Multiple sequence alignment - TraesCS2D01G119600

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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 TraesCS2D01G119600 chr2D 100.000 3023 0 0 1 3023 68906032 68903010 0.000000e+00 5583.0
1 TraesCS2D01G119600 chr2D 84.925 398 26 18 2207 2597 69148492 69148862 3.680000e-99 372.0
2 TraesCS2D01G119600 chr2D 79.534 386 40 17 2304 2680 64731781 64732136 3.890000e-59 239.0
3 TraesCS2D01G119600 chr2D 83.721 215 11 7 2810 3021 64732239 64732432 6.660000e-42 182.0
4 TraesCS2D01G119600 chr2D 92.593 108 5 1 2914 3021 65265936 65265832 5.220000e-33 152.0
5 TraesCS2D01G119600 chr2D 75.486 257 49 14 1001 1250 67442923 67443172 2.460000e-21 113.0
6 TraesCS2D01G119600 chr2D 75.385 260 50 14 998 1250 67452971 67453223 2.460000e-21 113.0
7 TraesCS2D01G119600 chr2D 90.000 70 3 3 2925 2994 69148928 69148993 1.490000e-13 87.9
8 TraesCS2D01G119600 chr2B 88.986 1489 75 47 691 2143 101453396 101454831 0.000000e+00 1759.0
9 TraesCS2D01G119600 chr2B 82.962 1033 91 40 2012 2994 101434349 101433352 0.000000e+00 854.0
10 TraesCS2D01G119600 chr2B 83.215 983 87 37 2057 2994 101420401 101419452 0.000000e+00 830.0
11 TraesCS2D01G119600 chr2B 86.207 754 55 21 2261 2994 101453119 101452395 0.000000e+00 771.0
12 TraesCS2D01G119600 chr2B 85.714 588 37 23 11 593 101455804 101455259 7.270000e-161 577.0
13 TraesCS2D01G119600 chr2B 78.499 493 50 26 2304 2771 101072334 101072795 3.840000e-69 272.0
14 TraesCS2D01G119600 chr2B 82.791 215 12 8 2809 3021 101072794 101072985 5.180000e-38 169.0
15 TraesCS2D01G119600 chr2B 75.465 269 53 13 998 1259 103900776 103900514 5.290000e-23 119.0
16 TraesCS2D01G119600 chr2B 75.093 269 54 13 998 1259 103866503 103866241 2.460000e-21 113.0
17 TraesCS2D01G119600 chr2A 88.041 1062 56 37 755 1790 65814300 65813284 0.000000e+00 1192.0
18 TraesCS2D01G119600 chr2A 89.401 434 29 9 2571 2994 65703889 65703463 5.740000e-147 531.0
19 TraesCS2D01G119600 chr2A 81.799 478 31 22 209 653 65814825 65814371 1.720000e-92 350.0
20 TraesCS2D01G119600 chr2A 82.487 394 35 16 1788 2162 65813316 65812938 6.290000e-82 315.0
21 TraesCS2D01G119600 chr2A 84.298 242 17 10 2299 2524 65704127 65703891 1.830000e-52 217.0
22 TraesCS2D01G119600 chr2A 83.246 191 20 6 11 189 65815064 65814874 6.700000e-37 165.0
23 TraesCS2D01G119600 chr2A 76.604 265 50 12 1001 1259 66915011 66914753 5.260000e-28 135.0
24 TraesCS2D01G119600 chr2A 74.468 329 60 19 998 1308 66004233 66003911 1.470000e-23 121.0
25 TraesCS2D01G119600 chr2A 75.000 268 56 11 998 1259 66909339 66909077 2.460000e-21 113.0


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 TraesCS2D01G119600 chr2D 68903010 68906032 3022 True 5583.00 5583 100.00000 1 3023 1 chr2D.!!$R2 3022
1 TraesCS2D01G119600 chr2D 69148492 69148993 501 False 229.95 372 87.46250 2207 2994 2 chr2D.!!$F4 787
2 TraesCS2D01G119600 chr2D 64731781 64732432 651 False 210.50 239 81.62750 2304 3021 2 chr2D.!!$F3 717
3 TraesCS2D01G119600 chr2B 101453396 101454831 1435 False 1759.00 1759 88.98600 691 2143 1 chr2B.!!$F1 1452
4 TraesCS2D01G119600 chr2B 101433352 101434349 997 True 854.00 854 82.96200 2012 2994 1 chr2B.!!$R2 982
5 TraesCS2D01G119600 chr2B 101419452 101420401 949 True 830.00 830 83.21500 2057 2994 1 chr2B.!!$R1 937
