Multiple sequence alignment - TraesCS2A01G013900

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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 TraesCS2A01G013900 chr2A 100.000 3485 0 0 1 3485 5650904 5654388 0.000000e+00 6436.0
1 TraesCS2A01G013900 chr2A 99.924 1311 1 0 1450 2760 5642842 5641532 0.000000e+00 2416.0
2 TraesCS2A01G013900 chr2A 94.014 735 27 7 1845 2579 62697106 62697823 0.000000e+00 1098.0
3 TraesCS2A01G013900 chr2A 89.775 577 53 3 1900 2476 5647408 5646838 0.000000e+00 734.0
4 TraesCS2A01G013900 chr2A 99.648 284 1 0 2477 2760 5646866 5646583 1.430000e-143 520.0
5 TraesCS2A01G013900 chr2A 86.308 409 39 12 1435 1833 62696292 62696693 2.490000e-116 429.0
6 TraesCS2A01G013900 chr2A 84.424 321 32 14 1006 1314 62695909 62696223 2.030000e-77 300.0
7 TraesCS2A01G013900 chr2A 85.946 185 21 5 2581 2760 62697881 62698065 3.550000e-45 193.0
8 TraesCS2A01G013900 chr2D 95.216 1066 28 7 779 1835 7155410 7154359 0.000000e+00 1664.0
9 TraesCS2A01G013900 chr2D 93.266 787 25 4 1845 2631 7153944 7153186 0.000000e+00 1134.0
10 TraesCS2A01G013900 chr2D 89.383 405 39 4 305 708 7157050 7156649 1.120000e-139 507.0
11 TraesCS2A01G013900 chr2B 92.479 1170 60 8 1435 2603 2090385 2091527 0.000000e+00 1648.0
12 TraesCS2A01G013900 chr2B 91.798 1146 58 14 1474 2603 1983784 1984909 0.000000e+00 1563.0
13 TraesCS2A01G013900 chr2B 84.548 1029 89 26 1255 2251 2065939 2066929 0.000000e+00 955.0
14 TraesCS2A01G013900 chr2B 90.732 615 53 2 1862 2476 2108099 2108709 0.000000e+00 817.0
15 TraesCS2A01G013900 chr2B 83.671 888 83 30 1862 2739 1988965 1989800 0.000000e+00 780.0
16 TraesCS2A01G013900 chr2B 94.708 359 18 1 1845 2203 1979493 1979850 1.090000e-154 556.0
17 TraesCS2A01G013900 chr2B 89.573 422 29 9 1426 1841 2107491 2107903 3.990000e-144 521.0
18 TraesCS2A01G013900 chr2B 88.030 401 27 10 1455 1841 1972837 1973230 4.100000e-124 455.0
19 TraesCS2A01G013900 chr2B 86.073 438 29 18 1406 1841 1988361 1988768 3.190000e-120 442.0
20 TraesCS2A01G013900 chr2B 85.987 314 27 9 999 1303 2107168 2107473 1.560000e-83 320.0
21 TraesCS2A01G013900 chr2B 91.071 224 17 1 1001 1224 2089981 2090201 2.030000e-77 300.0
22 TraesCS2A01G013900 chr2B 85.274 292 32 8 1021 1303 1988071 1988360 1.220000e-74 291.0
23 TraesCS2A01G013900 chr2B 88.158 228 15 6 997 1224 1983329 1983544 9.590000e-66 261.0
24 TraesCS2A01G013900 chr2B 86.528 193 26 0 2284 2476 2068264 2068456 2.720000e-51 213.0
25 TraesCS2A01G013900 chr2B 84.685 222 16 8 997 1218 1982576 1982779 4.560000e-49 206.0
26 TraesCS2A01G013900 chr2B 81.818 198 30 5 1024 1219 2065383 2065576 1.000000e-35 161.0
27 TraesCS2A01G013900 chr2B 89.157 83 1 1 2678 2760 2070827 2070901 2.860000e-16 97.1
28 TraesCS2A01G013900 chr7D 94.444 558 23 5 2793 3342 446882246 446881689 0.000000e+00 852.0
29 TraesCS2A01G013900 chr7D 93.739 559 26 5 2793 3342 162679152 162679710 0.000000e+00 830.0
30 TraesCS2A01G013900 chr7D 96.552 145 5 0 3340 3484 162681532 162681676 1.250000e-59 241.0
31 TraesCS2A01G013900 chr7D 96.552 145 5 0 3340 3484 446879869 446879725 1.250000e-59 241.0
32 TraesCS2A01G013900 chr1D 94.086 558 25 5 2793 3342 145174640 145174083 0.000000e+00 841.0
