Multiple sequence alignment - TraesCS7D01G110300

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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 TraesCS7D01G110300 chr7D 100.000 3704 0 0 1 3704 66549027 66545324 0.000000e+00 6841.0
1 TraesCS7D01G110300 chr7D 89.488 1779 83 22 708 2474 68897328 68899014 0.000000e+00 2154.0
2 TraesCS7D01G110300 chr7D 79.019 1244 177 45 963 2142 68901905 68903128 0.000000e+00 774.0
3 TraesCS7D01G110300 chr7D 93.359 512 22 6 2410 2920 68909348 68909848 0.000000e+00 747.0
4 TraesCS7D01G110300 chr7D 90.305 557 30 8 3150 3704 68910470 68911004 0.000000e+00 708.0
5 TraesCS7D01G110300 chr7D 81.720 837 116 25 830 1639 85345139 85345965 0.000000e+00 664.0
6 TraesCS7D01G110300 chr7D 87.335 529 34 16 2329 2851 580779374 580779875 3.210000e-160 575.0
7 TraesCS7D01G110300 chr7D 79.929 842 120 33 830 1639 83602703 83601879 1.150000e-159 573.0
8 TraesCS7D01G110300 chr7D 78.501 814 116 36 834 1612 66105589 66104800 2.590000e-131 479.0
9 TraesCS7D01G110300 chr7D 77.009 809 112 38 831 1612 69019110 69019871 2.680000e-106 396.0
10 TraesCS7D01G110300 chr7D 82.540 441 58 12 829 1263 68983429 68983856 1.620000e-98 370.0
11 TraesCS7D01G110300 chr7D 90.036 281 25 3 850 1130 85281475 85281752 9.780000e-96 361.0
12 TraesCS7D01G110300 chr7D 87.170 265 23 10 3416 3672 68922177 68922438 1.300000e-74 291.0
13 TraesCS7D01G110300 chr7D 85.600 250 22 6 3459 3697 68803955 68804201 2.210000e-62 250.0
14 TraesCS7D01G110300 chr7B 91.344 2172 93 25 701 2848 8448854 8446754 0.000000e+00 2881.0
15 TraesCS7D01G110300 chr7B 91.106 1383 62 16 1107 2474 10061120 10062456 0.000000e+00 1816.0
16 TraesCS7D01G110300 chr7B 91.462 691 58 1 5 695 107561491 107560802 0.000000e+00 948.0
17 TraesCS7D01G110300 chr7B 90.791 695 64 0 1 695 41166046 41165352 0.000000e+00 929.0
18 TraesCS7D01G110300 chr7B 87.968 507 37 13 2329 2822 648443037 648443532 8.920000e-161 577.0
19 TraesCS7D01G110300 chr7B 79.975 794 124 27 830 1601 32898642 32897862 1.500000e-153 553.0
20 TraesCS7D01G110300 chr7B 83.411 645 47 28 3074 3704 10070477 10071075 9.050000e-151 544.0
21 TraesCS7D01G110300 chr7B 76.144 1136 181 64 933 2006 34889055 34890162 7.090000e-142 514.0
22 TraesCS7D01G110300 chr7B 88.693 398 29 10 2462 2851 715226358 715225969 4.330000e-129 472.0
23 TraesCS7D01G110300 chr7B 88.432 389 30 8 3185 3573 10172844 10173217 4.360000e-124 455.0
24 TraesCS7D01G110300 chr7B 84.694 294 31 11 3415 3697 10104077 10104367 7.830000e-72 281.0
25 TraesCS7D01G110300 chr7B 89.231 130 14 0 3575 3704 10173248 10173377 2.960000e-36 163.0
26 TraesCS7D01G110300 chr7A 89.829 875 51 12 1335 2180 74548618 74549483 0.000000e+00 1088.0
27 TraesCS7D01G110300 chr7A 93.669 695 44 0 1 695 118245414 118246108 0.000000e+00 1040.0
28 TraesCS7D01G110300 chr7A 87.695 642 47 14 701 1341 74546739 74547349 0.000000e+00 719.0
