Multiple sequence alignment - TraesCS3A01G138200

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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 TraesCS3A01G138200 chr3A 100.000 6592 0 0 1 6592 115167786 115161195 0.000000e+00 12174.0
1 TraesCS3A01G138200 chr3A 95.940 3399 118 10 3207 6592 115392320 115388929 0.000000e+00 5494.0
2 TraesCS3A01G138200 chr3A 95.800 3405 118 10 3207 6592 115841936 115838538 0.000000e+00 5472.0
3 TraesCS3A01G138200 chr3A 95.794 3400 121 10 3207 6592 115613782 115610391 0.000000e+00 5467.0
4 TraesCS3A01G138200 chr3A 98.631 1972 25 2 1 1972 115394274 115392305 0.000000e+00 3491.0
5 TraesCS3A01G138200 chr3A 98.127 1975 32 4 1 1972 115615739 115613767 0.000000e+00 3437.0
6 TraesCS3A01G138200 chr3A 95.055 1719 76 6 257 1972 115843633 115841921 0.000000e+00 2695.0
7 TraesCS3A01G138200 chr3A 94.990 998 40 5 1970 2957 19766269 19765272 0.000000e+00 1557.0
8 TraesCS3A01G138200 chr3A 95.515 981 33 6 1972 2942 720943097 720944076 0.000000e+00 1557.0
9 TraesCS3A01G138200 chr3A 95.311 981 35 6 1972 2942 720968504 720969483 0.000000e+00 1546.0
10 TraesCS3A01G138200 chr3A 95.311 981 35 6 1972 2942 721012925 721013904 0.000000e+00 1546.0
11 TraesCS3A01G138200 chr3A 95.209 981 36 6 1972 2942 720905646 720906625 0.000000e+00 1541.0
12 TraesCS3A01G138200 chr3A 94.478 996 45 4 1972 2957 673216680 673215685 0.000000e+00 1526.0
13 TraesCS3A01G138200 chr3A 81.356 1770 271 35 3983 5733 116075567 116073838 0.000000e+00 1386.0
14 TraesCS3A01G138200 chr3A 81.967 854 111 29 1118 1937 116077263 116076419 0.000000e+00 684.0
15 TraesCS3A01G138200 chr3A 83.074 579 77 16 3210 3775 116076396 116075826 2.120000e-139 507.0
16 TraesCS3A01G138200 chr3A 97.101 276 8 0 2913 3188 720873336 720873611 3.600000e-127 466.0
17 TraesCS3A01G138200 chr3A 96.739 276 9 0 2913 3188 720906638 720906913 1.670000e-125 460.0
18 TraesCS3A01G138200 chr3A 96.703 273 9 0 2913 3185 19765274 19765002 7.790000e-124 455.0
19 TraesCS3A01G138200 chr3A 96.377 276 10 0 2913 3188 720944089 720944364 7.790000e-124 455.0
20 TraesCS3A01G138200 chr3A 96.691 272 9 0 2913 3184 694974728 694974999 2.800000e-123 453.0
21 TraesCS3A01G138200 chr3A 96.014 276 11 0 2913 3188 719807230 719807505 3.630000e-122 449.0
22 TraesCS3A01G138200 chr3A 81.863 408 59 10 6086 6486 597188592 597188193 4.930000e-86 329.0
23 TraesCS3A01G138200 chr3A 79.091 220 42 3 4 221 663450319 663450536 1.480000e-31 148.0
24 TraesCS3A01G138200 chr4A 95.358 991 41 4 1972 2957 105227031 105228021 0.000000e+00 1570.0
25 TraesCS3A01G138200 chr4A 83.601 311 45 6 6123 6430 723799932 723800239 3.010000e-73 287.0
26 TraesCS3A01G138200 chr6A 94.880 996 38 8 1972 2957 24830651 24831643 0.000000e+00 1544.0
27 TraesCS3A01G138200 chr6A 97.048 271 8 0 2913 3183 10111726 10111456 2.170000e-124 457.0
28 TraesCS3A01G138200 chr6A 76.522 805 178 10 4798 5593 106737141 106737943 4.720000e-116 429.0
29 TraesCS3A01G138200 chr6A 89.091 110 12 0 1167 1276 185249011 185248902 3.210000e-28 137.0
30 TraesCS3A01G138200 chr6A 78.125 224 40 8 6178 6397 478016333 478016551 4.150000e-27 134.0
