Multiple sequence alignment - TraesCS3D01G483700

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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 TraesCS3D01G483700 chr3D 100.000 3168 0 0 1 3168 581014606 581011439 0.000000e+00 5851.0
1 TraesCS3D01G483700 chr3D 82.099 972 98 42 548 1487 581060540 581059613 0.000000e+00 761.0
2 TraesCS3D01G483700 chr3D 84.942 777 66 21 2128 2881 580991820 580991072 0.000000e+00 739.0
3 TraesCS3D01G483700 chr3D 87.648 591 38 15 847 1416 581069545 581068969 0.000000e+00 654.0
4 TraesCS3D01G483700 chr3D 86.050 595 72 9 2123 2709 581058410 581057819 2.070000e-176 628.0
5 TraesCS3D01G483700 chr3D 81.415 721 86 19 2013 2696 580911499 580910790 2.150000e-151 545.0
6 TraesCS3D01G483700 chr3D 93.466 352 21 2 393 743 581084754 581084404 3.620000e-144 521.0
7 TraesCS3D01G483700 chr3D 78.843 709 84 36 1309 1991 580912237 580911569 4.890000e-113 418.0
8 TraesCS3D01G483700 chr3D 87.368 380 24 9 10 389 581085644 581085289 6.320000e-112 414.0
9 TraesCS3D01G483700 chr3D 85.751 393 28 10 694 1059 580974144 580973753 1.070000e-104 390.0
10 TraesCS3D01G483700 chr3D 84.865 370 30 8 540 901 580919657 580919306 1.810000e-92 350.0
11 TraesCS3D01G483700 chr3D 77.465 710 78 28 531 1231 580994957 580994321 1.810000e-92 350.0
12 TraesCS3D01G483700 chr3D 81.948 349 41 11 1541 1873 581059594 581059252 3.110000e-70 276.0
13 TraesCS3D01G483700 chr3D 80.053 376 37 18 1465 1815 581068965 581068603 8.780000e-61 244.0
14 TraesCS3D01G483700 chr3D 79.733 375 44 14 937 1284 580918854 580918485 3.160000e-60 243.0
15 TraesCS3D01G483700 chr3D 81.538 260 30 12 1416 1661 581093398 581093143 6.930000e-47 198.0
16 TraesCS3D01G483700 chr3D 88.535 157 14 2 749 901 580987935 580987779 1.500000e-43 187.0
17 TraesCS3D01G483700 chr3D 80.460 261 15 10 926 1178 580987287 580987055 1.950000e-37 167.0
18 TraesCS3D01G483700 chr3D 81.347 193 33 3 1 192 74326446 74326636 1.520000e-33 154.0
19 TraesCS3D01G483700 chr3D 91.228 114 9 1 323 436 581060652 581060540 1.520000e-33 154.0
20 TraesCS3D01G483700 chr3D 92.941 85 6 0 3084 3168 580990861 580990777 1.190000e-24 124.0
21 TraesCS3D01G483700 chr3D 96.875 64 2 0 526 589 581074847 581074784 1.200000e-19 108.0
22 TraesCS3D01G483700 chr3D 83.186 113 12 4 919 1028 581083547 581083439 2.600000e-16 97.1
23 TraesCS3D01G483700 chr3D 100.000 31 0 0 2071 2101 580991858 580991828 1.230000e-04 58.4
24 TraesCS3D01G483700 chr3B 83.080 1773 178 58 1195 2881 777756301 777758037 0.000000e+00 1500.0
25 TraesCS3D01G483700 chr3B 80.838 1503 170 59 540 2001 777653617 777655042 0.000000e+00 1072.0
26 TraesCS3D01G483700 chr3B 88.799 741 66 12 2013 2749 777655096 777655823 0.000000e+00 893.0
27 TraesCS3D01G483700 chr3B 84.673 672 56 28 548 1204 777755153 777755792 7.460000e-176 627.0
28 TraesCS3D01G483700 chr3B 83.105 438 48 9 1 436 777690474 777690887 2.980000e-100 375.0
29 TraesCS3D01G483700 chr3B 83.551 383 37 11 550 921 777690889 777691256 5.060000e-88 335.0
30 TraesCS3D01G483700 chr3B 86.063 287 23 8 2885 3168 777758087 777758359 3.090000e-75 292.0
31 TraesCS3D01G483700 chr3B 82.470 251 27 11 1416 1658 777630123 777630364 1.490000e-48 204.0
32 TraesCS3D01G483700 chr3B 85.714 119 14 2 320 436 777755036 777755153 4.290000e-24 122.0
33 TraesCS3D01G483700 chr3A 80.657 1401 162 62 749 2091 716806873 716808222 0.000000e+00 985.0
34 TraesCS3D01G483700 chr3A 87.010 893 56 21 548 1414 716792117 716792975 0.000000e+00 952.0
35 TraesCS3D01G483700 chr3A 79.389 786 83 30 2123 2870 716800314 716801058 6.150000e-132 481.0
36 TraesCS3D01G483700 chr3A 83.399 506 57 10 10 504 716786163 716786652 8.060000e-121 444.0
37 TraesCS3D01G483700 chr3A 78.431 765 82 41 526 1247 716794481 716795205 3.780000e-114 422.0
38 TraesCS3D01G483700 chr3A 79.383 616 61 38 1319 1921 716795234 716795796 1.070000e-99 374.0
39 TraesCS3D01G483700 chr3A 82.339 436 47 13 1 436 716790030 716790435 5.030000e-93 351.0
40 TraesCS3D01G483700 chr3A 86.864 236 17 2 528 763 716786789 716787010 5.250000e-63 252.0
41 TraesCS3D01G483700 chr3A 91.071 168 11 2 924 1090 716787088 716787252 1.140000e-54 224.0
42 TraesCS3D01G483700 chr3A 80.408 245 24 9 1417 1658 716777811 716778034 7.030000e-37 165.0
43 TraesCS3D01G483700 chr3A 88.889 81 9 0 2127 2207 716808309 716808389 2.010000e-17 100.0
