Multiple sequence alignment - TraesCS2B01G114600

Loading Multiple Alignment...

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 TraesCS2B01G114600 chr2B 100.000 2483 0 0 1 2483 77885238 77882756 0.000000e+00 4586
1 TraesCS2B01G114600 chr2B 98.062 929 17 1 1 929 77895170 77894243 0.000000e+00 1615
2 TraesCS2B01G114600 chr2B 78.531 1430 295 11 935 2359 683594217 683592795 0.000000e+00 929
3 TraesCS2B01G114600 chr7A 98.172 930 16 1 1 929 591653056 591653985 0.000000e+00 1622
4 TraesCS2B01G114600 chr7B 97.957 930 17 2 1 929 368664345 368665273 0.000000e+00 1611
5 TraesCS2B01G114600 chr7B 97.950 927 18 1 1 926 368671098 368672024 0.000000e+00 1605
6 TraesCS2B01G114600 chr7B 97.634 930 20 2 1 929 501491799 501492727 0.000000e+00 1594
7 TraesCS2B01G114600 chr7B 83.894 1428 224 6 934 2359 697866493 697865070 0.000000e+00 1358
8 TraesCS2B01G114600 chr5B 97.845 928 18 2 1 927 542762040 542761114 0.000000e+00 1602
9 TraesCS2B01G114600 chr5B 98.438 128 2 0 2356 2483 557744283 557744156 2.480000e-55 226
10 TraesCS2B01G114600 chr5B 98.400 125 2 0 2356 2480 678547010 678547134 1.160000e-53 220
11 TraesCS2B01G114600 chr3A 97.742 930 20 1 1 929 40344068 40343139 0.000000e+00 1600
12 TraesCS2B01G114600 chr1B 97.843 927 17 3 1 926 359607133 359608057 0.000000e+00 1598
13 TraesCS2B01G114600 chr1B 98.438 128 2 0 2356 2483 20447926 20448053 2.480000e-55 226
14 TraesCS2B01G114600 chr1B 97.656 128 3 0 2356 2483 153539665 153539792 1.160000e-53 220
15 TraesCS2B01G114600 chr1B 97.656 128 3 0 2356 2483 292504227 292504100 1.160000e-53 220
16 TraesCS2B01G114600 chr4B 97.740 929 18 3 1 927 673428681 673429608 0.000000e+00 1596
17 TraesCS2B01G114600 chr4B 98.438 128 1 1 2356 2483 517720525 517720651 8.940000e-55 224
18 TraesCS2B01G114600 chr5A 84.749 1436 213 6 926 2358 475601956 475600524 0.000000e+00 1434
19 TraesCS2B01G114600 chr5A 85.866 1316 178 5 1046 2359 673676503 673677812 0.000000e+00 1393
20 TraesCS2B01G114600 chr6B 83.693 1435 231 3 926 2359 702199986 702198554 0.000000e+00 1351
21 TraesCS2B01G114600 chr6A 83.438 1437 229 8 926 2359 530255157 530253727 0.000000e+00 1327
22 TraesCS2B01G114600 chr4A 81.463 1435 263 3 926 2359 739441802 739440370 0.000000e+00 1173
23 TraesCS2B01G114600 chr4A 86.137 1082 146 4 926 2005 506705313 506704234 0.000000e+00 1164
24 TraesCS2B01G114600 chr3D 79.804 1431 277 12 935 2359 67071397 67072821 0.000000e+00 1031
25 TraesCS2B01G114600 chr1A 98.438 128 2 0 2356 2483 565242999 565242872 2.480000e-55 226
26 TraesCS2B01G114600 chr3B 98.425 127 2 0 2356 2482 89822573 89822447 8.940000e-55 224
27 TraesCS2B01G114600 chr3B 97.656 128 3 0 2356 2483 219128289 219128416 1.160000e-53 220


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 TraesCS2B01G114600 chr2B 77882756 77885238 2482 True 4586 4586 100.000 1 2483 1 chr2B.!!$R1 2482
1 TraesCS2B01G114600 chr2B 77894243 77895170 927 True 1615 1615 98.062 1 929 1 chr2B.!!$R2 928
2 TraesCS2B01G114600 chr2B 683592795 683594217 1422 True 929 929 78.531 935 2359 1 chr2B.!!$R3 1424
3 TraesCS2B01G114600 chr7A 591653056 591653985 929 False 1622 1622 98.172 1 929 1 chr7A.!!$F1 928
4 TraesCS2B01G114600 chr7B 368664345 368665273 928 False 1611 1611 97.957 1 929 1 chr7B.!!$F1 928
5 TraesCS2B01G114600 chr7B 368671098 368672024 926 False 1605 1605 97.950 1 926 1 chr7B.!!$F2 925
6 TraesCS2B01G114600 chr7B 501491799 501492727 928 False 1594 1594 97.634 1 929 1 chr7B.!!$F3 928
7 TraesCS2B01G114600 chr7B 697865070 697866493 1423 True 1358 1358 83.894 934 2359 1 chr7B.!!$R1 1425