31 TraesCS3A01G138200 chr5A 94.300 1000 47 5 1968 2957 134575147 134574148 0.000000e+00 1522.0
32 TraesCS3A01G138200 chr3B 89.487 1189 89 17 798 1972 148547224 148546058 0.000000e+00 1471.0
33 TraesCS3A01G138200 chr3B 89.487 1189 89 17 798 1972 148583673 148582507 0.000000e+00 1471.0
34 TraesCS3A01G138200 chr3B 89.487 1189 89 17 798 1972 148625010 148623844 0.000000e+00 1471.0
35 TraesCS3A01G138200 chr3B 89.478 1188 90 17 798 1972 148660959 148659794 0.000000e+00 1469.0
36 TraesCS3A01G138200 chr3B 85.000 1180 161 10 4765 5931 148658227 148657051 0.000000e+00 1184.0
37 TraesCS3A01G138200 chr3B 85.878 871 107 10 5074 5931 148543747 148542880 0.000000e+00 913.0
38 TraesCS3A01G138200 chr3B 93.830 470 29 0 3207 3676 148546073 148545604 0.000000e+00 708.0
39 TraesCS3A01G138200 chr3B 93.830 470 29 0 3207 3676 148582522 148582053 0.000000e+00 708.0
40 TraesCS3A01G138200 chr3B 93.830 470 29 0 3207 3676 148623859 148623390 0.000000e+00 708.0
41 TraesCS3A01G138200 chr3B 93.191 470 31 1 3207 3676 148659809 148659341 0.000000e+00 689.0
42 TraesCS3A01G138200 chr3B 90.415 386 25 6 409 791 148661380 148661004 1.280000e-136 497.0
43 TraesCS3A01G138200 chr3B 90.390 385 25 6 409 791 148584092 148583718 4.590000e-136 496.0
44 TraesCS3A01G138200 chr3B 90.390 385 25 6 409 791 148625429 148625055 4.590000e-136 496.0
45 TraesCS3A01G138200 chr3B 89.896 386 26 7 409 791 148547644 148547269 9.940000e-133 484.0
46 TraesCS3A01G138200 chr3B 87.027 185 22 2 235 417 148685082 148684898 2.410000e-49 207.0
47 TraesCS3A01G138200 chr3D 88.991 1199 101 15 799 1972 98150583 98149391 0.000000e+00 1454.0
48 TraesCS3A01G138200 chr3D 82.730 1575 178 37 3208 4705 98149405 98147848 0.000000e+00 1315.0
49 TraesCS3A01G138200 chr3D 83.974 1223 164 22 4725 5931 98147857 98146651 0.000000e+00 1144.0
50 TraesCS3A01G138200 chr3D 91.083 471 37 3 221 688 98151877 98151409 3.350000e-177 632.0
51 TraesCS3A01G138200 chr3D 79.279 222 44 2 1 221 529502112 529502332 3.180000e-33 154.0
52 TraesCS3A01G138200 chr3D 81.183 186 34 1 40 224 462818933 462819118 1.480000e-31 148.0
53 TraesCS3A01G138200 chr3D 85.455 110 16 0 3 112 17597179 17597288 1.500000e-21 115.0
54 TraesCS3A01G138200 chr3D 94.444 54 3 0 742 795 98150676 98150623 4.240000e-12 84.2
55 TraesCS3A01G138200 chr7B 82.675 1241 155 30 1970 3178 74343 73131 0.000000e+00 1046.0
56 TraesCS3A01G138200 chr7B 81.333 225 36 6 1 221 417834503 417834281 1.890000e-40 178.0
57 TraesCS3A01G138200 chr7B 74.818 413 86 16 1529 1934 12366071 12365670 3.160000e-38 171.0
58 TraesCS3A01G138200 chr7B 84.971 173 21 5 1 170 440349846 440350016 3.160000e-38 171.0
59 TraesCS3A01G138200 chr5D 97.091 275 6 2 2913 3186 468838898 468839171 4.660000e-126 462.0
60 TraesCS3A01G138200 chr5D 82.100 419 64 8 6079 6486 42085983 42085565 1.360000e-91 348.0
61 TraesCS3A01G138200 chr5D 83.558 371 54 6 6121 6486 509653099 509652731 2.280000e-89 340.0
62 TraesCS3A01G138200 chr5D 85.586 111 16 0 2 112 333379186 333379076 4.180000e-22 117.0
63 TraesCS3A01G138200 chr5D 87.952 83 7 3 46 127 466589253 466589173 1.960000e-15 95.3
64 TraesCS3A01G138200 chr7A 76.847 812 177 10 4790 5593 76355870 76355062 1.300000e-121 448.0
