Multiple sequence alignment - TraesCS7B01G314900

Loading Multiple Alignment...

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 TraesCS7B01G314900 chr7B 100.000 3815 0 0 1 3815 562410442 562406628 0.000000e+00 7046.0
1 TraesCS7B01G314900 chr7D 92.190 1959 114 20 968 2920 525774602 525772677 0.000000e+00 2734.0
2 TraesCS7B01G314900 chr7D 91.910 445 22 7 479 918 525775334 525774899 9.060000e-171 610.0
3 TraesCS7B01G314900 chr7D 85.179 641 38 27 3211 3815 525772316 525771697 4.220000e-169 604.0
4 TraesCS7B01G314900 chr7D 88.750 320 36 0 1033 1352 525989239 525988920 3.570000e-105 392.0
5 TraesCS7B01G314900 chr7D 87.500 64 3 1 3017 3075 525772610 525772547 6.840000e-08 69.4
6 TraesCS7B01G314900 chr7A 92.723 1594 77 19 1048 2611 606331062 606329478 0.000000e+00 2265.0
7 TraesCS7B01G314900 chr7A 90.846 1016 54 17 37 1024 606332506 606331502 0.000000e+00 1325.0
8 TraesCS7B01G314900 chr7A 83.121 1333 89 57 2543 3815 606329513 606328257 0.000000e+00 1090.0
9 TraesCS7B01G314900 chr6D 84.834 1022 140 15 1088 2101 60168277 60167263 0.000000e+00 1014.0
10 TraesCS7B01G314900 chr6B 84.375 1024 141 17 1088 2101 134000320 133999306 0.000000e+00 987.0
11 TraesCS7B01G314900 chr6A 83.965 1029 145 16 1088 2101 76638901 76637878 0.000000e+00 968.0
12 TraesCS7B01G314900 chr1D 78.933 731 142 11 1107 1834 119010762 119010041 1.590000e-133 486.0
13 TraesCS7B01G314900 chr1B 78.729 724 140 13 1115 1834 181218229 181217516 4.460000e-129 472.0
14 TraesCS7B01G314900 chr3D 79.815 649 120 11 1103 1747 75355796 75356437 2.680000e-126 462.0
15 TraesCS7B01G314900 chr1A 78.279 732 145 13 1107 1834 131521550 131520829 3.470000e-125 459.0


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 TraesCS7B01G314900 chr7B 562406628 562410442 3814 True 7046.00 7046 100.000000 1 3815 1 chr7B.!!$R1 3814
1 TraesCS7B01G314900 chr7D 525771697 525775334 3637 True 1004.35 2734 89.194750 479 3815 4 chr7D.!!$R2 3336
2 TraesCS7B01G314900 chr7A 606328257 606332506 4249 True 1560.00 2265 88.896667 37 3815 3 chr7A.!!$R1 3778
3 TraesCS7B01G314900 chr6D 60167263 60168277 1014 True 1014.00 1014 84.834000 1088 2101 1 chr6D.!!$R1 1013
4 TraesCS7B01G314900 chr6B 133999306 134000320 1014 True 987.00 987 84.375000 1088 2101 1 chr6B.!!$R1 1013
5 TraesCS7B01G314900 chr6A 76637878 76638901 1023 True 968.00 968 83.965000 1088 2101 1 chr6A.!!$R1 1013
6 TraesCS7B01G314900 chr1D 119010041 119010762 721 True 486.00 486 78.933000 1107 1834 1 chr1D.!!$R1 727
7 TraesCS7B01G314900 chr1B 181217516 181218229 713 True 472.00 472 78.729000 1115 1834 1 chr1B.!!$R1 719
8 TraesCS7B01G314900 chr3D 75355796 75356437 641 False 462.00 462 79.815000 1103 1747 1 chr3D.!!$F1 644
9 TraesCS7B01G314900 chr1A 131520829 131521550 721 True 459.00 459 78.279000 1107 1834 1 chr1A.!!$R1 727


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
870 890 0.120377 TAACCCTCCATGTGACCCCT 59.880 55.000 0.00 0.0 0.00 4.79 F
1540 2245 1.005394 TTCAACGAGTTCGAGGGCC 60.005 57.895 8.72 0.0 43.02 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 2794 0.390340 GCTGATTCCTGACACTGCGA 60.390 55.0 0.0 0.0 0.0 5.10 R
3138 3940 0.178885 AACTAGTACCCCAGTGCCCA 60.179 55.0 0.0 0.0 0.0 5.36 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
18 19 1.059681 GACGACAGAGACTCGAGCG 59.940 63.158 13.61 8.60 35.08 5.03
19 20 1.352882 GACGACAGAGACTCGAGCGA 61.353 60.000 13.61 0.00 35.08 4.93
