Multiple sequence alignment - TraesCS1B01G285600

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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 TraesCS1B01G285600 chr1B 100.000 7050 0 0 1 7050 496568991 496561942 0.000000e+00 13020.0
1 TraesCS1B01G285600 chr1B 82.105 190 24 6 4968 5154 496565007 496565189 3.410000e-33 154.0
2 TraesCS1B01G285600 chr1B 88.235 85 8 1 5062 5146 68251287 68251369 4.500000e-17 100.0
3 TraesCS1B01G285600 chr1D 92.914 6393 274 80 741 7047 371756743 371750444 0.000000e+00 9130.0
4 TraesCS1B01G285600 chr1D 86.945 766 58 22 1 726 371782778 371782015 0.000000e+00 822.0
5 TraesCS1B01G285600 chr1D 84.946 186 24 4 3803 3985 371752321 371752505 1.210000e-42 185.0
6 TraesCS1B01G285600 chr1D 83.770 191 20 7 4968 5154 371753489 371753672 3.380000e-38 171.0
7 TraesCS1B01G285600 chr1A 92.528 2824 118 33 923 3669 471494383 471491576 0.000000e+00 3960.0
8 TraesCS1B01G285600 chr1A 87.326 1870 130 50 5240 7050 471490837 471489016 0.000000e+00 2041.0
9 TraesCS1B01G285600 chr1A 86.544 981 65 33 1 937 471504418 471503461 0.000000e+00 1018.0
10 TraesCS1B01G285600 chr1A 84.422 199 27 4 3795 3993 374253243 374253049 7.220000e-45 193.0
11 TraesCS1B01G285600 chr1A 89.032 155 12 5 3668 3817 471491417 471491263 3.360000e-43 187.0
12 TraesCS1B01G285600 chr1A 90.566 106 8 2 5147 5251 471491278 471491174 9.540000e-29 139.0
13 TraesCS1B01G285600 chr4A 83.333 852 91 22 1115 1955 592755925 592756736 0.000000e+00 739.0
14 TraesCS1B01G285600 chr4A 83.216 852 92 22 1115 1955 592477118 592477929 0.000000e+00 734.0
15 TraesCS1B01G285600 chr4A 83.099 852 93 22 1115 1955 593044005 593044816 0.000000e+00 728.0
16 TraesCS1B01G285600 chr4A 82.807 855 98 22 1115 1958 591566157 591565341 0.000000e+00 719.0
17 TraesCS1B01G285600 chr4A 90.270 370 34 2 3808 4176 609933409 609933777 3.820000e-132 483.0
18 TraesCS1B01G285600 chr4A 81.474 502 48 20 1467 1958 702672401 702671935 3.110000e-98 370.0
19 TraesCS1B01G285600 chrUn 83.099 852 93 22 1115 1955 332730711 332731522 0.000000e+00 728.0
20 TraesCS1B01G285600 chrUn 84.000 100 14 2 5510 5608 123881566 123881468 2.090000e-15 95.3
21 TraesCS1B01G285600 chrUn 78.049 164 26 8 5447 5608 131896546 131896701 2.090000e-15 95.3
22 TraesCS1B01G285600 chr3D 88.546 454 34 8 1242 1684 575279277 575278831 1.040000e-147 534.0
23 TraesCS1B01G285600 chr3D 84.483 174 24 3 3810 3982 607884089 607884260 1.220000e-37 169.0
24 TraesCS1B01G285600 chr5D 87.225 454 37 9 1242 1684 112835303 112834860 1.370000e-136 497.0
25 TraesCS1B01G285600 chr5D 87.037 162 18 3 3808 3969 263282872 263283030 5.620000e-41 180.0
26 TraesCS1B01G285600 chr6A 88.214 280 32 1 3900 4179 614766547 614766269 4.080000e-87 333.0
27 TraesCS1B01G285600 chr6A 87.805 164 19 1 3807 3969 112757825 112757988 2.600000e-44 191.0
28 TraesCS1B01G285600 chr6A 83.616 177 27 2 3813 3989 112759390 112759216 1.570000e-36 165.0
29 TraesCS1B01G285600 chr6A 83.243 185 21 7 4971 5152 112758000 112757823 2.040000e-35 161.0
30 TraesCS1B01G285600 chr6A 81.215 181 25 6 4967 5145 112759218 112759391 3.430000e-28 137.0
31 TraesCS1B01G285600 chr6B 82.967 182 21 7 4972 5150 231369762 231369588 9.470000e-34 156.0
32 TraesCS1B01G285600 chr6B 95.789 95 4 0 1864 1958 663794126 663794220 3.410000e-33 154.0
33 TraesCS1B01G285600 chr2D 80.000 165 24 6 4993 5154 398210636 398210794 5.780000e-21 113.0
34 TraesCS1B01G285600 chr2B 86.170 94 11 1 5062 5155 212162123 212162032 4.500000e-17 100.0
35 TraesCS1B01G285600 chr3B 78.049 164 26 8 5447 5608 515214511 515214666 2.090000e-15 95.3
36 TraesCS1B01G285600 chr3B 78.049 164 26 8 5447 5608 515474763 515474918 2.090000e-15 95.3
37 TraesCS1B01G285600 chr3B 78.049 164 26 8 5447 5608 515999739 515999894 2.090000e-15 95.3
38 TraesCS1B01G285600 chr3B 78.049 164 26 8 5447 5608 516472744 516472899 2.090000e-15 95.3
39 TraesCS1B01G285600 chr3B 84.000 100 14 2 5510 5608 518914406 518914308 2.090000e-15 95.3


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 TraesCS1B01G285600 chr1B 496561942 496568991 7049 True 13020.00 13020 100.000 1 7050 1 chr1B.!!$R1 7049
1 TraesCS1B01G285600 chr1D 371750444 371756743 6299 True 9130.00 9130 92.914 741 7047 1 chr1D.!!$R1 6306
2 TraesCS1B01G285600 chr1D 371782015 371782778 763 True 822.00 822 86.945 1 726 1 chr1D.!!$R2 725
