Multiple sequence alignment - TraesCS1A01G059000

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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 TraesCS1A01G059000 chr1A 100.000 2189 0 0 755 2943 39821607 39823795 0.000000e+00 4043
1 TraesCS1A01G059000 chr1A 91.844 797 45 12 1168 1951 39832218 39833007 0.000000e+00 1094
2 TraesCS1A01G059000 chr1A 100.000 386 0 0 1 386 39820853 39821238 0.000000e+00 713
3 TraesCS1A01G059000 chr1A 92.020 401 30 2 1551 1951 39790140 39790538 1.980000e-156 562
4 TraesCS1A01G059000 chr1A 84.264 591 54 17 1370 1951 31945896 31946456 9.280000e-150 540
5 TraesCS1A01G059000 chr3A 95.178 954 44 1 1981 2934 533975015 533975966 0.000000e+00 1506
6 TraesCS1A01G059000 chr3A 95.728 913 37 2 2032 2943 460150922 460150011 0.000000e+00 1469
7 TraesCS1A01G059000 chr7A 94.237 989 42 10 1955 2943 642898028 642899001 0.000000e+00 1496
8 TraesCS1A01G059000 chr2A 94.704 963 51 0 1981 2943 261186479 261185517 0.000000e+00 1496
9 TraesCS1A01G059000 chr2A 95.064 932 42 3 2010 2941 607478479 607479406 0.000000e+00 1463
10 TraesCS1A01G059000 chr2A 97.150 386 11 0 1 386 111452708 111453093 0.000000e+00 652
11 TraesCS1A01G059000 chr2A 96.597 382 9 3 3 382 167345527 167345148 5.350000e-177 630
12 TraesCS1A01G059000 chr2A 97.297 370 8 1 1 370 41007260 41006893 6.920000e-176 627
13 TraesCS1A01G059000 chr5A 94.502 964 51 2 1981 2943 331953662 331954624 0.000000e+00 1485
14 TraesCS1A01G059000 chr5A 94.532 951 49 2 1981 2931 495325968 495325021 0.000000e+00 1465
15 TraesCS1A01G059000 chr5A 93.548 961 57 4 1983 2943 444920896 444921851 0.000000e+00 1426
16 TraesCS1A01G059000 chr5A 96.597 382 10 2 3 382 641761659 641761279 5.350000e-177 630
17 TraesCS1A01G059000 chr1B 89.370 1223 72 25 756 1951 60047475 60048666 0.000000e+00 1485
18 TraesCS1A01G059000 chr1B 89.289 1223 73 25 756 1951 59961039 59962230 0.000000e+00 1480
19 TraesCS1A01G059000 chr1B 90.508 885 71 8 1080 1951 59912796 59913680 0.000000e+00 1157
20 TraesCS1A01G059000 chr1B 90.282 885 73 8 1080 1951 59855327 59856211 0.000000e+00 1146
21 TraesCS1A01G059000 chr1B 90.155 711 62 3 1249 1951 59918450 59919160 0.000000e+00 918
22 TraesCS1A01G059000 chr1B 87.151 179 20 3 758 935 59855031 59855207 1.790000e-47 200
23 TraesCS1A01G059000 chr1B 86.592 179 21 3 758 935 59912500 59912676 8.320000e-46 195
24 TraesCS1A01G059000 chr1B 84.946 186 18 5 758 933 60534800 60534615 2.330000e-41 180
25 TraesCS1A01G059000 chr6A 94.427 951 51 1 1981 2931 526211850 526210902 0.000000e+00 1461
26 TraesCS1A01G059000 chr6A 95.812 382 12 3 3 382 158409978 158409599 5.390000e-172 614
27 TraesCS1A01G059000 chr1D 91.798 890 64 4 1068 1951 40325706 40326592 0.000000e+00 1230
28 TraesCS1A01G059000 chr1D 91.348 890 68 4 1068 1951 40244367 40245253 0.000000e+00 1208
29 TraesCS1A01G059000 chr1D 90.848 896 67 6 1068 1951 40380707 40381599 0.000000e+00 1186
30 TraesCS1A01G059000 chr1D 91.628 872 43 8 1080 1951 40489219 40490060 0.000000e+00 1179
31 TraesCS1A01G059000 chr1D 91.324 876 53 12 1080 1951 40433333 40434189 0.000000e+00 1175
32 TraesCS1A01G059000 chr1D 91.210 876 54 12 1080 1951 40228654 40229510 0.000000e+00 1170
33 TraesCS1A01G059000 chr1D 88.274 921 69 18 1047 1951 40202183 40203080 0.000000e+00 1066
34 TraesCS1A01G059000 chr1D 86.387 191 13 9 756 935 40228353 40228541 2.310000e-46 196
35 TraesCS1A01G059000 chr1D 87.273 165 13 6 783 940 40201967 40202130 6.480000e-42 182
36 TraesCS1A01G059000 chr1D 82.286 175 26 4 765 935 40488939 40489112 2.360000e-31 147
