Multiple sequence alignment - TraesCS3B01G240900

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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 TraesCS3B01G240900 chr3B 100.000 8638 0 0 1 8638 380002343 379993706 0.000000e+00 15952
1 TraesCS3B01G240900 chr3A 93.259 6809 298 56 22 6743 375825133 375818399 0.000000e+00 9882
2 TraesCS3B01G240900 chr3A 92.774 1896 75 22 6740 8600 375818243 375816375 0.000000e+00 2686
3 TraesCS3B01G240900 chr3D 95.240 5861 148 24 2440 8252 287058438 287052661 0.000000e+00 9156
4 TraesCS3B01G240900 chr3D 94.659 2434 85 23 5 2415 287060841 287058430 0.000000e+00 3733
5 TraesCS3B01G240900 chr3D 94.375 160 8 1 8480 8638 287029878 287029719 2.410000e-60 244
6 TraesCS3B01G240900 chr3D 85.039 127 17 2 8363 8488 287050356 287050231 2.530000e-25 128


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 TraesCS3B01G240900 chr3B 379993706 380002343 8637 True 15952 15952 100.0000 1 8638 1 chr3B.!!$R1 8637
1 TraesCS3B01G240900 chr3A 375816375 375825133 8758 True 6284 9882 93.0165 22 8600 2 chr3A.!!$R1 8578
2 TraesCS3B01G240900 chr3D 287050231 287060841 10610 True 4339 9156 91.6460 5 8488 3 chr3D.!!$R2 8483

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
513 520 0.106967 GGCTGATGGAGAAGGGGAAC 60.107 60.000 0.00 0.00 0.00 3.62 F
895 923 1.383248 CTCCCGATCCACCCTCCTT 60.383 63.158 0.00 0.00 0.00 3.36 F
1323 1356 1.683385 GGATGGAGTAAATGCCTTGGC 59.317 52.381 4.43 4.43 0.00 4.52 F
2186 2232 2.472695 TGAGATAGCTGCAACCGTTT 57.527 45.000 1.02 0.00 0.00 3.60 F
3536 3604 1.679944 GCTGGGTCTAGCTTTCATGCA 60.680 52.381 0.00 0.00 40.52 3.96 F
4317 4402 2.205022 TTCAGCAGGGAAGTCCATTG 57.795 50.000 0.00 0.00 38.24 2.82 F
5000 5094 0.925466 CTTACGGATGTTTACGCCCG 59.075 55.000 10.01 10.01 46.65 6.13 F
5805 5909 1.007479 ACCAAGAATGCCCCATCATGT 59.993 47.619 0.00 0.00 0.00 3.21 F
5806 5910 1.411246 CCAAGAATGCCCCATCATGTG 59.589 52.381 0.00 0.00 0.00 3.21 F
7400 7664 1.601663 CCTATCTCTGAAGCTTCGCCG 60.602 57.143 21.11 12.12 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2065 2108 1.271871 TGCCACCCATGTAAACCTCAG 60.272 52.381 0.00 0.00 0.00 3.35 R
2186 2232 2.543777 AGCGACTGTGCTTCCTTTAA 57.456 45.000 0.00 0.00 44.46 1.52 R
2564 2612 3.305110 GCCAATTTGGTTTGACAGTACG 58.695 45.455 16.62 0.00 40.46 3.67 R
3875 3956 0.970640 TTCCCGAACTCACCGATGAA 59.029 50.000 0.00 0.00 33.30 2.57 R
5000 5094 0.744771 GTCGATGTTTCCCCAGAGGC 60.745 60.000 0.00 0.00 34.51 4.70 R
5806 5910 1.008079 GCTGCACACAAGAGGCAAC 60.008 57.895 0.00 0.00 37.06 4.17 R
6841 7105 1.810606 CGTCCGGATCATCTCCCAGG 61.811 65.000 7.81 0.00 41.49 4.45 R
7516 7780 0.443869 CCCGACTGCATCAGTTTTCG 59.556 55.000 0.66 0.98 45.44 3.46 R
7631 7913 0.608130 ATACGCTGCCACTTCACTCA 59.392 50.000 0.00 0.00 0.00 3.41 R
8580 11089 0.107643 TTGGAGTTGTCGCATGGTGA 59.892 50.000 0.00 0.00 0.00 4.02 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
87 88 2.520069 TGTGTGTTCCTCTCTCTCTCC 58.480 52.381 0.00 0.00 0.00 3.71
91 92 2.025321 GTGTTCCTCTCTCTCTCCCTCT 60.025 54.545 0.00 0.00 0.00 3.69
92 93 2.241176 TGTTCCTCTCTCTCTCCCTCTC 59.759 54.545 0.00 0.00 0.00 3.20
94 95 2.787956 TCCTCTCTCTCTCCCTCTCAT 58.212 52.381 0.00 0.00 0.00 2.90
95 96 3.130450 TCCTCTCTCTCTCCCTCTCATT 58.870 50.000 0.00 0.00 0.00 2.57
96 97 3.531397 TCCTCTCTCTCTCCCTCTCATTT 59.469 47.826 0.00 0.00 0.00 2.32
97 98 4.016666 TCCTCTCTCTCTCCCTCTCATTTT 60.017 45.833 0.00 0.00 0.00 1.82
98 99 4.099881 CCTCTCTCTCTCCCTCTCATTTTG 59.900 50.000 0.00 0.00 0.00 2.44
99 100 4.029520 TCTCTCTCTCCCTCTCATTTTGG 58.970 47.826 0.00 0.00 0.00 3.28
100 101 2.503356 TCTCTCTCCCTCTCATTTTGGC 59.497 50.000 0.00 0.00 0.00 4.52
101 102 1.208052 TCTCTCCCTCTCATTTTGGCG 59.792 52.381 0.00 0.00 0.00 5.69
102 103 0.984230 TCTCCCTCTCATTTTGGCGT 59.016 50.000 0.00 0.00 0.00 5.68
112 113 0.814457 ATTTTGGCGTGTGTGTGTGT 59.186 45.000 0.00 0.00 0.00 3.72
120 121 1.065551 CGTGTGTGTGTGTGAGAGAGA 59.934 52.381 0.00 0.00 0.00 3.10
