Multiple sequence alignment - TraesCS6B01G130200

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 TraesCS6B01G130200 chr6B 100.000 3185 0 0 1 3185 126719286 126716102 0.000000e+00 5882
1 TraesCS6B01G130200 chr2D 82.028 3244 496 56 1 3182 387059466 387056248 0.000000e+00 2680
2 TraesCS6B01G130200 chr2D 80.895 3219 530 49 5 3165 215773839 215777030 0.000000e+00 2459
3 TraesCS6B01G130200 chr2D 79.874 3170 566 51 1 3142 378125196 378128321 0.000000e+00 2254
4 TraesCS6B01G130200 chr2D 81.612 794 92 34 2403 3150 245356522 245357307 2.720000e-170 608
5 TraesCS6B01G130200 chr6D 81.406 3200 508 50 1 3146 297037786 297040952 0.000000e+00 2532
6 TraesCS6B01G130200 chr6D 80.573 3248 536 71 1 3184 142733858 142730642 0.000000e+00 2414
7 TraesCS6B01G130200 chr6D 82.671 554 83 11 2590 3140 427436026 427435483 2.220000e-131 479
8 TraesCS6B01G130200 chr4D 80.622 3215 528 65 1 3163 101449725 101452896 0.000000e+00 2398
9 TraesCS6B01G130200 chr4D 80.524 3204 549 58 3 3150 383909885 383913069 0.000000e+00 2390
10 TraesCS6B01G130200 chr4D 80.364 3244 543 59 3 3184 65218537 65215326 0.000000e+00 2375
11 TraesCS6B01G130200 chr4D 84.296 554 74 12 2590 3140 300203666 300203123 2.180000e-146 529
12 TraesCS6B01G130200 chr7D 79.809 3249 549 69 1 3183 472527193 472530400 0.000000e+00 2266
13 TraesCS6B01G130200 chr7D 83.307 629 76 23 2573 3184 124715222 124715838 1.290000e-153 553
14 TraesCS6B01G130200 chr5A 79.213 3175 569 67 3 3136 227267593 227264469 0.000000e+00 2122
15 TraesCS6B01G130200 chr5A 81.255 2534 449 26 2 2526 213801480 213803996 0.000000e+00 2025
16 TraesCS6B01G130200 chr5A 79.534 987 191 10 1 981 452013265 452012284 0.000000e+00 693
17 TraesCS6B01G130200 chr3D 79.193 3172 568 58 1 3136 269250516 269247401 0.000000e+00 2117
18 TraesCS6B01G130200 chr3D 83.459 532 68 9 2669 3185 28097061 28096535 7.990000e-131 477
19 TraesCS6B01G130200 chr6A 78.863 3255 578 88 1 3184 122340687 122337472 0.000000e+00 2098
20 TraesCS6B01G130200 chr2A 78.428 3231 605 72 1 3183 165671826 165675012 0.000000e+00 2021
21 TraesCS6B01G130200 chr7A 78.384 3243 598 67 1 3183 463127105 463130304 0.000000e+00 2010
22 TraesCS6B01G130200 chr7A 81.722 569 85 18 2624 3184 136232816 136233373 1.040000e-124 457
23 TraesCS6B01G130200 chr1A 81.010 2554 440 36 1 2531 368961879 368959348 0.000000e+00 1988
24 TraesCS6B01G130200 chr5D 80.757 2193 350 45 1042 3183 286090493 286092664 0.000000e+00 1646


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 TraesCS6B01G130200 chr6B 126716102 126719286 3184 True 5882 5882 100.000 1 3185 1 chr6B.!!$R1 3184
1 TraesCS6B01G130200 chr2D 387056248 387059466 3218 True 2680 2680 82.028 1 3182 1 chr2D.!!$R1 3181
2 TraesCS6B01G130200 chr2D 215773839 215777030 3191 False 2459 2459 80.895 5 3165 1 chr2D.!!$F1 3160
3 TraesCS6B01G130200 chr2D 378125196 378128321 3125 False 2254 2254 79.874 1 3142 1 chr2D.!!$F3 3141
4 TraesCS6B01G130200 chr2D 245356522 245357307 785 False 608 608 81.612 2403 3150 1 chr2D.!!$F2 747
5 TraesCS6B01G130200 chr6D 297037786 297040952 3166 False 2532 2532 81.406 1 3146 1 chr6D.!!$F1 3145
6 TraesCS6B01G130200 chr6D 142730642 142733858 3216 True 2414 2414 80.573 1 3184 1 chr6D.!!$R1 3183
7 TraesCS6B01G130200 chr6D 427435483 427436026 543 True 479 479 82.671 2590 3140 1 chr6D.!!$R2 550
8 TraesCS6B01G130200 chr4D 101449725 101452896 3171 False 2398 2398 80.622 1 3163 1 chr4D.!!$F1 3162
9 TraesCS6B01G130200 chr4D 383909885 383913069 3184 False 2390 2390 80.524 3 3150 1 chr4D.!!$F2 3147
