Multiple sequence alignment - TraesCS5B01G368900

Loading Multiple Alignment...

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 TraesCS5B01G368900 chr5B 100.000 5912 0 0 1 5912 547652176 547658087 0.000000e+00 10918.0
1 TraesCS5B01G368900 chr5B 94.527 1608 53 6 3419 5014 547808277 547809861 0.000000e+00 2449.0
2 TraesCS5B01G368900 chr5B 92.586 1659 83 15 4290 5912 547823869 547825523 0.000000e+00 2346.0
3 TraesCS5B01G368900 chr5B 96.189 866 26 3 2526 3390 547807137 547807996 0.000000e+00 1410.0
4 TraesCS5B01G368900 chr5B 83.478 920 104 24 4514 5390 547859241 547860155 0.000000e+00 813.0
5 TraesCS5B01G368900 chr5B 94.444 504 28 0 1 504 666456010 666455507 0.000000e+00 776.0
6 TraesCS5B01G368900 chr5B 89.223 399 31 7 5012 5405 547809893 547810284 6.890000e-134 488.0
7 TraesCS5B01G368900 chr5B 93.960 298 14 2 545 842 547645105 547645398 1.170000e-121 448.0
8 TraesCS5B01G368900 chr5B 88.449 303 25 4 541 842 547639034 547639327 2.030000e-94 357.0
9 TraesCS5B01G368900 chr5B 90.909 198 12 5 5414 5607 547672984 547673179 1.630000e-65 261.0
10 TraesCS5B01G368900 chr5B 81.375 349 34 8 5577 5903 547673183 547673522 7.600000e-64 255.0
11 TraesCS5B01G368900 chr5B 81.375 349 34 8 5577 5903 547828153 547828492 7.600000e-64 255.0
12 TraesCS5B01G368900 chr5B 90.306 196 16 3 5414 5607 547827955 547828149 2.730000e-63 254.0
13 TraesCS5B01G368900 chr5B 95.000 40 2 0 5367 5406 547794855 547794894 4.950000e-06 63.9
14 TraesCS5B01G368900 chr5A 91.317 2073 101 28 1382 3400 566701735 566703782 0.000000e+00 2758.0
15 TraesCS5B01G368900 chr5A 92.356 1609 97 14 3419 5014 566703977 566705572 0.000000e+00 2266.0
16 TraesCS5B01G368900 chr5A 87.176 811 86 4 4169 4976 566781066 566781861 0.000000e+00 905.0
17 TraesCS5B01G368900 chr5A 88.092 655 49 13 752 1380 566701027 566701678 0.000000e+00 750.0
18 TraesCS5B01G368900 chr5A 88.476 538 58 2 4481 5014 566734021 566734558 0.000000e+00 647.0
19 TraesCS5B01G368900 chr5A 87.065 402 38 9 5012 5406 566734591 566734985 5.440000e-120 442.0
20 TraesCS5B01G368900 chr5A 90.136 294 25 1 4568 4861 566795210 566795499 4.320000e-101 379.0
21 TraesCS5B01G368900 chr5A 87.879 330 21 9 5082 5406 566705752 566706067 2.600000e-98 370.0
22 TraesCS5B01G368900 chr5A 82.902 193 16 7 5219 5406 566796019 566796199 2.210000e-34 158.0
23 TraesCS5B01G368900 chr5A 93.814 97 5 1 5142 5238 566782553 566782648 1.720000e-30 145.0
24 TraesCS5B01G368900 chr5A 91.509 106 5 4 539 644 566700588 566700689 6.180000e-30 143.0
25 TraesCS5B01G368900 chr5A 88.235 102 10 1 5307 5406 566733075 566733176 2.890000e-23 121.0
26 TraesCS5B01G368900 chr5D 90.188 1274 67 20 1382 2606 448449868 448451132 0.000000e+00 1607.0
27 TraesCS5B01G368900 chr5D 88.329 1251 94 25 4195 5406 448453439 448454676 0.000000e+00 1454.0
28 TraesCS5B01G368900 chr5D 95.663 784 26 2 3420 4195 448452710 448453493 0.000000e+00 1253.0
29 TraesCS5B01G368900 chr5D 92.946 808 43 10 539 1345 448448966 448449760 0.000000e+00 1164.0
30 TraesCS5B01G368900 chr5D 95.312 576 22 4 2828 3398 448451941 448452516 0.000000e+00 909.0
31 TraesCS5B01G368900 chr5D 97.368 152 4 0 2604 2755 448451436 448451587 5.880000e-65 259.0
32 TraesCS5B01G368900 chr5D 80.208 192 28 5 539 730 448370286 448370467 1.030000e-27 135.0
33 TraesCS5B01G368900 chr2D 95.635 504 22 0 1 504 640914375 640914878 0.000000e+00 809.0
34 TraesCS5B01G368900 chr2B 95.219 502 23 1 4 504 745555370 745555871 0.000000e+00 793.0
35 TraesCS5B01G368900 chr7B 94.653 505 26 1 1 504 640303021 640302517 0.000000e+00 782.0
36 TraesCS5B01G368900 chr7B 94.455 505 27 1 1 504 6812107 6812611 0.000000e+00 776.0
37 TraesCS5B01G368900 chr3B 94.643 504 27 0 1 504 89314286 89314789 0.000000e+00 782.0
