Multiple sequence alignment - TraesCS3B01G337200

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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 TraesCS3B01G337200 chr3B 100.000 4849 0 0 1 4849 543541939 543537091 0.000000e+00 8955.0
1 TraesCS3B01G337200 chr3D 95.434 2234 92 8 1763 3991 417204907 417202679 0.000000e+00 3552.0
2 TraesCS3B01G337200 chr3D 89.781 548 47 2 656 1194 417209365 417208818 0.000000e+00 693.0
3 TraesCS3B01G337200 chr3D 90.746 389 26 3 1194 1582 417208775 417208397 1.200000e-140 510.0
4 TraesCS3B01G337200 chr3D 91.176 136 9 2 1633 1767 417208259 417208392 1.070000e-41 182.0
5 TraesCS3B01G337200 chr3A 92.761 2086 108 23 1918 3993 533631465 533633517 0.000000e+00 2976.0
6 TraesCS3B01G337200 chr3A 97.552 858 20 1 3993 4849 140958007 140958864 0.000000e+00 1467.0
7 TraesCS3B01G337200 chr3A 87.526 481 32 10 659 1121 533629893 533630363 9.240000e-147 531.0
8 TraesCS3B01G337200 chr3A 82.673 404 43 15 1196 1582 533630458 533630851 2.800000e-87 333.0
9 TraesCS3B01G337200 chr4A 97.552 858 20 1 3993 4849 301818674 301819531 0.000000e+00 1467.0
10 TraesCS3B01G337200 chr4A 94.308 650 33 2 2 650 711325327 711325973 0.000000e+00 992.0
11 TraesCS3B01G337200 chr6B 97.219 863 22 2 3989 4849 584057376 584056514 0.000000e+00 1459.0
12 TraesCS3B01G337200 chr6B 97.322 859 21 2 3993 4849 275927399 275928257 0.000000e+00 1458.0
13 TraesCS3B01G337200 chr6B 97.093 860 24 1 3991 4849 77660871 77661730 0.000000e+00 1448.0
14 TraesCS3B01G337200 chr6B 96.984 862 23 3 3989 4849 153400259 153399400 0.000000e+00 1445.0
15 TraesCS3B01G337200 chr7B 97.213 861 23 1 3990 4849 48114848 48115708 0.000000e+00 1456.0
16 TraesCS3B01G337200 chr7B 94.915 649 33 0 1 649 637698317 637697669 0.000000e+00 1016.0
17 TraesCS3B01G337200 chr5B 97.316 857 22 1 3994 4849 446984663 446985519 0.000000e+00 1454.0
18 TraesCS3B01G337200 chr5B 91.489 47 3 1 1064 1110 196466203 196466248 4.050000e-06 63.9
19 TraesCS3B01G337200 chr4B 97.310 855 22 1 3996 4849 646603720 646602866 0.000000e+00 1450.0
20 TraesCS3B01G337200 chr4B 94.325 652 33 3 1 650 568734577 568735226 0.000000e+00 996.0
21 TraesCS3B01G337200 chr4B 93.991 649 39 0 2 650 5275708 5276356 0.000000e+00 983.0
22 TraesCS3B01G337200 chr4B 93.798 645 40 0 6 650 403105199 403104555 0.000000e+00 970.0
23 TraesCS3B01G337200 chr2B 94.255 644 37 0 7 650 393873026 393873669 0.000000e+00 985.0
24 TraesCS3B01G337200 chr2B 94.009 651 36 2 1 650 665917087 665917735 0.000000e+00 983.0
25 TraesCS3B01G337200 chr1B 93.865 652 37 3 1 650 549442969 549443619 0.000000e+00 979.0
26 TraesCS3B01G337200 chr1B 93.702 651 40 1 1 650 667349486 667350136 0.000000e+00 974.0
27 TraesCS3B01G337200 chr5D 91.489 47 3 1 1064 1110 192265157 192265202 4.050000e-06 63.9
28 TraesCS3B01G337200 chr5A 91.489 47 3 1 1064 1110 230067686 230067731 4.050000e-06 63.9


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 TraesCS3B01G337200 chr3B 543537091 543541939 4848 True 8955 8955 100.000000 1 4849 1 chr3B.!!$R1 4848
1 TraesCS3B01G337200 chr3D 417202679 417209365 6686 True 1585 3552 91.987000 656 3991 3 chr3D.!!$R1 3335
2 TraesCS3B01G337200 chr3A 140958007 140958864 857 False 1467 1467 97.552000 3993 4849 1 chr3A.!!$F1 856
3 TraesCS3B01G337200 chr3A 533629893 533633517 3624 False 1280 2976 87.653333 659 3993 3 chr3A.!!$F2 3334
4 TraesCS3B01G337200 chr4A 301818674 301819531 857 False 1467 1467 97.552000 3993 4849 1 chr4A.!!$F1 856
5 TraesCS3B01G337200 chr4A 711325327 711325973 646 False 992 992 94.308000 2 650 1 chr4A.!!$F2 648
6 TraesCS3B01G337200 chr6B 584056514 584057376 862 True 1459 1459 97.219000 3989 4849 1 chr6B.!!$R2 860
7 TraesCS3B01G337200 chr6B 275927399 275928257 858 False 1458 1458 97.322000 3993 4849 1 chr6B.!!$F2 856
8 TraesCS3B01G337200 chr6B 77660871 77661730 859 False 1448 1448 97.093000 3991 4849 1 chr6B.!!$F1 858
9 TraesCS3B01G337200 chr6B 153399400 153400259 859 True 1445 1445 96.984000 3989 4849 1 chr6B.!!$R1 860
10 TraesCS3B01G337200 chr7B 48114848 48115708 860 False 1456 1456 97.213000 3990 4849 1 chr7B.!!$F1 859
