Multiple sequence alignment - TraesCS3D01G540100

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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 TraesCS3D01G540100 chr3D 100.000 4124 0 0 1 4124 611569569 611565446 0.000000e+00 7616.0
1 TraesCS3D01G540100 chr3D 86.619 1121 78 35 772 1869 611558265 611559336 0.000000e+00 1173.0
2 TraesCS3D01G540100 chr3D 87.500 144 6 3 86 228 611557797 611557929 5.520000e-34 156.0
3 TraesCS3D01G540100 chr3D 88.350 103 3 1 491 593 611581707 611581614 9.370000e-22 115.0
4 TraesCS3D01G540100 chr3A 94.660 1573 51 12 2581 4124 746353031 746354599 0.000000e+00 2409.0
5 TraesCS3D01G540100 chr3A 87.006 708 42 24 1746 2442 746352086 746352754 0.000000e+00 752.0
6 TraesCS3D01G540100 chr3A 89.127 561 41 14 1307 1853 746313390 746313944 0.000000e+00 680.0
7 TraesCS3D01G540100 chr3A 97.838 370 8 0 1307 1676 746351632 746352001 1.250000e-179 640.0
8 TraesCS3D01G540100 chr3A 97.838 370 8 0 1307 1676 746363827 746363458 1.250000e-179 640.0
9 TraesCS3D01G540100 chr3A 80.305 919 67 44 373 1221 746350759 746351633 1.280000e-164 590.0
10 TraesCS3D01G540100 chr3A 83.523 352 26 15 902 1221 746364177 746363826 2.410000e-77 300.0
11 TraesCS3D01G540100 chr3A 93.401 197 13 0 1351 1547 315281077 315281273 4.030000e-75 292.0
12 TraesCS3D01G540100 chr3A 88.546 227 17 5 995 1221 746313174 746313391 2.440000e-67 267.0
13 TraesCS3D01G540100 chr3A 90.909 198 17 1 1351 1547 314776782 314776979 8.790000e-67 265.0
14 TraesCS3D01G540100 chr3A 98.113 106 1 1 1749 1853 746363370 746363265 2.530000e-42 183.0
15 TraesCS3D01G540100 chr3A 76.587 252 25 20 660 906 746364423 746364201 1.570000e-19 108.0
16 TraesCS3D01G540100 chr3B 87.453 1331 95 36 1307 2587 829288973 829287665 0.000000e+00 1467.0
17 TraesCS3D01G540100 chr3B 97.487 557 14 0 3568 4124 829286717 829286161 0.000000e+00 952.0
18 TraesCS3D01G540100 chr3B 94.983 598 28 2 2909 3505 829287316 829286720 0.000000e+00 937.0
19 TraesCS3D01G540100 chr3B 88.579 718 49 22 1307 2012 829273685 829274381 0.000000e+00 841.0
20 TraesCS3D01G540100 chr3B 78.629 744 83 39 489 1221 829273008 829273686 1.370000e-114 424.0
21 TraesCS3D01G540100 chr3B 77.139 783 66 56 491 1221 829289693 829288972 2.360000e-92 350.0
22 TraesCS3D01G540100 chr3B 77.540 374 34 22 237 596 829296527 829296190 3.280000e-41 180.0
23 TraesCS3D01G540100 chr3B 87.349 166 8 6 227 386 829272571 829272729 1.180000e-40 178.0
24 TraesCS3D01G540100 chr3B 85.246 183 11 7 56 228 829290208 829290032 1.520000e-39 174.0
25 TraesCS3D01G540100 chr4A 89.114 542 50 5 3581 4122 13757161 13757693 0.000000e+00 665.0
26 TraesCS3D01G540100 chr4A 86.022 93 12 1 3284 3376 13756678 13756769 9.430000e-17 99.0
27 TraesCS3D01G540100 chr4B 90.342 497 45 2 3626 4122 566980577 566980084 0.000000e+00 649.0
28 TraesCS3D01G540100 chr4B 90.342 497 45 2 3626 4122 566983089 566982596 0.000000e+00 649.0
29 TraesCS3D01G540100 chr4B 90.000 90 8 1 3287 3376 566980947 566980859 9.370000e-22 115.0
30 TraesCS3D01G540100 chr4B 90.000 90 8 1 3287 3376 566983459 566983371 9.370000e-22 115.0
31 TraesCS3D01G540100 chr4D 90.909 473 40 1 3650 4122 453321195 453320726 2.090000e-177 632.0
32 TraesCS3D01G540100 chrUn 87.786 393 30 15 1526 1907 480633103 480633488 1.050000e-120 444.0
33 TraesCS3D01G540100 chr6A 88.797 241 26 1 1307 1547 361909802 361909563 1.120000e-75 294.0
34 TraesCS3D01G540100 chr1B 91.262 103 9 0 1762 1864 663374728 663374626 1.550000e-29 141.0
35 TraesCS3D01G540100 chr1B 90.667 75 7 0 1117 1191 492306378 492306452 2.620000e-17 100.0
36 TraesCS3D01G540100 chr1D 90.667 75 7 0 1117 1191 367847819 367847893 2.620000e-17 100.0
37 TraesCS3D01G540100 chr1D 89.855 69 7 0 1306 1374 367848044 367848112 5.680000e-14 89.8
38 TraesCS3D01G540100 chr1A 90.667 75 7 0 1117 1191 467184655 467184729 2.620000e-17 100.0
39 TraesCS3D01G540100 chr1A 89.855 69 7 0 1306 1374 467184860 467184928 5.680000e-14 89.8
40 TraesCS3D01G540100 chr2B 92.754 69 4 1 1797 1864 680916011 680915943 9.430000e-17 99.0


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 TraesCS3D01G540100 chr3D 611565446 611569569 4123 True 7616.00 7616 100.000000 1 4124 1 chr3D.!!$R1 4123
1 TraesCS3D01G540100 chr3D 611557797 611559336 1539 False 664.50 1173 87.059500 86 1869 2 chr3D.!!$F1 1783
2 TraesCS3D01G540100 chr3A 746350759 746354599 3840 False 1097.75 2409 89.952250 373 4124 4 chr3A.!!$F4 3751
3 TraesCS3D01G540100 chr3A 746313174 746313944 770 False 473.50 680 88.836500 995 1853 2 chr3A.!!$F3 858
4 TraesCS3D01G540100 chr3A 746363265 746364423 1158 True 307.75 640 89.015250 660 1853 4 chr3A.!!$R1 1193
5 TraesCS3D01G540100 chr3B 829286161 829290208 4047 True 776.00 1467 88.461600 56 4124 5 chr3B.!!$R2 4068
