Multiple sequence alignment - TraesCS3D01G341400

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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 TraesCS3D01G341400 chr3D 100.000 7082 0 0 1 7082 454696754 454689673 0.000000e+00 13079
1 TraesCS3D01G341400 chr3B 94.219 4999 194 41 378 5322 597474036 597469079 0.000000e+00 7542
2 TraesCS3D01G341400 chr3B 90.473 1312 67 23 5319 6591 597468526 597467234 0.000000e+00 1677
3 TraesCS3D01G341400 chr3B 84.073 496 48 18 6595 7082 597467168 597466696 3.900000e-122 449
4 TraesCS3D01G341400 chr3B 90.850 153 14 0 1 153 597474668 597474516 9.310000e-49 206
5 TraesCS3D01G341400 chr3A 94.421 3083 113 18 3440 6481 596766002 596762938 0.000000e+00 4686
6 TraesCS3D01G341400 chr3A 94.084 2586 119 19 871 3442 596768727 596766162 0.000000e+00 3897
7 TraesCS3D01G341400 chr3A 87.685 406 23 5 384 774 596769185 596768792 1.400000e-121 448
8 TraesCS3D01G341400 chr3A 90.541 296 15 4 6595 6888 596762646 596762362 5.180000e-101 379
9 TraesCS3D01G341400 chr3A 85.930 199 10 5 81 275 596769561 596769377 5.600000e-46 196
10 TraesCS3D01G341400 chr3A 91.045 134 8 2 6487 6620 596762803 596762674 2.030000e-40 178
11 TraesCS3D01G341400 chr1B 80.917 545 96 5 2532 3075 530475928 530476465 2.360000e-114 424
12 TraesCS3D01G341400 chr1B 83.103 290 44 5 1270 1555 530474203 530474491 7.050000e-65 259
13 TraesCS3D01G341400 chr1D 80.627 542 97 5 2535 3075 392136976 392136442 5.110000e-111 412
14 TraesCS3D01G341400 chr1A 84.483 290 40 5 1270 1555 493211950 493212238 1.500000e-71 281


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 TraesCS3D01G341400 chr3D 454689673 454696754 7081 True 13079.000000 13079 100.000000 1 7082 1 chr3D.!!$R1 7081
1 TraesCS3D01G341400 chr3B 597466696 597474668 7972 True 2468.500000 7542 89.903750 1 7082 4 chr3B.!!$R1 7081
2 TraesCS3D01G341400 chr3A 596762362 596769561 7199 True 1630.666667 4686 90.617667 81 6888 6 chr3A.!!$R1 6807
3 TraesCS3D01G341400 chr1B 530474203 530476465 2262 False 341.500000 424 82.010000 1270 3075 2 chr1B.!!$F1 1805
4 TraesCS3D01G341400 chr1D 392136442 392136976 534 True 412.000000 412 80.627000 2535 3075 1 chr1D.!!$R1 540

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
239 244 0.108329 ACAATTACGCGGCACTAGCT 60.108 50.000 12.47 0.00 41.70 3.32 F
835 1311 0.174617 GGAGAGGTGAGAAGAAGGCG 59.825 60.000 0.00 0.00 0.00 5.52 F
840 1316 0.243095 GGTGAGAAGAAGGCGTACGT 59.757 55.000 17.90 0.00 0.00 3.57 F
843 1319 1.131883 TGAGAAGAAGGCGTACGTAGC 59.868 52.381 17.90 1.78 0.00 3.58 F
852 1328 1.134530 GCGTACGTAGCTCTGCTGTG 61.135 60.000 17.90 0.00 40.10 3.66 F
2580 3738 1.747924 GCAGAAGGAATCAAAGGCCTC 59.252 52.381 5.23 0.00 0.00 4.70 F
4130 5452 0.413037 TGGGCCAGAATTGGGACATT 59.587 50.000 0.00 0.00 45.16 2.71 F
4220 5542 1.004440 AGCTGGAGTTGCTTCGGAC 60.004 57.895 0.00 0.00 37.52 4.79 F
5737 7634 0.047176 TGATCCACCCCAACCCCTAT 59.953 55.000 0.00 0.00 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 3051 2.289002 GGAAGTATTGCAAGGCTGATCG 59.711 50.000 4.94 0.00 35.98 3.69 R
2021 3052 3.549794 AGGAAGTATTGCAAGGCTGATC 58.450 45.455 4.94 1.26 39.77 2.92 R
2022 3053 3.549794 GAGGAAGTATTGCAAGGCTGAT 58.450 45.455 4.94 0.00 39.77 2.90 R
2501 3549 8.608844 ATTAAGTACTTTTCACCACAGAGAAG 57.391 34.615 14.49 0.00 36.22 2.85 R
2850 4008 1.909700 TTCTGGCAGGAACACCAATC 58.090 50.000 15.73 0.00 36.40 2.67 R
4220 5542 1.524986 CGACGAGCAGCATACAAAACG 60.525 52.381 0.00 0.00 0.00 3.60 R
5357 7248 0.758734 TCCTAGGATTGACATGGCGG 59.241 55.000 7.62 0.00 0.00 6.13 R
6012 7919 1.926511 CTTCTGCCGTGCCACATTCC 61.927 60.000 0.00 0.00 0.00 3.01 R
7017 9178 0.179089 GCTGCGAGGATGTCATGTCT 60.179 55.000 0.00 0.00 0.00 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
31 32 4.151335 GTGATTTAGGCGATATGTGCAGAG 59.849 45.833 0.00 0.00 0.00 3.35
46 47 1.609320 GCAGAGACAGTTTCCACTCCC 60.609 57.143 0.00 0.00 0.00 4.30
63 64 3.621419 CCCAAGGGGCATTGAGATT 57.379 52.632 0.00 0.00 35.35 2.40
83 84 5.713861 AGATTGGTCAAGGATTTTCTTGGAG 59.286 40.000 4.99 0.00 43.05 3.86
143 148 6.317391 CAGGAAAGATAGAACAAATCCTGGAC 59.683 42.308 10.35 0.00 45.49 4.02
