Multiple sequence alignment - TraesCS3B01G390800

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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 TraesCS3B01G390800 chr3B 100.000 4994 0 0 1 4994 615770968 615775961 0.000000e+00 9223.0
1 TraesCS3B01G390800 chr3B 97.788 3843 50 27 1 3839 616312854 616309043 0.000000e+00 6593.0
2 TraesCS3B01G390800 chr3B 93.705 2081 85 33 1773 3839 615749642 615751690 0.000000e+00 3075.0
3 TraesCS3B01G390800 chr3B 89.024 492 22 10 979 1441 615748825 615749313 9.320000e-162 580.0
4 TraesCS3B01G390800 chr3B 100.000 38 0 0 4074 4111 156575407 156575444 2.490000e-08 71.3
5 TraesCS3B01G390800 chr3D 95.082 2196 73 15 1775 3955 463191735 463189560 0.000000e+00 3424.0
6 TraesCS3B01G390800 chr3D 95.829 1894 66 8 1775 3657 462850915 462852806 0.000000e+00 3048.0
7 TraesCS3B01G390800 chr3D 91.053 950 58 9 1 925 463193997 463193050 0.000000e+00 1258.0
8 TraesCS3B01G390800 chr3D 91.224 433 26 5 954 1379 462849902 462850329 3.350000e-161 579.0
9 TraesCS3B01G390800 chr3D 91.224 433 26 5 954 1379 463192748 463192321 3.350000e-161 579.0
10 TraesCS3B01G390800 chr3D 87.925 265 17 6 4475 4733 463188527 463188272 1.050000e-76 298.0
11 TraesCS3B01G390800 chr3D 85.185 135 13 4 4717 4849 463187714 463187585 1.130000e-26 132.0
12 TraesCS3B01G390800 chr3A 90.112 2326 143 46 1553 3848 606436338 606434070 0.000000e+00 2940.0
13 TraesCS3B01G390800 chr3A 89.779 949 71 11 1 925 606438120 606437174 0.000000e+00 1192.0
14 TraesCS3B01G390800 chr3A 88.150 481 50 7 385 861 51887381 51887858 2.610000e-157 566.0
15 TraesCS3B01G390800 chr3A 86.848 479 58 5 385 861 124337552 124338027 9.520000e-147 531.0
16 TraesCS3B01G390800 chr3A 88.915 424 26 10 970 1376 606436888 606436469 2.080000e-138 503.0
17 TraesCS3B01G390800 chr1B 89.675 1753 169 7 1878 3628 512174641 512172899 0.000000e+00 2224.0
18 TraesCS3B01G390800 chr1B 86.929 482 51 11 385 862 502784500 502784973 9.520000e-147 531.0
19 TraesCS3B01G390800 chr1B 94.146 205 12 0 1118 1322 512175818 512175614 3.750000e-81 313.0
20 TraesCS3B01G390800 chr1B 95.146 103 5 0 4849 4951 306076901 306076799 4.000000e-36 163.0
21 TraesCS3B01G390800 chr1B 95.000 40 2 0 4075 4114 633131108 633131147 4.170000e-06 63.9
22 TraesCS3B01G390800 chr1A 89.459 1755 171 8 1878 3629 482337730 482335987 0.000000e+00 2204.0
23 TraesCS3B01G390800 chr1A 93.659 205 13 0 1118 1322 482338966 482338762 1.750000e-79 307.0
24 TraesCS3B01G390800 chr1A 100.000 37 0 0 4074 4110 291255937 291255973 8.970000e-08 69.4
25 TraesCS3B01G390800 chr1D 89.435 1751 169 10 1879 3625 382236377 382234639 0.000000e+00 2194.0
26 TraesCS3B01G390800 chr1D 93.780 209 12 1 1118 1325 382237628 382237420 3.750000e-81 313.0
27 TraesCS3B01G390800 chr4A 86.323 1784 218 21 1862 3631 110638851 110637080 0.000000e+00 1919.0
28 TraesCS3B01G390800 chr4A 86.667 480 55 9 385 861 275392966 275392493 1.590000e-144 523.0
29 TraesCS3B01G390800 chr4A 86.207 58 5 3 4076 4131 104100325 104100269 5.400000e-05 60.2
30 TraesCS3B01G390800 chr4D 87.917 480 50 8 385 861 405211559 405212033 4.370000e-155 558.0
31 TraesCS3B01G390800 chr4D 88.514 148 15 2 4848 4994 366329989 366329843 1.430000e-40 178.0
32 TraesCS3B01G390800 chr7A 87.164 483 55 7 385 864 70197163 70196685 4.400000e-150 542.0
33 TraesCS3B01G390800 chr7A 91.216 148 12 1 4848 4994 552974987 552975134 3.050000e-47 200.0
34 TraesCS3B01G390800 chr7A 90.152 132 11 1 4849 4980 206929159 206929030 2.390000e-38 171.0
35 TraesCS3B01G390800 chr7A 97.222 36 1 0 862 897 432698342 432698307 1.500000e-05 62.1
36 TraesCS3B01G390800 chr2B 89.030 237 19 6 1097 1330 534839206 534839438 2.280000e-73 287.0
37 TraesCS3B01G390800 chr2D 94.483 145 8 0 4850 4994 373890072 373890216 1.810000e-54 224.0
38 TraesCS3B01G390800 chr2D 100.000 35 0 0 4075 4109 376051370 376051404 1.160000e-06 65.8
39 TraesCS3B01G390800 chr5B 95.000 140 6 1 4856 4994 345349892 345350031 8.420000e-53 219.0
40 TraesCS3B01G390800 chr5B 97.368 38 1 0 4074 4111 490761043 490761080 1.160000e-06 65.8
41 TraesCS3B01G390800 chr4B 89.189 148 15 1 4848 4994 599442072 599442219 3.070000e-42 183.0
42 TraesCS3B01G390800 chr4B 88.514 148 14 3 4848 4994 450926100 450925955 5.140000e-40 176.0
43 TraesCS3B01G390800 chr7B 85.417 144 21 0 4851 4994 622266676 622266819 3.110000e-32 150.0
44 TraesCS3B01G390800 chr7D 93.333 45 3 0 4076 4120 625914841 625914797 3.230000e-07 67.6
45 TraesCS3B01G390800 chr6A 86.441 59 7 1 4074 4132 54785220 54785163 4.170000e-06 63.9
46 TraesCS3B01G390800 chr6A 97.143 35 1 0 3985 4019 63560037 63560003 5.400000e-05 60.2
47 TraesCS3B01G390800 chrUn 84.127 63 7 3 4071 4132 69441227 69441287 1.940000e-04 58.4


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 TraesCS3B01G390800 chr3B 615770968 615775961 4993 False 9223.0 9223 100.0000 1 4994 1 chr3B.!!$F2 4993
1 TraesCS3B01G390800 chr3B 616309043 616312854 3811 True 6593.0 6593 97.7880 1 3839 1 chr3B.!!$R1 3838
2 TraesCS3B01G390800 chr3B 615748825 615751690 2865 False 1827.5 3075 91.3645 979 3839 2 chr3B.!!$F3 2860
3 TraesCS3B01G390800 chr3D 462849902 462852806 2904 False 1813.5 3048 93.5265 954 3657 2 chr3D.!!$F1 2703
