Multiple sequence alignment - TraesCS5D01G240800

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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 TraesCS5D01G240800 chr5D 100.000 5865 0 0 1 5865 349869631 349863767 0.000000e+00 10831
1 TraesCS5D01G240800 chr5D 96.094 128 5 0 191 318 59944480 59944353 5.960000e-50 209
2 TraesCS5D01G240800 chr5A 92.844 5310 214 72 613 5865 450168608 450163408 0.000000e+00 7548
3 TraesCS5D01G240800 chr5A 90.306 196 6 4 375 557 450168915 450168720 1.630000e-60 244
4 TraesCS5D01G240800 chr5A 90.341 176 2 7 18 193 450169209 450169049 3.560000e-52 217
5 TraesCS5D01G240800 chr5A 92.908 141 5 5 192 329 546534499 546534637 3.580000e-47 200
6 TraesCS5D01G240800 chr5A 98.333 60 1 0 328 387 450168989 450168930 8.040000e-19 106
7 TraesCS5D01G240800 chr5B 95.323 4426 148 23 1478 5860 410534848 410530439 0.000000e+00 6972
8 TraesCS5D01G240800 chr5B 82.391 920 79 40 613 1480 410535823 410534935 0.000000e+00 725
9 TraesCS5D01G240800 chr5B 88.889 261 16 3 310 557 410536199 410535939 5.710000e-80 309
10 TraesCS5D01G240800 chr5B 94.643 168 8 1 15 182 410536596 410536430 5.830000e-65 259
11 TraesCS5D01G240800 chr5B 96.183 131 4 1 192 321 338489450 338489580 4.600000e-51 213
12 TraesCS5D01G240800 chr1D 89.355 1193 102 17 2932 4118 455130759 455129586 0.000000e+00 1476
13 TraesCS5D01G240800 chr1D 84.273 674 85 8 2265 2937 455143401 455142748 6.410000e-179 638
14 TraesCS5D01G240800 chr1D 87.402 381 36 3 1891 2262 455143881 455143504 1.510000e-115 427
15 TraesCS5D01G240800 chr1D 89.881 168 11 2 4196 4363 455129555 455129394 1.660000e-50 211
16 TraesCS5D01G240800 chr7B 87.392 1158 109 21 2259 3413 646035996 646034873 0.000000e+00 1295
17 TraesCS5D01G240800 chr7B 95.420 131 6 0 189 319 730035517 730035387 5.960000e-50 209
18 TraesCS5D01G240800 chr7B 83.529 170 18 8 400 559 227819050 227818881 3.660000e-32 150
19 TraesCS5D01G240800 chr7B 89.744 117 10 2 3358 3474 646034869 646034755 1.320000e-31 148
20 TraesCS5D01G240800 chr6B 87.392 1158 106 22 2259 3413 124630896 124629776 0.000000e+00 1293
21 TraesCS5D01G240800 chr6B 86.587 753 62 19 3622 4363 481663763 481663039 0.000000e+00 795
22 TraesCS5D01G240800 chr6B 84.898 245 22 7 328 559 457271622 457271864 3.530000e-57 233
23 TraesCS5D01G240800 chr6B 88.889 117 11 2 3358 3474 124629772 124629658 6.130000e-30 143
24 TraesCS5D01G240800 chr2A 84.946 651 92 5 2778 3425 753425659 753426306 0.000000e+00 654
25 TraesCS5D01G240800 chr2A 95.455 132 4 2 190 320 628400081 628400211 5.960000e-50 209
26 TraesCS5D01G240800 chr1A 90.107 374 32 3 1891 2262 549126181 549125811 1.140000e-131 481
27 TraesCS5D01G240800 chr1A 85.577 208 27 2 2265 2471 549125426 549125221 1.280000e-51 215
28 TraesCS5D01G240800 chr1A 89.655 116 10 2 2671 2785 549119559 549119445 4.740000e-31 147
29 TraesCS5D01G240800 chr3D 87.600 250 31 0 2277 2526 501136674 501136425 2.070000e-74 291
30 TraesCS5D01G240800 chr3D 95.455 132 4 2 190 320 545361625 545361755 5.960000e-50 209
31 TraesCS5D01G240800 chr3D 88.636 132 13 1 2519 2650 501136403 501136274 6.080000e-35 159
32 TraesCS5D01G240800 chr4D 88.066 243 15 4 329 557 331661829 331661587 5.790000e-70 276
33 TraesCS5D01G240800 chr2B 84.490 245 23 7 328 559 516320913 516320671 1.640000e-55 228
34 TraesCS5D01G240800 chr2B 92.908 141 10 0 188 328 783655428 783655568 7.700000e-49 206
35 TraesCS5D01G240800 chr3B 96.212 132 5 0 187 318 184611580 184611449 3.560000e-52 217
