Multiple sequence alignment - TraesCS3B01G581400

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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 TraesCS3B01G581400 chr3B 100.000 2444 0 0 1 2444 810138658 810141101 0.000000e+00 4514
1 TraesCS3B01G581400 chr3B 86.417 427 56 2 242 666 224153135 224153561 1.320000e-127 466
2 TraesCS3B01G581400 chr1B 93.321 1587 97 7 862 2444 394907042 394908623 0.000000e+00 2335
3 TraesCS3B01G581400 chr1B 88.017 1644 174 10 821 2444 678554974 678556614 0.000000e+00 1923
4 TraesCS3B01G581400 chr1B 92.245 245 19 0 1 245 145355556 145355312 5.000000e-92 348
5 TraesCS3B01G581400 chr1B 82.061 262 45 2 2178 2438 449370052 449370312 3.160000e-54 222
6 TraesCS3B01G581400 chr4B 92.839 1550 97 3 908 2444 621966700 621968248 0.000000e+00 2235
7 TraesCS3B01G581400 chr4B 81.282 577 71 22 242 814 345278518 345277975 1.340000e-117 433
8 TraesCS3B01G581400 chr2B 89.640 1641 145 15 824 2444 534244927 534243292 0.000000e+00 2065
9 TraesCS3B01G581400 chr1A 84.893 1635 227 11 825 2444 341018991 341020620 0.000000e+00 1633
10 TraesCS3B01G581400 chr1A 91.020 245 22 0 1 245 230147354 230147598 5.040000e-87 331
11 TraesCS3B01G581400 chr2D 85.660 1046 133 9 817 1849 71256104 71255063 0.000000e+00 1085
12 TraesCS3B01G581400 chr2D 80.865 601 97 4 1845 2444 71245946 71245363 7.970000e-125 457
13 TraesCS3B01G581400 chr2D 83.810 315 43 7 2134 2444 155158919 155158609 2.380000e-75 292
14 TraesCS3B01G581400 chr2D 78.481 237 30 6 568 804 284555867 284556082 4.240000e-28 135
15 TraesCS3B01G581400 chr4D 84.549 576 75 10 242 811 387793456 387794023 2.120000e-155 558
16 TraesCS3B01G581400 chr4D 91.837 245 20 0 1 245 387793283 387793527 2.330000e-90 342
17 TraesCS3B01G581400 chr1D 84.331 568 83 6 242 804 225417353 225416787 3.550000e-153 551
18 TraesCS3B01G581400 chr7A 82.923 568 86 11 242 802 421559928 421559365 3.630000e-138 501
19 TraesCS3B01G581400 chr7A 83.908 522 69 10 242 752 86234875 86234358 3.650000e-133 484
20 TraesCS3B01G581400 chr7A 91.429 245 21 0 1 245 82997776 82997532 1.080000e-88 337
21 TraesCS3B01G581400 chr3A 82.783 575 85 3 1870 2444 63453528 63454088 3.630000e-138 501
22 TraesCS3B01G581400 chr3A 92.245 245 19 0 1 245 17166223 17166467 5.000000e-92 348
23 TraesCS3B01G581400 chr3A 82.527 372 58 5 242 611 313519208 313519574 1.090000e-83 320
24 TraesCS3B01G581400 chr7B 83.716 522 71 9 242 752 34829710 34829192 4.730000e-132 481
25 TraesCS3B01G581400 chr7D 84.055 508 69 9 242 742 591558220 591558722 1.700000e-131 479
26 TraesCS3B01G581400 chr7D 91.837 245 16 3 1 245 591558047 591558287 3.010000e-89 339
27 TraesCS3B01G581400 chr4A 92.245 245 19 0 1 245 734097384 734097628 5.000000e-92 348
28 TraesCS3B01G581400 chrUn 91.429 245 21 0 1 245 334758546 334758302 1.080000e-88 337
29 TraesCS3B01G581400 chr6A 91.429 245 21 0 1 245 587753377 587753621 1.080000e-88 337


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 TraesCS3B01G581400 chr3B 810138658 810141101 2443 False 4514 4514 100.000 1 2444 1 chr3B.!!$F2 2443
