Multiple sequence alignment - TraesCS3D01G391200

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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 TraesCS3D01G391200 chr3D 100.000 2657 0 0 1 2657 506160036 506162692 0.000000e+00 4907.0
1 TraesCS3D01G391200 chr3D 93.333 120 7 1 683 801 381640807 381640926 2.720000e-40 176.0
2 TraesCS3D01G391200 chr3D 79.861 144 18 7 235 369 74754089 74753948 7.830000e-16 95.3
3 TraesCS3D01G391200 chr3A 93.352 1399 54 13 849 2227 644779947 644781326 0.000000e+00 2032.0
4 TraesCS3D01G391200 chr3A 87.031 586 45 14 1 562 644779241 644779819 1.340000e-177 632.0
5 TraesCS3D01G391200 chr3A 84.444 180 17 4 2403 2581 644783365 644783534 1.640000e-37 167.0
6 TraesCS3D01G391200 chr3A 86.897 145 15 4 649 791 572594388 572594246 2.740000e-35 159.0
7 TraesCS3D01G391200 chr3A 87.379 103 12 1 977 1079 644696523 644696624 1.670000e-22 117.0
8 TraesCS3D01G391200 chr3B 92.236 1288 64 15 793 2060 667855741 667857012 0.000000e+00 1792.0
9 TraesCS3D01G391200 chr3B 87.337 537 42 8 2051 2574 667859520 667860043 2.280000e-165 592.0
10 TraesCS3D01G391200 chr3B 84.603 617 55 24 1 591 667854109 667854711 6.380000e-161 577.0
11 TraesCS3D01G391200 chr2B 80.366 382 46 17 21 376 94253350 94252972 2.030000e-66 263.0
12 TraesCS3D01G391200 chr6B 81.818 330 39 17 20 336 707006106 707005785 9.440000e-65 257.0
13 TraesCS3D01G391200 chr6B 94.262 122 7 0 680 801 599445613 599445734 1.260000e-43 187.0
14 TraesCS3D01G391200 chr6D 78.747 367 45 20 31 367 463758751 463758388 5.760000e-52 215.0
15 TraesCS3D01G391200 chr7B 93.496 123 7 1 681 802 715085592 715085470 5.840000e-42 182.0
16 TraesCS3D01G391200 chr5D 91.603 131 9 2 681 810 532242613 532242484 2.100000e-41 180.0
17 TraesCS3D01G391200 chrUn 94.068 118 6 1 685 801 77508706 77508823 7.560000e-41 178.0
18 TraesCS3D01G391200 chr7A 94.783 115 4 2 678 792 701211516 701211628 7.560000e-41 178.0
19 TraesCS3D01G391200 chr7A 91.339 127 9 2 665 791 192671838 192671962 3.520000e-39 172.0
20 TraesCS3D01G391200 chr4D 94.737 114 6 0 682 795 474591214 474591327 7.560000e-41 178.0
21 TraesCS3D01G391200 chr4D 80.162 247 30 15 95 328 503521239 503521479 1.640000e-37 167.0
22 TraesCS3D01G391200 chr4B 77.439 328 34 22 31 328 649252082 649252399 2.740000e-35 159.0
23 TraesCS3D01G391200 chr5A 85.106 141 16 4 225 364 533268072 533268208 3.570000e-29 139.0
24 TraesCS3D01G391200 chr1B 78.333 240 31 16 105 335 35568780 35569007 4.610000e-28 135.0
25 TraesCS3D01G391200 chr1B 91.667 60 3 2 20 77 171207425 171207366 6.100000e-12 82.4


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 TraesCS3D01G391200 chr3D 506160036 506162692 2656 False 4907.000000 4907 100.000000 1 2657 1 chr3D.!!$F2 2656
1 TraesCS3D01G391200 chr3A 644779241 644783534 4293 False 943.666667 2032 88.275667 1 2581 3 chr3A.!!$F2 2580
2 TraesCS3D01G391200 chr3B 667854109 667860043 5934 False 987.000000 1792 88.058667 1 2574 3 chr3B.!!$F1 2573

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
701 1740 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.0 14.79 0.04 33.41 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2275 7764 0.25077 GGACCGGATAAATGGAGGGC 60.251 60.0 9.46 0.0 0.0 5.19 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 60 1.217585 CGAGCTCATATGCACCCACG 61.218 60.000 15.40 0.00 34.99 4.94
136 140 2.488937 TGAATTCTGAACATGCGTGCAT 59.511 40.909 5.64 0.51 37.08 3.96
271 295 8.211116 TGTTGTTTCTTCATGAAATTTTGCAT 57.789 26.923 9.88 0.00 45.19 3.96
272 296 8.336806 TGTTGTTTCTTCATGAAATTTTGCATC 58.663 29.630 9.88 4.62 45.19 3.91
273 297 8.336806 GTTGTTTCTTCATGAAATTTTGCATCA 58.663 29.630 9.88 0.00 45.19 3.07
285 310 8.714179 TGAAATTTTGCATCATGTTCTGAATTC 58.286 29.630 0.00 0.00 37.44 2.17
292 317 5.680229 GCATCATGTTCTGAATTCGTCAATC 59.320 40.000 0.04 0.00 37.44 2.67
297 322 5.451908 TGTTCTGAATTCGTCAATCTTTGC 58.548 37.500 0.04 0.00 35.22 3.68
300 325 5.931532 TCTGAATTCGTCAATCTTTGCTTC 58.068 37.500 0.04 0.00 35.22 3.86
369 413 0.833409 TGAGCTCAGGTGCAGAAGGA 60.833 55.000 13.74 0.00 34.99 3.36
370 414 0.390998 GAGCTCAGGTGCAGAAGGAC 60.391 60.000 9.40 0.00 34.99 3.85
376 420 2.092429 TCAGGTGCAGAAGGACACTTTT 60.092 45.455 0.00 0.00 37.91 2.27
614 1653 2.145536 GACGGGGAATTTACACACGTT 58.854 47.619 0.00 0.00 32.84 3.99
635 1674 5.061684 CGTTGTGTACAGATAAAATCGCAGA 59.938 40.000 0.00 0.00 45.75 4.26
