Multiple sequence alignment - TraesCS3D01G250200

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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 TraesCS3D01G250200 chr3D 100.000 2694 0 0 1 2694 350736958 350734265 0.000000e+00 4975.0
1 TraesCS3D01G250200 chr3D 89.325 637 57 6 1000 1635 349860468 349861094 0.000000e+00 789.0
2 TraesCS3D01G250200 chr3D 90.795 239 20 1 1808 2046 168853121 168853357 4.330000e-83 318.0
3 TraesCS3D01G250200 chr3B 94.724 1687 52 14 1 1672 449157867 449156203 0.000000e+00 2588.0
4 TraesCS3D01G250200 chr3B 87.736 636 69 4 1000 1635 448773585 448774211 0.000000e+00 734.0
5 TraesCS3D01G250200 chr3A 94.444 1548 51 8 106 1648 468318326 468316809 0.000000e+00 2350.0
6 TraesCS3D01G250200 chr3A 84.243 806 100 7 1815 2600 468310008 468309210 0.000000e+00 760.0
7 TraesCS3D01G250200 chr3A 87.284 637 70 3 1000 1635 468003308 468003934 0.000000e+00 717.0
8 TraesCS3D01G250200 chr3A 100.000 30 0 0 1708 1737 468315632 468315603 3.750000e-04 56.5
9 TraesCS3D01G250200 chr6B 89.627 241 21 3 1809 2048 276229253 276229490 1.210000e-78 303.0
10 TraesCS3D01G250200 chr5D 87.448 239 29 1 1809 2046 538171536 538171774 9.500000e-70 274.0
11 TraesCS3D01G250200 chr6A 86.695 233 29 2 1808 2039 614103073 614102842 9.570000e-65 257.0
12 TraesCS3D01G250200 chr2D 83.137 255 40 3 1795 2046 14087323 14087069 2.090000e-56 230.0
13 TraesCS3D01G250200 chr2D 85.646 209 27 3 1809 2015 209145957 209145750 1.620000e-52 217.0
14 TraesCS3D01G250200 chr4D 83.333 246 39 2 1804 2048 177493748 177493992 2.700000e-55 226.0
15 TraesCS3D01G250200 chr1A 82.917 240 39 2 1808 2046 64940195 64940433 5.840000e-52 215.0
16 TraesCS3D01G250200 chr6D 82.773 238 40 1 1800 2036 219089378 219089141 7.560000e-51 211.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G250200 chr3D 350734265 350736958 2693 True 4975.00 4975 100.000 1 2694 1 chr3D.!!$R1 2693
1 TraesCS3D01G250200 chr3D 349860468 349861094 626 False 789.00 789 89.325 1000 1635 1 chr3D.!!$F2 635
2 TraesCS3D01G250200 chr3B 449156203 449157867 1664 True 2588.00 2588 94.724 1 1672 1 chr3B.!!$R1 1671
3 TraesCS3D01G250200 chr3B 448773585 448774211 626 False 734.00 734 87.736 1000 1635 1 chr3B.!!$F1 635
4 TraesCS3D01G250200 chr3A 468315603 468318326 2723 True 1203.25 2350 97.222 106 1737 2 chr3A.!!$R2 1631
5 TraesCS3D01G250200 chr3A 468309210 468310008 798 True 760.00 760 84.243 1815 2600 1 chr3A.!!$R1 785
6 TraesCS3D01G250200 chr3A 468003308 468003934 626 False 717.00 717 87.284 1000 1635 1 chr3A.!!$F1 635

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
805 814 1.329599 GTAAGCCGTAGCAAAATCCGG 59.67 52.381 0.0 0.0 43.56 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2604 3792 0.105964 TCGCTAATCATTGGGTCCGG 59.894 55.0 0.0 0.0 0.0 5.14 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
27 28 6.239176 GCCTAGACACACTCAATATCTAGCTT 60.239 42.308 0.00 0.00 38.26 3.74
28 29 7.367285 CCTAGACACACTCAATATCTAGCTTC 58.633 42.308 0.00 0.00 38.26 3.86
35 36 4.202305 ACTCAATATCTAGCTTCAGCCCAC 60.202 45.833 0.00 0.00 43.38 4.61
50 51 5.250200 TCAGCCCACGTAGTAATTTTCATT 58.750 37.500 0.00 0.00 41.61 2.57
51 52 5.123186 TCAGCCCACGTAGTAATTTTCATTG 59.877 40.000 0.00 0.00 41.61 2.82
53 54 5.708230 AGCCCACGTAGTAATTTTCATTGAA 59.292 36.000 0.00 0.00 41.61 2.69
54 55 6.027749 GCCCACGTAGTAATTTTCATTGAAG 58.972 40.000 0.00 0.00 41.61 3.02
55 56 6.349033 GCCCACGTAGTAATTTTCATTGAAGT 60.349 38.462 0.00 0.00 41.61 3.01
57 58 7.021196 CCACGTAGTAATTTTCATTGAAGTGG 58.979 38.462 11.78 11.78 41.61 4.00
58 59 7.308348 CCACGTAGTAATTTTCATTGAAGTGGT 60.308 37.037 15.32 1.80 41.61 4.16
59 60 8.714179 CACGTAGTAATTTTCATTGAAGTGGTA 58.286 33.333 0.00 0.00 41.61 3.25
60 61 9.275398 ACGTAGTAATTTTCATTGAAGTGGTAA 57.725 29.630 0.00 0.00 41.94 2.85
98 100 5.904362 ATGCAGAAAACCCAATCTTACTC 57.096 39.130 0.00 0.00 0.00 2.59
103 105 4.695928 AGAAAACCCAATCTTACTCGCTTC 59.304 41.667 0.00 0.00 0.00 3.86
217 219 1.957177 TGCAAGGATTTAACACGGCAA 59.043 42.857 0.00 0.00 0.00 4.52
392 394 2.570284 TTCCTCCGCACGCAGAAGA 61.570 57.895 0.00 0.00 0.00 2.87
746 755 2.760092 ACGCTTATGGCAACCATGAATT 59.240 40.909 9.39 0.00 44.84 2.17
753 762 2.971330 TGGCAACCATGAATTTTGTCCT 59.029 40.909 0.00 0.00 0.00 3.85
805 814 1.329599 GTAAGCCGTAGCAAAATCCGG 59.670 52.381 0.00 0.00 43.56 5.14
1025 1045 2.223112 CGCCATGAAGGTTCGAAATCTG 60.223 50.000 0.00 0.48 40.61 2.90
1107 1127 1.613928 TGGATACCCCTCGGTTGCA 60.614 57.895 0.00 0.00 40.58 4.08
1156 1176 2.744202 CCAAATTCTCCGTTCAGGTCAG 59.256 50.000 0.00 0.00 41.99 3.51
