Multiple sequence alignment - TraesCS5B01G315900

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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 TraesCS5B01G315900 chr5B 100.000 4450 0 0 1 4450 497939609 497935160 0.000000e+00 8218.0
1 TraesCS5B01G315900 chr5D 91.755 3129 161 49 766 3831 413075750 413072656 0.000000e+00 4259.0
2 TraesCS5B01G315900 chr5D 90.717 474 27 9 3866 4339 413072661 413072205 2.270000e-172 616.0
3 TraesCS5B01G315900 chr5D 90.226 266 23 2 28 291 413078849 413078585 1.190000e-90 344.0
4 TraesCS5B01G315900 chr5D 89.706 272 14 8 289 555 413078490 413078228 7.130000e-88 335.0
5 TraesCS5B01G315900 chr5A 93.444 1388 72 11 2201 3580 525124359 525122983 0.000000e+00 2041.0
6 TraesCS5B01G315900 chr5A 90.171 1170 53 23 966 2091 525125570 525124419 0.000000e+00 1467.0
7 TraesCS5B01G315900 chr5A 93.287 432 20 7 3688 4116 525122862 525122437 2.920000e-176 628.0
8 TraesCS5B01G315900 chr5A 90.087 343 26 1 480 822 525126354 525126020 5.280000e-119 438.0
9 TraesCS5B01G315900 chr5A 94.372 231 13 0 4126 4356 525120952 525120722 5.470000e-94 355.0
10 TraesCS5B01G315900 chr5A 93.496 123 1 2 843 965 525125959 525125844 4.570000e-40 176.0
11 TraesCS5B01G315900 chr4D 87.500 96 7 5 4360 4450 48682218 48682313 6.090000e-19 106.0
12 TraesCS5B01G315900 chr4D 83.929 112 3 5 4353 4450 56943279 56943169 4.740000e-15 93.5
13 TraesCS5B01G315900 chr4D 84.259 108 3 6 4357 4450 102105189 102105296 4.740000e-15 93.5
14 TraesCS5B01G315900 chr1D 85.088 114 3 4 4351 4450 429021876 429021763 2.190000e-18 104.0
15 TraesCS5B01G315900 chr1D 83.333 108 4 4 4357 4450 80887641 80887748 2.210000e-13 87.9
16 TraesCS5B01G315900 chr1D 82.301 113 6 4 4352 4450 482486729 482486841 7.930000e-13 86.1
17 TraesCS5B01G315900 chr1D 82.407 108 4 6 4357 4450 338636583 338636477 3.690000e-11 80.5
18 TraesCS5B01G315900 chr2B 83.036 112 5 4 4353 4450 612691803 612691914 6.130000e-14 89.8
19 TraesCS5B01G315900 chr2B 96.154 52 2 0 4399 4450 479888320 479888371 7.930000e-13 86.1


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 TraesCS5B01G315900 chr5B 497935160 497939609 4449 True 8218.000000 8218 100.000000 1 4450 1 chr5B.!!$R1 4449
1 TraesCS5B01G315900 chr5D 413072205 413078849 6644 True 1388.500000 4259 90.601000 28 4339 4 chr5D.!!$R1 4311
2 TraesCS5B01G315900 chr5A 525120722 525126354 5632 True 850.833333 2041 92.476167 480 4356 6 chr5A.!!$R1 3876

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
67 68 0.105593 TCGATGGGAGCTTGATCTGC 59.894 55.000 0.00 0.0 0.00 4.26 F
86 87 0.670546 CGTGTCTCTGTGCGGGATTT 60.671 55.000 0.00 0.0 0.00 2.17 F
259 262 0.680280 GTCAGGTCGTGAGAGGGCTA 60.680 60.000 0.00 0.0 43.49 3.93 F
465 567 0.693092 TAGGCACATCCCTACCCACC 60.693 60.000 0.00 0.0 36.41 4.61 F
1762 4527 1.077005 TGAGGGGTTTCAATTGGGAGG 59.923 52.381 5.42 0.0 0.00 4.30 F
2625 5423 0.555769 TTGGAGGGAGCAAAGTGGTT 59.444 50.000 0.00 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1790 4555 0.032217 TGGAAGGATTTGGGGATGGC 60.032 55.000 0.00 0.0 0.00 4.40 R
1860 4625 0.041839 GTGAGCAGCAACAAGTGTCG 60.042 55.000 0.00 0.0 0.00 4.35 R
2180 4966 0.969149 AGTGAGACGATGTGGAAGCA 59.031 50.000 0.00 0.0 0.00 3.91 R
2232 5019 2.730715 GCATCGGCGAATAAAAAGCACA 60.731 45.455 15.93 0.0 0.00 4.57 R
3360 6158 0.466543 ACAGTTCCGCACCAACTACA 59.533 50.000 0.00 0.0 32.61 2.74 R
4369 8684 0.033796 AGCTACTGTAGGGTACGGCA 60.034 55.000 16.09 0.0 38.64 5.69 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 1.289380 CGGGAGGTTAGCGATAGGC 59.711 63.158 0.00 0.00 44.05 3.93
67 68 0.105593 TCGATGGGAGCTTGATCTGC 59.894 55.000 0.00 0.00 0.00 4.26
75 76 0.894141 AGCTTGATCTGCGTGTCTCT 59.106 50.000 0.00 0.00 35.28 3.10
80 81 1.409227 GATCTGCGTGTCTCTGTGCG 61.409 60.000 0.00 0.00 0.00 5.34
86 87 0.670546 CGTGTCTCTGTGCGGGATTT 60.671 55.000 0.00 0.00 0.00 2.17
161 162 5.129485 TCTTCAAGAGTAGATGCCCTTTAGG 59.871 44.000 0.00 0.00 39.47 2.69
163 164 4.406003 TCAAGAGTAGATGCCCTTTAGGAC 59.594 45.833 0.00 0.00 38.24 3.85
176 177 4.094476 CCTTTAGGACAGTTGGTCTAGGA 58.906 47.826 0.00 0.00 46.16 2.94
192 195 5.995897 GGTCTAGGAGAAAAACTAAGCACAA 59.004 40.000 0.00 0.00 0.00 3.33
198 201 6.826741 AGGAGAAAAACTAAGCACAACTAACA 59.173 34.615 0.00 0.00 0.00 2.41
211 214 5.003804 CACAACTAACAACCCAGATAAGCT 58.996 41.667 0.00 0.00 0.00 3.74
213 216 5.473504 ACAACTAACAACCCAGATAAGCTTG 59.526 40.000 9.86 0.00 0.00 4.01
220 223 2.158900 ACCCAGATAAGCTTGATGACGG 60.159 50.000 9.86 4.07 0.00 4.79
247 250 0.804989 CGGCCAGAAATTGTCAGGTC 59.195 55.000 2.24 0.00 35.33 3.85
