Multiple sequence alignment - TraesCS3D01G280900

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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 TraesCS3D01G280900 chr3D 100.000 4744 0 0 1 4744 388795723 388790980 0.000000e+00 8761.0
1 TraesCS3D01G280900 chr3D 94.068 118 7 0 1875 1992 315480460 315480577 3.770000e-41 180.0
2 TraesCS3D01G280900 chr3D 98.276 58 1 0 3717 3774 388791949 388791892 8.400000e-18 102.0
3 TraesCS3D01G280900 chr3D 98.276 58 1 0 3775 3832 388792007 388791950 8.400000e-18 102.0
4 TraesCS3D01G280900 chr3D 89.362 47 1 4 1841 1886 609076737 609076780 6.630000e-04 56.5
5 TraesCS3D01G280900 chr3A 94.837 3370 100 20 465 3781 509866797 509863449 0.000000e+00 5192.0
6 TraesCS3D01G280900 chr3A 98.061 619 12 0 1 619 509867660 509867042 0.000000e+00 1077.0
7 TraesCS3D01G280900 chr3A 94.017 468 21 5 3775 4241 509863510 509863049 0.000000e+00 702.0
8 TraesCS3D01G280900 chr3A 89.020 255 8 7 4493 4744 509862759 509862522 9.980000e-77 298.0
9 TraesCS3D01G280900 chr3A 92.308 117 8 1 4235 4350 688902022 688901906 1.060000e-36 165.0
10 TraesCS3D01G280900 chr3B 94.597 1388 32 9 708 2086 506197264 506195911 0.000000e+00 2108.0
11 TraesCS3D01G280900 chr3B 96.237 1063 33 5 2113 3171 506195846 506194787 0.000000e+00 1735.0
12 TraesCS3D01G280900 chr3B 97.165 635 18 0 1 635 506198201 506197567 0.000000e+00 1074.0
13 TraesCS3D01G280900 chr3B 91.274 573 42 6 3205 3774 506194660 506194093 0.000000e+00 774.0
14 TraesCS3D01G280900 chr3B 86.458 480 41 10 3775 4241 506194149 506193681 5.480000e-139 505.0
15 TraesCS3D01G280900 chr3B 82.979 282 19 19 4471 4732 506193528 506193256 1.330000e-55 228.0
16 TraesCS3D01G280900 chr3B 93.220 118 8 0 1875 1992 245935494 245935611 1.750000e-39 174.0
17 TraesCS3D01G280900 chr3B 93.220 118 8 0 1875 1992 404830436 404830319 1.750000e-39 174.0
18 TraesCS3D01G280900 chr3B 94.444 36 1 1 1847 1882 651256238 651256204 2.000000e-03 54.7
19 TraesCS3D01G280900 chr6B 95.690 116 5 0 4236 4351 506128092 506127977 2.250000e-43 187.0
20 TraesCS3D01G280900 chr6B 93.750 112 7 0 4237 4348 204159245 204159134 8.160000e-38 169.0
21 TraesCS3D01G280900 chr6B 83.761 117 17 1 4344 4458 457661620 457661736 5.020000e-20 110.0
22 TraesCS3D01G280900 chr6B 86.517 89 9 3 4362 4448 91022516 91022429 1.410000e-15 95.3
23 TraesCS3D01G280900 chr6B 89.855 69 6 1 4362 4429 217169140 217169072 2.350000e-13 87.9
24 TraesCS3D01G280900 chrUn 96.364 110 4 0 4236 4345 94181980 94181871 1.050000e-41 182.0
25 TraesCS3D01G280900 chr6D 93.966 116 7 0 4236 4351 318149815 318149930 4.880000e-40 176.0
26 TraesCS3D01G280900 chr6D 86.842 152 18 2 1843 1992 296196852 296197003 8.160000e-38 169.0
27 TraesCS3D01G280900 chr6D 91.667 120 8 2 4227 4345 388542912 388543030 1.060000e-36 165.0
28 TraesCS3D01G280900 chr6D 86.047 86 10 2 4362 4445 357026449 357026364 1.820000e-14 91.6
29 TraesCS3D01G280900 chr6D 89.855 69 6 1 4362 4429 123159114 123159046 2.350000e-13 87.9
30 TraesCS3D01G280900 chr5D 87.821 156 11 3 1845 1992 204323227 204323382 4.880000e-40 176.0
31 TraesCS3D01G280900 chr5D 91.045 134 6 3 1875 2003 233044473 233044605 4.880000e-40 176.0
32 TraesCS3D01G280900 chr4A 93.966 116 7 0 1877 1992 48905873 48905988 4.880000e-40 176.0
33 TraesCS3D01G280900 chr4A 82.022 89 13 3 4362 4448 483944772 483944685 6.590000e-09 73.1
34 TraesCS3D01G280900 chr7D 95.413 109 4 1 4238 4346 60693479 60693372 6.310000e-39 172.0
35 TraesCS3D01G280900 chr1D 95.370 108 5 0 4238 4345 465596911 465596804 6.310000e-39 172.0
36 TraesCS3D01G280900 chr1A 92.982 114 8 0 4238 4351 498166988 498166875 2.940000e-37 167.0
37 TraesCS3D01G280900 chr1A 86.813 91 11 1 4344 4433 498534337 498534427 3.020000e-17 100.0
38 TraesCS3D01G280900 chr2D 84.393 173 21 6 1836 2005 342571197 342571366 1.060000e-36 165.0
39 TraesCS3D01G280900 chr2A 85.535 159 20 3 1836 1992 452797740 452797897 3.800000e-36 163.0
40 TraesCS3D01G280900 chr6A 82.906 117 17 2 4344 4458 427619766 427619651 8.400000e-18 102.0
41 TraesCS3D01G280900 chr6A 95.652 46 1 1 4195 4239 81185465 81185510 6.590000e-09 73.1
42 TraesCS3D01G280900 chr6A 94.444 36 1 1 1847 1882 498584375 498584409 2.000000e-03 54.7
43 TraesCS3D01G280900 chr7B 88.235 85 8 2 4362 4444 481536518 481536602 3.020000e-17 100.0
44 TraesCS3D01G280900 chr7B 82.022 89 13 2 4362 4448 743860068 743860155 6.590000e-09 73.1
45 TraesCS3D01G280900 chr5B 86.517 89 9 3 4362 4448 35428471 35428558 1.410000e-15 95.3


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 TraesCS3D01G280900 chr3D 388790980 388795723 4743 True 2988.333333 8761 98.850667 1 4744 3 chr3D.!!$R1 4743
1 TraesCS3D01G280900 chr3A 509862522 509867660 5138 True 1817.250000 5192 93.983750 1 4744 4 chr3A.!!$R2 4743
2 TraesCS3D01G280900 chr3B 506193256 506198201 4945 True 1070.666667 2108 91.451667 1 4732 6 chr3B.!!$R3 4731

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
98 99 0.538584 TCCATGGTGCTAGTCTGCTG 59.461 55.0 12.58 0.0 0.00 4.41 F
1026 1656 1.059913 ACTGGAGTGAAAGTGAGGGG 58.940 55.0 0.00 0.0 0.00 4.79 F
1439 2069 0.480690 TGCCCCAAGTACAACCATGT 59.519 50.0 0.00 0.0 43.74 3.21 F