153 158 1.241315 AATCCTGGACCGCAAAACCG 61.241 55.000 0.00 0.00 0.00 4.44
154 159 2.119484 ATCCTGGACCGCAAAACCGA 62.119 55.000 0.00 0.00 0.00 4.69
155 160 2.613506 CCTGGACCGCAAAACCGAC 61.614 63.158 0.00 0.00 0.00 4.79
156 161 1.890041 CTGGACCGCAAAACCGACA 60.890 57.895 0.00 0.00 0.00 4.35
157 162 2.113131 CTGGACCGCAAAACCGACAC 62.113 60.000 0.00 0.00 0.00 3.67
158 163 2.181521 GGACCGCAAAACCGACACA 61.182 57.895 0.00 0.00 0.00 3.72
159 164 1.512156 GGACCGCAAAACCGACACAT 61.512 55.000 0.00 0.00 0.00 3.21
162 167 0.110238 CCGCAAAACCGACACATCTG 60.110 55.000 0.00 0.00 0.00 2.90
167 172 3.300009 CAAAACCGACACATCTGCTTTC 58.700 45.455 0.00 0.00 0.00 2.62
239 244 0.108329 ACAATTACGCGGCACTAGCT 60.108 50.000 12.47 0.00 41.70 3.32
263 575 0.251634 GGAGTTCCCTGCTTCCTGAG 59.748 60.000 0.00 0.00 0.00 3.35
275 587 5.279406 CCTGCTTCCTGAGAGAACCATATAG 60.279 48.000 0.00 0.00 0.00 1.31
276 588 4.039730 TGCTTCCTGAGAGAACCATATAGC 59.960 45.833 0.00 0.00 0.00 2.97
277 589 4.039730 GCTTCCTGAGAGAACCATATAGCA 59.960 45.833 0.00 0.00 0.00 3.49
287 599 7.215789 AGAGAACCATATAGCACATGAGAAAG 58.784 38.462 0.00 0.00 0.00 2.62
300 738 7.663081 AGCACATGAGAAAGATTCTTTTCAGTA 59.337 33.333 12.73 0.38 40.87 2.74
335 773 3.351020 CAGGCTTGCATTTGCTATCTC 57.649 47.619 3.94 0.00 42.66 2.75
336 774 1.945394 AGGCTTGCATTTGCTATCTCG 59.055 47.619 3.94 0.00 42.66 4.04
337 775 1.942657 GGCTTGCATTTGCTATCTCGA 59.057 47.619 3.94 0.00 42.66 4.04
338 776 2.032204 GGCTTGCATTTGCTATCTCGAG 60.032 50.000 5.93 5.93 42.66 4.04
339 777 2.868583 GCTTGCATTTGCTATCTCGAGA 59.131 45.455 19.19 19.19 42.66 4.04
340 778 3.497640 GCTTGCATTTGCTATCTCGAGAT 59.502 43.478 29.58 29.58 42.66 2.75
341 779 4.610905 GCTTGCATTTGCTATCTCGAGATG 60.611 45.833 33.22 23.72 42.66 2.90
342 780 4.063998 TGCATTTGCTATCTCGAGATGT 57.936 40.909 33.22 15.40 42.66 3.06
343 781 5.200368 TGCATTTGCTATCTCGAGATGTA 57.800 39.130 33.22 20.63 42.66 2.29
344 782 5.787380 TGCATTTGCTATCTCGAGATGTAT 58.213 37.500 33.22 14.30 42.66 2.29
345 783 6.226052 TGCATTTGCTATCTCGAGATGTATT 58.774 36.000 33.22 13.93 42.66 1.89
346 784 6.707608 TGCATTTGCTATCTCGAGATGTATTT 59.292 34.615 33.22 13.20 42.66 1.40
347 785 7.227314 TGCATTTGCTATCTCGAGATGTATTTT 59.773 33.333 33.22 12.48 42.66 1.82
348 786 7.743838 GCATTTGCTATCTCGAGATGTATTTTC 59.256 37.037 33.22 15.89 38.21 2.29
349 787 7.715265 TTTGCTATCTCGAGATGTATTTTCC 57.285 36.000 33.22 14.51 36.05 3.13
350 788 6.656632 TGCTATCTCGAGATGTATTTTCCT 57.343 37.500 33.22 10.32 36.05 3.36
351 789 7.055667 TGCTATCTCGAGATGTATTTTCCTT 57.944 36.000 33.22 9.81 36.05 3.36
352 790 7.500992 TGCTATCTCGAGATGTATTTTCCTTT 58.499 34.615 33.22 9.61 36.05 3.11
353 791 7.439356 TGCTATCTCGAGATGTATTTTCCTTTG 59.561 37.037 33.22 9.31 36.05 2.77
354 792 7.439655 GCTATCTCGAGATGTATTTTCCTTTGT 59.560 37.037 33.22 8.55 36.05 2.83
355 793 9.319143 CTATCTCGAGATGTATTTTCCTTTGTT 57.681 33.333 33.22 8.18 36.05 2.83
356 794 7.979444 TCTCGAGATGTATTTTCCTTTGTTT 57.021 32.000 12.08 0.00 0.00 2.83
357 795 8.391075 TCTCGAGATGTATTTTCCTTTGTTTT 57.609 30.769 12.08 0.00 0.00 2.43
358 796 8.504005 TCTCGAGATGTATTTTCCTTTGTTTTC 58.496 33.333 12.08 0.00 0.00 2.29
359 797 8.391075 TCGAGATGTATTTTCCTTTGTTTTCT 57.609 30.769 0.00 0.00 0.00 2.52
360 798 8.846211 TCGAGATGTATTTTCCTTTGTTTTCTT 58.154 29.630 0.00 0.00 0.00 2.52
361 799 9.463443 CGAGATGTATTTTCCTTTGTTTTCTTT 57.537 29.630 0.00 0.00 0.00 2.52
365 803 8.940768 TGTATTTTCCTTTGTTTTCTTTCAGG 57.059 30.769 0.00 0.00 0.00 3.86
366 804 8.754080 TGTATTTTCCTTTGTTTTCTTTCAGGA 58.246 29.630 0.00 0.00 0.00 3.86
367 805 9.594478 GTATTTTCCTTTGTTTTCTTTCAGGAA 57.406 29.630 0.00 0.00 33.05 3.36
369 807 8.546597 TTTTCCTTTGTTTTCTTTCAGGAAAG 57.453 30.769 14.17 14.17 46.82 2.62
370 808 6.220726 TCCTTTGTTTTCTTTCAGGAAAGG 57.779 37.500 18.74 0.00 45.80 3.11
371 809 5.128663 TCCTTTGTTTTCTTTCAGGAAAGGG 59.871 40.000 18.74 10.96 45.80 3.95
372 810 5.128663 CCTTTGTTTTCTTTCAGGAAAGGGA 59.871 40.000 18.74 7.91 45.80 4.20
373 811 6.183361 CCTTTGTTTTCTTTCAGGAAAGGGAT 60.183 38.462 18.74 0.00 45.80 3.85
374 812 6.806668 TTGTTTTCTTTCAGGAAAGGGATT 57.193 33.333 18.74 0.00 45.80 3.01
