Multiple sequence alignment - TraesCS5D01G396900

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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 TraesCS5D01G396900 chr5D 100.000 4437 0 0 1 4437 464076233 464080669 0.000000e+00 8194
1 TraesCS5D01G396900 chr5B 90.344 3428 227 51 1079 4437 570934754 570938146 0.000000e+00 4401
2 TraesCS5D01G396900 chr5B 92.153 1542 102 6 1899 3433 571173722 571175251 0.000000e+00 2159
3 TraesCS5D01G396900 chr5B 85.315 1791 186 36 160 1903 571121826 571123586 0.000000e+00 1779
4 TraesCS5D01G396900 chr5B 88.745 924 50 14 160 1044 570933749 570934657 0.000000e+00 1081
5 TraesCS5D01G396900 chr5B 84.017 463 23 19 4023 4437 571175949 571176408 8.940000e-107 398
6 TraesCS5D01G396900 chr5B 90.476 252 11 4 3424 3662 571175419 571175670 1.990000e-83 320
7 TraesCS5D01G396900 chr5B 90.058 171 8 4 3829 3991 571175782 571175951 3.480000e-51 213
8 TraesCS5D01G396900 chr5A 91.052 2034 113 31 2268 4261 584508105 584510109 0.000000e+00 2684
9 TraesCS5D01G396900 chr5A 86.654 1019 122 10 1079 2088 584507055 584508068 0.000000e+00 1116
10 TraesCS5D01G396900 chr5A 91.760 716 37 14 160 867 584491054 584491755 0.000000e+00 976
11 TraesCS5D01G396900 chr5A 89.844 128 13 0 1 128 584490928 584491055 9.870000e-37 165
12 TraesCS5D01G396900 chr5A 98.649 74 1 0 4253 4326 584510043 584510116 1.000000e-26 132
13 TraesCS5D01G396900 chr3B 88.321 1310 136 12 2271 3576 671746429 671745133 0.000000e+00 1555
14 TraesCS5D01G396900 chr2B 88.082 1225 132 8 2270 3491 752829850 752828637 0.000000e+00 1441
15 TraesCS5D01G396900 chr2B 83.636 770 91 20 160 929 752831747 752831013 0.000000e+00 691
16 TraesCS5D01G396900 chr2B 76.705 1056 197 25 1083 2112 752830889 752829857 3.900000e-150 542
17 TraesCS5D01G396900 chr2B 85.345 116 17 0 13 128 752831861 752831746 2.170000e-23 121
18 TraesCS5D01G396900 chr2D 88.663 1129 128 0 2298 3426 617072810 617071682 0.000000e+00 1376
19 TraesCS5D01G396900 chr2D 81.771 768 97 25 162 929 617074728 617074004 1.770000e-168 603
20 TraesCS5D01G396900 chr2D 76.600 1000 182 27 1117 2088 617073851 617072876 1.840000e-138 503
21 TraesCS5D01G396900 chr2D 85.185 162 22 1 2119 2280 600403942 600403783 9.870000e-37 165
22 TraesCS5D01G396900 chr2A 88.683 1131 123 5 2298 3426 747143693 747142566 0.000000e+00 1375
23 TraesCS5D01G396900 chr2A 81.582 771 101 25 160 929 747145620 747144890 2.280000e-167 599
24 TraesCS5D01G396900 chr2A 77.974 849 144 23 1083 1907 747144766 747143937 3.990000e-135 492
25 TraesCS5D01G396900 chr2A 78.846 416 73 10 1199 1603 746977518 746977107 2.630000e-67 267
26 TraesCS5D01G396900 chr2A 87.395 119 15 0 1 119 747145743 747145625 2.150000e-28 137
27 TraesCS5D01G396900 chr3A 82.983 1093 176 5 2323 3407 10952685 10951595 0.000000e+00 979
28 TraesCS5D01G396900 chr3D 82.208 1096 179 11 2323 3407 5007046 5005956 0.000000e+00 929
29 TraesCS5D01G396900 chr7D 85.806 155 18 3 2122 2274 436459777 436459625 1.280000e-35 161
30 TraesCS5D01G396900 chr4D 88.028 142 10 6 2137 2274 341693265 341693403 1.280000e-35 161
31 TraesCS5D01G396900 chr1B 85.526 152 22 0 2122 2273 437601170 437601019 4.590000e-35 159
32 TraesCS5D01G396900 chr7A 85.256 156 18 4 2122 2274 113028229 113028382 5.940000e-34 156
33 TraesCS5D01G396900 chr4A 87.324 142 11 6 2137 2274 125039933 125039795 5.940000e-34 156
34 TraesCS5D01G396900 chr1A 83.942 137 18 3 2141 2275 385659154 385659288 1.300000e-25 128


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 TraesCS5D01G396900 chr5D 464076233 464080669 4436 False 8194.000000 8194 100.000000 1 4437 1 chr5D.!!$F1 4436
