Multiple sequence alignment - TraesCS5A01G286500

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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 TraesCS5A01G286500 chr5A 100.000 6471 0 0 1 6471 494380792 494387262 0.000000e+00 11950.0
1 TraesCS5A01G286500 chr5A 90.205 1950 137 21 406 2341 512974143 512976052 0.000000e+00 2494.0
2 TraesCS5A01G286500 chr5A 92.090 1239 71 9 1584 2810 512972899 512974122 0.000000e+00 1720.0
3 TraesCS5A01G286500 chr5A 94.361 1064 47 7 1 1060 512971832 512972886 0.000000e+00 1620.0
4 TraesCS5A01G286500 chr5A 83.299 964 123 24 137 1081 649851653 649850709 0.000000e+00 854.0
5 TraesCS5A01G286500 chr5A 83.484 442 56 11 3384 3820 649849960 649849531 4.700000e-106 396.0
6 TraesCS5A01G286500 chr5A 90.222 225 19 3 1346 1569 649850661 649850439 2.280000e-74 291.0
7 TraesCS5A01G286500 chr5D 92.417 5842 274 82 1 5762 391040640 391046392 0.000000e+00 8178.0
8 TraesCS5A01G286500 chr5D 83.855 607 75 17 479 1081 521497268 521496681 2.040000e-154 556.0
9 TraesCS5A01G286500 chr5D 83.902 615 43 28 5797 6376 391048019 391048612 2.660000e-148 536.0
10 TraesCS5A01G286500 chr5D 83.747 443 54 10 3384 3821 521495952 521495523 2.810000e-108 403.0
11 TraesCS5A01G286500 chr5D 75.854 820 155 36 773 1573 409334409 409335204 1.700000e-100 377.0
12 TraesCS5A01G286500 chr5D 79.601 451 71 11 1683 2129 521496402 521495969 2.930000e-78 303.0
13 TraesCS5A01G286500 chr5D 91.031 223 18 2 1348 1569 521496646 521496425 3.790000e-77 300.0
14 TraesCS5A01G286500 chr5B 90.858 4594 248 83 1899 6371 471301764 471306306 0.000000e+00 5999.0
15 TraesCS5A01G286500 chr5B 94.424 1901 74 11 1 1897 471299815 471301687 0.000000e+00 2894.0
16 TraesCS5A01G286500 chr1D 93.085 188 9 2 4850 5033 24597713 24597900 8.270000e-69 272.0
17 TraesCS5A01G286500 chr3B 92.553 188 10 2 4850 5033 807979568 807979381 3.850000e-67 267.0
18 TraesCS5A01G286500 chr3B 92.818 181 11 1 4855 5033 456362257 456362437 1.790000e-65 261.0
19 TraesCS5A01G286500 chr4A 92.818 181 11 1 4855 5033 661952273 661952453 1.790000e-65 261.0
20 TraesCS5A01G286500 chr7B 91.489 188 12 2 4850 5033 614501080 614501267 8.330000e-64 255.0
21 TraesCS5A01G286500 chr7B 91.489 188 12 2 4850 5033 614555565 614555752 8.330000e-64 255.0
22 TraesCS5A01G286500 chr6D 91.489 188 12 2 4850 5033 467430051 467429864 8.330000e-64 255.0
23 TraesCS5A01G286500 chr6D 95.349 86 4 0 3475 3560 187493911 187493996 3.150000e-28 137.0
24 TraesCS5A01G286500 chr1B 90.957 188 13 2 4850 5033 638550321 638550134 3.870000e-62 250.0
25 TraesCS5A01G286500 chr1A 90.957 188 13 2 4850 5033 251741880 251742067 3.870000e-62 250.0
26 TraesCS5A01G286500 chr2B 100.000 29 0 0 3335 3363 777647579 777647607 3.000000e-03 54.7


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 TraesCS5A01G286500 chr5A 494380792 494387262 6470 False 11950.000000 11950 100.000000 1 6471 1 chr5A.!!$F1 6470
1 TraesCS5A01G286500 chr5A 512971832 512976052 4220 False 1944.666667 2494 92.218667 1 2810 3 chr5A.!!$F2 2809
2 TraesCS5A01G286500 chr5A 649849531 649851653 2122 True 513.666667 854 85.668333 137 3820 3 chr5A.!!$R1 3683
3 TraesCS5A01G286500 chr5D 391040640 391048612 7972 False 4357.000000 8178 88.159500 1 6376 2 chr5D.!!$F2 6375
4 TraesCS5A01G286500 chr5D 521495523 521497268 1745 True 390.500000 556 84.558500 479 3821 4 chr5D.!!$R1 3342
5 TraesCS5A01G286500 chr5D 409334409 409335204 795 False 377.000000 377 75.854000 773 1573 1 chr5D.!!$F1 800
6 TraesCS5A01G286500 chr5B 471299815 471306306 6491 False 4446.500000 5999 92.641000 1 6371 2 chr5B.!!$F1 6370

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
908 938 1.384989 CGGCACTAGGTCAGGATCGT 61.385 60.0 0.00 0.00 0.00 3.73 F
2605 4670 0.037326 GACAAGATGAGCGTGGGTCA 60.037 55.0 0.00 0.00 44.17 4.02 F
4144 6255 1.616159 TTAAGTGAAGTTGGCCAGCC 58.384 50.0 16.95 6.15 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2829 4898 1.573108 ACGATCCACTTCAGATGGGT 58.427 50.0 0.00 0.00 37.85 4.51 R
4479 6600 0.388659 GTGTGAACTGGCATGGCAAA 59.611 50.0 23.47 6.47 0.00 3.68 R
5965 9720 0.033504 TGGCGAGAGAAGAAAACGCT 59.966 50.0 0.00 0.00 46.71 5.07 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
142 143 8.934507 ATCTTCTCTGTAGTTTACAAGTATGC 57.065 34.615 0.00 0.00 38.38 3.14
270 271 9.442047 AAACTCTAGTCTCCTTGTTTGATATTG 57.558 33.333 0.00 0.00 0.00 1.90
290 296 4.301072 TGCTGCTTTTAGTAGTTGGGAT 57.699 40.909 0.00 0.00 30.12 3.85
380 393 4.762251 GCTGGGTGGTTCATTTCCTATATC 59.238 45.833 0.00 0.00 0.00 1.63
416 430 9.813080 GTCTTGTTTACATTTCTCTTGTACATC 57.187 33.333 0.00 0.00 29.60 3.06
908 938 1.384989 CGGCACTAGGTCAGGATCGT 61.385 60.000 0.00 0.00 0.00 3.73
966 2895 8.059798 ACATTCTGCTTGACATTTATTAGCTT 57.940 30.769 0.00 0.00 33.15 3.74
967 2896 7.972277 ACATTCTGCTTGACATTTATTAGCTTG 59.028 33.333 0.00 0.00 33.15 4.01
1114 3076 8.721478 TGAGCTCATTCAATTAGTTTACTGTTC 58.279 33.333 13.74 0.00 0.00 3.18
1306 3269 3.244112 GGTGGAGTTTGCTAGTGTGTAGT 60.244 47.826 0.00 0.00 0.00 2.73
1332 3295 2.015736 AGTTGGACTGACATCGATGC 57.984 50.000 25.11 17.40 0.00 3.91
1340 3303 2.133553 CTGACATCGATGCTGGATCAC 58.866 52.381 25.11 7.26 0.00 3.06
1548 3511 5.049267 CCTTTTTGGATGCTTGGATTTGTTG 60.049 40.000 0.00 0.00 38.35 3.33
