Multiple sequence alignment - TraesCS3A01G270400

Loading Multiple Alignment...

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 TraesCS3A01G270400 chr3A 100.000 4664 0 0 1 4664 497653149 497648486 0.000000e+00 8613.0
1 TraesCS3A01G270400 chr3A 95.556 45 2 0 3587 3631 497649519 497649475 6.470000e-09 73.1
2 TraesCS3A01G270400 chr3A 95.556 45 2 0 3631 3675 497649563 497649519 6.470000e-09 73.1
3 TraesCS3A01G270400 chr3D 95.562 2704 81 19 1873 4558 374930664 374927982 0.000000e+00 4292.0
4 TraesCS3A01G270400 chr3D 91.334 1177 58 22 649 1801 374931848 374930692 0.000000e+00 1568.0
5 TraesCS3A01G270400 chr3D 92.157 255 19 1 291 544 374932403 374932149 4.440000e-95 359.0
6 TraesCS3A01G270400 chr3D 91.213 239 12 5 1 233 374932640 374932405 2.710000e-82 316.0
7 TraesCS3A01G270400 chr3D 97.778 45 1 0 3587 3631 374928917 374928873 1.390000e-10 78.7
8 TraesCS3A01G270400 chr3B 95.897 1779 60 10 1881 3656 488537159 488535391 0.000000e+00 2868.0
9 TraesCS3A01G270400 chr3B 90.710 1098 56 20 737 1817 488538256 488537188 0.000000e+00 1421.0
10 TraesCS3A01G270400 chr3B 95.688 719 19 4 3882 4591 488532461 488531746 0.000000e+00 1146.0
11 TraesCS3A01G270400 chr3B 90.261 421 22 10 1 404 488541480 488541062 2.470000e-147 532.0
12 TraesCS3A01G270400 chr3B 91.531 307 10 7 3591 3884 488535388 488535085 4.340000e-110 409.0
13 TraesCS3A01G270400 chr3B 92.593 54 2 2 3629 3682 488535462 488535411 5.000000e-10 76.8
14 TraesCS3A01G270400 chr3B 93.478 46 1 2 3637 3682 488535386 488535343 3.010000e-07 67.6
15 TraesCS3A01G270400 chr2D 91.011 178 12 4 81 256 357970516 357970691 2.170000e-58 237.0
16 TraesCS3A01G270400 chr2D 86.275 102 10 2 2633 2731 22421368 22421468 1.770000e-19 108.0
17 TraesCS3A01G270400 chr6D 90.000 180 14 4 81 256 414629431 414629252 3.630000e-56 230.0
18 TraesCS3A01G270400 chr6D 89.944 179 13 5 81 256 187256074 187256250 4.700000e-55 226.0
19 TraesCS3A01G270400 chr6D 87.129 101 11 2 2630 2729 32649680 32649779 3.810000e-21 113.0
20 TraesCS3A01G270400 chr4A 90.000 180 15 3 80 256 576036369 576036548 3.630000e-56 230.0
21 TraesCS3A01G270400 chr4A 89.773 176 16 2 81 254 715713840 715713665 1.690000e-54 224.0
22 TraesCS3A01G270400 chr4A 96.000 75 3 0 4590 4664 596636642 596636568 6.340000e-24 122.0
23 TraesCS3A01G270400 chr6B 89.888 178 14 4 82 256 645643287 645643463 4.700000e-55 226.0
24 TraesCS3A01G270400 chr7B 89.071 183 16 4 77 256 706527844 706527663 1.690000e-54 224.0
25 TraesCS3A01G270400 chr5A 97.333 75 2 0 4590 4664 600889901 600889827 1.360000e-25 128.0
26 TraesCS3A01G270400 chr2A 94.872 78 3 1 4584 4660 590934615 590934538 2.280000e-23 121.0
27 TraesCS3A01G270400 chr2A 97.143 70 2 0 4590 4659 114625777 114625846 8.200000e-23 119.0
28 TraesCS3A01G270400 chr2A 86.905 84 7 3 2649 2729 539973499 539973581 1.790000e-14 91.6
29 TraesCS3A01G270400 chr1A 97.183 71 2 0 4590 4660 519270472 519270402 2.280000e-23 121.0
30 TraesCS3A01G270400 chr1A 94.667 75 4 0 4585 4659 380891947 380891873 2.950000e-22 117.0
31 TraesCS3A01G270400 chr1A 82.075 106 15 4 2625 2729 8335105 8335003 2.310000e-13 87.9
32 TraesCS3A01G270400 chr1B 95.890 73 3 0 4586 4658 155628096 155628168 8.200000e-23 119.0
33 TraesCS3A01G270400 chr1B 82.653 98 15 2 2633 2729 268582908 268583004 8.310000e-13 86.1
34 TraesCS3A01G270400 chr4B 94.667 75 4 0 4590 4664 167934381 167934307 2.950000e-22 117.0
35 TraesCS3A01G270400 chr7D 94.667 75 3 1 4590 4663 602101074 602101000 1.060000e-21 115.0
36 TraesCS3A01G270400 chr6A 86.139 101 11 3 2630 2729 37058736 37058834 6.380000e-19 106.0
37 TraesCS3A01G270400 chr2B 86.047 86 9 3 2647 2730 482952444 482952360 6.430000e-14 89.8


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 TraesCS3A01G270400 chr3A 497648486 497653149 4663 True 2919.733333 8613 97.037333 1 4664 3 chr3A.!!$R1 4663
1 TraesCS3A01G270400 chr3D 374927982 374932640 4658 True 1322.740000 4292 93.608800 1 4558 5 chr3D.!!$R1 4557
2 TraesCS3A01G270400 chr3B 488531746 488541480 9734 True 931.485714 2868 92.879714 1 4591 7 chr3B.!!$R1 4590

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
696 3344 0.535780 TGACTACGTCGACCACACCT 60.536 55.0 10.58 0.00 34.95 4.00 F
1130 3840 0.603975 GAGAGGCCACACACAAGGTC 60.604 60.0 5.01 0.00 0.00 3.85 F
2505 5235 0.321653 AGGACATTGTCGGGCAAGTC 60.322 55.0 10.56 13.13 40.86 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1527 4250 0.250727 TCTTTGGCGGGAGTTCAAGG 60.251 55.0 0.00 0.0 0.0 3.61 R
2994 5724 0.037326 TCGCGTTTCTCCAAGCTGAT 60.037 50.0 5.77 0.0 0.0 2.90 R
4390 9830 0.179081 GGGCGAAGACATACCCAGAC 60.179 60.0 0.00 0.0 37.0 3.51 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
85 94 8.300286 TGTTGTAACACTTCACTTTGATTTTCA 58.700 29.630 0.00 0.00 33.17 2.69
112 121 4.643334 AGGGGCGCTTTATTACTTAAAAGG 59.357 41.667 7.64 0.00 34.07 3.11
182 192 3.963129 ACAAGGTCCTCTCACAAAAACA 58.037 40.909 0.00 0.00 0.00 2.83
239 257 3.023119 TCTGTATAACGCCTAAACCGGA 58.977 45.455 9.46 0.00 0.00 5.14
