Multiple sequence alignment - TraesCS5B01G194600

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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 TraesCS5B01G194600 chr5B 100.000 4489 0 0 1 4489 351473585 351478073 0.000000e+00 8290.0
1 TraesCS5B01G194600 chr5B 93.182 44 1 1 747 790 351474259 351474300 3.750000e-06 63.9
2 TraesCS5B01G194600 chr5B 93.182 44 1 1 675 716 351474331 351474374 3.750000e-06 63.9
3 TraesCS5B01G194600 chr5A 92.233 4197 200 61 342 4489 391546920 391542801 0.000000e+00 5829.0
4 TraesCS5B01G194600 chr5A 86.364 308 12 16 1 300 391547551 391547266 4.360000e-80 309.0
5 TraesCS5B01G194600 chr5A 96.875 32 1 0 758 789 391546584 391546553 2.000000e-03 54.7
6 TraesCS5B01G194600 chr5D 91.078 4136 219 67 403 4486 306190949 306194986 0.000000e+00 5456.0
7 TraesCS5B01G194600 chr3D 84.170 259 27 8 3836 4091 443308458 443308705 5.800000e-59 239.0
8 TraesCS5B01G194600 chr1D 84.170 259 26 9 3836 4091 126870508 126870262 2.090000e-58 237.0
9 TraesCS5B01G194600 chr3A 85.068 221 23 9 3836 4052 562982036 562982250 2.720000e-52 217.0
10 TraesCS5B01G194600 chrUn 83.043 230 20 14 3836 4052 302550463 302550240 1.650000e-44 191.0
11 TraesCS5B01G194600 chr6A 82.609 230 21 15 3836 4052 561434039 561434262 7.670000e-43 185.0
12 TraesCS5B01G194600 chr6A 82.609 230 21 15 3836 4052 561619837 561619614 7.670000e-43 185.0
13 TraesCS5B01G194600 chr7B 86.986 146 16 3 3836 3979 44379278 44379134 1.290000e-35 161.0


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 TraesCS5B01G194600 chr5B 351473585 351478073 4488 False 2805.933333 8290 95.454667 1 4489 3 chr5B.!!$F1 4488
1 TraesCS5B01G194600 chr5A 391542801 391547551 4750 True 2064.233333 5829 91.824000 1 4489 3 chr5A.!!$R1 4488
2 TraesCS5B01G194600 chr5D 306190949 306194986 4037 False 5456.000000 5456 91.078000 403 4486 1 chr5D.!!$F1 4083

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
328 337 0.105964 TTCCAACTGTAGCAGTGCGT 59.894 50.0 10.00 0.00 44.62 5.24 F
329 338 0.319555 TCCAACTGTAGCAGTGCGTC 60.320 55.0 10.00 7.53 44.62 5.19 F
331 340 0.319900 CAACTGTAGCAGTGCGTCCT 60.320 55.0 10.00 0.00 44.62 3.85 F
332 341 0.319900 AACTGTAGCAGTGCGTCCTG 60.320 55.0 10.00 8.08 44.62 3.86 F
1350 1672 0.468226 TGGAGGAGTTTGCAGAACGT 59.532 50.0 6.24 0.00 0.00 3.99 F
1770 2092 0.622154 TACCTGGTATGTGGGGTGGG 60.622 60.0 1.49 0.00 33.74 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1575 1897 1.065854 AGATCACAGTGGTAGCCAAGC 60.066 52.381 0.00 0.00 34.18 4.01 R
2037 2360 3.094386 GGCACCAAGTGACAAGACA 57.906 52.632 0.00 0.00 41.94 3.41 R
2199 2544 4.744570 TGTCAGCTCCAAATACTAGTTCG 58.255 43.478 0.00 0.00 0.00 3.95 R
2212 2557 5.009010 TCAGTTCTCAAAAATTGTCAGCTCC 59.991 40.000 0.00 0.00 0.00 4.70 R
3044 3427 0.835276 TAGCATCACTGATGGCAGCT 59.165 50.000 18.74 12.45 46.26 4.24 R
3713 4102 0.106149 AAAACTGTTCTCCCGTCGCT 59.894 50.000 0.00 0.00 0.00 4.93 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
85 90 2.296471 ACTCACTACTTGGACGTCCTTG 59.704 50.000 33.39 26.15 36.82 3.61
119 124 9.823647 ACTGTACATTTCTCTAATTGGATGTAG 57.176 33.333 0.00 0.00 32.50 2.74
146 151 9.435570 TTTTGCTAGAGATTATAGGAAGTAGGT 57.564 33.333 0.00 0.00 33.01 3.08
171 176 9.939802 GTTATATATCTCTAATTGGAAACCGGT 57.060 33.333 0.00 0.00 0.00 5.28
172 177 9.938280 TTATATATCTCTAATTGGAAACCGGTG 57.062 33.333 8.52 0.00 0.00 4.94
173 178 2.706890 TCTCTAATTGGAAACCGGTGC 58.293 47.619 8.52 2.88 0.00 5.01
178 187 4.629523 TGGAAACCGGTGCGTCCC 62.630 66.667 22.92 14.24 0.00 4.46
197 206 4.075793 TCTCCCCTGGGGTCTCGG 62.076 72.222 30.69 16.16 44.74 4.63
264 273 6.343716 TCACTGATGTTTATTGTGCCAATT 57.656 33.333 5.85 0.00 0.00 2.32
266 275 7.215789 TCACTGATGTTTATTGTGCCAATTTT 58.784 30.769 5.85 0.00 0.00 1.82
267 276 7.171167 TCACTGATGTTTATTGTGCCAATTTTG 59.829 33.333 5.85 0.00 0.00 2.44
268 277 6.073112 ACTGATGTTTATTGTGCCAATTTTGC 60.073 34.615 5.85 0.00 0.00 3.68
269 278 5.996513 TGATGTTTATTGTGCCAATTTTGCT 59.003 32.000 5.85 0.00 0.00 3.91
270 279 5.670149 TGTTTATTGTGCCAATTTTGCTG 57.330 34.783 5.85 0.00 0.00 4.41
271 280 5.121811 TGTTTATTGTGCCAATTTTGCTGT 58.878 33.333 5.85 0.00 0.00 4.40
272 281 5.007430 TGTTTATTGTGCCAATTTTGCTGTG 59.993 36.000 5.85 0.00 0.00 3.66
277 286 3.373439 TGTGCCAATTTTGCTGTGTTTTC 59.627 39.130 0.00 0.00 0.00 2.29
278 287 3.373439 GTGCCAATTTTGCTGTGTTTTCA 59.627 39.130 0.00 0.00 0.00 2.69
296 305 8.447053 GTGTTTTCATTGTTGTTATGGTGTTTT 58.553 29.630 0.00 0.00 0.00 2.43
