Multiple sequence alignment - TraesCS5B01G067100

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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 TraesCS5B01G067100 chr5B 100.000 6032 0 0 1 6032 75205558 75211589 0.000000e+00 11140
1 TraesCS5B01G067100 chr5B 94.788 825 38 5 2653 3474 664880869 664881691 0.000000e+00 1280
2 TraesCS5B01G067100 chr5B 94.125 834 43 6 2653 3483 63251598 63252428 0.000000e+00 1264
3 TraesCS5B01G067100 chr5A 96.019 1909 64 5 3480 5383 60109368 60111269 0.000000e+00 3094
4 TraesCS5B01G067100 chr5A 92.296 1895 96 26 804 2660 60107507 60109389 0.000000e+00 2645
5 TraesCS5B01G067100 chr5A 93.750 848 45 8 2644 3487 653659163 653660006 0.000000e+00 1266
6 TraesCS5B01G067100 chr5A 87.731 432 39 4 323 741 60096463 60096893 5.430000e-135 492
7 TraesCS5B01G067100 chr5A 81.560 423 55 7 5426 5848 60111269 60111668 1.620000e-85 327
8 TraesCS5B01G067100 chr5A 95.480 177 8 0 1 177 60095562 60095738 3.560000e-72 283
9 TraesCS5B01G067100 chr5A 77.805 401 69 16 5415 5799 264083077 264082681 4.700000e-56 230
10 TraesCS5B01G067100 chr5D 95.499 1622 62 6 3724 5340 69327614 69329229 0.000000e+00 2580
11 TraesCS5B01G067100 chr5D 92.148 917 41 17 821 1710 69326360 69327272 0.000000e+00 1266
12 TraesCS5B01G067100 chr5D 86.552 699 61 12 1 681 69323426 69324109 0.000000e+00 739
13 TraesCS5B01G067100 chr5D 95.455 330 13 1 1740 2069 69327271 69327598 5.360000e-145 525
14 TraesCS5B01G067100 chr5D 85.407 418 46 5 5402 5809 69346310 69346722 2.600000e-113 420
15 TraesCS5B01G067100 chr5D 79.455 404 61 15 5415 5801 205869485 205869087 3.580000e-67 267
16 TraesCS5B01G067100 chr2D 89.788 1038 78 12 3480 4508 49190921 49189903 0.000000e+00 1304
17 TraesCS5B01G067100 chr2D 87.668 373 25 11 1677 2036 49193147 49192783 1.210000e-111 414
18 TraesCS5B01G067100 chr2D 90.033 301 24 6 2333 2631 49191239 49190943 9.480000e-103 385
19 TraesCS5B01G067100 chr2D 87.500 160 14 4 2142 2297 49191384 49191227 4.800000e-41 180
20 TraesCS5B01G067100 chr2B 94.604 834 37 7 2653 3483 750057075 750056247 0.000000e+00 1284
21 TraesCS5B01G067100 chr3B 94.272 838 39 8 2649 3484 461613611 461614441 0.000000e+00 1273
22 TraesCS5B01G067100 chr3B 93.757 849 45 7 2648 3493 689004381 689003538 0.000000e+00 1267
23 TraesCS5B01G067100 chr3B 93.662 852 45 9 2645 3489 171120921 171120072 0.000000e+00 1266
24 TraesCS5B01G067100 chr4A 93.349 857 46 9 2637 3490 729257530 729258378 0.000000e+00 1256
25 TraesCS5B01G067100 chr3A 93.522 849 43 12 2647 3490 522044215 522043374 0.000000e+00 1253
26 TraesCS5B01G067100 chr6B 81.905 735 100 19 5278 5996 204940874 204940157 1.870000e-164 590
27 TraesCS5B01G067100 chr6D 77.636 313 40 16 5398 5694 187551053 187550755 4.840000e-36 163


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 TraesCS5B01G067100 chr5B 75205558 75211589 6031 False 11140.00 11140 100.000000 1 6032 1 chr5B.!!$F2 6031
1 TraesCS5B01G067100 chr5B 664880869 664881691 822 False 1280.00 1280 94.788000 2653 3474 1 chr5B.!!$F3 821
2 TraesCS5B01G067100 chr5B 63251598 63252428 830 False 1264.00 1264 94.125000 2653 3483 1 chr5B.!!$F1 830
3 TraesCS5B01G067100 chr5A 60107507 60111668 4161 False 2022.00 3094 89.958333 804 5848 3 chr5A.!!$F3 5044
4 TraesCS5B01G067100 chr5A 653659163 653660006 843 False 1266.00 1266 93.750000 2644 3487 1 chr5A.!!$F1 843
5 TraesCS5B01G067100 chr5A 60095562 60096893 1331 False 387.50 492 91.605500 1 741 2 chr5A.!!$F2 740
6 TraesCS5B01G067100 chr5D 69323426 69329229 5803 False 1277.50 2580 92.413500 1 5340 4 chr5D.!!$F2 5339
7 TraesCS5B01G067100 chr2D 49189903 49193147 3244 True 570.75 1304 88.747250 1677 4508 4 chr2D.!!$R1 2831
8 TraesCS5B01G067100 chr2B 750056247 750057075 828 True 1284.00 1284 94.604000 2653 3483 1 chr2B.!!$R1 830
9 TraesCS5B01G067100 chr3B 461613611 461614441 830 False 1273.00 1273 94.272000 2649 3484 1 chr3B.!!$F1 835
10 TraesCS5B01G067100 chr3B 689003538 689004381 843 True 1267.00 1267 93.757000 2648 3493 1 chr3B.!!$R2 845
11 TraesCS5B01G067100 chr3B 171120072 171120921 849 True 1266.00 1266 93.662000 2645 3489 1 chr3B.!!$R1 844