10 TraesCS6B01G130200 chr4D 65215326 65218537 3211 True 2375 2375 80.364 3 3184 1 chr4D.!!$R1 3181
11 TraesCS6B01G130200 chr4D 300203123 300203666 543 True 529 529 84.296 2590 3140 1 chr4D.!!$R2 550
12 TraesCS6B01G130200 chr7D 472527193 472530400 3207 False 2266 2266 79.809 1 3183 1 chr7D.!!$F2 3182
13 TraesCS6B01G130200 chr7D 124715222 124715838 616 False 553 553 83.307 2573 3184 1 chr7D.!!$F1 611
14 TraesCS6B01G130200 chr5A 227264469 227267593 3124 True 2122 2122 79.213 3 3136 1 chr5A.!!$R1 3133
15 TraesCS6B01G130200 chr5A 213801480 213803996 2516 False 2025 2025 81.255 2 2526 1 chr5A.!!$F1 2524
16 TraesCS6B01G130200 chr5A 452012284 452013265 981 True 693 693 79.534 1 981 1 chr5A.!!$R2 980
17 TraesCS6B01G130200 chr3D 269247401 269250516 3115 True 2117 2117 79.193 1 3136 1 chr3D.!!$R2 3135
18 TraesCS6B01G130200 chr3D 28096535 28097061 526 True 477 477 83.459 2669 3185 1 chr3D.!!$R1 516
19 TraesCS6B01G130200 chr6A 122337472 122340687 3215 True 2098 2098 78.863 1 3184 1 chr6A.!!$R1 3183
20 TraesCS6B01G130200 chr2A 165671826 165675012 3186 False 2021 2021 78.428 1 3183 1 chr2A.!!$F1 3182
21 TraesCS6B01G130200 chr7A 463127105 463130304 3199 False 2010 2010 78.384 1 3183 1 chr7A.!!$F2 3182
22 TraesCS6B01G130200 chr7A 136232816 136233373 557 False 457 457 81.722 2624 3184 1 chr7A.!!$F1 560
23 TraesCS6B01G130200 chr1A 368959348 368961879 2531 True 1988 1988 81.010 1 2531 1 chr1A.!!$R1 2530
24 TraesCS6B01G130200 chr5D 286090493 286092664 2171 False 1646 1646 80.757 1042 3183 1 chr5D.!!$F1 2141

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
277 287 0.317479 GGTAGAATATCCACGGCGCT 59.683 55.0 6.9 0.0 0.0 5.92 F
1011 1030 0.032815 TCGTGTCCATGTGCGAGAAA 59.967 50.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1764 1805 0.108585 GCCACTCTCCACTTTCACCA 59.891 55.0 0.00 0.0 0.00 4.17 R
2802 2974 0.027716 CGGACCGACTGATAGACGTG 59.972 60.0 8.64 0.0 31.81 4.49 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
103 104 2.548480 GGTTCAAGGTTCGAGTGAAAGG 59.452 50.000 4.98 0.00 35.46 3.11
108 109 0.673956 GGTTCGAGTGAAAGGGGAGC 60.674 60.000 0.00 0.00 35.46 4.70
127 128 1.914634 CTGAAGATGGTTCCGACTCG 58.085 55.000 0.00 0.00 0.00 4.18
131 132 2.586258 AGATGGTTCCGACTCGATTG 57.414 50.000 0.00 0.00 0.00 2.67
134 135 3.446161 AGATGGTTCCGACTCGATTGTTA 59.554 43.478 0.00 0.00 0.00 2.41
144 145 1.927174 CTCGATTGTTAGTGCTTCGGG 59.073 52.381 0.00 0.00 0.00 5.14
161 163 2.303022 TCGGGAGCATCTTATTGGGATC 59.697 50.000 0.00 0.00 33.73 3.36
174 176 1.224592 GGGATCGGTGAACCATGCT 59.775 57.895 0.00 0.00 35.14 3.79
207 212 5.305585 ACTTCTTTTTCAGTCGCCTTGATA 58.694 37.500 0.00 0.00 0.00 2.15
240 247 3.575630 TGTCGAGTGAGTTTGCTGATAC 58.424 45.455 0.00 0.00 0.00 2.24
244 251 2.600867 GAGTGAGTTTGCTGATACGCTC 59.399 50.000 0.00 0.00 0.00 5.03
252 260 0.875908 GCTGATACGCTCCGAATGCA 60.876 55.000 0.00 0.00 0.00 3.96
256 265 2.224042 TGATACGCTCCGAATGCAGATT 60.224 45.455 0.00 0.00 0.00 2.40
262 271 2.289002 GCTCCGAATGCAGATTTGGTAG 59.711 50.000 6.27 4.57 42.17 3.18
265 274 4.780815 TCCGAATGCAGATTTGGTAGAAT 58.219 39.130 6.27 0.00 42.17 2.40
270 280 6.427853 CGAATGCAGATTTGGTAGAATATCCA 59.572 38.462 0.00 0.00 0.00 3.41
277 287 0.317479 GGTAGAATATCCACGGCGCT 59.683 55.000 6.90 0.00 0.00 5.92
282 292 1.732259 GAATATCCACGGCGCTATTGG 59.268 52.381 6.90 11.76 0.00 3.16
290 300 2.711924 GCGCTATTGGCTGCACTC 59.288 61.111 0.00 0.00 39.15 3.51
367 378 0.374758 CACAGCGAATGGAACGGATG 59.625 55.000 0.00 0.00 0.00 3.51
374 385 0.911769 AATGGAACGGATGAGGCAGA 59.088 50.000 0.00 0.00 0.00 4.26
