Multiple sequence alignment - TraesCS6D01G217000

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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 TraesCS6D01G217000 chr6D 100.000 4610 0 0 1 4610 306713237 306708628 0.000000e+00 8514
1 TraesCS6D01G217000 chr6B 93.136 1923 102 17 2701 4610 474178265 474176360 0.000000e+00 2793
2 TraesCS6D01G217000 chr6B 90.825 1079 55 27 786 1837 474180225 474179164 0.000000e+00 1404
3 TraesCS6D01G217000 chr6B 90.864 799 62 10 1892 2684 474179140 474178347 0.000000e+00 1061
4 TraesCS6D01G217000 chr6B 91.429 770 57 7 68 834 474187745 474186982 0.000000e+00 1048
5 TraesCS6D01G217000 chr6B 96.629 89 3 0 686 774 474183003 474182915 1.030000e-31 148
6 TraesCS6D01G217000 chr6A 93.181 1921 97 17 2701 4610 442398122 442396225 0.000000e+00 2791
7 TraesCS6D01G217000 chr6A 88.348 1931 145 51 772 2684 442400072 442398204 0.000000e+00 2246
8 TraesCS6D01G217000 chr6A 91.137 519 45 1 6 523 442401020 442400502 0.000000e+00 702


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 TraesCS6D01G217000 chr6D 306708628 306713237 4609 True 8514.0 8514 100.000000 1 4610 1 chr6D.!!$R1 4609
1 TraesCS6D01G217000 chr6B 474176360 474187745 11385 True 1290.8 2793 92.576600 68 4610 5 chr6B.!!$R1 4542
2 TraesCS6D01G217000 chr6A 442396225 442401020 4795 True 1913.0 2791 90.888667 6 4610 3 chr6A.!!$R1 4604

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
748 881 1.400494 AGATCGTGTTATTTTGCGGCC 59.600 47.619 0.00 0.00 0.0 6.13 F
1861 8919 0.106819 CCCATGCCCTTCTCCTTCTG 60.107 60.000 0.00 0.00 0.0 3.02 F
1999 9060 0.322187 TCCGTTCTTTAGGCCTTGGC 60.322 55.000 12.58 2.49 0.0 4.52 F
3297 10432 1.623811 TCTGTCCCTCTTTAGTGTGGC 59.376 52.381 0.00 0.00 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 9040 0.322187 GCCAAGGCCTAAAGAACGGA 60.322 55.000 5.16 0.0 34.56 4.69 R
3297 10432 0.798776 GTTGCCTCAACCATCTCACG 59.201 55.000 0.00 0.0 38.30 4.35 R
3305 10440 3.334583 TCATGTCTAGTTGCCTCAACC 57.665 47.619 6.12 0.0 44.49 3.77 R
4384 11527 1.898574 CTTTCACCCGGTGCTGCTT 60.899 57.895 13.19 0.0 32.98 3.91 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
53 54 6.874288 GCTTGTTAGATATGAGCCATTTCT 57.126 37.500 11.00 11.00 36.46 2.52
64 65 4.401022 TGAGCCATTTCTAGCCCAATATG 58.599 43.478 0.00 0.00 0.00 1.78
65 66 3.160269 AGCCATTTCTAGCCCAATATGC 58.840 45.455 0.00 0.00 0.00 3.14
66 67 2.892852 GCCATTTCTAGCCCAATATGCA 59.107 45.455 0.00 0.00 0.00 3.96
71 72 6.660521 CCATTTCTAGCCCAATATGCATCTAA 59.339 38.462 0.19 0.00 0.00 2.10
76 77 5.972107 AGCCCAATATGCATCTAAACATC 57.028 39.130 0.19 0.00 0.00 3.06
85 86 9.445878 AATATGCATCTAAACATCTGTGATAGG 57.554 33.333 0.19 0.00 0.00 2.57
110 111 7.278424 GGTTACATTTAGCATTGCACATCATTT 59.722 33.333 11.91 0.00 0.00 2.32
144 145 7.715249 AGTTTTCTTTGTAACTATGCAGTGAGA 59.285 33.333 0.00 0.00 34.36 3.27
147 148 6.935167 TCTTTGTAACTATGCAGTGAGATCA 58.065 36.000 0.00 0.00 34.36 2.92
149 150 7.877612 TCTTTGTAACTATGCAGTGAGATCAAA 59.122 33.333 0.00 0.00 34.36 2.69
151 152 5.874810 TGTAACTATGCAGTGAGATCAAACC 59.125 40.000 0.00 0.00 34.36 3.27
153 154 2.479566 ATGCAGTGAGATCAAACCGT 57.520 45.000 0.00 0.00 0.00 4.83
156 157 2.289631 TGCAGTGAGATCAAACCGTCAT 60.290 45.455 0.00 0.00 0.00 3.06
171 172 5.290493 ACCGTCATAATGCTAATCTCCAA 57.710 39.130 0.00 0.00 0.00 3.53
172 173 5.869579 ACCGTCATAATGCTAATCTCCAAT 58.130 37.500 0.00 0.00 0.00 3.16
177 178 8.961092 CGTCATAATGCTAATCTCCAATTTTTG 58.039 33.333 0.00 0.00 0.00 2.44
301 302 1.496060 TTACACGAGGGAGATGCCAT 58.504 50.000 0.00 0.00 38.95 4.40
393 394 5.830457 TCCTGTACAGATGATCAGACCTAAG 59.170 44.000 24.68 1.53 0.00 2.18
464 465 4.162651 AGAGCTCACAATTTTCCCCAATT 58.837 39.130 17.77 0.00 0.00 2.32
566 697 8.985315 AATGCTAATGATGTCTCCTGATTAAA 57.015 30.769 0.00 0.00 0.00 1.52
617 748 7.630026 TGTTATCGATGCATAAAAAGCTACAG 58.370 34.615 8.54 0.00 0.00 2.74
644 775 4.212425 TGTCTATACAAACAGTTGCGTTGG 59.788 41.667 0.00 0.00 38.39 3.77
685 816 2.094894 CCGATGCAAGTTCTGTAAGCAG 59.905 50.000 0.00 0.00 43.87 4.24
733 866 3.321497 GCTATGAAGGTTGCCTAGATCG 58.679 50.000 0.00 0.00 31.13 3.69
738 871 3.512329 TGAAGGTTGCCTAGATCGTGTTA 59.488 43.478 0.00 0.00 31.13 2.41
748 881 1.400494 AGATCGTGTTATTTTGCGGCC 59.600 47.619 0.00 0.00 0.00 6.13
803 1002 1.643832 CTTATGCGCGCTCTTTCCC 59.356 57.895 33.29 0.00 0.00 3.97
844 7848 4.632538 AGTTTCTTGTTACAGTGTTGGC 57.367 40.909 0.00 0.00 0.00 4.52
