Multiple sequence alignment - TraesCS2A01G055300

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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 TraesCS2A01G055300 chr2A 100.000 1708 0 0 986 2693 23826122 23827829 0.000000e+00 3155.0
1 TraesCS2A01G055300 chr2A 90.060 1006 72 18 1013 1990 23864367 23865372 0.000000e+00 1279.0
2 TraesCS2A01G055300 chr2A 100.000 682 0 0 1 682 23825137 23825818 0.000000e+00 1260.0
3 TraesCS2A01G055300 chr2A 90.041 241 17 4 1992 2232 23865455 23865688 3.370000e-79 305.0
4 TraesCS2A01G055300 chr2A 82.727 330 33 16 355 682 23863992 23864299 3.420000e-69 272.0
5 TraesCS2A01G055300 chr2D 95.020 984 49 0 1007 1990 21617456 21618439 0.000000e+00 1546.0
6 TraesCS2A01G055300 chr2D 91.823 1015 69 9 987 1990 21639783 21640794 0.000000e+00 1402.0
7 TraesCS2A01G055300 chr2D 94.927 887 42 1 986 1872 21743108 21743991 0.000000e+00 1386.0
8 TraesCS2A01G055300 chr2D 94.589 887 45 1 986 1872 21770843 21771726 0.000000e+00 1369.0
9 TraesCS2A01G055300 chr2D 90.828 1014 81 9 986 1990 21662185 21663195 0.000000e+00 1347.0
10 TraesCS2A01G055300 chr2D 90.828 1014 81 9 986 1990 21678600 21679610 0.000000e+00 1347.0
11 TraesCS2A01G055300 chr2D 90.665 707 46 13 1992 2693 21618521 21619212 0.000000e+00 922.0
12 TraesCS2A01G055300 chr2D 88.226 603 46 16 1992 2574 21663277 21663874 0.000000e+00 697.0
13 TraesCS2A01G055300 chr2D 88.226 603 46 16 1992 2574 21679692 21680289 0.000000e+00 697.0
14 TraesCS2A01G055300 chr2D 88.060 603 47 16 1992 2574 21640878 21641475 0.000000e+00 691.0
15 TraesCS2A01G055300 chr2D 86.071 481 35 13 1992 2469 21744217 21744668 3.120000e-134 488.0
16 TraesCS2A01G055300 chr2D 85.386 479 38 12 1992 2469 21771952 21772399 4.060000e-128 468.0
17 TraesCS2A01G055300 chr2D 90.415 313 21 5 373 682 21742754 21743060 1.160000e-108 403.0
18 TraesCS2A01G055300 chr2D 90.096 313 22 5 373 682 21770489 21770795 5.400000e-107 398.0
19 TraesCS2A01G055300 chr2D 88.179 313 27 6 354 662 21661842 21662148 5.480000e-97 364.0
20 TraesCS2A01G055300 chr2D 88.179 313 27 6 354 662 21678257 21678563 5.480000e-97 364.0
21 TraesCS2A01G055300 chr2D 88.538 253 14 6 1 241 21770243 21770492 2.620000e-75 292.0
22 TraesCS2A01G055300 chr2D 87.747 253 15 7 1 241 21742509 21742757 5.680000e-72 281.0
23 TraesCS2A01G055300 chr2D 90.476 210 16 3 354 561 21635847 21636054 9.500000e-70 274.0
24 TraesCS2A01G055300 chr2D 92.896 183 9 2 1 182 21633819 21633998 2.060000e-66 263.0
25 TraesCS2A01G055300 chr2D 92.896 183 9 4 1 182 21659801 21659980 2.060000e-66 263.0
26 TraesCS2A01G055300 chr2D 92.350 183 10 4 1 182 21676205 21676384 9.570000e-65 257.0
27 TraesCS2A01G055300 chr2D 92.537 67 5 0 175 241 21635744 21635810 2.210000e-16 97.1
28 TraesCS2A01G055300 chr2B 91.829 1028 56 9 986 1990 34867109 34866087 0.000000e+00 1408.0
29 TraesCS2A01G055300 chr2B 91.243 708 59 3 1172 1878 34954092 34953387 0.000000e+00 961.0
30 TraesCS2A01G055300 chr2B 87.168 452 40 13 2124 2572 34865906 34865470 5.180000e-137 497.0
31 TraesCS2A01G055300 chr2B 90.062 322 27 5 1995 2314 34953160 34952842 1.930000e-111 412.0
32 TraesCS2A01G055300 chr2B 92.381 210 16 0 391 600 34867411 34867202 1.570000e-77 300.0