3 TraesCS1B01G285600 chr1A 471489016 471494383 5367 True 1581.75 3960 89.863 923 7050 4 chr1A.!!$R3 6127
4 TraesCS1B01G285600 chr1A 471503461 471504418 957 True 1018.00 1018 86.544 1 937 1 chr1A.!!$R2 936
5 TraesCS1B01G285600 chr4A 592755925 592756736 811 False 739.00 739 83.333 1115 1955 1 chr4A.!!$F2 840
6 TraesCS1B01G285600 chr4A 592477118 592477929 811 False 734.00 734 83.216 1115 1955 1 chr4A.!!$F1 840
7 TraesCS1B01G285600 chr4A 593044005 593044816 811 False 728.00 728 83.099 1115 1955 1 chr4A.!!$F3 840
8 TraesCS1B01G285600 chr4A 591565341 591566157 816 True 719.00 719 82.807 1115 1958 1 chr4A.!!$R1 843
9 TraesCS1B01G285600 chrUn 332730711 332731522 811 False 728.00 728 83.099 1115 1955 1 chrUn.!!$F2 840

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
985 1051 0.402121 AGAAAACCAGTCCAGAGCCC 59.598 55.000 0.00 0.00 0.00 5.19 F
1949 2076 1.064906 AGCATGGATGGTCTGTTCCAG 60.065 52.381 0.00 0.00 44.87 3.86 F
1976 2103 1.074405 TGAGAACAGCTGGCAATCCTT 59.926 47.619 19.93 0.18 0.00 3.36 F
3703 4018 1.111277 AACACCTGGAAAGCACCAAC 58.889 50.000 0.00 0.00 39.59 3.77 F
4218 4535 0.342313 TACCCCTCCCTTCTCTTCCC 59.658 60.000 0.00 0.00 0.00 3.97 F
4305 4622 0.673333 CACGCTGCCACCATAGACAA 60.673 55.000 0.00 0.00 0.00 3.18 F
5020 5340 0.746659 AGCAAACCACCTGAGCAAAC 59.253 50.000 0.00 0.00 0.00 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1958 2085 1.074405 TGAAGGATTGCCAGCTGTTCT 59.926 47.619 13.81 0.0 36.29 3.01 R
3918 4235 2.239681 AAACAAACCCACCCAAGACA 57.760 45.000 0.00 0.0 0.00 3.41 R
3972 4289 0.322546 GGGCCCTACTGGTCAACAAG 60.323 60.000 17.04 0.0 42.20 3.16 R
4797 5114 0.108329 ATACGGTTTGGTCTCCAGCG 60.108 55.000 0.00 0.0 33.81 5.18 R
5763 6440 0.032678 CCGCGATCAGAAGCCTATGT 59.967 55.000 8.23 0.0 0.00 2.29 R
5806 6483 0.385974 ATCAGCTGCGCAAAAACGTC 60.386 50.000 13.05 0.0 34.88 4.34 R
6817 7559 0.846693 AGTGAAGCCAAGAAGGTGGT 59.153 50.000 0.00 0.0 41.12 4.16 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
40 42 1.099295 ACGCATGGCATCATCCACAG 61.099 55.000 0.00 0.00 39.25 3.66
53 55 5.628797 TCATCCACAGGCTAATAACATGA 57.371 39.130 0.00 0.00 0.00 3.07
77 79 2.025887 CCCCTTTCAGGTGAGCATAACT 60.026 50.000 0.00 0.00 31.93 2.24
146 148 1.374947 GCAGGTACACCCTCTTGCA 59.625 57.895 5.69 0.00 43.86 4.08
148 150 2.014068 GCAGGTACACCCTCTTGCATC 61.014 57.143 5.69 0.00 43.86 3.91
222 228 3.859414 GCTCAGGCTGGAGGCGAT 61.859 66.667 15.73 0.00 46.23 4.58
225 231 2.249413 CTCAGGCTGGAGGCGATGTT 62.249 60.000 15.73 0.00 46.23 2.71
258 264 2.500910 CAGCTCCAGGTTCTCTTCATCT 59.499 50.000 0.00 0.00 0.00 2.90
286 292 4.729918 AAGGCCCGAAGCTGCAGG 62.730 66.667 17.12 0.00 43.05 4.85
316 322 1.810030 CTACAGCGGAAAGGGCGTC 60.810 63.158 0.00 0.00 35.00 5.19
318 324 4.697756 CAGCGGAAAGGGCGTCCA 62.698 66.667 9.71 0.00 34.56 4.02
335 341 0.991920 CCAGGGTTTTCCAGAGGCTA 59.008 55.000 0.00 0.00 42.91 3.93
339 345 1.819288 GGGTTTTCCAGAGGCTAAAGC 59.181 52.381 0.00 0.00 42.91 3.51
340 346 2.514803 GGTTTTCCAGAGGCTAAAGCA 58.485 47.619 4.07 0.00 40.63 3.91
341 347 3.092301 GGTTTTCCAGAGGCTAAAGCAT 58.908 45.455 4.07 0.00 40.63 3.79
343 369 4.021104 GGTTTTCCAGAGGCTAAAGCATTT 60.021 41.667 4.07 0.00 40.63 2.32
363 397 4.836125 TTTTTCCAGTGTCATGAGCTTC 57.164 40.909 0.00 0.00 0.00 3.86
364 398 3.777106 TTTCCAGTGTCATGAGCTTCT 57.223 42.857 0.00 0.00 0.00 2.85
365 399 3.325293 TTCCAGTGTCATGAGCTTCTC 57.675 47.619 0.00 0.00 0.00 2.87
366 400 2.250924 TCCAGTGTCATGAGCTTCTCA 58.749 47.619 0.00 0.00 44.99 3.27
367 401 2.233186 TCCAGTGTCATGAGCTTCTCAG 59.767 50.000 0.00 0.00 44.08 3.35
368 402 2.028294 CCAGTGTCATGAGCTTCTCAGT 60.028 50.000 0.00 0.00 44.08 3.41
369 403 3.556633 CCAGTGTCATGAGCTTCTCAGTT 60.557 47.826 0.00 0.00 44.08 3.16
370 404 3.679025 CAGTGTCATGAGCTTCTCAGTTC 59.321 47.826 0.00 0.00 44.08 3.01
371 405 2.999355 GTGTCATGAGCTTCTCAGTTCC 59.001 50.000 0.00 0.00 44.08 3.62
375 409 4.400884 GTCATGAGCTTCTCAGTTCCTCTA 59.599 45.833 0.00 0.00 44.08 2.43
383 417 3.892284 TCTCAGTTCCTCTAGCAGTAGG 58.108 50.000 0.00 0.00 0.00 3.18
396 430 3.990318 GCAGTAGGCTCTTTGTTTTGT 57.010 42.857 0.00 0.00 40.25 2.83
397 431 4.307443 GCAGTAGGCTCTTTGTTTTGTT 57.693 40.909 0.00 0.00 40.25 2.83
399 433 4.740205 GCAGTAGGCTCTTTGTTTTGTTTC 59.260 41.667 0.00 0.00 40.25 2.78
400 434 4.970003 CAGTAGGCTCTTTGTTTTGTTTCG 59.030 41.667 0.00 0.00 0.00 3.46
401 435 4.638865 AGTAGGCTCTTTGTTTTGTTTCGT 59.361 37.500 0.00 0.00 0.00 3.85