259 262 0.680280 GTCAGGTCGTGAGAGGGCTA 60.680 60.000 0.00 0.00 43.49 3.93
277 280 3.069586 GGCTAGGTTTTGGCTCAGTTTTT 59.930 43.478 0.00 0.00 0.00 1.94
280 283 4.655762 AGGTTTTGGCTCAGTTTTTCTC 57.344 40.909 0.00 0.00 0.00 2.87
334 434 1.959710 TTATACTCCCACAGGCACCA 58.040 50.000 0.00 0.00 0.00 4.17
348 448 0.935196 GCACCATCGTTATCCGGTTC 59.065 55.000 0.00 0.00 37.11 3.62
375 475 0.825410 TGTGATGCCATTGCCAATCC 59.175 50.000 0.00 0.00 36.33 3.01
385 485 2.496899 TTGCCAATCCCTCTTGTCTC 57.503 50.000 0.00 0.00 0.00 3.36
420 522 7.537596 AAATCATCATTGTGTTCACCCTTTA 57.462 32.000 0.37 0.00 0.00 1.85
421 523 7.722949 AATCATCATTGTGTTCACCCTTTAT 57.277 32.000 0.37 0.00 0.00 1.40
422 524 8.821686 AATCATCATTGTGTTCACCCTTTATA 57.178 30.769 0.37 0.00 0.00 0.98
423 525 7.624360 TCATCATTGTGTTCACCCTTTATAC 57.376 36.000 0.37 0.00 0.00 1.47
424 526 6.601613 TCATCATTGTGTTCACCCTTTATACC 59.398 38.462 0.37 0.00 0.00 2.73
425 527 5.882040 TCATTGTGTTCACCCTTTATACCA 58.118 37.500 0.37 0.00 0.00 3.25
427 529 6.951198 TCATTGTGTTCACCCTTTATACCATT 59.049 34.615 0.37 0.00 0.00 3.16
428 530 8.110271 TCATTGTGTTCACCCTTTATACCATTA 58.890 33.333 0.37 0.00 0.00 1.90
429 531 8.912988 CATTGTGTTCACCCTTTATACCATTAT 58.087 33.333 0.37 0.00 0.00 1.28
431 533 9.976776 TTGTGTTCACCCTTTATACCATTATTA 57.023 29.630 0.37 0.00 0.00 0.98
464 566 2.925078 TAGGCACATCCCTACCCAC 58.075 57.895 0.00 0.00 36.41 4.61
465 567 0.693092 TAGGCACATCCCTACCCACC 60.693 60.000 0.00 0.00 36.41 4.61
466 568 2.001269 GGCACATCCCTACCCACCT 61.001 63.158 0.00 0.00 0.00 4.00
563 672 1.568504 CAGAGGGTTAGGTAGGTGCA 58.431 55.000 0.00 0.00 0.00 4.57
652 3008 1.279527 CTCGCCACGTTCGCTACAAA 61.280 55.000 3.11 0.00 0.00 2.83
663 3019 5.851177 ACGTTCGCTACAAATTTCATTTCAG 59.149 36.000 0.00 0.00 0.00 3.02
664 3020 5.283717 CGTTCGCTACAAATTTCATTTCAGG 59.716 40.000 0.00 0.00 0.00 3.86
665 3021 5.957842 TCGCTACAAATTTCATTTCAGGT 57.042 34.783 0.00 0.00 0.00 4.00
666 3022 7.302524 GTTCGCTACAAATTTCATTTCAGGTA 58.697 34.615 0.00 0.00 0.00 3.08
667 3023 7.441890 TCGCTACAAATTTCATTTCAGGTAA 57.558 32.000 0.00 0.00 0.00 2.85
668 3024 7.302524 TCGCTACAAATTTCATTTCAGGTAAC 58.697 34.615 0.00 0.00 0.00 2.50
669 3025 7.041030 TCGCTACAAATTTCATTTCAGGTAACA 60.041 33.333 0.00 0.00 41.41 2.41
670 3026 7.060633 CGCTACAAATTTCATTTCAGGTAACAC 59.939 37.037 0.00 0.00 41.41 3.32
778 3184 2.534042 TCTTCTCCTTCGGTCTCCAT 57.466 50.000 0.00 0.00 0.00 3.41
902 3348 2.004583 CGACATTCTTTACCTCGCCA 57.995 50.000 0.00 0.00 0.00 5.69
909 3355 2.253403 CTTTACCTCGCCACTCCCCC 62.253 65.000 0.00 0.00 0.00 5.40
1017 3739 4.911522 CCCCTCCCCTTTTATATACACTGA 59.088 45.833 0.00 0.00 0.00 3.41
1269 4000 2.678934 CGTTCCTCGGGGGTCTCA 60.679 66.667 0.00 0.00 36.25 3.27
1270 4001 2.711922 CGTTCCTCGGGGGTCTCAG 61.712 68.421 0.00 0.00 36.25 3.35
1284 4015 1.478510 GTCTCAGCCCTGAATTCTCGA 59.521 52.381 7.05 0.00 39.39 4.04
1290 4021 1.416401 GCCCTGAATTCTCGATACCCA 59.584 52.381 7.05 0.00 0.00 4.51
1326 4057 4.107051 GGCGCTGCGAATTGTGCT 62.107 61.111 28.07 0.00 39.38 4.40
1328 4059 1.730547 GCGCTGCGAATTGTGCTTT 60.731 52.632 28.07 0.00 36.83 3.51
1469 4213 1.676967 CAGCCAAGTCCCCTGCTTC 60.677 63.158 0.00 0.00 30.08 3.86
1535 4289 2.931649 TCCCTTCCCCGGTTGTCC 60.932 66.667 0.00 0.00 0.00 4.02
1613 4367 5.534654 ACATCCCCCAATTATTGTACAATCG 59.465 40.000 24.00 11.35 32.50 3.34
1631 4386 2.719739 TCGTACTCTCTTTCATCCGGT 58.280 47.619 0.00 0.00 0.00 5.28
1706 4461 4.640789 TCATTGTAACCGCAAAAACAGT 57.359 36.364 0.00 0.00 31.63 3.55
1708 4463 5.753744 TCATTGTAACCGCAAAAACAGTAG 58.246 37.500 0.00 0.00 31.63 2.57
1709 4464 5.297278 TCATTGTAACCGCAAAAACAGTAGT 59.703 36.000 0.00 0.00 31.63 2.73
1711 4466 5.655893 TGTAACCGCAAAAACAGTAGTAC 57.344 39.130 0.00 0.00 0.00 2.73
1741 4506 1.559682 TCCAGATGGTTAGGCTCCAAC 59.440 52.381 0.00 0.00 38.52 3.77
1755 4520 2.819348 GCTCCAACTGAGGGGTTTCAAT 60.819 50.000 0.00 0.00 41.73 2.57
1756 4521 3.500343 CTCCAACTGAGGGGTTTCAATT 58.500 45.455 0.00 0.00 37.45 2.32
1757 4522 3.230134 TCCAACTGAGGGGTTTCAATTG 58.770 45.455 0.00 0.00 34.89 2.32
1758 4523 2.299867 CCAACTGAGGGGTTTCAATTGG 59.700 50.000 5.42 2.37 44.82 3.16
1759 4524 2.299867 CAACTGAGGGGTTTCAATTGGG 59.700 50.000 5.42 0.00 32.33 4.12
1760 4525 1.786441 ACTGAGGGGTTTCAATTGGGA 59.214 47.619 5.42 0.00 0.00 4.37
1761 4526 2.225117 ACTGAGGGGTTTCAATTGGGAG 60.225 50.000 5.42 0.00 0.00 4.30
1762 4527 1.077005 TGAGGGGTTTCAATTGGGAGG 59.923 52.381 5.42 0.00 0.00 4.30
1763 4528 1.077169 GAGGGGTTTCAATTGGGAGGT 59.923 52.381 5.42 0.00 0.00 3.85