215 222 5.779241 TCCCTGACATTTCCTAATGACTT 57.221 39.130 4.99 0.00 43.12 3.01
235 242 0.931702 CTCTCTCGAGACGTGCGTAT 59.068 55.000 12.08 0.00 39.74 3.06
296 303 2.209273 CCATGTATTGGCGATTCACGA 58.791 47.619 0.00 0.00 44.44 4.35
314 321 1.982073 GAAAGCGATGGCCAACTCGG 61.982 60.000 25.76 11.12 41.24 4.63
417 424 1.374252 ACTGGCCACGTCGATTGAC 60.374 57.895 0.00 2.65 41.91 3.18
420 427 2.264794 GCCACGTCGATTGACCCT 59.735 61.111 7.54 0.00 42.37 4.34
441 448 0.969894 CTTGTGGAGACGGAGGAGTT 59.030 55.000 0.00 0.00 0.00 3.01
474 481 1.537202 CCGCAAGAGGGAAGAAACAAG 59.463 52.381 0.00 0.00 43.02 3.16
477 484 2.519013 CAAGAGGGAAGAAACAAGGGG 58.481 52.381 0.00 0.00 0.00 4.79
480 487 1.641192 GAGGGAAGAAACAAGGGGGAT 59.359 52.381 0.00 0.00 0.00 3.85
513 520 0.106967 GGCTGATGGAGAAGGGGAAC 60.107 60.000 0.00 0.00 0.00 3.62
561 568 7.271438 GGTTGTTTTCTCGCTTATTTCTTCATC 59.729 37.037 0.00 0.00 0.00 2.92
563 570 7.870826 TGTTTTCTCGCTTATTTCTTCATCAA 58.129 30.769 0.00 0.00 0.00 2.57
708 736 5.003804 ACAAGTGAGCAAATAATTCGACCT 58.996 37.500 0.00 0.00 0.00 3.85
895 923 1.383248 CTCCCGATCCACCCTCCTT 60.383 63.158 0.00 0.00 0.00 3.36
897 925 2.797278 CCCGATCCACCCTCCTTCG 61.797 68.421 0.00 0.00 0.00 3.79
1219 1252 4.072131 TCGCTTGCTCTTATTTTGTTCCT 58.928 39.130 0.00 0.00 0.00 3.36
1323 1356 1.683385 GGATGGAGTAAATGCCTTGGC 59.317 52.381 4.43 4.43 0.00 4.52
1400 1433 3.502356 TGTGTAGACGGGGATGCATATA 58.498 45.455 0.00 0.00 0.00 0.86
1681 1724 6.348132 CGTTGATATTGTGTTCAGTTGCCTTA 60.348 38.462 0.00 0.00 0.00 2.69
1684 1727 7.592938 TGATATTGTGTTCAGTTGCCTTAAAG 58.407 34.615 0.00 0.00 0.00 1.85
1721 1764 4.937620 TCAATCATCCAAACTCAGCTGTAC 59.062 41.667 14.67 0.00 0.00 2.90
1740 1783 6.734502 TGTACCCGGAATTGTCTGATAATA 57.265 37.500 0.73 0.00 30.94 0.98
2065 2108 4.770795 TCCTTGAGCTTCTGTTATTAGCC 58.229 43.478 0.00 0.00 35.53 3.93
2092 2135 4.161377 GGTTTACATGGGTGGCATGTTTAT 59.839 41.667 0.00 0.00 42.53 1.40
2186 2232 2.472695 TGAGATAGCTGCAACCGTTT 57.527 45.000 1.02 0.00 0.00 3.60
2195 2241 3.049912 GCTGCAACCGTTTTAAAGGAAG 58.950 45.455 1.38 0.00 0.00 3.46
2428 2474 7.289782 AGGATCACTATTTTCTGAGTATGCTCT 59.710 37.037 12.30 0.00 42.13 4.09
2437 2483 4.348486 TCTGAGTATGCTCTTCTTGAGGT 58.652 43.478 12.30 0.00 42.87 3.85
2439 2485 5.247110 TCTGAGTATGCTCTTCTTGAGGTTT 59.753 40.000 12.30 0.00 42.87 3.27
2461 2507 7.015877 GGTTTAACTGTTTCTATTCCCCCTTTT 59.984 37.037 0.00 0.00 0.00 2.27
2544 2592 4.397103 TGATGCCTTCTGAGCAAATACAAG 59.603 41.667 0.00 0.00 44.83 3.16
2545 2593 3.754965 TGCCTTCTGAGCAAATACAAGT 58.245 40.909 0.00 0.00 37.28 3.16
2586 2634 2.908688 ACTGTCAAACCAAATTGGCC 57.091 45.000 12.67 0.00 42.67 5.36
2606 2654 3.323243 CCCGTTGAGTTTTCGTGATAGT 58.677 45.455 0.00 0.00 0.00 2.12
2656 2704 9.959721 ATATAGTAAATACCTATGTTGGCCTTG 57.040 33.333 3.32 0.00 0.00 3.61
2805 2856 3.664107 TGTTGAAGAAGTTCCGGATGAG 58.336 45.455 4.15 0.00 0.00 2.90
2835 2886 2.099141 AGCGCTCTTTCAAGTATGCA 57.901 45.000 2.64 0.00 0.00 3.96
3271 3334 6.350629 TCTGATGTTGAGACTTCATCTTGA 57.649 37.500 13.41 10.25 38.70 3.02
3394 3457 8.279970 TGAATTATGTTCAGGTATTCCTTGTG 57.720 34.615 0.00 0.00 43.07 3.33
3536 3604 1.679944 GCTGGGTCTAGCTTTCATGCA 60.680 52.381 0.00 0.00 40.52 3.96
3694 3765 8.594881 CATCTGTAATGGAGGTAAGATGTAAC 57.405 38.462 0.00 0.00 37.38 2.50
3730 3811 2.987413 TTGATGTTTTGGCTGCTACG 57.013 45.000 0.00 0.00 0.00 3.51
3806 3887 5.545335 TGGTGCTGATGAGACCATATATTCT 59.455 40.000 0.00 0.00 34.75 2.40
3875 3956 6.582636 TGGAATGATCGCAGATAAGTTTAGT 58.417 36.000 0.00 0.00 45.12 2.24
3889 3970 7.760340 AGATAAGTTTAGTTCATCGGTGAGTTC 59.240 37.037 0.00 0.00 35.39 3.01
3940 4022 8.720562 GCATTTATTTGTTTATCTTGCCTTGTT 58.279 29.630 0.00 0.00 0.00 2.83
4006 4089 7.707893 GCATACAAACCTAGCATTTCATTTGAT 59.292 33.333 0.00 0.00 32.63 2.57
4125 4209 9.066892 TGTTTCTAGCAGAAATTTGACATACTT 57.933 29.630 12.42 0.00 44.94 2.24
4284 4369 8.303876 GCCTTCACAGTTTTAATCTTTATTGGA 58.696 33.333 0.00 0.00 0.00 3.53
4317 4402 2.205022 TTCAGCAGGGAAGTCCATTG 57.795 50.000 0.00 0.00 38.24 2.82