4 TraesCS3B01G390800 chr3D 463187585 463193997 6412 True 1138.2 3424 90.0938 1 4849 5 chr3D.!!$R1 4848
5 TraesCS3B01G390800 chr3A 606434070 606438120 4050 True 1545.0 2940 89.6020 1 3848 3 chr3A.!!$R1 3847
6 TraesCS3B01G390800 chr1B 512172899 512175818 2919 True 1268.5 2224 91.9105 1118 3628 2 chr1B.!!$R2 2510
7 TraesCS3B01G390800 chr1A 482335987 482338966 2979 True 1255.5 2204 91.5590 1118 3629 2 chr1A.!!$R1 2511
8 TraesCS3B01G390800 chr1D 382234639 382237628 2989 True 1253.5 2194 91.6075 1118 3625 2 chr1D.!!$R1 2507
9 TraesCS3B01G390800 chr4A 110637080 110638851 1771 True 1919.0 1919 86.3230 1862 3631 1 chr4A.!!$R2 1769

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
478 514 0.179121 TCATCGGTTCGATTGTCGGG 60.179 55.000 0.00 0.00 44.59 5.14 F
739 776 1.135660 GCTTTCTAGAAAACCAGCCGC 60.136 52.381 18.25 12.36 0.00 6.53 F
1332 1693 3.696084 GGTACGTCCTCCTGCACT 58.304 61.111 0.00 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1332 1693 4.861196 TCTAAGCTAGAAGAAGAGGAGCA 58.139 43.478 0.0 0.0 35.55 4.26 R
3447 4608 2.359602 TCCTCGAACTCGTCCGCT 60.360 61.111 0.0 0.0 40.80 5.52 R
3993 5241 0.766674 TTATGGGACGGAGGGATGGG 60.767 60.000 0.0 0.0 0.00 4.00 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
323 347 3.676646 GGGTAACAACAGTAGTAGCAACG 59.323 47.826 0.00 0.00 39.74 4.10
478 514 0.179121 TCATCGGTTCGATTGTCGGG 60.179 55.000 0.00 0.00 44.59 5.14
739 776 1.135660 GCTTTCTAGAAAACCAGCCGC 60.136 52.381 18.25 12.36 0.00 6.53
1332 1693 3.696084 GGTACGTCCTCCTGCACT 58.304 61.111 0.00 0.00 0.00 4.40
3447 4608 3.936203 ACCAACCAGCTCGCGGAA 61.936 61.111 6.13 0.00 0.00 4.30
3495 4656 2.270205 CTGGAGGGCGTCTGCAAT 59.730 61.111 7.19 0.00 43.27 3.56
3498 4659 2.586792 GAGGGCGTCTGCAATCCT 59.413 61.111 0.00 0.00 45.35 3.24
3525 4686 1.078497 CAAGATGTACCAGGGCGCA 60.078 57.895 10.83 0.00 0.00 6.09
3680 4880 5.240623 GTCTGAAGTCTCTGAACTCTGAAGA 59.759 44.000 0.00 0.00 31.99 2.87
3708 4918 3.821033 GGATTGTAGTGTTTGGCTGTTCT 59.179 43.478 0.00 0.00 0.00 3.01
3785 4995 5.700832 TGTCAGTGTTGTTGATGTAATCCTC 59.299 40.000 0.00 0.00 44.73 3.71
3810 5020 5.657474 ACTTTCGATCGATTTAAGTAGCCA 58.343 37.500 24.87 3.15 0.00 4.75
3821 5031 0.389426 AAGTAGCCAGCGTTGTACCG 60.389 55.000 0.00 0.00 0.00 4.02
3848 5058 6.803807 GTGTTTGCTTGGATCAAGTTATCTTC 59.196 38.462 9.07 0.00 42.77 2.87
3855 5065 6.139679 TGGATCAAGTTATCTTCCCTGTTT 57.860 37.500 0.00 0.00 0.00 2.83
3860 5070 5.699458 TCAAGTTATCTTCCCTGTTTCGTTC 59.301 40.000 0.00 0.00 0.00 3.95
3863 5073 5.701290 AGTTATCTTCCCTGTTTCGTTCTTG 59.299 40.000 0.00 0.00 0.00 3.02
3905 5119 0.439985 CCGCACGATCAACTGACTTG 59.560 55.000 0.00 0.00 0.00 3.16
3960 5208 5.368256 GACGTTCACTACAGAAAGTCCTA 57.632 43.478 10.32 0.00 45.25 2.94
3963 5211 7.458409 ACGTTCACTACAGAAAGTCCTATTA 57.542 36.000 0.00 0.00 35.77 0.98
3974 5222 9.660180 ACAGAAAGTCCTATTAGAGATTTCAAC 57.340 33.333 12.72 0.00 30.44 3.18
3987 5235 9.886132 TTAGAGATTTCAACATAAACTACTCCC 57.114 33.333 0.00 0.00 0.00 4.30
3988 5236 8.152023 AGAGATTTCAACATAAACTACTCCCT 57.848 34.615 0.00 0.00 0.00 4.20
3989 5237 8.261522 AGAGATTTCAACATAAACTACTCCCTC 58.738 37.037 0.00 0.00 0.00 4.30
3990 5238 7.339482 AGATTTCAACATAAACTACTCCCTCC 58.661 38.462 0.00 0.00 0.00 4.30
3991 5239 4.730949 TCAACATAAACTACTCCCTCCG 57.269 45.455 0.00 0.00 0.00 4.63
3993 5241 4.159135 TCAACATAAACTACTCCCTCCGTC 59.841 45.833 0.00 0.00 0.00 4.79
3994 5242 3.029570 ACATAAACTACTCCCTCCGTCC 58.970 50.000 0.00 0.00 0.00 4.79
3995 5243 2.149973 TAAACTACTCCCTCCGTCCC 57.850 55.000 0.00 0.00 0.00 4.46
3996 5244 0.115745 AAACTACTCCCTCCGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37
3997 5245 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
3998 5246 0.106116 ACTACTCCCTCCGTCCCATC 60.106 60.000 0.00 0.00 0.00 3.51
3999 5247 0.828343 CTACTCCCTCCGTCCCATCC 60.828 65.000 0.00 0.00 0.00 3.51
4000 5248 2.308118 TACTCCCTCCGTCCCATCCC 62.308 65.000 0.00 0.00 0.00 3.85
4001 5249 3.364964 TCCCTCCGTCCCATCCCT 61.365 66.667 0.00 0.00 0.00 4.20
4002 5250 2.844839 CCCTCCGTCCCATCCCTC 60.845 72.222 0.00 0.00 0.00 4.30
4003 5251 2.844839 CCTCCGTCCCATCCCTCC 60.845 72.222 0.00 0.00 0.00 4.30
4004 5252 3.227276 CTCCGTCCCATCCCTCCG 61.227 72.222 0.00 0.00 0.00 4.63
4005 5253 4.070265 TCCGTCCCATCCCTCCGT 62.070 66.667 0.00 0.00 0.00 4.69
4006 5254 3.537874 CCGTCCCATCCCTCCGTC 61.538 72.222 0.00 0.00 0.00 4.79
4007 5255 3.537874 CGTCCCATCCCTCCGTCC 61.538 72.222 0.00 0.00 0.00 4.79
4008 5256 3.162154 GTCCCATCCCTCCGTCCC 61.162 72.222 0.00 0.00 0.00 4.46
4009 5257 3.690206 TCCCATCCCTCCGTCCCA 61.690 66.667 0.00 0.00 0.00 4.37
4010 5258 2.448542 CCCATCCCTCCGTCCCAT 60.449 66.667 0.00 0.00 0.00 4.00
4011 5259 1.152118 CCCATCCCTCCGTCCCATA 60.152 63.158 0.00 0.00 0.00 2.74
4012 5260 0.766674 CCCATCCCTCCGTCCCATAA 60.767 60.000 0.00 0.00 0.00 1.90
4013 5261 1.362224 CCATCCCTCCGTCCCATAAT 58.638 55.000 0.00 0.00 0.00 1.28
4014 5262 2.546899 CCATCCCTCCGTCCCATAATA 58.453 52.381 0.00 0.00 0.00 0.98
4015 5263 3.115390 CCATCCCTCCGTCCCATAATAT 58.885 50.000 0.00 0.00 0.00 1.28
4016 5264 4.295201 CCATCCCTCCGTCCCATAATATA 58.705 47.826 0.00 0.00 0.00 0.86
