Multiple sequence alignment - TraesCS1D01G068100

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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 TraesCS1D01G068100 chr1D 100.000 3458 0 0 1 3458 49763689 49767146 0.000000e+00 6386.0
1 TraesCS1D01G068100 chr1D 90.311 1899 150 17 750 2643 33984427 33986296 0.000000e+00 2457.0
2 TraesCS1D01G068100 chr1D 95.302 745 29 5 1 743 78985211 78984471 0.000000e+00 1177.0
3 TraesCS1D01G068100 chr1D 93.818 275 6 4 2643 2910 157783475 157783745 1.490000e-108 403.0
4 TraesCS1D01G068100 chr1D 93.190 279 5 6 2643 2910 446802754 446803029 6.950000e-107 398.0
5 TraesCS1D01G068100 chr1D 91.429 280 12 5 2641 2912 110983147 110983422 1.170000e-99 374.0
6 TraesCS1D01G068100 chr1B 94.865 1928 66 10 746 2643 70232867 70234791 0.000000e+00 2981.0
7 TraesCS1D01G068100 chr1B 89.756 1923 158 20 750 2642 4954376 4952463 0.000000e+00 2423.0
8 TraesCS1D01G068100 chr1B 89.245 1934 165 19 746 2647 4597502 4595580 0.000000e+00 2379.0
9 TraesCS1D01G068100 chr1B 88.986 1943 166 24 745 2643 46830270 46828332 0.000000e+00 2359.0
10 TraesCS1D01G068100 chr1B 88.987 1916 170 23 750 2640 4110266 4112165 0.000000e+00 2331.0
11 TraesCS1D01G068100 chr1B 90.191 1784 152 12 750 2527 4518911 4517145 0.000000e+00 2303.0
12 TraesCS1D01G068100 chr1B 93.659 552 22 7 2910 3458 70234789 70235330 0.000000e+00 813.0
13 TraesCS1D01G068100 chr5D 92.006 1914 108 20 746 2634 57819620 57821513 0.000000e+00 2645.0
14 TraesCS1D01G068100 chr5D 95.161 744 32 3 1 743 117191902 117191162 0.000000e+00 1171.0
15 TraesCS1D01G068100 chr5D 94.814 752 33 5 1 750 260982999 260983746 0.000000e+00 1168.0
16 TraesCS1D01G068100 chr5D 90.370 540 38 6 2928 3458 535495093 535494559 0.000000e+00 697.0
17 TraesCS1D01G068100 chr5D 93.190 279 5 4 2643 2910 341635185 341634910 6.950000e-107 398.0
18 TraesCS1D01G068100 chr5D 92.727 275 10 4 2643 2910 209326749 209326478 4.190000e-104 388.0
19 TraesCS1D01G068100 chr5B 91.898 1913 114 18 746 2634 60825903 60824008 0.000000e+00 2636.0
20 TraesCS1D01G068100 chr1A 89.942 1899 156 16 750 2642 32545671 32547540 0.000000e+00 2416.0
21 TraesCS1D01G068100 chr1A 90.828 1679 127 7 989 2643 3013330 3015005 0.000000e+00 2222.0
22 TraesCS1D01G068100 chr1A 91.197 284 14 4 2641 2916 370889270 370888990 3.260000e-100 375.0
23 TraesCS1D01G068100 chr3D 89.219 1920 162 16 750 2643 560024797 560022897 0.000000e+00 2357.0
24 TraesCS1D01G068100 chr6D 88.854 1920 167 19 750 2643 51343000 51344898 0.000000e+00 2316.0
25 TraesCS1D01G068100 chr6D 88.646 1920 170 24 750 2643 51068277 51070174 0.000000e+00 2294.0
26 TraesCS1D01G068100 chr6D 85.560 464 44 16 2928 3382 53174022 53173573 6.760000e-127 464.0
27 TraesCS1D01G068100 chr6D 94.615 260 2 4 2643 2893 345168379 345168635 3.240000e-105 392.0
28 TraesCS1D01G068100 chr6D 85.028 354 34 10 3116 3458 50958572 50958917 3.300000e-90 342.0
29 TraesCS1D01G068100 chr6D 73.457 324 52 22 2928 3229 51350778 51351089 1.320000e-14 91.6
30 TraesCS1D01G068100 chr6D 75.229 218 34 13 3022 3229 50951186 50951393 6.150000e-13 86.1
31 TraesCS1D01G068100 chr6B 89.065 1829 153 18 835 2638 120317314 120315508 0.000000e+00 2226.0
32 TraesCS1D01G068100 chr6B 76.098 205 32 12 3034 3229 120310484 120310288 1.320000e-14 91.6
33 TraesCS1D01G068100 chr7B 89.157 1780 145 25 750 2527 591461715 591463448 0.000000e+00 2174.0
34 TraesCS1D01G068100 chr4D 95.618 753 29 4 1 750 360627182 360626431 0.000000e+00 1205.0
35 TraesCS1D01G068100 chr4D 95.053 748 31 5 1 746 41531803 41531060 0.000000e+00 1171.0
36 TraesCS1D01G068100 chr7D 95.225 754 29 6 1 750 296730714 296729964 0.000000e+00 1186.0
37 TraesCS1D01G068100 chr7D 95.315 747 28 5 1 743 307924136 307924879 0.000000e+00 1179.0
38 TraesCS1D01G068100 chr7D 95.073 751 32 4 1 749 545129487 545128740 0.000000e+00 1177.0
39 TraesCS1D01G068100 chr2D 94.702 755 35 5 1 752 492236108 492235356 0.000000e+00 1168.0
40 TraesCS1D01G068100 chr2D 95.349 258 2 3 2643 2893 478093520 478093774 5.380000e-108 401.0
41 TraesCS1D01G068100 chr6A 83.425 543 57 21 2928 3456 64165867 64165344 1.120000e-129 473.0
42 TraesCS1D01G068100 chr6A 91.901 284 12 4 2641 2916 55294552 55294832 1.510000e-103 387.0
43 TraesCS1D01G068100 chr6A 77.880 217 29 13 3022 3229 64172707 64172501 2.180000e-22 117.0


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 TraesCS1D01G068100 chr1D 49763689 49767146 3457 False 6386 6386 100.000 1 3458 1 chr1D.!!$F2 3457
1 TraesCS1D01G068100 chr1D 33984427 33986296 1869 False 2457 2457 90.311 750 2643 1 chr1D.!!$F1 1893
2 TraesCS1D01G068100 chr1D 78984471 78985211 740 True 1177 1177 95.302 1 743 1 chr1D.!!$R1 742
3 TraesCS1D01G068100 chr1B 4952463 4954376 1913 True 2423 2423 89.756 750 2642 1 chr1B.!!$R3 1892
4 TraesCS1D01G068100 chr1B 4595580 4597502 1922 True 2379 2379 89.245 746 2647 1 chr1B.!!$R2 1901
5 TraesCS1D01G068100 chr1B 46828332 46830270 1938 True 2359 2359 88.986 745 2643 1 chr1B.!!$R4 1898
6 TraesCS1D01G068100 chr1B 4110266 4112165 1899 False 2331 2331 88.987 750 2640 1 chr1B.!!$F1 1890
7 TraesCS1D01G068100 chr1B 4517145 4518911 1766 True 2303 2303 90.191 750 2527 1 chr1B.!!$R1 1777
8 TraesCS1D01G068100 chr1B 70232867 70235330 2463 False 1897 2981 94.262 746 3458 2 chr1B.!!$F2 2712
9 TraesCS1D01G068100 chr5D 57819620 57821513 1893 False 2645 2645 92.006 746 2634 1 chr5D.!!$F1 1888