380 399 5.956642 ACAAGTCCAAAAACAACGTTACAT 58.043 33.333 0.00 0.00 0.00 2.29
432 2883 1.221840 CACCCTAACTGATGCGCCT 59.778 57.895 4.18 0.00 0.00 5.52
436 2887 1.097547 CCTAACTGATGCGCCTTGGG 61.098 60.000 4.18 0.00 0.00 4.12
487 2939 0.907704 TCCCCTGTCACCAACGCTAT 60.908 55.000 0.00 0.00 0.00 2.97
509 2961 9.952030 GCTATTTAATAAAGGGAGAGAGCTAAT 57.048 33.333 0.00 0.00 0.00 1.73
521 2973 3.383185 AGAGAGCTAATCACCTGCACTAC 59.617 47.826 0.00 0.00 0.00 2.73
544 2996 3.258372 TCTCAATTCAAGTACGGCTCACT 59.742 43.478 0.00 0.00 0.00 3.41
545 2997 3.585862 TCAATTCAAGTACGGCTCACTC 58.414 45.455 0.00 0.00 0.00 3.51
546 2998 3.258372 TCAATTCAAGTACGGCTCACTCT 59.742 43.478 0.00 0.00 0.00 3.24
547 2999 3.963428 ATTCAAGTACGGCTCACTCTT 57.037 42.857 0.00 0.00 0.00 2.85
548 3000 3.299340 TTCAAGTACGGCTCACTCTTC 57.701 47.619 0.00 0.00 0.00 2.87
549 3001 2.515854 TCAAGTACGGCTCACTCTTCT 58.484 47.619 0.00 0.00 0.00 2.85
550 3002 2.488545 TCAAGTACGGCTCACTCTTCTC 59.511 50.000 0.00 0.00 0.00 2.87
555 3007 2.726351 GGCTCACTCTTCTCCCCCG 61.726 68.421 0.00 0.00 0.00 5.73
562 3014 0.543749 CTCTTCTCCCCCGCATTCTT 59.456 55.000 0.00 0.00 0.00 2.52
575 3027 5.508994 CCCCGCATTCTTAAAAACCATATCC 60.509 44.000 0.00 0.00 0.00 2.59
592 3044 4.918201 CGATCCAAGGGGGCGCTC 62.918 72.222 7.64 1.18 36.21 5.03
606 3058 2.499685 GCTCCAGCGACGGGTAAT 59.500 61.111 0.00 0.00 0.00 1.89
618 3070 3.549625 CGACGGGTAATTCTAGCCTACAC 60.550 52.174 0.00 0.00 42.60 2.90
619 3071 3.368248 ACGGGTAATTCTAGCCTACACA 58.632 45.455 0.00 0.00 42.60 3.72
665 3313 1.747206 GCGGCCTGTGGTGATTAGAAT 60.747 52.381 0.00 0.00 0.00 2.40
683 3331 5.606348 AGAATGTCCAGGAGATTGACTAC 57.394 43.478 16.59 2.01 0.00 2.73
696 3344 0.535780 TGACTACGTCGACCACACCT 60.536 55.000 10.58 0.00 34.95 4.00
711 3359 0.886490 CACCTTCGCTCAACCTTGCT 60.886 55.000 0.00 0.00 0.00 3.91
748 3396 3.012934 TCATGTCGACCTCCATGACTA 57.987 47.619 14.12 0.00 41.77 2.59
784 3485 5.568620 AAACCCTCTCTGTTTATGTCAGT 57.431 39.130 0.00 0.00 34.32 3.41
786 3487 5.923733 ACCCTCTCTGTTTATGTCAGTAG 57.076 43.478 0.00 0.00 34.86 2.57
803 3505 4.021456 TCAGTAGGTGTTGTAGACATGGTG 60.021 45.833 0.00 0.00 41.10 4.17
828 3530 9.317936 TGAGATCATGTTCATGATTAGTGTAAC 57.682 33.333 23.37 11.92 41.02 2.50
859 3561 7.554959 TTAGATCTAACAGTTTCAACCTCCT 57.445 36.000 11.24 0.00 0.00 3.69
998 3705 3.782244 GGCGCATCGATGATCGGC 61.782 66.667 29.20 27.84 40.88 5.54
1035 3744 2.037871 CTCCCCAACAAAACCACGG 58.962 57.895 0.00 0.00 0.00 4.94
1064 3774 3.249189 ACGGGAGAAGGCAGCCAA 61.249 61.111 15.80 0.00 0.00 4.52
1130 3840 0.603975 GAGAGGCCACACACAAGGTC 60.604 60.000 5.01 0.00 0.00 3.85
1138 3848 1.355210 CACACAAGGTCGCAACACC 59.645 57.895 0.00 0.00 36.58 4.16
1300 4014 1.153939 CCTGAACAGAGCCTCGACG 60.154 63.158 3.19 0.00 0.00 5.12
1331 4045 1.964373 GTTGCCGGGTCATGACGTT 60.964 57.895 19.33 0.00 0.00 3.99
1359 4076 1.036707 CCCTCTCGTCATCCTTCTCC 58.963 60.000 0.00 0.00 0.00 3.71
1360 4077 1.410932 CCCTCTCGTCATCCTTCTCCT 60.411 57.143 0.00 0.00 0.00 3.69
1361 4078 1.953686 CCTCTCGTCATCCTTCTCCTC 59.046 57.143 0.00 0.00 0.00 3.71
1362 4079 1.953686 CTCTCGTCATCCTTCTCCTCC 59.046 57.143 0.00 0.00 0.00 4.30
1398 4115 4.063230 CGGTCGTCGTCGTCGTCA 62.063 66.667 11.41 0.00 38.33 4.35
1399 4116 2.477845 GGTCGTCGTCGTCGTCAT 59.522 61.111 11.41 0.00 38.33 3.06
1400 4117 1.154338 GGTCGTCGTCGTCGTCATT 60.154 57.895 11.41 0.00 38.33 2.57
1446 4163 2.892640 CGGAGCATGGACGAGGAA 59.107 61.111 0.00 0.00 0.00 3.36
1550 4273 2.183858 GAACTCCCGCCAAAGAACGC 62.184 60.000 0.00 0.00 0.00 4.84
1584 4307 0.393808 GGCCGCCTTCAGGTTTGATA 60.394 55.000 0.71 0.00 37.57 2.15
1585 4308 1.680338 GCCGCCTTCAGGTTTGATAT 58.320 50.000 0.00 0.00 37.57 1.63
1587 4310 2.427095 GCCGCCTTCAGGTTTGATATTT 59.573 45.455 0.00 0.00 37.57 1.40
1588 4311 3.734902 GCCGCCTTCAGGTTTGATATTTG 60.735 47.826 0.00 0.00 37.57 2.32
1589 4312 3.181487 CCGCCTTCAGGTTTGATATTTGG 60.181 47.826 0.00 0.00 37.57 3.28
1590 4313 3.443681 CGCCTTCAGGTTTGATATTTGGT 59.556 43.478 0.00 0.00 37.57 3.67
1591 4314 4.082245 CGCCTTCAGGTTTGATATTTGGTT 60.082 41.667 0.00 0.00 37.57 3.67
1593 4316 5.869344 GCCTTCAGGTTTGATATTTGGTTTC 59.131 40.000 0.00 0.00 37.57 2.78
1594 4317 6.398095 CCTTCAGGTTTGATATTTGGTTTCC 58.602 40.000 0.00 0.00 32.27 3.13
1595 4318 6.014669 CCTTCAGGTTTGATATTTGGTTTCCA 60.015 38.462 0.00 0.00 32.27 3.53
1596 4319 7.310609 CCTTCAGGTTTGATATTTGGTTTCCAT 60.311 37.037 0.00 0.00 30.26 3.41
1597 4320 6.934056 TCAGGTTTGATATTTGGTTTCCATG 58.066 36.000 0.00 0.00 31.53 3.66
1598 4321 6.496565 TCAGGTTTGATATTTGGTTTCCATGT 59.503 34.615 0.00 0.00 31.53 3.21
1599 4322 6.591062 CAGGTTTGATATTTGGTTTCCATGTG 59.409 38.462 0.00 0.00 31.53 3.21
1600 4323 6.269769 AGGTTTGATATTTGGTTTCCATGTGT 59.730 34.615 0.00 0.00 31.53 3.72
1607 4330 1.137872 TGGTTTCCATGTGTTGTTGGC 59.862 47.619 0.00 0.00 32.80 4.52
1608 4331 1.412343 GGTTTCCATGTGTTGTTGGCT 59.588 47.619 0.00 0.00 32.80 4.75
1633 4356 1.289109 CCGTGGCAGTTGGTTCGTAG 61.289 60.000 0.00 0.00 0.00 3.51
1641 4368 3.187637 GCAGTTGGTTCGTAGTTGCATAA 59.812 43.478 0.00 0.00 0.00 1.90
