Multiple sequence alignment - TraesCS5B01G285000

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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 TraesCS5B01G285000 chr5B 100.000 2755 0 0 1 2755 470511106 470513860 0.000000e+00 5088.0
1 TraesCS5B01G285000 chr5B 100.000 2257 0 0 2954 5210 470514059 470516315 0.000000e+00 4169.0
2 TraesCS5B01G285000 chr5B 86.199 1268 90 47 735 1989 470435768 470436963 0.000000e+00 1293.0
3 TraesCS5B01G285000 chr5B 84.318 829 103 18 4393 5204 382378673 382379491 0.000000e+00 785.0
4 TraesCS5B01G285000 chr5B 81.742 356 30 19 1193 1547 470604048 470604369 1.110000e-66 265.0
5 TraesCS5B01G285000 chr5D 94.475 2027 69 15 1 2003 390416845 390418852 0.000000e+00 3083.0
6 TraesCS5B01G285000 chr5D 91.895 1678 123 7 3541 5210 390421092 390422764 0.000000e+00 2333.0
7 TraesCS5B01G285000 chr5D 85.951 1267 85 43 735 1995 390371256 390372435 0.000000e+00 1267.0
8 TraesCS5B01G285000 chr5D 81.113 1006 131 38 997 1981 390504139 390505106 0.000000e+00 750.0
9 TraesCS5B01G285000 chr5D 94.577 461 21 4 2254 2713 390419665 390420122 0.000000e+00 710.0
10 TraesCS5B01G285000 chr5D 87.002 577 57 6 2960 3530 390420389 390420953 7.360000e-178 634.0
11 TraesCS5B01G285000 chr5D 79.385 650 101 18 100 718 416590136 416589489 1.340000e-115 427.0
12 TraesCS5B01G285000 chr5D 85.751 386 45 10 3036 3416 398892732 398892352 2.920000e-107 399.0
13 TraesCS5B01G285000 chr5D 90.299 134 11 2 2476 2608 390372535 390372667 1.930000e-39 174.0
14 TraesCS5B01G285000 chr5A 95.300 1149 41 7 861 2003 493779210 493780351 0.000000e+00 1810.0
15 TraesCS5B01G285000 chr5A 89.124 1462 112 11 3300 4737 493781602 493783040 0.000000e+00 1775.0
16 TraesCS5B01G285000 chr5A 85.031 1276 104 43 735 1989 493661920 493663129 0.000000e+00 1218.0
17 TraesCS5B01G285000 chr5A 90.356 674 39 13 2065 2729 493780356 493781012 0.000000e+00 861.0
18 TraesCS5B01G285000 chr5A 85.472 826 111 5 4393 5210 673834737 673835561 0.000000e+00 852.0
19 TraesCS5B01G285000 chr5A 84.607 903 79 29 1 863 493775703 493776585 0.000000e+00 843.0
20 TraesCS5B01G285000 chr5A 80.948 1013 130 41 994 1985 493817929 493816959 0.000000e+00 743.0
21 TraesCS5B01G285000 chr5A 86.398 397 44 10 3026 3416 301232679 301232287 4.820000e-115 425.0
22 TraesCS5B01G285000 chr5A 87.252 353 38 4 2960 3306 493781071 493781422 3.780000e-106 396.0
23 TraesCS5B01G285000 chr5A 80.261 537 69 25 998 1532 492637158 492636657 2.290000e-98 370.0
24 TraesCS5B01G285000 chr5A 75.038 665 114 34 103 729 592063499 592062849 1.440000e-65 261.0
25 TraesCS5B01G285000 chr5A 76.109 586 87 28 103 639 378486790 378486209 1.860000e-64 257.0
26 TraesCS5B01G285000 chr5A 92.500 40 2 1 2014 2053 659456052 659456014 7.290000e-04 56.5
27 TraesCS5B01G285000 chr7D 85.000 820 102 13 4403 5210 632809231 632808421 0.000000e+00 813.0
28 TraesCS5B01G285000 chr7D 84.337 830 111 11 4392 5210 498253570 498252749 0.000000e+00 795.0
29 TraesCS5B01G285000 chr7D 84.856 383 51 7 3030 3408 592054585 592054964 3.810000e-101 379.0
30 TraesCS5B01G285000 chr7D 77.424 660 89 39 114 717 206682797 206683452 6.460000e-89 339.0
31 TraesCS5B01G285000 chr7D 91.489 47 4 0 2014 2060 554683994 554683948 1.210000e-06 65.8
32 TraesCS5B01G285000 chr7D 87.500 48 6 0 2014 2061 376561662 376561615 7.290000e-04 56.5
33 TraesCS5B01G285000 chr7D 89.130 46 3 2 2017 2061 629030254 629030298 7.290000e-04 56.5