37 TraesCS1A01G059000 chrUn 89.052 886 52 20 1073 1951 335950959 335950112 0.000000e+00 1057
38 TraesCS1A01G059000 chr4A 97.120 382 10 1 3 384 673148156 673147776 0.000000e+00 643
39 TraesCS1A01G059000 chr6B 96.597 382 10 2 3 382 482829896 482829516 5.350000e-177 630
40 TraesCS1A01G059000 chr5B 96.335 382 13 1 3 384 707454679 707454299 6.920000e-176 627
41 TraesCS1A01G059000 chr2B 96.073 382 12 2 3 382 616514708 616514328 1.160000e-173 619
42 TraesCS1A01G059000 chr6D 81.086 571 60 27 1379 1922 25514286 25513737 2.110000e-111 412


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 TraesCS1A01G059000 chr1A 39820853 39823795 2942 False 2378 4043 100.0000 1 2943 2 chr1A.!!$F4 2942
1 TraesCS1A01G059000 chr1A 39832218 39833007 789 False 1094 1094 91.8440 1168 1951 1 chr1A.!!$F3 783
2 TraesCS1A01G059000 chr1A 31945896 31946456 560 False 540 540 84.2640 1370 1951 1 chr1A.!!$F1 581
3 TraesCS1A01G059000 chr3A 533975015 533975966 951 False 1506 1506 95.1780 1981 2934 1 chr3A.!!$F1 953
4 TraesCS1A01G059000 chr3A 460150011 460150922 911 True 1469 1469 95.7280 2032 2943 1 chr3A.!!$R1 911
5 TraesCS1A01G059000 chr7A 642898028 642899001 973 False 1496 1496 94.2370 1955 2943 1 chr7A.!!$F1 988
6 TraesCS1A01G059000 chr2A 261185517 261186479 962 True 1496 1496 94.7040 1981 2943 1 chr2A.!!$R3 962
7 TraesCS1A01G059000 chr2A 607478479 607479406 927 False 1463 1463 95.0640 2010 2941 1 chr2A.!!$F2 931
8 TraesCS1A01G059000 chr5A 331953662 331954624 962 False 1485 1485 94.5020 1981 2943 1 chr5A.!!$F1 962
9 TraesCS1A01G059000 chr5A 495325021 495325968 947 True 1465 1465 94.5320 1981 2931 1 chr5A.!!$R1 950
10 TraesCS1A01G059000 chr5A 444920896 444921851 955 False 1426 1426 93.5480 1983 2943 1 chr5A.!!$F2 960
11 TraesCS1A01G059000 chr1B 60047475 60048666 1191 False 1485 1485 89.3700 756 1951 1 chr1B.!!$F3 1195
12 TraesCS1A01G059000 chr1B 59961039 59962230 1191 False 1480 1480 89.2890 756 1951 1 chr1B.!!$F2 1195
13 TraesCS1A01G059000 chr1B 59918450 59919160 710 False 918 918 90.1550 1249 1951 1 chr1B.!!$F1 702
14 TraesCS1A01G059000 chr1B 59912500 59913680 1180 False 676 1157 88.5500 758 1951 2 chr1B.!!$F5 1193
15 TraesCS1A01G059000 chr1B 59855031 59856211 1180 False 673 1146 88.7165 758 1951 2 chr1B.!!$F4 1193
16 TraesCS1A01G059000 chr6A 526210902 526211850 948 True 1461 1461 94.4270 1981 2931 1 chr6A.!!$R2 950
17 TraesCS1A01G059000 chr1D 40325706 40326592 886 False 1230 1230 91.7980 1068 1951 1 chr1D.!!$F2 883
18 TraesCS1A01G059000 chr1D 40244367 40245253 886 False 1208 1208 91.3480 1068 1951 1 chr1D.!!$F1 883
19 TraesCS1A01G059000 chr1D 40380707 40381599 892 False 1186 1186 90.8480 1068 1951 1 chr1D.!!$F3 883
20 TraesCS1A01G059000 chr1D 40433333 40434189 856 False 1175 1175 91.3240 1080 1951 1 chr1D.!!$F4 871
21 TraesCS1A01G059000 chr1D 40228353 40229510 1157 False 683 1170 88.7985 756 1951 2 chr1D.!!$F6 1195
22 TraesCS1A01G059000 chr1D 40488939 40490060 1121 False 663 1179 86.9570 765 1951 2 chr1D.!!$F7 1186
23 TraesCS1A01G059000 chr1D 40201967 40203080 1113 False 624 1066 87.7735 783 1951 2 chr1D.!!$F5 1168
24 TraesCS1A01G059000 chrUn 335950112 335950959 847 True 1057 1057 89.0520 1073 1951 1 chrUn.!!$R1 878
25 TraesCS1A01G059000 chr6D 25513737 25514286 549 True 412 412 81.0860 1379 1922 1 chr6D.!!$R1 543

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
246 247 0.103572 GATGCCGCTAGGGTTTCGTA 59.896 55.0 6.02 0.0 38.44 3.43 F