1 TraesCS3B01G581400 chr1B 394907042 394908623 1581 False 2335 2335 93.321 862 2444 1 chr1B.!!$F1 1582
2 TraesCS3B01G581400 chr1B 678554974 678556614 1640 False 1923 1923 88.017 821 2444 1 chr1B.!!$F3 1623
3 TraesCS3B01G581400 chr4B 621966700 621968248 1548 False 2235 2235 92.839 908 2444 1 chr4B.!!$F1 1536
4 TraesCS3B01G581400 chr4B 345277975 345278518 543 True 433 433 81.282 242 814 1 chr4B.!!$R1 572
5 TraesCS3B01G581400 chr2B 534243292 534244927 1635 True 2065 2065 89.640 824 2444 1 chr2B.!!$R1 1620
6 TraesCS3B01G581400 chr1A 341018991 341020620 1629 False 1633 1633 84.893 825 2444 1 chr1A.!!$F2 1619
7 TraesCS3B01G581400 chr2D 71255063 71256104 1041 True 1085 1085 85.660 817 1849 1 chr2D.!!$R2 1032
8 TraesCS3B01G581400 chr2D 71245363 71245946 583 True 457 457 80.865 1845 2444 1 chr2D.!!$R1 599
9 TraesCS3B01G581400 chr4D 387793283 387794023 740 False 450 558 88.193 1 811 2 chr4D.!!$F1 810
10 TraesCS3B01G581400 chr1D 225416787 225417353 566 True 551 551 84.331 242 804 1 chr1D.!!$R1 562
11 TraesCS3B01G581400 chr7A 421559365 421559928 563 True 501 501 82.923 242 802 1 chr7A.!!$R3 560
12 TraesCS3B01G581400 chr7A 86234358 86234875 517 True 484 484 83.908 242 752 1 chr7A.!!$R2 510
13 TraesCS3B01G581400 chr3A 63453528 63454088 560 False 501 501 82.783 1870 2444 1 chr3A.!!$F2 574
14 TraesCS3B01G581400 chr7B 34829192 34829710 518 True 481 481 83.716 242 752 1 chr7B.!!$R1 510
15 TraesCS3B01G581400 chr7D 591558047 591558722 675 False 409 479 87.946 1 742 2 chr7D.!!$F1 741

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
204 205 0.03759 CCAAGTTCCCGTGGGATGAA 59.962 55.0 8.81 0.0 44.74 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1985 2027 0.321564 CTCCATGGTCGTTCCTGCAA 60.322 55.0 12.58 0.0 37.07 4.08 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
50 51 4.634004 CGAGTATGTTAACAAGGCCATTGA 59.366 41.667 13.23 0.00 41.83 2.57
52 53 6.455360 AGTATGTTAACAAGGCCATTGATG 57.545 37.500 13.23 6.48 41.83 3.07
62 63 1.483415 GGCCATTGATGCCTTCATGTT 59.517 47.619 0.00 0.00 45.70 2.71
63 64 2.546778 GCCATTGATGCCTTCATGTTG 58.453 47.619 0.00 0.00 33.34 3.33
124 125 2.515523 CTCAGAATGGGGCGGCAG 60.516 66.667 12.47 0.00 36.16 4.85
173 174 3.124921 CCGGGCGGTGATGTTCAC 61.125 66.667 0.00 0.00 46.23 3.18
174 175 2.047274 CGGGCGGTGATGTTCACT 60.047 61.111 7.51 0.00 46.19 3.41
175 176 1.216977 CGGGCGGTGATGTTCACTA 59.783 57.895 7.51 0.00 46.19 2.74
176 177 1.082117 CGGGCGGTGATGTTCACTAC 61.082 60.000 7.51 0.89 46.19 2.73
177 178 1.082117 GGGCGGTGATGTTCACTACG 61.082 60.000 7.51 5.09 46.19 3.51
178 179 0.108992 GGCGGTGATGTTCACTACGA 60.109 55.000 7.51 0.00 46.19 3.43
179 180 1.670674 GGCGGTGATGTTCACTACGAA 60.671 52.381 7.51 0.00 46.19 3.85
180 181 2.268298 GCGGTGATGTTCACTACGAAT 58.732 47.619 7.51 0.00 46.19 3.34
181 182 2.029244 GCGGTGATGTTCACTACGAATG 59.971 50.000 7.51 0.00 46.19 2.67
182 183 3.250744 CGGTGATGTTCACTACGAATGT 58.749 45.455 7.51 0.00 46.19 2.71
183 184 3.060761 CGGTGATGTTCACTACGAATGTG 59.939 47.826 7.51 0.00 46.19 3.21
184 185 3.181520 GGTGATGTTCACTACGAATGTGC 60.182 47.826 7.51 0.00 46.19 4.57