415 469 2.051423 GTTTCGTTGCAAGCTTTAGGC 58.949 47.619 0.00 0.00 42.19 3.93
444 498 5.171476 ACTGTGTGTGTGATAGCATTAGAC 58.829 41.667 0.00 0.00 0.00 2.59
456 510 8.777413 GTGATAGCATTAGACTGCATATGAAAA 58.223 33.333 6.97 0.00 44.77 2.29
458 512 6.382869 AGCATTAGACTGCATATGAAAACC 57.617 37.500 6.97 0.00 44.77 3.27
466 520 8.218338 AGACTGCATATGAAAACCTATCTTTG 57.782 34.615 6.97 0.00 0.00 2.77
478 532 4.243270 ACCTATCTTTGTCAGCGTGTAAC 58.757 43.478 0.00 0.00 0.00 2.50
480 534 2.605837 TCTTTGTCAGCGTGTAACCA 57.394 45.000 0.00 0.00 0.00 3.67
481 535 3.120321 TCTTTGTCAGCGTGTAACCAT 57.880 42.857 0.00 0.00 0.00 3.55
482 536 3.064207 TCTTTGTCAGCGTGTAACCATC 58.936 45.455 0.00 0.00 0.00 3.51
499 554 1.688735 CATCCATGGCGGTCTCTTCTA 59.311 52.381 6.96 0.00 35.57 2.10
507 562 1.866063 GCGGTCTCTTCTAAGCCATCG 60.866 57.143 0.00 0.00 0.00 3.84
508 563 1.859383 GGTCTCTTCTAAGCCATCGC 58.141 55.000 0.00 0.00 0.00 4.58
524 579 2.274645 CGCATGGCCCTGTTTGGAA 61.275 57.895 9.95 0.00 38.35 3.53
528 583 1.273327 CATGGCCCTGTTTGGAACTTC 59.727 52.381 0.00 0.00 38.35 3.01
529 584 0.555769 TGGCCCTGTTTGGAACTTCT 59.444 50.000 0.00 0.00 38.35 2.85
563 619 5.447818 CGGGAAATAAGCTGATTCTTGTGAC 60.448 44.000 0.00 0.00 0.00 3.67
573 629 3.433274 TGATTCTTGTGACATTCTCGTGC 59.567 43.478 0.00 0.00 0.00 5.34
575 631 2.407090 TCTTGTGACATTCTCGTGCTG 58.593 47.619 0.00 0.00 0.00 4.41
591 647 2.435938 TGGAAACGCGCCTGGATC 60.436 61.111 5.73 0.00 0.00 3.36
687 743 2.884894 AGACGACGAGGTTTTGAACT 57.115 45.000 0.00 0.00 0.00 3.01
690 746 2.728318 GACGACGAGGTTTTGAACTACC 59.272 50.000 0.00 0.00 34.54 3.18
732 791 4.335315 ACATTTTCTCTTGCTTTGTCACGA 59.665 37.500 0.00 0.00 0.00 4.35
739 799 2.605837 TGCTTTGTCACGACCAAGTA 57.394 45.000 11.38 5.54 36.69 2.24
764 824 4.132336 CCTGAATCGTGAATCACATGGAT 58.868 43.478 14.24 5.41 38.05 3.41
765 825 5.299949 CCTGAATCGTGAATCACATGGATA 58.700 41.667 14.24 0.00 34.28 2.59
766 826 5.407691 CCTGAATCGTGAATCACATGGATAG 59.592 44.000 14.24 4.26 34.28 2.08
767 827 5.299949 TGAATCGTGAATCACATGGATAGG 58.700 41.667 14.24 0.00 34.28 2.57
768 828 3.751479 TCGTGAATCACATGGATAGGG 57.249 47.619 14.24 0.00 34.28 3.53
769 829 3.304829 TCGTGAATCACATGGATAGGGA 58.695 45.455 14.24 0.00 34.28 4.20
770 830 3.903714 TCGTGAATCACATGGATAGGGAT 59.096 43.478 14.24 0.00 34.28 3.85
790 850 3.385384 TGGTCGAGGCAGCTCAGG 61.385 66.667 0.00 0.00 0.00 3.86
791 851 3.386237 GGTCGAGGCAGCTCAGGT 61.386 66.667 0.00 0.00 0.00 4.00
795 861 2.503546 GAGGCAGCTCAGGTAGGC 59.496 66.667 0.00 0.00 0.00 3.93
985 1051 0.402121 AGAAAACCAGTCCAGAGCCC 59.598 55.000 0.00 0.00 0.00 5.19
1149 1228 3.147595 CGCTGGGAGTCGGATCCA 61.148 66.667 13.41 0.00 41.52 3.41
1210 1289 2.711922 TTCGGCTCCTTCTCTCCGC 61.712 63.158 0.00 0.00 41.49 5.54
1277 1357 1.901650 CTTCGGTTGCTTGTCTCGCC 61.902 60.000 0.00 0.00 0.00 5.54
1357 1437 1.535833 GGAGCTCGGGAATCTATCGA 58.464 55.000 7.83 0.00 0.00 3.59
1378 1458 1.197721 CGTGATTGTTTCTGCCTGGAC 59.802 52.381 0.00 0.00 0.00 4.02
1551 1639 1.891919 GGTGCACGCCTTCTGTTCA 60.892 57.895 11.45 0.00 0.00 3.18
1617 1716 3.055458 TGCTAATGTGGTACAAGCTAGCA 60.055 43.478 18.83 14.46 44.16 3.49
1624 1723 2.680805 TGGTACAAGCTAGCAATCAGCC 60.681 50.000 18.83 11.80 39.36 4.85
1628 1727 3.928441 TACAAGCTAGCAATCAGCCTGTG 60.928 47.826 18.83 1.58 42.26 3.66
1688 1798 7.289084 AGGATTTCTCTTGATAAGTACTCCCTC 59.711 40.741 0.00 0.00 0.00 4.30
1708 1818 7.371043 TCCCTCTGTAAGGTCTTATATTCCTT 58.629 38.462 0.00 0.00 44.56 3.36
1717 1827 7.619512 AGGTCTTATATTCCTTTACAGAGGG 57.380 40.000 0.00 0.00 37.41 4.30
1721 1831 8.145122 GTCTTATATTCCTTTACAGAGGGAGTG 58.855 40.741 0.00 0.00 37.41 3.51
1739 1849 5.298026 GGGAGTGCTTCTTTCTCCATAATTC 59.702 44.000 11.65 0.00 46.61 2.17
1771 1884 4.635765 TCTTGTATCCTGCAATTACTGTGC 59.364 41.667 0.00 0.00 42.55 4.57
1882 2009 7.989741 GGACTCTTAATCTCTGAATTTCCATGA 59.010 37.037 0.00 0.00 0.00 3.07
1949 2076 1.064906 AGCATGGATGGTCTGTTCCAG 60.065 52.381 0.00 0.00 44.87 3.86
1958 2085 2.637382 TGGTCTGTTCCAGTTAGCATGA 59.363 45.455 0.00 0.00 33.19 3.07
1961 2088 4.563580 GGTCTGTTCCAGTTAGCATGAGAA 60.564 45.833 0.00 0.00 32.61 2.87
1976 2103 1.074405 TGAGAACAGCTGGCAATCCTT 59.926 47.619 19.93 0.18 0.00 3.36
2142 2280 3.040147 AGTATGCAAGCACGTACAGTT 57.960 42.857 0.00 0.00 34.98 3.16
2176 2314 4.384208 CCCCAGTTTCCTAGAGGTTATGTG 60.384 50.000 0.00 0.00 36.34 3.21
