Multiple sequence alignment - TraesCS5D01G033800

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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 TraesCS5D01G033800 chr5D 100.000 5387 0 0 1 5387 32691188 32696574 0.000000e+00 9949.0
1 TraesCS5D01G033800 chr5D 88.707 549 58 2 1577 2124 483514874 483515419 0.000000e+00 667.0
2 TraesCS5D01G033800 chr5D 97.674 129 2 1 5214 5342 32696156 32696283 2.530000e-53 220.0
3 TraesCS5D01G033800 chr5D 97.674 129 2 1 4969 5096 32696401 32696529 2.530000e-53 220.0
4 TraesCS5D01G033800 chr5D 83.125 160 27 0 11 170 372093970 372094129 4.350000e-31 147.0
5 TraesCS5D01G033800 chr5D 97.619 42 0 1 4921 4962 32695986 32696026 2.690000e-08 71.3
6 TraesCS5D01G033800 chr5D 97.619 42 0 1 4799 4839 32696108 32696149 2.690000e-08 71.3
7 TraesCS5D01G033800 chr5B 97.522 4156 84 8 758 4911 24096916 24101054 0.000000e+00 7086.0
8 TraesCS5D01G033800 chr5B 95.960 297 11 1 5088 5384 24101059 24101354 1.050000e-131 481.0
9 TraesCS5D01G033800 chr5B 86.068 323 17 5 5088 5384 24094868 24095188 6.730000e-84 322.0
10 TraesCS5D01G033800 chr5B 85.581 215 19 3 4694 4908 24094654 24094856 1.180000e-51 215.0
11 TraesCS5D01G033800 chr5B 94.574 129 6 1 4969 5096 24101184 24101312 1.180000e-46 198.0
12 TraesCS5D01G033800 chr5A 97.281 4156 90 9 756 4908 21407816 21411951 0.000000e+00 7027.0
13 TraesCS5D01G033800 chr5A 89.021 419 42 3 336 751 637103000 637102583 2.880000e-142 516.0
14 TraesCS5D01G033800 chr5A 89.130 414 41 4 336 747 637103830 637103419 3.720000e-141 512.0
15 TraesCS5D01G033800 chr5A 88.489 417 38 5 332 747 637104644 637104237 3.750000e-136 496.0
16 TraesCS5D01G033800 chr5A 91.290 310 21 4 1 307 21407467 21407773 8.350000e-113 418.0
17 TraesCS5D01G033800 chr5A 85.507 276 13 6 5088 5337 21411963 21412237 4.140000e-66 263.0
18 TraesCS5D01G033800 chr5A 85.075 134 7 2 4969 5089 21412101 21412234 2.040000e-24 124.0
19 TraesCS5D01G033800 chrUn 100.000 418 0 0 3983 4400 477032214 477031797 0.000000e+00 773.0
20 TraesCS5D01G033800 chrUn 92.011 363 26 2 362 721 9906492 9906854 1.730000e-139 507.0
21 TraesCS5D01G033800 chr7B 92.180 422 30 3 332 751 1365187 1365607 1.290000e-165 593.0
22 TraesCS5D01G033800 chr2D 90.974 421 30 4 332 751 582151661 582151248 1.310000e-155 560.0
23 TraesCS5D01G033800 chr1D 88.471 425 40 5 334 751 37961531 37961109 6.230000e-139 505.0
24 TraesCS5D01G033800 chr2A 87.972 424 45 5 332 751 136338417 136337996 3.750000e-136 496.0
25 TraesCS5D01G033800 chr7D 87.775 409 42 7 335 738 71840810 71841215 6.320000e-129 472.0
26 TraesCS5D01G033800 chr7D 100.000 28 0 0 1390 1417 248426305 248426332 1.000000e-02 52.8
27 TraesCS5D01G033800 chr6A 81.818 176 32 0 8 183 56069020 56069195 1.210000e-31 148.0
28 TraesCS5D01G033800 chr6D 80.571 175 34 0 9 183 103206248 103206422 9.410000e-28 135.0
29 TraesCS5D01G033800 chr3B 78.723 188 40 0 12 199 49304626 49304439 5.660000e-25 126.0
30 TraesCS5D01G033800 chr1B 77.576 165 37 0 11 175 199569975 199570139 3.430000e-17 100.0
31 TraesCS5D01G033800 chr7A 97.561 41 1 0 4622 4662 617552679 617552719 2.690000e-08 71.3


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 TraesCS5D01G033800 chr5D 32691188 32696574 5386 False 2106.32 9949 98.11720 1 5387 5 chr5D.!!$F3 5386
1 TraesCS5D01G033800 chr5D 483514874 483515419 545 False 667.00 667 88.70700 1577 2124 1 chr5D.!!$F2 547
2 TraesCS5D01G033800 chr5B 24094654 24101354 6700 False 1660.40 7086 91.94100 758 5384 5 chr5B.!!$F1 4626
3 TraesCS5D01G033800 chr5A 21407467 21412237 4770 False 1958.00 7027 89.78825 1 5337 4 chr5A.!!$F1 5336
4 TraesCS5D01G033800 chr5A 637102583 637104644 2061 True 508.00 516 88.88000 332 751 3 chr5A.!!$R1 419

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
183 184 0.105039 GTTGTCGCTAGCTGGCCTAT 59.895 55.000 17.22 0.0 0.00 2.57 F
752 1566 1.003580 TCTCATGCAAGTCTTCCCCAC 59.996 52.381 0.00 0.0 0.00 4.61 F
830 3637 1.337917 GGAGGACCCTGAAACGAGAAC 60.338 57.143 0.00 0.0 0.00 3.01 F
837 3644 1.344763 CCTGAAACGAGAACTGGGACT 59.655 52.381 0.00 0.0 0.00 3.85 F
2799 5609 0.035439 CGGTGGTATGGGTTTCAGCT 60.035 55.000 0.00 0.0 0.00 4.24 F
3495 6411 0.034756 GGGTTTTGCCATGGGTGTTC 59.965 55.000 15.13 0.0 39.65 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1732 4542 0.321671 CGGTTCTTGAAGCTGGAGGA 59.678 55.000 10.24 0.0 0.00 3.71 R
1824 4634 0.817013 ACACTGGCACAAACAACAGG 59.183 50.000 0.00 0.0 38.70 4.00 R
2667 5477 7.550906 ACAGATAATCTTCTTACAAGAGCCAAC 59.449 37.037 0.00 0.0 36.22 3.77 R
2865 5675 3.044156 AGCTTGCCAGATCTTCATCCTA 58.956 45.455 0.00 0.0 0.00 2.94 R
3981 6897 0.107643 TGTCACCGAATCCTGCAACA 59.892 50.000 0.00 0.0 0.00 3.33 R
5070 7990 0.040067 CAACAAGTCGAAAGCTGGCC 60.040 55.000 0.00 0.0 0.00 5.36 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
45 46 1.859427 ATTGCTGTTCTGGTGCGCTG 61.859 55.000 9.73 0.00 0.00 5.18
81 82 7.148787 GGTCTTAACACGATGACTTTCTAACTG 60.149 40.741 0.00 0.00 0.00 3.16
95 96 9.182933 GACTTTCTAACTGTCTAGTACAACAAG 57.817 37.037 0.00 0.00 37.74 3.16
99 100 8.015185 TCTAACTGTCTAGTACAACAAGGTTT 57.985 34.615 0.00 0.00 37.74 3.27
102 103 6.053650 ACTGTCTAGTACAACAAGGTTTTCC 58.946 40.000 0.00 0.00 37.74 3.13
111 112 1.074951 AAGGTTTTCCCAGCTCCGG 59.925 57.895 0.00 0.00 41.86 5.14
134 135 2.872388 CGAGGGACGATGATGGGGG 61.872 68.421 0.00 0.00 45.77 5.40
