Multiple sequence alignment - TraesCS4B01G109600

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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 TraesCS4B01G109600 chr4B 100.000 5150 0 0 1 5150 122301280 122296131 0.000000e+00 9511.0
1 TraesCS4B01G109600 chr4B 97.688 173 2 2 4828 4998 658178157 658178329 3.900000e-76 296.0
2 TraesCS4B01G109600 chr4A 95.306 4857 153 26 3 4830 498989765 498984955 0.000000e+00 7637.0
3 TraesCS4B01G109600 chr4A 99.401 167 0 1 4832 4997 515656268 515656102 8.380000e-78 302.0
4 TraesCS4B01G109600 chr4A 96.629 178 4 2 4832 5007 594145373 594145196 1.400000e-75 294.0
5 TraesCS4B01G109600 chr4A 97.015 67 2 0 5029 5095 498984933 498984867 4.210000e-21 113.0
6 TraesCS4B01G109600 chr4A 100.000 29 0 0 4993 5021 498984956 498984928 3.000000e-03 54.7
7 TraesCS4B01G109600 chr4D 96.765 4173 127 7 3 4173 85176553 85172387 0.000000e+00 6951.0
8 TraesCS4B01G109600 chr4D 93.821 4402 246 13 115 4512 85263725 85259346 0.000000e+00 6599.0
9 TraesCS4B01G109600 chr4D 89.434 530 19 5 4335 4830 85167007 85166481 7.270000e-178 634.0
10 TraesCS4B01G109600 chr4D 88.868 530 22 5 4335 4830 84990120 84990646 7.330000e-173 617.0
11 TraesCS4B01G109600 chr4D 96.703 182 4 1 4158 4339 85172369 85172190 8.380000e-78 302.0
12 TraesCS4B01G109600 chr4D 85.517 290 15 4 4568 4830 85259325 85259036 1.410000e-70 278.0
13 TraesCS4B01G109600 chr4D 96.835 158 5 0 4993 5150 85166482 85166325 1.100000e-66 265.0
14 TraesCS4B01G109600 chr4D 96.203 158 6 0 4993 5150 84990645 84990802 5.120000e-65 259.0
15 TraesCS4B01G109600 chr4D 94.915 59 3 0 5092 5150 85258971 85258913 5.490000e-15 93.5
16 TraesCS4B01G109600 chr4D 100.000 31 0 0 4993 5023 85259037 85259007 2.000000e-04 58.4
17 TraesCS4B01G109600 chrUn 75.513 2630 586 47 1079 3682 75441564 75444161 0.000000e+00 1236.0
18 TraesCS4B01G109600 chr3D 75.294 2635 584 61 1080 3682 26271121 26273720 0.000000e+00 1197.0
19 TraesCS4B01G109600 chr3D 75.206 2545 560 59 1080 3585 26300877 26303389 0.000000e+00 1138.0
20 TraesCS4B01G109600 chr3D 74.113 2565 603 53 1078 3612 26218334 26215801 0.000000e+00 1002.0
21 TraesCS4B01G109600 chr3D 79.354 1269 242 17 2330 3588 26282540 26283798 0.000000e+00 874.0
22 TraesCS4B01G109600 chr3A 75.199 2637 583 61 1080 3682 36300277 36302876 0.000000e+00 1181.0
23 TraesCS4B01G109600 chr6D 81.598 1114 179 18 3016 4108 473271868 473270760 0.000000e+00 898.0
24 TraesCS4B01G109600 chr6A 98.837 172 1 1 4826 4996 1830022 1829851 6.480000e-79 305.0
25 TraesCS4B01G109600 chr2A 98.824 170 1 1 4830 4998 770971700 770971531 8.380000e-78 302.0
26 TraesCS4B01G109600 chr5B 98.246 171 2 1 4825 4994 656461946 656461776 1.080000e-76 298.0
27 TraesCS4B01G109600 chr7A 97.159 176 4 1 4831 5005 493942302 493942127 3.900000e-76 296.0
28 TraesCS4B01G109600 chr1A 97.688 173 3 1 4826 4997 575653156 575652984 3.900000e-76 296.0
29 TraesCS4B01G109600 chr1A 96.648 179 3 3 4819 4996 219372617 219372793 1.400000e-75 294.0
30 TraesCS4B01G109600 chr5A 95.109 184 5 4 4830 5012 35196947 35197127 2.350000e-73 287.0


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 TraesCS4B01G109600 chr4B 122296131 122301280 5149 True 9511.000000 9511 100.000000 1 5150 1 chr4B.!!$R1 5149
1 TraesCS4B01G109600 chr4A 498984867 498989765 4898 True 2601.566667 7637 97.440333 3 5095 3 chr4A.!!$R3 5092
