Multiple sequence alignment - TraesCS1B01G264200

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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 TraesCS1B01G264200 chr1B 100.000 4393 0 0 1 4393 465096045 465100437 0.000000e+00 8113.0
1 TraesCS1B01G264200 chr1B 85.845 1752 188 31 1687 3412 465240249 465241966 0.000000e+00 1807.0
2 TraesCS1B01G264200 chr1B 85.284 1427 176 26 2009 3415 465244800 465246212 0.000000e+00 1441.0
3 TraesCS1B01G264200 chr1B 86.231 857 103 10 3549 4393 27159297 27158444 0.000000e+00 915.0
4 TraesCS1B01G264200 chr1B 84.809 915 117 15 2483 3381 465362647 465363555 0.000000e+00 900.0
5 TraesCS1B01G264200 chr1B 87.037 594 72 5 963 1552 465243241 465243833 0.000000e+00 665.0
6 TraesCS1B01G264200 chr1B 87.478 567 63 4 981 1546 465239493 465240052 0.000000e+00 647.0
7 TraesCS1B01G264200 chr1B 84.139 517 60 11 981 1496 465246727 465247222 8.550000e-132 481.0
8 TraesCS1B01G264200 chr1B 87.356 87 11 0 74 160 391066204 391066290 2.800000e-17 100.0
9 TraesCS1B01G264200 chr1A 94.246 3441 157 24 926 4346 445656424 445653005 0.000000e+00 5219.0
10 TraesCS1B01G264200 chr1A 86.921 1361 154 18 2069 3415 445543098 445541748 0.000000e+00 1506.0
11 TraesCS1B01G264200 chr1A 89.407 944 99 1 2473 3415 445547915 445546972 0.000000e+00 1188.0
12 TraesCS1B01G264200 chr1A 85.124 847 104 14 3561 4393 77653902 77654740 0.000000e+00 846.0
13 TraesCS1B01G264200 chr1A 78.783 1216 190 48 1687 2855 445535760 445534566 0.000000e+00 754.0
14 TraesCS1B01G264200 chr1A 86.949 590 73 4 963 1549 445544608 445544020 0.000000e+00 660.0
15 TraesCS1B01G264200 chr1A 87.324 568 64 4 980 1546 445549569 445549009 1.030000e-180 643.0
16 TraesCS1B01G264200 chr1A 85.225 555 49 21 1838 2385 445548663 445548135 1.390000e-149 540.0
17 TraesCS1B01G264200 chr1D 95.808 1455 52 7 926 2377 345481802 345480354 0.000000e+00 2340.0
18 TraesCS1B01G264200 chr1D 97.032 1112 33 0 2416 3527 345480355 345479244 0.000000e+00 1871.0
19 TraesCS1B01G264200 chr1D 84.732 1454 185 26 1984 3415 345432507 345431069 0.000000e+00 1421.0
20 TraesCS1B01G264200 chr1D 86.656 1244 138 15 2188 3415 345436584 345435353 0.000000e+00 1352.0
21 TraesCS1B01G264200 chr1D 83.138 1281 160 31 2264 3509 345416864 345415605 0.000000e+00 1118.0
22 TraesCS1B01G264200 chr1D 85.461 846 99 11 3561 4393 6670114 6669280 0.000000e+00 859.0
23 TraesCS1B01G264200 chr1D 87.542 594 69 5 963 1552 345433738 345433146 0.000000e+00 682.0
24 TraesCS1B01G264200 chr1D 87.784 573 58 8 981 1552 345430537 345429976 0.000000e+00 660.0
25 TraesCS1B01G264200 chr1D 82.805 663 98 8 1 652 345485273 345484616 2.950000e-161 579.0
26 TraesCS1B01G264200 chr1D 77.039 331 69 7 74 400 120951308 120951635 2.700000e-42 183.0
27 TraesCS1B01G264200 chr1D 73.835 558 95 36 1685 2203 345425250 345424705 1.620000e-39 174.0
28 TraesCS1B01G264200 chr1D 81.343 134 24 1 603 735 435541269 435541402 1.670000e-19 108.0
29 TraesCS1B01G264200 chrUn 88.521 845 84 8 3557 4393 103279149 103278310 0.000000e+00 1011.0
30 TraesCS1B01G264200 chrUn 77.644 331 67 7 74 400 99854713 99855040 1.250000e-45 195.0
31 TraesCS1B01G264200 chr2A 87.796 844 87 11 3560 4393 750731026 750730189 0.000000e+00 974.0
32 TraesCS1B01G264200 chr3B 87.089 821 91 10 3582 4393 328403452 328404266 0.000000e+00 915.0
33 TraesCS1B01G264200 chr3B 79.341 334 62 7 74 403 250470906 250471236 1.230000e-55 228.0
34 TraesCS1B01G264200 chr3B 86.154 65 5 4 83 144 696590415 696590352 2.840000e-07 67.6
35 TraesCS1B01G264200 chr5D 85.151 862 111 11 3544 4393 313221983 313222839 0.000000e+00 867.0
36 TraesCS1B01G264200 chr4A 85.528 843 100 13 3563 4393 627482155 627481323 0.000000e+00 861.0
37 TraesCS1B01G264200 chr3D 79.624 319 54 6 79 387 566475854 566475537 7.400000e-53 219.0
38 TraesCS1B01G264200 chr5A 77.576 330 68 6 74 400 687274688 687275014 1.250000e-45 195.0
39 TraesCS1B01G264200 chr4B 77.151 337 64 11 74 403 672321546 672321216 2.700000e-42 183.0


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 TraesCS1B01G264200 chr1B 465096045 465100437 4392 False 8113.000000 8113 100.000000 1 4393 1 chr1B.!!$F2 4392
1 TraesCS1B01G264200 chr1B 465239493 465247222 7729 False 1008.200000 1807 85.956600 963 3415 5 chr1B.!!$F4 2452
2 TraesCS1B01G264200 chr1B 27158444 27159297 853 True 915.000000 915 86.231000 3549 4393 1 chr1B.!!$R1 844
3 TraesCS1B01G264200 chr1B 465362647 465363555 908 False 900.000000 900 84.809000 2483 3381 1 chr1B.!!$F3 898
4 TraesCS1B01G264200 chr1A 445653005 445656424 3419 True 5219.000000 5219 94.246000 926 4346 1 chr1A.!!$R2 3420
5 TraesCS1B01G264200 chr1A 445541748 445549569 7821 True 907.400000 1506 87.165200 963 3415 5 chr1A.!!$R3 2452