180 181 0.806492 GTAGTTGTCGCTAGCTGGCC 60.806 60.000 17.22 3.79 0.00 5.36
181 182 0.970937 TAGTTGTCGCTAGCTGGCCT 60.971 55.000 17.22 9.62 0.00 5.19
182 183 0.970937 AGTTGTCGCTAGCTGGCCTA 60.971 55.000 17.22 1.68 0.00 3.93
183 184 0.105039 GTTGTCGCTAGCTGGCCTAT 59.895 55.000 17.22 0.00 0.00 2.57
184 185 1.340248 GTTGTCGCTAGCTGGCCTATA 59.660 52.381 17.22 0.22 0.00 1.31
201 202 9.739276 CTGGCCTATAAAACTGGATATAATCAA 57.261 33.333 3.32 0.00 0.00 2.57
225 226 4.565166 TGTTACTTCTTGTGTTCTGTCACG 59.435 41.667 0.00 0.00 40.74 4.35
226 227 3.520290 ACTTCTTGTGTTCTGTCACGA 57.480 42.857 0.00 0.00 40.74 4.35
355 359 3.259374 GGGAGACTTGTGTGAGATCTCAA 59.741 47.826 26.70 14.14 41.85 3.02
466 875 7.826260 TTGATGTTCAACCTCAAAAAGTTTC 57.174 32.000 5.83 0.00 31.43 2.78
482 891 5.966742 AAGTTTCAGCTCCTAATTCAACC 57.033 39.130 0.00 0.00 0.00 3.77
525 934 4.906618 AGACAAAACGGGATGTGAATAGT 58.093 39.130 0.00 0.00 0.00 2.12
575 1389 6.209192 TGCCACTATTCACATCTGAATTTGTT 59.791 34.615 1.29 0.00 43.48 2.83
615 1429 7.440523 AAAATACTTCGAGTTTTGAGCTGAT 57.559 32.000 0.00 0.00 0.00 2.90
647 1461 5.392703 GGAGTTGTAGACATACGTCACATGA 60.393 44.000 0.00 0.00 45.23 3.07
739 1553 9.304731 GATCTCATCTAATGTAAGATCTCATGC 57.695 37.037 0.00 0.00 33.87 4.06
747 1561 7.551035 AATGTAAGATCTCATGCAAGTCTTC 57.449 36.000 0.00 0.00 32.02 2.87
748 1562 5.423015 TGTAAGATCTCATGCAAGTCTTCC 58.577 41.667 0.00 0.00 32.02 3.46
749 1563 3.557228 AGATCTCATGCAAGTCTTCCC 57.443 47.619 0.00 0.00 0.00 3.97
750 1564 2.172293 AGATCTCATGCAAGTCTTCCCC 59.828 50.000 0.00 0.00 0.00 4.81
751 1565 1.361204 TCTCATGCAAGTCTTCCCCA 58.639 50.000 0.00 0.00 0.00 4.96
752 1566 1.003580 TCTCATGCAAGTCTTCCCCAC 59.996 52.381 0.00 0.00 0.00 4.61
754 1568 1.003580 TCATGCAAGTCTTCCCCACTC 59.996 52.381 0.00 0.00 0.00 3.51
761 1575 3.767309 AGTCTTCCCCACTCTACAGAT 57.233 47.619 0.00 0.00 0.00 2.90
788 3594 5.485662 ACTCGAAAGGAAAGAAAACACAG 57.514 39.130 0.00 0.00 0.00 3.66
809 3616 2.055042 CAGTCCCTAGGCTCTGCGT 61.055 63.158 15.20 0.00 0.00 5.24
815 3622 1.754621 CTAGGCTCTGCGTGGAGGA 60.755 63.158 0.00 0.00 34.21 3.71
830 3637 1.337917 GGAGGACCCTGAAACGAGAAC 60.338 57.143 0.00 0.00 0.00 3.01
836 3643 1.608283 CCCTGAAACGAGAACTGGGAC 60.608 57.143 0.00 0.00 42.69 4.46
837 3644 1.344763 CCTGAAACGAGAACTGGGACT 59.655 52.381 0.00 0.00 0.00 3.85
906 3713 1.689243 CGATCTGGGCCATCCTGTCA 61.689 60.000 6.72 0.00 36.08 3.58
1047 3857 3.934962 GGCCGCCTCCTCATCTCC 61.935 72.222 0.71 0.00 0.00 3.71
1195 4005 4.039357 CACACTCGTCCGGCTCGT 62.039 66.667 15.93 0.06 0.00 4.18
1392 4202 3.121030 CAGGGCGCCTTCTTCACG 61.121 66.667 28.56 0.76 0.00 4.35
1722 4532 3.131223 TGGTCTTCTATTGGCTCTTCTCG 59.869 47.826 0.00 0.00 0.00 4.04
1824 4634 1.509787 CTGCGTGCATGCGTTGTAC 60.510 57.895 25.05 3.98 37.56 2.90
2710 5520 1.417890 CTGTTGACCAGAGAGTTGGGT 59.582 52.381 0.00 0.00 44.49 4.51
2751 5561 9.784531 ATCTTGACTTGTCTCTATTCTTCAAAA 57.215 29.630 2.35 0.00 0.00 2.44
2799 5609 0.035439 CGGTGGTATGGGTTTCAGCT 60.035 55.000 0.00 0.00 0.00 4.24
3027 5837 1.832883 TGTTGTCTGGTGTTGCTTGT 58.167 45.000 0.00 0.00 0.00 3.16
3076 5886 0.035881 TGCCCAGTCAGCAAAGAGAG 59.964 55.000 0.00 0.00 37.28 3.20
3330 6246 2.040278 TGAGTTGAGGGCTTTGTATGCT 59.960 45.455 0.00 0.00 0.00 3.79
3456 6372 7.169982 GCAGTCTTTATAGTATTCACGCATCTT 59.830 37.037 0.00 0.00 0.00 2.40
3495 6411 0.034756 GGGTTTTGCCATGGGTGTTC 59.965 55.000 15.13 0.00 39.65 3.18
3520 6436 6.123651 TCTTTGTTAGTAGCTTTGTTCCCAA 58.876 36.000 0.00 0.00 0.00 4.12
3566 6482 0.687427 AGGGCCAACAGTTTTGCAGT 60.687 50.000 6.18 0.00 0.00 4.40
3567 6483 0.177836 GGGCCAACAGTTTTGCAGTT 59.822 50.000 4.39 0.00 0.00 3.16
3901 6817 3.490439 TCATCTGCCTTGTTCTCAACA 57.510 42.857 0.00 0.00 40.21 3.33
3978 6894 7.020827 TCTACTTTTGAACCAGGATTCAGAT 57.979 36.000 0.00 0.00 39.68 2.90
3981 6897 9.401058 CTACTTTTGAACCAGGATTCAGATATT 57.599 33.333 0.00 0.00 39.68 1.28
4518 7436 7.552687 TGGTAATCACTTTTGTACTGGATGATC 59.447 37.037 0.00 0.00 0.00 2.92
4785 7703 0.393944 CCCGTTAGCTTTTCCCCTCC 60.394 60.000 0.00 0.00 0.00 4.30
4881 7801 2.297315 AGATCGAGTCACTGTTTGAGCA 59.703 45.455 0.00 0.00 33.71 4.26
4911 7831 5.420455 AGAGAGACATAGAGGAGGGATAGA 58.580 45.833 0.00 0.00 0.00 1.98
4912 7832 6.038609 AGAGAGACATAGAGGAGGGATAGAT 58.961 44.000 0.00 0.00 0.00 1.98
4913 7833 6.508920 AGAGAGACATAGAGGAGGGATAGATT 59.491 42.308 0.00 0.00 0.00 2.40
4914 7834 6.493166 AGAGACATAGAGGAGGGATAGATTG 58.507 44.000 0.00 0.00 0.00 2.67
4915 7835 6.276806 AGAGACATAGAGGAGGGATAGATTGA 59.723 42.308 0.00 0.00 0.00 2.57
4916 7836 6.493166 AGACATAGAGGAGGGATAGATTGAG 58.507 44.000 0.00 0.00 0.00 3.02
4917 7837 6.046643 AGACATAGAGGAGGGATAGATTGAGT 59.953 42.308 0.00 0.00 0.00 3.41
4919 7839 4.823364 AGAGGAGGGATAGATTGAGTCA 57.177 45.455 0.00 0.00 0.00 3.41
4920 7840 4.479158 AGAGGAGGGATAGATTGAGTCAC 58.521 47.826 0.00 0.00 0.00 3.67
4921 7841 4.169856 AGAGGAGGGATAGATTGAGTCACT 59.830 45.833 0.00 0.00 0.00 3.41
4922 7842 4.222336 AGGAGGGATAGATTGAGTCACTG 58.778 47.826 0.00 0.00 0.00 3.66
4923 7843 3.964031 GGAGGGATAGATTGAGTCACTGT 59.036 47.826 0.00 0.00 0.00 3.55
4924 7844 4.407296 GGAGGGATAGATTGAGTCACTGTT 59.593 45.833 0.00 0.00 0.00 3.16
4925 7845 5.104735 GGAGGGATAGATTGAGTCACTGTTT 60.105 44.000 0.00 0.00 0.00 2.83
4926 7846 5.738909 AGGGATAGATTGAGTCACTGTTTG 58.261 41.667 0.00 0.00 0.00 2.93
