Multiple sequence alignment - TraesCS7D01G455100

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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 TraesCS7D01G455100 chr7D 100.000 2798 0 0 1 2798 573968376 573971173 0.000000e+00 5168.0
1 TraesCS7D01G455100 chr7D 100.000 616 0 0 2183 2798 574248186 574248801 0.000000e+00 1138.0
2 TraesCS7D01G455100 chr7D 84.688 1169 96 31 700 1834 548560696 548561815 0.000000e+00 1090.0
3 TraesCS7D01G455100 chr7D 86.373 1020 76 28 792 1788 530430732 530429753 0.000000e+00 1055.0
4 TraesCS7D01G455100 chr7D 82.567 1262 105 37 538 1765 548324748 548325928 0.000000e+00 1005.0
5 TraesCS7D01G455100 chr7D 84.359 390 47 8 2341 2726 530429278 530428899 1.220000e-98 370.0
6 TraesCS7D01G455100 chr7D 85.013 387 25 9 24 410 574068089 574068442 2.050000e-96 363.0
7 TraesCS7D01G455100 chr7D 87.288 236 25 4 2493 2726 548326684 548326916 5.940000e-67 265.0
8 TraesCS7D01G455100 chr7D 87.892 223 18 7 2510 2726 548065078 548064859 1.290000e-63 254.0
9 TraesCS7D01G455100 chr7D 92.265 181 8 5 2550 2726 530358128 530357950 4.630000e-63 252.0
10 TraesCS7D01G455100 chr7D 93.793 145 9 0 538 682 530431002 530430858 4.690000e-53 219.0
11 TraesCS7D01G455100 chr7D 87.234 188 21 2 2061 2247 548326351 548326536 7.850000e-51 211.0
12 TraesCS7D01G455100 chr7D 89.404 151 9 1 538 681 543731448 543731598 1.710000e-42 183.0
13 TraesCS7D01G455100 chr7D 91.150 113 10 0 2196 2308 548093446 548093334 1.340000e-33 154.0
14 TraesCS7D01G455100 chr7D 92.000 75 6 0 2724 2798 548327427 548327501 3.810000e-19 106.0
15 TraesCS7D01G455100 chr7D 90.667 75 7 0 2724 2798 530428389 530428315 1.770000e-17 100.0
16 TraesCS7D01G455100 chr7D 93.182 44 3 0 722 765 530361678 530361635 6.470000e-07 65.8
17 TraesCS7D01G455100 chr7D 91.304 46 4 0 2366 2411 548065273 548065228 2.330000e-06 63.9
18 TraesCS7D01G455100 chr7B 89.623 1696 74 34 697 2322 633000999 633002662 0.000000e+00 2063.0
19 TraesCS7D01G455100 chr7B 89.646 1130 48 18 693 1793 632800689 632799600 0.000000e+00 1375.0
20 TraesCS7D01G455100 chr7B 87.346 972 74 18 835 1786 591566145 591567087 0.000000e+00 1068.0
21 TraesCS7D01G455100 chr7B 85.531 1016 84 30 792 1787 569439782 569438810 0.000000e+00 1003.0
22 TraesCS7D01G455100 chr7B 85.531 1016 84 30 792 1787 569481658 569480686 0.000000e+00 1003.0
23 TraesCS7D01G455100 chr7B 85.949 975 77 24 835 1786 591684376 591685313 0.000000e+00 987.0
24 TraesCS7D01G455100 chr7B 88.391 491 38 8 1837 2322 632799494 632799018 8.690000e-160 573.0
25 TraesCS7D01G455100 chr7B 86.905 420 26 16 1 410 632999442 632999842 7.110000e-121 444.0
26 TraesCS7D01G455100 chr7B 86.253 371 39 8 2356 2726 591055239 591054881 2.610000e-105 392.0
27 TraesCS7D01G455100 chr7B 84.783 368 42 12 2341 2703 569437106 569436748 9.530000e-95 357.0
