Multiple sequence alignment - TraesCS3D01G538600

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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 TraesCS3D01G538600 chr3D 100.000 4546 0 0 1 4546 611200344 611195799 0.000000e+00 8395.0
1 TraesCS3D01G538600 chr3D 75.106 1888 362 74 1736 3561 611212052 611210211 0.000000e+00 784.0
2 TraesCS3D01G538600 chr3D 75.678 1254 223 59 2119 3344 611217726 611216527 6.650000e-153 551.0
3 TraesCS3D01G538600 chr3D 83.072 319 44 8 1731 2043 611253484 611253170 9.630000e-72 281.0
4 TraesCS3D01G538600 chr3D 81.871 171 23 6 3827 3993 317748531 317748365 2.210000e-28 137.0
5 TraesCS3D01G538600 chr3D 97.500 40 0 1 197 236 293182982 293182944 2.940000e-07 67.6
6 TraesCS3D01G538600 chr3D 100.000 30 0 0 207 236 480127066 480127095 6.350000e-04 56.5
7 TraesCS3D01G538600 chr3B 94.791 4473 179 20 1 4452 828952637 828948198 0.000000e+00 6920.0
8 TraesCS3D01G538600 chr3B 77.596 1281 224 50 2135 3375 829038780 829040037 0.000000e+00 717.0
9 TraesCS3D01G538600 chr3B 76.037 1494 266 57 2129 3561 828993310 828991848 0.000000e+00 691.0
10 TraesCS3D01G538600 chr3B 74.724 1088 205 49 1404 2465 828919733 828918690 5.440000e-114 422.0
11 TraesCS3D01G538600 chr3B 94.231 52 1 1 4403 4452 816746043 816745992 1.360000e-10 78.7
12 TraesCS3D01G538600 chr3A 94.362 1880 67 18 2018 3886 746146510 746144659 0.000000e+00 2848.0
13 TraesCS3D01G538600 chr3A 93.825 1004 36 8 1 987 746153086 746152092 0.000000e+00 1487.0
14 TraesCS3D01G538600 chr3A 90.506 790 44 9 972 1756 746152068 746151305 0.000000e+00 1014.0
15 TraesCS3D01G538600 chr3A 97.227 577 13 2 3875 4451 746144465 746143892 0.000000e+00 974.0
16 TraesCS3D01G538600 chr3A 77.911 1254 205 49 2135 3344 746187563 746188788 0.000000e+00 715.0
17 TraesCS3D01G538600 chr3A 73.725 1530 284 86 2111 3600 746169255 746167804 1.470000e-134 490.0
18 TraesCS3D01G538600 chr3A 82.927 246 10 15 1778 2023 746147267 746147054 4.640000e-45 193.0
19 TraesCS3D01G538600 chrUn 85.882 255 21 5 1 246 311284117 311283869 1.620000e-64 257.0
20 TraesCS3D01G538600 chrUn 82.609 207 20 8 3833 4038 94749171 94748980 7.820000e-38 169.0
21 TraesCS3D01G538600 chr6B 87.324 213 22 5 3828 4038 23022248 23022039 5.880000e-59 239.0
22 TraesCS3D01G538600 chr6B 82.659 173 21 7 3820 3989 418184147 418183981 1.320000e-30 145.0
23 TraesCS3D01G538600 chr4B 85.876 177 21 4 3833 4008 378989087 378988914 7.770000e-43 185.0
24 TraesCS3D01G538600 chr4B 92.308 52 3 1 3 54 149037486 149037436 6.310000e-09 73.1
25 TraesCS3D01G538600 chr4B 90.385 52 4 1 3 54 149001262 149001212 2.940000e-07 67.6
26 TraesCS3D01G538600 chr7A 82.530 166 25 4 3828 3993 601517548 601517387 4.740000e-30 143.0
27 TraesCS3D01G538600 chr7A 97.436 39 1 0 4490 4528 719177451 719177489 2.940000e-07 67.6
28 TraesCS3D01G538600 chr7D 81.395 172 18 9 3824 3988 494212716 494212552 1.330000e-25 128.0
29 TraesCS3D01G538600 chr2B 79.365 126 24 2 3883 4008 725746898 725747021 2.250000e-13 87.9
30 TraesCS3D01G538600 chr1A 97.368 38 1 0 203 240 280078456 280078493 1.060000e-06 65.8
