Multiple sequence alignment - TraesCS3D01G274000

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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 TraesCS3D01G274000 chr3D 100.000 3229 0 0 1 3229 380047190 380043962 0.000000e+00 5963.0
1 TraesCS3D01G274000 chr3D 92.008 1051 61 13 2192 3225 537901430 537900386 0.000000e+00 1454.0
2 TraesCS3D01G274000 chr3D 91.029 1059 77 12 2184 3229 124043908 124042855 0.000000e+00 1413.0
3 TraesCS3D01G274000 chr3D 88.780 205 15 7 346 545 582707424 582707625 8.950000e-61 244.0
4 TraesCS3D01G274000 chr3D 86.449 214 23 5 348 556 132187667 132187455 2.510000e-56 230.0
5 TraesCS3D01G274000 chr3D 87.317 205 21 5 345 544 562514718 562514922 2.510000e-56 230.0
6 TraesCS3D01G274000 chr3D 87.624 202 18 6 349 544 573814386 573814586 9.010000e-56 228.0
7 TraesCS3D01G274000 chr3D 86.256 211 22 6 349 558 590975106 590975310 4.190000e-54 222.0
8 TraesCS3D01G274000 chr3D 95.349 43 0 2 218 258 310684004 310683962 2.080000e-07 67.6
9 TraesCS3D01G274000 chr3D 87.931 58 6 1 297 354 427448673 427448617 2.080000e-07 67.6
10 TraesCS3D01G274000 chr2D 92.784 1649 77 24 561 2192 36112247 36113870 0.000000e+00 2348.0
11 TraesCS3D01G274000 chr2D 93.499 1046 54 9 2195 3229 435294640 435295682 0.000000e+00 1543.0
12 TraesCS3D01G274000 chr2D 94.909 825 40 2 1372 2195 36123887 36123064 0.000000e+00 1290.0
13 TraesCS3D01G274000 chr2D 89.000 200 16 2 39 237 36111967 36112161 3.220000e-60 243.0
14 TraesCS3D01G274000 chr2D 81.592 201 32 4 573 769 36111589 36111788 9.270000e-36 161.0
15 TraesCS3D01G274000 chr2D 89.333 75 2 4 1300 1372 36152093 36152023 4.440000e-14 89.8
16 TraesCS3D01G274000 chr2D 93.023 43 1 2 218 258 109223301 109223343 9.670000e-06 62.1
17 TraesCS3D01G274000 chr2B 96.051 1418 49 5 781 2195 61340314 61338901 0.000000e+00 2302.0
18 TraesCS3D01G274000 chr2B 93.292 1118 37 16 781 1892 61285157 61284072 0.000000e+00 1615.0
19 TraesCS3D01G274000 chr2B 83.420 766 106 16 889 1642 23597882 23597126 0.000000e+00 691.0
20 TraesCS3D01G274000 chr2B 94.498 309 16 1 38 345 61340890 61340582 2.910000e-130 475.0
21 TraesCS3D01G274000 chr2B 95.089 224 10 1 561 783 61285410 61285187 5.130000e-93 351.0
22 TraesCS3D01G274000 chr2B 93.860 228 9 2 561 783 61340571 61340344 3.990000e-89 339.0
23 TraesCS3D01G274000 chr2B 87.083 240 22 5 1 237 61285729 61285496 2.470000e-66 263.0
24 TraesCS3D01G274000 chr2B 87.081 209 19 6 347 549 246954260 246954466 2.510000e-56 230.0
25 TraesCS3D01G274000 chr2B 83.333 180 24 5 598 772 61286041 61285863 9.270000e-36 161.0
26 TraesCS3D01G274000 chr2B 97.500 40 1 0 297 336 464902395 464902356 5.780000e-08 69.4
27 TraesCS3D01G274000 chr2B 97.436 39 1 0 297 335 110829720 110829758 2.080000e-07 67.6
28 TraesCS3D01G274000 chr2B 90.000 50 4 1 297 345 198720738 198720689 2.690000e-06 63.9
29 TraesCS3D01G274000 chr2B 87.500 56 5 1 218 271 616933885 616933940 2.690000e-06 63.9
30 TraesCS3D01G274000 chr1D 96.042 1036 41 0 2193 3228 388158992 388160027 0.000000e+00 1687.0
31 TraesCS3D01G274000 chr1D 94.909 1041 48 3 2193 3229 324063989 324062950 0.000000e+00 1624.0
32 TraesCS3D01G274000 chr1D 95.455 44 1 1 300 343 438938042 438938000 5.780000e-08 69.4
33 TraesCS3D01G274000 chr4D 94.450 1045 52 1 2191 3229 332871568 332870524 0.000000e+00 1604.0
34 TraesCS3D01G274000 chr4D 92.176 1048 70 3 2193 3229 400555040 400556086 0.000000e+00 1471.0
35 TraesCS3D01G274000 chr4D 91.210 1058 67 18 2193 3229 265592361 265593413 0.000000e+00 1415.0
36 TraesCS3D01G274000 chr4D 88.462 208 19 5 353 557 46672157 46672362 2.490000e-61 246.0
37 TraesCS3D01G274000 chr5D 91.325 1049 79 3 2192 3229 403211105 403210058 0.000000e+00 1423.0
38 TraesCS3D01G274000 chr5D 93.953 215 7 4 348 561 486817946 486817737 1.450000e-83 320.0
39 TraesCS3D01G274000 chr2A 92.692 780 24 10 1413 2192 39468942 39469688 0.000000e+00 1094.0
40 TraesCS3D01G274000 chr2A 94.761 649 28 2 781 1427 39468269 39468913 0.000000e+00 1005.0
41 TraesCS3D01G274000 chr2A 83.567 499 69 8 1703 2195 15011957 15011466 3.800000e-124 455.0
42 TraesCS3D01G274000 chr2A 92.308 234 15 3 553 783 39468006 39468239 2.400000e-86 329.0
43 TraesCS3D01G274000 chr2A 83.776 339 51 3 1308 1646 15012382 15012048 5.200000e-83 318.0
44 TraesCS3D01G274000 chr2A 87.712 236 21 4 1 236 39467701 39467928 5.310000e-68 268.0
45 TraesCS3D01G274000 chr2A 84.685 111 17 0 659 769 39467456 39467566 9.470000e-21 111.0
46 TraesCS3D01G274000 chr2A 93.023 43 1 2 218 258 507086241 507086283 9.670000e-06 62.1
47 TraesCS3D01G274000 chr7D 88.614 202 16 6 348 544 379845480 379845679 4.160000e-59 239.0
48 TraesCS3D01G274000 chr7A 95.556 45 0 2 218 260 214220793 214220749 1.610000e-08 71.3
