Multiple sequence alignment - TraesCS5D01G302000

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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 TraesCS5D01G302000 chr5D 100.000 6546 0 0 1 6546 398524021 398530566 0.000000e+00 12089.0
1 TraesCS5D01G302000 chr5A 94.638 5614 215 31 2 5562 503517045 503522625 0.000000e+00 8621.0
2 TraesCS5D01G302000 chr5A 81.351 992 85 40 5561 6545 503522660 503523558 0.000000e+00 715.0
3 TraesCS5D01G302000 chr5B 93.337 5268 232 41 2 5219 478475275 478480473 0.000000e+00 7673.0
4 TraesCS5D01G302000 chr5B 87.252 706 49 19 5561 6245 478480877 478481562 0.000000e+00 767.0
5 TraesCS5D01G302000 chr5B 93.729 303 14 1 6249 6546 478481832 478482134 3.600000e-122 449.0
6 TraesCS5D01G302000 chr5B 93.511 262 16 1 5301 5562 478480582 478480842 7.960000e-104 388.0
7 TraesCS5D01G302000 chr4B 87.226 1049 119 13 4171 5216 2220170 2219134 0.000000e+00 1181.0
8 TraesCS5D01G302000 chr4B 86.121 807 99 7 4424 5218 2209752 2208947 0.000000e+00 857.0
9 TraesCS5D01G302000 chr4B 86.121 807 99 7 4424 5218 2239742 2238937 0.000000e+00 857.0
10 TraesCS5D01G302000 chr4B 75.486 926 154 32 3509 4386 2210737 2209837 2.860000e-103 387.0
11 TraesCS5D01G302000 chr4B 75.486 926 154 32 3509 4386 2240727 2239827 2.860000e-103 387.0
12 TraesCS5D01G302000 chr4B 79.221 539 87 21 2399 2926 643021609 643022133 1.040000e-92 351.0
13 TraesCS5D01G302000 chr4B 77.007 548 91 24 2399 2926 2221786 2221254 1.390000e-71 281.0
14 TraesCS5D01G302000 chr4B 87.398 246 27 3 5321 5562 2218591 2218346 5.000000e-71 279.0
15 TraesCS5D01G302000 chr4B 85.656 244 33 2 5321 5562 643024894 643025137 8.420000e-64 255.0
16 TraesCS5D01G302000 chr4B 75.174 431 80 21 1727 2146 2227210 2226796 1.880000e-40 178.0
17 TraesCS5D01G302000 chr4B 75.174 431 80 21 1727 2146 2244325 2243911 1.880000e-40 178.0
18 TraesCS5D01G302000 chr4B 97.826 46 0 1 6469 6514 643147738 643147782 1.960000e-10 78.7
19 TraesCS5D01G302000 chr4D 87.202 1047 120 11 4174 5218 1652601 1651567 0.000000e+00 1179.0
20 TraesCS5D01G302000 chr4D 78.368 1789 288 45 3499 5218 499893192 499891434 0.000000e+00 1068.0
21 TraesCS5D01G302000 chr4D 87.611 791 88 3 4171 4961 499902988 499902208 0.000000e+00 909.0
22 TraesCS5D01G302000 chr4D 86.381 793 98 5 4436 5218 1641951 1641159 0.000000e+00 857.0
23 TraesCS5D01G302000 chr4D 79.962 524 82 18 2414 2926 499904615 499904104 1.340000e-96 364.0
24 TraesCS5D01G302000 chr4D 82.301 339 46 10 2399 2731 1654413 1654083 1.390000e-71 281.0
25 TraesCS5D01G302000 chr4D 89.401 217 23 0 5346 5562 1651032 1650816 2.330000e-69 274.0
26 TraesCS5D01G302000 chr4D 86.585 246 29 2 5321 5562 499901505 499901260 1.080000e-67 268.0
27 TraesCS5D01G302000 chr4D 75.410 366 69 18 1795 2152 1645712 1645360 2.440000e-34 158.0
28 TraesCS5D01G302000 chr4D 74.272 412 86 17 1755 2152 1655336 1654931 8.790000e-34 156.0
29 TraesCS5D01G302000 chr4A 82.001 1389 194 29 3881 5218 603340728 603342111 0.000000e+00 1129.0
30 TraesCS5D01G302000 chr4A 85.759 316 35 6 4278 4592 603284782 603285088 6.330000e-85 326.0
31 TraesCS5D01G302000 chr4A 86.585 246 29 3 5321 5562 603286176 603286421 1.080000e-67 268.0
32 TraesCS5D01G302000 chr4A 74.390 410 79 22 1755 2152 603333883 603334278 1.140000e-32 152.0
