Multiple sequence alignment - TraesCS3B01G037100

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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 TraesCS3B01G037100 chr3B 100.000 2449 0 0 1 2449 18027603 18025155 0.000000e+00 4523.0
1 TraesCS3B01G037100 chr3A 87.998 1683 134 32 736 2391 24747990 24749631 0.000000e+00 1927.0
2 TraesCS3B01G037100 chr3A 93.631 738 46 1 7 743 646114683 646113946 0.000000e+00 1101.0
3 TraesCS3B01G037100 chr3A 93.154 745 45 6 1 743 664700609 664701349 0.000000e+00 1088.0
4 TraesCS3B01G037100 chr3A 80.759 369 36 18 904 1262 24645173 24644830 3.130000e-64 255.0
5 TraesCS3B01G037100 chr3D 87.136 1306 101 30 817 2095 12432794 12431529 0.000000e+00 1419.0
6 TraesCS3B01G037100 chr3D 80.959 709 73 26 780 1447 12458568 12459255 2.810000e-139 505.0
7 TraesCS3B01G037100 chr3D 88.750 240 24 2 1187 1426 12701160 12700924 8.570000e-75 291.0
8 TraesCS3B01G037100 chr3D 85.714 133 17 2 1006 1137 12422369 12422238 3.280000e-29 139.0
9 TraesCS3B01G037100 chr3D 92.632 95 7 0 739 833 12432906 12432812 1.180000e-28 137.0
10 TraesCS3B01G037100 chr5D 93.540 743 44 3 1 741 537321367 537320627 0.000000e+00 1103.0
11 TraesCS3B01G037100 chr5D 93.182 748 48 3 1 746 370460851 370460105 0.000000e+00 1096.0
12 TraesCS3B01G037100 chr5D 93.127 742 49 2 1 741 291354647 291353907 0.000000e+00 1086.0
13 TraesCS3B01G037100 chr5D 94.286 35 2 0 1896 1930 195658057 195658091 1.000000e-03 54.7
14 TraesCS3B01G037100 chr2D 94.199 724 39 3 20 741 365796010 365796732 0.000000e+00 1101.0
15 TraesCS3B01G037100 chr2D 93.029 746 45 4 1 744 118536740 118537480 0.000000e+00 1083.0
16 TraesCS3B01G037100 chr2D 85.909 220 26 5 2234 2449 177911225 177911443 1.890000e-56 230.0
17 TraesCS3B01G037100 chr4D 93.405 743 44 4 1 741 437945010 437945749 0.000000e+00 1096.0
18 TraesCS3B01G037100 chr4D 93.506 154 8 2 2296 2449 211148194 211148043 6.810000e-56 228.0
19 TraesCS3B01G037100 chr5B 93.048 748 48 3 1 744 382571353 382570606 0.000000e+00 1090.0
20 TraesCS3B01G037100 chr2A 94.805 154 6 2 2296 2449 714638434 714638585 3.150000e-59 239.0
21 TraesCS3B01G037100 chr2A 91.515 165 10 4 2288 2449 297225729 297225892 8.810000e-55 224.0
22 TraesCS3B01G037100 chr5A 94.156 154 7 2 2296 2449 478301831 478301982 1.460000e-57 233.0
23 TraesCS3B01G037100 chr5A 85.973 221 24 5 2235 2449 607503435 607503654 1.890000e-56 230.0
24 TraesCS3B01G037100 chr5A 94.286 35 2 0 1896 1930 232841656 232841690 1.000000e-03 54.7
25 TraesCS3B01G037100 chr1A 94.156 154 7 2 2296 2449 474278276 474278125 1.460000e-57 233.0
26 TraesCS3B01G037100 chr7A 93.506 154 8 2 2296 2449 640066842 640066691 6.810000e-56 228.0
27 TraesCS3B01G037100 chr6A 93.506 154 8 2 2296 2449 420275586 420275737 6.810000e-56 228.0


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 TraesCS3B01G037100 chr3B 18025155 18027603 2448 True 4523 4523 100.000 1 2449 1 chr3B.!!$R1 2448
1 TraesCS3B01G037100 chr3A 24747990 24749631 1641 False 1927 1927 87.998 736 2391 1 chr3A.!!$F1 1655
2 TraesCS3B01G037100 chr3A 646113946 646114683 737 True 1101 1101 93.631 7 743 1 chr3A.!!$R2 736
3 TraesCS3B01G037100 chr3A 664700609 664701349 740 False 1088 1088 93.154 1 743 1 chr3A.!!$F2 742
