Multiple sequence alignment - TraesCS4D01G192100

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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 TraesCS4D01G192100 chr4D 100.000 4783 0 0 1 4783 335342238 335337456 0.000000e+00 8833.0
1 TraesCS4D01G192100 chr4B 91.652 2204 123 27 710 2886 413492314 413490145 0.000000e+00 2994.0
2 TraesCS4D01G192100 chr4B 86.772 1081 47 39 2941 4000 413490161 413489156 0.000000e+00 1116.0
3 TraesCS4D01G192100 chr4B 92.420 752 29 7 1 752 413493030 413492307 0.000000e+00 1048.0
4 TraesCS4D01G192100 chr4B 91.041 413 18 9 4076 4484 413472482 413472085 1.510000e-149 540.0
5 TraesCS4D01G192100 chr4A 91.189 1203 51 21 710 1883 137533397 137534573 0.000000e+00 1583.0
6 TraesCS4D01G192100 chr4A 89.227 789 41 19 3998 4783 137537971 137538718 0.000000e+00 946.0
7 TraesCS4D01G192100 chr4A 89.907 753 46 6 1 752 137532681 137533404 0.000000e+00 942.0
8 TraesCS4D01G192100 chr4A 92.722 632 29 6 1881 2502 137534830 137535454 0.000000e+00 896.0
9 TraesCS4D01G192100 chr4A 92.920 452 20 7 3561 4000 137537256 137537707 0.000000e+00 647.0
10 TraesCS4D01G192100 chr4A 88.430 363 33 3 2531 2886 137535453 137535813 3.420000e-116 429.0
11 TraesCS4D01G192100 chr4A 91.554 296 24 1 3240 3534 137536961 137537256 1.600000e-109 407.0
12 TraesCS4D01G192100 chr4A 85.574 305 28 9 2941 3237 137535797 137536093 6.010000e-79 305.0
13 TraesCS4D01G192100 chr2B 92.229 489 36 2 1003 1490 65313860 65314347 0.000000e+00 691.0
14 TraesCS4D01G192100 chr2B 80.000 370 50 13 1937 2298 65316014 65316367 7.950000e-63 252.0
15 TraesCS4D01G192100 chr2D 91.820 489 38 2 1003 1490 37533505 37533992 0.000000e+00 680.0
16 TraesCS4D01G192100 chr2D 79.714 350 52 13 1946 2289 37536177 37536513 8.000000e-58 235.0
17 TraesCS4D01G192100 chr2A 91.457 398 32 2 1094 1490 42398352 42398748 3.250000e-151 545.0
18 TraesCS4D01G192100 chr2A 79.167 360 56 13 1946 2299 42400979 42401325 1.040000e-56 231.0
19 TraesCS4D01G192100 chr2A 100.000 31 0 0 2525 2555 91138836 91138866 1.860000e-04 58.4
20 TraesCS4D01G192100 chr6A 82.154 622 49 25 1 621 81120765 81121325 1.200000e-130 477.0
21 TraesCS4D01G192100 chr6D 81.529 628 49 23 1 621 63767905 63768472 5.640000e-124 455.0
22 TraesCS4D01G192100 chr6B 86.563 387 24 14 1 383 137458701 137459063 7.460000e-108 401.0
23 TraesCS4D01G192100 chr5A 73.516 219 40 15 2578 2786 221611449 221611659 3.090000e-07 67.6


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 TraesCS4D01G192100 chr4D 335337456 335342238 4782 True 8833.000000 8833 100.000000 1 4783 1 chr4D.!!$R1 4782
1 TraesCS4D01G192100 chr4B 413489156 413493030 3874 True 1719.333333 2994 90.281333 1 4000 3 chr4B.!!$R2 3999
2 TraesCS4D01G192100 chr4A 137532681 137538718 6037 False 769.375000 1583 90.190375 1 4783 8 chr4A.!!$F1 4782
3 TraesCS4D01G192100 chr2B 65313860 65316367 2507 False 471.500000 691 86.114500 1003 2298 2 chr2B.!!$F1 1295
4 TraesCS4D01G192100 chr2D 37533505 37536513 3008 False 457.500000 680 85.767000 1003 2289 2 chr2D.!!$F1 1286
5 TraesCS4D01G192100 chr2A 42398352 42401325 2973 False 388.000000 545 85.312000 1094 2299 2 chr2A.!!$F2 1205
6 TraesCS4D01G192100 chr6A 81120765 81121325 560 False 477.000000 477 82.154000 1 621 1 chr6A.!!$F1 620
7 TraesCS4D01G192100 chr6D 63767905 63768472 567 False 455.000000 455 81.529000 1 621 1 chr6D.!!$F1 620

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
764 815 0.179037 GCTACCCGGTTCCAATACCC 60.179 60.0 0.00 0.0 34.56 3.69 F
810 865 0.324183 CTGGACTGGAGAGCTGGAGA 60.324 60.0 0.00 0.0 0.00 3.71 F
1182 1243 0.465705 GCATCCGTTCCATCTCCTCA 59.534 55.0 0.00 0.0 0.00 3.86 F
1714 2172 1.589803 GTTTGGTACTTGCGAGTGGT 58.410 50.0 17.36 0.0 36.60 4.16 F
2856 5394 2.094545 GCTAACCTTGCTTCCAATGTGG 60.095 50.0 0.00 0.0 39.43 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2753 5291 2.438021 CCCTCCGGTCCAAAATATCAGA 59.562 50.000 0.00 0.0 0.00 3.27 R
2786 5324 4.202567 GGATATAAAAGGATCCACCCAGCA 60.203 45.833 15.82 0.0 41.24 4.41 R
2921 5460 0.658897 GTTCCCGTCTTTTCAACGCA 59.341 50.000 0.00 0.0 38.77 5.24 R
2922 5461 0.658897 TGTTCCCGTCTTTTCAACGC 59.341 50.000 0.00 0.0 38.77 4.84 R
4343 8063 0.033504 GTCAGCCTCAAACGACTCCA 59.966 55.000 0.00 0.0 0.00 3.86 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
243 255 2.248248 TGAGTTGGAGGTGGTGAGTAG 58.752 52.381 0.00 0.00 0.00 2.57
244 256 2.158370 TGAGTTGGAGGTGGTGAGTAGA 60.158 50.000 0.00 0.00 0.00 2.59
245 257 2.494073 GAGTTGGAGGTGGTGAGTAGAG 59.506 54.545 0.00 0.00 0.00 2.43
246 258 2.110188 AGTTGGAGGTGGTGAGTAGAGA 59.890 50.000 0.00 0.00 0.00 3.10
247 259 2.897969 GTTGGAGGTGGTGAGTAGAGAA 59.102 50.000 0.00 0.00 0.00 2.87
248 260 2.808919 TGGAGGTGGTGAGTAGAGAAG 58.191 52.381 0.00 0.00 0.00 2.85
511 523 1.332997 GATCGCTGGAAAGGCAATGAG 59.667 52.381 0.00 0.00 0.00 2.90
