Multiple sequence alignment - TraesCS6A01G277000

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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 TraesCS6A01G277000 chr6A 100.000 2998 0 0 1 2998 503835863 503832866 0.000000e+00 5537
1 TraesCS6A01G277000 chr6B 90.283 1451 89 21 614 2054 545279970 545278562 0.000000e+00 1851
2 TraesCS6A01G277000 chr6B 91.272 951 74 8 2053 2998 545277758 545276812 0.000000e+00 1288
3 TraesCS6A01G277000 chr6B 93.590 156 4 2 38 193 545282648 545282499 8.360000e-56 228
4 TraesCS6A01G277000 chr6D 89.812 1276 82 24 812 2060 363321094 363319840 0.000000e+00 1592
5 TraesCS6A01G277000 chr6D 83.729 842 83 23 2188 2998 363319576 363318758 0.000000e+00 747
6 TraesCS6A01G277000 chr6D 92.913 127 6 1 55 181 363322790 363322667 6.600000e-42 182
7 TraesCS6A01G277000 chr7B 84.831 178 21 3 1579 1756 334798533 334798704 1.100000e-39 174
8 TraesCS6A01G277000 chr7B 83.429 175 25 3 381 554 48281316 48281145 3.090000e-35 159
9 TraesCS6A01G277000 chr7B 83.432 169 24 3 381 548 736726804 736726969 1.440000e-33 154
10 TraesCS6A01G277000 chr3B 83.929 168 25 1 381 548 674990136 674989971 3.090000e-35 159
11 TraesCS6A01G277000 chr3B 83.432 169 24 3 381 548 624022878 624023043 1.440000e-33 154
12 TraesCS6A01G277000 chr5B 83.735 166 25 1 383 548 566789476 566789639 4.000000e-34 156
13 TraesCS6A01G277000 chr5B 78.571 238 38 10 2241 2473 688042743 688042514 8.660000e-31 145
14 TraesCS6A01G277000 chr2A 84.049 163 25 1 384 546 39164544 39164705 4.000000e-34 156
15 TraesCS6A01G277000 chr4B 83.529 170 22 4 381 548 499224665 499224500 1.440000e-33 154
16 TraesCS6A01G277000 chr4B 83.333 168 26 1 381 548 549841919 549841754 1.440000e-33 154
17 TraesCS6A01G277000 chr2B 85.065 154 19 3 378 531 368413409 368413558 1.440000e-33 154


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 TraesCS6A01G277000 chr6A 503832866 503835863 2997 True 5537.000000 5537 100.000 1 2998 1 chr6A.!!$R1 2997
1 TraesCS6A01G277000 chr6B 545276812 545282648 5836 True 1122.333333 1851 91.715 38 2998 3 chr6B.!!$R1 2960
2 TraesCS6A01G277000 chr6D 363318758 363322790 4032 True 840.333333 1592 88.818 55 2998 3 chr6D.!!$R1 2943

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
286 1613 0.03213 TCTAATCGGCATCGGTCTGC 59.968 55.0 0.0 0.0 41.53 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2176 5427 0.108396 AAAACTTTGTGGCCCCATGC 59.892 50.0 0.0 0.0 40.16 4.06 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
23 24 5.661056 ACTGTCTCCGTCTTGATGAATAA 57.339 39.130 0.00 0.00 0.00 1.40
24 25 5.655488 ACTGTCTCCGTCTTGATGAATAAG 58.345 41.667 0.00 0.00 0.00 1.73
25 26 5.186021 ACTGTCTCCGTCTTGATGAATAAGT 59.814 40.000 0.00 0.00 0.00 2.24
26 27 5.651530 TGTCTCCGTCTTGATGAATAAGTC 58.348 41.667 0.00 0.00 0.00 3.01
27 28 5.185056 TGTCTCCGTCTTGATGAATAAGTCA 59.815 40.000 0.00 0.00 41.67 3.41
51 52 0.937304 GCGTAGTACGTGGGATCGTA 59.063 55.000 22.81 0.00 44.73 3.43
52 53 1.532868 GCGTAGTACGTGGGATCGTAT 59.467 52.381 22.81 0.00 45.61 3.06
53 54 2.736721 GCGTAGTACGTGGGATCGTATA 59.263 50.000 22.81 0.00 45.61 1.47
64 65 1.136029 GGATCGTATACTCGTCGCTGG 60.136 57.143 0.56 0.00 0.00 4.85
65 66 1.530293 GATCGTATACTCGTCGCTGGT 59.470 52.381 0.56 0.00 0.00 4.00
127 128 2.407428 CGAGCTCGTGCCTCCTACA 61.407 63.158 27.79 0.00 40.80 2.74
186 187 2.988549 GCGCGTGACGTGTGAGAAG 61.989 63.158 20.13 0.00 46.11 2.85
187 188 1.370051 CGCGTGACGTGTGAGAAGA 60.370 57.895 10.79 0.00 36.87 2.87
188 189 0.933047 CGCGTGACGTGTGAGAAGAA 60.933 55.000 10.79 0.00 36.87 2.52
189 190 1.205657 GCGTGACGTGTGAGAAGAAA 58.794 50.000 6.91 0.00 0.00 2.52
190 191 1.591158 GCGTGACGTGTGAGAAGAAAA 59.409 47.619 6.91 0.00 0.00 2.29
191 192 2.221055 GCGTGACGTGTGAGAAGAAAAT 59.779 45.455 6.91 0.00 0.00 1.82
203 204 8.244113 GTGTGAGAAGAAAATAAAATACCAGGG 58.756 37.037 0.00 0.00 0.00 4.45
236 1563 1.411612 AGCTCACTCATGATCGATGCA 59.588 47.619 0.54 0.83 33.22 3.96
237 1564 2.037381 AGCTCACTCATGATCGATGCAT 59.963 45.455 0.54 0.00 33.22 3.96
238 1565 2.157863 GCTCACTCATGATCGATGCATG 59.842 50.000 21.81 21.81 43.39 4.06
239 1566 2.140717 TCACTCATGATCGATGCATGC 58.859 47.619 22.49 11.82 42.13 4.06
254 1581 0.039527 CATGCGCATGTGATGGATGG 60.040 55.000 36.45 12.04 34.23 3.51
255 1582 0.179012 ATGCGCATGTGATGGATGGA 60.179 50.000 24.69 0.00 0.00 3.41
256 1583 0.179012 TGCGCATGTGATGGATGGAT 60.179 50.000 5.66 0.00 0.00 3.41
257 1584 0.240145 GCGCATGTGATGGATGGATG 59.760 55.000 11.26 0.00 0.00 3.51
259 1586 2.433436 CGCATGTGATGGATGGATGAT 58.567 47.619 0.00 0.00 0.00 2.45
260 1587 2.817844 CGCATGTGATGGATGGATGATT 59.182 45.455 0.00 0.00 0.00 2.57
261 1588 3.119955 CGCATGTGATGGATGGATGATTC 60.120 47.826 0.00 0.00 0.00 2.52
