Multiple sequence alignment - TraesCS5A01G032000

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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 TraesCS5A01G032000 chr5A 100.000 3284 0 0 1 3284 29625599 29628882 0.000000e+00 6065.0
1 TraesCS5A01G032000 chr5A 91.729 133 11 0 2143 2275 23823663 23823531 5.600000e-43 185.0
2 TraesCS5A01G032000 chr5D 89.649 1739 109 42 874 2595 41296718 41298402 0.000000e+00 2148.0
3 TraesCS5A01G032000 chr5D 92.956 653 42 3 2633 3284 483217568 483218217 0.000000e+00 948.0
4 TraesCS5A01G032000 chr5D 85.633 703 82 13 2 694 41295728 41296421 0.000000e+00 721.0
5 TraesCS5A01G032000 chr5B 84.688 1685 113 74 943 2583 35288608 35290191 0.000000e+00 1548.0
6 TraesCS5A01G032000 chr5B 85.237 359 32 14 2249 2595 35508465 35508814 1.880000e-92 350.0
7 TraesCS5A01G032000 chr5B 82.168 286 33 11 1999 2275 26445640 26445364 2.550000e-56 230.0
8 TraesCS5A01G032000 chr5B 100.000 34 0 0 2596 2629 35520574 35520607 2.740000e-06 63.9
9 TraesCS5A01G032000 chr2A 98.015 655 12 1 2631 3284 52590414 52589760 0.000000e+00 1136.0
10 TraesCS5A01G032000 chr2A 88.571 245 16 2 1132 1373 92831111 92831346 1.490000e-73 287.0
11 TraesCS5A01G032000 chr2A 80.893 403 36 26 2140 2518 720384515 720384900 2.500000e-71 279.0
12 TraesCS5A01G032000 chr2A 86.939 245 20 2 1132 1373 31373085 31372850 6.990000e-67 265.0
13 TraesCS5A01G032000 chr2A 87.037 162 17 3 939 1099 720383134 720383292 2.600000e-41 180.0
14 TraesCS5A01G032000 chr2A 92.222 90 6 1 1972 2061 21091147 21091235 3.440000e-25 126.0
15 TraesCS5A01G032000 chr2A 91.398 93 7 1 1972 2064 774247842 774247751 3.440000e-25 126.0
16 TraesCS5A01G032000 chr2A 86.792 106 12 2 1963 2068 720384302 720384405 2.070000e-22 117.0
17 TraesCS5A01G032000 chr7A 97.863 655 13 1 2631 3284 510908018 510908672 0.000000e+00 1131.0
18 TraesCS5A01G032000 chr6A 97.252 655 17 1 2631 3284 549290503 549291157 0.000000e+00 1109.0
19 TraesCS5A01G032000 chr6D 93.916 641 38 1 2645 3284 106696695 106696055 0.000000e+00 966.0
20 TraesCS5A01G032000 chr2B 91.437 654 55 1 2632 3284 689477093 689476440 0.000000e+00 896.0
21 TraesCS5A01G032000 chr2B 91.358 162 10 2 993 1150 109347421 109347260 5.520000e-53 219.0
22 TraesCS5A01G032000 chr3A 96.642 536 17 1 2750 3284 25375013 25374478 0.000000e+00 889.0
23 TraesCS5A01G032000 chr3A 84.096 459 43 7 1153 1611 734395470 734395898 1.820000e-112 416.0
24 TraesCS5A01G032000 chr3A 83.224 459 47 8 1153 1611 403130926 403130498 8.540000e-106 394.0
25 TraesCS5A01G032000 chr1B 89.242 660 63 6 2628 3284 15569914 15570568 0.000000e+00 819.0
26 TraesCS5A01G032000 chr1B 90.722 97 7 2 1972 2068 685034709 685034803 9.560000e-26 128.0
27 TraesCS5A01G032000 chr2D 90.033 602 59 1 2684 3284 336903892 336904493 0.000000e+00 778.0
28 TraesCS5A01G032000 chr3B 86.615 650 57 16 993 1633 545652016 545651388 0.000000e+00 691.0
29 TraesCS5A01G032000 chr3B 86.068 646 64 10 995 1633 545532313 545531687 0.000000e+00 671.0
30 TraesCS5A01G032000 chr3B 83.442 459 46 8 1153 1611 356351945 356352373 1.840000e-107 399.0
31 TraesCS5A01G032000 chr3B 89.362 235 15 4 993 1220 335361217 335360986 1.490000e-73 287.0
32 TraesCS5A01G032000 chr3B 83.813 278 35 5 1359 1636 335360984 335360717 4.210000e-64 255.0
33 TraesCS5A01G032000 chr3B 99.065 107 1 0 993 1099 356349493 356349599 3.340000e-45 193.0
34 TraesCS5A01G032000 chrUn 87.840 551 44 7 1639 2182 290597829 290597295 2.780000e-175 625.0
35 TraesCS5A01G032000 chrUn 91.748 412 27 3 2184 2595 331823850 331823446 1.710000e-157 566.0
36 TraesCS5A01G032000 chrUn 83.261 460 45 9 1153 1611 11987979 11987551 8.540000e-106 394.0