33 TraesCS5D01G302000 chr2D 82.424 165 22 4 1726 1890 32292097 32291940 3.180000e-28 137.0
34 TraesCS5D01G302000 chr2A 81.818 165 23 4 1726 1890 34516555 34516398 1.480000e-26 132.0


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 TraesCS5D01G302000 chr5D 398524021 398530566 6545 False 12089.000000 12089 100.000000 1 6546 1 chr5D.!!$F1 6545
1 TraesCS5D01G302000 chr5A 503517045 503523558 6513 False 4668.000000 8621 87.994500 2 6545 2 chr5A.!!$F1 6543
2 TraesCS5D01G302000 chr5B 478475275 478482134 6859 False 2319.250000 7673 91.957250 2 6546 4 chr5B.!!$F1 6544
3 TraesCS5D01G302000 chr4B 2208947 2210737 1790 True 622.000000 857 80.803500 3509 5218 2 chr4B.!!$R2 1709
4 TraesCS5D01G302000 chr4B 2218346 2221786 3440 True 580.333333 1181 83.877000 2399 5562 3 chr4B.!!$R3 3163
5 TraesCS5D01G302000 chr4B 2238937 2244325 5388 True 474.000000 857 78.927000 1727 5218 3 chr4B.!!$R4 3491
6 TraesCS5D01G302000 chr4B 643021609 643025137 3528 False 303.000000 351 82.438500 2399 5562 2 chr4B.!!$F2 3163
7 TraesCS5D01G302000 chr4D 499891434 499893192 1758 True 1068.000000 1068 78.368000 3499 5218 1 chr4D.!!$R1 1719
8 TraesCS5D01G302000 chr4D 499901260 499904615 3355 True 513.666667 909 84.719333 2414 5562 3 chr4D.!!$R4 3148
9 TraesCS5D01G302000 chr4D 1641159 1645712 4553 True 507.500000 857 80.895500 1795 5218 2 chr4D.!!$R2 3423
10 TraesCS5D01G302000 chr4D 1650816 1655336 4520 True 472.500000 1179 83.294000 1755 5562 4 chr4D.!!$R3 3807
11 TraesCS5D01G302000 chr4A 603340728 603342111 1383 False 1129.000000 1129 82.001000 3881 5218 1 chr4A.!!$F2 1337
12 TraesCS5D01G302000 chr4A 603284782 603286421 1639 False 297.000000 326 86.172000 4278 5562 2 chr4A.!!$F3 1284

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
93 94 0.169009 GAGTGCTTCGGTTCCAATGC 59.831 55.0 0.00 0.0 0.00 3.56 F
633 637 0.959553 GGTGATATCTTCTCCGCCGA 59.040 55.0 3.98 0.0 0.00 5.54 F
1387 1423 0.327259 AGGTAAAAGGGTCCGGCTTC 59.673 55.0 0.00 0.0 0.00 3.86 F
2811 4524 1.017387 GCATCCAGGTCTTTTAGGCG 58.983 55.0 0.00 0.0 0.00 5.52 F
3683 6585 0.463654 TTGAGCAACTGCACCGAGTT 60.464 50.0 4.22 0.0 45.16 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1266 1302 0.534412 CGAGGTTGGATCTGCTGTCT 59.466 55.0 0.00 0.00 0.00 3.41 R
1668 1716 0.875059 GGGGAGTGCTTTCTGAAACG 59.125 55.0 0.00 0.00 0.00 3.60 R
3377 5543 0.476338 TTGTGCTAGGACCAAAGCCA 59.524 50.0 12.28 9.91 37.97 4.75 R
4106 7128 1.633852 CTTTCTCACGCTGCAGCTCC 61.634 60.0 34.22 8.48 39.32 4.70 R
5644 9560 1.557099 TGTACATCACTTCTCGGCCT 58.443 50.0 0.00 0.00 0.00 5.19 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
33 34 3.022287 GGTGACCACACGCAACTG 58.978 61.111 0.00 0.00 46.77 3.16
35 36 0.884704 GGTGACCACACGCAACTGAT 60.885 55.000 0.00 0.00 46.77 2.90
38 39 1.270785 TGACCACACGCAACTGATCAT 60.271 47.619 0.00 0.00 0.00 2.45
54 55 5.587844 ACTGATCATACAAGAAGATGCCAAC 59.412 40.000 0.00 0.00 0.00 3.77
93 94 0.169009 GAGTGCTTCGGTTCCAATGC 59.831 55.000 0.00 0.00 0.00 3.56
134 136 9.869844 GCTGACAGCAAAGTTATATAGTTAATG 57.130 33.333 22.62 0.00 41.89 1.90
233 235 7.482743 CACATTATGTAATCAGTTCAGCAACAC 59.517 37.037 0.00 0.00 34.60 3.32
246 248 1.334869 AGCAACACTGTTACTTGCTGC 59.665 47.619 13.53 6.75 46.93 5.25
279 281 1.011333 GGTCATTGCATTGCATTGCC 58.989 50.000 26.06 21.45 42.06 4.52