4017 5265 4.719773 CCATCCCTCCGTCCCATAATATAA 59.280 45.833 0.00 0.00 0.00 0.98
4018 5266 5.163301 CCATCCCTCCGTCCCATAATATAAG 60.163 48.000 0.00 0.00 0.00 1.73
4019 5267 5.019657 TCCCTCCGTCCCATAATATAAGT 57.980 43.478 0.00 0.00 0.00 2.24
4020 5268 6.156554 TCCCTCCGTCCCATAATATAAGTA 57.843 41.667 0.00 0.00 0.00 2.24
4021 5269 6.192773 TCCCTCCGTCCCATAATATAAGTAG 58.807 44.000 0.00 0.00 0.00 2.57
4022 5270 6.011362 TCCCTCCGTCCCATAATATAAGTAGA 60.011 42.308 0.00 0.00 0.00 2.59
4023 5271 6.839657 CCCTCCGTCCCATAATATAAGTAGAT 59.160 42.308 0.00 0.00 0.00 1.98
4024 5272 8.003044 CCCTCCGTCCCATAATATAAGTAGATA 58.997 40.741 0.00 0.00 0.00 1.98
4025 5273 9.589461 CCTCCGTCCCATAATATAAGTAGATAT 57.411 37.037 0.00 0.00 0.00 1.63
4051 5299 7.746034 TGAATACGGTTGTATATCGACGTATTC 59.254 37.037 28.38 28.38 44.11 1.75
4054 5302 6.825584 ACGGTTGTATATCGACGTATTCTAG 58.174 40.000 0.00 0.00 0.00 2.43
4064 5312 7.966246 ATCGACGTATTCTAGAGTGTAGATT 57.034 36.000 0.00 0.00 0.00 2.40
4067 5315 7.042858 TCGACGTATTCTAGAGTGTAGATTCAC 60.043 40.741 0.00 0.00 38.46 3.18
4080 5328 7.827701 AGTGTAGATTCACTCTTTCGTATTGA 58.172 34.615 0.00 0.00 44.07 2.57
4081 5329 8.304596 AGTGTAGATTCACTCTTTCGTATTGAA 58.695 33.333 0.00 0.00 44.07 2.69
4086 5334 9.442047 AGATTCACTCTTTCGTATTGAAATCTT 57.558 29.630 0.00 0.00 45.21 2.40
4096 5587 9.974980 TTTCGTATTGAAATCTTTAAAAAGGCT 57.025 25.926 2.77 0.00 41.59 4.58
4138 5629 7.499563 AGAGAGTACTTTTTCTTTTGTTCCTCC 59.500 37.037 0.00 0.00 0.00 4.30
4160 5651 2.203337 GACAGGGTTGCTGTGCCA 60.203 61.111 0.00 0.00 34.88 4.92
4192 5684 2.028385 TCTCGGTAAACTTCCCTGAAGC 60.028 50.000 3.82 0.00 42.79 3.86
4199 5691 0.896226 ACTTCCCTGAAGCGAGTACC 59.104 55.000 3.82 0.00 42.79 3.34
4203 5695 1.517257 CCTGAAGCGAGTACCAGCG 60.517 63.158 4.77 0.90 38.61 5.18
4219 5711 2.245096 CAGCGCTGTACTGAATTTTGC 58.755 47.619 29.24 0.00 37.32 3.68
4228 5720 7.308435 GCTGTACTGAATTTTGCTTGAATACT 58.692 34.615 3.61 0.00 0.00 2.12
4229 5721 7.483059 GCTGTACTGAATTTTGCTTGAATACTC 59.517 37.037 3.61 0.00 0.00 2.59
4233 5725 6.857964 ACTGAATTTTGCTTGAATACTCGTTG 59.142 34.615 0.00 0.00 0.00 4.10
4280 5790 0.676151 GGAGCAGCCTTGGTTGAGAG 60.676 60.000 7.69 0.00 34.61 3.20
4286 5796 3.152341 CAGCCTTGGTTGAGAGTGAATT 58.848 45.455 0.00 0.00 0.00 2.17
4287 5797 3.571401 CAGCCTTGGTTGAGAGTGAATTT 59.429 43.478 0.00 0.00 0.00 1.82
4288 5798 3.571401 AGCCTTGGTTGAGAGTGAATTTG 59.429 43.478 0.00 0.00 0.00 2.32
4289 5799 3.858503 GCCTTGGTTGAGAGTGAATTTGC 60.859 47.826 0.00 0.00 0.00 3.68
4290 5800 3.571401 CCTTGGTTGAGAGTGAATTTGCT 59.429 43.478 0.00 0.00 0.00 3.91
4291 5801 4.320788 CCTTGGTTGAGAGTGAATTTGCTC 60.321 45.833 2.99 2.99 0.00 4.26
4293 5803 2.808543 GGTTGAGAGTGAATTTGCTCGT 59.191 45.455 5.08 0.00 36.88 4.18
4294 5804 3.251004 GGTTGAGAGTGAATTTGCTCGTT 59.749 43.478 5.08 0.00 36.88 3.85
4295 5805 4.458708 GTTGAGAGTGAATTTGCTCGTTC 58.541 43.478 5.08 0.00 36.88 3.95
4296 5806 3.727726 TGAGAGTGAATTTGCTCGTTCA 58.272 40.909 5.08 0.00 36.88 3.18
4297 5807 3.742882 TGAGAGTGAATTTGCTCGTTCAG 59.257 43.478 5.08 0.00 35.22 3.02
4298 5808 3.070018 AGAGTGAATTTGCTCGTTCAGG 58.930 45.455 5.08 0.00 35.22 3.86
4300 5810 2.151202 GTGAATTTGCTCGTTCAGGGA 58.849 47.619 0.00 0.00 35.22 4.20
4301 5811 2.160417 GTGAATTTGCTCGTTCAGGGAG 59.840 50.000 0.00 0.00 35.22 4.30
4302 5812 2.224523 TGAATTTGCTCGTTCAGGGAGT 60.225 45.455 0.00 0.00 34.00 3.85
4303 5813 1.813513 ATTTGCTCGTTCAGGGAGTG 58.186 50.000 0.00 0.00 34.00 3.51
4305 5815 0.756294 TTGCTCGTTCAGGGAGTGAA 59.244 50.000 0.00 0.00 43.26 3.18
4333 5858 5.047872 TGCAAAGCAGATTCTAGCAAATTCA 60.048 36.000 9.67 1.25 33.32 2.57
4353 5878 1.838112 TGGGATCATTGTTGCTCCAC 58.162 50.000 0.00 0.00 39.47 4.02
4369 5894 3.810743 GCTCCACTGTCTTTGGTACCATT 60.811 47.826 17.17 0.00 35.42 3.16
4370 5895 4.003648 CTCCACTGTCTTTGGTACCATTC 58.996 47.826 17.17 7.25 35.42 2.67
4426 6138 7.872113 ATCTTTTAAATCACTAAGCTCCCTG 57.128 36.000 0.00 0.00 0.00 4.45
4433 6145 2.834549 TCACTAAGCTCCCTGGAAGAAG 59.165 50.000 0.00 0.00 34.07 2.85
4438 6150 1.905894 AGCTCCCTGGAAGAAGAACTC 59.094 52.381 0.00 0.00 34.07 3.01
4439 6151 1.404851 GCTCCCTGGAAGAAGAACTCG 60.405 57.143 0.00 0.00 34.07 4.18
4449 6161 5.046304 TGGAAGAAGAACTCGAGGAATCAAT 60.046 40.000 18.41 5.44 0.00 2.57
4461 6173 5.065602 TCGAGGAATCAATTGAAGCTCAATG 59.934 40.000 13.09 3.75 45.57 2.82
4463 6175 5.962433 AGGAATCAATTGAAGCTCAATGTG 58.038 37.500 13.09 10.80 45.57 3.21
4464 6176 5.713389 AGGAATCAATTGAAGCTCAATGTGA 59.287 36.000 13.09 14.07 45.57 3.58
4465 6177 6.034591 GGAATCAATTGAAGCTCAATGTGAG 58.965 40.000 13.09 0.72 45.57 3.51
4485 6257 2.607635 AGCTGGTACAAATACGAATGCG 59.392 45.455 0.00 0.00 38.70 4.73
4505 6277 4.822498 CGTTTCGCTAAAGAAAACGAAC 57.178 40.909 18.28 3.99 43.48 3.95
4632 6409 3.542875 CGATCAAAGAGTACGCAATGCTG 60.543 47.826 2.94 0.00 0.00 4.41
4641 6418 2.047939 GCAATGCTGGTGTTGGCC 60.048 61.111 0.00 0.00 0.00 5.36
4642 6419 2.870119 GCAATGCTGGTGTTGGCCA 61.870 57.895 0.00 0.00 36.97 5.36
4643 6420 1.747145 CAATGCTGGTGTTGGCCAA 59.253 52.632 16.05 16.05 38.18 4.52
4644 6421 0.320073 CAATGCTGGTGTTGGCCAAG 60.320 55.000 21.21 7.88 38.18 3.61
