Multiple sequence alignment - TraesCS3B01G241800

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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 TraesCS3B01G241800 chr3B 100.000 4415 0 0 1947 6361 381754095 381758509 0.000000e+00 8154.0
1 TraesCS3B01G241800 chr3B 100.000 1568 0 0 1 1568 381752149 381753716 0.000000e+00 2896.0
2 TraesCS3B01G241800 chr3B 100.000 672 0 0 6670 7341 381758818 381759489 0.000000e+00 1242.0
3 TraesCS3B01G241800 chr3B 91.398 93 7 1 2610 2702 228206183 228206274 7.730000e-25 126.0
4 TraesCS3B01G241800 chr3B 87.838 74 9 0 2904 2977 707251945 707252018 3.650000e-13 87.9
5 TraesCS3B01G241800 chr3B 100.000 44 0 0 6996 7039 381759102 381759145 1.700000e-11 82.4
6 TraesCS3B01G241800 chr3B 100.000 44 0 0 6954 6997 381759144 381759187 1.700000e-11 82.4
7 TraesCS3B01G241800 chr3D 95.609 4486 68 24 1947 6361 289102997 289107424 0.000000e+00 7073.0
8 TraesCS3B01G241800 chr3D 95.707 1584 50 6 1 1568 289101309 289102890 0.000000e+00 2532.0
9 TraesCS3B01G241800 chr3D 97.806 319 7 0 6679 6997 289107542 289107860 1.080000e-152 551.0
10 TraesCS3B01G241800 chr3D 91.908 346 27 1 6996 7341 289107817 289108161 3.980000e-132 483.0
11 TraesCS3B01G241800 chr3D 91.954 87 7 0 2613 2699 381989158 381989072 1.000000e-23 122.0
12 TraesCS3B01G241800 chr3A 94.371 3837 104 34 2595 6361 379821586 379825380 0.000000e+00 5786.0
13 TraesCS3B01G241800 chr3A 96.883 738 17 4 836 1568 379819737 379820473 0.000000e+00 1230.0
14 TraesCS3B01G241800 chr3A 96.206 659 17 4 1947 2600 379820894 379821549 0.000000e+00 1072.0
15 TraesCS3B01G241800 chr3A 88.208 865 68 14 1 842 379818716 379819569 0.000000e+00 1002.0
16 TraesCS3B01G241800 chr3A 95.000 140 6 1 6678 6817 379825608 379825746 1.240000e-52 219.0
17 TraesCS3B01G241800 chr3A 83.770 191 29 2 4190 4378 384188712 384188522 5.850000e-41 180.0
18 TraesCS3B01G241800 chr3A 94.595 74 4 0 6818 6891 379825785 379825858 1.670000e-21 115.0
19 TraesCS3B01G241800 chr3A 95.556 45 1 1 6919 6963 379825851 379825894 3.670000e-08 71.3
20 TraesCS3B01G241800 chr6D 75.479 1097 179 51 3373 4413 127485237 127484175 3.120000e-123 453.0
21 TraesCS3B01G241800 chr6D 80.300 467 62 18 3006 3458 157159002 157158552 7.100000e-85 326.0
22 TraesCS3B01G241800 chr6D 86.503 163 22 0 3571 3733 157158565 157158403 5.850000e-41 180.0
23 TraesCS3B01G241800 chr6D 81.548 168 23 8 4684 4845 415457732 415457567 1.660000e-26 132.0
24 TraesCS3B01G241800 chr2B 80.769 598 68 24 3111 3689 398710646 398710077 2.450000e-114 424.0
25 TraesCS3B01G241800 chr2B 79.630 486 64 16 3949 4413 398709888 398709417 4.270000e-82 316.0
26 TraesCS3B01G241800 chr2B 94.118 85 5 0 2614 2698 723392895 723392979 5.980000e-26 130.0
27 TraesCS3B01G241800 chr2B 78.431 204 37 6 4638 4837 793184226 793184426 7.730000e-25 126.0
28 TraesCS3B01G241800 chr2B 91.209 91 8 0 2607 2697 723392985 723392895 2.780000e-24 124.0
29 TraesCS3B01G241800 chr2B 79.286 140 24 5 4707 4843 198641627 198641490 7.840000e-15 93.5
30 TraesCS3B01G241800 chr6B 82.077 491 47 19 2984 3436 184357346 184357833 1.490000e-101 381.0
31 TraesCS3B01G241800 chr6B 78.905 493 66 23 2984 3460 279923180 279922710 4.310000e-77 300.0
32 TraesCS3B01G241800 chr6B 80.669 269 37 3 3400 3668 313173925 313174178 2.090000e-45 195.0
33 TraesCS3B01G241800 chr6B 83.333 108 14 3 4738 4843 349465624 349465729 6.060000e-16 97.1
34 TraesCS3B01G241800 chr6A 80.694 461 60 15 3062 3505 521859975 521860423 1.530000e-86 331.0