11 TraesCS3B01G337200 chr7B 637697669 637698317 648 True 1016 1016 94.915000 1 649 1 chr7B.!!$R1 648
12 TraesCS3B01G337200 chr5B 446984663 446985519 856 False 1454 1454 97.316000 3994 4849 1 chr5B.!!$F2 855
13 TraesCS3B01G337200 chr4B 646602866 646603720 854 True 1450 1450 97.310000 3996 4849 1 chr4B.!!$R2 853
14 TraesCS3B01G337200 chr4B 568734577 568735226 649 False 996 996 94.325000 1 650 1 chr4B.!!$F2 649
15 TraesCS3B01G337200 chr4B 5275708 5276356 648 False 983 983 93.991000 2 650 1 chr4B.!!$F1 648
16 TraesCS3B01G337200 chr4B 403104555 403105199 644 True 970 970 93.798000 6 650 1 chr4B.!!$R1 644
17 TraesCS3B01G337200 chr2B 393873026 393873669 643 False 985 985 94.255000 7 650 1 chr2B.!!$F1 643
18 TraesCS3B01G337200 chr2B 665917087 665917735 648 False 983 983 94.009000 1 650 1 chr2B.!!$F2 649
19 TraesCS3B01G337200 chr1B 549442969 549443619 650 False 979 979 93.865000 1 650 1 chr1B.!!$F1 649
20 TraesCS3B01G337200 chr1B 667349486 667350136 650 False 974 974 93.702000 1 650 1 chr1B.!!$F2 649

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
653 658 0.238817 TGGGCGTTAACATTTCGTGC 59.761 50.0 6.39 0.00 0.00 5.34 F
1121 1154 0.039074 GATCGATCGAGCGGGATTGT 60.039 55.0 24.18 2.57 0.00 2.71 F
1735 5563 0.179032 ACCGGTGTCAGCATTGTTCA 60.179 50.0 6.12 0.00 0.00 3.18 F
2534 6375 0.669619 TCCTCGTGCAGTGAAACGTA 59.330 50.0 15.63 5.27 45.86 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2444 6285 0.112995 AATTCTCTGGTGGCAGGCAA 59.887 50.000 0.00 0.0 0.00 4.52 R
2534 6375 2.280592 GCCCCGACGTTTGACTGT 60.281 61.111 0.00 0.0 0.00 3.55 R
3491 7332 0.040204 CTGGATTTGGAGCCCAACCT 59.960 55.000 6.19 0.0 43.82 3.50 R
3882 7723 0.250234 TCCACCTACTGATGCTGTGC 59.750 55.000 0.00 0.0 0.00 4.57 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
101 102 1.066002 CATCGCCAAATCGCCTGAATT 59.934 47.619 0.00 0.00 0.00 2.17
291 294 3.068691 CGTCGCCTTCTCCCCTCA 61.069 66.667 0.00 0.00 0.00 3.86
363 367 2.477880 GGTGAGTAAATGGCACCGG 58.522 57.895 0.00 0.00 42.20 5.28
564 569 2.289547 CAGAAAAACGACCGGATTGTGT 59.710 45.455 9.46 0.00 0.00 3.72
650 655 1.723384 CGTGTGGGCGTTAACATTTCG 60.723 52.381 6.39 0.00 0.00 3.46
651 656 1.264826 GTGTGGGCGTTAACATTTCGT 59.735 47.619 6.39 0.00 0.00 3.85
652 657 1.264557 TGTGGGCGTTAACATTTCGTG 59.735 47.619 6.39 0.00 0.00 4.35
653 658 0.238817 TGGGCGTTAACATTTCGTGC 59.761 50.000 6.39 0.00 0.00 5.34
654 659 0.238817 GGGCGTTAACATTTCGTGCA 59.761 50.000 6.39 0.00 0.00 4.57
696 701 2.025605 TCCTTACTCCGAGCTAAGTGGA 60.026 50.000 6.22 2.02 0.00 4.02
808 824 2.046892 CCACCGTGCTCCTTCCAG 60.047 66.667 0.00 0.00 0.00 3.86
900 916 2.114616 CACTTACATCTCCCCTGAGCT 58.885 52.381 0.00 0.00 38.58 4.09
902 918 2.292521 ACTTACATCTCCCCTGAGCTGA 60.293 50.000 0.00 0.00 36.98 4.26
934 950 4.057224 GACACCATTGGCGTCACA 57.943 55.556 17.10 0.00 35.13 3.58
1121 1154 0.039074 GATCGATCGAGCGGGATTGT 60.039 55.000 24.18 2.57 0.00 2.71
1127 1160 1.227263 CGAGCGGGATTGTGGGTAG 60.227 63.158 0.00 0.00 0.00 3.18
1134 1167 1.276989 GGGATTGTGGGTAGTTCGACA 59.723 52.381 0.00 0.00 0.00 4.35
1142 1175 0.456312 GGTAGTTCGACAGACTGCCG 60.456 60.000 4.61 4.61 0.00 5.69
1153 1186 1.749258 GACTGCCGGAACAATCCCC 60.749 63.158 5.05 0.00 43.37 4.81
1188 1223 2.490991 GGTTCAGTGGTAGTTGTCACC 58.509 52.381 0.00 0.00 34.67 4.02
1221 1299 5.300969 TGCATTGACTGAAAGCATAGTTC 57.699 39.130 0.00 0.00 37.60 3.01
1286 1371 1.724429 GCTGAAGCAACTCTGAGGAG 58.276 55.000 9.85 2.01 42.00 3.69
1302 1387 7.125792 TCTGAGGAGTTTCTTAGTTCAGTTT 57.874 36.000 0.00 0.00 33.94 2.66
1303 1388 7.565680 TCTGAGGAGTTTCTTAGTTCAGTTTT 58.434 34.615 0.00 0.00 33.94 2.43
1304 1389 7.495934 TCTGAGGAGTTTCTTAGTTCAGTTTTG 59.504 37.037 0.00 0.00 33.94 2.44
1400 1489 6.037062 CAGAACATTCGTTGCAGATAACCATA 59.963 38.462 0.00 0.00 34.75 2.74
1401 1490 6.767902 AGAACATTCGTTGCAGATAACCATAT 59.232 34.615 0.00 0.00 34.75 1.78
1402 1491 7.931407 AGAACATTCGTTGCAGATAACCATATA 59.069 33.333 0.00 0.00 34.75 0.86
1403 1492 8.445275 AACATTCGTTGCAGATAACCATATAA 57.555 30.769 0.00 0.00 32.81 0.98
1404 1493 8.087982 ACATTCGTTGCAGATAACCATATAAG 57.912 34.615 0.00 0.00 0.00 1.73
