Multiple sequence alignment - TraesCS5B01G438300

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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 TraesCS5B01G438300 chr5B 100.000 2922 0 0 1 2922 611076553 611079474 0.000000e+00 5397.0
1 TraesCS5B01G438300 chr5B 83.065 1240 179 19 660 1876 610965520 610966751 0.000000e+00 1098.0
2 TraesCS5B01G438300 chr5B 82.785 1156 184 12 707 1857 610922960 610924105 0.000000e+00 1018.0
3 TraesCS5B01G438300 chr5B 83.829 1076 158 9 720 1784 611045395 611046465 0.000000e+00 1009.0
4 TraesCS5B01G438300 chr5B 81.472 1155 190 12 707 1843 611323101 611324249 0.000000e+00 926.0
5 TraesCS5B01G438300 chr5B 82.168 1116 161 22 698 1785 610927120 610928225 0.000000e+00 924.0
6 TraesCS5B01G438300 chr5B 84.563 881 128 6 923 1799 610876840 610877716 0.000000e+00 867.0
7 TraesCS5B01G438300 chr5B 77.805 829 145 25 632 1433 611129317 611130133 2.630000e-130 475.0
8 TraesCS5B01G438300 chr5B 87.449 247 20 10 2480 2724 69805675 69805438 1.030000e-69 274.0
9 TraesCS5B01G438300 chr5A 84.885 1310 157 25 657 1941 618273171 618274464 0.000000e+00 1284.0
10 TraesCS5B01G438300 chr5A 82.877 1168 173 17 707 1857 618270565 618271722 0.000000e+00 1024.0
11 TraesCS5B01G438300 chr5A 82.681 1022 155 17 869 1876 618430316 618431329 0.000000e+00 887.0
12 TraesCS5B01G438300 chr5A 78.700 831 136 22 632 1433 618307143 618307961 1.550000e-142 516.0
13 TraesCS5B01G438300 chr5A 85.955 178 24 1 457 634 580202256 580202432 3.840000e-44 189.0
14 TraesCS5B01G438300 chr5A 92.913 127 6 2 2107 2232 618274839 618274963 6.430000e-42 182.0
15 TraesCS5B01G438300 chr1A 99.844 643 1 0 1 643 585617504 585616862 0.000000e+00 1182.0
16 TraesCS5B01G438300 chr1A 81.356 885 137 13 988 1855 589394272 589393399 0.000000e+00 695.0
17 TraesCS5B01G438300 chr7A 99.843 635 1 0 1 635 725612567 725613201 0.000000e+00 1168.0
18 TraesCS5B01G438300 chr7A 80.531 113 22 0 523 635 501317298 501317410 1.440000e-13 87.9
19 TraesCS5B01G438300 chr5D 83.261 1159 176 15 707 1857 494684783 494685931 0.000000e+00 1050.0
20 TraesCS5B01G438300 chr5D 82.192 1168 173 25 658 1799 494654325 494655483 0.000000e+00 972.0
21 TraesCS5B01G438300 chr5D 81.385 1155 191 14 707 1843 494761773 494762921 0.000000e+00 920.0
22 TraesCS5B01G438300 chr5D 80.404 1189 173 35 707 1847 494773752 494774928 0.000000e+00 850.0
23 TraesCS5B01G438300 chr5D 79.846 1171 174 33 707 1854 494645925 494647056 0.000000e+00 798.0
24 TraesCS5B01G438300 chr5D 79.487 741 140 9 707 1438 494687144 494687881 1.550000e-142 516.0
25 TraesCS5B01G438300 chr5D 85.789 190 18 4 452 639 491723860 491724042 2.970000e-45 193.0
26 TraesCS5B01G438300 chr1D 98.222 450 7 1 1 449 393687165 393687614 0.000000e+00 785.0
27 TraesCS5B01G438300 chr1D 96.277 188 6 1 447 634 393687665 393687851 1.020000e-79 307.0
28 TraesCS5B01G438300 chr1D 82.456 171 30 0 457 627 58120694 58120524 1.810000e-32 150.0
29 TraesCS5B01G438300 chr2D 86.357 667 56 6 2260 2922 567786944 567786309 0.000000e+00 695.0
