Multiple sequence alignment - TraesCS1B01G471100

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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 TraesCS1B01G471100 chr1B 100.000 3935 0 0 1 3935 679275163 679271229 0.000000e+00 7267
1 TraesCS1B01G471100 chr1B 93.284 134 5 2 397 526 679287415 679287282 1.120000e-45 195
2 TraesCS1B01G471100 chr1D 96.692 1693 27 7 1480 3165 487634785 487633115 0.000000e+00 2789
3 TraesCS1B01G471100 chr1D 90.818 1100 60 19 397 1479 487635910 487634835 0.000000e+00 1434
4 TraesCS1B01G471100 chr1D 93.662 568 32 4 3369 3934 487631058 487630493 0.000000e+00 846
5 TraesCS1B01G471100 chr1D 92.965 199 14 0 3169 3367 487631560 487631362 1.380000e-74 291
6 TraesCS1B01G471100 chr1A 88.057 1616 129 35 1516 3104 585822529 585820951 0.000000e+00 1857
7 TraesCS1B01G471100 chr1A 87.163 1410 119 28 87 1452 585824017 585822626 0.000000e+00 1544
8 TraesCS1B01G471100 chr1A 85.968 1012 106 23 2111 3103 585755108 585754114 0.000000e+00 1050
9 TraesCS1B01G471100 chr1A 76.393 682 144 14 3267 3935 585754109 585753432 6.260000e-93 351
10 TraesCS1B01G471100 chr1A 80.889 225 31 8 2949 3163 589120082 589120304 2.430000e-37 167
11 TraesCS1B01G471100 chr7A 81.333 225 30 8 2949 3163 68910766 68910544 5.230000e-39 172
12 TraesCS1B01G471100 chr6B 81.166 223 34 5 2949 3163 4883187 4882965 5.230000e-39 172
13 TraesCS1B01G471100 chr6A 81.333 225 30 9 2949 3163 578655294 578655072 5.230000e-39 172
14 TraesCS1B01G471100 chr5B 81.250 224 32 6 2949 3163 678522852 678523074 5.230000e-39 172
15 TraesCS1B01G471100 chr4A 80.889 225 31 8 2949 3163 706611595 706611817 2.430000e-37 167
16 TraesCS1B01G471100 chr7D 80.357 224 34 6 2949 3163 24342189 24342411 1.130000e-35 161
17 TraesCS1B01G471100 chr7D 80.357 224 34 6 2949 3163 32055367 32055145 1.130000e-35 161
18 TraesCS1B01G471100 chr5D 80.357 224 34 6 2949 3163 438688143 438687921 1.130000e-35 161
19 TraesCS1B01G471100 chr2D 80.357 224 34 6 2949 3163 585120191 585120413 1.130000e-35 161
20 TraesCS1B01G471100 chr2D 80.357 224 34 6 2949 3163 598076028 598076250 1.130000e-35 161
21 TraesCS1B01G471100 chr4D 79.911 224 35 6 2949 3163 449044084 449044306 5.260000e-34 156
22 TraesCS1B01G471100 chr2B 80.000 225 33 8 2949 3163 787524055 787524277 5.260000e-34 156
23 TraesCS1B01G471100 chr3B 79.556 225 34 8 2949 3163 577731075 577730853 2.450000e-32 150


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 TraesCS1B01G471100 chr1B 679271229 679275163 3934 True 7267.0 7267 100.00000 1 3935 1 chr1B.!!$R1 3934
1 TraesCS1B01G471100 chr1D 487630493 487635910 5417 True 1340.0 2789 93.53425 397 3934 4 chr1D.!!$R1 3537
2 TraesCS1B01G471100 chr1A 585820951 585824017 3066 True 1700.5 1857 87.61000 87 3104 2 chr1A.!!$R2 3017
3 TraesCS1B01G471100 chr1A 585753432 585755108 1676 True 700.5 1050 81.18050 2111 3935 2 chr1A.!!$R1 1824

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
129 130 0.031721 ACAGTCAACTCCGTCGTTCC 59.968 55.0 0.00 0.00 0.00 3.62 F
134 135 0.032952 CAACTCCGTCGTTCCTCCAA 59.967 55.0 0.00 0.00 0.00 3.53 F
267 268 0.037975 ACCTAACACGCCCTTACACG 60.038 55.0 0.00 0.00 0.00 4.49 F
848 871 0.039165 TGATCGGATCAGCGATTCCG 60.039 55.0 16.44 7.47 46.06 4.30 F
1161 1212 0.302288 TGAACGAAACGACTTTGGCG 59.698 50.0 0.00 0.00 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1407 1458 1.005340 GCACCTGAGCAGAGAATTCG 58.995 55.000 0.00 0.00 0.00 3.34 R
1463 1514 3.005554 GGCAATTCATCATCGATCGGAT 58.994 45.455 16.41 8.18 35.09 4.18 R
2125 2241 4.023878 CCAAATCCCAAACAGCAAAATGTG 60.024 41.667 0.00 0.00 32.52 3.21 R
2543 2664 1.367599 GCCACTGCTGCTAGCTGAAG 61.368 60.000 24.19 24.19 41.94 3.02 R
3048 3193 2.066262 ACTACGACAACAATTGCGAGG 58.934 47.619 5.05 2.74 35.33 4.63 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
22 23 5.982465 GGAGAGTGAACATTGAGATAAGC 57.018 43.478 0.00 0.00 0.00 3.09
23 24 4.505922 GGAGAGTGAACATTGAGATAAGCG 59.494 45.833 0.00 0.00 0.00 4.68
24 25 5.330455 AGAGTGAACATTGAGATAAGCGA 57.670 39.130 0.00 0.00 0.00 4.93
25 26 5.347342 AGAGTGAACATTGAGATAAGCGAG 58.653 41.667 0.00 0.00 0.00 5.03
26 27 5.126222 AGAGTGAACATTGAGATAAGCGAGA 59.874 40.000 0.00 0.00 0.00 4.04
27 28 5.724328 AGTGAACATTGAGATAAGCGAGAA 58.276 37.500 0.00 0.00 0.00 2.87
28 29 5.809562 AGTGAACATTGAGATAAGCGAGAAG 59.190 40.000 0.00 0.00 0.00 2.85
