Multiple sequence alignment - TraesCS4B01G009000

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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 TraesCS4B01G009000 chr4B 100.000 4421 0 0 1 4421 5782833 5778413 0.000000e+00 8165.0
1 TraesCS4B01G009000 chr4B 77.011 174 30 5 1563 1727 616970778 616970950 1.690000e-14 91.6
2 TraesCS4B01G009000 chrUn 93.485 3607 154 40 853 4419 60989212 60985647 0.000000e+00 5284.0
3 TraesCS4B01G009000 chrUn 83.159 861 75 20 2 828 60990028 60989204 0.000000e+00 723.0
4 TraesCS4B01G009000 chr4A 94.645 915 37 7 1747 2651 601248032 601247120 0.000000e+00 1408.0
5 TraesCS4B01G009000 chr4A 95.460 815 28 4 2649 3460 601243822 601243014 0.000000e+00 1291.0
6 TraesCS4B01G009000 chr4A 86.744 694 51 21 842 1523 601248687 601248023 0.000000e+00 734.0
7 TraesCS4B01G009000 chr4A 82.512 852 84 31 2 819 601249691 601248871 0.000000e+00 688.0
8 TraesCS4B01G009000 chr4A 80.755 265 37 10 234 490 601250850 601250592 1.250000e-45 195.0
9 TraesCS4B01G009000 chr4A 91.803 122 10 0 3644 3765 601242981 601242860 2.110000e-38 171.0
10 TraesCS4B01G009000 chr5A 79.885 1044 157 26 2674 3689 601432589 601433607 0.000000e+00 715.0
11 TraesCS4B01G009000 chr5A 82.255 479 69 9 1921 2398 601432041 601432504 2.480000e-107 399.0
12 TraesCS4B01G009000 chr5A 85.841 226 28 3 2738 2960 601458254 601458478 2.060000e-58 237.0
13 TraesCS4B01G009000 chr5A 78.788 264 44 7 1267 1527 601431624 601431878 2.740000e-37 167.0
14 TraesCS4B01G009000 chr5A 78.603 229 26 16 920 1136 601430908 601431125 3.590000e-26 130.0
15 TraesCS4B01G009000 chr5A 84.091 88 13 1 1639 1725 565500402 565500315 2.830000e-12 84.2
16 TraesCS4B01G009000 chr5D 81.291 914 134 21 2674 3563 481812344 481813244 0.000000e+00 706.0
17 TraesCS4B01G009000 chr5D 80.153 262 42 4 1267 1527 481811379 481811631 2.100000e-43 187.0
18 TraesCS4B01G009000 chr5D 76.174 298 42 21 920 1201 481810680 481810964 3.590000e-26 130.0
19 TraesCS4B01G009000 chr5B 80.744 914 139 20 2677 3564 591108273 591109175 0.000000e+00 678.0
20 TraesCS4B01G009000 chr5B 82.952 481 62 14 1921 2398 591107722 591108185 2.460000e-112 416.0
21 TraesCS4B01G009000 chr5B 78.244 262 47 6 1267 1527 591107307 591107559 4.580000e-35 159.0
22 TraesCS4B01G009000 chr5B 80.645 186 19 9 962 1136 591106602 591106781 1.290000e-25 128.0
23 TraesCS4B01G009000 chr3A 83.140 172 22 3 1563 1727 728745536 728745707 2.750000e-32 150.0
24 TraesCS4B01G009000 chr3A 94.872 39 2 0 1563 1601 509862789 509862827 1.330000e-05 62.1
25 TraesCS4B01G009000 chr6B 83.133 166 25 1 1563 1725 151294679 151294514 9.910000e-32 148.0
26 TraesCS4B01G009000 chr7B 82.659 173 21 8 1563 1727 66880292 66880121 1.280000e-30 145.0
27 TraesCS4B01G009000 chr7B 78.404 213 36 6 1317 1528 630108855 630108652 3.590000e-26 130.0
28 TraesCS4B01G009000 chr2A 77.273 264 48 8 1267 1528 21730917 21730664 1.280000e-30 145.0
29 TraesCS4B01G009000 chr2A 77.457 173 31 2 1563 1727 165010965 165011137 3.640000e-16 97.1
30 TraesCS4B01G009000 chr2A 74.153 236 50 10 4112 4343 743114865 743115093 2.190000e-13 87.9
31 TraesCS4B01G009000 chr3D 80.925 173 25 5 1563 1727 558285124 558284952 3.590000e-26 130.0
