Multiple sequence alignment - TraesCS4D01G149600

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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 TraesCS4D01G149600 chr4D 100.000 3476 0 0 636 4111 157652095 157648620 0.000000e+00 6420
1 TraesCS4D01G149600 chr4D 100.000 154 0 0 1 154 157652730 157652577 6.730000e-73 285
2 TraesCS4D01G149600 chr4B 94.686 1543 56 8 2241 3757 216796428 216797970 0.000000e+00 2372
3 TraesCS4D01G149600 chr4B 98.201 778 14 0 960 1737 216792582 216793359 0.000000e+00 1360
4 TraesCS4D01G149600 chr4B 95.181 498 13 4 1753 2242 216793404 216793898 0.000000e+00 776
5 TraesCS4D01G149600 chr4B 84.365 307 39 9 3567 3866 667548246 667547942 4.020000e-75 292
6 TraesCS4D01G149600 chr4B 93.252 163 10 1 3949 4111 216798084 216798245 5.310000e-59 239
7 TraesCS4D01G149600 chr4B 88.344 163 10 4 1 154 14276210 14276372 1.950000e-43 187
8 TraesCS4D01G149600 chr4A 95.894 1242 33 8 2241 3465 346686994 346688234 0.000000e+00 1995
9 TraesCS4D01G149600 chr4A 95.838 913 17 6 960 1872 346684240 346685131 0.000000e+00 1456
10 TraesCS4D01G149600 chr4A 83.884 484 67 9 3459 3935 346745524 346746003 6.270000e-123 451
11 TraesCS4D01G149600 chr4A 95.023 221 6 3 2024 2242 346686615 346686832 3.940000e-90 342
12 TraesCS4D01G149600 chr4A 84.416 308 39 9 3567 3867 572708415 572708720 1.120000e-75 294
13 TraesCS4D01G149600 chr4A 96.226 159 6 0 1873 2031 346685292 346685450 1.130000e-65 261
14 TraesCS4D01G149600 chr4A 90.196 153 6 3 10 153 742062105 742062257 1.510000e-44 191
15 TraesCS4D01G149600 chr4A 86.905 168 15 7 3949 4111 346745990 346746155 9.080000e-42 182
16 TraesCS4D01G149600 chr3D 93.609 266 13 4 636 897 300669321 300669056 1.070000e-105 394
17 TraesCS4D01G149600 chr3D 88.710 248 24 3 647 890 55159772 55160019 2.400000e-77 300
18 TraesCS4D01G149600 chr3D 84.194 310 42 6 3566 3869 488120896 488121204 1.120000e-75 294
19 TraesCS4D01G149600 chr1D 90.566 265 21 4 636 896 462963484 462963220 8.460000e-92 348
20 TraesCS4D01G149600 chr1D 94.839 155 7 1 1 154 462963665 462963511 1.480000e-59 241
21 TraesCS4D01G149600 chr2B 90.637 267 16 5 636 894 765758875 765759140 3.040000e-91 346
22 TraesCS4D01G149600 chr5B 90.458 262 18 3 636 891 588829990 588830250 5.090000e-89 339
23 TraesCS4D01G149600 chr6A 89.961 259 22 4 636 890 616107986 616108244 8.520000e-87 331
24 TraesCS4D01G149600 chr5A 88.417 259 26 3 636 890 547539037 547539295 3.990000e-80 309
25 TraesCS4D01G149600 chr5A 83.810 315 44 7 3564 3872 299294794 299295107 4.020000e-75 292
26 TraesCS4D01G149600 chr5A 94.194 155 8 1 1 154 17285855 17285701 6.870000e-58 235
27 TraesCS4D01G149600 chr5A 93.333 150 9 1 6 154 438848852 438848703 1.920000e-53 220
28 TraesCS4D01G149600 chr3A 85.065 308 36 10 3566 3866 515737081 515736777 5.160000e-79 305
29 TraesCS4D01G149600 chr5D 84.365 307 42 6 3567 3868 536022336 536022031 3.110000e-76 296
30 TraesCS4D01G149600 chr1A 84.244 311 41 8 3567 3871 548573483 548573175 3.110000e-76 296
31 TraesCS4D01G149600 chr1A 87.259 259 29 3 636 890 19702935 19703193 4.020000e-75 292
32 TraesCS4D01G149600 chr6B 87.259 259 27 5 636 890 117537388 117537132 1.450000e-74 291
33 TraesCS4D01G149600 chr7B 93.506 154 9 1 1 153 1816927 1816774 1.150000e-55 228
34 TraesCS4D01G149600 chr7B 92.903 155 10 1 1 154 621402983 621403137 1.490000e-54 224
35 TraesCS4D01G149600 chr7A 88.344 163 10 1 1 154 6958730 6958892 1.950000e-43 187
36 TraesCS4D01G149600 chr1B 92.969 128 8 1 1 127 231662753 231662880 7.020000e-43 185


