Multiple sequence alignment - TraesCS3B01G480000

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G480000 chr3B 100.000 2984 0 0 1 2984 728198187 728201170 0.000000e+00 5511.0
1 TraesCS3B01G480000 chr3B 96.248 613 23 0 1 613 661735944 661736556 0.000000e+00 1005.0
2 TraesCS3B01G480000 chr3B 95.114 614 28 2 1 613 661768635 661769247 0.000000e+00 966.0
3 TraesCS3B01G480000 chr3B 94.805 616 29 1 1 613 96853665 96853050 0.000000e+00 957.0
4 TraesCS3B01G480000 chr3B 95.507 601 24 3 1 600 711726347 711725749 0.000000e+00 957.0
5 TraesCS3B01G480000 chr3B 91.250 240 21 0 2276 2515 728457297 728457536 7.980000e-86 327.0
6 TraesCS3B01G480000 chr3B 73.269 722 132 39 1222 1920 727464010 727463327 1.080000e-49 207.0
7 TraesCS3B01G480000 chr3B 91.549 71 6 0 1817 1887 727422092 727422022 6.810000e-17 99.0
8 TraesCS3B01G480000 chr3A 91.822 1394 65 18 659 2027 686253728 686255097 0.000000e+00 1897.0
9 TraesCS3B01G480000 chr3A 82.292 768 74 29 2276 2984 686255538 686256302 2.540000e-170 608.0
10 TraesCS3B01G480000 chr3A 87.228 368 36 7 2224 2587 686419945 686420305 2.770000e-110 409.0
11 TraesCS3B01G480000 chr3A 86.885 366 36 8 2226 2587 686487015 686487372 1.670000e-107 399.0
12 TraesCS3B01G480000 chr3A 71.777 737 135 50 1222 1920 686162637 686161936 1.120000e-29 141.0
13 TraesCS3B01G480000 chr3D 91.541 1395 71 16 659 2027 548964799 548966172 0.000000e+00 1879.0
14 TraesCS3B01G480000 chr3D 85.427 398 42 9 2195 2587 548966305 548966691 1.670000e-107 399.0
15 TraesCS3B01G480000 chr3D 86.376 367 41 7 2224 2587 549042695 549043055 2.790000e-105 392.0
16 TraesCS3B01G480000 chr3D 81.503 519 43 18 1205 1723 45043499 45043034 7.810000e-101 377.0
17 TraesCS3B01G480000 chr3D 87.164 335 27 4 1205 1539 582244948 582244630 1.690000e-97 366.0
18 TraesCS3B01G480000 chr3D 85.315 286 24 8 2714 2984 548972133 548972415 2.270000e-71 279.0
19 TraesCS3B01G480000 chr3D 72.752 723 134 39 1222 1920 548674569 548673886 5.080000e-43 185.0
20 TraesCS3B01G480000 chr3D 79.275 193 29 5 2586 2768 548971924 548972115 1.120000e-24 124.0
21 TraesCS3B01G480000 chr3D 75.636 275 52 11 1619 1887 548634970 548634705 4.040000e-24 122.0
22 TraesCS3B01G480000 chr3D 85.567 97 7 6 1593 1689 285172274 285172185 8.810000e-16 95.3
23 TraesCS3B01G480000 chr1B 96.091 614 23 1 1 613 546144545 546145158 0.000000e+00 1000.0
24 TraesCS3B01G480000 chr1B 95.440 614 26 2 1 613 2432523 2433135 0.000000e+00 977.0
25 TraesCS3B01G480000 chr4A 95.759 613 26 0 1 613 726957557 726958169 0.000000e+00 989.0
26 TraesCS3B01G480000 chr4A 94.788 614 30 2 1 613 690241400 690240788 0.000000e+00 955.0
27 TraesCS3B01G480000 chr7B 95.114 614 29 1 1 613 198540610 198539997 0.000000e+00 966.0
28 TraesCS3B01G480000 chr7D 87.041 517 40 16 1205 1721 72914381 72914870 2.600000e-155 558.0
29 TraesCS3B01G480000 chr7D 87.761 335 25 4 1205 1539 153764353 153764035 7.810000e-101 377.0
30 TraesCS3B01G480000 chr6D 87.066 518 38 10 1205 1721 38539602 38540091 2.600000e-155 558.0
31 TraesCS3B01G480000 chr5D 86.640 509 41 12 1205 1713 51641000 51641481 3.380000e-149 538.0
32 TraesCS3B01G480000 chr2B 82.274 519 39 19 1205 1723 132336202 132336667 1.670000e-107 399.0
33 TraesCS3B01G480000 chr7A 81.118 519 45 19 1205 1723 669866234 669866699 1.690000e-97 366.0


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 TraesCS3B01G480000 chr3B 728198187 728201170 2983 False 5511.0 5511 100.000 1 2984 1 chr3B.!!$F3 2983
1 TraesCS3B01G480000 chr3B 661735944 661736556 612 False 1005.0 1005 96.248 1 613 1 chr3B.!!$F1 612
2 TraesCS3B01G480000 chr3B 661768635 661769247 612 False 966.0 966 95.114 1 613 1 chr3B.!!$F2 612
3 TraesCS3B01G480000 chr3B 96853050 96853665 615 True 957.0 957 94.805 1 613 1 chr3B.!!$R1 612
4 TraesCS3B01G480000 chr3B 711725749 711726347 598 True 957.0 957 95.507 1 600 1 chr3B.!!$R2 599
5 TraesCS3B01G480000 chr3B 727463327 727464010 683 True 207.0 207 73.269 1222 1920 1 chr3B.!!$R4 698
6 TraesCS3B01G480000 chr3A 686253728 686256302 2574 False 1252.5 1897 87.057 659 2984 2 chr3A.!!$F3 2325
7 TraesCS3B01G480000 chr3D 548964799 548966691 1892 False 1139.0 1879 88.484 659 2587 2 chr3D.!!$F2 1928
8 TraesCS3B01G480000 chr1B 546144545 546145158 613 False 1000.0 1000 96.091 1 613 1 chr1B.!!$F2 612
9 TraesCS3B01G480000 chr1B 2432523 2433135 612 False 977.0 977 95.440 1 613 1 chr1B.!!$F1 612
10 TraesCS3B01G480000 chr4A 726957557 726958169 612 False 989.0 989 95.759 1 613 1 chr4A.!!$F1 612
11 TraesCS3B01G480000 chr4A 690240788 690241400 612 True 955.0 955 94.788 1 613 1 chr4A.!!$R1 612
12 TraesCS3B01G480000 chr7B 198539997 198540610 613 True 966.0 966 95.114 1 613 1 chr7B.!!$R1 612

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
