Multiple sequence alignment - TraesCS1B01G279600

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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 TraesCS1B01G279600 chr1B 100.000 9002 0 0 1 9002 488207308 488216309 0.000000e+00 16624.0
1 TraesCS1B01G279600 chr1D 94.061 3553 121 33 2142 5637 364764136 364767655 0.000000e+00 5310.0
2 TraesCS1B01G279600 chr1D 95.555 2137 71 6 6884 8997 364769043 364771178 0.000000e+00 3398.0
3 TraesCS1B01G279600 chr1D 91.302 1851 96 23 303 2146 364762307 364764099 0.000000e+00 2466.0
4 TraesCS1B01G279600 chr1D 94.072 1282 40 8 5636 6885 364767684 364768961 0.000000e+00 1914.0
5 TraesCS1B01G279600 chr1D 89.103 312 30 3 1 311 364761912 364762220 1.420000e-102 385.0
6 TraesCS1B01G279600 chr1A 94.183 2166 65 14 6887 9002 463826044 463828198 0.000000e+00 3245.0
7 TraesCS1B01G279600 chr1A 94.795 1902 72 10 1738 3615 463821475 463823373 0.000000e+00 2939.0
8 TraesCS1B01G279600 chr1A 91.650 2012 90 36 4197 6165 463824073 463826049 0.000000e+00 2713.0
9 TraesCS1B01G279600 chr1A 90.375 1413 79 22 303 1676 463820083 463821477 0.000000e+00 1803.0
10 TraesCS1B01G279600 chr1A 93.761 545 21 7 3659 4203 463823385 463823916 0.000000e+00 806.0
11 TraesCS1B01G279600 chr3B 74.720 803 164 28 7177 7964 652909897 652909119 1.130000e-83 322.0
12 TraesCS1B01G279600 chr3A 75.994 654 127 19 7320 7964 633848536 633847904 2.440000e-80 311.0
13 TraesCS1B01G279600 chr3A 88.793 116 10 3 5475 5590 630924423 630924311 1.220000e-28 139.0
14 TraesCS1B01G279600 chr3D 76.070 631 125 17 7339 7964 491958820 491958211 1.140000e-78 305.0
15 TraesCS1B01G279600 chr5A 81.443 291 49 4 5 291 169969751 169969462 5.430000e-57 233.0
16 TraesCS1B01G279600 chr5D 86.550 171 20 3 4 172 135091594 135091763 1.540000e-42 185.0
17 TraesCS1B01G279600 chr7A 92.920 113 7 1 5472 5584 305708933 305708822 7.230000e-36 163.0
18 TraesCS1B01G279600 chr7A 91.150 113 9 1 5472 5584 296604237 296604348 1.570000e-32 152.0
19 TraesCS1B01G279600 chr7A 90.265 113 10 1 5472 5584 299568613 299568502 7.280000e-31 147.0
20 TraesCS1B01G279600 chr7B 90.000 110 10 1 5474 5583 570465365 570465257 3.390000e-29 141.0
21 TraesCS1B01G279600 chr7B 78.947 114 17 4 121 230 87010835 87010945 4.510000e-08 71.3
22 TraesCS1B01G279600 chr6B 91.346 104 8 1 5482 5585 617173719 617173821 3.390000e-29 141.0
23 TraesCS1B01G279600 chr6A 89.381 113 11 1 5472 5584 58306515 58306626 3.390000e-29 141.0
24 TraesCS1B01G279600 chr7D 89.091 110 11 1 5475 5584 397578521 397578629 1.580000e-27 135.0
25 TraesCS1B01G279600 chr4D 86.207 58 5 3 146 201 509059308 509059364 9.760000e-05 60.2


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 TraesCS1B01G279600 chr1B 488207308 488216309 9001 False 16624.0 16624 100.0000 1 9002 1 chr1B.!!$F1 9001
1 TraesCS1B01G279600 chr1D 364761912 364771178 9266 False 2694.6 5310 92.8186 1 8997 5 chr1D.!!$F1 8996
2 TraesCS1B01G279600 chr1A 463820083 463828198 8115 False 2301.2 3245 92.9528 303 9002 5 chr1A.!!$F1 8699
3 TraesCS1B01G279600 chr3B 652909119 652909897 778 True 322.0 322 74.7200 7177 7964 1 chr3B.!!$R1 787
4 TraesCS1B01G279600 chr3A 633847904 633848536 632 True 311.0 311 75.9940 7320 7964 1 chr3A.!!$R2 644
5 TraesCS1B01G279600 chr3D 491958211 491958820 609 True 305.0 305 76.0700 7339 7964 1 chr3D.!!$R1 625


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
664 783 0.168128 GACAAGAAATTGGGCGTCCG 59.832 55.000 0.00 0.00 35.24 4.79 F
1158 1319 0.108424 CGAAGAGGGTGGAAGAGCAG 60.108 60.000 0.00 0.00 0.00 4.24 F
1159 1320 0.392327 GAAGAGGGTGGAAGAGCAGC 60.392 60.000 0.00 0.00 0.00 5.25 F
1380 1541 1.069500 GTGCCGCATTTCGTTAACTGT 60.069 47.619 3.71 0.00 36.19 3.55 F
2364 2568 1.134670 GGTAGAGCTAGCACTGTTGGG 60.135 57.143 23.03 0.00 34.00 4.12 F
2412 2616 1.628340 ACACTTGGTAGTAGCATGGCA 59.372 47.619 16.78 0.00 31.96 4.92 F
3233 3443 2.807108 GCGTCAGAAAGAACTTCCCAGT 60.807 50.000 0.00 0.00 34.21 4.00 F
4287 4711 2.230992 TCAATGATTTGTGGGCTTTCCG 59.769 45.455 0.00 0.00 38.76 4.30 F
4822 5246 1.538950 CAGGAAGTGAAGAGCCAAAGC 59.461 52.381 0.00 0.00 40.32 3.51 F
5322 5748 1.606601 GGGGTTGGTTCTCTTGCCC 60.607 63.158 0.00 0.00 35.52 5.36 F
5594 6034 2.224402 GGAGGGAGTATGTTCCATGCTC 60.224 54.545 12.22 12.22 36.57 4.26 F