1405 1494 7.715249 ACATTCGTTGCAGATAACCATATAAGT 59.285 33.333 0.00 0.00 0.00 2.24
1446 1535 7.653311 GGAAATAATGGGTTGCTTAATGCTTAG 59.347 37.037 0.00 0.00 43.37 2.18
1447 1536 7.660030 AATAATGGGTTGCTTAATGCTTAGT 57.340 32.000 0.00 0.00 43.37 2.24
1448 1537 4.989279 ATGGGTTGCTTAATGCTTAGTG 57.011 40.909 0.00 0.00 43.37 2.74
1451 1543 4.217550 TGGGTTGCTTAATGCTTAGTGTTC 59.782 41.667 0.00 0.00 43.37 3.18
1526 1621 1.761244 TATGCAGCGCCGACGAATTG 61.761 55.000 2.29 0.00 43.93 2.32
1539 1634 4.411327 CGACGAATTGGCATATGTTTGTT 58.589 39.130 4.29 0.00 0.00 2.83
1551 1646 7.812191 TGGCATATGTTTGTTTGTTCATAACTC 59.188 33.333 4.29 0.00 0.00 3.01
1577 1672 7.246311 CACAGTGCATTAAATCCTGAACTTAG 58.754 38.462 5.35 0.00 28.28 2.18
1582 1677 6.152661 TGCATTAAATCCTGAACTTAGGTTGG 59.847 38.462 0.00 0.00 38.99 3.77
1583 1678 6.564328 CATTAAATCCTGAACTTAGGTTGGC 58.436 40.000 0.00 0.00 38.99 4.52
1584 1679 3.806949 AATCCTGAACTTAGGTTGGCA 57.193 42.857 0.00 0.00 38.99 4.92
1585 1680 4.322057 AATCCTGAACTTAGGTTGGCAT 57.678 40.909 0.00 0.00 38.99 4.40
1596 1741 1.066908 AGGTTGGCATGTTTTGACACG 59.933 47.619 0.00 0.00 45.38 4.49
1598 1743 2.288152 GGTTGGCATGTTTTGACACGAT 60.288 45.455 0.00 0.00 45.38 3.73
1617 1762 4.541779 CGATAGTAGCATTTCTCGCTCTT 58.458 43.478 0.00 0.00 40.96 2.85
1618 1763 4.381270 CGATAGTAGCATTTCTCGCTCTTG 59.619 45.833 0.00 0.00 40.96 3.02
1619 1764 2.275318 AGTAGCATTTCTCGCTCTTGC 58.725 47.619 0.00 0.00 40.96 4.01
1620 1765 2.002586 GTAGCATTTCTCGCTCTTGCA 58.997 47.619 0.00 0.00 40.96 4.08
1622 1767 2.910199 AGCATTTCTCGCTCTTGCATA 58.090 42.857 0.00 0.00 39.64 3.14
1623 1768 3.474600 AGCATTTCTCGCTCTTGCATAT 58.525 40.909 0.00 0.00 39.64 1.78
1626 1771 5.704515 AGCATTTCTCGCTCTTGCATATTAT 59.295 36.000 0.00 0.00 39.64 1.28
1628 1773 6.347969 GCATTTCTCGCTCTTGCATATTATCA 60.348 38.462 0.00 0.00 39.64 2.15
1629 1774 7.625817 GCATTTCTCGCTCTTGCATATTATCAT 60.626 37.037 0.00 0.00 39.64 2.45
1630 1775 6.716898 TTCTCGCTCTTGCATATTATCATG 57.283 37.500 0.00 0.00 39.64 3.07
1633 1778 3.181503 CGCTCTTGCATATTATCATGGCC 60.182 47.826 0.00 0.00 39.64 5.36
1635 1780 5.188434 GCTCTTGCATATTATCATGGCCTA 58.812 41.667 3.32 0.00 39.41 3.93
1636 1781 5.649395 GCTCTTGCATATTATCATGGCCTAA 59.351 40.000 3.32 0.00 39.41 2.69
1637 1782 6.404074 GCTCTTGCATATTATCATGGCCTAAC 60.404 42.308 3.32 0.00 39.41 2.34
1638 1783 6.782986 TCTTGCATATTATCATGGCCTAACT 58.217 36.000 3.32 0.00 0.00 2.24
1639 1784 7.917003 TCTTGCATATTATCATGGCCTAACTA 58.083 34.615 3.32 0.00 0.00 2.24
1643 1788 7.770433 TGCATATTATCATGGCCTAACTATCAC 59.230 37.037 3.32 0.00 0.00 3.06
1645 1790 6.605471 ATTATCATGGCCTAACTATCACGA 57.395 37.500 3.32 0.00 0.00 4.35
1646 1791 6.605471 TTATCATGGCCTAACTATCACGAT 57.395 37.500 3.32 0.00 0.00 3.73
1647 1792 4.955811 TCATGGCCTAACTATCACGATT 57.044 40.909 3.32 0.00 0.00 3.34
1648 1793 6.605471 ATCATGGCCTAACTATCACGATTA 57.395 37.500 3.32 0.00 0.00 1.75
1649 1794 5.779922 TCATGGCCTAACTATCACGATTAC 58.220 41.667 3.32 0.00 0.00 1.89
1650 1795 5.538813 TCATGGCCTAACTATCACGATTACT 59.461 40.000 3.32 0.00 0.00 2.24
1651 1796 5.449107 TGGCCTAACTATCACGATTACTC 57.551 43.478 3.32 0.00 0.00 2.59
1653 1798 5.241064 TGGCCTAACTATCACGATTACTCTC 59.759 44.000 3.32 0.00 0.00 3.20
1658 1803 7.658167 CCTAACTATCACGATTACTCTCTCTCA 59.342 40.741 0.00 0.00 0.00 3.27
1659 1804 7.867305 AACTATCACGATTACTCTCTCTCAA 57.133 36.000 0.00 0.00 0.00 3.02
1660 1805 7.254227 ACTATCACGATTACTCTCTCTCAAC 57.746 40.000 0.00 0.00 0.00 3.18
1661 1806 6.824196 ACTATCACGATTACTCTCTCTCAACA 59.176 38.462 0.00 0.00 0.00 3.33
1662 1807 5.959618 TCACGATTACTCTCTCTCAACAA 57.040 39.130 0.00 0.00 0.00 2.83
1663 1808 6.327279 TCACGATTACTCTCTCTCAACAAA 57.673 37.500 0.00 0.00 0.00 2.83
1664 1809 6.745116 TCACGATTACTCTCTCTCAACAAAA 58.255 36.000 0.00 0.00 0.00 2.44
1665 1810 7.207383 TCACGATTACTCTCTCTCAACAAAAA 58.793 34.615 0.00 0.00 0.00 1.94
1694 5522 6.263168 ACACTTCAAACCTGTAGAAATGGAAG 59.737 38.462 0.00 0.00 36.28 3.46
1699 5527 4.640771 ACCTGTAGAAATGGAAGCAAGA 57.359 40.909 0.00 0.00 0.00 3.02
1700 5528 4.583871 ACCTGTAGAAATGGAAGCAAGAG 58.416 43.478 0.00 0.00 0.00 2.85