375 813 6.160576 TGTTTTCTTTCAGGAAAGGGATTG 57.839 37.500 18.74 0.00 45.80 2.67
376 814 5.070313 TGTTTTCTTTCAGGAAAGGGATTGG 59.930 40.000 18.74 0.00 45.80 3.16
377 815 3.456380 TCTTTCAGGAAAGGGATTGGG 57.544 47.619 18.74 0.00 45.80 4.12
378 816 2.721906 TCTTTCAGGAAAGGGATTGGGT 59.278 45.455 18.74 0.00 45.80 4.51
379 817 3.142028 TCTTTCAGGAAAGGGATTGGGTT 59.858 43.478 18.74 0.00 45.80 4.11
380 818 3.628832 TTCAGGAAAGGGATTGGGTTT 57.371 42.857 0.00 0.00 0.00 3.27
381 819 2.888212 TCAGGAAAGGGATTGGGTTTG 58.112 47.619 0.00 0.00 0.00 2.93
382 820 2.448961 TCAGGAAAGGGATTGGGTTTGA 59.551 45.455 0.00 0.00 0.00 2.69
452 897 1.374758 GACGAGGCTGACTGGTTGG 60.375 63.158 0.00 0.00 38.35 3.77
577 1022 3.261951 GACGCCGCGTATGCATGT 61.262 61.111 20.22 1.45 41.37 3.21
583 1028 0.589729 CCGCGTATGCATGTTCAAGC 60.590 55.000 10.16 1.99 42.97 4.01
593 1038 3.423154 GTTCAAGCTCCCGCCACG 61.423 66.667 0.00 0.00 36.60 4.94
615 1060 1.096416 ACCCGAAGAACGAGAGCTAG 58.904 55.000 0.00 0.00 45.77 3.42
628 1073 3.436704 CGAGAGCTAGTTGCCATGAAAAA 59.563 43.478 0.00 0.00 44.23 1.94
662 1108 1.797348 CGAATTCCGCCCAAAAATCCG 60.797 52.381 0.00 0.00 0.00 4.18
733 1197 1.726853 CCTCTTTGTCCGCTACTTGG 58.273 55.000 0.00 0.00 0.00 3.61
816 1292 5.389859 TGATTTTTACTGGGCATGTCTTG 57.610 39.130 0.00 0.00 0.00 3.02
830 1306 3.244887 TGTCTTGGAGAGGTGAGAAGA 57.755 47.619 0.00 0.00 0.00 2.87
831 1307 3.576861 TGTCTTGGAGAGGTGAGAAGAA 58.423 45.455 0.00 0.00 0.00 2.52
833 1309 3.056179 GTCTTGGAGAGGTGAGAAGAAGG 60.056 52.174 0.00 0.00 0.00 3.46
834 1310 1.270907 TGGAGAGGTGAGAAGAAGGC 58.729 55.000 0.00 0.00 0.00 4.35
835 1311 0.174617 GGAGAGGTGAGAAGAAGGCG 59.825 60.000 0.00 0.00 0.00 5.52
837 1313 2.093106 GAGAGGTGAGAAGAAGGCGTA 58.907 52.381 0.00 0.00 0.00 4.42
838 1314 1.819903 AGAGGTGAGAAGAAGGCGTAC 59.180 52.381 0.00 0.00 0.00 3.67
839 1315 0.526662 AGGTGAGAAGAAGGCGTACG 59.473 55.000 11.84 11.84 0.00 3.67
840 1316 0.243095 GGTGAGAAGAAGGCGTACGT 59.757 55.000 17.90 0.00 0.00 3.57
841 1317 1.470098 GGTGAGAAGAAGGCGTACGTA 59.530 52.381 17.90 0.00 0.00 3.57
842 1318 2.477525 GGTGAGAAGAAGGCGTACGTAG 60.478 54.545 17.90 0.00 0.00 3.51
843 1319 1.131883 TGAGAAGAAGGCGTACGTAGC 59.868 52.381 17.90 1.78 0.00 3.58
849 1325 1.313812 AAGGCGTACGTAGCTCTGCT 61.314 55.000 17.90 0.00 43.41 4.24
852 1328 1.134530 GCGTACGTAGCTCTGCTGTG 61.135 60.000 17.90 0.00 40.10 3.66
956 1445 3.787001 CCTCGCTCCACTTCCCCC 61.787 72.222 0.00 0.00 0.00 5.40
1085 1574 4.500116 GCCACTCTCTCCCGCGTC 62.500 72.222 4.92 0.00 0.00 5.19
1086 1575 3.827898 CCACTCTCTCCCGCGTCC 61.828 72.222 4.92 0.00 0.00 4.79
1087 1576 2.752238 CACTCTCTCCCGCGTCCT 60.752 66.667 4.92 0.00 0.00 3.85
1088 1577 2.438795 ACTCTCTCCCGCGTCCTC 60.439 66.667 4.92 0.00 0.00 3.71
1089 1578 3.213402 CTCTCTCCCGCGTCCTCC 61.213 72.222 4.92 0.00 0.00 4.30
1233 1728 3.797353 GATGAGAAGCCGGCCCCA 61.797 66.667 26.15 16.35 0.00 4.96
1595 2105 5.651530 TGCACTTTTTGTTAATTGGAACGA 58.348 33.333 0.00 0.00 31.59 3.85
1619 2129 3.412237 TTACCTGTTCCTAGTTGCCAC 57.588 47.619 0.00 0.00 0.00 5.01
1651 2161 7.925703 AATTCTAACCGAGATACGTACAATG 57.074 36.000 0.00 0.00 40.78 2.82
1804 2321 8.294577 ACAGAAAATTTTATACCTCGTGGAAAC 58.705 33.333 11.17 0.00 37.04 2.78
1898 2928 8.955388 TGATTTGAATTAATTTGGATCTCGTCA 58.045 29.630 1.43 0.00 0.00 4.35
1908 2938 6.633500 TTTGGATCTCGTCAGAAATTTTGT 57.367 33.333 0.00 0.00 30.24 2.83
1933 2963 3.312736 ACAAACATTTCAGGACCCACT 57.687 42.857 0.00 0.00 0.00 4.00
1950 2980 7.947890 AGGACCCACTGAATTTAAGAAAACATA 59.052 33.333 0.00 0.00 0.00 2.29
2007 3038 6.209589 GGGAATAGTGTATGTCTATGAGAGCA 59.790 42.308 0.00 0.00 0.00 4.26
2019 3050 8.969260 TGTCTATGAGAGCAATTGTGATTTAT 57.031 30.769 7.40 0.00 0.00 1.40
2020 3051 9.049523 TGTCTATGAGAGCAATTGTGATTTATC 57.950 33.333 7.40 0.00 0.00 1.75
2021 3052 8.219769 GTCTATGAGAGCAATTGTGATTTATCG 58.780 37.037 7.40 0.00 0.00 2.92
2022 3053 8.143835 TCTATGAGAGCAATTGTGATTTATCGA 58.856 33.333 7.40 0.00 0.00 3.59
2388 3421 2.514205 GCTGGCAAGCTTTTTCTTGA 57.486 45.000 5.60 0.00 46.60 3.02
2483 3531 6.617782 AGTATTCTGATATGCAGCCATACT 57.382 37.500 0.00 0.00 44.52 2.12
2580 3738 1.747924 GCAGAAGGAATCAAAGGCCTC 59.252 52.381 5.23 0.00 0.00 4.70