1764 4529 1.507742 AGGGGTTTCAATTGGGAGGTT 59.492 47.619 5.42 0.00 0.00 3.50
1765 4530 2.090210 AGGGGTTTCAATTGGGAGGTTT 60.090 45.455 5.42 0.00 0.00 3.27
1766 4531 2.301870 GGGGTTTCAATTGGGAGGTTTC 59.698 50.000 5.42 0.00 0.00 2.78
1767 4532 2.969262 GGGTTTCAATTGGGAGGTTTCA 59.031 45.455 5.42 0.00 0.00 2.69
1768 4533 3.389656 GGGTTTCAATTGGGAGGTTTCAA 59.610 43.478 5.42 0.00 0.00 2.69
1784 4549 2.916702 TCAAGCTCAACTGAAGCTCA 57.083 45.000 0.00 0.00 38.01 4.26
1790 4555 2.149578 CTCAACTGAAGCTCACCAAGG 58.850 52.381 0.00 0.00 0.00 3.61
1818 4583 2.622452 CCAAATCCTTCCAGATGGCTGT 60.622 50.000 0.00 0.00 40.63 4.40
1860 4625 6.966021 TCCTTGCTTTACATGTAGAACAAAC 58.034 36.000 11.89 0.00 0.00 2.93
1927 4692 2.175878 TCTGCTCTTTGCTGTCTTCC 57.824 50.000 0.00 0.00 43.37 3.46
1990 4755 7.475137 ACTCTAAGAGATAAGCACTTCAAGT 57.525 36.000 0.00 0.00 33.32 3.16
2155 4941 6.881065 ACTTTAATGAGCTACAGATCTTTGCA 59.119 34.615 12.15 0.00 31.68 4.08
2157 4943 7.870509 TTAATGAGCTACAGATCTTTGCAAT 57.129 32.000 0.00 0.00 31.68 3.56
2180 4966 5.108385 GCATTTAGCAAAGCGTATATGGT 57.892 39.130 0.00 0.00 44.79 3.55
2232 5019 2.239654 TCGAAGGGAGCCAAAATGATCT 59.760 45.455 0.00 0.00 0.00 2.75
2437 5224 3.688694 ATAAAGTGCCCGTTGTCAGTA 57.311 42.857 0.00 0.00 0.00 2.74
2443 5230 3.252458 AGTGCCCGTTGTCAGTATTTTTC 59.748 43.478 0.00 0.00 0.00 2.29
2514 5310 4.264253 TGTCTATTTTCCCTGCATCTGTG 58.736 43.478 0.00 0.00 0.00 3.66
2518 5314 2.957402 TTTCCCTGCATCTGTGTCTT 57.043 45.000 0.00 0.00 0.00 3.01
2521 5317 2.783135 TCCCTGCATCTGTGTCTTTTC 58.217 47.619 0.00 0.00 0.00 2.29
2524 5322 3.571401 CCCTGCATCTGTGTCTTTTCTTT 59.429 43.478 0.00 0.00 0.00 2.52
2534 5332 7.810658 TCTGTGTCTTTTCTTTGATATTGCTC 58.189 34.615 0.00 0.00 0.00 4.26
2541 5339 7.613022 TCTTTTCTTTGATATTGCTCATGGAGT 59.387 33.333 0.00 0.00 31.39 3.85
2579 5377 3.507622 AGCCACTTTCTTATTCAGTTGCC 59.492 43.478 0.00 0.00 31.14 4.52
2582 5380 4.278170 CCACTTTCTTATTCAGTTGCCACA 59.722 41.667 0.00 0.00 0.00 4.17
2587 5385 7.439056 ACTTTCTTATTCAGTTGCCACAAATTG 59.561 33.333 0.00 0.00 0.00 2.32
2591 5389 4.597404 TTCAGTTGCCACAAATTGCATA 57.403 36.364 0.00 0.00 37.33 3.14
2613 5411 7.094205 GCATATTCAGGTATTTATGTTGGAGGG 60.094 40.741 0.00 0.00 0.00 4.30
2625 5423 0.555769 TTGGAGGGAGCAAAGTGGTT 59.444 50.000 0.00 0.00 0.00 3.67
2653 5451 6.988622 TTACACGAAAGAAGGAAGTTGAAA 57.011 33.333 0.00 0.00 0.00 2.69
2757 5555 2.954868 GCCGATAGTGGCGTCGTG 60.955 66.667 0.00 0.00 46.75 4.35
2934 5732 2.027837 GCTTCAGAATGGGTTTGGCAAT 60.028 45.455 0.00 0.00 36.16 3.56
2943 5741 3.687125 TGGGTTTGGCAATTACGACATA 58.313 40.909 0.00 0.00 0.00 2.29
2970 5768 0.798776 AGAATTGCGAGGACTTTGCG 59.201 50.000 0.00 0.00 39.21 4.85
3006 5804 1.134788 GGACTTGTACCCGTGGATGAG 60.135 57.143 0.00 0.00 0.00 2.90
3007 5805 0.902531 ACTTGTACCCGTGGATGAGG 59.097 55.000 0.00 0.00 0.00 3.86
3036 5834 2.437359 GTGAGCGGGCAAGCATCT 60.437 61.111 6.94 0.00 40.15 2.90
3075 5873 1.376553 GGCAGCTCTTCTGTCCACC 60.377 63.158 0.00 0.00 44.66 4.61
3102 5900 2.033448 ATTTTCGCTGCCGGTCCA 59.967 55.556 1.90 0.00 34.56 4.02
3156 5954 2.362397 CTGTGCCGGTAGATACATCACT 59.638 50.000 1.90 0.00 0.00 3.41
3359 6157 0.179197 CTTCTCTGCGCTTCGTCGTA 60.179 55.000 9.73 0.00 0.00 3.43
3360 6158 0.450583 TTCTCTGCGCTTCGTCGTAT 59.549 50.000 9.73 0.00 0.00 3.06
3457 6260 5.738619 TGTAACTATGGAACTTGCTCTCA 57.261 39.130 0.00 0.00 0.00 3.27
3519 6322 2.996621 CTCCGAACTGGTTCTGTGAATC 59.003 50.000 11.03 0.00 39.52 2.52
3528 6331 7.869429 GAACTGGTTCTGTGAATCAAATTCAAT 59.131 33.333 4.05 0.00 41.97 2.57
3554 6357 8.989653 ACTAGTTTGTTCAGTAATCTTAGCTC 57.010 34.615 0.00 0.00 0.00 4.09
3580 6383 5.680594 TTTTCTTACTGCCCGGTCTATTA 57.319 39.130 0.00 0.00 0.00 0.98
3581 6384 4.931661 TTCTTACTGCCCGGTCTATTAG 57.068 45.455 0.00 0.00 0.00 1.73
3582 6385 3.907221 TCTTACTGCCCGGTCTATTAGT 58.093 45.455 0.00 0.00 0.00 2.24
3583 6386 5.052693 TCTTACTGCCCGGTCTATTAGTA 57.947 43.478 0.00 0.00 0.00 1.82
3584 6387 5.638133 TCTTACTGCCCGGTCTATTAGTAT 58.362 41.667 0.00 0.00 0.00 2.12
3586 6389 3.840991 ACTGCCCGGTCTATTAGTATGA 58.159 45.455 0.00 0.00 0.00 2.15
3594 6397 3.490399 GTCTATTAGTATGACGGCTCGC 58.510 50.000 0.00 0.00 0.00 5.03
3611 6414 1.206115 CGCGTTCAAGGTGTTTTGCC 61.206 55.000 0.00 0.00 0.00 4.52
3685 6525 1.202940 GGTTTTCCTTCTGGGCTCTGT 60.203 52.381 0.00 0.00 36.94 3.41
3748 6588 2.238521 GAGTCACCCAAGATGGCAAAA 58.761 47.619 0.00 0.00 35.79 2.44
3761 6601 2.193536 GCAAAACTGTCGGCAGGGT 61.194 57.895 22.98 5.74 46.62 4.34
3819 6659 2.057922 AGTTTATCCCTGGATCGGCAT 58.942 47.619 0.99 0.00 36.17 4.40