4393 4482 8.522542 TCTAATCCTTTACTTGTAGAGAGTCC 57.477 38.462 0.62 0.00 0.00 3.85
4394 4483 8.114102 TCTAATCCTTTACTTGTAGAGAGTCCA 58.886 37.037 0.62 0.00 0.00 4.02
4395 4484 7.741554 AATCCTTTACTTGTAGAGAGTCCAT 57.258 36.000 0.62 0.00 0.00 3.41
4396 4485 6.531503 TCCTTTACTTGTAGAGAGTCCATG 57.468 41.667 0.62 0.00 0.00 3.66
4397 4486 6.017192 TCCTTTACTTGTAGAGAGTCCATGT 58.983 40.000 0.00 0.00 0.00 3.21
4398 4487 6.153000 TCCTTTACTTGTAGAGAGTCCATGTC 59.847 42.308 0.00 0.00 0.00 3.06
4399 4488 5.916661 TTACTTGTAGAGAGTCCATGTCC 57.083 43.478 0.00 0.00 0.00 4.02
4400 4489 3.779444 ACTTGTAGAGAGTCCATGTCCA 58.221 45.455 0.00 0.00 0.00 4.02
4401 4490 4.160329 ACTTGTAGAGAGTCCATGTCCAA 58.840 43.478 0.00 0.00 0.00 3.53
4402 4491 4.780021 ACTTGTAGAGAGTCCATGTCCAAT 59.220 41.667 0.00 0.00 0.00 3.16
4403 4492 5.249393 ACTTGTAGAGAGTCCATGTCCAATT 59.751 40.000 0.00 0.00 0.00 2.32
4404 4493 5.762179 TGTAGAGAGTCCATGTCCAATTT 57.238 39.130 0.00 0.00 0.00 1.82
4405 4494 6.867519 TGTAGAGAGTCCATGTCCAATTTA 57.132 37.500 0.00 0.00 0.00 1.40
4406 4495 7.437713 TGTAGAGAGTCCATGTCCAATTTAT 57.562 36.000 0.00 0.00 0.00 1.40
4407 4496 7.275183 TGTAGAGAGTCCATGTCCAATTTATG 58.725 38.462 0.00 0.00 0.00 1.90
4408 4497 5.128919 AGAGAGTCCATGTCCAATTTATGC 58.871 41.667 0.00 0.00 0.00 3.14
4409 4498 5.104193 AGAGAGTCCATGTCCAATTTATGCT 60.104 40.000 0.00 0.00 0.00 3.79
4410 4499 5.513233 AGAGTCCATGTCCAATTTATGCTT 58.487 37.500 0.00 0.00 0.00 3.91
4411 4500 5.359009 AGAGTCCATGTCCAATTTATGCTTG 59.641 40.000 0.00 0.00 0.00 4.01
4412 4501 5.018809 AGTCCATGTCCAATTTATGCTTGT 58.981 37.500 0.00 0.00 0.00 3.16
4413 4502 6.186957 AGTCCATGTCCAATTTATGCTTGTA 58.813 36.000 0.00 0.00 0.00 2.41
4414 4503 6.663093 AGTCCATGTCCAATTTATGCTTGTAA 59.337 34.615 0.00 0.00 0.00 2.41
4415 4504 7.178274 AGTCCATGTCCAATTTATGCTTGTAAA 59.822 33.333 0.00 0.00 0.00 2.01
4499 4588 4.526970 ACATAGATGGTTACAAAGCCCTG 58.473 43.478 0.00 0.00 0.00 4.45
4518 4607 5.010282 CCCTGCATTTACAAGTAGGTTTCT 58.990 41.667 0.00 0.00 36.07 2.52
4562 4651 7.502226 TGGATCTGAAATATTTATGCTCCGTTT 59.498 33.333 0.00 0.00 0.00 3.60
4823 4912 7.923878 GTGCAAGATTTTGTTAGGAAAACCTTA 59.076 33.333 0.00 0.00 36.65 2.69
5000 5094 0.925466 CTTACGGATGTTTACGCCCG 59.075 55.000 10.01 10.01 46.65 6.13
5286 5385 4.388577 ACCATTTCTTTTCACCTAGCCT 57.611 40.909 0.00 0.00 0.00 4.58
5340 5439 3.510719 TGCTCTTAAATTTCGGCAATGC 58.489 40.909 0.00 0.00 0.00 3.56
5360 5459 7.370383 CAATGCTGTAGTGTCTTGGTAATTTT 58.630 34.615 0.00 0.00 0.00 1.82
5487 5588 1.331756 CAATCGGCAATAAAGCGCTCT 59.668 47.619 12.06 0.00 34.64 4.09
5600 5701 7.387397 CACAGGTACCCGTATAACAACTTTTTA 59.613 37.037 8.74 0.00 0.00 1.52
5709 5810 3.386078 TGTTGGTAAAATTCTTGCTGCCA 59.614 39.130 0.00 0.00 0.00 4.92
5744 5845 6.419484 TCTTTGTCAACAGAGTCTAATGGA 57.581 37.500 0.00 0.00 30.87 3.41
5805 5909 1.007479 ACCAAGAATGCCCCATCATGT 59.993 47.619 0.00 0.00 0.00 3.21
5806 5910 1.411246 CCAAGAATGCCCCATCATGTG 59.589 52.381 0.00 0.00 0.00 3.21
5986 6090 5.874810 GTGCATCCACTCAATACTTTGTCTA 59.125 40.000 0.00 0.00 38.93 2.59
5987 6091 5.874810 TGCATCCACTCAATACTTTGTCTAC 59.125 40.000 0.00 0.00 34.32 2.59
6127 6231 3.960102 TGGAGAATGTTTATCATTGGGCC 59.040 43.478 0.00 0.00 45.49 5.80
6383 6487 7.148755 GCCAATGTGCTAGTTTTGTTAGATTTG 60.149 37.037 0.00 0.00 0.00 2.32
6390 6494 8.637986 TGCTAGTTTTGTTAGATTTGATGGTTT 58.362 29.630 0.00 0.00 0.00 3.27
6426 6531 7.693969 AATATTTATCCCTGCATCTTGCTAC 57.306 36.000 0.75 0.00 45.31 3.58
6604 6709 7.535139 CGATTAAATGTTGAGGCTTTCCTAAA 58.465 34.615 0.00 0.00 44.46 1.85
6721 6826 8.924511 ACATTATGGTTAGTTTATCCATGGAG 57.075 34.615 21.33 2.38 41.34 3.86
6733 6838 7.663081 AGTTTATCCATGGAGTGTATAATGCAG 59.337 37.037 21.33 0.00 0.00 4.41
6735 6840 3.136260 TCCATGGAGTGTATAATGCAGCA 59.864 43.478 11.44 0.00 0.00 4.41
6841 7105 2.143925 GTGGTAATATCTTCCCTGCGC 58.856 52.381 0.00 0.00 0.00 6.09
7025 7289 2.472695 TCAATGACCGTTTAGCTGCT 57.527 45.000 7.57 7.57 0.00 4.24
