Multiple sequence alignment - TraesCS5D01G511300

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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 TraesCS5D01G511300 chr5D 100.000 3592 0 0 1 3592 535995617 535999208 0.000000e+00 6634.0
1 TraesCS5D01G511300 chr5D 78.747 1101 155 47 1533 2604 536025747 536026797 0.000000e+00 664.0
2 TraesCS5D01G511300 chr5D 77.534 1095 173 42 1533 2604 536279623 536278579 3.090000e-165 592.0
3 TraesCS5D01G511300 chr5D 77.916 1046 162 41 1593 2604 536254269 536253259 4.000000e-164 588.0
4 TraesCS5D01G511300 chr5D 81.629 626 77 19 2000 2609 536048214 536048817 5.390000e-133 484.0
5 TraesCS5D01G511300 chr5D 83.013 312 28 11 998 1306 536280170 536279881 3.560000e-65 259.0
6 TraesCS5D01G511300 chr5D 82.043 323 36 16 999 1304 536254882 536254565 4.600000e-64 255.0
7 TraesCS5D01G511300 chr5D 82.524 309 29 11 998 1303 536025200 536025486 7.700000e-62 248.0
8 TraesCS5D01G511300 chr5D 85.294 68 10 0 2520 2587 536088815 536088882 1.790000e-08 71.3
9 TraesCS5D01G511300 chr5D 92.857 42 3 0 2649 2690 536048825 536048866 1.080000e-05 62.1
10 TraesCS5D01G511300 chr5D 89.130 46 4 1 2646 2690 536253252 536253207 5.010000e-04 56.5
11 TraesCS5D01G511300 chr5B 89.245 2873 200 43 766 3592 676461115 676463924 0.000000e+00 3493.0
12 TraesCS5D01G511300 chr5B 77.890 692 113 22 1543 2210 676537445 676536770 9.350000e-106 394.0
13 TraesCS5D01G511300 chr5B 82.663 323 29 11 988 1306 676549475 676549176 9.890000e-66 261.0
14 TraesCS5D01G511300 chr5B 91.304 46 3 1 2646 2690 676536381 676536336 1.080000e-05 62.1
15 TraesCS5D01G511300 chr4A 88.530 1979 152 30 185 2130 633377547 633379483 0.000000e+00 2327.0
16 TraesCS5D01G511300 chr4A 87.711 1953 183 27 1661 3589 635863530 635861611 0.000000e+00 2224.0
17 TraesCS5D01G511300 chr4A 87.206 1532 132 27 147 1656 635865445 635863956 0.000000e+00 1685.0
18 TraesCS5D01G511300 chr4A 75.952 1759 286 81 916 2604 635303400 635301709 0.000000e+00 778.0
19 TraesCS5D01G511300 chr4A 75.782 1759 289 82 916 2604 635744848 635743157 0.000000e+00 761.0
20 TraesCS5D01G511300 chr4A 92.338 509 26 7 3085 3592 633485510 633486006 0.000000e+00 712.0
21 TraesCS5D01G511300 chr4A 92.141 509 27 7 3085 3592 633444519 633445015 0.000000e+00 706.0
22 TraesCS5D01G511300 chr4A 91.749 509 29 7 3085 3592 633401618 633402114 0.000000e+00 695.0
23 TraesCS5D01G511300 chr4A 79.015 1096 160 43 1543 2604 635275101 635274042 0.000000e+00 686.0
24 TraesCS5D01G511300 chr4A 91.356 509 31 7 3085 3592 633646231 633646727 0.000000e+00 684.0
25 TraesCS5D01G511300 chr4A 91.159 509 32 7 3085 3592 633601008 633601504 0.000000e+00 678.0
26 TraesCS5D01G511300 chr4A 91.159 509 32 7 3085 3592 633708147 633708643 0.000000e+00 678.0
27 TraesCS5D01G511300 chr4A 89.058 329 26 5 2129 2456 633444181 633444500 2.010000e-107 399.0
28 TraesCS5D01G511300 chr4A 88.754 329 27 5 2129 2456 633401280 633401599 9.350000e-106 394.0
29 TraesCS5D01G511300 chr4A 88.754 329 27 5 2129 2456 633485172 633485491 9.350000e-106 394.0
30 TraesCS5D01G511300 chr4A 88.580 324 27 5 2134 2456 633645898 633646212 5.630000e-103 385.0
31 TraesCS5D01G511300 chr4A 88.272 324 28 5 2134 2456 633600675 633600989 2.620000e-101 379.0
32 TraesCS5D01G511300 chr4A 87.842 329 30 5 2129 2456 633707809 633708128 9.410000e-101 377.0
33 TraesCS5D01G511300 chr4A 78.935 432 51 25 904 1304 635275787 635275365 1.280000e-64 257.0
34 TraesCS5D01G511300 chr4A 82.796 279 34 7 2308 2582 635300221 635299953 1.670000e-58 237.0
35 TraesCS5D01G511300 chr4A 86.765 68 9 0 2520 2587 635724570 635724503 3.850000e-10 76.8
36 TraesCS5D01G511300 chr4A 86.765 68 3 3 2646 2712 635743150 635743088 1.790000e-08 71.3
37 TraesCS5D01G511300 chr4A 89.796 49 5 0 2642 2690 635301700 635301652 2.990000e-06 63.9
38 TraesCS5D01G511300 chr4A 91.304 46 3 1 2646 2690 635274035 635273990 1.080000e-05 62.1
39 TraesCS5D01G511300 chr6A 85.009 527 69 8 231 751 551626998 551627520 8.830000e-146 527.0
40 TraesCS5D01G511300 chrUn 84.211 532 73 9 154 679 350568299 350568825 1.150000e-139 507.0
41 TraesCS5D01G511300 chrUn 84.211 532 73 9 154 679 359467127 359467653 1.150000e-139 507.0
42 TraesCS5D01G511300 chr7A 84.211 532 73 9 154 679 31517575 31518101 1.150000e-139 507.0
43 TraesCS5D01G511300 chr7A 84.211 532 73 9 154 679 31536016 31536542 1.150000e-139 507.0