375 386 1.135094 ATGGAACGGATGAGGCAGAT 58.865 50.000 0.00 0.00 0.00 2.90
419 430 4.728102 TTGCCACGTACCGAGCGG 62.728 66.667 7.48 7.48 42.03 5.52
446 457 2.213499 GCTACGGGATTTGACAGGATG 58.787 52.381 0.00 0.00 46.00 3.51
477 488 1.587054 CAGTCAGTCACTCGGGGAC 59.413 63.158 0.00 0.00 30.26 4.46
492 503 3.652581 GGACCAGGCCCATATAAGC 57.347 57.895 0.00 0.00 0.00 3.09
560 572 0.543883 TCCTCTGCTTCTCCACTGCT 60.544 55.000 0.00 0.00 0.00 4.24
640 652 1.275291 GACAAGATGACGACCCTGGAA 59.725 52.381 0.00 0.00 0.00 3.53
691 703 1.382692 GCAAGAAGATGAGCCAGGGC 61.383 60.000 0.97 0.97 42.33 5.19
781 794 3.127791 AGGATGACCTGGAAGATCTGT 57.872 47.619 0.00 0.00 45.92 3.41
812 826 1.480954 GCTGATTCCTCACGGTTCCTA 59.519 52.381 0.00 0.00 0.00 2.94
822 836 2.189784 GGTTCCTAGCGGCTTCCC 59.810 66.667 8.26 0.00 0.00 3.97
832 846 2.971452 GGCTTCCCGAGAACGAGT 59.029 61.111 0.00 0.00 42.66 4.18
868 882 1.979693 GAGGGTGAGTGCGTCCTCT 60.980 63.158 0.00 0.00 41.76 3.69
870 884 1.374758 GGGTGAGTGCGTCCTCTTG 60.375 63.158 5.32 0.00 32.50 3.02
981 1000 4.040047 TCTCTCCCAACACCATCACATAT 58.960 43.478 0.00 0.00 0.00 1.78
986 1005 4.018506 TCCCAACACCATCACATATCTTGT 60.019 41.667 0.00 0.00 39.91 3.16
989 1008 5.183713 CCAACACCATCACATATCTTGTTGT 59.816 40.000 9.88 0.00 40.34 3.32
1011 1030 0.032815 TCGTGTCCATGTGCGAGAAA 59.967 50.000 0.00 0.00 0.00 2.52
1023 1042 0.940833 GCGAGAAATTCCTAGGCTGC 59.059 55.000 2.96 0.00 0.00 5.25
1029 1048 1.984288 AATTCCTAGGCTGCCGACCC 61.984 60.000 13.96 0.00 0.00 4.46
1077 1097 2.031157 CACTTGTCGTTCCCAATTGGTC 60.031 50.000 22.91 11.72 34.77 4.02
1108 1128 0.252197 TCCGAGTGATGAGAGGACGA 59.748 55.000 0.00 0.00 0.00 4.20
1119 1139 2.035632 GAGAGGACGAAGGTGATCCAT 58.964 52.381 0.00 0.00 34.73 3.41
1152 1173 1.557681 TAGGGATCCAGATGAGGGGA 58.442 55.000 15.23 0.00 37.64 4.81
1182 1203 0.988145 TCCCCGCCATGATTCTTCCT 60.988 55.000 0.00 0.00 0.00 3.36
1188 1209 3.474600 CGCCATGATTCTTCCTGATTCT 58.525 45.455 0.00 0.00 0.00 2.40
1207 1228 3.006728 TTAGGGGGTGGCAGTCGG 61.007 66.667 0.00 0.00 0.00 4.79
1274 1295 3.149981 GCCTCCCACCATTTTCTATAGC 58.850 50.000 0.00 0.00 0.00 2.97
1284 1305 4.500887 CCATTTTCTATAGCCCGAGTCGAA 60.501 45.833 15.64 0.00 0.00 3.71
1291 1312 2.101233 GCCCGAGTCGAAAAGCCTC 61.101 63.158 15.64 0.00 0.00 4.70
1293 1314 1.292223 CCGAGTCGAAAAGCCTCCA 59.708 57.895 15.64 0.00 0.00 3.86
1294 1315 0.320421 CCGAGTCGAAAAGCCTCCAA 60.320 55.000 15.64 0.00 0.00 3.53
1319 1340 1.831652 AAAGTGACCCCGGCTGAGAG 61.832 60.000 0.00 0.00 0.00 3.20
1338 1359 4.809193 AGAGAGTGGAGGTGAATATGCTA 58.191 43.478 0.00 0.00 0.00 3.49
1344 1365 3.318275 TGGAGGTGAATATGCTAGTCGAC 59.682 47.826 7.70 7.70 0.00 4.20
1371 1392 2.401766 CCAGCTTGTCCATGACGGC 61.402 63.158 0.00 0.25 34.95 5.68
1410 1431 3.005472 TGTTAGAGGTGTTTCTCAGACGG 59.995 47.826 0.00 0.00 36.30 4.79
1416 1437 2.334838 GTGTTTCTCAGACGGCGTATT 58.665 47.619 14.74 0.48 0.00 1.89
1422 1443 0.892755 TCAGACGGCGTATTCAACCT 59.107 50.000 14.74 0.00 0.00 3.50
1461 1482 1.545428 CCCATGTGGATGTATTCGGGG 60.545 57.143 0.00 0.00 37.39 5.73
1479 1500 2.289444 GGGGATTGAAGACAACACTCGA 60.289 50.000 0.00 0.00 38.90 4.04
1525 1546 2.203139 CGGTGGTGCAGTGGTTGA 60.203 61.111 0.00 0.00 0.00 3.18
1536 1557 4.076394 TGCAGTGGTTGAAAGGTATTACC 58.924 43.478 4.57 4.57 38.99 2.85
1574 1595 1.289530 CAGGGGGTCTAGGAGAGTTCT 59.710 57.143 0.00 0.00 0.00 3.01
1601 1622 2.117941 GACAGCACCAACGAACCAGC 62.118 60.000 0.00 0.00 0.00 4.85
1614 1635 0.846693 AACCAGCCAAGGTCTGACTT 59.153 50.000 7.85 0.00 42.25 3.01
