Multiple sequence alignment - TraesCS5D01G360900

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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 TraesCS5D01G360900 chr5D 100.000 2312 0 0 1 2312 440376441 440374130 0.000000e+00 4270
1 TraesCS5D01G360900 chr5D 85.897 702 68 24 630 1316 436824460 436823775 0.000000e+00 719
2 TraesCS5D01G360900 chr5D 85.324 695 78 16 630 1314 436349175 436349855 0.000000e+00 697
3 TraesCS5D01G360900 chr5A 91.827 881 40 20 585 1462 556534720 556533869 0.000000e+00 1199
4 TraesCS5D01G360900 chr5A 86.246 698 68 23 635 1316 552078817 552078132 0.000000e+00 732
5 TraesCS5D01G360900 chr5A 90.930 441 25 6 1860 2291 556533548 556533114 1.540000e-161 579
6 TraesCS5D01G360900 chr5B 90.517 928 48 24 599 1522 535715794 535714903 0.000000e+00 1190
7 TraesCS5D01G360900 chr5B 86.187 695 69 20 636 1315 530974451 530973769 0.000000e+00 726
8 TraesCS5D01G360900 chr5B 93.348 466 30 1 1 465 111686895 111686430 0.000000e+00 688
9 TraesCS5D01G360900 chr5B 84.682 581 49 11 1732 2299 535714663 535714110 5.620000e-151 544
10 TraesCS5D01G360900 chr4D 98.236 567 8 2 1 566 64730920 64730355 0.000000e+00 990
11 TraesCS5D01G360900 chr6D 98.217 561 10 0 1 561 81943479 81944039 0.000000e+00 981
12 TraesCS5D01G360900 chr7D 97.354 567 9 2 1 566 422203881 422204442 0.000000e+00 959
13 TraesCS5D01G360900 chr7A 96.460 565 19 1 1 565 158443615 158444178 0.000000e+00 931
14 TraesCS5D01G360900 chrUn 86.532 594 52 23 773 1344 103772343 103771756 1.510000e-176 628
15 TraesCS5D01G360900 chr6B 85.949 548 54 16 771 1315 54877186 54876659 4.310000e-157 564
16 TraesCS5D01G360900 chr6B 84.034 595 60 29 777 1344 55651463 55650877 7.270000e-150 540
17 TraesCS5D01G360900 chr7B 96.073 331 11 2 987 1316 589740539 589740210 2.610000e-149 538
18 TraesCS5D01G360900 chr1B 93.557 357 19 3 987 1339 398836682 398837038 1.570000e-146 529
19 TraesCS5D01G360900 chr1B 91.304 322 28 0 243 564 296671856 296672177 7.580000e-120 440
20 TraesCS5D01G360900 chr1B 91.903 247 17 3 1 245 296658321 296658566 2.200000e-90 342


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 TraesCS5D01G360900 chr5D 440374130 440376441 2311 True 4270 4270 100.0000 1 2312 1 chr5D.!!$R2 2311
1 TraesCS5D01G360900 chr5D 436823775 436824460 685 True 719 719 85.8970 630 1316 1 chr5D.!!$R1 686
2 TraesCS5D01G360900 chr5D 436349175 436349855 680 False 697 697 85.3240 630 1314 1 chr5D.!!$F1 684
3 TraesCS5D01G360900 chr5A 556533114 556534720 1606 True 889 1199 91.3785 585 2291 2 chr5A.!!$R2 1706
4 TraesCS5D01G360900 chr5A 552078132 552078817 685 True 732 732 86.2460 635 1316 1 chr5A.!!$R1 681
5 TraesCS5D01G360900 chr5B 535714110 535715794 1684 True 867 1190 87.5995 599 2299 2 chr5B.!!$R3 1700
6 TraesCS5D01G360900 chr5B 530973769 530974451 682 True 726 726 86.1870 636 1315 1 chr5B.!!$R2 679
7 TraesCS5D01G360900 chr4D 64730355 64730920 565 True 990 990 98.2360 1 566 1 chr4D.!!$R1 565
8 TraesCS5D01G360900 chr6D 81943479 81944039 560 False 981 981 98.2170 1 561 1 chr6D.!!$F1 560
9 TraesCS5D01G360900 chr7D 422203881 422204442 561 False 959 959 97.3540 1 566 1 chr7D.!!$F1 565
10 TraesCS5D01G360900 chr7A 158443615 158444178 563 False 931 931 96.4600 1 565 1 chr7A.!!$F1 564
11 TraesCS5D01G360900 chrUn 103771756 103772343 587 True 628 628 86.5320 773 1344 1 chrUn.!!$R1 571
12 TraesCS5D01G360900 chr6B 54876659 54877186 527 True 564 564 85.9490 771 1315 1 chr6B.!!$R1 544
13 TraesCS5D01G360900 chr6B 55650877 55651463 586 True 540 540 84.0340 777 1344 1 chr6B.!!$R2 567


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
581 587 0.744281 AAAACCAGTTTCGTGGCCTG 59.256 50.0 3.32 0.0 41.9 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 1517 0.106918 AAGACGGGAGCAAACACCAA 60.107 50.0 0.0 0.0 0.0 3.67 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
64 65 5.692115 AACCAAAGGAAGGTTTTGTCAAT 57.308 34.783 0.00 0.00 46.85 2.57
580 586 1.480789 AAAAACCAGTTTCGTGGCCT 58.519 45.000 3.32 0.00 41.90 5.19
