Multiple sequence alignment - TraesCS2A01G266900

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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 TraesCS2A01G266900 chr2A 100.000 2426 0 0 1 2426 424445042 424442617 0.000000e+00 4481.0
1 TraesCS2A01G266900 chr2A 88.571 105 6 5 1703 1801 424443304 424443200 3.280000e-24 122.0
2 TraesCS2A01G266900 chr2A 88.571 105 6 5 1739 1843 424443340 424443242 3.280000e-24 122.0
3 TraesCS2A01G266900 chr2B 94.615 1040 39 5 514 1550 380258529 380259554 0.000000e+00 1594.0
4 TraesCS2A01G266900 chr2B 91.367 139 4 3 1543 1673 380259601 380259739 1.480000e-42 183.0
5 TraesCS2A01G266900 chr2B 86.538 104 7 5 41 138 783551278 783551380 9.170000e-20 108.0
6 TraesCS2A01G266900 chr2D 94.363 887 36 3 666 1550 312447365 312448239 0.000000e+00 1349.0
7 TraesCS2A01G266900 chr2D 85.533 629 83 8 1802 2426 400064428 400063804 0.000000e+00 651.0
8 TraesCS2A01G266900 chr2D 82.861 671 64 29 7 656 312446522 312447162 2.730000e-154 555.0
9 TraesCS2A01G266900 chr2D 93.382 136 4 2 1543 1673 312448286 312448421 1.900000e-46 196.0
10 TraesCS2A01G266900 chr2D 91.209 91 7 1 41 130 112935380 112935290 3.280000e-24 122.0
11 TraesCS2A01G266900 chr3D 85.692 629 82 8 1802 2426 481931342 481931966 0.000000e+00 656.0
12 TraesCS2A01G266900 chr3D 85.646 627 83 7 1802 2426 566100324 566099703 0.000000e+00 652.0
13 TraesCS2A01G266900 chr3D 84.810 158 21 2 133 290 98598178 98598332 3.230000e-34 156.0
14 TraesCS2A01G266900 chrUn 85.806 620 83 5 1805 2423 27187011 27187626 0.000000e+00 652.0
15 TraesCS2A01G266900 chr7D 85.646 627 82 8 1802 2426 169776490 169775870 0.000000e+00 652.0
16 TraesCS2A01G266900 chr7D 85.308 633 87 6 1795 2426 555875807 555875180 0.000000e+00 649.0
17 TraesCS2A01G266900 chr7D 76.692 266 60 2 135 400 458524314 458524051 1.940000e-31 147.0
18 TraesCS2A01G266900 chr1D 85.692 629 79 8 1802 2426 116449905 116449284 0.000000e+00 652.0
19 TraesCS2A01G266900 chr1D 81.356 236 40 3 133 365 465779651 465779885 3.180000e-44 189.0
20 TraesCS2A01G266900 chr5D 85.354 635 83 8 1795 2426 440886368 440885741 0.000000e+00 649.0
21 TraesCS2A01G266900 chr5D 85.174 634 87 7 1795 2426 120811549 120810921 0.000000e+00 643.0
22 TraesCS2A01G266900 chr5D 86.413 184 22 1 137 320 288178655 288178835 5.290000e-47 198.0
23 TraesCS2A01G266900 chr5B 78.351 194 40 2 138 330 707890804 707890612 9.110000e-25 124.0
24 TraesCS2A01G266900 chr5B 88.298 94 7 2 41 130 600484406 600484313 2.550000e-20 110.0
25 TraesCS2A01G266900 chr4A 88.000 100 10 2 41 138 622165418 622165319 1.520000e-22 117.0
26 TraesCS2A01G266900 chr4A 91.045 67 5 1 137 203 603334504 603334569 3.320000e-14 89.8
27 TraesCS2A01G266900 chr3A 88.298 94 7 4 41 130 589838428 589838335 2.550000e-20 110.0
28 TraesCS2A01G266900 chr5A 91.667 72 4 2 41 110 601481853 601481782 5.520000e-17 99.0
29 TraesCS2A01G266900 chr4B 85.333 75 9 2 129 203 622898798 622898870 2.590000e-10 76.8
30 TraesCS2A01G266900 chr6D 73.208 265 47 20 132 383 411769886 411769633 9.300000e-10 75.0
31 TraesCS2A01G266900 chr1B 78.824 85 16 1 137 221 572305993 572305911 3.370000e-04 56.5


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 TraesCS2A01G266900 chr2A 424442617 424445042 2425 True 1575.0 4481 92.380667 1 2426 3 chr2A.!!$R1 2425
1 TraesCS2A01G266900 chr2B 380258529 380259739 1210 False 888.5 1594 92.991000 514 1673 2 chr2B.!!$F2 1159
2 TraesCS2A01G266900 chr2D 312446522 312448421 1899 False 700.0 1349 90.202000 7 1673 3 chr2D.!!$F1 1666
3 TraesCS2A01G266900 chr2D 400063804 400064428 624 True 651.0 651 85.533000 1802 2426 1 chr2D.!!$R2 624
4 TraesCS2A01G266900 chr3D 481931342 481931966 624 False 656.0 656 85.692000 1802 2426 1 chr3D.!!$F2 624
5 TraesCS2A01G266900 chr3D 566099703 566100324 621 True 652.0 652 85.646000 1802 2426 1 chr3D.!!$R1 624
6 TraesCS2A01G266900 chrUn 27187011 27187626 615 False 652.0 652 85.806000 1805 2423 1 chrUn.!!$F1 618
7 TraesCS2A01G266900 chr7D 169775870 169776490 620 True 652.0 652 85.646000 1802 2426 1 chr7D.!!$R1 624
8 TraesCS2A01G266900 chr7D 555875180 555875807 627 True 649.0 649 85.308000 1795 2426 1 chr7D.!!$R3 631
9 TraesCS2A01G266900 chr1D 116449284 116449905 621 True 652.0 652 85.692000 1802 2426 1 chr1D.!!$R1 624