34 TraesCS5B01G285000 chr3A 84.514 833 101 19 4393 5210 96000079 96000898 0.000000e+00 798.0
35 TraesCS5B01G285000 chr3A 84.173 834 98 24 4393 5210 96228087 96228902 0.000000e+00 778.0
36 TraesCS5B01G285000 chr7B 84.653 808 107 10 4392 5187 99137675 99138477 0.000000e+00 789.0
37 TraesCS5B01G285000 chr6B 84.268 820 114 11 4393 5204 690025961 690026773 0.000000e+00 785.0
38 TraesCS5B01G285000 chr6B 91.489 47 4 0 2014 2060 212165894 212165940 1.210000e-06 65.8
39 TraesCS5B01G285000 chr3D 82.201 618 64 25 996 1604 564806674 564807254 1.690000e-134 490.0
40 TraesCS5B01G285000 chr4D 85.166 391 50 8 3033 3416 390259964 390259575 1.360000e-105 394.0
41 TraesCS5B01G285000 chr2B 85.090 389 51 7 3033 3416 474556785 474556399 1.760000e-104 390.0
42 TraesCS5B01G285000 chr2B 75.657 571 108 17 103 645 772831037 772830470 6.700000e-64 255.0
43 TraesCS5B01G285000 chr2B 93.684 95 6 0 100 194 93106039 93106133 5.440000e-30 143.0
44 TraesCS5B01G285000 chr2B 82.069 145 24 2 502 645 89009474 89009331 7.080000e-24 122.0
45 TraesCS5B01G285000 chr6A 84.131 397 57 6 3026 3416 409673962 409673566 3.810000e-101 379.0
46 TraesCS5B01G285000 chr6D 84.595 383 51 8 3026 3403 125083113 125082734 1.770000e-99 374.0
47 TraesCS5B01G285000 chr6D 85.366 82 12 0 564 645 433352130 433352049 9.300000e-13 86.1
48 TraesCS5B01G285000 chr4B 77.975 563 89 18 100 631 380691446 380692004 2.340000e-83 320.0
49 TraesCS5B01G285000 chr4B 80.315 381 63 9 113 485 116060644 116060268 1.430000e-70 278.0
50 TraesCS5B01G285000 chr4B 89.130 46 5 0 2015 2060 57796908 57796863 2.030000e-04 58.4
51 TraesCS5B01G285000 chr2D 78.870 407 66 12 285 679 348288271 348287873 1.860000e-64 257.0
52 TraesCS5B01G285000 chr2D 89.855 69 7 0 3424 3492 147350225 147350293 7.190000e-14 89.8
53 TraesCS5B01G285000 chr4A 79.275 386 55 13 103 466 174106737 174106355 4.030000e-61 246.0
54 TraesCS5B01G285000 chr2A 75.398 565 108 16 103 645 760931907 760931352 1.450000e-60 244.0
55 TraesCS5B01G285000 chr2A 73.159 611 116 25 90 660 318038917 318038315 5.360000e-40 176.0
56 TraesCS5B01G285000 chr2A 78.814 118 19 5 2071 2185 172532843 172532957 2.010000e-09 75.0
57 TraesCS5B01G285000 chr1B 74.286 595 113 28 104 660 297335204 297335796 1.140000e-51 215.0
58 TraesCS5B01G285000 chr1B 94.444 36 2 0 2015 2050 409956029 409955994 7.290000e-04 56.5
59 TraesCS5B01G285000 chr3B 78.899 218 43 3 502 717 684418798 684418582 1.510000e-30 145.0
60 TraesCS5B01G285000 chr3B 75.145 346 62 12 106 446 165244806 165244480 1.960000e-29 141.0
61 TraesCS5B01G285000 chr3B 97.059 34 1 0 2014 2047 728587326 728587293 2.030000e-04 58.4
62 TraesCS5B01G285000 chr1D 90.000 70 7 0 3423 3492 479523214 479523145 2.000000e-14 91.6
63 TraesCS5B01G285000 chr1D 91.489 47 4 0 2014 2060 7756992 7756946 1.210000e-06 65.8


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 TraesCS5B01G285000 chr5B 470511106 470516315 5209 False 4628.5 5088 100.00000 1 5210 2 chr5B.!!$F4 5209
1 TraesCS5B01G285000 chr5B 470435768 470436963 1195 False 1293.0 1293 86.19900 735 1989 1 chr5B.!!$F2 1254
2 TraesCS5B01G285000 chr5B 382378673 382379491 818 False 785.0 785 84.31800 4393 5204 1 chr5B.!!$F1 811
3 TraesCS5B01G285000 chr5D 390416845 390422764 5919 False 1690.0 3083 91.98725 1 5210 4 chr5D.!!$F3 5209
