Multiple sequence alignment - TraesCS2A01G554900

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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 TraesCS2A01G554900 chr2A 100.000 3144 0 0 1 3144 759734819 759731676 0.000000e+00 5806
1 TraesCS2A01G554900 chr2D 90.142 2252 150 35 782 3011 632083517 632081316 0.000000e+00 2863
2 TraesCS2A01G554900 chr2D 86.129 310 30 9 147 453 632085333 632085034 3.910000e-84 322
3 TraesCS2A01G554900 chr2D 84.127 252 23 3 504 743 632083763 632083517 8.770000e-56 228
4 TraesCS2A01G554900 chr2B 86.436 2691 187 85 516 3144 775495282 775492708 0.000000e+00 2784
5 TraesCS2A01G554900 chr2B 80.635 315 38 11 83 392 775496538 775496242 4.080000e-54 222
6 TraesCS2A01G554900 chr3B 81.138 668 59 29 2506 3140 776905700 776906333 1.020000e-129 473
7 TraesCS2A01G554900 chr3B 81.016 669 58 28 2506 3140 776887743 776888376 4.750000e-128 468
8 TraesCS2A01G554900 chr3B 81.875 160 18 9 2506 2658 28922976 28923131 1.180000e-24 124
9 TraesCS2A01G554900 chr4B 80.328 671 64 28 2506 3140 656073057 656073695 2.220000e-121 446
10 TraesCS2A01G554900 chr4A 82.667 525 46 17 2506 2994 661833963 661834478 1.040000e-114 424
11 TraesCS2A01G554900 chr7B 86.471 340 28 10 2509 2833 152914353 152914017 1.070000e-94 357
12 TraesCS2A01G554900 chr7B 88.152 211 15 6 2943 3144 265946433 265946642 3.130000e-60 243
13 TraesCS2A01G554900 chr7B 80.168 358 38 11 2506 2833 65395266 65395620 1.460000e-58 237
14 TraesCS2A01G554900 chr3D 92.233 206 12 1 2943 3144 385610015 385610220 3.970000e-74 289
15 TraesCS2A01G554900 chr7D 91.748 206 13 1 2943 3144 335465995 335466200 1.850000e-72 283
16 TraesCS2A01G554900 chr5D 91.346 208 11 2 2943 3144 425528287 425528081 8.590000e-71 278
17 TraesCS2A01G554900 chr6D 89.904 208 15 1 2943 3144 19061961 19062168 2.400000e-66 263
18 TraesCS2A01G554900 chr4D 95.395 152 7 0 2943 3094 492075374 492075223 3.130000e-60 243
19 TraesCS2A01G554900 chr7A 92.763 152 10 1 2943 3094 689138573 689138723 5.280000e-53 219
20 TraesCS2A01G554900 chr7A 91.447 152 12 1 2943 3094 234254991 234255141 1.140000e-49 207
21 TraesCS2A01G554900 chr1B 92.105 152 9 2 2943 3094 520949695 520949843 8.830000e-51 211


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 TraesCS2A01G554900 chr2A 759731676 759734819 3143 True 5806.000000 5806 100.000000 1 3144 1 chr2A.!!$R1 3143
1 TraesCS2A01G554900 chr2D 632081316 632085333 4017 True 1137.666667 2863 86.799333 147 3011 3 chr2D.!!$R1 2864
2 TraesCS2A01G554900 chr2B 775492708 775496538 3830 True 1503.000000 2784 83.535500 83 3144 2 chr2B.!!$R1 3061
3 TraesCS2A01G554900 chr3B 776905700 776906333 633 False 473.000000 473 81.138000 2506 3140 1 chr3B.!!$F3 634
4 TraesCS2A01G554900 chr3B 776887743 776888376 633 False 468.000000 468 81.016000 2506 3140 1 chr3B.!!$F2 634
5 TraesCS2A01G554900 chr4B 656073057 656073695 638 False 446.000000 446 80.328000 2506 3140 1 chr4B.!!$F1 634
6 TraesCS2A01G554900 chr4A 661833963 661834478 515 False 424.000000 424 82.667000 2506 2994 1 chr4A.!!$F1 488

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
71 72 0.040067 GCTTGTGAAAACCTGGCTCG 60.040 55.0 0.00 0.00 0.00 5.03 F
729 1982 0.040425 AGCGCACAACCACGAATTTC 60.040 50.0 11.47 0.00 0.00 2.17 F
870 2129 0.307146 CCCGACCTTATCTCGACGTC 59.693 60.0 5.18 5.18 32.65 4.34 F
2108 3399 0.633921 CCAATAATCCCACCCACCCA 59.366 55.0 0.00 0.00 0.00 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1122 2386 0.319727 GCTGGATCGAGCTGATGGAG 60.320 60.0 21.18 0.0 37.47 3.86 R
2107 3398 0.040942 TTTGGGGATGATGGTGGGTG 59.959 55.0 0.00 0.0 0.00 4.61 R
2119 3410 0.192064 TTGGCTTGGGATTTTGGGGA 59.808 50.0 0.00 0.0 0.00 4.81 R
3105 4478 0.038892 CCATGTGGCAGCAACAGTTC 60.039 55.0 9.00 0.0 0.00 3.01 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
18 19 3.482765 CTTTTACGTTTTGGGGGCG 57.517 52.632 0.00 0.00 0.00 6.13
19 20 0.953003 CTTTTACGTTTTGGGGGCGA 59.047 50.000 0.00 0.00 0.00 5.54
20 21 0.953003 TTTTACGTTTTGGGGGCGAG 59.047 50.000 0.00 0.00 0.00 5.03
21 22 1.517210 TTTACGTTTTGGGGGCGAGC 61.517 55.000 0.00 0.00 0.00 5.03
22 23 2.400269 TTACGTTTTGGGGGCGAGCT 62.400 55.000 0.00 0.00 0.00 4.09
23 24 2.791501 TACGTTTTGGGGGCGAGCTC 62.792 60.000 2.73 2.73 0.00 4.09
24 25 3.431725 GTTTTGGGGGCGAGCTCG 61.432 66.667 31.37 31.37 43.27 5.03
25 26 4.715523 TTTTGGGGGCGAGCTCGG 62.716 66.667 35.10 18.35 40.23 4.63
34 35 4.767255 CGAGCTCGGCTTGGGCTT 62.767 66.667 28.40 0.00 39.88 4.35
35 36 3.130160 GAGCTCGGCTTGGGCTTG 61.130 66.667 0.00 0.00 39.88 4.01
36 37 4.729918 AGCTCGGCTTGGGCTTGG 62.730 66.667 0.00 0.00 33.89 3.61
38 39 4.729918 CTCGGCTTGGGCTTGGCT 62.730 66.667 0.00 0.00 38.73 4.75
