Multiple sequence alignment - TraesCS1B01G164300

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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 TraesCS1B01G164300 chr1B 100.000 4103 0 0 1 4103 286714975 286710873 0.000000e+00 7577.0
1 TraesCS1B01G164300 chr1B 100.000 2332 0 0 4382 6713 286710594 286708263 0.000000e+00 4307.0
2 TraesCS1B01G164300 chr1B 96.797 281 8 1 1833 2113 478710593 478710872 1.020000e-127 468.0
3 TraesCS1B01G164300 chr1B 95.833 288 9 3 1833 2120 328141822 328142106 4.740000e-126 462.0
4 TraesCS1B01G164300 chr1B 91.935 62 4 1 4005 4066 60129220 60129160 1.200000e-12 86.1
5 TraesCS1B01G164300 chr1B 91.935 62 4 1 4005 4066 60275527 60275587 1.200000e-12 86.1
6 TraesCS1B01G164300 chr1B 91.935 62 2 3 4007 4067 614503617 614503558 4.310000e-12 84.2
7 TraesCS1B01G164300 chr1B 92.727 55 4 0 4013 4067 675450456 675450402 5.580000e-11 80.5
8 TraesCS1B01G164300 chr1D 97.102 4106 77 12 3 4103 199873309 199869241 0.000000e+00 6885.0
9 TraesCS1B01G164300 chr1D 98.803 2340 14 4 4382 6713 199869046 199866713 0.000000e+00 4154.0
10 TraesCS1B01G164300 chr1D 86.916 321 28 8 457 770 194536143 194535830 1.390000e-91 348.0
11 TraesCS1B01G164300 chr1D 97.484 159 4 0 6429 6587 356185779 356185937 8.580000e-69 272.0
12 TraesCS1B01G164300 chr1D 96.855 159 5 0 6429 6587 285371014 285371172 3.990000e-67 267.0
13 TraesCS1B01G164300 chr1D 95.266 169 7 1 6429 6596 466603296 466603464 3.990000e-67 267.0
14 TraesCS1B01G164300 chr1D 90.805 87 7 1 5856 5941 320589945 320590031 1.530000e-21 115.0
15 TraesCS1B01G164300 chr1D 90.385 52 2 3 4017 4067 405082767 405082816 1.560000e-06 65.8
16 TraesCS1B01G164300 chr1D 100.000 31 0 0 4012 4042 323463627 323463597 2.610000e-04 58.4
17 TraesCS1B01G164300 chr1A 96.175 2013 56 12 4427 6428 252504883 252502881 0.000000e+00 3271.0
18 TraesCS1B01G164300 chr1A 95.018 1987 56 15 2108 4073 252513761 252511797 0.000000e+00 3081.0
19 TraesCS1B01G164300 chr1A 92.508 961 36 12 821 1771 252518200 252517266 0.000000e+00 1343.0
20 TraesCS1B01G164300 chr1A 98.742 159 2 0 6429 6587 586112571 586112413 3.960000e-72 283.0
21 TraesCS1B01G164300 chr1A 95.808 167 7 0 6429 6595 312863771 312863605 3.090000e-68 270.0
22 TraesCS1B01G164300 chr1A 83.448 145 6 2 6585 6713 252502883 252502741 1.180000e-22 119.0
23 TraesCS1B01G164300 chr1A 95.652 46 2 0 1777 1822 252513890 252513845 2.600000e-09 75.0
24 TraesCS1B01G164300 chr6B 97.173 283 7 1 1833 2115 64197583 64197864 1.690000e-130 477.0
25 TraesCS1B01G164300 chr6B 86.646 322 31 7 452 767 407244913 407245228 4.980000e-91 346.0
26 TraesCS1B01G164300 chr6B 93.333 180 9 2 6429 6608 603896884 603896708 5.160000e-66 263.0