377 379 0.174617 ACAAACGGCACAAAGGGTTG 59.825 50.0 0.0 0.0 40.84 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2171 2290 0.03601 ACAAGCGGTTCCATGAGGAG 60.036 55.0 0.0 0.0 46.74 3.69 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
192 193 0.745845 ACATCATCTTCCTGGCGCAC 60.746 55.000 10.83 0.00 0.00 5.34
216 218 4.228567 TTCGACACCACTGCGCCA 62.229 61.111 4.18 0.00 0.00 5.69
312 314 2.324330 CCACGGCATTCTTCGCACA 61.324 57.895 0.00 0.00 0.00 4.57
377 379 0.174617 ACAAACGGCACAAAGGGTTG 59.825 50.000 0.00 0.00 40.84 3.77
487 492 1.929836 CTTGCCTTCGGATTCTTCTCG 59.070 52.381 0.00 0.00 0.00 4.04
600 606 3.135712 TCTGGCTTGTCTTGTACTCCAAA 59.864 43.478 0.00 0.00 31.20 3.28
603 609 5.626142 TGGCTTGTCTTGTACTCCAAATAA 58.374 37.500 0.00 0.00 31.20 1.40
614 620 9.722056 CTTGTACTCCAAATAAATCATTGTAGC 57.278 33.333 0.00 0.00 31.20 3.58
615 621 8.800370 TGTACTCCAAATAAATCATTGTAGCA 57.200 30.769 0.00 0.00 0.00 3.49
616 622 9.237187 TGTACTCCAAATAAATCATTGTAGCAA 57.763 29.630 0.00 0.00 0.00 3.91
645 651 7.125792 TCAACTATTCCACTAAATCTCTCCC 57.874 40.000 0.00 0.00 0.00 4.30
646 652 6.903534 TCAACTATTCCACTAAATCTCTCCCT 59.096 38.462 0.00 0.00 0.00 4.20
647 653 6.987403 ACTATTCCACTAAATCTCTCCCTC 57.013 41.667 0.00 0.00 0.00 4.30
648 654 5.841783 ACTATTCCACTAAATCTCTCCCTCC 59.158 44.000 0.00 0.00 0.00 4.30
649 655 3.047695 TCCACTAAATCTCTCCCTCCC 57.952 52.381 0.00 0.00 0.00 4.30
650 656 2.592512 TCCACTAAATCTCTCCCTCCCT 59.407 50.000 0.00 0.00 0.00 4.20
651 657 3.797845 TCCACTAAATCTCTCCCTCCCTA 59.202 47.826 0.00 0.00 0.00 3.53
652 658 3.898741 CCACTAAATCTCTCCCTCCCTAC 59.101 52.174 0.00 0.00 0.00 3.18
653 659 4.388118 CCACTAAATCTCTCCCTCCCTACT 60.388 50.000 0.00 0.00 0.00 2.57
654 660 5.162969 CCACTAAATCTCTCCCTCCCTACTA 60.163 48.000 0.00 0.00 0.00 1.82
655 661 6.374588 CACTAAATCTCTCCCTCCCTACTAA 58.625 44.000 0.00 0.00 0.00 2.24
656 662 6.265876 CACTAAATCTCTCCCTCCCTACTAAC 59.734 46.154 0.00 0.00 0.00 2.34
657 663 4.901785 AATCTCTCCCTCCCTACTAACA 57.098 45.455 0.00 0.00 0.00 2.41
717 724 4.641396 TGATGATCATCCACCCGAATAAC 58.359 43.478 28.61 4.49 37.02 1.89
756 770 7.904558 AAGAACAAGGAAGGAGAAGAAAATT 57.095 32.000 0.00 0.00 0.00 1.82
794 808 3.072666 GCTCCGCTCGCGAAGAAAC 62.073 63.158 11.33 0.00 42.83 2.78
827 841 4.568152 GGCATACCGCAACATAATTTCT 57.432 40.909 0.00 0.00 45.17 2.52
867 881 1.550976 GACCAACGGAAGACTCCAGAT 59.449 52.381 0.00 0.00 42.58 2.90
894 908 2.897326 TCCCAAGTCGTCTCATGAGAAA 59.103 45.455 26.70 15.17 39.48 2.52
936 950 1.095600 CCTCTCGACCATCGACAAGA 58.904 55.000 0.00 0.00 44.82 3.02
937 951 1.678627 CCTCTCGACCATCGACAAGAT 59.321 52.381 0.00 0.00 44.82 2.40
938 952 2.879026 CCTCTCGACCATCGACAAGATA 59.121 50.000 0.00 0.00 44.82 1.98
939 953 3.304123 CCTCTCGACCATCGACAAGATAC 60.304 52.174 0.00 0.00 44.82 2.24
940 954 3.275999 TCTCGACCATCGACAAGATACA 58.724 45.455 0.00 0.00 44.82 2.29
941 955 3.883489 TCTCGACCATCGACAAGATACAT 59.117 43.478 0.00 0.00 44.82 2.29
942 956 4.338400 TCTCGACCATCGACAAGATACATT 59.662 41.667 0.00 0.00 44.82 2.71
943 957 5.529800 TCTCGACCATCGACAAGATACATTA 59.470 40.000 0.00 0.00 44.82 1.90
944 958 5.516996 TCGACCATCGACAAGATACATTAC 58.483 41.667 0.00 0.00 44.82 1.89
945 959 5.298527 TCGACCATCGACAAGATACATTACT 59.701 40.000 0.00 0.00 44.82 2.24
962 976 1.540267 ACTACAAGCGCACTCTCTCT 58.460 50.000 11.47 0.00 0.00 3.10
1074 1110 4.117661 GGCTTCGTCGCGGACTCT 62.118 66.667 6.13 0.00 0.00 3.24
1075 1111 2.126424 GCTTCGTCGCGGACTCTT 60.126 61.111 6.13 0.00 0.00 2.85
1140 1176 4.363990 CTCGTGCTCGCCCACACT 62.364 66.667 2.69 0.00 35.47 3.55
1431 1473 0.388134 CCGTCCCGGCGTATTATCTG 60.388 60.000 6.01 0.00 41.17 2.90
1437 1479 1.887198 CCGGCGTATTATCTGGACTCT 59.113 52.381 6.01 0.00 0.00 3.24
1531 1585 4.742649 TCCTCGCCACGCTCCTCT 62.743 66.667 0.00 0.00 0.00 3.69
1922 2001 2.355108 CCATTCCACTGACGATGAAGGT 60.355 50.000 0.00 0.00 0.00 3.50
1973 2052 7.651027 ATTCTCTGAAATTGATTAAGGGTGG 57.349 36.000 0.00 0.00 0.00 4.61
2003 2085 6.877855 GCCTGAAGAATCTATGATGAATAGCA 59.122 38.462 0.00 0.00 38.57 3.49
2045 2164 0.109132 GGAGCTCGGGTGCAAATTTG 60.109 55.000 14.03 14.03 34.99 2.32
2063 2182 7.012327 GCAAATTTGTGGCTATGTAGATAGTGA 59.988 37.037 19.03 0.00 34.94 3.41
2072 2191 6.656693 GGCTATGTAGATAGTGAAAATGGCAT 59.343 38.462 8.56 0.00 34.94 4.40
2073 2192 7.824289 GGCTATGTAGATAGTGAAAATGGCATA 59.176 37.037 0.00 0.00 34.94 3.14
2074 2193 9.388506 GCTATGTAGATAGTGAAAATGGCATAT 57.611 33.333 0.00 0.00 34.94 1.78
2078 2197 9.725019 TGTAGATAGTGAAAATGGCATATTAGG 57.275 33.333 0.00 0.00 0.00 2.69
2079 2198 7.693969 AGATAGTGAAAATGGCATATTAGGC 57.306 36.000 0.00 0.00 0.00 3.93
2092 2211 4.083590 GCATATTAGGCACTCTAGCTTTGC 60.084 45.833 0.00 0.00 41.75 3.68
2105 2224 3.492102 AGCTTTGCTCAGGTTTCAGTA 57.508 42.857 0.00 0.00 30.62 2.74
2126 2245 4.718940 AAAATTTCTAGGTCCGCCATTG 57.281 40.909 0.00 0.00 37.19 2.82
