Multiple sequence alignment - TraesCS3A01G525600

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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 TraesCS3A01G525600 chr3A 100.000 3555 0 0 1 3555 739570253 739566699 0.000000e+00 6565.0
1 TraesCS3A01G525600 chr3A 93.663 505 30 2 1 504 144295866 144295363 0.000000e+00 754.0
2 TraesCS3A01G525600 chr3A 77.830 424 63 16 2290 2707 739613981 739613583 2.130000e-57 233.0
3 TraesCS3A01G525600 chr3A 80.345 290 45 6 2266 2551 739666258 739665977 3.600000e-50 209.0
4 TraesCS3A01G525600 chr3A 89.024 82 9 0 3061 3142 739663297 739663216 6.280000e-18 102.0
5 TraesCS3A01G525600 chr3A 100.000 35 0 0 2133 2167 739568035 739568001 8.240000e-07 65.8
6 TraesCS3A01G525600 chr3A 100.000 35 0 0 2219 2253 739568121 739568087 8.240000e-07 65.8
7 TraesCS3A01G525600 chr3B 94.511 838 39 4 2723 3555 816607878 816607043 0.000000e+00 1286.0
8 TraesCS3A01G525600 chr3B 93.688 507 26 5 2 504 682963221 682962717 0.000000e+00 754.0
9 TraesCS3A01G525600 chr3B 92.967 455 27 2 2272 2723 816608433 816607981 0.000000e+00 658.0
10 TraesCS3A01G525600 chr3B 87.069 580 40 8 943 1516 816609511 816608961 1.080000e-174 623.0
11 TraesCS3A01G525600 chr3B 88.065 310 22 7 1702 1998 816608846 816608539 1.570000e-93 353.0
12 TraesCS3A01G525600 chr3B 82.445 319 30 13 610 903 816610002 816609685 4.550000e-64 255.0
13 TraesCS3A01G525600 chr3B 88.947 190 14 2 2029 2211 816608539 816608350 9.930000e-56 228.0
14 TraesCS3A01G525600 chr3B 79.494 356 46 13 2266 2616 816613248 816612915 9.930000e-56 228.0
15 TraesCS3A01G525600 chr3B 90.244 82 8 0 3061 3142 816610696 816610615 1.350000e-19 108.0
16 TraesCS3A01G525600 chr3D 94.478 833 29 7 2723 3555 607205415 607204600 0.000000e+00 1267.0
17 TraesCS3A01G525600 chr3D 91.325 853 45 16 2723 3555 607097789 607096946 0.000000e+00 1138.0
18 TraesCS3A01G525600 chr3D 86.673 983 70 28 942 1878 607100919 607099952 0.000000e+00 1033.0
19 TraesCS3A01G525600 chr3D 86.528 720 59 18 1519 2211 607098969 607098261 0.000000e+00 758.0
20 TraesCS3A01G525600 chr3D 84.634 820 55 30 1452 2211 607099944 607099136 0.000000e+00 750.0
21 TraesCS3A01G525600 chr3D 86.034 716 63 18 1519 2210 607206580 607205878 0.000000e+00 734.0
22 TraesCS3A01G525600 chr3D 91.810 525 26 7 1702 2211 607207269 607206747 0.000000e+00 715.0
23 TraesCS3A01G525600 chr3D 94.505 455 19 3 2272 2722 607098344 607097892 0.000000e+00 697.0
24 TraesCS3A01G525600 chr3D 91.111 450 31 4 2272 2718 607205960 607205517 5.080000e-168 601.0
25 TraesCS3A01G525600 chr3D 84.652 632 46 20 892 1516 607207967 607207380 1.840000e-162 582.0
26 TraesCS3A01G525600 chr3D 85.808 458 20 14 504 930 607208412 607207969 9.060000e-121 444.0
27 TraesCS3A01G525600 chr3D 82.069 290 40 6 2266 2551 607224994 607224713 1.650000e-58 237.0
28 TraesCS3A01G525600 chr3D 85.057 174 18 5 692 857 607101246 607101073 1.700000e-38 171.0
29 TraesCS3A01G525600 chr3D 94.595 111 3 2 2266 2375 607206836 607206728 6.100000e-38 169.0
30 TraesCS3A01G525600 chr3D 94.393 107 4 1 2266 2372 607099225 607099121 2.840000e-36 163.0
31 TraesCS3A01G525600 chr3D 77.256 277 28 18 3061 3333 607210578 607210333 2.880000e-26 130.0
32 TraesCS3A01G525600 chr3D 100.000 35 0 0 2219 2253 607205955 607205921 8.240000e-07 65.8
33 TraesCS3A01G525600 chr1D 94.695 509 22 3 1 505 449707297 449706790 0.000000e+00 785.0
34 TraesCS3A01G525600 chr1D 93.478 506 27 5 2 505 280706122 280705621 0.000000e+00 747.0