6 TraesCS1B01G264200 chr1A 77653902 77654740 838 False 846.000000 846 85.124000 3561 4393 1 chr1A.!!$F1 832
7 TraesCS1B01G264200 chr1A 445534566 445535760 1194 True 754.000000 754 78.783000 1687 2855 1 chr1A.!!$R1 1168
8 TraesCS1B01G264200 chr1D 345479244 345485273 6029 True 1596.666667 2340 91.881667 1 3527 3 chr1D.!!$R5 3526
9 TraesCS1B01G264200 chr1D 345415605 345416864 1259 True 1118.000000 1118 83.138000 2264 3509 1 chr1D.!!$R2 1245
10 TraesCS1B01G264200 chr1D 345429976 345436584 6608 True 1028.750000 1421 86.678500 963 3415 4 chr1D.!!$R4 2452
11 TraesCS1B01G264200 chr1D 6669280 6670114 834 True 859.000000 859 85.461000 3561 4393 1 chr1D.!!$R1 832
12 TraesCS1B01G264200 chrUn 103278310 103279149 839 True 1011.000000 1011 88.521000 3557 4393 1 chrUn.!!$R1 836
13 TraesCS1B01G264200 chr2A 750730189 750731026 837 True 974.000000 974 87.796000 3560 4393 1 chr2A.!!$R1 833
14 TraesCS1B01G264200 chr3B 328403452 328404266 814 False 915.000000 915 87.089000 3582 4393 1 chr3B.!!$F2 811
15 TraesCS1B01G264200 chr5D 313221983 313222839 856 False 867.000000 867 85.151000 3544 4393 1 chr5D.!!$F1 849
16 TraesCS1B01G264200 chr4A 627481323 627482155 832 True 861.000000 861 85.528000 3563 4393 1 chr4A.!!$R1 830

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
748 760 0.036010 AGGTGCACACATGGTAGAGC 60.036 55.000 20.43 0.0 0.00 4.09 F
803 826 0.317160 TGCGACTTCGATTGTCCTGT 59.683 50.000 2.02 0.0 43.02 4.00 F
992 3590 0.383231 CCATTCAGAATCGCCAAGCC 59.617 55.000 0.00 0.0 0.00 4.35 F
2224 4918 1.470098 AGTGCGGATGTCATTTCTTGC 59.530 47.619 0.00 0.0 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2224 4918 1.453155 AGCTACTTCCAAATGCCACG 58.547 50.000 0.00 0.00 0.00 4.94 R
2757 11121 1.475280 TGATTCAATGCCAGCAGAAGC 59.525 47.619 0.00 0.88 42.56 3.86 R
2773 11137 3.555586 GCCTTGTGTTGCCATTCTTGATT 60.556 43.478 0.00 0.00 0.00 2.57 R
3993 17273 1.093972 TTTATGGGCACATGAGCGTG 58.906 50.000 12.99 0.00 37.97 5.34 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
31 32 7.739498 TTAAAACCTGAAGTACTCATGAACC 57.261 36.000 0.00 0.00 32.14 3.62
35 36 4.223032 ACCTGAAGTACTCATGAACCGAAT 59.777 41.667 0.00 0.00 32.14 3.34
53 54 4.546570 CGAATTCAGAAAACCCTGGTTTC 58.453 43.478 14.34 4.52 46.22 2.78
54 55 4.558697 CGAATTCAGAAAACCCTGGTTTCC 60.559 45.833 14.34 2.14 46.22 3.13
62 63 6.376864 CAGAAAACCCTGGTTTCCAAAAATTT 59.623 34.615 14.34 0.00 46.22 1.82
63 64 6.376864 AGAAAACCCTGGTTTCCAAAAATTTG 59.623 34.615 14.34 0.00 46.22 2.32
66 67 5.436175 ACCCTGGTTTCCAAAAATTTGAAG 58.564 37.500 7.44 0.00 40.55 3.02
68 69 6.157123 ACCCTGGTTTCCAAAAATTTGAAGTA 59.843 34.615 7.44 0.00 40.55 2.24
69 70 7.147391 ACCCTGGTTTCCAAAAATTTGAAGTAT 60.147 33.333 7.44 0.00 40.55 2.12
70 71 8.371699 CCCTGGTTTCCAAAAATTTGAAGTATA 58.628 33.333 7.44 0.00 40.55 1.47
71 72 9.203421 CCTGGTTTCCAAAAATTTGAAGTATAC 57.797 33.333 7.44 0.00 40.55 1.47
114 115 9.364989 CAATGTTCAAACCTAGAAACAGAAAAA 57.635 29.630 0.00 0.00 0.00 1.94
120 121 8.912988 TCAAACCTAGAAACAGAAAAATCACAT 58.087 29.630 0.00 0.00 0.00 3.21
160 161 1.922135 AAAAATCGCCGTCGCTGCAT 61.922 50.000 0.00 0.00 35.26 3.96
165 166 4.865761 GCCGTCGCTGCATCCGTA 62.866 66.667 0.00 0.00 0.00 4.02
169 170 1.472276 CGTCGCTGCATCCGTAGAAC 61.472 60.000 0.00 0.00 0.00 3.01
175 176 2.743183 GCTGCATCCGTAGAACATCCTT 60.743 50.000 0.00 0.00 0.00 3.36
178 179 2.866762 GCATCCGTAGAACATCCTTCAC 59.133 50.000 0.00 0.00 0.00 3.18
179 180 3.458189 CATCCGTAGAACATCCTTCACC 58.542 50.000 0.00 0.00 0.00 4.02
183 184 2.921754 CGTAGAACATCCTTCACCGTTC 59.078 50.000 0.00 0.00 38.40 3.95
185 186 3.703001 AGAACATCCTTCACCGTTCAT 57.297 42.857 0.00 0.00 40.14 2.57
201 202 4.443457 CCGTTCATGGTATCAATGACCTCT 60.443 45.833 0.00 0.00 37.88 3.69
203 204 6.280643 CGTTCATGGTATCAATGACCTCTAA 58.719 40.000 0.00 0.00 37.88 2.10
204 205 6.761242 CGTTCATGGTATCAATGACCTCTAAA 59.239 38.462 0.00 0.00 37.88 1.85
206 207 9.125026 GTTCATGGTATCAATGACCTCTAAATT 57.875 33.333 0.00 0.00 37.88 1.82
221 222 9.543783 GACCTCTAAATTGTCGGAGTTAATAAT 57.456 33.333 0.00 0.00 0.00 1.28
222 223 9.326413 ACCTCTAAATTGTCGGAGTTAATAATG 57.674 33.333 0.00 0.00 0.00 1.90
228 229 8.786826 AATTGTCGGAGTTAATAATGAGACAA 57.213 30.769 9.59 9.59 46.66 3.18
234 235 7.498900 TCGGAGTTAATAATGAGACAATTGCAT 59.501 33.333 5.05 0.00 0.00 3.96
243 244 2.883386 GAGACAATTGCATCCCATCCTC 59.117 50.000 5.05 0.00 0.00 3.71
245 246 2.621998 GACAATTGCATCCCATCCTCTG 59.378 50.000 5.05 0.00 0.00 3.35
246 247 1.340248 CAATTGCATCCCATCCTCTGC 59.660 52.381 0.00 0.00 35.21 4.26
265 266 1.722011 CGCAAGGGACAACTCGTATT 58.278 50.000 0.00 0.00 0.00 1.89
