Multiple sequence alignment - TraesCS5A01G374300

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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 TraesCS5A01G374300 chr5A 100.000 9596 0 0 1 9596 572811705 572821300 0.000000e+00 17721.0
1 TraesCS5A01G374300 chr5A 94.985 678 27 5 8920 9596 680199042 680199713 0.000000e+00 1057.0
2 TraesCS5A01G374300 chr5A 100.000 34 0 0 8597 8630 572820266 572820299 8.050000e-06 63.9
3 TraesCS5A01G374300 chr5A 100.000 34 0 0 8562 8595 572820301 572820334 8.050000e-06 63.9
4 TraesCS5A01G374300 chr5D 96.815 6343 139 29 1958 8270 453774176 453780485 0.000000e+00 10536.0
5 TraesCS5A01G374300 chr5D 92.988 1911 73 31 1 1896 453772033 453773897 0.000000e+00 2730.0
6 TraesCS5A01G374300 chr5D 94.118 204 8 2 8393 8596 453780571 453780770 3.370000e-79 307.0
7 TraesCS5A01G374300 chr5D 94.286 105 6 0 8809 8913 453781017 453781121 2.770000e-35 161.0
8 TraesCS5A01G374300 chr5D 92.453 106 5 3 8597 8701 453780736 453780839 2.160000e-31 148.0
9 TraesCS5A01G374300 chr5D 100.000 69 0 0 1895 1963 453774078 453774146 2.810000e-25 128.0
10 TraesCS5A01G374300 chr5D 85.714 105 6 5 8707 8809 453780898 453780995 1.700000e-17 102.0
11 TraesCS5A01G374300 chr5B 96.001 6501 166 35 1895 8327 554205596 554212070 0.000000e+00 10479.0
12 TraesCS5A01G374300 chr5B 93.893 1228 44 16 676 1896 554204211 554205414 0.000000e+00 1823.0
13 TraesCS5A01G374300 chr5B 93.908 476 21 4 223 690 554203779 554204254 0.000000e+00 712.0
14 TraesCS5A01G374300 chr5B 93.750 320 14 5 8282 8596 554212088 554212406 8.720000e-130 475.0
15 TraesCS5A01G374300 chr5B 93.722 223 6 4 8697 8913 554212527 554212747 2.580000e-85 327.0
16 TraesCS5A01G374300 chr5B 97.143 105 2 1 8597 8701 554212372 554212475 9.900000e-40 176.0
17 TraesCS5A01G374300 chr7A 95.864 677 25 2 8920 9596 22949874 22949201 0.000000e+00 1092.0
18 TraesCS5A01G374300 chr7A 95.308 682 25 7 8915 9596 44758217 44758891 0.000000e+00 1075.0
19 TraesCS5A01G374300 chr2A 95.864 677 25 3 8920 9596 120228406 120227733 0.000000e+00 1092.0
20 TraesCS5A01G374300 chr2A 95.852 675 24 4 8922 9596 71752070 71751400 0.000000e+00 1088.0
21 TraesCS5A01G374300 chr6A 95.294 680 26 6 8920 9596 86403862 86404538 0.000000e+00 1074.0
22 TraesCS5A01G374300 chr3A 95.280 678 28 3 8919 9596 749613370 749614043 0.000000e+00 1072.0
23 TraesCS5A01G374300 chr3A 94.100 678 37 3 8920 9596 658634532 658635207 0.000000e+00 1027.0
24 TraesCS5A01G374300 chr4A 95.448 659 26 4 8920 9577 38291169 38290514 0.000000e+00 1048.0
25 TraesCS5A01G374300 chr1D 88.889 63 6 1 8321 8383 218898628 218898567 1.030000e-09 76.8


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 TraesCS5A01G374300 chr5A 572811705 572821300 9595 False 5949.6 17721 100.000000 1 9596 3 chr5A.!!$F2 9595
1 TraesCS5A01G374300 chr5A 680199042 680199713 671 False 1057.0 1057 94.985000 8920 9596 1 chr5A.!!$F1 676
2 TraesCS5A01G374300 chr5D 453772033 453781121 9088 False 2016.0 10536 93.767714 1 8913 7 chr5D.!!$F1 8912
3 TraesCS5A01G374300 chr5B 554203779 554212747 8968 False 2332.0 10479 94.736167 223 8913 6 chr5B.!!$F1 8690
4 TraesCS5A01G374300 chr7A 22949201 22949874 673 True 1092.0 1092 95.864000 8920 9596 1 chr7A.!!$R1 676
5 TraesCS5A01G374300 chr7A 44758217 44758891 674 False 1075.0 1075 95.308000 8915 9596 1 chr7A.!!$F1 681
6 TraesCS5A01G374300 chr2A 120227733 120228406 673 True 1092.0 1092 95.864000 8920 9596 1 chr2A.!!$R2 676
7 TraesCS5A01G374300 chr2A 71751400 71752070 670 True 1088.0 1088 95.852000 8922 9596 1 chr2A.!!$R1 674
8 TraesCS5A01G374300 chr6A 86403862 86404538 676 False 1074.0 1074 95.294000 8920 9596 1 chr6A.!!$F1 676
9 TraesCS5A01G374300 chr3A 749613370 749614043 673 False 1072.0 1072 95.280000 8919 9596 1 chr3A.!!$F2 677
10 TraesCS5A01G374300 chr3A 658634532 658635207 675 False 1027.0 1027 94.100000 8920 9596 1 chr3A.!!$F1 676
11 TraesCS5A01G374300 chr4A 38290514 38291169 655 True 1048.0 1048 95.448000 8920 9577 1 chr4A.!!$R1 657

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
798 822 1.109920 TAAAAACAGGCCCAGCGCAA 61.110 50.000 11.47 0.00 40.31 4.85 F
1278 1304 0.316522 CCATGCAGGAGATCGTCGAT 59.683 55.000 7.63 7.63 41.22 3.59 F
1675 1704 0.470341 AAGCTCCCTTTCGGATAGCC 59.530 55.000 0.00 0.00 41.00 3.93 F