8 TraesCS2B01G114600 chr5B 542761114 542762040 926 True 1602 1602 97.845 1 927 1 chr5B.!!$R1 926
9 TraesCS2B01G114600 chr3A 40343139 40344068 929 True 1600 1600 97.742 1 929 1 chr3A.!!$R1 928
10 TraesCS2B01G114600 chr1B 359607133 359608057 924 False 1598 1598 97.843 1 926 1 chr1B.!!$F3 925
11 TraesCS2B01G114600 chr4B 673428681 673429608 927 False 1596 1596 97.740 1 927 1 chr4B.!!$F2 926
12 TraesCS2B01G114600 chr5A 475600524 475601956 1432 True 1434 1434 84.749 926 2358 1 chr5A.!!$R1 1432
13 TraesCS2B01G114600 chr5A 673676503 673677812 1309 False 1393 1393 85.866 1046 2359 1 chr5A.!!$F1 1313
14 TraesCS2B01G114600 chr6B 702198554 702199986 1432 True 1351 1351 83.693 926 2359 1 chr6B.!!$R1 1433
15 TraesCS2B01G114600 chr6A 530253727 530255157 1430 True 1327 1327 83.438 926 2359 1 chr6A.!!$R1 1433
16 TraesCS2B01G114600 chr4A 739440370 739441802 1432 True 1173 1173 81.463 926 2359 1 chr4A.!!$R2 1433
17 TraesCS2B01G114600 chr4A 506704234 506705313 1079 True 1164 1164 86.137 926 2005 1 chr4A.!!$R1 1079
18 TraesCS2B01G114600 chr3D 67071397 67072821 1424 False 1031 1031 79.804 935 2359 1 chr3D.!!$F1 1424

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
529 534 0.716591 TCCATACCTGAGTCCCTGGT 59.283 55.0 5.18 5.18 46.97 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 1671 0.042581 TAGATGACCCCAGACCAGCA 59.957 55.0 0.0 0.0 0.0 4.41 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
35 36 5.279156 CGTAGGGTCTACACACTTAAGGTTT 60.279 44.000 7.53 0.00 37.49 3.27
116 117 0.744874 GATGAGATCCCGGACGTCAA 59.255 55.000 18.91 0.00 0.00 3.18
529 534 0.716591 TCCATACCTGAGTCCCTGGT 59.283 55.000 5.18 5.18 46.97 4.00
930 936 1.939838 GCTACGTTCCCCAACAGTGAG 60.940 57.143 0.00 0.00 32.14 3.51
931 937 1.616865 CTACGTTCCCCAACAGTGAGA 59.383 52.381 0.00 0.00 32.14 3.27
943 949 4.546570 CAACAGTGAGAAGTATGTGTCGA 58.453 43.478 0.00 0.00 0.00 4.20
963 969 5.007724 GTCGATGGGAAACATGGAAATACTC 59.992 44.000 0.00 0.00 44.38 2.59
975 981 5.617528 TGGAAATACTCATTAAGGCGGTA 57.382 39.130 0.00 0.00 0.00 4.02
993 999 2.817258 GGTAGCACAAGCAATACCAACA 59.183 45.455 0.00 0.00 45.49 3.33
1008 1014 4.002906 ACCAACATACGTGATGAGTGTT 57.997 40.909 0.00 0.00 39.06 3.32
1021 1027 2.975799 GTGTTTTCCGCCTGCCGA 60.976 61.111 0.00 0.00 40.02 5.54
1026 1032 2.739849 TTTTCCGCCTGCCGACATCA 62.740 55.000 0.00 0.00 40.02 3.07
1029 1035 2.494445 CGCCTGCCGACATCAGTA 59.506 61.111 0.00 0.00 40.02 2.74
1041 1047 3.427638 CGACATCAGTATGTGACGACCTT 60.428 47.826 0.00 0.00 46.49 3.50
1098 1104 0.918310 AGGGCAAGAGGAAGATGGCT 60.918 55.000 0.00 0.00 39.38 4.75
1104 1110 2.490903 CAAGAGGAAGATGGCTTGGTTG 59.509 50.000 0.00 0.00 35.34 3.77
1122 1128 3.389329 GGTTGAGCTGGGAGAAGATGATA 59.611 47.826 0.00 0.00 0.00 2.15
1212 1218 7.416664 GCAAATCAGGCTTGGAGATTATTACAA 60.417 37.037 0.00 0.00 32.11 2.41
1273 1279 6.814043 AGATACTACCCAAACGGTAATCTTC 58.186 40.000 0.00 0.00 46.85 2.87
1287 1293 5.425630 GGTAATCTTCTGGATACGGTGTTT 58.574 41.667 0.00 0.00 45.94 2.83
1322 1328 5.174037 TCTACGGTTTGGAAAGGAATCAT 57.826 39.130 0.00 0.00 0.00 2.45
1323 1329 5.183228 TCTACGGTTTGGAAAGGAATCATC 58.817 41.667 0.00 0.00 0.00 2.92
1368 1374 2.108952 AGGCTTGATTTGGAGAGTTGGT 59.891 45.455 0.00 0.00 0.00 3.67
1425 1431 0.846427 TCCCCAGGAGGCATGACTTT 60.846 55.000 0.41 0.00 0.00 2.66
1458 1464 5.032170 ACCCCAAAAGGAAATTGCAGATAT 58.968 37.500 0.00 0.00 38.24 1.63
1467 1473 6.435164 AGGAAATTGCAGATATAACTGGGTT 58.565 36.000 11.54 0.00 38.22 4.11
1531 1537 3.559384 GCTAAGGCAGTACTTTTGGGAGT 60.559 47.826 0.00 0.00 38.54 3.85
1539 1545 2.430248 ACTTTTGGGAGTTGGACGTT 57.570 45.000 0.00 0.00 0.00 3.99