1 TraesCS5D01G396900 chr5B 570933749 570938146 4397 False 2741.000000 4401 89.544500 160 4437 2 chr5B.!!$F2 4277
2 TraesCS5D01G396900 chr5B 571121826 571123586 1760 False 1779.000000 1779 85.315000 160 1903 1 chr5B.!!$F1 1743
3 TraesCS5D01G396900 chr5B 571173722 571176408 2686 False 772.500000 2159 89.176000 1899 4437 4 chr5B.!!$F3 2538
4 TraesCS5D01G396900 chr5A 584507055 584510116 3061 False 1310.666667 2684 92.118333 1079 4326 3 chr5A.!!$F2 3247
5 TraesCS5D01G396900 chr5A 584490928 584491755 827 False 570.500000 976 90.802000 1 867 2 chr5A.!!$F1 866
6 TraesCS5D01G396900 chr3B 671745133 671746429 1296 True 1555.000000 1555 88.321000 2271 3576 1 chr3B.!!$R1 1305
7 TraesCS5D01G396900 chr2B 752828637 752831861 3224 True 698.750000 1441 83.442000 13 3491 4 chr2B.!!$R1 3478
8 TraesCS5D01G396900 chr2D 617071682 617074728 3046 True 827.333333 1376 82.344667 162 3426 3 chr2D.!!$R2 3264
9 TraesCS5D01G396900 chr2A 747142566 747145743 3177 True 650.750000 1375 83.908500 1 3426 4 chr2A.!!$R2 3425
10 TraesCS5D01G396900 chr3A 10951595 10952685 1090 True 979.000000 979 82.983000 2323 3407 1 chr3A.!!$R1 1084
11 TraesCS5D01G396900 chr3D 5005956 5007046 1090 True 929.000000 929 82.208000 2323 3407 1 chr3D.!!$R1 1084

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
137 138 0.388520 CGGTGTCAGCTGTGATCGAA 60.389 55.0 14.67 0.0 34.36 3.71 F
1921 2118 0.105778 GCAGCTCATACCCTGGAGAC 59.894 60.0 0.00 0.0 32.87 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2023 2220 0.038159 AGCGTAGTGAGTGAAGGTGC 60.038 55.0 0.0 0.0 0.00 5.01 R
3784 4246 0.389426 CTTCAGTTGGGCTGCAATGC 60.389 55.0 0.0 0.0 44.66 3.56 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
77 78 1.142748 CTCCCTTGAGCAGCCTACG 59.857 63.158 0.00 0.00 0.00 3.51
81 82 1.515020 CTTGAGCAGCCTACGAGCT 59.485 57.895 0.00 0.00 46.45 4.09
126 127 1.665916 CAGCTGTGGTCGGTGTCAG 60.666 63.158 5.25 0.00 0.00 3.51
127 128 3.044305 GCTGTGGTCGGTGTCAGC 61.044 66.667 0.00 0.00 44.50 4.26
128 129 2.737180 CTGTGGTCGGTGTCAGCT 59.263 61.111 0.00 0.00 0.00 4.24
129 130 1.665916 CTGTGGTCGGTGTCAGCTG 60.666 63.158 7.63 7.63 0.00 4.24
130 131 2.369257 CTGTGGTCGGTGTCAGCTGT 62.369 60.000 14.67 0.00 0.00 4.40
131 132 1.956170 GTGGTCGGTGTCAGCTGTG 60.956 63.158 14.67 0.10 0.00 3.66
132 133 2.131067 TGGTCGGTGTCAGCTGTGA 61.131 57.895 14.67 2.60 0.00 3.58
133 134 1.293498 GGTCGGTGTCAGCTGTGAT 59.707 57.895 14.67 0.00 34.36 3.06
134 135 0.737715 GGTCGGTGTCAGCTGTGATC 60.738 60.000 14.67 0.55 34.36 2.92
135 136 1.073216 GTCGGTGTCAGCTGTGATCG 61.073 60.000 14.67 13.31 34.36 3.69
136 137 1.212751 CGGTGTCAGCTGTGATCGA 59.787 57.895 14.67 0.00 34.36 3.59
137 138 0.388520 CGGTGTCAGCTGTGATCGAA 60.389 55.000 14.67 0.00 34.36 3.71
138 139 1.737029 CGGTGTCAGCTGTGATCGAAT 60.737 52.381 14.67 0.00 34.36 3.34
139 140 1.662629 GGTGTCAGCTGTGATCGAATG 59.337 52.381 14.67 0.00 34.36 2.67
140 141 2.341257 GTGTCAGCTGTGATCGAATGT 58.659 47.619 14.67 0.00 34.36 2.71
141 142 2.738846 GTGTCAGCTGTGATCGAATGTT 59.261 45.455 14.67 0.00 34.36 2.71
142 143 2.738314 TGTCAGCTGTGATCGAATGTTG 59.262 45.455 14.67 0.00 34.36 3.33
143 144 2.738846 GTCAGCTGTGATCGAATGTTGT 59.261 45.455 14.67 0.00 34.36 3.32
144 145 2.738314 TCAGCTGTGATCGAATGTTGTG 59.262 45.455 14.67 0.00 0.00 3.33
145 146 2.079158 AGCTGTGATCGAATGTTGTGG 58.921 47.619 0.00 0.00 0.00 4.17
146 147 1.131126 GCTGTGATCGAATGTTGTGGG 59.869 52.381 0.00 0.00 0.00 4.61
147 148 2.698803 CTGTGATCGAATGTTGTGGGA 58.301 47.619 0.00 0.00 0.00 4.37
148 149 3.273434 CTGTGATCGAATGTTGTGGGAT 58.727 45.455 0.00 0.00 0.00 3.85
149 150 3.684908 TGTGATCGAATGTTGTGGGATT 58.315 40.909 0.00 0.00 0.00 3.01