2 TraesCS4B01G109600 chr4D 85172190 85176553 4363 True 3626.500000 6951 96.734000 3 4339 2 chr4D.!!$R2 4336
3 TraesCS4B01G109600 chr4D 85258913 85263725 4812 True 1757.225000 6599 93.563250 115 5150 4 chr4D.!!$R3 5035
4 TraesCS4B01G109600 chr4D 85166325 85167007 682 True 449.500000 634 93.134500 4335 5150 2 chr4D.!!$R1 815
5 TraesCS4B01G109600 chr4D 84990120 84990802 682 False 438.000000 617 92.535500 4335 5150 2 chr4D.!!$F1 815
6 TraesCS4B01G109600 chrUn 75441564 75444161 2597 False 1236.000000 1236 75.513000 1079 3682 1 chrUn.!!$F1 2603
7 TraesCS4B01G109600 chr3D 26271121 26273720 2599 False 1197.000000 1197 75.294000 1080 3682 1 chr3D.!!$F1 2602
8 TraesCS4B01G109600 chr3D 26300877 26303389 2512 False 1138.000000 1138 75.206000 1080 3585 1 chr3D.!!$F3 2505
9 TraesCS4B01G109600 chr3D 26215801 26218334 2533 True 1002.000000 1002 74.113000 1078 3612 1 chr3D.!!$R1 2534
10 TraesCS4B01G109600 chr3D 26282540 26283798 1258 False 874.000000 874 79.354000 2330 3588 1 chr3D.!!$F2 1258
11 TraesCS4B01G109600 chr3A 36300277 36302876 2599 False 1181.000000 1181 75.199000 1080 3682 1 chr3A.!!$F1 2602
12 TraesCS4B01G109600 chr6D 473270760 473271868 1108 True 898.000000 898 81.598000 3016 4108 1 chr6D.!!$R1 1092

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
182 183 0.734889 GTCAAACGATGGCAGGATGG 59.265 55.000 0.00 0.00 35.86 3.51 F
1206 1216 1.144708 TGGGAAGGTGTTCATTGCAGA 59.855 47.619 0.00 0.00 33.93 4.26 F
2080 2094 1.909700 ACAAGGCCACATACCAAGTG 58.090 50.000 5.01 0.00 36.76 3.16 F
2241 2258 4.265856 TCCTCAATGGTTAGGAGCTCTA 57.734 45.455 14.64 1.13 36.97 2.43 F
4032 4071 2.770164 ATGACCTGGACTGTGTAAGC 57.230 50.000 0.00 0.00 0.00 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1329 1339 2.024941 GGATGGAGGAATTGTCCCAGTT 60.025 50.000 1.71 0.00 46.3 3.16 R
2401 2418 3.504906 AGATTGTTGCTGGACATGTTCAG 59.495 43.478 27.25 27.25 0.0 3.02 R
4032 4071 1.009829 GCCCGATGTTTAGCACTGAG 58.990 55.000 0.00 0.00 0.0 3.35 R
4086 4125 1.825090 CAGCCACTTCCTGCATGTTA 58.175 50.000 0.00 0.00 0.0 2.41 R
4982 5089 1.223501 TCCTCATCTACTCCCTCCGT 58.776 55.000 0.00 0.00 0.0 4.69 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
74 75 8.743085 AGTAGATATTGCCATGCCTATAAATG 57.257 34.615 0.00 0.00 0.00 2.32
79 80 4.451891 TGCCATGCCTATAAATGAAGGA 57.548 40.909 0.00 0.00 34.58 3.36
182 183 0.734889 GTCAAACGATGGCAGGATGG 59.265 55.000 0.00 0.00 35.86 3.51
213 214 3.067106 ACATGAACTCAAGGTGCGTTAG 58.933 45.455 0.00 0.00 0.00 2.34
220 221 3.440872 ACTCAAGGTGCGTTAGTCTCTAG 59.559 47.826 0.00 0.00 0.00 2.43
242 243 9.538508 TCTAGTAACTTTTGAGTCTTGTAAACC 57.461 33.333 0.00 0.00 0.00 3.27
442 447 6.686484 AGTATGATGATTACTGTATGCCCA 57.314 37.500 0.00 0.00 0.00 5.36
556 561 7.073208 TGTATCTCCTTATAACAGGTCATCCA 58.927 38.462 0.00 0.00 35.15 3.41
642 647 5.559770 ACATATTGGTCCATATGCGATTGA 58.440 37.500 15.63 0.00 34.90 2.57
646 651 3.466836 TGGTCCATATGCGATTGAGTTC 58.533 45.455 0.00 0.00 0.00 3.01
676 681 4.193826 CTGCTTCAGTAGTTTAGGCAGA 57.806 45.455 6.21 0.00 45.54 4.26
722 729 5.719563 TCACATGATTGTAGGACTGTAGGAA 59.280 40.000 0.00 0.00 33.76 3.36
723 730 6.212589 TCACATGATTGTAGGACTGTAGGAAA 59.787 38.462 0.00 0.00 33.76 3.13
859 866 1.270907 CAGTAGGCAAGTCCTGAGGT 58.729 55.000 0.00 0.00 46.98 3.85
862 869 2.312140 AGTAGGCAAGTCCTGAGGTAGA 59.688 50.000 0.00 0.00 46.98 2.59
871 878 5.199982 AGTCCTGAGGTAGAGATTGAAGA 57.800 43.478 0.00 0.00 0.00 2.87