44 TraesCS5D01G511300 chr7A 84.023 532 74 9 154 679 31554457 31554983 5.350000e-138 501.0
45 TraesCS5D01G511300 chr3D 80.519 616 92 20 158 751 302053884 302054493 7.070000e-122 448.0
46 TraesCS5D01G511300 chr3D 79.836 610 103 17 153 751 347448138 347447538 9.220000e-116 427.0
47 TraesCS5D01G511300 chr3D 96.599 147 3 2 1 146 326133138 326132993 3.580000e-60 243.0
48 TraesCS5D01G511300 chr4D 96.644 149 5 0 1 149 211043043 211042895 7.700000e-62 248.0
49 TraesCS5D01G511300 chr4D 96.575 146 5 0 1 146 500810402 500810257 3.580000e-60 243.0
50 TraesCS5D01G511300 chr4D 91.071 168 13 2 1 167 443538920 443538754 3.610000e-55 226.0
51 TraesCS5D01G511300 chr2D 97.260 146 4 0 1 146 412469983 412470128 7.700000e-62 248.0
52 TraesCS5D01G511300 chr1A 97.260 146 4 0 1 146 117160922 117161067 7.700000e-62 248.0
53 TraesCS5D01G511300 chr7D 97.241 145 2 2 1 143 68847391 68847247 9.960000e-61 244.0
54 TraesCS5D01G511300 chr7D 94.805 154 7 1 1 153 109115884 109116037 4.630000e-59 239.0
55 TraesCS5D01G511300 chr7B 91.279 172 10 5 1 167 636926413 636926584 2.790000e-56 230.0
56 TraesCS5D01G511300 chr2B 92.308 52 3 1 701 751 470909279 470909330 4.970000e-09 73.1


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 TraesCS5D01G511300 chr5D 535995617 535999208 3591 False 6634.000000 6634 100.000000 1 3592 1 chr5D.!!$F1 3591
1 TraesCS5D01G511300 chr5D 536025200 536026797 1597 False 456.000000 664 80.635500 998 2604 2 chr5D.!!$F3 1606
2 TraesCS5D01G511300 chr5D 536278579 536280170 1591 True 425.500000 592 80.273500 998 2604 2 chr5D.!!$R2 1606
3 TraesCS5D01G511300 chr5D 536253207 536254882 1675 True 299.833333 588 83.029667 999 2690 3 chr5D.!!$R1 1691
4 TraesCS5D01G511300 chr5D 536048214 536048866 652 False 273.050000 484 87.243000 2000 2690 2 chr5D.!!$F4 690
5 TraesCS5D01G511300 chr5B 676461115 676463924 2809 False 3493.000000 3493 89.245000 766 3592 1 chr5B.!!$F1 2826
6 TraesCS5D01G511300 chr5B 676536336 676537445 1109 True 228.050000 394 84.597000 1543 2690 2 chr5B.!!$R2 1147
7 TraesCS5D01G511300 chr4A 633377547 633379483 1936 False 2327.000000 2327 88.530000 185 2130 1 chr4A.!!$F1 1945
8 TraesCS5D01G511300 chr4A 635861611 635865445 3834 True 1954.500000 2224 87.458500 147 3589 2 chr4A.!!$R5 3442
9 TraesCS5D01G511300 chr4A 633485172 633486006 834 False 553.000000 712 90.546000 2129 3592 2 chr4A.!!$F4 1463
10 TraesCS5D01G511300 chr4A 633444181 633445015 834 False 552.500000 706 90.599500 2129 3592 2 chr4A.!!$F3 1463
11 TraesCS5D01G511300 chr4A 633401280 633402114 834 False 544.500000 695 90.251500 2129 3592 2 chr4A.!!$F2 1463
12 TraesCS5D01G511300 chr4A 633645898 633646727 829 False 534.500000 684 89.968000 2134 3592 2 chr4A.!!$F6 1458
13 TraesCS5D01G511300 chr4A 633600675 633601504 829 False 528.500000 678 89.715500 2134 3592 2 chr4A.!!$F5 1458
14 TraesCS5D01G511300 chr4A 633707809 633708643 834 False 527.500000 678 89.500500 2129 3592 2 chr4A.!!$F7 1463
15 TraesCS5D01G511300 chr4A 635743088 635744848 1760 True 416.150000 761 81.273500 916 2712 2 chr4A.!!$R4 1796
16 TraesCS5D01G511300 chr4A 635299953 635303400 3447 True 359.633333 778 82.848000 916 2690 3 chr4A.!!$R3 1774
17 TraesCS5D01G511300 chr4A 635273990 635275787 1797 True 335.033333 686 83.084667 904 2690 3 chr4A.!!$R2 1786
18 TraesCS5D01G511300 chr6A 551626998 551627520 522 False 527.000000 527 85.009000 231 751 1 chr6A.!!$F1 520
19 TraesCS5D01G511300 chrUn 350568299 350568825 526 False 507.000000 507 84.211000 154 679 1 chrUn.!!$F1 525
20 TraesCS5D01G511300 chrUn 359467127 359467653 526 False 507.000000 507 84.211000 154 679 1 chrUn.!!$F2 525
21 TraesCS5D01G511300 chr7A 31517575 31518101 526 False 507.000000 507 84.211000 154 679 1 chr7A.!!$F1 525
22 TraesCS5D01G511300 chr7A 31536016 31536542 526 False 507.000000 507 84.211000 154 679 1 chr7A.!!$F2 525
23 TraesCS5D01G511300 chr7A 31554457 31554983 526 False 501.000000 501 84.023000 154 679 1 chr7A.!!$F3 525
24 TraesCS5D01G511300 chr3D 302053884 302054493 609 False 448.000000 448 80.519000 158 751 1 chr3D.!!$F1 593
25 TraesCS5D01G511300 chr3D 347447538 347448138 600 True 427.000000 427 79.836000 153 751 1 chr3D.!!$R2 598

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
31 32 0.028902 GTTGTCAAACGCTTCCGCTT 59.971 50.0 0.00 0.00 38.22 4.68 F