262 1589 3.192844 GCATGTGATGGATGGATGATTCC 59.807 47.826 0.00 0.00 42.94 3.01
264 1591 5.805424 GCATGTGATGGATGGATGATTCCTA 60.805 44.000 0.00 0.00 43.07 2.94
266 1593 4.909695 TGTGATGGATGGATGATTCCTAGT 59.090 41.667 0.00 0.00 43.07 2.57
268 1595 5.936956 GTGATGGATGGATGATTCCTAGTTC 59.063 44.000 0.00 0.00 43.07 3.01
269 1596 5.848369 TGATGGATGGATGATTCCTAGTTCT 59.152 40.000 0.00 0.00 43.07 3.01
270 1597 7.018769 TGATGGATGGATGATTCCTAGTTCTA 58.981 38.462 0.00 0.00 43.07 2.10
271 1598 7.513781 TGATGGATGGATGATTCCTAGTTCTAA 59.486 37.037 0.00 0.00 43.07 2.10
272 1599 7.878621 TGGATGGATGATTCCTAGTTCTAAT 57.121 36.000 0.00 0.00 43.07 1.73
273 1600 7.911651 TGGATGGATGATTCCTAGTTCTAATC 58.088 38.462 0.00 0.00 43.07 1.75
282 1609 2.296471 CCTAGTTCTAATCGGCATCGGT 59.704 50.000 0.00 0.00 36.95 4.69
283 1610 2.510768 AGTTCTAATCGGCATCGGTC 57.489 50.000 0.00 0.00 36.95 4.79
286 1613 0.032130 TCTAATCGGCATCGGTCTGC 59.968 55.000 0.00 0.00 41.53 4.26
310 1637 4.360027 GCGAGTGCTGCGTGTGTG 62.360 66.667 0.00 0.00 38.39 3.82
312 1639 2.628106 GAGTGCTGCGTGTGTGTG 59.372 61.111 0.00 0.00 0.00 3.82
313 1640 2.125147 AGTGCTGCGTGTGTGTGT 60.125 55.556 0.00 0.00 0.00 3.72
317 1644 3.563088 CTGCGTGTGTGTGTGCGT 61.563 61.111 0.00 0.00 0.00 5.24
318 1645 3.772000 CTGCGTGTGTGTGTGCGTG 62.772 63.158 0.00 0.00 0.00 5.34
319 1646 3.860125 GCGTGTGTGTGTGCGTGT 61.860 61.111 0.00 0.00 0.00 4.49
320 1647 2.021243 CGTGTGTGTGTGCGTGTG 59.979 61.111 0.00 0.00 0.00 3.82
321 1648 2.735677 CGTGTGTGTGTGCGTGTGT 61.736 57.895 0.00 0.00 0.00 3.72
323 1650 0.109964 GTGTGTGTGTGCGTGTGTTT 60.110 50.000 0.00 0.00 0.00 2.83
324 1651 0.593618 TGTGTGTGTGCGTGTGTTTT 59.406 45.000 0.00 0.00 0.00 2.43
325 1652 0.981240 GTGTGTGTGCGTGTGTTTTG 59.019 50.000 0.00 0.00 0.00 2.44
326 1653 0.109551 TGTGTGTGCGTGTGTTTTGG 60.110 50.000 0.00 0.00 0.00 3.28
329 1656 0.988439 GTGTGCGTGTGTTTTGGTTG 59.012 50.000 0.00 0.00 0.00 3.77
330 1657 0.881796 TGTGCGTGTGTTTTGGTTGA 59.118 45.000 0.00 0.00 0.00 3.18
331 1658 1.135546 TGTGCGTGTGTTTTGGTTGAG 60.136 47.619 0.00 0.00 0.00 3.02
352 1709 2.487762 GTGCCCGATGATTTGACTTGAA 59.512 45.455 0.00 0.00 0.00 2.69
365 1722 3.909430 TGACTTGAACGACTCCACATAC 58.091 45.455 0.00 0.00 0.00 2.39
374 1731 3.057456 ACGACTCCACATACAGTTGACTC 60.057 47.826 0.00 0.00 0.00 3.36
375 1732 3.502920 GACTCCACATACAGTTGACTCG 58.497 50.000 0.00 0.00 0.00 4.18
378 1735 3.086282 TCCACATACAGTTGACTCGCTA 58.914 45.455 0.00 0.00 0.00 4.26
380 1737 3.366985 CCACATACAGTTGACTCGCTACA 60.367 47.826 0.00 0.00 0.00 2.74
382 1739 4.266265 CACATACAGTTGACTCGCTACATG 59.734 45.833 0.00 0.00 0.00 3.21
383 1740 4.082190 ACATACAGTTGACTCGCTACATGT 60.082 41.667 2.69 2.69 0.00 3.21
384 1741 5.124936 ACATACAGTTGACTCGCTACATGTA 59.875 40.000 5.25 5.25 0.00 2.29
385 1742 3.834610 ACAGTTGACTCGCTACATGTAC 58.165 45.455 0.08 0.00 0.00 2.90
387 1744 4.099120 CAGTTGACTCGCTACATGTACTC 58.901 47.826 0.08 0.00 0.00 2.59
388 1745 3.128938 AGTTGACTCGCTACATGTACTCC 59.871 47.826 0.08 0.00 0.00 3.85
389 1746 2.718563 TGACTCGCTACATGTACTCCA 58.281 47.619 0.08 0.00 0.00 3.86
390 1747 3.288092 TGACTCGCTACATGTACTCCAT 58.712 45.455 0.08 0.00 0.00 3.41
392 1749 2.623889 ACTCGCTACATGTACTCCATCC 59.376 50.000 0.08 0.00 0.00 3.51
393 1750 1.607148 TCGCTACATGTACTCCATCCG 59.393 52.381 0.08 0.00 0.00 4.18
394 1751 1.337071 CGCTACATGTACTCCATCCGT 59.663 52.381 0.08 0.00 0.00 4.69
396 1753 3.381949 GCTACATGTACTCCATCCGTTC 58.618 50.000 0.08 0.00 0.00 3.95
397 1754 2.579207 ACATGTACTCCATCCGTTCG 57.421 50.000 0.00 0.00 0.00 3.95
399 1756 3.018856 ACATGTACTCCATCCGTTCGTA 58.981 45.455 0.00 0.00 0.00 3.43
401 1758 4.082081 ACATGTACTCCATCCGTTCGTAAA 60.082 41.667 0.00 0.00 0.00 2.01
402 1759 3.836949 TGTACTCCATCCGTTCGTAAAC 58.163 45.455 0.00 0.00 0.00 2.01
403 1760 3.255395 TGTACTCCATCCGTTCGTAAACA 59.745 43.478 0.00 0.00 34.93 2.83
404 1761 3.604875 ACTCCATCCGTTCGTAAACAT 57.395 42.857 0.00 0.00 34.93 2.71
405 1762 4.724074 ACTCCATCCGTTCGTAAACATA 57.276 40.909 0.00 0.00 34.93 2.29
406 1763 5.075858 ACTCCATCCGTTCGTAAACATAA 57.924 39.130 0.00 0.00 34.93 1.90
407 1764 5.481105 ACTCCATCCGTTCGTAAACATAAA 58.519 37.500 0.00 0.00 34.93 1.40
408 1765 6.110707 ACTCCATCCGTTCGTAAACATAAAT 58.889 36.000 0.00 0.00 34.93 1.40
409 1766 6.257193 ACTCCATCCGTTCGTAAACATAAATC 59.743 38.462 0.00 0.00 34.93 2.17
410 1767 6.342906 TCCATCCGTTCGTAAACATAAATCT 58.657 36.000 0.00 0.00 34.93 2.40
411 1768 6.819649 TCCATCCGTTCGTAAACATAAATCTT 59.180 34.615 0.00 0.00 34.93 2.40
413 1770 7.638683 CCATCCGTTCGTAAACATAAATCTTTC 59.361 37.037 0.00 0.00 34.93 2.62
416 1773 9.421806 TCCGTTCGTAAACATAAATCTTTCTAA 57.578 29.630 0.00 0.00 34.93 2.10
