Multiple sequence alignment - TraesCS1A01G266600

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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 TraesCS1A01G266600 chr1A 100.000 5919 0 0 1 5919 462006023 462000105 0.000000e+00 10931.0
1 TraesCS1A01G266600 chr1D 89.699 6116 311 140 1 5919 362493934 362487941 0.000000e+00 7509.0
2 TraesCS1A01G266600 chr1B 92.806 1668 76 17 3833 5471 485289761 485288109 0.000000e+00 2375.0
3 TraesCS1A01G266600 chr1B 89.870 1461 63 30 1318 2713 485292424 485290984 0.000000e+00 1799.0
4 TraesCS1A01G266600 chr1B 93.023 989 42 13 2849 3836 485290825 485289863 0.000000e+00 1419.0
5 TraesCS1A01G266600 chr1B 84.440 1401 71 50 1 1321 485293795 485292462 0.000000e+00 1243.0
6 TraesCS1A01G266600 chr1B 96.347 438 10 3 5471 5908 485288047 485287616 0.000000e+00 715.0
7 TraesCS1A01G266600 chr1B 90.816 98 4 4 2757 2850 485290981 485290885 6.230000e-25 126.0
8 TraesCS1A01G266600 chr3A 85.151 963 141 2 3889 4850 653853001 653852040 0.000000e+00 985.0
9 TraesCS1A01G266600 chr3D 83.017 1054 163 9 3889 4934 518153052 518152007 0.000000e+00 941.0
10 TraesCS1A01G266600 chr3B 82.716 1053 168 9 3889 4934 682787559 682786514 0.000000e+00 924.0
11 TraesCS1A01G266600 chr5B 75.076 654 141 18 4124 4766 87979484 87978842 9.710000e-73 285.0
12 TraesCS1A01G266600 chr5A 74.740 673 145 20 4124 4783 74679282 74678622 1.620000e-70 278.0
13 TraesCS1A01G266600 chr5D 74.886 657 136 23 4124 4766 78121095 78120454 7.560000e-69 272.0
14 TraesCS1A01G266600 chr6D 82.927 123 9 5 2739 2850 14468135 14468256 3.770000e-17 100.0
15 TraesCS1A01G266600 chr6A 89.552 67 6 1 2785 2850 15917169 15917103 3.800000e-12 84.2


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 TraesCS1A01G266600 chr1A 462000105 462006023 5918 True 10931.0 10931 100.000 1 5919 1 chr1A.!!$R1 5918
1 TraesCS1A01G266600 chr1D 362487941 362493934 5993 True 7509.0 7509 89.699 1 5919 1 chr1D.!!$R1 5918
2 TraesCS1A01G266600 chr1B 485287616 485293795 6179 True 1279.5 2375 91.217 1 5908 6 chr1B.!!$R1 5907
3 TraesCS1A01G266600 chr3A 653852040 653853001 961 True 985.0 985 85.151 3889 4850 1 chr3A.!!$R1 961
4 TraesCS1A01G266600 chr3D 518152007 518153052 1045 True 941.0 941 83.017 3889 4934 1 chr3D.!!$R1 1045
5 TraesCS1A01G266600 chr3B 682786514 682787559 1045 True 924.0 924 82.716 3889 4934 1 chr3B.!!$R1 1045
6 TraesCS1A01G266600 chr5B 87978842 87979484 642 True 285.0 285 75.076 4124 4766 1 chr5B.!!$R1 642
7 TraesCS1A01G266600 chr5A 74678622 74679282 660 True 278.0 278 74.740 4124 4783 1 chr5A.!!$R1 659
8 TraesCS1A01G266600 chr5D 78120454 78121095 641 True 272.0 272 74.886 4124 4766 1 chr5D.!!$R1 642

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
337 338 0.107214 TTCGGTTCATCCATGGAGGC 60.107 55.000 21.65 8.46 37.29 4.70 F
789 843 0.378257 GCGTGTTGATCGATGCCATT 59.622 50.000 0.54 0.00 0.00 3.16 F
2160 2361 1.071699 AGCAAAACTGCTTCCCTACGA 59.928 47.619 0.00 0.00 43.52 3.43 F
3251 3520 0.244450 AGGCGCATGGTTTGATGTTG 59.756 50.000 10.83 0.00 0.00 3.33 F
3325 3594 0.679002 GGCTCCATTTGCAGCTCTCA 60.679 55.000 0.00 0.00 35.82 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 2360 0.031449 GGTGGCGAGCTCTCATACTC 59.969 60.0 12.85 0.0 0.00 2.59 R
2727 2929 0.249120 CCGCCACTGGTCTACATCAA 59.751 55.0 0.00 0.0 0.00 2.57 R
3331 3600 0.250338 AAGAGGTCACGGCCAGTTTC 60.250 55.0 2.24 0.0 0.00 2.78 R
4518 4911 0.100861 GTAGTGGAGCACGTAGAGGC 59.899 60.0 0.00 0.0 39.64 4.70 R
5037 5436 0.954452 GCAACAGAGGAGGGTTTGTG 59.046 55.0 0.00 0.0 0.00 3.33 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
33 34 1.075600 CCTCCTCCCCTCCTGAGAC 60.076 68.421 0.00 0.00 31.26 3.36
84 85 1.369209 CTTTTGCGTGAGTGCGTGG 60.369 57.895 0.00 0.00 37.81 4.94
94 95 0.732571 GAGTGCGTGGAGAGAGAGAG 59.267 60.000 0.00 0.00 0.00 3.20
95 96 0.326595 AGTGCGTGGAGAGAGAGAGA 59.673 55.000 0.00 0.00 0.00 3.10
96 97 0.732571 GTGCGTGGAGAGAGAGAGAG 59.267 60.000 0.00 0.00 0.00 3.20
97 98 0.615850 TGCGTGGAGAGAGAGAGAGA 59.384 55.000 0.00 0.00 0.00 3.10
99 100 1.953559 CGTGGAGAGAGAGAGAGAGG 58.046 60.000 0.00 0.00 0.00 3.69
100 101 1.484653 CGTGGAGAGAGAGAGAGAGGA 59.515 57.143 0.00 0.00 0.00 3.71
103 104 2.293519 TGGAGAGAGAGAGAGAGGAGGA 60.294 54.545 0.00 0.00 0.00 3.71
104 105 2.370189 GGAGAGAGAGAGAGAGGAGGAG 59.630 59.091 0.00 0.00 0.00 3.69