29 30 5.006165 GTGAACATTGAGATAAGCGAGAAGG 59.994 44.000 0.00 0.00 0.00 3.46
30 31 4.065321 ACATTGAGATAAGCGAGAAGGG 57.935 45.455 0.00 0.00 0.00 3.95
31 32 3.706594 ACATTGAGATAAGCGAGAAGGGA 59.293 43.478 0.00 0.00 0.00 4.20
32 33 4.346418 ACATTGAGATAAGCGAGAAGGGAT 59.654 41.667 0.00 0.00 0.00 3.85
33 34 5.163258 ACATTGAGATAAGCGAGAAGGGATT 60.163 40.000 0.00 0.00 0.00 3.01
34 35 5.359194 TTGAGATAAGCGAGAAGGGATTT 57.641 39.130 0.00 0.00 0.00 2.17
35 36 6.479972 TTGAGATAAGCGAGAAGGGATTTA 57.520 37.500 0.00 0.00 0.00 1.40
36 37 6.672266 TGAGATAAGCGAGAAGGGATTTAT 57.328 37.500 0.00 0.00 0.00 1.40
37 38 6.459066 TGAGATAAGCGAGAAGGGATTTATG 58.541 40.000 0.00 0.00 0.00 1.90
38 39 6.267699 TGAGATAAGCGAGAAGGGATTTATGA 59.732 38.462 0.00 0.00 0.00 2.15
39 40 6.459923 AGATAAGCGAGAAGGGATTTATGAC 58.540 40.000 0.00 0.00 0.00 3.06
40 41 3.099267 AGCGAGAAGGGATTTATGACG 57.901 47.619 0.00 0.00 0.00 4.35
41 42 1.527311 GCGAGAAGGGATTTATGACGC 59.473 52.381 0.00 0.00 37.11 5.19
42 43 1.787155 CGAGAAGGGATTTATGACGCG 59.213 52.381 3.53 3.53 0.00 6.01
43 44 2.135933 GAGAAGGGATTTATGACGCGG 58.864 52.381 12.47 0.00 0.00 6.46
44 45 0.586802 GAAGGGATTTATGACGCGGC 59.413 55.000 12.47 8.67 0.00 6.53
45 46 0.180406 AAGGGATTTATGACGCGGCT 59.820 50.000 15.80 0.26 0.00 5.52
46 47 0.180406 AGGGATTTATGACGCGGCTT 59.820 50.000 15.80 10.28 0.00 4.35
47 48 1.021968 GGGATTTATGACGCGGCTTT 58.978 50.000 15.80 2.72 0.00 3.51
48 49 1.268539 GGGATTTATGACGCGGCTTTG 60.269 52.381 15.80 0.00 0.00 2.77
49 50 1.668751 GGATTTATGACGCGGCTTTGA 59.331 47.619 15.80 0.00 0.00 2.69
50 51 2.286418 GGATTTATGACGCGGCTTTGAG 60.286 50.000 15.80 0.00 0.00 3.02
51 52 2.087501 TTTATGACGCGGCTTTGAGA 57.912 45.000 15.80 0.00 0.00 3.27
52 53 2.087501 TTATGACGCGGCTTTGAGAA 57.912 45.000 15.80 0.00 0.00 2.87
53 54 2.087501 TATGACGCGGCTTTGAGAAA 57.912 45.000 15.80 0.00 0.00 2.52
54 55 0.517316 ATGACGCGGCTTTGAGAAAC 59.483 50.000 15.80 0.00 0.00 2.78
55 56 0.812014 TGACGCGGCTTTGAGAAACA 60.812 50.000 15.80 0.00 0.00 2.83
56 57 0.110644 GACGCGGCTTTGAGAAACAG 60.111 55.000 12.47 0.00 0.00 3.16
57 58 1.441016 CGCGGCTTTGAGAAACAGC 60.441 57.895 0.00 0.00 0.00 4.40
58 59 1.441016 GCGGCTTTGAGAAACAGCG 60.441 57.895 0.00 0.00 0.00 5.18
59 60 1.441016 CGGCTTTGAGAAACAGCGC 60.441 57.895 0.00 0.00 0.00 5.92
60 61 1.441016 GGCTTTGAGAAACAGCGCG 60.441 57.895 0.00 0.00 0.00 6.86
61 62 1.569493 GCTTTGAGAAACAGCGCGA 59.431 52.632 12.10 0.00 0.00 5.87
62 63 0.722799 GCTTTGAGAAACAGCGCGAC 60.723 55.000 12.10 0.04 0.00 5.19
63 64 0.581529 CTTTGAGAAACAGCGCGACA 59.418 50.000 12.10 0.00 0.00 4.35
64 65 1.195448 CTTTGAGAAACAGCGCGACAT 59.805 47.619 12.10 0.00 0.00 3.06
65 66 0.790207 TTGAGAAACAGCGCGACATC 59.210 50.000 12.10 0.00 0.00 3.06
66 67 0.319469 TGAGAAACAGCGCGACATCA 60.319 50.000 12.10 0.00 0.00 3.07
67 68 0.093705 GAGAAACAGCGCGACATCAC 59.906 55.000 12.10 0.00 0.00 3.06
68 69 1.132640 GAAACAGCGCGACATCACC 59.867 57.895 12.10 0.00 0.00 4.02
69 70 2.240612 GAAACAGCGCGACATCACCC 62.241 60.000 12.10 0.00 0.00 4.61
75 76 4.796231 GCGACATCACCCGCTCGT 62.796 66.667 0.00 0.00 46.96 4.18
76 77 2.579787 CGACATCACCCGCTCGTC 60.580 66.667 0.00 0.00 0.00 4.20
77 78 2.202756 GACATCACCCGCTCGTCC 60.203 66.667 0.00 0.00 0.00 4.79
78 79 3.718210 GACATCACCCGCTCGTCCC 62.718 68.421 0.00 0.00 0.00 4.46
79 80 4.530857 CATCACCCGCTCGTCCCC 62.531 72.222 0.00 0.00 0.00 4.81
80 81 4.779733 ATCACCCGCTCGTCCCCT 62.780 66.667 0.00 0.00 0.00 4.79
129 130 0.031721 ACAGTCAACTCCGTCGTTCC 59.968 55.000 0.00 0.00 0.00 3.62
131 132 0.597072 AGTCAACTCCGTCGTTCCTC 59.403 55.000 0.00 0.00 0.00 3.71
132 133 0.388263 GTCAACTCCGTCGTTCCTCC 60.388 60.000 0.00 0.00 0.00 4.30
134 135 0.032952 CAACTCCGTCGTTCCTCCAA 59.967 55.000 0.00 0.00 0.00 3.53
137 138 1.005394 TCCGTCGTTCCTCCAAAGC 60.005 57.895 0.00 0.00 0.00 3.51
139 140 1.301401 CGTCGTTCCTCCAAAGCCA 60.301 57.895 0.00 0.00 0.00 4.75
144 145 1.610624 CGTTCCTCCAAAGCCAAGCTA 60.611 52.381 0.00 0.00 38.25 3.32
147 148 1.915489 TCCTCCAAAGCCAAGCTATGA 59.085 47.619 0.00 0.00 38.25 2.15
150 151 0.743097 CCAAAGCCAAGCTATGAGCC 59.257 55.000 0.00 0.00 43.77 4.70
151 152 0.379669 CAAAGCCAAGCTATGAGCCG 59.620 55.000 0.00 0.00 43.77 5.52
155 156 1.780025 GCCAAGCTATGAGCCGCTTC 61.780 60.000 0.00 0.00 44.06 3.86