65 TraesCS3A01G138200 chr7A 76.630 813 179 10 4790 5594 76420077 76419268 7.850000e-119 438.0
66 TraesCS3A01G138200 chr7A 76.493 804 178 10 4790 5585 76453543 76452743 1.700000e-115 427.0
67 TraesCS3A01G138200 chr2B 83.292 407 60 7 6087 6486 519694255 519693850 1.040000e-97 368.0
68 TraesCS3A01G138200 chr2B 85.612 278 35 5 6086 6360 39845551 39845276 3.010000e-73 287.0
69 TraesCS3A01G138200 chr4B 83.260 227 34 4 6170 6394 87677771 87677547 8.660000e-49 206.0
70 TraesCS3A01G138200 chr4B 80.556 180 24 9 47 221 558714285 558714112 1.930000e-25 128.0
71 TraesCS3A01G138200 chr4B 89.855 69 7 0 44 112 105726847 105726779 9.100000e-14 89.8
72 TraesCS3A01G138200 chr1A 81.905 210 38 0 8 217 550833525 550833316 1.890000e-40 178.0
73 TraesCS3A01G138200 chr1A 90.789 76 7 0 37 112 540295963 540296038 1.170000e-17 102.0
74 TraesCS3A01G138200 chr7D 81.308 214 34 4 5 215 583052852 583053062 1.140000e-37 169.0
75 TraesCS3A01G138200 chr2D 80.543 221 35 2 1 221 8636362 8636574 5.290000e-36 163.0
76 TraesCS3A01G138200 chr2D 78.481 158 30 3 38 193 481062103 481061948 4.210000e-17 100.0
77 TraesCS3A01G138200 chr1B 79.592 196 35 5 2 196 421369213 421369022 1.150000e-27 135.0
78 TraesCS3A01G138200 chr1B 93.617 47 1 1 6261 6307 684100534 684100490 1.190000e-07 69.4
79 TraesCS3A01G138200 chr6B 88.182 110 13 0 1167 1276 240392373 240392264 1.490000e-26 132.0
80 TraesCS3A01G138200 chr6B 80.645 155 30 0 67 221 37666364 37666210 3.230000e-23 121.0
81 TraesCS3A01G138200 chr1D 87.013 77 8 2 37 112 483253580 483253505 1.180000e-12 86.1
82 TraesCS3A01G138200 chr1D 88.525 61 4 3 53 112 139140787 139140729 3.300000e-08 71.3
83 TraesCS3A01G138200 chr6D 80.189 106 21 0 1168 1273 464011058 464010953 5.480000e-11 80.5


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 TraesCS3A01G138200 chr3A 115161195 115167786 6591 True 12174.000000 12174 100.000000 1 6592 1 chr3A.!!$R1 6591
1 TraesCS3A01G138200 chr3A 115388929 115394274 5345 True 4492.500000 5494 97.285500 1 6592 2 chr3A.!!$R5 6591
2 TraesCS3A01G138200 chr3A 115610391 115615739 5348 True 4452.000000 5467 96.960500 1 6592 2 chr3A.!!$R6 6591
3 TraesCS3A01G138200 chr3A 115838538 115843633 5095 True 4083.500000 5472 95.427500 257 6592 2 chr3A.!!$R7 6335
4 TraesCS3A01G138200 chr3A 720968504 720969483 979 False 1546.000000 1546 95.311000 1972 2942 1 chr3A.!!$F5 970
5 TraesCS3A01G138200 chr3A 721012925 721013904 979 False 1546.000000 1546 95.311000 1972 2942 1 chr3A.!!$F6 970
6 TraesCS3A01G138200 chr3A 673215685 673216680 995 True 1526.000000 1526 94.478000 1972 2957 1 chr3A.!!$R3 985
7 TraesCS3A01G138200 chr3A 19765002 19766269 1267 True 1006.000000 1557 95.846500 1970 3185 2 chr3A.!!$R4 1215
8 TraesCS3A01G138200 chr3A 720943097 720944364 1267 False 1006.000000 1557 95.946000 1972 3188 2 chr3A.!!$F8 1216
9 TraesCS3A01G138200 chr3A 720905646 720906913 1267 False 1000.500000 1541 95.974000 1972 3188 2 chr3A.!!$F7 1216
10 TraesCS3A01G138200 chr3A 116073838 116077263 3425 True 859.000000 1386 82.132333 1118 5733 3 chr3A.!!$R8 4615
11 TraesCS3A01G138200 chr4A 105227031 105228021 990 False 1570.000000 1570 95.358000 1972 2957 1 chr4A.!!$F1 985