10 TraesCS2A01G266900 chr5D 440885741 440886368 627 True 649.0 649 85.354000 1795 2426 1 chr5D.!!$R2 631
11 TraesCS2A01G266900 chr5D 120810921 120811549 628 True 643.0 643 85.174000 1795 2426 1 chr5D.!!$R1 631

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
801 1014 0.819582 CCAGCAACCACATGGAATCC 59.18 55.0 4.53 0.0 36.09 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1675 1960 0.248215 CGTTCATGATTTGCTCCGGC 60.248 55.0 0.0 0.0 39.26 6.13 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
57 58 8.909708 TGTTTTTGTGACAAATGTTCTAAGAG 57.090 30.769 11.97 0.00 0.00 2.85
62 63 6.494842 TGTGACAAATGTTCTAAGAGTTTGC 58.505 36.000 0.00 0.00 34.12 3.68
66 67 8.031864 TGACAAATGTTCTAAGAGTTTGCAAAA 58.968 29.630 14.67 0.00 34.12 2.44
80 82 9.415544 AGAGTTTGCAAAATTTCATCAGTAATC 57.584 29.630 14.67 0.00 0.00 1.75
84 86 9.491675 TTTGCAAAATTTCATCAGTAATCACAT 57.508 25.926 10.02 0.00 0.00 3.21
90 92 8.991243 AATTTCATCAGTAATCACATTTGTGG 57.009 30.769 10.60 0.00 45.65 4.17
130 135 7.719778 AAAATCAGTGCTCCAAAATTCTTTC 57.280 32.000 0.00 0.00 0.00 2.62
133 138 6.409524 TCAGTGCTCCAAAATTCTTTCAAT 57.590 33.333 0.00 0.00 0.00 2.57
140 145 9.077885 TGCTCCAAAATTCTTTCAATAGTACTT 57.922 29.630 0.00 0.00 0.00 2.24
149 154 6.628185 TCTTTCAATAGTACTTCCTCCGTTC 58.372 40.000 0.00 0.00 0.00 3.95
150 155 4.996788 TCAATAGTACTTCCTCCGTTCC 57.003 45.455 0.00 0.00 0.00 3.62
152 157 4.960469 TCAATAGTACTTCCTCCGTTCCAT 59.040 41.667 0.00 0.00 0.00 3.41
161 166 4.665833 TCCTCCGTTCCATAATGTAGTG 57.334 45.455 0.00 0.00 0.00 2.74
165 170 4.126437 TCCGTTCCATAATGTAGTGCATG 58.874 43.478 0.00 0.00 37.96 4.06
168 173 5.177511 CCGTTCCATAATGTAGTGCATGTAG 59.822 44.000 0.00 0.00 37.96 2.74
170 175 6.646653 CGTTCCATAATGTAGTGCATGTAGAT 59.353 38.462 0.00 0.00 37.96 1.98
204 209 7.410120 AAGTCAAACCTCAGAAACTTTGATT 57.590 32.000 0.00 0.00 35.61 2.57
214 219 8.981647 CCTCAGAAACTTTGATTAAATTTGTGG 58.018 33.333 0.00 0.00 0.00 4.17
223 228 9.748708 CTTTGATTAAATTTGTGGAGAGAAACA 57.251 29.630 0.00 0.00 0.00 2.83
240 246 9.377312 GAGAGAAACATTTAAGTCTAGAATGCT 57.623 33.333 0.00 0.00 34.86 3.79
246 252 9.515226 AACATTTAAGTCTAGAATGCTAAACCA 57.485 29.630 0.00 0.00 34.86 3.67
386 392 9.817809 AGAAATATATACGCACTACATTATGGG 57.182 33.333 0.00 0.00 35.06 4.00
399 405 5.832539 ACATTATGGGATGAAGGGAGTAG 57.167 43.478 0.00 0.00 0.00 2.57
408 414 4.949856 GGATGAAGGGAGTAGCATTTTCAA 59.050 41.667 0.00 0.00 0.00 2.69
414 420 7.336931 TGAAGGGAGTAGCATTTTCAAAGTATC 59.663 37.037 0.00 0.00 0.00 2.24
415 421 6.721318 AGGGAGTAGCATTTTCAAAGTATCA 58.279 36.000 0.00 0.00 0.00 2.15
447 453 8.472007 TTTTTCTTTTTACCATGCCTTCTAGA 57.528 30.769 0.00 0.00 0.00 2.43
457 463 7.573968 ACCATGCCTTCTAGAAATGTTATTC 57.426 36.000 6.63 0.00 0.00 1.75
489 495 8.296713 TGAAAATTTGCAAGTTCCTAGTACATC 58.703 33.333 7.72 0.00 0.00 3.06
490 496 6.759497 AATTTGCAAGTTCCTAGTACATCC 57.241 37.500 0.65 0.00 0.00 3.51
493 499 4.018490 TGCAAGTTCCTAGTACATCCGTA 58.982 43.478 0.00 0.00 0.00 4.02
528 547 6.687081 TTTCATCTTTTTACTGTTCACCGT 57.313 33.333 0.00 0.00 0.00 4.83
534 553 4.325028 TTTTACTGTTCACCGTAGCTCA 57.675 40.909 0.00 0.00 0.00 4.26
593 612 2.175202 CCAGATATTCTCCCGCTAGCT 58.825 52.381 13.93 0.00 0.00 3.32
600 619 6.770785 AGATATTCTCCCGCTAGCTTAGATAG 59.229 42.308 13.93 0.00 0.00 2.08
657 677 5.408604 CAGTGGTAGTTAGTAACCTGCAAAG 59.591 44.000 9.46 0.00 36.67 2.77
690 903 1.929836 GGATCGACATCAGTTGAGCAC 59.070 52.381 3.84 0.00 44.57 4.40
697 910 4.507710 GACATCAGTTGAGCACCAGATAA 58.492 43.478 0.00 0.00 0.00 1.75
704 917 1.432270 GAGCACCAGATAAGCGCACC 61.432 60.000 11.47 0.00 0.00 5.01
801 1014 0.819582 CCAGCAACCACATGGAATCC 59.180 55.000 4.53 0.00 36.09 3.01
926 1144 2.852714 TAAATACCCACCTCCTCCGA 57.147 50.000 0.00 0.00 0.00 4.55
944 1162 3.325425 TCCGAACCAATCTTTGTCCACTA 59.675 43.478 0.00 0.00 0.00 2.74
1128 1346 2.998949 GCCGGGGGATTCTTCAGT 59.001 61.111 2.18 0.00 0.00 3.41
1365 1583 1.521616 CCATGGGAAAAATGGCGGG 59.478 57.895 2.85 0.00 38.32 6.13
1438 1660 1.133513 ACTGCTGATCCAACCAACCAA 60.134 47.619 0.00 0.00 0.00 3.67
1439 1661 1.270550 CTGCTGATCCAACCAACCAAC 59.729 52.381 0.00 0.00 0.00 3.77
1440 1662 0.603065 GCTGATCCAACCAACCAACC 59.397 55.000 0.00 0.00 0.00 3.77
