Multiple sequence alignment - TraesCS4A01G242100

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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 TraesCS4A01G242100 chr4A 100.000 2339 0 0 1 2339 552213597 552215935 0.000000e+00 4320
1 TraesCS4A01G242100 chr4A 97.535 852 20 1 1 852 236930606 236929756 0.000000e+00 1456
2 TraesCS4A01G242100 chr4A 96.962 790 24 0 852 1641 448545803 448546592 0.000000e+00 1327
3 TraesCS4A01G242100 chr4A 96.713 791 26 0 852 1642 2974108 2974898 0.000000e+00 1317
4 TraesCS4A01G242100 chr4A 96.429 700 24 1 1640 2339 236929771 236929073 0.000000e+00 1153
5 TraesCS4A01G242100 chr4A 89.944 537 45 5 311 839 494015535 494016070 0.000000e+00 684
6 TraesCS4A01G242100 chr4A 86.373 499 61 4 1640 2135 721009184 721008690 2.640000e-149 538
7 TraesCS4A01G242100 chr4A 90.303 330 27 5 2 329 46173331 46173005 5.970000e-116 427
8 TraesCS4A01G242100 chr2A 98.005 852 16 1 1 852 360449176 360448326 0.000000e+00 1478
9 TraesCS4A01G242100 chr2A 96.143 700 24 3 1640 2339 360448341 360447645 0.000000e+00 1140
10 TraesCS4A01G242100 chr5A 96.338 792 28 1 852 1642 702079101 702079892 0.000000e+00 1301
11 TraesCS4A01G242100 chr5A 95.202 792 38 0 852 1643 457937952 457938743 0.000000e+00 1253
12 TraesCS4A01G242100 chr5A 94.843 795 30 2 849 1642 480183510 480182726 0.000000e+00 1230
13 TraesCS4A01G242100 chr5A 90.274 329 30 2 1 329 610086661 610086987 1.660000e-116 429
14 TraesCS4A01G242100 chr6A 95.707 792 32 2 852 1641 176176312 176177103 0.000000e+00 1273
15 TraesCS4A01G242100 chr7A 95.575 791 35 0 852 1642 663372403 663371613 0.000000e+00 1267
16 TraesCS4A01G242100 chr7A 91.489 329 25 3 1 329 660438620 660438945 1.270000e-122 449
17 TraesCS4A01G242100 chr2B 94.170 789 44 2 849 1636 452233671 452234458 0.000000e+00 1201
18 TraesCS4A01G242100 chr2B 93.182 528 31 2 314 839 51056003 51056527 0.000000e+00 771
19 TraesCS4A01G242100 chr2B 88.889 558 53 5 1789 2339 51056635 51057190 0.000000e+00 678
20 TraesCS4A01G242100 chr1D 89.741 887 54 20 1 852 469032484 469031600 0.000000e+00 1099
21 TraesCS4A01G242100 chr6B 91.195 795 62 6 852 1641 300863 300072 0.000000e+00 1074
22 TraesCS4A01G242100 chr7B 88.701 885 49 18 1 852 645259326 645260192 0.000000e+00 1033
23 TraesCS4A01G242100 chr7B 92.057 705 50 3 1640 2339 645260177 645260880 0.000000e+00 987
24 TraesCS4A01G242100 chr1A 89.758 537 46 5 311 839 118278618 118278083 0.000000e+00 678
25 TraesCS4A01G242100 chr1A 87.500 448 53 2 1680 2124 568464712 568464265 4.460000e-142 514
26 TraesCS4A01G242100 chr1A 90.937 331 24 6 1 329 546998457 546998783 7.670000e-120 440
27 TraesCS4A01G242100 chr7D 89.758 537 44 6 311 839 28800919 28801452 0.000000e+00 676
28 TraesCS4A01G242100 chr7D 88.471 425 46 1 1640 2061 28801449 28801873 5.770000e-141 510
29 TraesCS4A01G242100 chr3D 89.572 537 47 5 311 839 550034940 550034405 0.000000e+00 673
30 TraesCS4A01G242100 chr1B 89.882 425 40 1 1640 2061 90433742 90434166 5.680000e-151 544
31 TraesCS4A01G242100 chr2D 87.104 442 53 2 1640 2078 618899554 618899994 4.490000e-137 497
32 TraesCS4A01G242100 chr6D 91.429 315 26 1 15 329 470412022 470411709 4.620000e-117 431
33 TraesCS4A01G242100 chr5B 90.244 328 29 2 2 329 462315798 462315474 2.150000e-115 425


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 TraesCS4A01G242100 chr4A 552213597 552215935 2338 False 4320.0 4320 100.0000 1 2339 1 chr4A.!!$F4 2338
1 TraesCS4A01G242100 chr4A 448545803 448546592 789 False 1327.0 1327 96.9620 852 1641 1 chr4A.!!$F2 789
2 TraesCS4A01G242100 chr4A 2974108 2974898 790 False 1317.0 1317 96.7130 852 1642 1 chr4A.!!$F1 790
3 TraesCS4A01G242100 chr4A 236929073 236930606 1533 True 1304.5 1456 96.9820 1 2339 2 chr4A.!!$R3 2338
4 TraesCS4A01G242100 chr4A 494015535 494016070 535 False 684.0 684 89.9440 311 839 1 chr4A.!!$F3 528
5 TraesCS4A01G242100 chr2A 360447645 360449176 1531 True 1309.0 1478 97.0740 1 2339 2 chr2A.!!$R1 2338
6 TraesCS4A01G242100 chr5A 702079101 702079892 791 False 1301.0 1301 96.3380 852 1642 1 chr5A.!!$F3 790
7 TraesCS4A01G242100 chr5A 457937952 457938743 791 False 1253.0 1253 95.2020 852 1643 1 chr5A.!!$F1 791
8 TraesCS4A01G242100 chr5A 480182726 480183510 784 True 1230.0 1230 94.8430 849 1642 1 chr5A.!!$R1 793
9 TraesCS4A01G242100 chr6A 176176312 176177103 791 False 1273.0 1273 95.7070 852 1641 1 chr6A.!!$F1 789
10 TraesCS4A01G242100 chr7A 663371613 663372403 790 True 1267.0 1267 95.5750 852 1642 1 chr7A.!!$R1 790
11 TraesCS4A01G242100 chr2B 452233671 452234458 787 False 1201.0 1201 94.1700 849 1636 1 chr2B.!!$F1 787
