Multiple sequence alignment - TraesCS2B01G616900

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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 TraesCS2B01G616900 chr2B 100.000 3963 0 0 1 3963 793796057 793800019 0.000000e+00 7319.0
1 TraesCS2B01G616900 chr2B 77.859 411 35 24 612 988 16375543 16375155 1.870000e-48 204.0
2 TraesCS2B01G616900 chrUn 92.225 2521 126 24 771 3246 124816927 124814432 0.000000e+00 3506.0
3 TraesCS2B01G616900 chrUn 87.888 644 29 23 3245 3870 124814391 124813779 0.000000e+00 712.0
4 TraesCS2B01G616900 chr2D 90.146 1441 76 27 549 1939 635780714 635782138 0.000000e+00 1814.0
5 TraesCS2B01G616900 chr2D 91.542 1206 73 16 2042 3242 635782296 635783477 0.000000e+00 1635.0
6 TraesCS2B01G616900 chr2D 88.468 607 14 21 3245 3843 635783521 635784079 0.000000e+00 682.0
7 TraesCS2B01G616900 chr2D 77.253 466 53 27 4 443 635780204 635780642 1.430000e-54 224.0
8 TraesCS2B01G616900 chr2D 81.304 230 22 9 15 231 635778923 635779144 2.450000e-37 167.0
9 TraesCS2B01G616900 chr2D 92.857 112 4 2 3852 3963 635784170 635784277 4.100000e-35 159.0
10 TraesCS2B01G616900 chr1A 81.085 719 84 27 878 1589 475473215 475472542 9.750000e-146 527.0
11 TraesCS2B01G616900 chr1A 82.295 610 73 19 990 1589 475452744 475452160 2.750000e-136 496.0
12 TraesCS2B01G616900 chr1A 77.859 411 32 27 612 988 315060528 315060143 2.420000e-47 200.0
13 TraesCS2B01G616900 chr1D 80.056 717 95 27 878 1589 376183948 376183275 4.600000e-134 488.0
14 TraesCS2B01G616900 chr6D 81.977 344 54 6 1249 1588 2498878 2499217 6.480000e-73 285.0
15 TraesCS2B01G616900 chr6D 89.524 105 11 0 2059 2163 2499806 2499910 2.480000e-27 134.0
16 TraesCS2B01G616900 chr6A 81.924 343 56 3 1249 1588 1673147 1673486 6.480000e-73 285.0
17 TraesCS2B01G616900 chr6B 86.111 144 14 1 2062 2199 291330 291473 2.470000e-32 150.0
18 TraesCS2B01G616900 chr3D 83.495 103 11 5 613 715 112212439 112212343 1.520000e-14 91.6
19 TraesCS2B01G616900 chr3B 94.118 34 2 0 717 750 533559037 533559004 7.000000e-03 52.8


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 TraesCS2B01G616900 chr2B 793796057 793800019 3962 False 7319.000000 7319 100.000000 1 3963 1 chr2B.!!$F1 3962
1 TraesCS2B01G616900 chrUn 124813779 124816927 3148 True 2109.000000 3506 90.056500 771 3870 2 chrUn.!!$R1 3099
2 TraesCS2B01G616900 chr2D 635778923 635784277 5354 False 780.166667 1814 86.928333 4 3963 6 chr2D.!!$F1 3959
3 TraesCS2B01G616900 chr1A 475472542 475473215 673 True 527.000000 527 81.085000 878 1589 1 chr1A.!!$R3 711
4 TraesCS2B01G616900 chr1A 475452160 475452744 584 True 496.000000 496 82.295000 990 1589 1 chr1A.!!$R2 599
5 TraesCS2B01G616900 chr1D 376183275 376183948 673 True 488.000000 488 80.056000 878 1589 1 chr1D.!!$R1 711
6 TraesCS2B01G616900 chr6D 2498878 2499910 1032 False 209.500000 285 85.750500 1249 2163 2 chr6D.!!$F1 914

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
360 1667 0.031515 TCCCATCCCATCTACGGTGT 60.032 55.0 0.00 0.00 0.00 4.16 F
1672 3056 0.318445 AACTACACGTCCAGCGACAC 60.318 55.0 0.00 0.00 44.77 3.67 F
2509 4054 0.875908 GTCCGCTGCATGCTTATCGA 60.876 55.0 20.33 5.15 40.11 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 3514 0.250684 TGGCGCCAACAGAAGATCAA 60.251 50.0 30.74 0.0 0.00 2.57 R
2896 4442 0.810031 CGCTACTATGGCCAACGCTT 60.810 55.0 10.96 0.0 34.44 4.68 R
3340 4946 0.901124 ACCACCATGCTCTCTCTCAC 59.099 55.0 0.00 0.0 0.00 3.51 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.690985 CCTCCCTCCCTTCCTGTCC 60.691 68.421 0.00 0.00 0.00 4.02
41 42 0.689412 CTCCCTTCCTGTCCTCCTCC 60.689 65.000 0.00 0.00 0.00 4.30
52 53 0.104144 TCCTCCTCCTCCAACCCAAA 60.104 55.000 0.00 0.00 0.00 3.28
53 54 0.329596 CCTCCTCCTCCAACCCAAAG 59.670 60.000 0.00 0.00 0.00 2.77
54 55 1.362224 CTCCTCCTCCAACCCAAAGA 58.638 55.000 0.00 0.00 0.00 2.52
55 56 1.705186 CTCCTCCTCCAACCCAAAGAA 59.295 52.381 0.00 0.00 0.00 2.52
56 57 2.108250 CTCCTCCTCCAACCCAAAGAAA 59.892 50.000 0.00 0.00 0.00 2.52
57 58 2.516277 TCCTCCTCCAACCCAAAGAAAA 59.484 45.455 0.00 0.00 0.00 2.29
62 63 1.407258 TCCAACCCAAAGAAAACAGCG 59.593 47.619 0.00 0.00 0.00 5.18
64 65 0.104120 AACCCAAAGAAAACAGCGGC 59.896 50.000 0.00 0.00 0.00 6.53
222 1521 4.525949 GGCGGCGTAAGTCCCTCC 62.526 72.222 9.37 0.00 40.39 4.30
223 1522 4.525949 GCGGCGTAAGTCCCTCCC 62.526 72.222 9.37 0.00 40.39 4.30
224 1523 2.758737 CGGCGTAAGTCCCTCCCT 60.759 66.667 0.00 0.00 40.39 4.20
225 1524 2.783288 CGGCGTAAGTCCCTCCCTC 61.783 68.421 0.00 0.00 40.39 4.30
226 1525 2.433146 GGCGTAAGTCCCTCCCTCC 61.433 68.421 0.00 0.00 41.68 4.30
230 1529 0.398806 GTAAGTCCCTCCCTCCCTCC 60.399 65.000 0.00 0.00 0.00 4.30
234 1533 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
235 1534 3.368501 CCTCCCTCCCTCCCTCCA 61.369 72.222 0.00 0.00 0.00 3.86
236 1535 2.285180 CTCCCTCCCTCCCTCCAG 59.715 72.222 0.00 0.00 0.00 3.86