28 TraesCS7D01G455100 chr7B 85.081 248 31 3 1520 1767 591577722 591577963 5.980000e-62 248.0
29 TraesCS7D01G455100 chr7B 86.842 228 17 7 2338 2564 632799035 632798820 2.780000e-60 243.0
30 TraesCS7D01G455100 chr7B 86.842 228 17 7 2338 2564 633002645 633002860 2.780000e-60 243.0
31 TraesCS7D01G455100 chr7B 88.144 194 19 2 2061 2253 569480374 569480184 7.800000e-56 228.0
32 TraesCS7D01G455100 chr7B 82.745 255 16 14 538 765 569481907 569481654 4.730000e-48 202.0
33 TraesCS7D01G455100 chr7B 86.813 182 21 2 2061 2241 348751317 348751138 1.700000e-47 200.0
34 TraesCS7D01G455100 chr7B 92.793 111 2 3 541 645 569440074 569439964 3.730000e-34 156.0
35 TraesCS7D01G455100 chr7B 85.211 142 14 1 538 672 587464340 587464481 3.760000e-29 139.0
36 TraesCS7D01G455100 chr7B 85.211 142 14 1 538 672 587503619 587503760 3.760000e-29 139.0
37 TraesCS7D01G455100 chr7B 80.193 207 17 12 626 813 591565949 591566150 1.750000e-27 134.0
38 TraesCS7D01G455100 chr7B 92.593 81 6 0 592 672 587479511 587479591 1.760000e-22 117.0
39 TraesCS7D01G455100 chr7B 92.000 75 6 0 2724 2798 569436226 569436152 3.810000e-19 106.0
40 TraesCS7D01G455100 chr7B 92.000 75 6 0 2724 2798 569479103 569479029 3.810000e-19 106.0
41 TraesCS7D01G455100 chr7B 92.063 63 5 0 703 765 569439840 569439778 3.840000e-14 89.8
42 TraesCS7D01G455100 chr7B 100.000 47 0 0 1791 1837 591567129 591567175 1.380000e-13 87.9
43 TraesCS7D01G455100 chr7B 100.000 47 0 0 1791 1837 591685355 591685401 1.380000e-13 87.9
44 TraesCS7D01G455100 chr7B 100.000 47 0 0 1791 1837 632799577 632799531 1.380000e-13 87.9
45 TraesCS7D01G455100 chr7B 81.928 83 9 3 2366 2448 569480126 569480050 6.470000e-07 65.8
46 TraesCS7D01G455100 chr7B 91.304 46 4 0 2366 2411 591055420 591055375 2.330000e-06 63.9
47 TraesCS7D01G455100 chr7B 94.872 39 2 0 450 488 591057170 591057132 8.370000e-06 62.1
48 TraesCS7D01G455100 chr7A 88.836 1048 53 29 756 1793 663750871 663749878 0.000000e+00 1229.0
49 TraesCS7D01G455100 chr7A 84.491 1109 91 29 703 1786 632265735 632266787 0.000000e+00 1020.0
50 TraesCS7D01G455100 chr7A 84.884 1032 74 32 700 1700 632187993 632188973 0.000000e+00 966.0
51 TraesCS7D01G455100 chr7A 80.942 1380 106 59 838 2142 617551876 617550579 0.000000e+00 946.0
52 TraesCS7D01G455100 chr7A 85.874 807 73 12 775 1562 631872522 631871738 0.000000e+00 821.0
53 TraesCS7D01G455100 chr7A 92.929 198 8 2 407 604 663574548 663574739 1.640000e-72 283.0
54 TraesCS7D01G455100 chr7A 87.556 225 16 7 2 224 663757279 663757065 1.660000e-62 250.0
55 TraesCS7D01G455100 chr7A 87.113 194 22 2 2061 2253 631848916 631848725 1.690000e-52 217.0
56 TraesCS7D01G455100 chr7A 86.264 182 17 6 2550 2725 617549674 617549495 1.020000e-44 191.0
57 TraesCS7D01G455100 chr7A 85.870 184 21 4 2502 2681 630673455 630673637 1.020000e-44 191.0
58 TraesCS7D01G455100 chr7A 86.740 181 8 6 1 174 663573461 663573632 1.320000e-43 187.0