2133 2252 2.359850 GTCCGCCATTGGTGAGCA 60.360 61.111 17.90 0.00 34.74 4.26
2135 2254 2.046023 CCGCCATTGGTGAGCAGA 60.046 61.111 17.90 0.00 34.74 4.26
2136 2255 1.452651 CCGCCATTGGTGAGCAGAT 60.453 57.895 17.90 0.00 34.74 2.90
2137 2256 1.033746 CCGCCATTGGTGAGCAGATT 61.034 55.000 17.90 0.00 34.74 2.40
2138 2257 0.813184 CGCCATTGGTGAGCAGATTT 59.187 50.000 10.90 0.00 34.74 2.17
2139 2258 1.203052 CGCCATTGGTGAGCAGATTTT 59.797 47.619 10.90 0.00 34.74 1.82
2140 2259 2.423185 CGCCATTGGTGAGCAGATTTTA 59.577 45.455 10.90 0.00 34.74 1.52
2141 2260 3.488047 CGCCATTGGTGAGCAGATTTTAG 60.488 47.826 10.90 0.00 34.74 1.85
2142 2261 3.445096 GCCATTGGTGAGCAGATTTTAGT 59.555 43.478 4.26 0.00 0.00 2.24
2143 2262 4.082026 GCCATTGGTGAGCAGATTTTAGTT 60.082 41.667 4.26 0.00 0.00 2.24
2144 2263 5.567423 GCCATTGGTGAGCAGATTTTAGTTT 60.567 40.000 4.26 0.00 0.00 2.66
2145 2264 6.095377 CCATTGGTGAGCAGATTTTAGTTTC 58.905 40.000 0.00 0.00 0.00 2.78
2146 2265 6.294675 CCATTGGTGAGCAGATTTTAGTTTCA 60.295 38.462 0.00 0.00 0.00 2.69
2147 2266 5.947228 TGGTGAGCAGATTTTAGTTTCAG 57.053 39.130 0.00 0.00 0.00 3.02
2148 2267 4.216257 TGGTGAGCAGATTTTAGTTTCAGC 59.784 41.667 0.00 0.00 33.55 4.26
2149 2268 4.457257 GGTGAGCAGATTTTAGTTTCAGCT 59.543 41.667 0.00 0.00 37.41 4.24
2150 2269 5.391416 GGTGAGCAGATTTTAGTTTCAGCTC 60.391 44.000 9.53 9.53 46.06 4.09
2151 2270 5.869753 GAGCAGATTTTAGTTTCAGCTCA 57.130 39.130 11.06 0.00 45.52 4.26
2152 2271 6.246420 GAGCAGATTTTAGTTTCAGCTCAA 57.754 37.500 11.06 0.00 45.52 3.02
2153 2272 6.830873 AGCAGATTTTAGTTTCAGCTCAAT 57.169 33.333 0.00 0.00 29.87 2.57
2154 2273 7.928307 AGCAGATTTTAGTTTCAGCTCAATA 57.072 32.000 0.00 0.00 29.87 1.90
2155 2274 8.340618 AGCAGATTTTAGTTTCAGCTCAATAA 57.659 30.769 0.00 0.00 29.87 1.40
2156 2275 8.457261 AGCAGATTTTAGTTTCAGCTCAATAAG 58.543 33.333 0.00 0.00 29.87 1.73
2157 2276 7.699812 GCAGATTTTAGTTTCAGCTCAATAAGG 59.300 37.037 0.00 0.00 0.00 2.69
2158 2277 7.699812 CAGATTTTAGTTTCAGCTCAATAAGGC 59.300 37.037 0.00 0.00 0.00 4.35
2159 2278 6.892658 TTTTAGTTTCAGCTCAATAAGGCA 57.107 33.333 0.00 0.00 0.00 4.75
2160 2279 7.466746 TTTTAGTTTCAGCTCAATAAGGCAT 57.533 32.000 0.00 0.00 0.00 4.40
2161 2280 7.466746 TTTAGTTTCAGCTCAATAAGGCATT 57.533 32.000 0.00 0.00 0.00 3.56
2162 2281 8.574251 TTTAGTTTCAGCTCAATAAGGCATTA 57.426 30.769 0.00 0.00 0.00 1.90
2163 2282 8.574251 TTAGTTTCAGCTCAATAAGGCATTAA 57.426 30.769 0.00 0.00 0.00 1.40
2164 2283 7.651027 AGTTTCAGCTCAATAAGGCATTAAT 57.349 32.000 0.00 0.00 0.00 1.40
2165 2284 8.752005 AGTTTCAGCTCAATAAGGCATTAATA 57.248 30.769 0.00 0.00 0.00 0.98
2166 2285 9.359653 AGTTTCAGCTCAATAAGGCATTAATAT 57.640 29.630 0.00 0.00 0.00 1.28
2167 2286 9.617975 GTTTCAGCTCAATAAGGCATTAATATC 57.382 33.333 0.00 0.00 0.00 1.63
2168 2287 9.578576 TTTCAGCTCAATAAGGCATTAATATCT 57.421 29.630 0.00 0.00 0.00 1.98
2169 2288 8.783833 TCAGCTCAATAAGGCATTAATATCTC 57.216 34.615 0.00 0.00 0.00 2.75
2170 2289 7.826252 TCAGCTCAATAAGGCATTAATATCTCC 59.174 37.037 0.00 0.00 0.00 3.71
2171 2290 7.066766 CAGCTCAATAAGGCATTAATATCTCCC 59.933 40.741 0.00 0.00 0.00 4.30
2172 2291 7.037008 AGCTCAATAAGGCATTAATATCTCCCT 60.037 37.037 0.00 0.00 0.00 4.20
2173 2292 7.281999 GCTCAATAAGGCATTAATATCTCCCTC 59.718 40.741 0.00 0.00 0.00 4.30
2174 2293 7.633789 TCAATAAGGCATTAATATCTCCCTCC 58.366 38.462 0.00 0.00 0.00 4.30
2175 2294 7.462328 TCAATAAGGCATTAATATCTCCCTCCT 59.538 37.037 0.00 0.00 0.00 3.69
2176 2295 5.770685 AAGGCATTAATATCTCCCTCCTC 57.229 43.478 0.00 0.00 0.00 3.71
2177 2296 4.767908 AGGCATTAATATCTCCCTCCTCA 58.232 43.478 0.00 0.00 0.00 3.86
2178 2297 5.357440 AGGCATTAATATCTCCCTCCTCAT 58.643 41.667 0.00 0.00 0.00 2.90
2179 2298 5.191323 AGGCATTAATATCTCCCTCCTCATG 59.809 44.000 0.00 0.00 0.00 3.07
2180 2299 5.435291 GCATTAATATCTCCCTCCTCATGG 58.565 45.833 0.00 0.00 0.00 3.66
2181 2300 5.190528 GCATTAATATCTCCCTCCTCATGGA 59.809 44.000 0.00 0.00 40.69 3.41
2182 2301 6.296662 GCATTAATATCTCCCTCCTCATGGAA 60.297 42.308 0.00 0.00 42.66 3.53
2183 2302 6.688073 TTAATATCTCCCTCCTCATGGAAC 57.312 41.667 0.00 0.00 42.66 3.62
2184 2303 1.813102 ATCTCCCTCCTCATGGAACC 58.187 55.000 0.00 0.00 42.66 3.62
2185 2304 0.687757 TCTCCCTCCTCATGGAACCG 60.688 60.000 0.00 0.00 42.66 4.44
2186 2305 2.190578 CCCTCCTCATGGAACCGC 59.809 66.667 0.00 0.00 42.66 5.68
2187 2306 2.370445 CCCTCCTCATGGAACCGCT 61.370 63.158 0.00 0.00 42.66 5.52
2188 2307 1.604378 CCTCCTCATGGAACCGCTT 59.396 57.895 0.00 0.00 42.66 4.68
2189 2308 0.745845 CCTCCTCATGGAACCGCTTG 60.746 60.000 0.00 0.00 42.66 4.01
2190 2309 0.036010 CTCCTCATGGAACCGCTTGT 60.036 55.000 0.00 0.00 42.66 3.16
2191 2310 0.036388 TCCTCATGGAACCGCTTGTC 60.036 55.000 0.00 0.00 39.87 3.18
2192 2311 0.321564 CCTCATGGAACCGCTTGTCA 60.322 55.000 0.00 0.00 34.57 3.58
