Multiple sequence alignment - TraesCS5D01G159300

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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 TraesCS5D01G159300 chr5D 100.000 3878 0 0 1 3878 247751263 247755140 0.000000e+00 7162.0
1 TraesCS5D01G159300 chr5A 93.131 1354 84 4 1716 3065 331748354 331749702 0.000000e+00 1977.0
2 TraesCS5D01G159300 chr5A 91.147 689 55 2 1 689 331728290 331728972 0.000000e+00 929.0
3 TraesCS5D01G159300 chr5A 85.180 695 47 19 758 1434 331729528 331730184 0.000000e+00 662.0
4 TraesCS5D01G159300 chr5A 89.362 423 16 6 1016 1434 331731900 331732297 4.470000e-139 505.0
5 TraesCS5D01G159300 chr5A 88.416 423 20 6 1016 1434 331738228 331738625 2.100000e-132 483.0
6 TraesCS5D01G159300 chr5A 88.180 423 21 6 1016 1434 331734014 331734411 9.750000e-131 477.0
7 TraesCS5D01G159300 chr5A 87.972 424 20 8 1016 1435 331744487 331744883 4.540000e-129 472.0
8 TraesCS5D01G159300 chr5A 87.707 423 22 7 1016 1434 331736128 331736524 2.110000e-127 466.0
9 TraesCS5D01G159300 chr5A 87.707 423 23 6 1016 1434 331742413 331742810 2.110000e-127 466.0
10 TraesCS5D01G159300 chr5A 87.234 423 24 7 1016 1434 331740313 331740709 4.570000e-124 455.0
11 TraesCS5D01G159300 chr5A 94.570 221 9 2 1511 1729 331741794 331742013 4.800000e-89 339.0
12 TraesCS5D01G159300 chr5A 93.778 225 10 3 1507 1729 331745968 331746190 6.210000e-88 335.0
13 TraesCS5D01G159300 chr5A 94.118 221 10 2 1511 1729 331731270 331731489 2.230000e-87 333.0
14 TraesCS5D01G159300 chr5A 94.118 221 10 2 1511 1729 331737609 331737828 2.230000e-87 333.0
15 TraesCS5D01G159300 chr5A 93.333 225 11 3 1507 1729 331733379 331733601 2.890000e-86 329.0
16 TraesCS5D01G159300 chr5A 92.444 225 13 3 1507 1729 331735494 331735716 6.250000e-83 318.0
17 TraesCS5D01G159300 chr5A 92.444 225 13 3 1507 1729 331739679 331739901 6.250000e-83 318.0
18 TraesCS5D01G159300 chr5A 92.000 225 14 3 1507 1729 331743864 331744086 2.910000e-81 313.0
19 TraesCS5D01G159300 chr5A 93.506 77 5 0 688 764 331729192 331729268 8.800000e-22 115.0
20 TraesCS5D01G159300 chr7B 88.613 1370 146 6 1704 3065 56360322 56361689 0.000000e+00 1657.0
21 TraesCS5D01G159300 chr7B 89.022 1339 130 12 1737 3065 56995164 56993833 0.000000e+00 1642.0
22 TraesCS5D01G159300 chr7B 76.042 384 47 25 1005 1353 56359334 56359707 1.440000e-34 158.0
23 TraesCS5D01G159300 chr2D 92.467 823 51 5 3064 3876 462257789 462258610 0.000000e+00 1166.0
24 TraesCS5D01G159300 chr2D 79.128 1308 244 16 1775 3065 551874506 551873211 0.000000e+00 876.0
25 TraesCS5D01G159300 chr2D 78.691 718 134 15 1818 2527 551428269 551428975 9.820000e-126 460.0
26 TraesCS5D01G159300 chr2D 82.578 287 42 4 1 285 383562443 383562163 2.990000e-61 246.0
27 TraesCS5D01G159300 chr3D 92.242 825 46 10 3064 3878 600494731 600493915 0.000000e+00 1153.0
28 TraesCS5D01G159300 chr3D 80.000 105 17 3 538 641 550455100 550455201 1.490000e-09 75.0
29 TraesCS5D01G159300 chr7D 91.908 828 48 13 3064 3878 127643727 127644548 0.000000e+00 1140.0
30 TraesCS5D01G159300 chr7D 91.495 823 54 10 3067 3878 624917571 624916754 0.000000e+00 1118.0
31 TraesCS5D01G159300 chr7D 90.777 824 58 8 3063 3877 627018178 627018992 0.000000e+00 1085.0
32 TraesCS5D01G159300 chr7D 90.476 672 57 2 2398 3065 100649793 100650461 0.000000e+00 880.0
33 TraesCS5D01G159300 chr7D 88.682 698 77 2 1704 2401 100647581 100648276 0.000000e+00 850.0
34 TraesCS5D01G159300 chr7D 81.743 241 23 8 1473 1708 100647331 100647555 8.560000e-42 182.0