30 TraesCS5B01G438300 chr2D 84.812 665 75 9 2262 2922 7204409 7205051 0.000000e+00 645.0
31 TraesCS5B01G438300 chr7D 89.011 182 19 1 454 635 591227557 591227737 1.050000e-54 224.0
32 TraesCS5B01G438300 chr6A 87.222 180 23 0 457 636 10591887 10591708 3.820000e-49 206.0
33 TraesCS5B01G438300 chr2B 78.832 274 53 5 2647 2917 711165505 711165234 2.310000e-41 180.0
34 TraesCS5B01G438300 chr2B 72.821 677 125 25 2260 2922 237036431 237035800 2.990000e-40 176.0


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 TraesCS5B01G438300 chr5B 611076553 611079474 2921 False 5397 5397 100.000000 1 2922 1 chr5B.!!$F4 2921
1 TraesCS5B01G438300 chr5B 610965520 610966751 1231 False 1098 1098 83.065000 660 1876 1 chr5B.!!$F2 1216
2 TraesCS5B01G438300 chr5B 611045395 611046465 1070 False 1009 1009 83.829000 720 1784 1 chr5B.!!$F3 1064
3 TraesCS5B01G438300 chr5B 610922960 610928225 5265 False 971 1018 82.476500 698 1857 2 chr5B.!!$F7 1159
4 TraesCS5B01G438300 chr5B 611323101 611324249 1148 False 926 926 81.472000 707 1843 1 chr5B.!!$F6 1136
5 TraesCS5B01G438300 chr5B 610876840 610877716 876 False 867 867 84.563000 923 1799 1 chr5B.!!$F1 876
6 TraesCS5B01G438300 chr5B 611129317 611130133 816 False 475 475 77.805000 632 1433 1 chr5B.!!$F5 801
7 TraesCS5B01G438300 chr5A 618430316 618431329 1013 False 887 887 82.681000 869 1876 1 chr5A.!!$F3 1007
8 TraesCS5B01G438300 chr5A 618270565 618274963 4398 False 830 1284 86.891667 657 2232 3 chr5A.!!$F4 1575
9 TraesCS5B01G438300 chr5A 618307143 618307961 818 False 516 516 78.700000 632 1433 1 chr5A.!!$F2 801
10 TraesCS5B01G438300 chr1A 585616862 585617504 642 True 1182 1182 99.844000 1 643 1 chr1A.!!$R1 642
11 TraesCS5B01G438300 chr1A 589393399 589394272 873 True 695 695 81.356000 988 1855 1 chr1A.!!$R2 867
12 TraesCS5B01G438300 chr7A 725612567 725613201 634 False 1168 1168 99.843000 1 635 1 chr7A.!!$F2 634
13 TraesCS5B01G438300 chr5D 494654325 494655483 1158 False 972 972 82.192000 658 1799 1 chr5D.!!$F3 1141
14 TraesCS5B01G438300 chr5D 494761773 494762921 1148 False 920 920 81.385000 707 1843 1 chr5D.!!$F4 1136
15 TraesCS5B01G438300 chr5D 494773752 494774928 1176 False 850 850 80.404000 707 1847 1 chr5D.!!$F5 1140
16 TraesCS5B01G438300 chr5D 494645925 494647056 1131 False 798 798 79.846000 707 1854 1 chr5D.!!$F2 1147
17 TraesCS5B01G438300 chr5D 494684783 494687881 3098 False 783 1050 81.374000 707 1857 2 chr5D.!!$F6 1150
18 TraesCS5B01G438300 chr1D 393687165 393687851 686 False 546 785 97.249500 1 634 2 chr1D.!!$F1 633
19 TraesCS5B01G438300 chr2D 567786309 567786944 635 True 695 695 86.357000 2260 2922 1 chr2D.!!$R1 662
20 TraesCS5B01G438300 chr2D 7204409 7205051 642 False 645 645 84.812000 2262 2922 1 chr2D.!!$F1 660

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
863 966 0.771127 CCCCTTTCAGTGTTGGAGGA 59.229 55.0 0.0 0.0 32.86 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2098 5156 0.173255 CATGCCCAACCATCCGAAAC 59.827 55.0 0.0 0.0 0.0 2.78 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