3851 6691 2.165641 CAGGCTCCGTGATTGTAGTGTA 59.834 50.000 0.00 0.00 0.00 2.90
3929 6769 5.993055 TCTGCATGTGGAAGAATGAAGATA 58.007 37.500 0.00 0.00 34.18 1.98
3982 6822 2.760650 CCTGCTCCCTTGGAAATTTACC 59.239 50.000 0.00 0.00 0.00 2.85
3990 6830 4.264217 CCCTTGGAAATTTACCCTGTACCT 60.264 45.833 0.00 0.00 0.00 3.08
3996 6836 5.889289 GGAAATTTACCCTGTACCTGCATTA 59.111 40.000 0.00 0.00 0.00 1.90
4002 6842 1.539065 CCTGTACCTGCATTAGCCTCG 60.539 57.143 0.00 0.00 41.13 4.63
4010 6850 0.382158 GCATTAGCCTCGCCCTTTTC 59.618 55.000 0.00 0.00 33.58 2.29
4011 6851 1.750193 CATTAGCCTCGCCCTTTTCA 58.250 50.000 0.00 0.00 0.00 2.69
4012 6852 1.401905 CATTAGCCTCGCCCTTTTCAC 59.598 52.381 0.00 0.00 0.00 3.18
4014 6854 1.198759 TAGCCTCGCCCTTTTCACCT 61.199 55.000 0.00 0.00 0.00 4.00
4015 6855 2.335712 GCCTCGCCCTTTTCACCTG 61.336 63.158 0.00 0.00 0.00 4.00
4016 6856 2.335712 CCTCGCCCTTTTCACCTGC 61.336 63.158 0.00 0.00 0.00 4.85
4018 6858 2.282462 CGCCCTTTTCACCTGCCT 60.282 61.111 0.00 0.00 0.00 4.75
4034 6874 3.065648 CCTGCCTCTTCGTCTTCTAGTAC 59.934 52.174 0.00 0.00 0.00 2.73
4041 6881 7.228308 GCCTCTTCGTCTTCTAGTACCTTTATA 59.772 40.741 0.00 0.00 0.00 0.98
4116 6956 0.476771 ACCGATCCTCTCCTCTCCTC 59.523 60.000 0.00 0.00 0.00 3.71
4117 6957 0.771127 CCGATCCTCTCCTCTCCTCT 59.229 60.000 0.00 0.00 0.00 3.69
4118 6958 1.144913 CCGATCCTCTCCTCTCCTCTT 59.855 57.143 0.00 0.00 0.00 2.85
4131 8446 3.638160 CTCTCCTCTTCTGGATCTCAAGG 59.362 52.174 0.00 0.00 35.30 3.61
4265 8580 8.141909 TCAGAAAATATTATCACTGGGTCTACG 58.858 37.037 0.00 0.00 0.00 3.51
4303 8618 9.495754 GCACAAGAAATTATTATTCTGTCAGTC 57.504 33.333 0.00 0.00 37.22 3.51
4316 8631 1.272490 TGTCAGTCGTGGATCTGGTTC 59.728 52.381 0.00 0.00 33.13 3.62
4323 8638 1.168714 GTGGATCTGGTTCACTTGGC 58.831 55.000 0.00 0.00 0.00 4.52
4341 8656 2.575108 CCTGTACTGTACCGGCTGA 58.425 57.895 14.25 0.00 0.00 4.26
4347 8662 4.018490 TGTACTGTACCGGCTGAATTCTA 58.982 43.478 14.91 0.00 0.00 2.10
4356 8671 5.360591 ACCGGCTGAATTCTAAAGTCTATG 58.639 41.667 0.00 0.00 0.00 2.23
4357 8672 4.752101 CCGGCTGAATTCTAAAGTCTATGG 59.248 45.833 7.05 0.00 0.00 2.74
4358 8673 4.752101 CGGCTGAATTCTAAAGTCTATGGG 59.248 45.833 7.05 0.00 0.00 4.00
4359 8674 4.517075 GGCTGAATTCTAAAGTCTATGGGC 59.483 45.833 7.05 0.00 0.00 5.36
4360 8675 4.212214 GCTGAATTCTAAAGTCTATGGGCG 59.788 45.833 7.05 0.00 0.00 6.13
4361 8676 5.353394 TGAATTCTAAAGTCTATGGGCGT 57.647 39.130 7.05 0.00 0.00 5.68
4362 8677 5.116180 TGAATTCTAAAGTCTATGGGCGTG 58.884 41.667 7.05 0.00 0.00 5.34
4363 8678 4.755266 ATTCTAAAGTCTATGGGCGTGT 57.245 40.909 0.00 0.00 0.00 4.49
4364 8679 4.546829 TTCTAAAGTCTATGGGCGTGTT 57.453 40.909 0.00 0.00 0.00 3.32
4365 8680 4.546829 TCTAAAGTCTATGGGCGTGTTT 57.453 40.909 0.00 0.00 0.00 2.83
4366 8681 4.250464 TCTAAAGTCTATGGGCGTGTTTG 58.750 43.478 0.00 0.00 0.00 2.93
4367 8682 1.821216 AAGTCTATGGGCGTGTTTGG 58.179 50.000 0.00 0.00 0.00 3.28
4368 8683 0.690762 AGTCTATGGGCGTGTTTGGT 59.309 50.000 0.00 0.00 0.00 3.67
4369 8684 1.073284 AGTCTATGGGCGTGTTTGGTT 59.927 47.619 0.00 0.00 0.00 3.67
4370 8685 1.199097 GTCTATGGGCGTGTTTGGTTG 59.801 52.381 0.00 0.00 0.00 3.77
4371 8686 0.109319 CTATGGGCGTGTTTGGTTGC 60.109 55.000 0.00 0.00 0.00 4.17
4372 8687 1.528292 TATGGGCGTGTTTGGTTGCC 61.528 55.000 0.00 0.00 46.82 4.52
4374 8689 3.894947 GGCGTGTTTGGTTGCCGT 61.895 61.111 0.00 0.00 37.81 5.68
4375 8690 2.544698 GGCGTGTTTGGTTGCCGTA 61.545 57.895 0.00 0.00 37.81 4.02
4376 8691 1.369568 GCGTGTTTGGTTGCCGTAC 60.370 57.895 0.00 0.00 0.00 3.67
4377 8692 1.280444 CGTGTTTGGTTGCCGTACC 59.720 57.895 0.00 0.00 38.73 3.34
4378 8693 1.655885 GTGTTTGGTTGCCGTACCC 59.344 57.895 0.00 0.00 37.39 3.69
4379 8694 0.820482 GTGTTTGGTTGCCGTACCCT 60.820 55.000 0.00 0.00 37.39 4.34
4380 8695 0.763652 TGTTTGGTTGCCGTACCCTA 59.236 50.000 0.00 0.00 37.39 3.53
4381 8696 1.159285 GTTTGGTTGCCGTACCCTAC 58.841 55.000 0.00 0.00 37.39 3.18
4382 8697 0.763652 TTTGGTTGCCGTACCCTACA 59.236 50.000 0.00 0.00 37.39 2.74
4383 8698 0.322322 TTGGTTGCCGTACCCTACAG 59.678 55.000 0.00 0.00 37.39 2.74
4384 8699 0.832983 TGGTTGCCGTACCCTACAGT 60.833 55.000 0.00 0.00 37.39 3.55
4385 8700 1.185315 GGTTGCCGTACCCTACAGTA 58.815 55.000 0.00 0.00 31.71 2.74
4386 8701 1.135721 GGTTGCCGTACCCTACAGTAG 59.864 57.143 0.00 0.00 31.71 2.57
4387 8702 0.819582 TTGCCGTACCCTACAGTAGC 59.180 55.000 1.50 0.00 0.00 3.58
4388 8703 0.033796 TGCCGTACCCTACAGTAGCT 60.034 55.000 1.50 0.00 0.00 3.32
4389 8704 0.384669 GCCGTACCCTACAGTAGCTG 59.615 60.000 1.50 0.00 37.52 4.24