37 TraesCS5A01G032000 chrUn 82.353 459 51 7 1153 1611 11894752 11895180 4.000000e-99 372.0
38 TraesCS5A01G032000 chr3D 81.383 376 36 17 2140 2492 25523435 25523799 3.230000e-70 276.0
39 TraesCS5A01G032000 chr3D 90.722 97 7 2 1972 2068 111997895 111997989 9.560000e-26 128.0
40 TraesCS5A01G032000 chr7D 80.749 374 38 16 2140 2490 37663100 37662738 9.040000e-66 261.0
41 TraesCS5A01G032000 chr7D 88.272 162 17 2 939 1099 37664450 37664290 3.340000e-45 193.0
42 TraesCS5A01G032000 chr4A 83.784 296 22 14 2140 2415 687317207 687317496 1.170000e-64 257.0
43 TraesCS5A01G032000 chr4A 90.278 144 14 0 956 1099 687315804 687315947 4.330000e-44 189.0
44 TraesCS5A01G032000 chr4A 90.647 139 10 3 1227 1363 687316017 687316154 7.240000e-42 182.0
45 TraesCS5A01G032000 chr4A 74.568 405 66 22 1674 2068 687316705 687317082 3.420000e-30 143.0
46 TraesCS5A01G032000 chr6B 79.688 128 22 4 1253 1377 630549414 630549540 4.510000e-14 89.8


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 TraesCS5A01G032000 chr5A 29625599 29628882 3283 False 6065.0 6065 100.0000 1 3284 1 chr5A.!!$F1 3283
1 TraesCS5A01G032000 chr5D 41295728 41298402 2674 False 1434.5 2148 87.6410 2 2595 2 chr5D.!!$F2 2593
2 TraesCS5A01G032000 chr5D 483217568 483218217 649 False 948.0 948 92.9560 2633 3284 1 chr5D.!!$F1 651
3 TraesCS5A01G032000 chr5B 35288608 35290191 1583 False 1548.0 1548 84.6880 943 2583 1 chr5B.!!$F1 1640
4 TraesCS5A01G032000 chr2A 52589760 52590414 654 True 1136.0 1136 98.0150 2631 3284 1 chr2A.!!$R2 653
5 TraesCS5A01G032000 chr7A 510908018 510908672 654 False 1131.0 1131 97.8630 2631 3284 1 chr7A.!!$F1 653
6 TraesCS5A01G032000 chr6A 549290503 549291157 654 False 1109.0 1109 97.2520 2631 3284 1 chr6A.!!$F1 653
7 TraesCS5A01G032000 chr6D 106696055 106696695 640 True 966.0 966 93.9160 2645 3284 1 chr6D.!!$R1 639
8 TraesCS5A01G032000 chr2B 689476440 689477093 653 True 896.0 896 91.4370 2632 3284 1 chr2B.!!$R2 652
9 TraesCS5A01G032000 chr3A 25374478 25375013 535 True 889.0 889 96.6420 2750 3284 1 chr3A.!!$R1 534
10 TraesCS5A01G032000 chr1B 15569914 15570568 654 False 819.0 819 89.2420 2628 3284 1 chr1B.!!$F1 656
11 TraesCS5A01G032000 chr2D 336903892 336904493 601 False 778.0 778 90.0330 2684 3284 1 chr2D.!!$F1 600
12 TraesCS5A01G032000 chr3B 545651388 545652016 628 True 691.0 691 86.6150 993 1633 1 chr3B.!!$R2 640
13 TraesCS5A01G032000 chr3B 545531687 545532313 626 True 671.0 671 86.0680 995 1633 1 chr3B.!!$R1 638
14 TraesCS5A01G032000 chr3B 356349493 356352373 2880 False 296.0 399 91.2535 993 1611 2 chr3B.!!$F1 618
15 TraesCS5A01G032000 chr3B 335360717 335361217 500 True 271.0 287 86.5875 993 1636 2 chr3B.!!$R3 643
16 TraesCS5A01G032000 chrUn 290597295 290597829 534 True 625.0 625 87.8400 1639 2182 1 chrUn.!!$R2 543
17 TraesCS5A01G032000 chr7D 37662738 37664450 1712 True 227.0 261 84.5105 939 2490 2 chr7D.!!$R1 1551

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
645 655 0.248539 GCGACAGATACTCCACGTCC 60.249 60.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2548 5359 0.392998 GCAATGTCCTCACGGTGGAT 60.393 55.0 8.5 0.0 35.87 3.41 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
29 35 4.213564 ACATGAGTGATTTCTCTCACCC 57.786 45.455 12.97 0.00 45.54 4.61
33 39 3.515502 TGAGTGATTTCTCTCACCCGATT 59.484 43.478 7.96 0.00 45.41 3.34
40 46 4.720649 TTCTCTCACCCGATTTCAGTAG 57.279 45.455 0.00 0.00 0.00 2.57
47 53 5.842907 TCACCCGATTTCAGTAGTATGATG 58.157 41.667 0.00 0.00 0.00 3.07
48 54 5.596772 TCACCCGATTTCAGTAGTATGATGA 59.403 40.000 0.00 0.00 0.00 2.92
