Multiple sequence alignment - TraesCS2B01G537200

Loading Multiple Alignment...

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 TraesCS2B01G537200 chr2B 100.000 3454 0 0 1 3454 732594025 732590572 0.000000e+00 6379.0
1 TraesCS2B01G537200 chr2B 87.077 975 122 4 2482 3454 755914483 755915455 0.000000e+00 1099.0
2 TraesCS2B01G537200 chr2B 86.855 1027 68 29 1374 2389 732892973 732893943 0.000000e+00 1086.0
3 TraesCS2B01G537200 chr2B 97.812 320 6 1 2404 2722 732586409 732586090 5.040000e-153 551.0
4 TraesCS2B01G537200 chr2B 83.940 467 51 11 1398 1855 732864642 732865093 3.190000e-115 425.0
5 TraesCS2B01G537200 chr2B 87.077 325 42 0 2072 2396 732865352 732865676 5.450000e-98 368.0
6 TraesCS2B01G537200 chr2B 81.595 163 12 11 907 1063 732892469 732892619 6.060000e-23 119.0
7 TraesCS2B01G537200 chr2A 98.488 1058 15 1 2398 3454 684429097 684430154 0.000000e+00 1864.0
8 TraesCS2B01G537200 chr2A 91.955 1156 71 11 225 1370 734989980 734988837 0.000000e+00 1600.0
9 TraesCS2B01G537200 chr2A 93.788 998 50 4 1412 2401 734988832 734987839 0.000000e+00 1489.0
10 TraesCS2B01G537200 chr2A 87.012 1024 72 27 1374 2389 735244264 735245234 0.000000e+00 1098.0
11 TraesCS2B01G537200 chr2A 85.714 455 46 9 1393 1841 735238331 735238772 2.430000e-126 462.0
12 TraesCS2B01G537200 chr2A 97.807 228 5 0 2404 2631 684434323 684434550 8.980000e-106 394.0
13 TraesCS2B01G537200 chr2A 85.345 348 42 4 2054 2401 735261955 735262293 5.480000e-93 351.0
14 TraesCS2B01G537200 chr2A 100.000 31 0 0 802 832 713643365 713643335 1.340000e-04 58.4
15 TraesCS2B01G537200 chr6B 93.443 976 56 8 2482 3454 714304198 714303228 0.000000e+00 1441.0
16 TraesCS2B01G537200 chr6B 77.914 978 203 13 2482 3454 101611641 101610672 6.380000e-167 597.0
17 TraesCS2B01G537200 chr6B 78.947 171 29 2 432 602 38976927 38977090 3.640000e-20 110.0
18 TraesCS2B01G537200 chrUn 93.238 976 59 7 2482 3454 79546543 79545572 0.000000e+00 1430.0
19 TraesCS2B01G537200 chrUn 88.085 235 21 7 2482 2713 79541329 79541099 4.390000e-69 272.0
20 TraesCS2B01G537200 chr5A 83.765 579 88 6 2482 3058 614546861 614546287 8.430000e-151 544.0
21 TraesCS2B01G537200 chr5A 87.466 367 46 0 3084 3450 614523228 614522862 1.150000e-114 424.0
22 TraesCS2B01G537200 chr5A 86.792 371 49 0 3084 3454 614546288 614545918 6.900000e-112 414.0
23 TraesCS2B01G537200 chr2D 83.656 465 53 13 1413 1868 602648245 602648695 1.920000e-112 416.0
24 TraesCS2B01G537200 chr2D 86.239 327 45 0 2072 2398 602648830 602649156 4.240000e-94 355.0
25 TraesCS2B01G537200 chr2D 84.309 376 44 10 2024 2393 602253428 602253062 1.520000e-93 353.0
26 TraesCS2B01G537200 chr4A 78.618 608 124 6 2452 3057 607624179 607624782 6.950000e-107 398.0
27 TraesCS2B01G537200 chr5D 80.519 154 21 3 424 576 509290113 509290258 3.640000e-20 110.0
28 TraesCS2B01G537200 chr1A 84.286 70 8 3 1152 1220 9697476 9697409 8.000000e-07 65.8
29 TraesCS2B01G537200 chr5B 93.023 43 3 0 803 845 592293561 592293603 2.880000e-06 63.9
30 TraesCS2B01G537200 chr7B 100.000 30 0 0 803 832 429215397 429215426 4.820000e-04 56.5
31 TraesCS2B01G537200 chr1B 100.000 30 0 0 803 832 558522166 558522137 4.820000e-04 56.5


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 TraesCS2B01G537200 chr2B 732590572 732594025 3453 True 6379.0 6379 100.0000 1 3454 1 chr2B.!!$R2 3453
1 TraesCS2B01G537200 chr2B 755914483 755915455 972 False 1099.0 1099 87.0770 2482 3454 1 chr2B.!!$F1 972
2 TraesCS2B01G537200 chr2B 732892469 732893943 1474 False 602.5 1086 84.2250 907 2389 2 chr2B.!!$F3 1482
3 TraesCS2B01G537200 chr2B 732864642 732865676 1034 False 396.5 425 85.5085 1398 2396 2 chr2B.!!$F2 998