82 83 0.107456 CCCCTCTCGTTGCTATGCAT 59.893 55.0 3.79 3.79 38.76 3.96 F
176 177 0.111061 AGGATCAACACCAAGCAGCA 59.889 50.0 0.00 0.00 0.00 4.41 F
752 782 0.249238 GTCCGGCTGTAGATGCTCAG 60.249 60.0 0.00 0.00 35.12 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1439 1595 0.179121 TAACTGACGCGCCCTATGTG 60.179 55.0 5.73 0.00 0.00 3.21 R
1477 1633 0.249911 GCCGGCCACTACTATTCCAG 60.250 60.0 18.11 0.00 0.00 3.86 R
1659 2288 0.535335 TTAGATCGCCAGGTGACACC 59.465 55.0 17.43 17.43 38.99 4.16 R
2627 3319 0.180406 AATAAACCGCCGATGGAGCT 59.820 50.0 0.00 0.00 0.00 4.09 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
21 22 3.414549 ACATCAACCACGTTGTCAAAC 57.585 42.857 4.56 0.00 43.23 2.93
29 30 4.205584 GTTGTCAAACGCTTCCGC 57.794 55.556 0.00 0.00 38.22 5.54
30 31 1.647084 GTTGTCAAACGCTTCCGCT 59.353 52.632 0.00 0.00 38.22 5.52
31 32 0.028902 GTTGTCAAACGCTTCCGCTT 59.971 50.000 0.00 0.00 38.22 4.68
32 33 0.736053 TTGTCAAACGCTTCCGCTTT 59.264 45.000 0.00 0.00 38.22 3.51
33 34 0.306533 TGTCAAACGCTTCCGCTTTC 59.693 50.000 0.00 0.00 38.22 2.62
34 35 0.721483 GTCAAACGCTTCCGCTTTCG 60.721 55.000 0.00 0.00 38.22 3.46
55 56 2.696989 TCTACGAGGATACGTGGACA 57.303 50.000 0.00 0.00 45.53 4.02
56 57 2.283298 TCTACGAGGATACGTGGACAC 58.717 52.381 0.00 0.00 45.53 3.67
57 58 2.011947 CTACGAGGATACGTGGACACA 58.988 52.381 0.00 0.00 44.98 3.72
58 59 0.524862 ACGAGGATACGTGGACACAC 59.475 55.000 0.00 0.00 44.84 3.82
59 60 0.809385 CGAGGATACGTGGACACACT 59.191 55.000 0.00 0.00 45.50 3.55
60 61 1.202154 CGAGGATACGTGGACACACTC 60.202 57.143 0.00 0.00 45.50 3.51
61 62 2.093106 GAGGATACGTGGACACACTCT 58.907 52.381 0.00 0.00 45.50 3.24
62 63 2.093106 AGGATACGTGGACACACTCTC 58.907 52.381 0.00 0.00 45.50 3.20
63 64 1.134560 GGATACGTGGACACACTCTCC 59.865 57.143 0.00 0.00 45.50 3.71
64 65 1.134560 GATACGTGGACACACTCTCCC 59.865 57.143 0.00 0.00 45.50 4.30
65 66 0.896940 TACGTGGACACACTCTCCCC 60.897 60.000 0.00 0.00 45.50 4.81
66 67 2.943978 CGTGGACACACTCTCCCCC 61.944 68.421 3.12 0.00 45.50 5.40
67 68 1.536662 GTGGACACACTCTCCCCCT 60.537 63.158 0.00 0.00 44.29 4.79
68 69 1.229209 TGGACACACTCTCCCCCTC 60.229 63.158 0.00 0.00 0.00 4.30
69 70 1.079438 GGACACACTCTCCCCCTCT 59.921 63.158 0.00 0.00 0.00 3.69
70 71 0.973496 GGACACACTCTCCCCCTCTC 60.973 65.000 0.00 0.00 0.00 3.20
71 72 1.304547 ACACACTCTCCCCCTCTCG 60.305 63.158 0.00 0.00 0.00 4.04
72 73 1.304547 CACACTCTCCCCCTCTCGT 60.305 63.158 0.00 0.00 0.00 4.18
73 74 0.900647 CACACTCTCCCCCTCTCGTT 60.901 60.000 0.00 0.00 0.00 3.85
74 75 0.900647 ACACTCTCCCCCTCTCGTTG 60.901 60.000 0.00 0.00 0.00 4.10
75 76 1.985116 ACTCTCCCCCTCTCGTTGC 60.985 63.158 0.00 0.00 0.00 4.17
76 77 1.684049 CTCTCCCCCTCTCGTTGCT 60.684 63.158 0.00 0.00 0.00 3.91
77 78 0.395862 CTCTCCCCCTCTCGTTGCTA 60.396 60.000 0.00 0.00 0.00 3.49
78 79 0.261991 TCTCCCCCTCTCGTTGCTAT 59.738 55.000 0.00 0.00 0.00 2.97
79 80 0.390860 CTCCCCCTCTCGTTGCTATG 59.609 60.000 0.00 0.00 0.00 2.23
80 81 1.227674 CCCCCTCTCGTTGCTATGC 60.228 63.158 0.00 0.00 0.00 3.14
81 82 1.522092 CCCCTCTCGTTGCTATGCA 59.478 57.895 0.00 0.00 36.47 3.96
82 83 0.107456 CCCCTCTCGTTGCTATGCAT 59.893 55.000 3.79 3.79 38.76 3.96
83 84 1.506493 CCCTCTCGTTGCTATGCATC 58.494 55.000 0.19 0.00 38.76 3.91
84 85 1.069823 CCCTCTCGTTGCTATGCATCT 59.930 52.381 0.19 0.00 38.76 2.90
85 86 2.402305 CCTCTCGTTGCTATGCATCTC 58.598 52.381 0.19 0.00 38.76 2.75
86 87 2.402305 CTCTCGTTGCTATGCATCTCC 58.598 52.381 0.19 0.00 38.76 3.71
87 88 2.034878 TCTCGTTGCTATGCATCTCCT 58.965 47.619 0.19 0.00 38.76 3.69
88 89 3.222603 TCTCGTTGCTATGCATCTCCTA 58.777 45.455 0.19 0.00 38.76 2.94
89 90 3.254411 TCTCGTTGCTATGCATCTCCTAG 59.746 47.826 0.19 0.00 38.76 3.02
90 91 3.222603 TCGTTGCTATGCATCTCCTAGA 58.777 45.455 0.19 0.00 38.76 2.43
91 92 3.829026 TCGTTGCTATGCATCTCCTAGAT 59.171 43.478 0.19 0.00 38.76 1.98
92 93 5.010282 TCGTTGCTATGCATCTCCTAGATA 58.990 41.667 0.19 0.00 38.76 1.98
93 94 5.124617 TCGTTGCTATGCATCTCCTAGATAG 59.875 44.000 0.19 0.00 38.76 2.08
94 95 5.124617 CGTTGCTATGCATCTCCTAGATAGA 59.875 44.000 0.19 0.00 38.76 1.98
95 96 6.183360 CGTTGCTATGCATCTCCTAGATAGAT 60.183 42.308 0.19 0.00 38.76 1.98
96 97 6.957920 TGCTATGCATCTCCTAGATAGATC 57.042 41.667 0.19 0.00 32.12 2.75
97 98 6.671605 TGCTATGCATCTCCTAGATAGATCT 58.328 40.000 0.19 0.00 32.12 2.75
98 99 7.124721 TGCTATGCATCTCCTAGATAGATCTT 58.875 38.462 0.19 0.00 32.12 2.40