185 186 3.000041 TGATGTTCACTACGAATGTGCC 59.000 45.455 0.00 0.00 35.63 5.01
186 187 1.803334 TGTTCACTACGAATGTGCCC 58.197 50.000 0.00 0.00 35.63 5.36
187 188 1.070914 TGTTCACTACGAATGTGCCCA 59.929 47.619 0.00 0.00 35.63 5.36
188 189 2.147958 GTTCACTACGAATGTGCCCAA 58.852 47.619 0.00 0.00 35.63 4.12
189 190 2.093306 TCACTACGAATGTGCCCAAG 57.907 50.000 0.00 0.00 35.58 3.61
190 191 1.346395 TCACTACGAATGTGCCCAAGT 59.654 47.619 0.00 0.00 35.58 3.16
191 192 2.151202 CACTACGAATGTGCCCAAGTT 58.849 47.619 0.00 0.00 0.00 2.66
192 193 2.159627 CACTACGAATGTGCCCAAGTTC 59.840 50.000 0.00 0.00 0.00 3.01
193 194 1.737793 CTACGAATGTGCCCAAGTTCC 59.262 52.381 0.00 0.00 0.00 3.62
194 195 0.893727 ACGAATGTGCCCAAGTTCCC 60.894 55.000 0.00 0.00 0.00 3.97
195 196 1.883021 GAATGTGCCCAAGTTCCCG 59.117 57.895 0.00 0.00 0.00 5.14
196 197 0.893727 GAATGTGCCCAAGTTCCCGT 60.894 55.000 0.00 0.00 0.00 5.28
197 198 1.178534 AATGTGCCCAAGTTCCCGTG 61.179 55.000 0.00 0.00 0.00 4.94
198 199 2.983592 GTGCCCAAGTTCCCGTGG 60.984 66.667 0.00 0.00 39.65 4.94
202 203 4.319133 CCAAGTTCCCGTGGGATG 57.681 61.111 8.81 4.22 44.74 3.51
203 204 1.682849 CCAAGTTCCCGTGGGATGA 59.317 57.895 8.81 0.00 44.74 2.92
204 205 0.037590 CCAAGTTCCCGTGGGATGAA 59.962 55.000 8.81 0.00 44.74 2.57
205 206 1.453155 CAAGTTCCCGTGGGATGAAG 58.547 55.000 8.81 0.00 44.74 3.02
206 207 0.322546 AAGTTCCCGTGGGATGAAGC 60.323 55.000 8.81 0.00 44.74 3.86
207 208 1.201429 AGTTCCCGTGGGATGAAGCT 61.201 55.000 8.81 0.11 44.74 3.74
208 209 1.026718 GTTCCCGTGGGATGAAGCTG 61.027 60.000 8.81 0.00 44.74 4.24
209 210 1.488705 TTCCCGTGGGATGAAGCTGT 61.489 55.000 8.81 0.00 44.74 4.40
210 211 1.746615 CCCGTGGGATGAAGCTGTG 60.747 63.158 0.00 0.00 37.50 3.66
211 212 1.296392 CCGTGGGATGAAGCTGTGA 59.704 57.895 0.00 0.00 0.00 3.58
212 213 0.107508 CCGTGGGATGAAGCTGTGAT 60.108 55.000 0.00 0.00 0.00 3.06
213 214 1.012086 CGTGGGATGAAGCTGTGATG 58.988 55.000 0.00 0.00 0.00 3.07
214 215 1.405933 CGTGGGATGAAGCTGTGATGA 60.406 52.381 0.00 0.00 0.00 2.92
215 216 2.744166 CGTGGGATGAAGCTGTGATGAT 60.744 50.000 0.00 0.00 0.00 2.45
216 217 2.617308 GTGGGATGAAGCTGTGATGATG 59.383 50.000 0.00 0.00 0.00 3.07
217 218 2.228059 GGGATGAAGCTGTGATGATGG 58.772 52.381 0.00 0.00 0.00 3.51
218 219 1.607628 GGATGAAGCTGTGATGATGGC 59.392 52.381 0.00 0.00 0.00 4.40
219 220 1.607628 GATGAAGCTGTGATGATGGCC 59.392 52.381 0.00 0.00 0.00 5.36
220 221 0.328926 TGAAGCTGTGATGATGGCCA 59.671 50.000 8.56 8.56 0.00 5.36
221 222 0.737219 GAAGCTGTGATGATGGCCAC 59.263 55.000 8.16 2.36 0.00 5.01
222 223 0.682209 AAGCTGTGATGATGGCCACC 60.682 55.000 8.16 0.00 32.61 4.61
223 224 1.077212 GCTGTGATGATGGCCACCT 60.077 57.895 8.16 0.00 32.61 4.00
224 225 0.682209 GCTGTGATGATGGCCACCTT 60.682 55.000 8.16 0.00 32.61 3.50
225 226 1.386533 CTGTGATGATGGCCACCTTC 58.613 55.000 8.16 6.87 32.61 3.46
226 227 0.994247 TGTGATGATGGCCACCTTCT 59.006 50.000 8.16 0.00 32.61 2.85
227 228 1.355381 TGTGATGATGGCCACCTTCTT 59.645 47.619 8.16 0.00 32.61 2.52
228 229 1.747355 GTGATGATGGCCACCTTCTTG 59.253 52.381 8.16 0.00 0.00 3.02
229 230 1.634973 TGATGATGGCCACCTTCTTGA 59.365 47.619 8.16 0.00 0.00 3.02