443 1800 8.859090 AGATTCTGATAAGGATTACACAGAGAG 58.141 37.037 0.00 0.00 43.11 3.20
444 1801 7.962995 TTCTGATAAGGATTACACAGAGAGT 57.037 36.000 0.00 0.00 43.11 3.24
445 1802 9.647918 ATTCTGATAAGGATTACACAGAGAGTA 57.352 33.333 0.00 0.00 43.11 2.59
446 1803 9.475620 TTCTGATAAGGATTACACAGAGAGTAA 57.524 33.333 0.00 0.00 43.11 2.24
447 1804 9.475620 TCTGATAAGGATTACACAGAGAGTAAA 57.524 33.333 0.00 0.00 40.08 2.01
449 1806 9.871238 TGATAAGGATTACACAGAGAGTAAAAC 57.129 33.333 0.00 0.00 35.33 2.43
450 1807 9.871238 GATAAGGATTACACAGAGAGTAAAACA 57.129 33.333 0.00 0.00 35.33 2.83
452 1809 8.608844 AAGGATTACACAGAGAGTAAAACAAG 57.391 34.615 0.00 0.00 35.33 3.16
453 1810 7.736893 AGGATTACACAGAGAGTAAAACAAGT 58.263 34.615 0.00 0.00 35.33 3.16
454 1811 7.657761 AGGATTACACAGAGAGTAAAACAAGTG 59.342 37.037 0.00 0.00 35.33 3.16
455 1812 7.656137 GGATTACACAGAGAGTAAAACAAGTGA 59.344 37.037 0.00 0.00 35.33 3.41
456 1813 8.958119 ATTACACAGAGAGTAAAACAAGTGAA 57.042 30.769 0.00 0.00 35.33 3.18
457 1814 8.958119 TTACACAGAGAGTAAAACAAGTGAAT 57.042 30.769 0.00 0.00 0.00 2.57
458 1815 7.484035 ACACAGAGAGTAAAACAAGTGAATC 57.516 36.000 0.00 0.00 0.00 2.52
459 1816 7.275920 ACACAGAGAGTAAAACAAGTGAATCT 58.724 34.615 0.00 0.00 0.00 2.40
460 1817 8.421784 ACACAGAGAGTAAAACAAGTGAATCTA 58.578 33.333 0.00 0.00 0.00 1.98
461 1818 8.704234 CACAGAGAGTAAAACAAGTGAATCTAC 58.296 37.037 0.00 0.00 0.00 2.59
462 1819 8.421784 ACAGAGAGTAAAACAAGTGAATCTACA 58.578 33.333 0.00 0.00 0.00 2.74
463 1820 8.704234 CAGAGAGTAAAACAAGTGAATCTACAC 58.296 37.037 0.00 0.00 40.60 2.90
477 1834 8.240883 GTGAATCTACACTTCAAAATACGTCT 57.759 34.615 0.00 0.00 37.73 4.18
478 1835 9.350357 GTGAATCTACACTTCAAAATACGTCTA 57.650 33.333 0.00 0.00 37.73 2.59
498 1855 9.311916 ACGTCTATATAGATCCGTATGTAGTTC 57.688 37.037 20.72 2.99 34.59 3.01
499 1856 9.310716 CGTCTATATAGATCCGTATGTAGTTCA 57.689 37.037 15.43 0.00 34.39 3.18
511 1868 9.692749 TCCGTATGTAGTTCATATTGAAATCTC 57.307 33.333 0.00 0.00 38.22 2.75
512 1869 9.698309 CCGTATGTAGTTCATATTGAAATCTCT 57.302 33.333 0.00 0.00 38.22 3.10
550 1907 5.548706 TTAAAGACAGAGAGAGTAGTCGC 57.451 43.478 0.00 0.00 36.18 5.19
551 1908 3.343941 AAGACAGAGAGAGTAGTCGCT 57.656 47.619 3.16 3.16 35.18 4.93
552 1909 4.475051 AAGACAGAGAGAGTAGTCGCTA 57.525 45.455 3.56 0.00 32.14 4.26
553 1910 4.475051 AGACAGAGAGAGTAGTCGCTAA 57.525 45.455 3.56 0.00 32.14 3.09
554 1911 4.439057 AGACAGAGAGAGTAGTCGCTAAG 58.561 47.826 3.56 2.82 32.14 2.18
555 1912 4.160814 AGACAGAGAGAGTAGTCGCTAAGA 59.839 45.833 3.56 0.00 32.14 2.10
556 1913 4.439057 ACAGAGAGAGTAGTCGCTAAGAG 58.561 47.826 3.56 0.00 32.14 2.85
557 1914 4.081309 ACAGAGAGAGTAGTCGCTAAGAGT 60.081 45.833 3.56 0.00 32.14 3.24
558 1915 5.127519 ACAGAGAGAGTAGTCGCTAAGAGTA 59.872 44.000 3.56 0.00 32.14 2.59
559 1916 5.690409 CAGAGAGAGTAGTCGCTAAGAGTAG 59.310 48.000 3.56 0.00 35.57 2.57
560 1917 5.361857 AGAGAGAGTAGTCGCTAAGAGTAGT 59.638 44.000 3.56 0.00 40.26 2.73
561 1918 5.981174 AGAGAGTAGTCGCTAAGAGTAGTT 58.019 41.667 1.46 0.00 38.27 2.24
562 1919 7.068593 AGAGAGAGTAGTCGCTAAGAGTAGTTA 59.931 40.741 3.56 0.00 38.27 2.24
563 1920 6.980397 AGAGAGTAGTCGCTAAGAGTAGTTAC 59.020 42.308 1.46 0.00 38.27 2.50
564 1921 5.748152 AGAGTAGTCGCTAAGAGTAGTTACG 59.252 44.000 0.00 0.00 38.27 3.18
565 1922 5.415221 AGTAGTCGCTAAGAGTAGTTACGT 58.585 41.667 0.00 0.00 35.44 3.57
566 1923 6.565234 AGTAGTCGCTAAGAGTAGTTACGTA 58.435 40.000 0.00 0.00 35.44 3.57
567 1924 5.710613 AGTCGCTAAGAGTAGTTACGTAC 57.289 43.478 0.00 0.00 0.00 3.67
568 1925 5.415221 AGTCGCTAAGAGTAGTTACGTACT 58.585 41.667 0.00 0.00 41.04 2.73
569 1926 5.872070 AGTCGCTAAGAGTAGTTACGTACTT 59.128 40.000 0.00 0.00 38.33 2.24
570 1927 6.370166 AGTCGCTAAGAGTAGTTACGTACTTT 59.630 38.462 0.00 0.00 38.33 2.66
571 1928 7.545965 AGTCGCTAAGAGTAGTTACGTACTTTA 59.454 37.037 0.00 0.00 38.33 1.85
575 1932 9.056306 GCTAAGAGTAGTTACGTACTTTACAAC 57.944 37.037 0.00 0.00 38.33 3.32
581 1938 8.770828 AGTAGTTACGTACTTTACAACTACGAA 58.229 33.333 20.93 0.00 44.46 3.85
582 1939 9.543018 GTAGTTACGTACTTTACAACTACGAAT 57.457 33.333 15.61 0.00 37.88 3.34
598 1955 9.953825 CAACTACGAATATTTACTGAACACTTC 57.046 33.333 0.00 0.00 0.00 3.01
599 1956 8.390854 ACTACGAATATTTACTGAACACTTCG 57.609 34.615 0.00 0.00 39.87 3.79
622 2918 4.427312 ACATAACGTCGTGGTATTTCCTC 58.573 43.478 0.00 0.00 37.07 3.71
713 3009 1.290203 CTTGTGCGTTCGCTATCCAT 58.710 50.000 17.63 0.00 0.00 3.41
714 3010 1.004610 CTTGTGCGTTCGCTATCCATG 60.005 52.381 17.63 7.98 0.00 3.66
718 3014 3.004944 TGTGCGTTCGCTATCCATGTATA 59.995 43.478 17.63 0.00 0.00 1.47
727 3023 4.499399 CGCTATCCATGTATATGCGTACAC 59.501 45.833 11.31 0.00 37.40 2.90