247 248 0.179092 ATGCCGCTAGGGTTTCGTAC 60.179 55.0 6.02 0.0 38.44 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1450 1649 1.144716 TGCCCTCTGATGACGATGC 59.855 57.895 0.0 0.0 0.00 3.91 R
1951 2226 1.503542 GCGCCTGTTGGAGATGTTG 59.496 57.895 0.0 0.0 34.95 3.33 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
28 29 4.364409 GCGTTTCACCGGCGACAC 62.364 66.667 9.30 0.00 0.00 3.67
29 30 4.054455 CGTTTCACCGGCGACACG 62.054 66.667 15.85 15.85 33.33 4.49
30 31 2.659244 GTTTCACCGGCGACACGA 60.659 61.111 9.30 0.00 35.47 4.35
31 32 2.659244 TTTCACCGGCGACACGAC 60.659 61.111 9.30 0.00 35.47 4.34
43 44 2.415843 CACGACGTGTGGGTGACT 59.584 61.111 19.77 0.00 45.21 3.41
44 45 1.655885 CACGACGTGTGGGTGACTA 59.344 57.895 19.77 0.00 45.21 2.59
45 46 0.662374 CACGACGTGTGGGTGACTAC 60.662 60.000 19.77 0.00 45.21 2.73
46 47 1.441515 CGACGTGTGGGTGACTACG 60.442 63.158 0.00 0.00 46.30 3.51
47 48 1.080974 GACGTGTGGGTGACTACGG 60.081 63.158 0.00 0.00 46.30 4.02
48 49 1.518056 GACGTGTGGGTGACTACGGA 61.518 60.000 0.00 0.00 46.30 4.69
49 50 1.080974 CGTGTGGGTGACTACGGAC 60.081 63.158 0.00 0.00 46.30 4.79
50 51 1.080974 GTGTGGGTGACTACGGACG 60.081 63.158 0.00 0.00 46.30 4.79
51 52 2.126189 GTGGGTGACTACGGACGC 60.126 66.667 0.00 0.00 29.82 5.19
52 53 3.376078 TGGGTGACTACGGACGCC 61.376 66.667 0.00 0.00 37.13 5.68
71 72 4.707791 TCGGTGCTCACGACTAGA 57.292 55.556 0.00 0.00 35.12 2.43
72 73 2.168947 TCGGTGCTCACGACTAGAC 58.831 57.895 0.00 0.00 35.12 2.59
73 74 1.226046 CGGTGCTCACGACTAGACG 60.226 63.158 13.02 13.02 39.31 4.18
74 75 1.136984 GGTGCTCACGACTAGACGG 59.863 63.158 18.36 7.93 37.61 4.79
75 76 1.136984 GTGCTCACGACTAGACGGG 59.863 63.158 18.36 14.82 38.09 5.28
76 77 2.102553 GCTCACGACTAGACGGGC 59.897 66.667 18.36 14.47 36.57 6.13
77 78 2.697761 GCTCACGACTAGACGGGCA 61.698 63.158 18.36 4.52 36.57 5.36
78 79 1.136984 CTCACGACTAGACGGGCAC 59.863 63.158 18.36 0.00 36.57 5.01
97 98 4.986645 TCGGGGTCGACGTCGTGA 62.987 66.667 34.40 22.08 40.88 4.35
98 99 4.748679 CGGGGTCGACGTCGTGAC 62.749 72.222 34.40 26.06 40.80 3.67
134 135 2.186903 CGTTGATGCCGCTAGGGT 59.813 61.111 6.02 0.00 38.44 4.34
135 136 1.449601 CGTTGATGCCGCTAGGGTT 60.450 57.895 6.02 0.00 38.44 4.11
136 137 1.024579 CGTTGATGCCGCTAGGGTTT 61.025 55.000 6.02 0.00 38.44 3.27
137 138 0.733150 GTTGATGCCGCTAGGGTTTC 59.267 55.000 6.02 0.64 38.44 2.78
138 139 0.393808 TTGATGCCGCTAGGGTTTCC 60.394 55.000 6.02 0.00 38.44 3.13
139 140 1.271840 TGATGCCGCTAGGGTTTCCT 61.272 55.000 6.02 0.00 46.96 3.36
140 141 0.756903 GATGCCGCTAGGGTTTCCTA 59.243 55.000 6.02 0.00 44.38 2.94
146 147 4.386591 TAGGGTTTCCTAGGCGGG 57.613 61.111 2.96 0.00 44.38 6.13
147 148 1.383525 TAGGGTTTCCTAGGCGGGG 60.384 63.158 2.96 0.00 44.38 5.73
148 149 1.889010 TAGGGTTTCCTAGGCGGGGA 61.889 60.000 2.96 0.00 44.38 4.81
149 150 2.076803 GGGTTTCCTAGGCGGGGAT 61.077 63.158 2.96 0.00 32.41 3.85
150 151 1.148498 GGTTTCCTAGGCGGGGATG 59.852 63.158 2.96 0.00 32.41 3.51
151 152 1.148498 GTTTCCTAGGCGGGGATGG 59.852 63.158 2.96 0.00 32.41 3.51
152 153 2.076184 TTTCCTAGGCGGGGATGGG 61.076 63.158 2.96 0.00 32.41 4.00
153 154 4.574614 TCCTAGGCGGGGATGGGG 62.575 72.222 2.96 0.00 0.00 4.96
154 155 4.900259 CCTAGGCGGGGATGGGGT 62.900 72.222 0.00 0.00 0.00 4.95
155 156 3.560251 CTAGGCGGGGATGGGGTG 61.560 72.222 0.00 0.00 0.00 4.61
156 157 4.424867 TAGGCGGGGATGGGGTGT 62.425 66.667 0.00 0.00 0.00 4.16
161 162 3.335729 GGGGATGGGGTGTCGGTT 61.336 66.667 0.00 0.00 0.00 4.44
162 163 2.761160 GGGATGGGGTGTCGGTTT 59.239 61.111 0.00 0.00 0.00 3.27
163 164 1.378119 GGGATGGGGTGTCGGTTTC 60.378 63.158 0.00 0.00 0.00 2.78