845 7849 3.064820 AGTTTCTTGTTACAGTGTTGGCG 59.935 43.478 0.00 0.00 0.00 5.69
848 7852 1.448922 TTGTTACAGTGTTGGCGGGC 61.449 55.000 0.00 0.00 0.00 6.13
902 7907 1.976404 GGGGCATTCCTACCTACCTAC 59.024 57.143 0.00 0.00 35.33 3.18
1085 8099 2.480426 CTTCTGGTTTCGTCGCGTGC 62.480 60.000 5.77 0.00 0.00 5.34
1086 8100 4.409588 CTGGTTTCGTCGCGTGCG 62.410 66.667 16.80 16.80 41.35 5.34
1111 8142 1.772182 GTGTGTGTTCTCCTGACTCG 58.228 55.000 0.00 0.00 0.00 4.18
1321 8374 6.764877 GCATTTGCATCTTATTCATTCCAG 57.235 37.500 0.00 0.00 41.59 3.86
1322 8375 6.278363 GCATTTGCATCTTATTCATTCCAGT 58.722 36.000 0.00 0.00 41.59 4.00
1325 8378 7.707624 TTTGCATCTTATTCATTCCAGTCTT 57.292 32.000 0.00 0.00 0.00 3.01
1326 8379 6.688637 TGCATCTTATTCATTCCAGTCTTG 57.311 37.500 0.00 0.00 0.00 3.02
1327 8380 6.182627 TGCATCTTATTCATTCCAGTCTTGT 58.817 36.000 0.00 0.00 0.00 3.16
1328 8381 6.317140 TGCATCTTATTCATTCCAGTCTTGTC 59.683 38.462 0.00 0.00 0.00 3.18
1329 8382 6.541641 GCATCTTATTCATTCCAGTCTTGTCT 59.458 38.462 0.00 0.00 0.00 3.41
1330 8383 7.466996 GCATCTTATTCATTCCAGTCTTGTCTG 60.467 40.741 0.00 0.00 35.45 3.51
1331 8384 7.244886 TCTTATTCATTCCAGTCTTGTCTGA 57.755 36.000 0.00 0.00 37.61 3.27
1332 8385 7.855375 TCTTATTCATTCCAGTCTTGTCTGAT 58.145 34.615 0.00 0.00 37.61 2.90
1333 8386 7.984050 TCTTATTCATTCCAGTCTTGTCTGATC 59.016 37.037 0.00 0.00 37.61 2.92
1334 8387 4.115401 TCATTCCAGTCTTGTCTGATCG 57.885 45.455 0.00 0.00 37.61 3.69
1335 8388 2.370281 TTCCAGTCTTGTCTGATCGC 57.630 50.000 0.00 0.00 37.61 4.58
1336 8389 0.532573 TCCAGTCTTGTCTGATCGCC 59.467 55.000 0.00 0.00 37.61 5.54
1337 8390 0.247460 CCAGTCTTGTCTGATCGCCA 59.753 55.000 0.00 0.00 37.61 5.69
1338 8391 1.134580 CCAGTCTTGTCTGATCGCCAT 60.135 52.381 0.00 0.00 37.61 4.40
1339 8392 2.200067 CAGTCTTGTCTGATCGCCATC 58.800 52.381 0.00 0.00 37.61 3.51
1340 8393 2.106566 AGTCTTGTCTGATCGCCATCT 58.893 47.619 0.00 0.00 0.00 2.90
1341 8394 2.100584 AGTCTTGTCTGATCGCCATCTC 59.899 50.000 0.00 0.00 0.00 2.75
1342 8395 1.410517 TCTTGTCTGATCGCCATCTCC 59.589 52.381 0.00 0.00 0.00 3.71
1343 8396 1.411977 CTTGTCTGATCGCCATCTCCT 59.588 52.381 0.00 0.00 0.00 3.69
1344 8397 1.035923 TGTCTGATCGCCATCTCCTC 58.964 55.000 0.00 0.00 0.00 3.71
1345 8398 1.327303 GTCTGATCGCCATCTCCTCT 58.673 55.000 0.00 0.00 0.00 3.69
1346 8399 1.000385 GTCTGATCGCCATCTCCTCTG 60.000 57.143 0.00 0.00 0.00 3.35
1351 8404 1.107114 TCGCCATCTCCTCTGAACTC 58.893 55.000 0.00 0.00 0.00 3.01
1354 8407 1.830477 GCCATCTCCTCTGAACTCTGT 59.170 52.381 0.00 0.00 0.00 3.41
1358 8411 2.530701 TCTCCTCTGAACTCTGTTCCC 58.469 52.381 7.81 0.00 0.00 3.97
1361 8414 2.368875 TCCTCTGAACTCTGTTCCCAAC 59.631 50.000 7.81 0.00 0.00 3.77
1435 8490 3.304123 GGTCCGTATCACAATCTCTCTCG 60.304 52.174 0.00 0.00 0.00 4.04
1436 8491 2.290916 TCCGTATCACAATCTCTCTCGC 59.709 50.000 0.00 0.00 0.00 5.03
1437 8492 2.292016 CCGTATCACAATCTCTCTCGCT 59.708 50.000 0.00 0.00 0.00 4.93
1438 8493 3.550561 CGTATCACAATCTCTCTCGCTC 58.449 50.000 0.00 0.00 0.00 5.03
1439 8494 3.249799 CGTATCACAATCTCTCTCGCTCT 59.750 47.826 0.00 0.00 0.00 4.09
1440 8495 3.988379 ATCACAATCTCTCTCGCTCTC 57.012 47.619 0.00 0.00 0.00 3.20
1455 8511 2.777094 GCTCTCTCCTTTTGCTTCACT 58.223 47.619 0.00 0.00 0.00 3.41
1459 8515 2.883386 CTCTCCTTTTGCTTCACTGCTT 59.117 45.455 0.00 0.00 0.00 3.91
1542 8598 0.969894 AAGGAGTGACCGAGTTCCAG 59.030 55.000 0.00 0.00 44.74 3.86
1707 8763 2.046604 GGGAAGCCCGTGTACCAC 60.047 66.667 0.00 0.00 32.13 4.16
1752 8808 1.177256 AGTACGCGGTTGTCCACTCT 61.177 55.000 12.47 0.00 0.00 3.24
1834 8892 1.685820 GCCTCTGCAGGTACCCTTT 59.314 57.895 15.13 0.00 42.74 3.11
1851 8909 0.116143 TTTACTTTGCCCCATGCCCT 59.884 50.000 0.00 0.00 40.16 5.19
1855 8913 1.305213 TTTGCCCCATGCCCTTCTC 60.305 57.895 0.00 0.00 40.16 2.87
1856 8914 2.803593 TTTGCCCCATGCCCTTCTCC 62.804 60.000 0.00 0.00 40.16 3.71
1857 8915 3.424105 GCCCCATGCCCTTCTCCT 61.424 66.667 0.00 0.00 0.00 3.69
1858 8916 3.001358 GCCCCATGCCCTTCTCCTT 62.001 63.158 0.00 0.00 0.00 3.36
1861 8919 0.106819 CCCATGCCCTTCTCCTTCTG 60.107 60.000 0.00 0.00 0.00 3.02
1862 8920 0.914644 CCATGCCCTTCTCCTTCTGA 59.085 55.000 0.00 0.00 0.00 3.27
1863 8921 1.283029 CCATGCCCTTCTCCTTCTGAA 59.717 52.381 0.00 0.00 0.00 3.02
1864 8922 2.641305 CATGCCCTTCTCCTTCTGAAG 58.359 52.381 10.46 10.46 40.23 3.02
1865 8923 0.326264 TGCCCTTCTCCTTCTGAAGC 59.674 55.000 11.93 0.00 39.47 3.86
1866 8924 0.617935 GCCCTTCTCCTTCTGAAGCT 59.382 55.000 11.93 0.00 39.47 3.74
