Multiple sequence alignment - TraesCS2D01G315400

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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 TraesCS2D01G315400 chr2D 100.000 5985 0 0 1 5985 405061108 405067092 0.000000e+00 11053.0
1 TraesCS2D01G315400 chr2D 94.118 51 3 0 5511 5561 405066565 405066615 1.790000e-10 78.7
2 TraesCS2D01G315400 chr2D 94.118 51 3 0 5458 5508 405066618 405066668 1.790000e-10 78.7
3 TraesCS2D01G315400 chr2B 95.329 2890 96 12 1 2866 479851359 479854233 0.000000e+00 4553.0
4 TraesCS2D01G315400 chr2B 96.196 1183 41 4 2915 4097 479854334 479855512 0.000000e+00 1932.0
5 TraesCS2D01G315400 chr2B 88.548 978 55 20 4391 5358 479856019 479856949 0.000000e+00 1133.0
6 TraesCS2D01G315400 chr2B 96.786 280 6 2 4098 4375 479855592 479855870 1.170000e-126 464.0
7 TraesCS2D01G315400 chr2B 87.179 78 10 0 1300 1377 692460437 692460514 8.260000e-14 89.8
8 TraesCS2D01G315400 chr2B 93.103 58 4 0 5928 5985 479857683 479857740 1.070000e-12 86.1
9 TraesCS2D01G315400 chr2A 94.424 2134 72 11 1 2095 543119385 543121510 0.000000e+00 3238.0
10 TraesCS2D01G315400 chr2A 94.740 1464 46 8 2915 4375 543122647 543124082 0.000000e+00 2248.0
11 TraesCS2D01G315400 chr2A 95.634 733 28 3 2137 2866 543121813 543122544 0.000000e+00 1173.0
12 TraesCS2D01G315400 chr2A 87.475 982 59 20 4370 5335 543124179 543125112 0.000000e+00 1074.0
13 TraesCS2D01G315400 chr5D 82.274 519 73 11 5480 5985 232590894 232590382 1.190000e-116 431.0
14 TraesCS2D01G315400 chr5D 92.135 89 7 0 1289 1377 356619784 356619872 6.300000e-25 126.0
15 TraesCS2D01G315400 chr5D 85.507 69 5 4 335 402 284155355 284155419 3.870000e-07 67.6
16 TraesCS2D01G315400 chr6D 76.642 411 56 25 994 1393 234427921 234427540 2.200000e-44 191.0
17 TraesCS2D01G315400 chr6B 74.245 563 87 37 848 1393 357126102 357125581 3.680000e-42 183.0
18 TraesCS2D01G315400 chr6A 75.728 412 57 25 996 1393 356210146 356209764 3.710000e-37 167.0
19 TraesCS2D01G315400 chr5B 92.135 89 7 0 1289 1377 421447269 421447357 6.300000e-25 126.0
20 TraesCS2D01G315400 chr5B 84.058 69 6 4 335 402 321986957 321987021 1.800000e-05 62.1
21 TraesCS2D01G315400 chr5A 92.135 89 7 0 1289 1377 458102696 458102784 6.300000e-25 126.0
22 TraesCS2D01G315400 chr4D 85.714 77 7 4 5392 5466 11000386 11000460 1.790000e-10 78.7


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 TraesCS2D01G315400 chr2D 405061108 405067092 5984 False 3736.80 11053 96.078667 1 5985 3 chr2D.!!$F1 5984
1 TraesCS2D01G315400 chr2B 479851359 479857740 6381 False 1633.62 4553 93.992400 1 5985 5 chr2B.!!$F2 5984
2 TraesCS2D01G315400 chr2A 543119385 543125112 5727 False 1933.25 3238 93.068250 1 5335 4 chr2A.!!$F1 5334
3 TraesCS2D01G315400 chr5D 232590382 232590894 512 True 431.00 431 82.274000 5480 5985 1 chr5D.!!$R1 505

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
682 713 0.250295 CAGCAACAAGACTCCCGGAA 60.250 55.000 0.73 0.0 0.00 4.30 F
1522 1566 0.040514 TTTGCTGTCGTTTGATGCGG 60.041 50.000 0.00 0.0 31.73 5.69 F
2691 3008 1.003839 TGCAGCCCTAAACTGTCCG 60.004 57.895 0.00 0.0 37.47 4.79 F
4572 5281 0.107643 TCATTGGGCACACTTGTCGA 59.892 50.000 0.00 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2307 2624 1.892338 GGTGTTGGGCATCACATGG 59.108 57.895 0.0 0.0 36.43 3.66 R
2835 3156 0.817654 CACTACGACAGCATCAGGGA 59.182 55.000 0.0 0.0 0.00 4.20 R
4664 5373 1.007387 GCAAAGGCAACCCGTCTTG 60.007 57.895 0.0 0.0 39.14 3.02 R
5749 6595 0.102300 GCAGCGGTTTTGAAGTTGGT 59.898 50.000 0.0 0.0 0.00 3.67 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
28 29 4.322080 AAATATCCATGACGCGAAGAGA 57.678 40.909 15.93 2.72 0.00 3.10
59 60 2.112928 TGGCACGCAAGACCATGT 59.887 55.556 0.00 0.00 41.03 3.21
92 93 3.866883 AACCATGCAAACCTTAATCCG 57.133 42.857 0.00 0.00 0.00 4.18
124 133 7.413657 GGTCATGTTGTGGTACAATGTACATAC 60.414 40.741 23.04 19.91 44.16 2.39
283 294 0.458889 TTCGATTTACAGGTCGGGCG 60.459 55.000 0.00 0.00 38.34 6.13
405 417 5.806286 ACATATAGTGTTTGCGCATACAAC 58.194 37.500 30.72 22.84 38.01 3.32
406 418 5.352846 ACATATAGTGTTTGCGCATACAACA 59.647 36.000 30.72 25.00 38.01 3.33
407 419 4.963276 ATAGTGTTTGCGCATACAACAT 57.037 36.364 30.72 23.14 0.00 2.71
408 420 7.225734 ACATATAGTGTTTGCGCATACAACATA 59.774 33.333 30.72 26.98 38.01 2.29
409 421 4.078363 AGTGTTTGCGCATACAACATAC 57.922 40.909 30.72 19.49 0.00 2.39
473 485 9.533253 AGAAAATCATGTCGAACTTTCAAAAAT 57.467 25.926 0.00 0.00 34.34 1.82
536 559 1.271543 CCACCTCATTTCACAGCCTCA 60.272 52.381 0.00 0.00 0.00 3.86