59 TraesCS7D01G455100 chr7A 81.250 256 20 14 450 679 630671264 630671517 6.160000e-42 182.0
60 TraesCS7D01G455100 chr7A 83.178 214 17 9 483 682 631652759 631652551 7.960000e-41 178.0
61 TraesCS7D01G455100 chr7A 93.966 116 5 2 1844 1957 663749753 663749638 1.030000e-39 174.0
62 TraesCS7D01G455100 chr7A 88.079 151 11 2 538 681 625642209 625642359 3.710000e-39 172.0
63 TraesCS7D01G455100 chr7A 77.364 349 39 17 1824 2163 632266892 632267209 1.330000e-38 171.0
64 TraesCS7D01G455100 chr7A 93.548 93 6 0 2230 2322 663749646 663749554 3.760000e-29 139.0
65 TraesCS7D01G455100 chr7A 93.243 74 5 0 2725 2798 630674182 630674255 2.950000e-20 110.0
66 TraesCS7D01G455100 chr7A 94.203 69 4 0 2338 2406 663749571 663749503 3.810000e-19 106.0
67 TraesCS7D01G455100 chr7A 80.272 147 11 7 1 147 663573754 663573882 8.250000e-16 95.3
68 TraesCS7D01G455100 chr7A 94.737 57 3 0 461 517 663750924 663750868 3.840000e-14 89.8
69 TraesCS7D01G455100 chr7A 97.872 47 1 0 1791 1837 663749850 663749804 6.420000e-12 82.4
70 TraesCS7D01G455100 chr7A 97.619 42 1 0 1791 1832 632266831 632266872 3.870000e-09 73.1
71 TraesCS7D01G455100 chr7A 89.130 46 5 0 2366 2411 630622993 630623038 1.080000e-04 58.4
72 TraesCS7D01G455100 chrUn 87.410 969 73 18 838 1786 355335270 355334331 0.000000e+00 1068.0
73 TraesCS7D01G455100 chrUn 86.008 972 76 24 838 1786 337590797 337589863 0.000000e+00 987.0
74 TraesCS7D01G455100 chrUn 79.710 207 18 12 626 813 355335469 355335268 8.130000e-26 128.0
75 TraesCS7D01G455100 chrUn 100.000 47 0 0 1791 1837 337589821 337589775 1.380000e-13 87.9
76 TraesCS7D01G455100 chrUn 100.000 47 0 0 1791 1837 355334289 355334243 1.380000e-13 87.9
77 TraesCS7D01G455100 chr4A 81.994 1394 117 47 450 1785 141909140 141907823 0.000000e+00 1061.0
78 TraesCS7D01G455100 chr4B 86.170 188 23 2 2061 2247 158048899 158048714 1.700000e-47 200.0
79 TraesCS7D01G455100 chr2B 86.264 182 22 2 2061 2241 49036099 49036278 7.910000e-46 195.0
80 TraesCS7D01G455100 chr2B 86.264 182 22 2 2061 2241 742367445 742367266 7.910000e-46 195.0
81 TraesCS7D01G455100 chr2B 80.000 115 17 5 1844 1954 684004657 684004545 2.310000e-11 80.5
82 TraesCS7D01G455100 chr1D 87.500 152 12 1 538 682 110905208 110905359 4.790000e-38 169.0
83 TraesCS7D01G455100 chr1B 88.281 128 8 1 540 660 169024994 169025121 2.250000e-31 147.0
84 TraesCS7D01G455100 chr5D 89.691 97 7 2 226 321 227705363 227705269 1.360000e-23 121.0


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 TraesCS7D01G455100 chr7D 573968376 573971173 2797 False 5168.000000 5168 100.000000 1 2798 1 chr7D.!!$F3 2797
1 TraesCS7D01G455100 chr7D 574248186 574248801 615 False 1138.000000 1138 100.000000 2183 2798 1 chr7D.!!$F5 615
2 TraesCS7D01G455100 chr7D 548560696 548561815 1119 False 1090.000000 1090 84.688000 700 1834 1 chr7D.!!$F2 1134
