Multiple sequence alignment - TraesCS3D01G117200

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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 TraesCS3D01G117200 chr3D 100.000 2738 0 0 1 2738 70717442 70714705 0.000000e+00 5057.0
1 TraesCS3D01G117200 chr3A 90.751 1957 91 41 793 2738 82396643 82394766 0.000000e+00 2529.0
2 TraesCS3D01G117200 chr3A 88.068 352 34 3 286 637 82397083 82396740 7.060000e-111 411.0
3 TraesCS3D01G117200 chr3A 93.243 74 5 0 686 759 82396711 82396638 2.880000e-20 110.0
4 TraesCS3D01G117200 chr3A 100.000 29 0 0 642 670 82396720 82396692 1.000000e-03 54.7
5 TraesCS3D01G117200 chr3B 93.032 1263 58 16 706 1964 116151839 116150603 0.000000e+00 1818.0
6 TraesCS3D01G117200 chr3B 81.321 787 96 25 1964 2738 116149971 116149224 2.350000e-165 592.0
7 TraesCS3D01G117200 chr3B 86.353 447 26 12 1964 2409 116150562 116150150 3.210000e-124 455.0
8 TraesCS3D01G117200 chr3B 84.524 336 32 8 209 538 116153815 116153494 5.690000e-82 315.0
9 TraesCS3D01G117200 chr3B 90.076 131 7 1 543 667 116153381 116153251 6.070000e-37 165.0
10 TraesCS3D01G117200 chr2D 95.215 209 8 1 1 209 383334518 383334724 2.030000e-86 329.0
11 TraesCS3D01G117200 chr2B 94.712 208 8 1 1 208 37947821 37947617 1.220000e-83 320.0
12 TraesCS3D01G117200 chr1B 94.258 209 9 2 1 209 562368950 562368745 1.580000e-82 316.0
13 TraesCS3D01G117200 chr1B 90.909 209 16 2 1 209 349353414 349353619 7.470000e-71 278.0
14 TraesCS3D01G117200 chr1B 97.222 72 2 0 1 72 204453764 204453835 3.700000e-24 122.0
15 TraesCS3D01G117200 chr6A 92.925 212 15 0 1 212 214926266 214926055 2.650000e-80 309.0
16 TraesCS3D01G117200 chr7A 96.711 152 4 1 19 170 22184279 22184129 4.530000e-63 252.0
17 TraesCS3D01G117200 chr6B 92.763 152 8 1 1 152 620570238 620570090 1.650000e-52 217.0


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 TraesCS3D01G117200 chr3D 70714705 70717442 2737 True 5057.000 5057 100.0000 1 2738 1 chr3D.!!$R1 2737
1 TraesCS3D01G117200 chr3A 82394766 82397083 2317 True 776.175 2529 93.0155 286 2738 4 chr3A.!!$R1 2452
2 TraesCS3D01G117200 chr3B 116149224 116153815 4591 True 669.000 1818 87.0612 209 2738 5 chr3B.!!$R1 2529

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
144 145 0.032678 CACGATGGGGAAGATCCTCG 59.967 60.0 0.0 5.34 40.96 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 3533 0.976641 TGTGTTCTAGACAGGCCCTG 59.023 55.0 9.83 9.83 39.39 4.45 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
22 23 4.996434 GTGCAGCAGCCACGGAGT 62.996 66.667 0.00 0.00 41.13 3.85
23 24 4.687215 TGCAGCAGCCACGGAGTC 62.687 66.667 0.00 0.00 35.98 3.36
25 26 4.767255 CAGCAGCCACGGAGTCCC 62.767 72.222 2.80 0.00 41.61 4.46
27 28 4.767255 GCAGCCACGGAGTCCCAG 62.767 72.222 2.80 0.00 41.61 4.45
28 29 4.767255 CAGCCACGGAGTCCCAGC 62.767 72.222 2.80 4.02 41.61 4.85
34 35 2.439701 CGGAGTCCCAGCCGTAGA 60.440 66.667 2.80 0.00 42.49 2.59
35 36 1.828660 CGGAGTCCCAGCCGTAGAT 60.829 63.158 2.80 0.00 42.49 1.98
36 37 1.797211 CGGAGTCCCAGCCGTAGATC 61.797 65.000 2.80 0.00 42.49 2.75
37 38 1.655329 GAGTCCCAGCCGTAGATCG 59.345 63.158 0.00 0.00 39.52 3.69
38 39 2.027751 GTCCCAGCCGTAGATCGC 59.972 66.667 0.00 0.00 38.35 4.58
39 40 3.224324 TCCCAGCCGTAGATCGCC 61.224 66.667 0.00 0.00 38.35 5.54
40 41 4.647615 CCCAGCCGTAGATCGCCG 62.648 72.222 0.71 0.71 38.35 6.46
41 42 4.647615 CCAGCCGTAGATCGCCGG 62.648 72.222 18.33 18.33 46.90 6.13
57 58 3.878667 GGATCCCGCCCTCCCTTG 61.879 72.222 0.00 0.00 0.00 3.61
58 59 4.570874 GATCCCGCCCTCCCTTGC 62.571 72.222 0.00 0.00 0.00 4.01