4927 7847 5.249393 AGGGATAGATTGAGTCACTGTTTGT 59.751 40.000 0.00 0.00 0.00 2.83
4928 7848 5.940470 GGGATAGATTGAGTCACTGTTTGTT 59.060 40.000 0.00 0.00 0.00 2.83
4929 7849 6.431234 GGGATAGATTGAGTCACTGTTTGTTT 59.569 38.462 0.00 0.00 0.00 2.83
4930 7850 7.301054 GGATAGATTGAGTCACTGTTTGTTTG 58.699 38.462 0.00 0.00 0.00 2.93
4931 7851 5.505173 AGATTGAGTCACTGTTTGTTTGG 57.495 39.130 0.00 0.00 0.00 3.28
4932 7852 5.192927 AGATTGAGTCACTGTTTGTTTGGA 58.807 37.500 0.00 0.00 0.00 3.53
4933 7853 5.652014 AGATTGAGTCACTGTTTGTTTGGAA 59.348 36.000 0.00 0.00 0.00 3.53
4934 7854 5.913137 TTGAGTCACTGTTTGTTTGGAAT 57.087 34.783 0.00 0.00 0.00 3.01
4935 7855 5.913137 TGAGTCACTGTTTGTTTGGAATT 57.087 34.783 0.00 0.00 0.00 2.17
4936 7856 6.279513 TGAGTCACTGTTTGTTTGGAATTT 57.720 33.333 0.00 0.00 0.00 1.82
4937 7857 6.696411 TGAGTCACTGTTTGTTTGGAATTTT 58.304 32.000 0.00 0.00 0.00 1.82
4938 7858 6.811170 TGAGTCACTGTTTGTTTGGAATTTTC 59.189 34.615 0.00 0.00 0.00 2.29
4939 7859 6.935167 AGTCACTGTTTGTTTGGAATTTTCT 58.065 32.000 0.00 0.00 0.00 2.52
4940 7860 7.386059 AGTCACTGTTTGTTTGGAATTTTCTT 58.614 30.769 0.00 0.00 0.00 2.52
4941 7861 7.877612 AGTCACTGTTTGTTTGGAATTTTCTTT 59.122 29.630 0.00 0.00 0.00 2.52
4942 7862 8.503196 GTCACTGTTTGTTTGGAATTTTCTTTT 58.497 29.630 0.00 0.00 0.00 2.27
4943 7863 8.716909 TCACTGTTTGTTTGGAATTTTCTTTTC 58.283 29.630 0.00 0.00 0.00 2.29
4944 7864 8.502387 CACTGTTTGTTTGGAATTTTCTTTTCA 58.498 29.630 0.00 0.00 0.00 2.69
4945 7865 8.720562 ACTGTTTGTTTGGAATTTTCTTTTCAG 58.279 29.630 0.00 0.00 0.00 3.02
4946 7866 7.525759 TGTTTGTTTGGAATTTTCTTTTCAGC 58.474 30.769 0.00 0.00 0.00 4.26
4947 7867 6.676237 TTGTTTGGAATTTTCTTTTCAGCC 57.324 33.333 0.00 0.00 0.00 4.85
4948 7868 4.808364 TGTTTGGAATTTTCTTTTCAGCCG 59.192 37.500 0.00 0.00 0.00 5.52
4949 7869 3.658757 TGGAATTTTCTTTTCAGCCGG 57.341 42.857 0.00 0.00 0.00 6.13
4950 7870 2.962421 TGGAATTTTCTTTTCAGCCGGT 59.038 40.909 1.90 0.00 0.00 5.28
4951 7871 3.386402 TGGAATTTTCTTTTCAGCCGGTT 59.614 39.130 1.90 0.00 0.00 4.44
4952 7872 3.987868 GGAATTTTCTTTTCAGCCGGTTC 59.012 43.478 1.90 0.00 0.00 3.62
4953 7873 4.500716 GGAATTTTCTTTTCAGCCGGTTCA 60.501 41.667 1.90 0.00 0.00 3.18
4954 7874 3.708563 TTTTCTTTTCAGCCGGTTCAG 57.291 42.857 1.90 0.00 0.00 3.02
4955 7875 0.951558 TTCTTTTCAGCCGGTTCAGC 59.048 50.000 1.90 0.00 0.00 4.26
4956 7876 0.889186 TCTTTTCAGCCGGTTCAGCC 60.889 55.000 1.90 0.00 0.00 4.85
4957 7877 0.890996 CTTTTCAGCCGGTTCAGCCT 60.891 55.000 1.90 0.00 34.25 4.58
4958 7878 0.467290 TTTTCAGCCGGTTCAGCCTT 60.467 50.000 1.90 0.00 34.25 4.35
4959 7879 0.467290 TTTCAGCCGGTTCAGCCTTT 60.467 50.000 1.90 0.00 34.25 3.11
4960 7880 0.467290 TTCAGCCGGTTCAGCCTTTT 60.467 50.000 1.90 0.00 34.25 2.27
4961 7881 0.889186 TCAGCCGGTTCAGCCTTTTC 60.889 55.000 1.90 0.00 34.25 2.29
4962 7882 1.966451 AGCCGGTTCAGCCTTTTCG 60.966 57.895 1.90 0.00 34.25 3.46
4963 7883 2.258726 GCCGGTTCAGCCTTTTCGT 61.259 57.895 1.90 0.00 34.25 3.85
4964 7884 1.792118 GCCGGTTCAGCCTTTTCGTT 61.792 55.000 1.90 0.00 34.25 3.85
4965 7885 1.515081 CCGGTTCAGCCTTTTCGTTA 58.485 50.000 0.00 0.00 34.25 3.18
4966 7886 2.081462 CCGGTTCAGCCTTTTCGTTAT 58.919 47.619 0.00 0.00 34.25 1.89
4967 7887 2.486592 CCGGTTCAGCCTTTTCGTTATT 59.513 45.455 0.00 0.00 34.25 1.40
4968 7888 3.685756 CCGGTTCAGCCTTTTCGTTATTA 59.314 43.478 0.00 0.00 34.25 0.98
4969 7889 4.334481 CCGGTTCAGCCTTTTCGTTATTAT 59.666 41.667 0.00 0.00 34.25 1.28
4970 7890 5.263185 CGGTTCAGCCTTTTCGTTATTATG 58.737 41.667 0.00 0.00 34.25 1.90
4971 7891 5.163794 CGGTTCAGCCTTTTCGTTATTATGT 60.164 40.000 0.00 0.00 34.25 2.29
4972 7892 6.617879 GGTTCAGCCTTTTCGTTATTATGTT 58.382 36.000 0.00 0.00 0.00 2.71
4973 7893 6.526674 GGTTCAGCCTTTTCGTTATTATGTTG 59.473 38.462 0.00 0.00 0.00 3.33
4974 7894 5.636837 TCAGCCTTTTCGTTATTATGTTGC 58.363 37.500 0.00 0.00 0.00 4.17
4975 7895 5.414454 TCAGCCTTTTCGTTATTATGTTGCT 59.586 36.000 0.00 0.00 0.00 3.91
4976 7896 5.512788 CAGCCTTTTCGTTATTATGTTGCTG 59.487 40.000 0.00 0.00 35.88 4.41
4977 7897 5.183140 AGCCTTTTCGTTATTATGTTGCTGT 59.817 36.000 0.00 0.00 0.00 4.40
4978 7898 5.861787 GCCTTTTCGTTATTATGTTGCTGTT 59.138 36.000 0.00 0.00 0.00 3.16
4979 7899 6.364976 GCCTTTTCGTTATTATGTTGCTGTTT 59.635 34.615 0.00 0.00 0.00 2.83
4980 7900 7.619161 GCCTTTTCGTTATTATGTTGCTGTTTG 60.619 37.037 0.00 0.00 0.00 2.93
4981 7901 7.381139 CCTTTTCGTTATTATGTTGCTGTTTGT 59.619 33.333 0.00 0.00 0.00 2.83
4982 7902 7.616103 TTTCGTTATTATGTTGCTGTTTGTG 57.384 32.000 0.00 0.00 0.00 3.33
4983 7903 6.307031 TCGTTATTATGTTGCTGTTTGTGT 57.693 33.333 0.00 0.00 0.00 3.72
4984 7904 6.730175 TCGTTATTATGTTGCTGTTTGTGTT 58.270 32.000 0.00 0.00 0.00 3.32
4985 7905 6.853872 TCGTTATTATGTTGCTGTTTGTGTTC 59.146 34.615 0.00 0.00 0.00 3.18
4986 7906 6.855914 CGTTATTATGTTGCTGTTTGTGTTCT 59.144 34.615 0.00 0.00 0.00 3.01
4987 7907 7.149144 CGTTATTATGTTGCTGTTTGTGTTCTG 60.149 37.037 0.00 0.00 0.00 3.02
4988 7908 5.574891 TTATGTTGCTGTTTGTGTTCTGT 57.425 34.783 0.00 0.00 0.00 3.41
4989 7909 3.932545 TGTTGCTGTTTGTGTTCTGTT 57.067 38.095 0.00 0.00 0.00 3.16
4990 7910 3.573598 TGTTGCTGTTTGTGTTCTGTTG 58.426 40.909 0.00 0.00 0.00 3.33
4991 7911 3.005261 TGTTGCTGTTTGTGTTCTGTTGT 59.995 39.130 0.00 0.00 0.00 3.32
4992 7912 3.485947 TGCTGTTTGTGTTCTGTTGTC 57.514 42.857 0.00 0.00 0.00 3.18
4993 7913 2.163412 TGCTGTTTGTGTTCTGTTGTCC 59.837 45.455 0.00 0.00 0.00 4.02