576 588 2.093394 GCTACTTGTCCTCCTTCCCTTC 60.093 54.545 0.00 0.00 0.00 3.46
613 628 1.966451 CCAAGAAAAGAGGCGGCGT 60.966 57.895 9.37 0.00 0.00 5.68
660 676 3.535629 CTGGTGCGTGCCTCTTCCA 62.536 63.158 0.00 0.00 0.00 3.53
717 733 4.392166 TCTGCTCCCCGCTACCCA 62.392 66.667 0.00 0.00 40.11 4.51
722 738 1.377229 CTCCCCGCTACCCAAACAA 59.623 57.895 0.00 0.00 0.00 2.83
724 740 1.074248 CCCCGCTACCCAAACAAGT 59.926 57.895 0.00 0.00 0.00 3.16
730 781 1.084289 CTACCCAAACAAGTAGGCGC 58.916 55.000 0.00 0.00 33.73 6.53
735 786 1.135402 CCAAACAAGTAGGCGCATTCC 60.135 52.381 10.83 0.00 0.00 3.01
764 815 0.179037 GCTACCCGGTTCCAATACCC 60.179 60.000 0.00 0.00 34.56 3.69
768 819 2.110352 CCGGTTCCAATACCCGTGC 61.110 63.158 0.00 0.00 40.10 5.34
797 852 2.122954 GTGGGGGAGGACTGGACT 59.877 66.667 0.00 0.00 0.00 3.85
800 855 2.450243 GGGGAGGACTGGACTGGA 59.550 66.667 0.00 0.00 0.00 3.86
801 856 1.687493 GGGGAGGACTGGACTGGAG 60.687 68.421 0.00 0.00 0.00 3.86
802 857 1.388531 GGGAGGACTGGACTGGAGA 59.611 63.158 0.00 0.00 0.00 3.71
804 859 1.326951 GGAGGACTGGACTGGAGAGC 61.327 65.000 0.00 0.00 0.00 4.09
805 860 0.324275 GAGGACTGGACTGGAGAGCT 60.324 60.000 0.00 0.00 0.00 4.09
806 861 0.614415 AGGACTGGACTGGAGAGCTG 60.614 60.000 0.00 0.00 0.00 4.24
807 862 1.612395 GGACTGGACTGGAGAGCTGG 61.612 65.000 0.00 0.00 0.00 4.85
808 863 0.613292 GACTGGACTGGAGAGCTGGA 60.613 60.000 0.00 0.00 0.00 3.86
809 864 0.614415 ACTGGACTGGAGAGCTGGAG 60.614 60.000 0.00 0.00 0.00 3.86
810 865 0.324183 CTGGACTGGAGAGCTGGAGA 60.324 60.000 0.00 0.00 0.00 3.71
811 866 0.613292 TGGACTGGAGAGCTGGAGAC 60.613 60.000 0.00 0.00 0.00 3.36
812 867 1.326951 GGACTGGAGAGCTGGAGACC 61.327 65.000 0.00 0.00 0.00 3.85
813 868 1.305718 ACTGGAGAGCTGGAGACCC 60.306 63.158 0.00 0.00 0.00 4.46
877 938 2.476619 CACCAAGAGAGTACAACAAGCG 59.523 50.000 0.00 0.00 0.00 4.68
1182 1243 0.465705 GCATCCGTTCCATCTCCTCA 59.534 55.000 0.00 0.00 0.00 3.86
1467 1528 4.530857 GACCCCGACGCCATCCTG 62.531 72.222 0.00 0.00 0.00 3.86
1541 1602 7.094848 GGTTACCCACCAATTTTCATGATTTTG 60.095 37.037 0.00 1.15 46.42 2.44
1593 1711 6.403527 CGATGTCTTGACCTGATTAAATGCAA 60.404 38.462 0.00 0.00 0.00 4.08
1712 2170 1.878953 AGGTTTGGTACTTGCGAGTG 58.121 50.000 17.36 0.00 36.60 3.51
1714 2172 1.589803 GTTTGGTACTTGCGAGTGGT 58.410 50.000 17.36 0.00 36.60 4.16
1744 2207 7.454260 AATGGACCAAATGAACTTTCTAGTC 57.546 36.000 0.00 0.00 31.99 2.59
2097 4617 2.174639 TGGGGTGCTCCATATTAAGGTG 59.825 50.000 7.20 0.00 37.22 4.00
2122 4642 5.056553 AGTTAACCCTGTTTCTGCCTTTA 57.943 39.130 0.88 0.00 0.00 1.85
2123 4643 5.451354 AGTTAACCCTGTTTCTGCCTTTAA 58.549 37.500 0.88 0.00 0.00 1.52
2125 4645 3.876309 ACCCTGTTTCTGCCTTTAAGA 57.124 42.857 0.00 0.00 0.00 2.10
2128 4648 5.887754 ACCCTGTTTCTGCCTTTAAGATTA 58.112 37.500 0.00 0.00 0.00 1.75
2129 4649 6.311735 ACCCTGTTTCTGCCTTTAAGATTAA 58.688 36.000 0.00 0.00 0.00 1.40
2258 4786 5.069251 GCTAGTTGCTCCTCCTCTTTATGTA 59.931 44.000 0.00 0.00 38.95 2.29
2292 4820 2.135933 CTCTCGACAAGGTTGGTGTTC 58.864 52.381 0.00 0.00 0.00 3.18
2329 4857 4.527427 TCCATGATTCATGTTGGCTTTGAA 59.473 37.500 21.95 0.00 39.94 2.69
2356 4884 4.835615 AGGTATCCTGCTCGATTGATTAGT 59.164 41.667 0.00 0.00 29.57 2.24
2358 4886 5.406780 GGTATCCTGCTCGATTGATTAGTTG 59.593 44.000 0.00 0.00 0.00 3.16
2367 4895 7.496920 TGCTCGATTGATTAGTTGATCTGATTT 59.503 33.333 0.00 0.00 0.00 2.17
2403 4932 6.648725 GGATGCTCCTAGTTTGACATAGATTC 59.351 42.308 0.00 0.00 32.53 2.52
2405 4934 6.577103 TGCTCCTAGTTTGACATAGATTCAG 58.423 40.000 0.00 0.00 0.00 3.02
2418 4947 9.904198 TGACATAGATTCAGGATTTAACAATCA 57.096 29.630 0.00 0.00 40.77 2.57
2424 4953 9.739276 AGATTCAGGATTTAACAATCACACTAA 57.261 29.630 0.00 0.00 40.77 2.24
2503 5033 8.539770 TTAGAAAGAAGCTTCTAATGTGTCAG 57.460 34.615 28.67 0.00 41.04 3.51
2504 5034 6.763355 AGAAAGAAGCTTCTAATGTGTCAGA 58.237 36.000 28.67 0.00 36.28 3.27
2530 5061 8.536340 AGATTTAAGATTACGAGTTACTCCCT 57.464 34.615 6.80 0.00 0.00 4.20
2533 5064 7.951347 TTAAGATTACGAGTTACTCCCTCTT 57.049 36.000 6.80 11.27 0.00 2.85
2538 5069 2.230750 ACGAGTTACTCCCTCTTTTCCG 59.769 50.000 6.80 0.00 0.00 4.30
2700 5232 9.603921 ATGATTGGATTTTGGAAACATTGATAC 57.396 29.630 0.00 0.00 42.32 2.24
2799 5337 3.299503 ACATTATTTGCTGGGTGGATCC 58.700 45.455 4.20 4.20 0.00 3.36
2801 5339 3.756082 TTATTTGCTGGGTGGATCCTT 57.244 42.857 14.23 0.00 36.25 3.36
2810 5348 4.811063 GCTGGGTGGATCCTTTTATATCCC 60.811 50.000 14.23 11.40 40.91 3.85
2823 5361 9.182642 TCCTTTTATATCCCAACTATCAGGAAT 57.817 33.333 0.00 0.00 32.26 3.01
2833 5371 6.998074 CCCAACTATCAGGAATGCTGTTATAA 59.002 38.462 0.85 0.00 0.00 0.98
2834 5372 7.041098 CCCAACTATCAGGAATGCTGTTATAAC 60.041 40.741 8.75 8.75 0.00 1.89
2838 5376 5.270893 TCAGGAATGCTGTTATAACGCTA 57.729 39.130 23.27 14.89 32.44 4.26
2856 5394 2.094545 GCTAACCTTGCTTCCAATGTGG 60.095 50.000 0.00 0.00 39.43 4.17