1540 1546 2.294979 ACTTTTGGGAGTTGGACGTTC 58.705 47.619 0.00 0.00 0.00 3.95
1572 1578 0.978146 AGATCCGGACTTCACCCAGG 60.978 60.000 6.12 0.00 0.00 4.45
1602 1609 2.093500 GGATTTTCTGGCATGGTTTCCC 60.093 50.000 0.00 0.00 0.00 3.97
1605 1612 0.322456 TTCTGGCATGGTTTCCCGAG 60.322 55.000 0.00 0.00 0.00 4.63
1614 1623 0.685660 GGTTTCCCGAGAAGAGTGGT 59.314 55.000 0.00 0.00 32.35 4.16
1635 1644 5.648526 TGGTTGTTTTACAGTTAGAAGTGCA 59.351 36.000 0.00 0.00 32.54 4.57
1647 1656 4.530857 AGTGCATACCGGCTCGCC 62.531 66.667 0.00 0.00 32.81 5.54
1656 1665 2.584418 CGGCTCGCCACATCTGAG 60.584 66.667 8.87 0.00 35.37 3.35
1662 1671 2.599597 GCCACATCTGAGGGGCAT 59.400 61.111 14.20 0.00 45.70 4.40
1665 1674 1.226542 CACATCTGAGGGGCATGCT 59.773 57.895 18.92 0.00 0.00 3.79
1699 1708 2.798445 TAGTGCGGCTCCAGAAGGGA 62.798 60.000 0.00 0.00 45.89 4.20
1718 1727 0.482446 AACCAGGTGATTTGGAGGCA 59.518 50.000 0.00 0.00 39.08 4.75
1730 1739 2.799126 TGGAGGCATATTTGGAACGT 57.201 45.000 0.00 0.00 0.00 3.99
1735 1744 4.497507 GGAGGCATATTTGGAACGTTAAGC 60.498 45.833 0.00 0.00 0.00 3.09
1741 1750 0.109723 TTGGAACGTTAAGCTGCCCT 59.890 50.000 0.00 0.00 0.00 5.19
1756 1765 3.668447 CTGCCCTTGAAGATGCGTATAT 58.332 45.455 0.00 0.00 0.00 0.86
1758 1767 4.460263 TGCCCTTGAAGATGCGTATATTT 58.540 39.130 0.00 0.00 0.00 1.40
1767 1776 4.067896 AGATGCGTATATTTGCCTGGAAG 58.932 43.478 0.00 0.00 0.00 3.46
1819 1828 6.319405 TGCATGCAAGAAATACAGACACATAT 59.681 34.615 20.30 0.00 0.00 1.78
1833 1842 4.936411 AGACACATATCTACGAGGGATACG 59.064 45.833 0.00 0.00 37.60 3.06
1861 1870 1.768275 TGTGTGGCTCAGAGAAGGAAA 59.232 47.619 0.00 0.00 0.00 3.13
1926 1935 1.409064 TGGTCTCATATGCGTCAGGTC 59.591 52.381 0.00 0.00 0.00 3.85
1932 1941 2.369257 ATATGCGTCAGGTCTGGCCG 62.369 60.000 0.00 2.48 43.70 6.13
1971 1980 0.105658 TGAGGGATACGGGGAAGGAG 60.106 60.000 0.00 0.00 37.60 3.69
1997 2006 5.755861 GGCTCCTAAACATACTGATGAACTC 59.244 44.000 0.00 0.00 36.48 3.01
2012 2021 6.823497 TGATGAACTCTGATGATGCTATGAA 58.177 36.000 0.00 0.00 0.00 2.57
2016 2025 5.883685 ACTCTGATGATGCTATGAAGGAA 57.116 39.130 0.00 0.00 0.00 3.36
2022 2031 2.874086 TGATGCTATGAAGGAATGCACG 59.126 45.455 0.00 0.00 36.44 5.34
2057 2066 0.798776 AGAATTTGGTCGCTTCGCAG 59.201 50.000 0.00 0.00 0.00 5.18
2088 2097 2.431057 CCACGCTAAGTCTATCCCAACT 59.569 50.000 0.00 0.00 0.00 3.16
2090 2099 4.098960 CCACGCTAAGTCTATCCCAACTAA 59.901 45.833 0.00 0.00 0.00 2.24
2092 2101 4.954826 ACGCTAAGTCTATCCCAACTAACT 59.045 41.667 0.00 0.00 0.00 2.24
2096 2105 6.097129 GCTAAGTCTATCCCAACTAACTCTGT 59.903 42.308 0.00 0.00 0.00 3.41
2125 2134 7.522236 CGGCAGATTATCTACAGAGTTACATGA 60.522 40.741 0.00 0.00 0.00 3.07
2127 2136 8.356657 GCAGATTATCTACAGAGTTACATGACT 58.643 37.037 0.00 0.00 0.00 3.41
2137 2146 7.896811 ACAGAGTTACATGACTTCAATACAGA 58.103 34.615 0.00 0.00 0.00 3.41
2169 2178 9.482175 AGAAGGTACACTACAGAAGAGATAATT 57.518 33.333 0.00 0.00 0.00 1.40
2182 2191 8.566260 CAGAAGAGATAATTAAAGGCAAGATGG 58.434 37.037 0.00 0.00 0.00 3.51
2193 2202 1.742831 GGCAAGATGGCAATGTTCGTA 59.257 47.619 0.00 0.00 43.14 3.43
2201 2210 1.068610 GGCAATGTTCGTAGCAAAGCA 60.069 47.619 0.00 0.00 0.00 3.91
2203 2212 3.244976 GCAATGTTCGTAGCAAAGCAAT 58.755 40.909 0.00 0.00 0.00 3.56
2210 2219 5.411361 TGTTCGTAGCAAAGCAATCTAATGT 59.589 36.000 0.00 0.00 0.00 2.71
2223 2232 4.737855 ATCTAATGTACGAACACCTGCT 57.262 40.909 0.00 0.00 38.78 4.24
2225 2234 3.762288 TCTAATGTACGAACACCTGCTCT 59.238 43.478 0.00 0.00 38.78 4.09
2274 2283 1.724582 GCCAAACAGCACTGTCGGTT 61.725 55.000 16.37 1.82 44.13 4.44