2600 3758 4.244862 CTCTCAAAAGAGCAGAGGAAGTC 58.755 47.826 0.00 0.00 42.54 3.01
2850 4008 2.432874 TGTTATGTATGGGTCACGAGGG 59.567 50.000 0.00 0.00 0.00 4.30
3088 4246 2.420687 CCCCAGGTTATCACTTGCTCTC 60.421 54.545 0.00 0.00 0.00 3.20
3153 4311 6.509418 AACTGTAACATGCCGTAAATGATT 57.491 33.333 0.00 0.00 0.00 2.57
3406 4565 6.093495 TGAATTGATTCACCGATTCCAAGTAC 59.907 38.462 2.39 0.00 41.51 2.73
3437 4596 4.635699 TTACTCTTTCACTCCTTTCCCC 57.364 45.455 0.00 0.00 0.00 4.81
3457 4778 8.808240 TTCCCCTGTAGTTATCTATTTATGGT 57.192 34.615 0.00 0.00 0.00 3.55
3558 4879 3.328382 TCAGAACTGTTTATGGACGGG 57.672 47.619 0.00 0.00 0.00 5.28
3742 5063 3.378427 GCCTTGAGCGGTCTAATTGATTT 59.622 43.478 16.64 0.00 0.00 2.17
4130 5452 0.413037 TGGGCCAGAATTGGGACATT 59.587 50.000 0.00 0.00 45.16 2.71
4148 5470 5.357878 GGACATTAACCAGAGATTTGCATCA 59.642 40.000 0.00 0.00 0.00 3.07
4220 5542 1.004440 AGCTGGAGTTGCTTCGGAC 60.004 57.895 0.00 0.00 37.52 4.79
4500 5824 1.866601 CTGTCGAGTTGCACATGTGAA 59.133 47.619 29.80 17.53 0.00 3.18
4582 5906 6.823689 GGATGAATGAGTTAGTCTAAAGGCAA 59.176 38.462 0.00 0.00 0.00 4.52
4620 5945 4.194640 CTGCAACTGGTATGCTATCAAGT 58.805 43.478 0.00 0.00 44.14 3.16
4633 5958 4.314740 CTATCAAGTAGCCTGTCCAGTC 57.685 50.000 0.00 0.00 0.00 3.51
4679 6004 4.555262 TCACAATTTCGCCTTCCATTTTC 58.445 39.130 0.00 0.00 0.00 2.29
4712 6037 5.630121 TGCAATATCTAACATTTCCCCGAT 58.370 37.500 0.00 0.00 0.00 4.18
4739 6064 3.411446 TGTTAAGGTCATTGCTGGTCTG 58.589 45.455 0.00 0.00 0.00 3.51
4875 6200 4.798574 CCACTTCTGCATTTTGTACTTCC 58.201 43.478 0.00 0.00 0.00 3.46
4941 6269 9.743057 CTGGTTGAACTAAACAAACAAATATCA 57.257 29.630 0.00 0.00 42.94 2.15
5261 6596 2.068519 TCAACACATGTCATCTCGCAC 58.931 47.619 0.00 0.00 0.00 5.34
5262 6597 1.799994 CAACACATGTCATCTCGCACA 59.200 47.619 0.00 0.00 0.00 4.57
5263 6598 2.391616 ACACATGTCATCTCGCACAT 57.608 45.000 0.00 0.00 33.29 3.21
5264 6599 3.525268 ACACATGTCATCTCGCACATA 57.475 42.857 0.00 0.00 31.78 2.29
5265 6600 3.190079 ACACATGTCATCTCGCACATAC 58.810 45.455 0.00 0.00 31.78 2.39
5266 6601 3.189285 CACATGTCATCTCGCACATACA 58.811 45.455 0.00 0.00 31.78 2.29
5356 7247 3.937079 GTGTCACTCCGTTTTAATAGGGG 59.063 47.826 5.04 0.00 0.00 4.79
5357 7248 2.941064 GTCACTCCGTTTTAATAGGGGC 59.059 50.000 5.04 0.00 0.00 5.80
5455 7346 1.452773 CAACACGCACATTGTTGCATC 59.547 47.619 3.30 0.00 45.36 3.91
5559 7450 1.134220 TCATCCTACGGGTCAAATGCC 60.134 52.381 0.00 0.00 0.00 4.40
5572 7463 1.066573 CAAATGCCCCGCACCATTTAA 60.067 47.619 0.00 0.00 43.04 1.52
5675 7567 0.106519 ATTGAGCCGCTAGCCCATTT 60.107 50.000 9.66 0.00 45.47 2.32
5707 7599 1.953138 GGTGCAGATCGCTCATCCG 60.953 63.158 10.16 0.00 43.06 4.18
5737 7634 0.047176 TGATCCACCCCAACCCCTAT 59.953 55.000 0.00 0.00 0.00 2.57
5766 7670 3.656559 TCTGGTAGAACCGTTGCTAAAC 58.343 45.455 0.00 0.00 42.58 2.01
5800 7704 7.094506 GGGACAGAAATAAAAATCCTACAACGT 60.095 37.037 0.00 0.00 0.00 3.99
5823 7729 7.488471 ACGTAATGACTTATTTCTGCAGTCTAC 59.512 37.037 14.67 2.14 38.24 2.59
5829 7735 7.612244 TGACTTATTTCTGCAGTCTACTACTCT 59.388 37.037 14.67 0.00 38.24 3.24
5832 7738 8.803397 TTATTTCTGCAGTCTACTACTCTACA 57.197 34.615 14.67 0.00 35.76 2.74
6012 7919 6.037940 CCATCTCATCAGAAATACCAGTGTTG 59.962 42.308 0.00 0.00 30.24 3.33
6035 7942 1.301401 GTGGCACGGCAGAAGTACA 60.301 57.895 0.00 0.00 0.00 2.90
6090 7997 2.040278 TGAGCAGACATAGCCAAAAGGT 59.960 45.455 0.00 0.00 0.00 3.50
6124 8032 3.559171 GGCATCCAACTCAAGGAACAGTA 60.559 47.826 0.00 0.00 38.93 2.74
6207 8136 2.295909 TGCATTGTTTTTCGGGAAGGAG 59.704 45.455 0.00 0.00 0.00 3.69
6250 8179 8.340618 AGCAGAGTTTTTATTTGAGCATTCTA 57.659 30.769 0.00 0.00 0.00 2.10
6283 8213 6.655425 GGCTAAAAGGACTTCTTCTACACATT 59.345 38.462 0.00 0.00 33.94 2.71
6344 8276 4.730042 CAGTCAGATTTTGAAACACACACG 59.270 41.667 0.00 0.00 37.61 4.49
6345 8277 4.394920 AGTCAGATTTTGAAACACACACGT 59.605 37.500 0.00 0.00 37.61 4.49
6389 8322 3.530265 TCATCTTGGATTGCATTTGGC 57.470 42.857 0.00 0.00 45.13 4.52
6417 8350 7.040823 ACAGAAGTTGAGTTTCCATGAGAAATC 60.041 37.037 11.07 6.96 45.99 2.17
6418 8351 6.432472 AGAAGTTGAGTTTCCATGAGAAATCC 59.568 38.462 11.07 7.81 45.99 3.01