4 TraesCS3B01G037100 chr3D 12431529 12432906 1377 True 778 1419 89.884 739 2095 2 chr3D.!!$R3 1356
5 TraesCS3B01G037100 chr3D 12458568 12459255 687 False 505 505 80.959 780 1447 1 chr3D.!!$F1 667
6 TraesCS3B01G037100 chr5D 537320627 537321367 740 True 1103 1103 93.540 1 741 1 chr5D.!!$R3 740
7 TraesCS3B01G037100 chr5D 370460105 370460851 746 True 1096 1096 93.182 1 746 1 chr5D.!!$R2 745
8 TraesCS3B01G037100 chr5D 291353907 291354647 740 True 1086 1086 93.127 1 741 1 chr5D.!!$R1 740
9 TraesCS3B01G037100 chr2D 365796010 365796732 722 False 1101 1101 94.199 20 741 1 chr2D.!!$F3 721
10 TraesCS3B01G037100 chr2D 118536740 118537480 740 False 1083 1083 93.029 1 744 1 chr2D.!!$F1 743
11 TraesCS3B01G037100 chr4D 437945010 437945749 739 False 1096 1096 93.405 1 741 1 chr4D.!!$F1 740
12 TraesCS3B01G037100 chr5B 382570606 382571353 747 True 1090 1090 93.048 1 744 1 chr5B.!!$R1 743

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
651 660 0.034477 GGTCACCACATCCCGGAAAT 60.034 55.0 0.73 0.0 0.0 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2385 2536 0.109179 ATACGCGCACTTAACGGTCA 60.109 50.0 5.73 0.0 0.0 4.02 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
28 29 0.251297 CAACCACTGCCCAAGGATGA 60.251 55.000 0.00 0.00 0.00 2.92
117 118 4.142381 GGGGTATGTGCTCTTTTTAGCTTG 60.142 45.833 0.00 0.00 43.19 4.01
125 126 4.890581 TGCTCTTTTTAGCTTGGGTTTGTA 59.109 37.500 0.00 0.00 43.19 2.41
133 135 4.538746 AGCTTGGGTTTGTACTCTAGAC 57.461 45.455 0.00 0.00 30.23 2.59
310 312 5.751028 CACTTGTTGCTAGATTAGAGGCTAC 59.249 44.000 0.00 0.00 0.00 3.58
398 403 1.767681 GAGCCTCCTCCACAGATCAAT 59.232 52.381 0.00 0.00 31.68 2.57
450 455 3.274288 CTCAAGGGAGCAGTTATGGAAC 58.726 50.000 0.00 0.00 33.67 3.62
517 522 4.277423 TGGCCTTGCTTTACTAGTCAAAAC 59.723 41.667 3.32 0.00 0.00 2.43
529 534 6.946229 ACTAGTCAAAACGTGATGATGTAC 57.054 37.500 6.79 0.00 38.90 2.90
531 536 7.823665 ACTAGTCAAAACGTGATGATGTACTA 58.176 34.615 6.79 4.21 38.90 1.82
651 660 0.034477 GGTCACCACATCCCGGAAAT 60.034 55.000 0.73 0.00 0.00 2.17
726 735 2.355481 GTCCGTTTGAGGTCGCGT 60.355 61.111 5.77 0.00 0.00 6.01
748 757 1.225376 TGAAGTTGGCCTAACGTGCG 61.225 55.000 3.32 0.00 44.15 5.34
766 775 1.811266 GTGCTGCACATCGGACGAT 60.811 57.895 26.70 0.65 34.08 3.73
767 776 0.527600 GTGCTGCACATCGGACGATA 60.528 55.000 26.70 0.00 34.08 2.92
807 818 2.596904 TTAGATTCAGTAGGTGCGGC 57.403 50.000 0.00 0.00 0.00 6.53
823 834 0.671796 CGGCCATTGATCATGCACAT 59.328 50.000 2.24 0.00 0.00 3.21
836 882 2.118313 TGCACATCTCATTGTCAGGG 57.882 50.000 0.00 0.00 0.00 4.45
853 899 1.612513 GGTACCCATGTGGCCATCA 59.387 57.895 9.72 9.85 37.83 3.07
854 900 0.466189 GGTACCCATGTGGCCATCAG 60.466 60.000 9.72 0.73 37.83 2.90
856 902 0.918799 TACCCATGTGGCCATCAGGT 60.919 55.000 9.72 16.42 38.04 4.00
865 911 0.184451 GGCCATCAGGTCCACATCAT 59.816 55.000 0.00 0.00 37.19 2.45
935 982 2.502947 TCATGCTTAGCTGATCCACTGT 59.497 45.455 5.60 0.00 0.00 3.55
984 1038 0.308993 GCACAGGCAAAGTCAGTGAC 59.691 55.000 15.78 15.78 40.72 3.67
985 1039 1.667236 CACAGGCAAAGTCAGTGACA 58.333 50.000 24.73 0.00 34.60 3.58
1022 1079 2.435805 TGGGGATGAAGAGATGCAGTAC 59.564 50.000 0.00 0.00 0.00 2.73