237 1536 3.368501 TCCCTCCCTCCCTCCAGG 61.369 72.222 0.00 0.00 0.00 4.45
239 1538 4.101077 CCTCCCTCCCTCCAGGCT 62.101 72.222 0.00 0.00 34.51 4.58
240 1539 2.445654 CTCCCTCCCTCCAGGCTC 60.446 72.222 0.00 0.00 34.51 4.70
242 1541 4.421554 CCCTCCCTCCAGGCTCCA 62.422 72.222 0.00 0.00 34.51 3.86
243 1542 2.767496 CCTCCCTCCAGGCTCCAG 60.767 72.222 0.00 0.00 34.51 3.86
244 1543 3.478274 CTCCCTCCAGGCTCCAGC 61.478 72.222 0.00 0.00 41.14 4.85
254 1553 2.991540 GCTCCAGCCCCCAACAAC 60.992 66.667 0.00 0.00 34.31 3.32
255 1554 2.846532 CTCCAGCCCCCAACAACT 59.153 61.111 0.00 0.00 0.00 3.16
256 1555 1.153756 CTCCAGCCCCCAACAACTT 59.846 57.895 0.00 0.00 0.00 2.66
257 1556 1.152567 TCCAGCCCCCAACAACTTG 60.153 57.895 0.00 0.00 0.00 3.16
259 1558 1.048160 CCAGCCCCCAACAACTTGTT 61.048 55.000 1.00 1.00 42.08 2.83
260 1559 0.389025 CAGCCCCCAACAACTTGTTC 59.611 55.000 4.06 0.00 38.77 3.18
261 1560 0.759060 AGCCCCCAACAACTTGTTCC 60.759 55.000 4.06 0.00 38.77 3.62
263 1562 1.788229 CCCCCAACAACTTGTTCCTT 58.212 50.000 4.06 0.00 38.77 3.36
264 1563 1.686587 CCCCCAACAACTTGTTCCTTC 59.313 52.381 4.06 0.00 38.77 3.46
265 1564 1.336755 CCCCAACAACTTGTTCCTTCG 59.663 52.381 4.06 0.00 38.77 3.79
266 1565 1.269051 CCCAACAACTTGTTCCTTCGC 60.269 52.381 4.06 0.00 38.77 4.70
267 1566 1.269051 CCAACAACTTGTTCCTTCGCC 60.269 52.381 4.06 0.00 38.77 5.54
268 1567 1.029681 AACAACTTGTTCCTTCGCCC 58.970 50.000 1.00 0.00 35.27 6.13
269 1568 0.182775 ACAACTTGTTCCTTCGCCCT 59.817 50.000 0.00 0.00 0.00 5.19
270 1569 1.418637 ACAACTTGTTCCTTCGCCCTA 59.581 47.619 0.00 0.00 0.00 3.53
271 1570 2.076863 CAACTTGTTCCTTCGCCCTAG 58.923 52.381 0.00 0.00 0.00 3.02
272 1571 1.640917 ACTTGTTCCTTCGCCCTAGA 58.359 50.000 0.00 0.00 0.00 2.43
273 1572 2.188817 ACTTGTTCCTTCGCCCTAGAT 58.811 47.619 0.00 0.00 0.00 1.98
274 1573 2.093447 ACTTGTTCCTTCGCCCTAGATG 60.093 50.000 0.00 0.00 0.00 2.90
279 1580 2.526432 TCCTTCGCCCTAGATGGATAC 58.474 52.381 0.00 0.00 38.88 2.24
311 1612 6.577103 TCTCTGTTTCAATGCTCGATTCTAT 58.423 36.000 0.00 0.00 0.00 1.98
322 1629 7.881643 ATGCTCGATTCTATGAGTTATCAAC 57.118 36.000 0.00 0.00 39.39 3.18
332 1639 8.818141 TCTATGAGTTATCAACGGAATGAATC 57.182 34.615 0.00 0.00 39.39 2.52
333 1640 6.867662 ATGAGTTATCAACGGAATGAATCC 57.132 37.500 0.00 0.00 41.15 3.01
335 1642 5.110814 AGTTATCAACGGAATGAATCCCA 57.889 39.130 0.00 0.00 46.39 4.37
336 1643 5.694995 AGTTATCAACGGAATGAATCCCAT 58.305 37.500 0.00 0.00 46.39 4.00
337 1644 5.765182 AGTTATCAACGGAATGAATCCCATC 59.235 40.000 0.00 0.00 46.39 3.51
338 1645 2.930950 TCAACGGAATGAATCCCATCC 58.069 47.619 0.00 0.00 46.39 3.51
339 1646 1.956477 CAACGGAATGAATCCCATCCC 59.044 52.381 0.00 0.00 46.39 3.85
354 1661 2.565631 CATCCCATCCCATCCCATCTA 58.434 52.381 0.00 0.00 0.00 1.98
355 1662 2.044793 TCCCATCCCATCCCATCTAC 57.955 55.000 0.00 0.00 0.00 2.59
356 1663 0.615331 CCCATCCCATCCCATCTACG 59.385 60.000 0.00 0.00 0.00 3.51
359 1666 1.002430 CATCCCATCCCATCTACGGTG 59.998 57.143 0.00 0.00 0.00 4.94
360 1667 0.031515 TCCCATCCCATCTACGGTGT 60.032 55.000 0.00 0.00 0.00 4.16
361 1668 1.218450 TCCCATCCCATCTACGGTGTA 59.782 52.381 0.00 0.00 0.00 2.90
362 1669 1.618837 CCCATCCCATCTACGGTGTAG 59.381 57.143 0.00 0.00 0.00 2.74
363 1670 2.317040 CCATCCCATCTACGGTGTAGT 58.683 52.381 4.08 0.00 0.00 2.73
364 1671 3.493334 CCATCCCATCTACGGTGTAGTA 58.507 50.000 4.08 0.00 0.00 1.82
378 1685 6.895209 CGGTGTAGTACGTATTATTTACCG 57.105 41.667 23.34 23.34 40.84 4.02
401 1711 8.155510 ACCGTCTAATATCTGTATCTGTCTGTA 58.844 37.037 0.00 0.00 0.00 2.74
443 1753 0.376152 CAGTTCGCACATCTGCATCC 59.624 55.000 0.00 0.00 44.50 3.51
455 1765 1.664306 TGCATCCGCATTGCACAAA 59.336 47.368 9.69 0.00 45.36 2.83
458 1768 1.854126 GCATCCGCATTGCACAAATAC 59.146 47.619 9.69 0.00 39.90 1.89
459 1769 2.734809 GCATCCGCATTGCACAAATACA 60.735 45.455 9.69 0.00 39.90 2.29
461 1771 4.792380 GCATCCGCATTGCACAAATACATA 60.792 41.667 9.69 0.00 39.90 2.29
462 1772 4.285807 TCCGCATTGCACAAATACATAC 57.714 40.909 9.69 0.00 0.00 2.39
463 1773 3.691609 TCCGCATTGCACAAATACATACA 59.308 39.130 9.69 0.00 0.00 2.29
469 1779 8.014517 CGCATTGCACAAATACATACATACATA 58.985 33.333 9.69 0.00 0.00 2.29
470 1780 9.333497 GCATTGCACAAATACATACATACATAG 57.667 33.333 3.15 0.00 0.00 2.23
475 1785 9.435688 GCACAAATACATACATACATAGATGGA 57.564 33.333 0.00 0.00 0.00 3.41
515 1825 9.456147 ACATACATAGATAGATACCTGTCTGTC 57.544 37.037 0.00 0.00 40.47 3.51
516 1826 9.679661 CATACATAGATAGATACCTGTCTGTCT 57.320 37.037 8.01 8.01 45.18 3.41
517 1827 9.899661 ATACATAGATAGATACCTGTCTGTCTC 57.100 37.037 6.47 0.00 43.11 3.36
518 1828 7.172342 ACATAGATAGATACCTGTCTGTCTCC 58.828 42.308 6.47 0.00 43.11 3.71
519 1829 4.993028 AGATAGATACCTGTCTGTCTCCC 58.007 47.826 0.00 0.00 41.16 4.30
520 1830 2.060050 AGATACCTGTCTGTCTCCCG 57.940 55.000 0.00 0.00 0.00 5.14
521 1831 1.285373 AGATACCTGTCTGTCTCCCGT 59.715 52.381 0.00 0.00 0.00 5.28
