Multiple sequence alignment - TraesCS1A01G098900

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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 TraesCS1A01G098900 chr1A 100.000 5738 0 0 1 5738 95058109 95063846 0.000000e+00 10597
1 TraesCS1A01G098900 chr1A 90.030 672 60 6 5049 5719 481170546 481169881 0.000000e+00 863
2 TraesCS1A01G098900 chr1A 95.833 96 4 0 3016 3111 6047668 6047763 7.700000e-34 156
3 TraesCS1A01G098900 chr1D 94.868 3040 91 18 1 3017 99665984 99668981 0.000000e+00 4689
4 TraesCS1A01G098900 chr1D 94.956 1804 73 9 3099 4895 99668980 99670772 0.000000e+00 2811
5 TraesCS1A01G098900 chr1B 94.415 3044 109 13 1 3017 152802366 152799357 0.000000e+00 4623
6 TraesCS1A01G098900 chr1B 95.356 1852 76 8 3099 4943 152799358 152797510 0.000000e+00 2935
7 TraesCS1A01G098900 chr4A 91.260 778 55 2 4961 5738 566814859 566814095 0.000000e+00 1048
8 TraesCS1A01G098900 chr4A 88.250 783 70 14 4961 5725 543056739 543057517 0.000000e+00 917
9 TraesCS1A01G098900 chr5A 88.317 796 71 10 4961 5736 223060092 223060885 0.000000e+00 935
10 TraesCS1A01G098900 chr5A 90.449 691 61 5 5049 5736 533604553 533603865 0.000000e+00 905
11 TraesCS1A01G098900 chr5A 89.689 708 67 6 4961 5664 223066431 223067136 0.000000e+00 898
12 TraesCS1A01G098900 chr5A 90.172 641 57 6 5100 5736 145417066 145417704 0.000000e+00 830
13 TraesCS1A01G098900 chr5A 90.506 632 51 9 5049 5674 145423080 145423708 0.000000e+00 826
14 TraesCS1A01G098900 chr5A 89.783 646 60 6 5093 5735 524899846 524899204 0.000000e+00 822
15 TraesCS1A01G098900 chr5A 88.060 134 16 0 5605 5738 178456199 178456332 5.950000e-35 159
16 TraesCS1A01G098900 chr5A 94.737 95 3 2 3016 3110 25892360 25892268 4.630000e-31 147
17 TraesCS1A01G098900 chr5A 81.667 180 26 7 1128 1304 694983152 694982977 5.990000e-30 143
18 TraesCS1A01G098900 chr6A 88.030 802 69 9 4961 5736 480928012 480928812 0.000000e+00 924
19 TraesCS1A01G098900 chr6A 90.213 705 65 4 4961 5662 480916180 480916883 0.000000e+00 917
20 TraesCS1A01G098900 chr6A 88.050 318 34 4 4961 5274 480909139 480909456 1.950000e-99 374
21 TraesCS1A01G098900 chr3A 88.750 720 68 9 5022 5736 573153470 573152759 0.000000e+00 869
22 TraesCS1A01G098900 chr5D 83.037 731 91 26 5018 5735 399694190 399693480 2.920000e-177 632
23 TraesCS1A01G098900 chr2D 81.989 744 96 31 4993 5719 555327196 555327918 1.060000e-166 597
24 TraesCS1A01G098900 chr2D 95.876 97 4 0 3004 3100 538279159 538279255 2.140000e-34 158
25 TraesCS1A01G098900 chr2D 97.727 44 0 1 4939 4981 255796566 255796523 2.220000e-09 75
26 TraesCS1A01G098900 chr7A 87.462 327 28 9 4961 5274 66075080 66075406 1.170000e-96 364
27 TraesCS1A01G098900 chr7A 96.739 92 3 0 3013 3104 30061255 30061346 2.770000e-33 154
28 TraesCS1A01G098900 chr6D 98.864 88 1 0 3013 3100 68082858 68082945 2.140000e-34 158
29 TraesCS1A01G098900 chr2A 96.842 95 2 1 3016 3109 127212317 127212223 2.140000e-34 158
30 TraesCS1A01G098900 chrUn 95.833 96 3 1 3013 3107 27602653 27602558 2.770000e-33 154
31 TraesCS1A01G098900 chr7D 94.845 97 5 0 3012 3108 11420213 11420117 9.960000e-33 152
32 TraesCS1A01G098900 chr3B 87.805 123 10 4 3003 3124 59025819 59025937 7.750000e-29 139