39 40 4.284550 TCGGCTTGGGCTTGGCTT 62.285 61.111 0.00 0.00 38.73 4.35
40 41 3.305516 CGGCTTGGGCTTGGCTTT 61.306 61.111 0.00 0.00 38.73 3.51
41 42 2.871253 CGGCTTGGGCTTGGCTTTT 61.871 57.895 0.00 0.00 38.73 2.27
42 43 1.531739 CGGCTTGGGCTTGGCTTTTA 61.532 55.000 0.00 0.00 38.73 1.52
43 44 0.904649 GGCTTGGGCTTGGCTTTTAT 59.095 50.000 0.00 0.00 38.73 1.40
44 45 2.107366 GGCTTGGGCTTGGCTTTTATA 58.893 47.619 0.00 0.00 38.73 0.98
45 46 2.101415 GGCTTGGGCTTGGCTTTTATAG 59.899 50.000 0.00 0.00 38.73 1.31
46 47 2.101415 GCTTGGGCTTGGCTTTTATAGG 59.899 50.000 0.00 0.00 35.22 2.57
47 48 2.452600 TGGGCTTGGCTTTTATAGGG 57.547 50.000 0.00 0.00 0.00 3.53
48 49 1.040646 GGGCTTGGCTTTTATAGGGC 58.959 55.000 0.00 0.00 0.00 5.19
49 50 1.040646 GGCTTGGCTTTTATAGGGCC 58.959 55.000 0.00 0.00 45.45 5.80
52 53 4.494515 GGCTTTTATAGGGCCGGG 57.505 61.111 2.18 0.00 36.37 5.73
53 54 1.901948 GGCTTTTATAGGGCCGGGC 60.902 63.158 22.00 22.00 36.37 6.13
54 55 1.150764 GCTTTTATAGGGCCGGGCT 59.849 57.895 28.80 16.07 0.00 5.19
55 56 0.467474 GCTTTTATAGGGCCGGGCTT 60.467 55.000 28.80 23.94 0.00 4.35
56 57 1.318576 CTTTTATAGGGCCGGGCTTG 58.681 55.000 28.80 2.89 0.00 4.01
57 58 0.626916 TTTTATAGGGCCGGGCTTGT 59.373 50.000 28.80 21.50 0.00 3.16
58 59 0.106918 TTTATAGGGCCGGGCTTGTG 60.107 55.000 28.80 0.00 0.00 3.33
59 60 0.983905 TTATAGGGCCGGGCTTGTGA 60.984 55.000 28.80 13.03 0.00 3.58
60 61 0.983905 TATAGGGCCGGGCTTGTGAA 60.984 55.000 28.80 5.20 0.00 3.18
61 62 1.858739 ATAGGGCCGGGCTTGTGAAA 61.859 55.000 28.80 4.76 0.00 2.69
62 63 2.070399 TAGGGCCGGGCTTGTGAAAA 62.070 55.000 28.80 0.00 0.00 2.29
63 64 2.338620 GGCCGGGCTTGTGAAAAC 59.661 61.111 22.87 0.00 0.00 2.43
64 65 2.338620 GCCGGGCTTGTGAAAACC 59.661 61.111 12.87 0.00 0.00 3.27
65 66 2.200337 GCCGGGCTTGTGAAAACCT 61.200 57.895 12.87 0.00 0.00 3.50
66 67 1.659794 CCGGGCTTGTGAAAACCTG 59.340 57.895 0.00 0.00 0.00 4.00
67 68 1.659794 CGGGCTTGTGAAAACCTGG 59.340 57.895 0.00 0.00 0.00 4.45
68 69 1.367471 GGGCTTGTGAAAACCTGGC 59.633 57.895 0.00 0.00 0.00 4.85
69 70 1.115326 GGGCTTGTGAAAACCTGGCT 61.115 55.000 0.00 0.00 0.00 4.75
70 71 0.315251 GGCTTGTGAAAACCTGGCTC 59.685 55.000 0.00 0.00 0.00 4.70
71 72 0.040067 GCTTGTGAAAACCTGGCTCG 60.040 55.000 0.00 0.00 0.00 5.03
72 73 0.593128 CTTGTGAAAACCTGGCTCGG 59.407 55.000 0.00 0.00 0.00 4.63
73 74 0.181587 TTGTGAAAACCTGGCTCGGA 59.818 50.000 0.00 0.00 0.00 4.55
74 75 0.181587 TGTGAAAACCTGGCTCGGAA 59.818 50.000 0.00 0.00 0.00 4.30
75 76 1.314730 GTGAAAACCTGGCTCGGAAA 58.685 50.000 0.00 0.00 0.00 3.13
76 77 1.679153 GTGAAAACCTGGCTCGGAAAA 59.321 47.619 0.00 0.00 0.00 2.29
77 78 2.296190 GTGAAAACCTGGCTCGGAAAAT 59.704 45.455 0.00 0.00 0.00 1.82
78 79 3.504520 GTGAAAACCTGGCTCGGAAAATA 59.495 43.478 0.00 0.00 0.00 1.40
79 80 3.504520 TGAAAACCTGGCTCGGAAAATAC 59.495 43.478 0.00 0.00 0.00 1.89
80 81 2.124277 AACCTGGCTCGGAAAATACC 57.876 50.000 0.00 0.00 0.00 2.73
81 82 0.255033 ACCTGGCTCGGAAAATACCC 59.745 55.000 0.00 0.00 0.00 3.69
97 98 8.343366 GGAAAATACCCGTCTAATTTGAAGATC 58.657 37.037 4.57 0.00 0.00 2.75
100 101 9.543783 AAATACCCGTCTAATTTGAAGATCTAC 57.456 33.333 0.00 0.00 0.00 2.59
128 129 4.322057 AAGTCTTGGGCTCAACCATATT 57.678 40.909 0.00 0.00 40.91 1.28
130 131 4.677182 AGTCTTGGGCTCAACCATATTTT 58.323 39.130 0.00 0.00 40.91 1.82
131 132 4.706962 AGTCTTGGGCTCAACCATATTTTC 59.293 41.667 0.00 0.00 40.91 2.29
132 133 4.706962 GTCTTGGGCTCAACCATATTTTCT 59.293 41.667 0.00 0.00 40.91 2.52
133 134 5.885912 GTCTTGGGCTCAACCATATTTTCTA 59.114 40.000 0.00 0.00 40.91 2.10
134 135 6.038714 GTCTTGGGCTCAACCATATTTTCTAG 59.961 42.308 0.00 0.00 40.91 2.43
135 136 5.708736 TGGGCTCAACCATATTTTCTAGA 57.291 39.130 0.00 0.00 42.05 2.43
136 137 6.073447 TGGGCTCAACCATATTTTCTAGAA 57.927 37.500 0.00 0.00 42.05 2.10
137 138 6.489603 TGGGCTCAACCATATTTTCTAGAAA 58.510 36.000 13.99 13.99 42.05 2.52
138 139 6.951198 TGGGCTCAACCATATTTTCTAGAAAA 59.049 34.615 28.07 28.07 41.55 2.29
139 140 7.619302 TGGGCTCAACCATATTTTCTAGAAAAT 59.381 33.333 34.31 34.31 45.30 1.82
140 141 9.131791 GGGCTCAACCATATTTTCTAGAAAATA 57.868 33.333 35.69 35.69 43.44 1.40
188 189 7.691213 TGTGGTCTATTTGGTACATAGGAAAA 58.309 34.615 0.00 0.00 39.30 2.29
234 235 4.177783 GTTGGAAGTTTTCTTTTGGCGAA 58.822 39.130 0.00 0.00 40.61 4.70
280 281 5.805728 ACGAATGGAGTAGAGGAAAAACAT 58.194 37.500 0.00 0.00 0.00 2.71
283 284 6.480320 CGAATGGAGTAGAGGAAAAACATAGG 59.520 42.308 0.00 0.00 0.00 2.57
284 285 7.510675 AATGGAGTAGAGGAAAAACATAGGA 57.489 36.000 0.00 0.00 0.00 2.94
285 286 7.698163 ATGGAGTAGAGGAAAAACATAGGAT 57.302 36.000 0.00 0.00 0.00 3.24
321 322 7.887996 ATTCGCATTTGAAACAATAACACAT 57.112 28.000 0.00 0.00 0.00 3.21