6 TraesCS2D01G119600 chr2B 101452395 101455804 3409 True 674.00 771 85.96050 11 2994 2 chr2B.!!$R5 2983
7 TraesCS2D01G119600 chr2B 101072334 101072985 651 False 220.50 272 80.64500 2304 3021 2 chr2B.!!$F2 717
8 TraesCS2D01G119600 chr2A 65812938 65815064 2126 True 505.50 1192 83.89325 11 2162 4 chr2A.!!$R5 2151
9 TraesCS2D01G119600 chr2A 65703463 65704127 664 True 374.00 531 86.84950 2299 2994 2 chr2A.!!$R4 695

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
348 410 0.036577 AAGCAGCTCAGTGGCACTAG 60.037 55.0 21.59 17.73 34.17 2.57 F
914 1192 0.103208 CACGAGCTAGCTAACCCCAG 59.897 60.0 19.38 5.90 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1452 1750 0.535328 CATGAGGATGAGGCTGCTGG 60.535 60.0 0.0 0.0 0.0 4.85 R
2738 4129 0.747255 ATCTCGTTCTCATGGGGTCG 59.253 55.0 0.0 0.0 0.0 4.79 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
44 48 3.655810 CTGACCAGACCAGCGCCTC 62.656 68.421 2.29 0.00 0.00 4.70
45 49 3.695606 GACCAGACCAGCGCCTCA 61.696 66.667 2.29 0.00 0.00 3.86
51 55 0.674895 AGACCAGCGCCTCACAATTC 60.675 55.000 2.29 0.00 0.00 2.17
52 56 1.648467 GACCAGCGCCTCACAATTCC 61.648 60.000 2.29 0.00 0.00 3.01
53 57 1.675310 CCAGCGCCTCACAATTCCA 60.675 57.895 2.29 0.00 0.00 3.53
55 59 0.957395 CAGCGCCTCACAATTCCACT 60.957 55.000 2.29 0.00 0.00 4.00
56 60 0.613260 AGCGCCTCACAATTCCACTA 59.387 50.000 2.29 0.00 0.00 2.74
57 61 1.009829 GCGCCTCACAATTCCACTAG 58.990 55.000 0.00 0.00 0.00 2.57
61 65 1.656652 CTCACAATTCCACTAGGCGG 58.343 55.000 0.00 0.00 33.74 6.13
62 66 1.207089 CTCACAATTCCACTAGGCGGA 59.793 52.381 0.00 0.00 33.74 5.54
63 67 1.837439 TCACAATTCCACTAGGCGGAT 59.163 47.619 4.16 0.00 30.99 4.18
65 69 1.134098 ACAATTCCACTAGGCGGATGG 60.134 52.381 4.16 0.00 30.99 3.51
114 127 2.711922 CGCTTCTGGCCGTAGTCCT 61.712 63.158 0.00 0.00 37.74 3.85
189 202 5.220796 GGTCAAAGTTGGTCAAGTGAAGTAC 60.221 44.000 0.00 0.00 0.00 2.73
190 203 4.569162 TCAAAGTTGGTCAAGTGAAGTACG 59.431 41.667 0.00 0.00 0.00 3.67
192 205 4.924305 AGTTGGTCAAGTGAAGTACGTA 57.076 40.909 0.00 0.00 0.00 3.57
240 282 1.674651 GCTTTCCCGGACAGGAACC 60.675 63.158 0.73 0.00 45.65 3.62
269 314 2.093394 TGCGAATTTCGAAGGGTGGATA 60.093 45.455 22.25 0.00 43.74 2.59
271 316 2.538449 CGAATTTCGAAGGGTGGATACG 59.462 50.000 13.45 0.00 43.74 3.06
348 410 0.036577 AAGCAGCTCAGTGGCACTAG 60.037 55.000 21.59 17.73 34.17 2.57
374 436 6.398918 CAACATAGGACTACTATATGGTGGC 58.601 44.000 1.31 0.00 40.42 5.01
375 437 5.651303 ACATAGGACTACTATATGGTGGCA 58.349 41.667 1.31 0.00 40.42 4.92
376 438 6.264528 ACATAGGACTACTATATGGTGGCAT 58.735 40.000 1.31 0.00 40.42 4.40
377 439 6.155221 ACATAGGACTACTATATGGTGGCATG 59.845 42.308 1.31 4.29 40.42 4.06
406 468 3.119096 GCAGCCCTCGGTCGTTTC 61.119 66.667 0.00 0.00 0.00 2.78
434 496 7.908827 TTTGGATGTACTTTTATGCTCGTAA 57.091 32.000 0.00 0.00 0.00 3.18
488 550 1.888215 AACTGACATGCACACTCCTG 58.112 50.000 0.00 0.00 0.00 3.86
568 639 2.223688 TGCAAACAAAAGATGACCACCG 60.224 45.455 0.00 0.00 0.00 4.94
600 850 7.258441 ACTTTGAAGCAGTTTAGTTCCTTTTC 58.742 34.615 0.00 0.00 0.00 2.29
608 858 7.545615 AGCAGTTTAGTTCCTTTTCTTTGTTTG 59.454 33.333 0.00 0.00 0.00 2.93
610 860 9.849166 CAGTTTAGTTCCTTTTCTTTGTTTGTA 57.151 29.630 0.00 0.00 0.00 2.41
651 902 5.577164 ACAGAAACAACTTATTCTCGATCGG 59.423 40.000 16.41 6.26 33.73 4.18
653 904 5.577164 AGAAACAACTTATTCTCGATCGGTG 59.423 40.000 16.41 8.93 30.16 4.94
