Multiple sequence alignment - TraesCS1B01G297800

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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 TraesCS1B01G297800 chr1B 100.000 5779 0 0 1 5779 518175548 518181326 0.000000e+00 10672
1 TraesCS1B01G297800 chr1D 96.358 3020 89 11 774 3785 385802967 385805973 0.000000e+00 4948
2 TraesCS1B01G297800 chr1D 93.921 1793 93 10 3779 5567 385806000 385807780 0.000000e+00 2693
3 TraesCS1B01G297800 chr1D 85.084 771 62 19 1 736 385801881 385802633 0.000000e+00 737
4 TraesCS1B01G297800 chr1A 95.792 3018 92 12 778 3785 485353191 485356183 0.000000e+00 4837
5 TraesCS1B01G297800 chr1A 94.361 1791 87 7 3779 5567 485356210 485357988 0.000000e+00 2736
6 TraesCS1B01G297800 chr1A 89.267 382 38 2 1 380 485352284 485352664 5.240000e-130 475
7 TraesCS1B01G297800 chr1A 90.141 284 12 9 457 730 485352661 485352938 7.120000e-94 355
8 TraesCS1B01G297800 chr1A 94.643 112 3 2 5565 5675 485357944 485358053 2.770000e-38 171


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 TraesCS1B01G297800 chr1B 518175548 518181326 5778 False 10672.000000 10672 100.000000 1 5779 1 chr1B.!!$F1 5778
1 TraesCS1B01G297800 chr1D 385801881 385807780 5899 False 2792.666667 4948 91.787667 1 5567 3 chr1D.!!$F1 5566
2 TraesCS1B01G297800 chr1A 485352284 485358053 5769 False 1714.800000 4837 92.840800 1 5675 5 chr1A.!!$F1 5674

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
89 91 0.247301 GAAGCGCGAATCCTTTGTCG 60.247 55.0 12.10 0.0 40.24 4.35 F
602 638 1.091537 TTTTCCATTTAGCCGCTCCG 58.908 50.0 0.00 0.0 0.00 4.63 F
1644 1987 0.690192 TGGCACATTTCGAGGAGGAA 59.310 50.0 0.00 0.0 0.00 3.36 F
3094 3437 0.175302 CTCTGTACAGGAGCAGCAGG 59.825 60.0 22.48 0.0 33.09 4.85 F
4170 4582 0.108585 GGAACAAGTCAGCTGTCCCA 59.891 55.0 14.67 0.0 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1055 1394 0.322816 GGCATCAGAACCCTGCTTGA 60.323 55.0 0.00 0.0 40.20 3.02 R
2345 2688 0.979665 CTCTGGAGGAGGCACTTCAA 59.020 55.0 0.00 0.0 41.55 2.69 R
3369 3712 0.877071 CCTTTTCAGCATCAGCACGT 59.123 50.0 0.00 0.0 45.49 4.49 R
4694 5106 0.031178 CTGCGCTTTTCTTGGCTGTT 59.969 50.0 9.73 0.0 0.00 3.16 R
5699 6114 0.104304 CGTATTAAGCAGGCGACCCT 59.896 55.0 0.00 0.0 44.25 4.34 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
27 28 6.238484 GGGTTTGCATATATATCCGCTCATTC 60.238 42.308 6.60 0.00 0.00 2.67
57 59 1.895020 TACTTCTGGCGGCCGTTGAT 61.895 55.000 28.70 10.67 0.00 2.57
68 70 2.360350 CGTTGATGCCCTGCCTGT 60.360 61.111 0.00 0.00 0.00 4.00
79 81 1.446099 CTGCCTGTAGAAGCGCGAA 60.446 57.895 12.10 0.00 0.00 4.70
89 91 0.247301 GAAGCGCGAATCCTTTGTCG 60.247 55.000 12.10 0.00 40.24 4.35
105 107 1.554617 TGTCGAAGGAGCCATGAATCA 59.445 47.619 0.00 0.00 0.00 2.57
114 116 1.572415 AGCCATGAATCACCTTGGGAT 59.428 47.619 3.82 0.00 33.41 3.85
116 118 2.313317 CCATGAATCACCTTGGGATGG 58.687 52.381 0.00 0.00 0.00 3.51
161 163 6.637658 GGCGACTAGATTAGACATGAGTTAAC 59.362 42.308 0.00 0.00 0.00 2.01
167 169 9.469807 CTAGATTAGACATGAGTTAACCATCAC 57.530 37.037 0.00 2.90 0.00 3.06
181 183 8.211629 AGTTAACCATCACAGTTTCTTACTTCT 58.788 33.333 0.88 0.00 33.85 2.85
186 188 6.931281 CCATCACAGTTTCTTACTTCTCTTGA 59.069 38.462 0.00 0.00 33.85 3.02
209 211 3.389002 AGGTAAACTCACGGTGTAAAGGT 59.611 43.478 8.17 0.00 0.00 3.50
213 215 3.547054 ACTCACGGTGTAAAGGTTTCA 57.453 42.857 8.17 0.00 0.00 2.69
229 231 3.558033 GTTTCACCTTAACCTTGACCCA 58.442 45.455 0.00 0.00 0.00 4.51
232 234 2.041081 TCACCTTAACCTTGACCCATGG 59.959 50.000 4.14 4.14 35.21 3.66
268 270 7.097128 CGAGGTTCGTCTAAATACGTCAAATAG 60.097 40.741 0.00 0.00 43.31 1.73
381 383 7.769272 TGACACTTTGCCTCTTTTATTTTTG 57.231 32.000 0.00 0.00 0.00 2.44
382 384 7.327214 TGACACTTTGCCTCTTTTATTTTTGT 58.673 30.769 0.00 0.00 0.00 2.83
383 385 7.821846 TGACACTTTGCCTCTTTTATTTTTGTT 59.178 29.630 0.00 0.00 0.00 2.83
384 386 7.973601 ACACTTTGCCTCTTTTATTTTTGTTG 58.026 30.769 0.00 0.00 0.00 3.33
385 387 7.606073 ACACTTTGCCTCTTTTATTTTTGTTGT 59.394 29.630 0.00 0.00 0.00 3.32
386 388 9.092876 CACTTTGCCTCTTTTATTTTTGTTGTA 57.907 29.630 0.00 0.00 0.00 2.41
387 389 9.830975 ACTTTGCCTCTTTTATTTTTGTTGTAT 57.169 25.926 0.00 0.00 0.00 2.29
601 637 1.816224 TGTTTTCCATTTAGCCGCTCC 59.184 47.619 0.00 0.00 0.00 4.70
602 638 1.091537 TTTTCCATTTAGCCGCTCCG 58.908 50.000 0.00 0.00 0.00 4.63
605 641 3.279875 CATTTAGCCGCTCCGCCC 61.280 66.667 0.00 0.00 0.00 6.13
607 643 3.338275 ATTTAGCCGCTCCGCCCAA 62.338 57.895 0.00 0.00 0.00 4.12
608 644 4.770874 TTAGCCGCTCCGCCCAAC 62.771 66.667 0.00 0.00 0.00 3.77
933 1270 1.110442 CGTGGCTGATCTTCTCTCCT 58.890 55.000 0.00 0.00 0.00 3.69