33 TraesCS1A01G098900 chr4D 81.111 180 27 7 1128 1304 508695077 508694902 2.790000e-28 137
34 TraesCS1A01G098900 chr4B 80.328 183 29 7 1128 1307 659165883 659165705 1.300000e-26 132


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 TraesCS1A01G098900 chr1A 95058109 95063846 5737 False 10597 10597 100.0000 1 5738 1 chr1A.!!$F2 5737
1 TraesCS1A01G098900 chr1A 481169881 481170546 665 True 863 863 90.0300 5049 5719 1 chr1A.!!$R1 670
2 TraesCS1A01G098900 chr1D 99665984 99670772 4788 False 3750 4689 94.9120 1 4895 2 chr1D.!!$F1 4894
3 TraesCS1A01G098900 chr1B 152797510 152802366 4856 True 3779 4623 94.8855 1 4943 2 chr1B.!!$R1 4942
4 TraesCS1A01G098900 chr4A 566814095 566814859 764 True 1048 1048 91.2600 4961 5738 1 chr4A.!!$R1 777
5 TraesCS1A01G098900 chr4A 543056739 543057517 778 False 917 917 88.2500 4961 5725 1 chr4A.!!$F1 764
6 TraesCS1A01G098900 chr5A 223060092 223060885 793 False 935 935 88.3170 4961 5736 1 chr5A.!!$F4 775
7 TraesCS1A01G098900 chr5A 533603865 533604553 688 True 905 905 90.4490 5049 5736 1 chr5A.!!$R3 687
8 TraesCS1A01G098900 chr5A 223066431 223067136 705 False 898 898 89.6890 4961 5664 1 chr5A.!!$F5 703
9 TraesCS1A01G098900 chr5A 145417066 145417704 638 False 830 830 90.1720 5100 5736 1 chr5A.!!$F1 636
10 TraesCS1A01G098900 chr5A 145423080 145423708 628 False 826 826 90.5060 5049 5674 1 chr5A.!!$F2 625
11 TraesCS1A01G098900 chr5A 524899204 524899846 642 True 822 822 89.7830 5093 5735 1 chr5A.!!$R2 642
12 TraesCS1A01G098900 chr6A 480928012 480928812 800 False 924 924 88.0300 4961 5736 1 chr6A.!!$F3 775
13 TraesCS1A01G098900 chr6A 480916180 480916883 703 False 917 917 90.2130 4961 5662 1 chr6A.!!$F2 701
14 TraesCS1A01G098900 chr3A 573152759 573153470 711 True 869 869 88.7500 5022 5736 1 chr3A.!!$R1 714
15 TraesCS1A01G098900 chr5D 399693480 399694190 710 True 632 632 83.0370 5018 5735 1 chr5D.!!$R1 717
16 TraesCS1A01G098900 chr2D 555327196 555327918 722 False 597 597 81.9890 4993 5719 1 chr2D.!!$F2 726

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
152 169 0.875059 CTTTGAGCACCGGTTCTTCC 59.125 55.000 8.54 0.0 0.00 3.46 F
337 355 1.004394 CCGGGGAAAGCCTCTTTACTT 59.996 52.381 0.00 0.0 29.87 2.24 F
1800 1831 0.179067 TTGCCGAGTTCAACTTCCGT 60.179 50.000 0.00 0.0 0.00 4.69 F
2176 2209 0.032540 CTTGAACCTTGCCAGCCAAC 59.967 55.000 0.00 0.0 0.00 3.77 F
3277 3313 0.690192 TCTACATGGGTGTGTGGGTG 59.310 55.000 0.00 0.0 39.39 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 1777 0.870393 CAGAAGAAGCATGCACACGT 59.130 50.0 21.98 8.62 0.00 4.49 R
1979 2012 0.888619 GAGTCAGACCATGGACGTGA 59.111 55.0 21.47 14.57 39.01 4.35 R
2866 2899 0.394488 TTGGGCTCGTTCCACAAACA 60.394 50.0 0.00 0.00 37.77 2.83 R
3495 3534 0.469705 TGCTTTGCCAGATTGGTGGT 60.470 50.0 0.00 0.00 40.46 4.16 R
4934 4979 0.107361 GGTATTCCCCGACACCAAGG 60.107 60.0 0.00 0.00 0.00 3.61 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
152 169 0.875059 CTTTGAGCACCGGTTCTTCC 59.125 55.000 8.54 0.00 0.00 3.46
236 253 7.483018 AGATGTATCCCTCCTCAACAGTATAT 58.517 38.462 0.00 0.00 0.00 0.86
237 254 8.624670 AGATGTATCCCTCCTCAACAGTATATA 58.375 37.037 0.00 0.00 0.00 0.86
