Multiple sequence alignment - TraesCS2B01G546800

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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 TraesCS2B01G546800 chr2B 100.000 8168 0 0 1 8168 743735279 743727112 0.000000e+00 15084.0
1 TraesCS2B01G546800 chr2B 89.015 264 25 4 1056 1317 181699290 181699551 2.840000e-84 324.0
2 TraesCS2B01G546800 chr2A 95.701 4024 119 23 920 4920 742138219 742134227 0.000000e+00 6423.0
3 TraesCS2B01G546800 chr2A 95.212 1086 22 10 4918 5978 742134193 742133113 0.000000e+00 1690.0
4 TraesCS2B01G546800 chr2A 89.880 1334 68 30 5976 7303 742133075 742131803 0.000000e+00 1653.0
5 TraesCS2B01G546800 chr2A 96.240 718 20 3 7454 8168 741379824 741379111 0.000000e+00 1170.0
6 TraesCS2B01G546800 chr2A 91.540 792 33 8 7380 8168 742131487 742130727 0.000000e+00 1061.0
7 TraesCS2B01G546800 chr2A 87.895 190 12 3 6834 7023 741416255 741416077 6.420000e-51 213.0
8 TraesCS2B01G546800 chr2A 91.667 144 12 0 6563 6706 741417871 741417728 5.000000e-47 200.0
9 TraesCS2B01G546800 chr2A 97.087 103 3 0 7354 7456 742131797 742131695 3.030000e-39 174.0
10 TraesCS2B01G546800 chr2A 89.011 91 1 7 5828 5911 726911052 726910964 4.030000e-18 104.0
11 TraesCS2B01G546800 chr2D 95.534 3426 110 18 1511 4920 609438992 609435594 0.000000e+00 5439.0
12 TraesCS2B01G546800 chr2D 91.507 1307 69 13 5976 7277 609434435 609433166 0.000000e+00 1760.0
13 TraesCS2B01G546800 chr2D 94.766 1089 28 5 4918 5978 609435560 609434473 0.000000e+00 1668.0
14 TraesCS2B01G546800 chr2D 96.325 898 23 6 7278 8168 609432979 609432085 0.000000e+00 1467.0
15 TraesCS2B01G546800 chr2D 95.420 524 15 5 920 1441 609439865 609439349 0.000000e+00 826.0
16 TraesCS2B01G546800 chr2D 84.885 741 58 18 206 928 609466327 609465623 0.000000e+00 699.0
17 TraesCS2B01G546800 chr2D 94.211 190 9 1 16 205 609466809 609466622 1.040000e-73 289.0
18 TraesCS2B01G546800 chr2D 89.011 91 1 7 5828 5911 272795895 272795807 4.030000e-18 104.0
19 TraesCS2B01G546800 chr1B 91.270 252 22 0 1066 1317 217554382 217554633 2.180000e-90 344.0
20 TraesCS2B01G546800 chr7A 89.888 89 2 6 5828 5911 352183806 352183720 3.120000e-19 108.0
21 TraesCS2B01G546800 chr6A 88.889 90 2 7 5828 5911 445904343 445904256 4.030000e-18 104.0
22 TraesCS2B01G546800 chr3B 89.011 91 1 7 5828 5911 201525008 201525096 4.030000e-18 104.0
23 TraesCS2B01G546800 chrUn 88.043 92 1 7 5828 5911 23290155 23290066 5.220000e-17 100.0
24 TraesCS2B01G546800 chrUn 88.043 92 1 7 5828 5911 93411634 93411545 5.220000e-17 100.0
25 TraesCS2B01G546800 chrUn 75.141 177 28 14 7854 8019 279543594 279543423 1.470000e-07 69.4
26 TraesCS2B01G546800 chrUn 97.436 39 1 0 7981 8019 154542770 154542732 5.290000e-07 67.6
27 TraesCS2B01G546800 chrUn 100.000 36 0 0 7981 8016 189561740 189561775 5.290000e-07 67.6
28 TraesCS2B01G546800 chrUn 97.436 39 1 0 7981 8019 201369324 201369286 5.290000e-07 67.6
29 TraesCS2B01G546800 chrUn 97.436 39 1 0 7981 8019 363337042 363337004 5.290000e-07 67.6
30 TraesCS2B01G546800 chr4B 100.000 34 0 0 7981 8014 654707069 654707102 6.840000e-06 63.9


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 TraesCS2B01G546800 chr2B 743727112 743735279 8167 True 15084.0 15084 100.0000 1 8168 1 chr2B.!!$R1 8167
1 TraesCS2B01G546800 chr2A 742130727 742138219 7492 True 2200.2 6423 93.8840 920 8168 5 chr2A.!!$R4 7248
2 TraesCS2B01G546800 chr2A 741379111 741379824 713 True 1170.0 1170 96.2400 7454 8168 1 chr2A.!!$R2 714
3 TraesCS2B01G546800 chr2A 741416077 741417871 1794 True 206.5 213 89.7810 6563 7023 2 chr2A.!!$R3 460
4 TraesCS2B01G546800 chr2D 609432085 609439865 7780 True 2232.0 5439 94.7104 920 8168 5 chr2D.!!$R2 7248
5 TraesCS2B01G546800 chr2D 609465623 609466809 1186 True 494.0 699 89.5480 16 928 2 chr2D.!!$R3 912

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
59 60 0.744771 GTTGGCTCTTCCGTCCATCC 60.745 60.000 0.00 0.0 37.80 3.51 F
1568 2185 0.107945 GAGCAGGATCTTCGCTTGGT 60.108 55.000 5.71 0.0 35.75 3.67 F
2488 3114 0.538287 GTGTTGCCAGGAAGCCTTCT 60.538 55.000 4.15 0.0 0.00 2.85 F
2761 3387 1.067142 TCCACGCGCTTCAGATTACTT 60.067 47.619 5.73 0.0 0.00 2.24 F
3513 4144 1.482593 CGTAGAAGGGAGCAGGACATT 59.517 52.381 0.00 0.0 0.00 2.71 F
4537 5169 0.394565 ACACAGAAGGTCAGAGGCAC 59.605 55.000 0.00 0.0 0.00 5.01 F
4540 5172 0.534412 CAGAAGGTCAGAGGCACGAT 59.466 55.000 0.00 0.0 0.00 3.73 F