3022 3278 0.743345 GCGCGAAAGGGGTCAGTAAT 60.743 55.000 12.10 0.00 45.27 1.89 F
3763 4029 1.382629 GCCCCATGTTGGTGTAGGT 59.617 57.895 0.00 0.00 35.17 3.08 F
4722 4995 0.111061 TGATGTGCCCTGCTGAAACT 59.889 50.000 0.00 0.00 0.00 2.66 F
5541 5830 3.508762 AGTTGGTGTCGTTCGTGATATC 58.491 45.455 0.00 0.00 0.00 1.63 F
7035 7335 0.251922 ACCACCGGTAAGTAGAGGCA 60.252 55.000 6.87 0.00 32.11 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2014 2265 0.465460 AACAGCACCCACATCAACGT 60.465 50.000 0.0 0.0 0.00 3.99 R
2081 2335 0.823356 TTCAGAACTTGTGGGGCAGC 60.823 55.000 0.0 0.0 0.00 5.25 R
3494 3757 1.594331 AGTTCCAACCGAAGCTCAAC 58.406 50.000 0.0 0.0 0.00 3.18 R
3924 4190 2.079158 CGACCAAGAGCACACATCAAT 58.921 47.619 0.0 0.0 0.00 2.57 R
4765 5038 2.226437 CCATTGACCAACTCCTTTGACG 59.774 50.000 0.0 0.0 37.39 4.35 R
6191 6487 3.689161 TGCAGTGGATTAGCATTGTGTAC 59.311 43.478 0.0 0.0 32.55 2.90 R
7154 7454 4.201990 GCATCATCTTGTGGAATTGGAGAC 60.202 45.833 0.0 0.0 0.00 3.36 R
8624 8995 0.042188 CAACACTCGAAGCACAACGG 60.042 55.000 0.0 0.0 0.00 4.44 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
125 126 4.081031 ACTGTTCATCAGAGAGCATGTGAT 60.081 41.667 1.79 0.00 46.27 3.06
148 149 4.999950 TCTCAGGATCAAAAGAGCACTTTC 59.000 41.667 9.66 0.00 44.32 2.62
149 150 4.717877 TCAGGATCAAAAGAGCACTTTCA 58.282 39.130 9.66 0.56 44.32 2.69
150 151 4.516698 TCAGGATCAAAAGAGCACTTTCAC 59.483 41.667 9.66 2.57 44.32 3.18
151 152 3.499918 AGGATCAAAAGAGCACTTTCACG 59.500 43.478 9.66 2.53 44.32 4.35
159 160 5.401531 AAGAGCACTTTCACGGTATCTTA 57.598 39.130 0.00 0.00 31.71 2.10
255 256 6.715718 AGACTTGTAGCACTGTAACTTCTCTA 59.284 38.462 0.00 0.00 0.00 2.43
379 390 7.891183 ACATGGAAAGCTCATATACGATTAC 57.109 36.000 0.00 0.00 0.00 1.89
392 403 5.907197 ATACGATTACAGTTGTAGCATGC 57.093 39.130 10.51 10.51 0.00 4.06
397 408 4.443913 TTACAGTTGTAGCATGCGAGTA 57.556 40.909 13.01 2.40 0.00 2.59
490 504 8.548721 AGTAACAATTGACTGAAACTAAGAACG 58.451 33.333 13.59 0.00 0.00 3.95
583 601 9.880157 AAACGCCTTATATAAGTTTACAGAAGA 57.120 29.630 18.91 0.00 33.84 2.87
602 620 8.934697 ACAGAAGAGGTAGTGCCATTTTATATA 58.065 33.333 0.00 0.00 40.61 0.86
681 705 3.793819 TTTTTAGGGTATATCCGGCCC 57.206 47.619 5.98 5.98 42.64 5.80
687 711 3.063510 GGGTATATCCGGCCCTTTTAC 57.936 52.381 6.83 0.00 39.31 2.01
688 712 2.372837 GGGTATATCCGGCCCTTTTACA 59.627 50.000 6.83 0.00 39.31 2.41
689 713 3.009805 GGGTATATCCGGCCCTTTTACAT 59.990 47.826 6.83 0.00 39.31 2.29
690 714 4.507869 GGGTATATCCGGCCCTTTTACATT 60.508 45.833 6.83 0.00 39.31 2.71
691 715 5.074804 GGTATATCCGGCCCTTTTACATTT 58.925 41.667 0.00 0.00 0.00 2.32
692 716 5.537295 GGTATATCCGGCCCTTTTACATTTT 59.463 40.000 0.00 0.00 0.00 1.82
693 717 6.041182 GGTATATCCGGCCCTTTTACATTTTT 59.959 38.462 0.00 0.00 0.00 1.94
725 749 1.385528 CGGCCCTTTTACATGGTACC 58.614 55.000 4.43 4.43 0.00 3.34
783 807 2.223745 GTCACCAAACGAGGCCTAAAA 58.776 47.619 4.42 0.00 0.00 1.52
784 808 2.619646 GTCACCAAACGAGGCCTAAAAA 59.380 45.455 4.42 0.00 0.00 1.94
798 822 1.109920 TAAAAACAGGCCCAGCGCAA 61.110 50.000 11.47 0.00 40.31 4.85
799 823 2.642996 AAAAACAGGCCCAGCGCAAC 62.643 55.000 11.47 0.00 40.31 4.17
802 826 3.604667 CAGGCCCAGCGCAACAAA 61.605 61.111 11.47 0.00 40.31 2.83
803 827 3.605664 AGGCCCAGCGCAACAAAC 61.606 61.111 11.47 0.00 40.31 2.93
804 828 3.910490 GGCCCAGCGCAACAAACA 61.910 61.111 11.47 0.00 40.31 2.83
805 829 2.658268 GCCCAGCGCAACAAACAC 60.658 61.111 11.47 0.00 37.47 3.32
1014 1040 2.024871 GCGATGGAGGACGACGAG 59.975 66.667 0.00 0.00 0.00 4.18
1278 1304 0.316522 CCATGCAGGAGATCGTCGAT 59.683 55.000 7.63 7.63 41.22 3.59
1416 1442 1.004679 GTCGGTTAGGGTTTGGCGA 60.005 57.895 0.00 0.00 0.00 5.54
1444 1470 3.372554 GACTAGCTGGTGACGGGCC 62.373 68.421 7.76 0.00 37.13 5.80
1486 1512 3.539604 GCTGCTCAAATAGATGACCAGT 58.460 45.455 0.00 0.00 36.06 4.00
1549 1576 2.490902 GGTGGGGGTCTGAGAATTTTGT 60.491 50.000 0.00 0.00 0.00 2.83
1567 1594 9.584839 GAATTTTGTCAATGATTAAGCAACAAC 57.415 29.630 8.54 3.17 0.00 3.32
1568 1595 8.659925 ATTTTGTCAATGATTAAGCAACAACA 57.340 26.923 8.54 4.10 0.00 3.33
1615 1642 8.090214 GGTTGGATTGAATTTTGATTCTGAAGA 58.910 33.333 0.00 0.00 0.00 2.87
1651 1680 1.552337 TGTGTTCAGATGAGAGCTCCC 59.448 52.381 10.93 0.00 0.00 4.30