33 TraesCS2A01G013900 chr1D 95.172 145 7 0 3340 3484 145172266 145172122 2.710000e-56 230.0
34 TraesCS2A01G013900 chr3B 93.466 551 30 4 2793 3338 754015977 754015428 0.000000e+00 813.0
35 TraesCS2A01G013900 chr3B 94.483 145 8 0 3340 3484 754014713 754014569 1.260000e-54 224.0
36 TraesCS2A01G013900 chr4D 93.202 559 26 9 2793 3342 479419486 479418931 0.000000e+00 811.0
37 TraesCS2A01G013900 chr4D 96.552 145 5 0 3340 3484 479417113 479416969 1.250000e-59 241.0
38 TraesCS2A01G013900 chr6D 93.011 558 31 5 2793 3342 143831055 143831612 0.000000e+00 808.0
39 TraesCS2A01G013900 chr6D 96.552 145 5 0 3340 3484 143833431 143833575 1.250000e-59 241.0
40 TraesCS2A01G013900 chr4B 89.567 508 31 8 2848 3342 93298713 93298215 2.950000e-175 625.0
41 TraesCS2A01G013900 chr4B 88.166 507 29 9 2848 3342 370704205 370703718 3.020000e-160 575.0
42 TraesCS2A01G013900 chr6B 90.323 248 15 5 2513 2760 717939165 717938927 2.020000e-82 316.0


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 TraesCS2A01G013900 chr2A 5650904 5654388 3484 False 6436.000000 6436 100.000000 1 3485 1 chr2A.!!$F1 3484
1 TraesCS2A01G013900 chr2A 5641532 5647408 5876 True 1223.333333 2416 96.449000 1450 2760 3 chr2A.!!$R1 1310
2 TraesCS2A01G013900 chr2A 62695909 62698065 2156 False 505.000000 1098 87.673000 1006 2760 4 chr2A.!!$F2 1754
3 TraesCS2A01G013900 chr2D 7153186 7157050 3864 True 1101.666667 1664 92.621667 305 2631 3 chr2D.!!$R1 2326
4 TraesCS2A01G013900 chr2B 2089981 2091527 1546 False 974.000000 1648 91.775000 1001 2603 2 chr2B.!!$F4 1602
5 TraesCS2A01G013900 chr2B 1979493 1989800 10307 False 585.571429 1563 87.766714 997 2739 7 chr2B.!!$F2 1742
6 TraesCS2A01G013900 chr2B 2107168 2108709 1541 False 552.666667 817 88.764000 999 2476 3 chr2B.!!$F5 1477
7 TraesCS2A01G013900 chr2B 2065383 2070901 5518 False 356.525000 955 85.512750 1024 2760 4 chr2B.!!$F3 1736
8 TraesCS2A01G013900 chr7D 446879725 446882246 2521 True 546.500000 852 95.498000 2793 3484 2 chr7D.!!$R1 691
9 TraesCS2A01G013900 chr7D 162679152 162681676 2524 False 535.500000 830 95.145500 2793 3484 2 chr7D.!!$F1 691
10 TraesCS2A01G013900 chr1D 145172122 145174640 2518 True 535.500000 841 94.629000 2793 3484 2 chr1D.!!$R1 691
11 TraesCS2A01G013900 chr3B 754014569 754015977 1408 True 518.500000 813 93.974500 2793 3484 2 chr3B.!!$R1 691
12 TraesCS2A01G013900 chr4D 479416969 479419486 2517 True 526.000000 811 94.877000 2793 3484 2 chr4D.!!$R1 691
13 TraesCS2A01G013900 chr6D 143831055 143833575 2520 False 524.500000 808 94.781500 2793 3484 2 chr6D.!!$F1 691

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
324 325 0.396435 AAAGACATGGTGACGGCTCA 59.604 50.000 0.00 0.0 0.0 4.26 F
358 359 1.473677 ACACCACTACTAACGCGCATA 59.526 47.619 5.73 0.0 0.0 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1166 4005 1.066136 GAAGCGGGTGAAGACGTAAC 58.934 55.0 0.00 0.00 0.00 2.50 R
2766 14864 1.482621 CGAATAGCGCGAGTGCACAT 61.483 55.0 21.04 3.82 42.97 3.21 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
24 25 6.662414 TTTTTCGTCATGGCTCATAACTAG 57.338 37.500 0.00 0.00 0.00 2.57
27 28 3.951680 TCGTCATGGCTCATAACTAGTGA 59.048 43.478 0.00 0.00 0.00 3.41