342 345 3.277652 GGAAACGTTGACCTCGTCA 57.722 52.632 0.00 0.00 41.09 4.35
352 355 4.457496 CCTCGTCACGCCCAGCAT 62.457 66.667 0.00 0.00 0.00 3.79
353 356 3.190849 CTCGTCACGCCCAGCATG 61.191 66.667 0.00 0.00 0.00 4.06
439 442 1.530323 GCCACAAAGATACCGTTGGT 58.470 50.000 0.00 0.00 40.16 3.67
523 526 5.450412 GCTCTCTGTTGACTGAAGGAGATAG 60.450 48.000 9.78 0.00 30.93 2.08
527 530 3.196469 TGTTGACTGAAGGAGATAGCAGG 59.804 47.826 0.00 0.00 32.82 4.85
531 534 1.070445 CTGAAGGAGATAGCAGGGCTG 59.930 57.143 0.07 0.00 40.10 4.85
633 637 0.959553 GGTGATATCTTCTCCGCCGA 59.040 55.000 3.98 0.00 0.00 5.54
701 705 1.673329 GGAGAACGACCTTGAAGCTCC 60.673 57.143 0.00 0.00 34.35 4.70
735 739 5.522456 TCTTGTTTGTTTCTGCATCACATC 58.478 37.500 0.00 0.00 0.00 3.06
736 740 5.300034 TCTTGTTTGTTTCTGCATCACATCT 59.700 36.000 0.00 0.00 0.00 2.90
745 749 6.732531 TTCTGCATCACATCTACAGAAAAG 57.267 37.500 0.00 0.00 42.63 2.27
805 809 0.962855 GTTTGCTCCTCCTTGCTCCC 60.963 60.000 0.00 0.00 0.00 4.30
844 848 1.639280 CTGCCAACACCAACAACAAC 58.361 50.000 0.00 0.00 0.00 3.32
845 849 0.969149 TGCCAACACCAACAACAACA 59.031 45.000 0.00 0.00 0.00 3.33
886 890 7.148323 GGGTATGCACTTTTTCACTTTTGTTTT 60.148 33.333 0.00 0.00 0.00 2.43
1006 1042 2.117206 GGTGGTTCCACATGGCCA 59.883 61.111 21.25 8.56 38.59 5.36
1023 1059 4.479993 ATGGTCAGCAGAGCCCGC 62.480 66.667 5.81 0.00 41.53 6.13
1050 1086 2.180769 CCTTCGCCGTCATCGTCA 59.819 61.111 0.00 0.00 35.01 4.35
1254 1290 2.488355 CTGTATGTCGCCGTCGGT 59.512 61.111 13.94 0.00 36.13 4.69
1266 1302 1.673626 GCCGTCGGTAAGGACATCAAA 60.674 52.381 13.94 0.00 36.73 2.69
1275 1311 3.777106 AAGGACATCAAAGACAGCAGA 57.223 42.857 0.00 0.00 0.00 4.26
1306 1342 3.394836 GGGCAGCTCGGAACCTCT 61.395 66.667 0.00 0.00 0.00 3.69
1338 1374 1.248785 CCAAGCTTGTCCTGCTGCAT 61.249 55.000 24.35 0.00 41.03 3.96
1387 1423 0.327259 AGGTAAAAGGGTCCGGCTTC 59.673 55.000 0.00 0.00 0.00 3.86
1432 1471 2.163010 CCATCTGCATCAACTTGACCAC 59.837 50.000 0.00 0.00 0.00 4.16
1440 1479 1.070134 TCAACTTGACCACGGAGAAGG 59.930 52.381 0.00 0.00 0.00 3.46
1442 1481 1.645710 ACTTGACCACGGAGAAGGAT 58.354 50.000 0.00 0.00 0.00 3.24
1443 1482 1.550976 ACTTGACCACGGAGAAGGATC 59.449 52.381 0.00 0.00 0.00 3.36
1444 1483 1.550524 CTTGACCACGGAGAAGGATCA 59.449 52.381 0.00 0.00 0.00 2.92
1485 1528 6.545504 TTCTTGTTATTTCTGTCAGCACTC 57.454 37.500 0.00 0.00 0.00 3.51
1503 1546 4.810790 CACTCCAGTCGTTTCAGAAGTAT 58.189 43.478 0.00 0.00 0.00 2.12
1504 1547 5.621555 GCACTCCAGTCGTTTCAGAAGTATA 60.622 44.000 0.00 0.00 0.00 1.47
1523 1566 6.650120 AGTATATTTTGCGTATCTATGGGGG 58.350 40.000 0.00 0.00 0.00 5.40
1531 1575 3.314357 GCGTATCTATGGGGGAAAAACAC 59.686 47.826 0.00 0.00 0.00 3.32
1636 1681 4.927425 CAAATGAAATTAGCAGCAAGCAGT 59.073 37.500 0.00 0.00 40.63 4.40
1668 1716 1.461127 GTTCGATGTTGCTGTCAGACC 59.539 52.381 3.32 0.00 0.00 3.85
1703 1751 1.073284 TCCCCTGTTTTCAGTAGGCAC 59.927 52.381 0.00 0.00 45.68 5.01
1724 1772 5.625311 GCACTGCAAATACTTGTTCAGTAAC 59.375 40.000 0.00 0.00 41.56 2.50
1940 2803 5.739752 TCTGAAATCATATTCACTTGCGG 57.260 39.130 0.00 0.00 35.55 5.69
2581 4257 6.057533 TCATGCATCCCTAAGTCAACATAAG 58.942 40.000 0.00 0.00 0.00 1.73
2603 4308 6.515272 AGGCAAATACTACACAGAATTTGG 57.485 37.500 8.28 0.00 38.92 3.28