586 611 7.964545 AAATGCCGTATTTATTTCGTTCTTC 57.035 32.000 0.00 0.00 37.22 2.87
672 703 4.971830 CGCATCATATAAACCAGCAACAAG 59.028 41.667 0.00 0.00 0.00 3.16
679 710 0.535102 AACCAGCAACAAGACTCCCG 60.535 55.000 0.00 0.00 0.00 5.14
680 711 1.672356 CCAGCAACAAGACTCCCGG 60.672 63.158 0.00 0.00 0.00 5.73
681 712 1.371183 CAGCAACAAGACTCCCGGA 59.629 57.895 0.73 0.00 0.00 5.14
682 713 0.250295 CAGCAACAAGACTCCCGGAA 60.250 55.000 0.73 0.00 0.00 4.30
683 714 0.472471 AGCAACAAGACTCCCGGAAA 59.528 50.000 0.73 0.00 0.00 3.13
684 715 1.133915 AGCAACAAGACTCCCGGAAAA 60.134 47.619 0.73 0.00 0.00 2.29
723 766 0.693049 ACTTTCCAATCGCACTCCCT 59.307 50.000 0.00 0.00 0.00 4.20
768 812 2.767505 GCTATAACGGCAGCTACCAAT 58.232 47.619 3.30 0.00 34.86 3.16
841 885 2.424601 CCATTCAATCAACGACCAGCAT 59.575 45.455 0.00 0.00 0.00 3.79
842 886 3.431856 CATTCAATCAACGACCAGCATG 58.568 45.455 0.00 0.00 0.00 4.06
1513 1557 2.869233 ATTTTGTGCTTTGCTGTCGT 57.131 40.000 0.00 0.00 0.00 4.34
1522 1566 0.040514 TTTGCTGTCGTTTGATGCGG 60.041 50.000 0.00 0.00 31.73 5.69
1762 1815 5.052481 AGTTTGGTTAGTACTCGTTTGGAC 58.948 41.667 0.00 0.00 0.00 4.02
1777 1830 2.664436 GGACGAAACGGTCTTGGCG 61.664 63.158 0.00 0.00 37.12 5.69
1837 1893 7.973388 GCTAGTTATTGCATTTTGGTGATTACA 59.027 33.333 0.00 0.00 0.00 2.41
1902 1958 2.817258 TGAAAGCCTTGACCAATTACGG 59.183 45.455 0.00 0.00 0.00 4.02
1953 2009 2.235016 CGTGGACAGGAATTGGGAAAA 58.765 47.619 0.00 0.00 0.00 2.29
2007 2063 1.860676 AGAAAGCAAGTTGTACGCGA 58.139 45.000 15.93 0.00 0.00 5.87
2133 2189 4.970860 TTTTTCCCCTTCAATCATTGCA 57.029 36.364 0.00 0.00 0.00 4.08
2147 2464 9.797556 TTCAATCATTGCATATTTCTTCTCTTG 57.202 29.630 0.00 0.00 0.00 3.02
2152 2469 3.949754 TGCATATTTCTTCTCTTGCCCAG 59.050 43.478 0.00 0.00 0.00 4.45
2307 2624 3.092301 AGCCCTTCAGAATTTTACTGGC 58.908 45.455 0.00 0.00 36.22 4.85
2325 2642 1.892338 CCATGTGATGCCCAACACC 59.108 57.895 6.27 0.00 36.35 4.16
2532 2849 2.058675 CCGTTCTAGGGGCTATGGG 58.941 63.158 0.00 0.00 0.00 4.00
2605 2922 4.927425 TGAACGGTGTTTATTGCTCTACTC 59.073 41.667 0.00 0.00 0.00 2.59
2631 2948 2.048597 CGCGTAGGACCTGCAACA 60.049 61.111 10.45 0.00 0.00 3.33
2689 3006 1.807142 GTTCTGCAGCCCTAAACTGTC 59.193 52.381 9.47 0.00 37.47 3.51
2691 3008 1.003839 TGCAGCCCTAAACTGTCCG 60.004 57.895 0.00 0.00 37.47 4.79
2692 3009 1.745489 GCAGCCCTAAACTGTCCGG 60.745 63.158 0.00 0.00 37.47 5.14
2756 3076 8.220755 ACAAGTGCTTGAACTTTCACTAAATA 57.779 30.769 17.62 0.00 42.93 1.40
2844 3165 2.717639 ACCTTGTATGTCCCTGATGC 57.282 50.000 0.00 0.00 0.00 3.91
2871 3260 8.025445 TGTCGTAGTGTTCTCCTATTAGTTTTC 58.975 37.037 0.00 0.00 0.00 2.29
2872 3261 8.242739 GTCGTAGTGTTCTCCTATTAGTTTTCT 58.757 37.037 0.00 0.00 0.00 2.52
2873 3262 8.242053 TCGTAGTGTTCTCCTATTAGTTTTCTG 58.758 37.037 0.00 0.00 0.00 3.02
2875 3264 7.554959 AGTGTTCTCCTATTAGTTTTCTGGA 57.445 36.000 0.00 0.00 0.00 3.86
2900 3289 9.696917 GAACACATCCTGTTTTTAATGAAGAAT 57.303 29.630 0.00 0.00 43.60 2.40
2902 3291 8.090214 ACACATCCTGTTTTTAATGAAGAATGG 58.910 33.333 0.00 0.00 0.00 3.16
2904 3293 8.090214 ACATCCTGTTTTTAATGAAGAATGGTG 58.910 33.333 0.00 0.00 0.00 4.17
2906 3295 6.267471 TCCTGTTTTTAATGAAGAATGGTGCT 59.733 34.615 0.00 0.00 0.00 4.40
2907 3296 6.930722 CCTGTTTTTAATGAAGAATGGTGCTT 59.069 34.615 0.00 0.00 0.00 3.91
2908 3297 7.442062 CCTGTTTTTAATGAAGAATGGTGCTTT 59.558 33.333 0.00 0.00 0.00 3.51
2909 3298 8.364129 TGTTTTTAATGAAGAATGGTGCTTTC 57.636 30.769 0.00 0.00 0.00 2.62
2910 3299 8.203485 TGTTTTTAATGAAGAATGGTGCTTTCT 58.797 29.630 0.00 0.00 34.95 2.52
2911 3300 9.045223 GTTTTTAATGAAGAATGGTGCTTTCTT 57.955 29.630 0.00 0.00 44.09 2.52
2926 3315 7.177216 TGGTGCTTTCTTCTGTTATTGATCATT 59.823 33.333 0.00 0.00 0.00 2.57
2957 3346 4.338400 ACTTGTTTTGCCTTTCTGGACTAC 59.662 41.667 0.00 0.00 38.35 2.73
2971 3360 3.943381 CTGGACTACGTACATGACCTGTA 59.057 47.826 0.00 0.00 39.39 2.74
2972 3361 3.943381 TGGACTACGTACATGACCTGTAG 59.057 47.826 0.00 8.46 40.99 2.74
2978 3367 5.916661 ACGTACATGACCTGTAGAGATTT 57.083 39.130 0.00 0.00 40.99 2.17
3038 3427 1.825474 TGCTAGTGTTCCTACTGCCTC 59.175 52.381 0.00 0.00 32.19 4.70
3067 3456 3.181516 CGCCAGTTCTACTGCTTCAATTC 60.182 47.826 1.31 0.00 44.63 2.17
3235 3624 0.474184 CTGGTTCCTCAACACCTGGT 59.526 55.000 0.00 0.00 33.70 4.00
3306 3695 6.627395 TCCATAGTGTTTGTTAACCTTGTG 57.373 37.500 2.48 0.00 33.15 3.33
3311 3700 4.221924 AGTGTTTGTTAACCTTGTGGCTTT 59.778 37.500 2.48 0.00 36.63 3.51
3319 3708 8.064336 TGTTAACCTTGTGGCTTTTTAGTTTA 57.936 30.769 2.48 0.00 36.63 2.01
3479 3868 4.787598 CTTTGTTCAGTATGTCAACAGGC 58.212 43.478 0.00 0.00 37.40 4.85