581 587 0.744281 AAAACCAGTTTCGTGGCCTG 59.256 50.000 3.32 0.00 41.90 4.85
582 588 1.734388 AAACCAGTTTCGTGGCCTGC 61.734 55.000 3.32 0.00 41.90 4.85
583 589 2.594303 CCAGTTTCGTGGCCTGCA 60.594 61.111 3.32 0.00 0.00 4.41
718 731 1.032657 ATCCACCCAGACGAGACTCG 61.033 60.000 22.97 22.97 46.93 4.18
977 1040 0.926293 ATCCAATCCAATCCCACCGT 59.074 50.000 0.00 0.00 0.00 4.83
983 1046 1.776662 TCCAATCCCACCGTAGAGAG 58.223 55.000 0.00 0.00 0.00 3.20
994 1060 1.737201 GTAGAGAGGGGAGAAGCGC 59.263 63.158 0.00 0.00 0.00 5.92
1324 1409 2.444256 GGCTAGGCCGAGGGTTCAT 61.444 63.158 15.29 0.00 39.62 2.57
1368 1457 0.656785 CCGACCGAGAGTAGTAGTGC 59.343 60.000 0.00 0.00 0.00 4.40
1409 1498 2.315386 GGTTCGTGGTTCTCCGTGC 61.315 63.158 0.00 0.00 36.30 5.34
1411 1500 1.144276 TTCGTGGTTCTCCGTGCAA 59.856 52.632 0.00 0.00 36.30 4.08
1413 1502 1.300620 CGTGGTTCTCCGTGCAAGA 60.301 57.895 0.00 0.00 36.30 3.02
1427 1516 1.946745 GCAAGAGCAGTGGTATCTCC 58.053 55.000 0.00 0.00 41.58 3.71
1428 1517 1.484240 GCAAGAGCAGTGGTATCTCCT 59.516 52.381 0.00 0.00 41.58 3.69
1435 1525 2.290323 GCAGTGGTATCTCCTTGGTGTT 60.290 50.000 0.00 0.00 37.07 3.32
1462 1552 1.136141 CGTCTTGTGAGCTGATGTTGC 60.136 52.381 0.00 0.00 0.00 4.17
1463 1553 2.149578 GTCTTGTGAGCTGATGTTGCT 58.850 47.619 0.00 0.00 44.24 3.91
1464 1554 2.095869 GTCTTGTGAGCTGATGTTGCTG 60.096 50.000 0.00 0.00 41.30 4.41
1465 1555 1.878088 CTTGTGAGCTGATGTTGCTGT 59.122 47.619 0.00 0.00 41.30 4.40
1466 1556 1.971481 TGTGAGCTGATGTTGCTGTT 58.029 45.000 0.00 0.00 41.30 3.16
1467 1557 1.605232 TGTGAGCTGATGTTGCTGTTG 59.395 47.619 0.00 0.00 41.30 3.33
1468 1558 1.605710 GTGAGCTGATGTTGCTGTTGT 59.394 47.619 0.00 0.00 41.30 3.32
1469 1559 2.807967 GTGAGCTGATGTTGCTGTTGTA 59.192 45.455 0.00 0.00 41.30 2.41
1470 1560 3.069289 TGAGCTGATGTTGCTGTTGTAG 58.931 45.455 0.00 0.00 41.30 2.74
1471 1561 3.244181 TGAGCTGATGTTGCTGTTGTAGA 60.244 43.478 0.00 0.00 41.30 2.59
1472 1562 3.332919 AGCTGATGTTGCTGTTGTAGAG 58.667 45.455 0.00 0.00 39.56 2.43
1473 1563 3.007290 AGCTGATGTTGCTGTTGTAGAGA 59.993 43.478 0.00 0.00 39.56 3.10
1474 1564 3.937706 GCTGATGTTGCTGTTGTAGAGAT 59.062 43.478 0.00 0.00 0.00 2.75
1475 1565 4.201792 GCTGATGTTGCTGTTGTAGAGATG 60.202 45.833 0.00 0.00 0.00 2.90
1487 1577 6.925211 TGTTGTAGAGATGTACTGGAAGAAG 58.075 40.000 0.00 0.00 37.43 2.85
1507 1597 3.667360 AGTTTGGAATGGAAATTGCAGC 58.333 40.909 0.00 0.00 33.53 5.25
1510 1600 2.250031 TGGAATGGAAATTGCAGCAGT 58.750 42.857 0.00 0.00 0.00 4.40
1522 1612 3.153369 TGCAGCAGTTTATCCCTGAAA 57.847 42.857 0.00 0.00 31.38 2.69
1524 1614 4.088634 TGCAGCAGTTTATCCCTGAAATT 58.911 39.130 0.00 0.00 31.38 1.82
1527 1617 5.105595 GCAGCAGTTTATCCCTGAAATTCTT 60.106 40.000 0.00 0.00 31.38 2.52
1528 1618 6.558909 CAGCAGTTTATCCCTGAAATTCTTC 58.441 40.000 0.00 0.00 31.38 2.87
1529 1619 6.376581 CAGCAGTTTATCCCTGAAATTCTTCT 59.623 38.462 0.00 0.00 32.33 2.85
1530 1620 6.376581 AGCAGTTTATCCCTGAAATTCTTCTG 59.623 38.462 0.00 0.00 32.33 3.02
1533 1623 8.404000 CAGTTTATCCCTGAAATTCTTCTGATG 58.596 37.037 0.00 0.00 33.51 3.07
1535 1625 7.870509 TTATCCCTGAAATTCTTCTGATGTG 57.129 36.000 0.00 0.00 33.51 3.21
1536 1626 5.503634 TCCCTGAAATTCTTCTGATGTGA 57.496 39.130 0.00 0.00 33.51 3.58
1537 1627 5.879763 TCCCTGAAATTCTTCTGATGTGAA 58.120 37.500 0.00 0.00 33.51 3.18
1538 1628 6.487828 TCCCTGAAATTCTTCTGATGTGAAT 58.512 36.000 0.00 0.00 33.51 2.57
1539 1629 6.376299 TCCCTGAAATTCTTCTGATGTGAATG 59.624 38.462 0.00 0.00 33.51 2.67
1540 1630 6.034591 CCTGAAATTCTTCTGATGTGAATGC 58.965 40.000 0.00 0.00 33.51 3.56
1543 1633 6.209986 TGAAATTCTTCTGATGTGAATGCCTT 59.790 34.615 0.00 0.00 31.70 4.35
1544 1634 5.831702 ATTCTTCTGATGTGAATGCCTTC 57.168 39.130 0.00 0.00 0.00 3.46
1545 1635 3.614092 TCTTCTGATGTGAATGCCTTCC 58.386 45.455 0.00 0.00 0.00 3.46
1546 1636 3.009363 TCTTCTGATGTGAATGCCTTCCA 59.991 43.478 0.00 0.00 0.00 3.53
1547 1637 2.995283 TCTGATGTGAATGCCTTCCAG 58.005 47.619 0.00 0.22 0.00 3.86
1549 1639 2.422479 CTGATGTGAATGCCTTCCAGTG 59.578 50.000 0.00 0.00 0.00 3.66