12 TraesCS5B01G067100 chr4A 729257530 729258378 848 False 1256.00 1256 93.349000 2637 3490 1 chr4A.!!$F1 853
13 TraesCS5B01G067100 chr3A 522043374 522044215 841 True 1253.00 1253 93.522000 2647 3490 1 chr3A.!!$R1 843
14 TraesCS5B01G067100 chr6B 204940157 204940874 717 True 590.00 590 81.905000 5278 5996 1 chr6B.!!$R1 718

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
244 520 1.006220 CTCGTTGGGGGCAAAAAGC 60.006 57.895 0.00 0.0 44.65 3.51 F
691 3407 1.068250 CACCTTAGCCTAGCGCCTC 59.932 63.158 2.29 0.0 38.78 4.70 F
1627 4385 0.460311 CTTCCTCGACGCCAAGGTAT 59.540 55.000 1.45 0.0 34.12 2.73 F
1903 4675 0.533755 GCTGAGCCGCATATCAACCT 60.534 55.000 0.00 0.0 0.00 3.50 F
3417 7568 0.099259 CATGCGATGACGTGGCAATT 59.901 50.000 8.50 0.0 44.94 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1627 4385 0.032130 GCATTCCTCTCACGCCGATA 59.968 55.000 0.0 0.0 0.00 2.92 R
1890 4662 0.659427 CTGCACAGGTTGATATGCGG 59.341 55.000 0.0 0.0 41.07 5.69 R
2893 7039 0.458669 CATCATGGCAACTTCTGGGC 59.541 55.000 0.0 0.0 37.61 5.36 R
3878 8032 2.223876 TGACGTAGAAAGCAGACGGTTT 60.224 45.455 0.0 0.0 45.26 3.27 R
5251 9411 0.316522 TGCGGCATCTGCTAGAGATC 59.683 55.000 0.0 0.0 39.64 2.75 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
30 31 9.635404 ATTTTGGGATATCTAAATTACCACGAA 57.365 29.630 2.05 0.00 0.00 3.85
34 35 6.653740 GGGATATCTAAATTACCACGAAAGGG 59.346 42.308 2.05 0.00 0.00 3.95
48 49 5.861787 CCACGAAAGGGTCATAATTTTTCAC 59.138 40.000 0.00 0.00 0.00 3.18
165 166 3.134081 ACGACCTCCTTGAGTCAAAGAAA 59.866 43.478 7.06 0.00 0.00 2.52
177 178 6.738114 TGAGTCAAAGAAAAGCTTATGGTTG 58.262 36.000 0.00 3.01 35.24 3.77
192 468 1.073923 TGGTTGGCCTTCTCTCCTTTC 59.926 52.381 3.32 0.00 35.27 2.62
204 480 3.060602 CTCTCCTTTCGAGACACCAAAC 58.939 50.000 0.00 0.00 42.97 2.93
222 498 2.370281 ACGCACGAGATCATGAACTT 57.630 45.000 6.96 0.00 0.00 2.66
244 520 1.006220 CTCGTTGGGGGCAAAAAGC 60.006 57.895 0.00 0.00 44.65 3.51
259 535 4.111916 CAAAAAGCGAACAACAATGTCCT 58.888 39.130 0.00 0.00 39.40 3.85
263 539 2.290641 AGCGAACAACAATGTCCTCAAC 59.709 45.455 0.00 0.00 39.40 3.18
279 555 6.204688 TGTCCTCAACTGACATTTGACAATAC 59.795 38.462 4.24 2.39 37.80 1.89
333 915 8.175925 TCATCAACAACATTAAACAGGAATCA 57.824 30.769 0.00 0.00 0.00 2.57
362 944 4.299586 TGTGATTCACCAAGAAGCCATA 57.700 40.909 14.05 0.00 41.89 2.74
426 1011 6.418057 CTCCAGAAGCTAAGAATCCATAGT 57.582 41.667 0.00 0.00 0.00 2.12
434 1019 5.594725 AGCTAAGAATCCATAGTCGACAAGA 59.405 40.000 19.50 8.73 0.00 3.02
513 1110 7.440523 AAAGAATTGAAGCGTCTGTTATTCT 57.559 32.000 0.31 7.42 33.59 2.40
562 1160 2.906354 ACCAGCCATTCGATACTTGAC 58.094 47.619 0.00 0.00 0.00 3.18
572 1170 7.530010 CCATTCGATACTTGACATTTCAACTT 58.470 34.615 0.00 0.00 36.79 2.66
614 1212 3.784338 CCACGGTCGCTACCTATTTTTA 58.216 45.455 5.79 0.00 44.35 1.52
624 1222 5.176958 CGCTACCTATTTTTAATCCCTGACG 59.823 44.000 0.00 0.00 0.00 4.35
654 1252 2.358737 GCTCCAACCACCCGTCAG 60.359 66.667 0.00 0.00 0.00 3.51
657 1255 2.203280 CCAACCACCCGTCAGCAA 60.203 61.111 0.00 0.00 0.00 3.91
674 1272 3.258872 CAGCAAGGAAATCAATCCCAACA 59.741 43.478 0.00 0.00 40.59 3.33
690 3406 1.265454 AACACCTTAGCCTAGCGCCT 61.265 55.000 2.29 0.00 38.78 5.52
691 3407 1.068250 CACCTTAGCCTAGCGCCTC 59.932 63.158 2.29 0.00 38.78 4.70
692 3408 2.336809 CCTTAGCCTAGCGCCTCG 59.663 66.667 2.29 0.00 38.78 4.63
742 3458 7.471721 ACAATGTATCATCGGTGTAAACAATG 58.528 34.615 11.58 11.58 0.00 2.82
743 3459 7.120579 ACAATGTATCATCGGTGTAAACAATGT 59.879 33.333 12.49 12.49 29.88 2.71
744 3460 8.608317 CAATGTATCATCGGTGTAAACAATGTA 58.392 33.333 0.00 0.00 0.00 2.29
745 3461 8.902540 ATGTATCATCGGTGTAAACAATGTAT 57.097 30.769 0.00 0.00 0.00 2.29
748 3464 9.472361 GTATCATCGGTGTAAACAATGTATAGT 57.528 33.333 0.00 0.00 0.00 2.12
749 3465 7.997107 TCATCGGTGTAAACAATGTATAGTC 57.003 36.000 0.00 0.00 0.00 2.59
750 3466 6.693978 TCATCGGTGTAAACAATGTATAGTCG 59.306 38.462 0.00 0.00 0.00 4.18
753 3469 5.005012 CGGTGTAAACAATGTATAGTCGGTG 59.995 44.000 0.00 0.00 0.00 4.94
755 3471 7.035004 GGTGTAAACAATGTATAGTCGGTGTA 58.965 38.462 0.00 0.00 0.00 2.90
756 3472 7.707893 GGTGTAAACAATGTATAGTCGGTGTAT 59.292 37.037 0.00 0.00 0.00 2.29