163 164 1.320344 ATGAGCCGCTTCGAGTACCA 61.320 55.000 0.00 0.00 0.00 3.25
168 169 0.384309 CCGCTTCGAGTACCATGCTA 59.616 55.000 0.00 0.00 0.00 3.49
175 176 1.517242 GAGTACCATGCTATGCAGGC 58.483 55.000 7.40 7.40 43.65 4.85
177 178 0.890996 GTACCATGCTATGCAGGCCC 60.891 60.000 0.00 0.00 43.65 5.80
185 186 1.304052 TATGCAGGCCCAACCACAC 60.304 57.895 0.00 0.00 43.14 3.82
187 188 4.947147 GCAGGCCCAACCACACGA 62.947 66.667 0.00 0.00 43.14 4.35
192 193 2.425592 CCCAACCACACGAGCAGA 59.574 61.111 0.00 0.00 0.00 4.26
200 201 2.224426 ACCACACGAGCAGATAACCAAA 60.224 45.455 0.00 0.00 0.00 3.28
201 202 2.416547 CCACACGAGCAGATAACCAAAG 59.583 50.000 0.00 0.00 0.00 2.77
202 203 2.076863 ACACGAGCAGATAACCAAAGC 58.923 47.619 0.00 0.00 0.00 3.51
204 205 0.652592 CGAGCAGATAACCAAAGCGG 59.347 55.000 0.00 0.00 42.50 5.52
205 206 0.378610 GAGCAGATAACCAAAGCGGC 59.621 55.000 0.00 0.00 39.03 6.53
207 208 2.004808 GCAGATAACCAAAGCGGCCC 62.005 60.000 0.00 0.00 39.03 5.80
210 211 0.172578 GATAACCAAAGCGGCCCAAC 59.827 55.000 0.00 0.00 39.03 3.77
220 221 2.495866 GGCCCAACATTGCATCCG 59.504 61.111 0.00 0.00 0.00 4.18
224 225 0.680921 CCCAACATTGCATCCGAGGT 60.681 55.000 0.00 0.00 0.00 3.85
228 229 0.179000 ACATTGCATCCGAGGTCCTC 59.821 55.000 9.05 9.05 0.00 3.71
244 245 1.091771 CCTCGCTGGGTGTTATGCAG 61.092 60.000 0.00 0.00 0.00 4.41
251 252 0.611896 GGGTGTTATGCAGGCAACCT 60.612 55.000 12.94 0.00 37.05 3.50
267 268 0.037975 ACCTAACACGCCCTTACACG 60.038 55.000 0.00 0.00 0.00 4.49
268 269 0.738412 CCTAACACGCCCTTACACGG 60.738 60.000 0.00 0.00 0.00 4.94
299 300 3.987547 CAGCCAGACTGGTACATAGATG 58.012 50.000 22.58 0.02 43.19 2.90
310 323 2.760634 ACATAGATGTTGCACGTGGA 57.239 45.000 18.88 12.78 37.90 4.02
330 343 3.503748 GGACCACCTGAAAAGTTCATCTG 59.496 47.826 0.00 0.00 39.30 2.90
331 344 3.490348 ACCACCTGAAAAGTTCATCTGG 58.510 45.455 10.96 10.96 39.93 3.86
332 345 2.821969 CCACCTGAAAAGTTCATCTGGG 59.178 50.000 14.86 8.49 39.30 4.45
342 357 9.527157 TGAAAAGTTCATCTGGGAATTAACATA 57.473 29.630 0.00 0.00 34.08 2.29
473 493 1.928706 GAACGGCGCTCTCACTCTCT 61.929 60.000 6.90 0.00 0.00 3.10
494 514 3.183793 TGATGTAACATCTCGCATGCT 57.816 42.857 17.13 0.00 0.00 3.79
505 525 6.102663 ACATCTCGCATGCTAATAATAGGAC 58.897 40.000 17.13 0.00 31.77 3.85
530 550 2.884639 GCAGGAGCACAAAGTAAAGGAA 59.115 45.455 0.00 0.00 41.58 3.36
540 560 7.036829 GCACAAAGTAAAGGAACCAGTTAAAA 58.963 34.615 0.00 0.00 0.00 1.52
611 631 2.102588 CACCACTAATCTCTTACCCGGG 59.897 54.545 22.25 22.25 0.00 5.73
665 685 0.326927 GACCATTCTCCGGTGGGAAA 59.673 55.000 13.03 0.00 43.27 3.13
682 702 4.028131 GGGAAATTTTCGGGGAGGTAATT 58.972 43.478 3.17 0.00 0.00 1.40
683 703 5.202765 GGGAAATTTTCGGGGAGGTAATTA 58.797 41.667 3.17 0.00 0.00 1.40
684 704 5.657745 GGGAAATTTTCGGGGAGGTAATTAA 59.342 40.000 3.17 0.00 0.00 1.40
685 705 6.325545 GGGAAATTTTCGGGGAGGTAATTAAT 59.674 38.462 3.17 0.00 0.00 1.40
686 706 7.207383 GGAAATTTTCGGGGAGGTAATTAATG 58.793 38.462 3.17 0.00 0.00 1.90
687 707 5.784578 ATTTTCGGGGAGGTAATTAATGC 57.215 39.130 0.00 0.00 0.00 3.56
688 708 4.513406 TTTCGGGGAGGTAATTAATGCT 57.487 40.909 0.00 0.00 0.00 3.79
689 709 3.764237 TCGGGGAGGTAATTAATGCTC 57.236 47.619 0.00 0.00 0.00 4.26
701 721 9.950496 AGGTAATTAATGCTCATACTAGATTGG 57.050 33.333 0.00 0.00 0.00 3.16
702 722 9.167311 GGTAATTAATGCTCATACTAGATTGGG 57.833 37.037 0.00 0.00 0.00 4.12
707 727 6.692849 ATGCTCATACTAGATTGGGAATCA 57.307 37.500 0.00 0.00 40.42 2.57
715 735 2.201830 AGATTGGGAATCACCGGGTTA 58.798 47.619 6.32 0.00 40.42 2.85
717 737 2.428544 TTGGGAATCACCGGGTTATG 57.571 50.000 6.32 0.00 40.11 1.90
730 750 3.004734 CCGGGTTATGATTCTTCCATTGC 59.995 47.826 0.00 0.00 0.00 3.56
731 751 3.631686 CGGGTTATGATTCTTCCATTGCA 59.368 43.478 0.00 0.00 0.00 4.08
755 778 8.534778 GCATCGTTGATCCAATTTATTTTCTTC 58.465 33.333 0.00 0.00 0.00 2.87
757 780 7.812648 TCGTTGATCCAATTTATTTTCTTCGT 58.187 30.769 0.00 0.00 0.00 3.85
840 863 7.776933 TTGAATTAGTTCTTGATCGGATCAG 57.223 36.000 19.15 13.82 35.05 2.90
842 865 2.215907 AGTTCTTGATCGGATCAGCG 57.784 50.000 19.15 14.65 40.94 5.18
848 871 0.039165 TGATCGGATCAGCGATTCCG 60.039 55.000 16.44 7.47 46.06 4.30
869 892 5.465390 TCCGCATTATTTTAGTCCTTGATCG 59.535 40.000 0.00 0.00 0.00 3.69
874 897 9.387123 GCATTATTTTAGTCCTTGATCGAATTC 57.613 33.333 0.00 0.00 0.00 2.17