238 255 9.427821 GATGTATCCCTCCTCAACAGTATATAT 57.572 37.037 0.00 0.00 0.00 0.86
337 355 1.004394 CCGGGGAAAGCCTCTTTACTT 59.996 52.381 0.00 0.00 29.87 2.24
338 356 2.554564 CCGGGGAAAGCCTCTTTACTTT 60.555 50.000 0.00 0.00 38.78 2.66
339 357 3.154710 CGGGGAAAGCCTCTTTACTTTT 58.845 45.455 2.02 0.00 36.28 2.27
340 358 3.572682 CGGGGAAAGCCTCTTTACTTTTT 59.427 43.478 2.02 0.00 36.28 1.94
524 548 4.615588 AGAGAGGCCATAGAGTTATTGC 57.384 45.455 5.01 0.00 0.00 3.56
581 607 2.576832 GCAAACTGCTGGGGTGCAT 61.577 57.895 0.00 0.00 42.48 3.96
619 645 4.919774 TTGGGTAAATCTGGCTCAAGTA 57.080 40.909 0.00 0.00 0.00 2.24
647 674 5.692814 TGAAACTTTGAATGCGATTCTGAG 58.307 37.500 9.34 9.02 39.96 3.35
653 680 7.492524 ACTTTGAATGCGATTCTGAGTATCTA 58.507 34.615 9.34 0.00 39.96 1.98
656 683 8.893219 TTGAATGCGATTCTGAGTATCTAAAT 57.107 30.769 9.34 0.00 39.96 1.40
822 850 5.188434 CAGGCTGTGAATTCCAGAAATAGA 58.812 41.667 21.24 0.00 31.38 1.98
1123 1153 9.817809 TCTTTAGAGAATATATGACTTGCGTTT 57.182 29.630 0.00 0.00 0.00 3.60
1201 1231 9.565213 GACCAAGATCTTTTTCATGATTTACAG 57.435 33.333 4.86 0.00 0.00 2.74
1312 1342 4.517453 GGTCATGCAAAGGTAACACAGTTA 59.483 41.667 0.00 0.00 41.41 2.24
1361 1391 7.393327 CAAATTTCGTAACCATGATGAATTGC 58.607 34.615 0.00 0.00 0.00 3.56
1746 1777 7.700234 GGAATACGCATTTTGTGACATAATTGA 59.300 33.333 0.00 0.00 0.00 2.57
1800 1831 0.179067 TTGCCGAGTTCAACTTCCGT 60.179 50.000 0.00 0.00 0.00 4.69
2073 2106 8.006298 TGTAGTTCAATTCATTTCAAAGGTGT 57.994 30.769 0.00 0.00 0.00 4.16
2176 2209 0.032540 CTTGAACCTTGCCAGCCAAC 59.967 55.000 0.00 0.00 0.00 3.77
2275 2308 8.439971 TCTGGAATATAACATAGAGGTTGCAAT 58.560 33.333 0.59 0.00 32.29 3.56
2276 2309 8.995027 TGGAATATAACATAGAGGTTGCAATT 57.005 30.769 0.59 0.00 32.29 2.32
2445 2478 2.813754 TGAAGTTGCGGGAAATCAAGAG 59.186 45.455 0.00 0.00 0.00 2.85
2491 2524 3.014037 CCAACATGGTTGTGTCCGA 57.986 52.632 8.16 0.00 35.83 4.55
2866 2899 4.792521 AGATCTTTTCAGCGTGAGTAGT 57.207 40.909 0.00 0.00 0.00 2.73
2875 2908 1.411246 AGCGTGAGTAGTGTTTGTGGA 59.589 47.619 0.00 0.00 0.00 4.02
2925 2958 4.889995 GGGAGAATTTGGATAGGTCCTTTG 59.110 45.833 0.00 0.00 45.32 2.77
2972 3005 8.571461 TTCATCTTTGATTTGAGCTATGTTCT 57.429 30.769 0.00 0.00 0.00 3.01
3022 3055 2.716217 GCAATGTGCTTTCTACTCCCT 58.284 47.619 0.00 0.00 40.96 4.20
3023 3056 2.680339 GCAATGTGCTTTCTACTCCCTC 59.320 50.000 0.00 0.00 40.96 4.30
3024 3057 3.620966 GCAATGTGCTTTCTACTCCCTCT 60.621 47.826 0.00 0.00 40.96 3.69
3025 3058 3.902881 ATGTGCTTTCTACTCCCTCTG 57.097 47.619 0.00 0.00 0.00 3.35
3026 3059 2.609747 TGTGCTTTCTACTCCCTCTGT 58.390 47.619 0.00 0.00 0.00 3.41
3027 3060 3.774734 TGTGCTTTCTACTCCCTCTGTA 58.225 45.455 0.00 0.00 0.00 2.74
3028 3061 4.157246 TGTGCTTTCTACTCCCTCTGTAA 58.843 43.478 0.00 0.00 0.00 2.41
3029 3062 4.591498 TGTGCTTTCTACTCCCTCTGTAAA 59.409 41.667 0.00 0.00 0.00 2.01
3030 3063 4.930405 GTGCTTTCTACTCCCTCTGTAAAC 59.070 45.833 0.00 0.00 0.00 2.01
3031 3064 4.838986 TGCTTTCTACTCCCTCTGTAAACT 59.161 41.667 0.00 0.00 0.00 2.66
3032 3065 6.014647 TGCTTTCTACTCCCTCTGTAAACTA 58.985 40.000 0.00 0.00 0.00 2.24
3033 3066 6.495872 TGCTTTCTACTCCCTCTGTAAACTAA 59.504 38.462 0.00 0.00 0.00 2.24
