Multiple sequence alignment - TraesCS7D01G404000

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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 TraesCS7D01G404000 chr7D 100.000 6868 0 0 1 6868 520875211 520882078 0.000000e+00 12683.0
1 TraesCS7D01G404000 chr7D 89.090 4088 311 50 1882 5915 520945471 520949477 0.000000e+00 4953.0
2 TraesCS7D01G404000 chr7D 86.767 1859 153 38 4047 5860 521709794 521711604 0.000000e+00 1984.0
3 TraesCS7D01G404000 chr7D 91.185 1350 71 23 476 1800 521707407 521708733 0.000000e+00 1790.0
4 TraesCS7D01G404000 chr7D 93.271 1070 65 6 1882 2950 521708732 521709795 0.000000e+00 1570.0
5 TraesCS7D01G404000 chr7D 83.344 1621 190 36 4533 6123 521593694 521595264 0.000000e+00 1424.0
6 TraesCS7D01G404000 chr7D 86.935 1240 93 33 2949 4147 521576090 521577301 0.000000e+00 1328.0
7 TraesCS7D01G404000 chr7D 88.380 1136 88 13 4257 5368 521577302 521578417 0.000000e+00 1327.0
8 TraesCS7D01G404000 chr7D 83.212 1233 150 29 4917 6122 521523630 521524832 0.000000e+00 1077.0
9 TraesCS7D01G404000 chr7D 90.588 595 35 10 1224 1800 520944881 520945472 0.000000e+00 769.0
10 TraesCS7D01G404000 chr7D 87.250 651 37 15 477 1111 521570932 521571552 0.000000e+00 701.0
11 TraesCS7D01G404000 chr7D 92.308 481 33 2 1 480 521557586 521558063 0.000000e+00 680.0
12 TraesCS7D01G404000 chr7D 93.350 406 24 3 1 406 521706866 521707268 1.270000e-166 597.0
13 TraesCS7D01G404000 chr7D 82.429 700 84 19 5454 6126 521586503 521587190 5.970000e-160 575.0
14 TraesCS7D01G404000 chr7D 96.629 89 3 0 1796 1884 519264543 519264631 1.540000e-31 148.0
15 TraesCS7D01G404000 chr7D 100.000 43 0 0 1178 1220 520876445 520876487 5.710000e-11 80.5
16 TraesCS7D01G404000 chr7D 97.436 39 1 0 1182 1220 521571550 521571588 4.450000e-07 67.6
17 TraesCS7D01G404000 chr7B 97.523 4279 87 10 1882 6154 554360760 554365025 0.000000e+00 7297.0
18 TraesCS7D01G404000 chr7B 89.027 4101 309 53 1882 5915 554779007 554783033 0.000000e+00 4950.0
19 TraesCS7D01G404000 chr7B 89.625 2294 170 33 1882 4147 555217480 555219733 0.000000e+00 2856.0
20 TraesCS7D01G404000 chr7B 95.199 1812 45 12 1 1800 554358980 554360761 0.000000e+00 2826.0
21 TraesCS7D01G404000 chr7B 88.987 1353 108 11 4039 5368 555419333 555420667 0.000000e+00 1635.0
22 TraesCS7D01G404000 chr7B 89.665 1074 60 26 756 1800 555417191 555418242 0.000000e+00 1321.0
23 TraesCS7D01G404000 chr7B 82.009 1623 210 40 4531 6123 555308249 555309819 0.000000e+00 1304.0
24 TraesCS7D01G404000 chr7B 92.769 650 26 7 537 1179 554777778 554778413 0.000000e+00 920.0
25 TraesCS7D01G404000 chr7B 89.482 599 36 12 1222 1800 554778417 554779008 0.000000e+00 732.0
26 TraesCS7D01G404000 chr7B 88.428 579 39 13 1239 1800 555216914 555217481 0.000000e+00 673.0
27 TraesCS7D01G404000 chr7B 91.684 481 36 3 1 480 555215589 555216066 0.000000e+00 664.0
28 TraesCS7D01G404000 chr7B 84.551 712 57 21 5458 6122 555420880 555421585 0.000000e+00 656.0
29 TraesCS7D01G404000 chr7B 90.909 462 25 9 756 1207 595521260 595520806 7.620000e-169 604.0
30 TraesCS7D01G404000 chr7B 92.629 407 25 5 1 406 555416263 555416665 1.280000e-161 580.0
31 TraesCS7D01G404000 chr7B 92.950 383 14 1 6175 6557 554365324 554365693 4.680000e-151 545.0
32 TraesCS7D01G404000 chr7B 81.714 700 85 22 5454 6126 555224861 555225544 1.680000e-150 544.0
