Multiple sequence alignment - TraesCS7D01G380200

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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 TraesCS7D01G380200 chr7D 100.000 2481 0 0 1 2481 492767090 492764610 0.000000e+00 4582
1 TraesCS7D01G380200 chr7D 98.398 999 16 0 1 999 490651923 490652921 0.000000e+00 1757
2 TraesCS7D01G380200 chr7D 98.298 999 17 0 1 999 490642072 490643070 0.000000e+00 1751
3 TraesCS7D01G380200 chr7D 98.100 1000 17 2 1 1000 494000027 494001024 0.000000e+00 1740
4 TraesCS7D01G380200 chr7D 97.203 1001 25 3 1 999 179390625 179391624 0.000000e+00 1690
5 TraesCS7D01G380200 chr7D 93.245 681 45 1 1512 2191 204671781 204671101 0.000000e+00 1002
6 TraesCS7D01G380200 chr7D 92.679 683 50 0 1509 2191 375340335 375339653 0.000000e+00 985
7 TraesCS7D01G380200 chr3D 98.098 999 17 2 1 999 472774463 472773467 0.000000e+00 1738
8 TraesCS7D01G380200 chr3D 98.098 999 17 2 1 999 472784297 472783301 0.000000e+00 1738
9 TraesCS7D01G380200 chr3D 92.464 690 51 1 1503 2192 525785044 525785732 0.000000e+00 985
10 TraesCS7D01G380200 chr3D 86.942 291 31 5 2192 2481 515844202 515844486 1.110000e-83 320
11 TraesCS7D01G380200 chr2D 97.405 1002 22 3 1 999 410861439 410862439 0.000000e+00 1703
12 TraesCS7D01G380200 chr2D 92.219 694 53 1 1502 2194 333235157 333234464 0.000000e+00 981
13 TraesCS7D01G380200 chr2D 94.706 510 22 2 1000 1508 190430073 190429568 0.000000e+00 787
14 TraesCS7D01G380200 chrUn 97.400 1000 24 2 1 999 364457597 364456599 0.000000e+00 1701
15 TraesCS7D01G380200 chrUn 97.200 1000 26 2 1 999 364509883 364508885 0.000000e+00 1690
16 TraesCS7D01G380200 chrUn 86.942 291 35 3 2192 2481 420396047 420395759 8.560000e-85 324
17 TraesCS7D01G380200 chr5D 92.982 684 48 0 1510 2193 418805191 418805874 0.000000e+00 998
18 TraesCS7D01G380200 chr5D 92.857 686 49 0 1509 2194 302776531 302775846 0.000000e+00 996
19 TraesCS7D01G380200 chr5D 92.826 683 48 1 1509 2191 527202939 527202258 0.000000e+00 989
20 TraesCS7D01G380200 chr5D 94.466 506 23 2 1000 1504 189272501 189272000 0.000000e+00 774
21 TraesCS7D01G380200 chr5D 94.269 506 23 3 1000 1504 189461303 189460803 0.000000e+00 769
22 TraesCS7D01G380200 chr1B 93.068 678 47 0 1512 2189 641696590 641695913 0.000000e+00 992
23 TraesCS7D01G380200 chr1B 86.254 291 36 4 2192 2481 188691291 188691578 1.850000e-81 313
24 TraesCS7D01G380200 chr1A 92.230 695 54 0 1497 2191 377673072 377673766 0.000000e+00 985
25 TraesCS7D01G380200 chr3A 93.465 505 29 3 1000 1504 691087867 691088367 0.000000e+00 747
26 TraesCS7D01G380200 chr3A 86.942 291 35 3 2192 2481 439273137 439273425 8.560000e-85 324
27 TraesCS7D01G380200 chr7A 93.083 506 30 4 1000 1504 427519850 427519349 0.000000e+00 736
28 TraesCS7D01G380200 chr7A 90.037 271 24 3 2212 2481 546340665 546340933 5.080000e-92 348
29 TraesCS7D01G380200 chr5A 93.083 506 29 3 1000 1505 81480735 81481234 0.000000e+00 736
30 TraesCS7D01G380200 chr5A 93.083 506 30 4 1000 1504 429969334 429968833 0.000000e+00 736
31 TraesCS7D01G380200 chr5A 92.885 506 31 4 1000 1504 676897615 676897114 0.000000e+00 730
32 TraesCS7D01G380200 chr4A 92.475 505 35 2 1000 1504 352263211 352262710 0.000000e+00 719
33 TraesCS7D01G380200 chr4B 88.660 291 29 4 2192 2481 147689474 147689761 3.930000e-93 351
34 TraesCS7D01G380200 chr3B 87.329 292 32 5 2192 2481 182819254 182818966 1.840000e-86 329
35 TraesCS7D01G380200 chr5B 86.942 291 35 3 2192 2481 116949619 116949331 8.560000e-85 324
36 TraesCS7D01G380200 chr4D 87.868 272 32 1 2210 2481 125161058 125160788 3.980000e-83 318


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 TraesCS7D01G380200 chr7D 492764610 492767090 2480 True 4582 4582 100.000 1 2481 1 chr7D.!!$R3 2480
1 TraesCS7D01G380200 chr7D 490651923 490652921 998 False 1757 1757 98.398 1 999 1 chr7D.!!$F3 998
2 TraesCS7D01G380200 chr7D 490642072 490643070 998 False 1751 1751 98.298 1 999 1 chr7D.!!$F2 998
3 TraesCS7D01G380200 chr7D 494000027 494001024 997 False 1740 1740 98.100 1 1000 1 chr7D.!!$F4 999
4 TraesCS7D01G380200 chr7D 179390625 179391624 999 False 1690 1690 97.203 1 999 1 chr7D.!!$F1 998
5 TraesCS7D01G380200 chr7D 204671101 204671781 680 True 1002 1002 93.245 1512 2191 1 chr7D.!!$R1 679
6 TraesCS7D01G380200 chr7D 375339653 375340335 682 True 985 985 92.679 1509 2191 1 chr7D.!!$R2 682
7 TraesCS7D01G380200 chr3D 472773467 472774463 996 True 1738 1738 98.098 1 999 1 chr3D.!!$R1 998
8 TraesCS7D01G380200 chr3D 472783301 472784297 996 True 1738 1738 98.098 1 999 1 chr3D.!!$R2 998
9 TraesCS7D01G380200 chr3D 525785044 525785732 688 False 985 985 92.464 1503 2192 1 chr3D.!!$F2 689
10 TraesCS7D01G380200 chr2D 410861439 410862439 1000 False 1703 1703 97.405 1 999 1 chr2D.!!$F1 998
11 TraesCS7D01G380200 chr2D 333234464 333235157 693 True 981 981 92.219 1502 2194 1 chr2D.!!$R2 692
12 TraesCS7D01G380200 chr2D 190429568 190430073 505 True 787 787 94.706 1000 1508 1 chr2D.!!$R1 508
13 TraesCS7D01G380200 chrUn 364456599 364457597 998 True 1701 1701 97.400 1 999 1 chrUn.!!$R1 998
14 TraesCS7D01G380200 chrUn 364508885 364509883 998 True 1690 1690 97.200 1 999 1 chrUn.!!$R2 998
15 TraesCS7D01G380200 chr5D 418805191 418805874 683 False 998 998 92.982 1510 2193 1 chr5D.!!$F1 683