375 378 6.867816 TCTTAGAAATACTACGCACGGAAAAA 59.132 34.615 0.00 0.00 0.00 1.94
400 403 9.495572 AAAAGACTGGTATCTTTAGTTTCAGAG 57.504 33.333 1.41 0.00 46.02 3.35
439 443 4.634199 AGATTCATGTGTTTTGCCTTTGG 58.366 39.130 0.00 0.00 0.00 3.28
453 457 9.051679 GTTTTGCCTTTGGTTTGACTATATTTT 57.948 29.630 0.00 0.00 0.00 1.82
454 458 8.600449 TTTGCCTTTGGTTTGACTATATTTTG 57.400 30.769 0.00 0.00 0.00 2.44
455 459 6.162777 TGCCTTTGGTTTGACTATATTTTGC 58.837 36.000 0.00 0.00 0.00 3.68
456 460 5.580691 GCCTTTGGTTTGACTATATTTTGCC 59.419 40.000 0.00 0.00 0.00 4.52
457 461 6.574269 GCCTTTGGTTTGACTATATTTTGCCT 60.574 38.462 0.00 0.00 0.00 4.75
458 462 7.386059 CCTTTGGTTTGACTATATTTTGCCTT 58.614 34.615 0.00 0.00 0.00 4.35
459 463 7.877612 CCTTTGGTTTGACTATATTTTGCCTTT 59.122 33.333 0.00 0.00 0.00 3.11
460 464 8.600449 TTTGGTTTGACTATATTTTGCCTTTG 57.400 30.769 0.00 0.00 0.00 2.77
461 465 6.696411 TGGTTTGACTATATTTTGCCTTTGG 58.304 36.000 0.00 0.00 0.00 3.28
462 466 6.268847 TGGTTTGACTATATTTTGCCTTTGGT 59.731 34.615 0.00 0.00 0.00 3.67
466 470 7.531857 TGACTATATTTTGCCTTTGGTTTGA 57.468 32.000 0.00 0.00 0.00 2.69
467 471 7.375053 TGACTATATTTTGCCTTTGGTTTGAC 58.625 34.615 0.00 0.00 0.00 3.18
469 473 8.644374 ACTATATTTTGCCTTTGGTTTGACTA 57.356 30.769 0.00 0.00 0.00 2.59
480 490 9.313118 GCCTTTGGTTTGACTATATTTATTTGG 57.687 33.333 0.00 0.00 0.00 3.28
509 1747 7.095695 ACATAGGATTTTTGAAATGTACCGG 57.904 36.000 0.00 0.00 0.00 5.28
514 1752 5.047590 GGATTTTTGAAATGTACCGGACCTT 60.048 40.000 9.46 0.00 0.00 3.50
552 1793 3.228453 AGATCCAATCATGCATGGGAAC 58.772 45.455 25.97 20.99 37.31 3.62
601 1851 1.795162 GCACAACTGCATATTGCCGAC 60.795 52.381 10.05 0.00 44.23 4.79
610 1860 4.782156 TGCATATTGCCGACGATATTTTG 58.218 39.130 0.00 0.00 44.23 2.44
639 1889 5.887598 TCTGATTTGATCTATTTGGTGGTGG 59.112 40.000 0.00 0.00 0.00 4.61
661 1914 1.004394 GTGGTAGGGTTTCCAGGGAAG 59.996 57.143 0.42 0.00 35.38 3.46
662 1915 0.624254 GGTAGGGTTTCCAGGGAAGG 59.376 60.000 0.42 0.00 35.38 3.46
663 1916 0.624254 GTAGGGTTTCCAGGGAAGGG 59.376 60.000 0.42 0.00 35.38 3.95
664 1917 0.499147 TAGGGTTTCCAGGGAAGGGA 59.501 55.000 0.42 0.00 35.38 4.20
665 1918 0.404346 AGGGTTTCCAGGGAAGGGAA 60.404 55.000 0.42 0.00 42.49 3.97
729 1982 0.040425 AGCGCACAACCACGAATTTC 60.040 50.000 11.47 0.00 0.00 2.17
732 1985 2.307049 CGCACAACCACGAATTTCTTC 58.693 47.619 0.00 0.00 0.00 2.87
755 2008 1.396996 CAGTAACCGCATTTTCTCCCG 59.603 52.381 0.00 0.00 0.00 5.14
757 2010 1.664151 GTAACCGCATTTTCTCCCGAG 59.336 52.381 0.00 0.00 0.00 4.63
762 2015 1.659098 CGCATTTTCTCCCGAGTGTAC 59.341 52.381 0.00 0.00 0.00 2.90
763 2016 1.659098 GCATTTTCTCCCGAGTGTACG 59.341 52.381 0.00 0.00 0.00 3.67
777 2030 0.735978 TGTACGCGGCAAGACATCTG 60.736 55.000 12.47 0.00 0.00 2.90
790 2043 2.762887 AGACATCTGAATCCGAAGCTCA 59.237 45.455 0.00 0.00 0.00 4.26
795 2048 0.824109 TGAATCCGAAGCTCATCCGT 59.176 50.000 0.00 0.00 0.00 4.69
804 2057 2.550830 AGCTCATCCGTTCAAAGTGT 57.449 45.000 0.00 0.00 0.00 3.55
806 2059 4.002906 AGCTCATCCGTTCAAAGTGTTA 57.997 40.909 0.00 0.00 0.00 2.41
864 2123 3.878160 GGATGATCCCGACCTTATCTC 57.122 52.381 0.00 0.00 0.00 2.75
865 2124 2.164624 GGATGATCCCGACCTTATCTCG 59.835 54.545 0.00 0.00 0.00 4.04
867 2126 2.228059 TGATCCCGACCTTATCTCGAC 58.772 52.381 0.00 0.00 32.65 4.20
870 2129 0.307146 CCCGACCTTATCTCGACGTC 59.693 60.000 5.18 5.18 32.65 4.34
875 2134 2.422832 GACCTTATCTCGACGTCAACCT 59.577 50.000 17.16 0.00 0.00 3.50
885 2144 2.091588 CGACGTCAACCTCCAAATTACG 59.908 50.000 17.16 0.00 35.17 3.18
888 2147 2.786777 GTCAACCTCCAAATTACGGGT 58.213 47.619 0.00 0.00 0.00 5.28
905 2164 7.527568 TTACGGGTGTAATTTTCTTCCAAAT 57.472 32.000 0.00 0.00 35.67 2.32
928 2187 1.621301 CCCTGATCGCGATCGCATTC 61.621 60.000 36.05 29.89 40.63 2.67
995 2254 0.818040 AAAATATGGTCGCCGCCCTC 60.818 55.000 0.00 0.00 0.00 4.30
1072 2332 4.087892 CTCTGCCCACCACCTCCG 62.088 72.222 0.00 0.00 0.00 4.63
1100 2364 4.200283 CTCGCCGCTCCACTCCTC 62.200 72.222 0.00 0.00 0.00 3.71
1127 2391 4.162690 GCCGTCGGGAAGCTCCAT 62.163 66.667 14.38 0.00 38.64 3.41
1146 2410 3.465403 AGCTCGATCCAGCGGCTT 61.465 61.111 6.68 0.00 44.82 4.35
1148 2412 2.496341 CTCGATCCAGCGGCTTGA 59.504 61.111 6.21 6.21 0.00 3.02
1423 2690 4.722700 CACAAGGACCCCTGGGCG 62.723 72.222 7.39 3.20 39.32 6.13
1636 2906 1.304217 GGTCGTCTCCCCTGTCTCA 60.304 63.158 0.00 0.00 0.00 3.27
1638 2908 1.187087 GTCGTCTCCCCTGTCTCATT 58.813 55.000 0.00 0.00 0.00 2.57
1855 3137 3.400590 GCCGACGACAACCACGAC 61.401 66.667 0.00 0.00 34.70 4.34
1856 3138 3.095278 CCGACGACAACCACGACG 61.095 66.667 0.00 0.00 44.67 5.12
1857 3139 3.095278 CGACGACAACCACGACGG 61.095 66.667 0.00 0.00 42.50 4.79