4 TraesCS2B01G537200 chr2A 684429097 684430154 1057 False 1864.0 1864 98.4880 2398 3454 1 chr2A.!!$F1 1056
5 TraesCS2B01G537200 chr2A 734987839 734989980 2141 True 1544.5 1600 92.8715 225 2401 2 chr2A.!!$R2 2176
6 TraesCS2B01G537200 chr2A 735244264 735245234 970 False 1098.0 1098 87.0120 1374 2389 1 chr2A.!!$F4 1015
7 TraesCS2B01G537200 chr6B 714303228 714304198 970 True 1441.0 1441 93.4430 2482 3454 1 chr6B.!!$R2 972
8 TraesCS2B01G537200 chr6B 101610672 101611641 969 True 597.0 597 77.9140 2482 3454 1 chr6B.!!$R1 972
9 TraesCS2B01G537200 chrUn 79545572 79546543 971 True 1430.0 1430 93.2380 2482 3454 1 chrUn.!!$R2 972
10 TraesCS2B01G537200 chr5A 614545918 614546861 943 True 479.0 544 85.2785 2482 3454 2 chr5A.!!$R2 972
11 TraesCS2B01G537200 chr2D 602648245 602649156 911 False 385.5 416 84.9475 1413 2398 2 chr2D.!!$F1 985
12 TraesCS2B01G537200 chr4A 607624179 607624782 603 False 398.0 398 78.6180 2452 3057 1 chr4A.!!$F1 605


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 0.401738 CCACCTCACCTTCACCATGT 59.598 55.0 0.0 0.0 0.0 3.21 F
209 210 0.478072 TCACCTTCACCATGTTGCCT 59.522 50.0 0.0 0.0 0.0 4.75 F
1520 1622 0.034896 ACGGGCTTGTCACGAAGATT 59.965 50.0 0.0 0.0 0.0 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1282 1327 0.301687 TCGTCGACTCCGCGTTATAC 59.698 55.000 14.70 0.0 36.92 1.47 R
2037 2265 0.817654 TGAGCTCACATACTGGACCG 59.182 55.000 13.74 0.0 0.00 4.79 R
2711 2941 4.033709 CAAGTCTCAAGGAGAGGGGAATA 58.966 47.826 0.00 0.0 44.81 1.75 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
78 79 8.497554 ACATTACAACAAAATCAATGAACATGC 58.502 29.630 0.00 0.00 32.29 4.06
79 80 8.496751 CATTACAACAAAATCAATGAACATGCA 58.503 29.630 0.00 0.00 0.00 3.96
80 81 8.604640 TTACAACAAAATCAATGAACATGCAT 57.395 26.923 0.00 0.00 0.00 3.96
81 82 7.124347 ACAACAAAATCAATGAACATGCATC 57.876 32.000 0.00 0.00 0.00 3.91
82 83 6.706716 ACAACAAAATCAATGAACATGCATCA 59.293 30.769 0.00 4.45 0.00 3.07
83 84 7.226918 ACAACAAAATCAATGAACATGCATCAA 59.773 29.630 0.00 0.00 0.00 2.57
84 85 7.915293 ACAAAATCAATGAACATGCATCAAT 57.085 28.000 0.00 0.00 0.00 2.57
85 86 8.330466 ACAAAATCAATGAACATGCATCAATT 57.670 26.923 0.00 0.00 0.00 2.32
86 87 8.233868 ACAAAATCAATGAACATGCATCAATTG 58.766 29.630 0.00 0.00 0.00 2.32
87 88 8.447053 CAAAATCAATGAACATGCATCAATTGA 58.553 29.630 11.26 11.26 33.31 2.57
88 89 8.554835 AAATCAATGAACATGCATCAATTGAA 57.445 26.923 13.09 0.00 32.93 2.69
89 90 7.770801 ATCAATGAACATGCATCAATTGAAG 57.229 32.000 13.09 9.46 32.93 3.02
90 91 5.579119 TCAATGAACATGCATCAATTGAAGC 59.421 36.000 24.90 24.90 39.04 3.86
96 97 3.581024 TGCATCAATTGAAGCAGGTTC 57.419 42.857 29.07 5.33 42.83 3.62
97 98 2.892215 TGCATCAATTGAAGCAGGTTCA 59.108 40.909 29.07 11.11 42.83 3.18
98 99 3.512329 TGCATCAATTGAAGCAGGTTCAT 59.488 39.130 29.07 0.00 44.89 2.57
99 100 4.020928 TGCATCAATTGAAGCAGGTTCATT 60.021 37.500 29.07 9.64 44.89 2.57
100 101 4.933400 GCATCAATTGAAGCAGGTTCATTT 59.067 37.500 26.25 14.78 44.89 2.32
106 107 5.787953 TTGAAGCAGGTTCATTTGATTGA 57.212 34.783 15.71 0.00 44.89 2.57
107 108 5.988310 TGAAGCAGGTTCATTTGATTGAT 57.012 34.783 11.11 0.00 40.45 2.57
108 109 7.465353 TTGAAGCAGGTTCATTTGATTGATA 57.535 32.000 15.71 0.00 44.89 2.15
109 110 7.649533 TGAAGCAGGTTCATTTGATTGATAT 57.350 32.000 11.11 0.00 40.45 1.63
110 111 8.070034 TGAAGCAGGTTCATTTGATTGATATT 57.930 30.769 11.11 0.00 40.45 1.28
111 112 9.187996 TGAAGCAGGTTCATTTGATTGATATTA 57.812 29.630 11.11 0.00 40.45 0.98
112 113 9.674824 GAAGCAGGTTCATTTGATTGATATTAG 57.325 33.333 7.51 0.00 34.97 1.73
113 114 8.757982 AGCAGGTTCATTTGATTGATATTAGT 57.242 30.769 0.00 0.00 0.00 2.24