34 35 8.432013 TCATGGCTCATAACTAGTGACAAATAT 58.568 33.333 0.00 0.00 0.00 1.28
70 71 9.618890 AGTTCACAGTATATGTTGATGCTTAAT 57.381 29.630 0.00 0.00 41.41 1.40
124 125 7.881775 AGTTTAAGTTCAATTGGTTCTCTGT 57.118 32.000 5.42 0.00 0.00 3.41
125 126 7.707104 AGTTTAAGTTCAATTGGTTCTCTGTG 58.293 34.615 5.42 0.00 0.00 3.66
126 127 7.339466 AGTTTAAGTTCAATTGGTTCTCTGTGT 59.661 33.333 5.42 0.00 0.00 3.72
127 128 7.639113 TTAAGTTCAATTGGTTCTCTGTGTT 57.361 32.000 5.42 0.00 0.00 3.32
128 129 5.757850 AGTTCAATTGGTTCTCTGTGTTC 57.242 39.130 5.42 0.00 0.00 3.18
129 130 5.440610 AGTTCAATTGGTTCTCTGTGTTCT 58.559 37.500 5.42 0.00 0.00 3.01
130 131 5.888161 AGTTCAATTGGTTCTCTGTGTTCTT 59.112 36.000 5.42 0.00 0.00 2.52
132 133 7.556275 AGTTCAATTGGTTCTCTGTGTTCTTTA 59.444 33.333 5.42 0.00 0.00 1.85
133 134 8.352942 GTTCAATTGGTTCTCTGTGTTCTTTAT 58.647 33.333 5.42 0.00 0.00 1.40
137 138 7.639113 TTGGTTCTCTGTGTTCTTTATTTGT 57.361 32.000 0.00 0.00 0.00 2.83
141 142 7.432252 GGTTCTCTGTGTTCTTTATTTGTTGTG 59.568 37.037 0.00 0.00 0.00 3.33
143 144 8.725405 TCTCTGTGTTCTTTATTTGTTGTGTA 57.275 30.769 0.00 0.00 0.00 2.90
146 147 8.898761 TCTGTGTTCTTTATTTGTTGTGTACAT 58.101 29.630 0.00 0.00 36.44 2.29
147 148 9.515020 CTGTGTTCTTTATTTGTTGTGTACATT 57.485 29.630 0.00 0.00 36.44 2.71
162 163 7.759489 TGTGTACATTCTTGATTTTTAGCCT 57.241 32.000 0.00 0.00 0.00 4.58
165 166 9.774742 GTGTACATTCTTGATTTTTAGCCTAAG 57.225 33.333 0.00 0.00 0.00 2.18
166 167 8.458843 TGTACATTCTTGATTTTTAGCCTAAGC 58.541 33.333 0.00 0.00 40.32 3.09
168 169 8.071177 ACATTCTTGATTTTTAGCCTAAGCAT 57.929 30.769 0.00 0.00 43.56 3.79
169 170 7.977853 ACATTCTTGATTTTTAGCCTAAGCATG 59.022 33.333 0.00 0.00 43.56 4.06
170 171 5.894807 TCTTGATTTTTAGCCTAAGCATGC 58.105 37.500 10.51 10.51 43.56 4.06
171 172 5.653769 TCTTGATTTTTAGCCTAAGCATGCT 59.346 36.000 16.30 16.30 43.56 3.79
172 173 6.828273 TCTTGATTTTTAGCCTAAGCATGCTA 59.172 34.615 23.00 8.60 43.56 3.49
189 190 6.974932 CATGCTATCATGTATGGTACCTTC 57.025 41.667 14.36 4.14 43.85 3.46
190 191 6.466812 CATGCTATCATGTATGGTACCTTCA 58.533 40.000 14.36 9.80 43.85 3.02
192 193 7.790782 TGCTATCATGTATGGTACCTTCATA 57.209 36.000 14.36 0.00 0.00 2.15
193 194 7.611770 TGCTATCATGTATGGTACCTTCATAC 58.388 38.462 14.36 12.95 44.19 2.39
194 195 7.042335 GCTATCATGTATGGTACCTTCATACC 58.958 42.308 14.36 0.00 43.63 2.73
195 196 7.093289 GCTATCATGTATGGTACCTTCATACCT 60.093 40.741 14.36 3.39 44.43 3.08
196 197 7.633018 ATCATGTATGGTACCTTCATACCTT 57.367 36.000 14.36 1.28 44.43 3.50
198 199 7.867921 TCATGTATGGTACCTTCATACCTTTT 58.132 34.615 14.36 0.00 44.43 2.27
201 202 4.210724 TGGTACCTTCATACCTTTTCGG 57.789 45.455 14.36 0.00 44.43 4.30
204 205 5.248020 TGGTACCTTCATACCTTTTCGGTTA 59.752 40.000 14.36 0.00 46.37 2.85
206 207 6.825213 GGTACCTTCATACCTTTTCGGTTATT 59.175 38.462 4.06 0.00 46.37 1.40
207 208 7.337689 GGTACCTTCATACCTTTTCGGTTATTT 59.662 37.037 4.06 0.00 46.37 1.40
218 219 8.680001 ACCTTTTCGGTTATTTTATATGGACAC 58.320 33.333 0.00 0.00 46.37 3.67
222 223 8.966069 TTCGGTTATTTTATATGGACACATCA 57.034 30.769 0.00 0.00 38.53 3.07
236 237 5.598005 TGGACACATCAAAATTTCTTGGAGT 59.402 36.000 0.00 0.00 0.00 3.85
237 238 6.098124 TGGACACATCAAAATTTCTTGGAGTT 59.902 34.615 0.00 0.00 0.00 3.01
