Multiple sequence alignment - TraesCS3A01G154400

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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 TraesCS3A01G154400 chr3A 100.000 1341 0 0 976 2316 145667222 145668562 0.000000e+00 2477
1 TraesCS3A01G154400 chr3A 100.000 549 0 0 1 549 145666247 145666795 0.000000e+00 1014
2 TraesCS3A01G154400 chr3A 86.813 182 21 3 104 282 149265562 149265743 1.570000e-47 200
3 TraesCS3A01G154400 chr3A 87.429 175 20 1 112 284 291796848 291796674 1.570000e-47 200
4 TraesCS3A01G154400 chr3A 100.000 105 0 0 2490 2594 145668736 145668840 7.320000e-46 195
5 TraesCS3A01G154400 chr3B 91.973 1358 49 25 976 2316 188877202 188878516 0.000000e+00 1849
6 TraesCS3A01G154400 chr3B 97.508 321 8 0 981 1301 189921636 189921316 1.360000e-152 549
7 TraesCS3A01G154400 chr3B 93.281 253 17 0 292 544 188876936 188877188 8.770000e-100 374
8 TraesCS3A01G154400 chr3B 88.104 269 16 4 278 544 189917403 189917149 3.240000e-79 305
9 TraesCS3A01G154400 chr3B 89.091 165 18 0 118 282 505009094 505008930 3.380000e-49 206
10 TraesCS3A01G154400 chr3B 95.575 113 5 0 1 113 188876804 188876916 5.700000e-42 182
11 TraesCS3A01G154400 chr3B 93.694 111 7 0 3 113 189917513 189917403 1.600000e-37 167
12 TraesCS3A01G154400 chr3D 91.920 1349 53 22 976 2315 132275106 132276407 0.000000e+00 1836
13 TraesCS3A01G154400 chr3D 92.727 275 17 3 278 549 132274711 132274985 6.730000e-106 394
14 TraesCS3A01G154400 chr3D 89.091 165 17 1 118 282 170236968 170236805 1.220000e-48 204
15 TraesCS3A01G154400 chr3D 95.575 113 5 0 1 113 132274599 132274711 5.700000e-42 182
16 TraesCS3A01G154400 chr7D 84.698 562 67 11 989 1545 470837422 470837969 6.310000e-151 544
17 TraesCS3A01G154400 chr7D 88.235 170 19 1 117 286 518793748 518793916 4.380000e-48 202
18 TraesCS3A01G154400 chr7B 84.135 561 72 9 989 1545 494434785 494435332 6.360000e-146 527
19 TraesCS3A01G154400 chr7B 88.304 171 19 1 116 286 563740015 563739846 1.220000e-48 204
20 TraesCS3A01G154400 chr7A 84.135 561 72 9 989 1545 527995927 527995380 6.360000e-146 527
21 TraesCS3A01G154400 chr1B 80.186 323 48 12 1220 1534 373628644 373628958 7.220000e-56 228
22 TraesCS3A01G154400 chr1B 77.656 273 53 8 1131 1399 529998501 529998233 2.670000e-35 159
23 TraesCS3A01G154400 chr6B 88.462 182 17 3 107 286 54875261 54875440 1.560000e-52 217
24 TraesCS3A01G154400 chr6D 88.554 166 18 1 117 282 289352700 289352864 1.570000e-47 200
25 TraesCS3A01G154400 chr2B 86.857 175 22 1 113 287 9033415 9033588 7.320000e-46 195
26 TraesCS3A01G154400 chr1D 77.656 273 53 8 1131 1399 392697091 392697359 2.670000e-35 159
27 TraesCS3A01G154400 chr1A 76.923 273 55 8 1131 1399 492652702 492652434 5.780000e-32 148


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 TraesCS3A01G154400 chr3A 145666247 145668840 2593 False 1228.666667 2477 100.000000 1 2594 3 chr3A.!!$F2 2593
1 TraesCS3A01G154400 chr3B 188876804 188878516 1712 False 801.666667 1849 93.609667 1 2316 3 chr3B.!!$F1 2315
2 TraesCS3A01G154400 chr3B 189917149 189921636 4487 True 340.333333 549 93.102000 3 1301 3 chr3B.!!$R2 1298
3 TraesCS3A01G154400 chr3D 132274599 132276407 1808 False 804.000000 1836 93.407333 1 2315 3 chr3D.!!$F1 2314
4 TraesCS3A01G154400 chr7D 470837422 470837969 547 False 544.000000 544 84.698000 989 1545 1 chr7D.!!$F1 556
5 TraesCS3A01G154400 chr7B 494434785 494435332 547 False 527.000000 527 84.135000 989 1545 1 chr7B.!!$F1 556