757 3473 9.090692 GTGTAAACAATGTATAGTCGGTGTATT 57.909 33.333 0.00 0.00 0.00 1.89
758 3474 9.089601 TGTAAACAATGTATAGTCGGTGTATTG 57.910 33.333 0.00 0.00 0.00 1.90
768 3494 5.526506 AGTCGGTGTATTGGATAAGTACC 57.473 43.478 0.00 0.00 0.00 3.34
769 3495 4.343239 AGTCGGTGTATTGGATAAGTACCC 59.657 45.833 0.00 0.00 0.00 3.69
778 3504 2.247111 TGGATAAGTACCCCCTCCGTAA 59.753 50.000 0.00 0.00 0.00 3.18
780 3506 3.711190 GGATAAGTACCCCCTCCGTAAAA 59.289 47.826 0.00 0.00 0.00 1.52
781 3507 4.349048 GGATAAGTACCCCCTCCGTAAAAT 59.651 45.833 0.00 0.00 0.00 1.82
786 3512 6.425210 AGTACCCCCTCCGTAAAATAATAC 57.575 41.667 0.00 0.00 0.00 1.89
792 3518 6.408891 CCCCCTCCGTAAAATAATACAAGAGT 60.409 42.308 0.00 0.00 29.89 3.24
794 3520 6.018180 CCCTCCGTAAAATAATACAAGAGTGC 60.018 42.308 0.00 0.00 29.89 4.40
803 3529 9.905713 AAAATAATACAAGAGTGCTTAGATCCA 57.094 29.630 0.00 0.00 31.81 3.41
804 3530 9.553064 AAATAATACAAGAGTGCTTAGATCCAG 57.447 33.333 0.00 0.00 31.81 3.86
805 3531 6.798427 AATACAAGAGTGCTTAGATCCAGA 57.202 37.500 0.00 0.00 31.81 3.86
806 3532 4.734398 ACAAGAGTGCTTAGATCCAGAG 57.266 45.455 0.00 0.00 31.81 3.35
807 3533 4.348486 ACAAGAGTGCTTAGATCCAGAGA 58.652 43.478 0.00 0.00 31.81 3.10
808 3534 4.402155 ACAAGAGTGCTTAGATCCAGAGAG 59.598 45.833 0.00 0.00 31.81 3.20
809 3535 3.565307 AGAGTGCTTAGATCCAGAGAGG 58.435 50.000 0.00 0.00 39.47 3.69
838 3564 7.165483 CACAAATATACTCCGACGTCTAAGTTC 59.835 40.741 20.35 0.00 0.00 3.01
853 3583 4.980434 TCTAAGTTCGCAGTACAGAACAAC 59.020 41.667 22.11 8.41 46.54 3.32
862 3592 4.278419 GCAGTACAGAACAACCAATTTCCT 59.722 41.667 0.00 0.00 0.00 3.36
987 3732 1.577328 CCGCATTTTGTCGAGCACCT 61.577 55.000 0.00 0.00 0.00 4.00
1016 3761 2.586792 GATGCCGCTCTTCCACCT 59.413 61.111 0.00 0.00 0.00 4.00
1320 4065 2.420628 TCGTATTCGACACGGTTTGT 57.579 45.000 16.26 0.00 43.10 2.83
1338 4089 3.322466 CCCTTCACCCTCACGCCT 61.322 66.667 0.00 0.00 0.00 5.52
1383 4141 2.415608 CGCGAGCCTCACTCCCTTA 61.416 63.158 0.00 0.00 43.01 2.69
1384 4142 1.142097 GCGAGCCTCACTCCCTTAC 59.858 63.158 0.00 0.00 43.01 2.34
1514 4272 2.232298 GAGCGACCAGAGGTTCCAGG 62.232 65.000 0.00 0.00 35.25 4.45
1585 4343 2.755876 ATCGGTGAGCTCGAGGCA 60.756 61.111 15.58 0.00 44.79 4.75
1621 4379 1.315690 CTATACCTTCCTCGACGCCA 58.684 55.000 0.00 0.00 0.00 5.69
1627 4385 0.460311 CTTCCTCGACGCCAAGGTAT 59.540 55.000 1.45 0.00 34.12 2.73
1681 4439 1.813862 GCAATGCTGCCCGAGGTATAA 60.814 52.381 0.00 0.00 43.26 0.98
1796 4562 8.906636 TGTAGAGCGTAGTGACTAAATTTTAG 57.093 34.615 13.44 13.44 0.00 1.85
1798 4564 9.994432 GTAGAGCGTAGTGACTAAATTTTAGTA 57.006 33.333 19.21 4.05 0.00 1.82
1799 4565 8.908172 AGAGCGTAGTGACTAAATTTTAGTAC 57.092 34.615 19.21 16.39 0.00 2.73
1836 4602 6.440647 TGGAGTTTAGTCCATCAGTCACTTAT 59.559 38.462 2.11 0.00 41.99 1.73
1837 4603 7.618117 TGGAGTTTAGTCCATCAGTCACTTATA 59.382 37.037 2.11 0.00 41.99 0.98
1880 4652 4.873817 TCACTTTCATGGCTGTTCATTTG 58.126 39.130 0.00 0.00 0.00 2.32
1890 4662 2.669364 CTGTTCATTTGGTTGCTGAGC 58.331 47.619 0.00 0.00 0.00 4.26
1903 4675 0.533755 GCTGAGCCGCATATCAACCT 60.534 55.000 0.00 0.00 0.00 3.50
2138 4952 2.887152 AGTGTTTTCCAATCTGCTCCAC 59.113 45.455 0.00 0.00 0.00 4.02
2212 6335 2.486592 GGATTTTGTCCACCTGGTTACG 59.513 50.000 0.00 0.00 46.96 3.18
2214 6337 0.881159 TTTGTCCACCTGGTTACGCG 60.881 55.000 3.53 3.53 36.34 6.01
2238 6361 4.837860 TGCACCCTGTTTCTTGGAATAATT 59.162 37.500 0.00 0.00 0.00 1.40
2307 6430 5.532406 GGATACATATTGTTGGATGCAGTGT 59.468 40.000 0.00 0.00 29.23 3.55
2337 6460 9.493206 CATGCAAAATTTGAGGCAAAAATATAC 57.507 29.630 10.26 0.00 40.02 1.47
2338 6461 8.845413 TGCAAAATTTGAGGCAAAAATATACT 57.155 26.923 10.26 0.00 36.90 2.12
2339 6462 9.935241 TGCAAAATTTGAGGCAAAAATATACTA 57.065 25.926 10.26 0.00 36.90 1.82
2411 6534 6.523201 CAGACTGCGTAAATGTACCATTTTTC 59.477 38.462 7.43 2.33 0.00 2.29
2438 6563 9.941325 TTTCATGGAGCACACAATTAAATATTT 57.059 25.926 5.89 5.89 0.00 1.40
2884 7028 6.458206 CCCATGTTGATATGTTTCGACGAAAT 60.458 38.462 24.48 13.13 33.97 2.17
2978 7127 8.533965 CATGTGGCAATTTTAATTTGTAGATCG 58.466 33.333 0.00 0.00 0.00 3.69
3290 7440 3.798202 ACATGGGATCTAGTTTCGAAGC 58.202 45.455 3.49 3.49 0.00 3.86