267 268 1.737793 GCAAGGGACAACTCGTATTGG 59.262 52.381 6.41 0.00 33.63 3.16
295 296 3.403936 GCTTCCGCCATTAGGACAT 57.596 52.632 0.00 0.00 37.53 3.06
296 297 1.230324 GCTTCCGCCATTAGGACATC 58.770 55.000 0.00 0.00 37.53 3.06
303 304 1.888215 CCATTAGGACATCTGCGCAT 58.112 50.000 12.24 0.00 36.89 4.73
304 305 1.534163 CCATTAGGACATCTGCGCATG 59.466 52.381 12.24 10.56 36.89 4.06
313 314 2.627221 ACATCTGCGCATGAGTCTATCT 59.373 45.455 17.46 0.00 0.00 1.98
315 316 3.808466 TCTGCGCATGAGTCTATCTTT 57.192 42.857 12.24 0.00 0.00 2.52
322 323 5.220931 GCGCATGAGTCTATCTTTCCATTTT 60.221 40.000 0.30 0.00 0.00 1.82
326 327 7.498570 GCATGAGTCTATCTTTCCATTTTCTCT 59.501 37.037 0.00 0.00 0.00 3.10
327 328 9.393512 CATGAGTCTATCTTTCCATTTTCTCTT 57.606 33.333 0.00 0.00 0.00 2.85
428 437 1.656652 CCAAGGCATCGGACTACTTG 58.343 55.000 9.25 9.25 38.52 3.16
443 452 7.649306 TCGGACTACTTGAGTTTTAACTACAAC 59.351 37.037 0.00 0.00 39.06 3.32
460 471 6.879400 ACTACAACAGTTTTAAAAATGGCCA 58.121 32.000 26.64 8.56 38.22 5.36
477 488 1.457455 CACCAAACTGGGCCCAAGT 60.457 57.895 28.29 22.31 43.37 3.16
481 492 0.829990 CAAACTGGGCCCAAGTGTTT 59.170 50.000 26.95 26.95 0.00 2.83
485 496 0.890683 CTGGGCCCAAGTGTTTCATC 59.109 55.000 28.29 0.00 0.00 2.92
496 507 6.316390 CCCAAGTGTTTCATCTTCTATACACC 59.684 42.308 0.00 0.00 37.25 4.16
499 510 7.246171 AGTGTTTCATCTTCTATACACCACT 57.754 36.000 0.00 0.00 37.25 4.00
508 519 2.430694 TCTATACACCACTGAAGCGCAT 59.569 45.455 11.47 0.00 0.00 4.73
509 520 2.113860 ATACACCACTGAAGCGCATT 57.886 45.000 11.47 0.00 0.00 3.56
523 534 3.290098 GCATTACTGCGAACCAACG 57.710 52.632 0.00 0.00 38.92 4.10
525 536 1.724654 GCATTACTGCGAACCAACGTG 60.725 52.381 0.00 0.00 38.92 4.49
527 538 2.505628 TTACTGCGAACCAACGTGTA 57.494 45.000 0.00 0.00 35.59 2.90
531 542 2.032377 ACTGCGAACCAACGTGTAATTG 60.032 45.455 0.00 0.00 35.59 2.32
540 551 4.757799 CAACGTGTAATTGGATGGTTGA 57.242 40.909 0.00 0.00 36.34 3.18
544 555 4.020573 ACGTGTAATTGGATGGTTGAGAGA 60.021 41.667 0.00 0.00 0.00 3.10
546 557 5.586243 CGTGTAATTGGATGGTTGAGAGAAT 59.414 40.000 0.00 0.00 0.00 2.40
557 568 7.202047 GGATGGTTGAGAGAATAGTGGTATCTT 60.202 40.741 0.00 0.00 0.00 2.40
561 572 8.207545 GGTTGAGAGAATAGTGGTATCTTCAAT 58.792 37.037 0.00 0.00 0.00 2.57
565 576 8.503428 AGAGAATAGTGGTATCTTCAATCCAT 57.497 34.615 0.00 0.00 32.45 3.41
567 578 7.382110 AGAATAGTGGTATCTTCAATCCATCG 58.618 38.462 0.00 0.00 32.45 3.84
568 579 6.672266 ATAGTGGTATCTTCAATCCATCGT 57.328 37.500 0.00 0.00 32.45 3.73
569 580 4.697514 AGTGGTATCTTCAATCCATCGTG 58.302 43.478 0.00 0.00 32.45 4.35
576 587 4.393834 TCTTCAATCCATCGTGGTTCAAA 58.606 39.130 4.33 0.00 39.03 2.69
578 589 5.476599 TCTTCAATCCATCGTGGTTCAAATT 59.523 36.000 4.33 0.00 39.03 1.82
579 590 5.720371 TCAATCCATCGTGGTTCAAATTT 57.280 34.783 4.33 0.00 39.03 1.82
586 597 6.488683 TCCATCGTGGTTCAAATTTTAGACTT 59.511 34.615 4.33 0.00 39.03 3.01
587 598 7.013846 TCCATCGTGGTTCAAATTTTAGACTTT 59.986 33.333 4.33 0.00 39.03 2.66
589 600 9.113876 CATCGTGGTTCAAATTTTAGACTTTAC 57.886 33.333 0.00 0.00 0.00 2.01
622 634 9.674824 GCTCATATTATTCTGGATTTGTTTCAG 57.325 33.333 0.00 0.00 0.00 3.02
630 642 4.065088 CTGGATTTGTTTCAGACTTCCGA 58.935 43.478 0.00 0.00 0.00 4.55
635 647 4.508461 TTGTTTCAGACTTCCGACGATA 57.492 40.909 0.00 0.00 0.00 2.92
639 651 3.604065 TCAGACTTCCGACGATATTCG 57.396 47.619 0.00 0.00 46.93 3.34
649 661 3.951115 CGATATTCGTTCGGTGGGA 57.049 52.632 0.00 0.00 34.72 4.37
650 662 1.767289 CGATATTCGTTCGGTGGGAG 58.233 55.000 0.00 0.00 34.72 4.30
651 663 1.602165 CGATATTCGTTCGGTGGGAGG 60.602 57.143 0.00 0.00 34.72 4.30
652 664 1.684983 GATATTCGTTCGGTGGGAGGA 59.315 52.381 0.00 0.00 0.00 3.71
653 665 1.108776 TATTCGTTCGGTGGGAGGAG 58.891 55.000 0.00 0.00 0.00 3.69
654 666 0.613853 ATTCGTTCGGTGGGAGGAGA 60.614 55.000 0.00 0.00 0.00 3.71
655 667 0.828762 TTCGTTCGGTGGGAGGAGAA 60.829 55.000 0.00 0.00 0.00 2.87
656 668 1.215647 CGTTCGGTGGGAGGAGAAG 59.784 63.158 0.00 0.00 0.00 2.85
657 669 1.533469 CGTTCGGTGGGAGGAGAAGT 61.533 60.000 0.00 0.00 0.00 3.01
658 670 0.685660 GTTCGGTGGGAGGAGAAGTT 59.314 55.000 0.00 0.00 0.00 2.66
659 671 1.071857 GTTCGGTGGGAGGAGAAGTTT 59.928 52.381 0.00 0.00 0.00 2.66
660 672 0.974383 TCGGTGGGAGGAGAAGTTTC 59.026 55.000 0.00 0.00 0.00 2.78
661 673 0.036294 CGGTGGGAGGAGAAGTTTCC 60.036 60.000 0.00 0.00 37.52 3.13
662 674 0.036294 GGTGGGAGGAGAAGTTTCCG 60.036 60.000 0.00 0.00 42.29 4.30
663 675 0.685660 GTGGGAGGAGAAGTTTCCGT 59.314 55.000 0.00 0.00 42.29 4.69
664 676 0.974383 TGGGAGGAGAAGTTTCCGTC 59.026 55.000 0.00 0.00 42.29 4.79
665 677 0.108756 GGGAGGAGAAGTTTCCGTCG 60.109 60.000 0.00 0.00 42.29 5.12