1867 8925 1.834263 GCCCTTCTCCTTCTGAAGCTA 59.166 52.381 11.93 1.63 39.47 3.32
1868 8926 2.437651 GCCCTTCTCCTTCTGAAGCTAT 59.562 50.000 11.93 0.00 39.47 2.97
1869 8927 3.643792 GCCCTTCTCCTTCTGAAGCTATA 59.356 47.826 11.93 0.00 39.47 1.31
1870 8928 4.285775 GCCCTTCTCCTTCTGAAGCTATAT 59.714 45.833 11.93 0.00 39.47 0.86
1871 8929 5.482175 GCCCTTCTCCTTCTGAAGCTATATA 59.518 44.000 11.93 0.00 39.47 0.86
1872 8930 6.350949 GCCCTTCTCCTTCTGAAGCTATATAG 60.351 46.154 11.93 5.30 39.47 1.31
1873 8931 6.723977 CCCTTCTCCTTCTGAAGCTATATAGT 59.276 42.308 11.93 0.00 39.47 2.12
1874 8932 7.891183 CCCTTCTCCTTCTGAAGCTATATAGTA 59.109 40.741 11.93 0.00 39.47 1.82
1875 8933 8.956426 CCTTCTCCTTCTGAAGCTATATAGTAG 58.044 40.741 11.93 5.62 39.47 2.57
1876 8934 9.515226 CTTCTCCTTCTGAAGCTATATAGTAGT 57.485 37.037 11.93 0.00 35.21 2.73
1889 8947 9.490379 AGCTATATAGTAGTATTTGTTTGGTGC 57.510 33.333 11.38 0.00 0.00 5.01
1890 8948 8.433126 GCTATATAGTAGTATTTGTTTGGTGCG 58.567 37.037 11.38 0.00 0.00 5.34
1926 8986 8.514594 TGGTGTTCAAATTATTCAGTCATCTTC 58.485 33.333 0.00 0.00 0.00 2.87
1931 8991 6.316140 TCAAATTATTCAGTCATCTTCCGTGG 59.684 38.462 0.00 0.00 0.00 4.94
1932 8992 4.819105 TTATTCAGTCATCTTCCGTGGT 57.181 40.909 0.00 0.00 0.00 4.16
1943 9003 1.883275 CTTCCGTGGTGGCATGTTTTA 59.117 47.619 0.00 0.00 37.80 1.52
1961 9021 7.728847 TGTTTTAATGGTATCTGATCATCCG 57.271 36.000 0.00 0.00 0.00 4.18
1970 9030 6.210584 TGGTATCTGATCATCCGCTGTTTATA 59.789 38.462 0.00 0.00 0.00 0.98
1971 9031 7.093333 TGGTATCTGATCATCCGCTGTTTATAT 60.093 37.037 0.00 0.00 0.00 0.86
1972 9032 7.223582 GGTATCTGATCATCCGCTGTTTATATG 59.776 40.741 0.00 0.00 0.00 1.78
1974 9034 6.524734 TCTGATCATCCGCTGTTTATATGTT 58.475 36.000 0.00 0.00 0.00 2.71
1975 9035 7.666623 TCTGATCATCCGCTGTTTATATGTTA 58.333 34.615 0.00 0.00 0.00 2.41
1976 9036 8.314021 TCTGATCATCCGCTGTTTATATGTTAT 58.686 33.333 0.00 0.00 0.00 1.89
1977 9037 9.586435 CTGATCATCCGCTGTTTATATGTTATA 57.414 33.333 0.00 0.00 0.00 0.98
1978 9038 9.936759 TGATCATCCGCTGTTTATATGTTATAA 57.063 29.630 0.00 0.00 0.00 0.98
1999 9060 0.322187 TCCGTTCTTTAGGCCTTGGC 60.322 55.000 12.58 2.49 0.00 4.52
2062 9123 7.037873 AGTGTAGTTATATTTGGTCTGGGAACA 60.038 37.037 0.00 0.00 39.59 3.18
2087 9148 3.626670 AGGACTTTCGGTGAGTATCTACG 59.373 47.826 0.00 0.00 36.54 3.51
2090 9151 3.626670 ACTTTCGGTGAGTATCTACGGAG 59.373 47.826 0.00 0.00 36.05 4.63
2314 9379 3.194005 ACTTACTTGGTGTGTCTGTGG 57.806 47.619 0.00 0.00 0.00 4.17
2361 9426 7.027778 ACAGATTTTATTAATCCTGCCGAAC 57.972 36.000 0.00 0.00 0.00 3.95
2369 9434 2.322355 ATCCTGCCGAACTGAATGAG 57.678 50.000 0.00 0.00 0.00 2.90
2417 9482 4.426416 AGTTTTTGGGTTTGCTTCGTTAC 58.574 39.130 0.00 0.00 0.00 2.50
2418 9483 4.082136 AGTTTTTGGGTTTGCTTCGTTACA 60.082 37.500 0.00 0.00 0.00 2.41
2507 9573 9.832445 AAATTGACTGAGAAACTTGAACTACTA 57.168 29.630 0.00 0.00 0.00 1.82
2572 9638 5.567534 GTGTACAATTGGCATTCTGTTTACG 59.432 40.000 10.83 0.00 0.00 3.18
2593 9659 2.791004 GCAAACAAACTGATGTGCTCAC 59.209 45.455 0.00 0.00 32.81 3.51
2598 9664 4.898320 ACAAACTGATGTGCTCACTCATA 58.102 39.130 1.47 0.00 30.33 2.15
2604 9670 3.766051 TGATGTGCTCACTCATAGACTGT 59.234 43.478 1.47 0.00 30.33 3.55
2605 9671 3.582714 TGTGCTCACTCATAGACTGTG 57.417 47.619 1.47 0.00 0.00 3.66
2611 9677 4.380973 GCTCACTCATAGACTGTGCTAACA 60.381 45.833 0.00 0.00 34.34 2.41
2612 9678 5.680922 GCTCACTCATAGACTGTGCTAACAT 60.681 44.000 0.00 0.00 35.22 2.71
2661 9728 9.822185 ATAAAGCAAGATCACAAAAGTTCTTTT 57.178 25.926 4.91 4.91 0.00 2.27
2670 9737 5.654650 TCACAAAAGTTCTTTTCCTAGGCAA 59.345 36.000 2.96 0.00 0.00 4.52
2684 9751 4.227300 TCCTAGGCAATACTTGTCCAACAT 59.773 41.667 2.96 0.00 35.39 2.71
2685 9752 5.427157 TCCTAGGCAATACTTGTCCAACATA 59.573 40.000 2.96 0.00 35.39 2.29
2686 9753 5.527582 CCTAGGCAATACTTGTCCAACATAC 59.472 44.000 0.00 0.00 35.39 2.39
2689 9756 6.010219 AGGCAATACTTGTCCAACATACTTT 58.990 36.000 0.00 0.00 35.39 2.66
2690 9757 6.071952 AGGCAATACTTGTCCAACATACTTTG 60.072 38.462 0.00 0.00 35.39 2.77
2691 9758 5.572896 GCAATACTTGTCCAACATACTTTGC 59.427 40.000 0.00 0.00 30.35 3.68
2694 9761 3.569701 ACTTGTCCAACATACTTTGCCAG 59.430 43.478 0.00 0.00 0.00 4.85
2695 9762 3.222173 TGTCCAACATACTTTGCCAGT 57.778 42.857 0.00 0.00 39.87 4.00
2696 9763 4.359434 TGTCCAACATACTTTGCCAGTA 57.641 40.909 0.00 0.00 42.49 2.74
2699 9766 6.112734 TGTCCAACATACTTTGCCAGTATAG 58.887 40.000 5.55 4.22 45.63 1.31