49 TraesCS3D01G274000 chr5A 77.519 129 19 6 221 343 536122039 536122163 5.780000e-08 69.4
50 TraesCS3D01G274000 chr7B 95.349 43 0 2 217 257 89573451 89573493 2.080000e-07 67.6
51 TraesCS3D01G274000 chr1A 97.436 39 1 0 297 335 104852437 104852475 2.080000e-07 67.6
52 TraesCS3D01G274000 chr5B 89.796 49 3 1 289 337 706729520 706729474 9.670000e-06 62.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G274000 chr3D 380043962 380047190 3228 True 5963.000000 5963 100.00000 1 3229 1 chr3D.!!$R4 3228
1 TraesCS3D01G274000 chr3D 537900386 537901430 1044 True 1454.000000 1454 92.00800 2192 3225 1 chr3D.!!$R6 1033
2 TraesCS3D01G274000 chr3D 124042855 124043908 1053 True 1413.000000 1413 91.02900 2184 3229 1 chr3D.!!$R1 1045
3 TraesCS3D01G274000 chr2D 435294640 435295682 1042 False 1543.000000 1543 93.49900 2195 3229 1 chr2D.!!$F2 1034
4 TraesCS3D01G274000 chr2D 36123064 36123887 823 True 1290.000000 1290 94.90900 1372 2195 1 chr2D.!!$R1 823
5 TraesCS3D01G274000 chr2D 36111589 36113870 2281 False 917.333333 2348 87.79200 39 2192 3 chr2D.!!$F3 2153
6 TraesCS3D01G274000 chr2B 61338901 61340890 1989 True 1038.666667 2302 94.80300 38 2195 3 chr2B.!!$R5 2157
7 TraesCS3D01G274000 chr2B 23597126 23597882 756 True 691.000000 691 83.42000 889 1642 1 chr2B.!!$R1 753
8 TraesCS3D01G274000 chr2B 61284072 61286041 1969 True 597.500000 1615 89.69925 1 1892 4 chr2B.!!$R4 1891
9 TraesCS3D01G274000 chr1D 388158992 388160027 1035 False 1687.000000 1687 96.04200 2193 3228 1 chr1D.!!$F1 1035
10 TraesCS3D01G274000 chr1D 324062950 324063989 1039 True 1624.000000 1624 94.90900 2193 3229 1 chr1D.!!$R1 1036
11 TraesCS3D01G274000 chr4D 332870524 332871568 1044 True 1604.000000 1604 94.45000 2191 3229 1 chr4D.!!$R1 1038
12 TraesCS3D01G274000 chr4D 400555040 400556086 1046 False 1471.000000 1471 92.17600 2193 3229 1 chr4D.!!$F3 1036
13 TraesCS3D01G274000 chr4D 265592361 265593413 1052 False 1415.000000 1415 91.21000 2193 3229 1 chr4D.!!$F2 1036
14 TraesCS3D01G274000 chr5D 403210058 403211105 1047 True 1423.000000 1423 91.32500 2192 3229 1 chr5D.!!$R1 1037
15 TraesCS3D01G274000 chr2A 39467456 39469688 2232 False 561.400000 1094 90.43160 1 2192 5 chr2A.!!$F2 2191
16 TraesCS3D01G274000 chr2A 15011466 15012382 916 True 386.500000 455 83.67150 1308 2195 2 chr2A.!!$R1 887

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
546 893 0.105964 CCACCGAAGACAACACCTCA 59.894 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2371 2868 1.002502 GGCGGTTTAGCTCCTGGTT 60.003 57.895 0.0 0.0 37.29 3.67 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 428 4.218417 GGCTCTGAAGTTTGAAAATAGGCA 59.782 41.667 0.00 0.00 0.00 4.75
145 486 5.567138 ATCAACTTCAGCCCTTAATTTCG 57.433 39.130 0.00 0.00 0.00 3.46
184 525 3.874383 TCCACAAGTTCCCATTCAGAA 57.126 42.857 0.00 0.00 0.00 3.02
193 534 7.508977 ACAAGTTCCCATTCAGAAGGAAATTTA 59.491 33.333 12.06 0.00 43.36 1.40
194 535 8.534496 CAAGTTCCCATTCAGAAGGAAATTTAT 58.466 33.333 12.06 0.00 43.36 1.40
195 536 8.670521 AGTTCCCATTCAGAAGGAAATTTATT 57.329 30.769 5.62 0.00 41.21 1.40
196 537 9.104713 AGTTCCCATTCAGAAGGAAATTTATTT 57.895 29.630 5.62 0.00 41.21 1.40
197 538 9.725019 GTTCCCATTCAGAAGGAAATTTATTTT 57.275 29.630 5.62 0.00 41.21 1.82
281 628 5.246656 ACAGCCATTTTGATCCATTTCTTCA 59.753 36.000 0.00 0.00 0.00 3.02
345 692 6.424032 GGATGGAGGAAGTACCAAATTACTT 58.576 40.000 0.00 0.00 43.59 2.24
346 693 6.890268 GGATGGAGGAAGTACCAAATTACTTT 59.110 38.462 0.00 0.00 41.46 2.66
347 694 7.396339 GGATGGAGGAAGTACCAAATTACTTTT 59.604 37.037 0.00 0.00 41.46 2.27
348 695 8.721133 ATGGAGGAAGTACCAAATTACTTTTT 57.279 30.769 0.00 0.00 41.46 1.94
379 726 8.529102 TCGACAAAGCGAATATATTAATATCGC 58.471 33.333 24.42 24.42 40.71 4.58
380 727 7.519612 CGACAAAGCGAATATATTAATATCGCG 59.480 37.037 24.97 19.92 42.67 5.87
381 728 8.402326 ACAAAGCGAATATATTAATATCGCGA 57.598 30.769 24.97 13.09 42.67 5.87
382 729 8.865978 ACAAAGCGAATATATTAATATCGCGAA 58.134 29.630 24.97 2.68 42.67 4.70
383 730 9.346231 CAAAGCGAATATATTAATATCGCGAAG 57.654 33.333 24.97 18.12 42.67 3.79
384 731 8.851960 AAGCGAATATATTAATATCGCGAAGA 57.148 30.769 24.97 4.32 42.67 2.87
385 732 9.464714 AAGCGAATATATTAATATCGCGAAGAT 57.535 29.630 24.97 7.02 42.67 2.40
395 742 9.647797 ATTAATATCGCGAAGATACCAATTACA 57.352 29.630 15.24 0.00 43.93 2.41
396 743 6.946229 ATATCGCGAAGATACCAATTACAC 57.054 37.500 15.24 0.00 43.93 2.90
397 744 3.450578 TCGCGAAGATACCAATTACACC 58.549 45.455 6.20 0.00 0.00 4.16
398 745 2.542595 CGCGAAGATACCAATTACACCC 59.457 50.000 0.00 0.00 0.00 4.61
399 746 2.542595 GCGAAGATACCAATTACACCCG 59.457 50.000 0.00 0.00 0.00 5.28