2110 2775 1.060713 CTGTACCAACGACTCAAGCG 58.939 55.0 0.00 0.0 0.00 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1134 1764 0.179081 GAACCCAGGTACATCGCTCC 60.179 60.0 0.00 0.0 0.00 4.70 R
2250 2934 0.183492 TTCCTCAAGTGGCAGCTTGT 59.817 50.0 21.09 0.0 44.41 3.16 R
2856 3543 0.528017 GCTAGCCCTCACAAAAAGGC 59.472 55.0 2.29 0.0 46.13 4.35 R
3779 4561 0.035881 CAGCTTCCCTTCAGCACTCA 59.964 55.0 0.00 0.0 39.99 3.41 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
52 53 7.113404 CAGTTAACACCACAATTCAAAGAATCG 59.887 37.037 8.61 0.00 0.00 3.34
98 99 0.538584 TCCATGGTGCTAGTCTGCTG 59.461 55.000 12.58 0.00 0.00 4.41
112 113 1.344438 TCTGCTGGACGTTGATGAAGT 59.656 47.619 0.00 0.00 0.00 3.01
255 256 5.181056 TCTTTTGAACTGCATTCGCTCATTA 59.819 36.000 0.00 0.00 40.56 1.90
297 298 2.238942 ATAAATCATGGCACGCGAGA 57.761 45.000 15.93 0.45 0.00 4.04
1026 1656 1.059913 ACTGGAGTGAAAGTGAGGGG 58.940 55.000 0.00 0.00 0.00 4.79
1079 1709 4.705519 CAGCCAAAACTGCCGCCG 62.706 66.667 0.00 0.00 0.00 6.46
1112 1742 1.548357 TTCTGCAGGGAGAGGAGCAC 61.548 60.000 15.13 0.00 32.87 4.40
1134 1764 0.803768 ATGCTGCTGTTACTCGCTCG 60.804 55.000 0.00 0.00 0.00 5.03
1409 2039 2.038952 ACTTGGAGAAGTATGCTGCACA 59.961 45.455 3.57 0.00 44.32 4.57
1439 2069 0.480690 TGCCCCAAGTACAACCATGT 59.519 50.000 0.00 0.00 43.74 3.21
1800 2434 8.519799 TTCCCCTCTATCATTATTGTTTTGAC 57.480 34.615 0.00 0.00 0.00 3.18
1928 2570 6.183360 ACGTTTTAGTGTGTTTCTTCACTCAG 60.183 38.462 1.08 0.00 42.77 3.35
1932 2574 5.091261 AGTGTGTTTCTTCACTCAGTTCT 57.909 39.130 0.00 0.00 40.28 3.01
1942 2584 4.790765 TCACTCAGTTCTGTCTGTATGG 57.209 45.455 0.00 0.00 36.85 2.74
1948 2590 3.511540 CAGTTCTGTCTGTATGGAGTCCA 59.488 47.826 15.88 15.88 38.19 4.02
1992 2634 6.299141 TCTTATATTTGTGAATGGAGGGAGC 58.701 40.000 0.00 0.00 0.00 4.70
2000 2642 4.210331 GTGAATGGAGGGAGCATATGTTT 58.790 43.478 4.29 0.00 0.00 2.83
2013 2655 8.045176 GGAGCATATGTTTCCCAATACTAATC 57.955 38.462 14.19 0.00 0.00 1.75
2014 2656 7.121315 GGAGCATATGTTTCCCAATACTAATCC 59.879 40.741 14.19 0.00 0.00 3.01
2015 2657 7.759607 AGCATATGTTTCCCAATACTAATCCT 58.240 34.615 4.29 0.00 0.00 3.24
2016 2658 8.890472 AGCATATGTTTCCCAATACTAATCCTA 58.110 33.333 4.29 0.00 0.00 2.94
2017 2659 9.686683 GCATATGTTTCCCAATACTAATCCTAT 57.313 33.333 4.29 0.00 0.00 2.57
2021 2663 8.561536 TGTTTCCCAATACTAATCCTATGAGA 57.438 34.615 0.00 0.00 0.00 3.27
2070 2715 6.610830 AGGTGTCCCCTGGTTAATATATTTG 58.389 40.000 2.68 0.00 44.08 2.32
2110 2775 1.060713 CTGTACCAACGACTCAAGCG 58.939 55.000 0.00 0.00 0.00 4.68
2149 2832 6.479884 AGGGAGGCATAATATCTGAAATCAC 58.520 40.000 0.00 0.00 0.00 3.06
2203 2887 2.956132 TCAAGGCCAAATTGGTTCTCA 58.044 42.857 14.17 0.55 40.46 3.27
2250 2934 4.274147 TGTGCAAAGTTCAGGGTTAAGAA 58.726 39.130 0.00 0.00 0.00 2.52
2319 3006 4.883585 TCCATTGCTGCCTATTAGTCTTTG 59.116 41.667 0.00 0.00 0.00 2.77
2360 3047 3.052455 TCATTTCCACGCATGTGTACT 57.948 42.857 12.39 0.00 44.92 2.73
2683 3370 1.620323 AGCAAGCATCCCTTCCAAAAC 59.380 47.619 0.00 0.00 0.00 2.43
2824 3511 8.466086 AGAGAAATTTGTGCCGATTAATTTTC 57.534 30.769 0.00 0.00 32.14 2.29
2856 3543 7.837202 ATCATTAAGTCCAAATGTTGCATTG 57.163 32.000 0.00 0.00 36.07 2.82
3262 4042 4.800249 GCTGCAATTTCTCCATTGGTTGAA 60.800 41.667 1.86 6.24 35.07 2.69
3384 4164 1.053424 ACAAGAGCAACGTCCCCTTA 58.947 50.000 0.00 0.00 0.00 2.69
3445 4225 7.881142 ACGAATTAAAATGACAGTTGGATGAA 58.119 30.769 0.00 0.00 0.00 2.57
3446 4226 8.356657 ACGAATTAAAATGACAGTTGGATGAAA 58.643 29.630 0.00 0.00 0.00 2.69
3447 4227 9.190858 CGAATTAAAATGACAGTTGGATGAAAA 57.809 29.630 0.00 0.00 0.00 2.29
3450 4230 9.829507 ATTAAAATGACAGTTGGATGAAAAACA 57.170 25.926 0.00 0.00 0.00 2.83
3451 4231 9.658799 TTAAAATGACAGTTGGATGAAAAACAA 57.341 25.926 0.00 0.00 0.00 2.83
3453 4233 7.718272 AATGACAGTTGGATGAAAAACAATG 57.282 32.000 0.00 0.00 0.00 2.82
3454 4234 5.049167 TGACAGTTGGATGAAAAACAATGC 58.951 37.500 0.00 0.00 0.00 3.56
3473 4255 1.458398 CAACCTGTGTGTGTTGACCA 58.542 50.000 0.00 0.00 43.50 4.02
3503 4285 8.492673 TGTCTGTCATATGTCAGTTTTATTCC 57.507 34.615 23.46 8.32 33.84 3.01
3538 4320 1.916651 CGTGCTCTTCTCTGAATCGTG 59.083 52.381 0.00 0.00 0.00 4.35
3754 4536 4.615834 GCTCTAGCTCCGGTCGCG 62.616 72.222 0.00 0.00 38.21 5.87
3756 4538 4.790962 TCTAGCTCCGGTCGCGGT 62.791 66.667 6.13 0.00 0.00 5.68
3757 4539 3.823330 CTAGCTCCGGTCGCGGTT 61.823 66.667 6.13 0.00 0.00 4.44
3758 4540 3.352338 CTAGCTCCGGTCGCGGTTT 62.352 63.158 6.13 0.00 0.00 3.27
3759 4541 3.636313 TAGCTCCGGTCGCGGTTTG 62.636 63.158 6.13 0.00 0.00 2.93
3761 4543 2.663852 CTCCGGTCGCGGTTTGTT 60.664 61.111 6.13 0.00 0.00 2.83
3762 4544 2.203042 TCCGGTCGCGGTTTGTTT 60.203 55.556 6.13 0.00 0.00 2.83
3763 4545 2.051703 CCGGTCGCGGTTTGTTTG 60.052 61.111 6.13 0.00 0.00 2.93
3764 4546 2.724358 CGGTCGCGGTTTGTTTGC 60.724 61.111 6.13 0.00 0.00 3.68
3765 4547 2.354188 GGTCGCGGTTTGTTTGCC 60.354 61.111 6.13 0.00 0.00 4.52
3766 4548 2.409651 GTCGCGGTTTGTTTGCCA 59.590 55.556 6.13 0.00 0.00 4.92
3767 4549 1.007849 GTCGCGGTTTGTTTGCCAT 60.008 52.632 6.13 0.00 0.00 4.40
3768 4550 1.007964 TCGCGGTTTGTTTGCCATG 60.008 52.632 6.13 0.00 0.00 3.66