33 TraesCS7D01G404000 chr7B 82.746 284 38 8 6204 6486 714333366 714333093 6.880000e-60 243.0
34 TraesCS7D01G404000 chr7B 96.825 126 3 1 6546 6671 554368316 554368440 6.980000e-50 209.0
35 TraesCS7D01G404000 chr7B 82.171 258 20 11 5893 6126 555229332 555229587 1.510000e-46 198.0
36 TraesCS7D01G404000 chr7B 92.248 129 9 1 6669 6797 554368726 554368853 1.520000e-41 182.0
37 TraesCS7D01G404000 chr7B 100.000 43 0 0 1178 1220 554360185 554360227 5.710000e-11 80.5
38 TraesCS7D01G404000 chr7A 97.412 4211 88 12 1882 6085 598951034 598955230 0.000000e+00 7153.0
39 TraesCS7D01G404000 chr7A 97.387 4209 84 9 1882 6085 599500756 599504943 0.000000e+00 7140.0
40 TraesCS7D01G404000 chr7A 88.777 4375 337 58 1882 6200 600553010 600557286 0.000000e+00 5217.0
41 TraesCS7D01G404000 chr7A 97.627 1812 28 4 1 1800 599498949 599500757 0.000000e+00 3094.0
42 TraesCS7D01G404000 chr7A 97.143 1820 28 6 1 1800 598949220 598951035 0.000000e+00 3051.0
43 TraesCS7D01G404000 chr7A 89.948 2288 167 32 1890 4147 601467359 601469613 0.000000e+00 2892.0
44 TraesCS7D01G404000 chr7A 93.470 1072 61 8 1882 2950 602021601 602022666 0.000000e+00 1583.0
45 TraesCS7D01G404000 chr7A 88.044 1355 100 26 4039 5368 602022692 602024009 0.000000e+00 1548.0
46 TraesCS7D01G404000 chr7A 90.017 1212 73 20 613 1800 602020415 602021602 0.000000e+00 1524.0
47 TraesCS7D01G404000 chr7A 88.380 1136 87 15 4257 5368 601469614 601470728 0.000000e+00 1325.0
48 TraesCS7D01G404000 chr7A 93.416 805 40 10 6070 6868 598955246 598956043 0.000000e+00 1181.0
49 TraesCS7D01G404000 chr7A 92.980 812 40 8 6070 6868 599504959 599505766 0.000000e+00 1168.0
50 TraesCS7D01G404000 chr7A 81.377 1235 171 32 4917 6122 600639481 600640685 0.000000e+00 952.0
51 TraesCS7D01G404000 chr7A 88.201 678 35 11 537 1179 600550920 600551587 0.000000e+00 767.0
52 TraesCS7D01G404000 chr7A 87.749 653 32 9 476 1111 601466162 601466783 0.000000e+00 719.0
53 TraesCS7D01G404000 chr7A 92.964 469 29 3 15 482 601465471 601465936 0.000000e+00 680.0
54 TraesCS7D01G404000 chr7A 87.713 586 39 13 1239 1801 601466781 601467356 0.000000e+00 652.0
55 TraesCS7D01G404000 chr7A 93.350 406 24 3 1 406 602019694 602020096 1.270000e-166 597.0
56 TraesCS7D01G404000 chr7A 86.607 224 12 6 1593 1800 600552790 600553011 1.490000e-56 231.0
57 TraesCS7D01G404000 chr7A 82.437 279 29 11 5866 6126 601478245 601478521 6.930000e-55 226.0
58 TraesCS7D01G404000 chr7A 97.674 86 2 0 1799 1884 477234932 477234847 1.540000e-31 148.0
59 TraesCS7D01G404000 chr7A 93.684 95 6 0 476 570 602020235 602020329 7.180000e-30 143.0
60 TraesCS7D01G404000 chr7A 100.000 43 0 0 1178 1220 599500181 599500223 5.710000e-11 80.5
61 TraesCS7D01G404000 chr7A 97.436 39 1 0 1182 1220 601466781 601466819 4.450000e-07 67.6
62 TraesCS7D01G404000 chr7A 100.000 34 0 0 476 509 600550887 600550920 5.750000e-06 63.9
63 TraesCS7D01G404000 chr2B 91.429 385 22 1 6495 6868 403698331 403698715 1.020000e-142 518.0
64 TraesCS7D01G404000 chr2B 95.604 91 4 0 1796 1886 435504868 435504958 5.550000e-31 147.0
65 TraesCS7D01G404000 chr2A 91.429 385 22 3 6495 6868 446068234 446068618 1.020000e-142 518.0
66 TraesCS7D01G404000 chr2A 82.432 296 39 10 6194 6486 601387856 601387571 5.320000e-61 246.0
67 TraesCS7D01G404000 chr2A 92.857 98 6 1 1788 1885 16861350 16861446 2.580000e-29 141.0