38 TraesCS5B01G368900 chr3B 94.643 504 26 1 1 504 713334438 713333936 0.000000e+00 780.0
39 TraesCS5B01G368900 chr3B 89.091 110 11 1 4338 4446 581966093 581965984 1.030000e-27 135.0
40 TraesCS5B01G368900 chr3B 83.721 129 13 5 5433 5557 667679927 667679803 1.350000e-21 115.0
41 TraesCS5B01G368900 chr1B 94.643 504 27 0 1 504 545445066 545444563 0.000000e+00 782.0
42 TraesCS5B01G368900 chr1B 94.444 504 28 0 1 504 41969941 41969438 0.000000e+00 776.0
43 TraesCS5B01G368900 chr7D 89.623 106 11 0 4338 4443 79629834 79629939 1.030000e-27 135.0
44 TraesCS5B01G368900 chr3A 89.623 106 10 1 4338 4442 557420797 557420902 3.720000e-27 134.0
45 TraesCS5B01G368900 chr1D 88.785 107 12 0 4337 4443 478885943 478886049 1.340000e-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 TraesCS5B01G368900 chr5B 547652176 547658087 5911 False 10918.000000 10918 100.000000 1 5912 1 chr5B.!!$F3 5911
1 TraesCS5B01G368900 chr5B 547807137 547810284 3147 False 1449.000000 2449 93.313000 2526 5405 3 chr5B.!!$F7 2879
2 TraesCS5B01G368900 chr5B 547823869 547828492 4623 False 951.666667 2346 88.089000 4290 5912 3 chr5B.!!$F8 1622
3 TraesCS5B01G368900 chr5B 547859241 547860155 914 False 813.000000 813 83.478000 4514 5390 1 chr5B.!!$F5 876
4 TraesCS5B01G368900 chr5B 666455507 666456010 503 True 776.000000 776 94.444000 1 504 1 chr5B.!!$R1 503
5 TraesCS5B01G368900 chr5B 547672984 547673522 538 False 258.000000 261 86.142000 5414 5903 2 chr5B.!!$F6 489
6 TraesCS5B01G368900 chr5A 566700588 566706067 5479 False 1257.400000 2758 90.230600 539 5406 5 chr5A.!!$F1 4867
7 TraesCS5B01G368900 chr5A 566781066 566782648 1582 False 525.000000 905 90.495000 4169 5238 2 chr5A.!!$F3 1069
8 TraesCS5B01G368900 chr5A 566733075 566734985 1910 False 403.333333 647 87.925333 4481 5406 3 chr5A.!!$F2 925
9 TraesCS5B01G368900 chr5A 566795210 566796199 989 False 268.500000 379 86.519000 4568 5406 2 chr5A.!!$F4 838
10 TraesCS5B01G368900 chr5D 448448966 448454676 5710 False 1107.666667 1607 93.301000 539 5406 6 chr5D.!!$F2 4867
11 TraesCS5B01G368900 chr2D 640914375 640914878 503 False 809.000000 809 95.635000 1 504 1 chr2D.!!$F1 503
12 TraesCS5B01G368900 chr2B 745555370 745555871 501 False 793.000000 793 95.219000 4 504 1 chr2B.!!$F1 500
13 TraesCS5B01G368900 chr7B 640302517 640303021 504 True 782.000000 782 94.653000 1 504 1 chr7B.!!$R1 503
14 TraesCS5B01G368900 chr7B 6812107 6812611 504 False 776.000000 776 94.455000 1 504 1 chr7B.!!$F1 503
15 TraesCS5B01G368900 chr3B 89314286 89314789 503 False 782.000000 782 94.643000 1 504 1 chr3B.!!$F1 503
16 TraesCS5B01G368900 chr3B 713333936 713334438 502 True 780.000000 780 94.643000 1 504 1 chr3B.!!$R3 503
17 TraesCS5B01G368900 chr1B 545444563 545445066 503 True 782.000000 782 94.643000 1 504 1 chr1B.!!$R2 503
18 TraesCS5B01G368900 chr1B 41969438 41969941 503 True 776.000000 776 94.444000 1 504 1 chr1B.!!$R1 503

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
706 708 1.667154 CGTCTCGCCATTCCTCTGGA 61.667 60.000 0.0 0.0 38.69 3.86 F
1371 1652 0.897401 TTGCCAATTGCCACGGATGA 60.897 50.000 0.0 0.0 40.16 2.92 F
2139 2524 0.251341 GGGATGGAACCACAACAGCT 60.251 55.000 0.0 0.0 0.00 4.24 F
3667 4898 1.691434 GACCAGAGATTGAGGCTAGGG 59.309 57.143 0.0 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1525 1861 1.001633 TCAAAGTGCGGAAGTAGGGAC 59.998 52.381 0.00 0.00 0.00 4.46 R
2202 2587 1.039856 TGCCCTTTCTCAAAGCAACC 58.960 50.000 0.00 0.00 37.18 3.77 R
3950 5190 3.328050 GCTGCCCCTACCTGAATAATACT 59.672 47.826 0.00 0.00 0.00 2.12 R
5362 10248 0.036199 TTATAAACACCGCGCAGGGT 60.036 50.000 19.73 8.04 46.96 4.34 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