29 TraesCS7D01G110300 chr7A 91.245 514 26 10 2415 2920 74594054 74594556 0.000000e+00 682.0
30 TraesCS7D01G110300 chr7A 80.947 845 116 21 830 1639 86466403 86467237 8.730000e-176 627.0
31 TraesCS7D01G110300 chr7A 90.931 408 31 4 1891 2297 681276906 681276504 9.050000e-151 544.0
32 TraesCS7D01G110300 chr7A 89.461 408 36 5 1891 2297 483184712 483184311 3.300000e-140 508.0
33 TraesCS7D01G110300 chr7A 78.339 831 128 29 829 1639 70238183 70237385 1.200000e-134 490.0
34 TraesCS7D01G110300 chr7A 89.744 273 11 5 3433 3704 74594636 74594892 2.130000e-87 333.0
35 TraesCS7D01G110300 chr7A 75.122 820 141 32 994 1791 70777239 70776461 3.570000e-85 326.0
36 TraesCS7D01G110300 chr7A 83.275 287 28 12 3415 3690 71120527 71120250 2.860000e-61 246.0
37 TraesCS7D01G110300 chr7A 84.000 250 24 10 3459 3696 74603760 74604005 3.720000e-55 226.0
38 TraesCS7D01G110300 chr7A 82.917 240 32 7 1374 1610 74673342 74673575 1.350000e-49 207.0
39 TraesCS7D01G110300 chr7A 75.931 349 61 12 1837 2183 74593407 74593734 1.380000e-34 158.0
40 TraesCS7D01G110300 chr7A 75.938 320 63 9 1745 2050 70237204 70236885 6.410000e-33 152.0
41 TraesCS7D01G110300 chr4D 93.669 695 44 0 1 695 450497727 450498421 0.000000e+00 1040.0
42 TraesCS7D01G110300 chr4D 91.841 429 32 2 1891 2318 273129671 273130097 2.460000e-166 595.0
43 TraesCS7D01G110300 chr1A 90.258 698 65 3 1 695 462115684 462116381 0.000000e+00 909.0
44 TraesCS7D01G110300 chr3B 90.216 695 68 0 1 695 201879773 201880467 0.000000e+00 907.0
45 TraesCS7D01G110300 chr3B 87.931 696 83 1 1 695 141073325 141072630 0.000000e+00 819.0
46 TraesCS7D01G110300 chr3B 92.056 428 27 5 1891 2317 751774316 751773895 2.460000e-166 595.0
47 TraesCS7D01G110300 chr3B 90.443 429 24 7 2425 2845 276882030 276882449 1.940000e-152 549.0
48 TraesCS7D01G110300 chr3B 90.443 429 24 8 2425 2845 276908646 276909065 1.940000e-152 549.0
49 TraesCS7D01G110300 chr5B 88.235 697 80 1 1 695 608346328 608347024 0.000000e+00 832.0
50 TraesCS7D01G110300 chr2D 87.914 695 84 0 1 695 595434520 595435214 0.000000e+00 819.0
51 TraesCS7D01G110300 chr2B 83.071 827 105 24 847 1645 76517518 76516699 0.000000e+00 719.0
52 TraesCS7D01G110300 chr6B 90.452 398 23 6 2462 2851 29807390 29807780 9.180000e-141 510.0
53 TraesCS7D01G110300 chr2A 89.294 411 36 5 1891 2300 46537469 46537066 3.300000e-140 508.0
54 TraesCS7D01G110300 chr2A 94.915 59 3 0 2952 3010 51384876 51384818 3.940000e-15 93.5
55 TraesCS7D01G110300 chr4A 82.154 622 64 19 2315 2911 656758178 656758777 1.200000e-134 490.0
56 TraesCS7D01G110300 chrUn 84.925 398 36 10 2526 2920 305656385 305656761 7.510000e-102 381.0
57 TraesCS7D01G110300 chrUn 84.428 411 38 12 2526 2933 308149934 308149547 7.510000e-102 381.0
58 TraesCS7D01G110300 chr5D 94.521 219 10 1 2100 2318 504136042 504136258 1.650000e-88 337.0
59 TraesCS7D01G110300 chr1D 84.921 252 23 12 3458 3697 486923895 486923647 1.330000e-59 241.0


