Multiple sequence alignment - TraesCS3D01G031300

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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 TraesCS3D01G031300 chr3D 100.000 6656 0 0 1 6656 11450907 11444252 0.000000e+00 12292.0
1 TraesCS3D01G031300 chr3D 100.000 30 0 0 6243 6272 11435423 11435394 1.000000e-03 56.5
2 TraesCS3D01G031300 chr3A 91.704 6039 385 64 1 5974 25870995 25876982 0.000000e+00 8270.0
3 TraesCS3D01G031300 chr3A 93.077 390 25 2 6261 6649 25877183 25877571 2.690000e-158 569.0
4 TraesCS3D01G031300 chr3A 93.839 211 12 1 5995 6204 25876973 25877183 3.870000e-82 316.0
5 TraesCS3D01G031300 chr3B 91.149 5220 364 59 574 5748 25166735 25171901 0.000000e+00 6990.0
6 TraesCS3D01G031300 chr3B 91.647 5088 322 55 708 5748 16137743 16132712 0.000000e+00 6946.0
7 TraesCS3D01G031300 chr3B 88.647 414 26 4 1 397 16138659 16138250 1.000000e-132 484.0
8 TraesCS3D01G031300 chr3B 87.440 414 27 5 1 397 25166255 25166660 2.830000e-123 453.0
9 TraesCS3D01G031300 chr3B 88.073 109 13 0 5903 6011 25194168 25194276 5.420000e-26 130.0
10 TraesCS3D01G031300 chr3B 86.239 109 15 0 5903 6011 16113461 16113353 1.170000e-22 119.0
11 TraesCS3D01G031300 chr3B 97.619 42 0 1 3223 3263 16135279 16135238 3.330000e-08 71.3
12 TraesCS3D01G031300 chr3B 97.619 42 0 1 3223 3263 25169341 25169382 3.330000e-08 71.3
13 TraesCS3D01G031300 chr7B 90.909 77 5 1 5758 5832 388898925 388899001 1.180000e-17 102.0
14 TraesCS3D01G031300 chr7B 83.721 86 9 4 5758 5841 695368961 695369043 7.160000e-10 76.8
15 TraesCS3D01G031300 chr6B 82.857 105 13 4 6060 6162 15107516 15107415 9.190000e-14 89.8
16 TraesCS3D01G031300 chr6B 82.022 89 11 3 5748 5831 47866031 47865943 3.330000e-08 71.3
17 TraesCS3D01G031300 chr7A 93.333 60 3 1 5759 5817 699292350 699292291 3.310000e-13 87.9
18 TraesCS3D01G031300 chr1B 89.041 73 5 3 5761 5831 561388819 561388890 3.310000e-13 87.9
19 TraesCS3D01G031300 chr5B 86.076 79 10 1 5755 5832 550144290 550144368 4.280000e-12 84.2
20 TraesCS3D01G031300 chrUn 86.486 74 8 1 5758 5831 19084970 19084899 5.530000e-11 80.5
21 TraesCS3D01G031300 chr6A 86.486 74 7 3 5759 5831 609594898 609594969 1.990000e-10 78.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G031300 chr3D 11444252 11450907 6655 True 12292.000000 12292 100.000000 1 6656 1 chr3D.!!$R2 6655
1 TraesCS3D01G031300 chr3A 25870995 25877571 6576 False 3051.666667 8270 92.873333 1 6649 3 chr3A.!!$F1 6648
2 TraesCS3D01G031300 chr3B 25166255 25171901 5646 False 2504.766667 6990 92.069333 1 5748 3 chr3B.!!$F2 5747
3 TraesCS3D01G031300 chr3B 16132712 16138659 5947 True 2500.433333 6946 92.637667 1 5748 3 chr3B.!!$R2 5747

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
335 354 0.179051 ACAGGACGCACCGGTTTTTA 60.179 50.0 2.97 0.0 44.16 1.52 F
1063 1512 0.117140 TGGAGGCAAAGAGGAGGAGA 59.883 55.0 0.00 0.0 0.00 3.71 F
2659 3131 0.106569 TGAGCCCATGGATTTCGCAT 60.107 50.0 15.22 0.0 0.00 4.73 F
3724 4207 0.319469 CCACCGGCATGTGTTTTTCC 60.319 55.0 0.00 0.0 34.35 3.13 F
4478 4970 0.108019 GGTCGAACTCCCACCAAGTT 59.892 55.0 0.00 0.0 39.61 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1184 1633 2.039418 CAACGGTGGATCTAGATGGGA 58.961 52.381 10.74 0.0 0.00 4.37 R
2804 3279 1.238439 AGTTTGGATGAACCGCAGTG 58.762 50.000 0.00 0.0 42.61 3.66 R
4457 4949 0.396811 CTTGGTGGGAGTTCGACCTT 59.603 55.000 4.01 0.0 43.63 3.50 R
5572 6075 0.405585 ACAAGCCCACCACTAAGCAT 59.594 50.000 0.00 0.0 0.00 3.79 R
6210 6718 0.030101 GCTTACGGCTGCAAACAACA 59.970 50.000 0.50 0.0 38.06 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
32 34 7.862873 CGTAACATCTATGTAAGAGCTTCATCA 59.137 37.037 0.00 0.00 40.80 3.07
36 38 8.089597 ACATCTATGTAAGAGCTTCATCATCAG 58.910 37.037 0.00 0.00 39.68 2.90
40 42 4.958581 TGTAAGAGCTTCATCATCAGGAGA 59.041 41.667 0.00 0.00 0.00 3.71
66 68 9.840427 ACACACATATTTTACTTACAAAGATGC 57.160 29.630 1.00 0.00 36.65 3.91
207 226 3.947196 ACATGTCAAGAAAACTGCACTCA 59.053 39.130 0.00 0.00 0.00 3.41
321 340 0.392863 CCCATCAACGATGCACAGGA 60.393 55.000 0.00 0.00 38.59 3.86
335 354 0.179051 ACAGGACGCACCGGTTTTTA 60.179 50.000 2.97 0.00 44.16 1.52
415 434 8.798859 TTCCCATTTTCAAAAACATTTTCAGA 57.201 26.923 0.00 0.00 0.00 3.27
417 436 9.406113 TCCCATTTTCAAAAACATTTTCAGAAT 57.594 25.926 0.00 0.00 29.97 2.40
435 454 8.861033 TTCAGAATTTCAATTTGTTCTGTCTG 57.139 30.769 19.51 15.06 44.78 3.51
450 469 6.785191 GTTCTGTCTGTCTGAACATTTTTGA 58.215 36.000 15.65 0.00 46.79 2.69
454 473 7.970061 TCTGTCTGTCTGAACATTTTTGAAAAG 59.030 33.333 0.00 0.00 34.13 2.27
455 474 7.825681 TGTCTGTCTGAACATTTTTGAAAAGA 58.174 30.769 0.00 0.00 34.13 2.52
459 479 8.824159 TGTCTGAACATTTTTGAAAAGAACAA 57.176 26.923 0.00 0.00 0.00 2.83
461 481 9.528847 GTCTGAACATTTTTGAAAAGAACAAAC 57.471 29.630 0.00 0.00 37.05 2.93
501 521 9.844257 ATGAACAATTTTCTTAAATTCCAACCA 57.156 25.926 0.00 0.00 40.97 3.67
772 1219 1.758280 GAAAGGTTTCCAAAACCGGGT 59.242 47.619 6.32 0.00 44.82 5.28
773 1220 1.116308 AAGGTTTCCAAAACCGGGTG 58.884 50.000 6.32 0.00 44.82 4.61