2193 2312 1.081892 CTCATGGAACCGCTTGTCAG 58.918 55.000 0.00 0.00 0.00 3.51
2201 2320 0.463654 ACCGCTTGTCAGAGTTGCAA 60.464 50.000 0.00 0.00 0.00 4.08
2213 2332 4.644234 TCAGAGTTGCAATCCAAACTTCAA 59.356 37.500 0.59 0.00 34.68 2.69
2390 2741 3.717707 TCTCACTGTCAGGTTTTTCGAG 58.282 45.455 4.53 0.00 0.00 4.04
2443 2794 8.340618 AGTATTTGTGTTCAATGCTCTGTATT 57.659 30.769 0.00 0.00 33.32 1.89
2453 2804 3.407424 TGCTCTGTATTCACTGTGCTT 57.593 42.857 2.12 0.00 41.18 3.91
2456 2807 3.616379 GCTCTGTATTCACTGTGCTTCTC 59.384 47.826 2.12 0.00 38.98 2.87
2457 2808 3.838120 TCTGTATTCACTGTGCTTCTCG 58.162 45.455 2.12 0.00 0.00 4.04
2460 2811 3.255888 TGTATTCACTGTGCTTCTCGAGT 59.744 43.478 13.13 0.00 0.00 4.18
2464 2815 0.038709 ACTGTGCTTCTCGAGTCAGC 60.039 55.000 24.09 24.09 34.91 4.26
2469 2820 2.481952 GTGCTTCTCGAGTCAGCAAAAT 59.518 45.455 30.71 0.00 44.99 1.82
2501 2852 0.609662 CCAAACAGGGGCTTGGAATG 59.390 55.000 0.00 0.00 44.16 2.67
2502 2853 1.631405 CAAACAGGGGCTTGGAATGA 58.369 50.000 0.00 0.00 0.00 2.57
2507 2866 2.181975 CAGGGGCTTGGAATGATTTGT 58.818 47.619 0.00 0.00 0.00 2.83
2518 2877 5.927819 TGGAATGATTTGTTTCCAAAGCTT 58.072 33.333 0.00 0.00 45.07 3.74
2521 2880 6.652062 GGAATGATTTGTTTCCAAAGCTTGAT 59.348 34.615 0.00 0.00 45.07 2.57
2543 2902 1.676014 CCTGGACTCGGGCAGTTAAAG 60.676 57.143 0.00 0.00 34.41 1.85
2544 2903 0.321298 TGGACTCGGGCAGTTAAAGC 60.321 55.000 0.00 0.00 34.41 3.51
2545 2904 0.321298 GGACTCGGGCAGTTAAAGCA 60.321 55.000 3.87 0.00 34.41 3.91
2556 2915 5.050159 GGGCAGTTAAAGCAAATTGTTCAAG 60.050 40.000 0.00 0.00 0.00 3.02
2559 2918 6.697019 GCAGTTAAAGCAAATTGTTCAAGAGA 59.303 34.615 0.00 0.00 0.00 3.10
2575 2934 8.509690 TGTTCAAGAGATCAGCTAAAGAATTTG 58.490 33.333 0.00 0.00 39.63 2.32
2587 2946 6.780522 AGCTAAAGAATTTGGGTTGGTCTTTA 59.219 34.615 0.00 0.00 45.03 1.85
2609 2993 2.924290 GAGAGCGACGCAAGAAAATACT 59.076 45.455 23.70 6.44 43.62 2.12
2611 2995 2.666508 GAGCGACGCAAGAAAATACTGA 59.333 45.455 23.70 0.00 43.62 3.41
2613 2997 3.120649 AGCGACGCAAGAAAATACTGAAC 60.121 43.478 23.70 0.00 43.62 3.18
2614 2998 3.732943 CGACGCAAGAAAATACTGAACC 58.267 45.455 0.00 0.00 43.62 3.62
2615 2999 3.720920 CGACGCAAGAAAATACTGAACCG 60.721 47.826 0.00 0.00 43.62 4.44
2621 3006 5.506649 GCAAGAAAATACTGAACCGAACCAA 60.507 40.000 0.00 0.00 0.00 3.67
2624 3009 6.500910 AGAAAATACTGAACCGAACCAAAAC 58.499 36.000 0.00 0.00 0.00 2.43
2627 3012 2.661718 ACTGAACCGAACCAAAACCAT 58.338 42.857 0.00 0.00 0.00 3.55
2631 3016 2.074729 ACCGAACCAAAACCATGGAA 57.925 45.000 21.47 0.00 43.54 3.53
2634 3019 3.197983 ACCGAACCAAAACCATGGAAAAA 59.802 39.130 21.47 0.00 43.54 1.94
2641 3026 4.886489 CCAAAACCATGGAAAAACATTGGT 59.114 37.500 21.47 0.00 43.54 3.67
2650 3035 5.415221 TGGAAAAACATTGGTCACAGAAAC 58.585 37.500 0.00 0.00 0.00 2.78
2655 3040 7.920160 AAAACATTGGTCACAGAAACAAAAT 57.080 28.000 0.00 0.00 0.00 1.82
2657 3042 6.219417 ACATTGGTCACAGAAACAAAATCA 57.781 33.333 0.00 0.00 0.00 2.57
2697 3087 5.776716 AGTTCCACACAAATCAATCCAGAAT 59.223 36.000 0.00 0.00 0.00 2.40
2698 3088 6.268387 AGTTCCACACAAATCAATCCAGAATT 59.732 34.615 0.00 0.00 0.00 2.17
2699 3089 6.271488 TCCACACAAATCAATCCAGAATTC 57.729 37.500 0.00 0.00 0.00 2.17
2702 3092 6.097356 CACACAAATCAATCCAGAATTCCAG 58.903 40.000 0.65 0.00 0.00 3.86
2703 3093 6.012113 ACACAAATCAATCCAGAATTCCAGA 58.988 36.000 0.65 0.00 0.00 3.86
2705 3095 7.835682 ACACAAATCAATCCAGAATTCCAGATA 59.164 33.333 0.65 0.00 0.00 1.98
2706 3096 8.689061 CACAAATCAATCCAGAATTCCAGATAA 58.311 33.333 0.65 0.00 0.00 1.75
2707 3097 9.430399 ACAAATCAATCCAGAATTCCAGATAAT 57.570 29.630 0.65 0.65 0.00 1.28
2708 3098 9.909644 CAAATCAATCCAGAATTCCAGATAATC 57.090 33.333 0.65 0.00 0.00 1.75
2709 3099 9.650714 AAATCAATCCAGAATTCCAGATAATCA 57.349 29.630 0.65 0.00 0.00 2.57
2710 3100 8.632906 ATCAATCCAGAATTCCAGATAATCAC 57.367 34.615 0.65 0.00 0.00 3.06
2712 3102 7.718314 TCAATCCAGAATTCCAGATAATCACTG 59.282 37.037 0.65 0.00 35.43 3.66
2716 3110 6.996879 CCAGAATTCCAGATAATCACTGTCAT 59.003 38.462 0.65 0.00 34.04 3.06
2725 3119 9.368674 CCAGATAATCACTGTCATAGATCAATC 57.631 37.037 0.00 0.00 34.04 2.67
2743 3137 2.099141 TCCAACAAGCTCCTTGATCG 57.901 50.000 11.56 0.00 43.42 3.69
2752 3146 2.636893 AGCTCCTTGATCGCCATTATCT 59.363 45.455 0.00 0.00 0.00 1.98
2754 3148 3.805108 GCTCCTTGATCGCCATTATCTGT 60.805 47.826 0.00 0.00 0.00 3.41
2755 3149 4.561530 GCTCCTTGATCGCCATTATCTGTA 60.562 45.833 0.00 0.00 0.00 2.74
2772 3166 3.067320 TCTGTATCCTTCATCTGCTCACG 59.933 47.826 0.00 0.00 0.00 4.35
2783 3177 2.507324 GCTCACGAAGTCGCCTCC 60.507 66.667 0.00 0.00 41.61 4.30
2797 3191 2.117156 CCTCCGGCAGCTCCAATTG 61.117 63.158 0.00 0.00 34.01 2.32
2805 3199 1.660167 CAGCTCCAATTGATCGCTCA 58.340 50.000 7.12 0.00 0.00 4.26
2806 3200 2.219458 CAGCTCCAATTGATCGCTCAT 58.781 47.619 7.12 0.00 0.00 2.90