150 151 3.439825 TGTGATCGAATGTTGTGGGATTG 59.560 43.478 0.00 0.00 0.00 2.67
151 152 3.440173 GTGATCGAATGTTGTGGGATTGT 59.560 43.478 0.00 0.00 0.00 2.71
152 153 4.634004 GTGATCGAATGTTGTGGGATTGTA 59.366 41.667 0.00 0.00 0.00 2.41
153 154 5.296780 GTGATCGAATGTTGTGGGATTGTAT 59.703 40.000 0.00 0.00 0.00 2.29
154 155 5.296531 TGATCGAATGTTGTGGGATTGTATG 59.703 40.000 0.00 0.00 0.00 2.39
155 156 3.944650 TCGAATGTTGTGGGATTGTATGG 59.055 43.478 0.00 0.00 0.00 2.74
156 157 3.944650 CGAATGTTGTGGGATTGTATGGA 59.055 43.478 0.00 0.00 0.00 3.41
157 158 4.580167 CGAATGTTGTGGGATTGTATGGAT 59.420 41.667 0.00 0.00 0.00 3.41
158 159 5.506151 CGAATGTTGTGGGATTGTATGGATG 60.506 44.000 0.00 0.00 0.00 3.51
437 450 2.180769 CATCGAGACGGCGGACAA 59.819 61.111 13.24 0.00 0.00 3.18
503 516 2.438434 CCGGTTCCATGGCTGACC 60.438 66.667 6.96 13.65 0.00 4.02
554 567 7.451877 AGAAATATACTCATCTTTCTCCCGCTA 59.548 37.037 0.00 0.00 34.27 4.26
682 698 2.158755 CCCCTGTCCATGAGTCAATACC 60.159 54.545 0.00 0.00 0.00 2.73
685 701 4.567537 CCCTGTCCATGAGTCAATACCAAA 60.568 45.833 0.00 0.00 0.00 3.28
691 707 5.724370 TCCATGAGTCAATACCAAACTCCTA 59.276 40.000 0.00 0.00 38.91 2.94
748 777 1.849219 GTCGCTGTAGATCAAGCTTCG 59.151 52.381 0.00 0.00 0.00 3.79
787 818 4.163078 ACATTAGAATCCCAGACCTGACAG 59.837 45.833 0.00 0.00 0.00 3.51
935 989 2.029739 TGGCAGCAGTGATGTTTTCATG 60.030 45.455 10.56 0.00 41.05 3.07
941 1004 6.854892 GCAGCAGTGATGTTTTCATGTATATC 59.145 38.462 10.56 0.00 41.05 1.63
959 1022 8.117813 TGTATATCTATCTGGCACGTATTTCA 57.882 34.615 0.00 0.00 0.00 2.69
965 1028 3.669536 TCTGGCACGTATTTCATTGTGA 58.330 40.909 0.00 0.00 34.29 3.58
970 1033 4.142708 GGCACGTATTTCATTGTGATGACA 60.143 41.667 0.00 0.00 41.84 3.58
971 1034 5.449041 GGCACGTATTTCATTGTGATGACAT 60.449 40.000 0.00 0.00 41.84 3.06
972 1035 6.238347 GGCACGTATTTCATTGTGATGACATA 60.238 38.462 0.00 0.00 41.84 2.29
973 1036 7.355017 GCACGTATTTCATTGTGATGACATAT 58.645 34.615 0.00 0.00 41.84 1.78
1003 1066 0.319555 AGTGATGTGGACGTTCACCG 60.320 55.000 24.06 0.00 44.03 4.94
1036 1119 6.231211 CAGGTCTTTCTACAGGCTCTTTTTA 58.769 40.000 0.00 0.00 0.00 1.52
1040 1123 8.577296 GGTCTTTCTACAGGCTCTTTTTAAATT 58.423 33.333 0.00 0.00 0.00 1.82
1050 1133 5.346011 GGCTCTTTTTAAATTTTCTCCAGCG 59.654 40.000 0.00 0.00 0.00 5.18
1057 1148 2.586648 ATTTTCTCCAGCGTCCCTTT 57.413 45.000 0.00 0.00 0.00 3.11
1062 1155 0.951040 CTCCAGCGTCCCTTTGTGTC 60.951 60.000 0.00 0.00 0.00 3.67
1086 1235 4.573201 TGTTTTCACCCTTCTTCTACAACG 59.427 41.667 0.00 0.00 0.00 4.10
1099 1248 2.946329 TCTACAACGAAGCCAAAGCAAA 59.054 40.909 0.00 0.00 43.56 3.68
1113 1262 5.007528 GCCAAAGCAAAAGCTAAACAATCAA 59.992 36.000 0.00 0.00 39.53 2.57
1114 1263 6.293571 GCCAAAGCAAAAGCTAAACAATCAAT 60.294 34.615 0.00 0.00 39.53 2.57
1115 1264 7.293018 CCAAAGCAAAAGCTAAACAATCAATC 58.707 34.615 0.00 0.00 0.00 2.67
1172 1328 2.046314 GCCTGGCCGCTGTTCTTA 60.046 61.111 7.66 0.00 0.00 2.10
1175 1331 1.003839 CTGGCCGCTGTTCTTACCA 60.004 57.895 0.00 0.00 0.00 3.25
1215 1401 1.075525 ATAGGTACGCCTGCCCTCA 60.076 57.895 0.00 0.00 46.47 3.86
1263 1449 2.511600 CTACCCTTTCCGCCTGCG 60.512 66.667 4.20 4.20 39.44 5.18
1305 1491 0.393944 TCTCCGTCATACGAGCTGGT 60.394 55.000 6.61 6.61 46.05 4.00
1388 1574 5.634896 TCGACTACGAACTTTCATACTTCC 58.365 41.667 0.00 0.00 45.74 3.46
1399 1585 0.750850 CATACTTCCGGGTCGTGGAT 59.249 55.000 0.00 0.00 34.91 3.41
1492 1678 4.540153 CCCAACGGCTTCATCGAT 57.460 55.556 0.00 0.00 0.00 3.59
1496 1682 1.538276 CAACGGCTTCATCGATTTGC 58.462 50.000 0.00 0.00 0.00 3.68
1519 1708 4.787286 CCCGCGGTTACATGGGCA 62.787 66.667 26.12 0.00 34.25 5.36