736 3032 0.170784 TATGCGTACACGAAGCCGAA 59.829 50.000 5.84 0.00 43.02 4.30
747 3043 3.062042 ACGAAGCCGAAGTAAAATCGTT 58.938 40.909 0.00 0.00 38.74 3.85
769 3066 6.349280 CGTTTTCAGCCATCTCCTTTTGATTA 60.349 38.462 0.00 0.00 0.00 1.75
795 3092 4.140994 TCTCCTTCTACCCTCGGAACATAT 60.141 45.833 0.00 0.00 0.00 1.78
796 3093 5.074102 TCTCCTTCTACCCTCGGAACATATA 59.926 44.000 0.00 0.00 0.00 0.86
797 3094 5.900437 TCCTTCTACCCTCGGAACATATAT 58.100 41.667 0.00 0.00 0.00 0.86
802 3099 3.786553 ACCCTCGGAACATATATAGCCA 58.213 45.455 0.00 0.00 0.00 4.75
803 3100 3.769844 ACCCTCGGAACATATATAGCCAG 59.230 47.826 0.00 0.00 0.00 4.85
804 3101 3.430929 CCCTCGGAACATATATAGCCAGC 60.431 52.174 0.00 0.00 0.00 4.85
805 3102 3.430929 CCTCGGAACATATATAGCCAGCC 60.431 52.174 0.00 0.00 0.00 4.85
806 3103 3.169908 TCGGAACATATATAGCCAGCCA 58.830 45.455 0.00 0.00 0.00 4.75
807 3104 3.580895 TCGGAACATATATAGCCAGCCAA 59.419 43.478 0.00 0.00 0.00 4.52
808 3105 4.225042 TCGGAACATATATAGCCAGCCAAT 59.775 41.667 0.00 0.00 0.00 3.16
809 3106 4.943705 CGGAACATATATAGCCAGCCAATT 59.056 41.667 0.00 0.00 0.00 2.32
810 3107 5.415701 CGGAACATATATAGCCAGCCAATTT 59.584 40.000 0.00 0.00 0.00 1.82
848 3145 2.486592 CGCTTTCCTAATTCCAACCGTT 59.513 45.455 0.00 0.00 0.00 4.44
862 3159 4.404715 TCCAACCGTTAAATTCCAAACCAA 59.595 37.500 0.00 0.00 0.00 3.67
868 3165 5.813157 CCGTTAAATTCCAAACCAACAAAGT 59.187 36.000 0.00 0.00 0.00 2.66
1027 3333 2.049228 CGTGTACGTGAGTTGAGTTCC 58.951 52.381 0.00 0.00 46.40 3.62
1068 3374 3.065786 TGCGACCGACGATCTTAATTAGT 59.934 43.478 0.00 0.00 45.77 2.24
1069 3375 4.273235 TGCGACCGACGATCTTAATTAGTA 59.727 41.667 0.00 0.00 45.77 1.82
1070 3376 4.845060 GCGACCGACGATCTTAATTAGTAG 59.155 45.833 0.00 0.00 45.77 2.57
1090 3402 4.250116 AGAGCTAATCAAATCGAGCGAT 57.750 40.909 0.00 0.00 39.96 4.58
1093 3405 4.233789 AGCTAATCAAATCGAGCGATCTC 58.766 43.478 5.79 0.00 39.96 2.75
1095 3407 4.089780 GCTAATCAAATCGAGCGATCTCAG 59.910 45.833 5.79 0.51 39.30 3.35
1113 3425 4.022503 TCTCAGCTAATCATGGTCAGATCG 60.023 45.833 0.00 0.00 0.00 3.69
1117 3429 0.752658 AATCATGGTCAGATCGGCGA 59.247 50.000 13.87 13.87 0.00 5.54
1123 3435 0.526524 GGTCAGATCGGCGAGTCTTG 60.527 60.000 17.22 10.73 0.00 3.02
1160 3472 7.258022 TGATTAATTAGCTACGTACGTGGTA 57.742 36.000 30.25 23.44 0.00 3.25
1307 3619 0.037882 GGAGCCAAAGCCAAAAGAGC 60.038 55.000 0.00 0.00 41.25 4.09
1338 3659 3.471806 GAGGAGGAAGGGGCGTCC 61.472 72.222 0.00 0.00 41.85 4.79
1549 3870 1.668101 CTCGTCGAAGAAGGGGAGGG 61.668 65.000 1.95 0.00 39.69 4.30
1674 4007 1.817099 CTACTACGACGCCGAGGGT 60.817 63.158 0.00 0.00 39.50 4.34
1766 4101 4.776322 CAACGCCTGATCGCCCCA 62.776 66.667 0.00 0.00 0.00 4.96
1828 4164 1.685148 GACTTGGCCAAGATCCATCC 58.315 55.000 44.50 22.12 40.79 3.51
1829 4165 1.002069 ACTTGGCCAAGATCCATCCA 58.998 50.000 44.50 9.49 40.79 3.41
1830 4166 1.572415 ACTTGGCCAAGATCCATCCAT 59.428 47.619 44.50 21.27 40.79 3.41
1831 4167 1.961394 CTTGGCCAAGATCCATCCATG 59.039 52.381 37.60 9.12 40.79 3.66
1832 4168 0.468585 TGGCCAAGATCCATCCATGC 60.469 55.000 0.61 0.00 0.00 4.06
1833 4169 1.183676 GGCCAAGATCCATCCATGCC 61.184 60.000 0.00 0.00 0.00 4.40
1834 4170 0.178970 GCCAAGATCCATCCATGCCT 60.179 55.000 0.00 0.00 0.00 4.75
1851 4187 1.329171 CCTCTCCCTCTGCCTCACTG 61.329 65.000 0.00 0.00 0.00 3.66
1939 4275 1.500512 TTTTGGCGTGCGTAGTGACC 61.501 55.000 0.00 0.00 0.00 4.02
2013 4349 9.516314 TGTTACTAAATCTCAGTCGATGTTATG 57.484 33.333 0.00 0.00 0.00 1.90
2016 4352 8.635877 ACTAAATCTCAGTCGATGTTATGTTC 57.364 34.615 0.00 0.00 0.00 3.18
2076 5327 6.620877 ACATGTTCTTCTACCCACTAATGA 57.379 37.500 0.00 0.00 0.00 2.57
2082 5333 3.090210 TCTACCCACTAATGACACCGA 57.910 47.619 0.00 0.00 0.00 4.69
2110 5361 2.685017 AGGCACGCAGATGGGAGA 60.685 61.111 3.67 0.00 0.00 3.71
2123 5374 3.132563 GATGGGAGAGCGCATATTTGCT 61.133 50.000 11.47 0.00 46.33 3.91
2135 5386 1.990799 TATTTGCTCAGTCGTGTCGG 58.009 50.000 0.00 0.00 0.00 4.79
2141 5392 2.807045 CAGTCGTGTCGGCAGCTC 60.807 66.667 0.00 0.00 32.13 4.09
2148 5399 3.918220 GTCGGCAGCTCGATTGCG 61.918 66.667 13.76 10.19 42.42 4.85
2165 5416 1.017177 GCGCCGTGATCCACAAAGTA 61.017 55.000 0.00 0.00 33.40 2.24
2166 5417 1.651987 CGCCGTGATCCACAAAGTAT 58.348 50.000 0.00 0.00 33.40 2.12
2184 5435 1.402107 ATTTGGATTCCGCATGGGGC 61.402 55.000 23.55 10.31 39.90 5.80
2220 5471 9.930693 TTAGGTTTCAAAACTTGTGTTATTGTT 57.069 25.926 0.00 0.00 38.89 2.83
2250 5503 2.750301 AAGTTTTCGTCGTTTGCTCC 57.250 45.000 0.00 0.00 0.00 4.70
2267 5520 2.226674 GCTCCTACCAAGTTTCAACAGC 59.773 50.000 0.00 0.00 0.00 4.40
2344 5598 2.290896 TGAAAGCCCTCATCGGAAACAT 60.291 45.455 0.00 0.00 33.16 2.71
2357 5611 5.635417 TCGGAAACATGAATATGCAAACA 57.365 34.783 0.00 0.00 37.85 2.83
