Multiple sequence alignment - TraesCS6B01G178700

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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 TraesCS6B01G178700 chr6B 100.000 2630 0 0 1 2630 198921961 198919332 0.000000e+00 4857.0
1 TraesCS6B01G178700 chr6B 97.293 665 17 1 4 667 198934583 198933919 0.000000e+00 1127.0
2 TraesCS6B01G178700 chr6B 95.082 671 30 2 1 668 499264110 499264780 0.000000e+00 1053.0
3 TraesCS6B01G178700 chr6A 87.031 1172 96 33 696 1833 134552589 134551440 0.000000e+00 1271.0
4 TraesCS6B01G178700 chr7B 96.557 668 21 2 1 667 102954516 102953850 0.000000e+00 1105.0
5 TraesCS6B01G178700 chr7B 95.659 668 23 4 1 667 335324145 335323483 0.000000e+00 1068.0
6 TraesCS6B01G178700 chr7B 95.210 668 30 2 1 667 158810973 158811639 0.000000e+00 1055.0
7 TraesCS6B01G178700 chr7B 81.765 340 35 19 1011 1342 544973194 544973514 2.600000e-65 259.0
8 TraesCS6B01G178700 chr7B 81.115 323 37 18 1030 1342 675148547 675148855 1.220000e-58 237.0
9 TraesCS6B01G178700 chr5B 96.257 668 22 2 1 667 518494052 518493387 0.000000e+00 1092.0
10 TraesCS6B01G178700 chr3B 95.104 674 32 1 4 676 382197502 382196829 0.000000e+00 1061.0
11 TraesCS6B01G178700 chr3B 95.210 668 31 1 1 667 556523813 556524480 0.000000e+00 1055.0
12 TraesCS6B01G178700 chr2B 95.495 666 26 2 1 665 193030899 193031561 0.000000e+00 1061.0
13 TraesCS6B01G178700 chr2B 81.065 338 41 17 1011 1342 811187 810867 5.620000e-62 248.0
14 TraesCS6B01G178700 chr6D 95.215 627 16 8 751 1366 110161054 110160431 0.000000e+00 979.0
15 TraesCS6B01G178700 chr6D 82.620 748 99 23 1845 2571 110159787 110159050 1.330000e-177 632.0
16 TraesCS6B01G178700 chr6D 100.000 36 0 0 2595 2630 110159044 110159009 1.690000e-07 67.6
17 TraesCS6B01G178700 chr7D 83.383 337 33 16 1011 1342 596674654 596674972 9.210000e-75 291.0
18 TraesCS6B01G178700 chr2A 82.544 338 36 17 1011 1342 23796359 23796679 2.580000e-70 276.0
19 TraesCS6B01G178700 chr1A 82.196 337 40 13 1011 1342 11025908 11025587 3.340000e-69 272.0
20 TraesCS6B01G178700 chr1A 81.361 338 40 16 1011 1342 531839876 531839556 1.210000e-63 254.0
21 TraesCS6B01G178700 chr1B 82.059 340 34 19 1011 1342 658503957 658503637 5.580000e-67 265.0
22 TraesCS6B01G178700 chr7A 81.657 338 39 14 1011 1342 707844566 707844886 2.600000e-65 259.0
23 TraesCS6B01G178700 chr7A 81.341 343 37 20 1011 1342 689905329 689905655 1.210000e-63 254.0
24 TraesCS6B01G178700 chrUn 81.121 339 39 19 1011 1342 325844815 325844495 5.620000e-62 248.0


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 TraesCS6B01G178700 chr6B 198919332 198921961 2629 True 4857.000000 4857 100.000000 1 2630 1 chr6B.!!$R1 2629
1 TraesCS6B01G178700 chr6B 198933919 198934583 664 True 1127.000000 1127 97.293000 4 667 1 chr6B.!!$R2 663
2 TraesCS6B01G178700 chr6B 499264110 499264780 670 False 1053.000000 1053 95.082000 1 668 1 chr6B.!!$F1 667
3 TraesCS6B01G178700 chr6A 134551440 134552589 1149 True 1271.000000 1271 87.031000 696 1833 1 chr6A.!!$R1 1137
4 TraesCS6B01G178700 chr7B 102953850 102954516 666 True 1105.000000 1105 96.557000 1 667 1 chr7B.!!$R1 666
5 TraesCS6B01G178700 chr7B 335323483 335324145 662 True 1068.000000 1068 95.659000 1 667 1 chr7B.!!$R2 666
6 TraesCS6B01G178700 chr7B 158810973 158811639 666 False 1055.000000 1055 95.210000 1 667 1 chr7B.!!$F1 666
7 TraesCS6B01G178700 chr5B 518493387 518494052 665 True 1092.000000 1092 96.257000 1 667 1 chr5B.!!$R1 666
8 TraesCS6B01G178700 chr3B 382196829 382197502 673 True 1061.000000 1061 95.104000 4 676 1 chr3B.!!$R1 672
9 TraesCS6B01G178700 chr3B 556523813 556524480 667 False 1055.000000 1055 95.210000 1 667 1 chr3B.!!$F1 666
10 TraesCS6B01G178700 chr2B 193030899 193031561 662 False 1061.000000 1061 95.495000 1 665 1 chr2B.!!$F1 664
11 TraesCS6B01G178700 chr6D 110159009 110161054 2045 True 559.533333 979 92.611667 751 2630 3 chr6D.!!$R1 1879

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
896 916 0.321919 TCATCAGTCTGCAAGCCCAC 60.322 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2566 2804 0.250727 TAGTTTGTCTGGGTGCTGGC 60.251 55.0 0.0 0.0 0.0 4.85 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
214 215 1.825474 AGTGCCGCTACAGTATCAAGT 59.175 47.619 0.00 0.00 0.00 3.16
322 324 3.070446 CCAGCCGGATTACTATTGTACCA 59.930 47.826 5.05 0.00 0.00 3.25
400 411 7.906736 ACCTAGAGAGAGAGATAGACCAGATAT 59.093 40.741 0.00 0.00 0.00 1.63
591 602 2.303549 CTTCGCCTCATCCCGCTTCT 62.304 60.000 0.00 0.00 0.00 2.85
621 632 1.131883 CGACGTTCTACTCGTTCCCAT 59.868 52.381 0.00 0.00 41.64 4.00
670 681 1.832998 GTATCCAACCCCCGACAACTA 59.167 52.381 0.00 0.00 0.00 2.24
671 682 1.364269 ATCCAACCCCCGACAACTAA 58.636 50.000 0.00 0.00 0.00 2.24
676 687 3.069289 CAACCCCCGACAACTAAGTAAC 58.931 50.000 0.00 0.00 0.00 2.50
677 688 2.613129 ACCCCCGACAACTAAGTAACT 58.387 47.619 0.00 0.00 0.00 2.24
678 689 2.974794 ACCCCCGACAACTAAGTAACTT 59.025 45.455 0.00 0.00 0.00 2.66
