Multiple sequence alignment - TraesCS6A01G018300

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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 TraesCS6A01G018300 chr6A 100.000 2729 0 0 1 2729 8995810 8993082 0.000000e+00 5040.0
1 TraesCS6A01G018300 chr6A 86.800 1000 123 7 986 1982 9350634 9351627 0.000000e+00 1107.0
2 TraesCS6A01G018300 chr6A 81.963 754 132 4 984 1735 9473542 9474293 1.070000e-178 636.0
3 TraesCS6A01G018300 chr6A 80.024 826 138 12 986 1802 30560153 30559346 1.090000e-163 586.0
4 TraesCS6A01G018300 chr6A 81.153 642 62 33 2096 2710 35567584 35566975 6.890000e-126 460.0
5 TraesCS6A01G018300 chr6A 91.916 334 17 6 653 986 9364560 9364883 2.480000e-125 459.0
6 TraesCS6A01G018300 chr6A 84.309 376 28 17 2346 2702 9366471 9366834 3.370000e-89 339.0
7 TraesCS6A01G018300 chr6A 77.904 439 49 26 1799 2218 30559218 30558809 2.110000e-56 230.0
8 TraesCS6A01G018300 chr6A 89.796 98 8 2 2609 2705 8622638 8622542 1.030000e-24 124.0
9 TraesCS6A01G018300 chr6A 87.356 87 6 3 1976 2061 8394440 8394358 8.040000e-16 95.3
10 TraesCS6A01G018300 chr6B 94.628 819 44 0 984 1802 53062095 53061277 0.000000e+00 1269.0
11 TraesCS6A01G018300 chr6B 92.868 631 25 10 2114 2728 53061229 53060603 0.000000e+00 898.0
12 TraesCS6A01G018300 chr6B 88.372 688 61 17 310 985 53062907 53062227 0.000000e+00 809.0
13 TraesCS6A01G018300 chr6B 84.802 783 113 5 1014 1793 65158636 65157857 0.000000e+00 782.0
14 TraesCS6A01G018300 chr6B 83.394 825 121 12 986 1802 16255667 16256483 0.000000e+00 750.0
15 TraesCS6A01G018300 chr6B 83.266 747 117 6 1008 1750 15219303 15218561 0.000000e+00 680.0
16 TraesCS6A01G018300 chr6B 82.718 515 48 23 2221 2712 53075017 53074521 1.170000e-113 420.0
17 TraesCS6A01G018300 chr6B 85.417 384 35 8 1799 2178 670577608 670577242 1.980000e-101 379.0
18 TraesCS6A01G018300 chr6B 82.160 426 43 19 2308 2712 670576965 670576552 4.350000e-88 335.0
19 TraesCS6A01G018300 chr6B 86.306 314 25 14 676 985 52981067 52980768 2.620000e-85 326.0
20 TraesCS6A01G018300 chr6B 82.443 393 38 14 2339 2711 15247783 15247402 5.670000e-82 315.0
21 TraesCS6A01G018300 chr6B 84.887 311 36 8 675 985 52568264 52567965 1.230000e-78 303.0
22 TraesCS6A01G018300 chr6B 82.972 323 52 3 658 979 26512122 26512442 3.440000e-74 289.0
23 TraesCS6A01G018300 chr6B 77.449 439 50 25 1799 2218 16256611 16257019 1.650000e-52 217.0
24 TraesCS6A01G018300 chr6B 95.506 89 4 0 222 310 53063029 53062941 2.830000e-30 143.0
25 TraesCS6A01G018300 chr6B 89.286 112 7 3 2110 2218 15248028 15247919 4.740000e-28 135.0
26 TraesCS6A01G018300 chr6B 90.698 86 6 2 1 85 670587425 670587341 2.220000e-21 113.0
27 TraesCS6A01G018300 chr6D 83.709 755 116 4 984 1735 8967994 8968744 0.000000e+00 706.0
28 TraesCS6A01G018300 chr6D 77.215 948 137 45 1799 2712 8817132 8818034 5.290000e-132 481.0
29 TraesCS6A01G018300 chr6D 90.756 357 27 4 223 577 33902338 33902690 3.180000e-129 472.0
30 TraesCS6A01G018300 chr6D 79.840 625 83 28 2110 2712 8577444 8576841 1.510000e-112 416.0
31 TraesCS6A01G018300 chr6D 91.333 300 23 2 686 985 8987219 8987515 9.100000e-110 407.0