16 TraesCS7D01G380200 chr5D 302775846 302776531 685 True 996 996 92.857 1509 2194 1 chr5D.!!$R3 685
17 TraesCS7D01G380200 chr5D 527202258 527202939 681 True 989 989 92.826 1509 2191 1 chr5D.!!$R4 682
18 TraesCS7D01G380200 chr5D 189272000 189272501 501 True 774 774 94.466 1000 1504 1 chr5D.!!$R1 504
19 TraesCS7D01G380200 chr5D 189460803 189461303 500 True 769 769 94.269 1000 1504 1 chr5D.!!$R2 504
20 TraesCS7D01G380200 chr1B 641695913 641696590 677 True 992 992 93.068 1512 2189 1 chr1B.!!$R1 677
21 TraesCS7D01G380200 chr1A 377673072 377673766 694 False 985 985 92.230 1497 2191 1 chr1A.!!$F1 694
22 TraesCS7D01G380200 chr3A 691087867 691088367 500 False 747 747 93.465 1000 1504 1 chr3A.!!$F2 504
23 TraesCS7D01G380200 chr7A 427519349 427519850 501 True 736 736 93.083 1000 1504 1 chr7A.!!$R1 504
24 TraesCS7D01G380200 chr5A 429968833 429969334 501 True 736 736 93.083 1000 1504 1 chr5A.!!$R1 504
25 TraesCS7D01G380200 chr5A 676897114 676897615 501 True 730 730 92.885 1000 1504 1 chr5A.!!$R2 504
26 TraesCS7D01G380200 chr4A 352262710 352263211 501 True 719 719 92.475 1000 1504 1 chr4A.!!$R1 504

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
868 874 2.358957 TGGCAGATCTTTGGTGAATCG 58.641 47.619 0.0 0.0 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1814 1821 0.708209 TGAGGCCTAGGGTCTGTACA 59.292 55.0 4.42 0.0 38.01 2.9 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
527 530 6.040247 GGAAAGAAGTTTGGTGGTAAAAGTG 58.960 40.000 0.00 0.00 0.00 3.16
840 846 9.803315 GAGTCAAATGAAAAGTAAAAACTTCCT 57.197 29.630 0.00 0.00 0.00 3.36
859 865 3.782523 TCCTAGACCAATGGCAGATCTTT 59.217 43.478 0.00 0.00 0.00 2.52
868 874 2.358957 TGGCAGATCTTTGGTGAATCG 58.641 47.619 0.00 0.00 0.00 3.34
1060 1067 1.474330 TGATCTGCTTAGAGGCACGA 58.526 50.000 0.00 0.00 37.29 4.35
1114 1121 0.958091 CATTGTTGGCGGAAGTTGGA 59.042 50.000 0.00 0.00 0.00 3.53
1116 1123 0.821711 TTGTTGGCGGAAGTTGGAGG 60.822 55.000 0.00 0.00 0.00 4.30
1212 1219 3.694889 GTGCAACCGCCTTATTGTC 57.305 52.632 0.00 0.00 37.32 3.18
1218 1225 2.811431 CAACCGCCTTATTGTCAACTCA 59.189 45.455 0.00 0.00 0.00 3.41
1230 1237 9.186323 CTTATTGTCAACTCAGATAATACGGAG 57.814 37.037 0.00 0.00 33.25 4.63
1237 1244 6.732896 ACTCAGATAATACGGAGGTGATTT 57.267 37.500 0.00 0.00 36.65 2.17
1265 1272 2.571653 TGAAGAATGGAGGACAATCGGT 59.428 45.455 0.00 0.00 34.12 4.69
1272 1279 1.613630 AGGACAATCGGTGGGAGCT 60.614 57.895 0.00 0.00 0.00 4.09
1273 1280 0.325296 AGGACAATCGGTGGGAGCTA 60.325 55.000 0.00 0.00 0.00 3.32
1274 1281 0.105039 GGACAATCGGTGGGAGCTAG 59.895 60.000 0.00 0.00 0.00 3.42
1275 1282 0.530870 GACAATCGGTGGGAGCTAGC 60.531 60.000 6.62 6.62 0.00 3.42
1316 1323 5.595257 TGATTGCTATTTTATGGCTTGCA 57.405 34.783 0.00 0.00 37.67 4.08
1333 1340 7.703328 TGGCTTGCAAATTTACTATTACTAGC 58.297 34.615 0.00 0.00 0.00 3.42
1389 1396 3.494048 GCTCATGAACATGCTAGGCTAGT 60.494 47.826 21.92 2.26 38.65 2.57
1439 1446 3.205056 TGAGGAGCCCATGGTTGATATTT 59.795 43.478 11.73 0.00 0.00 1.40
1616 1623 3.506455 TGGATAGATCGATCGGAAAGGAC 59.494 47.826 19.33 6.85 0.00 3.85
1625 1632 2.249844 TCGGAAAGGACAACTTGGTC 57.750 50.000 0.00 0.00 39.96 4.02
1630 1637 4.392138 CGGAAAGGACAACTTGGTCTTATC 59.608 45.833 0.00 0.00 39.96 1.75
1757 1764 1.658596 GTGATGCTTCATCGCACGTTA 59.341 47.619 13.58 0.00 46.70 3.18
1782 1789 8.469309 AAGGGATTGTTATGTGATCCAATTAG 57.531 34.615 4.23 0.00 40.88 1.73
1814 1821 3.808466 TGAGAGATTGCACTAGCGAAT 57.192 42.857 0.00 0.00 46.23 3.34
1846 1853 3.881937 AGGCCTCATTTTCAAGCATTC 57.118 42.857 0.00 0.00 0.00 2.67
1854 1861 6.351202 CCTCATTTTCAAGCATTCCAATACCA 60.351 38.462 0.00 0.00 0.00 3.25
2019 2027 0.600255 GTTGGGGACACACGAGACTG 60.600 60.000 0.00 0.00 42.67 3.51
2052 2060 1.967319 TGCAGGGTTGTTTGAGAGAC 58.033 50.000 0.00 0.00 0.00 3.36
2083 2091 2.050144 TCCTATGCCTCCCACAGATTC 58.950 52.381 0.00 0.00 0.00 2.52
2108 2116 3.983044 ACCTTAGGTCATCCACTTGAC 57.017 47.619 0.00 0.00 44.27 3.18
2117 2125 4.379499 GGTCATCCACTTGACGGAAAATTC 60.379 45.833 0.00 0.00 45.63 2.17
2169 2177 3.265791 GCCCAACATGAGTCTACAAGAG 58.734 50.000 0.00 0.00 0.00 2.85
2194 2202 6.398095 CAAGTTGTGTAGTAGACATCATGGA 58.602 40.000 10.23 0.00 41.14 3.41
2195 2203 6.798427 AGTTGTGTAGTAGACATCATGGAT 57.202 37.500 10.23 0.00 41.14 3.41
2196 2204 7.187824 AGTTGTGTAGTAGACATCATGGATT 57.812 36.000 10.23 0.00 41.14 3.01
2197 2205 7.268586 AGTTGTGTAGTAGACATCATGGATTC 58.731 38.462 10.23 0.00 41.14 2.52
2198 2206 6.790232 TGTGTAGTAGACATCATGGATTCA 57.210 37.500 0.00 0.00 41.14 2.57
2199 2207 7.181569 TGTGTAGTAGACATCATGGATTCAA 57.818 36.000 0.00 0.00 41.14 2.69
2200 2208 7.619965 TGTGTAGTAGACATCATGGATTCAAA 58.380 34.615 0.00 0.00 41.14 2.69
2201 2209 8.267183 TGTGTAGTAGACATCATGGATTCAAAT 58.733 33.333 0.00 0.00 41.14 2.32
2202 2210 9.113838 GTGTAGTAGACATCATGGATTCAAATT 57.886 33.333 0.00 0.00 41.14 1.82
2206 2214 8.790718 AGTAGACATCATGGATTCAAATTATGC 58.209 33.333 0.00 0.00 0.00 3.14
2207 2215 7.834881 AGACATCATGGATTCAAATTATGCT 57.165 32.000 0.00 0.00 0.00 3.79
2208 2216 8.929260 AGACATCATGGATTCAAATTATGCTA 57.071 30.769 0.00 0.00 0.00 3.49
2209 2217 9.529823 AGACATCATGGATTCAAATTATGCTAT 57.470 29.630 0.00 0.00 0.00 2.97
2210 2218 9.569167 GACATCATGGATTCAAATTATGCTATG 57.431 33.333 0.00 0.00 0.00 2.23