7198 7462 7.721402 TGTACCAAACAGACAAATTTTAGCAT 58.279 30.769 0.00 0.00 33.01 3.79
7397 7661 4.942852 ACAATCCTATCTCTGAAGCTTCG 58.057 43.478 21.11 15.42 0.00 3.79
7400 7664 1.601663 CCTATCTCTGAAGCTTCGCCG 60.602 57.143 21.11 12.12 0.00 6.46
7516 7780 4.455533 TGATGCAGTTGTGGATACTGAAAC 59.544 41.667 7.15 0.00 44.52 2.78
7536 7818 1.808411 GAAAACTGATGCAGTCGGGA 58.192 50.000 0.00 0.00 44.62 5.14
7915 8197 2.298729 CGTTTCATGGGGAACAATTGGT 59.701 45.455 10.83 1.89 34.56 3.67
7916 8198 3.244044 CGTTTCATGGGGAACAATTGGTT 60.244 43.478 10.83 1.71 44.10 3.67
7917 8199 4.064388 GTTTCATGGGGAACAATTGGTTG 58.936 43.478 10.83 0.00 40.63 3.77
7918 8200 3.251016 TCATGGGGAACAATTGGTTGA 57.749 42.857 10.83 0.12 40.63 3.18
7919 8201 3.788933 TCATGGGGAACAATTGGTTGAT 58.211 40.909 10.83 0.00 40.63 2.57
7920 8202 3.514706 TCATGGGGAACAATTGGTTGATG 59.485 43.478 10.83 4.76 40.63 3.07
7921 8203 1.622811 TGGGGAACAATTGGTTGATGC 59.377 47.619 10.83 0.00 40.63 3.91
8189 8471 4.796038 AATTGTTTCAGATCCAGCTTGG 57.204 40.909 0.00 0.00 39.43 3.61
8190 8472 1.538047 TGTTTCAGATCCAGCTTGGC 58.462 50.000 0.00 0.00 37.47 4.52
8227 8509 4.162320 TCTTGACCAGCTATTCCCTAACTG 59.838 45.833 0.00 0.00 0.00 3.16
8253 10598 7.380065 GTGTTGTTCCGATGCAAAATTTAGTTA 59.620 33.333 0.00 0.00 0.00 2.24
8256 10601 9.482627 TTGTTCCGATGCAAAATTTAGTTAAAT 57.517 25.926 0.00 0.00 37.49 1.40
8282 10628 6.180472 AGGTGGACTACTAAAAATCCATGTG 58.820 40.000 0.00 0.00 43.02 3.21
8359 10867 2.235650 TGAGAAGCTCAATCAGAGTGGG 59.764 50.000 0.00 0.00 46.47 4.61
8445 10953 3.185594 TCGCTTGGTCGACTTTAAACATG 59.814 43.478 16.46 7.08 33.02 3.21
8451 10959 4.876679 TGGTCGACTTTAAACATGTTCACA 59.123 37.500 16.46 0.00 0.00 3.58
8465 10973 8.970691 AACATGTTCACAATTAGCTTTGTATC 57.029 30.769 4.92 0.00 37.73 2.24
8519 11028 8.415553 TCCAAAGTTGCCATCTCATAATTATTG 58.584 33.333 0.00 0.00 0.00 1.90
8559 11068 2.952978 ACCAAAGTTATCACGTGGCAAA 59.047 40.909 17.00 4.89 36.76 3.68
8566 11075 5.113383 AGTTATCACGTGGCAAATTCGATA 58.887 37.500 17.00 0.00 0.00 2.92
8570 11079 3.935828 TCACGTGGCAAATTCGATATCAA 59.064 39.130 17.00 0.00 0.00 2.57
8572 11081 5.755861 TCACGTGGCAAATTCGATATCAATA 59.244 36.000 17.00 0.00 0.00 1.90
8575 11084 6.426633 ACGTGGCAAATTCGATATCAATATCA 59.573 34.615 3.12 0.00 39.23 2.15
8576 11085 6.738200 CGTGGCAAATTCGATATCAATATCAC 59.262 38.462 3.12 7.62 39.23 3.06
8577 11086 7.571059 CGTGGCAAATTCGATATCAATATCACA 60.571 37.037 3.12 0.00 39.23 3.58
8578 11087 8.075574 GTGGCAAATTCGATATCAATATCACAA 58.924 33.333 3.12 3.38 39.23 3.33
8579 11088 8.075574 TGGCAAATTCGATATCAATATCACAAC 58.924 33.333 3.12 0.00 39.23 3.32
8580 11089 8.292448 GGCAAATTCGATATCAATATCACAACT 58.708 33.333 3.12 0.00 39.23 3.16
8581 11090 9.322776 GCAAATTCGATATCAATATCACAACTC 57.677 33.333 3.12 0.00 39.23 3.01
8596 11105 1.195448 CAACTCACCATGCGACAACTC 59.805 52.381 0.00 0.00 0.00 3.01
8600 11109 0.950836 CACCATGCGACAACTCCAAA 59.049 50.000 0.00 0.00 0.00 3.28
8601 11110 1.336440 CACCATGCGACAACTCCAAAA 59.664 47.619 0.00 0.00 0.00 2.44
8602 11111 2.030007 CACCATGCGACAACTCCAAAAT 60.030 45.455 0.00 0.00 0.00 1.82
8603 11112 2.228822 ACCATGCGACAACTCCAAAATC 59.771 45.455 0.00 0.00 0.00 2.17
8604 11113 2.489329 CCATGCGACAACTCCAAAATCT 59.511 45.455 0.00 0.00 0.00 2.40
8605 11114 3.689161 CCATGCGACAACTCCAAAATCTA 59.311 43.478 0.00 0.00 0.00 1.98
8606 11115 4.155826 CCATGCGACAACTCCAAAATCTAA 59.844 41.667 0.00 0.00 0.00 2.10
8607 11116 5.163622 CCATGCGACAACTCCAAAATCTAAT 60.164 40.000 0.00 0.00 0.00 1.73
8608 11117 6.038161 CCATGCGACAACTCCAAAATCTAATA 59.962 38.462 0.00 0.00 0.00 0.98
8609 11118 7.255242 CCATGCGACAACTCCAAAATCTAATAT 60.255 37.037 0.00 0.00 0.00 1.28
8610 11119 7.624360 TGCGACAACTCCAAAATCTAATATT 57.376 32.000 0.00 0.00 0.00 1.28
8611 11120 7.471721 TGCGACAACTCCAAAATCTAATATTG 58.528 34.615 0.00 0.00 0.00 1.90
8612 11121 7.335673 TGCGACAACTCCAAAATCTAATATTGA 59.664 33.333 0.00 0.00 0.00 2.57
8613 11122 7.852945 GCGACAACTCCAAAATCTAATATTGAG 59.147 37.037 0.00 0.00 0.00 3.02