230 231 2.242965 TGATGATGGCCACCTTCTTGAT 59.757 45.455 8.16 0.00 0.00 2.57
231 232 2.425143 TGATGGCCACCTTCTTGATC 57.575 50.000 8.16 0.00 0.00 2.92
232 233 1.634973 TGATGGCCACCTTCTTGATCA 59.365 47.619 8.16 0.53 0.00 2.92
233 234 2.041485 TGATGGCCACCTTCTTGATCAA 59.959 45.455 8.16 8.12 0.00 2.57
234 235 1.909700 TGGCCACCTTCTTGATCAAC 58.090 50.000 0.00 0.00 0.00 3.18
235 236 1.177401 GGCCACCTTCTTGATCAACC 58.823 55.000 3.38 0.00 0.00 3.77
236 237 0.804989 GCCACCTTCTTGATCAACCG 59.195 55.000 3.38 0.00 0.00 4.44
237 238 0.804989 CCACCTTCTTGATCAACCGC 59.195 55.000 3.38 0.00 0.00 5.68
238 239 1.522668 CACCTTCTTGATCAACCGCA 58.477 50.000 3.38 0.00 0.00 5.69
239 240 1.197721 CACCTTCTTGATCAACCGCAC 59.802 52.381 3.38 0.00 0.00 5.34
240 241 0.443869 CCTTCTTGATCAACCGCACG 59.556 55.000 3.38 0.00 0.00 5.34
290 293 0.330604 AAGCTGTCATGATGGCCACT 59.669 50.000 8.16 0.00 0.00 4.00
320 323 4.823419 CGCACGCCATCCCGGTAA 62.823 66.667 0.00 0.00 36.97 2.85
328 333 1.697982 GCCATCCCGGTAAGAGGTATT 59.302 52.381 0.00 0.00 36.97 1.89
335 340 7.394816 CATCCCGGTAAGAGGTATTAAATCAT 58.605 38.462 0.00 0.00 0.00 2.45
336 341 7.383156 TCCCGGTAAGAGGTATTAAATCATT 57.617 36.000 0.00 0.00 0.00 2.57
360 365 7.581213 TGTGTGAGTTGGTTTTCATAGAAAT 57.419 32.000 0.00 0.00 0.00 2.17
393 398 1.822425 TCCCCCAAGGTGTTCTGTTA 58.178 50.000 0.00 0.00 36.75 2.41
402 407 5.448632 CCAAGGTGTTCTGTTACACTTGTTC 60.449 44.000 12.80 0.94 45.98 3.18
411 416 3.619483 TGTTACACTTGTTCTGTTCGTGG 59.381 43.478 0.00 0.00 0.00 4.94
425 430 1.199615 TCGTGGTCATAGGCCATCAA 58.800 50.000 5.01 0.00 38.40 2.57
508 513 1.282157 AGGTACAAATGCTGGAGTCCC 59.718 52.381 6.74 0.00 0.00 4.46
510 515 2.359900 GTACAAATGCTGGAGTCCCTG 58.640 52.381 6.74 0.40 34.81 4.45
541 546 3.428452 GGACATTTGTGAGCATGGATGTG 60.428 47.826 0.00 0.00 0.00 3.21
542 547 2.494471 ACATTTGTGAGCATGGATGTGG 59.506 45.455 0.00 0.00 0.00 4.17
558 563 0.802494 GTGGCGTTCCATGAATCGTT 59.198 50.000 0.00 0.00 45.62 3.85
607 613 5.105756 CCAAGTGTCTTGTTTGAAGACCTTT 60.106 40.000 11.13 4.22 44.47 3.11
630 636 3.009695 ACCAATGTCTCCCACCGAAAATA 59.990 43.478 0.00 0.00 0.00 1.40
633 639 1.065709 TGTCTCCCACCGAAAATAGGC 60.066 52.381 0.00 0.00 0.00 3.93
670 678 3.324170 GCACACAGATGCAGCAATC 57.676 52.632 4.07 0.00 45.39 2.67
674 685 2.030628 CACACAGATGCAGCAATCACAA 60.031 45.455 4.07 0.00 0.00 3.33
690 701 6.215121 CAATCACAATCACCTTTAGCAACAA 58.785 36.000 0.00 0.00 0.00 2.83
714 725 3.838317 TGGCTCAATAGTAACTCCTGTGT 59.162 43.478 0.00 0.00 0.00 3.72
720 731 6.017192 TCAATAGTAACTCCTGTGTCTCCTT 58.983 40.000 0.00 0.00 0.00 3.36
723 734 3.967987 AGTAACTCCTGTGTCTCCTTTGT 59.032 43.478 0.00 0.00 0.00 2.83
745 756 0.389817 CAAGCATCGACTTCCACCGA 60.390 55.000 0.00 0.00 39.25 4.69
755 766 1.271325 ACTTCCACCGATGATGTGCAA 60.271 47.619 0.00 0.00 32.30 4.08
778 795 1.133823 TGGCACAATGACACCAACTCT 60.134 47.619 0.00 0.00 31.92 3.24
804 821 1.070134 GTAGTGTGCTGAGGTGGACAA 59.930 52.381 0.00 0.00 39.83 3.18
805 822 0.767375 AGTGTGCTGAGGTGGACAAT 59.233 50.000 0.00 0.00 39.83 2.71