6731 7212 0.543277 CCATAAGGCCTGCAGACTGA 59.457 55.000 17.39 6.59 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1672 1835 0.035152 TGTACATGCTTCAGCCCCAG 60.035 55.000 0.00 0.0 41.18 4.45 R
3090 3300 0.546122 TCCAAGTTGTGCCACTGAGT 59.454 50.000 1.45 0.0 0.00 3.41 R
3233 3443 3.130633 CGGCATCTCGTTTCATGGAATA 58.869 45.455 0.00 0.0 0.00 1.75 R
3239 3449 1.471676 GGTCTCGGCATCTCGTTTCAT 60.472 52.381 0.00 0.0 0.00 2.57 R
3449 3659 1.541588 GACAACTGAAATGGCCCAGAC 59.458 52.381 13.03 0.0 34.65 3.51 R
3639 3867 3.441572 AGTACTGAAATCATGCAGCCAAC 59.558 43.478 0.00 0.0 35.57 3.77 R
4602 5026 1.149101 AAGCAACCAAGAGAAGGGGA 58.851 50.000 0.00 0.0 0.00 4.81 R
5686 6156 0.388778 TCATGCATGCACAAAAGCCG 60.389 50.000 25.37 4.3 0.00 5.52 R
6266 6738 0.671251 TTGGGTCCGCAATCAACAAC 59.329 50.000 0.00 0.0 0.00 3.32 R
6343 6815 1.230324 GGTGTCAAGTGTTGAGAGGC 58.770 55.000 0.00 0.0 41.01 4.70 R
7071 7656 1.418373 TCGCGATTCACAACTGTCTG 58.582 50.000 3.71 0.0 0.00 3.51 R
8699 9341 0.032017 TTGCCCTAGAGAGACCTCCC 60.032 60.000 0.00 0.0 40.30 4.30 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
17 18 3.763319 ACGGATTCTCGAAACGCG 58.237 55.556 3.53 3.53 42.69 6.01
18 19 1.804326 ACGGATTCTCGAAACGCGG 60.804 57.895 12.47 0.00 41.33 6.46
35 36 2.350498 CGCGGTTAGGAAAATCAACGAT 59.650 45.455 0.00 0.00 0.00 3.73
69 70 2.439409 TGTCTGTTCATGGGCATCTTG 58.561 47.619 0.00 0.00 0.00 3.02
72 73 3.084039 TCTGTTCATGGGCATCTTGTTC 58.916 45.455 0.00 0.00 0.00 3.18
83 84 3.350833 GCATCTTGTTCAGGAGGTGAAT 58.649 45.455 0.00 0.00 46.99 2.57
85 86 4.330250 CATCTTGTTCAGGAGGTGAATGT 58.670 43.478 0.00 0.00 46.99 2.71
86 87 5.491070 CATCTTGTTCAGGAGGTGAATGTA 58.509 41.667 0.00 0.00 46.99 2.29
89 90 7.252612 TCTTGTTCAGGAGGTGAATGTATTA 57.747 36.000 0.00 0.00 46.99 0.98
91 92 5.741011 TGTTCAGGAGGTGAATGTATTACC 58.259 41.667 0.00 0.00 46.99 2.85
130 131 1.874345 AAGGTAGTCTGGGTGCGACG 61.874 60.000 0.00 0.00 36.53 5.12
159 160 1.060713 CAAAGTCGCACACGTCCTAG 58.939 55.000 0.00 0.00 41.18 3.02
204 205 1.320507 TGTAAAACTTGGTTCCGGGC 58.679 50.000 0.00 0.00 0.00 6.13
229 230 2.094906 TCCGACATGTGTTAGTTCGGAG 60.095 50.000 16.08 0.00 42.32 4.63
271 272 5.914635 CGTGACTGTTGAATAAAACTGCAAT 59.085 36.000 0.00 0.00 33.62 3.56
282 283 9.638239 TGAATAAAACTGCAATAATTTCCACTC 57.362 29.630 0.00 0.00 0.00 3.51
286 287 7.951530 AAACTGCAATAATTTCCACTCAAAG 57.048 32.000 0.00 0.00 0.00 2.77
293 294 8.919661 GCAATAATTTCCACTCAAAGAAAGAAG 58.080 33.333 0.00 0.00 35.57 2.85
298 299 6.927294 TTCCACTCAAAGAAAGAAGAAGAC 57.073 37.500 0.00 0.00 0.00 3.01
299 300 5.368989 TCCACTCAAAGAAAGAAGAAGACC 58.631 41.667 0.00 0.00 0.00 3.85
300 301 5.131142 TCCACTCAAAGAAAGAAGAAGACCT 59.869 40.000 0.00 0.00 0.00 3.85
301 302 5.238214 CCACTCAAAGAAAGAAGAAGACCTG 59.762 44.000 0.00 0.00 0.00 4.00
466 560 1.684049 CGAAGCTCCTCTCCCCTGT 60.684 63.158 0.00 0.00 0.00 4.00
467 561 1.261238 CGAAGCTCCTCTCCCCTGTT 61.261 60.000 0.00 0.00 0.00 3.16
468 562 0.539518 GAAGCTCCTCTCCCCTGTTC 59.460 60.000 0.00 0.00 0.00 3.18
469 563 1.261238 AAGCTCCTCTCCCCTGTTCG 61.261 60.000 0.00 0.00 0.00 3.95
470 564 2.726351 GCTCCTCTCCCCTGTTCGG 61.726 68.421 0.00 0.00 0.00 4.30
488 582 3.382832 CTGTTCCCCGTCTCCGCT 61.383 66.667 0.00 0.00 0.00 5.52
490 584 3.069318 GTTCCCCGTCTCCGCTCT 61.069 66.667 0.00 0.00 0.00 4.09
517 611 2.104253 CCCAAATCCGTCGAACCCG 61.104 63.158 0.00 0.00 37.07 5.28
538 632 4.933064 GCCCAGCGACGATCTCCG 62.933 72.222 0.00 0.00 45.44 4.63
627 746 4.433615 TCAGATTCCGCTTCAAGTATCAC 58.566 43.478 0.00 0.00 0.00 3.06
661 780 2.296190 GGAAAGACAAGAAATTGGGCGT 59.704 45.455 0.00 0.00 0.00 5.68
662 781 3.565516 GAAAGACAAGAAATTGGGCGTC 58.434 45.455 0.00 0.00 0.00 5.19
663 782 1.534729 AGACAAGAAATTGGGCGTCC 58.465 50.000 0.00 0.00 0.00 4.79
664 783 0.168128 GACAAGAAATTGGGCGTCCG 59.832 55.000 0.00 0.00 35.24 4.79
665 784 0.536460 ACAAGAAATTGGGCGTCCGT 60.536 50.000 0.00 0.00 35.24 4.69
677 796 2.087009 CGTCCGTCGTTTCTGAGCC 61.087 63.158 0.00 0.00 34.52 4.70
680 799 2.733218 CGTCGTTTCTGAGCCGCA 60.733 61.111 0.00 0.00 0.00 5.69
786 934 2.915659 TGAGCTGGTCCGGTTCGT 60.916 61.111 9.75 0.00 0.00 3.85
791 939 2.203523 TGGTCCGGTTCGTCCTGA 60.204 61.111 0.00 0.00 0.00 3.86
802 950 2.178912 TCGTCCTGATTGGTTGGTTC 57.821 50.000 0.00 0.00 37.07 3.62