2878 5417 4.906065 CAACAGCTATTGCACCACATAT 57.094 40.909 1.12 0.00 42.74 1.78
2879 5418 4.852138 CAACAGCTATTGCACCACATATC 58.148 43.478 1.12 0.00 42.74 1.63
2880 5419 4.155063 ACAGCTATTGCACCACATATCA 57.845 40.909 1.12 0.00 42.74 2.15
2881 5420 4.722220 ACAGCTATTGCACCACATATCAT 58.278 39.130 1.12 0.00 42.74 2.45
2882 5421 4.517832 ACAGCTATTGCACCACATATCATG 59.482 41.667 1.12 0.00 42.74 3.07
2883 5422 4.517832 CAGCTATTGCACCACATATCATGT 59.482 41.667 1.12 0.00 42.72 3.21
2884 5423 5.009310 CAGCTATTGCACCACATATCATGTT 59.991 40.000 1.12 0.00 41.04 2.71
2885 5424 5.595542 AGCTATTGCACCACATATCATGTTT 59.404 36.000 1.12 0.00 41.04 2.83
2886 5425 6.097270 AGCTATTGCACCACATATCATGTTTT 59.903 34.615 1.12 0.00 41.04 2.43
2887 5426 6.757947 GCTATTGCACCACATATCATGTTTTT 59.242 34.615 0.00 0.00 39.34 1.94
2909 5448 5.964958 TTTCGAGAAAATGCAAAGGATCT 57.035 34.783 0.00 0.00 0.00 2.75
2910 5449 5.964958 TTCGAGAAAATGCAAAGGATCTT 57.035 34.783 0.00 0.00 0.00 2.40
2911 5450 5.964958 TCGAGAAAATGCAAAGGATCTTT 57.035 34.783 0.00 0.00 0.00 2.52
2912 5451 5.702865 TCGAGAAAATGCAAAGGATCTTTG 58.297 37.500 14.07 14.07 0.00 2.77
2923 5462 5.864986 CAAAGGATCTTTGCATTTCATTGC 58.135 37.500 7.35 0.00 43.07 3.56
2924 5463 3.777478 AGGATCTTTGCATTTCATTGCG 58.223 40.909 0.00 0.00 45.77 4.85
2925 5464 3.194116 AGGATCTTTGCATTTCATTGCGT 59.806 39.130 0.00 0.00 45.77 5.24
2926 5465 3.928375 GGATCTTTGCATTTCATTGCGTT 59.072 39.130 0.00 0.00 45.77 4.84
2927 5466 4.201647 GGATCTTTGCATTTCATTGCGTTG 60.202 41.667 0.00 0.00 45.77 4.10
2928 5467 3.974912 TCTTTGCATTTCATTGCGTTGA 58.025 36.364 0.00 0.00 45.77 3.18
2929 5468 4.366586 TCTTTGCATTTCATTGCGTTGAA 58.633 34.783 0.00 0.00 45.77 2.69
2930 5469 4.807834 TCTTTGCATTTCATTGCGTTGAAA 59.192 33.333 14.06 14.06 46.46 2.69
2931 5470 5.292834 TCTTTGCATTTCATTGCGTTGAAAA 59.707 32.000 15.25 0.55 45.77 2.29
2932 5471 4.712191 TGCATTTCATTGCGTTGAAAAG 57.288 36.364 15.25 12.70 45.77 2.27
2933 5472 4.366586 TGCATTTCATTGCGTTGAAAAGA 58.633 34.783 15.25 3.28 45.77 2.52
2934 5473 4.208873 TGCATTTCATTGCGTTGAAAAGAC 59.791 37.500 15.25 9.71 45.77 3.01
2935 5474 4.661402 GCATTTCATTGCGTTGAAAAGACG 60.661 41.667 15.25 7.83 45.77 4.18
2936 5475 2.679355 TCATTGCGTTGAAAAGACGG 57.321 45.000 0.00 0.00 40.66 4.79
2937 5476 1.265635 TCATTGCGTTGAAAAGACGGG 59.734 47.619 0.00 0.00 40.66 5.28
2938 5477 1.265635 CATTGCGTTGAAAAGACGGGA 59.734 47.619 0.00 0.00 40.66 5.14
2939 5478 1.380524 TTGCGTTGAAAAGACGGGAA 58.619 45.000 0.00 0.00 40.66 3.97
2940 5479 0.658897 TGCGTTGAAAAGACGGGAAC 59.341 50.000 0.00 0.00 40.66 3.62
2941 5480 0.658897 GCGTTGAAAAGACGGGAACA 59.341 50.000 0.00 0.00 40.66 3.18
2942 5481 1.596220 GCGTTGAAAAGACGGGAACAC 60.596 52.381 0.00 0.00 40.66 3.32
2943 5482 1.003223 CGTTGAAAAGACGGGAACACC 60.003 52.381 0.00 0.00 36.90 4.16
2944 5483 2.018515 GTTGAAAAGACGGGAACACCA 58.981 47.619 0.00 0.00 40.22 4.17
2945 5484 1.670791 TGAAAAGACGGGAACACCAC 58.329 50.000 0.00 0.00 40.22 4.16
2946 5485 1.065345 TGAAAAGACGGGAACACCACA 60.065 47.619 0.00 0.00 40.22 4.17
2947 5486 2.227194 GAAAAGACGGGAACACCACAT 58.773 47.619 0.00 0.00 40.22 3.21
2948 5487 3.181453 TGAAAAGACGGGAACACCACATA 60.181 43.478 0.00 0.00 40.22 2.29
2949 5488 3.713826 AAAGACGGGAACACCACATAT 57.286 42.857 0.00 0.00 40.22 1.78
2950 5489 2.981859 AGACGGGAACACCACATATC 57.018 50.000 0.00 0.00 40.22 1.63
2974 5513 7.950512 TCATGTTTGATAGTTTGTTGTCCATT 58.049 30.769 0.00 0.00 0.00 3.16
3027 5566 3.365472 AGAAATGGGGTTGATTGGCTAC 58.635 45.455 0.00 0.00 0.00 3.58
3042 5581 1.840635 GGCTACTCACCCAGAAGGATT 59.159 52.381 0.00 0.00 39.89 3.01
3043 5582 2.239907 GGCTACTCACCCAGAAGGATTT 59.760 50.000 0.00 0.00 39.89 2.17
3044 5583 3.274288 GCTACTCACCCAGAAGGATTTG 58.726 50.000 0.00 0.00 39.89 2.32
3045 5584 3.307762 GCTACTCACCCAGAAGGATTTGT 60.308 47.826 0.00 0.00 39.89 2.83
3060 5599 8.137437 AGAAGGATTTGTAATTGATAATTGCCG 58.863 33.333 0.00 0.00 33.23 5.69
3061 5600 6.215845 AGGATTTGTAATTGATAATTGCCGC 58.784 36.000 0.00 0.00 33.23 6.53
3095 5634 3.242867 TCTCTTCTGTGACCAAGGATGT 58.757 45.455 0.00 0.00 0.00 3.06
3175 5722 8.611051 AGGTAACAGAGGTTATTGAACTATCT 57.389 34.615 0.00 0.00 41.28 1.98
3177 5724 9.099454 GGTAACAGAGGTTATTGAACTATCTTG 57.901 37.037 0.00 0.00 41.28 3.02
3227 5774 2.882137 TGGTACAGTAAGTTGCTTTGGC 59.118 45.455 0.00 0.00 39.26 4.52
3243 6655 3.931907 TTGGCCTTACAGCTGTATGAT 57.068 42.857 31.11 9.80 0.00 2.45
3266 6703 5.486735 TTTTTAGACCCCACGTATCTGAA 57.513 39.130 0.00 0.00 0.00 3.02
3267 6704 5.687166 TTTTAGACCCCACGTATCTGAAT 57.313 39.130 0.00 0.00 0.00 2.57
3268 6705 5.687166 TTTAGACCCCACGTATCTGAATT 57.313 39.130 0.00 0.00 0.00 2.17
3269 6706 3.821421 AGACCCCACGTATCTGAATTC 57.179 47.619 0.00 0.00 0.00 2.17
3270 6707 3.104512 AGACCCCACGTATCTGAATTCA 58.895 45.455 8.12 8.12 0.00 2.57
3271 6708 3.711704 AGACCCCACGTATCTGAATTCAT 59.288 43.478 8.96 0.00 0.00 2.57