27 TraesCS1B01G164300 chr6B 91.860 86 6 1 5857 5941 512188589 512188504 1.180000e-22 119.0
28 TraesCS1B01G164300 chr2D 97.482 278 6 1 1833 2110 241688382 241688106 2.190000e-129 473.0
29 TraesCS1B01G164300 chr2D 86.686 338 32 9 443 773 251930727 251930396 4.950000e-96 363.0
30 TraesCS1B01G164300 chr7D 95.302 298 13 1 1833 2130 429475592 429475888 7.880000e-129 472.0
31 TraesCS1B01G164300 chr7D 86.145 332 33 8 443 767 492604685 492604360 4.980000e-91 346.0
32 TraesCS1B01G164300 chr7D 99.371 159 1 0 6429 6587 52255655 52255813 8.520000e-74 289.0
33 TraesCS1B01G164300 chr7D 98.718 156 2 0 6429 6584 454078709 454078554 1.840000e-70 278.0
34 TraesCS1B01G164300 chr7D 92.778 180 13 0 6429 6608 565469656 565469477 1.860000e-65 261.0
35 TraesCS1B01G164300 chr7D 90.588 85 7 1 5860 5943 612833392 612833308 1.980000e-20 111.0
36 TraesCS1B01G164300 chr7D 89.189 74 7 1 5857 5930 497972656 497972584 2.580000e-14 91.6
37 TraesCS1B01G164300 chr7D 90.909 55 4 1 4013 4067 28398702 28398755 9.340000e-09 73.1
38 TraesCS1B01G164300 chr7D 88.333 60 6 1 4008 4067 380924652 380924594 3.360000e-08 71.3
39 TraesCS1B01G164300 chr5B 97.122 278 7 1 1833 2110 342871819 342872095 1.020000e-127 468.0
40 TraesCS1B01G164300 chr5B 94.558 294 15 1 1833 2126 692693342 692693050 2.850000e-123 453.0
41 TraesCS1B01G164300 chr5B 91.379 58 5 0 4008 4065 306437662 306437605 5.580000e-11 80.5
42 TraesCS1B01G164300 chr3D 96.127 284 10 1 1833 2116 263802734 263802452 4.740000e-126 462.0
43 TraesCS1B01G164300 chr3D 86.687 323 30 8 457 773 204440316 204440001 4.980000e-91 346.0
44 TraesCS1B01G164300 chr3D 96.914 162 5 0 6429 6590 550509438 550509599 8.580000e-69 272.0
45 TraesCS1B01G164300 chr3D 88.506 87 9 1 5857 5942 48851074 48850988 3.310000e-18 104.0
46 TraesCS1B01G164300 chr3D 87.640 89 9 2 5859 5946 399377765 399377852 1.190000e-17 102.0
47 TraesCS1B01G164300 chr3D 92.857 56 4 0 4013 4068 433564296 433564241 1.550000e-11 82.4
48 TraesCS1B01G164300 chr3D 90.909 55 5 0 4013 4067 24872046 24871992 2.600000e-09 75.0
49 TraesCS1B01G164300 chr7A 87.658 316 32 5 458 767 176251515 176251829 1.780000e-95 361.0
50 TraesCS1B01G164300 chr7A 96.386 166 6 0 6429 6594 643187048 643186883 2.390000e-69 274.0
51 TraesCS1B01G164300 chr3A 87.697 317 28 6 457 767 408946458 408946147 6.400000e-95 359.0
52 TraesCS1B01G164300 chr4D 85.970 335 36 7 439 767 401027808 401027479 1.390000e-91 348.0
53 TraesCS1B01G164300 chr4D 96.894 161 5 0 6429 6589 93336842 93336682 3.090000e-68 270.0
54 TraesCS1B01G164300 chr4D 95.266 169 8 0 6429 6597 457481057 457481225 1.110000e-67 268.0
55 TraesCS1B01G164300 chr4D 95.181 166 8 0 6429 6594 423909740 423909575 5.160000e-66 263.0