1708 4435 0.461693 AGAGAGATTCGCCAAGCTGC 60.462 55.000 0.00 0.00 0.00 5.25
1817 4544 4.447724 AGTTAACGAGTGTACATGCAACAG 59.552 41.667 0.00 0.00 0.00 3.16
1818 4545 2.526304 ACGAGTGTACATGCAACAGT 57.474 45.000 0.00 8.47 33.21 3.55
1819 4546 3.653539 ACGAGTGTACATGCAACAGTA 57.346 42.857 0.00 0.00 30.68 2.74
1820 4547 3.314553 ACGAGTGTACATGCAACAGTAC 58.685 45.455 16.19 16.19 40.68 2.73
1821 4548 3.005472 ACGAGTGTACATGCAACAGTACT 59.995 43.478 20.80 11.00 40.84 2.73
1822 4549 3.608506 CGAGTGTACATGCAACAGTACTC 59.391 47.826 20.80 18.21 40.84 2.59
1823 4550 4.616143 CGAGTGTACATGCAACAGTACTCT 60.616 45.833 21.53 21.53 43.61 3.24
1824 4551 4.560128 AGTGTACATGCAACAGTACTCTG 58.440 43.478 21.09 4.49 41.08 3.35
1846 4573 3.923461 GTCGATCTCTTGTTCTGTTCCTG 59.077 47.826 0.00 0.00 0.00 3.86
1847 4574 3.574396 TCGATCTCTTGTTCTGTTCCTGT 59.426 43.478 0.00 0.00 0.00 4.00
1848 4575 4.039245 TCGATCTCTTGTTCTGTTCCTGTT 59.961 41.667 0.00 0.00 0.00 3.16
1849 4576 4.387256 CGATCTCTTGTTCTGTTCCTGTTC 59.613 45.833 0.00 0.00 0.00 3.18
1851 4578 3.711704 TCTCTTGTTCTGTTCCTGTTCCT 59.288 43.478 0.00 0.00 0.00 3.36
1852 4579 4.164221 TCTCTTGTTCTGTTCCTGTTCCTT 59.836 41.667 0.00 0.00 0.00 3.36
1853 4580 4.451900 TCTTGTTCTGTTCCTGTTCCTTC 58.548 43.478 0.00 0.00 0.00 3.46
1854 4581 3.208747 TGTTCTGTTCCTGTTCCTTCC 57.791 47.619 0.00 0.00 0.00 3.46
1857 4584 1.978580 TCTGTTCCTGTTCCTTCCCTC 59.021 52.381 0.00 0.00 0.00 4.30
1858 4585 1.981495 CTGTTCCTGTTCCTTCCCTCT 59.019 52.381 0.00 0.00 0.00 3.69
1859 4586 1.978580 TGTTCCTGTTCCTTCCCTCTC 59.021 52.381 0.00 0.00 0.00 3.20
1860 4587 1.279558 GTTCCTGTTCCTTCCCTCTCC 59.720 57.143 0.00 0.00 0.00 3.71
1861 4588 0.491823 TCCTGTTCCTTCCCTCTCCA 59.508 55.000 0.00 0.00 0.00 3.86
1862 4589 1.081174 TCCTGTTCCTTCCCTCTCCAT 59.919 52.381 0.00 0.00 0.00 3.41
1863 4590 1.211457 CCTGTTCCTTCCCTCTCCATG 59.789 57.143 0.00 0.00 0.00 3.66
1864 4591 2.191400 CTGTTCCTTCCCTCTCCATGA 58.809 52.381 0.00 0.00 0.00 3.07
1865 4592 1.909302 TGTTCCTTCCCTCTCCATGAC 59.091 52.381 0.00 0.00 0.00 3.06
1866 4593 1.909302 GTTCCTTCCCTCTCCATGACA 59.091 52.381 0.00 0.00 0.00 3.58
1867 4594 2.507471 GTTCCTTCCCTCTCCATGACAT 59.493 50.000 0.00 0.00 0.00 3.06
1868 4595 2.850833 TCCTTCCCTCTCCATGACATT 58.149 47.619 0.00 0.00 0.00 2.71
1869 4596 2.507058 TCCTTCCCTCTCCATGACATTG 59.493 50.000 0.00 0.00 0.00 2.82
1870 4597 2.240667 CCTTCCCTCTCCATGACATTGT 59.759 50.000 0.00 0.00 0.00 2.71
1871 4598 3.308688 CCTTCCCTCTCCATGACATTGTT 60.309 47.826 0.00 0.00 0.00 2.83
1872 4599 3.634397 TCCCTCTCCATGACATTGTTC 57.366 47.619 0.00 0.00 0.00 3.18
1873 4600 2.239654 TCCCTCTCCATGACATTGTTCC 59.760 50.000 0.00 0.00 0.00 3.62
1874 4601 2.240667 CCCTCTCCATGACATTGTTCCT 59.759 50.000 0.00 0.00 0.00 3.36
1875 4602 3.539604 CCTCTCCATGACATTGTTCCTC 58.460 50.000 0.00 0.00 0.00 3.71
1876 4603 3.539604 CTCTCCATGACATTGTTCCTCC 58.460 50.000 0.00 0.00 0.00 4.30
1879 4606 2.239654 TCCATGACATTGTTCCTCCCTC 59.760 50.000 0.00 0.00 0.00 4.30
1895 4622 4.583489 CCTCCCTCCTTCATGATGAAATTG 59.417 45.833 9.39 1.51 35.73 2.32
2086 4815 1.683917 AGGTCACTCACTGTCTCACAC 59.316 52.381 0.00 0.00 0.00 3.82
2127 4857 4.990543 TTTCTAGCACTCATCACAAACG 57.009 40.909 0.00 0.00 0.00 3.60
2274 5004 2.222886 TCCGCGATCCTTTTCAACAAA 58.777 42.857 8.23 0.00 0.00 2.83
2388 5118 1.587054 CAACGAGAGCGAGAAGGGT 59.413 57.895 0.00 0.00 41.64 4.34
2491 5221 2.061220 CTCCAGCACCAGAAGGACA 58.939 57.895 0.00 0.00 38.69 4.02
2505 5235 0.321653 AGGACATTGTCGGGCAAGTC 60.322 55.000 10.56 13.13 40.86 3.01
2701 5431 1.352083 AAAGCTGGACTAGAGCCACA 58.648 50.000 0.00 0.00 37.12 4.17
2738 5468 5.715753 GGATCGGAGGGAGTATTAATGTAGT 59.284 44.000 0.00 0.00 0.00 2.73
2877 5607 0.547075 TTTTGACCCCAACGGACTCA 59.453 50.000 0.00 0.00 34.64 3.41
3076 5806 1.952367 GCACAAGTTCCCTGGATCTGG 60.952 57.143 0.00 0.00 0.00 3.86
3092 5822 0.674581 CTGGCCAGTCATCGCTTGAA 60.675 55.000 25.53 0.00 35.70 2.69
3126 5856 6.436738 TCCAATACAACAAGGTACCACTTA 57.563 37.500 15.94 0.00 0.00 2.24
3127 5857 6.469410 TCCAATACAACAAGGTACCACTTAG 58.531 40.000 15.94 3.35 0.00 2.18
3128 5858 6.043474 TCCAATACAACAAGGTACCACTTAGT 59.957 38.462 15.94 9.43 0.00 2.24
3167 5900 1.673920 GTTTCAGTTGCTTTCCGGACA 59.326 47.619 1.83 0.00 0.00 4.02
3179 5912 2.745100 CGGACATGCTGCAGTGCT 60.745 61.111 17.60 0.00 0.00 4.40
3182 5915 0.316204 GGACATGCTGCAGTGCTTTT 59.684 50.000 17.60 0.00 0.00 2.27
3230 5963 6.317857 GTGTTTCCTATTCAATGTGCTCTTC 58.682 40.000 0.00 0.00 0.00 2.87
3338 6071 0.817654 CGTCCTCTATGCTGACACCA 59.182 55.000 0.00 0.00 0.00 4.17
3411 6144 0.455972 GACAGCACTGAGTCTCTCGC 60.456 60.000 4.31 1.31 32.35 5.03
3497 6230 3.797353 GGAGCCTGGATTCCGGCA 61.797 66.667 28.36 0.00 42.52 5.69
3506 6239 1.675641 GATTCCGGCAGTGGCAAGT 60.676 57.895 17.80 0.45 43.71 3.16
3553 6286 4.279671 AGGAGGAAATCTATGCACGTAGAG 59.720 45.833 5.85 0.00 34.41 2.43
3572 6305 2.160205 AGAAGGTCGAGATGAACGTGA 58.840 47.619 0.00 0.00 40.15 4.35
3573 6306 2.557056 AGAAGGTCGAGATGAACGTGAA 59.443 45.455 0.00 0.00 40.15 3.18