3769 4551 2.021039 CGCGGTTTGTTTGCCATGG 61.021 57.895 7.63 7.63 0.00 3.66
3770 4552 1.068921 GCGGTTTGTTTGCCATGGT 59.931 52.632 14.67 0.00 0.00 3.55
3771 4553 1.220817 GCGGTTTGTTTGCCATGGTG 61.221 55.000 14.67 0.00 0.00 4.17
3772 4554 0.387202 CGGTTTGTTTGCCATGGTGA 59.613 50.000 14.67 0.00 0.00 4.02
3773 4555 1.864565 GGTTTGTTTGCCATGGTGAC 58.135 50.000 14.67 10.18 0.00 3.67
3774 4556 1.486439 GTTTGTTTGCCATGGTGACG 58.514 50.000 14.67 0.00 0.00 4.35
3775 4557 0.249238 TTTGTTTGCCATGGTGACGC 60.249 50.000 14.67 0.00 0.00 5.19
3776 4558 1.387295 TTGTTTGCCATGGTGACGCA 61.387 50.000 14.67 0.92 0.00 5.24
3777 4559 1.081242 GTTTGCCATGGTGACGCAG 60.081 57.895 14.67 0.00 33.30 5.18
3789 4571 4.855105 ACGCAGTTGAGTGCTGAA 57.145 50.000 8.97 0.00 37.78 3.02
3790 4572 2.609825 ACGCAGTTGAGTGCTGAAG 58.390 52.632 8.97 0.00 37.78 3.02
3791 4573 0.882042 ACGCAGTTGAGTGCTGAAGG 60.882 55.000 8.97 0.00 37.78 3.46
3792 4574 1.572085 CGCAGTTGAGTGCTGAAGGG 61.572 60.000 8.97 0.00 41.62 3.95
3793 4575 0.250467 GCAGTTGAGTGCTGAAGGGA 60.250 55.000 3.61 0.00 40.54 4.20
3794 4576 1.815408 GCAGTTGAGTGCTGAAGGGAA 60.815 52.381 3.61 0.00 40.54 3.97
3795 4577 2.149578 CAGTTGAGTGCTGAAGGGAAG 58.850 52.381 0.00 0.00 36.12 3.46
3796 4578 0.877743 GTTGAGTGCTGAAGGGAAGC 59.122 55.000 0.00 0.00 41.22 3.86
3797 4579 0.767375 TTGAGTGCTGAAGGGAAGCT 59.233 50.000 0.00 0.00 41.42 3.74
3798 4580 0.035881 TGAGTGCTGAAGGGAAGCTG 59.964 55.000 0.00 0.00 41.42 4.24
3799 4581 0.036022 GAGTGCTGAAGGGAAGCTGT 59.964 55.000 0.00 0.00 41.42 4.40
3800 4582 1.276421 GAGTGCTGAAGGGAAGCTGTA 59.724 52.381 0.00 0.00 41.42 2.74
3801 4583 1.277557 AGTGCTGAAGGGAAGCTGTAG 59.722 52.381 0.00 0.00 41.42 2.74
3802 4584 0.036010 TGCTGAAGGGAAGCTGTAGC 60.036 55.000 0.00 0.00 41.42 3.58
3813 4595 4.554363 CTGTAGCTCCGGTCGCGG 62.554 72.222 6.13 0.00 0.00 6.46
3853 4635 2.045926 GAAGGCGTGCCATGGACT 60.046 61.111 18.40 1.47 38.92 3.85
3895 4677 3.965379 TGTGTAGGTTTGGCGAGAATA 57.035 42.857 0.00 0.00 0.00 1.75
3928 4712 0.606401 CGACTCCAGCCATGTGGTTT 60.606 55.000 2.52 0.00 38.88 3.27
3973 4757 3.467803 CCTTGGTAGTGCTTGTATAGGC 58.532 50.000 0.00 0.00 0.00 3.93
4057 4841 0.104855 TGCTGTGTATCATCCTCGGC 59.895 55.000 0.00 0.00 0.00 5.54
4067 4851 0.037605 CATCCTCGGCGGGGTAATAC 60.038 60.000 27.52 0.00 0.00 1.89
4145 4938 5.366768 TGGTTTTCCCTATATCAGGTCTCTG 59.633 44.000 0.00 0.00 43.80 3.35
4161 4954 3.247886 GTCTCTGTCCGTTTCTTTTCACC 59.752 47.826 0.00 0.00 0.00 4.02
4178 4971 6.713762 TTTCACCCTGCATATTAGATTTGG 57.286 37.500 0.00 0.00 0.00 3.28
4242 5037 6.699575 AAATGCCAACATCTACAATACTCC 57.300 37.500 0.00 0.00 34.62 3.85
4243 5038 4.150897 TGCCAACATCTACAATACTCCC 57.849 45.455 0.00 0.00 0.00 4.30
4244 5039 3.780294 TGCCAACATCTACAATACTCCCT 59.220 43.478 0.00 0.00 0.00 4.20
4245 5040 4.141711 TGCCAACATCTACAATACTCCCTC 60.142 45.833 0.00 0.00 0.00 4.30
4246 5041 4.743955 GCCAACATCTACAATACTCCCTCC 60.744 50.000 0.00 0.00 0.00 4.30
4247 5042 4.501571 CCAACATCTACAATACTCCCTCCG 60.502 50.000 0.00 0.00 0.00 4.63
4248 5043 3.912248 ACATCTACAATACTCCCTCCGT 58.088 45.455 0.00 0.00 0.00 4.69
4249 5044 4.287552 ACATCTACAATACTCCCTCCGTT 58.712 43.478 0.00 0.00 0.00 4.44
4250 5045 4.341520 ACATCTACAATACTCCCTCCGTTC 59.658 45.833 0.00 0.00 0.00 3.95
4251 5046 3.972133 TCTACAATACTCCCTCCGTTCA 58.028 45.455 0.00 0.00 0.00 3.18
4252 5047 3.698040 TCTACAATACTCCCTCCGTTCAC 59.302 47.826 0.00 0.00 0.00 3.18
4253 5048 2.537143 ACAATACTCCCTCCGTTCACT 58.463 47.619 0.00 0.00 0.00 3.41
4254 5049 2.904434 ACAATACTCCCTCCGTTCACTT 59.096 45.455 0.00 0.00 0.00 3.16
4255 5050 3.326880 ACAATACTCCCTCCGTTCACTTT 59.673 43.478 0.00 0.00 0.00 2.66
4256 5051 4.202430 ACAATACTCCCTCCGTTCACTTTT 60.202 41.667 0.00 0.00 0.00 2.27
4257 5052 5.012354 ACAATACTCCCTCCGTTCACTTTTA 59.988 40.000 0.00 0.00 0.00 1.52
4258 5053 5.952347 ATACTCCCTCCGTTCACTTTTAT 57.048 39.130 0.00 0.00 0.00 1.40
4259 5054 7.093201 ACAATACTCCCTCCGTTCACTTTTATA 60.093 37.037 0.00 0.00 0.00 0.98
4260 5055 5.750352 ACTCCCTCCGTTCACTTTTATAA 57.250 39.130 0.00 0.00 0.00 0.98
4261 5056 5.731591 ACTCCCTCCGTTCACTTTTATAAG 58.268 41.667 0.00 0.00 37.40 1.73
4262 5057 5.247792 ACTCCCTCCGTTCACTTTTATAAGT 59.752 40.000 0.00 0.00 45.40 2.24
4263 5058 5.727434 TCCCTCCGTTCACTTTTATAAGTC 58.273 41.667 0.00 0.00 42.67 3.01
4264 5059 4.565564 CCCTCCGTTCACTTTTATAAGTCG 59.434 45.833 0.00 0.00 42.67 4.18
4265 5060 5.166398 CCTCCGTTCACTTTTATAAGTCGT 58.834 41.667 0.00 0.00 42.67 4.34
4266 5061 5.636543 CCTCCGTTCACTTTTATAAGTCGTT 59.363 40.000 0.00 0.00 42.67 3.85
4267 5062 6.146673 CCTCCGTTCACTTTTATAAGTCGTTT 59.853 38.462 0.00 0.00 42.67 3.60
4268 5063 7.109006 TCCGTTCACTTTTATAAGTCGTTTC 57.891 36.000 0.00 0.00 42.67 2.78
4269 5064 6.700960 TCCGTTCACTTTTATAAGTCGTTTCA 59.299 34.615 0.00 0.00 42.67 2.69
4270 5065 7.007697 CCGTTCACTTTTATAAGTCGTTTCAG 58.992 38.462 0.00 0.00 42.67 3.02
4271 5066 7.095940 CCGTTCACTTTTATAAGTCGTTTCAGA 60.096 37.037 0.00 0.00 42.67 3.27
4272 5067 7.734726 CGTTCACTTTTATAAGTCGTTTCAGAC 59.265 37.037 0.00 0.00 42.67 3.51
4273 5068 8.545420 GTTCACTTTTATAAGTCGTTTCAGACA 58.455 33.333 0.00 0.00 42.67 3.41