20 21 1.346879 CGACAGAGACTCGAGCGAG 59.653 63.158 13.61 17.46 46.91 5.03
21 22 1.079317 CGACAGAGACTCGAGCGAGA 61.079 60.000 24.81 0.00 44.53 4.04
22 23 0.650512 GACAGAGACTCGAGCGAGAG 59.349 60.000 24.81 9.44 44.53 3.20
23 24 0.248012 ACAGAGACTCGAGCGAGAGA 59.752 55.000 24.81 0.00 44.53 3.10
24 25 0.930310 CAGAGACTCGAGCGAGAGAG 59.070 60.000 24.81 8.47 44.53 3.20
25 26 0.179084 AGAGACTCGAGCGAGAGAGG 60.179 60.000 24.81 0.86 44.53 3.69
26 27 1.153249 AGACTCGAGCGAGAGAGGG 60.153 63.158 24.81 0.14 44.53 4.30
27 28 1.153329 GACTCGAGCGAGAGAGGGA 60.153 63.158 24.81 0.00 44.53 4.20
28 29 0.745128 GACTCGAGCGAGAGAGGGAA 60.745 60.000 24.81 0.00 44.53 3.97
29 30 0.322636 ACTCGAGCGAGAGAGGGAAA 60.323 55.000 24.81 0.00 44.53 3.13
30 31 0.811915 CTCGAGCGAGAGAGGGAAAA 59.188 55.000 14.28 0.00 44.53 2.29
31 32 0.526662 TCGAGCGAGAGAGGGAAAAC 59.473 55.000 0.00 0.00 0.00 2.43
32 33 0.528470 CGAGCGAGAGAGGGAAAACT 59.472 55.000 0.00 0.00 0.00 2.66
33 34 1.067495 CGAGCGAGAGAGGGAAAACTT 60.067 52.381 0.00 0.00 0.00 2.66
34 35 2.610727 CGAGCGAGAGAGGGAAAACTTT 60.611 50.000 0.00 0.00 0.00 2.66
35 36 3.367087 CGAGCGAGAGAGGGAAAACTTTA 60.367 47.826 0.00 0.00 0.00 1.85
36 37 4.678309 CGAGCGAGAGAGGGAAAACTTTAT 60.678 45.833 0.00 0.00 0.00 1.40
37 38 5.167303 AGCGAGAGAGGGAAAACTTTATT 57.833 39.130 0.00 0.00 0.00 1.40
38 39 5.561679 AGCGAGAGAGGGAAAACTTTATTT 58.438 37.500 0.00 0.00 0.00 1.40
39 40 6.004574 AGCGAGAGAGGGAAAACTTTATTTT 58.995 36.000 0.00 0.00 0.00 1.82
40 41 6.490381 AGCGAGAGAGGGAAAACTTTATTTTT 59.510 34.615 0.00 0.00 0.00 1.94
41 42 6.802348 GCGAGAGAGGGAAAACTTTATTTTTC 59.198 38.462 0.00 0.58 42.45 2.29
42 43 7.308649 GCGAGAGAGGGAAAACTTTATTTTTCT 60.309 37.037 7.94 0.00 42.68 2.52
43 44 8.017946 CGAGAGAGGGAAAACTTTATTTTTCTG 58.982 37.037 7.94 0.00 42.68 3.02
44 45 8.996651 AGAGAGGGAAAACTTTATTTTTCTGA 57.003 30.769 7.94 0.00 42.68 3.27
64 65 7.351414 TCTGAATATGTTTGAAGAAGTCGTG 57.649 36.000 0.00 0.00 0.00 4.35
69 70 3.057019 TGTTTGAAGAAGTCGTGGATCG 58.943 45.455 0.00 0.00 41.41 3.69
90 91 2.273588 TTAATAGGGGCCCGGTGTGC 62.274 60.000 18.95 0.00 0.00 4.57
151 152 3.119495 GGTGCACACTACAAAATCCCATC 60.119 47.826 20.43 0.00 0.00 3.51
154 155 3.627577 GCACACTACAAAATCCCATCGAT 59.372 43.478 0.00 0.00 0.00 3.59
198 199 9.378551 TGTATTTTAGTCATCGATTAAAGTGCT 57.621 29.630 0.00 0.00 28.53 4.40
201 202 6.662414 TTAGTCATCGATTAAAGTGCTTGG 57.338 37.500 0.00 0.00 0.00 3.61
202 203 3.941483 AGTCATCGATTAAAGTGCTTGGG 59.059 43.478 0.00 0.00 0.00 4.12
211 212 6.349777 CGATTAAAGTGCTTGGGTTGGATTAA 60.350 38.462 0.00 0.00 0.00 1.40
217 218 3.768757 TGCTTGGGTTGGATTAAATCTGG 59.231 43.478 0.00 0.00 0.00 3.86
231 232 1.496060 ATCTGGCCGTAACCATCTCA 58.504 50.000 0.00 0.00 39.54 3.27
237 238 1.859080 GCCGTAACCATCTCAATCGAC 59.141 52.381 0.00 0.00 0.00 4.20
254 255 3.521560 TCGACCAACAATATGTGAGCTC 58.478 45.455 6.82 6.82 0.00 4.09
267 268 2.231235 TGTGAGCTCGTACACACATGAT 59.769 45.455 9.64 0.00 41.19 2.45
274 275 4.202020 GCTCGTACACACATGATAAGAGGA 60.202 45.833 0.00 0.00 0.00 3.71
275 276 5.500645 TCGTACACACATGATAAGAGGAG 57.499 43.478 0.00 0.00 0.00 3.69
281 282 4.406972 CACACATGATAAGAGGAGGGAAGA 59.593 45.833 0.00 0.00 0.00 2.87
307 308 4.499696 CCCGAGAAGTTCAAACAAATTGCT 60.500 41.667 5.50 0.00 38.98 3.91
366 367 8.024865 TCAACAATTAAGAACATGATCTGCTTG 58.975 33.333 6.22 12.00 0.00 4.01
370 371 9.282247 CAATTAAGAACATGATCTGCTTGTTAC 57.718 33.333 6.22 0.00 42.77 2.50