2261 2411 1.457303 CAGTTTGCTGACTGTACTCGC 59.543 52.381 10.66 0.00 45.28 5.03
2277 2427 5.708230 TGTACTCGCTGGATTTAATTTTGGT 59.292 36.000 0.00 0.00 0.00 3.67
2397 2547 5.471797 CGATACAGTATGAGAGAGATGTGGT 59.528 44.000 0.00 0.00 39.69 4.16
2488 2638 8.328758 AGTCCATTTATCCATGTTTCTGAGTTA 58.671 33.333 0.00 0.00 0.00 2.24
2504 2654 5.641209 TCTGAGTTAATCTGCTTCTTTCTGC 59.359 40.000 0.00 0.00 0.00 4.26
2598 2748 6.705302 TGCATTCTCTGATAAGTCAACTTCT 58.295 36.000 0.00 0.00 37.40 2.85
2722 2872 4.674281 AGAACTCCGAAATCTCCATACC 57.326 45.455 0.00 0.00 0.00 2.73
3192 3342 4.338012 TCAACCTACGTACATCAGGAAGA 58.662 43.478 8.31 2.98 33.44 2.87
3321 3473 6.766467 CCCAGTAATGACCTTCTATTGTTACC 59.234 42.308 0.00 0.00 0.00 2.85
3462 3614 3.010420 GCTGTCCTTGGTGAGTATTTCC 58.990 50.000 0.00 0.00 0.00 3.13
3647 3799 6.815089 TGTGTATTCTTTTTCTGTTGGCATT 58.185 32.000 0.00 0.00 0.00 3.56
3703 4018 1.111277 AACACCTGGAAAGCACCAAC 58.889 50.000 0.00 0.00 39.59 3.77
3793 4108 6.545504 TGTCAATTAAGAGAACACAGAAGC 57.454 37.500 0.00 0.00 0.00 3.86
3800 4115 4.186856 AGAGAACACAGAAGCTAAGCTC 57.813 45.455 0.00 0.00 38.25 4.09
3801 4116 3.576118 AGAGAACACAGAAGCTAAGCTCA 59.424 43.478 0.00 0.00 38.25 4.26
3802 4117 4.222588 AGAGAACACAGAAGCTAAGCTCAT 59.777 41.667 0.00 0.00 38.25 2.90
3804 4119 6.042638 AGAACACAGAAGCTAAGCTCATTA 57.957 37.500 0.00 0.00 38.25 1.90
3806 4121 6.936900 AGAACACAGAAGCTAAGCTCATTAAA 59.063 34.615 0.00 0.00 38.25 1.52
3807 4122 7.609532 AGAACACAGAAGCTAAGCTCATTAAAT 59.390 33.333 0.00 0.00 38.25 1.40
3808 4123 8.792830 AACACAGAAGCTAAGCTCATTAAATA 57.207 30.769 0.00 0.00 38.25 1.40
3811 4126 9.713740 CACAGAAGCTAAGCTCATTAAATAAAG 57.286 33.333 0.00 0.00 38.25 1.85
3907 4224 1.421646 CCCCCTGATCTGTCCAATACC 59.578 57.143 0.00 0.00 0.00 2.73
3918 4235 8.798402 TGATCTGTCCAATACCGTTTAAAAATT 58.202 29.630 0.00 0.00 0.00 1.82
3928 4245 5.353111 ACCGTTTAAAAATTGTCTTGGGTG 58.647 37.500 0.00 0.00 0.00 4.61
3972 4289 0.598065 GTGGATGTGGTCAAAGTGGC 59.402 55.000 0.00 0.00 0.00 5.01
3992 4309 1.785353 TTGTTGACCAGTAGGGCCCC 61.785 60.000 21.43 3.37 45.14 5.80
3998 4315 3.387947 CAGTAGGGCCCCGTCGTT 61.388 66.667 21.43 0.00 0.00 3.85
4012 4329 0.896226 GTCGTTAGGTGAAGAGGGCT 59.104 55.000 0.00 0.00 0.00 5.19
4017 4334 2.798445 TAGGTGAAGAGGGCTGCCGA 62.798 60.000 13.40 0.00 0.00 5.54
4045 4362 2.443203 TCATCCTCGGCCGCCTAA 60.443 61.111 23.51 5.98 0.00 2.69
4137 4454 0.971447 ACCTCCAGCGTCTACTTCCC 60.971 60.000 0.00 0.00 0.00 3.97
4152 4469 3.322466 CCCGGCCACCAGTTCTCT 61.322 66.667 2.24 0.00 0.00 3.10
4153 4470 2.046892 CCGGCCACCAGTTCTCTG 60.047 66.667 2.24 0.00 41.01 3.35
4162 4479 3.114558 CAGTTCTCTGGTCGTGCTC 57.885 57.895 0.00 0.00 37.97 4.26
4168 4485 1.213182 TCTCTGGTCGTGCTCTCCTAT 59.787 52.381 0.00 0.00 0.00 2.57
4181 4498 2.525381 CCTATGGCCCGGCTCTCT 60.525 66.667 9.86 0.00 0.00 3.10
4193 4510 1.161563 GGCTCTCTAGTCGGGACTCG 61.162 65.000 4.30 0.00 42.54 4.18
4215 4532 1.722851 TGACTACCCCTCCCTTCTCTT 59.277 52.381 0.00 0.00 0.00 2.85
4218 4535 0.342313 TACCCCTCCCTTCTCTTCCC 59.658 60.000 0.00 0.00 0.00 3.97
4220 4537 2.066999 CCCTCCCTTCTCTTCCCGG 61.067 68.421 0.00 0.00 0.00 5.73
4222 4539 1.990060 CTCCCTTCTCTTCCCGGCA 60.990 63.158 0.00 0.00 0.00 5.69
4259 4576 1.810532 CTCTAGACGAGGCCACCAC 59.189 63.158 5.01 0.00 36.06 4.16
4305 4622 0.673333 CACGCTGCCACCATAGACAA 60.673 55.000 0.00 0.00 0.00 3.18
4417 4734 1.447838 CACGCTTCACCGCTACCAT 60.448 57.895 0.00 0.00 0.00 3.55
4418 4735 1.447838 ACGCTTCACCGCTACCATG 60.448 57.895 0.00 0.00 0.00 3.66
4425 4742 3.797353 CCGCTACCATGGGCCAGT 61.797 66.667 18.09 8.15 0.00 4.00
4477 4794 2.033602 TCTCCTCACCGTCGCTCA 59.966 61.111 0.00 0.00 0.00 4.26
4500 4817 3.715097 GCTGTCCAGGCCTGCTCT 61.715 66.667 28.39 0.00 0.00 4.09
4568 4885 1.671742 GGAGTCAAACTGCCTCCGA 59.328 57.895 0.00 0.00 35.79 4.55
4585 4902 1.606531 GATGCTCCACAGCCTCCTT 59.393 57.895 0.00 0.00 46.26 3.36
4600 4917 1.438710 CCTTCAAAGTTCACGCGCG 60.439 57.895 30.96 30.96 0.00 6.86
4683 5000 1.457009 CCAGTCCGCTAGCCTAGGTC 61.457 65.000 11.31 2.69 0.00 3.85
4741 5058 1.903404 CTGGCTTGCCCGTTCCTTT 60.903 57.895 9.35 0.00 35.87 3.11
4803 5120 4.927782 GTGCACCACCACGCTGGA 62.928 66.667 5.22 0.00 40.96 3.86
4812 5129 1.966451 CCACGCTGGAGACCAAACC 60.966 63.158 0.00 0.00 40.96 3.27
4814 5131 2.030562 CGCTGGAGACCAAACCGT 59.969 61.111 0.00 0.00 30.80 4.83
