Multiple sequence alignment - TraesCS2D01G207300

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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 TraesCS2D01G207300 chr2D 100.000 3240 0 0 1 3240 160941520 160944759 0.000000e+00 5984.0
1 TraesCS2D01G207300 chr2D 99.332 2395 15 1 1 2394 161529978 161527584 0.000000e+00 4333.0
2 TraesCS2D01G207300 chr2D 96.154 468 9 3 2478 2945 161526000 161525542 0.000000e+00 756.0
3 TraesCS2D01G207300 chr2D 94.196 224 11 2 3016 3239 348946359 348946138 1.110000e-89 340.0
4 TraesCS2D01G207300 chr2D 98.876 89 1 0 2395 2483 161526248 161526160 3.350000e-35 159.0
5 TraesCS2D01G207300 chr4A 89.495 1209 92 17 1595 2780 332023790 332024986 0.000000e+00 1496.0
6 TraesCS2D01G207300 chr4A 89.809 628 40 9 992 1596 332022844 332023470 0.000000e+00 784.0
7 TraesCS2D01G207300 chr4A 93.035 201 13 1 2794 2993 332036852 332037052 3.160000e-75 292.0
8 TraesCS2D01G207300 chr4A 83.537 164 24 3 2848 3010 212830758 212830919 2.010000e-32 150.0
9 TraesCS2D01G207300 chr4A 88.660 97 9 1 2914 3010 198907507 198907413 2.040000e-22 117.0
10 TraesCS2D01G207300 chr4A 97.297 37 1 0 939 975 497881440 497881404 2.700000e-06 63.9
11 TraesCS2D01G207300 chr3B 91.443 1005 62 11 1595 2577 216402591 216403593 0.000000e+00 1358.0
12 TraesCS2D01G207300 chr3B 90.350 943 52 11 7 943 216400759 216401668 0.000000e+00 1201.0
13 TraesCS2D01G207300 chr3B 91.506 624 32 9 992 1596 216401651 216402272 0.000000e+00 839.0
14 TraesCS2D01G207300 chr3B 90.987 233 17 3 2779 3010 216403975 216404204 8.730000e-81 311.0
15 TraesCS2D01G207300 chr3B 90.625 128 9 3 2592 2717 216403856 216403982 2.000000e-37 167.0
16 TraesCS2D01G207300 chr6B 91.139 948 51 17 1 943 300368715 300367796 0.000000e+00 1254.0
17 TraesCS2D01G207300 chr6B 90.116 951 60 11 1595 2515 300366874 300365928 0.000000e+00 1205.0
18 TraesCS2D01G207300 chr6B 90.836 622 39 6 992 1596 300367813 300367193 0.000000e+00 817.0
19 TraesCS2D01G207300 chr6B 90.090 111 5 2 2900 3010 300365927 300365823 4.360000e-29 139.0
20 TraesCS2D01G207300 chr6D 88.620 949 90 14 1 943 184815475 184814539 0.000000e+00 1138.0
21 TraesCS2D01G207300 chr6D 87.671 949 100 13 1 943 183949625 183950562 0.000000e+00 1088.0
22 TraesCS2D01G207300 chr6D 86.971 875 92 15 1 867 165534116 165533256 0.000000e+00 965.0
23 TraesCS2D01G207300 chr6D 86.743 875 94 15 1 867 165546167 165545307 0.000000e+00 953.0
24 TraesCS2D01G207300 chr6D 86.240 625 65 12 992 1596 184814556 184813933 0.000000e+00 658.0
25 TraesCS2D01G207300 chr6D 80.123 976 114 40 1595 2516 183956315 183957264 0.000000e+00 654.0
26 TraesCS2D01G207300 chr6D 80.143 977 99 47 1595 2516 184813616 184812680 2.730000e-180 641.0
27 TraesCS2D01G207300 chr6D 85.531 622 71 9 994 1596 165457841 165457220 1.640000e-177 632.0