1218 1238 1.304713 GACCCCGTCTCCACTACCA 60.305 63.158 0.00 0.00 0.00 3.25
1219 1239 1.602327 GACCCCGTCTCCACTACCAC 61.602 65.000 0.00 0.00 0.00 4.16
1220 1240 1.305046 CCCCGTCTCCACTACCACT 60.305 63.158 0.00 0.00 0.00 4.00
1221 1241 0.033796 CCCCGTCTCCACTACCACTA 60.034 60.000 0.00 0.00 0.00 2.74
1222 1242 1.101331 CCCGTCTCCACTACCACTAC 58.899 60.000 0.00 0.00 0.00 2.73
1223 1243 1.101331 CCGTCTCCACTACCACTACC 58.899 60.000 0.00 0.00 0.00 3.18
1224 1244 1.615116 CCGTCTCCACTACCACTACCA 60.615 57.143 0.00 0.00 0.00 3.25
1443 1463 1.670949 GCTCAGAGACCAGATGGCGA 61.671 60.000 0.00 0.00 39.32 5.54
1624 1644 2.819595 CTCGGATGTTGCCCCGTG 60.820 66.667 0.00 0.00 45.48 4.94
1642 1662 3.236816 CGTGTTGGATGCAGTGATTTTC 58.763 45.455 0.00 0.00 0.00 2.29
1682 2851 8.974060 TTTTCTACCTAGTTATTTATGCAGGG 57.026 34.615 0.00 0.00 0.00 4.45
1683 2852 6.110411 TCTACCTAGTTATTTATGCAGGGC 57.890 41.667 0.00 0.00 0.00 5.19
1684 2853 5.844516 TCTACCTAGTTATTTATGCAGGGCT 59.155 40.000 0.00 0.00 0.00 5.19
1685 2854 5.388599 ACCTAGTTATTTATGCAGGGCTT 57.611 39.130 0.00 0.00 0.00 4.35
1686 2855 5.377478 ACCTAGTTATTTATGCAGGGCTTC 58.623 41.667 0.00 0.00 0.00 3.86
1687 2856 5.132816 ACCTAGTTATTTATGCAGGGCTTCT 59.867 40.000 0.00 0.00 0.00 2.85
1688 2857 6.329197 ACCTAGTTATTTATGCAGGGCTTCTA 59.671 38.462 0.00 0.00 0.00 2.10
1689 2858 7.147373 ACCTAGTTATTTATGCAGGGCTTCTAA 60.147 37.037 0.00 0.00 0.00 2.10
1690 2859 7.719633 CCTAGTTATTTATGCAGGGCTTCTAAA 59.280 37.037 0.00 0.00 0.00 1.85
1691 2860 7.954666 AGTTATTTATGCAGGGCTTCTAAAA 57.045 32.000 0.00 0.00 0.00 1.52
1692 2861 8.361169 AGTTATTTATGCAGGGCTTCTAAAAA 57.639 30.769 0.00 0.00 0.00 1.94
1737 2906 1.431633 TCCCAACCTGTCAGAGGACTA 59.568 52.381 0.00 0.00 46.33 2.59
1738 2907 2.158219 TCCCAACCTGTCAGAGGACTAA 60.158 50.000 0.00 0.00 46.33 2.24
1739 2908 2.637872 CCCAACCTGTCAGAGGACTAAA 59.362 50.000 0.00 0.00 46.33 1.85
1740 2909 3.072476 CCCAACCTGTCAGAGGACTAAAA 59.928 47.826 0.00 0.00 46.33 1.52
1741 2910 4.445735 CCCAACCTGTCAGAGGACTAAAAA 60.446 45.833 0.00 0.00 46.33 1.94
1742 2911 5.316987 CCAACCTGTCAGAGGACTAAAAAT 58.683 41.667 0.00 0.00 46.33 1.82
1743 2912 5.770162 CCAACCTGTCAGAGGACTAAAAATT 59.230 40.000 0.00 0.00 46.33 1.82
1744 2913 6.265422 CCAACCTGTCAGAGGACTAAAAATTT 59.735 38.462 0.00 0.00 46.33 1.82
1745 2914 7.363431 CAACCTGTCAGAGGACTAAAAATTTC 58.637 38.462 0.00 0.00 46.33 2.17
1746 2915 5.701290 ACCTGTCAGAGGACTAAAAATTTCG 59.299 40.000 0.00 0.00 46.33 3.46
1747 2916 5.122396 CCTGTCAGAGGACTAAAAATTTCGG 59.878 44.000 0.00 0.00 46.33 4.30
1748 2917 5.617252 TGTCAGAGGACTAAAAATTTCGGT 58.383 37.500 0.00 0.00 44.61 4.69
1749 2918 6.059484 TGTCAGAGGACTAAAAATTTCGGTT 58.941 36.000 0.00 0.00 44.61 4.44
1750 2919 6.544564 TGTCAGAGGACTAAAAATTTCGGTTT 59.455 34.615 0.00 0.00 44.61 3.27
1751 2920 7.716123 TGTCAGAGGACTAAAAATTTCGGTTTA 59.284 33.333 0.00 0.00 44.61 2.01
1752 2921 8.013947 GTCAGAGGACTAAAAATTTCGGTTTAC 58.986 37.037 0.00 0.00 40.99 2.01
1753 2922 7.935210 TCAGAGGACTAAAAATTTCGGTTTACT 59.065 33.333 0.00 0.00 0.00 2.24
1754 2923 8.228464 CAGAGGACTAAAAATTTCGGTTTACTC 58.772 37.037 0.00 0.00 0.00 2.59
1755 2924 7.935210 AGAGGACTAAAAATTTCGGTTTACTCA 59.065 33.333 0.00 0.00 0.00 3.41
1756 2925 8.631480 AGGACTAAAAATTTCGGTTTACTCAT 57.369 30.769 0.00 0.00 0.00 2.90
1757 2926 8.727910 AGGACTAAAAATTTCGGTTTACTCATC 58.272 33.333 0.00 0.00 0.00 2.92
1758 2927 8.727910 GGACTAAAAATTTCGGTTTACTCATCT 58.272 33.333 0.00 0.00 0.00 2.90
1763 2932 7.989416 AAATTTCGGTTTACTCATCTAACCA 57.011 32.000 0.00 0.00 41.06 3.67
1764 2933 7.611213 AATTTCGGTTTACTCATCTAACCAG 57.389 36.000 0.00 0.00 41.06 4.00
1765 2934 5.733620 TTCGGTTTACTCATCTAACCAGT 57.266 39.130 0.00 0.00 41.06 4.00
1766 2935 5.068234 TCGGTTTACTCATCTAACCAGTG 57.932 43.478 0.00 0.00 41.06 3.66
1767 2936 4.525487 TCGGTTTACTCATCTAACCAGTGT 59.475 41.667 0.00 0.00 41.06 3.55
1768 2937 4.863131 CGGTTTACTCATCTAACCAGTGTC 59.137 45.833 0.00 0.00 41.06 3.67
1769 2938 5.336531 CGGTTTACTCATCTAACCAGTGTCT 60.337 44.000 0.00 0.00 41.06 3.41
1770 2939 6.465084 GGTTTACTCATCTAACCAGTGTCTT 58.535 40.000 0.00 0.00 40.77 3.01
1771 2940 6.369065 GGTTTACTCATCTAACCAGTGTCTTG 59.631 42.308 0.00 0.00 40.77 3.02
1772 2941 3.931578 ACTCATCTAACCAGTGTCTTGC 58.068 45.455 0.00 0.00 0.00 4.01
1773 2942 3.265791 CTCATCTAACCAGTGTCTTGCC 58.734 50.000 0.00 0.00 0.00 4.52
1774 2943 2.002586 CATCTAACCAGTGTCTTGCCG 58.997 52.381 0.00 0.00 0.00 5.69
1775 2944 1.334160 TCTAACCAGTGTCTTGCCGA 58.666 50.000 0.00 0.00 0.00 5.54
1776 2945 1.689813 TCTAACCAGTGTCTTGCCGAA 59.310 47.619 0.00 0.00 0.00 4.30
1777 2946 2.069273 CTAACCAGTGTCTTGCCGAAG 58.931 52.381 0.00 0.00 0.00 3.79