75 76 4.200283 CCGGCGCCTCAGAGAGAC 62.200 72.222 26.68 0.00 0.00 3.36
76 77 3.137459 CGGCGCCTCAGAGAGACT 61.137 66.667 26.68 0.00 0.00 3.24
77 78 2.705821 CGGCGCCTCAGAGAGACTT 61.706 63.158 26.68 0.00 0.00 3.01
78 79 1.140804 GGCGCCTCAGAGAGACTTC 59.859 63.158 22.15 0.00 0.00 3.01
79 80 1.226547 GCGCCTCAGAGAGACTTCG 60.227 63.158 0.00 0.00 0.00 3.79
80 81 1.226547 CGCCTCAGAGAGACTTCGC 60.227 63.158 0.00 0.00 0.00 4.70
81 82 1.140804 GCCTCAGAGAGACTTCGCC 59.859 63.158 0.00 0.00 0.00 5.54
82 83 1.431440 CCTCAGAGAGACTTCGCCG 59.569 63.158 0.00 0.00 0.00 6.46
83 84 1.226547 CTCAGAGAGACTTCGCCGC 60.227 63.158 0.00 0.00 0.00 6.53
84 85 2.202676 CAGAGAGACTTCGCCGCC 60.203 66.667 0.00 0.00 0.00 6.13
85 86 2.361865 AGAGAGACTTCGCCGCCT 60.362 61.111 0.00 0.00 0.00 5.52
86 87 2.202676 GAGAGACTTCGCCGCCTG 60.203 66.667 0.00 0.00 0.00 4.85
87 88 2.676822 AGAGACTTCGCCGCCTGA 60.677 61.111 0.00 0.00 0.00 3.86
88 89 2.202676 GAGACTTCGCCGCCTGAG 60.203 66.667 0.00 0.00 0.00 3.35
89 90 4.443266 AGACTTCGCCGCCTGAGC 62.443 66.667 0.00 0.00 0.00 4.26
90 91 4.742201 GACTTCGCCGCCTGAGCA 62.742 66.667 0.00 0.00 39.83 4.26
91 92 4.087892 ACTTCGCCGCCTGAGCAT 62.088 61.111 0.00 0.00 39.83 3.79
92 93 3.267860 CTTCGCCGCCTGAGCATC 61.268 66.667 0.00 0.00 39.83 3.91
93 94 4.838152 TTCGCCGCCTGAGCATCC 62.838 66.667 0.00 0.00 39.83 3.51
113 114 4.116328 CGCCGTCGAAGAGCCAGA 62.116 66.667 0.00 0.00 36.95 3.86
114 115 2.496817 GCCGTCGAAGAGCCAGAT 59.503 61.111 0.00 0.00 36.95 2.90
115 116 1.590259 GCCGTCGAAGAGCCAGATC 60.590 63.158 0.00 0.00 36.95 2.75
116 117 1.066587 CCGTCGAAGAGCCAGATCC 59.933 63.158 0.00 0.00 36.95 3.36
117 118 1.298713 CGTCGAAGAGCCAGATCCG 60.299 63.158 0.00 0.00 36.95 4.18
118 119 1.590259 GTCGAAGAGCCAGATCCGC 60.590 63.158 0.00 0.00 36.95 5.54
119 120 2.279784 CGAAGAGCCAGATCCGCC 60.280 66.667 0.00 0.00 0.00 6.13
120 121 2.279784 GAAGAGCCAGATCCGCCG 60.280 66.667 0.00 0.00 0.00 6.46
121 122 4.537433 AAGAGCCAGATCCGCCGC 62.537 66.667 0.00 0.00 0.00 6.53
140 141 4.464262 GCCACGATGGGGAAGATC 57.536 61.111 6.23 0.00 38.19 2.75
141 142 1.227973 GCCACGATGGGGAAGATCC 60.228 63.158 6.23 0.00 38.19 3.36
142 143 1.700042 GCCACGATGGGGAAGATCCT 61.700 60.000 6.23 0.00 38.19 3.24
143 144 0.394565 CCACGATGGGGAAGATCCTC 59.605 60.000 0.00 0.00 37.60 3.71
144 145 0.032678 CACGATGGGGAAGATCCTCG 59.967 60.000 0.00 5.34 40.96 4.63
145 146 1.005630 CGATGGGGAAGATCCTCGC 60.006 63.158 0.00 0.00 40.96 5.03
146 147 1.373059 GATGGGGAAGATCCTCGCC 59.627 63.158 18.29 18.29 40.96 5.54
148 149 4.610714 GGGGAAGATCCTCGCCGC 62.611 72.222 11.34 2.41 38.51 6.53
149 150 4.610714 GGGAAGATCCTCGCCGCC 62.611 72.222 0.00 0.00 36.57 6.13
150 151 4.951963 GGAAGATCCTCGCCGCCG 62.952 72.222 0.00 0.00 32.53 6.46
163 164 4.776322 CGCCGCCATGGAAGTGGA 62.776 66.667 18.40 0.00 42.02 4.02
164 165 2.124151 GCCGCCATGGAAGTGGAT 60.124 61.111 18.40 0.00 42.02 3.41
165 166 2.189499 GCCGCCATGGAAGTGGATC 61.189 63.158 18.40 0.00 42.02 3.36
166 167 1.526917 CCGCCATGGAAGTGGATCC 60.527 63.158 18.40 4.20 42.02 3.36
167 168 1.528824 CGCCATGGAAGTGGATCCT 59.471 57.895 18.40 0.00 42.02 3.24
168 169 0.107017 CGCCATGGAAGTGGATCCTT 60.107 55.000 18.40 0.00 42.02 3.36
169 170 1.396653 GCCATGGAAGTGGATCCTTG 58.603 55.000 18.40 3.03 42.02 3.61
170 171 1.396653 CCATGGAAGTGGATCCTTGC 58.603 55.000 14.23 5.78 42.02 4.01
171 172 1.396653 CATGGAAGTGGATCCTTGCC 58.603 55.000 14.23 9.98 40.35 4.52
172 173 0.107017 ATGGAAGTGGATCCTTGCCG 60.107 55.000 14.23 0.00 40.35 5.69
173 174 1.299976 GGAAGTGGATCCTTGCCGT 59.700 57.895 14.23 0.00 36.50 5.68
174 175 0.744771 GGAAGTGGATCCTTGCCGTC 60.745 60.000 14.23 6.07 36.50 4.79