979 1318 3.013327 GCCCCGGTCCCCTTACTT 61.013 66.667 0.00 0.00 0.00 2.24
1070 1409 1.376466 GCCTCAAGCAGGGTTCTGA 59.624 57.895 0.00 0.00 43.70 3.27
1152 1491 2.435059 GCCGCTGAGGTCAAGGAC 60.435 66.667 0.00 0.00 43.70 3.85
1161 1500 4.097361 GTCAAGGACGAGGGGGCC 62.097 72.222 0.00 0.00 0.00 5.80
1220 1559 1.523258 GAGATGCGCCAGATGCTGT 60.523 57.895 4.18 0.00 38.05 4.40
1243 1582 4.087892 AAGAGGCAGATGCGGCGT 62.088 61.111 9.37 0.00 43.26 5.68
1309 1648 5.474532 GGCATGATTATTGCAGAAGGATGTA 59.525 40.000 0.00 0.00 41.95 2.29
1310 1649 6.376978 GCATGATTATTGCAGAAGGATGTAC 58.623 40.000 0.00 0.00 39.90 2.90
1398 1737 3.706373 GGCGAGCCTGAGTGGGAA 61.706 66.667 6.90 0.00 36.00 3.97
1472 1811 4.222847 CGGTAAGGAGGCTCCGGC 62.223 72.222 27.11 19.67 42.75 6.13
1546 1886 6.467682 GCGTTGAATAATATTTTCGCACTTCA 59.532 34.615 17.75 0.00 41.59 3.02
1558 1898 3.673902 TCGCACTTCATTTCAGAATCCA 58.326 40.909 0.00 0.00 0.00 3.41
1644 1987 0.690192 TGGCACATTTCGAGGAGGAA 59.310 50.000 0.00 0.00 0.00 3.36
1687 2030 1.142748 GCTCAGTGCGCCAGATACT 59.857 57.895 4.18 0.00 0.00 2.12
1718 2061 6.126863 TCCTCTTGATAAAGAAGGCTTTCA 57.873 37.500 11.53 0.00 43.08 2.69
1953 2296 2.194201 TGGATTCCTTTGTCGGTTCC 57.806 50.000 3.95 0.00 0.00 3.62
2313 2656 5.187967 GGATGATACGGATACTTCTCCCATT 59.812 44.000 0.00 0.00 31.04 3.16
2340 2683 4.497291 TGTAGTGGTTGAGGAAGTTGTT 57.503 40.909 0.00 0.00 0.00 2.83
2345 2688 3.632145 GTGGTTGAGGAAGTTGTTGTCAT 59.368 43.478 0.00 0.00 0.00 3.06
2569 2912 6.475504 TCTTTCAAGATTGGAGAGTGCATTA 58.524 36.000 0.00 0.00 0.00 1.90
2606 2949 4.754667 GACCGGGCCTTCGTCCAC 62.755 72.222 6.32 0.00 0.00 4.02
2609 2952 4.003788 CGGGCCTTCGTCCACTGT 62.004 66.667 0.84 0.00 0.00 3.55
2790 3133 0.392998 CGGTTGCCATAGAGCCAACT 60.393 55.000 0.00 0.00 0.00 3.16
3087 3430 4.753233 CAGATTTGTCCTCTGTACAGGAG 58.247 47.826 22.48 16.78 43.68 3.69
3094 3437 0.175302 CTCTGTACAGGAGCAGCAGG 59.825 60.000 22.48 0.00 33.09 4.85
3330 3673 9.273016 CCACTAAAAGAATCTGAAACTGAAGTA 57.727 33.333 0.00 0.00 0.00 2.24
3348 3691 6.966021 TGAAGTACAAAAGAGCACAAATACC 58.034 36.000 0.00 0.00 0.00 2.73
3448 3791 4.145876 TCGCTTCGTAGTTTTCGTCTAA 57.854 40.909 0.00 0.00 0.00 2.10
3606 3952 5.911378 TTGCATGCTTAAACCATGTGATA 57.089 34.783 20.33 0.00 41.56 2.15
3640 3986 1.527433 GGTCCAAGTGAGCCCAAAGC 61.527 60.000 0.00 0.00 44.25 3.51
3858 4270 3.428452 CCCAATTGCAACAGCTGATGTAG 60.428 47.826 23.35 6.77 43.00 2.74
4001 4413 3.110705 AGTTCCATCAGATGCTGTACCT 58.889 45.455 4.68 0.00 32.61 3.08
4051 4463 0.311790 GTCGAACACGTGGGTACAGA 59.688 55.000 21.57 7.36 0.00 3.41
4122 4534 2.807967 GCTGGGTTGAAAAAGCAAATCC 59.192 45.455 0.00 0.00 35.69 3.01
4170 4582 0.108585 GGAACAAGTCAGCTGTCCCA 59.891 55.000 14.67 0.00 0.00 4.37
4378 4790 4.039124 ACCAGGTGATGAAATGGAAAACAC 59.961 41.667 0.00 0.00 36.62 3.32
4499 4911 1.898574 CCAAGGTGAAACGGCTGCT 60.899 57.895 0.00 0.00 38.12 4.24
4532 4944 2.137523 GCTGAAATTGCAACAACTGGG 58.862 47.619 0.00 0.00 0.00 4.45
4538 4950 3.902881 ATTGCAACAACTGGGAAAACA 57.097 38.095 0.00 0.00 0.00 2.83
4562 4974 2.436911 AGAGGGTGTCGGTGTTAAAACT 59.563 45.455 0.00 0.00 0.00 2.66
4581 4993 3.018149 ACTCGAGGTAAGAAGGCTACAG 58.982 50.000 18.41 0.00 0.00 2.74
4639 5051 3.809324 GCACCAGGTAAGAAGGCTACAAA 60.809 47.826 0.00 0.00 0.00 2.83
4694 5106 1.746615 GCGGGATGAGAAAGCTGCA 60.747 57.895 1.02 0.00 0.00 4.41
4768 5180 0.904865 ATGACAGCCAAGGAGGACGA 60.905 55.000 0.00 0.00 41.22 4.20
4780 5192 0.753262 GAGGACGACATGGCATAGGT 59.247 55.000 0.00 0.00 0.00 3.08
4853 5265 4.665897 GCGAATTCTTGTTTCTGTCGGTAC 60.666 45.833 3.52 0.00 0.00 3.34
4864 5276 3.433343 TCTGTCGGTACCAAGGTAATCA 58.567 45.455 13.54 0.00 31.86 2.57
4896 5308 1.216990 GGTTCTCCCCATCAGGATGT 58.783 55.000 8.35 0.00 38.24 3.06
4914 5326 7.552687 TCAGGATGTCATGTTTTGTATAGGAAC 59.447 37.037 0.00 0.00 37.40 3.62
4924 5336 2.029623 TGTATAGGAACAGACGGGAGC 58.970 52.381 0.00 0.00 0.00 4.70
4948 5360 2.280457 GACCCTAGCATCGCAGCC 60.280 66.667 0.00 0.00 34.23 4.85
4996 5408 5.786311 CATATATTTGGCCCCTTTCACATG 58.214 41.667 0.00 0.00 0.00 3.21
5078 5490 1.861542 TTGGTGCGGCTTTTCCATCG 61.862 55.000 0.00 0.00 34.01 3.84
5180 5593 1.811266 CGGTGAATCTGCTGGGACG 60.811 63.158 0.00 0.00 0.00 4.79
5182 5595 0.321653 GGTGAATCTGCTGGGACGTT 60.322 55.000 0.00 0.00 0.00 3.99
5192 5605 3.997021 CTGCTGGGACGTTATATGATTCC 59.003 47.826 0.00 0.00 0.00 3.01
5271 5684 0.242825 TTCCTACCGCGACTCTTGTG 59.757 55.000 8.23 0.00 0.00 3.33
5279 5692 2.031683 CCGCGACTCTTGTGTTTTTCTT 59.968 45.455 8.23 0.00 0.00 2.52
5288 5701 7.931275 ACTCTTGTGTTTTTCTTACAGATTCC 58.069 34.615 0.00 0.00 0.00 3.01