1778 2947 0.180406 AACCAGTGTCTTGCCGAAGT 59.820 50.000 0.00 0.00 0.00 3.01
1779 2948 1.045407 ACCAGTGTCTTGCCGAAGTA 58.955 50.000 0.00 0.00 0.00 2.24
1780 2949 1.000955 ACCAGTGTCTTGCCGAAGTAG 59.999 52.381 0.00 0.00 0.00 2.57
1781 2950 1.000955 CCAGTGTCTTGCCGAAGTAGT 59.999 52.381 0.00 0.00 0.00 2.73
1782 2951 2.230508 CCAGTGTCTTGCCGAAGTAGTA 59.769 50.000 0.00 0.00 0.00 1.82
1783 2952 3.305813 CCAGTGTCTTGCCGAAGTAGTAA 60.306 47.826 0.00 0.00 0.00 2.24
1784 2953 4.304110 CAGTGTCTTGCCGAAGTAGTAAA 58.696 43.478 0.00 0.00 0.00 2.01
1785 2954 4.748102 CAGTGTCTTGCCGAAGTAGTAAAA 59.252 41.667 0.00 0.00 0.00 1.52
1786 2955 4.748600 AGTGTCTTGCCGAAGTAGTAAAAC 59.251 41.667 0.00 0.00 0.00 2.43
1787 2956 4.060205 TGTCTTGCCGAAGTAGTAAAACC 58.940 43.478 0.00 0.00 0.00 3.27
1788 2957 4.060205 GTCTTGCCGAAGTAGTAAAACCA 58.940 43.478 0.00 0.00 0.00 3.67
1789 2958 4.694037 GTCTTGCCGAAGTAGTAAAACCAT 59.306 41.667 0.00 0.00 0.00 3.55
1790 2959 5.180680 GTCTTGCCGAAGTAGTAAAACCATT 59.819 40.000 0.00 0.00 0.00 3.16
1791 2960 6.369615 GTCTTGCCGAAGTAGTAAAACCATTA 59.630 38.462 0.00 0.00 0.00 1.90
1792 2961 6.592607 TCTTGCCGAAGTAGTAAAACCATTAG 59.407 38.462 0.00 0.00 0.00 1.73
1793 2962 6.040209 TGCCGAAGTAGTAAAACCATTAGA 57.960 37.500 0.00 0.00 0.00 2.10
1794 2963 6.103997 TGCCGAAGTAGTAAAACCATTAGAG 58.896 40.000 0.00 0.00 0.00 2.43
1795 2964 5.522824 GCCGAAGTAGTAAAACCATTAGAGG 59.477 44.000 0.00 0.00 0.00 3.69
1796 2965 6.628844 GCCGAAGTAGTAAAACCATTAGAGGA 60.629 42.308 0.00 0.00 0.00 3.71
1797 2966 6.979238 CCGAAGTAGTAAAACCATTAGAGGAG 59.021 42.308 0.00 0.00 0.00 3.69
1798 2967 7.363617 CCGAAGTAGTAAAACCATTAGAGGAGT 60.364 40.741 0.00 0.00 0.00 3.85
1799 2968 8.680903 CGAAGTAGTAAAACCATTAGAGGAGTA 58.319 37.037 0.00 0.00 0.00 2.59
1800 2969 9.800433 GAAGTAGTAAAACCATTAGAGGAGTAC 57.200 37.037 0.00 0.00 0.00 2.73
1801 2970 9.544579 AAGTAGTAAAACCATTAGAGGAGTACT 57.455 33.333 0.00 0.00 32.24 2.73
1833 3002 4.439253 ACCTCTATCCTGGTTTATTGGC 57.561 45.455 0.00 0.00 31.62 4.52
1835 3004 3.138283 CCTCTATCCTGGTTTATTGGCCA 59.862 47.826 0.00 0.00 0.00 5.36
1837 3006 3.785887 TCTATCCTGGTTTATTGGCCACT 59.214 43.478 3.88 1.42 0.00 4.00
1840 3010 1.472480 CCTGGTTTATTGGCCACTTCG 59.528 52.381 3.88 0.00 0.00 3.79
1857 3029 7.220108 GGCCACTTCGTATTTTATGTCAAATTC 59.780 37.037 0.00 0.00 0.00 2.17
1859 3031 9.277565 CCACTTCGTATTTTATGTCAAATTCTG 57.722 33.333 0.00 0.00 0.00 3.02
1974 3146 6.528014 TTTTGTGACATGCATTGACATTTC 57.472 33.333 0.00 0.00 32.72 2.17
1975 3147 5.456548 TTGTGACATGCATTGACATTTCT 57.543 34.783 0.00 0.00 32.72 2.52
1987 3159 9.255304 TGCATTGACATTTCTTTAGTTAAAACC 57.745 29.630 0.00 0.00 0.00 3.27
1988 3160 9.255304 GCATTGACATTTCTTTAGTTAAAACCA 57.745 29.630 0.00 0.00 0.00 3.67
2032 3204 4.482952 ACGAAGGGGACTAATAAACCAG 57.517 45.455 0.00 0.00 42.68 4.00
2033 3205 3.199289 ACGAAGGGGACTAATAAACCAGG 59.801 47.826 0.00 0.00 42.68 4.45
2034 3206 3.453353 CGAAGGGGACTAATAAACCAGGA 59.547 47.826 0.00 0.00 42.68 3.86
2039 3211 3.390311 GGGACTAATAAACCAGGACGGAT 59.610 47.826 0.00 0.00 38.63 4.18
2040 3212 4.377897 GGACTAATAAACCAGGACGGATG 58.622 47.826 0.00 0.00 38.63 3.51
2049 3221 1.955080 CCAGGACGGATGTAGTACTCC 59.045 57.143 0.00 5.45 36.56 3.85
2060 3232 2.950309 TGTAGTACTCCGAGCTTCCATC 59.050 50.000 0.00 0.00 0.00 3.51
2061 3233 1.404843 AGTACTCCGAGCTTCCATCC 58.595 55.000 0.00 0.00 0.00 3.51
2086 3258 0.320946 TAAAAACACTCCCCCGCTCG 60.321 55.000 0.00 0.00 0.00 5.03
2089 3261 3.892104 AACACTCCCCCGCTCGGTA 62.892 63.158 7.59 0.00 0.00 4.02
2111 3283 1.664965 GAGTCAAACACGCTCGCCT 60.665 57.895 0.00 0.00 0.00 5.52
2114 3286 1.954146 TCAAACACGCTCGCCTCAC 60.954 57.895 0.00 0.00 0.00 3.51
2119 3291 2.361357 ACGCTCGCCTCACCTACT 60.361 61.111 0.00 0.00 0.00 2.57
2120 3292 2.103143 CGCTCGCCTCACCTACTG 59.897 66.667 0.00 0.00 0.00 2.74
2131 3303 4.514577 CCTACTGCCGCTCCACCG 62.515 72.222 0.00 0.00 0.00 4.94
2139 3311 3.508840 CGCTCCACCGCCCAAATC 61.509 66.667 0.00 0.00 0.00 2.17
2163 3335 2.035626 CCGCCACCCAAATCACCT 59.964 61.111 0.00 0.00 0.00 4.00
2188 3360 4.348486 CTGCCTCTTCCTATGGCTAGATA 58.652 47.826 0.00 0.00 46.23 1.98
2189 3361 4.090090 TGCCTCTTCCTATGGCTAGATAC 58.910 47.826 0.00 0.00 46.23 2.24
2190 3362 3.129638 GCCTCTTCCTATGGCTAGATACG 59.870 52.174 0.00 0.00 43.05 3.06
2191 3363 3.697045 CCTCTTCCTATGGCTAGATACGG 59.303 52.174 0.00 0.00 0.00 4.02
2192 3364 4.337145 CTCTTCCTATGGCTAGATACGGT 58.663 47.826 0.00 0.00 0.00 4.83
2195 3367 1.132643 CCTATGGCTAGATACGGTCGC 59.867 57.143 0.00 0.00 0.00 5.19
2242 3414 2.745884 TTTGCCAGCGGATCCACG 60.746 61.111 13.41 0.00 0.00 4.94
