Multiple sequence alignment - TraesCS5A01G055600

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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 TraesCS5A01G055600 chr5A 100.000 2520 0 0 1 2520 52007549 52005030 0.000000e+00 4654.0
1 TraesCS5A01G055600 chr5A 87.516 785 75 11 1552 2334 51809183 51808420 0.000000e+00 885.0
2 TraesCS5A01G055600 chr5A 85.849 848 57 19 570 1396 51810334 51809529 0.000000e+00 843.0
3 TraesCS5A01G055600 chr5A 83.403 476 61 13 914 1380 51748477 51748011 2.320000e-115 425.0
4 TraesCS5A01G055600 chr5A 79.940 334 35 20 570 873 52171828 52171497 1.520000e-52 217.0
5 TraesCS5A01G055600 chr5A 96.581 117 3 1 2404 2520 707269355 707269470 2.560000e-45 193.0
6 TraesCS5A01G055600 chr5A 95.726 117 4 1 2405 2520 517623230 517623114 1.190000e-43 187.0
7 TraesCS5A01G055600 chr5D 92.758 1864 96 16 570 2411 62132160 62130314 0.000000e+00 2658.0
8 TraesCS5A01G055600 chr5D 89.573 844 60 18 570 1397 61838734 61837903 0.000000e+00 1046.0
9 TraesCS5A01G055600 chr5D 95.431 569 26 0 1 569 286924630 286925198 0.000000e+00 907.0
10 TraesCS5A01G055600 chr5D 95.255 569 27 0 1 569 528885377 528884809 0.000000e+00 902.0
11 TraesCS5A01G055600 chr5D 93.995 383 20 3 1767 2147 93604928 93604547 6.040000e-161 577.0
12 TraesCS5A01G055600 chr5D 83.301 509 57 17 888 1385 61792722 61792231 6.400000e-121 444.0
13 TraesCS5A01G055600 chr5D 89.728 331 31 3 2006 2334 61836919 61836590 1.080000e-113 420.0
14 TraesCS5A01G055600 chr5D 87.097 310 38 2 570 878 62134177 62133869 1.430000e-92 350.0
15 TraesCS5A01G055600 chr5D 87.097 279 19 8 1440 1712 61837912 61837645 1.470000e-77 300.0
16 TraesCS5A01G055600 chr5D 88.293 205 23 1 1796 2000 61837167 61836964 6.960000e-61 244.0
17 TraesCS5A01G055600 chr5D 86.996 223 22 3 658 873 62136628 62136406 6.960000e-61 244.0
18 TraesCS5A01G055600 chr5D 79.819 332 38 13 570 873 61841370 61841040 5.460000e-52 215.0
19 TraesCS5A01G055600 chr5D 87.805 82 8 2 1720 1801 61837484 61837405 7.420000e-16 95.3
20 TraesCS5A01G055600 chr5D 97.619 42 1 0 1402 1443 386689368 386689327 3.480000e-09 73.1
21 TraesCS5A01G055600 chr5D 93.182 44 2 1 2354 2396 345933900 345933857 2.090000e-06 63.9
22 TraesCS5A01G055600 chr5B 92.438 1415 79 11 570 1971 68370797 68372196 0.000000e+00 1995.0
23 TraesCS5A01G055600 chr5B 91.935 806 46 6 1520 2323 68421687 68422475 0.000000e+00 1110.0
24 TraesCS5A01G055600 chr5B 89.464 522 31 7 1014 1532 68420912 68421412 2.730000e-179 638.0
25 TraesCS5A01G055600 chr5B 91.304 460 28 8 1955 2411 68372246 68372696 3.560000e-173 617.0
26 TraesCS5A01G055600 chr5B 85.032 314 37 5 570 873 68380932 68381245 6.770000e-81 311.0
27 TraesCS5A01G055600 chr5B 86.010 193 18 4 690 873 68368115 68368307 5.500000e-47 198.0
28 TraesCS5A01G055600 chr5B 95.495 111 5 0 913 1023 68416171 68416281 7.160000e-41 178.0
29 TraesCS5A01G055600 chr5B 90.323 62 4 1 2352 2411 68486840 68486901 2.080000e-11 80.5
30 TraesCS5A01G055600 chr7D 95.431 569 26 0 1 569 549830316 549829748 0.000000e+00 907.0
31 TraesCS5A01G055600 chr7D 95.088 570 28 0 1 570 58171985 58171416 0.000000e+00 898.0
32 TraesCS5A01G055600 chr7D 82.432 148 22 4 1782 1927 534466774 534466919 2.630000e-25 126.0
