Multiple sequence alignment - TraesCS3D01G284400

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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 TraesCS3D01G284400 chr3D 100.000 2588 0 0 1 2588 393561149 393563736 0.000000e+00 4780
1 TraesCS3D01G284400 chr3A 90.909 1100 59 19 697 1762 513539176 513540268 0.000000e+00 1439
2 TraesCS3D01G284400 chr3A 91.337 531 29 4 1797 2312 513540411 513540939 0.000000e+00 710
3 TraesCS3D01G284400 chr3A 89.434 530 23 10 195 711 513538644 513539153 2.810000e-179 638
4 TraesCS3D01G284400 chr3A 92.135 178 7 5 2411 2588 513543388 513543558 7.150000e-61 244
5 TraesCS3D01G284400 chr3A 88.344 163 17 2 15 176 721565259 721565420 7.310000e-46 195
6 TraesCS3D01G284400 chr3B 93.103 812 42 7 195 996 513530206 513531013 0.000000e+00 1177
7 TraesCS3D01G284400 chr3B 91.971 548 31 5 1263 1797 513531596 513532143 0.000000e+00 756
8 TraesCS3D01G284400 chr3B 92.478 452 17 7 1797 2233 513532224 513532673 4.700000e-177 630
9 TraesCS3D01G284400 chr3B 89.835 364 24 7 2229 2588 513533742 513534096 3.040000e-124 455
10 TraesCS3D01G284400 chr3B 94.262 244 14 0 985 1228 513531036 513531279 8.740000e-100 374
11 TraesCS3D01G284400 chr4B 89.809 157 14 2 21 176 109316755 109316600 1.570000e-47 200
12 TraesCS3D01G284400 chr2A 89.375 160 15 2 18 176 78553720 78553878 1.570000e-47 200
13 TraesCS3D01G284400 chr2A 89.375 160 15 2 18 176 780720817 780720975 1.570000e-47 200
14 TraesCS3D01G284400 chr2A 86.740 181 20 4 1 179 562090894 562091072 5.650000e-47 198
15 TraesCS3D01G284400 chr2A 86.441 177 21 3 1 176 61799270 61799096 9.450000e-45 191
16 TraesCS3D01G284400 chr5A 89.172 157 15 2 21 176 312262184 312262029 7.310000e-46 195
17 TraesCS3D01G284400 chr6B 86.857 175 20 3 3 176 544695714 544695886 2.630000e-45 193
18 TraesCS3D01G284400 chr1B 86.441 177 20 4 15 189 15190154 15190328 9.450000e-45 191


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 TraesCS3D01G284400 chr3D 393561149 393563736 2587 False 4780.00 4780 100.00000 1 2588 1 chr3D.!!$F1 2587
1 TraesCS3D01G284400 chr3A 513538644 513543558 4914 False 757.75 1439 90.95375 195 2588 4 chr3A.!!$F2 2393
2 TraesCS3D01G284400 chr3B 513530206 513534096 3890 False 678.40 1177 92.32980 195 2588 5 chr3B.!!$F1 2393

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
151 152 0.394565 ATATGCCGGCTCAGTTCTCC 59.605 55.0 29.70 0.00 0.00 3.71 F
1024 1139 0.108377 TTTGCTCGCGAGATGCCTTA 60.108 50.0 38.74 13.11 42.08 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1198 1313 0.657659 CGCGCATACGTACTCTGGAG 60.658 60.0 8.75 0.0 42.83 3.86 R
2329 6161 0.037326 CATGCACACCTACTCCACGT 60.037 55.0 0.00 0.0 0.00 4.49 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
23 24 5.789643 TCAGGATTTAAGTTTTTGCTGCT 57.210 34.783 0.00 0.00 0.00 4.24
24 25 5.772521 TCAGGATTTAAGTTTTTGCTGCTC 58.227 37.500 0.00 0.00 0.00 4.26
25 26 4.618489 CAGGATTTAAGTTTTTGCTGCTCG 59.382 41.667 0.00 0.00 0.00 5.03
26 27 3.364920 GGATTTAAGTTTTTGCTGCTCGC 59.635 43.478 0.00 0.00 39.77 5.03
35 36 3.840831 TGCTGCTCGCACTATTCTT 57.159 47.368 0.00 0.00 45.47 2.52
36 37 1.362768 TGCTGCTCGCACTATTCTTG 58.637 50.000 0.00 0.00 45.47 3.02
37 38 0.654683 GCTGCTCGCACTATTCTTGG 59.345 55.000 0.00 0.00 38.92 3.61
38 39 1.740380 GCTGCTCGCACTATTCTTGGA 60.740 52.381 0.00 0.00 38.92 3.53