648 1687 1.003839 CGCAGACCTTACCAAGCCA 60.004 57.895 0.00 0.00 0.00 4.75
679 1718 4.478371 CGCCAGCTGAGCCCATCA 62.478 66.667 17.39 0.00 36.21 3.07
680 1719 2.827642 GCCAGCTGAGCCCATCAC 60.828 66.667 17.39 0.00 33.22 3.06
681 1720 2.996395 CCAGCTGAGCCCATCACT 59.004 61.111 17.39 0.00 33.22 3.41
682 1721 1.976132 GCCAGCTGAGCCCATCACTA 61.976 60.000 17.39 0.00 33.22 2.74
683 1722 0.106335 CCAGCTGAGCCCATCACTAG 59.894 60.000 17.39 0.00 33.22 2.57
684 1723 0.829333 CAGCTGAGCCCATCACTAGT 59.171 55.000 8.42 0.00 33.22 2.57
685 1724 2.034878 CAGCTGAGCCCATCACTAGTA 58.965 52.381 8.42 0.00 33.22 1.82
686 1725 2.035632 AGCTGAGCCCATCACTAGTAC 58.964 52.381 0.00 0.00 33.22 2.73
687 1726 2.035632 GCTGAGCCCATCACTAGTACT 58.964 52.381 0.00 0.00 33.22 2.73
688 1727 2.035321 GCTGAGCCCATCACTAGTACTC 59.965 54.545 0.00 0.00 33.22 2.59
689 1728 2.625790 CTGAGCCCATCACTAGTACTCC 59.374 54.545 0.00 0.00 33.22 3.85
690 1729 1.964933 GAGCCCATCACTAGTACTCCC 59.035 57.143 0.00 0.00 0.00 4.30
691 1730 1.576272 AGCCCATCACTAGTACTCCCT 59.424 52.381 0.00 0.00 0.00 4.20
692 1731 1.964933 GCCCATCACTAGTACTCCCTC 59.035 57.143 0.00 0.00 0.00 4.30
693 1732 2.599677 CCCATCACTAGTACTCCCTCC 58.400 57.143 0.00 0.00 0.00 4.30
694 1733 2.231529 CCATCACTAGTACTCCCTCCG 58.768 57.143 0.00 0.00 0.00 4.63
695 1734 2.423088 CCATCACTAGTACTCCCTCCGT 60.423 54.545 0.00 0.00 0.00 4.69
696 1735 3.288964 CATCACTAGTACTCCCTCCGTT 58.711 50.000 0.00 0.00 0.00 4.44
697 1736 2.996631 TCACTAGTACTCCCTCCGTTC 58.003 52.381 0.00 0.00 0.00 3.95
698 1737 1.669779 CACTAGTACTCCCTCCGTTCG 59.330 57.143 0.00 0.00 0.00 3.95
699 1738 1.307097 CTAGTACTCCCTCCGTTCGG 58.693 60.000 0.00 4.74 0.00 4.30
700 1739 0.911769 TAGTACTCCCTCCGTTCGGA 59.088 55.000 13.34 13.34 0.00 4.55
701 1740 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
702 1741 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
703 1742 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
704 1743 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
705 1744 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
706 1745 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
707 1746 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
708 1747 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
709 1748 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
710 1749 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
711 1750 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
712 1751 2.030007 TCCGTTCGGAATTACTTGTCGT 60.030 45.455 11.66 0.00 0.00 4.34
713 1752 3.190327 TCCGTTCGGAATTACTTGTCGTA 59.810 43.478 11.66 0.00 0.00 3.43
714 1753 3.545078 CCGTTCGGAATTACTTGTCGTAG 59.455 47.826 5.19 0.00 0.00 3.51
715 1754 4.406069 CGTTCGGAATTACTTGTCGTAGA 58.594 43.478 0.00 0.00 0.00 2.59
716 1755 4.853196 CGTTCGGAATTACTTGTCGTAGAA 59.147 41.667 0.00 0.00 39.69 2.10
717 1756 5.003214 CGTTCGGAATTACTTGTCGTAGAAG 59.997 44.000 0.00 0.00 39.69 2.85
718 1757 5.633830 TCGGAATTACTTGTCGTAGAAGT 57.366 39.130 0.00 0.00 39.69 3.01
719 1758 5.396484 TCGGAATTACTTGTCGTAGAAGTG 58.604 41.667 0.00 0.00 39.69 3.16
720 1759 4.561606 CGGAATTACTTGTCGTAGAAGTGG 59.438 45.833 0.00 0.00 39.69 4.00
721 1760 5.620654 CGGAATTACTTGTCGTAGAAGTGGA 60.621 44.000 0.00 0.00 39.69 4.02
722 1761 6.338937 GGAATTACTTGTCGTAGAAGTGGAT 58.661 40.000 0.00 0.00 39.69 3.41
723 1762 6.255887 GGAATTACTTGTCGTAGAAGTGGATG 59.744 42.308 0.00 0.00 39.69 3.51
724 1763 5.717078 TTACTTGTCGTAGAAGTGGATGT 57.283 39.130 0.00 0.00 39.69 3.06
725 1764 6.822667 TTACTTGTCGTAGAAGTGGATGTA 57.177 37.500 0.00 0.00 39.69 2.29
726 1765 5.916661 ACTTGTCGTAGAAGTGGATGTAT 57.083 39.130 0.00 0.00 39.69 2.29
727 1766 5.892568 ACTTGTCGTAGAAGTGGATGTATC 58.107 41.667 0.00 0.00 39.69 2.24
728 1767 5.652891 ACTTGTCGTAGAAGTGGATGTATCT 59.347 40.000 0.00 0.00 39.69 1.98
729 1768 6.827251 ACTTGTCGTAGAAGTGGATGTATCTA 59.173 38.462 0.00 0.00 39.69 1.98
730 1769 6.862711 TGTCGTAGAAGTGGATGTATCTAG 57.137 41.667 0.00 0.00 39.69 2.43
731 1770 6.589135 TGTCGTAGAAGTGGATGTATCTAGA 58.411 40.000 0.00 0.00 39.69 2.43
732 1771 6.482641 TGTCGTAGAAGTGGATGTATCTAGAC 59.517 42.308 0.00 0.00 39.69 2.59
733 1772 5.695363 TCGTAGAAGTGGATGTATCTAGACG 59.305 44.000 0.00 0.00 0.00 4.18
734 1773 5.466058 CGTAGAAGTGGATGTATCTAGACGT 59.534 44.000 0.00 0.00 0.00 4.34