2444 5698 3.053291 GATGCGTTCCACCGGCAA 61.053 61.111 0.00 0.00 40.49 4.52
2541 5795 3.744660 GTCACCTCACAAGTTTCATCCT 58.255 45.455 0.00 0.00 0.00 3.24
2613 5871 3.478857 TTACCCTCTTTTCGAAGCACA 57.521 42.857 0.00 0.00 0.00 4.57
2687 5949 1.932011 GCAGGCACACACACACACAA 61.932 55.000 0.00 0.00 0.00 3.33
2712 5974 6.258727 ACAAGTTTGTATATGGAGATTGCTCG 59.741 38.462 0.00 0.00 39.82 5.03
2801 6063 4.532834 ACACAACACTTATCAACCACCTT 58.467 39.130 0.00 0.00 0.00 3.50
2811 6074 6.649557 ACTTATCAACCACCTTCGAGTTAAAG 59.350 38.462 0.00 0.00 0.00 1.85
2834 6097 3.568007 CCAACCAACGAATGAAGGAGAAA 59.432 43.478 0.00 0.00 0.00 2.52
2846 6109 7.094805 CGAATGAAGGAGAAAAGTGGTTAATCA 60.095 37.037 0.00 0.00 0.00 2.57
2864 6127 7.669722 GGTTAATCATGGGATGTAATATGTGGT 59.330 37.037 0.00 0.00 32.92 4.16
2866 6129 6.708885 ATCATGGGATGTAATATGTGGTCT 57.291 37.500 0.00 0.00 30.86 3.85
2867 6130 5.868454 TCATGGGATGTAATATGTGGTCTG 58.132 41.667 0.00 0.00 0.00 3.51
2910 6191 3.329225 TGGTTGATGAGACATTACCCACA 59.671 43.478 0.00 0.00 0.00 4.17
2934 6215 5.132144 ACTTGAAACCTTAGTCTTTGAGGGA 59.868 40.000 0.00 0.00 34.81 4.20
2949 6231 3.219281 TGAGGGATCAATGTCGACGATA 58.781 45.455 11.62 0.00 0.00 2.92
2954 6236 5.047021 AGGGATCAATGTCGACGATAATCAT 60.047 40.000 11.62 0.00 0.00 2.45
2976 6258 0.043334 TAGAGGGCAGCCTTCTCCTT 59.957 55.000 28.68 8.77 39.27 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.377429 ACTTATTCATCAAGACGGAGACAGTA 59.623 38.462 0.00 0.00 0.00 2.74
1 2 5.186021 ACTTATTCATCAAGACGGAGACAGT 59.814 40.000 0.00 0.00 0.00 3.55
2 3 5.655488 ACTTATTCATCAAGACGGAGACAG 58.345 41.667 0.00 0.00 0.00 3.51
3 4 5.185056 TGACTTATTCATCAAGACGGAGACA 59.815 40.000 0.00 0.00 0.00 3.41
4 5 5.651530 TGACTTATTCATCAAGACGGAGAC 58.348 41.667 0.00 0.00 0.00 3.36
5 6 5.914898 TGACTTATTCATCAAGACGGAGA 57.085 39.130 0.00 0.00 0.00 3.71
6 7 7.515841 CGAAATGACTTATTCATCAAGACGGAG 60.516 40.741 0.00 0.00 44.86 4.63
7 8 6.255670 CGAAATGACTTATTCATCAAGACGGA 59.744 38.462 0.00 0.00 44.86 4.69
8 9 6.414079 CGAAATGACTTATTCATCAAGACGG 58.586 40.000 0.00 0.00 44.86 4.79
9 10 5.898606 GCGAAATGACTTATTCATCAAGACG 59.101 40.000 0.00 0.00 44.86 4.18
10 11 5.898606 CGCGAAATGACTTATTCATCAAGAC 59.101 40.000 0.00 0.00 44.86 3.01
11 12 5.580691 ACGCGAAATGACTTATTCATCAAGA 59.419 36.000 15.93 0.00 44.86 3.02
12 13 5.799960 ACGCGAAATGACTTATTCATCAAG 58.200 37.500 15.93 0.00 44.86 3.02
13 14 5.794687 ACGCGAAATGACTTATTCATCAA 57.205 34.783 15.93 0.00 44.86 2.57
14 15 6.040247 ACTACGCGAAATGACTTATTCATCA 58.960 36.000 15.93 0.00 44.86 3.07
15 16 6.512177 ACTACGCGAAATGACTTATTCATC 57.488 37.500 15.93 0.00 44.86 2.92
16 17 6.141844 CGTACTACGCGAAATGACTTATTCAT 59.858 38.462 15.93 0.00 39.93 2.57
17 18 5.453266 CGTACTACGCGAAATGACTTATTCA 59.547 40.000 15.93 0.00 34.66 2.57
18 19 5.876597 CGTACTACGCGAAATGACTTATTC 58.123 41.667 15.93 0.00 33.65 1.75
19 20 5.861491 CGTACTACGCGAAATGACTTATT 57.139 39.130 15.93 0.00 33.65 1.40
51 52 2.158842 ACCTACTACCAGCGACGAGTAT 60.159 50.000 0.00 0.00 0.00 2.12
52 53 1.208052 ACCTACTACCAGCGACGAGTA 59.792 52.381 0.00 0.00 0.00 2.59
53 54 0.035630 ACCTACTACCAGCGACGAGT 60.036 55.000 0.00 0.00 0.00 4.18
64 65 4.689812 TGCGAGATAAGATCGACCTACTAC 59.310 45.833 0.00 0.00 42.76 2.73
65 66 4.891260 TGCGAGATAAGATCGACCTACTA 58.109 43.478 0.00 0.00 42.76 1.82
186 187 6.775594 AGCTGACCCTGGTATTTTATTTTC 57.224 37.500 0.00 0.00 0.00 2.29
187 188 7.553504 AAAGCTGACCCTGGTATTTTATTTT 57.446 32.000 0.00 0.00 0.00 1.82
188 189 7.147897 GCTAAAGCTGACCCTGGTATTTTATTT 60.148 37.037 0.00 0.00 38.21 1.40
189 190 6.321435 GCTAAAGCTGACCCTGGTATTTTATT 59.679 38.462 0.00 0.00 38.21 1.40
190 191 5.828328 GCTAAAGCTGACCCTGGTATTTTAT 59.172 40.000 0.00 0.00 38.21 1.40
191 192 5.190677 GCTAAAGCTGACCCTGGTATTTTA 58.809 41.667 0.00 0.00 38.21 1.52
215 1542 2.060284 GCATCGATCATGAGTGAGCTC 58.940 52.381 6.82 6.82 38.59 4.09
236 1563 0.179012 TCCATCCATCACATGCGCAT 60.179 50.000 19.28 19.28 0.00 4.73
237 1564 0.179012 ATCCATCCATCACATGCGCA 60.179 50.000 14.96 14.96 0.00 6.09
238 1565 0.240145 CATCCATCCATCACATGCGC 59.760 55.000 0.00 0.00 0.00 6.09
239 1566 1.886886 TCATCCATCCATCACATGCG 58.113 50.000 0.00 0.00 0.00 4.73
254 1581 5.784177 TGCCGATTAGAACTAGGAATCATC 58.216 41.667 0.00 0.00 31.25 2.92
255 1582 5.808366 TGCCGATTAGAACTAGGAATCAT 57.192 39.130 0.00 0.00 31.25 2.45
256 1583 5.564848 CGATGCCGATTAGAACTAGGAATCA 60.565 44.000 0.00 0.00 36.95 2.57
257 1584 4.859798 CGATGCCGATTAGAACTAGGAATC 59.140 45.833 0.00 0.00 38.22 2.52
259 1586 3.005472 CCGATGCCGATTAGAACTAGGAA 59.995 47.826 0.00 0.00 38.22 3.36
260 1587 2.557056 CCGATGCCGATTAGAACTAGGA 59.443 50.000 0.00 0.00 38.22 2.94