39 40 2.831333 CTGCTCGCACTATTCTTGGAT 58.169 47.619 0.00 0.00 0.00 3.41
40 41 3.201290 CTGCTCGCACTATTCTTGGATT 58.799 45.455 0.00 0.00 0.00 3.01
41 42 3.609853 TGCTCGCACTATTCTTGGATTT 58.390 40.909 0.00 0.00 0.00 2.17
42 43 4.765273 TGCTCGCACTATTCTTGGATTTA 58.235 39.130 0.00 0.00 0.00 1.40
43 44 5.368145 TGCTCGCACTATTCTTGGATTTAT 58.632 37.500 0.00 0.00 0.00 1.40
44 45 5.237127 TGCTCGCACTATTCTTGGATTTATG 59.763 40.000 0.00 0.00 0.00 1.90
45 46 5.237344 GCTCGCACTATTCTTGGATTTATGT 59.763 40.000 0.00 0.00 0.00 2.29
46 47 6.564873 GCTCGCACTATTCTTGGATTTATGTC 60.565 42.308 0.00 0.00 0.00 3.06
47 48 6.345298 TCGCACTATTCTTGGATTTATGTCA 58.655 36.000 0.00 0.00 0.00 3.58
48 49 6.479990 TCGCACTATTCTTGGATTTATGTCAG 59.520 38.462 0.00 0.00 0.00 3.51
49 50 6.293081 CGCACTATTCTTGGATTTATGTCAGG 60.293 42.308 0.00 0.00 0.00 3.86
50 51 6.767902 GCACTATTCTTGGATTTATGTCAGGA 59.232 38.462 0.00 0.00 0.00 3.86
51 52 7.446625 GCACTATTCTTGGATTTATGTCAGGAT 59.553 37.037 0.00 0.00 0.00 3.24
52 53 9.347240 CACTATTCTTGGATTTATGTCAGGATT 57.653 33.333 0.00 0.00 0.00 3.01
53 54 9.927081 ACTATTCTTGGATTTATGTCAGGATTT 57.073 29.630 0.00 0.00 0.00 2.17
56 57 8.648698 TTCTTGGATTTATGTCAGGATTTTCA 57.351 30.769 0.00 0.00 0.00 2.69
57 58 8.284945 TCTTGGATTTATGTCAGGATTTTCAG 57.715 34.615 0.00 0.00 0.00 3.02
58 59 6.455360 TGGATTTATGTCAGGATTTTCAGC 57.545 37.500 0.00 0.00 0.00 4.26
59 60 5.066375 TGGATTTATGTCAGGATTTTCAGCG 59.934 40.000 0.00 0.00 0.00 5.18
60 61 5.296780 GGATTTATGTCAGGATTTTCAGCGA 59.703 40.000 0.00 0.00 0.00 4.93
61 62 6.016777 GGATTTATGTCAGGATTTTCAGCGAT 60.017 38.462 0.00 0.00 0.00 4.58
62 63 5.739752 TTATGTCAGGATTTTCAGCGATG 57.260 39.130 0.00 0.00 0.00 3.84
63 64 1.739466 TGTCAGGATTTTCAGCGATGC 59.261 47.619 0.00 0.00 0.00 3.91
64 65 1.009078 TCAGGATTTTCAGCGATGCG 58.991 50.000 0.00 0.00 0.00 4.73
76 77 2.762360 CGATGCGCTTTTAGTGGGA 58.238 52.632 9.73 0.00 0.00 4.37
77 78 1.299541 CGATGCGCTTTTAGTGGGAT 58.700 50.000 9.73 0.00 0.00 3.85
78 79 1.003545 CGATGCGCTTTTAGTGGGATG 60.004 52.381 9.73 0.00 0.00 3.51
79 80 2.288666 GATGCGCTTTTAGTGGGATGA 58.711 47.619 9.73 0.00 0.00 2.92
80 81 1.737838 TGCGCTTTTAGTGGGATGAG 58.262 50.000 9.73 0.00 0.00 2.90
81 82 1.277842 TGCGCTTTTAGTGGGATGAGA 59.722 47.619 9.73 0.00 0.00 3.27
82 83 1.666189 GCGCTTTTAGTGGGATGAGAC 59.334 52.381 0.00 0.00 0.00 3.36
83 84 1.927174 CGCTTTTAGTGGGATGAGACG 59.073 52.381 0.00 0.00 0.00 4.18
84 85 2.674177 CGCTTTTAGTGGGATGAGACGT 60.674 50.000 0.00 0.00 0.00 4.34
85 86 3.335579 GCTTTTAGTGGGATGAGACGTT 58.664 45.455 0.00 0.00 0.00 3.99
86 87 3.371285 GCTTTTAGTGGGATGAGACGTTC 59.629 47.826 0.00 0.00 0.00 3.95
87 88 3.604875 TTTAGTGGGATGAGACGTTCC 57.395 47.619 0.00 0.00 0.00 3.62
100 101 2.080286 ACGTTCCCGTCAATGAAGAG 57.920 50.000 0.00 0.00 46.28 2.85
101 102 1.616865 ACGTTCCCGTCAATGAAGAGA 59.383 47.619 0.00 0.00 46.28 3.10
102 103 1.993370 CGTTCCCGTCAATGAAGAGAC 59.007 52.381 0.00 0.00 0.00 3.36
123 124 4.098532 CGCCTACGTGAATTCGTAAATC 57.901 45.455 0.00 0.00 43.89 2.17
124 125 3.795101 CGCCTACGTGAATTCGTAAATCT 59.205 43.478 0.00 0.00 43.89 2.40
125 126 4.085721 CGCCTACGTGAATTCGTAAATCTC 60.086 45.833 0.00 0.00 43.89 2.75
126 127 4.802039 GCCTACGTGAATTCGTAAATCTCA 59.198 41.667 0.00 0.00 43.89 3.27
127 128 5.290158 GCCTACGTGAATTCGTAAATCTCAA 59.710 40.000 0.00 0.00 43.89 3.02