877 884 8.865090 TCCTGAGGTAGAGATTGAAGAATAATC 58.135 37.037 0.00 0.00 35.32 1.75
913 920 9.462174 GTACTTGACATGACAAATGATTTTTCA 57.538 29.630 11.62 8.95 0.00 2.69
1071 1081 2.573009 TGGACATGTCATCATCTGTGGT 59.427 45.455 26.47 0.00 31.15 4.16
1206 1216 1.144708 TGGGAAGGTGTTCATTGCAGA 59.855 47.619 0.00 0.00 33.93 4.26
1264 1274 6.348213 CCTTACAAATCGAGGTTTAGTTGGTG 60.348 42.308 0.00 0.00 0.00 4.17
1290 1300 5.157940 TCTCTCCTTCACTTGGAAATCTG 57.842 43.478 0.00 0.00 34.44 2.90
1329 1339 3.175594 ACTCCTACCGACAAATGGGTTA 58.824 45.455 0.00 0.00 38.10 2.85
1476 1490 6.349300 GCTGGATAGAAATCAACTAGTTGGA 58.651 40.000 30.35 19.32 40.78 3.53
2080 2094 1.909700 ACAAGGCCACATACCAAGTG 58.090 50.000 5.01 0.00 36.76 3.16
2241 2258 4.265856 TCCTCAATGGTTAGGAGCTCTA 57.734 45.455 14.64 1.13 36.97 2.43
2513 2530 6.126409 ACAACTTCAATGGACAACTTCCTAA 58.874 36.000 0.00 0.00 46.10 2.69
3064 3081 5.468072 CCATCACTTGATAGAAATCTTCCCG 59.532 44.000 0.00 0.00 32.63 5.14
3746 3777 7.394923 AGAGTAACTTCTGCTCATACTAACACT 59.605 37.037 0.00 0.00 39.14 3.55
3768 3802 8.313292 ACACTGGAATTACATTATTGTTGCATT 58.687 29.630 0.00 0.00 37.28 3.56
4032 4071 2.770164 ATGACCTGGACTGTGTAAGC 57.230 50.000 0.00 0.00 0.00 3.09
4451 4524 2.092429 CCTTGTTGCTCCCCTGCTATTA 60.092 50.000 0.00 0.00 0.00 0.98
4627 4707 2.126734 GCGCGTAGTGTGGTACGT 60.127 61.111 8.43 0.00 46.12 3.57
4679 4786 2.685380 CCTCTTCCCACCGGAGCT 60.685 66.667 9.46 0.00 40.10 4.09
4719 4826 3.375299 GCACACATACTTCACATCCTTCC 59.625 47.826 0.00 0.00 0.00 3.46
4795 4902 2.111384 GGCAGGGAGAGACATACAAGA 58.889 52.381 0.00 0.00 0.00 3.02
4803 4910 5.183140 GGGAGAGACATACAAGAGATAGCTC 59.817 48.000 0.00 0.00 41.62 4.09
4823 4930 3.998341 CTCTAGACTGCTACGGATCCTAC 59.002 52.174 10.75 0.00 0.00 3.18
4828 4935 2.158445 ACTGCTACGGATCCTACCATCT 60.158 50.000 10.75 0.00 0.00 2.90
4829 4936 3.074094 ACTGCTACGGATCCTACCATCTA 59.926 47.826 10.75 0.00 0.00 1.98
4830 4937 3.418995 TGCTACGGATCCTACCATCTAC 58.581 50.000 10.75 0.00 0.00 2.59
4831 4938 3.074094 TGCTACGGATCCTACCATCTACT 59.926 47.826 10.75 0.00 0.00 2.57
4832 4939 4.287845 TGCTACGGATCCTACCATCTACTA 59.712 45.833 10.75 0.00 0.00 1.82
4833 4940 4.635324 GCTACGGATCCTACCATCTACTAC 59.365 50.000 10.75 0.00 0.00 2.73
4834 4941 4.997545 ACGGATCCTACCATCTACTACT 57.002 45.455 10.75 0.00 0.00 2.57
4835 4942 4.909001 ACGGATCCTACCATCTACTACTC 58.091 47.826 10.75 0.00 0.00 2.59
4836 4943 4.263418 ACGGATCCTACCATCTACTACTCC 60.263 50.000 10.75 0.00 0.00 3.85
4837 4944 4.602107 GGATCCTACCATCTACTACTCCC 58.398 52.174 3.84 0.00 0.00 4.30
4838 4945 4.292836 GGATCCTACCATCTACTACTCCCT 59.707 50.000 3.84 0.00 0.00 4.20
4839 4946 4.997545 TCCTACCATCTACTACTCCCTC 57.002 50.000 0.00 0.00 0.00 4.30
4840 4947 3.656751 TCCTACCATCTACTACTCCCTCC 59.343 52.174 0.00 0.00 0.00 4.30
4841 4948 2.660670 ACCATCTACTACTCCCTCCG 57.339 55.000 0.00 0.00 0.00 4.63
4842 4949 1.851653 ACCATCTACTACTCCCTCCGT 59.148 52.381 0.00 0.00 0.00 4.69
4843 4950 2.244252 ACCATCTACTACTCCCTCCGTT 59.756 50.000 0.00 0.00 0.00 4.44
4844 4951 2.885894 CCATCTACTACTCCCTCCGTTC 59.114 54.545 0.00 0.00 0.00 3.95
4845 4952 2.725221 TCTACTACTCCCTCCGTTCC 57.275 55.000 0.00 0.00 0.00 3.62
4846 4953 2.203584 TCTACTACTCCCTCCGTTCCT 58.796 52.381 0.00 0.00 0.00 3.36
4847 4954 3.387962 TCTACTACTCCCTCCGTTCCTA 58.612 50.000 0.00 0.00 0.00 2.94
4848 4955 3.782523 TCTACTACTCCCTCCGTTCCTAA 59.217 47.826 0.00 0.00 0.00 2.69