6509 7270 0.465460 AGAAGCTTTGCCCAACGACA 60.465 50.000 0.00 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1671 2293 0.890996 GGGTCCTTGACTTGCCACAG 60.891 60.000 0.00 0.00 32.47 3.66 R
2740 3366 0.924090 GTAATCTGAAGCGCGTGGAG 59.076 55.000 8.43 0.00 0.00 3.86 R
4224 4855 0.036732 AGGTGCAGAAAATCCGCTCA 59.963 50.000 0.00 0.00 0.00 4.26 R
4535 5167 0.249784 CAGATGGGAGCCAGATCGTG 60.250 60.000 0.00 0.00 36.75 4.35 R
5450 6119 0.179034 ATTCGCATTGGCTCTCCTCC 60.179 55.000 0.00 0.00 38.10 4.30 R
6509 7270 0.040058 TCATTGGCCATGGCTTCTGT 59.960 50.000 34.70 14.72 41.60 3.41 R
6517 7278 0.101759 CGGCTTCTTCATTGGCCATG 59.898 55.000 6.09 7.61 44.27 3.66 R
7345 9710 2.122768 CTCTAGCCTCCAACCTCCATT 58.877 52.381 0.00 0.00 0.00 3.16 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
59 60 0.744771 GTTGGCTCTTCCGTCCATCC 60.745 60.000 0.00 0.00 37.80 3.51
62 63 1.596934 GCTCTTCCGTCCATCCACA 59.403 57.895 0.00 0.00 0.00 4.17
77 78 4.564199 CCATCCACATCACGTCATCCATAT 60.564 45.833 0.00 0.00 0.00 1.78
78 79 5.337491 CCATCCACATCACGTCATCCATATA 60.337 44.000 0.00 0.00 0.00 0.86
79 80 5.799827 TCCACATCACGTCATCCATATAA 57.200 39.130 0.00 0.00 0.00 0.98
127 128 4.041815 TGGTAGTGTGTATTAAACTGCCCA 59.958 41.667 8.38 2.55 43.67 5.36
168 169 8.792830 TTCTTCTTCTCTTCTTTCTTCACAAA 57.207 30.769 0.00 0.00 0.00 2.83
219 514 4.216472 CCCCAGCTTACTTCTTTTCTTCAC 59.784 45.833 0.00 0.00 0.00 3.18
278 573 6.514947 CACTTCATCTCCTTGATCCTCTTAG 58.485 44.000 0.00 0.00 32.05 2.18
299 594 9.066892 TCTTAGAATAATTTGCGCCTTATTGAT 57.933 29.630 18.60 12.10 29.87 2.57
301 596 7.042797 AGAATAATTTGCGCCTTATTGATGT 57.957 32.000 18.60 1.67 29.87 3.06
303 598 8.796475 AGAATAATTTGCGCCTTATTGATGTAT 58.204 29.630 18.60 0.69 29.87 2.29
312 607 6.581370 CGCCTTATTGATGTATTGTTCTACG 58.419 40.000 0.00 0.00 0.00 3.51
407 702 3.055891 AGGAAAGTGCCAATTAATGCCAC 60.056 43.478 0.00 0.00 0.00 5.01
451 746 6.423302 GTGTGAAGATAATGCTCATCACCTAG 59.577 42.308 6.60 0.00 41.09 3.02
453 748 7.287696 TGTGAAGATAATGCTCATCACCTAGTA 59.712 37.037 6.60 0.00 41.09 1.82
480 775 5.231991 ACAATTCGTCAAACAAACAATGCTC 59.768 36.000 0.00 0.00 0.00 4.26
488 783 3.715628 ACAAACAATGCTCAACACCTC 57.284 42.857 0.00 0.00 0.00 3.85
511 806 5.650266 TCTTTAAAGCATATTCCGCCAAAGA 59.350 36.000 10.51 0.00 33.43 2.52
540 835 7.124147 CCCATCCAAAAGGTGATACTGTAAAAT 59.876 37.037 0.00 0.00 0.00 1.82
549 844 9.798994 AAGGTGATACTGTAAAATACTAAGTCG 57.201 33.333 0.00 0.00 0.00 4.18
597 905 8.937634 AGAAAAATCATAGAAAATGATGTGGC 57.062 30.769 1.46 0.00 38.62 5.01
612 920 2.627945 TGTGGCATGTATCTCGGTTTC 58.372 47.619 0.00 0.00 0.00 2.78
617 925 6.014584 TGTGGCATGTATCTCGGTTTCTATAT 60.015 38.462 0.00 0.00 0.00 0.86
618 926 6.311445 GTGGCATGTATCTCGGTTTCTATATG 59.689 42.308 0.00 0.00 0.00 1.78
620 928 7.097192 GGCATGTATCTCGGTTTCTATATGAA 58.903 38.462 0.00 0.00 0.00 2.57
682 990 8.141268 TCCAACAGATCCAAGTTAATGTTTTTC 58.859 33.333 0.00 0.00 0.00 2.29
684 992 9.533253 CAACAGATCCAAGTTAATGTTTTTCTT 57.467 29.630 0.00 0.00 0.00 2.52
707 1015 9.706691 TCTTATGAAACGTGAAAGATAGAAACT 57.293 29.630 0.00 0.00 0.00 2.66
749 1057 6.952773 AAAATACACTGCTACAACCAAAGA 57.047 33.333 0.00 0.00 0.00 2.52
750 1058 6.560253 AAATACACTGCTACAACCAAAGAG 57.440 37.500 0.00 0.00 0.00 2.85
751 1059 2.222027 ACACTGCTACAACCAAAGAGC 58.778 47.619 0.00 0.00 35.43 4.09
752 1060 2.158755 ACACTGCTACAACCAAAGAGCT 60.159 45.455 0.00 0.00 35.89 4.09
753 1061 2.481952 CACTGCTACAACCAAAGAGCTC 59.518 50.000 5.27 5.27 35.89 4.09
754 1062 2.370189 ACTGCTACAACCAAAGAGCTCT 59.630 45.455 11.45 11.45 35.89 4.09
755 1063 3.578716 ACTGCTACAACCAAAGAGCTCTA 59.421 43.478 18.59 0.00 35.89 2.43
756 1064 3.926616 TGCTACAACCAAAGAGCTCTAC 58.073 45.455 18.59 0.00 35.89 2.59
757 1065 3.323691 TGCTACAACCAAAGAGCTCTACA 59.676 43.478 18.59 0.24 35.89 2.74
758 1066 3.929610 GCTACAACCAAAGAGCTCTACAG 59.070 47.826 18.59 10.84 32.04 2.74
766 1074 5.221925 ACCAAAGAGCTCTACAGGAATTTCA 60.222 40.000 26.71 0.00 0.00 2.69
832 1140 5.220548 CCGCATTTTGTTGTTGTTGAATTCA 60.221 36.000 3.38 3.38 0.00 2.57
865 1174 8.660295 TCCTACAAATTAAAGAGTCCTGACTA 57.340 34.615 0.00 0.00 42.66 2.59
866 1175 8.750298 TCCTACAAATTAAAGAGTCCTGACTAG 58.250 37.037 0.00 0.00 42.66 2.57
867 1176 8.750298 CCTACAAATTAAAGAGTCCTGACTAGA 58.250 37.037 0.00 0.00 42.66 2.43
970 1285 7.529880 AACGAGTCCTACATAAATAAAACCG 57.470 36.000 0.00 0.00 0.00 4.44
971 1286 6.866480 ACGAGTCCTACATAAATAAAACCGA 58.134 36.000 0.00 0.00 0.00 4.69
991 1306 1.068741 ACTCGCTCGTTTTCTGTTCCT 59.931 47.619 0.00 0.00 0.00 3.36