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 TraesCS4D01G149600 chr4D 157648620 157652730 4110 True 3352.50 6420 100.00000 1 4111 2 chr4D.!!$R1 4110
1 TraesCS4D01G149600 chr4B 216792582 216798245 5663 False 1186.75 2372 95.33000 960 4111 4 chr4B.!!$F2 3151
2 TraesCS4D01G149600 chr4A 346684240 346688234 3994 False 1013.50 1995 95.74525 960 3465 4 chr4A.!!$F3 2505
3 TraesCS4D01G149600 chr4A 346745524 346746155 631 False 316.50 451 85.39450 3459 4111 2 chr4A.!!$F4 652

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
921 922 0.250166 CACCTTCTTTCCCGGTTCGT 60.250 55.000 0.0 0.0 0.0 3.85 F
922 923 0.471191 ACCTTCTTTCCCGGTTCGTT 59.529 50.000 0.0 0.0 0.0 3.85 F
930 931 0.814812 TCCCGGTTCGTTTGTTCACC 60.815 55.000 0.0 0.0 0.0 4.02 F
933 934 1.096386 CGGTTCGTTTGTTCACCCCA 61.096 55.000 0.0 0.0 0.0 4.96 F
939 940 1.135803 CGTTTGTTCACCCCATTAGCG 60.136 52.381 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1737 1738 3.492102 TCTACTGCAAGCCAAAGACTT 57.508 42.857 0.00 0.0 37.6 3.01 R
1738 1739 3.710209 ATCTACTGCAAGCCAAAGACT 57.290 42.857 0.00 0.0 37.6 3.24 R
2683 6587 4.507388 CCTTTGCGTCATTTTGTTGTGATT 59.493 37.500 0.00 0.0 0.0 2.57 R
2886 6790 4.988540 CAGACTTGTTTCGTGAAGGTGATA 59.011 41.667 0.00 0.0 0.0 2.15 R
3146 7050 0.791422 TACGGCGCATAAACACACAC 59.209 50.000 10.83 0.0 0.0 3.82 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
17 18 3.081409 TCGAGCCCACTAAGCCCC 61.081 66.667 0.00 0.00 0.00 5.80
18 19 4.530857 CGAGCCCACTAAGCCCCG 62.531 72.222 0.00 0.00 0.00 5.73
19 20 4.858680 GAGCCCACTAAGCCCCGC 62.859 72.222 0.00 0.00 0.00 6.13
62 63 3.443045 CAGCACCCAACGCCCATC 61.443 66.667 0.00 0.00 0.00 3.51
89 90 4.785453 CCGCCTCCTGGAAGCCAC 62.785 72.222 11.56 0.00 34.57 5.01
92 93 4.785453 CCTCCTGGAAGCCACGCC 62.785 72.222 0.00 0.00 34.57 5.68
130 131 4.759205 GCCCGCCCAAACCCAGAT 62.759 66.667 0.00 0.00 0.00 2.90
131 132 2.755469 CCCGCCCAAACCCAGATG 60.755 66.667 0.00 0.00 0.00 2.90
132 133 2.755469 CCGCCCAAACCCAGATGG 60.755 66.667 0.00 0.00 41.37 3.51
668 669 4.506255 CCAGGAATCCCCGCCACC 62.506 72.222 0.00 0.00 40.87 4.61
669 670 3.727258 CAGGAATCCCCGCCACCA 61.727 66.667 0.00 0.00 40.87 4.17
670 671 3.728373 AGGAATCCCCGCCACCAC 61.728 66.667 0.00 0.00 40.87 4.16
750 751 3.154473 CGAGAGGGGAATGGCCGA 61.154 66.667 0.00 0.00 37.63 5.54
751 752 2.825264 GAGAGGGGAATGGCCGAG 59.175 66.667 0.00 0.00 37.63 4.63
752 753 2.770048 AGAGGGGAATGGCCGAGG 60.770 66.667 0.00 0.00 37.63 4.63
753 754 3.878667 GAGGGGAATGGCCGAGGG 61.879 72.222 0.00 0.00 37.63 4.30
830 831 2.123033 GGGGGAGAGAGGGAGAGC 60.123 72.222 0.00 0.00 0.00 4.09
831 832 2.710826 GGGGGAGAGAGGGAGAGCT 61.711 68.421 0.00 0.00 0.00 4.09
832 833 1.457455 GGGGAGAGAGGGAGAGCTG 60.457 68.421 0.00 0.00 0.00 4.24
833 834 1.457455 GGGAGAGAGGGAGAGCTGG 60.457 68.421 0.00 0.00 0.00 4.85
834 835 2.133641 GGAGAGAGGGAGAGCTGGC 61.134 68.421 0.00 0.00 0.00 4.85
835 836 2.441901 AGAGAGGGAGAGCTGGCG 60.442 66.667 0.00 0.00 0.00 5.69
836 837 3.535962 GAGAGGGAGAGCTGGCGG 61.536 72.222 0.00 0.00 0.00 6.13
837 838 4.067512 AGAGGGAGAGCTGGCGGA 62.068 66.667 0.00 0.00 0.00 5.54
838 839 3.077556 GAGGGAGAGCTGGCGGAA 61.078 66.667 0.00 0.00 0.00 4.30
839 840 3.080121 AGGGAGAGCTGGCGGAAG 61.080 66.667 0.00 0.00 0.00 3.46
840 841 4.168291 GGGAGAGCTGGCGGAAGG 62.168 72.222 0.00 0.00 0.00 3.46
841 842 4.168291 GGAGAGCTGGCGGAAGGG 62.168 72.222 0.00 0.00 0.00 3.95
842 843 4.168291 GAGAGCTGGCGGAAGGGG 62.168 72.222 0.00 0.00 0.00 4.79