821 1269 1.577328 GCTGACCCATGTGTGGTTCG 61.577 60.000 0.00 0.00 44.48 3.95
825 1273 1.302431 CCCATGTGTGGTTCGCTCA 60.302 57.895 0.00 0.00 44.48 4.26
828 1276 1.229428 CATGTGTGGTTCGCTCACTT 58.771 50.000 0.00 0.00 36.21 3.16
833 1281 0.880278 GTGGTTCGCTCACTTGCTCA 60.880 55.000 0.00 0.00 32.78 4.26
847 1295 1.882912 TGCTCACTCTTTGTGCGAAT 58.117 45.000 0.00 0.00 45.96 3.34
848 1296 1.532437 TGCTCACTCTTTGTGCGAATG 59.468 47.619 0.00 0.00 45.96 2.67
871 1319 1.905922 GACAACTTGCCGCAGAGAGC 61.906 60.000 8.85 0.00 40.87 4.09
884 1332 0.470268 AGAGAGCGGGGAATAGGGTC 60.470 60.000 0.00 0.00 0.00 4.46
918 1367 1.404583 GCATTGGAAAGCCCATGTGAC 60.405 52.381 0.00 0.00 46.10 3.67
934 1383 4.394712 ACGAGCCCGCCAAGAAGG 62.395 66.667 0.00 0.00 39.95 3.46
963 1412 2.433604 CTGGCTCTCCGCATATATCCAT 59.566 50.000 0.00 0.00 41.67 3.41
969 1418 5.105957 GCTCTCCGCATATATCCATCGATAT 60.106 44.000 0.00 0.00 40.38 1.63
973 1422 8.678199 TCTCCGCATATATCCATCGATATAATC 58.322 37.037 0.00 0.18 43.79 1.75
988 1437 1.600511 TAATCGAGGCGACAGGCACA 61.601 55.000 0.00 0.00 46.16 4.57
1012 1461 6.212888 AGGTCCACATAATTTCTTCATTGC 57.787 37.500 0.00 0.00 0.00 3.56
1026 1475 2.730382 TCATTGCAGGAACATGAGCAT 58.270 42.857 0.00 0.00 36.80 3.79
1030 1479 3.286329 TGCAGGAACATGAGCATACAT 57.714 42.857 0.00 0.00 31.05 2.29
1051 1500 2.050144 GGGATTGAGAGTATGGAGGCA 58.950 52.381 0.00 0.00 0.00 4.75
1063 1512 0.117140 TGGAGGCAAAGAGGAGGAGA 59.883 55.000 0.00 0.00 0.00 3.71
1140 1589 0.537188 TTCTGCTTCGATCCCCTCAC 59.463 55.000 0.00 0.00 0.00 3.51
1184 1633 3.117360 CCTCCTCCTTTGCCCTAATTGAT 60.117 47.826 0.00 0.00 0.00 2.57
1201 1650 2.529632 TGATCCCATCTAGATCCACCG 58.470 52.381 1.03 0.00 39.56 4.94
1258 1708 9.074576 TCTAGGGTTCTATTTTTCTTGGAAAAC 57.925 33.333 5.14 0.00 31.88 2.43
1279 1730 7.619512 AAACCCCTAGAAGTTCATATAGAGG 57.380 40.000 5.50 1.48 0.00 3.69
1310 1761 5.525378 ACATGGAGCTGAAGTAAATCGAATC 59.475 40.000 0.00 0.00 0.00 2.52
1312 1763 5.674525 TGGAGCTGAAGTAAATCGAATCAT 58.325 37.500 0.00 0.00 0.00 2.45
1343 1794 4.262164 GGCACCAGACACAAATTTTGATCT 60.262 41.667 15.81 13.62 32.51 2.75
1396 1847 8.442632 AGAAAACAAAGTGTTACTAACTACCC 57.557 34.615 0.71 0.00 40.14 3.69
1404 1855 7.803487 AGTGTTACTAACTACCCCACTAAAT 57.197 36.000 0.71 0.00 30.45 1.40
1409 1860 2.801077 ACTACCCCACTAAATGCACC 57.199 50.000 0.00 0.00 0.00 5.01
1422 1873 0.548989 ATGCACCCCGCTTATGGTAA 59.451 50.000 0.00 0.00 43.06 2.85
1477 1929 4.961438 AGCAACATCACCAAAAAGGAAT 57.039 36.364 0.00 0.00 41.22 3.01
1496 1948 8.424274 AAGGAATGTTCAGTTTTGTGATTTTC 57.576 30.769 0.00 0.00 0.00 2.29
1498 1950 8.260114 AGGAATGTTCAGTTTTGTGATTTTCTT 58.740 29.630 0.00 0.00 0.00 2.52
1520 1972 7.442656 TCTTAAAACCAAACACCTGTTCAAAA 58.557 30.769 0.00 0.00 37.25 2.44
1522 1974 6.735678 AAAACCAAACACCTGTTCAAAATC 57.264 33.333 0.00 0.00 37.25 2.17
1548 2000 9.553759 CGCAAGATAAATTTTAAATTATGTGCG 57.446 29.630 20.77 20.77 41.29 5.34
1566 2018 2.874086 TGCGCTATCATTGTCATCTTGG 59.126 45.455 9.73 0.00 0.00 3.61
1650 2102 5.194432 TCTAGTAGTCCTTCAACTAGCCTG 58.806 45.833 0.00 0.00 41.53 4.85
1688 2143 7.452813 TCTCCATCTACATTGCTAGTACATCAT 59.547 37.037 0.00 0.00 0.00 2.45
1689 2144 7.966812 TCCATCTACATTGCTAGTACATCATT 58.033 34.615 0.00 0.00 0.00 2.57
1752 2207 1.618343 CAATCCTTTGTGGGTGGGAAC 59.382 52.381 0.00 0.00 36.20 3.62
1762 2217 1.227383 GGTGGGAACTATGGGCCAG 59.773 63.158 13.78 0.82 0.00 4.85
1793 2248 2.225496 TGAATTTTACCCCCACATGCCT 60.225 45.455 0.00 0.00 0.00 4.75
1902 2357 4.996758 AGTTTGCCATATGCCTTTTCAAAC 59.003 37.500 15.72 15.72 40.93 2.93
1959 2415 7.458409 AACATGACATGTATTCAAAGCTTCT 57.542 32.000 21.10 0.00 44.07 2.85
2001 2457 8.499162 CCTTAAATAATGCATCTCTCCTTAACG 58.501 37.037 0.00 0.00 0.00 3.18
2139 2599 7.285401 GGGTGATCAAACCATAACTCATTGTAT 59.715 37.037 11.75 0.00 42.47 2.29
2157 2617 7.502226 TCATTGTATAAATGTTAAGCCCTCCTG 59.498 37.037 0.00 0.00 0.00 3.86
2171 2631 3.668447 CCCTCCTGTATGGAAATCATCG 58.332 50.000 0.00 0.00 45.63 3.84
2192 2652 7.719193 TCATCGAATAAGGCCTTGAAATCATTA 59.281 33.333 28.77 4.58 0.00 1.90
2283 2743 3.728566 GCCATTTGAAATGCCGCAATTTC 60.729 43.478 12.26 15.60 43.76 2.17
2293 2753 3.737850 TGCCGCAATTTCAATTTCCTTT 58.262 36.364 0.00 0.00 0.00 3.11
2299 2759 5.333263 CGCAATTTCAATTTCCTTTGGTGAC 60.333 40.000 0.00 0.00 0.00 3.67
2375 2838 7.308435 CACCTCAAAGGAAATTGTAGAATGTC 58.692 38.462 0.00 0.00 37.67 3.06
2379 2842 5.904362 AAGGAAATTGTAGAATGTCCAGC 57.096 39.130 20.95 0.00 45.60 4.85
2581 3047 6.677781 TTGTAACCACTTCAACTCTTCTTG 57.322 37.500 0.00 0.00 0.00 3.02
2591 3058 9.956720 CACTTCAACTCTTCTTGTTTCATAATT 57.043 29.630 0.00 0.00 0.00 1.40
2634 3106 8.635765 AAGTTCCAATTGTTCATGTACTATGT 57.364 30.769 4.43 0.00 0.00 2.29
2659 3131 0.106569 TGAGCCCATGGATTTCGCAT 60.107 50.000 15.22 0.00 0.00 4.73
2804 3279 4.193826 TCTCAGTGTTAGCTCCATTGAC 57.806 45.455 7.23 0.00 0.00 3.18
2838 3313 6.811665 TCATCCAAACTTCATGTACTAACTCG 59.188 38.462 0.00 0.00 0.00 4.18
2990 3467 5.127682 GCATTTATCCTCCCAATCAGTGTTT 59.872 40.000 0.00 0.00 0.00 2.83