36 TraesCS5D01G240800 chr4A 96.850 127 4 0 192 318 589667294 589667168 4.600000e-51 213
37 TraesCS5D01G240800 chr1B 79.060 234 32 13 328 557 121743376 121743596 1.700000e-30 145


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 TraesCS5D01G240800 chr5D 349863767 349869631 5864 True 10831.00 10831 100.0000 1 5865 1 chr5D.!!$R2 5864
1 TraesCS5D01G240800 chr5A 450163408 450169209 5801 True 2028.75 7548 92.9560 18 5865 4 chr5A.!!$R1 5847
2 TraesCS5D01G240800 chr5B 410530439 410536596 6157 True 2066.25 6972 90.3115 15 5860 4 chr5B.!!$R1 5845
3 TraesCS5D01G240800 chr1D 455129394 455130759 1365 True 843.50 1476 89.6180 2932 4363 2 chr1D.!!$R1 1431
4 TraesCS5D01G240800 chr1D 455142748 455143881 1133 True 532.50 638 85.8375 1891 2937 2 chr1D.!!$R2 1046
5 TraesCS5D01G240800 chr7B 646034755 646035996 1241 True 721.50 1295 88.5680 2259 3474 2 chr7B.!!$R3 1215
6 TraesCS5D01G240800 chr6B 481663039 481663763 724 True 795.00 795 86.5870 3622 4363 1 chr6B.!!$R1 741
7 TraesCS5D01G240800 chr6B 124629658 124630896 1238 True 718.00 1293 88.1405 2259 3474 2 chr6B.!!$R2 1215
8 TraesCS5D01G240800 chr2A 753425659 753426306 647 False 654.00 654 84.9460 2778 3425 1 chr2A.!!$F2 647
9 TraesCS5D01G240800 chr1A 549125221 549126181 960 True 348.00 481 87.8420 1891 2471 2 chr1A.!!$R2 580

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
607 772 0.028902 AAAAACACAGTCCGCTTCGC 59.971 50.000 0.00 0.0 0.00 4.70 F
654 858 0.038744 ATCAACACAAGGGGAGGCAG 59.961 55.000 0.00 0.0 0.00 4.85 F
967 1185 0.179029 CCTCGTCTCCTCTCTCCTCC 60.179 65.000 0.00 0.0 0.00 4.30 F
2435 3225 0.034767 TCACCCCTGTACTCGACGAT 60.035 55.000 0.00 0.0 0.00 3.73 F
2852 3645 0.036483 TTGATAAGCTCGCCACTGCA 60.036 50.000 0.00 0.0 37.32 4.41 F
3796 4676 4.982295 TGGCGAATATCGAGTCACAAATAG 59.018 41.667 3.61 0.0 43.74 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2418 3208 0.255318 AGATCGTCGAGTACAGGGGT 59.745 55.000 0.00 0.0 0.00 4.95 R
2419 3209 0.663688 CAGATCGTCGAGTACAGGGG 59.336 60.000 0.00 0.0 0.00 4.79 R
2836 3629 1.019673 CATTGCAGTGGCGAGCTTAT 58.980 50.000 0.32 0.0 45.35 1.73 R
3557 4433 1.866925 GGCCCTTCTTTTCGTGACG 59.133 57.895 0.00 0.0 0.00 4.35 R
4421 5309 2.019948 GGTATCGCCGTTTTTCCTCT 57.980 50.000 0.00 0.0 0.00 3.69 R
5512 6409 0.317160 TTGCTTCCGTCATGTCGTCT 59.683 50.000 11.29 0.0 0.00 4.18 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
151 152 1.213678 AGTACAGCCATGGCATGATGT 59.786 47.619 37.18 31.29 44.88 3.06
187 188 3.064931 CCTCACTCGGTTAAAAGTGACC 58.935 50.000 10.84 0.00 45.18 4.02
203 215 1.320507 GACCATCTACTCCCTCCGTC 58.679 60.000 0.00 0.00 0.00 4.79
205 217 1.173444 CCATCTACTCCCTCCGTCCG 61.173 65.000 0.00 0.00 0.00 4.79
206 218 0.179026 CATCTACTCCCTCCGTCCGA 60.179 60.000 0.00 0.00 0.00 4.55
212 224 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
214 226 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
218 230 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
222 234 6.164876 TCCGTCCGAAAATACTTGTCATTAA 58.835 36.000 0.00 0.00 0.00 1.40
227 239 9.072294 GTCCGAAAATACTTGTCATTAAAATGG 57.928 33.333 3.00 0.00 37.03 3.16
228 240 9.015367 TCCGAAAATACTTGTCATTAAAATGGA 57.985 29.630 3.00 0.00 37.03 3.41
237 261 7.976734 ACTTGTCATTAAAATGGACAAAAACGA 59.023 29.630 15.23 2.46 36.72 3.85
250 274 9.620660 ATGGACAAAAACGAATGTATCTAAAAC 57.379 29.630 0.00 0.00 0.00 2.43
251 275 8.842280 TGGACAAAAACGAATGTATCTAAAACT 58.158 29.630 0.00 0.00 0.00 2.66