32 TraesCS4B01G009000 chr1B 76.046 263 53 6 1267 1528 519300889 519301142 1.290000e-25 128.0
33 TraesCS4B01G009000 chr3B 93.333 45 3 0 1683 1727 109380387 109380431 2.850000e-07 67.6


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 TraesCS4B01G009000 chr4B 5778413 5782833 4420 True 8165.000000 8165 100.000000 1 4421 1 chr4B.!!$R1 4420
1 TraesCS4B01G009000 chrUn 60985647 60990028 4381 True 3003.500000 5284 88.322000 2 4419 2 chrUn.!!$R1 4417
2 TraesCS4B01G009000 chr4A 601242860 601250850 7990 True 747.833333 1408 88.653167 2 3765 6 chr4A.!!$R1 3763
3 TraesCS4B01G009000 chr5A 601430908 601433607 2699 False 352.750000 715 79.882750 920 3689 4 chr5A.!!$F2 2769
4 TraesCS4B01G009000 chr5D 481810680 481813244 2564 False 341.000000 706 79.206000 920 3563 3 chr5D.!!$F1 2643
5 TraesCS4B01G009000 chr5B 591106602 591109175 2573 False 345.250000 678 80.646250 962 3564 4 chr5B.!!$F1 2602

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
743 1941 0.036388 TTTCCCAGAGATGGCACGAC 60.036 55.0 0.00 0.00 0.00 4.34 F
1081 2465 0.320374 CCACTTTCGCCACCTAGACA 59.680 55.0 0.00 0.00 0.00 3.41 F
1389 3177 0.605860 AGCTCAAGGTGCAGCTTCTG 60.606 55.0 27.52 21.89 43.80 3.02 F
1669 3474 1.157870 AGTGGCACAACCGACGAAAG 61.158 55.0 21.41 0.00 44.16 2.62 F
3221 8399 0.995024 AGGGACAGAATCAGGTTGGG 59.005 55.0 0.00 0.00 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1709 3514 1.535462 CAGACAACCGGTTTGGATGAC 59.465 52.381 19.55 7.37 42.97 3.06 R
1992 3815 3.565902 GCTTGTAGTAGGGCAATTGATCC 59.434 47.826 10.34 9.80 0.00 3.36 R
3100 8266 0.468214 TGCCCGGAACACATTTTGGA 60.468 50.000 0.73 0.00 0.00 3.53 R
3342 8520 2.560105 GGAGCCTTTTTCTTGATGCTGT 59.440 45.455 0.00 0.00 0.00 4.40 R
4259 9445 0.241213 TTCGTGAGTTCAGGAGCTCG 59.759 55.000 7.83 0.00 40.91 5.03 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
27 1186 5.982391 AGTAATCTAGATGGGATCCTCCAA 58.018 41.667 12.58 0.00 40.62 3.53
34 1193 4.801164 AGATGGGATCCTCCAAAGATTTG 58.199 43.478 12.58 0.00 40.62 2.32
91 1250 6.402222 GCATGTTTATTCCCAAATGTAACCA 58.598 36.000 0.00 0.00 0.00 3.67
131 1290 3.257624 GGTATCCCGGGTGTCTATACAAG 59.742 52.174 22.86 0.00 37.36 3.16
133 1292 0.106149 CCCGGGTGTCTATACAAGCC 59.894 60.000 14.18 0.00 37.36 4.35
135 1294 1.208535 CCGGGTGTCTATACAAGCCAA 59.791 52.381 0.00 0.00 37.36 4.52
167 1330 4.082665 CCACAGAGGTAGATTCATGCAT 57.917 45.455 0.00 0.00 0.00 3.96
195 1358 6.287589 ACAATCTCGAGTTAGATCAACCTT 57.712 37.500 13.13 0.00 37.93 3.50
196 1359 7.406031 ACAATCTCGAGTTAGATCAACCTTA 57.594 36.000 13.13 0.00 37.93 2.69
198 1361 7.976734 ACAATCTCGAGTTAGATCAACCTTAAG 59.023 37.037 13.13 0.00 37.93 1.85
206 1369 7.536855 AGTTAGATCAACCTTAAGTCTGTACG 58.463 38.462 0.97 0.00 37.93 3.67
218 1381 1.665679 GTCTGTACGCCATCCACAATG 59.334 52.381 0.00 0.00 34.93 2.82
224 1387 2.098614 ACGCCATCCACAATGCAATAA 58.901 42.857 0.00 0.00 33.71 1.40
227 1390 4.121317 CGCCATCCACAATGCAATAAAAT 58.879 39.130 0.00 0.00 33.71 1.82
228 1391 5.163468 ACGCCATCCACAATGCAATAAAATA 60.163 36.000 0.00 0.00 33.71 1.40
229 1392 5.175491 CGCCATCCACAATGCAATAAAATAC 59.825 40.000 0.00 0.00 33.71 1.89