164 165 1.377229 GGATGGGGTGTCGGTTTCA 59.623 57.895 0.00 0.00 0.00 2.69
165 166 0.958876 GGATGGGGTGTCGGTTTCAC 60.959 60.000 0.00 0.00 35.36 3.18
166 167 1.296056 GATGGGGTGTCGGTTTCACG 61.296 60.000 0.00 0.00 36.76 4.35
167 168 2.667199 GGGGTGTCGGTTTCACGG 60.667 66.667 0.00 0.00 36.76 4.94
168 169 3.351416 GGGTGTCGGTTTCACGGC 61.351 66.667 0.00 0.00 39.28 5.68
169 170 3.708734 GGTGTCGGTTTCACGGCG 61.709 66.667 4.80 4.80 42.29 6.46
170 171 4.364409 GTGTCGGTTTCACGGCGC 62.364 66.667 6.90 0.00 42.29 6.53
188 189 2.126189 GTGGGTGACTACGGACGC 60.126 66.667 0.00 0.00 29.82 5.19
189 190 3.376078 TGGGTGACTACGGACGCC 61.376 66.667 0.00 0.00 37.13 5.68
210 211 4.771356 CGATGTCGTGACGGCGGT 62.771 66.667 13.24 0.00 32.50 5.68
211 212 3.179265 GATGTCGTGACGGCGGTG 61.179 66.667 13.24 0.00 32.50 4.94
212 213 4.735132 ATGTCGTGACGGCGGTGG 62.735 66.667 13.24 0.00 32.50 4.61
240 241 2.186903 CGTTGATGCCGCTAGGGT 59.813 61.111 6.02 0.00 38.44 4.34
241 242 1.449601 CGTTGATGCCGCTAGGGTT 60.450 57.895 6.02 0.00 38.44 4.11
242 243 1.024579 CGTTGATGCCGCTAGGGTTT 61.025 55.000 6.02 0.00 38.44 3.27
243 244 0.733150 GTTGATGCCGCTAGGGTTTC 59.267 55.000 6.02 0.64 38.44 2.78
244 245 0.742990 TTGATGCCGCTAGGGTTTCG 60.743 55.000 6.02 0.00 38.44 3.46
245 246 1.153429 GATGCCGCTAGGGTTTCGT 60.153 57.895 6.02 0.00 38.44 3.85
246 247 0.103572 GATGCCGCTAGGGTTTCGTA 59.896 55.000 6.02 0.00 38.44 3.43
247 248 0.179092 ATGCCGCTAGGGTTTCGTAC 60.179 55.000 6.02 0.00 38.44 3.67
248 249 1.875364 GCCGCTAGGGTTTCGTACG 60.875 63.158 9.53 9.53 38.44 3.67
249 250 1.875364 CCGCTAGGGTTTCGTACGC 60.875 63.158 11.24 0.00 39.85 4.42
250 251 2.219562 CGCTAGGGTTTCGTACGCG 61.220 63.158 11.24 3.53 43.97 6.01
251 252 1.875364 GCTAGGGTTTCGTACGCGG 60.875 63.158 12.47 0.00 43.97 6.46
252 253 1.802636 CTAGGGTTTCGTACGCGGA 59.197 57.895 12.47 0.00 43.97 5.54
253 254 0.248377 CTAGGGTTTCGTACGCGGAG 60.248 60.000 12.47 0.36 43.97 4.63
254 255 0.676466 TAGGGTTTCGTACGCGGAGA 60.676 55.000 12.47 3.31 43.97 3.71
255 256 1.140375 GGGTTTCGTACGCGGAGAT 59.860 57.895 12.47 0.00 38.89 2.75
256 257 1.143969 GGGTTTCGTACGCGGAGATG 61.144 60.000 12.47 0.31 38.89 2.90
257 258 1.143969 GGTTTCGTACGCGGAGATGG 61.144 60.000 12.47 0.00 38.89 3.51
258 259 1.140161 TTTCGTACGCGGAGATGGG 59.860 57.895 12.47 0.00 38.89 4.00
259 260 2.287457 TTTCGTACGCGGAGATGGGG 62.287 60.000 12.47 0.00 38.89 4.96
260 261 3.524606 CGTACGCGGAGATGGGGT 61.525 66.667 12.47 0.00 0.00 4.95
261 262 2.106332 GTACGCGGAGATGGGGTG 59.894 66.667 12.47 0.00 0.00 4.61
262 263 2.363276 TACGCGGAGATGGGGTGT 60.363 61.111 12.47 0.00 0.00 4.16
263 264 2.420568 TACGCGGAGATGGGGTGTC 61.421 63.158 12.47 0.00 0.00 3.67
264 265 4.873129 CGCGGAGATGGGGTGTCG 62.873 72.222 0.00 0.00 0.00 4.35
265 266 4.530857 GCGGAGATGGGGTGTCGG 62.531 72.222 0.00 0.00 0.00 4.79
266 267 3.849951 CGGAGATGGGGTGTCGGG 61.850 72.222 0.00 0.00 0.00 5.14
267 268 3.480133 GGAGATGGGGTGTCGGGG 61.480 72.222 0.00 0.00 0.00 5.73
268 269 2.687566 GAGATGGGGTGTCGGGGT 60.688 66.667 0.00 0.00 0.00 4.95
269 270 3.009115 AGATGGGGTGTCGGGGTG 61.009 66.667 0.00 0.00 0.00 4.61
270 271 4.109675 GATGGGGTGTCGGGGTGG 62.110 72.222 0.00 0.00 0.00 4.61
280 281 4.024545 CGGGGTGGGGCGTACTTT 62.025 66.667 0.00 0.00 0.00 2.66
281 282 2.437449 GGGGTGGGGCGTACTTTT 59.563 61.111 0.00 0.00 0.00 2.27
282 283 1.228644 GGGGTGGGGCGTACTTTTT 60.229 57.895 0.00 0.00 0.00 1.94
300 301 3.784845 TTTTTCCTTTGCCGATCGC 57.215 47.368 10.32 6.08 38.31 4.58
308 309 3.135457 TGCCGATCGCACTACCGA 61.135 61.111 10.32 0.00 44.64 4.69