35 TraesCS3B01G241800 chr6A 79.579 475 63 21 2996 3454 211713891 211714347 7.150000e-80 309.0
36 TraesCS3B01G241800 chr6A 82.264 265 39 4 3455 3715 521860306 521860566 9.590000e-54 222.0
37 TraesCS3B01G241800 chr6A 86.093 151 21 0 3571 3721 211714338 211714488 5.890000e-36 163.0
38 TraesCS3B01G241800 chr6A 88.406 69 6 2 2956 3024 594466333 594466267 1.700000e-11 82.4
39 TraesCS3B01G241800 chr7A 78.244 501 78 17 3935 4413 138179914 138180405 7.200000e-75 292.0
40 TraesCS3B01G241800 chr7A 76.484 455 61 25 3956 4386 155509802 155509370 9.650000e-49 206.0
41 TraesCS3B01G241800 chr7A 86.614 127 14 2 2905 3029 25118235 25118110 3.570000e-28 137.0
42 TraesCS3B01G241800 chr7A 91.111 90 8 0 2610 2699 562274916 562275005 1.000000e-23 122.0
43 TraesCS3B01G241800 chr7A 85.185 81 12 0 2903 2983 25118326 25118246 4.720000e-12 84.2
44 TraesCS3B01G241800 chr4A 77.064 436 78 14 3976 4396 585593956 585593528 1.590000e-56 231.0
45 TraesCS3B01G241800 chr4A 89.333 75 8 0 2903 2977 175216401 175216327 2.180000e-15 95.3
46 TraesCS3B01G241800 chr2A 76.765 439 74 19 3976 4396 195742385 195741957 3.450000e-53 220.0
47 TraesCS3B01G241800 chr2A 77.231 325 69 5 7019 7341 496668747 496669068 1.260000e-42 185.0
48 TraesCS3B01G241800 chr2A 91.011 89 6 2 2609 2696 79308139 79308226 1.290000e-22 119.0
49 TraesCS3B01G241800 chr7D 80.464 302 44 9 3400 3689 83752412 83752710 4.460000e-52 217.0
50 TraesCS3B01G241800 chr7D 78.125 352 46 22 2919 3262 10926916 10927244 2.090000e-45 195.0
51 TraesCS3B01G241800 chr7D 80.545 257 44 3 3415 3668 586743472 586743725 7.520000e-45 193.0
52 TraesCS3B01G241800 chr7D 82.883 111 14 5 2921 3029 578797054 578796947 2.180000e-15 95.3
53 TraesCS3B01G241800 chr4B 75.105 478 71 18 3208 3666 262827743 262828191 5.850000e-41 180.0
54 TraesCS3B01G241800 chr1B 81.604 212 33 5 3546 3751 667439319 667439530 3.520000e-38 171.0
55 TraesCS3B01G241800 chr1B 81.429 210 26 5 3402 3602 443991237 443991032 7.620000e-35 159.0
56 TraesCS3B01G241800 chr1B 87.705 122 13 2 2903 3024 487173045 487172926 2.760000e-29 141.0
57 TraesCS3B01G241800 chr1D 76.000 375 60 13 4044 4399 139903054 139903417 4.560000e-37 167.0
58 TraesCS3B01G241800 chr1D 80.220 182 34 2 4661 4841 246946780 246946600 1.280000e-27 135.0
59 TraesCS3B01G241800 chr5A 76.205 332 56 13 3290 3602 85857460 85857133 3.550000e-33 154.0
60 TraesCS3B01G241800 chr5A 82.895 76 11 2 72 146 830722 830648 4.750000e-07 67.6
61 TraesCS3B01G241800 chr1A 81.921 177 23 9 4685 4854 267143269 267143095 2.760000e-29 141.0
62 TraesCS3B01G241800 chr1A 89.855 69 5 2 2962 3029 463196979 463196912 3.650000e-13 87.9
63 TraesCS3B01G241800 chr5D 91.765 85 7 0 2614 2698 252217192 252217276 1.290000e-22 119.0
64 TraesCS3B01G241800 chr5D 94.444 36 2 0 2568 2603 128641814 128641779 1.000000e-03 56.5
65 TraesCS3B01G241800 chr2D 76.395 233 40 13 4619 4844 208844155 208844379 2.170000e-20 111.0
66 TraesCS3B01G241800 chr2D 86.667 75 10 0 2902 2976 295898508 295898582 4.720000e-12 84.2
67 TraesCS3B01G241800 chrUn 88.406 69 7 1 2956 3024 389438364 389438431 1.700000e-11 82.4
68 TraesCS3B01G241800 chrUn 88.406 69 7 1 2956 3024 415837427 415837494 1.700000e-11 82.4


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 TraesCS3B01G241800 chr3B 381752149 381759489 7340 False 2491.360000 8154 100.000000 1 7341 5 chr3B.!!$F3 7340
1 TraesCS3B01G241800 chr3D 289101309 289108161 6852 False 2659.750000 7073 95.257500 1 7341 4 chr3D.!!$F1 7340