4274 5069 8.651391 TCACTTTTATAAGTCGTTTCAGACAA 57.349 30.769 0.00 0.00 42.67 3.18
4275 5070 8.761497 TCACTTTTATAAGTCGTTTCAGACAAG 58.239 33.333 0.00 0.00 42.67 3.16
4276 5071 8.548721 CACTTTTATAAGTCGTTTCAGACAAGT 58.451 33.333 0.00 0.00 42.67 3.16
4277 5072 8.548721 ACTTTTATAAGTCGTTTCAGACAAGTG 58.451 33.333 0.00 0.00 40.60 3.16
4278 5073 8.651391 TTTTATAAGTCGTTTCAGACAAGTGA 57.349 30.769 0.00 0.00 43.24 3.41
4279 5074 8.651391 TTTATAAGTCGTTTCAGACAAGTGAA 57.349 30.769 0.00 0.00 43.24 3.18
4280 5075 8.651391 TTATAAGTCGTTTCAGACAAGTGAAA 57.349 30.769 0.00 0.00 42.79 2.69
4281 5076 5.873179 AAGTCGTTTCAGACAAGTGAAAA 57.127 34.783 0.76 0.00 45.65 2.29
4282 5077 6.436843 AAGTCGTTTCAGACAAGTGAAAAT 57.563 33.333 0.76 0.00 45.65 1.82
4283 5078 5.810525 AGTCGTTTCAGACAAGTGAAAATG 58.189 37.500 0.76 0.00 45.65 2.32
4284 5079 5.584649 AGTCGTTTCAGACAAGTGAAAATGA 59.415 36.000 0.76 0.76 45.65 2.57
4285 5080 5.904080 GTCGTTTCAGACAAGTGAAAATGAG 59.096 40.000 0.76 0.00 45.65 2.90
4286 5081 4.672413 CGTTTCAGACAAGTGAAAATGAGC 59.328 41.667 0.76 0.00 45.65 4.26
4287 5082 5.504665 CGTTTCAGACAAGTGAAAATGAGCT 60.505 40.000 0.76 0.00 45.65 4.09
4288 5083 6.292865 CGTTTCAGACAAGTGAAAATGAGCTA 60.293 38.462 0.76 0.00 45.65 3.32
4289 5084 6.545504 TTCAGACAAGTGAAAATGAGCTAC 57.454 37.500 0.00 0.00 33.41 3.58
4290 5085 5.858381 TCAGACAAGTGAAAATGAGCTACT 58.142 37.500 0.00 0.00 0.00 2.57
4291 5086 6.291377 TCAGACAAGTGAAAATGAGCTACTT 58.709 36.000 0.00 0.00 32.23 2.24
4292 5087 6.767902 TCAGACAAGTGAAAATGAGCTACTTT 59.232 34.615 0.00 0.00 29.78 2.66
4293 5088 7.931407 TCAGACAAGTGAAAATGAGCTACTTTA 59.069 33.333 0.00 0.00 29.78 1.85
4294 5089 8.012241 CAGACAAGTGAAAATGAGCTACTTTAC 58.988 37.037 0.00 0.00 29.78 2.01
4295 5090 7.715249 AGACAAGTGAAAATGAGCTACTTTACA 59.285 33.333 0.00 0.00 29.78 2.41
4296 5091 7.639945 ACAAGTGAAAATGAGCTACTTTACAC 58.360 34.615 0.00 0.00 29.78 2.90
4297 5092 6.803154 AGTGAAAATGAGCTACTTTACACC 57.197 37.500 0.00 0.00 31.19 4.16
4298 5093 6.534634 AGTGAAAATGAGCTACTTTACACCT 58.465 36.000 0.00 0.00 31.19 4.00
4299 5094 6.998673 AGTGAAAATGAGCTACTTTACACCTT 59.001 34.615 0.00 0.00 31.19 3.50
4300 5095 7.041098 AGTGAAAATGAGCTACTTTACACCTTG 60.041 37.037 0.00 0.00 31.19 3.61
4301 5096 6.770785 TGAAAATGAGCTACTTTACACCTTGT 59.229 34.615 0.00 0.00 0.00 3.16
4302 5097 7.284489 TGAAAATGAGCTACTTTACACCTTGTT 59.716 33.333 0.00 0.00 0.00 2.83
4303 5098 7.582667 AAATGAGCTACTTTACACCTTGTTT 57.417 32.000 0.00 0.00 0.00 2.83
4304 5099 6.560253 ATGAGCTACTTTACACCTTGTTTG 57.440 37.500 0.00 0.00 0.00 2.93
4305 5100 5.676552 TGAGCTACTTTACACCTTGTTTGA 58.323 37.500 0.00 0.00 0.00 2.69
4306 5101 6.116806 TGAGCTACTTTACACCTTGTTTGAA 58.883 36.000 0.00 0.00 0.00 2.69
4307 5102 6.600032 TGAGCTACTTTACACCTTGTTTGAAA 59.400 34.615 0.00 0.00 0.00 2.69
4308 5103 7.284489 TGAGCTACTTTACACCTTGTTTGAAAT 59.716 33.333 0.00 0.00 0.00 2.17
4309 5104 7.425606 AGCTACTTTACACCTTGTTTGAAATG 58.574 34.615 0.00 0.00 0.00 2.32
4310 5105 7.068226 AGCTACTTTACACCTTGTTTGAAATGT 59.932 33.333 0.00 0.00 0.00 2.71
4311 5106 7.378728 GCTACTTTACACCTTGTTTGAAATGTC 59.621 37.037 0.00 0.00 0.00 3.06
4312 5107 7.404671 ACTTTACACCTTGTTTGAAATGTCT 57.595 32.000 0.00 0.00 0.00 3.41
4313 5108 7.836842 ACTTTACACCTTGTTTGAAATGTCTT 58.163 30.769 0.00 0.00 0.00 3.01
4314 5109 7.973944 ACTTTACACCTTGTTTGAAATGTCTTC 59.026 33.333 0.00 0.00 0.00 2.87
4315 5110 5.913137 ACACCTTGTTTGAAATGTCTTCA 57.087 34.783 0.00 0.00 0.00 3.02
4316 5111 6.279513 ACACCTTGTTTGAAATGTCTTCAA 57.720 33.333 0.00 0.00 36.71 2.69
4317 5112 6.332630 ACACCTTGTTTGAAATGTCTTCAAG 58.667 36.000 0.71 0.00 39.30 3.02
4318 5113 5.750067 CACCTTGTTTGAAATGTCTTCAAGG 59.250 40.000 21.45 21.45 43.58 3.61
4319 5114 4.746611 CCTTGTTTGAAATGTCTTCAAGGC 59.253 41.667 15.73 0.00 39.30 4.35
4320 5115 4.320608 TGTTTGAAATGTCTTCAAGGCC 57.679 40.909 0.00 0.00 39.30 5.19
4321 5116 3.960102 TGTTTGAAATGTCTTCAAGGCCT 59.040 39.130 0.00 0.00 39.30 5.19
4322 5117 4.405358 TGTTTGAAATGTCTTCAAGGCCTT 59.595 37.500 13.78 13.78 39.30 4.35
4323 5118 5.596361 TGTTTGAAATGTCTTCAAGGCCTTA 59.404 36.000 20.00 2.00 39.30 2.69
4324 5119 6.267471 TGTTTGAAATGTCTTCAAGGCCTTAT 59.733 34.615 20.00 3.68 39.30 1.73
4325 5120 7.450014 TGTTTGAAATGTCTTCAAGGCCTTATA 59.550 33.333 20.00 6.65 39.30 0.98
4326 5121 8.303876 GTTTGAAATGTCTTCAAGGCCTTATAA 58.696 33.333 20.00 14.54 39.30 0.98
4327 5122 8.415950 TTGAAATGTCTTCAAGGCCTTATAAA 57.584 30.769 20.00 11.96 33.90 1.40
4328 5123 8.415950 TGAAATGTCTTCAAGGCCTTATAAAA 57.584 30.769 20.00 9.43 0.00 1.52
4329 5124 8.522830 TGAAATGTCTTCAAGGCCTTATAAAAG 58.477 33.333 20.00 18.05 0.00 2.27
4330 5125 8.422577 AAATGTCTTCAAGGCCTTATAAAAGT 57.577 30.769 20.00 0.00 0.00 2.66
4331 5126 6.817765 TGTCTTCAAGGCCTTATAAAAGTG 57.182 37.500 20.00 3.72 0.00 3.16
4332 5127 6.539173 TGTCTTCAAGGCCTTATAAAAGTGA 58.461 36.000 20.00 6.54 0.00 3.41
4333 5128 7.001674 TGTCTTCAAGGCCTTATAAAAGTGAA 58.998 34.615 20.00 14.48 0.00 3.18
4334 5129 7.040686 TGTCTTCAAGGCCTTATAAAAGTGAAC 60.041 37.037 20.00 13.04 0.00 3.18
4335 5130 7.001674 TCTTCAAGGCCTTATAAAAGTGAACA 58.998 34.615 20.00 0.21 0.00 3.18