4390 8705 0.384669 CCGTACCCTACAGTAGCTGC 59.615 60.000 1.50 0.00 34.37 5.25
4391 8706 1.100510 CGTACCCTACAGTAGCTGCA 58.899 55.000 4.12 0.00 34.37 4.41
4392 8707 1.681793 CGTACCCTACAGTAGCTGCAT 59.318 52.381 4.12 0.00 34.37 3.96
4393 8708 2.100916 CGTACCCTACAGTAGCTGCATT 59.899 50.000 4.12 0.00 34.37 3.56
4394 8709 2.698855 ACCCTACAGTAGCTGCATTG 57.301 50.000 4.12 0.00 34.37 2.82
4395 8710 1.303309 CCCTACAGTAGCTGCATTGC 58.697 55.000 4.12 0.46 34.37 3.56
4396 8711 1.407299 CCCTACAGTAGCTGCATTGCA 60.407 52.381 11.50 11.50 34.37 4.08
4397 8712 2.569059 CCTACAGTAGCTGCATTGCAT 58.431 47.619 12.53 0.37 38.13 3.96
4398 8713 3.494924 CCCTACAGTAGCTGCATTGCATA 60.495 47.826 12.53 0.00 38.13 3.14
4399 8714 3.744942 CCTACAGTAGCTGCATTGCATAG 59.255 47.826 12.53 8.76 38.13 2.23
4400 8715 1.945394 ACAGTAGCTGCATTGCATAGC 59.055 47.619 12.53 13.03 38.13 2.97
4401 8716 1.266175 CAGTAGCTGCATTGCATAGCC 59.734 52.381 12.53 1.80 38.13 3.93
4402 8717 1.142465 AGTAGCTGCATTGCATAGCCT 59.858 47.619 12.53 8.78 38.13 4.58
4403 8718 1.952296 GTAGCTGCATTGCATAGCCTT 59.048 47.619 12.53 1.18 38.13 4.35
4404 8719 1.481871 AGCTGCATTGCATAGCCTTT 58.518 45.000 12.53 0.00 38.13 3.11
4405 8720 1.829222 AGCTGCATTGCATAGCCTTTT 59.171 42.857 12.53 0.00 38.13 2.27
4406 8721 2.159142 AGCTGCATTGCATAGCCTTTTC 60.159 45.455 12.53 0.00 38.13 2.29
4407 8722 2.417651 GCTGCATTGCATAGCCTTTTCA 60.418 45.455 12.53 0.00 38.13 2.69
4408 8723 3.740141 GCTGCATTGCATAGCCTTTTCAT 60.740 43.478 12.53 0.00 38.13 2.57
4409 8724 3.787785 TGCATTGCATAGCCTTTTCATG 58.212 40.909 7.38 0.00 31.71 3.07
4410 8725 2.542595 GCATTGCATAGCCTTTTCATGC 59.457 45.455 3.15 0.00 44.23 4.06
4415 8730 4.789095 GCATAGCCTTTTCATGCAAATG 57.211 40.909 0.00 0.00 43.59 2.32
4416 8731 3.001939 GCATAGCCTTTTCATGCAAATGC 59.998 43.478 9.42 9.42 43.59 3.56
4428 8743 0.725117 GCAAATGCAGCCTCAAATGC 59.275 50.000 0.00 0.00 42.86 3.56
4431 8746 3.368822 TGCAGCCTCAAATGCACC 58.631 55.556 0.00 0.00 46.97 5.01
4432 8747 1.531128 TGCAGCCTCAAATGCACCA 60.531 52.632 0.00 0.00 46.97 4.17
4433 8748 0.901114 TGCAGCCTCAAATGCACCAT 60.901 50.000 0.00 0.00 46.97 3.55
4434 8749 0.179119 GCAGCCTCAAATGCACCATC 60.179 55.000 0.00 0.00 42.11 3.51
4435 8750 1.471119 CAGCCTCAAATGCACCATCT 58.529 50.000 0.00 0.00 0.00 2.90
4436 8751 1.134367 CAGCCTCAAATGCACCATCTG 59.866 52.381 0.00 0.00 0.00 2.90
4446 8761 2.514205 GCACCATCTGCAAGTTGTTT 57.486 45.000 4.48 0.00 46.29 2.83
4447 8762 2.129607 GCACCATCTGCAAGTTGTTTG 58.870 47.619 4.48 0.00 46.29 2.93
4448 8763 2.746269 CACCATCTGCAAGTTGTTTGG 58.254 47.619 4.48 8.91 37.26 3.28
4449 8764 2.101249 CACCATCTGCAAGTTGTTTGGT 59.899 45.455 4.48 9.49 37.26 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.686224 TCGCTAACCTCCCGGAAAAA 59.314 50.000 0.73 0.00 0.00 1.94
7 8 0.906775 ATCGCTAACCTCCCGGAAAA 59.093 50.000 0.73 0.00 0.00 2.29
8 9 1.684983 CTATCGCTAACCTCCCGGAAA 59.315 52.381 0.73 0.00 0.00 3.13
9 10 1.325355 CTATCGCTAACCTCCCGGAA 58.675 55.000 0.73 0.00 0.00 4.30
10 11 0.538977 CCTATCGCTAACCTCCCGGA 60.539 60.000 0.73 0.00 0.00 5.14
11 12 1.965219 CCTATCGCTAACCTCCCGG 59.035 63.158 0.00 0.00 0.00 5.73
12 13 1.289380 GCCTATCGCTAACCTCCCG 59.711 63.158 0.00 0.00 0.00 5.14
13 14 1.289380 CGCCTATCGCTAACCTCCC 59.711 63.158 0.00 0.00 34.21 4.30
14 15 4.968197 CGCCTATCGCTAACCTCC 57.032 61.111 0.00 0.00 34.21 4.30
53 54 1.078848 ACACGCAGATCAAGCTCCC 60.079 57.895 8.29 0.00 0.00 4.30
60 61 0.389037 GCACAGAGACACGCAGATCA 60.389 55.000 0.00 0.00 0.00 2.92
67 68 0.670546 AAATCCCGCACAGAGACACG 60.671 55.000 0.00 0.00 0.00 4.49
75 76 1.271934 CCATTTGACAAATCCCGCACA 59.728 47.619 10.52 0.00 0.00 4.57
80 81 0.175531 CGGCCCATTTGACAAATCCC 59.824 55.000 10.52 10.18 0.00 3.85
86 87 2.497792 ATCTGCCGGCCCATTTGACA 62.498 55.000 26.77 0.00 0.00 3.58
161 162 5.612351 AGTTTTTCTCCTAGACCAACTGTC 58.388 41.667 0.00 0.00 44.82 3.51
163 164 6.147985 GCTTAGTTTTTCTCCTAGACCAACTG 59.852 42.308 0.00 0.00 32.15 3.16
176 177 7.255569 GGTTGTTAGTTGTGCTTAGTTTTTCT 58.744 34.615 0.00 0.00 0.00 2.52
192 195 5.499004 TCAAGCTTATCTGGGTTGTTAGT 57.501 39.130 0.00 0.00 41.25 2.24
198 201 3.535561 CGTCATCAAGCTTATCTGGGTT 58.464 45.455 0.00 0.00 0.00 4.11
211 214 0.107897 CCGTCCATTCCCGTCATCAA 60.108 55.000 0.00 0.00 0.00 2.57
213 216 1.887707 GCCGTCCATTCCCGTCATC 60.888 63.158 0.00 0.00 0.00 2.92
220 223 1.134946 CAATTTCTGGCCGTCCATTCC 59.865 52.381 0.00 0.00 42.51 3.01
233 236 3.306364 CCTCTCACGACCTGACAATTTCT 60.306 47.826 0.00 0.00 0.00 2.52
241 244 0.394488 CTAGCCCTCTCACGACCTGA 60.394 60.000 0.00 0.00 0.00 3.86