4 TraesCS5B01G285000 chr5D 390504139 390505106 967 False 750.0 750 81.11300 997 1981 1 chr5D.!!$F1 984
5 TraesCS5B01G285000 chr5D 390371256 390372667 1411 False 720.5 1267 88.12500 735 2608 2 chr5D.!!$F2 1873
6 TraesCS5B01G285000 chr5D 416589489 416590136 647 True 427.0 427 79.38500 100 718 1 chr5D.!!$R2 618
7 TraesCS5B01G285000 chr5A 493661920 493663129 1209 False 1218.0 1218 85.03100 735 1989 1 chr5A.!!$F1 1254
8 TraesCS5B01G285000 chr5A 493775703 493783040 7337 False 1137.0 1810 89.32780 1 4737 5 chr5A.!!$F3 4736
9 TraesCS5B01G285000 chr5A 673834737 673835561 824 False 852.0 852 85.47200 4393 5210 1 chr5A.!!$F2 817
10 TraesCS5B01G285000 chr5A 493816959 493817929 970 True 743.0 743 80.94800 994 1985 1 chr5A.!!$R4 991
11 TraesCS5B01G285000 chr5A 492636657 492637158 501 True 370.0 370 80.26100 998 1532 1 chr5A.!!$R3 534
12 TraesCS5B01G285000 chr5A 592062849 592063499 650 True 261.0 261 75.03800 103 729 1 chr5A.!!$R5 626
13 TraesCS5B01G285000 chr5A 378486209 378486790 581 True 257.0 257 76.10900 103 639 1 chr5A.!!$R2 536
14 TraesCS5B01G285000 chr7D 632808421 632809231 810 True 813.0 813 85.00000 4403 5210 1 chr7D.!!$R4 807
15 TraesCS5B01G285000 chr7D 498252749 498253570 821 True 795.0 795 84.33700 4392 5210 1 chr7D.!!$R2 818
16 TraesCS5B01G285000 chr7D 206682797 206683452 655 False 339.0 339 77.42400 114 717 1 chr7D.!!$F1 603
17 TraesCS5B01G285000 chr3A 96000079 96000898 819 False 798.0 798 84.51400 4393 5210 1 chr3A.!!$F1 817
18 TraesCS5B01G285000 chr3A 96228087 96228902 815 False 778.0 778 84.17300 4393 5210 1 chr3A.!!$F2 817
19 TraesCS5B01G285000 chr7B 99137675 99138477 802 False 789.0 789 84.65300 4392 5187 1 chr7B.!!$F1 795
20 TraesCS5B01G285000 chr6B 690025961 690026773 812 False 785.0 785 84.26800 4393 5204 1 chr6B.!!$F2 811
21 TraesCS5B01G285000 chr3D 564806674 564807254 580 False 490.0 490 82.20100 996 1604 1 chr3D.!!$F1 608
22 TraesCS5B01G285000 chr2B 772830470 772831037 567 True 255.0 255 75.65700 103 645 1 chr2B.!!$R3 542
23 TraesCS5B01G285000 chr4B 380691446 380692004 558 False 320.0 320 77.97500 100 631 1 chr4B.!!$F1 531
24 TraesCS5B01G285000 chr2A 760931352 760931907 555 True 244.0 244 75.39800 103 645 1 chr2A.!!$R2 542
25 TraesCS5B01G285000 chr1B 297335204 297335796 592 False 215.0 215 74.28600 104 660 1 chr1B.!!$F1 556

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
975 3701 0.594796 CAAAGCACCAAACCACGAGC 60.595 55.0 0.00 0.00 0.00 5.03 F
1014 3747 0.178932 CCGAGATGATAGGGTGGGGA 60.179 60.0 0.00 0.00 0.00 4.81 F
2437 6101 0.605319 TGCCACAAACGAGCTTAGGG 60.605 55.0 0.00 0.00 0.00 3.53 F
2736 6401 0.456221 CCTACTGTACACCAGCGGAG 59.544 60.0 0.00 0.00 45.68 4.63 F
3309 7187 1.225855 ATTTGTGCGCTCGAAGTCAA 58.774 45.0 16.51 4.98 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2346 6010 2.116827 AGTTGTTTCCGTGGACACAA 57.883 45.000 14.87 14.87 40.92 3.33 R
2729 6394 2.186384 CTCCAAGAGGCTCCGCTG 59.814 66.667 11.71 6.39 33.74 5.18 R
3396 7274 0.395311 TAGGGTCTGCGGTAGGACAG 60.395 60.000 0.00 0.00 34.49 3.51 R
3922 7929 0.593518 CGATAGACTGAGGCAGTGCG 60.594 60.000 9.45 0.00 45.44 5.34 R
4784 8805 0.039618 TTTTCCAGTGATGGGAGGGC 59.960 55.000 0.00 0.00 35.46 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
562 640 2.040412 CCCAAGAAGGCTACAACTCCTT 59.960 50.000 0.00 0.00 44.80 3.36
700 779 2.742372 GAGCTGGAAAGCGCCGAA 60.742 61.111 2.29 0.00 40.27 4.30