6 TraesCS3A01G154400 chr7A 527995380 527995927 547 True 527.000000 527 84.135000 989 1545 1 chr7A.!!$R1 556

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
338 344 1.095228 TAGGGTAGCTGCGCATTTGC 61.095 55.0 20.46 11.99 37.78 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1953 5194 0.036875 ACTCCAACTTGCACTAGGGC 59.963 55.0 10.98 10.98 0.0 5.19 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
29 30 5.972107 ATATGCATATTTTGAGGAGTGCC 57.028 39.130 13.63 0.00 0.00 5.01
30 31 3.084536 TGCATATTTTGAGGAGTGCCA 57.915 42.857 0.00 0.00 36.29 4.92
47 48 3.387699 GTGCCACCCCATATAAGCATTTT 59.612 43.478 0.00 0.00 32.11 1.82
104 105 4.852134 TGGTCAACAGTGAAATCCAATG 57.148 40.909 0.00 0.00 45.57 2.82
128 129 4.895668 TGTAAACAAATACTCCCTCCGT 57.104 40.909 0.00 0.00 0.00 4.69
129 130 5.231702 TGTAAACAAATACTCCCTCCGTT 57.768 39.130 0.00 0.00 0.00 4.44
130 131 5.623169 TGTAAACAAATACTCCCTCCGTTT 58.377 37.500 0.00 0.00 0.00 3.60
131 132 5.702209 TGTAAACAAATACTCCCTCCGTTTC 59.298 40.000 0.00 0.00 0.00 2.78
132 133 4.635699 AACAAATACTCCCTCCGTTTCT 57.364 40.909 0.00 0.00 0.00 2.52
133 134 5.750352 AACAAATACTCCCTCCGTTTCTA 57.250 39.130 0.00 0.00 0.00 2.10
134 135 5.750352 ACAAATACTCCCTCCGTTTCTAA 57.250 39.130 0.00 0.00 0.00 2.10
135 136 6.117975 ACAAATACTCCCTCCGTTTCTAAA 57.882 37.500 0.00 0.00 0.00 1.85
136 137 6.718294 ACAAATACTCCCTCCGTTTCTAAAT 58.282 36.000 0.00 0.00 0.00 1.40
137 138 7.854337 ACAAATACTCCCTCCGTTTCTAAATA 58.146 34.615 0.00 0.00 0.00 1.40
138 139 8.491958 ACAAATACTCCCTCCGTTTCTAAATAT 58.508 33.333 0.00 0.00 0.00 1.28
139 140 9.991906 CAAATACTCCCTCCGTTTCTAAATATA 57.008 33.333 0.00 0.00 0.00 0.86
140 141 9.993454 AAATACTCCCTCCGTTTCTAAATATAC 57.007 33.333 0.00 0.00 0.00 1.47
141 142 6.081872 ACTCCCTCCGTTTCTAAATATACG 57.918 41.667 0.00 0.00 0.00 3.06
142 143 5.595952 ACTCCCTCCGTTTCTAAATATACGT 59.404 40.000 0.00 0.00 32.45 3.57
143 144 6.076981 TCCCTCCGTTTCTAAATATACGTC 57.923 41.667 0.00 0.00 32.45 4.34
144 145 5.829924 TCCCTCCGTTTCTAAATATACGTCT 59.170 40.000 0.00 0.00 32.45 4.18
145 146 6.322201 TCCCTCCGTTTCTAAATATACGTCTT 59.678 38.462 0.00 0.00 32.45 3.01
146 147 6.982724 CCCTCCGTTTCTAAATATACGTCTTT 59.017 38.462 0.00 0.00 32.45 2.52
147 148 7.168804 CCCTCCGTTTCTAAATATACGTCTTTC 59.831 40.741 0.00 0.00 32.45 2.62
148 149 7.919621 CCTCCGTTTCTAAATATACGTCTTTCT 59.080 37.037 0.00 0.00 32.45 2.52
149 150 9.941664 CTCCGTTTCTAAATATACGTCTTTCTA 57.058 33.333 0.00 0.00 32.45 2.10
163 164 9.840427 ATACGTCTTTCTAAACATTTCAAATGG 57.160 29.630 14.70 0.00 0.00 3.16
164 165 7.936584 ACGTCTTTCTAAACATTTCAAATGGA 58.063 30.769 14.70 0.00 0.00 3.41
165 166 7.860872 ACGTCTTTCTAAACATTTCAAATGGAC 59.139 33.333 14.70 8.10 0.00 4.02
166 167 8.076178 CGTCTTTCTAAACATTTCAAATGGACT 58.924 33.333 14.70 1.17 0.00 3.85
177 178 9.607988 ACATTTCAAATGGACTACAATATACGA 57.392 29.630 14.70 0.00 0.00 3.43
181 182 9.607988 TTCAAATGGACTACAATATACGAATGT 57.392 29.630 0.00 0.00 0.00 2.71
277 278 9.689501 AAAATACTTATATTTGGAAACGGAGGA 57.310 29.630 0.00 0.00 39.61 3.71
278 279 9.689501 AAATACTTATATTTGGAAACGGAGGAA 57.310 29.630 0.00 0.00 39.16 3.36
279 280 8.904099 ATACTTATATTTGGAAACGGAGGAAG 57.096 34.615 0.00 0.00 0.00 3.46
285 286 3.887621 TGGAAACGGAGGAAGTAGATG 57.112 47.619 0.00 0.00 0.00 2.90
338 344 1.095228 TAGGGTAGCTGCGCATTTGC 61.095 55.000 20.46 11.99 37.78 3.68
350 356 2.348779 GCGCATTTGCTTTTCAGTTTGG 60.349 45.455 0.30 0.00 39.32 3.28