2211 2219 9.304335 ACATCATGGATTCAAATTATGCTATGA 57.696 29.630 0.00 0.00 0.00 2.15
2212 2220 9.788960 CATCATGGATTCAAATTATGCTATGAG 57.211 33.333 0.00 0.00 0.00 2.90
2213 2221 9.749340 ATCATGGATTCAAATTATGCTATGAGA 57.251 29.630 0.00 0.00 0.00 3.27
2214 2222 9.577222 TCATGGATTCAAATTATGCTATGAGAA 57.423 29.630 0.00 0.00 0.00 2.87
2218 2226 9.468532 GGATTCAAATTATGCTATGAGAAAACC 57.531 33.333 0.00 0.00 0.00 3.27
2222 2230 9.241919 TCAAATTATGCTATGAGAAAACCTTCA 57.758 29.630 0.00 0.00 33.64 3.02
2225 2233 8.985315 ATTATGCTATGAGAAAACCTTCATGA 57.015 30.769 0.00 0.00 33.64 3.07
2226 2234 6.690194 ATGCTATGAGAAAACCTTCATGAC 57.310 37.500 0.00 0.00 33.64 3.06
2227 2235 5.559770 TGCTATGAGAAAACCTTCATGACA 58.440 37.500 0.00 0.00 33.64 3.58
2228 2236 6.182627 TGCTATGAGAAAACCTTCATGACAT 58.817 36.000 0.00 0.00 33.64 3.06
2229 2237 6.317140 TGCTATGAGAAAACCTTCATGACATC 59.683 38.462 0.00 0.00 33.64 3.06
2230 2238 6.541641 GCTATGAGAAAACCTTCATGACATCT 59.458 38.462 0.00 0.00 33.64 2.90
2231 2239 6.998968 ATGAGAAAACCTTCATGACATCTC 57.001 37.500 0.00 3.59 33.64 2.75
2232 2240 5.248640 TGAGAAAACCTTCATGACATCTCC 58.751 41.667 0.00 0.00 33.64 3.71
2233 2241 5.013495 TGAGAAAACCTTCATGACATCTCCT 59.987 40.000 0.00 0.00 33.64 3.69
2234 2242 5.885465 AGAAAACCTTCATGACATCTCCTT 58.115 37.500 0.00 0.00 33.64 3.36
2235 2243 6.310149 AGAAAACCTTCATGACATCTCCTTT 58.690 36.000 0.00 0.00 33.64 3.11
2236 2244 5.972107 AAACCTTCATGACATCTCCTTTG 57.028 39.130 0.00 0.00 0.00 2.77
2237 2245 4.647564 ACCTTCATGACATCTCCTTTGT 57.352 40.909 0.00 0.00 0.00 2.83
2238 2246 4.583871 ACCTTCATGACATCTCCTTTGTC 58.416 43.478 0.00 0.00 43.04 3.18
2245 2253 5.947228 TGACATCTCCTTTGTCACAAATC 57.053 39.130 2.71 0.00 46.31 2.17
2246 2254 5.375773 TGACATCTCCTTTGTCACAAATCA 58.624 37.500 2.71 0.00 46.31 2.57
2247 2255 6.005823 TGACATCTCCTTTGTCACAAATCAT 58.994 36.000 2.71 0.00 46.31 2.45
2248 2256 6.491062 TGACATCTCCTTTGTCACAAATCATT 59.509 34.615 2.71 0.00 46.31 2.57
2249 2257 7.014518 TGACATCTCCTTTGTCACAAATCATTT 59.985 33.333 2.71 0.00 46.31 2.32
2250 2258 7.373493 ACATCTCCTTTGTCACAAATCATTTC 58.627 34.615 2.71 0.00 0.00 2.17
2251 2259 6.957920 TCTCCTTTGTCACAAATCATTTCA 57.042 33.333 2.71 0.00 0.00 2.69
2252 2260 7.345422 TCTCCTTTGTCACAAATCATTTCAA 57.655 32.000 2.71 0.00 0.00 2.69
2253 2261 7.780064 TCTCCTTTGTCACAAATCATTTCAAA 58.220 30.769 2.71 0.00 0.00 2.69
2254 2262 7.922278 TCTCCTTTGTCACAAATCATTTCAAAG 59.078 33.333 2.71 12.17 39.53 2.77
2255 2263 7.555087 TCCTTTGTCACAAATCATTTCAAAGT 58.445 30.769 15.61 0.00 38.75 2.66
2256 2264 8.690884 TCCTTTGTCACAAATCATTTCAAAGTA 58.309 29.630 15.61 3.56 38.75 2.24
2257 2265 8.755018 CCTTTGTCACAAATCATTTCAAAGTAC 58.245 33.333 15.61 0.00 38.75 2.73
2258 2266 9.520204 CTTTGTCACAAATCATTTCAAAGTACT 57.480 29.630 2.71 0.00 36.96 2.73
2259 2267 9.515020 TTTGTCACAAATCATTTCAAAGTACTC 57.485 29.630 0.00 0.00 0.00 2.59
2260 2268 8.219546 TGTCACAAATCATTTCAAAGTACTCA 57.780 30.769 0.00 0.00 0.00 3.41
2261 2269 8.128582 TGTCACAAATCATTTCAAAGTACTCAC 58.871 33.333 0.00 0.00 0.00 3.51
2262 2270 8.345565 GTCACAAATCATTTCAAAGTACTCACT 58.654 33.333 0.00 0.00 36.19 3.41
2263 2271 9.554395 TCACAAATCATTTCAAAGTACTCACTA 57.446 29.630 0.00 0.00 33.48 2.74
2296 2304 9.897744 TCTAATTCATTTCAAAGATTGTGTGAC 57.102 29.630 0.00 0.00 0.00 3.67
2297 2305 9.681692 CTAATTCATTTCAAAGATTGTGTGACA 57.318 29.630 0.00 0.00 0.00 3.58
2298 2306 8.583810 AATTCATTTCAAAGATTGTGTGACAG 57.416 30.769 0.00 0.00 0.00 3.51
2299 2307 6.075762 TCATTTCAAAGATTGTGTGACAGG 57.924 37.500 0.00 0.00 0.00 4.00
2300 2308 5.827267 TCATTTCAAAGATTGTGTGACAGGA 59.173 36.000 0.00 0.00 0.00 3.86
2301 2309 6.320926 TCATTTCAAAGATTGTGTGACAGGAA 59.679 34.615 0.00 0.00 0.00 3.36
2302 2310 6.713762 TTTCAAAGATTGTGTGACAGGAAT 57.286 33.333 0.00 0.00 0.00 3.01
2303 2311 6.713762 TTCAAAGATTGTGTGACAGGAATT 57.286 33.333 0.00 0.00 0.00 2.17
2304 2312 7.815840 TTCAAAGATTGTGTGACAGGAATTA 57.184 32.000 0.00 0.00 0.00 1.40
2305 2313 8.408043 TTCAAAGATTGTGTGACAGGAATTAT 57.592 30.769 0.00 0.00 0.00 1.28
2306 2314 8.044060 TCAAAGATTGTGTGACAGGAATTATC 57.956 34.615 0.00 0.00 0.00 1.75
2307 2315 7.884877 TCAAAGATTGTGTGACAGGAATTATCT 59.115 33.333 0.00 0.00 0.00 1.98
2308 2316 7.856145 AAGATTGTGTGACAGGAATTATCTC 57.144 36.000 0.00 0.00 0.00 2.75
2309 2317 6.950842 AGATTGTGTGACAGGAATTATCTCA 58.049 36.000 0.00 0.00 0.00 3.27
2310 2318 7.046652 AGATTGTGTGACAGGAATTATCTCAG 58.953 38.462 0.00 0.00 0.00 3.35
2311 2319 6.358974 TTGTGTGACAGGAATTATCTCAGA 57.641 37.500 0.00 0.00 0.00 3.27
2312 2320 5.724328 TGTGTGACAGGAATTATCTCAGAC 58.276 41.667 0.00 0.00 0.00 3.51
2313 2321 5.245977 TGTGTGACAGGAATTATCTCAGACA 59.754 40.000 0.00 0.00 32.61 3.41
2314 2322 5.578727 GTGTGACAGGAATTATCTCAGACAC 59.421 44.000 0.00 0.00 28.16 3.67
2315 2323 5.481824 TGTGACAGGAATTATCTCAGACACT 59.518 40.000 0.00 0.00 0.00 3.55
2316 2324 5.809562 GTGACAGGAATTATCTCAGACACTG 59.190 44.000 0.00 0.00 0.00 3.66
2317 2325 5.481824 TGACAGGAATTATCTCAGACACTGT 59.518 40.000 0.00 0.00 39.14 3.55
2318 2326 6.014242 TGACAGGAATTATCTCAGACACTGTT 60.014 38.462 0.00 0.00 36.85 3.16
2319 2327 6.169094 ACAGGAATTATCTCAGACACTGTTG 58.831 40.000 0.00 0.00 33.31 3.33