997 1313 3.532542 CTCGTTTTCTGTTCCTATCCCC 58.467 50.000 0.00 0.00 0.00 4.81
998 1314 2.237893 TCGTTTTCTGTTCCTATCCCCC 59.762 50.000 0.00 0.00 0.00 5.40
1029 1345 0.390860 CCAAACCCGCACCAAAATCA 59.609 50.000 0.00 0.00 0.00 2.57
1030 1346 1.001860 CCAAACCCGCACCAAAATCAT 59.998 47.619 0.00 0.00 0.00 2.45
1321 1649 3.009115 AGCAGGCCGGCCTAAAGA 61.009 61.111 46.42 0.00 46.28 2.52
1447 1775 4.459089 GGCTCTGGTGAGGGTCGC 62.459 72.222 0.00 0.00 40.53 5.19
1492 1821 1.182667 GAGGGGGTTTTGGATTTCCG 58.817 55.000 0.00 0.00 39.43 4.30
1499 1828 2.167693 GGTTTTGGATTTCCGGATTCCC 59.832 50.000 24.10 17.02 39.43 3.97
1500 1829 2.153034 TTTGGATTTCCGGATTCCCC 57.847 50.000 24.10 15.54 39.43 4.81
1501 1830 1.304891 TTGGATTTCCGGATTCCCCT 58.695 50.000 24.10 0.54 39.43 4.79
1502 1831 0.550914 TGGATTTCCGGATTCCCCTG 59.449 55.000 24.10 0.00 39.43 4.45
1503 1832 0.551396 GGATTTCCGGATTCCCCTGT 59.449 55.000 18.93 0.00 0.00 4.00
1505 1834 2.298610 GATTTCCGGATTCCCCTGTTC 58.701 52.381 4.15 0.00 0.00 3.18
1507 1836 0.618458 TTCCGGATTCCCCTGTTCTG 59.382 55.000 4.15 0.00 0.00 3.02
1509 1838 0.328258 CCGGATTCCCCTGTTCTGTT 59.672 55.000 0.00 0.00 0.00 3.16
1510 1839 1.679032 CCGGATTCCCCTGTTCTGTTC 60.679 57.143 0.00 0.00 0.00 3.18
1511 1840 1.679032 CGGATTCCCCTGTTCTGTTCC 60.679 57.143 0.00 0.00 0.00 3.62
1512 1841 1.341089 GGATTCCCCTGTTCTGTTCCC 60.341 57.143 0.00 0.00 0.00 3.97
1568 2185 0.107945 GAGCAGGATCTTCGCTTGGT 60.108 55.000 5.71 0.00 35.75 3.67
1631 2253 8.192774 TCTATATTATATTAACCGCGGGACAAG 58.807 37.037 31.76 2.56 0.00 3.16
1643 2265 2.034812 GCGGGACAAGAGATAAGATCGT 59.965 50.000 0.00 0.00 0.00 3.73
1736 2358 1.134946 GGTGGAGGCACACATTATTGC 59.865 52.381 13.18 0.00 43.08 3.56
1826 2448 3.885484 CACAAAGTAGTGTGGAAGCAG 57.115 47.619 0.00 0.00 44.29 4.24
1842 2464 2.225467 AGCAGGTGTTTCTTTCTCAGC 58.775 47.619 0.00 0.00 0.00 4.26
1850 2475 5.277731 GGTGTTTCTTTCTCAGCAAGAAGAG 60.278 44.000 0.00 0.00 44.69 2.85
1858 2483 1.538512 TCAGCAAGAAGAGCACAATGC 59.461 47.619 0.00 0.00 45.46 3.56
1887 2512 8.099537 AGTCTGTATGATTCAGAAACTCACAAT 58.900 33.333 3.24 0.00 42.42 2.71
1968 2593 1.470098 AGATTGCGTGCCTTGATTGAC 59.530 47.619 0.00 0.00 0.00 3.18
1992 2617 5.645067 CAGTGTGATGGTGATGATTAGTTGT 59.355 40.000 0.00 0.00 0.00 3.32
2065 2690 8.296713 GCAAATGTTTGTTCCTCAGTAATAGAA 58.703 33.333 7.26 0.00 40.24 2.10
2071 2696 8.880750 GTTTGTTCCTCAGTAATAGAATACCAC 58.119 37.037 0.00 0.00 0.00 4.16
2076 2701 8.319057 TCCTCAGTAATAGAATACCACAATGT 57.681 34.615 0.00 0.00 0.00 2.71
2285 2910 2.775890 CTCATCATGTGTGCTATCCCC 58.224 52.381 0.00 0.00 0.00 4.81
2488 3114 0.538287 GTGTTGCCAGGAAGCCTTCT 60.538 55.000 4.15 0.00 0.00 2.85
2647 3273 5.395768 GCTTCAACTGGATATAGTCTGGTGT 60.396 44.000 0.00 0.00 0.00 4.16
2653 3279 9.396022 CAACTGGATATAGTCTGGTGTTATTTT 57.604 33.333 0.00 0.00 0.00 1.82
2725 3351 5.780958 AGGCTAGGTTAGGATTTGAACTT 57.219 39.130 0.00 0.00 0.00 2.66
2728 3354 5.357314 GGCTAGGTTAGGATTTGAACTTTCC 59.643 44.000 0.00 0.00 0.00 3.13
2740 3366 3.469739 TGAACTTTCCCACGGTAAAGAC 58.530 45.455 8.02 3.17 36.43 3.01
2761 3387 1.067142 TCCACGCGCTTCAGATTACTT 60.067 47.619 5.73 0.00 0.00 2.24
2767 3393 2.898705 CGCTTCAGATTACTTCAGGCT 58.101 47.619 0.00 0.00 0.00 4.58
2813 3440 7.974504 TCTGTAAGACTCTTACCATCCTTTTT 58.025 34.615 21.34 0.00 38.67 1.94
2873 3504 5.423931 ACAGTTGTTTGGAGTGGGTATTTTT 59.576 36.000 0.00 0.00 0.00 1.94
2881 3512 4.717778 TGGAGTGGGTATTTTTATCGAGGA 59.282 41.667 0.00 0.00 0.00 3.71
2883 3514 4.704965 AGTGGGTATTTTTATCGAGGAGC 58.295 43.478 0.00 0.00 0.00 4.70
2955 3586 7.126421 AGAGGATCACCAGTTCATAGTGTAATT 59.874 37.037 0.00 0.00 37.82 1.40
3009 3640 2.749076 TGTTGCATGCACACCTCTAATC 59.251 45.455 22.58 1.83 0.00 1.75
3115 3746 8.331730 TCTAGCTTTAACTTACAATGTTTCCC 57.668 34.615 0.00 0.00 0.00 3.97
3513 4144 1.482593 CGTAGAAGGGAGCAGGACATT 59.517 52.381 0.00 0.00 0.00 2.71
3522 4153 2.550855 GGAGCAGGACATTGAGACACAA 60.551 50.000 0.00 0.00 42.95 3.33
3891 4522 3.067106 CTCTTTGCCACTTCTAGCGAAA 58.933 45.455 0.00 0.00 32.09 3.46
4067 4698 8.658499 AGAAAGTGTAGTTGAAAATCTACGTT 57.342 30.769 0.00 0.00 39.25 3.99
4124 4755 5.587388 ATGTTAGTGATGAAAGGCAATGG 57.413 39.130 0.00 0.00 0.00 3.16
4164 4795 5.412640 TCGTGCGGAATGATTTTCTTAGTA 58.587 37.500 0.00 0.00 0.00 1.82
4165 4796 6.046593 TCGTGCGGAATGATTTTCTTAGTAT 58.953 36.000 0.00 0.00 0.00 2.12
4167 4798 7.065324 TCGTGCGGAATGATTTTCTTAGTATTT 59.935 33.333 0.00 0.00 0.00 1.40