4908 5225 2.423446 GTGGCCGGCTGATAGAGG 59.577 66.667 28.56 0.00 0.00 3.69
4951 5270 8.810652 TTTTCTGTAAAATTAATGCCACAGAC 57.189 30.769 18.63 1.81 41.37 3.51
4954 5273 8.263940 TCTGTAAAATTAATGCCACAGACTAC 57.736 34.615 16.47 0.66 37.93 2.73
4958 5277 2.554806 TAATGCCACAGACTACGTCG 57.445 50.000 0.00 0.00 37.67 5.12
5020 5340 0.746659 AGCAAACCACCTGAGCAAAC 59.253 50.000 0.00 0.00 0.00 2.93
5027 5347 0.754957 CACCTGAGCAAACCACCCAA 60.755 55.000 0.00 0.00 0.00 4.12
5044 5364 3.254903 ACCCAAAACTATTTCTGAACGGC 59.745 43.478 0.00 0.00 0.00 5.68
5061 5381 1.561643 GGCATCGGATAGATCAGGGA 58.438 55.000 0.00 0.00 37.52 4.20
5062 5382 1.480137 GGCATCGGATAGATCAGGGAG 59.520 57.143 0.00 0.00 37.52 4.30
5063 5383 1.480137 GCATCGGATAGATCAGGGAGG 59.520 57.143 0.00 0.00 37.52 4.30
5064 5384 2.106566 CATCGGATAGATCAGGGAGGG 58.893 57.143 0.00 0.00 37.52 4.30
5254 5924 3.136123 CATGGGTGGGCAAGCTCG 61.136 66.667 0.00 0.00 0.00 5.03
5263 5933 3.418068 GCAAGCTCGCAGACGCTT 61.418 61.111 0.00 0.00 46.23 4.68
5269 5939 1.735920 CTCGCAGACGCTTGCTCTT 60.736 57.895 9.65 0.00 41.90 2.85
5284 5954 4.750021 TGCTCTTGCTCTATGTGAATCT 57.250 40.909 0.00 0.00 40.48 2.40
5355 6025 4.930963 TCTTTTGTAGGCAACACACATTG 58.069 39.130 0.00 0.00 38.00 2.82
5356 6026 4.400884 TCTTTTGTAGGCAACACACATTGT 59.599 37.500 0.00 0.00 41.74 2.71
5393 6063 5.794894 ACTGTTGATCGGTCAAGTTTATCT 58.205 37.500 12.34 0.00 44.58 1.98
5401 6071 9.878667 TGATCGGTCAAGTTTATCTATTTAACA 57.121 29.630 0.00 0.00 0.00 2.41
5503 6173 4.273148 ACCTAACAGGCAGAAGTTAGTG 57.727 45.455 10.37 5.78 43.44 2.74
5578 6250 5.573337 GCTTCTTCAGCTGATATGGTTTT 57.427 39.130 19.04 0.00 46.27 2.43
5626 6298 4.301505 GCCAAGTGAGGCGAATGA 57.698 55.556 0.00 0.00 46.12 2.57
5627 6299 2.555123 GCCAAGTGAGGCGAATGAA 58.445 52.632 0.00 0.00 46.12 2.57
5698 6370 3.614390 GCTCGGAGTACCCTTATGTATGC 60.614 52.174 6.90 0.00 0.00 3.14
5732 6404 2.126888 GTTGCATCGCACCAACCG 60.127 61.111 0.00 0.00 38.71 4.44
5743 6415 4.617875 CCAACCGGGTCTGTGATC 57.382 61.111 6.32 0.00 0.00 2.92
5744 6416 1.078426 CCAACCGGGTCTGTGATCC 60.078 63.158 6.32 0.00 0.00 3.36
5806 6483 3.257933 GCAGACAGAGGTTTGCCG 58.742 61.111 0.00 0.00 46.38 5.69
5846 6523 4.329545 TGTGGTTGGCTCCTCGGC 62.330 66.667 1.63 0.00 38.97 5.54
5869 6546 1.461268 TGACCCAGCACCAGAGGAA 60.461 57.895 0.00 0.00 0.00 3.36
5963 6640 0.744414 AACGATTGCCAGATCGGTGG 60.744 55.000 15.57 1.52 46.80 4.61
5982 6659 2.371841 TGGGATGAACAGTTACTGCAGT 59.628 45.455 25.12 25.12 34.37 4.40
6106 6783 1.834263 GCCTGTCTCTACCTGGTGATT 59.166 52.381 10.23 0.00 0.00 2.57
6107 6784 3.031736 GCCTGTCTCTACCTGGTGATTA 58.968 50.000 10.23 0.00 0.00 1.75
6142 6819 2.879907 CTTTGCTCATGGTGCCCG 59.120 61.111 8.67 0.00 0.00 6.13
6190 6879 4.343814 TGATTTGACCCGTATCAGATGCTA 59.656 41.667 0.00 0.00 0.00 3.49
6194 6883 4.403734 TGACCCGTATCAGATGCTACATA 58.596 43.478 0.00 0.00 0.00 2.29
6198 6887 4.218635 CCCGTATCAGATGCTACATACACT 59.781 45.833 0.00 0.00 0.00 3.55
6226 6915 4.156622 CTGATGTGCGGCACTGCG 62.157 66.667 30.81 14.51 37.81 5.18
6269 6969 1.588824 CTGGATGCGCCTTTGCTTCA 61.589 55.000 4.18 0.00 39.92 3.02
6455 7181 8.023128 CGAAATAAGAAGCAGAGGAAAAATTGA 58.977 33.333 0.00 0.00 0.00 2.57
6456 7182 9.866798 GAAATAAGAAGCAGAGGAAAAATTGAT 57.133 29.630 0.00 0.00 0.00 2.57
6791 7533 1.577922 CCGTCTGTTTCGTCGGAGA 59.422 57.895 0.00 0.00 44.86 3.71
6823 7565 3.075005 CCCGTCGATCCACCACCT 61.075 66.667 0.00 0.00 0.00 4.00
6828 7570 1.726853 GTCGATCCACCACCTTCTTG 58.273 55.000 0.00 0.00 0.00 3.02
6834 7576 0.178992 CCACCACCTTCTTGGCTTCA 60.179 55.000 0.00 0.00 40.77 3.02
6843 7585 3.626670 CCTTCTTGGCTTCACTGATGATC 59.373 47.826 0.00 0.00 33.85 2.92
6901 7652 2.488952 TGTTTGTTGCTGTAGATCGCA 58.511 42.857 0.00 0.00 0.00 5.10
7008 7769 1.614850 GGTCGATAGGTTTTTGGCCCA 60.615 52.381 0.00 0.00 0.00 5.36
7034 7795 7.695480 AGCACTATACTACTGTCCATATCAG 57.305 40.000 0.00 0.00 38.68 2.90
7040 7801 4.219115 ACTACTGTCCATATCAGGGTGAG 58.781 47.826 0.00 0.00 37.25 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 42 5.420739 TGAAAGGGGTTTCATGTTATTAGCC 59.579 40.000 0.00 0.00 36.15 3.93
77 79 4.309099 GCTTGAATCCAGTTGCAATCAAA 58.691 39.130 0.59 0.00 33.37 2.69
146 148 1.207329 GCAGAAAGTAGTCGGTGGGAT 59.793 52.381 0.00 0.00 0.00 3.85
148 150 0.608640 AGCAGAAAGTAGTCGGTGGG 59.391 55.000 0.00 0.00 0.00 4.61
244 250 2.843113 CCTGGGAAGATGAAGAGAACCT 59.157 50.000 0.00 0.00 0.00 3.50