31 TraesCS3D01G538600 chr2D 94.444 36 1 1 201 235 631006769 631006804 2.000000e-03 54.7


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 TraesCS3D01G538600 chr3D 611195799 611200344 4545 True 8395.000000 8395 100.000000 1 4546 1 chr3D.!!$R3 4545
1 TraesCS3D01G538600 chr3D 611210211 611212052 1841 True 784.000000 784 75.106000 1736 3561 1 chr3D.!!$R4 1825
2 TraesCS3D01G538600 chr3D 611216527 611217726 1199 True 551.000000 551 75.678000 2119 3344 1 chr3D.!!$R5 1225
3 TraesCS3D01G538600 chr3B 828948198 828952637 4439 True 6920.000000 6920 94.791000 1 4452 1 chr3B.!!$R3 4451
4 TraesCS3D01G538600 chr3B 829038780 829040037 1257 False 717.000000 717 77.596000 2135 3375 1 chr3B.!!$F1 1240
5 TraesCS3D01G538600 chr3B 828991848 828993310 1462 True 691.000000 691 76.037000 2129 3561 1 chr3B.!!$R4 1432
6 TraesCS3D01G538600 chr3B 828918690 828919733 1043 True 422.000000 422 74.724000 1404 2465 1 chr3B.!!$R2 1061
7 TraesCS3D01G538600 chr3A 746143892 746147267 3375 True 1338.333333 2848 91.505333 1778 4451 3 chr3A.!!$R2 2673
8 TraesCS3D01G538600 chr3A 746151305 746153086 1781 True 1250.500000 1487 92.165500 1 1756 2 chr3A.!!$R3 1755
9 TraesCS3D01G538600 chr3A 746187563 746188788 1225 False 715.000000 715 77.911000 2135 3344 1 chr3A.!!$F1 1209
10 TraesCS3D01G538600 chr3A 746167804 746169255 1451 True 490.000000 490 73.725000 2111 3600 1 chr3A.!!$R1 1489

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
578 587 0.109458 GTACGATGTGAGACCGTGCA 60.109 55.000 0.0 0.0 38.45 4.57 F
1091 1155 0.036388 CGCAGATGGTGGGTACTTGT 60.036 55.000 0.0 0.0 34.37 3.16 F
1843 1936 0.674581 TGATGCGGAAGGTCAAGCAG 60.675 55.000 0.0 0.0 43.20 4.24 F
2194 2911 1.004918 GCTGGTGGTCTAGCAACGT 60.005 57.895 0.0 0.0 45.49 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 1917 0.674581 CTGCTTGACCTTCCGCATCA 60.675 55.000 0.00 0.0 0.0 3.07 R
2194 2911 2.414058 AAATCGTCGCAATGCACAAA 57.586 40.000 5.91 0.0 0.0 2.83 R
3285 4106 0.679505 CCAAGAGACGTCAAGGACCA 59.320 55.000 19.50 0.0 0.0 4.02 R
4017 5072 6.433093 GGCAACCTAAGGAAAATAACTTCTCA 59.567 38.462 0.00 0.0 0.0 3.27 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
268 269 7.663827 AGTGGGATCACAATATGCAAATATTG 58.336 34.615 15.42 15.42 45.91 1.90
334 335 9.844257 TCCAAATTTTAGAAACCAAATCATTGT 57.156 25.926 0.00 0.00 34.60 2.71
468 471 7.016465 AGAGATGGAAATTTTCACCCATTTTGA 59.984 33.333 0.00 0.00 39.33 2.69
565 574 5.259632 AGTTAGTGGTTAGTGGAGTACGAT 58.740 41.667 0.00 0.00 0.00 3.73
578 587 0.109458 GTACGATGTGAGACCGTGCA 60.109 55.000 0.00 0.00 38.45 4.57
612 621 0.179197 CGTGCGTGAGTCTCGTGTAT 60.179 55.000 15.32 0.00 0.00 2.29
694 703 7.480760 AAATGTAGCCTATGTGGTTTTCATT 57.519 32.000 0.00 0.00 35.66 2.57
703 712 3.221771 TGTGGTTTTCATTGGGAGACAG 58.778 45.455 0.00 0.00 0.00 3.51
715 724 0.615850 GGAGACAGGGCAAAGCTAGT 59.384 55.000 0.00 0.00 0.00 2.57
755 775 3.006940 TCGTGAGAGAAGAAGAGAGAGC 58.993 50.000 0.00 0.00 34.84 4.09
906 926 6.972901 CACGAGCACTGTGTATATTAGAAGAA 59.027 38.462 9.86 0.00 32.68 2.52