354 360 5.277442 CGCATTTGCTTTTCAGTTTGGAAAT 60.277 36.000 0.51 0.00 39.32 2.17
355 361 6.138088 GCATTTGCTTTTCAGTTTGGAAATC 58.862 36.000 0.00 0.00 36.71 2.17
357 364 6.660887 TTTGCTTTTCAGTTTGGAAATCAC 57.339 33.333 0.00 0.00 36.71 3.06
366 373 5.048782 TCAGTTTGGAAATCACATTTCTCGG 60.049 40.000 8.50 1.02 46.03 4.63
396 403 6.528072 CGAATAGGAGCTCAAAAATGGAAAAC 59.472 38.462 17.19 0.00 0.00 2.43
452 459 3.408634 CCAACCATAAAAGGTGAGACGT 58.591 45.455 0.00 0.00 42.25 4.34
470 477 3.932710 GACGTCTCCAATCTGCAAATACA 59.067 43.478 8.70 0.00 0.00 2.29
480 487 4.782019 TCTGCAAATACAACATCAACCC 57.218 40.909 0.00 0.00 0.00 4.11
484 491 3.993736 GCAAATACAACATCAACCCCAAC 59.006 43.478 0.00 0.00 0.00 3.77
520 527 5.163713 GGCCTTCTCTTAGTTAATTGCACAG 60.164 44.000 0.00 0.00 0.00 3.66
521 528 5.643777 GCCTTCTCTTAGTTAATTGCACAGA 59.356 40.000 0.00 0.00 0.00 3.41
544 551 3.266772 AGCCAGAGAAGAGAGAGAGAGAA 59.733 47.826 0.00 0.00 0.00 2.87
545 552 3.629398 GCCAGAGAAGAGAGAGAGAGAAG 59.371 52.174 0.00 0.00 0.00 2.85
547 554 4.324563 CCAGAGAAGAGAGAGAGAGAAGGT 60.325 50.000 0.00 0.00 0.00 3.50
548 555 4.637534 CAGAGAAGAGAGAGAGAGAAGGTG 59.362 50.000 0.00 0.00 0.00 4.00
1014 1021 2.816958 CACATGGAGAGCGCGCTT 60.817 61.111 36.87 24.27 0.00 4.68
1555 4717 4.082523 CCATCGCGACCACCACCT 62.083 66.667 12.93 0.00 0.00 4.00
1569 4731 2.060980 CACCTCCTCCTCTTCCCCG 61.061 68.421 0.00 0.00 0.00 5.73
1602 4764 3.007635 TGAGCAAAGCTGATCATCAGTG 58.992 45.455 16.28 7.85 42.92 3.66
1603 4765 3.268330 GAGCAAAGCTGATCATCAGTGA 58.732 45.455 16.28 0.00 45.94 3.41
1604 4766 3.878103 GAGCAAAGCTGATCATCAGTGAT 59.122 43.478 16.28 5.39 45.94 3.06
1605 4767 4.270834 AGCAAAGCTGATCATCAGTGATT 58.729 39.130 16.28 6.34 45.94 2.57
1607 4769 4.095932 GCAAAGCTGATCATCAGTGATTGA 59.904 41.667 22.70 5.38 45.94 2.57
1608 4770 5.221067 GCAAAGCTGATCATCAGTGATTGAT 60.221 40.000 22.70 9.92 45.94 2.57
1610 4772 4.308265 AGCTGATCATCAGTGATTGATCG 58.692 43.478 24.66 21.54 45.94 3.69
1611 4773 4.056740 GCTGATCATCAGTGATTGATCGT 58.943 43.478 24.66 8.09 45.94 3.73
1612 4774 4.510711 GCTGATCATCAGTGATTGATCGTT 59.489 41.667 24.66 6.10 45.94 3.85
1614 4776 5.910614 TGATCATCAGTGATTGATCGTTCT 58.089 37.500 24.66 7.13 44.76 3.01
1615 4777 6.343703 TGATCATCAGTGATTGATCGTTCTT 58.656 36.000 24.66 6.65 44.76 2.52
1616 4778 6.257193 TGATCATCAGTGATTGATCGTTCTTG 59.743 38.462 24.66 7.82 44.76 3.02
1617 4779 4.872124 TCATCAGTGATTGATCGTTCTTGG 59.128 41.667 1.86 0.00 44.76 3.61
1618 4780 4.271696 TCAGTGATTGATCGTTCTTGGT 57.728 40.909 0.00 0.00 0.00 3.67
1619 4781 4.641396 TCAGTGATTGATCGTTCTTGGTT 58.359 39.130 0.00 0.00 0.00 3.67
1620 4782 5.063204 TCAGTGATTGATCGTTCTTGGTTT 58.937 37.500 0.00 0.00 0.00 3.27
1631 4868 0.322456 TCTTGGTTTCTCCATGGCCG 60.322 55.000 6.96 0.01 46.60 6.13
1632 4869 1.304052 TTGGTTTCTCCATGGCCGG 60.304 57.895 6.96 0.00 46.60 6.13
1633 4870 2.075355 TTGGTTTCTCCATGGCCGGT 62.075 55.000 6.96 0.00 46.60 5.28
1634 4871 1.749258 GGTTTCTCCATGGCCGGTC 60.749 63.158 6.96 0.00 35.97 4.79
1669 4906 1.341852 TGCATGCACTGTGATGCTTTT 59.658 42.857 28.39 2.80 46.28 2.27
1767 5006 4.202212 GGGTGCAAGTTGGTGTTATTTTCT 60.202 41.667 4.75 0.00 0.00 2.52
1773 5012 7.064016 TGCAAGTTGGTGTTATTTTCTGTTTTC 59.936 33.333 4.75 0.00 0.00 2.29
1775 5014 6.859017 AGTTGGTGTTATTTTCTGTTTTCGT 58.141 32.000 0.00 0.00 0.00 3.85
1814 5055 4.332543 TCCATCGTTATCTTGCAATGTCAC 59.667 41.667 0.00 0.00 0.00 3.67
1832 5073 6.801539 TGTCACCATGTTATCACTCTTTTC 57.198 37.500 0.00 0.00 0.00 2.29