10 TraesCS1D01G068100 chr5D 117191162 117191902 740 True 1171 1171 95.161 1 743 1 chr5D.!!$R1 742
11 TraesCS1D01G068100 chr5D 260982999 260983746 747 False 1168 1168 94.814 1 750 1 chr5D.!!$F2 749
12 TraesCS1D01G068100 chr5D 535494559 535495093 534 True 697 697 90.370 2928 3458 1 chr5D.!!$R4 530
13 TraesCS1D01G068100 chr5B 60824008 60825903 1895 True 2636 2636 91.898 746 2634 1 chr5B.!!$R1 1888
14 TraesCS1D01G068100 chr1A 32545671 32547540 1869 False 2416 2416 89.942 750 2642 1 chr1A.!!$F2 1892
15 TraesCS1D01G068100 chr1A 3013330 3015005 1675 False 2222 2222 90.828 989 2643 1 chr1A.!!$F1 1654
16 TraesCS1D01G068100 chr3D 560022897 560024797 1900 True 2357 2357 89.219 750 2643 1 chr3D.!!$R1 1893
17 TraesCS1D01G068100 chr6D 51343000 51344898 1898 False 2316 2316 88.854 750 2643 1 chr6D.!!$F4 1893
18 TraesCS1D01G068100 chr6D 51068277 51070174 1897 False 2294 2294 88.646 750 2643 1 chr6D.!!$F3 1893
19 TraesCS1D01G068100 chr6B 120315508 120317314 1806 True 2226 2226 89.065 835 2638 1 chr6B.!!$R2 1803
20 TraesCS1D01G068100 chr7B 591461715 591463448 1733 False 2174 2174 89.157 750 2527 1 chr7B.!!$F1 1777
21 TraesCS1D01G068100 chr4D 360626431 360627182 751 True 1205 1205 95.618 1 750 1 chr4D.!!$R2 749
22 TraesCS1D01G068100 chr4D 41531060 41531803 743 True 1171 1171 95.053 1 746 1 chr4D.!!$R1 745
23 TraesCS1D01G068100 chr7D 296729964 296730714 750 True 1186 1186 95.225 1 750 1 chr7D.!!$R1 749
24 TraesCS1D01G068100 chr7D 307924136 307924879 743 False 1179 1179 95.315 1 743 1 chr7D.!!$F1 742
25 TraesCS1D01G068100 chr7D 545128740 545129487 747 True 1177 1177 95.073 1 749 1 chr7D.!!$R2 748
26 TraesCS1D01G068100 chr2D 492235356 492236108 752 True 1168 1168 94.702 1 752 1 chr2D.!!$R1 751
27 TraesCS1D01G068100 chr6A 64165344 64165867 523 True 473 473 83.425 2928 3456 1 chr6A.!!$R1 528

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
315 321 2.336945 TAGTCTTGATCTCGCGGGTA 57.663 50.0 5.57 0.0 0.0 3.69 F
1180 1238 0.033920 AGCACTGACATCGTTCTGCA 59.966 50.0 0.00 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2136 2205 0.032678 CCTTCATCCCCTCGTCATCG 59.967 60.0 0.0 0.0 38.55 3.84 R
2913 3021 0.403271 AAGAATGAGTGGTGCCTGCT 59.597 50.0 0.0 0.0 0.00 4.24 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
53 54 6.049790 AGAGAACTTGACACTTGACCTTAAC 58.950 40.000 0.00 0.00 0.00 2.01
315 321 2.336945 TAGTCTTGATCTCGCGGGTA 57.663 50.000 5.57 0.00 0.00 3.69
799 819 6.972328 GCTTATGAAGAACACACAAGTTTTGA 59.028 34.615 0.00 0.00 0.00 2.69
808 828 5.757886 ACACACAAGTTTTGAATGGATACG 58.242 37.500 0.00 0.00 42.51 3.06
825 849 7.222000 TGGATACGGAAAATGCTAAAACTTT 57.778 32.000 0.00 0.00 42.51 2.66
1029 1087 4.154347 CCGGAGGCTCTGCTGACC 62.154 72.222 18.14 0.00 46.14 4.02
1139 1197 1.530323 GGTGCTATCCGTGTTGGTTT 58.470 50.000 0.00 0.00 39.52 3.27
1146 1204 3.495434 ATCCGTGTTGGTTTTGGTCTA 57.505 42.857 0.00 0.00 39.52 2.59
1180 1238 0.033920 AGCACTGACATCGTTCTGCA 59.966 50.000 0.00 0.00 0.00 4.41
1184 1242 0.320683 CTGACATCGTTCTGCACCCA 60.321 55.000 0.00 0.00 0.00 4.51
1339 1397 2.624838 TGCTCATGCATCGATGACTCTA 59.375 45.455 29.20 9.11 45.31 2.43
1465 1524 3.030291 AGTCTATCTGCTCTCCACCTTG 58.970 50.000 0.00 0.00 0.00 3.61
1470 1529 0.389166 CTGCTCTCCACCTTGTCGAC 60.389 60.000 9.11 9.11 0.00 4.20
1637 1697 5.360591 TGAGTTTGAGAGGAAAAGAGACAC 58.639 41.667 0.00 0.00 0.00 3.67
1665 1734 1.072173 TGTCTTCCAGGTGATGTGGTG 59.928 52.381 0.00 0.00 36.37 4.17
1691 1760 2.961741 ACTCCTCGTATGATGCTCACAT 59.038 45.455 0.00 0.00 39.98 3.21
1813 1882 5.006386 AGTGTAAAGGATTGGAGAAGCTTG 58.994 41.667 2.10 0.00 0.00 4.01
1814 1883 4.762251 GTGTAAAGGATTGGAGAAGCTTGT 59.238 41.667 2.10 0.00 0.00 3.16
1881 1950 3.429141 CGGAGCTGCAGCAACCTG 61.429 66.667 38.24 27.66 45.16 4.00
2026 2095 4.586001 AGACGGTAGACCTCAACTTTACAA 59.414 41.667 0.00 0.00 0.00 2.41
2086 2155 0.035458 AGAGGGTTTTCTGGTGCTCG 59.965 55.000 0.00 0.00 0.00 5.03
2136 2205 2.854805 GCTCAACAACGCCAACTTCTTC 60.855 50.000 0.00 0.00 0.00 2.87
2214 2283 5.560183 GCTTATATTGTGTCATGCGGTAACC 60.560 44.000 0.00 0.00 0.00 2.85
2226 2295 3.800826 GGTAACCGATGCTGGGATT 57.199 52.632 0.00 0.00 0.00 3.01
2263 2332 3.920231 TGCCATGCTTGAGTAATCTCT 57.080 42.857 0.22 0.00 40.98 3.10
2461 2531 8.716674 AATTGGTCTTGGCATCTATTAATGAT 57.283 30.769 0.00 0.00 0.00 2.45
2532 2626 0.897621 TCAGTGTGCATCATCCGACT 59.102 50.000 0.00 0.00 0.00 4.18
2548 2642 6.602009 TCATCCGACTTAGATTCACTTGTCTA 59.398 38.462 0.00 0.00 32.73 2.59
2643 2751 6.095377 GGCATCTGGTGAATGAAACTTTAAG 58.905 40.000 0.00 0.00 0.00 1.85
2647 2755 9.219603 CATCTGGTGAATGAAACTTTAAGACTA 57.780 33.333 0.00 0.00 0.00 2.59
2648 2756 8.603242 TCTGGTGAATGAAACTTTAAGACTAC 57.397 34.615 0.00 0.00 0.00 2.73
2649 2757 7.660208 TCTGGTGAATGAAACTTTAAGACTACC 59.340 37.037 0.00 0.00 0.00 3.18
2650 2758 6.713450 TGGTGAATGAAACTTTAAGACTACCC 59.287 38.462 0.00 0.00 0.00 3.69
2651 2759 6.713450 GGTGAATGAAACTTTAAGACTACCCA 59.287 38.462 0.00 0.00 0.00 4.51
2652 2760 7.308408 GGTGAATGAAACTTTAAGACTACCCAC 60.308 40.741 0.00 0.00 0.00 4.61
2653 2761 7.227910 GTGAATGAAACTTTAAGACTACCCACA 59.772 37.037 0.00 0.00 0.00 4.17
2654 2762 7.776030 TGAATGAAACTTTAAGACTACCCACAA 59.224 33.333 0.00 0.00 0.00 3.33
2655 2763 8.706322 AATGAAACTTTAAGACTACCCACAAT 57.294 30.769 0.00 0.00 0.00 2.71