68 TraesCS7D01G404000 chr2D 90.390 385 26 3 6495 6868 335685869 335686253 4.780000e-136 496.0
69 TraesCS7D01G404000 chr2D 92.157 102 7 1 1799 1900 15682984 15682884 7.180000e-30 143.0
70 TraesCS7D01G404000 chr3B 83.273 275 35 8 6204 6477 752398189 752398453 6.880000e-60 243.0
71 TraesCS7D01G404000 chr6A 82.437 279 35 9 6194 6467 5292548 5292817 1.490000e-56 231.0
72 TraesCS7D01G404000 chr6A 81.533 287 40 10 6194 6477 373657640 373657916 2.490000e-54 224.0
73 TraesCS7D01G404000 chr6A 80.743 296 44 10 6194 6486 373660302 373660017 1.160000e-52 219.0
74 TraesCS7D01G404000 chr5A 81.419 296 42 10 6194 6486 543418666 543418381 5.360000e-56 230.0
75 TraesCS7D01G404000 chr5D 98.901 91 1 0 1796 1886 527158665 527158575 5.510000e-36 163.0
76 TraesCS7D01G404000 chr3D 96.629 89 3 0 1795 1883 606604077 606604165 1.540000e-31 148.0
77 TraesCS7D01G404000 chr1B 96.629 89 3 0 1796 1884 436383753 436383665 1.540000e-31 148.0
78 TraesCS7D01G404000 chr4A 96.591 88 3 0 1796 1883 69329852 69329939 5.550000e-31 147.0


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 TraesCS7D01G404000 chr7D 520875211 520882078 6867 False 12683.000000 12683 100.000000 1 6868 1 chr7D.!!$F2 6867
1 TraesCS7D01G404000 chr7D 520944881 520949477 4596 False 2861.000000 4953 89.839000 1224 5915 2 chr7D.!!$F8 4691
2 TraesCS7D01G404000 chr7D 521706866 521711604 4738 False 1485.250000 1984 91.143250 1 5860 4 chr7D.!!$F11 5859
3 TraesCS7D01G404000 chr7D 521593694 521595264 1570 False 1424.000000 1424 83.344000 4533 6123 1 chr7D.!!$F7 1590
4 TraesCS7D01G404000 chr7D 521576090 521578417 2327 False 1327.500000 1328 87.657500 2949 5368 2 chr7D.!!$F10 2419
5 TraesCS7D01G404000 chr7D 521523630 521524832 1202 False 1077.000000 1077 83.212000 4917 6122 1 chr7D.!!$F4 1205
6 TraesCS7D01G404000 chr7D 521586503 521587190 687 False 575.000000 575 82.429000 5454 6126 1 chr7D.!!$F6 672
7 TraesCS7D01G404000 chr7D 521570932 521571588 656 False 384.300000 701 92.343000 477 1220 2 chr7D.!!$F9 743
8 TraesCS7D01G404000 chr7B 554777778 554783033 5255 False 2200.666667 4950 90.426000 537 5915 3 chr7B.!!$F3 5378
9 TraesCS7D01G404000 chr7B 554358980 554368853 9873 False 1856.583333 7297 95.790833 1 6797 6 chr7B.!!$F2 6796
10 TraesCS7D01G404000 chr7B 555215589 555219733 4144 False 1397.666667 2856 89.912333 1 4147 3 chr7B.!!$F4 4146
11 TraesCS7D01G404000 chr7B 555308249 555309819 1570 False 1304.000000 1304 82.009000 4531 6123 1 chr7B.!!$F1 1592
12 TraesCS7D01G404000 chr7B 555416263 555421585 5322 False 1048.000000 1635 88.958000 1 6122 4 chr7B.!!$F6 6121
13 TraesCS7D01G404000 chr7B 555224861 555229587 4726 False 371.000000 544 81.942500 5454 6126 2 chr7B.!!$F5 672
14 TraesCS7D01G404000 chr7A 598949220 598956043 6823 False 3795.000000 7153 95.990333 1 6868 3 chr7A.!!$F3 6867
15 TraesCS7D01G404000 chr7A 599498949 599505766 6817 False 2870.625000 7140 96.998500 1 6868 4 chr7A.!!$F4 6867
16 TraesCS7D01G404000 chr7A 600550887 600557286 6399 False 1569.725000 5217 90.896250 476 6200 4 chr7A.!!$F5 5724
17 TraesCS7D01G404000 chr7A 602019694 602024009 4315 False 1079.000000 1583 91.713000 1 5368 5 chr7A.!!$F7 5367
18 TraesCS7D01G404000 chr7A 601465471 601470728 5257 False 1055.933333 2892 90.698333 15 5368 6 chr7A.!!$F6 5353
19 TraesCS7D01G404000 chr7A 600639481 600640685 1204 False 952.000000 952 81.377000 4917 6122 1 chr7A.!!$F1 1205