2 TraesCS3B01G241800 chr3A 379818716 379825894 7178 False 1356.471429 5786 94.402714 1 6963 7 chr3A.!!$F1 6962
3 TraesCS3B01G241800 chr6D 127484175 127485237 1062 True 453.000000 453 75.479000 3373 4413 1 chr6D.!!$R1 1040
4 TraesCS3B01G241800 chr6D 157158403 157159002 599 True 253.000000 326 83.401500 3006 3733 2 chr6D.!!$R3 727
5 TraesCS3B01G241800 chr2B 398709417 398710646 1229 True 370.000000 424 80.199500 3111 4413 2 chr2B.!!$R3 1302
6 TraesCS3B01G241800 chr6A 521859975 521860566 591 False 276.500000 331 81.479000 3062 3715 2 chr6A.!!$F2 653
7 TraesCS3B01G241800 chr6A 211713891 211714488 597 False 236.000000 309 82.836000 2996 3721 2 chr6A.!!$F1 725

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
446 450 0.319641 GAGTCTTGTTCTTCGCGGGT 60.320 55.000 6.13 0.0 0.00 5.28 F
649 672 1.447314 CGGGGTTACTTGTCGCCTC 60.447 63.158 0.00 0.0 35.04 4.70 F
650 673 1.447314 GGGGTTACTTGTCGCCTCG 60.447 63.158 0.00 0.0 34.49 4.63 F
752 775 1.621814 CCTCCCTAGACACAACCGAAA 59.378 52.381 0.00 0.0 0.00 3.46 F
871 1081 2.362369 CCGCTGGTCTGGGACTGAT 61.362 63.158 0.00 0.0 38.85 2.90 F
2640 2964 3.071479 TCTGTCCCAAAATAAGTGTCGC 58.929 45.455 0.00 0.0 0.00 5.19 F
3685 4122 1.002134 CGTTGCACCCATTCCTCCT 60.002 57.895 0.00 0.0 0.00 3.69 F
4066 4662 0.322366 TCCTCGCAATGACAATGGCA 60.322 50.000 0.00 0.0 31.44 4.92 F
5847 6475 2.094390 TGCACTCAGGTAATACCGTCAC 60.094 50.000 3.47 0.0 44.90 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2011 2270 2.004583 TAACCTCAATTGGCTCGTCG 57.995 50.000 5.42 0.00 0.00 5.12 R
2105 2364 2.026169 TCCACTGATGACTAGAGACGGT 60.026 50.000 0.00 0.00 0.00 4.83 R
2106 2365 2.644676 TCCACTGATGACTAGAGACGG 58.355 52.381 0.00 0.00 0.00 4.79 R
2621 2945 2.811431 CAGCGACACTTATTTTGGGACA 59.189 45.455 0.00 0.00 0.00 4.02 R
2758 3083 0.097674 GCAAGAGCAATGCACTACGG 59.902 55.000 8.35 1.42 43.29 4.02 R
3873 4355 0.666374 TGTCGAGCTTTGTCACGAGA 59.334 50.000 0.00 0.00 35.52 4.04 R
5564 6192 2.597455 CCATTGTTCCAGGTCCTGTTT 58.403 47.619 17.85 0.00 0.00 2.83 R
5850 6478 0.514255 CCAGTGCATCGTGTTGTGAG 59.486 55.000 0.00 0.00 0.00 3.51 R
6984 7763 0.253207 AGAGGGGAGAAACCGGGATT 60.253 55.000 6.32 0.00 40.11 3.01 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
55 56 5.124036 TCCTTTACCCTCACCCAAATATG 57.876 43.478 0.00 0.00 0.00 1.78
69 70 7.998383 TCACCCAAATATGCACTATATCAAAGT 59.002 33.333 0.00 0.00 30.65 2.66
177 178 4.704965 GTGTTTCTAGTCACCCTCACTTT 58.295 43.478 0.00 0.00 0.00 2.66
279 283 6.041637 ACGTTCTAGCCCAGTCATATTCATTA 59.958 38.462 0.00 0.00 0.00 1.90
340 344 3.137360 GGTTGGATATGAGCTTTCTCCCT 59.863 47.826 0.00 0.00 38.58 4.20
405 409 1.074775 ATACCTCCCCGCCTAGCAA 60.075 57.895 0.00 0.00 0.00 3.91
446 450 0.319641 GAGTCTTGTTCTTCGCGGGT 60.320 55.000 6.13 0.00 0.00 5.28
531 547 2.606587 CCTCCCCAGTGGTTGAGGG 61.607 68.421 26.74 14.15 42.44 4.30
536 552 2.425592 CAGTGGTTGAGGGCGACA 59.574 61.111 0.00 0.00 0.00 4.35
556 572 3.128068 ACACCTTCTTTTGGTTGTTCGTC 59.872 43.478 0.00 0.00 35.28 4.20
595 618 3.179939 GAAGCCGTCTTCGTCGCC 61.180 66.667 0.00 0.00 39.29 5.54
649 672 1.447314 CGGGGTTACTTGTCGCCTC 60.447 63.158 0.00 0.00 35.04 4.70
650 673 1.447314 GGGGTTACTTGTCGCCTCG 60.447 63.158 0.00 0.00 34.49 4.63
709 732 4.025145 GTGAAGGAAAGAACGTTGTCGATT 60.025 41.667 5.00 0.00 40.62 3.34
711 734 5.754406 TGAAGGAAAGAACGTTGTCGATTTA 59.246 36.000 5.00 0.00 40.62 1.40
752 775 1.621814 CCTCCCTAGACACAACCGAAA 59.378 52.381 0.00 0.00 0.00 3.46
772 795 4.954118 TCACCACCCCCGTCAGCT 62.954 66.667 0.00 0.00 0.00 4.24