2320 2328 6.014242 ACAGGAATTATCTCAGACACTGTTGA 60.014 38.462 0.00 0.00 33.31 3.18
2321 2329 6.534436 CAGGAATTATCTCAGACACTGTTGAG 59.466 42.308 11.93 11.93 41.67 3.02
2322 2330 6.212388 AGGAATTATCTCAGACACTGTTGAGT 59.788 38.462 15.26 9.31 41.21 3.41
2333 2341 4.556942 CACTGTTGAGTGCATTGAAAGA 57.443 40.909 0.00 0.00 43.24 2.52
2334 2342 4.923893 CACTGTTGAGTGCATTGAAAGAA 58.076 39.130 0.00 0.00 43.24 2.52
2335 2343 5.526115 CACTGTTGAGTGCATTGAAAGAAT 58.474 37.500 0.00 0.00 43.24 2.40
2336 2344 5.628193 CACTGTTGAGTGCATTGAAAGAATC 59.372 40.000 0.00 0.00 43.24 2.52
2337 2345 5.125100 TGTTGAGTGCATTGAAAGAATCC 57.875 39.130 0.00 0.00 0.00 3.01
2338 2346 4.828939 TGTTGAGTGCATTGAAAGAATCCT 59.171 37.500 0.00 0.00 0.00 3.24
2339 2347 5.048504 TGTTGAGTGCATTGAAAGAATCCTC 60.049 40.000 0.00 0.00 0.00 3.71
2340 2348 3.686241 TGAGTGCATTGAAAGAATCCTCG 59.314 43.478 0.00 0.00 0.00 4.63
2341 2349 3.935203 GAGTGCATTGAAAGAATCCTCGA 59.065 43.478 0.00 0.00 0.00 4.04
2342 2350 4.326826 AGTGCATTGAAAGAATCCTCGAA 58.673 39.130 0.00 0.00 0.00 3.71
2343 2351 4.946157 AGTGCATTGAAAGAATCCTCGAAT 59.054 37.500 0.00 0.00 0.00 3.34
2344 2352 5.032863 GTGCATTGAAAGAATCCTCGAATG 58.967 41.667 0.00 0.00 0.00 2.67
2345 2353 4.943093 TGCATTGAAAGAATCCTCGAATGA 59.057 37.500 0.00 0.00 0.00 2.57
2346 2354 5.065602 TGCATTGAAAGAATCCTCGAATGAG 59.934 40.000 0.00 0.00 42.18 2.90
2347 2355 5.295292 GCATTGAAAGAATCCTCGAATGAGA 59.705 40.000 0.00 0.00 45.57 3.27
2348 2356 6.017275 GCATTGAAAGAATCCTCGAATGAGAT 60.017 38.462 0.00 0.00 45.57 2.75
2349 2357 7.574496 CATTGAAAGAATCCTCGAATGAGATC 58.426 38.462 0.00 0.00 45.57 2.75
2350 2358 6.225981 TGAAAGAATCCTCGAATGAGATCA 57.774 37.500 0.00 0.00 45.57 2.92
2351 2359 6.824553 TGAAAGAATCCTCGAATGAGATCAT 58.175 36.000 0.00 0.00 45.57 2.45
2352 2360 7.955918 TGAAAGAATCCTCGAATGAGATCATA 58.044 34.615 0.00 0.00 45.57 2.15
2353 2361 8.591940 TGAAAGAATCCTCGAATGAGATCATAT 58.408 33.333 0.00 0.00 45.57 1.78
2357 2365 9.418839 AGAATCCTCGAATGAGATCATATATCA 57.581 33.333 0.00 0.00 45.57 2.15
2360 2368 9.984190 ATCCTCGAATGAGATCATATATCAATG 57.016 33.333 0.00 0.00 45.57 2.82
2361 2369 8.975295 TCCTCGAATGAGATCATATATCAATGT 58.025 33.333 0.00 0.00 45.57 2.71
2362 2370 9.247126 CCTCGAATGAGATCATATATCAATGTC 57.753 37.037 0.00 0.00 45.57 3.06
2363 2371 9.798994 CTCGAATGAGATCATATATCAATGTCA 57.201 33.333 0.00 6.83 45.57 3.58
2364 2372 9.578439 TCGAATGAGATCATATATCAATGTCAC 57.422 33.333 0.00 0.00 33.76 3.67
2365 2373 9.583765 CGAATGAGATCATATATCAATGTCACT 57.416 33.333 0.00 0.00 33.76 3.41
2374 2382 9.846248 TCATATATCAATGTCACTCATACGAAG 57.154 33.333 0.00 0.00 35.48 3.79
2375 2383 9.846248 CATATATCAATGTCACTCATACGAAGA 57.154 33.333 0.00 0.00 35.48 2.87
2378 2386 9.770097 ATATCAATGTCACTCATACGAAGAATT 57.230 29.630 0.00 0.00 35.48 2.17
2380 2388 8.407457 TCAATGTCACTCATACGAAGAATTAC 57.593 34.615 0.00 0.00 35.48 1.89
2381 2389 7.491372 TCAATGTCACTCATACGAAGAATTACC 59.509 37.037 0.00 0.00 35.48 2.85
2382 2390 6.525578 TGTCACTCATACGAAGAATTACCT 57.474 37.500 0.00 0.00 0.00 3.08
2383 2391 6.931838 TGTCACTCATACGAAGAATTACCTT 58.068 36.000 0.00 0.00 0.00 3.50
2384 2392 6.811665 TGTCACTCATACGAAGAATTACCTTG 59.188 38.462 0.00 0.00 0.00 3.61
2385 2393 5.810587 TCACTCATACGAAGAATTACCTTGC 59.189 40.000 0.00 0.00 0.00 4.01
2386 2394 5.812642 CACTCATACGAAGAATTACCTTGCT 59.187 40.000 0.00 0.00 0.00 3.91
2387 2395 6.313905 CACTCATACGAAGAATTACCTTGCTT 59.686 38.462 0.00 0.00 0.00 3.91
2388 2396 6.535508 ACTCATACGAAGAATTACCTTGCTTC 59.464 38.462 0.00 0.00 34.80 3.86
2389 2397 5.815740 TCATACGAAGAATTACCTTGCTTCC 59.184 40.000 0.00 0.00 34.69 3.46
2390 2398 4.287766 ACGAAGAATTACCTTGCTTCCT 57.712 40.909 0.00 0.00 34.69 3.36
2391 2399 4.254492 ACGAAGAATTACCTTGCTTCCTC 58.746 43.478 0.00 0.00 34.69 3.71
2392 2400 3.623510 CGAAGAATTACCTTGCTTCCTCC 59.376 47.826 0.00 0.00 34.69 4.30
2393 2401 3.653835 AGAATTACCTTGCTTCCTCCC 57.346 47.619 0.00 0.00 0.00 4.30
2394 2402 2.919602 AGAATTACCTTGCTTCCTCCCA 59.080 45.455 0.00 0.00 0.00 4.37
2395 2403 3.333680 AGAATTACCTTGCTTCCTCCCAA 59.666 43.478 0.00 0.00 0.00 4.12
2396 2404 4.017130 AGAATTACCTTGCTTCCTCCCAAT 60.017 41.667 0.00 0.00 0.00 3.16
2397 2405 5.193728 AGAATTACCTTGCTTCCTCCCAATA 59.806 40.000 0.00 0.00 0.00 1.90
2398 2406 5.669798 ATTACCTTGCTTCCTCCCAATAT 57.330 39.130 0.00 0.00 0.00 1.28
2399 2407 6.780198 ATTACCTTGCTTCCTCCCAATATA 57.220 37.500 0.00 0.00 0.00 0.86
2400 2408 6.780198 TTACCTTGCTTCCTCCCAATATAT 57.220 37.500 0.00 0.00 0.00 0.86
2401 2409 5.669798 ACCTTGCTTCCTCCCAATATATT 57.330 39.130 0.00 0.00 0.00 1.28
2402 2410 6.030727 ACCTTGCTTCCTCCCAATATATTT 57.969 37.500 0.00 0.00 0.00 1.40
2403 2411 6.443832 ACCTTGCTTCCTCCCAATATATTTT 58.556 36.000 0.00 0.00 0.00 1.82
2404 2412 7.591821 ACCTTGCTTCCTCCCAATATATTTTA 58.408 34.615 0.00 0.00 0.00 1.52
2405 2413 8.234525 ACCTTGCTTCCTCCCAATATATTTTAT 58.765 33.333 0.00 0.00 0.00 1.40
2406 2414 8.526147 CCTTGCTTCCTCCCAATATATTTTATG 58.474 37.037 0.00 0.00 0.00 1.90
2407 2415 9.082313 CTTGCTTCCTCCCAATATATTTTATGT 57.918 33.333 0.00 0.00 0.00 2.29
2408 2416 8.408043 TGCTTCCTCCCAATATATTTTATGTG 57.592 34.615 0.00 0.00 0.00 3.21
2409 2417 7.039784 TGCTTCCTCCCAATATATTTTATGTGC 60.040 37.037 0.00 0.00 0.00 4.57
2410 2418 7.177392 GCTTCCTCCCAATATATTTTATGTGCT 59.823 37.037 0.00 0.00 0.00 4.40