843 844 4.722535 AGAGCTGGCGGAAGGGGA 62.723 66.667 0.00 0.00 0.00 4.81
844 845 3.717294 GAGCTGGCGGAAGGGGAA 61.717 66.667 0.00 0.00 0.00 3.97
845 846 3.017581 AGCTGGCGGAAGGGGAAT 61.018 61.111 0.00 0.00 0.00 3.01
846 847 2.517166 GCTGGCGGAAGGGGAATC 60.517 66.667 0.00 0.00 0.00 2.52
847 848 2.203070 CTGGCGGAAGGGGAATCG 60.203 66.667 0.00 0.00 0.00 3.34
848 849 3.757248 CTGGCGGAAGGGGAATCGG 62.757 68.421 0.00 0.00 0.00 4.18
849 850 4.564110 GGCGGAAGGGGAATCGGG 62.564 72.222 0.00 0.00 0.00 5.14
850 851 4.564110 GCGGAAGGGGAATCGGGG 62.564 72.222 0.00 0.00 0.00 5.73
851 852 4.564110 CGGAAGGGGAATCGGGGC 62.564 72.222 0.00 0.00 0.00 5.80
852 853 4.564110 GGAAGGGGAATCGGGGCG 62.564 72.222 0.00 0.00 0.00 6.13
896 897 4.816984 GGTCGCGAGAGGGGGAGA 62.817 72.222 10.24 0.00 43.49 3.71
897 898 3.213402 GTCGCGAGAGGGGGAGAG 61.213 72.222 10.24 0.00 43.49 3.20
898 899 4.507916 TCGCGAGAGGGGGAGAGG 62.508 72.222 3.71 0.00 45.20 3.69
899 900 4.824515 CGCGAGAGGGGGAGAGGT 62.825 72.222 0.00 0.00 40.85 3.85
900 901 2.835895 GCGAGAGGGGGAGAGGTC 60.836 72.222 0.00 0.00 0.00 3.85
901 902 2.123640 CGAGAGGGGGAGAGGTCC 60.124 72.222 0.00 0.00 43.05 4.46
915 916 1.002502 GGTCCCACCTTCTTTCCCG 60.003 63.158 0.00 0.00 34.73 5.14
916 917 1.002502 GTCCCACCTTCTTTCCCGG 60.003 63.158 0.00 0.00 0.00 5.73
917 918 1.462627 TCCCACCTTCTTTCCCGGT 60.463 57.895 0.00 0.00 0.00 5.28
918 919 1.063654 TCCCACCTTCTTTCCCGGTT 61.064 55.000 0.00 0.00 0.00 4.44
919 920 0.608308 CCCACCTTCTTTCCCGGTTC 60.608 60.000 0.00 0.00 0.00 3.62
920 921 0.953960 CCACCTTCTTTCCCGGTTCG 60.954 60.000 0.00 0.00 0.00 3.95
921 922 0.250166 CACCTTCTTTCCCGGTTCGT 60.250 55.000 0.00 0.00 0.00 3.85
922 923 0.471191 ACCTTCTTTCCCGGTTCGTT 59.529 50.000 0.00 0.00 0.00 3.85
923 924 1.134007 ACCTTCTTTCCCGGTTCGTTT 60.134 47.619 0.00 0.00 0.00 3.60
924 925 1.265905 CCTTCTTTCCCGGTTCGTTTG 59.734 52.381 0.00 0.00 0.00 2.93
925 926 1.944709 CTTCTTTCCCGGTTCGTTTGT 59.055 47.619 0.00 0.00 0.00 2.83
926 927 2.041251 TCTTTCCCGGTTCGTTTGTT 57.959 45.000 0.00 0.00 0.00 2.83
927 928 1.941975 TCTTTCCCGGTTCGTTTGTTC 59.058 47.619 0.00 0.00 0.00 3.18
928 929 1.671845 CTTTCCCGGTTCGTTTGTTCA 59.328 47.619 0.00 0.00 0.00 3.18
929 930 1.015868 TTCCCGGTTCGTTTGTTCAC 58.984 50.000 0.00 0.00 0.00 3.18
930 931 0.814812 TCCCGGTTCGTTTGTTCACC 60.815 55.000 0.00 0.00 0.00 4.02
931 932 1.650363 CCGGTTCGTTTGTTCACCC 59.350 57.895 0.00 0.00 0.00 4.61
932 933 1.650363 CGGTTCGTTTGTTCACCCC 59.350 57.895 0.00 0.00 0.00 4.95
933 934 1.096386 CGGTTCGTTTGTTCACCCCA 61.096 55.000 0.00 0.00 0.00 4.96
934 935 1.324383 GGTTCGTTTGTTCACCCCAT 58.676 50.000 0.00 0.00 0.00 4.00
935 936 1.684450 GGTTCGTTTGTTCACCCCATT 59.316 47.619 0.00 0.00 0.00 3.16
936 937 2.885894 GGTTCGTTTGTTCACCCCATTA 59.114 45.455 0.00 0.00 0.00 1.90
937 938 3.057806 GGTTCGTTTGTTCACCCCATTAG 60.058 47.826 0.00 0.00 0.00 1.73
938 939 2.156098 TCGTTTGTTCACCCCATTAGC 58.844 47.619 0.00 0.00 0.00 3.09
939 940 1.135803 CGTTTGTTCACCCCATTAGCG 60.136 52.381 0.00 0.00 0.00 4.26
940 941 1.883926 GTTTGTTCACCCCATTAGCGT 59.116 47.619 0.00 0.00 0.00 5.07
941 942 2.279935 TTGTTCACCCCATTAGCGTT 57.720 45.000 0.00 0.00 0.00 4.84
942 943 3.420300 TTGTTCACCCCATTAGCGTTA 57.580 42.857 0.00 0.00 0.00 3.18
943 944 3.637911 TGTTCACCCCATTAGCGTTAT 57.362 42.857 0.00 0.00 0.00 1.89
944 945 3.275143 TGTTCACCCCATTAGCGTTATG 58.725 45.455 0.00 0.00 0.00 1.90
945 946 3.055021 TGTTCACCCCATTAGCGTTATGA 60.055 43.478 0.00 0.00 0.00 2.15
946 947 4.134563 GTTCACCCCATTAGCGTTATGAT 58.865 43.478 0.00 0.00 0.00 2.45