735 1774 6.644181 CGTAGAAGTGGATGTATCTAGACGTA 59.356 42.308 0.00 0.00 0.00 3.57
736 1775 7.331440 CGTAGAAGTGGATGTATCTAGACGTAT 59.669 40.741 0.00 0.00 0.00 3.06
737 1776 9.001542 GTAGAAGTGGATGTATCTAGACGTATT 57.998 37.037 0.00 0.00 0.00 1.89
738 1777 8.466617 AGAAGTGGATGTATCTAGACGTATTT 57.533 34.615 0.00 0.00 0.00 1.40
739 1778 8.915036 AGAAGTGGATGTATCTAGACGTATTTT 58.085 33.333 0.00 0.00 0.00 1.82
742 1781 9.352191 AGTGGATGTATCTAGACGTATTTTAGT 57.648 33.333 0.00 0.00 0.00 2.24
743 1782 9.962783 GTGGATGTATCTAGACGTATTTTAGTT 57.037 33.333 0.00 0.00 0.00 2.24
776 1815 6.737254 TCCATTTTCGAGACAAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
777 1816 6.234920 TCCATTTTCGAGACAAGTAATTCCA 58.765 36.000 0.00 0.00 0.00 3.53
778 1817 6.712998 TCCATTTTCGAGACAAGTAATTCCAA 59.287 34.615 0.00 0.00 0.00 3.53
779 1818 7.229707 TCCATTTTCGAGACAAGTAATTCCAAA 59.770 33.333 0.00 0.00 0.00 3.28
780 1819 7.326063 CCATTTTCGAGACAAGTAATTCCAAAC 59.674 37.037 0.00 0.00 0.00 2.93
781 1820 5.585500 TTCGAGACAAGTAATTCCAAACG 57.415 39.130 0.00 0.00 0.00 3.60
782 1821 3.991773 TCGAGACAAGTAATTCCAAACGG 59.008 43.478 0.00 0.00 0.00 4.44
783 1822 3.991773 CGAGACAAGTAATTCCAAACGGA 59.008 43.478 0.00 0.00 0.00 4.69
784 1823 4.091509 CGAGACAAGTAATTCCAAACGGAG 59.908 45.833 0.00 0.00 32.88 4.63
785 1824 4.324267 AGACAAGTAATTCCAAACGGAGG 58.676 43.478 0.00 0.00 32.88 4.30
786 1825 4.041198 AGACAAGTAATTCCAAACGGAGGA 59.959 41.667 0.00 0.00 32.88 3.71
794 1833 4.525912 TTCCAAACGGAGGAAGTACTAC 57.474 45.455 0.00 0.00 40.11 2.73
795 1834 3.771216 TCCAAACGGAGGAAGTACTACT 58.229 45.455 0.00 0.00 30.71 2.57
796 1835 4.922206 TCCAAACGGAGGAAGTACTACTA 58.078 43.478 0.00 0.00 30.71 1.82
797 1836 5.324409 TCCAAACGGAGGAAGTACTACTAA 58.676 41.667 0.00 0.00 30.71 2.24
830 1869 2.982488 TGCAAACCCAAATACCCCAATT 59.018 40.909 0.00 0.00 0.00 2.32
838 1877 3.465588 CCAAATACCCCAATTCCTCCCTA 59.534 47.826 0.00 0.00 0.00 3.53
839 1878 4.078863 CCAAATACCCCAATTCCTCCCTAA 60.079 45.833 0.00 0.00 0.00 2.69
840 1879 5.524535 CAAATACCCCAATTCCTCCCTAAA 58.475 41.667 0.00 0.00 0.00 1.85
841 1880 5.824542 AATACCCCAATTCCTCCCTAAAA 57.175 39.130 0.00 0.00 0.00 1.52
876 1915 0.724549 CGCGGTCATTTGGATTTCGA 59.275 50.000 0.00 0.00 0.00 3.71
877 1916 1.267532 CGCGGTCATTTGGATTTCGAG 60.268 52.381 0.00 0.00 0.00 4.04
879 1918 1.064060 CGGTCATTTGGATTTCGAGGC 59.936 52.381 0.00 0.00 0.00 4.70
880 1919 2.369394 GGTCATTTGGATTTCGAGGCT 58.631 47.619 0.00 0.00 0.00 4.58
881 1920 2.098117 GGTCATTTGGATTTCGAGGCTG 59.902 50.000 0.00 0.00 0.00 4.85
882 1921 3.009723 GTCATTTGGATTTCGAGGCTGA 58.990 45.455 0.00 0.00 0.00 4.26
883 1922 3.440173 GTCATTTGGATTTCGAGGCTGAA 59.560 43.478 0.00 0.00 0.00 3.02
884 1923 4.078537 TCATTTGGATTTCGAGGCTGAAA 58.921 39.130 12.33 12.33 41.69 2.69
911 1951 4.357947 TCGCGCGTCTTCTTGCCT 62.358 61.111 30.98 0.00 0.00 4.75
972 2018 0.391130 CTTGCTCCCGATCGGTTTCA 60.391 55.000 31.22 21.39 0.00 2.69
978 2024 1.019278 CCCGATCGGTTTCAGTGGTG 61.019 60.000 31.22 9.25 0.00 4.17
1159 2214 3.998672 GGCCAGGGTCGTTCGACA 61.999 66.667 23.25 0.00 36.91 4.35
1165 2220 4.353437 GGTCGTTCGACAGCGGGT 62.353 66.667 23.25 0.00 36.91 5.28
1224 2279 4.899239 GAGCCCGATGCCAGGACG 62.899 72.222 0.00 0.00 42.71 4.79
1665 2720 1.676967 GCTCAAGTGAAGCCAGGGG 60.677 63.158 0.00 0.00 0.00 4.79
1705 2764 1.209019 AGCGATGAACAGAGCAGGATT 59.791 47.619 0.00 0.00 0.00 3.01
1759 2819 7.572724 GCTTGATTATTTAGCCTGAGCATACAG 60.573 40.741 0.00 0.00 43.56 2.74
1857 2917 7.336176 GTGATTCCCCCTTGTAACTAAGTAAAG 59.664 40.741 0.00 0.00 0.00 1.85
1861 2921 5.221986 CCCCCTTGTAACTAAGTAAAGTGGT 60.222 44.000 0.00 0.00 0.00 4.16
1894 2954 9.104965 TGTAATATACATTAGTTGGTCACTTGC 57.895 33.333 0.00 0.00 33.44 4.01
1961 3023 4.065088 GTTTGTCTTCAGTCCATGCTACA 58.935 43.478 0.00 0.00 0.00 2.74
1962 3024 3.319137 TGTCTTCAGTCCATGCTACAC 57.681 47.619 0.00 0.00 0.00 2.90
2035 3097 8.682936 AGAAATCTAACACTTGTGAAGAACAT 57.317 30.769 7.83 1.95 38.99 2.71
2152 5734 5.381757 ACTGGTAATTAAGTGGCAACTGAA 58.618 37.500 0.00 0.00 36.51 3.02
2190 5772 2.486472 ACAGCATCTCCAAGGACAAG 57.514 50.000 0.00 0.00 0.00 3.16
2275 7764 1.945354 TAGCCTCTTCTCCAACGGCG 61.945 60.000 4.80 4.80 45.16 6.46
2290 7779 1.966451 GGCGCCCTCCATTTATCCG 60.966 63.158 18.11 0.00 0.00 4.18
2347 7901 8.989653 TTTTCATTTCTTTAACCAAACTCGTT 57.010 26.923 0.00 0.00 0.00 3.85
2348 7902 7.979115 TTCATTTCTTTAACCAAACTCGTTG 57.021 32.000 0.00 0.00 36.94 4.10