32 TraesCS6A01G018300 chr6D 75.309 972 135 57 1801 2712 8970549 8971475 4.290000e-98 368.0
33 TraesCS6A01G018300 chr6D 80.651 522 57 21 2216 2712 34019297 34019799 5.550000e-97 364.0
34 TraesCS6A01G018300 chr6D 84.431 334 41 9 653 985 16775783 16775460 4.390000e-83 318.0
35 TraesCS6A01G018300 chr6D 86.598 291 30 6 695 985 8397155 8396874 2.040000e-81 313.0
36 TraesCS6A01G018300 chr6D 83.427 356 26 25 638 985 7477212 7476882 1.590000e-77 300.0
37 TraesCS6A01G018300 chr6D 83.234 334 33 19 654 983 8659857 8659543 4.450000e-73 285.0
38 TraesCS6A01G018300 chr6D 82.991 341 33 17 653 985 9061936 9062259 4.450000e-73 285.0
39 TraesCS6A01G018300 chr6D 84.878 205 26 3 780 983 8095669 8095469 4.610000e-48 202.0
40 TraesCS6A01G018300 chr6D 90.299 134 12 1 102 235 123795886 123795754 1.000000e-39 174.0
41 TraesCS6A01G018300 chr6D 79.612 206 24 12 653 858 8402453 8402266 6.130000e-27 132.0
42 TraesCS6A01G018300 chr6D 92.473 93 5 2 1 93 8986297 8986387 6.130000e-27 132.0
43 TraesCS6A01G018300 chr2B 83.398 777 113 12 986 1754 89500368 89501136 0.000000e+00 706.0
44 TraesCS6A01G018300 chr2B 80.680 823 150 7 986 1802 89495038 89495857 4.960000e-177 630.0
45 TraesCS6A01G018300 chr2B 81.603 761 136 4 977 1735 709425766 709425008 6.420000e-176 627.0
46 TraesCS6A01G018300 chr2B 79.516 620 85 30 2112 2712 709486289 709485693 1.180000e-108 403.0
47 TraesCS6A01G018300 chr2B 83.376 391 37 17 2339 2712 89496352 89496731 1.210000e-88 337.0
48 TraesCS6A01G018300 chr2B 86.378 323 18 12 1799 2118 800419558 800419259 2.030000e-86 329.0
49 TraesCS6A01G018300 chr2B 81.579 342 38 14 2392 2712 800298958 800298621 2.700000e-65 259.0
50 TraesCS6A01G018300 chr2B 81.525 341 40 13 2135 2462 800554958 800554628 2.700000e-65 259.0
51 TraesCS6A01G018300 chr2B 76.629 445 50 28 1799 2218 709454422 709454007 2.140000e-46 196.0
52 TraesCS6A01G018300 chr2B 89.172 157 16 1 1799 1954 574757690 574757846 7.710000e-46 195.0
53 TraesCS6A01G018300 chr2B 77.778 333 41 13 1801 2115 709423156 709422839 1.000000e-39 174.0
54 TraesCS6A01G018300 chr2B 81.070 243 23 10 1799 2019 66120803 66121044 3.610000e-39 172.0
55 TraesCS6A01G018300 chr2B 76.796 362 51 22 2369 2712 800418759 800418413 3.610000e-39 172.0
56 TraesCS6A01G018300 chr2B 87.500 112 9 3 2110 2218 89496107 89496216 1.030000e-24 124.0
57 TraesCS6A01G018300 chr5B 80.624 769 138 7 1034 1794 621235531 621234766 3.920000e-163 584.0
58 TraesCS6A01G018300 chr5B 83.756 394 31 10 2225 2602 621234155 621233779 2.600000e-90 342.0
59 TraesCS6A01G018300 chr5B 86.897 290 30 7 695 983 556628242 556627960 4.390000e-83 318.0
60 TraesCS6A01G018300 chr5D 82.915 398 27 14 2223 2602 499860763 499860389 1.220000e-83 320.0
61 TraesCS6A01G018300 chr5A 82.750 400 30 10 2223 2602 624201419 624201039 1.220000e-83 320.0
62 TraesCS6A01G018300 chr7B 88.750 160 17 1 1799 1957 413001459 413001300 7.710000e-46 195.0
63 TraesCS6A01G018300 chr7D 91.429 140 11 1 90 229 573081711 573081849 9.970000e-45 191.0
64 TraesCS6A01G018300 chrUn 88.125 160 18 1 1799 1957 55514472 55514313 3.590000e-44 189.0