309 310 2.103538 GCCGATCGCACTACCGAA 59.896 61.111 10.32 0.00 41.01 4.30
310 311 2.228914 GCCGATCGCACTACCGAAC 61.229 63.158 10.32 0.00 41.01 3.95
311 312 1.588139 CCGATCGCACTACCGAACC 60.588 63.158 10.32 0.00 41.01 3.62
312 313 1.937846 CGATCGCACTACCGAACCG 60.938 63.158 0.26 0.00 41.01 4.44
313 314 2.202703 ATCGCACTACCGAACCGC 60.203 61.111 0.00 0.00 41.01 5.68
314 315 2.877360 GATCGCACTACCGAACCGCA 62.877 60.000 0.00 0.00 41.01 5.69
315 316 3.475774 CGCACTACCGAACCGCAC 61.476 66.667 0.00 0.00 0.00 5.34
316 317 3.475774 GCACTACCGAACCGCACG 61.476 66.667 0.00 0.00 0.00 5.34
317 318 3.475774 CACTACCGAACCGCACGC 61.476 66.667 0.00 0.00 0.00 5.34
320 321 3.665825 CTACCGAACCGCACGCGTA 62.666 63.158 13.44 0.00 37.81 4.42
321 322 3.944526 TACCGAACCGCACGCGTAC 62.945 63.158 13.44 5.01 37.81 3.67
324 325 3.820164 GAACCGCACGCGTACGAC 61.820 66.667 31.90 18.29 43.93 4.34
334 335 2.021931 CGTACGACGCGGGAGTAC 59.978 66.667 22.34 22.34 37.83 2.73
335 336 2.021931 GTACGACGCGGGAGTACG 59.978 66.667 19.51 15.06 32.67 3.67
336 337 3.195002 TACGACGCGGGAGTACGG 61.195 66.667 12.47 0.00 0.00 4.02
384 385 4.783734 GACGGACGGCGGGTACAC 62.784 72.222 13.24 0.00 0.00 2.90
962 1022 2.568696 AACTCGTGGACTCATCATCG 57.431 50.000 0.00 0.00 0.00 3.84
963 1023 1.751437 ACTCGTGGACTCATCATCGA 58.249 50.000 0.00 0.00 33.02 3.59
965 1025 3.477530 ACTCGTGGACTCATCATCGATA 58.522 45.455 0.00 0.00 33.39 2.92
966 1026 3.500299 ACTCGTGGACTCATCATCGATAG 59.500 47.826 0.00 0.00 33.39 2.08
1027 1087 4.779819 GCAGGAGCATTGCTTTCG 57.220 55.556 13.35 5.28 39.88 3.46
1044 1104 0.319211 TCGTTTCTGGCGTTCGTCAT 60.319 50.000 0.00 0.00 0.00 3.06
1134 1216 2.217038 ACAAGCTCTTCTCCCGCCA 61.217 57.895 0.00 0.00 0.00 5.69
1284 1366 2.649034 GCCGACTTCGTCCACAGA 59.351 61.111 0.00 0.00 37.74 3.41
1418 1617 4.354587 GACTGGAACAAGAAGTGCAAAAG 58.645 43.478 0.00 0.00 38.70 2.27
1450 1649 2.473760 ATCTGCTCCTCGTCGTCGG 61.474 63.158 1.55 0.00 37.69 4.79
1546 1754 0.398318 GAAGAAGCCTCACACCACCT 59.602 55.000 0.00 0.00 0.00 4.00
1619 1845 2.355363 CGTCGAACGCTGGGACAA 60.355 61.111 0.00 0.00 33.65 3.18
1633 1859 4.199310 CTGGGACAACAAGAAGAAACTCA 58.801 43.478 0.00 0.00 38.70 3.41
1669 1904 3.716195 CCGTGCCCACAGATCCCA 61.716 66.667 0.00 0.00 0.00 4.37
1756 1997 1.322442 GGACTTGCACAAGAAGCCTT 58.678 50.000 16.95 0.00 40.79 4.35
1764 2005 1.379044 CAAGAAGCCTTGCCCGGAT 60.379 57.895 0.73 0.00 42.72 4.18
1790 2052 0.383949 GAGAAGCTGCCTCGGACTAG 59.616 60.000 0.00 0.00 0.00 2.57
1922 2191 2.158959 GTTCGCGTGCGCTCTGTAT 61.159 57.895 9.73 0.00 39.59 2.29
1951 2226 7.115095 GTCATTAAGTCCATTACAGCGATCTAC 59.885 40.741 0.00 0.00 0.00 2.59
1952 2227 6.459670 TTAAGTCCATTACAGCGATCTACA 57.540 37.500 0.00 0.00 0.00 2.74
1953 2228 5.339008 AAGTCCATTACAGCGATCTACAA 57.661 39.130 0.00 0.00 0.00 2.41
2002 2277 2.681660 CGCTCATCGCCTGATTTGA 58.318 52.632 0.00 0.00 32.10 2.69
2052 2331 2.098298 CTAAAATGCAGCGCGCGT 59.902 55.556 32.35 15.53 46.97 6.01
2225 2507 4.743151 CGAAAGCATAGATAAACTACGGCA 59.257 41.667 0.00 0.00 37.27 5.69
2236 2518 8.004087 AGATAAACTACGGCACAACTAGATAA 57.996 34.615 0.00 0.00 0.00 1.75
2315 2597 1.827969 GTGTCTAGCCAGATGTCCAGT 59.172 52.381 0.00 0.00 32.09 4.00
2327 2609 1.555967 TGTCCAGTCACCGATCATCA 58.444 50.000 0.00 0.00 0.00 3.07
2413 2695 1.896660 GCTGACGCCTTTCCAACCA 60.897 57.895 0.00 0.00 0.00 3.67
2900 3182 1.289530 GGAGAGGAAGAGGGGAAGAGA 59.710 57.143 0.00 0.00 0.00 3.10
2908 3190 2.977808 AGAGGGGAAGAGAAAGTGTGA 58.022 47.619 0.00 0.00 0.00 3.58
