Multiple sequence alignment - TraesCS2A01G205200

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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 TraesCS2A01G205200 chr2A 100.000 2567 0 0 1 2567 182889102 182891668 0.000000e+00 4741.0
1 TraesCS2A01G205200 chr2A 98.909 275 3 0 2075 2349 447006451 447006725 2.290000e-135 492.0
2 TraesCS2A01G205200 chr2A 84.298 121 14 3 1929 2049 549956895 549956780 2.090000e-21 113.0
3 TraesCS2A01G205200 chr2D 92.873 1824 77 32 272 2075 167706504 167704714 0.000000e+00 2599.0
4 TraesCS2A01G205200 chr2D 96.043 278 11 0 2072 2349 625246461 625246738 1.080000e-123 453.0
5 TraesCS2A01G205200 chr2D 91.575 273 9 3 3 263 167706817 167706547 5.220000e-97 364.0
6 TraesCS2A01G205200 chr2D 95.370 216 10 0 2348 2563 167704717 167704502 6.800000e-91 344.0
7 TraesCS2A01G205200 chr2D 86.290 124 12 2 1926 2049 469717407 469717289 2.070000e-26 130.0
8 TraesCS2A01G205200 chr2D 94.118 51 3 0 381 431 167706427 167706377 7.620000e-11 78.7
9 TraesCS2A01G205200 chr2B 88.323 2158 85 64 3 2075 230282556 230284631 0.000000e+00 2435.0
10 TraesCS2A01G205200 chr2B 90.566 212 11 4 2348 2555 230284628 230284834 3.250000e-69 272.0
11 TraesCS2A01G205200 chr4B 97.818 275 6 0 2075 2349 300941974 300942248 2.310000e-130 475.0
12 TraesCS2A01G205200 chrUn 97.455 275 7 0 2075 2349 288038219 288038493 1.080000e-128 470.0
13 TraesCS2A01G205200 chr7B 97.122 278 8 0 2072 2349 553109867 553110144 1.080000e-128 470.0
14 TraesCS2A01G205200 chr1B 96.043 278 11 0 2075 2352 345769542 345769265 1.080000e-123 453.0
15 TraesCS2A01G205200 chr4A 95.714 280 12 0 2075 2354 452593008 452592729 3.890000e-123 451.0
16 TraesCS2A01G205200 chr5B 95.088 285 13 1 2069 2352 110116378 110116094 5.040000e-122 448.0
17 TraesCS2A01G205200 chr3A 93.878 294 16 2 2069 2360 20324017 20323724 2.340000e-120 442.0
18 TraesCS2A01G205200 chr1D 88.710 124 9 2 1926 2049 464831400 464831282 2.060000e-31 147.0
19 TraesCS2A01G205200 chr5A 83.065 124 17 2 1926 2049 546795124 546795005 2.700000e-20 110.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G205200 chr2A 182889102 182891668 2566 False 4741.000 4741 100.0000 1 2567 1 chr2A.!!$F1 2566
1 TraesCS2A01G205200 chr2D 167704502 167706817 2315 True 846.425 2599 93.4840 3 2563 4 chr2D.!!$R2 2560
2 TraesCS2A01G205200 chr2B 230282556 230284834 2278 False 1353.500 2435 89.4445 3 2555 2 chr2B.!!$F1 2552


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
436 498 0.104487 TCCCGTTTCGTGTGCAGTAA 59.896 50.0 0.0 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2210 2318 0.029834 CACATAGCGCTTCCCAATGC 59.97 55.0 18.68 0.0 0.0 3.56 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
168 191 3.394062 CCGCGGCGCAAACAAAAG 61.394 61.111 32.61 12.47 0.00 2.27
173 196 1.061276 GCGGCGCAAACAAAAGAAAAA 59.939 42.857 29.21 0.00 0.00 1.94
174 197 2.286125 GCGGCGCAAACAAAAGAAAAAT 60.286 40.909 29.21 0.00 0.00 1.82
178 201 3.279126 CGCAAACAAAAGAAAAATGGCG 58.721 40.909 0.00 0.00 34.66 5.69
275 312 2.488952 GAGGATCTCCATCGAAAAGGC 58.511 52.381 0.00 0.00 38.89 4.35
280 317 1.369091 CTCCATCGAAAAGGCCACGG 61.369 60.000 5.01 0.00 0.00 4.94
308 366 0.875059 CAGCTTTCCTCCGTTGGTTC 59.125 55.000 0.00 0.00 0.00 3.62
366 428 0.879090 ATTTGCTTCCCGTTTCGTCC 59.121 50.000 0.00 0.00 0.00 4.79
383 445 2.197605 CCCGTCCGGTTGCCTTTTT 61.198 57.895 0.00 0.00 0.00 1.94
399 461 3.059120 CCTTTTTCTTCCCGTTTCGTCTC 60.059 47.826 0.00 0.00 0.00 3.36
435 497 0.319211 CTCCCGTTTCGTGTGCAGTA 60.319 55.000 0.00 0.00 0.00 2.74
436 498 0.104487 TCCCGTTTCGTGTGCAGTAA 59.896 50.000 0.00 0.00 0.00 2.24
437 499 1.153353 CCCGTTTCGTGTGCAGTAAT 58.847 50.000 0.00 0.00 0.00 1.89
451 513 0.401738 AGTAATGCAGTGCAGGTGGT 59.598 50.000 24.20 2.71 43.65 4.16
452 514 0.523072 GTAATGCAGTGCAGGTGGTG 59.477 55.000 24.20 0.00 43.65 4.17
515 577 1.065273 GCCGAGCCATCTGCATTTG 59.935 57.895 0.00 0.00 44.83 2.32
682 744 2.038426 CCAGTACTGTCCCAACATGTGA 59.962 50.000 21.18 0.00 34.13 3.58
685 747 2.727123 ACTGTCCCAACATGTGAACA 57.273 45.000 0.00 0.92 34.13 3.18
709 771 1.559682 ACCCACATGTCATCCCTACAC 59.440 52.381 0.00 0.00 0.00 2.90
712 774 3.454447 CCCACATGTCATCCCTACACTAA 59.546 47.826 0.00 0.00 0.00 2.24
715 777 5.070981 CCACATGTCATCCCTACACTAATCT 59.929 44.000 0.00 0.00 0.00 2.40
720 797 3.570125 TCATCCCTACACTAATCTCGCAG 59.430 47.826 0.00 0.00 0.00 5.18
731 810 6.145696 ACACTAATCTCGCAGTTCAAGTTAAC 59.854 38.462 0.00 0.00 0.00 2.01
732 811 6.145534 CACTAATCTCGCAGTTCAAGTTAACA 59.854 38.462 8.61 0.00 0.00 2.41
733 812 4.992381 ATCTCGCAGTTCAAGTTAACAC 57.008 40.909 8.61 0.00 0.00 3.32
734 813 3.787785 TCTCGCAGTTCAAGTTAACACA 58.212 40.909 8.61 0.00 0.00 3.72