12 TraesCS3A01G138200 chr6A 24830651 24831643 992 False 1544.000000 1544 94.880000 1972 2957 1 chr6A.!!$F1 985
13 TraesCS3A01G138200 chr6A 106737141 106737943 802 False 429.000000 429 76.522000 4798 5593 1 chr6A.!!$F2 795
14 TraesCS3A01G138200 chr5A 134574148 134575147 999 True 1522.000000 1522 94.300000 1968 2957 1 chr5A.!!$R1 989
15 TraesCS3A01G138200 chr3B 148657051 148661380 4329 True 959.750000 1469 89.521000 409 5931 4 chr3B.!!$R5 5522
16 TraesCS3A01G138200 chr3B 148542880 148547644 4764 True 894.000000 1471 89.772750 409 5931 4 chr3B.!!$R2 5522
17 TraesCS3A01G138200 chr3B 148582053 148584092 2039 True 891.666667 1471 91.235667 409 3676 3 chr3B.!!$R3 3267
18 TraesCS3A01G138200 chr3B 148623390 148625429 2039 True 891.666667 1471 91.235667 409 3676 3 chr3B.!!$R4 3267
19 TraesCS3A01G138200 chr3D 98146651 98151877 5226 True 925.840000 1454 88.244400 221 5931 5 chr3D.!!$R1 5710
20 TraesCS3A01G138200 chr7B 73131 74343 1212 True 1046.000000 1046 82.675000 1970 3178 1 chr7B.!!$R1 1208
21 TraesCS3A01G138200 chr7A 76355062 76355870 808 True 448.000000 448 76.847000 4790 5593 1 chr7A.!!$R1 803
22 TraesCS3A01G138200 chr7A 76419268 76420077 809 True 438.000000 438 76.630000 4790 5594 1 chr7A.!!$R2 804
23 TraesCS3A01G138200 chr7A 76452743 76453543 800 True 427.000000 427 76.493000 4790 5585 1 chr7A.!!$R3 795

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
94 95 1.131638 GCTGGATATGAGGGGTGTCA 58.868 55.000 0.00 0.00 0.00 3.58 F
223 226 2.104281 GCCCGGGTGTAGATGTTCTTAT 59.896 50.000 24.63 0.00 0.00 1.73 F
1794 2624 1.822371 ACTCCGTGCTTGGTTTTGTTT 59.178 42.857 0.00 0.00 0.00 2.83 F
2894 3747 0.037303 GTGATGGATCCATGCCCGAT 59.963 55.000 32.05 6.73 36.70 4.18 F
3213 4114 0.182537 CACACAACCCCTCACCTCAA 59.817 55.000 0.00 0.00 0.00 3.02 F
3215 4116 0.250901 CACAACCCCTCACCTCAAGG 60.251 60.000 0.00 0.00 42.17 3.61 F
3307 4208 0.531311 TGCAGGATGTGAGCTATGCG 60.531 55.000 0.00 0.00 39.31 4.73 F
5356 6865 0.643820 GCGGTCGGAACAACTTATCG 59.356 55.000 0.00 0.00 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1679 2496 0.464036 CCTGAATCGATCACCCCGAA 59.536 55.000 0.00 0.0 39.62 4.30 R
1977 2807 2.223758 CGGGATCGTCCTCCTTTTCTAC 60.224 54.545 4.41 0.0 36.57 2.59 R
3194 4095 0.182537 TTGAGGTGAGGGGTTGTGTG 59.817 55.000 0.00 0.0 0.00 3.82 R
4837 5901 1.066858 CACATAGGAGCCACGAACAGT 60.067 52.381 0.00 0.0 0.00 3.55 R
5145 6654 1.896465 GTCACTAGCTCTGTCTGGGTT 59.104 52.381 0.00 0.0 0.00 4.11 R
5356 6865 2.558313 GAGCTTCAAGCACCGCAC 59.442 61.111 13.10 0.0 45.56 5.34 R
5409 6918 2.423577 ACTACCTTTGGCGAATGTGAC 58.576 47.619 5.74 0.0 0.00 3.67 R
6486 8021 0.539438 ACTTTCGGGCAATTCCAGCA 60.539 50.000 0.00 0.0 36.21 4.41 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
94 95 1.131638 GCTGGATATGAGGGGTGTCA 58.868 55.000 0.00 0.00 0.00 3.58
223 226 2.104281 GCCCGGGTGTAGATGTTCTTAT 59.896 50.000 24.63 0.00 0.00 1.73
796 1546 3.127548 GGTCGACCTCGTGTCATTAAGTA 59.872 47.826 27.64 0.00 44.71 2.24
1024 1781 4.038522 TGGATTCGAGGATAGCTTTCTCTG 59.961 45.833 4.10 1.65 0.00 3.35
1349 2128 3.120095 TCTGCAACAGCAAAGATGAATCG 60.120 43.478 0.00 0.00 37.91 3.34