33 TraesCS2A01G055300 chr2B 88.189 254 18 8 1 244 35012171 35011920 2.620000e-75 292.0
34 TraesCS2A01G055300 chr2B 91.905 210 12 4 356 562 35011905 35011698 3.390000e-74 289.0
35 TraesCS2A01G055300 chrUn 89.641 251 17 5 435 682 477929041 477928797 7.240000e-81 311.0
36 TraesCS2A01G055300 chr6A 87.879 99 8 2 355 449 604579314 604579216 2.190000e-21 113.0
37 TraesCS2A01G055300 chr4B 97.143 35 1 0 92 126 530021697 530021663 2.900000e-05 60.2


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 TraesCS2A01G055300 chr2A 23825137 23827829 2692 False 2207.500000 3155 100.000000 1 2693 2 chr2A.!!$F1 2692
1 TraesCS2A01G055300 chr2A 23863992 23865688 1696 False 618.666667 1279 87.609333 355 2232 3 chr2A.!!$F2 1877
2 TraesCS2A01G055300 chr2D 21617456 21619212 1756 False 1234.000000 1546 92.842500 1007 2693 2 chr2D.!!$F1 1686
3 TraesCS2A01G055300 chr2D 21659801 21663874 4073 False 667.750000 1347 90.032250 1 2574 4 chr2D.!!$F3 2573
4 TraesCS2A01G055300 chr2D 21676205 21680289 4084 False 666.250000 1347 89.895750 1 2574 4 chr2D.!!$F4 2573
5 TraesCS2A01G055300 chr2D 21742509 21744668 2159 False 639.500000 1386 89.790000 1 2469 4 chr2D.!!$F5 2468
6 TraesCS2A01G055300 chr2D 21770243 21772399 2156 False 631.750000 1369 89.652250 1 2469 4 chr2D.!!$F6 2468
7 TraesCS2A01G055300 chr2D 21633819 21641475 7656 False 545.420000 1402 91.158400 1 2574 5 chr2D.!!$F2 2573
8 TraesCS2A01G055300 chr2B 34865470 34867411 1941 True 735.000000 1408 90.459333 391 2572 3 chr2B.!!$R1 2181
9 TraesCS2A01G055300 chr2B 34952842 34954092 1250 True 686.500000 961 90.652500 1172 2314 2 chr2B.!!$R2 1142

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
258 2042 0.025770 GCGTACACACACACACACAC 59.974 55.0 0.0 0.0 0.0 3.82 F
299 2083 0.173708 TACACTCACACACACGCACA 59.826 50.0 0.0 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1452 6879 1.236616 CCGTGAAGAAGGCATGCACA 61.237 55.000 21.36 6.44 0.0 4.57 R
2252 7799 2.845659 AGTGGGGGTATGATGAAGACA 58.154 47.619 0.00 0.00 0.0 3.41 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
69 71 1.315257 CGGAAATCAACCAGCCAGGG 61.315 60.000 0.00 0.00 43.89 4.45
76 78 2.227036 AACCAGCCAGGGGAGACAG 61.227 63.158 0.00 0.00 43.89 3.51
135 137 6.659668 TCCGTCCCATAATGTATTGTCAAAAA 59.340 34.615 0.00 0.00 0.00 1.94
210 1994 7.060518 CGATCGATGCTTATCTAGTTCTCTTTG 59.939 40.741 10.26 0.00 0.00 2.77
237 2021 3.821033 CCTTTCCGGAACAAGACTTGAAT 59.179 43.478 18.64 9.81 33.16 2.57
238 2022 5.001232 CCTTTCCGGAACAAGACTTGAATA 58.999 41.667 18.64 0.00 33.16 1.75
239 2023 5.122396 CCTTTCCGGAACAAGACTTGAATAG 59.878 44.000 18.64 6.55 33.16 1.73
240 2024 3.596214 TCCGGAACAAGACTTGAATAGC 58.404 45.455 21.95 5.75 0.00 2.97
241 2025 2.348666 CCGGAACAAGACTTGAATAGCG 59.651 50.000 21.95 1.04 0.00 4.26
242 2026 2.993899 CGGAACAAGACTTGAATAGCGT 59.006 45.455 21.95 0.00 0.00 5.07
243 2027 4.171005 CGGAACAAGACTTGAATAGCGTA 58.829 43.478 21.95 0.00 0.00 4.42
244 2028 4.031426 CGGAACAAGACTTGAATAGCGTAC 59.969 45.833 21.95 2.54 0.00 3.67
245 2029 4.927425 GGAACAAGACTTGAATAGCGTACA 59.073 41.667 21.95 0.00 0.00 2.90
246 2030 5.163982 GGAACAAGACTTGAATAGCGTACAC 60.164 44.000 21.95 0.00 0.00 2.90