282 284 3.031736 CCTCAGGGGATCGAGACTAAAA 58.968 50.000 0.00 0.00 37.23 1.52
285 287 4.094476 TCAGGGGATCGAGACTAAAAGTT 58.906 43.478 0.00 0.00 0.00 2.66
411 413 6.422776 AAATTGTTAACGATCGCAGAGAAT 57.577 33.333 16.60 8.25 43.63 2.40
414 416 6.954616 TTGTTAACGATCGCAGAGAATTAA 57.045 33.333 16.60 7.82 43.63 1.40
425 427 3.181439 GCAGAGAATTAATAGGGGGCAGT 60.181 47.826 0.00 0.00 0.00 4.40
458 460 4.174009 GCAGCTCACGATTAGTAAACAGA 58.826 43.478 0.00 0.00 0.00 3.41
466 468 9.952188 CTCACGATTAGTAAACAGATTCATCTA 57.048 33.333 0.00 0.00 34.85 1.98
473 475 9.890629 TTAGTAAACAGATTCATCTACATGCTT 57.109 29.630 0.00 0.00 34.85 3.91
504 506 7.384477 TGATGAATCAGAAGAGCTATACATGG 58.616 38.462 0.00 0.00 32.11 3.66
507 509 6.552725 TGAATCAGAAGAGCTATACATGGAGT 59.447 38.462 0.00 0.00 0.00 3.85
508 510 6.992664 ATCAGAAGAGCTATACATGGAGTT 57.007 37.500 0.00 0.00 0.00 3.01
511 513 6.381133 TCAGAAGAGCTATACATGGAGTTCAA 59.619 38.462 0.00 0.00 0.00 2.69
515 517 7.603180 AGAGCTATACATGGAGTTCAACATA 57.397 36.000 0.00 0.00 0.00 2.29
516 518 8.023021 AGAGCTATACATGGAGTTCAACATAA 57.977 34.615 0.00 0.00 0.00 1.90
517 519 8.654997 AGAGCTATACATGGAGTTCAACATAAT 58.345 33.333 0.00 0.00 0.00 1.28
518 520 8.839310 AGCTATACATGGAGTTCAACATAATC 57.161 34.615 0.00 0.00 0.00 1.75
519 521 7.880195 AGCTATACATGGAGTTCAACATAATCC 59.120 37.037 0.00 0.00 0.00 3.01
520 522 7.880195 GCTATACATGGAGTTCAACATAATCCT 59.120 37.037 0.00 0.00 0.00 3.24
521 523 9.212641 CTATACATGGAGTTCAACATAATCCTG 57.787 37.037 0.00 0.00 0.00 3.86
522 524 6.065976 ACATGGAGTTCAACATAATCCTGA 57.934 37.500 0.00 0.00 0.00 3.86
523 525 6.484288 ACATGGAGTTCAACATAATCCTGAA 58.516 36.000 0.00 0.00 0.00 3.02
524 526 7.121382 ACATGGAGTTCAACATAATCCTGAAT 58.879 34.615 0.00 0.00 32.08 2.57
525 527 7.067859 ACATGGAGTTCAACATAATCCTGAATG 59.932 37.037 0.00 0.00 32.08 2.67
526 528 5.887598 TGGAGTTCAACATAATCCTGAATGG 59.112 40.000 0.00 0.00 32.08 3.16
528 530 4.646492 AGTTCAACATAATCCTGAATGGGC 59.354 41.667 0.00 0.00 36.20 5.36
529 531 3.565307 TCAACATAATCCTGAATGGGCC 58.435 45.455 0.00 0.00 36.20 5.80
530 532 3.205056 TCAACATAATCCTGAATGGGCCT 59.795 43.478 4.53 0.00 36.20 5.19
531 533 3.962718 CAACATAATCCTGAATGGGCCTT 59.037 43.478 4.53 0.00 36.20 4.35
534 536 2.755952 AATCCTGAATGGGCCTTACC 57.244 50.000 4.53 0.00 36.20 2.85
535 537 1.912862 ATCCTGAATGGGCCTTACCT 58.087 50.000 4.53 0.00 39.10 3.08
536 538 2.579624 TCCTGAATGGGCCTTACCTA 57.420 50.000 4.53 0.00 39.10 3.08
539 541 2.241176 CCTGAATGGGCCTTACCTAACA 59.759 50.000 4.53 0.00 39.10 2.41
541 543 3.947834 CTGAATGGGCCTTACCTAACAAG 59.052 47.826 4.53 0.00 39.10 3.16
542 544 3.332485 TGAATGGGCCTTACCTAACAAGT 59.668 43.478 4.53 0.00 39.10 3.16
543 545 3.646736 ATGGGCCTTACCTAACAAGTC 57.353 47.619 4.53 0.00 39.10 3.01
591 593 6.319911 CCTCAAAAATCCCCTAAATCTCTCAC 59.680 42.308 0.00 0.00 0.00 3.51
706 708 1.667154 CGTCTCGCCATTCCTCTGGA 61.667 60.000 0.00 0.00 38.69 3.86
749 987 4.269523 GTGCTGCCACCAGGTCCA 62.270 66.667 0.00 0.00 39.54 4.02
750 988 3.497115 TGCTGCCACCAGGTCCAA 61.497 61.111 0.00 0.00 39.54 3.53
981 1235 3.508840 CCGGGGCACTGAATTCGC 61.509 66.667 0.00 0.00 0.00 4.70
983 1237 3.508840 GGGGCACTGAATTCGCGG 61.509 66.667 6.13 0.00 0.00 6.46
1015 1269 2.912956 ACCACCATGTCTCTTACCACAT 59.087 45.455 0.00 0.00 33.29 3.21
1093 1347 3.760035 CGTGCCGGCTGTCTAGGT 61.760 66.667 29.70 0.00 0.00 3.08
1234 1491 1.966451 CTCGGTCCCAAAGGTGTGC 60.966 63.158 0.00 0.00 0.00 4.57
1286 1551 8.764287 CAGATGCATCACTGTAATCGTAATTTA 58.236 33.333 27.81 0.00 0.00 1.40
1287 1552 9.494271 AGATGCATCACTGTAATCGTAATTTAT 57.506 29.630 27.81 0.00 0.00 1.40
1313 1578 8.948631 TTTTGCTCTAGTATTACTTCTGGATG 57.051 34.615 0.85 0.00 0.00 3.51