656 907 2.032620 ACTTATTCTCGATCGGTGGCT 58.967 47.619 16.41 0.00 0.00 4.75
663 936 1.661821 CGATCGGTGGCTCGGAATC 60.662 63.158 7.38 0.00 0.00 2.52
673 946 1.092345 GCTCGGAATCCAGAAGTGCC 61.092 60.000 0.00 0.00 0.00 5.01
686 959 4.036498 CCAGAAGTGCCATTTGATCTGATC 59.964 45.833 10.72 10.72 37.14 2.92
687 960 3.875727 AGAAGTGCCATTTGATCTGATCG 59.124 43.478 12.65 0.00 0.00 3.69
688 961 3.548745 AGTGCCATTTGATCTGATCGA 57.451 42.857 12.65 8.28 0.00 3.59
689 962 3.201290 AGTGCCATTTGATCTGATCGAC 58.799 45.455 12.65 0.53 0.00 4.20
699 972 2.768253 TCTGATCGACAAGTTGCCAT 57.232 45.000 1.81 0.00 0.00 4.40
712 985 5.595542 ACAAGTTGCCATGCACTATGAATAT 59.404 36.000 1.81 0.00 38.71 1.28
713 986 6.772233 ACAAGTTGCCATGCACTATGAATATA 59.228 34.615 1.81 0.00 38.71 0.86
714 987 7.285172 ACAAGTTGCCATGCACTATGAATATAA 59.715 33.333 1.81 0.00 38.71 0.98
715 988 8.301720 CAAGTTGCCATGCACTATGAATATAAT 58.698 33.333 0.00 0.00 38.71 1.28
716 989 8.048534 AGTTGCCATGCACTATGAATATAATC 57.951 34.615 0.00 0.00 38.71 1.75
732 1005 9.851686 TGAATATAATCCTGTGGGCATAATATC 57.148 33.333 0.00 0.00 0.00 1.63
733 1006 9.851686 GAATATAATCCTGTGGGCATAATATCA 57.148 33.333 0.00 0.00 0.00 2.15
734 1007 9.632638 AATATAATCCTGTGGGCATAATATCAC 57.367 33.333 0.00 0.00 0.00 3.06
743 1017 4.141413 TGGGCATAATATCACACAGCTCTT 60.141 41.667 0.00 0.00 0.00 2.85
747 1021 5.333952 GCATAATATCACACAGCTCTTGAGC 60.334 44.000 14.16 14.16 0.00 4.26
748 1022 2.680312 TATCACACAGCTCTTGAGCC 57.320 50.000 17.78 2.08 34.90 4.70
752 1026 1.071987 CACAGCTCTTGAGCCCACA 59.928 57.895 17.78 0.00 34.90 4.17
753 1027 1.072159 ACAGCTCTTGAGCCCACAC 59.928 57.895 17.78 0.00 34.90 3.82
763 1037 1.369091 GAGCCCACACTATGCAACCG 61.369 60.000 0.00 0.00 0.00 4.44
824 1099 4.351054 GTGGGCCCACACCTCCTG 62.351 72.222 43.88 0.00 45.53 3.86
841 1119 3.082548 TCCTGCTCCTATACATACGCTC 58.917 50.000 0.00 0.00 0.00 5.03
855 1133 4.021925 GCTCCCCGCTCAAGGTGT 62.022 66.667 0.00 0.00 35.14 4.16
859 1137 3.726517 CCCGCTCAAGGTGTTGCG 61.727 66.667 0.00 0.00 46.74 4.85
864 1142 1.574702 GCTCAAGGTGTTGCGTACCC 61.575 60.000 0.74 0.00 39.05 3.69
866 1144 2.031465 AAGGTGTTGCGTACCCCG 59.969 61.111 0.74 0.00 39.05 5.73
875 1153 2.047655 CGTACCCCGCAGCTTCAA 60.048 61.111 0.00 0.00 0.00 2.69
891 1169 2.972505 AAGCAAGCCACGACCACG 60.973 61.111 0.00 0.00 45.75 4.94
899 1177 4.337060 CACGACCACGAGGCACGA 62.337 66.667 20.92 0.00 45.77 4.35
900 1178 4.039357 ACGACCACGAGGCACGAG 62.039 66.667 20.92 2.57 45.77 4.18
902 1180 4.057428 GACCACGAGGCACGAGCT 62.057 66.667 12.15 0.00 45.77 4.09
903 1181 2.675423 ACCACGAGGCACGAGCTA 60.675 61.111 12.15 0.00 45.77 3.32
904 1182 2.103143 CCACGAGGCACGAGCTAG 59.897 66.667 12.15 0.00 45.77 3.42
905 1183 2.580867 CACGAGGCACGAGCTAGC 60.581 66.667 12.15 6.62 45.77 3.42
906 1184 2.752238 ACGAGGCACGAGCTAGCT 60.752 61.111 19.45 19.45 45.77 3.32
907 1185 1.451567 ACGAGGCACGAGCTAGCTA 60.452 57.895 19.38 0.00 45.77 3.32
908 1186 1.030488 ACGAGGCACGAGCTAGCTAA 61.030 55.000 19.38 0.00 45.77 3.09
909 1187 0.592754 CGAGGCACGAGCTAGCTAAC 60.593 60.000 19.38 5.15 45.77 2.34
910 1188 0.249114 GAGGCACGAGCTAGCTAACC 60.249 60.000 19.38 16.09 41.70 2.85
911 1189 1.227292 GGCACGAGCTAGCTAACCC 60.227 63.158 19.38 11.99 41.70 4.11
912 1190 1.227292 GCACGAGCTAGCTAACCCC 60.227 63.158 19.38 3.48 37.91 4.95
913 1191 1.956629 GCACGAGCTAGCTAACCCCA 61.957 60.000 19.38 0.00 37.91 4.96