3034 3067 7.180408 TGCTTTCTACTCCCTCTGTAAACTAAT 59.820 37.037 0.00 0.00 0.00 1.73
3035 3068 8.693625 GCTTTCTACTCCCTCTGTAAACTAATA 58.306 37.037 0.00 0.00 0.00 0.98
3042 3075 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
3043 3076 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
3044 3077 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
3045 3078 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
3046 3079 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
3091 3124 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
3092 3125 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
3093 3126 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
3094 3127 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
3095 3128 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
3096 3129 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
3097 3130 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
3098 3131 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
3099 3132 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
3111 3144 5.654497 ACGGAGGGAGTAGTAATTAAAACG 58.346 41.667 0.00 0.00 0.00 3.60
3277 3313 0.690192 TCTACATGGGTGTGTGGGTG 59.310 55.000 0.00 0.00 39.39 4.61
3646 3687 3.138283 TGGAAGACTCACACCTCCAATTT 59.862 43.478 0.00 0.00 0.00 1.82
3654 3695 7.505585 AGACTCACACCTCCAATTTTTGATAAA 59.494 33.333 0.00 0.00 0.00 1.40
3708 3749 3.879295 TGGATTGATCATTCGCTTTCTCC 59.121 43.478 10.63 1.81 0.00 3.71
3725 3766 4.111375 TCTCCGCTTCTAATTGAGTGAC 57.889 45.455 0.00 0.00 0.00 3.67
3798 3839 4.456911 CCTTGTGAGTTGTAATGAGTGCAT 59.543 41.667 0.00 0.00 35.92 3.96
3854 3895 8.773645 CCTCATCACATACTTATTATTTTCGCA 58.226 33.333 0.00 0.00 0.00 5.10
4038 4083 5.836821 TTATCAGAGCACTACACGATCTT 57.163 39.130 0.00 0.00 0.00 2.40
4098 4143 7.857389 GCATCAAACATTGTCGTGACATATTAT 59.143 33.333 3.14 0.00 41.52 1.28
4118 4163 3.340814 TGGGAGAGTGAAAATCAGAGC 57.659 47.619 0.00 0.00 30.01 4.09
4147 4192 5.221561 TGTTTCAAGAAGACCGTTCCTATGA 60.222 40.000 0.00 0.00 0.00 2.15
4169 4214 3.081061 TGCGCAAAAACTATGAGGATGT 58.919 40.909 8.16 0.00 0.00 3.06
4233 4278 7.816411 AGCTAACTATTATCCCCAAAGATGTT 58.184 34.615 0.00 0.00 0.00 2.71
4235 4280 7.502561 GCTAACTATTATCCCCAAAGATGTTGT 59.497 37.037 0.00 0.00 0.00 3.32
4302 4347 2.585247 GTGATAGGGACGCACGCC 60.585 66.667 0.00 0.00 0.00 5.68
4400 4445 7.775093 CCCTGAACTTAGGTCAAATATTCATGA 59.225 37.037 0.34 0.00 36.02 3.07
4410 4455 8.658619 AGGTCAAATATTCATGAAGCTCTAGAT 58.341 33.333 14.54 0.00 0.00 1.98
4566 4611 4.987408 TGCACACAGAATGGATAAATGG 57.013 40.909 0.00 0.00 43.62 3.16
4653 4698 7.931015 AATGATCTTACTGGTTACCTATCCA 57.069 36.000 2.07 0.00 0.00 3.41
4662 4707 5.072329 ACTGGTTACCTATCCAATGATCCTG 59.928 44.000 2.07 0.00 33.06 3.86
4725 4770 9.618890 CTGAAGGATTTGAATCTTCATAACCTA 57.381 33.333 10.89 0.04 39.32 3.08
4754 4799 7.058023 TCAAGTAACTCCAGCTTTTGTACTA 57.942 36.000 0.00 0.00 0.00 1.82
4884 4929 7.888424 TCATGCTTCATTCTGAATTTTTGAGA 58.112 30.769 0.00 0.00 35.59 3.27
4933 4978 3.822594 TCCGAAAATATGTGTGTGTGC 57.177 42.857 0.00 0.00 0.00 4.57
4934 4979 2.486203 TCCGAAAATATGTGTGTGTGCC 59.514 45.455 0.00 0.00 0.00 5.01