44 TraesCS3D01G483700 chr3A 96.226 53 1 1 2072 2123 716808227 716808279 5.630000e-13 86.1
45 TraesCS3D01G483700 chr2B 86.364 110 15 0 36 145 164093402 164093293 1.540000e-23 121.0
46 TraesCS3D01G483700 chr7B 88.636 88 10 0 40 127 34615224 34615137 1.200000e-19 108.0
47 TraesCS3D01G483700 chr7B 87.500 88 9 1 40 127 34619529 34619444 2.010000e-17 100.0
48 TraesCS3D01G483700 chr1A 83.654 104 17 0 29 132 534323524 534323421 7.230000e-17 99.0
49 TraesCS3D01G483700 chr1B 79.487 117 24 0 15 131 592498335 592498451 2.020000e-12 84.2
50 TraesCS3D01G483700 chr6A 97.143 35 0 1 2559 2593 109686219 109686186 1.230000e-04 58.4
51 TraesCS3D01G483700 chr6B 97.059 34 0 1 2560 2593 174985008 174984976 4.410000e-04 56.5


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 TraesCS3D01G483700 chr3D 581011439 581014606 3167 True 5851.000000 5851 100.000000 1 3168 1 chr3D.!!$R2 3167
1 TraesCS3D01G483700 chr3D 580910790 580912237 1447 True 481.500000 545 80.129000 1309 2696 2 chr3D.!!$R5 1387
2 TraesCS3D01G483700 chr3D 581057819 581060652 2833 True 454.750000 761 85.331250 323 2709 4 chr3D.!!$R8 2386
3 TraesCS3D01G483700 chr3D 581068603 581069545 942 True 449.000000 654 83.850500 847 1815 2 chr3D.!!$R9 968
4 TraesCS3D01G483700 chr3D 581083439 581085644 2205 True 344.033333 521 88.006667 10 1028 3 chr3D.!!$R10 1018
5 TraesCS3D01G483700 chr3D 580918485 580919657 1172 True 296.500000 350 82.299000 540 1284 2 chr3D.!!$R6 744
6 TraesCS3D01G483700 chr3D 580987055 580994957 7902 True 270.900000 739 87.390500 531 3168 6 chr3D.!!$R7 2637
7 TraesCS3D01G483700 chr3B 777653617 777655823 2206 False 982.500000 1072 84.818500 540 2749 2 chr3B.!!$F2 2209
8 TraesCS3D01G483700 chr3B 777755036 777758359 3323 False 635.250000 1500 84.882500 320 3168 4 chr3B.!!$F4 2848
9 TraesCS3D01G483700 chr3B 777690474 777691256 782 False 355.000000 375 83.328000 1 921 2 chr3B.!!$F3 920
10 TraesCS3D01G483700 chr3A 716800314 716801058 744 False 481.000000 481 79.389000 2123 2870 1 chr3A.!!$F2 747
11 TraesCS3D01G483700 chr3A 716786163 716795796 9633 False 431.285714 952 84.071000 1 1921 7 chr3A.!!$F3 1920
12 TraesCS3D01G483700 chr3A 716806873 716808389 1516 False 390.366667 985 88.590667 749 2207 3 chr3A.!!$F4 1458

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
309 320 0.107654 ACGGCCTTAATGTCAGAGCC 60.108 55.000 0.00 0.00 37.03 4.70 F
311 322 0.107654 GGCCTTAATGTCAGAGCCGT 60.108 55.000 0.00 0.00 0.00 5.68 F
488 1043 0.320374 ACCACCTTGATCTTTCGCGA 59.680 50.000 3.71 3.71 0.00 5.87 F
1361 11750 1.001520 TGTGTGTGCCTTACGTATGCT 59.998 47.619 15.86 0.00 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1822 12339 0.036388 AGTTGACTATGGGTGTGGCG 60.036 55.000 0.00 0.00 0.00 5.69 R
1997 12850 2.068834 ACCGATCGATGGACCTAACT 57.931 50.000 18.66 0.00 0.00 2.24 R
2001 12854 2.877866 AGATTACCGATCGATGGACCT 58.122 47.619 18.66 3.44 39.85 3.85 R
2933 15821 1.332195 GCTCCAGCCAGTTTTCCTTT 58.668 50.000 0.00 0.00 34.31 3.11 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
103 112 7.922505 TTTGAATTGTCTATGTTTGTTTCGG 57.077 32.000 0.00 0.00 0.00 4.30
145 154 4.816786 ATTGTTTGAGCAAATGTTTGGC 57.183 36.364 7.51 0.88 38.57 4.52
150 159 3.374220 TGAGCAAATGTTTGGCAGAAG 57.626 42.857 7.51 0.00 38.57 2.85
161 170 4.837860 TGTTTGGCAGAAGTGGGAAAATAT 59.162 37.500 0.00 0.00 0.00 1.28
164 173 6.713762 TTGGCAGAAGTGGGAAAATATATG 57.286 37.500 0.00 0.00 0.00 1.78
192 203 8.690203 TGAGAGATTAAGTTTGTTGGAAATCA 57.310 30.769 0.00 0.00 0.00 2.57
293 304 7.164230 AGAATAAAGGATATGCTAGAGACGG 57.836 40.000 0.00 0.00 0.00 4.79
296 307 1.076350 AGGATATGCTAGAGACGGCCT 59.924 52.381 0.00 0.00 0.00 5.19
297 308 1.896465 GGATATGCTAGAGACGGCCTT 59.104 52.381 0.00 0.00 0.00 4.35
298 309 3.090037 GGATATGCTAGAGACGGCCTTA 58.910 50.000 0.00 0.00 0.00 2.69
299 310 3.510360 GGATATGCTAGAGACGGCCTTAA 59.490 47.826 0.00 0.00 0.00 1.85
300 311 4.160626 GGATATGCTAGAGACGGCCTTAAT 59.839 45.833 0.00 0.00 0.00 1.40
301 312 2.890808 TGCTAGAGACGGCCTTAATG 57.109 50.000 0.00 0.00 0.00 1.90
302 313 2.108168 TGCTAGAGACGGCCTTAATGT 58.892 47.619 0.00 0.00 0.00 2.71
303 314 2.100916 TGCTAGAGACGGCCTTAATGTC 59.899 50.000 0.00 0.00 0.00 3.06
304 315 2.100916 GCTAGAGACGGCCTTAATGTCA 59.899 50.000 0.00 0.00 35.09 3.58
305 316 2.969628 AGAGACGGCCTTAATGTCAG 57.030 50.000 0.00 0.00 35.09 3.51