108 109 1.143073 GAGAGAGAGAGGAGGAGGGAC 59.857 61.905 0.00 0.00 0.00 4.46
109 110 0.179029 GAGAGAGAGGAGGAGGGACG 60.179 65.000 0.00 0.00 0.00 4.79
110 111 0.622154 AGAGAGAGGAGGAGGGACGA 60.622 60.000 0.00 0.00 0.00 4.20
111 112 0.179029 GAGAGAGGAGGAGGGACGAG 60.179 65.000 0.00 0.00 0.00 4.18
112 113 1.826487 GAGAGGAGGAGGGACGAGC 60.826 68.421 0.00 0.00 0.00 5.03
113 114 2.043852 GAGGAGGAGGGACGAGCA 60.044 66.667 0.00 0.00 0.00 4.26
140 141 2.197324 TTTCTTGCCGCCCACCTT 59.803 55.556 0.00 0.00 0.00 3.50
195 196 4.457496 ACTGCTCGTCCATGGCGG 62.457 66.667 22.59 16.06 38.21 6.13
202 203 4.554036 GTCCATGGCGGCTCCTCC 62.554 72.222 11.43 0.00 35.26 4.30
246 247 3.057245 GCTCCTTTCATTTGGTTCTGGAC 60.057 47.826 0.00 0.00 0.00 4.02
290 291 2.746375 GGGGTCATCCATGGCGACT 61.746 63.158 24.77 2.86 37.22 4.18
326 327 1.546923 TGGCTCTTATCGTTCGGTTCA 59.453 47.619 0.00 0.00 0.00 3.18
327 328 2.167693 TGGCTCTTATCGTTCGGTTCAT 59.832 45.455 0.00 0.00 0.00 2.57
328 329 2.795470 GGCTCTTATCGTTCGGTTCATC 59.205 50.000 0.00 0.00 0.00 2.92
329 330 2.795470 GCTCTTATCGTTCGGTTCATCC 59.205 50.000 0.00 0.00 0.00 3.51
330 331 3.737047 GCTCTTATCGTTCGGTTCATCCA 60.737 47.826 0.00 0.00 35.57 3.41
331 332 4.621991 CTCTTATCGTTCGGTTCATCCAT 58.378 43.478 0.00 0.00 35.57 3.41
333 334 1.953559 ATCGTTCGGTTCATCCATGG 58.046 50.000 4.97 4.97 35.57 3.66
334 335 0.899019 TCGTTCGGTTCATCCATGGA 59.101 50.000 18.88 18.88 35.57 3.41
336 337 1.668419 GTTCGGTTCATCCATGGAGG 58.332 55.000 20.49 20.49 39.47 4.30
337 338 0.107214 TTCGGTTCATCCATGGAGGC 60.107 55.000 21.65 8.46 37.29 4.70
338 339 1.224315 CGGTTCATCCATGGAGGCA 59.776 57.895 21.65 8.28 37.29 4.75
388 393 1.140161 CCATGGCGGTCATTTGCTG 59.860 57.895 0.00 0.00 32.92 4.41
394 399 0.874390 GCGGTCATTTGCTGTTCTCA 59.126 50.000 0.00 0.00 0.00 3.27
408 413 4.706527 CTGTTCTCATTTTCGAGAGTTGC 58.293 43.478 0.00 0.00 42.81 4.17
437 455 1.800286 GCATTTGCTTGATTCGCCTCC 60.800 52.381 0.00 0.00 38.21 4.30
490 533 4.889427 CGTCTTCCGTGCTGATGA 57.111 55.556 0.00 0.00 0.00 2.92
491 534 3.352447 CGTCTTCCGTGCTGATGAT 57.648 52.632 0.00 0.00 0.00 2.45
505 548 3.451556 ATGATCAGCGGCGGTCTGG 62.452 63.158 9.40 0.00 32.63 3.86
543 587 6.538742 TCTTCTCGAGCAGAAAAGAAAAGAAA 59.461 34.615 12.58 0.00 40.83 2.52
544 588 6.677781 TCTCGAGCAGAAAAGAAAAGAAAA 57.322 33.333 7.81 0.00 0.00 2.29
545 589 7.264373 TCTCGAGCAGAAAAGAAAAGAAAAT 57.736 32.000 7.81 0.00 0.00 1.82
546 590 8.378172 TCTCGAGCAGAAAAGAAAAGAAAATA 57.622 30.769 7.81 0.00 0.00 1.40
547 591 8.499162 TCTCGAGCAGAAAAGAAAAGAAAATAG 58.501 33.333 7.81 0.00 0.00 1.73
570 614 4.676924 GGAAGAAAACAGCAGATCGTTTTG 59.323 41.667 12.16 2.02 43.46 2.44
577 621 9.176181 GAAAACAGCAGATCGTTTTGTTTATTA 57.824 29.630 12.16 0.00 43.46 0.98
679 723 6.017523 GGTCTGCTCTGCCTTCTATTTTATTC 60.018 42.308 0.00 0.00 0.00 1.75
682 726 7.831193 TCTGCTCTGCCTTCTATTTTATTCTTT 59.169 33.333 0.00 0.00 0.00 2.52
683 727 8.353423 TGCTCTGCCTTCTATTTTATTCTTTT 57.647 30.769 0.00 0.00 0.00 2.27
684 728 8.806146 TGCTCTGCCTTCTATTTTATTCTTTTT 58.194 29.630 0.00 0.00 0.00 1.94
715 759 5.257082 TGTTTCTTACTTTTGCTTCCACC 57.743 39.130 0.00 0.00 0.00 4.61
716 760 4.098807 TGTTTCTTACTTTTGCTTCCACCC 59.901 41.667 0.00 0.00 0.00 4.61
717 761 3.876309 TCTTACTTTTGCTTCCACCCT 57.124 42.857 0.00 0.00 0.00 4.34
719 763 2.178912 TACTTTTGCTTCCACCCTCG 57.821 50.000 0.00 0.00 0.00 4.63
720 764 1.172812 ACTTTTGCTTCCACCCTCGC 61.173 55.000 0.00 0.00 0.00 5.03
721 765 0.890996 CTTTTGCTTCCACCCTCGCT 60.891 55.000 0.00 0.00 0.00 4.93
746 795 2.364448 GCCCTCTCGGTTCCCTCT 60.364 66.667 0.00 0.00 0.00 3.69
752 805 3.281787 TCGGTTCCCTCTCCCCCT 61.282 66.667 0.00 0.00 0.00 4.79
771 825 3.520862 CGCCCATCCATGGTGTGC 61.521 66.667 12.58 11.16 46.65 4.57
789 843 0.378257 GCGTGTTGATCGATGCCATT 59.622 50.000 0.54 0.00 0.00 3.16
790 844 1.597195 GCGTGTTGATCGATGCCATTA 59.403 47.619 0.54 0.00 0.00 1.90
792 846 2.032894 CGTGTTGATCGATGCCATTACC 60.033 50.000 0.54 0.00 0.00 2.85
793 847 2.942376 GTGTTGATCGATGCCATTACCA 59.058 45.455 0.54 0.00 0.00 3.25
802 867 3.551863 CGATGCCATTACCACTCTCTCTC 60.552 52.174 0.00 0.00 0.00 3.20
803 868 3.107402 TGCCATTACCACTCTCTCTCT 57.893 47.619 0.00 0.00 0.00 3.10
808 873 4.285863 CATTACCACTCTCTCTCTCCCTT 58.714 47.826 0.00 0.00 0.00 3.95