1669 1692 2.754946 TAGCTTCCGAAACCGATTGT 57.245 45.000 0.00 0.00 0.00 2.71
1670 1693 1.439679 AGCTTCCGAAACCGATTGTC 58.560 50.000 0.00 0.00 0.00 3.18
1673 1696 2.933906 GCTTCCGAAACCGATTGTCATA 59.066 45.455 0.00 0.00 0.00 2.15
1689 1712 2.162608 GTCATACACTCGACTCTGTGCT 59.837 50.000 2.69 0.00 37.68 4.40
1740 1769 0.035881 CCAACAGAGAGCAGGAGCAA 59.964 55.000 0.00 0.00 45.49 3.91
1746 1775 0.740516 GAGAGCAGGAGCAAGAGCAC 60.741 60.000 0.00 0.00 45.49 4.40
1764 1805 2.363147 GAGGGAGAGGCGAGTGGT 60.363 66.667 0.00 0.00 0.00 4.16
1776 1817 0.105964 CGAGTGGTGGTGAAAGTGGA 59.894 55.000 0.00 0.00 0.00 4.02
1813 1856 1.745864 GGAGAGGACGACGAGAGCA 60.746 63.158 0.00 0.00 0.00 4.26
1832 1875 2.548920 GCAAAGACTCTAGCAGTGGTGT 60.549 50.000 4.76 0.00 34.41 4.16
1861 1904 4.200283 CTCCACCTCGCTCGGAGC 62.200 72.222 19.92 19.92 39.95 4.70
1877 1920 3.353836 GCGGCGCTCCAAACTGAA 61.354 61.111 26.86 0.00 0.00 3.02
1887 1930 0.523072 CCAAACTGAAGCATGACCCG 59.477 55.000 0.00 0.00 0.00 5.28
1893 1936 0.955428 TGAAGCATGACCCGACAAGC 60.955 55.000 0.00 0.00 35.19 4.01
1897 1940 1.079819 CATGACCCGACAAGCGTCT 60.080 57.895 0.00 0.00 40.23 4.18
1926 1969 0.761323 TGGTTCCTCCGACTGGACAA 60.761 55.000 0.00 0.00 40.17 3.18
1947 1990 3.894547 TTCCAAGCGCCCTCGAACC 62.895 63.158 2.29 0.00 38.10 3.62
1956 1999 1.258445 GCCCTCGAACCTCTTCTCCA 61.258 60.000 0.00 0.00 0.00 3.86
1962 2005 0.687354 GAACCTCTTCTCCAGTGCCA 59.313 55.000 0.00 0.00 0.00 4.92
1964 2007 1.140312 ACCTCTTCTCCAGTGCCAAA 58.860 50.000 0.00 0.00 0.00 3.28
1996 2039 1.982073 GAAGCATCCCAAAGTCGCGG 61.982 60.000 6.13 0.00 0.00 6.46
2009 2052 3.041940 CGCGGCGTCAAAACCTCT 61.042 61.111 15.36 0.00 0.00 3.69
2044 2087 2.968675 AGATTAAAGTGAACGTCCCCG 58.031 47.619 0.00 0.00 40.83 5.73
2071 2114 3.355378 TCTGGGTAATCATTGTGCTTGG 58.645 45.455 0.00 0.00 0.00 3.61
2077 2120 5.402398 GGTAATCATTGTGCTTGGTTTCTC 58.598 41.667 0.00 0.00 0.00 2.87
2078 2121 5.048083 GGTAATCATTGTGCTTGGTTTCTCA 60.048 40.000 0.00 0.00 0.00 3.27
2083 2126 5.754406 TCATTGTGCTTGGTTTCTCAATTTG 59.246 36.000 0.00 0.00 0.00 2.32
2087 2132 4.268405 GTGCTTGGTTTCTCAATTTGTGTG 59.732 41.667 0.00 0.00 0.00 3.82
2098 2143 6.728200 TCTCAATTTGTGTGTGACTTGATTC 58.272 36.000 0.00 0.00 0.00 2.52
2104 2149 4.269183 TGTGTGTGACTTGATTCTTGGTT 58.731 39.130 0.00 0.00 0.00 3.67
2115 2160 6.774656 ACTTGATTCTTGGTTGATTCACTTCT 59.225 34.615 0.00 0.00 0.00 2.85
2170 2216 0.979665 CTGCTTCCTCTGGGACTTCA 59.020 55.000 0.00 0.00 42.05 3.02
2206 2255 7.133133 TGATGATGATGAAGAGATGGAAGAA 57.867 36.000 0.00 0.00 0.00 2.52
2224 2273 3.131396 AGAAGCAGTTACTTCCAACACG 58.869 45.455 0.83 0.00 45.95 4.49
2239 2288 3.191791 CCAACACGGGGTATAACTTTTGG 59.808 47.826 0.00 0.00 0.00 3.28
2242 2291 2.422127 CACGGGGTATAACTTTTGGCAG 59.578 50.000 0.00 0.00 0.00 4.85
2264 2313 3.063588 GCTTGCCTTTACTTTACTAGCCG 59.936 47.826 0.00 0.00 0.00 5.52
2268 2317 5.065235 TGCCTTTACTTTACTAGCCGTTTT 58.935 37.500 0.00 0.00 0.00 2.43
2299 2349 6.567701 GCCAACTGAACTTTTGTGATCGATTA 60.568 38.462 0.00 0.00 0.00 1.75
2300 2350 7.017645 CCAACTGAACTTTTGTGATCGATTAG 58.982 38.462 0.00 0.00 0.00 1.73
2315 2365 0.035056 ATTAGTTTGCAGCTCCGCCT 60.035 50.000 0.00 0.00 0.00 5.52
2327 2377 1.599542 GCTCCGCCTCATGTTATTGAC 59.400 52.381 0.00 0.00 0.00 3.18
2333 2383 2.614057 GCCTCATGTTATTGACCTTCCG 59.386 50.000 0.00 0.00 0.00 4.30
2350 2403 4.445453 CTTCCGGATGACAATGAAGATGA 58.555 43.478 11.88 0.00 35.56 2.92
2351 2404 4.486125 TCCGGATGACAATGAAGATGAA 57.514 40.909 0.00 0.00 0.00 2.57
2370 2423 2.414250 ACCACAAAAACCCATGGGAT 57.586 45.000 38.07 24.35 36.47 3.85