880 903 9.624697 TTTTAGTCCTTGATCGAATTCATTTTG 57.375 29.630 6.22 0.00 0.00 2.44
930 953 5.237344 CGATCCTATTCTGTTGTTGGGAATC 59.763 44.000 0.00 0.00 32.78 2.52
954 979 2.547430 CGTCCATCCAGGTCATGATCTG 60.547 54.545 26.34 26.34 39.23 2.90
1090 1115 1.514087 GTCAACGCTCCCGGTATCA 59.486 57.895 0.00 0.00 39.22 2.15
1101 1132 1.681793 CCCGGTATCAACTCATCGTCT 59.318 52.381 0.00 0.00 0.00 4.18
1103 1134 2.619177 CCGGTATCAACTCATCGTCTCT 59.381 50.000 0.00 0.00 0.00 3.10
1104 1135 3.066900 CCGGTATCAACTCATCGTCTCTT 59.933 47.826 0.00 0.00 0.00 2.85
1105 1136 4.440250 CCGGTATCAACTCATCGTCTCTTT 60.440 45.833 0.00 0.00 0.00 2.52
1109 1160 6.035112 GGTATCAACTCATCGTCTCTTTTCAC 59.965 42.308 0.00 0.00 0.00 3.18
1112 1163 2.557056 ACTCATCGTCTCTTTTCACGGA 59.443 45.455 0.00 0.00 36.64 4.69
1113 1164 3.193691 ACTCATCGTCTCTTTTCACGGAT 59.806 43.478 0.00 0.00 36.64 4.18
1116 1167 3.936372 TCGTCTCTTTTCACGGATCTT 57.064 42.857 0.00 0.00 36.64 2.40
1118 1169 2.668457 CGTCTCTTTTCACGGATCTTGG 59.332 50.000 0.00 0.00 32.19 3.61
1120 1171 3.433615 GTCTCTTTTCACGGATCTTGGTG 59.566 47.826 0.00 0.00 35.50 4.17
1130 1181 2.094026 CGGATCTTGGTGTGATCACAGA 60.094 50.000 28.54 21.21 45.45 3.41
1131 1182 3.265791 GGATCTTGGTGTGATCACAGAC 58.734 50.000 28.54 22.93 45.45 3.51
1161 1212 0.302288 TGAACGAAACGACTTTGGCG 59.698 50.000 0.00 0.00 0.00 5.69
1162 1213 0.990295 GAACGAAACGACTTTGGCGC 60.990 55.000 0.00 0.00 0.00 6.53
1163 1214 1.707239 AACGAAACGACTTTGGCGCA 61.707 50.000 10.83 0.00 0.00 6.09
1164 1215 1.206578 CGAAACGACTTTGGCGCAT 59.793 52.632 10.83 0.00 0.00 4.73
1350 1401 2.685850 ACAATGGTACCCTTAGCGAC 57.314 50.000 10.07 0.00 0.00 5.19
1434 1485 4.030452 GCTCAGGTGCGTGCCAAC 62.030 66.667 0.59 0.00 0.00 3.77
1438 1489 2.672996 AGGTGCGTGCCAACCATC 60.673 61.111 4.43 0.00 0.00 3.51
1460 1511 7.147461 CCATCCATCATCCTCTCATCTGAATAT 60.147 40.741 0.00 0.00 0.00 1.28
1461 1512 8.925338 CATCCATCATCCTCTCATCTGAATATA 58.075 37.037 0.00 0.00 0.00 0.86
1462 1513 9.677554 ATCCATCATCCTCTCATCTGAATATAT 57.322 33.333 0.00 0.00 0.00 0.86
1503 1603 3.074390 TGCCTTTGGATTCTTCCTTCTCA 59.926 43.478 0.00 0.00 43.07 3.27
1504 1604 4.264083 TGCCTTTGGATTCTTCCTTCTCAT 60.264 41.667 0.00 0.00 43.07 2.90
1505 1605 4.097589 GCCTTTGGATTCTTCCTTCTCATG 59.902 45.833 0.00 0.00 43.07 3.07
1506 1606 5.503927 CCTTTGGATTCTTCCTTCTCATGA 58.496 41.667 0.00 0.00 43.07 3.07
1507 1607 5.589452 CCTTTGGATTCTTCCTTCTCATGAG 59.411 44.000 17.07 17.07 43.07 2.90
1685 1785 3.858238 GTGCGTCTACTCTACCACAATTC 59.142 47.826 0.00 0.00 0.00 2.17
1992 2100 4.577152 CTGACAAACCAGGGCACA 57.423 55.556 0.00 0.00 0.00 4.57
2064 2172 0.892358 ACGCACCAGAGTAAGACCGA 60.892 55.000 0.00 0.00 0.00 4.69
2065 2173 0.456221 CGCACCAGAGTAAGACCGAT 59.544 55.000 0.00 0.00 0.00 4.18
2124 2240 3.141398 CTCAGTTTTGCTACCTTGCTCA 58.859 45.455 0.00 0.00 0.00 4.26
2125 2241 2.878406 TCAGTTTTGCTACCTTGCTCAC 59.122 45.455 0.00 0.00 0.00 3.51
2299 2415 4.817517 AGTCTTGTTACTTGGGTATCGTG 58.182 43.478 0.00 0.00 0.00 4.35
2302 2418 5.119743 GTCTTGTTACTTGGGTATCGTGTTC 59.880 44.000 0.00 0.00 0.00 3.18
2473 2592 3.573491 GCCGTCGCCAAGGTATGC 61.573 66.667 0.00 0.00 0.00 3.14
2543 2664 2.616842 ACCGAGGTTGTGTTTTCATGTC 59.383 45.455 0.00 0.00 0.00 3.06
2726 2847 4.636206 ACAAAGAAGCTTGAACGAACTCTT 59.364 37.500 2.10 0.00 0.00 2.85
2727 2848 4.802876 AAGAAGCTTGAACGAACTCTTG 57.197 40.909 2.10 0.00 0.00 3.02
2728 2849 2.545946 AGAAGCTTGAACGAACTCTTGC 59.454 45.455 2.10 0.00 0.00 4.01
2729 2850 1.953559 AGCTTGAACGAACTCTTGCA 58.046 45.000 0.00 0.00 0.00 4.08
3048 3193 9.979578 TTGATATATTCCATTGTGCAAAATACC 57.020 29.630 0.65 0.00 0.00 2.73
3052 3197 2.752354 TCCATTGTGCAAAATACCCTCG 59.248 45.455 0.65 0.00 0.00 4.63
3153 3299 8.677148 TTAACTAGTTTTCTGCAAAGATCACT 57.323 30.769 14.49 0.00 0.00 3.41
3165 3311 4.640647 GCAAAGATCACTAACCCCTTTAGG 59.359 45.833 0.00 0.00 41.58 2.69
3166 3312 4.505324 AAGATCACTAACCCCTTTAGGC 57.495 45.455 0.00 0.00 41.58 3.93
3167 3313 3.737263 AGATCACTAACCCCTTTAGGCT 58.263 45.455 0.00 0.00 41.58 4.58
3191 4888 7.488150 GCTTTACCATTTATCCAGTTGCTAAAC 59.512 37.037 0.00 0.00 36.47 2.01
3197 4894 8.190784 CCATTTATCCAGTTGCTAAACTAAAGG 58.809 37.037 0.00 0.00 45.07 3.11
3212 4909 5.125367 ACTAAAGGGTGGACAAAAGAGTT 57.875 39.130 0.00 0.00 0.00 3.01
3219 4916 4.082733 GGGTGGACAAAAGAGTTATTGCTC 60.083 45.833 0.00 0.00 35.82 4.26