666 678 0.886563 GGAGGAGAAGTTTCCGTCGA 59.113 55.000 0.00 0.00 42.29 4.20
667 679 1.402588 GGAGGAGAAGTTTCCGTCGAC 60.403 57.143 5.18 5.18 42.29 4.20
668 680 1.540707 GAGGAGAAGTTTCCGTCGACT 59.459 52.381 14.70 0.00 42.29 4.18
669 681 1.269998 AGGAGAAGTTTCCGTCGACTG 59.730 52.381 14.70 7.40 42.29 3.51
670 682 1.061485 GAGAAGTTTCCGTCGACTGC 58.939 55.000 14.70 0.00 0.00 4.40
671 683 0.663568 AGAAGTTTCCGTCGACTGCG 60.664 55.000 14.70 0.00 39.35 5.18
682 694 0.874175 TCGACTGCGAGGTGTTTGTG 60.874 55.000 0.00 0.00 42.51 3.33
691 703 1.947456 GAGGTGTTTGTGGTGACTTCC 59.053 52.381 0.00 0.00 0.00 3.46
700 712 6.605594 TGTTTGTGGTGACTTCCTAAAATCTT 59.394 34.615 0.00 0.00 0.00 2.40
707 719 8.383175 TGGTGACTTCCTAAAATCTTAAGATGT 58.617 33.333 18.61 10.66 34.49 3.06
712 724 9.939802 ACTTCCTAAAATCTTAAGATGTTACGT 57.060 29.630 19.95 13.15 34.12 3.57
717 729 3.155093 TCTTAAGATGTTACGTCGGCC 57.845 47.619 0.00 0.00 0.00 6.13
718 730 1.850441 CTTAAGATGTTACGTCGGCCG 59.150 52.381 22.12 22.12 44.03 6.13
720 732 0.179145 AAGATGTTACGTCGGCCGAG 60.179 55.000 31.97 24.07 40.70 4.63
735 747 4.004348 GAGTCTCTCGGAGGTGCA 57.996 61.111 4.96 0.00 0.00 4.57
740 752 0.900182 TCTCTCGGAGGTGCACACAT 60.900 55.000 20.43 3.33 0.00 3.21
743 755 2.032528 CGGAGGTGCACACATGGT 59.967 61.111 20.43 0.00 0.00 3.55
744 756 1.188871 TCGGAGGTGCACACATGGTA 61.189 55.000 20.43 0.00 0.00 3.25
745 757 0.740868 CGGAGGTGCACACATGGTAG 60.741 60.000 20.43 0.00 0.00 3.18
746 758 0.613260 GGAGGTGCACACATGGTAGA 59.387 55.000 20.43 0.00 0.00 2.59
748 760 0.036010 AGGTGCACACATGGTAGAGC 60.036 55.000 20.43 0.00 0.00 4.09
749 761 1.361668 GGTGCACACATGGTAGAGCG 61.362 60.000 20.43 0.00 0.00 5.03
750 762 0.670546 GTGCACACATGGTAGAGCGT 60.671 55.000 13.17 0.00 0.00 5.07
751 763 0.892063 TGCACACATGGTAGAGCGTA 59.108 50.000 0.00 0.00 0.00 4.42
752 764 1.278238 GCACACATGGTAGAGCGTAC 58.722 55.000 0.00 0.00 0.00 3.67
753 765 1.403647 GCACACATGGTAGAGCGTACA 60.404 52.381 0.00 0.00 0.00 2.90
757 770 1.480545 ACATGGTAGAGCGTACATGCA 59.519 47.619 0.00 0.00 43.28 3.96
761 774 1.570813 GTAGAGCGTACATGCATGCA 58.429 50.000 26.53 25.04 37.31 3.96
764 777 1.600957 AGAGCGTACATGCATGCATTC 59.399 47.619 30.32 22.51 37.31 2.67
779 792 1.741706 GCATTCATGGAGGTGAGTGTG 59.258 52.381 0.00 0.00 37.92 3.82
781 794 2.549064 TTCATGGAGGTGAGTGTGTG 57.451 50.000 0.00 0.00 0.00 3.82
784 797 0.767375 ATGGAGGTGAGTGTGTGCTT 59.233 50.000 0.00 0.00 0.00 3.91
788 811 1.887242 GGTGAGTGTGTGCTTGCGA 60.887 57.895 0.00 0.00 0.00 5.10
799 822 0.790207 TGCTTGCGACTTCGATTGTC 59.210 50.000 2.02 8.49 43.02 3.18
801 824 1.714794 CTTGCGACTTCGATTGTCCT 58.285 50.000 2.02 0.00 43.02 3.85
802 825 1.391485 CTTGCGACTTCGATTGTCCTG 59.609 52.381 2.02 2.90 43.02 3.86
803 826 0.317160 TGCGACTTCGATTGTCCTGT 59.683 50.000 2.02 0.00 43.02 4.00
804 827 0.716108 GCGACTTCGATTGTCCTGTG 59.284 55.000 2.02 2.07 43.02 3.66
805 828 1.935300 GCGACTTCGATTGTCCTGTGT 60.935 52.381 2.02 0.00 43.02 3.72
806 829 2.404215 CGACTTCGATTGTCCTGTGTT 58.596 47.619 11.75 0.00 43.02 3.32
807 830 3.571571 CGACTTCGATTGTCCTGTGTTA 58.428 45.455 11.75 0.00 43.02 2.41
808 831 3.985279 CGACTTCGATTGTCCTGTGTTAA 59.015 43.478 11.75 0.00 43.02 2.01
809 832 4.446385 CGACTTCGATTGTCCTGTGTTAAA 59.554 41.667 11.75 0.00 43.02 1.52
810 833 5.050634 CGACTTCGATTGTCCTGTGTTAAAA 60.051 40.000 11.75 0.00 43.02 1.52
811 834 6.510478 CGACTTCGATTGTCCTGTGTTAAAAA 60.510 38.462 11.75 0.00 43.02 1.94
839 862 2.661537 GGGCGCCACTTGCAAAAC 60.662 61.111 30.85 1.84 41.33 2.43
845 869 2.223226 GCGCCACTTGCAAAACAAAAAT 60.223 40.909 0.00 0.00 41.33 1.82
883 907 7.829725 TCCAATAGGAATCATGTGTTTCTTTG 58.170 34.615 0.00 2.51 42.23 2.77
885 909 4.525912 AGGAATCATGTGTTTCTTTGGC 57.474 40.909 0.00 0.00 0.00 4.52
886 910 3.896888 AGGAATCATGTGTTTCTTTGGCA 59.103 39.130 0.00 0.00 0.00 4.92
887 911 4.529377 AGGAATCATGTGTTTCTTTGGCAT 59.471 37.500 0.00 0.00 0.00 4.40
888 912 5.012354 AGGAATCATGTGTTTCTTTGGCATT 59.988 36.000 0.00 0.00 0.00 3.56
889 913 5.349543 GGAATCATGTGTTTCTTTGGCATTC 59.650 40.000 0.00 0.00 0.00 2.67
890 914 4.933505 TCATGTGTTTCTTTGGCATTCA 57.066 36.364 0.00 0.00 0.00 2.57
891 915 5.471556 TCATGTGTTTCTTTGGCATTCAT 57.528 34.783 0.00 0.00 0.00 2.57
892 916 5.856156 TCATGTGTTTCTTTGGCATTCATT 58.144 33.333 0.00 0.00 0.00 2.57
893 917 5.697178 TCATGTGTTTCTTTGGCATTCATTG 59.303 36.000 0.00 0.00 0.00 2.82
896 920 4.810491 GTGTTTCTTTGGCATTCATTGTGT 59.190 37.500 0.00 0.00 0.00 3.72
897 921 5.294060 GTGTTTCTTTGGCATTCATTGTGTT 59.706 36.000 0.00 0.00 0.00 3.32
898 922 5.879223 TGTTTCTTTGGCATTCATTGTGTTT 59.121 32.000 0.00 0.00 0.00 2.83
899 923 6.036953 TGTTTCTTTGGCATTCATTGTGTTTC 59.963 34.615 0.00 0.00 0.00 2.78