947 948 4.431416 TCACCCCATTAGCGTTATGATT 57.569 40.909 0.00 0.00 0.00 2.57
948 949 4.385825 TCACCCCATTAGCGTTATGATTC 58.614 43.478 0.00 0.00 0.00 2.52
949 950 4.102524 TCACCCCATTAGCGTTATGATTCT 59.897 41.667 0.00 0.00 0.00 2.40
950 951 4.214119 CACCCCATTAGCGTTATGATTCTG 59.786 45.833 0.00 0.00 0.00 3.02
951 952 3.753272 CCCCATTAGCGTTATGATTCTGG 59.247 47.826 0.00 0.00 0.00 3.86
952 953 3.753272 CCCATTAGCGTTATGATTCTGGG 59.247 47.826 0.00 0.00 32.33 4.45
953 954 4.389374 CCATTAGCGTTATGATTCTGGGT 58.611 43.478 0.00 0.00 0.00 4.51
954 955 4.821805 CCATTAGCGTTATGATTCTGGGTT 59.178 41.667 0.00 0.00 0.00 4.11
955 956 5.049405 CCATTAGCGTTATGATTCTGGGTTC 60.049 44.000 0.00 0.00 0.00 3.62
956 957 2.919228 AGCGTTATGATTCTGGGTTCC 58.081 47.619 0.00 0.00 0.00 3.62
957 958 1.597663 GCGTTATGATTCTGGGTTCCG 59.402 52.381 0.00 0.00 0.00 4.30
958 959 2.740580 GCGTTATGATTCTGGGTTCCGA 60.741 50.000 0.00 0.00 0.00 4.55
959 960 3.728845 CGTTATGATTCTGGGTTCCGAT 58.271 45.455 0.00 0.00 0.00 4.18
960 961 3.494626 CGTTATGATTCTGGGTTCCGATG 59.505 47.826 0.00 0.00 0.00 3.84
961 962 2.645838 ATGATTCTGGGTTCCGATGG 57.354 50.000 0.00 0.00 0.00 3.51
1014 1015 1.402896 CGGAGATGCCCTTGCTCCTA 61.403 60.000 0.00 0.00 44.73 2.94
1371 1372 3.256960 GTGCTCCTTCCCCCACCA 61.257 66.667 0.00 0.00 0.00 4.17
1671 1672 8.116753 CCTTTGTTGTATAATTCTACTCTTGCG 58.883 37.037 3.04 0.00 0.00 4.85
1737 1738 9.638239 CCTGAAAGCAATTTTAAGCATTTACTA 57.362 29.630 0.00 0.00 0.00 1.82
1747 1748 9.639601 ATTTTAAGCATTTACTAAGTCTTTGGC 57.360 29.630 0.00 0.00 0.00 4.52
1748 1749 7.996098 TTAAGCATTTACTAAGTCTTTGGCT 57.004 32.000 0.00 0.00 0.00 4.75
1749 1750 6.901081 AAGCATTTACTAAGTCTTTGGCTT 57.099 33.333 0.00 0.00 33.46 4.35
1750 1751 6.259550 AGCATTTACTAAGTCTTTGGCTTG 57.740 37.500 0.00 0.00 0.00 4.01
1751 1752 4.859245 GCATTTACTAAGTCTTTGGCTTGC 59.141 41.667 0.00 0.00 0.00 4.01
1765 1795 6.714810 TCTTTGGCTTGCAGTAGATTTTAGAA 59.285 34.615 0.00 0.00 0.00 2.10
1860 1890 3.319137 TCATGCTGTGTGAGAAGTACC 57.681 47.619 0.00 0.00 0.00 3.34
1939 2130 3.138468 AGCCTAAAGAACAGTCCTTTGGT 59.862 43.478 0.00 0.00 35.65 3.67
2302 6205 5.373812 AATACATTTTGAGAGGGATCGGT 57.626 39.130 0.00 0.00 0.00 4.69
2886 6790 4.277423 CCGTGAAAGACATAAACCAAAGGT 59.723 41.667 0.00 0.00 37.65 3.50
3146 7050 2.286872 CTGCAGCTGGAATCTAACTGG 58.713 52.381 17.12 0.00 0.00 4.00
3159 7063 5.880054 ATCTAACTGGTGTGTGTTTATGC 57.120 39.130 0.00 0.00 0.00 3.14
3223 7127 2.631160 TGGTTGTCGGTTCATGTTCT 57.369 45.000 0.00 0.00 0.00 3.01
3531 7455 1.065709 TGGACGCACCTCCCTTTTATC 60.066 52.381 1.15 0.00 39.86 1.75
3532 7456 1.065709 GGACGCACCTCCCTTTTATCA 60.066 52.381 0.00 0.00 35.41 2.15
3555 7479 3.378112 CACCAACAATATGCGTCTGGATT 59.622 43.478 10.82 0.00 0.00 3.01
3622 7549 7.862648 CGTATATACGTGCATATACTCATCCT 58.137 38.462 24.02 0.00 44.13 3.24
3686 7614 0.390860 AGACTGAGCCGGCATATCAC 59.609 55.000 31.54 14.88 0.00 3.06
3688 7618 0.833287 ACTGAGCCGGCATATCACTT 59.167 50.000 31.54 4.27 0.00 3.16
3698 7628 5.468746 GCCGGCATATCACTTAGATTTTACA 59.531 40.000 24.80 0.00 38.19 2.41
3713 7643 9.917129 TTAGATTTTACAAAGTCATCGTAGACA 57.083 29.630 11.41 0.00 42.51 3.41
3718 7648 3.172050 CAAAGTCATCGTAGACACCTCG 58.828 50.000 11.41 0.00 42.51 4.63
3723 7653 2.934553 TCATCGTAGACACCTCGTAGTG 59.065 50.000 6.12 6.12 42.51 2.74
3749 7679 3.025262 GGAACGTCTCCTCCTACTGAAT 58.975 50.000 8.87 0.00 41.61 2.57
3759 7689 3.553096 CCTCCTACTGAATGCGTATCACC 60.553 52.174 0.00 0.00 0.00 4.02
3769 7699 2.033372 TGCGTATCACCGGAAATCCTA 58.967 47.619 9.46 0.00 0.00 2.94