1075 1139 2.662596 GTCCATCAGACCACCGCA 59.337 61.111 0.00 0.00 39.84 5.69
1091 1155 0.036388 CGCAGATGGTGGGTACTTGT 60.036 55.000 0.00 0.00 34.37 3.16
1165 1229 4.539083 TGTTCGGCGTGCCACAGT 62.539 61.111 12.06 0.00 35.37 3.55
1266 1330 2.043450 CTCCAGAGAGGCTCCGGT 60.043 66.667 11.71 0.00 36.39 5.28
1267 1331 2.363018 TCCAGAGAGGCTCCGGTG 60.363 66.667 11.71 6.14 37.29 4.94
1268 1332 2.363018 CCAGAGAGGCTCCGGTGA 60.363 66.667 11.71 0.00 0.00 4.02
1269 1333 2.716017 CCAGAGAGGCTCCGGTGAC 61.716 68.421 11.71 3.92 0.00 3.67
1270 1334 1.979155 CAGAGAGGCTCCGGTGACA 60.979 63.158 12.81 0.00 0.00 3.58
1271 1335 1.680651 AGAGAGGCTCCGGTGACAG 60.681 63.158 12.81 0.00 0.00 3.51
1272 1336 3.363844 GAGAGGCTCCGGTGACAGC 62.364 68.421 12.81 8.33 34.65 4.40
1353 1429 2.939103 CCTGCATCTTTTTCCCTCTACG 59.061 50.000 0.00 0.00 0.00 3.51
1358 1434 5.128827 TGCATCTTTTTCCCTCTACGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
1359 1435 6.049790 GCATCTTTTTCCCTCTACGTATCTT 58.950 40.000 0.00 0.00 0.00 2.40
1360 1436 6.539103 GCATCTTTTTCCCTCTACGTATCTTT 59.461 38.462 0.00 0.00 0.00 2.52
1361 1437 7.065923 GCATCTTTTTCCCTCTACGTATCTTTT 59.934 37.037 0.00 0.00 0.00 2.27
1362 1438 8.947115 CATCTTTTTCCCTCTACGTATCTTTTT 58.053 33.333 0.00 0.00 0.00 1.94
1412 1488 5.779529 ATCAAAAGACATACATGATGGGC 57.220 39.130 0.00 0.00 40.18 5.36
1462 1538 5.163652 GGGCAATTAGTTGATGGACTTGTAC 60.164 44.000 1.56 0.00 37.53 2.90
1521 1602 5.232463 GCACAGTCAATGATTGTTCCAATT 58.768 37.500 8.72 0.00 30.26 2.32
1532 1613 7.156876 TGATTGTTCCAATTGTAGAATGTCC 57.843 36.000 4.43 0.00 0.00 4.02
1590 1671 2.293318 ACTGGCGCTGGAATCCTCA 61.293 57.895 7.64 0.00 0.00 3.86
1633 1714 8.783660 AATCCTGGTAATCACAGATACTTCTA 57.216 34.615 0.00 0.00 38.20 2.10
1698 1784 5.477607 TTTCATGTCCTTCTCTCCGTTTA 57.522 39.130 0.00 0.00 0.00 2.01
1722 1815 7.964604 ACCTGAATATTTAATACTTCTCGGC 57.035 36.000 0.00 0.00 0.00 5.54
1723 1816 7.736893 ACCTGAATATTTAATACTTCTCGGCT 58.263 34.615 0.00 0.00 0.00 5.52
1724 1817 7.873505 ACCTGAATATTTAATACTTCTCGGCTC 59.126 37.037 0.00 0.00 0.00 4.70
1725 1818 8.091449 CCTGAATATTTAATACTTCTCGGCTCT 58.909 37.037 0.00 0.00 0.00 4.09
1726 1819 9.134734 CTGAATATTTAATACTTCTCGGCTCTC 57.865 37.037 0.00 0.00 0.00 3.20
1727 1820 8.638873 TGAATATTTAATACTTCTCGGCTCTCA 58.361 33.333 0.00 0.00 0.00 3.27
1803 1896 0.815734 AAGCCTACGTGCGATACTGT 59.184 50.000 0.00 0.00 36.02 3.55
1815 1908 2.389059 CGATACTGTGATGGAGCTTCG 58.611 52.381 0.00 0.00 0.00 3.79
1824 1917 2.224523 TGATGGAGCTTCGTTTTCAGGT 60.225 45.455 0.00 0.00 0.00 4.00
1843 1936 0.674581 TGATGCGGAAGGTCAAGCAG 60.675 55.000 0.00 0.00 43.20 4.24
1911 2004 4.572985 TGCTTCAGGAGATGTTTTGTTG 57.427 40.909 0.00 0.00 0.00 3.33
2102 2819 4.739716 GTGCTACAAATGTTGTGAACAAGG 59.260 41.667 3.90 0.00 45.86 3.61
2194 2911 1.004918 GCTGGTGGTCTAGCAACGT 60.005 57.895 0.00 0.00 45.49 3.99
2196 2913 1.878953 CTGGTGGTCTAGCAACGTTT 58.121 50.000 0.00 0.00 36.15 3.60
2296 3013 6.475727 TCTTGACGTGTAAGACTCTTGAAAAG 59.524 38.462 0.00 0.00 35.82 2.27
2433 3183 1.496429 CCTCCAGGTTAGCCATTGGAT 59.504 52.381 6.95 1.78 38.13 3.41