4224 4855 5.178096 TCCAATGTGACATGTTCTATGGT 57.822 39.130 10.51 0.00 0.00 3.55
4451 5082 1.948145 GACCCGACTGAGTATGACGAT 59.052 52.381 0.00 0.00 0.00 3.73
4463 5095 8.187480 ACTGAGTATGACGATGATAGCATAATC 58.813 37.037 0.00 0.00 38.24 1.75
4467 5099 8.187480 AGTATGACGATGATAGCATAATCTGTC 58.813 37.037 0.00 0.00 34.11 3.51
4530 5162 4.587262 TCAGCTAGTTTACACAGAAGGTCA 59.413 41.667 0.00 0.00 0.00 4.02
4531 5163 4.926238 CAGCTAGTTTACACAGAAGGTCAG 59.074 45.833 0.00 0.00 0.00 3.51
4532 5164 4.833380 AGCTAGTTTACACAGAAGGTCAGA 59.167 41.667 0.00 0.00 0.00 3.27
4533 5165 5.047660 AGCTAGTTTACACAGAAGGTCAGAG 60.048 44.000 0.00 0.00 0.00 3.35
4534 5166 4.608948 AGTTTACACAGAAGGTCAGAGG 57.391 45.455 0.00 0.00 0.00 3.69
4535 5167 3.067833 GTTTACACAGAAGGTCAGAGGC 58.932 50.000 0.00 0.00 0.00 4.70
4536 5168 2.009681 TACACAGAAGGTCAGAGGCA 57.990 50.000 0.00 0.00 0.00 4.75
4537 5169 0.394565 ACACAGAAGGTCAGAGGCAC 59.605 55.000 0.00 0.00 0.00 5.01
4538 5170 0.668706 CACAGAAGGTCAGAGGCACG 60.669 60.000 0.00 0.00 0.00 5.34
4539 5171 0.827925 ACAGAAGGTCAGAGGCACGA 60.828 55.000 0.00 0.00 0.00 4.35
4540 5172 0.534412 CAGAAGGTCAGAGGCACGAT 59.466 55.000 0.00 0.00 0.00 3.73
4541 5173 0.820871 AGAAGGTCAGAGGCACGATC 59.179 55.000 0.00 0.00 0.00 3.69
4563 5195 2.902486 TGGCTCCCATCTGCTAGATAAG 59.098 50.000 0.00 0.00 32.12 1.73
4730 5363 0.535335 GATGCTCCGGTGTTCTGGTA 59.465 55.000 0.00 0.00 40.77 3.25
4827 5460 2.023741 CATGTCCAGCGCGATTGC 59.976 61.111 12.10 0.00 37.91 3.56
4882 5515 6.925165 CGTACCTGCATGCATATATATGATCA 59.075 38.462 22.97 14.40 35.75 2.92
4995 5664 6.427853 TGAAGTTGTCATCTTCATCGATGTTT 59.572 34.615 24.09 5.90 43.88 2.83
4997 5666 5.934043 AGTTGTCATCTTCATCGATGTTTGA 59.066 36.000 24.09 19.12 41.17 2.69
5384 6053 2.552743 GACAGGTTAACAGAAAGTGCCC 59.447 50.000 8.10 0.00 0.00 5.36
5390 6059 2.357517 CAGAAAGTGCCCGCGTCT 60.358 61.111 4.92 0.00 0.00 4.18
5450 6119 6.830838 AGGAAAAGCATGGACCTCTTTATTAG 59.169 38.462 0.00 0.00 30.66 1.73
5990 6751 4.143179 GGAGAAAGTGTTTGTAACCGATCG 60.143 45.833 8.51 8.51 0.00 3.69
6162 6923 2.820059 TCCTACCAAGATGCTATGCG 57.180 50.000 0.00 0.00 0.00 4.73
6257 7018 6.540914 ACTTCATGGTATGTATGGGTTTAACG 59.459 38.462 0.00 0.00 0.00 3.18
6509 7270 0.465460 AGAAGCTTTGCCCAACGACA 60.465 50.000 0.00 0.00 0.00 4.35
6517 7278 2.617274 GCCCAACGACACAGAAGCC 61.617 63.158 0.00 0.00 0.00 4.35
6518 7279 1.227823 CCCAACGACACAGAAGCCA 60.228 57.895 0.00 0.00 0.00 4.75
6519 7280 0.606401 CCCAACGACACAGAAGCCAT 60.606 55.000 0.00 0.00 0.00 4.40
6535 7296 0.462789 CCATGGCCAATGAAGAAGCC 59.537 55.000 10.96 0.00 45.96 4.35
6577 7341 1.546961 GTGACGAAGAGGAGGAGGAA 58.453 55.000 0.00 0.00 0.00 3.36
6670 7434 4.719369 AACGAGCTGACGGGCGAC 62.719 66.667 0.00 0.00 37.61 5.19
6685 7449 2.488820 GACGCCCTGGACGACTAC 59.511 66.667 10.02 0.00 0.00 2.73
6703 7467 3.070060 GACATCGACGTCGCCAAC 58.930 61.111 32.19 18.77 39.60 3.77
6745 7513 0.907230 ACCTGAGCCTTCTGGAGTCC 60.907 60.000 0.73 0.73 43.19 3.85
6851 9014 3.649277 CTCAGCCCGGGAGTTCGTG 62.649 68.421 29.31 10.84 0.00 4.35
6858 9021 1.300620 CGGGAGTTCGTGTGCTTGA 60.301 57.895 0.00 0.00 0.00 3.02
6878 9041 6.294564 GCTTGATAGGGTTCGATCTGTACATA 60.295 42.308 0.00 0.00 0.00 2.29
6879 9042 7.577807 GCTTGATAGGGTTCGATCTGTACATAT 60.578 40.741 0.00 0.00 0.00 1.78
6880 9043 7.158099 TGATAGGGTTCGATCTGTACATATG 57.842 40.000 0.00 0.00 0.00 1.78
6915 9078 3.003480 GGTGCTACCTTTTGTGAGCTAG 58.997 50.000 0.00 0.00 34.73 3.42
6916 9079 3.557264 GGTGCTACCTTTTGTGAGCTAGT 60.557 47.826 0.00 0.00 34.73 2.57
6917 9080 4.322499 GGTGCTACCTTTTGTGAGCTAGTA 60.322 45.833 0.00 0.00 34.73 1.82
6926 9089 1.538512 TGTGAGCTAGTACGTGACACC 59.461 52.381 0.00 0.00 0.00 4.16
6986 9149 4.257267 TGGACCGCATCTCACTATATTG 57.743 45.455 0.00 0.00 0.00 1.90
7002 9165 7.606456 TCACTATATTGCGAGTTCCTTTTCTTT 59.394 33.333 0.00 0.00 0.00 2.52
7007 9170 6.385649 TTGCGAGTTCCTTTTCTTTTGTAT 57.614 33.333 0.00 0.00 0.00 2.29
7082 9245 8.785329 AAATACCACCGCATATTTTTCATTTT 57.215 26.923 0.00 0.00 28.68 1.82
7131 9308 7.218014 GGTTTACTGTTGTAACCGTTTTTGTAC 59.782 37.037 0.00 0.00 38.26 2.90
7135 9312 4.456911 TGTTGTAACCGTTTTTGTACCACA 59.543 37.500 0.00 0.00 0.00 4.17
7151 9328 6.941857 TGTACCACATCTTCTGTTAATAGCA 58.058 36.000 0.00 0.00 35.29 3.49
7152 9329 7.390823 TGTACCACATCTTCTGTTAATAGCAA 58.609 34.615 0.00 0.00 35.29 3.91
7153 9330 7.880713 TGTACCACATCTTCTGTTAATAGCAAA 59.119 33.333 0.00 0.00 35.29 3.68