261 1588 2.296471 ACCGATGCCGATTAGAACTAGG 59.704 50.000 0.00 0.00 38.22 3.02
262 1589 3.253677 AGACCGATGCCGATTAGAACTAG 59.746 47.826 0.00 0.00 38.22 2.57
264 1591 2.032620 AGACCGATGCCGATTAGAACT 58.967 47.619 0.00 0.00 38.22 3.01
266 1593 1.538204 GCAGACCGATGCCGATTAGAA 60.538 52.381 0.00 0.00 40.43 2.10
268 1595 2.522060 GCAGACCGATGCCGATTAG 58.478 57.895 0.00 0.00 40.43 1.73
269 1596 4.750460 GCAGACCGATGCCGATTA 57.250 55.556 0.00 0.00 40.43 1.75
294 1621 2.961721 ACACACACGCAGCACTCG 60.962 61.111 0.00 0.00 0.00 4.18
300 1627 3.563088 ACGCACACACACACGCAG 61.563 61.111 0.00 0.00 0.00 5.18
302 1629 3.860125 ACACGCACACACACACGC 61.860 61.111 0.00 0.00 0.00 5.34
303 1630 2.021243 CACACGCACACACACACG 59.979 61.111 0.00 0.00 0.00 4.49
304 1631 0.109964 AAACACACGCACACACACAC 60.110 50.000 0.00 0.00 0.00 3.82
305 1632 0.593618 AAAACACACGCACACACACA 59.406 45.000 0.00 0.00 0.00 3.72
306 1633 0.981240 CAAAACACACGCACACACAC 59.019 50.000 0.00 0.00 0.00 3.82
307 1634 0.109551 CCAAAACACACGCACACACA 60.110 50.000 0.00 0.00 0.00 3.72
308 1635 0.109504 ACCAAAACACACGCACACAC 60.110 50.000 0.00 0.00 0.00 3.82
309 1636 0.598562 AACCAAAACACACGCACACA 59.401 45.000 0.00 0.00 0.00 3.72
310 1637 0.988439 CAACCAAAACACACGCACAC 59.012 50.000 0.00 0.00 0.00 3.82
312 1639 1.135517 ACTCAACCAAAACACACGCAC 60.136 47.619 0.00 0.00 0.00 5.34
313 1640 1.135546 CACTCAACCAAAACACACGCA 60.136 47.619 0.00 0.00 0.00 5.24
317 1644 0.820871 GGGCACTCAACCAAAACACA 59.179 50.000 0.00 0.00 0.00 3.72
318 1645 0.248866 CGGGCACTCAACCAAAACAC 60.249 55.000 0.00 0.00 0.00 3.32
319 1646 0.394488 TCGGGCACTCAACCAAAACA 60.394 50.000 0.00 0.00 0.00 2.83
320 1647 0.958822 ATCGGGCACTCAACCAAAAC 59.041 50.000 0.00 0.00 0.00 2.43
321 1648 0.958091 CATCGGGCACTCAACCAAAA 59.042 50.000 0.00 0.00 0.00 2.44
323 1650 0.327924 ATCATCGGGCACTCAACCAA 59.672 50.000 0.00 0.00 0.00 3.67
324 1651 0.327924 AATCATCGGGCACTCAACCA 59.672 50.000 0.00 0.00 0.00 3.67
325 1652 1.133025 CAAATCATCGGGCACTCAACC 59.867 52.381 0.00 0.00 0.00 3.77
326 1653 2.083774 TCAAATCATCGGGCACTCAAC 58.916 47.619 0.00 0.00 0.00 3.18
329 1656 2.029838 AGTCAAATCATCGGGCACTC 57.970 50.000 0.00 0.00 0.00 3.51
330 1657 2.086869 CAAGTCAAATCATCGGGCACT 58.913 47.619 0.00 0.00 0.00 4.40
331 1658 2.083774 TCAAGTCAAATCATCGGGCAC 58.916 47.619 0.00 0.00 0.00 5.01
352 1709 2.891580 AGTCAACTGTATGTGGAGTCGT 59.108 45.455 0.00 0.00 25.79 4.34
365 1722 4.098055 AGTACATGTAGCGAGTCAACTG 57.902 45.455 5.62 0.00 0.00 3.16
374 1731 1.337071 ACGGATGGAGTACATGTAGCG 59.663 52.381 5.62 0.00 40.72 4.26
375 1732 3.381949 GAACGGATGGAGTACATGTAGC 58.618 50.000 5.62 1.35 40.72 3.58
378 1735 1.822990 ACGAACGGATGGAGTACATGT 59.177 47.619 2.69 2.69 40.72 3.21
380 1737 4.082081 TGTTTACGAACGGATGGAGTACAT 60.082 41.667 0.00 0.00 39.57 2.29
382 1739 3.836949 TGTTTACGAACGGATGGAGTAC 58.163 45.455 0.00 0.00 38.65 2.73
383 1740 4.724074 ATGTTTACGAACGGATGGAGTA 57.276 40.909 0.00 0.00 38.65 2.59
384 1741 3.604875 ATGTTTACGAACGGATGGAGT 57.395 42.857 0.00 0.00 38.65 3.85
385 1742 6.479001 AGATTTATGTTTACGAACGGATGGAG 59.521 38.462 0.00 0.00 38.65 3.86
387 1744 6.598753 AGATTTATGTTTACGAACGGATGG 57.401 37.500 0.00 0.00 38.65 3.51
388 1745 8.388103 AGAAAGATTTATGTTTACGAACGGATG 58.612 33.333 0.00 0.00 38.65 3.51
389 1746 8.488651 AGAAAGATTTATGTTTACGAACGGAT 57.511 30.769 0.00 0.00 38.65 4.18
390 1747 7.894376 AGAAAGATTTATGTTTACGAACGGA 57.106 32.000 0.00 0.00 38.65 4.69
416 1773 9.206690 TCTCTGTGTAATCCTTATCAGAATCTT 57.793 33.333 0.00 0.00 32.75 2.40
419 1776 8.546083 ACTCTCTGTGTAATCCTTATCAGAAT 57.454 34.615 0.00 0.00 32.75 2.40
423 1780 9.871238 GTTTTACTCTCTGTGTAATCCTTATCA 57.129 33.333 0.00 0.00 31.13 2.15
424 1781 9.871238 TGTTTTACTCTCTGTGTAATCCTTATC 57.129 33.333 0.00 0.00 31.13 1.75
426 1783 9.706691 CTTGTTTTACTCTCTGTGTAATCCTTA 57.293 33.333 0.00 0.00 31.13 2.69
427 1784 8.211629 ACTTGTTTTACTCTCTGTGTAATCCTT 58.788 33.333 0.00 0.00 31.13 3.36
429 1786 7.656137 TCACTTGTTTTACTCTCTGTGTAATCC 59.344 37.037 0.00 0.00 31.13 3.01
430 1787 8.589335 TCACTTGTTTTACTCTCTGTGTAATC 57.411 34.615 0.00 0.00 31.13 1.75
431 1788 8.958119 TTCACTTGTTTTACTCTCTGTGTAAT 57.042 30.769 0.00 0.00 31.13 1.89
432 1789 8.958119 ATTCACTTGTTTTACTCTCTGTGTAA 57.042 30.769 0.00 0.00 0.00 2.41
433 1790 8.421784 AGATTCACTTGTTTTACTCTCTGTGTA 58.578 33.333 0.00 0.00 0.00 2.90
435 1792 7.721286 AGATTCACTTGTTTTACTCTCTGTG 57.279 36.000 0.00 0.00 0.00 3.66
436 1793 8.421784 TGTAGATTCACTTGTTTTACTCTCTGT 58.578 33.333 0.00 0.00 0.00 3.41
437 1794 8.704234 GTGTAGATTCACTTGTTTTACTCTCTG 58.296 37.037 0.00 0.00 35.68 3.35
438 1795 8.643324 AGTGTAGATTCACTTGTTTTACTCTCT 58.357 33.333 0.00 0.00 44.92 3.10