522 1832 2.508716 AGATACCTGTCTGTCTCCCGTA 59.491 50.000 0.00 0.00 0.00 4.02
523 1833 3.138653 AGATACCTGTCTGTCTCCCGTAT 59.861 47.826 0.00 0.00 0.00 3.06
524 1834 4.350225 AGATACCTGTCTGTCTCCCGTATA 59.650 45.833 0.00 0.00 0.00 1.47
525 1835 3.596940 ACCTGTCTGTCTCCCGTATAT 57.403 47.619 0.00 0.00 0.00 0.86
526 1836 4.719026 ACCTGTCTGTCTCCCGTATATA 57.281 45.455 0.00 0.00 0.00 0.86
527 1837 5.258216 ACCTGTCTGTCTCCCGTATATAT 57.742 43.478 0.00 0.00 0.00 0.86
528 1838 5.642165 ACCTGTCTGTCTCCCGTATATATT 58.358 41.667 0.00 0.00 0.00 1.28
529 1839 5.711036 ACCTGTCTGTCTCCCGTATATATTC 59.289 44.000 0.00 0.00 0.00 1.75
530 1840 5.710567 CCTGTCTGTCTCCCGTATATATTCA 59.289 44.000 0.00 0.00 0.00 2.57
531 1841 6.378564 CCTGTCTGTCTCCCGTATATATTCAT 59.621 42.308 0.00 0.00 0.00 2.57
532 1842 7.556635 CCTGTCTGTCTCCCGTATATATTCATA 59.443 40.741 0.00 0.00 0.00 2.15
533 1843 8.277490 TGTCTGTCTCCCGTATATATTCATAC 57.723 38.462 0.00 0.00 0.00 2.39
534 1844 7.886446 TGTCTGTCTCCCGTATATATTCATACA 59.114 37.037 0.00 0.00 31.96 2.29
535 1845 8.904834 GTCTGTCTCCCGTATATATTCATACAT 58.095 37.037 0.00 0.00 31.96 2.29
536 1846 9.475620 TCTGTCTCCCGTATATATTCATACATT 57.524 33.333 0.00 0.00 31.96 2.71
537 1847 9.737427 CTGTCTCCCGTATATATTCATACATTC 57.263 37.037 0.00 0.00 31.96 2.67
538 1848 9.250246 TGTCTCCCGTATATATTCATACATTCA 57.750 33.333 0.00 0.00 31.96 2.57
543 1853 9.698309 CCCGTATATATTCATACATTCATCTCC 57.302 37.037 0.00 0.00 31.96 3.71
544 1854 9.698309 CCGTATATATTCATACATTCATCTCCC 57.302 37.037 0.00 0.00 31.96 4.30
545 1855 9.399403 CGTATATATTCATACATTCATCTCCCG 57.601 37.037 0.00 0.00 31.96 5.14
608 1918 7.832769 ACATACATACATACATACATACGGCA 58.167 34.615 0.00 0.00 0.00 5.69
609 1919 8.474831 ACATACATACATACATACATACGGCAT 58.525 33.333 0.00 0.00 0.00 4.40
610 1920 8.968242 CATACATACATACATACATACGGCATC 58.032 37.037 0.00 0.00 0.00 3.91
622 1940 0.900182 ACGGCATCCTGTCTGTCTCA 60.900 55.000 0.00 0.00 0.00 3.27
628 1946 3.675775 GCATCCTGTCTGTCTCAACTCTC 60.676 52.174 0.00 0.00 0.00 3.20
632 1950 3.305950 CCTGTCTGTCTCAACTCTCAAGG 60.306 52.174 0.00 0.00 0.00 3.61
640 1958 5.129980 TGTCTCAACTCTCAAGGATGCATAT 59.870 40.000 0.00 0.00 0.00 1.78
641 1959 5.695816 GTCTCAACTCTCAAGGATGCATATC 59.304 44.000 0.00 0.00 0.00 1.63
643 1961 5.851720 TCAACTCTCAAGGATGCATATCTC 58.148 41.667 0.00 0.00 33.68 2.75
645 1963 6.099413 TCAACTCTCAAGGATGCATATCTCTT 59.901 38.462 0.00 0.00 33.68 2.85
646 1964 6.497624 ACTCTCAAGGATGCATATCTCTTT 57.502 37.500 0.00 0.00 33.68 2.52
651 1977 8.823794 TCTCAAGGATGCATATCTCTTTCATAT 58.176 33.333 0.00 0.00 33.68 1.78
712 2038 7.470192 TCCTCATACATACAGATACAGGATGA 58.530 38.462 0.00 0.00 39.69 2.92
713 2039 8.118600 TCCTCATACATACAGATACAGGATGAT 58.881 37.037 0.00 0.00 39.69 2.45
714 2040 8.196103 CCTCATACATACAGATACAGGATGATG 58.804 40.741 0.00 0.00 39.69 3.07
715 2041 8.071177 TCATACATACAGATACAGGATGATGG 57.929 38.462 0.00 0.00 39.69 3.51
723 2049 0.986527 ACAGGATGATGGTGCTCACA 59.013 50.000 2.21 0.00 39.69 3.58
746 2072 3.066621 TGTCTTCTGATGCCACAACAAAC 59.933 43.478 0.00 0.00 0.00 2.93
790 2116 3.932710 TGTCGCTCCTCATGTTCAATAAC 59.067 43.478 0.00 0.00 36.07 1.89
807 2133 9.693157 GTTCAATAACATTTATTTCAGCATTGC 57.307 29.630 0.00 0.00 35.56 3.56
817 2143 0.528924 TCAGCATTGCACCTGATTGC 59.471 50.000 11.91 1.04 43.31 3.56
818 2144 0.459585 CAGCATTGCACCTGATTGCC 60.460 55.000 11.91 0.00 42.25 4.52
829 2155 3.451894 GATTGCCCCACCCAAGCG 61.452 66.667 0.00 0.00 0.00 4.68
857 2193 1.380380 CCAATCCACCCCTGCTTCC 60.380 63.158 0.00 0.00 0.00 3.46
944 2290 5.866633 GCATCCATCTCATTACACTAGCTAC 59.133 44.000 0.00 0.00 0.00 3.58
1237 2600 4.440880 ACATTTCCAACCACAAACATGTG 58.559 39.130 0.00 2.03 39.37 3.21
1262 2634 4.439057 TGTGAGTGACTGTCCTACAAAAC 58.561 43.478 5.17 0.00 0.00 2.43
1306 2681 2.069273 CTTGGTTCAGCGAAATCGTCT 58.931 47.619 4.59 0.00 42.22 4.18
1589 2968 2.040278 AGACTGGTATGCTTCTTTGCCA 59.960 45.455 0.00 0.00 0.00 4.92
1590 2969 2.819608 GACTGGTATGCTTCTTTGCCAA 59.180 45.455 0.00 0.00 0.00 4.52
1591 2970 3.230134 ACTGGTATGCTTCTTTGCCAAA 58.770 40.909 0.00 0.00 0.00 3.28
1594 2973 4.567971 TGGTATGCTTCTTTGCCAAATTG 58.432 39.130 0.00 0.00 0.00 2.32
1672 3056 0.318445 AACTACACGTCCAGCGACAC 60.318 55.000 0.00 0.00 44.77 3.67
1765 3227 2.618709 AGACACAAGCTTTCCTTTTCCG 59.381 45.455 0.00 0.00 0.00 4.30
1876 3340 6.943718 TGTTTCTGGTAAATTAAATCCCGAGT 59.056 34.615 0.00 0.00 0.00 4.18
1898 3362 7.042321 CGAGTCTATATTTGGGAATTGCGTTAA 60.042 37.037 0.00 0.00 0.00 2.01
1919 3383 7.254151 CGTTAAGAGTAGCAAAGATAGAAAGGC 60.254 40.741 0.00 0.00 0.00 4.35
1973 3460 4.790718 ACCCACTTCTTAAACTGAAGGT 57.209 40.909 8.12 0.00 43.59 3.50
1979 3473 6.265577 CACTTCTTAAACTGAAGGTGGTTTG 58.734 40.000 8.12 0.00 43.59 2.93
1991 3485 3.023832 AGGTGGTTTGTTCTTCAACTGG 58.976 45.455 0.00 0.00 35.61 4.00
1992 3486 2.758423 GGTGGTTTGTTCTTCAACTGGT 59.242 45.455 0.00 0.00 35.61 4.00