4336 5131 6.817765 TCAAGGCCTTATAAAAGTGAACAG 57.182 37.500 20.00 0.00 0.00 3.16
4337 5132 6.539173 TCAAGGCCTTATAAAAGTGAACAGA 58.461 36.000 20.00 2.74 0.00 3.41
4338 5133 6.655003 TCAAGGCCTTATAAAAGTGAACAGAG 59.345 38.462 20.00 0.00 0.00 3.35
4339 5134 5.501156 AGGCCTTATAAAAGTGAACAGAGG 58.499 41.667 0.00 0.00 0.00 3.69
4340 5135 4.640647 GGCCTTATAAAAGTGAACAGAGGG 59.359 45.833 0.00 0.00 0.00 4.30
4341 5136 5.497474 GCCTTATAAAAGTGAACAGAGGGA 58.503 41.667 0.00 0.00 0.00 4.20
4342 5137 5.586643 GCCTTATAAAAGTGAACAGAGGGAG 59.413 44.000 0.00 0.00 0.00 4.30
4343 5138 6.712276 CCTTATAAAAGTGAACAGAGGGAGT 58.288 40.000 0.00 0.00 0.00 3.85
4344 5139 7.580882 GCCTTATAAAAGTGAACAGAGGGAGTA 60.581 40.741 0.00 0.00 0.00 2.59
4345 5140 7.764901 CCTTATAAAAGTGAACAGAGGGAGTAC 59.235 40.741 0.00 0.00 0.00 2.73
4346 5141 6.936968 ATAAAAGTGAACAGAGGGAGTACT 57.063 37.500 0.00 0.00 0.00 2.73
4347 5142 9.537852 TTATAAAAGTGAACAGAGGGAGTACTA 57.462 33.333 0.00 0.00 0.00 1.82
4348 5143 6.742559 AAAAGTGAACAGAGGGAGTACTAA 57.257 37.500 0.00 0.00 0.00 2.24
4349 5144 6.742559 AAAGTGAACAGAGGGAGTACTAAA 57.257 37.500 0.00 0.00 0.00 1.85
4350 5145 5.986501 AGTGAACAGAGGGAGTACTAAAG 57.013 43.478 0.00 0.00 0.00 1.85
4351 5146 5.642165 AGTGAACAGAGGGAGTACTAAAGA 58.358 41.667 0.00 0.00 0.00 2.52
4352 5147 5.477637 AGTGAACAGAGGGAGTACTAAAGAC 59.522 44.000 0.00 0.00 0.00 3.01
4358 5153 5.186021 CAGAGGGAGTACTAAAGACACACAT 59.814 44.000 0.00 0.00 0.00 3.21
4458 5276 6.613233 TCGCAAAGTTTGACTTTAGACAAAA 58.387 32.000 19.82 0.00 45.84 2.44
4459 5277 6.745450 TCGCAAAGTTTGACTTTAGACAAAAG 59.255 34.615 19.82 0.00 45.84 2.27
4460 5278 6.745450 CGCAAAGTTTGACTTTAGACAAAAGA 59.255 34.615 19.82 0.00 45.84 2.52
4461 5279 7.272515 CGCAAAGTTTGACTTTAGACAAAAGAA 59.727 33.333 19.82 0.00 45.84 2.52
4464 5282 8.981724 AAGTTTGACTTTAGACAAAAGAAACC 57.018 30.769 8.53 0.00 46.44 3.27
4465 5283 8.117813 AGTTTGACTTTAGACAAAAGAAACCA 57.882 30.769 8.53 0.00 46.44 3.67
4466 5284 8.581578 AGTTTGACTTTAGACAAAAGAAACCAA 58.418 29.630 8.53 1.63 46.44 3.67
4500 5339 0.871722 TTTCCTCGTGCATCAAACCG 59.128 50.000 0.00 0.00 0.00 4.44
4563 5523 2.961062 ACAAGATTCTGCTTTGGTGCTT 59.039 40.909 0.00 0.00 0.00 3.91
4656 5627 3.418675 TCGGCTACGAGCTTTTGAG 57.581 52.632 6.78 0.00 45.59 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 6.038271 ACATCTACCAAAGAATGATTTACGGC 59.962 38.462 0.00 0.00 37.89 5.68
98 99 3.152261 AGATCGACTTCATCAACGTCC 57.848 47.619 0.00 0.00 0.00 4.79
112 113 4.832248 ACTATTCACCTGCAAAAGATCGA 58.168 39.130 0.00 0.00 0.00 3.59
163 164 1.197721 GTGCTATGAACTGTGTGTGCC 59.802 52.381 0.00 0.00 0.00 5.01
255 256 1.762460 CCCTATCGAGTGCCCCAGT 60.762 63.158 0.00 0.00 0.00 4.00
297 298 4.321230 GCTAAAGCAACTGCAACAGGTAAT 60.321 41.667 4.22 0.00 45.16 1.89
1026 1656 6.071391 GGAAGATAGGATCATGGACTCTCTTC 60.071 46.154 19.79 19.79 40.67 2.87
1079 1709 1.888512 TGCAGAATTCTTCAACAGGCC 59.111 47.619 4.86 0.00 0.00 5.19
1112 1742 0.649475 GCGAGTAACAGCAGCATCTG 59.351 55.000 0.00 3.99 39.86 2.90
1134 1764 0.179081 GAACCCAGGTACATCGCTCC 60.179 60.000 0.00 0.00 0.00 4.70
1439 2069 0.973632 ATACTCTGCACGAACCACCA 59.026 50.000 0.00 0.00 0.00 4.17
1776 2406 7.638444 TGTCAAAACAATAATGATAGAGGGGA 58.362 34.615 0.00 0.00 30.70 4.81
1777 2407 7.880160 TGTCAAAACAATAATGATAGAGGGG 57.120 36.000 0.00 0.00 30.70 4.79
1892 2534 8.693542 AACACACTAAAACGTGTCTATATACC 57.306 34.615 0.00 0.00 45.74 2.73
1900 2542 5.731263 GTGAAGAAACACACTAAAACGTGTC 59.269 40.000 0.00 0.00 45.74 3.67
1918 2560 5.047731 CCATACAGACAGAACTGAGTGAAGA 60.048 44.000 8.87 0.00 40.63 2.87
1919 2561 5.047731 TCCATACAGACAGAACTGAGTGAAG 60.048 44.000 8.87 2.29 40.63 3.02
1928 2570 4.744795 ATGGACTCCATACAGACAGAAC 57.255 45.455 9.00 0.00 43.19 3.01
1983 2625 1.494721 GGGAAACATATGCTCCCTCCA 59.505 52.381 26.20 0.00 44.81 3.86
2000 2642 6.156949 GCCATCTCATAGGATTAGTATTGGGA 59.843 42.308 0.00 0.00 0.00 4.37
2004 2646 7.885399 GGTTTGCCATCTCATAGGATTAGTATT 59.115 37.037 0.00 0.00 34.09 1.89
2005 2647 7.238514 AGGTTTGCCATCTCATAGGATTAGTAT 59.761 37.037 0.00 0.00 37.19 2.12
2006 2648 6.558775 AGGTTTGCCATCTCATAGGATTAGTA 59.441 38.462 0.00 0.00 37.19 1.82
2007 2649 5.370880 AGGTTTGCCATCTCATAGGATTAGT 59.629 40.000 0.00 0.00 37.19 2.24
2008 2650 5.874093 AGGTTTGCCATCTCATAGGATTAG 58.126 41.667 0.00 0.00 37.19 1.73
2009 2651 5.912149 AGGTTTGCCATCTCATAGGATTA 57.088 39.130 0.00 0.00 37.19 1.75
2010 2652 4.803329 AGGTTTGCCATCTCATAGGATT 57.197 40.909 0.00 0.00 37.19 3.01
2011 2653 5.012561 GTCTAGGTTTGCCATCTCATAGGAT 59.987 44.000 0.00 0.00 37.19 3.24
2012 2654 4.345257 GTCTAGGTTTGCCATCTCATAGGA 59.655 45.833 0.00 0.00 37.19 2.94
2013 2655 4.346418 AGTCTAGGTTTGCCATCTCATAGG 59.654 45.833 0.00 0.00 37.19 2.57
2014 2656 5.543507 AGTCTAGGTTTGCCATCTCATAG 57.456 43.478 0.00 0.00 37.19 2.23
2015 2657 6.040955 CACTAGTCTAGGTTTGCCATCTCATA 59.959 42.308 11.61 0.00 37.19 2.15
2016 2658 4.965532 ACTAGTCTAGGTTTGCCATCTCAT 59.034 41.667 11.61 0.00 37.19 2.90
2017 2659 4.160439 CACTAGTCTAGGTTTGCCATCTCA 59.840 45.833 11.61 0.00 37.19 3.27
2018 2660 4.442192 CCACTAGTCTAGGTTTGCCATCTC 60.442 50.000 11.61 0.00 37.19 2.75