679 690 3.392285 ACCCCCGACAACTAAGTAACTTT 59.608 43.478 0.00 0.00 0.00 2.66
680 691 4.592778 ACCCCCGACAACTAAGTAACTTTA 59.407 41.667 0.00 0.00 0.00 1.85
681 692 5.249163 ACCCCCGACAACTAAGTAACTTTAT 59.751 40.000 0.00 0.00 0.00 1.40
682 693 6.175471 CCCCCGACAACTAAGTAACTTTATT 58.825 40.000 0.00 0.00 0.00 1.40
683 694 6.314648 CCCCCGACAACTAAGTAACTTTATTC 59.685 42.308 0.00 0.00 0.00 1.75
684 695 7.101700 CCCCGACAACTAAGTAACTTTATTCT 58.898 38.462 0.00 0.00 0.00 2.40
685 696 7.277319 CCCCGACAACTAAGTAACTTTATTCTC 59.723 40.741 0.00 0.00 0.00 2.87
686 697 7.816031 CCCGACAACTAAGTAACTTTATTCTCA 59.184 37.037 0.00 0.00 0.00 3.27
687 698 8.645487 CCGACAACTAAGTAACTTTATTCTCAC 58.355 37.037 0.00 0.00 0.00 3.51
688 699 9.188588 CGACAACTAAGTAACTTTATTCTCACA 57.811 33.333 0.00 0.00 0.00 3.58
720 731 0.602905 GGCTCCCCGGAATATTGTCG 60.603 60.000 0.73 0.00 0.00 4.35
822 842 3.740115 ACAGCAATACGAAAGTTGGTCT 58.260 40.909 0.00 0.00 46.40 3.85
879 899 1.691434 GCCCAAGTTGGTCCATTTTCA 59.309 47.619 20.54 0.00 35.17 2.69
896 916 0.321919 TCATCAGTCTGCAAGCCCAC 60.322 55.000 0.00 0.00 0.00 4.61
925 945 2.936202 TCCAAGAAAGCAGCAGACTTT 58.064 42.857 0.00 0.00 39.99 2.66
926 946 3.290710 TCCAAGAAAGCAGCAGACTTTT 58.709 40.909 0.00 0.00 37.47 2.27
987 1007 1.891919 GAGCAAACGCACCTCCACA 60.892 57.895 0.00 0.00 0.00 4.17
1214 1245 1.593006 GATCTGACGCCGTATGGTTTG 59.407 52.381 2.17 0.00 37.67 2.93
1377 1409 3.488090 GCTTCTTCGTTCCCCGCG 61.488 66.667 0.00 0.00 36.19 6.46
1399 1431 1.190833 CCCCTCCGATCTGGGATCTG 61.191 65.000 14.50 0.36 46.15 2.90
1411 1443 1.067142 TGGGATCTGGTTTCTTCGTCG 60.067 52.381 0.00 0.00 0.00 5.12
1413 1445 1.203994 GGATCTGGTTTCTTCGTCGGA 59.796 52.381 0.00 0.00 0.00 4.55
1421 1523 3.479949 GTTTCTTCGTCGGAAATTCTGC 58.520 45.455 0.00 0.00 35.55 4.26
1454 1556 1.333308 CTGATGCGTGTGTTTGTGGAA 59.667 47.619 0.00 0.00 0.00 3.53
1457 1559 2.025589 TGCGTGTGTTTGTGGAAGTA 57.974 45.000 0.00 0.00 0.00 2.24
1459 1561 1.333791 GCGTGTGTTTGTGGAAGTAGC 60.334 52.381 0.00 0.00 0.00 3.58
1463 1565 1.225376 TGTTTGTGGAAGTAGCGCGG 61.225 55.000 8.83 0.00 0.00 6.46
1466 1568 4.752879 GTGGAAGTAGCGCGGGCA 62.753 66.667 27.20 9.82 43.41 5.36
1471 1573 1.366111 GAAGTAGCGCGGGCAATTCA 61.366 55.000 27.20 2.97 43.41 2.57
1479 1581 1.219664 CGGGCAATTCACCGTCCTA 59.780 57.895 8.76 0.00 44.85 2.94
1480 1582 0.810031 CGGGCAATTCACCGTCCTAG 60.810 60.000 8.76 0.00 44.85 3.02
1481 1583 0.463833 GGGCAATTCACCGTCCTAGG 60.464 60.000 0.82 0.82 37.30 3.02
1484 1586 1.742750 GCAATTCACCGTCCTAGGACC 60.743 57.143 31.78 16.74 41.76 4.46
1490 1592 2.123382 CGTCCTAGGACCCTCCCC 60.123 72.222 31.78 9.56 41.76 4.81
1493 1595 1.230853 TCCTAGGACCCTCCCCTGA 60.231 63.158 7.62 0.00 37.19 3.86
1495 1597 1.595058 CCTAGGACCCTCCCCTGAGT 61.595 65.000 1.05 0.00 37.19 3.41
1499 1601 2.233178 AGGACCCTCCCCTGAGTTATA 58.767 52.381 0.00 0.00 37.19 0.98
1502 1604 0.969894 CCCTCCCCTGAGTTATAGCG 59.030 60.000 0.00 0.00 36.86 4.26
1537 1650 6.265422 TGTGAGATCTTGTTAGAACTGACTCA 59.735 38.462 0.00 0.00 37.96 3.41
1539 1652 7.328249 GTGAGATCTTGTTAGAACTGACTCAAG 59.672 40.741 0.00 0.00 35.52 3.02
1554 1667 8.902540 ACTGACTCAAGTTATGTTTGTTATGA 57.097 30.769 0.00 0.00 0.00 2.15
1555 1668 8.774586 ACTGACTCAAGTTATGTTTGTTATGAC 58.225 33.333 0.00 0.00 0.00 3.06
1559 1672 7.227910 ACTCAAGTTATGTTTGTTATGACCGTT 59.772 33.333 0.00 0.00 0.00 4.44
1565 1678 9.698617 GTTATGTTTGTTATGACCGTTTCTATC 57.301 33.333 0.00 0.00 0.00 2.08
1566 1679 9.661563 TTATGTTTGTTATGACCGTTTCTATCT 57.338 29.630 0.00 0.00 0.00 1.98
1582 1695 8.135529 CGTTTCTATCTGGTAGTGTGATTGATA 58.864 37.037 0.00 0.00 0.00 2.15
1585 1698 8.712228 TCTATCTGGTAGTGTGATTGATACAT 57.288 34.615 0.00 0.00 0.00 2.29
1586 1699 8.579863 TCTATCTGGTAGTGTGATTGATACATG 58.420 37.037 0.00 0.00 0.00 3.21
1593 1706 3.696051 GTGTGATTGATACATGGGTGCTT 59.304 43.478 0.00 0.00 0.00 3.91
1594 1707 3.947196 TGTGATTGATACATGGGTGCTTC 59.053 43.478 0.00 0.00 0.00 3.86
1595 1708 3.316308 GTGATTGATACATGGGTGCTTCC 59.684 47.826 0.00 0.00 0.00 3.46
1596 1709 3.202818 TGATTGATACATGGGTGCTTCCT 59.797 43.478 0.00 0.00 36.25 3.36
1597 1710 2.715749 TGATACATGGGTGCTTCCTG 57.284 50.000 0.00 0.00 36.25 3.86
1598 1711 1.312815 GATACATGGGTGCTTCCTGC 58.687 55.000 0.00 0.00 43.25 4.85
1599 1712 0.921896 ATACATGGGTGCTTCCTGCT 59.078 50.000 0.00 0.00 43.37 4.24
1600 1713 0.698238 TACATGGGTGCTTCCTGCTT 59.302 50.000 0.00 0.00 43.37 3.91
1610 1723 3.255642 GTGCTTCCTGCTTTGTTTGGATA 59.744 43.478 0.00 0.00 43.37 2.59
1615 1728 6.723298 TTCCTGCTTTGTTTGGATAAGAAA 57.277 33.333 0.00 0.00 0.00 2.52
1619 1739 6.930722 CCTGCTTTGTTTGGATAAGAAATTGT 59.069 34.615 0.00 0.00 0.00 2.71
1637 1757 3.278668 TGTTTCGTTTTCACCAGGGTA 57.721 42.857 0.00 0.00 0.00 3.69
1638 1758 3.618351 TGTTTCGTTTTCACCAGGGTAA 58.382 40.909 0.00 0.00 0.00 2.85
1639 1759 4.208746 TGTTTCGTTTTCACCAGGGTAAT 58.791 39.130 0.00 0.00 0.00 1.89
1640 1760 4.276431 TGTTTCGTTTTCACCAGGGTAATC 59.724 41.667 0.00 0.00 0.00 1.75