2527 3280 7.064847 TGCACTTCTCTAAAACACGACTTTTAA 59.935 33.333 0.00 0.00 0.00 1.52
2552 3308 7.404671 AAAAGGCTTTGTAAAACTCTTGAGA 57.595 32.000 14.19 0.00 0.00 3.27
2672 3440 9.334693 CTTCTGTATCTCACAAATTTTGCTAAC 57.665 33.333 9.04 1.11 36.48 2.34
2823 3597 9.821662 GTAAGTTCGTTAGCTGAAATAATTGTT 57.178 29.630 0.00 0.00 0.00 2.83
3144 3965 6.688637 TTCACTCTCATTAAGCATCAATGG 57.311 37.500 5.45 0.00 34.73 3.16
3285 4106 3.512329 TCATGCTTCACTCATTGCCAAAT 59.488 39.130 0.00 0.00 0.00 2.32
3588 4429 6.860080 TGGTCGAGGTTTACTATGTAAAGAG 58.140 40.000 3.49 0.00 0.00 2.85
3590 4437 6.750963 GGTCGAGGTTTACTATGTAAAGAGTG 59.249 42.308 3.49 0.00 0.00 3.51
3591 4438 6.253083 GTCGAGGTTTACTATGTAAAGAGTGC 59.747 42.308 3.49 0.00 0.00 4.40
3593 4440 6.588756 CGAGGTTTACTATGTAAAGAGTGCAA 59.411 38.462 3.49 0.00 0.00 4.08
3594 4441 7.201444 CGAGGTTTACTATGTAAAGAGTGCAAG 60.201 40.741 3.49 0.00 0.00 4.01
3715 4562 3.440173 GTGGATCGTGTGAAAATGTCCAT 59.560 43.478 0.00 0.00 36.73 3.41
3871 4721 1.905637 ACGGGCTAACCAGAAAAAGG 58.094 50.000 0.00 0.00 40.22 3.11
3886 4941 9.397280 ACCAGAAAAAGGATAAATAGCTTAGAC 57.603 33.333 0.00 0.00 0.00 2.59
3935 4990 9.527157 TCTGACCATTTAATAAATTGACTGGAA 57.473 29.630 8.75 0.00 0.00 3.53
3951 5006 9.959721 ATTGACTGGAAAACTCTATAGCTTTTA 57.040 29.630 0.00 0.00 0.00 1.52
4385 5440 1.134521 TGGAACTGAAGTCTGCACGTT 60.135 47.619 0.00 0.00 0.00 3.99
4457 5512 6.653273 CATCATCGTCTTTGATGTTGTAGT 57.347 37.500 5.67 0.00 44.82 2.73
4458 5513 6.700020 CATCATCGTCTTTGATGTTGTAGTC 58.300 40.000 5.67 0.00 44.82 2.59
4459 5514 5.168569 TCATCGTCTTTGATGTTGTAGTCC 58.831 41.667 3.90 0.00 44.82 3.85
4460 5515 4.594123 TCGTCTTTGATGTTGTAGTCCA 57.406 40.909 0.00 0.00 0.00 4.02
4461 5516 4.951254 TCGTCTTTGATGTTGTAGTCCAA 58.049 39.130 0.00 0.00 0.00 3.53
4462 5517 5.361427 TCGTCTTTGATGTTGTAGTCCAAA 58.639 37.500 0.00 0.00 34.07 3.28
4463 5518 5.818336 TCGTCTTTGATGTTGTAGTCCAAAA 59.182 36.000 0.00 0.00 34.07 2.44
4464 5519 6.316640 TCGTCTTTGATGTTGTAGTCCAAAAA 59.683 34.615 0.00 0.00 34.07 1.94
4483 5538 3.323751 AAATCTGCCAACAAATCTGCC 57.676 42.857 0.00 0.00 0.00 4.85
4484 5539 1.927487 ATCTGCCAACAAATCTGCCA 58.073 45.000 0.00 0.00 0.00 4.92
4485 5540 1.250328 TCTGCCAACAAATCTGCCAG 58.750 50.000 0.00 0.00 0.00 4.85
4486 5541 1.202915 TCTGCCAACAAATCTGCCAGA 60.203 47.619 0.00 0.00 0.00 3.86
4487 5542 0.961019 TGCCAACAAATCTGCCAGAC 59.039 50.000 0.00 0.00 0.00 3.51
4488 5543 0.109597 GCCAACAAATCTGCCAGACG 60.110 55.000 0.00 0.00 0.00 4.18
4489 5544 1.522668 CCAACAAATCTGCCAGACGA 58.477 50.000 0.00 0.00 0.00 4.20
4490 5545 1.879380 CCAACAAATCTGCCAGACGAA 59.121 47.619 0.00 0.00 0.00 3.85
4491 5546 2.489329 CCAACAAATCTGCCAGACGAAT 59.511 45.455 0.00 0.00 0.00 3.34
4492 5547 3.057315 CCAACAAATCTGCCAGACGAATT 60.057 43.478 0.00 0.00 0.00 2.17
4493 5548 4.549458 CAACAAATCTGCCAGACGAATTT 58.451 39.130 0.00 0.00 0.00 1.82
4494 5549 4.425577 ACAAATCTGCCAGACGAATTTC 57.574 40.909 0.00 0.00 0.00 2.17
4495 5550 3.191371 ACAAATCTGCCAGACGAATTTCC 59.809 43.478 0.00 0.00 0.00 3.13
4496 5551 3.356529 AATCTGCCAGACGAATTTCCT 57.643 42.857 0.00 0.00 0.00 3.36