3 TraesCS7D01G455100 chr7D 530428315 530431002 2687 True 436.000000 1055 88.798000 538 2798 4 chr7D.!!$R3 2260
4 TraesCS7D01G455100 chr7D 548324748 548327501 2753 False 396.750000 1005 87.272250 538 2798 4 chr7D.!!$F6 2260
5 TraesCS7D01G455100 chr7B 632999442 633002860 3418 False 916.666667 2063 87.790000 1 2564 3 chr7B.!!$F7 2563
6 TraesCS7D01G455100 chr7B 632798820 632800689 1869 True 569.725000 1375 91.219750 693 2564 4 chr7B.!!$R5 1871
7 TraesCS7D01G455100 chr7B 591684376 591685401 1025 False 537.450000 987 92.974500 835 1837 2 chr7B.!!$F6 1002
8 TraesCS7D01G455100 chr7B 591565949 591567175 1226 False 429.966667 1068 89.179667 626 1837 3 chr7B.!!$F5 1211
9 TraesCS7D01G455100 chr7B 569436152 569440074 3922 True 342.360000 1003 89.434000 541 2798 5 chr7B.!!$R2 2257
10 TraesCS7D01G455100 chr7B 569479029 569481907 2878 True 320.960000 1003 86.069600 538 2798 5 chr7B.!!$R3 2260
11 TraesCS7D01G455100 chr7A 632187993 632188973 980 False 966.000000 966 84.884000 700 1700 1 chr7A.!!$F3 1000
12 TraesCS7D01G455100 chr7A 631871738 631872522 784 True 821.000000 821 85.874000 775 1562 1 chr7A.!!$R3 787
13 TraesCS7D01G455100 chr7A 617549495 617551876 2381 True 568.500000 946 83.603000 838 2725 2 chr7A.!!$R5 1887
14 TraesCS7D01G455100 chr7A 632265735 632267209 1474 False 421.366667 1020 86.491333 703 2163 3 chr7A.!!$F5 1460
15 TraesCS7D01G455100 chr7A 663749503 663750924 1421 True 303.366667 1229 93.860333 461 2406 6 chr7A.!!$R6 1945
16 TraesCS7D01G455100 chrUn 337589775 337590797 1022 True 537.450000 987 93.004000 838 1837 2 chrUn.!!$R1 999
17 TraesCS7D01G455100 chrUn 355334243 355335469 1226 True 427.966667 1068 89.040000 626 1837 3 chrUn.!!$R2 1211
18 TraesCS7D01G455100 chr4A 141907823 141909140 1317 True 1061.000000 1061 81.994000 450 1785 1 chr4A.!!$R1 1335

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
762 1741 0.248215 GCCGCTGTTCAATCGGATTG 60.248 55.000 21.85 21.85 45.53 2.67 F
1236 2257 1.452833 GCTGAGGCTGGTTCCATCC 60.453 63.158 0.00 3.76 35.22 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1700 2796 1.222936 CTGGTGCACCTCCTGATCC 59.777 63.158 34.75 7.37 36.82 3.36 R
2147 3508 4.331443 TGTCATGGTTTGTCGTACATATGC 59.669 41.667 1.58 0.00 0.00 3.14 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
54 55 8.571336 ACCTTCATCAATCTTGACAGTAAAAAG 58.429 33.333 0.00 0.00 40.49 2.27
55 56 8.025445 CCTTCATCAATCTTGACAGTAAAAAGG 58.975 37.037 0.00 0.00 40.49 3.11
56 57 7.452880 TCATCAATCTTGACAGTAAAAAGGG 57.547 36.000 0.00 0.00 40.49 3.95
60 61 8.477419 TCAATCTTGACAGTAAAAAGGGAAAT 57.523 30.769 0.00 0.00 31.01 2.17
71 72 8.638873 CAGTAAAAAGGGAAATTCCTTAACACT 58.361 33.333 12.28 6.04 45.67 3.55
72 73 9.871175 AGTAAAAAGGGAAATTCCTTAACACTA 57.129 29.630 12.28 0.00 45.67 2.74