3391 7542 5.550290 TGAAAATCCAAAAAGATTCCTGCC 58.450 37.500 0.00 0.00 35.40 4.85
3417 7568 0.099259 CATGCGATGACGTGGCAATT 59.901 50.000 8.50 0.00 44.94 2.32
3456 7607 2.584391 GGTGCGTCTCCCTTCCTGT 61.584 63.158 0.00 0.00 0.00 4.00
3677 7829 1.337071 CCATGAGCACTGAATGGATGC 59.663 52.381 0.00 0.00 43.00 3.91
3844 7996 6.335934 ACCATATATATGTGTCCCCTGGTTA 58.664 40.000 19.11 0.00 30.56 2.85
3878 8032 3.697542 CTCATTGATCAGGGAAATGTGCA 59.302 43.478 0.00 0.00 33.84 4.57
4022 8180 5.999205 ATGCCCTCTATATTCAGAGACTG 57.001 43.478 4.35 0.00 44.11 3.51
4159 8317 2.036958 TGGATGGCCAACAATACTCG 57.963 50.000 10.96 0.00 42.49 4.18
4163 8321 2.107950 TGGCCAACAATACTCGGAAG 57.892 50.000 0.61 0.00 0.00 3.46
4318 8477 3.270877 GTTGCACTACTCCCTGTTATGG 58.729 50.000 0.00 0.00 0.00 2.74
4329 8488 5.044846 ACTCCCTGTTATGGTGAATTAAGCT 60.045 40.000 0.00 0.00 0.00 3.74
4470 8629 0.110486 TGGGGGAGTTGAACTTGCTC 59.890 55.000 0.00 0.00 0.00 4.26
4511 8670 3.734463 TCTTCAGCGACCATTTTACACA 58.266 40.909 0.00 0.00 0.00 3.72
4551 8710 3.503363 TGAGAATGCACACATTGGACTTC 59.497 43.478 0.00 0.00 46.59 3.01
4575 8734 8.958119 TCCATACCTGTTACTATTTCATCAAC 57.042 34.615 0.00 0.00 0.00 3.18
4666 8825 1.858910 TGCATATTTGATCCCCAGGGT 59.141 47.619 4.22 0.00 36.47 4.34
4827 8986 6.872020 TCGCATTTAACAAACTAGCTCTAAGT 59.128 34.615 0.00 0.00 0.00 2.24
4838 8997 8.614346 CAAACTAGCTCTAAGTTATACGAGTCT 58.386 37.037 0.84 1.89 0.00 3.24
5209 9369 0.395862 TTTCCTTTTGCGGGTCACCA 60.396 50.000 0.00 0.00 36.13 4.17
5212 9372 0.250553 CCTTTTGCGGGTCACCACTA 60.251 55.000 0.00 0.00 36.13 2.74
5219 9379 2.210116 GCGGGTCACCACTATATGTTG 58.790 52.381 0.00 0.00 36.13 3.33
5251 9411 7.600752 AGAGATTTCTTCTGAAACGTTAAGAGG 59.399 37.037 0.00 8.85 43.90 3.69
5319 9480 4.453136 ACGCATACTGTAAACCGAATTTGT 59.547 37.500 10.59 0.00 0.00 2.83
5331 9492 1.375551 GAATTTGTGGTACCGCGGAT 58.624 50.000 35.90 18.92 0.00 4.18
5353 9514 1.858091 CACGAAAGATCAGATCCGGG 58.142 55.000 6.80 1.19 0.00 5.73
5358 9519 3.430929 CGAAAGATCAGATCCGGGAAACT 60.431 47.826 6.80 0.62 0.00 2.66
5359 9520 3.828875 AAGATCAGATCCGGGAAACTC 57.171 47.619 6.80 0.00 0.00 3.01
5390 9552 9.365311 CACATAATTTAAACTACTAATTCGCGG 57.635 33.333 6.13 0.00 0.00 6.46
5391 9553 9.101655 ACATAATTTAAACTACTAATTCGCGGT 57.898 29.630 6.13 0.00 0.00 5.68
5401 9563 7.874940 ACTACTAATTCGCGGTACATACATTA 58.125 34.615 6.13 0.00 0.00 1.90
5403 9565 6.506147 ACTAATTCGCGGTACATACATTACA 58.494 36.000 6.13 0.00 0.00 2.41
5404 9566 7.149973 ACTAATTCGCGGTACATACATTACAT 58.850 34.615 6.13 0.00 0.00 2.29
5405 9567 8.298854 ACTAATTCGCGGTACATACATTACATA 58.701 33.333 6.13 0.00 0.00 2.29
5406 9568 6.939551 ATTCGCGGTACATACATTACATAC 57.060 37.500 6.13 0.00 0.00 2.39
5407 9569 5.435820 TCGCGGTACATACATTACATACA 57.564 39.130 6.13 0.00 0.00 2.29
5408 9570 6.016213 TCGCGGTACATACATTACATACAT 57.984 37.500 6.13 0.00 0.00 2.29
5409 9571 6.448852 TCGCGGTACATACATTACATACATT 58.551 36.000 6.13 0.00 0.00 2.71
5410 9572 6.363896 TCGCGGTACATACATTACATACATTG 59.636 38.462 6.13 0.00 0.00 2.82
5411 9573 6.363896 CGCGGTACATACATTACATACATTGA 59.636 38.462 0.00 0.00 0.00 2.57
5412 9574 7.062956 CGCGGTACATACATTACATACATTGAT 59.937 37.037 0.00 0.00 0.00 2.57
5413 9575 9.361315 GCGGTACATACATTACATACATTGATA 57.639 33.333 0.00 0.00 0.00 2.15
5459 9629 9.073475 TGACAAACTTAAAACATACCAGCTTAT 57.927 29.630 0.00 0.00 0.00 1.73
5489 9659 9.512588 AACCTAAATCTATTCATCATCATCACC 57.487 33.333 0.00 0.00 0.00 4.02
5535 9717 3.920231 TCCATCAATGAGTTGGAGAGG 57.080 47.619 1.65 0.00 40.39 3.69
5536 9718 3.453868 TCCATCAATGAGTTGGAGAGGA 58.546 45.455 1.65 0.00 40.39 3.71
5537 9719 3.198635 TCCATCAATGAGTTGGAGAGGAC 59.801 47.826 1.65 0.00 40.39 3.85
5538 9720 3.193263 CATCAATGAGTTGGAGAGGACG 58.807 50.000 0.00 0.00 35.99 4.79
5539 9721 2.525368 TCAATGAGTTGGAGAGGACGA 58.475 47.619 0.00 0.00 35.99 4.20
5540 9722 2.897326 TCAATGAGTTGGAGAGGACGAA 59.103 45.455 0.00 0.00 35.99 3.85
5541 9723 3.515502 TCAATGAGTTGGAGAGGACGAAT 59.484 43.478 0.00 0.00 35.99 3.34
5542 9724 3.533606 ATGAGTTGGAGAGGACGAATG 57.466 47.619 0.00 0.00 0.00 2.67