7154 9331 7.944729 ACCACATCTTCTGTTAATAGCAAAT 57.055 32.000 0.00 0.00 35.29 2.32
7155 9332 7.989826 ACCACATCTTCTGTTAATAGCAAATC 58.010 34.615 0.00 0.00 35.29 2.17
7156 9333 7.067494 ACCACATCTTCTGTTAATAGCAAATCC 59.933 37.037 0.00 0.00 35.29 3.01
7157 9334 7.128331 CACATCTTCTGTTAATAGCAAATCCG 58.872 38.462 0.00 0.00 35.29 4.18
7158 9335 6.823689 ACATCTTCTGTTAATAGCAAATCCGT 59.176 34.615 0.00 0.00 32.90 4.69
7159 9336 6.662414 TCTTCTGTTAATAGCAAATCCGTG 57.338 37.500 0.00 0.00 0.00 4.94
7160 9337 5.584649 TCTTCTGTTAATAGCAAATCCGTGG 59.415 40.000 0.00 0.00 0.00 4.94
7161 9338 5.092554 TCTGTTAATAGCAAATCCGTGGA 57.907 39.130 0.00 0.00 0.00 4.02
7162 9339 5.116180 TCTGTTAATAGCAAATCCGTGGAG 58.884 41.667 0.00 0.00 0.00 3.86
7163 9340 4.839121 TGTTAATAGCAAATCCGTGGAGT 58.161 39.130 0.00 0.00 0.00 3.85
7164 9341 5.250200 TGTTAATAGCAAATCCGTGGAGTT 58.750 37.500 0.00 0.00 32.32 3.01
7170 9347 3.980646 CAAATCCGTGGAGTTGTCAAA 57.019 42.857 18.33 0.00 42.84 2.69
7171 9348 4.300189 CAAATCCGTGGAGTTGTCAAAA 57.700 40.909 18.33 0.00 42.84 2.44
7172 9349 4.677584 CAAATCCGTGGAGTTGTCAAAAA 58.322 39.130 18.33 0.00 42.84 1.94
7206 9383 7.807907 GCAAATCCGTGGATATTAATACCAAAG 59.192 37.037 14.52 12.25 35.40 2.77
7228 9405 1.621107 CGCATGTGCTGAAAATCCAC 58.379 50.000 3.25 0.00 39.32 4.02
7459 10107 6.001460 TGGGTAGAAATCGTCACTTTTTGAT 58.999 36.000 0.00 0.00 36.32 2.57
7499 10147 2.942804 TGTTGTTCAAGGGAGCATTGA 58.057 42.857 0.00 0.00 34.05 2.57
7547 10195 6.405842 CCAGGATAAATAGTTTTGAGGTTGGC 60.406 42.308 0.00 0.00 0.00 4.52
7622 10273 8.147642 AGATGAATATCAAACGGAAAGATGAC 57.852 34.615 0.00 0.00 35.70 3.06
7752 10403 3.783478 TATGCGCGTCGGATGTGGG 62.783 63.158 4.79 0.98 38.55 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.701340 TGGATGCCATCACTTATATAGACAC 58.299 40.000 7.06 0.00 0.00 3.67
1 2 6.933514 TGGATGCCATCACTTATATAGACA 57.066 37.500 7.06 0.00 0.00 3.41
2 3 8.621532 TTTTGGATGCCATCACTTATATAGAC 57.378 34.615 7.06 0.00 31.53 2.59
3 4 7.884877 CCTTTTGGATGCCATCACTTATATAGA 59.115 37.037 7.06 0.00 44.07 1.98
4 5 7.362401 GCCTTTTGGATGCCATCACTTATATAG 60.362 40.741 7.06 0.00 44.07 1.31
5 6 6.434028 GCCTTTTGGATGCCATCACTTATATA 59.566 38.462 7.06 0.00 44.07 0.86
6 7 5.244626 GCCTTTTGGATGCCATCACTTATAT 59.755 40.000 7.06 0.00 44.07 0.86
7 8 4.584325 GCCTTTTGGATGCCATCACTTATA 59.416 41.667 7.06 0.00 44.07 0.98
8 9 3.385755 GCCTTTTGGATGCCATCACTTAT 59.614 43.478 7.06 0.00 44.07 1.73
9 10 2.760092 GCCTTTTGGATGCCATCACTTA 59.240 45.455 7.06 0.00 44.07 2.24
10 11 1.551883 GCCTTTTGGATGCCATCACTT 59.448 47.619 7.06 0.00 44.07 3.16
11 12 1.188863 GCCTTTTGGATGCCATCACT 58.811 50.000 7.06 0.00 44.07 3.41
12 13 0.896923 TGCCTTTTGGATGCCATCAC 59.103 50.000 7.06 0.00 44.07 3.06
13 14 1.187974 CTGCCTTTTGGATGCCATCA 58.812 50.000 7.06 0.00 44.07 3.07
14 15 1.477553 TCTGCCTTTTGGATGCCATC 58.522 50.000 0.00 0.00 44.07 3.51
59 60 5.541845 AGGTTATATGGATGACGTGATGTG 58.458 41.667 0.00 0.00 0.00 3.21
62 63 8.645814 TTACTAGGTTATATGGATGACGTGAT 57.354 34.615 0.00 0.00 0.00 3.06
199 200 4.212214 AGCGTGAAGAAAAGAAGTAAGCTG 59.788 41.667 0.00 0.00 0.00 4.24
200 201 4.381411 AGCGTGAAGAAAAGAAGTAAGCT 58.619 39.130 0.00 0.00 0.00 3.74
219 514 6.603237 TCAATATGTTAATGGACTTGAGCG 57.397 37.500 0.00 0.00 0.00 5.03
278 573 8.970691 ATACATCAATAAGGCGCAAATTATTC 57.029 30.769 10.83 0.00 30.95 1.75
324 619 8.087750 TGTCCAAACACAAAAATCCATATTCTC 58.912 33.333 0.00 0.00 0.00 2.87
341 636 9.922477 TGGTATGGTAATTAATATGTCCAAACA 57.078 29.630 0.00 0.00 40.38 2.83
381 676 5.237048 GCATTAATTGGCACTTTCCTCAAA 58.763 37.500 0.00 0.00 0.00 2.69
382 677 4.819769 GCATTAATTGGCACTTTCCTCAA 58.180 39.130 0.00 0.00 0.00 3.02
383 678 4.454728 GCATTAATTGGCACTTTCCTCA 57.545 40.909 0.00 0.00 0.00 3.86
395 690 5.065090 TCTCATCACTTCGTGGCATTAATTG 59.935 40.000 0.00 0.00 33.87 2.32
407 702 6.325596 TCACACTATTTCTCTCATCACTTCG 58.674 40.000 0.00 0.00 0.00 3.79
420 715 9.049523 TGATGAGCATTATCTTCACACTATTTC 57.950 33.333 0.00 0.00 30.77 2.17
451 746 9.193602 CATTGTTTGTTTGACGAATTGTTTTAC 57.806 29.630 0.00 0.00 0.00 2.01
453 748 6.740453 GCATTGTTTGTTTGACGAATTGTTTT 59.260 30.769 0.00 0.00 0.00 2.43
480 775 6.258160 CGGAATATGCTTTAAAGAGGTGTTG 58.742 40.000 19.48 0.00 0.00 3.33
488 783 5.743872 GTCTTTGGCGGAATATGCTTTAAAG 59.256 40.000 11.02 11.02 33.43 1.85
580 888 8.107399 AGATACATGCCACATCATTTTCTATG 57.893 34.615 0.00 0.00 0.00 2.23
590 898 2.533266 ACCGAGATACATGCCACATC 57.467 50.000 0.00 0.00 0.00 3.06