1701 5529 4.287067 ACCTGTAGAAATGGAAGCAAGAGA 59.713 41.667 0.00 0.00 0.00 3.10
1702 5530 5.221925 ACCTGTAGAAATGGAAGCAAGAGAA 60.222 40.000 0.00 0.00 0.00 2.87
1705 5533 6.169094 TGTAGAAATGGAAGCAAGAGAAGAG 58.831 40.000 0.00 0.00 0.00 2.85
1706 5534 4.009002 AGAAATGGAAGCAAGAGAAGAGC 58.991 43.478 0.00 0.00 0.00 4.09
1707 5535 3.430042 AATGGAAGCAAGAGAAGAGCA 57.570 42.857 0.00 0.00 0.00 4.26
1709 5537 1.417517 TGGAAGCAAGAGAAGAGCACA 59.582 47.619 0.00 0.00 0.00 4.57
1710 5538 2.075338 GGAAGCAAGAGAAGAGCACAG 58.925 52.381 0.00 0.00 0.00 3.66
1714 5542 1.130749 GCAAGAGAAGAGCACAGCATG 59.869 52.381 0.00 0.00 46.00 4.06
1723 5551 2.979676 CACAGCATGCACCGGTGT 60.980 61.111 33.92 14.47 45.48 4.16
1724 5552 2.669569 ACAGCATGCACCGGTGTC 60.670 61.111 33.92 25.53 40.97 3.67
1726 5554 2.359107 AGCATGCACCGGTGTCAG 60.359 61.111 33.92 23.57 0.00 3.51
1727 5555 4.107051 GCATGCACCGGTGTCAGC 62.107 66.667 33.92 28.33 0.00 4.26
1728 5556 2.669229 CATGCACCGGTGTCAGCA 60.669 61.111 33.92 26.09 41.73 4.41
1729 5557 2.352422 ATGCACCGGTGTCAGCAT 59.648 55.556 33.92 27.07 42.42 3.79
1730 5558 1.303561 ATGCACCGGTGTCAGCATT 60.304 52.632 33.92 15.07 44.63 3.56
1731 5559 1.588824 ATGCACCGGTGTCAGCATTG 61.589 55.000 33.92 7.53 44.63 2.82
1732 5560 2.260869 GCACCGGTGTCAGCATTGT 61.261 57.895 33.92 0.00 0.00 2.71
1733 5561 1.795170 GCACCGGTGTCAGCATTGTT 61.795 55.000 33.92 0.00 0.00 2.83
1734 5562 0.238289 CACCGGTGTCAGCATTGTTC 59.762 55.000 26.95 0.00 0.00 3.18
1735 5563 0.179032 ACCGGTGTCAGCATTGTTCA 60.179 50.000 6.12 0.00 0.00 3.18
1736 5564 0.950836 CCGGTGTCAGCATTGTTCAA 59.049 50.000 2.47 0.00 0.00 2.69
1737 5565 1.336440 CCGGTGTCAGCATTGTTCAAA 59.664 47.619 2.47 0.00 0.00 2.69
1738 5566 2.223688 CCGGTGTCAGCATTGTTCAAAA 60.224 45.455 2.47 0.00 0.00 2.44
1739 5567 3.044986 CGGTGTCAGCATTGTTCAAAAG 58.955 45.455 2.47 0.00 0.00 2.27
1740 5568 2.796593 GGTGTCAGCATTGTTCAAAAGC 59.203 45.455 0.00 5.59 0.00 3.51
1741 5569 3.446799 GTGTCAGCATTGTTCAAAAGCA 58.553 40.909 12.96 0.00 0.00 3.91
1742 5570 3.864583 GTGTCAGCATTGTTCAAAAGCAA 59.135 39.130 12.96 0.00 0.00 3.91
1743 5571 3.864583 TGTCAGCATTGTTCAAAAGCAAC 59.135 39.130 12.96 11.06 0.00 4.17
1744 5572 4.114794 GTCAGCATTGTTCAAAAGCAACT 58.885 39.130 12.96 0.00 0.00 3.16
1745 5573 5.163571 TGTCAGCATTGTTCAAAAGCAACTA 60.164 36.000 12.96 0.00 0.00 2.24
1746 5574 5.748152 GTCAGCATTGTTCAAAAGCAACTAA 59.252 36.000 12.96 0.00 0.00 2.24
1747 5575 6.421801 GTCAGCATTGTTCAAAAGCAACTAAT 59.578 34.615 12.96 0.00 0.00 1.73
1748 5576 6.985645 TCAGCATTGTTCAAAAGCAACTAATT 59.014 30.769 12.96 0.00 0.00 1.40
1749 5577 7.042590 TCAGCATTGTTCAAAAGCAACTAATTG 60.043 33.333 12.96 0.00 38.99 2.32
1766 5594 9.443283 CAACTAATTGCTAGATTCTTTATGCAC 57.557 33.333 0.00 0.00 0.00 4.57
1784 5612 2.476854 GCACTGAATCAATTCGGCACTC 60.477 50.000 10.76 0.00 44.97 3.51
1875 5704 6.348540 GGTCACACTTCAAATAAGGTAGCAAG 60.349 42.308 0.00 0.00 0.00 4.01
1876 5705 5.181245 TCACACTTCAAATAAGGTAGCAAGC 59.819 40.000 0.00 0.00 0.00 4.01
1877 5706 5.182001 CACACTTCAAATAAGGTAGCAAGCT 59.818 40.000 0.00 0.00 34.01 3.74
1878 5707 6.371548 CACACTTCAAATAAGGTAGCAAGCTA 59.628 38.462 0.00 0.00 31.75 3.32
1879 5708 7.066284 CACACTTCAAATAAGGTAGCAAGCTAT 59.934 37.037 4.93 0.00 31.75 2.97
1880 5709 7.066284 ACACTTCAAATAAGGTAGCAAGCTATG 59.934 37.037 4.93 0.00 31.75 2.23
1921 5752 1.474143 GCCCCAGCATAGTTCTCTGTC 60.474 57.143 0.00 0.00 39.53 3.51
2194 6035 6.916360 TTCTTTGCTCTCCATGGTTAAATT 57.084 33.333 12.58 0.00 0.00 1.82
2204 6045 6.920758 TCTCCATGGTTAAATTTGTTTCAACG 59.079 34.615 12.58 0.00 0.00 4.10
2370 6211 4.601406 TTGTAATAGGCTTGGTGGGATT 57.399 40.909 0.00 0.00 0.00 3.01
2468 6309 1.815003 CTGCCACCAGAGAATTGGAAC 59.185 52.381 0.00 0.00 41.77 3.62
2534 6375 0.669619 TCCTCGTGCAGTGAAACGTA 59.330 50.000 15.63 5.27 45.86 3.57
2704 6545 1.152118 TAGGGTGTGGCTGGACACT 60.152 57.895 8.11 0.00 44.81 3.55
2737 6578 3.384532 CAAGCCCATGGTGGTGGC 61.385 66.667 11.73 6.40 45.70 5.01
2800 6641 4.505742 GGAGAGAACAAAGATGGACCAACT 60.506 45.833 0.00 0.00 0.00 3.16