56 TraesCS1B01G164300 chr4D 95.181 166 7 1 6429 6594 3370923 3371087 1.860000e-65 261.0
57 TraesCS1B01G164300 chr4D 89.247 93 8 2 5854 5944 34699231 34699139 1.530000e-21 115.0
58 TraesCS1B01G164300 chr4D 90.698 86 7 1 5857 5941 459425898 459425983 5.500000e-21 113.0
59 TraesCS1B01G164300 chr4D 90.000 80 5 2 5858 5936 230473164 230473087 4.280000e-17 100.0
60 TraesCS1B01G164300 chr5D 98.765 162 2 0 6429 6590 117350455 117350616 8.520000e-74 289.0
61 TraesCS1B01G164300 chr5D 97.516 161 4 0 6429 6589 386859298 386859458 6.630000e-70 276.0
62 TraesCS1B01G164300 chr5D 97.500 160 4 0 6429 6588 48668972 48669131 2.390000e-69 274.0
63 TraesCS1B01G164300 chr5D 82.353 289 37 8 3686 3971 276311338 276311615 8.700000e-59 239.0
64 TraesCS1B01G164300 chr5D 88.889 54 4 2 4015 4067 343098806 343098858 1.560000e-06 65.8
65 TraesCS1B01G164300 chr6D 98.125 160 3 0 6429 6588 446533384 446533225 5.130000e-71 279.0
66 TraesCS1B01G164300 chr6D 98.113 159 3 0 6429 6587 305359633 305359791 1.840000e-70 278.0
67 TraesCS1B01G164300 chr6D 98.101 158 3 0 6430 6587 460864654 460864497 6.630000e-70 276.0
68 TraesCS1B01G164300 chr6D 96.855 159 5 0 6429 6587 218407368 218407210 3.990000e-67 267.0
69 TraesCS1B01G164300 chr6D 96.855 159 5 0 6429 6587 318765113 318764955 3.990000e-67 267.0
70 TraesCS1B01G164300 chr6D 96.273 161 6 0 6429 6589 104041168 104041328 1.440000e-66 265.0
71 TraesCS1B01G164300 chr6D 96.250 160 6 0 6429 6588 109240476 109240317 5.160000e-66 263.0
72 TraesCS1B01G164300 chr6D 96.226 159 6 0 6429 6587 7482492 7482650 1.860000e-65 261.0
73 TraesCS1B01G164300 chr6D 96.226 159 6 0 6429 6587 307366450 307366608 1.860000e-65 261.0
74 TraesCS1B01G164300 chr6D 88.889 72 5 3 5858 5927 384535005 384535075 1.200000e-12 86.1
75 TraesCS1B01G164300 chr6D 87.500 72 7 2 5863 5932 2894264 2894335 1.550000e-11 82.4
76 TraesCS1B01G164300 chr6D 87.324 71 5 4 3999 4067 90441875 90441807 2.010000e-10 78.7
77 TraesCS1B01G164300 chr6D 87.500 56 5 2 4013 4067 141388867 141388813 5.620000e-06 63.9
78 TraesCS1B01G164300 chr6D 88.462 52 3 3 4017 4067 165527323 165527274 7.270000e-05 60.2
79 TraesCS1B01G164300 chr6D 100.000 31 0 0 4012 4042 33545668 33545698 2.610000e-04 58.4
80 TraesCS1B01G164300 chr5A 93.333 180 10 2 6429 6607 526657797 526657975 1.440000e-66 265.0
81 TraesCS1B01G164300 chr5A 91.071 56 3 2 4013 4067 559075385 559075331 2.600000e-09 75.0
82 TraesCS1B01G164300 chr5A 91.071 56 3 2 4013 4067 559087610 559087556 2.600000e-09 75.0
83 TraesCS1B01G164300 chrUn 96.226 159 6 0 6429 6587 112299375 112299217 1.860000e-65 261.0
84 TraesCS1B01G164300 chrUn 95.597 159 7 0 6429 6587 92483858 92483700 8.640000e-64 255.0