35 TraesCS3A01G525600 chr6D 94.094 508 28 2 1 508 454868636 454869141 0.000000e+00 771.0
36 TraesCS3A01G525600 chr6B 94.257 505 28 1 2 505 548449580 548450084 0.000000e+00 771.0
37 TraesCS3A01G525600 chr7D 93.478 506 28 4 2 505 24352793 24353295 0.000000e+00 747.0
38 TraesCS3A01G525600 chr2D 93.465 505 28 4 2 504 422074781 422075282 0.000000e+00 745.0
39 TraesCS3A01G525600 chr4B 93.254 504 32 2 2 504 593201169 593200667 0.000000e+00 741.0
40 TraesCS3A01G525600 chrUn 89.344 366 34 3 1216 1581 264524269 264524629 4.180000e-124 455.0
41 TraesCS3A01G525600 chrUn 89.344 366 34 3 1216 1581 315310727 315311087 4.180000e-124 455.0
42 TraesCS3A01G525600 chr6A 83.200 375 31 8 945 1319 162859077 162858735 7.410000e-82 315.0
43 TraesCS3A01G525600 chr6A 80.328 183 34 2 952 1134 4670378 4670558 1.720000e-28 137.0
44 TraesCS3A01G525600 chr6A 90.385 104 8 2 1942 2043 101615295 101615192 6.190000e-28 135.0
45 TraesCS3A01G525600 chr1B 82.058 379 39 9 942 1320 13592439 13592788 2.680000e-76 296.0
46 TraesCS3A01G525600 chr1B 80.851 376 40 9 945 1320 663374557 663374214 2.100000e-67 267.0
47 TraesCS3A01G525600 chr2B 88.372 129 11 4 945 1072 680915874 680915749 6.150000e-33 152.0
48 TraesCS3A01G525600 chr7B 87.023 131 15 2 942 1072 633833054 633833182 2.860000e-31 147.0
49 TraesCS3A01G525600 chr5A 91.346 104 7 2 1942 2043 554380524 554380627 1.330000e-29 141.0
50 TraesCS3A01G525600 chr5A 90.385 104 8 2 1942 2043 541156221 541156324 6.190000e-28 135.0
51 TraesCS3A01G525600 chr5A 90.385 104 8 2 1942 2043 554435921 554436024 6.190000e-28 135.0


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 TraesCS3A01G525600 chr3A 739566699 739570253 3554 True 2232.200000 6565 100.000000 1 3555 3 chr3A.!!$R3 3554
1 TraesCS3A01G525600 chr3A 144295363 144295866 503 True 754.000000 754 93.663000 1 504 1 chr3A.!!$R1 503
2 TraesCS3A01G525600 chr3B 682962717 682963221 504 True 754.000000 754 93.688000 2 504 1 chr3B.!!$R1 502
3 TraesCS3A01G525600 chr3B 816607043 816613248 6205 True 467.375000 1286 87.967750 610 3555 8 chr3B.!!$R2 2945
4 TraesCS3A01G525600 chr3D 607096946 607101246 4300 True 672.857143 1138 89.016429 692 3555 7 chr3D.!!$R2 2863
5 TraesCS3A01G525600 chr3D 607204600 607210578 5978 True 523.088889 1267 89.527111 504 3555 9 chr3D.!!$R3 3051
6 TraesCS3A01G525600 chr1D 449706790 449707297 507 True 785.000000 785 94.695000 1 505 1 chr1D.!!$R2 504
7 TraesCS3A01G525600 chr1D 280705621 280706122 501 True 747.000000 747 93.478000 2 505 1 chr1D.!!$R1 503
8 TraesCS3A01G525600 chr6D 454868636 454869141 505 False 771.000000 771 94.094000 1 508 1 chr6D.!!$F1 507
9 TraesCS3A01G525600 chr6B 548449580 548450084 504 False 771.000000 771 94.257000 2 505 1 chr6B.!!$F1 503
10 TraesCS3A01G525600 chr7D 24352793 24353295 502 False 747.000000 747 93.478000 2 505 1 chr7D.!!$F1 503
11 TraesCS3A01G525600 chr2D 422074781 422075282 501 False 745.000000 745 93.465000 2 504 1 chr2D.!!$F1 502
12 TraesCS3A01G525600 chr4B 593200667 593201169 502 True 741.000000 741 93.254000 2 504 1 chr4B.!!$R1 502

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
678 3317 0.179070 GAATTCCTCCTCCGCTCCAC 60.179 60.0 0.0 0.0 0.00 4.02 F
1228 4066 0.457443 TCATCGATCAACAGCGAGCT 59.543 50.0 0.0 0.0 45.21 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1540 4412 1.081242 GCAAGTCAACATGGCACCG 60.081 57.895 0.00 0.0 0.0 4.94 R
2987 8257 0.974383 GAAGAACCGGGAGAGAACCA 59.026 55.000 6.32 0.0 0.0 3.67 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