1441 1663 1.823250 GCTGATCCAACCAACCAACCT 60.823 52.381 0.00 0.00 0.00 3.50
1491 1715 0.742281 ATGGATCGCTGCACTCACAC 60.742 55.000 0.00 0.00 0.00 3.82
1524 1748 2.760650 ACGAGACTGCCATGAACTGATA 59.239 45.455 0.00 0.00 0.00 2.15
1532 1756 7.284034 AGACTGCCATGAACTGATAAATTAAGG 59.716 37.037 0.00 0.00 0.00 2.69
1590 1868 6.604735 AATGGATGTAATAAACTGAGCGAC 57.395 37.500 0.00 0.00 0.00 5.19
1601 1879 0.319555 CTGAGCGACGGTTTTGAGGA 60.320 55.000 0.00 0.00 0.00 3.71
1650 1931 8.296713 ACCATGTTATAACTGTTTGTGATGAAC 58.703 33.333 16.33 0.00 0.00 3.18
1670 1955 1.443702 TCGCCTCATGTCGTGTTCG 60.444 57.895 0.00 0.00 38.55 3.95
1671 1956 1.443702 CGCCTCATGTCGTGTTCGA 60.444 57.895 0.00 0.00 44.12 3.71
1679 1964 3.556625 TCGTGTTCGAATTGCCGG 58.443 55.556 0.00 0.00 43.34 6.13
1680 1965 1.005984 TCGTGTTCGAATTGCCGGA 60.006 52.632 5.05 0.00 43.34 5.14
1681 1966 1.011968 TCGTGTTCGAATTGCCGGAG 61.012 55.000 5.05 0.00 43.34 4.63
1682 1967 1.134694 GTGTTCGAATTGCCGGAGC 59.865 57.895 5.05 0.00 40.48 4.70
1693 1978 3.629858 GCCGGAGCAAATCATGAAC 57.370 52.632 5.05 0.00 39.53 3.18
1694 1979 0.248215 GCCGGAGCAAATCATGAACG 60.248 55.000 5.05 0.00 39.53 3.95
1695 1980 0.248215 CCGGAGCAAATCATGAACGC 60.248 55.000 0.00 2.61 0.00 4.84
1696 1981 0.447406 CGGAGCAAATCATGAACGCA 59.553 50.000 14.50 0.00 0.00 5.24
1697 1982 1.791555 CGGAGCAAATCATGAACGCAC 60.792 52.381 14.50 9.30 0.00 5.34
1698 1983 1.527696 GAGCAAATCATGAACGCACG 58.472 50.000 14.50 0.00 0.00 5.34
1699 1984 1.128507 GAGCAAATCATGAACGCACGA 59.871 47.619 14.50 0.00 0.00 4.35
1700 1985 1.535028 AGCAAATCATGAACGCACGAA 59.465 42.857 14.50 0.00 0.00 3.85
1701 1986 2.031245 AGCAAATCATGAACGCACGAAA 60.031 40.909 14.50 0.00 0.00 3.46
1702 1987 2.339400 GCAAATCATGAACGCACGAAAG 59.661 45.455 0.00 0.00 0.00 2.62
1703 1988 3.809234 CAAATCATGAACGCACGAAAGA 58.191 40.909 0.00 0.00 0.00 2.52
1704 1989 4.406069 CAAATCATGAACGCACGAAAGAT 58.594 39.130 0.00 0.00 0.00 2.40
1705 1990 3.663464 ATCATGAACGCACGAAAGATG 57.337 42.857 0.00 0.00 0.00 2.90
1706 1991 1.128507 TCATGAACGCACGAAAGATGC 59.871 47.619 0.00 0.00 39.81 3.91
1707 1992 1.136000 CATGAACGCACGAAAGATGCA 60.136 47.619 0.00 0.00 43.57 3.96
1708 1993 0.940833 TGAACGCACGAAAGATGCAA 59.059 45.000 0.00 0.00 43.57 4.08
1709 1994 1.535028 TGAACGCACGAAAGATGCAAT 59.465 42.857 0.00 0.00 43.57 3.56
1710 1995 2.169179 GAACGCACGAAAGATGCAATC 58.831 47.619 0.00 0.00 46.04 2.67
1724 2009 5.973651 GATGCAATCACTACGATGAAAGA 57.026 39.130 0.00 0.00 44.70 2.52
1725 2010 5.972018 GATGCAATCACTACGATGAAAGAG 58.028 41.667 0.00 0.00 44.70 2.85
1726 2011 4.820897 TGCAATCACTACGATGAAAGAGT 58.179 39.130 0.00 0.00 33.40 3.24
1727 2012 5.961272 TGCAATCACTACGATGAAAGAGTA 58.039 37.500 0.00 0.00 33.40 2.59
1728 2013 6.573434 TGCAATCACTACGATGAAAGAGTAT 58.427 36.000 0.00 0.00 33.40 2.12
1729 2014 7.041721 TGCAATCACTACGATGAAAGAGTATT 58.958 34.615 0.00 0.00 33.40 1.89
1730 2015 8.194769 TGCAATCACTACGATGAAAGAGTATTA 58.805 33.333 0.00 0.00 33.40 0.98
1731 2016 9.197694 GCAATCACTACGATGAAAGAGTATTAT 57.802 33.333 0.00 0.00 33.40 1.28
1735 2020 9.841880 TCACTACGATGAAAGAGTATTATATGC 57.158 33.333 0.00 0.00 0.00 3.14
1736 2021 9.626045 CACTACGATGAAAGAGTATTATATGCA 57.374 33.333 0.00 0.00 0.00 3.96
1737 2022 9.627395 ACTACGATGAAAGAGTATTATATGCAC 57.373 33.333 0.00 0.00 0.00 4.57
1738 2023 7.568267 ACGATGAAAGAGTATTATATGCACG 57.432 36.000 0.00 0.00 0.00 5.34
1739 2024 7.368059 ACGATGAAAGAGTATTATATGCACGA 58.632 34.615 0.00 0.00 0.00 4.35
1740 2025 8.029522 ACGATGAAAGAGTATTATATGCACGAT 58.970 33.333 0.00 0.00 0.00 3.73
1741 2026 8.316753 CGATGAAAGAGTATTATATGCACGATG 58.683 37.037 0.00 0.00 0.00 3.84
1742 2027 7.351414 TGAAAGAGTATTATATGCACGATGC 57.649 36.000 0.00 0.00 45.29 3.91
1752 2037 3.786955 GCACGATGCAATCACTACG 57.213 52.632 0.00 0.00 45.97 3.51
1753 2038 1.277326 GCACGATGCAATCACTACGA 58.723 50.000 0.00 0.00 45.97 3.43
1754 2039 1.860950 GCACGATGCAATCACTACGAT 59.139 47.619 0.00 0.00 45.97 3.73
1755 2040 2.347939 GCACGATGCAATCACTACGATG 60.348 50.000 0.00 0.00 45.97 3.84
1756 2041 3.115554 CACGATGCAATCACTACGATGA 58.884 45.455 0.00 0.00 45.97 2.92
1757 2042 3.551485 CACGATGCAATCACTACGATGAA 59.449 43.478 0.00 0.00 45.97 2.57
1758 2043 4.032786 CACGATGCAATCACTACGATGAAA 59.967 41.667 0.00 0.00 45.97 2.69