306 317 2.457598 AGAGACGGCCTTAATGTCAGA 58.542 47.619 0.00 0.00 35.09 3.27
307 318 2.428890 AGAGACGGCCTTAATGTCAGAG 59.571 50.000 0.00 0.00 35.09 3.35
308 319 1.134670 AGACGGCCTTAATGTCAGAGC 60.135 52.381 0.00 0.00 35.09 4.09
309 320 0.107654 ACGGCCTTAATGTCAGAGCC 60.108 55.000 0.00 0.00 37.03 4.70
310 321 2.695314 GGCCTTAATGTCAGAGCCG 58.305 57.895 0.00 0.00 0.00 5.52
311 322 0.107654 GGCCTTAATGTCAGAGCCGT 60.108 55.000 0.00 0.00 0.00 5.68
312 323 1.291132 GCCTTAATGTCAGAGCCGTC 58.709 55.000 0.00 0.00 0.00 4.79
329 352 2.878406 CCGTCTTTGATGGTGACTGTTT 59.122 45.455 0.00 0.00 34.27 2.83
353 376 6.337356 TCAAAACGGAAGAAAAATTGCTTCT 58.663 32.000 12.48 6.59 40.20 2.85
383 406 1.208614 CTGCTCCAAAAGTGCGAGC 59.791 57.895 1.38 1.38 43.15 5.03
466 1021 7.846066 ACTAAGGAGCATCATCTTATATCACC 58.154 38.462 0.00 0.00 36.25 4.02
467 1022 6.692849 AAGGAGCATCATCTTATATCACCA 57.307 37.500 0.00 0.00 36.25 4.17
468 1023 6.047511 AGGAGCATCATCTTATATCACCAC 57.952 41.667 0.00 0.00 36.25 4.16
469 1024 5.545335 AGGAGCATCATCTTATATCACCACA 59.455 40.000 0.00 0.00 36.25 4.17
470 1025 5.641209 GGAGCATCATCTTATATCACCACAC 59.359 44.000 0.00 0.00 36.25 3.82
471 1026 5.555017 AGCATCATCTTATATCACCACACC 58.445 41.667 0.00 0.00 0.00 4.16
472 1027 5.072193 AGCATCATCTTATATCACCACACCA 59.928 40.000 0.00 0.00 0.00 4.17
473 1028 5.180117 GCATCATCTTATATCACCACACCAC 59.820 44.000 0.00 0.00 0.00 4.16
474 1029 5.290493 TCATCTTATATCACCACACCACC 57.710 43.478 0.00 0.00 0.00 4.61
475 1030 4.968719 TCATCTTATATCACCACACCACCT 59.031 41.667 0.00 0.00 0.00 4.00
476 1031 5.428457 TCATCTTATATCACCACACCACCTT 59.572 40.000 0.00 0.00 0.00 3.50
477 1032 5.097742 TCTTATATCACCACACCACCTTG 57.902 43.478 0.00 0.00 0.00 3.61
478 1033 4.780554 TCTTATATCACCACACCACCTTGA 59.219 41.667 0.00 0.00 0.00 3.02
479 1034 5.428457 TCTTATATCACCACACCACCTTGAT 59.572 40.000 0.00 0.00 0.00 2.57
480 1035 2.496899 ATCACCACACCACCTTGATC 57.503 50.000 0.00 0.00 0.00 2.92
481 1036 1.434188 TCACCACACCACCTTGATCT 58.566 50.000 0.00 0.00 0.00 2.75
482 1037 1.774254 TCACCACACCACCTTGATCTT 59.226 47.619 0.00 0.00 0.00 2.40
483 1038 2.174639 TCACCACACCACCTTGATCTTT 59.825 45.455 0.00 0.00 0.00 2.52
484 1039 2.554032 CACCACACCACCTTGATCTTTC 59.446 50.000 0.00 0.00 0.00 2.62
485 1040 1.806542 CCACACCACCTTGATCTTTCG 59.193 52.381 0.00 0.00 0.00 3.46
486 1041 1.197721 CACACCACCTTGATCTTTCGC 59.802 52.381 0.00 0.00 0.00 4.70
487 1042 0.443869 CACCACCTTGATCTTTCGCG 59.556 55.000 0.00 0.00 0.00 5.87
488 1043 0.320374 ACCACCTTGATCTTTCGCGA 59.680 50.000 3.71 3.71 0.00 5.87
489 1044 1.270625 ACCACCTTGATCTTTCGCGAA 60.271 47.619 19.38 19.38 0.00 4.70
490 1045 1.804151 CCACCTTGATCTTTCGCGAAA 59.196 47.619 30.47 30.47 0.00 3.46
491 1046 2.225491 CCACCTTGATCTTTCGCGAAAA 59.775 45.455 31.68 22.72 0.00 2.29
492 1047 3.304391 CCACCTTGATCTTTCGCGAAAAA 60.304 43.478 31.68 22.39 0.00 1.94
493 1048 3.908382 CACCTTGATCTTTCGCGAAAAAG 59.092 43.478 31.68 28.38 37.55 2.27
494 1049 3.813166 ACCTTGATCTTTCGCGAAAAAGA 59.187 39.130 30.89 26.87 46.31 2.52
495 1050 4.274950 ACCTTGATCTTTCGCGAAAAAGAA 59.725 37.500 30.89 21.56 45.62 2.52
496 1051 4.848299 CCTTGATCTTTCGCGAAAAAGAAG 59.152 41.667 30.89 26.58 45.62 2.85
497 1052 5.418310 TTGATCTTTCGCGAAAAAGAAGT 57.582 34.783 31.68 14.69 45.62 3.01
498 1053 5.018695 TGATCTTTCGCGAAAAAGAAGTC 57.981 39.130 31.68 21.36 45.62 3.01
499 1054 4.750098 TGATCTTTCGCGAAAAAGAAGTCT 59.250 37.500 31.68 13.69 45.62 3.24
500 1055 4.710528 TCTTTCGCGAAAAAGAAGTCTC 57.289 40.909 31.68 0.00 41.17 3.36
501 1056 3.493503 TCTTTCGCGAAAAAGAAGTCTCC 59.506 43.478 31.68 0.00 41.17 3.71
502 1057 2.519377 TCGCGAAAAAGAAGTCTCCA 57.481 45.000 6.20 0.00 0.00 3.86
503 1058 3.040147 TCGCGAAAAAGAAGTCTCCAT 57.960 42.857 6.20 0.00 0.00 3.41
504 1059 2.993899 TCGCGAAAAAGAAGTCTCCATC 59.006 45.455 6.20 0.00 0.00 3.51
505 1060 2.996621 CGCGAAAAAGAAGTCTCCATCT 59.003 45.455 0.00 0.00 0.00 2.90
506 1061 3.061429 CGCGAAAAAGAAGTCTCCATCTC 59.939 47.826 0.00 0.00 0.00 2.75
507 1062 3.061429 GCGAAAAAGAAGTCTCCATCTCG 59.939 47.826 0.00 0.00 0.00 4.04
508 1063 3.061429 CGAAAAAGAAGTCTCCATCTCGC 59.939 47.826 0.00 0.00 0.00 5.03
509 1064 2.682155 AAAGAAGTCTCCATCTCGCC 57.318 50.000 0.00 0.00 0.00 5.54
510 1065 1.561643 AAGAAGTCTCCATCTCGCCA 58.438 50.000 0.00 0.00 0.00 5.69
511 1066 1.110442 AGAAGTCTCCATCTCGCCAG 58.890 55.000 0.00 0.00 0.00 4.85