2616 4321 6.183360 ACACAGAATTTGGAAATTTCAGCTCA 60.183 34.615 19.49 5.71 38.34 4.26
2732 4442 1.275573 GAGTCACCCCGAAGTAGCTTT 59.724 52.381 0.00 0.00 0.00 3.51
2811 4524 1.017387 GCATCCAGGTCTTTTAGGCG 58.983 55.000 0.00 0.00 0.00 5.52
2829 4542 1.074951 GCTACAGGCCAACAACCCT 59.925 57.895 5.01 0.00 34.27 4.34
2957 4688 3.300388 CTCTACAGATCAACAGGCCCTA 58.700 50.000 0.00 0.00 0.00 3.53
3154 4889 4.947147 TGGTTCACCGGTGCCTGC 62.947 66.667 30.25 17.56 39.43 4.85
3239 4987 2.432146 TCTCTAAGCATAGCCACACCTG 59.568 50.000 0.00 0.00 0.00 4.00
3419 5585 4.003648 GTGTAGAGGGAAATGGTTGACAG 58.996 47.826 0.00 0.00 0.00 3.51
3442 5608 3.311871 CAGAATGTCTTCATGGCTGTAGC 59.688 47.826 0.00 0.00 34.99 3.58
3463 5631 3.309388 CAACTCTCAACCAGTAGTGTCG 58.691 50.000 0.00 0.00 0.00 4.35
3572 6453 5.530915 TGATCAACCAAGGTCTACTGTTTTG 59.469 40.000 0.00 0.00 0.00 2.44
3620 6502 8.618677 AGATAATGTTGTCATGCTTACTGAATG 58.381 33.333 0.00 0.00 34.19 2.67
3683 6585 0.463654 TTGAGCAACTGCACCGAGTT 60.464 50.000 4.22 0.00 45.16 3.01
3970 6992 4.019591 GGAGGTAGAGGAAAGGCTAACAAA 60.020 45.833 0.00 0.00 0.00 2.83
4037 7059 3.715854 GCAGAAGGCAAATGAGCAG 57.284 52.632 0.00 0.00 43.97 4.24
4105 7127 1.133976 AGAGCTCCAACAGTTGCAAGT 60.134 47.619 10.93 0.00 0.00 3.16
4106 7128 1.002033 GAGCTCCAACAGTTGCAAGTG 60.002 52.381 28.65 28.65 35.47 3.16
4241 7401 3.129638 ACACAGAGATAGAAGAAGCGACC 59.870 47.826 0.00 0.00 0.00 4.79
5040 8280 2.037687 CTGCAGGGGAATGGCCAA 59.962 61.111 10.96 0.00 38.95 4.52
5045 8285 0.251742 CAGGGGAATGGCCAACTGAA 60.252 55.000 10.96 0.00 42.52 3.02
5312 9192 3.788227 TGAAGTAAGGTGGTCAGCATT 57.212 42.857 2.96 0.00 0.00 3.56
5328 9208 3.983344 CAGCATTGTCACCTTTAGTTTGC 59.017 43.478 0.00 0.00 0.00 3.68
5644 9560 2.094100 TTCTCAATGTTTGGGCCCAA 57.906 45.000 34.07 34.07 0.00 4.12
5645 9561 1.631405 TCTCAATGTTTGGGCCCAAG 58.369 50.000 35.02 23.82 37.24 3.61
5646 9562 0.609662 CTCAATGTTTGGGCCCAAGG 59.390 55.000 35.02 22.53 37.24 3.61
5675 9595 4.894784 AGTGATGTACATGTTTTCGGTCT 58.105 39.130 14.43 0.00 0.00 3.85
5716 9636 3.201290 GACATGGCATGTAACTCTCCAG 58.799 50.000 31.48 2.23 45.03 3.86
5734 9654 6.478512 CTCCAGGAGAGAGTAGCTATTTTT 57.521 41.667 11.62 0.00 46.50 1.94
5756 9676 9.528018 TTTTTAGGTTCATTGAAAAGTGATGTC 57.472 29.630 0.00 0.00 0.00 3.06
5757 9677 7.815840 TTAGGTTCATTGAAAAGTGATGTCA 57.184 32.000 0.00 0.00 0.00 3.58
5759 9679 6.684686 AGGTTCATTGAAAAGTGATGTCATG 58.315 36.000 0.00 0.00 0.00 3.07
5762 9682 6.638096 TCATTGAAAAGTGATGTCATGTGT 57.362 33.333 0.00 0.00 0.00 3.72
5764 9684 8.339344 TCATTGAAAAGTGATGTCATGTGTAT 57.661 30.769 0.00 0.00 0.00 2.29
5765 9685 8.238631 TCATTGAAAAGTGATGTCATGTGTATG 58.761 33.333 0.00 0.00 35.57 2.39
5766 9686 7.742556 TTGAAAAGTGATGTCATGTGTATGA 57.257 32.000 0.00 0.00 40.92 2.15
5807 9727 6.065374 TCAGTTATGCAAAGTTGGGAGTTAA 58.935 36.000 0.00 0.00 0.00 2.01
5899 9820 9.607988 CGGCTTATAATAATGTGATTACCCATA 57.392 33.333 0.00 0.00 0.00 2.74
5918 9839 5.334879 CCCATAAATTAGCTATGCACGTTCC 60.335 44.000 0.00 0.00 0.00 3.62
5967 9888 5.358160 AGTTGATAATTCAAGGTAAGCTGCC 59.642 40.000 0.00 0.00 42.41 4.85
5968 9889 4.854173 TGATAATTCAAGGTAAGCTGCCA 58.146 39.130 9.86 0.00 0.00 4.92
5969 9890 5.448654 TGATAATTCAAGGTAAGCTGCCAT 58.551 37.500 9.86 0.00 0.00 4.40
6033 9957 2.032071 CCAGGTCGGCGGAAACTT 59.968 61.111 7.21 0.00 0.00 2.66