3226 4923 7.592903 GGACAAAAGAGTTATTGCTCAGAAAAG 59.407 37.037 0.00 0.00 37.94 2.27
3252 4949 7.623089 GCGAGATATGCAATTCCTATTCTCAAC 60.623 40.741 0.00 0.00 0.00 3.18
3534 5534 1.156736 CTCGCCATTCTCGGTTTGTT 58.843 50.000 0.00 0.00 0.00 2.83
3535 5535 0.871722 TCGCCATTCTCGGTTTGTTG 59.128 50.000 0.00 0.00 0.00 3.33
3536 5536 0.729140 CGCCATTCTCGGTTTGTTGC 60.729 55.000 0.00 0.00 0.00 4.17
3537 5537 0.388520 GCCATTCTCGGTTTGTTGCC 60.389 55.000 0.00 0.00 0.00 4.52
3654 5655 3.838903 CCCCTACCCAGATATGGTTAGAC 59.161 52.174 12.20 0.00 37.31 2.59
3665 5666 0.252330 TGGTTAGACCGGGATGGACA 60.252 55.000 6.32 0.00 42.58 4.02
3671 5672 1.537889 ACCGGGATGGACAAGACCA 60.538 57.895 6.32 0.00 44.41 4.02
3723 5725 2.359975 CCTTGAGGTTGGGGTCGC 60.360 66.667 0.00 0.00 0.00 5.19
3733 5737 3.467226 GGGGTCGCGGAAGATGGA 61.467 66.667 6.13 0.00 0.00 3.41
3734 5738 2.582436 GGGTCGCGGAAGATGGAA 59.418 61.111 6.13 0.00 0.00 3.53
3747 5751 2.532843 AGATGGAAGTTTTGCATGCCT 58.467 42.857 16.68 1.12 42.07 4.75
3754 5758 3.923017 AGTTTTGCATGCCTAGTTCAC 57.077 42.857 16.68 2.32 0.00 3.18
3783 5787 1.971167 GGCAGTCCATGTTCGCCAA 60.971 57.895 7.57 0.00 42.50 4.52
3843 5854 1.359848 CTCTATGTGACCAACGCCAC 58.640 55.000 0.00 0.00 0.00 5.01
3869 5880 4.503817 GGCAGCAGTATTATCCATCAGACA 60.504 45.833 0.00 0.00 0.00 3.41
3870 5881 4.689812 GCAGCAGTATTATCCATCAGACAG 59.310 45.833 0.00 0.00 0.00 3.51
3897 5908 2.597510 GGCACCAACCGGCTTCTT 60.598 61.111 0.00 0.00 34.57 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.505922 CGCTTATCTCAATGTTCACTCTCC 59.494 45.833 0.00 0.00 0.00 3.71
2 3 5.126222 TCTCGCTTATCTCAATGTTCACTCT 59.874 40.000 0.00 0.00 0.00 3.24
3 4 5.344066 TCTCGCTTATCTCAATGTTCACTC 58.656 41.667 0.00 0.00 0.00 3.51
4 5 5.330455 TCTCGCTTATCTCAATGTTCACT 57.670 39.130 0.00 0.00 0.00 3.41
6 7 5.111989 CCTTCTCGCTTATCTCAATGTTCA 58.888 41.667 0.00 0.00 0.00 3.18
7 8 4.509600 CCCTTCTCGCTTATCTCAATGTTC 59.490 45.833 0.00 0.00 0.00 3.18
8 9 4.162320 TCCCTTCTCGCTTATCTCAATGTT 59.838 41.667 0.00 0.00 0.00 2.71
9 10 3.706594 TCCCTTCTCGCTTATCTCAATGT 59.293 43.478 0.00 0.00 0.00 2.71
10 11 4.327982 TCCCTTCTCGCTTATCTCAATG 57.672 45.455 0.00 0.00 0.00 2.82
11 12 5.559148 AATCCCTTCTCGCTTATCTCAAT 57.441 39.130 0.00 0.00 0.00 2.57
12 13 5.359194 AAATCCCTTCTCGCTTATCTCAA 57.641 39.130 0.00 0.00 0.00 3.02
13 14 6.267699 TCATAAATCCCTTCTCGCTTATCTCA 59.732 38.462 0.00 0.00 0.00 3.27
14 15 6.588373 GTCATAAATCCCTTCTCGCTTATCTC 59.412 42.308 0.00 0.00 0.00 2.75
15 16 6.459923 GTCATAAATCCCTTCTCGCTTATCT 58.540 40.000 0.00 0.00 0.00 1.98
16 17 5.346281 CGTCATAAATCCCTTCTCGCTTATC 59.654 44.000 0.00 0.00 0.00 1.75
17 18 5.230942 CGTCATAAATCCCTTCTCGCTTAT 58.769 41.667 0.00 0.00 0.00 1.73
18 19 4.617959 CGTCATAAATCCCTTCTCGCTTA 58.382 43.478 0.00 0.00 0.00 3.09
19 20 3.458189 CGTCATAAATCCCTTCTCGCTT 58.542 45.455 0.00 0.00 0.00 4.68
20 21 2.803492 GCGTCATAAATCCCTTCTCGCT 60.803 50.000 0.00 0.00 38.46 4.93
21 22 1.527311 GCGTCATAAATCCCTTCTCGC 59.473 52.381 0.00 0.00 34.93 5.03
22 23 1.787155 CGCGTCATAAATCCCTTCTCG 59.213 52.381 0.00 0.00 0.00 4.04
23 24 2.135933 CCGCGTCATAAATCCCTTCTC 58.864 52.381 4.92 0.00 0.00 2.87
24 25 1.810412 GCCGCGTCATAAATCCCTTCT 60.810 52.381 4.92 0.00 0.00 2.85
25 26 0.586802 GCCGCGTCATAAATCCCTTC 59.413 55.000 4.92 0.00 0.00 3.46
26 27 0.180406 AGCCGCGTCATAAATCCCTT 59.820 50.000 4.92 0.00 0.00 3.95
27 28 0.180406 AAGCCGCGTCATAAATCCCT 59.820 50.000 4.92 0.00 0.00 4.20
28 29 1.021968 AAAGCCGCGTCATAAATCCC 58.978 50.000 4.92 0.00 0.00 3.85
29 30 1.668751 TCAAAGCCGCGTCATAAATCC 59.331 47.619 4.92 0.00 0.00 3.01
30 31 2.607635 TCTCAAAGCCGCGTCATAAATC 59.392 45.455 4.92 0.00 0.00 2.17
31 32 2.627945 TCTCAAAGCCGCGTCATAAAT 58.372 42.857 4.92 0.00 0.00 1.40
32 33 2.087501 TCTCAAAGCCGCGTCATAAA 57.912 45.000 4.92 0.00 0.00 1.40
33 34 2.087501 TTCTCAAAGCCGCGTCATAA 57.912 45.000 4.92 0.00 0.00 1.90
34 35 1.730064 GTTTCTCAAAGCCGCGTCATA 59.270 47.619 4.92 0.00 0.00 2.15
35 36 0.517316 GTTTCTCAAAGCCGCGTCAT 59.483 50.000 4.92 0.00 0.00 3.06
36 37 0.812014 TGTTTCTCAAAGCCGCGTCA 60.812 50.000 4.92 0.00 0.00 4.35
37 38 0.110644 CTGTTTCTCAAAGCCGCGTC 60.111 55.000 4.92 0.00 0.00 5.19
38 39 1.941812 CTGTTTCTCAAAGCCGCGT 59.058 52.632 4.92 0.00 0.00 6.01