1551 1641 1.236616 TGTGAATGCCTTCCAGTGCG 61.237 55.000 0.00 0.00 0.00 5.34
1552 1642 1.073025 TGAATGCCTTCCAGTGCGT 59.927 52.632 0.00 0.00 0.00 5.24
1553 1643 0.537143 TGAATGCCTTCCAGTGCGTT 60.537 50.000 0.00 0.00 39.31 4.84
1555 1645 1.577328 AATGCCTTCCAGTGCGTTCG 61.577 55.000 0.00 0.00 31.26 3.95
1556 1646 4.090057 GCCTTCCAGTGCGTTCGC 62.090 66.667 10.34 10.34 0.00 4.70
1557 1647 2.357517 CCTTCCAGTGCGTTCGCT 60.358 61.111 17.63 0.00 0.00 4.93
1565 1655 0.385974 AGTGCGTTCGCTGATTTTGC 60.386 50.000 17.63 0.00 0.00 3.68
1566 1656 0.660005 GTGCGTTCGCTGATTTTGCA 60.660 50.000 17.63 0.00 0.00 4.08
1568 1658 1.335780 TGCGTTCGCTGATTTTGCATT 60.336 42.857 17.63 0.00 0.00 3.56
1569 1659 1.318491 GCGTTCGCTGATTTTGCATTC 59.682 47.619 9.99 0.00 0.00 2.67
1570 1660 2.855180 CGTTCGCTGATTTTGCATTCT 58.145 42.857 0.00 0.00 0.00 2.40
1571 1661 2.842485 CGTTCGCTGATTTTGCATTCTC 59.158 45.455 0.00 0.00 0.00 2.87
1572 1662 3.425359 CGTTCGCTGATTTTGCATTCTCT 60.425 43.478 0.00 0.00 0.00 3.10
1573 1663 3.752412 TCGCTGATTTTGCATTCTCTG 57.248 42.857 0.00 0.00 0.00 3.35
1593 1683 3.492353 CCCCATCCATCGCCTGGT 61.492 66.667 0.00 0.00 46.08 4.00
1594 1684 2.111878 CCCATCCATCGCCTGGTC 59.888 66.667 0.00 0.00 46.08 4.02
1595 1685 2.446848 CCCATCCATCGCCTGGTCT 61.447 63.158 0.00 0.00 46.08 3.85
1607 1697 1.516110 CCTGGTCTGATTCCCCATCT 58.484 55.000 0.00 0.00 32.34 2.90
1608 1698 1.142465 CCTGGTCTGATTCCCCATCTG 59.858 57.143 0.00 0.00 32.34 2.90
1609 1699 2.121948 CTGGTCTGATTCCCCATCTGA 58.878 52.381 0.00 0.00 37.48 3.27
1610 1700 2.507058 CTGGTCTGATTCCCCATCTGAA 59.493 50.000 0.00 0.00 40.50 3.02
1611 1701 2.507058 TGGTCTGATTCCCCATCTGAAG 59.493 50.000 0.00 0.00 40.50 3.02
1623 1795 3.260380 CCCATCTGAAGTCTCTGAACTGT 59.740 47.826 0.00 0.00 33.72 3.55
1628 1800 5.595885 TCTGAAGTCTCTGAACTGTGAAAG 58.404 41.667 0.00 0.00 0.00 2.62
1629 1801 4.697514 TGAAGTCTCTGAACTGTGAAAGG 58.302 43.478 0.00 0.00 0.00 3.11
1634 1806 4.276926 GTCTCTGAACTGTGAAAGGCATTT 59.723 41.667 0.00 0.00 0.00 2.32
1644 1816 4.122046 GTGAAAGGCATTTGAGCTGTTTT 58.878 39.130 0.00 0.00 34.17 2.43
1645 1817 5.163468 TGTGAAAGGCATTTGAGCTGTTTTA 60.163 36.000 0.00 0.00 34.17 1.52
1646 1818 5.928264 GTGAAAGGCATTTGAGCTGTTTTAT 59.072 36.000 0.00 0.00 34.17 1.40
1649 1821 3.448660 AGGCATTTGAGCTGTTTTATCCC 59.551 43.478 0.00 0.00 34.17 3.85
1650 1822 3.448660 GGCATTTGAGCTGTTTTATCCCT 59.551 43.478 0.00 0.00 34.17 4.20
1651 1823 4.427312 GCATTTGAGCTGTTTTATCCCTG 58.573 43.478 0.00 0.00 0.00 4.45
1652 1824 4.158394 GCATTTGAGCTGTTTTATCCCTGA 59.842 41.667 0.00 0.00 0.00 3.86
1653 1825 5.336690 GCATTTGAGCTGTTTTATCCCTGAA 60.337 40.000 0.00 0.00 0.00 3.02
1654 1826 6.628844 GCATTTGAGCTGTTTTATCCCTGAAT 60.629 38.462 0.00 0.00 0.00 2.57
1655 1827 6.916360 TTTGAGCTGTTTTATCCCTGAATT 57.084 33.333 0.00 0.00 0.00 2.17
1656 1828 6.515272 TTGAGCTGTTTTATCCCTGAATTC 57.485 37.500 0.00 0.00 0.00 2.17
1659 1831 6.375455 TGAGCTGTTTTATCCCTGAATTCTTC 59.625 38.462 7.05 0.00 0.00 2.87
1660 1832 5.654209 AGCTGTTTTATCCCTGAATTCTTCC 59.346 40.000 7.05 0.00 0.00 3.46
1661 1833 5.654209 GCTGTTTTATCCCTGAATTCTTCCT 59.346 40.000 7.05 0.00 0.00 3.36
1662 1834 6.153510 GCTGTTTTATCCCTGAATTCTTCCTT 59.846 38.462 7.05 0.00 0.00 3.36
1663 1835 7.629437 GCTGTTTTATCCCTGAATTCTTCCTTC 60.629 40.741 7.05 0.00 0.00 3.46
1664 1836 7.237982 TGTTTTATCCCTGAATTCTTCCTTCA 58.762 34.615 7.05 0.00 0.00 3.02
1665 1837 7.728083 TGTTTTATCCCTGAATTCTTCCTTCAA 59.272 33.333 7.05 0.00 32.53 2.69
1666 1838 8.753133 GTTTTATCCCTGAATTCTTCCTTCAAT 58.247 33.333 7.05 0.00 32.53 2.57
1667 1839 8.525290 TTTATCCCTGAATTCTTCCTTCAATC 57.475 34.615 7.05 0.00 32.53 2.67
1668 1840 5.786121 TCCCTGAATTCTTCCTTCAATCT 57.214 39.130 7.05 0.00 32.53 2.40
1669 1841 5.749462 TCCCTGAATTCTTCCTTCAATCTC 58.251 41.667 7.05 0.00 32.53 2.75
1670 1842 5.490357 TCCCTGAATTCTTCCTTCAATCTCT 59.510 40.000 7.05 0.00 32.53 3.10
1671 1843 6.012157 TCCCTGAATTCTTCCTTCAATCTCTT 60.012 38.462 7.05 0.00 32.53 2.85