2807 3201 3.396560 CAGCTCCAATTGATCGCTCATA 58.603 45.455 7.12 0.00 0.00 2.15
2823 3217 4.348863 CTCATATAGCTGCTCCAAGGTT 57.651 45.455 4.91 0.00 0.00 3.50
2832 3226 3.367395 GCTGCTCCAAGGTTTTCATTACC 60.367 47.826 0.00 0.00 35.85 2.85
2840 3238 3.822940 AGGTTTTCATTACCCGTTCACA 58.177 40.909 0.00 0.00 36.27 3.58
2841 3239 4.208746 AGGTTTTCATTACCCGTTCACAA 58.791 39.130 0.00 0.00 36.27 3.33
2844 3242 1.434555 TCATTACCCGTTCACAAGCG 58.565 50.000 0.00 0.00 0.00 4.68
2845 3243 0.179200 CATTACCCGTTCACAAGCGC 60.179 55.000 0.00 0.00 0.00 5.92
2863 3271 2.429930 CCTTGTTCTGCGACCCCA 59.570 61.111 0.00 0.00 0.00 4.96
2875 3283 3.192630 ACCCCATGCACCCTGGTT 61.193 61.111 4.19 0.00 31.44 3.67
2894 3302 4.124238 GGTTTGTTTACCCTCCTTTTTGC 58.876 43.478 0.00 0.00 31.71 3.68
2899 3307 2.579410 TACCCTCCTTTTTGCCAGTC 57.421 50.000 0.00 0.00 0.00 3.51
2901 3309 1.251251 CCCTCCTTTTTGCCAGTCAG 58.749 55.000 0.00 0.00 0.00 3.51
2910 3318 2.638480 TTGCCAGTCAGCTTAACAGT 57.362 45.000 0.00 0.00 0.00 3.55
2911 3319 2.638480 TGCCAGTCAGCTTAACAGTT 57.362 45.000 0.00 0.00 0.00 3.16
2913 3321 3.287222 TGCCAGTCAGCTTAACAGTTTT 58.713 40.909 0.00 0.00 0.00 2.43
2939 3348 3.583380 TTGGCCTGGCAGCTTCCT 61.583 61.111 22.05 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
192 193 0.246635 CAGTGGTGTCGAAGTAGGGG 59.753 60.000 0.00 0.00 0.00 4.79
216 218 2.513897 GGGCGCCGAGTTAGCATT 60.514 61.111 22.54 0.00 0.00 3.56
312 314 3.450115 GCCGTGGTCGAGGTAGCT 61.450 66.667 0.00 0.00 39.71 3.32
342 344 0.322277 TTGTCGAGGTAGCCGAGAGT 60.322 55.000 5.87 0.00 36.66 3.24
460 465 4.735132 CCGAAGGCAAGCCGACGA 62.735 66.667 25.12 0.00 46.14 4.20
487 492 1.154188 GACGCAGACGGTGAGACTC 60.154 63.158 0.00 0.00 46.04 3.36
619 625 8.871125 GGGAGAGATTTAGTGGAATAGTTGATA 58.129 37.037 0.00 0.00 0.00 2.15
620 626 7.570607 AGGGAGAGATTTAGTGGAATAGTTGAT 59.429 37.037 0.00 0.00 0.00 2.57
621 627 6.903534 AGGGAGAGATTTAGTGGAATAGTTGA 59.096 38.462 0.00 0.00 0.00 3.18
622 628 7.130681 AGGGAGAGATTTAGTGGAATAGTTG 57.869 40.000 0.00 0.00 0.00 3.16
623 629 6.327887 GGAGGGAGAGATTTAGTGGAATAGTT 59.672 42.308 0.00 0.00 0.00 2.24
624 630 5.841783 GGAGGGAGAGATTTAGTGGAATAGT 59.158 44.000 0.00 0.00 0.00 2.12
625 631 5.247337 GGGAGGGAGAGATTTAGTGGAATAG 59.753 48.000 0.00 0.00 0.00 1.73
626 632 5.102609 AGGGAGGGAGAGATTTAGTGGAATA 60.103 44.000 0.00 0.00 0.00 1.75
627 633 3.977326 GGGAGGGAGAGATTTAGTGGAAT 59.023 47.826 0.00 0.00 0.00 3.01
628 634 3.014110 AGGGAGGGAGAGATTTAGTGGAA 59.986 47.826 0.00 0.00 0.00 3.53
629 635 2.592512 AGGGAGGGAGAGATTTAGTGGA 59.407 50.000 0.00 0.00 0.00 4.02
630 636 3.053359 AGGGAGGGAGAGATTTAGTGG 57.947 52.381 0.00 0.00 0.00 4.00
631 637 4.810345 AGTAGGGAGGGAGAGATTTAGTG 58.190 47.826 0.00 0.00 0.00 2.74
632 638 6.068379 TGTTAGTAGGGAGGGAGAGATTTAGT 60.068 42.308 0.00 0.00 0.00 2.24
633 639 6.265876 GTGTTAGTAGGGAGGGAGAGATTTAG 59.734 46.154 0.00 0.00 0.00 1.85
634 640 6.134754 GTGTTAGTAGGGAGGGAGAGATTTA 58.865 44.000 0.00 0.00 0.00 1.40
635 641 4.963628 GTGTTAGTAGGGAGGGAGAGATTT 59.036 45.833 0.00 0.00 0.00 2.17
636 642 4.016479 TGTGTTAGTAGGGAGGGAGAGATT 60.016 45.833 0.00 0.00 0.00 2.40
637 643 3.532232 TGTGTTAGTAGGGAGGGAGAGAT 59.468 47.826 0.00 0.00 0.00 2.75
638 644 2.924302 TGTGTTAGTAGGGAGGGAGAGA 59.076 50.000 0.00 0.00 0.00 3.10
639 645 3.383698 TGTGTTAGTAGGGAGGGAGAG 57.616 52.381 0.00 0.00 0.00 3.20
640 646 3.373877 GGATGTGTTAGTAGGGAGGGAGA 60.374 52.174 0.00 0.00 0.00 3.71
641 647 2.966516 GGATGTGTTAGTAGGGAGGGAG 59.033 54.545 0.00 0.00 0.00 4.30
642 648 2.316677 TGGATGTGTTAGTAGGGAGGGA 59.683 50.000 0.00 0.00 0.00 4.20
643 649 2.759355 TGGATGTGTTAGTAGGGAGGG 58.241 52.381 0.00 0.00 0.00 4.30
644 650 4.514401 GTTTGGATGTGTTAGTAGGGAGG 58.486 47.826 0.00 0.00 0.00 4.30
645 651 4.181578 CGTTTGGATGTGTTAGTAGGGAG 58.818 47.826 0.00 0.00 0.00 4.30
646 652 3.055675 CCGTTTGGATGTGTTAGTAGGGA 60.056 47.826 0.00 0.00 37.49 4.20
647 653 3.055675 TCCGTTTGGATGTGTTAGTAGGG 60.056 47.826 0.00 0.00 40.17 3.53
648 654 4.081862 TCTCCGTTTGGATGTGTTAGTAGG 60.082 45.833 0.00 0.00 45.33 3.18
649 655 4.863131 GTCTCCGTTTGGATGTGTTAGTAG 59.137 45.833 0.00 0.00 45.33 2.57
650 656 4.281435 TGTCTCCGTTTGGATGTGTTAGTA 59.719 41.667 0.00 0.00 45.33 1.82
651 657 3.070446 TGTCTCCGTTTGGATGTGTTAGT 59.930 43.478 0.00 0.00 45.33 2.24
652 658 3.659786 TGTCTCCGTTTGGATGTGTTAG 58.340 45.455 0.00 0.00 45.33 2.34
653 659 3.755112 TGTCTCCGTTTGGATGTGTTA 57.245 42.857 0.00 0.00 45.33 2.41
654 660 2.631160 TGTCTCCGTTTGGATGTGTT 57.369 45.000 0.00 0.00 45.33 3.32
655 661 2.631160 TTGTCTCCGTTTGGATGTGT 57.369 45.000 0.00 0.00 45.33 3.72
656 662 3.304659 CCTTTTGTCTCCGTTTGGATGTG 60.305 47.826 0.00 0.00 45.33 3.21
657 663 2.884639 CCTTTTGTCTCCGTTTGGATGT 59.115 45.455 0.00 0.00 45.33 3.06
717 724 1.305219 TTCTTTTCCGCGGCATGAGG 61.305 55.000 23.51 8.28 39.23 3.86