4936 4981 2.487762 CGAAAATATGTGTGTGTGCCCT 59.512 45.455 0.00 0.00 0.00 5.19
4937 4982 3.057596 CGAAAATATGTGTGTGTGCCCTT 60.058 43.478 0.00 0.00 0.00 3.95
4938 4983 3.940209 AAATATGTGTGTGTGCCCTTG 57.060 42.857 0.00 0.00 0.00 3.61
4939 4984 1.838112 ATATGTGTGTGTGCCCTTGG 58.162 50.000 0.00 0.00 0.00 3.61
4941 4986 1.108727 ATGTGTGTGTGCCCTTGGTG 61.109 55.000 0.00 0.00 0.00 4.17
4942 4987 1.752694 GTGTGTGTGCCCTTGGTGT 60.753 57.895 0.00 0.00 0.00 4.16
4943 4988 1.453015 TGTGTGTGCCCTTGGTGTC 60.453 57.895 0.00 0.00 0.00 3.67
4944 4989 2.203139 TGTGTGCCCTTGGTGTCG 60.203 61.111 0.00 0.00 0.00 4.35
4946 4991 4.263572 TGTGCCCTTGGTGTCGGG 62.264 66.667 0.00 0.00 43.60 5.14
4949 4994 3.961414 GCCCTTGGTGTCGGGGAA 61.961 66.667 0.97 0.00 42.58 3.97
4950 4995 3.087065 CCCTTGGTGTCGGGGAAT 58.913 61.111 0.00 0.00 42.58 3.01
4951 4996 1.917336 GCCCTTGGTGTCGGGGAATA 61.917 60.000 0.97 0.00 42.58 1.75
4952 4997 0.107361 CCCTTGGTGTCGGGGAATAC 60.107 60.000 0.00 0.00 42.58 1.89
4953 4998 0.107361 CCTTGGTGTCGGGGAATACC 60.107 60.000 0.00 0.00 39.11 2.73
5116 5183 1.633561 CGGCAGACACAGTCATGTAG 58.366 55.000 0.00 0.00 37.65 2.74
5163 5231 1.734465 GCAGACACAGTCATGTAAGCC 59.266 52.381 0.00 0.00 37.65 4.35
5164 5232 2.871637 GCAGACACAGTCATGTAAGCCA 60.872 50.000 0.00 0.00 37.65 4.75
5165 5233 2.998670 CAGACACAGTCATGTAAGCCAG 59.001 50.000 0.00 0.00 37.65 4.85
5166 5234 2.899900 AGACACAGTCATGTAAGCCAGA 59.100 45.455 0.00 0.00 37.65 3.86
5167 5235 3.517100 AGACACAGTCATGTAAGCCAGAT 59.483 43.478 0.00 0.00 37.65 2.90
5168 5236 4.711846 AGACACAGTCATGTAAGCCAGATA 59.288 41.667 0.00 0.00 37.65 1.98
5169 5237 5.016051 ACACAGTCATGTAAGCCAGATAG 57.984 43.478 0.00 0.00 37.65 2.08
5170 5238 4.467795 ACACAGTCATGTAAGCCAGATAGT 59.532 41.667 0.00 0.00 37.65 2.12
5171 5239 5.046304 ACACAGTCATGTAAGCCAGATAGTT 60.046 40.000 0.00 0.00 37.65 2.24
5172 5240 6.154534 ACACAGTCATGTAAGCCAGATAGTTA 59.845 38.462 0.00 0.00 37.65 2.24
5173 5241 7.041721 CACAGTCATGTAAGCCAGATAGTTAA 58.958 38.462 0.00 0.00 37.65 2.01
5174 5242 7.549134 CACAGTCATGTAAGCCAGATAGTTAAA 59.451 37.037 0.00 0.00 37.65 1.52
5357 5522 4.282703 AGTTGAACTCTACATGTAACCCGT 59.717 41.667 7.06 0.00 0.00 5.28
5381 5546 6.500751 GTCCCTTCAACATATATAAGGAGGGA 59.499 42.308 17.49 17.49 40.85 4.20
5478 5651 7.398618 ACGACTCCCTAATGATGATAATGAGAT 59.601 37.037 0.00 0.00 0.00 2.75
5493 5666 4.833478 ATGAGATCTAGCCACAAACAGT 57.167 40.909 0.00 0.00 0.00 3.55
5521 5694 5.261216 AGGATTGTTACCGGATGATGTTTT 58.739 37.500 9.46 0.00 0.00 2.43
5550 5723 3.561155 CGAAGCTGTCTAAATCTTCGC 57.439 47.619 9.73 0.00 47.00 4.70
5602 5776 1.134220 CCCCTTCAAGCTACCGCATAA 60.134 52.381 0.00 0.00 39.10 1.90
5620 5794 0.960364 AAATGCGTTGGCCTCACGAT 60.960 50.000 26.38 15.75 38.85 3.73
5676 5851 4.988598 CGACAGTTGGCGCCCACT 62.989 66.667 26.54 26.54 40.91 4.00
5710 5885 1.208535 ACGGTGGTGTTGAGTTCTTGA 59.791 47.619 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 169 4.926244 ACGCATCTGATACTGTAACAGAG 58.074 43.478 25.30 19.32 42.55 3.35
236 253 1.687123 GCGGGGAAGCTGAAGAGTATA 59.313 52.381 0.00 0.00 0.00 1.47
237 254 0.466124 GCGGGGAAGCTGAAGAGTAT 59.534 55.000 0.00 0.00 0.00 2.12