132 133 3.935203 CAGCACAGGTGATAAGTGGTAAG 59.065 47.826 3.10 0.00 41.51 2.34
133 134 3.583086 AGCACAGGTGATAAGTGGTAAGT 59.417 43.478 3.10 0.00 41.61 2.24
153 154 2.717639 ACAAGACAGGCAAACAGACT 57.282 45.000 0.00 0.00 33.98 3.24
194 195 1.142314 CCTTTGCCATGAATGCGGG 59.858 57.895 0.00 0.00 0.00 6.13
195 196 1.606885 CCTTTGCCATGAATGCGGGT 61.607 55.000 0.00 0.00 0.00 5.28
201 202 1.544537 GCCATGAATGCGGGTGGTATA 60.545 52.381 0.00 0.00 34.23 1.47
202 203 2.426522 CCATGAATGCGGGTGGTATAG 58.573 52.381 0.00 0.00 0.00 1.31
213 214 4.443034 GCGGGTGGTATAGTTCTGAAGATT 60.443 45.833 0.00 0.00 0.00 2.40
216 217 5.817816 GGGTGGTATAGTTCTGAAGATTGTG 59.182 44.000 0.00 0.00 0.00 3.33
218 219 6.535508 GGTGGTATAGTTCTGAAGATTGTGAC 59.464 42.308 0.00 0.00 0.00 3.67
220 221 8.467598 GTGGTATAGTTCTGAAGATTGTGACTA 58.532 37.037 0.00 0.00 0.00 2.59
221 222 9.201989 TGGTATAGTTCTGAAGATTGTGACTAT 57.798 33.333 6.77 6.77 0.00 2.12
222 223 9.469807 GGTATAGTTCTGAAGATTGTGACTATG 57.530 37.037 10.07 0.00 0.00 2.23
272 283 1.229428 ATGTCAACGTGCAAGACAGG 58.771 50.000 6.65 0.00 44.51 4.00
274 285 1.153269 TCAACGTGCAAGACAGGCA 60.153 52.632 6.65 0.00 37.69 4.75
275 286 0.746204 TCAACGTGCAAGACAGGCAA 60.746 50.000 6.65 0.00 43.91 4.52
290 301 2.466846 AGGCAAAACCCTGACAAAACT 58.533 42.857 0.00 0.00 40.58 2.66
306 317 1.534729 AACTTGATTCCTGCCGTTCC 58.465 50.000 0.00 0.00 0.00 3.62
342 353 7.400599 ACTACGTACAATCCTAGATGAAACA 57.599 36.000 0.00 0.00 0.00 2.83
361 372 9.607333 ATGAAACACTGAATCTCCTCCTATATA 57.393 33.333 0.00 0.00 0.00 0.86
362 373 9.607333 TGAAACACTGAATCTCCTCCTATATAT 57.393 33.333 0.00 0.00 0.00 0.86
365 376 7.846066 ACACTGAATCTCCTCCTATATATTGC 58.154 38.462 0.00 0.00 0.00 3.56
367 378 9.194972 CACTGAATCTCCTCCTATATATTGCTA 57.805 37.037 0.00 0.00 0.00 3.49
368 379 9.775539 ACTGAATCTCCTCCTATATATTGCTAA 57.224 33.333 0.00 0.00 0.00 3.09
396 407 3.145286 TGCAATGTGATGGTTTCGAAGA 58.855 40.909 0.00 0.00 0.00 2.87
397 408 3.189080 TGCAATGTGATGGTTTCGAAGAG 59.811 43.478 0.00 0.00 38.43 2.85
410 421 1.449601 GAAGAGGCGGATTTGCGGA 60.450 57.895 0.00 0.00 35.06 5.54
411 422 1.706287 GAAGAGGCGGATTTGCGGAC 61.706 60.000 0.00 0.00 35.06 4.79
412 423 2.435938 GAGGCGGATTTGCGGACA 60.436 61.111 0.00 0.00 35.06 4.02
413 424 2.746277 AGGCGGATTTGCGGACAC 60.746 61.111 0.00 0.00 35.06 3.67
414 425 3.810896 GGCGGATTTGCGGACACC 61.811 66.667 0.00 0.00 35.06 4.16
439 450 3.644606 CCAGCAGGCTCACCACCT 61.645 66.667 0.00 0.00 39.06 4.00
478 489 3.730761 GCCTCACGCAGCAGGTTG 61.731 66.667 0.00 0.00 37.47 3.77
533 1231 2.811317 GGCGAGCGGACTGAACAG 60.811 66.667 0.00 0.00 0.00 3.16
536 1234 1.506718 CGAGCGGACTGAACAGCTA 59.493 57.895 1.46 0.00 40.87 3.32
654 1574 1.775039 CGTCGATCATGGCGCCAATT 61.775 55.000 36.33 21.21 0.00 2.32
762 1741 0.248215 GCCGCTGTTCAATCGGATTG 60.248 55.000 21.85 21.85 45.53 2.67