2384 2437 2.190578 GGATGAAGGGGCAGGACG 59.809 66.667 0.00 0.00 0.00 4.79
2446 2499 0.600255 CCGGTGACAGAACCAGTGAC 60.600 60.000 0.00 0.00 40.53 3.67
2492 2545 2.415491 GGCTTCCGTTACTTTTGCCATC 60.415 50.000 0.00 0.00 38.79 3.51
2567 2737 4.043200 GCTGCGACTGGTTTGCCC 62.043 66.667 0.00 0.00 0.00 5.36
2570 2740 3.423154 GCGACTGGTTTGCCCTCG 61.423 66.667 0.00 0.00 37.15 4.63
2583 2753 1.073199 CCCTCGCCACTTTTCACCT 59.927 57.895 0.00 0.00 0.00 4.00
2587 2757 2.325082 CGCCACTTTTCACCTCCCG 61.325 63.158 0.00 0.00 0.00 5.14
2612 2782 1.089978 TCCCAGAGGACCAAGTAGGA 58.910 55.000 0.00 0.00 42.07 2.94
2622 2792 1.144913 ACCAAGTAGGAGCTGCCAAAA 59.855 47.619 0.00 0.00 41.22 2.44
2761 2931 3.126831 CGACTGATCCATTAGCTTGACC 58.873 50.000 0.00 0.00 0.00 4.02
2784 2954 6.330250 ACCCTTGTTCTGTTAGGATATGCTAT 59.670 38.462 4.64 0.00 0.00 2.97
2794 2964 9.237187 CTGTTAGGATATGCTATCTGAAGACTA 57.763 37.037 4.64 0.00 0.00 2.59
2802 2974 6.668541 TGCTATCTGAAGACTATTTGTTGC 57.331 37.500 0.00 0.00 0.00 4.17
2803 2975 6.172630 TGCTATCTGAAGACTATTTGTTGCA 58.827 36.000 0.00 0.00 0.00 4.08
2805 2977 4.990543 TCTGAAGACTATTTGTTGCACG 57.009 40.909 0.00 0.00 0.00 5.34
2811 2983 6.310467 TGAAGACTATTTGTTGCACGTCTATC 59.690 38.462 0.00 0.00 32.02 2.08
2812 2984 5.720202 AGACTATTTGTTGCACGTCTATCA 58.280 37.500 0.00 0.00 30.65 2.15
2816 2988 1.977188 TGTTGCACGTCTATCAGTCG 58.023 50.000 0.00 0.00 33.19 4.18
2823 2995 0.027716 CGTCTATCAGTCGGTCCGTG 59.972 60.000 11.88 3.08 0.00 4.94
2832 3004 0.949105 GTCGGTCCGTGTCTTGCATT 60.949 55.000 11.88 0.00 0.00 3.56
2838 3010 1.795872 TCCGTGTCTTGCATTTGTACG 59.204 47.619 0.00 0.00 0.00 3.67
2840 3012 1.194547 CGTGTCTTGCATTTGTACGCT 59.805 47.619 0.00 0.00 0.00 5.07
2854 3026 0.466543 TACGCTCACTGGGTGTGTTT 59.533 50.000 5.30 0.00 46.27 2.83
2855 3027 0.393808 ACGCTCACTGGGTGTGTTTT 60.394 50.000 0.00 0.00 46.27 2.43
2863 3036 6.531503 TCACTGGGTGTGTTTTAATTTTCA 57.468 33.333 0.00 0.00 46.27 2.69
2993 3181 2.481276 GCGGGGGTCTTGATAAAAATGC 60.481 50.000 0.00 0.00 0.00 3.56
3002 3190 7.095229 GGGTCTTGATAAAAATGCCTTGTTTTC 60.095 37.037 0.00 0.00 0.00 2.29
3142 3331 6.072673 GGTTGTGGTCTAAGAATAACTGTTGG 60.073 42.308 2.69 0.00 0.00 3.77
3155 3344 6.867662 ATAACTGTTGGTTCTCTTCTGTTG 57.132 37.500 2.69 0.00 39.17 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 0.462759 CGGAACCATCTTCAGCTCCC 60.463 60.000 0.00 0.00 0.00 4.30
108 109 1.472878 TCGAGTCGGAACCATCTTCAG 59.527 52.381 13.54 0.00 0.00 3.02
144 145 3.070018 CACCGATCCCAATAAGATGCTC 58.930 50.000 0.00 0.00 0.00 4.26
150 151 3.275617 TGGTTCACCGATCCCAATAAG 57.724 47.619 0.00 0.00 39.43 1.73
154 155 0.679640 GCATGGTTCACCGATCCCAA 60.680 55.000 0.00 0.00 39.43 4.12
156 157 0.468226 TAGCATGGTTCACCGATCCC 59.532 55.000 1.12 0.00 39.43 3.85
161 163 0.391661 AGCTGTAGCATGGTTCACCG 60.392 55.000 1.12 0.00 45.16 4.94
174 176 5.357257 ACTGAAAAAGAAGTCGAAGCTGTA 58.643 37.500 0.00 0.00 0.00 2.74
207 212 2.492088 TCACTCGACAATCTCGGAATGT 59.508 45.455 0.00 0.00 43.16 2.71
229 234 1.355971 TTCGGAGCGTATCAGCAAAC 58.644 50.000 0.00 0.00 40.15 2.93
240 247 0.028505 CCAAATCTGCATTCGGAGCG 59.971 55.000 0.00 0.00 33.85 5.03
244 251 6.128172 GGATATTCTACCAAATCTGCATTCGG 60.128 42.308 0.00 0.00 0.00 4.30
252 260 4.642429 GCCGTGGATATTCTACCAAATCT 58.358 43.478 0.00 0.00 37.94 2.40
256 265 1.539496 GCGCCGTGGATATTCTACCAA 60.539 52.381 0.00 0.00 37.94 3.67
262 271 1.732259 CCAATAGCGCCGTGGATATTC 59.268 52.381 14.75 0.00 34.05 1.75
265 274 1.301401 GCCAATAGCGCCGTGGATA 60.301 57.895 22.04 0.00 34.05 2.59