6419 8352 5.634118 AGTTGAGTTTCCATGAGAAATCCA 58.366 37.500 11.07 9.58 45.99 3.41
6420 8353 5.474876 AGTTGAGTTTCCATGAGAAATCCAC 59.525 40.000 11.07 8.00 45.99 4.02
6421 8354 4.335416 TGAGTTTCCATGAGAAATCCACC 58.665 43.478 11.07 1.44 45.99 4.61
6422 8355 3.696548 GAGTTTCCATGAGAAATCCACCC 59.303 47.826 11.07 0.91 45.99 4.61
6457 8395 7.092079 CAGCCATGAGTTGTATTTGATCAAAA 58.908 34.615 23.91 11.17 33.56 2.44
6501 8569 8.405531 CAATTTATACCATAACTGGAACTGGTG 58.594 37.037 3.41 0.00 46.37 4.17
6530 8598 5.458595 TGGACTGTATGACTGTATCTCCAT 58.541 41.667 0.00 0.00 30.17 3.41
6554 8622 1.774110 TTGTGTTTGGTGCCATCTGT 58.226 45.000 0.00 0.00 0.00 3.41
6591 8659 4.038763 TGTTTACACCAGTGACTAGTGAGG 59.961 45.833 17.69 1.06 35.47 3.86
6592 8660 2.677542 ACACCAGTGACTAGTGAGGA 57.322 50.000 17.69 0.00 35.47 3.71
6597 8727 3.099905 CCAGTGACTAGTGAGGAATCCA 58.900 50.000 0.00 0.00 0.00 3.41
6655 8785 1.032114 AAATCTAGCCCGCTGTTGCC 61.032 55.000 0.00 0.00 35.36 4.52
6656 8786 1.915078 AATCTAGCCCGCTGTTGCCT 61.915 55.000 0.00 0.00 35.36 4.75
6657 8787 2.599645 ATCTAGCCCGCTGTTGCCTG 62.600 60.000 0.00 0.00 35.36 4.85
6658 8788 3.612247 CTAGCCCGCTGTTGCCTGT 62.612 63.158 0.00 0.00 35.36 4.00
6659 8789 3.190738 TAGCCCGCTGTTGCCTGTT 62.191 57.895 0.00 0.00 35.36 3.16
6660 8790 4.347453 GCCCGCTGTTGCCTGTTG 62.347 66.667 0.00 0.00 35.36 3.33
6661 8791 4.347453 CCCGCTGTTGCCTGTTGC 62.347 66.667 0.00 0.00 41.77 4.17
6682 8812 3.071602 GCTATTGCCAGAGGAATCCAGTA 59.928 47.826 0.61 0.00 0.00 2.74
6769 8902 1.002921 ACCGATCCCTGGACCATCA 59.997 57.895 0.00 0.00 0.00 3.07
6888 9023 0.039256 GCAAATTGGCAACGCAGAGA 60.039 50.000 0.00 0.00 42.51 3.10
6889 9024 1.602668 GCAAATTGGCAACGCAGAGAA 60.603 47.619 0.00 0.00 42.51 2.87
6890 9025 2.741612 CAAATTGGCAACGCAGAGAAA 58.258 42.857 0.00 0.00 42.51 2.52
6891 9026 3.319755 CAAATTGGCAACGCAGAGAAAT 58.680 40.909 0.00 0.00 42.51 2.17
6892 9027 2.642139 ATTGGCAACGCAGAGAAATG 57.358 45.000 0.00 0.00 42.51 2.32
6893 9028 1.317613 TTGGCAACGCAGAGAAATGT 58.682 45.000 0.00 0.00 42.51 2.71
6894 9029 2.177394 TGGCAACGCAGAGAAATGTA 57.823 45.000 0.00 0.00 42.51 2.29
6895 9030 2.076100 TGGCAACGCAGAGAAATGTAG 58.924 47.619 0.00 0.00 42.51 2.74
6896 9031 2.076863 GGCAACGCAGAGAAATGTAGT 58.923 47.619 0.00 0.00 0.00 2.73
6897 9032 2.484264 GGCAACGCAGAGAAATGTAGTT 59.516 45.455 0.00 0.00 0.00 2.24
6898 9033 3.482786 GCAACGCAGAGAAATGTAGTTG 58.517 45.455 10.57 10.57 40.52 3.16
6899 9034 3.482786 CAACGCAGAGAAATGTAGTTGC 58.517 45.455 0.00 0.00 35.69 4.17
6900 9035 2.766313 ACGCAGAGAAATGTAGTTGCA 58.234 42.857 0.00 0.00 0.00 4.08
6901 9036 2.738846 ACGCAGAGAAATGTAGTTGCAG 59.261 45.455 0.00 0.00 0.00 4.41
6902 9037 2.995939 CGCAGAGAAATGTAGTTGCAGA 59.004 45.455 0.00 0.00 0.00 4.26
6903 9038 3.061831 CGCAGAGAAATGTAGTTGCAGAG 59.938 47.826 0.00 0.00 0.00 3.35
6904 9039 3.999663 GCAGAGAAATGTAGTTGCAGAGT 59.000 43.478 0.00 0.00 0.00 3.24
6905 9040 4.453819 GCAGAGAAATGTAGTTGCAGAGTT 59.546 41.667 0.00 0.00 0.00 3.01
6906 9041 5.616424 GCAGAGAAATGTAGTTGCAGAGTTG 60.616 44.000 0.00 0.00 0.00 3.16
6952 9113 5.371526 CAGCTGAAATATCCATGTGGTAGT 58.628 41.667 8.42 0.00 36.34 2.73
6955 9116 6.327626 AGCTGAAATATCCATGTGGTAGTACT 59.672 38.462 0.00 0.00 36.34 2.73
7006 9167 1.734465 GGCTCTTGATCTGAACCGTTG 59.266 52.381 0.00 0.00 0.00 4.10
7019 9180 2.732016 CGTTGGACACGGTGGAGA 59.268 61.111 13.48 0.00 45.89 3.71
7020 9181 1.663702 CGTTGGACACGGTGGAGAC 60.664 63.158 13.48 4.84 45.89 3.36
7021 9182 1.444250 GTTGGACACGGTGGAGACA 59.556 57.895 13.48 2.88 38.70 3.41
7022 9183 0.034896 GTTGGACACGGTGGAGACAT 59.965 55.000 13.48 0.00 46.14 3.06
7023 9184 0.034756 TTGGACACGGTGGAGACATG 59.965 55.000 13.48 0.00 46.14 3.21
7032 9193 1.202463 GGTGGAGACATGACATCCTCG 60.202 57.143 0.00 0.00 46.14 4.63
7039 9200 1.153289 ATGACATCCTCGCAGCACC 60.153 57.895 0.00 0.00 0.00 5.01
7047 9208 1.302033 CTCGCAGCACCTCAGGTTT 60.302 57.895 0.00 0.00 31.02 3.27
7063 9224 6.070951 TCAGGTTTGGATTTCATCTCTGAT 57.929 37.500 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.068281 CTGTCTCTGCACATATCGCCT 59.932 52.381 0.00 0.00 0.00 5.52
31 32 1.545651 CCTTGGGGAGTGGAAACTGTC 60.546 57.143 0.00 0.00 33.58 3.51