147 148 2.498167 ACTGTGCGCTCTTTCTTCATT 58.502 42.857 9.73 0.00 0.00 2.57
171 175 0.551879 TCCCACTGGGTTTTTCGGAA 59.448 50.000 14.25 0.00 44.74 4.30
289 296 2.850851 ATAGCCCCTCCCGTTTCCCA 62.851 60.000 0.00 0.00 0.00 4.37
304 311 5.179929 CCGTTTCCCATCTTTACGTTAAGTT 59.820 40.000 13.49 3.31 0.00 2.66
407 416 2.757950 GCTGGTCTCCTCCATATCTCCA 60.758 54.545 0.00 0.00 36.84 3.86
506 516 2.539338 GCGGAGTTGCGGAACACAA 61.539 57.895 22.29 0.00 34.17 3.33
507 517 1.852067 GCGGAGTTGCGGAACACAAT 61.852 55.000 22.29 0.14 31.24 2.71
509 519 0.521735 GGAGTTGCGGAACACAATCC 59.478 55.000 22.29 15.38 31.24 3.01
510 520 1.234821 GAGTTGCGGAACACAATCCA 58.765 50.000 22.29 0.00 39.61 3.41
527 2191 2.116125 ACCCACTGGCTTGGCTTC 59.884 61.111 0.52 0.00 35.00 3.86
550 2214 3.702045 CAGGGGCAAAACGGGAATTAATA 59.298 43.478 0.00 0.00 0.00 0.98
552 2216 4.966168 AGGGGCAAAACGGGAATTAATAAT 59.034 37.500 0.00 0.00 0.00 1.28
553 2217 5.053811 GGGGCAAAACGGGAATTAATAATG 58.946 41.667 0.00 0.00 0.00 1.90
564 2228 6.531021 GGGAATTAATAATGAGGAGAACCGA 58.469 40.000 0.00 0.00 41.83 4.69
593 2257 1.529948 AGCAAGCAAGCCAAGCAGA 60.530 52.632 0.00 0.00 34.23 4.26
595 2259 0.666577 GCAAGCAAGCCAAGCAGAAG 60.667 55.000 0.00 0.00 0.00 2.85
597 2261 1.111116 AAGCAAGCCAAGCAGAAGCA 61.111 50.000 0.00 0.00 45.49 3.91
677 3316 1.676678 CGAATTCCTCCTCCGCTCCA 61.677 60.000 0.00 0.00 0.00 3.86
678 3317 0.179070 GAATTCCTCCTCCGCTCCAC 60.179 60.000 0.00 0.00 0.00 4.02
679 3318 0.618968 AATTCCTCCTCCGCTCCACT 60.619 55.000 0.00 0.00 0.00 4.00
680 3319 1.045911 ATTCCTCCTCCGCTCCACTC 61.046 60.000 0.00 0.00 0.00 3.51
681 3320 3.151022 CCTCCTCCGCTCCACTCC 61.151 72.222 0.00 0.00 0.00 3.85
777 3435 4.570663 CCGCCGATCGACCAGGTC 62.571 72.222 18.66 9.92 41.67 3.85
879 3568 3.430779 CCCGACGTCTAGGGTTTTC 57.569 57.895 17.80 0.00 42.67 2.29
925 3614 3.680620 TTCGATTGCAGGGGCGAGG 62.681 63.158 0.00 0.00 45.35 4.63
951 3784 2.739943 TGGGAATCTCGTCTGACTGAT 58.260 47.619 6.21 6.77 0.00 2.90
1135 3969 1.069978 TCATGCAGTTCGACAAGGTCA 59.930 47.619 0.00 0.00 32.09 4.02
1136 3970 1.195448 CATGCAGTTCGACAAGGTCAC 59.805 52.381 0.00 0.00 32.09 3.67
1177 4011 1.672356 CCTTCCCTTCCACACGCTG 60.672 63.158 0.00 0.00 0.00 5.18
1179 4013 0.951040 CTTCCCTTCCACACGCTGTC 60.951 60.000 0.00 0.00 0.00 3.51
1180 4014 1.691195 TTCCCTTCCACACGCTGTCA 61.691 55.000 0.00 0.00 0.00 3.58
1181 4015 1.961277 CCCTTCCACACGCTGTCAC 60.961 63.158 0.00 0.00 0.00 3.67
1182 4016 1.069765 CCTTCCACACGCTGTCACT 59.930 57.895 0.00 0.00 0.00 3.41
1183 4017 1.224069 CCTTCCACACGCTGTCACTG 61.224 60.000 0.00 0.00 0.00 3.66
1195 4029 2.592574 TCACTGCACTGCACTGGC 60.593 61.111 0.00 0.00 41.68 4.85
1214 4048 1.535015 GCTCCTCTCCGAAACTCATCG 60.535 57.143 0.00 0.00 42.37 3.84
1222 4056 3.511699 TCCGAAACTCATCGATCAACAG 58.488 45.455 0.00 0.00 45.48 3.16
1223 4057 2.029728 CCGAAACTCATCGATCAACAGC 59.970 50.000 0.00 0.00 45.48 4.40
1224 4058 2.284684 CGAAACTCATCGATCAACAGCG 60.285 50.000 0.00 0.00 45.48 5.18
1228 4066 0.457443 TCATCGATCAACAGCGAGCT 59.543 50.000 0.00 0.00 45.21 4.09
1266 4115 3.636764 GGTGTTTTGATCCTGGTCTTGTT 59.363 43.478 0.00 0.00 0.00 2.83
1267 4116 4.099419 GGTGTTTTGATCCTGGTCTTGTTT 59.901 41.667 0.00 0.00 0.00 2.83
1268 4117 5.395214 GGTGTTTTGATCCTGGTCTTGTTTT 60.395 40.000 0.00 0.00 0.00 2.43
1273 4122 5.514274 TGATCCTGGTCTTGTTTTTGTTC 57.486 39.130 0.00 0.00 0.00 3.18
1326 4175 1.432514 GACAAGCATGTCGAGAGCAA 58.567 50.000 6.29 0.00 45.94 3.91
1331 4180 2.169789 CATGTCGAGAGCAAGGCCG 61.170 63.158 0.00 0.00 0.00 6.13