4849 4956 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
4850 4957 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
4851 4958 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
4852 4959 4.892345 ACTACTCCCTCCGTTCCTAAATAC 59.108 45.833 0.00 0.00 0.00 1.89
4853 4960 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
4854 4961 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
4855 4962 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
4856 4963 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
4857 4964 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
4858 4965 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
4859 4966 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
4860 4967 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
4861 4968 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
4862 4969 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
4863 4970 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
4864 4971 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
4865 4972 7.491696 CCGTTCCTAAATACTTGTCTTTCTAGG 59.508 40.741 0.00 0.00 0.00 3.02
4866 4973 7.010275 CGTTCCTAAATACTTGTCTTTCTAGGC 59.990 40.741 0.00 0.00 0.00 3.93
4867 4974 7.490657 TCCTAAATACTTGTCTTTCTAGGCA 57.509 36.000 0.00 0.00 33.22 4.75
4868 4975 8.090788 TCCTAAATACTTGTCTTTCTAGGCAT 57.909 34.615 0.00 0.00 35.56 4.40
4869 4976 8.548877 TCCTAAATACTTGTCTTTCTAGGCATT 58.451 33.333 0.00 0.00 35.56 3.56
4870 4977 9.178758 CCTAAATACTTGTCTTTCTAGGCATTT 57.821 33.333 0.00 0.00 35.56 2.32
4872 4979 8.635765 AAATACTTGTCTTTCTAGGCATTTCA 57.364 30.769 0.00 0.00 35.56 2.69
4873 4980 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
4874 4981 6.319141 ACTTGTCTTTCTAGGCATTTCAAC 57.681 37.500 0.00 0.00 35.56 3.18
4875 4982 5.827797 ACTTGTCTTTCTAGGCATTTCAACA 59.172 36.000 0.00 0.00 35.56 3.33
4876 4983 6.321181 ACTTGTCTTTCTAGGCATTTCAACAA 59.679 34.615 0.00 0.00 35.56 2.83
4877 4984 6.707440 TGTCTTTCTAGGCATTTCAACAAA 57.293 33.333 0.00 0.00 29.10 2.83
4878 4985 7.288810 TGTCTTTCTAGGCATTTCAACAAAT 57.711 32.000 0.00 0.00 29.10 2.32
4891 4998 7.915293 ATTTCAACAAATGACTACATACGGA 57.085 32.000 0.00 0.00 37.92 4.69
4892 4999 6.961359 TTCAACAAATGACTACATACGGAG 57.039 37.500 0.00 0.00 37.92 4.63
4893 5000 4.868171 TCAACAAATGACTACATACGGAGC 59.132 41.667 0.00 0.00 35.50 4.70
4894 5001 4.465632 ACAAATGACTACATACGGAGCA 57.534 40.909 0.00 0.00 35.50 4.26
4895 5002 4.827692 ACAAATGACTACATACGGAGCAA 58.172 39.130 0.00 0.00 35.50 3.91
4896 5003 5.242434 ACAAATGACTACATACGGAGCAAA 58.758 37.500 0.00 0.00 35.50 3.68
4897 5004 5.703592 ACAAATGACTACATACGGAGCAAAA 59.296 36.000 0.00 0.00 35.50 2.44
4898 5005 6.374333 ACAAATGACTACATACGGAGCAAAAT 59.626 34.615 0.00 0.00 35.50 1.82
4899 5006 5.991328 ATGACTACATACGGAGCAAAATG 57.009 39.130 0.00 0.00 34.71 2.32
4900 5007 5.079689 TGACTACATACGGAGCAAAATGA 57.920 39.130 0.00 0.00 0.00 2.57
4901 5008 5.109210 TGACTACATACGGAGCAAAATGAG 58.891 41.667 0.00 0.00 0.00 2.90
4902 5009 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
4903 5010 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
4904 5011 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
4905 5012 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
4906 5013 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
4907 5014 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