238 239 6.986231 GGACACATCAAAATTTCTTGGAGTTT 59.014 34.615 0.00 0.00 0.00 2.66
239 240 7.495606 GGACACATCAAAATTTCTTGGAGTTTT 59.504 33.333 0.00 0.00 0.00 2.43
240 241 8.791327 ACACATCAAAATTTCTTGGAGTTTTT 57.209 26.923 0.00 0.00 0.00 1.94
269 270 7.878127 TCCTTCATCTTCCACTTAGTAAAACTG 59.122 37.037 0.00 0.00 0.00 3.16
270 271 7.878127 CCTTCATCTTCCACTTAGTAAAACTGA 59.122 37.037 0.00 0.00 0.00 3.41
271 272 8.603242 TTCATCTTCCACTTAGTAAAACTGAC 57.397 34.615 0.00 0.00 0.00 3.51
272 273 7.159372 TCATCTTCCACTTAGTAAAACTGACC 58.841 38.462 0.00 0.00 0.00 4.02
274 275 5.367352 TCTTCCACTTAGTAAAACTGACCCA 59.633 40.000 0.00 0.00 0.00 4.51
275 276 5.836024 TCCACTTAGTAAAACTGACCCAT 57.164 39.130 0.00 0.00 0.00 4.00
276 277 6.195600 TCCACTTAGTAAAACTGACCCATT 57.804 37.500 0.00 0.00 0.00 3.16
277 278 6.607019 TCCACTTAGTAAAACTGACCCATTT 58.393 36.000 0.00 0.00 0.00 2.32
279 280 7.562088 TCCACTTAGTAAAACTGACCCATTTTT 59.438 33.333 0.00 0.00 32.55 1.94
319 320 3.602390 AAAACGAAAGACATGGTGACG 57.398 42.857 0.00 0.00 0.00 4.35
323 324 1.079503 GAAAGACATGGTGACGGCTC 58.920 55.000 0.00 0.00 0.00 4.70
324 325 0.396435 AAAGACATGGTGACGGCTCA 59.604 50.000 0.00 0.00 0.00 4.26
326 327 0.396435 AGACATGGTGACGGCTCAAA 59.604 50.000 0.00 0.00 0.00 2.69
344 345 5.350091 GCTCAAAAGAAGATCTAGACACCAC 59.650 44.000 0.00 0.00 0.00 4.16
346 347 7.577807 GCTCAAAAGAAGATCTAGACACCACTA 60.578 40.741 0.00 0.00 0.00 2.74
352 353 6.539464 AGAAGATCTAGACACCACTACTAACG 59.461 42.308 0.00 0.00 0.00 3.18
358 359 1.473677 ACACCACTACTAACGCGCATA 59.526 47.619 5.73 0.00 0.00 3.14
366 367 2.006888 ACTAACGCGCATATGCACTTT 58.993 42.857 26.52 18.63 42.21 2.66
372 373 4.523813 ACGCGCATATGCACTTTATTAAC 58.476 39.130 26.52 2.62 42.21 2.01
628 630 8.966868 CCTTAAAAAGGTATTCAAGCCTAATCA 58.033 33.333 0.00 0.00 43.95 2.57
644 646 8.995027 AGCCTAATCATCATAAAATGTTGGTA 57.005 30.769 0.00 0.00 32.27 3.25
708 710 5.911378 TTTGTAATGCTGGCATGAACATA 57.089 34.783 18.21 13.48 36.68 2.29
709 711 5.503662 TTGTAATGCTGGCATGAACATAG 57.496 39.130 18.21 0.00 36.68 2.23
712 714 2.495155 TGCTGGCATGAACATAGTGT 57.505 45.000 0.00 0.00 0.00 3.55
716 718 5.868454 TGCTGGCATGAACATAGTGTATAT 58.132 37.500 0.00 0.00 0.00 0.86
721 723 9.526713 CTGGCATGAACATAGTGTATATCTATC 57.473 37.037 0.00 0.00 0.00 2.08
722 724 9.259832 TGGCATGAACATAGTGTATATCTATCT 57.740 33.333 0.00 0.00 0.00 1.98
775 781 8.858003 TTCGTAAAGATCTCTAAAGTGCATAG 57.142 34.615 0.00 0.00 0.00 2.23
776 782 7.997482 TCGTAAAGATCTCTAAAGTGCATAGT 58.003 34.615 0.00 0.00 0.00 2.12
777 783 8.129840 TCGTAAAGATCTCTAAAGTGCATAGTC 58.870 37.037 0.00 0.00 0.00 2.59
1166 4005 4.778143 CGACCCCAAGGAAGGCGG 62.778 72.222 0.00 0.00 36.73 6.13
1233 4421 3.762247 TGTACGCCACTACGCCCC 61.762 66.667 0.00 0.00 36.19 5.80
1234 4422 4.519437 GTACGCCACTACGCCCCC 62.519 72.222 0.00 0.00 36.19 5.40
1235 4423 4.764771 TACGCCACTACGCCCCCT 62.765 66.667 0.00 0.00 36.19 4.79
1237 4425 2.852563 TACGCCACTACGCCCCCTTA 62.853 60.000 0.00 0.00 36.19 2.69
1238 4426 2.992164 GCCACTACGCCCCCTTAA 59.008 61.111 0.00 0.00 0.00 1.85
1239 4427 1.530283 GCCACTACGCCCCCTTAAT 59.470 57.895 0.00 0.00 0.00 1.40