2293 3465 1.558756 AGCCTGACTCCTTCCATTCAG 59.441 52.381 0.00 0.00 36.10 3.02
2294 3466 2.016096 GCCTGACTCCTTCCATTCAGC 61.016 57.143 0.00 0.00 35.18 4.26
2345 3517 1.663388 CAGTGCACTTGTACGGCGA 60.663 57.895 18.94 0.00 35.74 5.54
2347 3519 1.952133 GTGCACTTGTACGGCGACA 60.952 57.895 16.62 11.18 0.00 4.35
2348 3520 1.005512 TGCACTTGTACGGCGACAT 60.006 52.632 16.62 0.00 0.00 3.06
2374 3547 0.242825 TCGTAACTTCCCGACAGCTG 59.757 55.000 13.48 13.48 0.00 4.24
2388 3561 1.753078 AGCTGTCTACCGCCATCGA 60.753 57.895 0.00 0.00 38.10 3.59
2406 3579 2.351336 GAAGCCGTCGATGGACCGAT 62.351 60.000 28.06 7.30 40.91 4.18
2427 3600 4.269523 TGGCCACTCCACACCAGC 62.270 66.667 0.00 0.00 40.72 4.85
2448 3621 1.379977 CAGGAGGACCGAGTAGCCA 60.380 63.158 0.00 0.00 41.83 4.75
2454 3627 3.759766 GACCGAGTAGCCAGCGAGC 62.760 68.421 0.00 0.00 0.00 5.03
2468 3641 1.591059 CGAGCTTCTCATGGCGGAG 60.591 63.158 0.00 0.00 36.21 4.63
2505 3678 1.982395 ATGGTGGAGCTCCGTCGAA 60.982 57.895 27.43 14.42 39.43 3.71
2531 3719 4.735132 GAGCGCCGCCTGTACACA 62.735 66.667 4.98 0.00 0.00 3.72
2540 3728 1.873903 CGCCTGTACACAGAGTTTGCT 60.874 52.381 10.96 0.00 46.59 3.91
2541 3729 1.532868 GCCTGTACACAGAGTTTGCTG 59.467 52.381 10.96 0.00 46.59 4.41
2561 3749 1.078759 CACGCAGGACCGAAGTCATC 61.079 60.000 0.00 0.00 45.48 2.92
2601 3789 3.959478 GGTGACGTCAACAGAGACA 57.041 52.632 28.28 0.00 38.43 3.41
2602 3790 2.218953 GGTGACGTCAACAGAGACAA 57.781 50.000 28.28 0.00 38.43 3.18
2603 3791 1.859080 GGTGACGTCAACAGAGACAAC 59.141 52.381 28.28 7.79 38.43 3.32
2604 3792 1.859080 GTGACGTCAACAGAGACAACC 59.141 52.381 21.95 0.00 38.43 3.77
2605 3793 1.202486 TGACGTCAACAGAGACAACCC 60.202 52.381 17.62 0.00 38.43 4.11
2606 3794 0.249322 ACGTCAACAGAGACAACCCG 60.249 55.000 0.00 0.00 38.43 5.28
2607 3795 0.944311 CGTCAACAGAGACAACCCGG 60.944 60.000 0.00 0.00 38.43 5.73
2608 3796 0.391597 GTCAACAGAGACAACCCGGA 59.608 55.000 0.73 0.00 38.40 5.14
2609 3797 0.391597 TCAACAGAGACAACCCGGAC 59.608 55.000 0.73 0.00 0.00 4.79
2610 3798 0.602905 CAACAGAGACAACCCGGACC 60.603 60.000 0.73 0.00 0.00 4.46
2611 3799 1.765597 AACAGAGACAACCCGGACCC 61.766 60.000 0.73 0.00 0.00 4.46
2612 3800 2.203182 AGAGACAACCCGGACCCA 59.797 61.111 0.73 0.00 0.00 4.51
2613 3801 1.460689 AGAGACAACCCGGACCCAA 60.461 57.895 0.73 0.00 0.00 4.12
2614 3802 0.840722 AGAGACAACCCGGACCCAAT 60.841 55.000 0.73 0.00 0.00 3.16
2615 3803 0.676782 GAGACAACCCGGACCCAATG 60.677 60.000 0.73 0.00 0.00 2.82
2616 3804 1.131303 AGACAACCCGGACCCAATGA 61.131 55.000 0.73 0.00 0.00 2.57
2617 3805 0.034477 GACAACCCGGACCCAATGAT 60.034 55.000 0.73 0.00 0.00 2.45
2618 3806 0.407918 ACAACCCGGACCCAATGATT 59.592 50.000 0.73 0.00 0.00 2.57
2619 3807 1.636519 ACAACCCGGACCCAATGATTA 59.363 47.619 0.73 0.00 0.00 1.75
2620 3808 2.297701 CAACCCGGACCCAATGATTAG 58.702 52.381 0.73 0.00 0.00 1.73
2621 3809 0.182775 ACCCGGACCCAATGATTAGC 59.817 55.000 0.73 0.00 0.00 3.09
2622 3810 0.884704 CCCGGACCCAATGATTAGCG 60.885 60.000 0.73 0.00 0.00 4.26
2623 3811 0.105964 CCGGACCCAATGATTAGCGA 59.894 55.000 0.00 0.00 0.00 4.93
2624 3812 1.270839 CCGGACCCAATGATTAGCGAT 60.271 52.381 0.00 0.00 0.00 4.58
2625 3813 2.028476 CCGGACCCAATGATTAGCGATA 60.028 50.000 0.00 0.00 0.00 2.92
2626 3814 3.369471 CCGGACCCAATGATTAGCGATAT 60.369 47.826 0.00 0.00 0.00 1.63
2627 3815 3.618594 CGGACCCAATGATTAGCGATATG 59.381 47.826 0.00 0.00 0.00 1.78
2628 3816 4.620567 CGGACCCAATGATTAGCGATATGA 60.621 45.833 0.00 0.00 0.00 2.15
2629 3817 4.872691 GGACCCAATGATTAGCGATATGAG 59.127 45.833 0.00 0.00 0.00 2.90
2630 3818 5.482908 GACCCAATGATTAGCGATATGAGT 58.517 41.667 0.00 0.00 0.00 3.41
2631 3819 6.351033 GGACCCAATGATTAGCGATATGAGTA 60.351 42.308 0.00 0.00 0.00 2.59
2632 3820 6.634805 ACCCAATGATTAGCGATATGAGTAG 58.365 40.000 0.00 0.00 0.00 2.57
2633 3821 6.045318 CCCAATGATTAGCGATATGAGTAGG 58.955 44.000 0.00 0.00 0.00 3.18
2634 3822 6.045318 CCAATGATTAGCGATATGAGTAGGG 58.955 44.000 0.00 0.00 0.00 3.53
2635 3823 4.720649 TGATTAGCGATATGAGTAGGGC 57.279 45.455 0.00 0.00 0.00 5.19
2636 3824 3.128764 TGATTAGCGATATGAGTAGGGCG 59.871 47.826 0.00 0.00 0.00 6.13
2637 3825 1.460504 TAGCGATATGAGTAGGGCGG 58.539 55.000 0.00 0.00 0.00 6.13
2638 3826 0.251209 AGCGATATGAGTAGGGCGGA 60.251 55.000 0.00 0.00 0.00 5.54
2639 3827 0.601558 GCGATATGAGTAGGGCGGAA 59.398 55.000 0.00 0.00 0.00 4.30
2640 3828 1.204941 GCGATATGAGTAGGGCGGAAT 59.795 52.381 0.00 0.00 0.00 3.01
2641 3829 2.881074 CGATATGAGTAGGGCGGAATG 58.119 52.381 0.00 0.00 0.00 2.67
2642 3830 2.417379 CGATATGAGTAGGGCGGAATGG 60.417 54.545 0.00 0.00 0.00 3.16