653 708 5.300539 ACACAGCTCTGTACATAGGTAGATG 59.699 44.000 12.04 12.52 42.83 2.90
654 709 5.532779 CACAGCTCTGTACATAGGTAGATGA 59.467 44.000 12.04 0.00 42.83 2.92
655 710 5.533154 ACAGCTCTGTACATAGGTAGATGAC 59.467 44.000 12.04 0.00 42.90 3.06
667 722 2.677836 GGTAGATGACGATGCAGCAAAA 59.322 45.455 1.53 0.00 0.00 2.44
678 738 2.229792 TGCAGCAAAATCTTTCCTCGT 58.770 42.857 0.00 0.00 0.00 4.18
694 754 2.621055 CCTCGTCAGTCTTCCATCCTAG 59.379 54.545 0.00 0.00 0.00 3.02
695 755 3.546724 CTCGTCAGTCTTCCATCCTAGA 58.453 50.000 0.00 0.00 0.00 2.43
696 756 3.948473 CTCGTCAGTCTTCCATCCTAGAA 59.052 47.826 0.00 0.00 0.00 2.10
697 757 4.537751 TCGTCAGTCTTCCATCCTAGAAT 58.462 43.478 0.00 0.00 0.00 2.40
698 758 4.580995 TCGTCAGTCTTCCATCCTAGAATC 59.419 45.833 0.00 0.00 0.00 2.52
702 765 5.907662 TCAGTCTTCCATCCTAGAATCCAAT 59.092 40.000 0.00 0.00 0.00 3.16
718 788 1.077265 AATCCACCAAGCCCACCTG 59.923 57.895 0.00 0.00 0.00 4.00
734 804 4.313819 TGCAGAATGGCAGAGCAG 57.686 55.556 0.00 0.00 39.25 4.24
794 894 1.746615 CGTGCTCAAGGTGGATGGG 60.747 63.158 0.00 0.00 0.00 4.00
806 909 0.824109 TGGATGGGTACTCAAGAGCG 59.176 55.000 0.00 0.00 0.00 5.03
839 942 2.126071 AACGGCGAGTGGATGACG 60.126 61.111 16.62 0.00 0.00 4.35
863 966 0.771127 CCCCTTTCAGTGTTGGAGGA 59.229 55.000 0.00 0.00 32.86 3.71
887 990 0.907704 ACTGGGCCGTGGAATACTGA 60.908 55.000 0.00 0.00 0.00 3.41
893 996 2.365582 GCCGTGGAATACTGACCAAAT 58.634 47.619 0.00 0.00 37.94 2.32
910 1013 5.497464 CCAAATGGTTACCCAAAGGATTT 57.503 39.130 0.00 0.00 46.04 2.17
911 1014 6.613153 CCAAATGGTTACCCAAAGGATTTA 57.387 37.500 0.00 0.00 46.04 1.40
920 1023 5.198602 ACCCAAAGGATTTAGCTGATTCT 57.801 39.130 0.00 0.00 35.03 2.40
950 1053 8.976353 TCTCTTTATCTACTTCTTCAATCTGCT 58.024 33.333 0.00 0.00 0.00 4.24
1027 1133 0.749454 CCAGTGCCTTCATACAGCCC 60.749 60.000 0.00 0.00 0.00 5.19
1038 1144 3.186283 TCATACAGCCCTACCTCCAAAA 58.814 45.455 0.00 0.00 0.00 2.44
1044 1151 2.983898 AGCCCTACCTCCAAAACTGTAA 59.016 45.455 0.00 0.00 0.00 2.41
1059 1166 3.528597 CTGTAAGTACCTTCTCAGGGC 57.471 52.381 0.00 0.00 46.01 5.19
1069 1176 0.250901 TTCTCAGGGCAAGGTTCAGC 60.251 55.000 0.00 0.00 0.00 4.26
1076 1183 2.919494 GCAAGGTTCAGCCAACGGG 61.919 63.158 0.00 0.00 40.61 5.28
1089 1196 2.349580 GCCAACGGGTACGATAACTTTC 59.650 50.000 0.00 0.00 44.60 2.62
1106 1213 5.489792 ACTTTCTCAACAAGGCTGATCTA 57.510 39.130 0.00 0.00 0.00 1.98
1118 1225 1.067915 GCTGATCTAGAGGCATCGGTC 60.068 57.143 0.00 0.00 0.00 4.79
1126 1233 0.249657 GAGGCATCGGTCCATCTGAC 60.250 60.000 0.00 0.00 43.67 3.51
1157 1264 4.528206 TGTCTCACTATCAGGTGTGATGTT 59.472 41.667 0.00 0.00 43.66 2.71
1189 1326 1.314730 GGCGAAGAAACAAGGGTTCA 58.685 50.000 0.00 0.00 35.82 3.18
1277 1414 2.894765 TCAAGTCGGTGGACAGACATTA 59.105 45.455 11.80 0.00 45.92 1.90
1298 1437 1.532604 CGGCTCACAGGTGTGTCCTA 61.533 60.000 9.87 0.00 46.24 2.94
1361 1503 2.659016 CAGGAGAGTTCTGCCGCA 59.341 61.111 0.00 0.00 34.60 5.69
1438 1580 4.547406 TCATATACACCGACTCTGTTCG 57.453 45.455 0.00 0.00 38.80 3.95
1451 1617 0.861837 CTGTTCGTCCAGTGCTTGAC 59.138 55.000 0.00 0.00 0.00 3.18