3782 7712 7.284489 CACCGGAAATCCTAAAATAAATCCAGA 59.716 37.037 9.46 0.00 0.00 3.86
3810 7740 0.868406 GAGCACCAGTTCTTGAACCG 59.132 55.000 9.58 0.27 0.00 4.44
3811 7741 0.180406 AGCACCAGTTCTTGAACCGT 59.820 50.000 9.58 4.38 0.00 4.83
3813 7743 1.948104 CACCAGTTCTTGAACCGTGA 58.052 50.000 18.57 0.00 0.00 4.35
3816 7746 1.806542 CCAGTTCTTGAACCGTGATGG 59.193 52.381 9.58 7.01 46.41 3.51
3819 7749 0.608035 TTCTTGAACCGTGATGGGCC 60.608 55.000 0.00 0.00 44.64 5.80
3820 7750 2.034999 TTGAACCGTGATGGGCCC 59.965 61.111 17.59 17.59 44.64 5.80
3870 7800 2.905075 CCACAGATTGGTTCGCTATCA 58.095 47.619 0.00 0.00 41.10 2.15
3910 7840 5.129485 TCTCTCCAACCATAGCTTCTAAAGG 59.871 44.000 0.00 0.00 0.00 3.11
4004 7934 0.632835 ACCTCCCACCATTGCATCAT 59.367 50.000 0.00 0.00 0.00 2.45
4006 7936 1.133575 CCTCCCACCATTGCATCATCT 60.134 52.381 0.00 0.00 0.00 2.90
4040 7974 9.436957 TTCTCTCTCGCTAATAAAAACTGAAAT 57.563 29.630 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.858680 GCGGGGCTTAGTGGGCTC 62.859 72.222 0.00 0.00 0.00 4.70
45 46 3.443045 GATGGGCGTTGGGTGCTG 61.443 66.667 0.00 0.00 0.00 4.41
72 73 4.785453 GTGGCTTCCAGGAGGCGG 62.785 72.222 17.03 0.00 44.53 6.13
75 76 4.785453 GGCGTGGCTTCCAGGAGG 62.785 72.222 9.47 0.00 41.36 4.30
113 114 4.759205 ATCTGGGTTTGGGCGGGC 62.759 66.667 0.00 0.00 0.00 6.13
114 115 2.755469 CATCTGGGTTTGGGCGGG 60.755 66.667 0.00 0.00 0.00 6.13
115 116 2.755469 CCATCTGGGTTTGGGCGG 60.755 66.667 0.00 0.00 0.00 6.13
125 126 4.195334 CCTTCGGGCCCCATCTGG 62.195 72.222 18.66 7.92 0.00 3.86
126 127 4.195334 CCCTTCGGGCCCCATCTG 62.195 72.222 18.66 0.58 35.35 2.90
136 137 2.507944 CAGATCTGGGCCCTTCGG 59.492 66.667 25.70 13.94 0.00 4.30
651 652 4.506255 GGTGGCGGGGATTCCTGG 62.506 72.222 0.00 0.00 39.84 4.45
652 653 3.727258 TGGTGGCGGGGATTCCTG 61.727 66.667 2.01 0.00 42.40 3.86
653 654 3.728373 GTGGTGGCGGGGATTCCT 61.728 66.667 2.01 0.00 0.00 3.36
720 721 3.708220 CTCTCGGTTGCTCTCCGGC 62.708 68.421 0.00 0.00 46.82 6.13
721 722 2.492090 CTCTCGGTTGCTCTCCGG 59.508 66.667 12.90 0.00 46.82 5.14
723 724 2.726351 CCCCTCTCGGTTGCTCTCC 61.726 68.421 0.00 0.00 0.00 3.71
724 725 1.258445 TTCCCCTCTCGGTTGCTCTC 61.258 60.000 0.00 0.00 0.00 3.20
725 726 0.618968 ATTCCCCTCTCGGTTGCTCT 60.619 55.000 0.00 0.00 0.00 4.09
726 727 0.462759 CATTCCCCTCTCGGTTGCTC 60.463 60.000 0.00 0.00 0.00 4.26
727 728 1.604378 CATTCCCCTCTCGGTTGCT 59.396 57.895 0.00 0.00 0.00 3.91
728 729 1.452108 CCATTCCCCTCTCGGTTGC 60.452 63.158 0.00 0.00 0.00 4.17
729 730 1.452108 GCCATTCCCCTCTCGGTTG 60.452 63.158 0.00 0.00 0.00 3.77
730 731 2.680370 GGCCATTCCCCTCTCGGTT 61.680 63.158 0.00 0.00 0.00 4.44
731 732 3.090532 GGCCATTCCCCTCTCGGT 61.091 66.667 0.00 0.00 0.00 4.69
732 733 4.241555 CGGCCATTCCCCTCTCGG 62.242 72.222 2.24 0.00 0.00 4.63
733 734 3.154473 TCGGCCATTCCCCTCTCG 61.154 66.667 2.24 0.00 0.00 4.04
734 735 2.812619 CCTCGGCCATTCCCCTCTC 61.813 68.421 2.24 0.00 0.00 3.20
735 736 2.770048 CCTCGGCCATTCCCCTCT 60.770 66.667 2.24 0.00 0.00 3.69
736 737 3.878667 CCCTCGGCCATTCCCCTC 61.879 72.222 2.24 0.00 0.00 4.30
813 814 2.123033 GCTCTCCCTCTCTCCCCC 60.123 72.222 0.00 0.00 0.00 5.40
814 815 1.457455 CAGCTCTCCCTCTCTCCCC 60.457 68.421 0.00 0.00 0.00 4.81
815 816 1.457455 CCAGCTCTCCCTCTCTCCC 60.457 68.421 0.00 0.00 0.00 4.30
816 817 2.133641 GCCAGCTCTCCCTCTCTCC 61.134 68.421 0.00 0.00 0.00 3.71
817 818 2.489275 CGCCAGCTCTCCCTCTCTC 61.489 68.421 0.00 0.00 0.00 3.20
818 819 2.441901 CGCCAGCTCTCCCTCTCT 60.442 66.667 0.00 0.00 0.00 3.10