2010 3504 7.230510 TCAACTGGTAAAATTTAGCACTGATGT 59.769 33.333 12.91 7.13 0.00 3.06
2011 3505 6.913170 ACTGGTAAAATTTAGCACTGATGTG 58.087 36.000 12.91 5.33 46.37 3.21
2012 3506 6.714810 ACTGGTAAAATTTAGCACTGATGTGA 59.285 34.615 12.91 0.00 46.55 3.58
2013 3507 7.394359 ACTGGTAAAATTTAGCACTGATGTGAT 59.606 33.333 12.91 0.00 46.55 3.06
2014 3508 7.537715 TGGTAAAATTTAGCACTGATGTGATG 58.462 34.615 12.91 0.00 46.55 3.07
2015 3509 7.392953 TGGTAAAATTTAGCACTGATGTGATGA 59.607 33.333 12.91 0.00 46.55 2.92
2016 3510 8.408601 GGTAAAATTTAGCACTGATGTGATGAT 58.591 33.333 9.75 0.00 46.55 2.45
2017 3511 9.443283 GTAAAATTTAGCACTGATGTGATGATC 57.557 33.333 0.00 0.00 46.55 2.92
2018 3512 7.634671 AAATTTAGCACTGATGTGATGATCA 57.365 32.000 0.00 0.00 46.55 2.92
2019 3513 7.818997 AATTTAGCACTGATGTGATGATCAT 57.181 32.000 8.25 8.25 46.55 2.45
2020 3514 7.818997 ATTTAGCACTGATGTGATGATCATT 57.181 32.000 10.14 0.00 46.55 2.57
2028 3522 8.070769 CACTGATGTGATGATCATTTGATCTTC 58.929 37.037 21.00 21.00 46.42 2.87
2172 3714 7.349330 AGGAAGAGGAAGAGGAATTGAATGATA 59.651 37.037 0.00 0.00 0.00 2.15
2173 3715 7.995488 GGAAGAGGAAGAGGAATTGAATGATAA 59.005 37.037 0.00 0.00 0.00 1.75
2201 3743 2.629051 GACACTTCCTGTTTATCCCCG 58.371 52.381 0.00 0.00 31.03 5.73
2253 3795 2.110213 GACCAAGTCACGGTGGCA 59.890 61.111 15.98 0.00 38.58 4.92
2266 3808 1.210155 GTGGCATGTTGAACTCCGC 59.790 57.895 0.00 0.00 0.00 5.54
2334 3876 2.881513 TCTGTTTCGCCAGCAAATAACA 59.118 40.909 0.00 0.00 32.32 2.41
2337 3879 1.242989 TTCGCCAGCAAATAACAGCA 58.757 45.000 0.00 0.00 0.00 4.41
2338 3880 1.242989 TCGCCAGCAAATAACAGCAA 58.757 45.000 0.00 0.00 0.00 3.91
2446 3988 2.066262 TCGTCTTTCGACAAATCCTGC 58.934 47.619 0.00 0.00 44.01 4.85
2508 4051 1.153597 TGTCCGCTGCATGCTTATCG 61.154 55.000 20.33 15.37 40.11 2.92
2509 4054 0.875908 GTCCGCTGCATGCTTATCGA 60.876 55.000 20.33 5.15 40.11 3.59
2599 4145 1.659098 GATTTGACGACCGCTAACCAG 59.341 52.381 0.00 0.00 0.00 4.00
2874 4420 1.067749 CGCTGGATCTGGAGCTGAG 59.932 63.158 0.00 0.00 32.70 3.35
2896 4442 1.618837 CTTGGGGTCGAGTCTTCTGAA 59.381 52.381 0.00 0.00 0.00 3.02
2917 4463 1.143183 CGTTGGCCATAGTAGCGGT 59.857 57.895 6.09 0.00 0.00 5.68
3048 4598 9.389570 GTATTCTATTTGTGGTTGTGTGTTAAC 57.610 33.333 0.00 0.00 0.00 2.01
3055 4605 3.440872 GTGGTTGTGTGTTAACCTTGTGA 59.559 43.478 2.48 0.00 46.11 3.58
3056 4606 3.440872 TGGTTGTGTGTTAACCTTGTGAC 59.559 43.478 2.48 0.00 46.11 3.67
3058 4608 4.082679 GGTTGTGTGTTAACCTTGTGACAA 60.083 41.667 2.48 0.00 43.33 3.18
3059 4609 4.955925 TGTGTGTTAACCTTGTGACAAG 57.044 40.909 18.04 18.04 0.00 3.16
3060 4610 4.328536 TGTGTGTTAACCTTGTGACAAGT 58.671 39.130 22.40 8.91 0.00 3.16
3115 4665 1.261480 TGGTTGTTGTTGTTGCAGGT 58.739 45.000 0.00 0.00 0.00 4.00
3116 4666 1.067283 TGGTTGTTGTTGTTGCAGGTG 60.067 47.619 0.00 0.00 0.00 4.00
3117 4667 1.639280 GTTGTTGTTGTTGCAGGTGG 58.361 50.000 0.00 0.00 0.00 4.61
3246 4797 2.172505 TGTGTGAATATTGGGAGCGGAT 59.827 45.455 0.00 0.00 0.00 4.18
3247 4798 3.214328 GTGTGAATATTGGGAGCGGATT 58.786 45.455 0.00 0.00 0.00 3.01
3249 4800 2.554032 GTGAATATTGGGAGCGGATTGG 59.446 50.000 0.00 0.00 0.00 3.16
3250 4801 2.441375 TGAATATTGGGAGCGGATTGGA 59.559 45.455 0.00 0.00 0.00 3.53
3284 4885 3.615155 CATTGGTTTGGTTTGGTTTGGT 58.385 40.909 0.00 0.00 0.00 3.67
3336 4942 3.222603 TCAGGAGCGAGCATATACAGAA 58.777 45.455 0.00 0.00 0.00 3.02
3338 4944 3.986572 CAGGAGCGAGCATATACAGAAAG 59.013 47.826 0.00 0.00 0.00 2.62
3339 4945 3.891977 AGGAGCGAGCATATACAGAAAGA 59.108 43.478 0.00 0.00 0.00 2.52
3340 4946 4.022416 AGGAGCGAGCATATACAGAAAGAG 60.022 45.833 0.00 0.00 0.00 2.85
3341 4947 4.261825 GGAGCGAGCATATACAGAAAGAGT 60.262 45.833 0.00 0.00 0.00 3.24
3360 4966 2.103373 GTGAGAGAGAGCATGGTGGTA 58.897 52.381 0.00 0.00 0.00 3.25
3376 4982 4.202101 TGGTGGTACTGTTTTGCATTTCAG 60.202 41.667 9.81 9.81 0.00 3.02
3414 5020 3.095163 CTCTGGGCTGGGCTGGAT 61.095 66.667 0.00 0.00 0.00 3.41
3438 5048 2.695666 ACTGTAACAGCAGTGAGTCAGT 59.304 45.455 0.00 0.00 46.72 3.41
3439 5049 3.243569 ACTGTAACAGCAGTGAGTCAGTC 60.244 47.826 0.00 0.00 46.72 3.51
3440 5050 2.959030 TGTAACAGCAGTGAGTCAGTCT 59.041 45.455 0.00 0.00 0.00 3.24
3441 5051 4.142038 TGTAACAGCAGTGAGTCAGTCTA 58.858 43.478 0.00 0.00 0.00 2.59
3442 5052 3.932545 AACAGCAGTGAGTCAGTCTAG 57.067 47.619 0.00 0.00 0.00 2.43
3443 5053 3.147553 ACAGCAGTGAGTCAGTCTAGA 57.852 47.619 0.00 0.00 0.00 2.43
3444 5054 2.817258 ACAGCAGTGAGTCAGTCTAGAC 59.183 50.000 15.41 15.41 38.81 2.59
3550 5172 2.158279 TGTACCTTACCTGTCCTGACCA 60.158 50.000 0.00 0.00 0.00 4.02
3551 5173 2.112279 ACCTTACCTGTCCTGACCAA 57.888 50.000 0.00 0.00 0.00 3.67
3552 5174 2.414612 ACCTTACCTGTCCTGACCAAA 58.585 47.619 0.00 0.00 0.00 3.28
3553 5175 2.105993 ACCTTACCTGTCCTGACCAAAC 59.894 50.000 0.00 0.00 0.00 2.93
3554 5176 2.372172 CCTTACCTGTCCTGACCAAACT 59.628 50.000 0.00 0.00 0.00 2.66
3567 5189 3.574396 TGACCAAACTAGACTGAGACTGG 59.426 47.826 0.00 0.00 0.00 4.00