374 375 7.175347 AGAACATGATCTGCTTGTTACTAGA 57.825 36.000 4.45 0.00 42.77 2.43
378 379 8.067751 ACATGATCTGCTTGTTACTAGAACTA 57.932 34.615 0.00 0.00 31.44 2.24
381 382 7.763356 TGATCTGCTTGTTACTAGAACTAGAC 58.237 38.462 14.64 5.14 36.97 2.59
462 463 2.093658 TGGACGGGACTAATCTTTGAGC 60.094 50.000 0.00 0.00 0.00 4.26
496 500 5.049405 TGCGATTTTTCTCTCCTTGAAAGTC 60.049 40.000 0.00 0.00 35.27 3.01
502 506 7.568199 TTTTCTCTCCTTGAAAGTCGATTTT 57.432 32.000 5.50 5.50 35.27 1.82
531 535 2.802816 CAATTGGAGGCATAGCTCGTAC 59.197 50.000 0.00 0.00 0.00 3.67
532 536 1.776662 TTGGAGGCATAGCTCGTACT 58.223 50.000 0.00 0.00 0.00 2.73
535 539 2.158652 TGGAGGCATAGCTCGTACTACT 60.159 50.000 0.00 0.00 0.00 2.57
536 540 3.072038 TGGAGGCATAGCTCGTACTACTA 59.928 47.826 0.00 0.00 0.00 1.82
537 541 3.436359 GGAGGCATAGCTCGTACTACTAC 59.564 52.174 0.00 0.00 0.00 2.73
539 543 2.805099 GGCATAGCTCGTACTACTACGT 59.195 50.000 0.00 0.00 45.14 3.57
540 544 3.363772 GGCATAGCTCGTACTACTACGTG 60.364 52.174 0.00 1.85 45.14 4.49
541 545 3.363772 GCATAGCTCGTACTACTACGTGG 60.364 52.174 0.00 0.00 45.14 4.94
542 546 1.012841 AGCTCGTACTACTACGTGGC 58.987 55.000 0.00 11.26 45.14 5.01
543 547 0.315706 GCTCGTACTACTACGTGGCG 60.316 60.000 0.00 0.00 45.14 5.69
587 591 2.821969 CCTGGGGATGTCAAGTCTTTTG 59.178 50.000 0.00 0.00 0.00 2.44
653 662 2.038557 ACTCAACTAATGAAGCCACGGT 59.961 45.455 0.00 0.00 37.67 4.83
701 711 4.744137 TGCACGGATCAAACATTCAAAAAG 59.256 37.500 0.00 0.00 0.00 2.27
714 725 4.759516 TTCAAAAAGATTAGCACGGACC 57.240 40.909 0.00 0.00 0.00 4.46
760 774 2.601194 TTTGACTCTGCGGCCACACA 62.601 55.000 2.24 0.00 0.00 3.72
870 890 0.120377 TAACCCTCCATGTGACCCCT 59.880 55.000 0.00 0.00 0.00 4.79
1540 2245 1.005394 TTCAACGAGTTCGAGGGCC 60.005 57.895 8.72 0.00 43.02 5.80
1789 2494 1.225704 GGGATGCTCAGGAAGGTGG 59.774 63.158 0.00 0.00 0.00 4.61
2089 2794 2.356313 CGTTCGACTGCAGCAGGT 60.356 61.111 26.38 11.96 35.51 4.00
2102 2807 3.051210 CAGGTCGCAGTGTCAGGA 58.949 61.111 0.00 0.00 0.00 3.86
2104 2809 0.036952 CAGGTCGCAGTGTCAGGAAT 60.037 55.000 0.00 0.00 0.00 3.01
2107 2812 1.354040 GTCGCAGTGTCAGGAATCAG 58.646 55.000 0.00 0.00 0.00 2.90
2110 2815 1.085091 GCAGTGTCAGGAATCAGCAG 58.915 55.000 0.00 0.00 0.00 4.24
2111 2816 1.735386 CAGTGTCAGGAATCAGCAGG 58.265 55.000 0.00 0.00 0.00 4.85
2136 2841 2.825836 CCAGGCAAGGGATCGCAC 60.826 66.667 12.83 0.87 0.00 5.34
2137 2842 3.197790 CAGGCAAGGGATCGCACG 61.198 66.667 12.83 3.39 0.00 5.34
2138 2843 4.473520 AGGCAAGGGATCGCACGG 62.474 66.667 12.83 1.99 0.00 4.94
2139 2844 4.467084 GGCAAGGGATCGCACGGA 62.467 66.667 12.83 0.00 0.00 4.69
2191 2896 3.833645 CGAGGGGCCATCGTCGAA 61.834 66.667 30.65 0.00 44.61 3.71
2192 2897 2.107141 GAGGGGCCATCGTCGAAG 59.893 66.667 4.39 0.00 0.00 3.79
2194 2899 3.782443 GGGGCCATCGTCGAAGGT 61.782 66.667 17.19 0.00 0.00 3.50
2195 2900 2.202892 GGGCCATCGTCGAAGGTC 60.203 66.667 17.19 15.01 0.00 3.85
2196 2901 2.582498 GGCCATCGTCGAAGGTCG 60.582 66.667 17.19 0.00 42.10 4.79
2197 2902 3.255379 GCCATCGTCGAAGGTCGC 61.255 66.667 17.19 0.29 40.21 5.19
2200 2905 4.849329 ATCGTCGAAGGTCGCCGC 62.849 66.667 0.00 0.00 41.26 6.53
2371 3097 4.394712 CCTCCTCCGCACCACCAC 62.395 72.222 0.00 0.00 0.00 4.16
2557 3283 3.650950 CACCACCCCCTCCACCAG 61.651 72.222 0.00 0.00 0.00 4.00
2595 3354 3.036429 ATCCTCTCCACCAAGCGGC 62.036 63.158 0.00 0.00 34.57 6.53
2770 3529 2.270205 CTCCAATGCCGCTGGTCT 59.730 61.111 0.00 0.00 35.30 3.85