1555 1744 3.554692 CGGGCGATCACGAACAGC 61.555 66.667 0.00 0.00 42.66 4.40
1613 1802 4.377431 GCACTTCTTTCGTCTATGTGTTGG 60.377 45.833 0.00 0.00 0.00 3.77
1630 1819 7.667043 TGTGTTGGTCAACTCTTATTATGTC 57.333 36.000 13.96 0.00 41.67 3.06
1713 1902 1.260561 GTATGATAACGCAAGCCACGG 59.739 52.381 0.00 0.00 45.62 4.94
1768 1960 6.648502 TCGTGTTTTGTTTCCTTTATACGAC 58.351 36.000 0.00 0.00 32.74 4.34
1770 1962 6.355144 CGTGTTTTGTTTCCTTTATACGACAC 59.645 38.462 0.00 0.00 0.00 3.67
1809 2001 1.202746 GGGCTGCCTAAAGGATCTGAG 60.203 57.143 19.68 0.00 37.39 3.35
1866 2062 4.976116 GTGCTTCTGTTTTGGAACATACAC 59.024 41.667 0.00 0.00 44.30 2.90
1907 2104 4.708421 ACATTTTCTCCATTGTATGCAGCT 59.292 37.500 0.00 0.00 0.00 4.24
1910 2107 3.851458 TCTCCATTGTATGCAGCTCAT 57.149 42.857 0.00 4.45 39.17 2.90
1921 2118 0.105778 GCAGCTCATACCCTGGAGAC 59.894 60.000 0.00 0.00 32.87 3.36
1932 2129 1.216710 CTGGAGACTCGGTGGCTTC 59.783 63.158 0.00 0.00 31.30 3.86
1945 2142 1.213013 GGCTTCTCTTCTCGTGCGA 59.787 57.895 0.00 0.00 0.00 5.10
2021 2218 3.375299 AGCAGATAATTTGCGTTCCACTC 59.625 43.478 0.00 0.00 45.98 3.51
2023 2220 4.728882 GCAGATAATTTGCGTTCCACTCAG 60.729 45.833 0.00 0.00 0.00 3.35
2064 2261 2.296471 CTGCGATAGTATTCTCCCCGTT 59.704 50.000 0.00 0.00 39.35 4.44
2078 2275 5.353938 TCTCCCCGTTAATATTGAAGTTCG 58.646 41.667 0.00 0.00 0.00 3.95
2088 2285 8.395633 GTTAATATTGAAGTTCGTTGCTGGTAT 58.604 33.333 0.00 0.00 0.00 2.73
2106 2314 8.374743 TGCTGGTATGCTGATAGAATTACATAA 58.625 33.333 0.00 0.00 0.00 1.90
2134 2342 2.805194 ACGCTAGTACTCCCTCTGTTT 58.195 47.619 0.00 0.00 0.00 2.83
2135 2343 2.492484 ACGCTAGTACTCCCTCTGTTTG 59.508 50.000 0.00 0.00 0.00 2.93
2144 2352 7.630082 AGTACTCCCTCTGTTTGCAAATATAA 58.370 34.615 16.21 3.26 0.00 0.98
2145 2353 8.275040 AGTACTCCCTCTGTTTGCAAATATAAT 58.725 33.333 16.21 0.00 0.00 1.28
2180 2394 9.507329 ACTTTTCTGCGAATTGGATGTATATAT 57.493 29.630 0.00 0.00 0.00 0.86
2184 2398 6.313658 TCTGCGAATTGGATGTATATATGCAC 59.686 38.462 5.58 1.02 0.00 4.57
2185 2399 5.936956 TGCGAATTGGATGTATATATGCACA 59.063 36.000 5.58 0.00 0.00 4.57
2186 2400 6.128309 TGCGAATTGGATGTATATATGCACAC 60.128 38.462 5.58 3.05 0.00 3.82
2211 2425 7.920682 ACTTTAGTGTGTTTGTTCATCCATTTC 59.079 33.333 0.00 0.00 0.00 2.17
2214 2428 5.360714 AGTGTGTTTGTTCATCCATTTCAGT 59.639 36.000 0.00 0.00 0.00 3.41
2223 2437 4.441792 TCATCCATTTCAGTCCGTATGTG 58.558 43.478 0.00 0.00 0.00 3.21
2241 2455 9.443323 CCGTATGTGGTCCATATTGAAATATTA 57.557 33.333 6.41 0.00 38.29 0.98
2295 2518 4.415596 AGTTTCTTGGCAATCCCACATAA 58.584 39.130 0.00 0.00 45.34 1.90
2296 2519 4.837860 AGTTTCTTGGCAATCCCACATAAA 59.162 37.500 0.00 0.00 45.34 1.40
2297 2520 5.484998 AGTTTCTTGGCAATCCCACATAAAT 59.515 36.000 0.00 0.00 45.34 1.40
2298 2521 6.667414 AGTTTCTTGGCAATCCCACATAAATA 59.333 34.615 0.00 0.00 45.34 1.40
2347 2570 1.203389 AGGTTAGTGGTTGCTCCCCTA 60.203 52.381 0.00 0.00 34.77 3.53
2573 2796 1.285667 TCCATGTGGCCATCAAGATGT 59.714 47.619 9.72 0.00 37.11 3.06
2642 2865 1.995066 ACCATCGGCAGGATCCACA 60.995 57.895 15.82 0.00 31.28 4.17
2746 2969 8.691797 GGTTCTCTTGATAAGTACATCTTCTCT 58.308 37.037 0.00 0.00 37.56 3.10
2749 2972 6.499172 TCTTGATAAGTACATCTTCTCTGCG 58.501 40.000 0.00 0.00 37.56 5.18
2953 3176 3.659850 GGACAACAGTTTTGTGCCC 57.340 52.632 0.00 0.00 37.67 5.36
2954 3177 0.820871 GGACAACAGTTTTGTGCCCA 59.179 50.000 0.00 0.00 37.67 5.36
3286 3527 3.809234 CGAAGTCATAGAGATGCTCGAG 58.191 50.000 8.45 8.45 35.36 4.04
3298 3539 2.182030 CTCGAGGGGAGCGTTGAC 59.818 66.667 3.91 0.00 35.63 3.18
3514 3937 8.279970 TGAACTATGGAATGTGGATGTTTTAG 57.720 34.615 0.00 0.00 0.00 1.85