3000 3477 4.520111 CCCAATCAGTGTTTCAAGTCATCA 59.480 41.667 0.00 0.00 0.00 3.07
3077 3554 8.668353 TGTCTTCAATTCATCTTAATTTCTCCG 58.332 33.333 0.00 0.00 0.00 4.63
3096 3576 6.354938 TCTCCGACAGTGTGTTCTAGTATAT 58.645 40.000 0.00 0.00 0.00 0.86
3102 3582 8.775527 CGACAGTGTGTTCTAGTATATCACTAT 58.224 37.037 0.00 0.00 39.06 2.12
3126 3606 3.963129 ACAAAACTCCAGTGTCCAAGAA 58.037 40.909 0.00 0.00 0.00 2.52
3181 3662 9.482627 TTGAATGTTGTTAAAATATCCACCAAC 57.517 29.630 0.00 0.00 33.23 3.77
3189 3670 7.815068 TGTTAAAATATCCACCAACCAAATTCG 59.185 33.333 0.00 0.00 0.00 3.34
3297 3778 5.838521 ACTTTCCTTTTCATTTAGGCTTCCA 59.161 36.000 0.00 0.00 0.00 3.53
3324 3805 8.894768 TTAAACCAACATTAAAGTCCAAATGG 57.105 30.769 0.00 0.00 37.40 3.16
3444 3925 1.132689 AGCCCCCTAGATCTAACCCTG 60.133 57.143 3.57 0.00 0.00 4.45
3479 3960 2.617021 GCCAACGAAAATCCCTACCAGA 60.617 50.000 0.00 0.00 0.00 3.86
3480 3961 3.886123 CCAACGAAAATCCCTACCAGAT 58.114 45.455 0.00 0.00 0.00 2.90
3499 3980 7.229308 ACCAGATCATATATTGTGCAACTCAT 58.771 34.615 0.00 0.00 38.04 2.90
3512 3993 6.466812 TGTGCAACTCATTTCTAGAGAATGA 58.533 36.000 19.95 19.95 38.04 2.57
3513 3994 6.369890 TGTGCAACTCATTTCTAGAGAATGAC 59.630 38.462 18.46 12.87 38.04 3.06
3515 3996 7.761704 GTGCAACTCATTTCTAGAGAATGACTA 59.238 37.037 18.46 6.72 36.91 2.59
3517 3998 9.323985 GCAACTCATTTCTAGAGAATGACTATT 57.676 33.333 18.46 13.23 36.91 1.73
3606 4088 2.426431 TAACCTCTCCTCCAAACCCA 57.574 50.000 0.00 0.00 0.00 4.51
3709 4192 0.538516 TGCACACACCCATTACCACC 60.539 55.000 0.00 0.00 0.00 4.61
3717 4200 1.383456 CCCATTACCACCGGCATGTG 61.383 60.000 0.00 0.00 35.98 3.21
3722 4205 1.693627 TACCACCGGCATGTGTTTTT 58.306 45.000 0.00 0.00 34.35 1.94
3724 4207 0.319469 CCACCGGCATGTGTTTTTCC 60.319 55.000 0.00 0.00 34.35 3.13
3725 4208 0.673437 CACCGGCATGTGTTTTTCCT 59.327 50.000 0.00 0.00 0.00 3.36
3726 4209 1.883275 CACCGGCATGTGTTTTTCCTA 59.117 47.619 0.00 0.00 0.00 2.94
3727 4210 2.491693 CACCGGCATGTGTTTTTCCTAT 59.508 45.455 0.00 0.00 0.00 2.57
3728 4211 2.491693 ACCGGCATGTGTTTTTCCTATG 59.508 45.455 0.00 0.00 0.00 2.23
3766 4249 2.036475 CCTGTCTAAGATGATCCCACCG 59.964 54.545 0.00 0.00 0.00 4.94
3776 4259 1.616628 ATCCCACCGGGCTTCTTCT 60.617 57.895 6.32 0.00 43.94 2.85
3783 4266 2.632996 CACCGGGCTTCTTCTATATCCA 59.367 50.000 6.32 0.00 0.00 3.41
3787 4270 6.323996 CACCGGGCTTCTTCTATATCCATATA 59.676 42.308 6.32 0.00 0.00 0.86
3980 4471 5.324409 TCAAAATAGCAACCCAGATTCACT 58.676 37.500 0.00 0.00 0.00 3.41
3981 4472 5.183713 TCAAAATAGCAACCCAGATTCACTG 59.816 40.000 0.00 0.00 45.36 3.66
3982 4473 4.307032 AATAGCAACCCAGATTCACTGT 57.693 40.909 0.00 0.00 44.40 3.55
4041 4532 8.611051 ACTAGAAGAAACTGTATTAGGGATGT 57.389 34.615 0.00 0.00 0.00 3.06
4107 4599 6.239396 CAAGATATTCAATCATGAGCCCTCT 58.761 40.000 0.09 0.00 36.78 3.69
4180 4672 9.653287 TGTTAACATTTAGATCTCTTGTGTAGG 57.347 33.333 3.59 0.00 0.00 3.18
4182 4674 5.675538 ACATTTAGATCTCTTGTGTAGGCC 58.324 41.667 0.00 0.00 0.00 5.19
4231 4723 2.280628 CCGATTCTTGGCTAGGTTCAC 58.719 52.381 0.00 0.00 0.00 3.18
4339 4831 5.094387 ACCTCCATTAACTCTTTCTCCTCA 58.906 41.667 0.00 0.00 0.00 3.86
4351 4843 8.317776 ACTCTTTCTCCTCAGCTATCTTAATT 57.682 34.615 0.00 0.00 0.00 1.40
4457 4949 5.367352 TGTCTAGGAAACTGGGAGTACAAAA 59.633 40.000 0.00 0.00 43.88 2.44
4478 4970 0.108019 GGTCGAACTCCCACCAAGTT 59.892 55.000 0.00 0.00 39.61 2.66
4542 5034 1.065126 ACATCCTCTTAACTGCCAGGC 60.065 52.381 3.66 3.66 0.00 4.85
4560 5052 3.084786 AGGCAGTCTCCTTTGTTTATGC 58.915 45.455 0.00 0.00 30.82 3.14
4563 5055 3.667960 GCAGTCTCCTTTGTTTATGCGTG 60.668 47.826 0.00 0.00 0.00 5.34
4581 5073 5.701029 GCGTGTGCAAATATTTTAGCAAT 57.299 34.783 13.13 0.00 42.15 3.56
4584 5076 6.252441 GCGTGTGCAAATATTTTAGCAATGTA 59.748 34.615 13.13 1.29 42.15 2.29
4586 5078 8.471457 CGTGTGCAAATATTTTAGCAATGTATC 58.529 33.333 13.13 3.31 38.91 2.24
4587 5079 8.471457 GTGTGCAAATATTTTAGCAATGTATCG 58.529 33.333 13.13 0.00 38.91 2.92
4588 5080 8.401709 TGTGCAAATATTTTAGCAATGTATCGA 58.598 29.630 13.13 0.00 38.91 3.59
4674 5168 2.560504 GTCGGGCATGTGATATGTTCA 58.439 47.619 0.00 0.00 0.00 3.18
4830 5324 3.367087 GCACCGTCAAGACACACTACTAT 60.367 47.826 0.72 0.00 0.00 2.12
4866 5360 2.350522 GAGAAATCGTGTCCACATGCT 58.649 47.619 0.00 0.00 33.05 3.79
4914 5408 1.302033 CTTCGCAGGCTCAACCACT 60.302 57.895 0.00 0.00 43.14 4.00
4951 5445 1.159285 CACTGCCGATCACATGTTGT 58.841 50.000 0.00 0.00 0.00 3.32
5016 5510 2.154462 CAGGAAGGAATGCGTGTTCTT 58.846 47.619 2.74 0.00 0.00 2.52
5019 5513 2.749621 GGAAGGAATGCGTGTTCTTCAT 59.250 45.455 14.19 0.00 0.00 2.57
5114 5608 4.224991 TCTTGTGCATTGATCCTCATGA 57.775 40.909 0.00 0.00 0.00 3.07
5157 5651 4.682787 TCGAGTGCGATGTTGATTTCTAT 58.317 39.130 0.00 0.00 42.51 1.98
5208 5702 7.465353 TTCAAATTTCCAGATCATAAGCACA 57.535 32.000 0.00 0.00 0.00 4.57
5389 5890 0.813610 GCATATGTGTGGCGGCAGTA 60.814 55.000 13.91 0.80 0.00 2.74
5395 5896 1.208293 TGTGTGGCGGCAGTAATATGA 59.792 47.619 13.91 0.00 0.00 2.15
