Multiple sequence alignment - TraesCS4B01G153800

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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 TraesCS4B01G153800 chr4B 100.000 3041 0 0 1 3041 267668696 267671736 0.000000e+00 5616
1 TraesCS4B01G153800 chr4B 73.182 660 156 19 1370 2016 407808085 407807434 5.100000e-53 219
2 TraesCS4B01G153800 chr4D 94.529 2687 137 8 361 3041 246518879 246516197 0.000000e+00 4139
3 TraesCS4B01G153800 chr4D 73.979 661 149 21 1370 2016 328185283 328184632 2.340000e-61 246
4 TraesCS4B01G153800 chr4A 92.447 2701 170 23 361 3041 239579779 239577093 0.000000e+00 3827
5 TraesCS4B01G153800 chr4A 73.828 661 150 20 1370 2016 142344807 142345458 1.090000e-59 241
6 TraesCS4B01G153800 chr2B 81.308 856 125 17 1184 2011 135775629 135776477 0.000000e+00 662
7 TraesCS4B01G153800 chr2A 80.980 857 126 25 1184 2011 84646376 84647224 0.000000e+00 645
8 TraesCS4B01G153800 chr2A 75.887 282 59 6 2579 2853 564622038 564622317 5.290000e-28 135
9 TraesCS4B01G153800 chr2D 80.724 856 130 24 1184 2011 83859541 83860389 4.280000e-178 634
10 TraesCS4B01G153800 chr5B 84.110 472 59 9 2577 3041 109226480 109226942 2.780000e-120 442
11 TraesCS4B01G153800 chr3D 83.726 467 65 4 2579 3041 615235260 615234801 6.020000e-117 431
12 TraesCS4B01G153800 chr7D 78.509 456 91 4 2580 3030 175768955 175769408 2.970000e-75 292
13 TraesCS4B01G153800 chr7D 77.481 262 47 8 2579 2835 549510306 549510560 2.440000e-31 147
14 TraesCS4B01G153800 chr5D 77.681 457 95 4 2580 3031 416792359 416792813 3.860000e-69 272
15 TraesCS4B01G153800 chr3B 78.756 193 38 3 2579 2770 126926479 126926669 3.180000e-25 126


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 TraesCS4B01G153800 chr4B 267668696 267671736 3040 False 5616 5616 100.000 1 3041 1 chr4B.!!$F1 3040
1 TraesCS4B01G153800 chr4B 407807434 407808085 651 True 219 219 73.182 1370 2016 1 chr4B.!!$R1 646
2 TraesCS4B01G153800 chr4D 246516197 246518879 2682 True 4139 4139 94.529 361 3041 1 chr4D.!!$R1 2680
3 TraesCS4B01G153800 chr4D 328184632 328185283 651 True 246 246 73.979 1370 2016 1 chr4D.!!$R2 646
4 TraesCS4B01G153800 chr4A 239577093 239579779 2686 True 3827 3827 92.447 361 3041 1 chr4A.!!$R1 2680
5 TraesCS4B01G153800 chr4A 142344807 142345458 651 False 241 241 73.828 1370 2016 1 chr4A.!!$F1 646
6 TraesCS4B01G153800 chr2B 135775629 135776477 848 False 662 662 81.308 1184 2011 1 chr2B.!!$F1 827
7 TraesCS4B01G153800 chr2A 84646376 84647224 848 False 645 645 80.980 1184 2011 1 chr2A.!!$F1 827
8 TraesCS4B01G153800 chr2D 83859541 83860389 848 False 634 634 80.724 1184 2011 1 chr2D.!!$F1 827

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
470 472 0.033503 TCAGGCCGTCTCATAGACCA 60.034 55.0 0.0 0.0 42.12 4.02 F
1221 1235 0.322816 TGGACGCTAACTACCTCCGT 60.323 55.0 0.0 0.0 34.52 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1476 1490 1.142314 GTAGATAACCCGGCGCACA 59.858 57.895 10.83 0.0 0.00 4.57 R
2744 2791 0.100146 GAGGTGATCGGTGTACGTCC 59.900 60.000 0.00 0.0 44.69 4.79 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
54 55 3.998672 GGGTCGGCGGACACAGAA 61.999 66.667 23.82 0.00 46.22 3.02
55 56 2.432628 GGTCGGCGGACACAGAAG 60.433 66.667 23.82 0.00 45.28 2.85
56 57 2.432628 GTCGGCGGACACAGAAGG 60.433 66.667 18.61 0.00 42.91 3.46
57 58 2.599281 TCGGCGGACACAGAAGGA 60.599 61.111 7.21 0.00 0.00 3.36
58 59 2.125912 CGGCGGACACAGAAGGAG 60.126 66.667 0.00 0.00 0.00 3.69