1371 1652 0.897401 TTGCCAATTGCCACGGATGA 60.897 50.000 0.00 0.00 40.16 2.92
1380 1661 3.574284 TGCCACGGATGAATTCTTTTG 57.426 42.857 7.05 0.22 0.00 2.44
1421 1757 5.794687 TGTTATCTTTGGTAATCAGCACG 57.205 39.130 0.00 0.00 0.00 5.34
1525 1861 8.434661 GGTTTTGTATAAACATTTGTCATGCAG 58.565 33.333 0.00 0.00 34.97 4.41
1650 2010 6.575162 AAGCTTCCAATAGATCGTTTTTGT 57.425 33.333 0.00 0.00 0.00 2.83
1735 2111 4.651503 ACACACTGTTCCTGAGATATAGGG 59.348 45.833 0.00 0.00 35.96 3.53
1740 2116 4.878968 TGTTCCTGAGATATAGGGTCACA 58.121 43.478 0.00 0.00 35.96 3.58
1918 2294 3.620488 TGCAGGGAGGAATGTTGTTATC 58.380 45.455 0.00 0.00 0.00 1.75
1936 2312 6.581712 TGTTATCGATCAAGATGATGTTCCA 58.418 36.000 0.00 0.00 37.20 3.53
1966 2342 5.981088 TTAATGATGGTGTCACAATTGCT 57.019 34.783 5.05 0.00 40.28 3.91
2033 2418 5.297547 TGCTACTTCAAGAGGTACAGTTTG 58.702 41.667 0.00 0.00 0.00 2.93
2079 2464 5.401531 AACTGCTTCTGATTCATTGCAAT 57.598 34.783 5.99 5.99 0.00 3.56
2097 2482 4.201841 TGCAATCATGTCAAACAGATAGCG 60.202 41.667 0.00 0.00 0.00 4.26
2139 2524 0.251341 GGGATGGAACCACAACAGCT 60.251 55.000 0.00 0.00 0.00 4.24
2277 2662 4.766375 TGAAGACAAAATCTATCCCCGTC 58.234 43.478 0.00 0.00 36.27 4.79
2312 2697 6.346896 AGGACATAAAAGGTAATCTTCGTCC 58.653 40.000 0.00 0.00 38.89 4.79
2399 2784 2.766263 ACTTCGTCTGATATCTGCCCAA 59.234 45.455 3.98 0.00 0.00 4.12
2418 2803 7.801104 TGCCCAACAGATTATCATAACTAAGA 58.199 34.615 0.00 0.00 0.00 2.10
2457 2842 4.782019 TGTGTATTGAAATGGAACTGCC 57.218 40.909 0.00 0.00 37.10 4.85
2469 2854 3.161866 TGGAACTGCCCCTTACAAATTC 58.838 45.455 0.00 0.00 34.97 2.17
2511 2896 5.811018 CACCATCATGTGTTTTCTTTTCG 57.189 39.130 0.00 0.00 0.00 3.46
2528 2913 6.831769 TCTTTTCGTTTCTGTGCATATTCTC 58.168 36.000 0.00 0.00 0.00 2.87
2577 2962 9.056005 GTATGCATGTATTCTCCTGAAATGTTA 57.944 33.333 10.16 0.00 35.63 2.41
2829 3801 6.268617 CCCCCTACCCTAAGTATTGTAACTAC 59.731 46.154 0.00 0.00 0.00 2.73
3400 4377 2.677199 GCTCATGCTGCTAGCGTTATA 58.323 47.619 10.77 0.00 46.26 0.98
3401 4378 3.059884 GCTCATGCTGCTAGCGTTATAA 58.940 45.455 10.77 0.00 46.26 0.98
3402 4379 3.494626 GCTCATGCTGCTAGCGTTATAAA 59.505 43.478 10.77 0.00 46.26 1.40
3403 4380 4.153117 GCTCATGCTGCTAGCGTTATAAAT 59.847 41.667 10.77 0.00 46.26 1.40
3405 4382 6.128553 GCTCATGCTGCTAGCGTTATAAATTA 60.129 38.462 10.77 0.00 46.26 1.40
3406 4383 7.351414 TCATGCTGCTAGCGTTATAAATTAG 57.649 36.000 10.77 0.00 46.26 1.73
3407 4384 6.929049 TCATGCTGCTAGCGTTATAAATTAGT 59.071 34.615 10.77 0.00 46.26 2.24
3410 4387 7.981142 TGCTGCTAGCGTTATAAATTAGTTTT 58.019 30.769 10.77 0.00 46.26 2.43
3411 4388 8.455682 TGCTGCTAGCGTTATAAATTAGTTTTT 58.544 29.630 10.77 0.00 46.26 1.94
3639 4870 8.978874 AATCTACAACTATAATTGCACATCCA 57.021 30.769 0.00 0.00 32.47 3.41
3667 4898 1.691434 GACCAGAGATTGAGGCTAGGG 59.309 57.143 0.00 0.00 0.00 3.53
3878 5116 6.595716 AGTTTCAGGATACAGAAGTGCATAAC 59.404 38.462 0.00 0.00 43.46 1.89
3880 5118 4.401202 TCAGGATACAGAAGTGCATAACGA 59.599 41.667 0.00 0.00 41.41 3.85
3935 5175 2.543653 CCTGTTTCTTTCTTTGTGGGCG 60.544 50.000 0.00 0.00 0.00 6.13
3950 5190 1.314730 GGGCGTTTGAGGAGTTTTGA 58.685 50.000 0.00 0.00 0.00 2.69
4021 5261 1.205655 CTGAGAGTGGAGGATGCGAAA 59.794 52.381 0.00 0.00 0.00 3.46
4063 5303 2.401766 CGAAGGCATCACACCTGGC 61.402 63.158 0.00 0.00 37.67 4.85
4591 5839 8.099364 TCATCCTAACTCTGAAATTTGTGAAC 57.901 34.615 0.00 0.00 0.00 3.18
4798 6047 3.384467 GCTCCAGAACTCTGCTTCTATCT 59.616 47.826 0.89 0.00 42.47 1.98
4806 6055 2.036217 CTCTGCTTCTATCTCAGGGCTG 59.964 54.545 0.00 0.00 0.00 4.85
4917 6166 8.133627 CAGATAAATCAAAATGCTTAGGTCTGG 58.866 37.037 0.00 0.00 0.00 3.86
4944 6196 7.630924 CAATTCGTATCCTGTTATTGAAGGTC 58.369 38.462 0.00 0.00 34.94 3.85