2411 2419 8.408043 TTCCTCCCAATATATTTTATGTGCTG 57.592 34.615 0.00 0.00 0.00 4.41
2412 2420 7.754624 TCCTCCCAATATATTTTATGTGCTGA 58.245 34.615 0.00 0.00 0.00 4.26
2413 2421 8.393259 TCCTCCCAATATATTTTATGTGCTGAT 58.607 33.333 0.00 0.00 0.00 2.90
2414 2422 8.464404 CCTCCCAATATATTTTATGTGCTGATG 58.536 37.037 0.00 0.00 0.00 3.07
2415 2423 7.829725 TCCCAATATATTTTATGTGCTGATGC 58.170 34.615 0.00 0.00 40.20 3.91
2426 2434 2.336945 TGCTGATGCATACCTTCAGG 57.663 50.000 14.44 0.00 45.31 3.86
2427 2435 1.839354 TGCTGATGCATACCTTCAGGA 59.161 47.619 14.44 9.84 45.31 3.86
2428 2436 2.158856 TGCTGATGCATACCTTCAGGAG 60.159 50.000 14.44 0.00 45.31 3.69
2429 2437 2.809665 GCTGATGCATACCTTCAGGAGG 60.810 54.545 14.44 0.00 42.79 4.30
2430 2438 5.074307 GCTGATGCATACCTTCAGGAGGA 62.074 52.174 14.44 0.00 42.79 3.71
2431 2439 6.835882 GCTGATGCATACCTTCAGGAGGAG 62.836 54.167 14.44 0.00 42.79 3.69
2438 2446 3.953006 CTTCAGGAGGAGCTTGCTT 57.047 52.632 0.00 0.00 0.00 3.91
2439 2447 2.197283 CTTCAGGAGGAGCTTGCTTT 57.803 50.000 0.00 0.00 0.00 3.51
2440 2448 2.512705 CTTCAGGAGGAGCTTGCTTTT 58.487 47.619 0.00 0.00 0.00 2.27
2441 2449 1.901591 TCAGGAGGAGCTTGCTTTTG 58.098 50.000 0.00 0.00 0.00 2.44
2442 2450 1.143684 TCAGGAGGAGCTTGCTTTTGT 59.856 47.619 0.00 0.00 0.00 2.83
2443 2451 1.538950 CAGGAGGAGCTTGCTTTTGTC 59.461 52.381 0.00 0.00 0.00 3.18
2444 2452 1.423161 AGGAGGAGCTTGCTTTTGTCT 59.577 47.619 0.00 0.00 0.00 3.41
2445 2453 2.158549 AGGAGGAGCTTGCTTTTGTCTT 60.159 45.455 0.00 0.00 0.00 3.01
2446 2454 2.227626 GGAGGAGCTTGCTTTTGTCTTC 59.772 50.000 0.00 0.00 0.00 2.87
2447 2455 1.876156 AGGAGCTTGCTTTTGTCTTCG 59.124 47.619 0.00 0.00 0.00 3.79
2448 2456 1.604278 GGAGCTTGCTTTTGTCTTCGT 59.396 47.619 0.00 0.00 0.00 3.85
2449 2457 2.806244 GGAGCTTGCTTTTGTCTTCGTA 59.194 45.455 0.00 0.00 0.00 3.43
2450 2458 3.250040 GGAGCTTGCTTTTGTCTTCGTAA 59.750 43.478 0.00 0.00 0.00 3.18
2451 2459 4.083271 GGAGCTTGCTTTTGTCTTCGTAAT 60.083 41.667 0.00 0.00 0.00 1.89
2452 2460 5.438761 AGCTTGCTTTTGTCTTCGTAATT 57.561 34.783 0.00 0.00 0.00 1.40
2453 2461 6.348213 GGAGCTTGCTTTTGTCTTCGTAATTA 60.348 38.462 0.00 0.00 0.00 1.40
2454 2462 7.145932 AGCTTGCTTTTGTCTTCGTAATTAT 57.854 32.000 0.00 0.00 0.00 1.28
2455 2463 7.244192 AGCTTGCTTTTGTCTTCGTAATTATC 58.756 34.615 0.00 0.00 0.00 1.75
2456 2464 7.119846 AGCTTGCTTTTGTCTTCGTAATTATCT 59.880 33.333 0.00 0.00 0.00 1.98
2457 2465 7.426743 GCTTGCTTTTGTCTTCGTAATTATCTC 59.573 37.037 0.00 0.00 0.00 2.75
2458 2466 8.547967 TTGCTTTTGTCTTCGTAATTATCTCT 57.452 30.769 0.00 0.00 0.00 3.10
2459 2467 8.186178 TGCTTTTGTCTTCGTAATTATCTCTC 57.814 34.615 0.00 0.00 0.00 3.20
2460 2468 7.817478 TGCTTTTGTCTTCGTAATTATCTCTCA 59.183 33.333 0.00 0.00 0.00 3.27
2461 2469 8.111224 GCTTTTGTCTTCGTAATTATCTCTCAC 58.889 37.037 0.00 0.00 0.00 3.51
2462 2470 9.360093 CTTTTGTCTTCGTAATTATCTCTCACT 57.640 33.333 0.00 0.00 0.00 3.41
2463 2471 9.706691 TTTTGTCTTCGTAATTATCTCTCACTT 57.293 29.630 0.00 0.00 0.00 3.16
2464 2472 8.689251 TTGTCTTCGTAATTATCTCTCACTTG 57.311 34.615 0.00 0.00 0.00 3.16
2465 2473 6.752351 TGTCTTCGTAATTATCTCTCACTTGC 59.248 38.462 0.00 0.00 0.00 4.01
2466 2474 6.975772 GTCTTCGTAATTATCTCTCACTTGCT 59.024 38.462 0.00 0.00 0.00 3.91
2467 2475 8.129840 GTCTTCGTAATTATCTCTCACTTGCTA 58.870 37.037 0.00 0.00 0.00 3.49
2468 2476 8.851145 TCTTCGTAATTATCTCTCACTTGCTAT 58.149 33.333 0.00 0.00 0.00 2.97
2469 2477 9.469807 CTTCGTAATTATCTCTCACTTGCTATT 57.530 33.333 0.00 0.00 0.00 1.73
2477 2485 9.684448 TTATCTCTCACTTGCTATTATTCTTCG 57.316 33.333 0.00 0.00 0.00 3.79
2478 2486 5.980116 TCTCTCACTTGCTATTATTCTTCGC 59.020 40.000 0.00 0.00 0.00 4.70
2479 2487 5.660460 TCTCACTTGCTATTATTCTTCGCA 58.340 37.500 0.00 0.00 0.00 5.10
2480 2488 6.283694 TCTCACTTGCTATTATTCTTCGCAT 58.716 36.000 0.00 0.00 0.00 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 3.575247 ACCCCATGACCAACGCCA 61.575 61.111 0.00 0.00 0.00 5.69
527 530 7.041721 ACAAAGGAACTCCATTTTCTGTTTTC 58.958 34.615 0.00 0.00 38.49 2.29
840 846 3.889815 CCAAAGATCTGCCATTGGTCTA 58.110 45.455 13.65 0.00 37.99 2.59
859 865 5.062809 GCAAAAGTTTTGTTTCGATTCACCA 59.937 36.000 25.20 0.00 0.00 4.17
868 874 7.546778 TTCCTTATGGCAAAAGTTTTGTTTC 57.453 32.000 25.20 16.73 0.00 2.78
982 989 4.043561 ACCCATATGTGACACCCAAGTTTA 59.956 41.667 2.45 0.00 0.00 2.01
1060 1067 4.316823 TCTCAGGACTGCCCCCGT 62.317 66.667 0.00 0.00 34.66 5.28
1114 1121 2.281070 CGCACACCAGTCAAGCCT 60.281 61.111 0.00 0.00 0.00 4.58
1116 1123 1.672356 ATCCGCACACCAGTCAAGC 60.672 57.895 0.00 0.00 0.00 4.01
1212 1219 5.515797 TCACCTCCGTATTATCTGAGTTG 57.484 43.478 0.00 0.00 0.00 3.16
1218 1225 8.190326 TCATGTAAATCACCTCCGTATTATCT 57.810 34.615 0.00 0.00 0.00 1.98
1230 1237 7.255381 CCTCCATTCTTCATCATGTAAATCACC 60.255 40.741 0.00 0.00 0.00 4.02
1237 1244 5.955961 TGTCCTCCATTCTTCATCATGTA 57.044 39.130 0.00 0.00 0.00 2.29
1272 1279 1.074319 GAACAATGTCGTCGCCGCTA 61.074 55.000 0.00 0.00 0.00 4.26
1273 1280 2.357034 AACAATGTCGTCGCCGCT 60.357 55.556 0.00 0.00 0.00 5.52
1274 1281 2.095843 GAACAATGTCGTCGCCGC 59.904 61.111 0.00 0.00 0.00 6.53
1275 1282 1.410737 ATCGAACAATGTCGTCGCCG 61.411 55.000 2.87 0.00 41.80 6.46
1283 1290 9.454585 CATAAAATAGCAATCATCGAACAATGT 57.545 29.630 0.00 0.00 0.00 2.71