12 TraesCS4A01G242100 chr2B 51056003 51057190 1187 False 724.5 771 91.0355 314 2339 2 chr2B.!!$F2 2025
13 TraesCS4A01G242100 chr1D 469031600 469032484 884 True 1099.0 1099 89.7410 1 852 1 chr1D.!!$R1 851
14 TraesCS4A01G242100 chr6B 300072 300863 791 True 1074.0 1074 91.1950 852 1641 1 chr6B.!!$R1 789
15 TraesCS4A01G242100 chr7B 645259326 645260880 1554 False 1010.0 1033 90.3790 1 2339 2 chr7B.!!$F1 2338
16 TraesCS4A01G242100 chr1A 118278083 118278618 535 True 678.0 678 89.7580 311 839 1 chr1A.!!$R1 528
17 TraesCS4A01G242100 chr7D 28800919 28801873 954 False 593.0 676 89.1145 311 2061 2 chr7D.!!$F1 1750
18 TraesCS4A01G242100 chr3D 550034405 550034940 535 True 673.0 673 89.5720 311 839 1 chr3D.!!$R1 528

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
839 879 0.04109 AGCCACCCGGGATTCAAATT 59.959 50.0 32.02 0.0 40.01 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1771 1861 0.249489 AAGAAGTTCGCAGCTCGTGT 60.249 50.0 0.0 0.0 39.67 4.49 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
390 421 5.448654 AGCTCAAGGCCATACATTTCATTA 58.551 37.500 5.01 0.00 43.05 1.90
735 772 2.946329 TGCCGGTAATAATGCGACATTT 59.054 40.909 1.90 0.00 0.00 2.32
839 879 0.041090 AGCCACCCGGGATTCAAATT 59.959 50.000 32.02 0.00 40.01 1.82
840 880 1.286553 AGCCACCCGGGATTCAAATTA 59.713 47.619 32.02 0.00 40.01 1.40
842 882 2.100749 GCCACCCGGGATTCAAATTAAG 59.899 50.000 32.02 0.00 40.01 1.85
843 883 2.100749 CCACCCGGGATTCAAATTAAGC 59.899 50.000 32.02 0.00 40.01 3.09
844 884 2.100749 CACCCGGGATTCAAATTAAGCC 59.899 50.000 32.02 0.00 34.06 4.35
846 886 2.100749 CCCGGGATTCAAATTAAGCCAC 59.899 50.000 18.48 0.00 36.61 5.01
847 887 3.023832 CCGGGATTCAAATTAAGCCACT 58.976 45.455 0.00 0.00 36.61 4.00
848 888 3.066760 CCGGGATTCAAATTAAGCCACTC 59.933 47.826 0.00 0.00 36.61 3.51
850 890 4.157656 CGGGATTCAAATTAAGCCACTCAA 59.842 41.667 0.00 0.00 36.61 3.02
1104 1144 1.285280 ACTATACTGTTGGCCTGGCA 58.715 50.000 22.05 1.21 0.00 4.92
1383 1459 1.820056 TTGCCGCTGTCGTTTCCAA 60.820 52.632 0.00 0.00 0.00 3.53
1439 1516 5.181245 TGAGCTTTTGGTTGTAATAGACTGC 59.819 40.000 0.00 0.00 0.00 4.40
1477 1555 4.055360 CGTTGAACTATGGTGTTGTCAGA 58.945 43.478 0.00 0.00 0.00 3.27
1492 1570 0.331278 TCAGATTTTCGCCCCATGGT 59.669 50.000 11.73 0.00 0.00 3.55
1501 1579 1.801309 CGCCCCATGGTGTTCGTTTT 61.801 55.000 11.73 0.00 37.37 2.43
1592 1670 7.162761 TCCTATTTGTTTCTCGGAACAATGTA 58.837 34.615 4.47 1.75 45.76 2.29
1593 1671 7.827236 TCCTATTTGTTTCTCGGAACAATGTAT 59.173 33.333 4.47 0.00 45.76 2.29
1594 1672 8.458843 CCTATTTGTTTCTCGGAACAATGTATT 58.541 33.333 4.47 0.00 45.76 1.89
1595 1673 9.840427 CTATTTGTTTCTCGGAACAATGTATTT 57.160 29.630 4.47 0.00 45.76 1.40
1596 1674 8.742554 ATTTGTTTCTCGGAACAATGTATTTC 57.257 30.769 4.47 0.00 45.76 2.17
1597 1675 6.249035 TGTTTCTCGGAACAATGTATTTCC 57.751 37.500 0.00 0.00 36.64 3.13
1662 1752 7.951530 AAAATCCACAACTCAATTAGCTTTG 57.048 32.000 0.00 0.00 0.00 2.77
1663 1753 6.655078 AATCCACAACTCAATTAGCTTTGT 57.345 33.333 0.00 0.00 0.00 2.83
1664 1754 5.689383 TCCACAACTCAATTAGCTTTGTC 57.311 39.130 0.00 0.00 0.00 3.18
1665 1755 5.129634 TCCACAACTCAATTAGCTTTGTCA 58.870 37.500 0.00 0.00 0.00 3.58
1666 1756 5.008613 TCCACAACTCAATTAGCTTTGTCAC 59.991 40.000 0.00 0.00 0.00 3.67
1667 1757 5.221028 CCACAACTCAATTAGCTTTGTCACA 60.221 40.000 0.00 0.00 0.00 3.58
1668 1758 5.911280 CACAACTCAATTAGCTTTGTCACAG 59.089 40.000 0.00 0.00 0.00 3.66
1669 1759 4.756084 ACTCAATTAGCTTTGTCACAGC 57.244 40.909 2.58 2.58 37.56 4.40
1670 1760 4.136796 ACTCAATTAGCTTTGTCACAGCA 58.863 39.130 13.30 0.00 39.99 4.41
1671 1761 4.763793 ACTCAATTAGCTTTGTCACAGCAT 59.236 37.500 13.30 1.73 39.99 3.79
1672 1762 5.050644 TCAATTAGCTTTGTCACAGCATG 57.949 39.130 13.30 6.72 46.00 4.06
1673 1763 4.082625 TCAATTAGCTTTGTCACAGCATGG 60.083 41.667 13.30 0.00 43.62 3.66
1674 1764 2.566833 TAGCTTTGTCACAGCATGGT 57.433 45.000 13.30 0.00 43.62 3.55
1675 1765 1.696063 AGCTTTGTCACAGCATGGTT 58.304 45.000 13.30 0.00 43.62 3.67
1676 1766 1.338973 AGCTTTGTCACAGCATGGTTG 59.661 47.619 13.30 0.00 43.62 3.77
1688 1778 2.769893 GCATGGTTGCCTCAAAAATGT 58.230 42.857 0.00 0.00 43.38 2.71
1689 1779 2.738314 GCATGGTTGCCTCAAAAATGTC 59.262 45.455 0.00 0.00 43.38 3.06
1690 1780 3.803021 GCATGGTTGCCTCAAAAATGTCA 60.803 43.478 0.00 0.00 43.38 3.58
1691 1781 3.451141 TGGTTGCCTCAAAAATGTCAC 57.549 42.857 0.00 0.00 0.00 3.67
1692 1782 2.102252 TGGTTGCCTCAAAAATGTCACC 59.898 45.455 0.00 0.00 0.00 4.02
1693 1783 2.365293 GGTTGCCTCAAAAATGTCACCT 59.635 45.455 0.00 0.00 0.00 4.00