914 1192 0.103208 CACGAGCTAGCTAACCCCAG 59.897 60.000 19.38 5.90 0.00 4.45
915 1193 1.068250 CGAGCTAGCTAACCCCAGC 59.932 63.158 19.38 1.02 42.12 4.85
916 1194 1.676678 CGAGCTAGCTAACCCCAGCA 61.677 60.000 19.38 0.00 44.35 4.41
943 1232 3.165058 CTAATCCTAGCACACGAGCAA 57.835 47.619 0.00 0.00 36.85 3.91
945 1234 0.108138 ATCCTAGCACACGAGCAACC 60.108 55.000 0.00 0.00 36.85 3.77
957 1246 3.307242 CACGAGCAACCATCTAGCTTAAC 59.693 47.826 0.00 0.00 39.02 2.01
961 1250 5.450688 CGAGCAACCATCTAGCTTAACTACT 60.451 44.000 0.00 0.00 39.02 2.57
976 1265 6.568081 GCTTAACTACTTCGAGAGTGAGTGAA 60.568 42.308 9.58 7.89 39.48 3.18
984 1273 1.892474 GAGAGTGAGTGAACTCCAGCT 59.108 52.381 7.96 3.96 46.51 4.24
985 1274 3.085533 GAGAGTGAGTGAACTCCAGCTA 58.914 50.000 7.96 0.00 46.51 3.32
986 1275 3.501349 AGAGTGAGTGAACTCCAGCTAA 58.499 45.455 7.96 0.00 46.51 3.09
987 1276 4.093011 AGAGTGAGTGAACTCCAGCTAAT 58.907 43.478 7.96 0.00 46.51 1.73
988 1277 5.265191 AGAGTGAGTGAACTCCAGCTAATA 58.735 41.667 7.96 0.00 46.51 0.98
992 1290 6.014156 AGTGAGTGAACTCCAGCTAATAAAGT 60.014 38.462 7.96 0.00 42.20 2.66
996 1294 7.844993 GAGTGAACTCCAGCTAATAAAGTAGCA 60.845 40.741 11.55 0.00 41.57 3.49
1011 1309 0.534873 TAGCAAGCATGGCGTACAGA 59.465 50.000 0.00 0.00 42.81 3.41
1056 1354 1.512926 CCAGGAACCTCAAGAACGTG 58.487 55.000 0.00 0.00 0.00 4.49
1499 1806 3.737172 GCACCACGACCACATGCC 61.737 66.667 0.00 0.00 0.00 4.40
1500 1807 3.422303 CACCACGACCACATGCCG 61.422 66.667 0.00 0.00 0.00 5.69
1501 1808 3.621805 ACCACGACCACATGCCGA 61.622 61.111 0.00 0.00 0.00 5.54
1502 1809 2.815211 CCACGACCACATGCCGAG 60.815 66.667 0.00 0.00 0.00 4.63
1503 1810 3.490759 CACGACCACATGCCGAGC 61.491 66.667 0.00 0.00 0.00 5.03
1595 1911 2.279918 GTACGCCTACATGCCGGG 60.280 66.667 2.18 0.00 0.00 5.73
1806 2131 2.271497 CAGCTCCAAGCCTCTGGG 59.729 66.667 0.00 0.00 43.77 4.45
1856 2181 3.622826 AGCAGCCGGGTACAACGT 61.623 61.111 5.47 0.00 0.00 3.99
1857 2182 2.667199 GCAGCCGGGTACAACGTT 60.667 61.111 5.47 0.00 0.00 3.99
1858 2183 1.374505 GCAGCCGGGTACAACGTTA 60.375 57.895 5.47 0.00 0.00 3.18
1859 2184 0.950071 GCAGCCGGGTACAACGTTAA 60.950 55.000 5.47 0.00 0.00 2.01
1860 2185 0.792031 CAGCCGGGTACAACGTTAAC 59.208 55.000 5.47 2.11 0.00 2.01
1861 2186 0.667184 AGCCGGGTACAACGTTAACG 60.667 55.000 25.68 25.68 46.33 3.18
1865 2190 0.792031 GGGTACAACGTTAACGCAGG 59.208 55.000 27.07 18.24 44.43 4.85
1868 2193 1.888958 TACAACGTTAACGCAGGCGC 61.889 55.000 27.07 0.00 44.43 6.53
1871 2196 3.419759 CGTTAACGCAGGCGCCTT 61.420 61.111 30.60 15.99 44.19 4.35
1884 2348 2.045926 GCCTTGCCATGGACGACT 60.046 61.111 18.40 0.00 0.00 4.18
1892 2356 1.226802 CATGGACGACTGCGAGGAG 60.227 63.158 0.00 0.00 41.64 3.69
1944 2437 3.272334 GCCGGCGACATGATGTCC 61.272 66.667 19.01 11.79 44.20 4.02
2030 2657 1.386533 GCCGTGTACTAGCTAGTGGA 58.613 55.000 32.21 17.62 37.10 4.02
2148 3164 2.598045 CGAGCTATCGCAACTGCAT 58.402 52.632 2.12 0.00 42.97 3.96
2193 3298 2.159181 GGTGTGCGTAACAGCGAAT 58.841 52.632 6.79 0.00 46.54 3.34
2194 3299 0.179225 GGTGTGCGTAACAGCGAATG 60.179 55.000 6.79 0.00 46.54 2.67
2195 3300 0.789383 GTGTGCGTAACAGCGAATGC 60.789 55.000 0.00 0.00 40.26 3.56
2199 3304 1.715585 CGTAACAGCGAATGCCAGG 59.284 57.895 0.00 0.00 44.31 4.45
2201 3306 0.727398 GTAACAGCGAATGCCAGGAC 59.273 55.000 0.00 0.00 44.31 3.85