2349 7903 5.974751 TCATTTCTTTAACCAAACTCGTTGC 59.025 36.000 0.00 0.00 35.74 4.17
2352 7906 6.621316 TTCTTTAACCAAACTCGTTGCATA 57.379 33.333 0.00 0.00 35.74 3.14
2353 7907 6.236017 TCTTTAACCAAACTCGTTGCATAG 57.764 37.500 0.00 0.00 35.74 2.23
2354 7908 5.761234 TCTTTAACCAAACTCGTTGCATAGT 59.239 36.000 0.00 0.00 35.74 2.12
2355 7909 6.930164 TCTTTAACCAAACTCGTTGCATAGTA 59.070 34.615 0.00 0.00 35.74 1.82
2356 7910 6.715344 TTAACCAAACTCGTTGCATAGTAG 57.285 37.500 0.00 0.00 35.74 2.57
2357 7911 4.530710 ACCAAACTCGTTGCATAGTAGA 57.469 40.909 0.00 0.00 35.74 2.59
2358 7912 4.890088 ACCAAACTCGTTGCATAGTAGAA 58.110 39.130 0.00 0.00 35.74 2.10
2359 7913 5.302360 ACCAAACTCGTTGCATAGTAGAAA 58.698 37.500 0.00 0.00 35.74 2.52
2360 7914 5.408604 ACCAAACTCGTTGCATAGTAGAAAG 59.591 40.000 0.00 0.00 35.74 2.62
2361 7915 5.637810 CCAAACTCGTTGCATAGTAGAAAGA 59.362 40.000 0.00 0.00 35.74 2.52
2362 7916 6.313905 CCAAACTCGTTGCATAGTAGAAAGAT 59.686 38.462 0.00 0.00 35.74 2.40
2363 7917 6.893958 AACTCGTTGCATAGTAGAAAGATG 57.106 37.500 0.00 0.00 0.00 2.90
2364 7918 5.967088 ACTCGTTGCATAGTAGAAAGATGT 58.033 37.500 0.00 0.00 0.00 3.06
2365 7919 7.096884 ACTCGTTGCATAGTAGAAAGATGTA 57.903 36.000 0.00 0.00 0.00 2.29
2366 7920 7.197017 ACTCGTTGCATAGTAGAAAGATGTAG 58.803 38.462 0.00 0.00 0.00 2.74
2367 7921 7.067129 ACTCGTTGCATAGTAGAAAGATGTAGA 59.933 37.037 0.00 0.00 0.00 2.59
2368 7922 7.194278 TCGTTGCATAGTAGAAAGATGTAGAC 58.806 38.462 0.00 0.00 0.00 2.59
2369 7923 7.067129 TCGTTGCATAGTAGAAAGATGTAGACT 59.933 37.037 0.00 0.00 0.00 3.24
2370 7924 7.166638 CGTTGCATAGTAGAAAGATGTAGACTG 59.833 40.741 0.00 0.00 0.00 3.51
2371 7925 7.646548 TGCATAGTAGAAAGATGTAGACTGT 57.353 36.000 0.00 0.00 0.00 3.55
2372 7926 8.747538 TGCATAGTAGAAAGATGTAGACTGTA 57.252 34.615 0.00 0.00 0.00 2.74
2373 7927 8.622157 TGCATAGTAGAAAGATGTAGACTGTAC 58.378 37.037 0.00 0.00 0.00 2.90
2374 7928 8.622157 GCATAGTAGAAAGATGTAGACTGTACA 58.378 37.037 0.00 0.00 0.00 2.90
2450 8004 6.683883 CGAGTACATCGTTCAGACATAAAAC 58.316 40.000 0.00 0.00 46.62 2.43
2464 8018 6.792250 CAGACATAAAACTCAAACGACATCAC 59.208 38.462 0.00 0.00 0.00 3.06
2466 8020 7.173218 AGACATAAAACTCAAACGACATCACAT 59.827 33.333 0.00 0.00 0.00 3.21
2469 8023 9.773328 CATAAAACTCAAACGACATCACATATT 57.227 29.630 0.00 0.00 0.00 1.28
2478 8033 8.849490 CAAACGACATCACATATTTAAAGGTTG 58.151 33.333 0.00 0.00 0.00 3.77
2491 8046 7.658525 ATTTAAAGGTTGCCATGATGTATCA 57.341 32.000 0.00 0.00 41.70 2.15
2518 8073 3.646534 TGCTCCTGGAGATCATTGAGTA 58.353 45.455 27.53 0.00 30.99 2.59
2519 8074 3.640498 TGCTCCTGGAGATCATTGAGTAG 59.360 47.826 27.53 0.00 30.99 2.57
2520 8075 3.640967 GCTCCTGGAGATCATTGAGTAGT 59.359 47.826 27.53 0.00 30.99 2.73
2521 8076 4.100808 GCTCCTGGAGATCATTGAGTAGTT 59.899 45.833 27.53 0.00 30.99 2.24
2522 8077 5.599732 CTCCTGGAGATCATTGAGTAGTTG 58.400 45.833 19.13 0.00 0.00 3.16
2539 8094 3.262420 AGTTGTACATGCACTTCGATCC 58.738 45.455 0.00 0.00 0.00 3.36
2540 8095 2.309528 TGTACATGCACTTCGATCCC 57.690 50.000 0.00 0.00 0.00 3.85
2584 8139 4.160928 TGTGCAACATGCTCTGCA 57.839 50.000 12.31 12.31 45.67 4.41
2598 8153 4.946445 TGCTCTGCATCTTATTCTGAGAG 58.054 43.478 0.00 0.00 31.71 3.20
2599 8154 4.202233 TGCTCTGCATCTTATTCTGAGAGG 60.202 45.833 0.00 0.00 31.71 3.69
2600 8155 4.202243 GCTCTGCATCTTATTCTGAGAGGT 60.202 45.833 0.00 0.00 0.00 3.85
2601 8156 5.273674 TCTGCATCTTATTCTGAGAGGTG 57.726 43.478 0.00 0.00 0.00 4.00
2602 8157 4.100653 TCTGCATCTTATTCTGAGAGGTGG 59.899 45.833 0.00 0.00 0.00 4.61
2603 8158 4.033009 TGCATCTTATTCTGAGAGGTGGA 58.967 43.478 0.00 0.00 0.00 4.02
2604 8159 4.471025 TGCATCTTATTCTGAGAGGTGGAA 59.529 41.667 0.00 0.00 0.00 3.53
2605 8160 5.131642 TGCATCTTATTCTGAGAGGTGGAAT 59.868 40.000 0.00 0.00 34.59 3.01
2606 8161 5.469421 GCATCTTATTCTGAGAGGTGGAATG 59.531 44.000 0.00 0.00 32.78 2.67
2607 8162 6.590068 CATCTTATTCTGAGAGGTGGAATGT 58.410 40.000 0.00 0.00 32.78 2.71
2608 8163 7.687837 GCATCTTATTCTGAGAGGTGGAATGTA 60.688 40.741 0.00 0.00 32.78 2.29
2609 8164 7.113658 TCTTATTCTGAGAGGTGGAATGTAC 57.886 40.000 0.00 0.00 32.78 2.90
2610 8165 6.897966 TCTTATTCTGAGAGGTGGAATGTACT 59.102 38.462 0.00 0.00 32.78 2.73
2611 8166 5.606348 ATTCTGAGAGGTGGAATGTACTC 57.394 43.478 0.00 0.00 0.00 2.59
2612 8167 3.366396 TCTGAGAGGTGGAATGTACTCC 58.634 50.000 0.00 0.00 35.88 3.85