85 TraesCS1B01G164300 chrUn 93.976 166 9 1 6429 6593 24831255 24831420 4.020000e-62 250.0
86 TraesCS1B01G164300 chrUn 93.976 166 9 1 6429 6593 24833773 24833938 4.020000e-62 250.0
87 TraesCS1B01G164300 chrUn 94.969 159 8 0 6429 6587 105244428 105244586 4.020000e-62 250.0
88 TraesCS1B01G164300 chrUn 93.976 166 9 1 6429 6593 212860736 212860901 4.020000e-62 250.0
89 TraesCS1B01G164300 chrUn 94.969 159 8 0 6429 6587 407971341 407971183 4.020000e-62 250.0
90 TraesCS1B01G164300 chrUn 94.375 160 9 0 6429 6588 244963980 244963821 5.200000e-61 246.0
91 TraesCS1B01G164300 chrUn 94.872 156 8 0 6432 6587 12184896 12184741 1.870000e-60 244.0
92 TraesCS1B01G164300 chrUn 94.340 159 9 0 6429 6587 28615965 28616123 1.870000e-60 244.0
93 TraesCS1B01G164300 chrUn 94.340 159 9 0 6429 6587 70231874 70231716 1.870000e-60 244.0
94 TraesCS1B01G164300 chrUn 89.529 191 17 3 6429 6618 92777887 92777699 8.700000e-59 239.0
95 TraesCS1B01G164300 chrUn 86.813 91 10 2 5857 5945 39577913 39577823 4.280000e-17 100.0
96 TraesCS1B01G164300 chrUn 90.698 43 4 0 4024 4066 450225570 450225528 2.610000e-04 58.4
97 TraesCS1B01G164300 chr2B 92.941 85 5 1 5858 5941 754008534 754008450 9.140000e-24 122.0
98 TraesCS1B01G164300 chr6A 91.860 86 6 1 5857 5941 64260789 64260704 1.180000e-22 119.0
99 TraesCS1B01G164300 chr6A 88.525 61 3 4 4008 4067 68625737 68625680 3.360000e-08 71.3
100 TraesCS1B01G164300 chr4A 88.421 95 7 4 5854 5944 567678251 567678345 1.980000e-20 111.0
101 TraesCS1B01G164300 chr4A 94.643 56 3 0 4011 4066 346858293 346858238 3.330000e-13 87.9


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 TraesCS1B01G164300 chr1B 286708263 286714975 6712 True 5942.000000 7577 100.000000 1 6713 2 chr1B.!!$R4 6712
1 TraesCS1B01G164300 chr1D 199866713 199873309 6596 True 5519.500000 6885 97.952500 3 6713 2 chr1D.!!$R3 6710
2 TraesCS1B01G164300 chr1A 252502741 252504883 2142 True 1695.000000 3271 89.811500 4427 6713 2 chr1A.!!$R3 2286
3 TraesCS1B01G164300 chr1A 252511797 252518200 6403 True 1499.666667 3081 94.392667 821 4073 3 chr1A.!!$R4 3252
4 TraesCS1B01G164300 chrUn 24831255 24833938 2683 False 250.000000 250 93.976000 6429 6593 2 chrUn.!!$F4 164

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
358 361 0.310543 ATTGCATTGCACACGAACGT 59.689 45.000 11.66 0.0 38.71 3.99 F
423 426 0.998928 ATGTGCCAGGTGGTCCAATA 59.001 50.000 0.00 0.0 37.57 1.90 F
2053 5175 0.392461 TCGCCAAGCCTATCACAACC 60.392 55.000 0.00 0.0 0.00 3.77 F
2055 5177 0.034089 GCCAAGCCTATCACAACCCT 60.034 55.000 0.00 0.0 0.00 4.34 F
2357 5694 0.675083 TGAAGACTCGTGCGGGTTAA 59.325 50.000 0.00 0.0 0.00 2.01 F
3671 7011 4.389374 GCTTAGGGCATGCTTGTTATAGA 58.611 43.478 18.92 0.0 41.35 1.98 F