3715 4104 8.421784 TCTTTGATCGTTCCTTGCTATAGTATT 58.578 33.333 0.84 0.00 0.00 1.89
3741 4130 5.471556 TTGCATTGAACCAATCATCTTGT 57.528 34.783 0.00 0.00 38.03 3.16
3777 4166 7.259290 TGACCACTATGTTTGAAAACTCTTC 57.741 36.000 7.39 0.00 39.59 2.87
3824 4213 8.322091 GGCAGTAACCTATGGATGACTATAAAT 58.678 37.037 0.00 0.00 0.00 1.40
4020 4413 6.763355 TGCTATAATGGATCTGTTCCTTCTC 58.237 40.000 6.35 0.00 45.68 2.87
4027 4420 1.446272 CTGTTCCTTCTCGTCCCGC 60.446 63.158 0.00 0.00 0.00 6.13
4097 4490 7.390718 CCTTATGCTTGGTAGTTGTTTCTAGTT 59.609 37.037 0.00 0.00 0.00 2.24
4098 4491 6.560253 ATGCTTGGTAGTTGTTTCTAGTTG 57.440 37.500 0.00 0.00 0.00 3.16
4362 4836 1.337703 TGCTTGTTGACTGAATGCCAC 59.662 47.619 0.00 0.00 0.00 5.01
4413 5092 3.802948 CTGCGGAGTGTAGGATTAGTT 57.197 47.619 0.00 0.00 0.00 2.24
4414 5093 4.124851 CTGCGGAGTGTAGGATTAGTTT 57.875 45.455 0.00 0.00 0.00 2.66
4425 5134 7.069085 AGTGTAGGATTAGTTTACCAAGCGATA 59.931 37.037 0.00 0.00 0.00 2.92
4469 5178 8.421784 TGTTAAATCAGACATCTGTATAGGGAC 58.578 37.037 8.70 2.48 44.12 4.46
4470 5179 8.421784 GTTAAATCAGACATCTGTATAGGGACA 58.578 37.037 8.70 0.00 44.12 4.02
4476 5185 4.097418 ACATCTGTATAGGGACATAGGCC 58.903 47.826 0.00 0.00 0.00 5.19
4484 5193 0.545548 GGGACATAGGCCCTAGGAGG 60.546 65.000 11.48 0.00 42.56 4.30
4504 5213 5.012328 AGGCTTTTATCTCTTACCACTCG 57.988 43.478 0.00 0.00 0.00 4.18
4507 5216 5.463724 GGCTTTTATCTCTTACCACTCGATG 59.536 44.000 0.00 0.00 0.00 3.84
4558 5267 8.464770 TGTTCTTTCAAACAAGTTTCTCATTG 57.535 30.769 0.00 0.00 36.25 2.82
4570 5279 1.896220 TCTCATTGGGCACACTTGTC 58.104 50.000 0.00 0.00 0.00 3.18
4572 5281 0.107643 TCATTGGGCACACTTGTCGA 59.892 50.000 0.00 0.00 0.00 4.20
4595 5304 3.476295 ACATGAGCAAACATTAGCACG 57.524 42.857 0.00 0.00 0.00 5.34
4598 5307 0.521291 GAGCAAACATTAGCACGGCA 59.479 50.000 0.00 0.00 0.00 5.69
4607 5316 1.153353 TTAGCACGGCACTTGTTAGC 58.847 50.000 0.00 0.00 0.00 3.09
4622 5331 2.565834 TGTTAGCCTGTACTGGTCCTTC 59.434 50.000 18.89 3.34 0.00 3.46
4627 5336 3.844211 AGCCTGTACTGGTCCTTCAAATA 59.156 43.478 18.89 0.00 0.00 1.40
4634 5343 8.570068 TGTACTGGTCCTTCAAATATTAAACC 57.430 34.615 0.00 0.00 0.00 3.27
4639 5348 5.656859 GGTCCTTCAAATATTAAACCAGGCT 59.343 40.000 0.00 0.00 0.00 4.58
4655 5364 3.054878 CAGGCTGTGCAATTGTTCTTTC 58.945 45.455 6.28 0.00 0.00 2.62
4657 5366 2.036346 GGCTGTGCAATTGTTCTTTCCT 59.964 45.455 7.40 0.00 0.00 3.36
4661 5370 2.472488 GTGCAATTGTTCTTTCCTTGCG 59.528 45.455 7.40 0.00 43.87 4.85
4664 5373 0.603065 ATTGTTCTTTCCTTGCGGCC 59.397 50.000 0.00 0.00 0.00 6.13
4686 5395 1.908066 GACGGGTTGCCTTTGCTACG 61.908 60.000 0.00 0.00 43.05 3.51
4687 5396 1.669760 CGGGTTGCCTTTGCTACGA 60.670 57.895 0.00 0.00 43.05 3.43
4689 5398 1.583495 GGGTTGCCTTTGCTACGACC 61.583 60.000 0.00 0.00 43.05 4.79
4704 5414 5.162075 GCTACGACCCATCATATACTTGTC 58.838 45.833 0.00 0.00 0.00 3.18
4713 5423 8.768397 ACCCATCATATACTTGTCAACTCTTTA 58.232 33.333 0.00 0.00 0.00 1.85
4770 5481 7.970384 TGTAAAGTTATATTTGTCTTGCGGAG 58.030 34.615 0.00 0.00 0.00 4.63
4771 5482 7.604927 TGTAAAGTTATATTTGTCTTGCGGAGT 59.395 33.333 0.00 0.00 0.00 3.85
4772 5483 7.448748 AAAGTTATATTTGTCTTGCGGAGTT 57.551 32.000 0.00 0.00 0.00 3.01
4773 5484 6.422776 AGTTATATTTGTCTTGCGGAGTTG 57.577 37.500 0.00 0.00 0.00 3.16
4774 5485 5.938125 AGTTATATTTGTCTTGCGGAGTTGT 59.062 36.000 0.00 0.00 0.00 3.32
4775 5486 6.430000 AGTTATATTTGTCTTGCGGAGTTGTT 59.570 34.615 0.00 0.00 0.00 2.83
4776 5487 5.705609 ATATTTGTCTTGCGGAGTTGTTT 57.294 34.783 0.00 0.00 0.00 2.83
4777 5488 6.811253 ATATTTGTCTTGCGGAGTTGTTTA 57.189 33.333 0.00 0.00 0.00 2.01
4778 5489 5.705609 ATTTGTCTTGCGGAGTTGTTTAT 57.294 34.783 0.00 0.00 0.00 1.40
4779 5490 4.742438 TTGTCTTGCGGAGTTGTTTATC 57.258 40.909 0.00 0.00 0.00 1.75
4780 5491 3.071479 TGTCTTGCGGAGTTGTTTATCC 58.929 45.455 0.00 0.00 0.00 2.59
4781 5492 3.071479 GTCTTGCGGAGTTGTTTATCCA 58.929 45.455 0.00 0.00 35.14 3.41
4782 5493 3.689649 GTCTTGCGGAGTTGTTTATCCAT 59.310 43.478 0.00 0.00 35.14 3.41
4783 5494 4.156008 GTCTTGCGGAGTTGTTTATCCATT 59.844 41.667 0.00 0.00 35.14 3.16
4784 5495 4.394920 TCTTGCGGAGTTGTTTATCCATTC 59.605 41.667 0.00 0.00 35.14 2.67
4785 5496 3.680490 TGCGGAGTTGTTTATCCATTCA 58.320 40.909 0.00 0.00 35.14 2.57
4786 5497 3.438781 TGCGGAGTTGTTTATCCATTCAC 59.561 43.478 0.00 0.00 35.14 3.18
5041 5752 3.414269 GGAACAAGGTTTTGATCCGGTA 58.586 45.455 0.00 0.00 43.55 4.02
5071 5782 2.355197 CAGCGTCAGAAGAGAGAGAGA 58.645 52.381 0.00 0.00 0.00 3.10