788 811 3.008704 GTCAGCTGAAACCCTAACCCTAA 59.991 47.826 20.19 0.00 0.00 2.69
871 1081 2.362369 CCGCTGGTCTGGGACTGAT 61.362 63.158 0.00 0.00 38.85 2.90
1051 1268 3.769369 ATCTCGTCGCCGCCTCCTA 62.769 63.158 0.00 0.00 0.00 2.94
2108 2367 9.946165 AGAACTTACTTTCTTTCATTTTTACCG 57.054 29.630 0.00 0.00 31.39 4.02
2109 2368 9.726232 GAACTTACTTTCTTTCATTTTTACCGT 57.274 29.630 0.00 0.00 0.00 4.83
2110 2369 9.726232 AACTTACTTTCTTTCATTTTTACCGTC 57.274 29.630 0.00 0.00 0.00 4.79
2111 2370 9.117183 ACTTACTTTCTTTCATTTTTACCGTCT 57.883 29.630 0.00 0.00 0.00 4.18
2112 2371 9.595357 CTTACTTTCTTTCATTTTTACCGTCTC 57.405 33.333 0.00 0.00 0.00 3.36
2113 2372 7.803279 ACTTTCTTTCATTTTTACCGTCTCT 57.197 32.000 0.00 0.00 0.00 3.10
2114 2373 8.897872 ACTTTCTTTCATTTTTACCGTCTCTA 57.102 30.769 0.00 0.00 0.00 2.43
2115 2374 8.989980 ACTTTCTTTCATTTTTACCGTCTCTAG 58.010 33.333 0.00 0.00 0.00 2.43
2116 2375 8.897872 TTTCTTTCATTTTTACCGTCTCTAGT 57.102 30.769 0.00 0.00 0.00 2.57
2117 2376 8.530269 TTCTTTCATTTTTACCGTCTCTAGTC 57.470 34.615 0.00 0.00 0.00 2.59
2118 2377 7.663827 TCTTTCATTTTTACCGTCTCTAGTCA 58.336 34.615 0.00 0.00 0.00 3.41
2145 2423 8.204160 TCAGTGGATATAGAGTTGTAATGGTTG 58.796 37.037 0.00 0.00 0.00 3.77
2267 2545 8.018520 TGAAAAACAACGTAAGCAATAATCGAT 58.981 29.630 0.00 0.00 45.62 3.59
2464 2742 4.733850 TGTACACTGACTTATCTTCGCAG 58.266 43.478 0.00 0.00 0.00 5.18
2495 2773 9.134734 GAATGTTTTTCGCTATTATTGTGGAAA 57.865 29.630 0.00 0.00 0.00 3.13
2505 2783 6.701400 GCTATTATTGTGGAAATGCGGATTTT 59.299 34.615 16.39 1.93 31.58 1.82
2640 2964 3.071479 TCTGTCCCAAAATAAGTGTCGC 58.929 45.455 0.00 0.00 0.00 5.19
2763 3088 2.332063 ATTTGGTGGCATCTCCGTAG 57.668 50.000 0.00 0.00 37.80 3.51
2862 3188 8.997621 TTTAAGACAAGGTAGCTATACTGTTG 57.002 34.615 0.00 0.00 34.55 3.33
2890 3216 1.607148 CGTTGGGACAGGAGAAAAACC 59.393 52.381 0.00 0.00 42.39 3.27
3060 3398 1.741770 GTGCCGCTCTAACAGGTGG 60.742 63.158 0.00 0.00 36.31 4.61
3202 3555 8.509690 CCATAGCAAACATAGTTCATAATCCAG 58.490 37.037 0.00 0.00 0.00 3.86
3247 3602 6.153851 TCAAATCAAGCTCATGATCCAACAAT 59.846 34.615 1.39 0.00 39.08 2.71
3267 3634 9.796062 CAACAATTAAAAGTGCACATAAACATC 57.204 29.630 21.04 0.00 0.00 3.06
3299 3666 1.162800 GCATCCATCCTCTCCGTTGC 61.163 60.000 0.00 0.00 0.00 4.17
3668 4105 2.272146 CACCCATTCCACCTCCCG 59.728 66.667 0.00 0.00 0.00 5.14
3677 4114 4.263572 CACCTCCCGTTGCACCCA 62.264 66.667 0.00 0.00 0.00 4.51
3678 4115 3.256960 ACCTCCCGTTGCACCCAT 61.257 61.111 0.00 0.00 0.00 4.00
3679 4116 2.035626 CCTCCCGTTGCACCCATT 59.964 61.111 0.00 0.00 0.00 3.16
3680 4117 2.046285 CCTCCCGTTGCACCCATTC 61.046 63.158 0.00 0.00 0.00 2.67
3681 4118 2.034999 TCCCGTTGCACCCATTCC 59.965 61.111 0.00 0.00 0.00 3.01
3685 4122 1.002134 CGTTGCACCCATTCCTCCT 60.002 57.895 0.00 0.00 0.00 3.69
3686 4123 1.026718 CGTTGCACCCATTCCTCCTC 61.027 60.000 0.00 0.00 0.00 3.71
3688 4125 1.863155 TTGCACCCATTCCTCCTCCC 61.863 60.000 0.00 0.00 0.00 4.30
3689 4126 2.911143 CACCCATTCCTCCTCCCG 59.089 66.667 0.00 0.00 0.00 5.14
4066 4662 0.322366 TCCTCGCAATGACAATGGCA 60.322 50.000 0.00 0.00 31.44 4.92
4676 5294 2.322081 GCTGTTTTACTCGGCCGCA 61.322 57.895 23.51 9.97 0.00 5.69
5649 6277 7.255381 GCCAATCATAAGCTAACAAGATGATGT 60.255 37.037 0.00 0.00 37.33 3.06
5760 6388 2.957006 AGGTCGTGTCTTGTCAGTAAGT 59.043 45.455 0.00 0.00 0.00 2.24
5778 6406 6.746364 CAGTAAGTGACATCCTAAACGTAGAC 59.254 42.308 0.00 0.00 0.00 2.59
5844 6472 3.906720 ATTGCACTCAGGTAATACCGT 57.093 42.857 3.47 0.00 44.90 4.83