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
966 1449 1.619827 CCACCACAAACATTGGCAGAT 59.380 47.619 0.00 0.00 37.69 2.90 F
1813 3186 1.076677 GGATATACTCCCTCCGTCCCA 59.923 57.143 0.00 0.00 38.19 4.37 F
2408 3787 0.609406 TGAGGCAGTCTCTACACGCT 60.609 55.000 3.09 0.00 42.86 5.07 F
3031 4437 0.658897 TGCACTTTCCCGAACGAAAC 59.341 50.000 0.00 0.00 0.00 2.78 F
3943 5420 0.474184 ACAGTTACTGGCAGGCTTGT 59.526 50.000 20.34 13.91 35.51 3.16 F
4457 5942 1.839994 TGATGCTAGCAGTAGGGCTTT 59.160 47.619 23.89 2.02 42.71 3.51 F
4945 6456 2.231215 GCCTCTGCTATGTGGTACAG 57.769 55.000 0.00 0.00 34.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1865 3238 0.178970 GCTACTCCCTCCGTCCCATA 60.179 60.000 0.00 0.0 0.00 2.74 R
3201 4607 8.223330 AGCTTCCATCTCTACCAAATATTCATT 58.777 33.333 0.00 0.0 0.00 2.57 R
3943 5420 7.719633 GGAATCTTGACCCTTGTATTTAGCATA 59.280 37.037 0.00 0.0 0.00 3.14 R
4853 6364 0.255890 TAGAAGAGGCAACCCCATGC 59.744 55.000 0.00 0.0 45.67 4.06 R
5435 7030 0.464036 CTATACCGTCAAGCAGGGCA 59.536 55.000 0.00 0.0 32.67 5.36 R
5436 7031 0.750850 TCTATACCGTCAAGCAGGGC 59.249 55.000 0.00 0.0 32.67 5.19 R
6807 11874 0.675208 TTGGTGATGTGGCGCGTAAT 60.675 50.000 8.43 0.0 0.00 1.89 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
334 337 7.378966 TGAACACTAGGTACTGAATGAAGAAG 58.621 38.462 0.00 0.00 41.52 2.85
335 338 7.232737 TGAACACTAGGTACTGAATGAAGAAGA 59.767 37.037 0.00 0.00 41.52 2.87
336 339 7.540474 ACACTAGGTACTGAATGAAGAAGAA 57.460 36.000 0.00 0.00 41.52 2.52
511 750 6.980978 CGTGGTGATAGAGAACAGATAACATT 59.019 38.462 0.00 0.00 0.00 2.71
966 1449 1.619827 CCACCACAAACATTGGCAGAT 59.380 47.619 0.00 0.00 37.69 2.90
1173 1658 6.773200 AGTTGTTTTTAGAGGGAGAAGAAAGG 59.227 38.462 0.00 0.00 0.00 3.11
1314 1801 6.800408 CACAGTCACATCTGATCAAATTTCAC 59.200 38.462 0.00 0.00 38.63 3.18
1795 3168 5.538118 CAGCATATGTAGTTCGTAATGGGA 58.462 41.667 4.29 0.00 0.00 4.37
1797 3170 7.320399 CAGCATATGTAGTTCGTAATGGGATA 58.680 38.462 4.29 0.00 0.00 2.59
1799 3172 9.197306 AGCATATGTAGTTCGTAATGGGATATA 57.803 33.333 4.29 0.00 0.00 0.86
1800 3173 9.245962 GCATATGTAGTTCGTAATGGGATATAC 57.754 37.037 4.29 0.00 0.00 1.47
1803 3176 7.458409 TGTAGTTCGTAATGGGATATACTCC 57.542 40.000 0.00 0.00 44.11 3.85
1812 3185 1.849977 GGATATACTCCCTCCGTCCC 58.150 60.000 0.00 0.00 38.19 4.46
1813 3186 1.076677 GGATATACTCCCTCCGTCCCA 59.923 57.143 0.00 0.00 38.19 4.37
1816 3189 4.571362 GGATATACTCCCTCCGTCCCATAA 60.571 50.000 0.00 0.00 38.19 1.90
1817 3190 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
1818 3191 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
1819 3192 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
1820 3193 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
1823 3196 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
1824 3197 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
1826 3199 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
1827 3200 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
1828 3201 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
1829 3202 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
1830 3203 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
1831 3204 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
1832 3205 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