33 TraesCS5A01G055600 chr1D 95.431 569 26 0 1 569 79155055 79155623 0.000000e+00 907.0
34 TraesCS5A01G055600 chr1D 94.965 576 29 0 1 576 314156732 314157307 0.000000e+00 904.0
35 TraesCS5A01G055600 chr1D 91.489 47 3 1 2366 2411 371189032 371188986 2.090000e-06 63.9
36 TraesCS5A01G055600 chr4D 95.263 570 27 0 1 570 487308284 487307715 0.000000e+00 904.0
37 TraesCS5A01G055600 chr4D 97.436 39 0 1 2363 2401 16653163 16653126 5.820000e-07 65.8
38 TraesCS5A01G055600 chr4D 88.462 52 3 3 2362 2411 464203896 464203846 2.710000e-05 60.2
39 TraesCS5A01G055600 chr2D 95.255 569 26 1 1 569 649579359 649579926 0.000000e+00 900.0
40 TraesCS5A01G055600 chr2D 77.932 503 93 15 1740 2233 336734280 336734773 5.270000e-77 298.0
41 TraesCS5A01G055600 chr2D 81.633 147 25 2 1782 1927 623916038 623915893 1.220000e-23 121.0
42 TraesCS5A01G055600 chr6D 94.939 573 29 0 1 573 9097583 9097011 0.000000e+00 898.0
43 TraesCS5A01G055600 chrUn 80.538 483 66 14 922 1385 337950277 337950750 1.860000e-91 346.0
44 TraesCS5A01G055600 chrUn 80.538 483 66 14 922 1385 337959460 337958987 1.860000e-91 346.0
45 TraesCS5A01G055600 chr2B 77.041 588 82 34 1659 2233 404204171 404204718 3.170000e-74 289.0
46 TraesCS5A01G055600 chr2B 95.556 45 2 0 1398 1442 138655196 138655240 3.480000e-09 73.1
47 TraesCS5A01G055600 chr2B 91.304 46 3 1 2363 2407 107530851 107530896 7.530000e-06 62.1
48 TraesCS5A01G055600 chr2B 85.965 57 6 2 2362 2416 23330782 23330838 2.710000e-05 60.2
49 TraesCS5A01G055600 chr1A 97.368 114 3 0 2407 2520 41908048 41908161 7.110000e-46 195.0
50 TraesCS5A01G055600 chr1A 97.297 111 3 0 2410 2520 569419729 569419839 3.310000e-44 189.0
51 TraesCS5A01G055600 chr1A 89.286 56 5 1 1389 1444 13380723 13380777 4.500000e-08 69.4
52 TraesCS5A01G055600 chr7A 98.182 110 2 0 2411 2520 722651965 722652074 2.560000e-45 193.0
53 TraesCS5A01G055600 chr7A 96.491 114 4 0 2407 2520 734280287 734280174 3.310000e-44 189.0
54 TraesCS5A01G055600 chr4A 98.165 109 2 0 2412 2520 307267705 307267597 9.200000e-45 191.0
55 TraesCS5A01G055600 chr4A 91.111 45 3 1 2364 2407 577977981 577978025 2.710000e-05 60.2
56 TraesCS5A01G055600 chr3A 97.321 112 3 0 2409 2520 696395198 696395309 9.200000e-45 191.0
57 TraesCS5A01G055600 chr3A 91.837 49 2 2 2364 2411 728770974 728770927 1.620000e-07 67.6
58 TraesCS5A01G055600 chr3A 90.000 50 3 2 2363 2411 21364621 21364573 2.090000e-06 63.9
59 TraesCS5A01G055600 chr2A 95.690 116 4 1 2405 2520 70243820 70243706 4.280000e-43 185.0
60 TraesCS5A01G055600 chr6A 97.674 43 1 0 1399 1441 13681164 13681206 9.670000e-10 75.0
61 TraesCS5A01G055600 chr6B 97.500 40 1 0 1402 1441 466966479 466966440 4.500000e-08 69.4
62 TraesCS5A01G055600 chr1B 93.617 47 2 1 1387 1433 685131089 685131044 4.500000e-08 69.4
63 TraesCS5A01G055600 chr7B 97.297 37 1 0 2360 2396 563740019 563739983 2.090000e-06 63.9
64 TraesCS5A01G055600 chr4B 87.273 55 4 3 2364 2416 37318867 37318814 2.710000e-05 60.2


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 TraesCS5A01G055600 chr5A 52005030 52007549 2519 True 4654.000000 4654 100.000000 1 2520 1 chr5A.!!$R2 2519
1 TraesCS5A01G055600 chr5A 51808420 51810334 1914 True 864.000000 885 86.682500 570 2334 2 chr5A.!!$R5 1764