1675 1704 0.470341 AAGCTCCCTTTCGGATAGCC 59.530 55.000 0.00 0.00 41.00 3.93
1687 1716 1.230324 GGATAGCCGCTAAAGCTTGG 58.770 55.000 3.73 0.00 41.83 3.61
1712 1742 1.833630 CAGAGGTGGCACTAGGAATGA 59.166 52.381 18.45 0.00 0.00 2.57
1783 1813 3.199946 TCATGGGTATTTGTCTCAGGGTC 59.800 47.826 0.00 0.00 0.00 4.46
1786 1816 4.431378 TGGGTATTTGTCTCAGGGTCTTA 58.569 43.478 0.00 0.00 0.00 2.10
1787 1817 4.224370 TGGGTATTTGTCTCAGGGTCTTAC 59.776 45.833 0.00 0.00 0.00 2.34
1788 1818 4.470304 GGGTATTTGTCTCAGGGTCTTACT 59.530 45.833 0.00 0.00 0.00 2.24
1789 1819 5.659971 GGGTATTTGTCTCAGGGTCTTACTA 59.340 44.000 0.00 0.00 0.00 1.82
1790 1820 6.326843 GGGTATTTGTCTCAGGGTCTTACTAT 59.673 42.308 0.00 0.00 0.00 2.12
1791 1821 7.435305 GGTATTTGTCTCAGGGTCTTACTATC 58.565 42.308 0.00 0.00 0.00 2.08
1792 1822 7.069578 GGTATTTGTCTCAGGGTCTTACTATCA 59.930 40.741 0.00 0.00 0.00 2.15
1794 1824 6.531503 TTGTCTCAGGGTCTTACTATCAAG 57.468 41.667 0.00 0.00 0.00 3.02
1795 1825 5.827756 TGTCTCAGGGTCTTACTATCAAGA 58.172 41.667 0.00 0.00 32.11 3.02
1796 1826 6.436027 TGTCTCAGGGTCTTACTATCAAGAT 58.564 40.000 0.00 0.00 36.93 2.40
1828 1859 7.271511 TGTTATTTTGCCTGTTTTCATCAGTT 58.728 30.769 0.00 0.00 0.00 3.16
1976 2227 2.371841 TGGTGTCTCACTGGCTGTTATT 59.628 45.455 0.00 0.00 34.40 1.40
2014 2265 3.682858 GCCTATGCGAACAAGAACTACAA 59.317 43.478 0.00 0.00 0.00 2.41
2054 2305 8.117370 GCTGTTAAGCTTTAAGCAGTATAAGTC 58.883 37.037 19.63 3.54 45.56 3.01
2081 2335 6.935240 TCCACTATGGTAATAGGGAATGAG 57.065 41.667 0.00 0.00 41.68 2.90
2109 2363 4.380233 CCCACAAGTTCTGAAGATGAATGC 60.380 45.833 8.78 0.00 0.00 3.56
2112 2366 5.048921 CACAAGTTCTGAAGATGAATGCTGT 60.049 40.000 8.78 0.00 0.00 4.40
2355 2611 4.990426 CCCTTTCAGTTTAAACCATGCTTG 59.010 41.667 14.72 5.78 0.00 4.01
2680 2936 3.936564 TGACACATGCTTGTAGTATGCA 58.063 40.909 4.73 0.00 41.24 3.96
2770 3026 3.038017 CTGCACACTGTTTCAACAATCG 58.962 45.455 0.00 0.00 38.66 3.34
3022 3278 0.743345 GCGCGAAAGGGGTCAGTAAT 60.743 55.000 12.10 0.00 45.27 1.89
3047 3303 4.401925 ACTGAAGCCTTGCAAATAGTTCT 58.598 39.130 0.00 0.00 0.00 3.01
3076 3332 2.103094 TGCATGTGTATCAGTCTAGGGC 59.897 50.000 0.00 0.00 0.00 5.19
3077 3333 2.548920 GCATGTGTATCAGTCTAGGGCC 60.549 54.545 0.00 0.00 0.00 5.80
3078 3334 2.543037 TGTGTATCAGTCTAGGGCCA 57.457 50.000 6.18 0.00 0.00 5.36
3256 3512 5.932303 TGTGTTTAGAGCACTAGGATTTGTC 59.068 40.000 0.00 0.00 37.70 3.18
3375 3631 4.706476 TCAAAATCAGCAGGTATTCCTTGG 59.294 41.667 0.00 0.00 43.07 3.61
3380 3636 1.490910 AGCAGGTATTCCTTGGGCTAC 59.509 52.381 0.47 0.00 43.07 3.58
3421 3677 9.768662 AAATTGTTCTTTATCACTTGCAATCTT 57.231 25.926 0.00 0.00 0.00 2.40
3422 3678 8.752766 ATTGTTCTTTATCACTTGCAATCTTG 57.247 30.769 0.00 0.00 0.00 3.02
3456 3712 7.700505 TCACATCTGCTTGAATTTATGTCATC 58.299 34.615 0.00 0.00 0.00 2.92
3494 3757 3.420893 TCTTGTTGGGGCACATCTTAAG 58.579 45.455 0.00 0.00 0.00 1.85
3588 3854 3.777522 AGCCTTATCTGTAGGTTGCTCTT 59.222 43.478 0.00 0.00 35.13 2.85
3606 3872 4.245660 CTCTTGACTACATTGGAAAGCGA 58.754 43.478 0.00 0.00 0.00 4.93
3763 4029 1.382629 GCCCCATGTTGGTGTAGGT 59.617 57.895 0.00 0.00 35.17 3.08
3796 4062 8.780249 TGTGAAACTAAAAAGGCATACTACTTC 58.220 33.333 0.00 0.00 38.04 3.01
3806 4072 3.319972 GGCATACTACTTCGGGTATGTGA 59.680 47.826 12.56 0.00 43.96 3.58
3855 4121 9.195411 TGTCAATCAAAAAGTTTGCATTCTATC 57.805 29.630 0.00 0.00 0.00 2.08
3921 4187 8.536175 TCATTATGCAGGTATATTATTCACCGA 58.464 33.333 0.00 0.00 37.42 4.69
3924 4190 6.904463 TGCAGGTATATTATTCACCGACTA 57.096 37.500 0.00 0.00 37.42 2.59
4063 4329 5.042593 TGCTAGCAAATTTGAGTGTGTTTG 58.957 37.500 22.31 2.31 35.30 2.93
4108 4374 7.809806 GCTGTGAGCTTAATTATGTTGTTCTTT 59.190 33.333 0.00 0.00 38.45 2.52
4184 4450 4.276926 CAGAAGGTTTCTCCCTTGTTTCAG 59.723 45.833 0.00 0.00 44.91 3.02
4201 4467 1.973515 TCAGTGACCATGCTCTGTCTT 59.026 47.619 0.00 0.00 32.71 3.01
4253 4519 2.799126 TCTGTTGAACCCAGTGTGTT 57.201 45.000 0.00 0.00 0.00 3.32
4403 4669 5.700832 GTCTCAGGTGTGTACATTTTCATGA 59.299 40.000 0.00 0.00 34.11 3.07
4443 4716 7.278461 TGCTTTACTACAATTTGGTTTAGCA 57.722 32.000 0.78 5.46 0.00 3.49
4450 4723 7.430441 ACTACAATTTGGTTTAGCAAACGAAT 58.570 30.769 9.04 0.00 42.29 3.34
4464 4737 4.031652 GCAAACGAATGTTCCAATATGTGC 59.968 41.667 0.00 0.00 37.31 4.57