1759 2044 4.268644 ACGATGCAATCACTACGATGAAAG 59.731 41.667 0.00 0.00 45.97 2.62
1760 2045 4.504097 CGATGCAATCACTACGATGAAAGA 59.496 41.667 0.00 0.00 45.97 2.52
1761 2046 5.332130 CGATGCAATCACTACGATGAAAGAG 60.332 44.000 0.00 0.00 45.97 2.85
1762 2047 4.820897 TGCAATCACTACGATGAAAGAGT 58.179 39.130 0.00 0.00 33.40 3.24
1763 2048 5.961272 TGCAATCACTACGATGAAAGAGTA 58.039 37.500 0.00 0.00 33.40 2.59
1764 2049 6.573434 TGCAATCACTACGATGAAAGAGTAT 58.427 36.000 0.00 0.00 33.40 2.12
1765 2050 7.041721 TGCAATCACTACGATGAAAGAGTATT 58.958 34.615 0.00 0.00 33.40 1.89
1766 2051 8.194769 TGCAATCACTACGATGAAAGAGTATTA 58.805 33.333 0.00 0.00 33.40 0.98
1767 2052 9.197694 GCAATCACTACGATGAAAGAGTATTAT 57.802 33.333 0.00 0.00 33.40 1.28
1771 2056 9.841880 TCACTACGATGAAAGAGTATTATATGC 57.158 33.333 0.00 0.00 0.00 3.14
1772 2057 9.626045 CACTACGATGAAAGAGTATTATATGCA 57.374 33.333 0.00 0.00 0.00 3.96
1773 2058 9.627395 ACTACGATGAAAGAGTATTATATGCAC 57.373 33.333 0.00 0.00 0.00 4.57
1774 2059 7.568267 ACGATGAAAGAGTATTATATGCACG 57.432 36.000 0.00 0.00 0.00 5.34
1775 2060 7.368059 ACGATGAAAGAGTATTATATGCACGA 58.632 34.615 0.00 0.00 0.00 4.35
1776 2061 7.539022 ACGATGAAAGAGTATTATATGCACGAG 59.461 37.037 0.00 0.00 0.00 4.18
1777 2062 7.750903 CGATGAAAGAGTATTATATGCACGAGA 59.249 37.037 0.00 0.00 0.00 4.04
1778 2063 8.749841 ATGAAAGAGTATTATATGCACGAGAC 57.250 34.615 0.00 0.00 0.00 3.36
1779 2064 7.712797 TGAAAGAGTATTATATGCACGAGACA 58.287 34.615 0.00 0.00 0.00 3.41
1780 2065 8.194769 TGAAAGAGTATTATATGCACGAGACAA 58.805 33.333 0.00 0.00 0.00 3.18
1781 2066 7.932120 AAGAGTATTATATGCACGAGACAAC 57.068 36.000 0.00 0.00 0.00 3.32
1782 2067 7.039313 AGAGTATTATATGCACGAGACAACA 57.961 36.000 0.00 0.00 0.00 3.33
1783 2068 7.661968 AGAGTATTATATGCACGAGACAACAT 58.338 34.615 0.00 0.00 0.00 2.71
1784 2069 7.596621 AGAGTATTATATGCACGAGACAACATG 59.403 37.037 0.00 0.00 0.00 3.21
1785 2070 7.433680 AGTATTATATGCACGAGACAACATGA 58.566 34.615 0.00 0.00 0.00 3.07
1786 2071 5.966636 TTATATGCACGAGACAACATGAC 57.033 39.130 0.00 0.00 0.00 3.06
1787 2072 2.168326 ATGCACGAGACAACATGACA 57.832 45.000 0.00 0.00 0.00 3.58
1788 2073 2.168326 TGCACGAGACAACATGACAT 57.832 45.000 0.00 0.00 0.00 3.06
1789 2074 2.068519 TGCACGAGACAACATGACATC 58.931 47.619 0.00 0.00 0.00 3.06
1790 2075 2.289010 TGCACGAGACAACATGACATCT 60.289 45.455 0.00 0.00 0.00 2.90
1791 2076 2.738846 GCACGAGACAACATGACATCTT 59.261 45.455 0.00 0.00 0.00 2.40
1792 2077 3.926527 GCACGAGACAACATGACATCTTA 59.073 43.478 0.00 0.00 0.00 2.10
1793 2078 4.201628 GCACGAGACAACATGACATCTTAC 60.202 45.833 0.00 0.00 0.00 2.34
1821 2106 4.983671 AGAGTATTACATGCACGAGACA 57.016 40.909 0.00 0.00 0.00 3.41
1827 2112 2.168326 ACATGCACGAGACAACATGA 57.832 45.000 0.00 0.00 41.93 3.07
1829 2114 1.799994 CATGCACGAGACAACATGACA 59.200 47.619 0.00 0.00 41.93 3.58
1892 2178 8.360390 GGGCAATATATAAGAGTTTTTGAAGGG 58.640 37.037 0.00 0.00 0.00 3.95
1909 2195 5.596845 TGAAGGGCAAATAAACAAGTTGTC 58.403 37.500 9.40 0.00 37.05 3.18
1918 2204 7.581476 CAAATAAACAAGTTGTCCTCGTACAT 58.419 34.615 9.40 0.00 0.00 2.29
1924 2210 0.528924 TTGTCCTCGTACATGTCGGG 59.471 55.000 0.00 6.09 0.00 5.14
1927 2213 0.034767 TCCTCGTACATGTCGGGACT 60.035 55.000 16.07 0.00 0.00 3.85
1931 2217 2.421073 CTCGTACATGTCGGGACTAACA 59.579 50.000 0.00 0.00 0.00 2.41
1937 2223 4.394729 ACATGTCGGGACTAACACAAAAT 58.605 39.130 0.00 0.00 0.00 1.82
1940 2226 3.181453 TGTCGGGACTAACACAAAATCCA 60.181 43.478 0.00 0.00 0.00 3.41
1950 2236 4.985538 ACACAAAATCCAACACCGTTTA 57.014 36.364 0.00 0.00 0.00 2.01
1967 2253 6.017605 CACCGTTTATACTACGTCTAGTCCAT 60.018 42.308 0.00 0.00 37.30 3.41
1974 2263 5.697473 ACTACGTCTAGTCCATCATGATG 57.303 43.478 25.97 25.97 38.51 3.07
2011 2300 8.035394 CACAATTTACTAAGCTCTACCTTGAGA 58.965 37.037 0.00 0.00 36.23 3.27
2018 2307 8.135382 ACTAAGCTCTACCTTGAGACAAATTA 57.865 34.615 0.00 0.00 36.23 1.40
2022 2311 6.013293 AGCTCTACCTTGAGACAAATTACCTT 60.013 38.462 0.00 0.00 36.23 3.50
2059 2349 8.565416 AGAAAGTAAATAACTCCTTCCAAAACG 58.435 33.333 0.00 0.00 37.50 3.60
2072 2362 2.554893 TCCAAAACGGCATAAACACCTC 59.445 45.455 0.00 0.00 33.14 3.85
2084 2374 0.375803 AACACCTCGTGCGTCAAAAC 59.624 50.000 0.00 0.00 36.98 2.43
2093 2383 2.365582 GTGCGTCAAAACCCATAGGAT 58.634 47.619 0.00 0.00 36.73 3.24