99 100 7.068470 TGCTATGCATCTCCTAGATAGATCTTG 59.932 40.741 0.19 0.00 32.12 3.02
100 101 5.657826 TGCATCTCCTAGATAGATCTTGC 57.342 43.478 0.00 0.69 38.32 4.01
101 102 4.157472 TGCATCTCCTAGATAGATCTTGCG 59.843 45.833 0.00 0.00 36.48 4.85
102 103 4.157656 GCATCTCCTAGATAGATCTTGCGT 59.842 45.833 0.00 0.00 38.32 5.24
103 104 5.639757 CATCTCCTAGATAGATCTTGCGTG 58.360 45.833 0.00 0.00 38.32 5.34
104 105 4.974399 TCTCCTAGATAGATCTTGCGTGA 58.026 43.478 0.00 0.00 38.32 4.35
105 106 5.000591 TCTCCTAGATAGATCTTGCGTGAG 58.999 45.833 0.00 1.23 38.32 3.51
139 140 6.698359 TTTTTAAATTGCATGCTACGTTCC 57.302 33.333 20.33 0.00 0.00 3.62
140 141 2.939460 AAATTGCATGCTACGTTCCC 57.061 45.000 20.33 0.00 0.00 3.97
141 142 1.832883 AATTGCATGCTACGTTCCCA 58.167 45.000 20.33 0.00 0.00 4.37
142 143 1.832883 ATTGCATGCTACGTTCCCAA 58.167 45.000 20.33 1.11 0.00 4.12
143 144 1.610363 TTGCATGCTACGTTCCCAAA 58.390 45.000 20.33 0.00 0.00 3.28
144 145 0.878416 TGCATGCTACGTTCCCAAAC 59.122 50.000 20.33 0.00 0.00 2.93
145 146 0.878416 GCATGCTACGTTCCCAAACA 59.122 50.000 11.37 0.00 34.93 2.83
176 177 0.111061 AGGATCAACACCAAGCAGCA 59.889 50.000 0.00 0.00 0.00 4.41
177 178 1.180029 GGATCAACACCAAGCAGCAT 58.820 50.000 0.00 0.00 0.00 3.79
200 201 1.097232 CTCGGCATTTGAGCAATCCA 58.903 50.000 0.00 0.00 35.83 3.41
262 281 2.980233 GGCAAGCAAGACCGCACT 60.980 61.111 0.00 0.00 0.00 4.40
294 313 1.491670 CAAGGCTACATCGTCATCCG 58.508 55.000 0.00 0.00 38.13 4.18
441 464 8.840200 TCGCCCTCTCCTTTTATATAATCTAT 57.160 34.615 0.00 0.00 0.00 1.98
475 498 3.794270 CGATGTGCCGGATCGTTT 58.206 55.556 5.05 0.00 38.31 3.60
480 503 1.717194 TGTGCCGGATCGTTTAACTC 58.283 50.000 5.05 0.00 0.00 3.01
481 504 1.004595 GTGCCGGATCGTTTAACTCC 58.995 55.000 5.05 0.00 0.00 3.85
673 699 0.918619 CACGGATTTACGTAGTGCCG 59.081 55.000 22.29 22.29 46.75 5.69
751 781 0.684479 AGTCCGGCTGTAGATGCTCA 60.684 55.000 0.00 0.00 0.00 4.26
752 782 0.249238 GTCCGGCTGTAGATGCTCAG 60.249 60.000 0.00 0.00 35.12 3.35
754 784 0.678395 CCGGCTGTAGATGCTCAGAT 59.322 55.000 0.00 0.00 34.02 2.90
757 787 2.094803 CGGCTGTAGATGCTCAGATAGG 60.095 54.545 0.00 0.00 34.02 2.57
758 788 2.896685 GGCTGTAGATGCTCAGATAGGT 59.103 50.000 0.00 0.00 34.02 3.08
761 791 3.818210 CTGTAGATGCTCAGATAGGTCGT 59.182 47.826 0.00 0.00 34.02 4.34
780 810 1.135315 GTGTCGGACATGCCTAACGTA 60.135 52.381 14.78 0.00 0.00 3.57
789 820 0.806868 TGCCTAACGTACCGTCTCAG 59.193 55.000 0.00 0.00 39.99 3.35
819 856 1.073923 ACTCTCCGAAAACAATGGGCT 59.926 47.619 0.00 0.00 0.00 5.19
887 924 4.459089 GCTGCCTCGTCTGGGGAC 62.459 72.222 0.00 0.00 38.97 4.46
888 925 2.681778 CTGCCTCGTCTGGGGACT 60.682 66.667 0.00 0.00 40.10 3.85
889 926 2.997315 TGCCTCGTCTGGGGACTG 60.997 66.667 0.00 0.00 40.10 3.51
890 927 3.775654 GCCTCGTCTGGGGACTGG 61.776 72.222 0.00 0.00 40.10 4.00
892 929 3.077556 CTCGTCTGGGGACTGGGG 61.078 72.222 0.00 0.00 40.10 4.96
977 1019 4.679106 CGAGCAAGCTTTCCAGATCTCTAA 60.679 45.833 0.00 0.00 0.00 2.10
1250 1350 2.420967 CGGATCCCCAGGTAATTTCGTT 60.421 50.000 6.06 0.00 0.00 3.85
1465 1621 2.383527 GCGCGTCAGTTAGCAAGCT 61.384 57.895 8.43 0.00 0.00 3.74
1471 1627 3.181967 AGTTAGCAAGCTCGCGCG 61.182 61.111 26.76 26.76 42.32 6.86
1485 1642 2.320587 GCGCGCCCATCTGGAATAG 61.321 63.158 23.24 0.00 37.39 1.73
1576 1775 3.259374 TCAGCATATCTTGGTAGCTAGCC 59.741 47.826 19.78 12.11 33.85 3.93
1584 1783 1.966845 TGGTAGCTAGCCCTTTTCCT 58.033 50.000 19.78 0.00 0.00 3.36
1585 1784 2.275466 TGGTAGCTAGCCCTTTTCCTT 58.725 47.619 19.78 0.00 0.00 3.36
1586 1785 2.647802 TGGTAGCTAGCCCTTTTCCTTT 59.352 45.455 19.78 0.00 0.00 3.11
1587 1786 3.847780 TGGTAGCTAGCCCTTTTCCTTTA 59.152 43.478 19.78 0.00 0.00 1.85
1588 1787 4.290196 TGGTAGCTAGCCCTTTTCCTTTAA 59.710 41.667 19.78 0.00 0.00 1.52
1615 1821 9.454859 TTTGTTGACCTGTATTTTCCAAATTTT 57.545 25.926 0.00 0.00 0.00 1.82
1641 1849 2.015456 TCAGGTGGAGAAGCTCTTCA 57.985 50.000 11.69 0.00 41.84 3.02
1697 2326 2.868964 ACTGGCTATTCCTACCCAGA 57.131 50.000 12.07 0.00 46.04 3.86
1889 2548 1.228124 CAAGGGTTGGTTCTGCCGA 60.228 57.895 0.00 0.00 41.21 5.54
1991 2650 1.627297 GGAAGAGAGCCCCGGTCAAT 61.627 60.000 0.00 0.00 31.89 2.57
2143 2803 3.641648 TGCAACTTGATTTTAGTGCAGC 58.358 40.909 0.00 0.00 31.17 5.25
2167 2830 2.939103 AGGTACAAGCGAATGAATCAGC 59.061 45.455 0.00 0.00 0.00 4.26
2176 2839 2.292569 CGAATGAATCAGCCCATCAAGG 59.707 50.000 0.00 0.00 37.03 3.61