3569 5191 3.165875 CCAAACTAGACTGAGACTGGGA 58.834 50.000 0.00 0.00 0.00 4.37
3570 5192 3.056465 CCAAACTAGACTGAGACTGGGAC 60.056 52.174 0.00 0.00 0.00 4.46
3571 5193 3.818295 AACTAGACTGAGACTGGGACT 57.182 47.619 0.00 0.00 0.00 3.85
3572 5194 3.080300 ACTAGACTGAGACTGGGACTG 57.920 52.381 0.00 0.00 0.00 3.51
3573 5195 2.377193 ACTAGACTGAGACTGGGACTGT 59.623 50.000 0.00 0.00 45.09 3.55
3574 5196 1.626686 AGACTGAGACTGGGACTGTG 58.373 55.000 0.00 0.00 41.64 3.66
3575 5197 1.145945 AGACTGAGACTGGGACTGTGA 59.854 52.381 0.00 0.00 41.64 3.58
3576 5198 1.543802 GACTGAGACTGGGACTGTGAG 59.456 57.143 0.00 0.00 41.64 3.51
3577 5199 1.145945 ACTGAGACTGGGACTGTGAGA 59.854 52.381 0.00 0.00 41.64 3.27
3578 5200 1.543802 CTGAGACTGGGACTGTGAGAC 59.456 57.143 0.00 0.00 41.64 3.36
3620 5258 4.156373 ACAAACAAATTTTGCTTGCTTGCT 59.844 33.333 19.93 3.35 39.65 3.91
3621 5259 4.968812 AACAAATTTTGCTTGCTTGCTT 57.031 31.818 9.04 0.00 0.00 3.91
3622 5260 4.281525 ACAAATTTTGCTTGCTTGCTTG 57.718 36.364 9.04 2.26 0.00 4.01
3623 5261 3.040099 CAAATTTTGCTTGCTTGCTTGC 58.960 40.909 0.00 0.00 0.00 4.01
3739 5377 9.995003 TCCTTTATATTGCTGTTTGTTTCATTT 57.005 25.926 0.00 0.00 0.00 2.32
3810 5448 6.491745 TGGATGATTAGGCAAGACTAGTCTAG 59.508 42.308 25.42 5.27 39.39 2.43
3819 5457 5.334182 GGCAAGACTAGTCTAGTTTGTTTGC 60.334 44.000 25.42 24.67 39.59 3.68
3820 5458 5.467063 GCAAGACTAGTCTAGTTTGTTTGCT 59.533 40.000 25.42 13.28 39.59 3.91
3821 5459 6.017852 GCAAGACTAGTCTAGTTTGTTTGCTT 60.018 38.462 25.42 16.65 39.59 3.91
3822 5460 7.170998 GCAAGACTAGTCTAGTTTGTTTGCTTA 59.829 37.037 25.42 0.00 39.59 3.09
3850 5488 7.821652 TGTTTGTTTGTTGACTCATGTCTTAA 58.178 30.769 0.00 0.00 43.29 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.711782 AGGAAGGGAGGGAGGGGG 61.712 72.222 0.00 0.00 0.00 5.40
15 16 2.367512 CAGGAAGGGAGGGAGGGG 60.368 72.222 0.00 0.00 0.00 4.79
16 17 1.690985 GACAGGAAGGGAGGGAGGG 60.691 68.421 0.00 0.00 0.00 4.30
17 18 1.690985 GGACAGGAAGGGAGGGAGG 60.691 68.421 0.00 0.00 0.00 4.30
18 19 0.689412 GAGGACAGGAAGGGAGGGAG 60.689 65.000 0.00 0.00 0.00 4.30
19 20 1.392534 GAGGACAGGAAGGGAGGGA 59.607 63.158 0.00 0.00 0.00 4.20
20 21 1.690985 GGAGGACAGGAAGGGAGGG 60.691 68.421 0.00 0.00 0.00 4.30
21 22 0.689412 GAGGAGGACAGGAAGGGAGG 60.689 65.000 0.00 0.00 0.00 4.30
22 23 0.689412 GGAGGAGGACAGGAAGGGAG 60.689 65.000 0.00 0.00 0.00 4.30
23 24 1.156322 AGGAGGAGGACAGGAAGGGA 61.156 60.000 0.00 0.00 0.00 4.20
24 25 0.689412 GAGGAGGAGGACAGGAAGGG 60.689 65.000 0.00 0.00 0.00 3.95
25 26 0.689412 GGAGGAGGAGGACAGGAAGG 60.689 65.000 0.00 0.00 0.00 3.46
26 27 0.041833 TGGAGGAGGAGGACAGGAAG 59.958 60.000 0.00 0.00 0.00 3.46
27 28 0.491823 TTGGAGGAGGAGGACAGGAA 59.508 55.000 0.00 0.00 0.00 3.36
28 29 0.252284 GTTGGAGGAGGAGGACAGGA 60.252 60.000 0.00 0.00 0.00 3.86
29 30 1.268283 GGTTGGAGGAGGAGGACAGG 61.268 65.000 0.00 0.00 0.00 4.00
35 36 1.362224 TCTTTGGGTTGGAGGAGGAG 58.638 55.000 0.00 0.00 0.00 3.69
41 42 2.543653 CGCTGTTTTCTTTGGGTTGGAG 60.544 50.000 0.00 0.00 0.00 3.86
99 100 4.083862 GTGGTGGTCGGAGGAGGC 62.084 72.222 0.00 0.00 0.00 4.70
102 103 0.896940 GTAGTGTGGTGGTCGGAGGA 60.897 60.000 0.00 0.00 0.00 3.71
107 108 2.660802 GGGGTAGTGTGGTGGTCG 59.339 66.667 0.00 0.00 0.00 4.79
108 109 3.075186 GGGGGTAGTGTGGTGGTC 58.925 66.667 0.00 0.00 0.00 4.02
220 1519 3.368501 CCTGGAGGGAGGGAGGGA 61.369 72.222 0.00 0.00 37.23 4.20
222 1521 4.101077 AGCCTGGAGGGAGGGAGG 62.101 72.222 0.00 0.00 37.23 4.30
223 1522 2.445654 GAGCCTGGAGGGAGGGAG 60.446 72.222 0.00 0.00 37.23 4.30
224 1523 4.095400 GGAGCCTGGAGGGAGGGA 62.095 72.222 0.00 0.00 37.23 4.20
225 1524 4.421554 TGGAGCCTGGAGGGAGGG 62.422 72.222 0.00 0.00 37.23 4.30
226 1525 2.767496 CTGGAGCCTGGAGGGAGG 60.767 72.222 0.00 0.00 37.23 4.30
237 1536 2.991540 GTTGTTGGGGGCTGGAGC 60.992 66.667 0.00 0.00 41.14 4.70
238 1537 1.153756 AAGTTGTTGGGGGCTGGAG 59.846 57.895 0.00 0.00 0.00 3.86
239 1538 1.152567 CAAGTTGTTGGGGGCTGGA 60.153 57.895 0.00 0.00 0.00 3.86
240 1539 1.048160 AACAAGTTGTTGGGGGCTGG 61.048 55.000 20.26 0.00 39.45 4.85
242 1541 0.759060 GGAACAAGTTGTTGGGGGCT 60.759 55.000 25.46 0.00 41.28 5.19
243 1542 0.759060 AGGAACAAGTTGTTGGGGGC 60.759 55.000 25.46 10.52 41.28 5.80
244 1543 1.686587 GAAGGAACAAGTTGTTGGGGG 59.313 52.381 25.46 0.00 41.28 5.40
245 1544 1.336755 CGAAGGAACAAGTTGTTGGGG 59.663 52.381 25.46 6.71 41.28 4.96
246 1545 1.269051 GCGAAGGAACAAGTTGTTGGG 60.269 52.381 25.46 10.49 41.28 4.12
247 1546 1.269051 GGCGAAGGAACAAGTTGTTGG 60.269 52.381 25.46 10.17 41.28 3.77
249 1548 1.029681 GGGCGAAGGAACAAGTTGTT 58.970 50.000 21.00 21.00 44.37 2.83
252 1551 1.975680 TCTAGGGCGAAGGAACAAGTT 59.024 47.619 0.00 0.00 0.00 2.66
253 1552 1.640917 TCTAGGGCGAAGGAACAAGT 58.359 50.000 0.00 0.00 0.00 3.16
254 1553 2.555199 CATCTAGGGCGAAGGAACAAG 58.445 52.381 0.00 0.00 0.00 3.16
255 1554 1.209504 CCATCTAGGGCGAAGGAACAA 59.790 52.381 0.00 0.00 0.00 2.83