1052 1109 0.170561 CTGCTGATGCTTTCACTGGC 59.829 55.000 0.00 0.00 40.48 4.85
1068 1125 4.925861 GCGGCAGCCCTCCTCATC 62.926 72.222 5.63 0.00 37.42 2.92
1069 1126 4.598894 CGGCAGCCCTCCTCATCG 62.599 72.222 5.63 0.00 0.00 3.84
1070 1127 4.925861 GGCAGCCCTCCTCATCGC 62.926 72.222 0.00 0.00 0.00 4.58
1071 1128 4.925861 GCAGCCCTCCTCATCGCC 62.926 72.222 0.00 0.00 0.00 5.54
1072 1129 4.598894 CAGCCCTCCTCATCGCCG 62.599 72.222 0.00 0.00 0.00 6.46
1077 1134 4.899239 CTCCTCATCGCCGGCCAC 62.899 72.222 23.46 0.00 0.00 5.01
1122 1197 1.035932 CCATTCTCCTGCCAAGCCAG 61.036 60.000 0.00 0.00 0.00 4.85
1143 1231 2.618053 GACAAAGGTACGGTGATCCAG 58.382 52.381 0.00 0.00 0.00 3.86
1152 1240 4.760047 GTGATCCAGGCCACGCGT 62.760 66.667 5.58 5.58 0.00 6.01
1172 1260 3.658709 GTGTGGACTCCTTTCTCTTCTG 58.341 50.000 0.00 0.00 0.00 3.02
1227 1338 0.397941 TTGAGGACTTGCAGACCAGG 59.602 55.000 8.23 0.00 32.35 4.45
1228 1339 0.471780 TGAGGACTTGCAGACCAGGA 60.472 55.000 0.00 0.00 32.35 3.86
1229 1340 0.248843 GAGGACTTGCAGACCAGGAG 59.751 60.000 0.00 0.00 32.35 3.69
1331 1442 2.251642 GGACGTGGTGGACAACTGC 61.252 63.158 0.00 0.00 0.00 4.40
1467 1586 9.019764 GTAACTGAACTCTACGTACTACTCTAG 57.980 40.741 0.00 0.00 0.00 2.43
1468 1587 6.042143 ACTGAACTCTACGTACTACTCTAGC 58.958 44.000 0.00 0.00 0.00 3.42
1469 1588 5.970592 TGAACTCTACGTACTACTCTAGCA 58.029 41.667 0.00 0.00 0.00 3.49
1470 1589 5.809562 TGAACTCTACGTACTACTCTAGCAC 59.190 44.000 0.00 0.00 0.00 4.40
1477 1596 5.004255 CGTACTACTCTAGCACGTGTATC 57.996 47.826 18.38 0.00 39.93 2.24
1478 1597 4.744137 CGTACTACTCTAGCACGTGTATCT 59.256 45.833 18.38 8.42 39.93 1.98
1479 1598 5.917447 CGTACTACTCTAGCACGTGTATCTA 59.083 44.000 18.38 9.16 39.93 1.98
1480 1599 6.129221 CGTACTACTCTAGCACGTGTATCTAC 60.129 46.154 18.38 0.00 39.93 2.59
1481 1600 5.916318 ACTACTCTAGCACGTGTATCTACT 58.084 41.667 18.38 6.88 0.00 2.57
1488 1607 0.737219 ACGTGTATCTACTCGCACCC 59.263 55.000 10.68 0.00 44.26 4.61
1492 1611 1.402968 TGTATCTACTCGCACCCGTTC 59.597 52.381 0.00 0.00 35.54 3.95
1505 1627 1.024271 CCCGTTCGATCTACCGGTAA 58.976 55.000 16.65 7.33 38.79 2.85
1509 1631 0.664761 TTCGATCTACCGGTAAGCGG 59.335 55.000 23.99 11.88 0.00 5.52
1532 1654 3.749373 CGCCGTCGACGTGTGTTC 61.749 66.667 33.49 15.16 38.10 3.18
1550 1672 5.423931 TGTGTTCCTACATGAATGGCTACTA 59.576 40.000 0.00 0.00 36.50 1.82
1551 1673 5.986135 GTGTTCCTACATGAATGGCTACTAG 59.014 44.000 0.00 0.00 36.50 2.57
1552 1674 5.661312 TGTTCCTACATGAATGGCTACTAGT 59.339 40.000 0.00 0.00 0.00 2.57
1553 1675 6.837048 TGTTCCTACATGAATGGCTACTAGTA 59.163 38.462 0.00 1.89 0.00 1.82
1646 1779 3.455990 AAAAATAAAACGGGTGGCGTT 57.544 38.095 0.00 0.00 0.00 4.84
1717 1851 2.492088 TCCTGGATACGACAGTCAACAG 59.508 50.000 0.41 1.31 42.51 3.16
1803 1944 9.416284 ACATCCAGAAACTTACTAAAAAGGAAA 57.584 29.630 0.00 0.00 0.00 3.13
1854 1997 2.160813 GTCACTTCACTCTCGTCTCTCC 59.839 54.545 0.00 0.00 0.00 3.71
1870 2013 2.780040 CCCTGGGGATGCCTCCAT 60.780 66.667 10.44 0.00 44.08 3.41
1872 2015 2.519441 CTGGGGATGCCTCCATGG 59.481 66.667 4.97 4.97 44.08 3.66
1882 2025 2.183409 CCTCCATGGCGTCAAAAGG 58.817 57.895 6.96 2.52 0.00 3.11
1886 2029 1.501741 CATGGCGTCAAAAGGACCG 59.498 57.895 0.00 0.00 43.95 4.79
1900 2045 1.196766 GGACCGTCTTAAGGGGGTGT 61.197 60.000 19.08 4.04 34.60 4.16