5413 5914 1.893137 TGACGTGGTGCTACTTGAGAT 59.107 47.619 0.00 0.00 0.00 2.75
5572 6075 6.162079 TGTTGAACTTTGATGCTTGAAAACA 58.838 32.000 0.00 0.00 0.00 2.83
5576 6079 4.952460 ACTTTGATGCTTGAAAACATGCT 58.048 34.783 0.00 0.00 0.00 3.79
5623 6126 0.469494 ATGGATATCGCCAGCACACA 59.531 50.000 0.00 0.00 42.15 3.72
5624 6127 0.461870 TGGATATCGCCAGCACACAC 60.462 55.000 0.00 0.00 33.10 3.82
5641 6144 5.056480 CACACACTGGAGTATGTTTTGAGA 58.944 41.667 0.00 0.00 32.68 3.27
5748 6255 3.521560 CGTACAAGTATGATGTGCACCT 58.478 45.455 15.69 3.77 33.63 4.00
5771 6278 2.797786 AGGCATATACTCTCTCCGTCC 58.202 52.381 0.00 0.00 0.00 4.79
5788 6295 2.412325 CGTCCCAAAATAAGTGTCGTGC 60.412 50.000 0.00 0.00 0.00 5.34
5805 6312 2.285756 CGTGCTTGAACTAAAACCACGA 59.714 45.455 4.46 0.00 45.00 4.35
5817 6324 7.556733 ACTAAAACCACGACACTTATTTTGA 57.443 32.000 0.00 0.00 0.00 2.69
5832 6339 1.171308 TTTGAGACCGAGGGAGTACG 58.829 55.000 0.00 0.00 0.00 3.67
5858 6365 0.179113 AAAACAACCACAAGCAGCCG 60.179 50.000 0.00 0.00 0.00 5.52
5859 6366 2.015227 AAACAACCACAAGCAGCCGG 62.015 55.000 0.00 0.00 0.00 6.13
5860 6367 4.347453 CAACCACAAGCAGCCGGC 62.347 66.667 21.89 21.89 45.30 6.13
5924 6431 2.355481 GTCCTTGTCGTCGGCGTT 60.355 61.111 10.18 0.00 39.49 4.84
5974 6481 3.109619 GAGCTCCGATAAGACGAACAAG 58.890 50.000 0.87 0.00 35.09 3.16
5975 6482 1.588861 GCTCCGATAAGACGAACAAGC 59.411 52.381 0.00 0.00 35.09 4.01
5976 6483 2.194271 CTCCGATAAGACGAACAAGCC 58.806 52.381 0.00 0.00 35.09 4.35
5977 6484 0.921347 CCGATAAGACGAACAAGCCG 59.079 55.000 0.00 0.00 35.09 5.52
5978 6485 1.625616 CGATAAGACGAACAAGCCGT 58.374 50.000 0.00 0.00 43.56 5.68
5979 6486 1.990563 CGATAAGACGAACAAGCCGTT 59.009 47.619 0.00 0.00 40.67 4.44
5980 6487 2.222508 CGATAAGACGAACAAGCCGTTG 60.223 50.000 0.00 0.00 40.67 4.10
5981 6488 2.512485 TAAGACGAACAAGCCGTTGA 57.488 45.000 0.00 0.00 40.67 3.18
5982 6489 1.217882 AAGACGAACAAGCCGTTGAG 58.782 50.000 0.00 0.00 40.67 3.02
5983 6490 0.600255 AGACGAACAAGCCGTTGAGG 60.600 55.000 0.00 0.00 40.67 3.86
5996 6503 3.857052 CCGTTGAGGCAAACTGTATAGA 58.143 45.455 0.00 0.00 0.00 1.98
5997 6504 3.617263 CCGTTGAGGCAAACTGTATAGAC 59.383 47.826 0.00 0.00 0.00 2.59
5998 6505 3.303495 CGTTGAGGCAAACTGTATAGACG 59.697 47.826 0.00 0.00 0.00 4.18
5999 6506 3.520290 TGAGGCAAACTGTATAGACGG 57.480 47.619 0.00 0.00 38.01 4.79
6000 6507 3.093814 TGAGGCAAACTGTATAGACGGA 58.906 45.455 2.68 0.00 35.72 4.69
6001 6508 3.119245 TGAGGCAAACTGTATAGACGGAC 60.119 47.826 2.68 0.00 35.72 4.79
6002 6509 2.829720 AGGCAAACTGTATAGACGGACA 59.170 45.455 2.68 0.00 35.72 4.02
6003 6510 3.259876 AGGCAAACTGTATAGACGGACAA 59.740 43.478 2.68 0.00 35.72 3.18
6010 6517 3.567530 TGTATAGACGGACAACAACACG 58.432 45.455 0.00 0.00 0.00 4.49
6011 6518 1.425412 ATAGACGGACAACAACACGC 58.575 50.000 0.00 0.00 0.00 5.34
6106 6614 4.382793 GCAATTTCTAGTTCTACGGACCCT 60.383 45.833 0.00 0.00 0.00 4.34
6136 6644 3.741476 GCTTCAGCTGTTGGCCCG 61.741 66.667 14.67 0.00 43.05 6.13
6143 6651 4.410400 CTGTTGGCCCGGGGAGTC 62.410 72.222 25.28 4.65 0.00 3.36
6183 6691 2.728318 CGCTGAGAACACGGATATCATG 59.272 50.000 4.83 4.92 0.00 3.07
6204 6712 0.538057 TCTGCCAGACAAGCCCTTTG 60.538 55.000 0.00 0.00 42.68 2.77
6205 6713 1.530013 CTGCCAGACAAGCCCTTTGG 61.530 60.000 0.00 0.00 41.25 3.28
6217 6725 2.636647 CCCTTTGGGCAATGTTGTTT 57.363 45.000 0.00 0.00 35.35 2.83
6218 6726 2.220313 CCCTTTGGGCAATGTTGTTTG 58.780 47.619 0.00 0.00 35.35 2.93
6225 6733 3.271142 CAATGTTGTTTGCAGCCGT 57.729 47.368 0.00 0.00 0.00 5.68
6226 6734 2.414058 CAATGTTGTTTGCAGCCGTA 57.586 45.000 0.00 0.00 0.00 4.02
6227 6735 2.736978 CAATGTTGTTTGCAGCCGTAA 58.263 42.857 0.00 0.00 0.00 3.18
6228 6736 2.704725 ATGTTGTTTGCAGCCGTAAG 57.295 45.000 0.00 0.00 0.00 2.34
6229 6737 0.030101 TGTTGTTTGCAGCCGTAAGC 59.970 50.000 0.00 0.00 44.25 3.09
6246 6754 7.419204 GCCGTAAGCTTACTATATGATAGAGG 58.581 42.308 29.00 19.87 38.99 3.69
6247 6755 7.067251 GCCGTAAGCTTACTATATGATAGAGGT 59.933 40.741 29.00 0.00 38.99 3.85
6248 6756 8.399425 CCGTAAGCTTACTATATGATAGAGGTG 58.601 40.741 29.00 11.25 0.00 4.00
6249 6757 8.399425 CGTAAGCTTACTATATGATAGAGGTGG 58.601 40.741 29.00 8.09 0.00 4.61
6250 6758 7.726033 AAGCTTACTATATGATAGAGGTGGG 57.274 40.000 0.00 0.00 0.00 4.61
6251 6759 7.045693 AGCTTACTATATGATAGAGGTGGGA 57.954 40.000 0.00 0.00 0.00 4.37
6252 6760 7.122715 AGCTTACTATATGATAGAGGTGGGAG 58.877 42.308 0.00 0.00 0.00 4.30
6253 6761 6.893005 GCTTACTATATGATAGAGGTGGGAGT 59.107 42.308 0.00 0.00 0.00 3.85
6254 6762 8.053963 GCTTACTATATGATAGAGGTGGGAGTA 58.946 40.741 0.00 0.00 0.00 2.59
6255 6763 9.621629 CTTACTATATGATAGAGGTGGGAGTAG 57.378 40.741 0.00 0.00 0.00 2.57
6256 6764 7.832473 ACTATATGATAGAGGTGGGAGTAGA 57.168 40.000 0.00 0.00 0.00 2.59
6257 6765 8.233349 ACTATATGATAGAGGTGGGAGTAGAA 57.767 38.462 0.00 0.00 0.00 2.10
6258 6766 8.679725 ACTATATGATAGAGGTGGGAGTAGAAA 58.320 37.037 0.00 0.00 0.00 2.52
6259 6767 9.535170 CTATATGATAGAGGTGGGAGTAGAAAA 57.465 37.037 0.00 0.00 0.00 2.29
6260 6768 8.980832 ATATGATAGAGGTGGGAGTAGAAAAT 57.019 34.615 0.00 0.00 0.00 1.82