2778 3537 4.143333 CCGCTGGTCTACGGGGTG 62.143 72.222 0.00 0.00 45.74 4.61
2781 3540 2.882876 CTGGTCTACGGGGTGTCG 59.117 66.667 0.00 0.00 0.00 4.35
2929 3692 4.767255 CCAGCCAGCCAGTCCGTC 62.767 72.222 0.00 0.00 0.00 4.79
2930 3693 4.767255 CAGCCAGCCAGTCCGTCC 62.767 72.222 0.00 0.00 0.00 4.79
2933 3696 4.436998 CCAGCCAGTCCGTCCGTC 62.437 72.222 0.00 0.00 0.00 4.79
2934 3697 4.436998 CAGCCAGTCCGTCCGTCC 62.437 72.222 0.00 0.00 0.00 4.79
2937 3700 3.677648 CCAGTCCGTCCGTCCGTT 61.678 66.667 0.00 0.00 0.00 4.44
2938 3701 2.126580 CAGTCCGTCCGTCCGTTC 60.127 66.667 0.00 0.00 0.00 3.95
2939 3702 3.730761 AGTCCGTCCGTCCGTTCG 61.731 66.667 0.00 0.00 0.00 3.95
2940 3703 4.030452 GTCCGTCCGTCCGTTCGT 62.030 66.667 0.00 0.00 0.00 3.85
2941 3704 3.726517 TCCGTCCGTCCGTTCGTC 61.727 66.667 0.00 0.00 0.00 4.20
2942 3705 4.766088 CCGTCCGTCCGTTCGTCC 62.766 72.222 0.00 0.00 0.00 4.79
2944 3707 4.030452 GTCCGTCCGTTCGTCCGT 62.030 66.667 0.00 0.00 0.00 4.69
2945 3708 3.726517 TCCGTCCGTTCGTCCGTC 61.727 66.667 0.00 0.00 0.00 4.79
2946 3709 4.766088 CCGTCCGTTCGTCCGTCC 62.766 72.222 0.00 0.00 0.00 4.79
2948 3711 4.030452 GTCCGTTCGTCCGTCCGT 62.030 66.667 0.00 0.00 0.00 4.69
2949 3712 3.726517 TCCGTTCGTCCGTCCGTC 61.727 66.667 0.00 0.00 0.00 4.79
2950 3713 4.766088 CCGTTCGTCCGTCCGTCC 62.766 72.222 0.00 0.00 0.00 4.79
2952 3715 4.030452 GTTCGTCCGTCCGTCCGT 62.030 66.667 0.00 0.00 0.00 4.69
2953 3716 4.029186 TTCGTCCGTCCGTCCGTG 62.029 66.667 0.00 0.00 0.00 4.94
2960 3723 4.773117 GTCCGTCCGTGGCTCGTC 62.773 72.222 8.25 0.35 37.94 4.20
2979 3754 2.092323 TCCGTCACCAGTACATCTCTG 58.908 52.381 0.00 0.00 0.00 3.35
2987 3762 3.027412 CCAGTACATCTCTGCCTGTAGT 58.973 50.000 0.00 0.00 32.94 2.73
2993 3768 4.573900 ACATCTCTGCCTGTAGTTTCTTG 58.426 43.478 0.00 0.00 0.00 3.02
2994 3769 3.045601 TCTCTGCCTGTAGTTTCTTGC 57.954 47.619 0.00 0.00 0.00 4.01
2995 3770 2.634940 TCTCTGCCTGTAGTTTCTTGCT 59.365 45.455 0.00 0.00 0.00 3.91
2997 3772 2.634940 TCTGCCTGTAGTTTCTTGCTCT 59.365 45.455 0.00 0.00 0.00 4.09
2999 3774 2.289694 TGCCTGTAGTTTCTTGCTCTCC 60.290 50.000 0.00 0.00 0.00 3.71
3000 3775 2.027653 GCCTGTAGTTTCTTGCTCTCCT 60.028 50.000 0.00 0.00 0.00 3.69
3006 3781 2.831526 AGTTTCTTGCTCTCCTCCTCTC 59.168 50.000 0.00 0.00 0.00 3.20
3011 3786 0.707024 TGCTCTCCTCCTCTCCTTGA 59.293 55.000 0.00 0.00 0.00 3.02
3022 3797 5.705905 CCTCCTCTCCTTGAACGTTATTTTT 59.294 40.000 0.00 0.00 0.00 1.94
3086 3884 7.367285 CGAATTAAATTCCAAACAAGTCTCCA 58.633 34.615 0.00 0.00 35.89 3.86
3103 3901 2.985896 TCCACGGTGGATTCTTTCATC 58.014 47.619 25.53 0.00 42.67 2.92
3104 3902 2.304470 TCCACGGTGGATTCTTTCATCA 59.696 45.455 25.53 0.00 42.67 3.07
3105 3903 3.054434 TCCACGGTGGATTCTTTCATCAT 60.054 43.478 25.53 0.00 42.67 2.45
3108 3906 5.335127 CACGGTGGATTCTTTCATCATTTC 58.665 41.667 0.00 0.00 0.00 2.17
3115 3917 9.264719 GTGGATTCTTTCATCATTTCTGTTTTT 57.735 29.630 0.00 0.00 0.00 1.94
3136 3938 1.171549 TGCTCGATTGCTGTTTGCCA 61.172 50.000 0.00 0.00 42.00 4.92
3138 3940 0.877071 CTCGATTGCTGTTTGCCACT 59.123 50.000 0.00 0.00 42.00 4.00
3141 3943 0.037975 GATTGCTGTTTGCCACTGGG 60.038 55.000 0.00 0.00 42.00 4.45
3153 3955 2.207189 ACTGGGCACTGGGGTACT 59.793 61.111 0.00 0.00 0.00 2.73
3154 3956 0.907704 CACTGGGCACTGGGGTACTA 60.908 60.000 0.00 0.00 0.00 1.82
3158 3960 0.989602 GGGCACTGGGGTACTAGTTT 59.010 55.000 0.00 0.00 0.00 2.66
3166 3968 2.916934 TGGGGTACTAGTTTCCATGCTT 59.083 45.455 0.00 0.00 0.00 3.91