305 409 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
308 412 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
313 417 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
319 423 0.032813 TTCCGGACGGAGGGAGTATT 60.033 55.000 13.64 0.00 46.06 1.89
320 424 0.846015 TCCGGACGGAGGGAGTATTA 59.154 55.000 9.76 0.00 39.76 0.98
322 426 1.817447 CCGGACGGAGGGAGTATTATC 59.183 57.143 4.40 0.00 37.50 1.75
326 430 4.271661 GGACGGAGGGAGTATTATCCTAG 58.728 52.174 0.00 0.00 39.50 3.02
394 525 3.801114 AACCTTTTGTTGGTTCTCTGC 57.199 42.857 0.00 0.00 43.60 4.26
442 573 5.455392 ACTCAAATCATTTCAGCTTGAACG 58.545 37.500 0.00 0.00 35.89 3.95
515 657 0.967380 GACAAAGGCCACCCTCCATG 60.967 60.000 5.01 0.00 41.90 3.66
522 664 2.311854 CCACCCTCCATGGCCTCTT 61.312 63.158 6.96 0.00 0.00 2.85
557 701 2.224159 GCTCACTCCCAACCTCCCA 61.224 63.158 0.00 0.00 0.00 4.37
559 703 0.036875 CTCACTCCCAACCTCCCAAC 59.963 60.000 0.00 0.00 0.00 3.77
561 705 0.537371 CACTCCCAACCTCCCAACAC 60.537 60.000 0.00 0.00 0.00 3.32
564 725 0.631753 TCCCAACCTCCCAACACAAA 59.368 50.000 0.00 0.00 0.00 2.83
567 728 1.827969 CCAACCTCCCAACACAAACAA 59.172 47.619 0.00 0.00 0.00 2.83
571 736 2.107366 CCTCCCAACACAAACAACCTT 58.893 47.619 0.00 0.00 0.00 3.50
582 747 5.473504 ACACAAACAACCTTCCTATAAGCAG 59.526 40.000 0.00 0.00 0.00 4.24
598 763 0.179103 GCAGCTGGCAAAAACACAGT 60.179 50.000 17.12 0.00 43.97 3.55
600 765 0.746659 AGCTGGCAAAAACACAGTCC 59.253 50.000 0.00 0.00 34.79 3.85
603 768 1.034838 TGGCAAAAACACAGTCCGCT 61.035 50.000 0.00 0.00 0.00 5.52
605 770 1.477105 GCAAAAACACAGTCCGCTTC 58.523 50.000 0.00 0.00 0.00 3.86
606 771 1.741993 CAAAAACACAGTCCGCTTCG 58.258 50.000 0.00 0.00 0.00 3.79
607 772 0.028902 AAAAACACAGTCCGCTTCGC 59.971 50.000 0.00 0.00 0.00 4.70
608 773 0.814010 AAAACACAGTCCGCTTCGCT 60.814 50.000 0.00 0.00 0.00 4.93
609 774 0.814010 AAACACAGTCCGCTTCGCTT 60.814 50.000 0.00 0.00 0.00 4.68
610 775 1.222115 AACACAGTCCGCTTCGCTTC 61.222 55.000 0.00 0.00 0.00 3.86
611 776 1.373497 CACAGTCCGCTTCGCTTCT 60.373 57.895 0.00 0.00 0.00 2.85
623 827 2.474410 TCGCTTCTTCCTTTCCCTTC 57.526 50.000 0.00 0.00 0.00 3.46
642 846 0.652592 CCCATCGCTTCGATCAACAC 59.347 55.000 0.00 0.00 45.19 3.32
654 858 0.038744 ATCAACACAAGGGGAGGCAG 59.961 55.000 0.00 0.00 0.00 4.85
660 864 1.281867 CACAAGGGGAGGCAGACATAA 59.718 52.381 0.00 0.00 0.00 1.90
665 869 1.694696 GGGGAGGCAGACATAACCTAG 59.305 57.143 0.00 0.00 32.67 3.02
666 870 1.070914 GGGAGGCAGACATAACCTAGC 59.929 57.143 0.00 0.00 32.67 3.42
667 871 1.070914 GGAGGCAGACATAACCTAGCC 59.929 57.143 0.00 0.00 42.31 3.93
668 872 2.182516 AGGCAGACATAACCTAGCCT 57.817 50.000 0.00 0.00 46.89 4.58
669 873 2.246719 GGCAGACATAACCTAGCCTG 57.753 55.000 0.00 0.00 39.02 4.85
731 935 1.217244 CAAAGGGCTGCTGGCATTC 59.783 57.895 16.80 0.86 41.80 2.67
750 954 1.572447 GGTGCGCGTGCTTTTTCTA 59.428 52.632 23.16 0.00 43.34 2.10
752 956 0.234884 GTGCGCGTGCTTTTTCTACT 59.765 50.000 23.16 0.00 43.34 2.57
753 957 0.511221 TGCGCGTGCTTTTTCTACTC 59.489 50.000 23.16 0.00 43.34 2.59
754 958 0.790814 GCGCGTGCTTTTTCTACTCT 59.209 50.000 15.02 0.00 38.39 3.24
783 987 3.047695 TCCTAATCCCAAGGAGAGGAC 57.952 52.381 11.35 0.00 40.62 3.85
794 998 0.923358 GGAGAGGACAGGAGAGGAGA 59.077 60.000 0.00 0.00 0.00 3.71
795 999 1.409661 GGAGAGGACAGGAGAGGAGAC 60.410 61.905 0.00 0.00 0.00 3.36
796 1000 0.254747 AGAGGACAGGAGAGGAGACG 59.745 60.000 0.00 0.00 0.00 4.18