2210 2873 1.442184 AGCACACGTCGTCGATGAC 60.442 57.895 24.88 24.88 40.62 3.06
2211 2874 1.728074 GCACACGTCGTCGATGACA 60.728 57.895 31.32 0.01 38.84 3.58
2212 2875 1.272784 GCACACGTCGTCGATGACAA 61.273 55.000 31.32 0.00 38.84 3.18
2216 2879 2.158959 CGTCGTCGATGACAAGCCC 61.159 63.158 31.32 9.21 38.84 5.19
2217 2880 2.158959 GTCGTCGATGACAAGCCCG 61.159 63.158 28.64 6.43 38.75 6.13
2226 2889 1.301716 GACAAGCCCGCTCTCAACA 60.302 57.895 0.00 0.00 0.00 3.33
2229 2892 0.883833 CAAGCCCGCTCTCAACAATT 59.116 50.000 0.00 0.00 0.00 2.32
2235 2898 0.592637 CGCTCTCAACAATTGCACCA 59.407 50.000 5.05 0.00 0.00 4.17
2237 2900 2.730090 CGCTCTCAACAATTGCACCATC 60.730 50.000 5.05 0.00 0.00 3.51
2250 2931 0.752658 CACCATCGGGATCAGCAGTA 59.247 55.000 0.00 0.00 38.05 2.74
2252 2933 1.837439 ACCATCGGGATCAGCAGTAAA 59.163 47.619 0.00 0.00 38.05 2.01
2470 3151 1.446791 GGGATGAGGAGAGCAGCAG 59.553 63.158 0.00 0.00 0.00 4.24
2555 3239 1.734655 AGAAGAGGTGGAGAAAGCCA 58.265 50.000 0.00 0.00 35.02 4.75
2625 3317 1.412710 CTGGCTTCGGATTACCTAGCA 59.587 52.381 0.00 0.00 40.67 3.49
2627 3319 1.687123 GGCTTCGGATTACCTAGCAGA 59.313 52.381 0.00 0.00 40.67 4.26
2658 3350 4.510340 CGGCGGTTTATTATAGTTTGCTCT 59.490 41.667 0.00 0.00 0.00 4.09
2660 3352 5.526111 GGCGGTTTATTATAGTTTGCTCTGA 59.474 40.000 0.00 0.00 0.00 3.27
2757 3462 1.004560 GTCAGTGCAGTGCTGGCTA 60.005 57.895 17.07 0.00 35.84 3.93
2759 3464 0.108396 TCAGTGCAGTGCTGGCTAAA 59.892 50.000 17.07 0.00 34.89 1.85
2776 3481 8.604890 GCTGGCTAAAGTTAGAACTACATAAAG 58.395 37.037 2.18 0.00 38.57 1.85
2811 3517 2.002586 GTGTCTTGTCATCGTGATGGG 58.997 52.381 9.81 0.00 39.24 4.00
2812 3518 1.009829 GTCTTGTCATCGTGATGGGC 58.990 55.000 9.81 4.62 39.24 5.36
2873 3592 3.309121 CCCTAATTCAGTCAACCCATGGT 60.309 47.826 11.73 0.00 37.65 3.55
2877 3596 2.465860 TCAGTCAACCCATGGTTACG 57.534 50.000 11.73 0.00 45.01 3.18
2944 3663 1.137872 CTCTGATCTTCTTCACCCCCG 59.862 57.143 0.00 0.00 0.00 5.73
3030 3774 5.667400 CAGAATTTCTGCTCGTTCTTCGAAG 60.667 44.000 19.35 19.35 40.57 3.79
3062 3806 4.037446 TCATTAAACCACCAACAGCAAGAC 59.963 41.667 0.00 0.00 0.00 3.01
3105 3876 3.378742 CAGTAAGACTGGAGCACTACGAT 59.621 47.826 0.00 0.00 42.35 3.73
3129 3900 6.713762 TTCCGACGGTAGAAATAGGATTTA 57.286 37.500 14.79 0.00 0.00 1.40
3151 3922 0.250338 GCTCCCAGTGACGAAAACCT 60.250 55.000 0.00 0.00 0.00 3.50
3152 3923 1.001633 GCTCCCAGTGACGAAAACCTA 59.998 52.381 0.00 0.00 0.00 3.08
3153 3924 2.685100 CTCCCAGTGACGAAAACCTAC 58.315 52.381 0.00 0.00 0.00 3.18
3176 4738 2.311542 AGCATTACATTCCCCAAGACCA 59.688 45.455 0.00 0.00 0.00 4.02
3264 4983 1.274703 ATAGGCACCACTGTCCCCAG 61.275 60.000 0.00 0.00 44.68 4.45
3359 5078 3.489229 CGAAGGACATTAGACATCAGCGA 60.489 47.826 0.00 0.00 0.00 4.93
3373 5092 2.107366 TCAGCGACCATCATTCCTACA 58.893 47.619 0.00 0.00 0.00 2.74
3394 5113 3.128764 CAGGACATATATCGCGGCTTAGA 59.871 47.826 6.13 0.00 0.00 2.10
3399 5118 4.022242 ACATATATCGCGGCTTAGACACTT 60.022 41.667 6.13 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.414549 GTTTGACAACGTGGTTGATGT 57.585 42.857 14.79 0.00 45.28 3.06
27 28 0.381089 ATCCTCGTAGACCGAAAGCG 59.619 55.000 0.00 0.00 46.75 4.68
28 29 2.601741 CGTATCCTCGTAGACCGAAAGC 60.602 54.545 0.00 0.00 46.75 3.51
29 30 2.611292 ACGTATCCTCGTAGACCGAAAG 59.389 50.000 0.00 0.00 46.75 2.62
30 31 2.352651 CACGTATCCTCGTAGACCGAAA 59.647 50.000 0.00 0.00 46.75 3.46
31 32 1.935873 CACGTATCCTCGTAGACCGAA 59.064 52.381 0.00 0.00 46.75 4.30
32 33 1.575244 CACGTATCCTCGTAGACCGA 58.425 55.000 0.00 0.00 45.00 4.69
33 34 0.585357 CCACGTATCCTCGTAGACCG 59.415 60.000 0.00 0.00 42.27 4.79
34 35 1.601430 GTCCACGTATCCTCGTAGACC 59.399 57.143 6.55 0.00 42.92 3.85
35 36 2.031437 GTGTCCACGTATCCTCGTAGAC 59.969 54.545 9.85 9.85 46.47 2.59
36 37 2.283298 GTGTCCACGTATCCTCGTAGA 58.717 52.381 0.00 0.00 42.27 2.59
37 38 2.011947 TGTGTCCACGTATCCTCGTAG 58.988 52.381 0.00 0.00 42.27 3.51
38 39 1.739466 GTGTGTCCACGTATCCTCGTA 59.261 52.381 0.00 0.00 42.27 3.43
39 40 0.524862 GTGTGTCCACGTATCCTCGT 59.475 55.000 0.00 0.00 45.10 4.18
40 41 0.809385 AGTGTGTCCACGTATCCTCG 59.191 55.000 0.00 0.00 46.56 4.63
41 42 2.093106 AGAGTGTGTCCACGTATCCTC 58.907 52.381 0.00 0.00 46.56 3.71
42 43 2.093106 GAGAGTGTGTCCACGTATCCT 58.907 52.381 0.00 0.00 46.56 3.24
43 44 1.134560 GGAGAGTGTGTCCACGTATCC 59.865 57.143 0.00 0.00 46.56 2.59