3594 4030 5.509605 TGTGTATCGAGTGTGAAATTTCG 57.490 39.130 13.34 1.22 34.56 3.46
3627 4063 1.402787 CCAAAAGGGTGTGAGCAGTT 58.597 50.000 0.00 0.00 0.00 3.16
3676 4136 4.142447 ACACCAGAGACGTACATGACATAC 60.142 45.833 0.00 0.00 0.00 2.39
3692 4154 2.760650 ACATACTCTGAACTGATGGCGA 59.239 45.455 0.00 0.00 0.00 5.54
3694 4156 1.550327 ACTCTGAACTGATGGCGAGA 58.450 50.000 0.00 0.00 0.00 4.04
3695 4157 1.895798 ACTCTGAACTGATGGCGAGAA 59.104 47.619 0.00 0.00 0.00 2.87
3696 4158 2.266554 CTCTGAACTGATGGCGAGAAC 58.733 52.381 0.00 0.00 0.00 3.01
3697 4159 1.066858 TCTGAACTGATGGCGAGAACC 60.067 52.381 0.00 0.00 0.00 3.62
3698 4160 0.976641 TGAACTGATGGCGAGAACCT 59.023 50.000 0.00 0.00 0.00 3.50
3699 4161 1.338105 TGAACTGATGGCGAGAACCTG 60.338 52.381 0.00 0.00 0.00 4.00
3700 4162 0.976641 AACTGATGGCGAGAACCTGA 59.023 50.000 0.00 0.00 0.00 3.86
3701 4163 1.198713 ACTGATGGCGAGAACCTGAT 58.801 50.000 0.00 0.00 0.00 2.90
3702 4164 1.134580 ACTGATGGCGAGAACCTGATG 60.135 52.381 0.00 0.00 0.00 3.07
3703 4165 1.137675 CTGATGGCGAGAACCTGATGA 59.862 52.381 0.00 0.00 0.00 2.92
3704 4166 1.554617 TGATGGCGAGAACCTGATGAA 59.445 47.619 0.00 0.00 0.00 2.57
3705 4167 2.027285 TGATGGCGAGAACCTGATGAAA 60.027 45.455 0.00 0.00 0.00 2.69
3706 4168 2.099141 TGGCGAGAACCTGATGAAAG 57.901 50.000 0.00 0.00 0.00 2.62
3707 4169 1.623311 TGGCGAGAACCTGATGAAAGA 59.377 47.619 0.00 0.00 0.00 2.52
3708 4170 2.237143 TGGCGAGAACCTGATGAAAGAT 59.763 45.455 0.00 0.00 0.00 2.40
3709 4171 2.611292 GGCGAGAACCTGATGAAAGATG 59.389 50.000 0.00 0.00 0.00 2.90
3710 4172 2.031437 GCGAGAACCTGATGAAAGATGC 59.969 50.000 0.00 0.00 0.00 3.91
3711 4173 2.611292 CGAGAACCTGATGAAAGATGCC 59.389 50.000 0.00 0.00 0.00 4.40
3720 4182 0.035317 TGAAAGATGCCTCGTGCTGT 59.965 50.000 1.74 0.00 42.00 4.40
3727 4189 1.508632 TGCCTCGTGCTGTAGTTTTC 58.491 50.000 1.74 0.00 42.00 2.29
3757 4219 1.933181 GCTGTTTGTTGGTTTCCAAGC 59.067 47.619 1.16 0.00 44.82 4.01
3765 4227 1.145571 TGGTTTCCAAGCCCTGTAGT 58.854 50.000 0.00 0.00 0.00 2.73
3820 4282 4.458295 ACTGAAGAAGCATCAAACCATGAG 59.542 41.667 0.00 0.00 42.53 2.90
3822 4284 5.072055 TGAAGAAGCATCAAACCATGAGAA 58.928 37.500 0.00 0.00 42.53 2.87
3840 4303 5.293560 TGAGAATGTTCACACGTTATGACA 58.706 37.500 0.00 2.58 31.82 3.58
3863 4328 5.922739 AAAATGGCAGAAAAATTCGGAAC 57.077 34.783 0.00 0.00 34.02 3.62
3895 4361 6.590677 CCTACTAGGAGTAGTTGTTTTTCAGC 59.409 42.308 11.66 0.00 45.12 4.26
3920 4394 6.882610 TGCAATTACTTTCAACAGATCAGT 57.117 33.333 0.00 0.00 0.00 3.41
3952 4426 4.112634 GTTTTTCAGTGAGGTTTGCTTCC 58.887 43.478 0.00 0.00 0.00 3.46
3958 4432 2.441750 AGTGAGGTTTGCTTCCCTGTTA 59.558 45.455 0.00 0.00 0.00 2.41
3963 4437 2.164422 GGTTTGCTTCCCTGTTATCAGC 59.836 50.000 0.00 0.00 40.09 4.26
4059 4545 8.865978 TGACATGAATTACACTTTATCACGTAC 58.134 33.333 0.00 0.00 0.00 3.67
4078 4567 6.868864 CACGTACAGATCCCATAGATTAAAGG 59.131 42.308 0.00 0.00 34.42 3.11
4115 4607 9.569167 GTAGTAATAAATTTGGAGGAAACTTGC 57.431 33.333 0.00 0.00 44.43 4.01
4116 4608 8.189119 AGTAATAAATTTGGAGGAAACTTGCA 57.811 30.769 0.00 0.00 44.43 4.08
4216 4739 2.190313 GCCGCATCCAGGTCATCA 59.810 61.111 0.00 0.00 0.00 3.07
4231 4754 3.774959 ATCATCGCCGTCTGCCGTC 62.775 63.158 0.00 0.00 36.24 4.79
4277 4861 2.240500 GCATCCAGGTCATCGTCGC 61.241 63.158 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 2.025969 CGACCACAGCTGTGCTCTG 61.026 63.158 36.38 25.86 44.34 3.35
102 103 2.341543 CGACCACAGCTGTGCTCT 59.658 61.111 36.38 22.37 44.34 4.09
112 113 2.421314 CAGCTGACACCGACCACA 59.579 61.111 8.42 0.00 0.00 4.17
126 127 1.131126 CCCACAACATTCGATCACAGC 59.869 52.381 0.00 0.00 0.00 4.40