1858 3140 3.400590 GACGACAACCACGACGGC 61.401 66.667 0.00 0.00 39.03 5.68
1915 3206 1.011463 CATCATGCAGAAGACGCGC 60.011 57.895 5.73 0.00 0.00 6.86
2094 3385 2.124901 CTTCGGCCGGCACCAATA 60.125 61.111 30.85 0.00 0.00 1.90
2098 3389 2.551912 CGGCCGGCACCAATAATCC 61.552 63.158 30.85 5.23 0.00 3.01
2106 3397 1.775385 CACCAATAATCCCACCCACC 58.225 55.000 0.00 0.00 0.00 4.61
2107 3398 0.634465 ACCAATAATCCCACCCACCC 59.366 55.000 0.00 0.00 0.00 4.61
2108 3399 0.633921 CCAATAATCCCACCCACCCA 59.366 55.000 0.00 0.00 0.00 4.51
2109 3400 1.687996 CCAATAATCCCACCCACCCAC 60.688 57.143 0.00 0.00 0.00 4.61
2119 3410 2.625460 CCCACCCACCCACCATCAT 61.625 63.158 0.00 0.00 0.00 2.45
2123 3414 2.603008 CCACCCACCATCATCCCC 59.397 66.667 0.00 0.00 0.00 4.81
2134 3425 2.701951 CCATCATCCCCAAAATCCCAAG 59.298 50.000 0.00 0.00 0.00 3.61
2147 3438 2.619697 TCCCAAGCCAATCCAAATCA 57.380 45.000 0.00 0.00 0.00 2.57
2151 3443 4.103785 TCCCAAGCCAATCCAAATCAAAAA 59.896 37.500 0.00 0.00 0.00 1.94
2160 3452 6.402442 CCAATCCAAATCAAAAATTTCTCGGC 60.402 38.462 0.00 0.00 0.00 5.54
2207 3511 9.516546 TTAAATTAGTCTTTCTTCTTCCCTTCC 57.483 33.333 0.00 0.00 0.00 3.46
2221 3525 1.488705 CCTTCCTGGTGTGCCCTGTA 61.489 60.000 0.00 0.00 0.00 2.74
2225 3529 2.524640 TGGTGTGCCCTGTACCGA 60.525 61.111 0.00 0.00 37.29 4.69
2240 3544 4.637489 CGATCGCCGGAGCAGAGG 62.637 72.222 5.05 0.00 39.83 3.69
2389 3694 1.655484 AAAGTTGGTTGCTTGCTTGC 58.345 45.000 0.00 0.00 0.00 4.01
2393 3698 0.822811 TTGGTTGCTTGCTTGCTTGA 59.177 45.000 3.47 0.00 0.00 3.02
2395 3700 1.413445 TGGTTGCTTGCTTGCTTGATT 59.587 42.857 3.47 0.00 0.00 2.57
2396 3701 1.796459 GGTTGCTTGCTTGCTTGATTG 59.204 47.619 3.47 0.00 0.00 2.67
2397 3702 1.193874 GTTGCTTGCTTGCTTGATTGC 59.806 47.619 3.47 0.00 0.00 3.56
2398 3703 0.320073 TGCTTGCTTGCTTGATTGCC 60.320 50.000 3.47 0.00 0.00 4.52
2436 3741 0.880278 GAGTGAGTTGTCGCTTGCCA 60.880 55.000 0.00 0.00 43.89 4.92
2442 3747 0.380378 GTTGTCGCTTGCCACTTTGA 59.620 50.000 0.00 0.00 0.00 2.69
2554 3868 3.053826 ACCACTTAAGTTGGACCCTTCT 58.946 45.455 22.90 4.18 0.00 2.85
2555 3869 4.237018 ACCACTTAAGTTGGACCCTTCTA 58.763 43.478 22.90 0.00 0.00 2.10
2556 3870 4.041321 ACCACTTAAGTTGGACCCTTCTAC 59.959 45.833 22.90 0.00 0.00 2.59
2557 3871 4.286291 CCACTTAAGTTGGACCCTTCTACT 59.714 45.833 5.07 0.00 0.00 2.57
2558 3872 5.221864 CCACTTAAGTTGGACCCTTCTACTT 60.222 44.000 5.07 0.00 33.76 2.24
2559 3873 5.932883 CACTTAAGTTGGACCCTTCTACTTC 59.067 44.000 5.07 0.00 32.45 3.01
2560 3874 5.845065 ACTTAAGTTGGACCCTTCTACTTCT 59.155 40.000 1.12 0.00 32.45 2.85
2561 3875 6.329460 ACTTAAGTTGGACCCTTCTACTTCTT 59.671 38.462 1.12 0.00 32.45 2.52
2562 3876 4.893829 AGTTGGACCCTTCTACTTCTTC 57.106 45.455 0.00 0.00 0.00 2.87
2572 3886 5.105106 CCCTTCTACTTCTTCTTCTTCCTCC 60.105 48.000 0.00 0.00 0.00 4.30
2573 3887 5.393678 CCTTCTACTTCTTCTTCTTCCTCCG 60.394 48.000 0.00 0.00 0.00 4.63
2583 3897 0.902531 TCTTCCTCCGTCCATCCAAC 59.097 55.000 0.00 0.00 0.00 3.77
2585 3899 1.003118 CTTCCTCCGTCCATCCAACAA 59.997 52.381 0.00 0.00 0.00 2.83
2586 3900 1.285280 TCCTCCGTCCATCCAACAAT 58.715 50.000 0.00 0.00 0.00 2.71
2592 3906 3.141398 CCGTCCATCCAACAATGATAGG 58.859 50.000 0.00 0.00 0.00 2.57
2636 3963 8.422973 TTGTTGGTGAATTTCTGAAATTTCTG 57.577 30.769 24.57 17.57 40.97 3.02
2652 3982 6.718454 AATTTCTGTCAGAATCTTCAGTCG 57.282 37.500 15.95 0.00 33.67 4.18
2658 3988 4.039245 TGTCAGAATCTTCAGTCGGAAAGT 59.961 41.667 0.00 0.00 34.44 2.66
2661 3991 4.387256 CAGAATCTTCAGTCGGAAAGTGTC 59.613 45.833 0.00 0.00 34.44 3.67
2802 4158 3.743521 TGTGAAGGTTCTGGATGTTCTG 58.256 45.455 0.00 0.00 0.00 3.02
2809 4165 3.117738 GGTTCTGGATGTTCTGGATGGAT 60.118 47.826 0.00 0.00 0.00 3.41
2860 4216 3.554785 GGCTGGAGATGATCCTGACCTT 61.555 54.545 5.11 0.00 46.92 3.50
2907 4272 1.612950 TGGTGCATGCTTGGTTGTTAG 59.387 47.619 20.33 0.00 0.00 2.34
2908 4273 1.067635 GGTGCATGCTTGGTTGTTAGG 60.068 52.381 20.33 0.00 0.00 2.69
2909 4274 1.613437 GTGCATGCTTGGTTGTTAGGT 59.387 47.619 20.33 0.00 0.00 3.08
2910 4275 2.035832 GTGCATGCTTGGTTGTTAGGTT 59.964 45.455 20.33 0.00 0.00 3.50
2911 4276 3.254657 GTGCATGCTTGGTTGTTAGGTTA 59.745 43.478 20.33 0.00 0.00 2.85
2913 4278 4.157656 TGCATGCTTGGTTGTTAGGTTATC 59.842 41.667 20.33 0.00 0.00 1.75
2914 4279 4.399303 GCATGCTTGGTTGTTAGGTTATCT 59.601 41.667 11.37 0.00 0.00 1.98
2915 4280 5.449177 GCATGCTTGGTTGTTAGGTTATCTC 60.449 44.000 11.37 0.00 0.00 2.75
2916 4281 5.499004 TGCTTGGTTGTTAGGTTATCTCT 57.501 39.130 0.00 0.00 0.00 3.10
2917 4282 5.876357 TGCTTGGTTGTTAGGTTATCTCTT 58.124 37.500 0.00 0.00 0.00 2.85
2918 4283 6.303839 TGCTTGGTTGTTAGGTTATCTCTTT 58.696 36.000 0.00 0.00 0.00 2.52