128 129 6.508088 GCCTACGTGAATTCGTAAATCTCAAG 60.508 42.308 0.00 0.00 43.89 3.02
129 130 6.750501 CCTACGTGAATTCGTAAATCTCAAGA 59.249 38.462 0.00 0.00 43.89 3.02
130 131 7.435488 CCTACGTGAATTCGTAAATCTCAAGAT 59.565 37.037 0.00 0.00 43.89 2.40
131 132 6.993878 ACGTGAATTCGTAAATCTCAAGATG 58.006 36.000 0.04 0.00 42.35 2.90
132 133 6.811665 ACGTGAATTCGTAAATCTCAAGATGA 59.188 34.615 0.04 0.00 42.35 2.92
133 134 7.492669 ACGTGAATTCGTAAATCTCAAGATGAT 59.507 33.333 0.04 0.00 42.35 2.45
134 135 8.968242 CGTGAATTCGTAAATCTCAAGATGATA 58.032 33.333 0.04 0.00 34.49 2.15
137 138 9.752274 GAATTCGTAAATCTCAAGATGATATGC 57.248 33.333 0.00 0.00 34.49 3.14
138 139 7.658179 TTCGTAAATCTCAAGATGATATGCC 57.342 36.000 0.00 0.00 34.49 4.40
139 140 5.863935 TCGTAAATCTCAAGATGATATGCCG 59.136 40.000 0.00 0.00 34.49 5.69
140 141 5.062683 CGTAAATCTCAAGATGATATGCCGG 59.937 44.000 0.00 0.00 34.49 6.13
141 142 2.462456 TCTCAAGATGATATGCCGGC 57.538 50.000 22.73 22.73 0.00 6.13
142 143 1.973515 TCTCAAGATGATATGCCGGCT 59.026 47.619 29.70 15.76 0.00 5.52
143 144 2.028658 TCTCAAGATGATATGCCGGCTC 60.029 50.000 29.70 17.89 0.00 4.70
144 145 1.693606 TCAAGATGATATGCCGGCTCA 59.306 47.619 29.70 23.34 0.00 4.26
145 146 2.074576 CAAGATGATATGCCGGCTCAG 58.925 52.381 29.70 7.35 0.00 3.35
146 147 1.346062 AGATGATATGCCGGCTCAGT 58.654 50.000 29.70 13.44 0.00 3.41
147 148 1.696336 AGATGATATGCCGGCTCAGTT 59.304 47.619 29.70 9.04 0.00 3.16
148 149 2.072298 GATGATATGCCGGCTCAGTTC 58.928 52.381 29.70 14.27 0.00 3.01
149 150 1.123077 TGATATGCCGGCTCAGTTCT 58.877 50.000 29.70 4.90 0.00 3.01
150 151 1.069204 TGATATGCCGGCTCAGTTCTC 59.931 52.381 29.70 14.28 0.00 2.87
151 152 0.394565 ATATGCCGGCTCAGTTCTCC 59.605 55.000 29.70 0.00 0.00 3.71
152 153 1.686325 TATGCCGGCTCAGTTCTCCC 61.686 60.000 29.70 0.00 0.00 4.30
153 154 4.821589 GCCGGCTCAGTTCTCCCG 62.822 72.222 22.15 0.00 40.39 5.14
154 155 3.068691 CCGGCTCAGTTCTCCCGA 61.069 66.667 0.00 0.00 43.20 5.14
155 156 2.646175 CCGGCTCAGTTCTCCCGAA 61.646 63.158 0.00 0.00 43.20 4.30
156 157 1.153745 CGGCTCAGTTCTCCCGAAG 60.154 63.158 0.00 0.00 43.20 3.79
173 174 3.854666 CGAAGGTGCTCATAGGGATATG 58.145 50.000 0.00 0.00 0.00 1.78
174 175 3.368843 CGAAGGTGCTCATAGGGATATGG 60.369 52.174 0.00 0.00 0.00 2.74
175 176 3.282135 AGGTGCTCATAGGGATATGGT 57.718 47.619 0.00 0.00 0.00 3.55
176 177 3.602608 AGGTGCTCATAGGGATATGGTT 58.397 45.455 0.00 0.00 0.00 3.67
177 178 3.328931 AGGTGCTCATAGGGATATGGTTG 59.671 47.826 0.00 0.00 0.00 3.77
178 179 3.073062 GGTGCTCATAGGGATATGGTTGT 59.927 47.826 0.00 0.00 0.00 3.32
179 180 4.286032 GGTGCTCATAGGGATATGGTTGTA 59.714 45.833 0.00 0.00 0.00 2.41
180 181 5.238583 GTGCTCATAGGGATATGGTTGTAC 58.761 45.833 0.00 0.00 0.00 2.90
181 182 5.012148 GTGCTCATAGGGATATGGTTGTACT 59.988 44.000 0.00 0.00 0.00 2.73
182 183 6.210784 GTGCTCATAGGGATATGGTTGTACTA 59.789 42.308 0.00 0.00 0.00 1.82
183 184 6.959954 TGCTCATAGGGATATGGTTGTACTAT 59.040 38.462 0.00 0.00 0.00 2.12
184 185 7.093333 TGCTCATAGGGATATGGTTGTACTATG 60.093 40.741 0.00 0.00 38.27 2.23
185 186 7.093289 GCTCATAGGGATATGGTTGTACTATGT 60.093 40.741 0.00 0.00 38.16 2.29
186 187 8.736097 TCATAGGGATATGGTTGTACTATGTT 57.264 34.615 0.00 0.00 38.16 2.71
187 188 9.166222 TCATAGGGATATGGTTGTACTATGTTT 57.834 33.333 0.00 0.00 38.16 2.83
229 231 5.105917 CGCTTTATCCTTTACACACCCAATT 60.106 40.000 0.00 0.00 0.00 2.32