3574 6307 3.193691 AGAAGGTCGAGATGAACGTGAAT 59.806 43.478 0.00 0.00 40.15 2.57
3575 6308 2.881074 AGGTCGAGATGAACGTGAATG 58.119 47.619 0.00 0.00 40.15 2.67
3576 6309 2.231478 AGGTCGAGATGAACGTGAATGT 59.769 45.455 0.00 0.00 40.15 2.71
3577 6310 2.345641 GGTCGAGATGAACGTGAATGTG 59.654 50.000 0.00 0.00 0.00 3.21
3580 6313 2.731451 CGAGATGAACGTGAATGTGTGT 59.269 45.455 0.00 0.00 0.00 3.72
3585 6318 0.380378 AACGTGAATGTGTGTGGTGC 59.620 50.000 0.00 0.00 0.00 5.01
3695 6496 1.289066 CGTTGCTTCGACAGGGAGA 59.711 57.895 0.00 0.00 0.00 3.71
3708 6509 2.182827 CAGGGAGACATCTGGTGAAGA 58.817 52.381 0.00 0.00 39.94 2.87
3709 6510 2.168106 CAGGGAGACATCTGGTGAAGAG 59.832 54.545 0.00 0.00 38.67 2.85
3710 6511 2.043664 AGGGAGACATCTGGTGAAGAGA 59.956 50.000 0.00 0.00 38.67 3.10
3822 6636 1.448985 TGTCGCCCTAAAGCATCAAC 58.551 50.000 0.00 0.00 0.00 3.18
3823 6637 0.373716 GTCGCCCTAAAGCATCAACG 59.626 55.000 0.00 0.00 0.00 4.10
3835 6649 3.216147 GCATCAACGGTATGCTTGTTT 57.784 42.857 8.30 0.00 45.05 2.83
3866 6680 9.323985 AGCAGCAAAATCTAAATAACACAAAAA 57.676 25.926 0.00 0.00 0.00 1.94
3987 9427 1.344114 CCACCCACACCATTTTCCTTG 59.656 52.381 0.00 0.00 0.00 3.61
4011 9451 5.518848 ACAATCTCAGAATGTTTGCAACA 57.481 34.783 0.00 0.88 46.94 3.33
4028 9468 3.063316 GCAACACAACCAACAATTTGACC 59.937 43.478 2.79 0.00 34.24 4.02
4083 9523 9.577110 CATAAAGTACATGAAGAAATGCACATT 57.423 29.630 0.00 0.00 0.00 2.71
4103 9543 7.362920 GCACATTGACAATTTATTCCCACTAGT 60.363 37.037 0.00 0.00 0.00 2.57
4108 9548 9.444600 TTGACAATTTATTCCCACTAGTAGTTC 57.555 33.333 0.00 0.00 0.00 3.01
4390 9830 3.996150 AGGAACTTCACATGCTTGTTG 57.004 42.857 1.83 0.00 27.25 3.33
4535 9983 6.206829 TGAGGATAGTGTGTCCATTCGTATAG 59.793 42.308 0.00 0.00 38.25 1.31
4591 10039 0.163788 CCGTTCTGCGTTCACACATC 59.836 55.000 0.00 0.00 39.32 3.06
4592 10040 1.139989 CGTTCTGCGTTCACACATCT 58.860 50.000 0.00 0.00 35.54 2.90
4593 10041 1.526887 CGTTCTGCGTTCACACATCTT 59.473 47.619 0.00 0.00 35.54 2.40
4594 10042 2.410262 CGTTCTGCGTTCACACATCTTC 60.410 50.000 0.00 0.00 35.54 2.87
4595 10043 2.802816 GTTCTGCGTTCACACATCTTCT 59.197 45.455 0.00 0.00 0.00 2.85
4596 10044 3.934457 TCTGCGTTCACACATCTTCTA 57.066 42.857 0.00 0.00 0.00 2.10
4597 10045 4.456280 TCTGCGTTCACACATCTTCTAT 57.544 40.909 0.00 0.00 0.00 1.98
4598 10046 5.576447 TCTGCGTTCACACATCTTCTATA 57.424 39.130 0.00 0.00 0.00 1.31
4599 10047 6.149129 TCTGCGTTCACACATCTTCTATAT 57.851 37.500 0.00 0.00 0.00 0.86
4600 10048 6.209361 TCTGCGTTCACACATCTTCTATATC 58.791 40.000 0.00 0.00 0.00 1.63
4601 10049 6.039829 TCTGCGTTCACACATCTTCTATATCT 59.960 38.462 0.00 0.00 0.00 1.98
4602 10050 7.228706 TCTGCGTTCACACATCTTCTATATCTA 59.771 37.037 0.00 0.00 0.00 1.98
4603 10051 7.712797 TGCGTTCACACATCTTCTATATCTAA 58.287 34.615 0.00 0.00 0.00 2.10
4604 10052 8.194769 TGCGTTCACACATCTTCTATATCTAAA 58.805 33.333 0.00 0.00 0.00 1.85
4605 10053 9.197694 GCGTTCACACATCTTCTATATCTAAAT 57.802 33.333 0.00 0.00 0.00 1.40
4615 10063 9.663365 ATCTTCTATATCTAAATACCTAGCCCC 57.337 37.037 0.00 0.00 0.00 5.80
4616 10064 8.066247 TCTTCTATATCTAAATACCTAGCCCCC 58.934 40.741 0.00 0.00 0.00 5.40
4617 10065 7.306751 TCTATATCTAAATACCTAGCCCCCA 57.693 40.000 0.00 0.00 0.00 4.96
4618 10066 7.130775 TCTATATCTAAATACCTAGCCCCCAC 58.869 42.308 0.00 0.00 0.00 4.61
4619 10067 3.719368 TCTAAATACCTAGCCCCCACT 57.281 47.619 0.00 0.00 0.00 4.00
4620 10068 4.838105 TCTAAATACCTAGCCCCCACTA 57.162 45.455 0.00 0.00 0.00 2.74
4621 10069 5.160511 TCTAAATACCTAGCCCCCACTAA 57.839 43.478 0.00 0.00 0.00 2.24
4622 10070 4.903649 TCTAAATACCTAGCCCCCACTAAC 59.096 45.833 0.00 0.00 0.00 2.34
4623 10071 2.113807 ATACCTAGCCCCCACTAACC 57.886 55.000 0.00 0.00 0.00 2.85
4624 10072 1.021275 TACCTAGCCCCCACTAACCT 58.979 55.000 0.00 0.00 0.00 3.50
4625 10073 1.021275 ACCTAGCCCCCACTAACCTA 58.979 55.000 0.00 0.00 0.00 3.08
4626 10074 1.584105 ACCTAGCCCCCACTAACCTAT 59.416 52.381 0.00 0.00 0.00 2.57
4627 10075 2.021341 ACCTAGCCCCCACTAACCTATT 60.021 50.000 0.00 0.00 0.00 1.73
4628 10076 3.053826 CCTAGCCCCCACTAACCTATTT 58.946 50.000 0.00 0.00 0.00 1.40
4629 10077 3.072622 CCTAGCCCCCACTAACCTATTTC 59.927 52.174 0.00 0.00 0.00 2.17
4630 10078 2.859951 AGCCCCCACTAACCTATTTCT 58.140 47.619 0.00 0.00 0.00 2.52
4631 10079 2.778270 AGCCCCCACTAACCTATTTCTC 59.222 50.000 0.00 0.00 0.00 2.87
4632 10080 2.778270 GCCCCCACTAACCTATTTCTCT 59.222 50.000 0.00 0.00 0.00 3.10
4633 10081 3.181453 GCCCCCACTAACCTATTTCTCTC 60.181 52.174 0.00 0.00 0.00 3.20
4634 10082 4.037927 CCCCCACTAACCTATTTCTCTCA 58.962 47.826 0.00 0.00 0.00 3.27
4635 10083 4.473559 CCCCCACTAACCTATTTCTCTCAA 59.526 45.833 0.00 0.00 0.00 3.02
4636 10084 5.429130 CCCCACTAACCTATTTCTCTCAAC 58.571 45.833 0.00 0.00 0.00 3.18
4637 10085 5.045869 CCCCACTAACCTATTTCTCTCAACA 60.046 44.000 0.00 0.00 0.00 3.33
4638 10086 6.353082 CCCCACTAACCTATTTCTCTCAACAT 60.353 42.308 0.00 0.00 0.00 2.71
4639 10087 6.763610 CCCACTAACCTATTTCTCTCAACATC 59.236 42.308 0.00 0.00 0.00 3.06
4640 10088 6.763610 CCACTAACCTATTTCTCTCAACATCC 59.236 42.308 0.00 0.00 0.00 3.51