39 40 1.441016 GCTGTTTCTCAAAGCCGCG 60.441 57.895 0.00 0.00 0.00 6.46
40 41 1.441016 CGCTGTTTCTCAAAGCCGC 60.441 57.895 0.00 0.00 33.24 6.53
41 42 1.441016 GCGCTGTTTCTCAAAGCCG 60.441 57.895 0.00 0.00 33.24 5.52
42 43 1.441016 CGCGCTGTTTCTCAAAGCC 60.441 57.895 5.56 0.00 33.24 4.35
43 44 0.722799 GTCGCGCTGTTTCTCAAAGC 60.723 55.000 5.56 0.00 0.00 3.51
44 45 0.581529 TGTCGCGCTGTTTCTCAAAG 59.418 50.000 5.56 0.00 0.00 2.77
45 46 1.194547 GATGTCGCGCTGTTTCTCAAA 59.805 47.619 5.56 0.00 0.00 2.69
46 47 0.790207 GATGTCGCGCTGTTTCTCAA 59.210 50.000 5.56 0.00 0.00 3.02
47 48 0.319469 TGATGTCGCGCTGTTTCTCA 60.319 50.000 5.56 0.00 0.00 3.27
48 49 0.093705 GTGATGTCGCGCTGTTTCTC 59.906 55.000 5.56 0.00 0.00 2.87
49 50 1.291877 GGTGATGTCGCGCTGTTTCT 61.292 55.000 5.56 0.00 0.00 2.52
50 51 1.132640 GGTGATGTCGCGCTGTTTC 59.867 57.895 5.56 0.00 0.00 2.78
51 52 2.325082 GGGTGATGTCGCGCTGTTT 61.325 57.895 5.56 0.00 36.53 2.83
52 53 2.742372 GGGTGATGTCGCGCTGTT 60.742 61.111 5.56 0.00 36.53 3.16
59 60 2.579787 GACGAGCGGGTGATGTCG 60.580 66.667 0.00 0.00 38.40 4.35
60 61 2.202756 GGACGAGCGGGTGATGTC 60.203 66.667 0.00 0.00 0.00 3.06
61 62 3.771160 GGGACGAGCGGGTGATGT 61.771 66.667 0.00 0.00 0.00 3.06
62 63 4.530857 GGGGACGAGCGGGTGATG 62.531 72.222 0.00 0.00 0.00 3.07
63 64 4.779733 AGGGGACGAGCGGGTGAT 62.780 66.667 0.00 0.00 0.00 3.06
92 93 1.281899 GTTACCAGCGAGTCATGCTC 58.718 55.000 6.98 6.98 41.72 4.26
93 94 0.608130 TGTTACCAGCGAGTCATGCT 59.392 50.000 0.00 0.00 45.31 3.79
96 97 1.893137 TGACTGTTACCAGCGAGTCAT 59.107 47.619 0.00 0.00 42.81 3.06
104 105 2.814280 ACGGAGTTGACTGTTACCAG 57.186 50.000 0.00 0.00 37.78 4.00
108 109 2.287788 GGAACGACGGAGTTGACTGTTA 60.288 50.000 0.00 0.00 47.00 2.41
118 119 1.014564 GCTTTGGAGGAACGACGGAG 61.015 60.000 0.00 0.00 0.00 4.63
121 122 0.882927 TTGGCTTTGGAGGAACGACG 60.883 55.000 0.00 0.00 0.00 5.12
123 124 0.889186 GCTTGGCTTTGGAGGAACGA 60.889 55.000 0.00 0.00 0.00 3.85
129 130 1.674962 GCTCATAGCTTGGCTTTGGAG 59.325 52.381 0.00 9.17 40.44 3.86
131 132 0.743097 GGCTCATAGCTTGGCTTTGG 59.257 55.000 0.00 3.39 41.99 3.28
132 133 0.379669 CGGCTCATAGCTTGGCTTTG 59.620 55.000 0.00 0.53 41.99 2.77
134 135 1.821332 GCGGCTCATAGCTTGGCTT 60.821 57.895 0.00 0.00 41.99 4.35
144 145 1.320344 TGGTACTCGAAGCGGCTCAT 61.320 55.000 1.45 0.00 0.00 2.90
147 148 1.141881 CATGGTACTCGAAGCGGCT 59.858 57.895 0.00 0.00 0.00 5.52
150 151 2.054363 CATAGCATGGTACTCGAAGCG 58.946 52.381 6.80 0.00 0.00 4.68
151 152 1.795286 GCATAGCATGGTACTCGAAGC 59.205 52.381 6.80 1.71 0.00 3.86
155 156 1.788258 CCTGCATAGCATGGTACTCG 58.212 55.000 6.80 0.23 38.13 4.18
163 164 1.456331 GGTTGGGCCTGCATAGCAT 60.456 57.895 4.53 0.00 38.13 3.79
168 169 2.601367 GTGTGGTTGGGCCTGCAT 60.601 61.111 4.53 0.00 38.35 3.96
175 176 0.249120 TATCTGCTCGTGTGGTTGGG 59.751 55.000 0.00 0.00 0.00 4.12
177 178 1.732259 GGTTATCTGCTCGTGTGGTTG 59.268 52.381 0.00 0.00 0.00 3.77
185 186 0.652592 CCGCTTTGGTTATCTGCTCG 59.347 55.000 0.00 0.00 0.00 5.03
187 188 1.032114 GGCCGCTTTGGTTATCTGCT 61.032 55.000 0.00 0.00 41.21 4.24
192 193 0.540830 TGTTGGGCCGCTTTGGTTAT 60.541 50.000 0.00 0.00 41.21 1.89
200 201 2.681064 ATGCAATGTTGGGCCGCT 60.681 55.556 0.00 0.00 0.00 5.52
201 202 2.202783 GATGCAATGTTGGGCCGC 60.203 61.111 0.00 0.00 0.00 6.53
202 203 2.495866 GGATGCAATGTTGGGCCG 59.504 61.111 0.00 0.00 0.00 6.13
204 205 1.434696 CTCGGATGCAATGTTGGGC 59.565 57.895 0.00 0.00 0.00 5.36
205 206 0.680921 ACCTCGGATGCAATGTTGGG 60.681 55.000 0.00 0.00 0.00 4.12
207 208 0.734889 GGACCTCGGATGCAATGTTG 59.265 55.000 0.00 0.00 0.00 3.33
210 211 2.997899 GAGGACCTCGGATGCAATG 58.002 57.895 5.55 0.00 0.00 2.82
220 221 1.255667 TAACACCCAGCGAGGACCTC 61.256 60.000 11.87 11.87 41.22 3.85
224 225 1.220749 GCATAACACCCAGCGAGGA 59.779 57.895 1.68 0.00 41.22 3.71
228 229 2.764314 GCCTGCATAACACCCAGCG 61.764 63.158 0.00 0.00 0.00 5.18
244 245 0.321830 TAAGGGCGTGTTAGGTTGCC 60.322 55.000 0.00 0.00 46.82 4.52
251 252 4.992515 CCGTGTAAGGGCGTGTTA 57.007 55.556 0.00 0.00 33.71 2.41
282 283 4.568359 GTGCAACATCTATGTACCAGTCTG 59.432 45.833 0.00 0.00 40.80 3.51
285 286 3.056107 ACGTGCAACATCTATGTACCAGT 60.056 43.478 0.00 0.00 40.80 4.00
291 292 2.346803 GTCCACGTGCAACATCTATGT 58.653 47.619 10.91 0.00 44.20 2.29
292 293 1.665679 GGTCCACGTGCAACATCTATG 59.334 52.381 10.91 0.00 35.74 2.23