35 TraesCS5D01G159300 chr7D 90.265 113 10 1 1005 1117 100646619 100646730 3.120000e-31 147.0
36 TraesCS5D01G159300 chr7D 83.951 81 10 2 537 617 453286134 453286211 1.490000e-09 75.0
37 TraesCS5D01G159300 chr4B 91.383 824 53 12 3064 3878 449341276 449340462 0.000000e+00 1112.0
38 TraesCS5D01G159300 chr4B 91.283 826 56 10 3063 3877 498203817 498204637 0.000000e+00 1112.0
39 TraesCS5D01G159300 chr3B 91.352 821 57 10 3067 3878 521415319 521414504 0.000000e+00 1110.0
40 TraesCS5D01G159300 chr3B 91.363 822 56 9 3065 3878 521478622 521477808 0.000000e+00 1110.0
41 TraesCS5D01G159300 chr3B 81.350 311 44 10 1 305 263518883 263518581 1.390000e-59 241.0
42 TraesCS5D01G159300 chr3B 81.250 288 44 6 1 285 817611504 817611224 1.400000e-54 224.0
43 TraesCS5D01G159300 chr2B 79.419 1307 239 22 1775 3063 657080398 657079104 0.000000e+00 896.0
44 TraesCS5D01G159300 chr2B 79.589 1264 227 24 1818 3065 656942475 656943723 0.000000e+00 876.0
45 TraesCS5D01G159300 chr2B 79.094 1258 231 22 1830 3065 691011816 691010569 0.000000e+00 837.0
46 TraesCS5D01G159300 chr2B 77.822 1258 248 20 1830 3065 656611402 656610154 0.000000e+00 749.0
47 TraesCS5D01G159300 chr2B 78.182 165 28 7 479 641 759487171 759487329 8.870000e-17 99.0
48 TraesCS5D01G159300 chr2A 79.084 1310 240 20 1775 3065 692644797 692643503 0.000000e+00 870.0
49 TraesCS5D01G159300 chr7A 82.566 304 43 6 2 302 46250529 46250825 3.840000e-65 259.0
50 TraesCS5D01G159300 chr4D 82.828 297 42 5 8 302 37839194 37839483 1.380000e-64 257.0
51 TraesCS5D01G159300 chr4D 81.053 285 44 9 1 282 399530022 399530299 6.520000e-53 219.0
52 TraesCS5D01G159300 chr4D 86.792 53 5 2 540 591 15813669 15813618 1.500000e-04 58.4
53 TraesCS5D01G159300 chr1D 81.250 304 46 9 2 303 153718788 153719082 6.480000e-58 235.0
54 TraesCS5D01G159300 chr1D 80.672 119 12 10 539 654 417895715 417895605 8.930000e-12 82.4
55 TraesCS5D01G159300 chr6B 79.677 310 54 5 1 308 228225506 228225808 8.440000e-52 215.0
56 TraesCS5D01G159300 chr1A 84.211 133 13 7 532 662 124346913 124346787 5.260000e-24 122.0


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 TraesCS5D01G159300 chr5D 247751263 247755140 3877 False 7162.000000 7162 100.000000 1 3878 1 chr5D.!!$F1 3877
1 TraesCS5D01G159300 chr5A 331728290 331749702 21412 False 506.578947 1977 90.860368 1 3065 19 chr5A.!!$F1 3064
2 TraesCS5D01G159300 chr7B 56993833 56995164 1331 True 1642.000000 1642 89.022000 1737 3065 1 chr7B.!!$R1 1328
3 TraesCS5D01G159300 chr7B 56359334 56361689 2355 False 907.500000 1657 82.327500 1005 3065 2 chr7B.!!$F1 2060
4 TraesCS5D01G159300 chr2D 462257789 462258610 821 False 1166.000000 1166 92.467000 3064 3876 1 chr2D.!!$F1 812
5 TraesCS5D01G159300 chr2D 551873211 551874506 1295 True 876.000000 876 79.128000 1775 3065 1 chr2D.!!$R2 1290
6 TraesCS5D01G159300 chr2D 551428269 551428975 706 False 460.000000 460 78.691000 1818 2527 1 chr2D.!!$F2 709
7 TraesCS5D01G159300 chr3D 600493915 600494731 816 True 1153.000000 1153 92.242000 3064 3878 1 chr3D.!!$R1 814
8 TraesCS5D01G159300 chr7D 127643727 127644548 821 False 1140.000000 1140 91.908000 3064 3878 1 chr7D.!!$F1 814
9 TraesCS5D01G159300 chr7D 624916754 624917571 817 True 1118.000000 1118 91.495000 3067 3878 1 chr7D.!!$R1 811
10 TraesCS5D01G159300 chr7D 627018178 627018992 814 False 1085.000000 1085 90.777000 3063 3877 1 chr7D.!!$F3 814
11 TraesCS5D01G159300 chr7D 100646619 100650461 3842 False 514.750000 880 87.791500 1005 3065 4 chr7D.!!$F4 2060