5543 9725 1.066858 TGAGTTGGAGAGGACGAATGC 60.067 52.381 0.00 0.00 0.00 3.56
5544 9726 1.205893 GAGTTGGAGAGGACGAATGCT 59.794 52.381 0.00 0.00 0.00 3.79
5545 9727 2.427453 GAGTTGGAGAGGACGAATGCTA 59.573 50.000 0.00 0.00 0.00 3.49
5546 9728 2.428890 AGTTGGAGAGGACGAATGCTAG 59.571 50.000 0.00 0.00 0.00 3.42
5564 9746 2.506438 GTCGTTCTCCTTCGCCGG 60.506 66.667 0.00 0.00 0.00 6.13
5588 9779 1.122019 ACAGTGCCTTCTTCTCCGGT 61.122 55.000 0.00 0.00 0.00 5.28
5591 9782 2.436824 GCCTTCTTCTCCGGTGGC 60.437 66.667 0.00 1.66 0.00 5.01
5594 9785 2.920912 TTCTTCTCCGGTGGCGGT 60.921 61.111 0.00 0.00 0.00 5.68
5595 9786 2.450479 CTTCTTCTCCGGTGGCGGTT 62.450 60.000 0.00 0.00 0.00 4.44
5620 9811 2.467946 CTTCGCCTCGTACCACGTGT 62.468 60.000 15.65 5.35 43.14 4.49
5625 9816 1.579932 CTCGTACCACGTGTGCTCT 59.420 57.895 15.65 0.00 43.14 4.09
5631 9822 2.341543 CACGTGTGCTCTGCCTCT 59.658 61.111 7.58 0.00 0.00 3.69
5756 9947 2.311854 CCTTGCCCCACTCCTCCAT 61.312 63.158 0.00 0.00 0.00 3.41
5799 9990 2.092291 GGCTTCGTCGTCATTGCGA 61.092 57.895 0.00 0.14 38.68 5.10
5865 10056 0.647410 CATGACCAACGCTCGACATC 59.353 55.000 0.00 0.00 0.00 3.06
5866 10057 0.246360 ATGACCAACGCTCGACATCA 59.754 50.000 0.00 0.00 0.00 3.07
5870 10061 1.811266 CAACGCTCGACATCAGGGG 60.811 63.158 0.00 0.00 0.00 4.79
5872 10063 4.899239 CGCTCGACATCAGGGGGC 62.899 72.222 0.00 0.00 0.00 5.80
5873 10064 4.899239 GCTCGACATCAGGGGGCG 62.899 72.222 0.00 0.00 0.00 6.13
5874 10065 3.147595 CTCGACATCAGGGGGCGA 61.148 66.667 0.00 0.00 0.00 5.54
5906 10097 4.293626 GCGCACGCGACAAACTGT 62.294 61.111 15.93 0.00 42.83 3.55
5907 10098 2.323105 CGCACGCGACAAACTGTT 59.677 55.556 15.93 0.00 42.83 3.16
5937 10128 0.386113 GGAGGATTTCTCGTCGGAGG 59.614 60.000 0.00 0.00 43.34 4.30
5938 10129 0.386113 GAGGATTTCTCGTCGGAGGG 59.614 60.000 0.00 0.00 40.85 4.30
5941 10132 1.413077 GGATTTCTCGTCGGAGGGAAT 59.587 52.381 0.00 0.00 40.85 3.01
5950 10141 0.463654 TCGGAGGGAATGATTTGCGG 60.464 55.000 0.00 0.00 0.00 5.69
5952 10143 1.356624 GAGGGAATGATTTGCGGCG 59.643 57.895 0.51 0.51 0.00 6.46
5955 10146 1.356624 GGAATGATTTGCGGCGGAG 59.643 57.895 9.78 0.00 0.00 4.63
5973 10164 3.931707 GGGGGAAAGGGGAAGTGA 58.068 61.111 0.00 0.00 0.00 3.41
5974 10165 2.170052 GGGGGAAAGGGGAAGTGAA 58.830 57.895 0.00 0.00 0.00 3.18
5980 10171 2.095461 GAAAGGGGAAGTGAAGGATGC 58.905 52.381 0.00 0.00 0.00 3.91
5985 10176 1.087501 GGAAGTGAAGGATGCGAACC 58.912 55.000 0.00 0.00 0.00 3.62
5991 10182 3.078837 GTGAAGGATGCGAACCCTAAAA 58.921 45.455 0.00 0.00 31.36 1.52
5996 10187 2.477396 GCGAACCCTAAAACGCGG 59.523 61.111 12.47 0.00 41.49 6.46
5997 10188 2.477396 CGAACCCTAAAACGCGGC 59.523 61.111 12.47 0.00 0.00 6.53
5998 10189 2.477396 GAACCCTAAAACGCGGCG 59.523 61.111 22.36 22.36 0.00 6.46
5999 10190 3.030763 GAACCCTAAAACGCGGCGG 62.031 63.158 27.37 9.16 0.00 6.13
6023 10214 3.095032 CGTGAATTTACGGGCCGG 58.905 61.111 31.78 12.53 40.22 6.13
6024 10215 2.466140 CGTGAATTTACGGGCCGGG 61.466 63.158 31.78 3.37 40.22 5.73
6025 10216 2.438795 TGAATTTACGGGCCGGGC 60.439 61.111 31.78 22.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 7.593825 AGAAGTGAAAAATTATGACCCTTTCG 58.406 34.615 0.00 0.00 0.00 3.46
30 31 9.147732 AGAAAGAAGTGAAAAATTATGACCCTT 57.852 29.630 0.00 0.00 0.00 3.95
48 49 7.173907 TGCCATCTTCAAGTAGAAAGAAAGAAG 59.826 37.037 0.00 0.00 35.40 2.85
165 166 2.310052 AGAGAAGGCCAACCATAAGCTT 59.690 45.455 5.01 3.48 39.06 3.74
177 178 1.187087 TCTCGAAAGGAGAGAAGGCC 58.813 55.000 0.00 0.00 46.80 5.19
192 468 1.876453 CTCGTGCGTTTGGTGTCTCG 61.876 60.000 0.00 0.00 0.00 4.04
204 480 1.325640 CCAAGTTCATGATCTCGTGCG 59.674 52.381 6.75 0.00 33.05 5.34
244 520 3.559655 TCAGTTGAGGACATTGTTGTTCG 59.440 43.478 0.00 0.00 36.37 3.95
298 574 2.884012 TGTTGTTGATGATGAAGCGGTT 59.116 40.909 0.00 0.00 0.00 4.44
333 915 7.363268 GGCTTCTTGGTGAATCACATCTTTTAT 60.363 37.037 15.86 0.00 35.86 1.40
336 918 4.219288 GGCTTCTTGGTGAATCACATCTTT 59.781 41.667 15.86 0.00 35.86 2.52
426 1011 5.869344 CCAACAATGAAGATACTCTTGTCGA 59.131 40.000 0.00 0.00 36.73 4.20
434 1019 4.307032 AGTGCCCAACAATGAAGATACT 57.693 40.909 0.00 0.00 0.00 2.12
441 1026 0.675083 CTGCAAGTGCCCAACAATGA 59.325 50.000 0.00 0.00 41.18 2.57