6 TraesCS3D01G540100 chr3B 829272571 829274381 1810 False 481.00 841 84.852333 227 2012 3 chr3B.!!$F1 1785
7 TraesCS3D01G540100 chr4A 13756678 13757693 1015 False 382.00 665 87.568000 3284 4122 2 chr4A.!!$F1 838
8 TraesCS3D01G540100 chr4B 566980084 566983459 3375 True 382.00 649 90.171000 3287 4122 4 chr4B.!!$R1 835

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
936 1595 0.106149 CAGGCCCCGACTAACATACC 59.894 60.0 0.0 0.0 0.00 2.73 F
2796 3752 0.389556 ATGCTATCAGCGGCTCATCG 60.390 55.0 0.0 0.0 46.26 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2870 3857 0.040058 TGGCCTGCCACTCATGAAAT 59.960 50.0 6.8 0.0 41.89 2.17 R
3638 7373 5.815581 TGTATCTGCCTGTTTAGTGGAAAT 58.184 37.5 0.0 0.0 0.00 2.17 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
36 37 8.746530 CCGATATGGTATTTGGTAGTAGTATGT 58.253 37.037 0.00 0.00 0.00 2.29
53 54 9.775539 AGTAGTATGTATGATATGGAATCCAGT 57.224 33.333 8.40 0.00 36.75 4.00
104 109 4.659088 CCAGTACTATGTATGATACGCCG 58.341 47.826 0.00 0.00 0.00 6.46
162 176 4.284550 TGCTCTGGGGTGGTTGGC 62.285 66.667 0.00 0.00 0.00 4.52
164 178 3.953775 CTCTGGGGTGGTTGGCGT 61.954 66.667 0.00 0.00 0.00 5.68
165 179 3.491598 CTCTGGGGTGGTTGGCGTT 62.492 63.158 0.00 0.00 0.00 4.84
166 180 3.294493 CTGGGGTGGTTGGCGTTG 61.294 66.667 0.00 0.00 0.00 4.10
170 184 3.977244 GGTGGTTGGCGTTGGCTG 61.977 66.667 0.00 0.00 39.81 4.85
171 185 3.977244 GTGGTTGGCGTTGGCTGG 61.977 66.667 0.00 0.00 39.81 4.85
172 186 4.196778 TGGTTGGCGTTGGCTGGA 62.197 61.111 0.00 0.00 39.81 3.86
173 187 2.676471 GGTTGGCGTTGGCTGGAT 60.676 61.111 0.00 0.00 39.81 3.41
174 188 2.700773 GGTTGGCGTTGGCTGGATC 61.701 63.158 0.00 0.00 39.81 3.36
175 189 1.971167 GTTGGCGTTGGCTGGATCA 60.971 57.895 0.00 0.00 39.81 2.92
176 190 1.971167 TTGGCGTTGGCTGGATCAC 60.971 57.895 0.00 0.00 39.81 3.06
177 191 3.499737 GGCGTTGGCTGGATCACG 61.500 66.667 0.00 0.00 39.81 4.35
178 192 4.166011 GCGTTGGCTGGATCACGC 62.166 66.667 9.77 9.77 39.33 5.34
179 193 3.853330 CGTTGGCTGGATCACGCG 61.853 66.667 3.53 3.53 0.00 6.01
235 265 1.798813 GACCGTGCTTACAACAGAAGG 59.201 52.381 0.00 0.00 0.00 3.46
263 293 1.657181 GCCACCGACACGCAAAAAG 60.657 57.895 0.00 0.00 0.00 2.27
277 313 0.755327 AAAAAGGGCAGGCGACAGTT 60.755 50.000 0.00 0.00 0.00 3.16
278 314 1.455383 AAAAGGGCAGGCGACAGTTG 61.455 55.000 0.00 0.00 0.00 3.16
279 315 2.624674 AAAGGGCAGGCGACAGTTGT 62.625 55.000 0.00 0.00 0.00 3.32
280 316 1.764571 AAGGGCAGGCGACAGTTGTA 61.765 55.000 0.00 0.00 0.00 2.41
286 322 1.472878 CAGGCGACAGTTGTAGAGCTA 59.527 52.381 0.00 0.00 0.00 3.32
325 361 2.735663 GTGATGCACAACTCACTCTCAG 59.264 50.000 10.29 0.00 38.94 3.35
326 362 1.731160 GATGCACAACTCACTCTCAGC 59.269 52.381 0.00 0.00 0.00 4.26
329 365 1.413382 CACAACTCACTCTCAGCGAC 58.587 55.000 0.00 0.00 0.00 5.19
351 387 3.270877 GAATGGCGTGAAATACAGAGGT 58.729 45.455 0.00 0.00 0.00 3.85
381 646 3.878699 CACATCAAGCAGCCATACATACA 59.121 43.478 0.00 0.00 0.00 2.29
388 657 6.041523 TCAAGCAGCCATACATACATACAGTA 59.958 38.462 0.00 0.00 37.06 2.74
389 658 6.419484 AGCAGCCATACATACATACAGTAA 57.581 37.500 0.00 0.00 36.05 2.24
415 684 6.942532 AAAATGTGAGCACTCTACAGAAAA 57.057 33.333 1.99 0.00 0.00 2.29
416 685 6.551385 AAATGTGAGCACTCTACAGAAAAG 57.449 37.500 1.99 0.00 0.00 2.27
430 961 2.973224 CAGAAAAGTAACGCACATGCAC 59.027 45.455 4.49 0.00 42.21 4.57
432 963 2.399396 AAAGTAACGCACATGCACAC 57.601 45.000 4.49 0.00 42.21 3.82
433 964 0.234625 AAGTAACGCACATGCACACG 59.765 50.000 4.49 0.00 42.21 4.49
434 965 1.792057 GTAACGCACATGCACACGC 60.792 57.895 4.49 0.00 42.21 5.34
443 974 3.717899 TGCACACGCAGTCACTTC 58.282 55.556 0.00 0.00 45.36 3.01
444 975 1.143838 TGCACACGCAGTCACTTCT 59.856 52.632 0.00 0.00 45.36 2.85
445 976 1.153597 TGCACACGCAGTCACTTCTG 61.154 55.000 0.00 0.00 45.36 3.02
446 977 0.875908 GCACACGCAGTCACTTCTGA 60.876 55.000 0.00 0.00 41.61 3.27
447 978 1.788258 CACACGCAGTCACTTCTGAT 58.212 50.000 0.00 0.00 41.61 2.90
448 979 1.723542 CACACGCAGTCACTTCTGATC 59.276 52.381 0.00 0.00 41.61 2.92
449 980 1.337260 ACACGCAGTCACTTCTGATCC 60.337 52.381 0.00 0.00 41.61 3.36
450 981 0.969149 ACGCAGTCACTTCTGATCCA 59.031 50.000 0.00 0.00 29.74 3.41
451 982 1.067283 ACGCAGTCACTTCTGATCCAG 60.067 52.381 0.00 0.00 29.74 3.86
452 983 1.067283 CGCAGTCACTTCTGATCCAGT 60.067 52.381 0.00 0.00 37.61 4.00
453 984 2.615869 GCAGTCACTTCTGATCCAGTC 58.384 52.381 0.00 0.00 37.61 3.51
454 985 2.233431 GCAGTCACTTCTGATCCAGTCT 59.767 50.000 0.00 0.00 37.61 3.24
455 986 3.675775 GCAGTCACTTCTGATCCAGTCTC 60.676 52.174 0.00 0.00 37.61 3.36
456 987 3.096092 AGTCACTTCTGATCCAGTCTCC 58.904 50.000 0.00 0.00 32.61 3.71
457 988 3.096092 GTCACTTCTGATCCAGTCTCCT 58.904 50.000 0.00 0.00 32.61 3.69
458 989 3.130340 GTCACTTCTGATCCAGTCTCCTC 59.870 52.174 0.00 0.00 32.61 3.71
459 990 3.011144 TCACTTCTGATCCAGTCTCCTCT 59.989 47.826 0.00 0.00 32.61 3.69