2285 2294 1.346395 ACTGTCGGTTGATGGTGCTTA 59.654 47.619 0.00 0.00 0.00 3.09
2287 2296 0.719465 GTCGGTTGATGGTGCTTACG 59.281 55.000 0.00 0.00 0.00 3.18
2289 2298 1.019278 CGGTTGATGGTGCTTACGCT 61.019 55.000 0.00 0.00 36.97 5.07
2290 2299 1.737696 CGGTTGATGGTGCTTACGCTA 60.738 52.381 0.00 0.00 36.97 4.26
2331 2340 2.672996 GGGATGGTGCTGCAACGT 60.673 61.111 13.06 13.06 0.00 3.99
2359 2368 0.316196 GAGTGTCATATTTGCGGCGC 60.316 55.000 27.44 27.44 0.00 6.53
2360 2369 1.024046 AGTGTCATATTTGCGGCGCA 61.024 50.000 33.07 33.07 36.47 6.09
2361 2370 0.861450 GTGTCATATTTGCGGCGCAC 60.861 55.000 36.57 21.45 38.71 5.34
2362 2371 1.298339 GTCATATTTGCGGCGCACC 60.298 57.895 36.57 12.27 38.71 5.01
2363 2372 1.451207 TCATATTTGCGGCGCACCT 60.451 52.632 36.57 25.81 38.71 4.00
2364 2373 0.179070 TCATATTTGCGGCGCACCTA 60.179 50.000 36.57 27.09 38.71 3.08
2365 2374 0.660488 CATATTTGCGGCGCACCTAA 59.340 50.000 36.57 26.51 38.71 2.69
2366 2375 1.266718 CATATTTGCGGCGCACCTAAT 59.733 47.619 36.57 30.76 38.71 1.73
2367 2376 1.384525 TATTTGCGGCGCACCTAATT 58.615 45.000 36.57 18.12 38.71 1.40
2368 2377 0.530288 ATTTGCGGCGCACCTAATTT 59.470 45.000 36.57 9.64 38.71 1.82
2369 2378 0.387878 TTTGCGGCGCACCTAATTTG 60.388 50.000 36.57 0.00 38.71 2.32
2370 2379 2.102161 GCGGCGCACCTAATTTGG 59.898 61.111 29.21 4.22 0.00 3.28
2371 2380 2.696759 GCGGCGCACCTAATTTGGT 61.697 57.895 29.21 5.68 41.77 3.67
2372 2381 1.427819 CGGCGCACCTAATTTGGTC 59.572 57.895 10.83 3.95 38.45 4.02
2373 2382 1.302383 CGGCGCACCTAATTTGGTCA 61.302 55.000 10.83 0.00 38.45 4.02
2374 2383 1.102978 GGCGCACCTAATTTGGTCAT 58.897 50.000 10.83 0.00 38.45 3.06
2375 2384 1.476488 GGCGCACCTAATTTGGTCATT 59.524 47.619 10.83 0.00 38.45 2.57
2376 2385 2.685897 GGCGCACCTAATTTGGTCATTA 59.314 45.455 10.83 0.00 38.45 1.90
2377 2386 3.129638 GGCGCACCTAATTTGGTCATTAA 59.870 43.478 10.83 0.00 38.45 1.40
2378 2387 4.202111 GGCGCACCTAATTTGGTCATTAAT 60.202 41.667 10.83 0.00 38.45 1.40
2379 2388 4.739716 GCGCACCTAATTTGGTCATTAATG 59.260 41.667 8.74 9.29 38.45 1.90
2380 2389 5.280945 CGCACCTAATTTGGTCATTAATGG 58.719 41.667 15.36 0.00 38.45 3.16
2381 2390 5.049828 GCACCTAATTTGGTCATTAATGGC 58.950 41.667 15.36 13.62 38.45 4.40
2382 2391 5.280945 CACCTAATTTGGTCATTAATGGCG 58.719 41.667 15.36 1.09 38.45 5.69
2383 2392 4.202111 ACCTAATTTGGTCATTAATGGCGC 60.202 41.667 15.36 0.00 34.86 6.53
2384 2393 3.883830 AATTTGGTCATTAATGGCGCA 57.116 38.095 15.36 10.72 31.93 6.09
2385 2394 4.405116 AATTTGGTCATTAATGGCGCAT 57.595 36.364 15.36 3.83 31.93 4.73
2386 2395 3.883830 TTTGGTCATTAATGGCGCATT 57.116 38.095 15.36 9.96 37.80 3.56
2387 2396 4.991153 TTTGGTCATTAATGGCGCATTA 57.009 36.364 15.36 8.90 35.54 1.90
2388 2397 4.566545 TTGGTCATTAATGGCGCATTAG 57.433 40.909 15.36 1.69 37.57 1.73
2389 2398 3.550820 TGGTCATTAATGGCGCATTAGT 58.449 40.909 15.36 5.81 37.57 2.24
2390 2399 3.314913 TGGTCATTAATGGCGCATTAGTG 59.685 43.478 15.36 16.83 41.88 2.74
2391 2400 3.304659 GGTCATTAATGGCGCATTAGTGG 60.305 47.826 22.29 13.03 41.31 4.00
2392 2401 3.315191 GTCATTAATGGCGCATTAGTGGT 59.685 43.478 22.29 8.09 41.31 4.16
2393 2402 3.314913 TCATTAATGGCGCATTAGTGGTG 59.685 43.478 22.29 15.08 41.31 4.17
2394 2403 1.021202 TAATGGCGCATTAGTGGTGC 58.979 50.000 10.83 0.00 40.91 5.01
2410 2419 4.536687 GCGCCATTAGTGCCACGC 62.537 66.667 0.00 0.00 46.76 5.34
2411 2420 3.876198 CGCCATTAGTGCCACGCC 61.876 66.667 0.00 0.00 0.00 5.68
2412 2421 2.749839 GCCATTAGTGCCACGCCA 60.750 61.111 0.00 0.00 0.00 5.69
2413 2422 2.120909 GCCATTAGTGCCACGCCAT 61.121 57.895 0.00 0.00 0.00 4.40
2414 2423 1.666209 GCCATTAGTGCCACGCCATT 61.666 55.000 0.00 0.00 0.00 3.16