2643 3831 2.391926 TATGAGTAGGGCGGAATGGA 57.608 50.000 0.00 0.00 0.00 3.41
2644 3832 1.507140 ATGAGTAGGGCGGAATGGAA 58.493 50.000 0.00 0.00 0.00 3.53
2645 3833 0.830648 TGAGTAGGGCGGAATGGAAG 59.169 55.000 0.00 0.00 0.00 3.46
2646 3834 0.106894 GAGTAGGGCGGAATGGAAGG 59.893 60.000 0.00 0.00 0.00 3.46
2647 3835 1.526225 GTAGGGCGGAATGGAAGGC 60.526 63.158 0.00 0.00 0.00 4.35
2648 3836 1.998438 TAGGGCGGAATGGAAGGCA 60.998 57.895 0.00 0.00 0.00 4.75
2649 3837 2.265467 TAGGGCGGAATGGAAGGCAC 62.265 60.000 0.00 0.00 0.00 5.01
2651 3839 1.223487 GGCGGAATGGAAGGCACTA 59.777 57.895 0.00 0.00 38.49 2.74
2652 3840 0.815615 GGCGGAATGGAAGGCACTAG 60.816 60.000 0.00 0.00 38.49 2.57
2653 3841 0.178068 GCGGAATGGAAGGCACTAGA 59.822 55.000 0.00 0.00 38.49 2.43
2654 3842 1.808133 GCGGAATGGAAGGCACTAGAG 60.808 57.143 0.00 0.00 38.49 2.43
2655 3843 1.202580 CGGAATGGAAGGCACTAGAGG 60.203 57.143 0.00 0.00 38.49 3.69
2656 3844 2.119495 GGAATGGAAGGCACTAGAGGA 58.881 52.381 0.00 0.00 38.49 3.71
2657 3845 2.505819 GGAATGGAAGGCACTAGAGGAA 59.494 50.000 0.00 0.00 38.49 3.36
2658 3846 3.432890 GGAATGGAAGGCACTAGAGGAAG 60.433 52.174 0.00 0.00 38.49 3.46
2659 3847 2.623418 TGGAAGGCACTAGAGGAAGA 57.377 50.000 0.00 0.00 38.49 2.87
2660 3848 2.902608 TGGAAGGCACTAGAGGAAGAA 58.097 47.619 0.00 0.00 38.49 2.52
2661 3849 3.454858 TGGAAGGCACTAGAGGAAGAAT 58.545 45.455 0.00 0.00 38.49 2.40
2662 3850 3.452627 TGGAAGGCACTAGAGGAAGAATC 59.547 47.826 0.00 0.00 38.49 2.52
2663 3851 3.491792 GGAAGGCACTAGAGGAAGAATCG 60.492 52.174 0.00 0.00 38.49 3.34
2664 3852 2.035632 AGGCACTAGAGGAAGAATCGG 58.964 52.381 0.00 0.00 36.02 4.18
2665 3853 2.032620 GGCACTAGAGGAAGAATCGGA 58.967 52.381 0.00 0.00 0.00 4.55
2666 3854 2.223852 GGCACTAGAGGAAGAATCGGAC 60.224 54.545 0.00 0.00 0.00 4.79
2667 3855 2.691011 GCACTAGAGGAAGAATCGGACT 59.309 50.000 0.00 0.00 0.00 3.85
2668 3856 3.884091 GCACTAGAGGAAGAATCGGACTA 59.116 47.826 0.00 0.00 0.00 2.59
2669 3857 4.023536 GCACTAGAGGAAGAATCGGACTAG 60.024 50.000 0.00 0.00 33.55 2.57
2670 3858 4.517453 CACTAGAGGAAGAATCGGACTAGG 59.483 50.000 0.00 0.00 32.60 3.02
2671 3859 3.673543 AGAGGAAGAATCGGACTAGGT 57.326 47.619 0.00 0.00 0.00 3.08
2672 3860 3.983821 AGAGGAAGAATCGGACTAGGTT 58.016 45.455 0.00 0.00 0.00 3.50
2673 3861 4.354662 AGAGGAAGAATCGGACTAGGTTT 58.645 43.478 0.00 0.00 0.00 3.27
2674 3862 4.403113 AGAGGAAGAATCGGACTAGGTTTC 59.597 45.833 0.00 0.00 0.00 2.78
2675 3863 4.094476 AGGAAGAATCGGACTAGGTTTCA 58.906 43.478 0.00 0.00 0.00 2.69
2676 3864 4.530946 AGGAAGAATCGGACTAGGTTTCAA 59.469 41.667 0.00 0.00 0.00 2.69
2677 3865 5.012768 AGGAAGAATCGGACTAGGTTTCAAA 59.987 40.000 0.00 0.00 0.00 2.69
2678 3866 5.880887 GGAAGAATCGGACTAGGTTTCAAAT 59.119 40.000 0.00 0.00 0.00 2.32
2679 3867 6.374613 GGAAGAATCGGACTAGGTTTCAAATT 59.625 38.462 0.00 0.00 0.00 1.82
2680 3868 7.094334 GGAAGAATCGGACTAGGTTTCAAATTT 60.094 37.037 0.00 0.00 0.00 1.82
2681 3869 7.379098 AGAATCGGACTAGGTTTCAAATTTC 57.621 36.000 0.00 0.00 0.00 2.17
2682 3870 6.940298 AGAATCGGACTAGGTTTCAAATTTCA 59.060 34.615 0.00 0.00 0.00 2.69
2683 3871 7.611855 AGAATCGGACTAGGTTTCAAATTTCAT 59.388 33.333 0.00 0.00 0.00 2.57
2684 3872 7.703058 ATCGGACTAGGTTTCAAATTTCATT 57.297 32.000 0.00 0.00 0.00 2.57
2685 3873 7.519032 TCGGACTAGGTTTCAAATTTCATTT 57.481 32.000 0.00 0.00 0.00 2.32
2686 3874 7.590279 TCGGACTAGGTTTCAAATTTCATTTC 58.410 34.615 0.00 0.00 0.00 2.17
2687 3875 7.447238 TCGGACTAGGTTTCAAATTTCATTTCT 59.553 33.333 0.00 0.00 0.00 2.52
2688 3876 8.726988 CGGACTAGGTTTCAAATTTCATTTCTA 58.273 33.333 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.935520 TGAAGCTAGATATTGAGTGTGTCTAG 58.064 38.462 0.00 0.00 40.67 2.43
7 8 5.461737 GCTGAAGCTAGATATTGAGTGTGTC 59.538 44.000 0.00 0.00 38.21 3.67
11 12 4.202295 TGGGCTGAAGCTAGATATTGAGTG 60.202 45.833 1.74 0.00 41.70 3.51
27 28 4.274602 TGAAAATTACTACGTGGGCTGA 57.725 40.909 3.26 0.00 0.00 4.26
28 29 5.123186 TCAATGAAAATTACTACGTGGGCTG 59.877 40.000 3.26 0.00 0.00 4.85
73 74 7.066307 AGTAAGATTGGGTTTTCTGCATTTT 57.934 32.000 0.00 0.00 0.00 1.82
123 125 9.415544 GAACTTGTAATTTCTAGTAGGTTCGAA 57.584 33.333 0.00 0.00 0.00 3.71
125 127 8.983307 AGAACTTGTAATTTCTAGTAGGTTCG 57.017 34.615 0.00 0.00 35.82 3.95
137 139 9.751542 CGATCAGGACTATAGAACTTGTAATTT 57.248 33.333 6.78 0.00 0.00 1.82
155 157 4.171878 AGGTTAGAGATGACGATCAGGA 57.828 45.455 0.00 0.00 0.00 3.86
217 219 1.073025 TTGGATGCGCACAGAGGTT 59.927 52.632 14.90 0.00 0.00 3.50
746 755 1.362224 AGCTCAAGGCCTAGGACAAA 58.638 50.000 19.45 0.00 43.05 2.83
753 762 3.774766 TCTTGTCAATAGCTCAAGGCCTA 59.225 43.478 5.16 0.00 43.05 3.93