735 814 3.554324 TCTCGCAGTTCAAGTTAACACAC 59.446 43.478 8.61 0.00 0.00 3.82
737 816 3.554324 TCGCAGTTCAAGTTAACACACTC 59.446 43.478 8.61 0.00 0.00 3.51
738 817 3.555956 CGCAGTTCAAGTTAACACACTCT 59.444 43.478 8.61 0.00 0.00 3.24
739 818 4.743151 CGCAGTTCAAGTTAACACACTCTA 59.257 41.667 8.61 0.00 0.00 2.43
740 819 5.332355 CGCAGTTCAAGTTAACACACTCTAC 60.332 44.000 8.61 0.00 0.00 2.59
741 820 5.753921 GCAGTTCAAGTTAACACACTCTACT 59.246 40.000 8.61 0.00 0.00 2.57
742 821 6.921857 GCAGTTCAAGTTAACACACTCTACTA 59.078 38.462 8.61 0.00 0.00 1.82
743 822 7.599245 GCAGTTCAAGTTAACACACTCTACTAT 59.401 37.037 8.61 0.00 0.00 2.12
773 853 5.471556 TTAATTGGACAGTAGGACAACGA 57.528 39.130 0.00 0.00 0.00 3.85
795 876 3.386486 ACGAACAATCAGTGAAGCGTAA 58.614 40.909 0.00 0.00 32.88 3.18
796 877 3.805422 ACGAACAATCAGTGAAGCGTAAA 59.195 39.130 0.00 0.00 32.88 2.01
797 878 4.271533 ACGAACAATCAGTGAAGCGTAAAA 59.728 37.500 0.00 0.00 32.88 1.52
830 912 1.553706 ACATTCTACCGTCCTTCCGT 58.446 50.000 0.00 0.00 0.00 4.69
831 913 1.897802 ACATTCTACCGTCCTTCCGTT 59.102 47.619 0.00 0.00 0.00 4.44
832 914 2.094338 ACATTCTACCGTCCTTCCGTTC 60.094 50.000 0.00 0.00 0.00 3.95
833 915 0.890683 TTCTACCGTCCTTCCGTTCC 59.109 55.000 0.00 0.00 0.00 3.62
834 916 1.138247 CTACCGTCCTTCCGTTCCG 59.862 63.158 0.00 0.00 0.00 4.30
835 917 1.589716 CTACCGTCCTTCCGTTCCGT 61.590 60.000 0.00 0.00 0.00 4.69
902 984 4.217767 GGAACAAGAATAAAACCGGAAGCT 59.782 41.667 9.46 0.00 0.00 3.74
1107 1203 3.217743 GCCGTCCTCTACCTCCCG 61.218 72.222 0.00 0.00 0.00 5.14
1110 1206 3.902086 GTCCTCTACCTCCCGCGC 61.902 72.222 0.00 0.00 0.00 6.86
1222 1318 0.263468 GACCCTAGCTCCTCCTCCTT 59.737 60.000 0.00 0.00 0.00 3.36
1224 1320 0.471022 CCCTAGCTCCTCCTCCTTCC 60.471 65.000 0.00 0.00 0.00 3.46
1625 1730 1.326245 GCGTTGGCTTTGACAAAAACC 59.674 47.619 11.17 11.17 29.78 3.27
1680 1785 4.031878 CGAGTGCCGTTCTTTATTCTCTTC 59.968 45.833 0.00 0.00 0.00 2.87
1697 1805 8.900983 ATTCTCTTCATTACTTAGATGCTTCC 57.099 34.615 0.00 0.00 0.00 3.46
1808 1916 3.334691 TGGCGAGTTTAGTTTGATCCTG 58.665 45.455 0.00 0.00 0.00 3.86
1816 1924 7.483580 AGTTTAGTTTGATCCTGCTACTACT 57.516 36.000 0.00 0.00 0.00 2.57
1817 1925 7.908453 AGTTTAGTTTGATCCTGCTACTACTT 58.092 34.615 0.00 0.00 0.00 2.24
1919 2027 2.935201 CCAAGCATCTTGAGCTAGTGTC 59.065 50.000 8.04 0.00 42.53 3.67
1949 2057 0.456221 AGCACTACAAGATCGTCCGG 59.544 55.000 0.00 0.00 0.00 5.14
2049 2157 6.580041 CAGATTGTGCTTGAGTTTCATGTTAC 59.420 38.462 0.00 0.00 0.00 2.50
2050 2158 4.466567 TGTGCTTGAGTTTCATGTTACG 57.533 40.909 0.00 0.00 0.00 3.18
2052 2160 4.754618 TGTGCTTGAGTTTCATGTTACGAT 59.245 37.500 0.00 0.00 0.00 3.73
2053 2161 5.929415 TGTGCTTGAGTTTCATGTTACGATA 59.071 36.000 0.00 0.00 0.00 2.92
2075 2183 5.528043 AGATAGCTTGGTGATACACTGAG 57.472 43.478 0.00 0.00 34.40 3.35
2076 2184 4.343526 AGATAGCTTGGTGATACACTGAGG 59.656 45.833 0.00 0.00 34.40 3.86
2077 2185 1.065854 AGCTTGGTGATACACTGAGGC 60.066 52.381 0.00 0.00 34.40 4.70
2078 2186 1.065854 GCTTGGTGATACACTGAGGCT 60.066 52.381 0.00 0.00 34.40 4.58
2079 2187 2.625737 CTTGGTGATACACTGAGGCTG 58.374 52.381 0.00 0.00 34.40 4.85
2080 2188 0.904649 TGGTGATACACTGAGGCTGG 59.095 55.000 0.00 0.00 34.40 4.85
2081 2189 0.905357 GGTGATACACTGAGGCTGGT 59.095 55.000 0.00 0.00 34.40 4.00
2082 2190 1.134670 GGTGATACACTGAGGCTGGTC 60.135 57.143 0.00 0.00 34.40 4.02
2083 2191 1.550524 GTGATACACTGAGGCTGGTCA 59.449 52.381 0.00 0.00 0.00 4.02
2084 2192 2.169352 GTGATACACTGAGGCTGGTCAT 59.831 50.000 0.00 0.00 0.00 3.06
2085 2193 3.384789 GTGATACACTGAGGCTGGTCATA 59.615 47.826 0.00 0.00 0.00 2.15
2086 2194 3.638627 TGATACACTGAGGCTGGTCATAG 59.361 47.826 0.00 0.00 0.00 2.23
2087 2195 1.944177 ACACTGAGGCTGGTCATAGT 58.056 50.000 0.00 0.00 0.00 2.12
2088 2196 1.552337 ACACTGAGGCTGGTCATAGTG 59.448 52.381 0.00 0.00 31.88 2.74
2089 2197 1.134580 CACTGAGGCTGGTCATAGTGG 60.135 57.143 0.00 0.00 0.00 4.00
2090 2198 1.273267 ACTGAGGCTGGTCATAGTGGA 60.273 52.381 0.00 0.00 0.00 4.02
2091 2199 1.411977 CTGAGGCTGGTCATAGTGGAG 59.588 57.143 0.00 0.00 0.00 3.86
2092 2200 1.007118 TGAGGCTGGTCATAGTGGAGA 59.993 52.381 0.00 0.00 0.00 3.71
2093 2201 1.686052 GAGGCTGGTCATAGTGGAGAG 59.314 57.143 0.00 0.00 0.00 3.20
2094 2202 1.007721 AGGCTGGTCATAGTGGAGAGT 59.992 52.381 0.00 0.00 0.00 3.24
2095 2203 2.245028 AGGCTGGTCATAGTGGAGAGTA 59.755 50.000 0.00 0.00 0.00 2.59
2096 2204 3.031736 GGCTGGTCATAGTGGAGAGTAA 58.968 50.000 0.00 0.00 0.00 2.24
2097 2205 3.181474 GGCTGGTCATAGTGGAGAGTAAC 60.181 52.174 0.00 0.00 0.00 2.50
2098 2206 3.702045 GCTGGTCATAGTGGAGAGTAACT 59.298 47.826 0.00 0.00 0.00 2.24
2099 2207 4.160626 GCTGGTCATAGTGGAGAGTAACTT 59.839 45.833 0.00 0.00 0.00 2.66
2100 2208 5.360144 GCTGGTCATAGTGGAGAGTAACTTA 59.640 44.000 0.00 0.00 0.00 2.24