452 1809 8.240883 AGACGTATTTTGAAGTGTAGATTCAC 57.759 34.615 0.00 0.00 36.44 3.18
472 1829 9.311916 GAACTACATACGGATCTATATAGACGT 57.688 37.037 23.70 23.70 38.22 4.34
473 1830 9.310716 TGAACTACATACGGATCTATATAGACG 57.689 37.037 14.71 16.00 34.72 4.18
485 1842 9.692749 GAGATTTCAATATGAACTACATACGGA 57.307 33.333 0.00 0.00 43.12 4.69
486 1843 9.698309 AGAGATTTCAATATGAACTACATACGG 57.302 33.333 0.00 0.00 43.12 4.02
524 1881 8.347035 GCGACTACTCTCTCTGTCTTTAAATAT 58.653 37.037 0.00 0.00 0.00 1.28
525 1882 7.553402 AGCGACTACTCTCTCTGTCTTTAAATA 59.447 37.037 0.00 0.00 0.00 1.40
526 1883 6.376018 AGCGACTACTCTCTCTGTCTTTAAAT 59.624 38.462 0.00 0.00 0.00 1.40
527 1884 5.706369 AGCGACTACTCTCTCTGTCTTTAAA 59.294 40.000 0.00 0.00 0.00 1.52
528 1885 5.247084 AGCGACTACTCTCTCTGTCTTTAA 58.753 41.667 0.00 0.00 0.00 1.52
529 1886 4.834534 AGCGACTACTCTCTCTGTCTTTA 58.165 43.478 0.00 0.00 0.00 1.85
530 1887 3.681593 AGCGACTACTCTCTCTGTCTTT 58.318 45.455 0.00 0.00 0.00 2.52
531 1888 3.343941 AGCGACTACTCTCTCTGTCTT 57.656 47.619 0.00 0.00 0.00 3.01
532 1889 4.160814 TCTTAGCGACTACTCTCTCTGTCT 59.839 45.833 0.00 0.00 0.00 3.41
533 1890 4.435425 TCTTAGCGACTACTCTCTCTGTC 58.565 47.826 0.00 0.00 0.00 3.51
534 1891 4.081309 ACTCTTAGCGACTACTCTCTCTGT 60.081 45.833 0.00 0.00 0.00 3.41
535 1892 4.439057 ACTCTTAGCGACTACTCTCTCTG 58.561 47.826 0.00 0.00 0.00 3.35
536 1893 4.748277 ACTCTTAGCGACTACTCTCTCT 57.252 45.455 0.00 0.00 0.00 3.10
537 1894 5.594926 ACTACTCTTAGCGACTACTCTCTC 58.405 45.833 0.00 0.00 0.00 3.20
538 1895 5.603170 ACTACTCTTAGCGACTACTCTCT 57.397 43.478 0.00 0.00 0.00 3.10
539 1896 6.074888 CGTAACTACTCTTAGCGACTACTCTC 60.075 46.154 0.00 0.00 0.00 3.20
540 1897 5.748152 CGTAACTACTCTTAGCGACTACTCT 59.252 44.000 0.00 0.00 0.00 3.24
541 1898 5.518487 ACGTAACTACTCTTAGCGACTACTC 59.482 44.000 0.00 0.00 0.00 2.59
542 1899 5.415221 ACGTAACTACTCTTAGCGACTACT 58.585 41.667 0.00 0.00 0.00 2.57
543 1900 5.710613 ACGTAACTACTCTTAGCGACTAC 57.289 43.478 0.00 0.00 0.00 2.73
544 1901 6.565234 AGTACGTAACTACTCTTAGCGACTA 58.435 40.000 0.00 0.00 36.36 2.59
545 1902 5.415221 AGTACGTAACTACTCTTAGCGACT 58.585 41.667 0.00 0.00 36.36 4.18
546 1903 5.710613 AGTACGTAACTACTCTTAGCGAC 57.289 43.478 0.00 0.00 36.36 5.19
547 1904 6.727824 AAAGTACGTAACTACTCTTAGCGA 57.272 37.500 0.00 0.00 37.50 4.93
548 1905 7.456253 TGTAAAGTACGTAACTACTCTTAGCG 58.544 38.462 0.00 0.00 37.50 4.26
549 1906 9.056306 GTTGTAAAGTACGTAACTACTCTTAGC 57.944 37.037 0.00 0.00 37.50 3.09
571 1928 9.485206 AAGTGTTCAGTAAATATTCGTAGTTGT 57.515 29.630 0.00 0.00 0.00 3.32
575 1932 8.521860 GTCGAAGTGTTCAGTAAATATTCGTAG 58.478 37.037 0.00 0.00 39.30 3.51
578 1935 7.273188 TGTCGAAGTGTTCAGTAAATATTCG 57.727 36.000 0.00 0.00 39.55 3.34
581 1938 8.804743 CGTTATGTCGAAGTGTTCAGTAAATAT 58.195 33.333 0.00 0.00 0.00 1.28
582 1939 7.809331 ACGTTATGTCGAAGTGTTCAGTAAATA 59.191 33.333 0.00 0.00 34.70 1.40
583 1940 6.643770 ACGTTATGTCGAAGTGTTCAGTAAAT 59.356 34.615 0.00 0.00 34.70 1.40
584 1941 5.978919 ACGTTATGTCGAAGTGTTCAGTAAA 59.021 36.000 0.00 0.00 34.70 2.01
585 1942 5.522456 ACGTTATGTCGAAGTGTTCAGTAA 58.478 37.500 0.00 0.00 34.70 2.24
599 1956 4.427312 AGGAAATACCACGACGTTATGTC 58.573 43.478 0.00 0.00 41.91 3.06
658 2954 8.673711 CCCGTCAGAAATTTCTCAATTTATACA 58.326 33.333 17.91 0.00 41.79 2.29
659 2955 7.644157 GCCCGTCAGAAATTTCTCAATTTATAC 59.356 37.037 17.91 5.79 41.79 1.47
660 2956 7.556275 AGCCCGTCAGAAATTTCTCAATTTATA 59.444 33.333 17.91 0.00 41.79 0.98
662 2958 5.710099 AGCCCGTCAGAAATTTCTCAATTTA 59.290 36.000 17.91 0.00 41.79 1.40
664 2960 4.082125 AGCCCGTCAGAAATTTCTCAATT 58.918 39.130 17.91 0.00 34.74 2.32
665 2961 3.690460 AGCCCGTCAGAAATTTCTCAAT 58.310 40.909 17.91 0.00 34.74 2.57
667 2963 2.859165 AGCCCGTCAGAAATTTCTCA 57.141 45.000 17.91 1.97 34.74 3.27
668 2964 2.603560 CGTAGCCCGTCAGAAATTTCTC 59.396 50.000 17.91 7.23 34.74 2.87
669 2965 2.618053 CGTAGCCCGTCAGAAATTTCT 58.382 47.619 15.11 15.11 38.25 2.52
693 2989 0.037697 TGGATAGCGAACGCACAAGT 60.038 50.000 20.66 2.76 44.88 3.16
713 3009 2.734670 GGCTTCGTGTACGCATATACA 58.265 47.619 7.29 0.00 39.60 2.29
714 3010 1.712350 CGGCTTCGTGTACGCATATAC 59.288 52.381 7.29 0.00 39.60 1.47
718 3014 1.076533 CTTCGGCTTCGTGTACGCAT 61.077 55.000 7.29 0.00 39.60 4.73
727 3023 3.717350 AACGATTTTACTTCGGCTTCG 57.283 42.857 0.00 0.00 40.83 3.79
736 3032 5.123979 GGAGATGGCTGAAAACGATTTTACT 59.876 40.000 0.00 0.00 31.94 2.24
747 3043 9.071276 GATATAATCAAAAGGAGATGGCTGAAA 57.929 33.333 0.00 0.00 0.00 2.69
769 3066 4.140994 TGTTCCGAGGGTAGAAGGAGATAT 60.141 45.833 0.00 0.00 33.89 1.63
780 3077 4.938028 TGGCTATATATGTTCCGAGGGTA 58.062 43.478 0.00 0.00 0.00 3.69
782 3079 3.430929 GCTGGCTATATATGTTCCGAGGG 60.431 52.174 0.00 0.00 0.00 4.30