1672 1844 6.095160 CCCTGAATTCTTCCTTCAATCTCTTG 59.905 42.308 7.05 0.00 32.53 3.02
1673 1845 6.404513 CCTGAATTCTTCCTTCAATCTCTTGC 60.405 42.308 7.05 0.00 32.53 4.01
1674 1846 6.243900 TGAATTCTTCCTTCAATCTCTTGCT 58.756 36.000 7.05 0.00 32.11 3.91
1675 1847 6.373774 TGAATTCTTCCTTCAATCTCTTGCTC 59.626 38.462 7.05 0.00 32.11 4.26
1676 1848 5.495926 TTCTTCCTTCAATCTCTTGCTCT 57.504 39.130 0.00 0.00 32.11 4.09
1677 1849 4.829968 TCTTCCTTCAATCTCTTGCTCTG 58.170 43.478 0.00 0.00 32.11 3.35
1678 1850 4.285517 TCTTCCTTCAATCTCTTGCTCTGT 59.714 41.667 0.00 0.00 32.11 3.41
1679 1851 4.630644 TCCTTCAATCTCTTGCTCTGTT 57.369 40.909 0.00 0.00 32.11 3.16
1680 1852 4.321718 TCCTTCAATCTCTTGCTCTGTTG 58.678 43.478 0.00 0.00 32.11 3.33
1681 1853 3.119919 CCTTCAATCTCTTGCTCTGTTGC 60.120 47.826 0.00 0.00 32.11 4.17
1682 1854 3.413846 TCAATCTCTTGCTCTGTTGCT 57.586 42.857 0.00 0.00 32.11 3.91
1683 1855 3.072211 TCAATCTCTTGCTCTGTTGCTG 58.928 45.455 0.00 0.00 32.11 4.41
1684 1856 2.812591 CAATCTCTTGCTCTGTTGCTGT 59.187 45.455 0.00 0.00 0.00 4.40
1685 1857 1.875009 TCTCTTGCTCTGTTGCTGTG 58.125 50.000 0.00 0.00 0.00 3.66
1686 1858 0.873054 CTCTTGCTCTGTTGCTGTGG 59.127 55.000 0.00 0.00 0.00 4.17
1687 1859 0.469494 TCTTGCTCTGTTGCTGTGGA 59.531 50.000 0.00 0.00 0.00 4.02
1688 1860 1.072806 TCTTGCTCTGTTGCTGTGGAT 59.927 47.619 0.00 0.00 0.00 3.41
1689 1861 1.199327 CTTGCTCTGTTGCTGTGGATG 59.801 52.381 0.00 0.00 0.00 3.51
1690 1862 0.109153 TGCTCTGTTGCTGTGGATGT 59.891 50.000 0.00 0.00 0.00 3.06
1691 1863 0.520404 GCTCTGTTGCTGTGGATGTG 59.480 55.000 0.00 0.00 0.00 3.21
1692 1864 0.520404 CTCTGTTGCTGTGGATGTGC 59.480 55.000 0.00 0.00 0.00 4.57
1693 1865 1.208358 CTGTTGCTGTGGATGTGCG 59.792 57.895 0.00 0.00 0.00 5.34
1694 1866 2.126734 GTTGCTGTGGATGTGCGC 60.127 61.111 0.00 0.00 0.00 6.09
1695 1867 3.725459 TTGCTGTGGATGTGCGCG 61.725 61.111 0.00 0.00 0.00 6.86
1700 1872 4.541482 GTGGATGTGCGCGGCATG 62.541 66.667 19.61 0.00 41.91 4.06
1703 1875 3.271586 GATGTGCGCGGCATGCTA 61.272 61.111 18.92 0.00 41.91 3.49
1704 1876 2.822758 GATGTGCGCGGCATGCTAA 61.823 57.895 18.92 0.00 41.91 3.09
1705 1877 2.971744 GATGTGCGCGGCATGCTAAC 62.972 60.000 18.92 9.39 41.91 2.34
1706 1878 3.499737 GTGCGCGGCATGCTAACT 61.500 61.111 18.92 0.00 41.91 2.24
1707 1879 2.745884 TGCGCGGCATGCTAACTT 60.746 55.556 18.92 0.00 43.27 2.66
1708 1880 2.331893 TGCGCGGCATGCTAACTTT 61.332 52.632 18.92 0.00 43.27 2.66
1711 1883 0.523335 CGCGGCATGCTAACTTTTCC 60.523 55.000 18.92 0.00 43.27 3.13
1718 1890 3.524541 CATGCTAACTTTTCCCCATTGC 58.475 45.455 0.00 0.00 0.00 3.56
1720 1892 1.207089 GCTAACTTTTCCCCATTGCCC 59.793 52.381 0.00 0.00 0.00 5.36
1738 1940 1.734465 CCCGTCTCTGAATTTCAGTGC 59.266 52.381 22.44 15.49 44.58 4.40
1739 1941 2.613977 CCCGTCTCTGAATTTCAGTGCT 60.614 50.000 22.44 0.00 44.58 4.40
1740 1942 3.368427 CCCGTCTCTGAATTTCAGTGCTA 60.368 47.826 22.44 5.95 44.58 3.49
1755 1957 3.118112 CAGTGCTATTCTGAACCATCCCT 60.118 47.826 0.00 0.00 35.20 4.20
1760 1962 2.905415 TTCTGAACCATCCCTGCATT 57.095 45.000 0.00 0.00 0.00 3.56
1762 1964 2.726821 TCTGAACCATCCCTGCATTTC 58.273 47.619 0.00 0.00 0.00 2.17
1767 1969 1.103398 CCATCCCTGCATTTCCGTCC 61.103 60.000 0.00 0.00 0.00 4.79
1772 1974 1.376683 CTGCATTTCCGTCCCCGAA 60.377 57.895 0.00 0.00 35.63 4.30
1773 1975 0.748005 CTGCATTTCCGTCCCCGAAT 60.748 55.000 0.00 0.00 35.63 3.34
1779 1981 1.534336 TTCCGTCCCCGAATCGTGAA 61.534 55.000 0.82 0.00 35.63 3.18
1804 2009 3.012518 CCCACTTCGAGCTGATTCAAAT 58.987 45.455 0.00 0.00 0.00 2.32
1806 2011 4.437930 CCCACTTCGAGCTGATTCAAATTC 60.438 45.833 0.00 0.00 0.00 2.17
1809 2014 4.761739 ACTTCGAGCTGATTCAAATTCCAA 59.238 37.500 0.00 0.00 0.00 3.53
1815 2020 6.363167 AGCTGATTCAAATTCCAATTCCAA 57.637 33.333 0.00 0.00 0.00 3.53
1820 2025 7.687388 TGATTCAAATTCCAATTCCAAATCCA 58.313 30.769 0.00 0.00 0.00 3.41
1825 2030 6.736110 AATTCCAATTCCAAATCCATCGAT 57.264 33.333 0.00 0.00 0.00 3.59
1827 2032 5.518848 TCCAATTCCAAATCCATCGATTG 57.481 39.130 0.00 0.00 38.75 2.67