756 770 1.660355 GTCGAGGCATCCGCTCATA 59.340 57.895 0.00 0.00 38.60 2.15
794 808 1.506262 GTATGCCGTGCTGTTTGGG 59.494 57.895 0.00 0.00 0.00 4.12
827 841 1.140852 CAGTCAACTGAGTGGGTGGAA 59.859 52.381 4.05 0.00 46.59 3.53
854 868 3.434310 GGGATGGAAATCTGGAGTCTTCC 60.434 52.174 1.95 1.95 44.31 3.46
855 869 3.200825 TGGGATGGAAATCTGGAGTCTTC 59.799 47.826 0.00 0.00 0.00 2.87
867 881 1.974957 TGAGACGACTTGGGATGGAAA 59.025 47.619 0.00 0.00 0.00 3.13
894 908 0.680061 GTGGTCACCGGAGAAGAAGT 59.320 55.000 9.46 0.00 0.00 3.01
936 950 5.067936 AGAGAGTGCGCTTGTAGTAATGTAT 59.932 40.000 9.73 0.00 0.00 2.29
937 951 4.398358 AGAGAGTGCGCTTGTAGTAATGTA 59.602 41.667 9.73 0.00 0.00 2.29
938 952 3.193691 AGAGAGTGCGCTTGTAGTAATGT 59.806 43.478 9.73 0.00 0.00 2.71
939 953 3.775202 AGAGAGTGCGCTTGTAGTAATG 58.225 45.455 9.73 0.00 0.00 1.90
940 954 3.697045 AGAGAGAGTGCGCTTGTAGTAAT 59.303 43.478 9.73 0.00 0.00 1.89
941 955 3.082548 AGAGAGAGTGCGCTTGTAGTAA 58.917 45.455 9.73 0.00 0.00 2.24
942 956 2.420372 CAGAGAGAGTGCGCTTGTAGTA 59.580 50.000 9.73 0.00 0.00 1.82
943 957 1.201181 CAGAGAGAGTGCGCTTGTAGT 59.799 52.381 9.73 0.00 0.00 2.73
944 958 1.906757 CAGAGAGAGTGCGCTTGTAG 58.093 55.000 9.73 0.00 0.00 2.74
945 959 0.109086 GCAGAGAGAGTGCGCTTGTA 60.109 55.000 9.73 0.00 0.00 2.41
962 976 3.074281 CTAGGGGGTTTGGTCGCA 58.926 61.111 0.00 0.00 0.00 5.10
1074 1110 2.305607 CCGGGTGGGGAGGATCAAA 61.306 63.158 0.00 0.00 36.25 2.69
1075 1111 2.690881 CCGGGTGGGGAGGATCAA 60.691 66.667 0.00 0.00 36.25 2.57
1128 1164 2.665185 ACGAAAGTGTGGGCGAGC 60.665 61.111 0.00 0.00 46.97 5.03
1428 1470 2.696526 ACCTGTACCAAGAGTCCAGA 57.303 50.000 0.00 0.00 0.00 3.86
1431 1473 2.094130 GCTGTACCTGTACCAAGAGTCC 60.094 54.545 5.07 0.00 35.26 3.85
1437 1479 1.899814 CTCCAGCTGTACCTGTACCAA 59.100 52.381 13.81 0.00 35.26 3.67
1702 1778 3.097728 CACGACGCTCACCACGAC 61.098 66.667 0.00 0.00 0.00 4.34
1795 1871 1.553248 CAGAAGGAACCCGTACATCCA 59.447 52.381 0.00 0.00 35.62 3.41
1797 1873 1.653151 GCAGAAGGAACCCGTACATC 58.347 55.000 0.00 0.00 0.00 3.06
1798 1874 0.252197 GGCAGAAGGAACCCGTACAT 59.748 55.000 0.00 0.00 0.00 2.29
1896 1975 0.955428 TCGTCAGTGGAATGGCAAGC 60.955 55.000 0.00 0.00 0.00 4.01
1973 2052 4.527509 TCATAGATTCTTCAGGCGATCC 57.472 45.455 0.00 0.00 0.00 3.36
2003 2085 1.474677 CCAGGCGATTCAGAGCAGATT 60.475 52.381 0.00 0.00 34.54 2.40
2015 2101 2.790791 CGAGCTCCTTCCAGGCGAT 61.791 63.158 8.47 0.00 34.61 4.58
2027 2113 0.598065 ACAAATTTGCACCCGAGCTC 59.402 50.000 18.12 2.73 34.99 4.09
2045 2164 6.073003 GCCATTTTCACTATCTACATAGCCAC 60.073 42.308 0.00 0.00 36.18 5.01
2063 2182 5.474876 GCTAGAGTGCCTAATATGCCATTTT 59.525 40.000 0.00 0.00 0.00 1.82
2072 2191 4.405680 TGAGCAAAGCTAGAGTGCCTAATA 59.594 41.667 8.58 0.00 39.88 0.98
2073 2192 3.198635 TGAGCAAAGCTAGAGTGCCTAAT 59.801 43.478 8.58 0.00 39.88 1.73
2074 2193 2.567169 TGAGCAAAGCTAGAGTGCCTAA 59.433 45.455 8.58 0.00 39.88 2.69
2075 2194 2.167281 CTGAGCAAAGCTAGAGTGCCTA 59.833 50.000 8.58 0.00 39.88 3.93
2076 2195 0.979665 TGAGCAAAGCTAGAGTGCCT 59.020 50.000 8.58 0.00 39.88 4.75
2077 2196 1.367659 CTGAGCAAAGCTAGAGTGCC 58.632 55.000 8.58 3.07 39.88 5.01
2078 2197 1.338579 ACCTGAGCAAAGCTAGAGTGC 60.339 52.381 0.00 0.00 39.88 4.40
2079 2198 2.758736 ACCTGAGCAAAGCTAGAGTG 57.241 50.000 0.00 0.00 39.88 3.51
2080 2199 3.071602 TGAAACCTGAGCAAAGCTAGAGT 59.928 43.478 0.00 0.00 39.88 3.24
2081 2200 3.668447 TGAAACCTGAGCAAAGCTAGAG 58.332 45.455 0.00 0.00 39.88 2.43
2082 2201 3.071602 ACTGAAACCTGAGCAAAGCTAGA 59.928 43.478 0.00 0.00 39.88 2.43
2085 2204 2.355010 ACTGAAACCTGAGCAAAGCT 57.645 45.000 0.00 0.00 43.88 3.74
2092 2211 8.622948 ACCTAGAAATTTTACTGAAACCTGAG 57.377 34.615 0.00 0.00 0.00 3.35
2105 2224 3.447229 CCAATGGCGGACCTAGAAATTTT 59.553 43.478 0.00 0.00 36.63 1.82
2126 2245 4.457257 AGCTGAAACTAAAATCTGCTCACC 59.543 41.667 1.93 0.00 44.38 4.02
2133 2252 7.394359 TGCCTTATTGAGCTGAAACTAAAATCT 59.606 33.333 0.00 0.00 0.00 2.40
2135 2254 7.466746 TGCCTTATTGAGCTGAAACTAAAAT 57.533 32.000 0.00 0.00 0.00 1.82
2136 2255 6.892658 TGCCTTATTGAGCTGAAACTAAAA 57.107 33.333 0.00 0.00 0.00 1.52
2137 2256 7.466746 AATGCCTTATTGAGCTGAAACTAAA 57.533 32.000 0.00 0.00 0.00 1.85
2138 2257 8.574251 TTAATGCCTTATTGAGCTGAAACTAA 57.426 30.769 0.00 0.00 0.00 2.24
2139 2258 8.752005 ATTAATGCCTTATTGAGCTGAAACTA 57.248 30.769 0.00 0.00 0.00 2.24
2140 2259 7.651027 ATTAATGCCTTATTGAGCTGAAACT 57.349 32.000 0.00 0.00 0.00 2.66
2141 2260 9.617975 GATATTAATGCCTTATTGAGCTGAAAC 57.382 33.333 0.00 0.00 0.00 2.78
2142 2261 9.578576 AGATATTAATGCCTTATTGAGCTGAAA 57.421 29.630 0.00 0.00 0.00 2.69
2143 2262 9.224267 GAGATATTAATGCCTTATTGAGCTGAA 57.776 33.333 0.00 0.00 0.00 3.02
2144 2263 7.826252 GGAGATATTAATGCCTTATTGAGCTGA 59.174 37.037 0.00 0.00 0.00 4.26