1641 1761 3.773418 TCGTTTTCACCAGGGTAATCA 57.227 42.857 0.00 0.00 0.00 2.57
1643 1763 3.816523 TCGTTTTCACCAGGGTAATCAAC 59.183 43.478 0.00 0.00 0.00 3.18
1659 1779 8.202745 GGTAATCAACCTTAGTTCTTGAGATG 57.797 38.462 0.00 0.00 45.75 2.90
1660 1780 8.041323 GGTAATCAACCTTAGTTCTTGAGATGA 58.959 37.037 0.00 0.00 45.75 2.92
1676 1796 5.116882 TGAGATGATGCTCACTGAATTGAG 58.883 41.667 0.00 0.00 45.15 3.02
1679 1799 3.603532 TGATGCTCACTGAATTGAGTCC 58.396 45.455 0.00 0.00 44.34 3.85
1685 1805 1.800805 ACTGAATTGAGTCCAGTGCG 58.199 50.000 0.00 0.00 39.43 5.34
1686 1806 0.445436 CTGAATTGAGTCCAGTGCGC 59.555 55.000 0.00 0.00 0.00 6.09
1688 1808 1.160137 GAATTGAGTCCAGTGCGCTT 58.840 50.000 9.73 0.00 0.00 4.68
1690 1810 0.674895 ATTGAGTCCAGTGCGCTTCC 60.675 55.000 9.73 0.00 0.00 3.46
1691 1811 2.435059 GAGTCCAGTGCGCTTCCC 60.435 66.667 9.73 0.00 0.00 3.97
1692 1812 4.379243 AGTCCAGTGCGCTTCCCG 62.379 66.667 9.73 0.00 40.75 5.14
1693 1813 4.681978 GTCCAGTGCGCTTCCCGT 62.682 66.667 9.73 0.00 39.71 5.28
1713 1833 5.508153 CCCGTGTGATTTCCATTTTTGTGTA 60.508 40.000 0.00 0.00 0.00 2.90
1737 1863 2.158726 AGTTACTTGGTTTGGAGCCGAA 60.159 45.455 0.00 0.00 0.00 4.30
1742 1868 3.133901 ACTTGGTTTGGAGCCGAATTTTT 59.866 39.130 0.00 0.00 0.00 1.94
1752 1878 0.240945 CCGAATTTTTGGCGCTGACT 59.759 50.000 7.64 0.00 0.00 3.41
1778 1904 5.221621 GGTATTCTCATGCTCTTAGCCTCTT 60.222 44.000 0.00 0.00 41.51 2.85
1780 1906 5.528043 TTCTCATGCTCTTAGCCTCTTAG 57.472 43.478 0.00 0.00 41.51 2.18
1781 1907 4.541705 TCTCATGCTCTTAGCCTCTTAGT 58.458 43.478 0.00 0.00 41.51 2.24
1789 1915 6.095160 TGCTCTTAGCCTCTTAGTAGTTACAC 59.905 42.308 0.00 0.00 41.51 2.90
1801 1927 9.243105 TCTTAGTAGTTACACCGTTTACCTTAT 57.757 33.333 0.00 0.00 0.00 1.73
1813 1942 5.124776 CCGTTTACCTTATCCAGCATTGAAA 59.875 40.000 0.00 0.00 0.00 2.69
1817 1946 4.677182 ACCTTATCCAGCATTGAAACCTT 58.323 39.130 0.00 0.00 0.00 3.50
1822 1951 1.067354 CCAGCATTGAAACCTTGAGGC 60.067 52.381 0.00 0.00 39.32 4.70
1824 1953 0.598065 GCATTGAAACCTTGAGGCGT 59.402 50.000 0.00 0.00 39.32 5.68
1830 1959 1.531578 GAAACCTTGAGGCGTGAGTTC 59.468 52.381 0.00 0.00 39.32 3.01
1831 1960 0.759346 AACCTTGAGGCGTGAGTTCT 59.241 50.000 0.00 0.00 39.32 3.01
1833 1962 1.270358 ACCTTGAGGCGTGAGTTCTTC 60.270 52.381 0.00 0.00 39.32 2.87
1834 1963 1.001406 CCTTGAGGCGTGAGTTCTTCT 59.999 52.381 0.00 0.00 0.00 2.85
1836 1965 1.328279 TGAGGCGTGAGTTCTTCTGA 58.672 50.000 0.00 0.00 0.00 3.27
1837 1966 1.686587 TGAGGCGTGAGTTCTTCTGAA 59.313 47.619 0.00 0.00 0.00 3.02
1838 1967 2.300152 TGAGGCGTGAGTTCTTCTGAAT 59.700 45.455 0.00 0.00 34.40 2.57
1839 1968 3.244215 TGAGGCGTGAGTTCTTCTGAATT 60.244 43.478 0.00 0.00 34.40 2.17
1840 1969 3.070018 AGGCGTGAGTTCTTCTGAATTG 58.930 45.455 0.00 0.00 34.40 2.32
1841 1970 2.808543 GGCGTGAGTTCTTCTGAATTGT 59.191 45.455 0.00 0.00 34.40 2.71
1842 1971 3.994392 GGCGTGAGTTCTTCTGAATTGTA 59.006 43.478 0.00 0.00 34.40 2.41
1843 1972 4.092091 GGCGTGAGTTCTTCTGAATTGTAG 59.908 45.833 0.00 0.00 34.40 2.74
1852 2074 5.978814 TCTTCTGAATTGTAGTAAGGGAGC 58.021 41.667 0.00 0.00 0.00 4.70
1854 2076 3.132289 TCTGAATTGTAGTAAGGGAGCCG 59.868 47.826 0.00 0.00 0.00 5.52
1856 2078 1.497161 ATTGTAGTAAGGGAGCCGCT 58.503 50.000 0.00 0.00 0.00 5.52
1875 2097 5.625721 GCCGCTATAAGTAGTATATGCATCG 59.374 44.000 0.19 0.00 0.00 3.84
1876 2098 6.143496 CCGCTATAAGTAGTATATGCATCGG 58.857 44.000 0.19 0.21 0.00 4.18
1883 2105 4.528596 AGTAGTATATGCATCGGCTCCTTT 59.471 41.667 0.19 0.00 41.91 3.11
1887 2109 1.549203 ATGCATCGGCTCCTTTTGTT 58.451 45.000 0.00 0.00 41.91 2.83
1890 2112 1.402852 GCATCGGCTCCTTTTGTTTCC 60.403 52.381 0.00 0.00 36.96 3.13
1894 2116 3.757270 TCGGCTCCTTTTGTTTCCAATA 58.243 40.909 0.00 0.00 0.00 1.90
1914 2136 7.831690 TCCAATATTTCATTGTAACAGCCAGTA 59.168 33.333 0.00 0.00 0.00 2.74
1915 2137 8.632679 CCAATATTTCATTGTAACAGCCAGTAT 58.367 33.333 0.00 0.00 0.00 2.12
1920 2142 6.995511 TCATTGTAACAGCCAGTATAAACC 57.004 37.500 0.00 0.00 0.00 3.27
1929 2151 6.717289 ACAGCCAGTATAAACCTGAACAATA 58.283 36.000 0.00 0.00 31.38 1.90
1933 2155 8.491134 AGCCAGTATAAACCTGAACAATATGTA 58.509 33.333 0.00 0.00 31.38 2.29
1966 2188 5.207110 ACTATCCATAGCAAGCAGTAGTG 57.793 43.478 0.00 0.00 33.68 2.74
1978 2200 7.756558 AGCAAGCAGTAGTGATTTTCTTTATC 58.243 34.615 0.42 0.00 26.60 1.75
1980 2202 7.475840 CAAGCAGTAGTGATTTTCTTTATCCC 58.524 38.462 0.42 0.00 26.60 3.85
2015 2237 9.521503 GGTTCTTTATGAAATTAAATGCCTCTC 57.478 33.333 0.00 0.00 36.30 3.20
2020 2242 9.874205 TTTATGAAATTAAATGCCTCTCTTTGG 57.126 29.630 0.00 0.00 0.00 3.28
2021 2243 7.722949 ATGAAATTAAATGCCTCTCTTTGGA 57.277 32.000 0.00 0.00 0.00 3.53
2026 2248 2.797177 ATGCCTCTCTTTGGACCTTC 57.203 50.000 0.00 0.00 0.00 3.46
2031 2253 3.254411 GCCTCTCTTTGGACCTTCTTTTG 59.746 47.826 0.00 0.00 0.00 2.44
2032 2254 4.464947 CCTCTCTTTGGACCTTCTTTTGT 58.535 43.478 0.00 0.00 0.00 2.83
2034 2256 5.009110 CCTCTCTTTGGACCTTCTTTTGTTC 59.991 44.000 0.00 0.00 0.00 3.18
2035 2257 4.574828 TCTCTTTGGACCTTCTTTTGTTCG 59.425 41.667 0.00 0.00 0.00 3.95