298 307 7.778470 TTTCATTGTTGTTATGGTGTTTTCC 57.222 32.000 0.00 0.00 0.00 3.13
300 309 6.511416 TCATTGTTGTTATGGTGTTTTCCTG 58.489 36.000 0.00 0.00 0.00 3.86
301 310 4.314740 TGTTGTTATGGTGTTTTCCTGC 57.685 40.909 0.00 0.00 0.00 4.85
302 311 3.068873 TGTTGTTATGGTGTTTTCCTGCC 59.931 43.478 0.00 0.00 0.00 4.85
303 312 2.950781 TGTTATGGTGTTTTCCTGCCA 58.049 42.857 0.00 0.00 35.28 4.92
305 314 2.214376 TATGGTGTTTTCCTGCCAGG 57.786 50.000 3.69 3.69 36.46 4.45
313 322 1.371467 TTTCCTGCCAGGAGATTCCA 58.629 50.000 14.22 0.00 46.73 3.53
314 323 1.371467 TTCCTGCCAGGAGATTCCAA 58.629 50.000 14.22 0.00 46.73 3.53
315 324 0.620556 TCCTGCCAGGAGATTCCAAC 59.379 55.000 10.05 0.00 40.06 3.77
316 325 0.622665 CCTGCCAGGAGATTCCAACT 59.377 55.000 4.15 0.00 39.61 3.16
317 326 1.681166 CCTGCCAGGAGATTCCAACTG 60.681 57.143 4.15 0.00 39.61 3.16
318 327 1.004044 CTGCCAGGAGATTCCAACTGT 59.996 52.381 0.00 0.00 39.61 3.55
319 328 2.237143 CTGCCAGGAGATTCCAACTGTA 59.763 50.000 0.00 0.00 39.61 2.74
321 330 2.911484 CCAGGAGATTCCAACTGTAGC 58.089 52.381 0.00 0.00 39.61 3.58
322 331 2.237143 CCAGGAGATTCCAACTGTAGCA 59.763 50.000 0.00 0.00 39.61 3.49
323 332 3.529533 CAGGAGATTCCAACTGTAGCAG 58.470 50.000 0.00 0.00 39.61 4.24
326 335 2.675348 GAGATTCCAACTGTAGCAGTGC 59.325 50.000 7.13 7.13 44.62 4.40
328 337 0.105964 TTCCAACTGTAGCAGTGCGT 59.894 50.000 10.00 0.00 44.62 5.24
329 338 0.319555 TCCAACTGTAGCAGTGCGTC 60.320 55.000 10.00 7.53 44.62 5.19
330 339 1.291877 CCAACTGTAGCAGTGCGTCC 61.292 60.000 10.00 2.01 44.62 4.79
331 340 0.319900 CAACTGTAGCAGTGCGTCCT 60.320 55.000 10.00 0.00 44.62 3.85
332 341 0.319900 AACTGTAGCAGTGCGTCCTG 60.320 55.000 10.00 8.08 44.62 3.86
333 342 1.290324 CTGTAGCAGTGCGTCCTGT 59.710 57.895 10.00 0.00 34.84 4.00
334 343 1.006220 TGTAGCAGTGCGTCCTGTG 60.006 57.895 10.00 0.00 34.84 3.66
335 344 1.006102 GTAGCAGTGCGTCCTGTGT 60.006 57.895 10.00 0.00 34.84 3.72
336 345 1.009389 GTAGCAGTGCGTCCTGTGTC 61.009 60.000 10.00 0.00 34.84 3.67
337 346 1.179174 TAGCAGTGCGTCCTGTGTCT 61.179 55.000 10.00 0.00 34.84 3.41
338 347 1.595382 GCAGTGCGTCCTGTGTCTT 60.595 57.895 0.00 0.00 34.84 3.01
339 348 1.560860 GCAGTGCGTCCTGTGTCTTC 61.561 60.000 0.00 0.00 34.84 2.87
340 349 0.946221 CAGTGCGTCCTGTGTCTTCC 60.946 60.000 0.00 0.00 0.00 3.46
347 659 1.067071 GTCCTGTGTCTTCCGGTTAGG 60.067 57.143 0.00 0.31 42.97 2.69
350 662 2.165845 CCTGTGTCTTCCGGTTAGGTAG 59.834 54.545 0.00 0.00 41.99 3.18
423 735 6.320164 TGTTGCAGGTTAAATTTACTCACTGT 59.680 34.615 0.00 0.00 0.00 3.55
430 742 7.558444 AGGTTAAATTTACTCACTGTTTGGACA 59.442 33.333 0.00 0.00 0.00 4.02
433 745 7.581213 AAATTTACTCACTGTTTGGACATCA 57.419 32.000 0.00 0.00 34.72 3.07
483 795 4.275936 CGTTAGATGGAATTTTGCTAGGGG 59.724 45.833 0.00 0.00 0.00 4.79
495 807 6.397217 TTTTGCTAGGGGTTATAGGAAGTT 57.603 37.500 0.00 0.00 33.01 2.66
507 819 8.430431 GGGTTATAGGAAGTTGGCTATATATCC 58.570 40.741 0.00 0.00 0.00 2.59
543 855 3.237268 ACCAAATGCACAGTTCCCTTA 57.763 42.857 0.00 0.00 0.00 2.69
715 1027 5.636121 TGCCAGTTAACTTCACGTAGTTATG 59.364 40.000 5.07 7.87 41.61 1.90
728 1040 7.375834 TCACGTAGTTATGACTTGTTCAATCT 58.624 34.615 0.00 0.00 41.61 2.40
754 1066 0.770557 TTAAGCAGTGGTGGGAGGGT 60.771 55.000 0.00 0.00 0.00 4.34
761 1073 3.318313 CAGTGGTGGGAGGGTAGATAAT 58.682 50.000 0.00 0.00 0.00 1.28
762 1074 3.716872 CAGTGGTGGGAGGGTAGATAATT 59.283 47.826 0.00 0.00 0.00 1.40
763 1075 4.166144 CAGTGGTGGGAGGGTAGATAATTT 59.834 45.833 0.00 0.00 0.00 1.82
764 1076 4.794067 AGTGGTGGGAGGGTAGATAATTTT 59.206 41.667 0.00 0.00 0.00 1.82
766 1078 5.359860 GTGGTGGGAGGGTAGATAATTTTTG 59.640 44.000 0.00 0.00 0.00 2.44
767 1079 4.341235 GGTGGGAGGGTAGATAATTTTTGC 59.659 45.833 0.00 0.00 0.00 3.68
768 1080 4.341235 GTGGGAGGGTAGATAATTTTTGCC 59.659 45.833 0.00 0.00 0.00 4.52
769 1081 4.017037 TGGGAGGGTAGATAATTTTTGCCA 60.017 41.667 0.00 0.00 0.00 4.92
770 1082 4.584743 GGGAGGGTAGATAATTTTTGCCAG 59.415 45.833 0.00 0.00 0.00 4.85
771 1083 5.201243 GGAGGGTAGATAATTTTTGCCAGT 58.799 41.667 0.00 0.00 0.00 4.00
773 1085 6.831868 GGAGGGTAGATAATTTTTGCCAGTTA 59.168 38.462 0.00 0.00 0.00 2.24
775 1087 8.063200 AGGGTAGATAATTTTTGCCAGTTAAC 57.937 34.615 0.00 0.00 0.00 2.01
776 1088 7.893833 AGGGTAGATAATTTTTGCCAGTTAACT 59.106 33.333 1.12 1.12 0.00 2.24
777 1089 8.528643 GGGTAGATAATTTTTGCCAGTTAACTT 58.471 33.333 5.07 0.00 0.00 2.66
778 1090 9.569167 GGTAGATAATTTTTGCCAGTTAACTTC 57.431 33.333 5.07 1.49 0.00 3.01