12 TraesCS5D01G159300 chr4B 449340462 449341276 814 True 1112.000000 1112 91.383000 3064 3878 1 chr4B.!!$R1 814
13 TraesCS5D01G159300 chr4B 498203817 498204637 820 False 1112.000000 1112 91.283000 3063 3877 1 chr4B.!!$F1 814
14 TraesCS5D01G159300 chr3B 521414504 521415319 815 True 1110.000000 1110 91.352000 3067 3878 1 chr3B.!!$R2 811
15 TraesCS5D01G159300 chr3B 521477808 521478622 814 True 1110.000000 1110 91.363000 3065 3878 1 chr3B.!!$R3 813
16 TraesCS5D01G159300 chr2B 657079104 657080398 1294 True 896.000000 896 79.419000 1775 3063 1 chr2B.!!$R2 1288
17 TraesCS5D01G159300 chr2B 656942475 656943723 1248 False 876.000000 876 79.589000 1818 3065 1 chr2B.!!$F1 1247
18 TraesCS5D01G159300 chr2B 691010569 691011816 1247 True 837.000000 837 79.094000 1830 3065 1 chr2B.!!$R3 1235
19 TraesCS5D01G159300 chr2B 656610154 656611402 1248 True 749.000000 749 77.822000 1830 3065 1 chr2B.!!$R1 1235
20 TraesCS5D01G159300 chr2A 692643503 692644797 1294 True 870.000000 870 79.084000 1775 3065 1 chr2A.!!$R1 1290

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
891 1391 0.030773 GCTCGTGTGTGACTGTGAGA 59.969 55.0 0.0 0.0 0.0 3.27 F
1041 3654 0.111253 GGGAGATGGATTTGGGCGAT 59.889 55.0 0.0 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1870 20643 1.136110 TCAATCAGAGGTGCGCGATAA 59.864 47.619 12.1 0.0 0.00 1.75 R
2920 23242 0.618458 TAGTTGGCACCTCCATCCAC 59.382 55.000 0.0 0.0 46.04 4.02 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
19 20 3.656457 TGGCAGCTGATGACATGTT 57.344 47.368 20.43 0.00 44.15 2.71
22 23 2.290197 TGGCAGCTGATGACATGTTGTA 60.290 45.455 20.43 0.00 44.15 2.41
33 34 6.807720 TGATGACATGTTGTATCATTTTGCAC 59.192 34.615 13.90 0.00 33.21 4.57
44 45 9.872721 TTGTATCATTTTGCACAATATGATTGT 57.127 25.926 24.53 11.61 42.62 2.71
46 47 7.688478 ATCATTTTGCACAATATGATTGTCG 57.312 32.000 18.00 0.96 42.62 4.35
88 89 4.533311 AGCCCAAACCAATGATTTTGAGAT 59.467 37.500 8.32 0.00 35.13 2.75
178 179 8.442632 TGCATAAATTCAGAATCTTCGAGATT 57.557 30.769 9.07 9.07 46.84 2.40
206 207 1.732732 GCACACCGTAGCTACTCAGTG 60.733 57.143 25.06 25.06 0.00 3.66
211 212 3.378742 CACCGTAGCTACTCAGTGATCTT 59.621 47.826 23.61 0.00 0.00 2.40
331 332 3.479489 TGTATGATGGACATGCATGGAC 58.521 45.455 29.41 21.11 44.23 4.02
333 334 0.921166 TGATGGACATGCATGGACCT 59.079 50.000 30.71 21.72 32.43 3.85
334 335 2.126057 TGATGGACATGCATGGACCTA 58.874 47.619 30.71 22.29 32.43 3.08
351 352 6.173339 TGGACCTACATGAATTTGAGAGTTC 58.827 40.000 0.00 0.00 0.00 3.01
353 354 5.178797 ACCTACATGAATTTGAGAGTTCGG 58.821 41.667 0.00 0.00 0.00 4.30
361 362 5.412594 TGAATTTGAGAGTTCGGATTTGAGG 59.587 40.000 0.00 0.00 0.00 3.86
373 374 1.461127 GATTTGAGGCGTGTGACTGTC 59.539 52.381 0.00 0.00 28.75 3.51
374 375 0.874175 TTTGAGGCGTGTGACTGTCG 60.874 55.000 2.98 0.00 28.75 4.35
389 390 3.407967 TCGGGCAGGGGATTGTCC 61.408 66.667 0.00 0.00 39.50 4.02
439 440 2.669240 GCGGACATATAGGGGCCC 59.331 66.667 17.12 17.12 0.00 5.80
440 441 2.978824 CGGACATATAGGGGCCCG 59.021 66.667 18.95 4.63 0.00 6.13
451 452 1.608046 GGGGCCCGGATTTGTCAAA 60.608 57.895 17.79 0.00 0.00 2.69
473 474 7.652105 TCAAATCCGACTGTAGATGCTATAAAC 59.348 37.037 0.00 0.00 0.00 2.01
475 476 5.138276 TCCGACTGTAGATGCTATAAACCT 58.862 41.667 0.00 0.00 0.00 3.50
478 479 6.294787 CCGACTGTAGATGCTATAAACCTCAT 60.295 42.308 0.00 0.00 0.00 2.90
496 497 6.119536 ACCTCATGATTTTATTGGTCGCTAA 58.880 36.000 0.00 0.00 0.00 3.09