127 128 2.698803 TCCCACAACATTCGATCACAG 58.301 47.619 0.00 0.00 0.00 3.66
128 129 2.849294 TCCCACAACATTCGATCACA 57.151 45.000 0.00 0.00 0.00 3.58
129 130 3.440173 ACAATCCCACAACATTCGATCAC 59.560 43.478 0.00 0.00 0.00 3.06
130 131 3.684908 ACAATCCCACAACATTCGATCA 58.315 40.909 0.00 0.00 0.00 2.92
131 132 5.277974 CCATACAATCCCACAACATTCGATC 60.278 44.000 0.00 0.00 0.00 3.69
132 133 4.580167 CCATACAATCCCACAACATTCGAT 59.420 41.667 0.00 0.00 0.00 3.59
133 134 3.944650 CCATACAATCCCACAACATTCGA 59.055 43.478 0.00 0.00 0.00 3.71
134 135 3.944650 TCCATACAATCCCACAACATTCG 59.055 43.478 0.00 0.00 0.00 3.34
135 136 5.221303 CCATCCATACAATCCCACAACATTC 60.221 44.000 0.00 0.00 0.00 2.67
136 137 4.650588 CCATCCATACAATCCCACAACATT 59.349 41.667 0.00 0.00 0.00 2.71
137 138 4.217510 CCATCCATACAATCCCACAACAT 58.782 43.478 0.00 0.00 0.00 2.71
138 139 3.630168 CCATCCATACAATCCCACAACA 58.370 45.455 0.00 0.00 0.00 3.33
139 140 2.362077 GCCATCCATACAATCCCACAAC 59.638 50.000 0.00 0.00 0.00 3.32
140 141 2.665165 GCCATCCATACAATCCCACAA 58.335 47.619 0.00 0.00 0.00 3.33
141 142 1.133513 GGCCATCCATACAATCCCACA 60.134 52.381 0.00 0.00 0.00 4.17
142 143 1.620822 GGCCATCCATACAATCCCAC 58.379 55.000 0.00 0.00 0.00 4.61
143 144 0.110295 CGGCCATCCATACAATCCCA 59.890 55.000 2.24 0.00 0.00 4.37
144 145 0.609131 CCGGCCATCCATACAATCCC 60.609 60.000 2.24 0.00 0.00 3.85
145 146 0.110486 ACCGGCCATCCATACAATCC 59.890 55.000 0.00 0.00 0.00 3.01
146 147 1.238439 CACCGGCCATCCATACAATC 58.762 55.000 0.00 0.00 0.00 2.67
147 148 0.178992 CCACCGGCCATCCATACAAT 60.179 55.000 0.00 0.00 0.00 2.71
148 149 1.225983 CCACCGGCCATCCATACAA 59.774 57.895 0.00 0.00 0.00 2.41
149 150 1.998438 ACCACCGGCCATCCATACA 60.998 57.895 0.00 0.00 0.00 2.29
150 151 1.525995 CACCACCGGCCATCCATAC 60.526 63.158 0.00 0.00 0.00 2.39
151 152 1.275421 TTCACCACCGGCCATCCATA 61.275 55.000 0.00 0.00 0.00 2.74
152 153 2.611505 TTCACCACCGGCCATCCAT 61.612 57.895 0.00 0.00 0.00 3.41
153 154 3.253061 TTCACCACCGGCCATCCA 61.253 61.111 0.00 0.00 0.00 3.41
154 155 2.750237 GTTCACCACCGGCCATCC 60.750 66.667 0.00 0.00 0.00 3.51
155 156 1.303317 AAGTTCACCACCGGCCATC 60.303 57.895 0.00 0.00 0.00 3.51
156 157 1.603455 CAAGTTCACCACCGGCCAT 60.603 57.895 0.00 0.00 0.00 4.40
157 158 2.203280 CAAGTTCACCACCGGCCA 60.203 61.111 0.00 0.00 0.00 5.36
158 159 2.203294 ACAAGTTCACCACCGGCC 60.203 61.111 0.00 0.00 0.00 6.13
347 360 4.978580 AGTAACACATCATCATCGTCATCG 59.021 41.667 0.00 0.00 38.55 3.84
353 366 5.754890 TGATTCCAGTAACACATCATCATCG 59.245 40.000 0.00 0.00 0.00 3.84
437 450 6.832900 GGGAGGATCAAGATTTCTTCAGAAAT 59.167 38.462 13.54 13.54 46.53 2.17
455 468 2.262774 CTTCGGCAGCTTGGGAGGAT 62.263 60.000 0.00 0.00 0.00 3.24
554 567 1.830587 TTCATCCACCTCTGCAGCGT 61.831 55.000 9.47 4.48 0.00 5.07
691 707 8.639761 AGCCAAGTACTAGAAAACGATATGTAT 58.360 33.333 0.00 0.00 0.00 2.29
787 818 4.332819 GCCAAGGTAGTTGATACATGTCAC 59.667 45.833 0.00 0.00 38.60 3.67
889 920 3.503363 TGTCATCACAAAGAAGATGTGCC 59.497 43.478 1.91 0.00 46.05 5.01
935 989 9.587772 AATGAAATACGTGCCAGATAGATATAC 57.412 33.333 0.00 0.00 0.00 1.47
941 1004 5.523552 TCACAATGAAATACGTGCCAGATAG 59.476 40.000 0.00 0.00 31.82 2.08
945 1008 4.094739 TCATCACAATGAAATACGTGCCAG 59.905 41.667 0.00 0.00 38.97 4.85
959 1022 7.330262 TGCGTCCATATATATGTCATCACAAT 58.670 34.615 19.11 0.00 35.64 2.71
965 1028 6.530019 TCACTGCGTCCATATATATGTCAT 57.470 37.500 19.11 0.00 31.82 3.06
970 1033 5.422012 TCCACATCACTGCGTCCATATATAT 59.578 40.000 0.00 0.00 0.00 0.86
971 1034 4.770010 TCCACATCACTGCGTCCATATATA 59.230 41.667 0.00 0.00 0.00 0.86
972 1035 3.578282 TCCACATCACTGCGTCCATATAT 59.422 43.478 0.00 0.00 0.00 0.86