1694 1784 3.383761 GTTGCCTCAAAAATGTCACCTG 58.616 45.455 0.00 0.00 0.00 4.00
1695 1785 2.942804 TGCCTCAAAAATGTCACCTGA 58.057 42.857 0.00 0.00 0.00 3.86
1696 1786 2.622942 TGCCTCAAAAATGTCACCTGAC 59.377 45.455 0.00 0.00 44.97 3.51
1697 1787 2.887152 GCCTCAAAAATGTCACCTGACT 59.113 45.455 6.97 0.00 44.99 3.41
1698 1788 4.072131 GCCTCAAAAATGTCACCTGACTA 58.928 43.478 6.97 0.00 44.99 2.59
1699 1789 4.518970 GCCTCAAAAATGTCACCTGACTAA 59.481 41.667 6.97 0.00 44.99 2.24
1700 1790 5.009610 GCCTCAAAAATGTCACCTGACTAAA 59.990 40.000 6.97 0.00 44.99 1.85
1701 1791 6.294731 GCCTCAAAAATGTCACCTGACTAAAT 60.295 38.462 6.97 0.00 44.99 1.40
1702 1792 7.308435 CCTCAAAAATGTCACCTGACTAAATC 58.692 38.462 6.97 0.00 44.99 2.17
1703 1793 7.214467 TCAAAAATGTCACCTGACTAAATCC 57.786 36.000 6.97 0.00 44.99 3.01
1704 1794 6.208599 TCAAAAATGTCACCTGACTAAATCCC 59.791 38.462 6.97 0.00 44.99 3.85
1705 1795 3.933861 ATGTCACCTGACTAAATCCCC 57.066 47.619 6.97 0.00 44.99 4.81
1706 1796 2.626785 TGTCACCTGACTAAATCCCCA 58.373 47.619 6.97 0.00 44.99 4.96
1707 1797 2.304761 TGTCACCTGACTAAATCCCCAC 59.695 50.000 6.97 0.00 44.99 4.61
1708 1798 2.572104 GTCACCTGACTAAATCCCCACT 59.428 50.000 0.00 0.00 41.65 4.00
1709 1799 2.571653 TCACCTGACTAAATCCCCACTG 59.428 50.000 0.00 0.00 0.00 3.66
1710 1800 1.916181 ACCTGACTAAATCCCCACTGG 59.084 52.381 0.00 0.00 0.00 4.00
1711 1801 1.916181 CCTGACTAAATCCCCACTGGT 59.084 52.381 0.00 0.00 34.77 4.00
1712 1802 3.112263 CCTGACTAAATCCCCACTGGTA 58.888 50.000 0.00 0.00 34.77 3.25
1713 1803 3.521937 CCTGACTAAATCCCCACTGGTAA 59.478 47.826 0.00 0.00 34.77 2.85
1714 1804 4.514401 CTGACTAAATCCCCACTGGTAAC 58.486 47.826 0.00 0.00 34.77 2.50
1715 1805 3.264964 TGACTAAATCCCCACTGGTAACC 59.735 47.826 0.00 0.00 34.77 2.85
1716 1806 3.261962 ACTAAATCCCCACTGGTAACCA 58.738 45.455 0.00 0.00 34.77 3.67
1717 1807 3.856206 ACTAAATCCCCACTGGTAACCAT 59.144 43.478 0.00 0.00 30.82 3.55
1718 1808 5.041015 ACTAAATCCCCACTGGTAACCATA 58.959 41.667 0.00 0.00 30.82 2.74
1719 1809 4.519906 AAATCCCCACTGGTAACCATAG 57.480 45.455 0.00 0.00 30.82 2.23
1720 1810 1.887797 TCCCCACTGGTAACCATAGG 58.112 55.000 0.00 0.00 30.82 2.57
1721 1811 1.081513 TCCCCACTGGTAACCATAGGT 59.918 52.381 0.00 0.00 34.06 3.08
1722 1812 1.211949 CCCCACTGGTAACCATAGGTG 59.788 57.143 0.00 0.00 35.34 4.00
1723 1813 1.408266 CCCACTGGTAACCATAGGTGC 60.408 57.143 0.00 0.00 35.34 5.01
1724 1814 1.280710 CCACTGGTAACCATAGGTGCA 59.719 52.381 0.00 0.00 35.34 4.57
1725 1815 2.356135 CACTGGTAACCATAGGTGCAC 58.644 52.381 8.80 8.80 35.34 4.57
1726 1816 2.027192 CACTGGTAACCATAGGTGCACT 60.027 50.000 17.98 5.41 35.34 4.40
1727 1817 3.196901 CACTGGTAACCATAGGTGCACTA 59.803 47.826 17.98 7.61 35.34 2.74
1728 1818 3.841845 ACTGGTAACCATAGGTGCACTAA 59.158 43.478 17.98 5.40 35.34 2.24
1729 1819 4.189231 CTGGTAACCATAGGTGCACTAAC 58.811 47.826 17.98 2.29 35.34 2.34
1730 1820 3.583526 TGGTAACCATAGGTGCACTAACA 59.416 43.478 17.98 5.19 35.34 2.41
1731 1821 4.041815 TGGTAACCATAGGTGCACTAACAA 59.958 41.667 17.98 0.00 35.34 2.83
1732 1822 4.393990 GGTAACCATAGGTGCACTAACAAC 59.606 45.833 17.98 0.00 35.34 3.32
1733 1823 3.780804 ACCATAGGTGCACTAACAACA 57.219 42.857 17.98 0.00 32.98 3.33
1734 1824 4.301072 ACCATAGGTGCACTAACAACAT 57.699 40.909 17.98 0.00 32.98 2.71
1735 1825 4.261801 ACCATAGGTGCACTAACAACATC 58.738 43.478 17.98 0.00 32.98 3.06
1736 1826 4.019321 ACCATAGGTGCACTAACAACATCT 60.019 41.667 17.98 4.23 32.98 2.90
1737 1827 5.188948 ACCATAGGTGCACTAACAACATCTA 59.811 40.000 17.98 6.48 32.98 1.98
1738 1828 6.112734 CCATAGGTGCACTAACAACATCTAA 58.887 40.000 17.98 0.00 34.79 2.10
1739 1829 6.767902 CCATAGGTGCACTAACAACATCTAAT 59.232 38.462 17.98 0.00 34.79 1.73
1740 1830 7.041780 CCATAGGTGCACTAACAACATCTAATC 60.042 40.741 17.98 0.00 34.79 1.75
1741 1831 4.870426 AGGTGCACTAACAACATCTAATCG 59.130 41.667 17.98 0.00 0.00 3.34
1742 1832 4.868171 GGTGCACTAACAACATCTAATCGA 59.132 41.667 17.98 0.00 0.00 3.59
1743 1833 5.350365 GGTGCACTAACAACATCTAATCGAA 59.650 40.000 17.98 0.00 0.00 3.71
1744 1834 6.241385 GTGCACTAACAACATCTAATCGAAC 58.759 40.000 10.32 0.00 0.00 3.95
1745 1835 5.929415 TGCACTAACAACATCTAATCGAACA 59.071 36.000 0.00 0.00 0.00 3.18
1746 1836 6.593770 TGCACTAACAACATCTAATCGAACAT 59.406 34.615 0.00 0.00 0.00 2.71
1747 1837 7.119997 GCACTAACAACATCTAATCGAACATC 58.880 38.462 0.00 0.00 0.00 3.06
1748 1838 7.201522 GCACTAACAACATCTAATCGAACATCA 60.202 37.037 0.00 0.00 0.00 3.07
1749 1839 8.820933 CACTAACAACATCTAATCGAACATCAT 58.179 33.333 0.00 0.00 0.00 2.45