519 1116 1.433879 CGCCTGTAGTTAGCGCTCT 59.566 57.895 16.34 8.88 43.72 4.09
525 1122 3.187700 CTGGTTTAGCGCCTGTAGTTAG 58.812 50.000 2.29 0.00 0.00 2.34
554 1151 8.450578 TCTGAACAAGTTGAAATGTCAAGTAT 57.549 30.769 10.54 0.00 44.98 2.12
562 1160 5.772825 TTCCCTCTGAACAAGTTGAAATG 57.227 39.130 10.54 0.00 0.00 2.32
572 1170 3.222603 GCCTTTTCTTTCCCTCTGAACA 58.777 45.455 0.00 0.00 31.05 3.18
624 1222 2.029918 GGTTGGAGCAACAAATCCTGAC 60.030 50.000 0.00 0.00 45.11 3.51
654 1252 3.588955 GTGTTGGGATTGATTTCCTTGC 58.411 45.455 0.00 0.00 35.97 4.01
657 1255 3.833559 AGGTGTTGGGATTGATTTCCT 57.166 42.857 0.00 0.00 35.97 3.36
690 3406 0.459899 AGAGCATATGACCAACGCGA 59.540 50.000 15.93 0.00 0.00 5.87
691 3407 2.134201 TAGAGCATATGACCAACGCG 57.866 50.000 6.97 3.53 0.00 6.01
692 3408 3.717707 TCTTAGAGCATATGACCAACGC 58.282 45.455 6.97 0.00 0.00 4.84
693 3409 7.438160 TGTTTATCTTAGAGCATATGACCAACG 59.562 37.037 6.97 0.00 0.00 4.10
694 3410 8.662781 TGTTTATCTTAGAGCATATGACCAAC 57.337 34.615 6.97 0.00 0.00 3.77
696 3412 9.276590 CATTGTTTATCTTAGAGCATATGACCA 57.723 33.333 6.97 0.00 0.00 4.02
742 3458 8.239998 GGTACTTATCCAATACACCGACTATAC 58.760 40.741 0.00 0.00 0.00 1.47
743 3459 7.394359 GGGTACTTATCCAATACACCGACTATA 59.606 40.741 0.00 0.00 0.00 1.31
744 3460 6.210185 GGGTACTTATCCAATACACCGACTAT 59.790 42.308 0.00 0.00 0.00 2.12
745 3461 5.536161 GGGTACTTATCCAATACACCGACTA 59.464 44.000 0.00 0.00 0.00 2.59
748 3464 3.642848 GGGGTACTTATCCAATACACCGA 59.357 47.826 0.00 0.00 32.84 4.69
749 3465 3.244318 GGGGGTACTTATCCAATACACCG 60.244 52.174 0.00 0.00 42.43 4.94
750 3466 3.978672 AGGGGGTACTTATCCAATACACC 59.021 47.826 0.00 0.00 41.02 4.16
753 3469 3.260128 CGGAGGGGGTACTTATCCAATAC 59.740 52.174 0.00 0.00 0.00 1.89
755 3471 2.335933 CGGAGGGGGTACTTATCCAAT 58.664 52.381 0.00 0.00 0.00 3.16
756 3472 1.008693 ACGGAGGGGGTACTTATCCAA 59.991 52.381 0.00 0.00 0.00 3.53
757 3473 0.638292 ACGGAGGGGGTACTTATCCA 59.362 55.000 0.00 0.00 0.00 3.41
758 3474 2.683211 TACGGAGGGGGTACTTATCC 57.317 55.000 0.00 0.00 0.00 2.59
768 3494 6.482308 CACTCTTGTATTATTTTACGGAGGGG 59.518 42.308 0.00 0.00 33.11 4.79
769 3495 6.018180 GCACTCTTGTATTATTTTACGGAGGG 60.018 42.308 0.00 0.00 34.22 4.30
778 3504 9.553064 CTGGATCTAAGCACTCTTGTATTATTT 57.447 33.333 0.00 0.00 33.85 1.40
780 3506 8.484214 TCTGGATCTAAGCACTCTTGTATTAT 57.516 34.615 0.00 0.00 33.85 1.28
781 3507 7.780271 TCTCTGGATCTAAGCACTCTTGTATTA 59.220 37.037 0.00 0.00 33.85 0.98
786 3512 4.202141 CCTCTCTGGATCTAAGCACTCTTG 60.202 50.000 0.00 0.00 38.35 3.02
792 3518 2.315176 GCTCCTCTCTGGATCTAAGCA 58.685 52.381 0.00 0.00 45.16 3.91
794 3520 3.295093 TGTGCTCCTCTCTGGATCTAAG 58.705 50.000 0.00 0.00 45.16 2.18
801 3527 5.510520 GGAGTATATTTGTGCTCCTCTCTGG 60.511 48.000 4.56 0.00 44.66 3.86
802 3528 5.537188 GGAGTATATTTGTGCTCCTCTCTG 58.463 45.833 4.56 0.00 44.66 3.35
803 3529 4.279671 CGGAGTATATTTGTGCTCCTCTCT 59.720 45.833 9.17 0.00 45.53 3.10
804 3530 4.278669 TCGGAGTATATTTGTGCTCCTCTC 59.721 45.833 9.17 0.00 45.53 3.20
805 3531 4.038162 GTCGGAGTATATTTGTGCTCCTCT 59.962 45.833 9.17 0.00 45.53 3.69
806 3532 4.299978 GTCGGAGTATATTTGTGCTCCTC 58.700 47.826 9.17 0.84 45.53 3.71
807 3533 3.243434 CGTCGGAGTATATTTGTGCTCCT 60.243 47.826 9.17 0.00 45.53 3.69
808 3534 3.050619 CGTCGGAGTATATTTGTGCTCC 58.949 50.000 2.07 2.07 44.63 4.70
809 3535 3.703420 ACGTCGGAGTATATTTGTGCTC 58.297 45.455 0.00 0.00 0.00 4.26
826 3552 3.120408 TCTGTACTGCGAACTTAGACGTC 60.120 47.826 7.70 7.70 0.00 4.34
838 3564 3.896648 AATTGGTTGTTCTGTACTGCG 57.103 42.857 0.00 0.00 0.00 5.18
853 3583 9.717942 TGGTATTGTATTTTTCAAGGAAATTGG 57.282 29.630 0.00 0.00 39.54 3.16
862 3592 7.473735 TGCTCCATGGTATTGTATTTTTCAA 57.526 32.000 12.58 0.00 0.00 2.69
881 3611 3.550656 CGTTCTCACGGTTGCTCC 58.449 61.111 0.00 0.00 43.16 4.70
936 3680 4.530710 AGCAGACCGTTATCTGTTTACA 57.469 40.909 9.52 0.00 46.65 2.41
1318 4063 2.879233 GCGTGAGGGTGAAGGGACA 61.879 63.158 0.00 0.00 0.00 4.02
1320 4065 3.319198 GGCGTGAGGGTGAAGGGA 61.319 66.667 0.00 0.00 0.00 4.20
1371 4129 1.817209 GGCGAGTAAGGGAGTGAGG 59.183 63.158 0.00 0.00 0.00 3.86