460 991 3.381272 CACTTCTGATCCAGTCTCCTCTC 59.619 52.174 0.00 0.00 32.61 3.20
461 992 3.011144 ACTTCTGATCCAGTCTCCTCTCA 59.989 47.826 0.00 0.00 32.61 3.27
462 993 3.969466 TCTGATCCAGTCTCCTCTCAT 57.031 47.619 0.00 0.00 32.61 2.90
463 994 3.831323 TCTGATCCAGTCTCCTCTCATC 58.169 50.000 0.00 0.00 32.61 2.92
464 995 3.462954 TCTGATCCAGTCTCCTCTCATCT 59.537 47.826 0.00 0.00 32.61 2.90
465 996 3.822735 CTGATCCAGTCTCCTCTCATCTC 59.177 52.174 0.00 0.00 0.00 2.75
466 997 2.746279 TCCAGTCTCCTCTCATCTCC 57.254 55.000 0.00 0.00 0.00 3.71
467 998 1.925959 TCCAGTCTCCTCTCATCTCCA 59.074 52.381 0.00 0.00 0.00 3.86
468 999 2.091939 TCCAGTCTCCTCTCATCTCCAG 60.092 54.545 0.00 0.00 0.00 3.86
469 1000 2.309613 CAGTCTCCTCTCATCTCCAGG 58.690 57.143 0.00 0.00 0.00 4.45
470 1001 1.217689 AGTCTCCTCTCATCTCCAGGG 59.782 57.143 0.00 0.00 0.00 4.45
471 1002 1.063266 GTCTCCTCTCATCTCCAGGGT 60.063 57.143 0.00 0.00 0.00 4.34
472 1003 2.175931 GTCTCCTCTCATCTCCAGGGTA 59.824 54.545 0.00 0.00 0.00 3.69
473 1004 2.445145 TCTCCTCTCATCTCCAGGGTAG 59.555 54.545 0.00 0.00 0.00 3.18
474 1005 1.501170 TCCTCTCATCTCCAGGGTAGG 59.499 57.143 0.00 0.00 0.00 3.18
475 1006 1.501170 CCTCTCATCTCCAGGGTAGGA 59.499 57.143 0.00 0.00 36.00 2.94
481 1012 2.443781 TCCAGGGTAGGAGCGTGT 59.556 61.111 0.00 0.00 32.77 4.49
482 1013 1.982395 TCCAGGGTAGGAGCGTGTG 60.982 63.158 0.00 0.00 32.77 3.82
483 1014 2.125512 CAGGGTAGGAGCGTGTGC 60.126 66.667 0.00 0.00 43.24 4.57
534 1065 2.570181 GCAACATGCCTGCCTGAC 59.430 61.111 8.82 0.00 37.42 3.51
535 1066 2.998279 GCAACATGCCTGCCTGACC 61.998 63.158 8.82 0.00 37.42 4.02
536 1067 1.303888 CAACATGCCTGCCTGACCT 60.304 57.895 1.32 0.00 0.00 3.85
537 1068 0.896940 CAACATGCCTGCCTGACCTT 60.897 55.000 1.32 0.00 0.00 3.50
538 1069 0.698238 AACATGCCTGCCTGACCTTA 59.302 50.000 1.32 0.00 0.00 2.69
611 1154 2.037136 CGGAAGGCCAAGTCAGCAG 61.037 63.158 5.01 0.00 0.00 4.24
679 1241 4.845580 CGGCAGGCAGGCAGGTAG 62.846 72.222 4.02 0.00 44.47 3.18
695 1257 3.502979 CAGGTAGTCGAGGCCTATAAGAC 59.497 52.174 4.42 13.48 0.00 3.01
705 1267 0.969894 CCTATAAGACGGGAGGCAGG 59.030 60.000 0.00 0.00 44.00 4.85
711 1273 3.966930 GACGGGAGGCAGGGTCTCT 62.967 68.421 0.00 0.00 38.26 3.10
731 1300 3.259374 TCTTCTCCTCTCATCACCACAAC 59.741 47.826 0.00 0.00 0.00 3.32
735 1304 2.037641 TCCTCTCATCACCACAACACAG 59.962 50.000 0.00 0.00 0.00 3.66
764 1340 0.829182 TGAGTCCACAGCAGAGCAGA 60.829 55.000 0.00 0.00 0.00 4.26
765 1341 0.108709 GAGTCCACAGCAGAGCAGAG 60.109 60.000 0.00 0.00 0.00 3.35
766 1342 1.741032 GTCCACAGCAGAGCAGAGC 60.741 63.158 0.00 0.00 0.00 4.09
767 1343 2.212110 TCCACAGCAGAGCAGAGCA 61.212 57.895 0.00 0.00 0.00 4.26
768 1344 1.742140 CCACAGCAGAGCAGAGCAG 60.742 63.158 0.00 0.00 0.00 4.24
769 1345 1.292541 CACAGCAGAGCAGAGCAGA 59.707 57.895 0.00 0.00 0.00 4.26
770 1346 0.738063 CACAGCAGAGCAGAGCAGAG 60.738 60.000 0.00 0.00 0.00 3.35
771 1347 1.812093 CAGCAGAGCAGAGCAGAGC 60.812 63.158 0.00 0.00 0.00 4.09
772 1348 2.265109 GCAGAGCAGAGCAGAGCA 59.735 61.111 0.00 0.00 0.00 4.26
773 1349 1.812093 GCAGAGCAGAGCAGAGCAG 60.812 63.158 0.00 0.00 0.00 4.24
813 1389 5.001874 TCTACTCAACGCAAAGTCTCTCTA 58.998 41.667 0.00 0.00 0.00 2.43
814 1390 4.792521 ACTCAACGCAAAGTCTCTCTAT 57.207 40.909 0.00 0.00 0.00 1.98
851 1438 3.033764 TTGCGTTGCGTCGTCTCC 61.034 61.111 0.00 0.00 0.00 3.71
910 1525 1.419387 CATCTCCTCCACCCCAAGATC 59.581 57.143 0.00 0.00 0.00 2.75
911 1526 0.687757 TCTCCTCCACCCCAAGATCG 60.688 60.000 0.00 0.00 0.00 3.69
936 1595 0.106149 CAGGCCCCGACTAACATACC 59.894 60.000 0.00 0.00 0.00 2.73
997 1684 1.202533 GCGCTAGGCTGTAAGATCCAA 60.203 52.381 0.00 0.00 39.11 3.53
1023 1722 2.125912 CCCTCACAGGAAGTCGCG 60.126 66.667 0.00 0.00 37.67 5.87
1025 1724 2.811317 CTCACAGGAAGTCGCGGC 60.811 66.667 0.21 0.21 0.00 6.53
1026 1725 4.373116 TCACAGGAAGTCGCGGCC 62.373 66.667 7.31 3.34 0.00 6.13
1108 1816 4.740822 CCGCCCCCAAGACCAAGG 62.741 72.222 0.00 0.00 0.00 3.61
1676 2384 3.951663 TCTTCGAGGACTGTGAGTCATA 58.048 45.455 0.00 0.00 46.79 2.15
1678 2386 3.351794 TCGAGGACTGTGAGTCATACT 57.648 47.619 0.00 0.00 46.79 2.12
1679 2387 4.482952 TCGAGGACTGTGAGTCATACTA 57.517 45.455 0.00 0.00 46.79 1.82
1680 2388 4.190001 TCGAGGACTGTGAGTCATACTAC 58.810 47.826 0.00 0.00 46.79 2.73
1681 2389 4.081031 TCGAGGACTGTGAGTCATACTACT 60.081 45.833 0.00 0.00 46.79 2.57
1682 2390 4.034626 CGAGGACTGTGAGTCATACTACTG 59.965 50.000 0.00 0.00 46.79 2.74
1684 2392 3.697045 GGACTGTGAGTCATACTACTGCT 59.303 47.826 0.00 0.00 46.79 4.24
1685 2393 4.882427 GGACTGTGAGTCATACTACTGCTA 59.118 45.833 0.00 0.00 46.79 3.49
1686 2394 5.220892 GGACTGTGAGTCATACTACTGCTAC 60.221 48.000 0.00 0.00 46.79 3.58
1687 2395 5.502079 ACTGTGAGTCATACTACTGCTACT 58.498 41.667 0.00 0.00 0.00 2.57
1689 2397 6.127869 ACTGTGAGTCATACTACTGCTACTTG 60.128 42.308 0.00 0.00 0.00 3.16