2 TraesCS5A01G055600 chr5D 62130314 62136628 6314 True 1084.000000 2658 88.950333 570 2411 3 chr5D.!!$R7 1841
3 TraesCS5A01G055600 chr5D 286924630 286925198 568 False 907.000000 907 95.431000 1 569 1 chr5D.!!$F1 568
4 TraesCS5A01G055600 chr5D 528884809 528885377 568 True 902.000000 902 95.255000 1 569 1 chr5D.!!$R5 568
5 TraesCS5A01G055600 chr5D 61836590 61841370 4780 True 386.716667 1046 87.052500 570 2334 6 chr5D.!!$R6 1764
6 TraesCS5A01G055600 chr5B 68368115 68372696 4581 False 936.666667 1995 89.917333 570 2411 3 chr5B.!!$F4 1841
7 TraesCS5A01G055600 chr5B 68420912 68422475 1563 False 874.000000 1110 90.699500 1014 2323 2 chr5B.!!$F5 1309
8 TraesCS5A01G055600 chr7D 549829748 549830316 568 True 907.000000 907 95.431000 1 569 1 chr7D.!!$R2 568
9 TraesCS5A01G055600 chr7D 58171416 58171985 569 True 898.000000 898 95.088000 1 570 1 chr7D.!!$R1 569
10 TraesCS5A01G055600 chr1D 79155055 79155623 568 False 907.000000 907 95.431000 1 569 1 chr1D.!!$F1 568
11 TraesCS5A01G055600 chr1D 314156732 314157307 575 False 904.000000 904 94.965000 1 576 1 chr1D.!!$F2 575
12 TraesCS5A01G055600 chr4D 487307715 487308284 569 True 904.000000 904 95.263000 1 570 1 chr4D.!!$R3 569
13 TraesCS5A01G055600 chr2D 649579359 649579926 567 False 900.000000 900 95.255000 1 569 1 chr2D.!!$F2 568
14 TraesCS5A01G055600 chr6D 9097011 9097583 572 True 898.000000 898 94.939000 1 573 1 chr6D.!!$R1 572
15 TraesCS5A01G055600 chr2B 404204171 404204718 547 False 289.000000 289 77.041000 1659 2233 1 chr2B.!!$F4 574

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
295 296 1.004320 CATTGGTCCCGGTTCGTGA 60.004 57.895 0.00 0.0 0.0 4.35 F
316 317 1.557832 CATGAACCGGGACTAAAGGGA 59.442 52.381 6.32 0.0 0.0 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1154 5709 1.358402 CTGTCGCTGATCCTCCTCG 59.642 63.158 0.00 0.0 0.0 4.63 R
1652 6752 2.417586 CACGAGAGAAAATGCATGCTCA 59.582 45.455 20.33 0.0 0.0 4.26 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
137 138 8.529476 AGTTTCGATAGGAGAAAGCTTAACTAA 58.471 33.333 0.00 0.00 38.15 2.24
295 296 1.004320 CATTGGTCCCGGTTCGTGA 60.004 57.895 0.00 0.00 0.00 4.35
316 317 1.557832 CATGAACCGGGACTAAAGGGA 59.442 52.381 6.32 0.00 0.00 4.20
485 486 1.983224 CCTCACGAACCAGGACCAT 59.017 57.895 0.00 0.00 30.32 3.55
619 5131 9.132521 CTGCCAAATCTGAAGTTTTAAATACAG 57.867 33.333 0.00 0.00 0.00 2.74
632 5144 5.514059 TTAAATACAGCGGTTCGTTACAC 57.486 39.130 0.00 0.00 0.00 2.90
640 5152 2.863704 GCGGTTCGTTACACTAGTGGTT 60.864 50.000 26.12 9.42 34.19 3.67
664 5177 9.436957 GTTGATATTTCTCCAGACTACTTTCAA 57.563 33.333 0.00 0.00 0.00 2.69
726 5239 6.479972 TTTGTAGGTCCAATATCATCTCGT 57.520 37.500 0.00 0.00 0.00 4.18
732 5245 4.523173 GGTCCAATATCATCTCGTGGAGTA 59.477 45.833 0.00 0.00 39.02 2.59
753 5266 7.111247 AGTAAGAGAGATGTCCAATTCAGAG 57.889 40.000 0.00 0.00 0.00 3.35
760 5273 6.597280 AGAGATGTCCAATTCAGAGTTTAAGC 59.403 38.462 0.00 0.00 0.00 3.09
766 5279 6.150140 GTCCAATTCAGAGTTTAAGCACAGAT 59.850 38.462 0.00 0.00 0.00 2.90
771 5284 8.798859 ATTCAGAGTTTAAGCACAGATAATGT 57.201 30.769 0.00 0.00 45.43 2.71
786 5299 7.279536 CACAGATAATGTAGAAGTGAAGCATGT 59.720 37.037 0.00 0.00 41.41 3.21