301 303 1.401761 AACAAATGACAGTGGCAGCA 58.598 45.000 4.25 0.00 0.00 4.41
336 338 3.449737 AGTTTGCATCATAGCCAGCATTT 59.550 39.130 0.00 0.00 36.80 2.32
385 387 6.149474 CCATTTCCACGAGAACAAGTTATCTT 59.851 38.462 6.09 0.00 32.95 2.40
402 406 7.945134 AGTTATCTTCAGCAACAGAAAAATGT 58.055 30.769 0.00 0.00 33.96 2.71
433 437 6.805713 TGACTTTGCAAGAGTGATCGATATA 58.194 36.000 15.84 0.00 0.00 0.86
478 483 2.415825 TCGATCCACGATCAGGACC 58.584 57.895 6.06 0.00 46.45 4.46
534 547 3.756727 GCCCCTTTGCTGCTCTGC 61.757 66.667 0.00 0.00 0.00 4.26
689 705 5.624344 TCCGTATTATCCATCTTCTCGAC 57.376 43.478 0.00 0.00 0.00 4.20
714 762 6.236558 AGGGTACAAAAGGCTCTATTAGAC 57.763 41.667 0.00 0.00 0.00 2.59
924 1005 1.091537 TGCACGCCAGCCTATAAAAC 58.908 50.000 0.00 0.00 0.00 2.43
935 1016 4.571176 CAGCCTATAAAACGAACCCTCTTC 59.429 45.833 0.00 0.00 0.00 2.87
939 1020 6.043411 CCTATAAAACGAACCCTCTTCTCAG 58.957 44.000 0.00 0.00 0.00 3.35
940 1021 2.841442 AAACGAACCCTCTTCTCAGG 57.159 50.000 0.00 0.00 0.00 3.86
944 1025 1.825474 CGAACCCTCTTCTCAGGCTTA 59.175 52.381 0.00 0.00 31.23 3.09
948 1029 1.208293 CCCTCTTCTCAGGCTTACCAC 59.792 57.143 0.00 0.00 39.06 4.16
963 1044 0.684535 ACCACGATCATCACACCACA 59.315 50.000 0.00 0.00 0.00 4.17
964 1045 1.078709 CCACGATCATCACACCACAC 58.921 55.000 0.00 0.00 0.00 3.82
965 1046 1.607767 CCACGATCATCACACCACACA 60.608 52.381 0.00 0.00 0.00 3.72
966 1047 1.460743 CACGATCATCACACCACACAC 59.539 52.381 0.00 0.00 0.00 3.82
983 1064 3.195610 ACACACGCTCTCCTTTGATCATA 59.804 43.478 0.00 0.00 0.00 2.15
992 1073 6.685116 GCTCTCCTTTGATCATAGTAGCAAGT 60.685 42.308 18.72 0.00 0.00 3.16
1011 1126 2.484264 AGTTACGACAATGGCTTTGCTC 59.516 45.455 12.54 8.69 39.03 4.26
1024 1139 0.108377 TTTGCTCGCGAGATGCCTTA 60.108 50.000 38.74 13.11 42.08 2.69
1041 1156 1.626356 TTATGCTCTGCCTCGCCCTT 61.626 55.000 0.00 0.00 0.00 3.95
1054 1169 2.972819 GCCCTTGTGGTCCTCTCCC 61.973 68.421 0.00 0.00 36.04 4.30
1060 1175 3.615811 TGGTCCTCTCCCTGGGCT 61.616 66.667 8.22 0.00 0.00 5.19
1211 1326 1.452651 CCCCGCTCCAGAGTACGTA 60.453 63.158 0.00 0.00 0.00 3.57
1249 1371 1.811965 CCACGCTGATCAAACCATCAA 59.188 47.619 0.00 0.00 32.24 2.57
1254 1376 2.095059 GCTGATCAAACCATCAAGCGTT 60.095 45.455 0.00 0.00 32.24 4.84
1256 1378 4.549458 CTGATCAAACCATCAAGCGTTTT 58.451 39.130 0.00 0.00 32.24 2.43
1259 1381 3.963665 TCAAACCATCAAGCGTTTTCTG 58.036 40.909 0.00 0.00 29.85 3.02
1261 1383 4.278170 TCAAACCATCAAGCGTTTTCTGAT 59.722 37.500 0.00 0.00 29.85 2.90
1272 1669 3.737305 CGTTTTCTGATTTCGCCTCTTC 58.263 45.455 0.00 0.00 0.00 2.87
1278 1675 3.189287 TCTGATTTCGCCTCTTCTTTTGC 59.811 43.478 0.00 0.00 0.00 3.68
1279 1676 3.149196 TGATTTCGCCTCTTCTTTTGCT 58.851 40.909 0.00 0.00 0.00 3.91
1401 1798 3.114616 CAGTCAGCGCCCTTCACG 61.115 66.667 2.29 0.00 0.00 4.35
1566 1963 2.506438 GACTTCGTCTTCGGGCCG 60.506 66.667 22.51 22.51 37.69 6.13
1831 2351 3.302415 GCATTGTGGTTGAAAGAAAACGC 60.302 43.478 0.00 0.00 0.00 4.84
1832 2352 2.181426 TGTGGTTGAAAGAAAACGCG 57.819 45.000 3.53 3.53 29.57 6.01
1837 2357 1.064357 GTTGAAAGAAAACGCGGTCCA 59.936 47.619 12.47 0.00 0.00 4.02
1875 2409 7.406799 AGTTGCTTTTGGAAAATATTTGTCG 57.593 32.000 0.39 0.00 0.00 4.35
1918 2453 7.218145 TCTAATTTTGAATAACTCTCGCGAC 57.782 36.000 3.71 0.00 0.00 5.19
1954 2489 1.653094 GCGGATGTTGATTTGGCCGA 61.653 55.000 0.00 0.00 41.11 5.54