4994 7914 2.423538 GCTGTTTGTGTTCTGTTGTCCT 59.576 45.455 0.00 0.00 0.00 3.85
4995 7915 3.119495 GCTGTTTGTGTTCTGTTGTCCTT 60.119 43.478 0.00 0.00 0.00 3.36
4996 7916 4.414852 CTGTTTGTGTTCTGTTGTCCTTG 58.585 43.478 0.00 0.00 0.00 3.61
4997 7917 4.075682 TGTTTGTGTTCTGTTGTCCTTGA 58.924 39.130 0.00 0.00 0.00 3.02
4998 7918 4.704540 TGTTTGTGTTCTGTTGTCCTTGAT 59.295 37.500 0.00 0.00 0.00 2.57
4999 7919 5.163663 TGTTTGTGTTCTGTTGTCCTTGATC 60.164 40.000 0.00 0.00 0.00 2.92
5000 7920 4.422073 TGTGTTCTGTTGTCCTTGATCT 57.578 40.909 0.00 0.00 0.00 2.75
5001 7921 5.545063 TGTGTTCTGTTGTCCTTGATCTA 57.455 39.130 0.00 0.00 0.00 1.98
5002 7922 5.541845 TGTGTTCTGTTGTCCTTGATCTAG 58.458 41.667 0.00 0.00 0.00 2.43
5003 7923 5.070446 TGTGTTCTGTTGTCCTTGATCTAGT 59.930 40.000 3.47 0.00 0.00 2.57
5004 7924 5.992217 GTGTTCTGTTGTCCTTGATCTAGTT 59.008 40.000 3.47 0.00 0.00 2.24
5005 7925 6.146347 GTGTTCTGTTGTCCTTGATCTAGTTC 59.854 42.308 3.47 0.00 0.00 3.01
5006 7926 6.042093 TGTTCTGTTGTCCTTGATCTAGTTCT 59.958 38.462 3.47 0.00 0.00 3.01
5007 7927 6.274157 TCTGTTGTCCTTGATCTAGTTCTC 57.726 41.667 3.47 0.00 0.00 2.87
5008 7928 5.186021 TCTGTTGTCCTTGATCTAGTTCTCC 59.814 44.000 3.47 0.00 0.00 3.71
5009 7929 4.082190 TGTTGTCCTTGATCTAGTTCTCCG 60.082 45.833 3.47 0.00 0.00 4.63
5010 7930 3.964411 TGTCCTTGATCTAGTTCTCCGA 58.036 45.455 3.47 0.00 0.00 4.55
5011 7931 4.537751 TGTCCTTGATCTAGTTCTCCGAT 58.462 43.478 3.47 0.00 0.00 4.18
5012 7932 4.956700 TGTCCTTGATCTAGTTCTCCGATT 59.043 41.667 3.47 0.00 0.00 3.34
5013 7933 5.422331 TGTCCTTGATCTAGTTCTCCGATTT 59.578 40.000 3.47 0.00 0.00 2.17
5014 7934 5.751028 GTCCTTGATCTAGTTCTCCGATTTG 59.249 44.000 3.47 0.00 0.00 2.32
5015 7935 5.422331 TCCTTGATCTAGTTCTCCGATTTGT 59.578 40.000 3.47 0.00 0.00 2.83
5016 7936 5.751028 CCTTGATCTAGTTCTCCGATTTGTC 59.249 44.000 3.47 0.00 0.00 3.18
5017 7937 4.921547 TGATCTAGTTCTCCGATTTGTCG 58.078 43.478 2.61 0.00 0.00 4.35
5018 7938 4.638865 TGATCTAGTTCTCCGATTTGTCGA 59.361 41.667 0.00 0.00 34.64 4.20
5019 7939 4.352600 TCTAGTTCTCCGATTTGTCGAC 57.647 45.455 9.11 9.11 34.64 4.20
5020 7940 4.008330 TCTAGTTCTCCGATTTGTCGACT 58.992 43.478 17.92 0.00 34.64 4.18
5021 7941 2.947852 AGTTCTCCGATTTGTCGACTG 58.052 47.619 17.92 1.48 34.64 3.51
5022 7942 1.993370 GTTCTCCGATTTGTCGACTGG 59.007 52.381 17.92 10.56 34.64 4.00
5023 7943 0.530744 TCTCCGATTTGTCGACTGGG 59.469 55.000 17.92 7.55 34.64 4.45
5024 7944 0.246635 CTCCGATTTGTCGACTGGGT 59.753 55.000 17.92 0.00 34.64 4.51
5025 7945 0.682852 TCCGATTTGTCGACTGGGTT 59.317 50.000 17.92 0.00 34.64 4.11
5026 7946 1.076332 CCGATTTGTCGACTGGGTTC 58.924 55.000 17.92 5.89 34.64 3.62
5027 7947 1.076332 CGATTTGTCGACTGGGTTCC 58.924 55.000 17.92 0.00 34.64 3.62
5028 7948 1.337823 CGATTTGTCGACTGGGTTCCT 60.338 52.381 17.92 0.00 34.64 3.36
5029 7949 2.094390 CGATTTGTCGACTGGGTTCCTA 60.094 50.000 17.92 0.00 34.64 2.94
5030 7950 3.430374 CGATTTGTCGACTGGGTTCCTAT 60.430 47.826 17.92 0.00 34.64 2.57
5031 7951 3.604875 TTTGTCGACTGGGTTCCTATC 57.395 47.619 17.92 0.00 0.00 2.08
5032 7952 1.481871 TGTCGACTGGGTTCCTATCC 58.518 55.000 17.92 0.00 0.00 2.59
5033 7953 1.006758 TGTCGACTGGGTTCCTATCCT 59.993 52.381 17.92 0.00 0.00 3.24
5034 7954 2.242965 TGTCGACTGGGTTCCTATCCTA 59.757 50.000 17.92 0.00 0.00 2.94
5035 7955 2.885894 GTCGACTGGGTTCCTATCCTAG 59.114 54.545 8.70 0.00 39.08 3.02
5037 7957 2.610873 GACTGGGTTCCTATCCTAGGG 58.389 57.143 9.46 0.00 46.24 3.53
5038 7958 1.945317 ACTGGGTTCCTATCCTAGGGT 59.055 52.381 9.46 3.69 46.24 4.34
5039 7959 2.321296 ACTGGGTTCCTATCCTAGGGTT 59.679 50.000 9.46 0.00 46.24 4.11
5040 7960 3.246758 ACTGGGTTCCTATCCTAGGGTTT 60.247 47.826 9.46 0.00 46.24 3.27
5041 7961 3.120108 TGGGTTCCTATCCTAGGGTTTG 58.880 50.000 9.46 0.00 46.24 2.93
5042 7962 3.120898 GGGTTCCTATCCTAGGGTTTGT 58.879 50.000 9.46 0.00 46.24 2.83
5043 7963 3.118000 GGGTTCCTATCCTAGGGTTTGTG 60.118 52.174 9.46 0.00 46.24 3.33
5044 7964 3.522343 GGTTCCTATCCTAGGGTTTGTGT 59.478 47.826 9.46 0.00 46.24 3.72
5045 7965 4.514401 GTTCCTATCCTAGGGTTTGTGTG 58.486 47.826 9.46 0.00 46.24 3.82
5046 7966 4.069312 TCCTATCCTAGGGTTTGTGTGA 57.931 45.455 9.46 0.00 46.24 3.58
5047 7967 4.431378 TCCTATCCTAGGGTTTGTGTGAA 58.569 43.478 9.46 0.00 46.24 3.18
5048 7968 5.036916 TCCTATCCTAGGGTTTGTGTGAAT 58.963 41.667 9.46 0.00 46.24 2.57
5049 7969 5.104527 TCCTATCCTAGGGTTTGTGTGAATG 60.105 44.000 9.46 0.00 46.24 2.67
5050 7970 4.657814 ATCCTAGGGTTTGTGTGAATGT 57.342 40.909 9.46 0.00 0.00 2.71
5051 7971 5.772393 ATCCTAGGGTTTGTGTGAATGTA 57.228 39.130 9.46 0.00 0.00 2.29
5052 7972 5.160607 TCCTAGGGTTTGTGTGAATGTAG 57.839 43.478 9.46 0.00 0.00 2.74
5053 7973 4.019681 TCCTAGGGTTTGTGTGAATGTAGG 60.020 45.833 9.46 0.00 0.00 3.18
5054 7974 3.876309 AGGGTTTGTGTGAATGTAGGT 57.124 42.857 0.00 0.00 0.00 3.08
5055 7975 4.178956 AGGGTTTGTGTGAATGTAGGTT 57.821 40.909 0.00 0.00 0.00 3.50
5056 7976 4.542697 AGGGTTTGTGTGAATGTAGGTTT 58.457 39.130 0.00 0.00 0.00 3.27
5057 7977 4.340950 AGGGTTTGTGTGAATGTAGGTTTG 59.659 41.667 0.00 0.00 0.00 2.93
5058 7978 4.098807 GGGTTTGTGTGAATGTAGGTTTGT 59.901 41.667 0.00 0.00 0.00 2.83
5059 7979 5.040635 GGTTTGTGTGAATGTAGGTTTGTG 58.959 41.667 0.00 0.00 0.00 3.33
5060 7980 5.163602 GGTTTGTGTGAATGTAGGTTTGTGA 60.164 40.000 0.00 0.00 0.00 3.58
5061 7981 6.460953 GGTTTGTGTGAATGTAGGTTTGTGAT 60.461 38.462 0.00 0.00 0.00 3.06