1454 1620 4.957266 CGTCCAGTGCTTGACGTA 57.043 55.556 14.96 0.00 46.83 3.57
1500 1666 1.337728 CCGCTGACAGGTACAACATCA 60.338 52.381 4.26 0.00 0.00 3.07
1566 1732 1.786937 TTCCAACATGGTGGCAACTT 58.213 45.000 25.89 0.00 39.03 2.66
1567 1733 2.666272 TCCAACATGGTGGCAACTTA 57.334 45.000 25.89 3.33 39.03 2.24
1596 1762 1.686355 AGCCGAACAACATGGTTTCA 58.314 45.000 0.00 0.00 0.00 2.69
1674 4480 1.134521 TGATGGCGAGTGATGGTTACC 60.135 52.381 0.00 0.00 0.00 2.85
1745 4551 0.035152 TCATGCCGGCTGAACTGAAT 60.035 50.000 29.70 6.94 0.00 2.57
1746 4552 1.209261 TCATGCCGGCTGAACTGAATA 59.791 47.619 29.70 2.45 0.00 1.75
1919 4773 9.632638 TTGCTATTTTCCTTTCTTGCTAGATAT 57.367 29.630 0.00 0.00 0.00 1.63
1940 4794 9.678260 AGATATAAGAAAGCATTGTTGAGACTT 57.322 29.630 0.00 0.00 0.00 3.01
1941 4795 9.928236 GATATAAGAAAGCATTGTTGAGACTTC 57.072 33.333 0.00 0.00 0.00 3.01
1942 4796 5.444663 AAGAAAGCATTGTTGAGACTTCC 57.555 39.130 0.00 0.00 0.00 3.46
1943 4797 3.823304 AGAAAGCATTGTTGAGACTTCCC 59.177 43.478 0.00 0.00 0.00 3.97
1944 4798 2.957402 AGCATTGTTGAGACTTCCCA 57.043 45.000 0.00 0.00 0.00 4.37
1945 4799 3.446442 AGCATTGTTGAGACTTCCCAT 57.554 42.857 0.00 0.00 0.00 4.00
1946 4800 3.087031 AGCATTGTTGAGACTTCCCATG 58.913 45.455 0.00 0.00 0.00 3.66
1947 4801 2.821969 GCATTGTTGAGACTTCCCATGT 59.178 45.455 0.00 0.00 0.00 3.21
1948 4802 4.009675 GCATTGTTGAGACTTCCCATGTA 58.990 43.478 0.00 0.00 0.00 2.29
1949 4803 4.142600 GCATTGTTGAGACTTCCCATGTAC 60.143 45.833 0.00 0.00 0.00 2.90
1950 4804 3.313012 TGTTGAGACTTCCCATGTACG 57.687 47.619 0.00 0.00 0.00 3.67
1951 4805 2.631062 TGTTGAGACTTCCCATGTACGT 59.369 45.455 0.00 0.00 0.00 3.57
1952 4806 3.827876 TGTTGAGACTTCCCATGTACGTA 59.172 43.478 0.00 0.00 0.00 3.57
1953 4807 4.082408 TGTTGAGACTTCCCATGTACGTAG 60.082 45.833 0.00 0.00 0.00 3.51
1954 4808 2.426024 TGAGACTTCCCATGTACGTAGC 59.574 50.000 0.00 0.00 0.00 3.58
1955 4809 1.755380 AGACTTCCCATGTACGTAGCC 59.245 52.381 0.00 0.00 0.00 3.93
1956 4810 1.755380 GACTTCCCATGTACGTAGCCT 59.245 52.381 0.00 0.00 0.00 4.58
1957 4811 2.954318 GACTTCCCATGTACGTAGCCTA 59.046 50.000 0.00 0.00 0.00 3.93
1958 4812 2.692041 ACTTCCCATGTACGTAGCCTAC 59.308 50.000 0.00 0.00 0.00 3.18
1959 4813 2.742428 TCCCATGTACGTAGCCTACT 57.258 50.000 0.00 0.00 0.00 2.57
1962 4816 4.535781 TCCCATGTACGTAGCCTACTTAA 58.464 43.478 0.00 0.00 0.00 1.85
1972 4826 4.565564 CGTAGCCTACTTAACCATTGTGTC 59.434 45.833 0.00 0.00 0.00 3.67
1979 4833 9.169592 GCCTACTTAACCATTGTGTCTTTATTA 57.830 33.333 0.00 0.00 0.00 0.98
1997 5032 8.752254 TCTTTATTAAGTCGATTACTTCATGCG 58.248 33.333 0.00 0.00 45.64 4.73
2009 5044 1.163420 TTCATGCGTGCCGTTCTTGT 61.163 50.000 0.00 0.00 0.00 3.16
2023 5058 4.210537 CCGTTCTTGTTTTGTATCGTCACT 59.789 41.667 0.00 0.00 0.00 3.41
2039 5082 0.249155 CACTGCTGCCCTGTTTTGTG 60.249 55.000 0.00 0.00 0.00 3.33
2041 5084 0.249155 CTGCTGCCCTGTTTTGTGTG 60.249 55.000 0.00 0.00 0.00 3.82
2054 5097 2.983907 TTGTGTGGACCGACTACAAA 57.016 45.000 1.22 0.00 41.36 2.83
2056 5099 2.033372 TGTGTGGACCGACTACAAAGA 58.967 47.619 1.22 0.00 41.36 2.52