813 5327 2.337532 CACTGCCAGGCAAGCAAC 59.662 61.111 17.03 0.00 40.35 4.17
818 5332 2.290896 ACTGCCAGGCAAGCAACTTATA 60.291 45.455 17.03 0.00 40.35 0.98
819 5333 2.357009 CTGCCAGGCAAGCAACTTATAG 59.643 50.000 17.03 0.00 40.35 1.31
883 5417 9.422681 TCTCTGCTTTTAGGAGTAGTATATTGT 57.577 33.333 0.00 0.00 35.01 2.71
984 5526 3.656045 CACGGTTCGCACCCCAAC 61.656 66.667 0.00 0.00 40.52 3.77
1012 5554 5.045505 TCCAACTGGTGCCTATAAATACACA 60.046 40.000 0.00 0.00 34.69 3.72
1154 5709 2.287909 ACGTGAAGCAAGAGAGACTGAC 60.288 50.000 0.00 0.00 0.00 3.51
1366 5924 1.607628 GATGAAGCTGGATGGTCATGC 59.392 52.381 1.09 0.00 0.00 4.06
1395 5953 4.650972 TTTTGCTATGTGGTACTCCCTT 57.349 40.909 0.00 0.00 0.00 3.95
1400 5958 3.689649 GCTATGTGGTACTCCCTTTGTTG 59.310 47.826 0.00 0.00 0.00 3.33
1411 5969 5.892348 ACTCCCTTTGTTGGTGATCTAAAT 58.108 37.500 0.00 0.00 0.00 1.40
1415 5973 5.047092 CCCTTTGTTGGTGATCTAAATGCTT 60.047 40.000 0.00 0.00 0.00 3.91
1501 6059 6.272698 TCGTGAATTCGTGATCATGTTATG 57.727 37.500 14.52 0.00 34.80 1.90
1652 6752 5.106038 CCATACAACATTCATCTGCACAAGT 60.106 40.000 0.00 0.00 0.00 3.16
1656 6756 2.486982 ACATTCATCTGCACAAGTGAGC 59.513 45.455 4.04 0.00 0.00 4.26
1845 7342 4.625972 TCTTTTGAACCGAAAGTCCAAC 57.374 40.909 6.58 0.00 36.52 3.77
1846 7343 3.379057 TCTTTTGAACCGAAAGTCCAACC 59.621 43.478 6.58 0.00 36.52 3.77
1923 7420 9.959749 GACCACTCTTAAATACATTTTGACAAA 57.040 29.630 0.00 0.00 0.00 2.83
1985 7548 4.164221 ACACGATGAGGGATAAAATCACCT 59.836 41.667 0.00 0.00 34.14 4.00
2025 7648 8.991783 AAACTTAAAGCTCTAAACCCTAAACT 57.008 30.769 0.00 0.00 0.00 2.66
2150 7787 0.386858 TTCGAAAGTCCTCGTCGCAG 60.387 55.000 0.00 0.00 39.84 5.18
2297 7938 1.134098 AGTTGTATTCGGGGCCATCAG 60.134 52.381 4.39 0.00 0.00 2.90
2413 8055 6.500684 TCTTTTGCAGACTCCAAATATCAC 57.499 37.500 0.00 0.00 32.76 3.06
2414 8056 6.240894 TCTTTTGCAGACTCCAAATATCACT 58.759 36.000 0.00 0.00 32.76 3.41
2415 8057 7.394016 TCTTTTGCAGACTCCAAATATCACTA 58.606 34.615 0.00 0.00 32.76 2.74
2416 8058 7.550551 TCTTTTGCAGACTCCAAATATCACTAG 59.449 37.037 0.00 0.00 32.76 2.57
2417 8059 5.939764 TGCAGACTCCAAATATCACTAGT 57.060 39.130 0.00 0.00 0.00 2.57
2418 8060 7.418337 TTGCAGACTCCAAATATCACTAGTA 57.582 36.000 0.00 0.00 0.00 1.82
2419 8061 7.043961 TGCAGACTCCAAATATCACTAGTAG 57.956 40.000 0.00 0.00 0.00 2.57
2420 8062 6.833933 TGCAGACTCCAAATATCACTAGTAGA 59.166 38.462 3.59 0.00 0.00 2.59
2421 8063 7.342026 TGCAGACTCCAAATATCACTAGTAGAA 59.658 37.037 3.59 0.00 0.00 2.10
2422 8064 8.198109 GCAGACTCCAAATATCACTAGTAGAAA 58.802 37.037 3.59 0.00 0.00 2.52
2425 8067 9.535878 GACTCCAAATATCACTAGTAGAAAAGG 57.464 37.037 3.59 0.00 0.00 3.11
2426 8068 9.268282 ACTCCAAATATCACTAGTAGAAAAGGA 57.732 33.333 3.59 0.00 0.00 3.36
2427 8069 9.757227 CTCCAAATATCACTAGTAGAAAAGGAG 57.243 37.037 3.59 4.18 0.00 3.69
2428 8070 8.705594 TCCAAATATCACTAGTAGAAAAGGAGG 58.294 37.037 3.59 0.00 0.00 4.30
2429 8071 7.442666 CCAAATATCACTAGTAGAAAAGGAGGC 59.557 40.741 3.59 0.00 0.00 4.70
2430 8072 7.922699 AATATCACTAGTAGAAAAGGAGGCT 57.077 36.000 3.59 0.00 0.00 4.58
2431 8073 7.922699 ATATCACTAGTAGAAAAGGAGGCTT 57.077 36.000 3.59 0.00 0.00 4.35
2432 8074 6.628644 ATCACTAGTAGAAAAGGAGGCTTT 57.371 37.500 3.59 0.00 0.00 3.51