59 60 2.636412 CGGCGGACACAGAAGGAGA 61.636 63.158 0.00 0.00 0.00 3.71
60 61 1.216710 GGCGGACACAGAAGGAGAG 59.783 63.158 0.00 0.00 0.00 3.20
61 62 1.216710 GCGGACACAGAAGGAGAGG 59.783 63.158 0.00 0.00 0.00 3.69
62 63 1.251527 GCGGACACAGAAGGAGAGGA 61.252 60.000 0.00 0.00 0.00 3.71
63 64 0.814457 CGGACACAGAAGGAGAGGAG 59.186 60.000 0.00 0.00 0.00 3.69
64 65 1.190643 GGACACAGAAGGAGAGGAGG 58.809 60.000 0.00 0.00 0.00 4.30
65 66 1.272760 GGACACAGAAGGAGAGGAGGA 60.273 57.143 0.00 0.00 0.00 3.71
66 67 2.099405 GACACAGAAGGAGAGGAGGAG 58.901 57.143 0.00 0.00 0.00 3.69
67 68 0.823460 CACAGAAGGAGAGGAGGAGC 59.177 60.000 0.00 0.00 0.00 4.70
68 69 0.682855 ACAGAAGGAGAGGAGGAGCG 60.683 60.000 0.00 0.00 0.00 5.03
69 70 1.756561 AGAAGGAGAGGAGGAGCGC 60.757 63.158 0.00 0.00 0.00 5.92
70 71 3.132481 GAAGGAGAGGAGGAGCGCG 62.132 68.421 0.00 0.00 0.00 6.86
91 92 3.018973 GCTCAACGCCGTTGACAA 58.981 55.556 27.27 9.04 45.88 3.18
92 93 1.082756 GCTCAACGCCGTTGACAAG 60.083 57.895 27.27 18.90 45.88 3.16
93 94 1.569493 CTCAACGCCGTTGACAAGG 59.431 57.895 27.27 14.68 45.88 3.61
94 95 0.878523 CTCAACGCCGTTGACAAGGA 60.879 55.000 27.27 7.56 45.88 3.36
95 96 0.878523 TCAACGCCGTTGACAAGGAG 60.879 55.000 27.27 0.78 45.88 3.69
96 97 0.878523 CAACGCCGTTGACAAGGAGA 60.879 55.000 24.84 0.00 45.28 3.71
97 98 0.600255 AACGCCGTTGACAAGGAGAG 60.600 55.000 0.00 4.47 0.00 3.20
98 99 1.738099 CGCCGTTGACAAGGAGAGG 60.738 63.158 9.42 0.19 0.00 3.69
99 100 1.376037 GCCGTTGACAAGGAGAGGG 60.376 63.158 9.42 0.00 0.00 4.30
100 101 1.827399 GCCGTTGACAAGGAGAGGGA 61.827 60.000 9.42 0.00 0.00 4.20
101 102 0.037232 CCGTTGACAAGGAGAGGGAC 60.037 60.000 9.42 0.00 0.00 4.46
102 103 0.388649 CGTTGACAAGGAGAGGGACG 60.389 60.000 1.55 0.00 0.00 4.79
103 104 0.037232 GTTGACAAGGAGAGGGACGG 60.037 60.000 0.00 0.00 0.00 4.79
104 105 1.827399 TTGACAAGGAGAGGGACGGC 61.827 60.000 0.00 0.00 0.00 5.68
105 106 3.358076 GACAAGGAGAGGGACGGCG 62.358 68.421 4.80 4.80 0.00 6.46
106 107 3.068691 CAAGGAGAGGGACGGCGA 61.069 66.667 16.62 0.00 0.00 5.54
107 108 2.756283 AAGGAGAGGGACGGCGAG 60.756 66.667 16.62 0.00 0.00 5.03
108 109 4.824515 AGGAGAGGGACGGCGAGG 62.825 72.222 16.62 0.00 0.00 4.63
126 127 4.820744 CTCGTGGGGGCCATTGGG 62.821 72.222 4.39 0.00 35.28 4.12
134 135 4.315264 GGCCATTGGGGTGGTGGT 62.315 66.667 4.53 0.00 41.47 4.16
135 136 2.679996 GCCATTGGGGTGGTGGTC 60.680 66.667 4.53 0.00 41.47 4.02
136 137 2.361104 CCATTGGGGTGGTGGTCG 60.361 66.667 0.00 0.00 34.46 4.79
137 138 2.361104 CATTGGGGTGGTGGTCGG 60.361 66.667 0.00 0.00 0.00 4.79
138 139 4.360405 ATTGGGGTGGTGGTCGGC 62.360 66.667 0.00 0.00 0.00 5.54
161 162 4.847585 CGAGACGAGGCGACGACG 62.848 72.222 13.15 9.14 42.93 5.12
162 163 4.517703 GAGACGAGGCGACGACGG 62.518 72.222 14.43 0.00 40.15 4.79
200 201 3.379445 GACAGCGACGGAGGGGAA 61.379 66.667 0.00 0.00 0.00 3.97
201 202 3.358076 GACAGCGACGGAGGGGAAG 62.358 68.421 0.00 0.00 0.00 3.46
202 203 4.148825 CAGCGACGGAGGGGAAGG 62.149 72.222 0.00 0.00 0.00 3.46
203 204 4.377760 AGCGACGGAGGGGAAGGA 62.378 66.667 0.00 0.00 0.00 3.36
204 205 3.387947 GCGACGGAGGGGAAGGAA 61.388 66.667 0.00 0.00 0.00 3.36
205 206 2.893398 CGACGGAGGGGAAGGAAG 59.107 66.667 0.00 0.00 0.00 3.46
206 207 2.722201 CGACGGAGGGGAAGGAAGG 61.722 68.421 0.00 0.00 0.00 3.46
207 208 2.285442 ACGGAGGGGAAGGAAGGG 60.285 66.667 0.00 0.00 0.00 3.95
208 209 3.090532 CGGAGGGGAAGGAAGGGG 61.091 72.222 0.00 0.00 0.00 4.79
209 210 2.696504 GGAGGGGAAGGAAGGGGG 60.697 72.222 0.00 0.00 0.00 5.40