2202 3307 0.739462 TAACAGCGAATGCCAGGACG 60.739 55.000 0.00 0.00 44.31 4.79
2308 3650 6.874134 CCCTCATAAGACTTAATAATCACCCG 59.126 42.308 0.00 0.00 0.00 5.28
2336 3678 3.335579 CTCTTTTGGAGAAACCCTACCG 58.664 50.000 0.00 0.00 44.45 4.02
2362 3712 1.148157 CGCCGCAATCGACAAGATCT 61.148 55.000 0.00 0.00 38.98 2.75
2385 3741 1.533299 CGATCGTCTCGTGAGATCCAT 59.467 52.381 7.03 0.00 42.56 3.41
2386 3742 2.412195 CGATCGTCTCGTGAGATCCATC 60.412 54.545 7.03 4.67 42.56 3.51
2405 3763 2.049433 AGTCGACGAAACGCCCTG 60.049 61.111 10.46 0.00 0.00 4.45
2406 3764 2.049802 GTCGACGAAACGCCCTGA 60.050 61.111 0.00 0.00 0.00 3.86
2407 3765 2.049802 TCGACGAAACGCCCTGAC 60.050 61.111 0.00 0.00 0.00 3.51
2409 3767 2.342648 GACGAAACGCCCTGACCT 59.657 61.111 0.00 0.00 0.00 3.85
2410 3768 1.301479 GACGAAACGCCCTGACCTT 60.301 57.895 0.00 0.00 0.00 3.50
2411 3769 1.566018 GACGAAACGCCCTGACCTTG 61.566 60.000 0.00 0.00 0.00 3.61
2456 3820 3.084786 CAGTCCAATCCAAGGAAGAACC 58.915 50.000 0.00 0.00 36.80 3.62
2537 3910 4.413851 AGGAGAAGGAAAAACTCAAGGAGT 59.586 41.667 0.00 0.00 45.64 3.85
2538 3911 4.757657 GGAGAAGGAAAAACTCAAGGAGTC 59.242 45.833 0.00 0.00 42.59 3.36
2683 4059 4.175489 CGTCCGTCGCCTCGTGAT 62.175 66.667 0.00 0.00 0.00 3.06
2684 4060 2.278013 GTCCGTCGCCTCGTGATC 60.278 66.667 0.00 0.00 0.00 2.92
2685 4061 2.748647 TCCGTCGCCTCGTGATCA 60.749 61.111 0.00 0.00 0.00 2.92
2689 4065 1.803943 GTCGCCTCGTGATCAGTCT 59.196 57.895 0.00 0.00 0.00 3.24
2692 4068 0.316278 CGCCTCGTGATCAGTCTACG 60.316 60.000 0.00 0.00 39.04 3.51
2704 4080 2.014857 CAGTCTACGTCGATGGAAGGA 58.985 52.381 9.90 0.00 0.00 3.36
2711 4087 4.730949 ACGTCGATGGAAGGAAAATCTA 57.269 40.909 9.90 0.00 0.00 1.98
2738 4129 0.877743 GTCTCAGCCTGTTTCTTGCC 59.122 55.000 0.00 0.00 0.00 4.52
2793 4193 0.827507 GGCAGCAAGAAGGGGAAACA 60.828 55.000 0.00 0.00 0.00 2.83
2885 4285 0.673644 CCAAGACCAAGGCTACCACG 60.674 60.000 0.00 0.00 0.00 4.94
2935 4341 6.013898 ACGGTGATGATGATATGAAGAAGGAT 60.014 38.462 0.00 0.00 0.00 3.24
3013 4419 2.335712 GGCCAAGACCTTTGCCTCG 61.336 63.158 15.24 0.00 45.03 4.63
3021 4427 0.244721 ACCTTTGCCTCGTACCGTAC 59.755 55.000 0.00 0.00 0.00 3.67
3022 4428 0.244450 CCTTTGCCTCGTACCGTACA 59.756 55.000 9.34 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.308229 GCTGATGGGTTCAATAGCTTATTAGTG 60.308 40.741 0.00 0.00 34.88 2.74
1 2 6.712547 GCTGATGGGTTCAATAGCTTATTAGT 59.287 38.462 0.00 0.00 34.88 2.24
2 3 6.939163 AGCTGATGGGTTCAATAGCTTATTAG 59.061 38.462 0.00 0.00 40.75 1.73
3 4 6.712095 CAGCTGATGGGTTCAATAGCTTATTA 59.288 38.462 8.42 0.00 41.26 0.98
4 5 5.533903 CAGCTGATGGGTTCAATAGCTTATT 59.466 40.000 8.42 0.00 41.26 1.40
5 6 5.068636 CAGCTGATGGGTTCAATAGCTTAT 58.931 41.667 8.42 0.00 41.26 1.73
6 7 4.164030 TCAGCTGATGGGTTCAATAGCTTA 59.836 41.667 13.74 0.00 41.26 3.09
7 8 3.054139 TCAGCTGATGGGTTCAATAGCTT 60.054 43.478 13.74 0.00 41.26 3.74
8 9 2.507058 TCAGCTGATGGGTTCAATAGCT 59.493 45.455 13.74 0.00 42.77 3.32
9 10 2.615912 GTCAGCTGATGGGTTCAATAGC 59.384 50.000 21.47 0.00 36.67 2.97
41 45 1.656652 CGCCTAGTGGAATTGTGAGG 58.343 55.000 0.00 0.00 34.57 3.86
44 48 1.942657 CATCCGCCTAGTGGAATTGTG 59.057 52.381 0.23 0.00 45.75 3.33
45 49 1.134098 CCATCCGCCTAGTGGAATTGT 60.134 52.381 0.23 0.00 45.75 2.71
51 55 0.759436 AGTACCCATCCGCCTAGTGG 60.759 60.000 0.00 0.00 33.99 4.00
52 56 0.389391 CAGTACCCATCCGCCTAGTG 59.611 60.000 0.00 0.00 0.00 2.74