247 2031 4.878439 ACAAGACTTGAATAGCGTACACA 58.122 39.130 21.95 0.00 0.00 3.72
248 2032 4.684703 ACAAGACTTGAATAGCGTACACAC 59.315 41.667 21.95 0.00 0.00 3.82
249 2033 4.514781 AGACTTGAATAGCGTACACACA 57.485 40.909 0.00 0.00 0.00 3.72
250 2034 4.235360 AGACTTGAATAGCGTACACACAC 58.765 43.478 0.00 0.00 0.00 3.82
251 2035 3.985008 ACTTGAATAGCGTACACACACA 58.015 40.909 0.00 0.00 0.00 3.72
252 2036 3.739300 ACTTGAATAGCGTACACACACAC 59.261 43.478 0.00 0.00 0.00 3.82
253 2037 3.372660 TGAATAGCGTACACACACACA 57.627 42.857 0.00 0.00 0.00 3.72
254 2038 3.054166 TGAATAGCGTACACACACACAC 58.946 45.455 0.00 0.00 0.00 3.82
255 2039 2.804697 ATAGCGTACACACACACACA 57.195 45.000 0.00 0.00 0.00 3.72
256 2040 1.842720 TAGCGTACACACACACACAC 58.157 50.000 0.00 0.00 0.00 3.82
257 2041 0.108567 AGCGTACACACACACACACA 60.109 50.000 0.00 0.00 0.00 3.72
258 2042 0.025770 GCGTACACACACACACACAC 59.974 55.000 0.00 0.00 0.00 3.82
259 2043 1.351153 CGTACACACACACACACACA 58.649 50.000 0.00 0.00 0.00 3.72
260 2044 1.059979 CGTACACACACACACACACAC 59.940 52.381 0.00 0.00 0.00 3.82
261 2045 2.070028 GTACACACACACACACACACA 58.930 47.619 0.00 0.00 0.00 3.72
262 2046 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
263 2047 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
264 2048 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
265 2049 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
266 2050 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
267 2051 0.179227 CACACACACACACACACACG 60.179 55.000 0.00 0.00 0.00 4.49
268 2052 1.225991 CACACACACACACACACGC 60.226 57.895 0.00 0.00 0.00 5.34
269 2053 1.669437 ACACACACACACACACGCA 60.669 52.632 0.00 0.00 0.00 5.24
270 2054 1.225991 CACACACACACACACGCAC 60.226 57.895 0.00 0.00 0.00 5.34
271 2055 2.021243 CACACACACACACGCACG 59.979 61.111 0.00 0.00 0.00 5.34
272 2056 3.860125 ACACACACACACGCACGC 61.860 61.111 0.00 0.00 0.00 5.34
273 2057 3.858989 CACACACACACGCACGCA 61.859 61.111 0.00 0.00 0.00 5.24
274 2058 3.860125 ACACACACACGCACGCAC 61.860 61.111 0.00 0.00 0.00 5.34
275 2059 4.918060 CACACACACGCACGCACG 62.918 66.667 0.00 0.00 39.50 5.34
284 2068 4.696172 GCACGCACGCACGTACAC 62.696 66.667 2.78 0.00 46.34 2.90
285 2069 3.028019 CACGCACGCACGTACACT 61.028 61.111 2.78 0.00 46.34 3.55
286 2070 2.728383 ACGCACGCACGTACACTC 60.728 61.111 0.96 0.00 46.19 3.51
287 2071 2.728015 CGCACGCACGTACACTCA 60.728 61.111 0.00 0.00 0.00 3.41
288 2072 2.844146 GCACGCACGTACACTCAC 59.156 61.111 0.00 0.00 0.00 3.51
289 2073 1.947146 GCACGCACGTACACTCACA 60.947 57.895 0.00 0.00 0.00 3.58
290 2074 1.844003 CACGCACGTACACTCACAC 59.156 57.895 0.00 0.00 0.00 3.82
291 2075 0.868177 CACGCACGTACACTCACACA 60.868 55.000 0.00 0.00 0.00 3.72
292 2076 0.868602 ACGCACGTACACTCACACAC 60.869 55.000 0.00 0.00 0.00 3.82
293 2077 0.868177 CGCACGTACACTCACACACA 60.868 55.000 0.00 0.00 0.00 3.72
294 2078 0.575390 GCACGTACACTCACACACAC 59.425 55.000 0.00 0.00 0.00 3.82
295 2079 0.843872 CACGTACACTCACACACACG 59.156 55.000 0.00 0.00 35.62 4.49
296 2080 0.868602 ACGTACACTCACACACACGC 60.869 55.000 0.00 0.00 32.90 5.34
297 2081 0.868177 CGTACACTCACACACACGCA 60.868 55.000 0.00 0.00 0.00 5.24