65 TraesCS6A01G018300 chrUn 87.097 62 7 1 1958 2019 55514295 55514235 4.880000e-08 69.4
66 TraesCS6A01G018300 chr1B 88.535 157 17 1 1799 1954 257984964 257985120 3.590000e-44 189.0
67 TraesCS6A01G018300 chr1B 87.097 62 7 1 1958 2019 79092861 79092801 4.880000e-08 69.4
68 TraesCS6A01G018300 chr4A 90.441 136 13 0 94 229 625477197 625477332 2.160000e-41 180.0
69 TraesCS6A01G018300 chr1D 91.473 129 10 1 101 229 430422443 430422570 2.790000e-40 176.0
70 TraesCS6A01G018300 chr1D 92.500 120 9 0 101 220 493897908 493898027 3.610000e-39 172.0
71 TraesCS6A01G018300 chr1D 89.552 134 14 0 96 229 85640348 85640215 1.300000e-38 171.0
72 TraesCS6A01G018300 chr4D 90.698 129 11 1 101 229 427916656 427916529 1.300000e-38 171.0
73 TraesCS6A01G018300 chr2D 89.552 134 12 2 96 229 152879369 152879500 4.670000e-38 169.0
74 TraesCS6A01G018300 chr2D 88.971 136 13 1 94 229 9720383 9720516 1.680000e-37 167.0
75 TraesCS6A01G018300 chr4B 79.679 187 19 8 1851 2019 632312902 632312717 1.720000e-22 117.0


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 TraesCS6A01G018300 chr6A 8993082 8995810 2728 True 5040.00 5040 100.0000 1 2729 1 chr6A.!!$R3 2728
1 TraesCS6A01G018300 chr6A 9350634 9351627 993 False 1107.00 1107 86.8000 986 1982 1 chr6A.!!$F1 996
2 TraesCS6A01G018300 chr6A 9473542 9474293 751 False 636.00 636 81.9630 984 1735 1 chr6A.!!$F2 751
3 TraesCS6A01G018300 chr6A 35566975 35567584 609 True 460.00 460 81.1530 2096 2710 1 chr6A.!!$R4 614
4 TraesCS6A01G018300 chr6A 30558809 30560153 1344 True 408.00 586 78.9640 986 2218 2 chr6A.!!$R5 1232
5 TraesCS6A01G018300 chr6A 9364560 9366834 2274 False 399.00 459 88.1125 653 2702 2 chr6A.!!$F3 2049
6 TraesCS6A01G018300 chr6B 65157857 65158636 779 True 782.00 782 84.8020 1014 1793 1 chr6B.!!$R5 779
7 TraesCS6A01G018300 chr6B 53060603 53063029 2426 True 779.75 1269 92.8435 222 2728 4 chr6B.!!$R8 2506
8 TraesCS6A01G018300 chr6B 15218561 15219303 742 True 680.00 680 83.2660 1008 1750 1 chr6B.!!$R1 742
9 TraesCS6A01G018300 chr6B 16255667 16257019 1352 False 483.50 750 80.4215 986 2218 2 chr6B.!!$F2 1232
10 TraesCS6A01G018300 chr6B 670576552 670577608 1056 True 357.00 379 83.7885 1799 2712 2 chr6B.!!$R9 913
11 TraesCS6A01G018300 chr6B 15247402 15248028 626 True 225.00 315 85.8645 2110 2711 2 chr6B.!!$R7 601
12 TraesCS6A01G018300 chr6D 8967994 8971475 3481 False 537.00 706 79.5090 984 2712 2 chr6D.!!$F5 1728
13 TraesCS6A01G018300 chr6D 8817132 8818034 902 False 481.00 481 77.2150 1799 2712 1 chr6D.!!$F1 913
14 TraesCS6A01G018300 chr6D 8576841 8577444 603 True 416.00 416 79.8400 2110 2712 1 chr6D.!!$R5 602
15 TraesCS6A01G018300 chr6D 34019297 34019799 502 False 364.00 364 80.6510 2216 2712 1 chr6D.!!$F4 496
16 TraesCS6A01G018300 chr6D 8986297 8987515 1218 False 269.50 407 91.9030 1 985 2 chr6D.!!$F6 984
17 TraesCS6A01G018300 chr2B 89495038 89501136 6098 False 449.25 706 83.7385 986 2712 4 chr2B.!!$F3 1726
18 TraesCS6A01G018300 chr2B 709485693 709486289 596 True 403.00 403 79.5160 2112 2712 1 chr2B.!!$R2 600