1286 1293 6.917477 GCCATAAAATAGCAATCATCGAACAA 59.083 34.615 0.00 0.00 0.00 2.83
1333 1340 7.156876 TGCTTCCCTATTACAATGTTCAAAG 57.843 36.000 0.00 0.00 0.00 2.77
1376 1383 5.466058 CAGAGAATTTCACTAGCCTAGCATG 59.534 44.000 0.00 0.00 0.00 4.06
1377 1384 5.130145 ACAGAGAATTTCACTAGCCTAGCAT 59.870 40.000 0.00 0.00 0.00 3.79
1389 1396 6.409704 CAATCCCTAGTCACAGAGAATTTCA 58.590 40.000 0.00 0.00 0.00 2.69
1616 1623 9.877178 AGTTCATACTAAGATAAGACCAAGTTG 57.123 33.333 0.00 0.00 31.21 3.16
1630 1637 9.658799 TCAATCTTTCCAAGAGTTCATACTAAG 57.341 33.333 0.00 0.00 41.61 2.18
1757 1764 8.281531 TCTAATTGGATCACATAACAATCCCTT 58.718 33.333 0.00 0.00 38.56 3.95
1782 1789 5.970023 GTGCAATCTCTCAACAATGCTAATC 59.030 40.000 0.00 0.00 34.97 1.75
1814 1821 0.708209 TGAGGCCTAGGGTCTGTACA 59.292 55.000 4.42 0.00 38.01 2.90
1846 1853 4.789012 AAGTGAGCACAAATGGTATTGG 57.211 40.909 3.19 0.00 36.44 3.16
1854 1861 5.519927 GCAAGTAACAAAAGTGAGCACAAAT 59.480 36.000 3.19 0.00 0.00 2.32
2012 2020 4.675114 GCAACCAAATAACAAACAGTCTCG 59.325 41.667 0.00 0.00 0.00 4.04
2019 2027 4.066646 ACCCTGCAACCAAATAACAAAC 57.933 40.909 0.00 0.00 0.00 2.93
2052 2060 3.558746 GGAGGCATAGGATGAAGATGGTG 60.559 52.174 0.00 0.00 0.00 4.17
2083 2091 6.316390 GTCAAGTGGATGACCTAAGGTTTATG 59.684 42.308 0.00 0.00 43.11 1.90
2117 2125 4.246458 GCAGAGTTTTGTAGGACAGTAGG 58.754 47.826 0.00 0.00 0.00 3.18
2169 2177 5.063944 CCATGATGTCTACTACACAACTTGC 59.936 44.000 0.00 0.00 42.09 4.01
2196 2204 9.241919 TGAAGGTTTTCTCATAGCATAATTTGA 57.758 29.630 0.00 0.00 34.31 2.69
2199 2207 9.412460 TCATGAAGGTTTTCTCATAGCATAATT 57.588 29.630 0.00 0.00 34.31 1.40
2200 2208 8.844244 GTCATGAAGGTTTTCTCATAGCATAAT 58.156 33.333 0.00 0.00 34.31 1.28
2201 2209 7.828717 TGTCATGAAGGTTTTCTCATAGCATAA 59.171 33.333 0.00 0.00 34.31 1.90
2202 2210 7.337938 TGTCATGAAGGTTTTCTCATAGCATA 58.662 34.615 0.00 0.00 34.31 3.14
2203 2211 6.182627 TGTCATGAAGGTTTTCTCATAGCAT 58.817 36.000 0.00 0.00 34.31 3.79
2204 2212 5.559770 TGTCATGAAGGTTTTCTCATAGCA 58.440 37.500 0.00 0.00 34.31 3.49
2205 2213 6.541641 AGATGTCATGAAGGTTTTCTCATAGC 59.458 38.462 0.00 0.00 34.31 2.97
2206 2214 7.226325 GGAGATGTCATGAAGGTTTTCTCATAG 59.774 40.741 0.00 0.00 34.31 2.23
2207 2215 7.050377 GGAGATGTCATGAAGGTTTTCTCATA 58.950 38.462 0.00 0.00 34.31 2.15
2208 2216 5.884792 GGAGATGTCATGAAGGTTTTCTCAT 59.115 40.000 0.00 0.00 34.31 2.90
2209 2217 5.013495 AGGAGATGTCATGAAGGTTTTCTCA 59.987 40.000 0.00 0.00 34.31 3.27
2210 2218 5.495640 AGGAGATGTCATGAAGGTTTTCTC 58.504 41.667 0.00 3.47 34.31 2.87
2211 2219 5.511386 AGGAGATGTCATGAAGGTTTTCT 57.489 39.130 0.00 0.00 34.31 2.52
2212 2220 6.015940 ACAAAGGAGATGTCATGAAGGTTTTC 60.016 38.462 0.00 0.00 0.00 2.29
2213 2221 5.835280 ACAAAGGAGATGTCATGAAGGTTTT 59.165 36.000 0.00 0.00 0.00 2.43
2214 2222 5.388654 ACAAAGGAGATGTCATGAAGGTTT 58.611 37.500 0.00 0.00 0.00 3.27
2215 2223 4.990526 ACAAAGGAGATGTCATGAAGGTT 58.009 39.130 0.00 0.00 0.00 3.50
2216 2224 4.583871 GACAAAGGAGATGTCATGAAGGT 58.416 43.478 0.00 0.00 45.13 3.50
2224 2232 5.947228 TGATTTGTGACAAAGGAGATGTC 57.053 39.130 16.43 7.62 45.82 3.06
2225 2233 6.906157 AATGATTTGTGACAAAGGAGATGT 57.094 33.333 16.43 0.00 0.00 3.06
2226 2234 7.372714 TGAAATGATTTGTGACAAAGGAGATG 58.627 34.615 16.43 0.00 0.00 2.90
2227 2235 7.528996 TGAAATGATTTGTGACAAAGGAGAT 57.471 32.000 16.43 0.00 0.00 2.75
2228 2236 6.957920 TGAAATGATTTGTGACAAAGGAGA 57.042 33.333 16.43 0.80 0.00 3.71
2229 2237 7.707893 ACTTTGAAATGATTTGTGACAAAGGAG 59.292 33.333 22.61 8.87 43.51 3.69
2230 2238 7.555087 ACTTTGAAATGATTTGTGACAAAGGA 58.445 30.769 22.61 5.65 43.51 3.36
2231 2239 7.775397 ACTTTGAAATGATTTGTGACAAAGG 57.225 32.000 22.61 12.06 43.51 3.11
2232 2240 9.520204 AGTACTTTGAAATGATTTGTGACAAAG 57.480 29.630 16.43 19.62 44.23 2.77
2233 2241 9.515020 GAGTACTTTGAAATGATTTGTGACAAA 57.485 29.630 13.66 13.66 0.00 2.83
2234 2242 8.681806 TGAGTACTTTGAAATGATTTGTGACAA 58.318 29.630 0.00 0.00 0.00 3.18
2235 2243 8.128582 GTGAGTACTTTGAAATGATTTGTGACA 58.871 33.333 0.00 0.00 0.00 3.58
2236 2244 8.345565 AGTGAGTACTTTGAAATGATTTGTGAC 58.654 33.333 0.00 0.00 31.66 3.67
2237 2245 8.450578 AGTGAGTACTTTGAAATGATTTGTGA 57.549 30.769 0.00 0.00 31.66 3.58
2270 2278 9.897744 GTCACACAATCTTTGAAATGAATTAGA 57.102 29.630 0.00 0.00 0.00 2.10
2271 2279 9.681692 TGTCACACAATCTTTGAAATGAATTAG 57.318 29.630 0.00 0.00 0.00 1.73
2272 2280 9.681692 CTGTCACACAATCTTTGAAATGAATTA 57.318 29.630 0.00 0.00 0.00 1.40
2273 2281 7.654520 CCTGTCACACAATCTTTGAAATGAATT 59.345 33.333 0.00 0.00 0.00 2.17
2274 2282 7.014518 TCCTGTCACACAATCTTTGAAATGAAT 59.985 33.333 0.00 0.00 0.00 2.57
2275 2283 6.320926 TCCTGTCACACAATCTTTGAAATGAA 59.679 34.615 0.00 0.00 0.00 2.57
2276 2284 5.827267 TCCTGTCACACAATCTTTGAAATGA 59.173 36.000 0.00 0.00 0.00 2.57
2277 2285 6.075762 TCCTGTCACACAATCTTTGAAATG 57.924 37.500 0.00 0.00 0.00 2.32
2278 2286 6.713762 TTCCTGTCACACAATCTTTGAAAT 57.286 33.333 0.00 0.00 0.00 2.17
2279 2287 6.713762 ATTCCTGTCACACAATCTTTGAAA 57.286 33.333 0.00 0.00 0.00 2.69
2280 2288 6.713762 AATTCCTGTCACACAATCTTTGAA 57.286 33.333 0.00 0.00 0.00 2.69
2281 2289 7.884877 AGATAATTCCTGTCACACAATCTTTGA 59.115 33.333 0.00 0.00 0.00 2.69
2282 2290 8.048534 AGATAATTCCTGTCACACAATCTTTG 57.951 34.615 0.00 0.00 0.00 2.77