810 875 1.340600 ACCACTCTCTCTCTCCCTTCG 60.341 57.143 0.00 0.00 0.00 3.79
829 894 2.520904 TTTTGTTGCGCGCCTTTGC 61.521 52.632 30.77 14.12 0.00 3.68
830 895 4.940593 TTGTTGCGCGCCTTTGCC 62.941 61.111 30.77 10.11 0.00 4.52
836 901 3.357079 CGCGCCTTTGCCTCTTGT 61.357 61.111 0.00 0.00 0.00 3.16
837 902 2.908073 CGCGCCTTTGCCTCTTGTT 61.908 57.895 0.00 0.00 0.00 2.83
838 903 1.081175 GCGCCTTTGCCTCTTGTTC 60.081 57.895 0.00 0.00 0.00 3.18
874 945 1.633171 GCGCGTCTGACATGACATC 59.367 57.895 8.43 0.00 36.82 3.06
939 1035 1.527148 TGATCCTCCTCCTCGCTCG 60.527 63.158 0.00 0.00 0.00 5.03
950 1046 2.826287 TCGCTCGGAGCAGAGGAG 60.826 66.667 27.83 11.79 42.58 3.69
1078 1174 6.862608 CCCGCCCCGTTTTAATTAATAATTAC 59.137 38.462 5.04 0.00 33.32 1.89
1110 1206 3.473625 TCTTTCCCTTTTCTCGTTCCAC 58.526 45.455 0.00 0.00 0.00 4.02
1222 1318 1.827344 GCTTCCCCTTTTATTGCTGCT 59.173 47.619 0.00 0.00 0.00 4.24
1223 1319 2.417787 GCTTCCCCTTTTATTGCTGCTG 60.418 50.000 0.00 0.00 0.00 4.41
1224 1320 1.185315 TCCCCTTTTATTGCTGCTGC 58.815 50.000 8.89 8.89 40.20 5.25
1274 1370 2.535186 GCGCTTCGTAATCTCGCG 59.465 61.111 0.00 0.00 45.88 5.87
1278 1374 2.041966 CGCTTCGTAATCTCGCGTTAT 58.958 47.619 5.77 0.00 39.07 1.89
1279 1375 2.466571 CGCTTCGTAATCTCGCGTTATT 59.533 45.455 5.77 9.86 39.07 1.40
1300 1396 1.958205 GGGCGATCTTCTCATGCCG 60.958 63.158 0.00 0.00 46.66 5.69
1305 1401 2.398498 CGATCTTCTCATGCCGGTTAG 58.602 52.381 1.90 0.00 0.00 2.34
1321 1417 2.762887 GGTTAGGAGTTAGTTACCCGCT 59.237 50.000 0.00 0.00 0.00 5.52
1393 1529 3.443925 GCTTCCTTTCAGCCCGGC 61.444 66.667 0.00 0.00 0.00 6.13
1409 1548 1.823041 GGCTCATGGCTTCTCCTGC 60.823 63.158 6.20 0.00 41.46 4.85
1428 1567 4.742201 ACTGCTGCCGGCGTGTAG 62.742 66.667 26.67 26.67 45.43 2.74
1493 1651 4.545610 CTGTCAGTCTGAACTCTGAACTC 58.454 47.826 3.51 0.00 41.41 3.01
1507 1665 7.190920 ACTCTGAACTCCATTTTTAAACGAG 57.809 36.000 0.00 0.00 0.00 4.18
1514 1672 5.106673 ACTCCATTTTTAAACGAGCACTAGC 60.107 40.000 0.00 0.00 42.56 3.42
1531 1692 2.112815 GCGTGTAAGGCCCATGGAC 61.113 63.158 15.22 0.00 43.00 4.02
1552 1713 2.099098 CGAAGGTTCCAAGTTGTGCTTT 59.901 45.455 1.45 0.00 34.69 3.51
1558 1719 1.134848 TCCAAGTTGTGCTTTGCAACC 60.135 47.619 0.00 0.00 45.14 3.77
1616 1789 7.730364 AAGATTTGTCAGTTGTTAGGTACAG 57.270 36.000 0.00 0.00 38.19 2.74
1638 1811 2.812836 TCACCCATGTGATCAGCAAT 57.187 45.000 0.00 0.00 46.40 3.56
1679 1852 5.693769 TTTCGATCCCTGAAAGATAGGTT 57.306 39.130 0.00 0.00 34.07 3.50
1680 1853 4.939052 TCGATCCCTGAAAGATAGGTTC 57.061 45.455 0.00 0.00 34.07 3.62
1681 1854 3.318275 TCGATCCCTGAAAGATAGGTTCG 59.682 47.826 0.00 0.00 38.94 3.95
1682 1855 3.068307 CGATCCCTGAAAGATAGGTTCGT 59.932 47.826 0.00 0.00 35.78 3.85
1683 1856 4.277672 CGATCCCTGAAAGATAGGTTCGTA 59.722 45.833 0.00 0.00 35.78 3.43
1684 1857 5.563085 CGATCCCTGAAAGATAGGTTCGTAG 60.563 48.000 0.00 0.00 35.78 3.51
1736 1911 1.408969 TTGGAGTTTTCCTTGGTGCC 58.591 50.000 0.00 0.00 44.36 5.01
1739 1914 2.142357 GAGTTTTCCTTGGTGCCGGC 62.142 60.000 22.73 22.73 0.00 6.13
1757 1932 2.762745 GGCGACACTAGTTTCTTTGGA 58.237 47.619 7.41 0.00 0.00 3.53
1809 1996 1.284657 GCATCCAGCGATCGGATATG 58.715 55.000 18.30 9.19 41.48 1.78
1929 2116 8.712285 ATCAGCATTCCACTTATTTTGATTTG 57.288 30.769 0.00 0.00 0.00 2.32
1980 2167 9.774413 GTAGCACTACCTGTATATAAAACCATT 57.226 33.333 0.00 0.00 0.00 3.16
1982 2169 7.719633 AGCACTACCTGTATATAAAACCATTGG 59.280 37.037 0.00 0.00 0.00 3.16
1985 2172 6.959639 ACCTGTATATAAAACCATTGGCTG 57.040 37.500 1.54 0.00 0.00 4.85
2019 2220 2.197283 AGAAAGCAGGAGCCTGAAAG 57.803 50.000 20.29 0.00 46.30 2.62
2077 2278 4.326548 GCGGTTGTTTCTACAGACATCTAC 59.673 45.833 0.00 0.00 35.28 2.59
2078 2279 5.710984 CGGTTGTTTCTACAGACATCTACT 58.289 41.667 0.00 0.00 35.28 2.57
2079 2280 5.573282 CGGTTGTTTCTACAGACATCTACTG 59.427 44.000 0.00 0.00 40.68 2.74
2082 2283 8.251721 GGTTGTTTCTACAGACATCTACTGTAT 58.748 37.037 0.00 0.00 45.57 2.29
2144 2345 8.688151 TGCTTCTAACCTTTTTAGTTAAAGCAA 58.312 29.630 19.20 10.72 42.51 3.91
2159 2360 1.523758 AGCAAAACTGCTTCCCTACG 58.476 50.000 0.00 0.00 43.52 3.51
2160 2361 1.071699 AGCAAAACTGCTTCCCTACGA 59.928 47.619 0.00 0.00 43.52 3.43
2161 2362 1.464997 GCAAAACTGCTTCCCTACGAG 59.535 52.381 0.00 0.00 0.00 4.18
2162 2363 2.767505 CAAAACTGCTTCCCTACGAGT 58.232 47.619 0.00 0.00 0.00 4.18