817 1814 4.514577 CGATCGGGAGTGGCGCTT 62.515 66.667 7.64 0.00 0.00 4.68
942 1943 3.244840 CCCAATCTCTCCATCCAATCCTC 60.245 52.174 0.00 0.00 0.00 3.71
947 1952 1.582624 TCTCCATCCAATCCTCCCTCT 59.417 52.381 0.00 0.00 0.00 3.69
1236 2257 1.452833 GCTGAGGCTGGTTCCATCC 60.453 63.158 0.00 3.76 35.22 3.51
1596 2686 1.561643 TCTGCTCGGAGGACAAGATT 58.438 50.000 7.20 0.00 0.00 2.40
1700 2796 2.719979 GCCCAAGATGATGCAGCG 59.280 61.111 0.00 0.00 0.00 5.18
1701 2815 2.842256 GCCCAAGATGATGCAGCGG 61.842 63.158 0.00 0.00 0.00 5.52
1732 2846 4.651867 CCAGCTCCATGGTGAAGG 57.348 61.111 17.98 13.24 46.27 3.46
1837 3024 0.813184 ACATGCCATACTGCAGTTGC 59.187 50.000 27.06 23.82 45.93 4.17
1838 3025 1.100510 CATGCCATACTGCAGTTGCT 58.899 50.000 27.06 7.59 45.93 3.91
1839 3026 1.065102 CATGCCATACTGCAGTTGCTC 59.935 52.381 27.06 12.72 45.93 4.26
1841 3028 1.021390 GCCATACTGCAGTTGCTCGT 61.021 55.000 27.06 0.33 42.66 4.18
1842 3029 1.739035 GCCATACTGCAGTTGCTCGTA 60.739 52.381 27.06 4.97 42.66 3.43
1914 3169 7.689812 CGAGATTTACTGTTACAAATCTGCAAG 59.310 37.037 17.34 6.62 46.43 4.01
1968 3233 1.624336 AGATGCATGTGTTTGTGGCT 58.376 45.000 2.46 0.00 0.00 4.75
2011 3281 2.813061 CAACTGAGCAACCAACAAAGG 58.187 47.619 0.00 0.00 0.00 3.11
2031 3332 6.747414 AAGGCCTCCTTTTAAAATTCAGTT 57.253 33.333 5.23 0.00 41.69 3.16
2032 3333 6.747414 AGGCCTCCTTTTAAAATTCAGTTT 57.253 33.333 0.00 0.00 0.00 2.66
2033 3334 7.136822 AGGCCTCCTTTTAAAATTCAGTTTT 57.863 32.000 0.00 0.00 42.47 2.43
2034 3335 7.217200 AGGCCTCCTTTTAAAATTCAGTTTTC 58.783 34.615 0.00 0.00 40.40 2.29
2124 3480 8.482852 TCAAAATTGAGAAAATCCTCCTCTTT 57.517 30.769 0.00 0.00 32.50 2.52
2132 3488 6.605119 AGAAAATCCTCCTCTTTCTGTTTCA 58.395 36.000 0.00 0.00 37.86 2.69
2133 3489 6.488344 AGAAAATCCTCCTCTTTCTGTTTCAC 59.512 38.462 0.00 0.00 37.86 3.18
2135 3491 5.574970 ATCCTCCTCTTTCTGTTTCACTT 57.425 39.130 0.00 0.00 0.00 3.16
2136 3492 4.708177 TCCTCCTCTTTCTGTTTCACTTG 58.292 43.478 0.00 0.00 0.00 3.16
2139 3495 5.454755 CCTCCTCTTTCTGTTTCACTTGGTA 60.455 44.000 0.00 0.00 0.00 3.25
2140 3496 6.187727 TCCTCTTTCTGTTTCACTTGGTAT 57.812 37.500 0.00 0.00 0.00 2.73
2141 3497 7.311092 TCCTCTTTCTGTTTCACTTGGTATA 57.689 36.000 0.00 0.00 0.00 1.47
2147 3508 9.450807 CTTTCTGTTTCACTTGGTATAAAACTG 57.549 33.333 0.00 0.00 32.44 3.16
2169 3531 4.331443 TGCATATGTACGACAAACCATGAC 59.669 41.667 4.29 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 5.516591 GCTGGGAGCCTGGGATAATAAAATA 60.517 44.000 0.00 0.00 34.48 1.40
90 91 4.754160 GCTGGGAGCCTGGGATAATAAAAT 60.754 45.833 0.00 0.00 34.48 1.82
95 96 0.698886 TGCTGGGAGCCTGGGATAAT 60.699 55.000 0.00 0.00 41.51 1.28
99 100 4.980592 TGTGCTGGGAGCCTGGGA 62.981 66.667 0.00 0.00 41.51 4.37
100 101 4.421515 CTGTGCTGGGAGCCTGGG 62.422 72.222 0.00 0.00 41.51 4.45
101 102 4.421515 CCTGTGCTGGGAGCCTGG 62.422 72.222 0.00 0.00 41.51 4.45