4793 8137 3.011032 AGAAAGATGGCAGAAATGGAGGT 59.989 43.478 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2053 5175 0.688087 AGCCCGAGTAAAGGAGGAGG 60.688 60.000 0.00 0.0 0.00 4.30 R
2055 5177 0.902531 CAAGCCCGAGTAAAGGAGGA 59.097 55.000 0.00 0.0 0.00 3.71 R
3740 7080 0.731417 CTCCAATCTTTCAGCCGCAG 59.269 55.000 0.00 0.0 0.00 5.18 R
3741 7081 1.308069 GCTCCAATCTTTCAGCCGCA 61.308 55.000 0.00 0.0 0.00 5.69 R
3773 7113 2.213499 GCTACAGCGCATCTACCAAAT 58.787 47.619 11.47 0.0 0.00 2.32 R
5639 8983 6.922957 TGTGCCAAAAGCTCATTTTACTAAAG 59.077 34.615 0.00 0.0 44.23 1.85 R
6246 9594 1.269448 GTGTTCCCGATTGCAACACAT 59.731 47.619 0.00 0.0 46.11 3.21 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
30 31 2.840102 CTGGACTAGGCGGGGGAG 60.840 72.222 0.00 0.00 0.00 4.30
128 130 4.160635 GTGCGACCGGCCGAAATG 62.161 66.667 30.73 12.89 42.61 2.32
220 222 2.365941 AGAAAGATAGGTAGAAGGCGGC 59.634 50.000 0.00 0.00 0.00 6.53
226 228 2.398252 AGGTAGAAGGCGGCTAAAAC 57.602 50.000 13.71 10.40 0.00 2.43
233 235 0.328258 AGGCGGCTAAAACCAGTCAT 59.672 50.000 11.03 0.00 0.00 3.06
318 321 2.279741 TCTCATATCGTTTGGCAGCAC 58.720 47.619 0.00 0.00 0.00 4.40
321 324 2.816672 TCATATCGTTTGGCAGCACAAA 59.183 40.909 0.00 0.00 37.96 2.83
322 325 2.987413 TATCGTTTGGCAGCACAAAG 57.013 45.000 8.74 5.09 40.67 2.77
323 326 0.318955 ATCGTTTGGCAGCACAAAGC 60.319 50.000 8.74 4.90 40.67 3.51
357 360 0.976963 GATTGCATTGCACACGAACG 59.023 50.000 11.66 0.00 38.71 3.95
358 361 0.310543 ATTGCATTGCACACGAACGT 59.689 45.000 11.66 0.00 38.71 3.99
423 426 0.998928 ATGTGCCAGGTGGTCCAATA 59.001 50.000 0.00 0.00 37.57 1.90
486 489 6.729690 AGGGTTCAATTCAAAAATCTCACA 57.270 33.333 0.00 0.00 0.00 3.58
499 502 8.567948 TCAAAAATCTCACAAACCAAGATAGAC 58.432 33.333 0.00 0.00 0.00 2.59
503 506 6.769134 TCTCACAAACCAAGATAGACGATA 57.231 37.500 0.00 0.00 0.00 2.92
514 517 6.986817 CCAAGATAGACGATAAGTGGTGAAAT 59.013 38.462 0.00 0.00 0.00 2.17
516 519 9.529325 CAAGATAGACGATAAGTGGTGAAATAA 57.471 33.333 0.00 0.00 0.00 1.40
562 565 6.363357 ACTCAATTAATGCGCTTGTTTTCTTC 59.637 34.615 9.73 0.00 0.00 2.87
623 626 6.362210 TGCATGCATAAAGTACAGTACATG 57.638 37.500 18.46 8.93 37.35 3.21
629 632 8.432110 TGCATAAAGTACAGTACATGTATTGG 57.568 34.615 26.36 14.20 45.94 3.16
631 634 9.537192 GCATAAAGTACAGTACATGTATTGGTA 57.463 33.333 26.36 17.39 45.94 3.25
692 695 9.602568 TGCACCTTAAAATCTTAACGTATGATA 57.397 29.630 0.00 0.00 0.00 2.15
800 804 2.033801 ACGTTGTAGGATTATCGGACGG 59.966 50.000 0.00 0.00 33.95 4.79
1179 1185 3.771160 GAGGACGATGGCGGTGGT 61.771 66.667 0.00 0.00 43.17 4.16
1401 1413 3.088044 GACGACGACGACGAGGAT 58.912 61.111 25.15 3.47 42.66 3.24