781 1093 7.807907 AGATAATTTTTGCCAGTTAACTTCACG 59.192 33.333 5.07 0.00 0.00 4.35
782 1094 4.705337 TTTTTGCCAGTTAACTTCACGT 57.295 36.364 5.07 0.00 0.00 4.49
783 1095 5.814764 TTTTTGCCAGTTAACTTCACGTA 57.185 34.783 5.07 0.00 0.00 3.57
784 1096 5.412526 TTTTGCCAGTTAACTTCACGTAG 57.587 39.130 5.07 0.00 0.00 3.51
786 1098 4.062677 TGCCAGTTAACTTCACGTAGTT 57.937 40.909 5.07 8.66 41.61 2.24
862 1181 6.445451 AAATGATCTGGTGGACTATGCTAT 57.555 37.500 0.00 0.00 0.00 2.97
870 1189 7.118723 TCTGGTGGACTATGCTATTTCAAATT 58.881 34.615 0.00 0.00 0.00 1.82
908 1230 9.684448 CTTTATTCCTTGGAGTTTTTCTTCTTC 57.316 33.333 0.00 0.00 0.00 2.87
910 1232 5.124036 TCCTTGGAGTTTTTCTTCTTCCA 57.876 39.130 0.00 0.00 0.00 3.53
916 1238 7.181569 TGGAGTTTTTCTTCTTCCATTTTGT 57.818 32.000 0.00 0.00 0.00 2.83
968 1290 5.393068 AGCATAATTTGGGAGGATCTGAA 57.607 39.130 0.00 0.00 33.73 3.02
985 1307 6.429385 GGATCTGAATAAGGAAGCACATAAGG 59.571 42.308 0.00 0.00 0.00 2.69
1015 1337 8.116026 ACCTGTTCTTGATGGATAAAATACCTT 58.884 33.333 0.00 0.00 0.00 3.50
1017 1339 8.519799 TGTTCTTGATGGATAAAATACCTTCC 57.480 34.615 0.00 0.00 31.92 3.46
1075 1397 2.239400 AGGAAGCAAACCCTAGCAAAC 58.761 47.619 0.00 0.00 0.00 2.93
1206 1528 2.762327 CCCTGAATTCATCAACTTGGGG 59.238 50.000 15.67 12.89 36.57 4.96
1317 1639 3.354467 TGCAGCACATGTTATTGGATCA 58.646 40.909 0.00 0.00 0.00 2.92
1350 1672 0.468226 TGGAGGAGTTTGCAGAACGT 59.532 50.000 6.24 0.00 0.00 3.99
1551 1873 6.750039 GCTCTCTAGAAATTGTGTACTCTCAC 59.250 42.308 0.00 0.00 38.63 3.51
1770 2092 0.622154 TACCTGGTATGTGGGGTGGG 60.622 60.000 1.49 0.00 33.74 4.61
1838 2160 1.601759 GCCAGAGCAAGCTTGGACA 60.602 57.895 27.10 0.00 39.53 4.02
2028 2351 7.983484 GGGATGCTTAAACATGATCAAGAATTT 59.017 33.333 4.68 3.87 0.00 1.82
2079 2402 6.463331 CCCATTCCCATGTCCTAATTGAAATG 60.463 42.308 0.00 0.00 30.97 2.32
2117 2440 8.436046 TTTGTTGAATTGCTTGAGCTTTAAAT 57.564 26.923 4.44 0.00 42.66 1.40
2199 2544 8.519799 TGATAAACATTAGGAAATGAAGGGTC 57.480 34.615 5.18 0.00 44.50 4.46
2212 2557 7.201617 GGAAATGAAGGGTCGAACTAGTATTTG 60.202 40.741 0.00 0.00 0.00 2.32
2330 2681 4.607293 AAACCTTTGGAAATGAAGAGCC 57.393 40.909 0.00 0.00 0.00 4.70
2403 2756 4.272489 TGTTAAGCTTAGGATGCTGCATT 58.728 39.130 17.36 4.21 41.03 3.56
2405 2758 5.185635 TGTTAAGCTTAGGATGCTGCATTTT 59.814 36.000 17.36 10.43 41.03 1.82
2406 2759 3.795623 AGCTTAGGATGCTGCATTTTG 57.204 42.857 17.36 7.06 39.56 2.44
2408 2761 3.129988 AGCTTAGGATGCTGCATTTTGTC 59.870 43.478 17.36 4.00 39.56 3.18
2410 2763 4.669318 CTTAGGATGCTGCATTTTGTCTG 58.331 43.478 17.36 1.19 0.00 3.51
2411 2764 2.522185 AGGATGCTGCATTTTGTCTGT 58.478 42.857 17.36 0.00 0.00 3.41
2412 2765 2.895404 AGGATGCTGCATTTTGTCTGTT 59.105 40.909 17.36 0.00 0.00 3.16
2413 2766 3.322828 AGGATGCTGCATTTTGTCTGTTT 59.677 39.130 17.36 0.00 0.00 2.83
2414 2767 4.523943 AGGATGCTGCATTTTGTCTGTTTA 59.476 37.500 17.36 0.00 0.00 2.01
2415 2768 5.010922 AGGATGCTGCATTTTGTCTGTTTAA 59.989 36.000 17.36 0.00 0.00 1.52
2416 2769 5.346822 GGATGCTGCATTTTGTCTGTTTAAG 59.653 40.000 17.36 0.00 0.00 1.85
2417 2770 4.050553 TGCTGCATTTTGTCTGTTTAAGC 58.949 39.130 0.00 0.00 0.00 3.09
2418 2771 4.202141 TGCTGCATTTTGTCTGTTTAAGCT 60.202 37.500 0.00 0.00 0.00 3.74
2419 2772 4.149396 GCTGCATTTTGTCTGTTTAAGCTG 59.851 41.667 0.00 0.00 0.00 4.24
2420 2773 5.261209 TGCATTTTGTCTGTTTAAGCTGT 57.739 34.783 0.00 0.00 0.00 4.40
2421 2774 6.384258 TGCATTTTGTCTGTTTAAGCTGTA 57.616 33.333 0.00 0.00 0.00 2.74
2422 2775 6.205784 TGCATTTTGTCTGTTTAAGCTGTAC 58.794 36.000 0.00 0.00 0.00 2.90
2423 2776 6.183360 TGCATTTTGTCTGTTTAAGCTGTACA 60.183 34.615 0.00 0.00 0.00 2.90
2424 2777 6.695278 GCATTTTGTCTGTTTAAGCTGTACAA 59.305 34.615 0.00 8.71 0.00 2.41
2425 2778 7.382218 GCATTTTGTCTGTTTAAGCTGTACAAT 59.618 33.333 0.00 0.00 0.00 2.71
2426 2779 8.693504 CATTTTGTCTGTTTAAGCTGTACAATG 58.306 33.333 0.00 0.00 0.00 2.82
2427 2780 7.561021 TTTGTCTGTTTAAGCTGTACAATGA 57.439 32.000 0.00 0.00 0.00 2.57
2428 2781 7.744087 TTGTCTGTTTAAGCTGTACAATGAT 57.256 32.000 0.00 0.00 0.00 2.45
2429 2782 7.744087 TGTCTGTTTAAGCTGTACAATGATT 57.256 32.000 0.00 0.00 0.00 2.57
2430 2783 8.165239 TGTCTGTTTAAGCTGTACAATGATTT 57.835 30.769 0.00 0.00 0.00 2.17
2431 2784 8.289618 TGTCTGTTTAAGCTGTACAATGATTTC 58.710 33.333 0.00 0.00 0.00 2.17
2432 2785 8.289618 GTCTGTTTAAGCTGTACAATGATTTCA 58.710 33.333 0.00 0.00 0.00 2.69