5295 5708 2.760634 TCTTACAGATTCCGCTTGCA 57.239 45.000 0.00 0.00 0.00 4.08
5296 5709 2.346803 TCTTACAGATTCCGCTTGCAC 58.653 47.619 0.00 0.00 0.00 4.57
5297 5710 2.076100 CTTACAGATTCCGCTTGCACA 58.924 47.619 0.00 0.00 0.00 4.57
5339 5753 1.282875 GCTTGTTTGACACTCGCCC 59.717 57.895 0.00 0.00 0.00 6.13
5341 5755 1.308998 CTTGTTTGACACTCGCCCTT 58.691 50.000 0.00 0.00 0.00 3.95
5358 5772 3.056107 GCCCTTTTTATTCCTGGTGGTTC 60.056 47.826 0.00 0.00 34.23 3.62
5359 5773 4.416516 CCCTTTTTATTCCTGGTGGTTCT 58.583 43.478 0.00 0.00 34.23 3.01
5402 5816 4.188247 TGCGCTCACATACTTTCTAACT 57.812 40.909 9.73 0.00 0.00 2.24
5413 5827 6.973474 ACATACTTTCTAACTGATGTACTCGC 59.027 38.462 0.00 0.00 0.00 5.03
5417 5831 4.307443 TCTAACTGATGTACTCGCATGG 57.693 45.455 0.00 0.00 0.00 3.66
5428 5842 6.650427 TGTACTCGCATGGTAGAATTCTAT 57.350 37.500 17.95 0.85 0.00 1.98
5429 5843 6.678878 TGTACTCGCATGGTAGAATTCTATC 58.321 40.000 17.95 17.67 0.00 2.08
5435 5849 8.354711 TCGCATGGTAGAATTCTATCTAGATT 57.645 34.615 23.09 0.00 32.72 2.40
5457 5871 6.963049 TTAATAAAAGAGAGACAAGACGGC 57.037 37.500 0.00 0.00 0.00 5.68
5458 5872 2.910688 AAAAGAGAGACAAGACGGCA 57.089 45.000 0.00 0.00 0.00 5.69
5489 5903 7.716612 AGATTGTTTTCTGTCCTTTCGAAATT 58.283 30.769 11.70 0.00 0.00 1.82
5567 5981 5.435686 TGGATAGTAATGGCTGAGTTTGT 57.564 39.130 0.00 0.00 0.00 2.83
5568 5982 5.185454 TGGATAGTAATGGCTGAGTTTGTG 58.815 41.667 0.00 0.00 0.00 3.33
5569 5983 4.576463 GGATAGTAATGGCTGAGTTTGTGG 59.424 45.833 0.00 0.00 0.00 4.17
5570 5984 2.162681 AGTAATGGCTGAGTTTGTGGC 58.837 47.619 0.00 0.00 0.00 5.01
5571 5985 1.202348 GTAATGGCTGAGTTTGTGGCC 59.798 52.381 0.00 0.00 44.31 5.36
5573 5987 3.854856 GGCTGAGTTTGTGGCCAA 58.145 55.556 7.24 0.00 43.59 4.52
5574 5988 2.354902 GGCTGAGTTTGTGGCCAAT 58.645 52.632 7.24 0.00 43.59 3.16
5575 5989 0.681175 GGCTGAGTTTGTGGCCAATT 59.319 50.000 7.24 0.00 43.59 2.32
5576 5990 1.606224 GGCTGAGTTTGTGGCCAATTG 60.606 52.381 7.24 0.00 43.59 2.32
5577 5991 1.606224 GCTGAGTTTGTGGCCAATTGG 60.606 52.381 20.81 20.81 38.53 3.16
5578 5992 1.688197 CTGAGTTTGTGGCCAATTGGT 59.312 47.619 25.19 2.83 37.57 3.67
5579 5993 1.686052 TGAGTTTGTGGCCAATTGGTC 59.314 47.619 22.59 22.59 41.09 4.02
5585 5999 2.744062 TGGCCAATTGGTCAGGTTG 58.256 52.632 27.81 0.00 46.36 3.77
5586 6000 0.105760 TGGCCAATTGGTCAGGTTGT 60.106 50.000 27.81 0.00 46.36 3.32
5587 6001 1.047801 GGCCAATTGGTCAGGTTGTT 58.952 50.000 24.31 0.00 40.23 2.83
5588 6002 1.270252 GGCCAATTGGTCAGGTTGTTG 60.270 52.381 24.31 0.00 40.23 3.33
5589 6003 1.270252 GCCAATTGGTCAGGTTGTTGG 60.270 52.381 25.19 0.00 39.20 3.77
5590 6004 1.270252 CCAATTGGTCAGGTTGTTGGC 60.270 52.381 16.90 0.00 30.91 4.52
5591 6005 1.688197 CAATTGGTCAGGTTGTTGGCT 59.312 47.619 0.00 0.00 0.00 4.75
5592 6006 2.890311 CAATTGGTCAGGTTGTTGGCTA 59.110 45.455 0.00 0.00 0.00 3.93
5593 6007 2.270352 TTGGTCAGGTTGTTGGCTAG 57.730 50.000 0.00 0.00 0.00 3.42
5594 6008 1.136828 TGGTCAGGTTGTTGGCTAGT 58.863 50.000 0.00 0.00 0.00 2.57
5595 6009 2.331166 TGGTCAGGTTGTTGGCTAGTA 58.669 47.619 0.00 0.00 0.00 1.82
5596 6010 2.706723 TGGTCAGGTTGTTGGCTAGTAA 59.293 45.455 0.00 0.00 0.00 2.24
5597 6011 3.329520 TGGTCAGGTTGTTGGCTAGTAAT 59.670 43.478 0.00 0.00 0.00 1.89
5598 6012 3.689649 GGTCAGGTTGTTGGCTAGTAATG 59.310 47.826 0.00 0.00 0.00 1.90
5599 6013 3.689649 GTCAGGTTGTTGGCTAGTAATGG 59.310 47.826 0.00 0.00 0.00 3.16
5600 6014 2.423538 CAGGTTGTTGGCTAGTAATGGC 59.576 50.000 0.00 0.00 0.00 4.40
5601 6015 2.308866 AGGTTGTTGGCTAGTAATGGCT 59.691 45.455 0.00 0.00 0.00 4.75
5602 6016 2.423538 GGTTGTTGGCTAGTAATGGCTG 59.576 50.000 0.00 0.00 0.00 4.85
5615 6029 7.042389 GCTAGTAATGGCTGAGTTTGAAGATAC 60.042 40.741 0.00 0.00 0.00 2.24
5627 6041 4.985538 TTGAAGATACGAAGGACCTCTC 57.014 45.455 0.00 0.00 0.00 3.20
5628 6042 3.288964 TGAAGATACGAAGGACCTCTCC 58.711 50.000 0.00 0.00 36.71 3.71
5640 6054 4.230455 AGGACCTCTCCTTGATTCATAGG 58.770 47.826 0.00 7.98 45.77 2.57
5683 6098 3.981212 GATTGAAATCCTTTCCTCCCCA 58.019 45.455 0.00 0.00 38.90 4.96
5684 6099 3.456380 TTGAAATCCTTTCCTCCCCAG 57.544 47.619 0.00 0.00 38.90 4.45
5685 6100 2.642982 TGAAATCCTTTCCTCCCCAGA 58.357 47.619 0.00 0.00 38.90 3.86
5686 6101 2.993146 TGAAATCCTTTCCTCCCCAGAA 59.007 45.455 0.00 0.00 38.90 3.02
5687 6102 3.401002 TGAAATCCTTTCCTCCCCAGAAA 59.599 43.478 0.00 0.00 38.90 2.52
5688 6103 3.458044 AATCCTTTCCTCCCCAGAAAC 57.542 47.619 0.00 0.00 0.00 2.78
5689 6104 1.073098 TCCTTTCCTCCCCAGAAACC 58.927 55.000 0.00 0.00 0.00 3.27
5690 6105 0.777446 CCTTTCCTCCCCAGAAACCA 59.223 55.000 0.00 0.00 0.00 3.67
5691 6106 1.272147 CCTTTCCTCCCCAGAAACCAG 60.272 57.143 0.00 0.00 0.00 4.00