2656 2764 7.504924 TGAAACTTTAAGACTACCCACAATG 57.495 36.000 0.00 0.00 0.00 2.82
2657 2765 6.488683 TGAAACTTTAAGACTACCCACAATGG 59.511 38.462 0.00 0.00 37.25 3.16
2673 2781 6.601332 CCACAATGGGAATAACATAGGTAGT 58.399 40.000 0.00 0.00 32.67 2.73
2674 2782 7.741785 CCACAATGGGAATAACATAGGTAGTA 58.258 38.462 0.00 0.00 32.67 1.82
2675 2783 8.215050 CCACAATGGGAATAACATAGGTAGTAA 58.785 37.037 0.00 0.00 32.67 2.24
2676 2784 9.052759 CACAATGGGAATAACATAGGTAGTAAC 57.947 37.037 0.00 0.00 0.00 2.50
2677 2785 8.774183 ACAATGGGAATAACATAGGTAGTAACA 58.226 33.333 0.00 0.00 0.00 2.41
2678 2786 9.793259 CAATGGGAATAACATAGGTAGTAACAT 57.207 33.333 0.00 0.00 0.00 2.71
2680 2788 8.555896 TGGGAATAACATAGGTAGTAACATCA 57.444 34.615 0.00 0.00 0.00 3.07
2681 2789 8.426489 TGGGAATAACATAGGTAGTAACATCAC 58.574 37.037 0.00 0.00 0.00 3.06
2682 2790 8.426489 GGGAATAACATAGGTAGTAACATCACA 58.574 37.037 0.00 0.00 0.00 3.58
2683 2791 9.257651 GGAATAACATAGGTAGTAACATCACAC 57.742 37.037 0.00 0.00 0.00 3.82
2684 2792 9.811995 GAATAACATAGGTAGTAACATCACACA 57.188 33.333 0.00 0.00 0.00 3.72
2688 2796 9.982651 AACATAGGTAGTAACATCACACATATC 57.017 33.333 0.00 0.00 0.00 1.63
2689 2797 9.368416 ACATAGGTAGTAACATCACACATATCT 57.632 33.333 0.00 0.00 0.00 1.98
2693 2801 9.815306 AGGTAGTAACATCACACATATCTAGAT 57.185 33.333 10.73 10.73 0.00 1.98
2711 2819 7.839680 TCTAGATAAAGTAGATGATGTGGCA 57.160 36.000 0.00 0.00 0.00 4.92
2712 2820 8.250143 TCTAGATAAAGTAGATGATGTGGCAA 57.750 34.615 0.00 0.00 0.00 4.52
2713 2821 8.363390 TCTAGATAAAGTAGATGATGTGGCAAG 58.637 37.037 0.00 0.00 0.00 4.01
2714 2822 5.762218 AGATAAAGTAGATGATGTGGCAAGC 59.238 40.000 0.00 0.00 0.00 4.01
2715 2823 3.354948 AAGTAGATGATGTGGCAAGCA 57.645 42.857 0.00 0.00 0.00 3.91
2716 2824 3.354948 AGTAGATGATGTGGCAAGCAA 57.645 42.857 0.00 0.00 0.00 3.91
2717 2825 3.894759 AGTAGATGATGTGGCAAGCAAT 58.105 40.909 0.00 0.00 0.00 3.56
2718 2826 5.039920 AGTAGATGATGTGGCAAGCAATA 57.960 39.130 0.00 0.00 0.00 1.90
2719 2827 5.439721 AGTAGATGATGTGGCAAGCAATAA 58.560 37.500 0.00 0.00 0.00 1.40
2720 2828 5.887598 AGTAGATGATGTGGCAAGCAATAAA 59.112 36.000 0.00 0.00 0.00 1.40
2721 2829 5.864418 AGATGATGTGGCAAGCAATAAAT 57.136 34.783 0.00 0.00 0.00 1.40
2722 2830 5.597806 AGATGATGTGGCAAGCAATAAATG 58.402 37.500 0.00 0.00 0.00 2.32
2723 2831 5.361571 AGATGATGTGGCAAGCAATAAATGA 59.638 36.000 0.00 0.00 0.00 2.57
2724 2832 5.402997 TGATGTGGCAAGCAATAAATGAA 57.597 34.783 0.00 0.00 0.00 2.57
2725 2833 5.412640 TGATGTGGCAAGCAATAAATGAAG 58.587 37.500 0.00 0.00 0.00 3.02
2726 2834 5.185442 TGATGTGGCAAGCAATAAATGAAGA 59.815 36.000 0.00 0.00 0.00 2.87
2727 2835 5.465532 TGTGGCAAGCAATAAATGAAGAA 57.534 34.783 0.00 0.00 0.00 2.52
2728 2836 5.851720 TGTGGCAAGCAATAAATGAAGAAA 58.148 33.333 0.00 0.00 0.00 2.52
2729 2837 5.927689 TGTGGCAAGCAATAAATGAAGAAAG 59.072 36.000 0.00 0.00 0.00 2.62
2730 2838 6.158598 GTGGCAAGCAATAAATGAAGAAAGA 58.841 36.000 0.00 0.00 0.00 2.52
2731 2839 6.309737 GTGGCAAGCAATAAATGAAGAAAGAG 59.690 38.462 0.00 0.00 0.00 2.85
2732 2840 6.209192 TGGCAAGCAATAAATGAAGAAAGAGA 59.791 34.615 0.00 0.00 0.00 3.10
2733 2841 6.750963 GGCAAGCAATAAATGAAGAAAGAGAG 59.249 38.462 0.00 0.00 0.00 3.20
2734 2842 6.750963 GCAAGCAATAAATGAAGAAAGAGAGG 59.249 38.462 0.00 0.00 0.00 3.69
2735 2843 7.362401 GCAAGCAATAAATGAAGAAAGAGAGGA 60.362 37.037 0.00 0.00 0.00 3.71
2736 2844 8.517878 CAAGCAATAAATGAAGAAAGAGAGGAA 58.482 33.333 0.00 0.00 0.00 3.36
2737 2845 8.641498 AGCAATAAATGAAGAAAGAGAGGAAA 57.359 30.769 0.00 0.00 0.00 3.13
2738 2846 8.738106 AGCAATAAATGAAGAAAGAGAGGAAAG 58.262 33.333 0.00 0.00 0.00 2.62
2739 2847 8.518702 GCAATAAATGAAGAAAGAGAGGAAAGT 58.481 33.333 0.00 0.00 0.00 2.66
2745 2853 9.713713 AATGAAGAAAGAGAGGAAAGTAGTAAC 57.286 33.333 0.00 0.00 0.00 2.50
2746 2854 8.246430 TGAAGAAAGAGAGGAAAGTAGTAACA 57.754 34.615 0.00 0.00 0.00 2.41
2747 2855 8.871125 TGAAGAAAGAGAGGAAAGTAGTAACAT 58.129 33.333 0.00 0.00 0.00 2.71
2750 2858 8.471609 AGAAAGAGAGGAAAGTAGTAACATAGC 58.528 37.037 0.00 0.00 0.00 2.97
2751 2859 7.964666 AAGAGAGGAAAGTAGTAACATAGCT 57.035 36.000 0.00 0.00 0.00 3.32
2752 2860 9.476928 AAAGAGAGGAAAGTAGTAACATAGCTA 57.523 33.333 0.00 0.00 0.00 3.32
2753 2861 8.685838 AGAGAGGAAAGTAGTAACATAGCTAG 57.314 38.462 0.00 0.00 0.00 3.42
2754 2862 8.276477 AGAGAGGAAAGTAGTAACATAGCTAGT 58.724 37.037 0.00 0.00 0.00 2.57
2755 2863 9.558396 GAGAGGAAAGTAGTAACATAGCTAGTA 57.442 37.037 0.00 0.00 0.00 1.82
2756 2864 9.563748 AGAGGAAAGTAGTAACATAGCTAGTAG 57.436 37.037 0.00 0.00 0.00 2.57
2757 2865 9.341078 GAGGAAAGTAGTAACATAGCTAGTAGT 57.659 37.037 0.00 0.00 0.00 2.73
2770 2878 9.794719 ACATAGCTAGTAGTATGAGTAACATCA 57.205 33.333 18.64 0.00 40.07 3.07
2772 2880 9.794719 ATAGCTAGTAGTATGAGTAACATCACA 57.205 33.333 0.00 0.00 40.07 3.58
2773 2881 7.932335 AGCTAGTAGTATGAGTAACATCACAC 58.068 38.462 0.00 0.00 40.07 3.82
2774 2882 7.556635 AGCTAGTAGTATGAGTAACATCACACA 59.443 37.037 0.00 0.00 40.07 3.72
2775 2883 8.353684 GCTAGTAGTATGAGTAACATCACACAT 58.646 37.037 0.00 0.00 40.07 3.21
2781 2889 9.755804 AGTATGAGTAACATCACACATATCAAG 57.244 33.333 0.00 0.00 40.07 3.02
2782 2890 8.982685 GTATGAGTAACATCACACATATCAAGG 58.017 37.037 0.00 0.00 40.07 3.61
2783 2891 5.817296 TGAGTAACATCACACATATCAAGGC 59.183 40.000 0.00 0.00 0.00 4.35
2784 2892 5.744171 AGTAACATCACACATATCAAGGCA 58.256 37.500 0.00 0.00 0.00 4.75
2785 2893 6.179756 AGTAACATCACACATATCAAGGCAA 58.820 36.000 0.00 0.00 0.00 4.52