3227 4124 2.260154 TGGTTGTGGCATGCACGAG 61.260 57.895 21.36 0.00 0.00 4.18
3231 4128 3.857854 GTGGCATGCACGAGCGAG 61.858 66.667 21.36 0.00 46.23 5.03
3261 4162 0.247419 CATGCATGCGAGAACACGTC 60.247 55.000 14.93 0.00 35.59 4.34
3287 4188 1.709760 CACACGAGTTATGCTGGCG 59.290 57.895 0.00 0.00 0.00 5.69
3366 4275 3.897239 TGCCTAATGAATGGAACGGATT 58.103 40.909 0.00 0.00 0.00 3.01
3427 4336 3.317993 GTGGCGCCATTTATTTACTCCAT 59.682 43.478 35.23 0.00 0.00 3.41
3429 4338 3.308530 GCGCCATTTATTTACTCCATGC 58.691 45.455 0.00 0.00 0.00 4.06
3450 4359 1.388065 ATGGACTTCGAGCCTCTCCG 61.388 60.000 0.00 0.00 0.00 4.63
3451 4360 2.776913 GGACTTCGAGCCTCTCCGG 61.777 68.421 0.00 0.00 0.00 5.14
3452 4361 2.035940 ACTTCGAGCCTCTCCGGT 59.964 61.111 0.00 0.00 34.25 5.28
3458 4367 3.966930 GAGCCTCTCCGGTGGGTCT 62.967 68.421 24.57 10.68 45.00 3.85
3459 4368 3.462678 GCCTCTCCGGTGGGTCTC 61.463 72.222 0.00 0.00 34.25 3.36
3461 4370 2.037367 CTCTCCGGTGGGTCTCCA 59.963 66.667 0.00 0.00 41.58 3.86
3469 4378 2.447572 TGGGTCTCCACAGGTGCA 60.448 61.111 0.00 0.00 38.32 4.57
3525 4434 4.345859 ACCAGAACGTTATGACTTGGAA 57.654 40.909 23.78 0.00 0.00 3.53
3528 4437 4.627467 CCAGAACGTTATGACTTGGAAGAG 59.373 45.833 23.78 0.00 0.00 2.85
3532 4441 4.566987 ACGTTATGACTTGGAAGAGGTTC 58.433 43.478 0.00 0.00 0.00 3.62
3533 4442 4.283722 ACGTTATGACTTGGAAGAGGTTCT 59.716 41.667 0.00 0.00 32.72 3.01
3570 4498 2.955614 TCTTTCGAGGTCCGTGATTTC 58.044 47.619 0.00 0.00 39.75 2.17
3592 4528 2.362503 ACGTGGGAGCGGATGAGA 60.363 61.111 0.00 0.00 35.98 3.27
3595 4531 3.157252 TGGGAGCGGATGAGAGGC 61.157 66.667 0.00 0.00 0.00 4.70
3596 4532 3.934962 GGGAGCGGATGAGAGGCC 61.935 72.222 0.00 0.00 0.00 5.19
3614 4550 1.312815 CCCTAGTAATTGCTGCCTGC 58.687 55.000 6.28 0.00 43.25 4.85
3615 4551 1.312815 CCTAGTAATTGCTGCCTGCC 58.687 55.000 6.28 0.00 42.00 4.85
3616 4552 1.408683 CCTAGTAATTGCTGCCTGCCA 60.409 52.381 6.28 0.00 42.00 4.92
3617 4553 1.945394 CTAGTAATTGCTGCCTGCCAG 59.055 52.381 6.28 0.00 44.67 4.85
3660 4615 0.534877 TCTGCAACCACAACTGCGAT 60.535 50.000 0.00 0.00 41.63 4.58
3732 4698 4.662961 GCCGTTTGCCACCCAAGC 62.663 66.667 0.00 0.00 34.34 4.01
3733 4699 3.222855 CCGTTTGCCACCCAAGCA 61.223 61.111 0.00 0.00 38.81 3.91
3734 4700 2.027460 CGTTTGCCACCCAAGCAC 59.973 61.111 0.00 0.00 40.69 4.40
3787 4755 0.037790 GAGATCCTATGAGCGTGCCC 60.038 60.000 0.00 0.00 30.37 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.059681 CGCTCGAGTCTCTGTCGTC 59.940 63.158 15.13 0.00 38.60 4.20
1 2 1.355796 CTCGCTCGAGTCTCTGTCGT 61.356 60.000 15.13 0.00 38.60 4.34
2 3 1.079317 TCTCGCTCGAGTCTCTGTCG 61.079 60.000 15.13 7.15 42.49 4.35
3 4 0.650512 CTCTCGCTCGAGTCTCTGTC 59.349 60.000 15.13 0.00 42.49 3.51
4 5 0.248012 TCTCTCGCTCGAGTCTCTGT 59.752 55.000 15.13 0.00 42.49 3.41
5 6 0.930310 CTCTCTCGCTCGAGTCTCTG 59.070 60.000 15.13 2.59 42.49 3.35
6 7 0.179084 CCTCTCTCGCTCGAGTCTCT 60.179 60.000 15.13 0.00 42.49 3.10
7 8 1.157870 CCCTCTCTCGCTCGAGTCTC 61.158 65.000 15.13 0.00 42.49 3.36
9 10 0.745128 TTCCCTCTCTCGCTCGAGTC 60.745 60.000 15.13 5.54 42.49 3.36
10 11 0.322636 TTTCCCTCTCTCGCTCGAGT 60.323 55.000 15.13 0.00 42.49 4.18
11 12 0.811915 TTTTCCCTCTCTCGCTCGAG 59.188 55.000 8.45 8.45 43.21 4.04
12 13 0.526662 GTTTTCCCTCTCTCGCTCGA 59.473 55.000 0.00 0.00 0.00 4.04
13 14 0.528470 AGTTTTCCCTCTCTCGCTCG 59.472 55.000 0.00 0.00 0.00 5.03
14 15 2.753055 AAGTTTTCCCTCTCTCGCTC 57.247 50.000 0.00 0.00 0.00 5.03