1694 2402 6.800543 AGTCATACTACTGCTACTTGTCATG 58.199 40.000 0.00 0.00 0.00 3.07
1695 2403 6.378564 AGTCATACTACTGCTACTTGTCATGT 59.621 38.462 0.00 0.00 0.00 3.21
1696 2404 7.036220 GTCATACTACTGCTACTTGTCATGTT 58.964 38.462 0.00 0.00 0.00 2.71
1697 2405 7.545965 GTCATACTACTGCTACTTGTCATGTTT 59.454 37.037 0.00 0.00 0.00 2.83
1701 2409 8.084590 ACTACTGCTACTTGTCATGTTTTTAC 57.915 34.615 0.00 0.00 0.00 2.01
1703 2411 9.419297 CTACTGCTACTTGTCATGTTTTTACTA 57.581 33.333 0.00 0.00 0.00 1.82
1705 2413 7.931948 ACTGCTACTTGTCATGTTTTTACTACT 59.068 33.333 0.00 0.00 0.00 2.57
1706 2414 8.083462 TGCTACTTGTCATGTTTTTACTACTG 57.917 34.615 0.00 0.00 0.00 2.74
1707 2415 7.929245 TGCTACTTGTCATGTTTTTACTACTGA 59.071 33.333 0.00 0.00 0.00 3.41
1708 2416 8.221766 GCTACTTGTCATGTTTTTACTACTGAC 58.778 37.037 0.00 0.00 34.91 3.51
1710 2418 6.202188 ACTTGTCATGTTTTTACTACTGACCG 59.798 38.462 0.00 0.00 33.72 4.79
1712 2420 5.693104 TGTCATGTTTTTACTACTGACCGAC 59.307 40.000 0.00 0.00 33.72 4.79
1713 2421 5.924825 GTCATGTTTTTACTACTGACCGACT 59.075 40.000 0.00 0.00 0.00 4.18
1715 2423 4.053295 TGTTTTTACTACTGACCGACTGC 58.947 43.478 0.00 0.00 0.00 4.40
1717 2425 4.325028 TTTTACTACTGACCGACTGCAA 57.675 40.909 0.00 0.00 0.00 4.08
1724 2457 3.472652 ACTGACCGACTGCAATGTTTTA 58.527 40.909 0.00 0.00 0.00 1.52
1725 2458 3.498397 ACTGACCGACTGCAATGTTTTAG 59.502 43.478 0.00 0.00 0.00 1.85
1726 2459 3.734463 TGACCGACTGCAATGTTTTAGA 58.266 40.909 0.00 0.00 0.00 2.10
1730 2463 3.745975 CCGACTGCAATGTTTTAGACTGA 59.254 43.478 0.00 0.00 0.00 3.41
1732 2465 5.319139 CGACTGCAATGTTTTAGACTGATG 58.681 41.667 0.00 0.00 0.00 3.07
1737 2470 5.091431 GCAATGTTTTAGACTGATGCTGAC 58.909 41.667 0.00 0.00 32.68 3.51
1740 2473 5.213891 TGTTTTAGACTGATGCTGACTGA 57.786 39.130 0.00 0.00 0.00 3.41
1741 2474 4.991056 TGTTTTAGACTGATGCTGACTGAC 59.009 41.667 0.00 0.00 0.00 3.51
1742 2475 4.871933 TTTAGACTGATGCTGACTGACA 57.128 40.909 0.00 0.00 0.00 3.58
1743 2476 4.871933 TTAGACTGATGCTGACTGACAA 57.128 40.909 0.00 0.00 0.00 3.18
1965 2713 8.572185 TGATGACGTTTCATGATTTTTCCTTTA 58.428 29.630 0.00 0.00 42.95 1.85
2008 2756 1.480212 TTTGCGAGGGCCTGAGAAGA 61.480 55.000 12.95 0.00 38.85 2.87
2100 2882 7.962918 AGCGAACATACATACATTCTTGTTTTC 59.037 33.333 0.00 0.00 37.28 2.29
2101 2883 7.748683 GCGAACATACATACATTCTTGTTTTCA 59.251 33.333 0.00 0.00 37.28 2.69
2120 2902 5.950544 TTCAGTTACCTACCTGCATACAT 57.049 39.130 0.00 0.00 0.00 2.29
2122 2904 7.612065 TTCAGTTACCTACCTGCATACATAT 57.388 36.000 0.00 0.00 0.00 1.78
2123 2905 8.715190 TTCAGTTACCTACCTGCATACATATA 57.285 34.615 0.00 0.00 0.00 0.86
2124 2906 8.118976 TCAGTTACCTACCTGCATACATATAC 57.881 38.462 0.00 0.00 0.00 1.47
2311 3093 5.538118 TCTCTGCTGAGTCGTTTATTTTGA 58.462 37.500 18.82 0.00 40.98 2.69
2312 3094 5.989168 TCTCTGCTGAGTCGTTTATTTTGAA 59.011 36.000 18.82 0.00 40.98 2.69
2313 3095 6.650807 TCTCTGCTGAGTCGTTTATTTTGAAT 59.349 34.615 18.82 0.00 40.98 2.57
2314 3096 7.817478 TCTCTGCTGAGTCGTTTATTTTGAATA 59.183 33.333 18.82 0.00 40.98 1.75
2316 3098 8.227791 TCTGCTGAGTCGTTTATTTTGAATAAC 58.772 33.333 0.00 0.00 0.00 1.89
2317 3099 7.866729 TGCTGAGTCGTTTATTTTGAATAACA 58.133 30.769 0.00 0.00 0.00 2.41
2318 3100 8.346300 TGCTGAGTCGTTTATTTTGAATAACAA 58.654 29.630 0.00 0.00 36.65 2.83
2319 3101 9.176181 GCTGAGTCGTTTATTTTGAATAACAAA 57.824 29.630 0.00 0.00 45.22 2.83
2334 3123 8.014322 TGAATAACAAATCTACGAGTGTTGTC 57.986 34.615 0.00 0.00 35.82 3.18
2340 3129 6.071560 ACAAATCTACGAGTGTTGTCTGGATA 60.072 38.462 0.00 0.00 0.00 2.59
2341 3130 4.959596 TCTACGAGTGTTGTCTGGATAC 57.040 45.455 0.00 0.00 0.00 2.24
2349 3138 4.780021 AGTGTTGTCTGGATACTCTGGAAT 59.220 41.667 0.00 0.00 37.61 3.01
2362 3151 4.036518 ACTCTGGAATGCCTAGAATCACT 58.963 43.478 0.00 0.00 34.31 3.41
2378 3167 3.194005 TCACTTCACCAAAGTCAGTCC 57.806 47.619 0.00 0.00 45.28 3.85
2432 3222 2.664402 AGCAGTGGTGTTTCAATCCT 57.336 45.000 0.00 0.00 0.00 3.24
2442 3232 5.362143 TGGTGTTTCAATCCTTTCATCAACA 59.638 36.000 0.00 0.00 0.00 3.33
2452 3348 8.517878 CAATCCTTTCATCAACAGTGATAAGTT 58.482 33.333 0.00 0.00 42.88 2.66
2497 3393 7.680730 ACAGAAAGTACCTTCATCAACAGTAT 58.319 34.615 6.97 0.00 0.00 2.12
2501 3397 9.612620 GAAAGTACCTTCATCAACAGTATTTTG 57.387 33.333 0.00 0.00 0.00 2.44
2509 3405 9.903682 CTTCATCAACAGTATTTTGAGAATTGT 57.096 29.630 0.00 0.00 36.44 2.71
2510 3406 9.681692 TTCATCAACAGTATTTTGAGAATTGTG 57.318 29.630 0.00 0.00 36.44 3.33
2538 3434 6.988109 AATACAGAAAGACGCGTCATATAC 57.012 37.500 37.85 23.25 0.00 1.47
2546 3442 3.057456 AGACGCGTCATATACCATCTTCC 60.057 47.826 37.85 8.66 0.00 3.46
2582 3510 9.495754 CTTATAAAATCAGAAAAGAGAAAGGCG 57.504 33.333 0.00 0.00 0.00 5.52
2609 3540 9.079833 CATTTCACCTTTCATGCAGTAAAATAG 57.920 33.333 0.00 0.00 0.00 1.73