49 55 6.267699 TCACCCGATTTCAGTAGTATGATGAT 59.732 38.462 0.00 0.00 0.00 2.45
59 65 7.935520 TCAGTAGTATGATGATTGTCAGTCTC 58.064 38.462 0.00 0.00 0.00 3.36
71 77 2.029918 TGTCAGTCTCATCACAACGAGG 60.030 50.000 0.00 0.00 0.00 4.63
99 105 2.772739 CCTTCATTGGCTGGACTCG 58.227 57.895 0.00 0.00 0.00 4.18
101 107 0.392193 CTTCATTGGCTGGACTCGCT 60.392 55.000 0.00 0.00 0.00 4.93
123 129 3.761218 TCAAAAAGTTCTTGGTGCAGTCA 59.239 39.130 0.00 0.00 0.00 3.41
134 140 3.435275 TGGTGCAGTCATCTAGAAGACT 58.565 45.455 21.92 21.92 45.46 3.24
165 172 8.994429 TTTGTGAAGTTGCTAAAAGAAAATCA 57.006 26.923 0.00 0.00 0.00 2.57
240 247 7.755822 CACATACTACTACTTCTTGTGAACCTC 59.244 40.741 0.00 0.00 36.06 3.85
258 265 2.285220 CCTCGAAATGCAGGTCGTTATG 59.715 50.000 18.17 9.43 38.41 1.90
259 266 2.930040 CTCGAAATGCAGGTCGTTATGT 59.070 45.455 18.17 0.00 38.41 2.29
269 276 4.315803 CAGGTCGTTATGTGAAAGTCCTT 58.684 43.478 0.00 0.00 0.00 3.36
302 309 3.490933 CGAGCTCAAATGAACTCCGGATA 60.491 47.826 15.40 0.00 34.64 2.59
306 313 4.394920 GCTCAAATGAACTCCGGATAAACA 59.605 41.667 3.57 3.79 0.00 2.83
314 321 7.429636 TGAACTCCGGATAAACAGTAAAAAG 57.570 36.000 3.57 0.00 0.00 2.27
315 322 6.428771 TGAACTCCGGATAAACAGTAAAAAGG 59.571 38.462 3.57 0.00 0.00 3.11
412 420 4.246712 AGATGGCATTCTTGGAAGTCAT 57.753 40.909 0.00 0.00 0.00 3.06
506 514 3.361644 CGCAATTTCACGAATGTCCTTTG 59.638 43.478 0.00 0.00 0.00 2.77
512 520 5.550232 TTCACGAATGTCCTTTGATGATG 57.450 39.130 0.00 0.00 0.00 3.07
533 541 7.904094 TGATGAATTTTTACAAGCACACAAAC 58.096 30.769 0.00 0.00 0.00 2.93
545 553 6.257630 ACAAGCACACAAACCATTTATCAAAC 59.742 34.615 0.00 0.00 0.00 2.93
557 565 8.896320 ACCATTTATCAAACTTTACCAAAACC 57.104 30.769 0.00 0.00 0.00 3.27
568 578 1.868713 ACCAAAACCCCCGAAAGTTT 58.131 45.000 0.00 0.00 37.80 2.66
575 585 4.330944 AACCCCCGAAAGTTTTTGATTC 57.669 40.909 0.00 0.00 0.00 2.52
581 591 5.978322 CCCCGAAAGTTTTTGATTCGTTTTA 59.022 36.000 6.42 0.00 33.76 1.52
585 595 8.536407 CCGAAAGTTTTTGATTCGTTTTACAAT 58.464 29.630 6.42 0.00 33.76 2.71
586 596 9.894439 CGAAAGTTTTTGATTCGTTTTACAATT 57.106 25.926 0.00 0.00 0.00 2.32
615 625 4.842531 TCTTATGTTTCATCAGGGAGCA 57.157 40.909 0.00 0.00 0.00 4.26
616 626 5.378230 TCTTATGTTTCATCAGGGAGCAT 57.622 39.130 0.00 0.00 0.00 3.79
629 639 2.265739 AGCATTTGAGCTCGGCGA 59.734 55.556 10.14 10.14 42.18 5.54
645 655 0.248539 GCGACAGATACTCCACGTCC 60.249 60.000 0.00 0.00 0.00 4.79
650 660 1.094073 AGATACTCCACGTCCGTCCG 61.094 60.000 0.00 0.00 0.00 4.79
717 765 3.552875 AGATGAATGATGTGCCCTTCAG 58.447 45.455 0.00 0.00 31.69 3.02
720 768 3.765381 TGAATGATGTGCCCTTCAGAAA 58.235 40.909 0.00 0.00 0.00 2.52
751 799 3.206150 GAATGATGCAGTAATCCACCGT 58.794 45.455 0.00 0.00 0.00 4.83
754 802 4.209307 TGATGCAGTAATCCACCGTAAA 57.791 40.909 0.00 0.00 0.00 2.01
756 804 2.339418 TGCAGTAATCCACCGTAAACG 58.661 47.619 0.00 0.00 39.44 3.60
757 805 2.029200 TGCAGTAATCCACCGTAAACGA 60.029 45.455 3.65 0.00 43.02 3.85
758 806 2.995258 GCAGTAATCCACCGTAAACGAA 59.005 45.455 3.65 0.00 43.02 3.85
775 868 6.995511 AAACGAATCCAATTTCCTATCGAA 57.004 33.333 0.00 0.00 33.42 3.71
784 877 0.379669 TTCCTATCGAACGACGCTCC 59.620 55.000 0.00 0.00 42.26 4.70
1165 3625 1.061735 GGATCCCCTTCTTCCTCCTCT 60.062 57.143 0.00 0.00 0.00 3.69
1173 3642 2.239681 TCTTCCTCCTCTTCTGGTCC 57.760 55.000 0.00 0.00 0.00 4.46
1182 3652 0.530744 TCTTCTGGTCCCGTTGATCG 59.469 55.000 0.00 0.00 39.52 3.69
1211 3689 1.284982 GACTGATGCGTGCGTGTTCT 61.285 55.000 0.00 0.00 0.00 3.01
1379 3868 0.108756 CTCGTCGACTCCCCTTTTCC 60.109 60.000 14.70 0.00 0.00 3.13
1394 3883 3.380320 CCTTTTCCCTTCGTTTCTGTGTT 59.620 43.478 0.00 0.00 0.00 3.32