175 176 0.744771 GAAGTGGATCCTTGCCGTCC 60.745 60.000 14.23 0.00 0.00 4.79
176 177 2.124695 GTGGATCCTTGCCGTCCC 60.125 66.667 14.23 0.00 0.00 4.46
177 178 3.407967 TGGATCCTTGCCGTCCCC 61.408 66.667 14.23 0.00 0.00 4.81
178 179 4.547367 GGATCCTTGCCGTCCCCG 62.547 72.222 3.84 0.00 0.00 5.73
220 221 2.660064 CGCTGGCCACCCTAGTCTT 61.660 63.158 0.00 0.00 0.00 3.01
234 235 7.178451 CCACCCTAGTCTTTTGATATTTTTGGT 59.822 37.037 0.00 0.00 0.00 3.67
269 270 9.599866 TTGACCTAGATATTAGTCACACATTTG 57.400 33.333 0.00 0.00 38.88 2.32
270 271 7.710907 TGACCTAGATATTAGTCACACATTTGC 59.289 37.037 0.00 0.00 34.44 3.68
272 273 5.991328 AGATATTAGTCACACATTTGCGG 57.009 39.130 0.00 0.00 0.00 5.69
273 274 5.428253 AGATATTAGTCACACATTTGCGGT 58.572 37.500 0.00 0.00 0.00 5.68
274 275 5.880332 AGATATTAGTCACACATTTGCGGTT 59.120 36.000 0.00 0.00 0.00 4.44
275 276 4.846779 ATTAGTCACACATTTGCGGTTT 57.153 36.364 0.00 0.00 0.00 3.27
276 277 4.640789 TTAGTCACACATTTGCGGTTTT 57.359 36.364 0.00 0.00 0.00 2.43
277 278 2.808244 AGTCACACATTTGCGGTTTTG 58.192 42.857 0.00 0.00 0.00 2.44
278 279 1.257675 GTCACACATTTGCGGTTTTGC 59.742 47.619 0.00 0.00 0.00 3.68
279 280 0.229247 CACACATTTGCGGTTTTGCG 59.771 50.000 0.00 0.00 37.81 4.85
302 303 3.761218 CCTCTATGCGGTCATCTCATACT 59.239 47.826 0.00 0.00 34.22 2.12
307 308 2.297315 TGCGGTCATCTCATACTGATCC 59.703 50.000 0.00 0.00 0.00 3.36
318 319 7.353414 TCTCATACTGATCCAAAGACCTAAG 57.647 40.000 0.00 0.00 0.00 2.18
319 320 5.918608 TCATACTGATCCAAAGACCTAAGC 58.081 41.667 0.00 0.00 0.00 3.09
320 321 5.425217 TCATACTGATCCAAAGACCTAAGCA 59.575 40.000 0.00 0.00 0.00 3.91
321 322 4.851639 ACTGATCCAAAGACCTAAGCAT 57.148 40.909 0.00 0.00 0.00 3.79
322 323 4.775236 ACTGATCCAAAGACCTAAGCATC 58.225 43.478 0.00 0.00 0.00 3.91
345 346 3.181518 GCATTGCACATTACAACATTGGC 60.182 43.478 3.15 0.00 0.00 4.52
355 360 1.143684 ACAACATTGGCCAGTCAGTCT 59.856 47.619 5.11 0.00 0.00 3.24
359 364 1.542915 CATTGGCCAGTCAGTCTTTGG 59.457 52.381 5.11 0.00 35.06 3.28
413 418 3.012518 CAGCGAAATCTCAAGGGTTCAT 58.987 45.455 0.00 0.00 0.00 2.57
445 450 1.988293 TCTCGGAAAATTTGGTGGCA 58.012 45.000 0.00 0.00 0.00 4.92
446 451 2.311463 TCTCGGAAAATTTGGTGGCAA 58.689 42.857 0.00 0.00 0.00 4.52
448 453 4.082845 TCTCGGAAAATTTGGTGGCAATA 58.917 39.130 0.00 0.00 0.00 1.90
449 454 4.709397 TCTCGGAAAATTTGGTGGCAATAT 59.291 37.500 0.00 0.00 0.00 1.28
450 455 5.186797 TCTCGGAAAATTTGGTGGCAATATT 59.813 36.000 0.00 0.00 0.00 1.28
453 458 7.560368 TCGGAAAATTTGGTGGCAATATTATT 58.440 30.769 0.00 0.00 0.00 1.40
480 488 1.037493 TAATCATCCACCTCGGGTCG 58.963 55.000 0.00 0.00 31.02 4.79
521 529 4.212847 CGATCAAAATAGCTGACCATGAGG 59.787 45.833 0.00 0.00 42.21 3.86
541 549 7.615582 TGAGGTCAAATGATACATGTTTCTC 57.384 36.000 15.92 6.79 0.00 2.87
670 807 1.764134 TCCTGTGGGTTTACTGACGTT 59.236 47.619 0.00 0.00 0.00 3.99
671 808 2.171027 TCCTGTGGGTTTACTGACGTTT 59.829 45.455 0.00 0.00 0.00 3.60
672 809 2.946990 CCTGTGGGTTTACTGACGTTTT 59.053 45.455 0.00 0.00 0.00 2.43
673 810 3.379057 CCTGTGGGTTTACTGACGTTTTT 59.621 43.478 0.00 0.00 0.00 1.94
697 863 2.181125 TGAGCGTATCCTGTGGGTTTA 58.819 47.619 0.00 0.00 0.00 2.01
698 864 2.093869 TGAGCGTATCCTGTGGGTTTAC 60.094 50.000 0.00 0.00 0.00 2.01
702 2212 3.518590 CGTATCCTGTGGGTTTACTGAC 58.481 50.000 0.00 0.00 0.00 3.51
704 2214 1.416243 TCCTGTGGGTTTACTGACGT 58.584 50.000 0.00 0.00 0.00 4.34
722 2235 1.153842 TGGCGACACGTGAGCATAG 60.154 57.895 30.06 14.38 33.40 2.23
748 2261 3.700970 TCGACGCTCAATGGGCCA 61.701 61.111 9.61 9.61 0.00 5.36
761 2274 2.586792 GGCCAGAACGAGAGCCAT 59.413 61.111 0.00 0.00 45.07 4.40