19 TraesCS6A01G018300 chr2B 709422839 709425766 2927 True 400.50 627 79.6905 977 2115 2 chr2B.!!$R5 1138
20 TraesCS6A01G018300 chr2B 800418413 800419558 1145 True 250.50 329 81.5870 1799 2712 2 chr2B.!!$R6 913
21 TraesCS6A01G018300 chr5B 621233779 621235531 1752 True 463.00 584 82.1900 1034 2602 2 chr5B.!!$R2 1568

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
634 997 0.038166 ACCAGACCACGCAAATCCAT 59.962 50.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2277 6700 1.066257 GCCATTACCATGCAAGCGG 59.934 57.895 0.0 0.0 0.0 5.52 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
89 90 8.906867 ACATGGTCAATTCTCTTAAATACATGG 58.093 33.333 0.00 0.00 36.18 3.66
93 94 8.398665 GGTCAATTCTCTTAAATACATGGTGAC 58.601 37.037 0.00 0.00 0.00 3.67
118 119 3.357504 GCAGCCTTGCCATTGATTC 57.642 52.632 0.00 0.00 44.74 2.52
119 120 0.179092 GCAGCCTTGCCATTGATTCC 60.179 55.000 0.00 0.00 44.74 3.01
122 123 1.438814 CCTTGCCATTGATTCCCGC 59.561 57.895 0.00 0.00 0.00 6.13
124 125 2.340453 CTTGCCATTGATTCCCGCGG 62.340 60.000 21.04 21.04 0.00 6.46
125 126 3.595758 GCCATTGATTCCCGCGGG 61.596 66.667 39.13 39.13 0.00 6.13
140 141 2.107141 GGGAACCGAGGCGATGAG 59.893 66.667 0.00 0.00 40.86 2.90
141 142 2.107141 GGAACCGAGGCGATGAGG 59.893 66.667 0.00 0.00 0.00 3.86
142 143 2.423898 GGAACCGAGGCGATGAGGA 61.424 63.158 0.00 0.00 0.00 3.71
143 144 1.227002 GAACCGAGGCGATGAGGAC 60.227 63.158 0.00 0.00 0.00 3.85
144 145 2.938539 GAACCGAGGCGATGAGGACG 62.939 65.000 0.00 0.00 0.00 4.79
145 146 3.209812 CCGAGGCGATGAGGACGA 61.210 66.667 0.00 0.00 0.00 4.20
146 147 2.024871 CGAGGCGATGAGGACGAC 59.975 66.667 0.00 0.00 39.24 4.34
147 148 2.024871 GAGGCGATGAGGACGACG 59.975 66.667 0.00 0.00 44.04 5.12
149 150 1.989966 GAGGCGATGAGGACGACGAA 61.990 60.000 0.00 0.00 44.04 3.85
151 152 1.411493 GGCGATGAGGACGACGAAAC 61.411 60.000 0.00 0.00 0.00 2.78
152 153 1.730593 GCGATGAGGACGACGAAACG 61.731 60.000 0.00 0.00 39.31 3.60
154 155 0.109412 GATGAGGACGACGAAACGGT 60.109 55.000 0.00 0.00 37.61 4.83
156 157 1.008079 GAGGACGACGAAACGGTGT 60.008 57.895 0.00 0.00 37.61 4.16
157 158 1.000736 GAGGACGACGAAACGGTGTC 61.001 60.000 0.00 0.00 37.61 3.67
159 160 1.000736 GGACGACGAAACGGTGTCTC 61.001 60.000 0.00 0.00 36.14 3.36
160 161 1.325904 GACGACGAAACGGTGTCTCG 61.326 60.000 0.00 14.47 38.53 4.04
161 162 2.704193 CGACGAAACGGTGTCTCGC 61.704 63.158 7.06 1.83 36.03 5.03
162 163 1.371389 GACGAAACGGTGTCTCGCT 60.371 57.895 7.26 0.00 36.03 4.93
163 164 1.606350 GACGAAACGGTGTCTCGCTG 61.606 60.000 7.26 0.00 36.03 5.18
164 165 1.371267 CGAAACGGTGTCTCGCTGA 60.371 57.895 0.00 0.00 0.00 4.26
165 166 1.606350 CGAAACGGTGTCTCGCTGAC 61.606 60.000 0.00 2.16 45.54 3.51
167 168 0.318784 AAACGGTGTCTCGCTGACTC 60.319 55.000 9.20 6.09 45.54 3.36
168 169 2.202362 CGGTGTCTCGCTGACTCG 60.202 66.667 9.20 9.00 45.54 4.18
170 171 2.505118 GTGTCTCGCTGACTCGGC 60.505 66.667 0.00 0.00 45.54 5.54
193 194 3.427425 CATCCCCGTTCGCGCAAA 61.427 61.111 8.75 0.00 39.70 3.68
194 195 2.670251 ATCCCCGTTCGCGCAAAA 60.670 55.556 8.75 0.00 39.70 2.44