4908 5015 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
4909 5016 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
4910 5017 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
4911 5018 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
4912 5019 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
4936 5043 9.181805 CACTCTAAAATATGTCTACATACACCG 57.818 37.037 4.98 0.00 41.15 4.94
4937 5044 8.910944 ACTCTAAAATATGTCTACATACACCGT 58.089 33.333 4.98 0.00 41.15 4.83
4949 5056 7.719778 CTACATACACCGTATGTAGTAGTCA 57.280 40.000 29.53 12.06 47.00 3.41
4950 5057 8.320396 CTACATACACCGTATGTAGTAGTCAT 57.680 38.462 29.53 8.73 47.00 3.06
4951 5058 7.578310 ACATACACCGTATGTAGTAGTCATT 57.422 36.000 16.15 0.00 47.00 2.57
4952 5059 8.004087 ACATACACCGTATGTAGTAGTCATTT 57.996 34.615 16.15 0.00 47.00 2.32
4953 5060 7.919091 ACATACACCGTATGTAGTAGTCATTTG 59.081 37.037 16.15 0.00 47.00 2.32
4954 5061 6.519679 ACACCGTATGTAGTAGTCATTTGA 57.480 37.500 0.00 0.00 40.88 2.69
4955 5062 6.927416 ACACCGTATGTAGTAGTCATTTGAA 58.073 36.000 0.00 0.00 40.88 2.69
4956 5063 7.380536 ACACCGTATGTAGTAGTCATTTGAAA 58.619 34.615 0.00 0.00 40.88 2.69
4957 5064 8.038944 ACACCGTATGTAGTAGTCATTTGAAAT 58.961 33.333 0.00 0.00 40.88 2.17
4958 5065 8.328146 CACCGTATGTAGTAGTCATTTGAAATG 58.672 37.037 11.54 11.54 0.00 2.32
4959 5066 8.038944 ACCGTATGTAGTAGTCATTTGAAATGT 58.961 33.333 16.62 2.38 0.00 2.71
4960 5067 8.540492 CCGTATGTAGTAGTCATTTGAAATGTC 58.460 37.037 16.62 11.74 0.00 3.06
4961 5068 9.302345 CGTATGTAGTAGTCATTTGAAATGTCT 57.698 33.333 18.62 18.62 0.00 3.41
4985 5092 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
4986 5093 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
4987 5094 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
4988 5095 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
4989 5096 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
4990 5097 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
4991 5098 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
5128 5235 4.099419 AGTTGTCATCCATGCGTATCTGTA 59.901 41.667 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 2.351455 GAGCTGCTTGGTTACTCCTTC 58.649 52.381 2.53 0.00 37.07 3.46
79 80 2.541466 ACTAGGAGCTGCTTGGTTACT 58.459 47.619 14.85 0.00 0.00 2.24
182 183 1.202758 TGAGTTCATGTCCACCACCAC 60.203 52.381 0.00 0.00 0.00 4.16
213 214 9.962783 TTACAAGACTCAAAAGTTACTAGAGAC 57.037 33.333 13.65 9.04 35.28 3.36
220 221 8.837389 AGATGGTTTACAAGACTCAAAAGTTAC 58.163 33.333 0.00 0.00 35.28 2.50
242 243 7.364522 TCGATGGAACTCTAAAAACAAGATG 57.635 36.000 0.00 0.00 0.00 2.90
442 447 7.275920 ACTTCAGATATACTTTTTCGCCATCT 58.724 34.615 0.00 0.00 0.00 2.90
475 480 7.537596 TTGTGATCAGGATTGGTTATGTTTT 57.462 32.000 0.00 0.00 0.00 2.43
476 481 7.722949 ATTGTGATCAGGATTGGTTATGTTT 57.277 32.000 0.00 0.00 0.00 2.83
492 497 5.135383 TCAGATCCATCCCAAATTGTGATC 58.865 41.667 0.00 0.00 0.00 2.92
598 603 1.006832 ACGCGTATGGTCAATTCTGC 58.993 50.000 11.67 0.00 0.00 4.26
676 681 4.918810 AAGCTTTTGATTCACGAACCTT 57.081 36.364 0.00 0.00 0.00 3.50
859 866 9.144298 ACCTAACCGATTATTCTTCAATCTCTA 57.856 33.333 0.00 0.00 31.49 2.43
862 869 8.925338 ACTACCTAACCGATTATTCTTCAATCT 58.075 33.333 0.00 0.00 31.49 2.40
871 878 8.297470 TGTCAAGTACTACCTAACCGATTATT 57.703 34.615 0.00 0.00 0.00 1.40
877 884 5.106038 TGTCATGTCAAGTACTACCTAACCG 60.106 44.000 0.00 0.00 0.00 4.44