2613 8168 3.099905 CTGAGAGGTGGAATGTACTCCA 58.900 50.000 0.00 0.00 43.45 3.86
2614 8169 3.099905 TGAGAGGTGGAATGTACTCCAG 58.900 50.000 4.14 0.00 46.29 3.86
2615 8170 2.432510 GAGAGGTGGAATGTACTCCAGG 59.567 54.545 4.14 0.00 46.29 4.45
2616 8171 0.912486 AGGTGGAATGTACTCCAGGC 59.088 55.000 4.14 0.00 46.29 4.85
2617 8172 0.912486 GGTGGAATGTACTCCAGGCT 59.088 55.000 4.14 0.00 46.29 4.58
2618 8173 1.282157 GGTGGAATGTACTCCAGGCTT 59.718 52.381 4.14 0.00 46.29 4.35
2619 8174 2.633488 GTGGAATGTACTCCAGGCTTC 58.367 52.381 4.14 0.00 46.29 3.86
2620 8175 2.237392 GTGGAATGTACTCCAGGCTTCT 59.763 50.000 4.14 0.00 46.29 2.85
2621 8176 2.912956 TGGAATGTACTCCAGGCTTCTT 59.087 45.455 0.00 0.00 40.71 2.52
2622 8177 4.081087 GTGGAATGTACTCCAGGCTTCTTA 60.081 45.833 4.14 0.00 46.29 2.10
2623 8178 4.534500 TGGAATGTACTCCAGGCTTCTTAA 59.466 41.667 0.00 0.00 40.71 1.85
2624 8179 5.013704 TGGAATGTACTCCAGGCTTCTTAAA 59.986 40.000 0.00 0.00 40.71 1.52
2625 8180 5.944007 GGAATGTACTCCAGGCTTCTTAAAA 59.056 40.000 0.00 0.00 35.36 1.52
2626 8181 6.603599 GGAATGTACTCCAGGCTTCTTAAAAT 59.396 38.462 0.00 0.00 35.36 1.82
2627 8182 7.201741 GGAATGTACTCCAGGCTTCTTAAAATC 60.202 40.741 0.00 0.00 35.36 2.17
2628 8183 6.121776 TGTACTCCAGGCTTCTTAAAATCA 57.878 37.500 0.00 0.00 0.00 2.57
2629 8184 6.539173 TGTACTCCAGGCTTCTTAAAATCAA 58.461 36.000 0.00 0.00 0.00 2.57
2630 8185 7.001674 TGTACTCCAGGCTTCTTAAAATCAAA 58.998 34.615 0.00 0.00 0.00 2.69
2631 8186 6.332735 ACTCCAGGCTTCTTAAAATCAAAC 57.667 37.500 0.00 0.00 0.00 2.93
2632 8187 5.833131 ACTCCAGGCTTCTTAAAATCAAACA 59.167 36.000 0.00 0.00 0.00 2.83
2633 8188 6.494835 ACTCCAGGCTTCTTAAAATCAAACAT 59.505 34.615 0.00 0.00 0.00 2.71
2634 8189 7.015584 ACTCCAGGCTTCTTAAAATCAAACATT 59.984 33.333 0.00 0.00 0.00 2.71
2635 8190 8.415950 TCCAGGCTTCTTAAAATCAAACATTA 57.584 30.769 0.00 0.00 0.00 1.90
2636 8191 8.522830 TCCAGGCTTCTTAAAATCAAACATTAG 58.477 33.333 0.00 0.00 0.00 1.73
2637 8192 8.522830 CCAGGCTTCTTAAAATCAAACATTAGA 58.477 33.333 0.00 0.00 0.00 2.10
2650 8205 8.603242 ATCAAACATTAGATATACCGTCAACC 57.397 34.615 0.00 0.00 0.00 3.77
2651 8206 7.788026 TCAAACATTAGATATACCGTCAACCT 58.212 34.615 0.00 0.00 0.00 3.50
2652 8207 7.924412 TCAAACATTAGATATACCGTCAACCTC 59.076 37.037 0.00 0.00 0.00 3.85
2653 8208 6.971726 ACATTAGATATACCGTCAACCTCA 57.028 37.500 0.00 0.00 0.00 3.86
2654 8209 7.540474 ACATTAGATATACCGTCAACCTCAT 57.460 36.000 0.00 0.00 0.00 2.90
2655 8210 7.603651 ACATTAGATATACCGTCAACCTCATC 58.396 38.462 0.00 0.00 0.00 2.92
2656 8211 6.585695 TTAGATATACCGTCAACCTCATCC 57.414 41.667 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.946377 AGAAACTTCATGTCCCTTGTATTCC 59.054 40.000 0.00 0.00 0.00 3.01
271 295 7.300320 CAAAGATTGACGAATTCAGAACATGA 58.700 34.615 6.22 0.00 34.94 3.07
272 296 6.033196 GCAAAGATTGACGAATTCAGAACATG 59.967 38.462 6.22 0.00 34.94 3.21
273 297 6.072286 AGCAAAGATTGACGAATTCAGAACAT 60.072 34.615 6.22 0.00 34.94 2.71
338 382 0.970427 TGAGCTCATACGCACCCTCA 60.970 55.000 13.74 0.00 0.00 3.86
369 413 5.127682 AGAAATGTCTCCAAAGCAAAAGTGT 59.872 36.000 0.00 0.00 0.00 3.55
370 414 5.594926 AGAAATGTCTCCAAAGCAAAAGTG 58.405 37.500 0.00 0.00 0.00 3.16
376 420 6.707440 TTTACAAGAAATGTCTCCAAAGCA 57.293 33.333 0.00 0.00 42.70 3.91
583 661 7.119262 GTGTAAATTCCCCGTCTATTATGGATG 59.881 40.741 0.00 0.00 36.17 3.51
594 1633 1.799544 ACGTGTGTAAATTCCCCGTC 58.200 50.000 0.00 0.00 0.00 4.79
614 1653 4.868171 GGTCTGCGATTTTATCTGTACACA 59.132 41.667 0.00 0.00 0.00 3.72
617 1656 6.200475 GGTAAGGTCTGCGATTTTATCTGTAC 59.800 42.308 0.00 0.00 0.00 2.90
618 1657 6.127281 TGGTAAGGTCTGCGATTTTATCTGTA 60.127 38.462 0.00 0.00 0.00 2.74
619 1658 5.116882 GGTAAGGTCTGCGATTTTATCTGT 58.883 41.667 0.00 0.00 0.00 3.41
620 1659 5.116180 TGGTAAGGTCTGCGATTTTATCTG 58.884 41.667 0.00 0.00 0.00 2.90
621 1660 5.353394 TGGTAAGGTCTGCGATTTTATCT 57.647 39.130 0.00 0.00 0.00 1.98
622 1661 5.504173 GCTTGGTAAGGTCTGCGATTTTATC 60.504 44.000 0.00 0.00 0.00 1.75
623 1662 4.335594 GCTTGGTAAGGTCTGCGATTTTAT 59.664 41.667 0.00 0.00 0.00 1.40
624 1663 3.687698 GCTTGGTAAGGTCTGCGATTTTA 59.312 43.478 0.00 0.00 0.00 1.52
627 1666 1.679032 GGCTTGGTAAGGTCTGCGATT 60.679 52.381 0.00 0.00 0.00 3.34
635 1674 1.076727 GGCCTTGGCTTGGTAAGGT 59.923 57.895 11.71 0.00 44.21 3.50
664 1703 0.106335 CTAGTGATGGGCTCAGCTGG 59.894 60.000 15.13 5.82 33.51 4.85
676 1715 3.553904 GAACGGAGGGAGTACTAGTGAT 58.446 50.000 5.39 0.00 0.00 3.06