258 264 3.327404 GGGCCTTCGTCCTGGGAA 61.327 66.667 0.84 0.00 0.00 3.97
286 292 0.458025 CGCTGTAGGAACTCGGGAAC 60.458 60.000 0.00 0.00 41.75 3.62
316 322 0.991920 TAGCCTCTGGAAAACCCTGG 59.008 55.000 0.00 0.00 34.88 4.45
318 324 2.555448 GCTTTAGCCTCTGGAAAACCCT 60.555 50.000 0.00 0.00 33.18 4.34
343 369 4.067896 GAGAAGCTCATGACACTGGAAAA 58.932 43.478 0.00 0.00 0.00 2.29
360 394 4.338118 CCTACTGCTAGAGGAACTGAGAAG 59.662 50.000 0.00 0.00 41.55 2.85
361 395 4.274147 CCTACTGCTAGAGGAACTGAGAA 58.726 47.826 0.00 0.00 41.55 2.87
362 396 3.892284 CCTACTGCTAGAGGAACTGAGA 58.108 50.000 0.00 0.00 41.55 3.27
363 397 2.360801 GCCTACTGCTAGAGGAACTGAG 59.639 54.545 0.00 0.00 35.99 3.35
364 398 2.379972 GCCTACTGCTAGAGGAACTGA 58.620 52.381 0.00 0.00 35.99 3.41
365 399 2.880963 GCCTACTGCTAGAGGAACTG 57.119 55.000 0.00 0.00 35.99 3.16
383 417 3.366422 TGCAACGAAACAAAACAAAGAGC 59.634 39.130 0.00 0.00 0.00 4.09
389 423 2.953020 AGCTTGCAACGAAACAAAACA 58.047 38.095 0.00 0.00 0.00 2.83
393 427 3.701241 CCTAAAGCTTGCAACGAAACAA 58.299 40.909 0.00 0.00 0.00 2.83
396 430 1.334599 CGCCTAAAGCTTGCAACGAAA 60.335 47.619 0.00 0.00 40.39 3.46
397 431 0.237235 CGCCTAAAGCTTGCAACGAA 59.763 50.000 0.00 0.00 40.39 3.85
399 433 0.447801 ATCGCCTAAAGCTTGCAACG 59.552 50.000 0.00 2.57 40.39 4.10
400 434 2.936498 TCTATCGCCTAAAGCTTGCAAC 59.064 45.455 0.00 0.00 40.39 4.17
401 435 2.936498 GTCTATCGCCTAAAGCTTGCAA 59.064 45.455 0.00 0.00 40.39 4.08
415 469 4.038361 GCTATCACACACACAGTCTATCG 58.962 47.826 0.00 0.00 0.00 2.92
423 477 5.170748 CAGTCTAATGCTATCACACACACA 58.829 41.667 0.00 0.00 0.00 3.72
444 498 7.988737 TGACAAAGATAGGTTTTCATATGCAG 58.011 34.615 0.00 0.00 0.00 4.41
456 510 4.243270 GTTACACGCTGACAAAGATAGGT 58.757 43.478 0.00 0.00 0.00 3.08
458 512 4.242475 TGGTTACACGCTGACAAAGATAG 58.758 43.478 0.00 0.00 0.00 2.08
466 520 1.665679 CATGGATGGTTACACGCTGAC 59.334 52.381 0.00 0.00 0.00 3.51
480 534 2.088104 TAGAAGAGACCGCCATGGAT 57.912 50.000 18.40 0.00 42.00 3.41
481 535 1.757118 CTTAGAAGAGACCGCCATGGA 59.243 52.381 18.40 0.00 42.00 3.41
482 536 1.808133 GCTTAGAAGAGACCGCCATGG 60.808 57.143 7.63 7.63 46.41 3.66
507 562 1.187567 AGTTCCAAACAGGGCCATGC 61.188 55.000 19.26 0.00 38.24 4.06
508 563 1.273327 GAAGTTCCAAACAGGGCCATG 59.727 52.381 17.55 17.55 38.24 3.66
551 607 3.433274 GCACGAGAATGTCACAAGAATCA 59.567 43.478 0.00 0.00 0.00 2.57
563 619 0.179215 GCGTTTCCAGCACGAGAATG 60.179 55.000 0.00 0.00 40.20 2.67
573 629 2.436646 ATCCAGGCGCGTTTCCAG 60.437 61.111 8.43 0.00 0.00 3.86
575 631 3.564027 CGATCCAGGCGCGTTTCC 61.564 66.667 8.43 0.00 0.00 3.13
666 722 4.311816 AGTTCAAAACCTCGTCGTCTAA 57.688 40.909 0.00 0.00 0.00 2.10
687 743 5.702209 TGTCGAGATAATGCTACATACGGTA 59.298 40.000 0.00 0.00 0.00 4.02
690 746 7.568267 AAATGTCGAGATAATGCTACATACG 57.432 36.000 0.00 0.00 0.00 3.06
703 762 5.471456 ACAAAGCAAGAGAAAATGTCGAGAT 59.529 36.000 0.00 0.00 0.00 2.75
732 791 2.236146 TCACGATTCAGGCATACTTGGT 59.764 45.455 0.00 0.00 0.00 3.67
739 799 2.989909 TGTGATTCACGATTCAGGCAT 58.010 42.857 11.97 0.00 37.14 4.40
764 824 1.760875 GCCTCGACCACCATCCCTA 60.761 63.158 0.00 0.00 0.00 3.53
765 825 3.083997 GCCTCGACCACCATCCCT 61.084 66.667 0.00 0.00 0.00 4.20
766 826 3.391665 CTGCCTCGACCACCATCCC 62.392 68.421 0.00 0.00 0.00 3.85
767 827 2.187946 CTGCCTCGACCACCATCC 59.812 66.667 0.00 0.00 0.00 3.51
768 828 2.512515 GCTGCCTCGACCACCATC 60.513 66.667 0.00 0.00 0.00 3.51
769 829 3.005539 AGCTGCCTCGACCACCAT 61.006 61.111 0.00 0.00 0.00 3.55
770 830 3.695606 GAGCTGCCTCGACCACCA 61.696 66.667 0.00 0.00 0.00 4.17
790 850 2.031944 GCAGCTTAAAATAGGCGCCTAC 60.032 50.000 37.53 22.43 35.71 3.18
791 851 2.218603 GCAGCTTAAAATAGGCGCCTA 58.781 47.619 36.88 36.88 35.71 3.93
795 861 3.126858 TCAGTTGCAGCTTAAAATAGGCG 59.873 43.478 0.00 0.00 35.71 5.52
985 1051 0.036765 TCTCCGGTTGGTGGATTTCG 60.037 55.000 0.00 0.00 34.32 3.46
1210 1289 1.649664 CAGCAGATCACGAAAGGAGG 58.350 55.000 0.00 0.00 0.00 4.30
1353 1433 1.732259 GGCAGAAACAATCACGTCGAT 59.268 47.619 0.00 0.00 35.12 3.59
1357 1437 1.202758 TCCAGGCAGAAACAATCACGT 60.203 47.619 0.00 0.00 0.00 4.49
1378 1458 1.066002 CCTATTGGTCGCAAATGCCAG 59.934 52.381 0.00 0.00 37.91 4.85
1617 1716 1.001641 GTGGAGGCACAGGCTGATT 60.002 57.895 23.66 2.88 38.98 2.57
1624 1723 1.148310 CTGTAAACGTGGAGGCACAG 58.852 55.000 0.00 0.00 0.00 3.66
1628 1727 0.320697 ACCTCTGTAAACGTGGAGGC 59.679 55.000 16.32 0.00 46.54 4.70