1400 3889 4.039973 TCCCTTCGTTTCTGTGTTCTGTAT 59.960 41.667 0.00 0.00 0.00 2.29
1401 3890 4.152402 CCCTTCGTTTCTGTGTTCTGTATG 59.848 45.833 0.00 0.00 0.00 2.39
1402 3891 4.988540 CCTTCGTTTCTGTGTTCTGTATGA 59.011 41.667 0.00 0.00 0.00 2.15
1403 3892 5.465390 CCTTCGTTTCTGTGTTCTGTATGAA 59.535 40.000 0.00 0.00 0.00 2.57
1409 3898 5.411831 TCTGTGTTCTGTATGAATGCTCT 57.588 39.130 0.00 0.00 36.99 4.09
1410 3899 5.798132 TCTGTGTTCTGTATGAATGCTCTT 58.202 37.500 0.00 0.00 36.99 2.85
1411 3900 5.640783 TCTGTGTTCTGTATGAATGCTCTTG 59.359 40.000 0.00 0.00 36.99 3.02
1414 3988 5.182001 GTGTTCTGTATGAATGCTCTTGGTT 59.818 40.000 0.00 0.00 36.99 3.67
1470 4088 7.789202 TTCTCTATAGAATCAGGCTGCTTAT 57.211 36.000 10.34 6.54 36.80 1.73
1475 4093 3.973425 AGAATCAGGCTGCTTATGGTTT 58.027 40.909 10.34 0.00 0.00 3.27
1476 4094 5.116084 AGAATCAGGCTGCTTATGGTTTA 57.884 39.130 10.34 0.00 0.00 2.01
1477 4095 4.884164 AGAATCAGGCTGCTTATGGTTTAC 59.116 41.667 10.34 0.00 0.00 2.01
1627 4355 3.635433 TCGTGGCGACTATGTTAGC 57.365 52.632 0.00 0.00 0.00 3.09
1653 4381 4.462483 TGATCCCCTGTTTGCTGTTAATTC 59.538 41.667 0.00 0.00 0.00 2.17
1655 4383 3.826157 TCCCCTGTTTGCTGTTAATTCTG 59.174 43.478 0.00 0.00 0.00 3.02
1678 4407 5.222027 TGGTTGGACTCTGTTTTATGATGGA 60.222 40.000 0.00 0.00 0.00 3.41
1679 4408 5.355350 GGTTGGACTCTGTTTTATGATGGAG 59.645 44.000 0.00 0.00 0.00 3.86
1701 4430 4.634883 AGTGCTCAGATGATGCTAAAACAG 59.365 41.667 6.06 0.00 0.00 3.16
1751 4483 8.234546 TGAGGATTACAAAATCGAGCTTTTTAC 58.765 33.333 0.00 0.00 42.16 2.01
1788 4521 5.812127 GCCCCTTTAATGCTATGTTTTCTTG 59.188 40.000 0.00 0.00 0.00 3.02
1803 4541 3.988379 TTCTTGCAAACACATGTCCTC 57.012 42.857 0.00 0.00 0.00 3.71
1824 4562 2.609459 CTCTACTTGGTAATGCAAGCGG 59.391 50.000 0.00 0.00 32.03 5.52
1831 4569 1.000717 GGTAATGCAAGCGGTGTGTTT 60.001 47.619 0.00 0.00 0.00 2.83
1851 4592 2.820178 TCAAGTGCAGTCCTCTGGATA 58.180 47.619 0.00 0.00 43.40 2.59
1862 4603 5.471456 CAGTCCTCTGGATATTTATGGTTGC 59.529 44.000 0.00 0.00 37.97 4.17
1863 4604 4.762251 GTCCTCTGGATATTTATGGTTGCC 59.238 45.833 0.00 0.00 32.73 4.52
1864 4605 4.415179 TCCTCTGGATATTTATGGTTGCCA 59.585 41.667 0.00 0.00 38.19 4.92
1865 4606 4.520492 CCTCTGGATATTTATGGTTGCCAC 59.480 45.833 0.00 0.00 35.80 5.01
1866 4607 5.122707 TCTGGATATTTATGGTTGCCACA 57.877 39.130 0.00 0.00 35.80 4.17
1867 4608 5.704354 TCTGGATATTTATGGTTGCCACAT 58.296 37.500 0.00 0.00 35.80 3.21
1868 4609 6.135454 TCTGGATATTTATGGTTGCCACATT 58.865 36.000 0.00 0.00 35.80 2.71
1869 4610 6.610830 TCTGGATATTTATGGTTGCCACATTT 59.389 34.615 0.00 0.00 35.80 2.32
1870 4611 7.125507 TCTGGATATTTATGGTTGCCACATTTT 59.874 33.333 0.00 0.00 35.80 1.82
1871 4612 7.628234 TGGATATTTATGGTTGCCACATTTTT 58.372 30.769 0.00 0.00 35.80 1.94
1872 4613 8.762645 TGGATATTTATGGTTGCCACATTTTTA 58.237 29.630 0.00 0.00 35.80 1.52
1873 4614 9.040939 GGATATTTATGGTTGCCACATTTTTAC 57.959 33.333 0.00 0.00 35.80 2.01
1874 4615 9.816354 GATATTTATGGTTGCCACATTTTTACT 57.184 29.630 0.00 0.00 35.80 2.24
1876 4617 7.721286 TTTATGGTTGCCACATTTTTACTTG 57.279 32.000 0.00 0.00 35.80 3.16
1877 4618 4.065321 TGGTTGCCACATTTTTACTTGG 57.935 40.909 0.00 0.00 0.00 3.61
1882 4623 6.147000 GGTTGCCACATTTTTACTTGGTAATG 59.853 38.462 0.00 0.00 36.33 1.90
1950 4691 8.437360 TGTGCTACAAATAGGATTAGTCATTG 57.563 34.615 0.00 0.00 30.59 2.82
2067 4815 9.187455 TGTTTCAAAATCGAGCTTTTTAATACC 57.813 29.630 0.00 0.00 0.00 2.73
2090 4866 5.447279 CCGCTTCATTCCTATTTGTGTGTAC 60.447 44.000 0.00 0.00 0.00 2.90
2175 4963 0.828022 ATCGGTTTGAGATGCGGGTA 59.172 50.000 0.00 0.00 0.00 3.69