1402 1414 1.296722 GACGACGACGACGAGGATG 60.297 63.158 25.15 1.27 42.66 3.51
1403 1415 1.690283 GACGACGACGACGAGGATGA 61.690 60.000 25.15 0.00 42.66 2.92
1404 1416 1.296722 CGACGACGACGAGGATGAC 60.297 63.158 15.32 0.00 42.66 3.06
1405 1417 1.296722 GACGACGACGAGGATGACG 60.297 63.158 15.32 0.00 42.66 4.35
1406 1418 1.690283 GACGACGACGAGGATGACGA 61.690 60.000 15.32 0.00 42.66 4.20
1407 1419 1.296722 CGACGACGAGGATGACGAC 60.297 63.158 0.00 0.00 42.66 4.34
1409 1421 1.690283 GACGACGAGGATGACGACGA 61.690 60.000 16.55 0.00 46.85 4.20
1410 1422 1.296722 CGACGAGGATGACGACGAC 60.297 63.158 0.00 0.00 46.85 4.34
1411 1423 1.296722 GACGAGGATGACGACGACG 60.297 63.158 5.58 5.58 45.75 5.12
1412 1424 1.690283 GACGAGGATGACGACGACGA 61.690 60.000 15.32 0.00 42.66 4.20
1735 1755 7.611467 TGTTCTGCATGGTGTTATTCTAAGAAT 59.389 33.333 0.00 0.00 0.00 2.40
1811 1831 4.083110 CCAACTCTAGCCATGTTCAAACAG 60.083 45.833 1.69 0.00 43.04 3.16
1825 1845 4.916983 TCAAACAGAATGAGTTGTTGGG 57.083 40.909 0.00 0.00 39.69 4.12
1828 1848 5.598005 TCAAACAGAATGAGTTGTTGGGATT 59.402 36.000 0.00 0.00 39.69 3.01
2053 5175 0.392461 TCGCCAAGCCTATCACAACC 60.392 55.000 0.00 0.00 0.00 3.77
2055 5177 0.034089 GCCAAGCCTATCACAACCCT 60.034 55.000 0.00 0.00 0.00 4.34
2066 5188 2.986050 TCACAACCCTCCTCCTTTACT 58.014 47.619 0.00 0.00 0.00 2.24
2154 5473 3.301794 TGATGATGCTGGCCTTACAAT 57.698 42.857 3.32 0.00 0.00 2.71
2301 5638 3.797256 GTCGAATATCAACTAGCGTGCTT 59.203 43.478 0.00 0.00 0.00 3.91
2349 5686 3.774066 TGTGATGCTATGAAGACTCGTG 58.226 45.455 0.00 0.00 0.00 4.35
2357 5694 0.675083 TGAAGACTCGTGCGGGTTAA 59.325 50.000 0.00 0.00 0.00 2.01
3671 7011 4.389374 GCTTAGGGCATGCTTGTTATAGA 58.611 43.478 18.92 0.00 41.35 1.98
3782 7122 4.780815 CCAAGATACAGGCATTTGGTAGA 58.219 43.478 0.00 0.00 34.88 2.59
4554 7898 7.038302 TGGGTCTACTGTTATCTTGTGAATCTT 60.038 37.037 0.00 0.00 0.00 2.40
4712 8056 5.468540 ACGATCTGCCTAATAACTATGCA 57.531 39.130 0.00 0.00 31.26 3.96
4793 8137 3.011032 AGAAAGATGGCAGAAATGGAGGT 59.989 43.478 0.00 0.00 0.00 3.85
5685 9029 5.227805 CACAACAATGTTCTGTTTTCTGACG 59.772 40.000 0.00 0.00 37.43 4.35
6246 9594 0.608856 CTTGGTATGCCTGTGTGCCA 60.609 55.000 0.16 0.00 35.27 4.92
6338 9689 9.366513 GACGTCTTACATTTGTTTAAGACTTTC 57.633 33.333 17.70 12.60 43.55 2.62
6355 9706 3.199946 ACTTTCAGTTCACTGTCCTTGGA 59.800 43.478 6.84 0.00 44.12 3.53
6601 12470 6.492772 CGGAGGGAGTATTTACTTGGTAGTAT 59.507 42.308 0.00 0.00 36.76 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.664835 ATCTCCCCCGCCTAGTCCAG 62.665 65.000 0.00 0.00 0.00 3.86
30 31 1.950909 TCAAACACGTGTTCCCCAATC 59.049 47.619 32.36 0.00 37.25 2.67
137 139 1.143183 ACTAATAGGCGCCGGTGTG 59.857 57.895 23.20 15.11 0.00 3.82