4590 4863 8.149647 TGAAGGTTGATATTGCTCAAATTGTTT 58.850 29.630 0.00 0.00 36.92 2.83
4634 4907 0.464452 CCTGGTCGCCTTAGGGTTAG 59.536 60.000 0.00 0.00 34.45 2.34
4722 4995 0.111061 TGATGTGCCCTGCTGAAACT 59.889 50.000 0.00 0.00 0.00 2.66
4795 5068 8.664669 AAGGAGTTGGTCAATGGTTTATATTT 57.335 30.769 0.00 0.00 0.00 1.40
4869 5142 5.648092 GGTTTATATCACTGTTGGTTCTGCT 59.352 40.000 0.00 0.00 0.00 4.24
4972 5245 6.905076 GCATGCATTTTCATTTGCTTATCTTG 59.095 34.615 14.21 0.00 39.60 3.02
4985 5258 4.835615 TGCTTATCTTGCCCAAGGTTAAAA 59.164 37.500 8.06 0.00 38.88 1.52
5035 5308 5.119279 AGTCACTGATTTCGTTCTTGATTCG 59.881 40.000 0.00 0.00 0.00 3.34
5090 5363 6.855836 TCCTCAAGCTGCTAAAATATTTGTG 58.144 36.000 0.90 0.00 0.00 3.33
5329 5611 5.067805 CCTTCCATATGCAACCCTAACTTTC 59.932 44.000 0.00 0.00 0.00 2.62
5331 5613 5.826643 TCCATATGCAACCCTAACTTTCTT 58.173 37.500 0.00 0.00 0.00 2.52
5332 5614 6.252995 TCCATATGCAACCCTAACTTTCTTT 58.747 36.000 0.00 0.00 0.00 2.52
5333 5615 6.152661 TCCATATGCAACCCTAACTTTCTTTG 59.847 38.462 0.00 0.00 0.00 2.77
5334 5616 6.152661 CCATATGCAACCCTAACTTTCTTTGA 59.847 38.462 0.00 0.00 0.00 2.69
5341 5623 7.415653 GCAACCCTAACTTTCTTTGATATCTGG 60.416 40.741 3.98 0.00 0.00 3.86
5541 5830 3.508762 AGTTGGTGTCGTTCGTGATATC 58.491 45.455 0.00 0.00 0.00 1.63
5674 5963 6.264067 GCAGCAAAGGGTCTGATATTCTTTAT 59.736 38.462 0.00 0.00 32.26 1.40
5953 6243 8.224025 TCCATTCTATTGGCATTCCTTTACATA 58.776 33.333 0.00 0.00 36.66 2.29
6117 6413 5.125578 TGAGACTTATACGCACTGTGAGATT 59.874 40.000 18.40 7.27 0.00 2.40
6191 6487 1.553690 AACCAGGTGACTCATCCCCG 61.554 60.000 0.00 0.00 40.21 5.73
6712 7008 2.632996 TCGTGGGTTCTTCAGATCACTT 59.367 45.455 0.00 0.00 0.00 3.16
6813 7113 6.039270 TGCCCAATCTAATAATTCAAACTCCG 59.961 38.462 0.00 0.00 0.00 4.63
6842 7142 4.165758 AGAGATGAGGAAAAGAAGATGGGG 59.834 45.833 0.00 0.00 0.00 4.96
6951 7251 6.054295 AGCAGATCTGATGAACTAACATTCC 58.946 40.000 27.04 2.43 0.00 3.01
7035 7335 0.251922 ACCACCGGTAAGTAGAGGCA 60.252 55.000 6.87 0.00 32.11 4.75
7154 7454 5.237344 GGAAGATGTCATTATTGGGAAGACG 59.763 44.000 0.00 0.00 32.08 4.18
7269 7569 4.142049 TGGTGGATCAGGTTTGTTTGTTTC 60.142 41.667 0.00 0.00 0.00 2.78
7295 7595 4.549458 CTTTCTGCCACCACTTTTATGTG 58.451 43.478 0.00 0.00 37.66 3.21
7662 7962 7.539436 TCACTGATGTTACTGTGAGTAATCTC 58.461 38.462 0.00 0.00 42.06 2.75
7742 8042 6.701841 TCCTCATGTGATCTTTTAATAGCGTC 59.298 38.462 0.00 0.00 0.00 5.19
7760 8060 4.463186 AGCGTCTGTAACCTCTTGTCTAAT 59.537 41.667 0.00 0.00 0.00 1.73
7762 8062 5.638234 GCGTCTGTAACCTCTTGTCTAATTT 59.362 40.000 0.00 0.00 0.00 1.82
7795 8099 6.437928 ACTTAACTTGCAATGTATGTGTGTG 58.562 36.000 0.00 0.00 0.00 3.82
8233 8537 1.334869 AGAGGCTGCAAGAACAAAACG 59.665 47.619 0.50 0.00 34.07 3.60
8271 8575 9.011095 GGTAAGTAGGAACTTTATTTTGCTCTT 57.989 33.333 0.00 0.00 43.60 2.85
8278 8582 6.607600 GGAACTTTATTTTGCTCTTATCCCCT 59.392 38.462 0.00 0.00 0.00 4.79
8291 8595 7.015682 TGCTCTTATCCCCTCTTTAGTTCATAG 59.984 40.741 0.00 0.00 0.00 2.23
8436 8806 1.283029 CCTTGAGCCATCTTCCTTGGA 59.717 52.381 0.00 0.00 36.26 3.53
8438 8808 3.137176 CCTTGAGCCATCTTCCTTGGATA 59.863 47.826 0.00 0.00 36.26 2.59
8596 8967 1.404986 CGAGGGATAAGCACCGTTGAA 60.405 52.381 0.00 0.00 0.00 2.69
8597 8968 2.741878 CGAGGGATAAGCACCGTTGAAT 60.742 50.000 0.00 0.00 0.00 2.57
8598 8969 2.614057 GAGGGATAAGCACCGTTGAATG 59.386 50.000 0.00 0.00 0.00 2.67
8599 8970 2.238646 AGGGATAAGCACCGTTGAATGA 59.761 45.455 0.00 0.00 0.00 2.57
8600 8971 2.614057 GGGATAAGCACCGTTGAATGAG 59.386 50.000 0.00 0.00 0.00 2.90
8601 8972 2.614057 GGATAAGCACCGTTGAATGAGG 59.386 50.000 0.00 0.00 0.00 3.86
8602 8973 2.851263 TAAGCACCGTTGAATGAGGT 57.149 45.000 0.00 0.00 39.12 3.85
8603 8974 1.523758 AAGCACCGTTGAATGAGGTC 58.476 50.000 0.00 0.00 35.85 3.85
8604 8975 0.396435 AGCACCGTTGAATGAGGTCA 59.604 50.000 0.00 0.00 35.85 4.02
8605 8976 1.202758 AGCACCGTTGAATGAGGTCAA 60.203 47.619 0.00 0.00 35.85 3.18
8606 8977 1.197721 GCACCGTTGAATGAGGTCAAG 59.802 52.381 0.00 0.00 38.17 3.02
8607 8978 1.806542 CACCGTTGAATGAGGTCAAGG 59.193 52.381 0.00 0.00 41.10 3.61
8609 8980 2.185004 CGTTGAATGAGGTCAAGGGT 57.815 50.000 0.00 0.00 38.17 4.34
8610 8981 1.806542 CGTTGAATGAGGTCAAGGGTG 59.193 52.381 0.00 0.00 38.17 4.61
8611 8982 1.541588 GTTGAATGAGGTCAAGGGTGC 59.458 52.381 0.00 0.00 38.17 5.01