776 2289 1.906995 CCATTGGCCCATGGGTTTC 59.093 57.895 31.58 20.73 37.65 2.78
780 2293 2.283821 GGCCCATGGGTTTCTGCA 60.284 61.111 31.58 0.00 37.65 4.41
784 2297 0.819582 CCCATGGGTTTCTGCATGAC 59.180 55.000 23.93 0.00 0.00 3.06
787 2300 2.498481 CCATGGGTTTCTGCATGACAAT 59.502 45.455 2.85 0.00 0.00 2.71
791 2304 5.798125 TGGGTTTCTGCATGACAATAAAA 57.202 34.783 0.00 0.00 0.00 1.52
792 2305 5.782047 TGGGTTTCTGCATGACAATAAAAG 58.218 37.500 0.00 0.00 0.00 2.27
793 2306 5.538053 TGGGTTTCTGCATGACAATAAAAGA 59.462 36.000 0.00 0.00 0.00 2.52
796 2309 7.025963 GGTTTCTGCATGACAATAAAAGAGAG 58.974 38.462 0.00 0.00 0.00 3.20
797 2310 5.808042 TCTGCATGACAATAAAAGAGAGC 57.192 39.130 0.00 0.00 0.00 4.09
798 2311 5.247862 TCTGCATGACAATAAAAGAGAGCA 58.752 37.500 0.00 0.00 0.00 4.26
829 2342 1.740296 GCTTTCGCTGCCTAACCGA 60.740 57.895 0.00 0.00 0.00 4.69
849 2362 1.002990 CCACTGCATCAGCCACAGA 60.003 57.895 0.00 0.00 41.13 3.41
936 2450 2.571757 CGCCACTTCGCTCCACTA 59.428 61.111 0.00 0.00 0.00 2.74
955 2469 2.028561 ACCCAAATCCAAGCACCATT 57.971 45.000 0.00 0.00 0.00 3.16
988 2502 4.491676 CAACAAGATCTGCCAAATCCAAG 58.508 43.478 0.00 0.00 0.00 3.61
997 2512 0.756815 CCAAATCCAAGCCCCCTAGC 60.757 60.000 0.00 0.00 0.00 3.42
1067 2582 0.401738 CAAGTTGAAGGGGAGGAGCA 59.598 55.000 0.00 0.00 0.00 4.26
1122 2637 4.430765 GTCGACGTGCCCACCGAT 62.431 66.667 0.00 0.00 33.47 4.18
1150 2665 0.329596 GCAAGTTGGAGGGGATGAGT 59.670 55.000 4.75 0.00 0.00 3.41
1156 2671 4.593864 GAGGGGATGAGTCGGCGC 62.594 72.222 0.00 0.00 0.00 6.53
1211 2726 1.153568 CGATGGAGCAAGGCGAAGA 60.154 57.895 0.00 0.00 0.00 2.87
1221 2736 3.077556 GGCGAAGAGGAGGAGGCA 61.078 66.667 0.00 0.00 0.00 4.75
1222 2737 2.660064 GGCGAAGAGGAGGAGGCAA 61.660 63.158 0.00 0.00 0.00 4.52
1749 3267 3.074687 AGGTCACTTAGAGGTGTCTCTCA 59.925 47.826 0.00 0.00 46.79 3.27
1801 3319 7.614192 CCAAGTGGTTAAAATGTATTCCTACCT 59.386 37.037 0.00 0.00 0.00 3.08
1831 3349 4.636206 GTGATGGAAGTGGAACCTATGAAC 59.364 45.833 0.00 0.00 37.80 3.18
1884 3402 9.807921 TTTAACCTTACAAATTCCTCATCTCTT 57.192 29.630 0.00 0.00 0.00 2.85
1901 3419 5.883685 TCTCTTGCAAGGATCTGATATGT 57.116 39.130 25.73 0.00 0.00 2.29
1907 3425 3.370366 GCAAGGATCTGATATGTCATCGC 59.630 47.826 0.00 0.00 32.98 4.58
1932 3450 6.737254 TCTTTATTTAGGCTTGTGTAGTGC 57.263 37.500 0.00 0.00 0.00 4.40
1933 3451 5.350365 TCTTTATTTAGGCTTGTGTAGTGCG 59.650 40.000 0.00 0.00 0.00 5.34
1934 3452 2.823924 TTTAGGCTTGTGTAGTGCGA 57.176 45.000 0.00 0.00 0.00 5.10
1935 3453 3.328382 TTTAGGCTTGTGTAGTGCGAT 57.672 42.857 0.00 0.00 0.00 4.58
1936 3454 2.579207 TAGGCTTGTGTAGTGCGATC 57.421 50.000 0.00 0.00 0.00 3.69
1937 3455 0.898320 AGGCTTGTGTAGTGCGATCT 59.102 50.000 0.00 0.00 0.00 2.75
1951 3469 2.099098 TGCGATCTCGAATTCAGCAGTA 59.901 45.455 6.22 0.00 43.02 2.74
2099 3660 3.629142 ACTTGGTGGGTATTACAGAGC 57.371 47.619 0.00 0.00 0.00 4.09
2126 3687 2.099098 CCACAGTTCTTTGGTGGTTCAC 59.901 50.000 0.00 0.00 45.48 3.18
2127 3688 3.016736 CACAGTTCTTTGGTGGTTCACT 58.983 45.455 0.00 0.00 34.40 3.41
2128 3689 4.196193 CACAGTTCTTTGGTGGTTCACTA 58.804 43.478 0.00 0.00 34.40 2.74
2129 3690 4.273480 CACAGTTCTTTGGTGGTTCACTAG 59.727 45.833 0.00 0.00 34.40 2.57
2130 3691 3.815401 CAGTTCTTTGGTGGTTCACTAGG 59.185 47.826 0.00 0.00 34.40 3.02
2131 3692 3.714798 AGTTCTTTGGTGGTTCACTAGGA 59.285 43.478 0.00 0.00 34.40 2.94
2132 3693 4.351111 AGTTCTTTGGTGGTTCACTAGGAT 59.649 41.667 0.00 0.00 34.40 3.24
2133 3694 5.546499 AGTTCTTTGGTGGTTCACTAGGATA 59.454 40.000 0.00 0.00 34.40 2.59
2134 3695 5.677319 TCTTTGGTGGTTCACTAGGATAG 57.323 43.478 0.00 0.00 46.50 2.08