968 978 4.518211 AGCTGTCTTTGTTGAAGATCTTGG 59.482 41.667 14.00 0.00 45.66 3.61
1071 1081 4.782691 TCTGTCTCATTTCCATACAGGGAA 59.217 41.667 0.00 0.00 45.00 3.97
1128 1138 2.158813 GGATTGCTTTGGATCGAGGGTA 60.159 50.000 0.00 0.00 0.00 3.69
1206 1216 4.876107 GTGACACGGTATGGATTCTTCATT 59.124 41.667 0.00 0.00 0.00 2.57
1260 1270 4.505566 CCAAGTGAAGGAGAGATTTCACCA 60.506 45.833 12.27 0.00 43.37 4.17
1264 1274 6.883756 AGATTTCCAAGTGAAGGAGAGATTTC 59.116 38.462 0.00 0.00 36.33 2.17
1290 1300 8.890718 GGTAGGAGTAAATGTTTTAGGAATGTC 58.109 37.037 0.00 0.00 0.00 3.06
1329 1339 2.024941 GGATGGAGGAATTGTCCCAGTT 60.025 50.000 1.71 0.00 46.30 3.16
2080 2094 5.594926 CTGAATGGAAAGGTTGGATAATGC 58.405 41.667 0.00 0.00 0.00 3.56
2401 2418 3.504906 AGATTGTTGCTGGACATGTTCAG 59.495 43.478 27.25 27.25 0.00 3.02
2487 2504 5.281727 GGAAGTTGTCCATTGAAGTTGTTC 58.718 41.667 0.00 0.00 46.97 3.18
3064 3081 9.155975 TCTAGCAATATCACTGAAAGAAACTTC 57.844 33.333 0.00 0.00 37.43 3.01
3255 3275 1.867233 AGATTACGATGCCGCACATTC 59.133 47.619 0.00 0.00 39.84 2.67
3746 3777 9.716531 TTCAAATGCAACAATAATGTAATTCCA 57.283 25.926 0.00 0.00 39.40 3.53
3768 3802 4.275689 CCTGTTGCACATTCTGTAGTTCAA 59.724 41.667 0.00 0.00 0.00 2.69
4032 4071 1.009829 GCCCGATGTTTAGCACTGAG 58.990 55.000 0.00 0.00 0.00 3.35
4086 4125 1.825090 CAGCCACTTCCTGCATGTTA 58.175 50.000 0.00 0.00 0.00 2.41
4173 4245 6.644347 AGACTATAAATAACACTGCAGCACT 58.356 36.000 15.27 0.00 0.00 4.40
4404 4477 2.866762 GCTCGCATTTCTCGGTTTAGAT 59.133 45.455 0.00 0.00 0.00 1.98
4451 4524 3.900601 AGATGGATGGACTCGCTAGAAAT 59.099 43.478 0.00 0.00 0.00 2.17
4555 4635 2.987437 TGACCGGGTATCTCTCCTAGAT 59.013 50.000 6.32 0.00 46.95 1.98
4627 4707 2.565391 TGATCGCTGACCTGGAAAGTTA 59.435 45.455 0.00 0.00 0.00 2.24
4795 4902 3.325425 TCCGTAGCAGTCTAGAGCTATCT 59.675 47.826 14.73 8.39 44.32 1.98
4803 4910 3.075884 GGTAGGATCCGTAGCAGTCTAG 58.924 54.545 5.98 0.00 0.00 2.43
4823 4930 2.660670 ACGGAGGGAGTAGTAGATGG 57.339 55.000 0.00 0.00 0.00 3.51
4828 4935 4.591321 TTTAGGAACGGAGGGAGTAGTA 57.409 45.455 0.00 0.00 0.00 1.82
4829 4936 3.463048 TTTAGGAACGGAGGGAGTAGT 57.537 47.619 0.00 0.00 0.00 2.73
4830 4937 5.139001 AGTATTTAGGAACGGAGGGAGTAG 58.861 45.833 0.00 0.00 0.00 2.57
4831 4938 5.134725 AGTATTTAGGAACGGAGGGAGTA 57.865 43.478 0.00 0.00 0.00 2.59
4832 4939 3.991683 AGTATTTAGGAACGGAGGGAGT 58.008 45.455 0.00 0.00 0.00 3.85
4833 4940 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
4834 4941 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
4835 4942 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
4836 4943 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
4837 4944 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
4838 4945 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
4839 4946 7.491696 CCTAGAAAGACAAGTATTTAGGAACGG 59.508 40.741 4.01 0.00 26.70 4.44
4840 4947 7.010275 GCCTAGAAAGACAAGTATTTAGGAACG 59.990 40.741 11.40 0.00 26.70 3.95
4841 4948 7.822822 TGCCTAGAAAGACAAGTATTTAGGAAC 59.177 37.037 11.40 0.00 26.70 3.62
4842 4949 7.913789 TGCCTAGAAAGACAAGTATTTAGGAA 58.086 34.615 11.40 1.02 26.70 3.36
4843 4950 7.490657 TGCCTAGAAAGACAAGTATTTAGGA 57.509 36.000 11.40 0.00 26.70 2.94
4844 4951 8.738645 AATGCCTAGAAAGACAAGTATTTAGG 57.261 34.615 5.26 5.26 0.00 2.69
4846 4953 9.733556 TGAAATGCCTAGAAAGACAAGTATTTA 57.266 29.630 0.00 0.00 0.00 1.40
4847 4954 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