247 250 1.676014 CCAAAACCTAGCCCTCTCACG 60.676 57.143 0.00 0.00 0.00 4.35
259 262 4.281657 AGAGAAAAACTGAGCCAAAACCT 58.718 39.130 0.00 0.00 0.00 3.50
280 283 7.831193 CCCCTCAATTACATGGATATTTAGGAG 59.169 40.741 13.94 6.86 0.00 3.69
317 417 0.839946 GATGGTGCCTGTGGGAGTAT 59.160 55.000 0.00 0.00 33.58 2.12
348 448 1.028330 AATGGCATCACAGCTGACCG 61.028 55.000 23.35 8.50 34.17 4.79
454 556 2.542541 AGGGGAGGTGGGTAGGGA 60.543 66.667 0.00 0.00 0.00 4.20
455 557 2.040779 GAGGGGAGGTGGGTAGGG 60.041 72.222 0.00 0.00 0.00 3.53
456 558 2.040779 GGAGGGGAGGTGGGTAGG 60.041 72.222 0.00 0.00 0.00 3.18
457 559 2.040779 GGGAGGGGAGGTGGGTAG 60.041 72.222 0.00 0.00 0.00 3.18
458 560 2.847215 TAGGGGAGGGGAGGTGGGTA 62.847 65.000 0.00 0.00 0.00 3.69
460 562 2.501943 TTTAGGGGAGGGGAGGTGGG 62.502 65.000 0.00 0.00 0.00 4.61
461 563 0.551624 TTTTAGGGGAGGGGAGGTGG 60.552 60.000 0.00 0.00 0.00 4.61
462 564 1.378732 TTTTTAGGGGAGGGGAGGTG 58.621 55.000 0.00 0.00 0.00 4.00
463 565 3.950340 TTTTTAGGGGAGGGGAGGT 57.050 52.632 0.00 0.00 0.00 3.85
546 655 1.207329 CTGTGCACCTACCTAACCCTC 59.793 57.143 15.69 0.00 0.00 4.30
547 656 1.276622 CTGTGCACCTACCTAACCCT 58.723 55.000 15.69 0.00 0.00 4.34
563 672 2.111043 CACACCAACTCCGGCTGT 59.889 61.111 0.00 0.00 0.00 4.40
652 3008 4.457949 GGTCCGTGTTACCTGAAATGAAAT 59.542 41.667 0.00 0.00 33.97 2.17
663 3019 2.505557 CTCGCGGTCCGTGTTACC 60.506 66.667 23.47 0.00 38.57 2.85
664 3020 3.177249 GCTCGCGGTCCGTGTTAC 61.177 66.667 23.47 11.05 38.57 2.50
665 3021 4.424566 GGCTCGCGGTCCGTGTTA 62.425 66.667 23.47 5.40 38.57 2.41
749 3148 3.775202 CGAAGGAGAAGAATGATCACGT 58.225 45.455 0.00 0.00 0.00 4.49
992 3713 2.990998 TGTATATAAAAGGGGAGGGGGC 59.009 50.000 0.00 0.00 0.00 5.80
995 3717 5.607171 AGTCAGTGTATATAAAAGGGGAGGG 59.393 44.000 0.00 0.00 0.00 4.30
1264 3995 1.478510 TCGAGAATTCAGGGCTGAGAC 59.521 52.381 8.44 0.00 41.13 3.36
1265 3996 1.852633 TCGAGAATTCAGGGCTGAGA 58.147 50.000 8.44 0.00 41.13 3.27
1266 3997 2.906691 ATCGAGAATTCAGGGCTGAG 57.093 50.000 8.44 0.00 41.13 3.35
1267 3998 2.365617 GGTATCGAGAATTCAGGGCTGA 59.634 50.000 8.44 0.00 37.91 4.26
1268 3999 2.548920 GGGTATCGAGAATTCAGGGCTG 60.549 54.545 8.44 0.00 0.00 4.85
1269 4000 1.694696 GGGTATCGAGAATTCAGGGCT 59.305 52.381 8.44 0.00 0.00 5.19
1270 4001 1.416401 TGGGTATCGAGAATTCAGGGC 59.584 52.381 8.44 0.00 0.00 5.19
1316 4047 2.184448 CCCGCATTAAAGCACAATTCG 58.816 47.619 3.30 0.00 0.00 3.34
1404 4135 2.097680 TGCGAGATGAAACATGCAGA 57.902 45.000 0.00 0.00 0.00 4.26
1535 4289 3.059166 GGTAACTTGGCATTGCAAACTG 58.941 45.455 11.39 0.00 0.00 3.16
1587 4341 5.458451 TGTACAATAATTGGGGGATGTGA 57.542 39.130 0.00 0.00 34.12 3.58
1613 4367 3.870633 ACACCGGATGAAAGAGAGTAC 57.129 47.619 9.46 0.00 0.00 2.73
1706 4461 5.546499 ACCATCTGGAAGGAGTTTTGTACTA 59.454 40.000 2.55 0.00 36.44 1.82
1708 4463 4.652822 ACCATCTGGAAGGAGTTTTGTAC 58.347 43.478 2.55 0.00 38.94 2.90
1709 4464 4.993705 ACCATCTGGAAGGAGTTTTGTA 57.006 40.909 2.55 0.00 38.94 2.41
1711 4466 4.702131 CCTAACCATCTGGAAGGAGTTTTG 59.298 45.833 13.75 0.00 41.34 2.44
1741 4506 2.450476 CTCCCAATTGAAACCCCTCAG 58.550 52.381 7.12 0.00 0.00 3.35
1755 4520 2.091885 AGTTGAGCTTGAAACCTCCCAA 60.092 45.455 0.00 0.00 0.00 4.12
1756 4521 1.494721 AGTTGAGCTTGAAACCTCCCA 59.505 47.619 0.00 0.00 0.00 4.37
1757 4522 1.882623 CAGTTGAGCTTGAAACCTCCC 59.117 52.381 0.00 0.00 0.00 4.30
1758 4523 2.851195 TCAGTTGAGCTTGAAACCTCC 58.149 47.619 0.00 0.00 0.00 4.30
1759 4524 3.304324 GCTTCAGTTGAGCTTGAAACCTC 60.304 47.826 0.56 0.00 0.00 3.85
1760 4525 2.620585 GCTTCAGTTGAGCTTGAAACCT 59.379 45.455 0.56 0.00 0.00 3.50
1761 4526 2.620585 AGCTTCAGTTGAGCTTGAAACC 59.379 45.455 0.56 0.00 35.02 3.27
1762 4527 3.313526 TGAGCTTCAGTTGAGCTTGAAAC 59.686 43.478 0.00 0.73 39.21 2.78
1763 4528 3.313526 GTGAGCTTCAGTTGAGCTTGAAA 59.686 43.478 0.00 0.00 39.21 2.69
1764 4529 2.874701 GTGAGCTTCAGTTGAGCTTGAA 59.125 45.455 0.00 0.00 39.21 2.69
1765 4530 2.487934 GTGAGCTTCAGTTGAGCTTGA 58.512 47.619 0.00 0.00 39.21 3.02
1766 4531 1.534595 GGTGAGCTTCAGTTGAGCTTG 59.465 52.381 0.00 0.00 39.21 4.01
1767 4532 1.141657 TGGTGAGCTTCAGTTGAGCTT 59.858 47.619 0.00 0.00 39.21 3.74
1768 4533 0.761187 TGGTGAGCTTCAGTTGAGCT 59.239 50.000 0.00 0.00 42.13 4.09
1784 4549 0.325577 GATTTGGGGATGGCCTTGGT 60.326 55.000 3.32 0.00 0.00 3.67
1790 4555 0.032217 TGGAAGGATTTGGGGATGGC 60.032 55.000 0.00 0.00 0.00 4.40
1860 4625 0.041839 GTGAGCAGCAACAAGTGTCG 60.042 55.000 0.00 0.00 0.00 4.35
1965 4730 7.902087 ACTTGAAGTGCTTATCTCTTAGAGTT 58.098 34.615 9.25 3.58 0.00 3.01