8614 11123 7.852945 CGACAACTCCAAAATCTAATATTGAGC 59.147 37.037 0.00 0.00 0.00 4.26
8615 11124 8.814038 ACAACTCCAAAATCTAATATTGAGCT 57.186 30.769 0.00 0.00 0.00 4.09
8616 11125 8.897752 ACAACTCCAAAATCTAATATTGAGCTC 58.102 33.333 6.82 6.82 0.00 4.09
8617 11126 9.118300 CAACTCCAAAATCTAATATTGAGCTCT 57.882 33.333 16.19 0.00 0.00 4.09
8618 11127 8.900983 ACTCCAAAATCTAATATTGAGCTCTC 57.099 34.615 16.19 0.00 0.00 3.20
8619 11128 7.655328 ACTCCAAAATCTAATATTGAGCTCTCG 59.345 37.037 16.19 0.00 0.00 4.04
8620 11129 7.500992 TCCAAAATCTAATATTGAGCTCTCGT 58.499 34.615 16.19 3.33 0.00 4.18
8621 11130 8.638873 TCCAAAATCTAATATTGAGCTCTCGTA 58.361 33.333 16.19 5.57 0.00 3.43
8622 11131 8.920665 CCAAAATCTAATATTGAGCTCTCGTAG 58.079 37.037 16.19 9.24 0.00 3.51
8623 11132 9.684448 CAAAATCTAATATTGAGCTCTCGTAGA 57.316 33.333 16.19 13.78 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.096532 TGATTCGTCTCTGCCTAGTTACTG 59.903 45.833 0.00 0.00 0.00 2.74
3 4 4.634184 TGATTCGTCTCTGCCTAGTTAC 57.366 45.455 0.00 0.00 0.00 2.50
4 5 4.887655 TCATGATTCGTCTCTGCCTAGTTA 59.112 41.667 0.00 0.00 0.00 2.24
5 6 3.701542 TCATGATTCGTCTCTGCCTAGTT 59.298 43.478 0.00 0.00 0.00 2.24
6 7 3.291584 TCATGATTCGTCTCTGCCTAGT 58.708 45.455 0.00 0.00 0.00 2.57
7 8 3.998099 TCATGATTCGTCTCTGCCTAG 57.002 47.619 0.00 0.00 0.00 3.02
8 9 3.057946 CGATCATGATTCGTCTCTGCCTA 60.058 47.826 10.14 0.00 0.00 3.93
12 13 4.480386 TCTCGATCATGATTCGTCTCTG 57.520 45.455 10.14 5.67 0.00 3.35
87 88 1.069022 CACACACGCCAAAATGAGAGG 60.069 52.381 0.00 0.00 0.00 3.69
91 92 1.098869 ACACACACACGCCAAAATGA 58.901 45.000 0.00 0.00 0.00 2.57
92 93 1.198767 CACACACACACGCCAAAATG 58.801 50.000 0.00 0.00 0.00 2.32
94 95 0.109551 CACACACACACACGCCAAAA 60.110 50.000 0.00 0.00 0.00 2.44
95 96 0.955919 TCACACACACACACGCCAAA 60.956 50.000 0.00 0.00 0.00 3.28
96 97 1.365368 CTCACACACACACACGCCAA 61.365 55.000 0.00 0.00 0.00 4.52
97 98 1.813337 CTCACACACACACACGCCA 60.813 57.895 0.00 0.00 0.00 5.69
98 99 1.490693 CTCTCACACACACACACGCC 61.491 60.000 0.00 0.00 0.00 5.68
99 100 0.527600 TCTCTCACACACACACACGC 60.528 55.000 0.00 0.00 0.00 5.34
100 101 1.065551 TCTCTCTCACACACACACACG 59.934 52.381 0.00 0.00 0.00 4.49
101 102 2.871182 TCTCTCTCACACACACACAC 57.129 50.000 0.00 0.00 0.00 3.82
102 103 3.885724 TTTCTCTCTCACACACACACA 57.114 42.857 0.00 0.00 0.00 3.72
112 113 3.842732 TGCGTCGTAATTTCTCTCTCA 57.157 42.857 0.00 0.00 0.00 3.27
120 121 4.688879 TCTCTTCATGTTGCGTCGTAATTT 59.311 37.500 0.00 0.00 0.00 1.82
161 165 3.885484 AAGAATGAGAGCACAACAACG 57.115 42.857 0.00 0.00 0.00 4.10
261 268 4.074854 TGGTCCACCAACACCTGA 57.925 55.556 0.00 0.00 44.35 3.86
296 303 2.040544 CCGAGTTGGCCATCGCTTT 61.041 57.895 20.92 0.00 37.61 3.51
420 427 0.612174 CTCCTCCGTCTCCACAAGGA 60.612 60.000 0.00 0.00 43.21 3.36
452 459 1.351017 TGTTTCTTCCCTCTTGCGGAT 59.649 47.619 0.00 0.00 0.00 4.18
477 484 3.490759 CACACGCTCGCACCATCC 61.491 66.667 0.00 0.00 0.00 3.51
513 520 0.541392 TCCATCGTCTCCACCATTGG 59.459 55.000 0.00 0.00 45.56 3.16
517 524 2.710902 CGCTCCATCGTCTCCACCA 61.711 63.158 0.00 0.00 0.00 4.17
519 526 2.105128 CCGCTCCATCGTCTCCAC 59.895 66.667 0.00 0.00 0.00 4.02
561 568 7.409697 CCACGATTTAAACTCCTCACATATTG 58.590 38.462 0.00 0.00 0.00 1.90
563 570 6.055588 CCCACGATTTAAACTCCTCACATAT 58.944 40.000 0.00 0.00 0.00 1.78
577 587 3.927854 TGACGATTTCACCCACGATTTA 58.072 40.909 0.00 0.00 0.00 1.40
600 614 1.635487 TCAACCTTCTCTTCCCCATGG 59.365 52.381 4.14 4.14 0.00 3.66
603 617 1.423921 GGTTCAACCTTCTCTTCCCCA 59.576 52.381 0.00 0.00 34.73 4.96
646 667 8.463930 AAAATAAAGTCTGAACAATGGACTCA 57.536 30.769 0.00 0.00 39.09 3.41
1323 1356 5.226396 TGCAAAACATAACCAAATCCGAAG 58.774 37.500 0.00 0.00 0.00 3.79
1640 1683 8.971321 CAATATCAACGAATGGAATTGGAATTC 58.029 33.333 0.00 0.00 43.12 2.17
1681 1724 9.264719 GGATGATTGAACACAAGATTTTTCTTT 57.735 29.630 0.00 0.00 0.00 2.52
1684 1727 8.592105 TTGGATGATTGAACACAAGATTTTTC 57.408 30.769 0.00 0.00 0.00 2.29
1721 1764 9.938280 TTAGTAATATTATCAGACAATTCCGGG 57.062 33.333 0.00 0.00 0.00 5.73