2135 3696 4.469945 TCTTTGGTGGTTCACTAGGATAGG 59.530 45.833 0.00 0.00 44.97 2.57
2136 3697 3.484953 TGGTGGTTCACTAGGATAGGT 57.515 47.619 0.00 0.00 44.97 3.08
2137 3698 3.798515 TGGTGGTTCACTAGGATAGGTT 58.201 45.455 0.00 0.00 44.97 3.50
2138 3699 3.773119 TGGTGGTTCACTAGGATAGGTTC 59.227 47.826 0.00 0.00 44.97 3.62
2139 3700 3.134262 GGTGGTTCACTAGGATAGGTTCC 59.866 52.174 0.00 0.00 44.97 3.62
2140 3701 5.365966 GGTGGTTCACTAGGATAGGTTCCA 61.366 50.000 0.00 0.00 44.97 3.53
2141 3702 6.636910 GGTGGTTCACTAGGATAGGTTCCAT 61.637 48.000 0.00 0.00 44.97 3.41
2142 3703 8.367500 GGTGGTTCACTAGGATAGGTTCCATC 62.368 50.000 0.00 0.00 44.97 3.51
2193 3768 4.696479 ACTGAACAGGAAATGACAGTCT 57.304 40.909 1.31 0.00 41.91 3.24
2202 3777 8.083828 ACAGGAAATGACAGTCTATCTATTGT 57.916 34.615 1.31 0.00 0.00 2.71
2208 3783 5.664457 TGACAGTCTATCTATTGTTGCCTG 58.336 41.667 1.31 0.00 0.00 4.85
2213 3788 8.924303 ACAGTCTATCTATTGTTGCCTGTATTA 58.076 33.333 0.00 0.00 0.00 0.98
2267 3842 4.921470 TGTAGCGATTTTCAGCAGTTAC 57.079 40.909 0.00 0.00 35.48 2.50
2305 3880 4.065088 TGTCATAAGAGTGCTCCAACAAC 58.935 43.478 0.00 0.00 0.00 3.32
2322 3897 3.078837 ACAACGTTGCCCTTAGGTAATG 58.921 45.455 27.61 0.00 46.92 1.90
2456 4635 1.047002 TTGGGTGTTTGCATGGGAAG 58.953 50.000 0.00 0.00 0.00 3.46
2470 4649 3.071874 TGGGAAGCGAATCAATCAACT 57.928 42.857 0.00 0.00 0.00 3.16
2537 4716 2.618045 CCTAGTTGCAGTTAGTTGGGGG 60.618 54.545 6.01 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.996434 ACTCCGTGGCTGCTGCAC 62.996 66.667 17.89 11.99 41.91 4.57
6 7 4.687215 GACTCCGTGGCTGCTGCA 62.687 66.667 17.89 0.88 41.91 4.41
8 9 4.767255 GGGACTCCGTGGCTGCTG 62.767 72.222 0.00 0.00 0.00 4.41
10 11 4.767255 CTGGGACTCCGTGGCTGC 62.767 72.222 0.00 0.00 35.24 5.25
11 12 4.767255 GCTGGGACTCCGTGGCTG 62.767 72.222 0.00 0.00 35.24 4.85
17 18 1.797211 GATCTACGGCTGGGACTCCG 61.797 65.000 0.00 0.00 46.71 4.63
18 19 1.797211 CGATCTACGGCTGGGACTCC 61.797 65.000 0.00 0.00 38.46 3.85
19 20 1.655329 CGATCTACGGCTGGGACTC 59.345 63.158 0.00 0.00 38.46 3.36
20 21 2.491022 GCGATCTACGGCTGGGACT 61.491 63.158 0.00 0.00 42.83 3.85
21 22 2.027751 GCGATCTACGGCTGGGAC 59.972 66.667 0.00 0.00 42.83 4.46
29 30 2.567049 GGGATCCGGCGATCTACG 59.433 66.667 9.30 0.00 43.90 3.51
30 31 2.567049 CGGGATCCGGCGATCTAC 59.433 66.667 9.30 6.50 43.90 2.59
40 41 3.878667 CAAGGGAGGGCGGGATCC 61.879 72.222 1.92 1.92 34.64 3.36
41 42 4.570874 GCAAGGGAGGGCGGGATC 62.571 72.222 0.00 0.00 0.00 3.36
58 59 4.200283 GTCTCTCTGAGGCGCCGG 62.200 72.222 23.20 15.60 0.00 6.13
59 60 2.606155 GAAGTCTCTCTGAGGCGCCG 62.606 65.000 23.20 7.22 39.53 6.46
60 61 1.140804 GAAGTCTCTCTGAGGCGCC 59.859 63.158 21.89 21.89 39.53 6.53
61 62 1.226547 CGAAGTCTCTCTGAGGCGC 60.227 63.158 0.00 0.00 39.53 6.53
62 63 1.226547 GCGAAGTCTCTCTGAGGCG 60.227 63.158 4.59 0.00 39.53 5.52
63 64 1.140804 GGCGAAGTCTCTCTGAGGC 59.859 63.158 4.59 0.00 34.04 4.70
64 65 1.431440 CGGCGAAGTCTCTCTGAGG 59.569 63.158 0.00 0.00 0.00 3.86
65 66 1.226547 GCGGCGAAGTCTCTCTGAG 60.227 63.158 12.98 0.00 0.00 3.35
66 67 2.701780 GGCGGCGAAGTCTCTCTGA 61.702 63.158 12.98 0.00 0.00 3.27
67 68 2.202676 GGCGGCGAAGTCTCTCTG 60.203 66.667 12.98 0.00 0.00 3.35
68 69 2.361865 AGGCGGCGAAGTCTCTCT 60.362 61.111 12.98 0.00 0.00 3.10
69 70 2.202676 CAGGCGGCGAAGTCTCTC 60.203 66.667 12.98 0.00 0.00 3.20
70 71 2.676822 TCAGGCGGCGAAGTCTCT 60.677 61.111 12.98 0.00 0.00 3.10
71 72 2.202676 CTCAGGCGGCGAAGTCTC 60.203 66.667 12.98 0.00 0.00 3.36
72 73 4.443266 GCTCAGGCGGCGAAGTCT 62.443 66.667 12.98 0.00 0.00 3.24