3272 6709 4.164221 AGACCCCACGTATCTGAATTCATT 59.836 41.667 8.96 2.48 0.00 2.57
3273 6710 4.451900 ACCCCACGTATCTGAATTCATTC 58.548 43.478 8.96 0.00 37.31 2.67
3274 6711 4.164221 ACCCCACGTATCTGAATTCATTCT 59.836 41.667 8.96 0.00 37.67 2.40
3275 6712 5.365605 ACCCCACGTATCTGAATTCATTCTA 59.634 40.000 8.96 0.00 37.67 2.10
3276 6713 6.126883 ACCCCACGTATCTGAATTCATTCTAA 60.127 38.462 8.96 0.00 37.67 2.10
3277 6714 6.936900 CCCCACGTATCTGAATTCATTCTAAT 59.063 38.462 8.96 1.31 37.67 1.73
3315 6753 9.239551 GGTTTAGGGTTTTATGTATCAACTCTT 57.760 33.333 0.00 0.00 33.20 2.85
3409 6847 0.722469 CAGTTAAAGCGTGCACAGCG 60.722 55.000 18.64 3.96 40.04 5.18
3477 6915 0.863144 GCTGTAAGTTTTCGGCGTCA 59.137 50.000 6.85 0.00 35.30 4.35
3478 6916 1.398071 GCTGTAAGTTTTCGGCGTCAC 60.398 52.381 6.85 2.04 35.30 3.67
3547 6985 8.746052 TTGTATAAATGTATTAGCAAGGCTGT 57.254 30.769 0.07 0.00 40.10 4.40
3548 6986 9.839817 TTGTATAAATGTATTAGCAAGGCTGTA 57.160 29.630 0.07 0.00 40.10 2.74
3549 6987 9.268268 TGTATAAATGTATTAGCAAGGCTGTAC 57.732 33.333 0.07 5.08 40.10 2.90
3550 6988 7.745620 ATAAATGTATTAGCAAGGCTGTACC 57.254 36.000 0.07 0.00 40.10 3.34
3562 7000 3.646736 GGCTGTACCTCCTGGTTATTT 57.353 47.619 0.00 0.00 46.05 1.40
3570 7008 9.238368 CTGTACCTCCTGGTTATTTTCAAAATA 57.762 33.333 0.00 0.00 46.05 1.40
3592 7031 9.851686 AAATAATATAGCTGTTCCAGTTCATGA 57.148 29.630 0.00 0.00 33.43 3.07
3733 7172 6.857437 TGACAGTGAAGATGAGGAAGATAA 57.143 37.500 0.00 0.00 0.00 1.75
3734 7173 6.871844 TGACAGTGAAGATGAGGAAGATAAG 58.128 40.000 0.00 0.00 0.00 1.73
3811 7250 9.265901 CTACATTAGTCGATTTGGATGAGATTT 57.734 33.333 0.00 0.00 0.00 2.17
4007 7725 3.504906 CCAGTCTTGGCATGCCTATTATG 59.495 47.826 35.53 25.92 37.73 1.90
4008 7726 4.392047 CAGTCTTGGCATGCCTATTATGA 58.608 43.478 35.53 19.96 36.94 2.15
4013 7731 6.430925 GTCTTGGCATGCCTATTATGATGTTA 59.569 38.462 35.53 9.43 36.94 2.41
4017 7735 5.707298 GGCATGCCTATTATGATGTTAGTGT 59.293 40.000 29.98 0.00 0.00 3.55
4114 7832 4.828072 AGTACACCCCTTCTCTTCAATC 57.172 45.455 0.00 0.00 0.00 2.67
4115 7833 4.430441 AGTACACCCCTTCTCTTCAATCT 58.570 43.478 0.00 0.00 0.00 2.40
4129 7847 2.783135 TCAATCTTCTGCACCAAGACC 58.217 47.619 5.64 0.00 32.65 3.85
4202 7921 4.340666 TGTTTCCTGATTTTAGCACAAGCA 59.659 37.500 0.00 0.00 45.49 3.91
4231 7951 3.057734 CACTCGTAGTTCAAACTCACCC 58.942 50.000 0.00 0.00 40.37 4.61
4238 7958 5.008217 CGTAGTTCAAACTCACCCAAATGAA 59.992 40.000 0.00 0.00 40.37 2.57
4239 7959 5.520376 AGTTCAAACTCACCCAAATGAAG 57.480 39.130 0.00 0.00 32.86 3.02
4241 7961 5.835280 AGTTCAAACTCACCCAAATGAAGAT 59.165 36.000 0.00 0.00 32.86 2.40
4242 7962 7.004086 AGTTCAAACTCACCCAAATGAAGATA 58.996 34.615 0.00 0.00 32.86 1.98
4243 7963 7.671398 AGTTCAAACTCACCCAAATGAAGATAT 59.329 33.333 0.00 0.00 32.86 1.63
4244 7964 7.395190 TCAAACTCACCCAAATGAAGATATG 57.605 36.000 0.00 0.00 0.00 1.78
4245 7965 6.947733 TCAAACTCACCCAAATGAAGATATGT 59.052 34.615 0.00 0.00 0.00 2.29
4246 7966 7.451255 TCAAACTCACCCAAATGAAGATATGTT 59.549 33.333 0.00 0.00 0.00 2.71
4247 7967 7.781324 AACTCACCCAAATGAAGATATGTTT 57.219 32.000 0.00 0.00 0.00 2.83
4248 7968 7.396540 ACTCACCCAAATGAAGATATGTTTC 57.603 36.000 0.00 0.00 0.00 2.78
4249 7969 6.947733 ACTCACCCAAATGAAGATATGTTTCA 59.052 34.615 2.65 2.65 38.76 2.69
4250 7970 7.451255 ACTCACCCAAATGAAGATATGTTTCAA 59.549 33.333 3.99 0.00 38.01 2.69
4251 7971 7.829725 TCACCCAAATGAAGATATGTTTCAAG 58.170 34.615 3.99 0.00 38.01 3.02
4252 7972 7.451255 TCACCCAAATGAAGATATGTTTCAAGT 59.549 33.333 3.99 0.00 38.01 3.16
4253 7973 8.090214 CACCCAAATGAAGATATGTTTCAAGTT 58.910 33.333 3.99 0.63 38.01 2.66
4254 7974 8.306761 ACCCAAATGAAGATATGTTTCAAGTTC 58.693 33.333 3.99 0.00 38.01 3.01
4255 7975 7.485913 CCCAAATGAAGATATGTTTCAAGTTCG 59.514 37.037 3.99 0.00 38.01 3.95
4256 7976 7.008628 CCAAATGAAGATATGTTTCAAGTTCGC 59.991 37.037 3.99 0.00 38.01 4.70
4257 7977 6.992063 ATGAAGATATGTTTCAAGTTCGCT 57.008 33.333 3.99 0.00 38.01 4.93
4271 7991 7.311364 TCAAGTTCGCTAGTTAAACAAAGTT 57.689 32.000 0.00 0.00 0.00 2.66
4338 8058 8.418662 AGAAAGGCTACGTTTAAAATTTCCTTT 58.581 29.630 16.17 16.17 42.17 3.11
4339 8059 7.940178 AAGGCTACGTTTAAAATTTCCTTTG 57.060 32.000 0.00 0.00 0.00 2.77
4340 8060 7.279750 AGGCTACGTTTAAAATTTCCTTTGA 57.720 32.000 0.00 0.00 0.00 2.69
4342 8062 8.364894 AGGCTACGTTTAAAATTTCCTTTGATT 58.635 29.630 0.00 0.00 0.00 2.57
4343 8063 8.984764 GGCTACGTTTAAAATTTCCTTTGATTT 58.015 29.630 0.00 0.00 0.00 2.17
4344 8064 9.791838 GCTACGTTTAAAATTTCCTTTGATTTG 57.208 29.630 0.00 0.00 0.00 2.32
4370 8090 2.734606 CGTTTGAGGCTGACACGATTAA 59.265 45.455 6.83 0.00 32.51 1.40
4381 8101 5.029807 TGACACGATTAAATATGAGGGCA 57.970 39.130 0.00 0.00 0.00 5.36
4470 8191 1.278985 CAGTTCATCTAGCCCACCACA 59.721 52.381 0.00 0.00 0.00 4.17
4471 8192 1.985159 AGTTCATCTAGCCCACCACAA 59.015 47.619 0.00 0.00 0.00 3.33