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 TraesCS7D01G110300 chr7D 66545324 66549027 3703 True 6841.0 6841 100.0000 1 3704 1 chr7D.!!$R2 3703
1 TraesCS7D01G110300 chr7D 68897328 68903128 5800 False 1464.0 2154 84.2535 708 2474 2 chr7D.!!$F8 1766
2 TraesCS7D01G110300 chr7D 68909348 68911004 1656 False 727.5 747 91.8320 2410 3704 2 chr7D.!!$F9 1294
3 TraesCS7D01G110300 chr7D 85345139 85345965 826 False 664.0 664 81.7200 830 1639 1 chr7D.!!$F6 809
4 TraesCS7D01G110300 chr7D 580779374 580779875 501 False 575.0 575 87.3350 2329 2851 1 chr7D.!!$F7 522
5 TraesCS7D01G110300 chr7D 83601879 83602703 824 True 573.0 573 79.9290 830 1639 1 chr7D.!!$R3 809
6 TraesCS7D01G110300 chr7D 66104800 66105589 789 True 479.0 479 78.5010 834 1612 1 chr7D.!!$R1 778
7 TraesCS7D01G110300 chr7D 69019110 69019871 761 False 396.0 396 77.0090 831 1612 1 chr7D.!!$F4 781
8 TraesCS7D01G110300 chr7B 8446754 8448854 2100 True 2881.0 2881 91.3440 701 2848 1 chr7B.!!$R1 2147
9 TraesCS7D01G110300 chr7B 10061120 10062456 1336 False 1816.0 1816 91.1060 1107 2474 1 chr7B.!!$F1 1367
10 TraesCS7D01G110300 chr7B 107560802 107561491 689 True 948.0 948 91.4620 5 695 1 chr7B.!!$R4 690
11 TraesCS7D01G110300 chr7B 41165352 41166046 694 True 929.0 929 90.7910 1 695 1 chr7B.!!$R3 694
12 TraesCS7D01G110300 chr7B 32897862 32898642 780 True 553.0 553 79.9750 830 1601 1 chr7B.!!$R2 771
13 TraesCS7D01G110300 chr7B 10070477 10071075 598 False 544.0 544 83.4110 3074 3704 1 chr7B.!!$F2 630
14 TraesCS7D01G110300 chr7B 34889055 34890162 1107 False 514.0 514 76.1440 933 2006 1 chr7B.!!$F4 1073
15 TraesCS7D01G110300 chr7B 10172844 10173377 533 False 309.0 455 88.8315 3185 3704 2 chr7B.!!$F6 519
16 TraesCS7D01G110300 chr7A 118245414 118246108 694 False 1040.0 1040 93.6690 1 695 1 chr7A.!!$F4 694
17 TraesCS7D01G110300 chr7A 74546739 74549483 2744 False 903.5 1088 88.7620 701 2180 2 chr7A.!!$F5 1479
18 TraesCS7D01G110300 chr7A 86466403 86467237 834 False 627.0 627 80.9470 830 1639 1 chr7A.!!$F3 809
19 TraesCS7D01G110300 chr7A 74593407 74594892 1485 False 391.0 682 85.6400 1837 3704 3 chr7A.!!$F6 1867
20 TraesCS7D01G110300 chr7A 70776461 70777239 778 True 326.0 326 75.1220 994 1791 1 chr7A.!!$R1 797
21 TraesCS7D01G110300 chr7A 70236885 70238183 1298 True 321.0 490 77.1385 829 2050 2 chr7A.!!$R5 1221
22 TraesCS7D01G110300 chr4D 450497727 450498421 694 False 1040.0 1040 93.6690 1 695 1 chr4D.!!$F2 694
23 TraesCS7D01G110300 chr1A 462115684 462116381 697 False 909.0 909 90.2580 1 695 1 chr1A.!!$F1 694
24 TraesCS7D01G110300 chr3B 201879773 201880467 694 False 907.0 907 90.2160 1 695 1 chr3B.!!$F1 694
25 TraesCS7D01G110300 chr3B 141072630 141073325 695 True 819.0 819 87.9310 1 695 1 chr3B.!!$R1 694
26 TraesCS7D01G110300 chr5B 608346328 608347024 696 False 832.0 832 88.2350 1 695 1 chr5B.!!$F1 694
27 TraesCS7D01G110300 chr2D 595434520 595435214 694 False 819.0 819 87.9140 1 695 1 chr2D.!!$F1 694