400 747 3.128349 CGAAGATACCAATTACACCCGG 58.872 50.000 0.00 0.00 0.00 5.73
401 748 2.632987 AGATACCAATTACACCCGGC 57.367 50.000 0.00 0.00 0.00 6.13
402 749 1.142262 AGATACCAATTACACCCGGCC 59.858 52.381 0.00 0.00 0.00 6.13
403 750 1.142262 GATACCAATTACACCCGGCCT 59.858 52.381 0.00 0.00 0.00 5.19
404 751 0.542805 TACCAATTACACCCGGCCTC 59.457 55.000 0.00 0.00 0.00 4.70
405 752 1.205460 ACCAATTACACCCGGCCTCT 61.205 55.000 0.00 0.00 0.00 3.69
406 753 0.748005 CCAATTACACCCGGCCTCTG 60.748 60.000 0.00 0.00 0.00 3.35
407 754 1.077716 AATTACACCCGGCCTCTGC 60.078 57.895 0.00 0.00 0.00 4.26
408 755 1.847798 AATTACACCCGGCCTCTGCA 61.848 55.000 0.00 0.00 40.13 4.41
409 756 2.536997 ATTACACCCGGCCTCTGCAC 62.537 60.000 0.00 0.00 40.13 4.57
414 761 4.641645 CCGGCCTCTGCACCAACA 62.642 66.667 0.00 0.00 40.13 3.33
415 762 2.594303 CGGCCTCTGCACCAACAA 60.594 61.111 0.00 0.00 40.13 2.83
416 763 2.620112 CGGCCTCTGCACCAACAAG 61.620 63.158 0.00 0.00 40.13 3.16
417 764 1.228245 GGCCTCTGCACCAACAAGA 60.228 57.895 0.00 0.00 40.13 3.02
418 765 0.610232 GGCCTCTGCACCAACAAGAT 60.610 55.000 0.00 0.00 40.13 2.40
419 766 0.524862 GCCTCTGCACCAACAAGATG 59.475 55.000 0.00 0.00 37.47 2.90
420 767 1.901591 CCTCTGCACCAACAAGATGT 58.098 50.000 0.00 0.00 0.00 3.06
421 768 1.808945 CCTCTGCACCAACAAGATGTC 59.191 52.381 0.00 0.00 0.00 3.06
422 769 1.808945 CTCTGCACCAACAAGATGTCC 59.191 52.381 0.00 0.00 0.00 4.02
423 770 1.142667 TCTGCACCAACAAGATGTCCA 59.857 47.619 0.00 0.00 0.00 4.02
424 771 1.955778 CTGCACCAACAAGATGTCCAA 59.044 47.619 0.00 0.00 0.00 3.53
425 772 2.361757 CTGCACCAACAAGATGTCCAAA 59.638 45.455 0.00 0.00 0.00 3.28
426 773 2.361757 TGCACCAACAAGATGTCCAAAG 59.638 45.455 0.00 0.00 0.00 2.77
427 774 2.622942 GCACCAACAAGATGTCCAAAGA 59.377 45.455 0.00 0.00 0.00 2.52
428 775 3.256631 GCACCAACAAGATGTCCAAAGAT 59.743 43.478 0.00 0.00 0.00 2.40
429 776 4.458989 GCACCAACAAGATGTCCAAAGATA 59.541 41.667 0.00 0.00 0.00 1.98
430 777 5.126061 GCACCAACAAGATGTCCAAAGATAT 59.874 40.000 0.00 0.00 0.00 1.63
431 778 6.678900 GCACCAACAAGATGTCCAAAGATATC 60.679 42.308 0.00 0.00 40.08 1.63
432 779 6.375174 CACCAACAAGATGTCCAAAGATATCA 59.625 38.462 5.32 0.00 41.71 2.15
433 780 6.947733 ACCAACAAGATGTCCAAAGATATCAA 59.052 34.615 5.32 0.00 41.71 2.57
434 781 7.121759 ACCAACAAGATGTCCAAAGATATCAAG 59.878 37.037 5.32 0.00 41.71 3.02
435 782 7.415989 CCAACAAGATGTCCAAAGATATCAAGG 60.416 40.741 5.32 3.75 41.71 3.61
436 783 6.962182 ACAAGATGTCCAAAGATATCAAGGA 58.038 36.000 5.32 6.13 41.71 3.36
437 784 7.580910 ACAAGATGTCCAAAGATATCAAGGAT 58.419 34.615 5.32 0.00 41.71 3.24
438 785 7.501559 ACAAGATGTCCAAAGATATCAAGGATG 59.498 37.037 5.32 6.36 41.71 3.51
439 786 6.002704 AGATGTCCAAAGATATCAAGGATGC 58.997 40.000 5.32 3.48 41.71 3.91
440 787 5.114764 TGTCCAAAGATATCAAGGATGCA 57.885 39.130 5.32 0.00 0.00 3.96
441 788 4.883585 TGTCCAAAGATATCAAGGATGCAC 59.116 41.667 5.32 0.00 0.00 4.57
442 789 4.883585 GTCCAAAGATATCAAGGATGCACA 59.116 41.667 5.32 0.00 0.00 4.57
443 790 4.883585 TCCAAAGATATCAAGGATGCACAC 59.116 41.667 5.32 0.00 0.00 3.82
444 791 4.641541 CCAAAGATATCAAGGATGCACACA 59.358 41.667 5.32 0.00 0.00 3.72
445 792 5.125900 CCAAAGATATCAAGGATGCACACAA 59.874 40.000 5.32 0.00 0.00 3.33
446 793 5.824904 AAGATATCAAGGATGCACACAAC 57.175 39.130 5.32 0.00 0.00 3.32
447 794 4.202441 AGATATCAAGGATGCACACAACC 58.798 43.478 5.32 0.00 39.00 3.77
448 795 2.291209 ATCAAGGATGCACACAACCA 57.709 45.000 0.00 0.00 41.12 3.67
449 796 2.064434 TCAAGGATGCACACAACCAA 57.936 45.000 0.00 0.00 41.12 3.67
450 797 1.955778 TCAAGGATGCACACAACCAAG 59.044 47.619 0.00 0.00 41.12 3.61
451 798 1.955778 CAAGGATGCACACAACCAAGA 59.044 47.619 0.00 0.00 41.12 3.02
452 799 2.361757 CAAGGATGCACACAACCAAGAA 59.638 45.455 0.00 0.00 41.12 2.52
453 800 2.665165 AGGATGCACACAACCAAGAAA 58.335 42.857 0.00 0.00 41.12 2.52
454 801 3.030291 AGGATGCACACAACCAAGAAAA 58.970 40.909 0.00 0.00 41.12 2.29
455 802 3.450457 AGGATGCACACAACCAAGAAAAA 59.550 39.130 0.00 0.00 41.12 1.94
485 832 7.987750 ACAAGAGAGAAATAAAAAGAGACCC 57.012 36.000 0.00 0.00 0.00 4.46
486 833 6.943146 ACAAGAGAGAAATAAAAAGAGACCCC 59.057 38.462 0.00 0.00 0.00 4.95
487 834 5.735766 AGAGAGAAATAAAAAGAGACCCCG 58.264 41.667 0.00 0.00 0.00 5.73
488 835 5.248705 AGAGAGAAATAAAAAGAGACCCCGT 59.751 40.000 0.00 0.00 0.00 5.28
489 836 5.489249 AGAGAAATAAAAAGAGACCCCGTC 58.511 41.667 0.00 0.00 0.00 4.79
490 837 5.012768 AGAGAAATAAAAAGAGACCCCGTCA 59.987 40.000 0.00 0.00 34.60 4.35
491 838 5.001874 AGAAATAAAAAGAGACCCCGTCAC 58.998 41.667 0.00 0.00 34.60 3.67
492 839 2.443887 TAAAAAGAGACCCCGTCACG 57.556 50.000 0.00 0.00 34.60 4.35
494 841 1.405272 AAAAGAGACCCCGTCACGGT 61.405 55.000 16.87 0.00 46.80 4.83