2433 8075 5.794894 TCACTAGTAGAAAAGGAGGCTTTG 58.205 41.667 3.59 0.00 0.00 2.77
2434 8076 4.938226 CACTAGTAGAAAAGGAGGCTTTGG 59.062 45.833 3.59 0.00 0.00 3.28
2435 8077 4.597940 ACTAGTAGAAAAGGAGGCTTTGGT 59.402 41.667 3.59 0.00 0.00 3.67
2436 8078 4.455070 AGTAGAAAAGGAGGCTTTGGTT 57.545 40.909 0.00 0.00 0.00 3.67
2437 8079 4.399219 AGTAGAAAAGGAGGCTTTGGTTC 58.601 43.478 0.00 0.00 0.00 3.62
2438 8080 3.312736 AGAAAAGGAGGCTTTGGTTCA 57.687 42.857 0.00 0.00 0.00 3.18
2439 8081 3.225940 AGAAAAGGAGGCTTTGGTTCAG 58.774 45.455 0.00 0.00 0.00 3.02
2440 8082 2.001076 AAAGGAGGCTTTGGTTCAGG 57.999 50.000 0.00 0.00 0.00 3.86
2441 8083 0.540597 AAGGAGGCTTTGGTTCAGGC 60.541 55.000 0.00 0.00 37.08 4.85
2442 8084 1.979155 GGAGGCTTTGGTTCAGGCC 60.979 63.158 0.00 0.00 44.38 5.19
2444 8086 3.373565 GGCTTTGGTTCAGGCCGG 61.374 66.667 0.00 0.00 35.08 6.13
2445 8087 3.373565 GCTTTGGTTCAGGCCGGG 61.374 66.667 2.18 0.00 0.00 5.73
2446 8088 2.115266 CTTTGGTTCAGGCCGGGT 59.885 61.111 2.18 0.00 0.00 5.28
2447 8089 1.377229 CTTTGGTTCAGGCCGGGTA 59.623 57.895 2.18 0.00 0.00 3.69
2448 8090 0.250989 CTTTGGTTCAGGCCGGGTAA 60.251 55.000 2.18 0.00 0.00 2.85
2449 8091 0.250989 TTTGGTTCAGGCCGGGTAAG 60.251 55.000 2.18 0.00 0.00 2.34
2450 8092 2.437895 GGTTCAGGCCGGGTAAGC 60.438 66.667 2.18 0.00 0.00 3.09
2462 8104 3.700198 GGTAAGCCCATTAGTCCCG 57.300 57.895 0.00 0.00 0.00 5.14
2463 8105 0.108019 GGTAAGCCCATTAGTCCCGG 59.892 60.000 0.00 0.00 0.00 5.73
2464 8106 0.835276 GTAAGCCCATTAGTCCCGGT 59.165 55.000 0.00 0.00 0.00 5.28
2465 8107 1.211212 GTAAGCCCATTAGTCCCGGTT 59.789 52.381 0.00 0.00 0.00 4.44
2466 8108 0.255033 AAGCCCATTAGTCCCGGTTC 59.745 55.000 0.00 0.00 0.00 3.62
2467 8109 0.912487 AGCCCATTAGTCCCGGTTCA 60.912 55.000 0.00 0.00 0.00 3.18
2468 8110 0.463833 GCCCATTAGTCCCGGTTCAG 60.464 60.000 0.00 0.00 0.00 3.02
2469 8111 0.909623 CCCATTAGTCCCGGTTCAGT 59.090 55.000 0.00 0.00 0.00 3.41
2470 8112 1.134491 CCCATTAGTCCCGGTTCAGTC 60.134 57.143 0.00 0.00 0.00 3.51
2471 8113 1.134491 CCATTAGTCCCGGTTCAGTCC 60.134 57.143 0.00 0.00 0.00 3.85
2472 8114 1.553248 CATTAGTCCCGGTTCAGTCCA 59.447 52.381 0.00 0.00 0.00 4.02
2473 8115 1.263356 TTAGTCCCGGTTCAGTCCAG 58.737 55.000 0.00 0.00 0.00 3.86
2474 8116 0.406750 TAGTCCCGGTTCAGTCCAGA 59.593 55.000 0.00 0.00 0.00 3.86
2475 8117 0.471211 AGTCCCGGTTCAGTCCAGAA 60.471 55.000 0.00 0.00 0.00 3.02
2476 8118 0.320508 GTCCCGGTTCAGTCCAGAAC 60.321 60.000 0.00 0.00 45.50 3.01
2480 8122 4.695560 GTTCAGTCCAGAACCGGG 57.304 61.111 6.32 0.00 41.52 5.73
2481 8123 2.055299 GTTCAGTCCAGAACCGGGA 58.945 57.895 6.32 0.00 41.52 5.14
2486 8128 4.243550 TCCAGAACCGGGACCAAT 57.756 55.556 6.32 0.00 0.00 3.16
2487 8129 1.682849 TCCAGAACCGGGACCAATG 59.317 57.895 6.32 0.00 0.00 2.82
2488 8130 1.378514 CCAGAACCGGGACCAATGG 60.379 63.158 6.32 0.00 0.00 3.16
2489 8131 1.378514 CAGAACCGGGACCAATGGG 60.379 63.158 6.32 0.00 41.29 4.00
2502 8144 1.340889 CCAATGGGTGCATTTATCCCG 59.659 52.381 4.96 0.00 43.75 5.14
2503 8145 2.305928 CAATGGGTGCATTTATCCCGA 58.694 47.619 4.96 0.00 43.75 5.14
2504 8146 2.892852 CAATGGGTGCATTTATCCCGAT 59.107 45.455 4.96 0.00 43.75 4.18
2505 8147 2.746279 TGGGTGCATTTATCCCGATT 57.254 45.000 4.96 0.00 43.75 3.34