28 TraesCS7D01G110300 chr2B 76516699 76517518 819 True 719.0 719 83.0710 847 1645 1 chr2B.!!$R1 798
29 TraesCS7D01G110300 chr4A 656758178 656758777 599 False 490.0 490 82.1540 2315 2911 1 chr4A.!!$F1 596

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
748 755 0.596341 AAAACAACGATTGGGCGTGC 60.596 50.000 0.00 0.00 44.86 5.34 F
749 756 1.452145 AAACAACGATTGGGCGTGCT 61.452 50.000 0.00 0.00 44.86 4.40 F
1710 7690 1.374252 CCCTTCAACCACGACGAGG 60.374 63.158 9.97 9.97 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1690 7656 0.388649 CTCGTCGTGGTTGAAGGGAG 60.389 60.000 0.00 0.0 0.00 4.30 R
1797 7792 1.005037 CGTGCCTCAGCTGGTACAA 60.005 57.895 15.13 0.0 41.79 2.41 R
3183 9907 0.095245 CATGTACAGAACAAGCGCGG 59.905 55.000 8.83 0.0 42.70 6.46 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
299 303 1.966451 CCGGCTTTCGCTCACCTTT 60.966 57.895 0.00 0.00 37.59 3.11
531 538 1.072331 GAGTGACCCACATCAGTTGGT 59.928 52.381 0.00 0.00 45.74 3.67
614 621 1.828768 GCACTATCTCTGGGCAGCT 59.171 57.895 0.00 0.00 0.00 4.24
741 748 6.948353 TGAGAAAGAGAGAAAACAACGATTG 58.052 36.000 0.00 0.00 0.00 2.67
748 755 0.596341 AAAACAACGATTGGGCGTGC 60.596 50.000 0.00 0.00 44.86 5.34
749 756 1.452145 AAACAACGATTGGGCGTGCT 61.452 50.000 0.00 0.00 44.86 4.40
750 757 2.128853 AACAACGATTGGGCGTGCTG 62.129 55.000 0.00 0.00 44.86 4.41
751 758 3.055719 AACGATTGGGCGTGCTGG 61.056 61.111 0.00 0.00 44.86 4.85
754 761 3.818787 GATTGGGCGTGCTGGCTG 61.819 66.667 3.36 0.00 44.11 4.85
1104 5537 2.283676 GTCTCCCTCCACCACCGA 60.284 66.667 0.00 0.00 0.00 4.69
1144 5577 3.039588 GGGTGGTGCACGTGTACG 61.040 66.667 26.86 2.43 46.33 3.67
1344 7074 2.125773 ACGAAGTCTACCTCGACCAT 57.874 50.000 8.04 0.00 29.74 3.55
1497 7306 2.747855 CTTCCACCTCCGGCTTGC 60.748 66.667 0.00 0.00 0.00 4.01
1560 7399 1.469767 GCGAATTGGGTTCTTGGATGC 60.470 52.381 0.00 0.00 34.56 3.91
1690 7656 4.687215 TGCGACTCAGCTGCACCC 62.687 66.667 9.47 0.00 38.13 4.61
1710 7690 1.374252 CCCTTCAACCACGACGAGG 60.374 63.158 9.97 9.97 0.00 4.63
1790 7785 1.663739 CGTGTTCGTCTTCAGGGGA 59.336 57.895 0.00 0.00 0.00 4.81
2009 8247 2.158813 TCCTTTGGCAAGAAACTCGTCT 60.159 45.455 0.00 0.00 30.57 4.18
2010 8248 2.031682 CCTTTGGCAAGAAACTCGTCTG 60.032 50.000 0.00 0.00 30.57 3.51
2011 8249 1.593196 TTGGCAAGAAACTCGTCTGG 58.407 50.000 0.00 0.00 0.00 3.86
2012 8250 0.884704 TGGCAAGAAACTCGTCTGGC 60.885 55.000 0.00 0.00 42.97 4.85
2013 8251 0.884704 GGCAAGAAACTCGTCTGGCA 60.885 55.000 4.09 0.00 45.15 4.92
2014 8252 0.235926 GCAAGAAACTCGTCTGGCAC 59.764 55.000 0.00 0.00 43.16 5.01
2015 8253 1.871080 CAAGAAACTCGTCTGGCACT 58.129 50.000 0.00 0.00 0.00 4.40
2016 8254 1.795286 CAAGAAACTCGTCTGGCACTC 59.205 52.381 0.00 0.00 0.00 3.51
2017 8255 1.333177 AGAAACTCGTCTGGCACTCT 58.667 50.000 0.00 0.00 0.00 3.24
2018 8256 1.689273 AGAAACTCGTCTGGCACTCTT 59.311 47.619 0.00 0.00 0.00 2.85
2019 8257 2.062519 GAAACTCGTCTGGCACTCTTC 58.937 52.381 0.00 0.00 0.00 2.87