298 2082 0.575390 GTACACTCACACACACGCAC 59.425 55.000 0.00 0.00 0.00 5.34
299 2083 0.173708 TACACTCACACACACGCACA 59.826 50.000 0.00 0.00 0.00 4.57
300 2084 1.348250 CACTCACACACACGCACAC 59.652 57.895 0.00 0.00 0.00 3.82
302 2086 3.491508 CTCACACACACGCACACGC 62.492 63.158 0.00 0.00 45.53 5.34
303 2087 3.858989 CACACACACGCACACGCA 61.859 61.111 0.00 0.00 45.53 5.24
304 2088 3.860125 ACACACACGCACACGCAC 61.860 61.111 0.00 0.00 45.53 5.34
305 2089 4.918060 CACACACGCACACGCACG 62.918 66.667 0.00 0.00 45.53 5.34
307 2091 3.323903 CACACGCACACGCACGTA 61.324 61.111 0.00 0.00 45.53 3.57
308 2092 3.324671 ACACGCACACGCACGTAC 61.325 61.111 0.00 0.00 45.53 3.67
309 2093 3.323903 CACGCACACGCACGTACA 61.324 61.111 0.00 0.00 45.53 2.90
310 2094 3.324671 ACGCACACGCACGTACAC 61.325 61.111 0.00 0.00 45.53 2.90
311 2095 3.323903 CGCACACGCACGTACACA 61.324 61.111 0.00 0.00 38.40 3.72
312 2096 2.244382 GCACACGCACGTACACAC 59.756 61.111 0.00 0.00 38.36 3.82
313 2097 2.518312 GCACACGCACGTACACACA 61.518 57.895 0.00 0.00 38.36 3.72
314 2098 1.271549 CACACGCACGTACACACAC 59.728 57.895 0.00 0.00 0.00 3.82
315 2099 1.153804 ACACGCACGTACACACACA 60.154 52.632 0.00 0.00 0.00 3.72
316 2100 1.271549 CACGCACGTACACACACAC 59.728 57.895 0.00 0.00 0.00 3.82
317 2101 2.225555 ACGCACGTACACACACACG 61.226 57.895 0.00 0.00 43.63 4.49
318 2102 2.244382 GCACGTACACACACACGC 59.756 61.111 0.00 0.00 41.80 5.34
319 2103 2.518312 GCACGTACACACACACGCA 61.518 57.895 0.00 0.00 41.80 5.24
320 2104 1.271549 CACGTACACACACACGCAC 59.728 57.895 0.00 0.00 41.80 5.34
321 2105 1.153804 ACGTACACACACACGCACA 60.154 52.632 0.00 0.00 41.80 4.57
322 2106 1.271549 CGTACACACACACGCACAC 59.728 57.895 0.00 0.00 0.00 3.82
324 2108 2.518312 TACACACACACGCACACGC 61.518 57.895 0.00 0.00 45.53 5.34
346 2130 2.651863 GCACAAGCGCACACACAC 60.652 61.111 11.47 0.00 0.00 3.82
347 2131 2.790586 CACAAGCGCACACACACA 59.209 55.556 11.47 0.00 0.00 3.72
348 2132 1.583451 CACAAGCGCACACACACAC 60.583 57.895 11.47 0.00 0.00 3.82
349 2133 2.037702 ACAAGCGCACACACACACA 61.038 52.632 11.47 0.00 0.00 3.72
350 2134 1.583451 CAAGCGCACACACACACAC 60.583 57.895 11.47 0.00 0.00 3.82
351 2135 2.037702 AAGCGCACACACACACACA 61.038 52.632 11.47 0.00 0.00 3.72
352 2136 1.581727 AAGCGCACACACACACACAA 61.582 50.000 11.47 0.00 0.00 3.33
353 2137 1.583451 GCGCACACACACACACAAG 60.583 57.895 0.30 0.00 0.00 3.16
364 2148 3.491639 CACACACACAAGCCAATGAAATG 59.508 43.478 0.00 0.00 0.00 2.32
380 2232 5.530519 TGAAATGAACGTGCTAGCTTAAG 57.469 39.130 17.23 6.99 0.00 1.85
428 2280 9.145865 ACAATTTACACCAACTTTTAAACACAG 57.854 29.630 0.00 0.00 0.00 3.66
465 2318 3.979101 AACCAATCATCCGCCAAAAAT 57.021 38.095 0.00 0.00 0.00 1.82
505 2359 5.329399 TGACAAAATACTGCCACCCTTAAT 58.671 37.500 0.00 0.00 0.00 1.40
627 6049 2.739704 CGTGCATGCAGGTGTACCG 61.740 63.158 27.92 18.98 42.08 4.02
1007 6434 5.637104 CAGTACGTACTTACAATGGCATC 57.363 43.478 25.35 0.00 33.46 3.91
1008 6435 5.348986 CAGTACGTACTTACAATGGCATCT 58.651 41.667 25.35 0.00 33.46 2.90
1010 6437 6.312918 CAGTACGTACTTACAATGGCATCTTT 59.687 38.462 25.35 0.00 33.46 2.52
1152 6579 4.961511 AGCGTCGCGAACCTTGCA 62.962 61.111 12.06 0.00 0.00 4.08