6035 9959 1.301401 CAGGTCGGCGGAAACTTCA 60.301 57.895 7.21 0.00 0.00 3.02
6056 9980 4.883585 TCATAGGCAAAGTCATTTAGCTGG 59.116 41.667 0.00 0.00 0.00 4.85
6068 9992 4.777896 TCATTTAGCTGGTCTTACTCACCT 59.222 41.667 0.00 0.00 34.66 4.00
6069 9993 5.955959 TCATTTAGCTGGTCTTACTCACCTA 59.044 40.000 0.00 0.00 34.66 3.08
6070 9994 5.916661 TTTAGCTGGTCTTACTCACCTAG 57.083 43.478 0.00 0.00 34.66 3.02
6105 10029 3.063997 CCAATCCACTAGCGCTAACTTTG 59.936 47.826 19.37 15.86 0.00 2.77
6106 10030 3.611766 ATCCACTAGCGCTAACTTTGT 57.388 42.857 19.37 9.53 0.00 2.83
6110 10034 3.617263 CCACTAGCGCTAACTTTGTAAGG 59.383 47.826 19.37 7.10 0.00 2.69
6113 10037 5.062308 CACTAGCGCTAACTTTGTAAGGAAG 59.938 44.000 19.37 5.54 0.00 3.46
6114 10038 4.267349 AGCGCTAACTTTGTAAGGAAGA 57.733 40.909 8.99 0.00 0.00 2.87
6121 10045 6.313164 GCTAACTTTGTAAGGAAGAGCGTATT 59.687 38.462 0.00 0.00 0.00 1.89
6128 10052 4.663636 AAGGAAGAGCGTATTGTTTTCG 57.336 40.909 0.00 0.00 0.00 3.46
6129 10053 3.660865 AGGAAGAGCGTATTGTTTTCGT 58.339 40.909 0.00 0.00 0.00 3.85
6149 10073 4.039973 TCGTAGAAGGAAGGCAAAGAAAGA 59.960 41.667 0.00 0.00 0.00 2.52
6150 10074 4.938226 CGTAGAAGGAAGGCAAAGAAAGAT 59.062 41.667 0.00 0.00 0.00 2.40
6151 10075 5.412904 CGTAGAAGGAAGGCAAAGAAAGATT 59.587 40.000 0.00 0.00 0.00 2.40
6152 10076 6.594159 CGTAGAAGGAAGGCAAAGAAAGATTA 59.406 38.462 0.00 0.00 0.00 1.75
6153 10077 7.119262 CGTAGAAGGAAGGCAAAGAAAGATTAA 59.881 37.037 0.00 0.00 0.00 1.40
6158 10088 6.072452 AGGAAGGCAAAGAAAGATTAAGAACG 60.072 38.462 0.00 0.00 0.00 3.95
6167 10097 4.923264 AAGATTAAGAACGAACGGCTTC 57.077 40.909 7.57 0.16 0.00 3.86
6173 10103 0.234884 GAACGAACGGCTTCCAACAG 59.765 55.000 0.00 0.00 0.00 3.16
6200 10130 1.342174 AGGAACTTGCATGCCAAACAG 59.658 47.619 16.68 5.85 27.25 3.16
6204 10134 0.947180 CTTGCATGCCAAACAGCCAC 60.947 55.000 16.68 0.00 31.94 5.01
6218 10148 2.567615 ACAGCCACTTAAGGGTCTACTG 59.432 50.000 7.53 9.60 37.26 2.74
6219 10149 2.567615 CAGCCACTTAAGGGTCTACTGT 59.432 50.000 7.53 0.00 37.26 3.55
6245 10180 7.954666 AGATACCTATCTATCTTCCTTGAGC 57.045 40.000 0.00 0.00 41.05 4.26
6259 10460 2.344950 CTTGAGCTGAGCGAGAACATT 58.655 47.619 0.00 0.00 0.00 2.71
6379 10585 6.684111 GCAGAGAGGAGTTTAATTAGCAGCTA 60.684 42.308 0.00 0.00 0.00 3.32
6380 10586 7.441017 CAGAGAGGAGTTTAATTAGCAGCTAT 58.559 38.462 2.02 0.00 0.00 2.97
6403 10609 3.215151 CGGAGCAGAGAGGTCTTGTATA 58.785 50.000 0.00 0.00 44.16 1.47
6409 10622 5.896678 AGCAGAGAGGTCTTGTATAAGTCAT 59.103 40.000 0.00 0.00 35.38 3.06
6515 10728 1.892474 GCACTGTTGGGCAATTCCTTA 59.108 47.619 0.00 0.00 34.39 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.181010 CACCCGATCCAGGCCCAG 62.181 72.222 0.00 0.00 0.00 4.45
3 4 4.731853 TCACCCGATCCAGGCCCA 62.732 66.667 0.00 0.00 0.00 5.36
6 7 3.399181 TGGTCACCCGATCCAGGC 61.399 66.667 0.00 0.00 0.00 4.85
33 34 4.024556 CGGTTGGCATCTTCTTGTATGATC 60.025 45.833 0.00 0.00 0.00 2.92
35 36 3.270027 CGGTTGGCATCTTCTTGTATGA 58.730 45.455 0.00 0.00 0.00 2.15
38 39 2.107950 CCGGTTGGCATCTTCTTGTA 57.892 50.000 0.00 0.00 0.00 2.41
54 55 1.724082 CTGTTTTAAATTTGGCGCCGG 59.276 47.619 23.90 0.00 0.00 6.13
93 94 4.800914 GCTGTCAGCATAGGTTAGGGTATG 60.801 50.000 20.16 0.00 41.89 2.39
134 136 2.029918 GTGATGCTTCCCTGTTTGGTTC 60.030 50.000 0.00 0.00 0.00 3.62