4472 8193 2.084546 GTTCATCTAGCCCACCACAAC 58.915 52.381 0.00 0.00 0.00 3.32
4478 8199 1.004745 CTAGCCCACCACAACCATCTT 59.995 52.381 0.00 0.00 0.00 2.40
4479 8200 1.072266 AGCCCACCACAACCATCTTA 58.928 50.000 0.00 0.00 0.00 2.10
4480 8201 1.173913 GCCCACCACAACCATCTTAC 58.826 55.000 0.00 0.00 0.00 2.34
4484 8205 0.326927 ACCACAACCATCTTACCCCG 59.673 55.000 0.00 0.00 0.00 5.73
4519 8240 2.297033 CCACCCCTCACTGTCAATTTTG 59.703 50.000 0.00 0.00 0.00 2.44
4521 8242 1.895131 CCCCTCACTGTCAATTTTGGG 59.105 52.381 0.00 0.00 0.00 4.12
4522 8243 2.597455 CCCTCACTGTCAATTTTGGGT 58.403 47.619 0.00 0.00 0.00 4.51
4523 8244 3.499563 CCCCTCACTGTCAATTTTGGGTA 60.500 47.826 0.00 0.00 0.00 3.69
4524 8245 4.148838 CCCTCACTGTCAATTTTGGGTAA 58.851 43.478 0.00 0.00 0.00 2.85
4553 8274 7.337942 CCTAGGACAAATGCAAGAAACTCTAAT 59.662 37.037 1.05 0.00 0.00 1.73
4584 8305 1.203440 ACCCACCCCACAGATCTAACT 60.203 52.381 0.00 0.00 0.00 2.24
4593 8314 4.712337 CCCACAGATCTAACTACCTCAAGT 59.288 45.833 0.00 0.00 0.00 3.16
4596 8317 6.295349 CCACAGATCTAACTACCTCAAGTTGT 60.295 42.308 2.11 0.00 39.95 3.32
4599 8320 4.778534 TCTAACTACCTCAAGTTGTCGG 57.221 45.455 2.11 7.50 39.95 4.79
4601 8322 2.005370 ACTACCTCAAGTTGTCGGGA 57.995 50.000 15.17 8.26 27.17 5.14
4658 8379 3.243737 GGATTGTGGTGACAAGGAAAACC 60.244 47.826 0.00 0.00 45.29 3.27
4665 8386 4.010349 GGTGACAAGGAAAACCTAGATGG 58.990 47.826 0.00 0.00 42.93 3.51
4667 8388 2.678336 GACAAGGAAAACCTAGATGGCG 59.322 50.000 0.00 0.00 40.22 5.69
4711 8432 1.001597 CCGCGTCACTAGATAGAACCC 60.002 57.143 4.92 0.00 0.00 4.11
4712 8433 1.674441 CGCGTCACTAGATAGAACCCA 59.326 52.381 0.00 0.00 0.00 4.51
4713 8434 2.541178 CGCGTCACTAGATAGAACCCAC 60.541 54.545 0.00 0.00 0.00 4.61
4714 8435 2.541178 GCGTCACTAGATAGAACCCACG 60.541 54.545 0.00 0.00 0.00 4.94
4715 8436 2.033049 CGTCACTAGATAGAACCCACGG 59.967 54.545 0.00 0.00 0.00 4.94
4716 8437 2.361438 GTCACTAGATAGAACCCACGGG 59.639 54.545 0.00 0.00 42.03 5.28
4717 8438 2.242965 TCACTAGATAGAACCCACGGGA 59.757 50.000 9.72 0.00 38.96 5.14
4718 8439 2.361438 CACTAGATAGAACCCACGGGAC 59.639 54.545 9.72 2.54 38.96 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
243 255 2.000447 GTGTCATGGGTAACGCTTCTC 59.000 52.381 0.00 0.00 37.60 2.87
244 256 1.338769 GGTGTCATGGGTAACGCTTCT 60.339 52.381 0.00 0.00 37.60 2.85
245 257 1.084289 GGTGTCATGGGTAACGCTTC 58.916 55.000 0.00 0.00 37.60 3.86
246 258 0.672401 CGGTGTCATGGGTAACGCTT 60.672 55.000 0.00 0.00 37.60 4.68
247 259 1.079405 CGGTGTCATGGGTAACGCT 60.079 57.895 0.00 0.00 37.60 5.07
248 260 2.746803 GCGGTGTCATGGGTAACGC 61.747 63.158 10.45 10.45 38.70 4.84
495 507 0.529378 CCACTCATTGCCTTTCCAGC 59.471 55.000 0.00 0.00 0.00 4.85
511 523 1.756430 GGCTTCTTCTCCAATCCCAC 58.244 55.000 0.00 0.00 0.00 4.61
576 588 1.454201 GAGGGGAGGAAAAGAAAGCG 58.546 55.000 0.00 0.00 0.00 4.68
613 628 0.045162 ACCGGATCCCCTTCCCTTAA 59.955 55.000 9.46 0.00 31.61 1.85
660 676 2.284699 CCGGGGAGTGGGAAGACT 60.285 66.667 0.00 0.00 0.00 3.24
717 733 1.173913 GGGAATGCGCCTACTTGTTT 58.826 50.000 4.18 0.00 0.00 2.83
722 738 0.179000 CTCTTGGGAATGCGCCTACT 59.821 55.000 4.18 0.00 0.00 2.57
724 740 1.138266 GTACTCTTGGGAATGCGCCTA 59.862 52.381 4.18 0.00 0.00 3.93
730 781 2.483188 GGGTAGCGTACTCTTGGGAATG 60.483 54.545 0.00 0.00 0.00 2.67
735 786 1.318158 ACCGGGTAGCGTACTCTTGG 61.318 60.000 6.32 0.00 0.00 3.61
776 831 3.706373 CAGTCCTCCCCCACACGG 61.706 72.222 0.00 0.00 0.00 4.94
777 832 3.706373 CCAGTCCTCCCCCACACG 61.706 72.222 0.00 0.00 0.00 4.49
779 834 2.203938 GTCCAGTCCTCCCCCACA 60.204 66.667 0.00 0.00 0.00 4.17
781 836 2.122729 CAGTCCAGTCCTCCCCCA 59.877 66.667 0.00 0.00 0.00 4.96
783 838 1.687493 CTCCAGTCCAGTCCTCCCC 60.687 68.421 0.00 0.00 0.00 4.81
788 843 1.612395 CCAGCTCTCCAGTCCAGTCC 61.612 65.000 0.00 0.00 0.00 3.85
797 852 2.363018 CGGGTCTCCAGCTCTCCA 60.363 66.667 0.00 0.00 0.00 3.86
800 855 0.847373 TATCTCGGGTCTCCAGCTCT 59.153 55.000 0.00 0.00 0.00 4.09
801 856 1.816224 GATATCTCGGGTCTCCAGCTC 59.184 57.143 0.00 0.00 0.00 4.09
802 857 1.884497 CGATATCTCGGGTCTCCAGCT 60.884 57.143 0.34 0.00 41.27 4.24
813 868 2.289565 TCCGATGGATCCGATATCTCG 58.710 52.381 7.39 8.22 44.62 4.04
1170 1231 3.453717 CCTTGATGAGTGAGGAGATGGAA 59.546 47.826 0.00 0.00 32.11 3.53
1182 1243 2.579201 CGGCCGACCTTGATGAGT 59.421 61.111 24.07 0.00 0.00 3.41
1467 1528 0.103208 CCTCGTAGGTGAGCACATCC 59.897 60.000 2.75 0.00 34.56 3.51
1541 1602 5.973565 GTGCATGCATCAGAATTACTAAACC 59.026 40.000 25.64 0.00 0.00 3.27
2097 4617 2.747989 GGCAGAAACAGGGTTAACTAGC 59.252 50.000 5.42 0.00 0.00 3.42
2128 4648 8.034804 GCAACCCAAAGTGTTCAATTATATCTT 58.965 33.333 0.00 0.00 0.00 2.40
2129 4649 7.397192 AGCAACCCAAAGTGTTCAATTATATCT 59.603 33.333 0.00 0.00 0.00 1.98
2258 4786 3.630769 TGTCGAGAGTTTGTGTAGTCAGT 59.369 43.478 0.00 0.00 0.00 3.41
2292 4820 3.623906 TCATGGAAAGAGGCTGAAGAG 57.376 47.619 0.00 0.00 0.00 2.85