2433 2786 8.845227 TCTGTTTAAGCTGTACAATGATTTCAA 58.155 29.630 0.00 0.00 0.00 2.69
2439 2818 6.672147 AGCTGTACAATGATTTCAACTGTTC 58.328 36.000 0.00 1.77 31.28 3.18
2442 2821 7.566760 TGTACAATGATTTCAACTGTTCAGT 57.433 32.000 0.00 0.00 31.28 3.41
2443 2822 7.416817 TGTACAATGATTTCAACTGTTCAGTG 58.583 34.615 6.22 5.60 39.39 3.66
2469 2848 5.252547 TCAGATATTGTTTGGTGCAAGCTA 58.747 37.500 0.00 0.00 33.76 3.32
2470 2849 5.887598 TCAGATATTGTTTGGTGCAAGCTAT 59.112 36.000 0.00 0.00 33.76 2.97
2474 2853 5.720371 ATTGTTTGGTGCAAGCTATGTTA 57.280 34.783 0.00 0.00 33.76 2.41
2484 2863 4.943093 TGCAAGCTATGTTATCTGCTTTCA 59.057 37.500 4.55 0.00 42.89 2.69
2499 2878 8.693542 ATCTGCTTTCATTTTGTTAATGCTAC 57.306 30.769 0.00 0.00 0.00 3.58
2504 2883 8.977505 GCTTTCATTTTGTTAATGCTACTTCAA 58.022 29.630 0.00 0.00 0.00 2.69
2524 2907 9.143155 ACTTCAAAATGGTTACTCTGGTTATTT 57.857 29.630 0.00 0.00 0.00 1.40
2527 2910 6.909550 AAATGGTTACTCTGGTTATTTGCA 57.090 33.333 0.00 0.00 0.00 4.08
2528 2911 5.897377 ATGGTTACTCTGGTTATTTGCAC 57.103 39.130 0.00 0.00 0.00 4.57
2532 2915 6.149633 GGTTACTCTGGTTATTTGCACAAAG 58.850 40.000 1.92 0.00 33.32 2.77
2600 2983 8.962857 AATTGTTTGTTAAGCTTTGGTTTTTG 57.037 26.923 3.20 0.00 0.00 2.44
2753 3136 4.881920 AGTGTATGCAACAAAATGGGAAC 58.118 39.130 0.00 0.00 40.63 3.62
2762 3145 2.621526 ACAAAATGGGAACTCACGGAAC 59.378 45.455 0.00 0.00 0.00 3.62
2801 3184 7.168637 CACACCAAAGAAGAAATTGATGAACTG 59.831 37.037 0.00 0.00 0.00 3.16
2849 3232 5.013547 TCGGAAAAGAATATGCCAAAGGAA 58.986 37.500 0.00 0.00 0.00 3.36
2879 3262 7.332213 TCATATAAAACAAGCTGCAGCATTA 57.668 32.000 38.24 25.87 45.16 1.90
2897 3280 7.378181 CAGCATTAGTTGTAAAATTGGAAGGT 58.622 34.615 0.00 0.00 0.00 3.50
3017 3400 2.621338 CTTCATAGCAACCGAGCTCAA 58.379 47.619 15.40 0.00 45.26 3.02
3044 3427 2.371841 TCTTCTCCTGCAGCAACCTTTA 59.628 45.455 8.66 0.00 0.00 1.85
3422 3805 2.507058 TGGTGAGGATGATGAAAGGAGG 59.493 50.000 0.00 0.00 0.00 4.30
3424 3807 2.130193 TGAGGATGATGAAAGGAGGGG 58.870 52.381 0.00 0.00 0.00 4.79
3505 3888 2.031333 GCTGAGAAACAGGTTTGCAGAG 60.031 50.000 19.94 6.86 45.82 3.35
3583 3972 8.615878 AAGTGTAGTGTAATGCATGTAAGAAA 57.384 30.769 0.00 0.00 0.00 2.52
3624 4013 9.679661 TTTTTGAAGAATGGCTATGATACTACA 57.320 29.630 0.00 0.00 0.00 2.74
3625 4014 9.851686 TTTTGAAGAATGGCTATGATACTACAT 57.148 29.630 0.00 0.00 0.00 2.29
3626 4015 8.837788 TTGAAGAATGGCTATGATACTACATG 57.162 34.615 0.00 0.00 0.00 3.21
3627 4016 7.966812 TGAAGAATGGCTATGATACTACATGT 58.033 34.615 2.69 2.69 0.00 3.21
3635 4024 9.259832 TGGCTATGATACTACATGTCTATGATT 57.740 33.333 0.00 0.00 37.73 2.57
3706 4095 3.054655 GGAGTGGTAGAGTGGGCAAATAA 60.055 47.826 0.00 0.00 0.00 1.40
3707 4096 4.566907 GGAGTGGTAGAGTGGGCAAATAAA 60.567 45.833 0.00 0.00 0.00 1.40
3708 4097 4.332828 AGTGGTAGAGTGGGCAAATAAAC 58.667 43.478 0.00 0.00 0.00 2.01
3710 4099 4.521256 GTGGTAGAGTGGGCAAATAAACAA 59.479 41.667 0.00 0.00 0.00 2.83
3712 4101 5.777732 TGGTAGAGTGGGCAAATAAACAAAT 59.222 36.000 0.00 0.00 0.00 2.32
3713 4102 6.948886 TGGTAGAGTGGGCAAATAAACAAATA 59.051 34.615 0.00 0.00 0.00 1.40
3714 4103 7.122055 TGGTAGAGTGGGCAAATAAACAAATAG 59.878 37.037 0.00 0.00 0.00 1.73
3715 4104 5.965922 AGAGTGGGCAAATAAACAAATAGC 58.034 37.500 0.00 0.00 0.00 2.97
3716 4105 4.743493 AGTGGGCAAATAAACAAATAGCG 58.257 39.130 0.00 0.00 0.00 4.26
3717 4106 4.461081 AGTGGGCAAATAAACAAATAGCGA 59.539 37.500 0.00 0.00 0.00 4.93
3718 4107 4.561213 GTGGGCAAATAAACAAATAGCGAC 59.439 41.667 0.00 0.00 0.00 5.19
3719 4108 3.789224 GGGCAAATAAACAAATAGCGACG 59.211 43.478 0.00 0.00 0.00 5.12
3769 4158 9.958234 TGTAACTAAACGTTGTATGTACTGTAA 57.042 29.630 0.00 0.00 37.05 2.41
3779 4169 4.536888 TGTATGTACTGTAACCACCCCAAT 59.463 41.667 0.00 0.00 0.00 3.16
3795 4185 9.197306 ACCACCCCAATATATTCTTTAAGAAAC 57.803 33.333 11.63 0.00 37.82 2.78
3796 4186 8.349983 CCACCCCAATATATTCTTTAAGAAACG 58.650 37.037 11.63 0.00 37.82 3.60
3839 4230 4.689812 CCTCAGTGCTCAATCTATATGTGC 59.310 45.833 0.00 0.00 37.69 4.57
3917 4308 8.049117 AGAAAGGTGATGTTTCATTATAGCTGA 58.951 33.333 0.00 0.00 36.53 4.26
3965 4356 5.684704 CTTTCCTAATCCAGGCATCTGTTA 58.315 41.667 0.00 0.00 45.10 2.41
3983 4374 6.126409 TCTGTTATCTTTCAGGTTTTGGTGT 58.874 36.000 0.00 0.00 33.13 4.16
3984 4375 6.262273 TCTGTTATCTTTCAGGTTTTGGTGTC 59.738 38.462 0.00 0.00 33.13 3.67
3988 4379 8.573035 GTTATCTTTCAGGTTTTGGTGTCATTA 58.427 33.333 0.00 0.00 0.00 1.90
3991 4382 7.657336 TCTTTCAGGTTTTGGTGTCATTAATC 58.343 34.615 0.00 0.00 0.00 1.75