1932 2079 1.480212 TTGAGGCATGACCGGTCTGT 61.480 55.000 33.39 20.16 46.52 3.41
1974 2121 1.468520 CGCGGTCATCAAAAGAATGGT 59.531 47.619 0.00 0.00 0.00 3.55
1978 2125 3.501828 CGGTCATCAAAAGAATGGTCACA 59.498 43.478 0.00 0.00 0.00 3.58
1984 2131 8.134895 GTCATCAAAAGAATGGTCACAGTAAAA 58.865 33.333 0.00 0.00 0.00 1.52
2058 2206 9.181805 CTATATGAAGTTACCATGTCAACTACG 57.818 37.037 9.00 0.00 33.92 3.51
2061 2209 2.300723 AGTTACCATGTCAACTACGGCA 59.699 45.455 7.26 0.00 33.29 5.69
2073 2221 3.899052 ACTACGGCAAACCTAATAGCA 57.101 42.857 0.00 0.00 0.00 3.49
2089 2237 7.935755 ACCTAATAGCACACTCGTAGTTAGATA 59.064 37.037 0.00 0.00 0.00 1.98
2095 2243 8.392372 AGCACACTCGTAGTTAGATATATTCA 57.608 34.615 0.00 0.00 0.00 2.57
2158 2306 0.107752 TGATGTTGCGGCTCATGCTA 60.108 50.000 13.76 1.47 39.59 3.49
2163 2311 1.111277 TTGCGGCTCATGCTAGAGTA 58.889 50.000 0.00 0.00 37.94 2.59
2164 2312 1.111277 TGCGGCTCATGCTAGAGTAA 58.889 50.000 0.00 0.00 37.94 2.24
2167 2315 2.482142 GCGGCTCATGCTAGAGTAAACT 60.482 50.000 0.00 0.00 37.94 2.66
2168 2316 3.119291 CGGCTCATGCTAGAGTAAACTG 58.881 50.000 0.00 0.00 37.94 3.16
2171 2319 5.661458 GGCTCATGCTAGAGTAAACTGTAA 58.339 41.667 0.00 0.00 37.94 2.41
2194 2342 3.482436 TCTAGATCCCGCTTCTCTTCTC 58.518 50.000 0.00 0.00 0.00 2.87
2199 2347 2.096248 TCCCGCTTCTCTTCTCTCTTC 58.904 52.381 0.00 0.00 0.00 2.87
2205 2353 5.095490 CGCTTCTCTTCTCTCTTCTCTTTC 58.905 45.833 0.00 0.00 0.00 2.62
2222 2370 6.906848 TCTCTTTCCTTCAACTAGGGAAAAA 58.093 36.000 10.26 4.70 44.94 1.94
2223 2371 7.526918 TCTCTTTCCTTCAACTAGGGAAAAAT 58.473 34.615 10.26 0.00 44.94 1.82
2233 2381 8.279970 TCAACTAGGGAAAAATGTATGATGTG 57.720 34.615 0.00 0.00 0.00 3.21
2234 2382 8.106462 TCAACTAGGGAAAAATGTATGATGTGA 58.894 33.333 0.00 0.00 0.00 3.58
2247 2397 8.765488 ATGTATGATGTGACATTTTAATGGGA 57.235 30.769 0.00 0.00 40.70 4.37
2279 2429 7.284489 ACATTTATGTCACTAATTTACGCCCAT 59.716 33.333 0.00 0.00 35.87 4.00
2283 2433 5.250200 TGTCACTAATTTACGCCCATTCTT 58.750 37.500 0.00 0.00 0.00 2.52
2323 2474 4.016444 TCATGTACTCAAATTTGCCCCTC 58.984 43.478 13.54 3.81 0.00 4.30
2324 2475 3.806949 TGTACTCAAATTTGCCCCTCT 57.193 42.857 13.54 0.00 0.00 3.69
2325 2476 4.112634 TGTACTCAAATTTGCCCCTCTT 57.887 40.909 13.54 0.00 0.00 2.85
2326 2477 4.079253 TGTACTCAAATTTGCCCCTCTTC 58.921 43.478 13.54 0.04 0.00 2.87
2327 2478 2.529632 ACTCAAATTTGCCCCTCTTCC 58.470 47.619 13.54 0.00 0.00 3.46
2328 2479 1.474077 CTCAAATTTGCCCCTCTTCCG 59.526 52.381 13.54 0.00 0.00 4.30
2329 2480 1.203001 TCAAATTTGCCCCTCTTCCGT 60.203 47.619 13.54 0.00 0.00 4.69
2330 2481 1.618343 CAAATTTGCCCCTCTTCCGTT 59.382 47.619 5.01 0.00 0.00 4.44
2331 2482 2.823154 CAAATTTGCCCCTCTTCCGTTA 59.177 45.455 5.01 0.00 0.00 3.18
2332 2483 2.891191 ATTTGCCCCTCTTCCGTTAA 57.109 45.000 0.00 0.00 0.00 2.01
2333 2484 2.194201 TTTGCCCCTCTTCCGTTAAG 57.806 50.000 0.00 0.00 36.45 1.85
2334 2485 1.061546 TTGCCCCTCTTCCGTTAAGT 58.938 50.000 0.00 0.00 36.51 2.24
2335 2486 0.323629 TGCCCCTCTTCCGTTAAGTG 59.676 55.000 0.00 0.00 36.51 3.16
2336 2487 0.323957 GCCCCTCTTCCGTTAAGTGT 59.676 55.000 0.00 0.00 36.51 3.55
2349 2500 7.534085 TCCGTTAAGTGTGCTTATAGAAATG 57.466 36.000 0.00 0.00 37.09 2.32