4497 5552 2.386661 TCTGCCAGACGAATTTCCTC 57.613 50.000 0.00 0.00 0.00 3.71
4498 5553 1.623311 TCTGCCAGACGAATTTCCTCA 59.377 47.619 0.00 0.00 0.00 3.86
4499 5554 2.005451 CTGCCAGACGAATTTCCTCAG 58.995 52.381 0.00 0.00 0.00 3.35
4500 5555 1.347707 TGCCAGACGAATTTCCTCAGT 59.652 47.619 0.00 0.00 0.00 3.41
4501 5556 2.003301 GCCAGACGAATTTCCTCAGTC 58.997 52.381 0.00 0.00 0.00 3.51
4502 5557 2.612972 GCCAGACGAATTTCCTCAGTCA 60.613 50.000 0.00 0.00 34.56 3.41
4503 5558 3.257393 CCAGACGAATTTCCTCAGTCAG 58.743 50.000 0.00 0.00 34.56 3.51
4504 5559 3.056536 CCAGACGAATTTCCTCAGTCAGA 60.057 47.826 0.00 0.00 34.56 3.27
4505 5560 4.382470 CCAGACGAATTTCCTCAGTCAGAT 60.382 45.833 0.00 0.00 34.56 2.90
4506 5561 4.803088 CAGACGAATTTCCTCAGTCAGATC 59.197 45.833 0.00 0.00 34.56 2.75
4507 5562 3.775202 ACGAATTTCCTCAGTCAGATCG 58.225 45.455 0.00 0.00 0.00 3.69
4508 5563 3.119291 CGAATTTCCTCAGTCAGATCGG 58.881 50.000 0.00 0.00 0.00 4.18
4509 5564 2.611225 ATTTCCTCAGTCAGATCGGC 57.389 50.000 0.00 0.00 0.00 5.54
4510 5565 1.561643 TTTCCTCAGTCAGATCGGCT 58.438 50.000 0.00 0.00 0.00 5.52
4511 5566 0.820226 TTCCTCAGTCAGATCGGCTG 59.180 55.000 11.39 11.39 46.31 4.85
4512 5567 1.039785 TCCTCAGTCAGATCGGCTGG 61.040 60.000 15.72 8.87 44.98 4.85
4513 5568 1.326213 CCTCAGTCAGATCGGCTGGT 61.326 60.000 15.72 0.00 44.98 4.00
4514 5569 1.393603 CTCAGTCAGATCGGCTGGTA 58.606 55.000 15.72 1.58 44.98 3.25
4515 5570 1.066303 CTCAGTCAGATCGGCTGGTAC 59.934 57.143 15.72 0.00 44.98 3.34
4516 5571 0.103208 CAGTCAGATCGGCTGGTACC 59.897 60.000 4.43 4.43 44.98 3.34
4517 5572 0.324368 AGTCAGATCGGCTGGTACCA 60.324 55.000 15.39 15.39 44.98 3.25
4518 5573 0.535335 GTCAGATCGGCTGGTACCAA 59.465 55.000 17.11 0.39 44.98 3.67
4519 5574 0.535335 TCAGATCGGCTGGTACCAAC 59.465 55.000 17.11 11.85 44.98 3.77
4520 5575 0.249120 CAGATCGGCTGGTACCAACA 59.751 55.000 17.11 0.00 41.07 3.33
4521 5576 1.134401 CAGATCGGCTGGTACCAACAT 60.134 52.381 17.11 1.69 41.07 2.71
4522 5577 1.134401 AGATCGGCTGGTACCAACATG 60.134 52.381 17.11 8.18 0.00 3.21
4523 5578 0.748005 ATCGGCTGGTACCAACATGC 60.748 55.000 17.11 15.35 0.00 4.06
4524 5579 1.673993 CGGCTGGTACCAACATGCA 60.674 57.895 21.47 0.00 0.00 3.96
4525 5580 1.647545 CGGCTGGTACCAACATGCAG 61.648 60.000 21.47 15.50 0.00 4.41
4526 5581 1.315257 GGCTGGTACCAACATGCAGG 61.315 60.000 21.47 7.52 0.00 4.85
4527 5582 0.322456 GCTGGTACCAACATGCAGGA 60.322 55.000 17.11 0.00 0.00 3.86
4528 5583 1.886222 GCTGGTACCAACATGCAGGAA 60.886 52.381 17.11 0.00 0.00 3.36
4529 5584 2.086869 CTGGTACCAACATGCAGGAAG 58.913 52.381 17.11 0.00 0.00 3.46
4530 5585 1.702401 TGGTACCAACATGCAGGAAGA 59.298 47.619 13.60 0.00 0.00 2.87
4531 5586 2.308570 TGGTACCAACATGCAGGAAGAT 59.691 45.455 13.60 0.00 0.00 2.40
4532 5587 3.521531 TGGTACCAACATGCAGGAAGATA 59.478 43.478 13.60 0.00 0.00 1.98
4533 5588 4.165950 TGGTACCAACATGCAGGAAGATAT 59.834 41.667 13.60 0.00 0.00 1.63
4534 5589 5.133221 GGTACCAACATGCAGGAAGATATT 58.867 41.667 4.84 0.00 0.00 1.28
4535 5590 6.126623 TGGTACCAACATGCAGGAAGATATTA 60.127 38.462 13.60 0.00 0.00 0.98