2701 9768 5.190925 TCCAACATACTTTGCCAGTATAGGT 59.809 40.000 5.55 0.00 45.63 3.08
2702 9769 5.527582 CCAACATACTTTGCCAGTATAGGTC 59.472 44.000 5.55 0.00 45.63 3.85
2704 9771 6.308015 ACATACTTTGCCAGTATAGGTCAA 57.692 37.500 5.55 0.00 45.63 3.18
2705 9772 6.717289 ACATACTTTGCCAGTATAGGTCAAA 58.283 36.000 5.55 0.00 45.63 2.69
2706 9773 7.172342 ACATACTTTGCCAGTATAGGTCAAAA 58.828 34.615 5.55 0.00 45.63 2.44
2708 9775 9.337396 CATACTTTGCCAGTATAGGTCAAAATA 57.663 33.333 5.55 0.00 45.63 1.40
2712 9843 8.588290 TTTGCCAGTATAGGTCAAAATATTGT 57.412 30.769 0.00 0.00 37.79 2.71
2730 9861 7.775053 ATATTGTTGTGGTACTGGTTTTCAT 57.225 32.000 0.00 0.00 0.00 2.57
2734 9865 5.654650 TGTTGTGGTACTGGTTTTCATTTCT 59.345 36.000 0.00 0.00 0.00 2.52
2735 9866 6.829298 TGTTGTGGTACTGGTTTTCATTTCTA 59.171 34.615 0.00 0.00 0.00 2.10
2786 9920 6.607198 CCCAACCTAAACAACATAGGAATGAT 59.393 38.462 6.60 0.00 42.16 2.45
2866 10000 5.630121 TCTTTTGAATGTGTGGGTGATACT 58.370 37.500 0.00 0.00 0.00 2.12
2917 10051 9.065798 TCATGTTCTGATGTAATTTTCTGTTCA 57.934 29.630 0.00 0.00 0.00 3.18
3178 10313 5.292345 ACGCAAACAAGGTAATTTGGAAAAC 59.708 36.000 0.00 0.00 36.51 2.43
3211 10346 8.955388 AGAACCAAATGTTTTGTAATGCTTTTT 58.045 25.926 0.00 0.00 37.29 1.94
3297 10432 1.623811 TCTGTCCCTCTTTAGTGTGGC 59.376 52.381 0.00 0.00 0.00 5.01
3305 10440 2.926200 CTCTTTAGTGTGGCGTGAGATG 59.074 50.000 0.00 0.00 0.00 2.90
3308 10443 0.973632 TAGTGTGGCGTGAGATGGTT 59.026 50.000 0.00 0.00 0.00 3.67
3316 10451 0.798776 CGTGAGATGGTTGAGGCAAC 59.201 55.000 1.82 1.82 42.89 4.17
3361 10496 3.402110 ACGAGACATTGCAGAATCAACA 58.598 40.909 0.00 0.00 0.00 3.33
3362 10497 3.434641 ACGAGACATTGCAGAATCAACAG 59.565 43.478 0.00 0.00 0.00 3.16
3387 10523 8.028938 AGTTGCCACACAAAATAGATTCAATAC 58.971 33.333 0.00 0.00 40.82 1.89
3414 10550 8.341892 TGTGGCATGTGTAATATAGTTTTCAA 57.658 30.769 0.00 0.00 0.00 2.69
3418 10554 6.413818 GCATGTGTAATATAGTTTTCAACCGC 59.586 38.462 0.00 0.00 0.00 5.68
3435 10571 4.506886 ACCGCGACAAATTATTTGGAAA 57.493 36.364 20.00 0.00 44.81 3.13
3598 10734 1.621107 CGTGATTCACATGCCAAAGC 58.379 50.000 16.61 0.00 34.97 3.51
3727 10863 3.804325 TCAACATATTGAAGCTCTAGCGC 59.196 43.478 0.00 0.00 41.99 5.92
3755 10891 2.905415 ATTGGCATCTCACCTTGGAA 57.095 45.000 0.00 0.00 0.00 3.53
3798 10934 8.821894 GTTGAGGAGATTACAAATCATACTGAC 58.178 37.037 2.74 0.00 0.00 3.51
3842 10978 5.414789 TGTCCGACCTCAAGAATTATTCA 57.585 39.130 7.74 0.00 0.00 2.57
3945 11081 9.230932 GTTCTAATATTTGAGCTTCTTGATTGC 57.769 33.333 6.52 0.00 0.00 3.56
4068 11205 8.889717 TGGTCCTTCGTAATGAATTCTATTTTC 58.110 33.333 7.05 2.60 35.63 2.29
4092 11229 9.829507 TTCAAAATCATGAAACCTGTTATTTGT 57.170 25.926 0.00 0.00 36.42 2.83
4132 11269 3.054139 TCCTCGGCTAGTAACCACTCTTA 60.054 47.826 0.00 0.00 36.14 2.10
4134 11271 3.946558 CTCGGCTAGTAACCACTCTTAGT 59.053 47.826 0.00 0.00 36.14 2.24
4135 11272 5.102953 TCGGCTAGTAACCACTCTTAGTA 57.897 43.478 0.00 0.00 36.14 1.82
4136 11273 4.878397 TCGGCTAGTAACCACTCTTAGTAC 59.122 45.833 0.00 0.00 36.14 2.73
4228 11365 7.728847 TCCAACTATGTGTCATGTAATATGC 57.271 36.000 0.00 0.00 0.00 3.14
4229 11366 6.423604 TCCAACTATGTGTCATGTAATATGCG 59.576 38.462 0.00 0.00 0.00 4.73
4265 11405 9.319143 CATATAATTTCTCTTGAAGTTCTCCGT 57.681 33.333 4.17 0.00 34.63 4.69
4299 11441 5.751243 TCTCTTGAAGTTAAACAGGTTGC 57.249 39.130 0.00 0.00 0.00 4.17
4312 11454 1.075305 GGTTGCGGGTCCCCTTTTA 59.925 57.895 1.00 0.00 0.00 1.52
4323 11465 3.639561 GGTCCCCTTTTAGCACTTTTTGA 59.360 43.478 0.00 0.00 0.00 2.69
4327 11469 4.368315 CCCTTTTAGCACTTTTTGACACC 58.632 43.478 0.00 0.00 0.00 4.16
4384 11527 8.328758 ACTGAAATCCATCCTGTGATTTTAGTA 58.671 33.333 16.09 0.00 39.99 1.82
4396 11539 1.816074 TTTTAGTAAGCAGCACCGGG 58.184 50.000 6.32 0.00 0.00 5.73
4400 11543 1.302192 GTAAGCAGCACCGGGTGAA 60.302 57.895 30.65 5.13 45.29 3.18
4419 11562 5.471456 GGTGAAAGGATATACTGGATGCTTG 59.529 44.000 0.00 0.00 35.42 4.01
4428 11571 7.824289 GGATATACTGGATGCTTGCTTTATACA 59.176 37.037 0.00 0.00 0.00 2.29
4429 11572 6.867662 ATACTGGATGCTTGCTTTATACAC 57.132 37.500 0.00 0.00 0.00 2.90
4430 11573 4.588899 ACTGGATGCTTGCTTTATACACA 58.411 39.130 0.00 0.00 0.00 3.72
4440 11583 6.688813 GCTTGCTTTATACACATTTCTAGCAC 59.311 38.462 0.00 0.00 37.14 4.40
4494 11637 8.364129 AGCATTTGTGTAATTCAAACGAAAAT 57.636 26.923 0.00 0.00 37.56 1.82
4529 11672 2.544721 TGCTCTTCAGATCCTTGGACT 58.455 47.619 0.00 0.00 0.00 3.85