1480 4238 1.664965 GCTCGCGGTGAAGAACTGT 60.665 57.895 6.13 0.00 37.49 3.55
1514 4272 1.142748 CCCACTCATCGACCAGCTC 59.857 63.158 0.00 0.00 0.00 4.09
1585 4343 0.698238 TAGCTGTGAAATGGCCACCT 59.302 50.000 8.16 0.00 33.80 4.00
1621 4379 1.887198 CCTCTCACGCCGATATACCTT 59.113 52.381 0.00 0.00 0.00 3.50
1627 4385 0.032130 GCATTCCTCTCACGCCGATA 59.968 55.000 0.00 0.00 0.00 2.92
1681 4439 2.179427 TCCACAAGATGTCGACCTGAT 58.821 47.619 14.12 0.00 0.00 2.90
1738 4500 6.877236 TGATAATGTGATGCTGTAGTGAAGA 58.123 36.000 0.00 0.00 0.00 2.87
1799 4565 7.934578 TGGACTAAACTCCAACGAACAAATCG 61.935 42.308 0.00 0.00 45.23 3.34
1806 4572 4.039973 ACTGATGGACTAAACTCCAACGAA 59.960 41.667 0.00 0.00 43.79 3.85
1808 4574 3.926616 ACTGATGGACTAAACTCCAACG 58.073 45.455 0.00 0.00 43.79 4.10
1890 4662 0.659427 CTGCACAGGTTGATATGCGG 59.341 55.000 0.00 0.00 41.07 5.69
1903 4675 5.316167 ACTTTAATCAGGTCATTCTGCACA 58.684 37.500 0.00 0.00 34.91 4.57
2118 4932 2.622942 TGTGGAGCAGATTGGAAAACAC 59.377 45.455 0.00 0.00 0.00 3.32
2138 4952 2.697761 GCTGGCAGCCTGTCACATG 61.698 63.158 28.87 0.00 34.48 3.21
2169 6288 3.493334 TCTCTCGAGACACTTGGGTTTA 58.507 45.455 12.08 0.00 31.41 2.01
2212 6335 1.008538 CAAGAAACAGGGTGCACGC 60.009 57.895 25.22 25.22 0.00 5.34
2214 6337 1.398692 TTCCAAGAAACAGGGTGCAC 58.601 50.000 8.80 8.80 0.00 4.57
2247 6370 6.195613 GCAGCGATTTTAAAAATGTACGCATA 59.804 34.615 25.16 0.00 45.65 3.14
2307 6430 2.037381 TGCCTCAAATTTTGCATGCTCA 59.963 40.909 20.33 2.20 0.00 4.26
2367 6490 7.442656 CAGTCTGTTTTAGAAACTCTTCCCTA 58.557 38.462 5.30 0.00 37.12 3.53
2411 6534 9.590451 AATATTTAATTGTGTGCTCCATGAAAG 57.410 29.630 0.00 0.00 0.00 2.62
2438 6563 6.205464 TGTGAACCAGCAAAATTTTGAACAAA 59.795 30.769 30.40 13.78 40.55 2.83
2893 7039 0.458669 CATCATGGCAACTTCTGGGC 59.541 55.000 0.00 0.00 37.61 5.36
2967 7116 7.391148 ACTAAAATTGCCACGATCTACAAAT 57.609 32.000 0.00 0.00 0.00 2.32
3250 7400 7.772292 TCCCATGTTGATTTGTTTTGATGAAAA 59.228 29.630 0.00 0.00 0.00 2.29
3264 7414 5.989477 TCGAAACTAGATCCCATGTTGATT 58.011 37.500 0.00 0.00 0.00 2.57
3417 7568 5.464057 CACCACACGTCTCTAATGTAAACAA 59.536 40.000 0.00 0.00 0.00 2.83
3677 7829 4.277476 TGGCCTACTTCCACAAATTATGG 58.723 43.478 3.32 2.76 38.71 2.74
3799 7951 4.513318 GGTTGTCTTGGAGAAAAGTCAGAG 59.487 45.833 0.00 0.00 0.00 3.35
3844 7996 7.895429 TCCCTGATCAATGAGTTAAAAAGGATT 59.105 33.333 0.00 0.00 0.00 3.01
3878 8032 2.223876 TGACGTAGAAAGCAGACGGTTT 60.224 45.455 0.00 0.00 45.26 3.27
3969 8123 4.892934 AGTACTTGGAAGAGAGGATAGCTG 59.107 45.833 0.00 0.00 0.00 4.24
3971 8125 6.963083 TTAGTACTTGGAAGAGAGGATAGC 57.037 41.667 0.00 0.00 0.00 2.97
4022 8180 1.609320 GCCCAGACAGAACTCAACTCC 60.609 57.143 0.00 0.00 0.00 3.85
4159 8317 6.908481 TTTGTCTCCAAAGGGAAAAGCTTCC 61.908 44.000 0.00 0.00 44.38 3.46
4163 8321 3.132111 TGTTTGTCTCCAAAGGGAAAAGC 59.868 43.478 0.00 0.00 44.38 3.51
4187 8345 1.244019 AAAATGTCCAGCACTCGGGC 61.244 55.000 0.00 0.00 0.00 6.13
4318 8477 8.303876 TGGAAATTTCACCTTAGCTTAATTCAC 58.696 33.333 19.49 0.00 0.00 3.18
4352 8511 7.675619 AGAGAATTCCACTAAAAATGATGGGTT 59.324 33.333 0.65 0.00 32.73 4.11
4353 8512 7.184862 AGAGAATTCCACTAAAAATGATGGGT 58.815 34.615 0.65 0.00 32.73 4.51
4354 8513 7.651027 AGAGAATTCCACTAAAAATGATGGG 57.349 36.000 0.65 0.00 32.73 4.00
4470 8629 1.743321 GATCCTGTCGAGAGCCCCAG 61.743 65.000 3.56 0.00 0.00 4.45
4511 8670 6.665992 TTCTCATACCACAACTGTACTCTT 57.334 37.500 0.00 0.00 0.00 2.85
4551 8710 8.612619 GTGTTGATGAAATAGTAACAGGTATGG 58.387 37.037 0.00 0.00 32.54 2.74
4575 8734 6.677187 GCCGGAATGAATATCATCATCATGTG 60.677 42.308 5.05 0.00 39.08 3.21
4666 8825 1.073025 ACCACAAATGCCTGCTCGA 59.927 52.632 0.00 0.00 0.00 4.04
4827 8986 5.182950 TGTTAAACCGACCAGACTCGTATAA 59.817 40.000 0.00 0.00 31.35 0.98
5167 9327 2.126882 ACATACAGGGGCATCAGCTTA 58.873 47.619 0.00 0.00 41.70 3.09
5195 9355 3.275143 CATATAGTGGTGACCCGCAAAA 58.725 45.455 0.00 0.00 44.14 2.44
5219 9379 8.300495 ACGTTTCAGAAGAAATCTCTAAGAAC 57.700 34.615 0.00 0.00 44.87 3.01
5251 9411 0.316522 TGCGGCATCTGCTAGAGATC 59.683 55.000 0.00 0.00 39.64 2.75
5299 9460 6.249035 ACCACAAATTCGGTTTACAGTATG 57.751 37.500 0.00 0.00 34.76 2.39