592 900 2.236146 AGAAACCGAGATACATGCCACA 59.764 45.455 0.00 0.00 0.00 4.17
593 901 2.906354 AGAAACCGAGATACATGCCAC 58.094 47.619 0.00 0.00 0.00 5.01
595 903 6.631016 TCATATAGAAACCGAGATACATGCC 58.369 40.000 0.00 0.00 0.00 4.40
596 904 8.534333 TTTCATATAGAAACCGAGATACATGC 57.466 34.615 0.00 0.00 41.17 4.06
617 925 8.168790 TGTGAATCAAATGATGTCTCTTTTCA 57.831 30.769 0.00 0.00 34.49 2.69
647 955 7.307131 ACTTGGATCTGTTGGAAAATTTCAT 57.693 32.000 8.09 0.00 0.00 2.57
650 958 9.492973 CATTAACTTGGATCTGTTGGAAAATTT 57.507 29.630 0.00 0.00 0.00 1.82
651 959 8.650490 ACATTAACTTGGATCTGTTGGAAAATT 58.350 29.630 0.00 0.00 0.00 1.82
652 960 8.193953 ACATTAACTTGGATCTGTTGGAAAAT 57.806 30.769 0.00 0.00 0.00 1.82
691 999 9.234384 ACGTATGATTAGTTTCTATCTTTCACG 57.766 33.333 0.00 0.00 0.00 4.35
697 1005 9.352191 AGTACCACGTATGATTAGTTTCTATCT 57.648 33.333 0.00 0.00 0.00 1.98
736 1044 3.926616 TGTAGAGCTCTTTGGTTGTAGC 58.073 45.455 23.84 0.82 35.16 3.58
737 1045 4.220821 TCCTGTAGAGCTCTTTGGTTGTAG 59.779 45.833 23.84 8.56 0.00 2.74
738 1046 4.157246 TCCTGTAGAGCTCTTTGGTTGTA 58.843 43.478 23.84 0.00 0.00 2.41
739 1047 2.972713 TCCTGTAGAGCTCTTTGGTTGT 59.027 45.455 23.84 0.00 0.00 3.32
740 1048 3.685139 TCCTGTAGAGCTCTTTGGTTG 57.315 47.619 23.84 6.45 0.00 3.77
741 1049 4.917906 ATTCCTGTAGAGCTCTTTGGTT 57.082 40.909 23.84 10.63 0.00 3.67
742 1050 4.917906 AATTCCTGTAGAGCTCTTTGGT 57.082 40.909 23.84 0.00 0.00 3.67
743 1051 5.248640 TGAAATTCCTGTAGAGCTCTTTGG 58.751 41.667 23.84 20.12 0.00 3.28
744 1052 6.998968 ATGAAATTCCTGTAGAGCTCTTTG 57.001 37.500 23.84 12.01 0.00 2.77
745 1053 8.414629 AAAATGAAATTCCTGTAGAGCTCTTT 57.585 30.769 23.84 7.19 33.67 2.52
746 1054 9.692325 ATAAAATGAAATTCCTGTAGAGCTCTT 57.308 29.630 23.84 6.22 33.67 2.85
784 1092 7.883311 CGGGGTATAGGAATTCAACATTAGAAT 59.117 37.037 7.93 0.00 37.30 2.40
785 1093 7.221450 CGGGGTATAGGAATTCAACATTAGAA 58.779 38.462 7.93 0.00 0.00 2.10
787 1095 5.411669 GCGGGGTATAGGAATTCAACATTAG 59.588 44.000 7.93 0.00 0.00 1.73
789 1097 4.142038 GCGGGGTATAGGAATTCAACATT 58.858 43.478 7.93 0.00 0.00 2.71
790 1098 3.137544 TGCGGGGTATAGGAATTCAACAT 59.862 43.478 7.93 0.00 0.00 2.71
840 1149 7.554959 AGTCAGGACTCTTTAATTTGTAGGA 57.445 36.000 0.00 0.00 36.92 2.94
890 1199 9.216117 AGCGTAATTTTGGAACATATCTATACC 57.784 33.333 0.00 0.00 39.30 2.73
895 1204 7.624360 TGAAGCGTAATTTTGGAACATATCT 57.376 32.000 0.00 0.00 39.30 1.98
970 1285 1.456165 GGAACAGAAAACGAGCGAGTC 59.544 52.381 0.00 0.00 0.00 3.36
971 1286 1.068741 AGGAACAGAAAACGAGCGAGT 59.931 47.619 0.00 0.00 0.00 4.18
997 1313 2.203422 TTTGGGGTCTGTTGCGGG 60.203 61.111 0.00 0.00 0.00 6.13
998 1314 2.561037 GGTTTGGGGTCTGTTGCGG 61.561 63.158 0.00 0.00 0.00 5.69
999 1315 2.561037 GGGTTTGGGGTCTGTTGCG 61.561 63.158 0.00 0.00 0.00 4.85
1000 1316 2.561037 CGGGTTTGGGGTCTGTTGC 61.561 63.158 0.00 0.00 0.00 4.17
1006 1322 4.589675 TGGTGCGGGTTTGGGGTC 62.590 66.667 0.00 0.00 0.00 4.46
1029 1345 3.000819 TCGGCGAGTTGTGGGGAT 61.001 61.111 4.99 0.00 0.00 3.85
1030 1346 3.691342 CTCGGCGAGTTGTGGGGA 61.691 66.667 27.92 0.00 0.00 4.81
1071 1387 4.626081 GCCATCGATCGGGGTGGG 62.626 72.222 25.55 17.05 32.35 4.61
1159 1487 4.106925 CAGCTCCACCTCCAGGGC 62.107 72.222 0.00 0.00 40.27 5.19
1317 1645 2.032981 CACCTTGGCGTTGCTCTTT 58.967 52.632 0.00 0.00 0.00 2.52
1321 1649 2.980233 GAGCACCTTGGCGTTGCT 60.980 61.111 3.37 3.37 39.27 3.91
1447 1775 1.514678 CGATCAGAGAGGAGCGGAGG 61.515 65.000 0.00 0.00 42.51 4.30
1479 1807 2.167693 GGGGAATCCGGAAATCCAAAAC 59.832 50.000 30.24 18.10 34.82 2.43
1492 1821 1.341089 GGGAACAGAACAGGGGAATCC 60.341 57.143 0.00 0.00 0.00 3.01
1568 2185 5.190992 TCGGCGCTCATAATTTTAGACTA 57.809 39.130 7.64 0.00 0.00 2.59
1631 2253 3.125658 GGCGGAGAGTACGATCTTATCTC 59.874 52.174 0.00 8.74 36.50 2.75
1671 2293 0.890996 GGGTCCTTGACTTGCCACAG 60.891 60.000 0.00 0.00 32.47 3.66
1790 2412 3.902261 TTGTGTTGCTAGCATGTTCTG 57.098 42.857 20.13 0.00 0.00 3.02
1826 2448 4.576463 TCTTCTTGCTGAGAAAGAAACACC 59.424 41.667 16.04 0.00 43.56 4.16
1842 2464 2.292569 ACTGTGCATTGTGCTCTTCTTG 59.707 45.455 3.41 0.00 45.31 3.02
1850 2475 2.743664 TCATACAGACTGTGCATTGTGC 59.256 45.455 18.58 0.00 45.29 4.57
1858 2483 6.870439 TGAGTTTCTGAATCATACAGACTGTG 59.130 38.462 18.58 2.43 42.84 3.66
1968 2593 5.645067 ACAACTAATCATCACCATCACACTG 59.355 40.000 0.00 0.00 0.00 3.66
2004 2629 5.351233 TTGTGCCACTAACATTTTCTACG 57.649 39.130 0.00 0.00 0.00 3.51