2283 2291 7.884877 TGAGATAATTCCTGTCACACAATCTTT 59.115 33.333 0.00 0.00 0.00 2.52
2284 2292 7.397221 TGAGATAATTCCTGTCACACAATCTT 58.603 34.615 0.00 0.00 0.00 2.40
2285 2293 6.950842 TGAGATAATTCCTGTCACACAATCT 58.049 36.000 0.00 0.00 0.00 2.40
2286 2294 7.010923 GTCTGAGATAATTCCTGTCACACAATC 59.989 40.741 0.00 0.00 0.00 2.67
2287 2295 6.820656 GTCTGAGATAATTCCTGTCACACAAT 59.179 38.462 0.00 0.00 0.00 2.71
2288 2296 6.166279 GTCTGAGATAATTCCTGTCACACAA 58.834 40.000 0.00 0.00 0.00 3.33
2289 2297 5.245977 TGTCTGAGATAATTCCTGTCACACA 59.754 40.000 0.00 0.00 0.00 3.72
2290 2298 5.578727 GTGTCTGAGATAATTCCTGTCACAC 59.421 44.000 0.00 0.00 0.00 3.82
2291 2299 5.481824 AGTGTCTGAGATAATTCCTGTCACA 59.518 40.000 0.00 0.00 0.00 3.58
2292 2300 5.809562 CAGTGTCTGAGATAATTCCTGTCAC 59.190 44.000 0.00 0.00 32.44 3.67
2293 2301 5.481824 ACAGTGTCTGAGATAATTCCTGTCA 59.518 40.000 3.70 0.00 35.18 3.58
2294 2302 5.971763 ACAGTGTCTGAGATAATTCCTGTC 58.028 41.667 3.70 0.00 35.18 3.51
2295 2303 6.014242 TCAACAGTGTCTGAGATAATTCCTGT 60.014 38.462 0.00 0.00 35.18 4.00
2296 2304 6.401394 TCAACAGTGTCTGAGATAATTCCTG 58.599 40.000 0.00 0.00 35.18 3.86
2297 2305 6.212388 ACTCAACAGTGTCTGAGATAATTCCT 59.788 38.462 27.57 11.05 41.38 3.36
2298 2306 6.312426 CACTCAACAGTGTCTGAGATAATTCC 59.688 42.308 27.57 0.00 44.63 3.01
2299 2307 7.288317 CACTCAACAGTGTCTGAGATAATTC 57.712 40.000 27.57 0.00 44.63 2.17
2313 2321 5.278660 GGATTCTTTCAATGCACTCAACAGT 60.279 40.000 0.00 0.00 0.00 3.55
2314 2322 5.048224 AGGATTCTTTCAATGCACTCAACAG 60.048 40.000 0.00 0.00 0.00 3.16
2315 2323 4.828939 AGGATTCTTTCAATGCACTCAACA 59.171 37.500 0.00 0.00 0.00 3.33
2316 2324 5.382618 AGGATTCTTTCAATGCACTCAAC 57.617 39.130 0.00 0.00 0.00 3.18
2317 2325 4.154737 CGAGGATTCTTTCAATGCACTCAA 59.845 41.667 0.00 0.00 0.00 3.02
2318 2326 3.686241 CGAGGATTCTTTCAATGCACTCA 59.314 43.478 0.00 0.00 0.00 3.41
2319 2327 3.935203 TCGAGGATTCTTTCAATGCACTC 59.065 43.478 0.00 0.00 0.00 3.51
2320 2328 3.942829 TCGAGGATTCTTTCAATGCACT 58.057 40.909 0.00 0.00 0.00 4.40
2321 2329 4.685169 TTCGAGGATTCTTTCAATGCAC 57.315 40.909 0.00 0.00 0.00 4.57
2322 2330 4.943093 TCATTCGAGGATTCTTTCAATGCA 59.057 37.500 0.00 0.00 0.00 3.96
2323 2331 5.295292 TCTCATTCGAGGATTCTTTCAATGC 59.705 40.000 0.00 0.00 39.95 3.56
2324 2332 6.915544 TCTCATTCGAGGATTCTTTCAATG 57.084 37.500 0.00 0.00 39.95 2.82
2325 2333 7.278135 TGATCTCATTCGAGGATTCTTTCAAT 58.722 34.615 0.00 0.00 39.95 2.57
2326 2334 6.643388 TGATCTCATTCGAGGATTCTTTCAA 58.357 36.000 0.00 0.00 39.95 2.69
2327 2335 6.225981 TGATCTCATTCGAGGATTCTTTCA 57.774 37.500 0.00 0.00 39.95 2.69
2331 2339 9.418839 TGATATATGATCTCATTCGAGGATTCT 57.581 33.333 0.00 0.00 39.95 2.40
2334 2342 9.984190 CATTGATATATGATCTCATTCGAGGAT 57.016 33.333 0.00 0.00 39.95 3.24
2335 2343 8.975295 ACATTGATATATGATCTCATTCGAGGA 58.025 33.333 0.00 0.00 39.95 3.71
2336 2344 9.247126 GACATTGATATATGATCTCATTCGAGG 57.753 37.037 0.00 0.00 39.95 4.63
2337 2345 9.798994 TGACATTGATATATGATCTCATTCGAG 57.201 33.333 0.00 0.00 40.98 4.04
2338 2346 9.578439 GTGACATTGATATATGATCTCATTCGA 57.422 33.333 0.00 0.00 37.76 3.71
2339 2347 9.583765 AGTGACATTGATATATGATCTCATTCG 57.416 33.333 0.00 0.00 37.76 3.34
2348 2356 9.846248 CTTCGTATGAGTGACATTGATATATGA 57.154 33.333 0.00 0.00 40.07 2.15
2349 2357 9.846248 TCTTCGTATGAGTGACATTGATATATG 57.154 33.333 0.00 0.00 40.07 1.78
2352 2360 9.770097 AATTCTTCGTATGAGTGACATTGATAT 57.230 29.630 0.00 0.00 40.07 1.63
2354 2362 9.035607 GTAATTCTTCGTATGAGTGACATTGAT 57.964 33.333 0.00 0.00 40.07 2.57
2355 2363 7.491372 GGTAATTCTTCGTATGAGTGACATTGA 59.509 37.037 0.00 0.00 40.07 2.57
2356 2364 7.492669 AGGTAATTCTTCGTATGAGTGACATTG 59.507 37.037 0.00 0.00 40.07 2.82
2357 2365 7.556844 AGGTAATTCTTCGTATGAGTGACATT 58.443 34.615 0.00 0.00 40.07 2.71
2358 2366 7.113658 AGGTAATTCTTCGTATGAGTGACAT 57.886 36.000 0.00 0.00 42.39 3.06
2359 2367 6.525578 AGGTAATTCTTCGTATGAGTGACA 57.474 37.500 0.00 0.00 0.00 3.58
2360 2368 6.237861 GCAAGGTAATTCTTCGTATGAGTGAC 60.238 42.308 0.00 0.00 0.00 3.67
2361 2369 5.810587 GCAAGGTAATTCTTCGTATGAGTGA 59.189 40.000 0.00 0.00 0.00 3.41
2362 2370 5.812642 AGCAAGGTAATTCTTCGTATGAGTG 59.187 40.000 0.00 0.00 0.00 3.51
2363 2371 5.978814 AGCAAGGTAATTCTTCGTATGAGT 58.021 37.500 0.00 0.00 0.00 3.41
2364 2372 6.018669 GGAAGCAAGGTAATTCTTCGTATGAG 60.019 42.308 0.00 0.00 36.66 2.90
2365 2373 5.815740 GGAAGCAAGGTAATTCTTCGTATGA 59.184 40.000 0.00 0.00 36.66 2.15
2366 2374 5.817816 AGGAAGCAAGGTAATTCTTCGTATG 59.182 40.000 0.00 0.00 36.66 2.39
2367 2375 5.990668 AGGAAGCAAGGTAATTCTTCGTAT 58.009 37.500 0.00 0.00 36.66 3.06
2368 2376 5.416271 AGGAAGCAAGGTAATTCTTCGTA 57.584 39.130 0.00 0.00 36.66 3.43
2369 2377 4.254492 GAGGAAGCAAGGTAATTCTTCGT 58.746 43.478 0.00 0.00 36.66 3.85
2370 2378 3.623510 GGAGGAAGCAAGGTAATTCTTCG 59.376 47.826 0.00 0.00 36.66 3.79
2371 2379 3.948473 GGGAGGAAGCAAGGTAATTCTTC 59.052 47.826 0.00 0.00 35.45 2.87
2372 2380 3.333680 TGGGAGGAAGCAAGGTAATTCTT 59.666 43.478 0.00 0.00 0.00 2.52
2373 2381 2.919602 TGGGAGGAAGCAAGGTAATTCT 59.080 45.455 0.00 0.00 0.00 2.40
2374 2382 3.366052 TGGGAGGAAGCAAGGTAATTC 57.634 47.619 0.00 0.00 0.00 2.17
2375 2383 3.825908 TTGGGAGGAAGCAAGGTAATT 57.174 42.857 0.00 0.00 0.00 1.40