2101 2209 6.460399 GCTGGTCATAGTGGAGAGTAACTTAG 60.460 46.154 0.00 0.00 0.00 2.18
2102 2210 6.728411 TGGTCATAGTGGAGAGTAACTTAGA 58.272 40.000 0.00 0.00 0.00 2.10
2103 2211 6.602406 TGGTCATAGTGGAGAGTAACTTAGAC 59.398 42.308 0.00 0.00 32.58 2.59
2104 2212 6.829811 GGTCATAGTGGAGAGTAACTTAGACT 59.170 42.308 0.00 0.00 33.27 3.24
2105 2213 7.992033 GGTCATAGTGGAGAGTAACTTAGACTA 59.008 40.741 0.00 0.00 33.27 2.59
2106 2214 9.048446 GTCATAGTGGAGAGTAACTTAGACTAG 57.952 40.741 0.00 0.00 31.58 2.57
2107 2215 8.770322 TCATAGTGGAGAGTAACTTAGACTAGT 58.230 37.037 0.00 0.00 0.00 2.57
2110 2218 8.791327 AGTGGAGAGTAACTTAGACTAGTAAC 57.209 38.462 0.00 0.00 0.00 2.50
2111 2219 8.381636 AGTGGAGAGTAACTTAGACTAGTAACA 58.618 37.037 0.00 0.00 0.00 2.41
2112 2220 9.176460 GTGGAGAGTAACTTAGACTAGTAACAT 57.824 37.037 0.00 0.00 0.00 2.71
2113 2221 9.175312 TGGAGAGTAACTTAGACTAGTAACATG 57.825 37.037 0.00 0.00 0.00 3.21
2114 2222 9.176460 GGAGAGTAACTTAGACTAGTAACATGT 57.824 37.037 0.00 0.00 0.00 3.21
2151 2259 9.756571 AGTCTATATTACTACCTTCATAGTGGG 57.243 37.037 0.00 0.00 36.09 4.61
2152 2260 9.531158 GTCTATATTACTACCTTCATAGTGGGT 57.469 37.037 0.00 0.00 36.09 4.51
2162 2270 9.702253 CTACCTTCATAGTGGGTAGTATCATAT 57.298 37.037 9.46 0.00 44.30 1.78
2168 2276 9.421399 TCATAGTGGGTAGTATCATATATGTGG 57.579 37.037 12.42 0.00 0.00 4.17
2169 2277 9.201989 CATAGTGGGTAGTATCATATATGTGGT 57.798 37.037 12.42 0.00 0.00 4.16
2172 2280 9.032624 AGTGGGTAGTATCATATATGTGGTAAC 57.967 37.037 12.42 7.05 0.00 2.50
2211 2319 8.519492 TTTATTGCTTTGTAGACTCATTTTGC 57.481 30.769 0.00 0.00 0.00 3.68
2212 2320 5.512753 TTGCTTTGTAGACTCATTTTGCA 57.487 34.783 0.00 0.00 0.00 4.08
2213 2321 5.710513 TGCTTTGTAGACTCATTTTGCAT 57.289 34.783 0.00 0.00 0.00 3.96
2214 2322 6.088016 TGCTTTGTAGACTCATTTTGCATT 57.912 33.333 0.00 0.00 0.00 3.56
2215 2323 5.921976 TGCTTTGTAGACTCATTTTGCATTG 59.078 36.000 0.00 0.00 0.00 2.82
2216 2324 5.346822 GCTTTGTAGACTCATTTTGCATTGG 59.653 40.000 0.00 0.00 0.00 3.16
2217 2325 5.389859 TTGTAGACTCATTTTGCATTGGG 57.610 39.130 0.00 0.00 0.00 4.12
2218 2326 4.661222 TGTAGACTCATTTTGCATTGGGA 58.339 39.130 0.00 0.00 0.00 4.37
2219 2327 5.076182 TGTAGACTCATTTTGCATTGGGAA 58.924 37.500 0.00 0.00 0.00 3.97
2220 2328 4.796038 AGACTCATTTTGCATTGGGAAG 57.204 40.909 0.00 0.00 0.00 3.46
2221 2329 3.056322 AGACTCATTTTGCATTGGGAAGC 60.056 43.478 0.00 0.00 0.00 3.86
2222 2330 2.264813 CTCATTTTGCATTGGGAAGCG 58.735 47.619 0.00 0.00 0.00 4.68
2223 2331 0.722848 CATTTTGCATTGGGAAGCGC 59.277 50.000 0.00 0.00 0.00 5.92
2224 2332 0.609662 ATTTTGCATTGGGAAGCGCT 59.390 45.000 2.64 2.64 0.00 5.92
2225 2333 1.252175 TTTTGCATTGGGAAGCGCTA 58.748 45.000 12.05 0.00 0.00 4.26
2226 2334 1.473258 TTTGCATTGGGAAGCGCTAT 58.527 45.000 12.05 0.00 0.00 2.97
2227 2335 0.740149 TTGCATTGGGAAGCGCTATG 59.260 50.000 12.05 11.94 34.15 2.23
2228 2336 0.394216 TGCATTGGGAAGCGCTATGT 60.394 50.000 12.05 0.00 33.74 2.29
2229 2337 0.029834 GCATTGGGAAGCGCTATGTG 59.970 55.000 12.05 5.56 33.74 3.21
2230 2338 1.667236 CATTGGGAAGCGCTATGTGA 58.333 50.000 12.05 0.00 0.00 3.58
2231 2339 2.224606 CATTGGGAAGCGCTATGTGAT 58.775 47.619 12.05 0.00 0.00 3.06
2232 2340 1.667236 TTGGGAAGCGCTATGTGATG 58.333 50.000 12.05 0.00 0.00 3.07
2233 2341 0.179048 TGGGAAGCGCTATGTGATGG 60.179 55.000 12.05 0.00 0.00 3.51
2234 2342 0.179045 GGGAAGCGCTATGTGATGGT 60.179 55.000 12.05 0.00 0.00 3.55
2235 2343 1.070134 GGGAAGCGCTATGTGATGGTA 59.930 52.381 12.05 0.00 0.00 3.25
2236 2344 2.484770 GGGAAGCGCTATGTGATGGTAA 60.485 50.000 12.05 0.00 0.00 2.85
2237 2345 2.544267 GGAAGCGCTATGTGATGGTAAC 59.456 50.000 12.05 0.00 0.00 2.50
2266 2374 8.540507 TTATGTTACTCTATTTGCCTCTCTCT 57.459 34.615 0.00 0.00 0.00 3.10
2267 2375 6.859112 TGTTACTCTATTTGCCTCTCTCTT 57.141 37.500 0.00 0.00 0.00 2.85
2268 2376 6.868622 TGTTACTCTATTTGCCTCTCTCTTC 58.131 40.000 0.00 0.00 0.00 2.87
2269 2377 6.437477 TGTTACTCTATTTGCCTCTCTCTTCA 59.563 38.462 0.00 0.00 0.00 3.02
2270 2378 7.124901 TGTTACTCTATTTGCCTCTCTCTTCAT 59.875 37.037 0.00 0.00 0.00 2.57
2271 2379 6.558488 ACTCTATTTGCCTCTCTCTTCATT 57.442 37.500 0.00 0.00 0.00 2.57
2272 2380 7.667575 ACTCTATTTGCCTCTCTCTTCATTA 57.332 36.000 0.00 0.00 0.00 1.90
2273 2381 8.083828 ACTCTATTTGCCTCTCTCTTCATTAA 57.916 34.615 0.00 0.00 0.00 1.40
2274 2382 7.984617 ACTCTATTTGCCTCTCTCTTCATTAAC 59.015 37.037 0.00 0.00 0.00 2.01
2275 2383 8.083828 TCTATTTGCCTCTCTCTTCATTAACT 57.916 34.615 0.00 0.00 0.00 2.24
2276 2384 9.201989 TCTATTTGCCTCTCTCTTCATTAACTA 57.798 33.333 0.00 0.00 0.00 2.24
2277 2385 9.823647 CTATTTGCCTCTCTCTTCATTAACTAA 57.176 33.333 0.00 0.00 0.00 2.24
2279 2387 9.692325 ATTTGCCTCTCTCTTCATTAACTAATT 57.308 29.630 0.00 0.00 0.00 1.40