677 1716 2.679059 CGAACGGAGGGAGTACTAGTGA 60.679 54.545 5.39 0.00 0.00 3.41
679 1718 1.407989 CCGAACGGAGGGAGTACTAGT 60.408 57.143 7.53 0.00 37.50 2.57
680 1719 1.134280 TCCGAACGGAGGGAGTACTAG 60.134 57.143 12.04 0.00 39.76 2.57
681 1720 0.911769 TCCGAACGGAGGGAGTACTA 59.088 55.000 12.04 0.00 39.76 1.82
682 1721 0.038744 TTCCGAACGGAGGGAGTACT 59.961 55.000 15.34 0.00 46.06 2.73
683 1722 1.109609 ATTCCGAACGGAGGGAGTAC 58.890 55.000 15.34 0.00 46.06 2.73
684 1723 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
685 1724 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
686 1725 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
687 1726 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
688 1727 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
689 1728 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
690 1729 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
691 1730 2.030007 ACGACAAGTAATTCCGAACGGA 60.030 45.455 12.04 12.04 43.52 4.69
692 1731 2.331194 ACGACAAGTAATTCCGAACGG 58.669 47.619 6.94 6.94 0.00 4.44
693 1732 4.406069 TCTACGACAAGTAATTCCGAACG 58.594 43.478 0.00 0.00 34.45 3.95
694 1733 5.860716 ACTTCTACGACAAGTAATTCCGAAC 59.139 40.000 0.00 0.00 34.45 3.95
695 1734 5.860182 CACTTCTACGACAAGTAATTCCGAA 59.140 40.000 0.00 0.00 34.45 4.30
696 1735 5.396484 CACTTCTACGACAAGTAATTCCGA 58.604 41.667 0.00 0.00 34.45 4.55
697 1736 4.561606 CCACTTCTACGACAAGTAATTCCG 59.438 45.833 0.00 0.00 34.45 4.30
698 1737 5.717119 TCCACTTCTACGACAAGTAATTCC 58.283 41.667 0.00 0.00 34.45 3.01
699 1738 6.812160 ACATCCACTTCTACGACAAGTAATTC 59.188 38.462 0.00 0.00 34.45 2.17
700 1739 6.698380 ACATCCACTTCTACGACAAGTAATT 58.302 36.000 0.00 0.00 34.45 1.40
701 1740 6.282199 ACATCCACTTCTACGACAAGTAAT 57.718 37.500 0.00 0.00 34.45 1.89
702 1741 5.717078 ACATCCACTTCTACGACAAGTAA 57.283 39.130 0.00 0.00 34.45 2.24
703 1742 6.827251 AGATACATCCACTTCTACGACAAGTA 59.173 38.462 0.00 0.00 32.61 2.24
704 1743 5.652891 AGATACATCCACTTCTACGACAAGT 59.347 40.000 0.00 0.00 34.24 3.16
705 1744 6.137794 AGATACATCCACTTCTACGACAAG 57.862 41.667 0.00 0.00 0.00 3.16
706 1745 7.012138 GTCTAGATACATCCACTTCTACGACAA 59.988 40.741 0.00 0.00 0.00 3.18
707 1746 6.482641 GTCTAGATACATCCACTTCTACGACA 59.517 42.308 0.00 0.00 0.00 4.35
708 1747 6.346758 CGTCTAGATACATCCACTTCTACGAC 60.347 46.154 0.00 0.00 0.00 4.34
709 1748 5.695363 CGTCTAGATACATCCACTTCTACGA 59.305 44.000 0.00 0.00 0.00 3.43
710 1749 5.466058 ACGTCTAGATACATCCACTTCTACG 59.534 44.000 0.00 0.00 0.00 3.51
711 1750 6.864360 ACGTCTAGATACATCCACTTCTAC 57.136 41.667 0.00 0.00 0.00 2.59
712 1751 9.570468 AAATACGTCTAGATACATCCACTTCTA 57.430 33.333 0.00 0.00 0.00 2.10
713 1752 8.466617 AAATACGTCTAGATACATCCACTTCT 57.533 34.615 0.00 0.00 0.00 2.85
716 1755 9.352191 ACTAAAATACGTCTAGATACATCCACT 57.648 33.333 0.00 0.00 0.00 4.00
717 1756 9.962783 AACTAAAATACGTCTAGATACATCCAC 57.037 33.333 0.00 0.00 0.00 4.02
750 1789 9.057089 GGAATTACTTGTCTCGAAAATGGATAT 57.943 33.333 0.00 0.00 0.00 1.63
751 1790 8.044309 TGGAATTACTTGTCTCGAAAATGGATA 58.956 33.333 0.00 0.00 0.00 2.59
752 1791 6.884295 TGGAATTACTTGTCTCGAAAATGGAT 59.116 34.615 0.00 0.00 0.00 3.41
753 1792 6.234920 TGGAATTACTTGTCTCGAAAATGGA 58.765 36.000 0.00 0.00 0.00 3.41
754 1793 6.494893 TGGAATTACTTGTCTCGAAAATGG 57.505 37.500 0.00 0.00 0.00 3.16
755 1794 7.059488 CGTTTGGAATTACTTGTCTCGAAAATG 59.941 37.037 0.00 0.00 0.00 2.32
756 1795 7.075741 CGTTTGGAATTACTTGTCTCGAAAAT 58.924 34.615 0.00 0.00 0.00 1.82
757 1796 6.423862 CGTTTGGAATTACTTGTCTCGAAAA 58.576 36.000 0.00 0.00 0.00 2.29
758 1797 5.049954 CCGTTTGGAATTACTTGTCTCGAAA 60.050 40.000 0.00 0.00 37.49 3.46
759 1798 4.449743 CCGTTTGGAATTACTTGTCTCGAA 59.550 41.667 0.00 0.00 37.49 3.71
760 1799 3.991773 CCGTTTGGAATTACTTGTCTCGA 59.008 43.478 0.00 0.00 37.49 4.04
761 1800 3.991773 TCCGTTTGGAATTACTTGTCTCG 59.008 43.478 0.00 0.00 42.85 4.04
762 1801 4.392138 CCTCCGTTTGGAATTACTTGTCTC 59.608 45.833 0.00 0.00 45.87 3.36
763 1802 4.041198 TCCTCCGTTTGGAATTACTTGTCT 59.959 41.667 0.00 0.00 45.87 3.41
764 1803 4.320870 TCCTCCGTTTGGAATTACTTGTC 58.679 43.478 0.00 0.00 45.87 3.18
765 1804 4.360951 TCCTCCGTTTGGAATTACTTGT 57.639 40.909 0.00 0.00 45.87 3.16
766 1805 4.760204 ACTTCCTCCGTTTGGAATTACTTG 59.240 41.667 0.00 0.00 45.87 3.16
767 1806 4.981812 ACTTCCTCCGTTTGGAATTACTT 58.018 39.130 0.00 0.00 45.87 2.24