840 991 0.545309 TGAGTGGTTCCTGGAGGAGG 60.545 60.000 0.00 0.00 46.36 4.30
853 1004 1.464198 AGGAGGAGCTGTTTGGGGT 60.464 57.895 0.00 0.00 0.00 4.95
896 1047 2.548904 GGAGTCGCTAGATCGCTTTAGA 59.451 50.000 0.00 0.00 0.00 2.10
907 1058 3.973206 TCGCTTTAGATTTGTGGAGGA 57.027 42.857 0.00 0.00 0.00 3.71
913 1064 6.093495 CGCTTTAGATTTGTGGAGGATTACAA 59.907 38.462 0.00 0.00 35.20 2.41
937 1088 8.726068 CAAAATAATACGGTATCATGGTGCATA 58.274 33.333 0.30 0.00 0.00 3.14
988 1143 3.338214 TGGGGATCAGGGATTTTGGTTAA 59.662 43.478 0.00 0.00 0.00 2.01
989 1144 3.704566 GGGGATCAGGGATTTTGGTTAAC 59.295 47.826 0.00 0.00 0.00 2.01
1020 1175 1.380302 GGGAGGCCTCTGCTCAAAA 59.620 57.895 31.36 0.00 37.74 2.44
1154 1315 2.646175 CGGCGAAGAGGGTGGAAGA 61.646 63.158 0.00 0.00 0.00 2.87
1155 1316 1.219393 GGCGAAGAGGGTGGAAGAG 59.781 63.158 0.00 0.00 0.00 2.85
1156 1317 1.448717 GCGAAGAGGGTGGAAGAGC 60.449 63.158 0.00 0.00 0.00 4.09
1157 1318 1.975327 CGAAGAGGGTGGAAGAGCA 59.025 57.895 0.00 0.00 0.00 4.26
1158 1319 0.108424 CGAAGAGGGTGGAAGAGCAG 60.108 60.000 0.00 0.00 0.00 4.24
1159 1320 0.392327 GAAGAGGGTGGAAGAGCAGC 60.392 60.000 0.00 0.00 0.00 5.25
1160 1321 1.130054 AAGAGGGTGGAAGAGCAGCA 61.130 55.000 0.00 0.00 0.00 4.41
1161 1322 1.078567 GAGGGTGGAAGAGCAGCAG 60.079 63.158 0.00 0.00 0.00 4.24
1162 1323 2.749441 GGGTGGAAGAGCAGCAGC 60.749 66.667 0.00 0.00 42.56 5.25
1163 1324 2.033141 GGTGGAAGAGCAGCAGCA 59.967 61.111 3.17 0.00 45.49 4.41
1164 1325 2.039405 GGTGGAAGAGCAGCAGCAG 61.039 63.158 3.17 0.00 45.49 4.24
1165 1326 2.359602 TGGAAGAGCAGCAGCAGC 60.360 61.111 3.17 0.46 45.49 5.25
1283 1444 1.495584 GCTCGGACACTGTCGCAAAA 61.496 55.000 3.04 0.00 32.65 2.44
1380 1541 1.069500 GTGCCGCATTTCGTTAACTGT 60.069 47.619 3.71 0.00 36.19 3.55
1422 1583 5.126707 TCTCCGGTCCTTAGTTTGTTAGATC 59.873 44.000 0.00 0.00 0.00 2.75
1426 1587 6.460676 CCGGTCCTTAGTTTGTTAGATCGTAT 60.461 42.308 0.00 0.00 0.00 3.06
1659 1822 2.797156 GTGAGCGCATTGTATCGAATCT 59.203 45.455 11.47 0.00 0.00 2.40
1669 1832 7.167635 CGCATTGTATCGAATCTAACTGTAGTT 59.832 37.037 2.51 2.51 41.73 2.24
1672 1835 6.270815 TGTATCGAATCTAACTGTAGTTGGC 58.729 40.000 7.50 0.00 38.90 4.52
1760 1923 6.261826 CCTGGATATTTTCTGATCTTTTCGCT 59.738 38.462 0.00 0.00 0.00 4.93
1764 1927 8.778358 GGATATTTTCTGATCTTTTCGCTGTAT 58.222 33.333 0.00 0.00 0.00 2.29
1820 1983 5.997385 AGTTATAACTTCCAAGCAAACACG 58.003 37.500 12.50 0.00 35.21 4.49
1841 2004 6.910972 ACACGTCAATGAGTATATAACACTCG 59.089 38.462 11.28 4.21 44.44 4.18
1853 2016 1.601166 AACACTCGCCCCTGTTTAAC 58.399 50.000 0.00 0.00 0.00 2.01
1859 2022 1.156736 CGCCCCTGTTTAACAGTCTG 58.843 55.000 21.63 11.58 44.50 3.51
1873 2036 3.937814 ACAGTCTGGATTAACAATCGCA 58.062 40.909 4.53 0.00 38.82 5.10
1877 2040 5.580691 CAGTCTGGATTAACAATCGCAAGTA 59.419 40.000 0.00 0.00 38.82 2.24
1895 2058 7.274904 TCGCAAGTAGTTTTCAGTGATATGTAC 59.725 37.037 0.00 0.00 39.48 2.90
1900 2063 8.251721 AGTAGTTTTCAGTGATATGTACTGGTC 58.748 37.037 13.80 5.64 44.33 4.02
1903 2066 6.605471 TTTCAGTGATATGTACTGGTCAGT 57.395 37.500 13.80 8.74 44.33 3.41
2049 2212 2.694397 TCCTGGCTATCCTATGCAAGT 58.306 47.619 0.00 0.00 0.00 3.16
2242 2446 6.322491 GTGTACACTTGTCTTTGCTCTTTTT 58.678 36.000 18.92 0.00 0.00 1.94
2245 2449 5.402398 ACACTTGTCTTTGCTCTTTTTGAC 58.598 37.500 0.00 0.00 0.00 3.18
2364 2568 1.134670 GGTAGAGCTAGCACTGTTGGG 60.135 57.143 23.03 0.00 34.00 4.12
2412 2616 1.628340 ACACTTGGTAGTAGCATGGCA 59.372 47.619 16.78 0.00 31.96 4.92
2634 2838 3.338249 TGAACTACTTGAGATTGCAGCC 58.662 45.455 0.00 0.00 0.00 4.85
2779 2983 8.526978 TGCAGTTAATATTTCAATACTTTGCCA 58.473 29.630 0.00 0.00 32.61 4.92
2797 3001 4.148838 TGCCAGTACTTTAATGCTTTGGT 58.851 39.130 0.00 0.00 0.00 3.67
2844 3048 5.801720 TTTATAGGGGGATGCATGATGAT 57.198 39.130 2.46 0.00 0.00 2.45
2888 3093 6.166982 AGATTTAGTGCTACCTTTGTCTGTC 58.833 40.000 0.00 0.00 0.00 3.51
2895 3100 3.119245 GCTACCTTTGTCTGTCCGTATGA 60.119 47.826 0.00 0.00 0.00 2.15
2918 3123 8.371571 TGATAGGCTGATGACAGATATAACAT 57.628 34.615 0.00 0.00 46.03 2.71
2968 3173 7.201794 CCCAGTAGAACTGTATTCACTATTCGA 60.202 40.741 6.33 0.00 44.50 3.71
3233 3443 2.807108 GCGTCAGAAAGAACTTCCCAGT 60.807 50.000 0.00 0.00 34.21 4.00
3239 3449 5.309543 TCAGAAAGAACTTCCCAGTATTCCA 59.690 40.000 0.00 0.00 34.21 3.53
