Multiple sequence alignment - TraesCS1A01G315400

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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 TraesCS1A01G315400 chr1A 100.000 6449 0 0 1 6449 506997554 507004002 0.000000e+00 11910
1 TraesCS1A01G315400 chr1A 80.793 328 41 13 1026 1346 69080414 69080102 3.010000e-58 237
2 TraesCS1A01G315400 chr1D 92.460 6154 265 85 30 6097 410738023 410744063 0.000000e+00 8610
3 TraesCS1A01G315400 chr1D 83.704 270 18 11 6175 6433 410744302 410744556 1.400000e-56 231
4 TraesCS1A01G315400 chr1B 90.286 6475 333 123 144 6449 553553032 553559379 0.000000e+00 8200
5 TraesCS1A01G315400 chr7D 91.114 1508 93 23 4395 5879 370516628 370518117 0.000000e+00 2004
6 TraesCS1A01G315400 chr7D 81.121 339 26 12 1026 1349 233910318 233910003 3.010000e-58 237
7 TraesCS1A01G315400 chr7A 85.000 320 32 6 3064 3375 49508998 49509309 1.750000e-80 311
8 TraesCS1A01G315400 chr4B 86.667 270 21 4 864 1124 613179468 613179731 1.060000e-72 285
9 TraesCS1A01G315400 chr4B 84.444 270 24 6 864 1124 601913091 601913351 3.860000e-62 250
10 TraesCS1A01G315400 chr4B 79.944 354 46 17 1031 1377 8269944 8269609 3.010000e-58 237
11 TraesCS1A01G315400 chr4B 80.347 346 23 15 1026 1371 584525856 584525556 3.030000e-53 220
12 TraesCS1A01G315400 chrUn 81.768 362 34 12 1026 1381 102814447 102814112 2.290000e-69 274
13 TraesCS1A01G315400 chrUn 85.662 272 17 11 864 1124 49108228 49107968 3.830000e-67 267
14 TraesCS1A01G315400 chrUn 85.185 270 22 5 864 1124 49052742 49052482 1.780000e-65 261
15 TraesCS1A01G315400 chrUn 83.333 156 5 8 1026 1166 102816006 102815857 2.440000e-24 124
16 TraesCS1A01G315400 chr3D 82.286 350 31 10 1027 1368 609865941 609866267 2.290000e-69 274
17 TraesCS1A01G315400 chr6A 85.985 264 20 5 864 1119 558130485 558130739 3.830000e-67 267
18 TraesCS1A01G315400 chr3B 85.606 264 21 5 864 1119 673562882 673562628 1.780000e-65 261
19 TraesCS1A01G315400 chr3B 81.232 357 29 9 1027 1368 820860385 820860052 2.980000e-63 254
20 TraesCS1A01G315400 chr5B 85.606 264 13 7 1094 1357 647915704 647915942 2.980000e-63 254
21 TraesCS1A01G315400 chr2A 79.834 362 41 15 1026 1381 31354095 31354430 1.080000e-57 235
22 TraesCS1A01G315400 chr7B 83.333 270 27 6 864 1124 658838585 658838845 3.890000e-57 233
23 TraesCS1A01G315400 chr5A 81.955 266 32 10 1090 1348 302449477 302449733 1.820000e-50 211
24 TraesCS1A01G315400 chr3A 78.531 354 43 16 1026 1371 108076684 108076356 1.100000e-47 202
25 TraesCS1A01G315400 chr4D 81.410 156 8 5 1026 1166 5076627 5076478 2.460000e-19 108
26 TraesCS1A01G315400 chr6B 81.884 138 8 4 1026 1163 624142469 624142589 4.110000e-17 100


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 TraesCS1A01G315400 chr1A 506997554 507004002 6448 False 11910.0 11910 100.000 1 6449 1 chr1A.!!$F1 6448
1 TraesCS1A01G315400 chr1D 410738023 410744556 6533 False 4420.5 8610 88.082 30 6433 2 chr1D.!!$F1 6403