114 115 9.851686 AGCAGGTTCATTTGATTGATATTAGTA 57.148 29.630 0.00 0.00 0.00 1.82
149 150 8.691661 GAAGTTATCTTCAGATAGTCTCCTCT 57.308 38.462 8.40 0.00 46.50 3.69
150 151 8.691661 AAGTTATCTTCAGATAGTCTCCTCTC 57.308 38.462 0.00 0.00 38.18 3.20
151 152 7.231467 AGTTATCTTCAGATAGTCTCCTCTCC 58.769 42.308 0.00 0.00 38.18 3.71
152 153 5.930209 ATCTTCAGATAGTCTCCTCTCCT 57.070 43.478 0.00 0.00 32.01 3.69
153 154 5.304686 TCTTCAGATAGTCTCCTCTCCTC 57.695 47.826 0.00 0.00 0.00 3.71
154 155 4.104102 TCTTCAGATAGTCTCCTCTCCTCC 59.896 50.000 0.00 0.00 0.00 4.30
155 156 3.398490 TCAGATAGTCTCCTCTCCTCCA 58.602 50.000 0.00 0.00 0.00 3.86
156 157 3.137544 TCAGATAGTCTCCTCTCCTCCAC 59.862 52.174 0.00 0.00 0.00 4.02
157 158 2.445525 AGATAGTCTCCTCTCCTCCACC 59.554 54.545 0.00 0.00 0.00 4.61
158 159 0.927767 TAGTCTCCTCTCCTCCACCC 59.072 60.000 0.00 0.00 0.00 4.61
159 160 0.853586 AGTCTCCTCTCCTCCACCCT 60.854 60.000 0.00 0.00 0.00 4.34
160 161 0.686112 GTCTCCTCTCCTCCACCCTG 60.686 65.000 0.00 0.00 0.00 4.45
161 162 0.851332 TCTCCTCTCCTCCACCCTGA 60.851 60.000 0.00 0.00 0.00 3.86
162 163 0.686112 CTCCTCTCCTCCACCCTGAC 60.686 65.000 0.00 0.00 0.00 3.51
163 164 1.687493 CCTCTCCTCCACCCTGACC 60.687 68.421 0.00 0.00 0.00 4.02
164 165 1.687493 CTCTCCTCCACCCTGACCC 60.687 68.421 0.00 0.00 0.00 4.46
165 166 2.689034 CTCCTCCACCCTGACCCC 60.689 72.222 0.00 0.00 0.00 4.95
166 167 4.715130 TCCTCCACCCTGACCCCG 62.715 72.222 0.00 0.00 0.00 5.73
169 170 4.585216 TCCACCCTGACCCCGGTT 62.585 66.667 0.00 0.00 0.00 4.44
170 171 4.344865 CCACCCTGACCCCGGTTG 62.345 72.222 0.00 0.00 0.00 3.77
171 172 4.344865 CACCCTGACCCCGGTTGG 62.345 72.222 0.00 0.00 0.00 3.77
174 175 4.410400 CCTGACCCCGGTTGGCTC 62.410 72.222 0.00 0.00 0.00 4.70
175 176 4.760047 CTGACCCCGGTTGGCTCG 62.760 72.222 0.00 0.00 0.00 5.03
196 197 4.643387 GCCGTGCCACCTCACCTT 62.643 66.667 0.00 0.00 33.57 3.50
197 198 2.358737 CCGTGCCACCTCACCTTC 60.359 66.667 0.00 0.00 33.57 3.46
198 199 2.425592 CGTGCCACCTCACCTTCA 59.574 61.111 0.00 0.00 33.57 3.02
199 200 1.961277 CGTGCCACCTCACCTTCAC 60.961 63.158 0.00 0.00 33.57 3.18
200 201 1.600916 GTGCCACCTCACCTTCACC 60.601 63.158 0.00 0.00 0.00 4.02
201 202 2.075566 TGCCACCTCACCTTCACCA 61.076 57.895 0.00 0.00 0.00 4.17
202 203 1.380302 GCCACCTCACCTTCACCAT 59.620 57.895 0.00 0.00 0.00 3.55
203 204 0.962356 GCCACCTCACCTTCACCATG 60.962 60.000 0.00 0.00 0.00 3.66
204 205 0.401738 CCACCTCACCTTCACCATGT 59.598 55.000 0.00 0.00 0.00 3.21
205 206 1.202927 CCACCTCACCTTCACCATGTT 60.203 52.381 0.00 0.00 0.00 2.71
206 207 1.881973 CACCTCACCTTCACCATGTTG 59.118 52.381 0.00 0.00 0.00 3.33
207 208 0.883833 CCTCACCTTCACCATGTTGC 59.116 55.000 0.00 0.00 0.00 4.17
208 209 0.883833 CTCACCTTCACCATGTTGCC 59.116 55.000 0.00 0.00 0.00 4.52
209 210 0.478072 TCACCTTCACCATGTTGCCT 59.522 50.000 0.00 0.00 0.00 4.75
210 211 1.133513 TCACCTTCACCATGTTGCCTT 60.134 47.619 0.00 0.00 0.00 4.35
211 212 1.000060 CACCTTCACCATGTTGCCTTG 60.000 52.381 0.00 0.00 0.00 3.61
212 213 1.133513 ACCTTCACCATGTTGCCTTGA 60.134 47.619 0.00 0.00 0.00 3.02
213 214 1.962807 CCTTCACCATGTTGCCTTGAA 59.037 47.619 0.00 0.00 0.00 2.69
214 215 2.364970 CCTTCACCATGTTGCCTTGAAA 59.635 45.455 0.00 0.00 0.00 2.69
215 216 3.383761 CTTCACCATGTTGCCTTGAAAC 58.616 45.455 0.00 0.00 0.00 2.78
216 217 1.686052 TCACCATGTTGCCTTGAAACC 59.314 47.619 0.00 0.00 0.00 3.27
217 218 1.047801 ACCATGTTGCCTTGAAACCC 58.952 50.000 0.00 0.00 0.00 4.11
218 219 1.047002 CCATGTTGCCTTGAAACCCA 58.953 50.000 0.00 0.00 0.00 4.51
219 220 1.270252 CCATGTTGCCTTGAAACCCAC 60.270 52.381 0.00 0.00 0.00 4.61
220 221 1.411977 CATGTTGCCTTGAAACCCACA 59.588 47.619 0.00 0.00 0.00 4.17