3538 3748 6.966021 TGGATTTTTCTAGTAACTGTTGCAC 58.034 36.000 11.16 0.00 0.00 4.57
3561 3786 2.813754 TGCTCAAAGAACCATGTAGTGC 59.186 45.455 0.00 0.00 0.00 4.40
3565 3790 4.460263 TCAAAGAACCATGTAGTGCACTT 58.540 39.130 27.06 4.31 0.00 3.16
3576 3804 6.372659 CCATGTAGTGCACTTCTAGTTTGAAT 59.627 38.462 27.06 3.77 0.00 2.57
3781 4009 6.877611 TTTTTCGGCTTTTTCTAGATGTCT 57.122 33.333 0.00 0.00 0.00 3.41
3869 4126 7.538334 TGATTTCATGTTATTCACTTTGCTTCG 59.462 33.333 0.00 0.00 0.00 3.79
4031 4288 5.126067 TGTTTGATTTATCAGGCCTAGCTC 58.874 41.667 3.98 0.00 38.19 4.09
4105 4363 7.408756 AAGAAATAGAACATAAGCATTGCCA 57.591 32.000 4.70 0.00 0.00 4.92
4160 4420 2.869897 CAGTCTTCGACTAGGTTGCTC 58.130 52.381 0.00 0.00 41.37 4.26
4239 4663 3.751175 TGCCTTTCTTGTGTGCATAGTAC 59.249 43.478 0.00 0.00 0.00 2.73
4241 4665 4.142816 GCCTTTCTTGTGTGCATAGTACTG 60.143 45.833 5.39 0.00 0.00 2.74
4287 4711 2.230992 TCAATGATTTGTGGGCTTTCCG 59.769 45.455 0.00 0.00 38.76 4.30
4385 4809 6.253727 ACATAAGAATCGCGAGTTAAGTTCAG 59.746 38.462 16.66 6.54 0.00 3.02
4447 4871 4.192317 GGATGAGAAAATACGTTGGAGCT 58.808 43.478 0.00 0.00 0.00 4.09
4695 5119 6.529125 GGTTTCATTTGTCAGTATGCATTCAG 59.471 38.462 3.54 0.00 34.76 3.02
4767 5191 5.642063 TGACGAGCTAAAGGAAAACTTATGG 59.358 40.000 0.00 0.00 38.85 2.74
4779 5203 8.189119 AGGAAAACTTATGGTTTATTTGCAGA 57.811 30.769 0.00 0.00 46.18 4.26
4822 5246 1.538950 CAGGAAGTGAAGAGCCAAAGC 59.461 52.381 0.00 0.00 40.32 3.51
5116 5540 3.379372 CCTTTGGTCATGCTGGTATTGAG 59.621 47.826 0.00 0.00 0.00 3.02
5153 5577 7.042051 GCTGTCTTACAAGAGTGAATGTTGTTA 60.042 37.037 0.00 0.00 42.42 2.41
5225 5651 4.345854 ACTTCCCCCGCATATGTTTTAAA 58.654 39.130 4.29 0.00 0.00 1.52
5236 5662 8.057742 CCGCATATGTTTTAAAAATGCATTCTC 58.942 33.333 24.91 5.16 42.36 2.87
5322 5748 1.606601 GGGGTTGGTTCTCTTGCCC 60.607 63.158 0.00 0.00 35.52 5.36
5416 5842 3.953612 CCTTAGCCATGCAAAGGTAATGA 59.046 43.478 9.94 0.00 0.00 2.57
5451 5878 6.634805 AGATCATGTCTGAACTTATTCACGT 58.365 36.000 0.00 0.00 40.01 4.49
5484 5912 4.284178 GGACAAGGTACATACTACCTCCA 58.716 47.826 0.00 0.00 46.52 3.86
5500 5929 3.265995 ACCTCCATCCGGAATTACTTGTT 59.734 43.478 9.01 0.00 42.21 2.83
5517 5946 6.594788 ACTTGTTGCAGAAATGGATGTATT 57.405 33.333 0.00 0.00 0.00 1.89
5518 5947 6.996509 ACTTGTTGCAGAAATGGATGTATTT 58.003 32.000 0.00 0.00 33.19 1.40
5548 5988 9.978044 ACGTATTTTTAGTTCTAGATACATCCC 57.022 33.333 0.00 0.00 0.00 3.85
5572 6012 4.819105 TCTGTGACAAGTAATTCGGGAT 57.181 40.909 0.00 0.00 0.00 3.85
5594 6034 2.224402 GGAGGGAGTATGTTCCATGCTC 60.224 54.545 12.22 12.22 36.57 4.26
5602 6042 7.147983 GGGAGTATGTTCCATGCTCTAGTATAG 60.148 44.444 17.77 0.00 39.09 1.31
5666 6136 3.424703 ACTTGCTATGGAGTGTGCAATT 58.575 40.909 0.00 0.00 43.17 2.32
5667 6137 3.828451 ACTTGCTATGGAGTGTGCAATTT 59.172 39.130 0.00 0.00 43.17 1.82
5724 6194 3.958018 TGAACACACACTTTAACCCTGT 58.042 40.909 0.00 0.00 0.00 4.00
5972 6444 7.766738 TCAGATTGACACACTTGTAAGTTAACA 59.233 33.333 8.61 0.00 37.08 2.41
6054 6526 7.423844 TCTCTAATCCAAAGATGTCTGCTTA 57.576 36.000 0.00 0.00 31.29 3.09
6177 6649 7.439056 GGCACCCATTATCTTTTCATACATTTG 59.561 37.037 0.00 0.00 0.00 2.32
6209 6681 9.969001 TGAAGTTAAAATACTAAAGGGCACTAT 57.031 29.630 0.00 0.00 0.00 2.12
6219 6691 2.938956 AGGGCACTATGGCATTCTAC 57.061 50.000 4.78 0.00 45.76 2.59
6245 6717 3.443052 TGCACCATCATCTTTTTGGGAT 58.557 40.909 0.00 0.00 34.72 3.85
6343 6815 2.896168 ACCCGGTATTACAACATGACG 58.104 47.619 0.00 0.00 0.00 4.35
6353 6825 1.202639 ACAACATGACGCCTCTCAACA 60.203 47.619 0.00 0.00 0.00 3.33
6403 6875 2.285743 AAGACCCCTCTCCCCTGC 60.286 66.667 0.00 0.00 0.00 4.85
6453 6925 1.484038 AGGAGGTGAGCTAAGCTGAG 58.516 55.000 7.75 0.00 39.88 3.35
6457 6929 0.898320 GGTGAGCTAAGCTGAGTGGA 59.102 55.000 0.00 0.00 39.88 4.02
6485 6957 2.963854 CGTATGCTGCAGGCCTCG 60.964 66.667 17.12 0.00 40.92 4.63
6496 6968 3.917760 GGCCTCGCCGTGCTAGAT 61.918 66.667 0.00 0.00 39.62 1.98
6505 6977 1.948138 CGTGCTAGATGCTCAGCCG 60.948 63.158 0.00 0.00 43.37 5.52
6548 7020 3.790089 AAAACTAGTTCCTGTGGGGAG 57.210 47.619 8.95 0.00 46.01 4.30
6572 7053 2.478134 CAGTTCAACTTCCAAGAGCTCG 59.522 50.000 8.37 0.00 0.00 5.03
6578 7059 1.001406 ACTTCCAAGAGCTCGAACTGG 59.999 52.381 8.37 13.55 0.00 4.00
6638 7119 4.428209 CATGTACTGAGCCATCCGATATC 58.572 47.826 0.00 0.00 0.00 1.63