2357 2508 3.251004 GTGCTTATAGAAATGCCCTTCCG 59.749 47.826 0.00 0.00 0.00 4.30
2373 2524 2.373540 TCCGTACATTTTCCGTCCAG 57.626 50.000 0.00 0.00 0.00 3.86
2374 2525 1.619827 TCCGTACATTTTCCGTCCAGT 59.380 47.619 0.00 0.00 0.00 4.00
2375 2526 1.997606 CCGTACATTTTCCGTCCAGTC 59.002 52.381 0.00 0.00 0.00 3.51
2376 2527 1.652124 CGTACATTTTCCGTCCAGTCG 59.348 52.381 0.00 0.00 0.00 4.18
2377 2528 2.669113 CGTACATTTTCCGTCCAGTCGA 60.669 50.000 0.00 0.00 0.00 4.20
2378 2529 2.536761 ACATTTTCCGTCCAGTCGAA 57.463 45.000 0.00 0.00 0.00 3.71
2379 2530 2.413837 ACATTTTCCGTCCAGTCGAAG 58.586 47.619 0.00 0.00 0.00 3.79
2380 2531 2.036733 ACATTTTCCGTCCAGTCGAAGA 59.963 45.455 0.00 0.00 0.00 2.87
2396 2547 4.624015 TCGAAGACATTTGACCGTTAAGT 58.376 39.130 0.00 0.00 0.00 2.24
2397 2548 4.446385 TCGAAGACATTTGACCGTTAAGTG 59.554 41.667 0.00 0.00 0.00 3.16
2398 2549 4.464112 GAAGACATTTGACCGTTAAGTGC 58.536 43.478 0.00 0.00 0.00 4.40
2399 2550 2.478894 AGACATTTGACCGTTAAGTGCG 59.521 45.455 0.00 0.00 0.00 5.34
2400 2551 1.069500 ACATTTGACCGTTAAGTGCGC 60.069 47.619 0.00 0.00 0.00 6.09
2401 2552 0.165079 ATTTGACCGTTAAGTGCGCG 59.835 50.000 0.00 0.00 0.00 6.86
2402 2553 1.152989 TTTGACCGTTAAGTGCGCGT 61.153 50.000 8.43 0.00 0.00 6.01
2403 2554 0.318529 TTGACCGTTAAGTGCGCGTA 60.319 50.000 8.43 0.00 0.00 4.42
2404 2555 0.109179 TGACCGTTAAGTGCGCGTAT 60.109 50.000 8.43 0.00 0.00 3.06
2405 2556 1.132073 TGACCGTTAAGTGCGCGTATA 59.868 47.619 8.43 0.00 0.00 1.47
2406 2557 2.184448 GACCGTTAAGTGCGCGTATAA 58.816 47.619 8.43 0.00 0.00 0.98
2407 2558 2.598192 GACCGTTAAGTGCGCGTATAAA 59.402 45.455 8.43 0.00 0.00 1.40
2408 2559 2.992543 ACCGTTAAGTGCGCGTATAAAA 59.007 40.909 8.43 0.00 0.00 1.52
2409 2560 3.431572 ACCGTTAAGTGCGCGTATAAAAA 59.568 39.130 8.43 0.00 0.00 1.94
2440 2591 3.021451 AAAGGCCTTTGACTGGACG 57.979 52.632 29.91 0.00 37.76 4.79
2441 2592 0.537371 AAAGGCCTTTGACTGGACGG 60.537 55.000 29.91 0.00 37.76 4.79
2442 2593 1.415672 AAGGCCTTTGACTGGACGGA 61.416 55.000 13.78 0.00 37.76 4.69
2443 2594 1.072505 GGCCTTTGACTGGACGGAA 59.927 57.895 0.00 0.00 0.00 4.30
2444 2595 0.536460 GGCCTTTGACTGGACGGAAA 60.536 55.000 0.00 0.00 0.00 3.13
2445 2596 1.314730 GCCTTTGACTGGACGGAAAA 58.685 50.000 0.00 0.00 0.00 2.29
2446 2597 1.886542 GCCTTTGACTGGACGGAAAAT 59.113 47.619 0.00 0.00 0.00 1.82
2447 2598 2.351738 GCCTTTGACTGGACGGAAAATG 60.352 50.000 0.00 0.00 0.00 2.32
2448 2599 2.884639 CCTTTGACTGGACGGAAAATGT 59.115 45.455 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.706433 ATCATCCTTGGGCAGTGGTT 59.294 50.000 0.00 0.00 0.00 3.67
117 118 5.725325 AGTCAAGTCTAGAGTACAAACCC 57.275 43.478 0.00 0.00 0.00 4.11
125 126 5.074115 AGCACAACTAGTCAAGTCTAGAGT 58.926 41.667 0.00 0.00 39.57 3.24
133 135 6.844696 TTGAAGTTAGCACAACTAGTCAAG 57.155 37.500 11.40 0.00 30.57 3.02
177 179 5.356882 TCTTCTCAATACCAAAACTTGCG 57.643 39.130 0.00 0.00 0.00 4.85
398 403 2.483714 GGCCTTCTCGATGCACTCATTA 60.484 50.000 0.00 0.00 31.96 1.90
517 522 6.677913 TGGTACATGATAGTACATCATCACG 58.322 40.000 14.21 7.06 44.76 4.35
564 572 3.742882 GCATTTTTCCTTGCAAGTCCTTC 59.257 43.478 24.35 3.07 38.72 3.46
577 585 0.729140 CTGTCCGCGTGCATTTTTCC 60.729 55.000 4.92 0.00 0.00 3.13