221 222 1.561643 TGTTGCCTTGAAACCCACAA 58.438 45.000 0.00 0.00 0.00 3.33
222 223 2.114616 TGTTGCCTTGAAACCCACAAT 58.885 42.857 0.00 0.00 0.00 2.71
223 224 2.503356 TGTTGCCTTGAAACCCACAATT 59.497 40.909 0.00 0.00 0.00 2.32
227 228 3.181467 TGCCTTGAAACCCACAATTTGAG 60.181 43.478 2.79 0.00 0.00 3.02
234 235 2.348472 ACCCACAATTTGAGGAGAGGA 58.652 47.619 13.71 0.00 28.90 3.71
237 238 2.356535 CCACAATTTGAGGAGAGGAGGG 60.357 54.545 7.03 0.00 28.90 4.30
264 265 1.154150 GCTTCAACGCTGATGGCAC 60.154 57.895 8.68 0.00 41.91 5.01
279 280 1.064803 TGGCACACGAAATGTTGTCAC 59.935 47.619 0.00 0.00 40.64 3.67
293 294 0.806868 TGTCACATCCGACGGACTAC 59.193 55.000 21.02 14.75 38.84 2.73
314 316 4.143333 CCCGATCCAGGTTCGCGT 62.143 66.667 13.72 0.00 35.31 6.01
375 377 6.590292 TGAGTTCGACAGATTTATCCTTTCAC 59.410 38.462 0.00 0.00 0.00 3.18
376 378 6.464222 AGTTCGACAGATTTATCCTTTCACA 58.536 36.000 0.00 0.00 0.00 3.58
401 403 9.702726 CACATTATATTACAAAAACTCTCCACG 57.297 33.333 0.00 0.00 0.00 4.94
427 429 5.486526 AGAAGACATCTCAACAACTCCATC 58.513 41.667 0.00 0.00 30.46 3.51
430 432 3.341823 ACATCTCAACAACTCCATCTGC 58.658 45.455 0.00 0.00 0.00 4.26
451 453 0.963962 CTGGCCTTGACAAACAGCAT 59.036 50.000 3.32 0.00 0.00 3.79
491 494 1.073199 GTGGCTTACTGGTGGTGCT 59.927 57.895 0.00 0.00 0.00 4.40
513 516 4.832248 TGATGAAGCTACTTTGATTCCGT 58.168 39.130 0.00 0.00 32.04 4.69
585 588 3.217626 GCACCCTGCTGCTATTAAGAAT 58.782 45.455 0.00 0.00 40.96 2.40
639 642 2.679996 AAAGCCCATTCCCACCGC 60.680 61.111 0.00 0.00 0.00 5.68
672 675 3.207669 GGCCTGCCAGCGATTCTG 61.208 66.667 2.58 0.00 42.49 3.02
673 676 2.437359 GCCTGCCAGCGATTCTGT 60.437 61.111 0.00 0.00 41.25 3.41
731 734 2.175202 AGCTTGTGTTGTGGGTTTTGA 58.825 42.857 0.00 0.00 0.00 2.69
736 739 4.873746 TGTGTTGTGGGTTTTGAAAAGA 57.126 36.364 0.00 0.00 0.00 2.52
746 749 7.094805 TGTGGGTTTTGAAAAGAGAATAGATCG 60.095 37.037 0.00 0.00 0.00 3.69
761 764 1.278127 AGATCGTGATTTGGGACCGTT 59.722 47.619 0.00 0.00 0.00 4.44
764 767 0.519961 CGTGATTTGGGACCGTTTCC 59.480 55.000 0.00 0.00 45.00 3.13
832 835 9.585099 TTGAATTATTTGGATTGCTTATCACAC 57.415 29.630 2.57 0.00 34.77 3.82
837 840 5.981088 TTGGATTGCTTATCACACATGTT 57.019 34.783 0.00 0.00 34.77 2.71
839 842 6.435430 TGGATTGCTTATCACACATGTTAC 57.565 37.500 0.00 0.00 34.77 2.50
840 843 5.942826 TGGATTGCTTATCACACATGTTACA 59.057 36.000 0.00 0.00 34.77 2.41
904 907 6.642707 TTTTGTTCACTCGGTTATTCCATT 57.357 33.333 0.00 0.00 35.57 3.16
915 918 5.067153 TCGGTTATTCCATTTAGCCAATGTG 59.933 40.000 5.69 0.00 40.87 3.21
961 964 6.429692 TGACAAACATCAACAAATCCTACGAT 59.570 34.615 0.00 0.00 0.00 3.73
962 965 7.604545 TGACAAACATCAACAAATCCTACGATA 59.395 33.333 0.00 0.00 0.00 2.92
963 966 8.330466 ACAAACATCAACAAATCCTACGATAA 57.670 30.769 0.00 0.00 0.00 1.75
1303 1359 1.364626 ATAACGCGGAGTCGACGACT 61.365 55.000 29.59 29.59 46.42 4.18
1349 1440 5.419155 ACGACCATGTATATATCCACCTCTG 59.581 44.000 0.00 0.00 0.00 3.35
1364 1455 1.756538 CCTCTGCTTGTTGTGGGTTTT 59.243 47.619 0.00 0.00 0.00 2.43
1370 1461 5.091261 TGCTTGTTGTGGGTTTTAATGTT 57.909 34.783 0.00 0.00 0.00 2.71
1371 1462 6.096987 TCTGCTTGTTGTGGGTTTTAATGTTA 59.903 34.615 0.00 0.00 0.00 2.41
1372 1463 6.640518 TGCTTGTTGTGGGTTTTAATGTTAA 58.359 32.000 0.00 0.00 0.00 2.01
1383 1474 7.102993 GGGTTTTAATGTTAATGTGGCTTGAT 58.897 34.615 0.00 0.00 0.00 2.57
1391 1482 5.106197 TGTTAATGTGGCTTGATTGCAGTAG 60.106 40.000 0.00 0.00 34.04 2.57
1394 1485 3.334691 TGTGGCTTGATTGCAGTAGTAC 58.665 45.455 0.00 0.00 34.04 2.73
1396 1487 4.221924 TGTGGCTTGATTGCAGTAGTACTA 59.778 41.667 1.57 0.00 34.04 1.82
1398 1489 5.817816 GTGGCTTGATTGCAGTAGTACTAAT 59.182 40.000 3.61 0.00 34.04 1.73