2163 2364 3.863400 GCAAAACTGCTTCCCTACGAGTA 60.863 47.826 0.00 0.00 0.00 2.59
2164 2365 4.504858 CAAAACTGCTTCCCTACGAGTAT 58.495 43.478 0.00 0.00 0.00 2.12
2194 2395 1.271871 CCACCTGTGCCCTACAAATCA 60.272 52.381 0.00 0.00 39.20 2.57
2219 2420 2.052782 AACCGGCCCAAGATTATGAC 57.947 50.000 0.00 0.00 0.00 3.06
2255 2456 9.787532 TTCGTCAAAAGATTATGATTGGAAATC 57.212 29.630 0.00 0.00 0.00 2.17
2370 2571 8.778059 TCCAAGCTAAGGGATATTTTTCTTCTA 58.222 33.333 5.38 0.00 0.00 2.10
2406 2607 7.805071 CCTGTTTTAGACAAGCATAGTTCTTTG 59.195 37.037 0.00 0.00 37.93 2.77
2410 2611 4.973168 AGACAAGCATAGTTCTTTGGTGA 58.027 39.130 0.00 0.00 0.00 4.02
2420 2622 7.327032 GCATAGTTCTTTGGTGACAGATTTTTC 59.673 37.037 0.00 0.00 44.54 2.29
2496 2698 5.382664 ACTAAGAGAAGGACCACCAAAAA 57.617 39.130 0.00 0.00 38.94 1.94
2723 2925 3.556365 TGCGACACGTTAAAAGATGACAA 59.444 39.130 0.00 0.00 0.00 3.18
2735 2937 9.103048 GTTAAAAGATGACAAACGTTGATGTAG 57.897 33.333 0.00 0.00 0.00 2.74
2736 2938 7.490962 AAAAGATGACAAACGTTGATGTAGA 57.509 32.000 0.00 0.00 0.00 2.59
3251 3520 0.244450 AGGCGCATGGTTTGATGTTG 59.756 50.000 10.83 0.00 0.00 3.33
3310 3579 1.005340 CGAGAGATGTTGCAAGGCTC 58.995 55.000 0.00 7.20 0.00 4.70
3325 3594 0.679002 GGCTCCATTTGCAGCTCTCA 60.679 55.000 0.00 0.00 35.82 3.27
3563 3832 6.961359 AAGGTTTGTTGCTTTTTAGTCAAC 57.039 33.333 0.00 0.00 40.17 3.18
3594 3863 1.262950 CGTTTCTCATTTCCGTGCACA 59.737 47.619 18.64 0.00 0.00 4.57
3781 4069 6.775594 AGAATGGGGCTTGTTAGATTTTAC 57.224 37.500 0.00 0.00 0.00 2.01
3783 4071 6.378280 AGAATGGGGCTTGTTAGATTTTACTG 59.622 38.462 0.00 0.00 0.00 2.74
3790 4078 5.393135 GCTTGTTAGATTTTACTGCTTCCCC 60.393 44.000 0.00 0.00 0.00 4.81
3811 4099 8.817092 TCCCCGAATAAGATTAAAATTCAGTT 57.183 30.769 0.00 0.00 31.37 3.16
3907 4300 2.874701 TGCAGCAAGACTTTTCTCAGTC 59.125 45.455 0.00 0.00 43.26 3.51
3931 4324 2.805099 CCGAAGAAGAGAAGCATATGCC 59.195 50.000 23.96 9.90 43.38 4.40
3970 4363 4.498009 GCAAGTGAATATGTATGTGGTGCC 60.498 45.833 0.00 0.00 0.00 5.01
4012 4405 1.074405 AGGCAAGCAGGATCAACAAGA 59.926 47.619 0.00 0.00 0.00 3.02
4027 4420 4.838423 TCAACAAGAGACTTGGTCATCCTA 59.162 41.667 14.51 0.00 34.60 2.94
4045 4438 7.171678 GTCATCCTAGTTGATAACACCATAAGC 59.828 40.741 0.00 0.00 0.00 3.09
4090 4483 2.045536 GCAGGCTGGAAGGTCAGG 60.046 66.667 17.64 0.00 35.43 3.86
4126 4519 1.964373 GAACCCAAAAGCCGAGCGA 60.964 57.895 0.00 0.00 0.00 4.93
4246 4639 3.550656 GTGGACTTCCTGTTCGCG 58.449 61.111 0.00 0.00 36.82 5.87
4859 5255 2.032681 GCGAGGCCAAGAACCAGT 59.967 61.111 5.01 0.00 0.00 4.00
5018 5417 5.636965 CAGCTTGTATAGGTAGCTATGCTTG 59.363 44.000 24.36 18.58 43.04 4.01
5037 5436 3.455152 GGCCTTCCCCACACAAAC 58.545 61.111 0.00 0.00 0.00 2.93
5093 5499 1.152030 TCTGAGCCTTGGAGGTGGT 60.152 57.895 0.00 0.00 37.80 4.16
5129 5535 6.827586 TGGGTTGGTTTAGCTAATAAGTTG 57.172 37.500 7.08 0.00 0.00 3.16
5136 5542 6.148811 TGGTTTAGCTAATAAGTTGTCTGTGC 59.851 38.462 7.08 0.00 0.00 4.57
5201 5607 4.081406 ACAATGAAAGCTAATGGCAGTGA 58.919 39.130 0.00 0.00 44.79 3.41
5202 5608 4.523943 ACAATGAAAGCTAATGGCAGTGAA 59.476 37.500 0.00 0.00 44.79 3.18
5204 5610 5.726980 ATGAAAGCTAATGGCAGTGAAAA 57.273 34.783 0.00 0.00 44.79 2.29
5206 5612 5.472148 TGAAAGCTAATGGCAGTGAAAATG 58.528 37.500 0.00 0.00 44.79 2.32
5208 5614 5.473066 AAGCTAATGGCAGTGAAAATGTT 57.527 34.783 0.00 0.00 44.79 2.71
5213 5619 2.392662 TGGCAGTGAAAATGTTTCCCA 58.607 42.857 0.00 0.00 32.28 4.37
5214 5620 2.768527 TGGCAGTGAAAATGTTTCCCAA 59.231 40.909 0.00 0.00 32.28 4.12
5215 5621 3.130633 GGCAGTGAAAATGTTTCCCAAC 58.869 45.455 0.00 0.00 32.28 3.77
5216 5622 3.130633 GCAGTGAAAATGTTTCCCAACC 58.869 45.455 0.00 0.00 32.28 3.77
5217 5623 3.181466 GCAGTGAAAATGTTTCCCAACCT 60.181 43.478 0.00 0.00 32.28 3.50
5218 5624 4.620982 CAGTGAAAATGTTTCCCAACCTC 58.379 43.478 0.00 0.00 31.02 3.85
5219 5625 4.342092 CAGTGAAAATGTTTCCCAACCTCT 59.658 41.667 0.00 0.00 31.02 3.69
5233 5639 6.081356 TCCCAACCTCTGTTCCAAATTATTT 58.919 36.000 0.00 0.00 30.42 1.40
5234 5640 6.556874 TCCCAACCTCTGTTCCAAATTATTTT 59.443 34.615 0.00 0.00 30.42 1.82
5292 5726 3.351740 ACATGTTTGACATATTCCCGCA 58.648 40.909 0.00 0.00 36.53 5.69
5305 5739 1.737838 TCCCGCACATCAACTGAATC 58.262 50.000 0.00 0.00 0.00 2.52
5341 5775 6.575162 ATTTAACTTGGTAGTTTGGAGCAG 57.425 37.500 0.00 0.00 41.85 4.24