811 828 1.804372 GCTGAGGTGGACAATAGAGCG 60.804 57.143 0.00 0.00 0.00 5.03
814 831 1.751924 GAGGTGGACAATAGAGCGAGT 59.248 52.381 0.00 0.00 0.00 4.18
815 832 2.166664 GAGGTGGACAATAGAGCGAGTT 59.833 50.000 0.00 0.00 0.00 3.01
845 862 0.109913 GGGTTTTGAGTTCCTCCGGT 59.890 55.000 0.00 0.00 0.00 5.28
853 870 2.602267 TTCCTCCGGTGGCGAGAA 60.602 61.111 18.03 3.99 0.00 2.87
934 953 2.179517 CTCGTCTCTGGTCGTGGC 59.820 66.667 0.00 0.00 0.00 5.01
935 954 2.282251 TCGTCTCTGGTCGTGGCT 60.282 61.111 0.00 0.00 0.00 4.75
936 955 2.126307 CGTCTCTGGTCGTGGCTG 60.126 66.667 0.00 0.00 0.00 4.85
972 992 3.042682 TGGTGTTGTTCTACCCTCTCAA 58.957 45.455 0.00 0.00 36.10 3.02
1095 1115 3.242867 TCTGCAGGAAGAAGAAGAGGAA 58.757 45.455 15.13 0.00 0.00 3.36
1155 1175 1.141019 GGCGAAGTGGCTCGTGATA 59.859 57.895 0.00 0.00 40.99 2.15
1170 1190 4.439057 TCGTGATAGCAAAAGTCCATACC 58.561 43.478 0.00 0.00 0.00 2.73
1176 1196 7.225931 GTGATAGCAAAAGTCCATACCGATAAA 59.774 37.037 0.00 0.00 0.00 1.40
1205 1225 1.227380 CATCTGCCCTGTACTCGCC 60.227 63.158 0.00 0.00 0.00 5.54
1316 1336 1.225376 TGGAACACGGCGATGAACAC 61.225 55.000 16.62 0.00 0.00 3.32
1402 1422 6.037830 TCCAACTTCTGTAGTGCTTAACAAAC 59.962 38.462 0.00 0.00 37.12 2.93
1435 1455 3.012518 GCAAGAATCTTGAAGCTGCCTA 58.987 45.455 25.54 0.00 0.00 3.93
1443 1463 8.267894 AGAATCTTGAAGCTGCCTAATAACTAA 58.732 33.333 0.00 0.00 0.00 2.24
1468 1488 2.056223 CCTGCAGCAATCAAGGGGG 61.056 63.158 8.66 0.00 0.00 5.40
1514 1534 9.138596 GATCTTAGAGATTCAAACTACCCTACT 57.861 37.037 0.00 0.00 34.53 2.57
1545 1565 1.069227 GCAGGCGAATTTGTTCGAGTT 60.069 47.619 14.00 0.00 46.52 3.01
1815 1849 1.610624 GGTGATGCTGGAAGAAACGGA 60.611 52.381 0.00 0.00 34.07 4.69
1821 1855 1.270893 GCTGGAAGAAACGGAGAAGGT 60.271 52.381 0.00 0.00 34.07 3.50
1923 1965 9.809096 CGTCATAATGCTCTCTATAATAATGGT 57.191 33.333 0.00 0.00 0.00 3.55
1959 2001 5.043737 TGGCTACAGAAGGTAACACTTTT 57.956 39.130 0.00 0.00 41.41 2.27
1985 2027 4.219115 AGGACCGAGACTGATCATGTAAT 58.781 43.478 0.00 0.00 0.00 1.89
2013 2055 3.688553 GACCATGGAGTCGGATTCC 57.311 57.895 21.47 12.27 35.20 3.01
2032 2074 2.846206 TCCATGAATCTGCTGGGTAAGT 59.154 45.455 0.00 0.00 0.00 2.24
2148 2190 2.474816 GTGACCAATCTAGTGGATCGC 58.525 52.381 6.39 3.88 41.65 4.58
2266 2308 3.890756 TGCAGTTGACAATTCTGATGGTT 59.109 39.130 9.39 0.00 0.00 3.67
2270 2312 6.621596 GCAGTTGACAATTCTGATGGTTCTAC 60.622 42.308 9.39 0.00 0.00 2.59
2333 2375 4.261698 CCGGATGCAATGAAAATCATAGCA 60.262 41.667 0.00 0.00 35.76 3.49
2428 2470 3.744238 TGTGATGTTCTTGTCGGAGAA 57.256 42.857 0.00 0.00 39.69 2.87
2439 2481 1.676529 TGTCGGAGAATCACCTCGATC 59.323 52.381 0.00 0.00 39.69 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.107703 TCGGTGCCATTGTCAGATCC 60.108 55.000 0.00 0.00 0.00 3.36
50 51 2.173519 CCTTGTCCAACATGAAGGCAT 58.826 47.619 0.00 0.00 34.29 4.40
52 53 0.890683 CCCTTGTCCAACATGAAGGC 59.109 55.000 0.00 0.00 34.70 4.35
119 120 0.375106 GCGATTTTTCCTCTCTGCCG 59.625 55.000 0.00 0.00 0.00 5.69
124 125 1.740025 CAGGTGGCGATTTTTCCTCTC 59.260 52.381 0.00 0.00 0.00 3.20
156 157 3.124921 GTGAACATCACCGCCCGG 61.125 66.667 4.96 4.96 41.37 5.73