4536 5591 6.942576 GGTACCAACATGCAGGAAGATATTAT 59.057 38.462 4.84 0.00 0.00 1.28
4537 5592 7.448469 GGTACCAACATGCAGGAAGATATTATT 59.552 37.037 4.84 0.00 0.00 1.40
4538 5593 7.516198 ACCAACATGCAGGAAGATATTATTC 57.484 36.000 4.84 0.00 0.00 1.75
4539 5594 7.062322 ACCAACATGCAGGAAGATATTATTCA 58.938 34.615 4.84 0.00 0.00 2.57
4540 5595 7.230108 ACCAACATGCAGGAAGATATTATTCAG 59.770 37.037 4.84 0.00 0.00 3.02
4541 5596 6.814506 ACATGCAGGAAGATATTATTCAGC 57.185 37.500 4.84 7.30 32.87 4.26
4542 5597 6.301486 ACATGCAGGAAGATATTATTCAGCA 58.699 36.000 4.84 16.17 40.81 4.41
4543 5598 6.946583 ACATGCAGGAAGATATTATTCAGCAT 59.053 34.615 4.84 18.00 44.07 3.79
4544 5599 6.812879 TGCAGGAAGATATTATTCAGCATG 57.187 37.500 12.67 0.00 35.60 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.947645 CTCTGATTAGAGGAGGCAAGAAG 58.052 47.826 6.61 0.00 45.47 2.85
221 222 8.674607 CCACTTTATAAAAACTAGATGACACCC 58.325 37.037 0.00 0.00 0.00 4.61
300 301 5.452216 GGTTTCTAAAATTTGGAACCCGTGT 60.452 40.000 3.98 0.00 29.37 4.49
349 350 6.028146 TCATCCAATTCCATGAAGTTTGTG 57.972 37.500 0.00 0.00 0.00 3.33
350 351 6.862469 ATCATCCAATTCCATGAAGTTTGT 57.138 33.333 0.00 0.00 32.76 2.83
526 529 3.508793 ACTAACTCCACGCACTAAGCTAA 59.491 43.478 0.00 0.00 42.61 3.09
565 574 1.301637 CACCATGCACGGTCTCACA 60.302 57.895 0.00 0.00 37.07 3.58
638 647 4.320870 CCTCACGGCCTAAACTTTTTCTA 58.679 43.478 0.00 0.00 0.00 2.10
694 703 0.840288 TAGCTTTGCCCTGTCTCCCA 60.840 55.000 0.00 0.00 0.00 4.37
703 712 1.607148 ACGACAAAACTAGCTTTGCCC 59.393 47.619 16.67 9.24 39.46 5.36
715 724 3.617706 ACGAATACACACACACGACAAAA 59.382 39.130 0.00 0.00 0.00 2.44
755 775 1.224069 CCTCACGTTGCCTCACACAG 61.224 60.000 0.00 0.00 0.00 3.66
897 917 4.635324 GCTGCTGCTTCTTCTTCTTCTAAT 59.365 41.667 8.53 0.00 36.03 1.73
1040 1104 2.671177 CGAAGTTGGCACTGCTCCG 61.671 63.158 0.00 0.00 31.60 4.63
1075 1139 0.328258 GCCACAAGTACCCACCATCT 59.672 55.000 0.00 0.00 0.00 2.90
1184 1248 3.695606 GTGCGGCAGTGAGGAGGA 61.696 66.667 1.18 0.00 0.00 3.71
1261 1325 3.695606 GCTGGAGCTGTCACCGGA 61.696 66.667 9.46 0.00 38.21 5.14
1262 1326 3.947132 CTGCTGGAGCTGTCACCGG 62.947 68.421 0.00 0.00 42.66 5.28
1263 1327 2.433838 CTGCTGGAGCTGTCACCG 60.434 66.667 0.00 0.00 42.66 4.94
1264 1328 2.745492 GCTGCTGGAGCTGTCACC 60.745 66.667 14.33 0.00 45.21 4.02
1412 1488 6.680810 TCCTTGATTCAACTTGCTAAACATG 58.319 36.000 0.00 0.00 0.00 3.21
1462 1538 5.251601 TCCCTTGGTTGTTAAAGAAAACG 57.748 39.130 0.00 0.00 31.76 3.60
1532 1613 4.348656 TGAATTTAGACGAACCGAGATCG 58.651 43.478 0.00 0.00 45.47 3.69
1572 1653 2.249413 CTGAGGATTCCAGCGCCAGT 62.249 60.000 2.29 0.00 0.00 4.00
1633 1714 5.608437 AGATATATGGACTGGTGTGTGGAAT 59.392 40.000 0.00 0.00 0.00 3.01
1698 1784 7.736893 AGCCGAGAAGTATTAAATATTCAGGT 58.263 34.615 0.00 0.00 0.00 4.00
1719 1812 1.804372 GCAAGGACATAGTGAGAGCCG 60.804 57.143 0.00 0.00 0.00 5.52
1721 1814 2.093764 AGTGCAAGGACATAGTGAGAGC 60.094 50.000 0.00 0.00 0.00 4.09
1722 1815 3.883830 AGTGCAAGGACATAGTGAGAG 57.116 47.619 0.00 0.00 0.00 3.20
1723 1816 5.939764 ATTAGTGCAAGGACATAGTGAGA 57.060 39.130 0.00 0.00 0.00 3.27