1845 2060 2.927856 ACACCGATCCACCCAGCA 60.928 61.111 0.00 0.00 0.00 4.41
1847 2062 4.101448 ACCGATCCACCCAGCAGC 62.101 66.667 0.00 0.00 0.00 5.25
1848 2063 4.864334 CCGATCCACCCAGCAGCC 62.864 72.222 0.00 0.00 0.00 4.85
1850 2065 4.864334 GATCCACCCAGCAGCCGG 62.864 72.222 0.00 0.00 0.00 6.13
1854 2069 4.020617 CACCCAGCAGCCGGAGAA 62.021 66.667 5.05 0.00 0.00 2.87
1855 2070 4.021925 ACCCAGCAGCCGGAGAAC 62.022 66.667 5.05 0.00 0.00 3.01
1856 2071 4.785453 CCCAGCAGCCGGAGAACC 62.785 72.222 5.05 0.00 0.00 3.62
1925 2148 2.101640 AGCCCAAAACCTGTTTCCAT 57.898 45.000 0.00 0.00 31.45 3.41
1926 2149 3.252554 AGCCCAAAACCTGTTTCCATA 57.747 42.857 0.00 0.00 31.45 2.74
1969 2192 3.416156 GAGGTGCATTCTGTTCTCCTTT 58.584 45.455 0.00 0.00 0.00 3.11
1991 2214 0.233848 CCCTTCGTTTTCGTTCACGG 59.766 55.000 0.00 0.00 44.46 4.94
2009 2232 1.034292 GGCCCATGACTCTTGCTTCC 61.034 60.000 0.00 0.00 0.00 3.46
2139 2363 2.107141 CCTCTGCCCCGAATCGAC 59.893 66.667 3.36 0.00 0.00 4.20
2246 2470 5.812642 CAGCTTCGATTTGGTAGTTCATACT 59.187 40.000 0.00 0.00 38.44 2.12
2247 2471 6.978659 CAGCTTCGATTTGGTAGTTCATACTA 59.021 38.462 0.00 0.00 35.78 1.82
2273 2497 4.996758 AGCTTTATTGGTTGCAATTTGGAC 59.003 37.500 0.59 0.00 0.00 4.02
2295 2519 1.067821 CGCTACCAATCAGGACTCCTC 59.932 57.143 0.00 0.00 41.22 3.71
2299 2523 4.345257 GCTACCAATCAGGACTCCTCATAA 59.655 45.833 0.00 0.00 41.22 1.90
2300 2524 4.762289 ACCAATCAGGACTCCTCATAAC 57.238 45.455 0.00 0.00 41.22 1.89
2301 2525 4.104086 ACCAATCAGGACTCCTCATAACA 58.896 43.478 0.00 0.00 41.22 2.41
2302 2526 4.723789 ACCAATCAGGACTCCTCATAACAT 59.276 41.667 0.00 0.00 41.22 2.71
2303 2527 5.192522 ACCAATCAGGACTCCTCATAACATT 59.807 40.000 0.00 0.00 41.22 2.71
2304 2528 6.125029 CCAATCAGGACTCCTCATAACATTT 58.875 40.000 0.00 0.00 41.22 2.32
2305 2529 6.039047 CCAATCAGGACTCCTCATAACATTTG 59.961 42.308 0.00 0.00 41.22 2.32
2306 2530 6.566079 ATCAGGACTCCTCATAACATTTGA 57.434 37.500 0.00 0.00 0.00 2.69
2307 2531 6.373005 TCAGGACTCCTCATAACATTTGAA 57.627 37.500 0.00 0.00 0.00 2.69
2308 2532 6.173339 TCAGGACTCCTCATAACATTTGAAC 58.827 40.000 0.00 0.00 0.00 3.18
2309 2533 6.013379 TCAGGACTCCTCATAACATTTGAACT 60.013 38.462 0.00 0.00 0.00 3.01
2310 2534 6.093219 CAGGACTCCTCATAACATTTGAACTG 59.907 42.308 0.00 0.00 0.00 3.16
2311 2535 5.940470 GGACTCCTCATAACATTTGAACTGT 59.060 40.000 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 3.687698 GGAAGGCTGCGTCAAAGTTAATA 59.312 43.478 0.00 0.00 0.00 0.98
482 483 4.323417 ACCAAGTCGCATACAAATTCTGA 58.677 39.130 0.00 0.00 0.00 3.27
566 572 2.594303 TGCAGGCCACGAAACTGG 60.594 61.111 5.01 0.00 32.98 4.00
567 573 2.639286 GTGCAGGCCACGAAACTG 59.361 61.111 5.01 0.00 34.22 3.16
574 580 3.360340 GAGCTGTGTGCAGGCCAC 61.360 66.667 5.01 0.00 45.94 5.01
575 581 3.876236 TGAGCTGTGTGCAGGCCA 61.876 61.111 5.01 0.00 45.94 5.36
576 582 3.360340 GTGAGCTGTGTGCAGGCC 61.360 66.667 0.00 0.00 45.94 5.19
577 583 2.281345 AGTGAGCTGTGTGCAGGC 60.281 61.111 0.00 0.00 45.94 4.85
578 584 1.964891 CCAGTGAGCTGTGTGCAGG 60.965 63.158 0.00 0.00 45.94 4.85
579 585 2.614446 GCCAGTGAGCTGTGTGCAG 61.614 63.158 0.00 0.00 45.94 4.41
580 586 2.592574 GCCAGTGAGCTGTGTGCA 60.593 61.111 0.00 0.00 45.94 4.57
581 587 3.360340 GGCCAGTGAGCTGTGTGC 61.360 66.667 0.00 0.00 41.02 4.57
582 588 2.111669 TGGCCAGTGAGCTGTGTG 59.888 61.111 0.00 0.00 41.02 3.82
583 589 2.111878 GTGGCCAGTGAGCTGTGT 59.888 61.111 5.11 0.00 41.02 3.72
602 608 2.657237 GGAGACTGTCGGTGTGGG 59.343 66.667 1.52 0.00 0.00 4.61
800 816 2.122954 GAGGAGTGGGGGTGGAGT 59.877 66.667 0.00 0.00 0.00 3.85
977 1040 1.824329 CGCGCTTCTCCCCTCTCTA 60.824 63.158 5.56 0.00 0.00 2.43
1320 1405 1.299392 CGCGAGCTGGATCGATGAA 60.299 57.895 12.42 0.00 45.56 2.57
1321 1406 2.186826 TCGCGAGCTGGATCGATGA 61.187 57.895 3.71 6.05 45.56 2.92
1324 1409 4.237809 CGTCGCGAGCTGGATCGA 62.238 66.667 10.24 0.00 45.56 3.59
1368 1457 7.172342 ACCCTAGACAGCAACTAGATAGATAG 58.828 42.308 0.00 0.00 39.48 2.08
1409 1498 3.529533 CAAGGAGATACCACTGCTCTTG 58.470 50.000 0.00 0.00 42.04 3.02