138 140 1.143183 CACTAATAGGCGCCGGTGT 59.857 57.895 23.20 13.92 0.00 4.16
192 194 7.207383 GCCTTCTACCTATCTTTCTTCTCTTC 58.793 42.308 0.00 0.00 0.00 2.87
242 245 8.519526 TCGCCAAAAAGAGTTATTTATCACATT 58.480 29.630 0.00 0.00 0.00 2.71
301 304 2.917701 TTGTGCTGCCAAACGATATG 57.082 45.000 0.00 0.00 0.00 1.78
303 306 1.068610 GCTTTGTGCTGCCAAACGATA 60.069 47.619 10.79 0.00 38.95 2.92
318 321 5.571784 ATCATGTAGGTGAATGTGCTTTG 57.428 39.130 0.00 0.00 0.00 2.77
321 324 3.379372 GCAATCATGTAGGTGAATGTGCT 59.621 43.478 0.00 0.00 34.39 4.40
322 325 3.129113 TGCAATCATGTAGGTGAATGTGC 59.871 43.478 0.00 0.00 36.14 4.57
323 326 4.968812 TGCAATCATGTAGGTGAATGTG 57.031 40.909 0.00 0.00 32.78 3.21
324 327 5.680408 GCAATGCAATCATGTAGGTGAATGT 60.680 40.000 0.00 0.00 32.78 2.71
325 328 4.743151 GCAATGCAATCATGTAGGTGAATG 59.257 41.667 0.00 0.00 33.23 2.67
326 329 4.403113 TGCAATGCAATCATGTAGGTGAAT 59.597 37.500 5.01 0.00 34.76 2.57
327 330 3.762823 TGCAATGCAATCATGTAGGTGAA 59.237 39.130 5.01 0.00 34.76 3.18
357 360 3.135895 ACATAGGTGTAGCATTACCCCAC 59.864 47.826 0.00 0.00 36.63 4.61
358 361 3.389866 ACATAGGTGTAGCATTACCCCA 58.610 45.455 0.00 0.00 36.63 4.96
410 413 5.245977 ACCTCAAATTTTATTGGACCACCTG 59.754 40.000 0.00 0.00 37.04 4.00
464 467 7.254761 GGTTTGTGAGATTTTTGAATTGAACCC 60.255 37.037 0.00 0.00 0.00 4.11
467 470 8.783833 TTGGTTTGTGAGATTTTTGAATTGAA 57.216 26.923 0.00 0.00 0.00 2.69
486 489 6.070995 TCACCACTTATCGTCTATCTTGGTTT 60.071 38.462 0.00 0.00 33.77 3.27
516 519 8.715191 TGAGTGATTTTGCAAACTACAAAAAT 57.285 26.923 12.39 0.00 46.67 1.82
525 528 6.733280 CGCATTAATTGAGTGATTTTGCAAAC 59.267 34.615 12.39 0.37 31.65 2.93
728 731 8.936787 TCCAGTTTACGGGGATTATCTTAATTA 58.063 33.333 0.00 0.00 0.00 1.40
731 734 6.811634 TCCAGTTTACGGGGATTATCTTAA 57.188 37.500 0.00 0.00 0.00 1.85
733 736 5.703730 TTCCAGTTTACGGGGATTATCTT 57.296 39.130 0.00 0.00 0.00 2.40
740 744 1.626825 CTCCTTTCCAGTTTACGGGGA 59.373 52.381 0.00 0.00 0.00 4.81
744 748 2.302157 ACTCCCTCCTTTCCAGTTTACG 59.698 50.000 0.00 0.00 0.00 3.18
751 755 3.338824 TCCTAACTACTCCCTCCTTTCCA 59.661 47.826 0.00 0.00 0.00 3.53
1179 1185 4.041762 GGGGGTCCGACAATGGCA 62.042 66.667 0.00 0.00 0.00 4.92
1298 1304 3.812019 CGTCCTCGTCCTCCACCG 61.812 72.222 0.00 0.00 0.00 4.94
1398 1410 2.963498 TATCATCGTCGTCGTCATCC 57.037 50.000 1.33 0.00 38.33 3.51
1399 1411 3.120304 TCCATATCATCGTCGTCGTCATC 60.120 47.826 1.33 0.00 38.33 2.92
1400 1412 2.812011 TCCATATCATCGTCGTCGTCAT 59.188 45.455 1.33 0.00 38.33 3.06
1401 1413 2.215196 TCCATATCATCGTCGTCGTCA 58.785 47.619 1.33 0.00 38.33 4.35
1402 1414 2.963498 TCCATATCATCGTCGTCGTC 57.037 50.000 1.33 0.00 38.33 4.20