1332 4181 2.650116 ATGTCGAGAGCAAGGCCGT 61.650 57.895 0.00 0.00 0.00 5.68
1420 4279 6.347969 GCTATTGTGATGCACATACATACAGG 60.348 42.308 0.62 0.00 44.16 4.00
1491 4352 3.802329 GCTGTTGCTACCTGTCAGTGTAA 60.802 47.826 0.00 0.00 36.03 2.41
1516 4377 8.118720 AACTAGTTGTTATCCTGATGATGCAGG 61.119 40.741 7.48 4.06 45.57 4.85
1542 4414 6.198966 GCTTTTATGCCTTATGTTTGATTCGG 59.801 38.462 0.00 0.00 0.00 4.30
1568 4440 3.980646 TGTTGACTTGCGTGCTTAATT 57.019 38.095 0.00 0.00 0.00 1.40
1569 4441 3.626977 TGTTGACTTGCGTGCTTAATTG 58.373 40.909 0.00 0.00 0.00 2.32
1581 4453 6.920758 TGCGTGCTTAATTGTGAAGTAAATTT 59.079 30.769 0.00 0.00 0.00 1.82
1588 4460 5.957842 ATTGTGAAGTAAATTTCTCGGCA 57.042 34.783 0.00 0.00 0.00 5.69
1601 4473 3.410631 TCTCGGCACAGTTATTTTCCA 57.589 42.857 0.00 0.00 0.00 3.53
1606 4478 3.252215 CGGCACAGTTATTTTCCAACTCA 59.748 43.478 0.00 0.00 33.99 3.41
1618 4490 2.847234 AACTCACCACAGGGCCGA 60.847 61.111 0.00 0.00 37.90 5.54
1620 4492 3.625897 CTCACCACAGGGCCGACA 61.626 66.667 0.00 0.00 37.90 4.35
1622 4494 2.747460 CACCACAGGGCCGACATG 60.747 66.667 0.00 0.00 37.90 3.21
1634 4510 2.063266 GCCGACATGTGTTCGTTTAGA 58.937 47.619 1.15 0.00 0.00 2.10
1642 4518 5.470098 ACATGTGTTCGTTTAGAAGCAGATT 59.530 36.000 0.00 0.00 39.95 2.40
1646 4522 8.094798 TGTGTTCGTTTAGAAGCAGATTTATT 57.905 30.769 0.00 0.00 39.95 1.40
1650 4526 9.479278 GTTCGTTTAGAAGCAGATTTATTCTTC 57.521 33.333 0.00 0.00 39.95 2.87
1651 4527 8.197988 TCGTTTAGAAGCAGATTTATTCTTCC 57.802 34.615 0.00 0.00 36.50 3.46
1661 4537 6.098838 GCAGATTTATTCTTCCCCTGGAAAAT 59.901 38.462 0.00 3.64 41.54 1.82
1700 5109 9.812347 ATTATATATGGCAGGAGATTTGTTTCA 57.188 29.630 0.00 0.00 0.00 2.69
1710 5956 6.918022 CAGGAGATTTGTTTCAGTTAAACCAC 59.082 38.462 0.00 0.00 45.83 4.16
1722 5968 6.664515 TCAGTTAAACCACAATTTCGTGATC 58.335 36.000 0.00 0.00 39.34 2.92
1729 5975 6.241207 ACCACAATTTCGTGATCAGTTAAG 57.759 37.500 0.00 0.00 39.34 1.85
1869 6118 3.753294 TCCTGTCTTGTTCCTGACTTC 57.247 47.619 0.00 0.00 34.57 3.01
1912 6168 8.697846 TGATTTCACTCTTAACTTACATACGG 57.302 34.615 0.00 0.00 0.00 4.02
1926 6183 6.146673 ACTTACATACGGTAGTTTCTTGCAAC 59.853 38.462 0.00 0.00 32.49 4.17
1982 6243 8.322906 TGAGTTTTGGAGAACATACTGTATTG 57.677 34.615 0.00 0.00 31.94 1.90
1988 6249 6.177610 TGGAGAACATACTGTATTGAAACCC 58.822 40.000 0.00 0.00 0.00 4.11
2038 6300 2.812499 CATGGCCTGGCAAGCATC 59.188 61.111 22.05 1.86 0.00 3.91
2113 6375 4.142730 GCTTCACTCAAATAGTTCTGCCTG 60.143 45.833 0.00 0.00 35.76 4.85
2158 6420 9.725019 TTCAGAATACTGTCTTCACAATATTGT 57.275 29.630 15.47 15.47 35.53 2.71
2168 6430 9.098355 TGTCTTCACAATATTGTAATCTGTAGC 57.902 33.333 20.39 8.27 39.91 3.58
2178 6440 5.172687 TGTAATCTGTAGCCATGTTTCCA 57.827 39.130 0.00 0.00 0.00 3.53
2180 6442 5.589855 TGTAATCTGTAGCCATGTTTCCATG 59.410 40.000 0.00 0.00 46.65 3.66
2198 6460 8.332464 GTTTCCATGCATACATTGATTTCATTG 58.668 33.333 0.00 1.89 32.87 2.82
2211 6473 8.611757 CATTGATTTCATTGACATGCATGATTT 58.388 29.630 32.75 11.11 31.01 2.17
2212 6474 7.764695 TGATTTCATTGACATGCATGATTTC 57.235 32.000 32.75 19.72 0.00 2.17
2215 6477 7.589574 TTTCATTGACATGCATGATTTCTTG 57.410 32.000 32.75 19.47 0.00 3.02
2216 6478 5.656480 TCATTGACATGCATGATTTCTTGG 58.344 37.500 32.75 13.37 0.00 3.61
2217 6479 5.186215 TCATTGACATGCATGATTTCTTGGT 59.814 36.000 32.75 7.05 0.00 3.67
2266 7312 8.877864 TTGTAATCTGTAATGATTTCCTGGTT 57.122 30.769 0.00 0.00 37.73 3.67
2267 7313 8.877864 TGTAATCTGTAATGATTTCCTGGTTT 57.122 30.769 0.00 0.00 37.73 3.27
2268 7314 8.956426 TGTAATCTGTAATGATTTCCTGGTTTC 58.044 33.333 0.00 0.00 37.73 2.78