1896 5137 8.494016 ACTCATACTTTTAAGATAGCGCTTTT 57.506 30.769 18.68 11.03 0.00 2.27
1901 5142 6.745116 ACTTTTAAGATAGCGCTTTTGGTTT 58.255 32.000 18.68 4.89 0.00 3.27
1918 5159 9.497030 CTTTTGGTTTGGCATTTTAAAAAGTAC 57.503 29.630 4.44 0.00 31.78 2.73
1953 5194 2.551459 CCAAGGTCACAAGAAAGAGCAG 59.449 50.000 0.00 0.00 34.85 4.24
1993 5234 9.295825 TGGAGTTAATTGCTAAAAGAATTCAGA 57.704 29.630 8.44 0.00 0.00 3.27
2035 5276 4.537135 TCGTGTCTTTGCTTTATCCTCT 57.463 40.909 0.00 0.00 0.00 3.69
2036 5277 4.894784 TCGTGTCTTTGCTTTATCCTCTT 58.105 39.130 0.00 0.00 0.00 2.85
2037 5278 5.305585 TCGTGTCTTTGCTTTATCCTCTTT 58.694 37.500 0.00 0.00 0.00 2.52
2038 5279 6.460781 TCGTGTCTTTGCTTTATCCTCTTTA 58.539 36.000 0.00 0.00 0.00 1.85
2039 5280 7.103641 TCGTGTCTTTGCTTTATCCTCTTTAT 58.896 34.615 0.00 0.00 0.00 1.40
2154 5395 0.034337 TTCGGGTGTTGCTAGGTGTC 59.966 55.000 0.00 0.00 0.00 3.67
2188 5439 7.301054 GTCAAGTGACATAACATGGAAGAAAG 58.699 38.462 6.57 0.00 44.18 2.62
2231 5482 6.828502 TCGCATACATTTCACTGTAAGATC 57.171 37.500 0.00 0.00 35.37 2.75
2507 6136 3.562397 GGTCCGCTAACCCAATCAA 57.438 52.632 0.00 0.00 32.82 2.57
2508 6137 1.828979 GGTCCGCTAACCCAATCAAA 58.171 50.000 0.00 0.00 32.82 2.69
2509 6138 1.743394 GGTCCGCTAACCCAATCAAAG 59.257 52.381 0.00 0.00 32.82 2.77
2510 6139 1.743394 GTCCGCTAACCCAATCAAAGG 59.257 52.381 0.00 0.00 0.00 3.11
2511 6140 0.455815 CCGCTAACCCAATCAAAGGC 59.544 55.000 0.00 0.00 0.00 4.35
2512 6141 0.455815 CGCTAACCCAATCAAAGGCC 59.544 55.000 0.00 0.00 0.00 5.19
2513 6142 0.824109 GCTAACCCAATCAAAGGCCC 59.176 55.000 0.00 0.00 0.00 5.80
2514 6143 1.102978 CTAACCCAATCAAAGGCCCG 58.897 55.000 0.00 0.00 0.00 6.13
2515 6144 0.699399 TAACCCAATCAAAGGCCCGA 59.301 50.000 0.00 0.00 0.00 5.14
2516 6145 0.041090 AACCCAATCAAAGGCCCGAT 59.959 50.000 0.00 0.00 0.00 4.18
2517 6146 0.041090 ACCCAATCAAAGGCCCGATT 59.959 50.000 0.00 2.56 32.04 3.34
2518 6147 1.194218 CCCAATCAAAGGCCCGATTT 58.806 50.000 0.00 0.00 29.38 2.17
2519 6148 2.291930 ACCCAATCAAAGGCCCGATTTA 60.292 45.455 0.00 0.00 29.38 1.40
2520 6149 2.763448 CCCAATCAAAGGCCCGATTTAA 59.237 45.455 0.00 0.00 29.38 1.52
2521 6150 3.387699 CCCAATCAAAGGCCCGATTTAAT 59.612 43.478 0.00 0.00 29.38 1.40
2522 6151 4.370917 CCAATCAAAGGCCCGATTTAATG 58.629 43.478 0.00 0.00 29.38 1.90
2523 6152 4.141959 CCAATCAAAGGCCCGATTTAATGT 60.142 41.667 0.00 0.00 29.38 2.71
2524 6153 5.418676 CAATCAAAGGCCCGATTTAATGTT 58.581 37.500 0.00 0.00 29.38 2.71
2525 6154 4.712122 TCAAAGGCCCGATTTAATGTTC 57.288 40.909 0.00 0.00 0.00 3.18
2526 6155 4.340617 TCAAAGGCCCGATTTAATGTTCT 58.659 39.130 0.00 0.00 0.00 3.01
2527 6156 4.157656 TCAAAGGCCCGATTTAATGTTCTG 59.842 41.667 0.00 0.00 0.00 3.02
2528 6157 2.024414 AGGCCCGATTTAATGTTCTGC 58.976 47.619 0.00 0.00 0.00 4.26
2529 6158 1.067060 GGCCCGATTTAATGTTCTGCC 59.933 52.381 0.00 0.00 0.00 4.85
2530 6159 1.748493 GCCCGATTTAATGTTCTGCCA 59.252 47.619 0.00 0.00 0.00 4.92
2531 6160 2.165437 GCCCGATTTAATGTTCTGCCAA 59.835 45.455 0.00 0.00 0.00 4.52
2532 6161 3.181476 GCCCGATTTAATGTTCTGCCAAT 60.181 43.478 0.00 0.00 0.00 3.16
2533 6162 4.610945 CCCGATTTAATGTTCTGCCAATC 58.389 43.478 0.00 0.00 0.00 2.67
2534 6163 4.097741 CCCGATTTAATGTTCTGCCAATCA 59.902 41.667 0.00 0.00 0.00 2.57
2535 6164 5.276270 CCGATTTAATGTTCTGCCAATCAG 58.724 41.667 0.00 0.00 44.21 2.90
2543 6172 3.231734 CTGCCAATCAGAACCGTCA 57.768 52.632 0.00 0.00 45.72 4.35