819 820 3.535962 CCGCCAGCTCTCCCTCTC 61.536 72.222 0.00 0.00 0.00 3.20
820 821 3.608759 TTCCGCCAGCTCTCCCTCT 62.609 63.158 0.00 0.00 0.00 3.69
821 822 3.077556 TTCCGCCAGCTCTCCCTC 61.078 66.667 0.00 0.00 0.00 4.30
822 823 3.080121 CTTCCGCCAGCTCTCCCT 61.080 66.667 0.00 0.00 0.00 4.20
823 824 4.168291 CCTTCCGCCAGCTCTCCC 62.168 72.222 0.00 0.00 0.00 4.30
824 825 4.168291 CCCTTCCGCCAGCTCTCC 62.168 72.222 0.00 0.00 0.00 3.71
825 826 4.168291 CCCCTTCCGCCAGCTCTC 62.168 72.222 0.00 0.00 0.00 3.20
826 827 4.722535 TCCCCTTCCGCCAGCTCT 62.723 66.667 0.00 0.00 0.00 4.09
827 828 2.949705 GATTCCCCTTCCGCCAGCTC 62.950 65.000 0.00 0.00 0.00 4.09
828 829 3.017581 ATTCCCCTTCCGCCAGCT 61.018 61.111 0.00 0.00 0.00 4.24
829 830 2.517166 GATTCCCCTTCCGCCAGC 60.517 66.667 0.00 0.00 0.00 4.85
830 831 2.203070 CGATTCCCCTTCCGCCAG 60.203 66.667 0.00 0.00 0.00 4.85
831 832 3.792736 CCGATTCCCCTTCCGCCA 61.793 66.667 0.00 0.00 0.00 5.69
832 833 4.564110 CCCGATTCCCCTTCCGCC 62.564 72.222 0.00 0.00 0.00 6.13
833 834 4.564110 CCCCGATTCCCCTTCCGC 62.564 72.222 0.00 0.00 0.00 5.54
834 835 4.564110 GCCCCGATTCCCCTTCCG 62.564 72.222 0.00 0.00 0.00 4.30
835 836 4.564110 CGCCCCGATTCCCCTTCC 62.564 72.222 0.00 0.00 0.00 3.46
879 880 4.816984 TCTCCCCCTCTCGCGACC 62.817 72.222 3.71 0.00 0.00 4.79
880 881 3.213402 CTCTCCCCCTCTCGCGAC 61.213 72.222 3.71 0.00 0.00 5.19
881 882 4.507916 CCTCTCCCCCTCTCGCGA 62.508 72.222 9.26 9.26 0.00 5.87
882 883 4.824515 ACCTCTCCCCCTCTCGCG 62.825 72.222 0.00 0.00 0.00 5.87
883 884 2.835895 GACCTCTCCCCCTCTCGC 60.836 72.222 0.00 0.00 0.00 5.03
884 885 2.123640 GGACCTCTCCCCCTCTCG 60.124 72.222 0.00 0.00 0.00 4.04
897 898 1.002502 CGGGAAAGAAGGTGGGACC 60.003 63.158 0.00 0.00 38.99 4.46
898 899 1.002502 CCGGGAAAGAAGGTGGGAC 60.003 63.158 0.00 0.00 0.00 4.46
899 900 1.063654 AACCGGGAAAGAAGGTGGGA 61.064 55.000 6.32 0.00 38.44 4.37
900 901 0.608308 GAACCGGGAAAGAAGGTGGG 60.608 60.000 6.32 0.00 38.44 4.61
901 902 0.953960 CGAACCGGGAAAGAAGGTGG 60.954 60.000 6.32 0.00 38.44 4.61
902 903 0.250166 ACGAACCGGGAAAGAAGGTG 60.250 55.000 6.32 0.00 38.44 4.00
903 904 0.471191 AACGAACCGGGAAAGAAGGT 59.529 50.000 6.32 0.00 40.50 3.50
904 905 1.265905 CAAACGAACCGGGAAAGAAGG 59.734 52.381 6.32 0.00 0.00 3.46
905 906 1.944709 ACAAACGAACCGGGAAAGAAG 59.055 47.619 6.32 0.00 0.00 2.85
906 907 2.041251 ACAAACGAACCGGGAAAGAA 57.959 45.000 6.32 0.00 0.00 2.52
907 908 1.941975 GAACAAACGAACCGGGAAAGA 59.058 47.619 6.32 0.00 0.00 2.52
908 909 1.671845 TGAACAAACGAACCGGGAAAG 59.328 47.619 6.32 0.00 0.00 2.62
909 910 1.401199 GTGAACAAACGAACCGGGAAA 59.599 47.619 6.32 0.00 0.00 3.13
910 911 1.015868 GTGAACAAACGAACCGGGAA 58.984 50.000 6.32 0.00 0.00 3.97
911 912 0.814812 GGTGAACAAACGAACCGGGA 60.815 55.000 6.32 0.00 0.00 5.14
912 913 1.650363 GGTGAACAAACGAACCGGG 59.350 57.895 6.32 0.00 0.00 5.73
913 914 1.650363 GGGTGAACAAACGAACCGG 59.350 57.895 0.00 0.00 33.24 5.28
914 915 1.096386 TGGGGTGAACAAACGAACCG 61.096 55.000 0.00 0.00 33.24 4.44
915 916 1.324383 ATGGGGTGAACAAACGAACC 58.676 50.000 0.00 0.00 0.00 3.62
916 917 3.610821 GCTAATGGGGTGAACAAACGAAC 60.611 47.826 0.00 0.00 0.00 3.95
917 918 2.554893 GCTAATGGGGTGAACAAACGAA 59.445 45.455 0.00 0.00 0.00 3.85
918 919 2.156098 GCTAATGGGGTGAACAAACGA 58.844 47.619 0.00 0.00 0.00 3.85
919 920 1.135803 CGCTAATGGGGTGAACAAACG 60.136 52.381 0.00 0.00 0.00 3.60
920 921 1.883926 ACGCTAATGGGGTGAACAAAC 59.116 47.619 0.00 0.00 39.69 2.93
921 922 2.279935 ACGCTAATGGGGTGAACAAA 57.720 45.000 0.00 0.00 39.69 2.83