4073 4465 1.523258 CGCTTGCCTGCTGCTCTAT 60.523 57.895 0.00 0.00 42.00 1.98
4101 4493 8.871686 AAGCAAAATTAAGTTGTGGAAACTAG 57.128 30.769 0.00 0.00 0.00 2.57
4114 4506 5.658634 TGTGGAAACTAGATGAGTCTGCTAT 59.341 40.000 0.00 0.00 37.44 2.97
4115 4507 6.183360 TGTGGAAACTAGATGAGTCTGCTATC 60.183 42.308 0.00 0.00 37.44 2.08
4118 4510 5.940192 AACTAGATGAGTCTGCTATCGAG 57.060 43.478 0.00 0.00 37.44 4.04
4160 4553 4.955811 TCAAAGTATGTCTGGTGTCACT 57.044 40.909 2.35 0.00 0.00 3.41
4169 4562 3.386402 TGTCTGGTGTCACTGTATTGTCA 59.614 43.478 2.35 0.00 0.00 3.58
4202 4595 2.448926 GGCCAAAATTTAGCCGTTGT 57.551 45.000 14.47 0.00 36.84 3.32
4232 4625 3.531538 TGTTCTTTGGTCTGTGTGAGTC 58.468 45.455 0.00 0.00 0.00 3.36
4324 4717 9.751542 ACCTTAGTTCTATCTTAAACATCATCG 57.248 33.333 0.00 0.00 0.00 3.84
4370 4763 5.759763 TGAAGACGCAATGCAAGTGATATAT 59.240 36.000 5.91 0.00 30.28 0.86
4371 4764 6.928492 TGAAGACGCAATGCAAGTGATATATA 59.072 34.615 5.91 0.00 30.28 0.86
4387 4781 7.865889 AGTGATATATATCGTGCGTCTTGAAAA 59.134 33.333 16.21 0.00 35.48 2.29
4396 4790 4.444056 CGTGCGTCTTGAAAATTCCATTTT 59.556 37.500 0.00 0.00 44.56 1.82
4403 4797 5.236047 TCTTGAAAATTCCATTTTTGTGGCG 59.764 36.000 0.00 0.00 42.15 5.69
4412 4806 2.350899 TTTTTGTGGCGCAGATGATG 57.649 45.000 10.83 0.00 0.00 3.07
4420 4814 1.094073 GCGCAGATGATGGAGTGCTT 61.094 55.000 0.30 0.00 34.84 3.91
4425 4819 2.801111 CAGATGATGGAGTGCTTGATCG 59.199 50.000 0.00 0.00 0.00 3.69
4469 4863 8.887717 CCAGTTTACTCTTTGAGATATCTTTGG 58.112 37.037 6.70 0.00 33.32 3.28
4471 4865 8.826765 AGTTTACTCTTTGAGATATCTTTGGGA 58.173 33.333 6.70 3.44 33.32 4.37
4486 4880 1.105457 TGGGATATTTGCAGTGCAGC 58.895 50.000 18.81 6.67 40.61 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 124 9.699703 CCTACTTCCTATAATCTCTAGCAAAAC 57.300 37.037 0.00 0.00 0.00 2.43
146 151 9.938280 CACCGGTTTCCAATTAGAGATATATAA 57.062 33.333 2.97 0.00 0.00 0.98
197 206 3.207669 CTCATCAGCGCCAAGGGC 61.208 66.667 2.29 0.00 46.75 5.19
206 215 4.925861 GCCTCCCCGCTCATCAGC 62.926 72.222 0.00 0.00 42.96 4.26
207 216 4.598894 CGCCTCCCCGCTCATCAG 62.599 72.222 0.00 0.00 0.00 2.90
228 237 3.242518 CATCAGTGAAACAGCAGCATTG 58.757 45.455 0.00 0.00 41.43 2.82
233 242 6.361481 CACAATAAACATCAGTGAAACAGCAG 59.639 38.462 0.00 0.00 41.43 4.24
264 273 7.201591 CCATAACAACAATGAAAACACAGCAAA 60.202 33.333 0.00 0.00 0.00 3.68
266 275 5.752472 CCATAACAACAATGAAAACACAGCA 59.248 36.000 0.00 0.00 0.00 4.41
267 276 5.752955 ACCATAACAACAATGAAAACACAGC 59.247 36.000 0.00 0.00 0.00 4.40
268 277 6.756074 ACACCATAACAACAATGAAAACACAG 59.244 34.615 0.00 0.00 0.00 3.66
269 278 6.634805 ACACCATAACAACAATGAAAACACA 58.365 32.000 0.00 0.00 0.00 3.72
270 279 7.532682 AACACCATAACAACAATGAAAACAC 57.467 32.000 0.00 0.00 0.00 3.32
271 280 8.553459 AAAACACCATAACAACAATGAAAACA 57.447 26.923 0.00 0.00 0.00 2.83
272 281 8.119845 GGAAAACACCATAACAACAATGAAAAC 58.880 33.333 0.00 0.00 0.00 2.43
277 286 5.177327 GCAGGAAAACACCATAACAACAATG 59.823 40.000 0.00 0.00 0.00 2.82
278 287 5.296748 GCAGGAAAACACCATAACAACAAT 58.703 37.500 0.00 0.00 0.00 2.71
296 305 0.620556 GTTGGAATCTCCTGGCAGGA 59.379 55.000 33.02 33.02 43.43 3.86
298 307 1.004044 ACAGTTGGAATCTCCTGGCAG 59.996 52.381 7.75 7.75 37.46 4.85
300 309 2.911484 CTACAGTTGGAATCTCCTGGC 58.089 52.381 0.00 0.00 37.46 4.85
301 310 2.237143 TGCTACAGTTGGAATCTCCTGG 59.763 50.000 0.00 0.00 37.46 4.45
302 311 3.055530 ACTGCTACAGTTGGAATCTCCTG 60.056 47.826 0.00 0.00 42.59 3.86
303 312 3.055530 CACTGCTACAGTTGGAATCTCCT 60.056 47.826 0.00 0.00 42.59 3.69
305 314 2.675348 GCACTGCTACAGTTGGAATCTC 59.325 50.000 0.00 0.00 42.59 2.75
313 322 0.319900 CAGGACGCACTGCTACAGTT 60.320 55.000 0.00 0.00 42.59 3.16
314 323 1.290324 CAGGACGCACTGCTACAGT 59.710 57.895 0.00 0.00 46.51 3.55
315 324 1.010935 CACAGGACGCACTGCTACAG 61.011 60.000 6.84 0.00 42.21 2.74
316 325 1.006220 CACAGGACGCACTGCTACA 60.006 57.895 6.84 0.00 42.21 2.74
317 326 1.006102 ACACAGGACGCACTGCTAC 60.006 57.895 6.84 0.00 42.21 3.58
318 327 1.179174 AGACACAGGACGCACTGCTA 61.179 55.000 6.84 0.00 42.21 3.49
319 328 2.029666 GACACAGGACGCACTGCT 59.970 61.111 6.84 0.00 42.21 4.24
321 330 0.946221 GGAAGACACAGGACGCACTG 60.946 60.000 5.50 5.50 44.03 3.66
322 331 1.367840 GGAAGACACAGGACGCACT 59.632 57.895 0.00 0.00 0.00 4.40
323 332 2.022129 CGGAAGACACAGGACGCAC 61.022 63.158 0.00 0.00 0.00 5.34
326 335 0.599558 TAACCGGAAGACACAGGACG 59.400 55.000 9.46 0.00 0.00 4.79