2058 5101 2.993899 GTGTGGACCGACTACAAAGATG 59.006 50.000 1.22 0.00 41.36 2.90
2059 5102 2.894765 TGTGGACCGACTACAAAGATGA 59.105 45.455 0.00 0.00 37.06 2.92
2060 5103 3.322541 TGTGGACCGACTACAAAGATGAA 59.677 43.478 0.00 0.00 37.06 2.57
2065 5121 5.292101 GGACCGACTACAAAGATGAATTGAG 59.708 44.000 0.00 0.00 0.00 3.02
2090 5148 6.384224 CATCAACATTAGATGCTTGTGTTGT 58.616 36.000 13.99 2.55 45.86 3.32
2093 5151 7.935520 TCAACATTAGATGCTTGTGTTGTTTA 58.064 30.769 13.99 0.00 45.86 2.01
2094 5152 8.575589 TCAACATTAGATGCTTGTGTTGTTTAT 58.424 29.630 13.99 0.00 45.86 1.40
2096 5154 8.970691 ACATTAGATGCTTGTGTTGTTTATTC 57.029 30.769 0.00 0.00 0.00 1.75
2098 5156 9.069078 CATTAGATGCTTGTGTTGTTTATTCTG 57.931 33.333 0.00 0.00 0.00 3.02
2099 5157 6.639632 AGATGCTTGTGTTGTTTATTCTGT 57.360 33.333 0.00 0.00 0.00 3.41
2101 5159 7.491682 AGATGCTTGTGTTGTTTATTCTGTTT 58.508 30.769 0.00 0.00 0.00 2.83
2108 5166 5.856455 GTGTTGTTTATTCTGTTTCGGATGG 59.144 40.000 0.00 0.00 0.00 3.51
2110 5168 6.039941 TGTTGTTTATTCTGTTTCGGATGGTT 59.960 34.615 0.00 0.00 0.00 3.67
2112 5170 5.048364 TGTTTATTCTGTTTCGGATGGTTGG 60.048 40.000 0.00 0.00 0.00 3.77
2159 7353 1.611673 CCTGAACCACTCGAAGGCAAT 60.612 52.381 3.59 0.00 0.00 3.56
2183 7378 3.259123 TGAAGAGTGTGATAGCTTCAGCA 59.741 43.478 0.75 0.00 41.08 4.41
2232 7427 2.025037 AGGCAATTAGAATGTGAGGCCA 60.025 45.455 5.01 0.00 42.49 5.36
2234 7429 3.243636 GGCAATTAGAATGTGAGGCCATG 60.244 47.826 5.01 0.00 39.88 3.66
2237 7432 0.846015 TAGAATGTGAGGCCATGGGG 59.154 55.000 15.13 0.00 37.18 4.96
2238 7433 1.456331 GAATGTGAGGCCATGGGGG 60.456 63.158 15.13 0.00 40.85 5.40
2239 7434 1.935400 AATGTGAGGCCATGGGGGA 60.935 57.895 15.13 0.00 40.01 4.81
2241 7436 1.298906 ATGTGAGGCCATGGGGGAAT 61.299 55.000 15.13 0.00 40.01 3.01
2242 7437 1.311059 GTGAGGCCATGGGGGAATT 59.689 57.895 15.13 0.00 40.01 2.17
2243 7438 1.044790 GTGAGGCCATGGGGGAATTG 61.045 60.000 15.13 0.00 40.01 2.32
2244 7439 1.458209 GAGGCCATGGGGGAATTGG 60.458 63.158 15.13 0.00 40.01 3.16
2245 7440 2.446418 GGCCATGGGGGAATTGGG 60.446 66.667 15.13 0.00 40.01 4.12
2246 7441 2.695597 GCCATGGGGGAATTGGGA 59.304 61.111 15.13 0.00 40.01 4.37
2247 7442 1.002792 GCCATGGGGGAATTGGGAA 59.997 57.895 15.13 0.00 40.01 3.97
2249 7444 1.203237 CCATGGGGGAATTGGGAAAC 58.797 55.000 2.85 0.00 40.01 2.78
2250 7445 1.554353 CCATGGGGGAATTGGGAAACA 60.554 52.381 2.85 0.00 40.01 2.83
2251 7446 2.264455 CATGGGGGAATTGGGAAACAA 58.736 47.619 0.00 0.00 44.54 2.83
2252 7447 2.022718 TGGGGGAATTGGGAAACAAG 57.977 50.000 0.00 0.00 43.48 3.16
2253 7448 1.505538 TGGGGGAATTGGGAAACAAGA 59.494 47.619 0.00 0.00 43.48 3.02
2254 7449 2.113414 TGGGGGAATTGGGAAACAAGAT 59.887 45.455 0.00 0.00 43.48 2.40
2256 7451 3.704566 GGGGGAATTGGGAAACAAGATAC 59.295 47.826 0.00 0.00 43.48 2.24
2257 7452 4.349365 GGGGAATTGGGAAACAAGATACA 58.651 43.478 0.00 0.00 43.48 2.29
2258 7453 4.402474 GGGGAATTGGGAAACAAGATACAG 59.598 45.833 0.00 0.00 43.48 2.74
2326 8216 3.155167 CCGCCACCTCTCCTACCC 61.155 72.222 0.00 0.00 0.00 3.69
2347 8502 0.911525 CCTCTCTTGGCCTCCTTCCA 60.912 60.000 3.32 0.00 0.00 3.53