5391 5832 9.793259 ATCATTATACCGTGTCCAGAATTTAAT 57.207 29.630 0.00 0.00 0.00 1.40
5400 5841 8.836413 CCGTGTCCAGAATTTAATTATGTACAT 58.164 33.333 13.93 13.93 33.88 2.29
5435 5876 7.618502 AAAAACATACGTAGGCAATACATCA 57.381 32.000 7.23 0.00 33.65 3.07
5436 5877 7.618502 AAAACATACGTAGGCAATACATCAA 57.381 32.000 7.23 0.00 33.65 2.57
5437 5878 7.801716 AAACATACGTAGGCAATACATCAAT 57.198 32.000 7.23 0.00 33.65 2.57
5438 5879 6.785488 ACATACGTAGGCAATACATCAATG 57.215 37.500 7.23 0.00 33.65 2.82
5527 6030 4.098055 AGTACATACAGACTGAAGCACG 57.902 45.455 10.08 0.00 0.00 5.34
5673 6176 4.219264 AGAGAGAAAAGAATGCAGAGGG 57.781 45.455 0.00 0.00 0.00 4.30
5674 6177 3.054508 AGAGAGAAAAGAATGCAGAGGGG 60.055 47.826 0.00 0.00 0.00 4.79
5754 6257 1.812571 CTGACAAAACCGAAGATGGGG 59.187 52.381 0.00 0.00 0.00 4.96
5755 6258 1.173913 GACAAAACCGAAGATGGGGG 58.826 55.000 0.00 0.00 0.00 5.40
5846 6349 6.128063 GGATTTCAGACATGAAGAAAGGTCAG 60.128 42.308 0.00 0.00 45.89 3.51
5871 6374 6.694411 GCTCATCATCCAATAACAATGAACAC 59.306 38.462 0.00 0.00 33.44 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.878656 GAGTGGTGGTGAGTCGGAGG 61.879 65.000 0.00 0.00 0.00 4.30
84 85 2.370189 CCTCCTCCTCTCTCTCTCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
94 95 1.826487 GCTCGTCCCTCCTCCTCTC 60.826 68.421 0.00 0.00 0.00 3.20
95 96 2.156496 TTGCTCGTCCCTCCTCCTCT 62.156 60.000 0.00 0.00 0.00 3.69
96 97 1.671901 CTTGCTCGTCCCTCCTCCTC 61.672 65.000 0.00 0.00 0.00 3.71
97 98 1.684049 CTTGCTCGTCCCTCCTCCT 60.684 63.158 0.00 0.00 0.00 3.69
99 100 2.185608 GCTTGCTCGTCCCTCCTC 59.814 66.667 0.00 0.00 0.00 3.71
100 101 2.604686 TGCTTGCTCGTCCCTCCT 60.605 61.111 0.00 0.00 0.00 3.69
103 104 4.400961 GGCTGCTTGCTCGTCCCT 62.401 66.667 0.00 0.00 42.39 4.20
109 110 1.518903 AAGAAACGGGCTGCTTGCTC 61.519 55.000 0.00 0.00 42.39 4.26
110 111 1.529244 AAGAAACGGGCTGCTTGCT 60.529 52.632 0.00 0.00 42.39 3.91
111 112 1.372128 CAAGAAACGGGCTGCTTGC 60.372 57.895 0.00 0.00 41.94 4.01
112 113 1.372128 GCAAGAAACGGGCTGCTTG 60.372 57.895 0.00 7.55 40.40 4.01
113 114 2.564721 GGCAAGAAACGGGCTGCTT 61.565 57.895 0.00 0.00 0.00 3.91
195 196 1.223211 GGAAGAGCAAGGGAGGAGC 59.777 63.158 0.00 0.00 0.00 4.70
202 203 0.327591 AGAAGGCAGGAAGAGCAAGG 59.672 55.000 0.00 0.00 0.00 3.61
246 247 2.907917 CTCCGCCGGAGTCTAGGG 60.908 72.222 24.93 0.00 44.25 3.53
290 291 1.292223 CCAAGAAGAACGCGGAGGA 59.708 57.895 12.47 0.00 0.00 3.71
326 327 1.925888 GGAAGGTGCCTCCATGGAT 59.074 57.895 16.63 0.00 38.35 3.41
327 328 2.669133 CGGAAGGTGCCTCCATGGA 61.669 63.158 15.27 15.27 38.35 3.41
328 329 2.124570 CGGAAGGTGCCTCCATGG 60.125 66.667 4.97 4.97 39.02 3.66
329 330 2.825836 GCGGAAGGTGCCTCCATG 60.826 66.667 0.00 0.00 39.02 3.66
330 331 3.011517 AGCGGAAGGTGCCTCCAT 61.012 61.111 0.00 0.00 42.35 3.41
338 339 2.266055 GCTACTGCAGCGGAAGGT 59.734 61.111 15.27 0.00 41.37 3.50
349 350 1.469940 CCAGCACCTACGAAGCTACTG 60.470 57.143 0.00 0.00 36.73 2.74
388 393 4.952097 GAGCAACTCTCGAAAATGAGAAC 58.048 43.478 6.42 0.00 44.03 3.01
449 485 0.515564 CGCCACTAACCAAAACGAGG 59.484 55.000 0.00 0.00 0.00 4.63
450 486 1.504359 TCGCCACTAACCAAAACGAG 58.496 50.000 0.00 0.00 0.00 4.18
451 487 2.172851 ATCGCCACTAACCAAAACGA 57.827 45.000 0.00 0.00 0.00 3.85
453 489 3.187022 ACGTAATCGCCACTAACCAAAAC 59.813 43.478 0.00 0.00 41.18 2.43
458 497 2.573941 AGACGTAATCGCCACTAACC 57.426 50.000 0.00 0.00 41.18 2.85
489 532 4.148825 ACCAGACCGCCGCTGATC 62.149 66.667 0.00 0.00 35.39 2.92
490 533 4.457496 CACCAGACCGCCGCTGAT 62.457 66.667 0.00 0.00 35.39 2.90
499 542 2.569404 AGAGGAGAACAATCACCAGACC 59.431 50.000 0.00 0.00 38.65 3.85
505 548 4.420168 CTCGAGAAGAGGAGAACAATCAC 58.580 47.826 6.58 0.00 43.20 3.06
543 587 5.491982 ACGATCTGCTGTTTTCTTCCTATT 58.508 37.500 0.00 0.00 0.00 1.73
544 588 5.091261 ACGATCTGCTGTTTTCTTCCTAT 57.909 39.130 0.00 0.00 0.00 2.57
545 589 4.537135 ACGATCTGCTGTTTTCTTCCTA 57.463 40.909 0.00 0.00 0.00 2.94
546 590 3.409026 ACGATCTGCTGTTTTCTTCCT 57.591 42.857 0.00 0.00 0.00 3.36
547 591 4.489679 AAACGATCTGCTGTTTTCTTCC 57.510 40.909 0.00 0.00 34.82 3.46
570 614 9.967346 GCCTAGAAAATCAGGGAAATAATAAAC 57.033 33.333 0.00 0.00 32.15 2.01
577 621 3.555966 CGGCCTAGAAAATCAGGGAAAT 58.444 45.455 0.00 0.00 32.15 2.17
644 688 3.678951 GAGCAGACCAGCAGAGGGC 62.679 68.421 0.00 0.00 45.30 5.19
654 698 2.998316 AATAGAAGGCAGAGCAGACC 57.002 50.000 0.00 0.00 0.00 3.85