5084 6707 7.782897 ATCAACTATATGTAGGCTTGCTCTA 57.217 36.000 0.00 0.00 31.96 2.43
5180 6990 7.364144 GCAGAATCTCCCCAAACAGAAAATATT 60.364 37.037 0.00 0.00 0.00 1.28
5243 10123 9.620660 TGTAGCATGTAACATAGTATGATTACG 57.379 33.333 17.13 10.08 33.47 3.18
5248 10128 7.046292 TGTAACATAGTATGATTACGCTGGT 57.954 36.000 17.13 0.00 33.47 4.00
5257 10137 3.845178 TGATTACGCTGGTAGAACTGTG 58.155 45.455 0.00 0.00 0.00 3.66
5264 10144 2.881074 CTGGTAGAACTGTGATGTCGG 58.119 52.381 0.00 0.00 0.00 4.79
5292 10175 5.863935 CCCAAATGTTTAAGCTAACTCTTGC 59.136 40.000 1.29 0.00 0.00 4.01
5298 10181 6.765403 TGTTTAAGCTAACTCTTGCCTCTTA 58.235 36.000 1.29 0.00 0.00 2.10
5305 10188 6.773200 AGCTAACTCTTGCCTCTTAACTTTTT 59.227 34.615 0.00 0.00 0.00 1.94
5371 10257 3.124636 GGTAAAATCATATACCCTGCGCG 59.875 47.826 0.00 0.00 36.39 6.86
5428 10358 2.370849 GGAGTACCTTTTGTCAGGACCA 59.629 50.000 0.00 0.00 37.39 4.02
5486 10416 9.248291 GCTCTCAAATGAACAGTAAATTCAAAA 57.752 29.630 0.00 0.00 39.43 2.44
5553 10484 7.067532 TGTTTAAGTGAGTGTAACAAGTGTG 57.932 36.000 0.00 0.00 41.43 3.82
5570 10501 2.222445 GTGTGCTTCGTCGGTGTAAAAT 59.778 45.455 0.00 0.00 0.00 1.82
5574 10505 3.560481 TGCTTCGTCGGTGTAAAATCAAA 59.440 39.130 0.00 0.00 0.00 2.69
5627 10591 6.100134 TGGATCTGACCATGAACTCATCAATA 59.900 38.462 0.00 0.00 42.54 1.90
5630 10594 8.991783 ATCTGACCATGAACTCATCAATATTT 57.008 30.769 0.00 0.00 42.54 1.40
5670 10634 6.264970 ACATTAAAAAGGCATTTTTGGCATGT 59.735 30.769 27.07 24.99 45.80 3.21
5697 10661 4.904241 GCATATGCTCTTAGGACCTGAAT 58.096 43.478 20.64 0.00 38.21 2.57
5706 10670 5.755849 TCTTAGGACCTGAATTGGATTTCC 58.244 41.667 3.53 0.00 0.00 3.13
5715 10679 4.272489 TGAATTGGATTTCCGATCTGCTT 58.728 39.130 0.00 0.00 39.20 3.91
5718 10682 1.065199 TGGATTTCCGATCTGCTTGCT 60.065 47.619 0.00 0.00 39.43 3.91
5725 10689 1.945394 CCGATCTGCTTGCTGCTTTAT 59.055 47.619 0.00 0.00 43.37 1.40
5780 10744 1.502190 GCTTGTTTGGCCGACTAGC 59.498 57.895 22.44 22.44 38.34 3.42
5784 10748 1.975660 TGTTTGGCCGACTAGCTTTT 58.024 45.000 10.08 0.00 0.00 2.27
5788 10752 1.519408 TGGCCGACTAGCTTTTTGAC 58.481 50.000 0.00 0.00 0.00 3.18
5790 10754 2.084546 GGCCGACTAGCTTTTTGACAT 58.915 47.619 0.00 0.00 0.00 3.06
5791 10755 2.096013 GGCCGACTAGCTTTTTGACATC 59.904 50.000 0.00 0.00 0.00 3.06
5792 10756 2.096013 GCCGACTAGCTTTTTGACATCC 59.904 50.000 0.00 0.00 0.00 3.51
5793 10757 3.334691 CCGACTAGCTTTTTGACATCCA 58.665 45.455 0.00 0.00 0.00 3.41
5794 10758 3.751175 CCGACTAGCTTTTTGACATCCAA 59.249 43.478 0.00 0.00 0.00 3.53
5795 10759 4.396166 CCGACTAGCTTTTTGACATCCAAT 59.604 41.667 0.00 0.00 34.23 3.16
5827 10813 7.056635 AGCTAGCACACTAATAATTCACCAAT 58.943 34.615 18.83 0.00 0.00 3.16
5854 10840 9.824534 CAAAAGAAAATATTGCCACCAAAATAC 57.175 29.630 0.00 0.00 34.05 1.89
5863 10849 2.944094 GCCACCAAAATACCATCCGAGT 60.944 50.000 0.00 0.00 0.00 4.18
5877 10863 4.430908 CATCCGAGTAGGGACAAAACTAC 58.569 47.826 0.00 0.00 39.34 2.73
5878 10864 3.499338 TCCGAGTAGGGACAAAACTACA 58.501 45.455 0.00 0.00 41.49 2.74
5885 10871 1.546998 GGGACAAAACTACAGGGGGTG 60.547 57.143 0.00 0.00 0.00 4.61
5896 10882 1.758862 ACAGGGGGTGTTACTATACGC 59.241 52.381 0.00 0.00 34.94 4.42
5903 10889 2.605580 GGTGTTACTATACGCCGCCTAC 60.606 54.545 0.00 0.00 38.77 3.18
5904 10890 2.033299 GTGTTACTATACGCCGCCTACA 59.967 50.000 0.00 0.00 0.00 2.74
5905 10891 2.291465 TGTTACTATACGCCGCCTACAG 59.709 50.000 0.00 0.00 0.00 2.74
5906 10892 2.260844 TACTATACGCCGCCTACAGT 57.739 50.000 0.00 0.00 0.00 3.55
5907 10893 0.666913 ACTATACGCCGCCTACAGTG 59.333 55.000 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 9.903682 AAAATTTGTCTTGACAGTATGAAGATG 57.096 29.630 3.61 0.00 39.69 2.90
66 67 1.937278 TGGTCGCACGTTTTGAGTAA 58.063 45.000 0.00 0.00 0.00 2.24