512 1067 1.107114 GAAGTCTCCATCTCGCCAGA 58.893 55.000 0.00 0.00 0.00 3.86
513 1068 1.686052 GAAGTCTCCATCTCGCCAGAT 59.314 52.381 0.00 0.00 40.32 2.90
514 1069 2.666272 AGTCTCCATCTCGCCAGATA 57.334 50.000 0.00 0.00 37.25 1.98
515 1070 2.950781 AGTCTCCATCTCGCCAGATAA 58.049 47.619 0.00 0.00 37.25 1.75
516 1071 2.625790 AGTCTCCATCTCGCCAGATAAC 59.374 50.000 0.00 0.00 37.25 1.89
517 1072 2.625790 GTCTCCATCTCGCCAGATAACT 59.374 50.000 0.00 0.00 37.25 2.24
518 1073 3.068873 GTCTCCATCTCGCCAGATAACTT 59.931 47.826 0.00 0.00 37.25 2.66
519 1074 3.706594 TCTCCATCTCGCCAGATAACTTT 59.293 43.478 0.00 0.00 37.25 2.66
520 1075 4.162320 TCTCCATCTCGCCAGATAACTTTT 59.838 41.667 0.00 0.00 37.25 2.27
521 1076 4.843728 TCCATCTCGCCAGATAACTTTTT 58.156 39.130 0.00 0.00 37.25 1.94
604 1386 5.864418 ATATGGTTGCTTTGCATCTGAAT 57.136 34.783 0.00 0.00 38.76 2.57
608 1390 4.512198 TGGTTGCTTTGCATCTGAATTTTG 59.488 37.500 0.00 0.00 38.76 2.44
748 6853 3.243101 CGTACCATGTCGATCACTAGCTT 60.243 47.826 0.00 0.00 0.00 3.74
750 6855 2.497675 ACCATGTCGATCACTAGCTTGT 59.502 45.455 0.00 0.00 0.00 3.16
751 6856 3.699538 ACCATGTCGATCACTAGCTTGTA 59.300 43.478 0.00 0.00 0.00 2.41
764 6885 3.192541 AGCTTGTATGTGTGTGTGTCA 57.807 42.857 0.00 0.00 0.00 3.58
791 6912 1.818060 CAAACCTCGGCCATTGATTCA 59.182 47.619 2.24 0.00 0.00 2.57
914 7050 4.280174 GTGTGGAGAGAACCTTGTGTACTA 59.720 45.833 0.00 0.00 0.00 1.82
916 7052 6.152323 GTGTGGAGAGAACCTTGTGTACTATA 59.848 42.308 0.00 0.00 0.00 1.31
917 7053 6.152323 TGTGGAGAGAACCTTGTGTACTATAC 59.848 42.308 0.00 0.00 0.00 1.47
918 7054 6.377712 GTGGAGAGAACCTTGTGTACTATACT 59.622 42.308 0.00 0.00 0.00 2.12
919 7055 7.555554 GTGGAGAGAACCTTGTGTACTATACTA 59.444 40.741 0.00 0.00 0.00 1.82
920 7056 7.555554 TGGAGAGAACCTTGTGTACTATACTAC 59.444 40.741 0.00 0.00 0.00 2.73
922 7058 6.038050 AGAGAACCTTGTGTACTATACTACGC 59.962 42.308 0.00 0.00 0.00 4.42
972 8231 4.539083 TGCCTGTTGCGACGGTGT 62.539 61.111 12.06 0.00 45.60 4.16
1048 8321 2.359230 AAGAGCAGACAAGCGCCC 60.359 61.111 2.29 0.00 40.15 6.13
1049 8322 3.182590 AAGAGCAGACAAGCGCCCA 62.183 57.895 2.29 0.00 40.15 5.36
1050 8323 2.437359 GAGCAGACAAGCGCCCAT 60.437 61.111 2.29 0.00 40.15 4.00
1101 8382 4.529219 CTCGCCGGCCACAGCATA 62.529 66.667 23.46 0.00 42.56 3.14
1102 8383 4.089239 TCGCCGGCCACAGCATAA 62.089 61.111 23.46 0.00 42.56 1.90
1211 9015 3.284617 CCCCCAGGTTAGTTAATTTCCG 58.715 50.000 0.00 0.00 0.00 4.30
1232 9189 3.282021 GCCAGTTTTGATCTCCATGCTA 58.718 45.455 0.00 0.00 0.00 3.49
1301 11667 6.793203 GTCGTCGTCAGATGAGATAAAGATAC 59.207 42.308 0.00 0.00 42.54 2.24
1333 11720 5.981315 CGTACCTCAAGTTGTTGACTTTAGA 59.019 40.000 2.11 0.00 46.34 2.10
1361 11750 1.001520 TGTGTGTGCCTTACGTATGCT 59.998 47.619 15.86 0.00 0.00 3.79
1412 11808 4.025401 CAACGTCAAGGCGGTGGC 62.025 66.667 3.85 0.00 44.88 5.01
1453 11849 4.351054 GGGGAGCACCACCACCAG 62.351 72.222 1.58 0.00 42.91 4.00
1496 11903 1.562672 AAGGATGGTAAGCACGCCCT 61.563 55.000 0.00 0.00 0.00 5.19
1527 11944 1.674221 GCTCCATCGATCCATAGCACC 60.674 57.143 0.00 0.00 0.00 5.01
1537 11961 4.636249 GATCCATAGCACCTCCTTTGTAG 58.364 47.826 0.00 0.00 0.00 2.74
1538 11962 3.450904 TCCATAGCACCTCCTTTGTAGT 58.549 45.455 0.00 0.00 0.00 2.73
1539 11963 4.616553 TCCATAGCACCTCCTTTGTAGTA 58.383 43.478 0.00 0.00 0.00 1.82
1578 12002 1.002624 TGGTGATTTCCGGCCTGAC 60.003 57.895 0.00 0.00 0.00 3.51
1596 12026 2.253603 GACAATGTCTGAATTTGGCGC 58.746 47.619 6.07 0.00 0.00 6.53
1667 12102 1.291272 GACTAACCGCCCAAGACGT 59.709 57.895 0.00 0.00 0.00 4.34
1706 12163 5.865085 AGTACCTTTGAAGAGCATACACAA 58.135 37.500 0.00 0.00 0.00 3.33
1707 12164 6.476378 AGTACCTTTGAAGAGCATACACAAT 58.524 36.000 0.00 0.00 0.00 2.71
1708 12185 6.942576 AGTACCTTTGAAGAGCATACACAATT 59.057 34.615 0.00 0.00 0.00 2.32
1710 12189 7.145932 ACCTTTGAAGAGCATACACAATTAC 57.854 36.000 0.00 0.00 0.00 1.89
1712 12191 7.023575 CCTTTGAAGAGCATACACAATTACAC 58.976 38.462 0.00 0.00 0.00 2.90
1714 12193 7.686438 TTGAAGAGCATACACAATTACACAT 57.314 32.000 0.00 0.00 0.00 3.21
1716 12195 8.196802 TGAAGAGCATACACAATTACACATAC 57.803 34.615 0.00 0.00 0.00 2.39
1722 12201 7.708322 AGCATACACAATTACACATACAGAGAG 59.292 37.037 0.00 0.00 0.00 3.20
1745 12224 4.033014 GGAGAGTCGTTGCTTAATTACAGC 59.967 45.833 10.77 10.77 37.82 4.40
1757 12245 7.194278 TGCTTAATTACAGCGTTTGTTTGTTA 58.806 30.769 12.12 0.00 41.29 2.41