900 924 4.630111 TCTTTGGCATTCATTGTGTTTCC 58.370 39.130 0.00 0.00 0.00 3.13
907 3475 5.183904 GGCATTCATTGTGTTTCCTACTCTT 59.816 40.000 0.00 0.00 0.00 2.85
915 3483 4.246458 GTGTTTCCTACTCTTGCTACCTG 58.754 47.826 0.00 0.00 0.00 4.00
920 3488 3.053544 TCCTACTCTTGCTACCTGCTACT 60.054 47.826 0.00 0.00 43.37 2.57
923 3491 3.698289 ACTCTTGCTACCTGCTACTGTA 58.302 45.455 0.00 0.00 43.37 2.74
992 3590 0.383231 CCATTCAGAATCGCCAAGCC 59.617 55.000 0.00 0.00 0.00 4.35
1080 3678 2.805546 GCGCTCCACTCCATCGTA 59.194 61.111 0.00 0.00 0.00 3.43
1198 3796 4.659172 CCAAAGCCGCCCAGTCCA 62.659 66.667 0.00 0.00 0.00 4.02
1199 3797 2.597217 CAAAGCCGCCCAGTCCAA 60.597 61.111 0.00 0.00 0.00 3.53
1675 4301 5.406780 GGTGTGACATCTCTTTACAGAACTG 59.593 44.000 0.00 0.00 0.00 3.16
1676 4302 5.406780 GTGTGACATCTCTTTACAGAACTGG 59.593 44.000 6.76 0.00 34.19 4.00
1678 4304 5.866633 GTGACATCTCTTTACAGAACTGGAG 59.133 44.000 6.76 3.71 34.19 3.86
1680 4306 6.719829 TGACATCTCTTTACAGAACTGGAGTA 59.280 38.462 6.76 0.00 34.19 2.59
1681 4307 6.926313 ACATCTCTTTACAGAACTGGAGTAC 58.074 40.000 6.76 0.00 34.19 2.73
1725 4386 4.399303 ACTTGGTGCTGTTATTGAATAGGC 59.601 41.667 0.00 0.00 0.00 3.93
1936 4624 4.652822 ACTGGTTATTTCCCTCACAGTTC 58.347 43.478 0.00 0.00 34.36 3.01
2121 4815 9.717942 GATACCAGAAATATCAGCTATCACTTT 57.282 33.333 0.00 0.00 0.00 2.66
2224 4918 1.470098 AGTGCGGATGTCATTTCTTGC 59.530 47.619 0.00 0.00 0.00 4.01
2385 10733 6.591935 TGGGTCACCATTTATTCTCTATCAC 58.408 40.000 0.00 0.00 43.37 3.06
2388 10736 7.442666 GGGTCACCATTTATTCTCTATCACTTC 59.557 40.741 0.00 0.00 36.50 3.01
2389 10737 7.987458 GGTCACCATTTATTCTCTATCACTTCA 59.013 37.037 0.00 0.00 0.00 3.02
2392 10740 6.995091 ACCATTTATTCTCTATCACTTCAGGC 59.005 38.462 0.00 0.00 0.00 4.85
2393 10741 6.994496 CCATTTATTCTCTATCACTTCAGGCA 59.006 38.462 0.00 0.00 0.00 4.75
2394 10742 7.500227 CCATTTATTCTCTATCACTTCAGGCAA 59.500 37.037 0.00 0.00 0.00 4.52
2395 10743 8.557864 CATTTATTCTCTATCACTTCAGGCAAG 58.442 37.037 0.00 0.00 38.21 4.01
2396 10744 5.946942 ATTCTCTATCACTTCAGGCAAGA 57.053 39.130 0.00 0.00 35.82 3.02
2398 10746 5.273674 TCTCTATCACTTCAGGCAAGATG 57.726 43.478 0.00 0.00 35.82 2.90
2399 10747 4.958581 TCTCTATCACTTCAGGCAAGATGA 59.041 41.667 0.00 0.00 35.82 2.92
2634 10998 6.532826 AGATTCCAAAAATTTGCTTGGCTTA 58.467 32.000 14.41 5.52 41.65 3.09
2685 11049 7.753309 TGAGTTTAAAATGGGAATCGAAGAA 57.247 32.000 0.00 0.00 43.58 2.52
2721 11085 2.986479 CAAGACATTTTACTTTGCCGGC 59.014 45.455 22.73 22.73 0.00 6.13
2757 11121 2.507339 ATTTGTTGACTTGGGCAACG 57.493 45.000 10.99 0.00 46.46 4.10
2773 11137 0.890542 AACGCTTCTGCTGGCATTGA 60.891 50.000 0.00 0.00 36.97 2.57
2890 11259 9.860898 AAATTGTGAGCCTTATTTACTTGAATC 57.139 29.630 0.00 0.00 0.00 2.52
2993 11370 9.913310 TGATATCAGGTTAATATGGTGTTGAAA 57.087 29.630 0.00 0.00 0.00 2.69
3083 11460 1.779061 AACTTGACATCCCTGCGGGT 61.779 55.000 11.58 0.00 44.74 5.28
3112 11496 5.940470 AGGTCAATCTTCCTATTGTTGACAC 59.060 40.000 15.66 7.51 46.34 3.67
3281 11667 2.547642 GGCAAAGTTGGTGCTTGCAATA 60.548 45.455 0.00 0.00 41.88 1.90
3512 16175 9.114952 TGAACTTTGTAATGAAAGTGTGTATGA 57.885 29.630 0.00 0.00 43.83 2.15
3519 16182 8.145122 TGTAATGAAAGTGTGTATGAGTGTGTA 58.855 33.333 0.00 0.00 0.00 2.90
3523 16186 2.295070 AGTGTGTATGAGTGTGTACGCA 59.705 45.455 4.65 4.65 40.89 5.24
3548 16211 3.994392 CCGCGCTGATAAAAGGTATATGT 59.006 43.478 5.56 0.00 0.00 2.29
3631 16301 3.853355 AGCAGTGGGAGAGATAATTGG 57.147 47.619 0.00 0.00 0.00 3.16
3683 16353 1.032657 GGCGACAGAGTGAGGAGCTA 61.033 60.000 0.00 0.00 0.00 3.32
3730 16401 2.546795 CCCGTGAGATCTTGATAGTGGC 60.547 54.545 0.00 0.00 0.00 5.01
3866 17141 2.089854 GCACGGTTGCTTCGATCAT 58.910 52.632 0.00 0.00 46.17 2.45
3898 17173 6.023435 CACAACAACGTAATCAGATGGATTG 58.977 40.000 0.00 0.00 45.70 2.67
4146 17429 4.463891 CCTCCAGCAATAATTTGTGGAGTT 59.536 41.667 21.87 0.00 46.37 3.01
4172 17455 3.733224 CGTTCTGCTCATAATTCTCGAGG 59.267 47.826 13.56 0.00 0.00 4.63
4195 17478 5.183904 GGCAACTTCCTTATTCTCACACAAT 59.816 40.000 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.868757 TCGGTTCATGAGTACTTCAGG 57.131 47.619 0.00 0.00 39.68 3.86
14 15 5.869344 TGAATTCGGTTCATGAGTACTTCAG 59.131 40.000 0.00 0.00 41.79 3.02
22 23 5.393962 GGTTTTCTGAATTCGGTTCATGAG 58.606 41.667 13.95 0.00 45.36 2.90
31 32 4.546570 GAAACCAGGGTTTTCTGAATTCG 58.453 43.478 16.94 0.00 46.80 3.34
35 36 3.390175 TGGAAACCAGGGTTTTCTGAA 57.610 42.857 20.08 0.99 46.80 3.02
40 41 6.249192 TCAAATTTTTGGAAACCAGGGTTTT 58.751 32.000 16.94 2.23 41.02 2.43
45 46 9.203421 GTATACTTCAAATTTTTGGAAACCAGG 57.797 33.333 3.38 0.00 38.66 4.45
46 47 9.981114 AGTATACTTCAAATTTTTGGAAACCAG 57.019 29.630 0.00 0.00 38.66 4.00