8612 8983 0.321564 TGAATGAGGTCAAGGGTGCG 60.322 55.000 0.00 0.00 0.00 5.34
8613 8984 0.036388 GAATGAGGTCAAGGGTGCGA 60.036 55.000 0.00 0.00 0.00 5.10
8614 8985 0.036010 AATGAGGTCAAGGGTGCGAG 60.036 55.000 0.00 0.00 0.00 5.03
8615 8986 1.903877 ATGAGGTCAAGGGTGCGAGG 61.904 60.000 0.00 0.00 0.00 4.63
8616 8987 3.316573 GAGGTCAAGGGTGCGAGGG 62.317 68.421 0.00 0.00 0.00 4.30
8617 8988 3.319198 GGTCAAGGGTGCGAGGGA 61.319 66.667 0.00 0.00 0.00 4.20
8618 8989 2.670148 GGTCAAGGGTGCGAGGGAT 61.670 63.158 0.00 0.00 0.00 3.85
8619 8990 1.335132 GGTCAAGGGTGCGAGGGATA 61.335 60.000 0.00 0.00 0.00 2.59
8620 8991 0.539986 GTCAAGGGTGCGAGGGATAA 59.460 55.000 0.00 0.00 0.00 1.75
8621 8992 0.830648 TCAAGGGTGCGAGGGATAAG 59.169 55.000 0.00 0.00 0.00 1.73
8622 8993 0.815615 CAAGGGTGCGAGGGATAAGC 60.816 60.000 0.00 0.00 0.00 3.09
8623 8994 1.271840 AAGGGTGCGAGGGATAAGCA 61.272 55.000 0.00 0.00 38.71 3.91
8626 8997 2.499205 TGCGAGGGATAAGCACCG 59.501 61.111 0.00 0.00 35.81 4.94
8627 8998 2.355986 TGCGAGGGATAAGCACCGT 61.356 57.895 0.00 0.00 35.81 4.83
8628 8999 1.153429 GCGAGGGATAAGCACCGTT 60.153 57.895 0.00 0.00 0.00 4.44
8629 9000 1.429148 GCGAGGGATAAGCACCGTTG 61.429 60.000 0.00 0.00 0.00 4.10
8630 9001 0.108329 CGAGGGATAAGCACCGTTGT 60.108 55.000 0.00 0.00 0.00 3.32
8631 9002 1.369625 GAGGGATAAGCACCGTTGTG 58.630 55.000 0.00 0.00 45.65 3.33
8701 9072 3.852205 GCCTTGTTGCGGAACTTAAGAAC 60.852 47.826 20.82 8.70 32.79 3.01
8702 9073 3.564225 CCTTGTTGCGGAACTTAAGAACT 59.436 43.478 20.82 0.00 32.79 3.01
8743 9171 3.487372 TCTGGATACGTCAGATACCAGG 58.513 50.000 0.00 0.00 43.21 4.45
8862 9316 0.642800 GAGCTCAACTCGAACGATGC 59.357 55.000 9.40 0.00 35.18 3.91
8895 9349 3.642848 ACAGTTGCATGAATTTCTGGGTT 59.357 39.130 0.00 0.00 0.00 4.11
9070 9527 1.913419 AGAGGGACTTTTCGGCCAATA 59.087 47.619 2.24 0.00 41.55 1.90
9084 9541 1.668419 CCAATAGTTGGCCGAAGAGG 58.332 55.000 0.00 0.00 45.17 3.69
9085 9542 1.668419 CAATAGTTGGCCGAAGAGGG 58.332 55.000 0.00 0.00 41.48 4.30
9131 9588 1.201429 AGTCCCTCTTCGGCCAACAT 61.201 55.000 2.24 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.753452 GACATTCGTGGAGGTCTAGTGA 59.247 50.000 0.00 0.00 0.00 3.41
19 20 2.492088 TGACATTCGTGGAGGTCTAGTG 59.508 50.000 0.00 0.00 0.00 2.74
20 21 2.803956 TGACATTCGTGGAGGTCTAGT 58.196 47.619 0.00 0.00 0.00 2.57
22 23 4.676986 CGAAATGACATTCGTGGAGGTCTA 60.677 45.833 0.05 0.00 45.32 2.59
23 24 3.600388 GAAATGACATTCGTGGAGGTCT 58.400 45.455 0.05 0.00 0.00 3.85
24 25 2.348666 CGAAATGACATTCGTGGAGGTC 59.651 50.000 0.05 0.00 45.32 3.85
25 26 2.346803 CGAAATGACATTCGTGGAGGT 58.653 47.619 0.05 0.00 45.32 3.85
111 112 2.694109 TCCTGAGATCACATGCTCTCTG 59.306 50.000 16.84 15.88 37.96 3.35
125 126 4.630644 AAGTGCTCTTTTGATCCTGAGA 57.369 40.909 0.00 0.00 0.00 3.27
183 184 8.017946 GGTAGCACTATCAGAAAGTTGAAAAAG 58.982 37.037 0.00 0.00 0.00 2.27
184 185 7.500892 TGGTAGCACTATCAGAAAGTTGAAAAA 59.499 33.333 0.00 0.00 0.00 1.94
185 186 6.995686 TGGTAGCACTATCAGAAAGTTGAAAA 59.004 34.615 0.00 0.00 0.00 2.29
186 187 6.530120 TGGTAGCACTATCAGAAAGTTGAAA 58.470 36.000 0.00 0.00 0.00 2.69
255 256 6.770286 ATATCCTATTTGATGTGGACACCT 57.230 37.500 0.00 0.00 0.00 4.00
379 390 3.865164 TGAATACTCGCATGCTACAACTG 59.135 43.478 17.13 0.00 0.00 3.16
392 403 6.435430 TCATGTTCCCAAAATGAATACTCG 57.565 37.500 0.00 0.00 0.00 4.18
397 408 8.895737 GCATAATTTCATGTTCCCAAAATGAAT 58.104 29.630 3.24 0.00 39.40 2.57
444 455 9.990360 TGTTACTATGTTAGTCAATGAAGTCAA 57.010 29.630 0.00 0.00 40.14 3.18
692 716 1.203001 AGGGCCGGATTGTCTCAAAAA 60.203 47.619 5.05 0.00 0.00 1.94
693 717 0.404040 AGGGCCGGATTGTCTCAAAA 59.596 50.000 5.05 0.00 0.00 2.44
694 718 0.404040 AAGGGCCGGATTGTCTCAAA 59.596 50.000 5.05 0.00 0.00 2.69
695 719 0.404040 AAAGGGCCGGATTGTCTCAA 59.596 50.000 5.05 0.00 0.00 3.02
696 720 0.404040 AAAAGGGCCGGATTGTCTCA 59.596 50.000 5.05 0.00 0.00 3.27
697 721 2.014857 GTAAAAGGGCCGGATTGTCTC 58.985 52.381 5.05 0.00 0.00 3.36
698 722 1.353022 TGTAAAAGGGCCGGATTGTCT 59.647 47.619 5.05 0.00 0.00 3.41
699 723 1.828979 TGTAAAAGGGCCGGATTGTC 58.171 50.000 5.05 0.00 0.00 3.18
700 724 2.099405 CATGTAAAAGGGCCGGATTGT 58.901 47.619 5.05 0.00 0.00 2.71
701 725 1.408702 CCATGTAAAAGGGCCGGATTG 59.591 52.381 5.05 0.00 0.00 2.67