2046 4829 7.920682 GCAACTCTTCTGAAGTTGGAATAAAAA 59.079 33.333 18.77 0.00 42.05 1.94
2131 4917 7.312657 TGCAAAGATCTGTAGCTCATTAAAG 57.687 36.000 13.39 0.00 0.00 1.85
2140 4926 3.770263 TGCATTGCAAAGATCTGTAGC 57.230 42.857 9.33 1.33 34.76 3.58
2144 4930 5.637104 GCTAAATGCATTGCAAAGATCTG 57.363 39.130 16.46 0.00 43.62 2.90
2180 4966 0.969149 AGTGAGACGATGTGGAAGCA 59.031 50.000 0.00 0.00 0.00 3.91
2232 5019 2.730715 GCATCGGCGAATAAAAAGCACA 60.731 45.455 15.93 0.00 0.00 4.57
2363 5150 4.354893 AATGCAGCTTTTCCAATTTCCA 57.645 36.364 0.00 0.00 0.00 3.53
2364 5151 6.990341 AATAATGCAGCTTTTCCAATTTCC 57.010 33.333 0.00 0.00 0.00 3.13
2365 5152 7.809665 ACAAATAATGCAGCTTTTCCAATTTC 58.190 30.769 0.00 0.00 0.00 2.17
2366 5153 7.444792 TGACAAATAATGCAGCTTTTCCAATTT 59.555 29.630 0.00 0.00 0.00 1.82
2367 5154 6.935771 TGACAAATAATGCAGCTTTTCCAATT 59.064 30.769 0.00 0.00 0.00 2.32
2368 5155 6.465948 TGACAAATAATGCAGCTTTTCCAAT 58.534 32.000 0.00 0.00 0.00 3.16
2369 5156 5.851720 TGACAAATAATGCAGCTTTTCCAA 58.148 33.333 0.00 0.00 0.00 3.53
2514 5310 7.765307 TCCATGAGCAATATCAAAGAAAAGAC 58.235 34.615 0.00 0.00 31.76 3.01
2518 5314 8.806429 TTACTCCATGAGCAATATCAAAGAAA 57.194 30.769 0.00 0.00 32.04 2.52
2521 5317 8.627403 ACAATTACTCCATGAGCAATATCAAAG 58.373 33.333 0.00 0.00 32.04 2.77
2524 5322 7.994911 AGAACAATTACTCCATGAGCAATATCA 59.005 33.333 0.00 0.00 32.04 2.15
2534 5332 7.011482 GGCTAACACTAGAACAATTACTCCATG 59.989 40.741 0.00 0.00 0.00 3.66
2587 5385 7.094205 CCCTCCAACATAAATACCTGAATATGC 60.094 40.741 0.00 0.00 30.61 3.14
2591 5389 6.590656 TCCCTCCAACATAAATACCTGAAT 57.409 37.500 0.00 0.00 0.00 2.57
2613 5411 4.675114 CGTGTAAAATGAACCACTTTGCTC 59.325 41.667 0.00 0.00 0.00 4.26
2625 5423 7.281324 TCAACTTCCTTCTTTCGTGTAAAATGA 59.719 33.333 0.00 0.00 0.00 2.57
2653 5451 4.387026 TGGAGTTGGATGAATTGGAAGT 57.613 40.909 0.00 0.00 0.00 3.01
2658 5456 4.579340 CCAGAGATGGAGTTGGATGAATTG 59.421 45.833 0.00 0.00 32.34 2.32
2659 5457 4.789807 CCAGAGATGGAGTTGGATGAATT 58.210 43.478 0.00 0.00 32.34 2.17
2757 5555 0.964358 AGCAATCCAAGCAGGTGAGC 60.964 55.000 0.00 0.00 39.02 4.26
2943 5741 3.118956 AGTCCTCGCAATTCTTCTCGAAT 60.119 43.478 0.00 0.00 44.10 3.34
2970 5768 1.548269 AGTCCAGTCTTGCAGTAGAGC 59.452 52.381 0.00 0.00 0.00 4.09
3006 5804 2.757099 CTCACCCCAATGCCAGCC 60.757 66.667 0.00 0.00 0.00 4.85
3007 5805 3.455469 GCTCACCCCAATGCCAGC 61.455 66.667 0.00 0.00 0.00 4.85
3075 5873 1.729149 GCAGCGAAAATCTTGAACGGG 60.729 52.381 0.00 0.00 0.00 5.28
3117 5915 1.518572 GTACATCCCGGCTGTGACG 60.519 63.158 15.85 0.00 0.00 4.35
3156 5954 6.183360 CGACATCCTTTCTTACTCCTATGTCA 60.183 42.308 0.00 0.00 41.13 3.58
3359 6157 1.071699 ACAGTTCCGCACCAACTACAT 59.928 47.619 0.00 0.00 32.61 2.29
3360 6158 0.466543 ACAGTTCCGCACCAACTACA 59.533 50.000 0.00 0.00 32.61 2.74
3457 6260 1.001378 GAAGTGCGCACTCAACCAAAT 60.001 47.619 40.60 24.11 41.58 2.32
3529 6332 8.035984 GGAGCTAAGATTACTGAACAAACTAGT 58.964 37.037 0.00 0.00 0.00 2.57
3530 6333 8.254508 AGGAGCTAAGATTACTGAACAAACTAG 58.745 37.037 0.00 0.00 0.00 2.57
3562 6365 5.475909 TCATACTAATAGACCGGGCAGTAAG 59.524 44.000 11.69 5.68 0.00 2.34
3572 6375 3.670091 GCGAGCCGTCATACTAATAGACC 60.670 52.174 0.00 0.00 0.00 3.85
3594 6397 0.744281 AGGGCAAAACACCTTGAACG 59.256 50.000 0.00 0.00 31.68 3.95
3611 6414 1.882623 GCAGAAGGGAAAGAACACAGG 59.117 52.381 0.00 0.00 0.00 4.00
3685 6525 4.524714 GGAGGAATTCGAGTCCATCATAGA 59.475 45.833 16.95 0.00 37.65 1.98
3748 6588 2.265467 AAACACACCCTGCCGACAGT 62.265 55.000 0.00 0.00 42.81 3.55
3819 6659 0.744874 CGGAGCCTGGACGAAAGATA 59.255 55.000 0.00 0.00 0.00 1.98
3982 6822 1.539065 CGAGGCTAATGCAGGTACAGG 60.539 57.143 0.00 0.00 41.91 4.00
3990 6830 0.323360 AAAAGGGCGAGGCTAATGCA 60.323 50.000 7.95 0.00 41.91 3.96
3996 6836 2.034221 GGTGAAAAGGGCGAGGCT 59.966 61.111 0.00 0.00 0.00 4.58
4002 6842 0.540597 AAGAGGCAGGTGAAAAGGGC 60.541 55.000 0.00 0.00 0.00 5.19
4010 6850 0.605589 AGAAGACGAAGAGGCAGGTG 59.394 55.000 0.00 0.00 0.00 4.00
4011 6851 2.096248 CTAGAAGACGAAGAGGCAGGT 58.904 52.381 0.00 0.00 0.00 4.00
4012 6852 2.096248 ACTAGAAGACGAAGAGGCAGG 58.904 52.381 0.00 0.00 0.00 4.85
4014 6854 3.015327 GGTACTAGAAGACGAAGAGGCA 58.985 50.000 0.00 0.00 0.00 4.75
4015 6855 3.281158 AGGTACTAGAAGACGAAGAGGC 58.719 50.000 0.00 0.00 36.02 4.70
4016 6856 5.900865 AAAGGTACTAGAAGACGAAGAGG 57.099 43.478 0.00 0.00 38.49 3.69
4044 6884 2.949644 TCAGCTGCCAGATCAATGAATG 59.050 45.455 9.47 0.00 0.00 2.67
4046 6886 2.362736 GTCAGCTGCCAGATCAATGAA 58.637 47.619 9.47 0.00 0.00 2.57