1640 3603 7.359264 CGTCATAGTAAAGTAATACTGCATGCC 60.359 40.741 16.68 0.00 36.78 4.40
1653 3616 3.323691 ACTGCATGCCGACTGGTATAATA 59.676 43.478 16.68 0.00 38.71 0.98
1667 3630 7.749666 ACTGGTATAATATCAAAGATGTGGCT 58.250 34.615 0.00 0.00 0.00 4.75
1673 3636 5.936686 ATATCAAAGATGTGGCTTCATCG 57.063 39.130 14.03 4.82 45.96 3.84
1680 3645 1.795768 TGTGGCTTCATCGAGTGAAC 58.204 50.000 6.28 4.84 41.79 3.18
1681 3646 1.069978 TGTGGCTTCATCGAGTGAACA 59.930 47.619 6.28 2.64 41.79 3.18
1693 3658 3.258372 TCGAGTGAACAGCATAGGAGTTT 59.742 43.478 0.00 0.00 0.00 2.66
1806 3783 1.616159 TGCTGTTAGTTTTCCTGCCC 58.384 50.000 0.00 0.00 0.00 5.36
1864 3841 4.157840 AGTTGAGGTTTCAGTGTGGTTTTC 59.842 41.667 0.00 0.00 34.15 2.29
1881 3858 6.318648 GTGGTTTTCTCATATACATCCTGCAA 59.681 38.462 0.00 0.00 0.00 4.08
1970 4022 3.366985 GCTGTAACCAGTGGTAAAATGGC 60.367 47.826 17.09 11.61 41.02 4.40
1989 4042 1.949525 GCAATATCCTGACGTGGCAAT 59.050 47.619 0.00 0.00 0.00 3.56
1991 4044 2.945008 CAATATCCTGACGTGGCAATGT 59.055 45.455 0.00 0.00 0.00 2.71
2033 4087 5.043903 GCTTGTAAGATGATCAGAACGCTA 58.956 41.667 0.09 0.00 0.00 4.26
2080 4135 4.467438 CCAAATGCCAGAGGAGGTAATTTT 59.533 41.667 0.00 0.00 29.98 1.82
2128 4185 3.473923 TGTGCTGTTCTGATTCTGTCA 57.526 42.857 0.00 0.00 35.05 3.58
2136 4193 6.017934 GCTGTTCTGATTCTGTCACTTGTTTA 60.018 38.462 0.00 0.00 32.22 2.01
2182 4239 5.936187 AGCTGCTATACTATGATGATGCT 57.064 39.130 0.00 0.00 0.00 3.79
2224 4287 1.202580 AGTTATCGACAGCTGCCATCC 60.203 52.381 15.27 0.00 0.00 3.51
2488 4553 4.298103 ACAGCATCTGTCCAGAATTCTT 57.702 40.909 4.86 0.00 41.21 2.52
2598 4663 3.245519 CAGTGATGATGACAAGATGAGCG 59.754 47.826 0.00 0.00 0.00 5.03
2605 4670 0.037326 GACAAGATGAGCGTGGGTCA 60.037 55.000 0.00 0.00 44.17 4.02
2647 4715 4.611961 GGACACCGAGGTAAAGGC 57.388 61.111 0.00 0.00 0.00 4.35
2764 4832 8.729756 TGAAAATGTTCATGGTTAGACATACTG 58.270 33.333 0.00 0.00 38.88 2.74
2766 4834 9.733556 AAAATGTTCATGGTTAGACATACTGTA 57.266 29.630 0.00 0.00 0.00 2.74
2767 4835 9.905713 AAATGTTCATGGTTAGACATACTGTAT 57.094 29.630 0.00 0.00 0.00 2.29
2768 4836 9.905713 AATGTTCATGGTTAGACATACTGTATT 57.094 29.630 0.00 0.00 0.00 1.89
2769 4837 9.905713 ATGTTCATGGTTAGACATACTGTATTT 57.094 29.630 0.00 0.00 0.00 1.40
2770 4838 9.378551 TGTTCATGGTTAGACATACTGTATTTC 57.621 33.333 5.95 5.95 0.00 2.17
2771 4839 8.827677 GTTCATGGTTAGACATACTGTATTTCC 58.172 37.037 9.69 0.00 0.00 3.13
2802 4870 9.444600 TTTGTAATCTAAAGTATTCCCTGACAC 57.555 33.333 0.00 0.00 0.00 3.67
2816 4885 3.054434 CCCTGACACACATAATCCCTGAA 60.054 47.826 0.00 0.00 0.00 3.02
2829 4898 9.170890 ACATAATCCCTGAATCTATTAGGTTCA 57.829 33.333 16.56 16.56 27.69 3.18
2855 4924 2.815503 TCTGAAGTGGATCGTTACGTCA 59.184 45.455 4.24 10.04 34.86 4.35
2896 4965 6.208797 ACATTTATCCCATGATGCTCTCATTG 59.791 38.462 0.00 0.00 42.07 2.82
2905 4974 8.027189 CCCATGATGCTCTCATTGTATTTAATG 58.973 37.037 0.00 0.00 42.07 1.90
2929 4998 7.312154 TGTTTTTGGTGCTAATATACTTGCTG 58.688 34.615 0.00 0.00 0.00 4.41
2940 5009 2.566833 TACTTGCTGCAACAGATGGT 57.433 45.000 11.69 9.28 32.44 3.55
2944 5013 3.192001 ACTTGCTGCAACAGATGGTAATG 59.808 43.478 11.69 0.00 32.44 1.90
2973 5042 5.063880 GGTCAAAGTGGTACAAACTCAGAT 58.936 41.667 0.00 0.00 44.16 2.90
3047 5123 5.585820 TTTACACGCAGATGTGGTCTATA 57.414 39.130 0.00 0.00 44.21 1.31
3067 5147 7.592164 GTCTATATCCGTTTGCTCTTCTCTAAC 59.408 40.741 0.00 0.00 0.00 2.34
3076 5156 8.113062 CGTTTGCTCTTCTCTAACTTTCATATG 58.887 37.037 0.00 0.00 0.00 1.78
3226 5306 6.839124 TCATTGGTAATTCTTGCTGTCATT 57.161 33.333 0.00 0.00 0.00 2.57
3296 5377 2.522060 GTCACTGGACTTGTGAGCG 58.478 57.895 0.00 0.00 43.90 5.03
3332 5414 2.256117 AAGTGTTAGTCCACCAGTGC 57.744 50.000 0.00 0.00 35.93 4.40
3335 5417 2.903784 AGTGTTAGTCCACCAGTGCATA 59.096 45.455 0.00 0.00 35.93 3.14
3367 5449 5.183140 ACCATGCCTTGATACACTTTACAAC 59.817 40.000 0.00 0.00 0.00 3.32
3374 5456 7.469456 GCCTTGATACACTTTACAACTTTTCCA 60.469 37.037 0.00 0.00 0.00 3.53
3393 5475 2.289694 CCAGCCTGCTACTAACAACTGT 60.290 50.000 0.00 0.00 0.00 3.55
3489 5571 2.875094 AGCAGAGGCATTCTTTCTGT 57.125 45.000 3.07 0.00 44.61 3.41
3495 5577 5.007528 GCAGAGGCATTCTTTCTGTATTCTC 59.992 44.000 3.07 0.00 40.29 2.87
3574 5661 7.333672 AGGCTACTTAAAGATGGTTTACTTTCG 59.666 37.037 0.00 0.00 37.49 3.46
3631 5718 8.788325 AGGTCAACCTAAGTAACATTATTGTC 57.212 34.615 0.00 0.00 46.48 3.18
3791 5884 7.039152 AGTGGAGATCTGATGTATATGAAGGTG 60.039 40.741 0.00 0.00 0.00 4.00
3793 5886 6.295518 GGAGATCTGATGTATATGAAGGTGCA 60.296 42.308 0.00 0.00 0.00 4.57
3828 5938 4.659111 TGAATGTCAATGCATGGGAATC 57.341 40.909 0.00 2.26 0.00 2.52
3831 5941 2.658285 TGTCAATGCATGGGAATCTCC 58.342 47.619 0.00 0.00 35.23 3.71
3849 5959 3.392947 TCTCCCCTAACACAATGTTGTCA 59.607 43.478 4.46 0.00 41.30 3.58
4013 6123 5.352569 CAGGCAACAGAAGATTAGGTAACTG 59.647 44.000 0.00 0.00 46.40 3.16
4042 6152 9.436957 TGAACTTATCTTTATGAAGTCAACCTC 57.563 33.333 0.00 0.00 32.27 3.85
4045 6155 9.660180 ACTTATCTTTATGAAGTCAACCTCTTC 57.340 33.333 0.00 0.00 40.89 2.87
4054 6164 5.466728 TGAAGTCAACCTCTTCGAAAATCTG 59.533 40.000 0.00 0.00 42.68 2.90
4055 6165 4.962155 AGTCAACCTCTTCGAAAATCTGT 58.038 39.130 0.00 0.00 0.00 3.41
4061 6171 7.331934 TCAACCTCTTCGAAAATCTGTATGAAG 59.668 37.037 0.00 0.00 35.36 3.02