797 1001 0.253610 GAGGACAGGAGAGGAGACGA 59.746 60.000 0.00 0.00 0.00 4.20
939 1149 2.438614 GGCCTTTCCTCGCCTTCC 60.439 66.667 0.00 0.00 42.21 3.46
940 1150 2.438614 GCCTTTCCTCGCCTTCCC 60.439 66.667 0.00 0.00 0.00 3.97
941 1151 2.972819 GCCTTTCCTCGCCTTCCCT 61.973 63.158 0.00 0.00 0.00 4.20
942 1152 1.685820 CCTTTCCTCGCCTTCCCTT 59.314 57.895 0.00 0.00 0.00 3.95
944 1154 0.741221 CTTTCCTCGCCTTCCCTTCG 60.741 60.000 0.00 0.00 0.00 3.79
945 1155 2.798148 TTTCCTCGCCTTCCCTTCGC 62.798 60.000 0.00 0.00 0.00 4.70
947 1157 3.775654 CTCGCCTTCCCTTCGCCT 61.776 66.667 0.00 0.00 0.00 5.52
966 1184 0.834612 TCCTCGTCTCCTCTCTCCTC 59.165 60.000 0.00 0.00 0.00 3.71
967 1185 0.179029 CCTCGTCTCCTCTCTCCTCC 60.179 65.000 0.00 0.00 0.00 4.30
972 1190 0.986019 TCTCCTCTCTCCTCCGAGCT 60.986 60.000 0.00 0.00 35.94 4.09
979 1197 2.757508 TCCTCCGAGCTGCTCCTG 60.758 66.667 22.97 14.68 0.00 3.86
1088 1323 1.374758 GCTTCGTGCCACTGCTAGT 60.375 57.895 0.00 0.00 38.71 2.57
1120 1355 3.761218 TGAAGTAGAGCTCTGTTCTCTGG 59.239 47.826 26.78 0.00 40.78 3.86
1137 1373 6.159299 TCTCTGGAAACAAATTTTGCATCA 57.841 33.333 9.04 2.81 42.06 3.07
1138 1374 6.761312 TCTCTGGAAACAAATTTTGCATCAT 58.239 32.000 9.04 0.00 42.06 2.45
1139 1375 7.894708 TCTCTGGAAACAAATTTTGCATCATA 58.105 30.769 9.04 1.47 42.06 2.15
1140 1376 7.814107 TCTCTGGAAACAAATTTTGCATCATAC 59.186 33.333 9.04 0.00 42.06 2.39
1145 1381 7.761249 GGAAACAAATTTTGCATCATACTAGCT 59.239 33.333 9.04 0.00 0.00 3.32
1150 1386 9.962759 CAAATTTTGCATCATACTAGCTTTTTC 57.037 29.630 0.00 0.00 0.00 2.29
1186 1439 1.134670 CCCCATCTTCTCTCGGTGAAC 60.135 57.143 0.00 0.00 0.00 3.18
1238 1491 3.305094 CCAATTCGCATGCTTCATTTCAC 59.695 43.478 17.13 0.00 0.00 3.18
1246 1499 5.050904 CGCATGCTTCATTTCACAAGAAAAA 60.051 36.000 17.13 0.00 46.06 1.94
1247 1500 6.360329 GCATGCTTCATTTCACAAGAAAAAG 58.640 36.000 11.37 0.00 46.06 2.27
1256 1509 4.287238 TCACAAGAAAAAGTTCGGCTTC 57.713 40.909 0.00 0.00 38.90 3.86
1321 1584 4.322080 CACTGTGTTTGAGTGTCCTCTA 57.678 45.455 0.00 0.00 38.61 2.43
1354 1619 7.042335 AGACTAGAGAATCGGGTGTTATTTTG 58.958 38.462 0.00 0.00 42.67 2.44
1360 1625 8.294577 AGAGAATCGGGTGTTATTTTGTTTTAC 58.705 33.333 0.00 0.00 42.67 2.01
1362 1627 8.294577 AGAATCGGGTGTTATTTTGTTTTACTC 58.705 33.333 0.00 0.00 0.00 2.59
1385 1650 2.232941 GACATGGAACGAGGGTTGAGTA 59.767 50.000 0.00 0.00 36.24 2.59
1388 1653 3.604875 TGGAACGAGGGTTGAGTATTC 57.395 47.619 0.00 0.00 36.24 1.75
1389 1654 2.094390 TGGAACGAGGGTTGAGTATTCG 60.094 50.000 0.00 0.00 36.24 3.34
1417 1682 0.605319 CACAGGGCTGCGGAAAAGTA 60.605 55.000 0.00 0.00 0.00 2.24
1432 1697 7.166142 TGCGGAAAAGTAACAACTTTTTATTCG 59.834 33.333 15.25 15.78 46.28 3.34
1472 1737 3.117046 GAGCGAGTATTCCTTGTGTAGC 58.883 50.000 0.00 0.00 0.00 3.58
1633 1989 6.971726 TCCTTGATTCTATTCGGCTTAGTA 57.028 37.500 0.00 0.00 0.00 1.82
1634 1990 6.982852 TCCTTGATTCTATTCGGCTTAGTAG 58.017 40.000 0.00 0.00 0.00 2.57
1635 1991 6.550108 TCCTTGATTCTATTCGGCTTAGTAGT 59.450 38.462 0.00 0.00 0.00 2.73
1702 2063 8.837389 GTCAACTAATACTCTGTTTTTCACCTT 58.163 33.333 0.00 0.00 0.00 3.50
1776 2137 0.480252 ATTAAGATGCCCAGGGGAGC 59.520 55.000 7.28 7.28 37.50 4.70
1793 2154 2.429610 GGAGCACATGAATCAGGCAATT 59.570 45.455 0.00 0.00 0.00 2.32
1798 2159 4.563976 GCACATGAATCAGGCAATTGTAAC 59.436 41.667 7.40 0.00 0.00 2.50
1799 2160 5.712004 CACATGAATCAGGCAATTGTAACA 58.288 37.500 7.40 0.00 0.00 2.41
1804 2165 6.623486 TGAATCAGGCAATTGTAACAATCAG 58.377 36.000 7.40 0.00 0.00 2.90