293 294 1.277842 TGGTCCACGTGCAACATCTAT 59.722 47.619 10.91 0.00 35.74 1.98
294 295 0.682292 TGGTCCACGTGCAACATCTA 59.318 50.000 10.91 0.00 35.74 1.98
295 296 0.884704 GTGGTCCACGTGCAACATCT 60.885 55.000 10.91 0.00 35.74 2.90
297 298 1.896660 GGTGGTCCACGTGCAACAT 60.897 57.895 15.93 0.00 35.74 2.71
298 299 2.515057 GGTGGTCCACGTGCAACA 60.515 61.111 15.93 0.00 35.74 3.33
299 300 2.203153 AGGTGGTCCACGTGCAAC 60.203 61.111 16.35 10.35 34.83 4.17
310 323 3.490348 CCAGATGAACTTTTCAGGTGGT 58.510 45.455 9.65 0.00 43.98 4.16
389 404 7.406553 TGTTATTTATCGACATAAGCACTTGC 58.593 34.615 0.00 0.00 42.49 4.01
390 405 9.935682 ATTGTTATTTATCGACATAAGCACTTG 57.064 29.630 0.00 0.00 0.00 3.16
473 493 3.534554 AGCATGCGAGATGTTACATCAA 58.465 40.909 24.79 9.66 0.00 2.57
494 514 3.006537 GCTCCTGCCGTGTCCTATTATTA 59.993 47.826 0.00 0.00 0.00 0.98
505 525 0.602638 TACTTTGTGCTCCTGCCGTG 60.603 55.000 0.00 0.00 38.71 4.94
530 550 3.473625 CTCCTGTTCCGTTTTAACTGGT 58.526 45.455 10.44 0.00 43.01 4.00
611 631 1.657181 CAGCGGCGGTGTTTTGTTC 60.657 57.895 29.14 0.00 0.00 3.18
665 685 5.454966 AGCATTAATTACCTCCCCGAAAAT 58.545 37.500 0.00 0.00 0.00 1.82
682 702 8.097038 GTGATTCCCAATCTAGTATGAGCATTA 58.903 37.037 0.00 0.00 38.72 1.90
683 703 6.939163 GTGATTCCCAATCTAGTATGAGCATT 59.061 38.462 0.00 0.00 38.72 3.56
684 704 6.471146 GTGATTCCCAATCTAGTATGAGCAT 58.529 40.000 0.00 0.00 38.72 3.79
685 705 5.221722 GGTGATTCCCAATCTAGTATGAGCA 60.222 44.000 0.00 0.00 38.72 4.26
686 706 5.241662 GGTGATTCCCAATCTAGTATGAGC 58.758 45.833 0.00 0.00 38.72 4.26
687 707 5.473931 CGGTGATTCCCAATCTAGTATGAG 58.526 45.833 0.00 0.00 38.72 2.90
688 708 4.283467 CCGGTGATTCCCAATCTAGTATGA 59.717 45.833 0.00 0.00 38.72 2.15
689 709 4.563580 CCCGGTGATTCCCAATCTAGTATG 60.564 50.000 0.00 0.00 38.72 2.39
707 727 4.207165 CAATGGAAGAATCATAACCCGGT 58.793 43.478 0.00 0.00 0.00 5.28
715 735 4.641541 TCAACGATGCAATGGAAGAATCAT 59.358 37.500 0.00 0.00 0.00 2.45
717 737 4.621068 TCAACGATGCAATGGAAGAATC 57.379 40.909 0.00 0.00 0.00 2.52
730 750 8.736742 CGAAGAAAATAAATTGGATCAACGATG 58.263 33.333 0.00 0.00 0.00 3.84
731 751 8.458843 ACGAAGAAAATAAATTGGATCAACGAT 58.541 29.630 0.00 0.00 0.00 3.73
755 778 1.688735 TGCTAGATCCTCCAATCCACG 59.311 52.381 0.00 0.00 0.00 4.94
757 780 3.657610 TCTTGCTAGATCCTCCAATCCA 58.342 45.455 0.00 0.00 0.00 3.41
829 852 0.039165 CGGAATCGCTGATCCGATCA 60.039 55.000 10.67 10.67 46.29 2.92
842 865 7.259290 TCAAGGACTAAAATAATGCGGAATC 57.741 36.000 0.00 0.00 0.00 2.52
848 871 9.387123 GAATTCGATCAAGGACTAAAATAATGC 57.613 33.333 0.00 0.00 0.00 3.56
856 879 8.335532 ACAAAATGAATTCGATCAAGGACTAA 57.664 30.769 0.04 0.00 32.06 2.24
859 882 7.148755 CCAAACAAAATGAATTCGATCAAGGAC 60.149 37.037 0.04 0.00 32.06 3.85
862 885 6.091169 CCCCAAACAAAATGAATTCGATCAAG 59.909 38.462 0.04 0.00 32.06 3.02
869 892 6.237154 TCCAATCCCCAAACAAAATGAATTC 58.763 36.000 0.00 0.00 0.00 2.17
874 897 3.582208 TCCTCCAATCCCCAAACAAAATG 59.418 43.478 0.00 0.00 0.00 2.32
880 903 2.102578 CACATCCTCCAATCCCCAAAC 58.897 52.381 0.00 0.00 0.00 2.93
930 953 0.462581 CATGACCTGGATGGACGTGG 60.463 60.000 0.00 0.00 41.57 4.94
1090 1115 3.005472 TCCGTGAAAAGAGACGATGAGTT 59.995 43.478 0.00 0.00 37.81 3.01
1101 1132 3.138304 CACACCAAGATCCGTGAAAAGA 58.862 45.455 11.09 0.00 34.05 2.52
1103 1134 3.201353 TCACACCAAGATCCGTGAAAA 57.799 42.857 11.09 0.00 35.54 2.29
1104 1135 2.920724 TCACACCAAGATCCGTGAAA 57.079 45.000 11.09 0.00 35.54 2.69
1105 1136 2.301583 TGATCACACCAAGATCCGTGAA 59.698 45.455 11.09 1.54 41.39 3.18
1109 1160 2.094026 TCTGTGATCACACCAAGATCCG 60.094 50.000 24.56 11.54 45.40 4.18
1112 1163 3.326006 ACTGTCTGTGATCACACCAAGAT 59.674 43.478 24.56 9.46 45.40 2.40
1113 1164 2.700371 ACTGTCTGTGATCACACCAAGA 59.300 45.455 24.56 16.83 45.40 3.02
1116 1167 3.558931 AAACTGTCTGTGATCACACCA 57.441 42.857 24.56 20.60 45.40 4.17
1140 1191 2.571206 GCCAAAGTCGTTTCGTTCATC 58.429 47.619 0.00 0.00 0.00 2.92
1161 1212 2.882876 CCTCTGTTGCCTGCATGC 59.117 61.111 11.82 11.82 0.00 4.06
1162 1213 2.882876 GCCTCTGTTGCCTGCATG 59.117 61.111 0.00 0.00 0.00 4.06
1163 1214 2.749044 CGCCTCTGTTGCCTGCAT 60.749 61.111 0.00 0.00 0.00 3.96
1407 1458 1.005340 GCACCTGAGCAGAGAATTCG 58.995 55.000 0.00 0.00 0.00 3.34
1434 1485 3.838903 TCAGATGAGAGGATGATGGATGG 59.161 47.826 0.00 0.00 0.00 3.51