1240 4428 0.534427 GCCACTACGCCCCCTTAATC 60.534 60.000 0.00 0.00 0.00 1.75
1241 4429 1.129058 CCACTACGCCCCCTTAATCT 58.871 55.000 0.00 0.00 0.00 2.40
1242 4430 1.070289 CCACTACGCCCCCTTAATCTC 59.930 57.143 0.00 0.00 0.00 2.75
2760 14858 4.316205 TTGTTTCAGCACTCGAGTCTTA 57.684 40.909 16.96 5.04 0.00 2.10
2761 14859 4.521130 TGTTTCAGCACTCGAGTCTTAT 57.479 40.909 16.96 0.00 0.00 1.73
2762 14860 5.638596 TGTTTCAGCACTCGAGTCTTATA 57.361 39.130 16.96 0.00 0.00 0.98
2763 14861 6.208988 TGTTTCAGCACTCGAGTCTTATAT 57.791 37.500 16.96 0.00 0.00 0.86
2764 14862 7.329588 TGTTTCAGCACTCGAGTCTTATATA 57.670 36.000 16.96 0.00 0.00 0.86
2765 14863 7.941919 TGTTTCAGCACTCGAGTCTTATATAT 58.058 34.615 16.96 0.00 0.00 0.86
2766 14864 9.063615 TGTTTCAGCACTCGAGTCTTATATATA 57.936 33.333 16.96 0.00 0.00 0.86
2769 14867 8.794335 TCAGCACTCGAGTCTTATATATATGT 57.206 34.615 16.96 0.00 0.00 2.29
2770 14868 8.669243 TCAGCACTCGAGTCTTATATATATGTG 58.331 37.037 16.96 0.91 0.00 3.21
2771 14869 7.430793 CAGCACTCGAGTCTTATATATATGTGC 59.569 40.741 16.96 11.64 43.93 4.57
2772 14870 7.121315 AGCACTCGAGTCTTATATATATGTGCA 59.879 37.037 16.96 0.00 45.37 4.57
2773 14871 7.219154 GCACTCGAGTCTTATATATATGTGCAC 59.781 40.741 16.96 10.75 43.34 4.57
2774 14872 8.454894 CACTCGAGTCTTATATATATGTGCACT 58.545 37.037 16.96 6.22 0.00 4.40
2775 14873 8.670135 ACTCGAGTCTTATATATATGTGCACTC 58.330 37.037 19.41 9.65 0.00 3.51
2776 14874 7.884631 CGAGTCTTATATATATGTGCACTCG 57.115 40.000 19.41 21.09 43.15 4.18
2777 14875 6.412362 CGAGTCTTATATATATGTGCACTCGC 59.588 42.308 19.41 0.00 42.78 5.03
2778 14876 6.258899 AGTCTTATATATATGTGCACTCGCG 58.741 40.000 19.41 0.00 42.97 5.87
2785 14883 2.615618 GTGCACTCGCGCTATTCG 59.384 61.111 10.32 0.00 45.49 3.34
2786 14884 2.158959 GTGCACTCGCGCTATTCGT 61.159 57.895 10.32 0.00 45.49 3.85
2787 14885 1.872234 TGCACTCGCGCTATTCGTC 60.872 57.895 5.56 0.00 42.97 4.20
2788 14886 1.872234 GCACTCGCGCTATTCGTCA 60.872 57.895 5.56 0.00 41.07 4.35
2789 14887 1.910880 CACTCGCGCTATTCGTCAC 59.089 57.895 5.56 0.00 41.07 3.67
2790 14888 1.226603 ACTCGCGCTATTCGTCACC 60.227 57.895 5.56 0.00 41.07 4.02
2791 14889 1.944676 CTCGCGCTATTCGTCACCC 60.945 63.158 5.56 0.00 41.07 4.61
2813 14911 1.635817 TATTCCTCACCCCAGCCTGC 61.636 60.000 0.00 0.00 0.00 4.85
2918 15016 5.912955 CGTAAGTAAAAAGGCTTTGAAGGTG 59.087 40.000 14.19 0.00 0.00 4.00
2996 15094 1.719600 TTTGCTTTGTTTTGCGTGCT 58.280 40.000 0.00 0.00 0.00 4.40
3033 15131 7.399191 ACTGTGGATAGACTACTCAAATTACCA 59.601 37.037 0.00 0.00 0.00 3.25
3047 15145 9.823647 ACTCAAATTACCACTGTCTATAAGATG 57.176 33.333 0.00 0.00 0.00 2.90
3134 15235 5.177142 CCGAAGAAATGATGATAGAGTGCAG 59.823 44.000 0.00 0.00 0.00 4.41
3217 15318 2.516448 CAGGATGCTTCTCCGGGTA 58.484 57.895 0.00 0.00 40.46 3.69
3250 15354 4.166888 GCTCGGCCAGCTGATCCA 62.167 66.667 17.39 6.18 45.83 3.41
3266 15370 2.355599 CATAGAGAGCGCCGCCAG 60.356 66.667 4.98 0.00 0.00 4.85
3328 15432 7.712797 ACAAACAAGAACGTAGGAAATTTGAT 58.287 30.769 14.32 0.00 0.00 2.57
3331 15435 4.600012 AGAACGTAGGAAATTTGATGCG 57.400 40.909 0.00 1.74 0.00 4.73
3332 15436 4.250464 AGAACGTAGGAAATTTGATGCGA 58.750 39.130 13.99 0.00 0.00 5.10
3334 15438 5.180492 AGAACGTAGGAAATTTGATGCGAAA 59.820 36.000 13.99 0.00 0.00 3.46