6666 7147 4.500116 GGAGGACGTCTGGCGAGC 62.500 72.222 16.46 0.00 44.77 5.03
6731 7212 0.543277 CCATAAGGCCTGCAGACTGA 59.457 55.000 17.39 6.59 0.00 3.41
6857 7359 5.233225 CAGCTCATATTCGTGTGGTGATAT 58.767 41.667 2.99 0.00 41.19 1.63
7045 7630 1.555075 GAAGAGGTATGCCACACTGGA 59.445 52.381 1.54 0.00 40.96 3.86
7071 7656 4.738124 TCATATTCGCTGCTACTATGAGC 58.262 43.478 9.25 0.00 43.16 4.26
7116 7701 2.076100 TGCTGTGGAATCGTGAATCAC 58.924 47.619 2.75 2.75 0.00 3.06
7132 7717 4.098349 TGAATCACAATTCCTTGCTATGGC 59.902 41.667 0.00 0.00 40.57 4.40
7531 8123 2.158711 ACCCGGATCGAGACACTGTATA 60.159 50.000 0.73 0.00 0.00 1.47
7746 8338 2.905085 ACCAGAGGATCAGGATATGCTG 59.095 50.000 17.55 17.55 46.05 4.41
7806 8398 3.659444 GCAAAAGTCAAGAATTCGACACG 59.341 43.478 13.74 0.00 34.48 4.49
8008 8600 6.260936 TCAGTCAGGAATCAACTGAAAGAAAC 59.739 38.462 9.06 0.00 45.66 2.78
8041 8633 5.721960 ACCTGGATACTGTGTAGTCATCTTT 59.278 40.000 0.00 0.00 38.36 2.52
8081 8673 4.616835 GCTCTGGCAAGGATGTAAAAAGTG 60.617 45.833 0.00 0.00 38.54 3.16
8082 8674 3.255642 TCTGGCAAGGATGTAAAAAGTGC 59.744 43.478 0.00 0.00 0.00 4.40
8083 8675 2.961741 TGGCAAGGATGTAAAAAGTGCA 59.038 40.909 0.00 0.00 32.18 4.57
8106 8719 2.995574 ACCCGTCCGAGGTGAAGG 60.996 66.667 0.08 0.00 35.85 3.46
8331 8957 1.138859 TGTGGATGTAAGGCCGATCAG 59.861 52.381 0.00 0.00 0.00 2.90
8396 9022 6.618166 GCGAGCATTTAATTGTGCAAAATTGA 60.618 34.615 22.67 13.35 43.63 2.57
8409 9035 4.633565 TGCAAAATTGAAACCAAGTTCCAC 59.366 37.500 0.00 0.00 31.58 4.02
8418 9044 6.074648 TGAAACCAAGTTCCACTTATCCATT 58.925 36.000 0.00 0.00 36.03 3.16
8494 9121 1.573376 AGATCAGCTCAGACCCCTAGT 59.427 52.381 0.00 0.00 0.00 2.57
8561 9197 3.838317 GTGATGTAGGGATATAGCCACCA 59.162 47.826 9.69 2.22 0.00 4.17
8619 9261 5.429762 TCCAGAGAAATTGTCCTATGATGGT 59.570 40.000 0.00 0.00 0.00 3.55
8650 9292 2.409012 ACATTGTGATTGACGTGCGTA 58.591 42.857 0.00 0.00 0.00 4.42
8651 9293 2.156891 ACATTGTGATTGACGTGCGTAC 59.843 45.455 0.00 0.00 0.00 3.67
8655 9297 2.030981 TGTGATTGACGTGCGTACTACA 60.031 45.455 0.00 0.00 0.00 2.74
8666 9308 4.341099 GTGCGTACTACAGTGAGTATGAC 58.659 47.826 18.42 12.83 40.12 3.06
8768 9410 1.265365 GATAAGATGCGGAAAGCTGCC 59.735 52.381 0.00 0.00 46.06 4.85
8864 9506 2.552315 GACATCGGCTCAACTCCAAAAA 59.448 45.455 0.00 0.00 0.00 1.94
8872 9514 5.801947 CGGCTCAACTCCAAAAATTCTAATG 59.198 40.000 0.00 0.00 0.00 1.90
8912 9554 7.811653 TGCAGTTGATCGAAACATACAATTTA 58.188 30.769 3.01 0.00 32.21 1.40
8933 9575 1.539341 CGCAGTCACTGTCTACATCG 58.461 55.000 6.68 0.00 33.43 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.817148 TGATTTTCCTAACCGCGTTTC 57.183 42.857 4.92 0.00 0.00 2.78
13 14 1.461897 CGTTGATTTTCCTAACCGCGT 59.538 47.619 4.92 0.00 0.00 6.01
14 15 1.727880 TCGTTGATTTTCCTAACCGCG 59.272 47.619 0.00 0.00 0.00 6.46
17 18 6.192360 CGATTCATCGTTGATTTTCCTAACC 58.808 40.000 0.80 0.00 44.74 2.85
35 36 5.789521 TGAACAGACAAACCTATCGATTCA 58.210 37.500 1.71 0.00 0.00 2.57
42 43 3.245229 TGCCCATGAACAGACAAACCTAT 60.245 43.478 0.00 0.00 0.00 2.57
43 44 2.107378 TGCCCATGAACAGACAAACCTA 59.893 45.455 0.00 0.00 0.00 3.08
46 47 2.821969 AGATGCCCATGAACAGACAAAC 59.178 45.455 0.00 0.00 0.00 2.93
50 51 2.440409 ACAAGATGCCCATGAACAGAC 58.560 47.619 0.00 0.00 0.00 3.51
54 55 2.165030 CCTGAACAAGATGCCCATGAAC 59.835 50.000 0.00 0.00 0.00 3.18
69 70 4.809426 CGGTAATACATTCACCTCCTGAAC 59.191 45.833 0.00 0.00 41.87 3.18
72 73 4.665833 TCGGTAATACATTCACCTCCTG 57.334 45.455 0.00 0.00 0.00 3.86
130 131 2.851104 CGACTTTGTTCGCCGACC 59.149 61.111 0.00 0.00 31.03 4.79
159 160 4.765813 TTATTGTACAACCCTCCCTAGC 57.234 45.455 11.22 0.00 0.00 3.42
193 194 3.961414 GGAGGTGCCCGGAACCAA 61.961 66.667 23.47 0.00 40.40 3.67
204 205 2.743636 ACTAACACATGTCGGAGGTG 57.256 50.000 0.00 0.00 42.30 4.00
212 213 3.764237 AACCTCCGAACTAACACATGT 57.236 42.857 0.00 0.00 0.00 3.21
229 230 1.153568 GGCGTCCTTACCGGTAACC 60.154 63.158 23.17 17.72 0.00 2.85
237 238 0.319297 AACAGTCACGGCGTCCTTAC 60.319 55.000 10.85 6.39 0.00 2.34
239 240 1.594293 CAACAGTCACGGCGTCCTT 60.594 57.895 10.85 0.00 0.00 3.36
243 244 2.157834 TTATTCAACAGTCACGGCGT 57.842 45.000 6.77 6.77 0.00 5.68
271 272 9.627123 TCTTCTTCTTTCTTTGAGTGGAAATTA 57.373 29.630 0.00 0.00 32.15 1.40