256 1555 0.830648 CCATCTAGGGCGAAGGAACA 59.169 55.000 0.00 0.00 0.00 3.18
257 1556 1.120530 TCCATCTAGGGCGAAGGAAC 58.879 55.000 0.00 0.00 38.24 3.62
259 1558 2.158370 TGTATCCATCTAGGGCGAAGGA 60.158 50.000 0.00 0.00 35.50 3.36
260 1559 2.028930 GTGTATCCATCTAGGGCGAAGG 60.029 54.545 0.00 0.00 38.24 3.46
261 1560 2.628178 TGTGTATCCATCTAGGGCGAAG 59.372 50.000 0.00 0.00 38.24 3.79
263 1562 2.158519 TCTGTGTATCCATCTAGGGCGA 60.159 50.000 0.00 0.00 38.24 5.54
264 1563 2.239400 TCTGTGTATCCATCTAGGGCG 58.761 52.381 0.00 0.00 38.24 6.13
265 1564 4.093011 AGATCTGTGTATCCATCTAGGGC 58.907 47.826 0.00 0.00 38.24 5.19
266 1565 5.579047 AGAGATCTGTGTATCCATCTAGGG 58.421 45.833 0.00 0.00 38.24 3.53
267 1566 6.375174 CAGAGAGATCTGTGTATCCATCTAGG 59.625 46.154 0.00 0.00 33.12 3.02
268 1567 6.942005 ACAGAGAGATCTGTGTATCCATCTAG 59.058 42.308 10.63 0.00 46.83 2.43
269 1568 6.846988 ACAGAGAGATCTGTGTATCCATCTA 58.153 40.000 10.63 0.00 46.83 1.98
270 1569 5.704354 ACAGAGAGATCTGTGTATCCATCT 58.296 41.667 10.63 0.00 46.83 2.90
281 1582 4.268167 CGAGCATTGAAACAGAGAGATCTG 59.732 45.833 0.00 3.76 43.03 2.90
291 1592 6.108687 ACTCATAGAATCGAGCATTGAAACA 58.891 36.000 0.00 0.00 32.21 2.83
294 1595 8.143835 TGATAACTCATAGAATCGAGCATTGAA 58.856 33.333 0.00 0.00 32.21 2.69
311 1612 5.123227 GGGATTCATTCCGTTGATAACTCA 58.877 41.667 0.00 0.00 46.52 3.41
332 1639 1.151083 ATGGGATGGGATGGGATGGG 61.151 60.000 0.00 0.00 0.00 4.00
333 1640 0.333993 GATGGGATGGGATGGGATGG 59.666 60.000 0.00 0.00 0.00 3.51
335 1642 2.566746 GTAGATGGGATGGGATGGGAT 58.433 52.381 0.00 0.00 0.00 3.85
336 1643 1.831290 CGTAGATGGGATGGGATGGGA 60.831 57.143 0.00 0.00 0.00 4.37
337 1644 0.615331 CGTAGATGGGATGGGATGGG 59.385 60.000 0.00 0.00 0.00 4.00
338 1645 0.615331 CCGTAGATGGGATGGGATGG 59.385 60.000 0.00 0.00 0.00 3.51
339 1646 1.002430 CACCGTAGATGGGATGGGATG 59.998 57.143 0.00 0.00 0.00 3.51
354 1661 6.427150 CGGTAAATAATACGTACTACACCGT 58.573 40.000 18.26 0.00 40.11 4.83
355 1662 6.895209 CGGTAAATAATACGTACTACACCG 57.105 41.667 15.00 15.00 39.18 4.94
356 1663 7.639945 AGACGGTAAATAATACGTACTACACC 58.360 38.462 0.00 0.00 39.95 4.16
414 1724 4.977963 AGATGTGCGAACTGAATTTTGTTG 59.022 37.500 0.00 0.00 0.00 3.33
443 1753 6.197981 TGTATGTATGTATTTGTGCAATGCG 58.802 36.000 0.00 0.00 30.24 4.73
448 1758 9.218440 CCATCTATGTATGTATGTATTTGTGCA 57.782 33.333 0.00 0.00 0.00 4.57
449 1759 9.435688 TCCATCTATGTATGTATGTATTTGTGC 57.564 33.333 0.00 0.00 0.00 4.57
458 1768 9.774413 ATGTATGCATCCATCTATGTATGTATG 57.226 33.333 0.19 0.00 32.40 2.39
461 1771 8.761689 TGTATGTATGCATCCATCTATGTATGT 58.238 33.333 8.18 0.00 34.54 2.29
462 1772 9.774413 ATGTATGTATGCATCCATCTATGTATG 57.226 33.333 8.18 0.00 34.54 2.39
469 1779 8.761689 TGTATGTATGTATGTATGCATCCATCT 58.238 33.333 8.18 0.00 34.25 2.90
470 1780 8.947055 TGTATGTATGTATGTATGCATCCATC 57.053 34.615 8.18 1.97 34.25 3.51
489 1799 9.456147 GACAGACAGGTATCTATCTATGTATGT 57.544 37.037 3.35 3.35 43.45 2.29
490 1800 9.679661 AGACAGACAGGTATCTATCTATGTATG 57.320 37.037 0.00 0.00 30.51 2.39
491 1801 9.899661 GAGACAGACAGGTATCTATCTATGTAT 57.100 37.037 0.00 0.00 32.51 2.29
493 1803 7.172342 GGAGACAGACAGGTATCTATCTATGT 58.828 42.308 0.00 0.00 32.51 2.29
495 1805 6.577438 CGGGAGACAGACAGGTATCTATCTAT 60.577 46.154 0.00 0.00 32.51 1.98
497 1807 4.505918 CGGGAGACAGACAGGTATCTATCT 60.506 50.000 0.00 0.00 35.12 1.98
498 1808 3.754323 CGGGAGACAGACAGGTATCTATC 59.246 52.174 0.00 0.00 0.00 2.08
499 1809 3.138653 ACGGGAGACAGACAGGTATCTAT 59.861 47.826 0.00 0.00 0.00 1.98
500 1810 2.508716 ACGGGAGACAGACAGGTATCTA 59.491 50.000 0.00 0.00 0.00 1.98
501 1811 1.285373 ACGGGAGACAGACAGGTATCT 59.715 52.381 0.00 0.00 0.00 1.98
502 1812 1.765230 ACGGGAGACAGACAGGTATC 58.235 55.000 0.00 0.00 0.00 2.24
503 1813 3.596940 ATACGGGAGACAGACAGGTAT 57.403 47.619 0.00 0.00 0.00 2.73
505 1815 3.596940 ATATACGGGAGACAGACAGGT 57.403 47.619 0.00 0.00 0.00 4.00
507 1817 6.819397 TGAATATATACGGGAGACAGACAG 57.181 41.667 0.00 0.00 0.00 3.51
508 1818 7.886446 TGTATGAATATATACGGGAGACAGACA 59.114 37.037 0.00 0.00 36.54 3.41
509 1819 8.277490 TGTATGAATATATACGGGAGACAGAC 57.723 38.462 0.00 0.00 36.54 3.51
511 1821 9.737427 GAATGTATGAATATATACGGGAGACAG 57.263 37.037 0.00 0.00 36.54 3.51
517 1827 9.698309 GGAGATGAATGTATGAATATATACGGG 57.302 37.037 0.00 0.00 36.54 5.28
518 1828 9.698309 GGGAGATGAATGTATGAATATATACGG 57.302 37.037 0.00 0.00 36.54 4.02
519 1829 9.399403 CGGGAGATGAATGTATGAATATATACG 57.601 37.037 0.00 0.00 36.54 3.06
525 1835 9.653287 GAAATACGGGAGATGAATGTATGAATA 57.347 33.333 0.00 0.00 0.00 1.75
526 1836 8.378565 AGAAATACGGGAGATGAATGTATGAAT 58.621 33.333 0.00 0.00 0.00 2.57
527 1837 7.735917 AGAAATACGGGAGATGAATGTATGAA 58.264 34.615 0.00 0.00 0.00 2.57
528 1838 7.303182 AGAAATACGGGAGATGAATGTATGA 57.697 36.000 0.00 0.00 0.00 2.15
529 1839 7.442364 ACAAGAAATACGGGAGATGAATGTATG 59.558 37.037 0.00 0.00 0.00 2.39