2117 2408 9.315525 GATTAGTGAGAAATACCAACTAAGTCC 57.684 37.037 0.00 0.00 0.00 3.85
2128 2419 4.202284 ACCAACTAAGTCCGAGCAAAACTA 60.202 41.667 0.00 0.00 0.00 2.24
2143 2434 8.500773 CGAGCAAAACTAAAACTTATTGGTAGA 58.499 33.333 0.00 0.00 0.00 2.59
2169 2460 6.354938 ACTGACTTTGTCATCATATCAGCAT 58.645 36.000 0.65 0.00 41.94 3.79
2197 2488 9.605275 ATTATCATGCGTACTTATCTTGCATAT 57.395 29.630 2.46 0.00 43.89 1.78
2258 2550 8.510243 AGTGAATATAACATCAATGTGCTTCA 57.490 30.769 0.00 2.18 41.61 3.02
2273 2565 5.045872 TGTGCTTCATTCTCTCATGATACG 58.954 41.667 0.00 0.00 33.07 3.06
2280 2572 6.450545 TCATTCTCTCATGATACGTTGGATC 58.549 40.000 0.00 0.00 0.00 3.36
2346 2638 3.511146 GGGCAAGATGAATCTCCACAAAA 59.489 43.478 0.00 0.00 35.76 2.44
2347 2639 4.161001 GGGCAAGATGAATCTCCACAAAAT 59.839 41.667 0.00 0.00 35.76 1.82
2375 2667 7.981789 CAGTATACAAAGCTCTCAACCAGATAA 59.018 37.037 5.50 0.00 0.00 1.75
2387 2679 7.394016 TCTCAACCAGATAACTTCTTTGCATA 58.606 34.615 0.00 0.00 29.93 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 9.487790 TTGTCACAAAAACATTCTCTTCTTTTT 57.512 25.926 0.00 0.00 0.00 1.94
20 21 9.487790 TTTGTCACAAAAACATTCTCTTCTTTT 57.512 25.926 0.00 0.00 0.00 2.27
24 25 8.411318 ACATTTGTCACAAAAACATTCTCTTC 57.589 30.769 7.14 0.00 0.00 2.87
27 28 8.411318 AGAACATTTGTCACAAAAACATTCTC 57.589 30.769 7.14 0.00 0.00 2.87
30 31 9.868277 TCTTAGAACATTTGTCACAAAAACATT 57.132 25.926 7.14 0.00 0.00 2.71
31 32 9.520204 CTCTTAGAACATTTGTCACAAAAACAT 57.480 29.630 7.14 0.00 0.00 2.71
32 33 8.519526 ACTCTTAGAACATTTGTCACAAAAACA 58.480 29.630 7.14 0.00 0.00 2.83
33 34 8.911247 ACTCTTAGAACATTTGTCACAAAAAC 57.089 30.769 7.14 0.00 0.00 2.43
34 35 9.921637 AAACTCTTAGAACATTTGTCACAAAAA 57.078 25.926 7.14 0.00 0.00 1.94
39 40 6.494842 TGCAAACTCTTAGAACATTTGTCAC 58.505 36.000 12.04 1.60 33.70 3.67
57 58 8.763356 TGTGATTACTGATGAAATTTTGCAAAC 58.237 29.630 12.39 0.50 0.00 2.93
80 82 2.223456 TGCAACGACTTCCACAAATGTG 60.223 45.455 6.57 6.57 45.23 3.21
84 86 3.577649 TTTTGCAACGACTTCCACAAA 57.422 38.095 0.00 0.00 0.00 2.83
107 109 6.819284 TGAAAGAATTTTGGAGCACTGATTT 58.181 32.000 0.00 0.00 39.27 2.17
110 112 5.850557 TTGAAAGAATTTTGGAGCACTGA 57.149 34.783 0.00 0.00 39.27 3.41
111 113 7.373493 ACTATTGAAAGAATTTTGGAGCACTG 58.627 34.615 0.00 0.00 39.27 3.66
113 115 8.515414 AGTACTATTGAAAGAATTTTGGAGCAC 58.485 33.333 0.00 0.00 39.27 4.40
114 116 8.635765 AGTACTATTGAAAGAATTTTGGAGCA 57.364 30.769 0.00 0.00 39.27 4.26
115 117 9.561270 GAAGTACTATTGAAAGAATTTTGGAGC 57.439 33.333 0.00 0.00 39.27 4.70
117 119 9.807921 AGGAAGTACTATTGAAAGAATTTTGGA 57.192 29.630 0.00 0.00 39.27 3.53
120 122 8.947115 CGGAGGAAGTACTATTGAAAGAATTTT 58.053 33.333 0.00 0.00 39.27 1.82
125 130 6.350780 GGAACGGAGGAAGTACTATTGAAAGA 60.351 42.308 0.00 0.00 0.00 2.52
130 135 4.730949 TGGAACGGAGGAAGTACTATTG 57.269 45.455 0.00 0.00 0.00 1.90
133 138 5.895534 ACATTATGGAACGGAGGAAGTACTA 59.104 40.000 0.00 0.00 0.00 1.82
140 145 3.181469 GCACTACATTATGGAACGGAGGA 60.181 47.826 0.00 0.00 0.00 3.71
176 181 6.834168 AAGTTTCTGAGGTTTGACTTTTCA 57.166 33.333 0.00 0.00 0.00 2.69
214 219 9.377312 AGCATTCTAGACTTAAATGTTTCTCTC 57.623 33.333 0.00 0.00 33.82 3.20
361 367 9.811995 TCCCATAATGTAGTGCGTATATATTTC 57.188 33.333 0.00 0.00 0.00 2.17
366 372 7.418337 TCATCCCATAATGTAGTGCGTATAT 57.582 36.000 0.00 0.00 0.00 0.86
372 378 4.074970 CCCTTCATCCCATAATGTAGTGC 58.925 47.826 0.00 0.00 0.00 4.40
385 391 4.526970 TGAAAATGCTACTCCCTTCATCC 58.473 43.478 0.00 0.00 0.00 3.51
386 392 6.151817 ACTTTGAAAATGCTACTCCCTTCATC 59.848 38.462 0.00 0.00 0.00 2.92
414 420 9.449550 GGCATGGTAAAAAGAAAAAGAAAATTG 57.550 29.630 0.00 0.00 0.00 2.32
415 421 9.407380 AGGCATGGTAAAAAGAAAAAGAAAATT 57.593 25.926 0.00 0.00 0.00 1.82
421 427 8.576442 TCTAGAAGGCATGGTAAAAAGAAAAAG 58.424 33.333 0.00 0.00 0.00 2.27
422 428 8.472007 TCTAGAAGGCATGGTAAAAAGAAAAA 57.528 30.769 0.00 0.00 0.00 1.94
423 429 8.472007 TTCTAGAAGGCATGGTAAAAAGAAAA 57.528 30.769 0.00 0.00 0.00 2.29
424 430 8.472007 TTTCTAGAAGGCATGGTAAAAAGAAA 57.528 30.769 5.12 0.00 0.00 2.52
425 431 8.522830 CATTTCTAGAAGGCATGGTAAAAAGAA 58.477 33.333 5.12 0.00 0.00 2.52
426 432 7.669722 ACATTTCTAGAAGGCATGGTAAAAAGA 59.330 33.333 16.37 0.00 0.00 2.52
427 433 7.830739 ACATTTCTAGAAGGCATGGTAAAAAG 58.169 34.615 16.37 0.00 0.00 2.27