2280 2388 8.498054 TTGCCTCTCTCTTCATTAACTAATTG 57.502 34.615 0.00 0.00 0.00 2.32
2281 2389 6.540189 TGCCTCTCTCTTCATTAACTAATTGC 59.460 38.462 0.00 0.00 0.00 3.56
2282 2390 6.017523 GCCTCTCTCTTCATTAACTAATTGCC 60.018 42.308 0.00 0.00 0.00 4.52
2283 2391 7.050377 CCTCTCTCTTCATTAACTAATTGCCA 58.950 38.462 0.00 0.00 0.00 4.92
2284 2392 7.011857 CCTCTCTCTTCATTAACTAATTGCCAC 59.988 40.741 0.00 0.00 0.00 5.01
2285 2393 6.823689 TCTCTCTTCATTAACTAATTGCCACC 59.176 38.462 0.00 0.00 0.00 4.61
2286 2394 6.721318 TCTCTTCATTAACTAATTGCCACCT 58.279 36.000 0.00 0.00 0.00 4.00
2287 2395 6.823689 TCTCTTCATTAACTAATTGCCACCTC 59.176 38.462 0.00 0.00 0.00 3.85
2288 2396 6.480763 TCTTCATTAACTAATTGCCACCTCA 58.519 36.000 0.00 0.00 0.00 3.86
2289 2397 7.118723 TCTTCATTAACTAATTGCCACCTCAT 58.881 34.615 0.00 0.00 0.00 2.90
2290 2398 6.942532 TCATTAACTAATTGCCACCTCATC 57.057 37.500 0.00 0.00 0.00 2.92
2291 2399 6.422333 TCATTAACTAATTGCCACCTCATCA 58.578 36.000 0.00 0.00 0.00 3.07
2292 2400 6.318648 TCATTAACTAATTGCCACCTCATCAC 59.681 38.462 0.00 0.00 0.00 3.06
2293 2401 4.307032 AACTAATTGCCACCTCATCACT 57.693 40.909 0.00 0.00 0.00 3.41
2294 2402 4.307032 ACTAATTGCCACCTCATCACTT 57.693 40.909 0.00 0.00 0.00 3.16
2295 2403 4.666512 ACTAATTGCCACCTCATCACTTT 58.333 39.130 0.00 0.00 0.00 2.66
2296 2404 5.079643 ACTAATTGCCACCTCATCACTTTT 58.920 37.500 0.00 0.00 0.00 2.27
2297 2405 3.947910 ATTGCCACCTCATCACTTTTG 57.052 42.857 0.00 0.00 0.00 2.44
2298 2406 0.961019 TGCCACCTCATCACTTTTGC 59.039 50.000 0.00 0.00 0.00 3.68
2299 2407 1.251251 GCCACCTCATCACTTTTGCT 58.749 50.000 0.00 0.00 0.00 3.91
2300 2408 1.615392 GCCACCTCATCACTTTTGCTT 59.385 47.619 0.00 0.00 0.00 3.91
2301 2409 2.608752 GCCACCTCATCACTTTTGCTTG 60.609 50.000 0.00 0.00 0.00 4.01
2302 2410 2.624838 CCACCTCATCACTTTTGCTTGT 59.375 45.455 0.00 0.00 0.00 3.16
2303 2411 3.551454 CCACCTCATCACTTTTGCTTGTG 60.551 47.826 0.00 0.00 35.68 3.33
2304 2412 3.067180 CACCTCATCACTTTTGCTTGTGT 59.933 43.478 0.00 0.00 35.82 3.72
2305 2413 3.067180 ACCTCATCACTTTTGCTTGTGTG 59.933 43.478 0.00 0.00 35.82 3.82
2306 2414 3.551454 CCTCATCACTTTTGCTTGTGTGG 60.551 47.826 0.00 0.00 35.82 4.17
2307 2415 2.129607 CATCACTTTTGCTTGTGTGGC 58.870 47.619 0.00 0.00 35.82 5.01
2308 2416 1.180907 TCACTTTTGCTTGTGTGGCA 58.819 45.000 0.00 0.00 37.97 4.92
2309 2417 1.755959 TCACTTTTGCTTGTGTGGCAT 59.244 42.857 0.00 0.00 39.54 4.40
2310 2418 2.129607 CACTTTTGCTTGTGTGGCATC 58.870 47.619 0.00 0.00 39.54 3.91
2311 2419 2.034124 ACTTTTGCTTGTGTGGCATCT 58.966 42.857 0.00 0.00 39.54 2.90
2312 2420 3.004629 CACTTTTGCTTGTGTGGCATCTA 59.995 43.478 0.00 0.00 39.54 1.98
2313 2421 3.636300 ACTTTTGCTTGTGTGGCATCTAA 59.364 39.130 0.00 0.00 39.54 2.10
2314 2422 3.921119 TTTGCTTGTGTGGCATCTAAG 57.079 42.857 0.00 0.00 39.54 2.18
2315 2423 2.566833 TGCTTGTGTGGCATCTAAGT 57.433 45.000 0.00 0.00 34.56 2.24
2316 2424 2.862541 TGCTTGTGTGGCATCTAAGTT 58.137 42.857 0.00 0.00 34.56 2.66
2317 2425 4.014569 TGCTTGTGTGGCATCTAAGTTA 57.985 40.909 0.00 0.00 34.56 2.24
2318 2426 3.751175 TGCTTGTGTGGCATCTAAGTTAC 59.249 43.478 0.00 0.00 34.56 2.50
2319 2427 4.003648 GCTTGTGTGGCATCTAAGTTACT 58.996 43.478 0.00 0.00 0.00 2.24
2320 2428 5.175859 GCTTGTGTGGCATCTAAGTTACTA 58.824 41.667 0.00 0.00 0.00 1.82
2321 2429 5.063564 GCTTGTGTGGCATCTAAGTTACTAC 59.936 44.000 0.00 0.00 0.00 2.73
2322 2430 5.080969 TGTGTGGCATCTAAGTTACTACC 57.919 43.478 0.00 0.00 0.00 3.18
2323 2431 4.775780 TGTGTGGCATCTAAGTTACTACCT 59.224 41.667 0.00 0.00 0.00 3.08
2324 2432 5.953548 TGTGTGGCATCTAAGTTACTACCTA 59.046 40.000 0.00 0.00 0.00 3.08
2325 2433 6.610020 TGTGTGGCATCTAAGTTACTACCTAT 59.390 38.462 0.00 0.00 0.00 2.57
2326 2434 6.924060 GTGTGGCATCTAAGTTACTACCTATG 59.076 42.308 0.00 0.00 0.00 2.23
2327 2435 6.610020 TGTGGCATCTAAGTTACTACCTATGT 59.390 38.462 0.00 0.00 0.00 2.29
2328 2436 7.125204 TGTGGCATCTAAGTTACTACCTATGTT 59.875 37.037 0.00 0.00 0.00 2.71
2329 2437 8.636213 GTGGCATCTAAGTTACTACCTATGTTA 58.364 37.037 0.00 0.00 0.00 2.41
2330 2438 8.636213 TGGCATCTAAGTTACTACCTATGTTAC 58.364 37.037 0.00 0.00 0.00 2.50
2331 2439 8.858094 GGCATCTAAGTTACTACCTATGTTACT 58.142 37.037 0.00 0.00 0.00 2.24
2332 2440 9.896263 GCATCTAAGTTACTACCTATGTTACTC 57.104 37.037 0.00 0.00 0.00 2.59
2334 2442 8.986929 TCTAAGTTACTACCTATGTTACTCCC 57.013 38.462 0.00 0.00 0.00 4.30
2335 2443 8.560039 TCTAAGTTACTACCTATGTTACTCCCA 58.440 37.037 0.00 0.00 0.00 4.37
2336 2444 7.415592 AAGTTACTACCTATGTTACTCCCAC 57.584 40.000 0.00 0.00 0.00 4.61
2337 2445 6.739664 AGTTACTACCTATGTTACTCCCACT 58.260 40.000 0.00 0.00 0.00 4.00
2338 2446 7.876371 AGTTACTACCTATGTTACTCCCACTA 58.124 38.462 0.00 0.00 0.00 2.74
2339 2447 8.509441 AGTTACTACCTATGTTACTCCCACTAT 58.491 37.037 0.00 0.00 0.00 2.12