5073 5784 2.027192 AGCGTCAGAAGAGAGAGAGAGT 60.027 50.000 0.00 0.00 0.00 3.24
5261 5990 1.592669 GGTCGGAGCGTCATGGATG 60.593 63.158 0.00 0.00 0.00 3.51
5262 5991 1.141881 GTCGGAGCGTCATGGATGT 59.858 57.895 0.00 0.00 0.00 3.06
5263 5992 0.460284 GTCGGAGCGTCATGGATGTT 60.460 55.000 0.00 0.00 0.00 2.71
5358 6091 1.340017 TGGGTGGAGTGCTGCTTATTC 60.340 52.381 0.00 0.00 0.00 1.75
5360 6093 1.676014 GGTGGAGTGCTGCTTATTCGT 60.676 52.381 0.00 0.00 0.00 3.85
5362 6095 2.076100 TGGAGTGCTGCTTATTCGTTG 58.924 47.619 0.00 0.00 0.00 4.10
5363 6096 1.202076 GGAGTGCTGCTTATTCGTTGC 60.202 52.381 0.00 0.00 0.00 4.17
5365 6098 0.521242 GTGCTGCTTATTCGTTGCCG 60.521 55.000 0.00 0.00 0.00 5.69
5366 6099 0.953471 TGCTGCTTATTCGTTGCCGT 60.953 50.000 0.00 0.00 35.01 5.68
5390 6152 6.983474 TTTTTAGCCTATAAACACCGGTAC 57.017 37.500 6.87 0.00 0.00 3.34
5413 6175 1.142262 TCTGGCTGAGCATATGCATGT 59.858 47.619 28.62 9.14 45.16 3.21
5418 6180 4.401837 TGGCTGAGCATATGCATGTAAAAA 59.598 37.500 28.62 5.30 45.16 1.94
5442 6204 6.854496 ATCAATATTTGCATGTTGATTGCC 57.146 33.333 6.49 0.00 44.60 4.52
5443 6205 5.979993 TCAATATTTGCATGTTGATTGCCT 58.020 33.333 0.00 0.00 36.04 4.75
5444 6206 5.813157 TCAATATTTGCATGTTGATTGCCTG 59.187 36.000 0.00 0.00 36.04 4.85
5445 6207 3.965379 ATTTGCATGTTGATTGCCTGA 57.035 38.095 0.00 0.00 39.39 3.86
5446 6208 3.747854 TTTGCATGTTGATTGCCTGAA 57.252 38.095 0.00 0.00 39.39 3.02
5447 6209 3.965379 TTGCATGTTGATTGCCTGAAT 57.035 38.095 0.00 0.00 39.39 2.57
5448 6210 5.402997 TTTGCATGTTGATTGCCTGAATA 57.597 34.783 0.00 0.00 39.39 1.75
5449 6211 5.601583 TTGCATGTTGATTGCCTGAATAT 57.398 34.783 0.00 0.00 39.39 1.28
5450 6212 5.190992 TGCATGTTGATTGCCTGAATATC 57.809 39.130 0.00 0.00 39.39 1.63
5451 6213 4.038282 TGCATGTTGATTGCCTGAATATCC 59.962 41.667 0.00 0.00 39.39 2.59
5452 6214 4.280174 GCATGTTGATTGCCTGAATATCCT 59.720 41.667 0.00 0.00 33.95 3.24
5453 6215 5.564259 GCATGTTGATTGCCTGAATATCCTC 60.564 44.000 0.00 0.00 33.95 3.71
5454 6216 5.378230 TGTTGATTGCCTGAATATCCTCT 57.622 39.130 0.00 0.00 0.00 3.69
5455 6217 5.759059 TGTTGATTGCCTGAATATCCTCTT 58.241 37.500 0.00 0.00 0.00 2.85
5456 6218 5.591472 TGTTGATTGCCTGAATATCCTCTTG 59.409 40.000 0.00 0.00 0.00 3.02
5457 6219 4.139786 TGATTGCCTGAATATCCTCTTGC 58.860 43.478 0.00 0.00 0.00 4.01
5458 6220 3.939740 TTGCCTGAATATCCTCTTGCT 57.060 42.857 0.00 0.00 0.00 3.91
5459 6221 3.204306 TGCCTGAATATCCTCTTGCTG 57.796 47.619 0.00 0.00 0.00 4.41
5460 6222 1.878734 GCCTGAATATCCTCTTGCTGC 59.121 52.381 0.00 0.00 0.00 5.25
5461 6223 2.747467 GCCTGAATATCCTCTTGCTGCA 60.747 50.000 0.00 0.00 0.00 4.41
5462 6224 3.752665 CCTGAATATCCTCTTGCTGCAT 58.247 45.455 1.84 0.00 0.00 3.96
5463 6225 4.142790 CCTGAATATCCTCTTGCTGCATT 58.857 43.478 1.84 0.00 0.00 3.56
5464 6226 4.023107 CCTGAATATCCTCTTGCTGCATTG 60.023 45.833 1.84 0.00 0.00 2.82
5465 6227 4.529897 TGAATATCCTCTTGCTGCATTGT 58.470 39.130 1.84 0.00 0.00 2.71
5466 6228 5.683681 TGAATATCCTCTTGCTGCATTGTA 58.316 37.500 1.84 0.00 0.00 2.41
5467 6229 5.761726 TGAATATCCTCTTGCTGCATTGTAG 59.238 40.000 1.84 0.00 0.00 2.74
5468 6230 1.742761 TCCTCTTGCTGCATTGTAGC 58.257 50.000 18.52 18.52 41.49 3.58
5477 6239 2.508361 GCATTGTAGCAATGCCCCT 58.492 52.632 27.00 0.00 45.31 4.79
5478 6240 1.691196 GCATTGTAGCAATGCCCCTA 58.309 50.000 27.00 0.00 45.31 3.53
5496 6258 3.006752 CCCTATGCATTGTGTTTGGTTGT 59.993 43.478 3.54 0.00 0.00 3.32
5497 6259 4.502950 CCCTATGCATTGTGTTTGGTTGTT 60.503 41.667 3.54 0.00 0.00 2.83
5503 6265 4.438472 GCATTGTGTTTGGTTGTTTGCATT 60.438 37.500 0.00 0.00 0.00 3.56
5504 6266 4.675190 TTGTGTTTGGTTGTTTGCATTG 57.325 36.364 0.00 0.00 0.00 2.82
5505 6267 3.668447 TGTGTTTGGTTGTTTGCATTGT 58.332 36.364 0.00 0.00 0.00 2.71
5506 6268 4.820897 TGTGTTTGGTTGTTTGCATTGTA 58.179 34.783 0.00 0.00 0.00 2.41
5508 6270 6.573434 TGTGTTTGGTTGTTTGCATTGTATA 58.427 32.000 0.00 0.00 0.00 1.47
5524 6288 6.183360 GCATTGTATATCTGCATCGTAGCAAT 60.183 38.462 6.07 0.00 45.13 3.56
5551 6315 5.911752 TCTATGCATTGTGTTTGGTTGTTT 58.088 33.333 3.54 0.00 0.00 2.83
5566 6330 4.141846 TGGTTGTTTGCATTGTATGTGGTT 60.142 37.500 0.00 0.00 0.00 3.67
5578 6342 4.842574 TGTATGTGGTTACATGAGTGCAT 58.157 39.130 0.00 0.00 46.63 3.96
5613 6383 5.614324 AGCATATAGTTGTGCTCACCTTA 57.386 39.130 0.00 0.00 46.10 2.69
5621 6391 8.671987 ATAGTTGTGCTCACCTTATATCCTAT 57.328 34.615 0.00 0.00 0.00 2.57
5645 6415 3.209410 GGCGAGCTTACCTACTACTACA 58.791 50.000 0.00 0.00 0.00 2.74
5646 6416 3.003171 GGCGAGCTTACCTACTACTACAC 59.997 52.174 0.00 0.00 0.00 2.90
5648 6418 4.450053 CGAGCTTACCTACTACTACACCT 58.550 47.826 0.00 0.00 0.00 4.00