428 434 7.775053 ACATTTCTAGAAGGCATGGTAAAAA 57.225 32.000 16.37 0.00 0.00 1.94
437 443 9.866655 ATTATGGAATAACATTTCTAGAAGGCA 57.133 29.630 5.12 0.00 42.43 4.75
457 463 7.910441 AGGAACTTGCAAATTTTCATTATGG 57.090 32.000 0.00 0.00 27.25 2.74
464 470 7.755373 GGATGTACTAGGAACTTGCAAATTTTC 59.245 37.037 0.00 3.67 41.75 2.29
468 474 4.876107 CGGATGTACTAGGAACTTGCAAAT 59.124 41.667 0.00 0.00 41.75 2.32
472 478 3.521947 ACGGATGTACTAGGAACTTGC 57.478 47.619 0.00 0.00 41.75 4.01
473 479 7.894376 TTTTTACGGATGTACTAGGAACTTG 57.106 36.000 0.00 0.00 41.75 3.16
504 510 7.090953 ACGGTGAACAGTAAAAAGATGAAAA 57.909 32.000 0.00 0.00 0.00 2.29
505 511 6.687081 ACGGTGAACAGTAAAAAGATGAAA 57.313 33.333 0.00 0.00 0.00 2.69
508 514 5.408604 AGCTACGGTGAACAGTAAAAAGATG 59.591 40.000 0.00 0.00 0.00 2.90
509 515 5.548406 AGCTACGGTGAACAGTAAAAAGAT 58.452 37.500 0.00 0.00 0.00 2.40
511 517 4.748102 TGAGCTACGGTGAACAGTAAAAAG 59.252 41.667 0.00 0.00 0.00 2.27
512 518 4.695396 TGAGCTACGGTGAACAGTAAAAA 58.305 39.130 0.00 0.00 0.00 1.94
528 547 1.134699 CAGCCCGAGTCAAATGAGCTA 60.135 52.381 0.00 0.00 0.00 3.32
534 553 2.039084 AGTTTCTCAGCCCGAGTCAAAT 59.961 45.455 1.01 0.00 42.88 2.32
593 612 4.771903 TGTTAATTGCCGTGGCTATCTAA 58.228 39.130 12.84 8.57 42.51 2.10
600 619 1.341369 GCGTTGTTAATTGCCGTGGC 61.341 55.000 3.30 3.30 42.35 5.01
684 897 0.740868 GTGCGCTTATCTGGTGCTCA 60.741 55.000 9.73 0.00 40.39 4.26
690 903 0.596083 CTCTCGGTGCGCTTATCTGG 60.596 60.000 9.73 0.00 0.00 3.86
704 917 4.767841 AGCTCGCACGCACTCTCG 62.768 66.667 0.00 0.00 0.00 4.04
715 928 3.044305 GTGTCACCACCAGCTCGC 61.044 66.667 0.00 0.00 35.44 5.03
831 1049 2.910977 GGGGAAGGAAGAAAGGTAGTGA 59.089 50.000 0.00 0.00 0.00 3.41
832 1050 2.354805 CGGGGAAGGAAGAAAGGTAGTG 60.355 54.545 0.00 0.00 0.00 2.74
833 1051 1.907255 CGGGGAAGGAAGAAAGGTAGT 59.093 52.381 0.00 0.00 0.00 2.73
834 1052 1.407025 GCGGGGAAGGAAGAAAGGTAG 60.407 57.143 0.00 0.00 0.00 3.18
835 1053 0.616891 GCGGGGAAGGAAGAAAGGTA 59.383 55.000 0.00 0.00 0.00 3.08
891 1109 1.309499 TTTATGACTTTGGGCGCGGG 61.309 55.000 8.83 0.00 0.00 6.13
926 1144 4.506802 GGGAGTAGTGGACAAAGATTGGTT 60.507 45.833 0.00 0.00 34.12 3.67
944 1162 2.989571 AGGATTCTTGGAACTTGGGAGT 59.010 45.455 0.00 0.00 37.87 3.85
1128 1346 2.266372 CGGAACCACGGTATGCCA 59.734 61.111 0.00 0.00 34.09 4.92
1491 1715 0.891373 AGTCTCGTCCTGGATGTGTG 59.109 55.000 15.28 7.66 0.00 3.82
1524 1748 5.410439 CACGTACAACTAGTGGCCTTAATTT 59.590 40.000 3.32 0.00 32.68 1.82
1532 1756 1.790623 CACACACGTACAACTAGTGGC 59.209 52.381 0.00 0.00 39.95 5.01
1590 1868 1.535462 ACGCTCAAATCCTCAAAACCG 59.465 47.619 0.00 0.00 0.00 4.44
1601 1879 2.368439 ACACCATATGCACGCTCAAAT 58.632 42.857 0.00 0.00 0.00 2.32
1650 1931 1.674611 GAACACGACATGAGGCGACG 61.675 60.000 0.00 0.00 0.00 5.12
1675 1960 0.248215 CGTTCATGATTTGCTCCGGC 60.248 55.000 0.00 0.00 39.26 6.13
1676 1961 0.248215 GCGTTCATGATTTGCTCCGG 60.248 55.000 0.00 0.00 0.00 5.14
1677 1962 0.447406 TGCGTTCATGATTTGCTCCG 59.553 50.000 13.39 2.86 0.00 4.63
1678 1963 1.791555 CGTGCGTTCATGATTTGCTCC 60.792 52.381 13.39 5.64 0.00 4.70
1679 1964 1.128507 TCGTGCGTTCATGATTTGCTC 59.871 47.619 13.39 9.82 33.54 4.26
1680 1965 1.155889 TCGTGCGTTCATGATTTGCT 58.844 45.000 13.39 0.00 33.54 3.91
1681 1966 1.962412 TTCGTGCGTTCATGATTTGC 58.038 45.000 0.00 1.55 37.99 3.68
1682 1967 3.809234 TCTTTCGTGCGTTCATGATTTG 58.191 40.909 0.00 0.00 37.99 2.32
1683 1968 4.406069 CATCTTTCGTGCGTTCATGATTT 58.594 39.130 0.00 0.00 37.99 2.17
1684 1969 3.728864 GCATCTTTCGTGCGTTCATGATT 60.729 43.478 0.00 0.00 37.99 2.57
1685 1970 2.223112 GCATCTTTCGTGCGTTCATGAT 60.223 45.455 0.00 0.00 37.99 2.45
1686 1971 1.128507 GCATCTTTCGTGCGTTCATGA 59.871 47.619 0.00 0.00 36.50 3.07
1687 1972 1.136000 TGCATCTTTCGTGCGTTCATG 60.136 47.619 0.00 0.00 45.37 3.07
1688 1973 1.155889 TGCATCTTTCGTGCGTTCAT 58.844 45.000 0.00 0.00 45.37 2.57
1689 1974 0.940833 TTGCATCTTTCGTGCGTTCA 59.059 45.000 0.00 0.00 45.37 3.18
1690 1975 2.169179 GATTGCATCTTTCGTGCGTTC 58.831 47.619 0.00 0.00 45.37 3.95
1691 1976 1.535028 TGATTGCATCTTTCGTGCGTT 59.465 42.857 0.00 0.00 45.37 4.84
1692 1977 1.135972 GTGATTGCATCTTTCGTGCGT 60.136 47.619 0.00 0.00 45.37 5.24
1693 1978 1.129251 AGTGATTGCATCTTTCGTGCG 59.871 47.619 0.00 0.00 45.37 5.34