6270 6778 5.694006 GTGGGAGTAGAAAATCGATGATCAG 59.306 44.000 0.00 0.00 0.00 2.90
6294 6802 1.378119 GGCCGGGGATTCGAGTTTT 60.378 57.895 2.18 0.00 0.00 2.43
6297 6805 0.035820 CCGGGGATTCGAGTTTTCCA 60.036 55.000 0.00 0.00 0.00 3.53
6303 6811 0.451783 ATTCGAGTTTTCCATGCCGC 59.548 50.000 0.00 0.00 0.00 6.53
6313 6821 2.046023 CATGCCGCTTCTCCACCA 60.046 61.111 0.00 0.00 0.00 4.17
6347 6855 1.978580 ACATCAACGGAGGAAGAAGGT 59.021 47.619 0.00 0.00 0.00 3.50
6397 6905 0.979665 CATGAGACCACACCTGACCT 59.020 55.000 0.00 0.00 0.00 3.85
6422 6931 3.708403 TCTGTCAAATGCAGATGGAGT 57.292 42.857 0.00 0.00 37.98 3.85
6430 6939 1.690633 GCAGATGGAGTGGGGAGGA 60.691 63.158 0.00 0.00 0.00 3.71
6441 6950 3.454812 GAGTGGGGAGGACTTATTTAGCA 59.545 47.826 0.00 0.00 0.00 3.49
6483 6992 4.607293 AGCTTCATGACACACTAGACAA 57.393 40.909 0.00 0.00 0.00 3.18
6490 6999 3.473625 TGACACACTAGACAAGAGACGA 58.526 45.455 0.00 0.00 0.00 4.20
6510 7019 1.623686 ATTCCACCTCCCTGCCCAT 60.624 57.895 0.00 0.00 0.00 4.00
6596 7105 2.159421 GCACTAATGGAGTCGAGACGAA 60.159 50.000 0.00 0.00 37.72 3.85
6621 7130 0.597637 AGACGAAACCAGCAGTGACG 60.598 55.000 0.00 0.00 35.11 4.35
6627 7136 1.151777 AACCAGCAGTGACGTGAACG 61.152 55.000 0.00 0.40 46.33 3.95
6634 7143 4.953868 TGACGTGAACGCGGTGGG 62.954 66.667 12.47 0.00 44.43 4.61
6655 7164 2.923121 GCAAACAGAGGCCAGATATGA 58.077 47.619 5.01 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 34 9.601217 GTAAGTAAAATATGTGTGTCTCCTGAT 57.399 33.333 0.00 0.00 0.00 2.90
40 42 9.840427 GCATCTTTGTAAGTAAAATATGTGTGT 57.160 29.630 0.00 0.00 0.00 3.72
207 226 1.528292 GAGCCCACACTGAGAGTCGT 61.528 60.000 0.00 0.00 0.00 4.34
349 368 9.853177 ATGAAACCAAAAACCATTAAACCATTA 57.147 25.926 0.00 0.00 0.00 1.90
350 369 8.759481 ATGAAACCAAAAACCATTAAACCATT 57.241 26.923 0.00 0.00 0.00 3.16
351 370 8.759481 AATGAAACCAAAAACCATTAAACCAT 57.241 26.923 0.00 0.00 0.00 3.55
353 372 9.862371 AAAAATGAAACCAAAAACCATTAAACC 57.138 25.926 0.00 0.00 0.00 3.27
358 377 9.987272 TTTTGAAAAATGAAACCAAAAACCATT 57.013 22.222 0.00 0.00 34.87 3.16
413 432 8.133627 CAGACAGACAGAACAAATTGAAATTCT 58.866 33.333 0.00 0.00 31.53 2.40
414 433 8.131100 TCAGACAGACAGAACAAATTGAAATTC 58.869 33.333 0.00 0.00 0.00 2.17
415 434 7.999679 TCAGACAGACAGAACAAATTGAAATT 58.000 30.769 0.00 0.00 0.00 1.82
417 436 7.094420 TGTTCAGACAGACAGAACAAATTGAAA 60.094 33.333 8.10 0.00 46.52 2.69
418 437 6.374053 TGTTCAGACAGACAGAACAAATTGAA 59.626 34.615 8.10 0.00 46.52 2.69
419 438 5.879777 TGTTCAGACAGACAGAACAAATTGA 59.120 36.000 8.10 0.00 46.52 2.57
420 439 6.122850 TGTTCAGACAGACAGAACAAATTG 57.877 37.500 8.10 0.00 46.52 2.32
430 449 7.825681 TCTTTTCAAAAATGTTCAGACAGACA 58.174 30.769 0.00 0.00 39.58 3.41
431 450 8.587111 GTTCTTTTCAAAAATGTTCAGACAGAC 58.413 33.333 0.00 0.00 39.58 3.51
432 451 8.303156 TGTTCTTTTCAAAAATGTTCAGACAGA 58.697 29.630 0.00 0.00 39.58 3.41
433 452 8.464770 TGTTCTTTTCAAAAATGTTCAGACAG 57.535 30.769 0.00 0.00 39.58 3.51
435 454 9.528847 GTTTGTTCTTTTCAAAAATGTTCAGAC 57.471 29.630 0.00 0.00 36.71 3.51
772 1219 1.072489 TGGATTTACGTGCAAGGGACA 59.928 47.619 4.26 0.00 0.00 4.02
773 1220 1.816074 TGGATTTACGTGCAAGGGAC 58.184 50.000 4.26 0.00 0.00 4.46
821 1269 2.216898 ACAAAGAGTGAGCAAGTGAGC 58.783 47.619 0.00 0.00 0.00 4.26
833 1281 3.243873 TGTCTCTCATTCGCACAAAGAGT 60.244 43.478 0.00 0.00 35.91 3.24
847 1295 0.601046 CTGCGGCAAGTTGTCTCTCA 60.601 55.000 3.44 0.31 0.00 3.27
848 1296 0.319900 TCTGCGGCAAGTTGTCTCTC 60.320 55.000 3.44 0.00 0.00 3.20
871 1319 1.632018 TTGGCAGACCCTATTCCCCG 61.632 60.000 0.00 0.00 33.59 5.73
884 1332 1.466950 CCAATGCATTTTGCTTGGCAG 59.533 47.619 9.83 0.00 45.31 4.85
918 1367 4.394712 ACCTTCTTGGCGGGCTCG 62.395 66.667 0.00 0.00 40.22 5.03
934 1383 1.806568 CGGAGAGCCAGAGAGTGAC 59.193 63.158 0.00 0.00 0.00 3.67
969 1418 1.141019 GTGCCTGTCGCCTCGATTA 59.859 57.895 0.00 0.00 38.42 1.75
973 1422 3.114616 CTTGTGCCTGTCGCCTCG 61.115 66.667 0.00 0.00 36.24 4.63
983 1432 3.763897 AGAAATTATGTGGACCTTGTGCC 59.236 43.478 0.00 0.00 0.00 5.01
988 1437 6.211184 TGCAATGAAGAAATTATGTGGACCTT 59.789 34.615 0.00 0.00 0.00 3.50
1012 1461 2.882761 CCCATGTATGCTCATGTTCCTG 59.117 50.000 13.02 2.13 42.29 3.86
1026 1475 4.840680 CCTCCATACTCTCAATCCCATGTA 59.159 45.833 0.00 0.00 0.00 2.29
1030 1479 2.050144 GCCTCCATACTCTCAATCCCA 58.950 52.381 0.00 0.00 0.00 4.37
1051 1500 1.398799 TCTCCCCTCTCCTCCTCTTT 58.601 55.000 0.00 0.00 0.00 2.52
1063 1512 3.003763 GTGGCGGACTTCTCCCCT 61.004 66.667 0.00 0.00 31.93 4.79
1184 1633 2.039418 CAACGGTGGATCTAGATGGGA 58.961 52.381 10.74 0.00 0.00 4.37
1201 1650 3.181490 GGAAACCGAATCCCTTATGCAAC 60.181 47.826 0.00 0.00 0.00 4.17
1258 1708 8.903059 ATAACCTCTATATGAACTTCTAGGGG 57.097 38.462 2.26 2.26 37.77 4.79
1310 1761 3.201290 GTGTCTGGTGCCTAAGATGATG 58.799 50.000 0.00 0.00 0.00 3.07
1312 1763 2.256306 TGTGTCTGGTGCCTAAGATGA 58.744 47.619 0.00 0.00 0.00 2.92
1377 1828 5.861727 AGTGGGGTAGTTAGTAACACTTTG 58.138 41.667 15.28 0.00 34.36 2.77