2916 3198 3.460857 AGAGAAAGTGTGAAGAAGCGT 57.539 42.857 0.00 0.00 0.00 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.364409 GTGTCGCCGGTGAAACGC 62.364 66.667 22.10 13.15 38.12 4.84
12 13 4.054455 CGTGTCGCCGGTGAAACG 62.054 66.667 37.97 37.97 42.57 3.60
13 14 2.659244 TCGTGTCGCCGGTGAAAC 60.659 61.111 25.74 25.74 0.00 2.78
14 15 2.659244 GTCGTGTCGCCGGTGAAA 60.659 61.111 21.49 12.66 0.00 2.69
15 16 4.986587 CGTCGTGTCGCCGGTGAA 62.987 66.667 21.49 7.55 0.00 3.18
22 23 4.936823 ACCCACACGTCGTGTCGC 62.937 66.667 27.44 0.00 43.92 5.19
23 24 3.028019 CACCCACACGTCGTGTCG 61.028 66.667 27.44 21.09 43.92 4.35
24 25 1.947642 GTCACCCACACGTCGTGTC 60.948 63.158 27.44 12.06 43.92 3.67
26 27 0.662374 GTAGTCACCCACACGTCGTG 60.662 60.000 23.40 23.40 45.92 4.35
27 28 1.656441 GTAGTCACCCACACGTCGT 59.344 57.895 0.00 0.00 0.00 4.34
28 29 1.441515 CGTAGTCACCCACACGTCG 60.442 63.158 0.00 0.00 0.00 5.12
29 30 1.080974 CCGTAGTCACCCACACGTC 60.081 63.158 0.00 0.00 31.48 4.34
30 31 1.529010 TCCGTAGTCACCCACACGT 60.529 57.895 0.00 0.00 31.48 4.49
31 32 1.080974 GTCCGTAGTCACCCACACG 60.081 63.158 0.00 0.00 32.53 4.49
32 33 1.080974 CGTCCGTAGTCACCCACAC 60.081 63.158 0.00 0.00 0.00 3.82
33 34 2.922950 GCGTCCGTAGTCACCCACA 61.923 63.158 0.00 0.00 0.00 4.17
34 35 2.126189 GCGTCCGTAGTCACCCAC 60.126 66.667 0.00 0.00 0.00 4.61
35 36 3.376078 GGCGTCCGTAGTCACCCA 61.376 66.667 0.00 0.00 0.00 4.51
36 37 4.487412 CGGCGTCCGTAGTCACCC 62.487 72.222 9.69 0.00 42.73 4.61
54 55 1.632948 CGTCTAGTCGTGAGCACCGA 61.633 60.000 0.93 0.00 0.00 4.69
55 56 1.226046 CGTCTAGTCGTGAGCACCG 60.226 63.158 0.93 0.00 0.00 4.94
56 57 1.136984 CCGTCTAGTCGTGAGCACC 59.863 63.158 8.53 0.00 0.00 5.01
57 58 1.136984 CCCGTCTAGTCGTGAGCAC 59.863 63.158 8.53 0.00 0.00 4.40
58 59 2.697761 GCCCGTCTAGTCGTGAGCA 61.698 63.158 8.53 0.00 0.00 4.26
59 60 2.102553 GCCCGTCTAGTCGTGAGC 59.897 66.667 8.53 4.88 0.00 4.26
60 61 1.136984 GTGCCCGTCTAGTCGTGAG 59.863 63.158 8.53 0.00 0.00 3.51
61 62 2.683859 CGTGCCCGTCTAGTCGTGA 61.684 63.158 8.53 0.00 0.00 4.35
62 63 2.202440 CGTGCCCGTCTAGTCGTG 60.202 66.667 8.53 0.00 0.00 4.35
63 64 2.670934 ACGTGCCCGTCTAGTCGT 60.671 61.111 8.53 0.00 46.28 4.34
80 81 4.986645 TCACGACGTCGACCCCGA 62.987 66.667 41.52 24.79 43.02 5.14
81 82 4.748679 GTCACGACGTCGACCCCG 62.749 72.222 41.52 23.13 43.02 5.73
117 118 1.024579 AAACCCTAGCGGCATCAACG 61.025 55.000 1.45 0.00 33.26 4.10
118 119 0.733150 GAAACCCTAGCGGCATCAAC 59.267 55.000 1.45 0.00 33.26 3.18
119 120 0.393808 GGAAACCCTAGCGGCATCAA 60.394 55.000 1.45 0.00 33.26 2.57
120 121 1.223487 GGAAACCCTAGCGGCATCA 59.777 57.895 1.45 0.00 33.26 3.07
121 122 0.756903 TAGGAAACCCTAGCGGCATC 59.243 55.000 1.45 0.00 35.26 3.91
122 123 0.759346 CTAGGAAACCCTAGCGGCAT 59.241 55.000 1.45 0.00 44.75 4.40
123 124 2.208527 CTAGGAAACCCTAGCGGCA 58.791 57.895 1.45 0.00 44.75 5.69
129 130 1.383525 CCCCGCCTAGGAAACCCTA 60.384 63.158 14.75 0.00 45.00 3.53
130 131 2.562973 ATCCCCGCCTAGGAAACCCT 62.563 60.000 14.75 0.00 45.00 4.34
131 132 2.076803 ATCCCCGCCTAGGAAACCC 61.077 63.158 14.75 0.00 45.00 4.11
132 133 1.148498 CATCCCCGCCTAGGAAACC 59.852 63.158 14.75 0.00 45.00 3.27
133 134 1.148498 CCATCCCCGCCTAGGAAAC 59.852 63.158 14.75 0.00 45.00 2.78
134 135 2.076184 CCCATCCCCGCCTAGGAAA 61.076 63.158 14.75 0.00 45.00 3.13
135 136 2.447765 CCCATCCCCGCCTAGGAA 60.448 66.667 14.75 0.00 45.00 3.36
136 137 4.574614 CCCCATCCCCGCCTAGGA 62.575 72.222 14.75 0.00 45.00 2.94
137 138 4.900259 ACCCCATCCCCGCCTAGG 62.900 72.222 3.67 3.67 40.63 3.02
138 139 3.560251 CACCCCATCCCCGCCTAG 61.560 72.222 0.00 0.00 0.00 3.02