2269 7315 7.410120 AATCTGTAATGATTTCCTGGTTTCC 57.590 36.000 0.00 0.00 33.33 3.13
2270 7316 4.941263 TCTGTAATGATTTCCTGGTTTCCG 59.059 41.667 0.00 0.00 0.00 4.30
2271 7317 4.658063 TGTAATGATTTCCTGGTTTCCGT 58.342 39.130 0.00 0.00 0.00 4.69
2272 7318 4.698304 TGTAATGATTTCCTGGTTTCCGTC 59.302 41.667 0.00 0.00 0.00 4.79
2273 7319 2.940994 TGATTTCCTGGTTTCCGTCA 57.059 45.000 0.00 0.00 0.00 4.35
2274 7320 3.216187 TGATTTCCTGGTTTCCGTCAA 57.784 42.857 0.00 0.00 0.00 3.18
2275 7321 3.556999 TGATTTCCTGGTTTCCGTCAAA 58.443 40.909 0.00 0.00 0.00 2.69
2276 7322 4.148838 TGATTTCCTGGTTTCCGTCAAAT 58.851 39.130 0.00 0.00 0.00 2.32
2277 7323 4.586841 TGATTTCCTGGTTTCCGTCAAATT 59.413 37.500 0.00 0.00 0.00 1.82
2278 7324 4.577834 TTTCCTGGTTTCCGTCAAATTC 57.422 40.909 0.00 0.00 0.00 2.17
2279 7325 3.216187 TCCTGGTTTCCGTCAAATTCA 57.784 42.857 0.00 0.00 0.00 2.57
2280 7326 3.146066 TCCTGGTTTCCGTCAAATTCAG 58.854 45.455 0.00 0.00 32.35 3.02
2281 7327 3.146066 CCTGGTTTCCGTCAAATTCAGA 58.854 45.455 0.00 0.00 33.43 3.27
2282 7328 3.568007 CCTGGTTTCCGTCAAATTCAGAA 59.432 43.478 0.00 0.00 33.43 3.02
2283 7329 4.537015 CTGGTTTCCGTCAAATTCAGAAC 58.463 43.478 0.00 0.00 33.43 3.01
2284 7330 3.948473 TGGTTTCCGTCAAATTCAGAACA 59.052 39.130 0.00 0.00 0.00 3.18
2285 7331 4.201970 TGGTTTCCGTCAAATTCAGAACAC 60.202 41.667 0.00 0.00 0.00 3.32
2286 7332 4.036380 GGTTTCCGTCAAATTCAGAACACT 59.964 41.667 0.00 0.00 0.00 3.55
2287 7333 4.811555 TTCCGTCAAATTCAGAACACTG 57.188 40.909 0.00 0.00 0.00 3.66
2288 7334 3.804036 TCCGTCAAATTCAGAACACTGT 58.196 40.909 0.00 0.00 33.82 3.55
2289 7335 3.807622 TCCGTCAAATTCAGAACACTGTC 59.192 43.478 0.00 0.00 33.82 3.51
2290 7336 3.809832 CCGTCAAATTCAGAACACTGTCT 59.190 43.478 0.00 0.00 33.82 3.41
2291 7337 4.273480 CCGTCAAATTCAGAACACTGTCTT 59.727 41.667 0.00 0.00 33.82 3.01
2292 7338 5.435557 CGTCAAATTCAGAACACTGTCTTC 58.564 41.667 0.00 0.00 33.82 2.87
2293 7339 5.006649 CGTCAAATTCAGAACACTGTCTTCA 59.993 40.000 0.00 0.00 33.82 3.02
2294 7340 6.195165 GTCAAATTCAGAACACTGTCTTCAC 58.805 40.000 0.00 0.00 33.82 3.18
2295 7341 5.879777 TCAAATTCAGAACACTGTCTTCACA 59.120 36.000 0.00 0.00 33.82 3.58
2296 7342 6.374053 TCAAATTCAGAACACTGTCTTCACAA 59.626 34.615 0.00 0.00 33.82 3.33
2297 7343 6.949352 AATTCAGAACACTGTCTTCACAAT 57.051 33.333 0.00 0.00 33.82 2.71
2298 7344 8.344831 CAAATTCAGAACACTGTCTTCACAATA 58.655 33.333 0.00 0.00 33.82 1.90
2299 7345 8.627208 AATTCAGAACACTGTCTTCACAATAT 57.373 30.769 0.00 0.00 33.82 1.28
2300 7346 8.627208 ATTCAGAACACTGTCTTCACAATATT 57.373 30.769 0.00 0.00 33.82 1.28
2301 7347 7.425577 TCAGAACACTGTCTTCACAATATTG 57.574 36.000 14.01 14.01 33.82 1.90
2302 7348 6.427853 TCAGAACACTGTCTTCACAATATTGG 59.572 38.462 19.37 8.69 33.82 3.16
2303 7349 6.427853 CAGAACACTGTCTTCACAATATTGGA 59.572 38.462 19.37 10.76 29.82 3.53
2304 7350 6.998074 AGAACACTGTCTTCACAATATTGGAA 59.002 34.615 19.37 16.59 29.82 3.53
2305 7351 7.667219 AGAACACTGTCTTCACAATATTGGAAT 59.333 33.333 19.37 0.00 29.82 3.01
2306 7352 7.383102 ACACTGTCTTCACAATATTGGAATC 57.617 36.000 19.37 13.92 29.82 2.52
2307 7353 7.170965 ACACTGTCTTCACAATATTGGAATCT 58.829 34.615 19.37 0.00 29.82 2.40
2308 7354 7.120285 ACACTGTCTTCACAATATTGGAATCTG 59.880 37.037 19.37 16.93 29.82 2.90
2309 7355 7.120285 CACTGTCTTCACAATATTGGAATCTGT 59.880 37.037 19.37 17.37 29.82 3.41
2310 7356 8.321353 ACTGTCTTCACAATATTGGAATCTGTA 58.679 33.333 19.37 1.97 29.82 2.74
2311 7357 9.334947 CTGTCTTCACAATATTGGAATCTGTAT 57.665 33.333 19.37 0.00 29.82 2.29