804 3101 7.931994 GCGATAAGCCTGCCAAATTAAATTGG 61.932 42.308 16.67 16.67 45.42 3.16
805 3102 5.050837 GCGATAAGCCTGCCAAATTAAATTG 60.051 40.000 0.00 0.00 40.81 2.32
806 3103 5.049828 GCGATAAGCCTGCCAAATTAAATT 58.950 37.500 0.00 0.00 40.81 1.82
807 3104 4.620982 GCGATAAGCCTGCCAAATTAAAT 58.379 39.130 0.00 0.00 40.81 1.40
808 3105 4.040445 GCGATAAGCCTGCCAAATTAAA 57.960 40.909 0.00 0.00 40.81 1.52
809 3106 3.708563 GCGATAAGCCTGCCAAATTAA 57.291 42.857 0.00 0.00 40.81 1.40
824 3121 4.124238 CGGTTGGAATTAGGAAAGCGATA 58.876 43.478 0.00 0.00 43.96 2.92
848 3145 6.037098 CGTGACTTTGTTGGTTTGGAATTTA 58.963 36.000 0.00 0.00 0.00 1.40
862 3159 2.504367 AGCCTAATTGCGTGACTTTGT 58.496 42.857 0.00 0.00 36.02 2.83
868 3165 8.462811 TGAATTAAATTAAGCCTAATTGCGTGA 58.537 29.630 1.06 0.00 37.70 4.35
1026 3332 3.631144 CATTGTATGTATTTGCGGCTGG 58.369 45.455 0.00 0.00 0.00 4.85
1027 3333 3.044986 GCATTGTATGTATTTGCGGCTG 58.955 45.455 0.00 0.00 0.00 4.85
1068 3374 4.830826 TCGCTCGATTTGATTAGCTCTA 57.169 40.909 0.00 0.00 32.73 2.43
1069 3375 3.717400 TCGCTCGATTTGATTAGCTCT 57.283 42.857 0.00 0.00 32.73 4.09
1070 3376 4.233789 AGATCGCTCGATTTGATTAGCTC 58.766 43.478 6.22 0.00 34.60 4.09
1090 3402 4.022503 CGATCTGACCATGATTAGCTGAGA 60.023 45.833 0.00 0.00 0.00 3.27
1093 3405 3.324117 CCGATCTGACCATGATTAGCTG 58.676 50.000 0.00 0.00 0.00 4.24
1095 3407 2.072298 GCCGATCTGACCATGATTAGC 58.928 52.381 0.00 0.00 0.00 3.09
1528 3849 0.680280 CTCCCCTTCTTCGACGAGGA 60.680 60.000 5.45 5.45 32.11 3.71
1530 3851 1.668101 CCCTCCCCTTCTTCGACGAG 61.668 65.000 0.00 0.00 0.00 4.18
1804 4139 1.372087 GATCTTGGCCAAGTCGCAGG 61.372 60.000 37.97 17.60 39.38 4.85
1828 4164 2.042404 GAGGCAGAGGGAGAGGCATG 62.042 65.000 0.00 0.00 0.00 4.06
1829 4165 1.765657 GAGGCAGAGGGAGAGGCAT 60.766 63.158 0.00 0.00 0.00 4.40
1830 4166 2.364842 GAGGCAGAGGGAGAGGCA 60.365 66.667 0.00 0.00 0.00 4.75
1831 4167 2.364842 TGAGGCAGAGGGAGAGGC 60.365 66.667 0.00 0.00 0.00 4.70
1832 4168 1.001503 AGTGAGGCAGAGGGAGAGG 59.998 63.158 0.00 0.00 0.00 3.69
1833 4169 1.958902 GCAGTGAGGCAGAGGGAGAG 61.959 65.000 0.00 0.00 0.00 3.20
1834 4170 1.986757 GCAGTGAGGCAGAGGGAGA 60.987 63.158 0.00 0.00 0.00 3.71
1851 4187 5.006746 GCAATAGAACCATGTACAGTACAGC 59.993 44.000 18.30 8.65 42.77 4.40
2016 4352 6.849811 GCACGATTTTCATGTAAGATCTCATG 59.150 38.462 15.18 15.18 41.64 3.07
2032 4368 8.677300 ACATGTATTGAGATTTAGCACGATTTT 58.323 29.630 0.00 0.00 0.00 1.82
2076 5327 2.158871 TGCCTCTACAAGTTTTCGGTGT 60.159 45.455 0.00 0.00 0.00 4.16
2082 5333 1.873591 CTGCGTGCCTCTACAAGTTTT 59.126 47.619 0.00 0.00 0.00 2.43
2116 5367 1.990799 CCGACACGACTGAGCAAATA 58.009 50.000 0.00 0.00 0.00 1.40
2123 5374 3.268965 GAGCTGCCGACACGACTGA 62.269 63.158 0.00 0.00 0.00 3.41
2127 5378 2.989881 AATCGAGCTGCCGACACGA 61.990 57.895 13.83 9.75 41.70 4.35
2141 5392 2.889988 TGGATCACGGCGCAATCG 60.890 61.111 10.83 6.32 39.07 3.34
2148 5399 3.427503 CCAAATACTTTGTGGATCACGGC 60.428 47.826 0.00 0.00 38.98 5.68
2165 5416 1.402107 GCCCCATGCGGAATCCAAAT 61.402 55.000 0.00 0.00 0.00 2.32
2166 5417 2.057408 GCCCCATGCGGAATCCAAA 61.057 57.895 0.00 0.00 0.00 3.28
2174 5425 3.762247 CTTTGTGGCCCCATGCGG 61.762 66.667 0.00 0.00 42.61 5.69
2176 5427 0.108396 AAAACTTTGTGGCCCCATGC 59.892 50.000 0.00 0.00 40.16 4.06
2324 5577 1.821216 TGTTTCCGATGAGGGCTTTC 58.179 50.000 0.00 0.00 41.52 2.62
2334 5588 6.206395 TGTTTGCATATTCATGTTTCCGAT 57.794 33.333 0.00 0.00 34.40 4.18
2369 5623 9.471084 CGGTTATATCTTTTGAACCAAAACTTT 57.529 29.630 3.75 0.00 41.23 2.66
2548 5806 9.052759 GTCAAAGATACAAGAGTTAACAAGGAA 57.947 33.333 8.61 0.00 0.00 3.36
2604 5862 2.654749 CACATCTACCTGTGCTTCGA 57.345 50.000 0.00 0.00 40.03 3.71
2613 5871 6.374417 AATTACTGTTCCACACATCTACCT 57.626 37.500 0.00 0.00 33.76 3.08
2687 5949 6.258727 CGAGCAATCTCCATATACAAACTTGT 59.741 38.462 0.07 0.07 39.34 3.16
2776 6038 5.040635 GGTGGTTGATAAGTGTTGTGTTTG 58.959 41.667 0.00 0.00 0.00 2.93
2801 6063 1.868498 CGTTGGTTGGCTTTAACTCGA 59.132 47.619 0.00 0.00 0.00 4.04
2811 6074 1.200020 CTCCTTCATTCGTTGGTTGGC 59.800 52.381 0.00 0.00 0.00 4.52
2834 6097 9.300681 CATATTACATCCCATGATTAACCACTT 57.699 33.333 0.00 0.00 0.00 3.16
2846 6109 6.708885 ATCAGACCACATATTACATCCCAT 57.291 37.500 0.00 0.00 0.00 4.00
2910 6191 5.132144 TCCCTCAAAGACTAAGGTTTCAAGT 59.868 40.000 0.00 0.00 0.00 3.16
2934 6215 5.233225 AGCATGATTATCGTCGACATTGAT 58.767 37.500 17.16 12.48 0.00 2.57
2949 6231 0.110104 GGCTGCCCTCTAGCATGATT 59.890 55.000 7.66 0.00 43.09 2.57
2954 6236 1.306482 AGAAGGCTGCCCTCTAGCA 60.306 57.895 18.04 0.00 41.90 3.49


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

AutoCloner maintained by Alex Coulton.