282 283 6.458888 GGTGTTCAGGTCTTCTTCTTTCTTTG 60.459 42.308 0.00 0.00 0.00 2.77
286 287 4.273724 GTGGTGTTCAGGTCTTCTTCTTTC 59.726 45.833 0.00 0.00 0.00 2.62
293 294 2.325583 TGTGTGGTGTTCAGGTCTTC 57.674 50.000 0.00 0.00 0.00 2.87
294 295 2.799126 TTGTGTGGTGTTCAGGTCTT 57.201 45.000 0.00 0.00 0.00 3.01
296 297 4.385358 AATTTTGTGTGGTGTTCAGGTC 57.615 40.909 0.00 0.00 0.00 3.85
298 299 5.977129 GTCTAAATTTTGTGTGGTGTTCAGG 59.023 40.000 0.00 0.00 0.00 3.86
299 300 5.977129 GGTCTAAATTTTGTGTGGTGTTCAG 59.023 40.000 0.00 0.00 0.00 3.02
300 301 5.419155 TGGTCTAAATTTTGTGTGGTGTTCA 59.581 36.000 0.00 0.00 0.00 3.18
301 302 5.897050 TGGTCTAAATTTTGTGTGGTGTTC 58.103 37.500 0.00 0.00 0.00 3.18
350 444 3.452474 CCCAAATTGTTTCGTTGCTTCA 58.548 40.909 0.00 0.00 0.00 3.02
359 453 3.177997 ACACACAGCCCAAATTGTTTC 57.822 42.857 0.00 0.00 0.00 2.78
466 560 2.920912 AGACGGGGAACAGCCGAA 60.921 61.111 0.00 0.00 36.66 4.30
467 561 3.379445 GAGACGGGGAACAGCCGA 61.379 66.667 0.00 0.00 36.66 5.54
468 562 4.452733 GGAGACGGGGAACAGCCG 62.453 72.222 0.00 0.00 39.06 5.52
488 582 1.559682 CGGATTTGGGGAAGAGGAAGA 59.440 52.381 0.00 0.00 0.00 2.87
490 584 1.280998 GACGGATTTGGGGAAGAGGAA 59.719 52.381 0.00 0.00 0.00 3.36
649 768 1.740296 CGACGGACGCCCAATTTCT 60.740 57.895 0.00 0.00 34.51 2.52
661 780 2.257371 CGGCTCAGAAACGACGGA 59.743 61.111 0.00 0.00 0.00 4.69
662 781 3.479269 GCGGCTCAGAAACGACGG 61.479 66.667 0.00 0.00 0.00 4.79
663 782 2.733218 TGCGGCTCAGAAACGACG 60.733 61.111 0.00 0.00 0.00 5.12
664 783 2.668280 GGTGCGGCTCAGAAACGAC 61.668 63.158 0.00 0.00 0.00 4.34
665 784 2.357034 GGTGCGGCTCAGAAACGA 60.357 61.111 0.00 0.00 0.00 3.85
677 796 2.154427 GAAACCAGACGAACGGTGCG 62.154 60.000 7.04 7.04 35.08 5.34
680 799 0.249741 CCAGAAACCAGACGAACGGT 60.250 55.000 0.00 0.00 36.98 4.83
717 865 3.220110 CAGCAGCTCCAATCCATGTAAT 58.780 45.455 0.00 0.00 0.00 1.89
786 934 0.768622 ACCGAACCAACCAATCAGGA 59.231 50.000 0.00 0.00 41.22 3.86
791 939 0.476771 ACCTGACCGAACCAACCAAT 59.523 50.000 0.00 0.00 0.00 3.16
802 950 0.324943 AATCCACCAAGACCTGACCG 59.675 55.000 0.00 0.00 0.00 4.79
840 991 2.026262 TCCAGAATACCCCAAACAGCTC 60.026 50.000 0.00 0.00 0.00 4.09
841 992 1.992557 TCCAGAATACCCCAAACAGCT 59.007 47.619 0.00 0.00 0.00 4.24
842 993 2.507407 TCCAGAATACCCCAAACAGC 57.493 50.000 0.00 0.00 0.00 4.40
853 1004 4.272489 CAATTCCACCAGCTTCCAGAATA 58.728 43.478 0.00 0.00 0.00 1.75
913 1064 7.552687 CCTATGCACCATGATACCGTATTATTT 59.447 37.037 0.00 0.00 0.00 1.40
937 1088 1.062488 AACCCAACTGCTCACCTCCT 61.062 55.000 0.00 0.00 0.00 3.69
988 1143 1.308216 CTCCCATCCCCCTCCTTGT 60.308 63.158 0.00 0.00 0.00 3.16
989 1144 2.081161 CCTCCCATCCCCCTCCTTG 61.081 68.421 0.00 0.00 0.00 3.61
1020 1175 2.486203 CGACTTGTCTACTGCAGAGACT 59.514 50.000 29.73 18.96 43.19 3.24
1159 1320 1.516365 AAAGACTGCTGCTGCTGCTG 61.516 55.000 27.75 27.75 41.07 4.41
1160 1321 1.228184 AAAGACTGCTGCTGCTGCT 60.228 52.632 27.67 12.31 41.07 4.24
1161 1322 1.209640 GAAAGACTGCTGCTGCTGC 59.790 57.895 22.51 22.51 41.07 5.25
1162 1323 0.797542 GAGAAAGACTGCTGCTGCTG 59.202 55.000 18.66 18.66 42.70 4.41
1163 1324 0.669932 CGAGAAAGACTGCTGCTGCT 60.670 55.000 17.00 0.00 40.48 4.24
1164 1325 0.948141 ACGAGAAAGACTGCTGCTGC 60.948 55.000 8.89 8.89 40.20 5.25
1165 1326 1.458827 GAACGAGAAAGACTGCTGCTG 59.541 52.381 4.89 4.89 0.00 4.41
1218 1379 1.065272 TGCTCAGCATCTGCACCATTA 60.065 47.619 0.00 0.00 45.16 1.90
1283 1444 3.655211 CCTTGCCCAGACCAGCCT 61.655 66.667 0.00 0.00 0.00 4.58
1362 1523 2.325509 AACAGTTAACGAAATGCGGC 57.674 45.000 0.00 0.00 46.49 6.53
1380 1541 6.713450 ACCGGAGAATTACTTTGAAAAGCTAA 59.287 34.615 9.46 2.58 39.63 3.09
1422 1583 7.569408 GCCATATGTCACTACAATTGTGATACG 60.569 40.741 21.42 6.71 44.74 3.06
1426 1587 4.570369 CGCCATATGTCACTACAATTGTGA 59.430 41.667 21.42 7.24 39.58 3.58
1601 1764 1.281867 TGCACCATCTAGAACAAGGGG 59.718 52.381 0.00 0.00 0.00 4.79
1602 1765 2.290260 TGTGCACCATCTAGAACAAGGG 60.290 50.000 15.69 0.00 0.00 3.95
1659 1822 0.326927 GCCCCAGCCAACTACAGTTA 59.673 55.000 0.00 0.00 36.32 2.24
1669 1832 3.664888 ATGCTTCAGCCCCAGCCA 61.665 61.111 0.00 0.00 41.25 4.75
1672 1835 0.035152 TGTACATGCTTCAGCCCCAG 60.035 55.000 0.00 0.00 41.18 4.45
1718 1881 3.699538 TCCAGGCTACACAGTACAGTATG 59.300 47.826 0.00 0.00 46.00 2.39