4645 6422 0.469705 AATGCTGGTGTTGGCCAAGA 60.470 50.000 21.21 16.53 38.18 3.02
4646 6423 0.251922 ATGCTGGTGTTGGCCAAGAT 60.252 50.000 21.21 0.00 38.18 2.40
4647 6424 1.180456 TGCTGGTGTTGGCCAAGATG 61.180 55.000 21.21 13.08 38.18 2.90
4648 6425 1.880819 GCTGGTGTTGGCCAAGATGG 61.881 60.000 21.21 12.66 41.55 3.51
4664 6441 0.904865 ATGGCCACGAAGACTCAGGA 60.905 55.000 8.16 0.00 0.00 3.86
4720 6497 2.428925 CCACAAGCCATGATGCCCC 61.429 63.158 0.00 0.00 0.00 5.80
4760 7112 5.984725 TGTTCTCTTCCAGTTCAAGTGTTA 58.015 37.500 0.00 0.00 0.00 2.41
4764 7116 8.406297 GTTCTCTTCCAGTTCAAGTGTTATTTT 58.594 33.333 0.00 0.00 0.00 1.82
4765 7117 8.154649 TCTCTTCCAGTTCAAGTGTTATTTTC 57.845 34.615 0.00 0.00 0.00 2.29
4767 7119 9.273016 CTCTTCCAGTTCAAGTGTTATTTTCTA 57.727 33.333 0.00 0.00 0.00 2.10
4768 7120 9.621629 TCTTCCAGTTCAAGTGTTATTTTCTAA 57.378 29.630 0.00 0.00 0.00 2.10
4780 7132 9.959749 AGTGTTATTTTCTAAAAAGAATTGCGA 57.040 25.926 0.00 0.00 0.00 5.10
4791 7143 1.880027 AGAATTGCGAACCAACCTGTC 59.120 47.619 0.00 0.00 35.99 3.51
4792 7144 0.591170 AATTGCGAACCAACCTGTCG 59.409 50.000 0.00 0.00 35.99 4.35
4793 7145 0.534203 ATTGCGAACCAACCTGTCGT 60.534 50.000 0.00 0.00 35.99 4.34
4803 7155 2.525055 CAACCTGTCGTTGTTGGTTTG 58.475 47.619 0.00 0.00 45.79 2.93
4804 7156 1.099689 ACCTGTCGTTGTTGGTTTGG 58.900 50.000 0.00 0.00 0.00 3.28
4805 7157 1.099689 CCTGTCGTTGTTGGTTTGGT 58.900 50.000 0.00 0.00 0.00 3.67
4808 7160 2.678836 CTGTCGTTGTTGGTTTGGTGTA 59.321 45.455 0.00 0.00 0.00 2.90
4823 7177 3.804036 TGGTGTATAGTGGTAAGCATGC 58.196 45.455 10.51 10.51 0.00 4.06
4834 7188 4.036380 GTGGTAAGCATGCTAATTACCCAC 59.964 45.833 30.82 26.69 45.17 4.61
4841 7195 4.823989 GCATGCTAATTACCCACTCTTCAT 59.176 41.667 11.37 0.00 0.00 2.57
4849 7203 7.839680 AATTACCCACTCTTCATCAAACTTT 57.160 32.000 0.00 0.00 0.00 2.66
4850 7204 7.839680 ATTACCCACTCTTCATCAAACTTTT 57.160 32.000 0.00 0.00 0.00 2.27
4851 7205 7.654022 TTACCCACTCTTCATCAAACTTTTT 57.346 32.000 0.00 0.00 0.00 1.94
4872 7226 4.493074 TTTTTCGAGAAAACGCAAAAGC 57.507 36.364 10.18 0.00 39.70 3.51
4873 7227 3.414549 TTTCGAGAAAACGCAAAAGCT 57.585 38.095 0.00 0.00 0.00 3.74
4874 7228 3.414549 TTCGAGAAAACGCAAAAGCTT 57.585 38.095 0.00 0.00 0.00 3.74
4875 7229 3.414549 TCGAGAAAACGCAAAAGCTTT 57.585 38.095 5.69 5.69 0.00 3.51
4876 7230 3.105203 TCGAGAAAACGCAAAAGCTTTG 58.895 40.909 13.54 8.26 0.00 2.77
4877 7231 2.346649 CGAGAAAACGCAAAAGCTTTGC 60.347 45.455 13.54 16.43 41.71 3.68
4885 7239 3.656651 GCAAAAGCTTTGCGTTTCTTT 57.343 38.095 13.54 0.00 38.06 2.52
4886 7240 3.344852 GCAAAAGCTTTGCGTTTCTTTG 58.655 40.909 13.54 4.93 38.06 2.77
4887 7241 3.344852 CAAAAGCTTTGCGTTTCTTTGC 58.655 40.909 13.54 0.00 38.06 3.68
4888 7242 2.292103 AAGCTTTGCGTTTCTTTGCA 57.708 40.000 0.00 0.00 39.81 4.08
4889 7243 2.514205 AGCTTTGCGTTTCTTTGCAT 57.486 40.000 0.00 0.00 41.42 3.96
4890 7244 2.825205 AGCTTTGCGTTTCTTTGCATT 58.175 38.095 0.00 0.00 41.42 3.56
4891 7245 2.540931 AGCTTTGCGTTTCTTTGCATTG 59.459 40.909 0.00 0.00 41.42 2.82
4892 7246 2.539274 GCTTTGCGTTTCTTTGCATTGA 59.461 40.909 0.00 0.00 41.42 2.57
4893 7247 3.001127 GCTTTGCGTTTCTTTGCATTGAA 59.999 39.130 0.00 0.00 41.42 2.69
4894 7248 4.493872 GCTTTGCGTTTCTTTGCATTGAAA 60.494 37.500 9.61 9.61 41.42 2.69
4895 7249 5.536554 TTTGCGTTTCTTTGCATTGAAAA 57.463 30.435 13.75 0.00 41.42 2.29
4896 7250 5.536554 TTGCGTTTCTTTGCATTGAAAAA 57.463 30.435 13.75 5.34 41.42 1.94
4897 7251 5.731599 TGCGTTTCTTTGCATTGAAAAAT 57.268 30.435 13.75 0.00 35.90 1.82
4898 7252 5.499935 TGCGTTTCTTTGCATTGAAAAATG 58.500 33.333 13.75 9.45 35.90 2.32
4899 7253 5.292834 TGCGTTTCTTTGCATTGAAAAATGA 59.707 32.000 13.75 0.00 35.90 2.57
4900 7254 5.842327 GCGTTTCTTTGCATTGAAAAATGAG 59.158 36.000 13.75 7.00 34.52 2.90
4901 7255 6.357198 CGTTTCTTTGCATTGAAAAATGAGG 58.643 36.000 13.75 0.00 34.52 3.86
4902 7256 6.200665 CGTTTCTTTGCATTGAAAAATGAGGA 59.799 34.615 13.75 0.00 34.52 3.71
4903 7257 7.568134 CGTTTCTTTGCATTGAAAAATGAGGAG 60.568 37.037 13.75 0.00 34.52 3.69
4904 7258 6.409524 TCTTTGCATTGAAAAATGAGGAGT 57.590 33.333 2.69 0.00 31.98 3.85
4905 7259 6.819284 TCTTTGCATTGAAAAATGAGGAGTT 58.181 32.000 2.69 0.00 31.98 3.01
4906 7260 6.925165 TCTTTGCATTGAAAAATGAGGAGTTC 59.075 34.615 2.69 0.00 31.98 3.01
4907 7261 5.787953 TGCATTGAAAAATGAGGAGTTCA 57.212 34.783 2.69 0.00 40.85 3.18
4908 7262 5.775686 TGCATTGAAAAATGAGGAGTTCAG 58.224 37.500 2.69 0.00 39.68 3.02
4909 7263 5.302568 TGCATTGAAAAATGAGGAGTTCAGT 59.697 36.000 2.69 0.00 39.68 3.41
4910 7264 6.183360 TGCATTGAAAAATGAGGAGTTCAGTT 60.183 34.615 2.69 0.00 45.33 3.16
4911 7265 7.014134 TGCATTGAAAAATGAGGAGTTCAGTTA 59.986 33.333 2.69 0.00 42.82 2.24
4912 7266 7.327032 GCATTGAAAAATGAGGAGTTCAGTTAC 59.673 37.037 2.69 0.00 42.82 2.50
4913 7267 7.873719 TTGAAAAATGAGGAGTTCAGTTACA 57.126 32.000 0.00 0.00 42.82 2.41
4914 7268 7.873719 TGAAAAATGAGGAGTTCAGTTACAA 57.126 32.000 0.00 0.00 42.82 2.41
4915 7269 8.287439 TGAAAAATGAGGAGTTCAGTTACAAA 57.713 30.769 0.00 0.00 42.82 2.83
4916 7270 8.188139 TGAAAAATGAGGAGTTCAGTTACAAAC 58.812 33.333 0.00 0.00 42.82 2.93
4917 7271 5.924475 AATGAGGAGTTCAGTTACAAACG 57.076 39.130 0.00 0.00 39.68 3.60