2659 3593 7.277539 TGGTCAAAACAATGTGAATTCAAGAAC 59.722 33.333 10.35 0.00 0.00 3.01
2756 3700 3.004315 CCACAGGTGTGTACAAATGGAAC 59.996 47.826 9.22 0.00 44.21 3.62
2796 3752 0.389556 ATGCTATCAGCGGCTCATCG 60.390 55.000 0.00 0.00 46.26 3.84
2869 3856 4.600692 TTTCATCTCTTTCGTCCTGTGA 57.399 40.909 0.00 0.00 0.00 3.58
2870 3857 4.600692 TTCATCTCTTTCGTCCTGTGAA 57.399 40.909 0.00 0.00 0.00 3.18
2871 3858 4.808414 TCATCTCTTTCGTCCTGTGAAT 57.192 40.909 0.00 0.00 0.00 2.57
2872 3859 5.152623 TCATCTCTTTCGTCCTGTGAATT 57.847 39.130 0.00 0.00 0.00 2.17
2873 3860 5.551233 TCATCTCTTTCGTCCTGTGAATTT 58.449 37.500 0.00 0.00 0.00 1.82
2874 3861 5.639506 TCATCTCTTTCGTCCTGTGAATTTC 59.360 40.000 0.00 0.00 0.00 2.17
2875 3862 4.956085 TCTCTTTCGTCCTGTGAATTTCA 58.044 39.130 0.00 0.00 0.00 2.69
2876 3863 5.551233 TCTCTTTCGTCCTGTGAATTTCAT 58.449 37.500 1.78 0.00 0.00 2.57
2877 3864 5.409520 TCTCTTTCGTCCTGTGAATTTCATG 59.590 40.000 1.78 0.00 0.00 3.07
2878 3865 5.304778 TCTTTCGTCCTGTGAATTTCATGA 58.695 37.500 1.78 0.00 0.00 3.07
2879 3866 5.409520 TCTTTCGTCCTGTGAATTTCATGAG 59.590 40.000 1.78 2.38 0.00 2.90
2880 3867 4.271696 TCGTCCTGTGAATTTCATGAGT 57.728 40.909 1.78 0.00 0.00 3.41
2881 3868 3.996363 TCGTCCTGTGAATTTCATGAGTG 59.004 43.478 1.78 0.00 0.00 3.51
2882 3869 3.125829 CGTCCTGTGAATTTCATGAGTGG 59.874 47.826 1.78 1.95 0.00 4.00
2883 3870 3.084039 TCCTGTGAATTTCATGAGTGGC 58.916 45.455 1.78 0.00 0.00 5.01
2884 3871 2.821378 CCTGTGAATTTCATGAGTGGCA 59.179 45.455 1.78 0.00 0.00 4.92
2885 3872 3.119602 CCTGTGAATTTCATGAGTGGCAG 60.120 47.826 1.78 3.57 0.00 4.85
2886 3873 2.821378 TGTGAATTTCATGAGTGGCAGG 59.179 45.455 1.78 0.00 0.00 4.85
2887 3874 1.820519 TGAATTTCATGAGTGGCAGGC 59.179 47.619 0.00 0.00 0.00 4.85
2888 3875 1.135721 GAATTTCATGAGTGGCAGGCC 59.864 52.381 2.62 2.62 0.00 5.19
2889 3876 0.040058 ATTTCATGAGTGGCAGGCCA 59.960 50.000 9.35 9.35 45.02 5.36
2907 3894 2.442212 CATGTTTGCCATGTTCTGCA 57.558 45.000 0.00 0.00 44.96 4.41
3032 4058 1.816835 GGATCACTACGAGACCACACA 59.183 52.381 0.00 0.00 0.00 3.72
3037 4063 4.055360 TCACTACGAGACCACACAAAATG 58.945 43.478 0.00 0.00 0.00 2.32
3064 4090 7.121168 TCTCAGATAATCATTTTCACCCACAAC 59.879 37.037 0.00 0.00 0.00 3.32
3303 4329 5.636543 CCTAATCTGCCAAAAAGCAAGAAAG 59.363 40.000 0.00 0.00 43.52 2.62
3317 4343 3.698040 GCAAGAAAGACACATCCATGGAT 59.302 43.478 22.15 22.15 34.81 3.41
3322 4348 7.087895 AGAAAGACACATCCATGGATATGAT 57.912 36.000 34.42 21.15 36.36 2.45
3454 7039 6.925718 CGCTCTCCTCTTTCATAAACATCATA 59.074 38.462 0.00 0.00 0.00 2.15
3566 7295 1.580059 GGGTACTCCACATTCCAGGA 58.420 55.000 0.00 0.00 35.00 3.86
3593 7323 3.153919 CCGAGGGGTTCTTTCAAAATCA 58.846 45.455 0.00 0.00 0.00 2.57
3955 7690 2.674852 CTGTCCATGAATCTTGTCCACG 59.325 50.000 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.746530 ACATACTACTACCAAATACCATATCGG 58.253 37.037 0.00 0.00 42.50 4.18
27 28 9.775539 ACTGGATTCCATATCATACATACTACT 57.224 33.333 5.70 0.00 30.82 2.57
29 30 9.768215 TGACTGGATTCCATATCATACATACTA 57.232 33.333 5.70 0.00 30.82 1.82
30 31 8.670521 TGACTGGATTCCATATCATACATACT 57.329 34.615 5.70 0.00 30.82 2.12
31 32 8.535335 ACTGACTGGATTCCATATCATACATAC 58.465 37.037 16.28 0.00 31.20 2.39
32 33 8.534496 CACTGACTGGATTCCATATCATACATA 58.466 37.037 16.28 0.00 31.20 2.29
33 34 7.392418 CACTGACTGGATTCCATATCATACAT 58.608 38.462 16.28 4.78 31.20 2.29
34 35 6.239686 CCACTGACTGGATTCCATATCATACA 60.240 42.308 16.28 5.73 43.95 2.29
35 36 6.169094 CCACTGACTGGATTCCATATCATAC 58.831 44.000 16.28 2.29 43.95 2.39
36 37 5.846164 ACCACTGACTGGATTCCATATCATA 59.154 40.000 16.28 0.70 43.95 2.15
37 38 4.662179 ACCACTGACTGGATTCCATATCAT 59.338 41.667 16.28 7.67 43.95 2.45
38 39 4.040047 ACCACTGACTGGATTCCATATCA 58.960 43.478 5.70 11.94 43.95 2.15
39 40 4.696479 ACCACTGACTGGATTCCATATC 57.304 45.455 5.70 7.90 43.95 1.63
40 41 4.443457 CGAACCACTGACTGGATTCCATAT 60.443 45.833 5.70 0.00 43.95 1.78
41 42 3.118775 CGAACCACTGACTGGATTCCATA 60.119 47.826 5.70 0.00 43.95 2.74
42 43 2.355108 CGAACCACTGACTGGATTCCAT 60.355 50.000 5.70 0.00 43.95 3.41
43 44 1.001974 CGAACCACTGACTGGATTCCA 59.998 52.381 5.05 5.05 43.95 3.53
44 45 1.726853 CGAACCACTGACTGGATTCC 58.273 55.000 0.00 0.00 43.95 3.01
45 46 1.079503 GCGAACCACTGACTGGATTC 58.920 55.000 0.00 0.00 43.95 2.52
46 47 0.396435 TGCGAACCACTGACTGGATT 59.604 50.000 0.00 0.00 43.95 3.01
47 48 0.615331 ATGCGAACCACTGACTGGAT 59.385 50.000 0.00 0.00 43.95 3.41
48 49 0.320683 CATGCGAACCACTGACTGGA 60.321 55.000 0.00 0.00 43.95 3.86
50 51 1.229975 TGCATGCGAACCACTGACTG 61.230 55.000 14.09 0.00 0.00 3.51
51 52 0.321919 ATGCATGCGAACCACTGACT 60.322 50.000 14.09 0.00 0.00 3.41
52 53 0.179181 CATGCATGCGAACCACTGAC 60.179 55.000 14.93 0.00 0.00 3.51
53 54 0.606130 ACATGCATGCGAACCACTGA 60.606 50.000 26.53 0.00 0.00 3.41