5062 7982 6.707440 TTGTGTGAATGTAGGTTTGTGATT 57.293 33.333 0.00 0.00 0.00 2.57
5063 7983 6.707440 TGTGTGAATGTAGGTTTGTGATTT 57.293 33.333 0.00 0.00 0.00 2.17
5064 7984 7.106439 TGTGTGAATGTAGGTTTGTGATTTT 57.894 32.000 0.00 0.00 0.00 1.82
5065 7985 7.199766 TGTGTGAATGTAGGTTTGTGATTTTC 58.800 34.615 0.00 0.00 0.00 2.29
5066 7986 6.640907 GTGTGAATGTAGGTTTGTGATTTTCC 59.359 38.462 0.00 0.00 0.00 3.13
5067 7987 6.156519 GTGAATGTAGGTTTGTGATTTTCCC 58.843 40.000 0.00 0.00 0.00 3.97
5068 7988 5.835819 TGAATGTAGGTTTGTGATTTTCCCA 59.164 36.000 0.00 0.00 0.00 4.37
5069 7989 6.496565 TGAATGTAGGTTTGTGATTTTCCCAT 59.503 34.615 0.00 0.00 0.00 4.00
5070 7990 5.720371 TGTAGGTTTGTGATTTTCCCATG 57.280 39.130 0.00 0.00 0.00 3.66
5071 7991 4.526262 TGTAGGTTTGTGATTTTCCCATGG 59.474 41.667 4.14 4.14 0.00 3.66
5072 7992 2.302733 AGGTTTGTGATTTTCCCATGGC 59.697 45.455 6.09 0.00 0.00 4.40
5073 7993 2.615240 GGTTTGTGATTTTCCCATGGCC 60.615 50.000 6.09 0.00 0.00 5.36
5074 7994 2.021262 TTGTGATTTTCCCATGGCCA 57.979 45.000 8.56 8.56 0.00 5.36
5075 7995 1.559368 TGTGATTTTCCCATGGCCAG 58.441 50.000 13.05 3.10 0.00 4.85
5076 7996 0.176449 GTGATTTTCCCATGGCCAGC 59.824 55.000 13.05 0.00 0.00 4.85
5077 7997 0.041535 TGATTTTCCCATGGCCAGCT 59.958 50.000 13.05 0.00 0.00 4.24
5078 7998 1.197812 GATTTTCCCATGGCCAGCTT 58.802 50.000 13.05 0.00 0.00 3.74
5079 7999 1.556451 GATTTTCCCATGGCCAGCTTT 59.444 47.619 13.05 0.00 0.00 3.51
5080 8000 0.975887 TTTTCCCATGGCCAGCTTTC 59.024 50.000 13.05 0.00 0.00 2.62
5081 8001 1.250154 TTTCCCATGGCCAGCTTTCG 61.250 55.000 13.05 0.00 0.00 3.46
5082 8002 2.045045 CCCATGGCCAGCTTTCGA 60.045 61.111 13.05 0.00 0.00 3.71
5083 8003 2.409870 CCCATGGCCAGCTTTCGAC 61.410 63.158 13.05 0.00 0.00 4.20
5084 8004 1.377725 CCATGGCCAGCTTTCGACT 60.378 57.895 13.05 0.00 0.00 4.18
5085 8005 0.962356 CCATGGCCAGCTTTCGACTT 60.962 55.000 13.05 0.00 0.00 3.01
5086 8006 0.169672 CATGGCCAGCTTTCGACTTG 59.830 55.000 13.05 0.00 0.00 3.16
5111 8031 2.744202 GTGATTTGTTCTGCGATGTCCT 59.256 45.455 0.00 0.00 0.00 3.85
5182 8102 2.513897 CCTGCGGATTCGGTTCCC 60.514 66.667 0.00 0.00 36.79 3.97
5328 8274 2.409870 CCCATGGCCAGCTTTCGAC 61.410 63.158 13.05 0.00 0.00 4.20
5342 8288 5.621228 CAGCTTTCGACTTGTTTGTGTATTC 59.379 40.000 0.00 0.00 0.00 1.75
5354 8300 2.840511 TGTGTATTCAGGGGCTTCCTA 58.159 47.619 0.00 0.00 46.12 2.94
5362 8308 2.043939 TCAGGGGCTTCCTAGTTCTGTA 59.956 50.000 0.00 0.00 46.12 2.74
5373 8319 6.869206 TCCTAGTTCTGTAGGTTTTGCTAT 57.131 37.500 0.00 0.00 40.64 2.97
5376 8322 6.758886 CCTAGTTCTGTAGGTTTTGCTATGAG 59.241 42.308 0.00 0.00 35.67 2.90
5384 8330 8.630054 TGTAGGTTTTGCTATGAGTATTTTGT 57.370 30.769 0.00 0.00 0.00 2.83
5385 8331 8.511321 TGTAGGTTTTGCTATGAGTATTTTGTG 58.489 33.333 0.00 0.00 0.00 3.33
5386 8332 6.924111 AGGTTTTGCTATGAGTATTTTGTGG 58.076 36.000 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 5.370679 TGGGAAAACCTTGTTGTACTAGAC 58.629 41.667 0.00 0.00 41.11 2.59
111 112 2.203771 ATCATCGTCCCTCGCTCCC 61.204 63.158 0.00 0.00 39.67 4.30
112 113 1.006805 CATCATCGTCCCTCGCTCC 60.007 63.158 0.00 0.00 39.67 4.70
134 135 1.569479 GGAGCGAGTTGAAGGTGTGC 61.569 60.000 0.00 0.00 0.00 4.57
201 202 5.234329 CGTGACAGAACACAAGAAGTAACAT 59.766 40.000 0.00 0.00 40.34 2.71
225 226 7.322222 CGACTTCTGATTTGTTCATCAACTTTC 59.678 37.037 0.00 0.00 35.61 2.62
226 227 7.012327 TCGACTTCTGATTTGTTCATCAACTTT 59.988 33.333 0.00 0.00 35.61 2.66
266 270 4.386867 TTTCATGCTCCTCTAACCGTAG 57.613 45.455 0.00 0.00 0.00 3.51
313 317 5.160386 TCCCCCTCTGTAGAGTTACTTTTT 58.840 41.667 8.02 0.00 40.48 1.94
314 318 4.759953 TCCCCCTCTGTAGAGTTACTTTT 58.240 43.478 8.02 0.00 40.48 2.27
315 319 4.045590 TCTCCCCCTCTGTAGAGTTACTTT 59.954 45.833 8.02 0.00 40.48 2.66
316 320 3.596956 TCTCCCCCTCTGTAGAGTTACTT 59.403 47.826 8.02 0.00 40.48 2.24
317 321 3.053470 GTCTCCCCCTCTGTAGAGTTACT 60.053 52.174 8.02 0.00 40.48 2.24
318 322 3.053470 AGTCTCCCCCTCTGTAGAGTTAC 60.053 52.174 8.02 0.00 40.48 2.50
319 323 3.199671 AGTCTCCCCCTCTGTAGAGTTA 58.800 50.000 8.02 0.00 40.48 2.24
320 324 2.004589 AGTCTCCCCCTCTGTAGAGTT 58.995 52.381 8.02 0.00 40.48 3.01
321 325 1.688750 AGTCTCCCCCTCTGTAGAGT 58.311 55.000 8.02 0.00 40.48 3.24
322 326 2.291930 ACAAGTCTCCCCCTCTGTAGAG 60.292 54.545 1.86 1.86 41.71 2.43
323 327 1.717077 ACAAGTCTCCCCCTCTGTAGA 59.283 52.381 0.00 0.00 0.00 2.59
324 328 1.827969 CACAAGTCTCCCCCTCTGTAG 59.172 57.143 0.00 0.00 0.00 2.74
325 329 1.149288 ACACAAGTCTCCCCCTCTGTA 59.851 52.381 0.00 0.00 0.00 2.74
326 330 0.104934 ACACAAGTCTCCCCCTCTGT 60.105 55.000 0.00 0.00 0.00 3.41
327 331 0.322975 CACACAAGTCTCCCCCTCTG 59.677 60.000 0.00 0.00 0.00 3.35
328 332 0.191064 TCACACAAGTCTCCCCCTCT 59.809 55.000 0.00 0.00 0.00 3.69
329 333 0.610687 CTCACACAAGTCTCCCCCTC 59.389 60.000 0.00 0.00 0.00 4.30
330 334 0.191064 TCTCACACAAGTCTCCCCCT 59.809 55.000 0.00 0.00 0.00 4.79
462 871 5.938125 TGTAGGTTGAATTAGGAGCTGAAAC 59.062 40.000 0.00 0.00 0.00 2.78
466 875 8.682936 ATTAATGTAGGTTGAATTAGGAGCTG 57.317 34.615 0.00 0.00 0.00 4.24
512 921 6.407202 AGTACTTTGACACTATTCACATCCC 58.593 40.000 0.00 0.00 0.00 3.85
525 934 5.472137 GCTTTGGGTGAATAGTACTTTGACA 59.528 40.000 0.00 0.00 0.00 3.58
589 1403 7.132213 TCAGCTCAAAACTCGAAGTATTTTTG 58.868 34.615 0.00 0.00 0.00 2.44
593 1407 7.440523 AAATCAGCTCAAAACTCGAAGTATT 57.559 32.000 0.00 0.00 0.00 1.89