2340 2448 8.574737 GTTACTACCTATGTTACTCCCACTATG 58.425 40.741 0.00 0.00 0.00 2.23
2341 2449 6.919158 ACTACCTATGTTACTCCCACTATGA 58.081 40.000 0.00 0.00 0.00 2.15
2342 2450 6.776603 ACTACCTATGTTACTCCCACTATGAC 59.223 42.308 0.00 0.00 0.00 3.06
2343 2451 4.900054 ACCTATGTTACTCCCACTATGACC 59.100 45.833 0.00 0.00 0.00 4.02
2344 2452 4.899457 CCTATGTTACTCCCACTATGACCA 59.101 45.833 0.00 0.00 0.00 4.02
2345 2453 5.011125 CCTATGTTACTCCCACTATGACCAG 59.989 48.000 0.00 0.00 0.00 4.00
2346 2454 2.500098 TGTTACTCCCACTATGACCAGC 59.500 50.000 0.00 0.00 0.00 4.85
2347 2455 1.789523 TACTCCCACTATGACCAGCC 58.210 55.000 0.00 0.00 0.00 4.85
2348 2456 0.043334 ACTCCCACTATGACCAGCCT 59.957 55.000 0.00 0.00 0.00 4.58
2349 2457 0.467384 CTCCCACTATGACCAGCCTG 59.533 60.000 0.00 0.00 0.00 4.85
2350 2458 0.042581 TCCCACTATGACCAGCCTGA 59.957 55.000 0.00 0.00 0.00 3.86
2385 2493 3.066481 GCTGCTTGGATCTGGAGAAAATC 59.934 47.826 0.00 0.00 0.00 2.17
2417 2525 2.741517 TGGCGACACATGTGTAAAGATG 59.258 45.455 30.63 16.51 45.05 2.90
2419 2527 2.095853 GCGACACATGTGTAAAGATGGG 59.904 50.000 30.63 13.21 45.05 4.00
2477 2585 3.857052 TGCTCACGAAATTAGGTCGATT 58.143 40.909 5.09 0.00 41.02 3.34
2515 2627 1.630369 ACTCCTGCTGTGCCATCTAAA 59.370 47.619 0.00 0.00 0.00 1.85
2556 2668 2.961424 GCTGCTTTGCCTCCCTTTA 58.039 52.632 0.00 0.00 0.00 1.85
2563 2675 4.705023 TGCTTTGCCTCCCTTTAGAAATAC 59.295 41.667 0.00 0.00 0.00 1.89
2564 2676 4.705023 GCTTTGCCTCCCTTTAGAAATACA 59.295 41.667 0.00 0.00 0.00 2.29
2565 2677 5.360999 GCTTTGCCTCCCTTTAGAAATACAT 59.639 40.000 0.00 0.00 0.00 2.29
2566 2678 6.546034 GCTTTGCCTCCCTTTAGAAATACATA 59.454 38.462 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.708051 CTCAGGTCAGGTCGTACTGTA 58.292 52.381 8.51 0.00 39.48 2.74
1 2 1.535833 CTCAGGTCAGGTCGTACTGT 58.464 55.000 8.51 0.00 39.48 3.55
178 201 3.781162 GTTAACGTGTCGGGGCGC 61.781 66.667 0.00 0.00 0.00 6.53
235 259 2.410469 GTATCCGTCACCCGTCGG 59.590 66.667 3.60 3.60 46.93 4.79
280 317 2.436824 GGAAAGCTGACGGGCCTC 60.437 66.667 0.84 0.00 0.00 4.70
366 428 1.170290 AGAAAAAGGCAACCGGACGG 61.170 55.000 9.46 9.56 42.03 4.79
383 445 0.239347 GACGAGACGAAACGGGAAGA 59.761 55.000 0.00 0.00 0.00 2.87
399 461 1.574702 GAGGAAAAGGCAACCGGACG 61.575 60.000 9.46 0.00 37.17 4.79
435 497 1.904865 CCACCACCTGCACTGCATT 60.905 57.895 3.64 0.00 38.13 3.56
436 498 2.282674 CCACCACCTGCACTGCAT 60.283 61.111 3.64 0.00 38.13 3.96
642 704 4.202441 CTGGGGAAATTGACCAGTATCTG 58.798 47.826 12.74 0.00 45.21 2.90
685 747 0.552848 GGGATGACATGTGGGTCCAT 59.447 55.000 1.15 0.00 36.97 3.41
709 771 6.145534 TGTGTTAACTTGAACTGCGAGATTAG 59.854 38.462 7.22 0.00 0.00 1.73
712 774 4.211374 GTGTGTTAACTTGAACTGCGAGAT 59.789 41.667 7.22 0.00 0.00 2.75
715 777 3.527533 AGTGTGTTAACTTGAACTGCGA 58.472 40.909 7.22 0.00 0.00 5.10
763 843 3.979948 TGATTGTTCGTTCGTTGTCCTA 58.020 40.909 0.00 0.00 0.00 2.94
773 853 2.210116 ACGCTTCACTGATTGTTCGTT 58.790 42.857 0.00 0.00 0.00 3.85
795 876 5.066968 AGAATGTTGTGTTCAAACCGTTT 57.933 34.783 0.00 0.00 35.20 3.60
796 877 4.712122 AGAATGTTGTGTTCAAACCGTT 57.288 36.364 0.00 0.00 35.20 4.44
797 878 4.035909 GGTAGAATGTTGTGTTCAAACCGT 59.964 41.667 0.00 0.00 35.20 4.83
804 886 3.660865 AGGACGGTAGAATGTTGTGTTC 58.339 45.455 0.00 0.00 0.00 3.18
830 912 2.048597 CTGCAGGTACGCACGGAA 60.049 61.111 5.57 0.00 36.86 4.30
831 913 2.089887 TTTCTGCAGGTACGCACGGA 62.090 55.000 15.13 0.00 36.86 4.69
832 914 1.225376 TTTTCTGCAGGTACGCACGG 61.225 55.000 15.13 0.00 36.86 4.94
833 915 0.584396 TTTTTCTGCAGGTACGCACG 59.416 50.000 15.13 0.00 36.86 5.34
902 984 1.442184 GCAAACGAGACGAGCGAGA 60.442 57.895 0.00 0.00 0.00 4.04
963 1050 5.303165 AGTGTAGTAGTGGTTAAAGCCAAC 58.697 41.667 0.00 0.00 40.68 3.77
980 1072 1.481871 TTAAGGCGGGAGGAGTGTAG 58.518 55.000 0.00 0.00 0.00 2.74
981 1073 1.941377 TTTAAGGCGGGAGGAGTGTA 58.059 50.000 0.00 0.00 0.00 2.90
982 1074 1.065418 CATTTAAGGCGGGAGGAGTGT 60.065 52.381 0.00 0.00 0.00 3.55
1110 1206 3.972971 GAGCAGCTGCAGGAGTGGG 62.973 68.421 38.24 0.00 45.16 4.61
1113 1209 2.607134 AGGAGCAGCTGCAGGAGT 60.607 61.111 38.24 19.47 45.16 3.85
1209 1305 2.370633 GGGGAAGGAGGAGGAGCT 59.629 66.667 0.00 0.00 0.00 4.09
1298 1394 2.731691 GAACACGCTCTGGGGCTTCA 62.732 60.000 0.00 0.00 0.00 3.02
1625 1730 4.027458 CGCCGAATCAGCAAAATGTATTTG 60.027 41.667 0.00 0.00 0.00 2.32
1680 1785 4.454678 TGCAGGGAAGCATCTAAGTAATG 58.545 43.478 0.00 0.00 40.11 1.90
1693 1801 2.880890 GCCTATGTACATTGCAGGGAAG 59.119 50.000 20.07 7.84 0.00 3.46
1694 1802 2.509548 AGCCTATGTACATTGCAGGGAA 59.490 45.455 23.81 2.51 0.00 3.97
1695 1803 2.126882 AGCCTATGTACATTGCAGGGA 58.873 47.619 23.81 3.15 0.00 4.20
1696 1804 2.224606 CAGCCTATGTACATTGCAGGG 58.775 52.381 23.81 15.37 0.00 4.45