1833 3206 7.360361 GTCCCATAATATAAGAGCGTTTTTGG 58.640 38.462 0.00 0.00 0.00 3.28
1836 3209 8.287503 CCCATAATATAAGAGCGTTTTTGGTAC 58.712 37.037 0.00 0.00 0.00 3.34
1837 3210 9.052759 CCATAATATAAGAGCGTTTTTGGTACT 57.947 33.333 0.00 0.00 0.00 2.73
1841 3214 6.963049 ATAAGAGCGTTTTTGGTACTAGTG 57.037 37.500 5.39 0.00 0.00 2.74
1842 3215 4.332428 AGAGCGTTTTTGGTACTAGTGT 57.668 40.909 5.39 0.00 0.00 3.55
1843 3216 5.458041 AGAGCGTTTTTGGTACTAGTGTA 57.542 39.130 5.39 0.00 0.00 2.90
1844 3217 5.467705 AGAGCGTTTTTGGTACTAGTGTAG 58.532 41.667 5.39 0.00 0.00 2.74
1845 3218 5.010415 AGAGCGTTTTTGGTACTAGTGTAGT 59.990 40.000 5.39 0.00 42.68 2.73
1847 3220 4.746611 GCGTTTTTGGTACTAGTGTAGTGT 59.253 41.667 5.39 0.00 39.81 3.55
1848 3221 5.107722 GCGTTTTTGGTACTAGTGTAGTGTC 60.108 44.000 5.39 0.00 39.81 3.67
1851 3224 7.010367 CGTTTTTGGTACTAGTGTAGTGTCAAA 59.990 37.037 5.39 10.16 39.81 2.69
1852 3225 8.667463 GTTTTTGGTACTAGTGTAGTGTCAAAA 58.333 33.333 5.39 16.60 42.69 2.44
1854 3227 7.775397 TTGGTACTAGTGTAGTGTCAAAAAC 57.225 36.000 5.39 0.00 39.81 2.43
1855 3228 5.978919 TGGTACTAGTGTAGTGTCAAAAACG 59.021 40.000 5.39 0.00 39.81 3.60
1856 3229 5.979517 GGTACTAGTGTAGTGTCAAAAACGT 59.020 40.000 5.39 0.00 39.81 3.99
1857 3230 6.476706 GGTACTAGTGTAGTGTCAAAAACGTT 59.523 38.462 5.39 0.00 39.81 3.99
1858 3231 6.579491 ACTAGTGTAGTGTCAAAAACGTTC 57.421 37.500 0.00 0.00 37.69 3.95
1859 3232 6.335777 ACTAGTGTAGTGTCAAAAACGTTCT 58.664 36.000 0.00 0.00 37.69 3.01
1860 3233 6.815142 ACTAGTGTAGTGTCAAAAACGTTCTT 59.185 34.615 0.00 0.00 37.69 2.52
1861 3234 7.975616 ACTAGTGTAGTGTCAAAAACGTTCTTA 59.024 33.333 0.00 0.00 37.69 2.10
1862 3235 7.781548 AGTGTAGTGTCAAAAACGTTCTTAT 57.218 32.000 0.00 0.00 0.00 1.73
1863 3236 8.876275 AGTGTAGTGTCAAAAACGTTCTTATA 57.124 30.769 0.00 0.00 0.00 0.98
1864 3237 9.485206 AGTGTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 0.00 0.00 0.00 0.86
1870 3243 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
1871 3244 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
1872 3245 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
1873 3246 8.605746 TCAAAAACGTTCTTATATTATGGGACG 58.394 33.333 0.00 9.33 0.00 4.79
1875 3248 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
1876 3249 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
1877 3250 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
1878 3251 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
1879 3252 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
1880 3253 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2143 3520 1.048601 TCGAAACAGTGGAAGAGGCT 58.951 50.000 0.00 0.00 0.00 4.58
2267 3644 3.008923 TCACCACATCCTGAATGCACTTA 59.991 43.478 0.00 0.00 39.12 2.24
2408 3787 0.609406 TGAGGCAGTCTCTACACGCT 60.609 55.000 3.09 0.00 42.86 5.07
2749 4130 1.473965 GCTAACAGCTGCTATGGCTCA 60.474 52.381 15.27 0.00 38.45 4.26
3027 4433 1.006832 CCTATGCACTTTCCCGAACG 58.993 55.000 0.00 0.00 0.00 3.95
3028 4434 1.404986 CCTATGCACTTTCCCGAACGA 60.405 52.381 0.00 0.00 0.00 3.85
3029 4435 2.343101 CTATGCACTTTCCCGAACGAA 58.657 47.619 0.00 0.00 0.00 3.85
3030 4436 1.600023 ATGCACTTTCCCGAACGAAA 58.400 45.000 0.00 0.00 0.00 3.46
3031 4437 0.658897 TGCACTTTCCCGAACGAAAC 59.341 50.000 0.00 0.00 0.00 2.78
3090 4496 5.683876 TTCTGCTATAGCCTTGAAGTTCT 57.316 39.130 21.84 0.00 41.18 3.01