2020 2645 2.298729 TGCTTTCCACCTATTTTGTGCC 59.701 45.455 0.00 0.00 32.30 5.01
2065 2690 6.350949 GCATCCCTACAAAAACATTGTGGTAT 60.351 38.462 4.19 0.00 34.11 2.73
2071 2696 3.928375 GCAGCATCCCTACAAAAACATTG 59.072 43.478 0.00 0.00 0.00 2.82
2076 2701 2.591923 TGTGCAGCATCCCTACAAAAA 58.408 42.857 0.00 0.00 0.00 1.94
2283 2908 1.325476 GCCATCTTCAAAGCCCTGGG 61.325 60.000 8.86 8.86 0.00 4.45
2285 2910 1.101331 GAGCCATCTTCAAAGCCCTG 58.899 55.000 0.00 0.00 0.00 4.45
2459 3085 1.682854 CCTGGCAACACAACAGATGTT 59.317 47.619 0.00 0.00 46.17 2.71
2460 3086 1.133823 TCCTGGCAACACAACAGATGT 60.134 47.619 0.00 0.00 46.17 3.06
2488 3114 8.675705 TCAATGAGTTTATTGTCACAAAGAGA 57.324 30.769 0.00 0.00 38.77 3.10
2525 3151 6.574350 AGGTAACAGATAATTCTTCTCACGG 58.426 40.000 0.00 0.00 41.41 4.94
2597 3223 3.881688 GGCACATTATCAACTCTCTGCAT 59.118 43.478 0.00 0.00 0.00 3.96
2711 3337 4.076394 CCGTGGGAAAGTTCAAATCCTAA 58.924 43.478 0.00 0.00 33.61 2.69
2725 3351 1.345415 GTGGAGTCTTTACCGTGGGAA 59.655 52.381 0.00 0.00 0.00 3.97
2728 3354 1.012486 GCGTGGAGTCTTTACCGTGG 61.012 60.000 0.00 0.00 0.00 4.94
2740 3366 0.924090 GTAATCTGAAGCGCGTGGAG 59.076 55.000 8.43 0.00 0.00 3.86
2761 3387 4.783621 GCATGACGGGCAGCCTGA 62.784 66.667 28.29 5.57 33.36 3.86
2767 3393 1.153309 CAGATCTGCATGACGGGCA 60.153 57.895 10.38 0.00 39.32 5.36
2842 3469 4.510340 CCACTCCAAACAACTGTACAGTAC 59.490 45.833 28.13 3.49 41.58 2.73
2843 3470 4.443739 CCCACTCCAAACAACTGTACAGTA 60.444 45.833 28.13 10.35 41.58 2.74
2844 3471 3.541632 CCACTCCAAACAACTGTACAGT 58.458 45.455 22.95 22.95 44.94 3.55
2845 3472 2.878406 CCCACTCCAAACAACTGTACAG 59.122 50.000 21.44 21.44 0.00 2.74
2846 3473 2.240160 ACCCACTCCAAACAACTGTACA 59.760 45.455 0.00 0.00 0.00 2.90
2847 3474 2.927028 ACCCACTCCAAACAACTGTAC 58.073 47.619 0.00 0.00 0.00 2.90
2873 3504 6.209589 AGCAATTAGTTATCTGCTCCTCGATA 59.790 38.462 0.00 0.00 41.18 2.92
3009 3640 8.289618 TCTTAACGAAAATCCAACAAAGATCAG 58.710 33.333 0.00 0.00 0.00 2.90
3107 3738 5.393027 GCAGTTTTGATACATCGGGAAACAT 60.393 40.000 13.41 2.89 33.26 2.71
3115 3746 2.223340 GGGCAGCAGTTTTGATACATCG 60.223 50.000 0.00 0.00 0.00 3.84
3513 4144 8.035394 GGTTACATTATCTCTCTTTGTGTCTCA 58.965 37.037 0.00 0.00 0.00 3.27
3522 4153 9.388506 CAATGTGAAGGTTACATTATCTCTCTT 57.611 33.333 0.00 0.00 44.50 2.85
3612 4243 2.169769 TCCCTAGGATAACGCCAAACAG 59.830 50.000 11.48 0.00 0.00 3.16
3774 4405 5.825593 TGTAGGACTATGGGGATTTCATC 57.174 43.478 0.00 0.00 0.00 2.92
3891 4522 6.096846 GGACTTTCAACCCATAACAAGCATAT 59.903 38.462 0.00 0.00 0.00 1.78
4040 4671 8.762426 ACGTAGATTTTCAACTACACTTTCTTC 58.238 33.333 0.00 0.00 38.90 2.87
4124 4755 3.294627 GCACGAACGAAATGAACGAATTC 59.705 43.478 0.14 0.00 35.18 2.17
4164 4795 5.195001 ACGACATGGCAAAACTTACAAAT 57.805 34.783 0.00 0.00 0.00 2.32
4165 4796 4.640789 ACGACATGGCAAAACTTACAAA 57.359 36.364 0.00 0.00 0.00 2.83
4167 4798 3.628032 TGAACGACATGGCAAAACTTACA 59.372 39.130 0.00 0.00 0.00 2.41
4224 4855 0.036732 AGGTGCAGAAAATCCGCTCA 59.963 50.000 0.00 0.00 0.00 4.26
4451 5082 2.288152 TGCGCGACAGATTATGCTATCA 60.288 45.455 12.10 0.00 0.00 2.15
4467 5099 1.397693 GCTAGATAAACATGCTGCGCG 60.398 52.381 0.00 0.00 0.00 6.86
4530 5162 2.430610 GGAGCCAGATCGTGCCTCT 61.431 63.158 5.97 0.00 0.00 3.69
4531 5163 2.107953 GGAGCCAGATCGTGCCTC 59.892 66.667 5.97 1.30 0.00 4.70
4532 5164 3.474570 GGGAGCCAGATCGTGCCT 61.475 66.667 5.97 0.00 0.00 4.75
4533 5165 3.112205 ATGGGAGCCAGATCGTGCC 62.112 63.158 5.97 0.00 36.75 5.01
4534 5166 1.596477 GATGGGAGCCAGATCGTGC 60.596 63.158 1.70 1.70 36.75 5.34
4535 5167 0.249784 CAGATGGGAGCCAGATCGTG 60.250 60.000 0.00 0.00 36.75 4.35
4536 5168 2.037620 GCAGATGGGAGCCAGATCGT 62.038 60.000 0.00 0.00 36.75 3.73
4537 5169 1.301558 GCAGATGGGAGCCAGATCG 60.302 63.158 0.00 0.00 36.75 3.69
4538 5170 1.275856 CTAGCAGATGGGAGCCAGATC 59.724 57.143 0.00 0.00 36.75 2.75
4539 5171 1.132913 TCTAGCAGATGGGAGCCAGAT 60.133 52.381 0.00 0.00 36.75 2.90
4540 5172 0.262876 TCTAGCAGATGGGAGCCAGA 59.737 55.000 0.00 0.00 36.75 3.86
4541 5173 1.350071 ATCTAGCAGATGGGAGCCAG 58.650 55.000 0.00 0.00 36.75 4.85
4563 5195 5.186198 AGACATGGTGGCTAGTGAATTAAC 58.814 41.667 0.00 0.00 30.85 2.01
4730 5363 1.464198 AGAAGGGGTGCCAGGACTT 60.464 57.895 0.00 0.00 0.00 3.01
4858 5491 8.667076 TTGATCATATATATGCATGCAGGTAC 57.333 34.615 26.69 8.46 33.76 3.34
4882 5515 6.822442 TGAATCATGGATTGCATGCTTTATT 58.178 32.000 20.33 7.69 31.89 1.40
4995 5664 2.103373 GAGACAGCCACATACCTCTCA 58.897 52.381 0.00 0.00 0.00 3.27