1767 12271 7.546316 ACAGCGTTTGTTTGTTATTTTAGGTTT 59.454 29.630 0.00 0.00 36.31 3.27
1772 12276 6.275305 TGTTTGTTATTTTAGGTTTTGCGC 57.725 33.333 0.00 0.00 0.00 6.09
1773 12277 5.051641 TGTTTGTTATTTTAGGTTTTGCGCG 60.052 36.000 0.00 0.00 0.00 6.86
1822 12339 1.762222 GATGTCCATGTACCGTGCGC 61.762 60.000 0.00 0.00 0.00 6.09
1823 12340 3.550992 GTCCATGTACCGTGCGCG 61.551 66.667 13.88 13.88 37.95 6.86
1840 12357 1.644786 GCGCCACACCCATAGTCAAC 61.645 60.000 0.00 0.00 0.00 3.18
1888 12729 9.771534 GCTACTGTTGAAGATCCTCTAATTAAT 57.228 33.333 0.00 0.00 0.00 1.40
1914 12757 3.909430 ACATCTGCTGTGCAAAAATGAG 58.091 40.909 12.77 0.00 38.41 2.90
1982 12835 3.255888 TCACTTGTGCAGAGGTAGTAGTG 59.744 47.826 0.00 1.49 34.55 2.74
1997 12850 4.767578 AGTAGTGGTAGTGGTATCGAGA 57.232 45.455 0.00 0.00 0.00 4.04
2000 12853 3.965694 AGTGGTAGTGGTATCGAGAGTT 58.034 45.455 0.00 0.00 0.00 3.01
2001 12854 5.108187 AGTGGTAGTGGTATCGAGAGTTA 57.892 43.478 0.00 0.00 0.00 2.24
2003 12856 4.275443 GTGGTAGTGGTATCGAGAGTTAGG 59.725 50.000 0.00 0.00 0.00 2.69
2006 12859 3.553904 AGTGGTATCGAGAGTTAGGTCC 58.446 50.000 0.00 0.00 0.00 4.46
2009 12915 4.023021 GTGGTATCGAGAGTTAGGTCCATC 60.023 50.000 0.00 0.00 0.00 3.51
2011 12917 2.704464 TCGAGAGTTAGGTCCATCGA 57.296 50.000 0.00 0.00 36.90 3.59
2245 15004 2.646175 GCACCCTCCTGTCGCTACA 61.646 63.158 0.00 0.00 0.00 2.74
2389 15176 7.889469 AGAAAATGTTCACTGCACATTAGAAT 58.111 30.769 7.37 0.00 42.80 2.40
2390 15177 8.362639 AGAAAATGTTCACTGCACATTAGAATT 58.637 29.630 7.37 0.00 42.80 2.17
2391 15178 8.891671 AAAATGTTCACTGCACATTAGAATTT 57.108 26.923 7.37 0.00 42.80 1.82
2393 15180 9.979578 AAATGTTCACTGCACATTAGAATTTTA 57.020 25.926 7.37 0.00 42.80 1.52
2550 15344 9.533253 CTGAGACATTTTTAAAAAGGTTCATGT 57.467 29.630 26.32 19.35 42.21 3.21
2556 15350 9.715123 CATTTTTAAAAAGGTTCATGTGTTTCC 57.285 29.630 17.72 0.00 0.00 3.13
2762 15589 6.182507 TGGTTCTAGAACAACCTGTATTGT 57.817 37.500 31.30 0.00 44.76 2.71
2767 15594 8.784043 GTTCTAGAACAACCTGTATTGTGAAAT 58.216 33.333 27.12 0.00 42.01 2.17
2771 15598 7.871853 AGAACAACCTGTATTGTGAAATGTAC 58.128 34.615 0.00 0.00 42.01 2.90
2796 15636 8.215736 ACTATGTAAGAAAAACACAAGGTACCT 58.784 33.333 9.21 9.21 0.00 3.08
2804 15644 1.414919 ACACAAGGTACCTTCTCGCAA 59.585 47.619 24.73 0.00 33.42 4.85
2809 15649 4.222145 ACAAGGTACCTTCTCGCAATAGAA 59.778 41.667 24.73 0.00 33.42 2.10
2824 15664 4.746089 GCAATAGAAGATCACCAGATGGCT 60.746 45.833 0.00 0.00 39.32 4.75
2881 15721 2.164422 TCGTCTCACAGTAGGCAAGATG 59.836 50.000 0.00 0.00 0.00 2.90
2882 15722 2.736719 CGTCTCACAGTAGGCAAGATGG 60.737 54.545 0.00 0.00 0.00 3.51
2883 15723 2.234908 GTCTCACAGTAGGCAAGATGGT 59.765 50.000 0.00 0.00 0.00 3.55
2888 15774 2.501723 ACAGTAGGCAAGATGGTTCGAT 59.498 45.455 0.00 0.00 0.00 3.59
2914 15802 0.104120 CTGTCTTGTGTGTCCCGTGA 59.896 55.000 0.00 0.00 0.00 4.35
2991 15879 5.630121 TGGATGCAGACTTTCTTTCCTTTA 58.370 37.500 0.00 0.00 0.00 1.85
2993 15881 5.106118 GGATGCAGACTTTCTTTCCTTTACC 60.106 44.000 0.00 0.00 0.00 2.85
3114 16002 4.988716 TCACGCCTGGGTCGAGGT 62.989 66.667 9.58 0.00 35.29 3.85
3159 16048 1.003355 CCTTGCTGGTGTGGATCGT 60.003 57.895 0.00 0.00 0.00 3.73
3163 16052 1.005037 GCTGGTGTGGATCGTGACA 60.005 57.895 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 154 9.177608 TCTCAAACATATATTTTCCCACTTCTG 57.822 33.333 0.00 0.00 0.00 3.02
161 170 9.567776 TCCAACAAACTTAATCTCTCAAACATA 57.432 29.630 0.00 0.00 0.00 2.29
164 173 9.750125 ATTTCCAACAAACTTAATCTCTCAAAC 57.250 29.630 0.00 0.00 0.00 2.93
293 304 1.134670 AGACGGCTCTGACATTAAGGC 60.135 52.381 0.00 0.00 0.00 4.35
296 307 4.265904 TCAAAGACGGCTCTGACATTAA 57.734 40.909 0.00 0.00 0.00 1.40
297 308 3.953712 TCAAAGACGGCTCTGACATTA 57.046 42.857 0.00 0.00 0.00 1.90
298 309 2.839486 TCAAAGACGGCTCTGACATT 57.161 45.000 0.00 0.00 0.00 2.71
299 310 2.625737 CATCAAAGACGGCTCTGACAT 58.374 47.619 0.00 0.00 0.00 3.06
300 311 1.338105 CCATCAAAGACGGCTCTGACA 60.338 52.381 0.00 0.00 0.00 3.58
301 312 1.338200 ACCATCAAAGACGGCTCTGAC 60.338 52.381 0.00 0.00 0.00 3.51
302 313 0.976641 ACCATCAAAGACGGCTCTGA 59.023 50.000 0.00 0.00 0.00 3.27
303 314 1.081892 CACCATCAAAGACGGCTCTG 58.918 55.000 0.00 0.00 0.00 3.35
304 315 0.976641 TCACCATCAAAGACGGCTCT 59.023 50.000 0.00 0.00 0.00 4.09
305 316 1.079503 GTCACCATCAAAGACGGCTC 58.920 55.000 0.00 0.00 0.00 4.70