2297 5085 2.962421 ACCAGTAGAGAGCTATGCCTTC 59.038 50.000 0.00 0.00 0.00 3.46
2301 5107 5.396213 CCAGTAGAGAGCTATGCCTTCTTTT 60.396 44.000 0.00 0.00 0.00 2.27
2492 5303 7.123247 GCTGGATTGGATATTTATACATGGCTT 59.877 37.037 0.00 0.00 0.00 4.35
2494 5305 7.396907 TGGATTGGATATTTATACATGGCTTGG 59.603 37.037 5.31 0.00 0.00 3.61
2499 5310 9.461312 TGGATATTTATACATGGCTTGGTATTC 57.539 33.333 5.31 0.00 32.72 1.75
2548 5359 6.538021 CAGTTGTCAAAATTTCCATTGGTTGA 59.462 34.615 1.86 2.21 0.00 3.18
2595 5406 8.597167 TCAGCTAATATCAGGTGCAGTATTTAT 58.403 33.333 0.00 0.00 42.48 1.40
2596 5407 9.875691 CAGCTAATATCAGGTGCAGTATTTATA 57.124 33.333 0.00 0.00 37.24 0.98
2601 5412 9.507329 AATATCAGGTGCAGTATTTATAACCAG 57.493 33.333 0.00 0.00 0.00 4.00
2602 5413 6.308015 TCAGGTGCAGTATTTATAACCAGT 57.692 37.500 0.00 0.00 0.00 4.00
2603 5414 7.426606 TCAGGTGCAGTATTTATAACCAGTA 57.573 36.000 0.00 0.00 0.00 2.74
2604 5415 7.853299 TCAGGTGCAGTATTTATAACCAGTAA 58.147 34.615 0.00 0.00 0.00 2.24
2605 5416 7.985184 TCAGGTGCAGTATTTATAACCAGTAAG 59.015 37.037 0.00 0.00 0.00 2.34
2606 5417 7.769044 CAGGTGCAGTATTTATAACCAGTAAGT 59.231 37.037 0.00 0.00 0.00 2.24
2607 5418 7.985752 AGGTGCAGTATTTATAACCAGTAAGTC 59.014 37.037 0.00 0.00 0.00 3.01
2608 5419 7.042925 GGTGCAGTATTTATAACCAGTAAGTCG 60.043 40.741 0.00 0.00 0.00 4.18
2609 5420 6.982141 TGCAGTATTTATAACCAGTAAGTCGG 59.018 38.462 0.00 0.00 0.00 4.79
2610 5421 7.147863 TGCAGTATTTATAACCAGTAAGTCGGA 60.148 37.037 0.00 0.00 0.00 4.55
2611 5422 7.381678 GCAGTATTTATAACCAGTAAGTCGGAG 59.618 40.741 0.00 0.00 0.00 4.63
2612 5423 8.411683 CAGTATTTATAACCAGTAAGTCGGAGT 58.588 37.037 0.00 0.00 0.00 3.85
2613 5424 9.632638 AGTATTTATAACCAGTAAGTCGGAGTA 57.367 33.333 0.00 0.00 0.00 2.59
2614 5425 9.890352 GTATTTATAACCAGTAAGTCGGAGTAG 57.110 37.037 0.00 0.00 0.00 2.57
2615 5426 8.757982 ATTTATAACCAGTAAGTCGGAGTAGA 57.242 34.615 0.00 0.00 0.00 2.59
2616 5427 8.757982 TTTATAACCAGTAAGTCGGAGTAGAT 57.242 34.615 0.00 0.00 0.00 1.98
2617 5428 6.880942 ATAACCAGTAAGTCGGAGTAGATC 57.119 41.667 0.00 0.00 0.00 2.75
2618 5429 3.204526 ACCAGTAAGTCGGAGTAGATCG 58.795 50.000 0.00 0.00 0.00 3.69
2619 5430 3.204526 CCAGTAAGTCGGAGTAGATCGT 58.795 50.000 0.00 0.00 0.00 3.73
2620 5431 3.002451 CCAGTAAGTCGGAGTAGATCGTG 59.998 52.174 0.00 0.00 0.00 4.35
2621 5432 3.869832 CAGTAAGTCGGAGTAGATCGTGA 59.130 47.826 0.00 0.00 0.00 4.35
2622 5433 4.331992 CAGTAAGTCGGAGTAGATCGTGAA 59.668 45.833 0.00 0.00 0.00 3.18
2623 5434 5.007823 CAGTAAGTCGGAGTAGATCGTGAAT 59.992 44.000 0.00 0.00 0.00 2.57
2624 5435 4.985538 AAGTCGGAGTAGATCGTGAATT 57.014 40.909 0.00 0.00 0.00 2.17
2625 5436 4.555348 AGTCGGAGTAGATCGTGAATTC 57.445 45.455 0.00 0.00 0.00 2.17
2626 5437 3.315749 AGTCGGAGTAGATCGTGAATTCC 59.684 47.826 2.27 0.00 0.00 3.01
2627 5438 3.315749 GTCGGAGTAGATCGTGAATTCCT 59.684 47.826 2.27 0.00 0.00 3.36
2628 5439 3.952323 TCGGAGTAGATCGTGAATTCCTT 59.048 43.478 2.27 0.00 0.00 3.36
2629 5440 4.401519 TCGGAGTAGATCGTGAATTCCTTT 59.598 41.667 2.27 0.00 0.00 3.11
2791 5602 4.771903 TGGCTTACAGTGTTTTGACTACA 58.228 39.130 0.00 0.00 0.00 2.74
3071 5882 1.302366 GATCACGCAAGATCATGCCA 58.698 50.000 16.72 2.15 43.47 4.92
3105 5916 1.594331 GTCCGCTGAAACAAAGGAGT 58.406 50.000 0.00 0.00 0.00 3.85
3153 5964 0.106708 TTCAGGTCTCAGCCACACAC 59.893 55.000 0.00 0.00 0.00 3.82
3154 5965 0.760567 TCAGGTCTCAGCCACACACT 60.761 55.000 0.00 0.00 0.00 3.55
3264 6076 0.169009 GGCTCTTTGGCGATTGTCAC 59.831 55.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.509690 TGAGAGAAATCACTCATGTTTGAATTC 58.490 33.333 14.34 14.34 38.37 2.17
23 29 5.515797 TCATACTACTGAAATCGGGTGAG 57.484 43.478 0.00 0.00 0.00 3.51