635 1449 6.552859 TTTGACAACATTCATGTGACGTAT 57.447 33.333 0.00 0.00 41.61 3.06
699 1513 8.733092 TTAGATGAGATCATGAGATTAACCCT 57.267 34.615 0.09 0.00 36.57 4.34
720 1534 8.016301 AGACTTGCATGAGATCTTACATTAGA 57.984 34.615 6.60 0.00 0.00 2.10
728 1542 3.371380 GGGGAAGACTTGCATGAGATCTT 60.371 47.826 9.09 5.23 32.36 2.40
738 1552 1.623811 TGTAGAGTGGGGAAGACTTGC 59.376 52.381 0.00 0.00 0.00 4.01
739 1553 3.165875 TCTGTAGAGTGGGGAAGACTTG 58.834 50.000 0.00 0.00 0.00 3.16
747 1561 2.035632 GTCCTCATCTGTAGAGTGGGG 58.964 57.143 2.99 2.99 34.72 4.96
748 1562 2.955660 GAGTCCTCATCTGTAGAGTGGG 59.044 54.545 0.00 0.00 0.00 4.61
749 1563 2.616376 CGAGTCCTCATCTGTAGAGTGG 59.384 54.545 0.00 0.00 0.00 4.00
750 1564 3.536570 TCGAGTCCTCATCTGTAGAGTG 58.463 50.000 0.00 0.00 0.00 3.51
751 1565 3.916359 TCGAGTCCTCATCTGTAGAGT 57.084 47.619 0.00 0.00 0.00 3.24
752 1566 4.036262 CCTTTCGAGTCCTCATCTGTAGAG 59.964 50.000 0.00 0.00 0.00 2.43
754 1568 3.948473 TCCTTTCGAGTCCTCATCTGTAG 59.052 47.826 0.00 0.00 0.00 2.74
761 1575 4.682778 TTTCTTTCCTTTCGAGTCCTCA 57.317 40.909 0.00 0.00 0.00 3.86
809 3616 0.178944 TCTCGTTTCAGGGTCCTCCA 60.179 55.000 0.00 0.00 38.24 3.86
815 3622 0.396811 CCCAGTTCTCGTTTCAGGGT 59.603 55.000 0.00 0.00 0.00 4.34
836 3643 3.535561 AGCGATGTGGACCTGATTTTAG 58.464 45.455 0.00 0.00 0.00 1.85
837 3644 3.531538 GAGCGATGTGGACCTGATTTTA 58.468 45.455 0.00 0.00 0.00 1.52
906 3713 1.982938 CGGGGAGGAAGAAGACGGT 60.983 63.158 0.00 0.00 0.00 4.83
992 3802 3.482232 GAGGGATCCATGGCGGTGG 62.482 68.421 15.23 2.54 40.76 4.61
993 3803 2.111878 GAGGGATCCATGGCGGTG 59.888 66.667 15.23 0.00 35.57 4.94
994 3804 3.171388 GGAGGGATCCATGGCGGT 61.171 66.667 15.23 0.00 35.57 5.68
1032 3842 3.237741 GGGGAGATGAGGAGGCGG 61.238 72.222 0.00 0.00 0.00 6.13
1047 3857 4.692475 GGGGTTGACACCGACGGG 62.692 72.222 20.00 9.81 45.39 5.28
1168 3978 3.314331 CGAGTGTGGCCTGGAGGT 61.314 66.667 3.32 0.00 37.57 3.85
1179 3989 3.735029 GACGAGCCGGACGAGTGT 61.735 66.667 23.84 5.34 34.70 3.55
1656 4466 3.219198 GCATTGGCCATCCCGACC 61.219 66.667 6.09 0.00 35.87 4.79
1732 4542 0.321671 CGGTTCTTGAAGCTGGAGGA 59.678 55.000 10.24 0.00 0.00 3.71
1734 4544 2.169832 TTCGGTTCTTGAAGCTGGAG 57.830 50.000 10.24 0.00 0.00 3.86
1824 4634 0.817013 ACACTGGCACAAACAACAGG 59.183 50.000 0.00 0.00 38.70 4.00
2667 5477 7.550906 ACAGATAATCTTCTTACAAGAGCCAAC 59.449 37.037 0.00 0.00 36.22 3.77
2865 5675 3.044156 AGCTTGCCAGATCTTCATCCTA 58.956 45.455 0.00 0.00 0.00 2.94
3027 5837 2.770447 TGGAGTGCCACTATTGGGATA 58.230 47.619 0.00 0.00 46.45 2.59
3076 5886 2.032981 CCACAACAAGCACCAGGAC 58.967 57.895 0.00 0.00 0.00 3.85
3330 6246 4.019681 CCTAGTGTAATTCCAACTCCCACA 60.020 45.833 0.00 0.00 0.00 4.17
3456 6372 1.277273 CTTGTGCTGGACTCAGATGGA 59.723 52.381 0.00 0.00 43.49 3.41
3495 6411 5.763204 TGGGAACAAAGCTACTAACAAAGAG 59.237 40.000 0.00 0.00 37.44 2.85
3566 6482 4.040829 TGAACTTCTCTGCTTCATCCTCAA 59.959 41.667 0.00 0.00 0.00 3.02
3567 6483 3.580022 TGAACTTCTCTGCTTCATCCTCA 59.420 43.478 0.00 0.00 0.00 3.86
3901 6817 2.829720 TCGAGCCACCAGTAAGTGTTAT 59.170 45.455 0.00 0.00 35.93 1.89
3978 6894 3.006940 GTCACCGAATCCTGCAACAATA 58.993 45.455 0.00 0.00 0.00 1.90
3981 6897 0.107643 TGTCACCGAATCCTGCAACA 59.892 50.000 0.00 0.00 0.00 3.33
4518 7436 5.114081 CCTCAAGGGTAAACCAGTATAACG 58.886 45.833 0.81 0.00 43.89 3.18
4796 7715 6.652481 TGAAAAGAAAATTCCAAACAACAGCA 59.348 30.769 0.00 0.00 0.00 4.41
4807 7726 3.660501 ACCGGCTGAAAAGAAAATTCC 57.339 42.857 0.00 0.00 0.00 3.01
4881 7801 4.051478 TCCTCTATGTCTCTCTCCCTTCT 58.949 47.826 0.00 0.00 0.00 2.85
4911 7831 5.913137 TTCCAAACAAACAGTGACTCAAT 57.087 34.783 0.00 0.00 0.00 2.57
4912 7832 5.913137 ATTCCAAACAAACAGTGACTCAA 57.087 34.783 0.00 0.00 0.00 3.02
4913 7833 5.913137 AATTCCAAACAAACAGTGACTCA 57.087 34.783 0.00 0.00 0.00 3.41
4914 7834 7.035612 AGAAAATTCCAAACAAACAGTGACTC 58.964 34.615 0.00 0.00 0.00 3.36
4915 7835 6.935167 AGAAAATTCCAAACAAACAGTGACT 58.065 32.000 0.00 0.00 0.00 3.41
4916 7836 7.595311 AAGAAAATTCCAAACAAACAGTGAC 57.405 32.000 0.00 0.00 0.00 3.67
4917 7837 8.614469 AAAAGAAAATTCCAAACAAACAGTGA 57.386 26.923 0.00 0.00 0.00 3.41
4919 7839 8.614469 TGAAAAGAAAATTCCAAACAAACAGT 57.386 26.923 0.00 0.00 0.00 3.55
4920 7840 7.693536 GCTGAAAAGAAAATTCCAAACAAACAG 59.306 33.333 0.00 0.00 0.00 3.16
4921 7841 7.361628 GGCTGAAAAGAAAATTCCAAACAAACA 60.362 33.333 0.00 0.00 0.00 2.83
4922 7842 6.966632 GGCTGAAAAGAAAATTCCAAACAAAC 59.033 34.615 0.00 0.00 0.00 2.93
4923 7843 6.183360 CGGCTGAAAAGAAAATTCCAAACAAA 60.183 34.615 0.00 0.00 0.00 2.83
4924 7844 5.293079 CGGCTGAAAAGAAAATTCCAAACAA 59.707 36.000 0.00 0.00 0.00 2.83
4925 7845 4.808364 CGGCTGAAAAGAAAATTCCAAACA 59.192 37.500 0.00 0.00 0.00 2.83
4926 7846 4.211164 CCGGCTGAAAAGAAAATTCCAAAC 59.789 41.667 0.00 0.00 0.00 2.93
4927 7847 4.141824 ACCGGCTGAAAAGAAAATTCCAAA 60.142 37.500 0.00 0.00 0.00 3.28
4928 7848 3.386402 ACCGGCTGAAAAGAAAATTCCAA 59.614 39.130 0.00 0.00 0.00 3.53
4929 7849 2.962421 ACCGGCTGAAAAGAAAATTCCA 59.038 40.909 0.00 0.00 0.00 3.53
4930 7850 3.660501 ACCGGCTGAAAAGAAAATTCC 57.339 42.857 0.00 0.00 0.00 3.01
4931 7851 4.616953 TGAACCGGCTGAAAAGAAAATTC 58.383 39.130 0.00 0.00 0.00 2.17
4932 7852 4.620982 CTGAACCGGCTGAAAAGAAAATT 58.379 39.130 0.00 0.00 0.00 1.82
4933 7853 3.552890 GCTGAACCGGCTGAAAAGAAAAT 60.553 43.478 0.00 0.00 32.24 1.82