173 174 1.737793 GGAACTTGGGCACATTCGTAG 59.262 52.381 0.00 0.00 0.00 3.51
174 175 1.612199 GGGAACTTGGGCACATTCGTA 60.612 52.381 0.00 0.00 0.00 3.43
175 176 0.893727 GGGAACTTGGGCACATTCGT 60.894 55.000 0.00 0.00 0.00 3.85
176 177 1.883021 GGGAACTTGGGCACATTCG 59.117 57.895 0.00 0.00 0.00 3.34
177 178 0.893727 ACGGGAACTTGGGCACATTC 60.894 55.000 0.00 0.00 0.00 2.67
178 179 1.152830 ACGGGAACTTGGGCACATT 59.847 52.632 0.00 0.00 0.00 2.71
179 180 1.603455 CACGGGAACTTGGGCACAT 60.603 57.895 0.00 0.00 0.00 3.21
180 181 2.203280 CACGGGAACTTGGGCACA 60.203 61.111 0.00 0.00 0.00 4.57
181 182 2.983592 CCACGGGAACTTGGGCAC 60.984 66.667 0.00 0.00 45.66 5.01
192 193 1.746615 CACAGCTTCATCCCACGGG 60.747 63.158 0.00 0.00 0.00 5.28
193 194 0.107508 ATCACAGCTTCATCCCACGG 60.108 55.000 0.00 0.00 0.00 4.94
194 195 1.012086 CATCACAGCTTCATCCCACG 58.988 55.000 0.00 0.00 0.00 4.94
195 196 2.408271 TCATCACAGCTTCATCCCAC 57.592 50.000 0.00 0.00 0.00 4.61
196 197 2.422377 CCATCATCACAGCTTCATCCCA 60.422 50.000 0.00 0.00 0.00 4.37
197 198 2.228059 CCATCATCACAGCTTCATCCC 58.772 52.381 0.00 0.00 0.00 3.85
198 199 1.607628 GCCATCATCACAGCTTCATCC 59.392 52.381 0.00 0.00 0.00 3.51
199 200 1.607628 GGCCATCATCACAGCTTCATC 59.392 52.381 0.00 0.00 0.00 2.92
200 201 1.064240 TGGCCATCATCACAGCTTCAT 60.064 47.619 0.00 0.00 0.00 2.57
201 202 0.328926 TGGCCATCATCACAGCTTCA 59.671 50.000 0.00 0.00 0.00 3.02
202 203 0.737219 GTGGCCATCATCACAGCTTC 59.263 55.000 9.72 0.00 34.32 3.86
203 204 0.682209 GGTGGCCATCATCACAGCTT 60.682 55.000 12.38 0.00 35.74 3.74
204 205 1.077212 GGTGGCCATCATCACAGCT 60.077 57.895 12.38 0.00 35.74 4.24
205 206 0.682209 AAGGTGGCCATCATCACAGC 60.682 55.000 20.62 0.00 35.74 4.40
206 207 1.064906 AGAAGGTGGCCATCATCACAG 60.065 52.381 22.59 0.00 35.74 3.66
207 208 0.994247 AGAAGGTGGCCATCATCACA 59.006 50.000 22.59 0.00 35.74 3.58
208 209 1.747355 CAAGAAGGTGGCCATCATCAC 59.253 52.381 22.59 8.58 0.00 3.06
209 210 1.634973 TCAAGAAGGTGGCCATCATCA 59.365 47.619 22.59 0.00 0.00 3.07
210 211 2.425143 TCAAGAAGGTGGCCATCATC 57.575 50.000 20.62 16.89 0.00 2.92
211 212 2.242965 TGATCAAGAAGGTGGCCATCAT 59.757 45.455 20.62 5.94 0.00 2.45
212 213 1.634973 TGATCAAGAAGGTGGCCATCA 59.365 47.619 20.62 7.33 0.00 3.07
213 214 2.424956 GTTGATCAAGAAGGTGGCCATC 59.575 50.000 9.72 9.02 0.00 3.51
214 215 2.450476 GTTGATCAAGAAGGTGGCCAT 58.550 47.619 9.72 0.00 0.00 4.40
215 216 1.547675 GGTTGATCAAGAAGGTGGCCA 60.548 52.381 8.80 0.00 0.00 5.36
216 217 1.177401 GGTTGATCAAGAAGGTGGCC 58.823 55.000 8.80 0.00 0.00 5.36
217 218 0.804989 CGGTTGATCAAGAAGGTGGC 59.195 55.000 8.80 0.00 0.00 5.01
218 219 0.804989 GCGGTTGATCAAGAAGGTGG 59.195 55.000 8.80 0.00 0.00 4.61
219 220 1.197721 GTGCGGTTGATCAAGAAGGTG 59.802 52.381 8.80 0.00 0.00 4.00
220 221 1.523758 GTGCGGTTGATCAAGAAGGT 58.476 50.000 8.80 0.00 0.00 3.50
221 222 0.443869 CGTGCGGTTGATCAAGAAGG 59.556 55.000 8.80 0.00 0.00 3.46
222 223 0.179215 GCGTGCGGTTGATCAAGAAG 60.179 55.000 8.80 4.44 0.00 2.85
223 224 1.573829 GGCGTGCGGTTGATCAAGAA 61.574 55.000 8.80 0.00 0.00 2.52