2145 2264 7.066766 GGGAGATATTAATGCCTTATTGAGCTG 59.933 40.741 0.00 0.00 0.00 4.24
2146 2265 7.037008 AGGGAGATATTAATGCCTTATTGAGCT 60.037 37.037 0.00 0.00 32.63 4.09
2147 2266 7.115414 AGGGAGATATTAATGCCTTATTGAGC 58.885 38.462 0.00 0.00 32.63 4.26
2148 2267 7.772757 GGAGGGAGATATTAATGCCTTATTGAG 59.227 40.741 0.00 0.00 37.39 3.02
2149 2268 7.462328 AGGAGGGAGATATTAATGCCTTATTGA 59.538 37.037 0.00 0.00 37.39 2.57
2150 2269 7.637511 AGGAGGGAGATATTAATGCCTTATTG 58.362 38.462 0.00 0.00 37.39 1.90
2151 2270 7.462328 TGAGGAGGGAGATATTAATGCCTTATT 59.538 37.037 0.00 0.00 37.39 1.40
2152 2271 6.968248 TGAGGAGGGAGATATTAATGCCTTAT 59.032 38.462 0.00 0.00 37.39 1.73
2153 2272 6.331032 TGAGGAGGGAGATATTAATGCCTTA 58.669 40.000 0.00 0.00 37.39 2.69
2154 2273 5.165652 TGAGGAGGGAGATATTAATGCCTT 58.834 41.667 0.00 0.00 37.39 4.35
2155 2274 4.767908 TGAGGAGGGAGATATTAATGCCT 58.232 43.478 0.00 0.00 40.39 4.75
2156 2275 5.435291 CATGAGGAGGGAGATATTAATGCC 58.565 45.833 0.00 0.00 0.00 4.40
2157 2276 5.190528 TCCATGAGGAGGGAGATATTAATGC 59.809 44.000 0.00 0.00 39.61 3.56
2158 2277 6.881067 TCCATGAGGAGGGAGATATTAATG 57.119 41.667 0.00 0.00 39.61 1.90
2159 2278 6.216456 GGTTCCATGAGGAGGGAGATATTAAT 59.784 42.308 0.00 0.00 46.74 1.40
2160 2279 5.548056 GGTTCCATGAGGAGGGAGATATTAA 59.452 44.000 0.00 0.00 46.74 1.40
2161 2280 5.094387 GGTTCCATGAGGAGGGAGATATTA 58.906 45.833 0.00 0.00 46.74 0.98
2162 2281 3.913163 GGTTCCATGAGGAGGGAGATATT 59.087 47.826 0.00 0.00 46.74 1.28
2163 2282 3.525862 GGTTCCATGAGGAGGGAGATAT 58.474 50.000 0.00 0.00 46.74 1.63
2164 2283 2.756576 CGGTTCCATGAGGAGGGAGATA 60.757 54.545 0.00 0.00 46.74 1.98
2165 2284 1.813102 GGTTCCATGAGGAGGGAGAT 58.187 55.000 0.00 0.00 46.74 2.75
2166 2285 0.687757 CGGTTCCATGAGGAGGGAGA 60.688 60.000 0.00 0.00 46.74 3.71
2167 2286 1.826024 CGGTTCCATGAGGAGGGAG 59.174 63.158 0.00 0.00 46.74 4.30
2168 2287 2.367202 GCGGTTCCATGAGGAGGGA 61.367 63.158 0.00 0.00 46.74 4.20
2169 2288 1.915078 AAGCGGTTCCATGAGGAGGG 61.915 60.000 0.00 0.00 46.74 4.30
2170 2289 0.745845 CAAGCGGTTCCATGAGGAGG 60.746 60.000 0.00 0.00 46.74 4.30
2171 2290 0.036010 ACAAGCGGTTCCATGAGGAG 60.036 55.000 0.00 0.00 46.74 3.69
2172 2291 0.036388 GACAAGCGGTTCCATGAGGA 60.036 55.000 0.00 0.00 43.93 3.71
2173 2292 0.321564 TGACAAGCGGTTCCATGAGG 60.322 55.000 0.00 0.00 0.00 3.86
2174 2293 1.081892 CTGACAAGCGGTTCCATGAG 58.918 55.000 0.00 0.00 0.00 2.90
2175 2294 0.684535 TCTGACAAGCGGTTCCATGA 59.315 50.000 0.00 0.00 0.00 3.07
2176 2295 1.081892 CTCTGACAAGCGGTTCCATG 58.918 55.000 0.00 0.00 0.00 3.66
2177 2296 0.687354 ACTCTGACAAGCGGTTCCAT 59.313 50.000 0.00 0.00 0.00 3.41
2178 2297 0.468226 AACTCTGACAAGCGGTTCCA 59.532 50.000 0.00 0.00 0.00 3.53
2179 2298 0.868406 CAACTCTGACAAGCGGTTCC 59.132 55.000 0.00 0.00 0.00 3.62
2180 2299 0.235926 GCAACTCTGACAAGCGGTTC 59.764 55.000 0.00 0.00 0.00 3.62
2181 2300 0.463654 TGCAACTCTGACAAGCGGTT 60.464 50.000 0.00 0.00 0.00 4.44
2182 2301 0.463654 TTGCAACTCTGACAAGCGGT 60.464 50.000 0.00 0.00 0.00 5.68
2183 2302 0.877071 ATTGCAACTCTGACAAGCGG 59.123 50.000 0.00 0.00 0.00 5.52
2184 2303 1.135859 GGATTGCAACTCTGACAAGCG 60.136 52.381 0.00 0.00 30.60 4.68
2185 2304 1.881973 TGGATTGCAACTCTGACAAGC 59.118 47.619 0.00 0.00 0.00 4.01
2186 2305 4.037208 AGTTTGGATTGCAACTCTGACAAG 59.963 41.667 0.00 0.00 0.00 3.16
2187 2306 3.953612 AGTTTGGATTGCAACTCTGACAA 59.046 39.130 0.00 0.00 0.00 3.18
2188 2307 3.554934 AGTTTGGATTGCAACTCTGACA 58.445 40.909 0.00 0.00 0.00 3.58
2189 2308 4.036734 TGAAGTTTGGATTGCAACTCTGAC 59.963 41.667 0.00 0.00 31.79 3.51
2190 2309 4.206375 TGAAGTTTGGATTGCAACTCTGA 58.794 39.130 0.00 0.00 31.79 3.27
2191 2310 4.572985 TGAAGTTTGGATTGCAACTCTG 57.427 40.909 0.00 0.00 31.79 3.35
2192 2311 5.596836 TTTGAAGTTTGGATTGCAACTCT 57.403 34.783 0.00 0.00 31.79 3.24
2193 2312 5.812127 ACTTTTGAAGTTTGGATTGCAACTC 59.188 36.000 0.00 0.50 39.04 3.01
2201 2320 5.339990 CAACACGACTTTTGAAGTTTGGAT 58.660 37.500 0.00 0.00 43.03 3.41
2213 2332 2.550830 AGGATGAGCAACACGACTTT 57.449 45.000 0.00 0.00 0.00 2.66
2390 2741 5.659440 TTTTAAGTGAATGATGGCCTTCC 57.341 39.130 15.62 1.68 0.00 3.46
2432 2783 3.623906 AGCACAGTGAATACAGAGCAT 57.376 42.857 4.15 0.00 33.53 3.79
2443 2794 1.268079 CTGACTCGAGAAGCACAGTGA 59.732 52.381 21.68 0.00 31.93 3.41
2453 2804 6.612247 TTGTAAAATTTTGCTGACTCGAGA 57.388 33.333 21.68 0.00 0.00 4.04
2456 2807 5.630680 AGCATTGTAAAATTTTGCTGACTCG 59.369 36.000 18.09 4.51 41.79 4.18
2457 2808 6.089954 GGAGCATTGTAAAATTTTGCTGACTC 59.910 38.462 16.86 16.35 43.29 3.36
2460 2811 5.221601 TGGGAGCATTGTAAAATTTTGCTGA 60.222 36.000 16.86 8.17 43.29 4.26
2464 2815 7.256756 TGTTTGGGAGCATTGTAAAATTTTG 57.743 32.000 13.76 0.00 0.00 2.44
2469 2820 4.599047 CCTGTTTGGGAGCATTGTAAAA 57.401 40.909 0.00 0.00 0.00 1.52