2329 4857 4.667573 TCAATCGAGCAGGATACCTAGAT 58.332 43.478 0.00 0.00 29.64 1.98
2358 4886 8.419442 AGCATCCTTCCAAATAAAAATCAGATC 58.581 33.333 0.00 0.00 0.00 2.75
2403 4932 7.383102 AGCTTAGTGTGATTGTTAAATCCTG 57.617 36.000 0.00 0.00 41.40 3.86
2405 4934 9.774742 CTAAAGCTTAGTGTGATTGTTAAATCC 57.225 33.333 0.00 0.00 41.40 3.01
2476 5006 8.993121 TGACACATTAGAAGCTTCTTTCTAAAG 58.007 33.333 32.70 19.50 46.78 1.85
2503 5033 9.247126 GGGAGTAACTCGTAATCTTAAATCTTC 57.753 37.037 0.00 0.00 0.00 2.87
2504 5034 8.979534 AGGGAGTAACTCGTAATCTTAAATCTT 58.020 33.333 0.00 0.00 0.00 2.40
2700 5232 7.716612 ACTTTGACCAAGTTTATGGAGAAAAG 58.283 34.615 0.00 8.78 43.89 2.27
2753 5291 2.438021 CCCTCCGGTCCAAAATATCAGA 59.562 50.000 0.00 0.00 0.00 3.27
2786 5324 4.202567 GGATATAAAAGGATCCACCCAGCA 60.203 45.833 15.82 0.00 41.24 4.41
2799 5337 8.734386 GCATTCCTGATAGTTGGGATATAAAAG 58.266 37.037 0.00 0.00 0.00 2.27
2801 5339 7.884877 CAGCATTCCTGATAGTTGGGATATAAA 59.115 37.037 0.00 0.00 44.64 1.40
2810 5348 7.567571 CGTTATAACAGCATTCCTGATAGTTG 58.432 38.462 15.67 0.00 44.64 3.16
2823 5361 3.372822 GCAAGGTTAGCGTTATAACAGCA 59.627 43.478 24.22 13.47 37.38 4.41
2833 5371 1.812571 CATTGGAAGCAAGGTTAGCGT 59.187 47.619 0.00 0.00 37.01 5.07
2834 5372 1.812571 ACATTGGAAGCAAGGTTAGCG 59.187 47.619 0.00 0.00 37.01 4.26
2838 5376 0.681175 GCCACATTGGAAGCAAGGTT 59.319 50.000 0.00 0.00 40.96 3.50
2885 5424 6.748132 AGATCCTTTGCATTTTCTCGAAAAA 58.252 32.000 8.69 7.59 42.71 1.94
2886 5425 6.331369 AGATCCTTTGCATTTTCTCGAAAA 57.669 33.333 7.22 7.22 43.48 2.29
2887 5426 5.964958 AGATCCTTTGCATTTTCTCGAAA 57.035 34.783 0.00 0.00 0.00 3.46
2888 5427 5.964958 AAGATCCTTTGCATTTTCTCGAA 57.035 34.783 0.00 0.00 0.00 3.71
2889 5428 5.702865 CAAAGATCCTTTGCATTTTCTCGA 58.297 37.500 6.51 0.00 0.00 4.04
2900 5439 5.445407 CGCAATGAAATGCAAAGATCCTTTG 60.445 40.000 13.41 13.41 46.76 2.77
2901 5440 4.628333 CGCAATGAAATGCAAAGATCCTTT 59.372 37.500 0.00 0.00 46.76 3.11
2902 5441 4.178540 CGCAATGAAATGCAAAGATCCTT 58.821 39.130 0.00 0.00 46.76 3.36
2903 5442 3.194116 ACGCAATGAAATGCAAAGATCCT 59.806 39.130 0.00 0.00 46.76 3.24
2904 5443 3.514645 ACGCAATGAAATGCAAAGATCC 58.485 40.909 0.00 0.00 46.76 3.36
2905 5444 4.622313 TCAACGCAATGAAATGCAAAGATC 59.378 37.500 0.00 0.00 46.76 2.75
2906 5445 4.558178 TCAACGCAATGAAATGCAAAGAT 58.442 34.783 0.00 0.00 46.76 2.40
2907 5446 3.974912 TCAACGCAATGAAATGCAAAGA 58.025 36.364 0.00 0.00 46.76 2.52
2908 5447 4.712191 TTCAACGCAATGAAATGCAAAG 57.288 36.364 0.00 0.00 46.76 2.77
2909 5448 5.292834 TCTTTTCAACGCAATGAAATGCAAA 59.707 32.000 12.96 0.39 45.77 3.68
2910 5449 4.807834 TCTTTTCAACGCAATGAAATGCAA 59.192 33.333 12.96 0.68 45.77 4.08
2911 5450 4.208873 GTCTTTTCAACGCAATGAAATGCA 59.791 37.500 12.96 0.00 45.77 3.96
2912 5451 4.661402 CGTCTTTTCAACGCAATGAAATGC 60.661 41.667 12.96 10.64 45.77 3.56
2913 5452 4.143556 CCGTCTTTTCAACGCAATGAAATG 60.144 41.667 12.96 14.33 45.77 2.32
2914 5453 3.980775 CCGTCTTTTCAACGCAATGAAAT 59.019 39.130 12.96 0.00 45.77 2.17
2915 5454 3.367607 CCGTCTTTTCAACGCAATGAAA 58.632 40.909 9.22 9.22 45.07 2.69
2916 5455 2.287308 CCCGTCTTTTCAACGCAATGAA 60.287 45.455 0.00 0.00 38.77 2.57
2917 5456 1.265635 CCCGTCTTTTCAACGCAATGA 59.734 47.619 0.00 0.00 38.77 2.57
2918 5457 1.265635 TCCCGTCTTTTCAACGCAATG 59.734 47.619 0.00 0.00 38.77 2.82
2919 5458 1.600023 TCCCGTCTTTTCAACGCAAT 58.400 45.000 0.00 0.00 38.77 3.56
2920 5459 1.064357 GTTCCCGTCTTTTCAACGCAA 59.936 47.619 0.00 0.00 38.77 4.85
2921 5460 0.658897 GTTCCCGTCTTTTCAACGCA 59.341 50.000 0.00 0.00 38.77 5.24
2922 5461 0.658897 TGTTCCCGTCTTTTCAACGC 59.341 50.000 0.00 0.00 38.77 4.84
2923 5462 1.003223 GGTGTTCCCGTCTTTTCAACG 60.003 52.381 0.00 0.00 39.78 4.10
2924 5463 2.018515 TGGTGTTCCCGTCTTTTCAAC 58.981 47.619 0.00 0.00 35.15 3.18
2925 5464 2.018515 GTGGTGTTCCCGTCTTTTCAA 58.981 47.619 0.00 0.00 35.15 2.69
2926 5465 1.065345 TGTGGTGTTCCCGTCTTTTCA 60.065 47.619 0.00 0.00 35.15 2.69
2927 5466 1.670791 TGTGGTGTTCCCGTCTTTTC 58.329 50.000 0.00 0.00 35.15 2.29
2928 5467 2.358322 ATGTGGTGTTCCCGTCTTTT 57.642 45.000 0.00 0.00 35.15 2.27
2929 5468 3.008594 TGATATGTGGTGTTCCCGTCTTT 59.991 43.478 0.00 0.00 35.15 2.52
2930 5469 2.569853 TGATATGTGGTGTTCCCGTCTT 59.430 45.455 0.00 0.00 35.15 3.01
2931 5470 2.184533 TGATATGTGGTGTTCCCGTCT 58.815 47.619 0.00 0.00 35.15 4.18
2932 5471 2.684001 TGATATGTGGTGTTCCCGTC 57.316 50.000 0.00 0.00 35.15 4.79
2933 5472 2.238646 ACATGATATGTGGTGTTCCCGT 59.761 45.455 0.00 0.00 43.01 5.28
2934 5473 2.917933 ACATGATATGTGGTGTTCCCG 58.082 47.619 0.00 0.00 43.01 5.14
2935 5474 4.704540 TCAAACATGATATGTGGTGTTCCC 59.295 41.667 0.00 0.00 44.07 3.97
2936 5475 5.895636 TCAAACATGATATGTGGTGTTCC 57.104 39.130 0.00 0.00 44.07 3.62
2937 5476 8.213518 ACTATCAAACATGATATGTGGTGTTC 57.786 34.615 0.00 0.00 44.07 3.18