328 337 1.263356 CCTAACCGGAAGACACAGGA 58.737 55.000 9.46 0.00 33.16 3.86
329 338 0.974383 ACCTAACCGGAAGACACAGG 59.026 55.000 9.46 5.82 36.31 4.00
330 339 3.087031 TCTACCTAACCGGAAGACACAG 58.913 50.000 9.46 0.00 36.31 3.66
331 340 3.159213 TCTACCTAACCGGAAGACACA 57.841 47.619 9.46 0.00 36.31 3.72
332 341 3.698040 TCATCTACCTAACCGGAAGACAC 59.302 47.826 9.46 0.00 36.31 3.67
333 342 3.952323 CTCATCTACCTAACCGGAAGACA 59.048 47.826 9.46 0.00 36.31 3.41
334 343 3.243468 GCTCATCTACCTAACCGGAAGAC 60.243 52.174 9.46 0.00 36.31 3.01
335 344 2.957006 GCTCATCTACCTAACCGGAAGA 59.043 50.000 9.46 0.92 36.31 2.87
336 345 2.036089 GGCTCATCTACCTAACCGGAAG 59.964 54.545 9.46 4.81 36.31 3.46
337 346 2.037144 GGCTCATCTACCTAACCGGAA 58.963 52.381 9.46 0.00 36.31 4.30
338 347 1.700955 GGCTCATCTACCTAACCGGA 58.299 55.000 9.46 0.00 36.31 5.14
339 348 0.680061 GGGCTCATCTACCTAACCGG 59.320 60.000 0.00 0.00 39.35 5.28
340 349 0.314302 CGGGCTCATCTACCTAACCG 59.686 60.000 0.00 0.00 0.00 4.44
347 659 2.029470 CCATCTTCTCGGGCTCATCTAC 60.029 54.545 0.00 0.00 0.00 2.59
350 662 0.755686 ACCATCTTCTCGGGCTCATC 59.244 55.000 0.00 0.00 0.00 2.92
400 712 6.952773 ACAGTGAGTAAATTTAACCTGCAA 57.047 33.333 0.00 0.00 0.00 4.08
495 807 4.141413 GCATGGGTGATGGATATATAGCCA 60.141 45.833 21.49 21.49 46.96 4.75
507 819 1.548081 TGGTTCAAGCATGGGTGATG 58.452 50.000 0.00 0.00 34.84 3.07
638 950 8.547069 CAAAAATTACCAACACAACACATTAGG 58.453 33.333 0.00 0.00 0.00 2.69
677 989 9.476202 AAGTTAACTGGCAAAAATTATCAACTC 57.524 29.630 9.34 0.00 0.00 3.01
678 990 9.476202 GAAGTTAACTGGCAAAAATTATCAACT 57.524 29.630 9.34 0.00 0.00 3.16
680 992 9.255304 GTGAAGTTAACTGGCAAAAATTATCAA 57.745 29.630 9.34 0.00 0.00 2.57
682 994 7.593644 ACGTGAAGTTAACTGGCAAAAATTATC 59.406 33.333 9.34 0.00 0.00 1.75
683 995 7.430441 ACGTGAAGTTAACTGGCAAAAATTAT 58.570 30.769 9.34 0.00 0.00 1.28
684 996 6.797454 ACGTGAAGTTAACTGGCAAAAATTA 58.203 32.000 9.34 0.00 0.00 1.40
685 997 5.656480 ACGTGAAGTTAACTGGCAAAAATT 58.344 33.333 9.34 0.00 0.00 1.82
686 998 5.257082 ACGTGAAGTTAACTGGCAAAAAT 57.743 34.783 9.34 0.00 0.00 1.82
715 1027 6.858478 GCTTAAGTTTGGAGATTGAACAAGTC 59.142 38.462 4.02 0.00 0.00 3.01
728 1040 2.582052 CCACCACTGCTTAAGTTTGGA 58.418 47.619 19.88 0.00 40.14 3.53
761 1073 4.705337 ACGTGAAGTTAACTGGCAAAAA 57.295 36.364 9.34 0.00 0.00 1.94
762 1074 4.877251 ACTACGTGAAGTTAACTGGCAAAA 59.123 37.500 9.34 0.07 0.00 2.44
763 1075 4.444536 ACTACGTGAAGTTAACTGGCAAA 58.555 39.130 9.34 0.39 0.00 3.68
764 1076 4.062677 ACTACGTGAAGTTAACTGGCAA 57.937 40.909 9.34 0.00 0.00 4.52
766 1078 5.445540 GCATAACTACGTGAAGTTAACTGGC 60.446 44.000 9.34 11.22 43.30 4.85
767 1079 5.867716 AGCATAACTACGTGAAGTTAACTGG 59.132 40.000 9.34 1.99 43.30 4.00
768 1080 6.946229 AGCATAACTACGTGAAGTTAACTG 57.054 37.500 9.34 10.00 43.30 3.16
831 1150 5.044919 AGTCCACCAGATCATTTAATCCACA 60.045 40.000 0.00 0.00 0.00 4.17
902 1221 8.960591 ACCATAGTATCAACAAAATGGAAGAAG 58.039 33.333 6.18 0.00 36.71 2.85
908 1230 6.629128 TGCAACCATAGTATCAACAAAATGG 58.371 36.000 0.00 0.00 38.05 3.16
910 1232 8.065473 TCATGCAACCATAGTATCAACAAAAT 57.935 30.769 0.00 0.00 0.00 1.82
916 1238 5.694231 GCATCATGCAACCATAGTATCAA 57.306 39.130 4.20 0.00 44.26 2.57
948 1270 8.166061 TCCTTATTCAGATCCTCCCAAATTATG 58.834 37.037 0.00 0.00 0.00 1.90
968 1290 4.443034 GGTCGACCTTATGTGCTTCCTTAT 60.443 45.833 27.64 0.00 0.00 1.73
985 1307 2.743636 TCCATCAAGAACAGGTCGAC 57.256 50.000 7.13 7.13 0.00 4.20
999 1321 6.349363 GGCAATCGGAAGGTATTTTATCCATC 60.349 42.308 0.00 0.00 32.08 3.51
1015 1337 0.764890 CCAGGATAAGGGCAATCGGA 59.235 55.000 0.00 0.00 0.00 4.55
1017 1339 2.224621 ACATCCAGGATAAGGGCAATCG 60.225 50.000 0.00 0.00 0.00 3.34
1206 1528 2.621998 AGCTGCCATGCACTCAAATATC 59.378 45.455 0.00 0.00 33.79 1.63
1317 1639 7.766278 GCAAACTCCTCCATATTCATCGTATAT 59.234 37.037 0.00 0.00 0.00 0.86
1575 1897 1.065854 AGATCACAGTGGTAGCCAAGC 60.066 52.381 0.00 0.00 34.18 4.01
1770 2092 3.188048 CAGGTGAGTTCTCATTCACAAGC 59.812 47.826 5.80 0.00 44.23 4.01
1838 2160 6.891908 ACCAGAAATATTAGCAACATGACCTT 59.108 34.615 0.00 0.00 0.00 3.50
2037 2360 3.094386 GGCACCAAGTGACAAGACA 57.906 52.632 0.00 0.00 41.94 3.41
2079 2402 6.424812 GCAATTCAACAAATATAATCCAGGCC 59.575 38.462 0.00 0.00 0.00 5.19
2199 2544 4.744570 TGTCAGCTCCAAATACTAGTTCG 58.255 43.478 0.00 0.00 0.00 3.95
2212 2557 5.009010 TCAGTTCTCAAAAATTGTCAGCTCC 59.991 40.000 0.00 0.00 0.00 4.70