2786 2894 5.571784 AACATCACACATATCAAGGCAAG 57.428 39.130 0.00 0.00 0.00 4.01
2787 2895 4.847198 ACATCACACATATCAAGGCAAGA 58.153 39.130 0.00 0.00 0.00 3.02
2788 2896 5.443283 ACATCACACATATCAAGGCAAGAT 58.557 37.500 0.00 0.00 0.00 2.40
2789 2897 5.298527 ACATCACACATATCAAGGCAAGATG 59.701 40.000 0.00 0.00 36.24 2.90
2790 2898 4.847198 TCACACATATCAAGGCAAGATGT 58.153 39.130 2.43 0.00 0.00 3.06
2793 2901 5.165911 CACATATCAAGGCAAGATGTGTC 57.834 43.478 15.13 0.00 43.18 3.67
2795 2903 6.051074 CACATATCAAGGCAAGATGTGTCTA 58.949 40.000 15.13 0.00 43.11 2.59
2796 2904 6.709397 CACATATCAAGGCAAGATGTGTCTAT 59.291 38.462 15.13 0.00 43.11 1.98
2797 2905 7.874528 CACATATCAAGGCAAGATGTGTCTATA 59.125 37.037 15.13 0.00 43.11 1.31
2798 2906 8.093307 ACATATCAAGGCAAGATGTGTCTATAG 58.907 37.037 13.16 0.00 43.11 1.31
2799 2907 4.697514 TCAAGGCAAGATGTGTCTATAGC 58.302 43.478 0.00 0.00 43.11 2.97
2800 2908 3.760580 AGGCAAGATGTGTCTATAGCC 57.239 47.619 0.00 0.00 41.69 3.93
2801 2909 3.312890 AGGCAAGATGTGTCTATAGCCT 58.687 45.455 11.05 11.05 41.69 4.58
2802 2910 4.483950 AGGCAAGATGTGTCTATAGCCTA 58.516 43.478 13.74 0.00 46.63 3.93
2803 2911 4.901849 AGGCAAGATGTGTCTATAGCCTAA 59.098 41.667 13.74 0.00 46.63 2.69
2804 2912 5.545723 AGGCAAGATGTGTCTATAGCCTAAT 59.454 40.000 13.74 0.00 46.63 1.73
2805 2913 6.726299 AGGCAAGATGTGTCTATAGCCTAATA 59.274 38.462 13.74 0.00 46.63 0.98
2806 2914 7.235606 AGGCAAGATGTGTCTATAGCCTAATAA 59.764 37.037 13.74 0.00 46.63 1.40
2807 2915 7.878127 GGCAAGATGTGTCTATAGCCTAATAAA 59.122 37.037 0.00 0.00 40.78 1.40
2808 2916 9.442047 GCAAGATGTGTCTATAGCCTAATAAAT 57.558 33.333 0.00 0.00 33.30 1.40
2814 2922 9.764363 TGTGTCTATAGCCTAATAAATGAAGTG 57.236 33.333 0.00 0.00 0.00 3.16
2815 2923 9.765795 GTGTCTATAGCCTAATAAATGAAGTGT 57.234 33.333 0.00 0.00 0.00 3.55
2818 2926 9.273016 TCTATAGCCTAATAAATGAAGTGTTGC 57.727 33.333 0.00 0.00 0.00 4.17
2819 2927 7.880160 ATAGCCTAATAAATGAAGTGTTGCA 57.120 32.000 0.00 0.00 0.00 4.08
2820 2928 6.780457 AGCCTAATAAATGAAGTGTTGCAT 57.220 33.333 0.00 0.00 0.00 3.96
2821 2929 6.567050 AGCCTAATAAATGAAGTGTTGCATG 58.433 36.000 0.00 0.00 0.00 4.06
2822 2930 6.153340 AGCCTAATAAATGAAGTGTTGCATGT 59.847 34.615 0.00 0.00 0.00 3.21
2823 2931 6.813152 GCCTAATAAATGAAGTGTTGCATGTT 59.187 34.615 0.00 0.00 0.00 2.71
2824 2932 7.973388 GCCTAATAAATGAAGTGTTGCATGTTA 59.027 33.333 0.00 0.00 0.00 2.41
2825 2933 9.289303 CCTAATAAATGAAGTGTTGCATGTTAC 57.711 33.333 0.00 0.00 0.00 2.50
2826 2934 9.289303 CTAATAAATGAAGTGTTGCATGTTACC 57.711 33.333 0.00 0.00 0.00 2.85
2827 2935 5.528043 AAATGAAGTGTTGCATGTTACCA 57.472 34.783 0.00 0.00 0.00 3.25
2828 2936 3.980646 TGAAGTGTTGCATGTTACCAC 57.019 42.857 0.00 0.00 0.00 4.16
2829 2937 3.282885 TGAAGTGTTGCATGTTACCACA 58.717 40.909 0.00 0.00 37.31 4.17
2830 2938 3.066064 TGAAGTGTTGCATGTTACCACAC 59.934 43.478 7.36 7.36 35.03 3.82
2831 2939 2.649190 AGTGTTGCATGTTACCACACA 58.351 42.857 15.74 0.00 35.03 3.72
2832 2940 3.221771 AGTGTTGCATGTTACCACACAT 58.778 40.909 15.74 1.51 37.93 3.21
2833 2941 4.393834 AGTGTTGCATGTTACCACACATA 58.606 39.130 15.74 0.00 35.51 2.29
2834 2942 5.009631 AGTGTTGCATGTTACCACACATAT 58.990 37.500 15.74 0.00 35.51 1.78
2835 2943 5.094812 GTGTTGCATGTTACCACACATATG 58.905 41.667 10.02 0.00 35.51 1.78
2836 2944 4.764308 TGTTGCATGTTACCACACATATGT 59.236 37.500 1.41 1.41 40.80 2.29
2837 2945 5.242615 TGTTGCATGTTACCACACATATGTT 59.757 36.000 5.37 0.00 36.72 2.71
2838 2946 6.431234 TGTTGCATGTTACCACACATATGTTA 59.569 34.615 5.37 0.00 36.72 2.41
2839 2947 6.429791 TGCATGTTACCACACATATGTTAC 57.570 37.500 5.37 0.00 36.72 2.50
2840 2948 6.176896 TGCATGTTACCACACATATGTTACT 58.823 36.000 5.37 0.00 36.72 2.24
2841 2949 6.315144 TGCATGTTACCACACATATGTTACTC 59.685 38.462 5.37 0.00 36.72 2.59
2842 2950 6.238374 GCATGTTACCACACATATGTTACTCC 60.238 42.308 5.37 0.00 36.72 3.85
2843 2951 5.736813 TGTTACCACACATATGTTACTCCC 58.263 41.667 5.37 0.00 36.72 4.30
2844 2952 3.926058 ACCACACATATGTTACTCCCC 57.074 47.619 5.37 0.00 36.72 4.81
2845 2953 3.186283 ACCACACATATGTTACTCCCCA 58.814 45.455 5.37 0.00 36.72 4.96
2846 2954 3.054655 ACCACACATATGTTACTCCCCAC 60.055 47.826 5.37 0.00 36.72 4.61
2847 2955 3.199946 CCACACATATGTTACTCCCCACT 59.800 47.826 5.37 0.00 36.72 4.00
2848 2956 4.407621 CCACACATATGTTACTCCCCACTA 59.592 45.833 5.37 0.00 36.72 2.74
2849 2957 5.071788 CCACACATATGTTACTCCCCACTAT 59.928 44.000 5.37 0.00 36.72 2.12
2850 2958 6.269077 CCACACATATGTTACTCCCCACTATA 59.731 42.308 5.37 0.00 36.72 1.31
2851 2959 7.378966 CACACATATGTTACTCCCCACTATAG 58.621 42.308 5.37 0.00 36.72 1.31
2852 2960 7.232737 CACACATATGTTACTCCCCACTATAGA 59.767 40.741 5.37 0.00 36.72 1.98
2853 2961 7.451877 ACACATATGTTACTCCCCACTATAGAG 59.548 40.741 5.37 0.00 34.46 2.43
2854 2962 6.954684 ACATATGTTACTCCCCACTATAGAGG 59.045 42.308 6.78 8.10 31.70 3.69
2855 2963 4.894252 TGTTACTCCCCACTATAGAGGT 57.106 45.455 14.29 0.00 31.70 3.85
2856 2964 5.999987 TGTTACTCCCCACTATAGAGGTA 57.000 43.478 14.29 2.62 31.70 3.08
2857 2965 5.950023 TGTTACTCCCCACTATAGAGGTAG 58.050 45.833 14.29 12.87 31.70 3.18
2858 2966 5.434376 TGTTACTCCCCACTATAGAGGTAGT 59.566 44.000 18.82 18.82 35.34 2.73
2859 2967 6.621098 TGTTACTCCCCACTATAGAGGTAGTA 59.379 42.308 17.42 17.42 33.29 1.82
2860 2968 7.129349 TGTTACTCCCCACTATAGAGGTAGTAA 59.871 40.741 23.15 23.15 33.91 2.24