5692 6107 1.705186 CTTTCCTCCCCAGAAACCAGA 59.295 52.381 0.00 0.00 0.00 3.86
5693 6108 1.362224 TTCCTCCCCAGAAACCAGAG 58.638 55.000 0.00 0.00 0.00 3.35
5694 6109 1.201429 TCCTCCCCAGAAACCAGAGC 61.201 60.000 0.00 0.00 0.00 4.09
5695 6110 1.301293 CTCCCCAGAAACCAGAGCC 59.699 63.158 0.00 0.00 0.00 4.70
5696 6111 2.203549 CTCCCCAGAAACCAGAGCCC 62.204 65.000 0.00 0.00 0.00 5.19
5697 6112 2.234296 CCCCAGAAACCAGAGCCCT 61.234 63.158 0.00 0.00 0.00 5.19
5698 6113 1.770324 CCCAGAAACCAGAGCCCTT 59.230 57.895 0.00 0.00 0.00 3.95
5699 6114 0.991920 CCCAGAAACCAGAGCCCTTA 59.008 55.000 0.00 0.00 0.00 2.69
5700 6115 1.065126 CCCAGAAACCAGAGCCCTTAG 60.065 57.143 0.00 0.00 0.00 2.18
5701 6116 1.065126 CCAGAAACCAGAGCCCTTAGG 60.065 57.143 0.00 0.00 0.00 2.69
5709 6124 3.083997 AGCCCTTAGGGTCGCCTG 61.084 66.667 19.76 0.00 46.51 4.85
5710 6125 4.858680 GCCCTTAGGGTCGCCTGC 62.859 72.222 19.76 0.00 46.51 4.85
5711 6126 3.083997 CCCTTAGGGTCGCCTGCT 61.084 66.667 9.64 0.00 38.25 4.24
5712 6127 2.670148 CCCTTAGGGTCGCCTGCTT 61.670 63.158 9.64 0.00 38.25 3.91
5713 6128 1.335132 CCCTTAGGGTCGCCTGCTTA 61.335 60.000 9.64 0.00 38.25 3.09
5714 6129 0.539986 CCTTAGGGTCGCCTGCTTAA 59.460 55.000 0.00 0.00 0.00 1.85
5715 6130 1.141053 CCTTAGGGTCGCCTGCTTAAT 59.859 52.381 0.00 0.00 0.00 1.40
5716 6131 2.367567 CCTTAGGGTCGCCTGCTTAATA 59.632 50.000 0.00 0.00 0.00 0.98
5717 6132 3.391049 CTTAGGGTCGCCTGCTTAATAC 58.609 50.000 0.00 0.00 0.00 1.89
5718 6133 0.104304 AGGGTCGCCTGCTTAATACG 59.896 55.000 0.00 0.00 0.00 3.06
5719 6134 1.496403 GGGTCGCCTGCTTAATACGC 61.496 60.000 0.00 0.00 0.00 4.42
5720 6135 1.558383 GTCGCCTGCTTAATACGCG 59.442 57.895 3.53 3.53 44.00 6.01
5721 6136 1.590525 TCGCCTGCTTAATACGCGG 60.591 57.895 12.47 0.00 42.92 6.46
5722 6137 1.590525 CGCCTGCTTAATACGCGGA 60.591 57.895 12.47 0.00 39.20 5.54
5723 6138 1.149361 CGCCTGCTTAATACGCGGAA 61.149 55.000 12.47 0.00 39.20 4.30
5724 6139 1.011333 GCCTGCTTAATACGCGGAAA 58.989 50.000 12.47 0.00 35.81 3.13
5725 6140 1.399089 GCCTGCTTAATACGCGGAAAA 59.601 47.619 12.47 0.00 35.81 2.29
5726 6141 2.790123 GCCTGCTTAATACGCGGAAAAC 60.790 50.000 12.47 0.00 35.81 2.43
5727 6142 2.223180 CCTGCTTAATACGCGGAAAACC 60.223 50.000 12.47 0.00 35.81 3.27
5728 6143 2.417239 CTGCTTAATACGCGGAAAACCA 59.583 45.455 12.47 0.00 35.81 3.67
5729 6144 2.417239 TGCTTAATACGCGGAAAACCAG 59.583 45.455 12.47 0.00 0.00 4.00
5730 6145 2.223180 GCTTAATACGCGGAAAACCAGG 60.223 50.000 12.47 0.00 0.00 4.45
5731 6146 2.766345 TAATACGCGGAAAACCAGGT 57.234 45.000 12.47 0.00 0.00 4.00
5732 6147 1.161843 AATACGCGGAAAACCAGGTG 58.838 50.000 12.47 0.00 0.00 4.00
5733 6148 0.322322 ATACGCGGAAAACCAGGTGA 59.678 50.000 12.47 0.00 0.00 4.02
5734 6149 0.106335 TACGCGGAAAACCAGGTGAA 59.894 50.000 12.47 0.00 0.00 3.18
5735 6150 0.748729 ACGCGGAAAACCAGGTGAAA 60.749 50.000 12.47 0.00 0.00 2.69
5736 6151 0.317519 CGCGGAAAACCAGGTGAAAC 60.318 55.000 0.00 0.00 0.00 2.78
5737 6152 1.029681 GCGGAAAACCAGGTGAAACT 58.970 50.000 0.00 0.00 36.74 2.66
5738 6153 1.269051 GCGGAAAACCAGGTGAAACTG 60.269 52.381 0.00 0.00 36.74 3.16
5744 6159 3.365265 CAGGTGAAACTGGCCGGC 61.365 66.667 21.18 21.18 36.74 6.13
5745 6160 3.570212 AGGTGAAACTGGCCGGCT 61.570 61.111 28.56 5.35 36.74 5.52
5746 6161 3.365265 GGTGAAACTGGCCGGCTG 61.365 66.667 28.56 21.44 36.74 4.85
5747 6162 2.281484 GTGAAACTGGCCGGCTGA 60.281 61.111 28.56 12.71 0.00 4.26
5748 6163 2.032528 TGAAACTGGCCGGCTGAG 59.967 61.111 28.56 23.76 0.00 3.35
5749 6164 2.747855 GAAACTGGCCGGCTGAGG 60.748 66.667 28.56 15.81 0.00 3.86
5750 6165 3.249189 AAACTGGCCGGCTGAGGA 61.249 61.111 28.56 4.41 0.00 3.71
5751 6166 2.748058 GAAACTGGCCGGCTGAGGAA 62.748 60.000 28.56 4.37 0.00 3.36
5752 6167 2.351924 AAACTGGCCGGCTGAGGAAA 62.352 55.000 28.56 2.50 0.00 3.13
5753 6168 2.034066 CTGGCCGGCTGAGGAAAA 59.966 61.111 28.56 1.03 0.00 2.29
5754 6169 2.282180 TGGCCGGCTGAGGAAAAC 60.282 61.111 28.56 6.48 0.00 2.43
5755 6170 3.062466 GGCCGGCTGAGGAAAACC 61.062 66.667 28.56 0.41 0.00 3.27
5756 6171 3.431725 GCCGGCTGAGGAAAACCG 61.432 66.667 22.15 0.00 45.21 4.44
5757 6172 2.032071 CCGGCTGAGGAAAACCGT 59.968 61.111 0.00 0.00 44.14 4.83
5758 6173 2.325082 CCGGCTGAGGAAAACCGTG 61.325 63.158 0.00 0.00 44.14 4.94
5759 6174 2.954611 GGCTGAGGAAAACCGTGC 59.045 61.111 0.00 0.00 0.00 5.34
5760 6175 2.556287 GCTGAGGAAAACCGTGCG 59.444 61.111 0.00 0.00 0.00 5.34
5761 6176 2.966309 GCTGAGGAAAACCGTGCGG 61.966 63.158 9.29 9.29 42.03 5.69
5762 6177 1.301401 CTGAGGAAAACCGTGCGGA 60.301 57.895 18.16 0.00 38.96 5.54
5763 6178 0.882927 CTGAGGAAAACCGTGCGGAA 60.883 55.000 18.16 0.00 38.96 4.30