655 699 6.765512 AGAATAAAATAGAAGGCAGAGCAGAC 59.234 38.462 0.00 0.00 0.00 3.51
689 733 7.279981 GGTGGAAGCAAAAGTAAGAAACAAAAT 59.720 33.333 0.00 0.00 0.00 1.82
694 738 4.341235 AGGGTGGAAGCAAAAGTAAGAAAC 59.659 41.667 0.00 0.00 34.77 2.78
698 742 2.484264 CGAGGGTGGAAGCAAAAGTAAG 59.516 50.000 0.00 0.00 34.77 2.34
715 759 4.208686 GGGCCGAGTGTAGCGAGG 62.209 72.222 0.00 0.00 0.00 4.63
716 760 3.127352 GAGGGCCGAGTGTAGCGAG 62.127 68.421 0.00 0.00 0.00 5.03
717 761 3.138798 GAGGGCCGAGTGTAGCGA 61.139 66.667 0.00 0.00 0.00 4.93
719 763 2.809010 GAGAGGGCCGAGTGTAGC 59.191 66.667 0.00 0.00 0.00 3.58
720 764 3.111939 CGAGAGGGCCGAGTGTAG 58.888 66.667 0.00 0.00 0.00 2.74
771 825 2.032894 GGTAATGGCATCGATCAACACG 60.033 50.000 0.00 0.00 0.00 4.49
789 843 2.092861 CGAAGGGAGAGAGAGAGTGGTA 60.093 54.545 0.00 0.00 0.00 3.25
790 844 1.340600 CGAAGGGAGAGAGAGAGTGGT 60.341 57.143 0.00 0.00 0.00 4.16
792 846 2.122783 ACGAAGGGAGAGAGAGAGTG 57.877 55.000 0.00 0.00 0.00 3.51
793 847 2.891191 AACGAAGGGAGAGAGAGAGT 57.109 50.000 0.00 0.00 0.00 3.24
802 867 0.660300 GCGCAACAAAACGAAGGGAG 60.660 55.000 0.30 0.00 0.00 4.30
803 868 1.357334 GCGCAACAAAACGAAGGGA 59.643 52.632 0.30 0.00 0.00 4.20
808 873 2.600122 AAAGGCGCGCAACAAAACGA 62.600 50.000 34.42 0.00 0.00 3.85
810 875 1.272423 CAAAGGCGCGCAACAAAAC 59.728 52.632 34.42 13.69 0.00 2.43
829 894 1.470098 CCGGCATGAAAGAACAAGAGG 59.530 52.381 0.00 0.00 0.00 3.69
830 895 2.095567 CACCGGCATGAAAGAACAAGAG 60.096 50.000 0.00 0.00 0.00 2.85
921 1001 1.527148 CGAGCGAGGAGGAGGATCA 60.527 63.158 0.00 0.00 36.25 2.92
922 1002 2.265182 CCGAGCGAGGAGGAGGATC 61.265 68.421 0.00 0.00 0.00 3.36
923 1003 2.203422 CCGAGCGAGGAGGAGGAT 60.203 66.667 0.00 0.00 0.00 3.24
924 1004 3.408853 TCCGAGCGAGGAGGAGGA 61.409 66.667 0.00 0.00 34.92 3.71
939 1035 1.457455 CCTCTCCCTCCTCTGCTCC 60.457 68.421 0.00 0.00 0.00 4.70
950 1046 2.042843 TCTTCTCCCGCCTCTCCC 60.043 66.667 0.00 0.00 0.00 4.30
1078 1174 4.879197 AAAGGGAAAGAGCTTTGGATTG 57.121 40.909 0.00 0.00 32.11 2.67
1200 1296 1.134946 CAGCAATAAAAGGGGAAGCGG 59.865 52.381 0.00 0.00 0.00 5.52
1235 1331 2.325082 GCTAGCAACCACCACACCG 61.325 63.158 10.63 0.00 0.00 4.94
1274 1370 3.973657 TGAGAAGATCGCCCGTAATAAC 58.026 45.455 0.00 0.00 0.00 1.89
1278 1374 1.538204 GCATGAGAAGATCGCCCGTAA 60.538 52.381 0.00 0.00 0.00 3.18
1279 1375 0.032130 GCATGAGAAGATCGCCCGTA 59.968 55.000 0.00 0.00 0.00 4.02
1285 1381 2.398498 CTAACCGGCATGAGAAGATCG 58.602 52.381 0.00 0.00 0.00 3.69
1292 1388 2.431057 ACTAACTCCTAACCGGCATGAG 59.569 50.000 0.00 5.26 0.00 2.90
1300 1396 2.762887 AGCGGGTAACTAACTCCTAACC 59.237 50.000 0.00 0.00 0.00 2.85
1305 1401 2.028748 TCAACAGCGGGTAACTAACTCC 60.029 50.000 0.00 0.00 0.00 3.85
1321 1417 2.073716 AAGTCCACGGGGGTCAACA 61.074 57.895 2.42 0.00 38.11 3.33
1493 1651 4.088648 CGCTAGTGCTCGTTTAAAAATGG 58.911 43.478 0.00 0.00 36.97 3.16
1514 1672 1.813753 CGTCCATGGGCCTTACACG 60.814 63.158 11.65 8.17 0.00 4.49
1518 1676 0.912487 ACCTTCGTCCATGGGCCTTA 60.912 55.000 11.65 0.00 0.00 2.69
1524 1685 1.271379 ACTTGGAACCTTCGTCCATGG 60.271 52.381 4.97 4.97 34.28 3.66
1531 1692 1.308998 AGCACAACTTGGAACCTTCG 58.691 50.000 0.00 0.00 0.00 3.79
1558 1719 4.809496 AGGGAAGCATGGCTGGCG 62.809 66.667 0.00 0.00 39.62 5.69
1633 1806 4.084013 GCGTCGCCATAGTTTATTATTGCT 60.084 41.667 5.75 0.00 0.00 3.91
1636 1809 6.563381 CGAAAGCGTCGCCATAGTTTATTATT 60.563 38.462 14.86 0.00 44.14 1.40
1637 1810 5.107607 CGAAAGCGTCGCCATAGTTTATTAT 60.108 40.000 14.86 0.00 44.14 1.28
1638 1811 4.207635 CGAAAGCGTCGCCATAGTTTATTA 59.792 41.667 14.86 0.00 44.14 0.98
1661 1834 4.674281 ACGAACCTATCTTTCAGGGATC 57.326 45.455 0.00 0.00 37.51 3.36
1678 1851 4.031418 TCGTATTTTGCGATCCTACGAA 57.969 40.909 9.48 0.00 40.60 3.85
1679 1852 3.065786 ACTCGTATTTTGCGATCCTACGA 59.934 43.478 10.80 10.80 41.09 3.43
1680 1853 3.369385 ACTCGTATTTTGCGATCCTACG 58.631 45.455 0.00 0.00 37.74 3.51
1681 1854 3.421231 CGACTCGTATTTTGCGATCCTAC 59.579 47.826 0.00 0.00 37.74 3.18
1682 1855 3.549423 CCGACTCGTATTTTGCGATCCTA 60.549 47.826 0.00 0.00 37.74 2.94
1683 1856 2.460918 CGACTCGTATTTTGCGATCCT 58.539 47.619 0.00 0.00 37.74 3.24
1684 1857 1.521423 CCGACTCGTATTTTGCGATCC 59.479 52.381 0.00 0.00 37.74 3.36
1736 1911 1.459592 CCAAAGAAACTAGTGTCGCCG 59.540 52.381 7.43 0.17 0.00 6.46