70 71 9.349713 TGAACATTGTAATAGAGAACCAAAAGT 57.650 29.630 0.00 0.00 0.00 2.66
114 115 7.492524 ACGACTGTTATCATCTTGTATGTGAT 58.507 34.615 0.00 0.00 36.60 3.06
152 153 0.459899 ATGTTCTACGGATGCAGCGA 59.540 50.000 0.00 0.00 0.00 4.93
160 161 1.475280 CGGTGAAGGATGTTCTACGGA 59.525 52.381 0.00 0.00 0.00 4.69
163 164 3.921677 TGAACGGTGAAGGATGTTCTAC 58.078 45.455 5.66 0.00 40.93 2.59
165 166 3.338249 CATGAACGGTGAAGGATGTTCT 58.662 45.455 5.66 0.00 40.93 3.01
169 170 2.113860 ACCATGAACGGTGAAGGATG 57.886 50.000 0.00 0.00 38.07 3.51
175 176 4.188462 GTCATTGATACCATGAACGGTGA 58.812 43.478 0.00 0.00 40.39 4.02
178 179 3.808728 AGGTCATTGATACCATGAACGG 58.191 45.455 0.00 0.00 39.64 4.44
179 180 4.697514 AGAGGTCATTGATACCATGAACG 58.302 43.478 0.00 0.00 39.64 3.95
183 184 8.455903 ACAATTTAGAGGTCATTGATACCATG 57.544 34.615 0.00 0.00 39.64 3.66
185 186 6.761242 CGACAATTTAGAGGTCATTGATACCA 59.239 38.462 0.00 0.00 39.64 3.25
201 202 9.878667 TGTCTCATTATTAACTCCGACAATTTA 57.121 29.630 0.00 0.00 0.00 1.40
203 204 8.786826 TTGTCTCATTATTAACTCCGACAATT 57.213 30.769 0.00 0.00 35.84 2.32
204 205 8.964476 ATTGTCTCATTATTAACTCCGACAAT 57.036 30.769 0.00 0.00 42.59 2.71
206 207 7.201609 GCAATTGTCTCATTATTAACTCCGACA 60.202 37.037 7.40 0.00 0.00 4.35
221 222 2.242965 AGGATGGGATGCAATTGTCTCA 59.757 45.455 7.40 4.14 0.00 3.27
222 223 2.883386 GAGGATGGGATGCAATTGTCTC 59.117 50.000 7.40 4.23 0.00 3.36
228 229 0.536687 CGCAGAGGATGGGATGCAAT 60.537 55.000 0.00 0.00 44.43 3.56
234 235 2.586245 CTTGCGCAGAGGATGGGA 59.414 61.111 11.31 0.00 44.43 4.37
243 244 2.671177 CGAGTTGTCCCTTGCGCAG 61.671 63.158 11.31 4.92 0.00 5.18
245 246 0.739813 ATACGAGTTGTCCCTTGCGC 60.740 55.000 0.00 0.00 0.00 6.09
246 247 1.393539 CAATACGAGTTGTCCCTTGCG 59.606 52.381 0.00 0.00 0.00 4.85
265 266 2.436109 GGAAGCCTTGGCACTCCA 59.564 61.111 20.89 0.00 41.55 3.86
286 287 2.103771 ACTCATGCGCAGATGTCCTAAT 59.896 45.455 18.32 0.00 0.00 1.73
287 288 1.482182 ACTCATGCGCAGATGTCCTAA 59.518 47.619 18.32 0.00 0.00 2.69
288 289 1.067669 GACTCATGCGCAGATGTCCTA 59.932 52.381 18.32 0.00 0.00 2.94
295 296 3.491619 GGAAAGATAGACTCATGCGCAGA 60.492 47.826 18.32 12.61 0.00 4.26
296 297 2.799412 GGAAAGATAGACTCATGCGCAG 59.201 50.000 18.32 8.46 0.00 5.18
303 304 8.597167 TGAAGAGAAAATGGAAAGATAGACTCA 58.403 33.333 0.00 0.00 0.00 3.41
304 305 9.442047 TTGAAGAGAAAATGGAAAGATAGACTC 57.558 33.333 0.00 0.00 0.00 3.36
327 328 9.578576 CAGGGATGATAGAGGAAATTTTATTGA 57.421 33.333 0.00 0.00 0.00 2.57
362 363 3.512516 GCTCAGGGCATTGTCGGC 61.513 66.667 0.00 0.00 41.35 5.54
396 398 4.614946 GATGCCTTGGCAATGAATACTTC 58.385 43.478 18.76 4.51 0.00 3.01
419 428 8.652810 TGTTGTAGTTAAAACTCAAGTAGTCC 57.347 34.615 0.00 0.00 37.50 3.85
443 452 5.588246 AGTTTGGTGGCCATTTTTAAAACTG 59.412 36.000 9.72 10.48 31.53 3.16
453 464 2.216331 GCCCAGTTTGGTGGCCATT 61.216 57.895 9.72 0.00 39.30 3.16
454 465 2.604382 GCCCAGTTTGGTGGCCAT 60.604 61.111 9.72 0.00 39.30 4.40
460 471 1.457455 CACTTGGGCCCAGTTTGGT 60.457 57.895 26.87 16.39 35.17 3.67
477 488 7.239763 TCAGTGGTGTATAGAAGATGAAACA 57.760 36.000 0.00 0.00 0.00 2.83
481 492 5.450550 CGCTTCAGTGGTGTATAGAAGATGA 60.451 44.000 0.00 0.00 38.30 2.92
485 496 2.860735 GCGCTTCAGTGGTGTATAGAAG 59.139 50.000 0.00 0.00 38.88 2.85
496 507 3.593247 GCAGTAATGCGCTTCAGTG 57.407 52.632 9.73 2.38 0.00 3.66
508 519 2.505628 TACACGTTGGTTCGCAGTAA 57.494 45.000 0.00 0.00 0.00 2.24
509 520 2.505628 TTACACGTTGGTTCGCAGTA 57.494 45.000 0.00 0.00 0.00 2.74
523 534 7.770897 ACTATTCTCTCAACCATCCAATTACAC 59.229 37.037 0.00 0.00 0.00 2.90
525 536 7.227512 CCACTATTCTCTCAACCATCCAATTAC 59.772 40.741 0.00 0.00 0.00 1.89
527 538 6.125029 CCACTATTCTCTCAACCATCCAATT 58.875 40.000 0.00 0.00 0.00 2.32
531 542 4.762289 ACCACTATTCTCTCAACCATCC 57.238 45.455 0.00 0.00 0.00 3.51
539 550 7.957002 TGGATTGAAGATACCACTATTCTCTC 58.043 38.462 0.00 0.00 0.00 3.20
540 551 7.921041 TGGATTGAAGATACCACTATTCTCT 57.079 36.000 0.00 0.00 0.00 3.10
544 555 6.931281 CACGATGGATTGAAGATACCACTATT 59.069 38.462 0.00 0.00 35.19 1.73
546 557 5.221441 CCACGATGGATTGAAGATACCACTA 60.221 44.000 0.00 0.00 40.96 2.74
557 568 5.720371 AAATTTGAACCACGATGGATTGA 57.280 34.783 10.46 0.00 40.96 2.57
561 572 6.001460 AGTCTAAAATTTGAACCACGATGGA 58.999 36.000 10.46 0.00 40.96 3.41
565 576 8.211116 TGTAAAGTCTAAAATTTGAACCACGA 57.789 30.769 0.00 0.00 0.00 4.35
616 628 4.204573 CGAATATCGTCGGAAGTCTGAAAC 59.795 45.833 0.00 0.00 37.37 2.78
635 647 0.613853 TCTCCTCCCACCGAACGAAT 60.614 55.000 0.00 0.00 0.00 3.34
639 651 0.685660 AACTTCTCCTCCCACCGAAC 59.314 55.000 0.00 0.00 0.00 3.95
648 660 1.540707 AGTCGACGGAAACTTCTCCTC 59.459 52.381 10.46 0.00 32.82 3.71