238 255 0.902984 TGCGGGGAAGCTGAAGAGTA 60.903 55.000 0.00 0.00 38.13 2.59
239 256 1.768684 TTGCGGGGAAGCTGAAGAGT 61.769 55.000 0.00 0.00 38.13 3.24
341 359 7.712204 AAGAAGTAAAGAGTTCCCACAAAAA 57.288 32.000 0.00 0.00 35.86 1.94
342 360 7.712204 AAAGAAGTAAAGAGTTCCCACAAAA 57.288 32.000 0.00 0.00 35.86 2.44
343 361 7.712204 AAAAGAAGTAAAGAGTTCCCACAAA 57.288 32.000 0.00 0.00 35.86 2.83
344 362 8.846211 CATAAAAGAAGTAAAGAGTTCCCACAA 58.154 33.333 0.00 0.00 35.86 3.33
345 363 8.215050 TCATAAAAGAAGTAAAGAGTTCCCACA 58.785 33.333 0.00 0.00 35.86 4.17
346 364 8.617290 TCATAAAAGAAGTAAAGAGTTCCCAC 57.383 34.615 0.00 0.00 35.86 4.61
347 365 9.807921 ATTCATAAAAGAAGTAAAGAGTTCCCA 57.192 29.630 0.00 0.00 35.86 4.37
472 496 1.630148 ATCAGTCGAACTTACTGCGC 58.370 50.000 0.00 0.00 43.30 6.09
475 499 4.386049 GGACACAATCAGTCGAACTTACTG 59.614 45.833 0.00 0.00 44.66 2.74
477 501 4.304110 TGGACACAATCAGTCGAACTTAC 58.696 43.478 0.00 0.00 36.87 2.34
524 548 1.812922 GCATGCGGGACTGAGACAG 60.813 63.158 0.00 0.00 37.52 3.51
619 645 4.647424 TCGCATTCAAAGTTTCAAACCT 57.353 36.364 0.00 0.00 0.00 3.50
778 806 6.238593 GCCTGTGCCAAATTTTACAAAAATCA 60.239 34.615 0.00 0.00 0.00 2.57
822 850 5.700402 ACCATCTGCTCCTTACATAAACT 57.300 39.130 0.00 0.00 0.00 2.66
857 885 7.493645 CCTATTCCTTTGATCCAAAATTTGAGC 59.506 37.037 7.37 0.00 32.75 4.26
1123 1153 6.042552 TGAAAAGGAAAATCAATTAGCCACCA 59.957 34.615 0.00 0.00 0.00 4.17
1245 1275 8.906867 AGGATAATATTGTTCCATCAACACTTG 58.093 33.333 17.03 0.00 45.12 3.16
1432 1462 6.327386 AGTATTTCCATGTCCAATACTGGT 57.673 37.500 15.52 0.11 40.60 4.00
1746 1777 0.870393 CAGAAGAAGCATGCACACGT 59.130 50.000 21.98 8.62 0.00 4.49
1800 1831 8.298729 ACATATCATGTAGAACAGAGAGAACA 57.701 34.615 0.00 0.00 42.78 3.18
1924 1955 5.606749 TGCCCTCTTTTCTATCTATTAGCCA 59.393 40.000 0.00 0.00 0.00 4.75
1979 2012 0.888619 GAGTCAGACCATGGACGTGA 59.111 55.000 21.47 14.57 39.01 4.35
2149 2182 1.888512 GGCAAGGTTCAAGAATCTGCA 59.111 47.619 14.72 0.00 30.99 4.41
2176 2209 5.989477 TCTCCATTGTCCCAACACTAATAG 58.011 41.667 0.00 0.00 34.35 1.73
2363 2396 2.158623 TCTGCATCCACACCAAAGTTCT 60.159 45.455 0.00 0.00 0.00 3.01
2373 2406 3.431673 TTGGTATGTTCTGCATCCACA 57.568 42.857 0.00 0.00 38.94 4.17
2423 2456 3.218453 TCTTGATTTCCCGCAACTTCAA 58.782 40.909 0.00 0.00 0.00 2.69
2445 2478 3.243643 GCACAACATCTTTCACTGCAAAC 59.756 43.478 0.00 0.00 0.00 2.93
2491 2524 7.331687 CACAAAACAAACCTGATCAAGAAAAGT 59.668 33.333 0.00 0.00 0.00 2.66
2639 2672 1.907255 AGTGGTTACCAAGTAGGCTCC 59.093 52.381 5.33 0.00 43.14 4.70
2669 2702 8.458573 CAAGTATTGCCATGTTAAATACCCTA 57.541 34.615 14.20 0.00 40.39 3.53
2799 2832 8.519799 TTTTTCTTCCTCAATTCACAGTAAGT 57.480 30.769 0.00 0.00 0.00 2.24
2825 2858 8.667592 AGATCTACTTCCTAGTTGTTTTAGGT 57.332 34.615 0.00 0.00 39.01 3.08
2866 2899 0.394488 TTGGGCTCGTTCCACAAACA 60.394 50.000 0.00 0.00 37.77 2.83
2875 2908 2.159382 ACAATCGAATTTGGGCTCGTT 58.841 42.857 3.94 0.00 36.46 3.85
2972 3005 2.988636 TCAACAATGTTGGATGGGGA 57.011 45.000 23.89 1.98 0.00 4.81
3017 3050 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
3018 3051 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
3019 3052 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