216 218 7.123098 TCCCTGTTGAAGAACATCGTATAGTAA 59.877 37.037 0.00 0.00 41.33 2.24
282 284 5.458041 AAGCTAACAATTGACATGCAACT 57.542 34.783 13.59 0.00 39.78 3.16
285 287 4.142708 CCGTAAGCTAACAATTGACATGCA 60.143 41.667 13.59 0.00 0.00 3.96
343 345 4.877823 AGCATTCATCGCTTCTACAAATCA 59.122 37.500 0.00 0.00 35.82 2.57
349 351 7.382488 TCACTATTAAGCATTCATCGCTTCTAC 59.618 37.037 0.00 0.00 46.61 2.59
411 413 5.456186 GCTTCTCATTACTGCCCCCTATTAA 60.456 44.000 0.00 0.00 0.00 1.40
414 416 2.373502 GCTTCTCATTACTGCCCCCTAT 59.626 50.000 0.00 0.00 0.00 2.57
425 427 1.645034 GTGAGCTGCGCTTCTCATTA 58.355 50.000 26.29 8.89 39.88 1.90
441 443 9.731819 GTAGATGAATCTGTTTACTAATCGTGA 57.268 33.333 2.99 0.00 37.76 4.35
453 455 6.413052 ACTGAAGCATGTAGATGAATCTGTT 58.587 36.000 3.61 0.00 37.76 3.16
458 460 8.373220 TCATCATACTGAAGCATGTAGATGAAT 58.627 33.333 3.61 0.00 34.49 2.57
466 468 6.589135 TCTGATTCATCATACTGAAGCATGT 58.411 36.000 5.36 0.00 46.80 3.21
473 475 6.728089 AGCTCTTCTGATTCATCATACTGA 57.272 37.500 0.00 0.00 36.02 3.41
490 492 6.299805 TGTTGAACTCCATGTATAGCTCTT 57.700 37.500 0.00 0.00 0.00 2.85
504 506 5.221126 GCCCATTCAGGATTATGTTGAACTC 60.221 44.000 0.00 0.00 41.22 3.01
507 509 3.960102 GGCCCATTCAGGATTATGTTGAA 59.040 43.478 0.00 0.00 41.22 2.69
508 510 3.205056 AGGCCCATTCAGGATTATGTTGA 59.795 43.478 0.00 0.00 41.22 3.18
511 513 3.979501 AAGGCCCATTCAGGATTATGT 57.020 42.857 0.00 0.00 41.22 2.29
515 517 2.217776 AGGTAAGGCCCATTCAGGATT 58.782 47.619 0.00 0.00 41.22 3.01
516 518 1.912862 AGGTAAGGCCCATTCAGGAT 58.087 50.000 0.00 0.00 41.22 3.24
517 519 2.508300 GTTAGGTAAGGCCCATTCAGGA 59.492 50.000 0.00 0.00 41.22 3.86
518 520 2.241176 TGTTAGGTAAGGCCCATTCAGG 59.759 50.000 0.00 0.00 38.26 3.86
519 521 3.644966 TGTTAGGTAAGGCCCATTCAG 57.355 47.619 0.00 0.00 38.26 3.02
520 522 3.332485 ACTTGTTAGGTAAGGCCCATTCA 59.668 43.478 0.00 0.00 38.26 2.57
521 523 3.945921 GACTTGTTAGGTAAGGCCCATTC 59.054 47.826 0.00 0.00 38.26 2.67
522 524 3.621461 CGACTTGTTAGGTAAGGCCCATT 60.621 47.826 0.00 0.00 38.26 3.16
523 525 2.093128 CGACTTGTTAGGTAAGGCCCAT 60.093 50.000 0.00 0.00 38.26 4.00
524 526 1.276989 CGACTTGTTAGGTAAGGCCCA 59.723 52.381 0.00 0.00 38.26 5.36
525 527 1.551883 TCGACTTGTTAGGTAAGGCCC 59.448 52.381 0.00 0.00 38.26 5.80
526 528 3.323751 TTCGACTTGTTAGGTAAGGCC 57.676 47.619 0.00 0.00 29.05 5.19
528 530 5.121768 CACCAATTCGACTTGTTAGGTAAGG 59.878 44.000 13.66 0.00 0.00 2.69
529 531 5.121768 CCACCAATTCGACTTGTTAGGTAAG 59.878 44.000 13.66 0.00 0.00 2.34
530 532 4.998672 CCACCAATTCGACTTGTTAGGTAA 59.001 41.667 13.66 0.00 0.00 2.85
531 533 4.283978 TCCACCAATTCGACTTGTTAGGTA 59.716 41.667 13.66 2.20 0.00 3.08
534 536 5.682943 TTTCCACCAATTCGACTTGTTAG 57.317 39.130 13.66 2.41 0.00 2.34
535 537 5.182380 GGATTTCCACCAATTCGACTTGTTA 59.818 40.000 13.66 0.00 35.64 2.41
536 538 4.022329 GGATTTCCACCAATTCGACTTGTT 60.022 41.667 13.66 0.00 35.64 2.83
539 541 3.089284 GGGATTTCCACCAATTCGACTT 58.911 45.455 0.00 0.00 37.91 3.01
541 543 1.749063 GGGGATTTCCACCAATTCGAC 59.251 52.381 0.00 0.00 37.91 4.20
542 544 1.638589 AGGGGATTTCCACCAATTCGA 59.361 47.619 0.00 0.00 41.50 3.71
543 545 2.143876 AGGGGATTTCCACCAATTCG 57.856 50.000 0.00 0.00 41.50 3.34
591 593 0.539051 AATGGAGAAGAGTGGGCGAG 59.461 55.000 0.00 0.00 0.00 5.03
688 690 0.755686 ATCCAGAGGAATGGCGAGAC 59.244 55.000 0.00 0.00 40.41 3.36
747 985 4.025401 GGTGCGCGTTGGACTTGG 62.025 66.667 8.43 0.00 39.22 3.61
748 986 4.368808 CGGTGCGCGTTGGACTTG 62.369 66.667 8.43 0.00 39.22 3.16
773 1011 1.345715 GGGAGTAGTGGATGGGGGTG 61.346 65.000 0.00 0.00 0.00 4.61
774 1012 1.004361 GGGAGTAGTGGATGGGGGT 59.996 63.158 0.00 0.00 0.00 4.95