2264 2609 7.120579 TGCAGTTATCTCCAACGAAATTAATGT 59.879 33.333 0.00 0.00 33.50 2.71
2265 2610 7.471721 TGCAGTTATCTCCAACGAAATTAATG 58.528 34.615 0.00 0.00 33.50 1.90
2266 2611 7.624360 TGCAGTTATCTCCAACGAAATTAAT 57.376 32.000 0.00 0.00 33.50 1.40
2268 2613 7.441890 TTTGCAGTTATCTCCAACGAAATTA 57.558 32.000 0.00 0.00 33.50 1.40
2330 2681 7.064609 TCAGAAATTGGTAGCTCAAAATACTCG 59.935 37.037 0.00 0.00 0.00 4.18
2403 2756 7.561021 TCATTGTACAGCTTAAACAGACAAA 57.439 32.000 0.00 0.00 0.00 2.83
2405 2758 7.744087 AATCATTGTACAGCTTAAACAGACA 57.256 32.000 0.00 0.00 0.00 3.41
2406 2759 8.289618 TGAAATCATTGTACAGCTTAAACAGAC 58.710 33.333 0.00 0.00 0.00 3.51
2408 2761 8.905702 GTTGAAATCATTGTACAGCTTAAACAG 58.094 33.333 0.00 0.00 0.00 3.16
2410 2763 8.905702 CAGTTGAAATCATTGTACAGCTTAAAC 58.094 33.333 0.00 0.00 0.00 2.01
2411 2764 8.629158 ACAGTTGAAATCATTGTACAGCTTAAA 58.371 29.630 0.00 0.00 0.00 1.52
2412 2765 8.165239 ACAGTTGAAATCATTGTACAGCTTAA 57.835 30.769 0.00 0.00 0.00 1.85
2413 2766 7.744087 ACAGTTGAAATCATTGTACAGCTTA 57.256 32.000 0.00 0.00 0.00 3.09
2414 2767 6.639632 ACAGTTGAAATCATTGTACAGCTT 57.360 33.333 0.00 0.00 0.00 3.74
2415 2768 6.262944 TGAACAGTTGAAATCATTGTACAGCT 59.737 34.615 0.00 0.00 0.00 4.24
2416 2769 6.437928 TGAACAGTTGAAATCATTGTACAGC 58.562 36.000 0.00 0.00 0.00 4.40
2417 2770 7.588854 CACTGAACAGTTGAAATCATTGTACAG 59.411 37.037 4.63 0.00 40.20 2.74
2418 2771 7.066887 ACACTGAACAGTTGAAATCATTGTACA 59.933 33.333 4.63 0.00 40.20 2.90
2419 2772 7.417612 ACACTGAACAGTTGAAATCATTGTAC 58.582 34.615 4.63 0.00 40.20 2.90
2420 2773 7.566760 ACACTGAACAGTTGAAATCATTGTA 57.433 32.000 4.63 0.00 40.20 2.41
2421 2774 6.455360 ACACTGAACAGTTGAAATCATTGT 57.545 33.333 4.63 0.00 40.20 2.71
2422 2775 7.488792 TGAAACACTGAACAGTTGAAATCATTG 59.511 33.333 4.63 0.00 40.20 2.82
2423 2776 7.546358 TGAAACACTGAACAGTTGAAATCATT 58.454 30.769 4.63 0.00 40.20 2.57
2424 2777 7.067372 TCTGAAACACTGAACAGTTGAAATCAT 59.933 33.333 4.63 0.00 40.20 2.45
2425 2778 6.374053 TCTGAAACACTGAACAGTTGAAATCA 59.626 34.615 4.63 5.47 40.20 2.57
2426 2779 6.785191 TCTGAAACACTGAACAGTTGAAATC 58.215 36.000 4.63 1.60 40.20 2.17
2427 2780 6.757897 TCTGAAACACTGAACAGTTGAAAT 57.242 33.333 4.63 0.00 40.20 2.17
2428 2781 6.757897 ATCTGAAACACTGAACAGTTGAAA 57.242 33.333 4.63 0.00 40.20 2.69
2429 2782 8.344831 CAATATCTGAAACACTGAACAGTTGAA 58.655 33.333 4.63 0.00 40.20 2.69
2430 2783 7.498900 ACAATATCTGAAACACTGAACAGTTGA 59.501 33.333 4.63 0.00 40.20 3.18
2431 2784 7.642669 ACAATATCTGAAACACTGAACAGTTG 58.357 34.615 4.63 4.26 40.20 3.16
2432 2785 7.807977 ACAATATCTGAAACACTGAACAGTT 57.192 32.000 4.63 0.00 40.20 3.16
2433 2786 7.807977 AACAATATCTGAAACACTGAACAGT 57.192 32.000 1.32 1.32 43.61 3.55
2439 2818 5.630680 GCACCAAACAATATCTGAAACACTG 59.369 40.000 0.00 0.00 0.00 3.66
2442 2821 5.781210 TGCACCAAACAATATCTGAAACA 57.219 34.783 0.00 0.00 0.00 2.83
2443 2822 5.119125 GCTTGCACCAAACAATATCTGAAAC 59.881 40.000 0.00 0.00 0.00 2.78
2470 2849 8.924691 GCATTAACAAAATGAAAGCAGATAACA 58.075 29.630 2.01 0.00 0.00 2.41
2474 2853 8.526147 AGTAGCATTAACAAAATGAAAGCAGAT 58.474 29.630 2.01 0.00 0.00 2.90
2484 2863 9.777297 ACCATTTTGAAGTAGCATTAACAAAAT 57.223 25.926 0.00 0.00 43.65 1.82
2499 2878 9.410556 CAAATAACCAGAGTAACCATTTTGAAG 57.589 33.333 0.00 0.00 0.00 3.02
2504 2883 6.266558 TGTGCAAATAACCAGAGTAACCATTT 59.733 34.615 0.00 0.00 0.00 2.32
2569 2952 9.908152 ACCAAAGCTTAACAAACAATTATAGAC 57.092 29.630 0.00 0.00 0.00 2.59
2600 2983 6.640907 CACATGGGAAAAGCAACTAAAGTTAC 59.359 38.462 0.00 0.00 36.32 2.50
2753 3136 5.800941 GTGACTACTAATTGAGTTCCGTGAG 59.199 44.000 0.00 0.00 39.81 3.51
2762 3145 7.872993 TCTTCTTTGGTGTGACTACTAATTGAG 59.127 37.037 0.00 0.00 0.00 3.02
2849 3232 7.468357 GCTGCAGCTTGTTTTATATGAAGATCT 60.468 37.037 31.33 0.00 38.21 2.75
2879 3262 9.588096 AGAGAATTACCTTCCAATTTTACAACT 57.412 29.630 0.00 0.00 34.11 3.16
3017 3400 3.920231 TGCTGCAGGAGAAGATAACAT 57.080 42.857 17.12 0.00 0.00 2.71
3044 3427 0.835276 TAGCATCACTGATGGCAGCT 59.165 50.000 18.74 12.45 46.26 4.24
3354 3737 0.809241 GAGTCATCAGCCTCTTGCCG 60.809 60.000 0.00 0.00 42.71 5.69
3356 3739 1.206610 TCAGAGTCATCAGCCTCTTGC 59.793 52.381 0.00 0.00 35.90 4.01
3422 3805 3.272574 TCAGTTTCATCATCTGCTCCC 57.727 47.619 0.00 0.00 0.00 4.30
3424 3807 4.880120 TCCATTCAGTTTCATCATCTGCTC 59.120 41.667 0.00 0.00 0.00 4.26
3536 3925 9.678941 CACTTATTAGAAGGGAAAACAAAGTTC 57.321 33.333 0.00 0.00 0.00 3.01