2938 5477 8.579850 AACTATCAAACATGATATGTGGTGTT 57.420 30.769 0.00 0.00 44.07 3.32
2939 5478 8.461222 CAAACTATCAAACATGATATGTGGTGT 58.539 33.333 0.00 0.00 44.07 4.16
2940 5479 8.461222 ACAAACTATCAAACATGATATGTGGTG 58.539 33.333 0.00 0.00 44.07 4.17
2941 5480 8.579850 ACAAACTATCAAACATGATATGTGGT 57.420 30.769 0.00 0.00 44.07 4.16
2942 5481 9.292846 CAACAAACTATCAAACATGATATGTGG 57.707 33.333 0.00 0.00 44.07 4.17
2943 5482 9.844790 ACAACAAACTATCAAACATGATATGTG 57.155 29.630 0.00 2.06 44.07 3.21
2945 5484 9.507280 GGACAACAAACTATCAAACATGATATG 57.493 33.333 0.00 0.00 31.24 1.78
2946 5485 9.241919 TGGACAACAAACTATCAAACATGATAT 57.758 29.630 0.00 0.00 31.24 1.63
2947 5486 8.628630 TGGACAACAAACTATCAAACATGATA 57.371 30.769 0.00 0.00 0.00 2.15
2948 5487 7.523293 TGGACAACAAACTATCAAACATGAT 57.477 32.000 0.00 0.00 0.00 2.45
2949 5488 6.951062 TGGACAACAAACTATCAAACATGA 57.049 33.333 0.00 0.00 0.00 3.07
2950 5489 9.859427 ATAATGGACAACAAACTATCAAACATG 57.141 29.630 0.00 0.00 0.00 3.21
2974 5513 7.661437 ACAATGAGAAACAGCAAACTACAGATA 59.339 33.333 0.00 0.00 0.00 1.98
3027 5566 5.945784 TCAATTACAAATCCTTCTGGGTGAG 59.054 40.000 0.00 0.00 36.25 3.51
3042 5581 4.095036 TGACGCGGCAATTATCAATTACAA 59.905 37.500 15.11 0.00 0.00 2.41
3043 5582 3.623510 TGACGCGGCAATTATCAATTACA 59.376 39.130 15.11 0.00 0.00 2.41
3044 5583 4.203950 TGACGCGGCAATTATCAATTAC 57.796 40.909 15.11 0.00 0.00 1.89
3045 5584 4.884458 TTGACGCGGCAATTATCAATTA 57.116 36.364 26.47 0.00 0.00 1.40
3060 5599 5.566774 CACAGAAGAGAATGAAATTTGACGC 59.433 40.000 0.00 0.00 36.07 5.19
3061 5600 6.794158 GTCACAGAAGAGAATGAAATTTGACG 59.206 38.462 0.00 0.00 36.07 4.35
3144 5686 7.414222 TCAATAACCTCTGTTACCTAATCGT 57.586 36.000 0.00 0.00 39.66 3.73
3145 5687 7.980099 AGTTCAATAACCTCTGTTACCTAATCG 59.020 37.037 0.00 0.00 39.66 3.34
3159 5701 9.606631 GACAGAATCAAGATAGTTCAATAACCT 57.393 33.333 0.00 0.00 36.15 3.50
3172 5719 8.078596 GCTTGTACAAAAAGACAGAATCAAGAT 58.921 33.333 10.03 0.00 33.00 2.40
3175 5722 6.972328 GTGCTTGTACAAAAAGACAGAATCAA 59.028 34.615 10.03 0.00 0.00 2.57
3177 5724 6.729187 AGTGCTTGTACAAAAAGACAGAATC 58.271 36.000 10.03 0.00 0.00 2.52
3179 5726 5.645929 TGAGTGCTTGTACAAAAAGACAGAA 59.354 36.000 10.03 0.00 0.00 3.02
3188 5735 5.590663 TGTACCATTTGAGTGCTTGTACAAA 59.409 36.000 10.03 0.00 35.48 2.83
3253 6690 7.875041 AGATTAGAATGAATTCAGATACGTGGG 59.125 37.037 14.54 0.00 39.23 4.61
3254 6691 8.824159 AGATTAGAATGAATTCAGATACGTGG 57.176 34.615 14.54 0.00 39.23 4.94
3255 6692 9.468532 TGAGATTAGAATGAATTCAGATACGTG 57.531 33.333 14.54 0.00 39.23 4.49
3256 6693 9.689976 CTGAGATTAGAATGAATTCAGATACGT 57.310 33.333 14.54 0.00 39.23 3.57
3257 6694 9.689976 ACTGAGATTAGAATGAATTCAGATACG 57.310 33.333 14.54 0.00 39.23 3.06
3272 6709 9.670442 ACCCTAAACCATAATACTGAGATTAGA 57.330 33.333 0.00 0.00 0.00 2.10
3275 6712 9.990868 AAAACCCTAAACCATAATACTGAGATT 57.009 29.630 0.00 0.00 0.00 2.40
3329 6767 9.617975 CAAGGAGAAACATACAAAAGAAGATTC 57.382 33.333 0.00 0.00 0.00 2.52
3409 6847 5.529581 TTCCCTTGTGTTTTTCAATCTCC 57.470 39.130 0.00 0.00 0.00 3.71
3521 6959 9.184523 ACAGCCTTGCTAATACATTTATACAAA 57.815 29.630 0.00 0.00 36.40 2.83
3522 6960 8.746052 ACAGCCTTGCTAATACATTTATACAA 57.254 30.769 0.00 0.00 36.40 2.41
3523 6961 9.268268 GTACAGCCTTGCTAATACATTTATACA 57.732 33.333 0.00 0.00 36.40 2.29
3616 7055 6.934645 CCTCTCACTCACCTGTTTACAAAATA 59.065 38.462 0.00 0.00 0.00 1.40
3733 7172 0.608640 GTCGATATCGCCCATTCCCT 59.391 55.000 20.34 0.00 39.60 4.20
3734 7173 0.391263 GGTCGATATCGCCCATTCCC 60.391 60.000 19.81 7.14 37.34 3.97
3811 7250 4.486125 TCTTGGCTGATGCTATACAACA 57.514 40.909 0.00 0.00 39.59 3.33
3943 7382 9.634163 GTTTAGAAAACAAAACTCCAAAGAGAA 57.366 29.630 0.00 0.00 43.39 2.87
3949 7388 8.145122 ACACTTGTTTAGAAAACAAAACTCCAA 58.855 29.630 16.24 0.00 39.36 3.53
3951 7390 8.528917 AACACTTGTTTAGAAAACAAAACTCC 57.471 30.769 16.24 0.00 39.36 3.85
3958 7397 8.439286 GCATCAAAAACACTTGTTTAGAAAACA 58.561 29.630 7.75 1.21 46.47 2.83
3959 7398 7.902917 GGCATCAAAAACACTTGTTTAGAAAAC 59.097 33.333 7.75 0.00 46.47 2.43
3960 7399 7.065204 GGGCATCAAAAACACTTGTTTAGAAAA 59.935 33.333 7.75 0.00 46.47 2.29
3961 7400 6.536941 GGGCATCAAAAACACTTGTTTAGAAA 59.463 34.615 7.75 0.00 46.47 2.52
4007 7725 7.869937 ACTAGATGCACATGATACACTAACATC 59.130 37.037 0.00 0.00 33.31 3.06
4008 7726 7.730084 ACTAGATGCACATGATACACTAACAT 58.270 34.615 0.00 0.00 0.00 2.71
4013 7731 6.183360 TGCTTACTAGATGCACATGATACACT 60.183 38.462 0.00 0.00 33.49 3.55
4017 7735 6.996509 TGATGCTTACTAGATGCACATGATA 58.003 36.000 0.00 0.00 40.71 2.15
4094 7812 4.828072 AGATTGAAGAGAAGGGGTGTAC 57.172 45.455 0.00 0.00 0.00 2.90
4095 7813 5.046304 CAGAAGATTGAAGAGAAGGGGTGTA 60.046 44.000 0.00 0.00 0.00 2.90
4096 7814 3.913163 AGAAGATTGAAGAGAAGGGGTGT 59.087 43.478 0.00 0.00 0.00 4.16
4097 7815 4.260170 CAGAAGATTGAAGAGAAGGGGTG 58.740 47.826 0.00 0.00 0.00 4.61