1476 2281 8.519492 TGCTGTCTTTATATGTTTTTCTTTGC 57.481 30.769 0.00 0.00 0.00 3.68
1477 2282 8.140628 TGCTGTCTTTATATGTTTTTCTTTGCA 58.859 29.630 0.00 0.00 0.00 4.08
1679 2496 5.864474 GCGAATTACGGTGAAGATATCATCT 59.136 40.000 9.23 0.00 40.48 2.90
1786 2616 2.317609 CGGTTGACTCCGTGCTTGG 61.318 63.158 0.00 0.00 44.77 3.61
1794 2624 1.822371 ACTCCGTGCTTGGTTTTGTTT 59.178 42.857 0.00 0.00 0.00 2.83
1820 2650 4.300045 GCATATGGCCTGAATCACGAAGT 61.300 47.826 3.32 0.00 37.84 3.01
1897 2727 2.606795 CCGGAACAACGTTCAATGCAAT 60.607 45.455 0.00 0.00 0.00 3.56
2033 2864 1.535860 GCGATGCATACGGCCATTTTT 60.536 47.619 16.56 0.00 43.89 1.94
2074 2905 5.168569 ACCGTACAGAGTCATACAACAATG 58.831 41.667 0.00 0.00 0.00 2.82
2313 3144 1.856629 CCTGCCACCAATCCATCTTT 58.143 50.000 0.00 0.00 0.00 2.52
2409 3240 1.607801 CCTGCACGAGTCCATCTCCA 61.608 60.000 0.00 0.00 39.84 3.86
2485 3316 1.270571 TGTGTAAGATGAAGCACCGCA 60.271 47.619 0.00 0.00 0.00 5.69
2599 3431 5.492895 GTCATCCGATCTACTGATCTAGGA 58.507 45.833 0.00 5.21 45.10 2.94
2611 3443 2.158004 TGATCTAGGATTTCCCCCGGAT 60.158 50.000 0.73 0.00 36.42 4.18
2744 3577 3.323403 GGATCTGATCGAAGACCTCCATT 59.677 47.826 11.28 0.00 42.51 3.16
2760 3593 2.579657 ATTCCTCGTGCACGGGTCA 61.580 57.895 35.06 22.55 38.37 4.02
2827 3680 3.547787 AAGCCTCCCACCGAGACCT 62.548 63.158 0.00 0.00 41.63 3.85
2893 3746 1.451504 GTGATGGATCCATGCCCGA 59.548 57.895 32.05 7.37 36.70 5.14
2894 3747 0.037303 GTGATGGATCCATGCCCGAT 59.963 55.000 32.05 6.73 36.70 4.18
3200 4101 4.980805 GAGGGACGCCGCACACAA 62.981 66.667 0.00 0.00 0.00 3.33
3207 4108 4.947147 GCCGCACACAACCCCTCA 62.947 66.667 0.00 0.00 0.00 3.86
3208 4109 2.978010 CCGCACACAACCCCTCAC 60.978 66.667 0.00 0.00 0.00 3.51
3209 4110 2.978010 CGCACACAACCCCTCACC 60.978 66.667 0.00 0.00 0.00 4.02
3210 4111 2.515901 GCACACAACCCCTCACCT 59.484 61.111 0.00 0.00 0.00 4.00
3211 4112 1.600916 GCACACAACCCCTCACCTC 60.601 63.158 0.00 0.00 0.00 3.85
3212 4113 1.836391 CACACAACCCCTCACCTCA 59.164 57.895 0.00 0.00 0.00 3.86
3213 4114 0.182537 CACACAACCCCTCACCTCAA 59.817 55.000 0.00 0.00 0.00 3.02
3214 4115 0.474184 ACACAACCCCTCACCTCAAG 59.526 55.000 0.00 0.00 0.00 3.02
3215 4116 0.250901 CACAACCCCTCACCTCAAGG 60.251 60.000 0.00 0.00 42.17 3.61
3294 4195 3.700109 CGGAGGAGAAGTGCAGGA 58.300 61.111 0.00 0.00 0.00 3.86
3307 4208 0.531311 TGCAGGATGTGAGCTATGCG 60.531 55.000 0.00 0.00 39.31 4.73
3470 4371 2.427453 GTCTTATCGCTCTCACTGGGAA 59.573 50.000 0.00 0.00 0.00 3.97
3647 4548 4.410228 CCTTCCCAACCTTCATATCTCTCA 59.590 45.833 0.00 0.00 0.00 3.27
3695 4611 7.599630 TGTACGTTTCTTCAAGTACTTGTTT 57.400 32.000 29.83 12.21 41.16 2.83
3770 4711 6.352565 CCACTCTCAAGGAATAGAAACATCCT 60.353 42.308 0.00 0.00 45.43 3.24
3774 4715 6.384015 TCTCAAGGAATAGAAACATCCTAGCA 59.616 38.462 0.00 0.00 42.72 3.49
3957 4995 3.060363 GCCGAAACATAATCGTATAGGCG 59.940 47.826 0.00 0.00 38.60 5.52
4083 5139 4.144297 ACTTTAAGGAGCTTGTTCATGCA 58.856 39.130 11.97 0.00 0.00 3.96
4090 5146 1.074405 AGCTTGTTCATGCAGGAAGGA 59.926 47.619 15.13 5.14 0.00 3.36
4332 5388 2.660064 AAGGGCCTCATCTTCGCGT 61.660 57.895 6.46 0.00 0.00 6.01