195 196 2.262303 ATCCCCGTTCGCGCAAAAA 61.262 52.632 8.75 0.00 39.70 1.94
196 197 1.591504 ATCCCCGTTCGCGCAAAAAT 61.592 50.000 8.75 0.00 39.70 1.82
197 198 1.799916 CCCCGTTCGCGCAAAAATC 60.800 57.895 8.75 0.00 39.70 2.17
198 199 2.143458 CCCGTTCGCGCAAAAATCG 61.143 57.895 8.75 1.95 39.70 3.34
206 207 2.736890 CGCAAAAATCGCTTTCCCC 58.263 52.632 0.00 0.00 0.00 4.81
207 208 1.070471 CGCAAAAATCGCTTTCCCCG 61.070 55.000 0.00 0.00 0.00 5.73
208 209 0.735978 GCAAAAATCGCTTTCCCCGG 60.736 55.000 0.00 0.00 0.00 5.73
209 210 0.735978 CAAAAATCGCTTTCCCCGGC 60.736 55.000 0.00 0.00 0.00 6.13
266 458 2.694043 GCATTACGATCGTGTTTGCTC 58.306 47.619 30.23 9.09 0.00 4.26
302 494 3.030441 CGACGAACGAGCTTTAGATCTC 58.970 50.000 0.00 0.00 45.77 2.75
319 545 2.135139 TCTCGATTGCATTACATCGCC 58.865 47.619 12.56 0.00 36.58 5.54
323 549 0.670162 ATTGCATTACATCGCCTGCC 59.330 50.000 0.00 0.00 33.70 4.85
353 579 3.555795 GCCGGATCAATGCTCATTCTCTA 60.556 47.826 5.05 0.00 0.00 2.43
357 583 5.121925 CGGATCAATGCTCATTCTCTATTGG 59.878 44.000 0.00 0.00 31.47 3.16
466 739 7.879962 TTTTACGACAACAAAAACTCGTATG 57.120 32.000 0.00 0.00 40.33 2.39
507 780 1.729586 TTTAGGAGACAGGGTGCAGT 58.270 50.000 0.00 0.00 0.00 4.40
514 787 3.412386 GAGACAGGGTGCAGTATGTTTT 58.588 45.455 0.00 0.00 39.31 2.43
577 916 3.005554 CCAGCCCATTATTAGATGCGAG 58.994 50.000 0.00 0.00 0.00 5.03
578 917 3.557898 CCAGCCCATTATTAGATGCGAGT 60.558 47.826 0.00 0.00 0.00 4.18
579 918 4.322725 CCAGCCCATTATTAGATGCGAGTA 60.323 45.833 0.00 0.00 0.00 2.59
580 919 5.423015 CAGCCCATTATTAGATGCGAGTAT 58.577 41.667 0.00 0.00 0.00 2.12
581 920 5.292834 CAGCCCATTATTAGATGCGAGTATG 59.707 44.000 0.00 0.00 0.00 2.39
585 928 5.004821 CCATTATTAGATGCGAGTATGCGAC 59.995 44.000 0.00 0.00 37.81 5.19
595 938 2.223363 CGAGTATGCGACAGACACTGAT 60.223 50.000 5.76 0.00 35.18 2.90
596 939 3.002348 CGAGTATGCGACAGACACTGATA 59.998 47.826 5.76 0.00 35.18 2.15
598 941 2.215907 ATGCGACAGACACTGATAGC 57.784 50.000 5.76 7.95 35.18 2.97
627 990 2.110213 GTCCAACCAGACCACGCA 59.890 61.111 0.00 0.00 0.00 5.24
629 992 1.098712 GTCCAACCAGACCACGCAAA 61.099 55.000 0.00 0.00 0.00 3.68
630 993 0.179004 TCCAACCAGACCACGCAAAT 60.179 50.000 0.00 0.00 0.00 2.32
632 995 0.240945 CAACCAGACCACGCAAATCC 59.759 55.000 0.00 0.00 0.00 3.01
634 997 0.038166 ACCAGACCACGCAAATCCAT 59.962 50.000 0.00 0.00 0.00 3.41
635 998 0.734889 CCAGACCACGCAAATCCATC 59.265 55.000 0.00 0.00 0.00 3.51
636 999 0.734889 CAGACCACGCAAATCCATCC 59.265 55.000 0.00 0.00 0.00 3.51
637 1000 0.394352 AGACCACGCAAATCCATCCC 60.394 55.000 0.00 0.00 0.00 3.85
718 1100 1.448013 GCTCCGCCTCCACAAGTAC 60.448 63.158 0.00 0.00 0.00 2.73
736 1118 0.830444 ACGTCCTCACCCAACTGCTA 60.830 55.000 0.00 0.00 0.00 3.49
749 1134 1.187087 ACTGCTACCTTCTTCCTCCG 58.813 55.000 0.00 0.00 0.00 4.63
823 1208 2.681591 GTTTCCCCCACCCCTAGC 59.318 66.667 0.00 0.00 0.00 3.42
1002 1520 1.668337 CGCTTCCGCTCTAGATCCATG 60.668 57.143 0.00 0.00 0.00 3.66
1017 1535 0.609957 CCATGGTCTCCAAGCTGCAA 60.610 55.000 2.57 0.00 36.95 4.08
1048 1566 1.206849 CTCTCTTTGGGTCCTCTGAGC 59.793 57.143 0.00 0.00 38.29 4.26