5319 9480 4.460683 GTGCCATCCGCGGTACCA 62.461 66.667 27.15 15.15 42.08 3.25
5331 9492 1.471501 CGGATCTGATCTTTCGTGCCA 60.472 52.381 16.61 0.00 0.00 4.92
5401 9563 9.896645 ACTCTGTTGAATTCTATCAATGTATGT 57.103 29.630 7.05 0.00 41.09 2.29
5404 9566 9.942850 TGAACTCTGTTGAATTCTATCAATGTA 57.057 29.630 7.05 0.00 41.09 2.29
5405 9567 8.853077 TGAACTCTGTTGAATTCTATCAATGT 57.147 30.769 7.05 3.02 41.09 2.71
5412 9574 9.942850 TTGTCATATGAACTCTGTTGAATTCTA 57.057 29.630 7.07 0.00 30.60 2.10
5413 9575 8.853077 TTGTCATATGAACTCTGTTGAATTCT 57.147 30.769 7.07 0.00 30.60 2.40
5416 9578 8.627208 AGTTTGTCATATGAACTCTGTTGAAT 57.373 30.769 7.07 0.00 0.00 2.57
5475 9645 3.452264 AGAAGGACGGTGATGATGATGAA 59.548 43.478 0.00 0.00 0.00 2.57
5489 9659 3.193263 CATCTCCACATCAAGAAGGACG 58.807 50.000 0.00 0.00 0.00 4.79
5523 9693 1.066858 GCATTCGTCCTCTCCAACTCA 60.067 52.381 0.00 0.00 0.00 3.41
5537 9719 1.405821 AGGAGAACGACCTAGCATTCG 59.594 52.381 0.00 5.40 41.14 3.34
5538 9720 3.449632 GAAGGAGAACGACCTAGCATTC 58.550 50.000 0.00 0.00 36.67 2.67
5539 9721 2.159226 CGAAGGAGAACGACCTAGCATT 60.159 50.000 0.00 0.00 36.67 3.56
5540 9722 1.405821 CGAAGGAGAACGACCTAGCAT 59.594 52.381 0.00 0.00 36.67 3.79
5541 9723 0.809385 CGAAGGAGAACGACCTAGCA 59.191 55.000 0.00 0.00 36.67 3.49
5542 9724 0.525882 GCGAAGGAGAACGACCTAGC 60.526 60.000 0.00 0.00 36.67 3.42
5543 9725 0.100861 GGCGAAGGAGAACGACCTAG 59.899 60.000 0.00 0.00 36.67 3.02
5544 9726 1.651240 CGGCGAAGGAGAACGACCTA 61.651 60.000 0.00 0.00 36.67 3.08
5545 9727 2.971452 GGCGAAGGAGAACGACCT 59.029 61.111 0.00 0.00 39.69 3.85
5546 9728 2.506438 CGGCGAAGGAGAACGACC 60.506 66.667 0.00 0.00 33.67 4.79
5566 9748 0.957888 GGAGAAGAAGGCACTGTGGC 60.958 60.000 25.03 25.03 40.86 5.01
5573 9755 3.068881 CCACCGGAGAAGAAGGCA 58.931 61.111 9.46 0.00 0.00 4.75
5591 9782 4.394712 AGGCGAAGGAGGCAACCG 62.395 66.667 0.00 0.00 39.37 4.44
5594 9785 1.980232 TACGAGGCGAAGGAGGCAA 60.980 57.895 0.00 0.00 39.37 4.52
5595 9786 2.361992 TACGAGGCGAAGGAGGCA 60.362 61.111 0.00 0.00 39.37 4.75
5735 9926 3.927481 GAGGAGTGGGGCAAGGTGC 62.927 68.421 0.00 0.00 44.08 5.01
5744 9935 4.227134 CGCCGATGGAGGAGTGGG 62.227 72.222 0.00 0.00 0.00 4.61
5781 9972 2.092291 TCGCAATGACGACGAAGCC 61.092 57.895 0.00 0.00 37.09 4.35
5835 10026 4.129148 GGTCATGGGAGGGGTGGC 62.129 72.222 0.00 0.00 0.00 5.01
5848 10039 0.388520 CTGATGTCGAGCGTTGGTCA 60.389 55.000 0.00 0.00 0.00 4.02
5865 10056 3.064324 CCAAAGCTTCGCCCCCTG 61.064 66.667 0.00 0.00 0.00 4.45
5890 10081 1.998257 CAACAGTTTGTCGCGTGCG 60.998 57.895 5.77 8.14 41.35 5.34
5898 10089 3.117663 TCCTTCCTTAGGCAACAGTTTGT 60.118 43.478 0.00 0.00 44.37 2.83
5906 10097 3.852578 AGAAATCCTCCTTCCTTAGGCAA 59.147 43.478 0.00 0.00 44.37 4.52
5907 10098 3.456277 GAGAAATCCTCCTTCCTTAGGCA 59.544 47.826 0.00 0.00 44.37 4.75
5911 10102 3.380637 CGACGAGAAATCCTCCTTCCTTA 59.619 47.826 0.00 0.00 38.71 2.69
5931 10122 0.463654 CCGCAAATCATTCCCTCCGA 60.464 55.000 0.00 0.00 0.00 4.55
5937 10128 1.356624 CTCCGCCGCAAATCATTCC 59.643 57.895 0.00 0.00 0.00 3.01
5938 10129 1.356624 CCTCCGCCGCAAATCATTC 59.643 57.895 0.00 0.00 0.00 2.67
5941 10132 4.794648 CCCCTCCGCCGCAAATCA 62.795 66.667 0.00 0.00 0.00 2.57
5970 10161 2.396590 TTAGGGTTCGCATCCTTCAC 57.603 50.000 0.00 0.00 34.75 3.18
5972 10163 2.095372 CGTTTTAGGGTTCGCATCCTTC 59.905 50.000 0.00 0.00 34.75 3.46
5973 10164 2.081462 CGTTTTAGGGTTCGCATCCTT 58.919 47.619 0.00 0.00 34.75 3.36
5974 10165 1.734163 CGTTTTAGGGTTCGCATCCT 58.266 50.000 0.00 0.00 37.18 3.24
5980 10171 2.477396 GCCGCGTTTTAGGGTTCG 59.523 61.111 4.92 0.00 0.00 3.95
5998 10189 1.650314 CGTAAATTCACGGGTGCCCC 61.650 60.000 0.99 0.30 41.09 5.80
5999 10190 1.798087 CGTAAATTCACGGGTGCCC 59.202 57.895 0.00 0.00 38.26 5.36
6006 10197 2.466140 CCCGGCCCGTAAATTCACG 61.466 63.158 0.85 0.00 41.59 4.35
6007 10198 2.767445 GCCCGGCCCGTAAATTCAC 61.767 63.158 0.85 0.00 0.00 3.18
6008 10199 2.438795 GCCCGGCCCGTAAATTCA 60.439 61.111 0.85 0.00 0.00 2.57
6009 10200 3.214123 GGCCCGGCCCGTAAATTC 61.214 66.667 18.83 0.00 44.06 2.17


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

AutoCloner maintained by Alex Coulton.