1739 1914 3.741344 CAGGTCCAAAGAAACTAGTGTCG 59.259 47.826 7.43 0.00 0.00 4.35
1809 1996 4.535526 TTTAAAGGGAGGAAAATGCAGC 57.464 40.909 0.00 0.00 0.00 5.25
1895 2082 1.133699 TGGAATGCTGATAGGCCTTGG 60.134 52.381 12.58 0.00 0.00 3.61
1897 2084 1.849039 AGTGGAATGCTGATAGGCCTT 59.151 47.619 12.58 0.00 0.00 4.35
1929 2116 6.261118 CACATCATCCTTTAAGCTTTGCTAC 58.739 40.000 3.20 0.00 38.25 3.58
1977 2164 4.774124 TCTTCAAGATAGACCAGCCAATG 58.226 43.478 0.00 0.00 0.00 2.82
1980 2167 4.096681 TCTTCTTCAAGATAGACCAGCCA 58.903 43.478 0.00 0.00 33.38 4.75
1982 2169 5.064579 GCTTTCTTCTTCAAGATAGACCAGC 59.935 44.000 6.43 10.80 39.06 4.85
1985 2172 5.584251 CCTGCTTTCTTCTTCAAGATAGACC 59.416 44.000 6.43 0.00 39.06 3.85
2077 2278 3.302092 GCGTCGCAAAATCTCTCATACAG 60.302 47.826 13.44 0.00 0.00 2.74
2078 2279 2.603110 GCGTCGCAAAATCTCTCATACA 59.397 45.455 13.44 0.00 0.00 2.29
2079 2280 2.860735 AGCGTCGCAAAATCTCTCATAC 59.139 45.455 21.09 0.00 0.00 2.39
2080 2281 2.860136 CAGCGTCGCAAAATCTCTCATA 59.140 45.455 21.09 0.00 0.00 2.15
2082 2283 1.070821 CAGCGTCGCAAAATCTCTCA 58.929 50.000 21.09 0.00 0.00 3.27
2083 2284 1.350193 TCAGCGTCGCAAAATCTCTC 58.650 50.000 21.09 0.00 0.00 3.20
2084 2285 1.662629 CATCAGCGTCGCAAAATCTCT 59.337 47.619 21.09 0.00 0.00 3.10
2085 2286 1.853646 GCATCAGCGTCGCAAAATCTC 60.854 52.381 21.09 0.00 0.00 2.75
2086 2287 0.097674 GCATCAGCGTCGCAAAATCT 59.902 50.000 21.09 0.00 0.00 2.40
2087 2288 0.179192 TGCATCAGCGTCGCAAAATC 60.179 50.000 21.09 5.95 46.23 2.17
2088 2289 0.179181 CTGCATCAGCGTCGCAAAAT 60.179 50.000 21.09 6.59 46.23 1.82
2089 2290 1.207339 CTGCATCAGCGTCGCAAAA 59.793 52.632 21.09 4.22 46.23 2.44
2144 2345 3.767673 TCATACTCGTAGGGAAGCAGTTT 59.232 43.478 0.00 0.00 0.00 2.66
2159 2360 0.031449 GGTGGCGAGCTCTCATACTC 59.969 60.000 12.85 0.00 0.00 2.59
2160 2361 0.396417 AGGTGGCGAGCTCTCATACT 60.396 55.000 12.85 9.53 0.00 2.12
2161 2362 0.249238 CAGGTGGCGAGCTCTCATAC 60.249 60.000 12.85 6.95 0.00 2.39
2162 2363 0.684479 ACAGGTGGCGAGCTCTCATA 60.684 55.000 12.85 0.00 0.00 2.15
2163 2364 1.986757 ACAGGTGGCGAGCTCTCAT 60.987 57.895 12.85 0.00 0.00 2.90
2164 2365 2.601666 ACAGGTGGCGAGCTCTCA 60.602 61.111 12.85 7.34 0.00 3.27
2194 2395 3.945640 AATCTTGGGCCGGTTAACTAT 57.054 42.857 1.90 0.00 0.00 2.12
2250 2451 8.118607 CCTTTTCTTGCTTTTCACTTTGATTTC 58.881 33.333 0.00 0.00 0.00 2.17
2255 2456 5.868801 TGTCCTTTTCTTGCTTTTCACTTTG 59.131 36.000 0.00 0.00 0.00 2.77
2406 2607 5.412594 TGCTATCACAGAAAAATCTGTCACC 59.587 40.000 8.44 0.00 46.96 4.02
2496 2698 8.306761 AGTTCTCAACATCTTTGAAACTTTTGT 58.693 29.630 7.90 0.00 31.89 2.83
2723 2925 2.870435 GCCACTGGTCTACATCAACGTT 60.870 50.000 0.00 0.00 0.00 3.99
2727 2929 0.249120 CCGCCACTGGTCTACATCAA 59.751 55.000 0.00 0.00 0.00 2.57
2735 2937 1.153549 CTAAGCTCCGCCACTGGTC 60.154 63.158 0.00 0.00 0.00 4.02
2736 2938 0.613853 TACTAAGCTCCGCCACTGGT 60.614 55.000 0.00 0.00 0.00 4.00
2881 3150 3.825585 TGCAAAGCATACATGAACTTCCA 59.174 39.130 0.00 0.00 31.71 3.53
2883 3152 4.082571 ACCTGCAAAGCATACATGAACTTC 60.083 41.667 0.00 0.00 38.13 3.01
3251 3520 2.024414 ACAGGGAAGTTTCACAGCAAC 58.976 47.619 0.00 0.00 31.44 4.17
3310 3579 1.428219 CGCTGAGAGCTGCAAATGG 59.572 57.895 1.02 0.00 39.60 3.16
3331 3600 0.250338 AAGAGGTCACGGCCAGTTTC 60.250 55.000 2.24 0.00 0.00 2.78
3563 3832 6.452090 CGGAAATGAGAAACGTAGACTAAACG 60.452 42.308 0.00 0.00 45.64 3.60
3642 3929 9.396022 CTGAAAATAGTTGTACTGGGTATCATT 57.604 33.333 0.00 0.00 0.00 2.57
3743 4031 7.565680 AGCCCCATTCTATATAAATTCCTACG 58.434 38.462 0.00 0.00 0.00 3.51
3744 4032 9.178758 CAAGCCCCATTCTATATAAATTCCTAC 57.821 37.037 0.00 0.00 0.00 3.18
3766 4054 5.393135 GGGGAAGCAGTAAAATCTAACAAGC 60.393 44.000 0.00 0.00 0.00 4.01
3781 4069 6.693315 TTTTAATCTTATTCGGGGAAGCAG 57.307 37.500 0.00 0.00 0.00 4.24
3783 4071 7.712797 TGAATTTTAATCTTATTCGGGGAAGC 58.287 34.615 0.00 0.00 32.30 3.86
3811 4099 3.756082 AAATCTAACAGGGCCCATTCA 57.244 42.857 27.56 8.61 0.00 2.57
3883 4276 0.947244 AGAAAAGTCTTGCTGCACCG 59.053 50.000 0.00 0.00 0.00 4.94
3907 4300 2.285827 ATGCTTCTCTTCTTCGGTCG 57.714 50.000 0.00 0.00 0.00 4.79
3970 4363 0.391263 TGCTCTGAGCTGCTGTGATG 60.391 55.000 28.04 1.02 42.97 3.07
4012 4405 6.440647 TGTTATCAACTAGGATGACCAAGTCT 59.559 38.462 2.95 0.00 38.94 3.24