230 1393 6.047870 GCCATCCACAATGCAATAAAATACA 58.952 36.000 0.00 0.00 33.71 2.29
232 1395 7.227116 GCCATCCACAATGCAATAAAATACAAT 59.773 33.333 0.00 0.00 33.71 2.71
251 1414 6.575162 ACAATACATCCTTTTGAACAGTCC 57.425 37.500 0.00 0.00 0.00 3.85
266 1432 0.320421 AGTCCGGTGAACGTTCATGG 60.320 55.000 31.35 31.35 42.24 3.66
268 1434 0.967662 TCCGGTGAACGTTCATGGTA 59.032 50.000 33.38 23.87 42.24 3.25
274 1440 3.927142 GGTGAACGTTCATGGTAGAGAAG 59.073 47.826 31.81 0.00 39.73 2.85
282 1448 8.289939 ACGTTCATGGTAGAGAAGTTCTAATA 57.710 34.615 5.09 0.00 40.04 0.98
343 1509 8.182227 ACTACTAAACTTGCAGTCAAAAGAAAC 58.818 33.333 0.00 0.00 0.00 2.78
373 1539 9.778993 CCATCTTACTGAATGTTAATCAACTTG 57.221 33.333 0.00 0.00 35.56 3.16
379 1545 8.281212 ACTGAATGTTAATCAACTTGGTATCC 57.719 34.615 0.00 0.00 35.56 2.59
430 1614 4.555709 ACAGGCCGGTGAACGCAA 62.556 61.111 8.08 0.00 42.52 4.85
442 1626 3.129638 GGTGAACGCAAGGGCATATTTTA 59.870 43.478 0.00 0.00 46.39 1.52
444 1628 5.009210 GGTGAACGCAAGGGCATATTTTATA 59.991 40.000 0.00 0.00 46.39 0.98
445 1629 6.142817 GTGAACGCAAGGGCATATTTTATAG 58.857 40.000 0.00 0.00 46.39 1.31
446 1630 5.825679 TGAACGCAAGGGCATATTTTATAGT 59.174 36.000 0.00 0.00 46.39 2.12
447 1631 5.941948 ACGCAAGGGCATATTTTATAGTC 57.058 39.130 0.00 0.00 46.39 2.59
448 1632 5.621193 ACGCAAGGGCATATTTTATAGTCT 58.379 37.500 0.00 0.00 46.39 3.24
449 1633 5.701290 ACGCAAGGGCATATTTTATAGTCTC 59.299 40.000 0.00 0.00 46.39 3.36
477 1661 6.731919 TCTCAACTATTAAAGGGGAGTTGGTA 59.268 38.462 12.30 0.86 45.70 3.25
490 1674 3.120095 GGAGTTGGTAATTGTACGTTGGC 60.120 47.826 0.00 0.00 0.00 4.52
491 1675 2.481185 AGTTGGTAATTGTACGTTGGCG 59.519 45.455 0.00 0.00 44.93 5.69
492 1676 0.797542 TGGTAATTGTACGTTGGCGC 59.202 50.000 0.00 0.00 42.83 6.53
494 1678 0.247379 GTAATTGTACGTTGGCGCGG 60.247 55.000 8.83 0.00 42.83 6.46
495 1679 1.360194 TAATTGTACGTTGGCGCGGG 61.360 55.000 8.83 0.00 42.83 6.13
594 1790 2.489329 CGTGAAGCCTTGACCATTGAAT 59.511 45.455 0.00 0.00 0.00 2.57
641 1839 5.809562 AGTGAAAGAATAACTCTGCAGATCG 59.190 40.000 18.63 9.30 33.37 3.69
657 1855 5.643348 TGCAGATCGATAAGCTTTTCAGAAA 59.357 36.000 18.75 0.00 0.00 2.52
722 1920 0.388907 CCGAACAAGGGCATGCTTTG 60.389 55.000 24.27 24.27 0.00 2.77
733 1931 2.649331 CATGCTTTGCTTTCCCAGAG 57.351 50.000 0.00 0.00 0.00 3.35
735 1933 2.592102 TGCTTTGCTTTCCCAGAGAT 57.408 45.000 0.00 0.00 0.00 2.75
736 1934 2.165167 TGCTTTGCTTTCCCAGAGATG 58.835 47.619 0.00 0.00 0.00 2.90
737 1935 1.475682 GCTTTGCTTTCCCAGAGATGG 59.524 52.381 0.00 0.00 0.00 3.51
743 1941 0.036388 TTTCCCAGAGATGGCACGAC 60.036 55.000 0.00 0.00 0.00 4.34
770 1968 2.095567 GCAGTGCCAAGAACAGTACATG 60.096 50.000 2.85 0.00 0.00 3.21
774 1972 5.048504 CAGTGCCAAGAACAGTACATGAATT 60.049 40.000 0.00 0.00 0.00 2.17
776 1974 5.048782 GTGCCAAGAACAGTACATGAATTGA 60.049 40.000 0.00 0.00 0.00 2.57
783 1981 3.190535 ACAGTACATGAATTGAAACGCCC 59.809 43.478 0.00 0.00 0.00 6.13
809 2007 2.037641 GCCACAAGATCCAAAAGGCTTT 59.962 45.455 6.68 6.68 37.67 3.51
823 2021 4.362476 CTTTGCGCCAAGGCACCC 62.362 66.667 13.21 0.00 43.82 4.61
839 2037 2.125269 CCCGGCCCGACTACAAAG 60.125 66.667 3.71 0.00 0.00 2.77