210 211 3.421386 GAGGGGAAGGAAGGGGGC 61.421 72.222 0.00 0.00 0.00 5.80
228 229 4.699522 GCGCGAGGGAAAGGTGGT 62.700 66.667 12.10 0.00 0.00 4.16
229 230 2.975536 CGCGAGGGAAAGGTGGTA 59.024 61.111 0.00 0.00 0.00 3.25
230 231 1.153628 CGCGAGGGAAAGGTGGTAG 60.154 63.158 0.00 0.00 0.00 3.18
231 232 1.221021 GCGAGGGAAAGGTGGTAGG 59.779 63.158 0.00 0.00 0.00 3.18
232 233 1.905512 CGAGGGAAAGGTGGTAGGG 59.094 63.158 0.00 0.00 0.00 3.53
233 234 0.908180 CGAGGGAAAGGTGGTAGGGT 60.908 60.000 0.00 0.00 0.00 4.34
234 235 1.369403 GAGGGAAAGGTGGTAGGGTT 58.631 55.000 0.00 0.00 0.00 4.11
235 236 2.554563 GAGGGAAAGGTGGTAGGGTTA 58.445 52.381 0.00 0.00 0.00 2.85
236 237 2.914941 GAGGGAAAGGTGGTAGGGTTAA 59.085 50.000 0.00 0.00 0.00 2.01
237 238 3.526430 GAGGGAAAGGTGGTAGGGTTAAT 59.474 47.826 0.00 0.00 0.00 1.40
238 239 3.927322 AGGGAAAGGTGGTAGGGTTAATT 59.073 43.478 0.00 0.00 0.00 1.40
239 240 5.110206 AGGGAAAGGTGGTAGGGTTAATTA 58.890 41.667 0.00 0.00 0.00 1.40
240 241 5.193124 AGGGAAAGGTGGTAGGGTTAATTAG 59.807 44.000 0.00 0.00 0.00 1.73
241 242 5.443283 GGAAAGGTGGTAGGGTTAATTAGG 58.557 45.833 0.00 0.00 0.00 2.69
242 243 5.044624 GGAAAGGTGGTAGGGTTAATTAGGT 60.045 44.000 0.00 0.00 0.00 3.08
243 244 5.446260 AAGGTGGTAGGGTTAATTAGGTG 57.554 43.478 0.00 0.00 0.00 4.00
244 245 3.784202 AGGTGGTAGGGTTAATTAGGTGG 59.216 47.826 0.00 0.00 0.00 4.61
245 246 3.548770 GTGGTAGGGTTAATTAGGTGGC 58.451 50.000 0.00 0.00 0.00 5.01
246 247 2.171027 TGGTAGGGTTAATTAGGTGGCG 59.829 50.000 0.00 0.00 0.00 5.69
247 248 2.486013 GGTAGGGTTAATTAGGTGGCGG 60.486 54.545 0.00 0.00 0.00 6.13
248 249 1.292085 AGGGTTAATTAGGTGGCGGT 58.708 50.000 0.00 0.00 0.00 5.68
249 250 1.064979 AGGGTTAATTAGGTGGCGGTG 60.065 52.381 0.00 0.00 0.00 4.94
250 251 1.385528 GGTTAATTAGGTGGCGGTGG 58.614 55.000 0.00 0.00 0.00 4.61
251 252 1.385528 GTTAATTAGGTGGCGGTGGG 58.614 55.000 0.00 0.00 0.00 4.61
252 253 0.993470 TTAATTAGGTGGCGGTGGGT 59.007 50.000 0.00 0.00 0.00 4.51
253 254 0.542805 TAATTAGGTGGCGGTGGGTC 59.457 55.000 0.00 0.00 0.00 4.46
254 255 2.530958 AATTAGGTGGCGGTGGGTCG 62.531 60.000 0.00 0.00 0.00 4.79
313 314 4.873129 CGTGGCGGTCATCGGGAG 62.873 72.222 0.00 0.00 39.69 4.30
332 333 2.676471 GGCCACGCTTCAACCCAT 60.676 61.111 0.00 0.00 0.00 4.00
333 334 2.568090 GCCACGCTTCAACCCATG 59.432 61.111 0.00 0.00 0.00 3.66
334 335 2.268076 GCCACGCTTCAACCCATGT 61.268 57.895 0.00 0.00 0.00 3.21
335 336 0.958382 GCCACGCTTCAACCCATGTA 60.958 55.000 0.00 0.00 0.00 2.29
336 337 0.802494 CCACGCTTCAACCCATGTAC 59.198 55.000 0.00 0.00 0.00 2.90
337 338 1.518325 CACGCTTCAACCCATGTACA 58.482 50.000 0.00 0.00 0.00 2.90
338 339 1.464608 CACGCTTCAACCCATGTACAG 59.535 52.381 0.33 0.00 0.00 2.74
339 340 1.086696 CGCTTCAACCCATGTACAGG 58.913 55.000 0.33 0.00 0.00 4.00
346 347 3.660724 CCATGTACAGGGGAGGGG 58.339 66.667 18.94 0.00 0.00 4.79
347 348 2.757124 CCATGTACAGGGGAGGGGC 61.757 68.421 18.94 0.00 0.00 5.80
348 349 2.368329 ATGTACAGGGGAGGGGCC 60.368 66.667 0.33 0.00 0.00 5.80
380 381 1.078426 GGCCAGTGCGGTTAGACAT 60.078 57.895 0.00 0.00 38.85 3.06
392 393 1.003118 GTTAGACATGGGTGTGGCAGA 59.997 52.381 0.00 0.00 39.09 4.26
398 399 1.426251 ATGGGTGTGGCAGAGGTTCA 61.426 55.000 0.00 0.00 0.00 3.18
407 408 4.070552 AGAGGTTCAGACGCCCGC 62.071 66.667 0.00 0.00 0.00 6.13
424 425 3.049227 GCAAAGCGCCCCTTATTTG 57.951 52.632 2.29 8.57 36.07 2.32
425 426 0.246360 GCAAAGCGCCCCTTATTTGT 59.754 50.000 15.98 0.00 35.55 2.83