5764 6179 1.161563 TGAGGAAAACCGTGCGGAAC 61.162 55.000 18.16 5.32 38.96 3.62
5765 6180 0.883370 GAGGAAAACCGTGCGGAACT 60.883 55.000 18.16 7.22 38.96 3.01
5766 6181 1.164041 AGGAAAACCGTGCGGAACTG 61.164 55.000 18.16 0.00 38.96 3.16
5767 6182 1.281656 GAAAACCGTGCGGAACTGG 59.718 57.895 18.16 0.00 38.96 4.00
5768 6183 1.441732 GAAAACCGTGCGGAACTGGT 61.442 55.000 18.16 0.00 37.30 4.00
5769 6184 1.033202 AAAACCGTGCGGAACTGGTT 61.033 50.000 18.16 8.86 43.16 3.67
5770 6185 1.720694 AAACCGTGCGGAACTGGTTG 61.721 55.000 18.16 0.00 41.63 3.77
5771 6186 4.025401 CCGTGCGGAACTGGTTGC 62.025 66.667 4.35 0.00 37.50 4.17
5772 6187 3.276091 CGTGCGGAACTGGTTGCA 61.276 61.111 5.88 0.89 34.44 4.08
5773 6188 2.829206 CGTGCGGAACTGGTTGCAA 61.829 57.895 0.00 0.00 39.34 4.08
5774 6189 1.299089 GTGCGGAACTGGTTGCAAC 60.299 57.895 21.59 21.59 39.34 4.17
5775 6190 1.750780 TGCGGAACTGGTTGCAACA 60.751 52.632 29.55 15.29 33.80 3.33
5776 6191 1.299089 GCGGAACTGGTTGCAACAC 60.299 57.895 29.55 19.16 0.00 3.32
5777 6192 1.010125 CGGAACTGGTTGCAACACG 60.010 57.895 29.55 21.02 0.00 4.49
5778 6193 1.299089 GGAACTGGTTGCAACACGC 60.299 57.895 29.55 13.98 42.89 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 59 2.671070 GCTTCTACAGGCAGGGCA 59.329 61.111 0.00 0.00 0.00 5.36
68 70 2.268298 GACAAAGGATTCGCGCTTCTA 58.732 47.619 5.56 0.00 0.00 2.10
89 91 2.686915 CAAGGTGATTCATGGCTCCTTC 59.313 50.000 11.78 0.00 36.24 3.46
114 116 0.707024 TGTTTATGATGGGGGTGCCA 59.293 50.000 0.00 0.00 0.00 4.92
116 118 1.688197 CCATGTTTATGATGGGGGTGC 59.312 52.381 0.00 0.00 37.33 5.01
161 163 6.931281 TCAAGAGAAGTAAGAAACTGTGATGG 59.069 38.462 0.00 0.00 38.88 3.51
181 183 3.133362 ACACCGTGAGTTTACCTTCAAGA 59.867 43.478 5.28 0.00 0.00 3.02
186 188 4.141642 ACCTTTACACCGTGAGTTTACCTT 60.142 41.667 5.28 0.00 0.00 3.50
209 211 3.955524 TGGGTCAAGGTTAAGGTGAAA 57.044 42.857 0.00 0.00 0.00 2.69
213 215 1.272480 GCCATGGGTCAAGGTTAAGGT 60.272 52.381 15.13 0.00 0.00 3.50
232 234 2.954611 GAACCTCGGCACCAAAGC 59.045 61.111 0.00 0.00 0.00 3.51
344 346 2.897271 AGTGTCATATGGCCCAACAA 57.103 45.000 4.54 0.00 0.00 2.83
347 349 1.824230 GCAAAGTGTCATATGGCCCAA 59.176 47.619 4.54 0.00 0.00 4.12
470 478 2.555227 CCTTCCAGGGCTTCTGCTTTTA 60.555 50.000 2.74 0.00 42.05 1.52
474 482 3.085223 CCTTCCAGGGCTTCTGCT 58.915 61.111 2.74 0.00 42.05 4.24
482 490 1.420430 TCGTATTAGGCCTTCCAGGG 58.580 55.000 12.58 0.00 35.37 4.45
494 502 2.278726 CGGCCCGCGTTCGTATTA 60.279 61.111 4.92 0.00 0.00 0.98
569 605 6.421377 AAATGGAAAACAGTTGTTTCTTGC 57.579 33.333 10.38 3.00 46.47 4.01
601 637 1.362355 GGGAAACAGTTGTTGGGCG 59.638 57.895 0.00 0.00 38.44 6.13
602 638 1.745890 GGGGAAACAGTTGTTGGGC 59.254 57.895 0.00 0.00 38.44 5.36
605 641 2.315176 TGATGGGGGAAACAGTTGTTG 58.685 47.619 0.00 0.00 38.44 3.33
607 643 2.557452 GGATGATGGGGGAAACAGTTGT 60.557 50.000 0.00 0.00 0.00 3.32
608 644 2.102578 GGATGATGGGGGAAACAGTTG 58.897 52.381 0.00 0.00 0.00 3.16
610 646 0.631212 GGGATGATGGGGGAAACAGT 59.369 55.000 0.00 0.00 0.00 3.55
710 747 4.767255 GGGAGGGAGTGTGCGCTG 62.767 72.222 9.73 0.00 0.00 5.18
933 1270 1.221840 GGAGGATTTGCAGCGGAGA 59.778 57.895 0.00 0.00 0.00 3.71
979 1318 0.899717 GGAGCAAAATCACCCTGCCA 60.900 55.000 0.00 0.00 36.73 4.92
1055 1394 0.322816 GGCATCAGAACCCTGCTTGA 60.323 55.000 0.00 0.00 40.20 3.02
1199 1538 2.418777 CATCTGGCGCATCTCGGA 59.581 61.111 10.83 1.87 38.94 4.55
1200 1539 3.344215 GCATCTGGCGCATCTCGG 61.344 66.667 10.83 0.00 38.94 4.63
1291 1630 5.290493 TCGGTACATCCTTCTGCAATAAT 57.710 39.130 0.00 0.00 0.00 1.28
1294 1633 3.470709 CATCGGTACATCCTTCTGCAAT 58.529 45.455 0.00 0.00 0.00 3.56
1296 1635 1.138859 CCATCGGTACATCCTTCTGCA 59.861 52.381 0.00 0.00 0.00 4.41
1329 1668 2.118076 CTTCCAAGCCCAAGCCCA 59.882 61.111 0.00 0.00 41.25 5.36
1349 1688 2.034879 GCCTTGCTGTCGCTGCTAA 61.035 57.895 0.00 3.43 36.97 3.09
1398 1737 0.612229 CATCTCCTGCTGTGACCAGT 59.388 55.000 0.00 0.00 41.02 4.00
1412 1751 1.467734 CAGAAGCACCAGCAACATCTC 59.532 52.381 0.00 0.00 45.49 2.75
1472 1811 7.849804 ACTATAAGCAGTACATGAAAAGTGG 57.150 36.000 0.00 0.00 0.00 4.00
1481 1821 6.495181 AGTGGCATCTACTATAAGCAGTACAT 59.505 38.462 0.00 0.00 0.00 2.29
1546 1886 4.020218 TCCGAGTTCACTGGATTCTGAAAT 60.020 41.667 0.00 0.00 0.00 2.17
1558 1898 5.360999 TGACATGATATTCTCCGAGTTCACT 59.639 40.000 0.00 0.00 0.00 3.41
1603 1946 4.034394 CACACCATTATCCTGTCGTTCATG 59.966 45.833 0.00 0.00 0.00 3.07
1609 1952 1.299541 GCCACACCATTATCCTGTCG 58.700 55.000 0.00 0.00 0.00 4.35
1644 1987 5.188359 AGAAATTGCCAAGCCATTCTGTATT 59.812 36.000 0.00 0.00 0.00 1.89