139 140 4.424867 ACACCCCATCCCCGCCTA 62.425 66.667 0.00 0.00 0.00 3.93
144 145 2.831894 GAAACCGACACCCCATCCCC 62.832 65.000 0.00 0.00 0.00 4.81
145 146 1.378119 GAAACCGACACCCCATCCC 60.378 63.158 0.00 0.00 0.00 3.85
146 147 0.958876 GTGAAACCGACACCCCATCC 60.959 60.000 0.00 0.00 32.84 3.51
147 148 1.296056 CGTGAAACCGACACCCCATC 61.296 60.000 0.00 0.00 35.17 3.51
148 149 1.302192 CGTGAAACCGACACCCCAT 60.302 57.895 0.00 0.00 35.17 4.00
149 150 2.109387 CGTGAAACCGACACCCCA 59.891 61.111 0.00 0.00 35.17 4.96
150 151 2.667199 CCGTGAAACCGACACCCC 60.667 66.667 0.00 0.00 35.17 4.95
151 152 3.351416 GCCGTGAAACCGACACCC 61.351 66.667 0.00 0.00 35.17 4.61
152 153 3.708734 CGCCGTGAAACCGACACC 61.709 66.667 0.00 0.00 35.17 4.16
153 154 4.364409 GCGCCGTGAAACCGACAC 62.364 66.667 0.00 0.00 35.26 3.67
168 169 3.740397 TCCGTAGTCACCCACGCG 61.740 66.667 3.53 3.53 36.85 6.01
169 170 2.126189 GTCCGTAGTCACCCACGC 60.126 66.667 0.00 0.00 36.85 5.34
170 171 2.177531 CGTCCGTAGTCACCCACG 59.822 66.667 0.00 0.00 37.89 4.94
171 172 2.126189 GCGTCCGTAGTCACCCAC 60.126 66.667 0.00 0.00 0.00 4.61
172 173 3.376078 GGCGTCCGTAGTCACCCA 61.376 66.667 0.00 0.00 0.00 4.51
173 174 4.487412 CGGCGTCCGTAGTCACCC 62.487 72.222 9.69 0.00 42.73 4.61
193 194 4.771356 ACCGCCGTCACGACATCG 62.771 66.667 0.00 0.00 46.33 3.84
194 195 3.179265 CACCGCCGTCACGACATC 61.179 66.667 0.00 0.00 34.06 3.06
195 196 4.735132 CCACCGCCGTCACGACAT 62.735 66.667 0.00 0.00 34.06 3.06
223 224 1.024579 AAACCCTAGCGGCATCAACG 61.025 55.000 1.45 0.00 33.26 4.10
224 225 0.733150 GAAACCCTAGCGGCATCAAC 59.267 55.000 1.45 0.00 33.26 3.18
225 226 0.742990 CGAAACCCTAGCGGCATCAA 60.743 55.000 1.45 0.00 33.26 2.57
226 227 1.153449 CGAAACCCTAGCGGCATCA 60.153 57.895 1.45 0.00 33.26 3.07
227 228 0.103572 TACGAAACCCTAGCGGCATC 59.896 55.000 1.45 0.00 33.26 3.91
228 229 0.179092 GTACGAAACCCTAGCGGCAT 60.179 55.000 1.45 0.00 33.26 4.40
229 230 1.216178 GTACGAAACCCTAGCGGCA 59.784 57.895 1.45 0.00 33.26 5.69
230 231 1.875364 CGTACGAAACCCTAGCGGC 60.875 63.158 10.44 0.00 33.26 6.53
231 232 1.875364 GCGTACGAAACCCTAGCGG 60.875 63.158 21.65 0.00 37.81 5.52
232 233 2.219562 CGCGTACGAAACCCTAGCG 61.220 63.158 21.65 5.46 43.93 4.26
233 234 1.875364 CCGCGTACGAAACCCTAGC 60.875 63.158 21.65 0.00 43.93 3.42
234 235 0.248377 CTCCGCGTACGAAACCCTAG 60.248 60.000 21.65 1.77 43.93 3.02
235 236 0.676466 TCTCCGCGTACGAAACCCTA 60.676 55.000 21.65 0.00 43.93 3.53
236 237 1.318158 ATCTCCGCGTACGAAACCCT 61.318 55.000 21.65 0.00 43.93 4.34
237 238 1.140375 ATCTCCGCGTACGAAACCC 59.860 57.895 21.65 0.00 43.93 4.11
238 239 1.143969 CCATCTCCGCGTACGAAACC 61.144 60.000 21.65 0.00 43.93 3.27
239 240 1.143969 CCCATCTCCGCGTACGAAAC 61.144 60.000 21.65 0.00 43.93 2.78
240 241 1.140161 CCCATCTCCGCGTACGAAA 59.860 57.895 21.65 1.69 43.93 3.46
241 242 2.777972 CCCCATCTCCGCGTACGAA 61.778 63.158 21.65 2.09 43.93 3.85
242 243 3.214123 CCCCATCTCCGCGTACGA 61.214 66.667 21.65 0.00 43.93 3.43
243 244 3.524606 ACCCCATCTCCGCGTACG 61.525 66.667 11.84 11.84 39.67 3.67
244 245 2.106332 CACCCCATCTCCGCGTAC 59.894 66.667 4.92 0.00 0.00 3.67
245 246 2.363276 ACACCCCATCTCCGCGTA 60.363 61.111 4.92 0.00 0.00 4.42
246 247 3.771160 GACACCCCATCTCCGCGT 61.771 66.667 4.92 0.00 0.00 6.01
247 248 4.873129 CGACACCCCATCTCCGCG 62.873 72.222 0.00 0.00 0.00 6.46
248 249 4.530857 CCGACACCCCATCTCCGC 62.531 72.222 0.00 0.00 0.00 5.54
249 250 3.849951 CCCGACACCCCATCTCCG 61.850 72.222 0.00 0.00 0.00 4.63
250 251 3.480133 CCCCGACACCCCATCTCC 61.480 72.222 0.00 0.00 0.00 3.71