4641 10089 7.331026 CACTAACCTATTTCTCTCAACATCCA 58.669 38.462 0.00 0.00 0.00 3.41
4642 10090 7.824289 CACTAACCTATTTCTCTCAACATCCAA 59.176 37.037 0.00 0.00 0.00 3.53
4643 10091 8.043710 ACTAACCTATTTCTCTCAACATCCAAG 58.956 37.037 0.00 0.00 0.00 3.61
4644 10092 5.189180 ACCTATTTCTCTCAACATCCAAGC 58.811 41.667 0.00 0.00 0.00 4.01
4645 10093 5.188434 CCTATTTCTCTCAACATCCAAGCA 58.812 41.667 0.00 0.00 0.00 3.91
4646 10094 5.826737 CCTATTTCTCTCAACATCCAAGCAT 59.173 40.000 0.00 0.00 0.00 3.79
4647 10095 5.578005 ATTTCTCTCAACATCCAAGCATG 57.422 39.130 0.00 0.00 0.00 4.06
4648 10096 2.362736 TCTCTCAACATCCAAGCATGC 58.637 47.619 10.51 10.51 0.00 4.06
4649 10097 1.404391 CTCTCAACATCCAAGCATGCC 59.596 52.381 15.66 0.00 0.00 4.40
4650 10098 1.179152 CTCAACATCCAAGCATGCCA 58.821 50.000 15.66 0.00 0.00 4.92
4651 10099 0.889994 TCAACATCCAAGCATGCCAC 59.110 50.000 15.66 0.00 0.00 5.01
4652 10100 0.108520 CAACATCCAAGCATGCCACC 60.109 55.000 15.66 0.00 0.00 4.61
4653 10101 0.251922 AACATCCAAGCATGCCACCT 60.252 50.000 15.66 0.00 0.00 4.00
4654 10102 0.682209 ACATCCAAGCATGCCACCTC 60.682 55.000 15.66 0.00 0.00 3.85
4655 10103 0.681887 CATCCAAGCATGCCACCTCA 60.682 55.000 15.66 0.00 0.00 3.86
4656 10104 0.260816 ATCCAAGCATGCCACCTCAT 59.739 50.000 15.66 0.00 0.00 2.90
4657 10105 0.394762 TCCAAGCATGCCACCTCATC 60.395 55.000 15.66 0.00 0.00 2.92
4658 10106 0.681887 CCAAGCATGCCACCTCATCA 60.682 55.000 15.66 0.00 0.00 3.07
4659 10107 1.399714 CAAGCATGCCACCTCATCAT 58.600 50.000 15.66 0.00 0.00 2.45
4660 10108 1.067060 CAAGCATGCCACCTCATCATG 59.933 52.381 15.66 0.00 40.23 3.07
4661 10109 0.549469 AGCATGCCACCTCATCATGA 59.451 50.000 15.66 0.00 39.80 3.07
4662 10110 1.064240 AGCATGCCACCTCATCATGAA 60.064 47.619 15.66 0.00 39.80 2.57
4663 10111 1.752498 GCATGCCACCTCATCATGAAA 59.248 47.619 6.36 0.00 39.80 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 49 4.142359 ACAACAACTCACAAAACGCCATAA 60.142 37.500 0.00 0.00 0.00 1.90
85 94 7.885009 TTTAAGTAATAAAGCGCCCCTTATT 57.115 32.000 18.26 18.26 32.20 1.40
112 121 1.133598 GGCCGGGTGTAATGCTTAAAC 59.866 52.381 2.18 0.00 0.00 2.01
188 198 6.491403 ACATGTTTCTTGTATTTTGCCTCTCT 59.509 34.615 0.00 0.00 0.00 3.10
189 199 6.681777 ACATGTTTCTTGTATTTTGCCTCTC 58.318 36.000 0.00 0.00 0.00 3.20
191 201 7.816640 TCTACATGTTTCTTGTATTTTGCCTC 58.183 34.615 2.30 0.00 0.00 4.70
193 203 7.593825 ACTCTACATGTTTCTTGTATTTTGCC 58.406 34.615 2.30 0.00 0.00 4.52
195 205 9.817365 CAGACTCTACATGTTTCTTGTATTTTG 57.183 33.333 2.30 0.00 0.00 2.44
196 206 9.561069 ACAGACTCTACATGTTTCTTGTATTTT 57.439 29.630 2.30 0.00 0.00 1.82
246 264 4.887655 AGTGAAGTGTTTCTTTAGGGTTGG 59.112 41.667 0.00 0.00 36.40 3.77
284 302 4.209538 CTGCATTCACCCATTCCTCATTA 58.790 43.478 0.00 0.00 0.00 1.90
289 307 2.610438 AACTGCATTCACCCATTCCT 57.390 45.000 0.00 0.00 0.00 3.36
298 316 3.318886 TCGTTACGCTTAACTGCATTCA 58.681 40.909 10.92 0.00 36.22 2.57
364 382 4.295051 CCTCCCATGTAACGTTGTTTTTG 58.705 43.478 11.99 1.59 0.00 2.44
370 389 1.029947 GCCCCTCCCATGTAACGTTG 61.030 60.000 11.99 0.00 0.00 4.10
397 416 1.479323 GGTGGAGAGGCACGTACATTA 59.521 52.381 0.00 0.00 0.00 1.90
432 2883 2.474268 TTTAGGTGCCCCAGCCCAA 61.474 57.895 0.00 0.00 38.69 4.12
436 2887 0.830023 TTTGGTTTAGGTGCCCCAGC 60.830 55.000 0.00 0.00 40.48 4.85
438 2889 2.407340 AATTTGGTTTAGGTGCCCCA 57.593 45.000 0.00 0.00 0.00 4.96
487 2939 8.211629 GGTGATTAGCTCTCTCCCTTTATTAAA 58.788 37.037 0.00 0.00 0.00 1.52
509 2961 3.578282 TGAATTGAGAGTAGTGCAGGTGA 59.422 43.478 0.00 0.00 0.00 4.02
521 2973 3.614616 GTGAGCCGTACTTGAATTGAGAG 59.385 47.826 0.00 0.00 0.00 3.20
544 2996 1.874129 TAAGAATGCGGGGGAGAAGA 58.126 50.000 0.00 0.00 0.00 2.87
545 2997 2.710096 TTAAGAATGCGGGGGAGAAG 57.290 50.000 0.00 0.00 0.00 2.85
546 2998 3.443145 TTTTAAGAATGCGGGGGAGAA 57.557 42.857 0.00 0.00 0.00 2.87
547 2999 3.086282 GTTTTTAAGAATGCGGGGGAGA 58.914 45.455 0.00 0.00 0.00 3.71
548 3000 2.165641 GGTTTTTAAGAATGCGGGGGAG 59.834 50.000 0.00 0.00 0.00 4.30
549 3001 2.172679 GGTTTTTAAGAATGCGGGGGA 58.827 47.619 0.00 0.00 0.00 4.81
550 3002 1.896465 TGGTTTTTAAGAATGCGGGGG 59.104 47.619 0.00 0.00 0.00 5.40
555 3007 7.084486 GGATCGGATATGGTTTTTAAGAATGC 58.916 38.462 0.00 0.00 0.00 3.56
562 3014 5.381757 CCCTTGGATCGGATATGGTTTTTA 58.618 41.667 0.00 0.00 0.00 1.52
575 3027 4.918201 GAGCGCCCCCTTGGATCG 62.918 72.222 2.29 0.00 35.39 3.69
590 3042 0.460311 AGAATTACCCGTCGCTGGAG 59.540 55.000 0.00 0.00 0.00 3.86
592 3044 1.868519 GCTAGAATTACCCGTCGCTGG 60.869 57.143 0.00 0.00 0.00 4.85
595 3047 0.388294 AGGCTAGAATTACCCGTCGC 59.612 55.000 0.00 0.00 0.00 5.19
598 3050 3.131755 GTGTGTAGGCTAGAATTACCCGT 59.868 47.826 0.00 0.00 0.00 5.28
603 3055 4.703575 ACGACAGTGTGTAGGCTAGAATTA 59.296 41.667 0.00 0.00 0.00 1.40
606 3058 2.511659 ACGACAGTGTGTAGGCTAGAA 58.488 47.619 0.00 0.00 0.00 2.10
652 3300 4.162320 TCTCCTGGACATTCTAATCACCAC 59.838 45.833 0.00 0.00 0.00 4.16
665 3313 2.803956 ACGTAGTCAATCTCCTGGACA 58.196 47.619 0.00 0.00 29.74 4.02
683 3331 3.103911 GCGAAGGTGTGGTCGACG 61.104 66.667 9.92 0.00 39.64 5.12