495 842 2.095978 AAAGAGACCCCGTCACGGTG 62.096 60.000 16.87 6.25 46.80 4.94
496 843 2.987547 GAGACCCCGTCACGGTGA 60.988 66.667 16.87 6.76 46.80 4.02
497 844 2.283676 AGACCCCGTCACGGTGAT 60.284 61.111 16.87 0.00 46.80 3.06
498 845 2.125673 GACCCCGTCACGGTGATG 60.126 66.667 20.83 20.83 46.80 3.07
499 846 2.602267 ACCCCGTCACGGTGATGA 60.602 61.111 27.49 0.00 46.80 2.92
500 847 2.162338 GACCCCGTCACGGTGATGAA 62.162 60.000 27.49 0.00 46.80 2.57
501 848 1.004320 CCCCGTCACGGTGATGAAA 60.004 57.895 27.49 0.00 46.80 2.69
502 849 0.604243 CCCCGTCACGGTGATGAAAA 60.604 55.000 27.49 0.00 46.80 2.29
503 850 0.515564 CCCGTCACGGTGATGAAAAC 59.484 55.000 27.49 8.39 46.80 2.43
504 851 1.508632 CCGTCACGGTGATGAAAACT 58.491 50.000 27.49 0.00 42.73 2.66
505 852 1.459592 CCGTCACGGTGATGAAAACTC 59.540 52.381 27.49 6.50 42.73 3.01
506 853 2.131972 CGTCACGGTGATGAAAACTCA 58.868 47.619 22.80 0.00 35.46 3.41
507 854 2.096909 CGTCACGGTGATGAAAACTCAC 60.097 50.000 22.80 2.23 41.83 3.51
508 855 2.869801 GTCACGGTGATGAAAACTCACA 59.130 45.455 14.78 0.00 43.85 3.58
509 856 3.311322 GTCACGGTGATGAAAACTCACAA 59.689 43.478 14.78 0.00 43.85 3.33
510 857 3.311322 TCACGGTGATGAAAACTCACAAC 59.689 43.478 6.76 0.00 43.85 3.32
511 858 3.064682 CACGGTGATGAAAACTCACAACA 59.935 43.478 0.74 0.00 43.85 3.33
512 859 3.312421 ACGGTGATGAAAACTCACAACAG 59.688 43.478 5.87 0.00 43.85 3.16
513 860 3.632189 GGTGATGAAAACTCACAACAGC 58.368 45.455 5.87 0.00 43.85 4.40
514 861 3.066621 GGTGATGAAAACTCACAACAGCA 59.933 43.478 5.87 0.00 43.85 4.41
515 862 4.439974 GGTGATGAAAACTCACAACAGCAA 60.440 41.667 5.87 0.00 43.85 3.91
516 863 4.500477 GTGATGAAAACTCACAACAGCAAC 59.500 41.667 0.00 0.00 42.08 4.17
517 864 4.157472 TGATGAAAACTCACAACAGCAACA 59.843 37.500 0.00 0.00 0.00 3.33
518 865 3.832276 TGAAAACTCACAACAGCAACAC 58.168 40.909 0.00 0.00 0.00 3.32
519 866 3.505680 TGAAAACTCACAACAGCAACACT 59.494 39.130 0.00 0.00 0.00 3.55
520 867 3.764885 AAACTCACAACAGCAACACTC 57.235 42.857 0.00 0.00 0.00 3.51
521 868 2.698855 ACTCACAACAGCAACACTCT 57.301 45.000 0.00 0.00 0.00 3.24
522 869 3.819564 ACTCACAACAGCAACACTCTA 57.180 42.857 0.00 0.00 0.00 2.43
523 870 4.137116 ACTCACAACAGCAACACTCTAA 57.863 40.909 0.00 0.00 0.00 2.10
524 871 3.871594 ACTCACAACAGCAACACTCTAAC 59.128 43.478 0.00 0.00 0.00 2.34
525 872 3.202906 TCACAACAGCAACACTCTAACC 58.797 45.455 0.00 0.00 0.00 2.85
526 873 2.942376 CACAACAGCAACACTCTAACCA 59.058 45.455 0.00 0.00 0.00 3.67
527 874 2.943033 ACAACAGCAACACTCTAACCAC 59.057 45.455 0.00 0.00 0.00 4.16
528 875 2.256117 ACAGCAACACTCTAACCACC 57.744 50.000 0.00 0.00 0.00 4.61
529 876 1.488812 ACAGCAACACTCTAACCACCA 59.511 47.619 0.00 0.00 0.00 4.17
530 877 1.873591 CAGCAACACTCTAACCACCAC 59.126 52.381 0.00 0.00 0.00 4.16
531 878 1.202770 AGCAACACTCTAACCACCACC 60.203 52.381 0.00 0.00 0.00 4.61
532 879 1.508632 CAACACTCTAACCACCACCG 58.491 55.000 0.00 0.00 0.00 4.94
533 880 1.069513 CAACACTCTAACCACCACCGA 59.930 52.381 0.00 0.00 0.00 4.69
534 881 1.416243 ACACTCTAACCACCACCGAA 58.584 50.000 0.00 0.00 0.00 4.30
535 882 1.343465 ACACTCTAACCACCACCGAAG 59.657 52.381 0.00 0.00 0.00 3.79
536 883 1.616865 CACTCTAACCACCACCGAAGA 59.383 52.381 0.00 0.00 0.00 2.87
537 884 1.617357 ACTCTAACCACCACCGAAGAC 59.383 52.381 0.00 0.00 0.00 3.01
538 885 1.616865 CTCTAACCACCACCGAAGACA 59.383 52.381 0.00 0.00 0.00 3.41
539 886 2.036733 CTCTAACCACCACCGAAGACAA 59.963 50.000 0.00 0.00 0.00 3.18
540 887 2.140717 CTAACCACCACCGAAGACAAC 58.859 52.381 0.00 0.00 0.00 3.32
541 888 0.253610 AACCACCACCGAAGACAACA 59.746 50.000 0.00 0.00 0.00 3.33
542 889 0.463116 ACCACCACCGAAGACAACAC 60.463 55.000 0.00 0.00 0.00 3.32
543 890 1.164041 CCACCACCGAAGACAACACC 61.164 60.000 0.00 0.00 0.00 4.16
544 891 0.179056 CACCACCGAAGACAACACCT 60.179 55.000 0.00 0.00 0.00 4.00
545 892 0.106149 ACCACCGAAGACAACACCTC 59.894 55.000 0.00 0.00 0.00 3.85
546 893 0.105964 CCACCGAAGACAACACCTCA 59.894 55.000 0.00 0.00 0.00 3.86
547 894 1.474320 CCACCGAAGACAACACCTCAA 60.474 52.381 0.00 0.00 0.00 3.02
548 895 1.597663 CACCGAAGACAACACCTCAAC 59.402 52.381 0.00 0.00 0.00 3.18
549 896 1.485066 ACCGAAGACAACACCTCAACT 59.515 47.619 0.00 0.00 0.00 3.16
550 897 1.867233 CCGAAGACAACACCTCAACTG 59.133 52.381 0.00 0.00 0.00 3.16
551 898 1.261619 CGAAGACAACACCTCAACTGC 59.738 52.381 0.00 0.00 0.00 4.40
552 899 2.288666 GAAGACAACACCTCAACTGCA 58.711 47.619 0.00 0.00 0.00 4.41
553 900 2.418368 AGACAACACCTCAACTGCAA 57.582 45.000 0.00 0.00 0.00 4.08
554 901 2.722094 AGACAACACCTCAACTGCAAA 58.278 42.857 0.00 0.00 0.00 3.68
555 902 3.088532 AGACAACACCTCAACTGCAAAA 58.911 40.909 0.00 0.00 0.00 2.44
556 903 3.509575 AGACAACACCTCAACTGCAAAAA 59.490 39.130 0.00 0.00 0.00 1.94