4064 6174 6.020281 CCTCTTCGAAAATCTGTATGAAGTCG 60.020 42.308 0.00 0.00 35.51 4.18
4086 6196 4.537135 AAGATGCCTTCTTCGACTGTAA 57.463 40.909 0.00 0.00 40.86 2.41
4111 6221 5.011090 TCTATTCTTCTGGATGGTTCACG 57.989 43.478 0.00 0.00 0.00 4.35
4127 6237 7.317842 TGGTTCACGTGTTATTTGTTCTTTA 57.682 32.000 16.51 0.00 0.00 1.85
4138 6249 9.796120 TGTTATTTGTTCTTTAAGTGAAGTTGG 57.204 29.630 0.00 0.00 0.00 3.77
4144 6255 1.616159 TTAAGTGAAGTTGGCCAGCC 58.384 50.000 16.95 6.15 0.00 4.85
4168 6279 4.280929 AGTGGAAAAGAATAAACCAGCCAC 59.719 41.667 0.00 0.00 42.58 5.01
4176 6287 5.360591 AGAATAAACCAGCCACTAATCTCG 58.639 41.667 0.00 0.00 0.00 4.04
4178 6290 2.674796 AACCAGCCACTAATCTCGTC 57.325 50.000 0.00 0.00 0.00 4.20
4190 6302 7.437748 CCACTAATCTCGTCTTCATTTCCTAT 58.562 38.462 0.00 0.00 0.00 2.57
4221 6334 4.252073 GCTGTGAGACTCAAATGATCAGT 58.748 43.478 6.76 0.00 0.00 3.41
4278 6392 2.170607 TGTTGTATAGCTCCCCTGAAGC 59.829 50.000 0.00 0.00 0.00 3.86
4353 6467 7.709613 GCTGATCTTTCTTGGATAAAATGCATT 59.290 33.333 5.99 5.99 0.00 3.56
4377 6492 4.217118 AGCTGGAAAGCTTCATAGTTGTTG 59.783 41.667 0.00 0.00 43.52 3.33
4410 6525 9.722056 CTGCAAACTAATCATTGTTAGGATAAC 57.278 33.333 0.00 0.00 36.27 1.89
4412 6527 7.855904 GCAAACTAATCATTGTTAGGATAACCG 59.144 37.037 9.37 0.00 41.83 4.44
4431 6546 4.504858 ACCGATCCTGTCATTTTACTGTC 58.495 43.478 0.00 0.00 0.00 3.51
4434 6549 4.383118 CGATCCTGTCATTTTACTGTCCCT 60.383 45.833 0.00 0.00 0.00 4.20
4488 6610 5.581605 TCTAAATTCGATCTTTTGCCATGC 58.418 37.500 0.00 0.00 0.00 4.06
4493 6615 1.203052 CGATCTTTTGCCATGCCAGTT 59.797 47.619 0.00 0.00 0.00 3.16
4498 6620 0.388659 TTTGCCATGCCAGTTCACAC 59.611 50.000 0.00 0.00 0.00 3.82
4499 6621 1.462731 TTGCCATGCCAGTTCACACC 61.463 55.000 0.00 0.00 0.00 4.16
4514 6636 3.694926 TCACACCATCCATGTTATGCAA 58.305 40.909 0.00 0.00 0.00 4.08
4522 6644 8.579006 CACCATCCATGTTATGCAATTTACTAT 58.421 33.333 0.00 0.00 0.00 2.12
4552 6674 8.143193 TGTTCTCTTTACAAAATGCATGTCAAT 58.857 29.630 0.00 0.00 32.27 2.57
4562 6684 3.690475 TGCATGTCAATCTGTGTCTCT 57.310 42.857 0.00 0.00 0.00 3.10
4567 6689 2.028658 TGTCAATCTGTGTCTCTCAGGC 60.029 50.000 0.00 0.00 34.15 4.85
4582 6704 1.881973 TCAGGCAAAGCTGTCATTCAC 59.118 47.619 0.00 0.00 0.00 3.18
4618 6740 6.128063 CCAACAGAAAGCTCCTTGAGATAAAG 60.128 42.308 0.00 0.00 0.00 1.85
4648 6770 6.900568 CTGGAAGTTGATATCACTGAAGAC 57.099 41.667 4.48 0.00 0.00 3.01
4675 6797 2.676748 TGACCATTGGTTCCAAGCTTT 58.323 42.857 10.29 0.00 35.25 3.51
4742 6864 5.226396 CCGATCCATCTCAATCTCTGTTAC 58.774 45.833 0.00 0.00 0.00 2.50
4743 6865 4.914504 CGATCCATCTCAATCTCTGTTACG 59.085 45.833 0.00 0.00 0.00 3.18
4787 6909 1.542492 CAAGGCCTGCTGAGTTTGAT 58.458 50.000 5.69 0.00 0.00 2.57
4908 7032 7.280428 GCTAAACCCTAGAATTTACCTCTTGTC 59.720 40.741 0.00 0.00 0.00 3.18
4909 7033 5.340439 ACCCTAGAATTTACCTCTTGTCG 57.660 43.478 0.00 0.00 0.00 4.35
5063 7187 0.105039 GAGGTATGACCGAAGCCTGG 59.895 60.000 0.00 0.00 44.90 4.45
5105 7229 5.456822 GTCAAGAATTTTGCAGTGTTGAGAC 59.543 40.000 0.00 0.00 0.00 3.36
5106 7230 5.357878 TCAAGAATTTTGCAGTGTTGAGACT 59.642 36.000 0.00 0.00 0.00 3.24
5123 7249 2.453843 CTCTGAGCAAGAGCAACCG 58.546 57.895 3.75 0.00 45.93 4.44
5181 7307 2.982744 GCCTTTCTTGCAGTCGGCC 61.983 63.158 0.00 0.00 43.89 6.13
5275 7401 1.376037 GACAAGCGGACCAGGAAGG 60.376 63.158 0.00 0.00 45.67 3.46
5311 7437 5.188327 GAAAAAGTTCCACCTTCCTTCAG 57.812 43.478 0.00 0.00 0.00 3.02
5389 7515 6.238731 CCTTTCAGTTGCATCAGTTTAACAGA 60.239 38.462 0.00 0.00 0.00 3.41
5410 7551 0.331616 ACCATAAGCTTGACCACCCC 59.668 55.000 9.86 0.00 0.00 4.95
5415 7556 0.779997 AAGCTTGACCACCCCTGAAT 59.220 50.000 0.00 0.00 0.00 2.57
5518 7660 1.671054 GCCTCAGCGCAACTAACCA 60.671 57.895 11.47 0.00 0.00 3.67
5542 7684 0.320771 GGTCAGGCGAAGAAGCAGAA 60.321 55.000 0.00 0.00 39.27 3.02
5543 7685 1.677217 GGTCAGGCGAAGAAGCAGAAT 60.677 52.381 0.00 0.00 39.27 2.40
5544 7686 2.418746 GGTCAGGCGAAGAAGCAGAATA 60.419 50.000 0.00 0.00 39.27 1.75
5555 7697 3.385111 AGAAGCAGAATACCCCTAGTTCG 59.615 47.826 0.00 0.00 0.00 3.95
5614 7756 1.381872 ATAGCGACAGAGCACCCCT 60.382 57.895 0.00 0.00 40.15 4.79
5683 7829 3.886549 ACGTAAACGAGAGAGACTTGTG 58.113 45.455 9.86 0.00 41.89 3.33
5684 7830 2.657372 CGTAAACGAGAGAGACTTGTGC 59.343 50.000 0.00 0.00 41.89 4.57
5705 7851 0.179029 CCCCCTGAGACGTGTTGTTT 60.179 55.000 0.00 0.00 0.00 2.83
5731 7881 2.682856 TGTTTGTTTCACTGGAGACTGC 59.317 45.455 0.00 0.00 0.00 4.40
5756 9489 0.671472 GGCCACTTTTGCCTGAATGC 60.671 55.000 0.00 0.00 45.70 3.56
5787 9542 0.031994 AATGTTGGTTGCTTCACGCC 59.968 50.000 0.00 0.00 38.05 5.68
5788 9543 1.106351 ATGTTGGTTGCTTCACGCCA 61.106 50.000 0.00 0.00 38.05 5.69
5789 9544 1.106351 TGTTGGTTGCTTCACGCCAT 61.106 50.000 0.00 0.00 38.05 4.40
5790 9545 0.664166 GTTGGTTGCTTCACGCCATG 60.664 55.000 0.00 0.00 38.05 3.66
5791 9546 1.804396 TTGGTTGCTTCACGCCATGG 61.804 55.000 7.63 7.63 38.05 3.66
5792 9547 2.268076 GGTTGCTTCACGCCATGGT 61.268 57.895 14.67 0.00 38.05 3.55
5793 9548 1.659794 GTTGCTTCACGCCATGGTT 59.340 52.632 14.67 0.00 38.05 3.67
5794 9549 0.031994 GTTGCTTCACGCCATGGTTT 59.968 50.000 14.67 0.00 38.05 3.27
5795 9550 0.749649 TTGCTTCACGCCATGGTTTT 59.250 45.000 14.67 0.00 38.05 2.43