2 TraesCS1A01G315400 chr1B 553553032 553559379 6347 False 8200.0 8200 90.286 144 6449 1 chr1B.!!$F1 6305
3 TraesCS1A01G315400 chr7D 370516628 370518117 1489 False 2004.0 2004 91.114 4395 5879 1 chr7D.!!$F1 1484

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
282 291 0.037590 TTGCTGATAACCCAAGCCGT 59.962 50.000 0.00 0.00 0.00 5.68 F
520 557 0.662619 CGCACGTCCCATATGCAAAT 59.337 50.000 0.00 0.00 39.39 2.32 F
924 995 1.075600 CTCCTCCCTCCCTCTCACC 60.076 68.421 0.00 0.00 0.00 4.02 F
1369 1471 1.002379 AAGCAGCAGAAGCAGGAGG 60.002 57.895 0.00 0.00 45.49 4.30 F
2928 3041 0.937304 CCACTGTGAACACCTGAACG 59.063 55.000 9.86 0.00 0.00 3.95 F
3069 3182 5.403897 TGACTTTCTTGTTAGCGAAACTG 57.596 39.130 6.55 1.14 38.99 3.16 F
3995 4115 0.033503 TCTGTCTATGTCTGGCGGGA 60.034 55.000 0.00 0.00 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1288 1390 0.391661 GAATCTGCAGAGCCCGTGAA 60.392 55.000 22.96 0.0 0.00 3.18 R
1351 1453 1.002379 CCTCCTGCTTCTGCTGCTT 60.002 57.895 0.00 0.0 40.48 3.91 R
2304 2410 1.207329 GCTCCCAATACAGACGAAGGT 59.793 52.381 0.00 0.0 0.00 3.50 R
2971 3084 2.559668 CACAGAAGTGTTCCATGGCATT 59.440 45.455 6.96 0.0 40.92 3.56 R
3976 4095 0.033503 TCCCGCCAGACATAGACAGA 60.034 55.000 0.00 0.0 0.00 3.41 R
4482 4603 1.511850 CACTGCCATGTCGAGTTTGA 58.488 50.000 0.00 0.0 0.00 2.69 R
5884 6072 0.257328 TGTCAAAAGGCACAGGACCA 59.743 50.000 0.00 0.0 0.00 4.02 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
24 25 3.505184 CGCCGCGCCCAAAGTAAT 61.505 61.111 0.00 0.00 0.00 1.89
25 26 2.407616 GCCGCGCCCAAAGTAATC 59.592 61.111 0.00 0.00 0.00 1.75
26 27 3.107447 CCGCGCCCAAAGTAATCC 58.893 61.111 0.00 0.00 0.00 3.01
27 28 1.747367 CCGCGCCCAAAGTAATCCA 60.747 57.895 0.00 0.00 0.00 3.41
28 29 1.309499 CCGCGCCCAAAGTAATCCAA 61.309 55.000 0.00 0.00 0.00 3.53
39 40 2.632377 AGTAATCCAACCATGCAGACG 58.368 47.619 0.00 0.00 0.00 4.18
69 70 1.225475 CGACGCACGCATGAGAAAC 60.225 57.895 2.50 0.00 34.51 2.78
72 73 0.235665 ACGCACGCATGAGAAACAAG 59.764 50.000 2.50 0.00 0.00 3.16
141 147 2.194800 TCGATCGAAGCACTCATGAC 57.805 50.000 16.99 0.00 0.00 3.06
186 192 6.545298 GCAGGAAATCAGAAGAGAAATATGGT 59.455 38.462 0.00 0.00 0.00 3.55
206 212 4.403432 TGGTCTCTAAATACGGGAAATCGT 59.597 41.667 0.00 0.00 45.88 3.73
224 230 1.741706 CGTGGAGAGAAATGCATTGCT 59.258 47.619 20.41 20.41 0.00 3.91
260 266 3.941483 AGTGATAACATTTCAAGCGAGGG 59.059 43.478 0.00 0.00 0.00 4.30
282 291 0.037590 TTGCTGATAACCCAAGCCGT 59.962 50.000 0.00 0.00 0.00 5.68
354 373 7.721842 TCTTCTCTTCCAATACTAGATCGACAT 59.278 37.037 0.00 0.00 0.00 3.06
419 445 1.213094 ACGCCGAAGAACACAACTCG 61.213 55.000 0.00 0.00 0.00 4.18
513 550 4.840288 CGCGACGCACGTCCCATA 62.840 66.667 21.35 0.00 44.60 2.74
514 551 2.279252 GCGACGCACGTCCCATAT 60.279 61.111 16.42 0.00 44.60 1.78
515 552 2.585869 GCGACGCACGTCCCATATG 61.586 63.158 16.42 0.00 44.60 1.78
516 553 2.585869 CGACGCACGTCCCATATGC 61.586 63.158 16.81 0.00 41.76 3.14
517 554 1.520564 GACGCACGTCCCATATGCA 60.521 57.895 12.04 0.00 39.39 3.96