2019 2661 3.452627 CCACTAGTCTAGGTTTGCCATCT 59.547 47.826 11.61 0.00 37.19 2.90
2020 2662 3.798202 CCACTAGTCTAGGTTTGCCATC 58.202 50.000 11.61 0.00 37.19 3.51
2021 2663 2.092914 GCCACTAGTCTAGGTTTGCCAT 60.093 50.000 11.61 0.00 37.19 4.40
2070 2715 3.130693 AGACGACTCAGCAAGTATAACCC 59.869 47.826 0.00 0.00 38.74 4.11
2082 2727 1.534163 TCGTTGGTACAGACGACTCAG 59.466 52.381 16.02 0.00 42.95 3.35
2110 2775 3.628032 GCCTCCCTTAAGTTGATAAGCAC 59.372 47.826 0.97 0.00 32.62 4.40
2203 2887 2.019897 GCCAACTTTGCTGCAGGTGT 62.020 55.000 17.12 0.38 0.00 4.16
2250 2934 0.183492 TTCCTCAAGTGGCAGCTTGT 59.817 50.000 21.09 0.00 44.41 3.16
2352 3039 5.410067 GCCAAACAATATGCAAGTACACAT 58.590 37.500 0.00 0.00 0.00 3.21
2360 3047 2.612471 GCTGTGGCCAAACAATATGCAA 60.612 45.455 7.24 0.00 0.00 4.08
2683 3370 1.345415 AGAAAACCCTGGCTTGCATTG 59.655 47.619 0.00 0.00 0.00 2.82
2792 3479 3.983344 CGGCACAAATTTCTCTTTTCTGG 59.017 43.478 0.00 0.00 0.00 3.86
2824 3511 8.004087 ACATTTGGACTTAATGATTGGATCAG 57.996 34.615 0.00 0.00 43.53 2.90
2856 3543 0.528017 GCTAGCCCTCACAAAAAGGC 59.472 55.000 2.29 0.00 46.13 4.35
3064 3751 1.984570 TGACTTGAGCTCGAGGGGG 60.985 63.158 30.37 10.70 0.00 5.40
3198 3978 3.231207 GAGACTGGTGGATAGGCTCTA 57.769 52.381 0.00 0.00 45.07 2.43
3203 3983 0.755686 GGCAGAGACTGGTGGATAGG 59.244 60.000 0.00 0.00 31.21 2.57
3262 4042 1.048601 CCCGGATACACCTGCATAGT 58.951 55.000 0.73 0.00 36.31 2.12
3384 4164 5.743636 AAATGTAATGCACCTTCAACCAT 57.256 34.783 0.00 0.00 0.00 3.55
3445 4225 3.260740 CACACACAGGTTGCATTGTTTT 58.739 40.909 0.00 0.00 0.00 2.43
3446 4226 2.233431 ACACACACAGGTTGCATTGTTT 59.767 40.909 0.00 0.00 0.00 2.83
3447 4227 1.824230 ACACACACAGGTTGCATTGTT 59.176 42.857 0.00 0.00 0.00 2.83
3448 4228 1.473258 ACACACACAGGTTGCATTGT 58.527 45.000 0.00 0.00 0.00 2.71
3449 4229 2.159268 TCAACACACACAGGTTGCATTG 60.159 45.455 0.00 0.00 43.06 2.82
3450 4230 2.098614 TCAACACACACAGGTTGCATT 58.901 42.857 0.00 0.00 43.06 3.56
3451 4231 1.405105 GTCAACACACACAGGTTGCAT 59.595 47.619 0.00 0.00 43.06 3.96
3453 4233 0.100503 GGTCAACACACACAGGTTGC 59.899 55.000 0.00 0.00 43.06 4.17
3454 4234 1.458398 TGGTCAACACACACAGGTTG 58.542 50.000 0.00 0.00 44.35 3.77
3473 4255 6.477053 AACTGACATATGACAGACAGCTAT 57.523 37.500 32.43 12.59 39.55 2.97
3503 4285 1.685640 GCACGCAAATGCCCATTTCG 61.686 55.000 16.47 16.47 38.84 3.46
3681 4463 2.608825 CGATCCTCCTCGCGTCGAT 61.609 63.158 5.77 0.78 34.61 3.59
3704 4486 0.318120 TCAACTGCTGCTCGATGTCA 59.682 50.000 0.00 0.00 0.00 3.58
3754 4536 1.864565 GTCACCATGGCAAACAAACC 58.135 50.000 13.04 0.00 0.00 3.27
3756 4538 0.249238 GCGTCACCATGGCAAACAAA 60.249 50.000 13.04 0.00 0.00 2.83
3757 4539 1.361993 GCGTCACCATGGCAAACAA 59.638 52.632 13.04 0.00 0.00 2.83
3758 4540 1.794151 CTGCGTCACCATGGCAAACA 61.794 55.000 13.04 3.17 36.06 2.83
3759 4541 1.081242 CTGCGTCACCATGGCAAAC 60.081 57.895 13.04 6.67 36.06 2.93
3760 4542 1.106351 AACTGCGTCACCATGGCAAA 61.106 50.000 13.04 0.00 36.06 3.68
3761 4543 1.528076 AACTGCGTCACCATGGCAA 60.528 52.632 13.04 0.00 36.06 4.52
3762 4544 2.112928 AACTGCGTCACCATGGCA 59.887 55.556 13.04 2.10 35.07 4.92
3763 4545 1.915614 CTCAACTGCGTCACCATGGC 61.916 60.000 13.04 0.00 0.00 4.40
3764 4546 0.603707 ACTCAACTGCGTCACCATGG 60.604 55.000 11.19 11.19 0.00 3.66
3765 4547 0.514255 CACTCAACTGCGTCACCATG 59.486 55.000 0.00 0.00 0.00 3.66
3766 4548 1.230635 GCACTCAACTGCGTCACCAT 61.231 55.000 0.00 0.00 0.00 3.55
3767 4549 1.887242 GCACTCAACTGCGTCACCA 60.887 57.895 0.00 0.00 0.00 4.17
3768 4550 1.595382 AGCACTCAACTGCGTCACC 60.595 57.895 0.00 0.00 42.42 4.02
3769 4551 0.875908 TCAGCACTCAACTGCGTCAC 60.876 55.000 0.00 0.00 42.42 3.67
3770 4552 0.179086 TTCAGCACTCAACTGCGTCA 60.179 50.000 0.00 0.00 42.42 4.35
3771 4553 0.510359 CTTCAGCACTCAACTGCGTC 59.490 55.000 0.00 0.00 42.42 5.19
3772 4554 0.882042 CCTTCAGCACTCAACTGCGT 60.882 55.000 0.00 0.00 42.42 5.24
3773 4555 1.572085 CCCTTCAGCACTCAACTGCG 61.572 60.000 0.00 0.00 42.42 5.18
3774 4556 0.250467 TCCCTTCAGCACTCAACTGC 60.250 55.000 0.00 0.00 37.44 4.40
3775 4557 2.149578 CTTCCCTTCAGCACTCAACTG 58.850 52.381 0.00 0.00 36.44 3.16
3776 4558 1.544314 GCTTCCCTTCAGCACTCAACT 60.544 52.381 0.00 0.00 37.22 3.16
3777 4559 0.877743 GCTTCCCTTCAGCACTCAAC 59.122 55.000 0.00 0.00 37.22 3.18
3778 4560 0.767375 AGCTTCCCTTCAGCACTCAA 59.233 50.000 0.00 0.00 39.99 3.02
3779 4561 0.035881 CAGCTTCCCTTCAGCACTCA 59.964 55.000 0.00 0.00 39.99 3.41
3780 4562 0.036022 ACAGCTTCCCTTCAGCACTC 59.964 55.000 0.00 0.00 39.99 3.51
3781 4563 1.277557 CTACAGCTTCCCTTCAGCACT 59.722 52.381 0.00 0.00 39.99 4.40
3782 4564 1.731720 CTACAGCTTCCCTTCAGCAC 58.268 55.000 0.00 0.00 39.99 4.40
3783 4565 0.036010 GCTACAGCTTCCCTTCAGCA 60.036 55.000 0.00 0.00 39.99 4.41
3784 4566 2.774044 GCTACAGCTTCCCTTCAGC 58.226 57.895 0.00 0.00 38.21 4.26
3805 4587 2.724358 GCAAACAAACCGCGACCG 60.724 61.111 8.23 0.00 0.00 4.79
3806 4588 2.354188 GGCAAACAAACCGCGACC 60.354 61.111 8.23 0.00 0.00 4.79
3807 4589 1.007849 ATGGCAAACAAACCGCGAC 60.008 52.632 8.23 0.00 0.00 5.19
3808 4590 1.007964 CATGGCAAACAAACCGCGA 60.008 52.632 8.23 0.00 0.00 5.87