2415 2424 1.674359 CCATTAGTGCCACGCCATTA 58.326 50.000 0.00 0.00 0.00 1.90
2416 2425 1.603802 CCATTAGTGCCACGCCATTAG 59.396 52.381 0.00 0.00 0.00 1.73
2417 2426 2.288666 CATTAGTGCCACGCCATTAGT 58.711 47.619 0.00 0.00 0.00 2.24
2418 2427 3.462982 CATTAGTGCCACGCCATTAGTA 58.537 45.455 0.00 0.00 0.00 1.82
2419 2428 3.830744 TTAGTGCCACGCCATTAGTAT 57.169 42.857 0.00 0.00 0.00 2.12
2420 2429 4.940905 TTAGTGCCACGCCATTAGTATA 57.059 40.909 0.00 0.00 0.00 1.47
2421 2430 5.477607 TTAGTGCCACGCCATTAGTATAT 57.522 39.130 0.00 0.00 0.00 0.86
2422 2431 4.351874 AGTGCCACGCCATTAGTATATT 57.648 40.909 0.00 0.00 0.00 1.28
2423 2432 4.714632 AGTGCCACGCCATTAGTATATTT 58.285 39.130 0.00 0.00 0.00 1.40
2424 2433 5.130350 AGTGCCACGCCATTAGTATATTTT 58.870 37.500 0.00 0.00 0.00 1.82
2425 2434 6.292923 AGTGCCACGCCATTAGTATATTTTA 58.707 36.000 0.00 0.00 0.00 1.52
2426 2435 6.204108 AGTGCCACGCCATTAGTATATTTTAC 59.796 38.462 0.00 0.00 0.00 2.01
2427 2436 6.204108 GTGCCACGCCATTAGTATATTTTACT 59.796 38.462 0.00 0.00 0.00 2.24
2428 2437 7.385752 GTGCCACGCCATTAGTATATTTTACTA 59.614 37.037 0.00 0.00 0.00 1.82
2429 2438 7.932491 TGCCACGCCATTAGTATATTTTACTAA 59.068 33.333 8.55 8.55 42.18 2.24
2430 2439 8.943002 GCCACGCCATTAGTATATTTTACTAAT 58.057 33.333 11.52 11.52 46.06 1.73
2438 2447 6.796705 AGTATATTTTACTAATGGCGCACC 57.203 37.500 10.83 0.00 0.00 5.01
2439 2448 5.704053 AGTATATTTTACTAATGGCGCACCC 59.296 40.000 10.83 0.00 33.59 4.61
2440 2449 1.465794 TTTTACTAATGGCGCACCCC 58.534 50.000 10.83 0.00 33.59 4.95
2441 2450 0.621609 TTTACTAATGGCGCACCCCT 59.378 50.000 10.83 0.00 33.59 4.79
2442 2451 0.621609 TTACTAATGGCGCACCCCTT 59.378 50.000 10.83 0.00 33.59 3.95
2443 2452 0.107410 TACTAATGGCGCACCCCTTG 60.107 55.000 10.83 0.00 33.59 3.61
2444 2453 2.044451 TAATGGCGCACCCCTTGG 60.044 61.111 10.83 0.00 33.59 3.61
2453 2462 4.299796 ACCCCTTGGTGCGCCATT 62.300 61.111 21.95 0.00 45.58 3.16
2454 2463 2.044451 CCCCTTGGTGCGCCATTA 60.044 61.111 21.95 4.95 45.56 1.90
2455 2464 2.120909 CCCCTTGGTGCGCCATTAG 61.121 63.158 21.95 15.49 45.56 1.73
2456 2465 1.378514 CCCTTGGTGCGCCATTAGT 60.379 57.895 21.95 0.00 45.56 2.24
2457 2466 0.107410 CCCTTGGTGCGCCATTAGTA 60.107 55.000 21.95 3.22 45.56 1.82
2458 2467 1.476833 CCCTTGGTGCGCCATTAGTAT 60.477 52.381 21.95 0.00 45.56 2.12
2459 2468 1.873591 CCTTGGTGCGCCATTAGTATC 59.126 52.381 21.95 0.00 45.56 2.24
2460 2469 2.485479 CCTTGGTGCGCCATTAGTATCT 60.485 50.000 21.95 0.00 45.56 1.98
2461 2470 2.238942 TGGTGCGCCATTAGTATCTG 57.761 50.000 16.89 0.00 40.46 2.90
2462 2471 1.760029 TGGTGCGCCATTAGTATCTGA 59.240 47.619 16.89 0.00 40.46 3.27
2463 2472 2.368548 TGGTGCGCCATTAGTATCTGAT 59.631 45.455 16.89 0.00 40.46 2.90
2464 2473 3.576550 TGGTGCGCCATTAGTATCTGATA 59.423 43.478 16.89 0.00 40.46 2.15
2465 2474 4.222810 TGGTGCGCCATTAGTATCTGATAT 59.777 41.667 16.89 0.00 40.46 1.63
2466 2475 5.420739 TGGTGCGCCATTAGTATCTGATATA 59.579 40.000 16.89 0.00 40.46 0.86
2467 2476 5.749109 GGTGCGCCATTAGTATCTGATATAC 59.251 44.000 12.58 0.00 34.09 1.47
2468 2477 6.405953 GGTGCGCCATTAGTATCTGATATACT 60.406 42.308 12.58 0.00 35.52 2.12
2469 2478 7.201794 GGTGCGCCATTAGTATCTGATATACTA 60.202 40.741 12.58 0.00 34.32 1.82
2470 2479 8.188799 GTGCGCCATTAGTATCTGATATACTAA 58.811 37.037 16.03 16.03 45.52 2.24
2477 2486 6.775594 AGTATCTGATATACTAATGGCGCA 57.224 37.500 10.83 0.00 33.45 6.09
2478 2487 6.565234 AGTATCTGATATACTAATGGCGCAC 58.435 40.000 10.83 0.00 33.45 5.34
2479 2488 4.188247 TCTGATATACTAATGGCGCACC 57.812 45.455 10.83 0.00 0.00 5.01