3368 4799 5.547465 TCATTACACGATTCCTGAAGTTGT 58.453 37.500 0.00 0.00 0.00 3.32
3943 5420 0.474184 ACAGTTACTGGCAGGCTTGT 59.526 50.000 20.34 13.91 35.51 3.16
4457 5942 1.839994 TGATGCTAGCAGTAGGGCTTT 59.160 47.619 23.89 2.02 42.71 3.51
4760 6271 3.395607 AGGGCTATCAACATTATGCCAGA 59.604 43.478 0.00 0.00 41.86 3.86
4945 6456 2.231215 GCCTCTGCTATGTGGTACAG 57.769 55.000 0.00 0.00 34.00 2.74
5156 6667 2.435805 AGCACTTGATGGATATGGACGT 59.564 45.455 0.00 0.00 0.00 4.34
5258 6769 3.489355 TGACATGCAGAAAGACACCAAT 58.511 40.909 0.00 0.00 0.00 3.16
5435 7030 1.142465 CTGGTGGATCTAGCAGGCAAT 59.858 52.381 25.71 0.00 41.28 3.56
5436 7031 1.134007 TGGTGGATCTAGCAGGCAATG 60.134 52.381 6.89 0.00 0.00 2.82
5450 7045 1.973281 CAATGCCCTGCTTGACGGT 60.973 57.895 0.00 0.00 0.00 4.83
5514 7192 2.040278 CCTTTCAGTGACTGGGATTGGA 59.960 50.000 13.33 0.00 31.51 3.53
5909 7675 7.885922 TGGTGAAGTATAAGCAATAAAGGTTCA 59.114 33.333 0.00 0.00 0.00 3.18
5996 7763 3.392616 TGTGGCATTGGTTAAACCCATTT 59.607 39.130 0.00 0.00 37.50 2.32
6157 8005 6.875926 GGATTTCTTTGATTCAATCCAACG 57.124 37.500 9.96 0.00 42.97 4.10
6323 8457 9.701098 ACCATCAATGAATAAAATCATGTATGC 57.299 29.630 0.00 0.00 39.90 3.14
6345 8479 4.708177 CTGTTCTGGTCTTCTCCTTTTGA 58.292 43.478 0.00 0.00 0.00 2.69
6759 11815 7.973944 ACTCATTCAAACTTAGTGAACCAAAAC 59.026 33.333 0.00 0.00 37.80 2.43
6764 11820 8.527567 TCAAACTTAGTGAACCAAAACTTTTG 57.472 30.769 7.21 7.21 0.00 2.44
6768 11824 7.312899 ACTTAGTGAACCAAAACTTTTGACTG 58.687 34.615 14.71 2.40 0.00 3.51
6773 11829 2.831526 ACCAAAACTTTTGACTGGCAGT 59.168 40.909 22.26 22.26 0.00 4.40
6788 11844 4.344102 ACTGGCAGTGTTGAAGTAGACTTA 59.656 41.667 21.37 0.00 36.11 2.24
6790 11846 5.865085 TGGCAGTGTTGAAGTAGACTTATT 58.135 37.500 0.00 0.00 36.11 1.40
6792 11848 5.122396 GGCAGTGTTGAAGTAGACTTATTGG 59.878 44.000 0.00 0.00 36.11 3.16
6807 11874 7.568349 AGACTTATTGGCTAACTTGATGATGA 58.432 34.615 0.00 0.00 27.54 2.92
6818 11885 1.217001 TGATGATGATTACGCGCCAC 58.783 50.000 5.73 0.00 0.00 5.01
6824 11891 1.087202 TGATTACGCGCCACATCACC 61.087 55.000 5.73 0.00 0.00 4.02
6825 11892 1.078778 ATTACGCGCCACATCACCA 60.079 52.632 5.73 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
355 360 3.032265 TGCATGTTCTCCCTAGCTCTA 57.968 47.619 0.00 0.00 0.00 2.43
511 750 1.946984 ACCCTTCCCGTCATGACTTA 58.053 50.000 22.95 5.96 0.00 2.24
1173 1658 9.654663 CTTTTATAGTAGCCCCATGAATACTAC 57.345 37.037 0.00 0.77 34.49 2.73
1314 1801 9.027129 CACCAAACAGCAGAAATATGAAATATG 57.973 33.333 0.00 0.00 38.94 1.78
1795 3168 4.687262 TTATGGGACGGAGGGAGTATAT 57.313 45.455 0.00 0.00 0.00 0.86
1797 3170 3.562108 ATTATGGGACGGAGGGAGTAT 57.438 47.619 0.00 0.00 0.00 2.12
1799 3172 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
1800 3173 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
1801 3174 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
1802 3175 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
1803 3176 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
1804 3177 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
1805 3178 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
1806 3179 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
1807 3180 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