4934 7854 2.223711 GCTGAACCGGCTGAAAAGAAAA 60.224 45.455 0.00 0.00 32.24 2.29
4935 7855 1.336755 GCTGAACCGGCTGAAAAGAAA 59.663 47.619 0.00 0.00 32.24 2.52
4936 7856 0.951558 GCTGAACCGGCTGAAAAGAA 59.048 50.000 0.00 0.00 32.24 2.52
4937 7857 0.889186 GGCTGAACCGGCTGAAAAGA 60.889 55.000 0.00 0.00 35.82 2.52
4938 7858 0.890996 AGGCTGAACCGGCTGAAAAG 60.891 55.000 0.00 0.00 46.52 2.27
4939 7859 0.467290 AAGGCTGAACCGGCTGAAAA 60.467 50.000 0.00 0.00 46.52 2.29
4940 7860 0.467290 AAAGGCTGAACCGGCTGAAA 60.467 50.000 0.00 0.00 46.52 2.69
4941 7861 0.467290 AAAAGGCTGAACCGGCTGAA 60.467 50.000 0.00 0.00 46.52 3.02
4942 7862 0.889186 GAAAAGGCTGAACCGGCTGA 60.889 55.000 0.00 0.00 46.52 4.26
4943 7863 1.581447 GAAAAGGCTGAACCGGCTG 59.419 57.895 0.00 0.00 46.52 4.85
4944 7864 1.966451 CGAAAAGGCTGAACCGGCT 60.966 57.895 0.00 0.00 46.52 5.52
4945 7865 1.792118 AACGAAAAGGCTGAACCGGC 61.792 55.000 0.00 0.00 46.52 6.13
4946 7866 1.515081 TAACGAAAAGGCTGAACCGG 58.485 50.000 0.00 0.00 46.52 5.28
4947 7867 3.824414 AATAACGAAAAGGCTGAACCG 57.176 42.857 0.00 0.00 46.52 4.44
4948 7868 6.190954 ACATAATAACGAAAAGGCTGAACC 57.809 37.500 0.00 0.00 39.61 3.62
4949 7869 6.033513 GCAACATAATAACGAAAAGGCTGAAC 59.966 38.462 0.00 0.00 0.00 3.18
4950 7870 6.072175 AGCAACATAATAACGAAAAGGCTGAA 60.072 34.615 0.00 0.00 0.00 3.02
4951 7871 5.414454 AGCAACATAATAACGAAAAGGCTGA 59.586 36.000 0.00 0.00 0.00 4.26
4952 7872 5.512788 CAGCAACATAATAACGAAAAGGCTG 59.487 40.000 0.00 0.00 38.02 4.85
4953 7873 5.183140 ACAGCAACATAATAACGAAAAGGCT 59.817 36.000 0.00 0.00 0.00 4.58
4954 7874 5.399013 ACAGCAACATAATAACGAAAAGGC 58.601 37.500 0.00 0.00 0.00 4.35
4955 7875 7.381139 ACAAACAGCAACATAATAACGAAAAGG 59.619 33.333 0.00 0.00 0.00 3.11
4956 7876 8.207252 CACAAACAGCAACATAATAACGAAAAG 58.793 33.333 0.00 0.00 0.00 2.27
4957 7877 7.702772 ACACAAACAGCAACATAATAACGAAAA 59.297 29.630 0.00 0.00 0.00 2.29
4958 7878 7.197017 ACACAAACAGCAACATAATAACGAAA 58.803 30.769 0.00 0.00 0.00 3.46
4959 7879 6.730175 ACACAAACAGCAACATAATAACGAA 58.270 32.000 0.00 0.00 0.00 3.85
4960 7880 6.307031 ACACAAACAGCAACATAATAACGA 57.693 33.333 0.00 0.00 0.00 3.85
4961 7881 6.855914 AGAACACAAACAGCAACATAATAACG 59.144 34.615 0.00 0.00 0.00 3.18
4962 7882 7.647715 ACAGAACACAAACAGCAACATAATAAC 59.352 33.333 0.00 0.00 0.00 1.89
4963 7883 7.711846 ACAGAACACAAACAGCAACATAATAA 58.288 30.769 0.00 0.00 0.00 1.40
4964 7884 7.270757 ACAGAACACAAACAGCAACATAATA 57.729 32.000 0.00 0.00 0.00 0.98
4965 7885 6.147864 ACAGAACACAAACAGCAACATAAT 57.852 33.333 0.00 0.00 0.00 1.28
4966 7886 5.574891 ACAGAACACAAACAGCAACATAA 57.425 34.783 0.00 0.00 0.00 1.90
4967 7887 5.105957 ACAACAGAACACAAACAGCAACATA 60.106 36.000 0.00 0.00 0.00 2.29
4968 7888 4.175516 CAACAGAACACAAACAGCAACAT 58.824 39.130 0.00 0.00 0.00 2.71
4969 7889 3.005261 ACAACAGAACACAAACAGCAACA 59.995 39.130 0.00 0.00 0.00 3.33
4970 7890 3.574614 ACAACAGAACACAAACAGCAAC 58.425 40.909 0.00 0.00 0.00 4.17
4971 7891 3.366883 GGACAACAGAACACAAACAGCAA 60.367 43.478 0.00 0.00 0.00 3.91
4972 7892 2.163412 GGACAACAGAACACAAACAGCA 59.837 45.455 0.00 0.00 0.00 4.41
4973 7893 2.423538 AGGACAACAGAACACAAACAGC 59.576 45.455 0.00 0.00 0.00 4.40
4974 7894 4.155826 TCAAGGACAACAGAACACAAACAG 59.844 41.667 0.00 0.00 0.00 3.16
4975 7895 4.075682 TCAAGGACAACAGAACACAAACA 58.924 39.130 0.00 0.00 0.00 2.83
4976 7896 4.695217 TCAAGGACAACAGAACACAAAC 57.305 40.909 0.00 0.00 0.00 2.93
4977 7897 5.192927 AGATCAAGGACAACAGAACACAAA 58.807 37.500 0.00 0.00 0.00 2.83
4978 7898 4.780815 AGATCAAGGACAACAGAACACAA 58.219 39.130 0.00 0.00 0.00 3.33
4979 7899 4.422073 AGATCAAGGACAACAGAACACA 57.578 40.909 0.00 0.00 0.00 3.72
4980 7900 5.542779 ACTAGATCAAGGACAACAGAACAC 58.457 41.667 0.00 0.00 0.00 3.32
4981 7901 5.808366 ACTAGATCAAGGACAACAGAACA 57.192 39.130 0.00 0.00 0.00 3.18
4982 7902 6.459923 AGAACTAGATCAAGGACAACAGAAC 58.540 40.000 0.00 0.00 0.00 3.01
4983 7903 6.295349 GGAGAACTAGATCAAGGACAACAGAA 60.295 42.308 0.00 0.00 0.00 3.02
4984 7904 5.186021 GGAGAACTAGATCAAGGACAACAGA 59.814 44.000 0.00 0.00 0.00 3.41
4985 7905 5.415221 GGAGAACTAGATCAAGGACAACAG 58.585 45.833 0.00 0.00 0.00 3.16
4986 7906 4.082190 CGGAGAACTAGATCAAGGACAACA 60.082 45.833 0.00 0.00 0.00 3.33
4987 7907 4.158025 TCGGAGAACTAGATCAAGGACAAC 59.842 45.833 0.00 0.00 0.00 3.32
4988 7908 4.341487 TCGGAGAACTAGATCAAGGACAA 58.659 43.478 0.00 0.00 0.00 3.18
4989 7909 3.964411 TCGGAGAACTAGATCAAGGACA 58.036 45.455 0.00 0.00 0.00 4.02
4990 7910 5.523438 AATCGGAGAACTAGATCAAGGAC 57.477 43.478 0.00 0.00 43.58 3.85
4991 7911 5.422331 ACAAATCGGAGAACTAGATCAAGGA 59.578 40.000 0.00 0.00 43.58 3.36
4992 7912 5.665459 ACAAATCGGAGAACTAGATCAAGG 58.335 41.667 0.00 0.00 43.58 3.61
4993 7913 5.457148 CGACAAATCGGAGAACTAGATCAAG 59.543 44.000 0.00 0.00 44.99 3.02
4994 7914 5.340803 CGACAAATCGGAGAACTAGATCAA 58.659 41.667 0.00 0.00 44.99 2.57
4995 7915 4.921547 CGACAAATCGGAGAACTAGATCA 58.078 43.478 0.00 0.00 44.99 2.92
5009 7929 2.474410 AGGAACCCAGTCGACAAATC 57.526 50.000 19.50 8.17 0.00 2.17
5010 7930 3.118371 GGATAGGAACCCAGTCGACAAAT 60.118 47.826 19.50 0.00 0.00 2.32
5011 7931 2.235402 GGATAGGAACCCAGTCGACAAA 59.765 50.000 19.50 0.00 0.00 2.83
5012 7932 1.829222 GGATAGGAACCCAGTCGACAA 59.171 52.381 19.50 0.00 0.00 3.18
5013 7933 1.006758 AGGATAGGAACCCAGTCGACA 59.993 52.381 19.50 0.00 0.00 4.35