518 555 1.078778 ACGCACGTCCCATATGCAA 60.079 52.632 0.00 0.00 39.39 4.08
519 556 0.675208 ACGCACGTCCCATATGCAAA 60.675 50.000 0.00 0.00 39.39 3.68
520 557 0.662619 CGCACGTCCCATATGCAAAT 59.337 50.000 0.00 0.00 39.39 2.32
521 558 1.597690 CGCACGTCCCATATGCAAATG 60.598 52.381 0.00 0.00 39.39 2.32
522 559 1.865248 GCACGTCCCATATGCAAATGC 60.865 52.381 0.00 0.00 39.23 3.56
548 585 1.152943 GCCTCCTCCCCGGAAAATC 60.153 63.158 0.73 0.00 42.53 2.17
688 733 1.431496 TTTTCCTACCGTACGCAAGC 58.569 50.000 10.49 0.00 45.62 4.01
707 752 5.431309 CAAGCCGCAAGTTAAAATTTTGTC 58.569 37.500 13.76 6.41 0.00 3.18
924 995 1.075600 CTCCTCCCTCCCTCTCACC 60.076 68.421 0.00 0.00 0.00 4.02
925 996 2.041405 CCTCCCTCCCTCTCACCC 60.041 72.222 0.00 0.00 0.00 4.61
926 997 2.443016 CTCCCTCCCTCTCACCCG 60.443 72.222 0.00 0.00 0.00 5.28
927 998 4.779733 TCCCTCCCTCTCACCCGC 62.780 72.222 0.00 0.00 0.00 6.13
1185 1283 4.459089 GGTGGCGGTGAGAGCTCC 62.459 72.222 10.93 2.40 34.52 4.70
1220 1322 4.271816 CCGCCGACTCATCTCCCG 62.272 72.222 0.00 0.00 0.00 5.14
1288 1390 2.546494 GCTGACTGGCTTGCGTGTT 61.546 57.895 0.00 0.00 0.00 3.32
1368 1470 1.025647 GGAAGCAGCAGAAGCAGGAG 61.026 60.000 0.00 0.00 45.49 3.69
1369 1471 1.002379 AAGCAGCAGAAGCAGGAGG 60.002 57.895 0.00 0.00 45.49 4.30
1370 1472 1.486997 AAGCAGCAGAAGCAGGAGGA 61.487 55.000 0.00 0.00 45.49 3.71
1371 1473 1.224039 GCAGCAGAAGCAGGAGGAT 59.776 57.895 0.00 0.00 45.49 3.24
1496 1598 4.179599 CCCCTCCTCCCTCCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
1497 1599 4.179599 CCCTCCTCCCTCCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
1498 1600 4.179599 CCTCCTCCCTCCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
1499 1601 4.179599 CTCCTCCCTCCCCTCCCC 62.180 77.778 0.00 0.00 0.00 4.81
1555 1660 2.162338 TTGCCGATTTCCCGTCGTCT 62.162 55.000 0.00 0.00 37.39 4.18
1678 1783 3.062466 CTCACCTCGTCGGGCTCA 61.062 66.667 0.00 0.00 36.97 4.26
1744 1849 2.342648 GCTCGGGTTTCTCGTGGT 59.657 61.111 0.00 0.00 0.00 4.16
1952 2057 2.261671 GGGTCGATCGCCGCATAT 59.738 61.111 11.09 0.00 38.37 1.78
2103 2209 2.268920 CCCGGCTCTTTGCTGCTA 59.731 61.111 0.00 0.00 46.34 3.49
2137 2243 3.211865 TCTGAATGATCTTGCCATGCTC 58.788 45.455 0.00 0.00 0.00 4.26
2206 2312 4.578871 TCATCATGTCGAATGGTTCTGTT 58.421 39.130 0.00 0.00 0.00 3.16
2207 2313 4.631377 TCATCATGTCGAATGGTTCTGTTC 59.369 41.667 0.00 0.00 0.00 3.18
2208 2314 4.271696 TCATGTCGAATGGTTCTGTTCT 57.728 40.909 0.00 0.00 0.00 3.01
2209 2315 5.400066 TCATGTCGAATGGTTCTGTTCTA 57.600 39.130 0.00 0.00 0.00 2.10
2210 2316 5.977635 TCATGTCGAATGGTTCTGTTCTAT 58.022 37.500 0.00 0.00 0.00 1.98
2273 2379 2.554142 CAGCGCATGTAAGATCTTCCA 58.446 47.619 12.24 7.30 0.00 3.53
2304 2410 1.133945 TCAGTTTTGTAGCAGGTGCCA 60.134 47.619 0.00 0.00 43.38 4.92
2550 2657 0.999406 CCTCGGTACTGAAATGCACG 59.001 55.000 5.76 0.00 0.00 5.34
2692 2805 3.058708 CAGATTGTAGCACACACACCTTG 60.059 47.826 0.00 0.00 36.69 3.61