779 1018 0.620410 TGGGTGGGGAGTAGTGGATG 60.620 60.000 0.00 0.00 0.00 3.51
885 1139 3.077907 CTTGGGGCCGGAAGAAGA 58.922 61.111 5.05 0.00 0.00 2.87
1033 1287 1.494960 GAGGAGGATGAGGAGCAAGT 58.505 55.000 0.00 0.00 0.00 3.16
1086 1340 2.439883 ACCCTCGCCGACCTAGAC 60.440 66.667 0.00 0.00 0.00 2.59
1087 1341 2.124403 GACCCTCGCCGACCTAGA 60.124 66.667 0.00 0.00 0.00 2.43
1089 1343 2.439701 CAGACCCTCGCCGACCTA 60.440 66.667 0.00 0.00 0.00 3.08
1253 1518 2.224843 ACAGTGATGCATCTGACCCAAA 60.225 45.455 26.32 1.49 35.84 3.28
1256 1521 2.988010 TACAGTGATGCATCTGACCC 57.012 50.000 26.32 9.86 35.84 4.46
1287 1552 9.383519 CATCCAGAAGTAATACTAGAGCAAAAA 57.616 33.333 0.00 0.00 0.00 1.94
1295 1560 8.768955 GCAAACATCATCCAGAAGTAATACTAG 58.231 37.037 0.00 0.00 0.00 2.57
1313 1578 8.577296 TCTAGACTATACACCATAGCAAACATC 58.423 37.037 0.00 0.00 40.42 3.06
1371 1652 7.312899 CAATTTACGGCTCTACCAAAAGAATT 58.687 34.615 0.00 0.00 39.03 2.17
1380 1661 3.340928 ACAACCAATTTACGGCTCTACC 58.659 45.455 0.00 0.00 0.00 3.18
1481 1817 4.823790 AACCGGAGAACAATTACACAAC 57.176 40.909 9.46 0.00 0.00 3.32
1525 1861 1.001633 TCAAAGTGCGGAAGTAGGGAC 59.998 52.381 0.00 0.00 0.00 4.46
1669 2029 8.693542 ATTTGAGGCGAAAATCTTTATGAAAG 57.306 30.769 0.00 0.00 39.88 2.62
1685 2045 2.002586 CAGTACACTGGATTTGAGGCG 58.997 52.381 1.21 0.00 40.20 5.52
1710 2086 6.323996 CCCTATATCTCAGGAACAGTGTGTTA 59.676 42.308 0.00 0.00 41.28 2.41
1735 2111 3.774066 GCAGAGGGCATAATTTTGTGAC 58.226 45.455 0.00 0.00 43.97 3.67
1765 2141 6.569179 TGGTAACAGATTTAACAAGGAAGC 57.431 37.500 0.00 0.00 46.17 3.86
1814 2190 5.072741 GGCATATATGATCCCAACAACACT 58.927 41.667 17.10 0.00 0.00 3.55
1815 2191 5.048504 CAGGCATATATGATCCCAACAACAC 60.049 44.000 17.10 0.00 0.00 3.32
1918 2294 6.187125 ACTTTTGGAACATCATCTTGATCG 57.813 37.500 0.00 0.00 39.30 3.69
1966 2342 8.548877 AGTGAATTTGGAAGTTCTATAGCCTTA 58.451 33.333 2.25 0.00 0.00 2.69
2067 2452 6.809689 TCTGTTTGACATGATTGCAATGAATC 59.190 34.615 18.59 11.27 33.59 2.52
2079 2464 3.056179 TGGACGCTATCTGTTTGACATGA 60.056 43.478 0.00 0.00 0.00 3.07
2139 2524 6.775142 TGATGATTTCTCGGGCCAAAATAATA 59.225 34.615 4.39 0.00 0.00 0.98
2202 2587 1.039856 TGCCCTTTCTCAAAGCAACC 58.960 50.000 0.00 0.00 37.18 3.77
2277 2662 6.238648 ACCTTTTATGTCCTCCTTTGTACTG 58.761 40.000 0.00 0.00 0.00 2.74
2429 2814 9.507280 CAGTTCCATTTCAATACACATAACATC 57.493 33.333 0.00 0.00 0.00 3.06
2435 2820 4.160252 GGGCAGTTCCATTTCAATACACAT 59.840 41.667 0.00 0.00 36.21 3.21
2439 2824 3.365472 AGGGGCAGTTCCATTTCAATAC 58.635 45.455 0.00 0.00 36.21 1.89
2457 2842 8.403236 CCCTTTATTACTTCGAATTTGTAAGGG 58.597 37.037 20.30 20.30 31.03 3.95
2469 2854 4.035208 GGTGTGCATCCCTTTATTACTTCG 59.965 45.833 0.00 0.00 0.00 3.79
2500 2885 5.949233 ATGCACAGAAACGAAAAGAAAAC 57.051 34.783 0.00 0.00 0.00 2.43
2502 2887 7.648142 AGAATATGCACAGAAACGAAAAGAAA 58.352 30.769 0.00 0.00 0.00 2.52
2503 2888 7.173218 AGAGAATATGCACAGAAACGAAAAGAA 59.827 33.333 0.00 0.00 0.00 2.52
2511 2896 7.912250 CCACAATTAGAGAATATGCACAGAAAC 59.088 37.037 0.00 0.00 0.00 2.78
2554 2939 7.936496 TTAACATTTCAGGAGAATACATGCA 57.064 32.000 0.00 0.00 32.89 3.96
2565 2950 9.739276 AATCTGACTATGTTTAACATTTCAGGA 57.261 29.630 29.07 21.90 42.20 3.86
2577 2962 8.543774 ACCAAGATGACTAATCTGACTATGTTT 58.456 33.333 0.00 0.00 45.37 2.83
3412 4389 7.533923 AAATTAAAGTATAGTCCTTGGGGGA 57.466 36.000 0.00 0.00 42.77 4.81
3413 4390 7.417456 GCAAAATTAAAGTATAGTCCTTGGGGG 60.417 40.741 0.00 0.00 0.00 5.40
3414 4391 7.123547 TGCAAAATTAAAGTATAGTCCTTGGGG 59.876 37.037 0.00 0.00 0.00 4.96
3415 4392 8.062065 TGCAAAATTAAAGTATAGTCCTTGGG 57.938 34.615 0.00 0.00 0.00 4.12
3639 4870 4.527816 GCCTCAATCTCTGGTCTCATAGAT 59.472 45.833 0.00 0.00 38.12 1.98