1228 6655 1.374252 AACTACGGCAAGTGCGAGG 60.374 57.895 0.00 0.00 43.26 4.63
1414 6841 2.761809 AGCAGGAGTGGAATGATCTCT 58.238 47.619 0.00 0.00 0.00 3.10
1452 6879 0.538287 GCCTTCAGCCACTGGACTTT 60.538 55.000 0.00 0.00 34.35 2.66
1645 7073 2.711009 AGGAAGGGCATCGGATTCAATA 59.289 45.455 0.00 0.00 0.00 1.90
1651 7079 2.032030 GGCATCGGATTCAATAACACGG 60.032 50.000 0.00 0.00 0.00 4.94
1668 7096 2.665603 GCTCCTCGCCAGAAGGTT 59.334 61.111 0.00 0.00 37.19 3.50
1732 7160 6.428159 AGAACAAAAGATCAGTGAAAGCGTAT 59.572 34.615 0.00 0.00 0.00 3.06
1733 7161 6.560253 ACAAAAGATCAGTGAAAGCGTATT 57.440 33.333 0.00 0.00 0.00 1.89
1783 7211 8.694540 AGTGTTCATAAATTTTATGCTGCCATA 58.305 29.630 19.83 3.23 32.85 2.74
1805 7233 8.501904 CCATATAATATGATGGGGTGGATGTTA 58.498 37.037 0.00 0.00 39.23 2.41
1857 7285 3.818210 TGCTATCAACTTTTTCGCTCCAA 59.182 39.130 0.00 0.00 0.00 3.53
1871 7327 2.096268 CGCTCCAAAGTGTGTGTATGTG 60.096 50.000 0.00 0.00 0.00 3.21
1887 7343 8.736244 GTGTGTATGTGGGTTTCTTAATATTGT 58.264 33.333 0.00 0.00 0.00 2.71
1888 7344 8.735315 TGTGTATGTGGGTTTCTTAATATTGTG 58.265 33.333 0.00 0.00 0.00 3.33
1891 7347 6.582677 TGTGGGTTTCTTAATATTGTGTGG 57.417 37.500 0.00 0.00 0.00 4.17
1911 7367 3.945285 TGGATTCACTATTTTCTTCCCGC 59.055 43.478 0.00 0.00 0.00 6.13
1921 7378 2.787473 TTCTTCCCGCATCATCAACT 57.213 45.000 0.00 0.00 0.00 3.16
1937 7395 5.296780 TCATCAACTTGTTCAACTTCCAGTC 59.703 40.000 0.00 0.00 0.00 3.51
1956 7414 5.124776 CCAGTCTCTTGTTTGTTGTAACCAA 59.875 40.000 0.00 0.00 0.00 3.67
2252 7799 4.772886 ACACAACACTTCTTCCTTACCT 57.227 40.909 0.00 0.00 0.00 3.08
2438 8004 4.436242 TGTTCCGCTTGTGTAAAACAAA 57.564 36.364 0.00 0.00 44.97 2.83
2482 8048 6.314018 TCTAGTACATACGTAACAACCAACG 58.686 40.000 0.00 0.00 44.47 4.10
2491 8057 1.842052 AACAACCAACGTCCAACCTT 58.158 45.000 0.00 0.00 0.00 3.50
2576 8144 6.088085 CGCTTTGGTTTCTCATTAATGTGAAC 59.912 38.462 25.13 20.15 39.23 3.18
2598 8166 6.126863 ACTATTTTCCAATCAGAGGTGACA 57.873 37.500 0.00 0.00 34.75 3.58
2601 8169 8.328758 ACTATTTTCCAATCAGAGGTGACATTA 58.671 33.333 0.00 0.00 34.75 1.90
2624 8192 2.032681 GGCGAGGCCTGTTTCAGT 59.967 61.111 12.00 0.00 46.69 3.41
2626 8194 1.598130 GCGAGGCCTGTTTCAGTGT 60.598 57.895 12.00 0.00 0.00 3.55
2636 8204 2.609459 CTGTTTCAGTGTTGAGCTTCGT 59.391 45.455 0.00 0.00 34.15 3.85
2650 8218 2.499289 AGCTTCGTGACTCCAATCTCAT 59.501 45.455 0.00 0.00 0.00 2.90
2652 8220 3.799420 GCTTCGTGACTCCAATCTCATAC 59.201 47.826 0.00 0.00 0.00 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 71 2.879103 TGAATTTCCCACCTGTCTCC 57.121 50.000 0.00 0.00 0.00 3.71
76 78 6.399639 TTTAACTCACTTGAATTTCCCACC 57.600 37.500 0.00 0.00 0.00 4.61
108 110 4.651962 TGACAATACATTATGGGACGGAGA 59.348 41.667 0.00 0.00 0.00 3.71
145 147 4.768968 TGTACTCCCTCCGCCTAATATAAC 59.231 45.833 0.00 0.00 0.00 1.89
148 150 3.537795 TGTACTCCCTCCGCCTAATAT 57.462 47.619 0.00 0.00 0.00 1.28
151 153 2.176364 AGTATGTACTCCCTCCGCCTAA 59.824 50.000 0.00 0.00 0.00 2.69
152 154 1.779092 AGTATGTACTCCCTCCGCCTA 59.221 52.381 0.00 0.00 0.00 3.93
154 156 1.411041 AAGTATGTACTCCCTCCGCC 58.589 55.000 0.00 0.00 34.99 6.13