557 904 3.848726 ACAACACCTCAACTGCAAAAAG 58.151 40.909 0.00 0.00 0.00 2.27
558 905 3.189285 CAACACCTCAACTGCAAAAAGG 58.811 45.455 0.00 0.00 0.00 3.11
559 906 1.756538 ACACCTCAACTGCAAAAAGGG 59.243 47.619 8.46 2.09 0.00 3.95
753 1105 2.045561 TTCTGTTGCCGGTGAGAAAA 57.954 45.000 1.90 0.00 0.00 2.29
764 1116 1.527311 GGTGAGAAAAGTGCTCGTGAC 59.473 52.381 0.00 0.00 35.15 3.67
774 1126 3.414700 CTCGTGACGCACAAGGCC 61.415 66.667 0.00 0.00 40.31 5.19
790 1175 2.868196 CCGAGTCAGCGTCTTCGA 59.132 61.111 5.51 0.00 39.71 3.71
851 1242 4.346127 TGGGATGTCTCACTCCATCTAATG 59.654 45.833 0.00 0.00 38.02 1.90
977 1368 2.443255 ACAACATCCCTTGAACCAGAGT 59.557 45.455 0.00 0.00 0.00 3.24
991 1386 0.987294 CAGAGTCCCACCCAACTCAT 59.013 55.000 5.42 0.00 43.52 2.90
996 1391 3.773119 GAGTCCCACCCAACTCATTAGTA 59.227 47.826 0.00 0.00 41.26 1.82
1026 1424 3.371595 CCAATTTCCAGATAACTCCCCGT 60.372 47.826 0.00 0.00 0.00 5.28
1125 1523 6.552725 AGAATCAGTCAGGCATAATAGACTCA 59.447 38.462 0.00 0.00 39.17 3.41
1189 1587 1.276138 CGATATGTGATGGCCCTAGCA 59.724 52.381 0.00 0.00 42.56 3.49
1224 1622 4.697756 GCACGTGCACAGGGCCTA 62.698 66.667 34.52 0.00 43.89 3.93
1266 1664 5.500234 TGGCAGAATACTTTCAGCATAACT 58.500 37.500 5.64 0.00 43.89 2.24
1306 1706 6.769608 ACGTACACATATGCATTCATACAG 57.230 37.500 3.54 1.71 37.94 2.74
1360 1770 9.701098 TCTTCATGTTGATTACTTAAACTACGT 57.299 29.630 0.00 0.00 0.00 3.57
1660 2146 7.675962 TGAATAACCAACATGTACAACTACC 57.324 36.000 0.00 0.00 0.00 3.18
1792 2282 1.452108 GGGTGGAAATGGAGGCTCG 60.452 63.158 8.69 0.00 0.00 5.03
1808 2298 2.223735 GGCTCGGATAAAGACATCGTCA 60.224 50.000 0.00 0.00 34.60 4.35
1846 2337 2.168106 AGAGAGCATCACAGTTAGCAGG 59.832 50.000 0.00 0.00 37.82 4.85
2123 2619 8.856153 ACAACCACAACATAATAACATCACTA 57.144 30.769 0.00 0.00 0.00 2.74
2168 2664 2.282180 GGGCCTTTCGGACAAGCA 60.282 61.111 0.84 0.00 41.63 3.91
2256 2752 1.070445 GTGGAGCCATCGCAGCTAT 59.930 57.895 0.00 0.00 41.75 2.97
2371 2868 4.274602 TGTATTGCTTAGGGTTTCGACA 57.725 40.909 0.00 0.00 0.00 4.35
2430 2927 2.397413 CTTGCCTGTCCCTGAACCGT 62.397 60.000 0.00 0.00 0.00 4.83
2433 2930 2.571216 CCTGTCCCTGAACCGTCGT 61.571 63.158 0.00 0.00 0.00 4.34
2487 2984 2.438614 CGGCTCTCAGAGTCCCGA 60.439 66.667 20.13 0.00 37.45 5.14
2503 3000 0.742505 CCGACCGGCTCATAACAGTA 59.257 55.000 0.00 0.00 0.00 2.74
2506 3003 2.293677 CGACCGGCTCATAACAGTATCT 59.706 50.000 0.00 0.00 0.00 1.98
2513 3010 3.004839 GCTCATAACAGTATCTGGCTCGA 59.995 47.826 1.90 0.00 35.51 4.04
2537 3034 5.903810 ACTCCTAACTATTCTTGCCTTACG 58.096 41.667 0.00 0.00 0.00 3.18
2556 3053 3.873910 ACGCTACAAGTCTTGCCATAAT 58.126 40.909 12.66 0.00 0.00 1.28
2558 3055 3.871006 CGCTACAAGTCTTGCCATAATGA 59.129 43.478 12.66 0.00 0.00 2.57
2620 3117 2.124693 CCATTATTGGCCCGCCGTT 61.125 57.895 0.00 0.00 39.42 4.44
2657 3154 0.807667 GCTTCGCGTGATGACCATCT 60.808 55.000 15.34 0.00 38.60 2.90
2865 3364 6.280643 CCATGACGTCATCTTCCATTAAGTA 58.719 40.000 27.79 0.00 36.51 2.24
2920 3420 2.638480 TCTTTAATGGCCATCCCGAG 57.362 50.000 21.08 14.47 35.87 4.63
3096 3619 2.342279 CGCGTCCCTTGTCTTCCA 59.658 61.111 0.00 0.00 0.00 3.53
3217 3741 1.834896 TCCGCATTTAGGGTTCTGCTA 59.165 47.619 0.00 0.00 32.48 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 394 2.149578 CTTCAGAGCCCAAGTGTCTTG 58.850 52.381 2.90 2.90 0.00 3.02
87 428 0.322975 GAGATAGGGCCATGCATCGT 59.677 55.000 6.18 0.00 0.00 3.73
95 436 2.832838 TGTTCAAGAGAGATAGGGCCA 58.167 47.619 6.18 0.00 0.00 5.36
260 607 8.721019 TTATTGAAGAAATGGATCAAAATGGC 57.279 30.769 0.00 0.00 0.00 4.40
353 700 8.529102 GCGATATTAATATATTCGCTTTGTCGA 58.471 33.333 24.48 0.00 38.61 4.20
355 702 8.529102 TCGCGATATTAATATATTCGCTTTGTC 58.471 33.333 26.80 8.90 39.00 3.18
356 703 8.402326 TCGCGATATTAATATATTCGCTTTGT 57.598 30.769 26.80 0.00 39.00 2.83
357 704 9.346231 CTTCGCGATATTAATATATTCGCTTTG 57.654 33.333 26.80 17.57 39.00 2.77
358 705 9.297586 TCTTCGCGATATTAATATATTCGCTTT 57.702 29.630 26.80 1.04 39.00 3.51
359 706 8.851960 TCTTCGCGATATTAATATATTCGCTT 57.148 30.769 26.80 1.64 39.00 4.68
369 716 9.647797 TGTAATTGGTATCTTCGCGATATTAAT 57.352 29.630 10.88 6.36 36.99 1.40
370 717 8.918658 GTGTAATTGGTATCTTCGCGATATTAA 58.081 33.333 10.88 4.38 36.99 1.40
371 718 7.543172 GGTGTAATTGGTATCTTCGCGATATTA 59.457 37.037 10.88 0.00 36.99 0.98
372 719 6.367969 GGTGTAATTGGTATCTTCGCGATATT 59.632 38.462 10.88 0.00 36.99 1.28
373 720 5.867716 GGTGTAATTGGTATCTTCGCGATAT 59.132 40.000 10.88 9.80 36.99 1.63
374 721 5.224888 GGTGTAATTGGTATCTTCGCGATA 58.775 41.667 10.88 0.85 33.48 2.92
375 722 4.056050 GGTGTAATTGGTATCTTCGCGAT 58.944 43.478 10.88 0.00 36.11 4.58
376 723 3.450578 GGTGTAATTGGTATCTTCGCGA 58.549 45.455 3.71 3.71 0.00 5.87