4116 6956 1.746516 GCCAGCCTTGAGATCCAGAAG 60.747 57.143 0.00 0.00 0.00 2.85
4117 6957 0.254178 GCCAGCCTTGAGATCCAGAA 59.746 55.000 0.00 0.00 0.00 3.02
4118 6958 0.619832 AGCCAGCCTTGAGATCCAGA 60.620 55.000 0.00 0.00 0.00 3.86
4144 8459 1.412710 TCTCCACTCACAACCTGTCAC 59.587 52.381 0.00 0.00 0.00 3.67
4147 8462 2.301296 CAGATCTCCACTCACAACCTGT 59.699 50.000 0.00 0.00 0.00 4.00
4265 8580 2.743636 TCTTGTGCTGTAGCCTGTAC 57.256 50.000 0.80 0.00 41.18 2.90
4303 8618 1.442769 CCAAGTGAACCAGATCCACG 58.557 55.000 0.00 0.00 36.06 4.94
4316 8631 1.671850 CGGTACAGTACAGGCCAAGTG 60.672 57.143 12.89 5.75 0.00 3.16
4323 8638 0.892755 TTCAGCCGGTACAGTACAGG 59.107 55.000 22.08 22.08 45.31 4.00
4339 8654 5.116180 CACGCCCATAGACTTTAGAATTCA 58.884 41.667 8.44 0.00 0.00 2.57
4340 8655 5.116882 ACACGCCCATAGACTTTAGAATTC 58.883 41.667 0.00 0.00 0.00 2.17
4341 8656 5.099042 ACACGCCCATAGACTTTAGAATT 57.901 39.130 0.00 0.00 0.00 2.17
4347 8662 2.159382 CCAAACACGCCCATAGACTTT 58.841 47.619 0.00 0.00 0.00 2.66
4356 8671 4.639171 CGGCAACCAAACACGCCC 62.639 66.667 0.00 0.00 41.71 6.13
4357 8672 2.544698 TACGGCAACCAAACACGCC 61.545 57.895 0.00 0.00 41.30 5.68
4358 8673 1.369568 GTACGGCAACCAAACACGC 60.370 57.895 0.00 0.00 0.00 5.34
4359 8674 1.280444 GGTACGGCAACCAAACACG 59.720 57.895 1.29 0.00 39.50 4.49
4360 8675 0.820482 AGGGTACGGCAACCAAACAC 60.820 55.000 8.16 0.00 41.67 3.32
4361 8676 0.763652 TAGGGTACGGCAACCAAACA 59.236 50.000 8.16 0.00 41.67 2.83
4362 8677 1.159285 GTAGGGTACGGCAACCAAAC 58.841 55.000 8.16 2.25 41.67 2.93
4363 8678 0.763652 TGTAGGGTACGGCAACCAAA 59.236 50.000 8.16 0.00 41.67 3.28
4364 8679 0.322322 CTGTAGGGTACGGCAACCAA 59.678 55.000 8.16 0.00 41.67 3.67
4365 8680 0.832983 ACTGTAGGGTACGGCAACCA 60.833 55.000 8.16 0.00 41.67 3.67
4366 8681 1.135721 CTACTGTAGGGTACGGCAACC 59.864 57.143 6.95 0.00 38.64 3.77
4367 8682 1.470458 GCTACTGTAGGGTACGGCAAC 60.470 57.143 16.09 0.00 38.64 4.17
4368 8683 0.819582 GCTACTGTAGGGTACGGCAA 59.180 55.000 16.09 0.00 38.64 4.52
4369 8684 0.033796 AGCTACTGTAGGGTACGGCA 60.034 55.000 16.09 0.00 38.64 5.69
4370 8685 0.384669 CAGCTACTGTAGGGTACGGC 59.615 60.000 16.09 1.27 38.64 5.68
4371 8686 0.384669 GCAGCTACTGTAGGGTACGG 59.615 60.000 16.09 2.17 40.88 4.02
4372 8687 1.100510 TGCAGCTACTGTAGGGTACG 58.899 55.000 16.09 0.00 33.43 3.67
4373 8688 3.458189 CAATGCAGCTACTGTAGGGTAC 58.542 50.000 16.09 0.01 33.43 3.34
4374 8689 2.158957 GCAATGCAGCTACTGTAGGGTA 60.159 50.000 16.09 0.00 33.43 3.69
4375 8690 1.407437 GCAATGCAGCTACTGTAGGGT 60.407 52.381 16.09 0.77 33.43 4.34
4376 8691 1.303309 GCAATGCAGCTACTGTAGGG 58.697 55.000 16.09 0.00 33.43 3.53
4377 8692 2.028420 TGCAATGCAGCTACTGTAGG 57.972 50.000 16.09 2.23 33.32 3.18
4378 8693 3.186001 GCTATGCAATGCAGCTACTGTAG 59.814 47.826 14.98 10.48 43.65 2.74
4379 8694 3.133691 GCTATGCAATGCAGCTACTGTA 58.866 45.455 14.98 0.00 43.65 2.74
4380 8695 1.945394 GCTATGCAATGCAGCTACTGT 59.055 47.619 14.98 0.00 43.65 3.55
4381 8696 1.266175 GGCTATGCAATGCAGCTACTG 59.734 52.381 14.98 1.20 43.65 2.74
4382 8697 1.142465 AGGCTATGCAATGCAGCTACT 59.858 47.619 14.98 6.76 43.65 2.57
4383 8698 1.602311 AGGCTATGCAATGCAGCTAC 58.398 50.000 14.98 4.40 43.65 3.58
4384 8699 2.353357 AAGGCTATGCAATGCAGCTA 57.647 45.000 14.98 0.85 43.65 3.32
4385 8700 1.481871 AAAGGCTATGCAATGCAGCT 58.518 45.000 14.98 0.00 43.65 4.24
4386 8701 2.199236 GAAAAGGCTATGCAATGCAGC 58.801 47.619 14.98 12.50 43.65 5.25
4387 8702 3.513680 TGAAAAGGCTATGCAATGCAG 57.486 42.857 14.98 1.61 43.65 4.41
4388 8703 3.787785 CATGAAAAGGCTATGCAATGCA 58.212 40.909 11.44 11.44 44.86 3.96
4389 8704 2.542595 GCATGAAAAGGCTATGCAATGC 59.457 45.455 13.67 9.85 44.88 3.56
4394 8709 3.001939 GCATTTGCATGAAAAGGCTATGC 59.998 43.478 25.09 15.54 42.10 3.14
4395 8710 4.789095 GCATTTGCATGAAAAGGCTATG 57.211 40.909 25.09 9.96 42.10 2.23
4409 8724 0.725117 GCATTTGAGGCTGCATTTGC 59.275 50.000 0.50 0.00 38.28 3.68
4410 8725 2.087501 TGCATTTGAGGCTGCATTTG 57.912 45.000 0.50 0.00 43.11 2.32
4414 8729 0.901114 ATGGTGCATTTGAGGCTGCA 60.901 50.000 0.50 0.00 45.60 4.41
4415 8730 0.179119 GATGGTGCATTTGAGGCTGC 60.179 55.000 0.00 0.00 38.87 5.25
4416 8731 1.134367 CAGATGGTGCATTTGAGGCTG 59.866 52.381 0.00 0.00 28.98 4.85
4417 8732 1.471119 CAGATGGTGCATTTGAGGCT 58.529 50.000 0.00 0.00 28.98 4.58
4428 8743 2.101249 ACCAAACAACTTGCAGATGGTG 59.899 45.455 7.29 3.43 38.22 4.17
4429 8744 2.387757 ACCAAACAACTTGCAGATGGT 58.612 42.857 0.00 0.00 34.98 3.55


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

AutoCloner maintained by Alex Coulton.