2544 6173 1.742761 CTGCCAATCAGAACCGTCAT 58.257 50.000 0.00 0.00 45.72 3.06
2545 6174 1.667724 CTGCCAATCAGAACCGTCATC 59.332 52.381 0.00 0.00 45.72 2.92
2546 6175 0.652592 GCCAATCAGAACCGTCATCG 59.347 55.000 0.00 0.00 0.00 3.84
2547 6176 0.652592 CCAATCAGAACCGTCATCGC 59.347 55.000 0.00 0.00 35.54 4.58
2548 6177 0.652592 CAATCAGAACCGTCATCGCC 59.347 55.000 0.00 0.00 35.54 5.54
2549 6178 0.462047 AATCAGAACCGTCATCGCCC 60.462 55.000 0.00 0.00 35.54 6.13
2550 6179 1.613317 ATCAGAACCGTCATCGCCCA 61.613 55.000 0.00 0.00 35.54 5.36
2551 6180 2.100631 CAGAACCGTCATCGCCCAC 61.101 63.158 0.00 0.00 35.54 4.61
2552 6181 2.047655 GAACCGTCATCGCCCACA 60.048 61.111 0.00 0.00 35.54 4.17
2553 6182 1.669760 GAACCGTCATCGCCCACAA 60.670 57.895 0.00 0.00 35.54 3.33
2554 6183 1.228003 AACCGTCATCGCCCACAAA 60.228 52.632 0.00 0.00 35.54 2.83
2555 6184 1.512156 AACCGTCATCGCCCACAAAC 61.512 55.000 0.00 0.00 35.54 2.93
2556 6185 1.671054 CCGTCATCGCCCACAAACT 60.671 57.895 0.00 0.00 35.54 2.66
2557 6186 1.497278 CGTCATCGCCCACAAACTG 59.503 57.895 0.00 0.00 0.00 3.16
2558 6187 1.210155 GTCATCGCCCACAAACTGC 59.790 57.895 0.00 0.00 0.00 4.40
2559 6188 1.971167 TCATCGCCCACAAACTGCC 60.971 57.895 0.00 0.00 0.00 4.85
2560 6189 2.676471 ATCGCCCACAAACTGCCC 60.676 61.111 0.00 0.00 0.00 5.36
2561 6190 4.966787 TCGCCCACAAACTGCCCC 62.967 66.667 0.00 0.00 0.00 5.80
2580 6209 4.803426 CGCACGTCCTGCCTCTCC 62.803 72.222 0.00 0.00 43.84 3.71
2581 6210 3.386237 GCACGTCCTGCCTCTCCT 61.386 66.667 0.00 0.00 40.42 3.69
2582 6211 2.575993 CACGTCCTGCCTCTCCTG 59.424 66.667 0.00 0.00 0.00 3.86
2583 6212 1.979155 CACGTCCTGCCTCTCCTGA 60.979 63.158 0.00 0.00 0.00 3.86
2584 6213 1.000993 ACGTCCTGCCTCTCCTGAT 59.999 57.895 0.00 0.00 0.00 2.90
2585 6214 0.259065 ACGTCCTGCCTCTCCTGATA 59.741 55.000 0.00 0.00 0.00 2.15
2586 6215 0.958091 CGTCCTGCCTCTCCTGATAG 59.042 60.000 0.00 0.00 0.00 2.08
2587 6216 1.477740 CGTCCTGCCTCTCCTGATAGA 60.478 57.143 0.00 0.00 0.00 1.98
2588 6217 1.960689 GTCCTGCCTCTCCTGATAGAC 59.039 57.143 0.00 0.00 0.00 2.59
2589 6218 1.133325 TCCTGCCTCTCCTGATAGACC 60.133 57.143 0.00 0.00 0.00 3.85
2590 6219 0.958091 CTGCCTCTCCTGATAGACCG 59.042 60.000 0.00 0.00 0.00 4.79
2591 6220 0.259065 TGCCTCTCCTGATAGACCGT 59.741 55.000 0.00 0.00 0.00 4.83
2592 6221 1.493446 TGCCTCTCCTGATAGACCGTA 59.507 52.381 0.00 0.00 0.00 4.02
2593 6222 2.156098 GCCTCTCCTGATAGACCGTAG 58.844 57.143 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 6.774656 AGAGAGAAAAATGCTTATATGGGGTG 59.225 38.462 0.00 0.00 0.00 4.61
30 31 6.774656 CAGAGAGAAAAATGCTTATATGGGGT 59.225 38.462 0.00 0.00 0.00 4.95
75 76 6.183360 GGATTTCACTGTTGACCATGGAATAG 60.183 42.308 21.47 13.25 0.00 1.73
104 105 4.393990 CGGAGGGAGTATTTGTTTACAACC 59.606 45.833 0.00 0.00 35.28 3.77
113 114 8.904099 ATATTTAGAAACGGAGGGAGTATTTG 57.096 34.615 0.00 0.00 0.00 2.32
114 115 9.993454 GTATATTTAGAAACGGAGGGAGTATTT 57.007 33.333 0.00 0.00 0.00 1.40
116 117 7.449704 ACGTATATTTAGAAACGGAGGGAGTAT 59.550 37.037 0.00 0.00 39.57 2.12
117 118 6.772716 ACGTATATTTAGAAACGGAGGGAGTA 59.227 38.462 0.00 0.00 39.57 2.59
118 119 5.595952 ACGTATATTTAGAAACGGAGGGAGT 59.404 40.000 0.00 0.00 39.57 3.85
119 120 6.016443 AGACGTATATTTAGAAACGGAGGGAG 60.016 42.308 0.00 0.00 39.57 4.30
120 121 5.829924 AGACGTATATTTAGAAACGGAGGGA 59.170 40.000 0.00 0.00 39.57 4.20
121 122 6.081872 AGACGTATATTTAGAAACGGAGGG 57.918 41.667 0.00 0.00 39.57 4.30
122 123 7.919621 AGAAAGACGTATATTTAGAAACGGAGG 59.080 37.037 0.00 0.00 39.57 4.30