53 57 0.032416 ACAGTACCCATCCGCCTAGT 60.032 55.000 0.00 0.00 0.00 2.57
55 59 0.032912 TGACAGTACCCATCCGCCTA 60.033 55.000 0.00 0.00 0.00 3.93
56 60 1.305802 TGACAGTACCCATCCGCCT 60.306 57.895 0.00 0.00 0.00 5.52
57 61 1.153429 GTGACAGTACCCATCCGCC 60.153 63.158 0.00 0.00 0.00 6.13
61 65 4.160439 TCAATCTCAGTGACAGTACCCATC 59.840 45.833 0.00 0.00 0.00 3.51
62 66 4.096681 TCAATCTCAGTGACAGTACCCAT 58.903 43.478 0.00 0.00 0.00 4.00
63 67 3.506398 TCAATCTCAGTGACAGTACCCA 58.494 45.455 0.00 0.00 0.00 4.51
65 69 5.126222 TCATCTCAATCTCAGTGACAGTACC 59.874 44.000 0.00 0.00 0.00 3.34
100 109 1.541310 CCAACAGGACTACGGCCAGA 61.541 60.000 2.24 0.00 0.00 3.86
144 157 2.216488 CGACATGGATCGTGATTTCGTC 59.784 50.000 0.00 0.00 37.33 4.20
155 168 2.420022 CCAACTTTGACCGACATGGATC 59.580 50.000 0.00 0.00 42.00 3.36
162 175 2.031683 CACTTGACCAACTTTGACCGAC 59.968 50.000 0.00 0.00 0.00 4.79
189 202 7.852945 CGGTTAAAATGGAGTACTACTACTACG 59.147 40.741 6.66 0.00 36.67 3.51
190 203 7.645735 GCGGTTAAAATGGAGTACTACTACTAC 59.354 40.741 6.66 0.00 34.62 2.73
192 205 6.567959 GCGGTTAAAATGGAGTACTACTACT 58.432 40.000 6.66 0.00 35.77 2.57
240 282 3.464053 CTTCGAAATTCGCATAGCATCG 58.536 45.455 10.93 0.00 40.21 3.84
348 410 6.398918 CACCATATAGTAGTCCTATGTTGGC 58.601 44.000 6.50 0.00 40.75 4.52
358 420 4.271696 TGCATGCCACCATATAGTAGTC 57.728 45.455 16.68 0.00 0.00 2.59
406 468 5.949735 AGCATAAAAGTACATCCAAAACGG 58.050 37.500 0.00 0.00 0.00 4.44
421 483 8.377681 CGAGTTATCAACTTTACGAGCATAAAA 58.622 33.333 0.00 0.00 43.03 1.52
434 496 6.837471 ACTACCTCTTCGAGTTATCAACTT 57.163 37.500 0.00 0.00 43.03 2.66
452 514 9.570488 CATGTCAGTTAAAGTTCTACTACTACC 57.430 37.037 0.00 0.00 0.00 3.18
454 516 8.799367 TGCATGTCAGTTAAAGTTCTACTACTA 58.201 33.333 0.00 0.00 0.00 1.82
455 517 7.599245 GTGCATGTCAGTTAAAGTTCTACTACT 59.401 37.037 0.00 0.00 0.00 2.57
488 550 4.548451 TGATCCATCTATGCATCTCCAC 57.452 45.455 0.19 0.00 0.00 4.02
520 587 3.055385 TGGGTTGAGCTGTGGATAACTAC 60.055 47.826 0.00 0.00 0.00 2.73
521 588 3.178046 TGGGTTGAGCTGTGGATAACTA 58.822 45.455 0.00 0.00 0.00 2.24
522 589 1.985159 TGGGTTGAGCTGTGGATAACT 59.015 47.619 0.00 0.00 0.00 2.24
568 639 6.036470 ACTAAACTGCTTCAAAGTTCAAAGC 58.964 36.000 12.84 12.84 44.41 3.51
647 898 2.032860 CTGGATTCCGAGCCACCGAT 62.033 60.000 0.00 0.00 36.14 4.18
651 902 0.250513 ACTTCTGGATTCCGAGCCAC 59.749 55.000 0.00 0.00 36.14 5.01
653 904 1.092345 GCACTTCTGGATTCCGAGCC 61.092 60.000 0.00 0.00 0.00 4.70
656 907 0.911769 ATGGCACTTCTGGATTCCGA 59.088 50.000 0.00 0.00 0.00 4.55
663 936 3.349927 TCAGATCAAATGGCACTTCTGG 58.650 45.455 11.57 0.00 33.19 3.86
673 946 5.026462 GCAACTTGTCGATCAGATCAAATG 58.974 41.667 11.12 2.46 0.00 2.32
686 959 1.155889 TAGTGCATGGCAACTTGTCG 58.844 50.000 0.00 0.00 41.47 4.35
687 960 2.749076 TCATAGTGCATGGCAACTTGTC 59.251 45.455 0.00 0.00 41.47 3.18
688 961 2.794103 TCATAGTGCATGGCAACTTGT 58.206 42.857 0.00 0.00 41.47 3.16
689 962 3.853831 TTCATAGTGCATGGCAACTTG 57.146 42.857 0.00 0.00 41.47 3.16
699 972 6.475504 CCCACAGGATTATATTCATAGTGCA 58.524 40.000 0.00 0.00 33.47 4.57
712 985 6.183361 TGTGTGATATTATGCCCACAGGATTA 60.183 38.462 0.00 0.00 39.79 1.75
713 986 5.072741 GTGTGATATTATGCCCACAGGATT 58.927 41.667 0.00 0.00 39.79 3.01
714 987 4.104579 TGTGTGATATTATGCCCACAGGAT 59.895 41.667 0.00 0.00 39.79 3.24