2427 7473 0.814457 GACAGCGAGTGGACTCTCAT 59.186 55.000 5.30 0.00 40.75 2.90
2448 7494 5.827267 TCATCCTGAGAAACACAACATTCAA 59.173 36.000 0.00 0.00 0.00 2.69
2565 7611 1.078848 GCCAGTAGTCCAGCACCTG 60.079 63.158 0.00 0.00 0.00 4.00
2584 7633 4.904251 ACCTGTAGCCATACTCTTCATGAT 59.096 41.667 0.00 0.00 32.75 2.45
2708 7758 5.694816 TGAATTTGTTATCGTTTGCATCGT 58.305 33.333 10.66 3.17 0.00 3.73
2714 7764 6.171932 TGTTATCGTTTGCATCGTTTATGT 57.828 33.333 10.66 0.00 37.93 2.29
2766 8021 2.777845 CGAATCGAATGCGGTTGAATTG 59.222 45.455 0.00 0.00 41.72 2.32
2788 8044 9.683069 AATTGTGACAAGTTCATTAAGATTCAC 57.317 29.630 3.74 0.00 36.32 3.18
2791 8047 6.147164 GTGACAAGTTCATTAAGATTCACGGA 59.853 38.462 0.00 0.00 36.32 4.69
2975 8245 1.595382 GGTTGTCACGCTGCACTCT 60.595 57.895 0.00 0.00 0.00 3.24
2987 8257 2.614987 GCTGCACTCTGACTTGGAGAAT 60.615 50.000 7.09 0.00 33.22 2.40
3211 8481 2.615747 GCTGGGGGTCTAGACAAAGAAC 60.616 54.545 23.91 5.67 32.05 3.01
3235 8505 5.626142 TGAATGGGAGCACTTACAGTAAAA 58.374 37.500 0.00 0.00 0.00 1.52
3303 8573 2.509964 CCTCCAGGGTGCCTTTATACTT 59.490 50.000 0.00 0.00 0.00 2.24
3304 8574 3.545703 CTCCAGGGTGCCTTTATACTTG 58.454 50.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
171 175 5.241403 TCCGTATATCCATGCCTCAAAAT 57.759 39.130 0.00 0.00 0.00 1.82
304 311 2.787035 GGGGGTCAAGGGATAAATACCA 59.213 50.000 0.00 0.00 31.13 3.25
407 416 6.037720 TGAACACGTGAAAGTAAATGACACAT 59.962 34.615 25.01 0.00 0.00 3.21
527 2191 1.191489 AATTCCCGTTTTGCCCCTGG 61.191 55.000 0.00 0.00 0.00 4.45
550 2214 0.108615 CTGCGTCGGTTCTCCTCATT 60.109 55.000 0.00 0.00 0.00 2.57
552 2216 0.607217 TACTGCGTCGGTTCTCCTCA 60.607 55.000 0.00 0.00 0.00 3.86
553 2217 0.099082 CTACTGCGTCGGTTCTCCTC 59.901 60.000 0.00 0.00 0.00 3.71
564 2228 2.743928 GCTTGCTGGCTACTGCGT 60.744 61.111 0.00 0.00 43.66 5.24
570 2234 1.228521 TTGGCTTGCTTGCTGGCTA 60.229 52.632 11.77 4.19 0.00 3.93
677 3316 3.647771 GGGGTTTGGGAGCGGAGT 61.648 66.667 0.00 0.00 0.00 3.85
678 3317 4.778143 CGGGGTTTGGGAGCGGAG 62.778 72.222 0.00 0.00 0.00 4.63
777 3435 2.470362 CGGAATGCAGCCAGCTCTG 61.470 63.158 8.88 0.00 45.94 3.35
925 3614 2.125106 ACGAGATTCCCAAGCCGC 60.125 61.111 0.00 0.00 0.00 6.53
1011 3845 2.665777 CTGCCGGTACAGTTCGATG 58.334 57.895 1.90 0.00 32.78 3.84
1056 3890 0.388520 TCACCATCTCGTTCAGCGTG 60.389 55.000 0.00 0.00 42.13 5.34
1135 3969 1.544151 GAAGGGAAGGGAAGGGGGT 60.544 63.158 0.00 0.00 0.00 4.95
1136 3970 2.317378 GGAAGGGAAGGGAAGGGGG 61.317 68.421 0.00 0.00 0.00 5.40
1180 4014 2.281345 GAGCCAGTGCAGTGCAGT 60.281 61.111 20.42 20.16 43.59 4.40
1181 4015 3.054503 GGAGCCAGTGCAGTGCAG 61.055 66.667 20.42 8.40 40.08 4.41
1182 4016 3.541950 GAGGAGCCAGTGCAGTGCA 62.542 63.158 15.37 15.37 41.13 4.57
1183 4017 2.745492 GAGGAGCCAGTGCAGTGC 60.745 66.667 16.47 8.58 41.13 4.40
1195 4029 2.017782 TCGATGAGTTTCGGAGAGGAG 58.982 52.381 0.00 0.00 39.56 3.69
1214 4048 1.791785 GATGCTAGCTCGCTGTTGATC 59.208 52.381 17.23 3.22 0.00 2.92
1266 4115 6.422400 GGACTGAAACAACAACAAGAACAAAA 59.578 34.615 0.00 0.00 0.00 2.44
1267 4116 5.923684 GGACTGAAACAACAACAAGAACAAA 59.076 36.000 0.00 0.00 0.00 2.83
1268 4117 5.010112 TGGACTGAAACAACAACAAGAACAA 59.990 36.000 0.00 0.00 0.00 2.83
1273 4122 5.505173 AGATGGACTGAAACAACAACAAG 57.495 39.130 0.00 0.00 0.00 3.16
1326 4175 2.032681 GCACCTTGAAGACGGCCT 59.967 61.111 0.00 0.00 0.00 5.19
1331 4180 1.398692 TTGGTTGGCACCTTGAAGAC 58.601 50.000 0.00 0.00 44.61 3.01
1332 4181 2.151502 TTTGGTTGGCACCTTGAAGA 57.848 45.000 0.00 0.00 44.61 2.87