123 124 8.853469 AGAAAGACGTATATTTAGAAACGGAG 57.147 34.615 0.00 0.00 39.57 4.63
137 138 9.840427 CCATTTGAAATGTTTAGAAAGACGTAT 57.160 29.630 15.93 0.00 0.00 3.06
138 139 9.058174 TCCATTTGAAATGTTTAGAAAGACGTA 57.942 29.630 15.93 0.00 0.00 3.57
139 140 7.860872 GTCCATTTGAAATGTTTAGAAAGACGT 59.139 33.333 15.93 0.00 0.00 4.34
140 141 8.076178 AGTCCATTTGAAATGTTTAGAAAGACG 58.924 33.333 15.93 0.00 0.00 4.18
151 152 9.607988 TCGTATATTGTAGTCCATTTGAAATGT 57.392 29.630 15.93 1.43 0.00 2.71
155 156 9.607988 ACATTCGTATATTGTAGTCCATTTGAA 57.392 29.630 0.00 0.00 0.00 2.69
251 252 9.689501 TCCTCCGTTTCCAAATATAAGTATTTT 57.310 29.630 0.00 0.00 38.21 1.82
252 253 9.689501 TTCCTCCGTTTCCAAATATAAGTATTT 57.310 29.630 0.00 0.00 40.31 1.40
253 254 9.338622 CTTCCTCCGTTTCCAAATATAAGTATT 57.661 33.333 0.00 0.00 31.89 1.89
254 255 8.491958 ACTTCCTCCGTTTCCAAATATAAGTAT 58.508 33.333 0.00 0.00 0.00 2.12
255 256 7.854337 ACTTCCTCCGTTTCCAAATATAAGTA 58.146 34.615 0.00 0.00 0.00 2.24
256 257 6.718294 ACTTCCTCCGTTTCCAAATATAAGT 58.282 36.000 0.00 0.00 0.00 2.24
257 258 8.202137 TCTACTTCCTCCGTTTCCAAATATAAG 58.798 37.037 0.00 0.00 0.00 1.73
258 259 8.081517 TCTACTTCCTCCGTTTCCAAATATAA 57.918 34.615 0.00 0.00 0.00 0.98
259 260 7.664552 TCTACTTCCTCCGTTTCCAAATATA 57.335 36.000 0.00 0.00 0.00 0.86
260 261 6.555463 TCTACTTCCTCCGTTTCCAAATAT 57.445 37.500 0.00 0.00 0.00 1.28
261 262 6.070424 ACATCTACTTCCTCCGTTTCCAAATA 60.070 38.462 0.00 0.00 0.00 1.40
262 263 4.903045 TCTACTTCCTCCGTTTCCAAAT 57.097 40.909 0.00 0.00 0.00 2.32
263 264 4.041198 ACATCTACTTCCTCCGTTTCCAAA 59.959 41.667 0.00 0.00 0.00 3.28
264 265 3.581332 ACATCTACTTCCTCCGTTTCCAA 59.419 43.478 0.00 0.00 0.00 3.53
265 266 3.170717 ACATCTACTTCCTCCGTTTCCA 58.829 45.455 0.00 0.00 0.00 3.53
266 267 3.889520 ACATCTACTTCCTCCGTTTCC 57.110 47.619 0.00 0.00 0.00 3.13
267 268 7.845066 ATTTAACATCTACTTCCTCCGTTTC 57.155 36.000 0.00 0.00 0.00 2.78
303 309 2.047296 ACCCTATTCCTTTCCTCAGGGA 59.953 50.000 11.36 0.00 44.71 4.20
310 316 2.807108 CGCAGCTACCCTATTCCTTTCC 60.807 54.545 0.00 0.00 0.00 3.13
350 356 3.307242 CGTCCTCCGAGAAATGTGATTTC 59.693 47.826 0.00 0.00 46.90 2.17
354 360 1.541379 TCGTCCTCCGAGAAATGTGA 58.459 50.000 0.00 0.00 41.60 3.58
366 373 3.802948 TTTGAGCTCCTATTCGTCCTC 57.197 47.619 12.15 0.00 0.00 3.71
396 403 0.523072 CGGGCTTGATGGTGTCTTTG 59.477 55.000 0.00 0.00 0.00 2.77
452 459 5.945191 TGATGTTGTATTTGCAGATTGGAGA 59.055 36.000 0.00 0.00 0.00 3.71
470 477 2.223745 GTGTACGTTGGGGTTGATGTT 58.776 47.619 0.00 0.00 0.00 2.71
480 487 1.001633 AGGCCTACTTGTGTACGTTGG 59.998 52.381 1.29 0.00 0.00 3.77
484 491 2.492484 AGAGAAGGCCTACTTGTGTACG 59.508 50.000 5.16 0.00 40.21 3.67
520 527 3.620488 TCTCTCTCTCTTCTCTGGCTTC 58.380 50.000 0.00 0.00 0.00 3.86
521 528 3.266772 TCTCTCTCTCTCTTCTCTGGCTT 59.733 47.826 0.00 0.00 0.00 4.35
975 982 1.122227 GCTCCATGCTCTTCCTCTCT 58.878 55.000 0.00 0.00 38.95 3.10
976 983 0.106521 GGCTCCATGCTCTTCCTCTC 59.893 60.000 0.00 0.00 42.39 3.20
977 984 1.344191 GGGCTCCATGCTCTTCCTCT 61.344 60.000 0.00 0.00 39.58 3.69
978 985 1.148048 GGGCTCCATGCTCTTCCTC 59.852 63.158 0.00 0.00 39.58 3.71
979 986 2.381941 GGGGCTCCATGCTCTTCCT 61.382 63.158 0.00 0.00 43.07 3.36
1545 4707 0.545548 AAGAGGAGGAGGTGGTGGTC 60.546 60.000 0.00 0.00 0.00 4.02
1599 4761 5.308825 AGAAACCAAGAACGATCAATCACT 58.691 37.500 0.00 0.00 0.00 3.41
1602 4764 4.695455 TGGAGAAACCAAGAACGATCAATC 59.305 41.667 0.00 0.00 46.75 2.67