1460 1511 5.985530 GGCAATTCATCATCGATCGGATATA 59.014 40.000 16.41 0.00 32.85 0.86
1461 1512 4.813161 GGCAATTCATCATCGATCGGATAT 59.187 41.667 16.41 3.25 32.85 1.63
1462 1513 4.081476 AGGCAATTCATCATCGATCGGATA 60.081 41.667 16.41 0.67 32.85 2.59
1463 1514 3.005554 GGCAATTCATCATCGATCGGAT 58.994 45.455 16.41 8.18 35.09 4.18
1503 1603 6.342338 TGAGATCGATCAATCATGACTCAT 57.658 37.500 26.47 1.35 38.69 2.90
1504 1604 5.779529 TGAGATCGATCAATCATGACTCA 57.220 39.130 26.47 14.76 38.69 3.41
1505 1605 6.401260 GCAATGAGATCGATCAATCATGACTC 60.401 42.308 26.47 12.45 38.69 3.36
1506 1606 5.408909 GCAATGAGATCGATCAATCATGACT 59.591 40.000 26.47 10.46 38.69 3.41
1507 1607 5.390673 GGCAATGAGATCGATCAATCATGAC 60.391 44.000 26.47 19.45 38.69 3.06
1740 1848 7.765307 AGAATCGATCGGTAAGTTACAGTTAA 58.235 34.615 16.41 0.00 0.00 2.01
1741 1849 7.325660 AGAATCGATCGGTAAGTTACAGTTA 57.674 36.000 16.41 0.00 0.00 2.24
1742 1850 6.205101 AGAATCGATCGGTAAGTTACAGTT 57.795 37.500 16.41 5.96 0.00 3.16
1743 1851 5.831702 AGAATCGATCGGTAAGTTACAGT 57.168 39.130 16.41 2.31 0.00 3.55
2064 2172 9.681062 TTAAGAAAAAGAATTCATAGGGTCGAT 57.319 29.630 8.44 0.00 0.00 3.59
2065 2173 9.681062 ATTAAGAAAAAGAATTCATAGGGTCGA 57.319 29.630 8.44 0.00 0.00 4.20
2124 2240 4.420522 AATCCCAAACAGCAAAATGTGT 57.579 36.364 0.00 0.00 32.52 3.72
2125 2241 4.023878 CCAAATCCCAAACAGCAAAATGTG 60.024 41.667 0.00 0.00 32.52 3.21
2302 2418 8.899771 ACCGATAAGTTTATCCAAAGGTTATTG 58.100 33.333 6.35 0.00 36.95 1.90
2473 2592 2.684001 TGCCGGATTTACTACAGTGG 57.316 50.000 5.05 0.00 0.00 4.00
2543 2664 1.367599 GCCACTGCTGCTAGCTGAAG 61.368 60.000 24.19 24.19 41.94 3.02
3048 3193 2.066262 ACTACGACAACAATTGCGAGG 58.934 47.619 5.05 2.74 35.33 4.63
3052 3197 2.806244 AGGACACTACGACAACAATTGC 59.194 45.455 5.05 0.00 0.00 3.56
3165 3311 5.582689 AGCAACTGGATAAATGGTAAAGC 57.417 39.130 0.00 0.00 0.00 3.51
3166 3312 8.739972 AGTTTAGCAACTGGATAAATGGTAAAG 58.260 33.333 8.68 0.00 42.74 1.85
3167 3313 8.644374 AGTTTAGCAACTGGATAAATGGTAAA 57.356 30.769 5.26 5.26 42.05 2.01
3191 4888 7.593825 CAATAACTCTTTTGTCCACCCTTTAG 58.406 38.462 0.00 0.00 0.00 1.85
3197 4894 4.518970 TGAGCAATAACTCTTTTGTCCACC 59.481 41.667 0.00 0.00 37.58 4.61
3212 4909 5.178252 GCATATCTCGCTTTTCTGAGCAATA 59.822 40.000 0.00 0.00 42.83 1.90
3219 4916 5.008415 AGGAATTGCATATCTCGCTTTTCTG 59.992 40.000 0.00 0.00 0.00 3.02
3226 4923 5.871524 TGAGAATAGGAATTGCATATCTCGC 59.128 40.000 15.71 3.02 0.00 5.03
3296 4993 4.330250 TGCTCTTTTCCTTCTCTTCCATG 58.670 43.478 0.00 0.00 0.00 3.66
3367 5064 1.985159 AGCTAATCCAACACCCAGACA 59.015 47.619 0.00 0.00 0.00 3.41
3368 5065 2.359900 CAGCTAATCCAACACCCAGAC 58.640 52.381 0.00 0.00 0.00 3.51
3372 5069 1.098050 CTGCAGCTAATCCAACACCC 58.902 55.000 0.00 0.00 0.00 4.61
3534 5534 3.706373 GGCTGGAGTTCCTCGGCA 61.706 66.667 0.00 0.00 33.85 5.69
3535 5535 3.394836 AGGCTGGAGTTCCTCGGC 61.395 66.667 0.00 3.53 36.82 5.54
3536 5536 2.581354 CAGGCTGGAGTTCCTCGG 59.419 66.667 6.61 0.00 36.82 4.63
3537 5537 1.984570 TCCAGGCTGGAGTTCCTCG 60.985 63.158 32.01 3.57 42.67 4.63
3582 5582 1.369321 GGCTAGAGCAGGGATTCCG 59.631 63.158 3.54 0.00 44.36 4.30
3585 5585 2.812619 GCGGGCTAGAGCAGGGATT 61.813 63.158 3.54 0.00 44.36 3.01
3605 5605 4.680537 AGGCGTCGGTGGGAGACT 62.681 66.667 0.00 0.00 36.53 3.24
3631 5632 2.133858 AACCATATCTGGGTAGGGGG 57.866 55.000 1.74 0.00 42.20 5.40
3654 5655 0.464373 CATGGTCTTGTCCATCCCGG 60.464 60.000 0.00 0.00 45.23 5.73
3671 5672 5.221422 GGTCGAGAAGAAGATCATTCCTCAT 60.221 44.000 0.00 0.00 0.00 2.90
3723 5725 3.504863 CATGCAAAACTTCCATCTTCCG 58.495 45.455 0.00 0.00 0.00 4.30
3733 5737 3.891366 AGTGAACTAGGCATGCAAAACTT 59.109 39.130 21.36 3.24 0.00 2.66
3734 5738 3.254166 CAGTGAACTAGGCATGCAAAACT 59.746 43.478 21.36 9.77 0.00 2.66
3754 5758 4.394712 GACTGCCCCCACCGACAG 62.395 72.222 0.00 0.00 36.22 3.51
3821 5832 1.090052 GCGTTGGTCACATAGAGGGC 61.090 60.000 0.00 0.00 0.00 5.19
3843 5854 2.820059 TGGATAATACTGCTGCCGAG 57.180 50.000 0.00 0.00 0.00 4.63
3869 5880 4.043859 TGGTGCCGCCAGTATACT 57.956 55.556 0.00 0.00 43.61 2.12
3887 5898 1.448540 CGCAGATCAAGAAGCCGGT 60.449 57.895 1.90 0.00 0.00 5.28
3897 5908 0.104120 CCACCGTAATCCGCAGATCA 59.896 55.000 0.00 0.00 34.38 2.92


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

AutoCloner maintained by Alex Coulton.