1708 1818 3.904339 AGAAAGAAGCACTCCCTCTGTAA 59.096 43.478 0.00 0.00 0.00 2.41
1717 1827 5.882557 TGGAATTATGGAGAAAGAAGCACTC 59.117 40.000 0.00 0.00 0.00 3.51
1721 1831 7.176340 AGCATATGGAATTATGGAGAAAGAAGC 59.824 37.037 4.56 0.00 31.50 3.86
1739 1849 4.392047 TGCAGGATACAAGAAGCATATGG 58.608 43.478 4.56 0.00 41.41 2.74
1807 1922 7.039644 TGGGAGAAAAACAAGAAAACTGTAACA 60.040 33.333 0.00 0.00 0.00 2.41
1851 1971 9.877178 GAAATTCAGAGATTAAGAGTCCTTACA 57.123 33.333 0.00 0.00 34.80 2.41
1855 1975 7.502060 TGGAAATTCAGAGATTAAGAGTCCT 57.498 36.000 0.00 0.00 0.00 3.85
1949 2076 1.399791 GCCAGCTGTTCTCATGCTAAC 59.600 52.381 13.81 3.74 35.05 2.34
1958 2085 1.074405 TGAAGGATTGCCAGCTGTTCT 59.926 47.619 13.81 0.00 36.29 3.01
1961 2088 2.226962 ATTGAAGGATTGCCAGCTGT 57.773 45.000 13.81 0.00 36.29 4.40
2142 2280 3.725267 AGGAAACTGGGGGAACTCTTAAA 59.275 43.478 0.00 0.00 41.13 1.52
2261 2411 5.181056 GCAACCCAACCAAAATTAAATCCAG 59.819 40.000 0.00 0.00 0.00 3.86
2277 2427 1.271871 CCATCCTGTACAGCAACCCAA 60.272 52.381 17.86 0.00 0.00 4.12
2397 2547 2.799017 TGGTAGTTCCGAGAGCAGTAA 58.201 47.619 0.00 0.00 39.52 2.24
2488 2638 5.979288 AGAAATGCAGAAAGAAGCAGATT 57.021 34.783 0.00 0.00 44.94 2.40
2622 2772 6.333416 CGCTATAGCTCTAATGAATTGCCTA 58.667 40.000 21.98 0.00 39.32 3.93
2646 2796 2.795329 TCCACCTCAGAAATTTGCTCC 58.205 47.619 0.00 0.00 0.00 4.70
2722 2872 1.630369 TCCATCCTGTTCACTTGAGGG 59.370 52.381 0.00 0.00 0.00 4.30
2875 3025 7.862873 TGAATATCTGAGTTCACGTGATGTATC 59.137 37.037 20.80 14.69 29.93 2.24
2881 3031 4.705023 TCCTGAATATCTGAGTTCACGTGA 59.295 41.667 15.76 15.76 31.55 4.35
3238 3389 2.624838 ACAAGCTGAAACAATGTCTGGG 59.375 45.455 0.00 0.00 0.00 4.45
3321 3473 3.562973 CAGCAATACATAGTCTGCAAGGG 59.437 47.826 0.00 0.00 37.26 3.95
3634 3786 6.014755 TGGAACATAATGAATGCCAACAGAAA 60.015 34.615 0.00 0.00 39.39 2.52
3807 4122 9.871175 AGGGTAGTAAAATGGACTTTTTCTTTA 57.129 29.630 0.00 0.00 38.09 1.85
3808 4123 8.638873 CAGGGTAGTAAAATGGACTTTTTCTTT 58.361 33.333 0.00 0.00 38.09 2.52
3811 4126 7.754851 TCAGGGTAGTAAAATGGACTTTTTC 57.245 36.000 0.00 0.00 38.09 2.29
3907 4224 4.747605 CCCACCCAAGACAATTTTTAAACG 59.252 41.667 0.00 0.00 0.00 3.60
3918 4235 2.239681 AAACAAACCCACCCAAGACA 57.760 45.000 0.00 0.00 0.00 3.41
3928 4245 3.868661 CAGCAAACCACTTAAACAAACCC 59.131 43.478 0.00 0.00 0.00 4.11
3972 4289 0.322546 GGGCCCTACTGGTCAACAAG 60.323 60.000 17.04 0.00 42.20 3.16
3992 4309 0.458025 GCCCTCTTCACCTAACGACG 60.458 60.000 0.00 0.00 0.00 5.12
3998 4315 2.359169 CGGCAGCCCTCTTCACCTA 61.359 63.158 5.63 0.00 0.00 3.08
4012 4329 3.749064 GAGGACTGAGCGTCGGCA 61.749 66.667 0.00 0.00 43.79 5.69
4017 4334 1.380403 CGAGGATGAGGACTGAGCGT 61.380 60.000 0.00 0.00 0.00 5.07
4152 4469 1.676678 GCCATAGGAGAGCACGACCA 61.677 60.000 0.00 0.00 0.00 4.02
4153 4470 1.068250 GCCATAGGAGAGCACGACC 59.932 63.158 0.00 0.00 0.00 4.79
4162 4479 2.525381 AGAGCCGGGCCATAGGAG 60.525 66.667 17.02 0.00 0.00 3.69
4168 4485 2.442272 GACTAGAGAGCCGGGCCA 60.442 66.667 17.02 0.00 0.00 5.36
4188 4505 1.320507 GGAGGGGTAGTCATCGAGTC 58.679 60.000 0.00 0.00 0.00 3.36
4193 4510 2.090999 AGAGAAGGGAGGGGTAGTCATC 60.091 54.545 0.00 0.00 0.00 2.92
4195 4512 1.394532 AGAGAAGGGAGGGGTAGTCA 58.605 55.000 0.00 0.00 0.00 3.41
4218 4535 4.227134 CCTCGTCCCCATCTGCCG 62.227 72.222 0.00 0.00 0.00 5.69
4220 4537 3.453070 GAGCCTCGTCCCCATCTGC 62.453 68.421 0.00 0.00 0.00 4.26
4222 4539 1.456705 GAGAGCCTCGTCCCCATCT 60.457 63.158 0.00 0.00 0.00 2.90
4305 4622 3.391382 CGGGGAGCTCCGGACTTT 61.391 66.667 26.36 0.00 45.78 2.66
4339 4656 1.752694 ACGGTTGGTGCTTTGCAGT 60.753 52.632 0.00 0.00 40.08 4.40
4363 4680 2.653115 CTGCAGAGGCTCACACGA 59.347 61.111 18.26 0.00 41.91 4.35
4385 4702 2.032528 CGTGGCTTTCCTGGAGCA 59.967 61.111 9.78 0.00 41.89 4.26
4530 4847 2.825387 GCCATGATGTGCCTCGCA 60.825 61.111 0.00 0.00 35.60 5.10
4538 4855 0.994247 TTGACTCCTGGCCATGATGT 59.006 50.000 5.51 9.31 0.00 3.06
4585 4902 2.938823 GCTCGCGCGTGAACTTTGA 61.939 57.895 33.22 9.01 0.00 2.69
4741 5058 1.068610 CCGCTGCAATTTTCTTCCGAA 60.069 47.619 0.00 0.00 0.00 4.30
4797 5114 0.108329 ATACGGTTTGGTCTCCAGCG 60.108 55.000 0.00 0.00 33.81 5.18
4803 5120 4.442706 CAGCATCTTATACGGTTTGGTCT 58.557 43.478 0.00 0.00 0.00 3.85
4908 5225 5.010933 AGAAAAGCCCCTAAAAGCTAGAAC 58.989 41.667 0.00 0.00 38.74 3.01
4954 5273 1.266786 GACCAGTGTTGACGTCGACG 61.267 60.000 34.58 34.58 46.33 5.12