805 814 1.308998 CCGGCCAATATTCTGGTGAC 58.691 55.000 2.24 0.00 38.86 3.67
932 952 2.338500 GTCCATCTCTCCACGTGTTTC 58.662 52.381 15.65 0.00 0.00 2.78
1107 1127 1.572447 CGTTCACGCGGAAAACCAT 59.428 52.632 12.47 0.00 37.23 3.55
1218 1238 1.274447 GTTGAAGGCGGTACTGGTAGT 59.726 52.381 3.34 0.00 0.00 2.73
1219 1239 1.274167 TGTTGAAGGCGGTACTGGTAG 59.726 52.381 3.34 0.00 0.00 3.18
1220 1240 1.340088 TGTTGAAGGCGGTACTGGTA 58.660 50.000 3.34 0.00 0.00 3.25
1221 1241 0.690762 ATGTTGAAGGCGGTACTGGT 59.309 50.000 3.34 0.00 0.00 4.00
1222 1242 1.821216 AATGTTGAAGGCGGTACTGG 58.179 50.000 3.34 0.00 0.00 4.00
1223 1243 2.676342 GGTAATGTTGAAGGCGGTACTG 59.324 50.000 0.00 0.00 0.00 2.74
1224 1244 2.355412 GGGTAATGTTGAAGGCGGTACT 60.355 50.000 0.00 0.00 0.00 2.73
1624 1644 4.619973 TGTTGAAAATCACTGCATCCAAC 58.380 39.130 0.00 0.00 34.83 3.77
1691 2860 5.394115 CGGCTCCCTGCATAAATAACTTTTT 60.394 40.000 0.00 0.00 45.15 1.94
1692 2861 4.097892 CGGCTCCCTGCATAAATAACTTTT 59.902 41.667 0.00 0.00 45.15 2.27
1693 2862 3.632145 CGGCTCCCTGCATAAATAACTTT 59.368 43.478 0.00 0.00 45.15 2.66
1694 2863 3.118038 TCGGCTCCCTGCATAAATAACTT 60.118 43.478 0.00 0.00 45.15 2.66
1695 2864 2.438021 TCGGCTCCCTGCATAAATAACT 59.562 45.455 0.00 0.00 45.15 2.24
1696 2865 2.846193 TCGGCTCCCTGCATAAATAAC 58.154 47.619 0.00 0.00 45.15 1.89
1697 2866 3.559171 GGATCGGCTCCCTGCATAAATAA 60.559 47.826 0.00 0.00 45.15 1.40
1698 2867 2.027192 GGATCGGCTCCCTGCATAAATA 60.027 50.000 0.00 0.00 45.15 1.40
1699 2868 1.271597 GGATCGGCTCCCTGCATAAAT 60.272 52.381 0.00 0.00 45.15 1.40
1700 2869 0.108585 GGATCGGCTCCCTGCATAAA 59.891 55.000 0.00 0.00 45.15 1.40
1701 2870 1.754745 GGATCGGCTCCCTGCATAA 59.245 57.895 0.00 0.00 45.15 1.90
1702 2871 3.471620 GGATCGGCTCCCTGCATA 58.528 61.111 0.00 0.00 45.15 3.14
1737 2906 8.852135 TGGTTAGATGAGTAAACCGAAATTTTT 58.148 29.630 0.00 0.00 44.62 1.94
1738 2907 8.398878 TGGTTAGATGAGTAAACCGAAATTTT 57.601 30.769 0.00 0.00 44.62 1.82
1739 2908 7.664318 ACTGGTTAGATGAGTAAACCGAAATTT 59.336 33.333 0.00 0.00 44.62 1.82
1740 2909 7.119262 CACTGGTTAGATGAGTAAACCGAAATT 59.881 37.037 0.00 0.00 44.62 1.82
1741 2910 6.594159 CACTGGTTAGATGAGTAAACCGAAAT 59.406 38.462 0.00 0.00 44.62 2.17
1742 2911 5.929992 CACTGGTTAGATGAGTAAACCGAAA 59.070 40.000 0.00 0.00 44.62 3.46
1743 2912 5.011329 ACACTGGTTAGATGAGTAAACCGAA 59.989 40.000 0.00 0.00 44.62 4.30
1744 2913 4.525487 ACACTGGTTAGATGAGTAAACCGA 59.475 41.667 0.00 0.00 44.62 4.69
1745 2914 4.817517 ACACTGGTTAGATGAGTAAACCG 58.182 43.478 0.00 0.00 44.62 4.44
1746 2915 6.038997 AGACACTGGTTAGATGAGTAAACC 57.961 41.667 0.00 0.00 42.49 3.27
1747 2916 6.128526 GCAAGACACTGGTTAGATGAGTAAAC 60.129 42.308 0.00 0.00 0.00 2.01
1748 2917 5.932303 GCAAGACACTGGTTAGATGAGTAAA 59.068 40.000 0.00 0.00 0.00 2.01
1749 2918 5.479306 GCAAGACACTGGTTAGATGAGTAA 58.521 41.667 0.00 0.00 0.00 2.24
1750 2919 4.081642 GGCAAGACACTGGTTAGATGAGTA 60.082 45.833 0.00 0.00 0.00 2.59
1751 2920 3.307059 GGCAAGACACTGGTTAGATGAGT 60.307 47.826 0.00 0.00 0.00 3.41
1752 2921 3.265791 GGCAAGACACTGGTTAGATGAG 58.734 50.000 0.00 0.00 0.00 2.90
1753 2922 2.353704 CGGCAAGACACTGGTTAGATGA 60.354 50.000 0.00 0.00 0.00 2.92
1754 2923 2.002586 CGGCAAGACACTGGTTAGATG 58.997 52.381 0.00 0.00 0.00 2.90
1755 2924 1.899814 TCGGCAAGACACTGGTTAGAT 59.100 47.619 0.00 0.00 0.00 1.98
1756 2925 1.334160 TCGGCAAGACACTGGTTAGA 58.666 50.000 0.00 0.00 0.00 2.10
1757 2926 2.069273 CTTCGGCAAGACACTGGTTAG 58.931 52.381 0.00 0.00 0.00 2.34
1758 2927 1.414919 ACTTCGGCAAGACACTGGTTA 59.585 47.619 4.13 0.00 33.34 2.85
1759 2928 0.180406 ACTTCGGCAAGACACTGGTT 59.820 50.000 4.13 0.00 33.34 3.67
1760 2929 1.000955 CTACTTCGGCAAGACACTGGT 59.999 52.381 4.13 0.00 33.34 4.00
1761 2930 1.000955 ACTACTTCGGCAAGACACTGG 59.999 52.381 4.13 0.00 33.34 4.00
1762 2931 2.440539 ACTACTTCGGCAAGACACTG 57.559 50.000 4.13 0.00 33.34 3.66
1763 2932 4.595762 TTTACTACTTCGGCAAGACACT 57.404 40.909 4.13 0.00 33.34 3.55
1764 2933 4.084171 GGTTTTACTACTTCGGCAAGACAC 60.084 45.833 4.13 0.00 33.34 3.67
1765 2934 4.060205 GGTTTTACTACTTCGGCAAGACA 58.940 43.478 4.13 0.00 33.34 3.41
1766 2935 4.060205 TGGTTTTACTACTTCGGCAAGAC 58.940 43.478 4.13 0.00 33.34 3.01
1767 2936 4.339872 TGGTTTTACTACTTCGGCAAGA 57.660 40.909 4.13 0.00 33.34 3.02
1768 2937 5.622770 AATGGTTTTACTACTTCGGCAAG 57.377 39.130 0.00 0.00 35.50 4.01
1769 2938 6.465948 TCTAATGGTTTTACTACTTCGGCAA 58.534 36.000 0.00 0.00 0.00 4.52
1770 2939 6.040209 TCTAATGGTTTTACTACTTCGGCA 57.960 37.500 0.00 0.00 0.00 5.69
1771 2940 5.522824 CCTCTAATGGTTTTACTACTTCGGC 59.477 44.000 0.00 0.00 0.00 5.54