1098 1622 2.296073 ACCTTCTCTCGTCTGACCTT 57.704 50.000 1.55 0.00 0.00 3.50
1196 1720 2.282251 TCGACCAGGTCTGCTCGT 60.282 61.111 17.95 0.00 39.11 4.18
1220 1744 1.267574 AATCCAGAGCGCTTCCAGGA 61.268 55.000 13.26 16.95 35.65 3.86
1320 1847 0.179127 TCAGCAAAGAGGAGATCGCG 60.179 55.000 0.00 0.00 0.00 5.87
1392 1919 1.134995 GGCATTGCTGTTTCTAAGGCC 60.135 52.381 8.82 0.00 42.86 5.19
1518 2045 2.032620 CTCACGTATAGCTTGGAGGGT 58.967 52.381 0.00 0.00 0.00 4.34
1604 2137 0.875059 GGCTACTTTGGTGCAGTCAC 59.125 55.000 0.00 0.00 42.40 3.67
2043 6140 8.954950 TCTTCTAAGCTGAAATATTCCTTCTG 57.045 34.615 0.00 0.00 0.00 3.02
2048 6145 3.317430 GCTGAAATATTCCTTCTGCCTGG 59.683 47.826 6.33 0.00 40.12 4.45
2049 6146 4.785301 CTGAAATATTCCTTCTGCCTGGA 58.215 43.478 0.00 0.00 0.00 3.86
2050 6147 4.785301 TGAAATATTCCTTCTGCCTGGAG 58.215 43.478 0.00 0.00 33.46 3.86
2051 6148 4.228210 TGAAATATTCCTTCTGCCTGGAGT 59.772 41.667 0.00 0.00 33.46 3.85
2052 6149 5.428457 TGAAATATTCCTTCTGCCTGGAGTA 59.572 40.000 0.00 0.00 33.46 2.59
2053 6150 5.559148 AATATTCCTTCTGCCTGGAGTAG 57.441 43.478 0.00 0.00 33.46 2.57
2054 6151 0.905357 TTCCTTCTGCCTGGAGTAGC 59.095 55.000 0.00 0.00 33.46 3.58
2055 6152 0.041833 TCCTTCTGCCTGGAGTAGCT 59.958 55.000 0.00 0.00 0.00 3.32
2056 6153 0.908198 CCTTCTGCCTGGAGTAGCTT 59.092 55.000 0.00 0.00 0.00 3.74
2057 6154 1.280421 CCTTCTGCCTGGAGTAGCTTT 59.720 52.381 0.00 0.00 0.00 3.51
2058 6155 2.501723 CCTTCTGCCTGGAGTAGCTTTA 59.498 50.000 0.00 0.00 0.00 1.85
2059 6156 3.135530 CCTTCTGCCTGGAGTAGCTTTAT 59.864 47.826 0.00 0.00 0.00 1.40
2070 6167 7.654116 CCTGGAGTAGCTTTATTAGTAGCTTTC 59.346 40.741 1.59 1.76 45.03 2.62
2218 6599 7.968956 TGATCTCGAAACTGAATAGTTGAGTAC 59.031 37.037 0.00 0.00 46.14 2.73
2229 6610 3.026630 AGTTGAGTACATCACCACGTG 57.973 47.619 9.08 9.08 37.77 4.49
2250 6631 4.272748 GTGAACAGATATTTCTAACGCCCC 59.727 45.833 0.00 0.00 0.00 5.80
2252 6633 2.433239 ACAGATATTTCTAACGCCCCGT 59.567 45.455 0.00 0.00 43.97 5.28
2277 6700 4.553351 GCTTTTGTTGGAGAAGCAAATTGC 60.553 41.667 10.41 10.41 43.89 3.56
2284 6707 3.955775 AAGCAAATTGCCGCTTGC 58.044 50.000 15.04 7.55 46.41 4.01
2306 6761 0.740737 GGTAATGGCATGGTGCTGAC 59.259 55.000 0.00 0.00 44.28 3.51
2355 6810 6.659824 AGGGAAGTTATGTTATGGTAACCTG 58.340 40.000 0.00 0.00 32.54 4.00
2466 7092 4.414846 AGATTGTGAGGGCATCTTTATCCT 59.585 41.667 0.00 0.00 0.00 3.24
2551 7217 5.528600 TCTGGAAAGTTGGAATGGGAATA 57.471 39.130 0.00 0.00 0.00 1.75
2702 7371 3.557228 AGGAAATGAGATCTCAGGTGC 57.443 47.619 28.26 22.22 43.61 5.01
2705 7374 2.593346 AATGAGATCTCAGGTGCGTC 57.407 50.000 28.26 0.00 43.61 5.19
2728 7442 5.356190 TCCTTGCATTTAAAGATCAGCTCTG 59.644 40.000 0.00 0.00 33.29 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 1.699656 GCTGCTACGCTGTCACCATG 61.700 60.000 0.00 0.00 0.00 3.66
89 90 1.374758 AAGGCTGCTACGCTGTCAC 60.375 57.895 0.00 0.00 34.63 3.67
103 104 1.438814 CGGGAATCAATGGCAAGGC 59.561 57.895 0.00 0.00 0.00 4.35
105 106 1.064621 CGCGGGAATCAATGGCAAG 59.935 57.895 0.00 0.00 0.00 4.01
109 110 2.191908 TCCCGCGGGAATCAATGG 59.808 61.111 43.93 15.54 42.05 3.16