3667 4898 8.425577 TCTAGATCTTGCTTTAGTTGCATAAC 57.574 34.615 0.00 0.00 40.34 1.89
3792 5023 5.363005 TCAGTAGGAAGAACTATTAGGTGGC 59.637 44.000 0.00 0.00 0.00 5.01
3878 5116 9.787532 AATACCACAATTACAATGATTTCTTCG 57.212 29.630 0.00 0.00 0.00 3.79
3950 5190 3.328050 GCTGCCCCTACCTGAATAATACT 59.672 47.826 0.00 0.00 0.00 2.12
4063 5303 4.693566 AGTTCAACATATGTTACACCACCG 59.306 41.667 20.39 6.39 36.32 4.94
4798 6047 2.439507 GGGTCATTAGAATCAGCCCTGA 59.560 50.000 0.00 0.00 44.59 3.86
4806 6055 6.040166 ACATCATTGCTTGGGTCATTAGAATC 59.960 38.462 0.00 0.00 0.00 2.52
4878 6127 1.609635 TTATCTGCAACGGCGGGAGA 61.610 55.000 13.24 11.02 46.76 3.71
4917 6166 6.371809 TTCAATAACAGGATACGAATTGCC 57.628 37.500 0.00 0.00 46.39 4.52
4944 6196 7.270047 AGCAAAATGATCTTCACATTTATGGG 58.730 34.615 0.00 0.00 43.94 4.00
5084 6707 9.127277 TGCACCTAACAGTACTAAAAAGAAAAT 57.873 29.630 0.00 0.00 0.00 1.82
5180 6990 6.509418 GGTGATGAAAATACTGCACCTAAA 57.491 37.500 0.00 0.00 41.82 1.85
5200 7010 5.468592 TGCTACAAAAATATTGTGCAGGTG 58.531 37.500 4.19 0.00 34.27 4.00
5243 10123 2.263077 CGACATCACAGTTCTACCAGC 58.737 52.381 0.00 0.00 0.00 4.85
5248 10128 3.306502 GGGAAACCGACATCACAGTTCTA 60.307 47.826 0.00 0.00 43.64 2.10
5264 10144 7.658261 AGAGTTAGCTTAAACATTTGGGAAAC 58.342 34.615 0.00 0.00 0.00 2.78
5292 10175 9.046296 ACGATGAGCATATAAAAAGTTAAGAGG 57.954 33.333 0.00 0.00 0.00 3.69
5298 10181 7.254795 GGCTACACGATGAGCATATAAAAAGTT 60.255 37.037 8.89 0.00 40.64 2.66
5305 10188 3.431415 AGGGCTACACGATGAGCATATA 58.569 45.455 8.89 0.00 40.64 0.86
5321 10206 7.716799 TTCATTATGTATCAAACAAAGGGCT 57.283 32.000 0.00 0.00 42.70 5.19
5359 10245 0.822811 TAAACACCGCGCAGGGTATA 59.177 50.000 19.73 6.50 46.96 1.47
5362 10248 0.036199 TTATAAACACCGCGCAGGGT 60.036 50.000 19.73 8.04 46.96 4.34
5437 10367 0.965439 TGATCCCCAAAGCCAAAACG 59.035 50.000 0.00 0.00 0.00 3.60
5535 10466 3.543680 AGCACACTTGTTACACTCACT 57.456 42.857 0.00 0.00 0.00 3.41
5538 10469 2.864343 ACGAAGCACACTTGTTACACTC 59.136 45.455 0.00 0.00 35.82 3.51
5553 10484 3.799137 TTGATTTTACACCGACGAAGC 57.201 42.857 0.00 0.00 0.00 3.86
5641 10605 8.131731 TGCCAAAAATGCCTTTTTAATGTAAAC 58.868 29.630 11.42 0.00 41.49 2.01
5642 10606 8.225603 TGCCAAAAATGCCTTTTTAATGTAAA 57.774 26.923 11.42 0.00 41.49 2.01
5647 10611 6.294620 CCACATGCCAAAAATGCCTTTTTAAT 60.295 34.615 11.42 4.73 41.49 1.40
5649 10613 4.518211 CCACATGCCAAAAATGCCTTTTTA 59.482 37.500 11.42 0.00 41.49 1.52
5655 10619 0.324285 TCCCACATGCCAAAAATGCC 59.676 50.000 0.00 0.00 0.00 4.40
5656 10620 1.729284 CTCCCACATGCCAAAAATGC 58.271 50.000 0.00 0.00 0.00 3.56
5662 10626 1.694844 CATATGCTCCCACATGCCAA 58.305 50.000 0.00 0.00 0.00 4.52
5686 10650 3.778075 TCGGAAATCCAATTCAGGTCCTA 59.222 43.478 0.00 0.00 35.14 2.94
5691 10655 3.004106 GCAGATCGGAAATCCAATTCAGG 59.996 47.826 0.00 0.00 35.14 3.86
5697 10661 1.745087 GCAAGCAGATCGGAAATCCAA 59.255 47.619 0.00 0.00 35.14 3.53
5715 10679 1.271108 TGTGGGTTCGATAAAGCAGCA 60.271 47.619 0.00 0.00 37.09 4.41
5718 10682 1.271108 TGCTGTGGGTTCGATAAAGCA 60.271 47.619 0.00 0.00 37.09 3.91
5801 10765 7.119709 TGGTGAATTATTAGTGTGCTAGCTA 57.880 36.000 17.23 1.87 0.00 3.32
5827 10813 8.688747 ATTTTGGTGGCAATATTTTCTTTTGA 57.311 26.923 0.00 0.00 0.00 2.69
5854 10840 2.236395 AGTTTTGTCCCTACTCGGATGG 59.764 50.000 0.00 0.00 33.48 3.51
5863 10849 2.271777 CCCCCTGTAGTTTTGTCCCTA 58.728 52.381 0.00 0.00 0.00 3.53
5877 10863 1.069668 GGCGTATAGTAACACCCCCTG 59.930 57.143 0.00 0.00 0.00 4.45
5878 10864 1.417288 GGCGTATAGTAACACCCCCT 58.583 55.000 0.00 0.00 0.00 4.79
5885 10871 2.291741 ACTGTAGGCGGCGTATAGTAAC 59.708 50.000 24.28 7.10 27.75 2.50


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

AutoCloner maintained by Alex Coulton.