3809 4591 2.021039 CCATGGCAAACAAACCGCG 61.021 57.895 0.00 0.00 0.00 6.46
3810 4592 1.068921 ACCATGGCAAACAAACCGC 59.931 52.632 13.04 0.00 0.00 5.68
3811 4593 0.387202 TCACCATGGCAAACAAACCG 59.613 50.000 13.04 0.00 0.00 4.44
3812 4594 1.137872 TGTCACCATGGCAAACAAACC 59.862 47.619 13.04 0.00 0.00 3.27
3813 4595 2.159114 ACTGTCACCATGGCAAACAAAC 60.159 45.455 13.04 0.32 28.17 2.93
3814 4596 2.106566 ACTGTCACCATGGCAAACAAA 58.893 42.857 13.04 0.00 28.17 2.83
3837 4619 2.202236 ATCAGTCCATGGCACGCCTT 62.202 55.000 6.96 0.00 36.94 4.35
3853 4635 9.671279 ACACATATATTCACAAACTCAAGATCA 57.329 29.630 0.00 0.00 0.00 2.92
3895 4677 2.290641 TGGAGTCGGCAAACATGGTATT 60.291 45.455 0.00 0.00 0.00 1.89
3928 4712 1.368641 CAACACAGCATAGCCGCTTA 58.631 50.000 0.00 0.00 41.38 3.09
4042 4826 1.006102 CCCGCCGAGGATGATACAC 60.006 63.158 0.00 0.00 45.00 2.90
4057 4841 4.011023 TGTCAAAACATGGTATTACCCCG 58.989 43.478 10.37 4.00 37.50 5.73
4067 4851 1.545582 AGCCCGATTGTCAAAACATGG 59.454 47.619 0.00 0.00 34.73 3.66
4138 4922 3.247886 GTGAAAAGAAACGGACAGAGACC 59.752 47.826 0.00 0.00 0.00 3.85
4145 4938 1.001706 GCAGGGTGAAAAGAAACGGAC 60.002 52.381 0.00 0.00 0.00 4.79
4161 4954 8.450578 TGACTTAACCAAATCTAATATGCAGG 57.549 34.615 0.00 0.00 0.00 4.85
4224 5019 4.501571 CGGAGGGAGTATTGTAGATGTTGG 60.502 50.000 0.00 0.00 0.00 3.77
4241 5036 4.565564 CGACTTATAAAAGTGAACGGAGGG 59.434 45.833 0.00 0.00 46.09 4.30
4242 5037 5.166398 ACGACTTATAAAAGTGAACGGAGG 58.834 41.667 0.00 0.00 46.09 4.30
4243 5038 6.701432 AACGACTTATAAAAGTGAACGGAG 57.299 37.500 0.00 0.00 46.09 4.63
4244 5039 6.700960 TGAAACGACTTATAAAAGTGAACGGA 59.299 34.615 0.00 0.00 46.09 4.69
4245 5040 6.879962 TGAAACGACTTATAAAAGTGAACGG 58.120 36.000 0.00 0.00 46.09 4.44
4246 5041 7.734726 GTCTGAAACGACTTATAAAAGTGAACG 59.265 37.037 0.00 0.00 46.09 3.95
4247 5042 8.545420 TGTCTGAAACGACTTATAAAAGTGAAC 58.455 33.333 0.00 0.00 46.09 3.18
4248 5043 8.651391 TGTCTGAAACGACTTATAAAAGTGAA 57.349 30.769 0.00 0.00 46.09 3.18
4249 5044 8.651391 TTGTCTGAAACGACTTATAAAAGTGA 57.349 30.769 0.00 0.00 46.09 3.41
4250 5045 8.548721 ACTTGTCTGAAACGACTTATAAAAGTG 58.451 33.333 0.00 0.00 46.09 3.16
4252 5047 8.761497 TCACTTGTCTGAAACGACTTATAAAAG 58.239 33.333 0.00 0.00 38.77 2.27
4253 5048 8.651391 TCACTTGTCTGAAACGACTTATAAAA 57.349 30.769 0.00 0.00 35.00 1.52
4254 5049 8.651391 TTCACTTGTCTGAAACGACTTATAAA 57.349 30.769 0.00 0.00 35.00 1.40
4255 5050 8.651391 TTTCACTTGTCTGAAACGACTTATAA 57.349 30.769 0.00 0.00 35.63 0.98
4256 5051 8.651391 TTTTCACTTGTCTGAAACGACTTATA 57.349 30.769 0.00 0.00 39.37 0.98
4257 5052 7.548196 TTTTCACTTGTCTGAAACGACTTAT 57.452 32.000 0.00 0.00 39.37 1.73
4258 5053 6.971527 TTTTCACTTGTCTGAAACGACTTA 57.028 33.333 0.00 0.00 39.37 2.24
4259 5054 5.873179 TTTTCACTTGTCTGAAACGACTT 57.127 34.783 0.00 0.00 39.37 3.01
4260 5055 5.584649 TCATTTTCACTTGTCTGAAACGACT 59.415 36.000 0.00 0.00 39.37 4.18
4261 5056 5.806286 TCATTTTCACTTGTCTGAAACGAC 58.194 37.500 0.00 0.00 39.37 4.34
4262 5057 5.504010 GCTCATTTTCACTTGTCTGAAACGA 60.504 40.000 0.00 0.00 39.37 3.85
4263 5058 4.672413 GCTCATTTTCACTTGTCTGAAACG 59.328 41.667 0.00 0.00 39.37 3.60
4264 5059 5.825507 AGCTCATTTTCACTTGTCTGAAAC 58.174 37.500 0.00 0.00 39.37 2.78
4265 5060 6.767902 AGTAGCTCATTTTCACTTGTCTGAAA 59.232 34.615 0.00 0.00 38.18 2.69
4266 5061 6.291377 AGTAGCTCATTTTCACTTGTCTGAA 58.709 36.000 0.00 0.00 0.00 3.02
4267 5062 5.858381 AGTAGCTCATTTTCACTTGTCTGA 58.142 37.500 0.00 0.00 0.00 3.27
4268 5063 6.551385 AAGTAGCTCATTTTCACTTGTCTG 57.449 37.500 0.00 0.00 0.00 3.51
4269 5064 7.715249 TGTAAAGTAGCTCATTTTCACTTGTCT 59.285 33.333 0.00 0.00 30.20 3.41
4270 5065 7.798982 GTGTAAAGTAGCTCATTTTCACTTGTC 59.201 37.037 18.25 7.84 35.24 3.18
4271 5066 7.255139 GGTGTAAAGTAGCTCATTTTCACTTGT 60.255 37.037 21.73 7.63 37.07 3.16
4272 5067 7.041098 AGGTGTAAAGTAGCTCATTTTCACTTG 60.041 37.037 21.73 0.00 37.07 3.16
4273 5068 6.998673 AGGTGTAAAGTAGCTCATTTTCACTT 59.001 34.615 21.73 16.31 37.07 3.16
4274 5069 6.534634 AGGTGTAAAGTAGCTCATTTTCACT 58.465 36.000 21.73 5.54 37.07 3.41
4275 5070 6.803154 AGGTGTAAAGTAGCTCATTTTCAC 57.197 37.500 17.70 17.70 36.52 3.18
4276 5071 6.770785 ACAAGGTGTAAAGTAGCTCATTTTCA 59.229 34.615 0.00 0.00 0.00 2.69
4277 5072 7.203255 ACAAGGTGTAAAGTAGCTCATTTTC 57.797 36.000 0.00 0.00 0.00 2.29
4278 5073 7.582667 AACAAGGTGTAAAGTAGCTCATTTT 57.417 32.000 0.00 0.00 0.00 1.82
4279 5074 7.284489 TCAAACAAGGTGTAAAGTAGCTCATTT 59.716 33.333 0.00 0.00 0.00 2.32
4280 5075 6.770785 TCAAACAAGGTGTAAAGTAGCTCATT 59.229 34.615 0.00 0.00 0.00 2.57
4281 5076 6.296026 TCAAACAAGGTGTAAAGTAGCTCAT 58.704 36.000 0.00 0.00 0.00 2.90
4282 5077 5.676552 TCAAACAAGGTGTAAAGTAGCTCA 58.323 37.500 0.00 0.00 0.00 4.26
4283 5078 6.613755 TTCAAACAAGGTGTAAAGTAGCTC 57.386 37.500 0.00 0.00 0.00 4.09
4284 5079 7.068226 ACATTTCAAACAAGGTGTAAAGTAGCT 59.932 33.333 0.00 0.00 0.00 3.32
4285 5080 7.200455 ACATTTCAAACAAGGTGTAAAGTAGC 58.800 34.615 0.00 0.00 0.00 3.58
4286 5081 8.621286 AGACATTTCAAACAAGGTGTAAAGTAG 58.379 33.333 0.00 0.00 0.00 2.57
4287 5082 8.514330 AGACATTTCAAACAAGGTGTAAAGTA 57.486 30.769 0.00 0.00 0.00 2.24