1396 1847 3.196648 GCGGGGTGCATTTAGTGG 58.803 61.111 0.00 0.00 45.45 4.00
1409 1860 5.099575 GTGAAACAAATTACCATAAGCGGG 58.900 41.667 0.00 0.00 36.32 6.13
1496 1948 7.659652 TTTTGAACAGGTGTTTGGTTTTAAG 57.340 32.000 0.00 0.00 38.56 1.85
1498 1950 6.531948 CGATTTTGAACAGGTGTTTGGTTTTA 59.468 34.615 0.00 0.00 38.56 1.52
1510 1962 7.816945 AATTTATCTTGCGATTTTGAACAGG 57.183 32.000 0.00 0.00 0.00 4.00
1522 1974 9.553759 CGCACATAATTTAAAATTTATCTTGCG 57.446 29.630 19.93 19.93 39.01 4.85
1548 2000 5.411977 CCTGATCCAAGATGACAATGATAGC 59.588 44.000 0.00 0.00 0.00 2.97
1551 2003 5.641789 TCCTGATCCAAGATGACAATGAT 57.358 39.130 0.00 0.00 0.00 2.45
1556 2008 5.370584 ACCATATTCCTGATCCAAGATGACA 59.629 40.000 5.69 0.00 0.00 3.58
1566 2018 6.175471 TGCATATGACACCATATTCCTGATC 58.825 40.000 6.97 0.00 41.83 2.92
1607 2059 7.339482 ACTAGAAGAATATTTTGAGGGTGGTC 58.661 38.462 0.00 0.00 0.00 4.02
1660 2115 6.806751 TGTACTAGCAATGTAGATGGAGAAC 58.193 40.000 0.00 0.00 0.00 3.01
1752 2207 2.620115 CAATGCTTGTACTGGCCCATAG 59.380 50.000 0.00 0.00 0.00 2.23
1762 2217 5.046950 TGGGGGTAAAATTCAATGCTTGTAC 60.047 40.000 0.00 0.00 0.00 2.90
1774 2229 2.640284 AGGCATGTGGGGGTAAAATT 57.360 45.000 0.00 0.00 0.00 1.82
1918 2373 9.715121 ATGTCATGTTAAAAAGCAAAGATCAAT 57.285 25.926 0.00 0.00 0.00 2.57
1923 2378 9.979578 AATACATGTCATGTTAAAAAGCAAAGA 57.020 25.926 23.05 1.44 41.63 2.52
1935 2391 7.458409 AGAAGCTTTGAATACATGTCATGTT 57.542 32.000 23.05 6.82 41.63 2.71
1973 2429 6.770286 AGGAGAGATGCATTATTTAAGGGA 57.230 37.500 0.00 0.00 0.00 4.20
1987 2443 6.090088 CAGACAACTTTCGTTAAGGAGAGATG 59.910 42.308 19.21 18.74 38.23 2.90
1988 2444 6.015350 TCAGACAACTTTCGTTAAGGAGAGAT 60.015 38.462 19.21 7.51 38.23 2.75
2001 2457 7.606456 TGTCATACCCTTATTCAGACAACTTTC 59.394 37.037 0.00 0.00 32.26 2.62
2139 2599 5.430417 TCCATACAGGAGGGCTTAACATTTA 59.570 40.000 0.00 0.00 43.07 1.40
2157 2617 5.940470 AGGCCTTATTCGATGATTTCCATAC 59.060 40.000 0.00 0.00 35.17 2.39
2222 2682 4.218312 GGCCCTAATGGATTCACTTCAAT 58.782 43.478 0.00 0.00 35.39 2.57
2283 2743 5.857268 AGGAATTGTCACCAAAGGAAATTG 58.143 37.500 0.00 0.00 33.44 2.32
2581 3047 8.485976 AGCTGAACTAGACAGAATTATGAAAC 57.514 34.615 19.72 0.00 37.54 2.78
2591 3058 5.416326 GGAACTTAGAGCTGAACTAGACAGA 59.584 44.000 19.72 2.77 37.54 3.41
2592 3059 5.184096 TGGAACTTAGAGCTGAACTAGACAG 59.816 44.000 14.07 14.07 38.27 3.51
2634 3106 3.069586 CGAAATCCATGGGCTCACTACTA 59.930 47.826 13.02 0.00 0.00 1.82
2703 3178 8.723942 AATATGAATGCCTCGTATAGAATTCC 57.276 34.615 0.65 0.00 35.54 3.01
2804 3279 1.238439 AGTTTGGATGAACCGCAGTG 58.762 50.000 0.00 0.00 42.61 3.66
2838 3313 9.157104 CTCTTAATTCTGAAGGAAGGACTAAAC 57.843 37.037 11.83 0.00 37.36 2.01
2899 3376 8.816894 ACCTTTGTATATAGATACATGGGACAG 58.183 37.037 23.88 10.68 45.77 3.51
2990 3467 9.465199 TTTGAGAAATTGGATATGATGACTTGA 57.535 29.630 0.00 0.00 0.00 3.02
3096 3576 7.179516 TGGACACTGGAGTTTTGTATATAGTGA 59.820 37.037 0.00 0.00 38.08 3.41
3102 3582 6.428083 TCTTGGACACTGGAGTTTTGTATA 57.572 37.500 0.00 0.00 0.00 1.47
3162 3642 9.495572 GAATTTGGTTGGTGGATATTTTAACAA 57.504 29.630 0.00 0.00 0.00 2.83
3206 3687 7.559897 ACAAATCTGAAACTTTCAAGGGTTCTA 59.440 33.333 5.72 0.00 39.58 2.10
3269 3750 5.602561 AGCCTAAATGAAAAGGAAAGTTGGT 59.397 36.000 0.00 0.00 34.58 3.67
3283 3764 5.636123 TGGTTTAAGTGGAAGCCTAAATGA 58.364 37.500 0.00 0.00 31.34 2.57
3289 3770 3.306472 TGTTGGTTTAAGTGGAAGCCT 57.694 42.857 0.00 0.00 31.34 4.58
3297 3778 9.541143 CATTTGGACTTTAATGTTGGTTTAAGT 57.459 29.630 0.00 0.00 34.67 2.24
3324 3805 8.560374 AGCAGTACAAGATAAGAAAACAAACTC 58.440 33.333 0.00 0.00 0.00 3.01
3407 3888 3.381590 GGGGCTATTTCTTGGTGTCAATC 59.618 47.826 0.00 0.00 31.75 2.67
3411 3892 1.285078 AGGGGGCTATTTCTTGGTGTC 59.715 52.381 0.00 0.00 0.00 3.67
3709 4192 3.848272 ACATAGGAAAAACACATGCCG 57.152 42.857 0.00 0.00 0.00 5.69
3750 4233 3.878774 AAGCCCGGTGGGATCATCTTAG 61.879 54.545 5.94 0.00 42.68 2.18
3752 4235 1.281925 AAGCCCGGTGGGATCATCTT 61.282 55.000 5.94 0.00 42.68 2.40
3963 4454 4.366377 GCAACAGTGAATCTGGGTTGCTA 61.366 47.826 20.42 0.00 44.98 3.49
3980 4471 1.216064 AGATGGCCTCCTATGCAACA 58.784 50.000 3.32 0.00 0.00 3.33
3981 4472 3.406764 CTTAGATGGCCTCCTATGCAAC 58.593 50.000 3.32 0.00 0.00 4.17
3982 4473 2.224621 GCTTAGATGGCCTCCTATGCAA 60.225 50.000 24.28 7.43 36.58 4.08
4041 4532 8.198109 GTGCCAAGAATGACTCTAGTAAGATAA 58.802 37.037 0.00 0.00 32.46 1.75
4107 4599 3.305403 GGTGTGACAGATTGAAGTCTCGA 60.305 47.826 0.00 0.00 35.81 4.04
4177 4669 4.998051 ACTTCAAAAATCAGGAAGGCCTA 58.002 39.130 5.16 0.00 44.80 3.93
4180 4672 7.378181 TCATTTACTTCAAAAATCAGGAAGGC 58.622 34.615 0.00 0.00 41.73 4.35
4231 4723 4.645535 TGAGGAAGAGAACCAAATGACTG 58.354 43.478 0.00 0.00 0.00 3.51
4316 4808 5.094387 TGAGGAGAAAGAGTTAATGGAGGT 58.906 41.667 0.00 0.00 0.00 3.85
4351 4843 6.312918 GCAAGAGTTCCTACGACAATTAATCA 59.687 38.462 0.00 0.00 0.00 2.57
4362 4854 3.305398 AAGACAGCAAGAGTTCCTACG 57.695 47.619 0.00 0.00 0.00 3.51
4457 4949 0.396811 CTTGGTGGGAGTTCGACCTT 59.603 55.000 4.01 0.00 43.63 3.50