135 137 1.963515 GTGATGCTTCCCTGTTTGGTT 59.036 47.619 0.00 0.00 0.00 3.67
233 235 3.257393 CCTGACTAGCAGCAAGTAACAG 58.743 50.000 8.23 0.00 43.50 3.16
244 246 1.538876 ACCTTGGGCCTGACTAGCA 60.539 57.895 4.53 0.00 0.00 3.49
245 247 1.222113 GACCTTGGGCCTGACTAGC 59.778 63.158 4.53 0.00 0.00 3.42
246 248 1.207791 ATGACCTTGGGCCTGACTAG 58.792 55.000 4.53 0.00 0.00 2.57
279 281 4.154918 CCTTAACTGCTGCTAACCAGAAAG 59.845 45.833 0.00 0.13 44.64 2.62
352 355 1.277273 CAGCCAGTGATCTCAAGACCA 59.723 52.381 0.00 0.00 0.00 4.02
353 356 1.406614 CCAGCCAGTGATCTCAAGACC 60.407 57.143 0.00 0.00 0.00 3.85
495 498 3.494048 CCTTCAGTCAACAGAGAGCAGTT 60.494 47.826 0.00 0.00 0.00 3.16
497 500 2.298446 TCCTTCAGTCAACAGAGAGCAG 59.702 50.000 0.00 0.00 0.00 4.24
527 530 1.382692 GGCCATCTCTTTCAGCAGCC 61.383 60.000 0.00 0.00 0.00 4.85
531 534 1.078143 ACGGGCCATCTCTTTCAGC 60.078 57.895 4.39 0.00 0.00 4.26
633 637 7.770433 TCCATCGTAGATGTCATTCAGAATTTT 59.230 33.333 8.91 0.00 45.12 1.82
701 705 2.021457 ACAAACAAGAAGTTGGTCCCG 58.979 47.619 0.00 0.00 40.41 5.14
735 739 2.423577 CGGGGGTCAACTTTTCTGTAG 58.576 52.381 0.00 0.00 0.00 2.74
736 740 1.072648 CCGGGGGTCAACTTTTCTGTA 59.927 52.381 0.00 0.00 0.00 2.74
745 749 4.410400 CTCAGCCCGGGGGTCAAC 62.410 72.222 25.28 3.55 37.65 3.18
765 769 0.524862 AATGGCTGCTTTCTCTTGCG 59.475 50.000 0.00 0.00 0.00 4.85
844 848 4.142381 GCATACCCTTAGCCTTTGAGTTTG 60.142 45.833 0.00 0.00 0.00 2.93
845 849 4.017126 GCATACCCTTAGCCTTTGAGTTT 58.983 43.478 0.00 0.00 0.00 2.66
886 890 9.787232 GCATATGCAATCTCCCAAGAGAAGAGA 62.787 44.444 22.84 0.00 45.82 3.10
925 961 3.025978 CCTCTCAGAGTGCAGAGAAGAT 58.974 50.000 0.00 0.00 40.13 2.40
1006 1042 4.479993 GCGGGCTCTGCTGACCAT 62.480 66.667 12.04 0.00 0.00 3.55
1023 1059 2.202810 GGCGAAGGGAGAGAAGCG 60.203 66.667 0.00 0.00 0.00 4.68
1050 1086 2.044946 GAGAAGGCCGGCAATGGT 60.045 61.111 30.85 8.17 0.00 3.55
1084 1120 1.875422 ATCCTCTCCACCACCTCGGA 61.875 60.000 0.00 0.00 38.63 4.55
1094 1130 1.215382 CGCGTGAACATCCTCTCCA 59.785 57.895 0.00 0.00 0.00 3.86
1254 1290 4.890158 TCTGCTGTCTTTGATGTCCTTA 57.110 40.909 0.00 0.00 0.00 2.69
1266 1302 0.534412 CGAGGTTGGATCTGCTGTCT 59.466 55.000 0.00 0.00 0.00 3.41
1275 1311 1.903877 CTGCCCAGACGAGGTTGGAT 61.904 60.000 0.00 0.00 36.55 3.41
1306 1342 2.267642 CTTGGGATCACCGGCGAA 59.732 61.111 9.30 0.00 44.64 4.70
1411 1450 2.163010 GTGGTCAAGTTGATGCAGATGG 59.837 50.000 9.18 0.00 0.00 3.51
1432 1471 1.967066 ACTAGCCATGATCCTTCTCCG 59.033 52.381 0.00 0.00 0.00 4.63
1440 1479 7.441017 AGAAAATCAGACTACTAGCCATGATC 58.559 38.462 0.00 0.00 0.00 2.92
1442 1481 6.798427 AGAAAATCAGACTACTAGCCATGA 57.202 37.500 0.00 0.00 0.00 3.07
1443 1482 6.820656 ACAAGAAAATCAGACTACTAGCCATG 59.179 38.462 0.00 0.00 0.00 3.66
1444 1483 6.951971 ACAAGAAAATCAGACTACTAGCCAT 58.048 36.000 0.00 0.00 0.00 4.40
1485 1528 6.961554 GCAAAATATACTTCTGAAACGACTGG 59.038 38.462 0.00 0.00 0.00 4.00
1503 1546 5.570205 TTCCCCCATAGATACGCAAAATA 57.430 39.130 0.00 0.00 0.00 1.40
1504 1547 4.447138 TTCCCCCATAGATACGCAAAAT 57.553 40.909 0.00 0.00 0.00 1.82
1523 1566 6.262273 TCCAGTAAGATCAAGGTGTGTTTTTC 59.738 38.462 0.00 0.00 0.00 2.29
1531 1575 7.256756 GATCAAATCCAGTAAGATCAAGGTG 57.743 40.000 0.00 0.00 36.13 4.00