2036 2258 4.266714 TCTTTGGACCTTCTTTTGTTCGT 58.733 39.130 0.00 0.00 0.00 3.85
2037 2259 4.095782 TCTTTGGACCTTCTTTTGTTCGTG 59.904 41.667 0.00 0.00 0.00 4.35
2038 2260 2.294074 TGGACCTTCTTTTGTTCGTGG 58.706 47.619 0.00 0.00 0.00 4.94
2039 2261 2.092861 TGGACCTTCTTTTGTTCGTGGA 60.093 45.455 0.00 0.00 0.00 4.02
2040 2262 2.946990 GGACCTTCTTTTGTTCGTGGAA 59.053 45.455 0.00 0.00 0.00 3.53
2041 2263 3.003378 GGACCTTCTTTTGTTCGTGGAAG 59.997 47.826 0.00 0.00 34.82 3.46
2042 2264 3.875134 GACCTTCTTTTGTTCGTGGAAGA 59.125 43.478 0.00 0.00 36.48 2.87
2045 2267 5.215160 CCTTCTTTTGTTCGTGGAAGATTG 58.785 41.667 0.00 0.00 36.48 2.67
2047 2269 6.443934 TTCTTTTGTTCGTGGAAGATTGAA 57.556 33.333 0.00 0.00 0.00 2.69
2049 2271 6.494842 TCTTTTGTTCGTGGAAGATTGAAAG 58.505 36.000 0.00 0.00 0.00 2.62
2050 2272 5.828299 TTTGTTCGTGGAAGATTGAAAGT 57.172 34.783 0.00 0.00 0.00 2.66
2051 2273 4.811555 TGTTCGTGGAAGATTGAAAGTG 57.188 40.909 0.00 0.00 0.00 3.16
2052 2274 3.003275 TGTTCGTGGAAGATTGAAAGTGC 59.997 43.478 0.00 0.00 0.00 4.40
2053 2275 2.844946 TCGTGGAAGATTGAAAGTGCA 58.155 42.857 0.00 0.00 0.00 4.57
2056 2278 3.058016 CGTGGAAGATTGAAAGTGCACAT 60.058 43.478 21.04 3.48 32.44 3.21
2068 2290 2.430465 AGTGCACATACTTCCAAGCTG 58.570 47.619 21.04 0.00 0.00 4.24
2076 2298 6.294473 CACATACTTCCAAGCTGATATCCTT 58.706 40.000 0.00 0.00 0.00 3.36
2078 2300 6.995091 ACATACTTCCAAGCTGATATCCTTTC 59.005 38.462 0.00 0.00 0.00 2.62
2084 2313 6.957631 TCCAAGCTGATATCCTTTCAACTTA 58.042 36.000 0.00 0.00 30.49 2.24
2103 2332 8.267894 TCAACTTAATCTGCTTTAGAGGCTTAT 58.732 33.333 0.00 0.00 39.20 1.73
2117 2346 6.029346 AGAGGCTTATTGTGGTTTTCATTG 57.971 37.500 0.00 0.00 0.00 2.82
2120 2349 6.591001 AGGCTTATTGTGGTTTTCATTGTTT 58.409 32.000 0.00 0.00 0.00 2.83
2122 2351 8.374743 AGGCTTATTGTGGTTTTCATTGTTTAT 58.625 29.630 0.00 0.00 0.00 1.40
2125 2354 8.893219 TTATTGTGGTTTTCATTGTTTATGCA 57.107 26.923 0.00 0.00 34.06 3.96
2131 2360 8.821894 GTGGTTTTCATTGTTTATGCAGTTTTA 58.178 29.630 0.00 0.00 34.06 1.52
2143 2372 9.793252 GTTTATGCAGTTTTAATCATCATGACT 57.207 29.630 0.00 0.00 0.00 3.41
2162 2391 4.338118 TGACTTTGTTTCATTCAGTGACCC 59.662 41.667 0.00 0.00 36.32 4.46
2163 2392 4.277476 ACTTTGTTTCATTCAGTGACCCA 58.723 39.130 0.00 0.00 36.32 4.51
2164 2393 4.895297 ACTTTGTTTCATTCAGTGACCCAT 59.105 37.500 0.00 0.00 36.32 4.00
2171 2400 4.104086 TCATTCAGTGACCCATTCTACCT 58.896 43.478 0.00 0.00 0.00 3.08
2173 2402 3.981071 TCAGTGACCCATTCTACCTTG 57.019 47.619 0.00 0.00 0.00 3.61
2180 2409 7.993183 CAGTGACCCATTCTACCTTGTATAAAT 59.007 37.037 0.00 0.00 0.00 1.40
2183 2412 9.762381 TGACCCATTCTACCTTGTATAAATTTT 57.238 29.630 0.00 0.00 0.00 1.82
2193 2422 7.532571 ACCTTGTATAAATTTTCAACGTAGGC 58.467 34.615 0.00 0.00 0.00 3.93
2199 2428 2.570415 TTTTCAACGTAGGCCCATGA 57.430 45.000 0.00 0.00 0.00 3.07
2213 2442 6.398655 AGGCCCATGATGATGATAAGTTAT 57.601 37.500 0.00 0.00 0.00 1.89
2218 2447 7.337689 GCCCATGATGATGATAAGTTATGCTTA 59.662 37.037 0.00 0.00 43.13 3.09
2247 2476 5.846203 ACTGCATGTGAAAGCATACTTTTT 58.154 33.333 0.00 0.00 46.20 1.94
2271 2500 5.390387 TGCACCAGGTCCTTTTAAATAACT 58.610 37.500 0.00 0.00 0.00 2.24
2279 2508 9.391006 CAGGTCCTTTTAAATAACTGTATGCTA 57.609 33.333 0.00 0.00 0.00 3.49
2306 2537 8.620116 TTTACAAGAATTCATGTGATCAGTCA 57.380 30.769 23.03 1.18 0.00 3.41
2307 2538 6.738832 ACAAGAATTCATGTGATCAGTCAG 57.261 37.500 15.13 0.00 34.36 3.51
2315 2547 4.640201 TCATGTGATCAGTCAGACGACATA 59.360 41.667 0.00 0.00 45.23 2.29
2330 2562 9.231297 TCAGACGACATACATCTGATATATCAA 57.769 33.333 16.08 8.15 41.84 2.57
2352 2588 7.383687 TCAATATCTTGACTCCTTACGTTTGT 58.616 34.615 0.00 0.00 36.46 2.83
2353 2589 7.330946 TCAATATCTTGACTCCTTACGTTTGTG 59.669 37.037 0.00 0.00 36.46 3.33
2358 2594 5.883503 TGACTCCTTACGTTTGTGTTTTT 57.116 34.783 0.00 0.00 0.00 1.94
2363 2599 9.934190 GACTCCTTACGTTTGTGTTTTTATTTA 57.066 29.630 0.00 0.00 0.00 1.40
2376 2612 9.689976 TGTGTTTTTATTTATGATTGTGTCTGG 57.310 29.630 0.00 0.00 0.00 3.86
2387 2623 2.455674 TGTGTCTGGTTCTGGATTCG 57.544 50.000 0.00 0.00 0.00 3.34
2402 2638 4.331108 TGGATTCGGAAAACATGTGATCA 58.669 39.130 0.00 0.00 0.00 2.92
2403 2639 4.155826 TGGATTCGGAAAACATGTGATCAC 59.844 41.667 19.27 19.27 0.00 3.06
2405 2641 4.747540 TTCGGAAAACATGTGATCACAG 57.252 40.909 30.63 23.62 45.48 3.66
2426 2662 7.985184 TCACAGATTGTTGAACTACATATACCC 59.015 37.037 0.00 0.00 0.00 3.69
2463 2701 6.375455 ACTTTGCAACTTCTGATGGTATAAGG 59.625 38.462 0.00 0.00 0.00 2.69
2490 2728 8.230472 TGGAATATGCCAAATGTTTTTGTTTT 57.770 26.923 0.00 0.00 40.55 2.43
2500 2738 7.012232 CCAAATGTTTTTGTTTTGATAGCCTGT 59.988 33.333 0.00 0.00 40.55 4.00
2503 2741 8.816640 ATGTTTTTGTTTTGATAGCCTGTAAG 57.183 30.769 0.00 0.00 0.00 2.34
2514 2752 8.446599 TTGATAGCCTGTAAGTTATTTTAGCC 57.553 34.615 0.00 0.00 0.00 3.93
2515 2753 6.996282 TGATAGCCTGTAAGTTATTTTAGCCC 59.004 38.462 0.00 0.00 0.00 5.19
2521 2759 7.277760 GCCTGTAAGTTATTTTAGCCCAATTTG 59.722 37.037 0.00 0.00 0.00 2.32