696 3344 1.100463 TGCAAGCAAGGTTGAGCGAA 61.100 50.000 15.44 0.00 35.48 4.70
725 3373 2.387757 TCATGGAGGTCGACATGATCA 58.612 47.619 18.91 8.78 46.05 2.92
748 3396 3.587506 AGAGGGTTTAGTGGTGCAATACT 59.412 43.478 8.88 8.88 0.00 2.12
784 3485 4.412843 TCTCACCATGTCTACAACACCTA 58.587 43.478 0.00 0.00 41.75 3.08
786 3487 3.678056 TCTCACCATGTCTACAACACC 57.322 47.619 0.00 0.00 41.75 4.16
828 3530 7.962964 TGAAACTGTTAGATCTAAAGTGTGG 57.037 36.000 16.73 6.45 0.00 4.17
945 3652 9.066892 CCACACCAAATATAAGCAACATACTAT 57.933 33.333 0.00 0.00 0.00 2.12
1015 3722 1.362355 GTGGTTTTGTTGGGGAGCG 59.638 57.895 0.00 0.00 0.00 5.03
1048 3757 2.747855 GTTGGCTGCCTTCTCCCG 60.748 66.667 21.03 0.00 0.00 5.14
1050 3759 1.676967 CTGGTTGGCTGCCTTCTCC 60.677 63.158 21.03 15.80 0.00 3.71
1089 3799 2.562912 GACGTACGACCGGCTGAA 59.437 61.111 24.41 0.00 31.58 3.02
1091 3801 4.824166 CCGACGTACGACCGGCTG 62.824 72.222 29.16 14.34 45.77 4.85
1130 3840 2.568090 GCCTTGGATGGTGTTGCG 59.432 61.111 0.00 0.00 0.00 4.85
1138 3848 2.280079 GGGGGAAGGCCTTGGATG 59.720 66.667 26.25 0.00 0.00 3.51
1243 3957 0.531532 CGCAGGTATGAGGGAAGCTG 60.532 60.000 0.00 0.00 42.67 4.24
1300 4014 0.529992 CGGCAACTCGGTAGGAATCC 60.530 60.000 0.00 0.00 0.00 3.01
1320 4034 0.038526 ACGGACTGAACGTCATGACC 60.039 55.000 20.03 6.94 44.68 4.02
1331 4045 1.376942 GACGAGAGGGACGGACTGA 60.377 63.158 0.00 0.00 34.93 3.41
1398 4115 2.037136 GCTGCACTGCGAGGACAAT 61.037 57.895 0.00 0.00 0.00 2.71
1399 4116 2.666190 GCTGCACTGCGAGGACAA 60.666 61.111 0.00 0.00 0.00 3.18
1400 4117 3.927548 TGCTGCACTGCGAGGACA 61.928 61.111 0.00 0.00 35.36 4.02
1517 4240 2.671963 GTTCAAGGTGCCGTCCCC 60.672 66.667 0.00 0.00 0.00 4.81
1521 4244 2.430367 GGGAGTTCAAGGTGCCGT 59.570 61.111 0.00 0.00 0.00 5.68
1527 4250 0.250727 TCTTTGGCGGGAGTTCAAGG 60.251 55.000 0.00 0.00 0.00 3.61
1528 4251 1.266989 GTTCTTTGGCGGGAGTTCAAG 59.733 52.381 0.00 0.00 0.00 3.02
1529 4252 1.314730 GTTCTTTGGCGGGAGTTCAA 58.685 50.000 0.00 0.00 0.00 2.69
1530 4253 0.882927 CGTTCTTTGGCGGGAGTTCA 60.883 55.000 0.00 0.00 0.00 3.18
1531 4254 1.866925 CGTTCTTTGGCGGGAGTTC 59.133 57.895 0.00 0.00 0.00 3.01
1566 4289 1.680338 ATATCAAACCTGAAGGCGGC 58.320 50.000 0.00 0.00 39.32 6.53
1580 4303 6.662865 ACAACACATGGAAACCAAATATCA 57.337 33.333 0.00 0.00 36.95 2.15
1584 4307 4.450053 CCAACAACACATGGAAACCAAAT 58.550 39.130 0.00 0.00 39.12 2.32
1585 4308 3.866651 CCAACAACACATGGAAACCAAA 58.133 40.909 0.00 0.00 39.12 3.28
1587 4310 1.137872 GCCAACAACACATGGAAACCA 59.862 47.619 0.00 0.00 39.12 3.67
1588 4311 1.412343 AGCCAACAACACATGGAAACC 59.588 47.619 0.00 0.00 39.12 3.27
1589 4312 2.472816 CAGCCAACAACACATGGAAAC 58.527 47.619 0.00 0.00 39.12 2.78
1590 4313 1.202510 GCAGCCAACAACACATGGAAA 60.203 47.619 0.00 0.00 39.12 3.13
1591 4314 0.388659 GCAGCCAACAACACATGGAA 59.611 50.000 0.00 0.00 39.12 3.53
1593 4316 0.319211 CAGCAGCCAACAACACATGG 60.319 55.000 0.00 0.00 39.80 3.66
1594 4317 0.319211 CCAGCAGCCAACAACACATG 60.319 55.000 0.00 0.00 0.00 3.21
1595 4318 2.043625 CCAGCAGCCAACAACACAT 58.956 52.632 0.00 0.00 0.00 3.21
1596 4319 2.784356 GCCAGCAGCCAACAACACA 61.784 57.895 0.00 0.00 34.35 3.72
1597 4320 2.028043 GCCAGCAGCCAACAACAC 59.972 61.111 0.00 0.00 34.35 3.32
1615 4338 0.599204 ACTACGAACCAACTGCCACG 60.599 55.000 0.00 0.00 0.00 4.94
1619 4342 0.941542 TGCAACTACGAACCAACTGC 59.058 50.000 0.00 0.00 0.00 4.40
1625 4348 5.849604 GTCAAAACTTATGCAACTACGAACC 59.150 40.000 0.00 0.00 0.00 3.62
1633 4356 2.724174 GCCACGTCAAAACTTATGCAAC 59.276 45.455 0.00 0.00 0.00 4.17
1641 4368 2.542907 CGGCAGCCACGTCAAAACT 61.543 57.895 13.30 0.00 0.00 2.66
1708 4435 2.303549 GACATGTCCTCCCCGAGCAG 62.304 65.000 15.31 0.00 0.00 4.24
1817 4544 5.106475 ACAGAACAAGAGATCGACAGAGTAC 60.106 44.000 0.00 0.00 0.00 2.73
1818 4545 5.004448 ACAGAACAAGAGATCGACAGAGTA 58.996 41.667 0.00 0.00 0.00 2.59
1819 4546 3.823873 ACAGAACAAGAGATCGACAGAGT 59.176 43.478 0.00 0.00 0.00 3.24
1820 4547 4.433186 ACAGAACAAGAGATCGACAGAG 57.567 45.455 0.00 0.00 0.00 3.35
1821 4548 4.321304 GGAACAGAACAAGAGATCGACAGA 60.321 45.833 0.00 0.00 0.00 3.41
1822 4549 3.923461 GGAACAGAACAAGAGATCGACAG 59.077 47.826 0.00 0.00 0.00 3.51
1823 4550 3.574396 AGGAACAGAACAAGAGATCGACA 59.426 43.478 0.00 0.00 0.00 4.35
1824 4551 3.923461 CAGGAACAGAACAAGAGATCGAC 59.077 47.826 0.00 0.00 0.00 4.20
1825 4552 3.574396 ACAGGAACAGAACAAGAGATCGA 59.426 43.478 0.00 0.00 0.00 3.59
1826 4553 3.919216 ACAGGAACAGAACAAGAGATCG 58.081 45.455 0.00 0.00 0.00 3.69
1827 4554 4.693095 GGAACAGGAACAGAACAAGAGATC 59.307 45.833 0.00 0.00 0.00 2.75
1828 4555 4.349342 AGGAACAGGAACAGAACAAGAGAT 59.651 41.667 0.00 0.00 0.00 2.75
1829 4556 3.711704 AGGAACAGGAACAGAACAAGAGA 59.288 43.478 0.00 0.00 0.00 3.10
1830 4557 4.078639 AGGAACAGGAACAGAACAAGAG 57.921 45.455 0.00 0.00 0.00 2.85
1846 4573 1.909302 TGTCATGGAGAGGGAAGGAAC 59.091 52.381 0.00 0.00 0.00 3.62
1847 4574 2.342406 TGTCATGGAGAGGGAAGGAA 57.658 50.000 0.00 0.00 0.00 3.36
1848 4575 2.507058 CAATGTCATGGAGAGGGAAGGA 59.493 50.000 0.00 0.00 0.00 3.36