581 582 1.247567 ATTTGAAAGCTCCCACCACG 58.752 50.000 0.00 0.00 0.00 4.94
589 590 1.228657 GCTCCCACCACGAGAAACAC 61.229 60.000 0.00 0.00 0.00 3.32
592 593 1.219522 CCCACCACGAGAAACACGAC 61.220 60.000 0.00 0.00 34.70 4.34
593 594 1.545614 CCACCACGAGAAACACGACG 61.546 60.000 0.00 0.00 34.70 5.12
595 596 0.101040 ACCACGAGAAACACGACGAA 59.899 50.000 0.00 0.00 34.70 3.85
596 597 1.269413 ACCACGAGAAACACGACGAAT 60.269 47.619 0.00 0.00 34.70 3.34
597 598 2.030893 ACCACGAGAAACACGACGAATA 60.031 45.455 0.00 0.00 34.70 1.75
598 599 3.176708 CCACGAGAAACACGACGAATAT 58.823 45.455 0.00 0.00 34.70 1.28
599 600 3.001070 CCACGAGAAACACGACGAATATG 60.001 47.826 0.00 0.00 34.70 1.78
609 610 5.457140 ACACGACGAATATGCAAACAAAAT 58.543 33.333 0.00 0.00 0.00 1.82
671 672 6.595716 TCAAAAATCAAAAGCCGGAAGAAAAA 59.404 30.769 5.05 0.00 0.00 1.94
700 922 4.641541 TGCGTGCTACTAGTACAAATCCTA 59.358 41.667 0.00 0.00 29.68 2.94
729 951 2.037367 CCTCCACCTCGGTCCTCA 59.963 66.667 0.00 0.00 35.57 3.86
730 952 2.352032 CCTCCACCTCGGTCCTCAC 61.352 68.421 0.00 0.00 35.57 3.51
737 959 1.153939 CTCGGTCCTCACAGAAGCG 60.154 63.158 0.00 0.00 35.38 4.68
751 973 1.202359 AGAAGCGAAAGATCTCTCCGC 60.202 52.381 21.26 21.26 45.39 5.54
764 986 0.326595 TCTCCGCAGTTGGCCATTAA 59.673 50.000 6.09 0.00 40.31 1.40
765 987 1.173043 CTCCGCAGTTGGCCATTAAA 58.827 50.000 6.09 0.00 40.31 1.52
766 988 0.885196 TCCGCAGTTGGCCATTAAAC 59.115 50.000 6.09 0.37 40.31 2.01
767 989 0.600557 CCGCAGTTGGCCATTAAACA 59.399 50.000 6.09 0.00 40.31 2.83
768 990 1.668628 CCGCAGTTGGCCATTAAACAC 60.669 52.381 6.09 0.00 40.31 3.32
769 991 1.668628 CGCAGTTGGCCATTAAACACC 60.669 52.381 6.09 0.00 40.31 4.16
770 992 1.337728 GCAGTTGGCCATTAAACACCC 60.338 52.381 6.09 0.00 36.11 4.61
821 1312 1.446272 CGACTCGAAGCAACCTCCC 60.446 63.158 0.00 0.00 0.00 4.30
827 1318 2.930562 AAGCAACCTCCCGCTCCT 60.931 61.111 0.00 0.00 37.54 3.69
839 1330 4.851214 GCTCCTCCTCGCCCTCCT 62.851 72.222 0.00 0.00 0.00 3.69
840 1331 2.042435 CTCCTCCTCGCCCTCCTT 60.042 66.667 0.00 0.00 0.00 3.36
841 1332 1.687493 CTCCTCCTCGCCCTCCTTT 60.687 63.158 0.00 0.00 0.00 3.11
867 1367 3.319926 GACTGCCGCTTGCTTGCTC 62.320 63.158 0.00 0.00 42.00 4.26
873 1373 4.773117 GCTTGCTTGCTCCGCTGC 62.773 66.667 0.00 0.00 0.00 5.25
884 1384 3.406361 CCGCTGCTCGTGTGTGAC 61.406 66.667 0.00 0.00 36.19 3.67
885 1385 2.355126 CGCTGCTCGTGTGTGACT 60.355 61.111 0.00 0.00 0.00 3.41
887 1387 1.592669 GCTGCTCGTGTGTGACTGT 60.593 57.895 0.00 0.00 0.00 3.55
888 1388 1.825285 GCTGCTCGTGTGTGACTGTG 61.825 60.000 0.00 0.00 0.00 3.66
889 1389 0.249031 CTGCTCGTGTGTGACTGTGA 60.249 55.000 0.00 0.00 0.00 3.58
890 1390 0.249031 TGCTCGTGTGTGACTGTGAG 60.249 55.000 0.00 0.00 0.00 3.51
891 1391 0.030773 GCTCGTGTGTGACTGTGAGA 59.969 55.000 0.00 0.00 0.00 3.27
892 1392 1.928152 GCTCGTGTGTGACTGTGAGAG 60.928 57.143 0.00 0.00 0.00 3.20
893 1393 0.668535 TCGTGTGTGACTGTGAGAGG 59.331 55.000 0.00 0.00 0.00 3.69
894 1394 0.941463 CGTGTGTGACTGTGAGAGGC 60.941 60.000 0.00 0.00 0.00 4.70
895 1395 0.601311 GTGTGTGACTGTGAGAGGCC 60.601 60.000 0.00 0.00 0.00 5.19
923 1423 2.421388 CCATGCCGAAACTCCCTTCATA 60.421 50.000 0.00 0.00 0.00 2.15
969 1469 0.600255 CTCGCGTGTGAGGGAAAAGT 60.600 55.000 5.77 0.00 32.64 2.66
977 1477 3.314357 GTGTGAGGGAAAAGTTAAAGCGT 59.686 43.478 0.00 0.00 0.00 5.07
978 1478 3.314080 TGTGAGGGAAAAGTTAAAGCGTG 59.686 43.478 0.00 0.00 0.00 5.34
979 1479 3.314357 GTGAGGGAAAAGTTAAAGCGTGT 59.686 43.478 0.00 0.00 0.00 4.49