2861 2969 5.951204 ACTCCCCACTATAGAGGTAGTAAC 58.049 45.833 14.29 0.00 33.29 2.50
2862 2970 5.434376 ACTCCCCACTATAGAGGTAGTAACA 59.566 44.000 14.29 0.00 33.29 2.41
2863 2971 6.104392 ACTCCCCACTATAGAGGTAGTAACAT 59.896 42.308 14.29 0.00 33.29 2.71
2864 2972 7.296628 ACTCCCCACTATAGAGGTAGTAACATA 59.703 40.741 14.29 0.00 33.29 2.29
2865 2973 7.696981 TCCCCACTATAGAGGTAGTAACATAG 58.303 42.308 14.29 0.00 33.29 2.23
2866 2974 7.518653 TCCCCACTATAGAGGTAGTAACATAGA 59.481 40.741 14.29 0.00 33.29 1.98
2867 2975 8.168725 CCCCACTATAGAGGTAGTAACATAGAA 58.831 40.741 14.29 0.00 33.29 2.10
2868 2976 9.584008 CCCACTATAGAGGTAGTAACATAGAAA 57.416 37.037 14.29 0.00 33.29 2.52
2882 2990 8.368668 AGTAACATAGAAACTAGTATCATGGGC 58.631 37.037 0.00 0.00 0.00 5.36
2883 2991 6.747414 ACATAGAAACTAGTATCATGGGCA 57.253 37.500 0.00 0.00 0.00 5.36
2884 2992 7.321717 ACATAGAAACTAGTATCATGGGCAT 57.678 36.000 0.00 0.00 0.00 4.40
2885 2993 7.164122 ACATAGAAACTAGTATCATGGGCATG 58.836 38.462 0.00 0.00 40.09 4.06
2886 2994 5.636903 AGAAACTAGTATCATGGGCATGT 57.363 39.130 0.00 0.00 39.72 3.21
2887 2995 6.006275 AGAAACTAGTATCATGGGCATGTT 57.994 37.500 0.00 0.00 39.72 2.71
2888 2996 6.426587 AGAAACTAGTATCATGGGCATGTTT 58.573 36.000 0.00 0.00 39.72 2.83
2889 2997 7.573710 AGAAACTAGTATCATGGGCATGTTTA 58.426 34.615 0.00 0.00 39.72 2.01
2890 2998 7.499232 AGAAACTAGTATCATGGGCATGTTTAC 59.501 37.037 0.00 0.00 39.72 2.01
2891 2999 6.500589 ACTAGTATCATGGGCATGTTTACT 57.499 37.500 0.00 5.66 39.57 2.24
2892 3000 7.612065 ACTAGTATCATGGGCATGTTTACTA 57.388 36.000 0.00 6.50 38.48 1.82
2893 3001 7.442656 ACTAGTATCATGGGCATGTTTACTAC 58.557 38.462 0.00 0.00 38.48 2.73
2894 3002 5.621193 AGTATCATGGGCATGTTTACTACC 58.379 41.667 2.05 0.00 37.22 3.18
2895 3003 3.290948 TCATGGGCATGTTTACTACCC 57.709 47.619 0.00 0.00 39.72 3.69
2898 3006 3.748645 TGGGCATGTTTACTACCCATT 57.251 42.857 1.22 0.00 45.65 3.16
2899 3007 3.360867 TGGGCATGTTTACTACCCATTG 58.639 45.455 1.22 0.00 45.65 2.82
2900 3008 3.245443 TGGGCATGTTTACTACCCATTGT 60.245 43.478 1.22 0.00 45.65 2.71
2901 3009 3.130340 GGGCATGTTTACTACCCATTGTG 59.870 47.826 0.00 0.00 40.52 3.33
2902 3010 3.130340 GGCATGTTTACTACCCATTGTGG 59.870 47.826 0.00 0.00 37.25 4.17
2903 3011 3.428862 GCATGTTTACTACCCATTGTGGC 60.429 47.826 0.00 0.00 35.79 5.01
2904 3012 3.799432 TGTTTACTACCCATTGTGGCT 57.201 42.857 0.00 0.00 35.79 4.75
2905 3013 4.912317 TGTTTACTACCCATTGTGGCTA 57.088 40.909 0.00 0.00 35.79 3.93
2906 3014 4.839121 TGTTTACTACCCATTGTGGCTAG 58.161 43.478 0.00 0.00 35.79 3.42
2907 3015 4.287585 TGTTTACTACCCATTGTGGCTAGT 59.712 41.667 8.55 8.55 35.79 2.57
2908 3016 4.748277 TTACTACCCATTGTGGCTAGTC 57.252 45.455 7.13 0.00 35.79 2.59
2909 3017 2.834113 ACTACCCATTGTGGCTAGTCT 58.166 47.619 0.00 0.00 35.79 3.24
2910 3018 3.990369 ACTACCCATTGTGGCTAGTCTA 58.010 45.455 0.00 0.00 35.79 2.59
2911 3019 4.359105 ACTACCCATTGTGGCTAGTCTAA 58.641 43.478 0.00 0.00 35.79 2.10
2912 3020 4.969359 ACTACCCATTGTGGCTAGTCTAAT 59.031 41.667 0.00 0.00 35.79 1.73
2913 3021 6.141083 ACTACCCATTGTGGCTAGTCTAATA 58.859 40.000 0.00 0.00 35.79 0.98
2922 3030 3.033368 GCTAGTCTAATAGCAGGCACC 57.967 52.381 4.66 0.00 46.12 5.01
2933 3041 0.807496 GCAGGCACCACTCATTCTTC 59.193 55.000 0.00 0.00 0.00 2.87
2954 3062 9.871238 TTCTTCTTGCGTAATTTCTACTCTATT 57.129 29.630 0.00 0.00 0.00 1.73
3026 3134 6.472686 TTGCCTGTTTGGTAGTATTGTTTT 57.527 33.333 0.00 0.00 38.35 2.43
3028 3141 6.276847 TGCCTGTTTGGTAGTATTGTTTTTG 58.723 36.000 0.00 0.00 38.35 2.44
3070 3183 5.648960 CCTTTTTACTACGCAGGGGATTTTA 59.351 40.000 0.00 0.00 0.00 1.52
3083 3196 8.665685 CGCAGGGGATTTTAAAGACATATATAC 58.334 37.037 0.00 0.00 0.00 1.47
3156 3269 2.557924 TCAATGTTTCACATGGACCTGC 59.442 45.455 0.00 0.00 37.97 4.85
3199 3314 9.949174 GCTTGTTTTGTTGGAATTGATTTATTT 57.051 25.926 0.00 0.00 0.00 1.40
3204 3319 6.942163 TGTTGGAATTGATTTATTTGGGGA 57.058 33.333 0.00 0.00 0.00 4.81
3205 3320 7.507797 TGTTGGAATTGATTTATTTGGGGAT 57.492 32.000 0.00 0.00 0.00 3.85
3325 3440 2.489938 TGGAAGCTGATGTACAACCC 57.510 50.000 0.00 0.00 0.00 4.11
3348 3463 2.949447 ACTTGAACCACTGAAGGCATT 58.051 42.857 0.00 0.00 0.00 3.56
3349 3464 4.098914 ACTTGAACCACTGAAGGCATTA 57.901 40.909 0.00 0.00 0.00 1.90
3351 3466 4.278419 ACTTGAACCACTGAAGGCATTAAC 59.722 41.667 0.00 0.00 0.00 2.01
3352 3467 3.826524 TGAACCACTGAAGGCATTAACA 58.173 40.909 0.00 0.00 0.00 2.41
3353 3468 4.406456 TGAACCACTGAAGGCATTAACAT 58.594 39.130 0.00 0.00 0.00 2.71
3354 3469 5.565509 TGAACCACTGAAGGCATTAACATA 58.434 37.500 0.00 0.00 0.00 2.29
3355 3470 5.647658 TGAACCACTGAAGGCATTAACATAG 59.352 40.000 0.00 0.00 0.00 2.23
3356 3471 5.435686 ACCACTGAAGGCATTAACATAGA 57.564 39.130 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
148 150 5.752036 ATCAAGAAGTGATCCTGAACTCA 57.248 39.130 0.00 0.00 44.01 3.41
315 321 2.106566 ACGAGGACTCAGCAATCTCAT 58.893 47.619 0.00 0.00 0.00 2.90
715 727 1.202348 CACGATGCGGCTATATCTCCA 59.798 52.381 0.00 0.00 0.00 3.86
743 755 7.187376 GCTTTATTAAGGTAGCTAGCCAGCTT 61.187 42.308 26.51 26.51 42.45 3.74
767 783 3.691118 TGTGTTCTTCATAAGCATGGAGC 59.309 43.478 0.00 0.00 37.65 4.70
799 819 7.404671 AGTTTTAGCATTTTCCGTATCCATT 57.595 32.000 0.00 0.00 0.00 3.16
808 828 9.476202 AGTATTGACAAAGTTTTAGCATTTTCC 57.524 29.630 0.00 0.00 0.00 3.13
983 1039 5.945784 TCCTCCATCGAACAAATTCAATTCT 59.054 36.000 0.00 0.00 34.14 2.40
1029 1087 3.382865 TGGTGATCCTCTTGAGAATCTCG 59.617 47.826 5.73 0.00 32.71 4.04