5845 6473 2.953466 TGCACTCAGGTAATACCGTC 57.047 50.000 3.47 0.00 44.90 4.79
5846 6474 2.172679 TGCACTCAGGTAATACCGTCA 58.827 47.619 3.47 0.00 44.90 4.35
5847 6475 2.094390 TGCACTCAGGTAATACCGTCAC 60.094 50.000 3.47 0.00 44.90 3.67
5848 6476 2.094390 GCACTCAGGTAATACCGTCACA 60.094 50.000 3.47 0.00 44.90 3.58
5849 6477 3.615592 GCACTCAGGTAATACCGTCACAA 60.616 47.826 3.47 0.00 44.90 3.33
5850 6478 3.924686 CACTCAGGTAATACCGTCACAAC 59.075 47.826 3.47 0.00 44.90 3.32
6902 7681 2.957006 GTCTATCGCTTCCTTGACCCTA 59.043 50.000 0.00 0.00 0.00 3.53
6922 7701 1.449778 GCGGGTAGGGCAAACTCTC 60.450 63.158 0.00 0.00 0.00 3.20
6986 7765 4.129148 GGCGGCCTGGAGGGAAAT 62.129 66.667 12.87 0.00 37.23 2.17
6987 7766 2.517166 GCGGCCTGGAGGGAAATC 60.517 66.667 0.00 0.00 37.23 2.17
6988 7767 2.193248 CGGCCTGGAGGGAAATCC 59.807 66.667 0.00 0.00 40.03 3.01
6999 7778 3.186345 GGAAATCCCGGTTTCTCCC 57.814 57.895 15.01 0.00 38.02 4.30
7000 7779 0.395311 GGAAATCCCGGTTTCTCCCC 60.395 60.000 15.01 0.00 38.02 4.81
7001 7780 0.624254 GAAATCCCGGTTTCTCCCCT 59.376 55.000 9.67 0.00 35.67 4.79
7002 7781 0.624254 AAATCCCGGTTTCTCCCCTC 59.376 55.000 0.00 0.00 0.00 4.30
7003 7782 0.253207 AATCCCGGTTTCTCCCCTCT 60.253 55.000 0.00 0.00 0.00 3.69
7004 7783 0.983378 ATCCCGGTTTCTCCCCTCTG 60.983 60.000 0.00 0.00 0.00 3.35
7005 7784 2.670148 CCCGGTTTCTCCCCTCTGG 61.670 68.421 0.00 0.00 0.00 3.86
7006 7785 2.269241 CGGTTTCTCCCCTCTGGC 59.731 66.667 0.00 0.00 0.00 4.85
7007 7786 2.592993 CGGTTTCTCCCCTCTGGCA 61.593 63.158 0.00 0.00 0.00 4.92
7008 7787 1.301293 GGTTTCTCCCCTCTGGCAG 59.699 63.158 8.58 8.58 0.00 4.85
7009 7788 1.492993 GGTTTCTCCCCTCTGGCAGT 61.493 60.000 15.27 0.00 0.00 4.40
7010 7789 0.035915 GTTTCTCCCCTCTGGCAGTC 60.036 60.000 15.27 0.00 0.00 3.51
7011 7790 1.544825 TTTCTCCCCTCTGGCAGTCG 61.545 60.000 15.27 6.98 0.00 4.18
7012 7791 3.465403 CTCCCCTCTGGCAGTCGG 61.465 72.222 15.27 15.42 0.00 4.79
7045 7824 1.545841 AATCCCGGTTTCTTTGCTCC 58.454 50.000 0.00 0.00 0.00 4.70
7052 7831 1.199327 GGTTTCTTTGCTCCGGTTAGC 59.801 52.381 8.18 8.18 43.08 3.09
7069 7848 6.402875 CCGGTTAGCAGTTTAGGTTATTGTTC 60.403 42.308 0.00 0.00 0.00 3.18
7070 7849 6.540205 GGTTAGCAGTTTAGGTTATTGTTCG 58.460 40.000 0.00 0.00 0.00 3.95
7119 7898 2.661594 GAATGGCGACGCTTTTTCTTT 58.338 42.857 20.77 6.82 0.00 2.52
7123 7902 1.045477 GCGACGCTTTTTCTTTGAGC 58.955 50.000 13.73 0.00 0.00 4.26
7133 7912 6.038985 GCTTTTTCTTTGAGCTTGTCTTTCT 58.961 36.000 0.00 0.00 33.72 2.52
7146 7925 6.492772 AGCTTGTCTTTCTGATTTCAATCCTT 59.507 34.615 0.00 0.00 34.50 3.36
7158 7937 6.600822 TGATTTCAATCCTTCTTGAGTCCATC 59.399 38.462 0.00 0.00 36.55 3.51
7162 7941 1.825474 TCCTTCTTGAGTCCATCCGTC 59.175 52.381 0.00 0.00 0.00 4.79
7183 7962 3.126514 TCTGGACATAGTCGACGAAACTC 59.873 47.826 10.46 2.56 32.65 3.01
7186 7965 3.427243 GACATAGTCGACGAAACTCCAG 58.573 50.000 10.46 0.00 0.00 3.86
7206 7985 1.588861 GCGTAGATTCTTGCCGTCTTC 59.411 52.381 0.00 0.00 0.00 2.87
7207 7986 2.876091 CGTAGATTCTTGCCGTCTTCA 58.124 47.619 0.00 0.00 0.00 3.02
7215 7994 4.166011 GCCGTCTTCATGGTGCGC 62.166 66.667 0.00 0.00 0.00 6.09
7218 7997 4.505217 GTCTTCATGGTGCGCGCG 62.505 66.667 28.44 28.44 0.00 6.86
7232 8011 1.416050 CGCGCGAGGTTAGGGTTTAC 61.416 60.000 28.94 0.00 0.00 2.01
7240 8019 4.322499 CGAGGTTAGGGTTTACTGTCATGT 60.322 45.833 0.00 0.00 0.00 3.21
7241 8020 4.906618 AGGTTAGGGTTTACTGTCATGTG 58.093 43.478 0.00 0.00 0.00 3.21
7256 8035 3.189287 GTCATGTGGTGAGATTTGGTGTC 59.811 47.826 0.00 0.00 37.56 3.67