2414 8573 3.408853 GGCGGGGCCTTACCTTCT 61.409 66.667 0.84 0.00 46.69 2.85
2416 8575 2.124695 CGGGGCCTTACCTTCTGC 60.125 66.667 0.84 0.00 39.10 4.26
2450 8609 3.550431 GAGCGGGCCAGCCTATCA 61.550 66.667 25.09 0.00 38.01 2.15
2455 8614 3.161450 GGCCAGCCTATCACCCGA 61.161 66.667 0.00 0.00 0.00 5.14
2473 8632 2.625460 AAGGCCCTGGCTTATGGCA 61.625 57.895 8.29 4.74 46.45 4.92
2487 8646 4.201122 GGCAGGGCCTAGCAGCAT 62.201 66.667 23.25 0.00 46.69 3.79
2488 8647 2.822637 GGCAGGGCCTAGCAGCATA 61.823 63.158 23.25 0.00 46.69 3.14
2795 8956 3.872603 TGCTGGCCGACCACTTGT 61.873 61.111 0.00 0.00 42.67 3.16
2876 9287 4.540153 GCAGGCGGCAATCTTCTA 57.460 55.556 13.08 0.00 43.97 2.10
2879 9290 1.147153 AGGCGGCAATCTTCTAGGC 59.853 57.895 13.08 0.00 0.00 3.93
2883 9294 0.755686 CGGCAATCTTCTAGGCCTCT 59.244 55.000 9.68 0.00 44.23 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
653 708 3.119708 AGGAAAGATTTTGCTGCATCGTC 60.120 43.478 1.84 1.83 0.00 4.20
654 709 2.821969 AGGAAAGATTTTGCTGCATCGT 59.178 40.909 1.84 0.00 0.00 3.73
655 710 3.432782 GAGGAAAGATTTTGCTGCATCG 58.567 45.455 1.84 0.00 0.00 3.84
667 722 3.165875 TGGAAGACTGACGAGGAAAGAT 58.834 45.455 0.00 0.00 0.00 2.40
678 738 4.883759 TGGATTCTAGGATGGAAGACTGA 58.116 43.478 0.00 0.00 39.58 3.41
694 754 1.114627 GGGCTTGGTGGATTGGATTC 58.885 55.000 0.00 0.00 0.00 2.52
695 755 0.413037 TGGGCTTGGTGGATTGGATT 59.587 50.000 0.00 0.00 0.00 3.01
696 756 0.324645 GTGGGCTTGGTGGATTGGAT 60.325 55.000 0.00 0.00 0.00 3.41
697 757 1.076549 GTGGGCTTGGTGGATTGGA 59.923 57.895 0.00 0.00 0.00 3.53
698 758 1.984026 GGTGGGCTTGGTGGATTGG 60.984 63.158 0.00 0.00 0.00 3.16
702 765 4.284550 GCAGGTGGGCTTGGTGGA 62.285 66.667 0.00 0.00 0.00 4.02
718 788 1.801332 CACTGCTCTGCCATTCTGC 59.199 57.895 0.00 0.00 0.00 4.26
734 804 0.675837 TGGCAGCAGAGATCTTGCAC 60.676 55.000 23.08 16.91 0.00 4.57
794 894 2.654939 CGCCTTCGCTCTTGAGTAC 58.345 57.895 0.00 0.00 0.00 2.73
806 909 0.992802 CGTTCTTGAGTAGCGCCTTC 59.007 55.000 2.29 0.00 0.00 3.46
839 942 0.954452 CAACACTGAAAGGGGCAGAC 59.046 55.000 0.00 0.00 46.65 3.51
950 1053 1.741401 CTTCACATCTTCGGCGCCA 60.741 57.895 28.98 11.20 0.00 5.69
1027 1133 6.356186 AGGTACTTACAGTTTTGGAGGTAG 57.644 41.667 0.00 0.00 31.02 3.18
1059 1166 0.250553 TACCCGTTGGCTGAACCTTG 60.251 55.000 0.00 0.00 40.22 3.61
1069 1176 3.853475 AGAAAGTTATCGTACCCGTTGG 58.147 45.455 0.00 0.00 35.01 3.77
1072 1179 4.022068 TGTTGAGAAAGTTATCGTACCCGT 60.022 41.667 0.00 0.00 35.01 5.28
1073 1180 4.487948 TGTTGAGAAAGTTATCGTACCCG 58.512 43.478 0.00 0.00 0.00 5.28
1076 1183 5.638234 AGCCTTGTTGAGAAAGTTATCGTAC 59.362 40.000 0.00 0.00 0.00 3.67
1089 1196 3.740764 GCCTCTAGATCAGCCTTGTTGAG 60.741 52.174 0.00 0.00 0.00 3.02
1106 1213 0.397675 TCAGATGGACCGATGCCTCT 60.398 55.000 0.00 0.00 0.00 3.69
1126 1233 4.644234 ACCTGATAGTGAGACAGTCATCTG 59.356 45.833 2.66 1.14 46.18 2.90
1142 1249 3.764972 TGACGGTAACATCACACCTGATA 59.235 43.478 0.00 0.00 35.17 2.15
1189 1326 1.376424 CAGTGCAGGTCGCTTGGAT 60.376 57.895 0.00 0.00 43.06 3.41