4461 5520 2.034305 ACAGAGTAAGAAGTCGCGTTGT 59.966 45.455 5.77 0.00 0.00 3.32
4552 5616 3.372440 AGGAATCCCATTGTGAAGGTC 57.628 47.619 0.00 0.00 33.88 3.85
4656 5720 2.116238 TCCAGGCATACTCAAGGTACC 58.884 52.381 2.73 2.73 32.72 3.34
4750 5814 4.851010 TGCGGTGCTTTTTAACTAACTTC 58.149 39.130 0.00 0.00 0.00 3.01
4758 5822 6.600032 TGCTTTTTAACTAACTTCTGTGACCA 59.400 34.615 0.00 0.00 0.00 4.02
4762 5826 8.974060 TTTTAACTAACTTCTGTGACCATCTT 57.026 30.769 0.00 0.00 0.00 2.40
4812 5876 1.816074 TTTGACAGCCCGACATAACC 58.184 50.000 0.00 0.00 0.00 2.85
4837 5901 2.627945 CGGGTGTTAGCATCTTAGCAA 58.372 47.619 0.00 0.00 36.85 3.91
5356 6865 0.643820 GCGGTCGGAACAACTTATCG 59.356 55.000 0.00 0.00 0.00 2.92
5379 6888 2.564471 GTGCTTGAAGCTCCAGCAT 58.436 52.632 18.94 0.00 42.97 3.79
5529 7038 2.241176 TGGTCAGATGGAAATACCCACC 59.759 50.000 0.00 0.00 39.34 4.61
5541 7050 4.519906 AATACCCACCCAGTTAGGATTG 57.480 45.455 0.00 0.00 41.22 2.67
5576 7085 7.484035 AAGAACTGTGATACAAGACTTTGTC 57.516 36.000 0.00 0.00 44.00 3.18
5577 7086 6.582636 AGAACTGTGATACAAGACTTTGTCA 58.417 36.000 0.00 0.00 44.00 3.58
5760 7286 2.958355 ACTAGCAAAACATTGTGTGGCT 59.042 40.909 13.43 13.43 37.07 4.75
5778 7304 1.948104 CTTGACCACGTGTCCAAAGA 58.052 50.000 15.65 0.00 43.78 2.52
5803 7330 8.814038 AGAGCACATACTTCAGGAAATTTTAT 57.186 30.769 0.00 0.00 0.00 1.40
5843 7371 1.339610 CGTCTCTCCTTAGATGGCAGG 59.660 57.143 0.00 0.00 0.00 4.85
5881 7410 6.208599 CCCCTTATGTCACAGTACATTTTGTT 59.791 38.462 0.00 0.00 40.52 2.83
5975 7504 4.156190 TGGCACGACTTTGTAACAGAAAAA 59.844 37.500 0.00 0.00 0.00 1.94
6125 7654 1.309950 CTCAGATGAGCCAAGGCATG 58.690 55.000 14.40 4.17 44.88 4.06
6142 7671 3.426159 GGCATGAACAGTACCGTGAATTG 60.426 47.826 0.00 0.00 0.00 2.32
6148 7677 7.359262 TGAACAGTACCGTGAATTGAAATAG 57.641 36.000 0.00 0.00 0.00 1.73
6209 7739 0.531974 TGTTCCTGTGCGTGAACTCC 60.532 55.000 0.00 0.00 41.10 3.85
6234 7764 7.201600 CCGTTCAAAATTTTGTGAAGTTTGGAT 60.202 33.333 25.98 0.00 39.18 3.41
6296 7826 8.862550 ATGTCTGAGAAACTTTTGAAAATCAC 57.137 30.769 0.00 0.00 0.00 3.06
6298 7828 7.754924 TGTCTGAGAAACTTTTGAAAATCACAC 59.245 33.333 0.00 0.00 0.00 3.82
6306 7836 6.686630 ACTTTTGAAAATCACACTGTTCACA 58.313 32.000 0.00 0.00 30.00 3.58
6367 7897 6.998968 TCCAAACTTCACAAAATTTTGCAT 57.001 29.167 26.94 9.25 41.79 3.96
6386 7916 1.328279 TGGAGCTCACGAACAGAAGA 58.672 50.000 17.19 0.00 0.00 2.87
6486 8021 2.499693 CCGGGCTTTGGGTTGAATTATT 59.500 45.455 0.00 0.00 0.00 1.40
6500 8044 3.181477 TGAATTATTGCTGGAATTGCCCG 60.181 43.478 0.00 0.00 34.97 6.13
6506 8050 1.271652 TGCTGGAATTGCCCGAAAGTA 60.272 47.619 0.00 0.00 34.97 2.24
6580 8124 3.535629 CTCTGGTGTTCTGCCCGCA 62.536 63.158 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
182 185 4.446889 GGGCCTCTTGTATCCATCTCAAAT 60.447 45.833 0.84 0.00 0.00 2.32
223 226 5.395990 GGTTCGGTTAGGGATATGAACAGAA 60.396 44.000 5.42 0.00 37.91 3.02
796 1546 6.883744 ACCACCATTAAACAACTTGAAACAT 58.116 32.000 0.00 0.00 0.00 2.71
1024 1781 1.449246 CCAGTAGCAGAGCACAGCC 60.449 63.158 0.00 0.00 0.00 4.85
1349 2128 8.511465 TGTAACTGTAAACTATCGACTTCAAC 57.489 34.615 0.00 0.00 0.00 3.18
1471 2276 6.515272 AACATATAAAGACACCCTGCAAAG 57.485 37.500 0.00 0.00 0.00 2.77