44 45 1.134560 GGGAGAGTGTGTCCACGTATC 59.865 57.143 0.00 0.00 46.56 2.24
45 46 1.183549 GGGAGAGTGTGTCCACGTAT 58.816 55.000 0.00 0.00 46.56 3.06
46 47 0.896940 GGGGAGAGTGTGTCCACGTA 60.897 60.000 0.00 0.00 46.56 3.57
47 48 2.207924 GGGGAGAGTGTGTCCACGT 61.208 63.158 0.00 0.00 46.56 4.49
48 49 2.657237 GGGGAGAGTGTGTCCACG 59.343 66.667 0.00 0.00 46.56 4.94
49 50 1.536662 AGGGGGAGAGTGTGTCCAC 60.537 63.158 0.00 0.00 42.17 4.02
50 51 1.229209 GAGGGGGAGAGTGTGTCCA 60.229 63.158 0.00 0.00 35.57 4.02
51 52 0.973496 GAGAGGGGGAGAGTGTGTCC 60.973 65.000 0.00 0.00 0.00 4.02
52 53 1.316706 CGAGAGGGGGAGAGTGTGTC 61.317 65.000 0.00 0.00 0.00 3.67
53 54 1.304547 CGAGAGGGGGAGAGTGTGT 60.305 63.158 0.00 0.00 0.00 3.72
54 55 0.900647 AACGAGAGGGGGAGAGTGTG 60.901 60.000 0.00 0.00 0.00 3.82
55 56 0.900647 CAACGAGAGGGGGAGAGTGT 60.901 60.000 0.00 0.00 0.00 3.55
56 57 1.893786 CAACGAGAGGGGGAGAGTG 59.106 63.158 0.00 0.00 0.00 3.51
57 58 1.985116 GCAACGAGAGGGGGAGAGT 60.985 63.158 0.00 0.00 0.00 3.24
58 59 0.395862 TAGCAACGAGAGGGGGAGAG 60.396 60.000 0.00 0.00 0.00 3.20
59 60 0.261991 ATAGCAACGAGAGGGGGAGA 59.738 55.000 0.00 0.00 0.00 3.71
60 61 0.390860 CATAGCAACGAGAGGGGGAG 59.609 60.000 0.00 0.00 0.00 4.30
61 62 1.686325 GCATAGCAACGAGAGGGGGA 61.686 60.000 0.00 0.00 0.00 4.81
62 63 1.227674 GCATAGCAACGAGAGGGGG 60.228 63.158 0.00 0.00 0.00 5.40
63 64 0.107456 ATGCATAGCAACGAGAGGGG 59.893 55.000 0.00 0.00 43.62 4.79
64 65 1.069823 AGATGCATAGCAACGAGAGGG 59.930 52.381 0.00 0.00 43.62 4.30
65 66 2.402305 GAGATGCATAGCAACGAGAGG 58.598 52.381 0.00 0.00 43.62 3.69
66 67 2.035704 AGGAGATGCATAGCAACGAGAG 59.964 50.000 0.00 0.00 43.62 3.20
67 68 2.034878 AGGAGATGCATAGCAACGAGA 58.965 47.619 0.00 0.00 43.62 4.04
68 69 2.522836 AGGAGATGCATAGCAACGAG 57.477 50.000 0.00 0.00 43.62 4.18
69 70 3.222603 TCTAGGAGATGCATAGCAACGA 58.777 45.455 0.00 0.00 43.62 3.85
70 71 3.650070 TCTAGGAGATGCATAGCAACG 57.350 47.619 0.00 0.00 43.62 4.10
71 72 6.522625 TCTATCTAGGAGATGCATAGCAAC 57.477 41.667 0.00 0.00 43.62 4.17
72 73 7.124721 AGATCTATCTAGGAGATGCATAGCAA 58.875 38.462 0.00 0.00 37.47 3.91
73 74 6.671605 AGATCTATCTAGGAGATGCATAGCA 58.328 40.000 0.00 0.00 38.03 3.49
74 75 7.428020 CAAGATCTATCTAGGAGATGCATAGC 58.572 42.308 0.00 0.00 35.37 2.97
75 76 7.428020 GCAAGATCTATCTAGGAGATGCATAG 58.572 42.308 0.00 0.00 35.37 2.23
76 77 6.039159 CGCAAGATCTATCTAGGAGATGCATA 59.961 42.308 0.00 0.00 35.65 3.14
77 78 5.163530 CGCAAGATCTATCTAGGAGATGCAT 60.164 44.000 0.00 0.00 35.65 3.96
78 79 4.157472 CGCAAGATCTATCTAGGAGATGCA 59.843 45.833 11.48 0.00 35.65 3.96
79 80 4.157656 ACGCAAGATCTATCTAGGAGATGC 59.842 45.833 11.48 9.81 36.70 3.91
80 81 5.414144 TCACGCAAGATCTATCTAGGAGATG 59.586 44.000 11.48 2.82 36.70 2.90
81 82 5.565509 TCACGCAAGATCTATCTAGGAGAT 58.434 41.667 0.00 7.55 38.77 2.75
82 83 4.974399 TCACGCAAGATCTATCTAGGAGA 58.026 43.478 0.00 0.00 43.62 3.71
83 84 4.379394 GCTCACGCAAGATCTATCTAGGAG 60.379 50.000 0.00 0.94 43.62 3.69
84 85 3.504134 GCTCACGCAAGATCTATCTAGGA 59.496 47.826 0.00 0.00 43.62 2.94
85 86 3.669290 CGCTCACGCAAGATCTATCTAGG 60.669 52.174 0.00 0.00 43.62 3.02
86 87 3.058570 ACGCTCACGCAAGATCTATCTAG 60.059 47.826 0.00 0.00 45.53 2.43
87 88 2.879026 ACGCTCACGCAAGATCTATCTA 59.121 45.455 0.00 0.00 45.53 1.98
88 89 1.678627 ACGCTCACGCAAGATCTATCT 59.321 47.619 0.00 0.00 45.53 1.98
89 90 2.126914 ACGCTCACGCAAGATCTATC 57.873 50.000 0.00 0.00 45.53 2.08
90 91 2.030717 CCTACGCTCACGCAAGATCTAT 60.031 50.000 0.00 0.00 45.53 1.98
91 92 1.333931 CCTACGCTCACGCAAGATCTA 59.666 52.381 0.00 0.00 45.53 1.98
92 93 0.101399 CCTACGCTCACGCAAGATCT 59.899 55.000 0.00 0.00 45.53 2.75
93 94 0.100682 TCCTACGCTCACGCAAGATC 59.899 55.000 0.00 0.00 45.53 2.75
94 95 0.530744 TTCCTACGCTCACGCAAGAT 59.469 50.000 0.00 0.00 45.53 2.40
95 96 0.315886 TTTCCTACGCTCACGCAAGA 59.684 50.000 0.00 0.00 45.53 3.02
96 97 1.359848 ATTTCCTACGCTCACGCAAG 58.640 50.000 0.00 0.00 45.53 4.01
97 98 1.803334 AATTTCCTACGCTCACGCAA 58.197 45.000 0.00 0.00 45.53 4.85
98 99 1.803334 AAATTTCCTACGCTCACGCA 58.197 45.000 0.00 0.00 45.53 5.24
99 100 2.894307 AAAATTTCCTACGCTCACGC 57.106 45.000 0.00 0.00 45.53 5.34
116 117 5.635700 GGGAACGTAGCATGCAATTTAAAAA 59.364 36.000 21.98 0.00 0.00 1.94
117 118 5.164954 GGGAACGTAGCATGCAATTTAAAA 58.835 37.500 21.98 0.00 0.00 1.52