73 74 4.742201 TGCTCAGGCGGCGAAGTC 62.742 66.667 12.98 0.00 42.25 3.01
74 75 4.087892 ATGCTCAGGCGGCGAAGT 62.088 61.111 12.98 0.00 42.25 3.01
75 76 3.267860 GATGCTCAGGCGGCGAAG 61.268 66.667 12.98 6.29 42.25 3.79
76 77 4.838152 GGATGCTCAGGCGGCGAA 62.838 66.667 12.98 0.00 42.25 4.70
96 97 3.417275 ATCTGGCTCTTCGACGGCG 62.417 63.158 2.87 2.87 39.35 6.46
97 98 1.590259 GATCTGGCTCTTCGACGGC 60.590 63.158 0.00 0.00 0.00 5.68
98 99 1.066587 GGATCTGGCTCTTCGACGG 59.933 63.158 0.00 0.00 0.00 4.79
99 100 1.298713 CGGATCTGGCTCTTCGACG 60.299 63.158 0.00 0.00 0.00 5.12
100 101 1.590259 GCGGATCTGGCTCTTCGAC 60.590 63.158 3.14 0.00 0.00 4.20
101 102 2.786495 GGCGGATCTGGCTCTTCGA 61.786 63.158 20.39 0.00 0.00 3.71
102 103 2.279784 GGCGGATCTGGCTCTTCG 60.280 66.667 20.39 0.00 0.00 3.79
103 104 2.279784 CGGCGGATCTGGCTCTTC 60.280 66.667 24.17 0.00 0.00 2.87
104 105 4.537433 GCGGCGGATCTGGCTCTT 62.537 66.667 24.17 0.00 0.00 2.85
121 122 2.996168 GATCTTCCCCATCGTGGCGG 62.996 65.000 0.00 2.96 35.79 6.13
122 123 1.595382 GATCTTCCCCATCGTGGCG 60.595 63.158 0.00 0.00 35.79 5.69
123 124 1.227973 GGATCTTCCCCATCGTGGC 60.228 63.158 0.00 0.00 35.79 5.01
124 125 0.394565 GAGGATCTTCCCCATCGTGG 59.605 60.000 0.00 0.00 37.19 4.94
125 126 0.032678 CGAGGATCTTCCCCATCGTG 59.967 60.000 0.00 0.00 37.19 4.35
126 127 1.749334 GCGAGGATCTTCCCCATCGT 61.749 60.000 0.00 0.00 37.19 3.73
127 128 1.005630 GCGAGGATCTTCCCCATCG 60.006 63.158 0.00 0.00 37.19 3.84
128 129 1.373059 GGCGAGGATCTTCCCCATC 59.627 63.158 3.73 0.00 37.19 3.51
129 130 2.511452 CGGCGAGGATCTTCCCCAT 61.511 63.158 0.00 0.00 37.19 4.00
130 131 3.154473 CGGCGAGGATCTTCCCCA 61.154 66.667 0.00 0.00 37.19 4.96
131 132 4.610714 GCGGCGAGGATCTTCCCC 62.611 72.222 12.98 0.00 37.19 4.81
132 133 4.610714 GGCGGCGAGGATCTTCCC 62.611 72.222 12.98 1.21 37.19 3.97
133 134 4.951963 CGGCGGCGAGGATCTTCC 62.952 72.222 29.19 0.00 36.58 3.46
146 147 4.776322 TCCACTTCCATGGCGGCG 62.776 66.667 6.96 0.51 39.85 6.46
147 148 2.124151 ATCCACTTCCATGGCGGC 60.124 61.111 6.96 0.00 39.85 6.53
148 149 1.526917 GGATCCACTTCCATGGCGG 60.527 63.158 6.96 4.90 39.85 6.13
149 150 0.107017 AAGGATCCACTTCCATGGCG 60.107 55.000 15.82 2.80 39.85 5.69
150 151 1.396653 CAAGGATCCACTTCCATGGC 58.603 55.000 15.82 0.00 39.85 4.40
151 152 1.396653 GCAAGGATCCACTTCCATGG 58.603 55.000 15.82 4.97 41.57 3.66
152 153 1.396653 GGCAAGGATCCACTTCCATG 58.603 55.000 15.82 2.34 38.32 3.66
153 154 0.107017 CGGCAAGGATCCACTTCCAT 60.107 55.000 15.82 0.00 38.32 3.41
154 155 1.299648 CGGCAAGGATCCACTTCCA 59.700 57.895 15.82 0.00 38.32 3.53
155 156 0.744771 GACGGCAAGGATCCACTTCC 60.745 60.000 15.82 8.30 35.90 3.46
156 157 0.744771 GGACGGCAAGGATCCACTTC 60.745 60.000 15.82 4.30 32.35 3.01
157 158 1.299976 GGACGGCAAGGATCCACTT 59.700 57.895 15.82 0.00 32.35 3.16
158 159 2.670148 GGGACGGCAAGGATCCACT 61.670 63.158 15.82 0.00 33.87 4.00
159 160 2.124695 GGGACGGCAAGGATCCAC 60.125 66.667 15.82 2.41 33.87 4.02
160 161 3.407967 GGGGACGGCAAGGATCCA 61.408 66.667 15.82 0.00 33.87 3.41
199 200 4.162690 CTAGGGTGGCCAGCGGTC 62.163 72.222 27.67 14.77 0.00 4.79
201 202 4.162690 GACTAGGGTGGCCAGCGG 62.163 72.222 27.67 21.09 0.00 5.52
202 203 2.185310 AAAGACTAGGGTGGCCAGCG 62.185 60.000 27.67 16.95 0.00 5.18
203 204 0.038310 AAAAGACTAGGGTGGCCAGC 59.962 55.000 27.04 27.04 0.00 4.85
204 205 1.351017 TCAAAAGACTAGGGTGGCCAG 59.649 52.381 5.11 0.00 0.00 4.85
205 206 1.440618 TCAAAAGACTAGGGTGGCCA 58.559 50.000 0.00 0.00 0.00 5.36
206 207 2.808906 ATCAAAAGACTAGGGTGGCC 57.191 50.000 0.00 0.00 0.00 5.36
207 208 6.775594 AAAATATCAAAAGACTAGGGTGGC 57.224 37.500 0.00 0.00 0.00 5.01