840 2038 2.818274 CCGGCCCGACTACAAAGC 60.818 66.667 3.71 0.00 0.00 3.51
846 2212 1.625616 CCCGACTACAAAGCAGTACG 58.374 55.000 0.00 0.00 0.00 3.67
879 2245 0.521659 CGACGAAGACTCCGAAGCTC 60.522 60.000 0.00 0.00 0.00 4.09
885 2251 0.894184 AGACTCCGAAGCTCGAACCA 60.894 55.000 7.07 0.00 43.74 3.67
886 2252 0.733223 GACTCCGAAGCTCGAACCAC 60.733 60.000 7.07 0.00 43.74 4.16
926 2298 3.744719 CTCCCGTCAACGCGAGGA 61.745 66.667 15.93 6.77 39.74 3.71
1053 2437 1.306997 CCTGGGCCTCCACTTCCTA 60.307 63.158 4.53 0.00 38.32 2.94
1056 2440 1.615424 GGGCCTCCACTTCCTACCA 60.615 63.158 0.84 0.00 0.00 3.25
1068 2452 0.770557 TCCTACCAGCCACCCACTTT 60.771 55.000 0.00 0.00 0.00 2.66
1076 2460 2.113139 CACCCACTTTCGCCACCT 59.887 61.111 0.00 0.00 0.00 4.00
1079 2463 0.834687 ACCCACTTTCGCCACCTAGA 60.835 55.000 0.00 0.00 0.00 2.43
1081 2465 0.320374 CCACTTTCGCCACCTAGACA 59.680 55.000 0.00 0.00 0.00 3.41
1092 2476 2.786495 CCTAGACAGCCGCGACCAT 61.786 63.158 8.23 0.00 0.00 3.55
1116 2509 1.930656 CACCTGGGTCCCCTTGGAT 60.931 63.158 17.72 4.14 44.28 3.41
1123 2516 1.689582 GTCCCCTTGGATCCCTCGT 60.690 63.158 9.90 0.00 44.28 4.18
1156 2552 3.402681 AGGTACTGCTGCCGCCAT 61.403 61.111 0.00 0.00 37.18 4.40
1167 2563 4.160635 CCGCCATGTTTCGCCGTC 62.161 66.667 0.00 0.00 0.00 4.79
1170 2566 3.496131 CCATGTTTCGCCGTCCCG 61.496 66.667 0.00 0.00 0.00 5.14
1171 2567 2.740826 CATGTTTCGCCGTCCCGT 60.741 61.111 0.00 0.00 0.00 5.28
1173 2569 2.939261 ATGTTTCGCCGTCCCGTCT 61.939 57.895 0.00 0.00 0.00 4.18
1174 2570 3.110178 GTTTCGCCGTCCCGTCTG 61.110 66.667 0.00 0.00 0.00 3.51
1190 2590 3.740495 CTGGCTCCCCGGCTCTCTA 62.740 68.421 0.00 0.00 39.32 2.43
1290 3078 2.060980 AGGATCTGTCCCACGAGGC 61.061 63.158 0.00 0.00 46.34 4.70
1297 3085 1.448013 GTCCCACGAGGCTACAAGC 60.448 63.158 0.00 0.00 41.46 4.01
1389 3177 0.605860 AGCTCAAGGTGCAGCTTCTG 60.606 55.000 27.52 21.89 43.80 3.02
1470 3262 9.787435 ACACAATTCAACCTTAACTACAGAATA 57.213 29.630 0.00 0.00 0.00 1.75
1571 3376 1.890979 CCTCCGACCTGATGCATGC 60.891 63.158 11.82 11.82 0.00 4.06
1627 3432 4.065088 TGTAATCCAGAACAAGCTCACAC 58.935 43.478 0.00 0.00 0.00 3.82
1669 3474 1.157870 AGTGGCACAACCGACGAAAG 61.158 55.000 21.41 0.00 44.16 2.62
1675 3480 6.827336 TGGCACAACCGACGAAAGTAGAAT 62.827 45.833 0.00 0.00 43.04 2.40
1691 3496 8.958119 AAAGTAGAATGAGTTGACTAAACACA 57.042 30.769 0.00 0.00 42.47 3.72
1709 3514 5.723672 ACACATATCCTATTACTGGACCG 57.276 43.478 0.00 0.00 36.30 4.79
1904 3726 3.630312 TCCAAGTACTTTTTGAGTGGTGC 59.370 43.478 5.07 0.00 39.48 5.01
1914 3736 4.584638 TTTGAGTGGTGCCTTATATGGT 57.415 40.909 6.53 0.00 0.00 3.55
2024 3847 4.273724 GCCCTACTACAAGCTAAAATCAGC 59.726 45.833 0.00 0.00 42.12 4.26
2050 3873 9.113838 CACTACCAGCTGATTCAAATATTACTT 57.886 33.333 17.39 0.00 0.00 2.24
2099 3923 8.496707 AAATGCTCATTTATTGTTGGAATTCC 57.503 30.769 18.17 18.17 39.08 3.01
2100 3924 6.602410 TGCTCATTTATTGTTGGAATTCCA 57.398 33.333 23.63 23.63 45.94 3.53
2156 3980 4.941263 AGCAAATCACGGACAAGCTAAATA 59.059 37.500 0.00 0.00 0.00 1.40
2441 4277 5.946972 AGCTGTCATAGTGAGTAGTAACTGT 59.053 40.000 0.00 0.00 35.56 3.55
2558 4395 9.650371 GAAAATTTTCCAGTCTTTAATTTGCAC 57.350 29.630 18.43 0.00 31.06 4.57