1399 1490 6.316390 GTGGCTTGATTGCAGTAGTACTAATT 59.684 38.462 3.61 0.00 34.04 1.40
1400 1491 7.494625 GTGGCTTGATTGCAGTAGTACTAATTA 59.505 37.037 3.61 0.00 34.04 1.40
1401 1492 8.044309 TGGCTTGATTGCAGTAGTACTAATTAA 58.956 33.333 3.61 1.94 34.04 1.40
1402 1493 8.336080 GGCTTGATTGCAGTAGTACTAATTAAC 58.664 37.037 3.61 0.00 34.04 2.01
1403 1494 8.056571 GCTTGATTGCAGTAGTACTAATTAACG 58.943 37.037 3.61 0.00 0.00 3.18
1404 1495 8.991243 TTGATTGCAGTAGTACTAATTAACGT 57.009 30.769 3.61 0.00 0.00 3.99
1438 1532 5.131784 GGTATACAGTGTAGCTAGTCTGGT 58.868 45.833 21.49 14.89 32.92 4.00
1508 1610 1.821216 CTTTGTATGTCCACGGGCTT 58.179 50.000 0.00 0.00 0.00 4.35
1520 1622 0.034896 ACGGGCTTGTCACGAAGATT 59.965 50.000 0.00 0.00 0.00 2.40
1525 1627 2.415512 GGCTTGTCACGAAGATTACCAC 59.584 50.000 0.00 0.00 0.00 4.16
1535 1637 4.825252 ATTACCACGGCGGCGGAC 62.825 66.667 35.05 0.00 39.03 4.79
1705 1813 1.589716 GCTTGCCAGAAATGGAGCGT 61.590 55.000 0.00 0.00 0.00 5.07
1787 1895 0.041238 TCGACTCCCACCTCATCCTT 59.959 55.000 0.00 0.00 0.00 3.36
1870 1990 1.810030 CCAGCGTTCTTCTACCGGC 60.810 63.158 0.00 0.00 0.00 6.13
1877 1997 4.077184 CTTCTACCGGCGGCACCA 62.077 66.667 28.71 7.97 39.03 4.17
1878 1998 4.382320 TTCTACCGGCGGCACCAC 62.382 66.667 28.71 0.00 39.03 4.16
1908 2028 1.890979 GCTGCATCTGCTATGGCGT 60.891 57.895 3.53 0.00 42.66 5.68
1950 2070 1.960763 CAGCTGCAGGTGCGTACAA 60.961 57.895 30.93 0.00 45.83 2.41
1967 2090 1.302832 AAACCCGCAGCCAGAAGAG 60.303 57.895 0.00 0.00 0.00 2.85
1973 2183 1.712977 CGCAGCCAGAAGAGCCATTC 61.713 60.000 0.00 0.00 0.00 2.67
2030 2258 5.894393 CCCATCGTCTTCCATATATAGGAGT 59.106 44.000 0.00 0.00 36.33 3.85
2037 2265 5.648526 TCTTCCATATATAGGAGTCTGCGAC 59.351 44.000 0.00 1.15 36.33 5.19
2068 2296 2.094390 TGTGAGCTCAACGTATGTACCC 60.094 50.000 20.19 1.49 0.00 3.69
2127 2355 1.237285 AACTTCGGCCATGTGCTCAC 61.237 55.000 2.24 0.00 40.92 3.51
2293 2521 2.351276 GACCACATCGTGCCCCTT 59.649 61.111 0.00 0.00 31.34 3.95
2610 2840 3.641906 GCTGCTTCCCTTATACCTACTCA 59.358 47.826 0.00 0.00 0.00 3.41
2620 2850 6.183361 CCCTTATACCTACTCAGTCCACTCTA 60.183 46.154 0.00 0.00 0.00 2.43
2711 2941 3.728373 GCCCACCCTTCCCGTGAT 61.728 66.667 0.00 0.00 32.77 3.06
2764 2994 3.882131 GCCACAGCTCTGGGAAATA 57.118 52.632 10.31 0.00 35.61 1.40
3368 3598 3.259374 TCAAATGGAGAAGAGCGAAGAGT 59.741 43.478 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 8.497554 GCATGTTCATTGATTTTGTTGTAATGT 58.502 29.630 0.00 0.00 32.22 2.71
53 54 8.496751 TGCATGTTCATTGATTTTGTTGTAATG 58.503 29.630 0.00 0.00 0.00 1.90
54 55 8.604640 TGCATGTTCATTGATTTTGTTGTAAT 57.395 26.923 0.00 0.00 0.00 1.89
55 56 8.604640 ATGCATGTTCATTGATTTTGTTGTAA 57.395 26.923 0.00 0.00 0.00 2.41
56 57 7.871463 TGATGCATGTTCATTGATTTTGTTGTA 59.129 29.630 2.46 0.00 0.00 2.41
57 58 6.706716 TGATGCATGTTCATTGATTTTGTTGT 59.293 30.769 2.46 0.00 0.00 3.32
58 59 7.123160 TGATGCATGTTCATTGATTTTGTTG 57.877 32.000 2.46 0.00 0.00 3.33
59 60 7.731882 TTGATGCATGTTCATTGATTTTGTT 57.268 28.000 2.46 0.00 0.00 2.83
60 61 7.915293 ATTGATGCATGTTCATTGATTTTGT 57.085 28.000 2.46 0.00 0.00 2.83
61 62 8.447053 TCAATTGATGCATGTTCATTGATTTTG 58.553 29.630 2.46 0.00 0.00 2.44
62 63 8.554835 TCAATTGATGCATGTTCATTGATTTT 57.445 26.923 2.46 0.00 0.00 1.82
63 64 8.554835 TTCAATTGATGCATGTTCATTGATTT 57.445 26.923 9.40 0.00 0.00 2.17
64 65 7.201609 GCTTCAATTGATGCATGTTCATTGATT 60.202 33.333 30.88 0.00 42.61 2.57
65 66 6.257849 GCTTCAATTGATGCATGTTCATTGAT 59.742 34.615 30.88 0.00 42.61 2.57
66 67 5.579119 GCTTCAATTGATGCATGTTCATTGA 59.421 36.000 30.88 9.37 42.61 2.57
67 68 5.350091 TGCTTCAATTGATGCATGTTCATTG 59.650 36.000 33.30 7.12 46.06 2.82