1830 2191 6.688637 TGCATTCTTGATTGATTACCTCTG 57.311 37.500 0.00 0.00 0.00 3.35
1877 2238 3.565482 ACCATGCATATAAGGTTGAAGCG 59.435 43.478 0.00 0.00 0.00 4.68
2068 2438 2.991540 GTGGCCACCAAGGAAGCC 60.992 66.667 26.31 14.50 45.96 4.35
2196 2568 1.239968 GGCTTCCTGAGTGGTTGCTG 61.240 60.000 0.00 0.00 36.19 4.41
2209 2581 1.228552 TTGCTGGGTTCCCTTGAGC 60.229 57.895 9.43 10.07 0.00 4.26
2226 2598 0.465824 AGCTGATGGAATCTGGCTGC 60.466 55.000 0.00 0.00 45.62 5.25
2264 3036 3.896888 TGATTCAAGTTGTGGATTGCCTT 59.103 39.130 2.11 0.00 34.31 4.35
2317 3103 5.091261 AGTAAATCTCTAGGCAACACCAG 57.909 43.478 0.00 0.00 43.14 4.00
2327 3113 3.412386 AGGCAACACCAGCTTACTTTAG 58.588 45.455 0.00 0.00 43.14 1.85
2368 3158 8.026026 TGCTTTTGTTAATTTATGATCGCTTGA 58.974 29.630 0.00 0.00 0.00 3.02
2399 3189 1.373748 GGGCTACGTGTCGCTCAAA 60.374 57.895 0.00 0.00 0.00 2.69
2414 3204 0.944386 TCAAAGAACAACTCGCTGCC 59.056 50.000 0.00 0.00 0.00 4.85
2418 3208 1.954146 GAACAACTCGCTGCCGTCA 60.954 57.895 0.00 0.00 35.54 4.35
2419 3209 2.159272 GAACAACTCGCTGCCGTCAC 62.159 60.000 0.00 0.00 35.54 3.67
2435 3225 0.034767 TCACCCCTGTACTCGACGAT 60.035 55.000 0.00 0.00 0.00 3.73
2528 3318 7.462109 CTCTGAGTTAAGTGAGCATAATGAC 57.538 40.000 0.00 0.00 0.00 3.06
2531 3321 7.877612 TCTGAGTTAAGTGAGCATAATGACAAA 59.122 33.333 0.00 0.00 0.00 2.83
2613 3403 2.613691 GCTACCAAGCGCAACTTAGTA 58.386 47.619 11.47 0.00 39.39 1.82
2638 3431 7.974504 ACTCTTCAGAAAGATAAGGTAAACCA 58.025 34.615 1.26 0.00 40.68 3.67
2772 3565 6.377327 TTCAGAAATGGTTCAACTCAGAAC 57.623 37.500 0.00 0.00 45.50 3.01
2852 3645 0.036483 TTGATAAGCTCGCCACTGCA 60.036 50.000 0.00 0.00 37.32 4.41
2902 3703 6.261118 GCTGCTGGTCATCTAATTTAAGTTG 58.739 40.000 0.00 0.00 0.00 3.16
2957 3759 8.939201 TTTCTTGTTTGCAATATTTTCAGTCA 57.061 26.923 0.00 0.00 33.65 3.41
3542 4418 8.584063 AGAGGTTAACAGAACTTAAAACCAAA 57.416 30.769 8.10 0.00 39.05 3.28
3566 4442 6.539649 AGATTGAAAGAAATCGTCACGAAA 57.460 33.333 2.76 0.00 40.75 3.46
3796 4676 4.982295 TGGCGAATATCGAGTCACAAATAG 59.018 41.667 3.61 0.00 43.74 1.73
4193 5081 8.708742 TCGTGTATTTCAGTTTAGTTCAATGAG 58.291 33.333 0.00 0.00 0.00 2.90
4325 5213 7.290014 TCTGATCAGTAGGGTAAGCATTTATCA 59.710 37.037 21.92 0.00 0.00 2.15
4421 5309 8.117813 ACAGACTTAACAGAAAACAAAAGGAA 57.882 30.769 0.00 0.00 0.00 3.36
4517 5405 7.678218 GCATATTCTGGTCTGAACATCACTTTC 60.678 40.741 0.00 0.00 0.00 2.62
4778 5666 0.836606 TGATTCAAGGCGGCTATCCA 59.163 50.000 13.71 3.59 0.00 3.41
4834 5722 6.358118 TCGACATTTACATCAATTAGTGGC 57.642 37.500 0.00 0.00 0.00 5.01
4876 5764 6.697641 TCTATGGGATAATTTCCTGGTACC 57.302 41.667 4.43 4.43 44.75 3.34
4995 5883 5.068198 CAGGTCAATCTATTGGGTCAATTGG 59.932 44.000 5.42 0.00 38.30 3.16
5196 6084 5.084519 AGGTGAAAGATGTAGTGAGTGGTA 58.915 41.667 0.00 0.00 0.00 3.25
5387 6275 7.182060 ACCCTTATTTTATGAGCAGAAAAGGA 58.818 34.615 8.67 0.00 35.36 3.36
5512 6409 8.043113 ACAGACATTAAAGAATATGCTCTGTCA 58.957 33.333 13.79 0.00 37.92 3.58
5533 6430 0.865769 ACGACATGACGGAAGCAAAC 59.134 50.000 20.92 0.00 37.61 2.93
5786 6683 4.500116 GTGAGGACCCGAGCGCTC 62.500 72.222 27.64 27.64 0.00 5.03
5808 6705 0.457853 TCTCCGGCAAAACTCGATCG 60.458 55.000 9.36 9.36 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.351276 CCCACAGCCACAGGGTAC 59.649 66.667 0.00 0.00 37.81 3.34
8 9 3.957586 TCCTGCCCACAGCCACAG 61.958 66.667 0.00 0.00 43.02 3.66
9 10 4.269523 GTCCTGCCCACAGCCACA 62.270 66.667 0.00 0.00 43.02 4.17