5649 6419 4.880696 CGAGCTTACCTACTACTACACCTT 59.119 45.833 0.00 0.00 0.00 3.50
5650 6420 6.051717 CGAGCTTACCTACTACTACACCTTA 58.948 44.000 0.00 0.00 0.00 2.69
5652 6422 7.307870 CGAGCTTACCTACTACTACACCTTATG 60.308 44.444 0.00 0.00 0.00 1.90
5653 6423 6.264970 AGCTTACCTACTACTACACCTTATGC 59.735 42.308 0.00 0.00 0.00 3.14
5654 6424 6.040166 GCTTACCTACTACTACACCTTATGCA 59.960 42.308 0.00 0.00 0.00 3.96
5655 6425 5.848833 ACCTACTACTACACCTTATGCAC 57.151 43.478 0.00 0.00 0.00 4.57
5656 6426 4.337555 ACCTACTACTACACCTTATGCACG 59.662 45.833 0.00 0.00 0.00 5.34
5665 6440 1.066430 ACCTTATGCACGAACACCGAT 60.066 47.619 0.00 0.00 41.76 4.18
5671 6446 2.803670 ACGAACACCGATCACGCG 60.804 61.111 3.53 3.53 41.76 6.01
5679 6488 3.474904 CGATCACGCGAACGCCAA 61.475 61.111 15.93 0.00 45.53 4.52
5699 6508 1.466856 AACACTGCAATGGCGATGAT 58.533 45.000 0.00 0.00 45.35 2.45
5731 6577 1.003118 TGATGGGAGTTCTTCAACCCG 59.997 52.381 0.00 0.00 44.70 5.28
5735 6581 1.520494 GGAGTTCTTCAACCCGAACC 58.480 55.000 0.00 0.00 40.18 3.62
5736 6582 1.202722 GGAGTTCTTCAACCCGAACCA 60.203 52.381 0.00 0.00 40.18 3.67
5744 6590 1.375013 AACCCGAACCAACGATCCG 60.375 57.895 0.00 0.00 35.09 4.18
5748 6594 0.801067 CCGAACCAACGATCCGTCTC 60.801 60.000 0.00 0.00 39.99 3.36
5749 6595 0.109458 CGAACCAACGATCCGTCTCA 60.109 55.000 0.00 0.00 39.99 3.27
5763 6609 2.032924 CCGTCTCACCAACTTCAAAACC 59.967 50.000 0.00 0.00 0.00 3.27
5808 6654 2.656560 TCGGAGTAAGCTTCTTCTGC 57.343 50.000 0.00 4.99 0.00 4.26
5844 6690 1.762708 AACCCTCTGTGGTTGTTGTG 58.237 50.000 4.07 0.00 46.76 3.33
5845 6691 0.106719 ACCCTCTGTGGTTGTTGTGG 60.107 55.000 0.00 0.00 33.91 4.17
5846 6692 0.106719 CCCTCTGTGGTTGTTGTGGT 60.107 55.000 0.00 0.00 0.00 4.16
5862 6708 2.158534 TGTGGTGCTTGTACCCTGAAAT 60.159 45.455 5.48 0.00 40.09 2.17
5865 6711 4.521256 GTGGTGCTTGTACCCTGAAATTTA 59.479 41.667 5.48 0.00 40.09 1.40
5872 6718 9.249053 TGCTTGTACCCTGAAATTTATTCATTA 57.751 29.630 0.00 0.00 0.00 1.90
5903 6749 7.496346 TCTCATAAACTGTAAACTCCAGGAT 57.504 36.000 0.00 0.00 34.16 3.24
5926 6979 2.872245 CCTTTCGATGAACACCGCATAT 59.128 45.455 0.00 0.00 0.00 1.78
5945 6998 2.871182 TCACTTATCCTAGCAGTGCG 57.129 50.000 10.00 0.00 38.27 5.34
5977 7030 7.771966 CAATAAGTTGAAGCACCAAGCAATGG 61.772 42.308 6.99 6.99 45.58 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.672961 TTTCTCTTCGCGTCATGGAT 57.327 45.000 5.77 0.00 0.00 3.41
21 22 8.651588 GTGCCATATACTATGATTTTCTCTTCG 58.348 37.037 0.00 0.00 0.00 3.79
28 29 6.710295 TCTTGCGTGCCATATACTATGATTTT 59.290 34.615 0.00 0.00 0.00 1.82
71 72 3.576550 ACGGATTAAGGTTTGCATGGTTT 59.423 39.130 0.00 0.00 0.00 3.27
84 85 5.123820 ACAACATGACCATCAACGGATTAAG 59.876 40.000 0.00 0.00 0.00 1.85
85 86 5.007034 ACAACATGACCATCAACGGATTAA 58.993 37.500 0.00 0.00 0.00 1.40
92 93 3.818210 TGTACCACAACATGACCATCAAC 59.182 43.478 0.00 0.00 0.00 3.18
124 133 6.512253 CGTTGATTCCAGAATGATGTGTATGG 60.512 42.308 0.00 0.00 39.69 2.74
275 286 0.179174 CTAAAAACATGCGCCCGACC 60.179 55.000 4.18 0.00 0.00 4.79
389 401 4.078363 AGTATGTTGTATGCGCAAACAC 57.922 40.909 24.09 17.94 0.00 3.32
440 452 7.365840 AGTTCGACATGATTTTCTAGGTTTC 57.634 36.000 0.00 0.00 0.00 2.78
473 485 3.720949 TGAAGTTCTTCCTTCGTTCGA 57.279 42.857 4.17 0.00 43.06 3.71
615 640 5.817296 TGCTGTCATAAATCAGTGTATGGTC 59.183 40.000 0.00 0.00 34.57 4.02
672 703 5.509716 TTTCTTTTTCTTTTCCGGGAGTC 57.490 39.130 0.00 0.00 0.00 3.36
723 766 1.772567 AGTGTGGGCCCTGTGGTTA 60.773 57.895 25.70 0.00 0.00 2.85
841 885 4.514441 GTCGGATCTAGGAGTTCGTTATCA 59.486 45.833 0.00 0.00 0.00 2.15
842 886 4.377226 CGTCGGATCTAGGAGTTCGTTATC 60.377 50.000 0.00 0.00 0.00 1.75
1378 1422 1.320344 CCGGATCGGGAGAGAACACA 61.320 60.000 13.96 0.00 44.15 3.72
1507 1551 4.334443 CTTTTATCCGCATCAAACGACAG 58.666 43.478 0.00 0.00 0.00 3.51
1513 1557 2.360844 TCGCCTTTTATCCGCATCAAA 58.639 42.857 0.00 0.00 0.00 2.69
1762 1815 4.424430 CGCGCCAAGACCGTTTCG 62.424 66.667 0.00 0.00 0.00 3.46
1837 1893 7.555195 CCCTCCAACCGTTATTTTACTTATTCT 59.445 37.037 0.00 0.00 0.00 2.40
1902 1958 5.360999 AGCAAACCTCCCAATAAAAGATAGC 59.639 40.000 0.00 0.00 0.00 2.97
1953 2009 2.438021 TCCAGACAAAGTACTTGCCACT 59.562 45.455 9.34 4.19 38.75 4.00
2007 2063 5.911752 TGCCAAATTGTACAAACACAAGAT 58.088 33.333 13.23 0.00 41.48 2.40
2043 2099 5.692115 ACCTATCATGGTTGATGTGTGTA 57.308 39.130 0.00 0.00 42.60 2.90
2117 2173 6.415206 AGAAATATGCAATGATTGAAGGGG 57.585 37.500 9.76 0.00 0.00 4.79
2118 2174 7.723324 AGAAGAAATATGCAATGATTGAAGGG 58.277 34.615 9.76 0.00 0.00 3.95