102 103 3.644606 ACCTGTGCTGGGAGCCTG 61.645 66.667 0.00 0.00 41.51 4.85
103 104 3.644606 CACCTGTGCTGGGAGCCT 61.645 66.667 0.00 0.00 41.51 4.58
104 105 1.626356 TATCACCTGTGCTGGGAGCC 61.626 60.000 0.00 0.00 41.51 4.70
105 106 0.253044 TTATCACCTGTGCTGGGAGC 59.747 55.000 0.00 0.00 42.82 4.70
106 107 1.556911 ACTTATCACCTGTGCTGGGAG 59.443 52.381 0.39 0.00 0.00 4.30
132 133 3.248602 CAGTCTGTTTGCCTGTCTTGTAC 59.751 47.826 0.00 0.00 0.00 2.90
133 134 3.133901 TCAGTCTGTTTGCCTGTCTTGTA 59.866 43.478 0.00 0.00 0.00 2.41
153 154 4.351874 AGGAATCGAACTTCCACTTTCA 57.648 40.909 17.84 0.00 46.02 2.69
171 172 1.826720 GCATTCATGGCAAAGGAAGGA 59.173 47.619 13.32 0.00 0.00 3.36
172 173 1.470285 CGCATTCATGGCAAAGGAAGG 60.470 52.381 0.00 0.00 0.00 3.46
173 174 1.470285 CCGCATTCATGGCAAAGGAAG 60.470 52.381 0.00 0.00 0.00 3.46
174 175 0.531657 CCGCATTCATGGCAAAGGAA 59.468 50.000 0.00 0.00 0.00 3.36
175 176 1.321805 CCCGCATTCATGGCAAAGGA 61.322 55.000 0.00 0.00 0.00 3.36
194 195 7.324178 AGTCACAATCTTCAGAACTATACCAC 58.676 38.462 0.00 0.00 0.00 4.16
195 196 7.482169 AGTCACAATCTTCAGAACTATACCA 57.518 36.000 0.00 0.00 0.00 3.25
201 202 8.128322 ACTACATAGTCACAATCTTCAGAACT 57.872 34.615 0.00 0.00 0.00 3.01
202 203 8.764524 AACTACATAGTCACAATCTTCAGAAC 57.235 34.615 0.00 0.00 34.99 3.01
213 214 6.600427 TCCGAGTTATGAACTACATAGTCACA 59.400 38.462 0.00 0.00 43.03 3.58
216 217 6.485984 TCCTCCGAGTTATGAACTACATAGTC 59.514 42.308 0.00 0.00 43.03 2.59
218 219 6.879276 TCCTCCGAGTTATGAACTACATAG 57.121 41.667 0.00 0.00 43.03 2.23
220 221 5.452077 GCTTCCTCCGAGTTATGAACTACAT 60.452 44.000 0.00 0.00 43.03 2.29
221 222 4.142227 GCTTCCTCCGAGTTATGAACTACA 60.142 45.833 0.00 0.00 43.03 2.74
222 223 4.098196 AGCTTCCTCCGAGTTATGAACTAC 59.902 45.833 0.00 0.00 43.03 2.73
223 224 4.098044 CAGCTTCCTCCGAGTTATGAACTA 59.902 45.833 0.00 0.00 43.03 2.24
272 283 3.855858 TCAAGTTTTGTCAGGGTTTTGC 58.144 40.909 0.00 0.00 0.00 3.68
274 285 5.425217 AGGAATCAAGTTTTGTCAGGGTTTT 59.575 36.000 0.00 0.00 0.00 2.43
275 286 4.962362 AGGAATCAAGTTTTGTCAGGGTTT 59.038 37.500 0.00 0.00 0.00 3.27
290 301 0.109532 TGTGGAACGGCAGGAATCAA 59.890 50.000 0.00 0.00 42.39 2.57
306 317 3.322369 TGTACGTAGTTTCCATGCTGTG 58.678 45.455 0.00 0.00 37.78 3.66
342 353 9.775539 TTAGCAATATATAGGAGGAGATTCAGT 57.224 33.333 0.00 0.00 0.00 3.41
368 379 5.406175 CGAAACCATCACATTGCAGATTTTT 59.594 36.000 0.00 0.00 0.00 1.94
381 392 0.721718 CGCCTCTTCGAAACCATCAC 59.278 55.000 0.00 0.00 0.00 3.06
389 400 1.358725 CGCAAATCCGCCTCTTCGAA 61.359 55.000 0.00 0.00 0.00 3.71
396 407 2.746277 GTGTCCGCAAATCCGCCT 60.746 61.111 0.00 0.00 0.00 5.52
397 408 3.810896 GGTGTCCGCAAATCCGCC 61.811 66.667 0.00 0.00 0.00 6.13
422 433 3.644606 AGGTGGTGAGCCTGCTGG 61.645 66.667 5.03 5.03 34.56 4.85
444 455 4.554363 CGTGCTACCTCGCCCTCG 62.554 72.222 0.00 0.00 0.00 4.63