427 428 2.870035 GCAAAGCGCCCCTTATTTGTTT 60.870 45.455 15.98 0.00 35.55 2.83
428 429 2.993220 CAAAGCGCCCCTTATTTGTTTC 59.007 45.455 2.29 0.00 32.20 2.78
430 431 0.179148 GCGCCCCTTATTTGTTTCCG 60.179 55.000 0.00 0.00 0.00 4.30
449 451 3.582714 CGGTTTACGGGAAGAAGTACT 57.417 47.619 0.00 0.00 39.42 2.73
461 463 2.249139 AGAAGTACTTTCAGGCCGTCT 58.751 47.619 10.02 0.00 38.31 4.18
462 464 2.231721 AGAAGTACTTTCAGGCCGTCTC 59.768 50.000 10.02 0.00 38.31 3.36
470 472 0.033503 TCAGGCCGTCTCATAGACCA 60.034 55.000 0.00 0.00 42.12 4.02
474 476 2.894126 AGGCCGTCTCATAGACCAATAG 59.106 50.000 0.00 0.00 42.12 1.73
482 484 7.382110 CGTCTCATAGACCAATAGAAATCCAT 58.618 38.462 1.63 0.00 42.12 3.41
483 485 8.523658 CGTCTCATAGACCAATAGAAATCCATA 58.476 37.037 1.63 0.00 42.12 2.74
506 517 2.210116 GGACGACACAACACATTCAGT 58.790 47.619 0.00 0.00 0.00 3.41
516 527 1.167851 CACATTCAGTCCGCATGGTT 58.832 50.000 0.00 0.00 36.30 3.67
518 529 1.271325 ACATTCAGTCCGCATGGTTCA 60.271 47.619 0.00 0.00 36.30 3.18
519 530 1.811965 CATTCAGTCCGCATGGTTCAA 59.188 47.619 0.00 0.00 36.30 2.69
525 536 1.735571 GTCCGCATGGTTCAAACGTAT 59.264 47.619 0.00 0.00 36.30 3.06
532 543 1.240256 GGTTCAAACGTATGTGGGCA 58.760 50.000 0.00 0.00 0.00 5.36
534 545 1.877443 GTTCAAACGTATGTGGGCAGT 59.123 47.619 0.00 0.00 0.00 4.40
547 558 1.891919 GGCAGTTTCACGGTGAGCA 60.892 57.895 18.10 5.45 0.00 4.26
568 579 4.037208 GCATTGGAGATGTCCTAATGTTGG 59.963 45.833 22.92 8.86 44.30 3.77
592 603 5.665459 CCCTGTTTCTAATCAGACAGTAGG 58.335 45.833 2.96 0.00 34.02 3.18
609 620 5.105756 ACAGTAGGTTGGCAAAGCATTAATC 60.106 40.000 0.00 0.00 36.20 1.75
614 625 4.176271 GTTGGCAAAGCATTAATCTGGAC 58.824 43.478 0.00 0.00 0.00 4.02
781 795 0.397675 TTGCCACCATGTTTGTCCCA 60.398 50.000 0.00 0.00 0.00 4.37
802 816 4.223923 CCATCTCCTCTTCACCTTACACTT 59.776 45.833 0.00 0.00 0.00 3.16
856 870 1.614226 CCTTCCTAACCCCGTCCCA 60.614 63.158 0.00 0.00 0.00 4.37
1013 1027 0.948623 CACACGATGCTTCCAACCGA 60.949 55.000 0.00 0.00 0.00 4.69
1041 1055 0.737367 TCTTCATTGCGCTCCTCGTG 60.737 55.000 9.73 0.00 41.07 4.35
1221 1235 0.322816 TGGACGCTAACTACCTCCGT 60.323 55.000 0.00 0.00 34.52 4.69
1476 1490 2.990479 GACACGCTTCCCCCTGAT 59.010 61.111 0.00 0.00 0.00 2.90
1542 1556 1.203523 GACATCCGCACACTCTTCTCT 59.796 52.381 0.00 0.00 0.00 3.10
1631 1654 1.472480 GGACACATTTTGGATGGACCG 59.528 52.381 0.00 0.00 42.61 4.79
1953 1997 4.660938 GGAAAGCCCTGGCACCGT 62.661 66.667 11.38 0.00 44.88 4.83
2031 2075 2.493030 CCATCGTCGCCGGTACTT 59.507 61.111 1.90 0.00 33.95 2.24
2224 2271 4.530581 TGCACACGCAGTTGAAGA 57.469 50.000 0.00 0.00 45.36 2.87
2234 2281 1.609072 GCAGTTGAAGAAAGGGTGGTC 59.391 52.381 0.00 0.00 0.00 4.02
2235 2282 2.930950 CAGTTGAAGAAAGGGTGGTCA 58.069 47.619 0.00 0.00 0.00 4.02
2325 2372 2.738013 ATTGCTCTTGCTTTTGCCTC 57.262 45.000 0.00 0.00 46.87 4.70
2376 2423 4.536364 TCTTGTTTTGTTCTGCTCTTCG 57.464 40.909 0.00 0.00 0.00 3.79
2435 2482 4.408821 TGCATGGTGGGAGGCGAC 62.409 66.667 0.00 0.00 0.00 5.19
2553 2600 6.632909 TGTTGATTGGAATCTTATTTGCCTG 58.367 36.000 1.26 0.00 36.39 4.85
2573 2620 6.196079 CCTGATAAGGCCTACTTTGTTTTC 57.804 41.667 5.16 0.00 40.64 2.29
2577 2624 3.434940 AGGCCTACTTTGTTTTCCGAT 57.565 42.857 1.29 0.00 0.00 4.18
2611 2658 6.442513 AGAAGGCAGAATACAAATACAAGC 57.557 37.500 0.00 0.00 0.00 4.01
2616 2663 5.493735 GCAGAATACAAATACAAGCGACTC 58.506 41.667 0.00 0.00 0.00 3.36
2624 2671 5.864474 ACAAATACAAGCGACTCTAACTCAG 59.136 40.000 0.00 0.00 0.00 3.35