29 35 8.579682 TGACAATCATCATACTACTGAAATCG 57.420 34.615 0.00 0.00 0.00 3.34
33 39 8.298729 AGACTGACAATCATCATACTACTGAA 57.701 34.615 0.00 0.00 0.00 3.02
47 53 4.237724 TCGTTGTGATGAGACTGACAATC 58.762 43.478 0.00 0.00 31.35 2.67
48 54 4.240888 CTCGTTGTGATGAGACTGACAAT 58.759 43.478 0.00 0.00 40.68 2.71
49 55 3.552890 CCTCGTTGTGATGAGACTGACAA 60.553 47.826 0.00 0.00 40.68 3.18
59 65 3.728864 GCAATACAAGCCTCGTTGTGATG 60.729 47.826 0.00 0.73 40.89 3.07
95 101 3.065371 CACCAAGAACTTTTTGAGCGAGT 59.935 43.478 0.00 0.00 0.00 4.18
99 105 3.118542 CTGCACCAAGAACTTTTTGAGC 58.881 45.455 0.00 0.00 0.00 4.26
101 107 3.761218 TGACTGCACCAAGAACTTTTTGA 59.239 39.130 0.00 0.00 0.00 2.69
142 148 8.994429 TTTGATTTTCTTTTAGCAACTTCACA 57.006 26.923 0.00 0.00 0.00 3.58
175 182 9.719355 ATTTTTCCTTGACTTTTTAACAACTGT 57.281 25.926 0.00 0.00 0.00 3.55
189 196 9.267084 TGCTGGTTTTATTTATTTTTCCTTGAC 57.733 29.630 0.00 0.00 0.00 3.18
191 198 9.050601 TGTGCTGGTTTTATTTATTTTTCCTTG 57.949 29.630 0.00 0.00 0.00 3.61
192 199 9.791801 ATGTGCTGGTTTTATTTATTTTTCCTT 57.208 25.926 0.00 0.00 0.00 3.36
210 217 5.807520 CACAAGAAGTAGTAGTATGTGCTGG 59.192 44.000 5.88 0.00 31.53 4.85
224 231 4.451096 GCATTTCGAGGTTCACAAGAAGTA 59.549 41.667 0.00 0.00 33.63 2.24
240 247 2.670905 TCACATAACGACCTGCATTTCG 59.329 45.455 13.89 13.89 41.14 3.46
293 300 4.698780 GCCTTTTTACTGTTTATCCGGAGT 59.301 41.667 11.34 3.31 0.00 3.85
294 301 4.698304 TGCCTTTTTACTGTTTATCCGGAG 59.302 41.667 11.34 0.00 0.00 4.63
350 357 7.544566 TCAAGCGTACAAAACATTTACCAAAAA 59.455 29.630 0.00 0.00 0.00 1.94
351 358 7.033791 TCAAGCGTACAAAACATTTACCAAAA 58.966 30.769 0.00 0.00 0.00 2.44
479 487 2.057316 CATTCGTGAAATTGCGGCAAA 58.943 42.857 20.48 0.00 0.00 3.68
480 488 1.000827 ACATTCGTGAAATTGCGGCAA 60.001 42.857 18.85 18.85 0.00 4.52
481 489 0.595588 ACATTCGTGAAATTGCGGCA 59.404 45.000 0.00 0.00 0.00 5.69
482 490 1.259316 GACATTCGTGAAATTGCGGC 58.741 50.000 0.00 0.00 0.00 6.53
484 492 2.900122 AGGACATTCGTGAAATTGCG 57.100 45.000 0.00 0.00 0.00 4.85
485 493 4.545610 TCAAAGGACATTCGTGAAATTGC 58.454 39.130 0.00 0.00 0.00 3.56
488 496 6.375174 TCATCATCAAAGGACATTCGTGAAAT 59.625 34.615 0.00 0.00 0.00 2.17
491 499 4.831107 TCATCATCAAAGGACATTCGTGA 58.169 39.130 0.00 0.00 0.00 4.35
506 514 7.872163 TGTGTGCTTGTAAAAATTCATCATC 57.128 32.000 0.00 0.00 0.00 2.92
512 520 6.654793 TGGTTTGTGTGCTTGTAAAAATTC 57.345 33.333 0.00 0.00 0.00 2.17
533 541 7.389330 GGGGTTTTGGTAAAGTTTGATAAATGG 59.611 37.037 0.00 0.00 0.00 3.16
545 553 2.960384 ACTTTCGGGGGTTTTGGTAAAG 59.040 45.455 0.00 0.00 0.00 1.85
556 564 2.295070 ACGAATCAAAAACTTTCGGGGG 59.705 45.455 8.84 0.00 39.21 5.40
557 565 3.636282 ACGAATCAAAAACTTTCGGGG 57.364 42.857 8.84 0.00 39.21 5.73
586 596 7.673504 TCCCTGATGAAACATAAGATCCAAAAA 59.326 33.333 0.00 0.00 0.00 1.94
595 605 6.095860 TCAAATGCTCCCTGATGAAACATAAG 59.904 38.462 0.00 0.00 0.00 1.73
597 607 5.508567 TCAAATGCTCCCTGATGAAACATA 58.491 37.500 0.00 0.00 0.00 2.29
599 609 3.760151 CTCAAATGCTCCCTGATGAAACA 59.240 43.478 0.00 0.00 0.00 2.83
600 610 3.428589 GCTCAAATGCTCCCTGATGAAAC 60.429 47.826 0.00 0.00 0.00 2.78
601 611 2.756760 GCTCAAATGCTCCCTGATGAAA 59.243 45.455 0.00 0.00 0.00 2.69
615 625 0.176680 ATCTGTCGCCGAGCTCAAAT 59.823 50.000 15.40 0.00 0.00 2.32
616 626 0.815095 TATCTGTCGCCGAGCTCAAA 59.185 50.000 15.40 0.00 0.00 2.69
628 638 1.063764 GACGGACGTGGAGTATCTGTC 59.936 57.143 0.53 0.00 40.53 3.51
629 639 1.093159 GACGGACGTGGAGTATCTGT 58.907 55.000 0.53 0.00 34.62 3.41
669 679 6.040729 TGAATGAATGCTTCCTTTCTTTGACA 59.959 34.615 0.00 0.00 0.00 3.58