2897 6738 4.282496 TGTTTTTCCAGCAACCTTTCCTA 58.718 39.130 0.00 0.00 0.00 2.94
2900 6741 3.586470 TTCCAGCAACCTTTCCTAACA 57.414 42.857 0.00 0.00 0.00 2.41
2976 6817 1.016627 TGTGCACTGACACTTGCTTC 58.983 50.000 19.41 0.00 41.30 3.86
3089 6930 2.034179 TGGAGAGCGTACCAATATCACG 59.966 50.000 0.00 0.00 38.66 4.35
3174 7015 3.627123 GCAGTATGTTATGTGGATGCACA 59.373 43.478 22.95 22.95 39.31 4.57
3188 7029 2.452813 GCACATCGACGACGGCAAT 61.453 57.895 7.55 0.00 40.21 3.56
3203 7044 4.261801 ACGGCAATTACACTAAAGCATCT 58.738 39.130 0.00 0.00 0.00 2.90
3311 7152 3.119955 TGACGATCTTCAAAGACGACGAT 60.120 43.478 0.00 0.00 37.98 3.73
3320 7161 2.202932 GACGACGATGGCATGGCT 60.203 61.111 21.08 5.86 0.00 4.75
3336 7177 3.008835 TGGCTTACCTCTTCTACGCTA 57.991 47.619 0.00 0.00 36.63 4.26
3389 7230 6.428159 GTCCATTGACAGCGGATTATCTTAAT 59.572 38.462 0.00 0.00 41.37 1.40
3401 7242 5.934625 GGATTATCTTAATGTCACATCGGCT 59.065 40.000 0.00 0.00 0.00 5.52
3404 7245 9.803315 GATTATCTTAATGTCACATCGGCTATA 57.197 33.333 0.00 0.00 0.00 1.31
3419 7260 7.399191 ACATCGGCTATAAGGAGAATATTGGTA 59.601 37.037 0.00 0.00 0.00 3.25
3483 7324 5.128827 GGAACCTACTACATGATCACCTCAA 59.871 44.000 0.00 0.00 37.44 3.02
3503 7344 2.853542 TGCTCAGGTTGGGCTCCA 60.854 61.111 2.28 0.00 46.08 3.86
3693 7534 0.604511 GTGGAACCCGTCGGATTTGT 60.605 55.000 14.39 0.00 0.00 2.83
3791 7632 1.664306 GTCGTGGTCGAGGGTTTCT 59.336 57.895 0.00 0.00 46.96 2.52
3842 7683 4.563786 CCTGAAGGTTGGAGGAAGAGTTAC 60.564 50.000 0.00 0.00 0.00 2.50
3881 7722 3.181473 GGGCATGGCGACGGTTATATATA 60.181 47.826 13.76 0.00 0.00 0.86
3882 7723 4.049186 GGCATGGCGACGGTTATATATAG 58.951 47.826 2.41 0.00 0.00 1.31
3935 7776 3.752747 TGCAGATACAGTGGTGATTGTTG 59.247 43.478 0.00 0.00 0.00 3.33
4056 7897 0.179094 CCAGGCAGCGTTACGGATAA 60.179 55.000 6.94 0.00 0.00 1.75
4074 7915 4.215613 GGATAACACAGGTTCACAGGAAAC 59.784 45.833 0.00 0.00 41.20 2.78
4077 7918 2.291282 ACACAGGTTCACAGGAAACCAA 60.291 45.455 7.69 0.00 41.87 3.67
4169 8010 0.250513 CGGGGAGGAGAAAGACCAAG 59.749 60.000 0.00 0.00 0.00 3.61
4170 8011 1.657804 GGGGAGGAGAAAGACCAAGA 58.342 55.000 0.00 0.00 0.00 3.02
4171 8012 1.985895 GGGGAGGAGAAAGACCAAGAA 59.014 52.381 0.00 0.00 0.00 2.52
4189 8030 0.743688 AATCCGCAAACAACAGCACA 59.256 45.000 0.00 0.00 0.00 4.57
4367 8209 4.487714 TGGGAAGGTAAGCTCAATAGTG 57.512 45.455 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 3.477530 TCCTCGCTCGAGATTCATAGAA 58.522 45.455 18.75 0.00 44.53 2.10
291 294 3.160679 CAAACCATTGGAGGAGAAGGT 57.839 47.619 10.37 0.00 32.69 3.50
564 569 2.548057 GGACTTTGTGCACGAATCTTGA 59.452 45.455 19.77 0.00 0.00 3.02
696 701 2.166664 GGAAATCAGACCGAGTAGCTGT 59.833 50.000 0.00 0.00 0.00 4.40
851 867 2.113986 GTGGGAAGTGGCAGCAGT 59.886 61.111 0.00 0.00 0.00 4.40
853 869 4.284550 GGGTGGGAAGTGGCAGCA 62.285 66.667 0.00 0.00 0.00 4.41
881 897 2.559381 AGCTCAGGGGAGATGTAAGT 57.441 50.000 0.00 0.00 44.26 2.24
900 916 3.367743 CGTCGTCGGGGGAAGTCA 61.368 66.667 0.00 0.00 0.00 3.41
902 918 3.368571 GTCGTCGTCGGGGGAAGT 61.369 66.667 1.55 0.00 37.69 3.01
957 973 3.940975 ATGTCACCGTCGTCGTCGC 62.941 63.158 6.36 0.00 36.96 5.19
958 974 2.144069 CATGTCACCGTCGTCGTCG 61.144 63.158 4.87 4.87 38.55 5.12
959 975 1.800315 CCATGTCACCGTCGTCGTC 60.800 63.158 0.71 0.00 35.01 4.20
960 976 2.257371 CCATGTCACCGTCGTCGT 59.743 61.111 0.71 0.00 35.01 4.34
961 977 1.800315 GACCATGTCACCGTCGTCG 60.800 63.158 0.00 0.00 32.09 5.12
962 978 1.800315 CGACCATGTCACCGTCGTC 60.800 63.158 13.02 0.04 43.29 4.20
963 979 2.257371 CGACCATGTCACCGTCGT 59.743 61.111 13.02 0.00 43.29 4.34
965 981 0.806868 TACTCGACCATGTCACCGTC 59.193 55.000 0.00 0.00 32.09 4.79
966 982 0.809385 CTACTCGACCATGTCACCGT 59.191 55.000 0.00 0.00 32.09 4.83
1121 1154 0.601558 GCAGTCTGTCGAACTACCCA 59.398 55.000 0.93 0.00 0.00 4.51
1134 1167 1.299976 GGGATTGTTCCGGCAGTCT 59.700 57.895 0.00 0.00 43.63 3.24
1142 1175 2.484742 ACAGTTACGGGGATTGTTCC 57.515 50.000 0.00 0.00 41.77 3.62
1153 1186 2.396601 TGAACCGCAGTTACAGTTACG 58.603 47.619 0.00 0.00 35.94 3.18
1188 1223 3.005050 TCAGTCAATGCAGCTGGAAAAAG 59.995 43.478 13.45 2.53 0.00 2.27