4958 5277 1.647346 TGTTGACCAGTGTTGACGTC 58.353 50.000 9.11 9.11 0.00 4.34
5020 5340 4.320935 CCGTTCAGAAATAGTTTTGGGTGG 60.321 45.833 0.00 0.00 0.00 4.61
5027 5347 3.374058 CCGATGCCGTTCAGAAATAGTTT 59.626 43.478 0.00 0.00 0.00 2.66
5044 5364 2.106566 CCCTCCCTGATCTATCCGATG 58.893 57.143 0.00 0.00 30.84 3.84
5061 5381 0.938192 TTTTGTTCCCTTGACCCCCT 59.062 50.000 0.00 0.00 0.00 4.79
5062 5382 1.796017 TTTTTGTTCCCTTGACCCCC 58.204 50.000 0.00 0.00 0.00 5.40
5088 5408 5.073965 GGTTGGTTCATATAACCCCCTGATA 59.926 44.000 4.55 0.00 39.54 2.15
5161 5482 5.232414 GTGCTAATGTCTATTGGTCGAGTTC 59.768 44.000 0.00 0.00 0.00 3.01
5254 5924 2.175322 GCAAGAGCAAGCGTCTGC 59.825 61.111 2.99 2.99 42.97 4.26
5262 5932 5.095145 AGATTCACATAGAGCAAGAGCAA 57.905 39.130 0.00 0.00 45.49 3.91
5263 5933 4.750021 AGATTCACATAGAGCAAGAGCA 57.250 40.909 0.00 0.00 45.49 4.26
5269 5939 9.136323 TCTATTGTCTTAGATTCACATAGAGCA 57.864 33.333 0.00 0.00 0.00 4.26
5284 5954 9.581289 TTTGGTCCAATCTTTTCTATTGTCTTA 57.419 29.630 4.80 0.00 33.37 2.10
5355 6025 6.562270 CGATCAACAGTCTGTGAGTAACAAAC 60.562 42.308 6.18 0.00 38.67 2.93
5356 6026 5.462068 CGATCAACAGTCTGTGAGTAACAAA 59.538 40.000 6.18 0.00 38.67 2.83
5362 6032 1.964223 ACCGATCAACAGTCTGTGAGT 59.036 47.619 6.18 0.00 0.00 3.41
5393 6063 7.175293 ACGTTGCCTACCAAAGAATGTTAAATA 59.825 33.333 0.00 0.00 36.57 1.40
5401 6071 6.826741 ACAATATACGTTGCCTACCAAAGAAT 59.173 34.615 0.00 0.00 36.57 2.40
5489 6159 3.328050 AGGTAAAGCACTAACTTCTGCCT 59.672 43.478 0.00 0.00 33.57 4.75
5503 6173 3.578688 CTTGGTTTGATGCAGGTAAAGC 58.421 45.455 12.57 12.57 33.68 3.51
5574 6246 1.069049 AGCCTGCAACATGGACAAAAC 59.931 47.619 0.00 0.00 0.00 2.43
5578 6250 2.343506 CAAGCCTGCAACATGGACA 58.656 52.632 0.00 0.00 0.00 4.02
5610 6282 0.449388 GCTTCATTCGCCTCACTTGG 59.551 55.000 0.00 0.00 0.00 3.61
5620 6292 6.696825 ATTAGATACATGTCGCTTCATTCG 57.303 37.500 0.00 0.00 0.00 3.34
5626 6298 6.038271 GGACCAAAATTAGATACATGTCGCTT 59.962 38.462 0.00 0.00 0.00 4.68
5627 6299 5.527582 GGACCAAAATTAGATACATGTCGCT 59.472 40.000 0.00 3.38 0.00 4.93
5673 6345 1.793134 ATAAGGGTACTCCGAGCGCG 61.793 60.000 0.00 0.00 41.52 6.86
5698 6370 1.431488 AACGCAGCGGCTGATACATG 61.431 55.000 32.72 15.68 38.10 3.21
5730 6402 1.522569 GGAAGGATCACAGACCCGG 59.477 63.158 0.00 0.00 0.00 5.73
5732 6404 2.176247 TAGGGAAGGATCACAGACCC 57.824 55.000 0.00 0.00 37.79 4.46
5763 6440 0.032678 CCGCGATCAGAAGCCTATGT 59.967 55.000 8.23 0.00 0.00 2.29
5806 6483 0.385974 ATCAGCTGCGCAAAAACGTC 60.386 50.000 13.05 0.00 34.88 4.34
5821 6498 2.026822 AGGAGCCAACCACAGTTATCAG 60.027 50.000 0.00 0.00 33.27 2.90
5846 6523 4.624364 TGGTGCTGGGTCACGCTG 62.624 66.667 0.00 0.00 37.83 5.18
5847 6524 4.320456 CTGGTGCTGGGTCACGCT 62.320 66.667 0.00 0.00 37.83 5.07
5869 6546 1.776662 TTAGCGGGAGTATCACAGCT 58.223 50.000 0.00 0.00 46.70 4.24
5963 6640 5.438761 AAAACTGCAGTAACTGTTCATCC 57.561 39.130 22.01 0.00 33.43 3.51
5982 6659 5.033589 AGGTTGCCACAATCAATCAAAAA 57.966 34.783 0.00 0.00 0.00 1.94
6029 6706 2.159071 TCCGTTCGAGTGGACTTTTCAA 60.159 45.455 3.76 0.00 0.00 2.69
6142 6819 5.091431 GCAAAACATAGCACAACAGAGATC 58.909 41.667 0.00 0.00 0.00 2.75
6190 6879 3.141398 CAGGCTTGTGTTCAGTGTATGT 58.859 45.455 0.00 0.00 0.00 2.29
6194 6883 2.224606 CATCAGGCTTGTGTTCAGTGT 58.775 47.619 0.00 0.00 0.00 3.55
6198 6887 0.953727 GCACATCAGGCTTGTGTTCA 59.046 50.000 17.94 0.00 44.96 3.18
6226 6915 2.258726 AAACTCAAAGCGGACCGGC 61.259 57.895 17.22 8.14 0.00 6.13
6227 6916 1.164041 ACAAACTCAAAGCGGACCGG 61.164 55.000 17.22 0.00 0.00 5.28
6277 6978 4.263572 CCACCTGCCGGTTCCACA 62.264 66.667 1.90 0.00 42.13 4.17
6289 6990 2.529389 GACACCAGGGACCCACCT 60.529 66.667 14.60 0.00 43.08 4.00
6300 7001 2.592993 GGGTAGGCTGCTGACACCA 61.593 63.158 16.09 0.00 0.00 4.17
6643 7369 2.570302 GCGCCTTATTAATAGGGGAGGA 59.430 50.000 21.55 0.00 45.78 3.71
6817 7559 0.846693 AGTGAAGCCAAGAAGGTGGT 59.153 50.000 0.00 0.00 41.12 4.16
6823 7565 3.055891 TCGATCATCAGTGAAGCCAAGAA 60.056 43.478 0.00 0.00 38.01 2.52
6828 7570 2.057316 CGATCGATCATCAGTGAAGCC 58.943 52.381 24.40 0.00 38.01 4.35
6901 7652 2.629656 GCGCATCACAACCAAGGCT 61.630 57.895 0.30 0.00 0.00 4.58
7008 7769 9.402320 CTGATATGGACAGTAGTATAGTGCTAT 57.598 37.037 0.00 0.00 45.90 2.97


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

AutoCloner maintained by Alex Coulton.