2637 2684 3.802139 TCTAACTCAGTGCGAACAACAAG 59.198 43.478 0.00 0.00 0.00 3.16
2644 2691 5.294356 TCAGTGCGAACAACAAGTATAGTT 58.706 37.500 0.00 0.00 0.00 2.24
2654 2701 6.303839 ACAACAAGTATAGTTCCAACACCAT 58.696 36.000 0.00 0.00 0.00 3.55
2662 2709 4.126520 AGTTCCAACACCATACCCAAAT 57.873 40.909 0.00 0.00 0.00 2.32
2672 2719 5.952947 ACACCATACCCAAATTAATCCGAAA 59.047 36.000 0.00 0.00 0.00 3.46
2678 2725 6.911250 ACCCAAATTAATCCGAAAAGAAGT 57.089 33.333 0.00 0.00 0.00 3.01
2734 2781 3.614092 CTGTCCTGACCATAGCAACAAT 58.386 45.455 0.00 0.00 0.00 2.71
2798 2845 1.128809 TAACCGGACTTCCCTTGCCA 61.129 55.000 9.46 0.00 0.00 4.92
2820 2867 0.037975 GCACCAACCAGCCTTGATTG 60.038 55.000 0.00 0.00 0.00 2.67
2884 2935 1.293062 AGCCACCATCTTGGACTCAT 58.707 50.000 0.00 0.00 40.96 2.90
2891 2942 0.179100 ATCTTGGACTCATCGGCGTG 60.179 55.000 6.85 4.88 0.00 5.34
2916 2967 0.827507 ACATTGCGCCCAAGAACCTT 60.828 50.000 4.18 0.00 33.80 3.50
2934 2985 2.358267 CCTTTACTCGGACTAGCGACAT 59.642 50.000 0.00 0.00 0.00 3.06
2960 3011 0.321653 GAGGACCGCATCACCAAACT 60.322 55.000 0.00 0.00 0.00 2.66
2968 3019 1.666888 GCATCACCAAACTTCCAAGCG 60.667 52.381 0.00 0.00 0.00 4.68
2978 3029 1.556911 ACTTCCAAGCGATGTCTCCAT 59.443 47.619 0.00 0.00 0.00 3.41
3036 3087 1.447838 CCATCACCGGTCCAAGACG 60.448 63.158 2.59 0.00 32.65 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 4.742201 CTGTGTCCGCCGACCCAG 62.742 72.222 3.62 3.62 38.01 4.45
37 38 3.934391 CTTCTGTGTCCGCCGACCC 62.934 68.421 2.66 0.00 38.32 4.46
38 39 2.432628 CTTCTGTGTCCGCCGACC 60.433 66.667 2.66 0.00 38.32 4.79
39 40 2.432628 CCTTCTGTGTCCGCCGAC 60.433 66.667 0.00 0.00 39.66 4.79
40 41 2.599281 TCCTTCTGTGTCCGCCGA 60.599 61.111 0.00 0.00 0.00 5.54
41 42 2.125912 CTCCTTCTGTGTCCGCCG 60.126 66.667 0.00 0.00 0.00 6.46
42 43 1.216710 CTCTCCTTCTGTGTCCGCC 59.783 63.158 0.00 0.00 0.00 6.13
43 44 1.216710 CCTCTCCTTCTGTGTCCGC 59.783 63.158 0.00 0.00 0.00 5.54
44 45 0.814457 CTCCTCTCCTTCTGTGTCCG 59.186 60.000 0.00 0.00 0.00 4.79
45 46 1.190643 CCTCCTCTCCTTCTGTGTCC 58.809 60.000 0.00 0.00 0.00 4.02
46 47 2.099405 CTCCTCCTCTCCTTCTGTGTC 58.901 57.143 0.00 0.00 0.00 3.67
47 48 1.894978 GCTCCTCCTCTCCTTCTGTGT 60.895 57.143 0.00 0.00 0.00 3.72
48 49 0.823460 GCTCCTCCTCTCCTTCTGTG 59.177 60.000 0.00 0.00 0.00 3.66
49 50 0.682855 CGCTCCTCCTCTCCTTCTGT 60.683 60.000 0.00 0.00 0.00 3.41
50 51 2.015227 GCGCTCCTCCTCTCCTTCTG 62.015 65.000 0.00 0.00 0.00 3.02
51 52 1.756561 GCGCTCCTCCTCTCCTTCT 60.757 63.158 0.00 0.00 0.00 2.85
52 53 2.811799 GCGCTCCTCCTCTCCTTC 59.188 66.667 0.00 0.00 0.00 3.46
53 54 3.144193 CGCGCTCCTCCTCTCCTT 61.144 66.667 5.56 0.00 0.00 3.36
77 78 0.878523 TCTCCTTGTCAACGGCGTTG 60.879 55.000 38.99 38.99 43.99 4.10
78 79 0.600255 CTCTCCTTGTCAACGGCGTT 60.600 55.000 21.19 21.19 0.00 4.84
79 80 1.006102 CTCTCCTTGTCAACGGCGT 60.006 57.895 6.77 6.77 0.00 5.68
80 81 1.738099 CCTCTCCTTGTCAACGGCG 60.738 63.158 4.80 4.80 0.00 6.46
81 82 1.376037 CCCTCTCCTTGTCAACGGC 60.376 63.158 0.00 0.00 0.00 5.68
82 83 0.037232 GTCCCTCTCCTTGTCAACGG 60.037 60.000 0.00 0.00 0.00 4.44
83 84 0.388649 CGTCCCTCTCCTTGTCAACG 60.389 60.000 0.00 0.00 0.00 4.10
84 85 0.037232 CCGTCCCTCTCCTTGTCAAC 60.037 60.000 0.00 0.00 0.00 3.18
85 86 1.827399 GCCGTCCCTCTCCTTGTCAA 61.827 60.000 0.00 0.00 0.00 3.18
86 87 2.283529 GCCGTCCCTCTCCTTGTCA 61.284 63.158 0.00 0.00 0.00 3.58
87 88 2.579738 GCCGTCCCTCTCCTTGTC 59.420 66.667 0.00 0.00 0.00 3.18