4098 7816 3.308046 GCAGAAGATTGAAGAGAAGGGGT 60.308 47.826 0.00 0.00 0.00 4.95
4099 7817 3.277715 GCAGAAGATTGAAGAGAAGGGG 58.722 50.000 0.00 0.00 0.00 4.79
4114 7832 0.890996 GGTGGGTCTTGGTGCAGAAG 60.891 60.000 0.00 0.00 0.00 2.85
4115 7833 1.150536 GGTGGGTCTTGGTGCAGAA 59.849 57.895 0.00 0.00 0.00 3.02
4129 7847 0.967380 GAATGTGGGCTTGGAGGTGG 60.967 60.000 0.00 0.00 0.00 4.61
4202 7921 9.121658 TGAGTTTGAACTACGAGTGATATCTAT 57.878 33.333 3.98 0.00 39.88 1.98
4231 7951 7.752239 AGCGAACTTGAAACATATCTTCATTTG 59.248 33.333 0.00 0.00 32.98 2.32
4238 7958 8.997621 TTAACTAGCGAACTTGAAACATATCT 57.002 30.769 0.00 0.00 0.00 1.98
4239 7959 9.474249 GTTTAACTAGCGAACTTGAAACATATC 57.526 33.333 0.00 0.00 0.00 1.63
4241 7961 8.367943 TGTTTAACTAGCGAACTTGAAACATA 57.632 30.769 0.00 0.00 32.29 2.29
4242 7962 7.254227 TGTTTAACTAGCGAACTTGAAACAT 57.746 32.000 0.00 0.00 32.29 2.71
4243 7963 6.665474 TGTTTAACTAGCGAACTTGAAACA 57.335 33.333 0.00 0.00 34.22 2.83
4244 7964 7.695201 ACTTTGTTTAACTAGCGAACTTGAAAC 59.305 33.333 0.00 0.00 0.00 2.78
4245 7965 7.754625 ACTTTGTTTAACTAGCGAACTTGAAA 58.245 30.769 0.00 0.00 0.00 2.69
4246 7966 7.311364 ACTTTGTTTAACTAGCGAACTTGAA 57.689 32.000 0.00 0.00 0.00 2.69
4247 7967 6.913873 ACTTTGTTTAACTAGCGAACTTGA 57.086 33.333 0.00 0.00 0.00 3.02
4248 7968 6.631636 GGAACTTTGTTTAACTAGCGAACTTG 59.368 38.462 0.00 0.00 0.00 3.16
4249 7969 6.316890 TGGAACTTTGTTTAACTAGCGAACTT 59.683 34.615 0.00 0.00 0.00 2.66
4250 7970 5.818857 TGGAACTTTGTTTAACTAGCGAACT 59.181 36.000 0.00 0.00 0.00 3.01
4251 7971 6.051646 TGGAACTTTGTTTAACTAGCGAAC 57.948 37.500 0.00 0.00 0.00 3.95
4252 7972 6.680874 TTGGAACTTTGTTTAACTAGCGAA 57.319 33.333 0.00 0.00 0.00 4.70
4253 7973 6.870971 ATTGGAACTTTGTTTAACTAGCGA 57.129 33.333 0.00 0.00 0.00 4.93
4254 7974 8.025243 TCTATTGGAACTTTGTTTAACTAGCG 57.975 34.615 0.00 0.00 0.00 4.26
4296 8016 9.067986 GTAGCCTTTCTATAAAATAACATGGCT 57.932 33.333 0.00 0.00 46.12 4.75
4335 8055 4.787598 CCTCAAACGACTCCAAATCAAAG 58.212 43.478 0.00 0.00 0.00 2.77
4338 8058 2.151202 GCCTCAAACGACTCCAAATCA 58.849 47.619 0.00 0.00 0.00 2.57
4339 8059 2.160417 CAGCCTCAAACGACTCCAAATC 59.840 50.000 0.00 0.00 0.00 2.17
4340 8060 2.154462 CAGCCTCAAACGACTCCAAAT 58.846 47.619 0.00 0.00 0.00 2.32
4342 8062 0.756294 TCAGCCTCAAACGACTCCAA 59.244 50.000 0.00 0.00 0.00 3.53
4343 8063 0.033504 GTCAGCCTCAAACGACTCCA 59.966 55.000 0.00 0.00 0.00 3.86
4344 8064 0.033504 TGTCAGCCTCAAACGACTCC 59.966 55.000 0.00 0.00 0.00 3.85
4345 8065 1.140816 GTGTCAGCCTCAAACGACTC 58.859 55.000 0.00 0.00 0.00 3.36
4430 8151 1.722034 CTTATGGGAGAGGGCTAGCA 58.278 55.000 18.24 0.00 0.00 3.49
4470 8191 1.077716 GCAGCGGGGTAAGATGGTT 60.078 57.895 0.00 0.00 0.00 3.67
4471 8192 0.689745 TAGCAGCGGGGTAAGATGGT 60.690 55.000 0.00 0.00 39.18 3.55
4472 8193 0.687354 ATAGCAGCGGGGTAAGATGG 59.313 55.000 0.00 0.00 32.33 3.51
4498 8219 2.292828 AAATTGACAGTGAGGGGTGG 57.707 50.000 0.00 0.00 0.00 4.61
4501 8222 1.895131 CCCAAAATTGACAGTGAGGGG 59.105 52.381 0.00 0.00 0.00 4.79
4507 8228 6.266786 CCTAGGTTTTACCCAAAATTGACAGT 59.733 38.462 0.00 0.00 39.75 3.55
4519 8240 4.083565 TGCATTTGTCCTAGGTTTTACCC 58.916 43.478 9.08 0.00 39.75 3.69
4521 8242 6.569179 TCTTGCATTTGTCCTAGGTTTTAC 57.431 37.500 9.08 0.00 0.00 2.01
4522 8243 7.286775 AGTTTCTTGCATTTGTCCTAGGTTTTA 59.713 33.333 9.08 0.00 0.00 1.52
4523 8244 6.098266 AGTTTCTTGCATTTGTCCTAGGTTTT 59.902 34.615 9.08 0.00 0.00 2.43
4524 8245 5.598417 AGTTTCTTGCATTTGTCCTAGGTTT 59.402 36.000 9.08 0.00 0.00 3.27
4553 8274 3.712907 GGTGGGTTGCGGCTAGGA 61.713 66.667 0.00 0.00 0.00 2.94
4584 8305 2.496070 CAGATCCCGACAACTTGAGGTA 59.504 50.000 0.00 0.00 0.00 3.08
4617 8338 0.321021 CAGTGTCTTGCCTCTGCTCT 59.679 55.000 0.00 0.00 38.71 4.09
4658 8379 2.923426 TTTCCAGCGCCGCCATCTAG 62.923 60.000 4.98 0.00 0.00 2.43
4665 8386 4.770874 TAGGGTTTCCAGCGCCGC 62.771 66.667 2.29 0.00 34.83 6.53
4667 8388 0.533085 GATCTAGGGTTTCCAGCGCC 60.533 60.000 2.29 0.00 34.83 6.53
4695 8416 2.361438 CCCGTGGGTTCTATCTAGTGAC 59.639 54.545 0.00 0.00 0.00 3.67
4711 8432 2.287393 TGATACACATTCGTCCCGTG 57.713 50.000 0.00 0.00 36.70 4.94
4712 8433 2.429250 TCATGATACACATTCGTCCCGT 59.571 45.455 0.00 0.00 37.07 5.28
4713 8434 3.052745 CTCATGATACACATTCGTCCCG 58.947 50.000 0.00 0.00 37.07 5.14
4714 8435 4.322080 TCTCATGATACACATTCGTCCC 57.678 45.455 0.00 0.00 37.07 4.46
4715 8436 6.851222 AAATCTCATGATACACATTCGTCC 57.149 37.500 0.00 0.00 37.07 4.79
4716 8437 7.909267 TGAAAATCTCATGATACACATTCGTC 58.091 34.615 0.00 0.00 37.07 4.20
4717 8438 7.848223 TGAAAATCTCATGATACACATTCGT 57.152 32.000 0.00 0.00 37.07 3.85
4718 8439 8.771766 AGATGAAAATCTCATGATACACATTCG 58.228 33.333 0.00 0.00 45.23 3.34
4750 8471 3.420893 TCGAAAAATTGACCATGGAGCT 58.579 40.909 21.47 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.