2506 8148 2.582052 TGGGTGCATTTATCCCGATTC 58.418 47.619 4.96 0.00 43.75 2.52
2507 8149 1.535462 GGGTGCATTTATCCCGATTCG 59.465 52.381 0.00 0.00 0.00 3.34
2508 8150 2.218603 GGTGCATTTATCCCGATTCGT 58.781 47.619 5.20 0.00 0.00 3.85
2509 8151 2.032030 GGTGCATTTATCCCGATTCGTG 60.032 50.000 5.20 0.00 0.00 4.35
2510 8152 1.601903 TGCATTTATCCCGATTCGTGC 59.398 47.619 5.20 6.93 0.00 5.34
2511 8153 1.398451 GCATTTATCCCGATTCGTGCG 60.398 52.381 5.20 0.00 0.00 5.34
2517 8159 3.309675 CCGATTCGTGCGGCTAAG 58.690 61.111 5.20 0.00 42.55 2.18
2518 8160 2.237751 CCGATTCGTGCGGCTAAGG 61.238 63.158 5.20 0.00 42.55 2.69
2519 8161 2.871427 CGATTCGTGCGGCTAAGGC 61.871 63.158 0.00 0.00 37.82 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.179265 CGCGCCGATCTCGTTGTT 61.179 61.111 0.00 0.00 37.74 2.83
119 120 6.070194 AGCCACATTAGTTAAGCTTTCTCCTA 60.070 38.462 3.20 0.00 0.00 2.94
137 138 0.396139 ATGAAATGCCCGAGCCACAT 60.396 50.000 0.00 0.00 38.69 3.21
295 296 1.280998 CCCTTTAGTCCCGGTTCATGT 59.719 52.381 0.00 0.00 0.00 3.21
316 317 1.228154 GAACCGGAACCACAGGCTT 60.228 57.895 9.46 0.00 37.36 4.35
463 464 2.358737 CCTGGTTCGTGAGGCCAC 60.359 66.667 5.01 0.00 39.86 5.01
478 479 2.691732 CATGGGGGCAATGGTCCT 59.308 61.111 0.00 0.00 39.39 3.85
499 501 2.028112 CCTGATTCAGTTCAGAACCGGA 60.028 50.000 9.46 5.48 44.88 5.14
619 5131 1.336240 ACCACTAGTGTAACGAACCGC 60.336 52.381 21.18 0.00 45.86 5.68
632 5144 7.118496 AGTCTGGAGAAATATCAACCACTAG 57.882 40.000 0.00 0.00 33.15 2.57
640 5152 9.658799 CTTTGAAAGTAGTCTGGAGAAATATCA 57.341 33.333 0.00 0.00 0.00 2.15
664 5177 0.893447 GGTAGGTGGTACTCGCACTT 59.107 55.000 0.00 0.00 0.00 3.16
708 5221 3.576118 CTCCACGAGATGATATTGGACCT 59.424 47.826 0.00 0.00 32.79 3.85
726 5239 5.721480 TGAATTGGACATCTCTCTTACTCCA 59.279 40.000 0.00 0.00 0.00 3.86
732 5245 6.371595 AACTCTGAATTGGACATCTCTCTT 57.628 37.500 0.00 0.00 0.00 2.85
753 5266 9.151471 TCACTTCTACATTATCTGTGCTTAAAC 57.849 33.333 0.00 0.00 38.92 2.01
760 5273 7.279536 ACATGCTTCACTTCTACATTATCTGTG 59.720 37.037 0.00 0.00 38.92 3.66
766 5279 7.041721 CCACTACATGCTTCACTTCTACATTA 58.958 38.462 0.00 0.00 0.00 1.90
771 5284 5.939764 ATCCACTACATGCTTCACTTCTA 57.060 39.130 0.00 0.00 0.00 2.10
981 5523 1.688197 AGGCACCAGTTGGAATTGTTG 59.312 47.619 4.92 0.00 38.94 3.33
984 5526 5.913137 TTTATAGGCACCAGTTGGAATTG 57.087 39.130 4.92 0.00 38.94 2.32
1012 5554 0.941542 GTTGGTGTGTGCATACGTGT 59.058 50.000 9.18 0.00 0.00 4.49
1154 5709 1.358402 CTGTCGCTGATCCTCCTCG 59.642 63.158 0.00 0.00 0.00 4.63
1308 5866 4.722700 GCAGCCGCTGGGGAAGAA 62.723 66.667 21.77 0.00 38.47 2.52
1366 5924 6.278363 AGTACCACATAGCAAAATACTACCG 58.722 40.000 0.00 0.00 0.00 4.02
1411 5969 8.795842 TCCTTCCGTAAAGAAATATAAAAGCA 57.204 30.769 0.00 0.00 37.12 3.91
1478 6036 5.810074 ACATAACATGATCACGAATTCACGA 59.190 36.000 6.22 1.13 37.03 4.35
1479 6037 6.036246 ACATAACATGATCACGAATTCACG 57.964 37.500 6.22 0.00 39.31 4.35
1480 6038 7.688372 AGAACATAACATGATCACGAATTCAC 58.312 34.615 6.22 0.00 34.84 3.18
1481 6039 7.848223 AGAACATAACATGATCACGAATTCA 57.152 32.000 6.22 0.00 34.84 2.57
1482 6040 8.177663 ACAAGAACATAACATGATCACGAATTC 58.822 33.333 0.00 0.00 34.84 2.17