4530 11673 3.713003 TGCTCTTCAGATCCTTGGACTA 58.287 45.455 0.00 0.00 0.00 2.59
4534 11678 4.357325 TCTTCAGATCCTTGGACTAGCTT 58.643 43.478 0.00 0.00 0.00 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 6.874288 AGAAATGGCTCATATCTAACAAGC 57.126 37.500 0.00 0.00 0.00 4.01
33 34 6.467677 GGCTAGAAATGGCTCATATCTAACA 58.532 40.000 0.00 0.00 0.00 2.41
34 35 5.877564 GGGCTAGAAATGGCTCATATCTAAC 59.122 44.000 0.00 0.00 0.00 2.34
36 37 5.093677 TGGGCTAGAAATGGCTCATATCTA 58.906 41.667 0.00 0.00 33.66 1.98
53 54 6.656270 CAGATGTTTAGATGCATATTGGGCTA 59.344 38.462 0.00 0.00 0.00 3.93
64 65 7.710907 TGTAACCTATCACAGATGTTTAGATGC 59.289 37.037 0.00 0.00 0.00 3.91
65 66 9.770097 ATGTAACCTATCACAGATGTTTAGATG 57.230 33.333 0.00 0.00 0.00 2.90
71 72 8.046708 TGCTAAATGTAACCTATCACAGATGTT 58.953 33.333 0.00 0.00 0.00 2.71
76 77 7.134815 GCAATGCTAAATGTAACCTATCACAG 58.865 38.462 0.00 0.00 0.00 3.66
85 86 7.760131 AATGATGTGCAATGCTAAATGTAAC 57.240 32.000 6.82 0.00 0.00 2.50
92 93 7.908827 ATTTTGAAATGATGTGCAATGCTAA 57.091 28.000 6.82 0.00 0.00 3.09
93 94 8.999220 TTATTTTGAAATGATGTGCAATGCTA 57.001 26.923 6.82 0.00 0.00 3.49
122 123 7.386059 TGATCTCACTGCATAGTTACAAAGAA 58.614 34.615 0.00 0.00 34.07 2.52
136 137 1.795768 TGACGGTTTGATCTCACTGC 58.204 50.000 0.00 0.00 0.00 4.40
139 140 4.572389 AGCATTATGACGGTTTGATCTCAC 59.428 41.667 0.00 0.00 0.00 3.51
140 141 4.769688 AGCATTATGACGGTTTGATCTCA 58.230 39.130 0.00 0.00 0.00 3.27
144 145 6.428159 GGAGATTAGCATTATGACGGTTTGAT 59.572 38.462 0.00 0.00 0.00 2.57
147 148 5.680619 TGGAGATTAGCATTATGACGGTTT 58.319 37.500 0.00 0.00 0.00 3.27
149 150 4.955811 TGGAGATTAGCATTATGACGGT 57.044 40.909 0.00 0.00 0.00 4.83
151 152 8.961092 CAAAAATTGGAGATTAGCATTATGACG 58.039 33.333 0.00 0.00 0.00 4.35
171 172 2.905736 AGTTGCCTGCATACCCAAAAAT 59.094 40.909 0.00 0.00 0.00 1.82
172 173 2.036992 CAGTTGCCTGCATACCCAAAAA 59.963 45.455 0.00 0.00 0.00 1.94
177 178 1.544724 TTTCAGTTGCCTGCATACCC 58.455 50.000 0.00 0.00 38.66 3.69
178 179 3.947834 ACTATTTCAGTTGCCTGCATACC 59.052 43.478 0.00 0.00 38.66 2.73
179 180 4.260375 CGACTATTTCAGTTGCCTGCATAC 60.260 45.833 0.00 0.00 37.72 2.39
301 302 4.415881 TCTCTGTGTGTTGCTTCCTTAA 57.584 40.909 0.00 0.00 0.00 1.85
617 748 7.464830 ACGCAACTGTTTGTATAGACATATC 57.535 36.000 0.00 0.00 34.86 1.63
733 866 0.800012 TCGAGGCCGCAAAATAACAC 59.200 50.000 7.44 0.00 35.37 3.32
738 871 1.135402 GTCAATTCGAGGCCGCAAAAT 60.135 47.619 7.44 2.65 35.37 1.82
748 881 4.319766 CCACCTGAAGTTTGTCAATTCGAG 60.320 45.833 0.00 0.00 0.00 4.04
803 1002 8.548721 AGAAACTTGAACAACTTATTACTGTCG 58.451 33.333 0.00 0.00 0.00 4.35
844 7848 4.189188 GCTCAATGCTGCTGCCCG 62.189 66.667 13.47 1.51 38.71 6.13
845 7849 2.642254 TTGCTCAATGCTGCTGCCC 61.642 57.895 13.47 0.00 43.37 5.36
848 7852 1.154093 CCGTTGCTCAATGCTGCTG 60.154 57.895 0.00 0.00 43.37 4.41
867 7871 3.912907 CCCTGCCGCTACCTACCG 61.913 72.222 0.00 0.00 0.00 4.02
902 7907 0.398098 TCGCTTTAGTAGGGGAGGGG 60.398 60.000 0.00 0.00 37.41 4.79
1086 8100 2.245532 GAGAACACACACGCGCAC 59.754 61.111 5.73 0.00 0.00 5.34
1091 8105 1.772182 GAGTCAGGAGAACACACACG 58.228 55.000 0.00 0.00 0.00 4.49
1093 8107 1.337071 GACGAGTCAGGAGAACACACA 59.663 52.381 0.00 0.00 0.00 3.72
1111 8142 2.898343 ACGCCACCAAACACCGAC 60.898 61.111 0.00 0.00 0.00 4.79
1285 8316 0.745845 CAAATGCAGGGGAGTCGGAG 60.746 60.000 0.00 0.00 0.00 4.63
1286 8317 1.299648 CAAATGCAGGGGAGTCGGA 59.700 57.895 0.00 0.00 0.00 4.55
1288 8319 3.190878 GCAAATGCAGGGGAGTCG 58.809 61.111 0.00 0.00 41.59 4.18
1315 8368 2.419297 GGCGATCAGACAAGACTGGAAT 60.419 50.000 0.00 0.00 38.31 3.01
1316 8369 1.066858 GGCGATCAGACAAGACTGGAA 60.067 52.381 0.00 0.00 38.31 3.53
1317 8370 0.532573 GGCGATCAGACAAGACTGGA 59.467 55.000 0.00 0.00 38.31 3.86
1318 8371 0.247460 TGGCGATCAGACAAGACTGG 59.753 55.000 0.00 0.00 32.75 4.00
1320 8373 2.100584 GAGATGGCGATCAGACAAGACT 59.899 50.000 11.55 0.00 44.01 3.24
1321 8374 2.468831 GAGATGGCGATCAGACAAGAC 58.531 52.381 11.55 0.00 44.01 3.01
1322 8375 1.410517 GGAGATGGCGATCAGACAAGA 59.589 52.381 11.55 0.00 44.01 3.02
1325 8378 1.035923 GAGGAGATGGCGATCAGACA 58.964 55.000 11.55 0.00 45.56 3.41
1326 8379 1.000385 CAGAGGAGATGGCGATCAGAC 60.000 57.143 11.55 0.75 0.00 3.51
1327 8380 1.133668 TCAGAGGAGATGGCGATCAGA 60.134 52.381 11.55 0.00 0.00 3.27
1328 8381 1.326328 TCAGAGGAGATGGCGATCAG 58.674 55.000 11.55 0.00 0.00 2.90