651 660 3.618750 GGGGTCGTGTCCGGACAA 61.619 66.667 37.75 21.85 43.77 3.18
704 713 0.595567 CGACCTCAAACGGACGTTCA 60.596 55.000 10.76 0.20 37.35 3.18
726 735 0.470766 ACGTTAGGCCAACTTCACCA 59.529 50.000 5.01 0.00 34.77 4.17
748 757 0.527600 TATCGTCCGATGTGCAGCAC 60.528 55.000 19.37 19.37 36.17 4.40
757 766 1.805345 GAGATGTCCGTATCGTCCGAT 59.195 52.381 7.41 7.41 38.54 4.18
766 775 1.472878 GCACTGTCAGAGATGTCCGTA 59.527 52.381 6.91 0.00 0.00 4.02
767 776 0.244994 GCACTGTCAGAGATGTCCGT 59.755 55.000 6.91 0.00 0.00 4.69
807 818 5.221244 ACAATGAGATGTGCATGATCAATGG 60.221 40.000 0.00 0.00 36.71 3.16
836 882 0.466189 CCTGATGGCCACATGGGTAC 60.466 60.000 8.16 0.00 37.47 3.34
853 899 2.024655 AGCCAATTGATGATGTGGACCT 60.025 45.455 7.12 0.00 32.54 3.85
854 900 2.360165 GAGCCAATTGATGATGTGGACC 59.640 50.000 7.12 0.00 32.54 4.46
856 902 2.242965 AGGAGCCAATTGATGATGTGGA 59.757 45.455 7.12 0.00 32.54 4.02
865 911 2.371784 TCCACGAGGAGCCAATTGA 58.628 52.632 7.12 0.00 39.61 2.57
914 961 2.502947 ACAGTGGATCAGCTAAGCATGA 59.497 45.455 0.00 0.00 0.00 3.07
935 982 3.004002 CCGTATATGTAGCCTCGTGACAA 59.996 47.826 0.00 0.00 0.00 3.18
984 1038 1.432514 CCATCGTTGGTCACTCACTG 58.567 55.000 4.23 0.00 38.30 3.66
985 1039 0.321671 CCCATCGTTGGTCACTCACT 59.678 55.000 11.51 0.00 41.91 3.41
1004 1061 3.640967 AGGAGTACTGCATCTCTTCATCC 59.359 47.826 17.34 0.00 0.00 3.51
1052 1109 4.598894 CGATGAGGAGGGCTGCCG 62.599 72.222 13.40 0.00 0.00 5.69
1122 1197 1.276989 TGGATCACCGTACCTTTGTCC 59.723 52.381 0.00 0.00 39.42 4.02
1152 1240 3.309296 ACAGAAGAGAAAGGAGTCCACA 58.691 45.455 12.86 0.00 0.00 4.17
1172 1260 6.752815 AGCGATAAGTTTAAACTGAGCTAGAC 59.247 38.462 25.23 12.17 39.66 2.59
1227 1338 4.408821 TGCCGCCATGACCACCTC 62.409 66.667 0.00 0.00 0.00 3.85
1228 1339 4.722700 GTGCCGCCATGACCACCT 62.723 66.667 0.00 0.00 0.00 4.00
1322 1433 2.617274 GGTTGGAGCGCAGTTGTCC 61.617 63.158 11.47 8.11 0.00 4.02
1467 1586 1.189403 GTGCGAGTAGATACACGTGC 58.811 55.000 17.22 0.00 41.28 5.34
1468 1587 1.533338 GGGTGCGAGTAGATACACGTG 60.533 57.143 15.48 15.48 41.28 4.49
1469 1588 0.737219 GGGTGCGAGTAGATACACGT 59.263 55.000 10.67 0.00 41.28 4.49
1470 1589 0.316772 CGGGTGCGAGTAGATACACG 60.317 60.000 5.61 5.61 41.95 4.49
1471 1590 0.737219 ACGGGTGCGAGTAGATACAC 59.263 55.000 0.00 0.00 0.00 2.90
1472 1591 1.402968 GAACGGGTGCGAGTAGATACA 59.597 52.381 0.00 0.00 0.00 2.29
1473 1592 1.596464 CGAACGGGTGCGAGTAGATAC 60.596 57.143 0.00 0.00 0.00 2.24
1474 1593 0.659427 CGAACGGGTGCGAGTAGATA 59.341 55.000 0.00 0.00 0.00 1.98
1475 1594 1.028330 TCGAACGGGTGCGAGTAGAT 61.028 55.000 0.00 0.00 32.13 1.98
1476 1595 1.028330 ATCGAACGGGTGCGAGTAGA 61.028 55.000 8.04 0.00 40.14 2.59
1477 1596 0.591741 GATCGAACGGGTGCGAGTAG 60.592 60.000 8.04 0.00 40.14 2.57
1478 1597 1.028330 AGATCGAACGGGTGCGAGTA 61.028 55.000 8.04 0.00 40.14 2.59
1479 1598 1.028330 TAGATCGAACGGGTGCGAGT 61.028 55.000 8.04 0.58 40.14 4.18
1480 1599 0.591741 GTAGATCGAACGGGTGCGAG 60.592 60.000 8.04 0.00 40.14 5.03
1481 1600 1.430632 GTAGATCGAACGGGTGCGA 59.569 57.895 4.08 4.08 41.14 5.10
1488 1607 1.751552 GCTTACCGGTAGATCGAACG 58.248 55.000 15.20 6.26 0.00 3.95
1532 1654 7.671302 ACATTACTAGTAGCCATTCATGTAGG 58.329 38.462 10.87 0.00 0.00 3.18