1697 1805 2.224606 CCAGCCTATGTACATTGCAGG 58.775 52.381 23.81 21.80 0.00 4.85
1808 1916 6.647895 TGGCACAAAAACTAGTAAGTAGTAGC 59.352 38.462 0.00 0.00 36.63 3.58
1919 2027 8.508062 ACGATCTTGTAGTGCTAATCATAGTAG 58.492 37.037 0.00 0.00 0.00 2.57
2049 2157 6.072452 TCAGTGTATCACCAAGCTATCTATCG 60.072 42.308 0.00 0.00 34.49 2.92
2050 2158 7.220741 TCAGTGTATCACCAAGCTATCTATC 57.779 40.000 0.00 0.00 34.49 2.08
2052 2160 5.536538 CCTCAGTGTATCACCAAGCTATCTA 59.463 44.000 0.00 0.00 34.49 1.98
2053 2161 4.343526 CCTCAGTGTATCACCAAGCTATCT 59.656 45.833 0.00 0.00 34.49 1.98
2075 2183 1.490574 ACTCTCCACTATGACCAGCC 58.509 55.000 0.00 0.00 0.00 4.85
2076 2184 3.702045 AGTTACTCTCCACTATGACCAGC 59.298 47.826 0.00 0.00 0.00 4.85
2077 2185 5.923733 AAGTTACTCTCCACTATGACCAG 57.076 43.478 0.00 0.00 0.00 4.00
2078 2186 6.602406 GTCTAAGTTACTCTCCACTATGACCA 59.398 42.308 0.00 0.00 0.00 4.02
2079 2187 6.829811 AGTCTAAGTTACTCTCCACTATGACC 59.170 42.308 0.00 0.00 31.22 4.02
2080 2188 7.868906 AGTCTAAGTTACTCTCCACTATGAC 57.131 40.000 0.00 0.00 0.00 3.06
2081 2189 8.770322 ACTAGTCTAAGTTACTCTCCACTATGA 58.230 37.037 0.00 0.00 0.00 2.15
2082 2190 8.967664 ACTAGTCTAAGTTACTCTCCACTATG 57.032 38.462 0.00 0.00 0.00 2.23
2084 2192 9.883142 GTTACTAGTCTAAGTTACTCTCCACTA 57.117 37.037 0.00 0.00 0.00 2.74
2085 2193 8.381636 TGTTACTAGTCTAAGTTACTCTCCACT 58.618 37.037 0.00 0.00 31.82 4.00
2086 2194 8.558973 TGTTACTAGTCTAAGTTACTCTCCAC 57.441 38.462 0.00 0.00 31.82 4.02
2087 2195 9.175312 CATGTTACTAGTCTAAGTTACTCTCCA 57.825 37.037 0.00 0.00 31.82 3.86
2088 2196 9.176460 ACATGTTACTAGTCTAAGTTACTCTCC 57.824 37.037 0.00 0.00 31.82 3.71
2125 2233 9.756571 CCCACTATGAAGGTAGTAATATAGACT 57.243 37.037 0.00 0.00 33.29 3.24
2126 2234 9.531158 ACCCACTATGAAGGTAGTAATATAGAC 57.469 37.037 0.00 0.00 33.29 2.59
2142 2250 9.421399 CCACATATATGATACTACCCACTATGA 57.579 37.037 19.63 0.00 0.00 2.15
2143 2251 9.201989 ACCACATATATGATACTACCCACTATG 57.798 37.037 19.63 1.97 0.00 2.23
2146 2254 9.032624 GTTACCACATATATGATACTACCCACT 57.967 37.037 19.63 0.00 0.00 4.00
2147 2255 8.809066 TGTTACCACATATATGATACTACCCAC 58.191 37.037 19.63 4.89 0.00 4.61
2148 2256 8.959676 TGTTACCACATATATGATACTACCCA 57.040 34.615 19.63 3.75 0.00 4.51
2185 2293 9.143631 GCAAAATGAGTCTACAAAGCAATAAAT 57.856 29.630 0.00 0.00 0.00 1.40
2186 2294 8.140628 TGCAAAATGAGTCTACAAAGCAATAAA 58.859 29.630 0.00 0.00 0.00 1.40
2187 2295 7.656412 TGCAAAATGAGTCTACAAAGCAATAA 58.344 30.769 0.00 0.00 0.00 1.40
2188 2296 7.213216 TGCAAAATGAGTCTACAAAGCAATA 57.787 32.000 0.00 0.00 0.00 1.90
2189 2297 6.088016 TGCAAAATGAGTCTACAAAGCAAT 57.912 33.333 0.00 0.00 0.00 3.56
2190 2298 5.512753 TGCAAAATGAGTCTACAAAGCAA 57.487 34.783 0.00 0.00 0.00 3.91
2191 2299 5.710513 ATGCAAAATGAGTCTACAAAGCA 57.289 34.783 0.00 0.00 0.00 3.91
2192 2300 5.346822 CCAATGCAAAATGAGTCTACAAAGC 59.653 40.000 0.00 0.00 0.00 3.51
2193 2301 5.865552 CCCAATGCAAAATGAGTCTACAAAG 59.134 40.000 0.00 0.00 0.00 2.77
2194 2302 5.538053 TCCCAATGCAAAATGAGTCTACAAA 59.462 36.000 0.00 0.00 0.00 2.83
2195 2303 5.076182 TCCCAATGCAAAATGAGTCTACAA 58.924 37.500 0.00 0.00 0.00 2.41
2196 2304 4.661222 TCCCAATGCAAAATGAGTCTACA 58.339 39.130 0.00 0.00 0.00 2.74
2197 2305 5.643379 TTCCCAATGCAAAATGAGTCTAC 57.357 39.130 0.00 0.00 0.00 2.59
2198 2306 4.158394 GCTTCCCAATGCAAAATGAGTCTA 59.842 41.667 0.00 0.00 0.00 2.59
2199 2307 3.056322 GCTTCCCAATGCAAAATGAGTCT 60.056 43.478 0.00 0.00 0.00 3.24
2200 2308 3.256558 GCTTCCCAATGCAAAATGAGTC 58.743 45.455 0.00 0.00 0.00 3.36
2201 2309 2.353011 CGCTTCCCAATGCAAAATGAGT 60.353 45.455 0.00 0.00 0.00 3.41
2202 2310 2.264813 CGCTTCCCAATGCAAAATGAG 58.735 47.619 0.00 0.00 0.00 2.90
2203 2311 1.672441 GCGCTTCCCAATGCAAAATGA 60.672 47.619 0.00 0.00 0.00 2.57
2204 2312 0.722848 GCGCTTCCCAATGCAAAATG 59.277 50.000 0.00 0.00 0.00 2.32
2205 2313 0.609662 AGCGCTTCCCAATGCAAAAT 59.390 45.000 2.64 0.00 0.00 1.82
2206 2314 1.252175 TAGCGCTTCCCAATGCAAAA 58.748 45.000 18.68 0.00 0.00 2.44
2207 2315 1.134753 CATAGCGCTTCCCAATGCAAA 59.865 47.619 18.68 0.00 0.00 3.68
2208 2316 0.740149 CATAGCGCTTCCCAATGCAA 59.260 50.000 18.68 0.00 0.00 4.08
2209 2317 0.394216 ACATAGCGCTTCCCAATGCA 60.394 50.000 18.68 0.00 0.00 3.96
2210 2318 0.029834 CACATAGCGCTTCCCAATGC 59.970 55.000 18.68 0.00 0.00 3.56
2211 2319 1.667236 TCACATAGCGCTTCCCAATG 58.333 50.000 18.68 15.83 0.00 2.82
2212 2320 2.224606 CATCACATAGCGCTTCCCAAT 58.775 47.619 18.68 0.00 0.00 3.16
2213 2321 1.667236 CATCACATAGCGCTTCCCAA 58.333 50.000 18.68 0.00 0.00 4.12
2214 2322 0.179048 CCATCACATAGCGCTTCCCA 60.179 55.000 18.68 0.00 0.00 4.37
2215 2323 0.179045 ACCATCACATAGCGCTTCCC 60.179 55.000 18.68 0.00 0.00 3.97
2216 2324 2.526304 TACCATCACATAGCGCTTCC 57.474 50.000 18.68 0.00 0.00 3.46