1752 1842 7.715265 ACAACATCTAATCGAACATCATACC 57.285 36.000 0.00 0.00 0.00 2.73
1753 1843 7.500992 ACAACATCTAATCGAACATCATACCT 58.499 34.615 0.00 0.00 0.00 3.08
1754 1844 7.987458 ACAACATCTAATCGAACATCATACCTT 59.013 33.333 0.00 0.00 0.00 3.50
1755 1845 8.491152 CAACATCTAATCGAACATCATACCTTC 58.509 37.037 0.00 0.00 0.00 3.46
1756 1846 7.726216 ACATCTAATCGAACATCATACCTTCA 58.274 34.615 0.00 0.00 0.00 3.02
1757 1847 7.869937 ACATCTAATCGAACATCATACCTTCAG 59.130 37.037 0.00 0.00 0.00 3.02
1758 1848 6.216569 TCTAATCGAACATCATACCTTCAGC 58.783 40.000 0.00 0.00 0.00 4.26
1759 1849 3.885724 TCGAACATCATACCTTCAGCA 57.114 42.857 0.00 0.00 0.00 4.41
1760 1850 4.200838 TCGAACATCATACCTTCAGCAA 57.799 40.909 0.00 0.00 0.00 3.91
1761 1851 3.932710 TCGAACATCATACCTTCAGCAAC 59.067 43.478 0.00 0.00 0.00 4.17
1762 1852 3.063997 CGAACATCATACCTTCAGCAACC 59.936 47.826 0.00 0.00 0.00 3.77
1763 1853 2.632377 ACATCATACCTTCAGCAACCG 58.368 47.619 0.00 0.00 0.00 4.44
1764 1854 2.236146 ACATCATACCTTCAGCAACCGA 59.764 45.455 0.00 0.00 0.00 4.69
1765 1855 2.672961 TCATACCTTCAGCAACCGAG 57.327 50.000 0.00 0.00 0.00 4.63
1766 1856 1.009829 CATACCTTCAGCAACCGAGC 58.990 55.000 0.00 0.00 0.00 5.03
1767 1857 0.613260 ATACCTTCAGCAACCGAGCA 59.387 50.000 0.00 0.00 36.85 4.26
1768 1858 0.320421 TACCTTCAGCAACCGAGCAC 60.320 55.000 0.00 0.00 36.85 4.40
1769 1859 2.671177 CCTTCAGCAACCGAGCACG 61.671 63.158 0.00 0.00 36.85 5.34
1770 1860 3.300667 CTTCAGCAACCGAGCACGC 62.301 63.158 0.00 0.00 38.29 5.34
1771 1861 4.600576 TCAGCAACCGAGCACGCA 62.601 61.111 0.00 0.00 38.29 5.24
1772 1862 4.374702 CAGCAACCGAGCACGCAC 62.375 66.667 0.00 0.00 38.29 5.34
1773 1863 4.908687 AGCAACCGAGCACGCACA 62.909 61.111 0.00 0.00 38.29 4.57
1774 1864 4.666532 GCAACCGAGCACGCACAC 62.667 66.667 0.00 0.00 38.29 3.82
1776 1866 4.578898 AACCGAGCACGCACACGA 62.579 61.111 0.00 0.00 43.93 4.35
1786 1876 3.038417 GCACACGAGCTGCGAACT 61.038 61.111 11.64 0.00 44.57 3.01
1787 1877 2.598632 GCACACGAGCTGCGAACTT 61.599 57.895 11.64 0.00 44.57 2.66
1788 1878 1.488957 CACACGAGCTGCGAACTTC 59.511 57.895 11.64 0.00 44.57 3.01
1789 1879 0.941463 CACACGAGCTGCGAACTTCT 60.941 55.000 11.64 0.00 44.57 2.85
1790 1880 0.249489 ACACGAGCTGCGAACTTCTT 60.249 50.000 11.64 0.00 44.57 2.52
1791 1881 0.436531 CACGAGCTGCGAACTTCTTC 59.563 55.000 11.64 0.00 44.57 2.87
1792 1882 0.667792 ACGAGCTGCGAACTTCTTCC 60.668 55.000 11.64 0.00 44.57 3.46
1793 1883 1.355066 CGAGCTGCGAACTTCTTCCC 61.355 60.000 0.00 0.00 44.57 3.97
1794 1884 1.355066 GAGCTGCGAACTTCTTCCCG 61.355 60.000 0.00 0.00 0.00 5.14
1795 1885 2.391389 GCTGCGAACTTCTTCCCGG 61.391 63.158 0.00 0.00 0.00 5.73
1796 1886 1.292223 CTGCGAACTTCTTCCCGGA 59.708 57.895 0.73 0.00 0.00 5.14
1797 1887 0.737715 CTGCGAACTTCTTCCCGGAG 60.738 60.000 0.73 0.00 34.50 4.63
1798 1888 2.101233 GCGAACTTCTTCCCGGAGC 61.101 63.158 0.73 0.00 0.00 4.70
1799 1889 1.805945 CGAACTTCTTCCCGGAGCG 60.806 63.158 0.73 0.00 0.00 5.03
1800 1890 1.590147 GAACTTCTTCCCGGAGCGA 59.410 57.895 0.73 0.00 0.00 4.93
1801 1891 0.736672 GAACTTCTTCCCGGAGCGAC 60.737 60.000 0.73 0.00 0.00 5.19
1802 1892 1.186267 AACTTCTTCCCGGAGCGACT 61.186 55.000 0.73 0.00 0.00 4.18
1803 1893 1.153745 CTTCTTCCCGGAGCGACTG 60.154 63.158 0.73 0.00 0.00 3.51
1804 1894 1.878656 CTTCTTCCCGGAGCGACTGT 61.879 60.000 0.73 0.00 0.00 3.55
1805 1895 2.125912 CTTCCCGGAGCGACTGTG 60.126 66.667 0.73 0.00 0.00 3.66
1806 1896 2.915659 TTCCCGGAGCGACTGTGT 60.916 61.111 0.73 0.00 0.00 3.72
1807 1897 3.220999 TTCCCGGAGCGACTGTGTG 62.221 63.158 0.73 0.00 0.00 3.82
1808 1898 3.680786 CCCGGAGCGACTGTGTGA 61.681 66.667 0.73 0.00 0.00 3.58
1809 1899 2.126307 CCGGAGCGACTGTGTGAG 60.126 66.667 0.00 0.00 0.00 3.51
1810 1900 2.807045 CGGAGCGACTGTGTGAGC 60.807 66.667 0.00 0.00 0.00 4.26
1811 1901 2.433318 GGAGCGACTGTGTGAGCC 60.433 66.667 0.00 0.00 0.00 4.70
1812 1902 2.340078 GAGCGACTGTGTGAGCCA 59.660 61.111 0.00 0.00 0.00 4.75
1813 1903 1.300931 GAGCGACTGTGTGAGCCAA 60.301 57.895 0.00 0.00 0.00 4.52
1814 1904 1.287730 GAGCGACTGTGTGAGCCAAG 61.288 60.000 0.00 0.00 0.00 3.61
1815 1905 2.959357 GCGACTGTGTGAGCCAAGC 61.959 63.158 0.00 0.00 0.00 4.01
1816 1906 1.595109 CGACTGTGTGAGCCAAGCA 60.595 57.895 0.00 0.00 0.00 3.91
1817 1907 1.835483 CGACTGTGTGAGCCAAGCAC 61.835 60.000 0.00 0.00 36.81 4.40
1818 1908 1.835483 GACTGTGTGAGCCAAGCACG 61.835 60.000 0.00 0.00 39.07 5.34
1819 1909 2.591429 TGTGTGAGCCAAGCACGG 60.591 61.111 0.00 0.00 39.07 4.94
1820 1910 3.357079 GTGTGAGCCAAGCACGGG 61.357 66.667 0.00 0.00 39.07 5.28
1821 1911 4.641645 TGTGAGCCAAGCACGGGG 62.642 66.667 0.00 0.00 39.07 5.73