2480 2489 8.718426 AGTATCTGATATACTAATGGCGCACCA 61.718 40.741 10.83 0.00 40.62 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 4.897076 TCCTTTATAACCCTAGCGTCATCA 59.103 41.667 0.00 0.00 0.00 3.07
116 117 1.555533 GGACCATTCCGAAACTCCTCT 59.444 52.381 0.00 0.00 29.98 3.69
768 774 1.822990 GGGTTGATGGAGTCGTACTCA 59.177 52.381 14.26 4.44 46.79 3.41
930 936 4.250464 TGTTTCCCATCGACACATACTTC 58.750 43.478 0.00 0.00 0.00 3.01
931 937 4.280436 TGTTTCCCATCGACACATACTT 57.720 40.909 0.00 0.00 0.00 2.24
943 949 8.837099 TTAATGAGTATTTCCATGTTTCCCAT 57.163 30.769 0.00 0.00 0.00 4.00
953 959 4.497291 ACCGCCTTAATGAGTATTTCCA 57.503 40.909 0.00 0.00 0.00 3.53
963 969 1.064060 GCTTGTGCTACCGCCTTAATG 59.936 52.381 0.00 0.00 36.03 1.90
975 981 3.126858 CGTATGTTGGTATTGCTTGTGCT 59.873 43.478 0.00 0.00 40.48 4.40
993 999 2.671396 GCGGAAAACACTCATCACGTAT 59.329 45.455 0.00 0.00 0.00 3.06
1008 1014 2.435938 GATGTCGGCAGGCGGAAA 60.436 61.111 17.49 5.54 0.00 3.13
1021 1027 9.657123 CCTTGTAAGGTCGTCACATACTGATGT 62.657 44.444 2.42 0.00 43.04 3.06
1026 1032 4.451629 CCTTGTAAGGTCGTCACATACT 57.548 45.455 2.42 0.00 41.41 2.12
1041 1047 6.013725 ACCAATACTGTCTCATCAACCTTGTA 60.014 38.462 0.00 0.00 0.00 2.41
1098 1104 1.434188 TCTTCTCCCAGCTCAACCAA 58.566 50.000 0.00 0.00 0.00 3.67
1104 1110 4.002316 GCAATATCATCTTCTCCCAGCTC 58.998 47.826 0.00 0.00 0.00 4.09
1180 1186 1.671850 CCAAGCCTGATTTGCAAGCAG 60.672 52.381 19.04 19.04 44.23 4.24
1191 1197 5.885912 GGTTTGTAATAATCTCCAAGCCTGA 59.114 40.000 0.00 0.00 35.88 3.86
1212 1218 1.615424 ACATAGGCTGTCCGGGGTT 60.615 57.895 0.00 0.00 37.47 4.11
1287 1293 1.323271 CCGTAGAAGAGCTGGCTGGA 61.323 60.000 0.00 0.00 0.00 3.86
1291 1297 1.079503 CAAACCGTAGAAGAGCTGGC 58.920 55.000 0.00 0.00 0.00 4.85
1329 1335 5.505181 AGCCTTTCTTCAATAGTTCCAGA 57.495 39.130 0.00 0.00 0.00 3.86
1368 1374 5.065859 CCACGTTCTTATCATTGTGCCATTA 59.934 40.000 0.00 0.00 0.00 1.90
1383 1389 0.903454 ACGGATCCCTCCACGTTCTT 60.903 55.000 6.06 0.00 42.19 2.52
1389 1395 1.749033 GATCCACGGATCCCTCCAC 59.251 63.158 14.18 0.00 43.71 4.02
1425 1431 7.634526 ATTTCCTTTTGGGGTTATTGGTTTA 57.365 32.000 0.00 0.00 40.87 2.01
1480 1486 2.550277 TTCCATGCTCCTGACTCCTA 57.450 50.000 0.00 0.00 0.00 2.94
1531 1537 7.655236 TCTTTAATATTTCACGAACGTCCAA 57.345 32.000 0.00 0.00 0.00 3.53
1539 1545 6.812998 AGTCCGGATCTTTAATATTTCACGA 58.187 36.000 7.81 0.00 0.00 4.35
1540 1546 7.223971 TGAAGTCCGGATCTTTAATATTTCACG 59.776 37.037 7.81 0.00 0.00 4.35
1572 1578 0.396278 CCAGAAAATCCTGCTCCCCC 60.396 60.000 0.00 0.00 32.97 5.40
1575 1581 1.407979 CATGCCAGAAAATCCTGCTCC 59.592 52.381 0.00 0.00 32.97 4.70
1581 1587 3.251479 GGAAACCATGCCAGAAAATCC 57.749 47.619 0.00 0.00 0.00 3.01
1602 1609 4.809426 ACTGTAAAACAACCACTCTTCTCG 59.191 41.667 0.00 0.00 0.00 4.04
1605 1612 7.781548 TCTAACTGTAAAACAACCACTCTTC 57.218 36.000 0.00 0.00 0.00 2.87
1614 1623 7.307514 CGGTATGCACTTCTAACTGTAAAACAA 60.308 37.037 0.00 0.00 0.00 2.83
1635 1644 2.134287 AGATGTGGCGAGCCGGTAT 61.134 57.895 9.78 3.63 39.42 2.73
1647 1656 1.101635 CAGCATGCCCCTCAGATGTG 61.102 60.000 15.66 0.00 0.00 3.21
1656 1665 4.828296 CCCAGACCAGCATGCCCC 62.828 72.222 15.66 0.79 31.97 5.80
1662 1671 0.042581 TAGATGACCCCAGACCAGCA 59.957 55.000 0.00 0.00 0.00 4.41
1665 1674 1.866015 CACTAGATGACCCCAGACCA 58.134 55.000 0.00 0.00 0.00 4.02
1699 1708 0.482446 TGCCTCCAAATCACCTGGTT 59.518 50.000 0.00 0.00 35.30 3.67
1718 1727 3.380320 GGGCAGCTTAACGTTCCAAATAT 59.620 43.478 2.82 0.00 0.00 1.28
1730 1739 2.094675 GCATCTTCAAGGGCAGCTTAA 58.905 47.619 0.00 0.00 0.00 1.85
1735 1744 1.959042 ATACGCATCTTCAAGGGCAG 58.041 50.000 3.39 0.00 0.00 4.85