4288 5083 7.404671 AGACATTTCAAACAAGGTGTAAAGT 57.595 32.000 0.00 0.00 0.00 2.66
4289 5084 7.973388 TGAAGACATTTCAAACAAGGTGTAAAG 59.027 33.333 0.00 0.00 0.00 1.85
4290 5085 7.831753 TGAAGACATTTCAAACAAGGTGTAAA 58.168 30.769 0.00 0.00 0.00 2.01
4291 5086 7.397892 TGAAGACATTTCAAACAAGGTGTAA 57.602 32.000 0.00 0.00 0.00 2.41
4292 5087 7.397892 TTGAAGACATTTCAAACAAGGTGTA 57.602 32.000 0.19 0.00 35.69 2.90
4293 5088 5.913137 TGAAGACATTTCAAACAAGGTGT 57.087 34.783 0.00 0.00 0.00 4.16
4294 5089 5.750067 CCTTGAAGACATTTCAAACAAGGTG 59.250 40.000 16.45 0.00 44.15 4.00
4295 5090 5.906073 CCTTGAAGACATTTCAAACAAGGT 58.094 37.500 16.45 0.00 44.15 3.50
4297 5092 4.746611 GGCCTTGAAGACATTTCAAACAAG 59.253 41.667 0.00 0.00 37.89 3.16
4298 5093 4.405358 AGGCCTTGAAGACATTTCAAACAA 59.595 37.500 0.00 0.00 37.89 2.83
4299 5094 3.960102 AGGCCTTGAAGACATTTCAAACA 59.040 39.130 0.00 0.00 37.89 2.83
4300 5095 4.590850 AGGCCTTGAAGACATTTCAAAC 57.409 40.909 0.00 0.47 37.89 2.93
4301 5096 6.916360 ATAAGGCCTTGAAGACATTTCAAA 57.084 33.333 28.77 2.42 37.89 2.69
4302 5097 8.415950 TTTATAAGGCCTTGAAGACATTTCAA 57.584 30.769 28.77 2.92 36.98 2.69
4303 5098 8.415950 TTTTATAAGGCCTTGAAGACATTTCA 57.584 30.769 28.77 3.15 0.00 2.69
4304 5099 8.523658 ACTTTTATAAGGCCTTGAAGACATTTC 58.476 33.333 28.77 0.00 35.61 2.17
4305 5100 8.306761 CACTTTTATAAGGCCTTGAAGACATTT 58.693 33.333 28.77 0.00 35.61 2.32
4306 5101 7.669722 TCACTTTTATAAGGCCTTGAAGACATT 59.330 33.333 28.77 0.00 35.61 2.71
4307 5102 7.175104 TCACTTTTATAAGGCCTTGAAGACAT 58.825 34.615 28.77 14.50 35.61 3.06
4308 5103 6.539173 TCACTTTTATAAGGCCTTGAAGACA 58.461 36.000 28.77 7.10 35.61 3.41
4309 5104 7.040686 TGTTCACTTTTATAAGGCCTTGAAGAC 60.041 37.037 28.77 17.56 35.61 3.01
4310 5105 7.001674 TGTTCACTTTTATAAGGCCTTGAAGA 58.998 34.615 28.77 15.87 35.61 2.87
4311 5106 7.174946 TCTGTTCACTTTTATAAGGCCTTGAAG 59.825 37.037 28.77 24.09 35.61 3.02
4312 5107 7.001674 TCTGTTCACTTTTATAAGGCCTTGAA 58.998 34.615 28.77 17.44 35.61 2.69
4313 5108 6.539173 TCTGTTCACTTTTATAAGGCCTTGA 58.461 36.000 28.77 11.98 35.61 3.02
4314 5109 6.127897 CCTCTGTTCACTTTTATAAGGCCTTG 60.128 42.308 28.77 12.48 35.61 3.61
4315 5110 5.946377 CCTCTGTTCACTTTTATAAGGCCTT 59.054 40.000 24.18 24.18 35.61 4.35
4316 5111 5.501156 CCTCTGTTCACTTTTATAAGGCCT 58.499 41.667 0.00 0.00 35.61 5.19
4317 5112 4.640647 CCCTCTGTTCACTTTTATAAGGCC 59.359 45.833 0.00 0.00 35.61 5.19
4318 5113 5.497474 TCCCTCTGTTCACTTTTATAAGGC 58.503 41.667 0.00 0.00 35.61 4.35
4319 5114 6.712276 ACTCCCTCTGTTCACTTTTATAAGG 58.288 40.000 0.00 0.00 35.61 2.69
4320 5115 8.532819 AGTACTCCCTCTGTTCACTTTTATAAG 58.467 37.037 0.00 0.00 37.40 1.73
4321 5116 8.431910 AGTACTCCCTCTGTTCACTTTTATAA 57.568 34.615 0.00 0.00 0.00 0.98
4322 5117 9.537852 TTAGTACTCCCTCTGTTCACTTTTATA 57.462 33.333 0.00 0.00 0.00 0.98
4323 5118 6.936968 AGTACTCCCTCTGTTCACTTTTAT 57.063 37.500 0.00 0.00 0.00 1.40
4324 5119 7.844493 TTAGTACTCCCTCTGTTCACTTTTA 57.156 36.000 0.00 0.00 0.00 1.52
4325 5120 6.742559 TTAGTACTCCCTCTGTTCACTTTT 57.257 37.500 0.00 0.00 0.00 2.27
4326 5121 6.553852 TCTTTAGTACTCCCTCTGTTCACTTT 59.446 38.462 0.00 0.00 0.00 2.66
4327 5122 6.015265 GTCTTTAGTACTCCCTCTGTTCACTT 60.015 42.308 0.00 0.00 0.00 3.16
4328 5123 5.477637 GTCTTTAGTACTCCCTCTGTTCACT 59.522 44.000 0.00 0.00 0.00 3.41
4329 5124 5.243283 TGTCTTTAGTACTCCCTCTGTTCAC 59.757 44.000 0.00 0.00 0.00 3.18
4330 5125 5.243283 GTGTCTTTAGTACTCCCTCTGTTCA 59.757 44.000 0.00 0.00 0.00 3.18
4331 5126 5.243283 TGTGTCTTTAGTACTCCCTCTGTTC 59.757 44.000 0.00 0.00 0.00 3.18
4332 5127 5.010820 GTGTGTCTTTAGTACTCCCTCTGTT 59.989 44.000 0.00 0.00 0.00 3.16
4333 5128 4.523558 GTGTGTCTTTAGTACTCCCTCTGT 59.476 45.833 0.00 0.00 0.00 3.41
4334 5129 4.523173 TGTGTGTCTTTAGTACTCCCTCTG 59.477 45.833 0.00 0.00 0.00 3.35
4335 5130 4.737578 TGTGTGTCTTTAGTACTCCCTCT 58.262 43.478 0.00 0.00 0.00 3.69
4336 5131 5.662674 ATGTGTGTCTTTAGTACTCCCTC 57.337 43.478 0.00 0.00 0.00 4.30
4337 5132 5.307196 ACAATGTGTGTCTTTAGTACTCCCT 59.693 40.000 0.00 0.00 34.38 4.20
4338 5133 5.408604 CACAATGTGTGTCTTTAGTACTCCC 59.591 44.000 5.00 0.00 43.08 4.30
4339 5134 6.467723 CACAATGTGTGTCTTTAGTACTCC 57.532 41.667 5.00 0.00 43.08 3.85
4349 5144 9.814899 TGAAATTAATTTTCACAATGTGTGTCT 57.185 25.926 14.45 0.00 46.80 3.41
4422 5218 4.547406 AACTTTGCGAGTTTGTAGGAAC 57.453 40.909 0.00 0.00 46.34 3.62
4463 5281 8.750298 ACGAGGAAATATATATACTCCTGTTGG 58.250 37.037 22.47 14.37 36.64 3.77
4464 5282 9.574458 CACGAGGAAATATATATACTCCTGTTG 57.426 37.037 22.47 16.70 36.64 3.33
4465 5283 8.251721 GCACGAGGAAATATATATACTCCTGTT 58.748 37.037 22.47 11.56 36.64 3.16
4466 5284 7.396339 TGCACGAGGAAATATATATACTCCTGT 59.604 37.037 22.47 18.16 36.64 4.00
4563 5523 7.120432 TGCAAGTGACATAACATAACATAAGCA 59.880 33.333 0.00 0.00 0.00 3.91
4597 5557 5.643777 GGAGCAAAGCAAGAGTAATTCTACA 59.356 40.000 0.00 0.00 34.14 2.74
4598 5558 5.643777 TGGAGCAAAGCAAGAGTAATTCTAC 59.356 40.000 0.00 0.00 34.14 2.59
4656 5627 2.264120 GAGGGGCCTCTTCTTGAGCC 62.264 65.000 6.58 0.00 41.35 4.70
4670 5641 0.105453 TGGCTAGCTAGGAAGAGGGG 60.105 60.000 22.10 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.