1988 2523 7.724305 TCCGTTTGGCTCTATATAATTTGTC 57.276 36.000 0.00 0.00 34.14 3.18
2061 2596 1.971167 GGGTTTCATGGCGCTGACA 60.971 57.895 7.64 0.00 0.00 3.58
2165 2700 0.447801 CAAACACCCACTAGCATCGC 59.552 55.000 0.00 0.00 0.00 4.58
2281 3889 0.478507 ACACCTTCCTTGGGGAGTTG 59.521 55.000 0.00 0.00 43.29 3.16
2312 3920 3.561725 GGCTATTGCGAGAAGTTAGCATT 59.438 43.478 5.99 1.95 40.83 3.56
2329 6161 4.441792 AGCATTGATATTGTAGCGTGTCA 58.558 39.130 0.00 0.00 0.00 3.58
2330 6162 4.271049 AGCATTGATATTGTAGCGTGTCAC 59.729 41.667 0.00 0.00 0.00 3.67
2353 6185 4.440940 CGTGGAGTAGGTGTGCATGTATTA 60.441 45.833 0.00 0.00 0.00 0.98
2379 6211 0.804933 GTAACATCGACGTGGAGGGC 60.805 60.000 16.45 3.03 0.00 5.19
2409 6367 6.997942 ACCCCCACTCTCTCTTTAATATAC 57.002 41.667 0.00 0.00 0.00 1.47
2441 6399 7.022979 CACATTCGTGCATATTCAAGAAGAAA 58.977 34.615 9.24 0.00 37.73 2.52
2442 6400 7.538334 CACATTCGTGCATATTCAAGAAGAAAA 59.462 33.333 9.24 0.00 37.73 2.29
2443 6401 8.081633 ACATTCGTGCATATTCAAGAAGAAAAA 58.918 29.630 9.24 0.00 40.22 1.94
2444 6402 9.079833 CATTCGTGCATATTCAAGAAGAAAAAT 57.920 29.630 9.24 0.00 40.22 1.82
2506 6464 7.458409 AATGCTCAGTTGTGTGAGATTTTAT 57.542 32.000 5.05 0.00 46.02 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.350629 AGCAGCAAAAACTTAAATCCTGAT 57.649 33.333 0.00 0.00 0.00 2.90
2 3 4.618489 CGAGCAGCAAAAACTTAAATCCTG 59.382 41.667 0.00 0.00 0.00 3.86
3 4 4.798574 CGAGCAGCAAAAACTTAAATCCT 58.201 39.130 0.00 0.00 0.00 3.24
19 20 2.299993 TCCAAGAATAGTGCGAGCAG 57.700 50.000 0.00 0.00 0.00 4.24
20 21 2.988010 ATCCAAGAATAGTGCGAGCA 57.012 45.000 0.00 0.00 0.00 4.26
21 22 5.237344 ACATAAATCCAAGAATAGTGCGAGC 59.763 40.000 0.00 0.00 0.00 5.03
22 23 6.479990 TGACATAAATCCAAGAATAGTGCGAG 59.520 38.462 0.00 0.00 0.00 5.03
23 24 6.345298 TGACATAAATCCAAGAATAGTGCGA 58.655 36.000 0.00 0.00 0.00 5.10
24 25 6.293081 CCTGACATAAATCCAAGAATAGTGCG 60.293 42.308 0.00 0.00 0.00 5.34
25 26 6.767902 TCCTGACATAAATCCAAGAATAGTGC 59.232 38.462 0.00 0.00 0.00 4.40
26 27 8.915057 ATCCTGACATAAATCCAAGAATAGTG 57.085 34.615 0.00 0.00 0.00 2.74
27 28 9.927081 AAATCCTGACATAAATCCAAGAATAGT 57.073 29.630 0.00 0.00 0.00 2.12
30 31 9.258629 TGAAAATCCTGACATAAATCCAAGAAT 57.741 29.630 0.00 0.00 0.00 2.40
31 32 8.648698 TGAAAATCCTGACATAAATCCAAGAA 57.351 30.769 0.00 0.00 0.00 2.52
32 33 7.148018 GCTGAAAATCCTGACATAAATCCAAGA 60.148 37.037 0.00 0.00 0.00 3.02
33 34 6.976925 GCTGAAAATCCTGACATAAATCCAAG 59.023 38.462 0.00 0.00 0.00 3.61
34 35 6.404623 CGCTGAAAATCCTGACATAAATCCAA 60.405 38.462 0.00 0.00 0.00 3.53
35 36 5.066375 CGCTGAAAATCCTGACATAAATCCA 59.934 40.000 0.00 0.00 0.00 3.41
36 37 5.296780 TCGCTGAAAATCCTGACATAAATCC 59.703 40.000 0.00 0.00 0.00 3.01
37 38 6.363577 TCGCTGAAAATCCTGACATAAATC 57.636 37.500 0.00 0.00 0.00 2.17
38 39 6.732154 CATCGCTGAAAATCCTGACATAAAT 58.268 36.000 0.00 0.00 0.00 1.40
39 40 5.449041 GCATCGCTGAAAATCCTGACATAAA 60.449 40.000 0.00 0.00 0.00 1.40
40 41 4.035558 GCATCGCTGAAAATCCTGACATAA 59.964 41.667 0.00 0.00 0.00 1.90
41 42 3.561310 GCATCGCTGAAAATCCTGACATA 59.439 43.478 0.00 0.00 0.00 2.29
42 43 2.357009 GCATCGCTGAAAATCCTGACAT 59.643 45.455 0.00 0.00 0.00 3.06
43 44 1.739466 GCATCGCTGAAAATCCTGACA 59.261 47.619 0.00 0.00 0.00 3.58
44 45 1.267732 CGCATCGCTGAAAATCCTGAC 60.268 52.381 0.00 0.00 0.00 3.51
45 46 1.009078 CGCATCGCTGAAAATCCTGA 58.991 50.000 0.00 0.00 0.00 3.86