1411 1500 2.114616 CCAAGGAGATACCACTGCTCT 58.885 52.381 0.00 0.00 42.04 4.09
1413 1502 1.556911 CACCAAGGAGATACCACTGCT 59.443 52.381 0.00 0.00 42.04 4.24
1420 1509 3.010420 GGAGCAAACACCAAGGAGATAC 58.990 50.000 0.00 0.00 0.00 2.24
1422 1511 1.272147 GGGAGCAAACACCAAGGAGAT 60.272 52.381 0.00 0.00 0.00 2.75
1423 1512 0.110486 GGGAGCAAACACCAAGGAGA 59.890 55.000 0.00 0.00 0.00 3.71
1424 1513 1.237285 CGGGAGCAAACACCAAGGAG 61.237 60.000 0.00 0.00 0.00 3.69
1425 1514 1.228124 CGGGAGCAAACACCAAGGA 60.228 57.895 0.00 0.00 0.00 3.36
1426 1515 1.515521 GACGGGAGCAAACACCAAGG 61.516 60.000 0.00 0.00 0.00 3.61
1427 1516 0.535102 AGACGGGAGCAAACACCAAG 60.535 55.000 0.00 0.00 0.00 3.61
1428 1517 0.106918 AAGACGGGAGCAAACACCAA 60.107 50.000 0.00 0.00 0.00 3.67
1462 1552 6.516739 TCTTCCAGTACATCTCTACAACAG 57.483 41.667 0.00 0.00 0.00 3.16
1463 1553 6.493802 ACTTCTTCCAGTACATCTCTACAACA 59.506 38.462 0.00 0.00 0.00 3.33
1464 1554 6.926313 ACTTCTTCCAGTACATCTCTACAAC 58.074 40.000 0.00 0.00 0.00 3.32
1465 1555 7.540474 AACTTCTTCCAGTACATCTCTACAA 57.460 36.000 0.00 0.00 0.00 2.41
1466 1556 7.378966 CAAACTTCTTCCAGTACATCTCTACA 58.621 38.462 0.00 0.00 0.00 2.74
1467 1557 6.814146 CCAAACTTCTTCCAGTACATCTCTAC 59.186 42.308 0.00 0.00 0.00 2.59
1468 1558 6.724441 TCCAAACTTCTTCCAGTACATCTCTA 59.276 38.462 0.00 0.00 0.00 2.43
1469 1559 5.544176 TCCAAACTTCTTCCAGTACATCTCT 59.456 40.000 0.00 0.00 0.00 3.10
1470 1560 5.794894 TCCAAACTTCTTCCAGTACATCTC 58.205 41.667 0.00 0.00 0.00 2.75
1471 1561 5.825593 TCCAAACTTCTTCCAGTACATCT 57.174 39.130 0.00 0.00 0.00 2.90
1472 1562 6.127897 CCATTCCAAACTTCTTCCAGTACATC 60.128 42.308 0.00 0.00 0.00 3.06
1473 1563 5.711976 CCATTCCAAACTTCTTCCAGTACAT 59.288 40.000 0.00 0.00 0.00 2.29
1474 1564 5.070001 CCATTCCAAACTTCTTCCAGTACA 58.930 41.667 0.00 0.00 0.00 2.90
1475 1565 5.313712 TCCATTCCAAACTTCTTCCAGTAC 58.686 41.667 0.00 0.00 0.00 2.73
1487 1577 3.401182 TGCTGCAATTTCCATTCCAAAC 58.599 40.909 0.00 0.00 0.00 2.93
1507 1597 7.928307 TCAGAAGAATTTCAGGGATAAACTG 57.072 36.000 0.00 0.00 35.70 3.16
1510 1600 8.108999 TCACATCAGAAGAATTTCAGGGATAAA 58.891 33.333 0.00 0.00 35.70 1.40
1522 1612 4.643784 GGAAGGCATTCACATCAGAAGAAT 59.356 41.667 13.81 0.00 37.15 2.40
1524 1614 3.009363 TGGAAGGCATTCACATCAGAAGA 59.991 43.478 13.81 0.00 37.15 2.87
1527 1617 2.306805 ACTGGAAGGCATTCACATCAGA 59.693 45.455 17.93 0.00 39.30 3.27
1528 1618 2.422479 CACTGGAAGGCATTCACATCAG 59.578 50.000 13.81 12.64 39.30 2.90
1529 1619 2.439409 CACTGGAAGGCATTCACATCA 58.561 47.619 13.81 0.54 39.30 3.07
1530 1620 1.133790 GCACTGGAAGGCATTCACATC 59.866 52.381 13.81 0.00 39.30 3.06
1533 1623 1.237285 ACGCACTGGAAGGCATTCAC 61.237 55.000 13.81 3.15 39.30 3.18
1535 1625 0.169009 GAACGCACTGGAAGGCATTC 59.831 55.000 1.60 1.60 39.30 2.67
1536 1626 1.577328 CGAACGCACTGGAAGGCATT 61.577 55.000 0.00 0.00 39.30 3.56
1537 1627 2.034879 CGAACGCACTGGAAGGCAT 61.035 57.895 0.00 0.00 39.30 4.40
1538 1628 2.664851 CGAACGCACTGGAAGGCA 60.665 61.111 0.00 0.00 39.30 4.75
1539 1629 4.090057 GCGAACGCACTGGAAGGC 62.090 66.667 14.26 0.00 39.30 4.35
1540 1630 2.357517 AGCGAACGCACTGGAAGG 60.358 61.111 20.66 0.00 44.88 3.46
1543 1633 0.602638 AAATCAGCGAACGCACTGGA 60.603 50.000 20.66 12.31 44.88 3.86
1544 1634 0.238289 AAAATCAGCGAACGCACTGG 59.762 50.000 20.66 7.70 44.88 4.00
1545 1635 1.321016 CAAAATCAGCGAACGCACTG 58.679 50.000 20.66 11.37 44.88 3.66
1546 1636 0.385974 GCAAAATCAGCGAACGCACT 60.386 50.000 20.66 0.00 44.88 4.40
1547 1637 0.660005 TGCAAAATCAGCGAACGCAC 60.660 50.000 20.66 1.37 44.88 5.34
1549 1639 1.318491 GAATGCAAAATCAGCGAACGC 59.682 47.619 11.31 11.31 42.33 4.84
1551 1641 3.850273 CAGAGAATGCAAAATCAGCGAAC 59.150 43.478 0.00 0.00 33.85 3.95
1552 1642 4.087510 CAGAGAATGCAAAATCAGCGAA 57.912 40.909 0.00 0.00 33.85 4.70
1553 1643 3.752412 CAGAGAATGCAAAATCAGCGA 57.248 42.857 0.00 0.00 33.85 4.93
1584 1674 1.700042 GGGGAATCAGACCAGGCGAT 61.700 60.000 0.00 0.00 0.00 4.58
1585 1675 2.367202 GGGGAATCAGACCAGGCGA 61.367 63.158 0.00 0.00 0.00 5.54