980 1480 3.314080 TGAGGGAAAAGTTAAAGCGTGTG 59.686 43.478 0.00 0.00 0.00 3.82
981 1481 3.547746 AGGGAAAAGTTAAAGCGTGTGA 58.452 40.909 0.00 0.00 0.00 3.58
982 1482 3.564225 AGGGAAAAGTTAAAGCGTGTGAG 59.436 43.478 0.00 0.00 0.00 3.51
983 1483 3.562557 GGGAAAAGTTAAAGCGTGTGAGA 59.437 43.478 0.00 0.00 0.00 3.27
984 1484 4.215613 GGGAAAAGTTAAAGCGTGTGAGAT 59.784 41.667 0.00 0.00 0.00 2.75
985 1485 5.147162 GGAAAAGTTAAAGCGTGTGAGATG 58.853 41.667 0.00 0.00 0.00 2.90
986 1486 4.749245 AAAGTTAAAGCGTGTGAGATGG 57.251 40.909 0.00 0.00 0.00 3.51
987 1487 2.076863 AGTTAAAGCGTGTGAGATGGC 58.923 47.619 0.00 0.00 0.00 4.40
988 1488 1.075542 TTAAAGCGTGTGAGATGGCG 58.924 50.000 0.00 0.00 0.00 5.69
989 1489 0.245266 TAAAGCGTGTGAGATGGCGA 59.755 50.000 0.00 0.00 0.00 5.54
990 1490 1.291877 AAAGCGTGTGAGATGGCGAC 61.292 55.000 0.00 0.00 0.00 5.19
991 1491 3.188786 GCGTGTGAGATGGCGACC 61.189 66.667 0.00 0.00 0.00 4.79
992 1492 2.509336 CGTGTGAGATGGCGACCC 60.509 66.667 0.00 0.00 0.00 4.46
993 1493 2.125106 GTGTGAGATGGCGACCCC 60.125 66.667 0.00 0.00 0.00 4.95
1041 3654 0.111253 GGGAGATGGATTTGGGCGAT 59.889 55.000 0.00 0.00 0.00 4.58
1109 3722 0.962356 AAAGGGCAGGTGCTCAATCG 60.962 55.000 4.30 0.00 46.01 3.34
1117 3730 0.250081 GGTGCTCAATCGATCCCTCC 60.250 60.000 0.00 0.00 0.00 4.30
1118 3731 0.250081 GTGCTCAATCGATCCCTCCC 60.250 60.000 0.00 0.00 0.00 4.30
1119 3732 0.399091 TGCTCAATCGATCCCTCCCT 60.399 55.000 0.00 0.00 0.00 4.20
1120 3733 0.320050 GCTCAATCGATCCCTCCCTC 59.680 60.000 0.00 0.00 0.00 4.30
1121 3734 0.972883 CTCAATCGATCCCTCCCTCC 59.027 60.000 0.00 0.00 0.00 4.30
1122 3735 0.471971 TCAATCGATCCCTCCCTCCC 60.472 60.000 0.00 0.00 0.00 4.30
1143 3775 0.811616 CCCTTGATAGTGCGAGTGGC 60.812 60.000 0.00 0.00 43.96 5.01
1149 3781 2.584261 ATAGTGCGAGTGGCTGCCAG 62.584 60.000 24.10 12.09 44.05 4.85
1227 10189 3.102097 GCGTCCAGCCATGCTTAC 58.898 61.111 0.00 0.00 36.40 2.34
1256 10234 4.428209 CTGATTGATGAGTCGCTTGTAGT 58.572 43.478 0.00 0.00 0.00 2.73
1259 10237 4.776795 TTGATGAGTCGCTTGTAGTACA 57.223 40.909 0.00 0.00 0.00 2.90
1354 10340 1.272425 TGCTAGGGTTTGGAATGGGTG 60.272 52.381 0.00 0.00 0.00 4.61
1379 10365 1.188863 GGCATGGCACTCAGGAAATT 58.811 50.000 15.47 0.00 0.00 1.82
1397 10383 0.993532 TTACGCGTGCCTGTAATTCG 59.006 50.000 24.59 0.00 0.00 3.34
1446 12516 6.861065 TGGATTCGGAAAACTAATGATAGC 57.139 37.500 0.00 0.00 31.96 2.97
1447 12517 6.591935 TGGATTCGGAAAACTAATGATAGCT 58.408 36.000 0.00 0.00 31.96 3.32
1451 12713 9.209175 GATTCGGAAAACTAATGATAGCTATGT 57.791 33.333 11.94 0.00 31.96 2.29
1518 13899 9.270640 TGATACACCAAATTTTCTTTCCAAATG 57.729 29.630 0.00 0.00 0.00 2.32
1720 18312 0.732538 GTATTTGGCCGCACAGTTGC 60.733 55.000 0.00 0.00 46.21 4.17
1751 20520 1.604604 AGTTGCATACCGTTTGTGCT 58.395 45.000 0.00 0.00 39.52 4.40
1772 20543 4.201724 GCTTTCACGTTGCTACATTCTAGG 60.202 45.833 0.00 0.00 0.00 3.02
1821 20594 9.127277 TCCCATTTACTGTTTTTATATGTAGGC 57.873 33.333 0.00 0.00 0.00 3.93
1870 20643 8.303780 TCTCACTTGATCACTATCTCAAATCT 57.696 34.615 0.00 0.00 31.40 2.40
1913 20686 1.800805 AACAAGGTCAGATCTGTGCG 58.199 50.000 21.92 10.02 0.00 5.34
2016 20789 2.102578 GGATGTGGACTTTGGGGATTG 58.897 52.381 0.00 0.00 0.00 2.67
2036 20809 2.407616 GGGCGGTTTATTCTGCGC 59.592 61.111 0.00 0.00 43.24 6.09
2048 20821 0.250234 TTCTGCGCAGGCTCATACTT 59.750 50.000 35.36 0.00 40.82 2.24
2054 20827 1.599542 CGCAGGCTCATACTTTAAGGC 59.400 52.381 0.00 0.00 35.94 4.35
2110 20883 1.476007 AAGCTGCGGAGGACTTCAGT 61.476 55.000 5.93 0.00 0.00 3.41