670 680 6.449698 TGAATGAATGCTTCCTTTCTTTGAC 58.550 36.000 0.00 0.00 0.00 3.18
671 681 6.653526 TGAATGAATGCTTCCTTTCTTTGA 57.346 33.333 0.00 0.00 0.00 2.69
672 682 7.654520 TCTTTGAATGAATGCTTCCTTTCTTTG 59.345 33.333 0.00 0.00 0.00 2.77
673 683 7.729116 TCTTTGAATGAATGCTTCCTTTCTTT 58.271 30.769 0.00 0.00 0.00 2.52
674 684 7.294017 TCTTTGAATGAATGCTTCCTTTCTT 57.706 32.000 0.00 0.00 0.00 2.52
675 685 6.906157 TCTTTGAATGAATGCTTCCTTTCT 57.094 33.333 0.00 0.00 0.00 2.52
720 768 8.411683 GGATTACTGCATCATTCATCTCTTTTT 58.588 33.333 0.00 0.00 0.00 1.94
725 773 5.180868 GGTGGATTACTGCATCATTCATCTC 59.819 44.000 0.00 0.00 0.00 2.75
740 788 4.183101 TGGATTCGTTTACGGTGGATTAC 58.817 43.478 2.09 0.00 40.29 1.89
751 799 7.254185 CGTTCGATAGGAAATTGGATTCGTTTA 60.254 37.037 0.00 0.00 36.14 2.01
754 802 4.506654 CGTTCGATAGGAAATTGGATTCGT 59.493 41.667 0.00 0.00 36.14 3.85
756 804 5.332355 CGTCGTTCGATAGGAAATTGGATTC 60.332 44.000 0.00 0.00 42.86 2.52
757 805 4.506654 CGTCGTTCGATAGGAAATTGGATT 59.493 41.667 0.00 0.00 42.86 3.01
758 806 4.049186 CGTCGTTCGATAGGAAATTGGAT 58.951 43.478 0.00 0.00 42.86 3.41
775 868 3.692406 GTTGGGAGGGAGCGTCGT 61.692 66.667 0.00 0.00 0.00 4.34
852 951 3.039011 GAGGGTTTCTGTATAGGCTGGA 58.961 50.000 0.00 0.00 0.00 3.86
898 1027 2.684104 CGAGGAGGGGAGTGGAGA 59.316 66.667 0.00 0.00 0.00 3.71
929 1058 2.366570 GGGAGGAGGAGAGCTGGT 59.633 66.667 0.00 0.00 0.00 4.00
932 1061 2.366570 GTGGGGAGGAGGAGAGCT 59.633 66.667 0.00 0.00 0.00 4.09
1159 3619 0.247736 CAACGGGACCAGAAGAGGAG 59.752 60.000 0.00 0.00 0.00 3.69
1182 3652 2.093310 CACGCATCAGTCAGATCAACAC 59.907 50.000 0.00 0.00 33.72 3.32
1367 3845 1.146452 AACGAAGGGAAAAGGGGAGT 58.854 50.000 0.00 0.00 0.00 3.85
1373 3851 4.335594 AGAACACAGAAACGAAGGGAAAAG 59.664 41.667 0.00 0.00 0.00 2.27
1379 3868 4.988540 TCATACAGAACACAGAAACGAAGG 59.011 41.667 0.00 0.00 0.00 3.46
1394 3883 5.528690 GCATAACCAAGAGCATTCATACAGA 59.471 40.000 0.00 0.00 0.00 3.41
1400 3889 3.119884 CGTTGCATAACCAAGAGCATTCA 60.120 43.478 0.00 0.00 36.80 2.57
1401 3890 3.126858 TCGTTGCATAACCAAGAGCATTC 59.873 43.478 0.00 0.00 36.80 2.67
1402 3891 3.081061 TCGTTGCATAACCAAGAGCATT 58.919 40.909 0.00 0.00 36.80 3.56
1403 3892 2.420022 GTCGTTGCATAACCAAGAGCAT 59.580 45.455 0.00 0.00 36.80 3.79
1409 3898 1.579084 GCCGGTCGTTGCATAACCAA 61.579 55.000 1.90 0.00 33.12 3.67
1410 3899 2.036006 GCCGGTCGTTGCATAACCA 61.036 57.895 1.90 0.00 33.12 3.67
1411 3900 2.789249 GCCGGTCGTTGCATAACC 59.211 61.111 1.90 0.00 33.12 2.85
1437 4011 6.973474 CCTGATTCTATAGAGAAACGTTCGTT 59.027 38.462 3.51 4.72 44.85 3.85
1438 4012 6.496571 CCTGATTCTATAGAGAAACGTTCGT 58.503 40.000 3.51 0.00 44.85 3.85
1439 4013 5.399892 GCCTGATTCTATAGAGAAACGTTCG 59.600 44.000 3.51 0.00 44.85 3.95
1440 4014 6.419413 CAGCCTGATTCTATAGAGAAACGTTC 59.581 42.308 3.51 0.00 44.85 3.95
1470 4088 5.216622 ACTGCCCTATCATCTAGTAAACCA 58.783 41.667 0.00 0.00 0.00 3.67
1475 4093 7.527196 GCCAATTTACTGCCCTATCATCTAGTA 60.527 40.741 0.00 0.00 0.00 1.82
1476 4094 6.745474 GCCAATTTACTGCCCTATCATCTAGT 60.745 42.308 0.00 0.00 0.00 2.57
1477 4095 5.645497 GCCAATTTACTGCCCTATCATCTAG 59.355 44.000 0.00 0.00 0.00 2.43
1576 4304 9.224058 GATCGATCACTAGTTCACTACTAAAAC 57.776 37.037 20.52 0.00 38.84 2.43
1619 4347 3.384168 ACAGGGGATCACTGCTAACATA 58.616 45.455 14.47 0.00 39.55 2.29
1627 4355 1.171308 CAGCAAACAGGGGATCACTG 58.829 55.000 13.32 13.32 41.64 3.66
1653 4381 5.124457 CCATCATAAAACAGAGTCCAACCAG 59.876 44.000 0.00 0.00 0.00 4.00
1655 4383 5.253330 TCCATCATAAAACAGAGTCCAACC 58.747 41.667 0.00 0.00 0.00 3.77
1678 4407 4.582869 TGTTTTAGCATCATCTGAGCACT 58.417 39.130 0.00 0.00 0.00 4.40