973 1036 2.962421 TCCACATCACTGCGTCCATATA 59.038 45.455 0.00 0.00 0.00 0.86
981 1044 0.943835 TGAACGTCCACATCACTGCG 60.944 55.000 0.00 0.00 0.00 5.18
1003 1066 4.342359 TGTAGAAAGACCTGGTAGGAGAC 58.658 47.826 0.00 0.00 37.67 3.36
1036 1119 2.586648 AGGGACGCTGGAGAAAATTT 57.413 45.000 0.00 0.00 0.00 1.82
1040 1123 0.472471 ACAAAGGGACGCTGGAGAAA 59.528 50.000 0.00 0.00 0.00 2.52
1050 1133 3.181490 GGTGAAAACAGACACAAAGGGAC 60.181 47.826 0.00 0.00 38.57 4.46
1057 1148 3.644966 AGAAGGGTGAAAACAGACACA 57.355 42.857 0.00 0.00 38.57 3.72
1062 1155 5.277345 CGTTGTAGAAGAAGGGTGAAAACAG 60.277 44.000 0.00 0.00 0.00 3.16
1099 1248 7.166628 CGATAGTCGATTGATTGTTTAGCTT 57.833 36.000 0.00 0.00 43.74 3.74
1133 1286 2.270257 GCAGCAGCAACCACCATGA 61.270 57.895 0.00 0.00 41.58 3.07
1155 1311 2.046314 TAAGAACAGCGGCCAGGC 60.046 61.111 1.26 1.26 0.00 4.85
1165 1321 4.567537 CCCTCAACATCCATGGTAAGAACA 60.568 45.833 12.58 0.00 0.00 3.18
1172 1328 1.307647 GCCCCTCAACATCCATGGT 59.692 57.895 12.58 0.00 0.00 3.55
1175 1331 1.224592 GTCGCCCCTCAACATCCAT 59.775 57.895 0.00 0.00 0.00 3.41
1215 1401 1.478105 GGAGATGGCCGCAAGAAAAAT 59.522 47.619 0.00 0.00 43.02 1.82
1263 1449 1.086634 GCACTCAGTTGGATCGCCTC 61.087 60.000 0.00 0.00 34.31 4.70
1388 1574 3.124921 GTTGGCATCCACGACCCG 61.125 66.667 0.00 0.00 30.78 5.28
1399 1585 1.303561 GCTCATGTCCAGGTTGGCA 60.304 57.895 0.00 0.00 37.47 4.92
1506 1695 2.035321 ACAAAGTTTGCCCATGTAACCG 59.965 45.455 15.59 0.00 0.00 4.44
1555 1744 1.508632 CCACCGGTTTGTAGTCACTG 58.491 55.000 2.97 0.00 0.00 3.66
1613 1802 6.975772 AGCTTCTCGACATAATAAGAGTTGAC 59.024 38.462 0.00 0.00 32.90 3.18
1630 1819 2.095053 GCAAGAAGGCTTAAGCTTCTCG 59.905 50.000 27.49 22.23 37.46 4.04
1693 1882 1.260561 CCGTGGCTTGCGTTATCATAC 59.739 52.381 0.00 0.00 0.00 2.39
1713 1902 3.194968 TCTGAGGGATCGTACCAAAGTTC 59.805 47.826 0.00 0.00 0.00 3.01
1741 1930 7.639461 TCGTATAAAGGAAACAAAACACGAAAC 59.361 33.333 0.00 0.00 32.42 2.78
1746 1935 6.355144 CGTGTCGTATAAAGGAAACAAAACAC 59.645 38.462 0.00 0.00 29.69 3.32
1768 1960 4.379243 AAGCTCCCAGGCGTCGTG 62.379 66.667 0.00 0.00 37.29 4.35
1770 1962 4.069232 TGAAGCTCCCAGGCGTCG 62.069 66.667 0.00 0.00 42.08 5.12
1809 2001 7.834068 ATGTATAGATCACAAACTCACACAC 57.166 36.000 0.00 0.00 0.00 3.82
1866 2062 7.714377 AGAAAATGTAGAGAAGTCAGGCATATG 59.286 37.037 0.00 0.00 0.00 1.78
1907 2104 0.629596 ACCGAGTCTCCAGGGTATGA 59.370 55.000 0.00 0.00 0.00 2.15
1910 2107 1.000019 CCACCGAGTCTCCAGGGTA 60.000 63.158 0.00 0.00 0.00 3.69
1921 2118 0.179150 CGAGAAGAGAAGCCACCGAG 60.179 60.000 0.00 0.00 0.00 4.63
1932 2129 0.459237 AAGCCATCGCACGAGAAGAG 60.459 55.000 0.00 0.00 37.52 2.85
1945 2142 3.440173 CCGTAAGAATGAACACAAGCCAT 59.560 43.478 0.00 0.00 43.02 4.40
2021 2218 1.702886 CGTAGTGAGTGAAGGTGCTG 58.297 55.000 0.00 0.00 0.00 4.41
2023 2220 0.038159 AGCGTAGTGAGTGAAGGTGC 60.038 55.000 0.00 0.00 0.00 5.01
2064 2261 7.466725 GCATACCAGCAACGAACTTCAATATTA 60.467 37.037 0.00 0.00 0.00 0.98
2078 2275 6.483307 TGTAATTCTATCAGCATACCAGCAAC 59.517 38.462 0.00 0.00 36.85 4.17
2119 2327 3.857157 TTTGCAAACAGAGGGAGTACT 57.143 42.857 8.05 0.00 0.00 2.73
2144 2352 8.184192 CCAATTCGCAGAAAAGTTAGAACATAT 58.816 33.333 0.00 0.00 45.90 1.78
2145 2353 7.389330 TCCAATTCGCAGAAAAGTTAGAACATA 59.611 33.333 0.00 0.00 45.90 2.29
2160 2368 6.092533 TGTGCATATATACATCCAATTCGCAG 59.907 38.462 0.00 0.00 0.00 5.18
2185 2399 6.959639 ATGGATGAACAAACACACTAAAGT 57.040 33.333 0.00 0.00 0.00 2.66
2186 2400 7.920151 TGAAATGGATGAACAAACACACTAAAG 59.080 33.333 0.00 0.00 0.00 1.85
2211 2425 4.058124 CAATATGGACCACATACGGACTG 58.942 47.826 0.00 0.00 44.41 3.51