1740 1783 5.129815 TGGAATAACGGAGCCACTTAGTAAT 59.870 40.000 0.00 0.00 0.00 1.89
2065 2108 1.271871 TGCCACCCATGTAAACCTCAG 60.272 52.381 0.00 0.00 0.00 3.35
2118 2161 6.605849 TGTTACTCTAGTACACACGATGAAC 58.394 40.000 0.00 0.00 0.00 3.18
2125 2168 9.694137 ATTCTTCTTTGTTACTCTAGTACACAC 57.306 33.333 0.00 0.00 0.00 3.82
2186 2232 2.543777 AGCGACTGTGCTTCCTTTAA 57.456 45.000 0.00 0.00 44.46 1.52
2195 2241 5.579511 TCCTTAACTTAATAAGCGACTGTGC 59.420 40.000 0.00 0.00 32.62 4.57
2259 2305 8.661352 AAACAGCAACTATTAAGTGCAAAAAT 57.339 26.923 0.00 0.00 35.62 1.82
2428 2474 9.063615 GGAATAGAAACAGTTAAACCTCAAGAA 57.936 33.333 0.00 0.00 0.00 2.52
2437 2483 8.008332 AGAAAAGGGGGAATAGAAACAGTTAAA 58.992 33.333 0.00 0.00 0.00 1.52
2439 2485 7.098845 AGAAAAGGGGGAATAGAAACAGTTA 57.901 36.000 0.00 0.00 0.00 2.24
2461 2507 7.516450 AGGAATCTATTTGGAGAGGAAAAGA 57.484 36.000 0.00 0.00 0.00 2.52
2564 2612 3.305110 GCCAATTTGGTTTGACAGTACG 58.695 45.455 16.62 0.00 40.46 3.67
2586 2634 4.446385 TGAACTATCACGAAAACTCAACGG 59.554 41.667 0.00 0.00 0.00 4.44
2606 2654 6.240145 TCACTCATTCATTCAACCAGATGAA 58.760 36.000 1.76 1.76 43.03 2.57
2656 2704 4.022068 TGGATGCCAACAGTCAAGAAAATC 60.022 41.667 0.00 0.00 0.00 2.17
2835 2886 6.819649 CAGGCAATGAATGTTAATGACCAATT 59.180 34.615 0.00 0.00 0.00 2.32
2993 3044 6.625873 AAGGACAAGAAAGCTTTTACTCTG 57.374 37.500 14.05 8.87 30.14 3.35
3185 3248 6.206395 ACAACGAATTTATGCCATGATTCA 57.794 33.333 12.90 0.00 0.00 2.57
3271 3334 8.190784 GCCTTGTAATAAATATGACAGCAACTT 58.809 33.333 0.00 0.00 29.11 2.66
3456 3519 7.542130 GCCCAAATATTCAAAGAAAGTACACTG 59.458 37.037 0.00 0.00 0.00 3.66
3536 3604 6.279513 TGTGACCACAGAAGAAAATTGTTT 57.720 33.333 0.00 0.00 36.21 2.83
3730 3811 1.299089 GCAACAGCGTCAACCAACC 60.299 57.895 0.00 0.00 0.00 3.77
3806 3887 5.759763 CCACTGCATTGTATCAGCATAGTTA 59.240 40.000 3.14 0.00 37.68 2.24
3875 3956 0.970640 TTCCCGAACTCACCGATGAA 59.029 50.000 0.00 0.00 33.30 2.57
3889 3970 7.521585 GCATTTCCCTAGTGTTAATATTTCCCG 60.522 40.741 0.00 0.00 0.00 5.14
4047 4130 9.700831 AACTGAATATTGTTATTTAGGAGGCTT 57.299 29.630 0.00 0.00 36.31 4.35
4125 4209 3.758554 GAGAGTCCTGCTTGGCAATTTAA 59.241 43.478 0.00 0.00 38.41 1.52
4170 4255 4.260743 CGAGTCACAGCACAAAGAATTTCA 60.261 41.667 0.00 0.00 35.03 2.69
4284 4369 1.063266 TGCTGAAAGGTTTTCCCCTGT 60.063 47.619 0.00 0.00 41.86 4.00
4386 4475 5.128919 AGCATAAATTGGACATGGACTCTC 58.871 41.667 0.00 0.00 0.00 3.20
4392 4481 7.546358 TCTTTACAAGCATAAATTGGACATGG 58.454 34.615 0.00 0.00 31.76 3.66
4393 4482 8.246180 ACTCTTTACAAGCATAAATTGGACATG 58.754 33.333 0.00 0.00 31.76 3.21
4394 4483 8.353423 ACTCTTTACAAGCATAAATTGGACAT 57.647 30.769 0.00 0.00 31.76 3.06
4395 4484 7.094377 GGACTCTTTACAAGCATAAATTGGACA 60.094 37.037 0.00 0.00 31.76 4.02
4396 4485 7.094377 TGGACTCTTTACAAGCATAAATTGGAC 60.094 37.037 0.00 0.00 31.76 4.02
4397 4486 6.945435 TGGACTCTTTACAAGCATAAATTGGA 59.055 34.615 0.00 0.00 31.76 3.53
4398 4487 7.156876 TGGACTCTTTACAAGCATAAATTGG 57.843 36.000 0.00 0.00 31.76 3.16
4399 4488 8.246180 ACATGGACTCTTTACAAGCATAAATTG 58.754 33.333 0.00 0.00 0.00 2.32
4400 4489 8.353423 ACATGGACTCTTTACAAGCATAAATT 57.647 30.769 0.00 0.00 0.00 1.82
4401 4490 7.067494 GGACATGGACTCTTTACAAGCATAAAT 59.933 37.037 0.00 0.00 0.00 1.40
4402 4491 6.374333 GGACATGGACTCTTTACAAGCATAAA 59.626 38.462 0.00 0.00 0.00 1.40
4403 4492 5.880332 GGACATGGACTCTTTACAAGCATAA 59.120 40.000 0.00 0.00 0.00 1.90
4404 4493 5.045942 TGGACATGGACTCTTTACAAGCATA 60.046 40.000 0.00 0.00 0.00 3.14
4405 4494 4.263462 TGGACATGGACTCTTTACAAGCAT 60.263 41.667 0.00 0.00 0.00 3.79
4406 4495 3.072330 TGGACATGGACTCTTTACAAGCA 59.928 43.478 0.00 0.00 0.00 3.91
4407 4496 3.674997 TGGACATGGACTCTTTACAAGC 58.325 45.455 0.00 0.00 0.00 4.01
4408 4497 6.824305 AATTGGACATGGACTCTTTACAAG 57.176 37.500 0.00 0.00 0.00 3.16
4409 4498 8.739039 CATAAATTGGACATGGACTCTTTACAA 58.261 33.333 0.00 0.00 0.00 2.41
4410 4499 7.148086 GCATAAATTGGACATGGACTCTTTACA 60.148 37.037 0.00 0.00 0.00 2.41