768 1807 4.635699 ACTTCCTCCGTTTGGAATTACT 57.364 40.909 0.00 0.00 45.87 2.24
769 1808 5.485620 AGTACTTCCTCCGTTTGGAATTAC 58.514 41.667 14.85 14.85 45.87 1.89
770 1809 5.750352 AGTACTTCCTCCGTTTGGAATTA 57.250 39.130 0.00 0.00 45.87 1.40
771 1810 4.635699 AGTACTTCCTCCGTTTGGAATT 57.364 40.909 0.00 0.00 45.87 2.17
772 1811 4.776308 AGTAGTACTTCCTCCGTTTGGAAT 59.224 41.667 0.00 0.00 45.87 3.01
773 1812 4.154942 AGTAGTACTTCCTCCGTTTGGAA 58.845 43.478 0.00 0.00 45.87 3.53
774 1813 3.771216 AGTAGTACTTCCTCCGTTTGGA 58.229 45.455 0.00 0.00 43.88 3.53
775 1814 5.649782 TTAGTAGTACTTCCTCCGTTTGG 57.350 43.478 8.40 0.00 0.00 3.28
776 1815 6.449698 TGTTTAGTAGTACTTCCTCCGTTTG 58.550 40.000 8.40 0.00 0.00 2.93
777 1816 6.655078 TGTTTAGTAGTACTTCCTCCGTTT 57.345 37.500 8.40 0.00 0.00 3.60
778 1817 6.847421 ATGTTTAGTAGTACTTCCTCCGTT 57.153 37.500 8.40 0.00 0.00 4.44
779 1818 6.628185 CAATGTTTAGTAGTACTTCCTCCGT 58.372 40.000 8.40 0.00 0.00 4.69
780 1819 5.519206 GCAATGTTTAGTAGTACTTCCTCCG 59.481 44.000 8.40 0.00 0.00 4.63
781 1820 6.403878 TGCAATGTTTAGTAGTACTTCCTCC 58.596 40.000 8.40 0.00 0.00 4.30
782 1821 7.900782 TTGCAATGTTTAGTAGTACTTCCTC 57.099 36.000 8.40 0.00 0.00 3.71
783 1822 8.863872 AATTGCAATGTTTAGTAGTACTTCCT 57.136 30.769 13.82 0.00 0.00 3.36
784 1823 9.341899 CAAATTGCAATGTTTAGTAGTACTTCC 57.658 33.333 13.82 0.00 0.00 3.46
785 1824 8.850452 GCAAATTGCAATGTTTAGTAGTACTTC 58.150 33.333 13.82 0.00 44.26 3.01
786 1825 8.742554 GCAAATTGCAATGTTTAGTAGTACTT 57.257 30.769 13.82 0.00 44.26 2.24
839 1878 3.258228 CGCGCCAGGGATTTTTATTTTT 58.742 40.909 0.00 0.00 0.00 1.94
840 1879 2.418060 CCGCGCCAGGGATTTTTATTTT 60.418 45.455 0.00 0.00 0.00 1.82
841 1880 1.136110 CCGCGCCAGGGATTTTTATTT 59.864 47.619 0.00 0.00 0.00 1.40
844 1883 1.001887 ACCGCGCCAGGGATTTTTA 60.002 52.632 0.00 0.00 35.02 1.52
848 1887 2.837031 AAATGACCGCGCCAGGGATT 62.837 55.000 0.00 1.56 35.02 3.01
855 1894 0.525455 GAAATCCAAATGACCGCGCC 60.525 55.000 0.00 0.00 0.00 6.53
876 1915 1.673168 GAGCGGATTCATTTCAGCCT 58.327 50.000 0.00 0.00 37.51 4.58
877 1916 0.305922 CGAGCGGATTCATTTCAGCC 59.694 55.000 0.00 0.00 37.51 4.85
879 1918 0.042708 CGCGAGCGGATTCATTTCAG 60.043 55.000 9.90 0.00 35.56 3.02
880 1919 2.005995 CGCGAGCGGATTCATTTCA 58.994 52.632 9.90 0.00 35.56 2.69
881 1920 4.880748 CGCGAGCGGATTCATTTC 57.119 55.556 9.90 0.00 35.56 2.17
972 2018 3.771160 GATCGGGGCGACACCACT 61.771 66.667 0.00 0.00 41.20 4.00
978 2024 4.593864 GGAGCAGATCGGGGCGAC 62.594 72.222 0.00 0.00 39.18 5.19
1224 2279 2.509561 GGACGCGGGCTCTTCTTC 60.510 66.667 12.47 0.00 0.00 2.87
1496 2551 2.814341 CAGCAGCAGCAGGACGAG 60.814 66.667 3.17 0.00 45.49 4.18
1502 2557 3.877357 CATCGGCAGCAGCAGCAG 61.877 66.667 12.41 7.92 45.49 4.24
1595 2650 4.692475 CCACCGTCCGAACCACCC 62.692 72.222 0.00 0.00 0.00 4.61
1597 2652 2.048503 CTCCACCGTCCGAACCAC 60.049 66.667 0.00 0.00 0.00 4.16
1705 2764 2.367241 TCTTCACTTGTTGGACGGATCA 59.633 45.455 0.00 0.00 0.00 2.92
1759 2819 4.703897 ACACTACACATACATATGGCACC 58.296 43.478 7.80 0.00 38.00 5.01
1872 2932 9.899661 TTAAGCAAGTGACCAACTAATGTATAT 57.100 29.630 0.00 0.00 38.56 0.86
1873 2933 9.899661 ATTAAGCAAGTGACCAACTAATGTATA 57.100 29.630 0.00 0.00 38.56 1.47
2035 3097 4.558226 AGGAATTGCTCACTGATGTACA 57.442 40.909 0.00 0.00 0.00 2.90
2152 5734 1.613437 GTTATGCAAGGCCACACAAGT 59.387 47.619 5.01 0.00 0.00 3.16
2190 5772 2.507407 TGGGGGCTCAAATTAGACAC 57.493 50.000 0.00 0.00 0.00 3.67
2244 7733 0.259938 AGAGGCTAAATGGGGCTTGG 59.740 55.000 0.00 0.00 39.69 3.61
2257 7746 2.665603 GCCGTTGGAGAAGAGGCT 59.334 61.111 0.00 0.00 44.06 4.58
2275 7764 0.250770 GGACCGGATAAATGGAGGGC 60.251 60.000 9.46 0.00 0.00 5.19
2321 7822 8.989653 ACGAGTTTGGTTAAAGAAATGAAAAA 57.010 26.923 0.00 0.00 0.00 1.94
2323 7824 7.009723 GCAACGAGTTTGGTTAAAGAAATGAAA 59.990 33.333 0.00 0.00 35.51 2.69
2339 7840 6.874134 ACATCTTTCTACTATGCAACGAGTTT 59.126 34.615 4.80 0.00 0.00 2.66
2347 7901 7.646548 ACAGTCTACATCTTTCTACTATGCA 57.353 36.000 0.00 0.00 0.00 3.96
2348 7902 8.622157 TGTACAGTCTACATCTTTCTACTATGC 58.378 37.037 0.00 0.00 0.00 3.14
2434 7988 5.749588 TCGTTTGAGTTTTATGTCTGAACGA 59.250 36.000 0.00 0.00 38.44 3.85
2435 7989 5.839239 GTCGTTTGAGTTTTATGTCTGAACG 59.161 40.000 0.00 0.00 35.83 3.95
2436 7990 6.711579 TGTCGTTTGAGTTTTATGTCTGAAC 58.288 36.000 0.00 0.00 0.00 3.18