251 252 2.687566 ACCCCGACACCCCATCTC 60.688 66.667 0.00 0.00 0.00 2.75
252 253 3.009115 CACCCCGACACCCCATCT 61.009 66.667 0.00 0.00 0.00 2.90
253 254 4.109675 CCACCCCGACACCCCATC 62.110 72.222 0.00 0.00 0.00 3.51
263 264 3.556298 AAAAGTACGCCCCACCCCG 62.556 63.158 0.00 0.00 0.00 5.73
264 265 1.228644 AAAAAGTACGCCCCACCCC 60.229 57.895 0.00 0.00 0.00 4.95
265 266 4.506039 AAAAAGTACGCCCCACCC 57.494 55.556 0.00 0.00 0.00 4.61
282 283 3.784845 GCGATCGGCAAAGGAAAAA 57.215 47.368 18.30 0.00 42.87 1.94
292 293 2.103538 TTCGGTAGTGCGATCGGC 59.896 61.111 18.30 9.85 43.96 5.54
293 294 1.588139 GGTTCGGTAGTGCGATCGG 60.588 63.158 18.30 0.00 0.00 4.18
294 295 1.937846 CGGTTCGGTAGTGCGATCG 60.938 63.158 11.69 11.69 0.00 3.69
295 296 2.228914 GCGGTTCGGTAGTGCGATC 61.229 63.158 0.00 0.00 0.00 3.69
296 297 2.202703 GCGGTTCGGTAGTGCGAT 60.203 61.111 0.00 0.00 0.00 4.58
297 298 3.672447 TGCGGTTCGGTAGTGCGA 61.672 61.111 0.00 0.00 0.00 5.10
298 299 3.475774 GTGCGGTTCGGTAGTGCG 61.476 66.667 0.00 0.00 0.00 5.34
299 300 3.475774 CGTGCGGTTCGGTAGTGC 61.476 66.667 0.00 0.00 0.00 4.40
300 301 3.475774 GCGTGCGGTTCGGTAGTG 61.476 66.667 0.00 0.00 0.00 2.74
302 303 3.665825 TACGCGTGCGGTTCGGTAG 62.666 63.158 24.59 0.00 44.69 3.18
303 304 3.731826 TACGCGTGCGGTTCGGTA 61.732 61.111 24.59 0.00 44.69 4.02
307 308 3.820164 GTCGTACGCGTGCGGTTC 61.820 66.667 40.89 28.76 44.69 3.62
317 318 2.021931 GTACTCCCGCGTCGTACG 59.978 66.667 9.53 9.53 45.88 3.67
318 319 2.021931 CGTACTCCCGCGTCGTAC 59.978 66.667 4.92 11.99 0.00 3.67
319 320 3.195002 CCGTACTCCCGCGTCGTA 61.195 66.667 4.92 0.00 0.00 3.43
364 365 4.769063 TACCCGCCGTCCGTCGTA 62.769 66.667 0.00 0.00 37.94 3.43
367 368 4.783734 GTGTACCCGCCGTCCGTC 62.784 72.222 0.00 0.00 34.38 4.79
793 794 6.507900 CGTATCTCCTTGTGATTAGTGATGT 58.492 40.000 0.00 0.00 0.00 3.06
979 1039 6.378582 GCGTGGAAAGAAATCAAGAAATACA 58.621 36.000 0.00 0.00 0.00 2.29
1027 1087 2.034842 CGATATGACGAACGCCAGAAAC 60.035 50.000 0.00 0.00 35.09 2.78
1044 1104 5.067283 TCGAGATTGTTTGATGGAGACGATA 59.933 40.000 0.00 0.00 0.00 2.92
1159 1241 1.449353 GGAGGATCGGCAGCATCTT 59.551 57.895 0.00 0.00 34.37 2.40
1284 1366 1.355720 CCCTTCTTGTTCCAGTCCCAT 59.644 52.381 0.00 0.00 0.00 4.00
1418 1617 2.194212 CAGATGGAGCTGCATGGCC 61.194 63.158 26.69 11.35 0.00 5.36
1450 1649 1.144716 TGCCCTCTGATGACGATGC 59.855 57.895 0.00 0.00 0.00 3.91
1546 1754 2.159435 ACGATGACGATGACGATGACAA 60.159 45.455 0.00 0.00 42.66 3.18
1619 1845 3.132289 TGAGGTCGTGAGTTTCTTCTTGT 59.868 43.478 0.00 0.00 0.00 3.16
1654 1880 2.439156 GCTGGGATCTGTGGGCAC 60.439 66.667 0.00 0.00 0.00 5.01
1756 1997 3.147595 CTCCGTCTGATCCGGGCA 61.148 66.667 0.00 0.00 45.51 5.36
1764 2005 1.599606 GAGGCAGCTTCTCCGTCTGA 61.600 60.000 0.00 0.00 0.00 3.27
1922 2191 6.869695 TCGCTGTAATGGACTTAATGACTTA 58.130 36.000 0.00 0.00 0.00 2.24
1951 2226 1.503542 GCGCCTGTTGGAGATGTTG 59.496 57.895 0.00 0.00 34.95 3.33
1952 2227 1.675641 GGCGCCTGTTGGAGATGTT 60.676 57.895 22.15 0.00 34.95 2.71
1953 2228 2.045926 GGCGCCTGTTGGAGATGT 60.046 61.111 22.15 0.00 34.95 3.06
2177 2459 7.148457 CGAACTATCTATCTAGTTGCACCGATA 60.148 40.741 1.47 0.00 41.00 2.92
2251 2533 7.052248 GGATGATAATGGTGATGATGATAGCA 58.948 38.462 0.00 0.00 0.00 3.49
2327 2609 2.126228 TCGTTCTTCGCGCCGAAT 60.126 55.556 13.51 0.00 44.85 3.34
2900 3182 1.670811 CCACACGCTTCTTCACACTTT 59.329 47.619 0.00 0.00 0.00 2.66
2908 3190 2.607892 GCTTCGCCACACGCTTCTT 61.608 57.895 0.00 0.00 43.23 2.52


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

AutoCloner maintained by Alex Coulton.