1694 1979 2.907910 AGTGATTGCATCTTTCGTGC 57.092 45.000 0.00 0.00 42.81 5.34
1695 1980 3.612423 TCGTAGTGATTGCATCTTTCGTG 59.388 43.478 0.00 0.00 0.00 4.35
1696 1981 3.845178 TCGTAGTGATTGCATCTTTCGT 58.155 40.909 0.00 0.00 0.00 3.85
1697 1982 4.504097 TCATCGTAGTGATTGCATCTTTCG 59.496 41.667 0.00 0.00 34.13 3.46
1698 1983 5.973651 TCATCGTAGTGATTGCATCTTTC 57.026 39.130 0.00 0.00 34.13 2.62
1699 1984 6.595326 TCTTTCATCGTAGTGATTGCATCTTT 59.405 34.615 0.00 0.00 34.13 2.52
1700 1985 6.108687 TCTTTCATCGTAGTGATTGCATCTT 58.891 36.000 0.00 0.00 34.13 2.40
1701 1986 5.664457 TCTTTCATCGTAGTGATTGCATCT 58.336 37.500 0.00 0.00 34.13 2.90
1702 1987 5.521735 ACTCTTTCATCGTAGTGATTGCATC 59.478 40.000 0.00 0.00 34.13 3.91
1703 1988 5.423015 ACTCTTTCATCGTAGTGATTGCAT 58.577 37.500 0.00 0.00 34.13 3.96
1704 1989 4.820897 ACTCTTTCATCGTAGTGATTGCA 58.179 39.130 0.00 0.00 34.13 4.08
1705 1990 7.470289 AATACTCTTTCATCGTAGTGATTGC 57.530 36.000 0.00 0.00 34.13 3.56
1709 1994 9.841880 GCATATAATACTCTTTCATCGTAGTGA 57.158 33.333 0.00 0.00 0.00 3.41
1710 1995 9.626045 TGCATATAATACTCTTTCATCGTAGTG 57.374 33.333 0.00 0.00 0.00 2.74
1711 1996 9.627395 GTGCATATAATACTCTTTCATCGTAGT 57.373 33.333 0.00 0.00 0.00 2.73
1712 1997 8.789743 CGTGCATATAATACTCTTTCATCGTAG 58.210 37.037 0.00 0.00 0.00 3.51
1713 1998 8.508875 TCGTGCATATAATACTCTTTCATCGTA 58.491 33.333 0.00 0.00 0.00 3.43
1714 1999 7.368059 TCGTGCATATAATACTCTTTCATCGT 58.632 34.615 0.00 0.00 0.00 3.73
1715 2000 7.796958 TCGTGCATATAATACTCTTTCATCG 57.203 36.000 0.00 0.00 0.00 3.84
1716 2001 8.113062 GCATCGTGCATATAATACTCTTTCATC 58.887 37.037 0.00 0.00 44.26 2.92
1717 2002 7.968246 GCATCGTGCATATAATACTCTTTCAT 58.032 34.615 0.00 0.00 44.26 2.57
1718 2003 7.351414 GCATCGTGCATATAATACTCTTTCA 57.649 36.000 0.00 0.00 44.26 2.69
1734 2019 1.277326 TCGTAGTGATTGCATCGTGC 58.723 50.000 0.00 3.44 45.29 5.34
1735 2020 3.115554 TCATCGTAGTGATTGCATCGTG 58.884 45.455 0.00 0.00 34.13 4.35
1736 2021 3.436700 TCATCGTAGTGATTGCATCGT 57.563 42.857 0.00 0.00 34.13 3.73
1737 2022 4.504097 TCTTTCATCGTAGTGATTGCATCG 59.496 41.667 0.00 0.00 34.13 3.84
1738 2023 5.521735 ACTCTTTCATCGTAGTGATTGCATC 59.478 40.000 0.00 0.00 34.13 3.91
1739 2024 5.423015 ACTCTTTCATCGTAGTGATTGCAT 58.577 37.500 0.00 0.00 34.13 3.96
1740 2025 4.820897 ACTCTTTCATCGTAGTGATTGCA 58.179 39.130 0.00 0.00 34.13 4.08
1741 2026 7.470289 AATACTCTTTCATCGTAGTGATTGC 57.530 36.000 0.00 0.00 34.13 3.56
1745 2030 9.841880 GCATATAATACTCTTTCATCGTAGTGA 57.158 33.333 0.00 0.00 0.00 3.41
1746 2031 9.626045 TGCATATAATACTCTTTCATCGTAGTG 57.374 33.333 0.00 0.00 0.00 2.74
1747 2032 9.627395 GTGCATATAATACTCTTTCATCGTAGT 57.373 33.333 0.00 0.00 0.00 2.73
1748 2033 8.789743 CGTGCATATAATACTCTTTCATCGTAG 58.210 37.037 0.00 0.00 0.00 3.51
1749 2034 8.508875 TCGTGCATATAATACTCTTTCATCGTA 58.491 33.333 0.00 0.00 0.00 3.43
1750 2035 7.368059 TCGTGCATATAATACTCTTTCATCGT 58.632 34.615 0.00 0.00 0.00 3.73
1751 2036 7.750903 TCTCGTGCATATAATACTCTTTCATCG 59.249 37.037 0.00 0.00 0.00 3.84
1752 2037 8.855279 GTCTCGTGCATATAATACTCTTTCATC 58.145 37.037 0.00 0.00 0.00 2.92
1753 2038 8.360390 TGTCTCGTGCATATAATACTCTTTCAT 58.640 33.333 0.00 0.00 0.00 2.57
1754 2039 7.712797 TGTCTCGTGCATATAATACTCTTTCA 58.287 34.615 0.00 0.00 0.00 2.69
1755 2040 8.480853 GTTGTCTCGTGCATATAATACTCTTTC 58.519 37.037 0.00 0.00 0.00 2.62
1756 2041 7.979537 TGTTGTCTCGTGCATATAATACTCTTT 59.020 33.333 0.00 0.00 0.00 2.52
1757 2042 7.489160 TGTTGTCTCGTGCATATAATACTCTT 58.511 34.615 0.00 0.00 0.00 2.85
1758 2043 7.039313 TGTTGTCTCGTGCATATAATACTCT 57.961 36.000 0.00 0.00 0.00 3.24
1759 2044 7.595130 TCATGTTGTCTCGTGCATATAATACTC 59.405 37.037 0.00 0.00 0.00 2.59
1760 2045 7.382488 GTCATGTTGTCTCGTGCATATAATACT 59.618 37.037 0.00 0.00 0.00 2.12
1761 2046 7.169140 TGTCATGTTGTCTCGTGCATATAATAC 59.831 37.037 0.00 0.00 0.00 1.89
1762 2047 7.206687 TGTCATGTTGTCTCGTGCATATAATA 58.793 34.615 0.00 0.00 0.00 0.98
1763 2048 6.048509 TGTCATGTTGTCTCGTGCATATAAT 58.951 36.000 0.00 0.00 0.00 1.28
1764 2049 5.415221 TGTCATGTTGTCTCGTGCATATAA 58.585 37.500 0.00 0.00 0.00 0.98
1765 2050 5.004922 TGTCATGTTGTCTCGTGCATATA 57.995 39.130 0.00 0.00 0.00 0.86
1766 2051 3.860641 TGTCATGTTGTCTCGTGCATAT 58.139 40.909 0.00 0.00 0.00 1.78