1550 1672 3.476552 CAGGACCACACACAACATTACT 58.523 45.455 0.00 0.00 0.00 2.24
1551 1673 2.031157 GCAGGACCACACACAACATTAC 60.031 50.000 0.00 0.00 0.00 1.89
1552 1674 2.226330 GCAGGACCACACACAACATTA 58.774 47.619 0.00 0.00 0.00 1.90
1553 1675 1.032014 GCAGGACCACACACAACATT 58.968 50.000 0.00 0.00 0.00 2.71
1646 1779 1.034356 CCATCCATCGTACGTACCCA 58.966 55.000 19.67 7.28 0.00 4.51
1717 1851 8.988934 TCATCTGTATTTTTGTATATCGGCTTC 58.011 33.333 0.00 0.00 0.00 3.86
1775 1911 9.416284 TCCTTTTTAGTAAGTTTCTGGATGTTT 57.584 29.630 0.00 0.00 0.00 2.83
1803 1944 2.073816 CGTACCAGTCCGCAGATTTTT 58.926 47.619 0.00 0.00 0.00 1.94
1804 1945 1.001633 ACGTACCAGTCCGCAGATTTT 59.998 47.619 0.00 0.00 0.00 1.82
1805 1946 0.606604 ACGTACCAGTCCGCAGATTT 59.393 50.000 0.00 0.00 0.00 2.17
1806 1947 0.606604 AACGTACCAGTCCGCAGATT 59.393 50.000 0.00 0.00 0.00 2.40
1807 1948 1.466856 TAACGTACCAGTCCGCAGAT 58.533 50.000 0.00 0.00 0.00 2.90
1808 1949 1.246649 TTAACGTACCAGTCCGCAGA 58.753 50.000 0.00 0.00 0.00 4.26
1854 1997 2.519441 CATGGAGGCATCCCCAGG 59.481 66.667 16.13 0.00 46.04 4.45
1870 2013 1.595929 GACGGTCCTTTTGACGCCA 60.596 57.895 0.00 0.00 45.46 5.69
1872 2015 1.787012 TAAGACGGTCCTTTTGACGC 58.213 50.000 4.14 0.00 45.46 5.19
1873 2016 2.735134 CCTTAAGACGGTCCTTTTGACG 59.265 50.000 3.36 0.00 45.46 4.35
1882 2025 1.479730 CTACACCCCCTTAAGACGGTC 59.520 57.143 3.36 0.00 0.00 4.79
1886 2029 4.608269 ACTACTCTACACCCCCTTAAGAC 58.392 47.826 3.36 0.00 0.00 3.01
1900 2045 7.272978 GGTCATGCCTCAAATTTACTACTCTA 58.727 38.462 0.00 0.00 0.00 2.43
1974 2121 9.917129 TTAGTATTTCTGACGATTTTACTGTGA 57.083 29.630 0.00 0.00 0.00 3.58
1978 2125 9.431887 TGCTTTAGTATTTCTGACGATTTTACT 57.568 29.630 0.00 0.00 0.00 2.24
1984 2131 6.407202 ACCTTGCTTTAGTATTTCTGACGAT 58.593 36.000 0.00 0.00 0.00 3.73
2058 2206 2.351726 CGAGTGTGCTATTAGGTTTGCC 59.648 50.000 0.00 0.00 0.00 4.52
2061 2209 5.656213 ACTACGAGTGTGCTATTAGGTTT 57.344 39.130 0.00 0.00 0.00 3.27
2095 2243 7.363443 GGGCCACACATTAATAACTTAACATGT 60.363 37.037 4.39 0.00 32.45 3.21
2100 2248 7.726033 AATGGGCCACACATTAATAACTTAA 57.274 32.000 9.28 0.00 36.82 1.85
2148 2296 4.130286 ACAGTTTACTCTAGCATGAGCC 57.870 45.455 0.00 0.00 43.56 4.70
2158 2306 7.470286 GCGGGATCTAGATTTACAGTTTACTCT 60.470 40.741 6.70 0.00 0.00 3.24
2163 2311 5.615925 AGCGGGATCTAGATTTACAGTTT 57.384 39.130 6.70 0.00 0.00 2.66
2164 2312 5.364157 AGAAGCGGGATCTAGATTTACAGTT 59.636 40.000 6.70 0.00 0.00 3.16
2167 2315 5.141182 AGAGAAGCGGGATCTAGATTTACA 58.859 41.667 6.70 0.00 0.00 2.41
2168 2316 5.715434 AGAGAAGCGGGATCTAGATTTAC 57.285 43.478 6.70 0.78 0.00 2.01
2171 2319 4.479158 AGAAGAGAAGCGGGATCTAGATT 58.521 43.478 6.70 0.00 0.00 2.40
2194 2342 5.482175 TCCCTAGTTGAAGGAAAGAGAAGAG 59.518 44.000 0.00 0.00 39.15 2.85
2205 2353 7.938140 TCATACATTTTTCCCTAGTTGAAGG 57.062 36.000 0.00 0.00 36.30 3.46
2222 2370 8.632679 GTCCCATTAAAATGTCACATCATACAT 58.367 33.333 0.00 0.00 37.94 2.29
2223 2371 7.613411 TGTCCCATTAAAATGTCACATCATACA 59.387 33.333 0.00 0.00 34.60 2.29
2262 2412 6.880484 TCTAAGAATGGGCGTAAATTAGTGA 58.120 36.000 0.00 0.00 0.00 3.41
2270 2420 6.043938 AGGGATAAATCTAAGAATGGGCGTAA 59.956 38.462 0.00 0.00 0.00 3.18
2272 2422 4.351111 AGGGATAAATCTAAGAATGGGCGT 59.649 41.667 0.00 0.00 0.00 5.68