5803 9558 3.761218 TCACGCCATGGTTTTAATGATGT 59.239 39.130 14.67 0.00 0.00 3.06
5834 9589 1.821753 ACTTCTGTACTGAGCAGCGAT 59.178 47.619 2.51 0.00 34.21 4.58
5941 9696 1.165270 GCTTGGCGTATGACCAAAGT 58.835 50.000 10.69 0.00 46.24 2.66
5947 9702 3.886505 TGGCGTATGACCAAAGTTTTTCT 59.113 39.130 0.00 0.00 33.12 2.52
5977 9732 0.663153 GTGGTGCAGCGTTTTCTTCT 59.337 50.000 11.91 0.00 0.00 2.85
5984 9739 0.033504 AGCGTTTTCTTCTCTCGCCA 59.966 50.000 0.00 0.00 46.49 5.69
5985 9740 0.440371 GCGTTTTCTTCTCTCGCCAG 59.560 55.000 0.00 0.00 40.83 4.85
5986 9741 0.440371 CGTTTTCTTCTCTCGCCAGC 59.560 55.000 0.00 0.00 0.00 4.85
5987 9742 0.799393 GTTTTCTTCTCTCGCCAGCC 59.201 55.000 0.00 0.00 0.00 4.85
5988 9743 0.321653 TTTTCTTCTCTCGCCAGCCC 60.322 55.000 0.00 0.00 0.00 5.19
5989 9744 1.194781 TTTCTTCTCTCGCCAGCCCT 61.195 55.000 0.00 0.00 0.00 5.19
5990 9745 1.608717 TTCTTCTCTCGCCAGCCCTC 61.609 60.000 0.00 0.00 0.00 4.30
5991 9746 3.423162 CTTCTCTCGCCAGCCCTCG 62.423 68.421 0.00 0.00 0.00 4.63
6042 9797 4.054085 CAGGCACACTGTCACCTG 57.946 61.111 11.66 11.66 43.45 4.00
6043 9798 3.970332 AGGCACACTGTCACCTGA 58.030 55.556 0.20 0.00 0.00 3.86
6044 9799 2.220953 AGGCACACTGTCACCTGAA 58.779 52.632 0.20 0.00 0.00 3.02
6045 9800 0.107456 AGGCACACTGTCACCTGAAG 59.893 55.000 0.20 0.00 0.00 3.02
6046 9801 0.886490 GGCACACTGTCACCTGAAGG 60.886 60.000 0.00 0.00 42.17 3.46
6047 9802 1.510480 GCACACTGTCACCTGAAGGC 61.510 60.000 0.00 0.00 39.32 4.35
6048 9803 0.886490 CACACTGTCACCTGAAGGCC 60.886 60.000 0.00 0.00 39.32 5.19
6051 9806 1.079543 CTGTCACCTGAAGGCCTCG 60.080 63.158 5.23 0.00 39.32 4.63
6069 9824 1.154205 CGCCTGGATCGTGTTGGATC 61.154 60.000 0.00 0.00 41.67 3.36
6091 9876 3.119101 CGTAGTGGTAGGCTTGAGTGATT 60.119 47.826 0.00 0.00 0.00 2.57
6099 9884 0.166814 GCTTGAGTGATTGCCGTGTC 59.833 55.000 0.00 0.00 0.00 3.67
6135 9920 0.320374 TCATTCCTTGTCGGCGTTCT 59.680 50.000 6.85 0.00 0.00 3.01
6148 9933 2.602878 GGCGTTCTGAGTTATTGACGA 58.397 47.619 0.00 0.00 0.00 4.20
6152 9937 4.673580 GCGTTCTGAGTTATTGACGAGGTA 60.674 45.833 0.00 0.00 0.00 3.08
6163 9948 1.270785 TGACGAGGTAGTGGTCACGTA 60.271 52.381 0.00 0.00 38.84 3.57
6166 9951 2.286872 CGAGGTAGTGGTCACGTATCT 58.713 52.381 0.00 0.00 36.20 1.98
6170 9968 2.223525 GGTAGTGGTCACGTATCTCTGC 60.224 54.545 0.00 0.00 36.20 4.26
6206 10004 4.798263 GCCGATTACATTTGATCCGGAGTA 60.798 45.833 11.34 2.17 0.00 2.59
6207 10005 4.923871 CCGATTACATTTGATCCGGAGTAG 59.076 45.833 11.34 0.00 0.00 2.57
6208 10006 5.509163 CCGATTACATTTGATCCGGAGTAGT 60.509 44.000 11.34 1.90 0.00 2.73
6226 10024 6.709846 GGAGTAGTACGTACTGGATCAACTAT 59.290 42.308 33.23 11.08 42.48 2.12
6227 10025 7.307870 GGAGTAGTACGTACTGGATCAACTATG 60.308 44.444 33.23 0.00 42.48 2.23
6229 10027 3.454371 ACGTACTGGATCAACTATGGC 57.546 47.619 0.00 0.00 0.00 4.40
6231 10029 2.548067 CGTACTGGATCAACTATGGCCC 60.548 54.545 0.00 0.00 0.00 5.80
6232 10030 1.898863 ACTGGATCAACTATGGCCCT 58.101 50.000 0.00 0.00 0.00 5.19
6233 10031 3.060479 ACTGGATCAACTATGGCCCTA 57.940 47.619 0.00 0.00 0.00 3.53
6290 10089 0.678366 TGTGCAACACGACAGGGTTT 60.678 50.000 0.00 0.00 45.67 3.27
6292 10091 0.736053 TGCAACACGACAGGGTTTTC 59.264 50.000 0.00 0.00 42.20 2.29
6293 10092 1.021968 GCAACACGACAGGGTTTTCT 58.978 50.000 0.00 0.00 42.20 2.52
6294 10093 1.404035 GCAACACGACAGGGTTTTCTT 59.596 47.619 0.00 0.00 42.20 2.52
6295 10094 2.540973 GCAACACGACAGGGTTTTCTTC 60.541 50.000 0.00 0.00 42.20 2.87
6296 10095 2.680841 CAACACGACAGGGTTTTCTTCA 59.319 45.455 0.00 0.00 42.20 3.02
6297 10096 2.993937 ACACGACAGGGTTTTCTTCAA 58.006 42.857 0.00 0.00 0.00 2.69
6299 10098 1.947456 ACGACAGGGTTTTCTTCAAGC 59.053 47.619 0.00 0.00 0.00 4.01
6300 10099 1.069906 CGACAGGGTTTTCTTCAAGCG 60.070 52.381 0.00 0.00 0.00 4.68
6342 10143 0.721718 GCTTCGCATCGTTAGCTTGT 59.278 50.000 0.00 0.00 34.71 3.16
6343 10144 1.527793 GCTTCGCATCGTTAGCTTGTG 60.528 52.381 0.00 0.00 34.71 3.33
6345 10146 2.293677 TCGCATCGTTAGCTTGTGAT 57.706 45.000 0.00 0.00 0.00 3.06
6350 10151 4.588278 GCATCGTTAGCTTGTGATAAACC 58.412 43.478 0.00 0.00 0.00 3.27
6378 10179 4.311816 TCGATAACGAAATCCAGTACCC 57.688 45.455 0.00 0.00 45.74 3.69
6379 10180 3.956199 TCGATAACGAAATCCAGTACCCT 59.044 43.478 0.00 0.00 45.74 4.34
6380 10181 5.132502 TCGATAACGAAATCCAGTACCCTA 58.867 41.667 0.00 0.00 45.74 3.53
6381 10182 5.593909 TCGATAACGAAATCCAGTACCCTAA 59.406 40.000 0.00 0.00 45.74 2.69
6382 10183 6.096705 TCGATAACGAAATCCAGTACCCTAAA 59.903 38.462 0.00 0.00 45.74 1.85
6383 10184 6.420008 CGATAACGAAATCCAGTACCCTAAAG 59.580 42.308 0.00 0.00 42.66 1.85
6384 10185 3.870274 ACGAAATCCAGTACCCTAAAGC 58.130 45.455 0.00 0.00 0.00 3.51
6385 10186 3.262405 ACGAAATCCAGTACCCTAAAGCA 59.738 43.478 0.00 0.00 0.00 3.91
6386 10187 4.080526 ACGAAATCCAGTACCCTAAAGCAT 60.081 41.667 0.00 0.00 0.00 3.79
6387 10188 4.881850 CGAAATCCAGTACCCTAAAGCATT 59.118 41.667 0.00 0.00 0.00 3.56
6388 10189 5.220854 CGAAATCCAGTACCCTAAAGCATTG 60.221 44.000 0.00 0.00 0.00 2.82
6389 10190 5.450818 AATCCAGTACCCTAAAGCATTGA 57.549 39.130 0.00 0.00 0.00 2.57
6390 10191 4.487714 TCCAGTACCCTAAAGCATTGAG 57.512 45.455 0.00 0.00 0.00 3.02
6391 10192 2.945668 CCAGTACCCTAAAGCATTGAGC 59.054 50.000 0.00 0.00 46.19 4.26
6400 10201 3.256936 GCATTGAGCTGTGTCGCA 58.743 55.556 0.00 0.00 41.15 5.10