68 69 5.483811 TGCTTCAATTGATGCATGTTCATT 58.516 33.333 33.30 0.00 46.06 2.57
69 70 5.079689 TGCTTCAATTGATGCATGTTCAT 57.920 34.783 33.30 0.00 46.06 2.57
70 71 4.522722 TGCTTCAATTGATGCATGTTCA 57.477 36.364 33.30 17.43 46.06 3.18
75 76 8.746927 CAAATGAACCTGCTTCAATTGATGCAT 61.747 37.037 35.40 26.15 46.51 3.96
76 77 7.506768 CAAATGAACCTGCTTCAATTGATGCA 61.507 38.462 33.94 33.94 46.51 3.96
77 78 3.581024 TGAACCTGCTTCAATTGATGC 57.419 42.857 29.80 29.80 43.15 3.91
78 79 6.160684 TCAAATGAACCTGCTTCAATTGATG 58.839 36.000 9.40 12.82 46.82 3.07
79 80 6.349243 TCAAATGAACCTGCTTCAATTGAT 57.651 33.333 9.40 0.00 46.82 2.57
81 82 6.647481 TCAATCAAATGAACCTGCTTCAATTG 59.353 34.615 0.00 0.00 45.58 2.32
82 83 6.761312 TCAATCAAATGAACCTGCTTCAATT 58.239 32.000 0.00 0.00 42.37 2.32
83 84 6.349243 TCAATCAAATGAACCTGCTTCAAT 57.651 33.333 0.00 0.00 42.37 2.57
84 85 5.787953 TCAATCAAATGAACCTGCTTCAA 57.212 34.783 0.00 0.00 42.37 2.69
85 86 5.988310 ATCAATCAAATGAACCTGCTTCA 57.012 34.783 0.00 0.00 43.28 3.02
86 87 9.674824 CTAATATCAATCAAATGAACCTGCTTC 57.325 33.333 0.00 0.00 32.06 3.86
87 88 9.193806 ACTAATATCAATCAAATGAACCTGCTT 57.806 29.630 0.00 0.00 32.06 3.91
88 89 8.757982 ACTAATATCAATCAAATGAACCTGCT 57.242 30.769 0.00 0.00 32.06 4.24
121 122 7.444183 AGGAGACTATCTGAAGATAACTTCGAG 59.556 40.741 8.08 6.95 46.79 4.04
122 123 7.284074 AGGAGACTATCTGAAGATAACTTCGA 58.716 38.462 8.08 8.46 46.79 3.71
123 124 7.504924 AGGAGACTATCTGAAGATAACTTCG 57.495 40.000 8.08 3.90 46.79 3.79
124 125 8.691661 AGAGGAGACTATCTGAAGATAACTTC 57.308 38.462 5.82 5.82 46.28 3.01
125 126 8.691661 GAGAGGAGACTATCTGAAGATAACTT 57.308 38.462 1.87 0.00 45.28 2.66
138 139 1.501604 GGGTGGAGGAGAGGAGACTAT 59.498 57.143 0.00 0.00 44.43 2.12
139 140 0.927767 GGGTGGAGGAGAGGAGACTA 59.072 60.000 0.00 0.00 44.43 2.59
141 142 0.686112 CAGGGTGGAGGAGAGGAGAC 60.686 65.000 0.00 0.00 0.00 3.36
142 143 0.851332 TCAGGGTGGAGGAGAGGAGA 60.851 60.000 0.00 0.00 0.00 3.71
143 144 0.686112 GTCAGGGTGGAGGAGAGGAG 60.686 65.000 0.00 0.00 0.00 3.69
144 145 1.388531 GTCAGGGTGGAGGAGAGGA 59.611 63.158 0.00 0.00 0.00 3.71
145 146 1.687493 GGTCAGGGTGGAGGAGAGG 60.687 68.421 0.00 0.00 0.00 3.69
146 147 1.687493 GGGTCAGGGTGGAGGAGAG 60.687 68.421 0.00 0.00 0.00 3.20
147 148 2.450243 GGGTCAGGGTGGAGGAGA 59.550 66.667 0.00 0.00 0.00 3.71
148 149 2.689034 GGGGTCAGGGTGGAGGAG 60.689 72.222 0.00 0.00 0.00 3.69
149 150 4.715130 CGGGGTCAGGGTGGAGGA 62.715 72.222 0.00 0.00 0.00 3.71
152 153 4.585216 AACCGGGGTCAGGGTGGA 62.585 66.667 6.32 0.00 36.45 4.02
153 154 4.344865 CAACCGGGGTCAGGGTGG 62.345 72.222 6.32 0.00 42.56 4.61
154 155 4.344865 CCAACCGGGGTCAGGGTG 62.345 72.222 6.32 0.00 45.73 4.61
179 180 4.643387 AAGGTGAGGTGGCACGGC 62.643 66.667 12.17 6.48 39.66 5.68
180 181 2.358737 GAAGGTGAGGTGGCACGG 60.359 66.667 12.17 0.00 39.66 4.94
181 182 1.961277 GTGAAGGTGAGGTGGCACG 60.961 63.158 12.17 0.00 39.66 5.34
182 183 1.600916 GGTGAAGGTGAGGTGGCAC 60.601 63.158 9.70 9.70 38.05 5.01
183 184 1.426251 ATGGTGAAGGTGAGGTGGCA 61.426 55.000 0.00 0.00 0.00 4.92
184 185 0.962356 CATGGTGAAGGTGAGGTGGC 60.962 60.000 0.00 0.00 0.00 5.01
185 186 0.401738 ACATGGTGAAGGTGAGGTGG 59.598 55.000 0.00 0.00 0.00 4.61
186 187 1.881973 CAACATGGTGAAGGTGAGGTG 59.118 52.381 4.15 0.00 0.00 4.00
187 188 1.819305 GCAACATGGTGAAGGTGAGGT 60.819 52.381 16.85 0.00 0.00 3.85
188 189 0.883833 GCAACATGGTGAAGGTGAGG 59.116 55.000 16.85 0.00 0.00 3.86
189 190 0.883833 GGCAACATGGTGAAGGTGAG 59.116 55.000 16.85 0.00 0.00 3.51
190 191 0.478072 AGGCAACATGGTGAAGGTGA 59.522 50.000 16.85 0.00 41.41 4.02