1206 1343 3.838271 GAGGTCGCCGAGATGCCA 61.838 66.667 0.00 0.00 0.00 4.92
1358 1500 2.936498 ACGGATTTCAATAGGACTTGCG 59.064 45.455 0.00 0.00 0.00 4.85
1361 1503 5.160607 TGTCACGGATTTCAATAGGACTT 57.839 39.130 0.00 0.00 0.00 3.01
1438 1580 1.000607 TCACTACGTCAAGCACTGGAC 60.001 52.381 0.00 0.00 0.00 4.02
1451 1617 2.584064 TGGCTGGCCATCACTACG 59.416 61.111 5.51 0.00 41.89 3.51
1478 1644 2.048597 TTGTACCTGTCAGCGGCG 60.049 61.111 0.51 0.51 0.00 6.46
1481 1647 2.078849 TGATGTTGTACCTGTCAGCG 57.921 50.000 0.00 0.00 0.00 5.18
1500 1666 2.780714 GCATATCTGCTTCAGCCTCAT 58.219 47.619 0.00 0.00 45.32 2.90
1583 1749 3.131396 GAGACGACTGAAACCATGTTGT 58.869 45.455 0.00 0.00 0.00 3.32
1596 1762 3.460857 ACAAGCTTCTTTGAGACGACT 57.539 42.857 0.00 0.00 0.00 4.18
1674 4480 1.065701 GCAGCTGGAATTGAGATGCTG 59.934 52.381 17.12 11.86 46.88 4.41
1745 4551 4.578871 CCATGATGATATCCTTTGCCGTA 58.421 43.478 0.00 0.00 0.00 4.02
1746 4552 3.415212 CCATGATGATATCCTTTGCCGT 58.585 45.455 0.00 0.00 0.00 5.68
1810 4619 7.195374 ACCAGTGCTACTAAAATTAGGATGA 57.805 36.000 5.27 0.00 35.08 2.92
1828 4644 2.766263 TGGAGAGGTAGCATAACCAGTG 59.234 50.000 5.79 0.00 42.40 3.66
1830 4646 3.389329 ACATGGAGAGGTAGCATAACCAG 59.611 47.826 0.00 0.00 42.40 4.00
1859 4675 7.533900 CACATGAGTAGTTTTGGAACGTAAATG 59.466 37.037 0.00 0.00 40.75 2.32
1865 4684 5.269459 CTCACATGAGTAGTTTTGGAACG 57.731 43.478 0.00 0.00 37.81 3.95
1919 4773 5.473504 GGGAAGTCTCAACAATGCTTTCTTA 59.526 40.000 0.00 0.00 0.00 2.10
1931 4785 3.314541 ACGTACATGGGAAGTCTCAAC 57.685 47.619 0.00 0.00 0.00 3.18
1940 4794 2.742428 AGTAGGCTACGTACATGGGA 57.258 50.000 18.41 0.00 0.00 4.37
1941 4795 4.500375 GGTTAAGTAGGCTACGTACATGGG 60.500 50.000 18.02 0.00 0.00 4.00
1942 4796 4.098349 TGGTTAAGTAGGCTACGTACATGG 59.902 45.833 18.02 0.00 0.00 3.66
1943 4797 5.252969 TGGTTAAGTAGGCTACGTACATG 57.747 43.478 18.02 0.00 0.00 3.21
1944 4798 6.127253 ACAATGGTTAAGTAGGCTACGTACAT 60.127 38.462 18.02 15.67 0.00 2.29
1945 4799 5.185635 ACAATGGTTAAGTAGGCTACGTACA 59.814 40.000 18.02 14.33 0.00 2.90
1946 4800 5.517770 CACAATGGTTAAGTAGGCTACGTAC 59.482 44.000 18.02 15.99 0.00 3.67
1947 4801 5.185635 ACACAATGGTTAAGTAGGCTACGTA 59.814 40.000 18.41 16.64 0.00 3.57
1948 4802 4.020839 ACACAATGGTTAAGTAGGCTACGT 60.021 41.667 18.41 17.69 0.00 3.57
1949 4803 4.501071 ACACAATGGTTAAGTAGGCTACG 58.499 43.478 18.41 4.18 0.00 3.51
1950 4804 5.731591 AGACACAATGGTTAAGTAGGCTAC 58.268 41.667 16.93 16.93 0.00 3.58
1951 4805 6.368779 AAGACACAATGGTTAAGTAGGCTA 57.631 37.500 0.00 0.00 0.00 3.93
1952 4806 4.910458 AGACACAATGGTTAAGTAGGCT 57.090 40.909 0.00 0.00 0.00 4.58
1953 4807 5.959618 AAAGACACAATGGTTAAGTAGGC 57.040 39.130 0.00 0.00 0.00 3.93
1958 4812 9.755064 CGACTTAATAAAGACACAATGGTTAAG 57.245 33.333 0.00 0.00 36.50 1.85
1959 4813 9.491675 TCGACTTAATAAAGACACAATGGTTAA 57.508 29.630 0.00 0.00 36.50 2.01
1962 4816 8.561738 AATCGACTTAATAAAGACACAATGGT 57.438 30.769 0.00 0.00 36.50 3.55
1997 5032 3.223157 CGATACAAAACAAGAACGGCAC 58.777 45.455 0.00 0.00 0.00 5.01
2009 5044 1.804151 GGCAGCAGTGACGATACAAAA 59.196 47.619 0.00 0.00 0.00 2.44