2507 2866 4.079253 GTCCAGGTATCAAGCTTTGGAAA 58.921 43.478 15.23 0.00 29.80 3.13
2514 2873 1.115467 CCGAGTCCAGGTATCAAGCT 58.885 55.000 0.00 0.00 0.00 3.74
2518 2877 1.001120 TGCCCGAGTCCAGGTATCA 59.999 57.895 0.00 0.00 0.00 2.15
2521 2880 0.040058 TAACTGCCCGAGTCCAGGTA 59.960 55.000 0.80 0.00 31.73 3.08
2543 2902 5.056894 AGCTGATCTCTTGAACAATTTGC 57.943 39.130 0.00 0.00 0.00 3.68
2544 2903 8.509690 TCTTTAGCTGATCTCTTGAACAATTTG 58.490 33.333 0.00 0.00 0.00 2.32
2545 2904 8.627208 TCTTTAGCTGATCTCTTGAACAATTT 57.373 30.769 0.00 0.00 0.00 1.82
2556 2915 6.405176 CCAACCCAAATTCTTTAGCTGATCTC 60.405 42.308 0.00 0.00 0.00 2.75
2559 2918 5.086621 ACCAACCCAAATTCTTTAGCTGAT 58.913 37.500 0.00 0.00 0.00 2.90
2575 2934 1.549170 TCGCTCTCTAAAGACCAACCC 59.451 52.381 0.00 0.00 0.00 4.11
2587 2946 2.086054 ATTTTCTTGCGTCGCTCTCT 57.914 45.000 19.50 0.00 0.00 3.10
2589 2948 2.668457 CAGTATTTTCTTGCGTCGCTCT 59.332 45.455 19.50 0.60 0.00 4.09
2596 2980 4.148891 GTTCGGTTCAGTATTTTCTTGCG 58.851 43.478 0.00 0.00 0.00 4.85
2609 2993 1.683917 CCATGGTTTTGGTTCGGTTCA 59.316 47.619 2.57 0.00 31.74 3.18
2611 2995 2.074729 TCCATGGTTTTGGTTCGGTT 57.925 45.000 12.58 0.00 38.01 4.44
2613 2997 3.460857 TTTTCCATGGTTTTGGTTCGG 57.539 42.857 12.58 0.00 38.01 4.30
2614 2998 4.184629 TGTTTTTCCATGGTTTTGGTTCG 58.815 39.130 12.58 0.00 38.01 3.95
2615 2999 6.459435 CCAATGTTTTTCCATGGTTTTGGTTC 60.459 38.462 12.58 0.00 38.01 3.62
2621 3006 5.122519 GTGACCAATGTTTTTCCATGGTTT 58.877 37.500 12.58 0.00 31.06 3.27
2624 3009 4.039004 TCTGTGACCAATGTTTTTCCATGG 59.961 41.667 4.97 4.97 0.00 3.66
2627 3012 5.047021 TGTTTCTGTGACCAATGTTTTTCCA 60.047 36.000 0.00 0.00 0.00 3.53
2631 3016 7.605691 TGATTTTGTTTCTGTGACCAATGTTTT 59.394 29.630 0.00 0.00 0.00 2.43
2634 3019 6.219417 TGATTTTGTTTCTGTGACCAATGT 57.781 33.333 0.00 0.00 0.00 2.71
2641 3026 5.984926 GCTCCATTTGATTTTGTTTCTGTGA 59.015 36.000 0.00 0.00 0.00 3.58
2650 3035 5.389859 TGTGTAGGCTCCATTTGATTTTG 57.610 39.130 0.00 0.00 0.00 2.44
2655 3040 3.788227 ACTTGTGTAGGCTCCATTTGA 57.212 42.857 0.00 0.00 0.00 2.69
2657 3042 3.181434 TGGAACTTGTGTAGGCTCCATTT 60.181 43.478 0.00 0.00 35.93 2.32
2697 3087 8.482852 TGATCTATGACAGTGATTATCTGGAA 57.517 34.615 0.00 0.00 37.25 3.53
2698 3088 8.482852 TTGATCTATGACAGTGATTATCTGGA 57.517 34.615 0.00 0.00 37.25 3.86
2699 3089 9.368674 GATTGATCTATGACAGTGATTATCTGG 57.631 37.037 0.00 0.00 37.25 3.86
2702 3092 9.716531 TTGGATTGATCTATGACAGTGATTATC 57.283 33.333 0.00 0.00 0.00 1.75
2703 3093 9.499479 GTTGGATTGATCTATGACAGTGATTAT 57.501 33.333 0.00 0.00 0.00 1.28
2705 3095 7.341030 TGTTGGATTGATCTATGACAGTGATT 58.659 34.615 0.00 0.00 0.00 2.57
2706 3096 6.892485 TGTTGGATTGATCTATGACAGTGAT 58.108 36.000 0.00 0.00 0.00 3.06
2707 3097 6.298441 TGTTGGATTGATCTATGACAGTGA 57.702 37.500 0.00 0.00 0.00 3.41
2708 3098 6.457934 GCTTGTTGGATTGATCTATGACAGTG 60.458 42.308 0.00 0.00 0.00 3.66
2709 3099 5.587844 GCTTGTTGGATTGATCTATGACAGT 59.412 40.000 0.00 0.00 0.00 3.55
2710 3100 5.821470 AGCTTGTTGGATTGATCTATGACAG 59.179 40.000 0.00 0.00 0.00 3.51
2712 3102 5.238214 GGAGCTTGTTGGATTGATCTATGAC 59.762 44.000 0.00 0.00 0.00 3.06
2716 3110 5.045651 TCAAGGAGCTTGTTGGATTGATCTA 60.046 40.000 8.64 0.00 41.66 1.98
2725 3119 0.449388 GCGATCAAGGAGCTTGTTGG 59.551 55.000 8.64 0.00 41.66 3.77
2743 3137 5.353678 GCAGATGAAGGATACAGATAATGGC 59.646 44.000 0.00 0.00 41.41 4.40
2752 3146 3.023832 TCGTGAGCAGATGAAGGATACA 58.976 45.455 0.00 0.00 41.41 2.29
2754 3148 3.701542 ACTTCGTGAGCAGATGAAGGATA 59.298 43.478 16.89 0.00 41.49 2.59
2755 3149 2.499289 ACTTCGTGAGCAGATGAAGGAT 59.501 45.455 16.89 0.29 41.49 3.24
2783 3177 1.645455 CGATCAATTGGAGCTGCCG 59.355 57.895 5.42 0.00 40.66 5.69
2805 3199 5.116084 TGAAAACCTTGGAGCAGCTATAT 57.884 39.130 0.00 0.00 0.00 0.86
2806 3200 4.568072 TGAAAACCTTGGAGCAGCTATA 57.432 40.909 0.00 0.00 0.00 1.31
2807 3201 3.439857 TGAAAACCTTGGAGCAGCTAT 57.560 42.857 0.00 0.00 0.00 2.97
2823 3217 2.224549 CGCTTGTGAACGGGTAATGAAA 59.775 45.455 0.00 0.00 0.00 2.69
2832 3226 2.978010 AAGGGCGCTTGTGAACGG 60.978 61.111 16.16 0.00 0.00 4.44
2840 3238 3.357079 CGCAGAACAAGGGCGCTT 61.357 61.111 10.73 10.73 44.49 4.68
2857 3255 2.730129 AAACCAGGGTGCATGGGGTC 62.730 60.000 9.58 0.00 42.48 4.46
2858 3256 2.789149 AAACCAGGGTGCATGGGGT 61.789 57.895 9.58 3.39 42.48 4.95
2863 3271 1.967779 GGTAAACAAACCAGGGTGCAT 59.032 47.619 0.00 0.00 39.50 3.96
2875 3283 3.375699 TGGCAAAAAGGAGGGTAAACAA 58.624 40.909 0.00 0.00 0.00 2.83
2927 3335 1.613836 ACTGAAAAGGAAGCTGCCAG 58.386 50.000 15.05 3.10 0.00 4.85
2929 3337 1.068954 CGAACTGAAAAGGAAGCTGCC 60.069 52.381 0.73 0.73 0.00 4.85
2939 3348 4.394920 AGAACAGCTCAAACGAACTGAAAA 59.605 37.500 0.00 0.00 32.13 2.29


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

AutoCloner maintained by Alex Coulton.