702 726 1.006639 ACCATGTAAAAGGGCCGGATT 59.993 47.619 5.05 0.00 30.67 3.01
725 749 4.603985 TGATGCGTATTAGTAACAGACCG 58.396 43.478 0.00 0.00 0.00 4.79
783 807 4.892965 TGTTGCGCTGGGCCTGTT 62.893 61.111 14.44 0.00 42.61 3.16
784 808 4.892965 TTGTTGCGCTGGGCCTGT 62.893 61.111 14.44 0.00 42.61 4.00
798 822 2.518349 CCAGTGCGGGGTGTTTGT 60.518 61.111 0.00 0.00 0.00 2.83
799 823 1.388065 TTTCCAGTGCGGGGTGTTTG 61.388 55.000 0.00 0.00 34.36 2.93
802 826 2.113139 CTTTCCAGTGCGGGGTGT 59.887 61.111 0.00 0.00 34.36 4.16
803 827 2.113139 ACTTTCCAGTGCGGGGTG 59.887 61.111 0.00 0.00 34.36 4.61
804 828 2.113139 CACTTTCCAGTGCGGGGT 59.887 61.111 0.00 0.00 44.16 4.95
844 868 5.509840 GCCGATCTGGTTCAGTCTATATTGT 60.510 44.000 5.66 0.00 41.21 2.71
939 963 4.436998 GGGTGTGTCGGCTCTCGG 62.437 72.222 0.00 0.00 39.77 4.63
940 964 3.680786 TGGGTGTGTCGGCTCTCG 61.681 66.667 0.00 0.00 40.90 4.04
1014 1040 2.704190 TCTCCATCCCCTCCTCATAC 57.296 55.000 0.00 0.00 0.00 2.39
1278 1304 2.748647 TCGATGTCGGCCGACTCA 60.749 61.111 46.72 34.23 44.80 3.41
1416 1442 1.183549 CCAGCTAGTCGTACCAAGGT 58.816 55.000 0.00 0.00 0.00 3.50
1444 1470 1.001406 GCCCCATCTAATCTGAGACCG 59.999 57.143 0.00 0.00 0.00 4.79
1486 1512 3.009253 TGAATACTCCCGCAAAACCCTAA 59.991 43.478 0.00 0.00 0.00 2.69
1615 1642 0.963962 CACAGCCAAGCAATTCCACT 59.036 50.000 0.00 0.00 0.00 4.00
1687 1716 2.501723 TCCTAGTGCCACCTCTGAAATC 59.498 50.000 0.00 0.00 0.00 2.17
1787 1817 9.294030 GCAAAATAACAGAAACCATCTTGATAG 57.706 33.333 0.00 0.00 35.73 2.08
1788 1818 8.250332 GGCAAAATAACAGAAACCATCTTGATA 58.750 33.333 0.00 0.00 35.73 2.15
1789 1819 7.038799 AGGCAAAATAACAGAAACCATCTTGAT 60.039 33.333 0.00 0.00 35.73 2.57
1790 1820 6.267471 AGGCAAAATAACAGAAACCATCTTGA 59.733 34.615 0.00 0.00 35.73 3.02
1791 1821 6.366877 CAGGCAAAATAACAGAAACCATCTTG 59.633 38.462 0.00 0.00 35.73 3.02
1792 1822 6.041979 ACAGGCAAAATAACAGAAACCATCTT 59.958 34.615 0.00 0.00 35.73 2.40
1794 1824 5.783111 ACAGGCAAAATAACAGAAACCATC 58.217 37.500 0.00 0.00 0.00 3.51
1795 1825 5.806654 ACAGGCAAAATAACAGAAACCAT 57.193 34.783 0.00 0.00 0.00 3.55
1796 1826 5.606348 AACAGGCAAAATAACAGAAACCA 57.394 34.783 0.00 0.00 0.00 3.67
1828 1859 8.698973 TTTCCCAGTACAATTCATCAGTTTAA 57.301 30.769 0.00 0.00 0.00 1.52
1976 2227 4.622695 GCATAGGCAGGCCATTTTGTTAAA 60.623 41.667 13.63 0.00 40.72 1.52
2014 2265 0.465460 AACAGCACCCACATCAACGT 60.465 50.000 0.00 0.00 0.00 3.99
2054 2305 8.992349 TCATTCCCTATTACCATAGTGGATATG 58.008 37.037 2.45 0.00 40.96 1.78
2081 2335 0.823356 TTCAGAACTTGTGGGGCAGC 60.823 55.000 0.00 0.00 0.00 5.25
2109 2363 1.250328 TCATGCCAGCCAGAAAACAG 58.750 50.000 0.00 0.00 0.00 3.16
2112 2366 2.097036 CTGATCATGCCAGCCAGAAAA 58.903 47.619 0.00 0.00 0.00 2.29
2329 2585 4.563374 GCATGGTTTAAACTGAAAGGGCAT 60.563 41.667 17.50 7.34 39.30 4.40
2725 2981 1.600957 CTAGAACGCAGCATGATTGGG 59.399 52.381 0.00 5.00 39.69 4.12
2770 3026 4.457257 CCAAGTTCTGTGAGATCCTTTTCC 59.543 45.833 0.00 0.00 0.00 3.13
3022 3278 6.490040 AGAACTATTTGCAAGGCTTCAGTAAA 59.510 34.615 0.00 0.00 0.00 2.01
3076 3332 8.049117 ACATATATATGCCATGTAAGAAGGTGG 58.951 37.037 20.46 0.00 37.19 4.61
3077 3333 8.886719 CACATATATATGCCATGTAAGAAGGTG 58.113 37.037 20.46 4.65 37.19 4.00
3078 3334 8.049117 CCACATATATATGCCATGTAAGAAGGT 58.951 37.037 20.46 0.00 37.19 3.50
3256 3512 3.738282 GCTCCAGTATATCTTTGTCAGCG 59.262 47.826 0.00 0.00 0.00 5.18
3375 3631 8.947115 ACAATTTAGTTTCACTTATCAGTAGCC 58.053 33.333 0.00 0.00 0.00 3.93
3416 3672 6.490381 AGCAGATGTGATATCAATGCAAGATT 59.510 34.615 24.01 9.57 36.91 2.40
3417 3673 6.004574 AGCAGATGTGATATCAATGCAAGAT 58.995 36.000 24.01 9.59 36.91 2.40
3418 3674 5.374071 AGCAGATGTGATATCAATGCAAGA 58.626 37.500 24.01 0.00 36.91 3.02
3419 3675 5.690997 AGCAGATGTGATATCAATGCAAG 57.309 39.130 24.01 10.34 36.91 4.01
3420 3676 5.591067 TCAAGCAGATGTGATATCAATGCAA 59.409 36.000 24.01 13.14 36.91 4.08
3421 3677 5.127491 TCAAGCAGATGTGATATCAATGCA 58.873 37.500 24.01 13.80 36.91 3.96
3422 3678 5.684550 TCAAGCAGATGTGATATCAATGC 57.315 39.130 18.61 18.61 35.66 3.56
3456 3712 8.603181 CCCAACAAGAAAGAACAATTTAGTTTG 58.397 33.333 0.00 0.00 0.00 2.93
3473 3729 3.181434 ACTTAAGATGTGCCCCAACAAGA 60.181 43.478 10.09 0.00 32.81 3.02
3478 3734 3.420893 CTCAACTTAAGATGTGCCCCAA 58.579 45.455 10.09 0.00 0.00 4.12