6414 10215 4.854399 TGTGTCGCAGAAAAATAAGGTTG 58.146 39.130 0.00 0.00 39.69 3.77
6415 10216 4.576873 TGTGTCGCAGAAAAATAAGGTTGA 59.423 37.500 0.00 0.00 39.69 3.18
6416 10217 5.147162 GTGTCGCAGAAAAATAAGGTTGAG 58.853 41.667 0.00 0.00 39.69 3.02
6417 10218 4.159120 GTCGCAGAAAAATAAGGTTGAGC 58.841 43.478 0.00 0.00 39.69 4.26
6418 10219 4.072131 TCGCAGAAAAATAAGGTTGAGCT 58.928 39.130 0.00 0.00 0.00 4.09
6419 10220 4.083324 TCGCAGAAAAATAAGGTTGAGCTG 60.083 41.667 0.00 0.00 0.00 4.24
6420 10221 4.083324 CGCAGAAAAATAAGGTTGAGCTGA 60.083 41.667 0.00 0.00 0.00 4.26
6421 10222 5.562696 CGCAGAAAAATAAGGTTGAGCTGAA 60.563 40.000 0.00 0.00 0.00 3.02
6422 10223 5.631096 GCAGAAAAATAAGGTTGAGCTGAAC 59.369 40.000 7.61 7.61 0.00 3.18
6423 10224 6.152379 CAGAAAAATAAGGTTGAGCTGAACC 58.848 40.000 25.83 25.83 45.16 3.62
6424 10225 5.833131 AGAAAAATAAGGTTGAGCTGAACCA 59.167 36.000 32.66 16.68 46.94 3.67
6425 10226 5.453567 AAAATAAGGTTGAGCTGAACCAC 57.546 39.130 32.66 10.69 46.94 4.16
6426 10227 2.163818 TAAGGTTGAGCTGAACCACG 57.836 50.000 32.66 0.00 46.94 4.94
6427 10228 1.166531 AAGGTTGAGCTGAACCACGC 61.167 55.000 32.66 9.63 46.94 5.34
6428 10229 2.617274 GGTTGAGCTGAACCACGCC 61.617 63.158 27.78 1.82 44.34 5.68
6429 10230 2.664851 TTGAGCTGAACCACGCCG 60.665 61.111 0.00 0.00 0.00 6.46
6430 10231 4.680237 TGAGCTGAACCACGCCGG 62.680 66.667 0.00 0.00 42.50 6.13
6450 10251 3.349488 GTTTCGAACCAAAGGTCTTGG 57.651 47.619 0.00 1.93 44.91 3.61
6451 10252 1.314730 TTCGAACCAAAGGTCTTGGC 58.685 50.000 3.40 0.00 43.23 4.52
6452 10253 0.472471 TCGAACCAAAGGTCTTGGCT 59.528 50.000 3.40 0.00 43.23 4.75
6453 10254 0.593128 CGAACCAAAGGTCTTGGCTG 59.407 55.000 3.40 0.00 43.23 4.85
6454 10255 0.961753 GAACCAAAGGTCTTGGCTGG 59.038 55.000 3.40 0.00 43.23 4.85
6455 10256 0.469892 AACCAAAGGTCTTGGCTGGG 60.470 55.000 3.40 0.00 43.23 4.45
6456 10257 1.607467 CCAAAGGTCTTGGCTGGGG 60.607 63.158 0.00 0.00 32.18 4.96
6457 10258 1.460255 CAAAGGTCTTGGCTGGGGA 59.540 57.895 0.00 0.00 0.00 4.81
6458 10259 0.895559 CAAAGGTCTTGGCTGGGGAC 60.896 60.000 0.00 0.00 0.00 4.46
6459 10260 1.360393 AAAGGTCTTGGCTGGGGACA 61.360 55.000 0.00 0.00 39.59 4.02
6460 10261 1.142688 AAGGTCTTGGCTGGGGACAT 61.143 55.000 0.00 0.00 41.51 3.06
6461 10262 1.142688 AGGTCTTGGCTGGGGACATT 61.143 55.000 0.00 0.00 41.51 2.71
6462 10263 0.681243 GGTCTTGGCTGGGGACATTC 60.681 60.000 0.00 0.00 41.51 2.67
6463 10264 0.329596 GTCTTGGCTGGGGACATTCT 59.670 55.000 0.00 0.00 41.51 2.40
6464 10265 0.620556 TCTTGGCTGGGGACATTCTC 59.379 55.000 0.00 0.00 41.51 2.87
6465 10266 0.622665 CTTGGCTGGGGACATTCTCT 59.377 55.000 0.00 0.00 41.51 3.10
6466 10267 1.005215 CTTGGCTGGGGACATTCTCTT 59.995 52.381 0.00 0.00 41.51 2.85
6467 10268 1.075601 TGGCTGGGGACATTCTCTTT 58.924 50.000 0.00 0.00 41.51 2.52
6468 10269 1.004745 TGGCTGGGGACATTCTCTTTC 59.995 52.381 0.00 0.00 41.51 2.62
6469 10270 1.004745 GGCTGGGGACATTCTCTTTCA 59.995 52.381 0.00 0.00 41.51 2.69
6470 10271 2.555227 GGCTGGGGACATTCTCTTTCAA 60.555 50.000 0.00 0.00 41.51 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 135 6.034256 GCATAGCACAAGAAAAAGCATACTTG 59.966 38.462 0.00 0.00 43.30 3.16
142 143 5.049198 TCTCACAGCATAGCACAAGAAAAAG 60.049 40.000 0.00 0.00 0.00 2.27
249 250 6.238320 GCAGCAATATCAAACAAGGAGACTAG 60.238 42.308 0.00 0.00 42.68 2.57
270 271 4.142381 CCAATCCCAACTACTAAAAGCAGC 60.142 45.833 0.00 0.00 0.00 5.25
416 430 3.598019 ACATTGCAATTTAGGGCACAG 57.402 42.857 9.83 0.00 40.23 3.66
929 968 9.836864 TGTCAAGCAGAATGTAGATATTACATT 57.163 29.630 16.49 16.49 46.99 2.71
931 970 9.836864 AATGTCAAGCAGAATGTAGATATTACA 57.163 29.630 0.00 1.83 39.31 2.41
966 2895 9.349713 ACAAATATAAGGTTGTTTGAGACTTCA 57.650 29.630 3.96 0.00 34.29 3.02
1306 3269 6.275494 TCGATGTCAGTCCAACTTAATACA 57.725 37.500 0.00 0.00 0.00 2.29
1332 3295 2.945080 ATGTAGGGCATGTGATCCAG 57.055 50.000 0.00 0.00 36.26 3.86
1340 3303 5.010314 ACATGATAAGCAAATGTAGGGCATG 59.990 40.000 0.00 0.00 37.96 4.06
1548 3511 5.297029 AGGAGCACAAAAGACTAACAAGAAC 59.703 40.000 0.00 0.00 0.00 3.01
1640 3603 7.148573 GCCACATCTTTGATATTATACCAGTCG 60.149 40.741 0.00 0.00 0.00 4.18
1653 3616 3.875727 CTCGATGAAGCCACATCTTTGAT 59.124 43.478 15.40 0.00 42.86 2.57
1667 3630 3.447229 TCCTATGCTGTTCACTCGATGAA 59.553 43.478 6.28 6.28 45.39 2.57
1672 3635 2.949451 ACTCCTATGCTGTTCACTCG 57.051 50.000 0.00 0.00 0.00 4.18
1673 3636 5.578727 CACTAAACTCCTATGCTGTTCACTC 59.421 44.000 0.00 0.00 0.00 3.51
1680 3645 5.482908 ACAGAACACTAAACTCCTATGCTG 58.517 41.667 0.00 0.00 0.00 4.41
1681 3646 5.746990 ACAGAACACTAAACTCCTATGCT 57.253 39.130 0.00 0.00 0.00 3.79
1716 3684 8.258007 CCTCCATATCTTAAGTTTCACACACTA 58.742 37.037 1.63 0.00 0.00 2.74
1717 3685 7.038302 TCCTCCATATCTTAAGTTTCACACACT 60.038 37.037 1.63 0.00 0.00 3.55
1723 3691 6.814954 AGCTCCTCCATATCTTAAGTTTCA 57.185 37.500 1.63 0.00 0.00 2.69
1724 3692 9.430623 GAATAGCTCCTCCATATCTTAAGTTTC 57.569 37.037 1.63 0.00 0.00 2.78
1806 3783 6.706055 TCAGTACTAGAATTTTGCAAGTCG 57.294 37.500 0.00 0.00 32.00 4.18
1970 4022 2.945008 ACATTGCCACGTCAGGATATTG 59.055 45.455 0.00 0.00 0.00 1.90
1989 4042 3.821033 GCAGAGCTCCTAAAAGGAAAACA 59.179 43.478 10.93 0.00 45.28 2.83
1991 4044 4.373156 AGCAGAGCTCCTAAAAGGAAAA 57.627 40.909 10.93 0.00 45.28 2.29