715 988 3.457749 TGTGTGATATTATGCCCACAGGA 59.542 43.478 0.00 0.00 39.79 3.86
716 989 3.817084 CTGTGTGATATTATGCCCACAGG 59.183 47.826 9.18 0.00 43.64 4.00
743 1017 0.322456 GGTTGCATAGTGTGGGCTCA 60.322 55.000 0.00 0.00 0.00 4.26
747 1021 2.406616 GCCGGTTGCATAGTGTGGG 61.407 63.158 1.90 0.00 40.77 4.61
748 1022 2.406616 GGCCGGTTGCATAGTGTGG 61.407 63.158 1.90 0.00 43.89 4.17
752 1026 4.483243 CCGGGCCGGTTGCATAGT 62.483 66.667 36.52 0.00 42.73 2.12
807 1082 4.351054 CAGGAGGTGTGGGCCCAC 62.351 72.222 42.81 42.81 46.33 4.61
824 1099 1.477295 GGGGAGCGTATGTATAGGAGC 59.523 57.143 0.00 0.00 0.00 4.70
841 1119 3.365265 GCAACACCTTGAGCGGGG 61.365 66.667 0.00 0.00 0.00 5.73
859 1137 2.399356 GCTTGAAGCTGCGGGGTAC 61.399 63.158 10.44 0.00 38.45 3.34
875 1153 3.865929 CTCGTGGTCGTGGCTTGCT 62.866 63.158 0.00 0.00 38.33 3.91
886 1164 2.675423 TAGCTCGTGCCTCGTGGT 60.675 61.111 5.73 9.30 44.00 4.16
887 1165 2.103143 CTAGCTCGTGCCTCGTGG 59.897 66.667 5.73 0.00 40.80 4.94
891 1169 0.249114 GGTTAGCTAGCTCGTGCCTC 60.249 60.000 23.26 4.98 40.80 4.70
894 1172 1.227292 GGGGTTAGCTAGCTCGTGC 60.227 63.158 23.26 9.69 40.05 5.34
895 1173 0.103208 CTGGGGTTAGCTAGCTCGTG 59.897 60.000 23.26 2.08 0.00 4.35
896 1174 1.677637 GCTGGGGTTAGCTAGCTCGT 61.678 60.000 23.26 0.00 40.52 4.18
897 1175 1.068250 GCTGGGGTTAGCTAGCTCG 59.932 63.158 23.26 4.39 40.52 5.03
898 1176 0.179070 GTGCTGGGGTTAGCTAGCTC 60.179 60.000 23.26 7.82 44.01 4.09
899 1177 0.909610 TGTGCTGGGGTTAGCTAGCT 60.910 55.000 23.12 23.12 44.01 3.32
900 1178 0.744771 GTGTGCTGGGGTTAGCTAGC 60.745 60.000 6.62 6.62 44.01 3.42
901 1179 0.107654 GGTGTGCTGGGGTTAGCTAG 60.108 60.000 0.00 0.00 44.01 3.42
902 1180 0.546747 AGGTGTGCTGGGGTTAGCTA 60.547 55.000 0.00 0.00 44.01 3.32
903 1181 1.847968 AGGTGTGCTGGGGTTAGCT 60.848 57.895 0.00 0.00 44.01 3.32
904 1182 1.675641 CAGGTGTGCTGGGGTTAGC 60.676 63.158 0.00 0.00 43.95 3.09
905 1183 4.722193 CAGGTGTGCTGGGGTTAG 57.278 61.111 0.00 0.00 0.00 2.34
929 1207 1.002366 GATGGTTGCTCGTGTGCTAG 58.998 55.000 0.00 0.00 0.00 3.42
930 1208 0.608130 AGATGGTTGCTCGTGTGCTA 59.392 50.000 0.00 0.00 0.00 3.49
932 1210 1.002366 CTAGATGGTTGCTCGTGTGC 58.998 55.000 0.00 0.00 0.00 4.57
933 1211 1.002366 GCTAGATGGTTGCTCGTGTG 58.998 55.000 0.00 0.00 0.00 3.82
934 1212 0.898320 AGCTAGATGGTTGCTCGTGT 59.102 50.000 0.00 0.00 30.41 4.49
935 1213 2.015736 AAGCTAGATGGTTGCTCGTG 57.984 50.000 0.00 0.00 35.85 4.35
936 1214 3.195825 AGTTAAGCTAGATGGTTGCTCGT 59.804 43.478 0.00 0.00 37.56 4.18
938 1216 5.908341 AGTAGTTAAGCTAGATGGTTGCTC 58.092 41.667 0.00 0.00 37.56 4.26
940 1218 5.232414 CGAAGTAGTTAAGCTAGATGGTTGC 59.768 44.000 0.00 0.00 37.56 4.17
943 1232 6.120905 TCTCGAAGTAGTTAAGCTAGATGGT 58.879 40.000 0.00 0.00 0.00 3.55
945 1234 7.011576 TCACTCTCGAAGTAGTTAAGCTAGATG 59.988 40.741 0.00 0.00 36.07 2.90
957 1246 4.142773 GGAGTTCACTCACTCTCGAAGTAG 60.143 50.000 9.18 0.00 44.60 2.57
961 1250 2.554462 CTGGAGTTCACTCACTCTCGAA 59.446 50.000 9.18 0.00 44.60 3.71
976 1265 5.119694 GCTTGCTACTTTATTAGCTGGAGT 58.880 41.667 0.00 0.00 44.26 3.85
984 1273 4.196193 ACGCCATGCTTGCTACTTTATTA 58.804 39.130 0.00 0.00 0.00 0.98
985 1274 3.016736 ACGCCATGCTTGCTACTTTATT 58.983 40.909 0.00 0.00 0.00 1.40
986 1275 2.643551 ACGCCATGCTTGCTACTTTAT 58.356 42.857 0.00 0.00 0.00 1.40
987 1276 2.107950 ACGCCATGCTTGCTACTTTA 57.892 45.000 0.00 0.00 0.00 1.85