1808 3181 7.012989 ACCAAAAACGCTCTTATATTATGGGAC 59.987 37.037 0.00 0.00 0.00 4.46
1809 3182 7.057894 ACCAAAAACGCTCTTATATTATGGGA 58.942 34.615 0.00 0.00 0.00 4.37
1810 3183 7.272037 ACCAAAAACGCTCTTATATTATGGG 57.728 36.000 0.00 0.00 0.00 4.00
1816 3189 8.255905 ACACTAGTACCAAAAACGCTCTTATAT 58.744 33.333 0.00 0.00 0.00 0.86
1817 3190 7.605449 ACACTAGTACCAAAAACGCTCTTATA 58.395 34.615 0.00 0.00 0.00 0.98
1818 3191 6.461640 ACACTAGTACCAAAAACGCTCTTAT 58.538 36.000 0.00 0.00 0.00 1.73
1819 3192 5.846203 ACACTAGTACCAAAAACGCTCTTA 58.154 37.500 0.00 0.00 0.00 2.10
1820 3193 4.700700 ACACTAGTACCAAAAACGCTCTT 58.299 39.130 0.00 0.00 0.00 2.85
1823 3196 4.986659 CACTACACTAGTACCAAAAACGCT 59.013 41.667 0.00 0.00 37.23 5.07
1824 3197 4.746611 ACACTACACTAGTACCAAAAACGC 59.253 41.667 0.00 0.00 37.23 4.84
1826 3199 7.775397 TTGACACTACACTAGTACCAAAAAC 57.225 36.000 0.00 0.00 37.23 2.43
1827 3200 8.789825 TTTTGACACTACACTAGTACCAAAAA 57.210 30.769 0.00 0.00 41.18 1.94
1828 3201 8.667463 GTTTTTGACACTACACTAGTACCAAAA 58.333 33.333 0.00 12.39 41.71 2.44
1829 3202 7.010367 CGTTTTTGACACTACACTAGTACCAAA 59.990 37.037 0.00 0.00 37.23 3.28
1830 3203 6.476380 CGTTTTTGACACTACACTAGTACCAA 59.524 38.462 0.00 0.00 37.23 3.67
1831 3204 5.978919 CGTTTTTGACACTACACTAGTACCA 59.021 40.000 0.00 0.00 37.23 3.25
1832 3205 5.979517 ACGTTTTTGACACTACACTAGTACC 59.020 40.000 0.00 0.00 37.23 3.34
1833 3206 7.433425 AGAACGTTTTTGACACTACACTAGTAC 59.567 37.037 0.46 0.00 37.23 2.73
1836 3209 6.823678 AGAACGTTTTTGACACTACACTAG 57.176 37.500 0.46 0.00 0.00 2.57
1837 3210 8.876275 ATAAGAACGTTTTTGACACTACACTA 57.124 30.769 13.87 0.00 0.00 2.74
1838 3211 7.781548 ATAAGAACGTTTTTGACACTACACT 57.218 32.000 13.87 0.00 0.00 3.55
1844 3217 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
1845 3218 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
1847 3220 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
1848 3221 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
1851 3224 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
1852 3225 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
1854 3227 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
1855 3228 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
1856 3229 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
1857 3230 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
1858 3231 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
1859 3232 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
1860 3233 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
1861 3234 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
1862 3235 3.816842 GCTACTCCCTCCGTCCCATAATA 60.817 52.174 0.00 0.00 0.00 0.98
1863 3236 2.890814 CTACTCCCTCCGTCCCATAAT 58.109 52.381 0.00 0.00 0.00 1.28
1864 3237 1.756690 GCTACTCCCTCCGTCCCATAA 60.757 57.143 0.00 0.00 0.00 1.90
1865 3238 0.178970 GCTACTCCCTCCGTCCCATA 60.179 60.000 0.00 0.00 0.00 2.74
1869 3242 1.174078 GCTAGCTACTCCCTCCGTCC 61.174 65.000 7.70 0.00 0.00 4.79
1870 3243 0.179012 AGCTAGCTACTCCCTCCGTC 60.179 60.000 17.69 0.00 0.00 4.79
1871 3244 0.466555 CAGCTAGCTACTCCCTCCGT 60.467 60.000 18.86 0.00 0.00 4.69
1872 3245 1.801309 GCAGCTAGCTACTCCCTCCG 61.801 65.000 18.86 2.47 41.15 4.63
1873 3246 2.046108 GCAGCTAGCTACTCCCTCC 58.954 63.158 18.86 0.00 41.15 4.30
2267 3644 3.008375 TGCTTACTGATGAGAGGCACTTT 59.992 43.478 0.00 0.00 41.55 2.66