270 271 1.062525 GCATAGAGGCGCAAAACCG 59.937 57.895 10.83 0.00 0.00 4.44
279 280 0.676184 TGAGATGACCGCATAGAGGC 59.324 55.000 0.00 0.00 34.11 4.70
302 303 3.797039 CGATGCTTAGGTCTTTGGATCA 58.203 45.455 0.00 0.00 0.00 2.92
307 308 3.688272 CAATGCGATGCTTAGGTCTTTG 58.312 45.455 0.00 0.00 0.00 2.77
318 319 2.191815 TGTAATGTGCAATGCGATGC 57.808 45.000 0.00 6.59 46.58 3.91
319 320 3.500014 TGTTGTAATGTGCAATGCGATG 58.500 40.909 0.00 0.00 0.00 3.84
320 321 3.846423 TGTTGTAATGTGCAATGCGAT 57.154 38.095 0.00 0.00 0.00 4.58
321 322 3.846423 ATGTTGTAATGTGCAATGCGA 57.154 38.095 0.00 0.00 0.00 5.10
322 323 3.061028 CCAATGTTGTAATGTGCAATGCG 59.939 43.478 0.00 0.00 0.00 4.73
345 346 0.532862 ACGCACCAAAGACTGACTGG 60.533 55.000 0.00 0.00 36.24 4.00
355 360 4.544689 GCACACGCACGCACCAAA 62.545 61.111 0.00 0.00 38.36 3.28
413 418 9.190858 CAAATTTTCCGAGATTATGTTTTGACA 57.809 29.630 0.00 0.00 0.00 3.58
423 428 4.082845 TGCCACCAAATTTTCCGAGATTA 58.917 39.130 0.00 0.00 0.00 1.75
448 453 9.965902 GAGGTGGATGATTAACCAGATAATAAT 57.034 33.333 0.00 0.00 36.82 1.28
449 454 8.094548 CGAGGTGGATGATTAACCAGATAATAA 58.905 37.037 0.00 0.00 36.82 1.40
450 455 7.310423 CCGAGGTGGATGATTAACCAGATAATA 60.310 40.741 0.00 0.00 42.00 0.98
453 458 4.283467 CCGAGGTGGATGATTAACCAGATA 59.717 45.833 0.00 0.00 42.00 1.98
496 504 5.427378 TCATGGTCAGCTATTTTGATCGAA 58.573 37.500 0.00 0.00 0.00 3.71
532 540 9.775854 AATCCATCTAGTGAATAGAGAAACATG 57.224 33.333 0.00 0.00 43.78 3.21
673 810 2.224670 ACCCACAGGATACGCTCAAAAA 60.225 45.455 0.00 0.00 46.39 1.94
679 845 2.093658 CAGTAAACCCACAGGATACGCT 60.094 50.000 0.00 0.00 46.39 5.07
680 846 2.093869 TCAGTAAACCCACAGGATACGC 60.094 50.000 0.00 0.00 46.39 4.42
683 849 3.056393 CACGTCAGTAAACCCACAGGATA 60.056 47.826 0.00 0.00 36.73 2.59
686 852 1.508632 CACGTCAGTAAACCCACAGG 58.491 55.000 0.00 0.00 40.04 4.00
691 857 1.005867 TCGCCACGTCAGTAAACCC 60.006 57.895 0.00 0.00 0.00 4.11
692 858 0.598158 TGTCGCCACGTCAGTAAACC 60.598 55.000 0.00 0.00 0.00 3.27
704 2214 1.153842 CTATGCTCACGTGTCGCCA 60.154 57.895 22.82 13.71 0.00 5.69
714 2224 0.249031 CGACGGTGATGCTATGCTCA 60.249 55.000 0.00 0.00 0.00 4.26
748 2261 4.625800 GCCAATGGCTCTCGTTCT 57.374 55.556 18.47 0.00 46.69 3.01
761 2274 1.912763 GCAGAAACCCATGGGCCAA 60.913 57.895 31.73 0.00 39.32 4.52
776 2289 5.556355 TGCTCTCTTTTATTGTCATGCAG 57.444 39.130 0.00 0.00 0.00 4.41
787 2300 7.779798 AGCCCAACATATATTTGCTCTCTTTTA 59.220 33.333 0.00 0.00 0.00 1.52
791 2304 5.316158 AGCCCAACATATATTTGCTCTCT 57.684 39.130 0.00 0.00 0.00 3.10
792 2305 6.396829 AAAGCCCAACATATATTTGCTCTC 57.603 37.500 0.00 0.00 0.00 3.20
793 2306 5.009010 CGAAAGCCCAACATATATTTGCTCT 59.991 40.000 0.00 0.00 0.00 4.09
823 2336 0.249120 CTGATGCAGTGGGTCGGTTA 59.751 55.000 0.00 0.00 0.00 2.85
829 2342 2.034687 GTGGCTGATGCAGTGGGT 59.965 61.111 0.00 0.00 41.91 4.51
849 2362 2.671963 GGCGCCGGAAGAAACCTT 60.672 61.111 12.58 0.00 0.00 3.50
928 2442 2.369394 CTTGGATTTGGGTAGTGGAGC 58.631 52.381 0.00 0.00 0.00 4.70
936 2450 1.901833 GAATGGTGCTTGGATTTGGGT 59.098 47.619 0.00 0.00 0.00 4.51
955 2469 1.209504 GATCTTGTTGGGGATGGACGA 59.790 52.381 0.00 0.00 0.00 4.20
1122 2637 2.664851 CCAACTTGCTCCGTCGCA 60.665 61.111 0.00 0.00 38.31 5.10
1127 2642 1.915078 ATCCCCTCCAACTTGCTCCG 61.915 60.000 0.00 0.00 0.00 4.63
1170 2685 2.891936 GCCGCATCATCGTCAGCA 60.892 61.111 0.00 0.00 0.00 4.41
1211 2726 1.002274 ATCTCCGTTGCCTCCTCCT 59.998 57.895 0.00 0.00 0.00 3.69
1221 2736 3.109612 CTCCGCGTCGATCTCCGTT 62.110 63.158 4.92 0.00 39.75 4.44