2273 2423 4.911390 AGGGATAAATCTAAGAATGGGCG 58.089 43.478 0.00 0.00 0.00 6.13
2305 2456 3.444034 GGAAGAGGGGCAAATTTGAGTAC 59.556 47.826 22.31 8.21 0.00 2.73
2323 2474 7.591006 TTTCTATAAGCACACTTAACGGAAG 57.409 36.000 0.00 0.00 41.62 3.46
2324 2475 7.413657 GCATTTCTATAAGCACACTTAACGGAA 60.414 37.037 0.00 0.00 41.62 4.30
2325 2476 6.036735 GCATTTCTATAAGCACACTTAACGGA 59.963 38.462 0.00 0.00 41.62 4.69
2326 2477 6.192360 GCATTTCTATAAGCACACTTAACGG 58.808 40.000 0.00 0.00 41.62 4.44
2327 2478 6.192360 GGCATTTCTATAAGCACACTTAACG 58.808 40.000 0.00 0.00 41.62 3.18
2328 2479 6.318900 AGGGCATTTCTATAAGCACACTTAAC 59.681 38.462 0.00 0.00 41.62 2.01
2329 2480 6.423182 AGGGCATTTCTATAAGCACACTTAA 58.577 36.000 0.00 0.00 41.62 1.85
2330 2481 6.001449 AGGGCATTTCTATAAGCACACTTA 57.999 37.500 0.00 0.00 42.47 2.24
2331 2482 4.860022 AGGGCATTTCTATAAGCACACTT 58.140 39.130 0.00 0.00 40.07 3.16
2332 2483 4.510167 AGGGCATTTCTATAAGCACACT 57.490 40.909 0.00 0.00 31.46 3.55
2333 2484 4.036852 GGAAGGGCATTTCTATAAGCACAC 59.963 45.833 0.00 0.00 31.46 3.82
2334 2485 4.207165 GGAAGGGCATTTCTATAAGCACA 58.793 43.478 0.00 0.00 31.46 4.57
2335 2486 3.251004 CGGAAGGGCATTTCTATAAGCAC 59.749 47.826 0.00 0.00 0.00 4.40
2336 2487 3.118038 ACGGAAGGGCATTTCTATAAGCA 60.118 43.478 0.00 0.00 0.00 3.91
2349 2500 0.730840 CGGAAAATGTACGGAAGGGC 59.269 55.000 0.00 0.00 0.00 5.19
2357 2508 2.950433 TCGACTGGACGGAAAATGTAC 58.050 47.619 0.00 0.00 0.00 2.90
2373 2524 4.446719 ACTTAACGGTCAAATGTCTTCGAC 59.553 41.667 0.00 0.00 0.00 4.20
2374 2525 4.446385 CACTTAACGGTCAAATGTCTTCGA 59.554 41.667 0.00 0.00 0.00 3.71
2375 2526 4.698276 CACTTAACGGTCAAATGTCTTCG 58.302 43.478 0.00 0.00 0.00 3.79
2376 2527 4.464112 GCACTTAACGGTCAAATGTCTTC 58.536 43.478 0.00 0.00 0.00 2.87
2377 2528 3.059188 CGCACTTAACGGTCAAATGTCTT 60.059 43.478 0.00 0.00 0.00 3.01
2378 2529 2.478894 CGCACTTAACGGTCAAATGTCT 59.521 45.455 0.00 0.00 0.00 3.41
2379 2530 2.834689 CGCACTTAACGGTCAAATGTC 58.165 47.619 0.00 0.00 0.00 3.06
2380 2531 1.069500 GCGCACTTAACGGTCAAATGT 60.069 47.619 0.30 0.00 0.00 2.71
2381 2532 1.602191 GCGCACTTAACGGTCAAATG 58.398 50.000 0.30 0.00 0.00 2.32
2382 2533 0.165079 CGCGCACTTAACGGTCAAAT 59.835 50.000 8.75 0.00 0.00 2.32
2383 2534 1.152989 ACGCGCACTTAACGGTCAAA 61.153 50.000 5.73 0.00 0.00 2.69
2384 2535 0.318529 TACGCGCACTTAACGGTCAA 60.319 50.000 5.73 0.00 0.00 3.18
2385 2536 0.109179 ATACGCGCACTTAACGGTCA 60.109 50.000 5.73 0.00 0.00 4.02
2386 2537 1.826327 TATACGCGCACTTAACGGTC 58.174 50.000 5.73 0.00 0.00 4.79
2387 2538 2.276472 TTATACGCGCACTTAACGGT 57.724 45.000 5.73 0.00 0.00 4.83
2388 2539 3.638080 TTTTATACGCGCACTTAACGG 57.362 42.857 5.73 0.00 0.00 4.44
2407 2558 4.149598 AGGCCTTTGACCGTTAGATTTTT 58.850 39.130 0.00 0.00 0.00 1.94
2408 2559 3.763057 AGGCCTTTGACCGTTAGATTTT 58.237 40.909 0.00 0.00 0.00 1.82
2409 2560 3.434940 AGGCCTTTGACCGTTAGATTT 57.565 42.857 0.00 0.00 0.00 2.17
2410 2561 3.434940 AAGGCCTTTGACCGTTAGATT 57.565 42.857 13.78 0.00 0.00 2.40
2411 2562 3.434940 AAAGGCCTTTGACCGTTAGAT 57.565 42.857 29.91 0.34 0.00 1.98
2412 2563 2.943036 AAAGGCCTTTGACCGTTAGA 57.057 45.000 29.91 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.