2217 2325 3.194861 TGTTACCATCACATAGCGCTTC 58.805 45.455 18.68 0.00 0.00 3.86
2218 2326 3.260475 TGTTACCATCACATAGCGCTT 57.740 42.857 18.68 0.00 0.00 4.68
2219 2327 2.979814 TGTTACCATCACATAGCGCT 57.020 45.000 17.26 17.26 0.00 5.92
2220 2328 5.862924 AATATGTTACCATCACATAGCGC 57.137 39.130 0.00 0.00 39.83 5.92
2221 2329 8.479313 ACATAATATGTTACCATCACATAGCG 57.521 34.615 0.00 0.00 41.63 4.26
2240 2348 9.153479 AGAGAGAGGCAAATAGAGTAACATAAT 57.847 33.333 0.00 0.00 0.00 1.28
2241 2349 8.540507 AGAGAGAGGCAAATAGAGTAACATAA 57.459 34.615 0.00 0.00 0.00 1.90
2242 2350 8.540507 AAGAGAGAGGCAAATAGAGTAACATA 57.459 34.615 0.00 0.00 0.00 2.29
2243 2351 7.124901 TGAAGAGAGAGGCAAATAGAGTAACAT 59.875 37.037 0.00 0.00 0.00 2.71
2244 2352 6.437477 TGAAGAGAGAGGCAAATAGAGTAACA 59.563 38.462 0.00 0.00 0.00 2.41
2245 2353 6.868622 TGAAGAGAGAGGCAAATAGAGTAAC 58.131 40.000 0.00 0.00 0.00 2.50
2246 2354 7.667575 ATGAAGAGAGAGGCAAATAGAGTAA 57.332 36.000 0.00 0.00 0.00 2.24
2247 2355 7.667575 AATGAAGAGAGAGGCAAATAGAGTA 57.332 36.000 0.00 0.00 0.00 2.59
2248 2356 6.558488 AATGAAGAGAGAGGCAAATAGAGT 57.442 37.500 0.00 0.00 0.00 3.24
2249 2357 8.203485 AGTTAATGAAGAGAGAGGCAAATAGAG 58.797 37.037 0.00 0.00 0.00 2.43
2250 2358 8.083828 AGTTAATGAAGAGAGAGGCAAATAGA 57.916 34.615 0.00 0.00 0.00 1.98
2251 2359 9.823647 TTAGTTAATGAAGAGAGAGGCAAATAG 57.176 33.333 0.00 0.00 0.00 1.73
2253 2361 9.692325 AATTAGTTAATGAAGAGAGAGGCAAAT 57.308 29.630 0.00 0.00 0.00 2.32
2254 2362 8.950210 CAATTAGTTAATGAAGAGAGAGGCAAA 58.050 33.333 0.00 0.00 0.00 3.68
2255 2363 7.066284 GCAATTAGTTAATGAAGAGAGAGGCAA 59.934 37.037 0.00 0.00 0.00 4.52
2256 2364 6.540189 GCAATTAGTTAATGAAGAGAGAGGCA 59.460 38.462 0.00 0.00 0.00 4.75
2257 2365 6.017523 GGCAATTAGTTAATGAAGAGAGAGGC 60.018 42.308 0.00 0.00 0.00 4.70
2258 2366 7.011857 GTGGCAATTAGTTAATGAAGAGAGAGG 59.988 40.741 0.00 0.00 0.00 3.69
2259 2367 7.011857 GGTGGCAATTAGTTAATGAAGAGAGAG 59.988 40.741 0.00 0.00 0.00 3.20
2260 2368 6.823689 GGTGGCAATTAGTTAATGAAGAGAGA 59.176 38.462 0.00 0.00 0.00 3.10
2261 2369 6.825721 AGGTGGCAATTAGTTAATGAAGAGAG 59.174 38.462 0.00 0.00 0.00 3.20
2262 2370 6.721318 AGGTGGCAATTAGTTAATGAAGAGA 58.279 36.000 0.00 0.00 0.00 3.10
2263 2371 6.599244 TGAGGTGGCAATTAGTTAATGAAGAG 59.401 38.462 0.00 0.00 0.00 2.85
2264 2372 6.480763 TGAGGTGGCAATTAGTTAATGAAGA 58.519 36.000 0.00 0.00 0.00 2.87
2265 2373 6.757897 TGAGGTGGCAATTAGTTAATGAAG 57.242 37.500 0.00 0.00 0.00 3.02
2266 2374 6.889177 TGATGAGGTGGCAATTAGTTAATGAA 59.111 34.615 0.00 0.00 0.00 2.57
2267 2375 6.318648 GTGATGAGGTGGCAATTAGTTAATGA 59.681 38.462 0.00 0.00 0.00 2.57
2268 2376 6.319658 AGTGATGAGGTGGCAATTAGTTAATG 59.680 38.462 0.00 0.00 0.00 1.90
2269 2377 6.426587 AGTGATGAGGTGGCAATTAGTTAAT 58.573 36.000 0.00 0.00 0.00 1.40
2270 2378 5.815581 AGTGATGAGGTGGCAATTAGTTAA 58.184 37.500 0.00 0.00 0.00 2.01
2271 2379 5.435686 AGTGATGAGGTGGCAATTAGTTA 57.564 39.130 0.00 0.00 0.00 2.24
2272 2380 4.307032 AGTGATGAGGTGGCAATTAGTT 57.693 40.909 0.00 0.00 0.00 2.24
2273 2381 4.307032 AAGTGATGAGGTGGCAATTAGT 57.693 40.909 0.00 0.00 0.00 2.24
2274 2382 5.404946 CAAAAGTGATGAGGTGGCAATTAG 58.595 41.667 0.00 0.00 0.00 1.73
2275 2383 4.321899 GCAAAAGTGATGAGGTGGCAATTA 60.322 41.667 0.00 0.00 0.00 1.40
2276 2384 3.555586 GCAAAAGTGATGAGGTGGCAATT 60.556 43.478 0.00 0.00 0.00 2.32
2277 2385 2.028748 GCAAAAGTGATGAGGTGGCAAT 60.029 45.455 0.00 0.00 0.00 3.56
2278 2386 1.340889 GCAAAAGTGATGAGGTGGCAA 59.659 47.619 0.00 0.00 0.00 4.52
2279 2387 0.961019 GCAAAAGTGATGAGGTGGCA 59.039 50.000 0.00 0.00 0.00 4.92
2280 2388 1.251251 AGCAAAAGTGATGAGGTGGC 58.749 50.000 0.00 0.00 0.00 5.01
2281 2389 2.624838 ACAAGCAAAAGTGATGAGGTGG 59.375 45.455 0.00 0.00 0.00 4.61
2282 2390 3.067180 ACACAAGCAAAAGTGATGAGGTG 59.933 43.478 0.00 0.00 39.03 4.00
2283 2391 3.067180 CACACAAGCAAAAGTGATGAGGT 59.933 43.478 0.00 0.00 39.03 3.85
2284 2392 3.551454 CCACACAAGCAAAAGTGATGAGG 60.551 47.826 0.00 0.00 39.03 3.86
2285 2393 3.635331 CCACACAAGCAAAAGTGATGAG 58.365 45.455 0.00 0.00 39.03 2.90
2286 2394 2.223782 GCCACACAAGCAAAAGTGATGA 60.224 45.455 0.00 0.00 39.03 2.92
2287 2395 2.129607 GCCACACAAGCAAAAGTGATG 58.870 47.619 0.00 0.00 39.03 3.07
2288 2396 1.755959 TGCCACACAAGCAAAAGTGAT 59.244 42.857 0.00 0.00 37.28 3.06
2289 2397 1.180907 TGCCACACAAGCAAAAGTGA 58.819 45.000 0.00 0.00 37.28 3.41
2290 2398 2.129607 GATGCCACACAAGCAAAAGTG 58.870 47.619 0.00 0.00 44.83 3.16
2291 2399 2.034124 AGATGCCACACAAGCAAAAGT 58.966 42.857 0.00 0.00 44.83 2.66
2292 2400 2.806608 AGATGCCACACAAGCAAAAG 57.193 45.000 0.00 0.00 44.83 2.27
2293 2401 3.636300 ACTTAGATGCCACACAAGCAAAA 59.364 39.130 0.00 0.00 44.83 2.44