4848 4955 8.515414 GTTGAAATGCCTAGAAAGACAAGTATT 58.485 33.333 0.00 0.00 0.00 1.89
4849 4956 7.665559 TGTTGAAATGCCTAGAAAGACAAGTAT 59.334 33.333 0.00 0.00 0.00 2.12
4850 4957 6.995686 TGTTGAAATGCCTAGAAAGACAAGTA 59.004 34.615 0.00 0.00 0.00 2.24
4851 4958 5.827797 TGTTGAAATGCCTAGAAAGACAAGT 59.172 36.000 0.00 0.00 0.00 3.16
4852 4959 6.317789 TGTTGAAATGCCTAGAAAGACAAG 57.682 37.500 0.00 0.00 0.00 3.16
4853 4960 6.707440 TTGTTGAAATGCCTAGAAAGACAA 57.293 33.333 0.00 0.00 0.00 3.18
4854 4961 6.707440 TTTGTTGAAATGCCTAGAAAGACA 57.293 33.333 0.00 0.00 0.00 3.41
4855 4962 7.327032 GTCATTTGTTGAAATGCCTAGAAAGAC 59.673 37.037 0.00 0.00 45.61 3.01
4856 4963 7.231317 AGTCATTTGTTGAAATGCCTAGAAAGA 59.769 33.333 0.00 0.00 45.61 2.52
4857 4964 7.373493 AGTCATTTGTTGAAATGCCTAGAAAG 58.627 34.615 0.00 0.00 45.61 2.62
4858 4965 7.288810 AGTCATTTGTTGAAATGCCTAGAAA 57.711 32.000 0.00 0.00 45.61 2.52
4859 4966 6.899393 AGTCATTTGTTGAAATGCCTAGAA 57.101 33.333 0.00 0.00 45.61 2.10
4860 4967 6.939730 TGTAGTCATTTGTTGAAATGCCTAGA 59.060 34.615 0.00 0.00 45.61 2.43
4861 4968 7.144722 TGTAGTCATTTGTTGAAATGCCTAG 57.855 36.000 0.00 0.00 45.61 3.02
4862 4969 7.701539 ATGTAGTCATTTGTTGAAATGCCTA 57.298 32.000 0.00 0.00 45.61 3.93
4863 4970 6.594788 ATGTAGTCATTTGTTGAAATGCCT 57.405 33.333 0.00 0.00 45.61 4.75
4864 4971 6.468956 CGTATGTAGTCATTTGTTGAAATGCC 59.531 38.462 0.00 0.00 45.61 4.40
4865 4972 6.468956 CCGTATGTAGTCATTTGTTGAAATGC 59.531 38.462 0.00 0.00 45.61 3.56
4866 4973 7.747888 TCCGTATGTAGTCATTTGTTGAAATG 58.252 34.615 0.00 0.00 46.84 2.32
4867 4974 7.414098 GCTCCGTATGTAGTCATTTGTTGAAAT 60.414 37.037 0.00 0.00 35.70 2.17
4868 4975 6.128391 GCTCCGTATGTAGTCATTTGTTGAAA 60.128 38.462 0.00 0.00 35.70 2.69
4869 4976 5.350365 GCTCCGTATGTAGTCATTTGTTGAA 59.650 40.000 0.00 0.00 35.70 2.69
4870 4977 4.868171 GCTCCGTATGTAGTCATTTGTTGA 59.132 41.667 0.00 0.00 35.70 3.18
4871 4978 4.629634 TGCTCCGTATGTAGTCATTTGTTG 59.370 41.667 0.00 0.00 35.70 3.33
4872 4979 4.827692 TGCTCCGTATGTAGTCATTTGTT 58.172 39.130 0.00 0.00 35.70 2.83
4873 4980 4.465632 TGCTCCGTATGTAGTCATTTGT 57.534 40.909 0.00 0.00 35.70 2.83
4874 4981 5.794687 TTTGCTCCGTATGTAGTCATTTG 57.205 39.130 0.00 0.00 35.70 2.32
4875 4982 6.597672 TCATTTTGCTCCGTATGTAGTCATTT 59.402 34.615 0.00 0.00 35.70 2.32
4876 4983 6.112734 TCATTTTGCTCCGTATGTAGTCATT 58.887 36.000 0.00 0.00 35.70 2.57
4877 4984 5.670485 TCATTTTGCTCCGTATGTAGTCAT 58.330 37.500 0.00 0.00 38.00 3.06
4878 4985 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
4879 4986 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
4880 4987 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
4881 4988 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
4882 4989 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
4883 4990 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
4884 4991 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
4885 4992 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
4886 4993 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
4887 4994 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
4888 4995 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
4889 4996 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
4890 4997 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
4910 5017 9.181805 CGGTGTATGTAGACATATTTTAGAGTG 57.818 37.037 5.69 0.00 40.53 3.51