46 47 1.117150 CCAATCTCAATGCCCCTTGG 58.883 55.000 0.00 0.00 0.00 3.61
56 57 6.015180 CCAAGAAAATCCTTGACCAATCTCAA 60.015 38.462 5.32 0.00 44.66 3.02
57 58 5.477984 CCAAGAAAATCCTTGACCAATCTCA 59.522 40.000 5.32 0.00 44.66 3.27
59 60 5.644188 TCCAAGAAAATCCTTGACCAATCT 58.356 37.500 5.32 0.00 44.66 2.40
60 61 5.105595 CCTCCAAGAAAATCCTTGACCAATC 60.106 44.000 5.32 0.00 44.66 2.67
61 62 4.774200 CCTCCAAGAAAATCCTTGACCAAT 59.226 41.667 5.32 0.00 44.66 3.16
62 63 4.151883 CCTCCAAGAAAATCCTTGACCAA 58.848 43.478 5.32 0.00 44.66 3.67
63 64 3.140144 ACCTCCAAGAAAATCCTTGACCA 59.860 43.478 5.32 0.00 44.66 4.02
83 84 2.240279 ACACATCCGGAGATAGCTACC 58.760 52.381 11.34 0.00 0.00 3.18
127 132 1.626321 TGCGGTCCAGGATTTGTTCTA 59.374 47.619 0.00 0.00 0.00 2.10
140 145 1.512156 ATGTGTCGGTTTTGCGGTCC 61.512 55.000 0.00 0.00 0.00 4.46
143 148 0.110238 CAGATGTGTCGGTTTTGCGG 60.110 55.000 0.00 0.00 0.00 5.69
153 158 2.873797 GGGGGAAAGCAGATGTGTC 58.126 57.895 0.00 0.00 0.00 3.67
193 198 6.369890 CAGAGAAAACTCAGCATTACAGCTAA 59.630 38.462 0.00 0.00 44.54 3.09
239 244 0.687354 GAAGCAGGGAACTCCAGTCA 59.313 55.000 0.00 0.00 40.21 3.41
240 245 0.035915 GGAAGCAGGGAACTCCAGTC 60.036 60.000 0.00 0.00 40.21 3.51
241 246 0.474660 AGGAAGCAGGGAACTCCAGT 60.475 55.000 0.00 0.00 40.21 4.00
242 247 0.035630 CAGGAAGCAGGGAACTCCAG 60.036 60.000 0.00 0.00 40.21 3.86
243 248 0.473694 TCAGGAAGCAGGGAACTCCA 60.474 55.000 0.00 0.00 40.21 3.86
244 249 0.251634 CTCAGGAAGCAGGGAACTCC 59.748 60.000 0.00 0.00 40.21 3.85
263 575 7.212976 TCTTTCTCATGTGCTATATGGTTCTC 58.787 38.462 0.00 0.00 0.00 2.87
275 587 6.675987 ACTGAAAAGAATCTTTCTCATGTGC 58.324 36.000 8.86 0.00 39.61 4.57
276 588 8.997323 AGTACTGAAAAGAATCTTTCTCATGTG 58.003 33.333 8.86 6.46 39.61 3.21
277 589 9.566432 AAGTACTGAAAAGAATCTTTCTCATGT 57.434 29.630 8.86 14.13 39.61 3.21
300 738 3.214696 AGCCTGCAACACTTCTTAAGT 57.785 42.857 1.63 0.00 44.06 2.24
333 771 8.507249 AGAAAACAAAGGAAAATACATCTCGAG 58.493 33.333 5.93 5.93 0.00 4.04
335 773 9.463443 AAAGAAAACAAAGGAAAATACATCTCG 57.537 29.630 0.00 0.00 0.00 4.04
339 777 9.546428 CCTGAAAGAAAACAAAGGAAAATACAT 57.454 29.630 0.00 0.00 34.07 2.29
340 778 8.754080 TCCTGAAAGAAAACAAAGGAAAATACA 58.246 29.630 0.00 0.00 34.07 2.29
341 779 9.594478 TTCCTGAAAGAAAACAAAGGAAAATAC 57.406 29.630 0.00 0.00 38.76 1.89
358 796 3.175438 ACCCAATCCCTTTCCTGAAAG 57.825 47.619 11.78 11.78 45.47 2.62
359 797 3.628832 AACCCAATCCCTTTCCTGAAA 57.371 42.857 0.00 0.00 0.00 2.69
360 798 3.116939 TCAAACCCAATCCCTTTCCTGAA 60.117 43.478 0.00 0.00 0.00 3.02
361 799 2.448961 TCAAACCCAATCCCTTTCCTGA 59.551 45.455 0.00 0.00 0.00 3.86
362 800 2.888212 TCAAACCCAATCCCTTTCCTG 58.112 47.619 0.00 0.00 0.00 3.86
363 801 3.852858 ATCAAACCCAATCCCTTTCCT 57.147 42.857 0.00 0.00 0.00 3.36
364 802 7.670364 CATAATATCAAACCCAATCCCTTTCC 58.330 38.462 0.00 0.00 0.00 3.13
365 803 7.015584 AGCATAATATCAAACCCAATCCCTTTC 59.984 37.037 0.00 0.00 0.00 2.62
366 804 6.845975 AGCATAATATCAAACCCAATCCCTTT 59.154 34.615 0.00 0.00 0.00 3.11
367 805 6.268387 CAGCATAATATCAAACCCAATCCCTT 59.732 38.462 0.00 0.00 0.00 3.95
368 806 5.776716 CAGCATAATATCAAACCCAATCCCT 59.223 40.000 0.00 0.00 0.00 4.20
369 807 5.567423 GCAGCATAATATCAAACCCAATCCC 60.567 44.000 0.00 0.00 0.00 3.85
370 808 5.473039 GCAGCATAATATCAAACCCAATCC 58.527 41.667 0.00 0.00 0.00 3.01
371 809 5.156355 CGCAGCATAATATCAAACCCAATC 58.844 41.667 0.00 0.00 0.00 2.67
372 810 5.125100 CGCAGCATAATATCAAACCCAAT 57.875 39.130 0.00 0.00 0.00 3.16
373 811 4.566545 CGCAGCATAATATCAAACCCAA 57.433 40.909 0.00 0.00 0.00 4.12
400 838 1.528309 ACCTTCCGCACAAACCTGG 60.528 57.895 0.00 0.00 0.00 4.45
452 897 1.442857 CGTCTCCGCGAGCATATCC 60.443 63.158 8.23 0.00 0.00 2.59
593 1038 1.069255 GCTCTCGTTCTTCGGGTTTC 58.931 55.000 0.00 0.00 41.36 2.78
628 1073 0.613572 AATTCGCCGGGGTGGAATTT 60.614 50.000 19.13 0.00 42.00 1.82
629 1074 1.000145 AATTCGCCGGGGTGGAATT 60.000 52.632 19.13 13.83 42.00 2.17
630 1075 1.453197 GAATTCGCCGGGGTGGAAT 60.453 57.895 19.13 8.23 42.00 3.01
662 1108 1.079266 CAGAGACAGGGACAGCAGC 60.079 63.158 0.00 0.00 0.00 5.25