1603 4765 4.651778 TGGAGAAACCAAGAACGATCAAT 58.348 39.130 0.00 0.00 46.75 2.57
1604 4766 4.079980 TGGAGAAACCAAGAACGATCAA 57.920 40.909 0.00 0.00 46.75 2.57
1605 4767 3.762407 TGGAGAAACCAAGAACGATCA 57.238 42.857 0.00 0.00 46.75 2.92
1616 4778 1.749258 GACCGGCCATGGAGAAACC 60.749 63.158 18.40 5.49 39.54 3.27
1617 4779 1.749258 GGACCGGCCATGGAGAAAC 60.749 63.158 18.40 2.93 36.34 2.78
1618 4780 2.674754 GGACCGGCCATGGAGAAA 59.325 61.111 18.40 0.00 36.34 2.52
1619 4781 3.407967 GGGACCGGCCATGGAGAA 61.408 66.667 18.40 0.00 38.95 2.87
1631 4868 2.350458 ATTGCATGCAACCGGGACC 61.350 57.895 34.10 0.00 38.88 4.46
1632 4869 1.153784 CATTGCATGCAACCGGGAC 60.154 57.895 34.10 0.00 38.88 4.46
1633 4870 3.286407 CATTGCATGCAACCGGGA 58.714 55.556 34.10 12.90 38.88 5.14
1669 4906 5.398603 TTTGGTGCAGAAAAGAAAACAGA 57.601 34.783 0.00 0.00 0.00 3.41
1814 5055 8.971321 CAAAAACAGAAAAGAGTGATAACATGG 58.029 33.333 0.00 0.00 0.00 3.66
1832 5073 3.822735 TGGAGAGAGATTGGCAAAAACAG 59.177 43.478 3.01 0.00 0.00 3.16
1896 5137 8.561738 TTTGTACTTTTTAAAATGCCAAACCA 57.438 26.923 18.34 6.77 0.00 3.67
1918 5159 5.240623 TGTGACCTTGGCAACTAATACTTTG 59.759 40.000 0.00 0.00 37.61 2.77
1953 5194 0.036875 ACTCCAACTTGCACTAGGGC 59.963 55.000 10.98 10.98 0.00 5.19
2038 5279 8.934507 TGTTGAACGGAAATGAAAAGTAAAAT 57.065 26.923 0.00 0.00 0.00 1.82
2039 5280 8.812329 CATGTTGAACGGAAATGAAAAGTAAAA 58.188 29.630 0.00 0.00 0.00 1.52
2128 5369 1.470051 AGCAACACCCGAAAACAGTT 58.530 45.000 0.00 0.00 0.00 3.16
2154 5395 2.492019 TGTCACTTGACTGTCGACTG 57.508 50.000 19.56 19.56 44.99 3.51
2204 5455 7.866729 TCTTACAGTGAAATGTATGCGAAAAA 58.133 30.769 0.00 0.00 35.65 1.94
2205 5456 7.428282 TCTTACAGTGAAATGTATGCGAAAA 57.572 32.000 0.00 0.00 35.65 2.29
2206 5457 7.549134 AGATCTTACAGTGAAATGTATGCGAAA 59.451 33.333 0.00 0.00 35.65 3.46
2207 5458 7.041721 AGATCTTACAGTGAAATGTATGCGAA 58.958 34.615 0.00 0.00 35.65 4.70
2209 5460 6.476706 TGAGATCTTACAGTGAAATGTATGCG 59.523 38.462 0.00 0.00 35.65 4.73
2210 5461 7.515841 CGTGAGATCTTACAGTGAAATGTATGC 60.516 40.741 16.95 0.00 35.65 3.14
2212 5463 7.772166 TCGTGAGATCTTACAGTGAAATGTAT 58.228 34.615 16.95 0.00 33.31 2.29
2214 5465 6.025749 TCGTGAGATCTTACAGTGAAATGT 57.974 37.500 16.95 0.00 34.12 2.71
2215 5466 6.951256 TTCGTGAGATCTTACAGTGAAATG 57.049 37.500 16.95 0.00 41.60 2.32
2217 5468 9.952188 CTATATTCGTGAGATCTTACAGTGAAA 57.048 33.333 16.95 4.26 41.60 2.69
2218 5469 9.121658 ACTATATTCGTGAGATCTTACAGTGAA 57.878 33.333 16.95 12.19 41.60 3.18
2219 5470 8.678593 ACTATATTCGTGAGATCTTACAGTGA 57.321 34.615 16.95 4.34 41.60 3.41
2222 5473 9.909043 CGATACTATATTCGTGAGATCTTACAG 57.091 37.037 16.95 9.98 41.60 2.74
2290 5541 6.506538 AGAGGTAGGATTTGCTCATATGTT 57.493 37.500 1.90 0.00 0.00 2.71
2489 6118 1.743394 CTTTGATTGGGTTAGCGGACC 59.257 52.381 3.21 3.21 39.04 4.46
2490 6119 1.743394 CCTTTGATTGGGTTAGCGGAC 59.257 52.381 0.00 0.00 0.00 4.79
2491 6120 1.953311 GCCTTTGATTGGGTTAGCGGA 60.953 52.381 0.00 0.00 0.00 5.54
2492 6121 0.455815 GCCTTTGATTGGGTTAGCGG 59.544 55.000 0.00 0.00 0.00 5.52
2493 6122 0.455815 GGCCTTTGATTGGGTTAGCG 59.544 55.000 0.00 0.00 0.00 4.26
2494 6123 0.824109 GGGCCTTTGATTGGGTTAGC 59.176 55.000 0.84 0.00 0.00 3.09
2495 6124 1.102978 CGGGCCTTTGATTGGGTTAG 58.897 55.000 0.84 0.00 0.00 2.34
2496 6125 0.699399 TCGGGCCTTTGATTGGGTTA 59.301 50.000 0.84 0.00 0.00 2.85
2497 6126 0.041090 ATCGGGCCTTTGATTGGGTT 59.959 50.000 0.84 0.00 0.00 4.11