377 724 2.542595 GGGTGTAATTGGTATCTTCGCG 59.457 50.000 0.00 0.00 0.00 5.87
378 725 2.542595 CGGGTGTAATTGGTATCTTCGC 59.457 50.000 0.00 0.00 0.00 4.70
379 726 3.128349 CCGGGTGTAATTGGTATCTTCG 58.872 50.000 0.00 0.00 0.00 3.79
380 727 2.876550 GCCGGGTGTAATTGGTATCTTC 59.123 50.000 2.18 0.00 0.00 2.87
381 728 2.422377 GGCCGGGTGTAATTGGTATCTT 60.422 50.000 2.18 0.00 0.00 2.40
382 729 1.142262 GGCCGGGTGTAATTGGTATCT 59.858 52.381 2.18 0.00 0.00 1.98
383 730 1.142262 AGGCCGGGTGTAATTGGTATC 59.858 52.381 2.18 0.00 0.00 2.24
384 731 1.142262 GAGGCCGGGTGTAATTGGTAT 59.858 52.381 2.18 0.00 0.00 2.73
385 732 0.542805 GAGGCCGGGTGTAATTGGTA 59.457 55.000 2.18 0.00 0.00 3.25
386 733 1.205460 AGAGGCCGGGTGTAATTGGT 61.205 55.000 2.18 0.00 0.00 3.67
387 734 0.748005 CAGAGGCCGGGTGTAATTGG 60.748 60.000 2.18 0.00 0.00 3.16
388 735 1.376609 GCAGAGGCCGGGTGTAATTG 61.377 60.000 2.18 0.00 0.00 2.32
389 736 1.077716 GCAGAGGCCGGGTGTAATT 60.078 57.895 2.18 0.00 0.00 1.40
390 737 2.297895 TGCAGAGGCCGGGTGTAAT 61.298 57.895 2.18 0.00 40.13 1.89
391 738 2.925706 TGCAGAGGCCGGGTGTAA 60.926 61.111 2.18 0.00 40.13 2.41
392 739 3.702048 GTGCAGAGGCCGGGTGTA 61.702 66.667 2.18 0.00 40.13 2.90
397 744 4.641645 TGTTGGTGCAGAGGCCGG 62.642 66.667 0.00 0.00 40.13 6.13
398 745 2.594303 TTGTTGGTGCAGAGGCCG 60.594 61.111 0.00 0.00 40.13 6.13
399 746 0.610232 ATCTTGTTGGTGCAGAGGCC 60.610 55.000 0.00 0.00 40.13 5.19
400 747 0.524862 CATCTTGTTGGTGCAGAGGC 59.475 55.000 0.00 0.00 41.68 4.70
401 748 1.808945 GACATCTTGTTGGTGCAGAGG 59.191 52.381 0.00 0.00 0.00 3.69
402 749 1.808945 GGACATCTTGTTGGTGCAGAG 59.191 52.381 0.00 0.00 0.00 3.35
403 750 1.142667 TGGACATCTTGTTGGTGCAGA 59.857 47.619 0.00 0.00 0.00 4.26
404 751 1.608055 TGGACATCTTGTTGGTGCAG 58.392 50.000 0.00 0.00 0.00 4.41
405 752 2.064434 TTGGACATCTTGTTGGTGCA 57.936 45.000 0.00 0.00 0.00 4.57
406 753 2.622942 TCTTTGGACATCTTGTTGGTGC 59.377 45.455 0.00 0.00 0.00 5.01
407 754 6.375174 TGATATCTTTGGACATCTTGTTGGTG 59.625 38.462 3.98 0.00 0.00 4.17
408 755 6.484288 TGATATCTTTGGACATCTTGTTGGT 58.516 36.000 3.98 0.00 0.00 3.67
409 756 7.395190 TTGATATCTTTGGACATCTTGTTGG 57.605 36.000 3.98 0.00 0.00 3.77
410 757 7.337689 TCCTTGATATCTTTGGACATCTTGTTG 59.662 37.037 3.98 0.00 0.00 3.33
411 758 7.405292 TCCTTGATATCTTTGGACATCTTGTT 58.595 34.615 3.98 0.00 0.00 2.83
412 759 6.962182 TCCTTGATATCTTTGGACATCTTGT 58.038 36.000 3.98 0.00 0.00 3.16
413 760 7.521748 GCATCCTTGATATCTTTGGACATCTTG 60.522 40.741 3.98 5.25 0.00 3.02
414 761 6.489361 GCATCCTTGATATCTTTGGACATCTT 59.511 38.462 3.98 0.00 0.00 2.40
415 762 6.002704 GCATCCTTGATATCTTTGGACATCT 58.997 40.000 3.98 0.00 0.00 2.90
416 763 5.766670 TGCATCCTTGATATCTTTGGACATC 59.233 40.000 3.98 3.38 0.00 3.06
417 764 5.533903 GTGCATCCTTGATATCTTTGGACAT 59.466 40.000 3.98 0.00 0.00 3.06
418 765 4.883585 GTGCATCCTTGATATCTTTGGACA 59.116 41.667 3.98 2.36 0.00 4.02
419 766 4.883585 TGTGCATCCTTGATATCTTTGGAC 59.116 41.667 3.98 6.49 0.00 4.02
420 767 4.883585 GTGTGCATCCTTGATATCTTTGGA 59.116 41.667 3.98 8.96 0.00 3.53
421 768 4.641541 TGTGTGCATCCTTGATATCTTTGG 59.358 41.667 3.98 3.86 0.00 3.28
422 769 5.823209 TGTGTGCATCCTTGATATCTTTG 57.177 39.130 3.98 0.00 0.00 2.77
423 770 5.126061 GGTTGTGTGCATCCTTGATATCTTT 59.874 40.000 3.98 0.00 32.94 2.52
424 771 4.641989 GGTTGTGTGCATCCTTGATATCTT 59.358 41.667 3.98 0.00 32.94 2.40
425 772 4.202441 GGTTGTGTGCATCCTTGATATCT 58.798 43.478 3.98 0.00 32.94 1.98
426 773 3.947196 TGGTTGTGTGCATCCTTGATATC 59.053 43.478 0.00 0.00 35.89 1.63
427 774 3.966979 TGGTTGTGTGCATCCTTGATAT 58.033 40.909 0.00 0.00 35.89 1.63
428 775 3.431673 TGGTTGTGTGCATCCTTGATA 57.568 42.857 0.00 0.00 35.89 2.15
429 776 2.291209 TGGTTGTGTGCATCCTTGAT 57.709 45.000 0.00 0.00 35.89 2.57
430 777 1.955778 CTTGGTTGTGTGCATCCTTGA 59.044 47.619 0.00 0.00 35.89 3.02
431 778 1.955778 TCTTGGTTGTGTGCATCCTTG 59.044 47.619 0.00 0.00 35.89 3.61
432 779 2.363306 TCTTGGTTGTGTGCATCCTT 57.637 45.000 0.00 0.00 35.89 3.36
433 780 2.363306 TTCTTGGTTGTGTGCATCCT 57.637 45.000 0.00 0.00 35.89 3.24
434 781 3.451141 TTTTCTTGGTTGTGTGCATCC 57.549 42.857 0.00 0.00 35.54 3.51
459 806 8.851145 GGGTCTCTTTTTATTTCTCTCTTGTTT 58.149 33.333 0.00 0.00 0.00 2.83
460 807 7.448777 GGGGTCTCTTTTTATTTCTCTCTTGTT 59.551 37.037 0.00 0.00 0.00 2.83
461 808 6.943146 GGGGTCTCTTTTTATTTCTCTCTTGT 59.057 38.462 0.00 0.00 0.00 3.16
462 809 6.092807 CGGGGTCTCTTTTTATTTCTCTCTTG 59.907 42.308 0.00 0.00 0.00 3.02
463 810 6.174049 CGGGGTCTCTTTTTATTTCTCTCTT 58.826 40.000 0.00 0.00 0.00 2.85
464 811 5.248705 ACGGGGTCTCTTTTTATTTCTCTCT 59.751 40.000 0.00 0.00 0.00 3.10
465 812 5.489249 ACGGGGTCTCTTTTTATTTCTCTC 58.511 41.667 0.00 0.00 0.00 3.20