1329 8382 1.410517 GTTCAGAGGAGATGGCGATCA 59.589 52.381 11.55 0.00 0.00 2.92
1330 8383 1.686052 AGTTCAGAGGAGATGGCGATC 59.314 52.381 0.00 0.00 0.00 3.69
1331 8384 1.686052 GAGTTCAGAGGAGATGGCGAT 59.314 52.381 0.00 0.00 0.00 4.58
1332 8385 1.107114 GAGTTCAGAGGAGATGGCGA 58.893 55.000 0.00 0.00 0.00 5.54
1333 8386 1.110442 AGAGTTCAGAGGAGATGGCG 58.890 55.000 0.00 0.00 0.00 5.69
1334 8387 1.830477 ACAGAGTTCAGAGGAGATGGC 59.170 52.381 0.00 0.00 0.00 4.40
1335 8388 3.118811 GGAACAGAGTTCAGAGGAGATGG 60.119 52.174 11.51 0.00 0.00 3.51
1336 8389 3.118811 GGGAACAGAGTTCAGAGGAGATG 60.119 52.174 11.51 0.00 0.00 2.90
1337 8390 3.103742 GGGAACAGAGTTCAGAGGAGAT 58.896 50.000 11.51 0.00 0.00 2.75
1338 8391 2.158310 TGGGAACAGAGTTCAGAGGAGA 60.158 50.000 11.51 0.00 35.01 3.71
1339 8392 2.251818 TGGGAACAGAGTTCAGAGGAG 58.748 52.381 11.51 0.00 35.01 3.69
1340 8393 2.368875 GTTGGGAACAGAGTTCAGAGGA 59.631 50.000 11.51 0.00 44.54 3.71
1341 8394 2.551071 GGTTGGGAACAGAGTTCAGAGG 60.551 54.545 11.51 0.00 44.54 3.69
1342 8395 2.772287 GGTTGGGAACAGAGTTCAGAG 58.228 52.381 11.51 0.00 44.54 3.35
1343 8396 1.070134 CGGTTGGGAACAGAGTTCAGA 59.930 52.381 11.51 0.00 44.54 3.27
1344 8397 1.512926 CGGTTGGGAACAGAGTTCAG 58.487 55.000 11.51 0.00 44.54 3.02
1345 8398 0.534203 GCGGTTGGGAACAGAGTTCA 60.534 55.000 11.51 0.00 44.54 3.18
1346 8399 0.534203 TGCGGTTGGGAACAGAGTTC 60.534 55.000 1.37 1.37 44.54 3.01
1351 8404 3.365265 GCCTGCGGTTGGGAACAG 61.365 66.667 0.00 0.00 44.54 3.16
1435 8490 2.483491 CAGTGAAGCAAAAGGAGAGAGC 59.517 50.000 0.00 0.00 0.00 4.09
1436 8491 2.483491 GCAGTGAAGCAAAAGGAGAGAG 59.517 50.000 0.00 0.00 0.00 3.20
1437 8492 2.105477 AGCAGTGAAGCAAAAGGAGAGA 59.895 45.455 0.00 0.00 36.85 3.10
1438 8493 2.502295 AGCAGTGAAGCAAAAGGAGAG 58.498 47.619 0.00 0.00 36.85 3.20
1439 8494 2.645838 AGCAGTGAAGCAAAAGGAGA 57.354 45.000 0.00 0.00 36.85 3.71
1440 8495 3.565482 TGTAAGCAGTGAAGCAAAAGGAG 59.435 43.478 0.00 0.00 36.85 3.69
1455 8511 3.003585 CAGCATTGTGACTTGTGTAAGCA 59.996 43.478 0.00 0.00 37.43 3.91
1459 8515 3.802866 TGTCAGCATTGTGACTTGTGTA 58.197 40.909 15.53 0.00 46.06 2.90
1707 8763 2.577112 CTCGACACGGCGCAGTAG 60.577 66.667 14.13 10.48 0.00 2.57
1863 8921 9.490379 GCACCAAACAAATACTACTATATAGCT 57.510 33.333 9.78 0.00 0.00 3.32
1864 8922 8.433126 CGCACCAAACAAATACTACTATATAGC 58.567 37.037 9.78 0.00 0.00 2.97
1865 8923 9.687210 TCGCACCAAACAAATACTACTATATAG 57.313 33.333 8.27 8.27 0.00 1.31
1867 8925 8.951787 TTCGCACCAAACAAATACTACTATAT 57.048 30.769 0.00 0.00 0.00 0.86
1868 8926 8.252417 TCTTCGCACCAAACAAATACTACTATA 58.748 33.333 0.00 0.00 0.00 1.31
1869 8927 7.101054 TCTTCGCACCAAACAAATACTACTAT 58.899 34.615 0.00 0.00 0.00 2.12
1870 8928 6.457355 TCTTCGCACCAAACAAATACTACTA 58.543 36.000 0.00 0.00 0.00 1.82
1871 8929 5.302360 TCTTCGCACCAAACAAATACTACT 58.698 37.500 0.00 0.00 0.00 2.57
1872 8930 5.600908 TCTTCGCACCAAACAAATACTAC 57.399 39.130 0.00 0.00 0.00 2.73
1873 8931 6.811253 ATTCTTCGCACCAAACAAATACTA 57.189 33.333 0.00 0.00 0.00 1.82
1874 8932 5.705609 ATTCTTCGCACCAAACAAATACT 57.294 34.783 0.00 0.00 0.00 2.12
1875 8933 5.689961 ACAATTCTTCGCACCAAACAAATAC 59.310 36.000 0.00 0.00 0.00 1.89
1876 8934 5.837437 ACAATTCTTCGCACCAAACAAATA 58.163 33.333 0.00 0.00 0.00 1.40
1877 8935 4.692228 ACAATTCTTCGCACCAAACAAAT 58.308 34.783 0.00 0.00 0.00 2.32
1878 8936 4.116747 ACAATTCTTCGCACCAAACAAA 57.883 36.364 0.00 0.00 0.00 2.83
1879 8937 3.791973 ACAATTCTTCGCACCAAACAA 57.208 38.095 0.00 0.00 0.00 2.83
1880 8938 3.443037 CAACAATTCTTCGCACCAAACA 58.557 40.909 0.00 0.00 0.00 2.83
1881 8939 2.794350 CCAACAATTCTTCGCACCAAAC 59.206 45.455 0.00 0.00 0.00 2.93
1882 8940 2.428890 ACCAACAATTCTTCGCACCAAA 59.571 40.909 0.00 0.00 0.00 3.28
1883 8941 2.028130 ACCAACAATTCTTCGCACCAA 58.972 42.857 0.00 0.00 0.00 3.67
1884 8942 1.336440 CACCAACAATTCTTCGCACCA 59.664 47.619 0.00 0.00 0.00 4.17
1885 8943 1.336755 ACACCAACAATTCTTCGCACC 59.663 47.619 0.00 0.00 0.00 5.01
1886 8944 2.774439 ACACCAACAATTCTTCGCAC 57.226 45.000 0.00 0.00 0.00 5.34
1887 8945 2.685388 TGAACACCAACAATTCTTCGCA 59.315 40.909 0.00 0.00 0.00 5.10
1888 8946 3.347958 TGAACACCAACAATTCTTCGC 57.652 42.857 0.00 0.00 0.00 4.70
1889 8947 6.826893 AATTTGAACACCAACAATTCTTCG 57.173 33.333 0.00 0.00 33.85 3.79
1926 8986 2.605030 CATTAAAACATGCCACCACGG 58.395 47.619 0.00 0.00 38.11 4.94
1931 8991 6.449635 TCAGATACCATTAAAACATGCCAC 57.550 37.500 0.00 0.00 0.00 5.01