118 119 4.218635 TGGGAACGTAGCATGCAATTTAAA 59.781 37.500 21.98 0.00 0.00 1.52
119 120 3.759086 TGGGAACGTAGCATGCAATTTAA 59.241 39.130 21.98 0.00 0.00 1.52
120 121 3.348119 TGGGAACGTAGCATGCAATTTA 58.652 40.909 21.98 0.00 0.00 1.40
121 122 2.166829 TGGGAACGTAGCATGCAATTT 58.833 42.857 21.98 7.02 0.00 1.82
122 123 1.832883 TGGGAACGTAGCATGCAATT 58.167 45.000 21.98 7.96 0.00 2.32
123 124 1.832883 TTGGGAACGTAGCATGCAAT 58.167 45.000 21.98 1.90 0.00 3.56
124 125 1.268352 GTTTGGGAACGTAGCATGCAA 59.732 47.619 21.98 0.00 0.00 4.08
125 126 0.878416 GTTTGGGAACGTAGCATGCA 59.122 50.000 21.98 2.77 0.00 3.96
126 127 0.878416 TGTTTGGGAACGTAGCATGC 59.122 50.000 10.51 10.51 38.65 4.06
127 128 1.136085 CGTGTTTGGGAACGTAGCATG 60.136 52.381 0.00 0.00 38.65 4.06
128 129 1.153353 CGTGTTTGGGAACGTAGCAT 58.847 50.000 0.00 0.00 38.65 3.79
129 130 0.104487 TCGTGTTTGGGAACGTAGCA 59.896 50.000 0.00 0.00 40.61 3.49
130 131 0.509929 GTCGTGTTTGGGAACGTAGC 59.490 55.000 0.00 0.00 40.61 3.58
131 132 0.780002 CGTCGTGTTTGGGAACGTAG 59.220 55.000 0.00 0.00 40.61 3.51
132 133 0.597118 CCGTCGTGTTTGGGAACGTA 60.597 55.000 0.00 0.00 40.61 3.57
133 134 1.884004 CCGTCGTGTTTGGGAACGT 60.884 57.895 0.00 0.00 40.61 3.99
134 135 1.824272 GACCGTCGTGTTTGGGAACG 61.824 60.000 0.00 0.00 38.65 3.95
135 136 1.501337 GGACCGTCGTGTTTGGGAAC 61.501 60.000 0.00 0.00 36.29 3.62
136 137 1.227615 GGACCGTCGTGTTTGGGAA 60.228 57.895 0.00 0.00 0.00 3.97
137 138 2.422591 GGACCGTCGTGTTTGGGA 59.577 61.111 0.00 0.00 0.00 4.37
138 139 3.039588 CGGACCGTCGTGTTTGGG 61.040 66.667 5.48 0.00 0.00 4.12
139 140 3.039588 CCGGACCGTCGTGTTTGG 61.040 66.667 13.94 0.00 0.00 3.28
140 141 2.019951 CTCCGGACCGTCGTGTTTG 61.020 63.158 13.94 0.00 0.00 2.93
141 142 2.337532 CTCCGGACCGTCGTGTTT 59.662 61.111 13.94 0.00 0.00 2.83
142 143 3.677648 CCTCCGGACCGTCGTGTT 61.678 66.667 13.94 0.00 0.00 3.32
143 144 3.933048 ATCCTCCGGACCGTCGTGT 62.933 63.158 13.94 0.00 32.98 4.49
144 145 3.122250 GATCCTCCGGACCGTCGTG 62.122 68.421 13.94 0.00 32.98 4.35
145 146 2.827642 GATCCTCCGGACCGTCGT 60.828 66.667 13.94 0.00 32.98 4.34
176 177 4.131376 CTCAAATGCCGAGCCGAT 57.869 55.556 0.00 0.00 0.00 4.18
190 191 1.078214 CTCCCGCTTGGATTGCTCA 60.078 57.895 0.00 0.00 44.07 4.26
294 313 3.213402 CGTCGGAGGAGGAGGAGC 61.213 72.222 0.00 0.00 0.00 4.70
409 431 1.612395 AAGGAGAGGGCGAGCTTCAG 61.612 60.000 0.00 0.00 0.00 3.02
441 464 7.380333 CGGCACATCGTAACTACATATTAGAAA 59.620 37.037 0.00 0.00 0.00 2.52
459 482 2.277084 AGTTAAACGATCCGGCACATC 58.723 47.619 0.00 0.00 0.00 3.06
475 498 1.135527 CGGGCATAAGTCACGGAGTTA 59.864 52.381 4.38 4.38 41.61 2.24
480 503 0.446222 CAAACGGGCATAAGTCACGG 59.554 55.000 0.00 0.00 0.00 4.94
481 504 0.446222 CCAAACGGGCATAAGTCACG 59.554 55.000 0.00 0.00 0.00 4.35
573 597 5.537300 ACTACATAGATCACCAAGCGATT 57.463 39.130 0.00 0.00 0.00 3.34
578 602 6.573434 TGCAACTACTACATAGATCACCAAG 58.427 40.000 0.00 0.00 34.65 3.61
622 648 6.139048 TCCACGTATCTCATATTTCGAACA 57.861 37.500 0.00 0.00 0.00 3.18
642 668 1.275666 AATCCGTGTCTCCACATCCA 58.724 50.000 0.00 0.00 41.93 3.41
664 690 2.126071 CACTGACCCGGCACTACG 60.126 66.667 0.00 0.00 0.00 3.51
666 692 2.280552 GGACACTGACCCGGCACTA 61.281 63.158 0.00 0.00 0.00 2.74
673 699 4.699522 GCCCACGGACACTGACCC 62.700 72.222 0.00 0.00 0.00 4.46
751 781 1.676529 CATGTCCGACACGACCTATCT 59.323 52.381 2.57 0.00 31.35 1.98
752 782 1.864435 GCATGTCCGACACGACCTATC 60.864 57.143 2.57 0.00 31.35 2.08
754 784 1.509463 GCATGTCCGACACGACCTA 59.491 57.895 2.57 0.00 31.35 3.08
757 787 0.108992 TTAGGCATGTCCGACACGAC 60.109 55.000 2.57 0.00 40.77 4.34
758 788 0.108992 GTTAGGCATGTCCGACACGA 60.109 55.000 2.57 0.00 40.77 4.35
761 791 1.135315 GTACGTTAGGCATGTCCGACA 60.135 52.381 3.10 3.10 40.77 4.35
780 810 3.456317 GTGGACACCTGAGACGGT 58.544 61.111 0.00 0.00 37.93 4.83
819 856 1.920325 CCCACTTGCCAGAGGAGGA 60.920 63.158 2.62 0.00 32.54 3.71
886 923 2.119495 GATGGATGTACAGACCCCAGT 58.881 52.381 16.03 5.66 32.76 4.00
887 924 1.417890 GGATGGATGTACAGACCCCAG 59.582 57.143 16.03 0.00 32.76 4.45
888 925 1.274126 TGGATGGATGTACAGACCCCA 60.274 52.381 16.03 14.08 33.48 4.96
889 926 1.141053 GTGGATGGATGTACAGACCCC 59.859 57.143 16.03 12.24 0.00 4.95
890 927 1.141053 GGTGGATGGATGTACAGACCC 59.859 57.143 16.03 10.83 0.00 4.46
892 929 3.197766 TGAAGGTGGATGGATGTACAGAC 59.802 47.826 0.33 0.00 0.00 3.51