28 TraesCS2D01G207300 chr6D 88.462 416 48 0 993 1408 183950546 183950961 1.340000e-138 503.0
29 TraesCS2D01G207300 chr6D 85.684 468 53 7 1595 2048 165456896 165456429 6.290000e-132 481.0
30 TraesCS2D01G207300 chr6D 88.384 396 46 0 994 1389 120840541 120840936 8.130000e-131 477.0
31 TraesCS2D01G207300 chr6D 91.018 167 13 2 2844 3010 165455647 165455483 1.170000e-54 224.0
32 TraesCS2D01G207300 chr6D 89.820 167 16 1 2844 3010 184811594 184811429 2.530000e-51 213.0
33 TraesCS2D01G207300 chr6D 90.566 159 13 2 2843 3001 183957533 183957689 3.280000e-50 209.0
34 TraesCS2D01G207300 chr6D 79.263 217 24 12 1400 1596 183955779 183955994 7.290000e-27 132.0
35 TraesCS2D01G207300 chr4B 87.158 950 106 14 1 943 210361887 210360947 0.000000e+00 1064.0
36 TraesCS2D01G207300 chr6A 86.328 885 102 14 65 938 158482797 158481921 0.000000e+00 946.0
37 TraesCS2D01G207300 chr6A 87.879 396 48 0 994 1389 158481931 158481536 1.760000e-127 466.0
38 TraesCS2D01G207300 chr5B 85.021 474 51 10 1594 2048 50230210 50230682 6.330000e-127 464.0
39 TraesCS2D01G207300 chr5B 89.062 128 13 1 2349 2475 50232220 50232347 1.200000e-34 158.0
40 TraesCS2D01G207300 chr7D 96.396 222 5 3 3016 3237 167988636 167988418 2.380000e-96 363.0
41 TraesCS2D01G207300 chr1D 95.536 224 6 3 3016 3239 56940231 56940450 3.980000e-94 355.0
42 TraesCS2D01G207300 chr1D 94.643 224 9 3 3016 3237 120856186 120855964 8.610000e-91 344.0
43 TraesCS2D01G207300 chr1D 94.222 225 10 3 3016 3239 39654604 39654826 1.110000e-89 340.0
44 TraesCS2D01G207300 chr7A 94.595 222 10 2 3016 3237 162374903 162374684 3.100000e-90 342.0
45 TraesCS2D01G207300 chr5D 94.196 224 11 2 3016 3239 430553257 430553478 1.110000e-89 340.0
46 TraesCS2D01G207300 chr3D 94.196 224 11 2 3016 3239 36731132 36730911 1.110000e-89 340.0
47 TraesCS2D01G207300 chr3D 91.667 60 4 1 939 997 519246035 519246094 7.450000e-12 82.4
48 TraesCS2D01G207300 chr5A 93.074 231 12 2 3010 3239 259300761 259300988 5.180000e-88 335.0
49 TraesCS2D01G207300 chr1B 89.583 96 10 0 2915 3010 283925201 283925296 4.390000e-24 122.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G207300 chr2D 160941520 160944759 3239 False 5984.000000 5984 100.000000 1 3240 1 chr2D.!!$F1 3239
1 TraesCS2D01G207300 chr2D 161525542 161529978 4436 True 1749.333333 4333 98.120667 1 2945 3 chr2D.!!$R2 2944
2 TraesCS2D01G207300 chr4A 332022844 332024986 2142 False 1140.000000 1496 89.652000 992 2780 2 chr4A.!!$F3 1788
3 TraesCS2D01G207300 chr3B 216400759 216404204 3445 False 775.200000 1358 90.982200 7 3010 5 chr3B.!!$F1 3003
4 TraesCS2D01G207300 chr6B 300365823 300368715 2892 True 853.750000 1254 90.545250 1 3010 4 chr6B.!!$R1 3009