3484 17423 5.451242 GGAAAGTTGGTGTATCAGCACAAAA 60.451 40.000 1.09 0.00 41.66 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.105513 TCACTAGTTATGAGCCATGACGAAA 60.106 40.000 0.00 0.00 35.85 3.46
4 5 4.401202 TCACTAGTTATGAGCCATGACGAA 59.599 41.667 0.00 0.00 35.85 3.85
6 7 4.045104 GTCACTAGTTATGAGCCATGACG 58.955 47.826 0.00 0.00 35.85 4.35
7 8 5.011090 TGTCACTAGTTATGAGCCATGAC 57.989 43.478 0.00 0.00 36.58 3.06
98 99 9.403583 ACAGAGAACCAATTGAACTTAAACTAA 57.596 29.630 7.12 0.00 0.00 2.24
101 102 7.480810 ACACAGAGAACCAATTGAACTTAAAC 58.519 34.615 7.12 0.00 0.00 2.01
102 103 7.639113 ACACAGAGAACCAATTGAACTTAAA 57.361 32.000 7.12 0.00 0.00 1.52
103 104 7.556275 AGAACACAGAGAACCAATTGAACTTAA 59.444 33.333 7.12 0.00 0.00 1.85
105 106 5.888161 AGAACACAGAGAACCAATTGAACTT 59.112 36.000 7.12 0.00 0.00 2.66
109 110 8.463930 AATAAAGAACACAGAGAACCAATTGA 57.536 30.769 7.12 0.00 0.00 2.57
110 111 8.971321 CAAATAAAGAACACAGAGAACCAATTG 58.029 33.333 0.00 0.00 0.00 2.32
116 117 7.968405 ACACAACAAATAAAGAACACAGAGAAC 59.032 33.333 0.00 0.00 0.00 3.01
118 119 7.624360 ACACAACAAATAAAGAACACAGAGA 57.376 32.000 0.00 0.00 0.00 3.10
119 120 8.394877 TGTACACAACAAATAAAGAACACAGAG 58.605 33.333 0.00 0.00 34.29 3.35
120 121 8.270080 TGTACACAACAAATAAAGAACACAGA 57.730 30.769 0.00 0.00 34.29 3.41
137 138 8.177119 AGGCTAAAAATCAAGAATGTACACAA 57.823 30.769 0.00 0.00 0.00 3.33
141 142 8.458843 TGCTTAGGCTAAAAATCAAGAATGTAC 58.541 33.333 8.54 0.00 39.59 2.90
143 144 7.466746 TGCTTAGGCTAAAAATCAAGAATGT 57.533 32.000 8.54 0.00 39.59 2.71
146 147 6.153340 AGCATGCTTAGGCTAAAAATCAAGAA 59.847 34.615 16.30 0.00 38.90 2.52
147 148 5.653769 AGCATGCTTAGGCTAAAAATCAAGA 59.346 36.000 16.30 0.00 38.90 3.02
150 151 6.772233 TGATAGCATGCTTAGGCTAAAAATCA 59.228 34.615 28.02 20.17 44.93 2.57
168 169 6.686484 ATGAAGGTACCATACATGATAGCA 57.314 37.500 15.94 0.00 0.00 3.49
169 170 7.042335 GGTATGAAGGTACCATACATGATAGC 58.958 42.308 15.94 7.47 44.88 2.97
170 171 8.367660 AGGTATGAAGGTACCATACATGATAG 57.632 38.462 15.94 0.00 45.35 2.08
171 172 8.736097 AAGGTATGAAGGTACCATACATGATA 57.264 34.615 15.94 0.00 45.35 2.15
172 173 7.633018 AAGGTATGAAGGTACCATACATGAT 57.367 36.000 15.94 4.62 45.35 2.45
177 178 5.756833 CCGAAAAGGTATGAAGGTACCATAC 59.243 44.000 15.94 12.90 45.35 2.39
178 179 5.920903 CCGAAAAGGTATGAAGGTACCATA 58.079 41.667 15.94 0.00 45.35 2.74
179 180 4.777463 CCGAAAAGGTATGAAGGTACCAT 58.223 43.478 15.94 0.42 45.35 3.55
180 181 4.210724 CCGAAAAGGTATGAAGGTACCA 57.789 45.455 15.94 0.00 45.35 3.25
196 197 9.397280 TGATGTGTCCATATAAAATAACCGAAA 57.603 29.630 0.00 0.00 0.00 3.46
198 199 8.966069 TTGATGTGTCCATATAAAATAACCGA 57.034 30.769 0.00 0.00 0.00 4.69
211 212 6.268387 ACTCCAAGAAATTTTGATGTGTCCAT 59.732 34.615 0.00 0.00 0.00 3.41
212 213 5.598005 ACTCCAAGAAATTTTGATGTGTCCA 59.402 36.000 0.00 0.00 0.00 4.02
213 214 6.089249 ACTCCAAGAAATTTTGATGTGTCC 57.911 37.500 0.00 0.00 0.00 4.02
214 215 8.424274 AAAACTCCAAGAAATTTTGATGTGTC 57.576 30.769 0.00 0.00 0.00 3.67
215 216 8.791327 AAAAACTCCAAGAAATTTTGATGTGT 57.209 26.923 0.00 0.00 0.00 3.72
239 240 9.635404 TTTACTAAGTGGAAGATGAAGGAAAAA 57.365 29.630 0.00 0.00 0.00 1.94