2332 3711 7.496346 ACACTCCTAGATTAATGAGTTTGGA 57.504 36.000 3.97 0.00 35.97 3.53
2408 3787 2.238521 GAAGCATGTTCCAAGGGTCAA 58.761 47.619 0.00 0.00 0.00 3.18
3029 4435 8.794335 TTAATTAGTGGCAAAAACAAAAGGTT 57.206 26.923 0.00 0.00 42.98 3.50
3030 4436 8.261522 TCTTAATTAGTGGCAAAAACAAAAGGT 58.738 29.630 0.00 0.00 0.00 3.50
3031 4437 8.655651 TCTTAATTAGTGGCAAAAACAAAAGG 57.344 30.769 0.00 0.00 0.00 3.11
3201 4607 8.223330 AGCTTCCATCTCTACCAAATATTCATT 58.777 33.333 0.00 0.00 0.00 2.57
3943 5420 7.719633 GGAATCTTGACCCTTGTATTTAGCATA 59.280 37.037 0.00 0.00 0.00 3.14
4760 6271 9.504708 GACATCATCTCAGATAATTCCTTCATT 57.495 33.333 0.00 0.00 0.00 2.57
4853 6364 0.255890 TAGAAGAGGCAACCCCATGC 59.744 55.000 0.00 0.00 45.67 4.06
5082 6593 6.986250 TGTATGACAGGCTCTCATTATAGTG 58.014 40.000 10.60 0.00 30.76 2.74
5156 6667 5.249163 TCTCTCCAGGTTGATGAAAATCTCA 59.751 40.000 0.00 0.00 38.81 3.27
5202 6713 2.089980 GATGACAATCTTGCCTGCTGT 58.910 47.619 0.00 0.00 0.00 4.40
5435 7030 0.464036 CTATACCGTCAAGCAGGGCA 59.536 55.000 0.00 0.00 32.67 5.36
5436 7031 0.750850 TCTATACCGTCAAGCAGGGC 59.249 55.000 0.00 0.00 32.67 5.19
5437 7032 1.754803 TGTCTATACCGTCAAGCAGGG 59.245 52.381 0.00 0.00 35.97 4.45
5440 7035 4.142315 GGTAGTTGTCTATACCGTCAAGCA 60.142 45.833 0.00 0.00 32.62 3.91
5443 7038 4.158394 GGTGGTAGTTGTCTATACCGTCAA 59.842 45.833 0.00 0.00 43.73 3.18
5445 7040 3.067320 GGGTGGTAGTTGTCTATACCGTC 59.933 52.174 0.00 0.00 43.73 4.79
5446 7041 3.026694 GGGTGGTAGTTGTCTATACCGT 58.973 50.000 0.00 0.00 43.73 4.83
5450 7045 2.034124 GCGGGGTGGTAGTTGTCTATA 58.966 52.381 0.00 0.00 0.00 1.31
5514 7192 4.757149 CGTCAAGAATTTCTCCACCTCTTT 59.243 41.667 0.00 0.00 0.00 2.52
5996 7763 5.223449 AGAAGTCTGGAAACCGATTAACA 57.777 39.130 0.00 0.00 0.00 2.41
6136 7984 5.782047 TGCGTTGGATTGAATCAAAGAAAT 58.218 33.333 7.56 0.00 0.00 2.17
6137 7985 5.193663 TGCGTTGGATTGAATCAAAGAAA 57.806 34.783 7.56 0.00 0.00 2.52
6170 8018 3.728385 AGGACTCAAATCCTCCCAAAG 57.272 47.619 0.00 0.00 46.92 2.77
6323 8457 4.708177 TCAAAAGGAGAAGACCAGAACAG 58.292 43.478 0.00 0.00 0.00 3.16
6345 8479 7.014230 CCAAATAATCCCCACGTTAATCTGAAT 59.986 37.037 0.00 0.00 0.00 2.57
6454 8588 3.119495 AGGTCCATGCAGTTATTTTTCGC 60.119 43.478 0.00 0.00 0.00 4.70
6587 11355 5.105392 AGGAACTGATGTTTTGCAAAGTCAA 60.105 36.000 12.41 0.00 37.18 3.18
6759 11815 3.129287 ACTTCAACACTGCCAGTCAAAAG 59.871 43.478 0.00 0.00 0.00 2.27
6764 11820 3.060602 GTCTACTTCAACACTGCCAGTC 58.939 50.000 0.00 0.00 0.00 3.51
6768 11824 5.122396 CCAATAAGTCTACTTCAACACTGCC 59.878 44.000 0.00 0.00 37.40 4.85
6773 11829 7.676947 AGTTAGCCAATAAGTCTACTTCAACA 58.323 34.615 0.00 0.00 37.40 3.33
6788 11844 6.293626 GCGTAATCATCATCAAGTTAGCCAAT 60.294 38.462 0.00 0.00 0.00 3.16
6790 11846 4.511454 GCGTAATCATCATCAAGTTAGCCA 59.489 41.667 0.00 0.00 0.00 4.75
6792 11848 4.692135 CGCGTAATCATCATCAAGTTAGC 58.308 43.478 0.00 0.00 0.00 3.09
6807 11874 0.675208 TTGGTGATGTGGCGCGTAAT 60.675 50.000 8.43 0.00 0.00 1.89
6818 11885 4.162812 CGGTCGGTTAAATTTTGGTGATG 58.837 43.478 0.00 0.00 0.00 3.07
6824 11891 1.269998 TGGCCGGTCGGTTAAATTTTG 59.730 47.619 11.25 0.00 37.65 2.44
6825 11892 1.542472 CTGGCCGGTCGGTTAAATTTT 59.458 47.619 6.75 0.00 37.65 1.82


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

AutoCloner maintained by Alex Coulton.