2919 4284 6.206634 TGCTTGGTTGTTAGGTTATCTCTTTG 59.793 38.462 0.00 0.00 0.00 2.77
2920 4285 6.206829 GCTTGGTTGTTAGGTTATCTCTTTGT 59.793 38.462 0.00 0.00 0.00 2.83
2921 4286 7.255486 GCTTGGTTGTTAGGTTATCTCTTTGTT 60.255 37.037 0.00 0.00 0.00 2.83
2944 4309 1.591768 TGGGTGGTTCTATTCCCCTC 58.408 55.000 0.00 0.00 39.20 4.30
2951 4316 2.197465 GTTCTATTCCCCTCTGGTGGT 58.803 52.381 0.00 0.00 34.77 4.16
2952 4317 1.879575 TCTATTCCCCTCTGGTGGTG 58.120 55.000 0.00 0.00 34.77 4.17
2953 4318 0.839946 CTATTCCCCTCTGGTGGTGG 59.160 60.000 0.00 0.00 34.77 4.61
2967 4332 2.439156 GTGGCCTGGACCTGCATC 60.439 66.667 3.32 0.00 0.00 3.91
3004 4373 7.069455 TGCTTTCCATACTACAGCTCTTATACA 59.931 37.037 0.00 0.00 0.00 2.29
3014 4383 9.355916 ACTACAGCTCTTATACAGATTATCACA 57.644 33.333 0.00 0.00 0.00 3.58
3016 4385 8.879342 ACAGCTCTTATACAGATTATCACAAC 57.121 34.615 0.00 0.00 0.00 3.32
3017 4386 8.478066 ACAGCTCTTATACAGATTATCACAACA 58.522 33.333 0.00 0.00 0.00 3.33
3018 4387 8.976471 CAGCTCTTATACAGATTATCACAACAG 58.024 37.037 0.00 0.00 0.00 3.16
3019 4388 8.700051 AGCTCTTATACAGATTATCACAACAGT 58.300 33.333 0.00 0.00 0.00 3.55
3020 4389 8.759641 GCTCTTATACAGATTATCACAACAGTG 58.240 37.037 0.00 0.00 34.56 3.66
3021 4390 8.648557 TCTTATACAGATTATCACAACAGTGC 57.351 34.615 0.00 0.00 33.28 4.40
3022 4391 8.478066 TCTTATACAGATTATCACAACAGTGCT 58.522 33.333 0.00 0.00 33.28 4.40
3023 4392 9.102757 CTTATACAGATTATCACAACAGTGCTT 57.897 33.333 0.00 0.00 33.28 3.91
3024 4393 7.928307 ATACAGATTATCACAACAGTGCTTT 57.072 32.000 0.00 0.00 33.28 3.51
3025 4394 6.639632 ACAGATTATCACAACAGTGCTTTT 57.360 33.333 0.00 0.00 33.28 2.27
3026 4395 7.042797 ACAGATTATCACAACAGTGCTTTTT 57.957 32.000 0.00 0.00 33.28 1.94
3047 4416 5.764487 TTTTATGACATCACAACAGTGCA 57.236 34.783 0.00 0.00 33.28 4.57
3058 4427 4.340666 TCACAACAGTGCAAATTATGGTGT 59.659 37.500 0.00 0.00 44.12 4.16
3063 4432 7.930865 ACAACAGTGCAAATTATGGTGTTAATT 59.069 29.630 0.00 0.00 40.58 1.40
3065 4434 7.665690 ACAGTGCAAATTATGGTGTTAATTCA 58.334 30.769 0.00 0.00 32.05 2.57
3066 4435 8.313292 ACAGTGCAAATTATGGTGTTAATTCAT 58.687 29.630 0.00 0.00 32.05 2.57
3067 4436 9.800433 CAGTGCAAATTATGGTGTTAATTCATA 57.200 29.630 0.00 0.00 32.05 2.15
3075 4444 8.704849 TTATGGTGTTAATTCATAATCCTGGG 57.295 34.615 0.00 0.00 31.03 4.45
3076 4445 5.454062 TGGTGTTAATTCATAATCCTGGGG 58.546 41.667 0.00 0.00 0.00 4.96
3077 4446 4.832823 GGTGTTAATTCATAATCCTGGGGG 59.167 45.833 0.00 0.00 0.00 5.40
3104 4477 2.819608 GGGTGTGTGTGCTTGTGATTAT 59.180 45.455 0.00 0.00 0.00 1.28
3105 4478 3.366273 GGGTGTGTGTGCTTGTGATTATG 60.366 47.826 0.00 0.00 0.00 1.90
3140 4513 2.011947 CATGGTGTGCCTCTGTATGTG 58.988 52.381 0.00 0.00 35.27 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.953003 TCGCCCCCAAAACGTAAAAG 59.047 50.000 0.00 0.00 0.00 2.27
3 4 1.967494 GCTCGCCCCCAAAACGTAA 60.967 57.895 0.00 0.00 0.00 3.18
4 5 2.358984 GCTCGCCCCCAAAACGTA 60.359 61.111 0.00 0.00 0.00 3.57
5 6 4.265056 AGCTCGCCCCCAAAACGT 62.265 61.111 0.00 0.00 0.00 3.99
6 7 3.431725 GAGCTCGCCCCCAAAACG 61.432 66.667 0.00 0.00 0.00 3.60
7 8 3.431725 CGAGCTCGCCCCCAAAAC 61.432 66.667 25.07 0.00 0.00 2.43
8 9 4.715523 CCGAGCTCGCCCCCAAAA 62.716 66.667 30.49 0.00 38.18 2.44
17 18 4.767255 AAGCCCAAGCCGAGCTCG 62.767 66.667 29.06 29.06 38.25 5.03
18 19 3.130160 CAAGCCCAAGCCGAGCTC 61.130 66.667 2.73 2.73 38.25 4.09
19 20 4.729918 CCAAGCCCAAGCCGAGCT 62.730 66.667 0.00 0.00 42.56 4.09
21 22 4.729918 AGCCAAGCCCAAGCCGAG 62.730 66.667 0.00 0.00 41.25 4.63
22 23 3.808218 AAAGCCAAGCCCAAGCCGA 62.808 57.895 0.00 0.00 41.25 5.54
23 24 1.531739 TAAAAGCCAAGCCCAAGCCG 61.532 55.000 0.00 0.00 41.25 5.52
24 25 0.904649 ATAAAAGCCAAGCCCAAGCC 59.095 50.000 0.00 0.00 41.25 4.35
25 26 2.101415 CCTATAAAAGCCAAGCCCAAGC 59.899 50.000 0.00 0.00 40.32 4.01
26 27 2.695147 CCCTATAAAAGCCAAGCCCAAG 59.305 50.000 0.00 0.00 0.00 3.61
27 28 2.745968 CCCTATAAAAGCCAAGCCCAA 58.254 47.619 0.00 0.00 0.00 4.12
28 29 1.687996 GCCCTATAAAAGCCAAGCCCA 60.688 52.381 0.00 0.00 0.00 5.36
29 30 1.040646 GCCCTATAAAAGCCAAGCCC 58.959 55.000 0.00 0.00 0.00 5.19
30 31 1.040646 GGCCCTATAAAAGCCAAGCC 58.959 55.000 0.00 0.00 46.34 4.35
35 36 1.901948 GCCCGGCCCTATAAAAGCC 60.902 63.158 0.00 0.00 43.53 4.35
36 37 0.467474 AAGCCCGGCCCTATAAAAGC 60.467 55.000 5.55 0.00 0.00 3.51
37 38 1.318576 CAAGCCCGGCCCTATAAAAG 58.681 55.000 5.55 0.00 0.00 2.27
38 39 0.626916 ACAAGCCCGGCCCTATAAAA 59.373 50.000 5.55 0.00 0.00 1.52
39 40 0.106918 CACAAGCCCGGCCCTATAAA 60.107 55.000 5.55 0.00 0.00 1.40
40 41 0.983905 TCACAAGCCCGGCCCTATAA 60.984 55.000 5.55 0.00 0.00 0.98
41 42 0.983905 TTCACAAGCCCGGCCCTATA 60.984 55.000 5.55 0.00 0.00 1.31