2523 2761 9.139174 CTGTAAGTTATTTTAGCCCAATTTGTG 57.861 33.333 0.00 0.00 0.00 3.33
2524 2762 7.600752 TGTAAGTTATTTTAGCCCAATTTGTGC 59.399 33.333 0.00 0.00 0.00 4.57
2528 2766 4.363991 TTTTAGCCCAATTTGTGCCAAT 57.636 36.364 0.00 0.00 0.00 3.16
2557 2795 8.986929 ATTCTAAACCTTGAATCCTGGATTAG 57.013 34.615 21.39 15.52 37.48 1.73
2562 2800 4.540099 ACCTTGAATCCTGGATTAGAACCA 59.460 41.667 21.39 12.06 31.89 3.67
2566 2804 7.446625 CCTTGAATCCTGGATTAGAACCATTAG 59.553 40.741 21.39 9.89 36.79 1.73
2571 2809 3.817647 CTGGATTAGAACCATTAGCCAGC 59.182 47.826 0.00 0.00 35.74 4.85
2572 2810 3.201930 TGGATTAGAACCATTAGCCAGCA 59.798 43.478 0.00 0.00 32.03 4.41
2574 2812 2.710096 TAGAACCATTAGCCAGCACC 57.290 50.000 0.00 0.00 0.00 5.01
2575 2813 0.034089 AGAACCATTAGCCAGCACCC 60.034 55.000 0.00 0.00 0.00 4.61
2576 2814 0.323360 GAACCATTAGCCAGCACCCA 60.323 55.000 0.00 0.00 0.00 4.51
2577 2815 0.323725 AACCATTAGCCAGCACCCAG 60.324 55.000 0.00 0.00 0.00 4.45
2578 2816 1.207488 ACCATTAGCCAGCACCCAGA 61.207 55.000 0.00 0.00 0.00 3.86
2579 2817 0.749454 CCATTAGCCAGCACCCAGAC 60.749 60.000 0.00 0.00 0.00 3.51
2580 2818 0.035152 CATTAGCCAGCACCCAGACA 60.035 55.000 0.00 0.00 0.00 3.41
2581 2819 0.698238 ATTAGCCAGCACCCAGACAA 59.302 50.000 0.00 0.00 0.00 3.18
2582 2820 0.476338 TTAGCCAGCACCCAGACAAA 59.524 50.000 0.00 0.00 0.00 2.83
2583 2821 0.250727 TAGCCAGCACCCAGACAAAC 60.251 55.000 0.00 0.00 0.00 2.93
2584 2822 1.529244 GCCAGCACCCAGACAAACT 60.529 57.895 0.00 0.00 0.00 2.66
2585 2823 0.250727 GCCAGCACCCAGACAAACTA 60.251 55.000 0.00 0.00 0.00 2.24
2586 2824 1.523758 CCAGCACCCAGACAAACTAC 58.476 55.000 0.00 0.00 0.00 2.73
2587 2825 1.072331 CCAGCACCCAGACAAACTACT 59.928 52.381 0.00 0.00 0.00 2.57
2588 2826 2.417719 CAGCACCCAGACAAACTACTC 58.582 52.381 0.00 0.00 0.00 2.59
2589 2827 2.047061 AGCACCCAGACAAACTACTCA 58.953 47.619 0.00 0.00 0.00 3.41
2590 2828 2.037772 AGCACCCAGACAAACTACTCAG 59.962 50.000 0.00 0.00 0.00 3.35
2591 2829 2.417719 CACCCAGACAAACTACTCAGC 58.582 52.381 0.00 0.00 0.00 4.26
2592 2830 1.348036 ACCCAGACAAACTACTCAGCC 59.652 52.381 0.00 0.00 0.00 4.85
2593 2831 1.339151 CCCAGACAAACTACTCAGCCC 60.339 57.143 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.263572 CGGCCCACCCACTGACAA 62.264 66.667 0.00 0.00 0.00 3.18
322 324 1.396662 TATATAGGCCTACCCCCGGT 58.603 55.000 16.61 0.00 40.16 5.28
400 411 0.627768 TAGCTCTCTCCTCCCTGGGA 60.628 60.000 16.13 16.13 36.20 4.37
507 518 2.365941 GGAGATAACACCCCTACTGCTC 59.634 54.545 0.00 0.00 0.00 4.26
591 602 4.424566 GAACGTCGCCGGTGCCTA 62.425 66.667 11.05 0.00 38.78 3.93
615 626 3.659195 AGGATGGCTTATCATGATGGGAA 59.341 43.478 18.72 3.88 37.54 3.97
671 682 9.372369 GCAGTTATCTGTGAGAATAAAGTTACT 57.628 33.333 2.85 0.00 43.05 2.24
676 687 7.201679 CCCAAGCAGTTATCTGTGAGAATAAAG 60.202 40.741 2.85 0.00 43.05 1.85
677 688 6.599244 CCCAAGCAGTTATCTGTGAGAATAAA 59.401 38.462 2.85 0.00 43.05 1.40
678 689 6.115446 CCCAAGCAGTTATCTGTGAGAATAA 58.885 40.000 2.85 0.00 43.05 1.40
679 690 5.674525 CCCAAGCAGTTATCTGTGAGAATA 58.325 41.667 2.85 0.00 43.05 1.75
680 691 4.521146 CCCAAGCAGTTATCTGTGAGAAT 58.479 43.478 2.85 0.00 43.05 2.40
681 692 3.869912 GCCCAAGCAGTTATCTGTGAGAA 60.870 47.826 2.85 0.00 43.05 2.87
682 693 2.355108 GCCCAAGCAGTTATCTGTGAGA 60.355 50.000 2.85 0.00 43.05 3.27
683 694 2.012673 GCCCAAGCAGTTATCTGTGAG 58.987 52.381 2.85 0.00 43.05 3.51
684 695 1.630369 AGCCCAAGCAGTTATCTGTGA 59.370 47.619 2.85 0.00 43.05 3.58
685 696 2.012673 GAGCCCAAGCAGTTATCTGTG 58.987 52.381 2.85 0.00 43.05 3.66
686 697 1.065126 GGAGCCCAAGCAGTTATCTGT 60.065 52.381 2.85 0.00 43.05 3.41
687 698 1.673168 GGAGCCCAAGCAGTTATCTG 58.327 55.000 0.00 0.00 43.56 2.90
688 699 0.548510 GGGAGCCCAAGCAGTTATCT 59.451 55.000 0.00 0.00 43.56 1.98
689 700 0.466372 GGGGAGCCCAAGCAGTTATC 60.466 60.000 8.02 0.00 44.65 1.75
690 701 1.615262 GGGGAGCCCAAGCAGTTAT 59.385 57.895 8.02 0.00 44.65 1.89
691 702 2.966732 CGGGGAGCCCAAGCAGTTA 61.967 63.158 8.02 0.00 45.83 2.24
692 703 4.351054 CGGGGAGCCCAAGCAGTT 62.351 66.667 8.02 0.00 45.83 3.16
716 727 3.407443 GGTTCCCTTGGAAACGACA 57.593 52.632 0.00 0.00 43.86 4.35
822 842 6.579666 ATTGCTTGCAGACTGAAGAAAATA 57.420 33.333 6.65 0.00 0.00 1.40
865 885 4.616835 GCAGACTGATGAAAATGGACCAAC 60.617 45.833 6.65 0.00 0.00 3.77
879 899 1.376424 CGTGGGCTTGCAGACTGAT 60.376 57.895 6.65 0.00 0.00 2.90
896 916 1.379642 GCTTTCTTGGATGGGCCTCG 61.380 60.000 4.53 0.00 37.63 4.63
925 945 4.212425 ACGATGCGTGTTTTAATGAGACAA 59.788 37.500 0.00 0.00 39.18 3.18
926 946 3.743911 ACGATGCGTGTTTTAATGAGACA 59.256 39.130 0.00 0.00 39.18 3.41
936 956 0.321210 TGGATGGACGATGCGTGTTT 60.321 50.000 0.00 0.00 41.37 2.83
987 1007 0.985490 GGAGAGGTGGGAGGCAGAAT 60.985 60.000 0.00 0.00 0.00 2.40
1214 1245 2.959357 GAACTCTGCACACGCCAGC 61.959 63.158 0.00 0.00 37.32 4.85
1380 1412 1.157276 AGATCCCAGATCGGAGGGG 59.843 63.158 17.43 12.91 45.51 4.79
1399 1431 3.667166 GCAGAATTTCCGACGAAGAAACC 60.667 47.826 0.00 0.00 36.13 3.27