2146 20919 6.320164 TGACATATTACTTGGCAATGGTTACC 59.680 38.462 0.00 0.00 0.00 2.85
2202 20978 5.993441 AGAAGCATTTCAAAATCAAGGTTGG 59.007 36.000 0.00 0.00 35.70 3.77
2291 21070 9.029368 TCATAACAAACATGTGGATATGGAAAA 57.971 29.630 19.19 6.00 32.32 2.29
2343 21122 4.790765 ATTTCACAGTGATCGAGTCTCA 57.209 40.909 3.45 0.00 0.00 3.27
2570 22888 8.592105 AATAAATCGCAAATGGATGTTATTGG 57.408 30.769 0.00 0.00 0.00 3.16
2658 22976 2.404559 ACTGGAAAGACCCACACTGTA 58.595 47.619 0.00 0.00 38.00 2.74
2749 23067 2.279935 AATTGGGGTTTGCACTCGTA 57.720 45.000 0.00 0.00 0.00 3.43
2867 23185 2.361119 TGGACATAACCGGAGATCTTCG 59.639 50.000 16.96 16.96 0.00 3.79
2884 23206 5.160607 TCTTCGGGAAGCTTAGATTTTCA 57.839 39.130 0.00 0.00 38.28 2.69
2886 23208 5.817816 TCTTCGGGAAGCTTAGATTTTCATC 59.182 40.000 0.00 0.00 38.28 2.92
2920 23242 6.772770 TGTTGAATGCTTTTCATCATTGTG 57.227 33.333 8.65 0.00 33.49 3.33
3022 23344 2.627945 TGGAAATAGTGATGCCGTGTC 58.372 47.619 0.00 0.00 0.00 3.67
3340 23678 9.941664 AATAATGCATTATCTGTCTTTCTTTCG 57.058 29.630 27.77 0.00 32.08 3.46
3602 23943 5.644636 AGGACATGCATGGCAAAAATTAAAG 59.355 36.000 32.84 2.01 43.62 1.85
3615 23960 5.680594 AAAATTAAAGAGGCATGCATGGA 57.319 34.783 27.34 0.00 0.00 3.41
3618 23964 5.881923 ATTAAAGAGGCATGCATGGAAAT 57.118 34.783 27.34 8.62 0.00 2.17
3622 23968 5.680594 AAGAGGCATGCATGGAAATAAAA 57.319 34.783 27.34 0.00 0.00 1.52
3719 24065 8.830580 CAAGAAATAGTGATGAAATATGGACGT 58.169 33.333 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 9.872721 ACAATCATATTGTGCAAAATGATACAA 57.127 25.926 12.62 0.00 0.00 2.41
19 20 9.518906 GACAATCATATTGTGCAAAATGATACA 57.481 29.630 12.62 0.00 31.96 2.29
22 23 7.482474 TCGACAATCATATTGTGCAAAATGAT 58.518 30.769 12.62 6.15 31.96 2.45
33 34 3.983988 CCTCGTCCTCGACAATCATATTG 59.016 47.826 0.00 0.00 41.35 1.90
43 44 0.312416 CCATCATCCTCGTCCTCGAC 59.688 60.000 0.00 0.00 41.35 4.20
44 45 0.823769 CCCATCATCCTCGTCCTCGA 60.824 60.000 0.00 0.00 44.12 4.04
46 47 1.889829 CTACCCATCATCCTCGTCCTC 59.110 57.143 0.00 0.00 0.00 3.71
88 89 1.211703 TGTGGACTTGTTCTTCAGGCA 59.788 47.619 0.00 0.00 0.00 4.75
185 186 0.526211 CTGAGTAGCTACGGTGTGCA 59.474 55.000 17.99 9.56 0.00 4.57
206 207 3.812053 GTCCACATATGCTCCACAAGATC 59.188 47.826 1.58 0.00 0.00 2.75
211 212 0.546122 GGGTCCACATATGCTCCACA 59.454 55.000 1.58 0.00 0.00 4.17
308 309 3.117963 TCCATGCATGTCCATCATACACA 60.118 43.478 24.58 0.00 33.29 3.72
320 321 3.650281 TTCATGTAGGTCCATGCATGT 57.350 42.857 24.58 9.25 42.07 3.21
331 332 5.419542 TCCGAACTCTCAAATTCATGTAGG 58.580 41.667 0.00 0.00 0.00 3.18
333 334 7.606073 TCAAATCCGAACTCTCAAATTCATGTA 59.394 33.333 0.00 0.00 0.00 2.29
334 335 6.430925 TCAAATCCGAACTCTCAAATTCATGT 59.569 34.615 0.00 0.00 0.00 3.21
351 352 0.670546 AGTCACACGCCTCAAATCCG 60.671 55.000 0.00 0.00 0.00 4.18
353 354 1.461127 GACAGTCACACGCCTCAAATC 59.539 52.381 0.00 0.00 0.00 2.17
361 362 4.961511 TGCCCGACAGTCACACGC 62.962 66.667 0.41 0.00 0.00 5.34
373 374 4.856801 CGGACAATCCCCTGCCCG 62.857 72.222 0.00 0.00 31.13 6.13
374 375 4.506255 CCGGACAATCCCCTGCCC 62.506 72.222 0.00 0.00 31.13 5.36
419 420 2.280552 GCCCCTATATGTCCGCGGA 61.281 63.158 27.28 27.28 0.00 5.54
451 452 5.775701 AGGTTTATAGCATCTACAGTCGGAT 59.224 40.000 0.00 0.00 0.00 4.18
473 474 6.618287 TTAGCGACCAATAAAATCATGAGG 57.382 37.500 0.09 0.00 0.00 3.86
475 476 7.717436 TGGTATTAGCGACCAATAAAATCATGA 59.283 33.333 0.00 0.00 44.08 3.07
551 552 8.037166 GTGGGAGCTTTCAAATAAGATTCATTT 58.963 33.333 0.00 0.00 0.00 2.32