4478 4970 9.372369 AGAAAATTTTGTTTTGGTTGAACGATA 57.628 25.926 8.47 0.00 0.00 2.92
4517 5009 2.819608 GGCAGTTAAGAGGATGTTTGCA 59.180 45.455 0.00 0.00 32.24 4.08
4542 5034 3.498397 ACACGCATAAACAAAGGAGACTG 59.502 43.478 0.00 0.00 42.68 3.51
4560 5052 6.630676 ACATTGCTAAAATATTTGCACACG 57.369 33.333 11.56 6.94 44.86 4.49
4563 5055 8.781067 TCGATACATTGCTAAAATATTTGCAC 57.219 30.769 11.56 1.28 44.86 4.57
4584 5076 9.814899 CTTGCCTATGAGAAAGATAATATCGAT 57.185 33.333 2.16 2.16 0.00 3.59
4586 5078 7.010923 GGCTTGCCTATGAGAAAGATAATATCG 59.989 40.741 4.11 0.00 0.00 2.92
4587 5079 7.281999 GGGCTTGCCTATGAGAAAGATAATATC 59.718 40.741 11.71 0.00 0.00 1.63
4588 5080 7.115414 GGGCTTGCCTATGAGAAAGATAATAT 58.885 38.462 11.71 0.00 0.00 1.28
4674 5168 1.760192 GGAGCTTGTGATGGCAAGAT 58.240 50.000 9.65 3.25 46.18 2.40
4734 5228 2.395360 GGCGATGCAGCGGTTGTAA 61.395 57.895 27.22 0.00 38.18 2.41
4830 5324 0.895559 TCTCGTGCTCCTCTTGCTGA 60.896 55.000 0.00 0.00 0.00 4.26
4914 5408 1.219124 GAGATGGCGCTGGAGTTGA 59.781 57.895 7.64 0.00 0.00 3.18
5016 5510 3.054361 GGCCACCTTCTTCTTTCCTATGA 60.054 47.826 0.00 0.00 0.00 2.15
5019 5513 1.633945 GGGCCACCTTCTTCTTTCCTA 59.366 52.381 4.39 0.00 0.00 2.94
5114 5608 4.499865 CGAACCTATGATTCTCCGTCACAT 60.500 45.833 0.00 0.00 0.00 3.21
5157 5651 2.510411 CATCCCATGGTGCGGCTA 59.490 61.111 11.73 0.00 0.00 3.93
5208 5702 2.491675 GGAACCCGTTGGAGAGATTT 57.508 50.000 0.00 0.00 34.81 2.17
5323 5817 1.137282 GCTAGTCACTTAGGGACAGGC 59.863 57.143 17.52 15.35 37.74 4.85
5389 5890 4.159693 TCTCAAGTAGCACCACGTCATATT 59.840 41.667 0.00 0.00 0.00 1.28
5395 5896 3.067106 CAAATCTCAAGTAGCACCACGT 58.933 45.455 0.00 0.00 0.00 4.49
5498 6001 3.333029 TCTTCCGAAGATGCACATGAA 57.667 42.857 6.75 0.00 31.20 2.57
5572 6075 0.405585 ACAAGCCCACCACTAAGCAT 59.594 50.000 0.00 0.00 0.00 3.79
5576 6079 1.071699 GAGTGACAAGCCCACCACTAA 59.928 52.381 0.00 0.00 39.67 2.24
5748 6255 4.325119 GACGGAGAGAGTATATGCCTACA 58.675 47.826 0.00 0.00 0.00 2.74
5771 6278 4.481930 TCAAGCACGACACTTATTTTGG 57.518 40.909 0.00 0.00 0.00 3.28
5788 6295 5.479716 AAGTGTCGTGGTTTTAGTTCAAG 57.520 39.130 0.00 0.00 0.00 3.02
5805 6312 3.581332 TCCCTCGGTCTCAAAATAAGTGT 59.419 43.478 0.00 0.00 0.00 3.55
5817 6324 1.487976 TGTATCGTACTCCCTCGGTCT 59.512 52.381 0.00 0.00 0.00 3.85
5832 6339 5.572896 GCTGCTTGTGGTTGTTTTATGTATC 59.427 40.000 0.00 0.00 0.00 2.24
5858 6365 4.438148 TGCTTTTTCTTTTGTTGTAGGCC 58.562 39.130 0.00 0.00 0.00 5.19
5859 6366 5.220586 GGTTGCTTTTTCTTTTGTTGTAGGC 60.221 40.000 0.00 0.00 0.00 3.93
5860 6367 5.005299 CGGTTGCTTTTTCTTTTGTTGTAGG 59.995 40.000 0.00 0.00 0.00 3.18
5861 6368 5.575218 ACGGTTGCTTTTTCTTTTGTTGTAG 59.425 36.000 0.00 0.00 0.00 2.74
5924 6431 8.603898 TGAAGATTTAGAAGGTCACCATAGTA 57.396 34.615 0.00 0.00 0.00 1.82
5960 6467 2.991190 TCAACGGCTTGTTCGTCTTATC 59.009 45.455 0.00 0.00 39.29 1.75
5975 6482 3.617263 GTCTATACAGTTTGCCTCAACGG 59.383 47.826 0.00 0.00 0.00 4.44
5976 6483 3.303495 CGTCTATACAGTTTGCCTCAACG 59.697 47.826 0.00 0.00 0.00 4.10
5977 6484 3.617263 CCGTCTATACAGTTTGCCTCAAC 59.383 47.826 0.00 0.00 0.00 3.18
5978 6485 3.512329 TCCGTCTATACAGTTTGCCTCAA 59.488 43.478 0.00 0.00 0.00 3.02
5979 6486 3.093814 TCCGTCTATACAGTTTGCCTCA 58.906 45.455 0.00 0.00 0.00 3.86
5980 6487 3.119245 TGTCCGTCTATACAGTTTGCCTC 60.119 47.826 0.00 0.00 0.00 4.70
5981 6488 2.829720 TGTCCGTCTATACAGTTTGCCT 59.170 45.455 0.00 0.00 0.00 4.75
5982 6489 3.241067 TGTCCGTCTATACAGTTTGCC 57.759 47.619 0.00 0.00 0.00 4.52
5983 6490 3.991773 TGTTGTCCGTCTATACAGTTTGC 59.008 43.478 0.00 0.00 0.00 3.68
5984 6491 5.464057 TGTTGTTGTCCGTCTATACAGTTTG 59.536 40.000 0.00 0.00 0.00 2.93
5985 6492 5.464389 GTGTTGTTGTCCGTCTATACAGTTT 59.536 40.000 0.00 0.00 0.00 2.66
5986 6493 4.986659 GTGTTGTTGTCCGTCTATACAGTT 59.013 41.667 0.00 0.00 0.00 3.16
5987 6494 4.553323 GTGTTGTTGTCCGTCTATACAGT 58.447 43.478 0.00 0.00 0.00 3.55
5988 6495 3.606777 CGTGTTGTTGTCCGTCTATACAG 59.393 47.826 0.00 0.00 0.00 2.74
5989 6496 3.567530 CGTGTTGTTGTCCGTCTATACA 58.432 45.455 0.00 0.00 0.00 2.29
5990 6497 2.343544 GCGTGTTGTTGTCCGTCTATAC 59.656 50.000 0.00 0.00 0.00 1.47
5991 6498 2.030096 TGCGTGTTGTTGTCCGTCTATA 60.030 45.455 0.00 0.00 0.00 1.31
5992 6499 1.269883 TGCGTGTTGTTGTCCGTCTAT 60.270 47.619 0.00 0.00 0.00 1.98
5993 6500 0.102663 TGCGTGTTGTTGTCCGTCTA 59.897 50.000 0.00 0.00 0.00 2.59
5994 6501 1.151777 CTGCGTGTTGTTGTCCGTCT 61.152 55.000 0.00 0.00 0.00 4.18
5995 6502 1.275657 CTGCGTGTTGTTGTCCGTC 59.724 57.895 0.00 0.00 0.00 4.79
5996 6503 2.177580 CCTGCGTGTTGTTGTCCGT 61.178 57.895 0.00 0.00 0.00 4.69
5997 6504 2.631428 CCTGCGTGTTGTTGTCCG 59.369 61.111 0.00 0.00 0.00 4.79
5998 6505 2.551912 CCCCTGCGTGTTGTTGTCC 61.552 63.158 0.00 0.00 0.00 4.02
5999 6506 3.030652 CCCCTGCGTGTTGTTGTC 58.969 61.111 0.00 0.00 0.00 3.18
6000 6507 3.216292 GCCCCTGCGTGTTGTTGT 61.216 61.111 0.00 0.00 0.00 3.32
6095 6603 0.682209 GTAGCCACAGGGTCCGTAGA 60.682 60.000 0.00 0.00 34.28 2.59