7259 8038 2.154462 GTGGTGAGATTTGGTGTCAGG 58.846 52.381 0.00 0.00 29.63 3.86
7261 8040 0.798776 GTGAGATTTGGTGTCAGGCG 59.201 55.000 0.00 0.00 29.63 5.52
7284 8063 4.394300 GCTTCAGATGTATGCAAGTGTTCT 59.606 41.667 0.00 0.00 0.00 3.01
7311 8090 4.514577 ATCGCGACTCCAAGGCCG 62.515 66.667 12.93 0.00 0.00 6.13
7317 8096 3.607370 GACTCCAAGGCCGTGGTCC 62.607 68.421 33.09 20.45 39.88 4.46
7325 8104 2.686106 GCCGTGGTCCTAAGGGGA 60.686 66.667 0.00 0.00 42.77 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.165112 AGGATCTCCCTCCCAATAGGA 58.835 52.381 0.00 0.00 43.31 2.94
55 56 7.096271 CGTCAGAGATGAACTTTGATATAGTGC 60.096 40.741 0.00 0.00 40.84 4.40
69 70 2.145397 ACTAGGCCGTCAGAGATGAA 57.855 50.000 8.79 0.00 0.00 2.57
177 178 5.584649 GTGGAAATATCTTTGTCCACATCGA 59.415 40.000 15.11 0.00 44.87 3.59
279 283 3.537206 AAGTTTGCTCGCCTCGGCT 62.537 57.895 6.35 0.00 39.32 5.52
340 344 6.476409 AGGGACTCATCTATGAAGATCCTA 57.524 41.667 13.32 0.00 40.65 2.94
405 409 1.278413 GGACCCTACTTCGAGCCTTTT 59.722 52.381 0.00 0.00 0.00 2.27
446 450 0.032130 GCGGTAGATCGGCTGAATCA 59.968 55.000 0.00 0.00 38.95 2.57
531 547 1.404035 ACAACCAAAAGAAGGTGTCGC 59.596 47.619 0.00 0.00 39.86 5.19
536 552 2.686405 GGACGAACAACCAAAAGAAGGT 59.314 45.455 0.00 0.00 42.34 3.50
650 673 4.632458 GCGGAGAGGACGATCGGC 62.632 72.222 20.98 17.86 35.12 5.54
687 710 3.167921 TCGACAACGTTCTTTCCTTCA 57.832 42.857 0.00 0.00 40.69 3.02
731 754 0.113776 TCGGTTGTGTCTAGGGAGGT 59.886 55.000 0.00 0.00 0.00 3.85
752 775 4.567597 TGACGGGGGTGGTGAGGT 62.568 66.667 0.00 0.00 0.00 3.85
772 795 4.446600 CCTTGTGTTAGGGTTAGGGTTTCA 60.447 45.833 0.00 0.00 0.00 2.69
788 811 2.974698 GCGACTGCAGCCTTGTGT 60.975 61.111 15.27 0.00 42.15 3.72
817 853 3.244105 CCACGAGGTGAAACGCTG 58.756 61.111 0.00 0.00 38.12 5.18
2011 2270 2.004583 TAACCTCAATTGGCTCGTCG 57.995 50.000 5.42 0.00 0.00 5.12
2100 2359 6.387465 CACTGATGACTAGAGACGGTAAAAA 58.613 40.000 0.00 0.00 0.00 1.94
2101 2360 5.105877 CCACTGATGACTAGAGACGGTAAAA 60.106 44.000 0.00 0.00 0.00 1.52
2102 2361 4.398358 CCACTGATGACTAGAGACGGTAAA 59.602 45.833 0.00 0.00 0.00 2.01
2103 2362 3.945921 CCACTGATGACTAGAGACGGTAA 59.054 47.826 0.00 0.00 0.00 2.85
2104 2363 3.199289 TCCACTGATGACTAGAGACGGTA 59.801 47.826 0.00 0.00 0.00 4.02
2105 2364 2.026169 TCCACTGATGACTAGAGACGGT 60.026 50.000 0.00 0.00 0.00 4.83
2106 2365 2.644676 TCCACTGATGACTAGAGACGG 58.355 52.381 0.00 0.00 0.00 4.79
2107 2366 7.100409 TCTATATCCACTGATGACTAGAGACG 58.900 42.308 0.00 0.00 32.18 4.18
2108 2367 8.100791 ACTCTATATCCACTGATGACTAGAGAC 58.899 40.741 16.77 0.00 37.68 3.36
2109 2368 8.213489 ACTCTATATCCACTGATGACTAGAGA 57.787 38.462 16.77 0.00 37.68 3.10
2110 2369 8.729756 CAACTCTATATCCACTGATGACTAGAG 58.270 40.741 0.00 0.00 39.21 2.43
2111 2370 8.221251 ACAACTCTATATCCACTGATGACTAGA 58.779 37.037 0.00 0.00 32.18 2.43
2112 2371 8.402798 ACAACTCTATATCCACTGATGACTAG 57.597 38.462 0.00 0.00 32.18 2.57
2113 2372 9.862149 TTACAACTCTATATCCACTGATGACTA 57.138 33.333 0.00 0.00 32.18 2.59
2114 2373 8.768501 TTACAACTCTATATCCACTGATGACT 57.231 34.615 0.00 0.00 32.18 3.41
2115 2374 9.416794 CATTACAACTCTATATCCACTGATGAC 57.583 37.037 0.00 0.00 32.18 3.06
2116 2375 8.588472 CCATTACAACTCTATATCCACTGATGA 58.412 37.037 0.00 0.00 32.18 2.92
2117 2376 8.370940 ACCATTACAACTCTATATCCACTGATG 58.629 37.037 0.00 0.00 32.18 3.07
2118 2377 8.497910 ACCATTACAACTCTATATCCACTGAT 57.502 34.615 0.00 0.00 34.87 2.90
2145 2423 5.948992 AAGCAAATCTTACACCTGAACTC 57.051 39.130 0.00 0.00 32.10 3.01