306 317 0.687354 AGTCACCATCAAAGACGGCT 59.313 50.000 0.00 0.00 37.36 5.52
307 318 0.798776 CAGTCACCATCAAAGACGGC 59.201 55.000 0.00 0.00 37.36 5.68
308 319 2.169832 ACAGTCACCATCAAAGACGG 57.830 50.000 0.00 0.00 37.36 4.79
309 320 3.559655 TGAAACAGTCACCATCAAAGACG 59.440 43.478 0.00 0.00 37.36 4.18
310 321 5.499139 TTGAAACAGTCACCATCAAAGAC 57.501 39.130 0.00 0.00 35.39 3.01
311 322 6.329496 GTTTTGAAACAGTCACCATCAAAGA 58.671 36.000 1.90 0.00 40.07 2.52
312 323 5.229887 CGTTTTGAAACAGTCACCATCAAAG 59.770 40.000 7.32 0.00 40.07 2.77
329 352 6.337356 AGAAGCAATTTTTCTTCCGTTTTGA 58.663 32.000 7.76 0.00 39.48 2.69
353 376 0.973632 TGGAGCAGCTTAACGGAGAA 59.026 50.000 0.00 0.00 0.00 2.87
383 406 2.994995 GTCCAAAAAGCCCCGGGG 60.995 66.667 37.09 37.09 38.57 5.73
440 995 8.972127 GGTGATATAAGATGATGCTCCTTAGTA 58.028 37.037 0.00 0.00 0.00 1.82
441 996 7.455953 TGGTGATATAAGATGATGCTCCTTAGT 59.544 37.037 0.00 0.00 0.00 2.24
442 997 7.763528 GTGGTGATATAAGATGATGCTCCTTAG 59.236 40.741 0.00 0.00 0.00 2.18
443 998 7.235399 TGTGGTGATATAAGATGATGCTCCTTA 59.765 37.037 0.00 0.00 0.00 2.69
444 999 6.043590 TGTGGTGATATAAGATGATGCTCCTT 59.956 38.462 0.00 0.00 0.00 3.36
445 1000 5.545335 TGTGGTGATATAAGATGATGCTCCT 59.455 40.000 0.00 0.00 0.00 3.69
446 1001 5.641209 GTGTGGTGATATAAGATGATGCTCC 59.359 44.000 0.00 0.00 0.00 4.70
447 1002 5.641209 GGTGTGGTGATATAAGATGATGCTC 59.359 44.000 0.00 0.00 0.00 4.26
448 1003 5.072193 TGGTGTGGTGATATAAGATGATGCT 59.928 40.000 0.00 0.00 0.00 3.79
449 1004 5.180117 GTGGTGTGGTGATATAAGATGATGC 59.820 44.000 0.00 0.00 0.00 3.91
450 1005 5.702670 GGTGGTGTGGTGATATAAGATGATG 59.297 44.000 0.00 0.00 0.00 3.07
451 1006 5.608437 AGGTGGTGTGGTGATATAAGATGAT 59.392 40.000 0.00 0.00 0.00 2.45
452 1007 4.968719 AGGTGGTGTGGTGATATAAGATGA 59.031 41.667 0.00 0.00 0.00 2.92
453 1008 5.296151 AGGTGGTGTGGTGATATAAGATG 57.704 43.478 0.00 0.00 0.00 2.90
454 1009 5.428457 TCAAGGTGGTGTGGTGATATAAGAT 59.572 40.000 0.00 0.00 0.00 2.40
455 1010 4.780554 TCAAGGTGGTGTGGTGATATAAGA 59.219 41.667 0.00 0.00 0.00 2.10
456 1011 5.097742 TCAAGGTGGTGTGGTGATATAAG 57.902 43.478 0.00 0.00 0.00 1.73
457 1012 5.428457 AGATCAAGGTGGTGTGGTGATATAA 59.572 40.000 0.00 0.00 0.00 0.98
458 1013 4.968719 AGATCAAGGTGGTGTGGTGATATA 59.031 41.667 0.00 0.00 0.00 0.86
459 1014 3.782523 AGATCAAGGTGGTGTGGTGATAT 59.217 43.478 0.00 0.00 0.00 1.63
460 1015 3.181329 AGATCAAGGTGGTGTGGTGATA 58.819 45.455 0.00 0.00 0.00 2.15
461 1016 1.988107 AGATCAAGGTGGTGTGGTGAT 59.012 47.619 0.00 0.00 0.00 3.06
462 1017 1.434188 AGATCAAGGTGGTGTGGTGA 58.566 50.000 0.00 0.00 0.00 4.02
463 1018 2.276732 AAGATCAAGGTGGTGTGGTG 57.723 50.000 0.00 0.00 0.00 4.17
464 1019 2.810400 CGAAAGATCAAGGTGGTGTGGT 60.810 50.000 0.00 0.00 0.00 4.16
465 1020 1.806542 CGAAAGATCAAGGTGGTGTGG 59.193 52.381 0.00 0.00 0.00 4.17
466 1021 1.197721 GCGAAAGATCAAGGTGGTGTG 59.802 52.381 0.00 0.00 0.00 3.82
467 1022 1.523758 GCGAAAGATCAAGGTGGTGT 58.476 50.000 0.00 0.00 0.00 4.16
468 1023 0.443869 CGCGAAAGATCAAGGTGGTG 59.556 55.000 0.00 0.00 0.00 4.17
469 1024 0.320374 TCGCGAAAGATCAAGGTGGT 59.680 50.000 6.20 0.00 0.00 4.16
470 1025 1.438651 TTCGCGAAAGATCAAGGTGG 58.561 50.000 21.14 0.00 0.00 4.61
471 1026 3.536158 TTTTCGCGAAAGATCAAGGTG 57.464 42.857 30.60 0.00 0.00 4.00
472 1027 3.813166 TCTTTTTCGCGAAAGATCAAGGT 59.187 39.130 29.33 0.00 39.90 3.50
473 1028 4.404507 TCTTTTTCGCGAAAGATCAAGG 57.595 40.909 29.33 19.35 39.90 3.61
474 1029 5.444122 ACTTCTTTTTCGCGAAAGATCAAG 58.556 37.500 30.60 28.27 43.15 3.02
475 1030 5.236478 AGACTTCTTTTTCGCGAAAGATCAA 59.764 36.000 30.60 21.70 43.15 2.57
476 1031 4.750098 AGACTTCTTTTTCGCGAAAGATCA 59.250 37.500 30.60 16.15 43.15 2.92
477 1032 5.270812 AGACTTCTTTTTCGCGAAAGATC 57.729 39.130 30.60 20.89 43.15 2.75
478 1033 4.152580 GGAGACTTCTTTTTCGCGAAAGAT 59.847 41.667 30.60 14.14 43.15 2.40
479 1034 3.493503 GGAGACTTCTTTTTCGCGAAAGA 59.506 43.478 30.60 26.07 42.28 2.52
480 1035 3.247648 TGGAGACTTCTTTTTCGCGAAAG 59.752 43.478 30.60 21.93 37.85 2.62
481 1036 3.199677 TGGAGACTTCTTTTTCGCGAAA 58.800 40.909 29.22 29.22 0.00 3.46
482 1037 2.828877 TGGAGACTTCTTTTTCGCGAA 58.171 42.857 19.38 19.38 0.00 4.70
483 1038 2.519377 TGGAGACTTCTTTTTCGCGA 57.481 45.000 3.71 3.71 0.00 5.87
484 1039 2.996621 AGATGGAGACTTCTTTTTCGCG 59.003 45.455 0.00 0.00 41.71 5.87