2080 4135 7.039434 TCCAATGTAACCAAAATACAGAATGCA 60.039 33.333 0.00 0.00 42.53 3.96
2128 4185 3.880490 TGGTTCGCTGAACATAAACAAGT 59.120 39.130 18.49 0.00 43.54 3.16
2136 4193 5.185454 TCATTAGAATGGTTCGCTGAACAT 58.815 37.500 18.49 2.92 43.54 2.71
2182 4239 4.150897 AGAAACAAAGGCACTCACTGTA 57.849 40.909 0.00 0.00 38.49 2.74
2488 4553 7.135591 AGAAATTGATCAAAAAGACCCCAAA 57.864 32.000 13.09 0.00 0.00 3.28
2598 4663 3.842869 GGTCTGACTCATGACCCAC 57.157 57.895 7.85 0.00 45.03 4.61
2721 4789 4.864704 TTTCATGCAAAAAGGAGGTACC 57.135 40.909 2.73 2.73 39.35 3.34
2802 4870 9.442047 GAACCTAATAGATTCAGGGATTATGTG 57.558 37.037 0.00 0.00 33.48 3.21
2816 4885 6.617371 ACTTCAGATGGGTGAACCTAATAGAT 59.383 38.462 0.00 0.00 41.11 1.98
2829 4898 1.573108 ACGATCCACTTCAGATGGGT 58.427 50.000 0.00 0.00 37.85 4.51
2855 4924 7.451566 GGGATAAATGTTACCATTAGGAGCAAT 59.548 37.037 0.00 0.00 40.42 3.56
2905 4974 6.253512 GCAGCAAGTATATTAGCACCAAAAAC 59.746 38.462 0.00 0.00 0.00 2.43
2929 4998 3.514645 CTTTGCCATTACCATCTGTTGC 58.485 45.455 0.00 0.00 0.00 4.17
2940 5009 3.571590 ACCACTTTGACCTTTGCCATTA 58.428 40.909 0.00 0.00 0.00 1.90
2944 5013 2.303175 TGTACCACTTTGACCTTTGCC 58.697 47.619 0.00 0.00 0.00 4.52
2973 5042 5.551233 CTCTCTTGAACCAATAACTGACCA 58.449 41.667 0.00 0.00 0.00 4.02
3023 5099 3.674997 AGACCACATCTGCGTGTAAAAT 58.325 40.909 0.00 0.00 35.81 1.82
3031 5107 2.229062 ACGGATATAGACCACATCTGCG 59.771 50.000 0.00 0.00 38.49 5.18
3037 5113 3.704566 AGAGCAAACGGATATAGACCACA 59.295 43.478 0.00 0.00 0.00 4.17
3047 5123 4.810191 AGTTAGAGAAGAGCAAACGGAT 57.190 40.909 0.00 0.00 0.00 4.18
3076 5156 5.180868 AGCATCTTGAGTTTCATCTGTGAAC 59.819 40.000 0.00 0.00 43.72 3.18
3152 5232 5.321102 TGAAGCATTAACAGTACCCATGTT 58.679 37.500 4.60 4.60 43.15 2.71
3284 5365 0.032130 TGTCACTCGCTCACAAGTCC 59.968 55.000 0.00 0.00 0.00 3.85
3296 5377 9.262358 ACTAACACTTAAAGAAATCTGTCACTC 57.738 33.333 0.00 0.00 0.00 3.51
3332 5414 6.889301 ATCAAGGCATGGTCTGTTTATATG 57.111 37.500 0.00 0.00 0.00 1.78
3335 5417 5.590259 GTGTATCAAGGCATGGTCTGTTTAT 59.410 40.000 0.00 0.00 0.00 1.40
3367 5449 3.674997 TGTTAGTAGCAGGCTGGAAAAG 58.325 45.455 17.64 0.00 0.00 2.27
3374 5456 3.771577 AACAGTTGTTAGTAGCAGGCT 57.228 42.857 0.00 0.00 36.32 4.58
3393 5475 6.183360 CCATTTCCTGCAAAACATTCAACAAA 60.183 34.615 0.00 0.00 0.00 2.83
3471 5553 4.880696 AGAATACAGAAAGAATGCCTCTGC 59.119 41.667 1.01 0.00 40.23 4.26
3519 5601 9.918630 CCAAAATATCTGAAAAGTGAGTCATTT 57.081 29.630 0.00 0.00 0.00 2.32
3574 5661 2.123982 CCATCCTTGCCTGCCCTC 60.124 66.667 0.00 0.00 0.00 4.30
3631 5718 7.495606 TGAAGAACAATATAGCATGTGTGGTAG 59.504 37.037 0.00 0.00 41.22 3.18
3674 5761 6.479972 TTGGGATCAGTAATCTGTAATCGT 57.520 37.500 0.00 0.00 41.91 3.73
3758 5851 4.573900 ACATCAGATCTCCACTGTTGTTC 58.426 43.478 0.00 0.00 42.07 3.18
3791 5884 3.826729 ACATTCAAGGGTTAAAGGACTGC 59.173 43.478 0.00 0.00 0.00 4.40
3793 5886 5.319043 TGACATTCAAGGGTTAAAGGACT 57.681 39.130 0.00 0.00 0.00 3.85
3828 5938 3.750371 TGACAACATTGTGTTAGGGGAG 58.250 45.455 1.07 0.00 42.43 4.30
3843 5953 4.097741 TGGTATAATGCCTGCAATGACAAC 59.902 41.667 0.00 0.00 0.00 3.32
3849 5959 1.608590 GCGTGGTATAATGCCTGCAAT 59.391 47.619 0.00 0.00 0.00 3.56
4013 6123 9.548208 GTTGACTTCATAAAGATAAGTTCAAGC 57.452 33.333 0.00 0.00 33.72 4.01
4020 6130 8.812329 CGAAGAGGTTGACTTCATAAAGATAAG 58.188 37.037 0.00 0.00 42.39 1.73
4027 6137 7.878127 AGATTTTCGAAGAGGTTGACTTCATAA 59.122 33.333 0.00 0.00 42.39 1.90
4042 6152 6.871044 TCGACTTCATACAGATTTTCGAAG 57.129 37.500 0.00 0.00 36.72 3.79
4045 6155 6.871044 TCTTCGACTTCATACAGATTTTCG 57.129 37.500 0.00 0.00 0.00 3.46
4086 6196 5.032846 TGAACCATCCAGAAGAATAGAGGT 58.967 41.667 0.00 0.00 0.00 3.85
4127 6237 0.825010 CTGGCTGGCCAACTTCACTT 60.825 55.000 15.47 0.00 46.63 3.16
4138 6249 1.260544 ATTCTTTTCCACTGGCTGGC 58.739 50.000 0.00 0.00 40.39 4.85
4144 6255 4.280677 TGGCTGGTTTATTCTTTTCCACTG 59.719 41.667 0.00 0.00 0.00 3.66
4151 6262 6.316390 CGAGATTAGTGGCTGGTTTATTCTTT 59.684 38.462 0.00 0.00 0.00 2.52
4176 6287 9.727627 CAGCAAATCTTTATAGGAAATGAAGAC 57.272 33.333 0.00 0.00 0.00 3.01
4178 6290 9.512435 CACAGCAAATCTTTATAGGAAATGAAG 57.488 33.333 0.00 0.00 0.00 3.02
4190 6302 7.445096 TCATTTGAGTCTCACAGCAAATCTTTA 59.555 33.333 0.78 0.00 38.49 1.85
4256 6370 3.742640 GCTTCAGGGGAGCTATACAACAG 60.743 52.174 0.00 0.00 0.00 3.16
4262 6376 2.700897 GTCTTGCTTCAGGGGAGCTATA 59.299 50.000 0.00 0.00 0.00 1.31
4268 6382 1.075601 AATGGTCTTGCTTCAGGGGA 58.924 50.000 0.00 0.00 0.00 4.81
4377 6492 3.536158 TGATTAGTTTGCAGCGAACAC 57.464 42.857 24.80 14.08 30.67 3.32
4410 6525 3.871594 GGACAGTAAAATGACAGGATCGG 59.128 47.826 0.00 0.00 0.00 4.18
4412 6527 5.104259 AGGGACAGTAAAATGACAGGATC 57.896 43.478 0.00 0.00 0.00 3.36
4468 6589 3.055963 TGGCATGGCAAAAGATCGAATTT 60.056 39.130 21.13 0.00 0.00 1.82
4478 6599 1.117994 TGTGAACTGGCATGGCAAAA 58.882 45.000 23.47 6.11 0.00 2.44
4479 6600 0.388659 GTGTGAACTGGCATGGCAAA 59.611 50.000 23.47 6.47 0.00 3.68
4483 6604 0.813184 GATGGTGTGAACTGGCATGG 59.187 55.000 0.00 0.00 0.00 3.66
4488 6610 2.205022 ACATGGATGGTGTGAACTGG 57.795 50.000 0.00 0.00 0.00 4.00
4493 6615 3.362870 TGCATAACATGGATGGTGTGA 57.637 42.857 5.66 0.00 38.69 3.58