1221 1299 5.577945 TCAAATTAGCTAACCGAAGTTACCG 59.422 40.000 8.70 0.00 37.42 4.02
1279 1364 7.281100 ACAAAACTGAACTAAGAAACTCCTCAG 59.719 37.037 0.00 0.00 35.92 3.35
1280 1365 7.065803 CACAAAACTGAACTAAGAAACTCCTCA 59.934 37.037 0.00 0.00 0.00 3.86
1289 1374 9.997482 GTTCAATTACACAAAACTGAACTAAGA 57.003 29.630 4.26 0.00 39.07 2.10
1446 1535 5.163854 CGTGGAAATCATGAACCTAGAACAC 60.164 44.000 0.00 1.05 34.35 3.32
1447 1536 4.935205 CGTGGAAATCATGAACCTAGAACA 59.065 41.667 0.00 0.00 34.35 3.18
1448 1537 4.935808 ACGTGGAAATCATGAACCTAGAAC 59.064 41.667 0.00 0.00 36.29 3.01
1451 1543 4.759782 AGACGTGGAAATCATGAACCTAG 58.240 43.478 0.00 5.35 36.29 3.02
1526 1621 7.275560 GGAGTTATGAACAAACAAACATATGCC 59.724 37.037 1.58 0.00 0.00 4.40
1539 1634 3.814625 TGCACTGTGGAGTTATGAACAA 58.185 40.909 10.21 0.00 0.00 2.83
1551 1646 4.460382 AGTTCAGGATTTAATGCACTGTGG 59.540 41.667 10.21 0.00 0.00 4.17
1577 1672 1.066303 TCGTGTCAAAACATGCCAACC 59.934 47.619 0.00 0.00 41.38 3.77
1582 1677 4.092821 TGCTACTATCGTGTCAAAACATGC 59.907 41.667 0.00 0.00 41.38 4.06
1583 1678 5.778161 TGCTACTATCGTGTCAAAACATG 57.222 39.130 0.00 0.00 42.71 3.21
1584 1679 6.985188 AATGCTACTATCGTGTCAAAACAT 57.015 33.333 0.00 0.00 37.81 2.71
1585 1680 6.649141 AGAAATGCTACTATCGTGTCAAAACA 59.351 34.615 0.00 0.00 0.00 2.83
1596 1741 4.149747 GCAAGAGCGAGAAATGCTACTATC 59.850 45.833 0.00 0.00 44.18 2.08
1598 1743 3.119137 TGCAAGAGCGAGAAATGCTACTA 60.119 43.478 0.00 0.00 44.18 1.82
1604 1749 7.125536 TGATAATATGCAAGAGCGAGAAATG 57.874 36.000 0.00 0.00 46.23 2.32
1605 1750 7.148289 CCATGATAATATGCAAGAGCGAGAAAT 60.148 37.037 0.00 0.00 46.23 2.17
1606 1751 6.148315 CCATGATAATATGCAAGAGCGAGAAA 59.852 38.462 0.00 0.00 46.23 2.52
1607 1752 5.640783 CCATGATAATATGCAAGAGCGAGAA 59.359 40.000 0.00 0.00 46.23 2.87
1608 1753 5.173664 CCATGATAATATGCAAGAGCGAGA 58.826 41.667 0.00 0.00 46.23 4.04
1609 1754 4.201792 GCCATGATAATATGCAAGAGCGAG 60.202 45.833 0.00 0.00 46.23 5.03
1610 1755 3.686241 GCCATGATAATATGCAAGAGCGA 59.314 43.478 0.00 0.00 46.23 4.93
1611 1756 3.181503 GGCCATGATAATATGCAAGAGCG 60.182 47.826 0.00 0.00 46.23 5.03
1613 1758 6.883217 AGTTAGGCCATGATAATATGCAAGAG 59.117 38.462 5.01 0.00 0.00 2.85
1614 1759 6.782986 AGTTAGGCCATGATAATATGCAAGA 58.217 36.000 5.01 0.00 0.00 3.02
1617 1762 7.770433 GTGATAGTTAGGCCATGATAATATGCA 59.230 37.037 5.01 0.00 0.00 3.96
1618 1763 7.042456 CGTGATAGTTAGGCCATGATAATATGC 60.042 40.741 5.01 0.00 0.00 3.14
1619 1764 8.197439 TCGTGATAGTTAGGCCATGATAATATG 58.803 37.037 5.01 0.00 0.00 1.78
1620 1765 8.306313 TCGTGATAGTTAGGCCATGATAATAT 57.694 34.615 5.01 0.00 0.00 1.28
1622 1767 6.605471 TCGTGATAGTTAGGCCATGATAAT 57.395 37.500 5.01 0.00 0.00 1.28
1623 1768 6.605471 ATCGTGATAGTTAGGCCATGATAA 57.395 37.500 5.01 0.00 34.56 1.75
1626 1771 4.955811 AATCGTGATAGTTAGGCCATGA 57.044 40.909 5.01 0.00 0.00 3.07
1628 1773 5.775701 AGAGTAATCGTGATAGTTAGGCCAT 59.224 40.000 5.01 0.00 0.00 4.40
1629 1774 5.138276 AGAGTAATCGTGATAGTTAGGCCA 58.862 41.667 5.01 0.00 0.00 5.36
1630 1775 5.474189 AGAGAGTAATCGTGATAGTTAGGCC 59.526 44.000 0.00 0.00 0.00 5.19
1633 1778 8.596271 TGAGAGAGAGTAATCGTGATAGTTAG 57.404 38.462 0.00 0.00 0.00 2.34
1635 1780 7.337184 TGTTGAGAGAGAGTAATCGTGATAGTT 59.663 37.037 0.00 0.00 0.00 2.24
1636 1781 6.824196 TGTTGAGAGAGAGTAATCGTGATAGT 59.176 38.462 0.00 0.00 0.00 2.12
1637 1782 7.252965 TGTTGAGAGAGAGTAATCGTGATAG 57.747 40.000 0.00 0.00 0.00 2.08
1638 1783 7.625828 TTGTTGAGAGAGAGTAATCGTGATA 57.374 36.000 0.00 0.00 0.00 2.15
1639 1784 6.516739 TTGTTGAGAGAGAGTAATCGTGAT 57.483 37.500 0.00 0.00 0.00 3.06
1664 1809 9.965824 CATTTCTACAGGTTTGAAGTGTATTTT 57.034 29.630 0.00 0.00 0.00 1.82
1665 1810 8.576442 CCATTTCTACAGGTTTGAAGTGTATTT 58.424 33.333 0.00 0.00 0.00 1.40
1667 1812 7.458397 TCCATTTCTACAGGTTTGAAGTGTAT 58.542 34.615 0.00 0.00 0.00 2.29
1669 1814 5.690865 TCCATTTCTACAGGTTTGAAGTGT 58.309 37.500 0.00 0.00 0.00 3.55
1671 1816 5.241728 GCTTCCATTTCTACAGGTTTGAAGT 59.758 40.000 0.00 0.00 31.65 3.01
1672 1817 5.241506 TGCTTCCATTTCTACAGGTTTGAAG 59.758 40.000 0.00 0.00 0.00 3.02
1673 1818 5.136828 TGCTTCCATTTCTACAGGTTTGAA 58.863 37.500 0.00 0.00 0.00 2.69