2133 2189 4.516652 AGCTGGGCAAGAGAAGAAATAT 57.483 40.909 0.00 0.00 0.00 1.28
2147 2464 3.430513 GGTGAGTAAACTAGTAGCTGGGC 60.431 52.174 0.00 0.00 0.00 5.36
2152 2469 6.699366 AGAAAAGGGTGAGTAAACTAGTAGC 58.301 40.000 0.00 0.00 0.00 3.58
2289 2606 4.463891 ACATGGCCAGTAAAATTCTGAAGG 59.536 41.667 13.05 0.00 35.20 3.46
2307 2624 1.892338 GGTGTTGGGCATCACATGG 59.108 57.895 0.00 0.00 36.43 3.66
2325 2642 3.927142 AGTTCAACTTAAAGGCTCGATCG 59.073 43.478 9.36 9.36 0.00 3.69
2532 2849 7.494625 TCGGTATCATCTCCAAATCTAACAAAC 59.505 37.037 0.00 0.00 0.00 2.93
2631 2948 4.949121 ACATACCAGAGGTTCTTCTAGGT 58.051 43.478 0.00 0.00 37.09 3.08
2689 3006 1.605232 ACGAACTAACAAAAAGGCCGG 59.395 47.619 0.00 0.00 0.00 6.13
2691 3008 2.619646 TCCACGAACTAACAAAAAGGCC 59.380 45.455 0.00 0.00 0.00 5.19
2692 3009 3.974871 TCCACGAACTAACAAAAAGGC 57.025 42.857 0.00 0.00 0.00 4.35
2747 3067 9.066892 GGCCATAAAATGAGTCATATTTAGTGA 57.933 33.333 5.94 0.00 0.00 3.41
2756 3076 5.422970 ACAATGTGGCCATAAAATGAGTCAT 59.577 36.000 9.72 0.00 0.00 3.06
2820 3140 5.687441 GCATCAGGGACATACAAGGTATGAA 60.687 44.000 19.94 2.61 0.00 2.57
2835 3156 0.817654 CACTACGACAGCATCAGGGA 59.182 55.000 0.00 0.00 0.00 4.20
2844 3165 6.680874 ACTAATAGGAGAACACTACGACAG 57.319 41.667 0.00 0.00 0.00 3.51
2900 3289 6.003326 TGATCAATAACAGAAGAAAGCACCA 58.997 36.000 0.00 0.00 0.00 4.17
2902 3291 8.976986 AAATGATCAATAACAGAAGAAAGCAC 57.023 30.769 0.00 0.00 0.00 4.40
2926 3315 7.255451 CCAGAAAGGCAAAACAAGTACAGATAA 60.255 37.037 0.00 0.00 0.00 1.75
2957 3346 6.792326 TGTAAATCTCTACAGGTCATGTACG 58.208 40.000 0.00 0.00 43.66 3.67
3038 3427 0.818296 AGTAGAACTGGCGCCACTAG 59.182 55.000 29.03 19.62 0.00 2.57
3155 3544 8.437575 ACAAGGGATTAAACATATACGGATCTT 58.562 33.333 0.00 0.00 0.00 2.40
3167 3556 1.957177 TGCGCAACAAGGGATTAAACA 59.043 42.857 8.16 0.00 0.00 2.83
3235 3624 8.578448 TGTTATTTGAATCACCATCTGAATGA 57.422 30.769 0.00 0.00 34.61 2.57
3319 3708 7.951347 AAGCAGGTTGAGAATTTCAGATTAT 57.049 32.000 0.00 0.00 37.07 1.28
3479 3868 4.449068 ACACATAAGAGCTTCAGAAACGTG 59.551 41.667 0.00 0.00 0.00 4.49
3715 4104 6.839124 AGATGATTGGTTCAATGCAAACTA 57.161 33.333 0.00 0.00 38.03 2.24
3777 4166 7.065683 ACTGCCAAATTTTCCAAACTTAACTTG 59.934 33.333 0.00 0.00 0.00 3.16
3824 4213 8.217799 AGGCTAATTTGCTATAGTACATCCAAA 58.782 33.333 11.61 2.88 0.00 3.28
4027 4420 5.893687 TGTGTTGGAATAATTGCTAGCATG 58.106 37.500 20.13 0.00 0.00 4.06
4097 4490 8.924691 GCATGTTCAAAGTTTATTTAGCATTCA 58.075 29.630 0.00 0.00 0.00 2.57
4098 4491 8.924691 TGCATGTTCAAAGTTTATTTAGCATTC 58.075 29.630 0.00 0.00 0.00 2.67
4425 5134 3.753294 ACAATGAAGTGAGAACCGAGT 57.247 42.857 0.00 0.00 0.00 4.18
4476 5185 5.602978 TGGTAAGAGATAAAAGCCTCCTAGG 59.397 44.000 0.82 0.82 38.80 3.02
4478 5187 6.203072 AGTGGTAAGAGATAAAAGCCTCCTA 58.797 40.000 0.00 0.00 0.00 2.94
4482 5191 4.710375 TCGAGTGGTAAGAGATAAAAGCCT 59.290 41.667 0.00 0.00 0.00 4.58
4484 5193 6.043411 ACATCGAGTGGTAAGAGATAAAAGC 58.957 40.000 0.00 0.00 0.00 3.51
4488 5197 9.788889 TTCTATACATCGAGTGGTAAGAGATAA 57.211 33.333 0.00 0.00 0.00 1.75
4534 5243 7.010460 CCCAATGAGAAACTTGTTTGAAAGAAC 59.990 37.037 3.27 0.00 0.00 3.01
4535 5244 7.041107 CCCAATGAGAAACTTGTTTGAAAGAA 58.959 34.615 3.27 0.00 0.00 2.52
4537 5246 5.234972 GCCCAATGAGAAACTTGTTTGAAAG 59.765 40.000 3.27 0.00 0.00 2.62
4545 5254 2.624838 AGTGTGCCCAATGAGAAACTTG 59.375 45.455 0.00 0.00 0.00 3.16
4547 5256 2.624838 CAAGTGTGCCCAATGAGAAACT 59.375 45.455 0.00 0.00 0.00 2.66
4548 5257 2.362077 ACAAGTGTGCCCAATGAGAAAC 59.638 45.455 0.00 0.00 0.00 2.78
4549 5258 2.622942 GACAAGTGTGCCCAATGAGAAA 59.377 45.455 0.00 0.00 0.00 2.52
4550 5259 2.229792 GACAAGTGTGCCCAATGAGAA 58.770 47.619 0.00 0.00 0.00 2.87
4558 5267 1.803334 TGTTATCGACAAGTGTGCCC 58.197 50.000 0.00 0.00 34.69 5.36
4570 5279 5.678483 GTGCTAATGTTTGCTCATGTTATCG 59.322 40.000 0.00 0.00 0.00 2.92
4572 5281 5.449041 CCGTGCTAATGTTTGCTCATGTTAT 60.449 40.000 0.00 0.00 0.00 1.89
4598 5307 2.302157 GGACCAGTACAGGCTAACAAGT 59.698 50.000 3.83 0.00 0.00 3.16
4607 5316 8.674607 GTTTAATATTTGAAGGACCAGTACAGG 58.325 37.037 2.14 2.14 0.00 4.00
4608 5317 8.674607 GGTTTAATATTTGAAGGACCAGTACAG 58.325 37.037 0.00 0.00 0.00 2.74
4622 5331 5.070770 TGCACAGCCTGGTTTAATATTTG 57.929 39.130 0.00 0.00 0.00 2.32
4627 5336 3.324556 ACAATTGCACAGCCTGGTTTAAT 59.675 39.130 5.05 0.00 0.00 1.40
4634 5343 2.806608 AAGAACAATTGCACAGCCTG 57.193 45.000 5.05 0.00 0.00 4.85
4639 5348 3.456280 GCAAGGAAAGAACAATTGCACA 58.544 40.909 5.05 0.00 44.32 4.57