1733 1896 6.261826 CGAAAAGATCAGAAAATATCCAGGCT 59.738 38.462 0.00 0.00 0.00 4.58
1820 1983 5.634020 GGGCGAGTGTTATATACTCATTGAC 59.366 44.000 14.46 4.44 43.65 3.18
1853 2016 4.393062 ACTTGCGATTGTTAATCCAGACTG 59.607 41.667 0.00 0.00 34.35 3.51
1859 2022 7.302524 TGAAAACTACTTGCGATTGTTAATCC 58.697 34.615 0.00 0.00 34.35 3.01
1873 2036 8.594550 ACCAGTACATATCACTGAAAACTACTT 58.405 33.333 13.35 0.00 45.10 2.24
1877 2040 7.004555 TGACCAGTACATATCACTGAAAACT 57.995 36.000 13.35 0.00 45.10 2.66
1895 2058 7.490962 TTGTTAATCACACTTAACTGACCAG 57.509 36.000 7.87 0.00 40.60 4.00
1948 2111 8.027524 AGATGATATGAGTTTTTCCTCAGCTA 57.972 34.615 0.00 0.00 44.25 3.32
1949 2112 6.897986 AGATGATATGAGTTTTTCCTCAGCT 58.102 36.000 0.00 0.00 44.25 4.24
2082 2245 1.025041 GCCCGAGAAGCCCAAAATAG 58.975 55.000 0.00 0.00 0.00 1.73
2147 2351 8.284693 GCTCACAAAAATTGCATCTTTTATTGT 58.715 29.630 7.66 7.04 0.00 2.71
2242 2446 3.244215 GGAATGAACACTCTGGACAGTCA 60.244 47.826 2.17 0.00 0.00 3.41
2245 2449 3.407424 TGGAATGAACACTCTGGACAG 57.593 47.619 0.00 0.00 0.00 3.51
2412 2616 4.440839 GCCACTGCTAGCATTTAAACTT 57.559 40.909 19.72 0.00 33.53 2.66
2634 2838 3.311322 TCAACACTTACCTTTTGTCAGCG 59.689 43.478 0.00 0.00 0.00 5.18
2779 2983 7.017319 ACTCCTACCAAAGCATTAAAGTACT 57.983 36.000 0.00 0.00 0.00 2.73
2797 3001 5.020795 TGACATGCTACCACTTAACTCCTA 58.979 41.667 0.00 0.00 0.00 2.94
2881 3086 2.623416 CAGCCTATCATACGGACAGACA 59.377 50.000 0.00 0.00 0.00 3.41
2888 3093 3.507622 TCTGTCATCAGCCTATCATACGG 59.492 47.826 0.00 0.00 41.10 4.02
2918 3123 7.170277 GGGTAATGAAACTACTCCCTTTGTTA 58.830 38.462 0.00 0.00 0.00 2.41
2968 3173 4.786425 AGAAAGGTTCTGCTGAAGTTCTT 58.214 39.130 6.24 8.15 38.91 2.52
3090 3300 0.546122 TCCAAGTTGTGCCACTGAGT 59.454 50.000 1.45 0.00 0.00 3.41
3233 3443 3.130633 CGGCATCTCGTTTCATGGAATA 58.869 45.455 0.00 0.00 0.00 1.75
3239 3449 1.471676 GGTCTCGGCATCTCGTTTCAT 60.472 52.381 0.00 0.00 0.00 2.57
3334 3544 8.896320 ACGGTACATAATGCAAATGACTTATA 57.104 30.769 16.80 0.00 0.00 0.98
3355 3565 8.544597 GTGCAAAATTTAAGTAATCAAAACGGT 58.455 29.630 0.00 0.00 0.00 4.83
3387 3597 6.640499 GTGCTAAATTCATTTGCACAGTTACA 59.360 34.615 21.86 0.00 44.51 2.41
3429 3639 6.258727 CCAGACATTGCTACGTTCTATTCATT 59.741 38.462 0.00 0.00 0.00 2.57
3449 3659 1.541588 GACAACTGAAATGGCCCAGAC 59.458 52.381 13.03 0.00 34.65 3.51
3538 3748 4.614535 GCACTACATGGTTCTTTGAGCAAG 60.615 45.833 0.00 0.00 0.00 4.01
3561 3786 6.888430 ACGCTTACAATTCAAACTAGAAGTG 58.112 36.000 0.00 3.01 45.94 3.16
3565 3790 7.485418 TTTGACGCTTACAATTCAAACTAGA 57.515 32.000 0.00 0.00 33.96 2.43
3576 3804 5.885881 ACTGAAAATGTTTGACGCTTACAA 58.114 33.333 0.00 0.00 0.00 2.41
3639 3867 3.441572 AGTACTGAAATCATGCAGCCAAC 59.558 43.478 0.00 0.00 35.57 3.77
3771 3999 7.869937 CAGAAGTTCAAAAGACAGACATCTAGA 59.130 37.037 5.50 0.00 0.00 2.43
3869 4126 5.112129 TGAGGGGAGAAAGGTAAATAAGC 57.888 43.478 0.00 0.00 0.00 3.09
4031 4288 6.137415 CAGCTAAAAACATGCAAAAATGTGG 58.863 36.000 0.00 0.00 39.89 4.17
4195 4455 6.377146 GGCATTACTCTGGGATGAGTTTTTAA 59.623 38.462 2.44 0.00 44.01 1.52
4239 4663 7.205737 TGCACCATATTATTGTATTCTGCAG 57.794 36.000 7.63 7.63 0.00 4.41
4241 4665 8.048534 AGATGCACCATATTATTGTATTCTGC 57.951 34.615 0.00 0.00 0.00 4.26
4385 4809 5.296151 TGGATGGTCTGGATTGATTAGAC 57.704 43.478 0.00 0.00 39.98 2.59
4447 4871 4.640364 TGTGTGAGTGATGATAGTGCAAA 58.360 39.130 0.00 0.00 0.00 3.68
4516 4940 4.710324 TGAAACGTCAAGATGTAAAGGGT 58.290 39.130 0.00 0.00 0.00 4.34
4602 5026 1.149101 AAGCAACCAAGAGAAGGGGA 58.851 50.000 0.00 0.00 0.00 4.81
4779 5203 6.820335 TGCTTTAGTATATGCAGACTGTCAT 58.180 36.000 10.88 14.18 0.00 3.06
5225 5651 9.199982 CTTAACAAAAGACATGAGAATGCATTT 57.800 29.630 14.33 3.59 0.00 2.32
5245 5671 5.359576 ACTGGCTGACATGAAAAACTTAACA 59.640 36.000 0.00 0.00 0.00 2.41
5322 5748 3.243907 GGAAACTGAGGGTCATCTATCCG 60.244 52.174 0.00 0.00 0.00 4.18
5403 5829 9.241919 TCTCAATAAAGATTCATTACCTTTGCA 57.758 29.630 0.00 0.00 32.92 4.08
5416 5842 9.902684 AGTTCAGACATGATCTCAATAAAGATT 57.097 29.630 0.00 0.00 36.13 2.40
5484 5912 3.950397 TCTGCAACAAGTAATTCCGGAT 58.050 40.909 4.15 0.00 0.00 4.18
5500 5929 6.597672 ACGTCTAAAATACATCCATTTCTGCA 59.402 34.615 0.00 0.00 0.00 4.41
5548 5988 4.994852 TCCCGAATTACTTGTCACAGAAAG 59.005 41.667 0.00 0.00 0.00 2.62