277 287 4.371786 CGAAGATAAGAGTGCAGCCAATA 58.628 43.478 0.00 0.00 0.00 1.90
282 292 2.586258 TCCGAAGATAAGAGTGCAGC 57.414 50.000 0.00 0.00 0.00 5.25
290 300 5.646577 ATCCCGTAAGATCCGAAGATAAG 57.353 43.478 0.00 0.00 43.02 1.73
346 357 1.375396 CCGTTCCATTCGCTGTGGA 60.375 57.895 0.00 0.00 43.77 4.02
361 372 2.107750 CGCATCTGCCTCATCCGT 59.892 61.111 0.00 0.00 37.91 4.69
427 438 3.458189 GACATCCTGTCAAATCCCGTAG 58.542 50.000 2.48 0.00 46.22 3.51
457 468 2.262915 CCCGAGTGACTGACTGGC 59.737 66.667 0.00 0.00 33.83 4.85
459 470 1.587054 GTCCCCGAGTGACTGACTG 59.413 63.158 0.00 0.00 33.83 3.51
477 488 0.110486 AACGGCTTATATGGGCCTGG 59.890 55.000 4.53 0.00 45.57 4.45
514 526 3.935828 GAGAAGAAATGGGAGTACTGTGC 59.064 47.826 0.00 0.00 0.00 4.57
515 527 5.413309 AGAGAAGAAATGGGAGTACTGTG 57.587 43.478 0.00 0.00 0.00 3.66
516 528 5.046231 GGAAGAGAAGAAATGGGAGTACTGT 60.046 44.000 0.00 0.00 0.00 3.55
517 529 5.188751 AGGAAGAGAAGAAATGGGAGTACTG 59.811 44.000 0.00 0.00 0.00 2.74
518 530 5.346270 AGGAAGAGAAGAAATGGGAGTACT 58.654 41.667 0.00 0.00 0.00 2.73
519 531 5.395879 GGAGGAAGAGAAGAAATGGGAGTAC 60.396 48.000 0.00 0.00 0.00 2.73
521 533 3.521531 GGAGGAAGAGAAGAAATGGGAGT 59.478 47.826 0.00 0.00 0.00 3.85
522 534 3.779738 AGGAGGAAGAGAAGAAATGGGAG 59.220 47.826 0.00 0.00 0.00 4.30
560 572 4.689549 TCGAGGGTGGAGGCGGAA 62.690 66.667 0.00 0.00 0.00 4.30
640 652 2.733593 GTCGCCTTCTTCACGCGT 60.734 61.111 5.58 5.58 45.85 6.01
691 703 2.408022 GATCTGGACGACGACCCG 59.592 66.667 13.72 7.64 0.00 5.28
765 778 2.231478 GTCGAACAGATCTTCCAGGTCA 59.769 50.000 0.00 0.00 0.00 4.02
774 787 3.617368 CCCCCGTCGAACAGATCT 58.383 61.111 0.00 0.00 0.00 2.75
801 815 2.221906 GAAGCCGCTAGGAACCGTGA 62.222 60.000 0.00 0.00 41.02 4.35
812 826 4.436998 CGTTCTCGGGAAGCCGCT 62.437 66.667 0.00 0.00 31.46 5.52
822 836 2.100603 GGCTCGGACTCGTTCTCG 59.899 66.667 0.00 0.00 37.69 4.04
846 860 1.666011 GACGCACTCACCCTCTTGA 59.334 57.895 0.00 0.00 0.00 3.02
868 882 1.602323 GGTCAACATGGGTCGCCAA 60.602 57.895 0.00 0.00 0.00 4.52
870 884 3.124921 CGGTCAACATGGGTCGCC 61.125 66.667 0.00 0.00 0.00 5.54
948 967 2.948315 GTTGGGAGAGAAATGATGGAGC 59.052 50.000 0.00 0.00 0.00 4.70
951 970 3.019564 GGTGTTGGGAGAGAAATGATGG 58.980 50.000 0.00 0.00 0.00 3.51
981 1000 2.388310 TGGACACGAACACAACAAGA 57.612 45.000 0.00 0.00 0.00 3.02
986 1005 0.660488 GCACATGGACACGAACACAA 59.340 50.000 0.00 0.00 0.00 3.33
989 1008 0.943835 CTCGCACATGGACACGAACA 60.944 55.000 0.00 0.00 33.61 3.18
1011 1030 2.444256 GGGTCGGCAGCCTAGGAAT 61.444 63.158 14.75 0.00 37.19 3.01
1029 1048 1.419387 TGTTTGAAAAGGCCCCAATGG 59.581 47.619 0.00 0.00 37.09 3.16
1077 1097 1.885887 TCACTCGGATTGGCCTTTTTG 59.114 47.619 3.32 0.00 0.00 2.44
1119 1139 3.714798 GGATCCCTAAACCTCCACACATA 59.285 47.826 0.00 0.00 0.00 2.29
1152 1173 1.045911 TGGCGGGGAAAGCACTTTTT 61.046 50.000 0.00 0.00 36.08 1.94
1182 1203 0.623723 GCCACCCCCTAACAGAATCA 59.376 55.000 0.00 0.00 0.00 2.57
1188 1209 2.589157 CGACTGCCACCCCCTAACA 61.589 63.158 0.00 0.00 0.00 2.41
1207 1228 3.007614 TGGTCCTTGTAGTAGAACCAAGC 59.992 47.826 0.00 0.00 35.39 4.01
1260 1281 3.243771 CGACTCGGGCTATAGAAAATGGT 60.244 47.826 3.21 0.00 0.00 3.55
1274 1295 4.187056 GAGGCTTTTCGACTCGGG 57.813 61.111 0.00 0.00 38.20 5.14
1284 1305 4.023291 TCACTTTCAAAGTTGGAGGCTTT 58.977 39.130 0.00 0.00 40.46 3.51
1291 1312 1.336755 CGGGGTCACTTTCAAAGTTGG 59.663 52.381 0.00 0.00 40.46 3.77
1293 1314 1.687563 CCGGGGTCACTTTCAAAGTT 58.312 50.000 0.00 0.00 40.46 2.66
1294 1315 0.822121 GCCGGGGTCACTTTCAAAGT 60.822 55.000 2.18 0.00 44.06 2.66