1483 6041 8.044060 ACAAGAACATAACATGATCACGAATT 57.956 30.769 0.00 0.00 34.84 2.17
1484 6042 7.201644 GGACAAGAACATAACATGATCACGAAT 60.202 37.037 0.00 0.00 34.84 3.34
1485 6043 6.092122 GGACAAGAACATAACATGATCACGAA 59.908 38.462 0.00 0.00 34.84 3.85
1501 6059 6.800408 GCTTTATTTCCTTAACGGACAAGAAC 59.200 38.462 0.00 0.00 42.97 3.01
1652 6752 2.417586 CACGAGAGAAAATGCATGCTCA 59.582 45.455 20.33 0.00 0.00 4.26
1656 6756 2.905959 TGCACGAGAGAAAATGCATG 57.094 45.000 0.00 0.00 42.92 4.06
1953 7450 3.138304 TCCCTCATCGTGTCAAGTTTTG 58.862 45.455 0.00 0.00 0.00 2.44
2150 7787 6.310224 AGTTTCGTTTGCATATTTATGGTTGC 59.690 34.615 0.00 0.00 34.32 4.17
2396 8037 7.278461 TCTACTAGTGATATTTGGAGTCTGC 57.722 40.000 5.39 0.00 0.00 4.26
2411 8053 4.938226 CCAAAGCCTCCTTTTCTACTAGTG 59.062 45.833 5.39 0.00 39.20 2.74
2412 8054 4.597940 ACCAAAGCCTCCTTTTCTACTAGT 59.402 41.667 0.00 0.00 39.20 2.57
2413 8055 5.167303 ACCAAAGCCTCCTTTTCTACTAG 57.833 43.478 0.00 0.00 39.20 2.57
2414 8056 5.072600 TGAACCAAAGCCTCCTTTTCTACTA 59.927 40.000 0.00 0.00 39.20 1.82
2415 8057 4.141251 TGAACCAAAGCCTCCTTTTCTACT 60.141 41.667 0.00 0.00 39.20 2.57
2416 8058 4.142038 TGAACCAAAGCCTCCTTTTCTAC 58.858 43.478 0.00 0.00 39.20 2.59
2417 8059 4.398319 CTGAACCAAAGCCTCCTTTTCTA 58.602 43.478 0.00 0.00 39.20 2.10
2418 8060 3.225940 CTGAACCAAAGCCTCCTTTTCT 58.774 45.455 0.00 0.00 39.20 2.52
2419 8061 2.297315 CCTGAACCAAAGCCTCCTTTTC 59.703 50.000 0.00 0.00 39.20 2.29
2420 8062 2.319844 CCTGAACCAAAGCCTCCTTTT 58.680 47.619 0.00 0.00 39.20 2.27
2421 8063 2.001076 CCTGAACCAAAGCCTCCTTT 57.999 50.000 0.00 0.00 41.86 3.11
2422 8064 0.540597 GCCTGAACCAAAGCCTCCTT 60.541 55.000 0.00 0.00 0.00 3.36
2423 8065 1.075659 GCCTGAACCAAAGCCTCCT 59.924 57.895 0.00 0.00 0.00 3.69
2424 8066 1.979155 GGCCTGAACCAAAGCCTCC 60.979 63.158 0.00 0.00 42.34 4.30
2425 8067 2.335712 CGGCCTGAACCAAAGCCTC 61.336 63.158 0.00 0.00 43.48 4.70
2426 8068 2.282462 CGGCCTGAACCAAAGCCT 60.282 61.111 0.00 0.00 43.48 4.58
2427 8069 3.373565 CCGGCCTGAACCAAAGCC 61.374 66.667 0.00 0.00 42.18 4.35
2428 8070 2.757980 TACCCGGCCTGAACCAAAGC 62.758 60.000 0.00 0.00 0.00 3.51
2429 8071 0.250989 TTACCCGGCCTGAACCAAAG 60.251 55.000 0.00 0.00 0.00 2.77
2430 8072 0.250989 CTTACCCGGCCTGAACCAAA 60.251 55.000 0.00 0.00 0.00 3.28
2431 8073 1.377229 CTTACCCGGCCTGAACCAA 59.623 57.895 0.00 0.00 0.00 3.67
2432 8074 3.074281 CTTACCCGGCCTGAACCA 58.926 61.111 0.00 0.00 0.00 3.67
2433 8075 2.437895 GCTTACCCGGCCTGAACC 60.438 66.667 0.00 0.00 0.00 3.62
2434 8076 2.437895 GGCTTACCCGGCCTGAAC 60.438 66.667 0.00 0.00 45.57 3.18
2444 8086 0.108019 CCGGGACTAATGGGCTTACC 59.892 60.000 0.00 0.00 40.81 2.85
2445 8087 0.835276 ACCGGGACTAATGGGCTTAC 59.165 55.000 6.32 0.00 0.00 2.34
2446 8088 1.487558 GAACCGGGACTAATGGGCTTA 59.512 52.381 6.32 0.00 0.00 3.09
2447 8089 0.255033 GAACCGGGACTAATGGGCTT 59.745 55.000 6.32 0.00 0.00 4.35
2448 8090 0.912487 TGAACCGGGACTAATGGGCT 60.912 55.000 6.32 0.00 0.00 5.19
2449 8091 0.463833 CTGAACCGGGACTAATGGGC 60.464 60.000 6.32 0.00 0.00 5.36
2450 8092 0.909623 ACTGAACCGGGACTAATGGG 59.090 55.000 6.32 0.00 0.00 4.00
2451 8093 1.134491 GGACTGAACCGGGACTAATGG 60.134 57.143 6.32 0.00 0.00 3.16
2452 8094 1.553248 TGGACTGAACCGGGACTAATG 59.447 52.381 6.32 0.00 0.00 1.90