1822 1912 4.329545 GTGAGCCAAGCACGGGGA 62.330 66.667 0.00 0.00 0.00 4.81
1823 1913 4.020617 TGAGCCAAGCACGGGGAG 62.021 66.667 0.00 0.00 0.00 4.30
1827 1917 4.473520 CCAAGCACGGGGAGCGAT 62.474 66.667 0.00 0.00 37.01 4.58
1828 1918 3.197790 CAAGCACGGGGAGCGATG 61.198 66.667 0.00 0.00 37.01 3.84
1829 1919 3.390521 AAGCACGGGGAGCGATGA 61.391 61.111 0.00 0.00 37.01 2.92
1830 1920 2.735772 AAGCACGGGGAGCGATGAT 61.736 57.895 0.00 0.00 37.01 2.45
1831 1921 2.203070 GCACGGGGAGCGATGATT 60.203 61.111 0.00 0.00 0.00 2.57
1832 1922 1.069090 GCACGGGGAGCGATGATTA 59.931 57.895 0.00 0.00 0.00 1.75
1833 1923 1.222115 GCACGGGGAGCGATGATTAC 61.222 60.000 0.00 0.00 0.00 1.89
1834 1924 0.939577 CACGGGGAGCGATGATTACG 60.940 60.000 0.00 0.00 0.00 3.18
1835 1925 1.372997 CGGGGAGCGATGATTACGG 60.373 63.158 0.00 0.00 0.00 4.02
1836 1926 1.668151 GGGGAGCGATGATTACGGC 60.668 63.158 0.00 0.00 0.00 5.68
1837 1927 2.022129 GGGAGCGATGATTACGGCG 61.022 63.158 4.80 4.80 0.00 6.46
1838 1928 2.022129 GGAGCGATGATTACGGCGG 61.022 63.158 13.24 0.00 0.00 6.13
1839 1929 2.022129 GAGCGATGATTACGGCGGG 61.022 63.158 13.24 0.00 0.00 6.13
1840 1930 3.712881 GCGATGATTACGGCGGGC 61.713 66.667 13.24 0.00 0.00 6.13
1841 1931 2.279851 CGATGATTACGGCGGGCA 60.280 61.111 13.24 3.59 0.00 5.36
1842 1932 2.594962 CGATGATTACGGCGGGCAC 61.595 63.158 13.24 0.28 0.00 5.01
1843 1933 1.522806 GATGATTACGGCGGGCACA 60.523 57.895 13.24 6.71 0.00 4.57
1844 1934 1.078072 ATGATTACGGCGGGCACAA 60.078 52.632 13.24 0.00 0.00 3.33
1845 1935 0.465460 ATGATTACGGCGGGCACAAT 60.465 50.000 13.24 2.19 0.00 2.71
1846 1936 1.355210 GATTACGGCGGGCACAATG 59.645 57.895 13.24 0.00 0.00 2.82
1849 1939 2.749706 TTACGGCGGGCACAATGGAA 62.750 55.000 13.24 0.00 0.00 3.53
1882 1972 1.415659 CAATTCGAGATGCCTCCTCCT 59.584 52.381 0.00 0.00 36.04 3.69
1890 1980 2.108425 AGATGCCTCCTCCTACATCGTA 59.892 50.000 0.00 0.00 42.91 3.43
2104 2194 0.561184 TGGTGGGGATAGGACGAGAT 59.439 55.000 0.00 0.00 0.00 2.75
2232 2322 2.688666 AGGAGGATGCTGGCGGAA 60.689 61.111 0.00 0.00 32.93 4.30
2295 2385 1.663739 GTCTCACCGCACACCACTA 59.336 57.895 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
390 421 6.536582 CGCATTTTCTATACTATATGCAGCCT 59.463 38.462 0.00 0.00 38.55 4.58
735 772 3.516586 TCCTGTGGTATTCTCAGGTTGA 58.483 45.455 12.08 0.00 46.04 3.18
839 879 5.512060 GCATCCTGAGATATTGAGTGGCTTA 60.512 44.000 0.00 0.00 0.00 3.09
840 880 4.746089 GCATCCTGAGATATTGAGTGGCTT 60.746 45.833 0.00 0.00 0.00 4.35
842 882 3.072944 GCATCCTGAGATATTGAGTGGC 58.927 50.000 0.00 0.00 0.00 5.01
843 883 4.202336 ACAGCATCCTGAGATATTGAGTGG 60.202 45.833 0.00 0.00 41.77 4.00
844 884 4.958509 ACAGCATCCTGAGATATTGAGTG 58.041 43.478 0.00 0.00 41.77 3.51
846 886 5.471556 AGACAGCATCCTGAGATATTGAG 57.528 43.478 0.00 0.00 41.77 3.02
847 887 5.364735 TCAAGACAGCATCCTGAGATATTGA 59.635 40.000 0.00 0.00 41.77 2.57
848 888 5.466058 GTCAAGACAGCATCCTGAGATATTG 59.534 44.000 0.00 0.00 41.77 1.90
850 890 4.900652 AGTCAAGACAGCATCCTGAGATAT 59.099 41.667 2.72 0.00 41.77 1.63
1206 1249 3.071602 GCTGAAGACCTGCCCAATATAGA 59.928 47.826 0.00 0.00 34.12 1.98
1383 1459 3.502211 CCAAATAGAAAACGGACAGCAGT 59.498 43.478 0.00 0.00 0.00 4.40
1426 1503 7.620880 ACCTGAAATACTGCAGTCTATTACAA 58.379 34.615 25.56 2.84 0.00 2.41
1439 1516 5.236478 AGTTCAACGACAACCTGAAATACTG 59.764 40.000 0.00 0.00 31.21 2.74
1477 1555 0.894835 GAACACCATGGGGCGAAAAT 59.105 50.000 15.93 0.00 37.90 1.82
1492 1570 0.589223 GCCCGACATCAAAACGAACA 59.411 50.000 0.00 0.00 0.00 3.18
1501 1579 4.365505 TGCGTTCGCCCGACATCA 62.366 61.111 14.44 0.00 0.00 3.07
1592 1670 4.533919 TCCATTGCAAATGAACGGAAAT 57.466 36.364 1.71 0.00 0.00 2.17
1593 1671 4.327982 TTCCATTGCAAATGAACGGAAA 57.672 36.364 1.71 0.00 0.00 3.13
1594 1672 4.305769 CTTTCCATTGCAAATGAACGGAA 58.694 39.130 1.71 6.48 0.00 4.30
1595 1673 3.305950 CCTTTCCATTGCAAATGAACGGA 60.306 43.478 22.21 11.81 0.00 4.69
1596 1674 2.995258 CCTTTCCATTGCAAATGAACGG 59.005 45.455 16.96 16.96 0.00 4.44
1597 1675 2.995258 CCCTTTCCATTGCAAATGAACG 59.005 45.455 1.71 7.00 0.00 3.95
1598 1676 3.244526 ACCCCTTTCCATTGCAAATGAAC 60.245 43.478 1.71 0.00 0.00 3.18
1599 1677 2.978278 ACCCCTTTCCATTGCAAATGAA 59.022 40.909 1.71 6.57 0.00 2.57
1600 1678 2.566724 GACCCCTTTCCATTGCAAATGA 59.433 45.455 1.71 0.00 0.00 2.57
1601 1679 2.302445 TGACCCCTTTCCATTGCAAATG 59.698 45.455 1.71 2.47 0.00 2.32
1643 1733 5.215160 GTGACAAAGCTAATTGAGTTGTGG 58.785 41.667 5.15 0.00 34.38 4.17
1644 1734 5.820131 TGTGACAAAGCTAATTGAGTTGTG 58.180 37.500 5.15 0.00 34.38 3.33