88 89 3.382832 CGCCGTCCCTCTCCTTGT 61.383 66.667 0.00 0.00 0.00 3.16
89 90 3.068691 TCGCCGTCCCTCTCCTTG 61.069 66.667 0.00 0.00 0.00 3.61
90 91 2.756283 CTCGCCGTCCCTCTCCTT 60.756 66.667 0.00 0.00 0.00 3.36
91 92 4.824515 CCTCGCCGTCCCTCTCCT 62.825 72.222 0.00 0.00 0.00 3.69
109 110 4.820744 CCCAATGGCCCCCACGAG 62.821 72.222 0.00 0.00 35.80 4.18
117 118 4.315264 ACCACCACCCCAATGGCC 62.315 66.667 0.00 0.00 44.33 5.36
118 119 2.679996 GACCACCACCCCAATGGC 60.680 66.667 0.00 0.00 44.33 4.40
119 120 2.361104 CGACCACCACCCCAATGG 60.361 66.667 0.00 0.00 46.10 3.16
120 121 2.361104 CCGACCACCACCCCAATG 60.361 66.667 0.00 0.00 0.00 2.82
121 122 4.360405 GCCGACCACCACCCCAAT 62.360 66.667 0.00 0.00 0.00 3.16
144 145 4.847585 CGTCGTCGCCTCGTCTCG 62.848 72.222 0.00 0.00 0.00 4.04
145 146 4.517703 CCGTCGTCGCCTCGTCTC 62.518 72.222 0.00 0.00 35.54 3.36
183 184 3.358076 CTTCCCCTCCGTCGCTGTC 62.358 68.421 0.00 0.00 0.00 3.51
184 185 3.382832 CTTCCCCTCCGTCGCTGT 61.383 66.667 0.00 0.00 0.00 4.40
185 186 4.148825 CCTTCCCCTCCGTCGCTG 62.149 72.222 0.00 0.00 0.00 5.18
186 187 3.899545 TTCCTTCCCCTCCGTCGCT 62.900 63.158 0.00 0.00 0.00 4.93
187 188 3.372554 CTTCCTTCCCCTCCGTCGC 62.373 68.421 0.00 0.00 0.00 5.19
188 189 2.722201 CCTTCCTTCCCCTCCGTCG 61.722 68.421 0.00 0.00 0.00 5.12
189 190 2.368011 CCCTTCCTTCCCCTCCGTC 61.368 68.421 0.00 0.00 0.00 4.79
190 191 2.285442 CCCTTCCTTCCCCTCCGT 60.285 66.667 0.00 0.00 0.00 4.69
191 192 3.090532 CCCCTTCCTTCCCCTCCG 61.091 72.222 0.00 0.00 0.00 4.63
192 193 2.696504 CCCCCTTCCTTCCCCTCC 60.697 72.222 0.00 0.00 0.00 4.30
193 194 3.421386 GCCCCCTTCCTTCCCCTC 61.421 72.222 0.00 0.00 0.00 4.30
211 212 3.305177 TACCACCTTTCCCTCGCGC 62.305 63.158 0.00 0.00 0.00 6.86
212 213 1.153628 CTACCACCTTTCCCTCGCG 60.154 63.158 0.00 0.00 0.00 5.87
213 214 1.221021 CCTACCACCTTTCCCTCGC 59.779 63.158 0.00 0.00 0.00 5.03
214 215 0.908180 ACCCTACCACCTTTCCCTCG 60.908 60.000 0.00 0.00 0.00 4.63
215 216 1.369403 AACCCTACCACCTTTCCCTC 58.631 55.000 0.00 0.00 0.00 4.30
216 217 2.747083 TAACCCTACCACCTTTCCCT 57.253 50.000 0.00 0.00 0.00 4.20
217 218 4.326600 AATTAACCCTACCACCTTTCCC 57.673 45.455 0.00 0.00 0.00 3.97
218 219 5.044624 ACCTAATTAACCCTACCACCTTTCC 60.045 44.000 0.00 0.00 0.00 3.13
219 220 5.884232 CACCTAATTAACCCTACCACCTTTC 59.116 44.000 0.00 0.00 0.00 2.62
220 221 5.281349 CCACCTAATTAACCCTACCACCTTT 60.281 44.000 0.00 0.00 0.00 3.11
221 222 4.228895 CCACCTAATTAACCCTACCACCTT 59.771 45.833 0.00 0.00 0.00 3.50
222 223 3.784202 CCACCTAATTAACCCTACCACCT 59.216 47.826 0.00 0.00 0.00 4.00
223 224 3.686405 GCCACCTAATTAACCCTACCACC 60.686 52.174 0.00 0.00 0.00 4.61
224 225 3.548770 GCCACCTAATTAACCCTACCAC 58.451 50.000 0.00 0.00 0.00 4.16
225 226 2.171027 CGCCACCTAATTAACCCTACCA 59.829 50.000 0.00 0.00 0.00 3.25
226 227 2.486013 CCGCCACCTAATTAACCCTACC 60.486 54.545 0.00 0.00 0.00 3.18
227 228 2.171237 ACCGCCACCTAATTAACCCTAC 59.829 50.000 0.00 0.00 0.00 3.18
228 229 2.171027 CACCGCCACCTAATTAACCCTA 59.829 50.000 0.00 0.00 0.00 3.53
229 230 1.064979 CACCGCCACCTAATTAACCCT 60.065 52.381 0.00 0.00 0.00 4.34
230 231 1.385528 CACCGCCACCTAATTAACCC 58.614 55.000 0.00 0.00 0.00 4.11
231 232 1.385528 CCACCGCCACCTAATTAACC 58.614 55.000 0.00 0.00 0.00 2.85
232 233 1.340308 ACCCACCGCCACCTAATTAAC 60.340 52.381 0.00 0.00 0.00 2.01
233 234 0.993470 ACCCACCGCCACCTAATTAA 59.007 50.000 0.00 0.00 0.00 1.40
234 235 0.542805 GACCCACCGCCACCTAATTA 59.457 55.000 0.00 0.00 0.00 1.40