649 661 1.269998 CAGTCGACGGAAACTTCTCCT 59.730 52.381 10.41 0.00 32.82 3.69
650 662 1.699343 CAGTCGACGGAAACTTCTCC 58.301 55.000 10.41 0.00 0.00 3.71
651 663 1.061485 GCAGTCGACGGAAACTTCTC 58.939 55.000 20.25 0.00 0.00 2.87
652 664 0.663568 CGCAGTCGACGGAAACTTCT 60.664 55.000 20.25 0.00 38.10 2.85
653 665 0.662374 TCGCAGTCGACGGAAACTTC 60.662 55.000 20.25 0.00 40.21 3.01
654 666 0.663568 CTCGCAGTCGACGGAAACTT 60.664 55.000 20.25 0.00 40.21 2.66
655 667 1.081376 CTCGCAGTCGACGGAAACT 60.081 57.895 20.25 0.00 40.21 2.66
656 668 2.087009 CCTCGCAGTCGACGGAAAC 61.087 63.158 20.25 0.77 40.21 2.78
657 669 2.257371 CCTCGCAGTCGACGGAAA 59.743 61.111 20.25 5.16 40.21 3.13
658 670 2.981909 ACCTCGCAGTCGACGGAA 60.982 61.111 20.25 5.52 40.21 4.30
659 671 3.733960 CACCTCGCAGTCGACGGA 61.734 66.667 20.25 12.65 40.21 4.69
660 672 3.553437 AACACCTCGCAGTCGACGG 62.553 63.158 11.64 11.64 40.21 4.79
661 673 1.660575 AAACACCTCGCAGTCGACG 60.661 57.895 10.46 6.47 40.21 5.12
662 674 0.874607 ACAAACACCTCGCAGTCGAC 60.875 55.000 7.70 7.70 40.21 4.20
663 675 0.874175 CACAAACACCTCGCAGTCGA 60.874 55.000 0.00 0.00 43.28 4.20
664 676 1.564622 CACAAACACCTCGCAGTCG 59.435 57.895 0.00 0.00 0.00 4.18
665 677 0.814010 ACCACAAACACCTCGCAGTC 60.814 55.000 0.00 0.00 0.00 3.51
666 678 1.095228 CACCACAAACACCTCGCAGT 61.095 55.000 0.00 0.00 0.00 4.40
667 679 0.813610 TCACCACAAACACCTCGCAG 60.814 55.000 0.00 0.00 0.00 5.18
668 680 1.092921 GTCACCACAAACACCTCGCA 61.093 55.000 0.00 0.00 0.00 5.10
669 681 0.814010 AGTCACCACAAACACCTCGC 60.814 55.000 0.00 0.00 0.00 5.03
670 682 1.597663 GAAGTCACCACAAACACCTCG 59.402 52.381 0.00 0.00 0.00 4.63
671 683 1.947456 GGAAGTCACCACAAACACCTC 59.053 52.381 0.00 0.00 0.00 3.85
675 687 6.126409 AGATTTTAGGAAGTCACCACAAACA 58.874 36.000 0.00 0.00 0.00 2.83
677 689 8.754991 TTAAGATTTTAGGAAGTCACCACAAA 57.245 30.769 0.00 0.00 0.00 2.83
682 694 8.794335 ACATCTTAAGATTTTAGGAAGTCACC 57.206 34.615 15.49 0.00 29.93 4.02
691 703 7.335491 GCCGACGTAACATCTTAAGATTTTAG 58.665 38.462 19.66 16.13 30.16 1.85
700 712 1.064505 CTCGGCCGACGTAACATCTTA 59.935 52.381 27.28 0.00 44.69 2.10
707 719 1.364626 GAGAGACTCGGCCGACGTAA 61.365 60.000 27.28 2.79 44.69 3.18
718 730 1.244697 TGTGCACCTCCGAGAGACTC 61.245 60.000 15.69 0.00 0.00 3.36
720 732 1.080434 GTGTGCACCTCCGAGAGAC 60.080 63.158 15.69 0.00 0.00 3.36
729 741 0.036010 GCTCTACCATGTGTGCACCT 60.036 55.000 15.69 0.00 0.00 4.00
735 747 2.738643 GCATGTACGCTCTACCATGTGT 60.739 50.000 0.00 0.00 0.00 3.72
740 752 1.806247 GCATGCATGTACGCTCTACCA 60.806 52.381 26.79 0.00 0.00 3.25
743 755 2.531522 ATGCATGCATGTACGCTCTA 57.468 45.000 31.74 0.00 35.03 2.43
744 756 1.600957 GAATGCATGCATGTACGCTCT 59.399 47.619 32.79 15.24 36.68 4.09
745 757 1.331447 TGAATGCATGCATGTACGCTC 59.669 47.619 32.79 23.98 36.68 5.03
746 758 1.381522 TGAATGCATGCATGTACGCT 58.618 45.000 32.79 16.78 36.68 5.07
757 770 2.025605 ACACTCACCTCCATGAATGCAT 60.026 45.455 0.00 0.00 28.78 3.96
761 774 2.877300 GCACACACTCACCTCCATGAAT 60.877 50.000 0.00 0.00 0.00 2.57
764 777 0.035881 AGCACACACTCACCTCCATG 59.964 55.000 0.00 0.00 0.00 3.66
767 780 1.510480 GCAAGCACACACTCACCTCC 61.510 60.000 0.00 0.00 0.00 4.30
769 782 1.889105 CGCAAGCACACACTCACCT 60.889 57.895 0.00 0.00 0.00 4.00
779 792 0.512952 ACAATCGAAGTCGCAAGCAC 59.487 50.000 0.00 0.00 39.60 4.40
781 794 0.095417 GGACAATCGAAGTCGCAAGC 59.905 55.000 13.20 0.00 39.60 4.01
784 797 0.317160 ACAGGACAATCGAAGTCGCA 59.683 50.000 13.20 0.00 39.60 5.10
788 811 6.687081 TTTTTAACACAGGACAATCGAAGT 57.313 33.333 0.00 0.00 0.00 3.01
810 833 0.543174 TGGCGCCCCTTGGTATTTTT 60.543 50.000 26.77 0.00 0.00 1.94
811 834 1.077625 TGGCGCCCCTTGGTATTTT 59.922 52.632 26.77 0.00 0.00 1.82
812 835 1.680989 GTGGCGCCCCTTGGTATTT 60.681 57.895 26.77 0.00 0.00 1.40
813 836 2.044352 GTGGCGCCCCTTGGTATT 60.044 61.111 26.77 0.00 0.00 1.89
814 837 2.612493 AAGTGGCGCCCCTTGGTAT 61.612 57.895 24.05 0.00 0.00 2.73
815 838 3.253838 AAGTGGCGCCCCTTGGTA 61.254 61.111 24.05 0.00 0.00 3.25
816 839 4.974721 CAAGTGGCGCCCCTTGGT 62.975 66.667 35.59 9.78 35.51 3.67
825 848 4.671250 ACAATTTTTGTTTTGCAAGTGGCG 60.671 37.500 0.00 0.00 43.73 5.69
826 849 4.558080 CACAATTTTTGTTTTGCAAGTGGC 59.442 37.500 0.00 0.00 43.23 5.01
827 850 5.697826 ACACAATTTTTGTTTTGCAAGTGG 58.302 33.333 0.00 0.00 43.23 4.00
845 869 7.669304 TGATTCCTATTGGATCTGAAAACACAA 59.331 33.333 0.00 0.00 42.81 3.33
869 893 4.933505 TGAATGCCAAAGAAACACATGA 57.066 36.364 0.00 0.00 0.00 3.07
870 894 5.467399 ACAATGAATGCCAAAGAAACACATG 59.533 36.000 0.00 0.00 0.00 3.21
871 895 5.467399 CACAATGAATGCCAAAGAAACACAT 59.533 36.000 0.00 0.00 0.00 3.21