3494 3757 1.594331 AGTTCCAACCGAAGCTCAAC 58.406 50.000 0.00 0.00 0.00 3.18
3588 3854 2.301870 ACCTCGCTTTCCAATGTAGTCA 59.698 45.455 0.00 0.00 0.00 3.41
3606 3872 2.704065 AGTTACACCAACTGTAGCACCT 59.296 45.455 0.00 0.00 46.01 4.00
3699 3965 8.308931 TCTCTTTCGCATACCTAAGAAGTTAAA 58.691 33.333 0.00 0.00 0.00 1.52
3706 3972 7.284716 TGAAGTATCTCTTTCGCATACCTAAGA 59.715 37.037 0.00 0.00 36.40 2.10
3707 3973 7.426410 TGAAGTATCTCTTTCGCATACCTAAG 58.574 38.462 0.00 0.00 36.40 2.18
3708 3974 7.342769 TGAAGTATCTCTTTCGCATACCTAA 57.657 36.000 0.00 0.00 36.40 2.69
3763 4029 7.106439 TGCCTTTTTAGTTTCACAGAATTCA 57.894 32.000 8.44 0.00 0.00 2.57
3806 4072 5.620738 ACAGACTAATGTGCAGTATGGAT 57.379 39.130 3.20 0.00 39.99 3.41
3869 4135 7.071824 AGGTAGGAAATTAGCTTATCTGCTTCT 59.928 37.037 0.00 0.00 43.74 2.85
3870 4136 7.220740 AGGTAGGAAATTAGCTTATCTGCTTC 58.779 38.462 0.00 0.00 43.74 3.86
3921 4187 4.256920 GACCAAGAGCACACATCAATAGT 58.743 43.478 0.00 0.00 0.00 2.12
3924 4190 2.079158 CGACCAAGAGCACACATCAAT 58.921 47.619 0.00 0.00 0.00 2.57
4108 4374 7.581213 TTCCTGAAAAGCTGATTTTGTAAGA 57.419 32.000 8.52 0.00 41.24 2.10
4112 4378 7.225341 GTCAATTTCCTGAAAAGCTGATTTTGT 59.775 33.333 8.52 0.00 41.24 2.83
4184 4450 3.817647 AGAAAAAGACAGAGCATGGTCAC 59.182 43.478 25.71 15.98 36.50 3.67
4201 4467 8.103305 AGTTAGCAATTATCAGGACTGAGAAAA 58.897 33.333 12.69 5.49 42.98 2.29
4253 4519 7.398618 TGCAAATTAACTTCCTTCCCATTATCA 59.601 33.333 0.00 0.00 0.00 2.15
4403 4669 5.874810 AGTAAAGCATACACGTGAATGTGAT 59.125 36.000 25.01 10.58 42.55 3.06
4443 4716 5.415701 AGAGCACATATTGGAACATTCGTTT 59.584 36.000 0.00 0.00 39.30 3.60
4590 4863 7.123547 GGTTTCAATGGGGAAGTAATGTATGAA 59.876 37.037 0.00 0.00 0.00 2.57
4765 5038 2.226437 CCATTGACCAACTCCTTTGACG 59.774 50.000 0.00 0.00 37.39 4.35
4795 5068 6.601613 CCACAAGCCTGAATAAAGGTGTATAA 59.398 38.462 0.00 0.00 39.75 0.98
4869 5142 7.941238 TCCAAAAATTCCAAAATAGGATTTGCA 59.059 29.630 0.00 0.00 38.64 4.08
4899 5172 3.008266 CCTCAAAATTTTCTGTGCCCCAT 59.992 43.478 0.00 0.00 0.00 4.00
4972 5245 3.985008 ACACGAAATTTTAACCTTGGGC 58.015 40.909 0.00 0.00 0.00 5.36
4985 5258 7.012515 TGTTGTAACTGGTAAATGACACGAAAT 59.987 33.333 0.00 0.00 0.00 2.17
5035 5308 5.220796 GCCGGTGATATCTCCTGTTAAAAAC 60.221 44.000 19.07 0.00 0.00 2.43
5090 5363 4.202305 TGAATTCCAACCCAACAACCATTC 60.202 41.667 2.27 0.00 0.00 2.67
5277 5552 9.859427 CAACAAAATCACATATTAATGGAGTGT 57.141 29.630 13.11 4.92 37.43 3.55
5361 5648 8.530311 ACATGTTTGCCATACATCTTGAAAATA 58.470 29.630 0.00 0.00 34.11 1.40
5462 5751 5.559770 TCAGCATGTAATTTTGAGACCTGA 58.440 37.500 0.00 0.00 37.40 3.86
5541 5830 4.796369 AGAGTCGAAGTTCTTTAAGACGG 58.204 43.478 0.56 0.00 33.96 4.79
5825 6115 9.702253 ATCATAGTAGTTTCTTCCTCTTCAGTA 57.298 33.333 0.00 0.00 0.00 2.74
5953 6243 6.791303 TGCAAATAGAACGAAGAAACAAAGT 58.209 32.000 0.00 0.00 0.00 2.66
6117 6413 4.042809 ACACCAAGTATCAATGAAGGGTGA 59.957 41.667 20.64 0.00 45.61 4.02
6191 6487 3.689161 TGCAGTGGATTAGCATTGTGTAC 59.311 43.478 0.00 0.00 32.55 2.90
6628 6924 8.224898 TGGTTATATCCAGAGTAGCATGCAATG 61.225 40.741 21.98 10.23 39.03 2.82
6813 7113 6.344500 TCTTCTTTTCCTCATCTCTGCATAC 58.656 40.000 0.00 0.00 0.00 2.39
7154 7454 4.201990 GCATCATCTTGTGGAATTGGAGAC 60.202 45.833 0.00 0.00 0.00 3.36
7295 7595 6.371809 TGAAACTGAAAACACCACATAGAC 57.628 37.500 0.00 0.00 0.00 2.59
7662 7962 4.500499 AGAAGATCAATGAGTCCCCAAG 57.500 45.455 0.00 0.00 0.00 3.61
7707 8007 8.850007 AAAGATCACATGAGGAGATTGATATG 57.150 34.615 0.00 0.00 0.00 1.78
7742 8042 6.801539 TGCAAATTAGACAAGAGGTTACAG 57.198 37.500 0.00 0.00 0.00 2.74
7762 8062 9.703892 ATACATTGCAAGTTAAGTTTAAATGCA 57.296 25.926 18.78 16.20 41.71 3.96
7780 8080 3.770263 ATGAGCACACACATACATTGC 57.230 42.857 0.00 0.00 0.00 3.56
7781 8081 8.692110 AAATTAATGAGCACACACATACATTG 57.308 30.769 0.00 0.00 31.85 2.82
8233 8537 9.372609 AAGTTCCTACTTACCTGGACAATGTCC 62.373 44.444 24.68 24.68 46.03 4.02
8271 8575 9.144298 CAAGTACTATGAACTAAAGAGGGGATA 57.856 37.037 0.00 0.00 0.00 2.59
8278 8582 8.248253 TCGCATTCAAGTACTATGAACTAAAGA 58.752 33.333 17.21 11.92 39.43 2.52
8291 8595 7.073342 AGATAAGGTTTTCGCATTCAAGTAC 57.927 36.000 0.00 0.00 0.00 2.73
8344 8714 8.658499 AAGACTAGTTTAGACGACAAAAACAT 57.342 30.769 14.52 4.10 35.93 2.71