240 241 9.635404 TTTTACTAAGTGGAAGATGAAGGAAAA 57.365 29.630 0.00 0.00 0.00 2.29
241 242 9.063615 GTTTTACTAAGTGGAAGATGAAGGAAA 57.936 33.333 0.00 0.00 0.00 3.13
244 245 7.878127 TCAGTTTTACTAAGTGGAAGATGAAGG 59.122 37.037 0.00 0.00 0.00 3.46
245 246 8.713271 GTCAGTTTTACTAAGTGGAAGATGAAG 58.287 37.037 0.00 0.00 0.00 3.02
246 247 7.660208 GGTCAGTTTTACTAAGTGGAAGATGAA 59.340 37.037 0.00 0.00 0.00 2.57
247 248 7.159372 GGTCAGTTTTACTAAGTGGAAGATGA 58.841 38.462 0.00 0.00 0.00 2.92
248 249 6.371825 GGGTCAGTTTTACTAAGTGGAAGATG 59.628 42.308 0.00 0.00 0.00 2.90
249 250 6.043938 TGGGTCAGTTTTACTAAGTGGAAGAT 59.956 38.462 0.00 0.00 0.00 2.40
250 251 5.367352 TGGGTCAGTTTTACTAAGTGGAAGA 59.633 40.000 0.00 0.00 0.00 2.87
252 253 5.633655 TGGGTCAGTTTTACTAAGTGGAA 57.366 39.130 0.00 0.00 0.00 3.53
253 254 5.836024 ATGGGTCAGTTTTACTAAGTGGA 57.164 39.130 0.00 0.00 0.00 4.02
254 255 6.894339 AAATGGGTCAGTTTTACTAAGTGG 57.106 37.500 0.00 0.00 0.00 4.00
295 296 5.966503 CGTCACCATGTCTTTCGTTTTAAAA 59.033 36.000 0.00 0.00 0.00 1.52
297 298 4.024725 CCGTCACCATGTCTTTCGTTTTAA 60.025 41.667 0.00 0.00 0.00 1.52
298 299 3.495377 CCGTCACCATGTCTTTCGTTTTA 59.505 43.478 0.00 0.00 0.00 1.52
302 303 0.949105 GCCGTCACCATGTCTTTCGT 60.949 55.000 0.00 0.00 0.00 3.85
309 310 1.202758 TCTTTTGAGCCGTCACCATGT 60.203 47.619 0.00 0.00 30.10 3.21
319 320 4.873259 GGTGTCTAGATCTTCTTTTGAGCC 59.127 45.833 0.00 0.00 0.00 4.70
323 324 7.607250 AGTAGTGGTGTCTAGATCTTCTTTTG 58.393 38.462 0.00 0.00 0.00 2.44
324 325 7.784470 AGTAGTGGTGTCTAGATCTTCTTTT 57.216 36.000 0.00 0.00 0.00 2.27
326 327 7.066043 CGTTAGTAGTGGTGTCTAGATCTTCTT 59.934 40.741 0.00 0.00 0.00 2.52
344 345 2.837337 GTGCATATGCGCGTTAGTAG 57.163 50.000 24.29 0.00 45.83 2.57
617 619 8.199449 ACCAACATTTTATGATGATTAGGCTTG 58.801 33.333 0.00 0.00 35.33 4.01
685 687 4.597404 TGTTCATGCCAGCATTACAAAA 57.403 36.364 12.50 0.00 33.90 2.44
691 693 3.359033 ACACTATGTTCATGCCAGCATT 58.641 40.909 1.47 0.00 33.90 3.56
695 697 9.526713 GATAGATATACACTATGTTCATGCCAG 57.473 37.037 6.16 0.00 31.76 4.85
751 757 7.997482 ACTATGCACTTTAGAGATCTTTACGA 58.003 34.615 0.00 0.00 0.00 3.43
752 758 8.132362 AGACTATGCACTTTAGAGATCTTTACG 58.868 37.037 0.00 0.00 0.00 3.18
761 767 9.853555 CCTATATTCAGACTATGCACTTTAGAG 57.146 37.037 0.00 0.00 0.00 2.43
766 772 5.280215 GGGCCTATATTCAGACTATGCACTT 60.280 44.000 0.84 0.00 0.00 3.16
775 781 4.457257 GCTGATTTGGGCCTATATTCAGAC 59.543 45.833 20.58 11.81 0.00 3.51
776 782 4.507335 GGCTGATTTGGGCCTATATTCAGA 60.507 45.833 20.58 0.00 44.48 3.27
777 783 3.760684 GGCTGATTTGGGCCTATATTCAG 59.239 47.826 15.09 15.09 44.48 3.02
836 2006 3.357079 GTCGTGCTGGCTTGGTGG 61.357 66.667 0.00 0.00 0.00 4.61
842 2012 0.108615 GTACATGAGTCGTGCTGGCT 60.109 55.000 12.41 0.00 0.00 4.75
851 2021 1.993370 GTCACGCCAAGTACATGAGTC 59.007 52.381 0.00 0.00 0.00 3.36
1166 4005 1.066136 GAAGCGGGTGAAGACGTAAC 58.934 55.000 0.00 0.00 0.00 2.50
2760 14858 3.510388 AGCGCGAGTGCACATATATAT 57.490 42.857 21.04 0.00 42.97 0.86
2761 14859 4.632538 ATAGCGCGAGTGCACATATATA 57.367 40.909 21.04 4.94 42.97 0.86
2762 14860 3.510388 ATAGCGCGAGTGCACATATAT 57.490 42.857 21.04 5.51 42.97 0.86
2763 14861 3.242518 GAATAGCGCGAGTGCACATATA 58.757 45.455 21.04 3.27 42.97 0.86