1403 1415 2.812011 TCATCCATATCATCGTCGTCGT 59.188 45.455 1.33 0.00 38.33 4.34
1404 1416 3.471495 TCATCCATATCATCGTCGTCG 57.529 47.619 0.00 0.00 38.55 5.12
1405 1417 4.986622 TCATCATCCATATCATCGTCGTC 58.013 43.478 0.00 0.00 0.00 4.20
1406 1418 5.126061 TCATCATCATCCATATCATCGTCGT 59.874 40.000 0.00 0.00 0.00 4.34
1407 1419 5.585390 TCATCATCATCCATATCATCGTCG 58.415 41.667 0.00 0.00 0.00 5.12
1408 1420 6.424207 CCATCATCATCATCCATATCATCGTC 59.576 42.308 0.00 0.00 0.00 4.20
1409 1421 6.289064 CCATCATCATCATCCATATCATCGT 58.711 40.000 0.00 0.00 0.00 3.73
1410 1422 5.701290 CCCATCATCATCATCCATATCATCG 59.299 44.000 0.00 0.00 0.00 3.84
1411 1423 6.004574 CCCCATCATCATCATCCATATCATC 58.995 44.000 0.00 0.00 0.00 2.92
1412 1424 5.674958 TCCCCATCATCATCATCCATATCAT 59.325 40.000 0.00 0.00 0.00 2.45
1735 1755 6.869913 CGGTATGTAACACTGGTAGAGAAAAA 59.130 38.462 0.00 0.00 0.00 1.94
1811 1831 3.940209 TGCAATCCCAACAACTCATTC 57.060 42.857 0.00 0.00 0.00 2.67
1825 1845 3.825328 ACTAGGATTGGGTGATGCAATC 58.175 45.455 0.00 0.00 45.83 2.67
1828 1848 3.384168 AGTACTAGGATTGGGTGATGCA 58.616 45.455 0.00 0.00 0.00 3.96
2053 5175 0.688087 AGCCCGAGTAAAGGAGGAGG 60.688 60.000 0.00 0.00 0.00 4.30
2055 5177 0.902531 CAAGCCCGAGTAAAGGAGGA 59.097 55.000 0.00 0.00 0.00 3.71
2301 5638 3.230134 CACCTTTGAAGATCACCCCAAA 58.770 45.455 0.00 0.00 0.00 3.28
2349 5686 4.428615 TGAAACTAGCAATTTAACCCGC 57.571 40.909 0.00 0.00 0.00 6.13
3538 6878 0.833834 AGAGTATGGCGGCATAGGCT 60.834 55.000 29.82 24.72 40.87 4.58
3739 7079 1.138247 CCAATCTTTCAGCCGCAGC 59.862 57.895 0.00 0.00 40.32 5.25
3740 7080 0.731417 CTCCAATCTTTCAGCCGCAG 59.269 55.000 0.00 0.00 0.00 5.18
3741 7081 1.308069 GCTCCAATCTTTCAGCCGCA 61.308 55.000 0.00 0.00 0.00 5.69
3773 7113 2.213499 GCTACAGCGCATCTACCAAAT 58.787 47.619 11.47 0.00 0.00 2.32
4554 7898 7.812690 ATGCTGCAGTTCTTATCATTATCAA 57.187 32.000 16.64 0.00 0.00 2.57
4712 8056 7.663081 TCTGAACTAAATGAAGCATTTGTCTCT 59.337 33.333 13.90 0.00 42.91 3.10
5639 8983 6.922957 TGTGCCAAAAGCTCATTTTACTAAAG 59.077 34.615 0.00 0.00 44.23 1.85
5685 9029 2.541762 GTCGCTGCATTAGATTCACTCC 59.458 50.000 0.00 0.00 0.00 3.85
6246 9594 1.269448 GTGTTCCCGATTGCAACACAT 59.731 47.619 0.00 0.00 46.11 3.21
6355 9706 8.507249 GCATTCGCTCTGGATTAATAACTAATT 58.493 33.333 0.00 0.00 30.27 1.40
6421 9772 9.139734 ACTTATATTTAGGAACGGAGTACATGA 57.860 33.333 0.00 0.00 45.00 3.07
6422 9773 9.408069 GACTTATATTTAGGAACGGAGTACATG 57.592 37.037 0.00 0.00 45.00 3.21
6423 9774 9.364653 AGACTTATATTTAGGAACGGAGTACAT 57.635 33.333 0.00 0.00 45.00 2.29
6424 9775 8.757982 AGACTTATATTTAGGAACGGAGTACA 57.242 34.615 0.00 0.00 45.00 2.90


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

AutoCloner maintained by Alex Coulton.