4522 6644 9.979578 ACATGCATTTTGTAAAGAGAACAAATA 57.020 25.926 0.00 0.00 44.05 1.40
4535 6657 6.207221 AGACACAGATTGACATGCATTTTGTA 59.793 34.615 0.00 0.00 0.00 2.41
4543 6665 3.593096 TGAGAGACACAGATTGACATGC 58.407 45.455 0.00 0.00 0.00 4.06
4552 6674 1.270518 GCTTTGCCTGAGAGACACAGA 60.271 52.381 0.00 0.00 37.54 3.41
4562 6684 1.881973 GTGAATGACAGCTTTGCCTGA 59.118 47.619 0.00 0.00 36.67 3.86
4567 6689 4.514441 ACTTCAGAGTGAATGACAGCTTTG 59.486 41.667 0.00 0.00 35.59 2.77
4582 6704 3.249559 GCTTTCTGTTGGTGACTTCAGAG 59.750 47.826 0.00 0.00 40.00 3.35
4618 6740 8.417106 TCAGTGATATCAACTTCCAGTATCTTC 58.583 37.037 7.07 0.00 0.00 2.87
4662 6784 0.459489 GTGCACAAAGCTTGGAACCA 59.541 50.000 13.17 0.00 45.94 3.67
4664 6786 2.618709 AGTAGTGCACAAAGCTTGGAAC 59.381 45.455 21.04 1.81 45.94 3.62
4742 6864 2.287188 GGTATCAATTGCCTGCATGACG 60.287 50.000 0.00 0.00 0.00 4.35
4743 6865 2.689471 TGGTATCAATTGCCTGCATGAC 59.311 45.455 0.00 0.00 0.00 3.06
4787 6909 0.389817 CCGTTTGGTGATCTCTGCGA 60.390 55.000 0.00 0.00 0.00 5.10
4799 6921 2.260869 CCACTCACCAGCCGTTTGG 61.261 63.158 1.19 1.19 44.09 3.28
4802 6924 3.414136 TTGCCACTCACCAGCCGTT 62.414 57.895 0.00 0.00 0.00 4.44
4804 6926 3.357079 GTTGCCACTCACCAGCCG 61.357 66.667 0.00 0.00 0.00 5.52
4830 6952 2.194859 AGAGCCTGAACATGGATGTCT 58.805 47.619 0.00 0.00 40.80 3.41
4831 6953 2.706339 AGAGCCTGAACATGGATGTC 57.294 50.000 0.00 0.00 40.80 3.06
4890 7014 5.517054 GTCTGCGACAAGAGGTAAATTCTAG 59.483 44.000 4.20 0.00 32.09 2.43
4894 7018 3.244422 TGGTCTGCGACAAGAGGTAAATT 60.244 43.478 10.14 0.00 33.68 1.82
4908 7032 2.426522 TCTTTCATTTCCTGGTCTGCG 58.573 47.619 0.00 0.00 0.00 5.18
4909 7033 3.129988 CCATCTTTCATTTCCTGGTCTGC 59.870 47.826 0.00 0.00 0.00 4.26
5006 7130 1.351017 TCCTGCTTGGGTCCTTGTTAG 59.649 52.381 0.00 0.00 36.20 2.34
5063 7187 2.370849 TGACTACTTGGGGAAGTCCAAC 59.629 50.000 0.00 0.00 41.44 3.77
5106 7230 1.669115 GCGGTTGCTCTTGCTCAGA 60.669 57.895 0.00 0.00 40.48 3.27
5123 7249 8.814235 ACGTTTCAACTATACTACATATGTTGC 58.186 33.333 14.77 0.00 35.02 4.17
5181 7307 2.973899 CCACTCTCCAGGGACGTG 59.026 66.667 0.00 6.19 0.00 4.49
5275 7401 2.562738 ACTTTTTCCTTACCATGCTGGC 59.437 45.455 2.50 0.00 42.67 4.85
5311 7437 8.600449 TTGTGGATTTGATCATTTTGGTTAAC 57.400 30.769 0.00 0.00 0.00 2.01
5389 7515 2.525368 GGGTGGTCAAGCTTATGGTTT 58.475 47.619 0.00 0.00 0.00 3.27
5410 7551 3.558505 CTTCACCTGCGACAAAATTCAG 58.441 45.455 0.00 0.00 0.00 3.02
5415 7556 1.593196 CTCCTTCACCTGCGACAAAA 58.407 50.000 0.00 0.00 0.00 2.44
5518 7660 0.526662 CTTCTTCGCCTGACCTACGT 59.473 55.000 0.00 0.00 0.00 3.57
5525 7667 2.418746 GGTATTCTGCTTCTTCGCCTGA 60.419 50.000 0.00 0.00 0.00 3.86
5530 7672 2.990066 AGGGGTATTCTGCTTCTTCG 57.010 50.000 0.00 0.00 0.00 3.79
5542 7684 5.103940 TGAAGTAGTACCGAACTAGGGGTAT 60.104 44.000 11.33 5.54 41.42 2.73
5543 7685 4.227300 TGAAGTAGTACCGAACTAGGGGTA 59.773 45.833 5.73 5.73 41.42 3.69
5544 7686 3.010584 TGAAGTAGTACCGAACTAGGGGT 59.989 47.826 7.43 7.43 41.42 4.95
5555 7697 4.022503 ACCTGAACGAACTGAAGTAGTACC 60.023 45.833 0.00 0.00 39.18 3.34
5614 7756 2.088104 AGGATCTACATCTGCCGGAA 57.912 50.000 5.05 0.00 0.00 4.30
5705 7851 6.427853 CAGTCTCCAGTGAAACAAACATCATA 59.572 38.462 0.00 0.00 41.43 2.15
5731 7881 2.644992 GCAAAAGTGGCCTCGGTG 59.355 61.111 3.32 2.64 0.00 4.94
5756 9489 3.896648 ACCAACATTGCTACGTTTCAG 57.103 42.857 0.00 0.00 0.00 3.02
5803 9558 8.749354 TGCTCAGTACAGAAGTTCAAATAGATA 58.251 33.333 5.50 0.00 0.00 1.98
5818 9573 2.392821 GATCATCGCTGCTCAGTACAG 58.607 52.381 0.00 0.00 38.22 2.74
5834 9589 1.956043 AAAAAGCTTGCGCCGATCA 59.044 47.368 4.18 0.00 36.60 2.92
5870 9625 3.366396 ACAGTACCTACAGCTACAGCAT 58.634 45.455 3.70 0.00 45.16 3.79
5919 9674 0.878416 TTGGTCATACGCCAAGCAAC 59.122 50.000 0.00 0.00 40.69 4.17
5941 9696 2.281900 CGGTCCCCGCCAGAAAAA 60.282 61.111 0.00 0.00 41.17 1.94
5962 9717 1.139989 CGAGAGAAGAAAACGCTGCA 58.860 50.000 0.00 0.00 0.00 4.41
5965 9720 0.033504 TGGCGAGAGAAGAAAACGCT 59.966 50.000 0.00 0.00 46.71 5.07
6026 9781 0.107456 CTTCAGGTGACAGTGTGCCT 59.893 55.000 0.00 5.23 0.00 4.75
6036 9791 3.706373 GGCGAGGCCTTCAGGTGA 61.706 66.667 6.77 0.00 46.69 4.02
6046 9801 3.665675 AACACGATCCAGGCGAGGC 62.666 63.158 0.00 0.00 0.00 4.70
6047 9802 1.811266 CAACACGATCCAGGCGAGG 60.811 63.158 0.00 0.00 0.00 4.63
6048 9803 1.811266 CCAACACGATCCAGGCGAG 60.811 63.158 0.00 0.00 0.00 5.03
6051 9806 1.154205 CGATCCAACACGATCCAGGC 61.154 60.000 0.00 0.00 36.13 4.85
6069 9824 1.816835 TCACTCAAGCCTACCACTACG 59.183 52.381 0.00 0.00 0.00 3.51
6091 9876 4.293648 CAGTGACCCGACACGGCA 62.294 66.667 4.57 0.00 46.86 5.69
6099 9884 0.317160 TGAACTGCTACAGTGACCCG 59.683 55.000 0.15 0.00 44.62 5.28
6135 9920 4.084287 ACCACTACCTCGTCAATAACTCA 58.916 43.478 0.00 0.00 0.00 3.41
6148 9933 3.280295 CAGAGATACGTGACCACTACCT 58.720 50.000 0.00 0.00 0.00 3.08
6152 9937 1.202582 GTGCAGAGATACGTGACCACT 59.797 52.381 0.00 0.00 0.00 4.00
6163 9948 2.581354 GACGCCCTGTGCAGAGAT 59.419 61.111 13.38 0.00 41.33 2.75
6178 9976 1.658994 TCAAATGTAATCGGCCGGAC 58.341 50.000 27.83 20.77 0.00 4.79
6189 9987 4.883585 ACGTACTACTCCGGATCAAATGTA 59.116 41.667 3.57 1.16 0.00 2.29
6191 9989 4.303086 ACGTACTACTCCGGATCAAATG 57.697 45.455 3.57 0.00 0.00 2.32