702 781 1.648467 GAGCTGGAAAGCGCCGAAAT 61.648 55.000 2.29 0.00 40.27 2.17
900 3624 3.737850 GAGTGGAGAGAATAATGGCAGG 58.262 50.000 0.00 0.00 0.00 4.85
901 3625 2.158696 AGTGGAGAGAATAATGGCAGGC 60.159 50.000 0.00 0.00 0.00 4.85
902 3626 1.845791 TGGAGAGAATAATGGCAGGCA 59.154 47.619 0.00 0.00 0.00 4.75
975 3701 0.594796 CAAAGCACCAAACCACGAGC 60.595 55.000 0.00 0.00 0.00 5.03
1014 3747 0.178932 CCGAGATGATAGGGTGGGGA 60.179 60.000 0.00 0.00 0.00 4.81
1551 4341 3.640407 GCCTGGCTGGAGGTGACA 61.640 66.667 15.36 0.00 38.35 3.58
1662 4624 4.812476 CGGAAGATGGCGGCGACA 62.812 66.667 21.84 21.84 0.00 4.35
1809 4783 4.225984 CAGCAGATTAGTGAGTAGCGATC 58.774 47.826 0.00 0.00 0.00 3.69
1818 4792 4.460263 AGTGAGTAGCGATCTTCTCTCAT 58.540 43.478 9.48 0.72 37.55 2.90
1855 4831 7.938715 ACAATTTATTCATCAGGCATTCTCTC 58.061 34.615 0.00 0.00 0.00 3.20
2003 5016 5.711036 ACCTACTACTCTCTTCGTTCACAAT 59.289 40.000 0.00 0.00 0.00 2.71
2004 5017 6.127952 ACCTACTACTCTCTTCGTTCACAATC 60.128 42.308 0.00 0.00 0.00 2.67
2005 5018 5.061920 ACTACTCTCTTCGTTCACAATCC 57.938 43.478 0.00 0.00 0.00 3.01
2006 5019 4.767928 ACTACTCTCTTCGTTCACAATCCT 59.232 41.667 0.00 0.00 0.00 3.24
2007 5020 4.181309 ACTCTCTTCGTTCACAATCCTC 57.819 45.455 0.00 0.00 0.00 3.71
2008 5021 3.056465 ACTCTCTTCGTTCACAATCCTCC 60.056 47.826 0.00 0.00 0.00 4.30
2009 5022 2.897326 TCTCTTCGTTCACAATCCTCCA 59.103 45.455 0.00 0.00 0.00 3.86
2010 5023 3.515502 TCTCTTCGTTCACAATCCTCCAT 59.484 43.478 0.00 0.00 0.00 3.41
2011 5024 3.861840 TCTTCGTTCACAATCCTCCATC 58.138 45.455 0.00 0.00 0.00 3.51
2012 5025 3.515502 TCTTCGTTCACAATCCTCCATCT 59.484 43.478 0.00 0.00 0.00 2.90
2013 5026 3.526931 TCGTTCACAATCCTCCATCTC 57.473 47.619 0.00 0.00 0.00 2.75
2014 5027 2.831526 TCGTTCACAATCCTCCATCTCA 59.168 45.455 0.00 0.00 0.00 3.27
2015 5028 3.260632 TCGTTCACAATCCTCCATCTCAA 59.739 43.478 0.00 0.00 0.00 3.02
2016 5029 4.002982 CGTTCACAATCCTCCATCTCAAA 58.997 43.478 0.00 0.00 0.00 2.69
2017 5030 4.455533 CGTTCACAATCCTCCATCTCAAAA 59.544 41.667 0.00 0.00 0.00 2.44
2018 5031 5.124457 CGTTCACAATCCTCCATCTCAAAAT 59.876 40.000 0.00 0.00 0.00 1.82
2019 5032 6.349611 CGTTCACAATCCTCCATCTCAAAATT 60.350 38.462 0.00 0.00 0.00 1.82
2020 5033 7.148255 CGTTCACAATCCTCCATCTCAAAATTA 60.148 37.037 0.00 0.00 0.00 1.40
2021 5034 8.689972 GTTCACAATCCTCCATCTCAAAATTAT 58.310 33.333 0.00 0.00 0.00 1.28
2022 5035 9.919416 TTCACAATCCTCCATCTCAAAATTATA 57.081 29.630 0.00 0.00 0.00 0.98
2023 5036 9.342308 TCACAATCCTCCATCTCAAAATTATAC 57.658 33.333 0.00 0.00 0.00 1.47
2024 5037 9.347240 CACAATCCTCCATCTCAAAATTATACT 57.653 33.333 0.00 0.00 0.00 2.12
2057 5070 9.503427 AAGACACTTATTTTGAAACGAAAGAAG 57.497 29.630 13.69 13.69 39.77 2.85
2058 5071 8.674607 AGACACTTATTTTGAAACGAAAGAAGT 58.325 29.630 14.64 14.64 44.65 3.01
2059 5072 9.925268 GACACTTATTTTGAAACGAAAGAAGTA 57.075 29.630 17.93 0.00 43.01 2.24
2165 5185 9.321562 TCCTATATAGAAATGTCCAAAACGTTC 57.678 33.333 11.53 0.00 36.03 3.95
2277 5937 7.329588 TCTACGACAACTTATCATGCTCTTA 57.670 36.000 0.00 0.00 0.00 2.10
2399 6063 3.568093 GTCACGCTTTTGTGGCAAT 57.432 47.368 0.00 0.00 43.83 3.56
2437 6101 0.605319 TGCCACAAACGAGCTTAGGG 60.605 55.000 0.00 0.00 0.00 3.53
2465 6129 1.135333 TGCCTGAAAACCAAAACGTCC 59.865 47.619 0.00 0.00 0.00 4.79
2693 6358 9.872757 ATAAAATACGTACACAACTTGAACTTG 57.127 29.630 0.00 0.00 0.00 3.16