78 79 0.603569 CCCTACACTTGTCGTGAGCT 59.396 55.000 0.00 0.00 46.81 4.09
137 138 2.558286 CGGGACATCATGCCATGGC 61.558 63.158 30.54 30.54 39.28 4.40
187 188 0.179026 TCGGACGGAGGGAGTAGATG 60.179 60.000 0.00 0.00 0.00 2.90
203 215 9.072294 GTCCATTTTAATGACAAGTATTTTCGG 57.928 33.333 4.07 0.00 38.70 4.30
212 224 8.346476 TCGTTTTTGTCCATTTTAATGACAAG 57.654 30.769 4.07 2.90 37.53 3.16
214 226 8.759641 CATTCGTTTTTGTCCATTTTAATGACA 58.240 29.630 4.07 4.41 38.70 3.58
279 303 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
280 304 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
282 306 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
283 307 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
284 308 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
286 310 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
290 394 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
294 398 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
295 399 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
296 400 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
297 401 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
302 406 1.817447 GATAATACTCCCTCCGTCCGG 59.183 57.143 0.00 0.00 0.00 5.14
303 407 1.817447 GGATAATACTCCCTCCGTCCG 59.183 57.143 0.00 0.00 0.00 4.79
305 409 4.920999 ACTAGGATAATACTCCCTCCGTC 58.079 47.826 0.00 0.00 35.79 4.79
308 412 7.452189 GCCATATACTAGGATAATACTCCCTCC 59.548 44.444 0.00 0.00 35.79 4.30
313 417 9.900710 CAATCGCCATATACTAGGATAATACTC 57.099 37.037 0.00 0.00 0.00 2.59
394 525 3.194116 AGCTGGTGCCAAATACTTTCATG 59.806 43.478 0.00 0.00 40.80 3.07
515 657 4.168291 CAGCGGAGGGAAGAGGCC 62.168 72.222 0.00 0.00 0.00 5.19
557 701 5.830991 TGCTTATAGGAAGGTTGTTTGTGTT 59.169 36.000 0.00 0.00 0.00 3.32
559 703 5.619981 GCTGCTTATAGGAAGGTTGTTTGTG 60.620 44.000 0.00 0.00 0.00 3.33
561 705 4.702131 AGCTGCTTATAGGAAGGTTGTTTG 59.298 41.667 0.00 0.00 0.00 2.93
564 725 3.370953 CCAGCTGCTTATAGGAAGGTTGT 60.371 47.826 8.66 0.00 0.00 3.32
567 728 1.141858 GCCAGCTGCTTATAGGAAGGT 59.858 52.381 8.66 0.00 36.87 3.50
571 736 3.364460 TTTTGCCAGCTGCTTATAGGA 57.636 42.857 8.66 0.00 42.00 2.94
582 747 0.594796 CGGACTGTGTTTTTGCCAGC 60.595 55.000 0.00 0.00 0.00 4.85
603 768 2.552373 GGAAGGGAAAGGAAGAAGCGAA 60.552 50.000 0.00 0.00 0.00 4.70
605 770 1.454201 GGAAGGGAAAGGAAGAAGCG 58.546 55.000 0.00 0.00 0.00 4.68
606 771 1.075536 TGGGAAGGGAAAGGAAGAAGC 59.924 52.381 0.00 0.00 0.00 3.86
607 772 3.625853 GATGGGAAGGGAAAGGAAGAAG 58.374 50.000 0.00 0.00 0.00 2.85
608 773 2.026262 CGATGGGAAGGGAAAGGAAGAA 60.026 50.000 0.00 0.00 0.00 2.52
609 774 1.559682 CGATGGGAAGGGAAAGGAAGA 59.440 52.381 0.00 0.00 0.00 2.87
610 775 2.019156 GCGATGGGAAGGGAAAGGAAG 61.019 57.143 0.00 0.00 0.00 3.46
611 776 0.034477 GCGATGGGAAGGGAAAGGAA 60.034 55.000 0.00 0.00 0.00 3.36
623 827 0.652592 GTGTTGATCGAAGCGATGGG 59.347 55.000 7.09 0.00 47.00 4.00
642 846 1.408822 GGTTATGTCTGCCTCCCCTTG 60.409 57.143 0.00 0.00 0.00 3.61
654 858 2.436173 AGAAGCCAGGCTAGGTTATGTC 59.564 50.000 16.56 5.83 38.25 3.06
660 864 0.833949 GCTTAGAAGCCAGGCTAGGT 59.166 55.000 16.56 4.75 46.20 3.08
731 935 2.165362 TAGAAAAAGCACGCGCACCG 62.165 55.000 5.73 0.00 42.27 4.94
738 942 6.532365 AAGAAGAAGAGTAGAAAAAGCACG 57.468 37.500 0.00 0.00 0.00 5.34
750 954 6.704056 TGGGATTAGGAAAAGAAGAAGAGT 57.296 37.500 0.00 0.00 0.00 3.24
752 956 6.274672 TCCTTGGGATTAGGAAAAGAAGAAGA 59.725 38.462 0.00 0.00 38.83 2.87