15 16 4.828072 ATAAAGTTTTCCCTCTCTCGCT 57.172 40.909 0.00 0.00 0.00 4.93
16 17 5.881777 AAATAAAGTTTTCCCTCTCTCGC 57.118 39.130 0.00 0.00 0.00 5.03
17 18 8.017946 CAGAAAAATAAAGTTTTCCCTCTCTCG 58.982 37.037 10.93 0.00 44.93 4.04
18 19 9.067986 TCAGAAAAATAAAGTTTTCCCTCTCTC 57.932 33.333 10.93 0.00 44.93 3.20
19 20 8.996651 TCAGAAAAATAAAGTTTTCCCTCTCT 57.003 30.769 10.93 0.00 44.93 3.10
36 37 9.663904 CGACTTCTTCAAACATATTCAGAAAAA 57.336 29.630 0.00 0.00 0.00 1.94
37 38 8.836413 ACGACTTCTTCAAACATATTCAGAAAA 58.164 29.630 0.00 0.00 0.00 2.29
38 39 8.282592 CACGACTTCTTCAAACATATTCAGAAA 58.717 33.333 0.00 0.00 0.00 2.52
39 40 7.095229 CCACGACTTCTTCAAACATATTCAGAA 60.095 37.037 0.00 0.00 0.00 3.02
40 41 6.368791 CCACGACTTCTTCAAACATATTCAGA 59.631 38.462 0.00 0.00 0.00 3.27
41 42 6.368791 TCCACGACTTCTTCAAACATATTCAG 59.631 38.462 0.00 0.00 0.00 3.02
42 43 6.227522 TCCACGACTTCTTCAAACATATTCA 58.772 36.000 0.00 0.00 0.00 2.57
43 44 6.721571 TCCACGACTTCTTCAAACATATTC 57.278 37.500 0.00 0.00 0.00 1.75
44 45 6.036083 CGATCCACGACTTCTTCAAACATATT 59.964 38.462 0.00 0.00 45.77 1.28
64 65 1.134491 CGGGCCCCTATTAATCGATCC 60.134 57.143 18.66 0.00 0.00 3.36
69 70 0.769247 ACACCGGGCCCCTATTAATC 59.231 55.000 18.66 0.00 0.00 1.75
71 72 1.916738 CACACCGGGCCCCTATTAA 59.083 57.895 18.66 0.00 0.00 1.40
90 91 1.691196 TTGAGGGTTTCAAGGCACAG 58.309 50.000 0.00 0.00 40.82 3.66
145 146 1.679680 GAACGGTAGTGATCGATGGGA 59.320 52.381 0.54 0.00 31.88 4.37
151 152 3.551890 CAGATTTGGAACGGTAGTGATCG 59.448 47.826 0.00 0.00 34.43 3.69
154 155 5.670792 ATACAGATTTGGAACGGTAGTGA 57.329 39.130 0.00 0.00 0.00 3.41
191 192 5.543790 AGATTTAATCCAACCCAAGCACTTT 59.456 36.000 0.78 0.00 0.00 2.66
198 199 3.103742 GGCCAGATTTAATCCAACCCAA 58.896 45.455 0.00 0.00 0.00 4.12
199 200 2.745968 GGCCAGATTTAATCCAACCCA 58.254 47.619 0.00 0.00 0.00 4.51
200 201 1.681264 CGGCCAGATTTAATCCAACCC 59.319 52.381 2.24 0.00 0.00 4.11
201 202 2.375146 ACGGCCAGATTTAATCCAACC 58.625 47.619 2.24 0.07 0.00 3.77
202 203 4.201980 GGTTACGGCCAGATTTAATCCAAC 60.202 45.833 2.24 0.00 0.00 3.77
211 212 1.837439 TGAGATGGTTACGGCCAGATT 59.163 47.619 2.24 0.00 42.47 2.40
217 218 1.859080 GTCGATTGAGATGGTTACGGC 59.141 52.381 0.00 0.00 0.00 5.68
231 232 4.517285 AGCTCACATATTGTTGGTCGATT 58.483 39.130 0.00 0.00 0.00 3.34
237 238 4.032900 GTGTACGAGCTCACATATTGTTGG 59.967 45.833 15.40 0.00 35.04 3.77
254 255 4.499865 CCCTCCTCTTATCATGTGTGTACG 60.500 50.000 0.00 0.00 0.00 3.67
261 262 3.970640 GGTCTTCCCTCCTCTTATCATGT 59.029 47.826 0.00 0.00 0.00 3.21
281 282 0.841289 TGTTTGAACTTCTCGGGGGT 59.159 50.000 0.00 0.00 0.00 4.95
344 345 9.282247 GTAACAAGCAGATCATGTTCTTAATTG 57.718 33.333 3.44 10.76 37.69 2.32
345 346 9.236006 AGTAACAAGCAGATCATGTTCTTAATT 57.764 29.630 3.44 0.00 37.69 1.40
347 348 9.371136 CTAGTAACAAGCAGATCATGTTCTTAA 57.629 33.333 3.44 0.00 37.69 1.85
350 351 7.175347 TCTAGTAACAAGCAGATCATGTTCT 57.825 36.000 0.16 0.16 37.69 3.01
432 433 2.249309 AGTCCCGTCCATTAGACCTT 57.751 50.000 0.00 0.00 43.08 3.50
496 500 4.277257 TCCAATTGCTCATCGAAAATCG 57.723 40.909 0.00 0.00 42.10 3.34
502 506 0.252761 TGCCTCCAATTGCTCATCGA 59.747 50.000 0.00 0.00 0.00 3.59
531 535 1.722636 GAGGGGACGCCACGTAGTAG 61.723 65.000 11.67 0.00 41.61 2.57
532 536 1.750399 GAGGGGACGCCACGTAGTA 60.750 63.158 11.67 0.00 41.61 1.82
541 545 1.158484 GCGATTTAAGGAGGGGACGC 61.158 60.000 0.00 0.00 38.23 5.19
542 546 0.464452 AGCGATTTAAGGAGGGGACG 59.536 55.000 0.00 0.00 0.00 4.79