485 1040 3.061429 CGAGATGGAGACTTCTTTTTCGC 59.939 47.826 0.00 0.00 44.20 4.70
486 1041 3.061429 GCGAGATGGAGACTTCTTTTTCG 59.939 47.826 0.00 0.00 44.20 3.46
487 1042 3.372514 GGCGAGATGGAGACTTCTTTTTC 59.627 47.826 0.00 0.00 44.20 2.29
488 1043 3.244561 TGGCGAGATGGAGACTTCTTTTT 60.245 43.478 0.00 0.00 44.20 1.94
489 1044 2.303022 TGGCGAGATGGAGACTTCTTTT 59.697 45.455 0.00 0.00 44.20 2.27
490 1045 1.902508 TGGCGAGATGGAGACTTCTTT 59.097 47.619 0.00 0.00 44.20 2.52
491 1046 1.480137 CTGGCGAGATGGAGACTTCTT 59.520 52.381 0.00 0.00 44.20 2.52
492 1047 1.110442 CTGGCGAGATGGAGACTTCT 58.890 55.000 0.00 0.00 46.58 2.85
493 1048 1.107114 TCTGGCGAGATGGAGACTTC 58.893 55.000 0.00 0.00 34.84 3.01
494 1049 1.786937 ATCTGGCGAGATGGAGACTT 58.213 50.000 10.78 0.00 37.56 3.01
495 1050 2.625790 GTTATCTGGCGAGATGGAGACT 59.374 50.000 20.31 0.00 39.44 3.24
496 1051 2.625790 AGTTATCTGGCGAGATGGAGAC 59.374 50.000 20.31 12.91 39.44 3.36
497 1052 2.950781 AGTTATCTGGCGAGATGGAGA 58.049 47.619 20.31 0.00 39.44 3.71
498 1053 3.742433 AAGTTATCTGGCGAGATGGAG 57.258 47.619 20.31 0.00 39.44 3.86
499 1054 4.487714 AAAAGTTATCTGGCGAGATGGA 57.512 40.909 20.31 6.96 39.44 3.41
521 1076 2.824689 TGATATTTGCTGGCCAGGAA 57.175 45.000 33.36 33.36 36.97 3.36
522 1077 2.760092 GTTTGATATTTGCTGGCCAGGA 59.240 45.455 33.46 29.53 0.00 3.86
523 1078 2.496871 TGTTTGATATTTGCTGGCCAGG 59.503 45.455 33.46 15.81 0.00 4.45
524 1079 3.777478 CTGTTTGATATTTGCTGGCCAG 58.223 45.455 29.34 29.34 0.00 4.85
525 1080 2.094078 GCTGTTTGATATTTGCTGGCCA 60.094 45.455 4.71 4.71 0.00 5.36
526 1081 2.543641 GCTGTTTGATATTTGCTGGCC 58.456 47.619 0.00 0.00 0.00 5.36
527 1082 2.543641 GGCTGTTTGATATTTGCTGGC 58.456 47.619 0.00 0.00 0.00 4.85
528 1083 2.423185 TCGGCTGTTTGATATTTGCTGG 59.577 45.455 0.00 0.00 0.00 4.85
529 1084 3.688272 CTCGGCTGTTTGATATTTGCTG 58.312 45.455 0.00 0.00 0.00 4.41
533 1088 2.024414 GGGCTCGGCTGTTTGATATTT 58.976 47.619 0.00 0.00 0.00 1.40
604 1386 5.869888 GGAGAAAGCTAACTCGAGATCAAAA 59.130 40.000 21.68 0.00 34.40 2.44
608 1390 3.549221 CCGGAGAAAGCTAACTCGAGATC 60.549 52.174 21.68 4.71 34.40 2.75
748 6853 2.102252 TGAGCTGACACACACACATACA 59.898 45.455 0.00 0.00 0.00 2.29
750 6855 3.130633 GTTGAGCTGACACACACACATA 58.869 45.455 0.00 0.00 0.00 2.29
751 6856 1.942657 GTTGAGCTGACACACACACAT 59.057 47.619 0.00 0.00 0.00 3.21
764 6885 1.600916 GGCCGAGGTTTGTTGAGCT 60.601 57.895 0.00 0.00 0.00 4.09
791 6912 2.431782 ACAAATGGAAAGTGTGCTGCTT 59.568 40.909 0.00 0.00 0.00 3.91
898 7021 6.183360 TGCGTAGTATAGTACACAAGGTTCTC 60.183 42.308 16.22 0.00 0.00 2.87
922 7058 8.224389 AGCACATAGATAGAGCATAGTAGATG 57.776 38.462 0.00 0.00 0.00 2.90
972 8231 3.774528 CTAGCTGCTCGCCACCCA 61.775 66.667 4.91 0.00 40.39 4.51
1048 8321 4.023107 GGTTTCAGCTGGATGATGATGATG 60.023 45.833 15.13 0.00 41.06 3.07
1049 8322 4.142790 GGTTTCAGCTGGATGATGATGAT 58.857 43.478 15.13 0.00 41.06 2.45
1050 8323 3.054213 TGGTTTCAGCTGGATGATGATGA 60.054 43.478 15.13 0.00 41.06 2.92
1092 8367 2.289002 GCGAGGAGAATTTATGCTGTGG 59.711 50.000 0.00 0.00 0.00 4.17
1101 8382 2.162716 GCGTGTGCGAGGAGAATTT 58.837 52.632 0.00 0.00 41.33 1.82
1102 8383 3.876300 GCGTGTGCGAGGAGAATT 58.124 55.556 0.00 0.00 41.33 2.17
1211 9015 2.097825 AGCATGGAGATCAAAACTGGC 58.902 47.619 0.00 0.00 0.00 4.85
1232 9189 4.090761 TCAGCCTCAGTTTTCAGACATT 57.909 40.909 0.00 0.00 0.00 2.71
1301 11667 0.170561 ACTTGAGGTACGTGCTAGCG 59.829 55.000 10.77 0.00 37.94 4.26
1333 11720 1.624336 AAGGCACACACATGAGCAAT 58.376 45.000 0.00 0.00 43.56 3.56
1361 11750 1.209504 GATGGGTAGTAGCCTGCACAA 59.790 52.381 18.90 0.00 40.28 3.33
1448 11844 4.641645 TTGTCGCCCCTGCTGGTG 62.642 66.667 9.00 0.00 37.24 4.17
1449 11845 4.335647 CTTGTCGCCCCTGCTGGT 62.336 66.667 9.00 0.00 34.43 4.00
1453 11849 3.645268 AATCCCTTGTCGCCCCTGC 62.645 63.158 0.00 0.00 0.00 4.85
1496 11903 1.907739 GATGGAGCAGCTGGTGGTA 59.092 57.895 25.60 9.48 36.87 3.25
1527 11944 8.923683 GTTAAGCAAGTTACTACTACAAAGGAG 58.076 37.037 0.00 0.00 39.89 3.69
1537 11961 4.922103 AGCGACAGTTAAGCAAGTTACTAC 59.078 41.667 0.00 0.00 0.00 2.73
1538 11962 4.921515 CAGCGACAGTTAAGCAAGTTACTA 59.078 41.667 0.00 0.00 0.00 1.82
1539 11963 3.741344 CAGCGACAGTTAAGCAAGTTACT 59.259 43.478 0.00 0.00 0.00 2.24
1578 12002 1.261989 CGCGCCAAATTCAGACATTG 58.738 50.000 0.00 0.00 0.00 2.82