1849 4576 2.240667 ACAATGTCATGGAGAGGGAAGG 59.759 50.000 0.00 0.00 0.00 3.46
1851 4578 3.308402 GGAACAATGTCATGGAGAGGGAA 60.308 47.826 0.00 0.00 0.00 3.97
1852 4579 2.239654 GGAACAATGTCATGGAGAGGGA 59.760 50.000 0.00 0.00 0.00 4.20
1853 4580 2.240667 AGGAACAATGTCATGGAGAGGG 59.759 50.000 0.00 0.00 0.00 4.30
1854 4581 3.539604 GAGGAACAATGTCATGGAGAGG 58.460 50.000 0.00 0.00 0.00 3.69
1857 4584 2.240667 AGGGAGGAACAATGTCATGGAG 59.759 50.000 0.00 0.00 0.00 3.86
1858 4585 2.239654 GAGGGAGGAACAATGTCATGGA 59.760 50.000 0.00 0.00 0.00 3.41
1859 4586 2.648059 GAGGGAGGAACAATGTCATGG 58.352 52.381 0.00 0.00 0.00 3.66
1860 4587 2.240667 AGGAGGGAGGAACAATGTCATG 59.759 50.000 0.00 0.00 0.00 3.07
1861 4588 2.566746 AGGAGGGAGGAACAATGTCAT 58.433 47.619 0.00 0.00 0.00 3.06
1862 4589 2.044793 AGGAGGGAGGAACAATGTCA 57.955 50.000 0.00 0.00 0.00 3.58
1863 4590 2.305927 TGAAGGAGGGAGGAACAATGTC 59.694 50.000 0.00 0.00 0.00 3.06
1864 4591 2.348472 TGAAGGAGGGAGGAACAATGT 58.652 47.619 0.00 0.00 0.00 2.71
1865 4592 3.054139 TCATGAAGGAGGGAGGAACAATG 60.054 47.826 0.00 0.00 0.00 2.82
1866 4593 3.192944 TCATGAAGGAGGGAGGAACAAT 58.807 45.455 0.00 0.00 0.00 2.71
1867 4594 2.631384 TCATGAAGGAGGGAGGAACAA 58.369 47.619 0.00 0.00 0.00 2.83
1868 4595 2.342406 TCATGAAGGAGGGAGGAACA 57.658 50.000 0.00 0.00 0.00 3.18
1869 4596 2.774234 TCATCATGAAGGAGGGAGGAAC 59.226 50.000 0.00 0.00 0.00 3.62
1870 4597 3.135161 TCATCATGAAGGAGGGAGGAA 57.865 47.619 0.00 0.00 0.00 3.36
1871 4598 2.875102 TCATCATGAAGGAGGGAGGA 57.125 50.000 0.00 0.00 0.00 3.71
1872 4599 3.939740 TTTCATCATGAAGGAGGGAGG 57.060 47.619 0.00 0.00 37.70 4.30
1873 4600 4.583489 CCAATTTCATCATGAAGGAGGGAG 59.417 45.833 0.00 0.00 37.70 4.30
1874 4601 4.539726 CCAATTTCATCATGAAGGAGGGA 58.460 43.478 0.00 0.00 37.70 4.20
1875 4602 3.640029 CCCAATTTCATCATGAAGGAGGG 59.360 47.826 14.99 14.99 37.70 4.30
1876 4603 3.069158 GCCCAATTTCATCATGAAGGAGG 59.931 47.826 7.44 7.18 37.70 4.30
1879 4606 4.186159 GTTGCCCAATTTCATCATGAAGG 58.814 43.478 0.00 0.00 37.70 3.46
2086 4815 3.366052 AAGCCTATTGGTGTTAGTGGG 57.634 47.619 0.00 0.00 35.27 4.61
2124 4854 4.032355 CGTGTGATAAAAGTTGCAACGTT 58.968 39.130 22.64 22.64 32.00 3.99
2126 4856 2.400408 GCGTGTGATAAAAGTTGCAACG 59.600 45.455 23.21 9.25 0.00 4.10
2127 4857 3.367607 TGCGTGTGATAAAAGTTGCAAC 58.632 40.909 22.17 22.17 0.00 4.17
2274 5004 4.021102 ACATCAACTTTGACTCGGGAAT 57.979 40.909 0.00 0.00 40.49 3.01
2491 5221 0.400213 TTGAGGACTTGCCCGACAAT 59.600 50.000 0.00 0.00 37.72 2.71
2505 5235 3.145551 GCCATGGCTGCCTTGAGG 61.146 66.667 29.98 20.94 38.26 3.86
2623 5353 7.496346 TGGATTGGAGAGAGTACTACATTTT 57.504 36.000 0.00 0.00 30.29 1.82
2689 5419 3.996480 AGAAAGTGTTGTGGCTCTAGTC 58.004 45.455 0.00 0.00 0.00 2.59
2701 5431 3.821033 CCTCCGATCCAAAAGAAAGTGTT 59.179 43.478 0.00 0.00 0.00 3.32
2745 5475 8.848474 TTAGAATTTCTTTCTGTCCGAAGAAT 57.152 30.769 3.86 0.00 44.54 2.40
2752 5482 7.923414 TTAGCCTTAGAATTTCTTTCTGTCC 57.077 36.000 3.86 0.00 44.54 4.02
2877 5607 2.371179 TCGATAGGTCTACGGAGTCCAT 59.629 50.000 13.71 4.83 43.93 3.41
2994 5724 0.037326 TCGCGTTTCTCCAAGCTGAT 60.037 50.000 5.77 0.00 0.00 2.90
3076 5806 3.790123 GCTTATTTCAAGCGATGACTGGC 60.790 47.826 0.00 0.00 37.92 4.85
3092 5822 7.397192 ACCTTGTTGTATTGGATCTTGCTTATT 59.603 33.333 0.00 0.00 0.00 1.40
3126 5856 5.350504 ACATTGCTGCTTCTCTATGTACT 57.649 39.130 0.00 0.00 29.50 2.73
3127 5857 6.092670 TGAAACATTGCTGCTTCTCTATGTAC 59.907 38.462 0.00 0.00 30.40 2.90
3128 5858 6.172630 TGAAACATTGCTGCTTCTCTATGTA 58.827 36.000 0.00 0.00 30.40 2.29
3206 5939 5.886960 AGAGCACATTGAATAGGAAACAC 57.113 39.130 0.00 0.00 0.00 3.32
3230 5963 3.305608 GCAAACCCAACATCCTGAAAGAG 60.306 47.826 0.00 0.00 34.07 2.85
3331 6064 2.016393 GATCCCGAGCGATGGTGTCA 62.016 60.000 0.00 0.00 0.00 3.58
3497 6230 3.416156 GGATCTTCTTCAACTTGCCACT 58.584 45.455 0.00 0.00 0.00 4.00
3506 6239 2.364324 CGATACGGGGGATCTTCTTCAA 59.636 50.000 0.00 0.00 0.00 2.69
3553 6286 2.631418 TCACGTTCATCTCGACCTTC 57.369 50.000 0.00 0.00 0.00 3.46
3572 6305 1.737355 GCACCAGCACCACACACATT 61.737 55.000 0.00 0.00 41.58 2.71
3573 6306 2.195567 GCACCAGCACCACACACAT 61.196 57.895 0.00 0.00 41.58 3.21
3574 6307 2.828095 GCACCAGCACCACACACA 60.828 61.111 0.00 0.00 41.58 3.72
3575 6308 2.516930 AGCACCAGCACCACACAC 60.517 61.111 0.00 0.00 45.49 3.82
3576 6309 2.516695 CAGCACCAGCACCACACA 60.517 61.111 0.00 0.00 45.49 3.72
3577 6310 3.289834 CCAGCACCAGCACCACAC 61.290 66.667 0.00 0.00 45.49 3.82
3580 6313 2.066700 TTGATCCAGCACCAGCACCA 62.067 55.000 0.00 0.00 45.49 4.17
3585 6318 1.093159 GCTTCTTGATCCAGCACCAG 58.907 55.000 0.00 0.00 33.45 4.00
3695 6496 2.235898 GCCTCTTCTCTTCACCAGATGT 59.764 50.000 0.00 0.00 0.00 3.06
3708 6509 2.789409 ATTTTACAGGCGCCTCTTCT 57.211 45.000 30.29 11.97 0.00 2.85
3709 6510 2.288186 GCTATTTTACAGGCGCCTCTTC 59.712 50.000 30.29 0.00 0.00 2.87
3710 6511 2.092914 AGCTATTTTACAGGCGCCTCTT 60.093 45.455 30.29 19.66 0.00 2.85
3835 6649 9.840427 GTGTTATTTAGATTTTGCTGCTTAAGA 57.160 29.630 6.67 0.00 0.00 2.10