2453 8095 1.831736 CTGGACTGAACCGGGACTAAT 59.168 52.381 6.32 0.00 33.06 1.73
2454 8096 1.203087 TCTGGACTGAACCGGGACTAA 60.203 52.381 6.32 0.00 36.97 2.24
2455 8097 0.406750 TCTGGACTGAACCGGGACTA 59.593 55.000 6.32 0.00 36.97 2.59
2456 8098 0.471211 TTCTGGACTGAACCGGGACT 60.471 55.000 6.32 0.00 36.97 3.85
2457 8099 0.320508 GTTCTGGACTGAACCGGGAC 60.321 60.000 6.32 0.00 40.10 4.46
2458 8100 2.055299 GTTCTGGACTGAACCGGGA 58.945 57.895 6.32 0.00 40.10 5.14
2459 8101 4.695560 GTTCTGGACTGAACCGGG 57.304 61.111 6.32 0.00 40.10 5.73
2463 8105 2.055299 TCCCGGTTCTGGACTGAAC 58.945 57.895 12.04 12.04 43.88 3.18
2464 8106 4.631493 TCCCGGTTCTGGACTGAA 57.369 55.556 0.00 0.00 36.72 3.02
2469 8111 1.682849 CATTGGTCCCGGTTCTGGA 59.317 57.895 0.00 0.00 0.00 3.86
2470 8112 1.378514 CCATTGGTCCCGGTTCTGG 60.379 63.158 0.00 0.00 0.00 3.86
2471 8113 1.378514 CCCATTGGTCCCGGTTCTG 60.379 63.158 0.00 0.00 0.00 3.02
2472 8114 1.850755 ACCCATTGGTCCCGGTTCT 60.851 57.895 0.00 0.00 43.06 3.01
2473 8115 1.677633 CACCCATTGGTCCCGGTTC 60.678 63.158 0.00 0.00 45.57 3.62
2474 8116 2.438795 CACCCATTGGTCCCGGTT 59.561 61.111 0.00 0.00 45.57 4.44
2475 8117 4.360405 GCACCCATTGGTCCCGGT 62.360 66.667 0.00 0.00 45.57 5.28
2476 8118 3.660422 ATGCACCCATTGGTCCCGG 62.660 63.158 1.20 0.00 45.57 5.73
2477 8119 1.257055 AAATGCACCCATTGGTCCCG 61.257 55.000 1.20 0.00 45.57 5.14
2478 8120 1.859302 TAAATGCACCCATTGGTCCC 58.141 50.000 1.20 0.00 45.57 4.46
2479 8121 2.365293 GGATAAATGCACCCATTGGTCC 59.635 50.000 1.20 0.00 45.57 4.46
2480 8122 2.365293 GGGATAAATGCACCCATTGGTC 59.635 50.000 4.47 0.00 45.57 4.02
2482 8124 1.340889 CGGGATAAATGCACCCATTGG 59.659 52.381 9.80 0.00 40.69 3.16
2483 8125 2.305928 TCGGGATAAATGCACCCATTG 58.694 47.619 9.80 0.00 40.69 2.82
2484 8126 2.746279 TCGGGATAAATGCACCCATT 57.254 45.000 9.80 0.00 43.32 3.16
2485 8127 2.978156 ATCGGGATAAATGCACCCAT 57.022 45.000 9.80 0.52 43.40 4.00
2486 8128 2.582052 GAATCGGGATAAATGCACCCA 58.418 47.619 9.80 0.00 43.40 4.51
2487 8129 1.535462 CGAATCGGGATAAATGCACCC 59.465 52.381 0.00 0.00 40.17 4.61
2488 8130 2.032030 CACGAATCGGGATAAATGCACC 60.032 50.000 7.80 0.00 28.17 5.01
2489 8131 2.602217 GCACGAATCGGGATAAATGCAC 60.602 50.000 9.93 0.00 28.17 4.57
2490 8132 1.601903 GCACGAATCGGGATAAATGCA 59.398 47.619 9.93 0.00 28.17 3.96
2491 8133 1.398451 CGCACGAATCGGGATAAATGC 60.398 52.381 9.93 5.53 28.17 3.56
2492 8134 1.194547 CCGCACGAATCGGGATAAATG 59.805 52.381 9.93 0.00 42.99 2.32
2493 8135 1.508632 CCGCACGAATCGGGATAAAT 58.491 50.000 9.93 0.00 42.99 1.40
2494 8136 1.155424 GCCGCACGAATCGGGATAAA 61.155 55.000 9.93 0.00 46.51 1.40
2495 8137 1.593209 GCCGCACGAATCGGGATAA 60.593 57.895 9.93 0.00 46.51 1.75
2496 8138 1.174078 TAGCCGCACGAATCGGGATA 61.174 55.000 9.93 0.00 46.51 2.59
2497 8139 2.023414 TTAGCCGCACGAATCGGGAT 62.023 55.000 9.93 0.00 46.51 3.85
2498 8140 2.622903 CTTAGCCGCACGAATCGGGA 62.623 60.000 9.93 0.00 46.51 5.14
2499 8141 2.202824 TTAGCCGCACGAATCGGG 60.203 61.111 7.80 3.33 46.51 5.14
2501 8143 2.871427 GCCTTAGCCGCACGAATCG 61.871 63.158 0.00 0.00 0.00 3.34
2502 8144 3.014856 GCCTTAGCCGCACGAATC 58.985 61.111 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.