1319 1340 4.557695 CGACTAGCATATTCACCTCCACTC 60.558 50.000 0.00 0.00 0.00 3.51
1338 1359 1.025647 GCTGGACTACTCGGTCGACT 61.026 60.000 16.46 0.00 37.12 4.18
1344 1365 0.173708 GGACAAGCTGGACTACTCGG 59.826 60.000 0.00 0.00 0.00 4.63
1371 1392 4.082523 AGGTCCATGCCGGTCACG 62.083 66.667 1.90 0.00 40.55 4.35
1387 1408 4.230657 CGTCTGAGAAACACCTCTAACAG 58.769 47.826 0.00 0.00 34.38 3.16
1410 1431 1.666189 GCTTGGAGAGGTTGAATACGC 59.334 52.381 0.00 0.00 0.00 4.42
1416 1437 1.841556 ACGGGCTTGGAGAGGTTGA 60.842 57.895 0.00 0.00 0.00 3.18
1422 1443 2.525629 TGGTCACGGGCTTGGAGA 60.526 61.111 0.00 0.00 0.00 3.71
1443 1464 2.928801 TCCCCGAATACATCCACATG 57.071 50.000 0.00 0.00 35.92 3.21
1455 1476 2.105821 AGTGTTGTCTTCAATCCCCGAA 59.894 45.455 0.00 0.00 35.92 4.30
1461 1482 4.690748 TGGATTCGAGTGTTGTCTTCAATC 59.309 41.667 0.00 0.00 35.92 2.67
1479 1500 1.229853 AACCTCCTCCGGGTGGATT 60.230 57.895 17.65 8.06 46.24 3.01
1525 1546 3.086282 CCTTGTTGCCGGTAATACCTTT 58.914 45.455 8.64 0.00 35.66 3.11
1536 1557 2.561037 GGGGTTGTCCTTGTTGCCG 61.561 63.158 0.00 0.00 35.33 5.69
1574 1595 1.234821 GTTGGTGCTGTCGAATGGAA 58.765 50.000 0.00 0.00 0.00 3.53
1614 1635 9.838339 AGAATAAGAAGACACTCAGAAGAAAAA 57.162 29.630 0.00 0.00 0.00 1.94
1646 1669 5.180271 ACAATCGGTTTCGGAAGCTAATAA 58.820 37.500 3.79 0.00 36.95 1.40
1656 1679 3.259064 AGTGTATGACAATCGGTTTCGG 58.741 45.455 0.00 0.00 36.95 4.30
1669 1692 2.437413 AGCACAGAGTCGAGTGTATGA 58.563 47.619 16.62 0.00 38.02 2.15
1670 1693 2.929531 AGCACAGAGTCGAGTGTATG 57.070 50.000 16.62 0.00 38.02 2.39
1673 1696 1.858091 CAAAGCACAGAGTCGAGTGT 58.142 50.000 16.62 0.00 38.02 3.55
1689 1712 5.411831 ACATCTCAGTGTAGATCTGCAAA 57.588 39.130 15.57 3.62 33.87 3.68
1740 1769 2.757917 GCCTCTCCCTCGTGCTCT 60.758 66.667 0.00 0.00 0.00 4.09
1746 1775 3.522731 CCACTCGCCTCTCCCTCG 61.523 72.222 0.00 0.00 0.00 4.63
1764 1805 0.108585 GCCACTCTCCACTTTCACCA 59.891 55.000 0.00 0.00 0.00 4.17
1813 1856 2.037772 CCACACCACTGCTAGAGTCTTT 59.962 50.000 0.00 0.00 29.75 2.52
1821 1864 1.532604 CGACCTCCACACCACTGCTA 61.533 60.000 0.00 0.00 0.00 3.49
1861 1904 2.863153 CTTCAGTTTGGAGCGCCG 59.137 61.111 2.29 0.00 36.79 6.46
1872 1915 0.396435 TTGTCGGGTCATGCTTCAGT 59.604 50.000 0.00 0.00 0.00 3.41
1874 1917 0.955428 GCTTGTCGGGTCATGCTTCA 60.955 55.000 0.00 0.00 36.18 3.02
1877 1920 2.434884 CGCTTGTCGGGTCATGCT 60.435 61.111 0.00 0.00 36.68 3.79
1887 1930 2.770587 CTTTGCCGCAGACGCTTGTC 62.771 60.000 0.00 0.00 43.21 3.18
1893 1936 2.443957 GAACCACTTTGCCGCAGACG 62.444 60.000 0.00 0.00 39.67 4.18
1897 1940 1.896660 GAGGAACCACTTTGCCGCA 60.897 57.895 0.00 0.00 0.00 5.69
1926 1969 2.358737 CGAGGGCGCTTGGAAGTT 60.359 61.111 7.64 0.00 0.00 2.66
1947 1990 3.063510 TCATTTGGCACTGGAGAAGAG 57.936 47.619 0.00 0.00 0.00 2.85
1996 2039 0.238553 GCCTTCAGAGGTTTTGACGC 59.761 55.000 0.00 0.00 45.44 5.19
2016 2059 3.751175 CGTTCACTTTAATCTTGGGCAGA 59.249 43.478 0.00 0.00 35.33 4.26
2017 2060 3.502211 ACGTTCACTTTAATCTTGGGCAG 59.498 43.478 0.00 0.00 0.00 4.85
2044 2087 4.737054 CACAATGATTACCCAGAAGCAAC 58.263 43.478 0.00 0.00 0.00 4.17
2071 2114 6.321717 TCAAGTCACACACAAATTGAGAAAC 58.678 36.000 0.00 0.00 0.00 2.78
2077 2120 6.199531 CCAAGAATCAAGTCACACACAAATTG 59.800 38.462 0.00 0.00 0.00 2.32
2078 2121 6.127366 ACCAAGAATCAAGTCACACACAAATT 60.127 34.615 0.00 0.00 0.00 1.82
2083 2126 4.335315 TCAACCAAGAATCAAGTCACACAC 59.665 41.667 0.00 0.00 0.00 3.82
2087 2132 6.016777 AGTGAATCAACCAAGAATCAAGTCAC 60.017 38.462 0.00 0.00 29.87 3.67
2098 2143 7.821359 TCAGAATAGAGAAGTGAATCAACCAAG 59.179 37.037 0.00 0.00 0.00 3.61