1932 8992 6.832900 TGATCAGATACCATTAAAACATGCCA 59.167 34.615 0.00 0.00 0.00 4.92
1943 9003 3.326006 ACAGCGGATGATCAGATACCATT 59.674 43.478 0.00 0.00 0.00 3.16
1970 9030 7.287810 AGGCCTAAAGAACGGATTTATAACAT 58.712 34.615 1.29 0.00 0.00 2.71
1971 9031 6.655930 AGGCCTAAAGAACGGATTTATAACA 58.344 36.000 1.29 0.00 0.00 2.41
1972 9032 7.415229 CAAGGCCTAAAGAACGGATTTATAAC 58.585 38.462 5.16 0.00 0.00 1.89
1974 9034 6.059484 CCAAGGCCTAAAGAACGGATTTATA 58.941 40.000 5.16 0.00 0.00 0.98
1975 9035 4.887655 CCAAGGCCTAAAGAACGGATTTAT 59.112 41.667 5.16 0.00 0.00 1.40
1976 9036 4.266714 CCAAGGCCTAAAGAACGGATTTA 58.733 43.478 5.16 0.00 0.00 1.40
1977 9037 3.089284 CCAAGGCCTAAAGAACGGATTT 58.911 45.455 5.16 0.00 0.00 2.17
1978 9038 2.723273 CCAAGGCCTAAAGAACGGATT 58.277 47.619 5.16 0.00 0.00 3.01
1980 9040 0.322187 GCCAAGGCCTAAAGAACGGA 60.322 55.000 5.16 0.00 34.56 4.69
1981 9041 1.644786 CGCCAAGGCCTAAAGAACGG 61.645 60.000 5.16 0.00 37.98 4.44
1999 9060 2.504681 GCAACATTCCAAGCCGCG 60.505 61.111 0.00 0.00 0.00 6.46
2062 9123 4.857679 AGATACTCACCGAAAGTCCTACT 58.142 43.478 0.00 0.00 0.00 2.57
2087 9148 4.962155 ACTTACATACAATAGCAGCCTCC 58.038 43.478 0.00 0.00 0.00 4.30
2090 9151 6.677781 TTCAACTTACATACAATAGCAGCC 57.322 37.500 0.00 0.00 0.00 4.85
2124 9187 2.100418 GGGCCTCAGAATTGCATTTCTC 59.900 50.000 18.56 9.29 33.69 2.87
2288 9352 4.271049 CAGACACACCAAGTAAGTTCACAG 59.729 45.833 0.00 0.00 0.00 3.66
2289 9353 4.188462 CAGACACACCAAGTAAGTTCACA 58.812 43.478 0.00 0.00 0.00 3.58
2290 9354 4.034048 CACAGACACACCAAGTAAGTTCAC 59.966 45.833 0.00 0.00 0.00 3.18
2291 9355 4.188462 CACAGACACACCAAGTAAGTTCA 58.812 43.478 0.00 0.00 0.00 3.18
2292 9356 3.560068 CCACAGACACACCAAGTAAGTTC 59.440 47.826 0.00 0.00 0.00 3.01
2314 9379 1.115326 ACCAAAAGCCTTCCCTGTGC 61.115 55.000 0.00 0.00 0.00 4.57
2417 9482 1.677576 CCCGGTTCCACAATCATCATG 59.322 52.381 0.00 0.00 0.00 3.07
2418 9483 2.023788 GCCCGGTTCCACAATCATCAT 61.024 52.381 0.00 0.00 0.00 2.45
2528 9594 6.992063 ACACCAAAGATGCAGTTAAGATAG 57.008 37.500 0.00 0.00 0.00 2.08
2572 9638 2.791004 GTGAGCACATCAGTTTGTTTGC 59.209 45.455 0.00 0.00 39.07 3.68
2634 9701 9.822185 AAAGAACTTTTGTGATCTTGCTTTATT 57.178 25.926 0.00 0.00 31.88 1.40
2646 9713 5.197451 TGCCTAGGAAAAGAACTTTTGTGA 58.803 37.500 14.75 2.07 42.26 3.58
2670 9737 5.321102 TGGCAAAGTATGTTGGACAAGTAT 58.679 37.500 0.00 0.00 0.00 2.12
2684 9751 9.914834 AATATTTTGACCTATACTGGCAAAGTA 57.085 29.630 1.41 1.41 45.47 2.24
2685 9752 8.686334 CAATATTTTGACCTATACTGGCAAAGT 58.314 33.333 0.00 0.00 37.72 2.66
2686 9753 8.686334 ACAATATTTTGACCTATACTGGCAAAG 58.314 33.333 2.69 0.00 35.88 2.77
2689 9756 7.613801 ACAACAATATTTTGACCTATACTGGCA 59.386 33.333 13.71 0.00 36.64 4.92
2690 9757 7.915397 CACAACAATATTTTGACCTATACTGGC 59.085 37.037 13.71 0.00 36.64 4.85
2691 9758 8.405531 CCACAACAATATTTTGACCTATACTGG 58.594 37.037 13.71 7.26 36.64 4.00
2696 9763 8.956426 CAGTACCACAACAATATTTTGACCTAT 58.044 33.333 13.71 0.00 36.64 2.57
2699 9766 6.015772 ACCAGTACCACAACAATATTTTGACC 60.016 38.462 13.71 0.00 36.64 4.02
2701 9768 7.589958 AACCAGTACCACAACAATATTTTGA 57.410 32.000 13.71 0.00 36.64 2.69
2702 9769 8.655651 AAAACCAGTACCACAACAATATTTTG 57.344 30.769 8.10 8.10 38.86 2.44
2704 9771 8.012957 TGAAAACCAGTACCACAACAATATTT 57.987 30.769 0.00 0.00 0.00 1.40
2705 9772 7.589958 TGAAAACCAGTACCACAACAATATT 57.410 32.000 0.00 0.00 0.00 1.28
2706 9773 7.775053 ATGAAAACCAGTACCACAACAATAT 57.225 32.000 0.00 0.00 0.00 1.28
2708 9775 6.478512 AATGAAAACCAGTACCACAACAAT 57.521 33.333 0.00 0.00 0.00 2.71
2709 9776 5.923733 AATGAAAACCAGTACCACAACAA 57.076 34.783 0.00 0.00 0.00 2.83
2712 9843 7.883391 TTAGAAATGAAAACCAGTACCACAA 57.117 32.000 0.00 0.00 0.00 3.33
2746 9877 8.581578 GTTTAGGTTGGGATCAATGAGTTAAAA 58.418 33.333 0.00 0.00 35.10 1.52
2747 9878 7.726291 TGTTTAGGTTGGGATCAATGAGTTAAA 59.274 33.333 0.00 0.00 35.10 1.52
2748 9879 7.235079 TGTTTAGGTTGGGATCAATGAGTTAA 58.765 34.615 0.00 0.00 35.10 2.01
2749 9880 6.785076 TGTTTAGGTTGGGATCAATGAGTTA 58.215 36.000 0.00 0.00 35.10 2.24
2750 9881 5.640147 TGTTTAGGTTGGGATCAATGAGTT 58.360 37.500 0.00 0.00 35.10 3.01
2751 9882 5.255397 TGTTTAGGTTGGGATCAATGAGT 57.745 39.130 0.00 0.00 35.10 3.41
2752 9883 5.476599 TGTTGTTTAGGTTGGGATCAATGAG 59.523 40.000 0.00 0.00 35.10 2.90
2753 9884 5.389520 TGTTGTTTAGGTTGGGATCAATGA 58.610 37.500 0.00 0.00 35.10 2.57
2754 9885 5.720371 TGTTGTTTAGGTTGGGATCAATG 57.280 39.130 0.00 0.00 35.10 2.82