1411 1443 4.536687 CGGGCGCGCAGAATTTCC 62.537 66.667 34.42 21.25 0.00 3.13
1413 1445 3.361977 AACGGGCGCGCAGAATTT 61.362 55.556 34.42 14.80 0.00 1.82
1421 1523 3.118454 ATCAGAACAACGGGCGCG 61.118 61.111 22.69 22.69 0.00 6.86
1454 1556 2.106683 GTGAATTGCCCGCGCTACT 61.107 57.895 5.56 0.00 35.36 2.57
1463 1565 0.539986 TCCTAGGACGGTGAATTGCC 59.460 55.000 7.62 0.00 0.00 4.52
1466 1568 1.201424 GGGTCCTAGGACGGTGAATT 58.799 55.000 31.00 0.00 45.41 2.17
1471 1573 2.688538 GGAGGGTCCTAGGACGGT 59.311 66.667 31.00 22.19 45.41 4.83
1477 1579 0.340208 AACTCAGGGGAGGGTCCTAG 59.660 60.000 0.00 0.00 45.81 3.02
1479 1581 1.027815 ATAACTCAGGGGAGGGTCCT 58.972 55.000 0.00 0.00 45.81 3.85
1480 1582 2.610873 CTATAACTCAGGGGAGGGTCC 58.389 57.143 0.00 0.00 45.81 4.46
1481 1583 1.972075 GCTATAACTCAGGGGAGGGTC 59.028 57.143 0.00 0.00 45.81 4.46
1484 1586 1.614413 GACGCTATAACTCAGGGGAGG 59.386 57.143 0.00 0.00 45.81 4.30
1490 1592 5.177881 ACAGATCTACGACGCTATAACTCAG 59.822 44.000 0.00 0.00 0.00 3.35
1493 1595 5.055144 TCACAGATCTACGACGCTATAACT 58.945 41.667 0.00 0.00 0.00 2.24
1495 1597 5.295152 TCTCACAGATCTACGACGCTATAA 58.705 41.667 0.00 0.00 0.00 0.98
1499 1601 2.025589 TCTCACAGATCTACGACGCT 57.974 50.000 0.00 0.00 0.00 5.07
1524 1637 8.958119 ACAAACATAACTTGAGTCAGTTCTAA 57.042 30.769 10.12 0.00 38.07 2.10
1537 1650 8.161699 AGAAACGGTCATAACAAACATAACTT 57.838 30.769 0.00 0.00 0.00 2.66
1539 1652 9.698617 GATAGAAACGGTCATAACAAACATAAC 57.301 33.333 0.00 0.00 0.00 1.89
1554 1667 4.084287 TCACACTACCAGATAGAAACGGT 58.916 43.478 0.00 0.00 34.65 4.83
1555 1668 4.713824 TCACACTACCAGATAGAAACGG 57.286 45.455 0.00 0.00 34.65 4.44
1559 1672 8.533569 TGTATCAATCACACTACCAGATAGAA 57.466 34.615 0.00 0.00 34.65 2.10
1565 1678 5.059161 CCCATGTATCAATCACACTACCAG 58.941 45.833 0.00 0.00 0.00 4.00
1566 1679 4.473196 ACCCATGTATCAATCACACTACCA 59.527 41.667 0.00 0.00 0.00 3.25
1593 1706 6.916360 ATTTCTTATCCAAACAAAGCAGGA 57.084 33.333 0.00 0.00 34.12 3.86
1594 1707 6.930722 ACAATTTCTTATCCAAACAAAGCAGG 59.069 34.615 0.00 0.00 0.00 4.85
1595 1708 7.951530 ACAATTTCTTATCCAAACAAAGCAG 57.048 32.000 0.00 0.00 0.00 4.24
1596 1709 8.729805 AAACAATTTCTTATCCAAACAAAGCA 57.270 26.923 0.00 0.00 0.00 3.91
1597 1710 8.003784 CGAAACAATTTCTTATCCAAACAAAGC 58.996 33.333 0.25 0.00 37.52 3.51
1598 1711 9.030301 ACGAAACAATTTCTTATCCAAACAAAG 57.970 29.630 0.00 0.00 37.52 2.77
1599 1712 8.934507 ACGAAACAATTTCTTATCCAAACAAA 57.065 26.923 0.00 0.00 37.52 2.83
1600 1713 8.934507 AACGAAACAATTTCTTATCCAAACAA 57.065 26.923 0.00 0.00 37.52 2.83
1610 1723 5.810074 CCTGGTGAAAACGAAACAATTTCTT 59.190 36.000 0.00 0.00 37.52 2.52
1615 1728 3.028130 ACCCTGGTGAAAACGAAACAAT 58.972 40.909 0.00 0.00 0.00 2.71
1619 1739 4.462133 TGATTACCCTGGTGAAAACGAAA 58.538 39.130 0.00 0.00 0.00 3.46
1637 1757 7.066766 GCATCATCTCAAGAACTAAGGTTGATT 59.933 37.037 0.00 0.00 35.58 2.57
1638 1758 6.541641 GCATCATCTCAAGAACTAAGGTTGAT 59.458 38.462 0.00 0.00 35.58 2.57
1639 1759 5.877012 GCATCATCTCAAGAACTAAGGTTGA 59.123 40.000 0.00 0.00 35.58 3.18
1640 1760 5.879223 AGCATCATCTCAAGAACTAAGGTTG 59.121 40.000 0.00 0.00 35.58 3.77
1641 1761 6.059787 AGCATCATCTCAAGAACTAAGGTT 57.940 37.500 0.00 0.00 38.52 3.50
1643 1763 5.668471 TGAGCATCATCTCAAGAACTAAGG 58.332 41.667 0.00 0.00 42.56 2.69
1676 1796 4.681978 ACGGGAAGCGCACTGGAC 62.682 66.667 11.47 0.00 0.00 4.02
1679 1799 3.716006 CACACGGGAAGCGCACTG 61.716 66.667 11.47 7.15 0.00 3.66
1684 1804 0.953471 TGGAAATCACACGGGAAGCG 60.953 55.000 0.00 0.00 0.00 4.68
1685 1805 1.463674 ATGGAAATCACACGGGAAGC 58.536 50.000 0.00 0.00 0.00 3.86
1686 1806 4.519540 AAAATGGAAATCACACGGGAAG 57.480 40.909 0.00 0.00 0.00 3.46
1688 1808 3.639094 ACAAAAATGGAAATCACACGGGA 59.361 39.130 0.00 0.00 0.00 5.14
1690 1810 4.367450 ACACAAAAATGGAAATCACACGG 58.633 39.130 0.00 0.00 0.00 4.94
1691 1811 6.205784 AGTACACAAAAATGGAAATCACACG 58.794 36.000 0.00 0.00 0.00 4.49
1692 1812 8.349983 ACTAGTACACAAAAATGGAAATCACAC 58.650 33.333 0.00 0.00 0.00 3.82
1693 1813 8.458573 ACTAGTACACAAAAATGGAAATCACA 57.541 30.769 0.00 0.00 0.00 3.58
1713 1833 3.556423 CGGCTCCAAACCAAGTAACTAGT 60.556 47.826 0.00 0.00 0.00 2.57
1737 1863 0.827507 ACCCAGTCAGCGCCAAAAAT 60.828 50.000 2.29 0.00 0.00 1.82
1742 1868 1.220749 GAATACCCAGTCAGCGCCA 59.779 57.895 2.29 0.00 0.00 5.69
1746 1872 2.158842 AGCATGAGAATACCCAGTCAGC 60.159 50.000 0.00 0.00 0.00 4.26
1750 1876 4.202305 GCTAAGAGCATGAGAATACCCAGT 60.202 45.833 0.00 0.00 41.89 4.00
1752 1878 3.071602 GGCTAAGAGCATGAGAATACCCA 59.928 47.826 0.00 0.00 44.75 4.51
1778 1904 7.613801 TGGATAAGGTAAACGGTGTAACTACTA 59.386 37.037 0.00 0.00 36.74 1.82
1780 1906 6.630071 TGGATAAGGTAAACGGTGTAACTAC 58.370 40.000 0.00 0.00 36.74 2.73
1781 1907 6.627953 GCTGGATAAGGTAAACGGTGTAACTA 60.628 42.308 0.00 0.00 36.74 2.24
1789 1915 4.196193 TCAATGCTGGATAAGGTAAACGG 58.804 43.478 0.00 0.00 0.00 4.44
1801 1927 2.517959 CCTCAAGGTTTCAATGCTGGA 58.482 47.619 0.00 0.00 0.00 3.86