5 TraesCS2D01G207300 chr6D 165533256 165534116 860 True 965.000000 965 86.971000 1 867 1 chr6D.!!$R1 866
6 TraesCS2D01G207300 chr6D 165545307 165546167 860 True 953.000000 953 86.743000 1 867 1 chr6D.!!$R2 866
7 TraesCS2D01G207300 chr6D 183949625 183950961 1336 False 795.500000 1088 88.066500 1 1408 2 chr6D.!!$F2 1407
8 TraesCS2D01G207300 chr6D 184811429 184815475 4046 True 662.500000 1138 86.205750 1 3010 4 chr6D.!!$R4 3009
9 TraesCS2D01G207300 chr6D 165455483 165457841 2358 True 445.666667 632 87.411000 994 3010 3 chr6D.!!$R3 2016
10 TraesCS2D01G207300 chr6D 183955779 183957689 1910 False 331.666667 654 83.317333 1400 3001 3 chr6D.!!$F3 1601
11 TraesCS2D01G207300 chr4B 210360947 210361887 940 True 1064.000000 1064 87.158000 1 943 1 chr4B.!!$R1 942
12 TraesCS2D01G207300 chr6A 158481536 158482797 1261 True 706.000000 946 87.103500 65 1389 2 chr6A.!!$R1 1324
13 TraesCS2D01G207300 chr5B 50230210 50232347 2137 False 311.000000 464 87.041500 1594 2475 2 chr5B.!!$F1 881

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
956 981 7.230747 TGAATGTCCCTCTCTTTTCAATACAA 58.769 34.615 0.0 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2475 5476 5.070981 TCAGTTGGCATATTTCCAAAAACCA 59.929 36.0 7.56 0.0 44.36 3.67 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
677 688 7.392113 TGTTTCGTTCCTTGGACATAATATTGT 59.608 33.333 0.00 0.00 0.00 2.71
748 768 9.956640 AATTTGGATATGCTTTCCACATTTTTA 57.043 25.926 8.02 0.00 39.48 1.52
956 981 7.230747 TGAATGTCCCTCTCTTTTCAATACAA 58.769 34.615 0.00 0.00 0.00 2.41
1099 1124 1.908340 CTGGCAGAAGTCCCCTCCTG 61.908 65.000 9.42 0.00 0.00 3.86
1118 1143 0.324645 GGAACCATTGTCATGCCCCT 60.325 55.000 0.00 0.00 0.00 4.79
1410 1436 7.664318 GGTACCACCAACCTTTATCCATTATAG 59.336 40.741 7.15 0.00 38.42 1.31
2480 5646 5.536497 AAGGAGATTGTATCCCTTGGTTT 57.464 39.130 0.00 0.00 38.04 3.27
2505 5671 9.434420 TTTTGGAAATATGCCAACTGAATTAAG 57.566 29.630 9.24 0.00 44.58 1.85
2614 6810 4.707105 TGCAAATGTATCATGGATCGTCT 58.293 39.130 0.00 0.00 0.00 4.18
2624 6820 3.632604 TCATGGATCGTCTAACCTGACTC 59.367 47.826 0.00 0.00 35.00 3.36
2933 7192 5.020795 ACCTAATTAAAGGCCGGATGTTTT 58.979 37.500 5.05 1.64 40.62 2.43
3024 7283 6.743575 ATAAATAGAAATAGATGGCGCACC 57.256 37.500 10.83 0.00 0.00 5.01
3046 7305 2.262915 GCTCTGTGCGCCACTACT 59.737 61.111 4.18 0.00 35.11 2.57
3047 7306 1.511305 GCTCTGTGCGCCACTACTA 59.489 57.895 4.18 0.00 35.11 1.82
3048 7307 0.108804 GCTCTGTGCGCCACTACTAA 60.109 55.000 4.18 0.00 35.11 2.24
3049 7308 1.630148 CTCTGTGCGCCACTACTAAC 58.370 55.000 4.18 0.00 35.11 2.34
3050 7309 0.963225 TCTGTGCGCCACTACTAACA 59.037 50.000 4.18 0.00 35.11 2.41
3051 7310 1.341852 TCTGTGCGCCACTACTAACAA 59.658 47.619 4.18 0.00 35.11 2.83
3052 7311 2.028476 TCTGTGCGCCACTACTAACAAT 60.028 45.455 4.18 0.00 35.11 2.71