1645 1735 5.506317 GCTGTGACAAAGCTAATTGAGTTGT 60.506 40.000 10.58 1.28 37.69 3.32
1646 1736 4.913924 GCTGTGACAAAGCTAATTGAGTTG 59.086 41.667 10.58 0.00 37.69 3.16
1647 1737 4.580167 TGCTGTGACAAAGCTAATTGAGTT 59.420 37.500 18.42 0.00 41.42 3.01
1648 1738 4.136796 TGCTGTGACAAAGCTAATTGAGT 58.863 39.130 18.42 0.00 41.42 3.41
1649 1739 4.754372 TGCTGTGACAAAGCTAATTGAG 57.246 40.909 18.42 0.00 41.42 3.02
1650 1740 4.082625 CCATGCTGTGACAAAGCTAATTGA 60.083 41.667 18.42 0.00 41.42 2.57
1651 1741 4.171005 CCATGCTGTGACAAAGCTAATTG 58.829 43.478 18.42 10.33 41.42 2.32
1652 1742 3.828451 ACCATGCTGTGACAAAGCTAATT 59.172 39.130 18.42 0.00 41.42 1.40
1653 1743 3.424703 ACCATGCTGTGACAAAGCTAAT 58.575 40.909 18.42 1.97 41.42 1.73
1654 1744 2.862541 ACCATGCTGTGACAAAGCTAA 58.137 42.857 18.42 0.00 41.42 3.09
1655 1745 2.553602 CAACCATGCTGTGACAAAGCTA 59.446 45.455 18.42 5.78 41.42 3.32
1656 1746 1.338973 CAACCATGCTGTGACAAAGCT 59.661 47.619 18.42 1.75 41.42 3.74
1657 1747 1.774639 CAACCATGCTGTGACAAAGC 58.225 50.000 10.94 10.94 41.22 3.51
1669 1759 3.742369 GTGACATTTTTGAGGCAACCATG 59.258 43.478 0.00 0.00 37.17 3.66
1670 1760 3.244181 GGTGACATTTTTGAGGCAACCAT 60.244 43.478 0.00 0.00 37.17 3.55
1671 1761 2.102252 GGTGACATTTTTGAGGCAACCA 59.898 45.455 0.00 0.00 37.17 3.67
1672 1762 2.365293 AGGTGACATTTTTGAGGCAACC 59.635 45.455 0.00 0.00 37.17 3.77
1673 1763 3.068024 TCAGGTGACATTTTTGAGGCAAC 59.932 43.478 0.00 0.00 0.00 4.17
1674 1764 3.068024 GTCAGGTGACATTTTTGAGGCAA 59.932 43.478 5.21 0.00 44.18 4.52
1675 1765 2.622942 GTCAGGTGACATTTTTGAGGCA 59.377 45.455 5.21 0.00 44.18 4.75
1676 1766 3.288809 GTCAGGTGACATTTTTGAGGC 57.711 47.619 5.21 0.00 44.18 4.70
1687 1777 2.572104 AGTGGGGATTTAGTCAGGTGAC 59.428 50.000 1.60 1.60 45.08 3.67
1688 1778 2.571653 CAGTGGGGATTTAGTCAGGTGA 59.428 50.000 0.00 0.00 0.00 4.02
1689 1779 2.356125 CCAGTGGGGATTTAGTCAGGTG 60.356 54.545 0.00 0.00 40.01 4.00
1690 1780 1.916181 CCAGTGGGGATTTAGTCAGGT 59.084 52.381 0.00 0.00 40.01 4.00
1691 1781 1.916181 ACCAGTGGGGATTTAGTCAGG 59.084 52.381 15.21 0.00 41.15 3.86
1692 1782 4.514401 GTTACCAGTGGGGATTTAGTCAG 58.486 47.826 15.21 0.00 41.15 3.51
1693 1783 3.264964 GGTTACCAGTGGGGATTTAGTCA 59.735 47.826 15.21 0.00 41.15 3.41
1694 1784 3.264964 TGGTTACCAGTGGGGATTTAGTC 59.735 47.826 15.21 0.00 41.15 2.59
1695 1785 3.261962 TGGTTACCAGTGGGGATTTAGT 58.738 45.455 15.21 0.00 41.15 2.24
1696 1786 4.519906 ATGGTTACCAGTGGGGATTTAG 57.480 45.455 15.21 0.00 41.15 1.85
1697 1787 4.414182 CCTATGGTTACCAGTGGGGATTTA 59.586 45.833 15.21 0.00 41.15 1.40
1698 1788 3.204382 CCTATGGTTACCAGTGGGGATTT 59.796 47.826 15.21 0.00 41.15 2.17
1699 1789 2.783510 CCTATGGTTACCAGTGGGGATT 59.216 50.000 15.21 0.00 41.15 3.01
1700 1790 2.294263 ACCTATGGTTACCAGTGGGGAT 60.294 50.000 22.78 3.96 36.75 3.85
1701 1791 1.081513 ACCTATGGTTACCAGTGGGGA 59.918 52.381 22.78 0.00 36.75 4.81
1702 1792 1.211949 CACCTATGGTTACCAGTGGGG 59.788 57.143 22.78 17.90 36.75 4.96
1703 1793 1.408266 GCACCTATGGTTACCAGTGGG 60.408 57.143 22.78 19.00 36.75 4.61
1704 1794 1.280710 TGCACCTATGGTTACCAGTGG 59.719 52.381 19.32 19.24 36.75 4.00
1705 1795 2.027192 AGTGCACCTATGGTTACCAGTG 60.027 50.000 14.63 13.44 36.75 3.66
1706 1796 2.266279 AGTGCACCTATGGTTACCAGT 58.734 47.619 14.63 0.00 36.75 4.00
1707 1797 4.189231 GTTAGTGCACCTATGGTTACCAG 58.811 47.826 14.63 0.00 36.75 4.00
1708 1798 3.583526 TGTTAGTGCACCTATGGTTACCA 59.416 43.478 14.63 6.53 38.19 3.25
1709 1799 4.210724 TGTTAGTGCACCTATGGTTACC 57.789 45.455 14.63 0.00 31.02 2.85
1710 1800 4.998672 TGTTGTTAGTGCACCTATGGTTAC 59.001 41.667 14.63 0.00 31.02 2.50
1711 1801 5.230323 TGTTGTTAGTGCACCTATGGTTA 57.770 39.130 14.63 0.00 31.02 2.85
1712 1802 4.093472 TGTTGTTAGTGCACCTATGGTT 57.907 40.909 14.63 0.00 31.02 3.67
1713 1803 3.780804 TGTTGTTAGTGCACCTATGGT 57.219 42.857 14.63 0.00 35.62 3.55
1714 1804 4.517285 AGATGTTGTTAGTGCACCTATGG 58.483 43.478 14.63 0.00 0.00 2.74
1715 1805 7.306807 CGATTAGATGTTGTTAGTGCACCTATG 60.307 40.741 14.63 0.00 0.00 2.23
1716 1806 6.701841 CGATTAGATGTTGTTAGTGCACCTAT 59.298 38.462 14.63 0.00 0.00 2.57
1717 1807 6.040247 CGATTAGATGTTGTTAGTGCACCTA 58.960 40.000 14.63 2.41 0.00 3.08
1718 1808 4.870426 CGATTAGATGTTGTTAGTGCACCT 59.130 41.667 14.63 3.48 0.00 4.00
1719 1809 4.868171 TCGATTAGATGTTGTTAGTGCACC 59.132 41.667 14.63 0.00 0.00 5.01
1720 1810 6.128661 TGTTCGATTAGATGTTGTTAGTGCAC 60.129 38.462 9.40 9.40 0.00 4.57
1721 1811 5.929415 TGTTCGATTAGATGTTGTTAGTGCA 59.071 36.000 0.00 0.00 0.00 4.57
1722 1812 6.403333 TGTTCGATTAGATGTTGTTAGTGC 57.597 37.500 0.00 0.00 0.00 4.40