6126 6634 4.410400 GACTCCCCGGGCCAACAG 62.410 72.222 17.73 7.53 0.00 3.16
6183 6691 0.034670 AAGGGCTTGTCTGGCAGATC 60.035 55.000 21.84 14.44 0.00 2.75
6207 6715 2.414058 TACGGCTGCAAACAACATTG 57.586 45.000 0.50 0.00 0.00 2.82
6208 6716 2.862140 GCTTACGGCTGCAAACAACATT 60.862 45.455 0.50 0.00 38.06 2.71
6209 6717 1.335872 GCTTACGGCTGCAAACAACAT 60.336 47.619 0.50 0.00 38.06 2.71
6210 6718 0.030101 GCTTACGGCTGCAAACAACA 59.970 50.000 0.50 0.00 38.06 3.33
6211 6719 2.796227 GCTTACGGCTGCAAACAAC 58.204 52.632 0.50 0.00 38.06 3.32
6221 6729 7.067251 ACCTCTATCATATAGTAAGCTTACGGC 59.933 40.741 26.66 7.63 38.65 5.68
6222 6730 8.399425 CACCTCTATCATATAGTAAGCTTACGG 58.601 40.741 26.66 19.54 38.65 4.02
6223 6731 8.399425 CCACCTCTATCATATAGTAAGCTTACG 58.601 40.741 26.66 14.73 38.65 3.18
6224 6732 8.688151 CCCACCTCTATCATATAGTAAGCTTAC 58.312 40.741 26.04 26.04 0.00 2.34
6225 6733 8.621073 TCCCACCTCTATCATATAGTAAGCTTA 58.379 37.037 0.86 0.86 0.00 3.09
6226 6734 7.479579 TCCCACCTCTATCATATAGTAAGCTT 58.520 38.462 3.48 3.48 0.00 3.74
6227 6735 7.045693 TCCCACCTCTATCATATAGTAAGCT 57.954 40.000 0.00 0.00 0.00 3.74
6228 6736 6.893005 ACTCCCACCTCTATCATATAGTAAGC 59.107 42.308 0.00 0.00 0.00 3.09
6229 6737 9.621629 CTACTCCCACCTCTATCATATAGTAAG 57.378 40.741 0.00 0.00 0.00 2.34
6230 6738 9.347777 TCTACTCCCACCTCTATCATATAGTAA 57.652 37.037 0.00 0.00 0.00 2.24
6231 6739 8.928672 TCTACTCCCACCTCTATCATATAGTA 57.071 38.462 0.00 0.00 0.00 1.82
6232 6740 7.832473 TCTACTCCCACCTCTATCATATAGT 57.168 40.000 0.00 0.00 0.00 2.12
6233 6741 9.535170 TTTTCTACTCCCACCTCTATCATATAG 57.465 37.037 0.00 0.00 0.00 1.31
6235 6743 8.980832 ATTTTCTACTCCCACCTCTATCATAT 57.019 34.615 0.00 0.00 0.00 1.78
6236 6744 7.176865 CGATTTTCTACTCCCACCTCTATCATA 59.823 40.741 0.00 0.00 0.00 2.15
6237 6745 6.015010 CGATTTTCTACTCCCACCTCTATCAT 60.015 42.308 0.00 0.00 0.00 2.45
6238 6746 5.302059 CGATTTTCTACTCCCACCTCTATCA 59.698 44.000 0.00 0.00 0.00 2.15
6239 6747 5.535406 TCGATTTTCTACTCCCACCTCTATC 59.465 44.000 0.00 0.00 0.00 2.08
6240 6748 5.455872 TCGATTTTCTACTCCCACCTCTAT 58.544 41.667 0.00 0.00 0.00 1.98
6241 6749 4.863548 TCGATTTTCTACTCCCACCTCTA 58.136 43.478 0.00 0.00 0.00 2.43
6242 6750 3.709587 TCGATTTTCTACTCCCACCTCT 58.290 45.455 0.00 0.00 0.00 3.69
6243 6751 4.099573 TCATCGATTTTCTACTCCCACCTC 59.900 45.833 0.00 0.00 0.00 3.85
6244 6752 4.030913 TCATCGATTTTCTACTCCCACCT 58.969 43.478 0.00 0.00 0.00 4.00
6245 6753 4.402056 TCATCGATTTTCTACTCCCACC 57.598 45.455 0.00 0.00 0.00 4.61
6246 6754 5.601662 TGATCATCGATTTTCTACTCCCAC 58.398 41.667 0.00 0.00 0.00 4.61
6247 6755 5.740224 GCTGATCATCGATTTTCTACTCCCA 60.740 44.000 0.00 0.00 0.00 4.37
6248 6756 4.688413 GCTGATCATCGATTTTCTACTCCC 59.312 45.833 0.00 0.00 0.00 4.30
6249 6757 4.688413 GGCTGATCATCGATTTTCTACTCC 59.312 45.833 0.00 0.00 0.00 3.85
6250 6758 4.384247 CGGCTGATCATCGATTTTCTACTC 59.616 45.833 11.66 0.00 0.00 2.59
6251 6759 4.038042 TCGGCTGATCATCGATTTTCTACT 59.962 41.667 14.64 0.00 0.00 2.57
6252 6760 4.299155 TCGGCTGATCATCGATTTTCTAC 58.701 43.478 14.64 0.00 0.00 2.59
6253 6761 4.584327 TCGGCTGATCATCGATTTTCTA 57.416 40.909 14.64 0.00 0.00 2.10
6254 6762 3.459232 TCGGCTGATCATCGATTTTCT 57.541 42.857 14.64 0.00 0.00 2.52
6255 6763 3.120408 CCATCGGCTGATCATCGATTTTC 60.120 47.826 23.03 0.00 40.99 2.29
6256 6764 2.810274 CCATCGGCTGATCATCGATTTT 59.190 45.455 23.03 8.58 40.99 1.82
6257 6765 2.420642 CCATCGGCTGATCATCGATTT 58.579 47.619 23.03 9.12 40.99 2.17
6258 6766 1.943046 GCCATCGGCTGATCATCGATT 60.943 52.381 23.03 11.70 46.69 3.34
6259 6767 0.390866 GCCATCGGCTGATCATCGAT 60.391 55.000 21.08 21.08 46.69 3.59
6260 6768 1.005748 GCCATCGGCTGATCATCGA 60.006 57.895 19.01 19.01 46.69 3.59
6281 6789 1.405463 GGCATGGAAAACTCGAATCCC 59.595 52.381 0.00 0.00 32.01 3.85
6284 6792 0.451783 GCGGCATGGAAAACTCGAAT 59.548 50.000 0.00 0.00 0.00 3.34
6294 6802 2.268920 GTGGAGAAGCGGCATGGA 59.731 61.111 1.45 0.00 0.00 3.41
6297 6805 1.153086 GATGGTGGAGAAGCGGCAT 60.153 57.895 1.45 0.00 0.00 4.40
6303 6811 1.611673 GGTGTGGTGATGGTGGAGAAG 60.612 57.143 0.00 0.00 0.00 2.85
6313 6821 3.149196 GTTGATGTTCTGGTGTGGTGAT 58.851 45.455 0.00 0.00 0.00 3.06
6347 6855 1.081175 CGACGAAGCTGAGAGTGCA 60.081 57.895 0.00 0.00 0.00 4.57
6422 6931 3.199946 CAGTGCTAAATAAGTCCTCCCCA 59.800 47.826 0.00 0.00 0.00 4.96
6430 6939 3.081804 GTGGTGGCAGTGCTAAATAAGT 58.918 45.455 16.11 0.00 0.00 2.24
6441 6950 1.494960 ATGTTTTTGGTGGTGGCAGT 58.505 45.000 0.00 0.00 0.00 4.40
6483 6992 1.686741 GGGAGGTGGAATCTCGTCTCT 60.687 57.143 0.00 0.00 32.34 3.10
6490 6999 2.003548 GGGCAGGGAGGTGGAATCT 61.004 63.158 0.00 0.00 0.00 2.40
6553 7062 2.974041 TATGCAACCCCGTCACCCC 61.974 63.158 0.00 0.00 0.00 4.95
6557 7066 3.167189 CATGTATGCAACCCCGTCA 57.833 52.632 0.00 0.00 0.00 4.35
6596 7105 0.387929 TGCTGGTTTCGTCTCGAGTT 59.612 50.000 13.13 0.00 37.14 3.01
6604 7113 1.143183 ACGTCACTGCTGGTTTCGT 59.857 52.632 0.00 0.00 32.74 3.85
6627 7136 3.365265 CTCTGTTTGCCCCACCGC 61.365 66.667 0.00 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.