568 569 0.250338 GTTTCTCGTGGTGGGAGCTT 60.250 55.000 0.00 0.00 0.00 3.74
571 572 0.944311 CGTGTTTCTCGTGGTGGGAG 60.944 60.000 0.00 0.00 0.00 4.30
574 575 1.545614 CGTCGTGTTTCTCGTGGTGG 61.546 60.000 0.00 0.00 0.00 4.61
581 582 4.577687 TTGCATATTCGTCGTGTTTCTC 57.422 40.909 0.00 0.00 0.00 2.87
589 590 9.950858 AATTAAATTTTGTTTGCATATTCGTCG 57.049 25.926 0.00 0.00 0.00 5.12
641 642 6.934048 TCCGGCTTTTGATTTTTGATTTTT 57.066 29.167 0.00 0.00 0.00 1.94
642 643 6.765512 TCTTCCGGCTTTTGATTTTTGATTTT 59.234 30.769 0.00 0.00 0.00 1.82
662 663 3.119708 AGCACGCATCATCTTTTTCTTCC 60.120 43.478 0.00 0.00 0.00 3.46
663 664 4.088823 AGCACGCATCATCTTTTTCTTC 57.911 40.909 0.00 0.00 0.00 2.87
671 672 3.883489 TGTACTAGTAGCACGCATCATCT 59.117 43.478 1.87 0.00 0.00 2.90
700 922 1.147817 AGGTGGAGGTTTTCTTGGCAT 59.852 47.619 0.00 0.00 0.00 4.40
729 951 2.159310 CGGAGAGATCTTTCGCTTCTGT 60.159 50.000 7.14 0.00 31.54 3.41
730 952 2.458951 CGGAGAGATCTTTCGCTTCTG 58.541 52.381 7.14 0.00 31.54 3.02
737 959 2.275318 CCAACTGCGGAGAGATCTTTC 58.725 52.381 12.26 4.66 0.00 2.62
751 973 1.275010 GGGGTGTTTAATGGCCAACTG 59.725 52.381 10.96 0.00 0.00 3.16
764 986 2.680805 CGTGATCAATAGCAGGGGTGTT 60.681 50.000 0.00 0.00 0.00 3.32
765 987 1.134401 CGTGATCAATAGCAGGGGTGT 60.134 52.381 0.00 0.00 0.00 4.16
766 988 1.586422 CGTGATCAATAGCAGGGGTG 58.414 55.000 0.00 0.00 0.00 4.61
767 989 0.179045 GCGTGATCAATAGCAGGGGT 60.179 55.000 12.45 0.00 0.00 4.95
768 990 0.179048 TGCGTGATCAATAGCAGGGG 60.179 55.000 15.12 0.00 34.39 4.79
769 991 0.940126 GTGCGTGATCAATAGCAGGG 59.060 55.000 18.31 0.00 40.53 4.45
770 992 0.578683 CGTGCGTGATCAATAGCAGG 59.421 55.000 18.31 19.12 40.53 4.85
806 1297 2.815647 GCGGGAGGTTGCTTCGAG 60.816 66.667 0.00 0.00 0.00 4.04
827 1318 0.684805 GAGAGAAAGGAGGGCGAGGA 60.685 60.000 0.00 0.00 0.00 3.71
833 1324 0.324830 AGTCCCGAGAGAAAGGAGGG 60.325 60.000 0.00 0.00 43.32 4.30
838 1329 4.921834 GGCAGTCCCGAGAGAAAG 57.078 61.111 0.00 0.00 0.00 2.62
867 1367 3.406361 GTCACACACGAGCAGCGG 61.406 66.667 4.06 0.00 46.49 5.52
869 1369 1.592669 ACAGTCACACACGAGCAGC 60.593 57.895 0.00 0.00 0.00 5.25
873 1373 1.335415 CCTCTCACAGTCACACACGAG 60.335 57.143 0.00 0.00 0.00 4.18
876 1376 0.601311 GGCCTCTCACAGTCACACAC 60.601 60.000 0.00 0.00 0.00 3.82
884 1384 3.324930 TGCTGGGGCCTCTCACAG 61.325 66.667 3.07 2.51 37.74 3.66
885 1385 3.640407 GTGCTGGGGCCTCTCACA 61.640 66.667 19.42 6.25 37.74 3.58
887 1387 4.980592 TGGTGCTGGGGCCTCTCA 62.981 66.667 3.07 0.00 37.74 3.27
888 1388 3.415087 ATGGTGCTGGGGCCTCTC 61.415 66.667 3.07 0.00 37.74 3.20
889 1389 3.736224 CATGGTGCTGGGGCCTCT 61.736 66.667 3.07 0.00 37.74 3.69
949 1449 1.901650 CTTTTCCCTCACACGCGAGC 61.902 60.000 15.93 0.00 0.00 5.03
952 1452 1.504359 TAACTTTTCCCTCACACGCG 58.496 50.000 3.53 3.53 0.00 6.01
954 1454 3.606153 CGCTTTAACTTTTCCCTCACACG 60.606 47.826 0.00 0.00 0.00 4.49
969 1469 1.075542 CGCCATCTCACACGCTTTAA 58.924 50.000 0.00 0.00 0.00 1.52
977 1477 2.606213 TGGGGTCGCCATCTCACA 60.606 61.111 4.12 0.00 0.00 3.58
978 1478 2.187946 CTGGGGTCGCCATCTCAC 59.812 66.667 9.40 0.00 0.00 3.51
979 1479 3.785859 GCTGGGGTCGCCATCTCA 61.786 66.667 9.40 0.00 0.00 3.27
980 1480 4.899239 CGCTGGGGTCGCCATCTC 62.899 72.222 9.40 1.44 0.00 2.75
1041 3654 1.847328 TCGACCAGGAGAGCACAATA 58.153 50.000 0.00 0.00 0.00 1.90
1109 3722 1.979389 AAGGGAGGGAGGGAGGGATC 61.979 65.000 0.00 0.00 0.00 3.36
1117 3730 0.761802 GCACTATCAAGGGAGGGAGG 59.238 60.000 0.00 0.00 0.00 4.30