54 55 1.085893 TACATGCATGCGAACCACTG 58.914 50.000 26.53 0.31 0.00 3.66
88 89 1.911464 CGTGCGGCGTATCATACATAG 59.089 52.381 9.37 0.00 35.54 2.23
104 109 2.201885 CGCTTTCGTCGTTCGTGC 60.202 61.111 0.00 5.77 40.80 5.34
162 176 3.853330 CGCGTGATCCAGCCAACG 61.853 66.667 0.00 0.84 0.00 4.10
163 177 3.499737 CCGCGTGATCCAGCCAAC 61.500 66.667 4.92 0.00 0.00 3.77
164 178 3.545124 AACCGCGTGATCCAGCCAA 62.545 57.895 4.92 0.00 0.00 4.52
165 179 3.545124 AAACCGCGTGATCCAGCCA 62.545 57.895 4.92 0.00 0.00 4.75
166 180 1.862602 AAAAACCGCGTGATCCAGCC 61.863 55.000 4.92 0.00 0.00 4.85
235 265 3.327404 TCGGTGGCCTTCCCTTCC 61.327 66.667 3.32 0.00 0.00 3.46
263 293 1.741770 CTACAACTGTCGCCTGCCC 60.742 63.158 0.00 0.00 0.00 5.36
277 313 3.263170 TGCCTGAATTTGGTAGCTCTACA 59.737 43.478 9.04 0.00 37.78 2.74
278 314 3.873910 TGCCTGAATTTGGTAGCTCTAC 58.126 45.455 0.00 0.00 35.40 2.59
279 315 4.778213 ATGCCTGAATTTGGTAGCTCTA 57.222 40.909 0.00 0.00 0.00 2.43
280 316 3.659183 ATGCCTGAATTTGGTAGCTCT 57.341 42.857 0.00 0.00 0.00 4.09
286 322 3.499338 TCACTGAATGCCTGAATTTGGT 58.501 40.909 1.31 0.00 0.00 3.67
329 365 2.285220 CCTCTGTATTTCACGCCATTCG 59.715 50.000 0.00 0.00 45.38 3.34
351 387 2.426522 GCTGCTTGATGTGGTTCTGTA 58.573 47.619 0.00 0.00 0.00 2.74
367 403 7.490962 TTTTACTGTATGTATGTATGGCTGC 57.509 36.000 0.00 0.00 0.00 5.25
402 671 4.743151 TGTGCGTTACTTTTCTGTAGAGTG 59.257 41.667 0.00 0.00 0.00 3.51
406 675 4.084066 TGCATGTGCGTTACTTTTCTGTAG 60.084 41.667 0.01 0.00 45.83 2.74
415 684 1.859398 CGTGTGCATGTGCGTTACT 59.141 52.632 0.00 0.00 45.83 2.24
416 685 1.792057 GCGTGTGCATGTGCGTTAC 60.792 57.895 0.00 0.00 45.83 2.50
430 961 1.337167 TGGATCAGAAGTGACTGCGTG 60.337 52.381 0.00 0.00 37.75 5.34
432 963 1.067283 ACTGGATCAGAAGTGACTGCG 60.067 52.381 1.59 0.00 37.75 5.18
433 964 2.233431 AGACTGGATCAGAAGTGACTGC 59.767 50.000 1.59 0.00 37.75 4.40
434 965 3.119173 GGAGACTGGATCAGAAGTGACTG 60.119 52.174 1.59 0.00 34.75 3.51
435 966 3.096092 GGAGACTGGATCAGAAGTGACT 58.904 50.000 1.59 0.00 34.75 3.41
436 967 3.096092 AGGAGACTGGATCAGAAGTGAC 58.904 50.000 1.59 0.00 41.13 3.67
437 968 3.011144 AGAGGAGACTGGATCAGAAGTGA 59.989 47.826 1.59 0.00 44.43 3.41
438 969 3.364549 AGAGGAGACTGGATCAGAAGTG 58.635 50.000 1.59 0.00 44.43 3.16
439 970 3.011144 TGAGAGGAGACTGGATCAGAAGT 59.989 47.826 1.59 0.00 44.43 3.01
440 971 3.630168 TGAGAGGAGACTGGATCAGAAG 58.370 50.000 1.59 0.00 44.43 2.85
441 972 3.746792 TGAGAGGAGACTGGATCAGAA 57.253 47.619 1.59 0.00 44.43 3.02
442 973 3.462954 AGATGAGAGGAGACTGGATCAGA 59.537 47.826 1.59 0.00 44.43 3.27
443 974 3.822735 GAGATGAGAGGAGACTGGATCAG 59.177 52.174 0.00 0.00 44.43 2.90
444 975 3.436325 GGAGATGAGAGGAGACTGGATCA 60.436 52.174 0.00 0.00 44.43 2.92
445 976 3.157087 GGAGATGAGAGGAGACTGGATC 58.843 54.545 0.00 0.00 44.43 3.36
446 977 2.517553 TGGAGATGAGAGGAGACTGGAT 59.482 50.000 0.00 0.00 44.43 3.41
447 978 1.925959 TGGAGATGAGAGGAGACTGGA 59.074 52.381 0.00 0.00 44.43 3.86
448 979 2.309613 CTGGAGATGAGAGGAGACTGG 58.690 57.143 0.00 0.00 44.43 4.00
449 980 2.309613 CCTGGAGATGAGAGGAGACTG 58.690 57.143 0.00 0.00 44.43 3.51
451 982 1.063266 ACCCTGGAGATGAGAGGAGAC 60.063 57.143 0.00 0.00 0.00 3.36
452 983 1.313889 ACCCTGGAGATGAGAGGAGA 58.686 55.000 0.00 0.00 0.00 3.71
453 984 2.490718 CCTACCCTGGAGATGAGAGGAG 60.491 59.091 0.00 0.00 0.00 3.69
454 985 1.501170 CCTACCCTGGAGATGAGAGGA 59.499 57.143 0.00 0.00 0.00 3.71
455 986 1.501170 TCCTACCCTGGAGATGAGAGG 59.499 57.143 0.00 0.00 0.00 3.69
464 995 1.982395 CACACGCTCCTACCCTGGA 60.982 63.158 0.00 0.00 34.52 3.86
465 996 2.579201 CACACGCTCCTACCCTGG 59.421 66.667 0.00 0.00 0.00 4.45
466 997 2.125512 GCACACGCTCCTACCCTG 60.126 66.667 0.00 0.00 34.30 4.45
480 1011 4.980903 CAACGCCAACGCCAGCAC 62.981 66.667 0.00 0.00 45.53 4.40
482 1013 4.683334 GTCAACGCCAACGCCAGC 62.683 66.667 0.00 0.00 45.53 4.85
483 1014 4.368808 CGTCAACGCCAACGCCAG 62.369 66.667 0.00 0.00 45.53 4.85
485 1016 4.659874 CACGTCAACGCCAACGCC 62.660 66.667 1.81 0.00 45.53 5.68
486 1017 4.659874 CCACGTCAACGCCAACGC 62.660 66.667 1.81 0.00 45.53 4.84
487 1018 4.659874 GCCACGTCAACGCCAACG 62.660 66.667 1.81 2.94 44.43 4.10
520 1051 0.921896 ATAAGGTCAGGCAGGCATGT 59.078 50.000 5.79 0.00 0.00 3.21
524 1055 1.149401 GGGATAAGGTCAGGCAGGC 59.851 63.158 0.00 0.00 0.00 4.85
527 1058 0.907704 ACGTGGGATAAGGTCAGGCA 60.908 55.000 0.00 0.00 0.00 4.75
528 1059 0.462047 CACGTGGGATAAGGTCAGGC 60.462 60.000 7.95 0.00 0.00 4.85
529 1060 0.178068 CCACGTGGGATAAGGTCAGG 59.822 60.000 27.57 0.00 40.01 3.86
531 1062 3.384937 TCCACGTGGGATAAGGTCA 57.615 52.632 33.40 8.84 42.15 4.02
611 1154 2.665185 AGAACGGCGGTGCTGAAC 60.665 61.111 13.24 0.00 38.46 3.18
672 1234 1.906990 TATAGGCCTCGACTACCTGC 58.093 55.000 9.68 0.00 34.92 4.85
676 1238 2.483491 CCGTCTTATAGGCCTCGACTAC 59.517 54.545 9.68 2.58 0.00 2.73