155 157 4.763793 TGTATAAGTATGTACTCCCTCCGC 59.236 45.833 0.00 0.00 34.99 5.54
156 158 5.766670 TGTGTATAAGTATGTACTCCCTCCG 59.233 44.000 0.00 0.00 34.99 4.63
157 159 7.592885 TTGTGTATAAGTATGTACTCCCTCC 57.407 40.000 0.00 0.00 34.99 4.30
210 1994 0.875059 CTTGTTCCGGAAAGGTCAGC 59.125 55.000 20.79 5.00 41.99 4.26
237 2021 1.134560 TGTGTGTGTGTGTGTACGCTA 59.865 47.619 8.10 0.00 38.15 4.26
238 2022 0.108567 TGTGTGTGTGTGTGTACGCT 60.109 50.000 8.10 0.00 38.15 5.07
239 2023 0.025770 GTGTGTGTGTGTGTGTACGC 59.974 55.000 0.00 0.00 37.82 4.42
240 2024 1.059979 GTGTGTGTGTGTGTGTGTACG 59.940 52.381 0.00 0.00 0.00 3.67
241 2025 2.070028 TGTGTGTGTGTGTGTGTGTAC 58.930 47.619 0.00 0.00 0.00 2.90
242 2026 2.070028 GTGTGTGTGTGTGTGTGTGTA 58.930 47.619 0.00 0.00 0.00 2.90
243 2027 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
244 2028 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
245 2029 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
246 2030 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
247 2031 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
248 2032 0.179227 CGTGTGTGTGTGTGTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
249 2033 1.906994 GCGTGTGTGTGTGTGTGTGT 61.907 55.000 0.00 0.00 0.00 3.72
250 2034 1.225991 GCGTGTGTGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
251 2035 1.669437 TGCGTGTGTGTGTGTGTGT 60.669 52.632 0.00 0.00 0.00 3.72
252 2036 1.225991 GTGCGTGTGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
253 2037 2.735677 CGTGCGTGTGTGTGTGTGT 61.736 57.895 0.00 0.00 0.00 3.72
254 2038 2.021243 CGTGCGTGTGTGTGTGTG 59.979 61.111 0.00 0.00 0.00 3.82
255 2039 3.860125 GCGTGCGTGTGTGTGTGT 61.860 61.111 0.00 0.00 0.00 3.72
256 2040 3.858989 TGCGTGCGTGTGTGTGTG 61.859 61.111 0.00 0.00 0.00 3.82
257 2041 3.860125 GTGCGTGCGTGTGTGTGT 61.860 61.111 0.00 0.00 0.00 3.72
258 2042 4.918060 CGTGCGTGCGTGTGTGTG 62.918 66.667 0.00 0.00 0.00 3.82
267 2051 4.696172 GTGTACGTGCGTGCGTGC 62.696 66.667 14.68 13.74 45.33 5.34
268 2052 2.983977 GAGTGTACGTGCGTGCGTG 61.984 63.158 14.68 0.00 45.33 5.34
270 2054 2.728015 TGAGTGTACGTGCGTGCG 60.728 61.111 7.55 0.00 33.40 5.34
271 2055 1.947146 TGTGAGTGTACGTGCGTGC 60.947 57.895 7.55 6.68 0.00 5.34
272 2056 0.868177 TGTGTGAGTGTACGTGCGTG 60.868 55.000 7.55 0.00 0.00 5.34
273 2057 0.868602 GTGTGTGAGTGTACGTGCGT 60.869 55.000 0.00 2.05 0.00 5.24
274 2058 0.868177 TGTGTGTGAGTGTACGTGCG 60.868 55.000 0.00 0.00 0.00 5.34
275 2059 0.575390 GTGTGTGTGAGTGTACGTGC 59.425 55.000 0.00 0.00 0.00 5.34
276 2060 0.843872 CGTGTGTGTGAGTGTACGTG 59.156 55.000 0.00 0.00 0.00 4.49
277 2061 0.868602 GCGTGTGTGTGAGTGTACGT 60.869 55.000 0.00 0.00 34.37 3.57
278 2062 0.868177 TGCGTGTGTGTGAGTGTACG 60.868 55.000 0.00 0.00 34.93 3.67
279 2063 0.575390 GTGCGTGTGTGTGAGTGTAC 59.425 55.000 0.00 0.00 0.00 2.90
280 2064 0.173708 TGTGCGTGTGTGTGAGTGTA 59.826 50.000 0.00 0.00 0.00 2.90
281 2065 1.079474 TGTGCGTGTGTGTGAGTGT 60.079 52.632 0.00 0.00 0.00 3.55
282 2066 1.348250 GTGTGCGTGTGTGTGAGTG 59.652 57.895 0.00 0.00 0.00 3.51
283 2067 2.164663 CGTGTGCGTGTGTGTGAGT 61.165 57.895 0.00 0.00 0.00 3.41
284 2068 2.620459 CGTGTGCGTGTGTGTGAG 59.380 61.111 0.00 0.00 0.00 3.51