1222 2737 3.574445 CTCCGCGTCGATCTCCGT 61.574 66.667 4.92 0.00 39.75 4.69
1332 2847 2.188207 GCCTCCGCTTCCTCCTTC 59.812 66.667 0.00 0.00 0.00 3.46
1333 2848 3.403558 GGCCTCCGCTTCCTCCTT 61.404 66.667 0.00 0.00 34.44 3.36
1749 3267 1.999735 CAGTTCATAATCACACGCGGT 59.000 47.619 12.47 2.05 0.00 5.68
1753 3271 2.674852 AGCAGCAGTTCATAATCACACG 59.325 45.455 0.00 0.00 0.00 4.49
1759 3277 3.693085 CACTTGGAGCAGCAGTTCATAAT 59.307 43.478 0.00 0.00 0.00 1.28
1884 3402 4.563061 CGATGACATATCAGATCCTTGCA 58.437 43.478 0.00 0.00 38.57 4.08
1901 3419 5.822519 ACAAGCCTAAATAAAGATGCGATGA 59.177 36.000 0.00 0.00 0.00 2.92
1907 3425 7.189512 GCACTACACAAGCCTAAATAAAGATG 58.810 38.462 0.00 0.00 0.00 2.90
1932 3450 5.896922 AATTACTGCTGAATTCGAGATCG 57.103 39.130 0.04 0.00 41.45 3.69
1933 3451 8.394121 AGAAAAATTACTGCTGAATTCGAGATC 58.606 33.333 0.04 0.00 0.00 2.75
1934 3452 8.273780 AGAAAAATTACTGCTGAATTCGAGAT 57.726 30.769 0.04 0.00 0.00 2.75
1935 3453 7.672983 AGAAAAATTACTGCTGAATTCGAGA 57.327 32.000 0.04 0.00 0.00 4.04
1936 3454 8.017373 TCAAGAAAAATTACTGCTGAATTCGAG 58.983 33.333 0.04 1.09 0.00 4.04
1937 3455 7.870826 TCAAGAAAAATTACTGCTGAATTCGA 58.129 30.769 0.04 0.00 0.00 3.71
1951 3469 9.211485 CCTGAAACATAATGCTCAAGAAAAATT 57.789 29.630 0.00 0.00 0.00 1.82
1974 3533 0.976641 TGTGTTCTAGACAGGCCCTG 59.023 55.000 9.83 9.83 39.39 4.45
2099 3660 2.091541 ACCAAAGAACTGTGGTGTGTG 58.908 47.619 14.99 0.00 46.53 3.82
2130 3691 5.751586 TGTAACAAAGGGATGGAACCTATC 58.248 41.667 0.00 0.00 37.35 2.08
2131 3692 5.491078 TCTGTAACAAAGGGATGGAACCTAT 59.509 40.000 0.00 0.00 37.35 2.57
2132 3693 4.847512 TCTGTAACAAAGGGATGGAACCTA 59.152 41.667 0.00 0.00 37.35 3.08
2133 3694 3.655777 TCTGTAACAAAGGGATGGAACCT 59.344 43.478 0.00 0.00 40.96 3.50
2134 3695 3.756963 GTCTGTAACAAAGGGATGGAACC 59.243 47.826 0.00 0.00 0.00 3.62
2135 3696 3.756963 GGTCTGTAACAAAGGGATGGAAC 59.243 47.826 0.00 0.00 0.00 3.62
2136 3697 3.655777 AGGTCTGTAACAAAGGGATGGAA 59.344 43.478 0.00 0.00 0.00 3.53
2137 3698 3.009033 CAGGTCTGTAACAAAGGGATGGA 59.991 47.826 0.00 0.00 0.00 3.41
2138 3699 3.347216 CAGGTCTGTAACAAAGGGATGG 58.653 50.000 0.00 0.00 0.00 3.51
2139 3700 2.749621 GCAGGTCTGTAACAAAGGGATG 59.250 50.000 0.00 0.00 0.00 3.51
2140 3701 2.644798 AGCAGGTCTGTAACAAAGGGAT 59.355 45.455 0.00 0.00 0.00 3.85
2141 3702 2.054799 AGCAGGTCTGTAACAAAGGGA 58.945 47.619 0.00 0.00 0.00 4.20
2142 3703 2.568623 AGCAGGTCTGTAACAAAGGG 57.431 50.000 0.00 0.00 0.00 3.95
2143 3704 4.385825 TGTTAGCAGGTCTGTAACAAAGG 58.614 43.478 16.23 0.00 35.86 3.11
2193 3768 9.860650 ACCAATTAATACAGGCAACAATAGATA 57.139 29.630 0.00 0.00 41.41 1.98
2202 3777 2.685897 GCGGACCAATTAATACAGGCAA 59.314 45.455 0.00 0.00 0.00 4.52
2208 3783 5.813080 AACTCTTGCGGACCAATTAATAC 57.187 39.130 0.00 0.00 31.91 1.89
2213 3788 3.950397 TCATAACTCTTGCGGACCAATT 58.050 40.909 0.00 0.00 31.91 2.32
2254 3829 2.543777 AGCCGAGTAACTGCTGAAAA 57.456 45.000 0.00 0.00 37.65 2.29
2267 3842 1.337167 TGACAGTGTTCATCAGCCGAG 60.337 52.381 0.00 0.00 0.00 4.63
2305 3880 3.118738 AGAGACATTACCTAAGGGCAACG 60.119 47.826 0.00 0.00 35.63 4.10
2322 3897 4.439016 CGTCTTAGCTTCCTAACCAGAGAC 60.439 50.000 0.00 0.00 30.63 3.36
2456 4635 7.805071 CCAATCCTAATAAGTTGATTGATTCGC 59.195 37.037 12.22 0.00 44.24 4.70
2470 4649 7.779798 CCTTGAAACTGATCCCAATCCTAATAA 59.220 37.037 0.00 0.00 0.00 1.40
2537 4716 8.252624 AGACTGGTTATAATCCTCTTTAGACC 57.747 38.462 0.00 0.00 0.00 3.85
2617 4797 3.007635 ACCCTTACAACTTTATGCGCTC 58.992 45.455 9.73 0.00 0.00 5.03
2684 4868 5.121105 CAGATCAGATAAGCCATGTTGACA 58.879 41.667 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.