2023 5058 1.674764 CCACACAAAACAGGGCAGCA 61.675 55.000 0.00 0.00 0.00 4.41
2039 5082 3.587797 TCATCTTTGTAGTCGGTCCAC 57.412 47.619 0.00 0.00 0.00 4.02
2041 5084 5.175859 TCAATTCATCTTTGTAGTCGGTCC 58.824 41.667 0.00 0.00 0.00 4.46
2054 5097 8.568794 CATCTAATGTTGATGCTCAATTCATCT 58.431 33.333 7.04 0.00 38.79 2.90
2090 5148 4.461081 CCCAACCATCCGAAACAGAATAAA 59.539 41.667 0.00 0.00 0.00 1.40
2093 5151 2.446435 CCCAACCATCCGAAACAGAAT 58.554 47.619 0.00 0.00 0.00 2.40
2094 5152 1.904287 CCCAACCATCCGAAACAGAA 58.096 50.000 0.00 0.00 0.00 3.02
2096 5154 0.893270 TGCCCAACCATCCGAAACAG 60.893 55.000 0.00 0.00 0.00 3.16
2098 5156 0.173255 CATGCCCAACCATCCGAAAC 59.827 55.000 0.00 0.00 0.00 2.78
2099 5157 0.969917 CCATGCCCAACCATCCGAAA 60.970 55.000 0.00 0.00 0.00 3.46
2101 5159 2.275089 CCATGCCCAACCATCCGA 59.725 61.111 0.00 0.00 0.00 4.55
2108 5166 2.078392 CAATGAAAAGCCATGCCCAAC 58.922 47.619 0.00 0.00 0.00 3.77
2110 5168 1.642112 TCAATGAAAAGCCATGCCCA 58.358 45.000 0.00 0.00 0.00 5.36
2112 5170 3.602483 ACAATCAATGAAAAGCCATGCC 58.398 40.909 0.00 0.00 0.00 4.40
2183 7378 4.574674 TCAGGTTCTTGATGCCAATACT 57.425 40.909 0.00 0.00 0.00 2.12
2232 7427 2.113414 TCTTGTTTCCCAATTCCCCCAT 59.887 45.455 0.00 0.00 31.20 4.00
2234 7429 2.319025 TCTTGTTTCCCAATTCCCCC 57.681 50.000 0.00 0.00 31.20 5.40
2237 7432 4.142160 GGCTGTATCTTGTTTCCCAATTCC 60.142 45.833 0.00 0.00 31.20 3.01
2238 7433 4.142160 GGGCTGTATCTTGTTTCCCAATTC 60.142 45.833 0.00 0.00 31.20 2.17
2239 7434 3.769300 GGGCTGTATCTTGTTTCCCAATT 59.231 43.478 0.00 0.00 31.20 2.32
2241 7436 2.556559 GGGGCTGTATCTTGTTTCCCAA 60.557 50.000 0.00 0.00 34.04 4.12
2242 7437 1.005450 GGGGCTGTATCTTGTTTCCCA 59.995 52.381 0.00 0.00 34.04 4.37
2243 7438 1.685180 GGGGGCTGTATCTTGTTTCCC 60.685 57.143 0.00 0.00 0.00 3.97
2244 7439 1.763968 GGGGGCTGTATCTTGTTTCC 58.236 55.000 0.00 0.00 0.00 3.13
2326 8216 1.617839 AAGGAGGCCAAGAGAGGGG 60.618 63.158 5.01 0.00 0.00 4.79
2434 8593 3.866582 GTGATAGGCTGGCCCGCT 61.867 66.667 19.30 7.65 39.21 5.52
2447 8606 3.411517 CCAGGGCCTTCGGGTGAT 61.412 66.667 1.32 0.00 37.45 3.06
2460 8619 2.520260 GCCCTGCCATAAGCCAGG 60.520 66.667 0.00 0.00 42.71 4.45
2473 8632 2.876945 CGCTATGCTGCTAGGCCCT 61.877 63.158 0.00 0.00 0.00 5.19
2477 8636 2.736236 CGCCGCTATGCTGCTAGG 60.736 66.667 0.00 0.00 36.66 3.02
2479 8638 4.219999 TGCGCCGCTATGCTGCTA 62.220 61.111 11.67 0.00 36.66 3.49
2598 8758 4.758251 CGTGCACCGCCAGATCCA 62.758 66.667 12.15 0.00 0.00 3.41
2718 8879 4.807039 CCACCGGCCGACGTAAGG 62.807 72.222 30.73 14.59 46.39 2.69
2753 8914 0.889186 GCCAAGTCCACCGATGTTGT 60.889 55.000 0.00 0.00 0.00 3.32
2759 8920 3.998672 GTCCGCCAAGTCCACCGA 61.999 66.667 0.00 0.00 0.00 4.69
2790 8951 4.003788 CCACCGGAGCCGACAAGT 62.004 66.667 9.46 0.00 42.83 3.16
2879 9290 4.760047 CGTCCACCGGCCAAGAGG 62.760 72.222 0.00 1.03 38.23 3.69
2902 9313 4.868116 ACGCAAGGCCACCAACGT 62.868 61.111 5.01 4.29 46.39 3.99


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

AutoCloner maintained by Alex Coulton.