733 1197 1.291877 AAGCTGGTCGACATTGCGTC 61.292 55.000 18.91 0.00 41.62 5.19
747 1211 2.378806 CGTTTGAAGTGCTTGAAGCTG 58.621 47.619 18.94 0.00 42.97 4.24
816 1292 0.174617 CGCCTTCTTCTCACCTCTCC 59.825 60.000 0.00 0.00 0.00 3.71
830 1306 1.139095 GCAGAGCTACGTACGCCTT 59.861 57.895 16.72 0.00 0.00 4.35
831 1307 1.749638 AGCAGAGCTACGTACGCCT 60.750 57.895 16.72 9.34 36.99 5.52
833 1309 1.134530 CACAGCAGAGCTACGTACGC 61.135 60.000 16.72 0.00 36.40 4.42
834 1310 1.134530 GCACAGCAGAGCTACGTACG 61.135 60.000 15.01 15.01 36.40 3.67
835 1311 0.109272 TGCACAGCAGAGCTACGTAC 60.109 55.000 0.00 0.00 36.40 3.67
837 1313 0.249868 TTTGCACAGCAGAGCTACGT 60.250 50.000 0.00 0.00 40.61 3.57
838 1314 0.164647 GTTTGCACAGCAGAGCTACG 59.835 55.000 0.00 0.00 40.61 3.51
839 1315 1.196354 CTGTTTGCACAGCAGAGCTAC 59.804 52.381 5.67 0.00 44.16 3.58
840 1316 1.516161 CTGTTTGCACAGCAGAGCTA 58.484 50.000 5.67 0.00 44.16 3.32
841 1317 2.328235 CTGTTTGCACAGCAGAGCT 58.672 52.632 5.67 0.00 44.16 4.09
842 1318 4.937781 CTGTTTGCACAGCAGAGC 57.062 55.556 5.67 0.00 44.16 4.09
849 1325 3.504134 ACAACTGTACAACTGTTTGCACA 59.496 39.130 0.00 0.00 38.03 4.57
867 1343 1.068474 CTACAGCACGGCAGTACAAC 58.932 55.000 0.00 0.00 29.63 3.32
928 1416 1.016653 GGAGCGAGGCAACAAGAGAC 61.017 60.000 0.00 0.00 41.41 3.36
1084 1573 4.144727 GCGGGAGGAGGAGGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
1218 1713 4.344865 GTTGGGGCCGGCTTCTCA 62.345 66.667 28.56 14.61 0.00 3.27
1595 2105 5.243060 GTGGCAACTAGGAACAGGTAAAATT 59.757 40.000 0.00 0.00 37.61 1.82
1619 2129 9.193133 ACGTATCTCGGTTAGAATTATGAATTG 57.807 33.333 0.00 0.00 44.69 2.32
1791 2307 6.642707 AATTCAAAATGTTTCCACGAGGTA 57.357 33.333 0.00 0.00 35.89 3.08
1840 2862 7.839680 ACTGGGTCTAATTCAGTGAATTTTT 57.160 32.000 30.62 14.48 41.64 1.94
1908 2938 5.242838 GTGGGTCCTGAAATGTTTGTTATCA 59.757 40.000 0.00 0.00 0.00 2.15
1995 3026 8.219769 CGATAAATCACAATTGCTCTCATAGAC 58.780 37.037 5.05 0.00 0.00 2.59
2007 3038 6.732154 CAAGGCTGATCGATAAATCACAATT 58.268 36.000 0.00 0.00 32.36 2.32
2019 3050 2.988010 AGTATTGCAAGGCTGATCGA 57.012 45.000 4.94 0.00 0.00 3.59
2020 3051 2.289002 GGAAGTATTGCAAGGCTGATCG 59.711 50.000 4.94 0.00 35.98 3.69
2021 3052 3.549794 AGGAAGTATTGCAAGGCTGATC 58.450 45.455 4.94 1.26 39.77 2.92
2022 3053 3.549794 GAGGAAGTATTGCAAGGCTGAT 58.450 45.455 4.94 0.00 39.77 2.90
2501 3549 8.608844 ATTAAGTACTTTTCACCACAGAGAAG 57.391 34.615 14.49 0.00 36.22 2.85
2850 4008 1.909700 TTCTGGCAGGAACACCAATC 58.090 50.000 15.73 0.00 36.40 2.67
3088 4246 5.543507 AGGAGTACCAAAGATATGCTGAG 57.456 43.478 0.00 0.00 38.94 3.35
3153 4311 8.594550 AGCTCATTACTGGTTTTCTAGAGTAAA 58.405 33.333 4.65 0.00 35.20 2.01
3189 4347 5.121221 AGCAAGTTTTTAGCTGCGTTAAT 57.879 34.783 0.00 0.00 37.20 1.40
3272 4430 7.925043 TCCTGCAATGAAATAAATGCAAAAT 57.075 28.000 0.00 0.00 46.97 1.82
3291 4450 8.320617 AGATCTATTCCTTTCTGAATATCCTGC 58.679 37.037 0.00 0.00 36.79 4.85
3530 4851 9.529325 CGTCCATAAACAGTTCTGATAGATTTA 57.471 33.333 6.83 1.82 0.00 1.40
3558 4879 2.479566 TGAAATCTGACAGGGCTGAC 57.520 50.000 1.81 0.00 0.00 3.51
3604 4925 3.576078 TCTGGCAGTTCTTTCCTTTCA 57.424 42.857 15.27 0.00 0.00 2.69
3742 5063 7.425224 AAGTTCTCCTAGCTATAAAGAGCAA 57.575 36.000 13.00 4.97 45.43 3.91
4061 5383 3.451178 GCAGTGACCCTAACAATCCTCTA 59.549 47.826 0.00 0.00 0.00 2.43
4130 5452 6.299805 AGTACTGATGCAAATCTCTGGTTA 57.700 37.500 0.00 0.00 0.00 2.85
4148 5470 3.537795 TTCAGACCACCCACTAGTACT 57.462 47.619 0.00 0.00 0.00 2.73
4220 5542 1.524986 CGACGAGCAGCATACAAAACG 60.525 52.381 0.00 0.00 0.00 3.60
4500 5824 4.080356 TGCTAAAGTTCCTATCATGTGCCT 60.080 41.667 0.00 0.00 0.00 4.75
4582 5906 1.602888 CAGCTGCAAGGCCTCAGTT 60.603 57.895 19.68 12.97 33.09 3.16
4620 5945 5.366477 TGATCATAAATGACTGGACAGGCTA 59.634 40.000 6.73 0.00 40.03 3.93
4658 5983 3.364621 CGAAAATGGAAGGCGAAATTGTG 59.635 43.478 0.00 0.00 0.00 3.33
4712 6037 8.052748 AGACCAGCAATGACCTTAACATATTTA 58.947 33.333 0.00 0.00 0.00 1.40
4781 6106 3.777478 CACATTAGCAAGAAATGGCTGG 58.223 45.455 0.00 0.00 41.25 4.85
4968 6296 3.996921 AACCTGCTCTCTGAATCACAT 57.003 42.857 0.00 0.00 0.00 3.21
5261 6596 5.723492 CATGTACAGGACACACATGTATG 57.277 43.478 1.67 1.67 45.23 2.39