3053 7312 2.742053 CTGTGCGCCACTACTAACAATT 59.258 45.455 4.18 0.00 35.11 2.32
3054 7313 3.142951 TGTGCGCCACTACTAACAATTT 58.857 40.909 4.18 0.00 35.11 1.82
3055 7314 3.566322 TGTGCGCCACTACTAACAATTTT 59.434 39.130 4.18 0.00 35.11 1.82
3056 7315 4.036971 TGTGCGCCACTACTAACAATTTTT 59.963 37.500 4.18 0.00 35.11 1.94
3090 7349 5.440234 TTTTCAAAACTAGTAATGGCGCA 57.560 34.783 10.83 0.00 0.00 6.09
3091 7350 5.637006 TTTCAAAACTAGTAATGGCGCAT 57.363 34.783 10.83 0.00 0.00 4.73
3092 7351 4.875544 TCAAAACTAGTAATGGCGCATC 57.124 40.909 10.83 0.00 0.00 3.91
3093 7352 4.513442 TCAAAACTAGTAATGGCGCATCT 58.487 39.130 10.83 1.91 0.00 2.90
3094 7353 4.332543 TCAAAACTAGTAATGGCGCATCTG 59.667 41.667 10.83 0.00 0.00 2.90
3095 7354 3.543680 AACTAGTAATGGCGCATCTGT 57.456 42.857 10.83 0.00 0.00 3.41
3096 7355 2.826428 ACTAGTAATGGCGCATCTGTG 58.174 47.619 10.83 0.00 0.00 3.66
3097 7356 2.168521 ACTAGTAATGGCGCATCTGTGT 59.831 45.455 10.83 0.00 0.00 3.72
3098 7357 2.979814 AGTAATGGCGCATCTGTGTA 57.020 45.000 10.83 0.00 0.00 2.90
3099 7358 3.260475 AGTAATGGCGCATCTGTGTAA 57.740 42.857 10.83 0.00 0.00 2.41
3100 7359 3.605634 AGTAATGGCGCATCTGTGTAAA 58.394 40.909 10.83 0.00 0.00 2.01
3101 7360 3.623060 AGTAATGGCGCATCTGTGTAAAG 59.377 43.478 10.83 0.00 0.00 1.85
3102 7361 2.113860 ATGGCGCATCTGTGTAAAGT 57.886 45.000 10.83 0.00 0.00 2.66
3103 7362 1.155889 TGGCGCATCTGTGTAAAGTG 58.844 50.000 10.83 0.00 0.00 3.16
3104 7363 0.179189 GGCGCATCTGTGTAAAGTGC 60.179 55.000 10.83 0.00 35.15 4.40
3106 7365 3.296516 GCATCTGTGTAAAGTGCGC 57.703 52.632 0.00 0.00 0.00 6.09
3107 7366 0.179189 GCATCTGTGTAAAGTGCGCC 60.179 55.000 4.18 0.00 0.00 6.53
3108 7367 1.155889 CATCTGTGTAAAGTGCGCCA 58.844 50.000 4.18 0.00 0.00 5.69
3109 7368 1.739466 CATCTGTGTAAAGTGCGCCAT 59.261 47.619 4.18 0.00 0.00 4.40
3110 7369 1.890876 TCTGTGTAAAGTGCGCCATT 58.109 45.000 4.18 0.00 0.00 3.16
3111 7370 3.046968 TCTGTGTAAAGTGCGCCATTA 57.953 42.857 4.18 0.00 0.00 1.90
3112 7371 2.739913 TCTGTGTAAAGTGCGCCATTAC 59.260 45.455 4.18 12.14 0.00 1.89
3113 7372 2.742053 CTGTGTAAAGTGCGCCATTACT 59.258 45.455 20.51 9.76 32.18 2.24
3114 7373 3.927854 TGTGTAAAGTGCGCCATTACTA 58.072 40.909 20.51 11.59 32.18 1.82
3115 7374 3.930229 TGTGTAAAGTGCGCCATTACTAG 59.070 43.478 20.51 0.00 32.18 2.57
3116 7375 3.930848 GTGTAAAGTGCGCCATTACTAGT 59.069 43.478 20.51 0.00 32.18 2.57
3117 7376 4.390909 GTGTAAAGTGCGCCATTACTAGTT 59.609 41.667 20.51 7.76 32.18 2.24
3118 7377 4.628333 TGTAAAGTGCGCCATTACTAGTTC 59.372 41.667 20.51 4.65 32.18 3.01
3119 7378 3.328382 AAGTGCGCCATTACTAGTTCA 57.672 42.857 4.18 0.00 0.00 3.18
3120 7379 3.328382 AGTGCGCCATTACTAGTTCAA 57.672 42.857 4.18 0.00 0.00 2.69
3121 7380 3.670625 AGTGCGCCATTACTAGTTCAAA 58.329 40.909 4.18 0.00 0.00 2.69