1767 2052 3.311486 TGTCATGTTGTCTCGTGCATA 57.689 42.857 0.00 0.00 0.00 3.14
1768 2053 2.168326 TGTCATGTTGTCTCGTGCAT 57.832 45.000 0.00 0.00 0.00 3.96
1769 2054 2.068519 GATGTCATGTTGTCTCGTGCA 58.931 47.619 0.00 0.00 0.00 4.57
1770 2055 2.341257 AGATGTCATGTTGTCTCGTGC 58.659 47.619 0.00 0.00 0.00 5.34
1771 2056 4.030641 CGTAAGATGTCATGTTGTCTCGTG 59.969 45.833 5.49 0.00 43.02 4.35
1772 2057 4.082949 TCGTAAGATGTCATGTTGTCTCGT 60.083 41.667 5.49 0.00 45.01 4.18
1773 2058 4.412207 TCGTAAGATGTCATGTTGTCTCG 58.588 43.478 5.49 5.60 45.01 4.04
1789 2074 8.269424 GTGCATGTAATACTCTTTCATCGTAAG 58.731 37.037 0.00 0.00 0.00 2.34
1790 2075 7.043656 CGTGCATGTAATACTCTTTCATCGTAA 60.044 37.037 0.00 0.00 0.00 3.18
1791 2076 6.416750 CGTGCATGTAATACTCTTTCATCGTA 59.583 38.462 0.00 0.00 0.00 3.43
1792 2077 5.232202 CGTGCATGTAATACTCTTTCATCGT 59.768 40.000 0.00 0.00 0.00 3.73
1793 2078 5.458779 TCGTGCATGTAATACTCTTTCATCG 59.541 40.000 5.68 0.00 0.00 3.84
1798 2083 5.720202 TGTCTCGTGCATGTAATACTCTTT 58.280 37.500 5.68 0.00 0.00 2.52
1800 2085 4.983671 TGTCTCGTGCATGTAATACTCT 57.016 40.909 5.68 0.00 0.00 3.24
1811 2096 2.068519 GATGTCATGTTGTCTCGTGCA 58.931 47.619 0.00 0.00 0.00 4.57
1865 2150 8.912988 CCTTCAAAAACTCTTATATATTGCCCA 58.087 33.333 0.00 0.00 0.00 5.36
1892 2178 4.855531 ACGAGGACAACTTGTTTATTTGC 58.144 39.130 0.00 0.00 41.13 3.68
1896 2182 6.228258 ACATGTACGAGGACAACTTGTTTAT 58.772 36.000 0.00 0.00 41.13 1.40
1909 2195 1.671979 TAGTCCCGACATGTACGAGG 58.328 55.000 16.06 14.68 0.00 4.63
1918 2204 3.181453 TGGATTTTGTGTTAGTCCCGACA 60.181 43.478 0.00 0.00 0.00 4.35
1924 2210 4.035909 ACGGTGTTGGATTTTGTGTTAGTC 59.964 41.667 0.00 0.00 0.00 2.59
1927 2213 4.985538 AACGGTGTTGGATTTTGTGTTA 57.014 36.364 0.00 0.00 0.00 2.41
1931 2217 6.887626 AGTATAAACGGTGTTGGATTTTGT 57.112 33.333 0.00 0.00 0.00 2.83
1937 2223 4.782019 ACGTAGTATAAACGGTGTTGGA 57.218 40.909 12.10 0.00 44.48 3.53
1950 2236 7.384439 CATCATGATGGACTAGACGTAGTAT 57.616 40.000 25.37 0.00 39.78 2.12
1974 2263 9.860898 AGCTTAGTAAATTGTGATTCAAATTCC 57.139 29.630 0.00 0.00 39.62 3.01
1982 2271 9.167311 CAAGGTAGAGCTTAGTAAATTGTGATT 57.833 33.333 0.00 0.00 0.00 2.57
1994 2283 7.492994 GGTAATTTGTCTCAAGGTAGAGCTTAG 59.507 40.741 0.00 0.00 35.59 2.18
1995 2284 7.180408 AGGTAATTTGTCTCAAGGTAGAGCTTA 59.820 37.037 0.00 0.00 35.59 3.09
1998 2287 5.735766 AGGTAATTTGTCTCAAGGTAGAGC 58.264 41.667 0.00 0.00 35.59 4.09
2002 2291 7.074653 ACTGAAGGTAATTTGTCTCAAGGTA 57.925 36.000 0.00 0.00 0.00 3.08
2050 2340 2.959707 AGGTGTTTATGCCGTTTTGGAA 59.040 40.909 0.00 0.00 42.00 3.53
2057 2347 1.296056 GCACGAGGTGTTTATGCCGT 61.296 55.000 0.00 0.00 35.75 5.68
2059 2349 1.296056 ACGCACGAGGTGTTTATGCC 61.296 55.000 0.00 0.00 36.69 4.40
2072 2362 0.446222 CCTATGGGTTTTGACGCACG 59.554 55.000 0.00 0.00 35.41 5.34
2084 2374 7.316393 TGGTATTTCTCACTAATCCTATGGG 57.684 40.000 0.00 0.00 0.00 4.00
2093 2383 7.177216 TCGGACTTAGTTGGTATTTCTCACTAA 59.823 37.037 0.00 0.00 0.00 2.24
2117 2408 8.500773 TCTACCAATAAGTTTTAGTTTTGCTCG 58.499 33.333 0.00 0.00 0.00 5.03
2143 2434 6.656270 TGCTGATATGATGACAAAGTCAGTTT 59.344 34.615 6.01 0.00 46.04 2.66
2169 2460 6.928492 TGCAAGATAAGTACGCATGATAATCA 59.072 34.615 0.00 0.00 0.00 2.57
2197 2488 8.347004 TGTTATTGCTGAAGGTGATTTGAATA 57.653 30.769 0.00 0.00 0.00 1.75
2198 2489 7.230849 TGTTATTGCTGAAGGTGATTTGAAT 57.769 32.000 0.00 0.00 0.00 2.57
2207 2498 4.471904 TCGAGATGTTATTGCTGAAGGT 57.528 40.909 0.00 0.00 0.00 3.50
2257 2549 5.636965 GGATCCAACGTATCATGAGAGAATG 59.363 44.000 6.95 0.00 0.00 2.67
2258 2550 5.541868 AGGATCCAACGTATCATGAGAGAAT 59.458 40.000 15.82 0.00 0.00 2.40
2273 2565 6.238759 GCCATATGTCTTACAAAGGATCCAAC 60.239 42.308 15.82 0.00 0.00 3.77
2280 2572 6.150976 TCAAAGTGCCATATGTCTTACAAAGG 59.849 38.462 1.24 0.00 0.00 3.11
2346 2638 6.711277 TGGTTGAGAGCTTTGTATACTGAAT 58.289 36.000 4.17 0.00 0.00 2.57
2347 2639 6.014584 TCTGGTTGAGAGCTTTGTATACTGAA 60.015 38.462 4.17 0.00 0.00 3.02
2360 2652 5.391416 GCAAAGAAGTTATCTGGTTGAGAGC 60.391 44.000 0.00 0.00 38.79 4.09
2375 2667 7.283354 GGCTATTTCTAAGGTATGCAAAGAAGT 59.717 37.037 0.00 0.00 0.00 3.01
2387 2679 7.171630 CCGAGTATATGGCTATTTCTAAGGT 57.828 40.000 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.