224 225 2.032634 GGCGTGCGGTTGATCAAGA 61.033 57.895 8.80 0.00 0.00 3.02
225 226 1.647545 ATGGCGTGCGGTTGATCAAG 61.648 55.000 8.80 0.00 0.00 3.02
226 227 1.673993 ATGGCGTGCGGTTGATCAA 60.674 52.632 3.38 3.38 0.00 2.57
227 228 2.046411 ATGGCGTGCGGTTGATCA 60.046 55.556 0.00 0.00 0.00 2.92
228 229 1.643868 TTCATGGCGTGCGGTTGATC 61.644 55.000 0.65 0.00 0.00 2.92
229 230 1.031571 ATTCATGGCGTGCGGTTGAT 61.032 50.000 0.65 0.00 0.00 2.57
230 231 1.673993 ATTCATGGCGTGCGGTTGA 60.674 52.632 0.65 0.00 0.00 3.18
231 232 1.514657 CATTCATGGCGTGCGGTTG 60.515 57.895 0.65 0.00 0.00 3.77
232 233 1.971167 ACATTCATGGCGTGCGGTT 60.971 52.632 0.65 0.00 0.00 4.44
233 234 2.359850 ACATTCATGGCGTGCGGT 60.360 55.556 0.65 0.00 0.00 5.68
234 235 2.100797 CACATTCATGGCGTGCGG 59.899 61.111 0.65 0.00 0.00 5.69
235 236 2.577644 GCACATTCATGGCGTGCG 60.578 61.111 15.81 0.00 45.69 5.34
237 238 1.875420 TTGGGCACATTCATGGCGTG 61.875 55.000 0.00 0.00 45.84 5.34
238 239 1.597797 CTTGGGCACATTCATGGCGT 61.598 55.000 0.00 0.00 45.84 5.68
239 240 1.140161 CTTGGGCACATTCATGGCG 59.860 57.895 0.00 0.00 45.84 5.69
240 241 0.609662 AACTTGGGCACATTCATGGC 59.390 50.000 0.00 0.00 44.21 4.40
267 268 1.607628 GGCCATCATGACAGCTTCATC 59.392 52.381 16.12 0.00 43.68 2.92
268 269 1.064240 TGGCCATCATGACAGCTTCAT 60.064 47.619 16.12 5.80 46.75 2.57
290 293 0.237235 GCGTGCGGTTGATCAAGAAA 59.763 50.000 8.80 0.00 0.00 2.52
319 322 9.520515 AACTCACACAATGATTTAATACCTCTT 57.479 29.630 0.00 0.00 36.48 2.85
320 323 8.950210 CAACTCACACAATGATTTAATACCTCT 58.050 33.333 0.00 0.00 36.48 3.69
328 333 7.776107 TGAAAACCAACTCACACAATGATTTA 58.224 30.769 0.00 0.00 36.48 1.40
335 340 7.397892 TTTCTATGAAAACCAACTCACACAA 57.602 32.000 0.00 0.00 0.00 3.33
336 341 7.581213 ATTTCTATGAAAACCAACTCACACA 57.419 32.000 0.00 0.00 0.00 3.72
360 365 5.076738 ACCTTGGGGGAAACTAGGAATTTAA 59.923 40.000 0.00 0.00 38.76 1.52
393 398 2.277084 GACCACGAACAGAACAAGTGT 58.723 47.619 0.00 0.00 0.00 3.55
402 407 0.249120 TGGCCTATGACCACGAACAG 59.751 55.000 3.32 0.00 30.29 3.16
411 416 4.641989 ACTTGTTGATTGATGGCCTATGAC 59.358 41.667 3.32 0.00 0.00 3.06
425 430 3.434309 CCCAAGGATCCAACTTGTTGAT 58.566 45.455 15.82 6.61 42.84 2.57
488 493 1.282157 GGGACTCCAGCATTTGTACCT 59.718 52.381 0.00 0.00 31.00 3.08
508 513 1.081892 CAAATGTCCGCCTCTCACAG 58.918 55.000 0.00 0.00 0.00 3.66
510 515 0.798776 CACAAATGTCCGCCTCTCAC 59.201 55.000 0.00 0.00 0.00 3.51
541 546 0.377203 GGAACGATTCATGGAACGCC 59.623 55.000 3.17 0.00 0.00 5.68
542 547 0.377203 GGGAACGATTCATGGAACGC 59.623 55.000 3.17 0.00 0.00 4.84
558 563 5.947663 TCAGTTTTCTCACCATAAAAGGGA 58.052 37.500 0.00 0.00 0.00 4.20
607 613 1.646912 TTCGGTGGGAGACATTGGTA 58.353 50.000 0.00 0.00 0.00 3.25
630 636 0.618968 CTACTCTCCCCACTTGGCCT 60.619 60.000 3.32 0.00 0.00 5.19
633 639 1.757699 GCTACTACTCTCCCCACTTGG 59.242 57.143 0.00 0.00 0.00 3.61
666 674 5.771469 TGTTGCTAAAGGTGATTGTGATTG 58.229 37.500 0.00 0.00 0.00 2.67
667 675 6.040842 ACTTGTTGCTAAAGGTGATTGTGATT 59.959 34.615 0.00 0.00 0.00 2.57
668 676 5.536161 ACTTGTTGCTAAAGGTGATTGTGAT 59.464 36.000 0.00 0.00 0.00 3.06