5266 6601 2.038952 AGCACATGTACAGGACACACAT 59.961 45.455 15.54 0.00 42.17 3.21
5356 7247 0.886490 CCTAGGATTGACATGGCGGC 60.886 60.000 1.05 0.00 0.00 6.53
5357 7248 0.758734 TCCTAGGATTGACATGGCGG 59.241 55.000 7.62 0.00 0.00 6.13
5455 7346 9.698617 CATGCACATATATTTAGACATTCATCG 57.301 33.333 0.00 0.00 0.00 3.84
5559 7450 1.999024 GTTGCATTTAAATGGTGCGGG 59.001 47.619 25.61 3.13 41.61 6.13
5737 7634 2.696707 ACGGTTCTACCAGAGACAAACA 59.303 45.455 0.00 0.00 38.47 2.83
5766 7670 7.201857 GGATTTTTATTTCTGTCCCTGGAGATG 60.202 40.741 0.00 0.00 0.00 2.90
5803 7709 7.612244 AGAGTAGTAGACTGCAGAAATAAGTCA 59.388 37.037 23.35 0.00 42.28 3.41
5806 7712 8.894731 TGTAGAGTAGTAGACTGCAGAAATAAG 58.105 37.037 23.35 0.00 39.06 1.73
5823 7729 7.089770 TGTATGAAGCTGAGTTGTAGAGTAG 57.910 40.000 0.00 0.00 0.00 2.57
5832 7738 9.948964 TGCATAATATATGTATGAAGCTGAGTT 57.051 29.630 14.18 0.00 31.71 3.01
6012 7919 1.926511 CTTCTGCCGTGCCACATTCC 61.927 60.000 0.00 0.00 0.00 3.01
6124 8032 7.004691 TGTGTCTATATGCCTGTACTGTAGAT 58.995 38.462 0.00 0.00 0.00 1.98
6157 8086 2.027192 TGGGATTCAGTCTTGCTGTACC 60.027 50.000 0.00 0.00 45.23 3.34
6207 8136 7.144000 ACTCTGCTCTTCAAAATTTCATGTTC 58.856 34.615 0.00 0.00 0.00 3.18
6250 8179 3.073274 AGTCCTTTTAGCCGCAAGAAT 57.927 42.857 0.00 0.00 43.02 2.40
6300 8230 8.536175 TGACTGTTTCCTGTTGATGTACATATA 58.464 33.333 8.71 0.00 0.00 0.86
6344 8276 9.250624 GATATCAAGAGTCTAAATGGTGTGTAC 57.749 37.037 0.00 0.00 0.00 2.90
6345 8277 8.977412 TGATATCAAGAGTCTAAATGGTGTGTA 58.023 33.333 1.98 0.00 0.00 2.90
6389 8322 7.415541 TTTCTCATGGAAACTCAACTTCTGTTG 60.416 37.037 5.55 2.83 44.28 3.33
6394 8327 6.207417 TGGATTTCTCATGGAAACTCAACTTC 59.793 38.462 10.37 4.52 45.29 3.01
6429 8362 2.428171 CAAATACAACTCATGGCTGGGG 59.572 50.000 0.00 0.00 0.00 4.96
6430 8363 3.355378 TCAAATACAACTCATGGCTGGG 58.645 45.455 0.00 0.00 0.00 4.45
6431 8364 4.641541 TGATCAAATACAACTCATGGCTGG 59.358 41.667 0.00 0.00 0.00 4.85
6501 8569 7.275920 AGATACAGTCATACAGTCCAATTTCC 58.724 38.462 0.00 0.00 0.00 3.13
6554 8622 6.747125 TGGTGTAAACAAGTATCGACAGTTA 58.253 36.000 0.00 0.00 0.00 2.24
6622 8752 5.915196 GGGCTAGATTTGTTCGATTAATTGC 59.085 40.000 0.00 0.00 0.00 3.56
6655 8785 2.408271 TCCTCTGGCAATAGCAACAG 57.592 50.000 0.00 0.00 44.61 3.16
6656 8786 2.877097 TTCCTCTGGCAATAGCAACA 57.123 45.000 0.00 0.00 44.61 3.33
6657 8787 2.620585 GGATTCCTCTGGCAATAGCAAC 59.379 50.000 0.00 0.00 44.61 4.17
6658 8788 2.241941 TGGATTCCTCTGGCAATAGCAA 59.758 45.455 3.95 0.00 44.61 3.91
6659 8789 1.845791 TGGATTCCTCTGGCAATAGCA 59.154 47.619 3.95 0.00 44.61 3.49
6660 8790 2.158696 ACTGGATTCCTCTGGCAATAGC 60.159 50.000 3.95 0.00 41.10 2.97
6661 8791 3.853355 ACTGGATTCCTCTGGCAATAG 57.147 47.619 3.95 0.00 0.00 1.73
6682 8812 2.063015 TTGGATGGCCGTGACTTGGT 62.063 55.000 0.00 0.00 36.79 3.67
6769 8902 4.159879 AGACTTCGGATATGTTCGTTCCTT 59.840 41.667 0.00 0.00 0.00 3.36
6832 8967 3.130227 CGGATCCGGTCCTCCTTC 58.870 66.667 26.95 0.00 45.46 3.46
6881 9016 2.995939 TCTGCAACTACATTTCTCTGCG 59.004 45.455 0.00 0.00 32.45 5.18
6911 9046 2.686915 GCTGCAGCTGGAATGTCTATTT 59.313 45.455 31.33 0.00 38.21 1.40
6970 9131 1.822186 GCCAGACCACAACCGTTGT 60.822 57.895 11.24 11.24 46.75 3.32
6973 9134 1.696097 AAGAGCCAGACCACAACCGT 61.696 55.000 0.00 0.00 0.00 4.83
6980 9141 1.942776 TCAGATCAAGAGCCAGACCA 58.057 50.000 0.00 0.00 0.00 4.02
7006 9167 0.389948 GTCATGTCTCCACCGTGTCC 60.390 60.000 0.00 0.00 0.00 4.02
7017 9178 0.179089 GCTGCGAGGATGTCATGTCT 60.179 55.000 0.00 0.00 0.00 3.41
7018 9179 0.460811 TGCTGCGAGGATGTCATGTC 60.461 55.000 0.00 0.00 0.00 3.06
7019 9180 0.742281 GTGCTGCGAGGATGTCATGT 60.742 55.000 0.00 0.00 0.00 3.21
7020 9181 1.434622 GGTGCTGCGAGGATGTCATG 61.435 60.000 0.00 0.00 0.00 3.07
7021 9182 1.153289 GGTGCTGCGAGGATGTCAT 60.153 57.895 0.00 0.00 0.00 3.06
7022 9183 2.230994 GAGGTGCTGCGAGGATGTCA 62.231 60.000 0.00 0.00 0.00 3.58
7023 9184 1.520342 GAGGTGCTGCGAGGATGTC 60.520 63.158 0.00 0.00 0.00 3.06
7032 9193 0.610232 ATCCAAACCTGAGGTGCTGC 60.610 55.000 4.15 0.00 35.34 5.25


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

AutoCloner maintained by Alex Coulton.