3020 3053 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
3065 3098 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
3066 3099 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
3067 3100 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
3068 3101 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
3069 3102 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
3070 3103 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
3071 3104 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
3072 3105 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
3073 3106 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
3074 3107 9.512588 CTACTCCCTCCGTAAACTAATATAAGA 57.487 37.037 0.00 0.00 0.00 2.10
3075 3108 9.294614 ACTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
3078 3111 9.819754 ATTACTACTCCCTCCGTAAACTAATAT 57.180 33.333 0.00 0.00 0.00 1.28
3079 3112 9.646522 AATTACTACTCCCTCCGTAAACTAATA 57.353 33.333 0.00 0.00 0.00 0.98
3080 3113 8.544687 AATTACTACTCCCTCCGTAAACTAAT 57.455 34.615 0.00 0.00 0.00 1.73
3081 3114 7.961326 AATTACTACTCCCTCCGTAAACTAA 57.039 36.000 0.00 0.00 0.00 2.24
3082 3115 9.474313 TTTAATTACTACTCCCTCCGTAAACTA 57.526 33.333 0.00 0.00 0.00 2.24
3083 3116 7.961326 TTAATTACTACTCCCTCCGTAAACT 57.039 36.000 0.00 0.00 0.00 2.66
3084 3117 8.873830 GTTTTAATTACTACTCCCTCCGTAAAC 58.126 37.037 0.00 0.00 0.00 2.01
3085 3118 7.759433 CGTTTTAATTACTACTCCCTCCGTAAA 59.241 37.037 0.00 0.00 0.00 2.01
3086 3119 7.093945 ACGTTTTAATTACTACTCCCTCCGTAA 60.094 37.037 0.00 0.00 0.00 3.18
3087 3120 6.377146 ACGTTTTAATTACTACTCCCTCCGTA 59.623 38.462 0.00 0.00 0.00 4.02
3088 3121 5.185828 ACGTTTTAATTACTACTCCCTCCGT 59.814 40.000 0.00 0.00 0.00 4.69
3089 3122 5.517770 CACGTTTTAATTACTACTCCCTCCG 59.482 44.000 0.00 0.00 0.00 4.63
3090 3123 5.292834 GCACGTTTTAATTACTACTCCCTCC 59.707 44.000 0.00 0.00 0.00 4.30
3091 3124 5.870978 TGCACGTTTTAATTACTACTCCCTC 59.129 40.000 0.00 0.00 0.00 4.30
3092 3125 5.797051 TGCACGTTTTAATTACTACTCCCT 58.203 37.500 0.00 0.00 0.00 4.20
3093 3126 6.314400 TGATGCACGTTTTAATTACTACTCCC 59.686 38.462 0.00 0.00 0.00 4.30
3094 3127 7.298507 TGATGCACGTTTTAATTACTACTCC 57.701 36.000 0.00 0.00 0.00 3.85
3095 3128 9.769093 AAATGATGCACGTTTTAATTACTACTC 57.231 29.630 0.00 0.00 34.50 2.59
3096 3129 9.554724 CAAATGATGCACGTTTTAATTACTACT 57.445 29.630 0.00 0.00 35.79 2.57
3097 3130 9.337091 ACAAATGATGCACGTTTTAATTACTAC 57.663 29.630 0.00 0.00 35.79 2.73
3098 3131 9.335891 CACAAATGATGCACGTTTTAATTACTA 57.664 29.630 0.00 0.00 35.79 1.82
3099 3132 7.865385 ACACAAATGATGCACGTTTTAATTACT 59.135 29.630 0.00 0.00 35.79 2.24
3111 3144 6.225703 TGCAAAATAACACAAATGATGCAC 57.774 33.333 0.00 0.00 36.46 4.57
3277 3313 1.953686 ACACACAAGCACATACCAACC 59.046 47.619 0.00 0.00 0.00 3.77
3384 3423 6.889019 CTACTAACTTGGCTTTAGTAGTGC 57.111 41.667 21.08 0.00 46.29 4.40
3495 3534 0.469705 TGCTTTGCCAGATTGGTGGT 60.470 50.000 0.00 0.00 40.46 4.16
3526 3565 6.924111 TGCAAAATAAAATGAGAGAGAACCC 58.076 36.000 0.00 0.00 0.00 4.11
3708 3749 1.324736 GCGGTCACTCAATTAGAAGCG 59.675 52.381 0.00 0.00 37.96 4.68
3725 3766 0.737019 GATGCCAACACCATTTGCGG 60.737 55.000 0.00 0.00 0.00 5.69