669 677 4.887071 ACTTGTTGCTAAAGGTGATTGTGA 59.113 37.500 0.00 0.00 0.00 3.58
670 678 4.977963 CACTTGTTGCTAAAGGTGATTGTG 59.022 41.667 0.00 0.00 0.00 3.33
674 685 2.558359 GCCACTTGTTGCTAAAGGTGAT 59.442 45.455 2.14 0.00 0.00 3.06
690 701 4.081420 CACAGGAGTTACTATTGAGCCACT 60.081 45.833 3.16 0.00 0.00 4.00
714 725 3.994392 GTCGATGCTTGTAACAAAGGAGA 59.006 43.478 0.00 0.00 30.50 3.71
720 731 3.496884 GTGGAAGTCGATGCTTGTAACAA 59.503 43.478 0.00 0.00 0.00 2.83
723 734 2.695359 GGTGGAAGTCGATGCTTGTAA 58.305 47.619 0.00 0.00 0.00 2.41
755 766 2.699846 AGTTGGTGTCATTGTGCCAATT 59.300 40.909 10.62 6.01 42.13 2.32
773 784 3.324846 TCAGCACACTACCAATCAGAGTT 59.675 43.478 0.00 0.00 0.00 3.01
778 795 1.977854 ACCTCAGCACACTACCAATCA 59.022 47.619 0.00 0.00 0.00 2.57
804 821 1.192428 ACGGGGAAAACTCGCTCTAT 58.808 50.000 0.00 0.00 0.00 1.98
805 822 0.971386 AACGGGGAAAACTCGCTCTA 59.029 50.000 0.00 0.00 0.00 2.43
853 870 2.352519 GGAGAAAGTTTACTCTCGGCGT 60.353 50.000 6.85 0.00 39.23 5.68
972 992 0.838987 TGCCCGAGAAACCCTAACCT 60.839 55.000 0.00 0.00 0.00 3.50
1029 1049 2.434774 GGTTCCTTCCTTGGGCGT 59.565 61.111 0.00 0.00 0.00 5.68
1151 1171 4.746535 TCGGTATGGACTTTTGCTATCA 57.253 40.909 0.00 0.00 0.00 2.15
1155 1175 4.881850 CCTTTATCGGTATGGACTTTTGCT 59.118 41.667 0.00 0.00 0.00 3.91
1170 1190 4.511826 GCAGATGGACTAAACCCTTTATCG 59.488 45.833 0.00 0.00 0.00 2.92
1176 1196 0.919710 GGGCAGATGGACTAAACCCT 59.080 55.000 0.00 0.00 34.52 4.34
1205 1225 2.093764 GGATTCCAGGCGGATCTCATAG 60.094 54.545 0.00 0.00 42.41 2.23
1402 1422 4.696479 AGATTCTTGCCCATACCACTAG 57.304 45.455 0.00 0.00 0.00 2.57
1435 1455 7.938140 TTGCTGCAGGAATTAGTTAGTTATT 57.062 32.000 17.55 0.00 0.00 1.40
1443 1463 3.698040 CCTTGATTGCTGCAGGAATTAGT 59.302 43.478 30.77 12.98 36.19 2.24
1468 1488 1.863155 TTCCCCATCTTCCTGCACCC 61.863 60.000 0.00 0.00 0.00 4.61
1469 1489 0.394899 CTTCCCCATCTTCCTGCACC 60.395 60.000 0.00 0.00 0.00 5.01
1545 1565 5.545063 TTGTGACATCAAGTTCCACTCTA 57.455 39.130 0.00 0.00 0.00 2.43
1580 1601 2.762887 TGCTTTGTGATCCCAACAAACA 59.237 40.909 5.89 6.89 31.21 2.83
1650 1672 3.640407 AGACCGCACTGCCCACAT 61.640 61.111 0.00 0.00 0.00 3.21
1815 1849 0.408309 GGCCCCTACCAAAACCTTCT 59.592 55.000 0.00 0.00 0.00 2.85
1821 1855 2.437002 CCACGGCCCCTACCAAAA 59.563 61.111 0.00 0.00 0.00 2.44
1959 2001 1.271926 TGATCAGTCTCGGTCCTCACA 60.272 52.381 0.00 0.00 0.00 3.58
1985 2027 0.321564 CTCCATGGTCGTTCCTGCAA 60.322 55.000 12.58 0.00 37.07 4.08
2008 2050 2.941480 ACCCAGCAGATTCATGGAATC 58.059 47.619 10.25 10.25 46.05 2.52
2013 2055 2.357009 GCACTTACCCAGCAGATTCATG 59.643 50.000 0.00 0.00 0.00 3.07
2032 2074 1.219124 GAGAATCAGGTGCCGAGCA 59.781 57.895 0.00 0.00 32.37 4.26
2041 2083 5.408356 CAATTTTTCTGCCAGAGAATCAGG 58.592 41.667 0.00 0.00 45.89 3.86
2148 2190 5.376625 TCCCCCGAATTATCTCTTTCAATG 58.623 41.667 0.00 0.00 0.00 2.82
2266 2308 4.083271 CGCCGATATCTCATGAGTTGTAGA 60.083 45.833 21.92 2.47 0.00 2.59
2270 2312 2.983136 GACGCCGATATCTCATGAGTTG 59.017 50.000 21.92 7.29 0.00 3.16


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

AutoCloner maintained by Alex Coulton.