2352 8623 6.816134 TTTGATGCTACTGTGCTTTGATTA 57.184 33.333 0.00 0.00 0.00 1.75
2386 8660 5.693104 AGTTTTGCAATTTGATGCTACTGTG 59.307 36.000 0.00 0.00 46.54 3.66
2387 8661 3.220507 TGCAATTTGATGCTACTGTGC 57.779 42.857 0.00 0.00 46.54 4.57
2717 9008 3.075884 CAGCGTAGAGAGATACCCCTAC 58.924 54.545 0.00 0.00 0.00 3.18
2834 9135 3.826466 GCAGTTCATTTGTTCCTGCTAC 58.174 45.455 0.00 0.00 43.89 3.58
2885 9186 5.952387 AGGATACCTATTTGCTTTGCCATA 58.048 37.500 0.00 0.00 28.47 2.74
2886 9187 6.555711 AGGATACCTATTTGCTTTGCCATAT 58.444 36.000 0.00 0.00 28.47 1.78
2927 9252 1.044725 GTTTGAGCAATGCGTTGACG 58.955 50.000 22.81 0.00 37.53 4.35
2943 9268 1.621317 TGACGATGGCCACTACTTCAA 59.379 47.619 8.16 0.00 0.00 2.69
2950 9275 0.237498 GCCACTACTTCAACGTTGCC 59.763 55.000 23.47 0.00 0.00 4.52
2953 9278 1.531149 CACTACTTCAACGTTGCCAGG 59.469 52.381 23.47 10.27 0.00 4.45
2965 9290 2.337532 GCCAGGTGCAAGCAGTTG 59.662 61.111 0.00 0.00 40.77 3.16
2968 9293 1.285023 CAGGTGCAAGCAGTTGAGC 59.715 57.895 0.00 0.00 35.46 4.26
2969 9294 1.152902 AGGTGCAAGCAGTTGAGCA 60.153 52.632 0.00 0.00 35.46 4.26
2972 9297 2.797837 TGCAAGCAGTTGAGCACTT 58.202 47.368 0.00 0.00 35.46 3.16
2975 9300 1.334779 GCAAGCAGTTGAGCACTTGAG 60.335 52.381 5.82 0.00 41.59 3.02
2976 9301 1.945394 CAAGCAGTTGAGCACTTGAGT 59.055 47.619 0.00 0.00 41.59 3.41
2977 9302 2.338577 AGCAGTTGAGCACTTGAGTT 57.661 45.000 0.00 0.00 36.85 3.01
2978 9303 2.648059 AGCAGTTGAGCACTTGAGTTT 58.352 42.857 0.00 0.00 36.85 2.66
2979 9304 3.808728 AGCAGTTGAGCACTTGAGTTTA 58.191 40.909 0.00 0.00 36.85 2.01
2980 9305 3.561725 AGCAGTTGAGCACTTGAGTTTAC 59.438 43.478 0.00 0.00 36.85 2.01
2981 9306 3.561725 GCAGTTGAGCACTTGAGTTTACT 59.438 43.478 0.00 0.00 30.92 2.24
2982 9307 4.750098 GCAGTTGAGCACTTGAGTTTACTA 59.250 41.667 0.00 0.00 30.92 1.82
2983 9308 5.107298 GCAGTTGAGCACTTGAGTTTACTAG 60.107 44.000 0.00 0.00 30.92 2.57
2984 9309 5.986135 CAGTTGAGCACTTGAGTTTACTAGT 59.014 40.000 0.00 0.00 30.92 2.57
2985 9310 5.986135 AGTTGAGCACTTGAGTTTACTAGTG 59.014 40.000 5.39 7.97 42.90 2.74
2991 9316 6.619801 CACTTGAGTTTACTAGTGCCTTTT 57.380 37.500 5.39 0.00 37.00 2.27
3006 9331 3.311322 TGCCTTTTACAGTTTCAGTCGTG 59.689 43.478 0.00 0.00 0.00 4.35
3012 9337 7.254658 CCTTTTACAGTTTCAGTCGTGTAACAT 60.255 37.037 0.00 0.00 36.64 2.71
3013 9338 6.519353 TTACAGTTTCAGTCGTGTAACATG 57.481 37.500 0.00 0.00 36.64 3.21
3014 9339 3.807622 ACAGTTTCAGTCGTGTAACATGG 59.192 43.478 0.00 0.00 36.64 3.66
3015 9340 3.807622 CAGTTTCAGTCGTGTAACATGGT 59.192 43.478 0.00 0.00 36.64 3.55
3016 9341 4.272504 CAGTTTCAGTCGTGTAACATGGTT 59.727 41.667 0.00 0.00 36.64 3.67
3017 9342 4.510340 AGTTTCAGTCGTGTAACATGGTTC 59.490 41.667 0.00 0.00 36.64 3.62
3018 9343 3.737032 TCAGTCGTGTAACATGGTTCA 57.263 42.857 0.00 0.00 35.74 3.18
3019 9344 4.265904 TCAGTCGTGTAACATGGTTCAT 57.734 40.909 0.00 0.00 35.74 2.57