3866 6680 5.312895 TGGTGCAGATTACTGTTTATGTGT 58.687 37.500 0.00 0.00 45.04 3.72
4011 9451 2.379972 TCCGGTCAAATTGTTGGTTGT 58.620 42.857 0.00 0.00 35.29 3.32
4028 9468 3.303395 GCAAGTGACTTCAGAGTTTTCCG 60.303 47.826 0.00 0.00 35.88 4.30
4083 9523 7.762615 CGAACTACTAGTGGGAATAAATTGTCA 59.237 37.037 11.30 0.00 0.00 3.58
4103 9543 3.462483 TTGAACTTGTCTGCCGAACTA 57.538 42.857 0.00 0.00 0.00 2.24
4108 9548 2.869801 TGTAGTTTGAACTTGTCTGCCG 59.130 45.455 1.20 0.00 40.37 5.69
4390 9830 0.179081 GGGCGAAGACATACCCAGAC 60.179 60.000 0.00 0.00 37.00 3.51
4574 10022 2.802816 AGAAGATGTGTGAACGCAGAAC 59.197 45.455 2.83 0.00 39.97 3.01
4578 10026 6.149129 AGATATAGAAGATGTGTGAACGCA 57.851 37.500 0.00 0.00 40.98 5.24
4591 10039 7.844779 TGGGGGCTAGGTATTTAGATATAGAAG 59.155 40.741 0.00 0.00 0.00 2.85
4592 10040 7.622479 GTGGGGGCTAGGTATTTAGATATAGAA 59.378 40.741 0.00 0.00 0.00 2.10
4593 10041 7.035320 AGTGGGGGCTAGGTATTTAGATATAGA 60.035 40.741 0.00 0.00 0.00 1.98
4594 10042 7.133483 AGTGGGGGCTAGGTATTTAGATATAG 58.867 42.308 0.00 0.00 0.00 1.31
4595 10043 7.065018 AGTGGGGGCTAGGTATTTAGATATA 57.935 40.000 0.00 0.00 0.00 0.86
4596 10044 5.928656 AGTGGGGGCTAGGTATTTAGATAT 58.071 41.667 0.00 0.00 0.00 1.63
4597 10045 5.364620 AGTGGGGGCTAGGTATTTAGATA 57.635 43.478 0.00 0.00 0.00 1.98
4598 10046 4.229718 AGTGGGGGCTAGGTATTTAGAT 57.770 45.455 0.00 0.00 0.00 1.98
4599 10047 3.719368 AGTGGGGGCTAGGTATTTAGA 57.281 47.619 0.00 0.00 0.00 2.10
4600 10048 4.041321 GGTTAGTGGGGGCTAGGTATTTAG 59.959 50.000 0.00 0.00 0.00 1.85
4601 10049 3.975982 GGTTAGTGGGGGCTAGGTATTTA 59.024 47.826 0.00 0.00 0.00 1.40
4602 10050 2.781757 GGTTAGTGGGGGCTAGGTATTT 59.218 50.000 0.00 0.00 0.00 1.40
4603 10051 2.021341 AGGTTAGTGGGGGCTAGGTATT 60.021 50.000 0.00 0.00 0.00 1.89
4604 10052 1.584105 AGGTTAGTGGGGGCTAGGTAT 59.416 52.381 0.00 0.00 0.00 2.73
4605 10053 1.021275 AGGTTAGTGGGGGCTAGGTA 58.979 55.000 0.00 0.00 0.00 3.08
4606 10054 1.021275 TAGGTTAGTGGGGGCTAGGT 58.979 55.000 0.00 0.00 0.00 3.08
4607 10055 2.417719 ATAGGTTAGTGGGGGCTAGG 57.582 55.000 0.00 0.00 0.00 3.02
4608 10056 3.974642 AGAAATAGGTTAGTGGGGGCTAG 59.025 47.826 0.00 0.00 0.00 3.42
4609 10057 3.971971 GAGAAATAGGTTAGTGGGGGCTA 59.028 47.826 0.00 0.00 0.00 3.93
4610 10058 2.778270 GAGAAATAGGTTAGTGGGGGCT 59.222 50.000 0.00 0.00 0.00 5.19
4611 10059 2.778270 AGAGAAATAGGTTAGTGGGGGC 59.222 50.000 0.00 0.00 0.00 5.80
4612 10060 4.037927 TGAGAGAAATAGGTTAGTGGGGG 58.962 47.826 0.00 0.00 0.00 5.40
4613 10061 5.045869 TGTTGAGAGAAATAGGTTAGTGGGG 60.046 44.000 0.00 0.00 0.00 4.96
4614 10062 6.049955 TGTTGAGAGAAATAGGTTAGTGGG 57.950 41.667 0.00 0.00 0.00 4.61
4615 10063 6.763610 GGATGTTGAGAGAAATAGGTTAGTGG 59.236 42.308 0.00 0.00 0.00 4.00
4616 10064 7.331026 TGGATGTTGAGAGAAATAGGTTAGTG 58.669 38.462 0.00 0.00 0.00 2.74
4617 10065 7.496346 TGGATGTTGAGAGAAATAGGTTAGT 57.504 36.000 0.00 0.00 0.00 2.24
4618 10066 7.011857 GCTTGGATGTTGAGAGAAATAGGTTAG 59.988 40.741 0.00 0.00 0.00 2.34
4619 10067 6.823689 GCTTGGATGTTGAGAGAAATAGGTTA 59.176 38.462 0.00 0.00 0.00 2.85
4620 10068 5.649831 GCTTGGATGTTGAGAGAAATAGGTT 59.350 40.000 0.00 0.00 0.00 3.50
4621 10069 5.189180 GCTTGGATGTTGAGAGAAATAGGT 58.811 41.667 0.00 0.00 0.00 3.08
4622 10070 5.188434 TGCTTGGATGTTGAGAGAAATAGG 58.812 41.667 0.00 0.00 0.00 2.57
4623 10071 6.726230 CATGCTTGGATGTTGAGAGAAATAG 58.274 40.000 0.00 0.00 0.00 1.73
4624 10072 5.066893 GCATGCTTGGATGTTGAGAGAAATA 59.933 40.000 11.37 0.00 0.00 1.40
4625 10073 4.142227 GCATGCTTGGATGTTGAGAGAAAT 60.142 41.667 11.37 0.00 0.00 2.17
4626 10074 3.192001 GCATGCTTGGATGTTGAGAGAAA 59.808 43.478 11.37 0.00 0.00 2.52
4627 10075 2.751259 GCATGCTTGGATGTTGAGAGAA 59.249 45.455 11.37 0.00 0.00 2.87
4628 10076 2.362736 GCATGCTTGGATGTTGAGAGA 58.637 47.619 11.37 0.00 0.00 3.10
4629 10077 1.404391 GGCATGCTTGGATGTTGAGAG 59.596 52.381 18.92 0.00 0.00 3.20
4630 10078 1.272037 TGGCATGCTTGGATGTTGAGA 60.272 47.619 18.92 0.00 0.00 3.27
4631 10079 1.135199 GTGGCATGCTTGGATGTTGAG 60.135 52.381 18.92 0.00 0.00 3.02
4632 10080 0.889994 GTGGCATGCTTGGATGTTGA 59.110 50.000 18.92 0.00 0.00 3.18
4633 10081 0.108520 GGTGGCATGCTTGGATGTTG 60.109 55.000 18.92 0.00 0.00 3.33
4634 10082 0.251922 AGGTGGCATGCTTGGATGTT 60.252 50.000 18.92 0.00 0.00 2.71
4635 10083 0.682209 GAGGTGGCATGCTTGGATGT 60.682 55.000 18.92 0.00 0.00 3.06
4636 10084 0.681887 TGAGGTGGCATGCTTGGATG 60.682 55.000 18.92 0.00 0.00 3.51
4637 10085 0.260816 ATGAGGTGGCATGCTTGGAT 59.739 50.000 18.92 0.00 0.00 3.41
4638 10086 0.394762 GATGAGGTGGCATGCTTGGA 60.395 55.000 18.92 0.00 0.00 3.53
4639 10087 0.681887 TGATGAGGTGGCATGCTTGG 60.682 55.000 18.92 0.00 0.00 3.61
4640 10088 1.067060 CATGATGAGGTGGCATGCTTG 59.933 52.381 18.92 0.00 33.81 4.01
4641 10089 1.064240 TCATGATGAGGTGGCATGCTT 60.064 47.619 18.92 0.65 39.30 3.91
4642 10090 0.549469 TCATGATGAGGTGGCATGCT 59.451 50.000 18.92 0.00 39.30 3.79
4643 10091 1.395635 TTCATGATGAGGTGGCATGC 58.604 50.000 9.90 9.90 39.30 4.06


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

AutoCloner maintained by Alex Coulton.