124 125 2.107141 CCTCATCGCCTCGGTTCC 59.893 66.667 0.00 0.00 0.00 3.62
125 126 1.227002 GTCCTCATCGCCTCGGTTC 60.227 63.158 0.00 0.00 0.00 3.62
128 129 3.209812 TCGTCCTCATCGCCTCGG 61.210 66.667 0.00 0.00 0.00 4.63
130 131 1.989966 TTCGTCGTCCTCATCGCCTC 61.990 60.000 0.00 0.00 0.00 4.70
131 132 1.592400 TTTCGTCGTCCTCATCGCCT 61.592 55.000 0.00 0.00 0.00 5.52
132 133 1.153901 TTTCGTCGTCCTCATCGCC 60.154 57.895 0.00 0.00 0.00 5.54
133 134 1.730593 CGTTTCGTCGTCCTCATCGC 61.731 60.000 0.00 0.00 0.00 4.58
135 136 0.109412 ACCGTTTCGTCGTCCTCATC 60.109 55.000 0.00 0.00 0.00 2.92
136 137 0.388134 CACCGTTTCGTCGTCCTCAT 60.388 55.000 0.00 0.00 0.00 2.90
137 138 1.008194 CACCGTTTCGTCGTCCTCA 60.008 57.895 0.00 0.00 0.00 3.86
139 140 1.008079 GACACCGTTTCGTCGTCCT 60.008 57.895 0.00 0.00 0.00 3.85
140 141 1.000736 GAGACACCGTTTCGTCGTCC 61.001 60.000 0.00 0.00 37.23 4.79
141 142 1.325904 CGAGACACCGTTTCGTCGTC 61.326 60.000 0.00 0.00 35.83 4.20
142 143 1.369689 CGAGACACCGTTTCGTCGT 60.370 57.895 0.00 0.00 35.83 4.34
143 144 2.704193 GCGAGACACCGTTTCGTCG 61.704 63.158 8.56 3.89 41.22 5.12
144 145 1.371389 AGCGAGACACCGTTTCGTC 60.371 57.895 8.56 2.33 41.22 4.20
145 146 1.660575 CAGCGAGACACCGTTTCGT 60.661 57.895 8.56 0.00 41.22 3.85
146 147 1.371267 TCAGCGAGACACCGTTTCG 60.371 57.895 2.97 2.97 41.90 3.46
147 148 2.142641 GTCAGCGAGACACCGTTTC 58.857 57.895 7.37 0.00 46.77 2.78
176 177 2.465097 TTTTTGCGCGAACGGGGATG 62.465 55.000 12.10 0.00 40.57 3.51
178 179 2.190101 GATTTTTGCGCGAACGGGGA 62.190 55.000 12.10 7.35 40.57 4.81
179 180 1.799916 GATTTTTGCGCGAACGGGG 60.800 57.895 12.10 0.00 40.57 5.73
180 181 2.143458 CGATTTTTGCGCGAACGGG 61.143 57.895 12.10 6.89 40.57 5.28
182 183 2.675405 GCGATTTTTGCGCGAACG 59.325 55.556 12.10 11.92 45.27 3.95
188 189 1.070471 CGGGGAAAGCGATTTTTGCG 61.070 55.000 0.00 0.00 37.44 4.85
189 190 0.735978 CCGGGGAAAGCGATTTTTGC 60.736 55.000 0.00 0.00 0.00 3.68
190 191 0.735978 GCCGGGGAAAGCGATTTTTG 60.736 55.000 2.18 0.00 0.00 2.44
191 192 1.589630 GCCGGGGAAAGCGATTTTT 59.410 52.632 2.18 0.00 0.00 1.94
266 458 2.190161 TCGTCGAGTGAAATAATGCCG 58.810 47.619 0.00 0.00 0.00 5.69
302 494 1.661178 GCAGGCGATGTAATGCAATCG 60.661 52.381 12.97 12.97 38.54 3.34
323 549 0.378257 CATTGATCCGGCCAAAGACG 59.622 55.000 2.24 0.00 0.00 4.18
353 579 7.125391 ACACCCTTGATAATATGTTGTCCAAT 58.875 34.615 0.00 0.00 0.00 3.16
357 583 7.865706 AAGACACCCTTGATAATATGTTGTC 57.134 36.000 0.00 0.00 32.92 3.18
514 787 3.609853 AGCGACTCATATGCCAGAAAAA 58.390 40.909 0.00 0.00 0.00 1.94
577 916 3.046390 GCTATCAGTGTCTGTCGCATAC 58.954 50.000 0.00 0.00 32.61 2.39
578 917 2.034685 GGCTATCAGTGTCTGTCGCATA 59.965 50.000 0.00 0.00 32.61 3.14
579 918 1.202463 GGCTATCAGTGTCTGTCGCAT 60.202 52.381 0.00 0.00 32.61 4.73
580 919 0.173481 GGCTATCAGTGTCTGTCGCA 59.827 55.000 0.00 0.00 32.61 5.10
581 920 0.528684 GGGCTATCAGTGTCTGTCGC 60.529 60.000 0.00 0.00 32.61 5.19
585 928 0.538584 TGCTGGGCTATCAGTGTCTG 59.461 55.000 0.00 0.00 37.12 3.51
595 938 0.913934 TGGACCTTGATGCTGGGCTA 60.914 55.000 0.00 0.00 0.00 3.93