2576 4413 4.580868 TGCACGAAACAGATTTACCCATA 58.419 39.130 0.00 0.00 0.00 2.74
3100 8266 5.105310 ACGTAGCTAATCAAAGGTCAGTGAT 60.105 40.000 0.00 0.00 36.00 3.06
3122 8288 1.864082 CAAAATGTGTTCCGGGCAAAC 59.136 47.619 0.00 0.00 0.00 2.93
3147 8313 8.267183 ACATATCCATCATCCGCATAAATTAGA 58.733 33.333 0.00 0.00 0.00 2.10
3221 8399 0.995024 AGGGACAGAATCAGGTTGGG 59.005 55.000 0.00 0.00 0.00 4.12
3342 8520 2.037121 TGTTTGCTCTGAAGATGACGGA 59.963 45.455 0.00 0.00 0.00 4.69
3567 8749 4.627035 TGCACATACAAGTGAAAGATCTCG 59.373 41.667 0.00 0.00 42.05 4.04
3603 8785 3.242381 GCTTGTGTGTGTTTTCCAAATGC 60.242 43.478 0.00 0.00 0.00 3.56
3746 8930 7.148705 CGAAATGTTGAATCAAATGTGCATTCT 60.149 33.333 0.00 0.00 0.00 2.40
3766 8950 5.252969 TCTGCACAGGAAATATTGCATTC 57.747 39.130 0.00 0.00 43.74 2.67
3820 9004 0.326238 AGGGCATCCGGTTTAGGAGA 60.326 55.000 0.00 0.00 44.55 3.71
3828 9012 1.502231 CGGTTTAGGAGATGATGGCG 58.498 55.000 0.00 0.00 0.00 5.69
3855 9039 1.375908 GCCCGCACAATCTGTCTCA 60.376 57.895 0.00 0.00 0.00 3.27
3869 9053 0.107703 GTCTCATGGGATGGCACGAA 60.108 55.000 0.00 0.00 0.00 3.85
3876 9060 1.595093 GGGATGGCACGAACCCAAAG 61.595 60.000 13.51 0.00 41.72 2.77
3886 9070 1.228154 AACCCAAAGGACCGCTGTC 60.228 57.895 0.00 0.00 40.98 3.51
3907 9091 1.228003 TGGTTCACATCGGCCGTTT 60.228 52.632 27.15 11.61 0.00 3.60
4180 9366 0.974383 AGGGACGAAACGAAGGTCAT 59.026 50.000 0.00 0.00 32.39 3.06
4183 9369 1.993370 GGACGAAACGAAGGTCATCAG 59.007 52.381 0.00 0.00 32.39 2.90
4215 9401 3.682292 GACATGGCGTCCAGTCCCC 62.682 68.421 0.00 0.00 38.85 4.81
4235 9421 7.510343 AGTCCCCAAATATATAAAGCATGCTTT 59.490 33.333 39.21 39.21 46.56 3.51
4259 9445 8.581057 TTGCTAGATTATGAGTCTCGAAATTC 57.419 34.615 0.00 0.00 0.00 2.17
4276 9462 0.241213 TTCGAGCTCCTGAACTCACG 59.759 55.000 8.47 0.00 32.98 4.35
4280 9466 1.000163 GAGCTCCTGAACTCACGAACA 60.000 52.381 0.87 0.00 32.98 3.18
4310 9496 5.049405 ACACAGAGTAAAAGCACTACAATGC 60.049 40.000 0.00 0.00 46.50 3.56
4405 9591 5.133941 ACAGTATGAGACGACATGTATCCT 58.866 41.667 0.00 0.00 38.04 3.24
4419 9605 6.893583 ACATGTATCCTTCTGCAGTTTAGAT 58.106 36.000 14.67 13.70 0.00 1.98
4420 9606 6.989169 ACATGTATCCTTCTGCAGTTTAGATC 59.011 38.462 14.67 7.23 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 1177 3.009723 TGCGACAAATCTTTGGAGGATC 58.990 45.455 7.51 0.00 42.34 3.36
22 1181 2.549754 AGTGTGCGACAAATCTTTGGAG 59.450 45.455 7.51 2.35 42.34 3.86
27 1186 2.254546 TGGAGTGTGCGACAAATCTT 57.745 45.000 0.00 0.00 0.00 2.40
34 1193 2.280797 TGCCTTGGAGTGTGCGAC 60.281 61.111 0.00 0.00 0.00 5.19
62 1221 5.012975 ACATTTGGGAATAAACATGCCAAGT 59.987 36.000 0.00 0.00 46.88 3.16
65 1224 6.402222 GTTACATTTGGGAATAAACATGCCA 58.598 36.000 0.00 0.00 36.40 4.92
109 1268 3.233507 TTGTATAGACACCCGGGATACC 58.766 50.000 32.02 13.17 45.48 2.73
113 1272 1.117150 GCTTGTATAGACACCCGGGA 58.883 55.000 32.02 3.67 34.48 5.14
117 1276 2.421529 CCCTTGGCTTGTATAGACACCC 60.422 54.545 0.00 0.00 43.26 4.61
133 1292 0.397941 TCTGTGGTCTGAAGCCCTTG 59.602 55.000 0.00 0.00 0.00 3.61
135 1294 1.197430 CCTCTGTGGTCTGAAGCCCT 61.197 60.000 0.00 0.00 0.00 5.19