2376 2384 5.669798 ATATTGGGAGGAAGCAAGGTAAT 57.330 39.130 0.00 0.00 0.00 1.89
2377 2385 6.780198 ATATATTGGGAGGAAGCAAGGTAA 57.220 37.500 0.00 0.00 0.00 2.85
2378 2386 6.780198 AATATATTGGGAGGAAGCAAGGTA 57.220 37.500 0.00 0.00 0.00 3.08
2379 2387 5.669798 AATATATTGGGAGGAAGCAAGGT 57.330 39.130 0.00 0.00 0.00 3.50
2380 2388 6.983906 AAAATATATTGGGAGGAAGCAAGG 57.016 37.500 0.00 0.00 0.00 3.61
2381 2389 9.082313 ACATAAAATATATTGGGAGGAAGCAAG 57.918 33.333 0.00 0.00 0.00 4.01
2382 2390 8.859090 CACATAAAATATATTGGGAGGAAGCAA 58.141 33.333 0.00 0.00 0.00 3.91
2383 2391 7.039784 GCACATAAAATATATTGGGAGGAAGCA 60.040 37.037 0.00 0.00 0.00 3.91
2384 2392 7.177392 AGCACATAAAATATATTGGGAGGAAGC 59.823 37.037 0.00 0.00 0.00 3.86
2385 2393 8.517878 CAGCACATAAAATATATTGGGAGGAAG 58.482 37.037 0.00 0.00 0.00 3.46
2386 2394 8.224025 TCAGCACATAAAATATATTGGGAGGAA 58.776 33.333 0.00 0.00 0.00 3.36
2387 2395 7.754624 TCAGCACATAAAATATATTGGGAGGA 58.245 34.615 0.00 0.00 0.00 3.71
2388 2396 8.464404 CATCAGCACATAAAATATATTGGGAGG 58.536 37.037 0.00 0.00 0.00 4.30
2389 2397 7.972277 GCATCAGCACATAAAATATATTGGGAG 59.028 37.037 0.00 0.00 41.58 4.30
2390 2398 7.829725 GCATCAGCACATAAAATATATTGGGA 58.170 34.615 0.00 0.00 41.58 4.37
2401 2409 9.695747 TCCTGAAGGTATGCATCAGCACATAAA 62.696 40.741 0.19 0.00 44.81 1.40
2402 2410 8.323000 TCCTGAAGGTATGCATCAGCACATAA 62.323 42.308 0.19 0.00 44.81 1.90
2403 2411 6.920302 TCCTGAAGGTATGCATCAGCACATA 61.920 44.000 0.19 0.00 44.81 2.29
2404 2412 6.212789 TCCTGAAGGTATGCATCAGCACAT 62.213 45.833 0.19 0.00 44.81 3.21
2405 2413 4.955497 TCCTGAAGGTATGCATCAGCACA 61.955 47.826 0.19 0.00 44.81 4.57
2406 2414 2.420547 TCCTGAAGGTATGCATCAGCAC 60.421 50.000 0.19 0.00 44.81 4.40
2407 2415 1.839354 TCCTGAAGGTATGCATCAGCA 59.161 47.619 0.19 0.00 45.55 4.41
2408 2416 2.492012 CTCCTGAAGGTATGCATCAGC 58.508 52.381 0.19 0.00 39.36 4.26
2409 2417 2.702478 TCCTCCTGAAGGTATGCATCAG 59.298 50.000 0.19 4.67 46.32 2.90
2410 2418 2.702478 CTCCTCCTGAAGGTATGCATCA 59.298 50.000 0.19 0.00 46.32 3.07
2411 2419 2.549778 GCTCCTCCTGAAGGTATGCATC 60.550 54.545 0.19 0.00 46.32 3.91
2412 2420 1.419387 GCTCCTCCTGAAGGTATGCAT 59.581 52.381 3.79 3.79 46.32 3.96
2413 2421 0.833287 GCTCCTCCTGAAGGTATGCA 59.167 55.000 0.00 0.00 46.32 3.96
2414 2422 1.127343 AGCTCCTCCTGAAGGTATGC 58.873 55.000 0.00 0.00 46.32 3.14
2415 2423 2.744494 GCAAGCTCCTCCTGAAGGTATG 60.744 54.545 0.00 0.00 46.32 2.39
2416 2424 1.488393 GCAAGCTCCTCCTGAAGGTAT 59.512 52.381 0.00 0.00 46.32 2.73
2417 2425 0.905357 GCAAGCTCCTCCTGAAGGTA 59.095 55.000 0.00 0.00 46.32 3.08
2418 2426 0.839853 AGCAAGCTCCTCCTGAAGGT 60.840 55.000 0.00 0.00 46.32 3.50
2420 2428 2.197283 AAAGCAAGCTCCTCCTGAAG 57.803 50.000 0.00 0.00 0.00 3.02
2421 2429 2.233271 CAAAAGCAAGCTCCTCCTGAA 58.767 47.619 0.00 0.00 0.00 3.02
2422 2430 1.143684 ACAAAAGCAAGCTCCTCCTGA 59.856 47.619 0.00 0.00 0.00 3.86
2423 2431 1.538950 GACAAAAGCAAGCTCCTCCTG 59.461 52.381 0.00 0.00 0.00 3.86
2424 2432 1.423161 AGACAAAAGCAAGCTCCTCCT 59.577 47.619 0.00 0.00 0.00 3.69
2425 2433 1.902938 AGACAAAAGCAAGCTCCTCC 58.097 50.000 0.00 0.00 0.00 4.30
2426 2434 2.096019 CGAAGACAAAAGCAAGCTCCTC 60.096 50.000 0.00 0.00 0.00 3.71
2427 2435 1.876156 CGAAGACAAAAGCAAGCTCCT 59.124 47.619 0.00 0.00 0.00 3.69
2428 2436 1.604278 ACGAAGACAAAAGCAAGCTCC 59.396 47.619 0.00 0.00 0.00 4.70
2429 2437 4.468095 TTACGAAGACAAAAGCAAGCTC 57.532 40.909 0.00 0.00 0.00 4.09
2430 2438 5.438761 AATTACGAAGACAAAAGCAAGCT 57.561 34.783 0.00 0.00 0.00 3.74
2431 2439 7.244192 AGATAATTACGAAGACAAAAGCAAGC 58.756 34.615 0.00 0.00 0.00 4.01
2432 2440 8.660373 AGAGATAATTACGAAGACAAAAGCAAG 58.340 33.333 0.00 0.00 0.00 4.01
2433 2441 8.547967 AGAGATAATTACGAAGACAAAAGCAA 57.452 30.769 0.00 0.00 0.00 3.91
2434 2442 7.817478 TGAGAGATAATTACGAAGACAAAAGCA 59.183 33.333 0.00 0.00 0.00 3.91
2435 2443 8.111224 GTGAGAGATAATTACGAAGACAAAAGC 58.889 37.037 0.00 0.00 0.00 3.51
2436 2444 9.360093 AGTGAGAGATAATTACGAAGACAAAAG 57.640 33.333 0.00 0.00 0.00 2.27
2437 2445 9.706691 AAGTGAGAGATAATTACGAAGACAAAA 57.293 29.630 0.00 0.00 0.00 2.44
2438 2446 9.140286 CAAGTGAGAGATAATTACGAAGACAAA 57.860 33.333 0.00 0.00 0.00 2.83
2439 2447 7.275779 GCAAGTGAGAGATAATTACGAAGACAA 59.724 37.037 0.00 0.00 0.00 3.18
2440 2448 6.752351 GCAAGTGAGAGATAATTACGAAGACA 59.248 38.462 0.00 0.00 0.00 3.41
2441 2449 6.975772 AGCAAGTGAGAGATAATTACGAAGAC 59.024 38.462 0.00 0.00 0.00 3.01
2442 2450 7.101652 AGCAAGTGAGAGATAATTACGAAGA 57.898 36.000 0.00 0.00 0.00 2.87
2443 2451 9.469807 AATAGCAAGTGAGAGATAATTACGAAG 57.530 33.333 0.00 0.00 0.00 3.79
2451 2459 9.684448 CGAAGAATAATAGCAAGTGAGAGATAA 57.316 33.333 0.00 0.00 0.00 1.75
2452 2460 7.810282 GCGAAGAATAATAGCAAGTGAGAGATA 59.190 37.037 0.00 0.00 0.00 1.98
2453 2461 6.644592 GCGAAGAATAATAGCAAGTGAGAGAT 59.355 38.462 0.00 0.00 0.00 2.75
2454 2462 5.980116 GCGAAGAATAATAGCAAGTGAGAGA 59.020 40.000 0.00 0.00 0.00 3.10
2455 2463 5.750547 TGCGAAGAATAATAGCAAGTGAGAG 59.249 40.000 0.00 0.00 34.66 3.20
2456 2464 5.660460 TGCGAAGAATAATAGCAAGTGAGA 58.340 37.500 0.00 0.00 34.66 3.27
2457 2465 5.973651 TGCGAAGAATAATAGCAAGTGAG 57.026 39.130 0.00 0.00 34.66 3.51


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

AutoCloner maintained by Alex Coulton.