2104 2149 5.652452 TCGGTCAGAATAGAGAAGTGAATCA 59.348 40.000 0.00 0.00 0.00 2.57
2115 2160 5.652452 TCAGAATTCACTCGGTCAGAATAGA 59.348 40.000 8.44 0.00 32.11 1.98
2156 2202 6.672218 TCTTTATACATTGAAGTCCCAGAGGA 59.328 38.462 0.00 0.00 41.08 3.71
2194 2243 5.729510 GAAGTAACTGCTTCTTCCATCTCT 58.270 41.667 0.80 0.00 41.07 3.10
2206 2255 1.542547 CCCGTGTTGGAAGTAACTGCT 60.543 52.381 0.00 0.00 42.00 4.24
2224 2273 2.735151 AGCTGCCAAAAGTTATACCCC 58.265 47.619 0.00 0.00 0.00 4.95
2239 2288 4.437524 GCTAGTAAAGTAAAGGCAAGCTGC 60.438 45.833 0.00 0.00 44.08 5.25
2242 2291 3.063588 CGGCTAGTAAAGTAAAGGCAAGC 59.936 47.826 0.00 0.00 34.40 4.01
2259 2308 1.271102 GTTGGCCATCAAAAACGGCTA 59.729 47.619 6.09 0.00 45.50 3.93
2264 2313 4.058721 AGTTCAGTTGGCCATCAAAAAC 57.941 40.909 16.12 14.71 37.08 2.43
2268 2317 3.450457 ACAAAAGTTCAGTTGGCCATCAA 59.550 39.130 16.12 0.00 0.00 2.57
2277 2326 7.730364 ACTAATCGATCACAAAAGTTCAGTT 57.270 32.000 0.00 0.00 0.00 3.16
2333 2383 4.701651 TGTGGTTCATCTTCATTGTCATCC 59.298 41.667 0.00 0.00 0.00 3.51
2350 2403 2.182516 TCCCATGGGTTTTTGTGGTT 57.817 45.000 30.28 0.00 36.47 3.67
2351 2404 1.977129 CATCCCATGGGTTTTTGTGGT 59.023 47.619 30.28 0.00 36.47 4.16
2370 2423 3.691342 CGACGTCCTGCCCCTTCA 61.691 66.667 10.58 0.00 0.00 3.02
2384 2437 1.726533 CTAGCGTCCTCCTTCCCGAC 61.727 65.000 0.00 0.00 0.00 4.79
2390 2443 2.726351 GCTGGCTAGCGTCCTCCTT 61.726 63.158 6.22 0.00 40.67 3.36
2446 2499 1.662438 GAGGTCTCCGGACTGCTGAG 61.662 65.000 0.00 0.00 41.82 3.35
2492 2545 0.666577 GACGTTCACTCGACAAGGGG 60.667 60.000 0.00 0.00 34.70 4.79
2546 2626 2.980233 AAACCAGTCGCAGCAGGC 60.980 61.111 0.00 0.00 39.90 4.85
2547 2627 2.949106 CAAACCAGTCGCAGCAGG 59.051 61.111 0.00 0.00 0.00 4.85
2562 2732 1.152860 TGAAAAGTGGCGAGGGCAA 60.153 52.632 0.00 0.00 40.46 4.52
2567 2737 0.955919 GGGAGGTGAAAAGTGGCGAG 60.956 60.000 0.00 0.00 0.00 5.03
2570 2740 1.228154 ACGGGAGGTGAAAAGTGGC 60.228 57.895 0.00 0.00 0.00 5.01
2583 2753 1.685765 CCTCTGGGACATGACGGGA 60.686 63.158 0.00 0.00 38.20 5.14
2733 2903 3.430218 GCTAATGGATCAGTCGGAAATCG 59.570 47.826 0.00 0.00 40.90 3.34
2750 2920 4.373156 ACAGAACAAGGGTCAAGCTAAT 57.627 40.909 0.00 0.00 0.00 1.73
2761 2931 7.601886 CAGATAGCATATCCTAACAGAACAAGG 59.398 40.741 0.00 0.00 0.00 3.61
2784 2954 4.377021 ACGTGCAACAAATAGTCTTCAGA 58.623 39.130 0.00 0.00 35.74 3.27
2794 2964 3.367932 CGACTGATAGACGTGCAACAAAT 59.632 43.478 0.00 0.00 35.74 2.32
2802 2974 0.027716 CGGACCGACTGATAGACGTG 59.972 60.000 8.64 0.00 31.81 4.49
2803 2975 0.392193 ACGGACCGACTGATAGACGT 60.392 55.000 23.38 0.00 31.81 4.34
2805 2977 1.063764 GACACGGACCGACTGATAGAC 59.936 57.143 23.38 0.00 0.00 2.59
2811 2983 2.022129 GCAAGACACGGACCGACTG 61.022 63.158 23.38 12.22 0.00 3.51
2812 2984 1.816863 ATGCAAGACACGGACCGACT 61.817 55.000 23.38 13.51 0.00 4.18
2816 2988 0.951558 ACAAATGCAAGACACGGACC 59.048 50.000 0.00 0.00 0.00 4.46
2823 2995 2.480419 AGTGAGCGTACAAATGCAAGAC 59.520 45.455 0.00 0.00 40.32 3.01
2832 3004 2.129620 ACACCCAGTGAGCGTACAA 58.870 52.632 0.96 0.00 36.96 2.41
2854 3026 9.691362 GTGGAAGAATTGCTTAGTGAAAATTAA 57.309 29.630 0.00 0.00 37.31 1.40
2855 3027 9.077885 AGTGGAAGAATTGCTTAGTGAAAATTA 57.922 29.630 0.00 0.00 37.31 1.40
2993 3181 3.954258 AGTGGAAGAACTGGAAAACAAGG 59.046 43.478 0.00 0.00 0.00 3.61
3002 3190 0.969894 AGACCGAGTGGAAGAACTGG 59.030 55.000 0.00 0.00 39.21 4.00
3083 3272 2.005960 GATCGTGGTCTCGGGGACTG 62.006 65.000 8.12 0.00 43.97 3.51


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

AutoCloner maintained by Alex Coulton.