4411 4500 7.067494 AGCATAAATTGGACATGGACTCTTTAC 59.933 37.037 0.00 0.00 0.00 2.01
4412 4501 7.118723 AGCATAAATTGGACATGGACTCTTTA 58.881 34.615 0.00 0.00 0.00 1.85
4413 4502 5.954150 AGCATAAATTGGACATGGACTCTTT 59.046 36.000 0.00 0.00 0.00 2.52
4414 4503 5.513233 AGCATAAATTGGACATGGACTCTT 58.487 37.500 0.00 0.00 0.00 2.85
4415 4504 5.121380 AGCATAAATTGGACATGGACTCT 57.879 39.130 0.00 0.00 0.00 3.24
4416 4505 5.126061 ACAAGCATAAATTGGACATGGACTC 59.874 40.000 0.00 0.00 31.76 3.36
4417 4506 5.018809 ACAAGCATAAATTGGACATGGACT 58.981 37.500 0.00 0.00 31.76 3.85
4418 4507 5.329035 ACAAGCATAAATTGGACATGGAC 57.671 39.130 0.00 0.00 31.76 4.02
4419 4508 7.395772 TCTTTACAAGCATAAATTGGACATGGA 59.604 33.333 0.00 0.00 31.76 3.41
4460 4549 9.646427 CCATCTATGTAAAGCCTCTTTAGATAC 57.354 37.037 10.32 0.00 0.00 2.24
4499 4588 7.169140 CCAACAAAGAAACCTACTTGTAAATGC 59.831 37.037 0.00 0.00 0.00 3.56
4562 4651 6.586344 TCCCAACAAAACTGCAATTTCATAA 58.414 32.000 0.00 0.00 0.00 1.90
4567 4656 3.199727 ACCTCCCAACAAAACTGCAATTT 59.800 39.130 0.00 0.00 0.00 1.82
4823 4912 7.690256 ACAAGGTCTACAATTGAGTAAGGAAT 58.310 34.615 13.59 0.00 0.00 3.01
4857 4948 1.202710 AGCAAACCATGACACACGGTA 60.203 47.619 0.00 0.00 31.12 4.02
4916 5010 8.007405 AGTTGAGCAAATTACCTACAAAAGTT 57.993 30.769 0.00 0.00 0.00 2.66
5000 5094 0.744771 GTCGATGTTTCCCCAGAGGC 60.745 60.000 0.00 0.00 34.51 4.70
5145 5241 4.654262 TCCAGACAACACTAAGAACCTTCT 59.346 41.667 0.00 0.00 39.74 2.85
5146 5242 4.750598 GTCCAGACAACACTAAGAACCTTC 59.249 45.833 0.00 0.00 0.00 3.46
5152 5248 3.321111 GGTCAGTCCAGACAACACTAAGA 59.679 47.826 0.00 0.00 40.29 2.10
5154 5250 3.305720 AGGTCAGTCCAGACAACACTAA 58.694 45.455 0.00 0.00 40.29 2.24
5266 5365 7.993183 TCTATAAGGCTAGGTGAAAAGAAATGG 59.007 37.037 0.00 0.00 0.00 3.16
5276 5375 7.941238 ACTAATACGTTCTATAAGGCTAGGTGA 59.059 37.037 0.00 0.00 0.00 4.02
5277 5376 8.021973 CACTAATACGTTCTATAAGGCTAGGTG 58.978 40.741 0.00 0.00 0.00 4.00
5340 5439 6.428159 AGCAGAAAATTACCAAGACACTACAG 59.572 38.462 0.00 0.00 0.00 2.74
5360 5459 1.148310 GCTTAACACAAGCGAGCAGA 58.852 50.000 0.00 0.00 33.20 4.26
5600 5701 7.933577 ACAATTATATTCTCGACATGATGGTGT 59.066 33.333 0.00 0.00 34.39 4.16
5709 5810 6.024552 TGTTGACAAAGAAGAAAGCTTGTT 57.975 33.333 0.00 0.00 39.07 2.83
5805 5909 1.727511 GCTGCACACAAGAGGCAACA 61.728 55.000 0.00 0.00 37.06 3.33
5806 5910 1.008079 GCTGCACACAAGAGGCAAC 60.008 57.895 0.00 0.00 37.06 4.17
6004 6108 6.206829 AGGTCAAAGTAAGGCATACAAAACTC 59.793 38.462 2.44 0.00 36.94 3.01
6127 6231 4.100279 AGGAAAGAAAACCTACCCACAG 57.900 45.455 0.00 0.00 34.47 3.66
6390 6494 9.231297 GCAGGGATAAATATTTTGATAGTAGCA 57.769 33.333 5.91 0.00 0.00 3.49
6426 6531 8.491152 GCATATACAATACAGCAGTAGAAACAG 58.509 37.037 0.00 0.00 32.86 3.16
6471 6576 2.159156 GCCTGCATTCAAATGATCAGCA 60.159 45.455 0.09 2.34 38.70 4.41
6628 6733 9.095065 ACTTTATAGTCGGCTTTTTGTACATAG 57.905 33.333 0.00 0.00 0.00 2.23
6721 6826 9.385902 CAATATACTTGTTGCTGCATTATACAC 57.614 33.333 1.84 0.00 0.00 2.90
6841 7105 1.810606 CGTCCGGATCATCTCCCAGG 61.811 65.000 7.81 0.00 41.49 4.45
7025 7289 1.893801 GGAGAGGACGAAGGAACAGAA 59.106 52.381 0.00 0.00 0.00 3.02
7198 7462 5.180117 GCACTTTCTAGTTGCTCATTCTCAA 59.820 40.000 0.00 0.00 30.26 3.02
7317 7581 1.550327 CCTGCCTGTGTCTCAGTAGA 58.450 55.000 1.48 0.00 42.19 2.59
7336 7600 4.154918 CAGCTGGTTTATCAACTGTTCTCC 59.845 45.833 5.57 0.00 32.90 3.71
7397 7661 1.233019 CATTGACATCAGGATCCGGC 58.767 55.000 7.07 0.00 0.00 6.13
7400 7664 2.441001 ACTCCCATTGACATCAGGATCC 59.559 50.000 2.48 2.48 0.00 3.36
7516 7780 0.443869 CCCGACTGCATCAGTTTTCG 59.556 55.000 0.66 0.98 45.44 3.46
7536 7818 3.057033 GCATCAGCTTTCACTCCAACATT 60.057 43.478 0.00 0.00 37.91 2.71
7631 7913 0.608130 ATACGCTGCCACTTCACTCA 59.392 50.000 0.00 0.00 0.00 3.41
7915 8197 3.190953 TGACATTTCGCATCAAGCATCAA 59.809 39.130 0.00 0.00 46.13 2.57
7916 8198 2.748532 TGACATTTCGCATCAAGCATCA 59.251 40.909 0.00 0.00 46.13 3.07