46 47 3.521534 CGCATCGCTGAAAATCCTG 57.478 52.632 0.00 0.00 0.00 3.86
58 59 1.003545 CATCCCACTAAAAGCGCATCG 60.004 52.381 11.47 0.00 0.00 3.84
59 60 2.288666 TCATCCCACTAAAAGCGCATC 58.711 47.619 11.47 0.00 0.00 3.91
60 61 2.092968 TCTCATCCCACTAAAAGCGCAT 60.093 45.455 11.47 0.00 0.00 4.73
61 62 1.277842 TCTCATCCCACTAAAAGCGCA 59.722 47.619 11.47 0.00 0.00 6.09
62 63 1.666189 GTCTCATCCCACTAAAAGCGC 59.334 52.381 0.00 0.00 0.00 5.92
63 64 1.927174 CGTCTCATCCCACTAAAAGCG 59.073 52.381 0.00 0.00 0.00 4.68
64 65 2.973945 ACGTCTCATCCCACTAAAAGC 58.026 47.619 0.00 0.00 0.00 3.51
65 66 3.933332 GGAACGTCTCATCCCACTAAAAG 59.067 47.826 0.00 0.00 0.00 2.27
66 67 3.934068 GGAACGTCTCATCCCACTAAAA 58.066 45.455 0.00 0.00 0.00 1.52
67 68 3.604875 GGAACGTCTCATCCCACTAAA 57.395 47.619 0.00 0.00 0.00 1.85
89 90 2.186076 CGTAGGCGTCTCTTCATTGAC 58.814 52.381 0.00 0.00 0.00 3.18
90 91 2.561733 CGTAGGCGTCTCTTCATTGA 57.438 50.000 0.00 0.00 0.00 2.57
102 103 3.795101 AGATTTACGAATTCACGTAGGCG 59.205 43.478 6.22 0.00 46.60 5.52
103 104 4.802039 TGAGATTTACGAATTCACGTAGGC 59.198 41.667 6.22 0.00 46.60 3.93
104 105 6.750501 TCTTGAGATTTACGAATTCACGTAGG 59.249 38.462 6.22 0.00 46.60 3.18
105 106 7.736031 TCTTGAGATTTACGAATTCACGTAG 57.264 36.000 6.22 0.00 46.60 3.51
106 107 7.971722 TCATCTTGAGATTTACGAATTCACGTA 59.028 33.333 6.22 0.60 38.89 3.57
107 108 6.811665 TCATCTTGAGATTTACGAATTCACGT 59.188 34.615 6.22 1.65 40.18 4.49
108 109 7.221828 TCATCTTGAGATTTACGAATTCACG 57.778 36.000 6.22 0.00 34.34 4.35
111 112 9.752274 GCATATCATCTTGAGATTTACGAATTC 57.248 33.333 0.00 0.00 31.21 2.17
112 113 8.725148 GGCATATCATCTTGAGATTTACGAATT 58.275 33.333 0.00 0.00 31.21 2.17
113 114 7.063898 CGGCATATCATCTTGAGATTTACGAAT 59.936 37.037 0.00 0.00 31.21 3.34
114 115 6.366061 CGGCATATCATCTTGAGATTTACGAA 59.634 38.462 0.00 0.00 31.21 3.85
115 116 5.863935 CGGCATATCATCTTGAGATTTACGA 59.136 40.000 0.00 0.00 31.21 3.43
116 117 5.062683 CCGGCATATCATCTTGAGATTTACG 59.937 44.000 0.00 0.00 31.21 3.18
117 118 5.163814 GCCGGCATATCATCTTGAGATTTAC 60.164 44.000 24.80 0.00 31.21 2.01
118 119 4.937620 GCCGGCATATCATCTTGAGATTTA 59.062 41.667 24.80 0.00 31.21 1.40
119 120 3.755378 GCCGGCATATCATCTTGAGATTT 59.245 43.478 24.80 0.00 31.21 2.17
120 121 3.008813 AGCCGGCATATCATCTTGAGATT 59.991 43.478 31.54 0.00 31.21 2.40
121 122 2.570752 AGCCGGCATATCATCTTGAGAT 59.429 45.455 31.54 0.00 34.56 2.75
122 123 1.973515 AGCCGGCATATCATCTTGAGA 59.026 47.619 31.54 0.00 0.00 3.27
123 124 2.289257 TGAGCCGGCATATCATCTTGAG 60.289 50.000 31.54 0.00 0.00 3.02
124 125 1.693606 TGAGCCGGCATATCATCTTGA 59.306 47.619 31.54 0.00 0.00 3.02
125 126 2.074576 CTGAGCCGGCATATCATCTTG 58.925 52.381 31.54 7.95 0.00 3.02
126 127 1.696336 ACTGAGCCGGCATATCATCTT 59.304 47.619 31.54 3.33 0.00 2.40
127 128 1.346062 ACTGAGCCGGCATATCATCT 58.654 50.000 31.54 4.27 0.00 2.90
128 129 2.072298 GAACTGAGCCGGCATATCATC 58.928 52.381 31.54 16.99 0.00 2.92
129 130 1.696336 AGAACTGAGCCGGCATATCAT 59.304 47.619 31.54 9.70 0.00 2.45
130 131 1.069204 GAGAACTGAGCCGGCATATCA 59.931 52.381 31.54 22.44 0.00 2.15
131 132 1.606737 GGAGAACTGAGCCGGCATATC 60.607 57.143 31.54 18.63 0.00 1.63
132 133 0.394565 GGAGAACTGAGCCGGCATAT 59.605 55.000 31.54 8.11 0.00 1.78
133 134 1.686325 GGGAGAACTGAGCCGGCATA 61.686 60.000 31.54 16.21 0.00 3.14
134 135 2.586792 GGAGAACTGAGCCGGCAT 59.413 61.111 31.54 14.28 0.00 4.40