1741 1750 4.275689 CCAGGCAAATATACGCATCTTCAA 59.724 41.667 0.00 0.00 0.00 2.69
1756 1765 1.152567 CCACCACCTTCCAGGCAAA 60.153 57.895 0.00 0.00 39.63 3.68
1758 1767 4.284550 GCCACCACCTTCCAGGCA 62.285 66.667 0.00 0.00 44.59 4.75
1819 1828 0.820891 GGGCACGTATCCCTCGTAGA 60.821 60.000 15.70 0.00 40.66 2.59
1861 1870 3.036819 TGATGAGAGCATGGAAGCTAGT 58.963 45.455 0.00 0.00 46.75 2.57
1863 1872 2.767960 TGTGATGAGAGCATGGAAGCTA 59.232 45.455 0.00 0.00 46.75 3.32
1898 1907 3.694566 ACGCATATGAGACCATAGCGATA 59.305 43.478 22.69 0.00 45.12 2.92
1909 1918 1.683385 CCAGACCTGACGCATATGAGA 59.317 52.381 13.81 0.00 0.00 3.27
1932 1941 2.089980 AGCATCTGATTGTCAGGCAAC 58.910 47.619 7.08 0.00 44.39 4.17
1938 1947 2.190538 TCCCTCAGCATCTGATTGTCA 58.809 47.619 0.00 0.00 39.92 3.58
1955 1964 1.408453 CCACTCCTTCCCCGTATCCC 61.408 65.000 0.00 0.00 0.00 3.85
1971 1980 5.023533 TCATCAGTATGTTTAGGAGCCAC 57.976 43.478 0.00 0.00 37.40 5.01
1980 1989 7.012138 GCATCATCAGAGTTCATCAGTATGTTT 59.988 37.037 0.00 0.00 37.40 2.83
1997 2006 4.760204 TGCATTCCTTCATAGCATCATCAG 59.240 41.667 0.00 0.00 0.00 2.90
2022 2031 5.450137 CCAAATTCTCCACAAGAGCATGATC 60.450 44.000 1.78 1.78 42.90 2.92
2057 2066 3.130693 AGACTTAGCGTGGGTAAGATCAC 59.869 47.826 18.29 8.65 43.64 3.06
2096 2105 4.207955 ACTCTGTAGATAATCTGCCGTCA 58.792 43.478 0.00 0.00 0.00 4.35
2125 2134 4.521146 CTTCTGGCCATCTGTATTGAAGT 58.479 43.478 5.51 0.00 0.00 3.01
2127 2136 3.266772 ACCTTCTGGCCATCTGTATTGAA 59.733 43.478 5.51 2.33 36.63 2.69
2137 2146 2.501723 CTGTAGTGTACCTTCTGGCCAT 59.498 50.000 5.51 0.00 36.63 4.40
2169 2178 3.119531 CGAACATTGCCATCTTGCCTTTA 60.120 43.478 0.00 0.00 0.00 1.85
2182 2191 2.330231 TGCTTTGCTACGAACATTGC 57.670 45.000 0.00 0.00 0.00 3.56
2193 2202 5.411361 TGTTCGTACATTAGATTGCTTTGCT 59.589 36.000 0.00 0.00 0.00 3.91
2201 2210 5.086104 AGCAGGTGTTCGTACATTAGATT 57.914 39.130 0.00 0.00 36.50 2.40
2203 2212 3.762288 AGAGCAGGTGTTCGTACATTAGA 59.238 43.478 0.00 0.00 36.50 2.10
2210 2219 2.741433 ACCAGAGCAGGTGTTCGTA 58.259 52.632 0.00 0.00 41.30 3.43
2223 2232 1.422977 TTGGCCAAGGTAGCACCAGA 61.423 55.000 16.05 0.00 41.95 3.86
2225 2234 0.539438 CTTTGGCCAAGGTAGCACCA 60.539 55.000 19.48 0.00 41.95 4.17
2253 2262 1.893808 CGACAGTGCTGTTTGGCCT 60.894 57.895 3.32 0.00 45.05 5.19
2262 2271 0.603707 CACCATCAACCGACAGTGCT 60.604 55.000 0.00 0.00 0.00 4.40
2287 2296 0.952984 GCTGATCCATCCGCCTTAGC 60.953 60.000 0.00 0.00 31.84 3.09
2289 2298 0.394192 CTGCTGATCCATCCGCCTTA 59.606 55.000 1.06 0.00 36.37 2.69
2290 2299 1.147824 CTGCTGATCCATCCGCCTT 59.852 57.895 1.06 0.00 36.37 4.35
2359 2368 5.280945 CGCCATTAATGACCAAATTAGGTG 58.719 41.667 17.23 0.00 43.38 4.00
2360 2369 4.202111 GCGCCATTAATGACCAAATTAGGT 60.202 41.667 17.23 0.00 46.82 3.08
2361 2370 4.202101 TGCGCCATTAATGACCAAATTAGG 60.202 41.667 17.23 0.00 0.00 2.69
2362 2371 4.930963 TGCGCCATTAATGACCAAATTAG 58.069 39.130 17.23 0.00 0.00 1.73
2363 2372 4.991153 TGCGCCATTAATGACCAAATTA 57.009 36.364 17.23 0.00 0.00 1.40
2364 2373 3.883830 TGCGCCATTAATGACCAAATT 57.116 38.095 17.23 0.00 0.00 1.82
2365 2374 4.405116 AATGCGCCATTAATGACCAAAT 57.595 36.364 17.23 1.55 31.77 2.32
2366 2375 3.883830 AATGCGCCATTAATGACCAAA 57.116 38.095 17.23 0.00 31.77 3.28
2367 2376 3.951037 ACTAATGCGCCATTAATGACCAA 59.049 39.130 17.23 0.56 36.14 3.67
2368 2377 3.314913 CACTAATGCGCCATTAATGACCA 59.685 43.478 17.23 10.39 36.16 4.02
2369 2378 3.304659 CCACTAATGCGCCATTAATGACC 60.305 47.826 17.23 6.52 36.16 4.02
2370 2379 3.315191 ACCACTAATGCGCCATTAATGAC 59.685 43.478 17.23 4.16 36.16 3.06
2371 2380 3.314913 CACCACTAATGCGCCATTAATGA 59.685 43.478 17.23 0.00 36.16 2.57