4911 5018 8.910944 ACGGTGTATGTAGACATATTTTAGAGT 58.089 33.333 5.69 0.00 40.53 3.24
4926 5033 8.681486 AATGACTACTACATACGGTGTATGTA 57.319 34.615 21.88 21.88 42.21 2.29
4927 5034 7.578310 AATGACTACTACATACGGTGTATGT 57.422 36.000 21.97 21.97 42.21 2.29
4928 5035 8.132995 TCAAATGACTACTACATACGGTGTATG 58.867 37.037 13.82 13.82 42.21 2.39
4929 5036 8.229253 TCAAATGACTACTACATACGGTGTAT 57.771 34.615 3.80 0.00 42.21 2.29
4930 5037 7.628769 TCAAATGACTACTACATACGGTGTA 57.371 36.000 3.41 3.41 42.29 2.90
4931 5038 6.519679 TCAAATGACTACTACATACGGTGT 57.480 37.500 1.35 1.35 44.95 4.16
4932 5039 7.821595 TTTCAAATGACTACTACATACGGTG 57.178 36.000 0.00 0.00 0.00 4.94
4933 5040 8.038944 ACATTTCAAATGACTACTACATACGGT 58.961 33.333 17.30 0.00 0.00 4.83
4934 5041 8.420374 ACATTTCAAATGACTACTACATACGG 57.580 34.615 17.30 0.00 0.00 4.02
4935 5042 9.302345 AGACATTTCAAATGACTACTACATACG 57.698 33.333 17.30 0.00 0.00 3.06
4959 5066 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
4960 5067 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
4961 5068 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
4962 5069 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
4963 5070 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
4964 5071 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
4965 5072 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
4966 5073 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
4967 5074 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
4968 5075 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
4969 5076 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
4970 5077 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
4971 5078 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
4972 5079 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
4973 5080 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
4974 5081 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
4975 5082 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
4976 5083 3.203710 TCATCTACTCCCTCCGTTCCTAA 59.796 47.826 0.00 0.00 0.00 2.69
4977 5084 2.781757 TCATCTACTCCCTCCGTTCCTA 59.218 50.000 0.00 0.00 0.00 2.94
4978 5085 1.569548 TCATCTACTCCCTCCGTTCCT 59.430 52.381 0.00 0.00 0.00 3.36
4979 5086 1.957877 CTCATCTACTCCCTCCGTTCC 59.042 57.143 0.00 0.00 0.00 3.62
4980 5087 1.957877 CCTCATCTACTCCCTCCGTTC 59.042 57.143 0.00 0.00 0.00 3.95
4981 5088 1.569548 TCCTCATCTACTCCCTCCGTT 59.430 52.381 0.00 0.00 0.00 4.44
4982 5089 1.223501 TCCTCATCTACTCCCTCCGT 58.776 55.000 0.00 0.00 0.00 4.69
4983 5090 2.166829 CATCCTCATCTACTCCCTCCG 58.833 57.143 0.00 0.00 0.00 4.63
4984 5091 2.896685 CACATCCTCATCTACTCCCTCC 59.103 54.545 0.00 0.00 0.00 4.30
4985 5092 3.571590 ACACATCCTCATCTACTCCCTC 58.428 50.000 0.00 0.00 0.00 4.30
4986 5093 3.697190 ACACATCCTCATCTACTCCCT 57.303 47.619 0.00 0.00 0.00 4.20
4987 5094 3.706594 TCAACACATCCTCATCTACTCCC 59.293 47.826 0.00 0.00 0.00 4.30
4988 5095 4.160439 TGTCAACACATCCTCATCTACTCC 59.840 45.833 0.00 0.00 0.00 3.85
4989 5096 5.330455 TGTCAACACATCCTCATCTACTC 57.670 43.478 0.00 0.00 0.00 2.59
4990 5097 5.946942 ATGTCAACACATCCTCATCTACT 57.053 39.130 0.00 0.00 39.15 2.57
5068 5175 4.785511 ACACTTAACGAGCTACATGACT 57.214 40.909 0.00 0.00 0.00 3.41
5128 5235 3.482436 TGTCTTGCCGTAATTTTGACCT 58.518 40.909 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.