4918 7272 4.395959 TGAGGAGTTCAGTTACAAACGT 57.604 40.909 0.00 0.00 36.23 3.99
4919 7273 4.365723 TGAGGAGTTCAGTTACAAACGTC 58.634 43.478 0.00 0.00 36.23 4.34
4920 7274 3.725490 AGGAGTTCAGTTACAAACGTCC 58.275 45.455 0.00 9.10 36.23 4.79
4921 7275 2.804527 GGAGTTCAGTTACAAACGTCCC 59.195 50.000 0.00 0.00 36.23 4.46
4922 7276 3.460103 GAGTTCAGTTACAAACGTCCCA 58.540 45.455 0.00 0.00 36.23 4.37
4923 7277 4.062991 GAGTTCAGTTACAAACGTCCCAT 58.937 43.478 0.00 0.00 36.23 4.00
4924 7278 3.813166 AGTTCAGTTACAAACGTCCCATG 59.187 43.478 0.00 0.00 36.23 3.66
4925 7279 3.755112 TCAGTTACAAACGTCCCATGA 57.245 42.857 0.00 0.00 36.23 3.07
4926 7280 3.395639 TCAGTTACAAACGTCCCATGAC 58.604 45.455 0.00 0.00 38.18 3.06
4934 7288 4.201951 GTCCCATGACGCGTGAAT 57.798 55.556 20.70 7.47 0.00 2.57
4935 7289 2.466867 GTCCCATGACGCGTGAATT 58.533 52.632 20.70 0.00 0.00 2.17
4936 7290 1.647346 GTCCCATGACGCGTGAATTA 58.353 50.000 20.70 0.00 0.00 1.40
4937 7291 1.326548 GTCCCATGACGCGTGAATTAC 59.673 52.381 20.70 0.06 0.00 1.89
4953 7307 6.986118 GTGAATTACGGTGTGATTAGTGTAC 58.014 40.000 0.00 0.00 0.00 2.90
4954 7308 6.587226 GTGAATTACGGTGTGATTAGTGTACA 59.413 38.462 0.00 0.00 0.00 2.90
4955 7309 7.277098 GTGAATTACGGTGTGATTAGTGTACAT 59.723 37.037 0.00 0.00 0.00 2.29
4956 7310 7.490079 TGAATTACGGTGTGATTAGTGTACATC 59.510 37.037 0.00 0.00 0.00 3.06
4957 7311 4.119442 ACGGTGTGATTAGTGTACATCC 57.881 45.455 0.00 0.00 0.00 3.51
4958 7312 3.118884 ACGGTGTGATTAGTGTACATCCC 60.119 47.826 0.00 0.00 0.00 3.85
4959 7313 3.118920 CGGTGTGATTAGTGTACATCCCA 60.119 47.826 0.00 0.00 0.00 4.37
4960 7314 4.442893 CGGTGTGATTAGTGTACATCCCAT 60.443 45.833 0.00 0.00 0.00 4.00
4961 7315 4.816385 GGTGTGATTAGTGTACATCCCATG 59.184 45.833 0.00 0.00 0.00 3.66
4962 7316 5.428253 GTGTGATTAGTGTACATCCCATGT 58.572 41.667 0.00 0.00 46.92 3.21
4963 7317 5.880332 GTGTGATTAGTGTACATCCCATGTT 59.120 40.000 0.00 0.00 41.63 2.71
4964 7318 6.374333 GTGTGATTAGTGTACATCCCATGTTT 59.626 38.462 0.00 0.00 41.63 2.83
4965 7319 6.374053 TGTGATTAGTGTACATCCCATGTTTG 59.626 38.462 0.00 0.00 41.63 2.93
4966 7320 6.374333 GTGATTAGTGTACATCCCATGTTTGT 59.626 38.462 0.00 0.00 41.63 2.83
4967 7321 6.374053 TGATTAGTGTACATCCCATGTTTGTG 59.626 38.462 0.00 0.00 41.63 3.33
4968 7322 3.420893 AGTGTACATCCCATGTTTGTGG 58.579 45.455 0.00 0.00 41.63 4.17
4969 7323 2.094752 GTGTACATCCCATGTTTGTGGC 60.095 50.000 0.00 0.00 41.63 5.01
4970 7324 2.166829 GTACATCCCATGTTTGTGGCA 58.833 47.619 0.00 0.00 41.63 4.92
4971 7325 1.259609 ACATCCCATGTTTGTGGCAG 58.740 50.000 0.00 0.00 41.63 4.85
4972 7326 1.259609 CATCCCATGTTTGTGGCAGT 58.740 50.000 0.00 0.00 37.96 4.40
4973 7327 2.224992 ACATCCCATGTTTGTGGCAGTA 60.225 45.455 0.00 0.00 41.63 2.74
4974 7328 1.904287 TCCCATGTTTGTGGCAGTAC 58.096 50.000 0.00 0.00 37.96 2.73
4975 7329 0.887933 CCCATGTTTGTGGCAGTACC 59.112 55.000 0.00 0.00 37.96 3.34
4984 7338 4.162690 GGCAGTACCAGCCGGAGG 62.163 72.222 5.05 9.11 46.77 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
323 347 0.801251 CTTGAGTTGCTACTGCTGCC 59.199 55.000 5.27 0.00 40.48 4.85
1332 1693 4.861196 TCTAAGCTAGAAGAAGAGGAGCA 58.139 43.478 0.00 0.00 35.55 4.26
3447 4608 2.359602 TCCTCGAACTCGTCCGCT 60.360 61.111 0.00 0.00 40.80 5.52
3629 4811 1.244019 GCCAAAATCACCACCGCTCT 61.244 55.000 0.00 0.00 0.00 4.09
3680 4880 3.758554 GCCAAACACTACAATCCATCACT 59.241 43.478 0.00 0.00 0.00 3.41
3723 4933 1.454201 CTCTCGACTCAGCCACACTA 58.546 55.000 0.00 0.00 0.00 2.74
3724 4934 1.247419 CCTCTCGACTCAGCCACACT 61.247 60.000 0.00 0.00 0.00 3.55
3785 4995 6.035650 TGGCTACTTAAATCGATCGAAAGTTG 59.964 38.462 28.80 26.83 32.85 3.16
3810 5020 1.146707 AAACACCCGGTACAACGCT 59.853 52.632 0.00 0.00 0.00 5.07
3821 5031 1.963515 ACTTGATCCAAGCAAACACCC 59.036 47.619 6.61 0.00 44.43 4.61
3848 5058 6.036083 CACAGATATACAAGAACGAAACAGGG 59.964 42.308 0.00 0.00 0.00 4.45
3855 5065 6.400621 CGTTTTGCACAGATATACAAGAACGA 60.401 38.462 0.00 0.00 37.95 3.85
3905 5119 2.026262 TCTGAAGCCTAAACCCATGGTC 60.026 50.000 11.73 0.00 33.12 4.02
3963 5211 8.152023 AGGGAGTAGTTTATGTTGAAATCTCT 57.848 34.615 0.00 0.00 0.00 3.10
3971 5219 4.430908 GACGGAGGGAGTAGTTTATGTTG 58.569 47.826 0.00 0.00 0.00 3.33
3974 5222 2.364647 GGGACGGAGGGAGTAGTTTATG 59.635 54.545 0.00 0.00 0.00 1.90
3983 5231 2.844839 GGGATGGGACGGAGGGAG 60.845 72.222 0.00 0.00 0.00 4.30
3984 5232 3.364964 AGGGATGGGACGGAGGGA 61.365 66.667 0.00 0.00 0.00 4.20
3985 5233 2.844839 GAGGGATGGGACGGAGGG 60.845 72.222 0.00 0.00 0.00 4.30
3986 5234 2.844839 GGAGGGATGGGACGGAGG 60.845 72.222 0.00 0.00 0.00 4.30
3987 5235 3.227276 CGGAGGGATGGGACGGAG 61.227 72.222 0.00 0.00 0.00 4.63
3988 5236 4.070265 ACGGAGGGATGGGACGGA 62.070 66.667 0.00 0.00 0.00 4.69
3989 5237 3.537874 GACGGAGGGATGGGACGG 61.538 72.222 0.00 0.00 0.00 4.79
3990 5238 3.537874 GGACGGAGGGATGGGACG 61.538 72.222 0.00 0.00 0.00 4.79
3991 5239 3.162154 GGGACGGAGGGATGGGAC 61.162 72.222 0.00 0.00 0.00 4.46
3993 5241 0.766674 TTATGGGACGGAGGGATGGG 60.767 60.000 0.00 0.00 0.00 4.00
3994 5242 1.362224 ATTATGGGACGGAGGGATGG 58.638 55.000 0.00 0.00 0.00 3.51
3995 5243 5.425539 ACTTATATTATGGGACGGAGGGATG 59.574 44.000 0.00 0.00 0.00 3.51