2267 2545 3.902881 ACAATGAAACTGGGCACAAAA 57.097 38.095 0.00 0.00 0.00 2.44
2464 2742 8.129211 ACAATAATAGCGAAAAACATTCTAGCC 58.871 33.333 0.00 0.00 0.00 3.93
2495 2773 6.512297 ACAAAACAGAGTTTAAAATCCGCAT 58.488 32.000 11.81 0.00 0.00 4.73
2621 2945 2.811431 CAGCGACACTTATTTTGGGACA 59.189 45.455 0.00 0.00 0.00 4.02
2758 3083 0.097674 GCAAGAGCAATGCACTACGG 59.902 55.000 8.35 1.42 43.29 4.02
2763 3088 2.872925 CGCGCAAGAGCAATGCAC 60.873 61.111 8.75 0.00 44.01 4.57
2862 3188 1.001633 TCCTGTCCCAACGTAAGAAGC 59.998 52.381 0.00 0.00 43.62 3.86
2890 3216 1.002430 TGCTCTTAGCCACAAGGTGAG 59.998 52.381 0.00 0.00 41.51 3.51
3060 3398 1.424403 GCCGTTGGCCATTTTTACAC 58.576 50.000 6.09 0.00 44.06 2.90
3227 3582 7.465353 TTTAATTGTTGGATCATGAGCTTGA 57.535 32.000 11.34 0.00 0.00 3.02
3267 3634 7.166851 AGAGGATGGATGCTATGTTTTATCTG 58.833 38.462 0.00 0.00 0.00 2.90
3299 3666 2.445427 TGTCCATAATGTGCCAAGTGG 58.555 47.619 0.00 0.00 38.53 4.00
3668 4105 0.681243 GGAGGAGGAATGGGTGCAAC 60.681 60.000 0.00 0.00 0.00 4.17
3676 4113 1.026718 GTGCAACGGGAGGAGGAATG 61.027 60.000 0.00 0.00 0.00 2.67
3677 4114 1.299976 GTGCAACGGGAGGAGGAAT 59.700 57.895 0.00 0.00 0.00 3.01
3678 4115 2.747686 GTGCAACGGGAGGAGGAA 59.252 61.111 0.00 0.00 0.00 3.36
3679 4116 3.319198 GGTGCAACGGGAGGAGGA 61.319 66.667 0.00 0.00 38.12 3.71
3680 4117 4.410400 GGGTGCAACGGGAGGAGG 62.410 72.222 0.00 0.00 38.12 4.30
3681 4118 2.484287 AATGGGTGCAACGGGAGGAG 62.484 60.000 0.00 0.00 38.12 3.69
3685 4122 2.034999 GGAATGGGTGCAACGGGA 59.965 61.111 0.00 0.00 38.12 5.14
3686 4123 2.035626 AGGAATGGGTGCAACGGG 59.964 61.111 0.00 0.00 38.12 5.28
3688 4125 1.002134 AGGAGGAATGGGTGCAACG 60.002 57.895 0.00 0.00 38.12 4.10
3689 4126 0.681243 GGAGGAGGAATGGGTGCAAC 60.681 60.000 0.00 0.00 0.00 4.17
3873 4355 0.666374 TGTCGAGCTTTGTCACGAGA 59.334 50.000 0.00 0.00 35.52 4.04
3874 4356 1.487482 TTGTCGAGCTTTGTCACGAG 58.513 50.000 0.00 0.00 35.52 4.18
4131 4727 1.606601 CCCCACTCCTCACTCGACA 60.607 63.158 0.00 0.00 0.00 4.35
4133 4729 2.680352 GCCCCACTCCTCACTCGA 60.680 66.667 0.00 0.00 0.00 4.04
4386 5000 9.512435 GCATATGTTCCTATAAATTGATGATGC 57.488 33.333 4.29 0.00 0.00 3.91
4478 5092 4.195334 GCCCCCATCTCACCGCAT 62.195 66.667 0.00 0.00 0.00 4.73
4676 5294 2.878406 GCAAATATACATCACCAGCCGT 59.122 45.455 0.00 0.00 0.00 5.68
4756 5382 6.765989 CCAAAAACGTCCCTCAATAGATGATA 59.234 38.462 0.00 0.00 37.44 2.15
5564 6192 2.597455 CCATTGTTCCAGGTCCTGTTT 58.403 47.619 17.85 0.00 0.00 2.83
5760 6388 3.181517 CGTCGTCTACGTTTAGGATGTCA 60.182 47.826 0.00 0.00 46.72 3.58
5778 6406 1.063806 CCAGAACTTTCAGCTCGTCG 58.936 55.000 0.00 0.00 0.00 5.12
5844 6472 1.597195 GCATCGTGTTGTGAGTTGTGA 59.403 47.619 0.00 0.00 0.00 3.58
5845 6473 1.330213 TGCATCGTGTTGTGAGTTGTG 59.670 47.619 0.00 0.00 0.00 3.33
5846 6474 1.330521 GTGCATCGTGTTGTGAGTTGT 59.669 47.619 0.00 0.00 0.00 3.32
5847 6475 1.599071 AGTGCATCGTGTTGTGAGTTG 59.401 47.619 0.00 0.00 0.00 3.16
5848 6476 1.599071 CAGTGCATCGTGTTGTGAGTT 59.401 47.619 0.00 0.00 0.00 3.01
5849 6477 1.220529 CAGTGCATCGTGTTGTGAGT 58.779 50.000 0.00 0.00 0.00 3.41
5850 6478 0.514255 CCAGTGCATCGTGTTGTGAG 59.486 55.000 0.00 0.00 0.00 3.51
6005 6636 0.532417 CTCCAGGTCTGCTATGCTGC 60.532 60.000 0.00 0.00 0.00 5.25
6251 6882 6.412072 GCATAAAGTGTCGCTTCATTATCAAC 59.588 38.462 0.00 0.00 36.17 3.18
6669 7300 5.335261 TGGTTATGGAAGGTACACTCAGTA 58.665 41.667 0.00 0.00 0.00 2.74
6670 7301 4.164981 TGGTTATGGAAGGTACACTCAGT 58.835 43.478 0.00 0.00 0.00 3.41