1139 1197 0.899019 TGTAGCGGTGCATAGACCAA 59.101 50.000 0.00 0.00 35.50 3.67
1180 1238 0.482446 TGCAGATTTGGGAAGTGGGT 59.518 50.000 0.00 0.00 0.00 4.51
1184 1242 3.571401 CACTTTCTGCAGATTTGGGAAGT 59.429 43.478 19.04 19.00 0.00 3.01
1470 1529 5.461526 TCTACAGTGTCGATTTTCTCACAG 58.538 41.667 0.00 0.00 33.84 3.66
1637 1697 6.017357 CACATCACCTGGAAGACAATCATATG 60.017 42.308 0.00 0.00 34.07 1.78
1665 1734 4.216472 TGAGCATCATACGAGGAGTCATAC 59.784 45.833 0.00 0.00 42.56 2.39
1691 1760 9.609346 CACAGCAGAAATCATATATATCCATGA 57.391 33.333 0.00 1.53 35.72 3.07
1813 1882 2.945668 GGGCATGAACATACTCAAGGAC 59.054 50.000 0.00 0.00 0.00 3.85
1814 1883 2.846206 AGGGCATGAACATACTCAAGGA 59.154 45.455 0.00 0.00 0.00 3.36
1881 1950 6.403746 GGTTGAGCCTAAGTAAGATGCTTTTC 60.404 42.308 0.00 0.00 31.23 2.29
2026 2095 1.566298 GGCCAGTCAGGGGAACATCT 61.566 60.000 0.00 0.00 38.09 2.90
2086 2155 1.880027 ACGAATTGGGCAAGACTGAAC 59.120 47.619 0.00 0.00 0.00 3.18
2136 2205 0.032678 CCTTCATCCCCTCGTCATCG 59.967 60.000 0.00 0.00 38.55 3.84
2214 2283 0.811219 TGAAGCGAATCCCAGCATCG 60.811 55.000 0.00 0.00 39.47 3.84
2243 2312 3.198417 TGAGAGATTACTCAAGCATGGCA 59.802 43.478 0.00 0.00 44.79 4.92
2461 2531 6.775142 TCATACTGAAAATTTTGGAGACCACA 59.225 34.615 8.47 0.00 30.78 4.17
2548 2642 6.628644 AAGGTAGAAGGCAATAGAAAGTCT 57.371 37.500 0.00 0.00 0.00 3.24
2649 2757 6.601332 ACTACCTATGTTATTCCCATTGTGG 58.399 40.000 0.00 0.00 37.25 4.17
2650 2758 9.052759 GTTACTACCTATGTTATTCCCATTGTG 57.947 37.037 0.00 0.00 0.00 3.33
2651 2759 8.774183 TGTTACTACCTATGTTATTCCCATTGT 58.226 33.333 0.00 0.00 0.00 2.71
2652 2760 9.793259 ATGTTACTACCTATGTTATTCCCATTG 57.207 33.333 0.00 0.00 0.00 2.82
2654 2762 9.166222 TGATGTTACTACCTATGTTATTCCCAT 57.834 33.333 0.00 0.00 0.00 4.00
2655 2763 8.426489 GTGATGTTACTACCTATGTTATTCCCA 58.574 37.037 0.00 0.00 0.00 4.37
2656 2764 8.426489 TGTGATGTTACTACCTATGTTATTCCC 58.574 37.037 0.00 0.00 0.00 3.97
2657 2765 9.257651 GTGTGATGTTACTACCTATGTTATTCC 57.742 37.037 0.00 0.00 0.00 3.01
2658 2766 9.811995 TGTGTGATGTTACTACCTATGTTATTC 57.188 33.333 0.00 0.00 0.00 1.75
2662 2770 9.982651 GATATGTGTGATGTTACTACCTATGTT 57.017 33.333 0.00 0.00 0.00 2.71
2663 2771 9.368416 AGATATGTGTGATGTTACTACCTATGT 57.632 33.333 0.00 0.00 0.00 2.29
2667 2775 9.815306 ATCTAGATATGTGTGATGTTACTACCT 57.185 33.333 2.53 0.00 0.00 3.08
2685 2793 9.533831 TGCCACATCATCTACTTTATCTAGATA 57.466 33.333 8.44 8.44 31.02 1.98
2686 2794 8.427902 TGCCACATCATCTACTTTATCTAGAT 57.572 34.615 10.73 10.73 32.13 1.98
2687 2795 7.839680 TGCCACATCATCTACTTTATCTAGA 57.160 36.000 0.00 0.00 0.00 2.43
2688 2796 7.117523 GCTTGCCACATCATCTACTTTATCTAG 59.882 40.741 0.00 0.00 0.00 2.43
2689 2797 6.931281 GCTTGCCACATCATCTACTTTATCTA 59.069 38.462 0.00 0.00 0.00 1.98
2690 2798 5.762218 GCTTGCCACATCATCTACTTTATCT 59.238 40.000 0.00 0.00 0.00 1.98
2691 2799 5.528690 TGCTTGCCACATCATCTACTTTATC 59.471 40.000 0.00 0.00 0.00 1.75
2692 2800 5.439721 TGCTTGCCACATCATCTACTTTAT 58.560 37.500 0.00 0.00 0.00 1.40
2693 2801 4.842574 TGCTTGCCACATCATCTACTTTA 58.157 39.130 0.00 0.00 0.00 1.85
2694 2802 3.689347 TGCTTGCCACATCATCTACTTT 58.311 40.909 0.00 0.00 0.00 2.66
2695 2803 3.354948 TGCTTGCCACATCATCTACTT 57.645 42.857 0.00 0.00 0.00 2.24
2696 2804 3.354948 TTGCTTGCCACATCATCTACT 57.645 42.857 0.00 0.00 0.00 2.57
2697 2805 5.756195 TTATTGCTTGCCACATCATCTAC 57.244 39.130 0.00 0.00 0.00 2.59
2698 2806 6.546772 TCATTTATTGCTTGCCACATCATCTA 59.453 34.615 0.00 0.00 0.00 1.98
2699 2807 5.361571 TCATTTATTGCTTGCCACATCATCT 59.638 36.000 0.00 0.00 0.00 2.90
2700 2808 5.593968 TCATTTATTGCTTGCCACATCATC 58.406 37.500 0.00 0.00 0.00 2.92
2701 2809 5.601583 TCATTTATTGCTTGCCACATCAT 57.398 34.783 0.00 0.00 0.00 2.45
2702 2810 5.185442 TCTTCATTTATTGCTTGCCACATCA 59.815 36.000 0.00 0.00 0.00 3.07
2703 2811 5.653507 TCTTCATTTATTGCTTGCCACATC 58.346 37.500 0.00 0.00 0.00 3.06
2704 2812 5.664294 TCTTCATTTATTGCTTGCCACAT 57.336 34.783 0.00 0.00 0.00 3.21
2705 2813 5.465532 TTCTTCATTTATTGCTTGCCACA 57.534 34.783 0.00 0.00 0.00 4.17
2706 2814 6.158598 TCTTTCTTCATTTATTGCTTGCCAC 58.841 36.000 0.00 0.00 0.00 5.01
2707 2815 6.209192 TCTCTTTCTTCATTTATTGCTTGCCA 59.791 34.615 0.00 0.00 0.00 4.92
2708 2816 6.624423 TCTCTTTCTTCATTTATTGCTTGCC 58.376 36.000 0.00 0.00 0.00 4.52
2709 2817 6.750963 CCTCTCTTTCTTCATTTATTGCTTGC 59.249 38.462 0.00 0.00 0.00 4.01
2710 2818 8.048534 TCCTCTCTTTCTTCATTTATTGCTTG 57.951 34.615 0.00 0.00 0.00 4.01
2711 2819 8.641498 TTCCTCTCTTTCTTCATTTATTGCTT 57.359 30.769 0.00 0.00 0.00 3.91
2712 2820 8.641498 TTTCCTCTCTTTCTTCATTTATTGCT 57.359 30.769 0.00 0.00 0.00 3.91
2713 2821 8.518702 ACTTTCCTCTCTTTCTTCATTTATTGC 58.481 33.333 0.00 0.00 0.00 3.56
2719 2827 9.713713 GTTACTACTTTCCTCTCTTTCTTCATT 57.286 33.333 0.00 0.00 0.00 2.57
2720 2828 8.871125 TGTTACTACTTTCCTCTCTTTCTTCAT 58.129 33.333 0.00 0.00 0.00 2.57
2721 2829 8.246430 TGTTACTACTTTCCTCTCTTTCTTCA 57.754 34.615 0.00 0.00 0.00 3.02
2724 2832 8.471609 GCTATGTTACTACTTTCCTCTCTTTCT 58.528 37.037 0.00 0.00 0.00 2.52
2725 2833 8.471609 AGCTATGTTACTACTTTCCTCTCTTTC 58.528 37.037 0.00 0.00 0.00 2.62
2726 2834 8.368962 AGCTATGTTACTACTTTCCTCTCTTT 57.631 34.615 0.00 0.00 0.00 2.52
2727 2835 7.964666 AGCTATGTTACTACTTTCCTCTCTT 57.035 36.000 0.00 0.00 0.00 2.85
2728 2836 8.276477 ACTAGCTATGTTACTACTTTCCTCTCT 58.724 37.037 0.00 0.00 0.00 3.10