2294 2402 3.221771 ACTTAGATGCCACACAAGCAAA 58.778 40.909 0.00 0.00 44.83 3.68
2295 2403 2.862541 ACTTAGATGCCACACAAGCAA 58.137 42.857 0.00 0.00 44.83 3.91
2296 2404 2.566833 ACTTAGATGCCACACAAGCA 57.433 45.000 0.00 0.00 45.94 3.91
2297 2405 4.003648 AGTAACTTAGATGCCACACAAGC 58.996 43.478 0.00 0.00 0.00 4.01
2298 2406 5.581085 GGTAGTAACTTAGATGCCACACAAG 59.419 44.000 0.00 0.00 0.00 3.16
2299 2407 5.247564 AGGTAGTAACTTAGATGCCACACAA 59.752 40.000 0.00 0.00 0.00 3.33
2300 2408 4.775780 AGGTAGTAACTTAGATGCCACACA 59.224 41.667 0.00 0.00 0.00 3.72
2301 2409 5.340439 AGGTAGTAACTTAGATGCCACAC 57.660 43.478 0.00 0.00 0.00 3.82
2302 2410 6.610020 ACATAGGTAGTAACTTAGATGCCACA 59.390 38.462 0.00 0.00 0.00 4.17
2303 2411 7.052142 ACATAGGTAGTAACTTAGATGCCAC 57.948 40.000 0.00 0.00 0.00 5.01
2304 2412 7.670605 AACATAGGTAGTAACTTAGATGCCA 57.329 36.000 0.00 0.00 0.00 4.92
2305 2413 8.858094 AGTAACATAGGTAGTAACTTAGATGCC 58.142 37.037 0.00 0.00 0.00 4.40
2306 2414 9.896263 GAGTAACATAGGTAGTAACTTAGATGC 57.104 37.037 0.00 0.00 0.00 3.91
2308 2416 9.585369 GGGAGTAACATAGGTAGTAACTTAGAT 57.415 37.037 0.00 0.00 0.00 1.98
2309 2417 8.560039 TGGGAGTAACATAGGTAGTAACTTAGA 58.440 37.037 0.00 0.00 0.00 2.10
2310 2418 8.628280 GTGGGAGTAACATAGGTAGTAACTTAG 58.372 40.741 0.00 0.00 0.00 2.18
2311 2419 8.339247 AGTGGGAGTAACATAGGTAGTAACTTA 58.661 37.037 0.00 0.00 0.00 2.24
2312 2420 7.187676 AGTGGGAGTAACATAGGTAGTAACTT 58.812 38.462 0.00 0.00 0.00 2.66
2313 2421 6.739664 AGTGGGAGTAACATAGGTAGTAACT 58.260 40.000 0.00 0.00 0.00 2.24
2314 2422 8.574737 CATAGTGGGAGTAACATAGGTAGTAAC 58.425 40.741 0.00 0.00 0.00 2.50
2315 2423 8.505246 TCATAGTGGGAGTAACATAGGTAGTAA 58.495 37.037 0.00 0.00 0.00 2.24
2316 2424 7.941238 GTCATAGTGGGAGTAACATAGGTAGTA 59.059 40.741 0.00 0.00 0.00 1.82
2317 2425 6.776603 GTCATAGTGGGAGTAACATAGGTAGT 59.223 42.308 0.00 0.00 0.00 2.73
2318 2426 6.208994 GGTCATAGTGGGAGTAACATAGGTAG 59.791 46.154 0.00 0.00 0.00 3.18
2319 2427 6.073314 GGTCATAGTGGGAGTAACATAGGTA 58.927 44.000 0.00 0.00 0.00 3.08
2320 2428 4.900054 GGTCATAGTGGGAGTAACATAGGT 59.100 45.833 0.00 0.00 0.00 3.08
2321 2429 4.899457 TGGTCATAGTGGGAGTAACATAGG 59.101 45.833 0.00 0.00 0.00 2.57
2322 2430 5.509840 GCTGGTCATAGTGGGAGTAACATAG 60.510 48.000 0.00 0.00 0.00 2.23
2323 2431 4.344102 GCTGGTCATAGTGGGAGTAACATA 59.656 45.833 0.00 0.00 0.00 2.29
2324 2432 3.134804 GCTGGTCATAGTGGGAGTAACAT 59.865 47.826 0.00 0.00 0.00 2.71
2325 2433 2.500098 GCTGGTCATAGTGGGAGTAACA 59.500 50.000 0.00 0.00 0.00 2.41
2326 2434 2.158943 GGCTGGTCATAGTGGGAGTAAC 60.159 54.545 0.00 0.00 0.00 2.50
2327 2435 2.116238 GGCTGGTCATAGTGGGAGTAA 58.884 52.381 0.00 0.00 0.00 2.24
2328 2436 1.291033 AGGCTGGTCATAGTGGGAGTA 59.709 52.381 0.00 0.00 0.00 2.59
2329 2437 0.043334 AGGCTGGTCATAGTGGGAGT 59.957 55.000 0.00 0.00 0.00 3.85
2330 2438 0.467384 CAGGCTGGTCATAGTGGGAG 59.533 60.000 6.61 0.00 0.00 4.30
2331 2439 0.042581 TCAGGCTGGTCATAGTGGGA 59.957 55.000 15.73 0.00 0.00 4.37
2332 2440 1.135094 ATCAGGCTGGTCATAGTGGG 58.865 55.000 15.73 0.00 0.00 4.61
2333 2441 2.968574 AGTATCAGGCTGGTCATAGTGG 59.031 50.000 15.73 0.00 0.00 4.00
2334 2442 4.830046 AGTAGTATCAGGCTGGTCATAGTG 59.170 45.833 15.73 0.00 0.00 2.74
2335 2443 5.068215 AGTAGTATCAGGCTGGTCATAGT 57.932 43.478 15.73 10.48 0.00 2.12
2336 2444 5.124776 GCTAGTAGTATCAGGCTGGTCATAG 59.875 48.000 15.73 7.35 0.00 2.23
2337 2445 5.010933 GCTAGTAGTATCAGGCTGGTCATA 58.989 45.833 15.73 2.30 0.00 2.15
2338 2446 3.829601 GCTAGTAGTATCAGGCTGGTCAT 59.170 47.826 15.73 3.37 0.00 3.06
2339 2447 3.117474 AGCTAGTAGTATCAGGCTGGTCA 60.117 47.826 15.73 0.00 0.00 4.02
2340 2448 3.492337 AGCTAGTAGTATCAGGCTGGTC 58.508 50.000 15.73 5.58 0.00 4.02
2341 2449 3.603965 AGCTAGTAGTATCAGGCTGGT 57.396 47.619 15.73 10.75 0.00 4.00
2342 2450 3.442273 GCTAGCTAGTAGTATCAGGCTGG 59.558 52.174 21.62 0.00 0.00 4.85
2343 2451 4.155826 CAGCTAGCTAGTAGTATCAGGCTG 59.844 50.000 18.86 14.72 37.65 4.85
2344 2452 4.331968 CAGCTAGCTAGTAGTATCAGGCT 58.668 47.826 18.86 6.79 0.00 4.58
2345 2453 3.119637 GCAGCTAGCTAGTAGTATCAGGC 60.120 52.174 18.86 8.24 41.15 4.85
2346 2454 4.695217 GCAGCTAGCTAGTAGTATCAGG 57.305 50.000 18.86 1.09 41.15 3.86
2385 2493 2.616960 TGTGTCGCCAAGCTACTAATG 58.383 47.619 0.00 0.00 0.00 1.90
2419 2527 4.906537 AACCACCAACCACCGGCC 62.907 66.667 0.00 0.00 0.00 6.13
2456 2564 3.520290 ATCGACCTAATTTCGTGAGCA 57.480 42.857 0.00 0.00 37.73 4.26
2477 2585 2.163010 GAGTATGTTCTCGTGGTCGGAA 59.837 50.000 0.00 0.00 37.69 4.30
2483 2591 1.478510 AGCAGGAGTATGTTCTCGTGG 59.521 52.381 14.91 2.03 44.98 4.94
2515 2627 6.886459 AGCCTGTCAGTATTAATTGAACATGT 59.114 34.615 0.00 0.00 0.00 3.21



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

AutoCloner maintained by Alex Coulton.