1420 4279 7.870445 TGCATTAACTATTCCCTTCAAACAAAC 59.130 33.333 0.00 0.00 0.00 2.93
1491 4352 6.239217 TGCATCATCAGGATAACAACTAGT 57.761 37.500 0.00 0.00 33.95 2.57
1517 4378 6.198966 CCGAATCAAACATAAGGCATAAAAGC 59.801 38.462 0.00 0.00 0.00 3.51
1539 4411 1.514678 GCAAGTCAACATGGCACCGA 61.515 55.000 0.00 0.00 0.00 4.69
1540 4412 1.081242 GCAAGTCAACATGGCACCG 60.081 57.895 0.00 0.00 0.00 4.94
1542 4414 4.539152 CGCAAGTCAACATGGCAC 57.461 55.556 0.00 0.00 0.00 5.01
1568 4440 4.130857 TGTGCCGAGAAATTTACTTCACA 58.869 39.130 0.00 0.07 0.00 3.58
1569 4441 4.213482 ACTGTGCCGAGAAATTTACTTCAC 59.787 41.667 0.00 0.00 0.00 3.18
1581 4453 3.410631 TGGAAAATAACTGTGCCGAGA 57.589 42.857 0.00 0.00 0.00 4.04
1588 4460 5.197451 TGTGGTGAGTTGGAAAATAACTGT 58.803 37.500 0.00 0.00 38.42 3.55
1601 4473 2.847234 TCGGCCCTGTGGTGAGTT 60.847 61.111 0.00 0.00 0.00 3.01
1606 4478 3.249189 ACATGTCGGCCCTGTGGT 61.249 61.111 0.00 0.00 0.00 4.16
1618 4490 4.377021 TCTGCTTCTAAACGAACACATGT 58.623 39.130 0.00 0.00 0.00 3.21
1620 4492 6.560253 AAATCTGCTTCTAAACGAACACAT 57.440 33.333 0.00 0.00 0.00 3.21
1622 4494 8.443937 AGAATAAATCTGCTTCTAAACGAACAC 58.556 33.333 0.00 0.00 36.88 3.32
1634 4510 4.230502 TCCAGGGGAAGAATAAATCTGCTT 59.769 41.667 0.00 0.00 38.79 3.91
1642 4518 7.398904 CAGGTTTATTTTCCAGGGGAAGAATAA 59.601 37.037 14.41 14.41 43.06 1.40
1646 4522 4.355588 TCAGGTTTATTTTCCAGGGGAAGA 59.644 41.667 0.00 0.00 43.06 2.87
1650 4526 4.156477 TGTTCAGGTTTATTTTCCAGGGG 58.844 43.478 0.00 0.00 0.00 4.79
1651 4527 5.799827 TTGTTCAGGTTTATTTTCCAGGG 57.200 39.130 0.00 0.00 0.00 4.45
1699 5108 6.434596 TGATCACGAAATTGTGGTTTAACTG 58.565 36.000 0.00 0.00 40.31 3.16
1700 5109 6.262273 ACTGATCACGAAATTGTGGTTTAACT 59.738 34.615 0.00 0.00 40.31 2.24
1710 5956 5.295431 TGCCTTAACTGATCACGAAATTG 57.705 39.130 0.00 0.00 0.00 2.32
1722 5968 3.634397 TCTCCTGGAATGCCTTAACTG 57.366 47.619 0.00 0.00 34.31 3.16
1729 5975 3.853475 CAAACAAATCTCCTGGAATGCC 58.147 45.455 0.00 0.00 0.00 4.40
1807 6054 4.893424 TGTTGCAGACAGTTTAACCTTC 57.107 40.909 0.00 0.00 33.40 3.46
1869 6118 5.768980 AATCATCCAGTAGGTCCATATGG 57.231 43.478 16.25 16.25 35.89 2.74
1912 6168 3.065648 TGGAAACGGTTGCAAGAAACTAC 59.934 43.478 4.35 0.00 31.30 2.73
1926 6183 7.119262 ACAAATTCAGATACTACTTGGAAACGG 59.881 37.037 0.00 0.00 0.00 4.44
2038 6300 9.941664 CTGAAATAATTAAACAGCATCACCTAG 57.058 33.333 0.00 0.00 0.00 3.02
2113 6375 5.815740 TCTGAATTTGACGGAAATACTAGCC 59.184 40.000 0.00 0.00 32.76 3.93
2178 6440 7.170828 GCATGTCAATGAAATCAATGTATGCAT 59.829 33.333 22.92 3.79 41.75 3.96
2180 6442 6.477360 TGCATGTCAATGAAATCAATGTATGC 59.523 34.615 22.04 22.04 42.05 3.14
2198 6460 5.472148 TGAAACCAAGAAATCATGCATGTC 58.528 37.500 25.43 16.05 0.00 3.06
2211 6473 6.706270 GTGAAGACAGTATTCTGAAACCAAGA 59.294 38.462 9.31 0.00 43.76 3.02
2212 6474 6.483307 TGTGAAGACAGTATTCTGAAACCAAG 59.517 38.462 9.31 0.00 43.76 3.61
2215 6477 6.861065 TTGTGAAGACAGTATTCTGAAACC 57.139 37.500 9.31 0.00 43.76 3.27
2253 7299 3.433306 TGACGGAAACCAGGAAATCAT 57.567 42.857 0.00 0.00 0.00 2.45
2254 7300 2.940994 TGACGGAAACCAGGAAATCA 57.059 45.000 0.00 0.00 0.00 2.57
2255 7301 4.783764 ATTTGACGGAAACCAGGAAATC 57.216 40.909 0.00 0.00 0.00 2.17
2256 7302 4.586841 TGAATTTGACGGAAACCAGGAAAT 59.413 37.500 0.00 0.00 0.00 2.17
2257 7303 3.954904 TGAATTTGACGGAAACCAGGAAA 59.045 39.130 0.00 0.00 0.00 3.13
2258 7304 3.556999 TGAATTTGACGGAAACCAGGAA 58.443 40.909 0.00 0.00 0.00 3.36
2259 7305 3.146066 CTGAATTTGACGGAAACCAGGA 58.854 45.455 0.00 0.00 29.93 3.86