5014 7934 1.777941 AGGATAGGAACCCAGTCGAC 58.222 55.000 7.70 7.70 0.00 4.20
5015 7935 3.225177 CTAGGATAGGAACCCAGTCGA 57.775 52.381 0.00 0.00 34.22 4.20
5027 7947 5.745227 ACATTCACACAAACCCTAGGATAG 58.255 41.667 11.48 0.00 38.80 2.08
5028 7948 5.772393 ACATTCACACAAACCCTAGGATA 57.228 39.130 11.48 0.00 0.00 2.59
5029 7949 4.657814 ACATTCACACAAACCCTAGGAT 57.342 40.909 11.48 0.00 0.00 3.24
5030 7950 4.019681 CCTACATTCACACAAACCCTAGGA 60.020 45.833 11.48 0.00 0.00 2.94
5031 7951 4.261801 CCTACATTCACACAAACCCTAGG 58.738 47.826 0.06 0.06 0.00 3.02
5032 7952 4.906618 ACCTACATTCACACAAACCCTAG 58.093 43.478 0.00 0.00 0.00 3.02
5033 7953 4.986054 ACCTACATTCACACAAACCCTA 57.014 40.909 0.00 0.00 0.00 3.53
5034 7954 3.876309 ACCTACATTCACACAAACCCT 57.124 42.857 0.00 0.00 0.00 4.34
5035 7955 4.098807 ACAAACCTACATTCACACAAACCC 59.901 41.667 0.00 0.00 0.00 4.11
5036 7956 5.040635 CACAAACCTACATTCACACAAACC 58.959 41.667 0.00 0.00 0.00 3.27
5037 7957 5.885881 TCACAAACCTACATTCACACAAAC 58.114 37.500 0.00 0.00 0.00 2.93
5038 7958 6.707440 ATCACAAACCTACATTCACACAAA 57.293 33.333 0.00 0.00 0.00 2.83
5039 7959 6.707440 AATCACAAACCTACATTCACACAA 57.293 33.333 0.00 0.00 0.00 3.33
5040 7960 6.707440 AAATCACAAACCTACATTCACACA 57.293 33.333 0.00 0.00 0.00 3.72
5041 7961 6.640907 GGAAAATCACAAACCTACATTCACAC 59.359 38.462 0.00 0.00 0.00 3.82
5042 7962 6.239176 GGGAAAATCACAAACCTACATTCACA 60.239 38.462 0.00 0.00 0.00 3.58
5043 7963 6.156519 GGGAAAATCACAAACCTACATTCAC 58.843 40.000 0.00 0.00 0.00 3.18
5044 7964 5.835819 TGGGAAAATCACAAACCTACATTCA 59.164 36.000 0.00 0.00 0.00 2.57
5045 7965 6.339587 TGGGAAAATCACAAACCTACATTC 57.660 37.500 0.00 0.00 0.00 2.67
5046 7966 6.295802 CCATGGGAAAATCACAAACCTACATT 60.296 38.462 2.85 0.00 31.08 2.71
5047 7967 5.187576 CCATGGGAAAATCACAAACCTACAT 59.812 40.000 2.85 0.00 31.08 2.29
5048 7968 4.526262 CCATGGGAAAATCACAAACCTACA 59.474 41.667 2.85 0.00 31.08 2.74
5049 7969 4.620567 GCCATGGGAAAATCACAAACCTAC 60.621 45.833 15.13 0.00 31.08 3.18
5050 7970 3.513515 GCCATGGGAAAATCACAAACCTA 59.486 43.478 15.13 0.00 31.08 3.08
5051 7971 2.302733 GCCATGGGAAAATCACAAACCT 59.697 45.455 15.13 0.00 31.08 3.50
5052 7972 2.615240 GGCCATGGGAAAATCACAAACC 60.615 50.000 15.13 0.00 31.08 3.27
5053 7973 2.038295 TGGCCATGGGAAAATCACAAAC 59.962 45.455 15.13 0.00 31.08 2.93
5054 7974 2.302445 CTGGCCATGGGAAAATCACAAA 59.698 45.455 15.13 0.00 31.08 2.83
5055 7975 1.901159 CTGGCCATGGGAAAATCACAA 59.099 47.619 15.13 0.00 31.08 3.33
5056 7976 1.559368 CTGGCCATGGGAAAATCACA 58.441 50.000 15.13 0.00 32.34 3.58
5057 7977 0.176449 GCTGGCCATGGGAAAATCAC 59.824 55.000 15.13 0.00 0.00 3.06
5058 7978 0.041535 AGCTGGCCATGGGAAAATCA 59.958 50.000 15.13 0.00 0.00 2.57
5059 7979 1.197812 AAGCTGGCCATGGGAAAATC 58.802 50.000 15.13 0.00 0.00 2.17
5060 7980 1.556451 GAAAGCTGGCCATGGGAAAAT 59.444 47.619 15.13 0.00 0.00 1.82
5061 7981 0.975887 GAAAGCTGGCCATGGGAAAA 59.024 50.000 15.13 0.00 0.00 2.29
5062 7982 1.250154 CGAAAGCTGGCCATGGGAAA 61.250 55.000 15.13 0.00 0.00 3.13
5063 7983 1.678635 CGAAAGCTGGCCATGGGAA 60.679 57.895 15.13 0.00 0.00 3.97
5064 7984 2.045045 CGAAAGCTGGCCATGGGA 60.045 61.111 15.13 0.00 0.00 4.37
5065 7985 2.045045 TCGAAAGCTGGCCATGGG 60.045 61.111 15.13 0.00 0.00 4.00
5066 7986 0.962356 AAGTCGAAAGCTGGCCATGG 60.962 55.000 5.51 7.63 0.00 3.66
5067 7987 0.169672 CAAGTCGAAAGCTGGCCATG 59.830 55.000 5.51 1.08 0.00 3.66
5068 7988 0.250901 ACAAGTCGAAAGCTGGCCAT 60.251 50.000 5.51 0.00 0.00 4.40
5069 7989 0.465460 AACAAGTCGAAAGCTGGCCA 60.465 50.000 4.71 4.71 0.00 5.36
5070 7990 0.040067 CAACAAGTCGAAAGCTGGCC 60.040 55.000 0.00 0.00 0.00 5.36
5071 7991 0.040067 CCAACAAGTCGAAAGCTGGC 60.040 55.000 0.00 0.00 0.00 4.85
5072 7992 1.002468 CACCAACAAGTCGAAAGCTGG 60.002 52.381 0.00 0.00 0.00 4.85
5073 7993 1.939934 TCACCAACAAGTCGAAAGCTG 59.060 47.619 0.00 0.00 0.00 4.24
5074 7994 2.325583 TCACCAACAAGTCGAAAGCT 57.674 45.000 0.00 0.00 0.00 3.74
5075 7995 3.626028 AATCACCAACAAGTCGAAAGC 57.374 42.857 0.00 0.00 0.00 3.51
5076 7996 4.920376 ACAAATCACCAACAAGTCGAAAG 58.080 39.130 0.00 0.00 0.00 2.62
5077 7997 4.974368 ACAAATCACCAACAAGTCGAAA 57.026 36.364 0.00 0.00 0.00 3.46
5078 7998 4.638421 AGAACAAATCACCAACAAGTCGAA 59.362 37.500 0.00 0.00 0.00 3.71
5079 7999 4.035091 CAGAACAAATCACCAACAAGTCGA 59.965 41.667 0.00 0.00 0.00 4.20
5080 8000 4.282068 CAGAACAAATCACCAACAAGTCG 58.718 43.478 0.00 0.00 0.00 4.18
5081 8001 4.044426 GCAGAACAAATCACCAACAAGTC 58.956 43.478 0.00 0.00 0.00 3.01
5082 8002 3.489059 CGCAGAACAAATCACCAACAAGT 60.489 43.478 0.00 0.00 0.00 3.16
5083 8003 3.044986 CGCAGAACAAATCACCAACAAG 58.955 45.455 0.00 0.00 0.00 3.16
5084 8004 2.685388 TCGCAGAACAAATCACCAACAA 59.315 40.909 0.00 0.00 0.00 2.83
5085 8005 2.293170 TCGCAGAACAAATCACCAACA 58.707 42.857 0.00 0.00 0.00 3.33
5086 8006 3.236816 CATCGCAGAACAAATCACCAAC 58.763 45.455 0.00 0.00 43.58 3.77
5111 8031 1.221840 GAGAGCTCCCAATCGCCAA 59.778 57.895 10.93 0.00 0.00 4.52
5182 8102 1.599797 GGGGTCAAACCACTCCACG 60.600 63.158 0.00 0.00 39.07 4.94
5328 8274 3.157087 AGCCCCTGAATACACAAACAAG 58.843 45.455 0.00 0.00 0.00 3.16
5354 8300 6.115448 ACTCATAGCAAAACCTACAGAACT 57.885 37.500 0.00 0.00 0.00 3.01
5362 8308 6.924111 CCACAAAATACTCATAGCAAAACCT 58.076 36.000 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.