1596 12026 2.255252 CCGCCAGGCTGAAAAACG 59.745 61.111 17.94 11.01 0.00 3.60
1664 12099 1.808531 TAGCACGGTAGCACCAACGT 61.809 55.000 6.21 0.00 38.47 3.99
1667 12102 1.203052 GTACTAGCACGGTAGCACCAA 59.797 52.381 3.23 0.00 38.47 3.67
1670 12105 1.101331 AGGTACTAGCACGGTAGCAC 58.899 55.000 12.75 1.03 39.30 4.40
1673 12108 4.157289 TCTTCAAAGGTACTAGCACGGTAG 59.843 45.833 1.79 1.79 38.49 3.18
1674 12109 4.081406 TCTTCAAAGGTACTAGCACGGTA 58.919 43.478 0.00 0.00 38.49 4.02
1677 12112 2.924290 GCTCTTCAAAGGTACTAGCACG 59.076 50.000 0.00 0.00 38.49 5.34
1706 12163 5.529430 CGACTCTCCTCTCTGTATGTGTAAT 59.471 44.000 0.00 0.00 0.00 1.89
1707 12164 4.876679 CGACTCTCCTCTCTGTATGTGTAA 59.123 45.833 0.00 0.00 0.00 2.41
1708 12185 4.081031 ACGACTCTCCTCTCTGTATGTGTA 60.081 45.833 0.00 0.00 0.00 2.90
1710 12189 3.275143 ACGACTCTCCTCTCTGTATGTG 58.725 50.000 0.00 0.00 0.00 3.21
1712 12191 3.488384 GCAACGACTCTCCTCTCTGTATG 60.488 52.174 0.00 0.00 0.00 2.39
1714 12193 2.085320 GCAACGACTCTCCTCTCTGTA 58.915 52.381 0.00 0.00 0.00 2.74
1716 12195 1.173043 AGCAACGACTCTCCTCTCTG 58.827 55.000 0.00 0.00 0.00 3.35
1722 12201 4.033014 GCTGTAATTAAGCAACGACTCTCC 59.967 45.833 12.10 0.00 40.52 3.71
1745 12224 7.368511 CGCAAAACCTAAAATAACAAACAAACG 59.631 33.333 0.00 0.00 0.00 3.60
1757 12245 4.469552 GTTACTCGCGCAAAACCTAAAAT 58.530 39.130 8.75 0.00 0.00 1.82
1767 12271 1.005294 GTTCTCGGTTACTCGCGCAA 61.005 55.000 8.75 0.00 0.00 4.85
1772 12276 1.154338 ACGCGTTCTCGGTTACTCG 60.154 57.895 5.58 0.00 37.56 4.18
1773 12277 1.671880 GCACGCGTTCTCGGTTACTC 61.672 60.000 10.22 0.00 37.56 2.59
1822 12339 0.036388 AGTTGACTATGGGTGTGGCG 60.036 55.000 0.00 0.00 0.00 5.69
1823 12340 2.200373 AAGTTGACTATGGGTGTGGC 57.800 50.000 0.00 0.00 0.00 5.01
1831 12348 3.006940 TGGCGCCTTAAAGTTGACTATG 58.993 45.455 29.70 0.00 0.00 2.23
1835 12352 2.785713 TTTGGCGCCTTAAAGTTGAC 57.214 45.000 29.70 0.00 0.00 3.18
1840 12357 3.550030 CCCGATAATTTGGCGCCTTAAAG 60.550 47.826 29.70 14.76 0.00 1.85
1888 12729 5.450592 TTTTTGCACAGCAGATGTTATCA 57.549 34.783 0.00 0.00 41.41 2.15
1914 12757 2.422832 CTCCCTCTGCAAATGAAAGCTC 59.577 50.000 0.00 0.00 0.00 4.09
1982 12835 4.459330 ACCTAACTCTCGATACCACTACC 58.541 47.826 0.00 0.00 0.00 3.18
1997 12850 2.068834 ACCGATCGATGGACCTAACT 57.931 50.000 18.66 0.00 0.00 2.24
2000 12853 4.030314 AGATTACCGATCGATGGACCTA 57.970 45.455 18.66 0.00 39.85 3.08
2001 12854 2.877866 AGATTACCGATCGATGGACCT 58.122 47.619 18.66 3.44 39.85 3.85
2003 12856 5.154932 CAACTAGATTACCGATCGATGGAC 58.845 45.833 18.66 5.12 39.85 4.02
2006 12859 5.399596 CACACAACTAGATTACCGATCGATG 59.600 44.000 18.66 2.80 39.85 3.84
2009 12915 3.486108 GCACACAACTAGATTACCGATCG 59.514 47.826 8.51 8.51 39.85 3.69
2011 12917 4.465632 TGCACACAACTAGATTACCGAT 57.534 40.909 0.00 0.00 0.00 4.18
2389 15176 9.327529 CTAATTTTGTACACCGCGTTAATAAAA 57.672 29.630 4.92 6.15 0.00 1.52
2390 15177 8.502387 ACTAATTTTGTACACCGCGTTAATAAA 58.498 29.630 4.92 0.00 0.00 1.40
2391 15178 8.027440 ACTAATTTTGTACACCGCGTTAATAA 57.973 30.769 4.92 0.00 0.00 1.40
2393 15180 6.484818 ACTAATTTTGTACACCGCGTTAAT 57.515 33.333 4.92 0.00 0.00 1.40
2542 15336 7.151308 TGAACATATTTGGAAACACATGAACC 58.849 34.615 0.00 0.00 42.67 3.62
2728 15539 8.669243 GGTTGTTCTAGAACCATTTTCAGATAG 58.331 37.037 28.43 0.00 42.26 2.08
2767 15594 8.967664 ACCTTGTGTTTTTCTTACATAGTACA 57.032 30.769 0.00 0.00 0.00 2.90
2771 15598 8.617290 AGGTACCTTGTGTTTTTCTTACATAG 57.383 34.615 9.21 0.00 0.00 2.23
2796 15636 4.402474 TCTGGTGATCTTCTATTGCGAGAA 59.598 41.667 0.00 0.00 34.30 2.87
2804 15644 4.620589 CAGCCATCTGGTGATCTTCTAT 57.379 45.455 0.00 0.00 45.48 1.98
2824 15664 4.141205 TCCTCATGAATCCATATTGTGCCA 60.141 41.667 0.00 0.00 0.00 4.92
2881 15721 2.939103 CAAGACAGGAATCCATCGAACC 59.061 50.000 0.61 0.00 0.00 3.62
2882 15722 3.372206 CACAAGACAGGAATCCATCGAAC 59.628 47.826 0.61 0.00 0.00 3.95
2883 15723 3.007940 ACACAAGACAGGAATCCATCGAA 59.992 43.478 0.61 0.00 0.00 3.71
2888 15774 2.224523 GGACACACAAGACAGGAATCCA 60.225 50.000 0.61 0.00 0.00 3.41
2933 15821 1.332195 GCTCCAGCCAGTTTTCCTTT 58.668 50.000 0.00 0.00 34.31 3.11
3009 15897 4.293648 TCGACCCACACAGCACGG 62.294 66.667 0.00 0.00 0.00 4.94
3067 15955 3.259314 TGATGCCACAGCCTGGGT 61.259 61.111 0.00 0.00 41.02 4.51
3114 16002 6.419791 ACCGGGTCATATTAAATTTCTGTCA 58.580 36.000 6.32 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.