1813 1942 0.759346 AAGAACTCACGCCTCAAGGT 59.241 50.000 0.00 0.00 37.57 3.50
1817 1946 1.328279 TCAGAAGAACTCACGCCTCA 58.672 50.000 0.00 0.00 0.00 3.86
1822 1951 7.062371 CCTTACTACAATTCAGAAGAACTCACG 59.938 40.741 0.00 0.00 36.39 4.35
1824 1953 7.234782 TCCCTTACTACAATTCAGAAGAACTCA 59.765 37.037 0.00 0.00 36.39 3.41
1830 1959 5.119694 GGCTCCCTTACTACAATTCAGAAG 58.880 45.833 0.00 0.00 0.00 2.85
1831 1960 4.382685 CGGCTCCCTTACTACAATTCAGAA 60.383 45.833 0.00 0.00 0.00 3.02
1833 1962 3.458189 CGGCTCCCTTACTACAATTCAG 58.542 50.000 0.00 0.00 0.00 3.02
1834 1963 2.419574 GCGGCTCCCTTACTACAATTCA 60.420 50.000 0.00 0.00 0.00 2.57
1836 1965 1.838077 AGCGGCTCCCTTACTACAATT 59.162 47.619 0.00 0.00 0.00 2.32
1837 1966 1.497161 AGCGGCTCCCTTACTACAAT 58.503 50.000 0.00 0.00 0.00 2.71
1838 1967 2.148446 TAGCGGCTCCCTTACTACAA 57.852 50.000 5.39 0.00 0.00 2.41
1839 1968 2.376695 ATAGCGGCTCCCTTACTACA 57.623 50.000 5.39 0.00 0.00 2.74
1840 1969 3.825585 ACTTATAGCGGCTCCCTTACTAC 59.174 47.826 5.39 0.00 0.00 2.73
1841 1970 4.109877 ACTTATAGCGGCTCCCTTACTA 57.890 45.455 5.39 0.00 0.00 1.82
1842 1971 2.960163 ACTTATAGCGGCTCCCTTACT 58.040 47.619 5.39 0.00 0.00 2.24
1843 1972 3.825585 ACTACTTATAGCGGCTCCCTTAC 59.174 47.826 5.39 0.00 30.75 2.34
1852 2074 6.143496 CCGATGCATATACTACTTATAGCGG 58.857 44.000 0.00 0.00 30.75 5.52
1854 2076 6.740110 AGCCGATGCATATACTACTTATAGC 58.260 40.000 0.00 0.00 41.13 2.97
1856 2078 7.061054 AGGAGCCGATGCATATACTACTTATA 58.939 38.462 0.00 0.00 41.13 0.98
1887 2109 7.178274 ACTGGCTGTTACAATGAAATATTGGAA 59.822 33.333 4.84 0.00 33.56 3.53
1894 2116 8.466798 GGTTTATACTGGCTGTTACAATGAAAT 58.533 33.333 1.31 0.00 0.00 2.17
1943 2165 6.068670 TCACTACTGCTTGCTATGGATAGTA 58.931 40.000 0.00 0.00 32.96 1.82
1954 2176 6.969473 GGATAAAGAAAATCACTACTGCTTGC 59.031 38.462 0.00 0.00 0.00 4.01
1955 2177 7.121168 TGGGATAAAGAAAATCACTACTGCTTG 59.879 37.037 0.00 0.00 0.00 4.01
1956 2178 7.175104 TGGGATAAAGAAAATCACTACTGCTT 58.825 34.615 0.00 0.00 0.00 3.91
1988 2210 9.034800 AGAGGCATTTAATTTCATAAAGAACCA 57.965 29.630 0.00 0.00 35.56 3.67
1989 2211 9.521503 GAGAGGCATTTAATTTCATAAAGAACC 57.478 33.333 0.00 0.00 35.56 3.62
1996 2218 8.686334 GTCCAAAGAGAGGCATTTAATTTCATA 58.314 33.333 0.00 0.00 0.00 2.15
2015 2237 4.351192 CACGAACAAAAGAAGGTCCAAAG 58.649 43.478 0.00 0.00 0.00 2.77
2020 2242 3.875134 TCTTCCACGAACAAAAGAAGGTC 59.125 43.478 0.00 0.00 35.68 3.85
2021 2243 3.881220 TCTTCCACGAACAAAAGAAGGT 58.119 40.909 0.00 0.00 35.68 3.50
2026 2248 6.197096 CACTTTCAATCTTCCACGAACAAAAG 59.803 38.462 0.00 0.00 0.00 2.27
2031 2253 3.003275 TGCACTTTCAATCTTCCACGAAC 59.997 43.478 0.00 0.00 0.00 3.95
2032 2254 3.003275 GTGCACTTTCAATCTTCCACGAA 59.997 43.478 10.32 0.00 0.00 3.85
2034 2256 2.290367 TGTGCACTTTCAATCTTCCACG 59.710 45.455 19.41 0.00 0.00 4.94
2035 2257 3.988379 TGTGCACTTTCAATCTTCCAC 57.012 42.857 19.41 0.00 0.00 4.02
2036 2258 5.316167 AGTATGTGCACTTTCAATCTTCCA 58.684 37.500 19.41 0.00 0.00 3.53
2037 2259 5.886960 AGTATGTGCACTTTCAATCTTCC 57.113 39.130 19.41 0.00 0.00 3.46
2038 2260 6.072508 TGGAAGTATGTGCACTTTCAATCTTC 60.073 38.462 19.41 18.26 40.36 2.87
2039 2261 5.769662 TGGAAGTATGTGCACTTTCAATCTT 59.230 36.000 19.41 11.92 40.36 2.40
2040 2262 5.316167 TGGAAGTATGTGCACTTTCAATCT 58.684 37.500 19.41 4.18 40.36 2.40
2041 2263 5.627499 TGGAAGTATGTGCACTTTCAATC 57.373 39.130 19.41 11.40 40.36 2.67
2045 2267 3.503748 AGCTTGGAAGTATGTGCACTTTC 59.496 43.478 19.41 15.07 38.86 2.62
2047 2269 2.816087 CAGCTTGGAAGTATGTGCACTT 59.184 45.455 19.41 14.68 41.44 3.16
2049 2271 2.426522 TCAGCTTGGAAGTATGTGCAC 58.573 47.619 10.75 10.75 0.00 4.57
2050 2272 2.857186 TCAGCTTGGAAGTATGTGCA 57.143 45.000 0.00 0.00 0.00 4.57
2051 2273 4.453819 GGATATCAGCTTGGAAGTATGTGC 59.546 45.833 4.83 0.00 0.00 4.57
2052 2274 5.862845 AGGATATCAGCTTGGAAGTATGTG 58.137 41.667 4.83 0.00 0.00 3.21
2053 2275 6.506538 AAGGATATCAGCTTGGAAGTATGT 57.493 37.500 4.83 0.00 0.00 2.29
2056 2278 6.560003 TGAAAGGATATCAGCTTGGAAGTA 57.440 37.500 4.83 0.00 0.00 2.24
2076 2298 6.476378 AGCCTCTAAAGCAGATTAAGTTGAA 58.524 36.000 0.00 0.00 31.13 2.69
2078 2300 6.749923 AAGCCTCTAAAGCAGATTAAGTTG 57.250 37.500 0.00 0.00 31.13 3.16
2084 2313 5.591877 CCACAATAAGCCTCTAAAGCAGATT 59.408 40.000 0.00 0.00 31.13 2.40
2103 2332 6.344500 ACTGCATAAACAATGAAAACCACAA 58.656 32.000 0.00 0.00 37.86 3.33
2117 2346 9.793252 AGTCATGATGATTAAAACTGCATAAAC 57.207 29.630 0.00 0.00 0.00 2.01
2120 2349 9.791820 CAAAGTCATGATGATTAAAACTGCATA 57.208 29.630 0.00 0.00 0.00 3.14
2122 2351 7.660112 ACAAAGTCATGATGATTAAAACTGCA 58.340 30.769 0.00 0.00 0.00 4.41
2131 2360 8.582437 ACTGAATGAAACAAAGTCATGATGATT 58.418 29.630 0.00 0.00 35.87 2.57
2138 2367 5.010012 GGGTCACTGAATGAAACAAAGTCAT 59.990 40.000 0.00 0.00 39.72 3.06
2143 2372 5.598005 AGAATGGGTCACTGAATGAAACAAA 59.402 36.000 0.00 0.00 39.72 2.83
2144 2373 5.139727 AGAATGGGTCACTGAATGAAACAA 58.860 37.500 0.00 0.00 39.72 2.83