543 547 1.954927 CAGCGATTTAAGGAGGGGAC 58.045 55.000 0.00 0.00 0.00 4.46
587 591 1.425428 GTGCGAACCATGTAGCTGC 59.575 57.895 0.00 0.00 0.00 5.25
653 662 5.351948 TCGAATCAGTGGTAAATGGATGA 57.648 39.130 0.00 0.00 0.00 2.92
701 711 3.006940 TGATGTTTGGTCCGTGCTAATC 58.993 45.455 0.00 0.00 0.00 1.75
714 725 0.717896 CGTGTGCGTCGTGATGTTTG 60.718 55.000 0.00 0.00 0.00 2.93
743 757 3.545574 TGTGTGGCCGCAGAGTCA 61.546 61.111 21.93 11.57 0.00 3.41
1789 2494 2.778679 GCTGACATCGAACACGGC 59.221 61.111 0.00 0.00 0.00 5.68
1920 2625 0.540830 AGTTCCTCAGACTCGGCAGT 60.541 55.000 0.00 0.00 34.57 4.40
2064 2769 4.379243 CAGTCGAACGGGCTGGCT 62.379 66.667 0.00 0.00 0.00 4.75
2089 2794 0.390340 GCTGATTCCTGACACTGCGA 60.390 55.000 0.00 0.00 0.00 5.10
2094 2799 1.028868 GCCCTGCTGATTCCTGACAC 61.029 60.000 0.00 0.00 0.00 3.67
2102 2807 4.453892 GGCCTGGCCCTGCTGATT 62.454 66.667 27.77 0.00 44.06 2.57
2119 2824 2.825836 GTGCGATCCCTTGCCTGG 60.826 66.667 0.00 0.00 0.00 4.45
2120 2825 3.197790 CGTGCGATCCCTTGCCTG 61.198 66.667 0.00 0.00 0.00 4.85
2121 2826 4.473520 CCGTGCGATCCCTTGCCT 62.474 66.667 0.00 0.00 0.00 4.75
2122 2827 4.467084 TCCGTGCGATCCCTTGCC 62.467 66.667 0.00 0.00 0.00 4.52
2125 2830 4.162690 GCCTCCGTGCGATCCCTT 62.163 66.667 0.00 0.00 0.00 3.95
2179 2884 2.582498 CGACCTTCGACGATGGCC 60.582 66.667 25.16 16.13 43.74 5.36
2202 2907 2.033602 GTAAACCAGCCTGGCGGT 59.966 61.111 23.39 23.39 42.67 5.68
2313 3039 4.988716 TCGCTGTGGGTCGGAGGT 62.989 66.667 0.00 0.00 0.00 3.85
2316 3042 3.062466 CTCTCGCTGTGGGTCGGA 61.062 66.667 0.00 0.00 0.00 4.55
2424 3150 2.668550 GGTTGGTGACTGGACGGC 60.669 66.667 0.00 0.00 0.00 5.68
2754 3513 1.220749 GTAGACCAGCGGCATTGGA 59.779 57.895 14.49 0.00 39.08 3.53
2765 3524 0.960364 GTACGACACCCCGTAGACCA 60.960 60.000 0.00 0.00 44.40 4.02
2770 3529 2.749839 CCCGTACGACACCCCGTA 60.750 66.667 18.76 0.00 43.20 4.02
2775 3534 4.783734 GGCGACCCGTACGACACC 62.784 72.222 18.76 6.92 38.75 4.16
2920 3683 3.621892 GAACGGACGGACGGACTGG 62.622 68.421 6.00 0.00 38.39 4.00
2922 3685 3.730761 CGAACGGACGGACGGACT 61.731 66.667 6.00 0.00 38.39 3.85
2927 3690 3.935665 GACGGACGAACGGACGGAC 62.936 68.421 14.41 6.96 38.39 4.79
2928 3691 3.726517 GACGGACGAACGGACGGA 61.727 66.667 14.41 0.00 38.39 4.69
2929 3692 4.766088 GGACGGACGAACGGACGG 62.766 72.222 14.41 8.07 38.39 4.79
2931 3694 3.935665 GACGGACGGACGAACGGAC 62.936 68.421 8.01 6.96 38.39 4.79
2932 3695 3.726517 GACGGACGGACGAACGGA 61.727 66.667 8.01 0.00 38.39 4.69
2933 3696 4.766088 GGACGGACGGACGAACGG 62.766 72.222 8.01 8.07 38.39 4.44
2935 3698 4.030452 ACGGACGGACGGACGAAC 62.030 66.667 15.02 2.13 38.39 3.95
2936 3699 4.029186 CACGGACGGACGGACGAA 62.029 66.667 15.02 0.00 38.39 3.85
2951 3714 3.916392 CTGGTGACGGACGAGCCAC 62.916 68.421 0.00 3.72 39.98 5.01
2952 3715 3.680786 CTGGTGACGGACGAGCCA 61.681 66.667 0.00 2.93 39.98 4.75
2953 3716 2.338015 TACTGGTGACGGACGAGCC 61.338 63.158 0.00 0.00 41.09 4.70
2954 3717 1.154073 GTACTGGTGACGGACGAGC 60.154 63.158 0.00 0.00 41.09 5.03
2955 3718 0.809385 ATGTACTGGTGACGGACGAG 59.191 55.000 0.00 0.00 41.09 4.18
2956 3719 0.806868 GATGTACTGGTGACGGACGA 59.193 55.000 0.00 0.00 41.09 4.20
2957 3720 0.809385 AGATGTACTGGTGACGGACG 59.191 55.000 0.00 0.00 41.09 4.79
2958 3721 2.093106 AGAGATGTACTGGTGACGGAC 58.907 52.381 0.00 0.00 41.09 4.79
2959 3722 2.092323 CAGAGATGTACTGGTGACGGA 58.908 52.381 0.00 0.00 41.09 4.69