6206 10004 4.037684 GCCATAGTTGATCCAGTACGTACT 59.962 45.833 22.45 22.45 36.90 2.73
6207 10005 4.296690 GCCATAGTTGATCCAGTACGTAC 58.703 47.826 18.10 18.10 0.00 3.67
6208 10006 3.319972 GGCCATAGTTGATCCAGTACGTA 59.680 47.826 0.00 0.00 0.00 3.57
6226 10024 1.116536 TGACAACAGACGTAGGGCCA 61.117 55.000 6.18 0.00 0.00 5.36
6227 10025 0.389948 CTGACAACAGACGTAGGGCC 60.390 60.000 0.00 0.00 46.03 5.80
6229 10027 0.389948 GCCTGACAACAGACGTAGGG 60.390 60.000 0.00 0.00 46.03 3.53
6231 10029 0.603569 AGGCCTGACAACAGACGTAG 59.396 55.000 3.11 0.00 46.03 3.51
6232 10030 0.317160 CAGGCCTGACAACAGACGTA 59.683 55.000 29.88 0.00 46.03 3.57
6233 10031 1.069765 CAGGCCTGACAACAGACGT 59.930 57.895 29.88 0.00 46.03 4.34
6286 10085 4.091424 CGATGATTCGCTTGAAGAAAACC 58.909 43.478 0.00 0.00 38.75 3.27
6342 10143 7.034685 TCGTTATCGATCTCTTGGTTTATCA 57.965 36.000 0.00 0.00 41.35 2.15
6343 10144 7.925703 TTCGTTATCGATCTCTTGGTTTATC 57.074 36.000 0.00 0.00 45.65 1.75
6345 10146 7.437267 GGATTTCGTTATCGATCTCTTGGTTTA 59.563 37.037 0.00 0.00 45.65 2.01
6350 10151 5.980116 ACTGGATTTCGTTATCGATCTCTTG 59.020 40.000 0.00 0.00 45.65 3.02
6383 10184 1.134075 CTGCGACACAGCTCAATGC 59.866 57.895 0.00 0.00 40.19 3.56
6384 10185 1.150827 TTCTGCGACACAGCTCAATG 58.849 50.000 0.00 0.00 46.76 2.82
6385 10186 1.882912 TTTCTGCGACACAGCTCAAT 58.117 45.000 0.00 0.00 46.76 2.57
6386 10187 1.662517 TTTTCTGCGACACAGCTCAA 58.337 45.000 0.00 0.00 46.76 3.02
6387 10188 1.662517 TTTTTCTGCGACACAGCTCA 58.337 45.000 0.00 0.00 46.76 4.26
6388 10189 2.977405 ATTTTTCTGCGACACAGCTC 57.023 45.000 0.00 0.00 46.76 4.09
6389 10190 3.189287 CCTTATTTTTCTGCGACACAGCT 59.811 43.478 0.00 0.00 46.76 4.24
6390 10191 3.058224 ACCTTATTTTTCTGCGACACAGC 60.058 43.478 0.00 0.00 46.76 4.40
6392 10193 4.576873 TCAACCTTATTTTTCTGCGACACA 59.423 37.500 0.00 0.00 0.00 3.72
6393 10194 5.103290 TCAACCTTATTTTTCTGCGACAC 57.897 39.130 0.00 0.00 0.00 3.67
6394 10195 4.320202 GCTCAACCTTATTTTTCTGCGACA 60.320 41.667 0.00 0.00 0.00 4.35
6395 10196 4.083271 AGCTCAACCTTATTTTTCTGCGAC 60.083 41.667 0.00 0.00 0.00 5.19
6396 10197 4.072131 AGCTCAACCTTATTTTTCTGCGA 58.928 39.130 0.00 0.00 0.00 5.10
6397 10198 4.083324 TCAGCTCAACCTTATTTTTCTGCG 60.083 41.667 0.00 0.00 0.00 5.18
6398 10199 5.376854 TCAGCTCAACCTTATTTTTCTGC 57.623 39.130 0.00 0.00 0.00 4.26
6399 10200 6.152379 GGTTCAGCTCAACCTTATTTTTCTG 58.848 40.000 13.00 0.00 42.46 3.02
6400 10201 5.833131 TGGTTCAGCTCAACCTTATTTTTCT 59.167 36.000 21.04 0.00 45.54 2.52
6401 10202 5.920840 GTGGTTCAGCTCAACCTTATTTTTC 59.079 40.000 21.04 0.00 45.54 2.29
6402 10203 5.507315 CGTGGTTCAGCTCAACCTTATTTTT 60.507 40.000 21.04 0.00 45.54 1.94
6403 10204 4.023193 CGTGGTTCAGCTCAACCTTATTTT 60.023 41.667 21.04 0.00 45.54 1.82
6404 10205 3.502211 CGTGGTTCAGCTCAACCTTATTT 59.498 43.478 21.04 0.00 45.54 1.40
6405 10206 3.074412 CGTGGTTCAGCTCAACCTTATT 58.926 45.455 21.04 0.00 45.54 1.40
6406 10207 2.699954 CGTGGTTCAGCTCAACCTTAT 58.300 47.619 21.04 0.00 45.54 1.73
6407 10208 1.876416 GCGTGGTTCAGCTCAACCTTA 60.876 52.381 21.04 0.00 45.54 2.69
6408 10209 1.166531 GCGTGGTTCAGCTCAACCTT 61.167 55.000 21.04 0.00 45.54 3.50
6409 10210 1.598130 GCGTGGTTCAGCTCAACCT 60.598 57.895 21.04 0.00 45.54 3.50
6410 10211 2.617274 GGCGTGGTTCAGCTCAACC 61.617 63.158 13.42 13.42 45.54 3.77
6411 10212 2.946762 GGCGTGGTTCAGCTCAAC 59.053 61.111 0.00 0.00 0.00 3.18
6412 10213 2.664851 CGGCGTGGTTCAGCTCAA 60.665 61.111 0.00 0.00 0.00 3.02
6413 10214 4.680237 CCGGCGTGGTTCAGCTCA 62.680 66.667 6.01 0.00 0.00 4.26
6422 10223 3.719144 GGTTCGAAACCGGCGTGG 61.719 66.667 0.32 0.00 42.62 4.94
6430 10231 2.543031 GCCAAGACCTTTGGTTCGAAAC 60.543 50.000 6.16 6.16 41.53 2.78
6431 10232 1.679153 GCCAAGACCTTTGGTTCGAAA 59.321 47.619 0.00 0.00 41.53 3.46
6432 10233 1.133915 AGCCAAGACCTTTGGTTCGAA 60.134 47.619 7.67 0.00 41.53 3.71
6433 10234 0.472471 AGCCAAGACCTTTGGTTCGA 59.528 50.000 7.67 0.00 41.53 3.71
6434 10235 0.593128 CAGCCAAGACCTTTGGTTCG 59.407 55.000 7.67 0.00 41.53 3.95
6435 10236 0.961753 CCAGCCAAGACCTTTGGTTC 59.038 55.000 7.67 0.00 41.53 3.62
6436 10237 0.469892 CCCAGCCAAGACCTTTGGTT 60.470 55.000 7.67 0.00 41.53 3.67
6437 10238 1.153756 CCCAGCCAAGACCTTTGGT 59.846 57.895 7.67 0.00 41.53 3.67
6438 10239 1.607467 CCCCAGCCAAGACCTTTGG 60.607 63.158 1.59 1.59 42.37 3.28
6439 10240 0.895559 GTCCCCAGCCAAGACCTTTG 60.896 60.000 0.00 0.00 0.00 2.77
6440 10241 1.360393 TGTCCCCAGCCAAGACCTTT 61.360 55.000 0.00 0.00 0.00 3.11
6441 10242 1.142688 ATGTCCCCAGCCAAGACCTT 61.143 55.000 0.00 0.00 0.00 3.50
6442 10243 1.142688 AATGTCCCCAGCCAAGACCT 61.143 55.000 0.00 0.00 0.00 3.85
6443 10244 0.681243 GAATGTCCCCAGCCAAGACC 60.681 60.000 0.00 0.00 0.00 3.85
6444 10245 0.329596 AGAATGTCCCCAGCCAAGAC 59.670 55.000 0.00 0.00 0.00 3.01
6445 10246 0.620556 GAGAATGTCCCCAGCCAAGA 59.379 55.000 0.00 0.00 0.00 3.02
6446 10247 0.622665 AGAGAATGTCCCCAGCCAAG 59.377 55.000 0.00 0.00 0.00 3.61
6447 10248 1.075601 AAGAGAATGTCCCCAGCCAA 58.924 50.000 0.00 0.00 0.00 4.52
6448 10249 1.004745 GAAAGAGAATGTCCCCAGCCA 59.995 52.381 0.00 0.00 0.00 4.75
6449 10250 1.004745 TGAAAGAGAATGTCCCCAGCC 59.995 52.381 0.00 0.00 0.00 4.85
6450 10251 2.496899 TGAAAGAGAATGTCCCCAGC 57.503 50.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.