2171 2400 6.433404 TGGGCCTACGTTGAAAATTTATACAA 59.567 34.615 4.53 0.00 0.00 2.41
2173 2402 6.439675 TGGGCCTACGTTGAAAATTTATAC 57.560 37.500 4.53 0.00 0.00 1.47
2180 2409 2.570415 TCATGGGCCTACGTTGAAAA 57.430 45.000 4.53 0.00 0.00 2.29
2183 2412 1.199615 TCATCATGGGCCTACGTTGA 58.800 50.000 4.53 0.00 0.00 3.18
2187 2416 2.775911 ATCATCATCATGGGCCTACG 57.224 50.000 4.53 0.00 0.00 3.51
2192 2421 5.651139 AGCATAACTTATCATCATCATGGGC 59.349 40.000 0.00 0.00 0.00 5.36
2193 2422 7.698506 AAGCATAACTTATCATCATCATGGG 57.301 36.000 0.00 0.00 36.62 4.00
2199 2428 8.509690 GTGCACATAAGCATAACTTATCATCAT 58.490 33.333 13.17 0.00 46.60 2.45
2213 2442 1.200484 CACATGCAGTGCACATAAGCA 59.800 47.619 22.44 21.79 43.04 3.91
2224 2453 5.458041 AAAAGTATGCTTTCACATGCAGT 57.542 34.783 9.35 0.00 43.52 4.40
2247 2476 5.836358 AGTTATTTAAAAGGACCTGGTGCAA 59.164 36.000 20.87 5.83 0.00 4.08
2284 2515 6.370994 GTCTGACTGATCACATGAATTCTTGT 59.629 38.462 18.53 18.53 35.02 3.16
2289 2520 4.867047 GTCGTCTGACTGATCACATGAATT 59.133 41.667 0.00 0.00 42.08 2.17
2330 2562 6.698380 ACACAAACGTAAGGAGTCAAGATAT 58.302 36.000 0.00 0.00 46.39 1.63
2331 2563 6.092955 ACACAAACGTAAGGAGTCAAGATA 57.907 37.500 0.00 0.00 46.39 1.98
2333 2565 4.395959 ACACAAACGTAAGGAGTCAAGA 57.604 40.909 0.00 0.00 46.39 3.02
2334 2566 5.479716 AAACACAAACGTAAGGAGTCAAG 57.520 39.130 0.00 0.00 46.39 3.02
2335 2567 5.883503 AAAACACAAACGTAAGGAGTCAA 57.116 34.783 0.00 0.00 46.39 3.18
2358 2594 7.629157 TCCAGAACCAGACACAATCATAAATA 58.371 34.615 0.00 0.00 0.00 1.40
2363 2599 4.581309 ATCCAGAACCAGACACAATCAT 57.419 40.909 0.00 0.00 0.00 2.45
2367 2603 2.549992 CCGAATCCAGAACCAGACACAA 60.550 50.000 0.00 0.00 0.00 3.33
2376 2612 4.215399 TCACATGTTTTCCGAATCCAGAAC 59.785 41.667 0.00 0.00 0.00 3.01
2380 2616 4.155826 GTGATCACATGTTTTCCGAATCCA 59.844 41.667 21.07 0.00 0.00 3.41
2387 2623 6.017400 ACAATCTGTGATCACATGTTTTCC 57.983 37.500 28.00 0.00 41.01 3.13
2402 2638 6.984474 CGGGTATATGTAGTTCAACAATCTGT 59.016 38.462 0.00 0.00 32.02 3.41
2403 2639 7.207383 TCGGGTATATGTAGTTCAACAATCTG 58.793 38.462 0.00 0.00 32.02 2.90
2405 2641 7.493320 TGTTCGGGTATATGTAGTTCAACAATC 59.507 37.037 0.00 0.00 32.02 2.67
2423 2659 3.444388 TGCAAAGTTTAGTTTGTTCGGGT 59.556 39.130 10.73 0.00 39.27 5.28
2424 2660 4.035278 TGCAAAGTTTAGTTTGTTCGGG 57.965 40.909 10.73 0.00 39.27 5.14
2426 2662 6.526674 AGAAGTTGCAAAGTTTAGTTTGTTCG 59.473 34.615 0.00 0.00 40.14 3.95
2463 2701 5.412286 ACAAAAACATTTGGCATATTCCAGC 59.588 36.000 6.29 0.00 37.44 4.85
2480 2718 8.642908 AACTTACAGGCTATCAAAACAAAAAC 57.357 30.769 0.00 0.00 0.00 2.43
2490 2728 6.996282 GGGCTAAAATAACTTACAGGCTATCA 59.004 38.462 0.00 0.00 0.00 2.15
2495 2733 5.907866 TTGGGCTAAAATAACTTACAGGC 57.092 39.130 0.00 0.00 0.00 4.85
2503 2741 5.703130 TTGGCACAAATTGGGCTAAAATAAC 59.297 36.000 20.35 0.99 44.32 1.89
2523 2761 9.914131 GGATTCAAGGTTTAGAATATAATTGGC 57.086 33.333 0.00 0.00 34.79 4.52
2557 2795 0.323360 TGGGTGCTGGCTAATGGTTC 60.323 55.000 0.00 0.00 0.00 3.62
2562 2800 0.698238 TTGTCTGGGTGCTGGCTAAT 59.302 50.000 0.00 0.00 0.00 1.73
2566 2804 0.250727 TAGTTTGTCTGGGTGCTGGC 60.251 55.000 0.00 0.00 0.00 4.85
2571 2809 2.417719 GCTGAGTAGTTTGTCTGGGTG 58.582 52.381 0.00 0.00 0.00 4.61
2572 2810 1.348036 GGCTGAGTAGTTTGTCTGGGT 59.652 52.381 0.00 0.00 0.00 4.51
2574 2812 1.347707 TGGGCTGAGTAGTTTGTCTGG 59.652 52.381 0.00 0.00 0.00 3.86
2575 2813 2.300152 TCTGGGCTGAGTAGTTTGTCTG 59.700 50.000 0.00 0.00 0.00 3.51
2576 2814 2.300437 GTCTGGGCTGAGTAGTTTGTCT 59.700 50.000 0.00 0.00 0.00 3.41
2577 2815 2.037251 TGTCTGGGCTGAGTAGTTTGTC 59.963 50.000 0.00 0.00 0.00 3.18
2578 2816 2.047061 TGTCTGGGCTGAGTAGTTTGT 58.953 47.619 0.00 0.00 0.00 2.83
2579 2817 2.839486 TGTCTGGGCTGAGTAGTTTG 57.161 50.000 0.00 0.00 0.00 2.93
2580 2818 2.706190 ACTTGTCTGGGCTGAGTAGTTT 59.294 45.455 0.00 0.00 0.00 2.66
2581 2819 2.330216 ACTTGTCTGGGCTGAGTAGTT 58.670 47.619 0.00 0.00 0.00 2.24
2582 2820 2.016905 ACTTGTCTGGGCTGAGTAGT 57.983 50.000 0.00 0.00 0.00 2.73
2583 2821 3.511934 ACTAACTTGTCTGGGCTGAGTAG 59.488 47.826 0.00 0.00 0.00 2.57
2584 2822 3.507411 ACTAACTTGTCTGGGCTGAGTA 58.493 45.455 0.00 0.00 0.00 2.59
2585 2823 2.300437 GACTAACTTGTCTGGGCTGAGT 59.700 50.000 0.00 0.00 34.39 3.41
2586 2824 2.300152 TGACTAACTTGTCTGGGCTGAG 59.700 50.000 0.00 0.00 37.79 3.35
2587 2825 2.325484 TGACTAACTTGTCTGGGCTGA 58.675 47.619 0.00 0.00 37.79 4.26
2588 2826 2.839486 TGACTAACTTGTCTGGGCTG 57.161 50.000 0.00 0.00 37.79 4.85
2589 2827 2.906389 TCATGACTAACTTGTCTGGGCT 59.094 45.455 0.00 0.00 37.79 5.19
2590 2828 3.265791 CTCATGACTAACTTGTCTGGGC 58.734 50.000 0.00 0.00 37.79 5.36
2591 2829 3.265791 GCTCATGACTAACTTGTCTGGG 58.734 50.000 0.00 0.00 37.79 4.45
2592 2830 3.265791 GGCTCATGACTAACTTGTCTGG 58.734 50.000 0.00 0.00 37.79 3.86
2593 2831 3.265791 GGGCTCATGACTAACTTGTCTG 58.734 50.000 0.00 0.00 37.79 3.51


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

AutoCloner maintained by Alex Coulton.