3122 7381 3.435671 AGTGCGCCATTACTAGTTCAAAC 59.564 43.478 4.18 0.00 0.00 2.93
3123 7382 3.435671 GTGCGCCATTACTAGTTCAAACT 59.564 43.478 4.18 0.46 42.91 2.66
3124 7383 4.628333 GTGCGCCATTACTAGTTCAAACTA 59.372 41.667 4.18 2.82 40.37 2.24
3135 7394 3.670625 AGTTCAAACTAGTAATGGCGCA 58.329 40.909 10.83 0.00 37.52 6.09
3136 7395 3.435671 AGTTCAAACTAGTAATGGCGCAC 59.564 43.478 10.83 0.00 37.52 5.34
3137 7396 2.352388 TCAAACTAGTAATGGCGCACC 58.648 47.619 10.83 0.00 0.00 5.01
3138 7397 7.993601 AGTTCAAACTAGTAATGGCGCACCA 62.994 44.000 10.83 0.00 44.04 4.17
3162 7421 3.776656 CGGTGCGCCACTACTAAC 58.223 61.111 18.18 0.00 34.40 2.34
3163 7422 1.214589 CGGTGCGCCACTACTAACT 59.785 57.895 18.18 0.00 34.40 2.24
3164 7423 0.452987 CGGTGCGCCACTACTAACTA 59.547 55.000 18.18 0.00 34.40 2.24
3165 7424 1.066605 CGGTGCGCCACTACTAACTAT 59.933 52.381 18.18 0.00 34.40 2.12
3166 7425 2.480759 CGGTGCGCCACTACTAACTATT 60.481 50.000 18.18 0.00 34.40 1.73
3167 7426 3.528532 GGTGCGCCACTACTAACTATTT 58.471 45.455 12.58 0.00 34.40 1.40
3168 7427 3.937079 GGTGCGCCACTACTAACTATTTT 59.063 43.478 12.58 0.00 34.40 1.82
3169 7428 4.393990 GGTGCGCCACTACTAACTATTTTT 59.606 41.667 12.58 0.00 34.40 1.94
3170 7429 5.321516 GTGCGCCACTACTAACTATTTTTG 58.678 41.667 4.18 0.00 0.00 2.44
3171 7430 4.998672 TGCGCCACTACTAACTATTTTTGT 59.001 37.500 4.18 0.00 0.00 2.83
3172 7431 5.470777 TGCGCCACTACTAACTATTTTTGTT 59.529 36.000 4.18 0.00 0.00 2.83
3173 7432 6.016943 TGCGCCACTACTAACTATTTTTGTTT 60.017 34.615 4.18 0.00 0.00 2.83
3174 7433 6.859508 GCGCCACTACTAACTATTTTTGTTTT 59.140 34.615 0.00 0.00 0.00 2.43
3175 7434 7.149031 GCGCCACTACTAACTATTTTTGTTTTG 60.149 37.037 0.00 0.00 0.00 2.44
3176 7435 7.149031 CGCCACTACTAACTATTTTTGTTTTGC 60.149 37.037 0.00 0.00 0.00 3.68
3177 7436 7.650104 GCCACTACTAACTATTTTTGTTTTGCA 59.350 33.333 0.00 0.00 0.00 4.08
3178 7437 9.522804 CCACTACTAACTATTTTTGTTTTGCAA 57.477 29.630 0.00 0.00 34.87 4.08
3191 7450 6.836577 TTGTTTTGCAAAACTAGTAATGGC 57.163 33.333 39.89 20.55 46.37 4.40
3192 7451 4.979197 TGTTTTGCAAAACTAGTAATGGCG 59.021 37.500 39.89 0.00 46.37 5.69
3193 7452 2.911819 TGCAAAACTAGTAATGGCGC 57.088 45.000 0.00 0.00 0.00 6.53
3194 7453 2.155279 TGCAAAACTAGTAATGGCGCA 58.845 42.857 10.83 0.00 0.00 6.09
3195 7454 2.095466 TGCAAAACTAGTAATGGCGCAC 60.095 45.455 10.83 0.00 0.00 5.34
3196 7455 2.731027 GCAAAACTAGTAATGGCGCACC 60.731 50.000 10.83 0.00 0.00 5.01
3205 7464 2.663520 TGGCGCACCACGTAACTG 60.664 61.111 10.83 0.00 42.67 3.16
3206 7465 3.419759 GGCGCACCACGTAACTGG 61.420 66.667 10.83 0.00 46.11 4.00
3207 7466 2.663852 GCGCACCACGTAACTGGT 60.664 61.111 0.30 0.00 46.18 4.00
3211 7470 2.663852 ACCACGTAACTGGTGCGC 60.664 61.111 2.32 0.00 43.38 6.09
3212 7471 3.419759 CCACGTAACTGGTGCGCC 61.420 66.667 10.11 10.11 34.08 6.53