2729 2837 8.454570 ACTAGCTATGTTACTACTTTCCTCTC 57.545 38.462 0.00 0.00 0.00 3.20
2730 2838 9.563748 CTACTAGCTATGTTACTACTTTCCTCT 57.436 37.037 0.00 0.00 0.00 3.69
2731 2839 9.341078 ACTACTAGCTATGTTACTACTTTCCTC 57.659 37.037 0.00 0.00 0.00 3.71
2744 2852 9.794719 TGATGTTACTCATACTACTAGCTATGT 57.205 33.333 0.00 0.00 36.83 2.29
2746 2854 9.794719 TGTGATGTTACTCATACTACTAGCTAT 57.205 33.333 0.00 0.00 36.83 2.97
2747 2855 9.053840 GTGTGATGTTACTCATACTACTAGCTA 57.946 37.037 0.00 0.00 36.83 3.32
2748 2856 7.556635 TGTGTGATGTTACTCATACTACTAGCT 59.443 37.037 0.00 0.00 37.92 3.32
2749 2857 7.704271 TGTGTGATGTTACTCATACTACTAGC 58.296 38.462 10.75 0.00 37.92 3.42
2755 2863 9.755804 CTTGATATGTGTGATGTTACTCATACT 57.244 33.333 10.75 3.32 38.84 2.12
2756 2864 8.982685 CCTTGATATGTGTGATGTTACTCATAC 58.017 37.037 0.00 5.35 38.84 2.39
2757 2865 7.657354 GCCTTGATATGTGTGATGTTACTCATA 59.343 37.037 0.00 0.00 39.73 2.15
2758 2866 6.484643 GCCTTGATATGTGTGATGTTACTCAT 59.515 38.462 0.00 0.00 38.11 2.90
2759 2867 5.817296 GCCTTGATATGTGTGATGTTACTCA 59.183 40.000 0.00 0.00 0.00 3.41
2760 2868 5.817296 TGCCTTGATATGTGTGATGTTACTC 59.183 40.000 0.00 0.00 0.00 2.59
2761 2869 5.744171 TGCCTTGATATGTGTGATGTTACT 58.256 37.500 0.00 0.00 0.00 2.24
2762 2870 6.316140 TCTTGCCTTGATATGTGTGATGTTAC 59.684 38.462 0.00 0.00 0.00 2.50
2763 2871 6.413892 TCTTGCCTTGATATGTGTGATGTTA 58.586 36.000 0.00 0.00 0.00 2.41
2764 2872 5.255687 TCTTGCCTTGATATGTGTGATGTT 58.744 37.500 0.00 0.00 0.00 2.71
2765 2873 4.847198 TCTTGCCTTGATATGTGTGATGT 58.153 39.130 0.00 0.00 0.00 3.06
2766 2874 5.298527 ACATCTTGCCTTGATATGTGTGATG 59.701 40.000 0.00 0.00 35.23 3.07
2767 2875 5.298527 CACATCTTGCCTTGATATGTGTGAT 59.701 40.000 0.00 0.00 41.46 3.06
2768 2876 4.637091 CACATCTTGCCTTGATATGTGTGA 59.363 41.667 0.00 0.00 41.46 3.58
2769 2877 4.916870 CACATCTTGCCTTGATATGTGTG 58.083 43.478 0.00 0.00 41.46 3.82
2772 2880 5.108187 AGACACATCTTGCCTTGATATGT 57.892 39.130 0.00 0.00 34.70 2.29
2773 2881 7.064371 GCTATAGACACATCTTGCCTTGATATG 59.936 40.741 3.21 0.00 36.29 1.78
2774 2882 7.102346 GCTATAGACACATCTTGCCTTGATAT 58.898 38.462 3.21 0.00 36.29 1.63
2775 2883 6.459066 GCTATAGACACATCTTGCCTTGATA 58.541 40.000 3.21 0.00 36.29 2.15
2776 2884 5.303971 GCTATAGACACATCTTGCCTTGAT 58.696 41.667 3.21 0.00 36.29 2.57
2777 2885 4.443457 GGCTATAGACACATCTTGCCTTGA 60.443 45.833 3.21 0.00 39.50 3.02
2778 2886 3.812053 GGCTATAGACACATCTTGCCTTG 59.188 47.826 3.21 0.00 39.50 3.61
2779 2887 3.713764 AGGCTATAGACACATCTTGCCTT 59.286 43.478 8.68 0.00 45.01 4.35
2780 2888 3.312890 AGGCTATAGACACATCTTGCCT 58.687 45.455 8.68 0.00 43.78 4.75
2781 2889 3.760580 AGGCTATAGACACATCTTGCC 57.239 47.619 8.68 0.00 41.26 4.52
2782 2890 8.833231 TTTATTAGGCTATAGACACATCTTGC 57.167 34.615 8.68 0.00 36.29 4.01
2788 2896 9.764363 CACTTCATTTATTAGGCTATAGACACA 57.236 33.333 8.68 0.00 0.00 3.72
2789 2897 9.765795 ACACTTCATTTATTAGGCTATAGACAC 57.234 33.333 8.68 0.00 0.00 3.67
2792 2900 9.273016 GCAACACTTCATTTATTAGGCTATAGA 57.727 33.333 3.21 0.00 0.00 1.98
2793 2901 9.056005 TGCAACACTTCATTTATTAGGCTATAG 57.944 33.333 0.00 0.00 0.00 1.31
2794 2902 8.972458 TGCAACACTTCATTTATTAGGCTATA 57.028 30.769 0.00 0.00 0.00 1.31
2795 2903 7.880160 TGCAACACTTCATTTATTAGGCTAT 57.120 32.000 0.00 0.00 0.00 2.97
2796 2904 7.339212 ACATGCAACACTTCATTTATTAGGCTA 59.661 33.333 0.00 0.00 0.00 3.93
2797 2905 6.153340 ACATGCAACACTTCATTTATTAGGCT 59.847 34.615 0.00 0.00 0.00 4.58
2798 2906 6.332630 ACATGCAACACTTCATTTATTAGGC 58.667 36.000 0.00 0.00 0.00 3.93
2799 2907 9.289303 GTAACATGCAACACTTCATTTATTAGG 57.711 33.333 0.00 0.00 0.00 2.69
2800 2908 9.289303 GGTAACATGCAACACTTCATTTATTAG 57.711 33.333 0.00 0.00 0.00 1.73
2801 2909 8.797438 TGGTAACATGCAACACTTCATTTATTA 58.203 29.630 0.00 0.00 46.17 0.98
2802 2910 7.665690 TGGTAACATGCAACACTTCATTTATT 58.334 30.769 0.00 0.00 46.17 1.40
2803 2911 7.225784 TGGTAACATGCAACACTTCATTTAT 57.774 32.000 0.00 0.00 46.17 1.40
2804 2912 6.641169 TGGTAACATGCAACACTTCATTTA 57.359 33.333 0.00 0.00 46.17 1.40
2805 2913 5.528043 TGGTAACATGCAACACTTCATTT 57.472 34.783 0.00 0.00 46.17 2.32
2821 2929 5.121105 GGGGAGTAACATATGTGTGGTAAC 58.879 45.833 9.63 1.91 38.92 2.50
2822 2930 4.783763 TGGGGAGTAACATATGTGTGGTAA 59.216 41.667 9.63 0.00 38.92 2.85
2823 2931 4.162698 GTGGGGAGTAACATATGTGTGGTA 59.837 45.833 9.63 0.00 38.92 3.25
2824 2932 3.054655 GTGGGGAGTAACATATGTGTGGT 60.055 47.826 9.63 0.00 38.92 4.16
2825 2933 3.199946 AGTGGGGAGTAACATATGTGTGG 59.800 47.826 9.63 0.00 38.92 4.17
2826 2934 4.487714 AGTGGGGAGTAACATATGTGTG 57.512 45.455 9.63 0.00 38.92 3.82
2827 2935 7.302948 TCTATAGTGGGGAGTAACATATGTGT 58.697 38.462 9.63 2.63 41.28 3.72
2828 2936 7.093727 CCTCTATAGTGGGGAGTAACATATGTG 60.094 44.444 9.63 0.00 0.00 3.21
2829 2937 6.954684 CCTCTATAGTGGGGAGTAACATATGT 59.045 42.308 12.29 1.41 0.00 2.29
2830 2938 6.954684 ACCTCTATAGTGGGGAGTAACATATG 59.045 42.308 21.82 0.00 33.22 1.78
2831 2939 7.117331 ACCTCTATAGTGGGGAGTAACATAT 57.883 40.000 21.82 0.00 33.22 1.78
2832 2940 6.541264 ACCTCTATAGTGGGGAGTAACATA 57.459 41.667 21.82 0.00 33.22 2.29
2833 2941 5.420215 ACCTCTATAGTGGGGAGTAACAT 57.580 43.478 21.82 0.00 33.22 2.71
2834 2942 4.894252 ACCTCTATAGTGGGGAGTAACA 57.106 45.455 21.82 0.00 33.22 2.41
2835 2943 5.951204 ACTACCTCTATAGTGGGGAGTAAC 58.049 45.833 22.09 0.00 34.02 2.50