4027 4420 5.523916 GTGATCGCTTATGGTGTTATCAACT 59.476 40.000 0.00 0.00 31.63 3.16
4045 4438 2.808315 CCTCTCCGGTGGTGATCG 59.192 66.667 0.00 0.00 0.00 3.69
4090 4483 6.129179 TGGGTTCCTGATCCTTTCAATTATC 58.871 40.000 0.00 0.00 32.78 1.75
4126 4519 0.892358 TCCACTCGTTGTAGGCGTCT 60.892 55.000 0.00 0.00 0.00 4.18
4246 4639 1.953138 CGCGGTGATCTCTGGCATC 60.953 63.158 0.00 0.00 0.00 3.91
4282 4675 1.176619 TGACGCCGGAGTTGAAGAGA 61.177 55.000 13.57 0.00 0.00 3.10
4518 4911 0.100861 GTAGTGGAGCACGTAGAGGC 59.899 60.000 0.00 0.00 39.64 4.70
4859 5255 4.735132 CGCGGGGTTGCTCTTCGA 62.735 66.667 0.00 0.00 0.00 3.71
4895 5291 1.081108 AGCTCGACGACAAGCTCAC 60.081 57.895 4.40 0.00 45.57 3.51
4964 5363 4.082408 TGCAGGTACGGTGCTATACATATC 60.082 45.833 17.05 0.00 41.78 1.63
5037 5436 0.954452 GCAACAGAGGAGGGTTTGTG 59.046 55.000 0.00 0.00 0.00 3.33
5087 5493 3.387699 CCCAAAAGAATTGTTGACCACCT 59.612 43.478 0.00 0.00 0.00 4.00
5093 5499 5.428184 AACCAACCCAAAAGAATTGTTGA 57.572 34.783 0.00 0.00 38.81 3.18
5129 5535 7.602517 AGTAAGAGAATTTACATGCACAGAC 57.397 36.000 0.00 0.00 36.27 3.51
5183 5589 5.010922 ACATTTTCACTGCCATTAGCTTTCA 59.989 36.000 0.00 0.00 44.23 2.69
5201 5607 4.100963 GGAACAGAGGTTGGGAAACATTTT 59.899 41.667 0.00 0.00 37.36 1.82
5202 5608 3.641436 GGAACAGAGGTTGGGAAACATTT 59.359 43.478 0.00 0.00 37.36 2.32
5204 5610 2.176798 TGGAACAGAGGTTGGGAAACAT 59.823 45.455 0.00 0.00 37.36 2.71
5206 5612 2.358322 TGGAACAGAGGTTGGGAAAC 57.642 50.000 0.00 0.00 37.36 2.78
5208 5614 3.611025 ATTTGGAACAGAGGTTGGGAA 57.389 42.857 0.00 0.00 42.39 3.97
5233 5639 6.969993 ATGAACTTGGGCAAACTTAACTAA 57.030 33.333 0.00 0.00 0.00 2.24
5234 5640 6.999272 TGTATGAACTTGGGCAAACTTAACTA 59.001 34.615 0.00 0.00 0.00 2.24
5289 5723 1.452110 TGGGATTCAGTTGATGTGCG 58.548 50.000 0.00 0.00 0.00 5.34
5292 5726 3.527253 TGGGTATGGGATTCAGTTGATGT 59.473 43.478 0.00 0.00 0.00 3.06
5305 5739 5.719563 ACCAAGTTAAATTTCTGGGTATGGG 59.280 40.000 4.48 0.00 36.35 4.00
5341 5775 1.067295 TGGTGCCCAGGGATATGATC 58.933 55.000 10.89 0.00 0.00 2.92
5416 5857 5.179182 TGCATTGATGTATTGCCTACGTATG 59.821 40.000 0.00 0.00 35.35 2.39
5418 5859 4.698575 TGCATTGATGTATTGCCTACGTA 58.301 39.130 0.00 0.00 35.35 3.57
5420 5861 4.550577 TTGCATTGATGTATTGCCTACG 57.449 40.909 0.00 0.00 35.35 3.51
5421 5862 5.894807 AGTTTGCATTGATGTATTGCCTAC 58.105 37.500 0.00 0.00 35.35 3.18
5422 5863 6.528537 AAGTTTGCATTGATGTATTGCCTA 57.471 33.333 0.00 0.00 35.35 3.93
5423 5864 5.410355 AAGTTTGCATTGATGTATTGCCT 57.590 34.783 0.00 0.00 35.35 4.75
5424 5865 6.484818 AAAAGTTTGCATTGATGTATTGCC 57.515 33.333 0.00 0.00 35.35 4.52
5425 5866 6.303733 GCAAAAAGTTTGCATTGATGTATTGC 59.696 34.615 18.31 2.72 44.34 3.56
5426 5867 6.517034 CGCAAAAAGTTTGCATTGATGTATTG 59.483 34.615 21.73 1.73 45.14 1.90
5427 5868 6.592166 CGCAAAAAGTTTGCATTGATGTATT 58.408 32.000 21.73 0.00 45.14 1.89
5428 5869 5.389725 GCGCAAAAAGTTTGCATTGATGTAT 60.390 36.000 21.73 0.00 45.14 2.29
5429 5870 4.084641 GCGCAAAAAGTTTGCATTGATGTA 60.085 37.500 21.73 0.00 45.14 2.29
5430 5871 3.303263 GCGCAAAAAGTTTGCATTGATGT 60.303 39.130 21.73 0.00 45.14 3.06
5431 5872 3.059461 AGCGCAAAAAGTTTGCATTGATG 60.059 39.130 21.73 8.50 45.14 3.07
5432 5873 3.132925 AGCGCAAAAAGTTTGCATTGAT 58.867 36.364 21.73 5.51 45.14 2.57
5433 5874 2.539274 GAGCGCAAAAAGTTTGCATTGA 59.461 40.909 21.73 0.00 45.14 2.57
5434 5875 2.284684 TGAGCGCAAAAAGTTTGCATTG 59.715 40.909 21.73 9.69 45.14 2.82
5435 5876 2.548875 TGAGCGCAAAAAGTTTGCATT 58.451 38.095 21.73 11.25 45.14 3.56
5436 5877 2.222007 TGAGCGCAAAAAGTTTGCAT 57.778 40.000 21.73 11.87 45.14 3.96
5437 5878 2.126467 GATGAGCGCAAAAAGTTTGCA 58.874 42.857 21.73 6.28 45.14 4.08
5438 5879 1.123038 CGATGAGCGCAAAAAGTTTGC 59.877 47.619 11.47 14.28 41.71 3.68
5673 6176 4.563140 TGATAGGTGGTTTAACTGGACC 57.437 45.455 0.00 0.00 36.45 4.46
5674 6177 6.885922 AGTATGATAGGTGGTTTAACTGGAC 58.114 40.000 0.00 0.00 0.00 4.02
5754 6257 0.470766 TGCCCCATACGTACATTCCC 59.529 55.000 0.00 0.00 0.00 3.97
5755 6258 2.335316 TTGCCCCATACGTACATTCC 57.665 50.000 0.00 0.00 0.00 3.01
5756 6259 3.942748 TCTTTTGCCCCATACGTACATTC 59.057 43.478 0.00 0.00 0.00 2.67
5846 6349 6.694411 GTGTTCATTGTTATTGGATGATGAGC 59.306 38.462 0.00 0.00 30.59 4.26
5871 6374 1.424403 TGTACCGATGCAGTTGAACG 58.576 50.000 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.