3213 7472 2.663520 CACGTAACTGGTGCGCCA 60.664 61.111 19.93 19.93 43.73 5.69
3214 7473 2.032634 CACGTAACTGGTGCGCCAT 61.033 57.895 21.54 8.76 45.05 4.40
3215 7474 1.302192 ACGTAACTGGTGCGCCATT 60.302 52.632 21.54 12.16 45.05 3.16
3216 7475 0.037139 ACGTAACTGGTGCGCCATTA 60.037 50.000 21.54 16.60 45.05 1.90
3217 7476 0.650512 CGTAACTGGTGCGCCATTAG 59.349 55.000 21.54 11.19 45.05 1.73
3218 7477 1.734163 GTAACTGGTGCGCCATTAGT 58.266 50.000 21.54 11.93 45.05 2.24
3219 7478 2.736081 CGTAACTGGTGCGCCATTAGTA 60.736 50.000 21.54 6.85 45.05 1.82
3220 7479 2.483014 AACTGGTGCGCCATTAGTAA 57.517 45.000 21.54 0.00 45.05 2.24
3221 7480 1.734163 ACTGGTGCGCCATTAGTAAC 58.266 50.000 21.54 0.00 45.05 2.50
3222 7481 0.650512 CTGGTGCGCCATTAGTAACG 59.349 55.000 21.54 0.85 45.05 3.18
3223 7482 0.246910 TGGTGCGCCATTAGTAACGA 59.753 50.000 16.89 0.00 40.46 3.85
3224 7483 0.928229 GGTGCGCCATTAGTAACGAG 59.072 55.000 12.58 0.00 34.09 4.18
3225 7484 0.928229 GTGCGCCATTAGTAACGAGG 59.072 55.000 4.18 0.00 0.00 4.63
3226 7485 0.179094 TGCGCCATTAGTAACGAGGG 60.179 55.000 4.18 0.00 0.00 4.30
3227 7486 0.179092 GCGCCATTAGTAACGAGGGT 60.179 55.000 0.00 0.00 0.00 4.34
3228 7487 1.741394 GCGCCATTAGTAACGAGGGTT 60.741 52.381 0.00 0.00 40.20 4.11
3229 7488 2.481795 GCGCCATTAGTAACGAGGGTTA 60.482 50.000 0.00 0.00 37.58 2.85
3238 7497 2.304751 AACGAGGGTTACTAATGGCG 57.695 50.000 0.00 0.00 33.72 5.69
3239 7498 1.188863 ACGAGGGTTACTAATGGCGT 58.811 50.000 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
956 981 3.695816 GCAAGAAGACTTTGCGTTTCTT 58.304 40.909 0.00 0.00 39.69 2.52
1099 1124 0.324645 AGGGGCATGACAATGGTTCC 60.325 55.000 0.00 0.00 34.09 3.62
1118 1143 2.503331 ACAACATTGAGCGACCATTCA 58.497 42.857 0.00 0.00 0.00 2.57
1410 1436 7.478044 CACAACAAAAACAACAATTGATGTCAC 59.522 33.333 20.10 0.00 42.99 3.67
2475 5476 5.070981 TCAGTTGGCATATTTCCAAAAACCA 59.929 36.000 7.56 0.00 44.36 3.67
2480 5646 8.811017 TCTTAATTCAGTTGGCATATTTCCAAA 58.189 29.630 7.56 0.00 44.36 3.28
3029 7288 0.108804 TTAGTAGTGGCGCACAGAGC 60.109 55.000 10.83 0.00 36.74 4.09
3030 7289 1.067846 TGTTAGTAGTGGCGCACAGAG 60.068 52.381 10.83 0.00 36.74 3.35
3031 7290 0.963225 TGTTAGTAGTGGCGCACAGA 59.037 50.000 10.83 0.00 36.74 3.41
3032 7291 1.790755 TTGTTAGTAGTGGCGCACAG 58.209 50.000 10.83 0.00 36.74 3.66
3033 7292 2.465860 ATTGTTAGTAGTGGCGCACA 57.534 45.000 10.83 1.22 36.74 4.57
3034 7293 3.824414 AAATTGTTAGTAGTGGCGCAC 57.176 42.857 10.83 5.73 34.10 5.34
3035 7294 4.839668 AAAAATTGTTAGTAGTGGCGCA 57.160 36.364 10.83 0.00 0.00 6.09
3067 7326 5.833082 TGCGCCATTACTAGTTTTGAAAAA 58.167 33.333 4.18 0.00 0.00 1.94
3068 7327 5.440234 TGCGCCATTACTAGTTTTGAAAA 57.560 34.783 4.18 0.00 0.00 2.29