3021 9346 5.972935 TCAGTCGTGTAACATGGTTCATAT 58.027 37.500 0.00 0.00 35.74 1.78
3022 9347 6.040247 TCAGTCGTGTAACATGGTTCATATC 58.960 40.000 0.00 0.00 35.74 1.63
3023 9348 5.234329 CAGTCGTGTAACATGGTTCATATCC 59.766 44.000 0.00 0.00 35.74 2.59
3024 9349 5.128827 AGTCGTGTAACATGGTTCATATCCT 59.871 40.000 0.00 0.00 35.74 3.24
3025 9350 5.234329 GTCGTGTAACATGGTTCATATCCTG 59.766 44.000 0.00 0.00 35.74 3.86
3029 9354 7.250569 GTGTAACATGGTTCATATCCTGTTTG 58.749 38.462 0.00 0.00 36.32 2.93
3033 9358 5.185635 ACATGGTTCATATCCTGTTTGTTGG 59.814 40.000 0.00 0.00 0.00 3.77
3034 9359 4.735369 TGGTTCATATCCTGTTTGTTGGT 58.265 39.130 0.00 0.00 0.00 3.67
3035 9360 5.144100 TGGTTCATATCCTGTTTGTTGGTT 58.856 37.500 0.00 0.00 0.00 3.67
3036 9361 5.242838 TGGTTCATATCCTGTTTGTTGGTTC 59.757 40.000 0.00 0.00 0.00 3.62
3037 9362 5.476945 GGTTCATATCCTGTTTGTTGGTTCT 59.523 40.000 0.00 0.00 0.00 3.01
3041 9399 2.733956 TCCTGTTTGTTGGTTCTGCTT 58.266 42.857 0.00 0.00 0.00 3.91
3048 9406 7.283625 TGTTTGTTGGTTCTGCTTGTATATT 57.716 32.000 0.00 0.00 0.00 1.28
3064 9422 1.568504 TATTCCAAGCAGACCGAGGT 58.431 50.000 0.00 0.00 0.00 3.85
3239 9963 7.394870 ACGATCGTGATAACTATTCAACATG 57.605 36.000 22.06 0.00 0.00 3.21
3294 10020 2.669240 GGTCGAAACCTCCCAGGG 59.331 66.667 0.00 0.00 42.80 4.45
3306 10032 1.689273 CTCCCAGGGTATACTGAGCAC 59.311 57.143 5.01 0.00 40.97 4.40
3447 10173 4.072131 TGGAAGGCAGTGTAATGAAACTC 58.928 43.478 0.00 0.00 0.00 3.01
3599 10363 8.122952 GGTATTTGCATTAGTTGTACAGATGAC 58.877 37.037 12.10 1.99 0.00 3.06
3627 10392 4.229876 GTTGTCTGAAGCTAATTGGTTGC 58.770 43.478 0.00 0.00 36.40 4.17
3628 10393 3.754965 TGTCTGAAGCTAATTGGTTGCT 58.245 40.909 0.00 0.00 36.40 3.91
3637 10402 1.813102 AATTGGTTGCTGGGGGAAAA 58.187 45.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.808945 CAAGGCATCATAAGGCGGATC 59.191 52.381 0.00 0.00 36.55 3.36
114 116 6.938507 TCTTAAAGCTGTTTACTATCCGGAA 58.061 36.000 9.01 0.00 0.00 4.30
299 303 4.325030 GGAAATTCTGGTGGGGATGTAAGA 60.325 45.833 0.00 0.00 0.00 2.10
339 344 3.636060 TCCCAAGGGGACTATGTGATCAT 60.636 47.826 5.08 0.00 46.17 2.45
531 538 8.500238 TCTCTAAGTGACAGATACTTGGGTATA 58.500 37.037 0.00 0.00 38.60 1.47
748 755 0.036732 TGCAAGTTAGACCCAGCCAG 59.963 55.000 0.00 0.00 0.00 4.85
749 756 0.698238 ATGCAAGTTAGACCCAGCCA 59.302 50.000 0.00 0.00 0.00 4.75
750 757 1.098050 CATGCAAGTTAGACCCAGCC 58.902 55.000 0.00 0.00 0.00 4.85
751 758 1.098050 CCATGCAAGTTAGACCCAGC 58.902 55.000 0.00 0.00 0.00 4.85
752 759 1.755179 CCCATGCAAGTTAGACCCAG 58.245 55.000 0.00 0.00 0.00 4.45
753 760 0.323360 GCCCATGCAAGTTAGACCCA 60.323 55.000 0.00 0.00 37.47 4.51
754 761 1.037579 GGCCCATGCAAGTTAGACCC 61.038 60.000 0.00 0.00 40.13 4.46
755 762 1.376609 CGGCCCATGCAAGTTAGACC 61.377 60.000 0.00 0.00 40.13 3.85
756 763 1.993369 GCGGCCCATGCAAGTTAGAC 61.993 60.000 0.00 0.00 40.13 2.59
757 764 1.748879 GCGGCCCATGCAAGTTAGA 60.749 57.895 0.00 0.00 40.13 2.10