1724 1817 5.877012 ACAATTAGTGCAAGGACATAGTGAG 59.123 40.000 0.00 0.00 0.00 3.51
1725 1818 5.804639 ACAATTAGTGCAAGGACATAGTGA 58.195 37.500 0.00 0.00 0.00 3.41
1726 1819 5.643348 TGACAATTAGTGCAAGGACATAGTG 59.357 40.000 0.00 0.00 0.00 2.74
1727 1820 5.804639 TGACAATTAGTGCAAGGACATAGT 58.195 37.500 0.00 0.00 0.00 2.12
1803 1896 2.224523 ACCTGAAAACGAAGCTCCATCA 60.225 45.455 0.00 0.00 0.00 3.07
1815 1908 1.200020 CCTTCCGCATCACCTGAAAAC 59.800 52.381 0.00 0.00 0.00 2.43
1824 1917 0.674581 CTGCTTGACCTTCCGCATCA 60.675 55.000 0.00 0.00 0.00 3.07
1843 1936 5.633830 TCAGAATGCAGAAAAATCACCTC 57.366 39.130 0.00 0.00 34.76 3.85
1911 2004 3.201266 TGGTTCCATCCTACACCATTACC 59.799 47.826 0.00 0.00 34.23 2.85
2194 2911 2.414058 AAATCGTCGCAATGCACAAA 57.586 40.000 5.91 0.00 0.00 2.83
2196 2913 2.482336 ACTAAAATCGTCGCAATGCACA 59.518 40.909 5.91 0.00 0.00 4.57
2433 3183 8.093927 AGGCATGCTATTAAAGTTTTAAGCAAA 58.906 29.630 18.92 0.00 37.36 3.68
2527 3280 7.836842 TCTCAAGAGTTTTACAAAGCCTTTTT 58.163 30.769 0.00 0.00 0.00 1.94
2552 3308 2.692557 TGCACAACTAACCACTTGCAAT 59.307 40.909 0.00 0.00 37.05 3.56
2823 3597 2.551504 GCGGGGAAGAAACACTAGGAAA 60.552 50.000 0.00 0.00 0.00 3.13
3285 4106 0.679505 CCAAGAGACGTCAAGGACCA 59.320 55.000 19.50 0.00 0.00 4.02
4017 5072 6.433093 GGCAACCTAAGGAAAATAACTTCTCA 59.567 38.462 0.00 0.00 0.00 3.27
4461 5516 4.067192 GGCAGATTTGTTGGCAGATTTTT 58.933 39.130 0.00 0.00 40.50 1.94
4462 5517 3.071312 TGGCAGATTTGTTGGCAGATTTT 59.929 39.130 0.00 0.00 44.86 1.82
4463 5518 2.633967 TGGCAGATTTGTTGGCAGATTT 59.366 40.909 0.00 0.00 44.86 2.17
4464 5519 2.250031 TGGCAGATTTGTTGGCAGATT 58.750 42.857 0.00 0.00 44.86 2.40
4465 5520 1.927487 TGGCAGATTTGTTGGCAGAT 58.073 45.000 0.00 0.00 44.86 2.90
4466 5521 3.435846 TGGCAGATTTGTTGGCAGA 57.564 47.368 0.00 0.00 44.86 4.26
4469 5524 0.109597 CGTCTGGCAGATTTGTTGGC 60.110 55.000 21.84 3.88 41.12 4.52
4470 5525 1.522668 TCGTCTGGCAGATTTGTTGG 58.477 50.000 21.84 4.71 0.00 3.77
4471 5526 3.837213 ATTCGTCTGGCAGATTTGTTG 57.163 42.857 21.84 6.95 0.00 3.33
4472 5527 4.321230 GGAAATTCGTCTGGCAGATTTGTT 60.321 41.667 21.84 11.30 0.00 2.83
4473 5528 3.191371 GGAAATTCGTCTGGCAGATTTGT 59.809 43.478 21.84 5.07 0.00 2.83
4474 5529 3.441572 AGGAAATTCGTCTGGCAGATTTG 59.558 43.478 21.84 13.66 0.00 2.32
4475 5530 3.690460 AGGAAATTCGTCTGGCAGATTT 58.310 40.909 21.84 16.42 0.00 2.17
4476 5531 3.274288 GAGGAAATTCGTCTGGCAGATT 58.726 45.455 21.84 10.38 0.00 2.40
4477 5532 2.237143 TGAGGAAATTCGTCTGGCAGAT 59.763 45.455 21.84 2.59 32.87 2.90
4478 5533 1.623311 TGAGGAAATTCGTCTGGCAGA 59.377 47.619 14.43 14.43 32.87 4.26
4479 5534 2.005451 CTGAGGAAATTCGTCTGGCAG 58.995 52.381 8.58 8.58 32.87 4.85
4480 5535 1.347707 ACTGAGGAAATTCGTCTGGCA 59.652 47.619 20.78 0.00 35.46 4.92
4481 5536 2.003301 GACTGAGGAAATTCGTCTGGC 58.997 52.381 20.78 16.60 35.46 4.85
4482 5537 3.056536 TCTGACTGAGGAAATTCGTCTGG 60.057 47.826 20.78 13.97 35.46 3.86
4483 5538 4.179926 TCTGACTGAGGAAATTCGTCTG 57.820 45.455 17.05 17.05 36.64 3.51