1474 2279 6.909550 AAAAACATATAAAGACACCCTGCA 57.090 33.333 0.00 0.00 0.00 4.41
1679 2496 0.464036 CCTGAATCGATCACCCCGAA 59.536 55.000 0.00 0.00 39.62 4.30
1820 2650 2.417239 GCCGTATCCGTTGTCATCAAAA 59.583 45.455 0.00 0.00 35.20 2.44
1897 2727 5.525012 CCGATGATCTTTCTATTGCAACTCA 59.475 40.000 0.00 0.00 0.00 3.41
1977 2807 2.223758 CGGGATCGTCCTCCTTTTCTAC 60.224 54.545 4.41 0.00 36.57 2.59
1994 2824 3.473647 CAGATGCAGAGGCCGGGA 61.474 66.667 2.18 0.00 40.13 5.14
2033 2864 8.604640 TGTACGGTCTTGTGTCAATAATTAAA 57.395 30.769 0.00 0.00 0.00 1.52
2074 2905 4.793028 GCTTGTTTTGGTGGCTTTAGACTC 60.793 45.833 0.00 0.00 0.00 3.36
2313 3144 1.067846 CGGTGCAGCAGTACAACTCTA 60.068 52.381 17.33 0.00 31.27 2.43
2409 3240 3.685214 GACTCGGCGTCTGATGCGT 62.685 63.158 15.13 8.03 39.61 5.24
2485 3316 1.068585 GGACGACGACTTTGGTGGT 59.931 57.895 0.00 0.00 37.11 4.16
2599 3431 0.474184 CTGCTACATCCGGGGGAAAT 59.526 55.000 0.00 0.00 34.34 2.17
2611 3443 0.610174 CAAGGCCACTCTCTGCTACA 59.390 55.000 5.01 0.00 0.00 2.74
2744 3577 3.986006 GTGACCCGTGCACGAGGA 61.986 66.667 37.06 22.06 43.02 3.71
3190 4091 4.947147 TGAGGGGTTGTGTGCGGC 62.947 66.667 0.00 0.00 0.00 6.53
3191 4092 2.978010 GTGAGGGGTTGTGTGCGG 60.978 66.667 0.00 0.00 0.00 5.69
3192 4093 2.978010 GGTGAGGGGTTGTGTGCG 60.978 66.667 0.00 0.00 0.00 5.34
3193 4094 1.600916 GAGGTGAGGGGTTGTGTGC 60.601 63.158 0.00 0.00 0.00 4.57
3194 4095 0.182537 TTGAGGTGAGGGGTTGTGTG 59.817 55.000 0.00 0.00 0.00 3.82
3195 4096 0.474184 CTTGAGGTGAGGGGTTGTGT 59.526 55.000 0.00 0.00 0.00 3.72
3196 4097 0.250901 CCTTGAGGTGAGGGGTTGTG 60.251 60.000 0.00 0.00 0.00 3.33
3197 4098 2.155065 CCTTGAGGTGAGGGGTTGT 58.845 57.895 0.00 0.00 0.00 3.32
3210 4111 3.678056 GTGACATGTACTCACCCTTGA 57.322 47.619 0.00 0.00 33.23 3.02
3216 4117 1.135083 CCCGAGGTGACATGTACTCAC 60.135 57.143 18.91 13.94 37.84 3.51
3217 4118 1.182667 CCCGAGGTGACATGTACTCA 58.817 55.000 18.91 4.03 0.00 3.41
3218 4119 1.471119 TCCCGAGGTGACATGTACTC 58.529 55.000 0.00 6.47 0.00 2.59
3219 4120 2.160721 ATCCCGAGGTGACATGTACT 57.839 50.000 0.00 0.00 0.00 2.73
3220 4121 2.981859 AATCCCGAGGTGACATGTAC 57.018 50.000 0.00 0.00 0.00 2.90
3221 4122 2.835156 TGAAATCCCGAGGTGACATGTA 59.165 45.455 0.00 0.00 0.00 2.29
3294 4195 1.121407 TAGGCCCGCATAGCTCACAT 61.121 55.000 0.00 0.00 0.00 3.21
3470 4371 3.402681 CTCATGACCGGCACCCCT 61.403 66.667 0.00 0.00 0.00 4.79
3647 4548 5.405935 ACCACAAGCTTTTCTTTGTTTCT 57.594 34.783 0.00 0.00 31.27 2.52
3851 4803 9.395707 CTATACGATTATGGTAAGTCAGTTGTC 57.604 37.037 0.00 0.00 0.00 3.18
4003 5059 4.331968 TGTCCCTGCGTTTAAGATCAAAT 58.668 39.130 0.00 0.00 0.00 2.32
4083 5139 2.301870 TGTGTTATGTCGCTTCCTTCCT 59.698 45.455 0.00 0.00 0.00 3.36
4090 5146 4.754618 TCAATTGAGTGTGTTATGTCGCTT 59.245 37.500 3.38 0.00 0.00 4.68
4185 5241 1.608283 GCTTGACGCTAACCACTCCTT 60.608 52.381 0.00 0.00 35.14 3.36
4332 5388 4.994852 GTCCAAGCTGTTCATGTTGTACTA 59.005 41.667 0.00 0.00 0.00 1.82
4461 5520 2.978978 TGAAGATTGACCCTGTTCCAGA 59.021 45.455 0.00 0.00 32.44 3.86
4552 5616 3.618594 CGACAACAATCATGGTAGGTGAG 59.381 47.826 4.61 0.00 0.00 3.51
4566 5630 2.135581 ACCCCGTCTCCGACAACAA 61.136 57.895 0.00 0.00 35.63 2.83