2372 2381 3.631144 CACCACTAATGCGCCATTAATG 58.369 45.455 4.18 8.58 36.14 1.90
2373 2382 2.034558 GCACCACTAATGCGCCATTAAT 59.965 45.455 4.18 0.00 36.14 1.40
2374 2383 1.403679 GCACCACTAATGCGCCATTAA 59.596 47.619 4.18 0.00 36.14 1.40
2375 2384 1.021202 GCACCACTAATGCGCCATTA 58.979 50.000 4.18 8.43 35.54 1.90
2376 2385 1.809207 GCACCACTAATGCGCCATT 59.191 52.632 4.18 7.63 37.80 3.16
2377 2386 3.513225 GCACCACTAATGCGCCAT 58.487 55.556 4.18 0.00 32.45 4.40
2396 2405 1.603802 CTAATGGCGTGGCACTAATGG 59.396 52.381 16.72 0.12 0.00 3.16
2397 2406 2.288666 ACTAATGGCGTGGCACTAATG 58.711 47.619 16.72 0.53 0.00 1.90
2398 2407 2.710096 ACTAATGGCGTGGCACTAAT 57.290 45.000 16.72 3.44 0.00 1.73
2399 2408 3.830744 ATACTAATGGCGTGGCACTAA 57.169 42.857 16.72 0.89 0.00 2.24
2400 2409 5.477607 AATATACTAATGGCGTGGCACTA 57.522 39.130 16.72 2.20 0.00 2.74
2401 2410 4.351874 AATATACTAATGGCGTGGCACT 57.648 40.909 16.72 0.00 0.00 4.40
2402 2411 5.432885 AAAATATACTAATGGCGTGGCAC 57.567 39.130 7.79 7.79 0.00 5.01
2403 2412 6.292923 AGTAAAATATACTAATGGCGTGGCA 58.707 36.000 0.00 0.00 0.00 4.92
2404 2413 6.796705 AGTAAAATATACTAATGGCGTGGC 57.203 37.500 0.00 0.00 0.00 5.01
2412 2421 8.943002 GGTGCGCCATTAGTAAAATATACTAAT 58.057 33.333 12.58 12.73 46.06 1.73
2413 2422 7.388500 GGGTGCGCCATTAGTAAAATATACTAA 59.612 37.037 19.98 9.72 42.18 2.24
2414 2423 6.875195 GGGTGCGCCATTAGTAAAATATACTA 59.125 38.462 19.98 0.00 36.17 1.82
2415 2424 5.704053 GGGTGCGCCATTAGTAAAATATACT 59.296 40.000 19.98 0.00 36.17 2.12
2416 2425 5.106436 GGGGTGCGCCATTAGTAAAATATAC 60.106 44.000 19.98 0.00 36.17 1.47
2417 2426 5.005094 GGGGTGCGCCATTAGTAAAATATA 58.995 41.667 19.98 0.00 36.17 0.86
2418 2427 3.824443 GGGGTGCGCCATTAGTAAAATAT 59.176 43.478 19.98 0.00 36.17 1.28
2419 2428 3.117813 AGGGGTGCGCCATTAGTAAAATA 60.118 43.478 19.98 0.00 36.17 1.40
2420 2429 2.028876 GGGGTGCGCCATTAGTAAAAT 58.971 47.619 19.98 0.00 36.17 1.82
2421 2430 1.004979 AGGGGTGCGCCATTAGTAAAA 59.995 47.619 19.98 0.00 36.17 1.52
2422 2431 0.621609 AGGGGTGCGCCATTAGTAAA 59.378 50.000 19.98 0.00 36.17 2.01
2423 2432 0.621609 AAGGGGTGCGCCATTAGTAA 59.378 50.000 19.98 0.00 36.17 2.24
2424 2433 0.107410 CAAGGGGTGCGCCATTAGTA 60.107 55.000 19.98 0.00 36.17 1.82
2425 2434 1.378514 CAAGGGGTGCGCCATTAGT 60.379 57.895 19.98 0.00 36.17 2.24
2426 2435 2.120909 CCAAGGGGTGCGCCATTAG 61.121 63.158 19.98 4.83 36.17 1.73
2427 2436 2.044451 CCAAGGGGTGCGCCATTA 60.044 61.111 19.98 0.00 36.17 1.90
2442 2451 8.718426 AGTATATCAGATACTAATGGCGCACCA 61.718 40.741 10.83 0.00 40.62 4.17
2443 2452 2.526304 TCAGATACTAATGGCGCACC 57.474 50.000 10.83 0.00 0.00 5.01
2444 2453 6.565234 AGTATATCAGATACTAATGGCGCAC 58.435 40.000 10.83 0.00 33.45 5.34
2445 2454 6.775594 AGTATATCAGATACTAATGGCGCA 57.224 37.500 10.83 0.00 33.45 6.09
2452 2461 8.188799 GTGCGCCATTAGTATATCAGATACTAA 58.811 37.037 13.13 13.13 45.52 2.24
2453 2462 7.201794 GGTGCGCCATTAGTATATCAGATACTA 60.202 40.741 12.58 0.00 34.32 1.82
2454 2463 6.405953 GGTGCGCCATTAGTATATCAGATACT 60.406 42.308 12.58 0.00 35.52 2.12
2455 2464 5.749109 GGTGCGCCATTAGTATATCAGATAC 59.251 44.000 12.58 0.00 34.09 2.24
2456 2465 5.420739 TGGTGCGCCATTAGTATATCAGATA 59.579 40.000 16.89 0.00 40.46 1.98
2457 2466 4.222810 TGGTGCGCCATTAGTATATCAGAT 59.777 41.667 16.89 0.00 40.46 2.90
2458 2467 3.576550 TGGTGCGCCATTAGTATATCAGA 59.423 43.478 16.89 0.00 40.46 3.27
2459 2468 3.925379 TGGTGCGCCATTAGTATATCAG 58.075 45.455 16.89 0.00 40.46 2.90


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

AutoCloner maintained by Alex Coulton.