4657 5366 4.572571 AACCCGTCTTGGCCGCAA 62.573 61.111 0.00 0.00 35.87 4.85
4661 5370 4.660938 AGGCAACCCGTCTTGGCC 62.661 66.667 11.00 0.00 45.58 5.36
4664 5373 1.007387 GCAAAGGCAACCCGTCTTG 60.007 57.895 0.00 0.00 39.14 3.02
4686 5395 6.821388 AGAGTTGACAAGTATATGATGGGTC 58.179 40.000 0.00 0.00 0.00 4.46
4687 5396 6.814954 AGAGTTGACAAGTATATGATGGGT 57.185 37.500 0.00 0.00 0.00 4.51
4746 5456 7.971455 ACTCCGCAAGACAAATATAACTTTAC 58.029 34.615 0.00 0.00 43.02 2.01
4752 5462 6.811253 AACAACTCCGCAAGACAAATATAA 57.189 33.333 0.00 0.00 43.02 0.98
4753 5463 6.811253 AAACAACTCCGCAAGACAAATATA 57.189 33.333 0.00 0.00 43.02 0.86
4754 5464 5.705609 AAACAACTCCGCAAGACAAATAT 57.294 34.783 0.00 0.00 43.02 1.28
4765 5475 3.689649 AGTGAATGGATAAACAACTCCGC 59.310 43.478 0.00 0.00 34.05 5.54
4766 5477 5.163754 GGAAGTGAATGGATAAACAACTCCG 60.164 44.000 0.00 0.00 34.05 4.63
4770 5481 7.029563 GTCATGGAAGTGAATGGATAAACAAC 58.970 38.462 0.00 0.00 0.00 3.32
4771 5482 6.128035 CGTCATGGAAGTGAATGGATAAACAA 60.128 38.462 0.00 0.00 0.00 2.83
4772 5483 5.353956 CGTCATGGAAGTGAATGGATAAACA 59.646 40.000 0.00 0.00 0.00 2.83
4773 5484 5.730568 GCGTCATGGAAGTGAATGGATAAAC 60.731 44.000 0.00 0.00 0.00 2.01
4774 5485 4.335315 GCGTCATGGAAGTGAATGGATAAA 59.665 41.667 0.00 0.00 0.00 1.40
4775 5486 3.876914 GCGTCATGGAAGTGAATGGATAA 59.123 43.478 0.00 0.00 0.00 1.75
4776 5487 3.134623 AGCGTCATGGAAGTGAATGGATA 59.865 43.478 0.00 0.00 0.00 2.59
4777 5488 2.092753 AGCGTCATGGAAGTGAATGGAT 60.093 45.455 0.00 0.00 0.00 3.41
4778 5489 1.278985 AGCGTCATGGAAGTGAATGGA 59.721 47.619 0.00 0.00 0.00 3.41
4779 5490 1.742761 AGCGTCATGGAAGTGAATGG 58.257 50.000 0.00 0.00 0.00 3.16
4780 5491 4.024556 GGATTAGCGTCATGGAAGTGAATG 60.025 45.833 0.00 0.00 0.00 2.67
4781 5492 4.130118 GGATTAGCGTCATGGAAGTGAAT 58.870 43.478 0.00 0.00 0.00 2.57
4782 5493 3.055458 TGGATTAGCGTCATGGAAGTGAA 60.055 43.478 0.00 0.00 0.00 3.18
4783 5494 2.499693 TGGATTAGCGTCATGGAAGTGA 59.500 45.455 0.00 0.00 0.00 3.41
4784 5495 2.609459 GTGGATTAGCGTCATGGAAGTG 59.391 50.000 0.00 0.00 0.00 3.16
4785 5496 2.501723 AGTGGATTAGCGTCATGGAAGT 59.498 45.455 0.00 0.00 0.00 3.01
4786 5497 2.868583 CAGTGGATTAGCGTCATGGAAG 59.131 50.000 0.00 0.00 0.00 3.46
5041 5752 0.820226 TCTGACGCTGCTATGCTCTT 59.180 50.000 0.00 0.00 0.00 2.85
5263 5992 8.767085 GCAAGTCAAAATTTCTTGAATGAATCA 58.233 29.630 17.71 0.00 40.35 2.57
5385 6126 2.490217 CTCAGCCAGACCGTACCG 59.510 66.667 0.00 0.00 0.00 4.02
5386 6127 1.961180 ATGCTCAGCCAGACCGTACC 61.961 60.000 0.00 0.00 0.00 3.34
5390 6152 1.226686 GCATATGCTCAGCCAGACCG 61.227 60.000 20.64 0.00 38.21 4.79
5396 6158 4.572985 TTTTACATGCATATGCTCAGCC 57.427 40.909 27.13 0.00 42.66 4.85
5420 6182 5.813157 CAGGCAATCAACATGCAAATATTGA 59.187 36.000 12.16 9.96 45.60 2.57
5424 6186 5.402997 TTCAGGCAATCAACATGCAAATA 57.597 34.783 0.00 0.00 45.60 1.40
5428 6190 4.038282 GGATATTCAGGCAATCAACATGCA 59.962 41.667 0.00 0.00 45.60 3.96
5429 6191 4.280174 AGGATATTCAGGCAATCAACATGC 59.720 41.667 0.00 0.00 43.08 4.06
5430 6192 5.768662 AGAGGATATTCAGGCAATCAACATG 59.231 40.000 0.00 0.00 0.00 3.21
5431 6193 5.950023 AGAGGATATTCAGGCAATCAACAT 58.050 37.500 0.00 0.00 0.00 2.71
5432 6194 5.378230 AGAGGATATTCAGGCAATCAACA 57.622 39.130 0.00 0.00 0.00 3.33
5433 6195 5.506982 GCAAGAGGATATTCAGGCAATCAAC 60.507 44.000 0.00 0.00 0.00 3.18
5434 6196 4.581824 GCAAGAGGATATTCAGGCAATCAA 59.418 41.667 0.00 0.00 0.00 2.57
5435 6197 4.139786 GCAAGAGGATATTCAGGCAATCA 58.860 43.478 0.00 0.00 0.00 2.57
5436 6198 4.215827 CAGCAAGAGGATATTCAGGCAATC 59.784 45.833 0.00 0.00 0.00 2.67
5437 6199 4.142790 CAGCAAGAGGATATTCAGGCAAT 58.857 43.478 0.00 0.00 0.00 3.56
5438 6200 3.548770 CAGCAAGAGGATATTCAGGCAA 58.451 45.455 0.00 0.00 0.00 4.52
5439 6201 2.747467 GCAGCAAGAGGATATTCAGGCA 60.747 50.000 0.00 0.00 0.00 4.75
5440 6202 1.878734 GCAGCAAGAGGATATTCAGGC 59.121 52.381 0.00 0.00 0.00 4.85
5441 6203 3.204306 TGCAGCAAGAGGATATTCAGG 57.796 47.619 0.00 0.00 0.00 3.86
5442 6204 4.579340 ACAATGCAGCAAGAGGATATTCAG 59.421 41.667 0.00 0.00 0.00 3.02
5443 6205 4.529897 ACAATGCAGCAAGAGGATATTCA 58.470 39.130 0.00 0.00 0.00 2.57
5444 6206 5.334724 GCTACAATGCAGCAAGAGGATATTC 60.335 44.000 0.00 0.00 38.93 1.75
5445 6207 4.518211 GCTACAATGCAGCAAGAGGATATT 59.482 41.667 0.00 0.00 38.93 1.28
5446 6208 4.070716 GCTACAATGCAGCAAGAGGATAT 58.929 43.478 0.00 0.00 38.93 1.63
5447 6209 3.118298 TGCTACAATGCAGCAAGAGGATA 60.118 43.478 5.56 0.00 45.71 2.59
5448 6210 2.295885 GCTACAATGCAGCAAGAGGAT 58.704 47.619 0.00 0.00 38.93 3.24