191 192 1.000060 CAAGGCAACATGGTGAAGGTG 60.000 52.381 16.85 2.22 41.41 4.00
192 193 1.133513 TCAAGGCAACATGGTGAAGGT 60.134 47.619 16.85 0.00 35.55 3.50
193 194 1.619654 TCAAGGCAACATGGTGAAGG 58.380 50.000 16.85 0.00 35.55 3.46
194 195 3.383761 GTTTCAAGGCAACATGGTGAAG 58.616 45.455 16.85 0.02 35.55 3.02
195 196 2.102252 GGTTTCAAGGCAACATGGTGAA 59.898 45.455 16.85 0.00 35.55 3.18
196 197 1.686052 GGTTTCAAGGCAACATGGTGA 59.314 47.619 16.85 0.00 35.55 4.02
197 198 1.270252 GGGTTTCAAGGCAACATGGTG 60.270 52.381 6.32 6.32 35.55 4.17
198 199 1.047801 GGGTTTCAAGGCAACATGGT 58.952 50.000 0.00 0.00 35.55 3.55
199 200 1.047002 TGGGTTTCAAGGCAACATGG 58.953 50.000 0.00 0.00 35.55 3.66
200 201 1.411977 TGTGGGTTTCAAGGCAACATG 59.588 47.619 0.00 0.00 41.41 3.21
201 202 1.786937 TGTGGGTTTCAAGGCAACAT 58.213 45.000 0.00 0.00 41.41 2.71
202 203 1.561643 TTGTGGGTTTCAAGGCAACA 58.438 45.000 0.00 0.00 41.41 3.33
203 204 2.908688 ATTGTGGGTTTCAAGGCAAC 57.091 45.000 0.00 0.00 0.00 4.17
204 205 3.198635 TCAAATTGTGGGTTTCAAGGCAA 59.801 39.130 0.00 0.00 0.00 4.52
205 206 2.768527 TCAAATTGTGGGTTTCAAGGCA 59.231 40.909 0.00 0.00 0.00 4.75
206 207 3.392882 CTCAAATTGTGGGTTTCAAGGC 58.607 45.455 0.00 0.00 0.00 4.35
207 208 3.640967 TCCTCAAATTGTGGGTTTCAAGG 59.359 43.478 13.36 0.35 32.20 3.61
208 209 4.584325 TCTCCTCAAATTGTGGGTTTCAAG 59.416 41.667 13.36 3.64 32.20 3.02
209 210 4.541705 TCTCCTCAAATTGTGGGTTTCAA 58.458 39.130 13.36 0.00 32.20 2.69
210 211 4.144297 CTCTCCTCAAATTGTGGGTTTCA 58.856 43.478 13.36 0.00 32.20 2.69
211 212 3.507622 CCTCTCCTCAAATTGTGGGTTTC 59.492 47.826 13.36 0.00 32.20 2.78
212 213 3.140144 TCCTCTCCTCAAATTGTGGGTTT 59.860 43.478 13.36 0.00 32.20 3.27
213 214 2.716424 TCCTCTCCTCAAATTGTGGGTT 59.284 45.455 13.36 0.00 32.20 4.11
214 215 2.307098 CTCCTCTCCTCAAATTGTGGGT 59.693 50.000 13.36 0.00 32.20 4.51
215 216 2.356535 CCTCCTCTCCTCAAATTGTGGG 60.357 54.545 13.36 7.63 32.20 4.61
216 217 2.356535 CCCTCCTCTCCTCAAATTGTGG 60.357 54.545 7.71 7.71 32.56 4.17
217 218 2.356535 CCCCTCCTCTCCTCAAATTGTG 60.357 54.545 0.00 0.00 0.00 3.33
218 219 1.918957 CCCCTCCTCTCCTCAAATTGT 59.081 52.381 0.00 0.00 0.00 2.71
219 220 1.213926 CCCCCTCCTCTCCTCAAATTG 59.786 57.143 0.00 0.00 0.00 2.32
220 221 1.601248 CCCCCTCCTCTCCTCAAATT 58.399 55.000 0.00 0.00 0.00 1.82
221 222 3.348938 CCCCCTCCTCTCCTCAAAT 57.651 57.895 0.00 0.00 0.00 2.32
222 223 4.919770 CCCCCTCCTCTCCTCAAA 57.080 61.111 0.00 0.00 0.00 2.69
242 243 2.044946 ATCAGCGTTGAAGCCCCC 60.045 61.111 5.91 0.00 36.78 5.40
256 257 1.952990 ACAACATTTCGTGTGCCATCA 59.047 42.857 0.00 0.00 41.14 3.07
274 275 0.806868 GTAGTCCGTCGGATGTGACA 59.193 55.000 18.75 0.00 38.84 3.58
275 276 0.100146 GGTAGTCCGTCGGATGTGAC 59.900 60.000 18.75 12.44 32.73 3.67
279 280 2.496291 GGGGGTAGTCCGTCGGATG 61.496 68.421 18.75 0.00 32.73 3.51
375 377 9.702726 CGTGGAGAGTTTTTGTAATATAATGTG 57.297 33.333 0.00 0.00 0.00 3.21
376 378 9.661563 TCGTGGAGAGTTTTTGTAATATAATGT 57.338 29.630 0.00 0.00 0.00 2.71
415 417 1.538512 CCAGTGCAGATGGAGTTGTTG 59.461 52.381 11.75 0.00 40.51 3.33
427 429 0.031178 GTTTGTCAAGGCCAGTGCAG 59.969 55.000 5.01 0.00 40.13 4.41
430 432 0.031178 GCTGTTTGTCAAGGCCAGTG 59.969 55.000 5.01 2.04 0.00 3.66
491 494 4.832248 ACGGAATCAAAGTAGCTTCATCA 58.168 39.130 0.00 0.00 0.00 3.07
511 514 0.171231 TCGCATCTCAGTCCTCAACG 59.829 55.000 0.00 0.00 0.00 4.10
513 516 2.102578 TCATCGCATCTCAGTCCTCAA 58.897 47.619 0.00 0.00 0.00 3.02
551 554 4.021925 GGTGCCTTCCGTGCCTCT 62.022 66.667 0.00 0.00 0.00 3.69
560 563 0.394899 AATAGCAGCAGGGTGCCTTC 60.395 55.000 18.77 0.00 46.52 3.46
585 588 7.402071 ACTCACCTGTCTATTTTCCCATACTTA 59.598 37.037 0.00 0.00 0.00 2.24