2698 6363 4.201773 CGTACACAACTTGAACTTGCTTCA 60.202 41.667 0.00 0.00 37.08 3.02
2729 6394 2.766828 AGCAGAATCCCTACTGTACACC 59.233 50.000 0.00 0.00 36.62 4.16
2730 6395 2.500098 GCAGAATCCCTACTGTACACCA 59.500 50.000 0.00 0.00 36.62 4.17
2734 6399 0.968901 TCCCTACTGTACACCAGCGG 60.969 60.000 0.00 0.00 45.68 5.52
2735 6400 0.968901 CCCTACTGTACACCAGCGGA 60.969 60.000 0.00 0.00 45.68 5.54
2736 6401 0.456221 CCTACTGTACACCAGCGGAG 59.544 60.000 0.00 0.00 45.68 4.63
2754 6419 4.751431 CCTCTTGGAGGCCAAAGG 57.249 61.111 5.01 6.67 43.44 3.11
2975 6661 3.906846 AGCCCATTTTTGGTACATTCCAA 59.093 39.130 0.00 0.00 44.48 3.53
3002 6692 5.515626 GTGAAGTATACTTTAGAGCACCACG 59.484 44.000 18.96 0.00 36.11 4.94
3003 6693 4.043037 AGTATACTTTAGAGCACCACGC 57.957 45.455 0.00 0.00 42.91 5.34
3004 6694 3.446161 AGTATACTTTAGAGCACCACGCA 59.554 43.478 0.00 0.00 46.13 5.24
3048 6738 3.263170 TGGTAGCTCCTTTTAGTGATGCA 59.737 43.478 0.00 0.00 37.07 3.96
3055 6745 5.643777 GCTCCTTTTAGTGATGCAGTAAAGA 59.356 40.000 0.00 3.43 39.43 2.52
3058 6748 8.458573 TCCTTTTAGTGATGCAGTAAAGAAAA 57.541 30.769 0.00 0.00 39.43 2.29
3082 6772 6.552445 AATAAGCATCTCACACCTACTTCT 57.448 37.500 0.00 0.00 0.00 2.85
3084 6774 4.899352 AGCATCTCACACCTACTTCTTT 57.101 40.909 0.00 0.00 0.00 2.52
3096 6786 3.451540 CCTACTTCTTTAGAGGTGACCCC 59.548 52.174 0.00 0.00 35.84 4.95
3153 6843 1.737363 CGGTGGTCTCTAGCAAGCTTC 60.737 57.143 0.00 0.00 34.25 3.86
3170 6861 5.819825 AGCTTCGTTAAAGGATCAATTCC 57.180 39.130 0.00 0.00 45.85 3.01
3257 6949 7.165485 AGTATGTGGTCTTAATGCTTACAACA 58.835 34.615 0.00 0.00 30.70 3.33
3278 6970 1.529226 TGTATTTGCGTTGGGACCAG 58.471 50.000 0.00 0.00 0.00 4.00
3298 6990 7.194607 ACCAGATATGATCTTAATTTGTGCG 57.805 36.000 0.00 0.00 37.58 5.34
3301 6993 7.014115 CAGATATGATCTTAATTTGTGCGCTC 58.986 38.462 9.73 5.51 37.58 5.03
3309 7187 1.225855 ATTTGTGCGCTCGAAGTCAA 58.774 45.000 16.51 4.98 0.00 3.18
3312 7190 2.733218 TGCGCTCGAAGTCAACCG 60.733 61.111 9.73 0.00 0.00 4.44
3323 7201 1.244816 AGTCAACCGTCGAGATGTGA 58.755 50.000 0.00 0.00 0.00 3.58
3342 7220 5.845103 TGTGATTGTTACTAACCGAAGTGA 58.155 37.500 0.00 0.00 0.00 3.41
3347 7225 3.256631 TGTTACTAACCGAAGTGAGGGAC 59.743 47.826 0.00 0.00 0.00 4.46
3394 7272 2.499289 ACGAGTCCTGCATCAAGAATCT 59.501 45.455 0.00 0.00 0.00 2.40
3395 7273 3.701542 ACGAGTCCTGCATCAAGAATCTA 59.298 43.478 0.00 0.00 0.00 1.98
3396 7274 4.047822 CGAGTCCTGCATCAAGAATCTAC 58.952 47.826 0.00 0.00 0.00 2.59
3410 7288 2.730934 ATCTACTGTCCTACCGCAGA 57.269 50.000 0.00 0.00 36.62 4.26
3429 7307 1.450312 CCCTACTGCGGGCTCAAAG 60.450 63.158 0.00 0.00 37.41 2.77
3520 7398 7.870509 AGAATATAACATTGAGCACACACAT 57.129 32.000 0.00 0.00 0.00 3.21
3533 7411 2.994699 CACATTAGTGGGCCGGGA 59.005 61.111 2.18 0.00 42.13 5.14
3545 7551 3.817084 GTGGGCCGGGAATAAATAGTAAC 59.183 47.826 2.18 0.00 0.00 2.50
3603 7609 8.147642 AGGAATTAACTGATTGATCGTGAATC 57.852 34.615 0.00 0.00 34.72 2.52
3616 7622 6.750667 GATCGTGAATCACACCGATCTGGT 62.751 50.000 20.35 3.75 44.97 4.00
3646 7652 3.093814 TGTAGGCTTGTTCATCGGTCTA 58.906 45.455 0.00 0.00 0.00 2.59
3667 7673 1.299926 GGACAAGCTCGTCGTGTGT 60.300 57.895 0.00 0.00 37.52 3.72
3679 7685 2.334946 CGTGTGTGGGCCTGGATTG 61.335 63.158 4.53 0.00 0.00 2.67
3760 7766 2.289257 GCTACTTTTGGGACTACGTGGT 60.289 50.000 3.40 3.40 0.00 4.16
3772 7778 2.758770 TACGTGGTGACCTTCTGCGC 62.759 60.000 2.11 0.00 0.00 6.09