5449 6211 1.003464 TGCTACAATGCAGCAAGAGGA 59.997 47.619 5.56 0.00 45.71 3.71
5450 6212 1.456296 TGCTACAATGCAGCAAGAGG 58.544 50.000 5.56 0.00 45.71 3.69
5460 6222 2.029649 GCATAGGGGCATTGCTACAATG 60.030 50.000 14.47 14.47 33.61 2.82
5461 6223 2.242043 GCATAGGGGCATTGCTACAAT 58.758 47.619 8.82 0.00 33.61 2.71
5462 6224 1.064091 TGCATAGGGGCATTGCTACAA 60.064 47.619 8.82 0.00 39.25 2.41
5463 6225 0.550432 TGCATAGGGGCATTGCTACA 59.450 50.000 8.82 0.00 39.25 2.74
5464 6226 3.419793 TGCATAGGGGCATTGCTAC 57.580 52.632 8.82 2.04 39.25 3.58
5472 6234 1.134729 CCAAACACAATGCATAGGGGC 60.135 52.381 0.00 0.00 0.00 5.80
5473 6235 2.178580 ACCAAACACAATGCATAGGGG 58.821 47.619 0.00 0.00 0.00 4.79
5474 6236 3.006752 ACAACCAAACACAATGCATAGGG 59.993 43.478 0.00 0.00 0.00 3.53
5475 6237 4.255833 ACAACCAAACACAATGCATAGG 57.744 40.909 0.00 0.00 0.00 2.57
5476 6238 5.558653 GCAAACAACCAAACACAATGCATAG 60.559 40.000 0.00 0.00 0.00 2.23
5477 6239 4.272018 GCAAACAACCAAACACAATGCATA 59.728 37.500 0.00 0.00 0.00 3.14
5478 6240 3.065095 GCAAACAACCAAACACAATGCAT 59.935 39.130 0.00 0.00 0.00 3.96
5484 6246 3.668447 ACAATGCAAACAACCAAACACA 58.332 36.364 0.00 0.00 0.00 3.72
5485 6247 5.982465 ATACAATGCAAACAACCAAACAC 57.018 34.783 0.00 0.00 0.00 3.32
5488 6250 6.589523 GCAGATATACAATGCAAACAACCAAA 59.410 34.615 0.00 0.00 39.75 3.28
5503 6265 4.627035 GCATTGCTACGATGCAGATATACA 59.373 41.667 13.66 0.00 46.96 2.29
5504 6266 5.136250 GCATTGCTACGATGCAGATATAC 57.864 43.478 13.66 0.00 46.96 1.47
5528 6292 5.528043 AACAACCAAACACAATGCATAGA 57.472 34.783 0.00 0.00 0.00 1.98
5536 6300 4.067896 ACAATGCAAACAACCAAACACAA 58.932 34.783 0.00 0.00 0.00 3.33
5551 6315 5.123661 CACTCATGTAACCACATACAATGCA 59.876 40.000 0.00 0.00 43.73 3.96
5578 6342 7.647318 CACAACTATATGCTCAACAAAACAACA 59.353 33.333 0.00 0.00 0.00 3.33
5613 6383 4.532521 AGGTAAGCTCGCCAAATAGGATAT 59.467 41.667 8.91 0.00 41.22 1.63
5621 6391 3.094572 AGTAGTAGGTAAGCTCGCCAAA 58.905 45.455 8.91 0.00 0.00 3.28
5645 6415 0.319083 TCGGTGTTCGTGCATAAGGT 59.681 50.000 0.00 0.00 40.32 3.50
5646 6416 1.593006 GATCGGTGTTCGTGCATAAGG 59.407 52.381 0.00 0.00 40.32 2.69
5648 6418 1.996898 GTGATCGGTGTTCGTGCATAA 59.003 47.619 0.00 0.00 40.32 1.90
5649 6419 1.635844 GTGATCGGTGTTCGTGCATA 58.364 50.000 0.00 0.00 40.32 3.14
5650 6420 1.351430 CGTGATCGGTGTTCGTGCAT 61.351 55.000 0.00 0.00 40.32 3.96
5652 6422 2.769617 CGTGATCGGTGTTCGTGC 59.230 61.111 0.00 0.00 40.32 5.34
5653 6423 2.769617 GCGTGATCGGTGTTCGTG 59.230 61.111 0.00 0.00 40.32 4.35
5654 6424 2.736343 TTCGCGTGATCGGTGTTCGT 62.736 55.000 5.77 0.00 40.32 3.85
5655 6425 2.084101 TTCGCGTGATCGGTGTTCG 61.084 57.895 5.77 0.00 40.90 3.95
5656 6426 1.414897 GTTCGCGTGATCGGTGTTC 59.585 57.895 5.77 0.00 37.56 3.18
5665 6440 2.325166 GTTTTGGCGTTCGCGTGA 59.675 55.556 5.77 0.00 43.62 4.35
5671 6446 1.522258 CATTGCAGTGTTTTGGCGTTC 59.478 47.619 0.13 0.00 0.00 3.95
5675 6450 2.237416 GCCATTGCAGTGTTTTGGC 58.763 52.632 8.53 13.95 45.31 4.52
5679 6488 1.246649 TCATCGCCATTGCAGTGTTT 58.753 45.000 8.53 0.00 37.32 2.83
5699 6508 3.099905 ACTCCCATCATCTTCGTTCAGA 58.900 45.455 0.00 0.00 0.00 3.27
5731 6577 1.347320 GTGAGACGGATCGTTGGTTC 58.653 55.000 0.00 0.00 41.37 3.62
5735 6581 1.068474 GTTGGTGAGACGGATCGTTG 58.932 55.000 0.00 0.00 41.37 4.10
5736 6582 0.966920 AGTTGGTGAGACGGATCGTT 59.033 50.000 0.00 0.00 41.37 3.85
5744 6590 2.540973 GCGGTTTTGAAGTTGGTGAGAC 60.541 50.000 0.00 0.00 0.00 3.36
5748 6594 1.838913 CAGCGGTTTTGAAGTTGGTG 58.161 50.000 0.00 0.00 0.00 4.17
5749 6595 0.102300 GCAGCGGTTTTGAAGTTGGT 59.898 50.000 0.00 0.00 0.00 3.67
5790 6636 1.646189 GGCAGAAGAAGCTTACTCCG 58.354 55.000 0.00 0.00 0.00 4.63
5808 6654 1.002624 TTTAAGACCAGGCAGGCGG 60.003 57.895 0.00 3.75 43.14 6.13
5844 6690 5.914898 ATAAATTTCAGGGTACAAGCACC 57.085 39.130 0.00 0.00 37.91 5.01
5845 6691 6.919721 TGAATAAATTTCAGGGTACAAGCAC 58.080 36.000 0.00 0.00 0.00 4.40
5846 6692 7.716799 ATGAATAAATTTCAGGGTACAAGCA 57.283 32.000 0.00 0.00 0.00 3.91
5865 6711 9.236006 ACAGTTTATGAGAAGCTTGTAATGAAT 57.764 29.630 2.10 0.00 0.00 2.57
5872 6718 7.173390 GGAGTTTACAGTTTATGAGAAGCTTGT 59.827 37.037 2.10 0.00 0.00 3.16
5885 6731 3.916989 AGGGATCCTGGAGTTTACAGTTT 59.083 43.478 12.58 0.00 34.16 2.66
5903 6749 0.672401 GCGGTGTTCATCGAAAGGGA 60.672 55.000 9.70 0.00 0.00 4.20
5926 6979 1.202417 GCGCACTGCTAGGATAAGTGA 60.202 52.381 0.30 0.00 43.22 3.41
5945 6998 3.916776 GTGCTTCAACTTATTGCTCTTGC 59.083 43.478 0.00 0.00 35.63 4.01


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

AutoCloner maintained by Alex Coulton.