285 2069 3.559344 GCGTGTGCGTGTGTGTGA 61.559 61.111 0.00 0.00 40.81 3.58
295 2079 2.244382 GTGTGTACGTGCGTGTGC 59.756 61.111 7.55 0.00 43.20 4.57
296 2080 1.271549 GTGTGTGTACGTGCGTGTG 59.728 57.895 7.55 0.00 0.00 3.82
297 2081 1.153804 TGTGTGTGTACGTGCGTGT 60.154 52.632 7.55 0.00 0.00 4.49
298 2082 1.271549 GTGTGTGTGTACGTGCGTG 59.728 57.895 7.55 0.00 0.00 5.34
299 2083 2.225555 CGTGTGTGTGTACGTGCGT 61.226 57.895 0.00 2.05 35.70 5.24
300 2084 2.537578 CGTGTGTGTGTACGTGCG 59.462 61.111 0.00 0.00 35.70 5.34
301 2085 2.244382 GCGTGTGTGTGTACGTGC 59.756 61.111 0.00 0.00 41.98 5.34
302 2086 1.271549 GTGCGTGTGTGTGTACGTG 59.728 57.895 0.00 0.00 41.98 4.49
303 2087 1.153804 TGTGCGTGTGTGTGTACGT 60.154 52.632 0.00 0.00 41.98 3.57
304 2088 1.271549 GTGTGCGTGTGTGTGTACG 59.728 57.895 0.00 0.00 42.79 3.67
305 2089 1.271549 CGTGTGCGTGTGTGTGTAC 59.728 57.895 0.00 0.00 0.00 2.90
306 2090 2.518312 GCGTGTGCGTGTGTGTGTA 61.518 57.895 0.00 0.00 40.81 2.90
307 2091 3.860125 GCGTGTGCGTGTGTGTGT 61.860 61.111 0.00 0.00 40.81 3.72
329 2113 2.651863 GTGTGTGTGCGCTTGTGC 60.652 61.111 9.73 0.00 0.00 4.57
330 2114 1.583451 GTGTGTGTGTGCGCTTGTG 60.583 57.895 9.73 0.00 0.00 3.33
331 2115 2.037702 TGTGTGTGTGTGCGCTTGT 61.038 52.632 9.73 0.00 0.00 3.16
332 2116 1.583451 GTGTGTGTGTGTGCGCTTG 60.583 57.895 9.73 0.00 0.00 4.01
333 2117 1.581727 TTGTGTGTGTGTGTGCGCTT 61.582 50.000 9.73 0.00 0.00 4.68
334 2118 1.980951 CTTGTGTGTGTGTGTGCGCT 61.981 55.000 9.73 0.00 0.00 5.92
335 2119 1.583451 CTTGTGTGTGTGTGTGCGC 60.583 57.895 0.00 0.00 0.00 6.09
336 2120 1.583451 GCTTGTGTGTGTGTGTGCG 60.583 57.895 0.00 0.00 0.00 5.34
337 2121 1.226660 GGCTTGTGTGTGTGTGTGC 60.227 57.895 0.00 0.00 0.00 4.57
338 2122 0.525311 TTGGCTTGTGTGTGTGTGTG 59.475 50.000 0.00 0.00 0.00 3.82
339 2123 1.134753 CATTGGCTTGTGTGTGTGTGT 59.865 47.619 0.00 0.00 0.00 3.72
340 2124 1.404748 TCATTGGCTTGTGTGTGTGTG 59.595 47.619 0.00 0.00 0.00 3.82
341 2125 1.761449 TCATTGGCTTGTGTGTGTGT 58.239 45.000 0.00 0.00 0.00 3.72
342 2126 2.867287 TTCATTGGCTTGTGTGTGTG 57.133 45.000 0.00 0.00 0.00 3.82
343 2127 3.384146 TCATTTCATTGGCTTGTGTGTGT 59.616 39.130 0.00 0.00 0.00 3.72
344 2128 3.979948 TCATTTCATTGGCTTGTGTGTG 58.020 40.909 0.00 0.00 0.00 3.82
345 2129 4.370917 GTTCATTTCATTGGCTTGTGTGT 58.629 39.130 0.00 0.00 0.00 3.72
346 2130 3.426191 CGTTCATTTCATTGGCTTGTGTG 59.574 43.478 0.00 0.00 0.00 3.82
347 2131 3.068024 ACGTTCATTTCATTGGCTTGTGT 59.932 39.130 0.00 0.00 0.00 3.72
348 2132 3.426191 CACGTTCATTTCATTGGCTTGTG 59.574 43.478 0.00 0.00 0.00 3.33
349 2133 3.641648 CACGTTCATTTCATTGGCTTGT 58.358 40.909 0.00 0.00 0.00 3.16
350 2134 2.409378 GCACGTTCATTTCATTGGCTTG 59.591 45.455 0.00 0.00 0.00 4.01
351 2135 2.297033 AGCACGTTCATTTCATTGGCTT 59.703 40.909 0.00 0.00 0.00 4.35
352 2136 1.888512 AGCACGTTCATTTCATTGGCT 59.111 42.857 0.00 0.00 0.00 4.75
353 2137 2.352503 AGCACGTTCATTTCATTGGC 57.647 45.000 0.00 0.00 0.00 4.52
364 2148 4.730657 TGACTACTTAAGCTAGCACGTTC 58.269 43.478 18.83 4.37 0.00 3.95
428 2280 4.457834 TGGTTTGAACTCTCTAGCTAGC 57.542 45.455 16.35 6.62 0.00 3.42
485 2339 7.227910 ACGTATATTAAGGGTGGCAGTATTTTG 59.772 37.037 0.00 0.00 0.00 2.44