2866 10000 2.130272 ATGCAGTCGAGACTACTCCA 57.870 50.000 5.34 2.23 40.20 3.86
3131 10266 6.530534 CGTACTTCTCCACTAACAAAGGTATG 59.469 42.308 0.00 0.00 0.00 2.39
3178 10313 4.630940 ACAAAACATTTGGTTCTGCAACAG 59.369 37.500 7.64 0.00 39.29 3.16
3297 10432 0.798776 GTTGCCTCAACCATCTCACG 59.201 55.000 0.00 0.00 38.30 4.35
3305 10440 3.334583 TCATGTCTAGTTGCCTCAACC 57.665 47.619 6.12 0.00 44.49 3.77
3308 10443 6.129874 ACTAGTATCATGTCTAGTTGCCTCA 58.870 40.000 16.13 0.00 42.52 3.86
3321 10456 8.947115 TGTCTCGTCCATTATACTAGTATCATG 58.053 37.037 22.35 22.35 30.72 3.07
3326 10461 7.229907 TGCAATGTCTCGTCCATTATACTAGTA 59.770 37.037 4.77 4.77 31.52 1.82
3342 10477 5.152097 CAACTGTTGATTCTGCAATGTCTC 58.848 41.667 15.26 0.00 0.00 3.36
3361 10496 6.403866 TTGAATCTATTTTGTGTGGCAACT 57.596 33.333 0.00 0.00 36.72 3.16
3362 10497 7.812191 TGTATTGAATCTATTTTGTGTGGCAAC 59.188 33.333 0.00 0.00 36.72 4.17
3387 10523 8.404765 TGAAAACTATATTACACATGCCACATG 58.595 33.333 6.03 6.03 0.00 3.21
3414 10550 4.481463 CTTTCCAAATAATTTGTCGCGGT 58.519 39.130 6.13 0.00 38.98 5.68
3418 10554 6.464834 GTCTACGCTTTCCAAATAATTTGTCG 59.535 38.462 0.00 0.00 38.98 4.35
3435 10571 3.819564 TGCATATTTGAGGTCTACGCT 57.180 42.857 0.00 0.00 0.00 5.07
3598 10734 7.570140 GCACTGATGTATAAATCAATCCTGTCG 60.570 40.741 7.03 0.00 36.16 4.35
3727 10863 4.070716 GGTGAGATGCCAATAGAGAATGG 58.929 47.826 0.00 0.00 39.80 3.16
3755 10891 8.768397 TCTCCTCAACAACTATAACACCATAAT 58.232 33.333 0.00 0.00 0.00 1.28
3881 11017 5.027737 CACCGAACATGCATACAACATTAC 58.972 41.667 0.00 0.00 0.00 1.89
3928 11064 3.752747 TCATCGCAATCAAGAAGCTCAAA 59.247 39.130 0.00 0.00 0.00 2.69
3990 11126 9.529325 TGTATAACTCGTCCATAAGAAGAAATG 57.471 33.333 0.00 0.00 32.26 2.32
4002 11138 9.836076 CGATCTAAATAATGTATAACTCGTCCA 57.164 33.333 0.00 0.00 0.00 4.02
4033 11170 7.637078 ATTCATTACGAAGGACCATACAATGGA 60.637 37.037 12.80 0.00 44.74 3.41
4068 11205 9.044150 ACACAAATAACAGGTTTCATGATTTTG 57.956 29.630 0.00 0.00 0.00 2.44
4074 11211 4.382457 CGCACACAAATAACAGGTTTCATG 59.618 41.667 0.00 0.00 0.00 3.07
4076 11213 3.793801 GCGCACACAAATAACAGGTTTCA 60.794 43.478 0.30 0.00 0.00 2.69
4082 11219 3.266541 TGAAGCGCACACAAATAACAG 57.733 42.857 11.47 0.00 0.00 3.16
4092 11229 0.744414 GATAGCCCTTGAAGCGCACA 60.744 55.000 11.47 6.70 34.64 4.57
4107 11244 3.488363 AGTGGTTACTAGCCGAGGATAG 58.512 50.000 12.39 12.39 39.71 2.08
4132 11269 9.477484 CACAGTTGAACTTTAACAGATAGTACT 57.523 33.333 0.00 0.00 0.00 2.73
4134 11271 8.644216 TCCACAGTTGAACTTTAACAGATAGTA 58.356 33.333 0.00 0.00 0.00 1.82
4135 11272 7.506114 TCCACAGTTGAACTTTAACAGATAGT 58.494 34.615 0.00 0.00 0.00 2.12
4136 11273 7.962964 TCCACAGTTGAACTTTAACAGATAG 57.037 36.000 0.00 0.00 0.00 2.08
4194 11331 9.859427 CATGACACATAGTTGGATAAAAACAAT 57.141 29.630 0.00 0.00 0.00 2.71
4214 11351 6.799926 ACATAATGCGCATATTACATGACA 57.200 33.333 25.61 0.00 0.00 3.58
4274 11414 6.858478 GCAACCTGTTTAACTTCAAGAGATTC 59.142 38.462 0.00 0.00 0.00 2.52
4342 11485 6.348868 GGATTTCAGTCCATTCTGTGAACTTC 60.349 42.308 0.00 0.00 38.20 3.01
4384 11527 1.898574 CTTTCACCCGGTGCTGCTT 60.899 57.895 13.19 0.00 32.98 3.91
4396 11539 5.049129 GCAAGCATCCAGTATATCCTTTCAC 60.049 44.000 0.00 0.00 0.00 3.18
4400 11543 4.989875 AGCAAGCATCCAGTATATCCTT 57.010 40.909 0.00 0.00 0.00 3.36
4419 11562 7.308782 ACTGTGCTAGAAATGTGTATAAAGC 57.691 36.000 0.00 0.00 0.00 3.51
4428 11571 3.149196 CCACCAACTGTGCTAGAAATGT 58.851 45.455 0.00 0.00 44.01 2.71
4429 11572 2.095059 GCCACCAACTGTGCTAGAAATG 60.095 50.000 0.00 0.00 44.01 2.32
4430 11573 2.162681 GCCACCAACTGTGCTAGAAAT 58.837 47.619 0.00 0.00 44.01 2.17
4440 11583 3.679389 ACAGATTTCTAGCCACCAACTG 58.321 45.455 0.00 0.00 0.00 3.16
4486 11629 7.334421 AGCATTGTACAGACAGATATTTTCGTT 59.666 33.333 0.00 0.00 36.76 3.85
4488 11631 7.223582 AGAGCATTGTACAGACAGATATTTTCG 59.776 37.037 0.00 0.00 36.76 3.46
4494 11637 6.378280 TCTGAAGAGCATTGTACAGACAGATA 59.622 38.462 0.00 0.00 36.76 1.98
4498 11641 4.871933 TCTGAAGAGCATTGTACAGACA 57.128 40.909 0.00 0.00 31.02 3.41
4529 11672 8.644374 ACCAGTTAAAATGAATTACCAAGCTA 57.356 30.769 0.00 0.00 0.00 3.32
4530 11673 7.539034 ACCAGTTAAAATGAATTACCAAGCT 57.461 32.000 0.00 0.00 0.00 3.74
4534 11678 6.711194 TGTCGACCAGTTAAAATGAATTACCA 59.289 34.615 14.12 0.00 0.00 3.25


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

AutoCloner maintained by Alex Coulton.