1250 1350 4.726254 CGAGGGGGTGGGGTGGTA 62.726 72.222 0.00 0.00 0.00 3.25
1434 1590 1.149964 GACGCGCCCTATGTGGTTAC 61.150 60.000 5.73 0.00 0.00 2.50
1435 1591 1.142314 GACGCGCCCTATGTGGTTA 59.858 57.895 5.73 0.00 0.00 2.85
1436 1592 2.125269 GACGCGCCCTATGTGGTT 60.125 61.111 5.73 0.00 0.00 3.67
1437 1593 3.371097 CTGACGCGCCCTATGTGGT 62.371 63.158 5.73 0.00 0.00 4.16
1438 1594 2.586079 CTGACGCGCCCTATGTGG 60.586 66.667 5.73 0.00 0.00 4.17
1439 1595 0.179121 TAACTGACGCGCCCTATGTG 60.179 55.000 5.73 0.00 0.00 3.21
1471 1627 2.551071 GCCACTACTATTCCAGATGGGC 60.551 54.545 0.00 0.00 36.21 5.36
1475 1631 1.971357 CCGGCCACTACTATTCCAGAT 59.029 52.381 2.24 0.00 0.00 2.90
1477 1633 0.249911 GCCGGCCACTACTATTCCAG 60.250 60.000 18.11 0.00 0.00 3.86
1478 1634 1.692173 GGCCGGCCACTACTATTCCA 61.692 60.000 40.73 0.00 35.81 3.53
1576 1775 7.272244 ACAGGTCAACAAATTAAAGGAAAAGG 58.728 34.615 0.00 0.00 0.00 3.11
1587 1786 9.625747 AATTTGGAAAATACAGGTCAACAAATT 57.374 25.926 0.00 0.00 39.65 1.82
1588 1787 9.625747 AAATTTGGAAAATACAGGTCAACAAAT 57.374 25.926 0.00 0.00 37.54 2.32
1615 1821 1.257743 CTTCTCCACCTGAAGGACGA 58.742 55.000 2.62 0.00 37.75 4.20
1641 1849 3.833070 ACACCGATGAAGTAAGTCTCCTT 59.167 43.478 0.00 0.00 34.56 3.36
1659 2288 0.535335 TTAGATCGCCAGGTGACACC 59.465 55.000 17.43 17.43 38.99 4.16
1991 2650 2.036098 TAGAACCCCTCGCCGACA 59.964 61.111 0.00 0.00 0.00 4.35
2143 2803 4.183865 TGATTCATTCGCTTGTACCTGAG 58.816 43.478 0.00 0.00 0.00 3.35
2210 2873 0.883833 AATTGTTGAGAGCGGGCTTG 59.116 50.000 0.00 0.00 0.00 4.01
2211 2874 0.883833 CAATTGTTGAGAGCGGGCTT 59.116 50.000 0.00 0.00 0.00 4.35
2212 2875 1.589716 GCAATTGTTGAGAGCGGGCT 61.590 55.000 7.40 0.00 0.00 5.19
2216 2879 0.592637 TGGTGCAATTGTTGAGAGCG 59.407 50.000 7.40 0.00 0.00 5.03
2217 2880 2.730090 CGATGGTGCAATTGTTGAGAGC 60.730 50.000 7.40 0.00 0.00 4.09
2226 2889 1.683943 CTGATCCCGATGGTGCAATT 58.316 50.000 0.00 0.00 0.00 2.32
2229 2892 2.190313 GCTGATCCCGATGGTGCA 59.810 61.111 0.00 0.00 0.00 4.57
2235 2898 3.643320 TCATCTTTACTGCTGATCCCGAT 59.357 43.478 0.00 0.00 0.00 4.18
2237 2900 3.126831 GTCATCTTTACTGCTGATCCCG 58.873 50.000 0.00 0.00 0.00 5.14
2250 2931 1.072331 AGGTTCTGGCACGTCATCTTT 59.928 47.619 0.00 0.00 0.00 2.52
2252 2933 0.247736 GAGGTTCTGGCACGTCATCT 59.752 55.000 0.00 0.00 32.77 2.90
2451 3132 2.366480 CTGCTGCTCTCCTCATCCCG 62.366 65.000 0.00 0.00 0.00 5.14
2470 3151 1.063649 CAGCCAAGCATGTCATCGC 59.936 57.895 0.00 0.55 0.00 4.58
2474 3155 0.245266 CATTGCAGCCAAGCATGTCA 59.755 50.000 0.00 0.00 45.19 3.58
2555 3239 3.591254 GAGCGACCGGGCTTTCACT 62.591 63.158 5.33 0.00 44.93 3.41
2625 3317 1.327690 TAAACCGCCGATGGAGCTCT 61.328 55.000 14.64 0.00 0.00 4.09
2627 3319 0.180406 AATAAACCGCCGATGGAGCT 59.820 50.000 0.00 0.00 0.00 4.09
2658 3350 4.202461 ACCAAAACTGGAGCAGACTAATCA 60.202 41.667 0.00 0.00 35.18 2.57
2660 3352 4.074970 CACCAAAACTGGAGCAGACTAAT 58.925 43.478 0.00 0.00 35.18 1.73
2727 3432 4.214980 CTGCACTGACAGTTAAAACAGG 57.785 45.455 5.04 0.00 35.08 4.00
2776 3481 7.708998 TGACAAGACACCTTTTAATAAACCAC 58.291 34.615 0.00 0.00 0.00 4.16
2783 3488 5.995282 TCACGATGACAAGACACCTTTTAAT 59.005 36.000 0.00 0.00 0.00 1.40
2812 3518 0.382158 CAATGGCTGCTGCATCTCAG 59.618 55.000 17.89 6.44 45.62 3.35
2847 3566 1.339727 GGTTGACTGAATTAGGGGCGT 60.340 52.381 0.00 0.00 0.00 5.68
2917 3636 7.093684 GGGGGTGAAGAAGATCAGAGTATATAC 60.094 44.444 4.60 4.60 0.00 1.47
2944 3663 1.608283 CCGTTGGGACTTGTTCCTCTC 60.608 57.143 0.00 0.00 45.09 3.20
3030 3774 6.763610 TGTTGGTGGTTTAATGACAATTTTCC 59.236 34.615 0.00 0.00 0.00 3.13
3105 3876 5.603170 AATCCTATTTCTACCGTCGGAAA 57.397 39.130 20.51 8.76 36.17 3.13
3129 3900 0.468226 TTTTCGTCACTGGGAGCAGT 59.532 50.000 0.00 0.00 35.49 4.40
3151 3922 5.163237 GGTCTTGGGGAATGTAATGCTAGTA 60.163 44.000 0.00 0.00 0.00 1.82
3152 3923 4.385310 GGTCTTGGGGAATGTAATGCTAGT 60.385 45.833 0.00 0.00 0.00 2.57
3153 3924 4.137543 GGTCTTGGGGAATGTAATGCTAG 58.862 47.826 0.00 0.00 0.00 3.42
3176 4738 7.063074 GTCGTAGTGCTTGATATTTACTGTTGT 59.937 37.037 0.00 0.00 0.00 3.32
3373 5092 3.128938 GTCTAAGCCGCGATATATGTCCT 59.871 47.826 8.23 0.00 0.00 3.85
3394 5113 1.893808 CTGGGCGTTGCTCAAGTGT 60.894 57.895 0.00 0.00 39.14 3.55
3486 5207 2.684001 TATCCTTAAGCCCACGTGTG 57.316 50.000 15.65 3.72 0.00 3.82


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

AutoCloner maintained by Alex Coulton.