677 1239 2.551721 CCCGTCTTATAGGCCTCGACTA 60.552 54.545 9.68 0.00 0.00 2.59
678 1240 1.606903 CCGTCTTATAGGCCTCGACT 58.393 55.000 9.68 0.00 0.00 4.18
679 1241 0.597072 CCCGTCTTATAGGCCTCGAC 59.403 60.000 9.68 11.34 0.00 4.20
695 1257 2.685380 AAGAGACCCTGCCTCCCG 60.685 66.667 0.00 0.00 0.00 5.14
705 1267 2.693074 GGTGATGAGAGGAGAAGAGACC 59.307 54.545 0.00 0.00 0.00 3.85
711 1273 2.972021 TGTTGTGGTGATGAGAGGAGAA 59.028 45.455 0.00 0.00 0.00 2.87
735 1304 4.687215 TGGACTCAGCGGCTGTGC 62.687 66.667 27.63 19.74 32.61 4.57
764 1340 2.027003 GAGAAGAATGCTGCTCTGCT 57.973 50.000 0.59 0.00 42.66 4.24
768 1344 2.983229 TGGAAGAGAAGAATGCTGCTC 58.017 47.619 0.00 0.00 45.80 4.26
769 1345 3.648507 ATGGAAGAGAAGAATGCTGCT 57.351 42.857 0.00 0.00 30.49 4.24
770 1346 3.946558 AGAATGGAAGAGAAGAATGCTGC 59.053 43.478 0.00 0.00 0.00 5.25
771 1347 6.347696 AGTAGAATGGAAGAGAAGAATGCTG 58.652 40.000 0.00 0.00 0.00 4.41
772 1348 6.155910 TGAGTAGAATGGAAGAGAAGAATGCT 59.844 38.462 0.00 0.00 0.00 3.79
773 1349 6.344500 TGAGTAGAATGGAAGAGAAGAATGC 58.656 40.000 0.00 0.00 0.00 3.56
813 1389 2.029290 ACGAAGCAAACGTACCTGAGAT 60.029 45.455 0.00 0.00 42.17 2.75
814 1390 1.338973 ACGAAGCAAACGTACCTGAGA 59.661 47.619 0.00 0.00 42.17 3.27
851 1438 2.069430 GGGGAAGAGCAGGAGGAGG 61.069 68.421 0.00 0.00 0.00 4.30
936 1595 1.154225 GCGAAAATGGAGGTGTGCG 60.154 57.895 0.00 0.00 0.00 5.34
997 1684 3.341629 CTGTGAGGGGGCCATGGT 61.342 66.667 14.67 0.00 0.00 3.55
1587 2295 2.283388 AAGTGGCGGTACTCGGGA 60.283 61.111 0.00 0.00 39.69 5.14
1676 2384 7.931948 AGTAAAAACATGACAAGTAGCAGTAGT 59.068 33.333 0.00 0.00 0.00 2.73
1678 2386 9.199982 GTAGTAAAAACATGACAAGTAGCAGTA 57.800 33.333 0.00 0.00 0.00 2.74
1679 2387 7.931948 AGTAGTAAAAACATGACAAGTAGCAGT 59.068 33.333 0.00 0.00 0.00 4.40
1680 2388 8.223769 CAGTAGTAAAAACATGACAAGTAGCAG 58.776 37.037 0.00 0.00 0.00 4.24
1681 2389 7.929245 TCAGTAGTAAAAACATGACAAGTAGCA 59.071 33.333 0.00 0.00 0.00 3.49
1682 2390 8.221766 GTCAGTAGTAAAAACATGACAAGTAGC 58.778 37.037 0.00 0.00 37.56 3.58
1684 2392 7.383029 CGGTCAGTAGTAAAAACATGACAAGTA 59.617 37.037 0.00 0.00 38.99 2.24
1685 2393 6.202188 CGGTCAGTAGTAAAAACATGACAAGT 59.798 38.462 0.00 0.00 38.99 3.16
1686 2394 6.422701 TCGGTCAGTAGTAAAAACATGACAAG 59.577 38.462 0.00 0.00 38.99 3.16
1687 2395 6.201425 GTCGGTCAGTAGTAAAAACATGACAA 59.799 38.462 0.00 0.00 38.99 3.18
1689 2397 5.924825 AGTCGGTCAGTAGTAAAAACATGAC 59.075 40.000 0.00 0.00 37.04 3.06
1694 2402 4.053295 TGCAGTCGGTCAGTAGTAAAAAC 58.947 43.478 0.00 0.00 0.00 2.43
1695 2403 4.325028 TGCAGTCGGTCAGTAGTAAAAA 57.675 40.909 0.00 0.00 0.00 1.94
1696 2404 4.325028 TTGCAGTCGGTCAGTAGTAAAA 57.675 40.909 0.00 0.00 0.00 1.52
1697 2405 4.242475 CATTGCAGTCGGTCAGTAGTAAA 58.758 43.478 0.00 0.00 0.00 2.01
1701 2409 2.370281 ACATTGCAGTCGGTCAGTAG 57.630 50.000 0.00 0.00 0.00 2.57
1703 2411 1.967319 AAACATTGCAGTCGGTCAGT 58.033 45.000 0.00 0.00 0.00 3.41
1705 2413 3.496884 GTCTAAAACATTGCAGTCGGTCA 59.503 43.478 0.00 0.00 0.00 4.02
1706 2414 3.746492 AGTCTAAAACATTGCAGTCGGTC 59.254 43.478 0.00 0.00 0.00 4.79
1707 2415 3.498397 CAGTCTAAAACATTGCAGTCGGT 59.502 43.478 0.00 0.00 0.00 4.69
1708 2416 3.745975 TCAGTCTAAAACATTGCAGTCGG 59.254 43.478 0.00 0.00 0.00 4.79
1710 2418 5.091431 GCATCAGTCTAAAACATTGCAGTC 58.909 41.667 0.00 0.00 32.62 3.51
1712 2420 5.093457 CAGCATCAGTCTAAAACATTGCAG 58.907 41.667 0.00 0.00 33.93 4.41
1713 2421 4.761227 TCAGCATCAGTCTAAAACATTGCA 59.239 37.500 0.00 0.00 33.93 4.08
1715 2423 6.148315 TCAGTCAGCATCAGTCTAAAACATTG 59.852 38.462 0.00 0.00 0.00 2.82
1717 2425 5.641209 GTCAGTCAGCATCAGTCTAAAACAT 59.359 40.000 0.00 0.00 0.00 2.71
1724 2457 3.977134 ATTGTCAGTCAGCATCAGTCT 57.023 42.857 0.00 0.00 0.00 3.24
1725 2458 5.368256 AAAATTGTCAGTCAGCATCAGTC 57.632 39.130 0.00 0.00 0.00 3.51
1726 2459 7.310664 CAATAAAATTGTCAGTCAGCATCAGT 58.689 34.615 0.00 0.00 0.00 3.41
1730 2463 5.105228 CCCCAATAAAATTGTCAGTCAGCAT 60.105 40.000 0.00 0.00 0.00 3.79
1732 2465 4.462483 TCCCCAATAAAATTGTCAGTCAGC 59.538 41.667 0.00 0.00 0.00 4.26
1737 2470 8.259411 TGATGAATTCCCCAATAAAATTGTCAG 58.741 33.333 2.27 0.00 0.00 3.51
1740 2473 8.260114 GTCTGATGAATTCCCCAATAAAATTGT 58.740 33.333 2.27 0.00 0.00 2.71
1741 2474 8.259411 TGTCTGATGAATTCCCCAATAAAATTG 58.741 33.333 2.27 0.00 0.00 2.32
1742 2475 8.378115 TGTCTGATGAATTCCCCAATAAAATT 57.622 30.769 2.27 0.00 0.00 1.82
1743 2476 7.976414 TGTCTGATGAATTCCCCAATAAAAT 57.024 32.000 2.27 0.00 0.00 1.82
1945 2693 6.586082 CCCTGTAAAGGAAAAATCATGAAACG 59.414 38.462 0.00 0.00 0.00 3.60
1949 2697 7.413446 AGATCCCTGTAAAGGAAAAATCATGA 58.587 34.615 0.00 0.00 36.85 3.07
1965 2713 1.061812 AGGTGGCATAGAGATCCCTGT 60.062 52.381 0.00 0.00 0.00 4.00
2030 2781 3.801997 ATCCTCCAGCAAGCGGGG 61.802 66.667 11.25 5.51 32.10 5.73