145 1308 9.056164 ATGTATGCATGAATCTACCTCTGTGGT 62.056 40.741 10.16 6.64 42.33 4.16
146 1309 3.548745 TGCATGAATCTACCTCTGTGG 57.451 47.619 0.00 0.00 42.93 4.17
147 1310 5.604565 TGTATGCATGAATCTACCTCTGTG 58.395 41.667 10.16 0.00 0.00 3.66
148 1311 5.876651 TGTATGCATGAATCTACCTCTGT 57.123 39.130 10.16 0.00 0.00 3.41
149 1312 7.381323 TGTATGTATGCATGAATCTACCTCTG 58.619 38.462 10.16 0.00 36.58 3.35
164 1327 8.023706 TGATCTAACTCGAGATTGTATGTATGC 58.976 37.037 21.68 0.00 36.27 3.14
167 1330 8.350722 GGTTGATCTAACTCGAGATTGTATGTA 58.649 37.037 21.68 0.00 36.27 2.29
195 1358 2.172679 TGTGGATGGCGTACAGACTTA 58.827 47.619 0.00 0.00 0.00 2.24
196 1359 0.973632 TGTGGATGGCGTACAGACTT 59.026 50.000 0.00 0.00 0.00 3.01
198 1361 1.665679 CATTGTGGATGGCGTACAGAC 59.334 52.381 0.00 0.00 31.83 3.51
206 1369 6.047870 TGTATTTTATTGCATTGTGGATGGC 58.952 36.000 0.00 0.00 36.21 4.40
227 1390 6.370442 CGGACTGTTCAAAAGGATGTATTGTA 59.630 38.462 0.00 0.00 0.00 2.41
228 1391 5.181245 CGGACTGTTCAAAAGGATGTATTGT 59.819 40.000 0.00 0.00 0.00 2.71
229 1392 5.391950 CCGGACTGTTCAAAAGGATGTATTG 60.392 44.000 0.00 0.00 0.00 1.90
230 1393 4.700213 CCGGACTGTTCAAAAGGATGTATT 59.300 41.667 0.00 0.00 0.00 1.89
232 1395 3.071892 ACCGGACTGTTCAAAAGGATGTA 59.928 43.478 9.46 0.00 0.00 2.29
234 1397 2.226437 CACCGGACTGTTCAAAAGGATG 59.774 50.000 9.46 0.00 0.00 3.51
235 1398 2.105821 TCACCGGACTGTTCAAAAGGAT 59.894 45.455 9.46 0.00 0.00 3.24
236 1399 1.487142 TCACCGGACTGTTCAAAAGGA 59.513 47.619 9.46 0.00 0.00 3.36
237 1400 1.961793 TCACCGGACTGTTCAAAAGG 58.038 50.000 9.46 0.00 0.00 3.11
238 1401 2.286184 CGTTCACCGGACTGTTCAAAAG 60.286 50.000 9.46 0.00 0.00 2.27
239 1402 1.666700 CGTTCACCGGACTGTTCAAAA 59.333 47.619 9.46 0.00 0.00 2.44
240 1403 1.292061 CGTTCACCGGACTGTTCAAA 58.708 50.000 9.46 0.00 0.00 2.69
241 1404 0.176219 ACGTTCACCGGACTGTTCAA 59.824 50.000 9.46 0.00 42.24 2.69
242 1405 0.176219 AACGTTCACCGGACTGTTCA 59.824 50.000 9.46 0.00 42.24 3.18
243 1406 0.857287 GAACGTTCACCGGACTGTTC 59.143 55.000 23.12 10.99 42.24 3.18
244 1407 0.176219 TGAACGTTCACCGGACTGTT 59.824 50.000 26.53 5.15 42.24 3.16
245 1408 0.391597 ATGAACGTTCACCGGACTGT 59.608 50.000 31.87 11.87 40.49 3.55
246 1409 0.790207 CATGAACGTTCACCGGACTG 59.210 55.000 31.87 20.83 40.49 3.51
247 1410 0.320421 CCATGAACGTTCACCGGACT 60.320 55.000 31.24 16.14 40.49 3.85
248 1411 0.601841 ACCATGAACGTTCACCGGAC 60.602 55.000 36.99 13.24 40.49 4.79
249 1412 0.967662 TACCATGAACGTTCACCGGA 59.032 50.000 36.99 24.45 40.49 5.14
250 1413 1.067425 TCTACCATGAACGTTCACCGG 60.067 52.381 32.21 32.21 40.49 5.28
251 1414 2.094906 TCTCTACCATGAACGTTCACCG 60.095 50.000 31.87 24.89 40.49 4.94
331 1497 3.214328 AGATGGCACGTTTCTTTTGACT 58.786 40.909 0.00 0.00 0.00 3.41
343 1509 5.794687 TTAACATTCAGTAAGATGGCACG 57.205 39.130 0.00 0.00 0.00 5.34
430 1614 8.884323 TGAGATTGAGACTATAAAATATGCCCT 58.116 33.333 0.00 0.00 0.00 5.19
444 1628 7.403231 TCCCCTTTAATAGTTGAGATTGAGACT 59.597 37.037 0.00 0.00 0.00 3.24
445 1629 7.565680 TCCCCTTTAATAGTTGAGATTGAGAC 58.434 38.462 0.00 0.00 0.00 3.36
446 1630 7.403231 ACTCCCCTTTAATAGTTGAGATTGAGA 59.597 37.037 0.00 0.00 0.00 3.27