2764 14862 2.061773 GAATAGCGCGAGTGCACATAT 58.938 47.619 21.04 0.00 42.97 1.78
2765 14863 1.487482 GAATAGCGCGAGTGCACATA 58.513 50.000 21.04 2.18 42.97 2.29
2766 14864 1.482621 CGAATAGCGCGAGTGCACAT 61.483 55.000 21.04 3.82 42.97 3.21
2767 14865 2.158330 CGAATAGCGCGAGTGCACA 61.158 57.895 21.04 0.00 42.97 4.57
2768 14866 2.067453 GACGAATAGCGCGAGTGCAC 62.067 60.000 12.10 9.40 46.04 4.57
2769 14867 1.872234 GACGAATAGCGCGAGTGCA 60.872 57.895 12.10 0.00 46.04 4.57
2770 14868 1.872234 TGACGAATAGCGCGAGTGC 60.872 57.895 12.10 0.00 46.04 4.40
2771 14869 1.472276 GGTGACGAATAGCGCGAGTG 61.472 60.000 12.10 0.00 46.04 3.51
2772 14870 1.226603 GGTGACGAATAGCGCGAGT 60.227 57.895 12.10 0.00 46.04 4.18
2773 14871 1.944676 GGGTGACGAATAGCGCGAG 60.945 63.158 12.10 0.00 46.04 5.03
2774 14872 2.103538 GGGTGACGAATAGCGCGA 59.896 61.111 12.10 0.00 46.04 5.87
2775 14873 2.901051 AAGGGGTGACGAATAGCGCG 62.901 60.000 0.00 0.00 46.04 6.86
2776 14874 0.103572 TAAGGGGTGACGAATAGCGC 59.896 55.000 0.00 0.00 46.04 5.92
2778 14876 3.071167 AGGAATAAGGGGTGACGAATAGC 59.929 47.826 0.00 0.00 0.00 2.97
2779 14877 4.344102 TGAGGAATAAGGGGTGACGAATAG 59.656 45.833 0.00 0.00 0.00 1.73
2780 14878 4.100498 GTGAGGAATAAGGGGTGACGAATA 59.900 45.833 0.00 0.00 0.00 1.75
2781 14879 3.112263 TGAGGAATAAGGGGTGACGAAT 58.888 45.455 0.00 0.00 0.00 3.34
2782 14880 2.235402 GTGAGGAATAAGGGGTGACGAA 59.765 50.000 0.00 0.00 0.00 3.85
2783 14881 1.829222 GTGAGGAATAAGGGGTGACGA 59.171 52.381 0.00 0.00 0.00 4.20
2784 14882 1.134491 GGTGAGGAATAAGGGGTGACG 60.134 57.143 0.00 0.00 0.00 4.35
2785 14883 1.212195 GGGTGAGGAATAAGGGGTGAC 59.788 57.143 0.00 0.00 0.00 3.67
2786 14884 1.591768 GGGTGAGGAATAAGGGGTGA 58.408 55.000 0.00 0.00 0.00 4.02
2787 14885 0.551396 GGGGTGAGGAATAAGGGGTG 59.449 60.000 0.00 0.00 0.00 4.61
2788 14886 0.122435 TGGGGTGAGGAATAAGGGGT 59.878 55.000 0.00 0.00 0.00 4.95
2789 14887 0.846693 CTGGGGTGAGGAATAAGGGG 59.153 60.000 0.00 0.00 0.00 4.79
2790 14888 0.183731 GCTGGGGTGAGGAATAAGGG 59.816 60.000 0.00 0.00 0.00 3.95
2791 14889 0.183731 GGCTGGGGTGAGGAATAAGG 59.816 60.000 0.00 0.00 0.00 2.69
2813 14911 1.162181 CGTGGCTGTAGATGCATGGG 61.162 60.000 2.46 0.00 0.00 4.00
2883 14981 7.933577 AGCCTTTTTACTTACGGTAGTTTTAGT 59.066 33.333 0.00 0.00 0.00 2.24
2918 15016 5.841957 ACCTCCATGCATCTTGTAAAATC 57.158 39.130 0.00 0.00 0.00 2.17
3033 15131 5.131067 TGCGGTAGACATCTTATAGACAGT 58.869 41.667 0.00 0.00 0.00 3.55
3047 15145 3.821600 TGATAGAGGAAGATGCGGTAGAC 59.178 47.826 0.00 0.00 0.00 2.59
3052 15150 3.257873 ACAGATGATAGAGGAAGATGCGG 59.742 47.826 0.00 0.00 0.00 5.69
3134 15235 3.701241 CATCTTGCCTCTCTCTTCGTAC 58.299 50.000 0.00 0.00 0.00 3.67
3241 15345 0.602562 GCGCTCTCTATGGATCAGCT 59.397 55.000 0.00 0.00 0.00 4.24
3250 15354 4.292178 GCTGGCGGCGCTCTCTAT 62.292 66.667 32.30 0.00 0.00 1.98
3266 15370 2.880268 TGTATCCATGCACATGCTAAGC 59.120 45.455 5.31 0.00 42.66 3.09
3374 17313 9.573166 TGGTCATGCTATTATAAAAACATAGCT 57.427 29.630 13.49 0.00 43.94 3.32
3397 17336 8.970859 TTTCATTTGACCACATTTTAATTGGT 57.029 26.923 8.22 8.22 46.67 3.67


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

AutoCloner maintained by Alex Coulton.