2836 2944 7.129349 TGTTACTACCTCTATAGTGGGGAGTAA 59.871 40.741 28.26 28.26 38.03 2.24
2837 2945 6.621098 TGTTACTACCTCTATAGTGGGGAGTA 59.379 42.308 23.32 23.32 36.09 2.59
2838 2946 5.434376 TGTTACTACCTCTATAGTGGGGAGT 59.566 44.000 24.72 24.72 36.09 3.85
2839 2947 5.950023 TGTTACTACCTCTATAGTGGGGAG 58.050 45.833 21.82 20.04 36.09 4.30
2840 2948 5.999987 TGTTACTACCTCTATAGTGGGGA 57.000 43.478 21.82 11.28 36.09 4.81
2841 2949 7.696981 TCTATGTTACTACCTCTATAGTGGGG 58.303 42.308 21.82 16.35 36.09 4.96
2842 2950 9.584008 TTTCTATGTTACTACCTCTATAGTGGG 57.416 37.037 21.82 16.23 36.09 4.61
2856 2964 8.368668 GCCCATGATACTAGTTTCTATGTTACT 58.631 37.037 13.52 0.00 0.00 2.24
2857 2965 8.148351 TGCCCATGATACTAGTTTCTATGTTAC 58.852 37.037 13.52 8.05 0.00 2.50
2858 2966 8.257602 TGCCCATGATACTAGTTTCTATGTTA 57.742 34.615 13.52 0.00 0.00 2.41
2859 2967 7.136822 TGCCCATGATACTAGTTTCTATGTT 57.863 36.000 13.52 0.00 0.00 2.71
2860 2968 6.747414 TGCCCATGATACTAGTTTCTATGT 57.253 37.500 13.52 0.00 0.00 2.29
2861 2969 7.164122 ACATGCCCATGATACTAGTTTCTATG 58.836 38.462 14.69 13.56 41.20 2.23
2862 2970 7.321717 ACATGCCCATGATACTAGTTTCTAT 57.678 36.000 14.69 4.32 41.20 1.98
2863 2971 6.747414 ACATGCCCATGATACTAGTTTCTA 57.253 37.500 14.69 2.38 41.20 2.10
2864 2972 5.636903 ACATGCCCATGATACTAGTTTCT 57.363 39.130 14.69 0.00 41.20 2.52
2865 2973 6.699575 AAACATGCCCATGATACTAGTTTC 57.300 37.500 14.69 3.09 41.20 2.78
2866 2974 7.346471 AGTAAACATGCCCATGATACTAGTTT 58.654 34.615 19.70 0.00 40.05 2.66
2867 2975 6.900194 AGTAAACATGCCCATGATACTAGTT 58.100 36.000 19.70 0.00 40.05 2.24
2868 2976 6.500589 AGTAAACATGCCCATGATACTAGT 57.499 37.500 19.70 0.00 40.05 2.57
2869 2977 6.874134 GGTAGTAAACATGCCCATGATACTAG 59.126 42.308 23.09 0.00 41.63 2.57
2870 2978 6.239772 GGGTAGTAAACATGCCCATGATACTA 60.240 42.308 21.01 21.01 41.01 1.82
2871 2979 5.456186 GGGTAGTAAACATGCCCATGATACT 60.456 44.000 22.23 22.23 42.09 2.12
2872 2980 4.760204 GGGTAGTAAACATGCCCATGATAC 59.240 45.833 14.69 14.82 41.20 2.24
2873 2981 4.413851 TGGGTAGTAAACATGCCCATGATA 59.586 41.667 14.69 5.17 43.75 2.15
2874 2982 3.204158 TGGGTAGTAAACATGCCCATGAT 59.796 43.478 14.69 0.18 43.75 2.45
2875 2983 2.578480 TGGGTAGTAAACATGCCCATGA 59.422 45.455 14.69 0.00 43.75 3.07
2876 2984 3.011566 TGGGTAGTAAACATGCCCATG 57.988 47.619 6.71 6.71 43.75 3.66
2879 2987 3.130340 CACAATGGGTAGTAAACATGCCC 59.870 47.826 0.00 0.00 39.73 5.36
2880 2988 3.130340 CCACAATGGGTAGTAAACATGCC 59.870 47.826 0.00 0.00 32.67 4.40
2881 2989 3.428862 GCCACAATGGGTAGTAAACATGC 60.429 47.826 0.00 0.00 38.19 4.06
2882 2990 4.370364 GCCACAATGGGTAGTAAACATG 57.630 45.455 0.00 0.00 38.19 3.21
2893 3001 4.202357 TGCTATTAGACTAGCCACAATGGG 60.202 45.833 0.00 0.00 42.85 4.00
2894 3002 4.960938 TGCTATTAGACTAGCCACAATGG 58.039 43.478 0.00 0.00 42.85 3.16
2895 3003 4.993584 CCTGCTATTAGACTAGCCACAATG 59.006 45.833 0.00 0.00 42.85 2.82
2896 3004 4.503991 GCCTGCTATTAGACTAGCCACAAT 60.504 45.833 0.00 0.00 42.85 2.71
2897 3005 3.181465 GCCTGCTATTAGACTAGCCACAA 60.181 47.826 0.00 0.00 42.85 3.33
2898 3006 2.365617 GCCTGCTATTAGACTAGCCACA 59.634 50.000 0.00 0.00 42.85 4.17
2899 3007 2.365617 TGCCTGCTATTAGACTAGCCAC 59.634 50.000 0.00 0.00 42.85 5.01
2900 3008 2.365617 GTGCCTGCTATTAGACTAGCCA 59.634 50.000 0.00 0.00 42.85 4.75
2901 3009 2.289133 GGTGCCTGCTATTAGACTAGCC 60.289 54.545 0.00 0.00 42.85 3.93
2902 3010 2.365617 TGGTGCCTGCTATTAGACTAGC 59.634 50.000 0.00 0.00 43.61 3.42
2903 3011 3.639094 AGTGGTGCCTGCTATTAGACTAG 59.361 47.826 0.00 0.00 0.00 2.57
2904 3012 3.637229 GAGTGGTGCCTGCTATTAGACTA 59.363 47.826 0.00 0.00 0.00 2.59
2905 3013 2.432510 GAGTGGTGCCTGCTATTAGACT 59.567 50.000 0.00 0.00 0.00 3.24
2906 3014 2.168521 TGAGTGGTGCCTGCTATTAGAC 59.831 50.000 0.00 0.00 0.00 2.59
2907 3015 2.466846 TGAGTGGTGCCTGCTATTAGA 58.533 47.619 0.00 0.00 0.00 2.10
2908 3016 2.988010 TGAGTGGTGCCTGCTATTAG 57.012 50.000 0.00 0.00 0.00 1.73
2909 3017 3.455910 AGAATGAGTGGTGCCTGCTATTA 59.544 43.478 0.00 0.00 0.00 0.98
2910 3018 2.240667 AGAATGAGTGGTGCCTGCTATT 59.759 45.455 0.00 0.00 0.00 1.73
2911 3019 1.842562 AGAATGAGTGGTGCCTGCTAT 59.157 47.619 0.00 0.00 0.00 2.97
2912 3020 1.279496 AGAATGAGTGGTGCCTGCTA 58.721 50.000 0.00 0.00 0.00 3.49
2913 3021 0.403271 AAGAATGAGTGGTGCCTGCT 59.597 50.000 0.00 0.00 0.00 4.24
2922 3030 6.835914 AGAAATTACGCAAGAAGAATGAGTG 58.164 36.000 0.00 0.00 43.62 3.51
2954 3062 8.439993 TTGTGCGGATTACAAAATAGCTATAA 57.560 30.769 6.68 0.00 35.29 0.98
3026 3134 6.783708 AAGGGTTCACAACATTTCTTACAA 57.216 33.333 0.00 0.00 0.00 2.41
3028 3141 9.027129 GTAAAAAGGGTTCACAACATTTCTTAC 57.973 33.333 0.00 0.00 0.00 2.34
3070 3183 5.832539 AGCAGGCAGGTATATATGTCTTT 57.167 39.130 0.00 0.00 0.00 2.52
3083 3196 1.131126 CACACGAAAATAGCAGGCAGG 59.869 52.381 0.00 0.00 0.00 4.85
3156 3269 1.137404 GCATGCCGCCTTTGTACTG 59.863 57.895 6.36 0.00 32.94 2.74
3199 3314 3.037549 AGCAACAAAAAGACAATCCCCA 58.962 40.909 0.00 0.00 0.00 4.96
3200 3315 3.751479 AGCAACAAAAAGACAATCCCC 57.249 42.857 0.00 0.00 0.00 4.81
3204 3319 7.903995 TTTTGAGAAGCAACAAAAAGACAAT 57.096 28.000 0.00 0.00 41.08 2.71
3205 3320 7.903995 ATTTTGAGAAGCAACAAAAAGACAA 57.096 28.000 0.00 0.00 44.91 3.18
3279 3394 7.607607 TGAGATGACTACACTGCATTTGTAATT 59.392 33.333 9.06 1.15 0.00 1.40
3325 3440 2.426738 TGCCTTCAGTGGTTCAAGTTTG 59.573 45.455 0.00 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.