922 923 2.279935 AACGCTAATGGGGTGAACAA 57.720 45.000 0.00 0.00 41.04 2.83
923 924 3.055021 TCATAACGCTAATGGGGTGAACA 60.055 43.478 0.00 0.00 41.04 3.18
924 925 3.537580 TCATAACGCTAATGGGGTGAAC 58.462 45.455 0.00 0.00 41.04 3.18
925 926 3.916359 TCATAACGCTAATGGGGTGAA 57.084 42.857 0.00 0.00 41.04 3.18
926 927 4.102524 AGAATCATAACGCTAATGGGGTGA 59.897 41.667 0.00 0.00 41.04 4.02
927 928 4.214119 CAGAATCATAACGCTAATGGGGTG 59.786 45.833 0.00 0.00 41.04 4.61
928 929 4.389374 CAGAATCATAACGCTAATGGGGT 58.611 43.478 0.00 0.00 43.11 4.95
929 930 3.753272 CCAGAATCATAACGCTAATGGGG 59.247 47.826 0.00 0.00 0.00 4.96
930 931 3.753272 CCCAGAATCATAACGCTAATGGG 59.247 47.826 0.00 0.00 38.98 4.00
931 932 4.389374 ACCCAGAATCATAACGCTAATGG 58.611 43.478 0.00 0.00 0.00 3.16
932 933 5.049405 GGAACCCAGAATCATAACGCTAATG 60.049 44.000 0.00 0.00 0.00 1.90
933 934 5.063880 GGAACCCAGAATCATAACGCTAAT 58.936 41.667 0.00 0.00 0.00 1.73
934 935 4.448210 GGAACCCAGAATCATAACGCTAA 58.552 43.478 0.00 0.00 0.00 3.09
935 936 3.491964 CGGAACCCAGAATCATAACGCTA 60.492 47.826 0.00 0.00 0.00 4.26
936 937 2.741878 CGGAACCCAGAATCATAACGCT 60.742 50.000 0.00 0.00 0.00 5.07
937 938 1.597663 CGGAACCCAGAATCATAACGC 59.402 52.381 0.00 0.00 0.00 4.84
938 939 3.173668 TCGGAACCCAGAATCATAACG 57.826 47.619 0.00 0.00 0.00 3.18
939 940 3.815401 CCATCGGAACCCAGAATCATAAC 59.185 47.826 0.00 0.00 0.00 1.89
940 941 3.181445 CCCATCGGAACCCAGAATCATAA 60.181 47.826 0.00 0.00 0.00 1.90
941 942 2.371841 CCCATCGGAACCCAGAATCATA 59.628 50.000 0.00 0.00 0.00 2.15
942 943 1.143684 CCCATCGGAACCCAGAATCAT 59.856 52.381 0.00 0.00 0.00 2.45
943 944 0.546122 CCCATCGGAACCCAGAATCA 59.454 55.000 0.00 0.00 0.00 2.57
944 945 0.819666 GCCCATCGGAACCCAGAATC 60.820 60.000 0.00 0.00 0.00 2.52
945 946 1.227383 GCCCATCGGAACCCAGAAT 59.773 57.895 0.00 0.00 0.00 2.40
946 947 2.674754 GCCCATCGGAACCCAGAA 59.325 61.111 0.00 0.00 0.00 3.02
947 948 3.781307 CGCCCATCGGAACCCAGA 61.781 66.667 0.00 0.00 33.78 3.86
956 957 0.655733 GTGTAAACATCCGCCCATCG 59.344 55.000 0.00 0.00 38.08 3.84
957 958 0.655733 CGTGTAAACATCCGCCCATC 59.344 55.000 0.00 0.00 0.00 3.51
958 959 1.373590 GCGTGTAAACATCCGCCCAT 61.374 55.000 6.80 0.00 35.98 4.00
959 960 2.036006 GCGTGTAAACATCCGCCCA 61.036 57.895 6.80 0.00 35.98 5.36
960 961 1.303091 AAGCGTGTAAACATCCGCCC 61.303 55.000 12.67 0.00 40.70 6.13
961 962 0.519961 AAAGCGTGTAAACATCCGCC 59.480 50.000 12.67 0.00 40.70 6.13
1014 1015 0.250513 GCGAAGTGGGGAGAGTGAAT 59.749 55.000 0.00 0.00 0.00 2.57
1215 1216 1.376424 CAGCACCTTGGACGCAGAT 60.376 57.895 8.11 0.00 0.00 2.90
1671 1672 1.815003 AGGACAATAAGCAAGCACAGC 59.185 47.619 0.00 0.00 0.00 4.40
1737 1738 3.492102 TCTACTGCAAGCCAAAGACTT 57.508 42.857 0.00 0.00 37.60 3.01
1738 1739 3.710209 ATCTACTGCAAGCCAAAGACT 57.290 42.857 0.00 0.00 37.60 3.24
1739 1740 4.773323 AAATCTACTGCAAGCCAAAGAC 57.227 40.909 0.00 0.00 37.60 3.01
1740 1741 6.237901 TCTAAAATCTACTGCAAGCCAAAGA 58.762 36.000 0.00 0.00 37.60 2.52
1741 1742 6.500684 TCTAAAATCTACTGCAAGCCAAAG 57.499 37.500 0.00 0.00 37.60 2.77
1742 1743 6.892658 TTCTAAAATCTACTGCAAGCCAAA 57.107 33.333 0.00 0.00 37.60 3.28
1743 1744 8.752005 ATATTCTAAAATCTACTGCAAGCCAA 57.248 30.769 0.00 0.00 37.60 4.52
1745 1746 8.624776 ACAATATTCTAAAATCTACTGCAAGCC 58.375 33.333 0.00 0.00 37.60 4.35
1765 1795 8.511604 AAGCATTTACAAGCAGACTACAATAT 57.488 30.769 0.00 0.00 0.00 1.28
1860 1890 9.469807 GACACCAATCTCATAGTACTTAAGATG 57.530 37.037 10.09 2.46 0.00 2.90