6671 7302 4.819105 TGGTTATGGAAGGTACACTCAG 57.181 45.455 0.00 0.00 0.00 3.35
6672 7303 4.564821 GCTTGGTTATGGAAGGTACACTCA 60.565 45.833 0.00 0.00 0.00 3.41
6673 7304 3.939592 GCTTGGTTATGGAAGGTACACTC 59.060 47.826 0.00 0.00 0.00 3.51
6674 7305 3.329520 TGCTTGGTTATGGAAGGTACACT 59.670 43.478 0.00 0.00 0.00 3.55
6675 7306 3.681593 TGCTTGGTTATGGAAGGTACAC 58.318 45.455 0.00 0.00 0.00 2.90
6676 7307 4.042311 TCTTGCTTGGTTATGGAAGGTACA 59.958 41.667 0.00 0.00 32.55 2.90
6677 7308 4.585879 TCTTGCTTGGTTATGGAAGGTAC 58.414 43.478 0.00 0.00 32.55 3.34
6739 7481 4.510038 ACAAATGCCTTGTTGTGATCTC 57.490 40.909 0.00 0.00 46.49 2.75
6902 7681 2.933834 AGTTTGCCCTACCCGCCT 60.934 61.111 0.00 0.00 0.00 5.52
6922 7701 2.487428 CTCGCTGGTCTGGAGACG 59.513 66.667 0.74 0.00 45.65 4.18
6981 7760 0.395311 GGGGAGAAACCGGGATTTCC 60.395 60.000 6.32 8.13 39.05 3.13
6982 7761 0.624254 AGGGGAGAAACCGGGATTTC 59.376 55.000 6.32 8.01 40.11 2.17
6983 7762 0.624254 GAGGGGAGAAACCGGGATTT 59.376 55.000 6.32 0.00 40.11 2.17
6984 7763 0.253207 AGAGGGGAGAAACCGGGATT 60.253 55.000 6.32 0.00 40.11 3.01
6985 7764 0.983378 CAGAGGGGAGAAACCGGGAT 60.983 60.000 6.32 0.00 40.11 3.85
6986 7765 1.612442 CAGAGGGGAGAAACCGGGA 60.612 63.158 6.32 0.00 40.11 5.14
6987 7766 2.670148 CCAGAGGGGAGAAACCGGG 61.670 68.421 6.32 0.00 40.01 5.73
6988 7767 2.990479 CCAGAGGGGAGAAACCGG 59.010 66.667 0.00 0.00 40.01 5.28
6989 7768 2.269241 GCCAGAGGGGAGAAACCG 59.731 66.667 0.00 0.00 40.01 4.44
6990 7769 3.495729 TGCCAGAGGGGAGAAACC 58.504 61.111 0.00 0.00 40.01 3.27
7011 7790 4.129148 ATTTCCCTCCAGGCCGCC 62.129 66.667 0.00 0.00 34.51 6.13
7012 7791 2.517166 GATTTCCCTCCAGGCCGC 60.517 66.667 0.00 0.00 34.51 6.53
7013 7792 2.193248 GGATTTCCCTCCAGGCCG 59.807 66.667 0.00 0.00 35.24 6.13
7045 7824 6.490566 AACAATAACCTAAACTGCTAACCG 57.509 37.500 0.00 0.00 0.00 4.44
7052 7831 8.985805 AGAACTAACGAACAATAACCTAAACTG 58.014 33.333 0.00 0.00 0.00 3.16
7089 7868 3.118454 CGCCATTCGCCTGAACGT 61.118 61.111 0.00 0.00 36.81 3.99
7119 7898 6.072286 GGATTGAAATCAGAAAGACAAGCTCA 60.072 38.462 5.46 0.00 37.15 4.26
7123 7902 8.108551 AGAAGGATTGAAATCAGAAAGACAAG 57.891 34.615 5.46 0.00 37.15 3.16
7133 7912 5.879763 TGGACTCAAGAAGGATTGAAATCA 58.120 37.500 5.46 0.00 38.66 2.57
7146 7925 1.186200 CCAGACGGATGGACTCAAGA 58.814 55.000 2.10 0.00 43.57 3.02
7158 7937 3.920144 GTCGACTATGTCCAGACGG 57.080 57.895 8.70 0.00 35.02 4.79
7162 7941 3.427243 GAGTTTCGTCGACTATGTCCAG 58.573 50.000 14.70 0.00 0.00 3.86
7183 7962 0.460284 ACGGCAAGAATCTACGCTGG 60.460 55.000 15.18 6.54 34.99 4.85
7186 7965 1.588861 GAAGACGGCAAGAATCTACGC 59.411 52.381 0.00 0.00 0.00 4.42
7207 7986 4.444838 TAACCTCGCGCGCACCAT 62.445 61.111 32.61 14.94 0.00 3.55
7215 7994 1.067354 ACAGTAAACCCTAACCTCGCG 60.067 52.381 0.00 0.00 0.00 5.87
7218 7997 4.935808 CACATGACAGTAAACCCTAACCTC 59.064 45.833 0.00 0.00 0.00 3.85
7232 8011 3.189910 CACCAAATCTCACCACATGACAG 59.810 47.826 0.00 0.00 32.37 3.51
7240 8019 1.545428 GCCTGACACCAAATCTCACCA 60.545 52.381 0.00 0.00 0.00 4.17
7241 8020 1.168714 GCCTGACACCAAATCTCACC 58.831 55.000 0.00 0.00 0.00 4.02
7256 8035 0.585357 GCATACATCTGAAGCGCCTG 59.415 55.000 2.29 0.00 0.00 4.85
7259 8038 1.667724 ACTTGCATACATCTGAAGCGC 59.332 47.619 0.00 0.00 0.00 5.92
7261 8040 4.394300 AGAACACTTGCATACATCTGAAGC 59.606 41.667 0.00 0.00 0.00 3.86
7317 8096 3.691609 GTCTTCATGCACTTTCCCCTTAG 59.308 47.826 0.00 0.00 0.00 2.18


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

AutoCloner maintained by Alex Coulton.