2960 3723 1.469940 GCAGAGATGTACTGGTGACGG 60.470 57.143 0.00 0.00 44.60 4.79
2979 3754 2.027653 AGGAGAGCAAGAAACTACAGGC 60.028 50.000 0.00 0.00 0.00 4.85
2987 3762 2.183679 GGAGAGGAGGAGAGCAAGAAA 58.816 52.381 0.00 0.00 0.00 2.52
2993 3768 1.480545 GTTCAAGGAGAGGAGGAGAGC 59.519 57.143 0.00 0.00 0.00 4.09
2994 3769 1.748493 CGTTCAAGGAGAGGAGGAGAG 59.252 57.143 0.00 0.00 0.00 3.20
2995 3770 1.075698 ACGTTCAAGGAGAGGAGGAGA 59.924 52.381 0.00 0.00 0.00 3.71
2997 3772 2.011122 AACGTTCAAGGAGAGGAGGA 57.989 50.000 0.00 0.00 0.00 3.71
2999 3774 6.803154 AAAAATAACGTTCAAGGAGAGGAG 57.197 37.500 2.82 0.00 0.00 3.69
3022 3797 5.913137 AACAAATGGACAACAGAGAACAA 57.087 34.783 0.00 0.00 0.00 2.83
3076 3874 4.288234 TCCACCGTGGAGACTTGT 57.712 55.556 16.73 0.00 42.67 3.16
3086 3884 5.124457 CAGAAATGATGAAAGAATCCACCGT 59.876 40.000 0.00 0.00 0.00 4.83
3115 3917 1.769733 GCAAACAGCAATCGAGCAAA 58.230 45.000 0.00 0.00 44.79 3.68
3136 3938 0.617820 CTAGTACCCCAGTGCCCAGT 60.618 60.000 0.00 0.00 0.00 4.00
3138 3940 0.178885 AACTAGTACCCCAGTGCCCA 60.179 55.000 0.00 0.00 0.00 5.36
3141 3943 1.626825 TGGAAACTAGTACCCCAGTGC 59.373 52.381 13.99 0.00 0.00 4.40
3142 3944 3.873910 CATGGAAACTAGTACCCCAGTG 58.126 50.000 13.99 9.62 0.00 3.66
3143 3945 2.238898 GCATGGAAACTAGTACCCCAGT 59.761 50.000 13.99 0.00 0.00 4.00
3144 3946 2.505819 AGCATGGAAACTAGTACCCCAG 59.494 50.000 13.99 7.05 0.00 4.45
3145 3947 2.557869 AGCATGGAAACTAGTACCCCA 58.442 47.619 13.99 12.83 0.00 4.96
3147 3949 4.216411 TCAAGCATGGAAACTAGTACCC 57.784 45.455 13.99 10.46 0.00 3.69
3148 3950 5.741388 CATCAAGCATGGAAACTAGTACC 57.259 43.478 10.86 10.86 0.00 3.34
3166 3968 3.172229 TGCGTCGTTATTCATCCATCA 57.828 42.857 0.00 0.00 0.00 3.07
3197 3999 2.380285 ACAACCACCGGTCCAAGGT 61.380 57.895 2.59 6.25 43.97 3.50
3227 4124 1.947013 CATGCATGTGATCCCTCGC 59.053 57.895 18.91 0.00 0.00 5.03
3231 4128 3.886044 CATGCATGCATGTGATCCC 57.114 52.632 40.30 10.36 46.20 3.85
3287 4188 9.307121 ACACTATGTATAGTATCGTATCGTACC 57.693 37.037 4.35 0.00 41.44 3.34
3300 4201 9.083422 ACTGCTTATCATCACACTATGTATAGT 57.917 33.333 0.00 0.00 44.03 2.12
3301 4202 9.351570 CACTGCTTATCATCACACTATGTATAG 57.648 37.037 0.00 0.00 36.46 1.31
3302 4203 9.077885 TCACTGCTTATCATCACACTATGTATA 57.922 33.333 0.00 0.00 0.00 1.47
3366 4275 9.613428 CCCTAATTGACTAGTCATTCAACATTA 57.387 33.333 25.68 20.99 39.64 1.90
3427 4336 0.391661 GAGGCTCGAAGTCCATTGCA 60.392 55.000 0.00 0.00 0.00 4.08
3429 4338 1.472376 GGAGAGGCTCGAAGTCCATTG 60.472 57.143 13.93 0.00 0.00 2.82
3452 4361 2.447572 TGCACCTGTGGAGACCCA 60.448 61.111 0.00 0.00 40.95 4.51
3458 4367 2.421314 CACGTCTGCACCTGTGGA 59.579 61.111 0.00 0.00 0.00 4.02
3459 4368 3.349006 GCACGTCTGCACCTGTGG 61.349 66.667 8.91 0.00 43.62 4.17
3467 4376 0.318699 TCACTGTACTGCACGTCTGC 60.319 55.000 0.00 0.00 44.52 4.26
3468 4377 2.134201 TTCACTGTACTGCACGTCTG 57.866 50.000 0.00 0.00 0.00 3.51
3469 4378 2.558795 AGATTCACTGTACTGCACGTCT 59.441 45.455 0.00 0.00 0.00 4.18
3570 4498 1.079127 ATCCGCTCCCACGTGAAAG 60.079 57.895 19.30 14.56 0.00 2.62
3592 4528 0.183731 GGCAGCAATTACTAGGGCCT 59.816 55.000 12.58 12.58 37.00 5.19
3595 4531 1.312815 GCAGGCAGCAATTACTAGGG 58.687 55.000 0.00 0.00 44.79 3.53
3660 4615 2.983030 AGGCCGACGCAATTGCAA 60.983 55.556 28.77 0.00 42.21 4.08
3730 4696 5.978814 AGTAATTAACTCCGATCAAGTGCT 58.021 37.500 0.00 0.00 30.33 4.40



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

AutoCloner maintained by Alex Coulton.