135 136 3.706373 GGGAGAACTGAGCCGGCA 61.706 66.667 31.54 7.98 0.00 5.69
136 137 4.821589 CGGGAGAACTGAGCCGGC 62.822 72.222 21.89 21.89 0.00 6.13
137 138 2.564553 CTTCGGGAGAACTGAGCCGG 62.565 65.000 0.00 0.00 45.39 6.13
138 139 1.153745 CTTCGGGAGAACTGAGCCG 60.154 63.158 0.00 0.00 45.39 5.52
139 140 1.219393 CCTTCGGGAGAACTGAGCC 59.781 63.158 0.00 0.00 45.39 4.70
140 141 0.390472 CACCTTCGGGAGAACTGAGC 60.390 60.000 0.00 0.00 45.39 4.26
141 142 0.390472 GCACCTTCGGGAGAACTGAG 60.390 60.000 0.00 0.00 45.39 3.35
142 143 0.832135 AGCACCTTCGGGAGAACTGA 60.832 55.000 0.00 0.00 45.39 3.41
143 144 0.390472 GAGCACCTTCGGGAGAACTG 60.390 60.000 0.00 0.00 45.39 3.16
144 145 0.832135 TGAGCACCTTCGGGAGAACT 60.832 55.000 0.00 0.00 45.39 3.01
145 146 0.250513 ATGAGCACCTTCGGGAGAAC 59.749 55.000 0.00 0.00 45.39 3.01
147 148 1.403814 CTATGAGCACCTTCGGGAGA 58.596 55.000 0.00 0.00 38.77 3.71
148 149 0.390860 CCTATGAGCACCTTCGGGAG 59.609 60.000 0.00 0.00 38.77 4.30
149 150 1.048724 CCCTATGAGCACCTTCGGGA 61.049 60.000 0.00 0.00 38.77 5.14
150 151 1.048724 TCCCTATGAGCACCTTCGGG 61.049 60.000 0.00 0.00 41.87 5.14
151 152 1.051812 ATCCCTATGAGCACCTTCGG 58.948 55.000 0.00 0.00 0.00 4.30
152 153 3.368843 CCATATCCCTATGAGCACCTTCG 60.369 52.174 0.00 0.00 37.51 3.79
153 154 3.584848 ACCATATCCCTATGAGCACCTTC 59.415 47.826 0.00 0.00 37.51 3.46
154 155 3.602608 ACCATATCCCTATGAGCACCTT 58.397 45.455 0.00 0.00 37.51 3.50
155 156 3.282135 ACCATATCCCTATGAGCACCT 57.718 47.619 0.00 0.00 37.51 4.00
156 157 3.073062 ACAACCATATCCCTATGAGCACC 59.927 47.826 0.00 0.00 37.51 5.01
157 158 4.357918 ACAACCATATCCCTATGAGCAC 57.642 45.455 0.00 0.00 37.51 4.40
158 159 5.155161 AGTACAACCATATCCCTATGAGCA 58.845 41.667 0.00 0.00 37.51 4.26
159 160 5.746990 AGTACAACCATATCCCTATGAGC 57.253 43.478 0.00 0.00 37.51 4.26
160 161 8.367660 ACATAGTACAACCATATCCCTATGAG 57.632 38.462 9.91 0.00 37.51 2.90
161 162 8.736097 AACATAGTACAACCATATCCCTATGA 57.264 34.615 9.91 0.00 37.51 2.15
192 193 5.557866 AGGATAAAGCGGAAAGTTGTACTT 58.442 37.500 0.00 0.00 40.80 2.24
193 194 5.161943 AGGATAAAGCGGAAAGTTGTACT 57.838 39.130 0.00 0.00 0.00 2.73
194 195 5.874895 AAGGATAAAGCGGAAAGTTGTAC 57.125 39.130 0.00 0.00 0.00 2.90
195 196 6.935771 TGTAAAGGATAAAGCGGAAAGTTGTA 59.064 34.615 0.00 0.00 0.00 2.41
196 197 5.766174 TGTAAAGGATAAAGCGGAAAGTTGT 59.234 36.000 0.00 0.00 0.00 3.32
229 231 3.188100 CAGCAATCGAAGCGCCGA 61.188 61.111 11.09 11.09 43.16 5.54
275 277 6.403866 TGCCACTGTCATTTGTTAATTCTT 57.596 33.333 0.00 0.00 0.00 2.52
276 278 5.565439 GCTGCCACTGTCATTTGTTAATTCT 60.565 40.000 0.00 0.00 0.00 2.40
402 406 2.031120 CTCTTGCAAAGTCAACCCCAA 58.969 47.619 0.00 0.00 46.34 4.12
433 437 1.192146 ATACATATCGCCGCCCCACT 61.192 55.000 0.00 0.00 0.00 4.00
478 483 1.522668 TGCAAAGGGATGTCTTCGTG 58.477 50.000 0.00 0.00 0.00 4.35
669 685 6.183360 CCCTAGTCGAGAAGATGGATAATACG 60.183 46.154 0.00 0.00 0.00 3.06
689 705 7.069578 TGTCTAATAGAGCCTTTTGTACCCTAG 59.930 40.741 0.00 0.00 0.00 3.02
751 799 1.107945 TCATTCATGCATGTGGCTGG 58.892 50.000 25.43 10.95 45.15 4.85
924 1005 2.281830 AGCCTGAGAAGAGGGTTCG 58.718 57.895 0.00 0.00 41.20 3.95
935 1016 2.101415 TGATGATCGTGGTAAGCCTGAG 59.899 50.000 0.00 0.00 35.27 3.35
939 1020 1.933853 GTGTGATGATCGTGGTAAGCC 59.066 52.381 0.00 0.00 0.00 4.35