3829 7835 2.254546 TGTTACAGGCTCACAACTGG 57.745 50.000 0.00 0.00 39.00 4.00
3922 7929 1.070289 CCTCGTTCCTATTGGTAGGCC 59.930 57.143 0.00 0.00 46.03 5.19
3959 7966 3.254470 TCGGGACATTTATCTTTGCGA 57.746 42.857 0.00 0.00 0.00 5.10
3973 7980 4.524053 TCTTTGCGAGAGAGTATGACCTA 58.476 43.478 0.00 0.00 0.00 3.08
4006 8013 4.708726 ACTCAGTACCGCGTAAGTAAAT 57.291 40.909 4.92 0.00 41.68 1.40
4115 8123 2.034179 ACAACTAAAACCGCTCTTTGCC 59.966 45.455 0.00 0.00 38.78 4.52
4119 8127 2.509052 AAAACCGCTCTTTGCCTTTC 57.491 45.000 0.00 0.00 38.78 2.62
4121 8129 0.467290 AACCGCTCTTTGCCTTTCCA 60.467 50.000 0.00 0.00 38.78 3.53
4155 8163 1.897423 CAGGGTGATAGTCGGCACA 59.103 57.895 0.00 0.00 36.76 4.57
4228 8236 9.725019 TCATGTGATTATGTTATATGTTCCTCC 57.275 33.333 0.00 0.00 0.00 4.30
4282 8294 4.215399 GTGTGCCTACAAGATGTAGCAAAA 59.785 41.667 11.19 4.29 46.72 2.44
4283 8295 4.824537 TGTGCCTACAAGATGTAGCAAAAA 59.175 37.500 11.19 2.47 46.72 1.94
4336 8349 6.372103 TGTGTTTTGGTCGTTCTTCTCTTTAA 59.628 34.615 0.00 0.00 0.00 1.52
4343 8356 6.990349 TGGTCGTTCTTCTCTTTAAGAAATGT 59.010 34.615 0.00 0.00 44.75 2.71
4423 8436 9.968870 CTATAACACTAAGCTCCCTAGTTTTAG 57.031 37.037 8.08 5.87 32.66 1.85
4460 8473 8.511604 TCAATTGAGGTCTCCAATTAGAATTC 57.488 34.615 3.38 0.00 40.91 2.17
4462 8475 5.677319 TGAGGTCTCCAATTAGAATTCGT 57.323 39.130 0.00 0.00 0.00 3.85
4467 8480 5.642063 GGTCTCCAATTAGAATTCGTTCACA 59.358 40.000 0.00 0.00 0.00 3.58
4498 8511 5.190992 ACCGGGTTAACAATTTCTCAAAC 57.809 39.130 6.32 0.00 0.00 2.93
4512 8526 7.684937 ATTTCTCAAACCTCTCTCATTCAAG 57.315 36.000 0.00 0.00 0.00 3.02
4514 8529 5.788450 TCTCAAACCTCTCTCATTCAAGTC 58.212 41.667 0.00 0.00 0.00 3.01
4620 8637 1.202651 ACCGGGTCAACACTTTCTCAG 60.203 52.381 6.32 0.00 0.00 3.35
4621 8638 0.868406 CGGGTCAACACTTTCTCAGC 59.132 55.000 0.00 0.00 0.00 4.26
4709 8727 9.928618 TGAGGTATTCAAATTTGGATATGGTTA 57.071 29.630 19.81 6.06 31.64 2.85
4783 8804 6.968904 GCCTATAAAACATATCAATCATGCGG 59.031 38.462 0.00 0.00 0.00 5.69
4784 8805 7.475015 CCTATAAAACATATCAATCATGCGGG 58.525 38.462 0.00 0.00 0.00 6.13
4815 8837 2.872245 CACTGGAAAAGAGAAGCGTCAA 59.128 45.455 1.61 0.00 0.00 3.18
4835 8857 5.586243 GTCAACATGTGATATTGTAGCACCT 59.414 40.000 0.00 0.00 44.02 4.00
4868 8890 3.243873 ACATGCGATCACCGACATAGAAT 60.244 43.478 0.00 0.00 41.76 2.40
4878 8900 2.612212 CCGACATAGAATTTTCCCCACG 59.388 50.000 0.00 0.00 0.00 4.94
4952 8976 8.026607 CCCACCAAATAACCGCATTATAAATAG 58.973 37.037 0.00 0.00 32.86 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 37 4.982701 GCCAGCCACCAACCAGCT 62.983 66.667 0.00 0.00 37.32 4.24
63 66 1.183030 ATGGTCGTCGTTGTCCTCCA 61.183 55.000 0.00 0.00 0.00 3.86
210 252 0.322008 CTCTTGGAGGAGTTGGTGGC 60.322 60.000 0.00 0.00 0.00 5.01
497 574 1.613925 TGCACTACTCTTCTCGCAGTT 59.386 47.619 0.00 0.00 0.00 3.16
498 575 1.068194 GTGCACTACTCTTCTCGCAGT 60.068 52.381 10.32 0.00 0.00 4.40
500 577 0.109735 CGTGCACTACTCTTCTCGCA 60.110 55.000 16.19 0.00 0.00 5.10
782 861 4.022416 TGCACCTTTCATACCAACATCAAC 60.022 41.667 0.00 0.00 0.00 3.18
1014 3747 1.068127 GACACCACCTTGTACACGTCT 59.932 52.381 0.00 0.00 0.00 4.18
1042 3775 4.189188 GGCGAAGTAGAGCGGCGA 62.189 66.667 12.98 0.00 42.98 5.54
1086 3819 1.271379 CGGGTGAAGAACTTCCACCAT 60.271 52.381 23.40 0.00 39.89 3.55
1236 3969 4.738345 GCGAGCACGACGACGAGT 62.738 66.667 15.32 0.00 42.66 4.18