4484 5539 4.439426 CGATCTGACTGAGGAAATTCGTCT 60.439 45.833 15.42 0.00 32.87 4.18
4485 5540 3.794028 CGATCTGACTGAGGAAATTCGTC 59.206 47.826 8.58 8.58 0.00 4.20
4486 5541 3.429547 CCGATCTGACTGAGGAAATTCGT 60.430 47.826 0.00 0.00 0.00 3.85
4487 5542 3.119291 CCGATCTGACTGAGGAAATTCG 58.881 50.000 0.00 0.00 0.00 3.34
4488 5543 2.869192 GCCGATCTGACTGAGGAAATTC 59.131 50.000 0.00 0.00 0.00 2.17
4489 5544 2.503356 AGCCGATCTGACTGAGGAAATT 59.497 45.455 0.00 0.00 0.00 1.82
4490 5545 2.114616 AGCCGATCTGACTGAGGAAAT 58.885 47.619 0.00 0.00 0.00 2.17
4491 5546 1.205655 CAGCCGATCTGACTGAGGAAA 59.794 52.381 1.42 0.00 45.72 3.13
4492 5547 0.820226 CAGCCGATCTGACTGAGGAA 59.180 55.000 1.42 0.00 45.72 3.36
4493 5548 1.039785 CCAGCCGATCTGACTGAGGA 61.040 60.000 7.77 0.00 45.72 3.71
4494 5549 1.326213 ACCAGCCGATCTGACTGAGG 61.326 60.000 7.77 0.00 45.72 3.86
4495 5550 1.066303 GTACCAGCCGATCTGACTGAG 59.934 57.143 7.77 2.42 45.72 3.35
4496 5551 1.103803 GTACCAGCCGATCTGACTGA 58.896 55.000 7.77 0.00 45.72 3.41
4497 5552 0.103208 GGTACCAGCCGATCTGACTG 59.897 60.000 7.15 0.00 45.72 3.51
4498 5553 0.324368 TGGTACCAGCCGATCTGACT 60.324 55.000 11.60 0.00 45.72 3.41
4499 5554 0.535335 TTGGTACCAGCCGATCTGAC 59.465 55.000 15.65 0.00 45.72 3.51
4500 5555 0.535335 GTTGGTACCAGCCGATCTGA 59.465 55.000 17.45 0.00 45.72 3.27
4501 5556 0.249120 TGTTGGTACCAGCCGATCTG 59.751 55.000 24.18 0.00 42.49 2.90
4502 5557 1.134401 CATGTTGGTACCAGCCGATCT 60.134 52.381 24.18 3.15 0.00 2.75
4503 5558 1.299541 CATGTTGGTACCAGCCGATC 58.700 55.000 24.18 8.77 0.00 3.69
4504 5559 0.748005 GCATGTTGGTACCAGCCGAT 60.748 55.000 24.18 10.61 0.00 4.18
4505 5560 1.376683 GCATGTTGGTACCAGCCGA 60.377 57.895 24.18 8.67 0.00 5.54
4506 5561 1.647545 CTGCATGTTGGTACCAGCCG 61.648 60.000 24.18 16.61 0.00 5.52
4507 5562 1.315257 CCTGCATGTTGGTACCAGCC 61.315 60.000 24.18 15.15 0.00 4.85
4508 5563 0.322456 TCCTGCATGTTGGTACCAGC 60.322 55.000 20.98 20.98 0.00 4.85
4509 5564 2.086869 CTTCCTGCATGTTGGTACCAG 58.913 52.381 15.65 4.48 0.00 4.00
4510 5565 1.702401 TCTTCCTGCATGTTGGTACCA 59.298 47.619 11.60 11.60 0.00 3.25
4511 5566 2.489938 TCTTCCTGCATGTTGGTACC 57.510 50.000 4.43 4.43 0.00 3.34
4512 5567 7.986085 ATAATATCTTCCTGCATGTTGGTAC 57.014 36.000 0.00 0.00 0.00 3.34
4513 5568 8.217111 TGAATAATATCTTCCTGCATGTTGGTA 58.783 33.333 0.00 0.00 0.00 3.25
4514 5569 7.062322 TGAATAATATCTTCCTGCATGTTGGT 58.938 34.615 0.00 0.00 0.00 3.67
4515 5570 7.514784 TGAATAATATCTTCCTGCATGTTGG 57.485 36.000 0.00 0.00 0.00 3.77
4516 5571 7.082602 GCTGAATAATATCTTCCTGCATGTTG 58.917 38.462 0.00 0.00 0.00 3.33
4517 5572 6.774170 TGCTGAATAATATCTTCCTGCATGTT 59.226 34.615 0.00 0.00 31.13 2.71
4518 5573 6.301486 TGCTGAATAATATCTTCCTGCATGT 58.699 36.000 0.00 0.00 31.13 3.21
4519 5574 6.812879 TGCTGAATAATATCTTCCTGCATG 57.187 37.500 0.00 0.00 31.13 4.06
4520 5575 7.173032 TCATGCTGAATAATATCTTCCTGCAT 58.827 34.615 15.13 15.13 39.80 3.96
4521 5576 6.536447 TCATGCTGAATAATATCTTCCTGCA 58.464 36.000 13.14 13.14 36.37 4.41


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

AutoCloner maintained by Alex Coulton.