466 813 5.012768 TGACGGGGTCTCTTTTTATTTCTCT 59.987 40.000 0.00 0.00 33.15 3.10
467 814 5.121925 GTGACGGGGTCTCTTTTTATTTCTC 59.878 44.000 0.00 0.00 33.15 2.87
468 815 5.001874 GTGACGGGGTCTCTTTTTATTTCT 58.998 41.667 0.00 0.00 33.15 2.52
469 816 4.142966 CGTGACGGGGTCTCTTTTTATTTC 60.143 45.833 0.00 0.00 33.15 2.17
470 817 3.749609 CGTGACGGGGTCTCTTTTTATTT 59.250 43.478 0.00 0.00 33.15 1.40
471 818 3.332034 CGTGACGGGGTCTCTTTTTATT 58.668 45.455 0.00 0.00 33.15 1.40
472 819 2.354403 CCGTGACGGGGTCTCTTTTTAT 60.354 50.000 17.80 0.00 44.15 1.40
473 820 1.001181 CCGTGACGGGGTCTCTTTTTA 59.999 52.381 17.80 0.00 44.15 1.52
474 821 0.250166 CCGTGACGGGGTCTCTTTTT 60.250 55.000 17.80 0.00 44.15 1.94
475 822 1.370064 CCGTGACGGGGTCTCTTTT 59.630 57.895 17.80 0.00 44.15 2.27
476 823 3.057337 CCGTGACGGGGTCTCTTT 58.943 61.111 17.80 0.00 44.15 2.52
485 832 5.180791 GTGAGTTTTCATCACCGTGACGG 62.181 52.174 24.23 24.23 43.64 4.79
486 833 2.096909 GTGAGTTTTCATCACCGTGACG 60.097 50.000 2.57 0.00 40.99 4.35
487 834 2.869801 TGTGAGTTTTCATCACCGTGAC 59.130 45.455 2.57 0.00 45.24 3.67
488 835 3.186702 TGTGAGTTTTCATCACCGTGA 57.813 42.857 3.10 3.10 45.24 4.35
489 836 3.064682 TGTTGTGAGTTTTCATCACCGTG 59.935 43.478 3.82 0.00 45.24 4.94
490 837 3.275143 TGTTGTGAGTTTTCATCACCGT 58.725 40.909 3.82 0.00 45.24 4.83
491 838 3.849645 GCTGTTGTGAGTTTTCATCACCG 60.850 47.826 3.82 0.00 45.24 4.94
492 839 3.066621 TGCTGTTGTGAGTTTTCATCACC 59.933 43.478 3.82 0.00 45.24 4.02
493 840 4.291540 TGCTGTTGTGAGTTTTCATCAC 57.708 40.909 0.00 0.00 45.88 3.06
494 841 4.157472 TGTTGCTGTTGTGAGTTTTCATCA 59.843 37.500 0.00 0.00 35.39 3.07
495 842 4.500477 GTGTTGCTGTTGTGAGTTTTCATC 59.500 41.667 0.00 0.00 35.39 2.92
496 843 4.158394 AGTGTTGCTGTTGTGAGTTTTCAT 59.842 37.500 0.00 0.00 35.39 2.57
497 844 3.505680 AGTGTTGCTGTTGTGAGTTTTCA 59.494 39.130 0.00 0.00 0.00 2.69
498 845 4.096732 AGTGTTGCTGTTGTGAGTTTTC 57.903 40.909 0.00 0.00 0.00 2.29
499 846 3.758554 AGAGTGTTGCTGTTGTGAGTTTT 59.241 39.130 0.00 0.00 0.00 2.43
500 847 3.347216 AGAGTGTTGCTGTTGTGAGTTT 58.653 40.909 0.00 0.00 0.00 2.66
501 848 2.991250 AGAGTGTTGCTGTTGTGAGTT 58.009 42.857 0.00 0.00 0.00 3.01
502 849 2.698855 AGAGTGTTGCTGTTGTGAGT 57.301 45.000 0.00 0.00 0.00 3.41
503 850 3.248602 GGTTAGAGTGTTGCTGTTGTGAG 59.751 47.826 0.00 0.00 0.00 3.51
504 851 3.202906 GGTTAGAGTGTTGCTGTTGTGA 58.797 45.455 0.00 0.00 0.00 3.58
505 852 2.942376 TGGTTAGAGTGTTGCTGTTGTG 59.058 45.455 0.00 0.00 0.00 3.33
506 853 2.943033 GTGGTTAGAGTGTTGCTGTTGT 59.057 45.455 0.00 0.00 0.00 3.32
507 854 2.290641 GGTGGTTAGAGTGTTGCTGTTG 59.709 50.000 0.00 0.00 0.00 3.33
508 855 2.092646 TGGTGGTTAGAGTGTTGCTGTT 60.093 45.455 0.00 0.00 0.00 3.16
509 856 1.488812 TGGTGGTTAGAGTGTTGCTGT 59.511 47.619 0.00 0.00 0.00 4.40
510 857 1.873591 GTGGTGGTTAGAGTGTTGCTG 59.126 52.381 0.00 0.00 0.00 4.41
511 858 1.202770 GGTGGTGGTTAGAGTGTTGCT 60.203 52.381 0.00 0.00 0.00 3.91
512 859 1.235724 GGTGGTGGTTAGAGTGTTGC 58.764 55.000 0.00 0.00 0.00 4.17
513 860 1.069513 TCGGTGGTGGTTAGAGTGTTG 59.930 52.381 0.00 0.00 0.00 3.33
514 861 1.416243 TCGGTGGTGGTTAGAGTGTT 58.584 50.000 0.00 0.00 0.00 3.32
515 862 1.343465 CTTCGGTGGTGGTTAGAGTGT 59.657 52.381 0.00 0.00 0.00 3.55
516 863 1.616865 TCTTCGGTGGTGGTTAGAGTG 59.383 52.381 0.00 0.00 0.00 3.51
517 864 1.617357 GTCTTCGGTGGTGGTTAGAGT 59.383 52.381 0.00 0.00 0.00 3.24
518 865 1.616865 TGTCTTCGGTGGTGGTTAGAG 59.383 52.381 0.00 0.00 0.00 2.43
519 866 1.707106 TGTCTTCGGTGGTGGTTAGA 58.293 50.000 0.00 0.00 0.00 2.10
520 867 2.140717 GTTGTCTTCGGTGGTGGTTAG 58.859 52.381 0.00 0.00 0.00 2.34
521 868 1.485480 TGTTGTCTTCGGTGGTGGTTA 59.515 47.619 0.00 0.00 0.00 2.85
522 869 0.253610 TGTTGTCTTCGGTGGTGGTT 59.746 50.000 0.00 0.00 0.00 3.67
523 870 0.463116 GTGTTGTCTTCGGTGGTGGT 60.463 55.000 0.00 0.00 0.00 4.16
524 871 1.164041 GGTGTTGTCTTCGGTGGTGG 61.164 60.000 0.00 0.00 0.00 4.61
525 872 0.179056 AGGTGTTGTCTTCGGTGGTG 60.179 55.000 0.00 0.00 0.00 4.17
526 873 0.106149 GAGGTGTTGTCTTCGGTGGT 59.894 55.000 0.00 0.00 0.00 4.16
527 874 0.105964 TGAGGTGTTGTCTTCGGTGG 59.894 55.000 0.00 0.00 0.00 4.61
528 875 1.597663 GTTGAGGTGTTGTCTTCGGTG 59.402 52.381 0.00 0.00 0.00 4.94
529 876 1.485066 AGTTGAGGTGTTGTCTTCGGT 59.515 47.619 0.00 0.00 0.00 4.69
530 877 1.867233 CAGTTGAGGTGTTGTCTTCGG 59.133 52.381 0.00 0.00 0.00 4.30
531 878 1.261619 GCAGTTGAGGTGTTGTCTTCG 59.738 52.381 0.00 0.00 0.00 3.79
532 879 2.288666 TGCAGTTGAGGTGTTGTCTTC 58.711 47.619 0.00 0.00 0.00 2.87
533 880 2.418368 TGCAGTTGAGGTGTTGTCTT 57.582 45.000 0.00 0.00 0.00 3.01
534 881 2.418368 TTGCAGTTGAGGTGTTGTCT 57.582 45.000 0.00 0.00 0.00 3.41
535 882 3.502191 TTTTGCAGTTGAGGTGTTGTC 57.498 42.857 0.00 0.00 0.00 3.18