7917 8199 3.409851 TGACATTTCGCATCAAGCATC 57.590 42.857 0.00 0.00 46.13 3.91
7918 8200 4.380841 AATGACATTTCGCATCAAGCAT 57.619 36.364 0.00 0.00 46.13 3.79
7919 8201 3.853831 AATGACATTTCGCATCAAGCA 57.146 38.095 0.00 0.00 46.13 3.91
7920 8202 3.305094 CCAAATGACATTTCGCATCAAGC 59.695 43.478 10.52 0.00 40.87 4.01
7921 8203 3.305094 GCCAAATGACATTTCGCATCAAG 59.695 43.478 21.16 5.02 36.55 3.02
8189 8471 3.546271 GGTCAAGAAAAAGACGTGTTTGC 59.454 43.478 11.84 7.26 35.63 3.68
8190 8472 4.728534 TGGTCAAGAAAAAGACGTGTTTG 58.271 39.130 11.84 0.00 35.63 2.93
8227 8509 5.689961 ACTAAATTTTGCATCGGAACAACAC 59.310 36.000 0.00 0.00 0.00 3.32
8253 10598 9.990868 ATGGATTTTTAGTAGTCCACCTAATTT 57.009 29.630 0.00 0.00 43.02 1.82
8256 10601 7.827236 CACATGGATTTTTAGTAGTCCACCTAA 59.173 37.037 0.00 0.00 43.02 2.69
8380 10888 0.592637 TTTCACCATGCTCACTTGCG 59.407 50.000 0.00 0.00 35.36 4.85
8407 10915 9.741168 CGACCAAGCGATTTAATAGTATAATTG 57.259 33.333 0.00 0.00 0.00 2.32
8408 10916 9.701098 TCGACCAAGCGATTTAATAGTATAATT 57.299 29.630 0.00 0.00 35.01 1.40
8412 10920 6.746120 AGTCGACCAAGCGATTTAATAGTAT 58.254 36.000 13.01 0.00 42.82 2.12
8413 10921 6.140303 AGTCGACCAAGCGATTTAATAGTA 57.860 37.500 13.01 0.00 42.82 1.82
8414 10922 5.007385 AGTCGACCAAGCGATTTAATAGT 57.993 39.130 13.01 0.00 42.82 2.12
8415 10923 5.968387 AAGTCGACCAAGCGATTTAATAG 57.032 39.130 13.01 0.00 42.82 1.73
8416 10924 7.830940 TTAAAGTCGACCAAGCGATTTAATA 57.169 32.000 13.01 0.00 42.82 0.98
8445 10953 7.295201 TCAACGATACAAAGCTAATTGTGAAC 58.705 34.615 13.00 4.73 43.13 3.18
8451 10959 6.407202 AGTCCTCAACGATACAAAGCTAATT 58.593 36.000 0.00 0.00 0.00 1.40
8465 10973 5.399604 AACTTTTTACGAAGTCCTCAACG 57.600 39.130 0.00 0.00 43.93 4.10
8519 11028 5.493133 TGGTACAACACAATGACAACTTC 57.507 39.130 0.00 0.00 31.92 3.01
8559 11068 8.150296 TGGTGAGTTGTGATATTGATATCGAAT 58.850 33.333 0.00 1.77 41.55 3.34
8566 11075 4.274214 CGCATGGTGAGTTGTGATATTGAT 59.726 41.667 0.00 0.00 0.00 2.57
8570 11079 3.198068 GTCGCATGGTGAGTTGTGATAT 58.802 45.455 0.00 0.00 35.09 1.63
8572 11081 1.270785 TGTCGCATGGTGAGTTGTGAT 60.271 47.619 0.00 0.00 35.09 3.06
8575 11084 0.944386 GTTGTCGCATGGTGAGTTGT 59.056 50.000 0.00 0.00 0.00 3.32
8576 11085 1.195448 GAGTTGTCGCATGGTGAGTTG 59.805 52.381 0.00 0.00 0.00 3.16
8577 11086 1.512926 GAGTTGTCGCATGGTGAGTT 58.487 50.000 0.00 0.00 0.00 3.01
8578 11087 0.320771 GGAGTTGTCGCATGGTGAGT 60.321 55.000 0.00 0.00 0.00 3.41
8579 11088 0.320683 TGGAGTTGTCGCATGGTGAG 60.321 55.000 0.00 0.00 0.00 3.51
8580 11089 0.107643 TTGGAGTTGTCGCATGGTGA 59.892 50.000 0.00 0.00 0.00 4.02
8581 11090 0.950836 TTTGGAGTTGTCGCATGGTG 59.049 50.000 0.00 0.00 0.00 4.17
8596 11105 7.721286 ACGAGAGCTCAATATTAGATTTTGG 57.279 36.000 17.77 0.00 0.00 3.28
8600 11109 8.856153 TCTCTACGAGAGCTCAATATTAGATT 57.144 34.615 17.77 0.00 42.04 2.40
8602 11111 9.945904 TTATCTCTACGAGAGCTCAATATTAGA 57.054 33.333 17.77 11.80 42.26 2.10
8603 11112 9.982291 GTTATCTCTACGAGAGCTCAATATTAG 57.018 37.037 17.77 8.73 42.26 1.73
8604 11113 9.727859 AGTTATCTCTACGAGAGCTCAATATTA 57.272 33.333 17.77 0.00 42.26 0.98
8605 11114 8.630054 AGTTATCTCTACGAGAGCTCAATATT 57.370 34.615 17.77 0.00 42.26 1.28
8606 11115 8.630054 AAGTTATCTCTACGAGAGCTCAATAT 57.370 34.615 17.77 0.52 42.26 1.28
8607 11116 8.346300 CAAAGTTATCTCTACGAGAGCTCAATA 58.654 37.037 17.77 4.00 42.26 1.90
8608 11117 6.952773 AAGTTATCTCTACGAGAGCTCAAT 57.047 37.500 17.77 2.88 42.26 2.57
8609 11118 6.556212 CAAAGTTATCTCTACGAGAGCTCAA 58.444 40.000 17.77 0.00 42.26 3.02
8610 11119 5.449314 GCAAAGTTATCTCTACGAGAGCTCA 60.449 44.000 17.77 0.00 42.26 4.26
8611 11120 4.973663 GCAAAGTTATCTCTACGAGAGCTC 59.026 45.833 5.27 5.27 42.26 4.09
8612 11121 4.642885 AGCAAAGTTATCTCTACGAGAGCT 59.357 41.667 6.93 0.00 42.26 4.09
8613 11122 4.927422 AGCAAAGTTATCTCTACGAGAGC 58.073 43.478 6.93 0.00 42.26 4.09
8614 11123 6.804534 CAAGCAAAGTTATCTCTACGAGAG 57.195 41.667 0.00 0.00 42.26 3.20


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

AutoCloner maintained by Alex Coulton.