605 5617 1.327460 GTACACCTGCATGCACGTATG 59.673 52.381 18.46 14.40 0.00 2.39
619 5631 0.320697 AAGTCCAAGCTCGGTACACC 59.679 55.000 0.00 0.00 0.00 4.16
627 6049 2.294512 CCAAAGTCCAAAGTCCAAGCTC 59.705 50.000 0.00 0.00 0.00 4.09
1006 6433 6.663734 ACCCAGAAGAAGAAGAAGAAAAAGA 58.336 36.000 0.00 0.00 0.00 2.52
1007 6434 6.543831 TGACCCAGAAGAAGAAGAAGAAAAAG 59.456 38.462 0.00 0.00 0.00 2.27
1008 6435 6.423182 TGACCCAGAAGAAGAAGAAGAAAAA 58.577 36.000 0.00 0.00 0.00 1.94
1010 6437 5.630415 TGACCCAGAAGAAGAAGAAGAAA 57.370 39.130 0.00 0.00 0.00 2.52
1117 6544 1.728971 GCTCGACATGACCTTGTTCAG 59.271 52.381 0.00 0.00 0.00 3.02
1203 6630 2.151202 CACTTGCCGTAGTTGGTGAAT 58.849 47.619 0.00 0.00 0.00 2.57
1319 6746 5.850614 AGCCGTAATATAGTTTTCCGTCAT 58.149 37.500 0.00 0.00 0.00 3.06
1320 6747 5.266733 AGCCGTAATATAGTTTTCCGTCA 57.733 39.130 0.00 0.00 0.00 4.35
1414 6841 2.218066 GGAGCCTCCGGAATTGGTA 58.782 57.895 5.23 0.00 0.00 3.25
1452 6879 1.236616 CCGTGAAGAAGGCATGCACA 61.237 55.000 21.36 6.44 0.00 4.57
1473 6900 3.016736 CGCCATTATGAGGAAAACCACT 58.983 45.455 0.00 0.00 0.00 4.00
1668 7096 3.593442 ACTTTGTTCAAGGGATGGACA 57.407 42.857 0.29 0.00 46.12 4.02
1732 7160 4.076394 GTCTAACATGGGTGGCAACTAAA 58.924 43.478 0.97 0.00 37.61 1.85
1733 7161 3.329520 AGTCTAACATGGGTGGCAACTAA 59.670 43.478 0.97 0.00 37.61 2.24
1783 7211 7.341885 TGTAACATCCACCCCATCATATTAT 57.658 36.000 0.00 0.00 0.00 1.28
1857 7285 4.164843 AGAAACCCACATACACACACTT 57.835 40.909 0.00 0.00 0.00 3.16
1871 7327 7.973944 GTGAATCCACACAATATTAAGAAACCC 59.026 37.037 0.00 0.00 42.72 4.11
1887 7343 4.941263 CGGGAAGAAAATAGTGAATCCACA 59.059 41.667 0.00 0.00 45.54 4.17
1888 7344 4.201920 GCGGGAAGAAAATAGTGAATCCAC 60.202 45.833 0.00 0.00 43.50 4.02
1891 7347 5.296780 TGATGCGGGAAGAAAATAGTGAATC 59.703 40.000 0.00 0.00 0.00 2.52
1911 7367 6.075762 TGGAAGTTGAACAAGTTGATGATG 57.924 37.500 10.54 0.00 34.36 3.07
1990 7448 4.130118 ACTTCATGTGTTTCTCTGGTGAC 58.870 43.478 0.00 0.00 0.00 3.67
2092 7638 4.347000 GGAGGTTGGGATGCTTACTACATA 59.653 45.833 0.00 0.00 0.00 2.29
2183 7730 5.954150 AGGCAAACTGGATTTAGTTCATGAT 59.046 36.000 0.00 0.00 39.86 2.45
2252 7799 2.845659 AGTGGGGGTATGATGAAGACA 58.154 47.619 0.00 0.00 0.00 3.41
2406 7967 2.916716 CAAGCGGAACATGTATTTGCAC 59.083 45.455 0.00 0.00 0.00 4.57
2482 8048 2.299867 ACCATGCAATCAAAGGTTGGAC 59.700 45.455 4.27 0.00 32.80 4.02
2491 8057 4.209538 CCATTCTCCTACCATGCAATCAA 58.790 43.478 0.00 0.00 0.00 2.57
2525 8092 0.595095 CTGGAGTTTGCTCTTGTGGC 59.405 55.000 0.00 0.00 41.38 5.01
2576 8144 7.636150 AATGTCACCTCTGATTGGAAAATAG 57.364 36.000 0.00 0.00 0.00 1.73
2617 8185 2.607635 TCACGAAGCTCAACACTGAAAC 59.392 45.455 0.00 0.00 0.00 2.78
2623 8191 1.140816 GGAGTCACGAAGCTCAACAC 58.859 55.000 0.00 0.00 33.66 3.32
2624 8192 0.750249 TGGAGTCACGAAGCTCAACA 59.250 50.000 0.00 0.00 33.66 3.33
2626 8194 2.300152 AGATTGGAGTCACGAAGCTCAA 59.700 45.455 0.00 0.00 27.39 3.02
2636 8204 5.876460 CACAATGTGTATGAGATTGGAGTCA 59.124 40.000 5.00 0.00 39.21 3.41
2650 8218 2.131972 GACGCACTCACACAATGTGTA 58.868 47.619 19.42 7.05 45.65 2.90


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

AutoCloner maintained by Alex Coulton.