3996 5244 5.600749 ACTTATATTATGGGACGGAGGGAT 58.399 41.667 0.00 0.00 0.00 3.85
3997 5245 5.019657 ACTTATATTATGGGACGGAGGGA 57.980 43.478 0.00 0.00 0.00 4.20
3998 5246 6.192773 TCTACTTATATTATGGGACGGAGGG 58.807 44.000 0.00 0.00 0.00 4.30
3999 5247 7.899648 ATCTACTTATATTATGGGACGGAGG 57.100 40.000 0.00 0.00 0.00 4.30
4020 5268 8.121086 CGTCGATATACAACCGTATTCATATCT 58.879 37.037 0.00 0.00 39.17 1.98
4021 5269 7.907045 ACGTCGATATACAACCGTATTCATATC 59.093 37.037 0.00 0.00 39.17 1.63
4022 5270 7.755591 ACGTCGATATACAACCGTATTCATAT 58.244 34.615 0.00 0.00 39.17 1.78
4023 5271 7.132694 ACGTCGATATACAACCGTATTCATA 57.867 36.000 0.00 0.00 39.17 2.15
4024 5272 6.005583 ACGTCGATATACAACCGTATTCAT 57.994 37.500 0.00 0.00 39.17 2.57
4025 5273 5.422666 ACGTCGATATACAACCGTATTCA 57.577 39.130 0.00 0.00 39.17 2.57
4028 5276 7.369803 AGAATACGTCGATATACAACCGTAT 57.630 36.000 0.00 7.41 41.62 3.06
4029 5277 6.785488 AGAATACGTCGATATACAACCGTA 57.215 37.500 0.00 3.61 35.57 4.02
4030 5278 5.679734 AGAATACGTCGATATACAACCGT 57.320 39.130 0.00 0.00 0.00 4.83
4031 5279 7.053710 TCTAGAATACGTCGATATACAACCG 57.946 40.000 0.00 0.00 0.00 4.44
4032 5280 7.956403 CACTCTAGAATACGTCGATATACAACC 59.044 40.741 0.00 0.00 0.00 3.77
4033 5281 8.494347 ACACTCTAGAATACGTCGATATACAAC 58.506 37.037 0.00 0.00 0.00 3.32
4034 5282 8.599055 ACACTCTAGAATACGTCGATATACAA 57.401 34.615 0.00 0.00 0.00 2.41
4035 5283 9.351570 CTACACTCTAGAATACGTCGATATACA 57.648 37.037 0.00 0.00 0.00 2.29
4036 5284 9.566530 TCTACACTCTAGAATACGTCGATATAC 57.433 37.037 0.00 0.00 0.00 1.47
4042 5290 7.042590 AGTGAATCTACACTCTAGAATACGTCG 60.043 40.741 0.00 0.00 46.36 5.12
4070 5318 9.974980 AGCCTTTTTAAAGATTTCAATACGAAA 57.025 25.926 3.84 0.00 39.22 3.46
4110 5601 9.244292 AGGAACAAAAGAAAAAGTACTCTCTTT 57.756 29.630 16.25 16.25 39.27 2.52
4111 5602 8.809468 AGGAACAAAAGAAAAAGTACTCTCTT 57.191 30.769 0.00 2.48 0.00 2.85
4112 5603 7.499563 GGAGGAACAAAAGAAAAAGTACTCTCT 59.500 37.037 0.00 0.00 0.00 3.10
4113 5604 7.499563 AGGAGGAACAAAAGAAAAAGTACTCTC 59.500 37.037 0.00 0.00 0.00 3.20
4114 5605 7.347252 AGGAGGAACAAAAGAAAAAGTACTCT 58.653 34.615 0.00 0.00 0.00 3.24
4118 5609 7.832187 TCTGAAGGAGGAACAAAAGAAAAAGTA 59.168 33.333 0.00 0.00 0.00 2.24
4129 5620 1.699634 CCCTGTCTGAAGGAGGAACAA 59.300 52.381 7.26 0.00 40.02 2.83
4160 5651 0.899720 TTACCGAGATCTTGGCCGTT 59.100 50.000 26.64 11.45 37.67 4.44
4192 5684 0.523546 CAGTACAGCGCTGGTACTCG 60.524 60.000 38.27 26.75 46.27 4.18
4199 5691 2.095567 AGCAAAATTCAGTACAGCGCTG 60.096 45.455 34.89 34.89 35.43 5.18
4203 5695 7.308435 AGTATTCAAGCAAAATTCAGTACAGC 58.692 34.615 0.00 0.00 0.00 4.40
4228 5720 4.827627 CGGTGAATGTCCTCGTCAACGA 62.828 54.545 4.39 5.02 43.24 3.85
4229 5721 1.068474 GGTGAATGTCCTCGTCAACG 58.932 55.000 0.00 0.00 41.45 4.10
4233 5725 1.078759 CTGCGGTGAATGTCCTCGTC 61.079 60.000 0.00 0.00 0.00 4.20
4261 5760 0.676151 CTCTCAACCAAGGCTGCTCC 60.676 60.000 0.00 0.00 0.00 4.70
4262 5761 0.036022 ACTCTCAACCAAGGCTGCTC 59.964 55.000 0.00 0.00 0.00 4.26
4263 5762 0.250640 CACTCTCAACCAAGGCTGCT 60.251 55.000 0.00 0.00 0.00 4.24
4264 5763 0.250467 TCACTCTCAACCAAGGCTGC 60.250 55.000 0.00 0.00 0.00 5.25
4265 5764 2.260844 TTCACTCTCAACCAAGGCTG 57.739 50.000 0.00 0.00 0.00 4.85
4266 5765 3.515602 AATTCACTCTCAACCAAGGCT 57.484 42.857 0.00 0.00 0.00 4.58
4267 5766 3.858503 GCAAATTCACTCTCAACCAAGGC 60.859 47.826 0.00 0.00 0.00 4.35
4269 5768 4.612259 CGAGCAAATTCACTCTCAACCAAG 60.612 45.833 6.22 0.00 0.00 3.61
4270 5769 3.250762 CGAGCAAATTCACTCTCAACCAA 59.749 43.478 6.22 0.00 0.00 3.67
4280 5790 2.151202 TCCCTGAACGAGCAAATTCAC 58.849 47.619 0.00 0.00 31.62 3.18
4286 5796 0.756294 TTCACTCCCTGAACGAGCAA 59.244 50.000 0.00 0.00 33.65 3.91
4287 5797 0.318441 CTTCACTCCCTGAACGAGCA 59.682 55.000 0.00 0.00 33.65 4.26
4288 5798 0.603569 TCTTCACTCCCTGAACGAGC 59.396 55.000 0.00 0.00 33.65 5.03
4289 5799 3.257393 CAATCTTCACTCCCTGAACGAG 58.743 50.000 0.00 0.00 33.65 4.18
4290 5800 2.612972 GCAATCTTCACTCCCTGAACGA 60.613 50.000 0.00 0.00 33.65 3.85
4291 5801 1.734465 GCAATCTTCACTCCCTGAACG 59.266 52.381 0.00 0.00 33.65 3.95
4293 5803 3.507162 TTGCAATCTTCACTCCCTGAA 57.493 42.857 0.00 0.00 36.46 3.02
4294 5804 3.415212 CTTTGCAATCTTCACTCCCTGA 58.585 45.455 0.00 0.00 0.00 3.86
4295 5805 2.094854 GCTTTGCAATCTTCACTCCCTG 60.095 50.000 0.00 0.00 0.00 4.45
4296 5806 2.165998 GCTTTGCAATCTTCACTCCCT 58.834 47.619 0.00 0.00 0.00 4.20
4297 5807 1.888512 TGCTTTGCAATCTTCACTCCC 59.111 47.619 0.00 0.00 34.76 4.30
4298 5808 2.816087 TCTGCTTTGCAATCTTCACTCC 59.184 45.455 0.00 0.00 38.41 3.85
4300 5810 4.765856 AGAATCTGCTTTGCAATCTTCACT 59.234 37.500 0.00 0.00 38.41 3.41
4301 5811 5.056894 AGAATCTGCTTTGCAATCTTCAC 57.943 39.130 0.00 0.00 38.41 3.18
4302 5812 5.163683 GCTAGAATCTGCTTTGCAATCTTCA 60.164 40.000 0.00 0.00 38.41 3.02
4303 5813 5.163683 TGCTAGAATCTGCTTTGCAATCTTC 60.164 40.000 0.00 0.00 38.41 2.87
4305 5815 4.267536 TGCTAGAATCTGCTTTGCAATCT 58.732 39.130 0.00 0.29 38.41 2.40
4369 5894 8.488668 TGATTCTGAATCATATGGTCTCTTTGA 58.511 33.333 25.05 1.23 42.69 2.69
4370 5895 8.672823 TGATTCTGAATCATATGGTCTCTTTG 57.327 34.615 25.05 0.00 42.69 2.77