1687 2030 4.104086 TCTTTATCAAGAGGAGGAAGGCA 58.896 43.478 0.00 0.00 33.80 4.75
1718 2061 3.395941 ACCCCAGACAAGATCAGAAACTT 59.604 43.478 0.00 0.00 0.00 2.66
1953 2296 5.931532 AGTTCTTCAAGTGCATAATTGACG 58.068 37.500 10.42 9.41 40.23 4.35
2313 2656 3.184382 TCCTCAACCACTACATCCTCA 57.816 47.619 0.00 0.00 0.00 3.86
2340 2683 1.003580 GGAGGAGGCACTTCAATGACA 59.996 52.381 0.00 0.00 41.55 3.58
2345 2688 0.979665 CTCTGGAGGAGGCACTTCAA 59.020 55.000 0.00 0.00 41.55 2.69
2602 2945 3.907474 TCATTCTGGGACTTTACAGTGGA 59.093 43.478 0.00 0.00 36.17 4.02
2606 2949 7.414098 CGGTATTTTCATTCTGGGACTTTACAG 60.414 40.741 0.00 0.00 36.07 2.74
2609 2952 5.355910 GCGGTATTTTCATTCTGGGACTTTA 59.644 40.000 0.00 0.00 0.00 1.85
2790 3133 2.499693 TGCCGAGAAGTTGTATCCATCA 59.500 45.455 0.00 0.00 0.00 3.07
2900 3243 4.748239 GCAAAACCCTCTTCTTTCTCCTCT 60.748 45.833 0.00 0.00 0.00 3.69
3094 3437 5.599999 TGTATCTCTTTCTTAGGAGCCAC 57.400 43.478 0.00 0.00 0.00 5.01
3330 3673 9.777297 ATTTTAATGGTATTTGTGCTCTTTTGT 57.223 25.926 0.00 0.00 0.00 2.83
3348 3691 7.578736 GCACGTTTCTTGAACACAATTTTAATG 59.421 33.333 0.00 0.00 38.18 1.90
3369 3712 0.877071 CCTTTTCAGCATCAGCACGT 59.123 50.000 0.00 0.00 45.49 4.49
3448 3791 6.042093 TCTCCTAGAGAAAACGGCATATTCAT 59.958 38.462 0.00 0.00 35.59 2.57
3606 3952 6.043243 TCACTTGGACCTAGAGAAAAGACATT 59.957 38.462 10.12 0.00 0.00 2.71
3858 4270 4.309099 TGATTTTCCATTGTTTGCTCAGC 58.691 39.130 0.00 0.00 0.00 4.26
4001 4413 5.007034 TCTGGTTGAACTTTTGAAGTGTCA 58.993 37.500 0.00 0.00 41.91 3.58
4051 4463 4.368391 CAGTGTCCGCTTCTGCTT 57.632 55.556 0.00 0.00 36.97 3.91
4094 4506 3.181476 GCTTTTTCAACCCAGCTTCTTGA 60.181 43.478 0.00 0.00 0.00 3.02
4122 4534 1.691196 TCAGCAGTTTTGGGTTCCAG 58.309 50.000 0.00 0.00 33.81 3.86
4170 4582 4.016444 TCTTCCACTTGAACAGTTTGCTT 58.984 39.130 0.00 0.00 30.92 3.91
4378 4790 0.656259 CAGTGATTCAGCTGCATCCG 59.344 55.000 21.37 8.19 0.00 4.18
4469 4881 1.988015 ACCTTGGGTGGACATACCG 59.012 57.895 0.00 0.00 41.79 4.02
4521 4933 1.134848 TGCTGTTTTCCCAGTTGTTGC 60.135 47.619 0.00 0.00 34.84 4.17
4532 4944 0.868406 CGACACCCTCTGCTGTTTTC 59.132 55.000 0.00 0.00 0.00 2.29
4538 4950 0.830444 TAACACCGACACCCTCTGCT 60.830 55.000 0.00 0.00 0.00 4.24
4562 4974 1.749634 GCTGTAGCCTTCTTACCTCGA 59.250 52.381 0.00 0.00 34.31 4.04
4581 4993 2.079925 CTCTACAGGTTTCTTGGCTGC 58.920 52.381 0.00 0.00 0.00 5.25
4639 5051 1.479389 CCTCCACTGGTTTCTTGGCTT 60.479 52.381 0.00 0.00 0.00 4.35
4667 5079 3.417275 CTCATCCCGCGCTTCGACT 62.417 63.158 5.56 0.00 41.67 4.18
4694 5106 0.031178 CTGCGCTTTTCTTGGCTGTT 59.969 50.000 9.73 0.00 0.00 3.16
4724 5136 3.417275 CTCATCCGGCGCTTCGACT 62.417 63.158 7.64 0.00 29.68 4.18
4758 5170 1.414181 CTATGCCATGTCGTCCTCCTT 59.586 52.381 0.00 0.00 0.00 3.36
4768 5180 0.848735 ATCAGCCACCTATGCCATGT 59.151 50.000 0.00 0.00 0.00 3.21
4780 5192 4.051167 CCACCTGCCCATCAGCCA 62.051 66.667 0.00 0.00 41.50 4.75
4853 5265 3.017048 TGGGCAGATTGATTACCTTGG 57.983 47.619 0.00 0.00 0.00 3.61
4864 5276 0.322546 GAGAACCGGTTGGGCAGATT 60.323 55.000 27.87 0.00 40.62 2.40
4896 5308 5.872617 CCGTCTGTTCCTATACAAAACATGA 59.127 40.000 0.00 0.00 32.85 3.07
4924 5336 0.387202 CGATGCTAGGGTCAGACAGG 59.613 60.000 2.17 0.00 0.00 4.00
4948 5360 3.197983 ACTGCCTTAGCTAACCTAACAGG 59.802 47.826 0.86 1.31 39.97 4.00
4996 5408 3.582208 ACCCTAGATGATTGATGGAGCTC 59.418 47.826 4.71 4.71 0.00 4.09
5036 5448 0.250901 AAGTTCCGCAACAGCTCCAT 60.251 50.000 0.00 0.00 34.60 3.41
5037 5449 0.884704 GAAGTTCCGCAACAGCTCCA 60.885 55.000 0.00 0.00 34.60 3.86
5078 5490 6.566197 CTGATTCAGGATGCTAATTAACCC 57.434 41.667 5.73 0.00 34.76 4.11
5192 5605 9.345517 CCAGTTTACAAATGACAATTCATACAG 57.654 33.333 0.00 0.00 42.00 2.74
5256 5669 2.228138 AAAACACAAGAGTCGCGGTA 57.772 45.000 6.13 0.00 0.00 4.02
5257 5670 1.329599 GAAAAACACAAGAGTCGCGGT 59.670 47.619 6.13 0.00 0.00 5.68
5258 5671 1.597663 AGAAAAACACAAGAGTCGCGG 59.402 47.619 6.13 0.00 0.00 6.46
5261 5674 6.583912 TCTGTAAGAAAAACACAAGAGTCG 57.416 37.500 0.00 0.00 42.31 4.18
5279 5692 2.401583 ATGTGCAAGCGGAATCTGTA 57.598 45.000 0.00 0.00 0.00 2.74
5295 5708 7.862512 AAAAATGTTGGTCACAAATCAATGT 57.137 28.000 0.00 0.00 39.50 2.71
5332 5746 2.041216 ACCAGGAATAAAAAGGGCGAGT 59.959 45.455 0.00 0.00 0.00 4.18
5334 5748 2.442413 CACCAGGAATAAAAAGGGCGA 58.558 47.619 0.00 0.00 0.00 5.54
5339 5753 5.770162 ACAGAGAACCACCAGGAATAAAAAG 59.230 40.000 0.00 0.00 38.69 2.27
5341 5755 5.070001 CACAGAGAACCACCAGGAATAAAA 58.930 41.667 0.00 0.00 38.69 1.52
5358 5772 2.099592 TGCTCAAACCAAAAGCACAGAG 59.900 45.455 0.00 0.00 40.91 3.35
5359 5773 2.098614 TGCTCAAACCAAAAGCACAGA 58.901 42.857 0.00 0.00 40.91 3.41