1679 4408 4.906423 CTGTTTTAGCATCATCTGAGCAC 58.094 43.478 0.00 0.00 0.00 4.40
1701 4430 2.416893 GAGAATCTCGGGAACAAGTTGC 59.583 50.000 1.81 0.00 0.00 4.17
1788 4521 3.931578 AGTAGAGAGGACATGTGTTTGC 58.068 45.455 1.15 0.00 0.00 3.68
1803 4541 2.609459 CCGCTTGCATTACCAAGTAGAG 59.391 50.000 0.00 0.00 43.17 2.43
1824 4562 2.017049 AGGACTGCACTTGAAACACAC 58.983 47.619 0.00 0.00 0.00 3.82
1831 4569 1.649321 ATCCAGAGGACTGCACTTGA 58.351 50.000 0.00 0.00 42.25 3.02
1851 4592 7.390162 CCAAGTAAAAATGTGGCAACCATAAAT 59.610 33.333 0.00 0.00 35.28 1.40
1862 4603 9.405587 CAAGTACATTACCAAGTAAAAATGTGG 57.594 33.333 9.22 0.00 41.38 4.17
1863 4604 8.911662 GCAAGTACATTACCAAGTAAAAATGTG 58.088 33.333 9.22 0.00 41.38 3.21
1864 4605 8.634444 TGCAAGTACATTACCAAGTAAAAATGT 58.366 29.630 0.00 5.07 43.17 2.71
1865 4606 8.911662 GTGCAAGTACATTACCAAGTAAAAATG 58.088 33.333 0.00 0.00 35.83 2.32
1866 4607 8.634444 TGTGCAAGTACATTACCAAGTAAAAAT 58.366 29.630 0.00 0.00 31.56 1.82
1867 4608 7.997482 TGTGCAAGTACATTACCAAGTAAAAA 58.003 30.769 0.00 0.00 31.56 1.94
1868 4609 7.569639 TGTGCAAGTACATTACCAAGTAAAA 57.430 32.000 0.00 0.00 31.56 1.52
1869 4610 7.753309 ATGTGCAAGTACATTACCAAGTAAA 57.247 32.000 0.00 0.00 38.05 2.01
1870 4611 7.753309 AATGTGCAAGTACATTACCAAGTAA 57.247 32.000 13.63 0.00 46.40 2.24
1882 4623 8.973378 TGCTGTTTAATAAAAATGTGCAAGTAC 58.027 29.630 0.00 0.00 0.00 2.73
1957 4698 6.481954 ACTGCTTCATTCTTAGTAAAACCG 57.518 37.500 0.00 0.00 0.00 4.44
2067 4815 4.685169 ACACACAAATAGGAATGAAGCG 57.315 40.909 0.00 0.00 0.00 4.68
2175 4963 1.374252 GTCGATCACCCGCTTGTGT 60.374 57.895 0.00 0.00 37.51 3.72
2301 5107 4.703897 CTGGTGTCTCTCCACTTGTAAAA 58.296 43.478 0.00 0.00 35.63 1.52
2492 5303 6.493115 ACCAAATCTCAAACACATGAATACCA 59.507 34.615 0.00 0.00 0.00 3.25
2494 5305 7.370383 ACACCAAATCTCAAACACATGAATAC 58.630 34.615 0.00 0.00 0.00 1.89
2499 5310 5.185668 TGACACCAAATCTCAAACACATG 57.814 39.130 0.00 0.00 0.00 3.21
2548 5359 0.392998 GCAATGTCCTCACGGTGGAT 60.393 55.000 8.50 0.00 35.87 3.41
2554 5365 0.445436 GCTGAAGCAATGTCCTCACG 59.555 55.000 0.00 0.00 41.59 4.35
2595 5406 4.813161 CGATCTACTCCGACTTACTGGTTA 59.187 45.833 0.00 0.00 0.00 2.85
2596 5407 3.626670 CGATCTACTCCGACTTACTGGTT 59.373 47.826 0.00 0.00 0.00 3.67
2597 5408 3.204526 CGATCTACTCCGACTTACTGGT 58.795 50.000 0.00 0.00 0.00 4.00
2598 5409 3.002451 CACGATCTACTCCGACTTACTGG 59.998 52.174 0.00 0.00 0.00 4.00
2599 5410 3.869832 TCACGATCTACTCCGACTTACTG 59.130 47.826 0.00 0.00 0.00 2.74
2600 5411 4.134379 TCACGATCTACTCCGACTTACT 57.866 45.455 0.00 0.00 0.00 2.24
2601 5412 4.871993 TTCACGATCTACTCCGACTTAC 57.128 45.455 0.00 0.00 0.00 2.34
2602 5413 5.008415 GGAATTCACGATCTACTCCGACTTA 59.992 44.000 7.93 0.00 0.00 2.24
2603 5414 4.202030 GGAATTCACGATCTACTCCGACTT 60.202 45.833 7.93 0.00 0.00 3.01
2604 5415 3.315749 GGAATTCACGATCTACTCCGACT 59.684 47.826 7.93 0.00 0.00 4.18
2605 5416 3.315749 AGGAATTCACGATCTACTCCGAC 59.684 47.826 7.93 0.00 0.00 4.79
2606 5417 3.552875 AGGAATTCACGATCTACTCCGA 58.447 45.455 7.93 0.00 0.00 4.55
2607 5418 3.992260 AGGAATTCACGATCTACTCCG 57.008 47.619 7.93 0.00 0.00 4.63
2608 5419 6.986904 AAAAAGGAATTCACGATCTACTCC 57.013 37.500 7.93 0.00 0.00 3.85
2861 5672 4.237843 AGGGAGAAATGGATAGATCTGCA 58.762 43.478 5.18 0.00 32.56 4.41
3105 5916 6.535150 GGACGATTGAAACTCAATACAGATGA 59.465 38.462 1.96 0.00 46.20 2.92
3153 5964 4.152402 CGTCTGAACTGGTAATTCCACAAG 59.848 45.833 0.00 0.00 41.93 3.16
3154 5965 4.062293 CGTCTGAACTGGTAATTCCACAA 58.938 43.478 0.00 0.00 41.93 3.33


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

AutoCloner maintained by Alex Coulton.