596 939 1.792757 TTGGACCTTGATGCTGGGCT 61.793 55.000 0.00 0.00 0.00 5.19
598 941 0.967380 GGTTGGACCTTGATGCTGGG 60.967 60.000 0.00 0.00 34.73 4.45
625 988 1.959282 GAGTGATGGGGATGGATTTGC 59.041 52.381 0.00 0.00 0.00 3.68
627 990 3.393941 GAGAGAGTGATGGGGATGGATTT 59.606 47.826 0.00 0.00 0.00 2.17
629 992 2.181865 AGAGAGAGTGATGGGGATGGAT 59.818 50.000 0.00 0.00 0.00 3.41
630 993 1.577729 AGAGAGAGTGATGGGGATGGA 59.422 52.381 0.00 0.00 0.00 3.41
632 995 2.892852 GAGAGAGAGAGTGATGGGGATG 59.107 54.545 0.00 0.00 0.00 3.51
634 997 1.216678 GGAGAGAGAGAGTGATGGGGA 59.783 57.143 0.00 0.00 0.00 4.81
635 998 1.703411 GGAGAGAGAGAGTGATGGGG 58.297 60.000 0.00 0.00 0.00 4.96
636 999 1.217689 AGGGAGAGAGAGAGTGATGGG 59.782 57.143 0.00 0.00 0.00 4.00
637 1000 2.586425 GAGGGAGAGAGAGAGTGATGG 58.414 57.143 0.00 0.00 0.00 3.51
682 1064 1.446099 CATGGCGTACTGCTGTCGT 60.446 57.895 0.00 0.00 45.43 4.34
684 1066 1.448540 AGCATGGCGTACTGCTGTC 60.449 57.895 6.54 0.00 46.55 3.51
718 1100 0.389948 GTAGCAGTTGGGTGAGGACG 60.390 60.000 0.00 0.00 0.00 4.79
736 1118 1.990614 GGAGGCGGAGGAAGAAGGT 60.991 63.158 0.00 0.00 0.00 3.50
992 1510 2.971330 AGCTTGGAGACCATGGATCTAG 59.029 50.000 21.47 16.33 31.53 2.43
1002 1520 2.409948 AGTATTGCAGCTTGGAGACC 57.590 50.000 0.00 0.00 0.00 3.85
1017 1535 4.104831 ACCCAAAGAGAGGCAAGTAGTAT 58.895 43.478 0.00 0.00 0.00 2.12
1098 1622 2.829384 GGGCTTGACCACACCCTCA 61.829 63.158 0.00 0.00 42.05 3.86
1196 1720 1.473965 GGAAGCGCTCTGGATTGATGA 60.474 52.381 12.06 0.00 0.00 2.92
1232 1756 1.472480 GCACACCTATGTTTTCGGCAT 59.528 47.619 0.00 0.00 36.72 4.40
1233 1757 0.878416 GCACACCTATGTTTTCGGCA 59.122 50.000 0.00 0.00 36.72 5.69
1296 1823 3.124297 CGATCTCCTCTTTGCTGAAACAC 59.876 47.826 0.00 0.00 0.00 3.32
1320 1847 1.198759 TCAAGTAGTCCACCCTGGCC 61.199 60.000 0.00 0.00 37.47 5.36
1392 1919 2.224066 GGACCTCGTCAGTATCAATGGG 60.224 54.545 0.00 0.00 33.68 4.00
1518 2045 4.051167 TACCGGGGTCTGAGCCGA 62.051 66.667 18.80 2.45 36.39 5.54
1604 2137 2.287069 ACGAATACCTTCTCGCTGATCG 60.287 50.000 0.00 0.00 38.64 3.69
2043 6140 5.231702 GCTACTAATAAAGCTACTCCAGGC 58.768 45.833 0.00 0.00 35.80 4.85
2218 6599 5.582269 AGAAATATCTGTTCACGTGGTGATG 59.418 40.000 17.00 3.08 37.15 3.07
2229 6610 3.493503 CGGGGCGTTAGAAATATCTGTTC 59.506 47.826 0.00 0.00 37.10 3.18
2250 6631 2.119457 GCTTCTCCAACAAAAGCAACG 58.881 47.619 1.68 0.00 43.77 4.10
2277 6700 1.066257 GCCATTACCATGCAAGCGG 59.934 57.895 0.00 0.00 0.00 5.52
2284 6707 1.067974 CAGCACCATGCCATTACCATG 59.932 52.381 0.00 0.00 46.52 3.66
2306 6761 5.163513 GTTGTATGAAATGCCCTCTGTTTG 58.836 41.667 0.00 0.00 0.00 2.93
2355 6810 5.669164 TGGTAATGCCATAACCCTTTTTC 57.331 39.130 0.00 0.00 43.61 2.29
2545 7194 3.584848 AGACTACATGGCATCCTATTCCC 59.415 47.826 0.00 0.00 0.00 3.97
2551 7217 2.180946 TCCAGACTACATGGCATCCT 57.819 50.000 0.00 0.00 37.76 3.24
2702 7371 4.095483 AGCTGATCTTTAAATGCAAGGACG 59.905 41.667 0.00 0.00 0.00 4.79
2705 7374 5.579718 CAGAGCTGATCTTTAAATGCAAGG 58.420 41.667 0.00 0.00 35.47 3.61


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

AutoCloner maintained by Alex Coulton.