530 1840 7.509546 ACAAGAAATACGGGAGATGAATGTAT 58.490 34.615 0.00 0.00 0.00 2.29
531 1841 6.884832 ACAAGAAATACGGGAGATGAATGTA 58.115 36.000 0.00 0.00 0.00 2.29
532 1842 5.745227 ACAAGAAATACGGGAGATGAATGT 58.255 37.500 0.00 0.00 0.00 2.71
533 1843 6.683974 AACAAGAAATACGGGAGATGAATG 57.316 37.500 0.00 0.00 0.00 2.67
534 1844 9.490379 GTATAACAAGAAATACGGGAGATGAAT 57.510 33.333 0.00 0.00 0.00 2.57
535 1845 8.479689 TGTATAACAAGAAATACGGGAGATGAA 58.520 33.333 0.00 0.00 32.34 2.57
536 1846 8.014070 TGTATAACAAGAAATACGGGAGATGA 57.986 34.615 0.00 0.00 32.34 2.92
537 1847 8.833231 ATGTATAACAAGAAATACGGGAGATG 57.167 34.615 0.00 0.00 32.34 2.90
538 1848 9.924650 GTATGTATAACAAGAAATACGGGAGAT 57.075 33.333 0.00 0.00 32.34 2.75
539 1849 8.916062 TGTATGTATAACAAGAAATACGGGAGA 58.084 33.333 0.00 0.00 32.34 3.71
540 1850 9.706691 ATGTATGTATAACAAGAAATACGGGAG 57.293 33.333 0.00 0.00 32.34 4.30
581 1891 9.961265 GCCGTATGTATGTATGTATGTATGTAT 57.039 33.333 0.00 0.00 0.00 2.29
582 1892 8.958506 TGCCGTATGTATGTATGTATGTATGTA 58.041 33.333 0.00 0.00 0.00 2.29
583 1893 7.832769 TGCCGTATGTATGTATGTATGTATGT 58.167 34.615 0.00 0.00 0.00 2.29
606 1916 2.233431 AGAGTTGAGACAGACAGGATGC 59.767 50.000 0.00 0.00 42.53 3.91
608 1918 3.772387 TGAGAGTTGAGACAGACAGGAT 58.228 45.455 0.00 0.00 0.00 3.24
609 1919 3.229697 TGAGAGTTGAGACAGACAGGA 57.770 47.619 0.00 0.00 0.00 3.86
610 1920 3.305950 CCTTGAGAGTTGAGACAGACAGG 60.306 52.174 0.00 0.00 0.00 4.00
622 1940 6.497624 AAGAGATATGCATCCTTGAGAGTT 57.502 37.500 0.19 0.00 0.00 3.01
683 2009 8.642432 TCCTGTATCTGTATGTATGAGGAAAAG 58.358 37.037 0.00 0.00 0.00 2.27
712 2038 2.303890 TCAGAAGACATGTGAGCACCAT 59.696 45.455 1.15 0.00 0.00 3.55
713 2039 1.693606 TCAGAAGACATGTGAGCACCA 59.306 47.619 1.15 0.00 0.00 4.17
714 2040 2.462456 TCAGAAGACATGTGAGCACC 57.538 50.000 1.15 0.00 0.00 5.01
715 2041 2.095532 GCATCAGAAGACATGTGAGCAC 59.904 50.000 1.15 0.00 34.38 4.40
723 2049 3.144657 TGTTGTGGCATCAGAAGACAT 57.855 42.857 0.00 0.00 0.00 3.06
746 2072 5.807520 ACACTGAAGAAAGCACATATAGTCG 59.192 40.000 0.00 0.00 0.00 4.18
790 2116 5.412640 TCAGGTGCAATGCTGAAATAAATG 58.587 37.500 6.82 0.00 0.00 2.32
794 2120 4.678574 GCAATCAGGTGCAATGCTGAAATA 60.679 41.667 6.82 0.00 44.29 1.40
807 2133 2.362889 GGGTGGGGCAATCAGGTG 60.363 66.667 0.00 0.00 0.00 4.00
817 2143 3.491598 AAGTGTCGCTTGGGTGGGG 62.492 63.158 0.00 0.00 35.80 4.96
818 2144 1.966451 GAAGTGTCGCTTGGGTGGG 60.966 63.158 2.68 0.00 37.59 4.61
829 2155 2.437413 GGGTGGATTGGAAGAAGTGTC 58.563 52.381 0.00 0.00 0.00 3.67
874 2210 8.753133 AGCTTAAATAAGAGAAAATGAAAGGGG 58.247 33.333 4.39 0.00 35.33 4.79
916 2257 6.206243 GCTAGTGTAATGAGATGGATGCAAAT 59.794 38.462 0.00 0.00 0.00 2.32
944 2290 6.765989 TGCCTTAACTATTGTATTGTGCTAGG 59.234 38.462 0.00 0.00 0.00 3.02
1176 2530 9.467030 AAGAGGGGGATAAGTAATAGAAAGAAT 57.533 33.333 0.00 0.00 0.00 2.40
1181 2540 9.684702 AATACAAGAGGGGGATAAGTAATAGAA 57.315 33.333 0.00 0.00 0.00 2.10
1237 2600 2.029020 TGTAGGACAGTCACTCACATGC 60.029 50.000 2.17 0.00 0.00 4.06
1262 2634 3.625764 TGAAGAAACAAACGGTCAGAAGG 59.374 43.478 0.00 0.00 0.00 3.46
1306 2681 1.906824 GAGATCCCCGGTCGGCATA 60.907 63.158 0.00 0.00 0.00 3.14
1672 3056 3.323000 CATGGCATGCTACGTCGG 58.677 61.111 18.92 0.00 0.00 4.79
1792 3254 5.163703 GGCACGTGTATTATTCCAATTGACA 60.164 40.000 18.38 0.00 0.00 3.58
1800 3262 4.026310 CGTTAGTGGCACGTGTATTATTCC 60.026 45.833 18.38 8.29 32.80 3.01
1872 3336 4.750098 ACGCAATTCCCAAATATAGACTCG 59.250 41.667 0.00 0.00 0.00 4.18
1876 3340 7.990886 ACTCTTAACGCAATTCCCAAATATAGA 59.009 33.333 0.00 0.00 0.00 1.98
1898 3362 4.141597 GGGCCTTTCTATCTTTGCTACTCT 60.142 45.833 0.84 0.00 0.00 3.24
1919 3383 6.511605 GCAATTCTTGTTTTTAGCTGTTTGGG 60.512 38.462 0.00 0.00 0.00 4.12
1973 3460 6.591750 TTTTACCAGTTGAAGAACAAACCA 57.408 33.333 0.00 0.00 40.36 3.67
1979 3473 8.135529 AGTGCTAAATTTTACCAGTTGAAGAAC 58.864 33.333 0.00 0.00 0.00 3.01
1991 3485 9.443283 GATCATCACATCAGTGCTAAATTTTAC 57.557 33.333 0.00 0.00 45.49 2.01
1992 3486 9.176460 TGATCATCACATCAGTGCTAAATTTTA 57.824 29.630 0.00 0.00 45.49 1.52
2015 3509 3.181493 GCGCCAACAGAAGATCAAATGAT 60.181 43.478 0.00 0.00 37.51 2.45
2016 3510 2.162208 GCGCCAACAGAAGATCAAATGA 59.838 45.455 0.00 0.00 0.00 2.57
2017 3511 2.523015 GCGCCAACAGAAGATCAAATG 58.477 47.619 0.00 0.00 0.00 2.32
2018 3512 1.474077 GGCGCCAACAGAAGATCAAAT 59.526 47.619 24.80 0.00 0.00 2.32
2019 3513 0.881118 GGCGCCAACAGAAGATCAAA 59.119 50.000 24.80 0.00 0.00 2.69
2020 3514 0.250684 TGGCGCCAACAGAAGATCAA 60.251 50.000 30.74 0.00 0.00 2.57
2028 3522 0.957395 AGAATCAGTGGCGCCAACAG 60.957 55.000 34.66 23.50 0.00 3.16
2172 3714 2.065799 ACAGGAAGTGTCCCCATTCTT 58.934 47.619 0.00 0.00 46.30 2.52
2173 3715 1.747444 ACAGGAAGTGTCCCCATTCT 58.253 50.000 0.00 0.00 46.30 2.40
2184 3726 1.558294 GGACGGGGATAAACAGGAAGT 59.442 52.381 0.00 0.00 0.00 3.01