940 1021 1.933853 GGTGTGATGATCGTGGTAAGC 59.066 52.381 0.00 0.00 0.00 3.09
944 1025 0.684535 TGTGGTGTGATGATCGTGGT 59.315 50.000 0.00 0.00 0.00 4.16
948 1029 0.715551 CGTGTGTGGTGTGATGATCG 59.284 55.000 0.00 0.00 0.00 3.69
963 1044 3.449018 ACTATGATCAAAGGAGAGCGTGT 59.551 43.478 0.00 0.00 0.00 4.49
964 1045 4.052159 ACTATGATCAAAGGAGAGCGTG 57.948 45.455 0.00 0.00 0.00 5.34
965 1046 4.261825 GCTACTATGATCAAAGGAGAGCGT 60.262 45.833 0.00 0.00 0.00 5.07
966 1047 4.233789 GCTACTATGATCAAAGGAGAGCG 58.766 47.826 0.00 0.00 0.00 5.03
983 1064 3.000727 GCCATTGTCGTAACTTGCTACT 58.999 45.455 0.00 0.00 0.00 2.57
992 1073 1.463056 CGAGCAAAGCCATTGTCGTAA 59.537 47.619 12.39 0.00 41.32 3.18
1024 1139 3.406200 AAGGGCGAGGCAGAGCAT 61.406 61.111 0.00 0.00 34.54 3.79
1041 1156 2.122729 CCCAGGGAGAGGACCACA 59.877 66.667 0.00 0.00 0.00 4.17
1060 1175 4.743018 GCTTTTGCTAGGGAGGCA 57.257 55.556 0.00 0.00 43.35 4.75
1198 1313 0.657659 CGCGCATACGTACTCTGGAG 60.658 60.000 8.75 0.00 42.83 3.86
1202 1317 2.352001 CGCGCGCATACGTACTCT 60.352 61.111 32.61 0.00 42.83 3.24
1233 1355 1.470098 ACGCTTGATGGTTTGATCAGC 59.530 47.619 0.00 0.00 33.86 4.26
1235 1357 4.278170 AGAAAACGCTTGATGGTTTGATCA 59.722 37.500 0.00 0.00 36.55 2.92
1249 1371 1.464997 GAGGCGAAATCAGAAAACGCT 59.535 47.619 14.71 5.04 46.71 5.07
1254 1376 5.762045 CAAAAGAAGAGGCGAAATCAGAAA 58.238 37.500 0.00 0.00 0.00 2.52
1256 1378 3.189287 GCAAAAGAAGAGGCGAAATCAGA 59.811 43.478 0.00 0.00 0.00 3.27
1259 1381 3.839051 AGCAAAAGAAGAGGCGAAATC 57.161 42.857 0.00 0.00 0.00 2.17
1261 1383 3.119849 GCATAGCAAAAGAAGAGGCGAAA 60.120 43.478 0.00 0.00 0.00 3.46
1272 1669 1.068127 GGGGCATCTGCATAGCAAAAG 59.932 52.381 4.33 0.00 44.36 2.27
1278 1675 2.670934 GCCGGGGCATCTGCATAG 60.671 66.667 2.18 0.00 44.36 2.23
1279 1676 4.624364 CGCCGGGGCATCTGCATA 62.624 66.667 5.22 0.00 44.36 3.14
1471 1868 4.016706 CGGCGACCCCTTGTTCCT 62.017 66.667 0.00 0.00 0.00 3.36
1566 1963 2.982744 GCACTTGCCGGGCTTCTTC 61.983 63.158 21.46 3.05 34.31 2.87
1591 1988 2.749621 GTGAAGCCCAAACTTGATCGAT 59.250 45.455 0.00 0.00 0.00 3.59
1678 2088 6.739331 TGTTTTGGAAAATACAAGGGTGAT 57.261 33.333 0.00 0.00 0.00 3.06
1762 2201 4.393062 ACATGCACTAGTTTCCTCAAATCG 59.607 41.667 0.00 0.00 0.00 3.34
1850 2370 7.381139 TCGACAAATATTTTCCAAAAGCAACTC 59.619 33.333 0.00 0.00 0.00 3.01
1918 2453 4.022464 TCCGCTTTTACAGTTGTGTTTG 57.978 40.909 0.00 0.00 38.19 2.93
1954 2489 4.019174 AGAGCCAAACGGATGAAATGAAT 58.981 39.130 0.00 0.00 0.00 2.57
1988 2523 3.621268 TGTTTCTCGGTCAAAAGTCAGTG 59.379 43.478 0.00 0.00 0.00 3.66
2118 2653 3.531982 CTTTTCAGTTTACGAGTGCACG 58.468 45.455 12.01 2.67 39.31 5.34
2165 2700 3.005367 GGCGTTATGGTTTGATTATGGGG 59.995 47.826 0.00 0.00 0.00 4.96
2281 3889 0.177141 TCGCAATAGCCCACACTACC 59.823 55.000 0.00 0.00 37.52 3.18
2329 6161 0.037326 CATGCACACCTACTCCACGT 60.037 55.000 0.00 0.00 0.00 4.49
2330 6162 0.037326 ACATGCACACCTACTCCACG 60.037 55.000 0.00 0.00 0.00 4.94
2353 6185 6.387465 CCTCCACGTCGATGTTACATATTAT 58.613 40.000 7.76 0.00 0.00 1.28
2379 6211 2.112190 GAGAGAGTGGGGGTAGAAAGG 58.888 57.143 0.00 0.00 0.00 3.11
2484 6442 6.486320 TCAATAAAATCTCACACAACTGAGCA 59.514 34.615 0.00 0.00 38.07 4.26
2506 6464 3.411446 ACATCAGCGATGAGGTTTTCAA 58.589 40.909 16.07 0.00 42.09 2.69


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

AutoCloner maintained by Alex Coulton.