988 1277 1.737793 GTACGCCATGCTTGCTACTTT 59.262 47.619 0.00 0.00 0.00 2.66
992 1290 0.534873 TCTGTACGCCATGCTTGCTA 59.465 50.000 0.00 0.00 0.00 3.49
996 1294 0.734889 GCATTCTGTACGCCATGCTT 59.265 50.000 13.13 0.00 39.20 3.91
1011 1309 4.257890 AGGGTCACCTCCAGCATT 57.742 55.556 0.00 0.00 46.95 3.56
1056 1354 2.125512 AGGCGCGACATGAGGTTC 60.126 61.111 17.71 0.00 0.00 3.62
1449 1747 2.827642 GGATGAGGCTGCTGGTGC 60.828 66.667 0.00 0.00 40.20 5.01
1450 1748 1.153208 GAGGATGAGGCTGCTGGTG 60.153 63.158 0.00 0.00 0.00 4.17
1451 1749 0.987081 ATGAGGATGAGGCTGCTGGT 60.987 55.000 0.00 0.00 0.00 4.00
1452 1750 0.535328 CATGAGGATGAGGCTGCTGG 60.535 60.000 0.00 0.00 0.00 4.85
1453 1751 1.167155 GCATGAGGATGAGGCTGCTG 61.167 60.000 0.00 0.00 0.00 4.41
1454 1752 1.148723 GCATGAGGATGAGGCTGCT 59.851 57.895 0.00 0.00 0.00 4.24
1647 1969 2.509336 GAGGACGACATGTGCCCG 60.509 66.667 1.15 2.97 40.31 6.13
1786 2111 3.317571 AGAGGCTTGGAGCTGCGT 61.318 61.111 0.00 0.00 41.99 5.24
1856 2181 3.732892 GCAAGGCGCCTGCGTTAA 61.733 61.111 33.60 0.00 46.70 2.01
1868 2193 2.401766 GCAGTCGTCCATGGCAAGG 61.402 63.158 6.96 1.41 0.00 3.61
1871 2196 3.647649 CTCGCAGTCGTCCATGGCA 62.648 63.158 6.96 0.00 36.96 4.92
1884 2348 2.571757 CTGCCGTTACTCCTCGCA 59.428 61.111 0.00 0.00 0.00 5.10
2030 2657 1.909302 AGGACTGATCAACCCGATGTT 59.091 47.619 13.02 0.00 37.80 2.71
2205 3310 1.977188 AAAATAGAAAACTGGCGCGC 58.023 45.000 25.94 25.94 0.00 6.86
2269 3611 3.039526 AGGGGCTAGCTCCTCCCT 61.040 66.667 31.55 25.19 45.46 4.20
2276 3618 2.785357 AGTCTTATGAGGGGCTAGCT 57.215 50.000 15.72 0.00 0.00 3.32
2279 3621 8.594550 GTGATTATTAAGTCTTATGAGGGGCTA 58.405 37.037 0.00 0.00 0.00 3.93
2308 3650 1.073098 TTCTCCAAAAGAGGGGTCCC 58.927 55.000 0.00 0.00 43.44 4.46
2385 3741 2.127118 GGCGTTTCGTCGACTCGA 60.127 61.111 14.70 3.72 35.78 4.04
2386 3742 3.170585 GGGCGTTTCGTCGACTCG 61.171 66.667 14.70 13.27 39.03 4.18
2405 3763 4.405358 ACTCTCCATCTCAATCTCAAGGTC 59.595 45.833 0.00 0.00 0.00 3.85
2406 3764 4.360889 ACTCTCCATCTCAATCTCAAGGT 58.639 43.478 0.00 0.00 0.00 3.50
2407 3765 5.509501 GCTACTCTCCATCTCAATCTCAAGG 60.510 48.000 0.00 0.00 0.00 3.61
2409 3767 4.037327 CGCTACTCTCCATCTCAATCTCAA 59.963 45.833 0.00 0.00 0.00 3.02
2410 3768 3.567585 CGCTACTCTCCATCTCAATCTCA 59.432 47.826 0.00 0.00 0.00 3.27
2411 3769 3.818210 TCGCTACTCTCCATCTCAATCTC 59.182 47.826 0.00 0.00 0.00 2.75
2537 3910 2.812609 CGACGACTCCGACTCCGA 60.813 66.667 0.00 0.00 39.50 4.55
2538 3911 3.862402 CCGACGACTCCGACTCCG 61.862 72.222 0.00 0.00 39.50 4.63
2683 4059 2.014857 CCTTCCATCGACGTAGACTGA 58.985 52.381 0.00 0.00 0.00 3.41
2684 4060 2.014857 TCCTTCCATCGACGTAGACTG 58.985 52.381 0.00 1.24 0.00 3.51
2685 4061 2.414994 TCCTTCCATCGACGTAGACT 57.585 50.000 0.00 0.00 0.00 3.24
2689 4065 4.730949 AGATTTTCCTTCCATCGACGTA 57.269 40.909 0.00 0.00 0.00 3.57
2692 4068 4.740695 CGAGTAGATTTTCCTTCCATCGAC 59.259 45.833 0.00 0.00 0.00 4.20
2704 4080 3.677424 GCTGAGACTGCCGAGTAGATTTT 60.677 47.826 0.00 0.00 30.16 1.82
2738 4129 0.747255 ATCTCGTTCTCATGGGGTCG 59.253 55.000 0.00 0.00 0.00 4.79
2793 4193 3.379445 CACCCGCACTACCTCCGT 61.379 66.667 0.00 0.00 0.00 4.69
2885 4285 3.503748 CCACCAGAGACATCAACCTTTTC 59.496 47.826 0.00 0.00 0.00 2.29
2935 4341 1.475034 GCCGATTTGCCTCTGTCCATA 60.475 52.381 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.