827 840 1.299541 AGGCGGATGTATTTCAAGCG 58.700 50.000 0.00 0.00 0.00 4.68
1160 5600 0.739561 GAGGAGTAGGTACGGCACAG 59.260 60.000 0.00 0.00 0.00 3.66
1275 5724 3.917072 GATTAGATCCACCTCCGGC 57.083 57.895 0.00 0.00 0.00 6.13
1560 7399 5.512788 GTCAAATTCCGATGCATGTTAACAG 59.487 40.000 14.65 7.46 0.00 3.16
1690 7656 0.388649 CTCGTCGTGGTTGAAGGGAG 60.389 60.000 0.00 0.00 0.00 4.30
1710 7690 2.032634 TGATTTCCCGCGACAGCAC 61.033 57.895 8.23 0.00 45.49 4.40
1790 7785 1.625818 CTCAGCTGGTACAAGGACCTT 59.374 52.381 15.13 0.00 40.46 3.50
1797 7792 1.005037 CGTGCCTCAGCTGGTACAA 60.005 57.895 15.13 0.00 41.79 2.41
1834 7829 4.098847 GGTGAGAGACGTCCACCT 57.901 61.111 26.08 16.07 45.08 4.00
2009 8247 3.214328 GAAAAGTTCCAGAAGAGTGCCA 58.786 45.455 0.00 0.00 0.00 4.92
2010 8248 3.906014 GAAAAGTTCCAGAAGAGTGCC 57.094 47.619 0.00 0.00 0.00 5.01
2075 8331 5.643777 ACAGATTATCCAAAGTTTCAGACGG 59.356 40.000 0.00 0.00 0.00 4.79
2166 8436 4.935808 ACCTACTGATTCGATTCAACAACC 59.064 41.667 10.90 0.00 0.00 3.77
2386 8660 3.195825 TCCAAAGTCTTCCACTAGCTAGC 59.804 47.826 20.91 6.62 32.30 3.42
2387 8661 5.046950 AGTTCCAAAGTCTTCCACTAGCTAG 60.047 44.000 19.44 19.44 32.30 3.42
2834 9135 6.094881 TGTCAGGAGAACAAACCAAGTTTAAG 59.905 38.462 0.00 0.00 33.70 1.85
2885 9186 7.745620 ACAGTTTCAGAATTTTAGAACCGAT 57.254 32.000 0.00 0.00 0.00 4.18
2886 9187 7.562454 AACAGTTTCAGAATTTTAGAACCGA 57.438 32.000 0.00 0.00 0.00 4.69
2927 9252 2.094762 ACGTTGAAGTAGTGGCCATC 57.905 50.000 9.72 1.58 0.00 3.51
2950 9275 1.285023 GCTCAACTGCTTGCACCTG 59.715 57.895 0.00 0.00 0.00 4.00
2953 9278 4.622364 GTGCTCAACTGCTTGCAC 57.378 55.556 0.00 0.00 46.66 4.57
2958 9283 2.338577 AACTCAAGTGCTCAACTGCT 57.661 45.000 0.00 0.00 39.81 4.24
2959 9284 3.561725 AGTAAACTCAAGTGCTCAACTGC 59.438 43.478 0.00 0.00 39.81 4.40
2960 9285 5.986135 ACTAGTAAACTCAAGTGCTCAACTG 59.014 40.000 0.00 0.00 39.81 3.16
2961 9286 5.986135 CACTAGTAAACTCAAGTGCTCAACT 59.014 40.000 0.00 0.00 42.60 3.16
2962 9287 6.216750 CACTAGTAAACTCAAGTGCTCAAC 57.783 41.667 0.00 0.00 33.59 3.18
2968 9293 6.619801 AAAAGGCACTAGTAAACTCAAGTG 57.380 37.500 0.00 8.17 38.49 3.16
2969 9294 7.277396 TGTAAAAGGCACTAGTAAACTCAAGT 58.723 34.615 0.00 0.00 38.49 3.16
2970 9295 7.441458 ACTGTAAAAGGCACTAGTAAACTCAAG 59.559 37.037 0.00 0.00 38.49 3.02
2972 9297 6.823497 ACTGTAAAAGGCACTAGTAAACTCA 58.177 36.000 0.00 0.00 38.49 3.41
2975 9300 7.922837 TGAAACTGTAAAAGGCACTAGTAAAC 58.077 34.615 0.00 0.00 38.49 2.01
2976 9301 7.771826 ACTGAAACTGTAAAAGGCACTAGTAAA 59.228 33.333 0.00 0.00 38.49 2.01
2977 9302 7.277396 ACTGAAACTGTAAAAGGCACTAGTAA 58.723 34.615 0.00 0.00 38.49 2.24
2978 9303 6.823497 ACTGAAACTGTAAAAGGCACTAGTA 58.177 36.000 0.00 0.00 38.49 1.82
2979 9304 5.681639 ACTGAAACTGTAAAAGGCACTAGT 58.318 37.500 0.00 0.00 38.49 2.57
2980 9305 5.107453 CGACTGAAACTGTAAAAGGCACTAG 60.107 44.000 0.00 0.00 38.49 2.57
2981 9306 4.748102 CGACTGAAACTGTAAAAGGCACTA 59.252 41.667 0.00 0.00 38.49 2.74