3069 7328 5.414454 AGATGCGCCATTACTAGTTTTGAAA 59.586 36.000 4.18 0.00 0.00 2.69
3070 7329 4.941263 AGATGCGCCATTACTAGTTTTGAA 59.059 37.500 4.18 0.00 0.00 2.69
3071 7330 4.332543 CAGATGCGCCATTACTAGTTTTGA 59.667 41.667 4.18 0.00 0.00 2.69
3072 7331 4.094887 ACAGATGCGCCATTACTAGTTTTG 59.905 41.667 4.18 0.00 0.00 2.44
3073 7332 4.094887 CACAGATGCGCCATTACTAGTTTT 59.905 41.667 4.18 0.00 0.00 2.43
3074 7333 3.623060 CACAGATGCGCCATTACTAGTTT 59.377 43.478 4.18 0.00 0.00 2.66
3075 7334 3.198068 CACAGATGCGCCATTACTAGTT 58.802 45.455 4.18 0.00 0.00 2.24
3076 7335 2.168521 ACACAGATGCGCCATTACTAGT 59.831 45.455 4.18 0.00 0.00 2.57
3077 7336 2.826428 ACACAGATGCGCCATTACTAG 58.174 47.619 4.18 0.00 0.00 2.57
3078 7337 2.979814 ACACAGATGCGCCATTACTA 57.020 45.000 4.18 0.00 0.00 1.82
3079 7338 2.979814 TACACAGATGCGCCATTACT 57.020 45.000 4.18 0.00 0.00 2.24
3080 7339 3.374058 ACTTTACACAGATGCGCCATTAC 59.626 43.478 4.18 0.00 0.00 1.89
3081 7340 3.373748 CACTTTACACAGATGCGCCATTA 59.626 43.478 4.18 0.00 0.00 1.90
3082 7341 2.162208 CACTTTACACAGATGCGCCATT 59.838 45.455 4.18 0.00 0.00 3.16
3083 7342 1.739466 CACTTTACACAGATGCGCCAT 59.261 47.619 4.18 0.00 0.00 4.40
3084 7343 1.155889 CACTTTACACAGATGCGCCA 58.844 50.000 4.18 0.00 0.00 5.69
3085 7344 0.179189 GCACTTTACACAGATGCGCC 60.179 55.000 4.18 0.00 0.00 6.53
3086 7345 3.296516 GCACTTTACACAGATGCGC 57.703 52.632 0.00 0.00 0.00 6.09
3088 7347 0.179189 GGCGCACTTTACACAGATGC 60.179 55.000 10.83 0.00 0.00 3.91
3089 7348 1.155889 TGGCGCACTTTACACAGATG 58.844 50.000 10.83 0.00 0.00 2.90
3090 7349 2.113860 ATGGCGCACTTTACACAGAT 57.886 45.000 10.83 0.00 0.00 2.90
3091 7350 1.890876 AATGGCGCACTTTACACAGA 58.109 45.000 10.83 0.00 0.00 3.41
3092 7351 2.742053 AGTAATGGCGCACTTTACACAG 59.258 45.455 23.53 0.00 40.37 3.66
3093 7352 2.773487 AGTAATGGCGCACTTTACACA 58.227 42.857 23.53 8.65 40.37 3.72
3094 7353 3.930848 ACTAGTAATGGCGCACTTTACAC 59.069 43.478 23.53 9.49 40.37 2.90
3095 7354 4.196626 ACTAGTAATGGCGCACTTTACA 57.803 40.909 23.53 9.82 40.37 2.41
3096 7355 4.628333 TGAACTAGTAATGGCGCACTTTAC 59.372 41.667 10.83 16.13 39.01 2.01
3097 7356 4.823157 TGAACTAGTAATGGCGCACTTTA 58.177 39.130 10.83 5.00 0.00 1.85
3098 7357 3.670625 TGAACTAGTAATGGCGCACTTT 58.329 40.909 10.83 6.01 0.00 2.66
3099 7358 3.328382 TGAACTAGTAATGGCGCACTT 57.672 42.857 10.83 4.06 0.00 3.16
3100 7359 3.328382 TTGAACTAGTAATGGCGCACT 57.672 42.857 10.83 6.53 0.00 4.40
3101 7360 3.435671 AGTTTGAACTAGTAATGGCGCAC 59.564 43.478 10.83 0.00 37.52 5.34
3102 7361 3.670625 AGTTTGAACTAGTAATGGCGCA 58.329 40.909 10.83 0.00 37.52 6.09
3112 7371 8.092173 GGTGCGCCATTACTAGTTTGAACTAG 62.092 46.154 22.87 22.87 46.85 2.57
3113 7372 4.628333 GTGCGCCATTACTAGTTTGAACTA 59.372 41.667 4.18 3.78 40.37 2.24