872 896 4.809958 CACAATGAATGCCAAAGAAACACA 59.190 37.500 0.00 0.00 0.00 3.72
873 897 4.810491 ACACAATGAATGCCAAAGAAACAC 59.190 37.500 0.00 0.00 0.00 3.32
874 898 5.021033 ACACAATGAATGCCAAAGAAACA 57.979 34.783 0.00 0.00 0.00 2.83
875 899 5.989551 AACACAATGAATGCCAAAGAAAC 57.010 34.783 0.00 0.00 0.00 2.78
876 900 5.526846 GGAAACACAATGAATGCCAAAGAAA 59.473 36.000 0.00 0.00 0.00 2.52
877 901 5.055812 GGAAACACAATGAATGCCAAAGAA 58.944 37.500 0.00 0.00 0.00 2.52
878 902 4.344679 AGGAAACACAATGAATGCCAAAGA 59.655 37.500 0.00 0.00 0.00 2.52
880 904 4.686191 AGGAAACACAATGAATGCCAAA 57.314 36.364 0.00 0.00 0.00 3.28
881 905 4.832266 AGTAGGAAACACAATGAATGCCAA 59.168 37.500 0.00 0.00 0.00 4.52
882 906 4.406456 AGTAGGAAACACAATGAATGCCA 58.594 39.130 0.00 0.00 0.00 4.92
883 907 4.702131 AGAGTAGGAAACACAATGAATGCC 59.298 41.667 0.00 0.00 0.00 4.40
885 909 6.072286 AGCAAGAGTAGGAAACACAATGAATG 60.072 38.462 0.00 0.00 0.00 2.67
886 910 6.006449 AGCAAGAGTAGGAAACACAATGAAT 58.994 36.000 0.00 0.00 0.00 2.57
887 911 5.376625 AGCAAGAGTAGGAAACACAATGAA 58.623 37.500 0.00 0.00 0.00 2.57
888 912 4.973168 AGCAAGAGTAGGAAACACAATGA 58.027 39.130 0.00 0.00 0.00 2.57
889 913 5.122396 GGTAGCAAGAGTAGGAAACACAATG 59.878 44.000 0.00 0.00 0.00 2.82
890 914 5.013183 AGGTAGCAAGAGTAGGAAACACAAT 59.987 40.000 0.00 0.00 0.00 2.71
891 915 4.347000 AGGTAGCAAGAGTAGGAAACACAA 59.653 41.667 0.00 0.00 0.00 3.33
892 916 3.901844 AGGTAGCAAGAGTAGGAAACACA 59.098 43.478 0.00 0.00 0.00 3.72
893 917 4.246458 CAGGTAGCAAGAGTAGGAAACAC 58.754 47.826 0.00 0.00 0.00 3.32
896 920 3.611766 GCAGGTAGCAAGAGTAGGAAA 57.388 47.619 0.00 0.00 44.79 3.13
915 3483 4.142556 GAGTTGACTCTCTGGTACAGTAGC 60.143 50.000 2.56 2.56 44.66 3.58
920 3488 3.527507 AGGAGTTGACTCTCTGGTACA 57.472 47.619 10.68 0.00 42.48 2.90
923 3491 2.370189 CCAAAGGAGTTGACTCTCTGGT 59.630 50.000 10.68 0.00 42.48 4.00
992 3590 4.236416 CGGCGCCCATTGCTTACG 62.236 66.667 23.46 0.00 38.05 3.18
1020 3618 0.885596 CGAGTAGACCGGCTAGGAGG 60.886 65.000 0.00 0.00 45.00 4.30
1155 3753 2.853150 GACGTATTCGGCCGCGTTC 61.853 63.158 25.41 16.19 39.49 3.95
1276 3874 2.280524 CCAGAACACGAACGGGCA 60.281 61.111 0.00 0.00 0.00 5.36
1478 4076 3.976701 ATGTTGAAGGCGGGCGAGG 62.977 63.158 0.00 0.00 0.00 4.63
1725 4386 4.591202 CTTGAAATAAGCGTGCATACTGG 58.409 43.478 0.00 0.00 0.00 4.00
2224 4918 1.453155 AGCTACTTCCAAATGCCACG 58.547 50.000 0.00 0.00 0.00 4.94
2385 10733 7.330900 AGAAATATGTTCATCTTGCCTGAAG 57.669 36.000 0.00 0.00 33.49 3.02
2388 10736 7.558161 TGTAGAAATATGTTCATCTTGCCTG 57.442 36.000 0.00 0.00 0.00 4.85
2389 10737 8.757982 AATGTAGAAATATGTTCATCTTGCCT 57.242 30.769 0.00 0.00 0.00 4.75
2685 11049 6.525578 AATGTCTTGCACTCATCAATGATT 57.474 33.333 0.00 0.00 36.02 2.57
2721 11085 5.799681 ACAAATTTGCAGTTGTTTCCTTG 57.200 34.783 18.12 0.00 37.99 3.61
2757 11121 1.475280 TGATTCAATGCCAGCAGAAGC 59.525 47.619 0.00 0.88 42.56 3.86
2773 11137 3.555586 GCCTTGTGTTGCCATTCTTGATT 60.556 43.478 0.00 0.00 0.00 2.57
2993 11370 1.412361 GGATACAGCCTGAGGGTCTCT 60.412 57.143 0.00 0.00 34.45 3.10
3083 11460 4.161565 ACAATAGGAAGATTGACCTGCGTA 59.838 41.667 3.27 0.00 38.83 4.42
3112 11496 2.531522 TATGCCGACATCATGGTGAG 57.468 50.000 14.29 6.10 37.74 3.51
3281 11667 2.980233 GCAAACCGCTGGAGCACT 60.980 61.111 0.00 0.00 42.21 4.40
3376 16005 1.606737 GGGCTCAGATCTTGCGGATAC 60.607 57.143 10.31 0.00 34.33 2.24
3523 16186 2.461110 CCTTTTATCAGCGCGGCGT 61.461 57.895 24.46 7.95 0.00 5.68
3631 16301 6.198966 GTGGAGATTGTTTTTGATGAACACAC 59.801 38.462 0.00 0.00 36.79 3.82
3683 16353 1.273606 CATGACCCGTGAGAAGACTGT 59.726 52.381 0.00 0.00 0.00 3.55
3780 16821 1.889530 GACAGAGGTGGACCCGGAAG 61.890 65.000 0.73 0.00 38.74 3.46
3781 16822 1.911766 GACAGAGGTGGACCCGGAA 60.912 63.158 0.73 0.00 38.74 4.30
3866 17141 4.882427 TGATTACGTTGTTGTGGGAGAAAA 59.118 37.500 0.00 0.00 0.00 2.29
3898 17173 5.630680 ACATAATTTATGCGCTGCAATTAGC 59.369 36.000 9.73 0.00 43.62 3.09
3937 17212 1.470285 GGACATTCAGGTTACGCGCTA 60.470 52.381 5.73 0.00 0.00 4.26
3986 17266 2.163412 GGGCACATGAGCGTGAAAATAA 59.837 45.455 9.09 0.00 39.34 1.40
3993 17273 1.093972 TTTATGGGCACATGAGCGTG 58.906 50.000 12.99 0.00 37.97 5.34
4045 17326 5.674052 TTGTGGGCACATGCTAATAAAAT 57.326 34.783 3.48 0.00 41.52 1.82
4146 17429 4.498177 CGAGAATTATGAGCAGAACGAGGA 60.498 45.833 0.00 0.00 0.00 3.71
4172 17455 5.689383 TTGTGTGAGAATAAGGAAGTTGC 57.311 39.130 0.00 0.00 0.00 4.17
4195 17478 7.674348 TCTCTAAGTTGTCTGGAAATAAGGAGA 59.326 37.037 0.00 0.00 0.00 3.71
4245 17528 9.971922 GAACAATCCCATCTTGGAATTTTATAG 57.028 33.333 0.00 0.00 40.96 1.31


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

AutoCloner maintained by Alex Coulton.