2498 6127 0.041090 AATCGGGCCTTTGATTGGGT 59.959 50.000 14.76 0.00 33.72 4.51
2499 6128 1.194218 AAATCGGGCCTTTGATTGGG 58.806 50.000 15.79 0.00 35.13 4.12
2500 6129 4.141959 ACATTAAATCGGGCCTTTGATTGG 60.142 41.667 15.79 10.26 35.13 3.16
2501 6130 5.009854 ACATTAAATCGGGCCTTTGATTG 57.990 39.130 15.79 9.04 35.13 2.67
2502 6131 5.422012 AGAACATTAAATCGGGCCTTTGATT 59.578 36.000 0.84 7.65 36.41 2.57
2503 6132 4.956075 AGAACATTAAATCGGGCCTTTGAT 59.044 37.500 0.84 0.70 0.00 2.57
2504 6133 4.157656 CAGAACATTAAATCGGGCCTTTGA 59.842 41.667 0.84 0.00 0.00 2.69
2505 6134 4.423732 CAGAACATTAAATCGGGCCTTTG 58.576 43.478 0.84 0.00 0.00 2.77
2506 6135 3.119137 GCAGAACATTAAATCGGGCCTTT 60.119 43.478 0.84 0.00 0.00 3.11
2507 6136 2.427095 GCAGAACATTAAATCGGGCCTT 59.573 45.455 0.84 0.00 0.00 4.35
2508 6137 2.024414 GCAGAACATTAAATCGGGCCT 58.976 47.619 0.84 0.00 0.00 5.19
2509 6138 1.067060 GGCAGAACATTAAATCGGGCC 59.933 52.381 0.00 0.00 35.07 5.80
2510 6139 1.748493 TGGCAGAACATTAAATCGGGC 59.252 47.619 6.20 6.20 36.96 6.13
2511 6140 4.097741 TGATTGGCAGAACATTAAATCGGG 59.902 41.667 0.00 0.00 0.00 5.14
2512 6141 5.247507 TGATTGGCAGAACATTAAATCGG 57.752 39.130 0.00 0.00 0.00 4.18
2525 6154 1.667724 GATGACGGTTCTGATTGGCAG 59.332 52.381 0.00 0.00 46.31 4.85
2526 6155 1.737838 GATGACGGTTCTGATTGGCA 58.262 50.000 0.00 0.00 0.00 4.92
2527 6156 0.652592 CGATGACGGTTCTGATTGGC 59.347 55.000 0.00 0.00 35.72 4.52
2528 6157 0.652592 GCGATGACGGTTCTGATTGG 59.347 55.000 0.00 0.00 40.15 3.16
2529 6158 0.652592 GGCGATGACGGTTCTGATTG 59.347 55.000 0.00 0.00 40.15 2.67
2530 6159 0.462047 GGGCGATGACGGTTCTGATT 60.462 55.000 0.00 0.00 40.15 2.57
2531 6160 1.144057 GGGCGATGACGGTTCTGAT 59.856 57.895 0.00 0.00 40.15 2.90
2532 6161 2.279810 TGGGCGATGACGGTTCTGA 61.280 57.895 0.00 0.00 40.15 3.27
2533 6162 2.100631 GTGGGCGATGACGGTTCTG 61.101 63.158 0.00 0.00 40.15 3.02
2534 6163 2.107041 TTGTGGGCGATGACGGTTCT 62.107 55.000 0.00 0.00 40.15 3.01
2535 6164 1.231958 TTTGTGGGCGATGACGGTTC 61.232 55.000 0.00 0.00 40.15 3.62
2536 6165 1.228003 TTTGTGGGCGATGACGGTT 60.228 52.632 0.00 0.00 40.15 4.44
2537 6166 1.964373 GTTTGTGGGCGATGACGGT 60.964 57.895 0.00 0.00 40.15 4.83
2538 6167 1.671054 AGTTTGTGGGCGATGACGG 60.671 57.895 0.00 0.00 40.15 4.79
2539 6168 1.497278 CAGTTTGTGGGCGATGACG 59.503 57.895 0.00 0.00 42.93 4.35
2540 6169 1.210155 GCAGTTTGTGGGCGATGAC 59.790 57.895 0.00 0.00 0.00 3.06
2541 6170 1.971167 GGCAGTTTGTGGGCGATGA 60.971 57.895 0.00 0.00 0.00 2.92
2542 6171 2.568090 GGCAGTTTGTGGGCGATG 59.432 61.111 0.00 0.00 0.00 3.84
2543 6172 2.676471 GGGCAGTTTGTGGGCGAT 60.676 61.111 0.00 0.00 0.00 4.58
2544 6173 4.966787 GGGGCAGTTTGTGGGCGA 62.967 66.667 0.00 0.00 0.00 5.54
2565 6194 1.326213 ATCAGGAGAGGCAGGACGTG 61.326 60.000 0.00 0.00 0.00 4.49
2566 6195 0.259065 TATCAGGAGAGGCAGGACGT 59.741 55.000 0.00 0.00 0.00 4.34
2567 6196 0.958091 CTATCAGGAGAGGCAGGACG 59.042 60.000 0.00 0.00 0.00 4.79
2568 6197 1.960689 GTCTATCAGGAGAGGCAGGAC 59.039 57.143 0.00 0.00 0.00 3.85
2569 6198 1.133325 GGTCTATCAGGAGAGGCAGGA 60.133 57.143 0.00 0.00 0.00 3.86
2570 6199 1.337118 GGTCTATCAGGAGAGGCAGG 58.663 60.000 0.00 0.00 0.00 4.85
2571 6200 0.958091 CGGTCTATCAGGAGAGGCAG 59.042 60.000 0.00 0.00 0.00 4.85
2572 6201 0.259065 ACGGTCTATCAGGAGAGGCA 59.741 55.000 0.00 0.00 0.00 4.75
2573 6202 2.156098 CTACGGTCTATCAGGAGAGGC 58.844 57.143 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.