2260 7306 3.146066 TCTGAATTTGACGGAAACCAGG 58.854 45.455 0.00 0.00 32.44 4.45
2261 7307 4.036262 TGTTCTGAATTTGACGGAAACCAG 59.964 41.667 0.00 0.00 34.97 4.00
2262 7308 3.948473 TGTTCTGAATTTGACGGAAACCA 59.052 39.130 0.00 0.00 34.97 3.67
2263 7309 4.036380 AGTGTTCTGAATTTGACGGAAACC 59.964 41.667 0.00 0.00 34.97 3.27
2264 7310 4.970003 CAGTGTTCTGAATTTGACGGAAAC 59.030 41.667 0.00 0.00 43.76 2.78
2265 7311 4.638421 ACAGTGTTCTGAATTTGACGGAAA 59.362 37.500 2.17 0.00 43.76 3.13
2266 7312 4.196193 ACAGTGTTCTGAATTTGACGGAA 58.804 39.130 2.17 0.00 43.76 4.30
2267 7313 3.804036 ACAGTGTTCTGAATTTGACGGA 58.196 40.909 2.17 0.00 43.76 4.69
2268 7314 3.809832 AGACAGTGTTCTGAATTTGACGG 59.190 43.478 0.00 0.00 43.76 4.79
2269 7315 5.006649 TGAAGACAGTGTTCTGAATTTGACG 59.993 40.000 11.51 0.00 43.76 4.35
2270 7316 6.183360 TGTGAAGACAGTGTTCTGAATTTGAC 60.183 38.462 11.51 0.19 43.76 3.18
2271 7317 5.879777 TGTGAAGACAGTGTTCTGAATTTGA 59.120 36.000 11.51 0.00 43.76 2.69
2272 7318 6.122850 TGTGAAGACAGTGTTCTGAATTTG 57.877 37.500 11.51 0.00 43.76 2.32
2273 7319 6.757897 TTGTGAAGACAGTGTTCTGAATTT 57.242 33.333 11.51 0.00 43.76 1.82
2274 7320 6.949352 ATTGTGAAGACAGTGTTCTGAATT 57.051 33.333 11.51 0.00 43.76 2.17
2275 7321 8.509690 CAATATTGTGAAGACAGTGTTCTGAAT 58.490 33.333 11.51 10.86 43.76 2.57
2276 7322 7.041167 CCAATATTGTGAAGACAGTGTTCTGAA 60.041 37.037 14.25 4.93 43.76 3.02
2277 7323 6.427853 CCAATATTGTGAAGACAGTGTTCTGA 59.572 38.462 14.25 0.00 43.76 3.27
2278 7324 6.427853 TCCAATATTGTGAAGACAGTGTTCTG 59.572 38.462 14.25 0.27 46.18 3.02
2279 7325 6.533730 TCCAATATTGTGAAGACAGTGTTCT 58.466 36.000 14.25 0.00 32.26 3.01
2280 7326 6.801539 TCCAATATTGTGAAGACAGTGTTC 57.198 37.500 14.25 3.40 32.26 3.18
2281 7327 7.667219 AGATTCCAATATTGTGAAGACAGTGTT 59.333 33.333 14.25 1.19 32.26 3.32
2282 7328 7.120285 CAGATTCCAATATTGTGAAGACAGTGT 59.880 37.037 14.25 0.00 32.26 3.55
2283 7329 7.120285 ACAGATTCCAATATTGTGAAGACAGTG 59.880 37.037 14.25 11.85 32.26 3.66
2284 7330 7.170965 ACAGATTCCAATATTGTGAAGACAGT 58.829 34.615 14.25 13.12 32.26 3.55
2285 7331 7.621428 ACAGATTCCAATATTGTGAAGACAG 57.379 36.000 14.25 12.67 32.26 3.51
2297 7343 9.778741 GGAAACATGACTATACAGATTCCAATA 57.221 33.333 0.00 0.00 33.73 1.90
2298 7344 8.274322 TGGAAACATGACTATACAGATTCCAAT 58.726 33.333 0.00 0.00 37.08 3.16
2299 7345 7.629157 TGGAAACATGACTATACAGATTCCAA 58.371 34.615 0.00 0.00 37.08 3.53
2300 7346 7.194112 TGGAAACATGACTATACAGATTCCA 57.806 36.000 0.00 0.00 37.36 3.53
2395 7441 1.344942 CGCTGTCGCAGAACCTGTAC 61.345 60.000 10.46 0.00 39.69 2.90
2427 7473 5.436175 TCTTGAATGTTGTGTTTCTCAGGA 58.564 37.500 0.00 0.00 0.00 3.86
2565 7611 6.209589 TGGTCTATCATGAAGAGTATGGCTAC 59.790 42.308 0.00 0.00 0.00 3.58
2708 7758 9.995957 CATCCACAAACATTATCGTTACATAAA 57.004 29.630 0.00 0.00 0.00 1.40
2714 7764 5.006261 CGCTCATCCACAAACATTATCGTTA 59.994 40.000 0.00 0.00 0.00 3.18
2766 8021 6.147164 TCCGTGAATCTTAATGAACTTGTCAC 59.853 38.462 0.00 0.00 39.72 3.67
2788 8044 3.735237 ATGTAGAGGTGCTAACATCCG 57.265 47.619 0.00 0.00 37.85 4.18
2791 8047 7.499232 GGATTTTGTATGTAGAGGTGCTAACAT 59.501 37.037 0.00 0.00 0.00 2.71
2874 8144 1.228367 AACAGCTGCCCTTGGAGTG 60.228 57.895 15.27 0.00 0.00 3.51
2987 8257 0.974383 GAAGAACCGGGAGAGAACCA 59.026 55.000 6.32 0.00 0.00 3.67
3235 8505 2.362632 AACGCTCGGGCTACCTCT 60.363 61.111 5.36 0.00 36.09 3.69
3420 8690 8.838365 CGACTAAATCATGGTAGACTAGTAGTT 58.162 37.037 3.85 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.