2437 7991 6.912203 TGTCGTTTGAGTTTTATGTCTGAA 57.088 33.333 0.00 0.00 0.00 3.02
2450 8004 8.450964 ACCTTTAAATATGTGATGTCGTTTGAG 58.549 33.333 0.00 0.00 0.00 3.02
2464 8018 9.630098 GATACATCATGGCAACCTTTAAATATG 57.370 33.333 0.00 0.00 0.00 1.78
2466 8020 8.759481 TGATACATCATGGCAACCTTTAAATA 57.241 30.769 0.00 0.00 0.00 1.40
2469 8023 7.473735 TTTGATACATCATGGCAACCTTTAA 57.526 32.000 0.00 0.00 36.56 1.52
2499 8054 5.128499 ACAACTACTCAATGATCTCCAGGAG 59.872 44.000 10.70 10.70 36.66 3.69
2518 8073 3.262420 GGATCGAAGTGCATGTACAACT 58.738 45.455 16.62 0.00 0.00 3.16
2519 8074 2.351726 GGGATCGAAGTGCATGTACAAC 59.648 50.000 16.62 8.28 0.00 3.32
2520 8075 2.627945 GGGATCGAAGTGCATGTACAA 58.372 47.619 16.62 0.00 0.00 2.41
2521 8076 1.470805 CGGGATCGAAGTGCATGTACA 60.471 52.381 16.62 0.00 39.00 2.90
2522 8077 1.202371 TCGGGATCGAAGTGCATGTAC 60.202 52.381 5.71 5.71 43.03 2.90
2539 8094 3.535561 AGAGATACATTGGCAACTTCGG 58.464 45.455 0.00 0.00 37.61 4.30
2540 8095 5.352284 ACTAGAGATACATTGGCAACTTCG 58.648 41.667 0.00 0.00 37.61 3.79
2581 8136 4.033009 TCCACCTCTCAGAATAAGATGCA 58.967 43.478 0.00 0.00 0.00 3.96
2582 8137 4.679373 TCCACCTCTCAGAATAAGATGC 57.321 45.455 0.00 0.00 0.00 3.91
2583 8138 6.590068 ACATTCCACCTCTCAGAATAAGATG 58.410 40.000 0.00 0.00 0.00 2.90
2584 8139 6.821616 ACATTCCACCTCTCAGAATAAGAT 57.178 37.500 0.00 0.00 0.00 2.40
2585 8140 6.897966 AGTACATTCCACCTCTCAGAATAAGA 59.102 38.462 0.00 0.00 0.00 2.10
2586 8141 7.118496 AGTACATTCCACCTCTCAGAATAAG 57.882 40.000 0.00 0.00 0.00 1.73
2587 8142 6.098409 GGAGTACATTCCACCTCTCAGAATAA 59.902 42.308 0.00 0.00 37.20 1.40
2588 8143 5.598830 GGAGTACATTCCACCTCTCAGAATA 59.401 44.000 0.00 0.00 37.20 1.75
2589 8144 4.407296 GGAGTACATTCCACCTCTCAGAAT 59.593 45.833 0.00 0.00 37.20 2.40
2590 8145 3.769844 GGAGTACATTCCACCTCTCAGAA 59.230 47.826 0.00 0.00 37.20 3.02
2591 8146 3.245622 TGGAGTACATTCCACCTCTCAGA 60.246 47.826 0.00 0.00 42.24 3.27
2592 8147 3.099905 TGGAGTACATTCCACCTCTCAG 58.900 50.000 0.00 0.00 42.24 3.35
2593 8148 3.099905 CTGGAGTACATTCCACCTCTCA 58.900 50.000 0.00 0.00 42.24 3.27
2594 8149 2.432510 CCTGGAGTACATTCCACCTCTC 59.567 54.545 0.00 0.00 42.24 3.20
2595 8150 2.472029 CCTGGAGTACATTCCACCTCT 58.528 52.381 0.00 0.00 42.24 3.69
2596 8151 1.134371 GCCTGGAGTACATTCCACCTC 60.134 57.143 0.00 0.00 42.24 3.85
2597 8152 0.912486 GCCTGGAGTACATTCCACCT 59.088 55.000 0.00 0.00 42.24 4.00
2598 8153 0.912486 AGCCTGGAGTACATTCCACC 59.088 55.000 0.00 0.00 42.24 4.61
2599 8154 2.237392 AGAAGCCTGGAGTACATTCCAC 59.763 50.000 0.00 0.00 42.24 4.02
2600 8155 2.551270 AGAAGCCTGGAGTACATTCCA 58.449 47.619 0.00 3.97 44.84 3.53
2601 8156 3.636153 AAGAAGCCTGGAGTACATTCC 57.364 47.619 0.00 0.00 37.77 3.01
2602 8157 7.336931 TGATTTTAAGAAGCCTGGAGTACATTC 59.663 37.037 0.00 0.00 0.00 2.67
2603 8158 7.175104 TGATTTTAAGAAGCCTGGAGTACATT 58.825 34.615 0.00 0.00 0.00 2.71
2604 8159 6.721318 TGATTTTAAGAAGCCTGGAGTACAT 58.279 36.000 0.00 0.00 0.00 2.29
2605 8160 6.121776 TGATTTTAAGAAGCCTGGAGTACA 57.878 37.500 0.00 0.00 0.00 2.90
2606 8161 7.040686 TGTTTGATTTTAAGAAGCCTGGAGTAC 60.041 37.037 0.00 0.00 0.00 2.73
2607 8162 7.001674 TGTTTGATTTTAAGAAGCCTGGAGTA 58.998 34.615 0.00 0.00 0.00 2.59
2608 8163 5.833131 TGTTTGATTTTAAGAAGCCTGGAGT 59.167 36.000 0.00 0.00 0.00 3.85
2609 8164 6.331369 TGTTTGATTTTAAGAAGCCTGGAG 57.669 37.500 0.00 0.00 0.00 3.86
2610 8165 6.916360 ATGTTTGATTTTAAGAAGCCTGGA 57.084 33.333 0.00 0.00 0.00 3.86
2611 8166 8.522830 TCTAATGTTTGATTTTAAGAAGCCTGG 58.477 33.333 0.00 0.00 0.00 4.45
2624 8179 9.052759 GGTTGACGGTATATCTAATGTTTGATT 57.947 33.333 0.00 0.00 0.00 2.57
2625 8180 8.429641 AGGTTGACGGTATATCTAATGTTTGAT 58.570 33.333 0.00 0.00 0.00 2.57
2626 8181 7.788026 AGGTTGACGGTATATCTAATGTTTGA 58.212 34.615 0.00 0.00 0.00 2.69
2627 8182 7.709182 TGAGGTTGACGGTATATCTAATGTTTG 59.291 37.037 0.00 0.00 0.00 2.93
2628 8183 7.788026 TGAGGTTGACGGTATATCTAATGTTT 58.212 34.615 0.00 0.00 0.00 2.83
2629 8184 7.356089 TGAGGTTGACGGTATATCTAATGTT 57.644 36.000 0.00 0.00 0.00 2.71
2630 8185 6.971726 TGAGGTTGACGGTATATCTAATGT 57.028 37.500 0.00 0.00 0.00 2.71
2631 8186 7.036220 GGATGAGGTTGACGGTATATCTAATG 58.964 42.308 0.00 0.00 0.00 1.90
2632 8187 7.171630 GGATGAGGTTGACGGTATATCTAAT 57.828 40.000 0.00 0.00 0.00 1.73
2633 8188 6.585695 GGATGAGGTTGACGGTATATCTAA 57.414 41.667 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.