42 43 1.858739 TTTCACAAGCCCGGCCCTAT 61.859 55.000 5.55 0.00 0.00 2.57
43 44 2.070399 TTTTCACAAGCCCGGCCCTA 62.070 55.000 5.55 0.00 0.00 3.53
44 45 3.444818 TTTTCACAAGCCCGGCCCT 62.445 57.895 5.55 0.00 0.00 5.19
45 46 2.915137 TTTTCACAAGCCCGGCCC 60.915 61.111 5.55 0.00 0.00 5.80
46 47 2.338620 GTTTTCACAAGCCCGGCC 59.661 61.111 5.55 0.00 0.00 6.13
47 48 2.200337 AGGTTTTCACAAGCCCGGC 61.200 57.895 0.00 0.00 33.70 6.13
48 49 1.659794 CAGGTTTTCACAAGCCCGG 59.340 57.895 0.00 0.00 33.70 5.73
49 50 1.659794 CCAGGTTTTCACAAGCCCG 59.340 57.895 0.00 0.00 33.70 6.13
50 51 1.115326 AGCCAGGTTTTCACAAGCCC 61.115 55.000 0.00 0.00 33.70 5.19
51 52 0.315251 GAGCCAGGTTTTCACAAGCC 59.685 55.000 0.00 0.00 33.40 4.35
52 53 0.040067 CGAGCCAGGTTTTCACAAGC 60.040 55.000 0.00 0.00 0.00 4.01
53 54 0.593128 CCGAGCCAGGTTTTCACAAG 59.407 55.000 0.00 0.00 0.00 3.16
54 55 0.181587 TCCGAGCCAGGTTTTCACAA 59.818 50.000 0.00 0.00 0.00 3.33
55 56 0.181587 TTCCGAGCCAGGTTTTCACA 59.818 50.000 0.00 0.00 0.00 3.58
56 57 1.314730 TTTCCGAGCCAGGTTTTCAC 58.685 50.000 0.00 0.00 0.00 3.18
57 58 2.060050 TTTTCCGAGCCAGGTTTTCA 57.940 45.000 0.00 0.00 0.00 2.69
58 59 3.119602 GGTATTTTCCGAGCCAGGTTTTC 60.120 47.826 0.00 0.00 0.00 2.29
59 60 2.823747 GGTATTTTCCGAGCCAGGTTTT 59.176 45.455 0.00 0.00 0.00 2.43
60 61 2.443416 GGTATTTTCCGAGCCAGGTTT 58.557 47.619 0.00 0.00 0.00 3.27
61 62 1.340697 GGGTATTTTCCGAGCCAGGTT 60.341 52.381 0.00 0.00 33.26 3.50
62 63 0.255033 GGGTATTTTCCGAGCCAGGT 59.745 55.000 0.00 0.00 33.26 4.00
63 64 3.095922 GGGTATTTTCCGAGCCAGG 57.904 57.895 0.00 0.00 33.26 4.45
71 72 7.619964 TCTTCAAATTAGACGGGTATTTTCC 57.380 36.000 0.00 0.00 0.00 3.13
72 73 9.110502 AGATCTTCAAATTAGACGGGTATTTTC 57.889 33.333 0.00 0.00 0.00 2.29
74 75 9.543783 GTAGATCTTCAAATTAGACGGGTATTT 57.456 33.333 0.00 0.00 0.00 1.40
75 76 8.148999 GGTAGATCTTCAAATTAGACGGGTATT 58.851 37.037 0.00 0.00 0.00 1.89
76 77 7.509659 AGGTAGATCTTCAAATTAGACGGGTAT 59.490 37.037 0.00 0.00 0.00 2.73
77 78 6.837568 AGGTAGATCTTCAAATTAGACGGGTA 59.162 38.462 0.00 0.00 0.00 3.69
78 79 5.661759 AGGTAGATCTTCAAATTAGACGGGT 59.338 40.000 0.00 0.00 0.00 5.28
79 80 6.163135 AGGTAGATCTTCAAATTAGACGGG 57.837 41.667 0.00 0.00 0.00 5.28
80 81 7.014422 ACCTAGGTAGATCTTCAAATTAGACGG 59.986 40.741 14.41 0.00 0.00 4.79
81 82 7.942990 ACCTAGGTAGATCTTCAAATTAGACG 58.057 38.462 14.41 0.00 0.00 4.18
97 98 3.637694 GAGCCCAAGACTTACCTAGGTAG 59.362 52.174 20.79 16.70 31.71 3.18
100 101 2.467880 TGAGCCCAAGACTTACCTAGG 58.532 52.381 7.41 7.41 0.00 3.02
110 111 4.934356 AGAAAATATGGTTGAGCCCAAGA 58.066 39.130 0.00 0.00 38.20 3.02
139 140 9.729281 ACAAAAATCTAGAAAATAAGACGGGTA 57.271 29.630 0.00 0.00 0.00 3.69
140 141 8.512138 CACAAAAATCTAGAAAATAAGACGGGT 58.488 33.333 0.00 0.00 0.00 5.28
141 142 7.968405 CCACAAAAATCTAGAAAATAAGACGGG 59.032 37.037 0.00 0.00 0.00 5.28
142 143 8.512138 ACCACAAAAATCTAGAAAATAAGACGG 58.488 33.333 0.00 0.00 0.00 4.79
143 144 9.543018 GACCACAAAAATCTAGAAAATAAGACG 57.457 33.333 0.00 0.00 0.00 4.18
234 235 8.310382 TCGTTTAAACCAAATGGATGATCATTT 58.690 29.630 10.14 0.00 45.11 2.32
317 318 8.649841 CCAAGTGCAAAGTAAAATTCATATGTG 58.350 33.333 1.90 0.00 0.00 3.21
321 322 7.232534 AGGTCCAAGTGCAAAGTAAAATTCATA 59.767 33.333 0.00 0.00 0.00 2.15
336 337 3.963428 TCTAAGAAGAGGTCCAAGTGC 57.037 47.619 0.00 0.00 0.00 4.40
375 378 8.871125 TCTCTGAAACTAAAGATACCAGTCTTT 58.129 33.333 7.03 7.03 46.88 2.52
408 412 8.243426 GGCAAAACACATGAATCTACAAATAGA 58.757 33.333 0.00 0.00 41.76 1.98
412 416 6.403866 AGGCAAAACACATGAATCTACAAA 57.596 33.333 0.00 0.00 0.00 2.83
428 432 9.050601 CAAAATATAGTCAAACCAAAGGCAAAA 57.949 29.630 0.00 0.00 0.00 2.44
439 443 8.495148 CAAACCAAAGGCAAAATATAGTCAAAC 58.505 33.333 0.00 0.00 0.00 2.93
453 457 9.868277 CAAATAAATATAGTCAAACCAAAGGCA 57.132 29.630 0.00 0.00 0.00 4.75
454 458 9.313118 CCAAATAAATATAGTCAAACCAAAGGC 57.687 33.333 0.00 0.00 0.00 4.35
483 493 8.032451 CCGGTACATTTCAAAAATCCTATGTTT 58.968 33.333 0.00 0.00 0.00 2.83
486 496 7.193595 GTCCGGTACATTTCAAAAATCCTATG 58.806 38.462 0.00 0.00 0.00 2.23
487 497 6.320418 GGTCCGGTACATTTCAAAAATCCTAT 59.680 38.462 0.00 0.00 0.00 2.57
488 498 5.648960 GGTCCGGTACATTTCAAAAATCCTA 59.351 40.000 0.00 0.00 0.00 2.94
489 499 4.461431 GGTCCGGTACATTTCAAAAATCCT 59.539 41.667 0.00 0.00 0.00 3.24
491 501 5.638596 AGGTCCGGTACATTTCAAAAATC 57.361 39.130 0.00 0.00 0.00 2.17
493 503 5.009210 CAGAAGGTCCGGTACATTTCAAAAA 59.991 40.000 0.00 0.00 30.81 1.94
494 504 4.517453 CAGAAGGTCCGGTACATTTCAAAA 59.483 41.667 0.00 0.00 30.81 2.44
498 508 3.604875 TCAGAAGGTCCGGTACATTTC 57.395 47.619 0.00 6.84 30.81 2.17
502 512 2.614481 GCATTTCAGAAGGTCCGGTACA 60.614 50.000 0.00 0.00 0.00 2.90