1586 1676 1.987807 ATGGGGAATCAGACCAGGCG 61.988 60.000 0.00 0.00 37.75 5.52
1588 1678 1.142465 CAGATGGGGAATCAGACCAGG 59.858 57.143 0.00 0.00 37.75 4.45
1590 1680 2.268796 TCAGATGGGGAATCAGACCA 57.731 50.000 0.00 0.00 37.81 4.02
1591 1681 2.507471 ACTTCAGATGGGGAATCAGACC 59.493 50.000 0.00 0.00 37.81 3.85
1592 1682 3.454082 AGACTTCAGATGGGGAATCAGAC 59.546 47.826 0.00 0.00 37.81 3.51
1593 1683 3.708631 GAGACTTCAGATGGGGAATCAGA 59.291 47.826 0.00 0.00 37.81 3.27
1594 1684 3.710677 AGAGACTTCAGATGGGGAATCAG 59.289 47.826 0.00 0.00 37.81 2.90
1595 1685 3.453717 CAGAGACTTCAGATGGGGAATCA 59.546 47.826 0.00 0.00 37.81 2.57
1607 1697 4.697514 CCTTTCACAGTTCAGAGACTTCA 58.302 43.478 0.00 0.00 0.00 3.02
1608 1698 3.496507 GCCTTTCACAGTTCAGAGACTTC 59.503 47.826 0.00 0.00 0.00 3.01
1609 1699 3.118261 TGCCTTTCACAGTTCAGAGACTT 60.118 43.478 0.00 0.00 0.00 3.01
1610 1700 2.435805 TGCCTTTCACAGTTCAGAGACT 59.564 45.455 0.00 0.00 0.00 3.24
1611 1701 2.838736 TGCCTTTCACAGTTCAGAGAC 58.161 47.619 0.00 0.00 0.00 3.36
1623 1795 4.405116 AAAACAGCTCAAATGCCTTTCA 57.595 36.364 0.00 0.00 0.00 2.69
1628 1800 3.448660 AGGGATAAAACAGCTCAAATGCC 59.551 43.478 0.00 0.00 0.00 4.40
1629 1801 4.158394 TCAGGGATAAAACAGCTCAAATGC 59.842 41.667 0.00 0.00 0.00 3.56
1634 1806 5.819991 AGAATTCAGGGATAAAACAGCTCA 58.180 37.500 8.44 0.00 0.00 4.26
1651 1823 6.598850 AGAGCAAGAGATTGAAGGAAGAATTC 59.401 38.462 0.00 0.00 46.67 2.17
1652 1824 6.374894 CAGAGCAAGAGATTGAAGGAAGAATT 59.625 38.462 0.00 0.00 0.00 2.17
1653 1825 5.881443 CAGAGCAAGAGATTGAAGGAAGAAT 59.119 40.000 0.00 0.00 0.00 2.40
1654 1826 5.221803 ACAGAGCAAGAGATTGAAGGAAGAA 60.222 40.000 0.00 0.00 0.00 2.52
1655 1827 4.285517 ACAGAGCAAGAGATTGAAGGAAGA 59.714 41.667 0.00 0.00 0.00 2.87
1656 1828 4.577875 ACAGAGCAAGAGATTGAAGGAAG 58.422 43.478 0.00 0.00 0.00 3.46
1659 1831 3.119919 GCAACAGAGCAAGAGATTGAAGG 60.120 47.826 0.00 0.00 0.00 3.46
1660 1832 3.752222 AGCAACAGAGCAAGAGATTGAAG 59.248 43.478 0.00 0.00 36.85 3.02
1661 1833 3.501062 CAGCAACAGAGCAAGAGATTGAA 59.499 43.478 0.00 0.00 36.85 2.69
1662 1834 3.072211 CAGCAACAGAGCAAGAGATTGA 58.928 45.455 0.00 0.00 36.85 2.57
1663 1835 2.812591 ACAGCAACAGAGCAAGAGATTG 59.187 45.455 0.00 0.00 36.85 2.67
1664 1836 2.812591 CACAGCAACAGAGCAAGAGATT 59.187 45.455 0.00 0.00 36.85 2.40
1665 1837 2.424557 CACAGCAACAGAGCAAGAGAT 58.575 47.619 0.00 0.00 36.85 2.75
1666 1838 1.541889 CCACAGCAACAGAGCAAGAGA 60.542 52.381 0.00 0.00 36.85 3.10
1667 1839 0.873054 CCACAGCAACAGAGCAAGAG 59.127 55.000 0.00 0.00 36.85 2.85
1668 1840 0.469494 TCCACAGCAACAGAGCAAGA 59.531 50.000 0.00 0.00 36.85 3.02
1669 1841 1.199327 CATCCACAGCAACAGAGCAAG 59.801 52.381 0.00 0.00 36.85 4.01
1670 1842 1.241165 CATCCACAGCAACAGAGCAA 58.759 50.000 0.00 0.00 36.85 3.91
1671 1843 0.109153 ACATCCACAGCAACAGAGCA 59.891 50.000 0.00 0.00 36.85 4.26
1672 1844 0.520404 CACATCCACAGCAACAGAGC 59.480 55.000 0.00 0.00 0.00 4.09
1673 1845 0.520404 GCACATCCACAGCAACAGAG 59.480 55.000 0.00 0.00 0.00 3.35
1674 1846 1.229975 CGCACATCCACAGCAACAGA 61.230 55.000 0.00 0.00 0.00 3.41
1675 1847 1.208358 CGCACATCCACAGCAACAG 59.792 57.895 0.00 0.00 0.00 3.16
1676 1848 2.906939 GCGCACATCCACAGCAACA 61.907 57.895 0.30 0.00 0.00 3.33
1677 1849 2.126734 GCGCACATCCACAGCAAC 60.127 61.111 0.30 0.00 0.00 4.17
1678 1850 3.725459 CGCGCACATCCACAGCAA 61.725 61.111 8.75 0.00 0.00 3.91
1683 1855 4.541482 CATGCCGCGCACATCCAC 62.541 66.667 8.75 0.00 43.04 4.02
1693 1865 0.179137 GGGAAAAGTTAGCATGCCGC 60.179 55.000 15.66 4.76 42.91 6.53
1694 1866 0.455815 GGGGAAAAGTTAGCATGCCG 59.544 55.000 15.66 0.00 0.00 5.69
1695 1867 1.555967 TGGGGAAAAGTTAGCATGCC 58.444 50.000 15.66 0.00 0.00 4.40
1696 1868 3.524541 CAATGGGGAAAAGTTAGCATGC 58.475 45.455 10.51 10.51 0.00 4.06
1697 1869 3.524541 GCAATGGGGAAAAGTTAGCATG 58.475 45.455 0.00 0.00 0.00 4.06
1698 1870 2.501316 GGCAATGGGGAAAAGTTAGCAT 59.499 45.455 0.00 0.00 0.00 3.79
1699 1871 1.899142 GGCAATGGGGAAAAGTTAGCA 59.101 47.619 0.00 0.00 0.00 3.49