1606 1651 6.486248 TGCTGCTAATTTCATTTGTATCGTC 58.514 36.000 0.00 0.00 0.00 4.20
1636 1681 4.447724 GCAACATCGAACAACAGAAGACTA 59.552 41.667 0.00 0.00 0.00 2.59
1668 1716 0.875059 GGGGAGTGCTTTCTGAAACG 59.125 55.000 0.00 0.00 0.00 3.60
1703 1751 6.560253 AGGTTACTGAACAAGTATTTGCAG 57.440 37.500 0.00 1.52 41.10 4.41
1724 1772 7.798596 AACATTAGAGTTGAATCAGCATAGG 57.201 36.000 0.00 0.00 0.00 2.57
1940 2803 9.297586 TCGTACAGATGACATATAACAAGAAAC 57.702 33.333 0.00 0.00 0.00 2.78
2556 4222 4.508551 TGTTGACTTAGGGATGCATGAT 57.491 40.909 2.46 0.00 0.00 2.45
2581 4257 6.509418 TCCAAATTCTGTGTAGTATTTGCC 57.491 37.500 11.51 0.00 44.09 4.52
2603 4308 6.006759 AGTAGTTGCTTGAGCTGAAATTTC 57.993 37.500 11.41 11.41 42.66 2.17
2732 4442 4.186926 GTTGATCTGAGATAGTGCTTGCA 58.813 43.478 0.00 0.00 0.00 4.08
2811 4524 0.539669 AAGGGTTGTTGGCCTGTAGC 60.540 55.000 3.32 0.00 42.60 3.58
2829 4542 2.592287 GTTGGACCGCCGTGGAAA 60.592 61.111 4.58 0.00 42.00 3.13
3377 5543 0.476338 TTGTGCTAGGACCAAAGCCA 59.524 50.000 12.28 9.91 37.97 4.75
3419 5585 2.089980 ACAGCCATGAAGACATTCTGC 58.910 47.619 0.00 0.00 37.71 4.26
3442 5608 3.309388 CGACACTACTGGTTGAGAGTTG 58.691 50.000 0.00 0.00 0.00 3.16
3564 6444 7.280356 AGTATTACAACTGAGACCAAAACAGT 58.720 34.615 0.00 0.00 45.02 3.55
3565 6445 7.730364 AGTATTACAACTGAGACCAAAACAG 57.270 36.000 0.00 0.00 37.62 3.16
3822 6726 7.447545 AGAAGAAAGGTTGGGAAAATACAGTAC 59.552 37.037 0.00 0.00 0.00 2.73
4037 7059 2.687700 TGCTCTCCAATTCTGCTCTC 57.312 50.000 0.00 0.00 0.00 3.20
4105 7127 2.381838 TTTCTCACGCTGCAGCTCCA 62.382 55.000 34.22 17.26 39.32 3.86
4106 7128 1.633852 CTTTCTCACGCTGCAGCTCC 61.634 60.000 34.22 8.48 39.32 4.70
4241 7401 4.811555 TTTGGAGTCATCAAAGTTGTCG 57.188 40.909 0.00 0.00 31.42 4.35
4599 7838 2.394563 GCTCTCTTTGGTGCTCGCC 61.395 63.158 0.00 0.00 0.00 5.54
5040 8280 4.202357 TGCCAACTCTTCAGTGTATTCAGT 60.202 41.667 0.00 0.00 31.06 3.41
5045 8285 4.623932 TCTTGCCAACTCTTCAGTGTAT 57.376 40.909 0.00 0.00 31.06 2.29
5102 8342 2.722094 TCATTTGCAAGATTAGGCCGT 58.278 42.857 0.00 0.00 0.00 5.68
5280 9160 7.787028 ACCACCTTACTTCAAAGCAAATAAAA 58.213 30.769 0.00 0.00 0.00 1.52
5312 9192 6.293955 GCAAGATTAGCAAACTAAAGGTGACA 60.294 38.462 0.00 0.00 41.62 3.58
5644 9560 1.557099 TGTACATCACTTCTCGGCCT 58.443 50.000 0.00 0.00 0.00 5.19
5645 9561 2.205074 CATGTACATCACTTCTCGGCC 58.795 52.381 5.07 0.00 0.00 6.13
5646 9562 2.893637 ACATGTACATCACTTCTCGGC 58.106 47.619 5.07 0.00 0.00 5.54
5675 9595 3.820467 GTCAGTTCATCCCAAACACATGA 59.180 43.478 0.00 0.00 0.00 3.07
5716 9636 7.783042 TGAACCTAAAAATAGCTACTCTCTCC 58.217 38.462 0.00 0.00 0.00 3.71
5725 9645 9.696917 CACTTTTCAATGAACCTAAAAATAGCT 57.303 29.630 0.00 0.00 0.00 3.32
5730 9650 9.528018 GACATCACTTTTCAATGAACCTAAAAA 57.472 29.630 0.00 0.00 0.00 1.94
5731 9651 8.690884 TGACATCACTTTTCAATGAACCTAAAA 58.309 29.630 0.00 0.00 0.00 1.52
5734 9654 7.448161 ACATGACATCACTTTTCAATGAACCTA 59.552 33.333 0.00 0.00 0.00 3.08
5755 9675 7.838696 AGGGAATTAAAATGGTCATACACATGA 59.161 33.333 0.00 0.00 38.90 3.07
5756 9676 8.010733 AGGGAATTAAAATGGTCATACACATG 57.989 34.615 0.00 0.00 0.00 3.21
5757 9677 8.061304 AGAGGGAATTAAAATGGTCATACACAT 58.939 33.333 0.00 0.00 0.00 3.21
5759 9679 7.556275 TGAGAGGGAATTAAAATGGTCATACAC 59.444 37.037 0.00 0.00 0.00 2.90