536 883 3.368323 CCTTTTTGCAGTTGAGGTGTTGT 60.368 43.478 0.00 0.00 0.00 3.32
537 884 3.189285 CCTTTTTGCAGTTGAGGTGTTG 58.811 45.455 0.00 0.00 0.00 3.33
538 885 2.168313 CCCTTTTTGCAGTTGAGGTGTT 59.832 45.455 6.71 0.00 0.00 3.32
539 886 1.756538 CCCTTTTTGCAGTTGAGGTGT 59.243 47.619 6.71 0.00 0.00 4.16
540 887 2.031120 TCCCTTTTTGCAGTTGAGGTG 58.969 47.619 6.71 0.73 0.00 4.00
541 888 2.031870 GTCCCTTTTTGCAGTTGAGGT 58.968 47.619 6.71 0.00 0.00 3.85
542 889 1.341209 GGTCCCTTTTTGCAGTTGAGG 59.659 52.381 0.00 0.00 0.00 3.86
543 890 2.310538 AGGTCCCTTTTTGCAGTTGAG 58.689 47.619 0.00 0.00 0.00 3.02
544 891 2.452600 AGGTCCCTTTTTGCAGTTGA 57.547 45.000 0.00 0.00 0.00 3.18
545 892 3.005791 CCTTAGGTCCCTTTTTGCAGTTG 59.994 47.826 0.00 0.00 0.00 3.16
546 893 3.117284 TCCTTAGGTCCCTTTTTGCAGTT 60.117 43.478 0.00 0.00 0.00 3.16
547 894 2.445525 TCCTTAGGTCCCTTTTTGCAGT 59.554 45.455 0.00 0.00 0.00 4.40
548 895 3.154827 TCCTTAGGTCCCTTTTTGCAG 57.845 47.619 0.00 0.00 0.00 4.41
549 896 3.697166 GATCCTTAGGTCCCTTTTTGCA 58.303 45.455 0.00 0.00 0.00 4.08
550 897 2.683362 CGATCCTTAGGTCCCTTTTTGC 59.317 50.000 0.00 0.00 0.00 3.68
551 898 3.951663 ACGATCCTTAGGTCCCTTTTTG 58.048 45.455 0.00 0.00 0.00 2.44
552 899 4.202535 ACAACGATCCTTAGGTCCCTTTTT 60.203 41.667 0.00 0.00 0.00 1.94
553 900 3.329814 ACAACGATCCTTAGGTCCCTTTT 59.670 43.478 0.00 0.00 0.00 2.27
554 901 2.910977 ACAACGATCCTTAGGTCCCTTT 59.089 45.455 0.00 0.00 0.00 3.11
555 902 2.547990 ACAACGATCCTTAGGTCCCTT 58.452 47.619 0.00 0.00 0.00 3.95
556 903 2.249309 ACAACGATCCTTAGGTCCCT 57.751 50.000 0.00 0.00 0.00 4.20
557 904 4.831710 AGTATACAACGATCCTTAGGTCCC 59.168 45.833 5.50 0.00 0.00 4.46
558 905 7.516198 TTAGTATACAACGATCCTTAGGTCC 57.484 40.000 5.50 0.00 0.00 4.46
559 906 8.790718 TCATTAGTATACAACGATCCTTAGGTC 58.209 37.037 5.50 0.00 0.00 3.85
587 938 5.018809 AGGATAAGATTTTTCCTGCAAGCA 58.981 37.500 0.00 0.00 38.46 3.91
764 1116 3.114616 CTGACTCGGCCTTGTGCG 61.115 66.667 0.00 0.00 42.61 5.34
774 1126 1.226156 CCTCGAAGACGCTGACTCG 60.226 63.158 0.00 0.00 39.58 4.18
790 1175 1.077212 GGATCAGCCATGTGCACCT 60.077 57.895 15.69 0.23 44.83 4.00
839 1224 4.592351 AGCATGTCTAGCATTAGATGGAGT 59.408 41.667 0.00 0.00 38.17 3.85
851 1242 1.602311 CCAATGGGAGCATGTCTAGC 58.398 55.000 0.00 0.00 35.59 3.42
977 1368 3.264964 GGTTACTAATGAGTTGGGTGGGA 59.735 47.826 0.00 0.00 37.10 4.37
991 1386 4.678256 TGGAAATTGGCCATGGTTACTAA 58.322 39.130 14.67 1.04 0.00 2.24
996 1391 2.323999 TCTGGAAATTGGCCATGGTT 57.676 45.000 14.67 0.00 34.33 3.67
1026 1424 4.717629 CTCTCCACGAACGCGGCA 62.718 66.667 12.47 0.00 43.17 5.69
1125 1523 3.822167 CACCCAAACCGGTAGTAACATTT 59.178 43.478 8.00 0.00 33.67 2.32
1189 1587 4.966787 AACAATGGTGGCGCCGGT 62.967 61.111 23.90 9.84 41.21 5.28
1224 1622 4.537135 CCAGTTACCGGCATAGATATGT 57.463 45.455 0.00 0.00 36.11 2.29
1266 1664 3.457610 ACGTACCTTTCAACCTCGAAA 57.542 42.857 0.00 0.00 33.89 3.46
1397 1807 6.370442 GTGGTTGTTAACTGTATCATGCACTA 59.630 38.462 7.22 0.00 0.00 2.74
1533 1987 5.441500 TGGAACTTTTTGTAGATGACACCA 58.558 37.500 0.00 0.00 37.96 4.17
1792 2282 3.309954 GTGCCTTGACGATGTCTTTATCC 59.690 47.826 0.00 0.00 33.15 2.59
1808 2298 1.546476 CTCTAGACGTCTTGGTGCCTT 59.454 52.381 25.44 0.00 0.00 4.35
1846 2337 6.395426 TTGATTGAATCAATGATAGTGCCC 57.605 37.500 16.04 0.00 43.84 5.36
2025 2517 1.710013 CCGAGTACGAACTGCATTGT 58.290 50.000 0.00 0.00 42.66 2.71
2168 2664 2.838637 TGGTGAAAGTGGTTCCCTTT 57.161 45.000 5.47 5.47 35.12 3.11
2256 2752 3.822167 CCGTTTAACCCCTTTAAGCTTCA 59.178 43.478 0.00 0.00 30.64 3.02
2371 2868 1.002502 GGCGGTTTAGCTCCTGGTT 60.003 57.895 0.00 0.00 37.29 3.67
2487 2984 2.365617 CCAGATACTGTTATGAGCCGGT 59.634 50.000 1.90 0.00 0.00 5.28
2503 3000 2.741145 AGTTAGGAGTTCGAGCCAGAT 58.259 47.619 0.00 0.00 0.00 2.90
2506 3003 4.279145 AGAATAGTTAGGAGTTCGAGCCA 58.721 43.478 0.00 0.00 0.00 4.75
2513 3010 6.338937 CGTAAGGCAAGAATAGTTAGGAGTT 58.661 40.000 0.00 0.00 0.00 3.01
2537 3034 4.260375 CGTCATTATGGCAAGACTTGTAGC 60.260 45.833 16.39 2.35 0.00 3.58
2556 3053 1.135024 GCCCGTAGTGATAAACCGTCA 60.135 52.381 0.00 0.00 0.00 4.35
2558 3055 0.176449 GGCCCGTAGTGATAAACCGT 59.824 55.000 0.00 0.00 0.00 4.83
2620 3117 1.144913 AGCCCAGTACCAAGCTTGAAA 59.855 47.619 28.05 12.11 29.27 2.69
2657 3154 1.880819 GAGGAGCCGGGTTACGTCAA 61.881 60.000 8.00 0.00 42.24 3.18
2865 3364 9.683870 TTGGGGTATAACGTAATAAAGAAATGT 57.316 29.630 0.00 0.00 0.00 2.71
2878 3377 2.391678 AGATCCGTTGGGGTATAACGT 58.608 47.619 9.06 0.00 46.81 3.99
3096 3619 4.892965 TGCAGCGGCCAAGGTTGT 62.893 61.111 6.32 0.00 40.13 3.32


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

AutoCloner maintained by Alex Coulton.