1700 1872 1.207089 GGGCAATGGGGAAAAGTTAGC 59.793 52.381 0.00 0.00 0.00 3.09
1701 1873 1.476488 CGGGCAATGGGGAAAAGTTAG 59.524 52.381 0.00 0.00 0.00 2.34
1702 1874 1.203075 ACGGGCAATGGGGAAAAGTTA 60.203 47.619 0.00 0.00 0.00 2.24
1703 1875 0.471022 ACGGGCAATGGGGAAAAGTT 60.471 50.000 0.00 0.00 0.00 2.66
1704 1876 0.898326 GACGGGCAATGGGGAAAAGT 60.898 55.000 0.00 0.00 0.00 2.66
1705 1877 0.611896 AGACGGGCAATGGGGAAAAG 60.612 55.000 0.00 0.00 0.00 2.27
1706 1878 0.610785 GAGACGGGCAATGGGGAAAA 60.611 55.000 0.00 0.00 0.00 2.29
1707 1879 1.001393 GAGACGGGCAATGGGGAAA 60.001 57.895 0.00 0.00 0.00 3.13
1708 1880 1.923395 AGAGACGGGCAATGGGGAA 60.923 57.895 0.00 0.00 0.00 3.97
1711 1883 0.107017 ATTCAGAGACGGGCAATGGG 60.107 55.000 0.00 0.00 0.00 4.00
1738 1940 3.565764 TGCAGGGATGGTTCAGAATAG 57.434 47.619 0.00 0.00 0.00 1.73
1739 1941 4.524802 AATGCAGGGATGGTTCAGAATA 57.475 40.909 0.00 0.00 0.00 1.75
1740 1942 3.393426 AATGCAGGGATGGTTCAGAAT 57.607 42.857 0.00 0.00 0.00 2.40
1767 1969 2.746803 GGGCGTTTCACGATTCGGG 61.747 63.158 11.29 6.48 46.05 5.14
1772 1974 1.289109 CGAAGTGGGCGTTTCACGAT 61.289 55.000 0.00 0.00 46.05 3.73
1773 1975 1.952133 CGAAGTGGGCGTTTCACGA 60.952 57.895 0.00 0.00 46.05 4.35
1779 1981 2.172483 ATCAGCTCGAAGTGGGCGTT 62.172 55.000 0.00 0.00 0.00 4.84
1789 1991 5.163622 GGAATTGGAATTTGAATCAGCTCGA 60.164 40.000 0.00 0.00 0.00 4.04
1804 2009 5.655974 TCAATCGATGGATTTGGAATTGGAA 59.344 36.000 0.00 0.00 40.90 3.53
1806 2011 5.163530 TGTCAATCGATGGATTTGGAATTGG 60.164 40.000 5.61 0.00 40.90 3.16
1809 2014 4.339247 GGTGTCAATCGATGGATTTGGAAT 59.661 41.667 5.61 0.00 40.90 3.01
1815 2020 2.979814 TCGGTGTCAATCGATGGATT 57.020 45.000 5.61 0.00 43.62 3.01
1820 2025 1.202533 GGTGGATCGGTGTCAATCGAT 60.203 52.381 10.83 10.83 46.96 3.59
1825 2030 1.676968 CTGGGTGGATCGGTGTCAA 59.323 57.895 0.00 0.00 0.00 3.18
1827 2032 2.125106 GCTGGGTGGATCGGTGTC 60.125 66.667 0.00 0.00 0.00 3.67
1850 2065 0.886563 TTCCGTTCTCCTCGGTTCTC 59.113 55.000 4.36 0.00 46.86 2.87
1852 2067 0.731855 CGTTCCGTTCTCCTCGGTTC 60.732 60.000 4.36 0.00 46.86 3.62
1853 2068 1.288127 CGTTCCGTTCTCCTCGGTT 59.712 57.895 4.36 0.00 46.86 4.44
1854 2069 2.633509 CCGTTCCGTTCTCCTCGGT 61.634 63.158 4.36 0.00 46.86 4.69
1856 2071 2.506438 GCCGTTCCGTTCTCCTCG 60.506 66.667 0.00 0.00 0.00 4.63
1857 2072 1.153804 GAGCCGTTCCGTTCTCCTC 60.154 63.158 0.00 0.00 0.00 3.71
1858 2073 2.971452 GAGCCGTTCCGTTCTCCT 59.029 61.111 0.00 0.00 0.00 3.69
1859 2074 2.506438 CGAGCCGTTCCGTTCTCC 60.506 66.667 0.00 0.00 0.00 3.71
1860 2075 1.800713 GACGAGCCGTTCCGTTCTC 60.801 63.158 1.80 0.00 41.37 2.87
1861 2076 2.257676 GACGAGCCGTTCCGTTCT 59.742 61.111 1.80 0.00 41.37 3.01
1862 2077 2.087009 CAGACGAGCCGTTCCGTTC 61.087 63.158 1.80 0.00 41.37 3.95
1863 2078 2.049433 CAGACGAGCCGTTCCGTT 60.049 61.111 1.80 0.00 41.37 4.44
1864 2079 4.719369 GCAGACGAGCCGTTCCGT 62.719 66.667 1.80 0.00 41.37 4.69
1865 2080 4.717629 TGCAGACGAGCCGTTCCG 62.718 66.667 1.80 0.00 41.37 4.30
1906 2121 3.625314 TGGAAACAGGTTTTGGGCT 57.375 47.368 0.00 0.00 35.01 5.19
1925 2148 2.063266 GTGTTCGACGAAATGGCTGTA 58.937 47.619 12.67 0.00 0.00 2.74
1926 2149 0.865769 GTGTTCGACGAAATGGCTGT 59.134 50.000 12.67 0.00 0.00 4.40
1969 2192 0.469070 TGAACGAAAACGAAGGGGGA 59.531 50.000 0.00 0.00 0.00 4.81
1991 2214 1.372087 CGGAAGCAAGAGTCATGGGC 61.372 60.000 0.00 0.00 0.00 5.36
2009 2232 1.002366 CTCGGCTCCAATCTGTTTCG 58.998 55.000 0.00 0.00 0.00 3.46
2097 2321 2.464459 CGCGATCCCAACTCAAGGC 61.464 63.158 0.00 0.00 0.00 4.35
2101 2325 2.434185 GCACGCGATCCCAACTCA 60.434 61.111 15.93 0.00 0.00 3.41
2139 2363 3.058160 CGGGAGCAGCAAAGTGGG 61.058 66.667 0.00 0.00 0.00 4.61
2246 2470 5.736951 AATTGCAACCAATAAAGCTGGTA 57.263 34.783 0.00 0.00 46.75 3.25
2248 2472 4.154556 CCAAATTGCAACCAATAAAGCTGG 59.845 41.667 0.00 0.00 40.69 4.85
2273 2497 0.872021 GAGTCCTGATTGGTAGCGCG 60.872 60.000 0.00 0.00 37.07 6.86



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

AutoCloner maintained by Alex Coulton.