2983 9308 3.311596 ACGACTGAAACTGTAAAAGGCAC 59.688 43.478 0.00 0.00 0.00 5.01
2984 9309 3.311322 CACGACTGAAACTGTAAAAGGCA 59.689 43.478 0.00 0.00 0.00 4.75
2985 9310 3.311596 ACACGACTGAAACTGTAAAAGGC 59.688 43.478 0.00 0.00 0.00 4.35
2986 9311 6.036300 TGTTACACGACTGAAACTGTAAAAGG 59.964 38.462 0.00 0.00 32.35 3.11
2987 9312 6.996106 TGTTACACGACTGAAACTGTAAAAG 58.004 36.000 0.00 0.00 32.35 2.27
2988 9313 6.964741 TGTTACACGACTGAAACTGTAAAA 57.035 33.333 0.00 0.00 32.35 1.52
2989 9314 6.018588 CCATGTTACACGACTGAAACTGTAAA 60.019 38.462 0.00 0.00 32.35 2.01
2990 9315 5.464057 CCATGTTACACGACTGAAACTGTAA 59.536 40.000 0.00 0.00 0.00 2.41
2991 9316 4.986034 CCATGTTACACGACTGAAACTGTA 59.014 41.667 0.00 0.00 0.00 2.74
3006 9331 7.391148 ACAAACAGGATATGAACCATGTTAC 57.609 36.000 0.00 0.00 32.75 2.50
3012 9337 4.735369 ACCAACAAACAGGATATGAACCA 58.265 39.130 0.00 0.00 0.00 3.67
3013 9338 5.476945 AGAACCAACAAACAGGATATGAACC 59.523 40.000 0.00 0.00 0.00 3.62
3014 9339 6.381801 CAGAACCAACAAACAGGATATGAAC 58.618 40.000 0.00 0.00 0.00 3.18
3015 9340 5.048083 GCAGAACCAACAAACAGGATATGAA 60.048 40.000 0.00 0.00 0.00 2.57
3016 9341 4.458989 GCAGAACCAACAAACAGGATATGA 59.541 41.667 0.00 0.00 0.00 2.15
3017 9342 4.460382 AGCAGAACCAACAAACAGGATATG 59.540 41.667 0.00 0.00 0.00 1.78
3018 9343 4.666512 AGCAGAACCAACAAACAGGATAT 58.333 39.130 0.00 0.00 0.00 1.63
3019 9344 4.098914 AGCAGAACCAACAAACAGGATA 57.901 40.909 0.00 0.00 0.00 2.59
3021 9346 2.426738 CAAGCAGAACCAACAAACAGGA 59.573 45.455 0.00 0.00 0.00 3.86
3022 9347 2.166254 ACAAGCAGAACCAACAAACAGG 59.834 45.455 0.00 0.00 0.00 4.00
3023 9348 3.508744 ACAAGCAGAACCAACAAACAG 57.491 42.857 0.00 0.00 0.00 3.16
3024 9349 6.892658 ATATACAAGCAGAACCAACAAACA 57.107 33.333 0.00 0.00 0.00 2.83
3025 9350 6.806739 GGAATATACAAGCAGAACCAACAAAC 59.193 38.462 0.00 0.00 0.00 2.93
3029 9354 6.509418 TTGGAATATACAAGCAGAACCAAC 57.491 37.500 0.00 0.00 31.39 3.77
3041 9399 3.069586 CCTCGGTCTGCTTGGAATATACA 59.930 47.826 0.00 0.00 0.00 2.29
3048 9406 3.377656 GACCTCGGTCTGCTTGGA 58.622 61.111 8.82 0.00 41.57 3.53
3183 9907 0.095245 CATGTACAGAACAAGCGCGG 59.905 55.000 8.83 0.00 42.70 6.46
3261 9986 1.917336 GACCTGGTCGGGCCCAAATA 61.917 60.000 24.92 3.87 33.11 1.40
3292 10018 0.529992 GCACCGTGCTCAGTATACCC 60.530 60.000 16.51 0.00 40.96 3.69
3294 10020 1.659098 GTTGCACCGTGCTCAGTATAC 59.341 52.381 23.52 0.00 45.31 1.47
3385 10111 4.597507 AGGTTCCTCTGACAAACCAATAGA 59.402 41.667 15.22 0.00 43.98 1.98
3397 10123 4.207891 GCTGAATAACAGGTTCCTCTGA 57.792 45.455 0.00 0.00 45.82 3.27
3431 10157 5.928839 TCTTCAGAGAGTTTCATTACACTGC 59.071 40.000 0.00 0.00 0.00 4.40
3599 10363 5.106396 CCAATTAGCTTCAGACAACCTTCTG 60.106 44.000 0.00 0.00 43.93 3.02
3627 10392 8.197439 GTGACTAATTTATTGATTTTCCCCCAG 58.803 37.037 0.00 0.00 0.00 4.45
3628 10393 7.676043 TGTGACTAATTTATTGATTTTCCCCCA 59.324 33.333 0.00 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.