605 608 2.937149 GCTTTCCTTTCGGATACTCACC 59.063 50.000 0.00 0.00 39.58 4.02
642 645 3.736224 AGGCCAGCTGGTCCATGG 61.736 66.667 33.78 4.97 41.83 3.66
720 723 7.094805 CGATCTATTCTCTTTTCAAAACCCACA 60.095 37.037 0.00 0.00 0.00 4.17
721 724 7.094762 ACGATCTATTCTCTTTTCAAAACCCAC 60.095 37.037 0.00 0.00 0.00 4.61
731 734 7.281100 GTCCCAAATCACGATCTATTCTCTTTT 59.719 37.037 0.00 0.00 0.00 2.27
736 739 4.501571 CGGTCCCAAATCACGATCTATTCT 60.502 45.833 0.00 0.00 0.00 2.40
761 764 9.720769 CTTAGTTAAGAAGGTTCATGTAAGGAA 57.279 33.333 0.00 0.00 35.33 3.36
813 816 6.534475 ACATGTGTGATAAGCAATCCAAAT 57.466 33.333 0.00 0.00 33.22 2.32
827 830 8.678593 TTAGTTAAACCATGTAACATGTGTGA 57.321 30.769 0.00 0.00 34.50 3.58
1282 1327 0.301687 TCGTCGACTCCGCGTTATAC 59.698 55.000 14.70 0.00 36.92 1.47
1349 1440 7.225734 ACATTAACATTAAAACCCACAACAAGC 59.774 33.333 0.00 0.00 0.00 4.01
1364 1455 6.071447 ACTGCAATCAAGCCACATTAACATTA 60.071 34.615 0.00 0.00 0.00 1.90
1370 1461 4.588899 ACTACTGCAATCAAGCCACATTA 58.411 39.130 0.00 0.00 0.00 1.90
1371 1462 3.424703 ACTACTGCAATCAAGCCACATT 58.575 40.909 0.00 0.00 0.00 2.71
1372 1463 3.077484 ACTACTGCAATCAAGCCACAT 57.923 42.857 0.00 0.00 0.00 3.21
1383 1474 7.062605 GCAAGACGTTAATTAGTACTACTGCAA 59.937 37.037 0.91 0.00 0.00 4.08
1391 1482 7.543520 ACCAACTAGCAAGACGTTAATTAGTAC 59.456 37.037 0.00 0.00 0.00 2.73
1394 1485 6.963049 ACCAACTAGCAAGACGTTAATTAG 57.037 37.500 0.00 0.00 0.00 1.73
1396 1487 8.036575 TGTATACCAACTAGCAAGACGTTAATT 58.963 33.333 0.00 0.00 0.00 1.40
1398 1489 6.923012 TGTATACCAACTAGCAAGACGTTAA 58.077 36.000 0.00 0.00 0.00 2.01
1399 1490 6.151648 ACTGTATACCAACTAGCAAGACGTTA 59.848 38.462 0.00 0.00 0.00 3.18
1400 1491 5.047519 ACTGTATACCAACTAGCAAGACGTT 60.048 40.000 0.00 0.00 0.00 3.99
1401 1492 4.461781 ACTGTATACCAACTAGCAAGACGT 59.538 41.667 0.00 0.00 0.00 4.34
1402 1493 4.798907 CACTGTATACCAACTAGCAAGACG 59.201 45.833 0.00 0.00 0.00 4.18
1403 1494 5.721232 ACACTGTATACCAACTAGCAAGAC 58.279 41.667 0.00 0.00 0.00 3.01
1404 1495 5.995565 ACACTGTATACCAACTAGCAAGA 57.004 39.130 0.00 0.00 0.00 3.02
1496 1598 2.110213 GTGACAAGCCCGTGGACA 59.890 61.111 0.00 0.00 0.00 4.02
1508 1610 1.670674 GCCGTGGTAATCTTCGTGACA 60.671 52.381 0.00 0.00 0.00 3.58
1685 1793 1.588824 CGCTCCATTTCTGGCAAGCA 61.589 55.000 5.98 0.00 40.69 3.91
1705 1813 0.947180 GTACAAGAACTTCCGGCGCA 60.947 55.000 10.83 0.00 0.00 6.09
1787 1895 0.913934 TGTGGCTGAGCAAGGGGATA 60.914 55.000 6.82 0.00 0.00 2.59
1836 1944 1.202545 GCTGGTAGGATTCGGAGGAAC 60.203 57.143 0.00 0.00 34.37 3.62
1870 1990 2.650196 CCATTGTTGGTGGTGCCG 59.350 61.111 0.00 0.00 41.21 5.69
1879 1999 3.495127 GCAGATGCAGCAACCATTGTTG 61.495 50.000 4.07 5.31 46.34 3.33
1950 2070 2.348998 CTCTTCTGGCTGCGGGTT 59.651 61.111 0.00 0.00 0.00 4.11
1967 2090 4.525912 AAACCAACAAGATGAGAATGGC 57.474 40.909 0.00 0.00 0.00 4.40
1973 2183 3.054878 GCTGCAAAACCAACAAGATGAG 58.945 45.455 0.00 0.00 0.00 2.90
2030 2258 0.963856 ACATACTGGACCGTCGCAGA 60.964 55.000 18.43 7.40 0.00 4.26
2037 2265 0.817654 TGAGCTCACATACTGGACCG 59.182 55.000 13.74 0.00 0.00 4.79
2175 2403 2.203788 TCTTGACGGCCACCTCCT 60.204 61.111 2.24 0.00 0.00 3.69
2185 2413 2.670414 GTGATTCTTCAGGCTCTTGACG 59.330 50.000 0.00 0.00 30.85 4.35
2258 2486 2.982130 GTGACGGAGGTGGCAGAT 59.018 61.111 0.00 0.00 0.00 2.90
2401 2629 5.568685 ATCCATCTTAGGATCGTATCACG 57.431 43.478 0.00 0.00 45.16 4.35
2711 2941 4.033709 CAAGTCTCAAGGAGAGGGGAATA 58.966 47.826 0.00 0.00 44.81 1.75
2764 2994 4.725810 AGATGAAGTCCCTCTGAAATCCAT 59.274 41.667 0.00 0.00 0.00 3.41



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

AutoCloner maintained by Alex Coulton.