3114 7373 3.435671 GTGCGCCATTACTAGTTTGAACT 59.564 43.478 4.18 1.60 42.91 3.01
3115 7374 3.425758 GGTGCGCCATTACTAGTTTGAAC 60.426 47.826 12.58 0.00 34.09 3.18
3116 7375 2.745281 GGTGCGCCATTACTAGTTTGAA 59.255 45.455 12.58 0.00 34.09 2.69
3117 7376 2.289756 TGGTGCGCCATTACTAGTTTGA 60.290 45.455 16.89 0.00 40.46 2.69
3118 7377 2.080693 TGGTGCGCCATTACTAGTTTG 58.919 47.619 16.89 0.00 40.46 2.93
3119 7378 2.483014 TGGTGCGCCATTACTAGTTT 57.517 45.000 16.89 0.00 40.46 2.66
3145 7404 0.452987 TAGTTAGTAGTGGCGCACCG 59.547 55.000 10.83 0.00 39.70 4.94
3146 7405 2.884894 ATAGTTAGTAGTGGCGCACC 57.115 50.000 10.83 0.00 34.49 5.01
3147 7406 5.106830 ACAAAAATAGTTAGTAGTGGCGCAC 60.107 40.000 10.83 5.73 34.10 5.34
3148 7407 4.998672 ACAAAAATAGTTAGTAGTGGCGCA 59.001 37.500 10.83 0.00 0.00 6.09
3149 7408 5.541098 ACAAAAATAGTTAGTAGTGGCGC 57.459 39.130 0.00 0.00 0.00 6.53
3150 7409 7.149031 GCAAAACAAAAATAGTTAGTAGTGGCG 60.149 37.037 0.00 0.00 0.00 5.69
3151 7410 7.650104 TGCAAAACAAAAATAGTTAGTAGTGGC 59.350 33.333 0.00 0.00 0.00 5.01
3152 7411 9.522804 TTGCAAAACAAAAATAGTTAGTAGTGG 57.477 29.630 0.00 0.00 34.56 4.00
3170 7429 4.143410 GCGCCATTACTAGTTTTGCAAAAC 60.143 41.667 36.64 36.64 46.54 2.43
3171 7430 3.984633 GCGCCATTACTAGTTTTGCAAAA 59.015 39.130 20.46 20.46 0.00 2.44
3172 7431 3.004839 TGCGCCATTACTAGTTTTGCAAA 59.995 39.130 8.05 8.05 0.00 3.68
3173 7432 2.554462 TGCGCCATTACTAGTTTTGCAA 59.446 40.909 4.18 0.00 0.00 4.08
3174 7433 2.095466 GTGCGCCATTACTAGTTTTGCA 60.095 45.455 4.18 0.72 0.00 4.08
3175 7434 2.515912 GTGCGCCATTACTAGTTTTGC 58.484 47.619 4.18 0.00 0.00 3.68
3176 7435 2.486203 TGGTGCGCCATTACTAGTTTTG 59.514 45.455 16.89 0.00 40.46 2.44
3177 7436 2.785562 TGGTGCGCCATTACTAGTTTT 58.214 42.857 16.89 0.00 40.46 2.43
3178 7437 2.483014 TGGTGCGCCATTACTAGTTT 57.517 45.000 16.89 0.00 40.46 2.66
3188 7447 2.663520 CAGTTACGTGGTGCGCCA 60.664 61.111 16.89 16.89 46.11 5.69
3189 7448 3.419759 CCAGTTACGTGGTGCGCC 61.420 66.667 10.11 10.11 46.11 6.53
3195 7454 3.419759 GGCGCACCAGTTACGTGG 61.420 66.667 10.83 0.00 44.01 4.94
3196 7455 2.663520 TGGCGCACCAGTTACGTG 60.664 61.111 10.83 0.00 42.67 4.49
3205 7464 0.928229 CTCGTTACTAATGGCGCACC 59.072 55.000 10.83 0.00 0.00 5.01
3206 7465 0.928229 CCTCGTTACTAATGGCGCAC 59.072 55.000 10.83 0.00 0.00 5.34
3207 7466 0.179094 CCCTCGTTACTAATGGCGCA 60.179 55.000 10.83 0.00 0.00 6.09
3208 7467 0.179092 ACCCTCGTTACTAATGGCGC 60.179 55.000 0.00 0.00 0.00 6.53
3209 7468 2.304751 AACCCTCGTTACTAATGGCG 57.695 50.000 0.00 0.00 0.00 5.69
3218 7477 2.760092 ACGCCATTAGTAACCCTCGTTA 59.240 45.455 0.00 0.00 33.17 3.18
3219 7478 1.551883 ACGCCATTAGTAACCCTCGTT 59.448 47.619 0.00 0.00 35.90 3.85
3220 7479 1.188863 ACGCCATTAGTAACCCTCGT 58.811 50.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.