5402 5816 4.937201 ATTCTACCATGCGAGTACATCA 57.063 40.909 0.00 0.00 0.00 3.07
5435 5849 6.032956 TGCCGTCTTGTCTCTCTTTTATTA 57.967 37.500 0.00 0.00 0.00 0.98
5437 5851 4.537135 TGCCGTCTTGTCTCTCTTTTAT 57.463 40.909 0.00 0.00 0.00 1.40
5438 5852 4.330944 TTGCCGTCTTGTCTCTCTTTTA 57.669 40.909 0.00 0.00 0.00 1.52
5442 5856 3.409026 AATTTGCCGTCTTGTCTCTCT 57.591 42.857 0.00 0.00 0.00 3.10
5443 5857 4.929808 TCTAAATTTGCCGTCTTGTCTCTC 59.070 41.667 0.00 0.00 0.00 3.20
5458 5872 9.463443 CGAAAGGACAGAAAACAATCTAAATTT 57.537 29.630 0.00 0.00 0.00 1.82
5489 5903 2.237143 CCAGACTGAAGTCCAGCCATAA 59.763 50.000 3.32 0.00 46.81 1.90
5509 5923 1.305930 GCCACAATCGTCAAGTCCCC 61.306 60.000 0.00 0.00 0.00 4.81
5510 5924 1.305930 GGCCACAATCGTCAAGTCCC 61.306 60.000 0.00 0.00 0.00 4.46
5517 5931 0.887933 ACCAATTGGCCACAATCGTC 59.112 50.000 24.79 0.00 46.25 4.20
5519 5933 0.887247 TGACCAATTGGCCACAATCG 59.113 50.000 24.79 0.00 46.25 3.34
5567 5981 0.105760 ACAACCTGACCAATTGGCCA 60.106 50.000 24.79 18.99 39.32 5.36
5568 5982 1.047801 AACAACCTGACCAATTGGCC 58.952 50.000 24.79 14.75 39.32 5.36
5569 5983 1.270252 CCAACAACCTGACCAATTGGC 60.270 52.381 24.79 16.89 39.32 4.52
5570 5984 1.270252 GCCAACAACCTGACCAATTGG 60.270 52.381 23.31 23.31 39.69 3.16
5571 5985 1.688197 AGCCAACAACCTGACCAATTG 59.312 47.619 0.00 0.00 0.00 2.32
5572 5986 2.086610 AGCCAACAACCTGACCAATT 57.913 45.000 0.00 0.00 0.00 2.32
5573 5987 2.108250 ACTAGCCAACAACCTGACCAAT 59.892 45.455 0.00 0.00 0.00 3.16
5574 5988 1.493022 ACTAGCCAACAACCTGACCAA 59.507 47.619 0.00 0.00 0.00 3.67
5575 5989 1.136828 ACTAGCCAACAACCTGACCA 58.863 50.000 0.00 0.00 0.00 4.02
5576 5990 3.412237 TTACTAGCCAACAACCTGACC 57.588 47.619 0.00 0.00 0.00 4.02
5577 5991 3.689649 CCATTACTAGCCAACAACCTGAC 59.310 47.826 0.00 0.00 0.00 3.51
5578 5992 3.872240 GCCATTACTAGCCAACAACCTGA 60.872 47.826 0.00 0.00 0.00 3.86
5579 5993 2.423538 GCCATTACTAGCCAACAACCTG 59.576 50.000 0.00 0.00 0.00 4.00
5580 5994 2.308866 AGCCATTACTAGCCAACAACCT 59.691 45.455 0.00 0.00 0.00 3.50
5581 5995 2.423538 CAGCCATTACTAGCCAACAACC 59.576 50.000 0.00 0.00 0.00 3.77
5582 5996 3.343617 TCAGCCATTACTAGCCAACAAC 58.656 45.455 0.00 0.00 0.00 3.32
5583 5997 3.009033 ACTCAGCCATTACTAGCCAACAA 59.991 43.478 0.00 0.00 0.00 2.83
5584 5998 2.571653 ACTCAGCCATTACTAGCCAACA 59.428 45.455 0.00 0.00 0.00 3.33
5585 5999 3.268023 ACTCAGCCATTACTAGCCAAC 57.732 47.619 0.00 0.00 0.00 3.77
5586 6000 4.009675 CAAACTCAGCCATTACTAGCCAA 58.990 43.478 0.00 0.00 0.00 4.52
5587 6001 3.263170 TCAAACTCAGCCATTACTAGCCA 59.737 43.478 0.00 0.00 0.00 4.75
5588 6002 3.873910 TCAAACTCAGCCATTACTAGCC 58.126 45.455 0.00 0.00 0.00 3.93
5589 6003 5.178797 TCTTCAAACTCAGCCATTACTAGC 58.821 41.667 0.00 0.00 0.00 3.42
5590 6004 7.168302 CGTATCTTCAAACTCAGCCATTACTAG 59.832 40.741 0.00 0.00 0.00 2.57
5591 6005 6.978659 CGTATCTTCAAACTCAGCCATTACTA 59.021 38.462 0.00 0.00 0.00 1.82
5592 6006 5.812642 CGTATCTTCAAACTCAGCCATTACT 59.187 40.000 0.00 0.00 0.00 2.24
5593 6007 5.810587 TCGTATCTTCAAACTCAGCCATTAC 59.189 40.000 0.00 0.00 0.00 1.89
5594 6008 5.972935 TCGTATCTTCAAACTCAGCCATTA 58.027 37.500 0.00 0.00 0.00 1.90
5595 6009 4.832248 TCGTATCTTCAAACTCAGCCATT 58.168 39.130 0.00 0.00 0.00 3.16
5596 6010 4.471904 TCGTATCTTCAAACTCAGCCAT 57.528 40.909 0.00 0.00 0.00 4.40
5597 6011 3.953712 TCGTATCTTCAAACTCAGCCA 57.046 42.857 0.00 0.00 0.00 4.75
5598 6012 3.619038 CCTTCGTATCTTCAAACTCAGCC 59.381 47.826 0.00 0.00 0.00 4.85
5599 6013 4.327627 GTCCTTCGTATCTTCAAACTCAGC 59.672 45.833 0.00 0.00 0.00 4.26
5600 6014 4.865365 GGTCCTTCGTATCTTCAAACTCAG 59.135 45.833 0.00 0.00 0.00 3.35
5601 6015 4.527038 AGGTCCTTCGTATCTTCAAACTCA 59.473 41.667 0.00 0.00 0.00 3.41
5602 6016 5.074584 AGGTCCTTCGTATCTTCAAACTC 57.925 43.478 0.00 0.00 0.00 3.01
5627 6041 6.483307 TGCTACGAAAATCCTATGAATCAAGG 59.517 38.462 0.00 5.49 0.00 3.61
5628 6042 7.482654 TGCTACGAAAATCCTATGAATCAAG 57.517 36.000 0.00 0.00 0.00 3.02
5640 6054 8.375465 CAATCCTTCAAAATTGCTACGAAAATC 58.625 33.333 0.00 0.00 0.00 2.17
5675 6090 1.201429 GCTCTGGTTTCTGGGGAGGA 61.201 60.000 0.00 0.00 0.00 3.71
5676 6091 1.301293 GCTCTGGTTTCTGGGGAGG 59.699 63.158 0.00 0.00 0.00 4.30
5677 6092 1.301293 GGCTCTGGTTTCTGGGGAG 59.699 63.158 0.00 0.00 0.00 4.30
5678 6093 2.231380 GGGCTCTGGTTTCTGGGGA 61.231 63.158 0.00 0.00 0.00 4.81
5679 6094 1.793820 AAGGGCTCTGGTTTCTGGGG 61.794 60.000 0.00 0.00 0.00 4.96
5680 6095 0.991920 TAAGGGCTCTGGTTTCTGGG 59.008 55.000 0.00 0.00 0.00 4.45
5681 6096 1.065126 CCTAAGGGCTCTGGTTTCTGG 60.065 57.143 0.00 0.00 0.00 3.86
