAAATTCTTCAGGCCCAAA 59.101 45.455 0.00 0.00 0.00 3.28
2359 5299 1.203287 GCACCTCAAATTCTTCAGGCC 59.797 52.381 0.00 0.00 0.00 5.19
2360 5300 1.888512 TGCACCTCAAATTCTTCAGGC 59.111 47.619 0.00 0.00 0.00 4.85
2361 5301 3.415212 TCTGCACCTCAAATTCTTCAGG 58.585 45.455 0.00 0.00 0.00 3.86
2387 5327 3.056821 TCTGTCGTAACTGAACCAGATGG 60.057 47.826 0.00 0.00 42.17 3.51
2388 5328 3.921021 GTCTGTCGTAACTGAACCAGATG 59.079 47.826 0.45 0.00 35.44 2.90
2389 5329 3.572682 TGTCTGTCGTAACTGAACCAGAT 59.427 43.478 0.45 0.00 35.44 2.90
2390 5330 2.953648 TGTCTGTCGTAACTGAACCAGA 59.046 45.455 0.45 0.00 35.44 3.86
2391 5331 3.309388 CTGTCTGTCGTAACTGAACCAG 58.691 50.000 0.00 0.00 35.44 4.00
2392 5332 2.035449 CCTGTCTGTCGTAACTGAACCA 59.965 50.000 0.00 0.00 35.44 3.67
2393 5333 2.673833 CCTGTCTGTCGTAACTGAACC 58.326 52.381 0.00 0.00 35.44 3.62
2407 5347 1.185618 TTCCTGTACGCTGCCTGTCT 61.186 55.000 0.00 0.00 0.00 3.41
2418 5358 4.202245 TGTAGCTGAACCATTCCTGTAC 57.798 45.455 0.00 0.00 0.00 2.90
2428 5368 2.012673 CTGATGCCTTGTAGCTGAACC 58.987 52.381 0.00 0.00 0.00 3.62
2430 5370 3.244526 TGTTCTGATGCCTTGTAGCTGAA 60.245 43.478 0.00 0.00 0.00 3.02
2431 5371 2.302733 TGTTCTGATGCCTTGTAGCTGA 59.697 45.455 0.00 0.00 0.00 4.26
2451 5461 1.953559 AATCGGTGGATGATCCGTTG 58.046 50.000 7.03 0.00 45.88 4.10
2454 5464 2.138320 CTGAAATCGGTGGATGATCCG 58.862 52.381 7.03 0.00 46.93 4.18
2460 5470 1.134280 CCAGCTCTGAAATCGGTGGAT 60.134 52.381 6.96 0.00 46.37 3.41
2469 5479 2.938086 TACGCGCCCAGCTCTGAAA 61.938 57.895 5.73 0.00 45.59 2.69
2481 5491 3.977568 GATGCAGCTCGTACGCGC 61.978 66.667 21.96 21.96 38.14 6.86
2485 5495 0.030773 TCCATCGATGCAGCTCGTAC 59.969 55.000 20.25 0.00 39.62 3.67
2488 5498 1.664017 CCTCCATCGATGCAGCTCG 60.664 63.158 20.25 1.10 39.99 5.03
2516 5527 1.148310 CAAGGCCGCGGTTCATATAG 58.852 55.000 28.70 5.11 0.00 1.31
2520 5531 4.344865 ACCAAGGCCGCGGTTCAT 62.345 61.111 28.70 9.85 28.43 2.57
2566 5577 2.954318 AGCACTTTCTGAATGTTGCTGT 59.046 40.909 21.00 8.40 0.00 4.40


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

AutoCloner maintained by Alex Coulton.