4404 6116 6.180472 TCCAGGGAGCTTAGTGATTTAAAAG 58.820 40.000 0.00 0.00 0.00 2.27
4426 6138 4.457834 TGATTCCTCGAGTTCTTCTTCC 57.542 45.455 12.31 0.00 0.00 3.46
4433 6145 4.633565 AGCTTCAATTGATTCCTCGAGTTC 59.366 41.667 9.40 6.03 0.00 3.01
4438 6150 4.952262 TTGAGCTTCAATTGATTCCTCG 57.048 40.909 9.40 0.00 30.26 4.63
4439 6151 6.034591 CACATTGAGCTTCAATTGATTCCTC 58.965 40.000 9.40 14.46 44.03 3.71
4461 6173 4.494199 GCATTCGTATTTGTACCAGCTCAC 60.494 45.833 0.00 0.00 0.00 3.51
4463 6175 3.302480 CGCATTCGTATTTGTACCAGCTC 60.302 47.826 0.00 0.00 0.00 4.09
4464 6176 2.607635 CGCATTCGTATTTGTACCAGCT 59.392 45.455 0.00 0.00 0.00 4.24
4465 6177 2.969055 CGCATTCGTATTTGTACCAGC 58.031 47.619 0.00 0.00 0.00 4.85
4485 6257 4.141861 CGTGTTCGTTTTCTTTAGCGAAAC 59.858 41.667 0.00 0.00 43.43 2.78
4493 6265 3.033185 CGCATTCGTGTTCGTTTTCTTT 58.967 40.909 0.00 0.00 38.33 2.52
4600 6377 1.129998 CTCTTTGATCGTGGCTGCAAG 59.870 52.381 0.50 0.00 0.00 4.01
4605 6382 1.736032 GCGTACTCTTTGATCGTGGCT 60.736 52.381 0.00 0.00 0.00 4.75
4610 6387 2.604914 AGCATTGCGTACTCTTTGATCG 59.395 45.455 2.38 0.00 0.00 3.69
4641 6418 1.338105 TGAGTCTTCGTGGCCATCTTG 60.338 52.381 9.72 0.00 0.00 3.02
4642 6419 0.976641 TGAGTCTTCGTGGCCATCTT 59.023 50.000 9.72 0.00 0.00 2.40
4643 6420 0.534412 CTGAGTCTTCGTGGCCATCT 59.466 55.000 9.72 0.68 0.00 2.90
4644 6421 0.460987 CCTGAGTCTTCGTGGCCATC 60.461 60.000 9.72 0.00 0.00 3.51
4645 6422 0.904865 TCCTGAGTCTTCGTGGCCAT 60.905 55.000 9.72 0.00 0.00 4.40
4646 6423 1.533033 TCCTGAGTCTTCGTGGCCA 60.533 57.895 0.00 0.00 0.00 5.36
4647 6424 1.079750 GTCCTGAGTCTTCGTGGCC 60.080 63.158 0.00 0.00 0.00 5.36
4648 6425 0.389166 CAGTCCTGAGTCTTCGTGGC 60.389 60.000 0.00 0.00 0.00 5.01
4649 6426 0.244994 CCAGTCCTGAGTCTTCGTGG 59.755 60.000 0.00 0.00 0.00 4.94
4650 6427 1.201181 CTCCAGTCCTGAGTCTTCGTG 59.799 57.143 0.00 0.00 0.00 4.35
4664 6441 0.388649 GTGATCGTTGTCGCTCCAGT 60.389 55.000 0.00 0.00 36.96 4.00
4692 6469 1.673665 GGCTTGTGGTGCCTCTCTG 60.674 63.158 0.00 0.00 46.38 3.35
4720 6497 6.352516 AGAGAACATCCATAAAAGCTGTAGG 58.647 40.000 0.00 0.00 0.00 3.18
4760 7112 8.547894 GTTGGTTCGCAATTCTTTTTAGAAAAT 58.452 29.630 0.00 0.00 0.00 1.82
4764 7116 5.300792 AGGTTGGTTCGCAATTCTTTTTAGA 59.699 36.000 0.00 0.00 0.00 2.10
4765 7117 5.402270 CAGGTTGGTTCGCAATTCTTTTTAG 59.598 40.000 0.00 0.00 0.00 1.85
4767 7119 4.119136 CAGGTTGGTTCGCAATTCTTTTT 58.881 39.130 0.00 0.00 0.00 1.94
4768 7120 3.132111 ACAGGTTGGTTCGCAATTCTTTT 59.868 39.130 0.00 0.00 0.00 2.27
4769 7121 2.693074 ACAGGTTGGTTCGCAATTCTTT 59.307 40.909 0.00 0.00 0.00 2.52
4770 7122 2.293399 GACAGGTTGGTTCGCAATTCTT 59.707 45.455 0.00 0.00 0.00 2.52
4771 7123 1.880027 GACAGGTTGGTTCGCAATTCT 59.120 47.619 0.00 0.00 0.00 2.40
4772 7124 1.399727 CGACAGGTTGGTTCGCAATTC 60.400 52.381 0.00 0.00 0.00 2.17
4773 7125 0.591170 CGACAGGTTGGTTCGCAATT 59.409 50.000 0.00 0.00 0.00 2.32
4774 7126 0.534203 ACGACAGGTTGGTTCGCAAT 60.534 50.000 0.00 0.00 0.00 3.56
4791 7143 4.319911 CCACTATACACCAAACCAACAACG 60.320 45.833 0.00 0.00 0.00 4.10
4792 7144 4.581409 ACCACTATACACCAAACCAACAAC 59.419 41.667 0.00 0.00 0.00 3.32
4793 7145 4.794334 ACCACTATACACCAAACCAACAA 58.206 39.130 0.00 0.00 0.00 2.83
4795 7147 5.106436 GCTTACCACTATACACCAAACCAAC 60.106 44.000 0.00 0.00 0.00 3.77
4796 7148 5.005094 GCTTACCACTATACACCAAACCAA 58.995 41.667 0.00 0.00 0.00 3.67
4797 7149 4.041815 TGCTTACCACTATACACCAAACCA 59.958 41.667 0.00 0.00 0.00 3.67
4798 7150 4.581868 TGCTTACCACTATACACCAAACC 58.418 43.478 0.00 0.00 0.00 3.27
4799 7151 5.448632 GCATGCTTACCACTATACACCAAAC 60.449 44.000 11.37 0.00 0.00 2.93
4801 7153 4.080582 AGCATGCTTACCACTATACACCAA 60.081 41.667 16.30 0.00 0.00 3.67
4803 7155 4.073293 AGCATGCTTACCACTATACACC 57.927 45.455 16.30 0.00 0.00 4.16
4804 7156 7.730364 AATTAGCATGCTTACCACTATACAC 57.270 36.000 28.02 0.00 0.00 2.90
4805 7157 7.876068 GGTAATTAGCATGCTTACCACTATACA 59.124 37.037 29.87 8.00 42.52 2.29
4808 7160 6.183361 TGGGTAATTAGCATGCTTACCACTAT 60.183 38.462 32.99 14.77 44.02 2.12
4823 7177 8.567285 AAGTTTGATGAAGAGTGGGTAATTAG 57.433 34.615 0.00 0.00 0.00 1.73
4851 7205 4.493074 GCTTTTGCGTTTTCTCGAAAAA 57.507 36.364 6.41 5.17 43.26 1.94
4865 7219 6.702292 TGCAAAGAAACGCAAAGCTTTTGC 62.702 41.667 9.53 13.69 39.66 3.68
4866 7220 3.181522 TGCAAAGAAACGCAAAGCTTTTG 60.182 39.130 9.53 7.81 34.59 2.44
4867 7221 2.999355 TGCAAAGAAACGCAAAGCTTTT 59.001 36.364 9.53 0.00 34.59 2.27
4868 7222 2.615869 TGCAAAGAAACGCAAAGCTTT 58.384 38.095 5.69 5.69 34.59 3.51
4869 7223 2.292103 TGCAAAGAAACGCAAAGCTT 57.708 40.000 0.00 0.00 34.59 3.74
4870 7224 2.514205 ATGCAAAGAAACGCAAAGCT 57.486 40.000 0.00 0.00 42.37 3.74
4871 7225 2.539274 TCAATGCAAAGAAACGCAAAGC 59.461 40.909 0.00 0.00 42.37 3.51
4872 7226 4.775440 TTCAATGCAAAGAAACGCAAAG 57.225 36.364 0.00 0.00 42.37 2.77
4873 7227 5.536554 TTTTCAATGCAAAGAAACGCAAA 57.463 30.435 14.28 0.53 42.37 3.68
4874 7228 5.536554 TTTTTCAATGCAAAGAAACGCAA 57.463 30.435 14.28 6.22 42.37 4.85
4875 7229 5.292834 TCATTTTTCAATGCAAAGAAACGCA 59.707 32.000 14.28 5.02 39.90 5.24
4876 7230 5.736338 TCATTTTTCAATGCAAAGAAACGC 58.264 33.333 14.28 0.00 39.90 4.84