753 957 6.485171 TCCTTGGGATTAGGAAAAGAAGAAG 58.515 40.000 0.00 0.00 38.83 2.85
754 958 6.274672 TCTCCTTGGGATTAGGAAAAGAAGAA 59.725 38.462 0.00 0.00 41.13 2.52
783 987 0.108089 TCGTCTCGTCTCCTCTCCTG 60.108 60.000 0.00 0.00 0.00 3.86
794 998 2.806608 TTTGTTTAGCCTCGTCTCGT 57.193 45.000 0.00 0.00 0.00 4.18
795 999 3.664537 GCTTTTTGTTTAGCCTCGTCTCG 60.665 47.826 0.00 0.00 0.00 4.04
796 1000 3.498777 AGCTTTTTGTTTAGCCTCGTCTC 59.501 43.478 0.00 0.00 38.14 3.36
797 1001 3.477530 AGCTTTTTGTTTAGCCTCGTCT 58.522 40.909 0.00 0.00 38.14 4.18
939 1149 2.776913 GGAGACGAGGAGGCGAAGG 61.777 68.421 0.00 0.00 34.83 3.46
940 1150 1.720694 GAGGAGACGAGGAGGCGAAG 61.721 65.000 0.00 0.00 34.83 3.79
941 1151 1.749638 GAGGAGACGAGGAGGCGAA 60.750 63.158 0.00 0.00 34.83 4.70
942 1152 2.124653 GAGGAGACGAGGAGGCGA 60.125 66.667 0.00 0.00 34.83 5.54
944 1154 0.818040 GAGAGAGGAGACGAGGAGGC 60.818 65.000 0.00 0.00 0.00 4.70
945 1155 0.179029 GGAGAGAGGAGACGAGGAGG 60.179 65.000 0.00 0.00 0.00 4.30
947 1157 0.834612 GAGGAGAGAGGAGACGAGGA 59.165 60.000 0.00 0.00 0.00 3.71
966 1184 3.699894 ACCACAGGAGCAGCTCGG 61.700 66.667 16.47 13.70 0.00 4.63
967 1185 2.433838 CACCACAGGAGCAGCTCG 60.434 66.667 16.47 6.05 0.00 5.03
972 1190 2.818169 GGACACCACCACAGGAGCA 61.818 63.158 0.00 0.00 0.00 4.26
979 1197 0.603975 GAAGCAGAGGACACCACCAC 60.604 60.000 0.00 0.00 0.00 4.16
1055 1289 0.240411 GAAGCAAAGGTGAGCAGCAG 59.760 55.000 0.00 0.00 0.00 4.24
1088 1323 7.113437 ACAGAGCTCTACTTCACTCAATACTA 58.887 38.462 17.75 0.00 0.00 1.82
1120 1355 8.693542 AGCTAGTATGATGCAAAATTTGTTTC 57.306 30.769 7.60 5.52 0.00 2.78
1137 1373 3.200165 AGAAGGCGGGAAAAAGCTAGTAT 59.800 43.478 0.00 0.00 0.00 2.12
1138 1374 2.570302 AGAAGGCGGGAAAAAGCTAGTA 59.430 45.455 0.00 0.00 0.00 1.82
1139 1375 1.351350 AGAAGGCGGGAAAAAGCTAGT 59.649 47.619 0.00 0.00 0.00 2.57
1140 1376 2.115343 AGAAGGCGGGAAAAAGCTAG 57.885 50.000 0.00 0.00 0.00 3.42
1165 1401 0.687757 TCACCGAGAGAAGATGGGGG 60.688 60.000 0.00 0.00 0.00 5.40
1166 1402 1.134670 GTTCACCGAGAGAAGATGGGG 60.135 57.143 0.00 0.00 0.00 4.96
1169 1405 3.919216 ACAAGTTCACCGAGAGAAGATG 58.081 45.455 0.00 0.00 0.00 2.90
1238 1491 3.708563 TGGAAGCCGAACTTTTTCTTG 57.291 42.857 0.00 0.00 39.29 3.02
1246 1499 1.208293 GGAAGAGATGGAAGCCGAACT 59.792 52.381 0.00 0.00 0.00 3.01
1247 1500 1.066143 TGGAAGAGATGGAAGCCGAAC 60.066 52.381 0.00 0.00 0.00 3.95
1256 1509 4.537751 TCACCTAGTACTGGAAGAGATGG 58.462 47.826 7.98 0.00 37.43 3.51
1283 1536 5.827797 ACACAGTGTAGTTCCAACAATGATT 59.172 36.000 3.69 0.00 43.64 2.57
1284 1537 5.376625 ACACAGTGTAGTTCCAACAATGAT 58.623 37.500 3.69 0.00 43.64 2.45
1321 1584 5.600484 ACCCGATTCTCTAGTCTCAAATCAT 59.400 40.000 0.00 0.00 0.00 2.45
1354 1619 4.389077 CCTCGTTCCATGTCAGAGTAAAAC 59.611 45.833 0.00 0.00 0.00 2.43
1360 1625 0.898320 ACCCTCGTTCCATGTCAGAG 59.102 55.000 0.00 0.00 0.00 3.35
1362 1627 1.001974 TCAACCCTCGTTCCATGTCAG 59.998 52.381 0.00 0.00 0.00 3.51
1385 1650 0.326927 CCCTGTGTAACCCCACGAAT 59.673 55.000 0.00 0.00 38.20 3.34
1388 1653 2.359478 GCCCTGTGTAACCCCACG 60.359 66.667 0.00 0.00 38.20 4.94
1389 1654 1.303317 CAGCCCTGTGTAACCCCAC 60.303 63.158 0.00 0.00 34.36 4.61
1417 1682 7.357303 ACGCAATACTCGAATAAAAAGTTGTT 58.643 30.769 0.00 0.00 0.00 2.83
1432 1697 2.256174 TCACGCTGTTACGCAATACTC 58.744 47.619 1.04 0.00 36.19 2.59
1633 1989 4.254709 TCAACTGCCTGGCGCACT 62.255 61.111 14.98 0.00 44.64 4.40
1634 1990 3.730761 CTCAACTGCCTGGCGCAC 61.731 66.667 14.98 0.00 44.64 5.34