447 1631 7.569240 ACTCCCCTTTAATAGTTGAGATTGAG 58.431 38.462 0.00 0.00 0.00 3.02
448 1632 7.510675 ACTCCCCTTTAATAGTTGAGATTGA 57.489 36.000 0.00 0.00 0.00 2.57
477 1661 2.682876 CCCGCGCCAACGTACAATT 61.683 57.895 0.00 0.00 42.83 2.32
494 1678 0.039618 TTTCATCAAGGGAGGTGGCC 59.960 55.000 0.00 0.00 0.00 5.36
495 1679 1.923356 TTTTCATCAAGGGAGGTGGC 58.077 50.000 0.00 0.00 0.00 5.01
703 1901 0.388907 CAAAGCATGCCCTTGTTCGG 60.389 55.000 15.66 0.00 0.00 4.30
722 1920 1.372087 CGTGCCATCTCTGGGAAAGC 61.372 60.000 0.00 0.00 45.45 3.51
724 1922 0.036388 GTCGTGCCATCTCTGGGAAA 60.036 55.000 0.00 0.00 45.45 3.13
726 1924 2.710902 CGTCGTGCCATCTCTGGGA 61.711 63.158 0.00 0.00 43.36 4.37
727 1925 2.202797 CGTCGTGCCATCTCTGGG 60.203 66.667 0.00 0.00 43.36 4.45
728 1926 2.887568 GCGTCGTGCCATCTCTGG 60.888 66.667 0.00 0.00 46.17 3.86
770 1968 0.588980 GCGATCGGGCGTTTCAATTC 60.589 55.000 18.30 0.00 0.00 2.17
774 1972 4.380781 TGGCGATCGGGCGTTTCA 62.381 61.111 18.30 0.00 46.04 2.69
776 1974 4.690719 TGTGGCGATCGGGCGTTT 62.691 61.111 18.30 0.00 46.04 3.60
783 1981 1.368641 TTTGGATCTTGTGGCGATCG 58.631 50.000 11.69 11.69 38.49 3.69
821 2019 3.675619 CTTTGTAGTCGGGCCGGGG 62.676 68.421 27.98 0.00 0.00 5.73
822 2020 2.125269 CTTTGTAGTCGGGCCGGG 60.125 66.667 27.98 0.00 0.00 5.73
823 2021 2.818274 GCTTTGTAGTCGGGCCGG 60.818 66.667 27.98 8.25 0.00 6.13
824 2022 2.047655 TGCTTTGTAGTCGGGCCG 60.048 61.111 22.51 22.51 0.00 6.13
831 2029 4.746611 GGTTTGTACGTACTGCTTTGTAGT 59.253 41.667 25.12 0.00 32.46 2.73
839 2037 0.785979 CGTGGGTTTGTACGTACTGC 59.214 55.000 25.12 14.76 35.70 4.40
840 2038 1.421382 CCGTGGGTTTGTACGTACTG 58.579 55.000 25.12 6.16 38.56 2.74
846 2212 2.660612 CGTCGCCGTGGGTTTGTAC 61.661 63.158 0.00 0.00 0.00 2.90
873 2239 2.100605 ATGGAAGTGGTTCGAGCTTC 57.899 50.000 0.00 5.99 38.22 3.86
879 2245 1.165270 GTGGGAATGGAAGTGGTTCG 58.835 55.000 0.00 0.00 32.92 3.95
885 2251 1.378762 CGGTGGTGGGAATGGAAGT 59.621 57.895 0.00 0.00 0.00 3.01
886 2252 2.046285 GCGGTGGTGGGAATGGAAG 61.046 63.158 0.00 0.00 0.00 3.46
953 2325 2.509336 ATGACGCGCTTTCCTCCG 60.509 61.111 5.73 0.00 0.00 4.63
956 2329 1.741770 GTGGATGACGCGCTTTCCT 60.742 57.895 18.81 0.00 0.00 3.36
957 2330 1.741770 AGTGGATGACGCGCTTTCC 60.742 57.895 5.73 10.62 33.90 3.13
958 2331 1.421485 CAGTGGATGACGCGCTTTC 59.579 57.895 5.73 1.81 33.90 2.62
959 2332 2.680913 GCAGTGGATGACGCGCTTT 61.681 57.895 5.73 0.00 33.90 3.51
960 2333 3.121030 GCAGTGGATGACGCGCTT 61.121 61.111 5.73 0.00 33.90 4.68
1036 2420 1.627297 GGTAGGAAGTGGAGGCCCAG 61.627 65.000 0.00 0.00 44.55 4.45
1053 2437 2.113139 CGAAAGTGGGTGGCTGGT 59.887 61.111 0.00 0.00 0.00 4.00
1056 2440 3.884774 TGGCGAAAGTGGGTGGCT 61.885 61.111 0.00 0.00 0.00 4.75
1076 2460 2.494445 CATGGTCGCGGCTGTCTA 59.506 61.111 11.94 0.00 0.00 2.59
1173 2569 3.740495 CTAGAGAGCCGGGGAGCCA 62.740 68.421 2.18 0.00 0.00 4.75
1174 2570 2.915137 CTAGAGAGCCGGGGAGCC 60.915 72.222 2.18 0.00 0.00 4.70
1176 2572 4.492604 CTCTAGAGAGCCGGGGAG 57.507 66.667 15.05 0.00 35.13 4.30
1190 2590 5.463154 AGAATACAGATAACAGGGAGCTCT 58.537 41.667 14.64 0.00 0.00 4.09
1228 2762 8.864087 CCCAGCTCTAGTAATATCATATGCATA 58.136 37.037 9.27 9.27 0.00 3.14