1674 1819 4.724399 TGCTTCCATTTCTACAGGTTTGA 58.276 39.130 0.00 0.00 0.00 2.69
1675 1820 5.241506 TCTTGCTTCCATTTCTACAGGTTTG 59.758 40.000 0.00 0.00 0.00 2.93
1676 1821 5.385198 TCTTGCTTCCATTTCTACAGGTTT 58.615 37.500 0.00 0.00 0.00 3.27
1677 1822 4.985538 TCTTGCTTCCATTTCTACAGGTT 58.014 39.130 0.00 0.00 0.00 3.50
1678 1823 4.287067 TCTCTTGCTTCCATTTCTACAGGT 59.713 41.667 0.00 0.00 0.00 4.00
1679 1824 4.836825 TCTCTTGCTTCCATTTCTACAGG 58.163 43.478 0.00 0.00 0.00 4.00
1680 1825 6.169094 TCTTCTCTTGCTTCCATTTCTACAG 58.831 40.000 0.00 0.00 0.00 2.74
1681 1826 6.114187 TCTTCTCTTGCTTCCATTTCTACA 57.886 37.500 0.00 0.00 0.00 2.74
1682 1827 5.064579 GCTCTTCTCTTGCTTCCATTTCTAC 59.935 44.000 0.00 0.00 0.00 2.59
1683 1828 5.181748 GCTCTTCTCTTGCTTCCATTTCTA 58.818 41.667 0.00 0.00 0.00 2.10
1684 1829 4.009002 GCTCTTCTCTTGCTTCCATTTCT 58.991 43.478 0.00 0.00 0.00 2.52
1694 5522 1.130749 CATGCTGTGCTCTTCTCTTGC 59.869 52.381 0.00 0.00 0.00 4.01
1706 5534 2.969806 GACACCGGTGCATGCTGTG 61.970 63.158 34.26 20.57 0.00 3.66
1707 5535 2.669569 GACACCGGTGCATGCTGT 60.670 61.111 34.26 13.33 0.00 4.40
1709 5537 2.359107 CTGACACCGGTGCATGCT 60.359 61.111 34.26 15.00 0.00 3.79
1710 5538 4.107051 GCTGACACCGGTGCATGC 62.107 66.667 34.26 28.08 0.00 4.06
1714 5542 1.795170 AACAATGCTGACACCGGTGC 61.795 55.000 34.26 25.37 0.00 5.01
1715 5543 0.238289 GAACAATGCTGACACCGGTG 59.762 55.000 32.83 32.83 0.00 4.94
1716 5544 0.179032 TGAACAATGCTGACACCGGT 60.179 50.000 0.00 0.00 0.00 5.28
1717 5545 0.950836 TTGAACAATGCTGACACCGG 59.049 50.000 0.00 0.00 0.00 5.28
1718 5546 2.772568 TTTGAACAATGCTGACACCG 57.227 45.000 0.00 0.00 0.00 4.94
1719 5547 2.796593 GCTTTTGAACAATGCTGACACC 59.203 45.455 0.00 0.00 0.00 4.16
1722 5550 4.114794 AGTTGCTTTTGAACAATGCTGAC 58.885 39.130 11.71 10.44 0.00 3.51
1723 5551 4.389890 AGTTGCTTTTGAACAATGCTGA 57.610 36.364 11.71 2.49 0.00 4.26
1724 5552 6.774354 ATTAGTTGCTTTTGAACAATGCTG 57.226 33.333 11.71 0.00 0.00 4.41
1740 5568 9.443283 GTGCATAAAGAATCTAGCAATTAGTTG 57.557 33.333 0.00 0.00 38.39 3.16
1741 5569 9.401058 AGTGCATAAAGAATCTAGCAATTAGTT 57.599 29.630 0.00 0.00 33.37 2.24
1742 5570 8.834465 CAGTGCATAAAGAATCTAGCAATTAGT 58.166 33.333 0.00 0.00 33.37 2.24
1743 5571 9.049523 TCAGTGCATAAAGAATCTAGCAATTAG 57.950 33.333 0.00 0.00 33.37 1.73
1744 5572 8.962884 TCAGTGCATAAAGAATCTAGCAATTA 57.037 30.769 0.00 0.00 33.37 1.40
1745 5573 7.870509 TCAGTGCATAAAGAATCTAGCAATT 57.129 32.000 0.00 0.00 33.37 2.32
1746 5574 7.870509 TTCAGTGCATAAAGAATCTAGCAAT 57.129 32.000 0.00 0.00 33.37 3.56
1747 5575 7.553760 TGATTCAGTGCATAAAGAATCTAGCAA 59.446 33.333 22.36 9.00 44.05 3.91
1748 5576 7.049754 TGATTCAGTGCATAAAGAATCTAGCA 58.950 34.615 22.36 9.64 44.05 3.49
1749 5577 7.488187 TGATTCAGTGCATAAAGAATCTAGC 57.512 36.000 22.36 7.99 44.05 3.42
1752 5580 8.127327 CGAATTGATTCAGTGCATAAAGAATCT 58.873 33.333 22.36 11.11 44.05 2.40
1753 5581 7.377928 CCGAATTGATTCAGTGCATAAAGAATC 59.622 37.037 18.47 18.47 44.01 2.52
1754 5582 7.198390 CCGAATTGATTCAGTGCATAAAGAAT 58.802 34.615 0.00 0.00 36.61 2.40
1755 5583 6.554419 CCGAATTGATTCAGTGCATAAAGAA 58.446 36.000 0.00 0.00 36.61 2.52
1756 5584 5.449041 GCCGAATTGATTCAGTGCATAAAGA 60.449 40.000 0.00 0.00 36.61 2.52
1757 5585 4.736793 GCCGAATTGATTCAGTGCATAAAG 59.263 41.667 0.00 0.00 36.61 1.85
1758 5586 4.157472 TGCCGAATTGATTCAGTGCATAAA 59.843 37.500 0.00 0.00 36.61 1.40
1759 5587 3.693578 TGCCGAATTGATTCAGTGCATAA 59.306 39.130 0.00 0.00 36.61 1.90
1760 5588 3.065233 GTGCCGAATTGATTCAGTGCATA 59.935 43.478 12.58 0.00 36.61 3.14
1761 5589 2.093890 TGCCGAATTGATTCAGTGCAT 58.906 42.857 0.00 0.00 36.61 3.96
1841 5670 3.025322 TGAAGTGTGACCCCAAATGTT 57.975 42.857 0.00 0.00 0.00 2.71
1875 5704 1.469335 ATGCAGCAATGGGGCATAGC 61.469 55.000 0.00 0.00 45.72 2.97
1876 5705 0.317160 CATGCAGCAATGGGGCATAG 59.683 55.000 0.00 0.00 45.81 2.23
1877 5706 0.397394 ACATGCAGCAATGGGGCATA 60.397 50.000 0.00 0.00 45.81 3.14
1879 5708 2.284039 ACATGCAGCAATGGGGCA 60.284 55.556 0.00 0.00 42.43 5.36
1880 5709 2.056223 AGACATGCAGCAATGGGGC 61.056 57.895 0.00 0.00 31.46 5.80