1723 1813 8.185003 TGATGTTCGATTAGATGTTGTTAGTG 57.815 34.615 0.00 0.00 0.00 2.74
1724 1814 8.948631 ATGATGTTCGATTAGATGTTGTTAGT 57.051 30.769 0.00 0.00 0.00 2.24
1726 1816 9.256477 GGTATGATGTTCGATTAGATGTTGTTA 57.744 33.333 0.00 0.00 0.00 2.41
1727 1817 7.987458 AGGTATGATGTTCGATTAGATGTTGTT 59.013 33.333 0.00 0.00 0.00 2.83
1728 1818 7.500992 AGGTATGATGTTCGATTAGATGTTGT 58.499 34.615 0.00 0.00 0.00 3.32
1729 1819 7.953158 AGGTATGATGTTCGATTAGATGTTG 57.047 36.000 0.00 0.00 0.00 3.33
1730 1820 8.204160 TGAAGGTATGATGTTCGATTAGATGTT 58.796 33.333 0.00 0.00 0.00 2.71
1731 1821 7.726216 TGAAGGTATGATGTTCGATTAGATGT 58.274 34.615 0.00 0.00 0.00 3.06
1732 1822 7.148672 GCTGAAGGTATGATGTTCGATTAGATG 60.149 40.741 0.00 0.00 0.00 2.90
1733 1823 6.870965 GCTGAAGGTATGATGTTCGATTAGAT 59.129 38.462 0.00 0.00 0.00 1.98
1734 1824 6.183360 TGCTGAAGGTATGATGTTCGATTAGA 60.183 38.462 0.00 0.00 0.00 2.10
1735 1825 5.985530 TGCTGAAGGTATGATGTTCGATTAG 59.014 40.000 0.00 0.00 0.00 1.73
1736 1826 5.912892 TGCTGAAGGTATGATGTTCGATTA 58.087 37.500 0.00 0.00 0.00 1.75
1737 1827 4.769688 TGCTGAAGGTATGATGTTCGATT 58.230 39.130 0.00 0.00 0.00 3.34
1738 1828 4.406648 TGCTGAAGGTATGATGTTCGAT 57.593 40.909 0.00 0.00 0.00 3.59
1739 1829 3.885724 TGCTGAAGGTATGATGTTCGA 57.114 42.857 0.00 0.00 0.00 3.71
1740 1830 3.063997 GGTTGCTGAAGGTATGATGTTCG 59.936 47.826 0.00 0.00 0.00 3.95
1741 1831 3.063997 CGGTTGCTGAAGGTATGATGTTC 59.936 47.826 0.00 0.00 0.00 3.18
1742 1832 3.009723 CGGTTGCTGAAGGTATGATGTT 58.990 45.455 0.00 0.00 0.00 2.71
1743 1833 2.236146 TCGGTTGCTGAAGGTATGATGT 59.764 45.455 0.00 0.00 0.00 3.06
1744 1834 2.868583 CTCGGTTGCTGAAGGTATGATG 59.131 50.000 0.00 0.00 0.00 3.07
1745 1835 2.743183 GCTCGGTTGCTGAAGGTATGAT 60.743 50.000 0.00 0.00 0.00 2.45
1746 1836 1.405526 GCTCGGTTGCTGAAGGTATGA 60.406 52.381 0.00 0.00 0.00 2.15
1747 1837 1.009829 GCTCGGTTGCTGAAGGTATG 58.990 55.000 0.00 0.00 0.00 2.39
1748 1838 0.613260 TGCTCGGTTGCTGAAGGTAT 59.387 50.000 0.00 0.00 0.00 2.73
1749 1839 0.320421 GTGCTCGGTTGCTGAAGGTA 60.320 55.000 0.00 0.00 0.00 3.08
1750 1840 1.598130 GTGCTCGGTTGCTGAAGGT 60.598 57.895 0.00 0.00 0.00 3.50
1751 1841 2.671177 CGTGCTCGGTTGCTGAAGG 61.671 63.158 0.00 0.00 0.00 3.46
1752 1842 2.856032 CGTGCTCGGTTGCTGAAG 59.144 61.111 0.00 0.00 0.00 3.02
1753 1843 3.345808 GCGTGCTCGGTTGCTGAA 61.346 61.111 10.52 0.00 37.56 3.02
1754 1844 4.600576 TGCGTGCTCGGTTGCTGA 62.601 61.111 10.52 0.00 37.56 4.26
1755 1845 4.374702 GTGCGTGCTCGGTTGCTG 62.375 66.667 10.52 0.00 37.56 4.41
1756 1846 4.908687 TGTGCGTGCTCGGTTGCT 62.909 61.111 10.52 0.00 37.56 3.91
1757 1847 4.666532 GTGTGCGTGCTCGGTTGC 62.667 66.667 10.52 0.00 37.56 4.17
1758 1848 4.354212 CGTGTGCGTGCTCGGTTG 62.354 66.667 10.52 0.00 37.56 3.77
1759 1849 4.578898 TCGTGTGCGTGCTCGGTT 62.579 61.111 10.52 0.00 39.49 4.44
1769 1859 2.486036 GAAGTTCGCAGCTCGTGTGC 62.486 60.000 5.66 0.00 39.67 4.57
1770 1860 0.941463 AGAAGTTCGCAGCTCGTGTG 60.941 55.000 0.00 0.00 39.67 3.82
1771 1861 0.249489 AAGAAGTTCGCAGCTCGTGT 60.249 50.000 0.00 0.00 39.67 4.49
1772 1862 0.436531 GAAGAAGTTCGCAGCTCGTG 59.563 55.000 0.00 0.00 39.67 4.35
1773 1863 0.667792 GGAAGAAGTTCGCAGCTCGT 60.668 55.000 0.00 0.00 39.67 4.18
1774 1864 1.355066 GGGAAGAAGTTCGCAGCTCG 61.355 60.000 0.00 0.00 43.49 5.03
1775 1865 1.355066 CGGGAAGAAGTTCGCAGCTC 61.355 60.000 0.00 0.00 44.07 4.09
1776 1866 1.374758 CGGGAAGAAGTTCGCAGCT 60.375 57.895 0.00 0.00 44.07 4.24
1777 1867 2.391389 CCGGGAAGAAGTTCGCAGC 61.391 63.158 0.00 0.00 44.07 5.25
1778 1868 0.737715 CTCCGGGAAGAAGTTCGCAG 60.738 60.000 0.00 0.00 44.07 5.18
1779 1869 1.292223 CTCCGGGAAGAAGTTCGCA 59.708 57.895 0.00 0.00 44.07 5.10
1780 1870 2.101233 GCTCCGGGAAGAAGTTCGC 61.101 63.158 0.00 0.00 41.21 4.70
1781 1871 1.805945 CGCTCCGGGAAGAAGTTCG 60.806 63.158 0.00 0.00 32.92 3.95
1782 1872 0.736672 GTCGCTCCGGGAAGAAGTTC 60.737 60.000 0.00 0.00 0.00 3.01
1783 1873 1.186267 AGTCGCTCCGGGAAGAAGTT 61.186 55.000 0.00 0.00 0.00 2.66
1784 1874 1.606889 AGTCGCTCCGGGAAGAAGT 60.607 57.895 0.00 0.00 0.00 3.01
1785 1875 1.153745 CAGTCGCTCCGGGAAGAAG 60.154 63.158 0.00 0.00 0.00 2.85
1786 1876 1.906824 ACAGTCGCTCCGGGAAGAA 60.907 57.895 0.00 0.00 0.00 2.52
1787 1877 2.282958 ACAGTCGCTCCGGGAAGA 60.283 61.111 0.00 0.00 0.00 2.87
1788 1878 2.125912 CACAGTCGCTCCGGGAAG 60.126 66.667 0.00 0.00 0.00 3.46
1789 1879 2.915659 ACACAGTCGCTCCGGGAA 60.916 61.111 0.00 0.00 0.00 3.97
1790 1880 3.680786 CACACAGTCGCTCCGGGA 61.681 66.667 0.00 0.00 0.00 5.14
1791 1881 3.633094 CTCACACAGTCGCTCCGGG 62.633 68.421 0.00 0.00 0.00 5.73