8345 8715 9.585099 TTAAGACTAGTTTAGACGACAAAAACA 57.415 29.630 14.52 4.48 35.93 2.83
8375 8745 2.519013 AGTACTCCCTCCGTAAAACGT 58.481 47.619 0.00 0.00 40.58 3.99
8376 8746 4.907879 ATAGTACTCCCTCCGTAAAACG 57.092 45.455 0.00 0.00 42.11 3.60
8377 8747 6.951062 AGTATAGTACTCCCTCCGTAAAAC 57.049 41.667 0.00 0.00 32.47 2.43
8378 8748 6.547510 GGAAGTATAGTACTCCCTCCGTAAAA 59.452 42.308 0.00 0.00 38.26 1.52
8381 8751 4.660303 TGGAAGTATAGTACTCCCTCCGTA 59.340 45.833 0.00 0.00 36.46 4.02
8387 8757 6.269307 TGGCTATTTGGAAGTATAGTACTCCC 59.731 42.308 0.00 0.00 38.26 4.30
8388 8758 7.299246 TGGCTATTTGGAAGTATAGTACTCC 57.701 40.000 0.00 0.00 38.26 3.85
8436 8806 6.889198 TGATTACTAACTCTGGCAAAGCTAT 58.111 36.000 0.00 0.00 0.00 2.97
8438 8808 5.165961 TGATTACTAACTCTGGCAAAGCT 57.834 39.130 0.00 0.00 0.00 3.74
8596 8967 1.599047 CTCGCACCCTTGACCTCAT 59.401 57.895 0.00 0.00 0.00 2.90
8597 8968 2.583441 CCTCGCACCCTTGACCTCA 61.583 63.158 0.00 0.00 0.00 3.86
8598 8969 2.266055 CCTCGCACCCTTGACCTC 59.734 66.667 0.00 0.00 0.00 3.85
8599 8970 3.322466 CCCTCGCACCCTTGACCT 61.322 66.667 0.00 0.00 0.00 3.85
8600 8971 1.335132 TATCCCTCGCACCCTTGACC 61.335 60.000 0.00 0.00 0.00 4.02
8601 8972 0.539986 TTATCCCTCGCACCCTTGAC 59.460 55.000 0.00 0.00 0.00 3.18
8602 8973 0.830648 CTTATCCCTCGCACCCTTGA 59.169 55.000 0.00 0.00 0.00 3.02
8603 8974 0.815615 GCTTATCCCTCGCACCCTTG 60.816 60.000 0.00 0.00 0.00 3.61
8604 8975 1.271840 TGCTTATCCCTCGCACCCTT 61.272 55.000 0.00 0.00 0.00 3.95
8605 8976 1.689233 TGCTTATCCCTCGCACCCT 60.689 57.895 0.00 0.00 0.00 4.34
8606 8977 1.523938 GTGCTTATCCCTCGCACCC 60.524 63.158 2.43 0.00 46.09 4.61
8607 8978 4.126524 GTGCTTATCCCTCGCACC 57.873 61.111 2.43 0.00 46.09 5.01
8609 8980 1.895020 AACGGTGCTTATCCCTCGCA 61.895 55.000 0.00 0.00 0.00 5.10
8610 8981 1.153429 AACGGTGCTTATCCCTCGC 60.153 57.895 0.00 0.00 0.00 5.03
8611 8982 0.108329 ACAACGGTGCTTATCCCTCG 60.108 55.000 0.00 0.00 0.00 4.63
8612 8983 1.369625 CACAACGGTGCTTATCCCTC 58.630 55.000 0.00 0.00 38.37 4.30
8613 8984 3.551259 CACAACGGTGCTTATCCCT 57.449 52.632 0.00 0.00 38.37 4.20
8623 8994 0.461339 AACACTCGAAGCACAACGGT 60.461 50.000 0.00 0.00 0.00 4.83
8624 8995 0.042188 CAACACTCGAAGCACAACGG 60.042 55.000 0.00 0.00 0.00 4.44
8625 8996 0.650512 ACAACACTCGAAGCACAACG 59.349 50.000 0.00 0.00 0.00 4.10
8626 8997 4.455124 GAATACAACACTCGAAGCACAAC 58.545 43.478 0.00 0.00 0.00 3.32
8627 8998 3.183574 CGAATACAACACTCGAAGCACAA 59.816 43.478 0.00 0.00 34.52 3.33
8628 8999 2.729360 CGAATACAACACTCGAAGCACA 59.271 45.455 0.00 0.00 34.52 4.57
8629 9000 2.092211 CCGAATACAACACTCGAAGCAC 59.908 50.000 0.00 0.00 34.52 4.40
8630 9001 2.333926 CCGAATACAACACTCGAAGCA 58.666 47.619 0.00 0.00 34.52 3.91
8631 9002 1.659098 CCCGAATACAACACTCGAAGC 59.341 52.381 0.00 0.00 34.52 3.86
8632 9003 2.666508 CACCCGAATACAACACTCGAAG 59.333 50.000 0.00 0.00 34.52 3.79
8633 9004 2.679450 CACCCGAATACAACACTCGAA 58.321 47.619 0.00 0.00 34.52 3.71
8634 9005 1.670674 GCACCCGAATACAACACTCGA 60.671 52.381 0.00 0.00 34.52 4.04
8635 9006 0.719465 GCACCCGAATACAACACTCG 59.281 55.000 0.00 0.00 0.00 4.18
8701 9072 6.482641 CCAGAACACAATCAGAAGGATGATAG 59.517 42.308 0.00 0.00 39.00 2.08
8702 9073 6.156775 TCCAGAACACAATCAGAAGGATGATA 59.843 38.462 0.00 0.00 39.00 2.15
8743 9171 4.192317 CCTAAGTAACTTCATGTCTGGGC 58.808 47.826 0.00 0.00 0.00 5.36
8862 9316 5.868043 TCATGCAACTGTCTTCATACAAG 57.132 39.130 0.00 0.00 0.00 3.16
8975 9429 7.151976 CGGGGTGATACTTTTGATTTTTCTTT 58.848 34.615 0.00 0.00 0.00 2.52
8976 9430 6.266786 ACGGGGTGATACTTTTGATTTTTCTT 59.733 34.615 0.00 0.00 0.00 2.52
9047 9504 0.036306 GGCCGAAAAGTCCCTCTTCA 59.964 55.000 0.00 0.00 35.02 3.02
9070 9527 1.128188 AAGTCCCTCTTCGGCCAACT 61.128 55.000 2.24 0.00 0.00 3.16
9078 9535 0.036306 TGGCCGAAAAGTCCCTCTTC 59.964 55.000 0.00 0.00 35.02 2.87
9081 9538 0.536460 TGTTGGCCGAAAAGTCCCTC 60.536 55.000 0.00 0.00 0.00 4.30
9084 9541 1.029681 AACTGTTGGCCGAAAAGTCC 58.970 50.000 9.54 0.00 0.00 3.85
9085 9542 1.269051 CCAACTGTTGGCCGAAAAGTC 60.269 52.381 25.21 0.00 45.17 3.01
9519 9981 9.209175 AGCTACTGATAACTAAACAGAAACAAG 57.791 33.333 0.00 0.00 35.85 3.16


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

AutoCloner maintained by Alex Coulton.