3541 3930 9.280174 CACTACACTTATTAGAAGGGAAAACAA 57.720 33.333 0.00 0.00 0.00 2.83
3548 3937 7.985184 TGCATTACACTACACTTATTAGAAGGG 59.015 37.037 0.00 0.00 0.00 3.95
3657 4046 7.573238 TGTTTGTAGGATAATTAGGGGATGGTA 59.427 37.037 0.00 0.00 0.00 3.25
3692 4081 5.393027 CGCTATTTGTTTATTTGCCCACTCT 60.393 40.000 0.00 0.00 0.00 3.24
3693 4082 4.798387 CGCTATTTGTTTATTTGCCCACTC 59.202 41.667 0.00 0.00 0.00 3.51
3706 4095 2.289195 TGTTCTCCCGTCGCTATTTGTT 60.289 45.455 0.00 0.00 0.00 2.83
3707 4096 1.274167 TGTTCTCCCGTCGCTATTTGT 59.726 47.619 0.00 0.00 0.00 2.83
3708 4097 1.927174 CTGTTCTCCCGTCGCTATTTG 59.073 52.381 0.00 0.00 0.00 2.32
3710 4099 1.183549 ACTGTTCTCCCGTCGCTATT 58.816 50.000 0.00 0.00 0.00 1.73
3712 4101 0.963962 AAACTGTTCTCCCGTCGCTA 59.036 50.000 0.00 0.00 0.00 4.26
3713 4102 0.106149 AAAACTGTTCTCCCGTCGCT 59.894 50.000 0.00 0.00 0.00 4.93
3714 4103 0.942252 AAAAACTGTTCTCCCGTCGC 59.058 50.000 0.00 0.00 0.00 5.19
3715 4104 4.034279 TGTTTAAAAACTGTTCTCCCGTCG 59.966 41.667 7.09 0.00 39.59 5.12
3716 4105 5.488645 TGTTTAAAAACTGTTCTCCCGTC 57.511 39.130 7.09 0.00 39.59 4.79
3717 4106 5.900865 TTGTTTAAAAACTGTTCTCCCGT 57.099 34.783 7.09 0.00 39.59 5.28
3718 4107 7.764695 ATTTTGTTTAAAAACTGTTCTCCCG 57.235 32.000 7.09 0.00 39.09 5.14
3719 4108 8.941977 ACAATTTTGTTTAAAAACTGTTCTCCC 58.058 29.630 7.09 0.00 38.47 4.30
3753 4142 3.928375 GGGTGGTTACAGTACATACAACG 59.072 47.826 0.00 0.00 0.00 4.10
3765 4154 9.635404 CTTAAAGAATATATTGGGGTGGTTACA 57.365 33.333 1.78 0.00 0.00 2.41
3769 4158 9.197306 GTTTCTTAAAGAATATATTGGGGTGGT 57.803 33.333 1.78 0.00 33.67 4.16
3795 4185 6.013842 AGGCAGGAAAAGTTTCTAATTTCG 57.986 37.500 3.92 0.00 37.35 3.46
3796 4186 6.981722 TGAGGCAGGAAAAGTTTCTAATTTC 58.018 36.000 3.92 0.00 37.35 2.17
3807 4197 1.163554 GAGCACTGAGGCAGGAAAAG 58.836 55.000 0.00 0.00 35.51 2.27
3839 4230 8.066595 GCAGATTGCTAAAGATTATGTGTGTAG 58.933 37.037 0.00 0.00 40.96 2.74
3853 4244 6.374333 AGGTAAAGAAATCGCAGATTGCTAAA 59.626 34.615 10.83 2.46 45.12 1.85
3871 4262 8.568794 CCTTTCTAAAGTCAGGAAAAGGTAAAG 58.431 37.037 0.00 0.00 34.20 1.85
3912 4303 2.862541 TGCCAGTTGTTTGTATCAGCT 58.137 42.857 0.00 0.00 0.00 4.24
3917 4308 4.082245 GCCATAGTTGCCAGTTGTTTGTAT 60.082 41.667 0.00 0.00 0.00 2.29
3965 4356 7.595819 TTAATGACACCAAAACCTGAAAGAT 57.404 32.000 0.00 0.00 34.07 2.40
3983 4374 7.913297 GCAAGCTTACCAAATAACGATTAATGA 59.087 33.333 0.00 0.00 0.00 2.57
3984 4375 7.915397 AGCAAGCTTACCAAATAACGATTAATG 59.085 33.333 0.00 0.00 0.00 1.90
3988 4379 5.648092 AGAGCAAGCTTACCAAATAACGATT 59.352 36.000 0.00 0.00 0.00 3.34
3991 4382 4.391830 TGAGAGCAAGCTTACCAAATAACG 59.608 41.667 0.00 0.00 0.00 3.18
4034 4426 1.843992 CTGCTTCTGTTGTTGTTGCC 58.156 50.000 0.00 0.00 0.00 4.52
4069 4461 8.855110 TCCACAACTTAATTTTGCTTTGATAGA 58.145 29.630 0.00 0.00 0.00 1.98
4073 4465 7.821846 AGTTTCCACAACTTAATTTTGCTTTGA 59.178 29.630 0.00 0.00 0.00 2.69
4101 4493 2.813754 AGCTCTCGATAGCAGACTCATC 59.186 50.000 22.93 0.00 45.30 2.92
4114 4506 5.907207 AGCTACATTTTTATGAGCTCTCGA 58.093 37.500 16.19 0.00 39.22 4.04
4115 4507 6.595772 AAGCTACATTTTTATGAGCTCTCG 57.404 37.500 16.19 0.00 42.56 4.04
4118 4510 8.970691 TTTGAAAGCTACATTTTTATGAGCTC 57.029 30.769 6.82 6.82 42.56 4.09
4160 4553 2.236893 TGCTCTCCATGCTGACAATACA 59.763 45.455 0.00 0.00 0.00 2.29
4169 4562 2.146146 TTGGCCTTGCTCTCCATGCT 62.146 55.000 3.32 0.00 0.00 3.79
4202 4595 0.400213 ACCAAAGAACATGGCGAGGA 59.600 50.000 0.00 0.00 41.89 3.71
4232 4625 2.951726 TCTCAAGAATCTGTCACAGCG 58.048 47.619 0.00 0.00 0.00 5.18
4244 4637 5.371526 AGAGCAAGACAACATTCTCAAGAA 58.628 37.500 0.00 0.00 38.56 2.52
4246 4639 5.237996 TCAAGAGCAAGACAACATTCTCAAG 59.762 40.000 0.00 0.00 0.00 3.02
4324 4717 6.913170 TCAAGGTAAAGCTCATTCACAAATC 58.087 36.000 0.00 0.00 0.00 2.17
4370 4763 3.997681 TGGAATTTTCAAGACGCACGATA 59.002 39.130 0.00 0.00 0.00 2.92
4371 4764 2.811431 TGGAATTTTCAAGACGCACGAT 59.189 40.909 0.00 0.00 0.00 3.73
4387 4781 1.617850 TCTGCGCCACAAAAATGGAAT 59.382 42.857 4.18 0.00 43.02 3.01
4396 4790 0.745486 CTCCATCATCTGCGCCACAA 60.745 55.000 4.18 0.00 0.00 3.33
4403 4797 2.034104 TCAAGCACTCCATCATCTGC 57.966 50.000 0.00 0.00 0.00 4.26
4420 4814 2.270352 AAGGTTTCCTGTTGCGATCA 57.730 45.000 0.00 0.00 32.13 2.92
4469 4863 0.029834 CCGCTGCACTGCAAATATCC 59.970 55.000 4.99 0.00 38.41 2.59


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

AutoCloner maintained by Alex Coulton.