1749 2110 4.580580 CCCTGGGCATCTTAATAAGTGTTC 59.419 45.833 0.00 0.00 0.00 3.18
1776 2137 5.712004 TGTTACAATTGCCTGATTCATGTG 58.288 37.500 5.05 0.00 0.00 3.21
1793 2154 7.451501 TCAAGAATGCATTCTGATTGTTACA 57.548 32.000 36.16 15.89 45.83 2.41
1798 2159 8.648557 AATCAATCAAGAATGCATTCTGATTG 57.351 30.769 40.71 40.71 45.83 2.67
1799 2160 9.745880 GTAATCAATCAAGAATGCATTCTGATT 57.254 29.630 33.39 33.39 45.83 2.57
1804 2165 7.861372 CAGAGGTAATCAATCAAGAATGCATTC 59.139 37.037 28.44 28.44 37.06 2.67
1830 2191 2.749280 AAATGCAAGGCTAAGGCAAC 57.251 45.000 11.62 0.00 41.43 4.17
1865 2226 3.267483 GAGTAATGGCGCTTCAACCTTA 58.733 45.455 7.64 0.00 0.00 2.69
1866 2227 2.084546 GAGTAATGGCGCTTCAACCTT 58.915 47.619 7.64 0.00 0.00 3.50
1877 2238 0.316204 GGGCATGCATGAGTAATGGC 59.684 55.000 30.64 14.86 43.92 4.40
2068 2438 1.534595 GCCATTAGCAATGCAACCTCG 60.535 52.381 8.35 0.00 42.97 4.63
2151 2521 1.611491 ACAACCAACCCAATTAGTGCG 59.389 47.619 0.00 0.00 0.00 5.34
2209 2581 1.309950 CAGCAGCCAGATTCCATCAG 58.690 55.000 0.00 0.00 0.00 2.90
2226 2598 5.313520 TGAATCATGCATGTTACCAACAG 57.686 39.130 25.43 0.00 45.95 3.16
2368 3158 1.338200 CGTAGCCCTTGTCTTTCTGCT 60.338 52.381 0.00 0.00 0.00 4.24
2399 3189 1.664965 GACGGCAGCGAGTTGTTCT 60.665 57.895 0.00 0.00 0.00 3.01
2414 3204 1.505353 GTCGAGTACAGGGGTGACG 59.495 63.158 0.00 0.00 0.00 4.35
2418 3208 0.255318 AGATCGTCGAGTACAGGGGT 59.745 55.000 0.00 0.00 0.00 4.95
2419 3209 0.663688 CAGATCGTCGAGTACAGGGG 59.336 60.000 0.00 0.00 0.00 4.79
2435 3225 6.547141 TCCTTTCTTCTTTCTTGCATTTCAGA 59.453 34.615 0.00 0.00 0.00 3.27
2528 3318 5.473162 TGGACTGTTTACATGATCACCTTTG 59.527 40.000 0.00 0.00 0.00 2.77
2531 3321 4.836825 CTGGACTGTTTACATGATCACCT 58.163 43.478 0.00 0.00 0.00 4.00
2613 3403 7.974504 TGGTTTACCTTATCTTTCTGAAGAGT 58.025 34.615 0.00 0.00 39.95 3.24
2836 3629 1.019673 CATTGCAGTGGCGAGCTTAT 58.980 50.000 0.32 0.00 45.35 1.73
2843 3636 1.199789 ACACATTACATTGCAGTGGCG 59.800 47.619 14.25 1.46 45.35 5.69
2852 3645 7.987458 CCCTAGACAGTTGATACACATTACATT 59.013 37.037 0.00 0.00 0.00 2.71
2902 3703 4.633565 CCAGTCAAGACTCAATCCTAAAGC 59.366 45.833 0.00 0.00 40.20 3.51
2917 3718 7.674705 GCAAACAAGAAAACATTTCCAGTCAAG 60.675 37.037 0.00 0.00 0.00 3.02
2984 3786 7.218773 CCACATAAAGAATGCACTTCATTTACG 59.781 37.037 10.26 7.72 44.95 3.18
3176 3985 4.513318 CACTGAGAAGAAAGGAACCTTGAC 59.487 45.833 6.88 5.16 36.26 3.18
3542 4418 6.539649 TTCGTGACGATTTCTTTCAATCTT 57.460 33.333 9.08 0.00 35.23 2.40
3557 4433 1.866925 GGCCCTTCTTTTCGTGACG 59.133 57.895 0.00 0.00 0.00 4.35
3566 4442 4.779993 ATCTTCTAATTCGGCCCTTCTT 57.220 40.909 0.00 0.00 0.00 2.52
3796 4676 5.491635 AGTGACTCTTCTTTTGCTTTCAC 57.508 39.130 0.00 0.00 33.76 3.18
4193 5081 4.414337 AGCTGAGAAAGATATGGGTCAC 57.586 45.455 0.00 0.00 0.00 3.67
4421 5309 2.019948 GGTATCGCCGTTTTTCCTCT 57.980 50.000 0.00 0.00 0.00 3.69
4517 5405 9.084164 CAATTTCTTCTGATCCTGCAAATAAAG 57.916 33.333 0.00 0.00 0.00 1.85
4778 5666 2.930040 CGCCGAAGTTCAGTTGTGATAT 59.070 45.455 3.32 0.00 30.85 1.63
4834 5722 2.843113 AGAAGGGGATTCTGGTTCAGAG 59.157 50.000 0.00 0.00 46.80 3.35
4995 5883 6.967199 GTCCATTTACAATGCTAAGTACTTGC 59.033 38.462 18.56 18.07 0.00 4.01
5387 6275 4.025360 TGCATTTTATGGCATGGACTCTT 58.975 39.130 10.98 0.00 34.58 2.85
5512 6409 0.317160 TTGCTTCCGTCATGTCGTCT 59.683 50.000 11.29 0.00 0.00 4.18
5808 6705 0.387565 GAGGAGACGAAGATGGAGGC 59.612 60.000 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.