4877 7231 6.200665 TCCTCATTTTTCAATGCAAAGAAACG 59.799 34.615 14.28 8.12 39.90 3.60
4878 7232 7.225341 ACTCCTCATTTTTCAATGCAAAGAAAC 59.775 33.333 14.28 0.00 39.90 2.78
4879 7233 7.274447 ACTCCTCATTTTTCAATGCAAAGAAA 58.726 30.769 11.53 11.53 39.90 2.52
4880 7234 6.819284 ACTCCTCATTTTTCAATGCAAAGAA 58.181 32.000 0.00 0.00 39.90 2.52
4881 7235 6.409524 ACTCCTCATTTTTCAATGCAAAGA 57.590 33.333 0.00 0.00 39.90 2.52
4882 7236 6.702723 TGAACTCCTCATTTTTCAATGCAAAG 59.297 34.615 0.00 0.00 39.90 2.77
4883 7237 6.580788 TGAACTCCTCATTTTTCAATGCAAA 58.419 32.000 0.00 0.00 39.90 3.68
4884 7238 6.159299 TGAACTCCTCATTTTTCAATGCAA 57.841 33.333 0.00 0.00 39.90 4.08
4885 7239 5.302568 ACTGAACTCCTCATTTTTCAATGCA 59.697 36.000 0.00 0.00 39.90 3.96
4886 7240 5.776744 ACTGAACTCCTCATTTTTCAATGC 58.223 37.500 0.00 0.00 39.90 3.56
4887 7241 8.352201 TGTAACTGAACTCCTCATTTTTCAATG 58.648 33.333 0.00 0.00 41.25 2.82
4888 7242 8.463930 TGTAACTGAACTCCTCATTTTTCAAT 57.536 30.769 0.00 0.00 32.14 2.57
4889 7243 7.873719 TGTAACTGAACTCCTCATTTTTCAA 57.126 32.000 0.00 0.00 32.14 2.69
4890 7244 7.873719 TTGTAACTGAACTCCTCATTTTTCA 57.126 32.000 0.00 0.00 32.14 2.69
4891 7245 7.376072 CGTTTGTAACTGAACTCCTCATTTTTC 59.624 37.037 0.00 0.00 32.14 2.29
4892 7246 7.148137 ACGTTTGTAACTGAACTCCTCATTTTT 60.148 33.333 0.00 0.00 32.14 1.94
4893 7247 6.317893 ACGTTTGTAACTGAACTCCTCATTTT 59.682 34.615 0.00 0.00 32.14 1.82
4894 7248 5.820947 ACGTTTGTAACTGAACTCCTCATTT 59.179 36.000 0.00 0.00 32.14 2.32
4895 7249 5.365619 ACGTTTGTAACTGAACTCCTCATT 58.634 37.500 0.00 0.00 32.14 2.57
4896 7250 4.957296 ACGTTTGTAACTGAACTCCTCAT 58.043 39.130 0.00 0.00 32.14 2.90
4897 7251 4.365723 GACGTTTGTAACTGAACTCCTCA 58.634 43.478 0.00 0.00 0.00 3.86
4898 7252 3.739810 GGACGTTTGTAACTGAACTCCTC 59.260 47.826 0.00 0.00 0.00 3.71
4899 7253 3.493873 GGGACGTTTGTAACTGAACTCCT 60.494 47.826 0.00 0.00 0.00 3.69
4900 7254 2.804527 GGGACGTTTGTAACTGAACTCC 59.195 50.000 0.00 0.00 0.00 3.85
4901 7255 3.460103 TGGGACGTTTGTAACTGAACTC 58.540 45.455 0.00 0.00 0.00 3.01
4902 7256 3.547054 TGGGACGTTTGTAACTGAACT 57.453 42.857 0.00 0.00 0.00 3.01
4903 7257 3.810941 TCATGGGACGTTTGTAACTGAAC 59.189 43.478 0.00 0.00 0.00 3.18
4904 7258 3.810941 GTCATGGGACGTTTGTAACTGAA 59.189 43.478 0.00 0.00 33.68 3.02
4905 7259 3.395639 GTCATGGGACGTTTGTAACTGA 58.604 45.455 0.00 0.00 33.68 3.41
4906 7260 3.806316 GTCATGGGACGTTTGTAACTG 57.194 47.619 0.00 0.00 33.68 3.16
4917 7271 1.326548 GTAATTCACGCGTCATGGGAC 59.673 52.381 9.86 0.00 40.77 4.46
4918 7272 1.647346 GTAATTCACGCGTCATGGGA 58.353 50.000 9.86 0.00 0.00 4.37
4919 7273 0.300491 CGTAATTCACGCGTCATGGG 59.700 55.000 9.86 0.00 45.03 4.00
4920 7274 3.779303 CGTAATTCACGCGTCATGG 57.221 52.632 9.86 0.00 45.03 3.66
4929 7283 6.587226 TGTACACTAATCACACCGTAATTCAC 59.413 38.462 0.00 0.00 0.00 3.18
4930 7284 6.689554 TGTACACTAATCACACCGTAATTCA 58.310 36.000 0.00 0.00 0.00 2.57
4931 7285 7.042925 GGATGTACACTAATCACACCGTAATTC 60.043 40.741 0.00 0.00 0.00 2.17
4932 7286 6.759827 GGATGTACACTAATCACACCGTAATT 59.240 38.462 0.00 0.00 0.00 1.40
4933 7287 6.278363 GGATGTACACTAATCACACCGTAAT 58.722 40.000 0.00 0.00 0.00 1.89
4934 7288 5.394443 GGGATGTACACTAATCACACCGTAA 60.394 44.000 0.00 0.00 0.00 3.18
4935 7289 4.098349 GGGATGTACACTAATCACACCGTA 59.902 45.833 0.00 0.00 0.00 4.02
4936 7290 3.118884 GGGATGTACACTAATCACACCGT 60.119 47.826 0.00 0.00 0.00 4.83
4937 7291 3.118920 TGGGATGTACACTAATCACACCG 60.119 47.826 0.00 0.00 31.27 4.94
4938 7292 4.481368 TGGGATGTACACTAATCACACC 57.519 45.455 0.00 0.00 31.27 4.16
4939 7293 5.428253 ACATGGGATGTACACTAATCACAC 58.572 41.667 0.00 0.00 42.78 3.82
4940 7294 5.692115 ACATGGGATGTACACTAATCACA 57.308 39.130 0.00 0.00 42.78 3.58
4941 7295 6.374333 ACAAACATGGGATGTACACTAATCAC 59.626 38.462 0.00 0.00 44.07 3.06
4942 7296 6.374053 CACAAACATGGGATGTACACTAATCA 59.626 38.462 0.00 0.00 44.07 2.57
4943 7297 6.183360 CCACAAACATGGGATGTACACTAATC 60.183 42.308 0.00 0.00 44.07 1.75
4944 7298 5.652014 CCACAAACATGGGATGTACACTAAT 59.348 40.000 0.00 0.00 44.07 1.73
4945 7299 5.007034 CCACAAACATGGGATGTACACTAA 58.993 41.667 0.00 0.00 44.07 2.24
4946 7300 4.584874 CCACAAACATGGGATGTACACTA 58.415 43.478 0.00 0.00 44.07 2.74
4947 7301 3.420893 CCACAAACATGGGATGTACACT 58.579 45.455 0.00 0.00 44.07 3.55
4948 7302 2.094752 GCCACAAACATGGGATGTACAC 60.095 50.000 0.00 0.00 44.07 2.90
4949 7303 2.166829 GCCACAAACATGGGATGTACA 58.833 47.619 0.00 0.00 44.07 2.90
4950 7304 2.164219 CTGCCACAAACATGGGATGTAC 59.836 50.000 0.00 0.00 44.07 2.90
4951 7305 2.224992 ACTGCCACAAACATGGGATGTA 60.225 45.455 0.00 0.00 44.07 2.29
4953 7307 1.259609 ACTGCCACAAACATGGGATG 58.740 50.000 0.00 0.00 39.66 3.51
4954 7308 2.446435 GTACTGCCACAAACATGGGAT 58.554 47.619 0.00 0.00 39.66 3.85
4955 7309 1.546773 GGTACTGCCACAAACATGGGA 60.547 52.381 0.00 0.00 40.43 4.37
4956 7310 0.887933 GGTACTGCCACAAACATGGG 59.112 55.000 0.00 0.00 40.43 4.00
4957 7311 1.541147 CTGGTACTGCCACAAACATGG 59.459 52.381 0.00 0.00 43.61 3.66
4958 7312 2.995466 CTGGTACTGCCACAAACATG 57.005 50.000 0.00 0.00 43.61 3.21


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

AutoCloner maintained by Alex Coulton.