2214 2428 5.360649 TTTCAATATGGACCACATACGGA 57.639 39.130 0.00 0.00 44.41 4.69
2263 2482 3.244582 TGCCAAGAAACTACTCCCTACA 58.755 45.455 0.00 0.00 0.00 2.74
2265 2484 4.080526 GGATTGCCAAGAAACTACTCCCTA 60.081 45.833 0.00 0.00 0.00 3.53
2296 2519 9.632638 ACTCCTGCACATATAGAACAATTTTAT 57.367 29.630 0.00 0.00 0.00 1.40
2298 2521 7.944729 ACTCCTGCACATATAGAACAATTTT 57.055 32.000 0.00 0.00 0.00 1.82
2347 2570 1.348036 GCCAGGAAGAACAGTACCACT 59.652 52.381 0.00 0.00 0.00 4.00
2642 2865 2.426522 CAGACGGACCACATTGACATT 58.573 47.619 0.00 0.00 0.00 2.71
3286 3527 4.681978 ACGCTGTCAACGCTCCCC 62.682 66.667 0.00 0.00 0.00 4.81
3347 3588 2.615986 TGGTAAGGCTCCACTACAGA 57.384 50.000 0.00 0.00 0.00 3.41
3439 3858 7.797123 CACAAGATAAGTTTTTCACCTCGTAAC 59.203 37.037 0.00 0.00 0.00 2.50
3594 4030 2.810032 CCTTTTGGGCAATGGGACAAAC 60.810 50.000 0.00 0.00 37.80 2.93
3676 4136 2.266554 GTTCTCGCCATCAGTTCAGAG 58.733 52.381 0.00 0.00 0.00 3.35
3692 4154 3.681034 CGAGGCATCTTTCATCAGGTTCT 60.681 47.826 0.00 0.00 0.00 3.01
3694 4156 2.026822 ACGAGGCATCTTTCATCAGGTT 60.027 45.455 0.00 0.00 0.00 3.50
3695 4157 1.556911 ACGAGGCATCTTTCATCAGGT 59.443 47.619 0.00 0.00 0.00 4.00
3696 4158 1.938577 CACGAGGCATCTTTCATCAGG 59.061 52.381 0.00 0.00 0.00 3.86
3697 4159 1.329906 GCACGAGGCATCTTTCATCAG 59.670 52.381 0.00 0.00 43.97 2.90
3698 4160 1.372582 GCACGAGGCATCTTTCATCA 58.627 50.000 0.00 0.00 43.97 3.07
3709 4171 1.727335 GAGAAAACTACAGCACGAGGC 59.273 52.381 0.00 0.00 45.30 4.70
3710 4172 3.305398 AGAGAAAACTACAGCACGAGG 57.695 47.619 0.00 0.00 0.00 4.63
3711 4173 4.384247 CAGAAGAGAAAACTACAGCACGAG 59.616 45.833 0.00 0.00 0.00 4.18
3720 4182 2.037251 ACAGCGCCAGAAGAGAAAACTA 59.963 45.455 2.29 0.00 0.00 2.24
3727 4189 0.947244 AACAAACAGCGCCAGAAGAG 59.053 50.000 2.29 0.00 0.00 2.85
3757 4219 0.911769 TGCCATCAGGAACTACAGGG 59.088 55.000 0.00 0.00 36.02 4.45
3765 4227 1.956636 GCAAGGATGTGCCATCAGGAA 60.957 52.381 14.57 0.00 38.66 3.36
3784 4246 0.389426 CTTCAGTTGGGCTGCAATGC 60.389 55.000 0.00 0.00 44.66 3.56
3785 4247 1.250328 TCTTCAGTTGGGCTGCAATG 58.750 50.000 0.50 0.00 44.66 2.82
3786 4248 1.891150 CTTCTTCAGTTGGGCTGCAAT 59.109 47.619 0.50 0.00 44.66 3.56
3787 4249 1.321474 CTTCTTCAGTTGGGCTGCAA 58.679 50.000 0.50 0.00 44.66 4.08
3788 4250 1.174712 GCTTCTTCAGTTGGGCTGCA 61.175 55.000 0.50 0.00 44.66 4.41
3820 4282 7.672351 TTTTTGTCATAACGTGTGAACATTC 57.328 32.000 5.57 0.00 0.00 2.67
3822 4284 6.640499 CCATTTTTGTCATAACGTGTGAACAT 59.360 34.615 5.57 0.00 0.00 2.71
3840 4303 5.238432 GGTTCCGAATTTTTCTGCCATTTTT 59.762 36.000 0.00 0.00 0.00 1.94
3863 4328 4.024670 AACTACTCCTAGTAGGTTGCAGG 58.975 47.826 16.02 5.79 45.96 4.85
3895 4361 7.365741 ACTGATCTGTTGAAAGTAATTGCAAG 58.634 34.615 4.94 0.00 0.00 4.01
3920 4394 5.359576 ACCTCACTGAAAAACAAGTGCATAA 59.640 36.000 0.00 0.00 32.16 1.90
3952 4426 2.528743 CGGCTGCGCTGATAACAGG 61.529 63.158 19.32 0.00 43.62 4.00
3963 4437 1.516169 GTTATTTTGCCCGGCTGCG 60.516 57.895 11.61 0.00 0.00 5.18
4024 4505 9.829507 AAAGTGTAATTCATGTCAAATCCAAAA 57.170 25.926 0.00 0.00 0.00 2.44
4059 4545 4.256920 CGCCCTTTAATCTATGGGATCTG 58.743 47.826 0.00 0.00 42.11 2.90
4078 4567 4.545823 TTTATTACTACATGCAAGCGCC 57.454 40.909 2.29 0.00 37.32 6.53
4115 4607 1.478105 GCTGCCTCACCCCTAAAAATG 59.522 52.381 0.00 0.00 0.00 2.32
4116 4608 1.359130 AGCTGCCTCACCCCTAAAAAT 59.641 47.619 0.00 0.00 0.00 1.82
4182 4704 3.536917 CGGCGAGGGGCATGTCTA 61.537 66.667 0.00 0.00 46.16 2.59
4237 4760 4.021925 GCGGTTGGCAGGGAGACT 62.022 66.667 0.00 0.00 42.87 3.24
4290 4874 0.616891 GCGAAAGGGGAGGTTAAGGA 59.383 55.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.