1855 4831 6.667370 TGCAAACGCATATAGGTTGATAATG 58.333 36.000 11.10 0.00 38.49 1.90
2031 5044 9.503427 CTTCTTTCGTTTCAAAATAAGTGTCTT 57.497 29.630 0.00 0.00 0.00 3.01
2032 5045 8.674607 ACTTCTTTCGTTTCAAAATAAGTGTCT 58.325 29.630 0.00 0.00 34.02 3.41
2033 5046 8.836959 ACTTCTTTCGTTTCAAAATAAGTGTC 57.163 30.769 0.00 0.00 34.02 3.67
2165 5185 5.531122 TCTCCCTCCGTTCACAAATATAG 57.469 43.478 0.00 0.00 0.00 1.31
2221 5241 3.633065 CCAAACCCCAAGACTTTCGTTAA 59.367 43.478 0.00 0.00 0.00 2.01
2227 5247 2.953453 GGTACCAAACCCCAAGACTTT 58.047 47.619 7.15 0.00 43.16 2.66
2277 5937 5.763204 AGTGTGATCGACCAACTAAACAAAT 59.237 36.000 0.00 0.00 0.00 2.32
2346 6010 2.116827 AGTTGTTTCCGTGGACACAA 57.883 45.000 14.87 14.87 40.92 3.33
2399 6063 3.465871 GCAAAGTTGGCCAAAAGATGAA 58.534 40.909 22.47 0.00 0.00 2.57
2729 6394 2.186384 CTCCAAGAGGCTCCGCTG 59.814 66.667 11.71 6.39 33.74 5.18
2730 6395 3.080121 CCTCCAAGAGGCTCCGCT 61.080 66.667 11.71 0.00 43.29 5.52
2954 6619 3.971245 TGGAATGTACCAAAAATGGGC 57.029 42.857 0.00 0.00 36.96 5.36
2975 6661 8.414778 GTGGTGCTCTAAAGTATACTTCACTAT 58.585 37.037 23.16 11.31 34.61 2.12
3002 6692 7.148407 CCAATAATATCCTCACGGTAAATCTGC 60.148 40.741 0.00 0.00 0.00 4.26
3003 6693 7.878127 ACCAATAATATCCTCACGGTAAATCTG 59.122 37.037 0.00 0.00 0.00 2.90
3004 6694 7.974504 ACCAATAATATCCTCACGGTAAATCT 58.025 34.615 0.00 0.00 0.00 2.40
3028 6718 4.508662 ACTGCATCACTAAAAGGAGCTAC 58.491 43.478 0.00 0.00 0.00 3.58
3031 6721 5.643777 TCTTTACTGCATCACTAAAAGGAGC 59.356 40.000 0.00 0.00 0.00 4.70
3058 6748 6.951971 AGAAGTAGGTGTGAGATGCTTATTT 58.048 36.000 0.00 0.00 0.00 1.40
3060 6750 6.552445 AAGAAGTAGGTGTGAGATGCTTAT 57.448 37.500 0.00 0.00 0.00 1.73
3061 6751 6.360370 AAAGAAGTAGGTGTGAGATGCTTA 57.640 37.500 0.00 0.00 0.00 3.09
3065 6755 6.153680 ACCTCTAAAGAAGTAGGTGTGAGATG 59.846 42.308 0.00 0.00 40.83 2.90
3082 6772 0.474273 AACCCGGGGTCACCTCTAAA 60.474 55.000 27.92 0.00 33.12 1.85
3084 6774 0.638292 ATAACCCGGGGTCACCTCTA 59.362 55.000 27.92 7.38 33.12 2.43
3132 6822 0.900647 AGCTTGCTAGAGACCACCGT 60.901 55.000 0.00 0.00 0.00 4.83
3135 6825 1.067495 ACGAAGCTTGCTAGAGACCAC 60.067 52.381 2.10 0.00 0.00 4.16
3232 6924 7.165485 TGTTGTAAGCATTAAGACCACATACT 58.835 34.615 0.00 0.00 28.70 2.12
3238 6930 6.892658 ACATTGTTGTAAGCATTAAGACCA 57.107 33.333 0.00 0.00 33.16 4.02
3257 6949 2.491693 CTGGTCCCAACGCAAATACATT 59.508 45.455 0.00 0.00 0.00 2.71
3278 6970 6.011879 CGAGCGCACAAATTAAGATCATATC 58.988 40.000 11.47 0.00 0.00 1.63
3298 6990 1.081641 TCGACGGTTGACTTCGAGC 60.082 57.895 0.00 0.00 36.87 5.03
3301 6993 1.260206 CATCTCGACGGTTGACTTCG 58.740 55.000 0.00 0.00 0.00 3.79
3309 7187 2.743636 AACAATCACATCTCGACGGT 57.256 45.000 0.00 0.00 0.00 4.83
3312 7190 5.229469 CGGTTAGTAACAATCACATCTCGAC 59.771 44.000 14.81 0.00 0.00 4.20
3323 7201 4.529377 TCCCTCACTTCGGTTAGTAACAAT 59.471 41.667 14.81 0.00 0.00 2.71
3347 7225 4.494035 CGGTCATGATGTTATTTGGACACG 60.494 45.833 0.00 0.00 0.00 4.49
3364 7242 2.680352 AGGACTCGTGCCGGTCAT 60.680 61.111 1.90 7.52 34.49 3.06
3394 7272 0.682209 GGGTCTGCGGTAGGACAGTA 60.682 60.000 0.00 0.00 35.37 2.74
3395 7273 1.982938 GGGTCTGCGGTAGGACAGT 60.983 63.158 0.00 0.00 35.37 3.55
3396 7274 0.395311 TAGGGTCTGCGGTAGGACAG 60.395 60.000 0.00 0.00 34.49 3.51
3420 7298 3.904339 TCTAGATACATCCCTTTGAGCCC 59.096 47.826 0.00 0.00 0.00 5.19
3452 7330 7.145985 GTCGCTGAAATGAATATACCTAGACA 58.854 38.462 0.00 0.00 0.00 3.41