4656 5720 7.461182 TTGAGTTATAAATTTCACAGTGGGG 57.539 36.000 0.00 0.00 0.00 4.96
4737 5801 8.974060 AAGATGGTCACAGAAGTTAGTTAAAA 57.026 30.769 0.00 0.00 0.00 1.52
4750 5814 5.292101 GTCTTAAATCCGAAGATGGTCACAG 59.708 44.000 0.00 0.00 35.46 3.66
4762 5826 7.764443 CCACAGAGATAAAAGTCTTAAATCCGA 59.236 37.037 4.29 0.00 0.00 4.55
4818 5882 3.375299 CAGTTGCTAAGATGCTAACACCC 59.625 47.826 0.00 0.00 31.43 4.61
4824 5888 3.926527 CACGAACAGTTGCTAAGATGCTA 59.073 43.478 0.00 0.00 0.00 3.49
4837 5901 1.066858 CACATAGGAGCCACGAACAGT 60.067 52.381 0.00 0.00 0.00 3.55
5145 6654 1.896465 GTCACTAGCTCTGTCTGGGTT 59.104 52.381 0.00 0.00 0.00 4.11
5356 6865 2.558313 GAGCTTCAAGCACCGCAC 59.442 61.111 13.10 0.00 45.56 5.34
5379 6888 2.747022 CACGGACATGACCACCCA 59.253 61.111 14.61 0.00 0.00 4.51
5409 6918 2.423577 ACTACCTTTGGCGAATGTGAC 58.576 47.619 5.74 0.00 0.00 3.67
5529 7038 1.009829 GCGACAGCAATCCTAACTGG 58.990 55.000 0.00 0.00 44.35 4.00
5702 7220 9.623000 ATCAACACATCTCATTAATCATGAAGA 57.377 29.630 0.00 0.00 41.66 2.87
5778 7304 8.814038 ATAAAATTTCCTGAAGTATGTGCTCT 57.186 30.769 0.00 0.00 0.00 4.09
5803 7330 2.863740 CGCGCAAGTACATATTTCCTGA 59.136 45.455 8.75 0.00 41.68 3.86
5843 7371 3.118149 ACATAAGGGGTTGACGGAATACC 60.118 47.826 0.00 0.00 0.00 2.73
5975 7504 7.056006 TGCCTTTTCTATGTCATGTGTCATAT 58.944 34.615 0.00 0.00 0.00 1.78
5995 7524 2.747799 GCTGCTAGCCTTCTTATGCCTT 60.748 50.000 13.29 0.00 34.48 4.35
6033 7562 3.065371 GGTCATGTCTAAATGCCTTTCCG 59.935 47.826 0.00 0.00 0.00 4.30
6125 7654 7.591006 TCTATTTCAATTCACGGTACTGTTC 57.409 36.000 4.06 0.00 0.00 3.18
6174 7704 5.304101 ACAGGAACATCTTGCACCATAAAAA 59.696 36.000 0.00 0.00 0.00 1.94
6192 7722 1.300620 CGGAGTTCACGCACAGGAA 60.301 57.895 0.00 0.00 0.00 3.36
6194 7724 2.029073 ACGGAGTTCACGCACAGG 59.971 61.111 0.00 0.00 37.78 4.00
6209 7739 7.054855 TCCAAACTTCACAAAATTTTGAACG 57.945 32.000 32.20 20.61 40.55 3.95
6268 7798 7.403312 TTTTCAAAAGTTTCTCAGACATCCA 57.597 32.000 0.00 0.00 0.00 3.41
6269 7799 8.137437 TGATTTTCAAAAGTTTCTCAGACATCC 58.863 33.333 0.00 0.00 0.00 3.51
6296 7826 5.883661 AGACAAAATCAAGTGTGAACAGTG 58.116 37.500 0.00 0.00 37.30 3.66
6298 7828 7.816945 AAAAGACAAAATCAAGTGTGAACAG 57.183 32.000 0.00 0.00 37.30 3.16
6340 7870 7.011295 TGCAAAATTTTGTGAAGTTTGGATCTC 59.989 33.333 27.13 9.19 40.24 2.75
6343 7873 6.998968 TGCAAAATTTTGTGAAGTTTGGAT 57.001 29.167 27.13 0.00 40.24 3.41
6367 7897 1.328279 TCTTCTGTTCGTGAGCTCCA 58.672 50.000 12.15 0.00 0.00 3.86
6386 7916 2.593346 TTTTTGTGCGGTGCAAGATT 57.407 40.000 0.00 0.00 41.47 2.40
6428 7959 8.492748 CACAATGAACAATTCCTTGATTTGAAG 58.507 33.333 11.87 0.00 37.44 3.02
6441 7975 2.884012 TCGGTGAGCACAATGAACAATT 59.116 40.909 2.75 0.00 0.00 2.32
6472 8007 6.171921 CAATTCCAGCAATAATTCAACCCAA 58.828 36.000 0.00 0.00 0.00 4.12
6486 8021 0.539438 ACTTTCGGGCAATTCCAGCA 60.539 50.000 0.00 0.00 36.21 4.41
6500 8044 6.445357 TGAGTTGGTTCCAAACTTACTTTC 57.555 37.500 5.81 0.00 0.00 2.62
6506 8050 2.365293 GGCATGAGTTGGTTCCAAACTT 59.635 45.455 5.81 0.53 0.00 2.66


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

AutoCloner maintained by Alex Coulton.