3812 3853 0.807496 GAGGTCAGACAAGCAATGGC 59.193 55.000 2.17 0.00 41.61 4.40
4070 4115 3.252944 TGTCACGACAATGTTTGATGCAT 59.747 39.130 0.00 0.00 38.56 3.96
4098 4143 2.909006 AGCTCTGATTTTCACTCTCCCA 59.091 45.455 0.00 0.00 0.00 4.37
4118 4163 2.549754 ACGGTCTTCTTGAAACATGCAG 59.450 45.455 0.00 0.00 0.00 4.41
4147 4192 3.696051 ACATCCTCATAGTTTTTGCGCAT 59.304 39.130 12.75 0.00 0.00 4.73
4169 4214 7.992608 ACAGTGTGTCCATAATAATATTGCTGA 59.007 33.333 0.00 0.00 0.00 4.26
4199 4244 7.346175 TGGGGATAATAGTTAGCTTGTAGTCAA 59.654 37.037 0.00 0.00 0.00 3.18
4233 4278 8.853077 ACTTCATCAATGAAAGTAGATGAACA 57.147 30.769 11.40 0.00 46.62 3.18
4400 4445 4.776837 CACCATAGGGATCATCTAGAGCTT 59.223 45.833 0.00 0.00 38.05 3.74
4410 4455 3.041211 CCAGTTCTCACCATAGGGATCA 58.959 50.000 0.00 0.00 38.05 2.92
4453 4498 5.470098 TGTAGAATGACTCCTTCAGCAAAAC 59.530 40.000 0.00 0.00 37.77 2.43
4522 4567 6.151144 GCAAGTGTGTTCCTATAAAACCTCAT 59.849 38.462 0.00 0.00 0.00 2.90
4566 4611 3.626028 ACATTCTGCAACGGTTTCTTC 57.374 42.857 0.00 0.00 0.00 2.87
4653 4698 1.134007 TGCATTCTCGGCAGGATCATT 60.134 47.619 0.00 0.00 36.11 2.57
4662 4707 2.079925 AGTTCTTCTTGCATTCTCGGC 58.920 47.619 0.00 0.00 0.00 5.54
4725 4770 6.152831 ACAAAAGCTGGAGTTACTTGAAGTTT 59.847 34.615 1.97 0.00 0.00 2.66
4754 4799 7.058023 TCACACAGTTACCAGTTACACTTAT 57.942 36.000 0.00 0.00 0.00 1.73
4813 4858 8.870075 AGATATTCTTTCAAACCTTTGTAGCT 57.130 30.769 0.00 0.00 39.18 3.32
4914 4959 2.415357 GGGCACACACACATATTTTCGG 60.415 50.000 0.00 0.00 0.00 4.30
4915 4960 2.487762 AGGGCACACACACATATTTTCG 59.512 45.455 0.00 0.00 0.00 3.46
4923 4968 1.752310 CACCAAGGGCACACACACA 60.752 57.895 0.00 0.00 0.00 3.72
4934 4979 0.107361 GGTATTCCCCGACACCAAGG 60.107 60.000 0.00 0.00 0.00 3.61
4981 5026 1.476085 TGCCGGCTTACCAATGAAATG 59.524 47.619 29.70 0.00 34.57 2.32
5116 5183 3.612247 ATGACTGTGTCTGCCGGGC 62.612 63.158 13.32 13.32 33.15 6.13
5167 5235 9.856488 CTGTCTGCTTAACTATCTGTTTAACTA 57.144 33.333 0.00 0.00 39.89 2.24
5168 5236 8.368668 ACTGTCTGCTTAACTATCTGTTTAACT 58.631 33.333 0.00 0.00 39.89 2.24
5169 5237 8.535690 ACTGTCTGCTTAACTATCTGTTTAAC 57.464 34.615 0.00 0.00 39.89 2.01
5172 5240 9.209175 CTTAACTGTCTGCTTAACTATCTGTTT 57.791 33.333 0.00 0.00 39.89 2.83
5173 5241 8.368668 ACTTAACTGTCTGCTTAACTATCTGTT 58.631 33.333 0.00 0.00 42.31 3.16
5174 5242 7.897864 ACTTAACTGTCTGCTTAACTATCTGT 58.102 34.615 0.00 0.00 0.00 3.41
5357 5522 6.500751 GTCCCTCCTTATATATGTTGAAGGGA 59.499 42.308 15.40 15.40 39.20 4.20
5381 5546 2.201210 CCTTTTGGGGTGCCCTGT 59.799 61.111 7.26 0.00 45.70 4.00
5462 5635 7.914859 TGTGGCTAGATCTCATTATCATCATT 58.085 34.615 0.00 0.00 0.00 2.57
5478 5651 5.020795 TCCTACATACTGTTTGTGGCTAGA 58.979 41.667 13.14 2.18 0.00 2.43
5493 5666 6.269077 ACATCATCCGGTAACAATCCTACATA 59.731 38.462 0.00 0.00 0.00 2.29
5501 5674 5.576447 GGAAAACATCATCCGGTAACAAT 57.424 39.130 0.00 0.00 0.00 2.71
5550 5723 0.110056 GAGTGACGCAACATGCAAGG 60.110 55.000 2.99 0.00 45.36 3.61
5602 5776 0.960364 AATCGTGAGGCCAACGCATT 60.960 50.000 22.28 18.56 36.38 3.56
5710 5885 3.073946 TCGAACCCTGAAAAAGATCCCTT 59.926 43.478 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.