1792 1882 2.126307 CTCACACAGTCGCTCCGG 60.126 66.667 0.00 0.00 0.00 5.14
1793 1883 2.807045 GCTCACACAGTCGCTCCG 60.807 66.667 0.00 0.00 0.00 4.63
1794 1884 2.433318 GGCTCACACAGTCGCTCC 60.433 66.667 0.00 0.00 0.00 4.70
1795 1885 1.287730 CTTGGCTCACACAGTCGCTC 61.288 60.000 0.00 0.00 0.00 5.03
1796 1886 1.301244 CTTGGCTCACACAGTCGCT 60.301 57.895 0.00 0.00 0.00 4.93
1797 1887 2.959357 GCTTGGCTCACACAGTCGC 61.959 63.158 0.00 0.00 0.00 5.19
1798 1888 1.595109 TGCTTGGCTCACACAGTCG 60.595 57.895 0.00 0.00 0.00 4.18
1799 1889 1.835483 CGTGCTTGGCTCACACAGTC 61.835 60.000 0.00 0.00 33.89 3.51
1800 1890 1.889105 CGTGCTTGGCTCACACAGT 60.889 57.895 0.00 0.00 33.89 3.55
1801 1891 2.610694 CCGTGCTTGGCTCACACAG 61.611 63.158 0.00 0.00 33.89 3.66
1802 1892 2.591429 CCGTGCTTGGCTCACACA 60.591 61.111 0.00 0.00 33.89 3.72
1803 1893 3.357079 CCCGTGCTTGGCTCACAC 61.357 66.667 6.09 0.00 34.27 3.82
1804 1894 4.641645 CCCCGTGCTTGGCTCACA 62.642 66.667 6.09 0.00 34.27 3.58
1805 1895 4.329545 TCCCCGTGCTTGGCTCAC 62.330 66.667 0.00 0.00 0.00 3.51
1806 1896 4.020617 CTCCCCGTGCTTGGCTCA 62.021 66.667 0.00 0.00 0.00 4.26
1810 1900 4.473520 ATCGCTCCCCGTGCTTGG 62.474 66.667 0.00 0.00 38.35 3.61
1811 1901 2.930385 ATCATCGCTCCCCGTGCTTG 62.930 60.000 0.00 0.00 38.35 4.01
1812 1902 2.257409 AATCATCGCTCCCCGTGCTT 62.257 55.000 0.00 0.00 38.35 3.91
1813 1903 1.399744 TAATCATCGCTCCCCGTGCT 61.400 55.000 0.00 0.00 38.35 4.40
1814 1904 1.069090 TAATCATCGCTCCCCGTGC 59.931 57.895 0.00 0.00 38.35 5.34
1815 1905 0.939577 CGTAATCATCGCTCCCCGTG 60.940 60.000 0.00 0.00 38.35 4.94
1816 1906 1.362717 CGTAATCATCGCTCCCCGT 59.637 57.895 0.00 0.00 38.35 5.28
1817 1907 1.372997 CCGTAATCATCGCTCCCCG 60.373 63.158 0.00 0.00 38.61 5.73
1818 1908 1.668151 GCCGTAATCATCGCTCCCC 60.668 63.158 0.00 0.00 0.00 4.81
1819 1909 2.022129 CGCCGTAATCATCGCTCCC 61.022 63.158 0.00 0.00 0.00 4.30
1820 1910 2.022129 CCGCCGTAATCATCGCTCC 61.022 63.158 0.00 0.00 0.00 4.70
1821 1911 2.022129 CCCGCCGTAATCATCGCTC 61.022 63.158 0.00 0.00 0.00 5.03
1822 1912 2.029073 CCCGCCGTAATCATCGCT 59.971 61.111 0.00 0.00 0.00 4.93
1823 1913 3.712881 GCCCGCCGTAATCATCGC 61.713 66.667 0.00 0.00 0.00 4.58
1824 1914 2.279851 TGCCCGCCGTAATCATCG 60.280 61.111 0.00 0.00 0.00 3.84
1825 1915 1.092921 TTGTGCCCGCCGTAATCATC 61.093 55.000 0.00 0.00 0.00 2.92
1826 1916 0.465460 ATTGTGCCCGCCGTAATCAT 60.465 50.000 0.00 0.00 0.00 2.45
1827 1917 1.078072 ATTGTGCCCGCCGTAATCA 60.078 52.632 0.00 0.00 0.00 2.57
1828 1918 1.355210 CATTGTGCCCGCCGTAATC 59.645 57.895 0.00 0.00 0.00 1.75
1829 1919 2.118404 CCATTGTGCCCGCCGTAAT 61.118 57.895 0.00 0.00 0.00 1.89
1830 1920 2.748251 CCATTGTGCCCGCCGTAA 60.748 61.111 0.00 0.00 0.00 3.18
1831 1921 2.544590 ATTCCATTGTGCCCGCCGTA 62.545 55.000 0.00 0.00 0.00 4.02
1832 1922 3.936772 ATTCCATTGTGCCCGCCGT 62.937 57.895 0.00 0.00 0.00 5.68
1833 1923 3.140141 ATTCCATTGTGCCCGCCG 61.140 61.111 0.00 0.00 0.00 6.46
1834 1924 1.603236 TTCATTCCATTGTGCCCGCC 61.603 55.000 0.00 0.00 0.00 6.13
1835 1925 0.461135 ATTCATTCCATTGTGCCCGC 59.539 50.000 0.00 0.00 0.00 6.13
1836 1926 2.026641 AGATTCATTCCATTGTGCCCG 58.973 47.619 0.00 0.00 0.00 6.13
1837 1927 2.033801 CGAGATTCATTCCATTGTGCCC 59.966 50.000 0.00 0.00 0.00 5.36
1838 1928 2.033801 CCGAGATTCATTCCATTGTGCC 59.966 50.000 0.00 0.00 0.00 5.01
1839 1929 2.684881 ACCGAGATTCATTCCATTGTGC 59.315 45.455 0.00 0.00 0.00 4.57
1840 1930 3.313526 GGACCGAGATTCATTCCATTGTG 59.686 47.826 0.00 0.00 0.00 3.33
1841 1931 3.054434 TGGACCGAGATTCATTCCATTGT 60.054 43.478 0.00 0.00 31.19 2.71
1842 1932 3.544684 TGGACCGAGATTCATTCCATTG 58.455 45.455 0.00 0.00 31.19 2.82
1843 1933 3.931907 TGGACCGAGATTCATTCCATT 57.068 42.857 0.00 0.00 31.19 3.16
1844 1934 3.931907 TTGGACCGAGATTCATTCCAT 57.068 42.857 0.00 0.00 36.25 3.41
1845 1935 3.931907 ATTGGACCGAGATTCATTCCA 57.068 42.857 0.00 0.00 34.46 3.53
1846 1936 3.248602 CGAATTGGACCGAGATTCATTCC 59.751 47.826 12.68 0.00 31.69 3.01
1849 1939 3.819564 TCGAATTGGACCGAGATTCAT 57.180 42.857 12.68 0.00 31.69 2.57
1882 1972 2.350484 GCGAGCTGCTGTATACGATGTA 60.350 50.000 7.01 0.00 41.73 2.29
1890 1980 0.318529 CGAGATGCGAGCTGCTGTAT 60.319 55.000 7.01 4.61 46.63 2.29
1989 2079 1.544825 GCTAGCTCCTGTCACCACCA 61.545 60.000 7.70 0.00 0.00 4.17
2051 2141 3.324108 GCCCTTACCCCCACGACA 61.324 66.667 0.00 0.00 0.00 4.35
2232 2322 5.752036 TTCTCCACTCATGACTTGATTCT 57.248 39.130 0.00 0.00 32.72 2.40
2295 2385 3.561725 CACTTTGCTTTCTCGGTTTCTCT 59.438 43.478 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.