5594 6034 9.449719 AAAAACCCAAGAACACATCTATACTAG 57.550 33.333 0.00 0.00 37.42 2.57
5602 6042 4.857037 GCGATAAAAACCCAAGAACACATC 59.143 41.667 0.00 0.00 0.00 3.06
5686 6156 0.388778 TCATGCATGCACAAAAGCCG 60.389 50.000 25.37 4.30 0.00 5.52
5955 6425 6.982141 TCCAGTAGTGTTAACTTACAAGTGTG 59.018 38.462 17.35 9.79 39.66 3.82
5972 6444 9.823647 CAGAATAGTTGTGATATTTCCAGTAGT 57.176 33.333 0.00 0.00 0.00 2.73
6038 6510 5.947228 TGAACTTAAGCAGACATCTTTGG 57.053 39.130 1.29 0.00 0.00 3.28
6183 6655 9.969001 ATAGTGCCCTTTAGTATTTTAACTTCA 57.031 29.630 0.00 0.00 0.00 3.02
6209 6681 2.238395 TGGTGCAGTATGTAGAATGCCA 59.762 45.455 0.00 0.00 39.31 4.92
6219 6691 5.345702 CCAAAAAGATGATGGTGCAGTATG 58.654 41.667 0.00 0.00 40.87 2.39
6266 6738 0.671251 TTGGGTCCGCAATCAACAAC 59.329 50.000 0.00 0.00 0.00 3.32
6277 6749 1.519408 AACTCACGATTTTGGGTCCG 58.481 50.000 0.00 0.00 26.58 4.79
6343 6815 1.230324 GGTGTCAAGTGTTGAGAGGC 58.770 55.000 0.00 0.00 41.01 4.70
6353 6825 2.031163 GCAGAGGCGGTGTCAAGT 59.969 61.111 0.00 0.00 0.00 3.16
6384 6856 2.285743 AGGGGAGAGGGGTCTTGC 60.286 66.667 0.00 0.00 0.00 4.01
6469 6941 3.275338 GCGAGGCCTGCAGCATAC 61.275 66.667 12.00 0.00 46.50 2.39
6548 7020 1.882623 CTCTTGGAAGTTGAACTGGGC 59.117 52.381 0.00 0.00 0.00 5.36
6572 7053 2.748058 TTTCAGGGAGCGGCCAGTTC 62.748 60.000 2.24 3.03 38.95 3.01
6578 7059 1.746991 CCTTCTTTCAGGGAGCGGC 60.747 63.158 0.00 0.00 0.00 6.53
6722 7203 3.483587 GGGGGTCTTCAGTCTGCA 58.516 61.111 0.00 0.00 0.00 4.41
6783 7285 5.163683 GCAACATCTGATAGTGCAATTGAGT 60.164 40.000 10.34 0.20 0.00 3.41
7045 7630 1.967066 AGTAGCAGCGAATATGAGCCT 59.033 47.619 0.00 0.00 0.00 4.58
7071 7656 1.418373 TCGCGATTCACAACTGTCTG 58.582 50.000 3.71 0.00 0.00 3.51
7116 7701 2.620115 ACATCGCCATAGCAAGGAATTG 59.380 45.455 0.00 0.00 39.83 2.32
7132 7717 8.703336 CATGTTCCAGTGTTATAAGATACATCG 58.297 37.037 0.00 0.00 0.00 3.84
7531 8123 3.326006 TCAGTCTTGTCCTTCTCAGCATT 59.674 43.478 0.00 0.00 0.00 3.56
7746 8338 3.746045 TTCCTGTACTTGACACACCTC 57.254 47.619 0.00 0.00 33.31 3.85
7806 8398 1.668751 TGTTTGTCGTGCCTTGACTTC 59.331 47.619 2.40 0.00 37.26 3.01
7869 8461 7.951347 AAATGATAGCAGATCTTTCCTGTTT 57.049 32.000 0.00 0.00 34.29 2.83
8008 8600 3.618594 CACAGTATCCAGGTTCATTCACG 59.381 47.826 0.00 0.00 0.00 4.35
8041 8633 5.513788 GCCAGAGCTATGGATTTCAGGATAA 60.514 44.000 31.31 0.00 43.57 1.75
8082 8674 4.760047 CTCGGACGGGTGGCCTTG 62.760 72.222 3.32 0.00 0.00 3.61
8106 8719 1.672881 CAGTTTGGCATACTGCTAGGC 59.327 52.381 22.06 0.00 44.28 3.93
8119 8732 4.073293 ACACCAGTTACTCTCAGTTTGG 57.927 45.455 0.00 0.00 32.63 3.28
8123 8736 3.497332 TGCTACACCAGTTACTCTCAGT 58.503 45.455 0.00 0.00 0.00 3.41
8124 8737 4.521130 TTGCTACACCAGTTACTCTCAG 57.479 45.455 0.00 0.00 0.00 3.35
8177 8790 5.874895 AGTTTTTACAATAACTCCGCTCC 57.125 39.130 0.00 0.00 28.79 4.70
8253 8866 5.300034 CAGGCCATGTATATTCACAACACAT 59.700 40.000 5.01 0.00 30.84 3.21
8302 8928 5.067153 CGGCCTTACATCCACATTTGAAATA 59.933 40.000 0.00 0.00 0.00 1.40
8331 8957 3.131046 CCCATGGCTACTTTGGTGAAATC 59.869 47.826 6.09 0.00 0.00 2.17
8360 8986 4.284123 TGCTCGCTCGCATTTTCT 57.716 50.000 0.00 0.00 34.44 2.52
8453 9080 5.550290 TCTGTATGAGCATGTGAAAGTTGA 58.450 37.500 0.00 0.00 0.00 3.18
8561 9197 8.547173 GTGGAATGAGGAATCTATTGAGGATAT 58.453 37.037 0.00 0.00 0.00 1.63
8619 9261 6.380995 GTCAATCACAATGTCATTTGTAGCA 58.619 36.000 0.00 0.00 37.73 3.49
8650 9292 4.263994 ACCAGAGGTCATACTCACTGTAGT 60.264 45.833 0.00 0.00 39.97 2.73
8651 9293 4.274147 ACCAGAGGTCATACTCACTGTAG 58.726 47.826 0.00 0.00 39.97 2.74
8655 9297 5.186021 CACTTTACCAGAGGTCATACTCACT 59.814 44.000 0.00 0.00 39.97 3.41
8666 9308 9.396022 ACAATGAATATAACACTTTACCAGAGG 57.604 33.333 0.00 0.00 0.00 3.69
8699 9341 0.032017 TTGCCCTAGAGAGACCTCCC 60.032 60.000 0.00 0.00 40.30 4.30
8843 9485 1.808411 TTTGGAGTTGAGCCGATGTC 58.192 50.000 0.00 0.00 0.00 3.06
8864 9506 8.579006 TGCAGTTCTTTGAAATGACATTAGAAT 58.421 29.630 12.16 0.00 0.00 2.40
8872 9514 5.581605 TCAACTGCAGTTCTTTGAAATGAC 58.418 37.500 28.97 4.30 35.83 3.06
8912 9554 1.202582 GATGTAGACAGTGACTGCGGT 59.797 52.381 13.37 0.00 34.37 5.68
8933 9575 5.677178 GGCATTTCGAAAACGATACAAGATC 59.323 40.000 15.66 0.00 0.00 2.75



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

AutoCloner maintained by Alex Coulton.