2253 3795 1.375523 GACCCGCGGAGTTCAACAT 60.376 57.895 30.73 0.00 0.00 2.71
2266 3808 3.353836 CGGCCAGTTGTTGACCCG 61.354 66.667 2.24 0.00 35.96 5.28
2295 3837 2.198304 GACAAGGAATCCCCACCGCT 62.198 60.000 0.00 0.00 37.41 5.52
2300 3842 2.552155 CGAAACAGACAAGGAATCCCCA 60.552 50.000 0.00 0.00 37.41 4.96
2446 3988 1.019673 CGATTGTCCATCTTGGCCTG 58.980 55.000 3.32 0.00 37.47 4.85
2562 4108 6.028368 GTCAAATCAGACTGCATCATCAAAG 58.972 40.000 0.00 0.00 35.65 2.77
2756 4302 0.917533 AGCAGGTCATTCAGCTCCAT 59.082 50.000 0.00 0.00 30.05 3.41
2874 4420 1.079057 GAAGACTCGACCCCAAGCC 60.079 63.158 0.00 0.00 0.00 4.35
2884 4430 1.457303 CCAACGCTTTCAGAAGACTCG 59.543 52.381 0.00 0.00 34.71 4.18
2896 4442 0.810031 CGCTACTATGGCCAACGCTT 60.810 55.000 10.96 0.00 34.44 4.68
3048 4598 6.989659 TCCTACTTTACTACTTGTCACAAGG 58.010 40.000 21.71 7.34 0.00 3.61
3055 4605 7.002879 TGTCAGTCTCCTACTTTACTACTTGT 58.997 38.462 0.00 0.00 35.76 3.16
3056 4606 7.450124 TGTCAGTCTCCTACTTTACTACTTG 57.550 40.000 0.00 0.00 35.76 3.16
3058 4608 6.660094 CCTTGTCAGTCTCCTACTTTACTACT 59.340 42.308 0.00 0.00 35.76 2.57
3059 4609 6.433716 ACCTTGTCAGTCTCCTACTTTACTAC 59.566 42.308 0.00 0.00 35.76 2.73
3060 4610 6.433404 CACCTTGTCAGTCTCCTACTTTACTA 59.567 42.308 0.00 0.00 35.76 1.82
3115 4665 1.367346 TGAAGAACCTACCCATGCCA 58.633 50.000 0.00 0.00 0.00 4.92
3116 4666 2.576615 GATGAAGAACCTACCCATGCC 58.423 52.381 0.00 0.00 0.00 4.40
3117 4667 2.213499 CGATGAAGAACCTACCCATGC 58.787 52.381 0.00 0.00 0.00 4.06
3246 4797 3.293337 CAATGCTTCTCCATCCATCCAA 58.707 45.455 0.00 0.00 0.00 3.53
3247 4798 2.423803 CCAATGCTTCTCCATCCATCCA 60.424 50.000 0.00 0.00 0.00 3.41
3249 4800 2.941480 ACCAATGCTTCTCCATCCATC 58.059 47.619 0.00 0.00 0.00 3.51
3250 4801 3.393426 AACCAATGCTTCTCCATCCAT 57.607 42.857 0.00 0.00 0.00 3.41
3315 4921 2.863809 TCTGTATATGCTCGCTCCTGA 58.136 47.619 0.00 0.00 0.00 3.86
3336 4942 2.496871 CACCATGCTCTCTCTCACTCTT 59.503 50.000 0.00 0.00 0.00 2.85
3338 4944 1.136695 CCACCATGCTCTCTCTCACTC 59.863 57.143 0.00 0.00 0.00 3.51
3339 4945 1.193323 CCACCATGCTCTCTCTCACT 58.807 55.000 0.00 0.00 0.00 3.41
3340 4946 0.901124 ACCACCATGCTCTCTCTCAC 59.099 55.000 0.00 0.00 0.00 3.51
3341 4947 2.103373 GTACCACCATGCTCTCTCTCA 58.897 52.381 0.00 0.00 0.00 3.27
3360 4966 5.852282 AACCTACTGAAATGCAAAACAGT 57.148 34.783 20.56 20.56 44.17 3.55
3434 5040 6.569127 AATCCACTCTAGAGTCTAGACTGA 57.431 41.667 29.84 18.76 42.66 3.41
3440 5050 9.868160 TCATTGATTAATCCACTCTAGAGTCTA 57.132 33.333 22.76 13.65 40.20 2.59
3441 5051 8.774546 TCATTGATTAATCCACTCTAGAGTCT 57.225 34.615 22.76 9.98 40.20 3.24
3442 5052 8.855110 TCTCATTGATTAATCCACTCTAGAGTC 58.145 37.037 22.76 9.46 40.20 3.36
3443 5053 8.774546 TCTCATTGATTAATCCACTCTAGAGT 57.225 34.615 20.00 20.00 43.61 3.24
3550 5172 3.829601 CAGTCCCAGTCTCAGTCTAGTTT 59.170 47.826 0.00 0.00 0.00 2.66
3551 5173 3.181427 ACAGTCCCAGTCTCAGTCTAGTT 60.181 47.826 0.00 0.00 0.00 2.24
3552 5174 2.377193 ACAGTCCCAGTCTCAGTCTAGT 59.623 50.000 0.00 0.00 0.00 2.57
3553 5175 2.752354 CACAGTCCCAGTCTCAGTCTAG 59.248 54.545 0.00 0.00 0.00 2.43
3554 5176 2.375509 TCACAGTCCCAGTCTCAGTCTA 59.624 50.000 0.00 0.00 0.00 2.59
3567 5189 4.397481 TCATCATCATGTCTCACAGTCC 57.603 45.455 0.00 0.00 0.00 3.85
3569 5191 5.453480 CCTCATCATCATCATGTCTCACAGT 60.453 44.000 0.00 0.00 0.00 3.55
3570 5192 4.991687 CCTCATCATCATCATGTCTCACAG 59.008 45.833 0.00 0.00 0.00 3.66
3571 5193 4.742743 GCCTCATCATCATCATGTCTCACA 60.743 45.833 0.00 0.00 0.00 3.58
3572 5194 3.747010 GCCTCATCATCATCATGTCTCAC 59.253 47.826 0.00 0.00 0.00 3.51
3573 5195 3.389983 TGCCTCATCATCATCATGTCTCA 59.610 43.478 0.00 0.00 0.00 3.27
3574 5196 4.004196 TGCCTCATCATCATCATGTCTC 57.996 45.455 0.00 0.00 0.00 3.36
3575 5197 4.432980 TTGCCTCATCATCATCATGTCT 57.567 40.909 0.00 0.00 0.00 3.41
3576 5198 4.337274 TGTTTGCCTCATCATCATCATGTC 59.663 41.667 0.00 0.00 0.00 3.06
3577 5199 4.274978 TGTTTGCCTCATCATCATCATGT 58.725 39.130 0.00 0.00 0.00 3.21
3578 5200 4.911514 TGTTTGCCTCATCATCATCATG 57.088 40.909 0.00 0.00 0.00 3.07
3739 5377 6.534793 GCACCTTTCTGAATCAACAAAAGAAA 59.465 34.615 11.60 4.29 35.96 2.52
3740 5378 6.042143 GCACCTTTCTGAATCAACAAAAGAA 58.958 36.000 11.60 0.00 0.00 2.52
3741 5379 5.126869 TGCACCTTTCTGAATCAACAAAAGA 59.873 36.000 11.60 0.00 0.00 2.52
3742 5380 5.350633 TGCACCTTTCTGAATCAACAAAAG 58.649 37.500 0.00 5.81 0.00 2.27
3810 5448 8.720909 ACAAACAAACAAATAAGCAAACAAAC 57.279 26.923 0.00 0.00 0.00 2.93
3819 5457 9.086336 ACATGAGTCAACAAACAAACAAATAAG 57.914 29.630 0.00 0.00 0.00 1.73
3820 5458 8.994429 ACATGAGTCAACAAACAAACAAATAA 57.006 26.923 0.00 0.00 0.00 1.40
3821 5459 8.627487 GACATGAGTCAACAAACAAACAAATA 57.373 30.769 0.00 0.00 44.34 1.40
3822 5460 7.524294 GACATGAGTCAACAAACAAACAAAT 57.476 32.000 0.00 0.00 44.34 2.32
3850 5488 4.033232 ACCTACCTACCTACCTACCTCT 57.967 50.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.