235 236 1.301954 GACCCACCGCCACCTAATT 59.698 57.895 0.00 0.00 0.00 1.40
236 237 2.995547 GACCCACCGCCACCTAAT 59.004 61.111 0.00 0.00 0.00 1.73
237 238 3.697747 CGACCCACCGCCACCTAA 61.698 66.667 0.00 0.00 0.00 2.69
296 297 4.873129 CTCCCGATGACCGCCACG 62.873 72.222 0.00 0.00 36.84 4.94
315 316 2.676471 ATGGGTTGAAGCGTGGCC 60.676 61.111 0.00 0.00 0.00 5.36
316 317 0.958382 TACATGGGTTGAAGCGTGGC 60.958 55.000 0.00 0.00 0.00 5.01
317 318 0.802494 GTACATGGGTTGAAGCGTGG 59.198 55.000 0.00 0.00 0.00 4.94
318 319 1.464608 CTGTACATGGGTTGAAGCGTG 59.535 52.381 0.00 0.00 0.00 5.34
319 320 1.610624 CCTGTACATGGGTTGAAGCGT 60.611 52.381 0.00 0.00 0.00 5.07
320 321 1.086696 CCTGTACATGGGTTGAAGCG 58.913 55.000 0.00 0.00 0.00 4.68
321 322 1.463674 CCCTGTACATGGGTTGAAGC 58.536 55.000 17.64 0.00 39.82 3.86
322 323 1.633432 TCCCCTGTACATGGGTTGAAG 59.367 52.381 29.09 13.79 43.09 3.02
323 324 1.633432 CTCCCCTGTACATGGGTTGAA 59.367 52.381 29.09 13.81 43.09 2.69
324 325 1.285280 CTCCCCTGTACATGGGTTGA 58.715 55.000 29.09 17.49 43.09 3.18
325 326 0.255890 CCTCCCCTGTACATGGGTTG 59.744 60.000 29.09 22.84 43.09 3.77
326 327 0.919289 CCCTCCCCTGTACATGGGTT 60.919 60.000 29.09 0.00 43.09 4.11
327 328 1.307866 CCCTCCCCTGTACATGGGT 60.308 63.158 29.09 0.00 43.09 4.51
328 329 2.078665 CCCCTCCCCTGTACATGGG 61.079 68.421 25.98 25.98 44.19 4.00
329 330 2.757124 GCCCCTCCCCTGTACATGG 61.757 68.421 10.06 10.06 0.00 3.66
330 331 2.757124 GGCCCCTCCCCTGTACATG 61.757 68.421 0.00 0.00 0.00 3.21
331 332 2.368329 GGCCCCTCCCCTGTACAT 60.368 66.667 0.00 0.00 0.00 2.29
357 358 2.819984 CTAACCGCACTGGCCCATGT 62.820 60.000 0.00 0.00 43.94 3.21
358 359 2.045438 TAACCGCACTGGCCCATG 60.045 61.111 0.00 0.00 43.94 3.66
359 360 2.272146 CTAACCGCACTGGCCCAT 59.728 61.111 0.00 0.00 43.94 4.00
380 381 2.055689 CTGAACCTCTGCCACACCCA 62.056 60.000 0.00 0.00 0.00 4.51
392 393 3.469863 TTTGCGGGCGTCTGAACCT 62.470 57.895 0.00 0.00 0.00 3.50
407 408 2.741759 AACAAATAAGGGGCGCTTTG 57.258 45.000 22.38 16.27 35.30 2.77
428 429 4.800582 AAAGTACTTCTTCCCGTAAACCGG 60.801 45.833 8.95 0.00 45.31 5.28
430 431 5.299949 TGAAAGTACTTCTTCCCGTAAACC 58.700 41.667 8.95 0.00 35.02 3.27
442 444 2.029290 TGAGACGGCCTGAAAGTACTTC 60.029 50.000 8.95 3.51 34.31 3.01
449 451 1.480954 GGTCTATGAGACGGCCTGAAA 59.519 52.381 0.00 0.00 45.96 2.69
461 463 9.964354 CCAATATGGATTTCTATTGGTCTATGA 57.036 33.333 11.46 0.00 44.84 2.15
482 484 4.381411 TGAATGTGTTGTGTCGTCCAATA 58.619 39.130 0.00 0.00 0.00 1.90
483 485 3.210227 TGAATGTGTTGTGTCGTCCAAT 58.790 40.909 0.00 0.00 0.00 3.16
506 517 1.735018 CATACGTTTGAACCATGCGGA 59.265 47.619 0.00 0.00 35.59 5.54
516 527 2.264005 AACTGCCCACATACGTTTGA 57.736 45.000 13.16 0.00 0.00 2.69
518 529 2.292292 GTGAAACTGCCCACATACGTTT 59.708 45.455 0.00 0.00 33.72 3.60
519 530 1.877443 GTGAAACTGCCCACATACGTT 59.123 47.619 0.00 0.00 33.72 3.99
525 536 1.821759 CACCGTGAAACTGCCCACA 60.822 57.895 0.00 0.00 33.13 4.17
532 543 1.202758 TCCAATGCTCACCGTGAAACT 60.203 47.619 2.19 0.00 31.75 2.66
534 545 1.071542 TCTCCAATGCTCACCGTGAAA 59.928 47.619 2.19 0.00 0.00 2.69
547 558 4.210331 GCCAACATTAGGACATCTCCAAT 58.790 43.478 0.00 0.00 39.39 3.16
568 579 3.944087 ACTGTCTGATTAGAAACAGGGC 58.056 45.455 10.06 0.00 33.54 5.19
592 603 4.082026 AGTCCAGATTAATGCTTTGCCAAC 60.082 41.667 0.00 0.00 0.00 3.77
609 620 2.260844 TTGGCTTCAGTTGAGTCCAG 57.739 50.000 5.14 0.00 31.96 3.86
614 625 6.769822 AGTAATATGGATTGGCTTCAGTTGAG 59.230 38.462 0.00 0.00 0.00 3.02