1772 2941 6.870769 TCCTCTAATGGTTTTACTACTTCGG 58.129 40.000 0.00 0.00 0.00 4.30
1773 2942 7.545489 ACTCCTCTAATGGTTTTACTACTTCG 58.455 38.462 0.00 0.00 0.00 3.79
1774 2943 9.800433 GTACTCCTCTAATGGTTTTACTACTTC 57.200 37.037 0.00 0.00 0.00 3.01
1775 2944 9.544579 AGTACTCCTCTAATGGTTTTACTACTT 57.455 33.333 0.00 0.00 0.00 2.24
1791 2960 9.994017 AGAGGTAGTAAATTTTAGTACTCCTCT 57.006 33.333 22.79 22.79 42.49 3.69
1799 2968 9.503369 ACCAGGATAGAGGTAGTAAATTTTAGT 57.497 33.333 0.00 2.27 36.07 2.24
1806 2975 8.711170 CCAATAAACCAGGATAGAGGTAGTAAA 58.289 37.037 0.00 0.00 37.07 2.01
1807 2976 7.202066 GCCAATAAACCAGGATAGAGGTAGTAA 60.202 40.741 0.00 0.00 37.07 2.24
1808 2977 6.269307 GCCAATAAACCAGGATAGAGGTAGTA 59.731 42.308 0.00 0.00 37.07 1.82
1809 2978 5.071923 GCCAATAAACCAGGATAGAGGTAGT 59.928 44.000 0.00 0.00 37.07 2.73
1810 2979 5.513267 GGCCAATAAACCAGGATAGAGGTAG 60.513 48.000 0.00 0.00 37.07 3.18
1811 2980 4.349930 GGCCAATAAACCAGGATAGAGGTA 59.650 45.833 0.00 0.00 37.07 3.08
1812 2981 3.138468 GGCCAATAAACCAGGATAGAGGT 59.862 47.826 0.00 0.00 40.61 3.85
1813 2982 3.138283 TGGCCAATAAACCAGGATAGAGG 59.862 47.826 0.61 0.00 0.00 3.69
1818 2987 3.365472 GAAGTGGCCAATAAACCAGGAT 58.635 45.455 7.24 0.00 36.38 3.24
1820 2989 1.472480 CGAAGTGGCCAATAAACCAGG 59.528 52.381 7.24 0.00 36.38 4.45
1824 2993 7.971722 ACATAAAATACGAAGTGGCCAATAAAC 59.028 33.333 7.24 0.32 45.73 2.01
1826 2995 7.337184 TGACATAAAATACGAAGTGGCCAATAA 59.663 33.333 7.24 0.00 45.73 1.40
1833 3002 9.277565 CAGAATTTGACATAAAATACGAAGTGG 57.722 33.333 0.00 0.00 45.73 4.00
1950 3122 6.762187 AGAAATGTCAATGCATGTCACAAAAA 59.238 30.769 0.00 0.00 35.96 1.94
1967 3139 9.406828 GACCATGGTTTTAACTAAAGAAATGTC 57.593 33.333 20.85 0.00 0.00 3.06
1996 3168 4.700213 CCCCTTCGTATTCAGTGTCAAATT 59.300 41.667 0.00 0.00 0.00 1.82
2005 3177 6.704937 GGTTTATTAGTCCCCTTCGTATTCAG 59.295 42.308 0.00 0.00 0.00 3.02
2006 3178 6.156602 TGGTTTATTAGTCCCCTTCGTATTCA 59.843 38.462 0.00 0.00 0.00 2.57
2039 3211 2.502142 TGGAAGCTCGGAGTACTACA 57.498 50.000 5.80 0.00 0.00 2.74
2040 3212 2.293955 GGATGGAAGCTCGGAGTACTAC 59.706 54.545 6.90 0.00 0.00 2.73
2049 3221 1.403814 TACTCCTGGATGGAAGCTCG 58.596 55.000 0.00 0.00 45.63 5.03
2086 3258 0.790814 GCGTGTTTGACTCAGCTACC 59.209 55.000 0.00 0.00 0.00 3.18
2089 3261 0.941463 CGAGCGTGTTTGACTCAGCT 60.941 55.000 0.00 0.00 37.69 4.24
2092 3264 1.954146 GGCGAGCGTGTTTGACTCA 60.954 57.895 0.00 0.00 0.00 3.41
2111 3283 2.283604 TGGAGCGGCAGTAGGTGA 60.284 61.111 1.45 0.00 0.00 4.02
2114 3286 4.514577 CGGTGGAGCGGCAGTAGG 62.515 72.222 1.45 0.00 0.00 3.18
2131 3303 3.068064 CGGGGTGGTGATTTGGGC 61.068 66.667 0.00 0.00 0.00 5.36
2163 3335 3.247424 CCATAGGAAGAGGCAGGGA 57.753 57.895 0.00 0.00 0.00 4.20
2209 3381 1.524848 CAAAGCATTGCATTTGGGCA 58.475 45.000 11.91 0.00 43.19 5.36
2243 3415 4.821589 GAGGAGGAGGCGTTGCGG 62.822 72.222 0.00 0.00 0.00 5.69
2244 3416 4.821589 GGAGGAGGAGGCGTTGCG 62.822 72.222 0.00 0.00 0.00 4.85
2246 3418 4.148825 CGGGAGGAGGAGGCGTTG 62.149 72.222 0.00 0.00 0.00 4.10
2279 3451 0.539051 CTCCGCTGAATGGAAGGAGT 59.461 55.000 1.91 0.00 42.48 3.85
2345 3517 0.457337 GAAGTTACGACCGGCGATGT 60.457 55.000 22.10 6.13 44.57 3.06
2347 3519 1.140375 GGAAGTTACGACCGGCGAT 59.860 57.895 22.10 0.00 44.57 4.58
2348 3520 2.568090 GGAAGTTACGACCGGCGA 59.432 61.111 22.10 5.96 44.57 5.54
2351 3523 3.277133 TCGGGAAGTTACGACCGG 58.723 61.111 0.00 0.00 45.97 5.28
2369 3542 1.589993 CGATGGCGGTAGACAGCTG 60.590 63.158 13.48 13.48 40.26 4.24
2374 3547 1.591863 GGCTTCGATGGCGGTAGAC 60.592 63.158 9.13 0.00 38.28 2.59
2388 3561 2.423898 ATCGGTCCATCGACGGCTT 61.424 57.895 0.00 0.00 42.21 4.35
2448 3621 2.202851 CGCCATGAGAAGCTCGCT 60.203 61.111 0.00 0.00 32.35 4.93
2454 3627 1.523258 CAGCCTCCGCCATGAGAAG 60.523 63.158 0.00 0.00 34.11 2.85
2483 3656 0.179108 GACGGAGCTCCACCATGTAC 60.179 60.000 31.67 11.31 35.14 2.90
2540 3728 3.858868 GACTTCGGTCCTGCGTGCA 62.859 63.158 0.00 0.00 38.93 4.57
2541 3729 3.112709 GACTTCGGTCCTGCGTGC 61.113 66.667 0.00 0.00 38.93 5.34
2567 3755 1.824329 ACCGTCCTCATCGCTCGAT 60.824 57.895 0.00 0.00 34.81 3.59
2590 3778 0.391597 GTCCGGGTTGTCTCTGTTGA 59.608 55.000 0.00 0.00 0.00 3.18
2594 3782 1.764571 TTGGGTCCGGGTTGTCTCTG 61.765 60.000 0.00 0.00 0.00 3.35
2600 3788 2.297701 CTAATCATTGGGTCCGGGTTG 58.702 52.381 0.00 0.00 0.00 3.77
2601 3789 1.409661 GCTAATCATTGGGTCCGGGTT 60.410 52.381 0.00 0.00 0.00 4.11
2602 3790 0.182775 GCTAATCATTGGGTCCGGGT 59.817 55.000 0.00 0.00 0.00 5.28
2603 3791 0.884704 CGCTAATCATTGGGTCCGGG 60.885 60.000 0.00 0.00 0.00 5.73
2604 3792 0.105964 TCGCTAATCATTGGGTCCGG 59.894 55.000 0.00 0.00 0.00 5.14