2031 2782 2.515523 CATCCTCCAGCAAGCGGG 60.516 66.667 4.78 4.78 0.00 6.13
2100 2882 8.531982 ATGTATATGTATGCAGGTAGGTAACTG 58.468 37.037 0.00 0.00 38.53 3.16
2101 2883 8.666129 ATGTATATGTATGCAGGTAGGTAACT 57.334 34.615 0.00 0.00 40.27 2.24
2166 2948 1.066143 TCTGGCTGCTACTGCCTTAAC 60.066 52.381 15.28 0.00 46.43 2.01
2311 3093 7.117812 CCAGACAACACTCGTAGATTTGTTATT 59.882 37.037 0.00 0.00 39.61 1.40
2312 3094 6.590292 CCAGACAACACTCGTAGATTTGTTAT 59.410 38.462 0.00 0.00 39.61 1.89
2313 3095 5.924254 CCAGACAACACTCGTAGATTTGTTA 59.076 40.000 0.00 0.00 39.61 2.41
2314 3096 4.750098 CCAGACAACACTCGTAGATTTGTT 59.250 41.667 0.00 0.00 41.46 2.83
2316 3098 4.556233 TCCAGACAACACTCGTAGATTTG 58.444 43.478 0.00 0.00 33.89 2.32
2317 3099 4.866508 TCCAGACAACACTCGTAGATTT 57.133 40.909 0.00 0.00 33.89 2.17
2318 3100 5.652891 AGTATCCAGACAACACTCGTAGATT 59.347 40.000 0.00 0.00 33.89 2.40
2319 3101 5.194432 AGTATCCAGACAACACTCGTAGAT 58.806 41.667 0.00 0.00 33.89 1.98
2320 3102 4.586884 AGTATCCAGACAACACTCGTAGA 58.413 43.478 0.00 0.00 0.00 2.59
2321 3103 4.636648 AGAGTATCCAGACAACACTCGTAG 59.363 45.833 0.00 0.00 40.41 3.51
2322 3104 4.395231 CAGAGTATCCAGACAACACTCGTA 59.605 45.833 0.00 0.00 40.41 3.43
2323 3105 3.191581 CAGAGTATCCAGACAACACTCGT 59.808 47.826 0.00 0.00 40.41 4.18
2324 3106 3.428180 CCAGAGTATCCAGACAACACTCG 60.428 52.174 0.00 0.00 40.41 4.18
2330 3119 3.118261 GGCATTCCAGAGTATCCAGACAA 60.118 47.826 0.00 0.00 33.66 3.18
2334 3123 4.155709 TCTAGGCATTCCAGAGTATCCAG 58.844 47.826 0.00 0.00 33.66 3.86
2340 3129 4.036518 AGTGATTCTAGGCATTCCAGAGT 58.963 43.478 0.00 0.00 33.74 3.24
2341 3130 4.686191 AGTGATTCTAGGCATTCCAGAG 57.314 45.455 0.00 0.00 33.74 3.35
2349 3138 4.202461 ACTTTGGTGAAGTGATTCTAGGCA 60.202 41.667 0.00 0.00 46.66 4.75
2362 3151 2.702592 AACGGACTGACTTTGGTGAA 57.297 45.000 0.00 0.00 0.00 3.18
2378 3167 0.456653 GCACAAGCATGCCCTTAACG 60.457 55.000 15.66 0.00 39.86 3.18
2481 3377 8.641498 ATTCTCAAAATACTGTTGATGAAGGT 57.359 30.769 0.00 0.00 34.59 3.50
2497 3393 7.939782 TCTGTATTTCAGCACAATTCTCAAAA 58.060 30.769 0.00 0.00 43.32 2.44
2501 3397 7.748241 GTCTTTCTGTATTTCAGCACAATTCTC 59.252 37.037 0.00 0.00 43.32 2.87
2509 3405 2.411748 CGCGTCTTTCTGTATTTCAGCA 59.588 45.455 0.00 0.00 43.32 4.41
2510 3406 2.412089 ACGCGTCTTTCTGTATTTCAGC 59.588 45.455 5.58 0.00 43.32 4.26
2582 3510 3.308438 ACTGCATGAAAGGTGAAATGC 57.692 42.857 0.00 0.00 44.49 3.56
2609 3540 3.305398 ACGGCGAGAGGATGATTTATC 57.695 47.619 16.62 0.00 34.93 1.75
2659 3593 4.976224 TGACTTGATGGCATGAAATCTG 57.024 40.909 3.81 0.00 0.00 2.90
2796 3752 2.670414 CGCAGAGGACAAAAGAGATGAC 59.330 50.000 0.00 0.00 0.00 3.06
2869 3856 1.188863 GGCCTGCCACTCATGAAATT 58.811 50.000 2.58 0.00 35.81 1.82
2870 3857 0.040058 TGGCCTGCCACTCATGAAAT 59.960 50.000 6.80 0.00 41.89 2.17
2871 3858 1.459812 TGGCCTGCCACTCATGAAA 59.540 52.632 6.80 0.00 41.89 2.69
2872 3859 3.169378 TGGCCTGCCACTCATGAA 58.831 55.556 6.80 0.00 41.89 2.57
2894 3881 2.104451 ACCAAATTTGCAGAACATGGCA 59.896 40.909 12.92 0.00 38.46 4.92
2895 3882 2.481185 CACCAAATTTGCAGAACATGGC 59.519 45.455 12.92 0.00 0.00 4.40
2896 3883 3.992643 TCACCAAATTTGCAGAACATGG 58.007 40.909 12.92 0.00 0.00 3.66
2897 3884 6.548441 AATTCACCAAATTTGCAGAACATG 57.452 33.333 19.34 5.73 33.69 3.21
2898 3885 8.851541 AATAATTCACCAAATTTGCAGAACAT 57.148 26.923 19.34 15.21 38.53 2.71
2899 3886 8.674263 AAATAATTCACCAAATTTGCAGAACA 57.326 26.923 19.34 13.42 38.53 3.18
2900 3887 8.772705 TGAAATAATTCACCAAATTTGCAGAAC 58.227 29.630 19.34 10.50 40.59 3.01
2901 3888 8.899427 TGAAATAATTCACCAAATTTGCAGAA 57.101 26.923 19.28 19.28 40.59 3.02
2985 4011 5.629435 TCGCTGATGCTAATTACTAACATCG 59.371 40.000 0.00 0.00 36.33 3.84
3037 4063 6.599244 TGTGGGTGAAAATGATTATCTGAGAC 59.401 38.462 0.00 0.00 0.00 3.36
3042 4068 6.493115 TGTGTTGTGGGTGAAAATGATTATCT 59.507 34.615 0.00 0.00 0.00 1.98
3064 4090 2.161012 GCATCTGACAAGTGGATGTGTG 59.839 50.000 11.63 0.00 39.04 3.82
3193 4219 1.374560 GTTTGTGCCAAAACCAACCC 58.625 50.000 2.47 0.00 34.58 4.11
3267 4293 3.128349 GCAGATTAGGCATGCCAAAATG 58.872 45.455 37.18 26.71 38.92 2.32
3303 4329 6.412214 TGATCATCATATCCATGGATGTGTC 58.588 40.000 36.39 29.17 42.09 3.67
3317 4343 7.991460 AGCAGAAGATTTCACTTGATCATCATA 59.009 33.333 0.00 0.00 0.00 2.15
3322 4348 4.155462 GCAGCAGAAGATTTCACTTGATCA 59.845 41.667 0.00 0.00 0.00 2.92
3384 4458 4.838423 TGTGAGATGAACAGGAACCTTCTA 59.162 41.667 0.00 0.00 0.00 2.10
3385 4459 3.648067 TGTGAGATGAACAGGAACCTTCT 59.352 43.478 0.00 0.00 0.00 2.85
3454 7039 5.684704 TCTCTGAGATTTTGACCAAGTTGT 58.315 37.500 2.58 0.00 0.00 3.32
3566 7295 1.763545 GAAAGAACCCCTCGGCTAGAT 59.236 52.381 0.00 0.00 0.00 1.98
3638 7373 5.815581 TGTATCTGCCTGTTTAGTGGAAAT 58.184 37.500 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.