1881 5710 1.813859 CAGACATGCAGCAATGGGG 59.186 57.895 0.00 0.00 31.46 4.96
1921 5752 8.373048 TCACATTAGTAACTTGTAAGGTTGTG 57.627 34.615 5.49 5.49 0.00 3.33
1975 5806 7.447594 AGCAAGAATCTGATCAACCAATTTTT 58.552 30.769 0.00 0.00 0.00 1.94
2048 5885 4.652822 ACCCTTATTCGGCAAGATATTCC 58.347 43.478 0.00 0.00 0.00 3.01
2169 6010 5.964958 TTAACCATGGAGAGCAAAGAAAG 57.035 39.130 21.47 0.00 0.00 2.62
2194 6035 6.565234 ACATCCATGTAAAACGTTGAAACAA 58.435 32.000 0.00 0.00 39.68 2.83
2370 6211 0.913934 TAGGCAGGCAATGAGGGTGA 60.914 55.000 0.00 0.00 0.00 4.02
2444 6285 0.112995 AATTCTCTGGTGGCAGGCAA 59.887 50.000 0.00 0.00 0.00 4.52
2468 6309 2.557920 AAGTGCTCTTCCTCAACCTG 57.442 50.000 0.00 0.00 0.00 4.00
2534 6375 2.280592 GCCCCGACGTTTGACTGT 60.281 61.111 0.00 0.00 0.00 3.55
2866 6707 5.167845 GTTGCTGGAAAAACAAAGAACAGA 58.832 37.500 0.00 0.00 0.00 3.41
2868 6709 4.020662 AGGTTGCTGGAAAAACAAAGAACA 60.021 37.500 0.00 0.00 0.00 3.18
2871 6712 4.817318 AAGGTTGCTGGAAAAACAAAGA 57.183 36.364 0.00 0.00 0.00 2.52
2872 6713 4.332543 GGAAAGGTTGCTGGAAAAACAAAG 59.667 41.667 0.00 0.00 0.00 2.77
2897 6738 7.724061 ACAGGTAATAAAAACCAGAGTCATGTT 59.276 33.333 0.00 0.00 39.64 2.71
2900 6741 7.724061 ACAACAGGTAATAAAAACCAGAGTCAT 59.276 33.333 0.00 0.00 39.64 3.06
3089 6930 5.597813 CCTTTGATATATGAAGGTCGTGC 57.402 43.478 13.07 0.00 36.13 5.34
3174 7015 1.135199 AGTGTAATTGCCGTCGTCGAT 60.135 47.619 2.98 0.00 39.71 3.59
3188 7029 4.242475 CACCGACAGATGCTTTAGTGTAA 58.758 43.478 0.00 0.00 0.00 2.41
3311 7152 1.289160 AGAAGAGGTAAGCCATGCCA 58.711 50.000 0.00 0.00 35.99 4.92
3320 7161 2.611292 GCGAGTAGCGTAGAAGAGGTAA 59.389 50.000 0.00 0.00 43.41 2.85
3352 7193 3.341823 GTCAATGGACTGACATGAAGCT 58.658 45.455 0.00 0.00 44.32 3.74
3375 7216 5.163953 CCGATGTGACATTAAGATAATCCGC 60.164 44.000 0.00 0.00 0.00 5.54
3376 7217 5.163953 GCCGATGTGACATTAAGATAATCCG 60.164 44.000 0.00 0.00 0.00 4.18
3377 7218 5.934625 AGCCGATGTGACATTAAGATAATCC 59.065 40.000 0.00 0.00 0.00 3.01
3389 7230 3.562182 TCTCCTTATAGCCGATGTGACA 58.438 45.455 0.00 0.00 0.00 3.58
3401 7242 8.716674 ACCGTCTTACCAATATTCTCCTTATA 57.283 34.615 0.00 0.00 0.00 0.98
3404 7245 5.952347 ACCGTCTTACCAATATTCTCCTT 57.048 39.130 0.00 0.00 0.00 3.36
3419 7260 1.536662 AGCCTCCCTGAACCGTCTT 60.537 57.895 0.00 0.00 0.00 3.01
3483 7324 2.856000 AGCCCAACCTGAGCACCT 60.856 61.111 0.00 0.00 0.00 4.00
3491 7332 0.040204 CTGGATTTGGAGCCCAACCT 59.960 55.000 6.19 0.00 43.82 3.50
3555 7396 2.344500 CACGCACGGGTTCCCTAA 59.656 61.111 6.31 0.00 0.00 2.69
3572 7413 1.002011 GAGGAAGTGGTTGCCTCCC 60.002 63.158 0.00 0.00 41.84 4.30
3653 7494 3.053842 ACCTGTCTGCCATGAAGATGAAT 60.054 43.478 0.00 0.00 0.00 2.57
3693 7534 1.379443 AGACATACCGGGAGTCGCA 60.379 57.895 6.32 0.00 37.36 5.10
3788 7629 5.652014 CCATTTCCTGTGCCAGTAAATAGAA 59.348 40.000 5.76 0.00 30.31 2.10
3791 7632 3.699038 GCCATTTCCTGTGCCAGTAAATA 59.301 43.478 5.76 0.00 30.31 1.40
3842 7683 1.597742 CCCATGGTAGAATTCAGGCG 58.402 55.000 11.73 0.00 0.00 5.52
3881 7722 0.251354 CCACCTACTGATGCTGTGCT 59.749 55.000 0.00 0.00 0.00 4.40
3882 7723 0.250234 TCCACCTACTGATGCTGTGC 59.750 55.000 0.00 0.00 0.00 4.57
3935 7776 4.965814 TGGATACATCAAGCAAGATCCTC 58.034 43.478 0.00 0.00 46.17 3.71
4048 7889 3.056393 CCTGTGAACCTGTGTTATCCGTA 60.056 47.826 0.00 0.00 33.97 4.02
4056 7897 1.283613 TGGTTTCCTGTGAACCTGTGT 59.716 47.619 7.45 0.00 45.39 3.72
4074 7915 2.348411 ACTCCTCTGTGTGGTTTTGG 57.652 50.000 0.00 0.00 0.00 3.28
4077 7918 5.130477 TCTCTTAAACTCCTCTGTGTGGTTT 59.870 40.000 0.00 0.00 34.95 3.27
4169 8010 1.268999 TGTGCTGTTGTTTGCGGATTC 60.269 47.619 0.00 0.00 0.00 2.52
4170 8011 0.743688 TGTGCTGTTGTTTGCGGATT 59.256 45.000 0.00 0.00 0.00 3.01
4171 8012 0.743688 TTGTGCTGTTGTTTGCGGAT 59.256 45.000 0.00 0.00 0.00 4.18
4189 8030 3.613030 ACGAACCCTGCCGTATAATTTT 58.387 40.909 0.00 0.00 37.23 1.82
4268 8110 0.747255 TGACTAAGGAGCCTGATCGC 59.253 55.000 0.00 0.00 0.00 4.58
4590 8432 2.559440 GCCAGGCTCTGAATTCTGTAG 58.441 52.381 3.29 7.11 32.44 2.74


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

AutoCloner maintained by Alex Coulton.