781 795 5.046231 GGAAAGTGTAAGGTGAAGAGGAGAT 60.046 44.000 0.00 0.00 0.00 2.75
802 816 3.284793 TCAAAACGGTGGAGAAAGGAA 57.715 42.857 0.00 0.00 0.00 3.36
835 849 1.335882 GGACGGGGTTAGGAAGGGAG 61.336 65.000 0.00 0.00 0.00 4.30
856 870 1.077265 CTGGTCCCTGGCAATGGTT 59.923 57.895 2.95 0.00 0.00 3.67
1013 1027 1.139989 CGCAATGAAGACGACACAGT 58.860 50.000 0.00 0.00 0.00 3.55
1024 1038 2.390599 GCACGAGGAGCGCAATGAA 61.391 57.895 11.47 0.00 46.04 2.57
1170 1184 1.525077 GTTCACCTTGTCACCGCCA 60.525 57.895 0.00 0.00 0.00 5.69
1473 1487 1.522806 GATAACCCGGCGCACATCA 60.523 57.895 10.83 0.00 0.00 3.07
1476 1490 1.142314 GTAGATAACCCGGCGCACA 59.858 57.895 10.83 0.00 0.00 4.57
1488 1502 2.145958 CGTCGGAGTCGAGGTAGATA 57.854 55.000 0.00 0.00 46.91 1.98
1517 1531 3.179265 GTGTGCGGATGTCGTCGG 61.179 66.667 0.00 0.00 41.72 4.79
1533 1547 1.540267 CGAGGTCCACAGAGAAGAGT 58.460 55.000 0.00 0.00 0.00 3.24
1860 1904 1.577328 CTTTGACATTGTCGCCGCCT 61.577 55.000 11.97 0.00 34.95 5.52
2031 2075 2.781431 TAGGTGCCGCTCACTCCTCA 62.781 60.000 6.04 0.00 44.98 3.86
2125 2171 7.168905 ACATCTCTCGTTAATTTCCTCCTTTT 58.831 34.615 0.00 0.00 0.00 2.27
2126 2172 6.712276 ACATCTCTCGTTAATTTCCTCCTTT 58.288 36.000 0.00 0.00 0.00 3.11
2129 2175 6.106673 TCAACATCTCTCGTTAATTTCCTCC 58.893 40.000 0.00 0.00 0.00 4.30
2224 2271 4.519906 TTCTCTTCTTTGACCACCCTTT 57.480 40.909 0.00 0.00 0.00 3.11
2234 2281 3.423645 GCACCGATCGTTTCTCTTCTTTG 60.424 47.826 15.09 0.00 0.00 2.77
2235 2282 2.737252 GCACCGATCGTTTCTCTTCTTT 59.263 45.455 15.09 0.00 0.00 2.52
2325 2372 6.547510 CCCAAGGGAGATAATAACCAAGAAAG 59.452 42.308 0.00 0.00 37.50 2.62
2376 2423 8.583810 TTATAGCATGACCTATACAAAACGAC 57.416 34.615 0.00 0.00 31.75 4.34
2435 2482 3.855689 ATTCTTGAGCACCAATTTCCG 57.144 42.857 0.00 0.00 33.68 4.30
2553 2600 4.939439 TCGGAAAACAAAGTAGGCCTTATC 59.061 41.667 12.58 1.81 31.48 1.75
2604 2651 4.675671 GCACTGAGTTAGAGTCGCTTGTAT 60.676 45.833 0.00 0.00 0.00 2.29
2611 2658 2.243407 GTTCGCACTGAGTTAGAGTCG 58.757 52.381 0.00 0.00 0.00 4.18
2616 2663 3.555956 ACTTGTTGTTCGCACTGAGTTAG 59.444 43.478 0.00 0.00 0.00 2.34
2624 2671 4.449743 TGGAACTATACTTGTTGTTCGCAC 59.550 41.667 0.00 0.00 39.50 5.34
2637 2684 5.362105 TGGGTATGGTGTTGGAACTATAC 57.638 43.478 3.12 3.12 41.36 1.47
2644 2691 5.659079 GGATTAATTTGGGTATGGTGTTGGA 59.341 40.000 0.00 0.00 0.00 3.53
2654 2701 7.666388 TGACTTCTTTTCGGATTAATTTGGGTA 59.334 33.333 0.00 0.00 0.00 3.69
2662 2709 3.434299 GCGGTGACTTCTTTTCGGATTAA 59.566 43.478 0.00 0.00 0.00 1.40
2672 2719 1.967319 AATGTGTGCGGTGACTTCTT 58.033 45.000 0.00 0.00 0.00 2.52
2678 2725 2.032302 GTGTTTGTAATGTGTGCGGTGA 59.968 45.455 0.00 0.00 0.00 4.02
2740 2787 1.723003 GTGATCGGTGTACGTCCAAAC 59.277 52.381 0.00 0.00 44.69 2.93
2744 2791 0.100146 GAGGTGATCGGTGTACGTCC 59.900 60.000 0.00 0.00 44.69 4.79
2798 2845 0.469705 TCAAGGCTGGTTGGTGCATT 60.470 50.000 0.00 0.00 33.32 3.56
2820 2867 1.734465 CACCCACTCGCAATCTTCTTC 59.266 52.381 0.00 0.00 0.00 2.87
2884 2935 1.444724 CAATGTACGTCCACGCCGA 60.445 57.895 0.00 0.00 44.43 5.54
2916 2967 1.674441 CCATGTCGCTAGTCCGAGTAA 59.326 52.381 0.00 0.00 37.99 2.24
2934 2985 2.284625 ATGCGGTCCTCCAGTCCA 60.285 61.111 0.00 0.00 0.00 4.02
2978 3029 0.770499 TCAGTTGGGAGCATTGTGGA 59.230 50.000 0.00 0.00 0.00 4.02
3023 3074 3.690745 CCTACGTCTTGGACCGGT 58.309 61.111 6.92 6.92 0.00 5.28


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

AutoCloner maintained by Alex Coulton.