2605 3793 2.169832 ATCGCTAATCATTGGGTCCG 57.830 50.000 0.00 0.00 0.00 4.79
2606 3794 4.832248 TCATATCGCTAATCATTGGGTCC 58.168 43.478 0.00 0.00 0.00 4.46
2607 3795 5.482908 ACTCATATCGCTAATCATTGGGTC 58.517 41.667 0.00 0.00 0.00 4.46
2608 3796 5.489792 ACTCATATCGCTAATCATTGGGT 57.510 39.130 0.00 0.00 0.00 4.51
2609 3797 6.045318 CCTACTCATATCGCTAATCATTGGG 58.955 44.000 0.00 0.00 0.00 4.12
2610 3798 6.045318 CCCTACTCATATCGCTAATCATTGG 58.955 44.000 0.00 0.00 0.00 3.16
2611 3799 5.521735 GCCCTACTCATATCGCTAATCATTG 59.478 44.000 0.00 0.00 0.00 2.82
2612 3800 5.665459 GCCCTACTCATATCGCTAATCATT 58.335 41.667 0.00 0.00 0.00 2.57
2613 3801 4.202060 CGCCCTACTCATATCGCTAATCAT 60.202 45.833 0.00 0.00 0.00 2.45
2614 3802 3.128764 CGCCCTACTCATATCGCTAATCA 59.871 47.826 0.00 0.00 0.00 2.57
2615 3803 3.489398 CCGCCCTACTCATATCGCTAATC 60.489 52.174 0.00 0.00 0.00 1.75
2616 3804 2.427453 CCGCCCTACTCATATCGCTAAT 59.573 50.000 0.00 0.00 0.00 1.73
2617 3805 1.816835 CCGCCCTACTCATATCGCTAA 59.183 52.381 0.00 0.00 0.00 3.09
2618 3806 1.003928 TCCGCCCTACTCATATCGCTA 59.996 52.381 0.00 0.00 0.00 4.26
2619 3807 0.251209 TCCGCCCTACTCATATCGCT 60.251 55.000 0.00 0.00 0.00 4.93
2620 3808 0.601558 TTCCGCCCTACTCATATCGC 59.398 55.000 0.00 0.00 0.00 4.58
2621 3809 2.417379 CCATTCCGCCCTACTCATATCG 60.417 54.545 0.00 0.00 0.00 2.92
2622 3810 2.832129 TCCATTCCGCCCTACTCATATC 59.168 50.000 0.00 0.00 0.00 1.63
2623 3811 2.902608 TCCATTCCGCCCTACTCATAT 58.097 47.619 0.00 0.00 0.00 1.78
2624 3812 2.391926 TCCATTCCGCCCTACTCATA 57.608 50.000 0.00 0.00 0.00 2.15
2625 3813 1.417890 CTTCCATTCCGCCCTACTCAT 59.582 52.381 0.00 0.00 0.00 2.90
2626 3814 0.830648 CTTCCATTCCGCCCTACTCA 59.169 55.000 0.00 0.00 0.00 3.41
2627 3815 0.106894 CCTTCCATTCCGCCCTACTC 59.893 60.000 0.00 0.00 0.00 2.59
2628 3816 1.984288 GCCTTCCATTCCGCCCTACT 61.984 60.000 0.00 0.00 0.00 2.57
2629 3817 1.526225 GCCTTCCATTCCGCCCTAC 60.526 63.158 0.00 0.00 0.00 3.18
2630 3818 1.998438 TGCCTTCCATTCCGCCCTA 60.998 57.895 0.00 0.00 0.00 3.53
2631 3819 3.338250 TGCCTTCCATTCCGCCCT 61.338 61.111 0.00 0.00 0.00 5.19
2632 3820 2.265467 TAGTGCCTTCCATTCCGCCC 62.265 60.000 0.00 0.00 0.00 6.13
2633 3821 0.815615 CTAGTGCCTTCCATTCCGCC 60.816 60.000 0.00 0.00 0.00 6.13
2634 3822 0.178068 TCTAGTGCCTTCCATTCCGC 59.822 55.000 0.00 0.00 0.00 5.54
2635 3823 1.202580 CCTCTAGTGCCTTCCATTCCG 60.203 57.143 0.00 0.00 0.00 4.30
2636 3824 2.119495 TCCTCTAGTGCCTTCCATTCC 58.881 52.381 0.00 0.00 0.00 3.01
2637 3825 3.452627 TCTTCCTCTAGTGCCTTCCATTC 59.547 47.826 0.00 0.00 0.00 2.67
2638 3826 3.454858 TCTTCCTCTAGTGCCTTCCATT 58.545 45.455 0.00 0.00 0.00 3.16
2639 3827 3.121929 TCTTCCTCTAGTGCCTTCCAT 57.878 47.619 0.00 0.00 0.00 3.41
2640 3828 2.623418 TCTTCCTCTAGTGCCTTCCA 57.377 50.000 0.00 0.00 0.00 3.53
2641 3829 3.491792 CGATTCTTCCTCTAGTGCCTTCC 60.492 52.174 0.00 0.00 0.00 3.46
2642 3830 3.491792 CCGATTCTTCCTCTAGTGCCTTC 60.492 52.174 0.00 0.00 0.00 3.46
2643 3831 2.432510 CCGATTCTTCCTCTAGTGCCTT 59.567 50.000 0.00 0.00 0.00 4.35
2644 3832 2.035632 CCGATTCTTCCTCTAGTGCCT 58.964 52.381 0.00 0.00 0.00 4.75
2645 3833 2.032620 TCCGATTCTTCCTCTAGTGCC 58.967 52.381 0.00 0.00 0.00 5.01
2646 3834 2.691011 AGTCCGATTCTTCCTCTAGTGC 59.309 50.000 0.00 0.00 0.00 4.40
2647 3835 4.517453 CCTAGTCCGATTCTTCCTCTAGTG 59.483 50.000 0.00 0.00 0.00 2.74
2648 3836 4.166531 ACCTAGTCCGATTCTTCCTCTAGT 59.833 45.833 0.00 0.00 0.00 2.57
2649 3837 4.721132 ACCTAGTCCGATTCTTCCTCTAG 58.279 47.826 0.00 0.00 0.00 2.43
2650 3838 4.792513 ACCTAGTCCGATTCTTCCTCTA 57.207 45.455 0.00 0.00 0.00 2.43
2651 3839 3.673543 ACCTAGTCCGATTCTTCCTCT 57.326 47.619 0.00 0.00 0.00 3.69
2652 3840 4.159879 TGAAACCTAGTCCGATTCTTCCTC 59.840 45.833 0.00 0.00 0.00 3.71
2653 3841 4.094476 TGAAACCTAGTCCGATTCTTCCT 58.906 43.478 0.00 0.00 0.00 3.36
2654 3842 4.467198 TGAAACCTAGTCCGATTCTTCC 57.533 45.455 0.00 0.00 0.00 3.46
2655 3843 6.986904 ATTTGAAACCTAGTCCGATTCTTC 57.013 37.500 0.00 0.00 0.00 2.87
2656 3844 7.447238 TGAAATTTGAAACCTAGTCCGATTCTT 59.553 33.333 0.00 0.00 0.00 2.52
2657 3845 6.940298 TGAAATTTGAAACCTAGTCCGATTCT 59.060 34.615 0.00 0.00 0.00 2.40
2658 3846 7.141100 TGAAATTTGAAACCTAGTCCGATTC 57.859 36.000 0.00 0.00 0.00 2.52
2659 3847 7.703058 ATGAAATTTGAAACCTAGTCCGATT 57.297 32.000 0.00 0.00 0.00 3.34
2660 3848 7.703058 AATGAAATTTGAAACCTAGTCCGAT 57.297 32.000 0.00 0.00 26.74 4.18
2661 3849 7.519032 AAATGAAATTTGAAACCTAGTCCGA 57.481 32.000 0.00 0.00 46.55 4.55


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

AutoCloner maintained by Alex Coulton.