5682 6097 1.065126 CCCTAAGGGCTCTGGTTTCTG 60.065 57.143 0.00 0.00 35.35 3.02
5683 6098 1.290134 CCCTAAGGGCTCTGGTTTCT 58.710 55.000 0.00 0.00 35.35 2.52
5684 6099 3.884226 CCCTAAGGGCTCTGGTTTC 57.116 57.895 0.00 0.00 35.35 2.78
5695 6110 0.539986 TTAAGCAGGCGACCCTAAGG 59.460 55.000 0.00 0.00 40.33 2.69
5696 6111 2.622064 ATTAAGCAGGCGACCCTAAG 57.378 50.000 0.00 0.00 40.33 2.18
5697 6112 2.223876 CGTATTAAGCAGGCGACCCTAA 60.224 50.000 0.00 0.00 40.33 2.69
5698 6113 1.338973 CGTATTAAGCAGGCGACCCTA 59.661 52.381 0.00 0.00 40.33 3.53
5699 6114 0.104304 CGTATTAAGCAGGCGACCCT 59.896 55.000 0.00 0.00 44.25 4.34
5700 6115 1.496403 GCGTATTAAGCAGGCGACCC 61.496 60.000 0.00 0.00 34.19 4.46
5701 6116 1.932277 GCGTATTAAGCAGGCGACC 59.068 57.895 0.00 0.00 34.19 4.79
5704 6119 1.149361 TTCCGCGTATTAAGCAGGCG 61.149 55.000 15.90 15.90 46.61 5.52
5705 6120 1.011333 TTTCCGCGTATTAAGCAGGC 58.989 50.000 4.92 0.00 34.19 4.85
5706 6121 2.223180 GGTTTTCCGCGTATTAAGCAGG 60.223 50.000 4.92 4.72 34.19 4.85
5707 6122 2.417239 TGGTTTTCCGCGTATTAAGCAG 59.583 45.455 4.92 0.00 44.36 4.24
5708 6123 2.417239 CTGGTTTTCCGCGTATTAAGCA 59.583 45.455 4.92 8.58 44.36 3.91
5709 6124 2.223180 CCTGGTTTTCCGCGTATTAAGC 60.223 50.000 4.92 4.13 44.36 3.09
5710 6125 3.004862 ACCTGGTTTTCCGCGTATTAAG 58.995 45.455 4.92 0.00 44.36 1.85
5711 6126 2.743126 CACCTGGTTTTCCGCGTATTAA 59.257 45.455 4.92 0.00 44.36 1.40
5712 6127 2.028294 TCACCTGGTTTTCCGCGTATTA 60.028 45.455 4.92 0.00 44.36 0.98
5713 6128 1.161843 CACCTGGTTTTCCGCGTATT 58.838 50.000 4.92 0.00 44.36 1.89
5714 6129 0.322322 TCACCTGGTTTTCCGCGTAT 59.678 50.000 4.92 0.00 44.36 3.06
5715 6130 0.106335 TTCACCTGGTTTTCCGCGTA 59.894 50.000 4.92 0.00 44.36 4.42
5716 6131 0.748729 TTTCACCTGGTTTTCCGCGT 60.749 50.000 4.92 0.00 44.36 6.01
5717 6132 0.317519 GTTTCACCTGGTTTTCCGCG 60.318 55.000 0.00 0.00 44.36 6.46
5718 6133 1.029681 AGTTTCACCTGGTTTTCCGC 58.970 50.000 0.00 0.00 44.36 5.54
5719 6134 1.336755 CCAGTTTCACCTGGTTTTCCG 59.663 52.381 0.00 0.00 45.81 4.30
5727 6142 3.365265 GCCGGCCAGTTTCACCTG 61.365 66.667 18.11 0.00 0.00 4.00
5728 6143 3.570212 AGCCGGCCAGTTTCACCT 61.570 61.111 26.15 0.00 0.00 4.00
5729 6144 3.365265 CAGCCGGCCAGTTTCACC 61.365 66.667 26.15 0.00 0.00 4.02
5730 6145 2.281484 TCAGCCGGCCAGTTTCAC 60.281 61.111 26.15 0.00 0.00 3.18
5731 6146 2.032528 CTCAGCCGGCCAGTTTCA 59.967 61.111 26.15 0.00 0.00 2.69
5732 6147 2.747855 CCTCAGCCGGCCAGTTTC 60.748 66.667 26.15 0.00 0.00 2.78
5733 6148 2.351924 TTTCCTCAGCCGGCCAGTTT 62.352 55.000 26.15 0.00 0.00 2.66
5734 6149 2.351924 TTTTCCTCAGCCGGCCAGTT 62.352 55.000 26.15 0.00 0.00 3.16
5735 6150 2.829384 TTTTCCTCAGCCGGCCAGT 61.829 57.895 26.15 0.18 0.00 4.00
5736 6151 2.034066 TTTTCCTCAGCCGGCCAG 59.966 61.111 26.15 19.65 0.00 4.85
5737 6152 2.282180 GTTTTCCTCAGCCGGCCA 60.282 61.111 26.15 9.57 0.00 5.36
5738 6153 3.062466 GGTTTTCCTCAGCCGGCC 61.062 66.667 26.15 5.07 36.94 6.13
5739 6154 3.431725 CGGTTTTCCTCAGCCGGC 61.432 66.667 21.89 21.89 40.45 6.13
5742 6157 2.954611 GCACGGTTTTCCTCAGCC 59.045 61.111 0.00 0.00 37.95 4.85
5743 6158 2.556287 CGCACGGTTTTCCTCAGC 59.444 61.111 0.00 0.00 37.95 4.26
5744 6159 0.882927 TTCCGCACGGTTTTCCTCAG 60.883 55.000 9.23 0.00 37.95 3.35
5745 6160 1.146485 TTCCGCACGGTTTTCCTCA 59.854 52.632 9.23 0.00 37.95 3.86
5746 6161 0.883370 AGTTCCGCACGGTTTTCCTC 60.883 55.000 9.23 0.00 37.95 3.71
5747 6162 1.147600 AGTTCCGCACGGTTTTCCT 59.852 52.632 9.23 0.00 37.95 3.36
5748 6163 1.281656 CAGTTCCGCACGGTTTTCC 59.718 57.895 9.23 0.00 36.47 3.13
5749 6164 1.281656 CCAGTTCCGCACGGTTTTC 59.718 57.895 9.23 0.00 36.47 2.29
5750 6165 1.033202 AACCAGTTCCGCACGGTTTT 61.033 50.000 9.23 0.00 38.40 2.43
5751 6166 1.452470 AACCAGTTCCGCACGGTTT 60.452 52.632 9.23 0.00 38.40 3.27
5752 6167 2.184167 CAACCAGTTCCGCACGGTT 61.184 57.895 9.23 0.00 40.65 4.44
5753 6168 2.590575 CAACCAGTTCCGCACGGT 60.591 61.111 9.23 0.00 34.82 4.83
5754 6169 4.025401 GCAACCAGTTCCGCACGG 62.025 66.667 1.73 1.73 0.00 4.94
5755 6170 2.829206 TTGCAACCAGTTCCGCACG 61.829 57.895 0.00 0.00 33.29 5.34
5756 6171 1.299089 GTTGCAACCAGTTCCGCAC 60.299 57.895 19.15 0.00 33.29 5.34
5757 6172 1.750780 TGTTGCAACCAGTTCCGCA 60.751 52.632 26.14 1.62 0.00 5.69
5758 6173 1.299089 GTGTTGCAACCAGTTCCGC 60.299 57.895 26.14 2.91 0.00 5.54
5759 6174 1.010125 CGTGTTGCAACCAGTTCCG 60.010 57.895 26.14 14.07 0.00 4.30
5760 6175 1.299089 GCGTGTTGCAACCAGTTCC 60.299 57.895 26.14 5.68 45.45 3.62
5761 6176 4.302154 GCGTGTTGCAACCAGTTC 57.698 55.556 26.14 10.58 45.45 3.01


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

AutoCloner maintained by Alex Coulton.