3472 7350 4.481368 TTGTCCCATATTAGTTGTCGCT 57.519 40.909 0.00 0.00 0.00 4.93
3492 7370 9.410556 GTGTGTGCTCAATGTTATATTCTTTTT 57.589 29.630 0.00 0.00 0.00 1.94
3495 7373 7.686438 TGTGTGTGCTCAATGTTATATTCTT 57.314 32.000 0.00 0.00 0.00 2.52
3499 7377 8.615211 CACTAATGTGTGTGCTCAATGTTATAT 58.385 33.333 0.00 0.00 39.24 0.86
3520 7398 3.717913 ACTATTTATTCCCGGCCCACTAA 59.282 43.478 0.00 0.00 0.00 2.24
3616 7622 4.720046 TGAACAAGCCTACAATACAACCA 58.280 39.130 0.00 0.00 0.00 3.67
3646 7652 1.007271 CACGACGAGCTTGTCCTGT 60.007 57.895 25.34 16.67 35.40 4.00
3667 7673 2.669133 CGAGGTCAATCCAGGCCCA 61.669 63.158 0.00 0.00 39.02 5.36
3679 7685 3.134127 GCCATGCCCAACGAGGTC 61.134 66.667 0.00 0.00 34.66 3.85
3760 7766 3.345808 GCAACGCGCAGAAGGTCA 61.346 61.111 5.73 0.00 41.79 4.02
3772 7778 3.331150 TGTTACCTGTAAGATGGCAACG 58.669 45.455 0.00 0.00 35.08 4.10
3810 7816 1.488812 ACCAGTTGTGAGCCTGTAACA 59.511 47.619 0.00 0.00 0.00 2.41
3864 7871 6.889301 TGATCTGGATATTTGGCTCAATTC 57.111 37.500 0.00 0.00 0.00 2.17
3922 7929 0.593518 CGATAGACTGAGGCAGTGCG 60.594 60.000 9.45 0.00 45.44 5.34
3959 7966 3.916035 TGGCATGTAGGTCATACTCTCT 58.084 45.455 0.00 0.00 34.67 3.10
3973 7980 4.799586 GCGGTACTGAGTATATTGGCATGT 60.800 45.833 5.68 0.00 0.00 3.21
4228 8236 6.911250 ACAAACCCCCAAAATAAACTAGAG 57.089 37.500 0.00 0.00 0.00 2.43
4284 8296 8.231837 GCAATTCTTGTTGATGCAAACATAATT 58.768 29.630 4.85 10.50 39.68 1.40
4285 8297 7.604927 AGCAATTCTTGTTGATGCAAACATAAT 59.395 29.630 4.85 5.88 39.68 1.28
4294 8306 3.645884 ACACAGCAATTCTTGTTGATGC 58.354 40.909 10.14 0.00 46.41 3.91
4296 8308 5.524646 CCAAAACACAGCAATTCTTGTTGAT 59.475 36.000 10.14 0.00 43.54 2.57
4315 8328 7.852971 TTCTTAAAGAGAAGAACGACCAAAA 57.147 32.000 0.00 0.00 39.87 2.44
4321 8334 8.833231 ATGACATTTCTTAAAGAGAAGAACGA 57.167 30.769 0.00 0.00 44.80 3.85
4336 8349 8.701908 ATACAATTAGCCATGATGACATTTCT 57.298 30.769 0.00 0.00 34.15 2.52
4423 8436 2.686915 CCTCAATTGAATGTGGGCTCTC 59.313 50.000 9.88 0.00 31.76 3.20
4462 8475 1.231221 CCCGGTCAAAATCGTGTGAA 58.769 50.000 0.00 0.00 0.00 3.18
4467 8480 2.848691 TGTTAACCCGGTCAAAATCGT 58.151 42.857 0.00 0.00 0.00 3.73
4533 8548 8.990163 ATTGTGAGACCTTAAAAGTTAGGAAA 57.010 30.769 0.00 0.00 35.45 3.13
4586 8602 1.341187 ACCCGGTCAAAACAGGTTGAA 60.341 47.619 0.00 0.00 39.18 2.69
4620 8637 9.091784 GAATTAAAAGAATTGAATGGAAGAGGC 57.908 33.333 0.00 0.00 0.00 4.70
4695 8713 8.966868 AGTCAAAATCGTTAACCATATCCAAAT 58.033 29.630 0.00 0.00 0.00 2.32
4703 8721 3.192633 GCCCAGTCAAAATCGTTAACCAT 59.807 43.478 0.00 0.00 0.00 3.55
4709 8727 1.339929 GTTGGCCCAGTCAAAATCGTT 59.660 47.619 0.00 0.00 0.00 3.85
4783 8804 1.863155 TTTCCAGTGATGGGAGGGCC 61.863 60.000 0.00 0.00 35.46 5.80
4784 8805 0.039618 TTTTCCAGTGATGGGAGGGC 59.960 55.000 0.00 0.00 35.46 5.19
4797 8818 2.912771 TGTTGACGCTTCTCTTTTCCA 58.087 42.857 0.00 0.00 0.00 3.53
4835 8857 7.010830 GTCGGTGATCGCATGTACTACTATATA 59.989 40.741 8.82 0.00 39.05 0.86
4868 8890 8.209802 ACCAATCTATATATACGTGGGGAAAA 57.790 34.615 0.00 0.00 0.00 2.29
4952 8976 9.788960 GGGAGATGATAAAGTGTGTTTTATTTC 57.211 33.333 0.00 0.00 34.31 2.17
4967 8991 1.415672 GGCGGGTGGGGAGATGATAA 61.416 60.000 0.00 0.00 0.00 1.75
5051 9083 1.876156 GCTCTGAACCTGGTCAAAGTG 59.124 52.381 0.00 0.77 0.00 3.16


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

AutoCloner maintained by Alex Coulton.