509 1747 3.091545 TGGATTGGCATTTCAGAAGGTC 58.908 45.455 0.00 0.00 0.00 3.85
514 1752 3.956199 GGATCTTGGATTGGCATTTCAGA 59.044 43.478 0.00 0.00 0.00 3.27
601 1851 8.504815 AGATCAAATCAGATCAGCAAAATATCG 58.495 33.333 6.70 0.00 45.39 2.92
610 1860 7.361127 CACCAAATAGATCAAATCAGATCAGC 58.639 38.462 6.70 0.00 45.39 4.26
628 1878 1.203001 CCTACCACACCACCACCAAAT 60.203 52.381 0.00 0.00 0.00 2.32
639 1889 0.037734 CCCTGGAAACCCTACCACAC 59.962 60.000 0.00 0.00 32.44 3.82
661 1914 1.859080 GATTACACAGCGTCGATTCCC 59.141 52.381 0.00 0.00 0.00 3.97
662 1915 1.859080 GGATTACACAGCGTCGATTCC 59.141 52.381 0.00 0.00 0.00 3.01
663 1916 1.859080 GGGATTACACAGCGTCGATTC 59.141 52.381 0.00 0.00 0.00 2.52
664 1917 1.801395 CGGGATTACACAGCGTCGATT 60.801 52.381 0.00 0.00 0.00 3.34
665 1918 0.248907 CGGGATTACACAGCGTCGAT 60.249 55.000 0.00 0.00 0.00 3.59
713 1966 2.307049 CGAAGAAATTCGTGGTTGTGC 58.693 47.619 2.35 0.00 39.41 4.57
719 1972 1.156736 ACTGCCGAAGAAATTCGTGG 58.843 50.000 9.27 0.00 42.44 4.94
734 1987 1.132453 GGGAGAAAATGCGGTTACTGC 59.868 52.381 9.54 9.54 0.00 4.40
740 1993 0.673644 CACTCGGGAGAAAATGCGGT 60.674 55.000 2.08 0.00 39.18 5.68
741 1994 0.673644 ACACTCGGGAGAAAATGCGG 60.674 55.000 2.08 0.00 39.18 5.69
743 1996 1.659098 CGTACACTCGGGAGAAAATGC 59.341 52.381 2.08 0.00 39.18 3.56
746 1999 0.387622 CGCGTACACTCGGGAGAAAA 60.388 55.000 0.00 0.00 44.40 2.29
755 2008 0.736325 ATGTCTTGCCGCGTACACTC 60.736 55.000 4.92 0.00 0.00 3.51
757 2010 0.736325 AGATGTCTTGCCGCGTACAC 60.736 55.000 4.92 0.00 0.00 2.90
762 2015 0.302890 GATTCAGATGTCTTGCCGCG 59.697 55.000 0.00 0.00 0.00 6.46
763 2016 0.659957 GGATTCAGATGTCTTGCCGC 59.340 55.000 0.00 0.00 0.00 6.53
777 2030 1.861575 GAACGGATGAGCTTCGGATTC 59.138 52.381 0.00 0.00 0.00 2.52
790 2043 6.149633 GCAGAAATTAACACTTTGAACGGAT 58.850 36.000 0.00 0.00 0.00 4.18
795 2048 6.127196 ACAAGGGCAGAAATTAACACTTTGAA 60.127 34.615 0.00 0.00 0.00 2.69
856 2115 2.223525 GGAGGTTGACGTCGAGATAAGG 60.224 54.545 11.62 0.00 0.00 2.69
864 2123 2.091588 CGTAATTTGGAGGTTGACGTCG 59.908 50.000 11.62 0.00 0.00 5.12
865 2124 2.414138 CCGTAATTTGGAGGTTGACGTC 59.586 50.000 9.11 9.11 0.00 4.34
867 2126 1.735571 CCCGTAATTTGGAGGTTGACG 59.264 52.381 0.00 0.00 0.00 4.35
870 2129 2.510613 ACACCCGTAATTTGGAGGTTG 58.489 47.619 0.00 0.00 0.00 3.77
905 2164 1.658114 CGATCGCGATCAGGGGTAA 59.342 57.895 39.26 4.50 40.82 2.85
928 2187 3.389221 CAAATTTGGAAGTTTCACCGGG 58.611 45.455 10.49 0.00 0.00 5.73
978 2237 2.426023 GAGGGCGGCGACCATATT 59.574 61.111 36.46 14.12 29.21 1.28
979 2238 3.626924 GGAGGGCGGCGACCATAT 61.627 66.667 36.46 14.60 29.21 1.78
995 2254 0.251165 CGGGGCTATTTATGGTGGGG 60.251 60.000 0.00 0.00 0.00 4.96
999 2259 0.400594 GGAGCGGGGCTATTTATGGT 59.599 55.000 0.00 0.00 39.88 3.55
1054 2314 3.721706 GGAGGTGGTGGGCAGAGG 61.722 72.222 0.00 0.00 0.00 3.69
1072 2332 2.806237 CGGCGAGGGAGGAGTAAC 59.194 66.667 0.00 0.00 0.00 2.50
1112 2376 1.227089 CTGATGGAGCTTCCCGACG 60.227 63.158 0.00 0.00 35.03 5.12
1113 2377 1.522580 GCTGATGGAGCTTCCCGAC 60.523 63.158 0.00 0.00 45.21 4.79
1114 2378 2.903357 GCTGATGGAGCTTCCCGA 59.097 61.111 0.00 0.00 45.21 5.14
1122 2386 0.319727 GCTGGATCGAGCTGATGGAG 60.320 60.000 21.18 0.00 37.47 3.86
1123 2387 1.744639 GCTGGATCGAGCTGATGGA 59.255 57.895 21.18 0.00 37.47 3.41
1124 2388 1.664017 CGCTGGATCGAGCTGATGG 60.664 63.158 24.73 7.54 37.47 3.51
1125 2389 1.664017 CCGCTGGATCGAGCTGATG 60.664 63.158 24.73 10.99 37.47 3.07
1126 2390 2.733301 CCGCTGGATCGAGCTGAT 59.267 61.111 24.73 0.00 41.06 2.90
1127 2391 4.212913 GCCGCTGGATCGAGCTGA 62.213 66.667 24.73 0.00 36.77 4.26
1148 2412 4.101448 GCTCCCCGACATGGCTGT 62.101 66.667 0.00 0.00 38.67 4.40
1695 2965 1.218047 GTGGCGATGTAGGCTGACA 59.782 57.895 0.00 0.00 37.59 3.58
1699 2969 4.530857 GCGGTGGCGATGTAGGCT 62.531 66.667 0.00 0.00 37.59 4.58
2094 3385 3.272847 GGGTGGGTGGGTGGGATT 61.273 66.667 0.00 0.00 0.00 3.01
2106 3397 1.873178 TTGGGGATGATGGTGGGTGG 61.873 60.000 0.00 0.00 0.00 4.61
2107 3398 0.040942 TTTGGGGATGATGGTGGGTG 59.959 55.000 0.00 0.00 0.00 4.61
2108 3399 0.789687 TTTTGGGGATGATGGTGGGT 59.210 50.000 0.00 0.00 0.00 4.51
2109 3400 2.041701 GATTTTGGGGATGATGGTGGG 58.958 52.381 0.00 0.00 0.00 4.61
2115 3406 2.401568 GCTTGGGATTTTGGGGATGAT 58.598 47.619 0.00 0.00 0.00 2.45
2119 3410 0.192064 TTGGCTTGGGATTTTGGGGA 59.808 50.000 0.00 0.00 0.00 4.81
2123 3414 3.699411 TTGGATTGGCTTGGGATTTTG 57.301 42.857 0.00 0.00 0.00 2.44
2134 3425 6.402442 CCGAGAAATTTTTGATTTGGATTGGC 60.402 38.462 0.00 0.00 0.00 4.52
2147 3438 6.385649 TCTTTACACAGCCGAGAAATTTTT 57.614 33.333 0.00 0.00 0.00 1.94
2151 3443 4.832248 TGATCTTTACACAGCCGAGAAAT 58.168 39.130 0.00 0.00 0.00 2.17