1939 2130 6.587206 TGATGTGTTGCCTTCATTGAAATA 57.413 33.333 0.01 0.00 0.00 1.40
2683 6587 4.507388 CCTTTGCGTCATTTTGTTGTGATT 59.493 37.500 0.00 0.00 0.00 2.57
2886 6790 4.988540 CAGACTTGTTTCGTGAAGGTGATA 59.011 41.667 0.00 0.00 0.00 2.15
3146 7050 0.791422 TACGGCGCATAAACACACAC 59.209 50.000 10.83 0.00 0.00 3.82
3159 7063 5.041287 TGATCTGATAGTTTCTTTACGGCG 58.959 41.667 4.80 4.80 0.00 6.46
3223 7127 0.548926 TTCCCCACTGTGGCATAGGA 60.549 55.000 21.47 18.28 35.79 2.94
3349 7269 4.124851 AGAACGATACACCAAGGATGAC 57.875 45.455 0.00 0.00 0.00 3.06
3366 7286 2.306847 TGGCTGGTGGAAAGAAAGAAC 58.693 47.619 0.00 0.00 0.00 3.01
3531 7455 2.159531 CCAGACGCATATTGTTGGTGTG 60.160 50.000 0.00 0.00 0.00 3.82
3532 7456 2.083774 CCAGACGCATATTGTTGGTGT 58.916 47.619 0.00 0.00 0.00 4.16
3613 7540 8.581578 TCATGCGTGTATTTATAAGGATGAGTA 58.418 33.333 5.68 0.00 32.91 2.59
3619 7546 5.756347 GTGGTCATGCGTGTATTTATAAGGA 59.244 40.000 5.68 0.00 0.00 3.36
3622 7549 5.429130 TGGTGGTCATGCGTGTATTTATAA 58.571 37.500 5.68 0.00 0.00 0.98
3634 7561 4.511527 CTCATAGGATATGGTGGTCATGC 58.488 47.826 0.00 0.00 37.30 4.06
3688 7618 9.350357 GTGTCTACGATGACTTTGTAAAATCTA 57.650 33.333 12.10 0.00 37.79 1.98
3698 7628 2.818432 ACGAGGTGTCTACGATGACTTT 59.182 45.455 12.10 1.09 37.79 2.66
3705 7635 1.276138 TCCACTACGAGGTGTCTACGA 59.724 52.381 10.41 0.34 35.63 3.43
3742 7672 2.025898 TCCGGTGATACGCATTCAGTA 58.974 47.619 0.00 0.00 0.00 2.74
3749 7679 0.828022 AGGATTTCCGGTGATACGCA 59.172 50.000 0.00 0.00 42.08 5.24
3769 7699 8.196771 TGCTCGCATTTATTCTGGATTTATTTT 58.803 29.630 0.00 0.00 0.00 1.82
3782 7712 3.347216 AGAACTGGTGCTCGCATTTATT 58.653 40.909 0.00 0.00 0.00 1.40
3810 7740 2.430367 GTATCCCGGGCCCATCAC 59.570 66.667 24.92 7.95 0.00 3.06
3811 7741 2.852075 GGTATCCCGGGCCCATCA 60.852 66.667 24.92 3.88 0.00 3.07
3813 7743 1.778383 AATGGTATCCCGGGCCCAT 60.778 57.895 25.21 25.21 39.34 4.00
3816 7746 0.822121 GAACAATGGTATCCCGGGCC 60.822 60.000 18.49 12.82 0.00 5.80
3819 7749 2.411628 TGTGAACAATGGTATCCCGG 57.588 50.000 0.00 0.00 0.00 5.73
3820 7750 4.274950 GGTTATGTGAACAATGGTATCCCG 59.725 45.833 0.00 0.00 0.00 5.14
3834 7764 3.329225 TCTGTGGTTGGATGGTTATGTGA 59.671 43.478 0.00 0.00 0.00 3.58
3870 7800 3.307762 GGAGAGATTACAAGTTGGGCAGT 60.308 47.826 7.96 0.00 0.00 4.40
3946 7876 9.025041 CCAACTCCTCTTTTTGTATTCCTAATT 57.975 33.333 0.00 0.00 0.00 1.40
3947 7877 8.170730 ACCAACTCCTCTTTTTGTATTCCTAAT 58.829 33.333 0.00 0.00 0.00 1.73
3948 7878 7.523415 ACCAACTCCTCTTTTTGTATTCCTAA 58.477 34.615 0.00 0.00 0.00 2.69
3949 7879 7.086685 ACCAACTCCTCTTTTTGTATTCCTA 57.913 36.000 0.00 0.00 0.00 2.94
3950 7880 5.953571 ACCAACTCCTCTTTTTGTATTCCT 58.046 37.500 0.00 0.00 0.00 3.36
3951 7881 6.940867 ACTACCAACTCCTCTTTTTGTATTCC 59.059 38.462 0.00 0.00 0.00 3.01
3952 7882 7.878644 AGACTACCAACTCCTCTTTTTGTATTC 59.121 37.037 0.00 0.00 0.00 1.75
3953 7883 7.746703 AGACTACCAACTCCTCTTTTTGTATT 58.253 34.615 0.00 0.00 0.00 1.89
3954 7884 7.317722 AGACTACCAACTCCTCTTTTTGTAT 57.682 36.000 0.00 0.00 0.00 2.29
3955 7885 6.742559 AGACTACCAACTCCTCTTTTTGTA 57.257 37.500 0.00 0.00 0.00 2.41
3956 7886 5.632034 AGACTACCAACTCCTCTTTTTGT 57.368 39.130 0.00 0.00 0.00 2.83
3957 7887 6.017026 GGAAAGACTACCAACTCCTCTTTTTG 60.017 42.308 0.00 0.00 32.55 2.44
3958 7888 6.062749 GGAAAGACTACCAACTCCTCTTTTT 58.937 40.000 0.00 0.00 32.55 1.94
4040 7974 5.419542 CGACATGAGAGGAAACCTTATTCA 58.580 41.667 0.00 0.00 31.76 2.57


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

AutoCloner maintained by Alex Coulton.