1290 3078 4.336993 AGGAGAAGACATCTACGCTTGTAG 59.663 45.833 0.00 0.00 44.51 2.74
1297 3085 5.563867 GCTTATCCAGGAGAAGACATCTACG 60.564 48.000 25.52 0.00 44.51 3.51
1396 3184 5.689383 AATTGCTGAAATACACGTGAAGT 57.311 34.783 25.01 1.74 0.00 3.01
1397 3185 6.417635 ACAAAATTGCTGAAATACACGTGAAG 59.582 34.615 25.01 10.18 0.00 3.02
1571 3376 6.156519 GTCACTTTGTTTAATAAAGGGGCTG 58.843 40.000 12.62 5.35 39.44 4.85
1604 3409 4.515191 GTGTGAGCTTGTTCTGGATTACAA 59.485 41.667 0.00 0.00 33.54 2.41
1691 3496 5.657302 GGATGACGGTCCAGTAATAGGATAT 59.343 44.000 5.55 0.00 37.52 1.63
1709 3514 1.535462 CAGACAACCGGTTTGGATGAC 59.465 52.381 19.55 7.37 42.97 3.06
1857 3673 4.495422 ACAAGACACGGCATAAGTTCTAG 58.505 43.478 0.00 0.00 0.00 2.43
1858 3674 4.219944 AGACAAGACACGGCATAAGTTCTA 59.780 41.667 0.00 0.00 0.00 2.10
1859 3675 3.006967 AGACAAGACACGGCATAAGTTCT 59.993 43.478 0.00 0.00 0.00 3.01
1904 3726 5.611374 AGGAAACACGATGACCATATAAGG 58.389 41.667 0.00 0.00 0.00 2.69
1914 3736 4.714632 AGAAGGAAAAGGAAACACGATGA 58.285 39.130 0.00 0.00 0.00 2.92
1992 3815 3.565902 GCTTGTAGTAGGGCAATTGATCC 59.434 47.826 10.34 9.80 0.00 3.36
2024 3847 8.668510 AGTAATATTTGAATCAGCTGGTAGTG 57.331 34.615 15.13 0.00 0.00 2.74
2050 3873 5.818678 AATCTGTGTGGTCACCTAGTAAA 57.181 39.130 0.00 0.00 43.26 2.01
2062 3885 9.590451 AATAAATGAGCATTTTAATCTGTGTGG 57.410 29.630 13.05 0.00 40.99 4.17
2099 3923 7.589958 AGAGGTAATAAGTATGAGGACACTG 57.410 40.000 0.00 0.00 0.00 3.66
2100 3924 7.839705 TGAAGAGGTAATAAGTATGAGGACACT 59.160 37.037 0.00 0.00 0.00 3.55
2156 3980 5.584551 AAGTTTCCTTCTGGAGTGGTAAT 57.415 39.130 0.00 0.00 44.24 1.89
2558 4395 9.632807 TTCAAAAATATGGGTAAATCTGTTTCG 57.367 29.630 0.00 0.00 0.00 3.46
3100 8266 0.468214 TGCCCGGAACACATTTTGGA 60.468 50.000 0.73 0.00 0.00 3.53
3122 8288 8.667076 TCTAATTTATGCGGATGATGGATATG 57.333 34.615 0.00 0.00 0.00 1.78
3342 8520 2.560105 GGAGCCTTTTTCTTGATGCTGT 59.440 45.455 0.00 0.00 0.00 4.40
3603 8785 9.234384 CAGTCTACCGTACAATATTTTAGTGAG 57.766 37.037 0.00 0.00 0.00 3.51
3828 9012 3.869473 TTGTGCGGGCGTGGACTAC 62.869 63.158 2.11 0.00 0.00 2.73
3855 9039 2.275418 GGGTTCGTGCCATCCCAT 59.725 61.111 0.00 0.00 39.68 4.00
3869 9053 2.430367 GACAGCGGTCCTTTGGGT 59.570 61.111 5.60 0.00 38.12 4.51
3886 9070 3.124921 GGCCGATGTGAACCACCG 61.125 66.667 0.00 0.00 32.73 4.94
3907 9091 0.041833 AGCACAGAGAGAAGGCCCTA 59.958 55.000 0.00 0.00 0.00 3.53
3957 9141 1.675552 ACTGTGTAACCCTGCACAAC 58.324 50.000 0.00 0.00 45.92 3.32
3988 9172 4.621068 CACACAAAGTGCAGAAAGAGAA 57.379 40.909 0.00 0.00 42.15 2.87
4140 9326 5.097529 CCTGCAAACATTGTGACATCATAC 58.902 41.667 0.00 0.00 0.00 2.39
4235 9421 6.858478 CGAATTTCGAGACTCATAATCTAGCA 59.142 38.462 13.45 0.00 43.74 3.49
4259 9445 0.241213 TTCGTGAGTTCAGGAGCTCG 59.759 55.000 7.83 0.00 40.91 5.03
4276 9462 8.743099 GTGCTTTTACTCTGTGTAATTTTGTTC 58.257 33.333 3.45 0.00 40.41 3.18
4280 9466 9.116067 TGTAGTGCTTTTACTCTGTGTAATTTT 57.884 29.630 3.45 0.00 40.41 1.82
4349 9535 0.737715 AAGACATCGAGAACCGCAGC 60.738 55.000 0.00 0.00 38.37 5.25


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

AutoCloner maintained by Alex Coulton.