2160 3452 9.799106 ATTTAAGGGGATATGATCTTTACACAG 57.201 33.333 0.00 0.00 0.00 3.66
2207 3511 1.899437 ATCGGTACAGGGCACACCAG 61.899 60.000 0.00 0.00 43.89 4.00
2389 3694 0.962356 AAGCAGTCCGGGCAATCAAG 60.962 55.000 9.71 0.00 0.00 3.02
2393 3698 1.228552 AACAAGCAGTCCGGGCAAT 60.229 52.632 9.71 0.00 0.00 3.56
2395 3700 2.594303 CAACAAGCAGTCCGGGCA 60.594 61.111 9.71 0.00 0.00 5.36
2396 3701 3.365265 CCAACAAGCAGTCCGGGC 61.365 66.667 0.00 0.00 0.00 6.13
2397 3702 3.365265 GCCAACAAGCAGTCCGGG 61.365 66.667 0.00 0.00 0.00 5.73
2398 3703 3.365265 GGCCAACAAGCAGTCCGG 61.365 66.667 0.00 0.00 0.00 5.14
2436 3741 1.247567 CCATCCCTTTGCGTCAAAGT 58.752 50.000 22.18 8.79 46.40 2.66
2442 3747 2.046314 CCGACCATCCCTTTGCGT 60.046 61.111 0.00 0.00 0.00 5.24
2554 3868 3.762823 GGACGGAGGAAGAAGAAGAAGTA 59.237 47.826 0.00 0.00 0.00 2.24
2555 3869 2.563620 GGACGGAGGAAGAAGAAGAAGT 59.436 50.000 0.00 0.00 0.00 3.01
2556 3870 2.563179 TGGACGGAGGAAGAAGAAGAAG 59.437 50.000 0.00 0.00 0.00 2.85
2557 3871 2.605257 TGGACGGAGGAAGAAGAAGAA 58.395 47.619 0.00 0.00 0.00 2.52
2558 3872 2.304221 TGGACGGAGGAAGAAGAAGA 57.696 50.000 0.00 0.00 0.00 2.87
2559 3873 2.159028 GGATGGACGGAGGAAGAAGAAG 60.159 54.545 0.00 0.00 0.00 2.85
2560 3874 1.831736 GGATGGACGGAGGAAGAAGAA 59.168 52.381 0.00 0.00 0.00 2.52
2561 3875 1.273041 TGGATGGACGGAGGAAGAAGA 60.273 52.381 0.00 0.00 0.00 2.87
2562 3876 1.195115 TGGATGGACGGAGGAAGAAG 58.805 55.000 0.00 0.00 0.00 2.85
2572 3886 4.071961 TCCTATCATTGTTGGATGGACG 57.928 45.455 0.00 0.00 0.00 4.79
2573 3887 5.440610 AGTTCCTATCATTGTTGGATGGAC 58.559 41.667 0.00 0.00 0.00 4.02
2583 3897 7.517614 TGACTCTAGCTAGTTCCTATCATTG 57.482 40.000 20.10 0.00 0.00 2.82
2585 3899 8.540507 TTTTGACTCTAGCTAGTTCCTATCAT 57.459 34.615 20.10 0.00 0.00 2.45
2586 3900 7.956328 TTTTGACTCTAGCTAGTTCCTATCA 57.044 36.000 20.10 12.28 0.00 2.15
2592 3906 7.173390 ACCAACAATTTTGACTCTAGCTAGTTC 59.827 37.037 20.10 16.92 0.00 3.01
2633 3960 3.421844 TCCGACTGAAGATTCTGACAGA 58.578 45.455 20.50 0.00 34.88 3.41
2636 3963 4.387256 CACTTTCCGACTGAAGATTCTGAC 59.613 45.833 6.48 0.22 33.63 3.51
2652 3982 4.218417 ACAAACATAGGCATGACACTTTCC 59.782 41.667 0.00 0.00 35.96 3.13
2658 3988 4.140536 TCACAACAAACATAGGCATGACA 58.859 39.130 0.00 0.00 35.96 3.58
2661 3991 5.531634 ACTTTCACAACAAACATAGGCATG 58.468 37.500 0.00 0.00 38.21 4.06
2802 4158 1.033746 CACAGCACCACCATCCATCC 61.034 60.000 0.00 0.00 0.00 3.51
2809 4165 1.460497 TAGTCCCACAGCACCACCA 60.460 57.895 0.00 0.00 0.00 4.17
2860 4216 6.649973 CCAAACCATCATTTCAGCACATTAAA 59.350 34.615 0.00 0.00 0.00 1.52
2921 4286 3.143168 AGGGGAATAGAACCACCCAAAAA 59.857 43.478 0.00 0.00 43.96 1.94
2944 4309 4.351054 GGTCCAGGCCACCACCAG 62.351 72.222 5.01 0.00 33.63 4.00
2951 4316 2.611800 AGATGCAGGTCCAGGCCA 60.612 61.111 5.01 0.00 0.00 5.36
2952 4317 2.124403 CAGATGCAGGTCCAGGCC 60.124 66.667 0.00 0.00 0.00 5.19
2953 4318 1.001641 AACAGATGCAGGTCCAGGC 60.002 57.895 0.00 0.00 0.00 4.85
2967 4332 4.520492 AGTATGGAAAGCAACCAAGAACAG 59.480 41.667 0.00 0.00 40.93 3.16
3024 4393 6.141560 TGCACTGTTGTGATGTCATAAAAA 57.858 33.333 0.00 0.00 46.55 1.94
3025 4394 5.764487 TGCACTGTTGTGATGTCATAAAA 57.236 34.783 0.00 0.00 46.55 1.52
3026 4395 5.764487 TTGCACTGTTGTGATGTCATAAA 57.236 34.783 0.00 0.00 46.55 1.40
3027 4396 5.764487 TTTGCACTGTTGTGATGTCATAA 57.236 34.783 0.00 0.00 46.55 1.90
3028 4397 5.963176 ATTTGCACTGTTGTGATGTCATA 57.037 34.783 0.00 0.00 46.55 2.15
3029 4398 4.859304 ATTTGCACTGTTGTGATGTCAT 57.141 36.364 0.00 0.00 46.55 3.06
3030 4399 4.652421 AATTTGCACTGTTGTGATGTCA 57.348 36.364 0.00 0.00 46.55 3.58
3031 4400 5.574055 CCATAATTTGCACTGTTGTGATGTC 59.426 40.000 0.00 0.00 46.55 3.06
3032 4401 5.010922 ACCATAATTTGCACTGTTGTGATGT 59.989 36.000 0.00 0.00 46.55 3.06
3033 4402 5.346551 CACCATAATTTGCACTGTTGTGATG 59.653 40.000 0.00 0.00 46.55 3.07
3034 4403 5.010922 ACACCATAATTTGCACTGTTGTGAT 59.989 36.000 0.00 0.00 46.55 3.06
3035 4404 4.340666 ACACCATAATTTGCACTGTTGTGA 59.659 37.500 0.00 0.00 46.55 3.58
3036 4405 4.619973 ACACCATAATTTGCACTGTTGTG 58.380 39.130 0.00 0.00 46.37 3.33
3074 4443 4.974721 CACACACCCACTGCCCCC 62.975 72.222 0.00 0.00 0.00 5.40
3075 4444 4.204028 ACACACACCCACTGCCCC 62.204 66.667 0.00 0.00 0.00 5.80
3076 4445 2.906897 CACACACACCCACTGCCC 60.907 66.667 0.00 0.00 0.00 5.36
3077 4446 3.595758 GCACACACACCCACTGCC 61.596 66.667 0.00 0.00 0.00 4.85
3078 4447 2.120909 AAGCACACACACCCACTGC 61.121 57.895 0.00 0.00 0.00 4.40
3104 4477 0.669619 CATGTGGCAGCAACAGTTCA 59.330 50.000 9.00 0.00 0.00 3.18
3105 4478 0.038892 CCATGTGGCAGCAACAGTTC 60.039 55.000 9.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.