445 456 4.874977 GCGTGCTACCTCGCCCTC 62.875 72.222 0.00 0.00 45.31 4.30
485 502 1.002379 CAGCAAGCAAGAGGAGGCT 60.002 57.895 0.00 0.00 43.46 4.58
526 1224 0.390340 TCAAGGCGCTAGCTGTTCAG 60.390 55.000 13.93 0.00 44.37 3.02
527 1225 0.670546 GTCAAGGCGCTAGCTGTTCA 60.671 55.000 13.93 0.00 44.37 3.18
528 1226 1.687494 CGTCAAGGCGCTAGCTGTTC 61.687 60.000 13.93 0.00 44.37 3.18
529 1227 1.738099 CGTCAAGGCGCTAGCTGTT 60.738 57.895 13.93 0.00 44.37 3.16
530 1228 2.125912 CGTCAAGGCGCTAGCTGT 60.126 61.111 13.93 0.00 44.37 4.40
533 1231 3.248171 CGTCGTCAAGGCGCTAGC 61.248 66.667 7.64 4.06 42.71 3.42
882 1879 3.075005 GCCTACCACGAGGGAGCA 61.075 66.667 5.43 0.00 45.39 4.26
885 1882 1.826921 GATCGCCTACCACGAGGGA 60.827 63.158 3.29 0.00 43.74 4.20
886 1883 2.728817 GATCGCCTACCACGAGGG 59.271 66.667 3.29 0.00 43.74 4.30
926 1927 1.977129 GAGGGAGGATTGGATGGAGAG 59.023 57.143 0.00 0.00 0.00 3.20
942 1943 1.127343 GGATGGAGAAGTGGAGAGGG 58.873 60.000 0.00 0.00 0.00 4.30
947 1952 1.203300 TGGAGTGGATGGAGAAGTGGA 60.203 52.381 0.00 0.00 0.00 4.02
1700 2796 1.222936 CTGGTGCACCTCCTGATCC 59.777 63.158 34.75 7.37 36.82 3.36
1701 2815 1.451028 GCTGGTGCACCTCCTGATC 60.451 63.158 34.75 7.84 39.41 2.92
1732 2846 2.289444 TGGTCCTGATCGACAAGGTTTC 60.289 50.000 13.49 7.02 34.24 2.78
1837 3024 7.807907 TCACATACATAACATGCATACTACGAG 59.192 37.037 0.00 0.00 0.00 4.18
1838 3025 7.653647 TCACATACATAACATGCATACTACGA 58.346 34.615 0.00 0.00 0.00 3.43
1839 3026 7.867445 TCACATACATAACATGCATACTACG 57.133 36.000 0.00 0.00 0.00 3.51
1841 3028 8.519526 TCGATCACATACATAACATGCATACTA 58.480 33.333 0.00 0.00 0.00 1.82
1842 3029 7.378181 TCGATCACATACATAACATGCATACT 58.622 34.615 0.00 0.00 0.00 2.12
1914 3169 4.544242 GAGCAATTTCTCTCGAAATCCC 57.456 45.455 0.00 0.00 46.36 3.85
1968 3233 8.332464 GTTGCGTGCAGAATTATACAGTAAATA 58.668 33.333 0.00 0.00 0.00 1.40
2011 3281 8.662781 AAGAAAACTGAATTTTAAAAGGAGGC 57.337 30.769 6.79 0.00 40.73 4.70
2124 3480 6.544197 TGCAGTTTTATACCAAGTGAAACAGA 59.456 34.615 0.00 0.00 41.43 3.41
2132 3488 7.982919 TCGTACATATGCAGTTTTATACCAAGT 59.017 33.333 1.58 0.00 0.00 3.16
2133 3489 8.273557 GTCGTACATATGCAGTTTTATACCAAG 58.726 37.037 1.58 0.00 0.00 3.61
2135 3491 7.266400 TGTCGTACATATGCAGTTTTATACCA 58.734 34.615 1.58 0.00 0.00 3.25
2136 3492 7.703298 TGTCGTACATATGCAGTTTTATACC 57.297 36.000 1.58 0.00 0.00 2.73
2139 3495 7.119992 TGGTTTGTCGTACATATGCAGTTTTAT 59.880 33.333 1.58 0.00 0.00 1.40
2140 3496 6.427242 TGGTTTGTCGTACATATGCAGTTTTA 59.573 34.615 1.58 0.00 0.00 1.52
2141 3497 5.239744 TGGTTTGTCGTACATATGCAGTTTT 59.760 36.000 1.58 0.00 0.00 2.43
2147 3508 4.331443 TGTCATGGTTTGTCGTACATATGC 59.669 41.667 1.58 0.00 0.00 3.14
2169 3531 8.712285 AAGATTTATCTTTTTGTGGATGCATG 57.288 30.769 2.46 0.00 44.28 4.06


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

AutoCloner maintained by Alex Coulton.