4997 5666 1.107114 CGAGACAGCCACATACCTCT 58.893 55.000 0.00 0.00 0.00 3.69
5067 5736 1.079750 GTCCTCCTTGACGGCTGAC 60.080 63.158 0.00 0.00 0.00 3.51
5320 5989 5.291905 ACCATATAAGTAGGACCTTGCAC 57.708 43.478 0.00 0.00 0.00 4.57
5384 6053 2.159572 CCCTAAAAATGGACAAGACGCG 60.160 50.000 3.53 3.53 0.00 6.01
5390 6059 8.499288 AAAGAATAACCCCTAAAAATGGACAA 57.501 30.769 0.00 0.00 0.00 3.18
5450 6119 0.179034 ATTCGCATTGGCTCTCCTCC 60.179 55.000 0.00 0.00 38.10 4.30
5901 6622 9.717942 GCTAGGAATAGATGTGTGAAATCTAAT 57.282 33.333 0.00 0.00 39.46 1.73
5990 6751 7.279981 ACTTCTCAAACCTGCAAAATTAAAACC 59.720 33.333 0.00 0.00 0.00 3.27
6162 6923 6.530181 CAGAACAAAAGGAAGTGTTAACAACC 59.470 38.462 10.51 13.68 38.07 3.77
6308 7069 0.974383 AAGACGTAGAAGGGGGTGTG 59.026 55.000 0.00 0.00 0.00 3.82
6509 7270 0.040058 TCATTGGCCATGGCTTCTGT 59.960 50.000 34.70 14.72 41.60 3.41
6517 7278 0.101759 CGGCTTCTTCATTGGCCATG 59.898 55.000 6.09 7.61 44.27 3.66
6518 7279 0.323725 ACGGCTTCTTCATTGGCCAT 60.324 50.000 6.09 0.00 44.27 4.40
6519 7280 1.074775 ACGGCTTCTTCATTGGCCA 59.925 52.632 0.00 0.00 44.27 5.36
6535 7296 1.948104 TGTCTTGGTCTTGGTTCACG 58.052 50.000 0.00 0.00 0.00 4.35
6559 7320 2.497675 CAATTCCTCCTCCTCTTCGTCA 59.502 50.000 0.00 0.00 0.00 4.35
6577 7341 1.202580 CCCGCTTCTTCCTCGATCAAT 60.203 52.381 0.00 0.00 0.00 2.57
6670 7434 3.129502 TCGTAGTCGTCCAGGGCG 61.130 66.667 7.30 7.30 38.33 6.13
6712 7476 2.758327 AGGTACTCCGCGATGGCA 60.758 61.111 8.23 0.00 39.92 4.92
6761 7532 4.527583 AGAGCTAGCAGCCGCAGC 62.528 66.667 18.83 0.00 43.77 5.25
6762 7533 2.172372 CAAGAGCTAGCAGCCGCAG 61.172 63.158 18.83 0.00 43.77 5.18
6763 7534 1.964608 ATCAAGAGCTAGCAGCCGCA 61.965 55.000 18.83 0.00 43.77 5.69
6764 7535 1.227497 ATCAAGAGCTAGCAGCCGC 60.227 57.895 18.83 0.42 43.77 6.53
6765 7536 0.179089 ACATCAAGAGCTAGCAGCCG 60.179 55.000 18.83 2.54 43.77 5.52
6766 7537 1.297664 CACATCAAGAGCTAGCAGCC 58.702 55.000 18.83 5.57 43.77 4.85
6767 7538 0.656785 GCACATCAAGAGCTAGCAGC 59.343 55.000 18.83 8.57 42.84 5.25
6768 7539 1.934525 CTGCACATCAAGAGCTAGCAG 59.065 52.381 18.83 3.78 41.45 4.24
6851 9014 3.126831 CAGATCGAACCCTATCAAGCAC 58.873 50.000 0.00 0.00 0.00 4.40
6858 9021 7.615757 TCATCATATGTACAGATCGAACCCTAT 59.384 37.037 0.00 0.00 0.00 2.57
6878 9041 8.098963 AGGTAGCACCATATTCATATCATCAT 57.901 34.615 7.86 0.00 41.95 2.45
6879 9042 7.500629 AGGTAGCACCATATTCATATCATCA 57.499 36.000 7.86 0.00 41.95 3.07
6880 9043 8.798859 AAAGGTAGCACCATATTCATATCATC 57.201 34.615 7.86 0.00 41.95 2.92
6915 9078 2.542595 CAGGTTTTCAGGTGTCACGTAC 59.457 50.000 0.00 0.00 0.00 3.67
6916 9079 2.168936 ACAGGTTTTCAGGTGTCACGTA 59.831 45.455 0.00 0.00 0.00 3.57
6917 9080 1.065709 ACAGGTTTTCAGGTGTCACGT 60.066 47.619 0.00 0.00 0.00 4.49
6926 9089 2.220133 CACGACGGTAACAGGTTTTCAG 59.780 50.000 0.00 0.00 0.00 3.02
6986 9149 7.975750 AGATATACAAAAGAAAAGGAACTCGC 58.024 34.615 0.00 0.00 38.49 5.03
7028 9191 9.984190 CCCTATAAAACCATCTACTAAGACTTC 57.016 37.037 0.00 0.00 33.57 3.01
7131 9308 7.420800 GGATTTGCTATTAACAGAAGATGTGG 58.579 38.462 0.00 0.00 43.00 4.17
7135 9312 6.260936 CCACGGATTTGCTATTAACAGAAGAT 59.739 38.462 0.00 0.00 0.00 2.40
7151 9328 4.993029 TTTTTGACAACTCCACGGATTT 57.007 36.364 0.00 0.00 0.00 2.17
7176 9353 9.826574 GGTATTAATATCCACGGATTTGCTATA 57.173 33.333 3.41 0.00 36.17 1.31
7177 9354 8.325787 TGGTATTAATATCCACGGATTTGCTAT 58.674 33.333 3.41 0.00 36.17 2.97
7178 9355 7.681679 TGGTATTAATATCCACGGATTTGCTA 58.318 34.615 3.41 0.00 36.17 3.49
7179 9356 6.539173 TGGTATTAATATCCACGGATTTGCT 58.461 36.000 3.41 0.00 36.17 3.91
7180 9357 6.811253 TGGTATTAATATCCACGGATTTGC 57.189 37.500 3.41 0.00 36.17 3.68
7181 9358 9.062524 TCTTTGGTATTAATATCCACGGATTTG 57.937 33.333 3.41 3.92 36.17 2.32
7345 9710 2.122768 CTCTAGCCTCCAACCTCCATT 58.877 52.381 0.00 0.00 0.00 3.16
7480 10128 3.569701 TCTTCAATGCTCCCTTGAACAAC 59.430 43.478 0.00 0.00 37.61 3.32
7499 10147 5.817816 GGTGATGTAATTCCATTCTCGTCTT 59.182 40.000 0.00 0.00 0.00 3.01
7538 10186 2.647683 TGTATTGTGTGCCAACCTCA 57.352 45.000 0.00 0.00 35.44 3.86
7547 10195 6.567687 TGGAAGGTGTAATTGTATTGTGTG 57.432 37.500 0.00 0.00 0.00 3.82
7695 10346 2.908688 AATCAAGGTTGTTGTTGGGC 57.091 45.000 0.00 0.00 0.00 5.36
7698 10349 6.966435 AGTTTGAAATCAAGGTTGTTGTTG 57.034 33.333 0.00 0.00 37.15 3.33
7752 10403 2.408022 CTGATCCGTCCGTCCGTC 59.592 66.667 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.