1118 3731 0.390860 CGCACTATCAAGGGAGGGAG 59.609 60.000 0.00 0.00 0.00 4.30
1119 3732 0.032515 TCGCACTATCAAGGGAGGGA 60.033 55.000 0.00 0.00 0.00 4.20
1120 3733 0.390860 CTCGCACTATCAAGGGAGGG 59.609 60.000 0.00 0.00 40.08 4.30
1121 3734 1.115467 ACTCGCACTATCAAGGGAGG 58.885 55.000 10.53 0.00 45.76 4.30
1122 3735 1.202463 CCACTCGCACTATCAAGGGAG 60.202 57.143 0.00 0.00 46.57 4.30
1143 3775 0.680280 AAGGATGCTCAAGCTGGCAG 60.680 55.000 10.94 10.94 41.88 4.85
1149 3781 2.165998 ACAGGAAAAGGATGCTCAAGC 58.834 47.619 0.00 0.00 42.50 4.01
1227 10189 2.604914 CGACTCATCAATCAGGGAAACG 59.395 50.000 0.00 0.00 0.00 3.60
1256 10234 1.062258 GCGGTGAAACGACGATTGTA 58.938 50.000 0.00 0.00 38.12 2.41
1259 10237 0.511221 CAAGCGGTGAAACGACGATT 59.489 50.000 0.00 0.00 38.12 3.34
1354 10340 2.332362 CTGAGTGCCATGCCGATTGC 62.332 60.000 0.00 0.00 41.77 3.56
1379 10365 0.109179 ACGAATTACAGGCACGCGTA 60.109 50.000 13.44 0.00 0.00 4.42
1397 10383 9.804758 ATAGTATATTTATTAGCTGGCTCGAAC 57.195 33.333 0.00 0.00 0.00 3.95
1461 12723 7.542130 TGTCAACATAGCTATCATTAGTATGCG 59.458 37.037 2.34 0.00 30.60 4.73
1462 12724 8.763049 TGTCAACATAGCTATCATTAGTATGC 57.237 34.615 2.34 0.00 30.60 3.14
1476 12738 7.312154 TGGTGTATCATTTTTGTCAACATAGC 58.688 34.615 0.00 0.00 0.00 2.97
1518 13899 2.884827 AGTATTCTGAAACGCCGGTAC 58.115 47.619 1.90 0.00 0.00 3.34
1572 13956 3.954258 CCTAACATCCCCCAACATTCTTC 59.046 47.826 0.00 0.00 0.00 2.87
1666 18226 1.486310 TGGCTACCATGACATGTCTCC 59.514 52.381 25.55 14.52 0.00 3.71
1751 20520 4.890088 ACCTAGAATGTAGCAACGTGAAA 58.110 39.130 0.00 0.00 0.00 2.69
1772 20543 9.529325 GGGAATATGGTTAAAGATAGCAAAAAC 57.471 33.333 0.00 0.00 0.00 2.43
1813 20586 4.133526 AGGAATAGCCTCAGCCTACATA 57.866 45.455 0.00 0.00 46.97 2.29
1814 20587 2.983296 AGGAATAGCCTCAGCCTACAT 58.017 47.619 0.00 0.00 46.97 2.29
1870 20643 1.136110 TCAATCAGAGGTGCGCGATAA 59.864 47.619 12.10 0.00 0.00 1.75
1913 20686 1.291877 ACGATGAGTTCAAGGCGTGC 61.292 55.000 0.00 0.00 33.37 5.34
2016 20789 1.807226 GCAGAATAAACCGCCCCAC 59.193 57.895 0.00 0.00 0.00 4.61
2036 20809 3.567164 CCATGCCTTAAAGTATGAGCCTG 59.433 47.826 3.92 0.00 0.00 4.85
2048 20821 6.892658 AATAAATACATCGCCATGCCTTAA 57.107 33.333 0.00 0.00 32.57 1.85
2054 20827 7.535258 GCTAGACAAAATAAATACATCGCCATG 59.465 37.037 0.00 0.00 35.92 3.66
2146 20919 1.665169 TCATCATCCATGCAAACGTCG 59.335 47.619 0.00 0.00 31.70 5.12
2202 20978 7.121907 AGTCTTCTTCCAAGCCAATATCTTTTC 59.878 37.037 0.00 0.00 0.00 2.29
2318 21097 4.926238 AGACTCGATCACTGTGAAATTGTC 59.074 41.667 15.31 18.22 0.00 3.18
2343 21122 1.615919 CCGAATTTGTGGGGGCTAAGT 60.616 52.381 0.00 0.00 0.00 2.24
2658 22976 2.362077 CAAAGCCCACAGTAAAGCACTT 59.638 45.455 0.00 0.00 34.26 3.16
2867 23185 7.284034 TCATTCAGATGAAAATCTAAGCTTCCC 59.716 37.037 0.00 0.00 39.29 3.97
2884 23206 6.585695 AGCATTCAACAAGTTCATTCAGAT 57.414 33.333 0.00 0.00 0.00 2.90
2886 23208 7.223193 TGAAAAGCATTCAACAAGTTCATTCAG 59.777 33.333 2.79 0.00 0.00 3.02
2920 23242 0.618458 TAGTTGGCACCTCCATCCAC 59.382 55.000 0.00 0.00 46.04 4.02
3285 23614 9.998106 TTAAGATTGCACCCTAGATAGTATTTC 57.002 33.333 0.00 0.00 0.00 2.17
3340 23678 3.378339 CAATCCGAATCACTACCGGTAC 58.622 50.000 11.16 0.00 43.40 3.34
3516 23855 3.161067 TCATCTTCATCGGATCTCCTCC 58.839 50.000 0.00 0.00 41.07 4.30
3530 23869 6.202570 GGAGAATAGCACAACATCTCATCTTC 59.797 42.308 0.00 0.00 38.58 2.87
3803 24153 9.899226 AAATACATGAAGAGCTGTTAAAAAGAC 57.101 29.630 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.