5762 9682 7.872138 ACTGAGAGGGAATTAAAATGGTCATA 58.128 34.615 0.00 0.00 0.00 2.15
5764 9684 6.139679 ACTGAGAGGGAATTAAAATGGTCA 57.860 37.500 0.00 0.00 0.00 4.02
5765 9685 8.624776 CATAACTGAGAGGGAATTAAAATGGTC 58.375 37.037 0.00 0.00 0.00 4.02
5766 9686 7.068716 GCATAACTGAGAGGGAATTAAAATGGT 59.931 37.037 0.00 0.00 0.00 3.55
5767 9687 7.068593 TGCATAACTGAGAGGGAATTAAAATGG 59.931 37.037 0.00 0.00 0.00 3.16
5807 9727 3.104519 TGGGACCATGCTGATTTGATT 57.895 42.857 0.00 0.00 0.00 2.57
5899 9820 5.590259 AGAATGGAACGTGCATAGCTAATTT 59.410 36.000 0.00 0.00 0.00 1.82
5918 9839 6.652062 TCATGCCTGTATATGCAGTAAGAATG 59.348 38.462 18.08 13.06 41.46 2.67
6033 9957 4.883585 CCAGCTAAATGACTTTGCCTATGA 59.116 41.667 0.00 0.00 0.00 2.15
6035 9959 4.860022 ACCAGCTAAATGACTTTGCCTAT 58.140 39.130 0.00 0.00 0.00 2.57
6056 9980 7.705752 GGCTAAATTGTACTAGGTGAGTAAGAC 59.294 40.741 0.00 0.00 42.43 3.01
6068 9992 5.192923 AGTGGATTGGGGCTAAATTGTACTA 59.807 40.000 0.00 0.00 0.00 1.82
6069 9993 4.017499 AGTGGATTGGGGCTAAATTGTACT 60.017 41.667 0.00 0.00 0.00 2.73
6070 9994 4.278310 AGTGGATTGGGGCTAAATTGTAC 58.722 43.478 0.00 0.00 0.00 2.90
6105 10029 5.119743 ACGAAAACAATACGCTCTTCCTTAC 59.880 40.000 0.00 0.00 0.00 2.34
6106 10030 5.232463 ACGAAAACAATACGCTCTTCCTTA 58.768 37.500 0.00 0.00 0.00 2.69
6110 10034 6.385537 TTCTACGAAAACAATACGCTCTTC 57.614 37.500 0.00 0.00 0.00 2.87
6113 10037 4.860907 TCCTTCTACGAAAACAATACGCTC 59.139 41.667 0.00 0.00 0.00 5.03
6114 10038 4.813027 TCCTTCTACGAAAACAATACGCT 58.187 39.130 0.00 0.00 0.00 5.07
6121 10045 3.478857 TGCCTTCCTTCTACGAAAACA 57.521 42.857 0.00 0.00 0.00 2.83
6128 10052 6.825944 AATCTTTCTTTGCCTTCCTTCTAC 57.174 37.500 0.00 0.00 0.00 2.59
6129 10053 8.383175 TCTTAATCTTTCTTTGCCTTCCTTCTA 58.617 33.333 0.00 0.00 0.00 2.10
6149 10073 3.048337 TGGAAGCCGTTCGTTCTTAAT 57.952 42.857 0.00 0.00 32.92 1.40
6150 10074 2.529780 TGGAAGCCGTTCGTTCTTAA 57.470 45.000 0.00 0.00 32.92 1.85
6151 10075 2.137523 GTTGGAAGCCGTTCGTTCTTA 58.862 47.619 0.00 0.00 32.92 2.10
6152 10076 0.942252 GTTGGAAGCCGTTCGTTCTT 59.058 50.000 0.00 0.00 32.92 2.52
6153 10077 0.179067 TGTTGGAAGCCGTTCGTTCT 60.179 50.000 0.00 0.00 32.92 3.01
6167 10097 4.761739 TGCAAGTTCCTAATCTTCTGTTGG 59.238 41.667 0.00 0.00 0.00 3.77
6173 10103 3.696051 TGGCATGCAAGTTCCTAATCTTC 59.304 43.478 21.36 0.00 0.00 2.87
6183 10113 0.249996 GGCTGTTTGGCATGCAAGTT 60.250 50.000 21.36 0.00 41.37 2.66
6200 10130 4.465305 TCTTACAGTAGACCCTTAAGTGGC 59.535 45.833 0.97 0.00 0.00 5.01
6204 10134 9.810870 ATAGGTATCTTACAGTAGACCCTTAAG 57.189 37.037 0.00 0.00 33.33 1.85
6219 10149 9.469097 GCTCAAGGAAGATAGATAGGTATCTTA 57.531 37.037 4.85 0.00 45.70 2.10
6245 10180 0.725686 CAGCCAATGTTCTCGCTCAG 59.274 55.000 0.00 0.00 0.00 3.35
6259 10460 0.825425 TTTGTTCGAATGCCCAGCCA 60.825 50.000 0.00 0.00 0.00 4.75
6379 10585 2.028130 CAAGACCTCTCTGCTCCGTAT 58.972 52.381 0.00 0.00 0.00 3.06
6380 10586 1.271982 ACAAGACCTCTCTGCTCCGTA 60.272 52.381 0.00 0.00 0.00 4.02
6403 10609 3.511540 TCTCATGGACGACTGAATGACTT 59.488 43.478 0.00 0.00 0.00 3.01
6409 10622 2.612972 GCCTTTCTCATGGACGACTGAA 60.613 50.000 0.00 0.00 0.00 3.02
6515 10728 1.537202 GGTGATTTTCTTGCGCAGAGT 59.463 47.619 11.31 1.19 31.12 3.24


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

AutoCloner maintained by Alex Coulton.