2724 2837 7.646654 TGATCCCCTTTGATCCAGATAATTA 57.353 36.000 0.00 0.00 40.37 1.40
2726 2839 8.681584 TGATCCCCTTTGATCCAGATAATTATT 58.318 33.333 0.00 0.00 40.37 1.40
2750 2863 4.420168 AGACATTGTTTTTGTTGACCACG 58.580 39.130 0.00 0.00 0.00 4.94
2756 2869 4.106197 TGTTTTTGTTGACCACGTATTGC 58.894 39.130 0.00 0.00 0.00 3.56
2773 2886 5.220006 CGTATTGCATGTCGTTTGGATTTTG 60.220 40.000 0.00 0.00 0.00 2.44
2777 2890 4.047822 GCATGTCGTTTGGATTTTGTTGA 58.952 39.130 0.00 0.00 0.00 3.18
2806 2919 7.564793 TGCTTAGATTTCTCAGCTGGTAAATA 58.435 34.615 20.28 8.99 42.19 1.40
2928 3041 0.937304 CCACTGTGAACACCTGAACG 59.063 55.000 9.86 0.00 0.00 3.95
3045 3158 5.603170 AATGCCAATTGGTAATGGAAGAG 57.397 39.130 25.19 0.00 39.12 2.85
3069 3182 5.403897 TGACTTTCTTGTTAGCGAAACTG 57.596 39.130 6.55 1.14 38.99 3.16
3109 3222 7.144722 TGTTTTCTCATGCAGGTTTATACTG 57.855 36.000 0.00 0.00 38.95 2.74
3286 3404 8.950210 AGGATAATGTGTTCTGTACATCTTTTG 58.050 33.333 0.00 0.00 39.39 2.44
3428 3546 7.304497 ACAAGAAACTAGGTAGAATGTCTGT 57.696 36.000 0.00 0.00 0.00 3.41
3598 3716 7.075741 GCGTTATTTGTCTACAGTGTCATTTT 58.924 34.615 0.00 0.00 0.00 1.82
3976 4095 6.402658 CGCAACAAAAAGGTTGGTTTATTTGT 60.403 34.615 7.99 0.00 46.36 2.83
3991 4111 6.183360 GGTTTATTTGTCTGTCTATGTCTGGC 60.183 42.308 0.00 0.00 0.00 4.85
3994 4114 0.103208 GTCTGTCTATGTCTGGCGGG 59.897 60.000 0.00 0.00 0.00 6.13
3995 4115 0.033503 TCTGTCTATGTCTGGCGGGA 60.034 55.000 0.00 0.00 0.00 5.14
3996 4116 0.824109 CTGTCTATGTCTGGCGGGAA 59.176 55.000 0.00 0.00 0.00 3.97
3997 4117 1.207089 CTGTCTATGTCTGGCGGGAAA 59.793 52.381 0.00 0.00 0.00 3.13
3998 4118 1.837439 TGTCTATGTCTGGCGGGAAAT 59.163 47.619 0.00 0.00 0.00 2.17
3999 4119 2.213499 GTCTATGTCTGGCGGGAAATG 58.787 52.381 0.00 0.00 0.00 2.32
4021 4141 4.889409 TGAAATTATCTGCCCTGGTCATTC 59.111 41.667 0.00 0.00 0.00 2.67
4022 4142 3.515602 ATTATCTGCCCTGGTCATTCC 57.484 47.619 0.00 0.00 0.00 3.01
4040 4160 6.797033 GTCATTCCGTATTTGTCTTCTTGTTG 59.203 38.462 0.00 0.00 0.00 3.33
4203 4323 2.047002 AGAAGAGAGGACGGACTAGC 57.953 55.000 0.00 0.00 0.00 3.42
4361 4481 2.103094 CACGATCATCCCCTGCTAAGAA 59.897 50.000 0.00 0.00 0.00 2.52
4482 4603 1.367102 CAAAAATGGCACCCGCAGT 59.633 52.632 0.00 0.00 41.24 4.40
4587 4708 6.992123 TCCGTAATGCTGATGAATTTGATACT 59.008 34.615 0.00 0.00 0.00 2.12
4605 4726 6.270815 TGATACTAAGGTAACAACAGATCGC 58.729 40.000 0.00 0.00 41.41 4.58
4611 4734 2.268298 GTAACAACAGATCGCCGACAT 58.732 47.619 0.00 0.00 0.00 3.06
4688 4819 9.118300 ACTTATGCTTTGGAAGATTCAGATTAG 57.882 33.333 0.00 0.00 0.00 1.73
4691 4822 7.849804 TGCTTTGGAAGATTCAGATTAGTAC 57.150 36.000 0.00 0.00 0.00 2.73
4714 4845 7.631717 ACTAAACATTCTAAAAGGCTGGATC 57.368 36.000 0.00 0.00 0.00 3.36
4724 4855 0.325296 AGGCTGGATCCGTCCTGTTA 60.325 55.000 20.27 0.00 45.32 2.41
4798 4929 2.421073 ACATCAGCACATGCACATACAC 59.579 45.455 6.64 0.00 45.16 2.90
5042 5177 1.261885 TGCCGTTTGTAATGTGACACG 59.738 47.619 0.22 0.00 0.00 4.49
5263 5402 1.563410 CTGGAAAGGCTCAAGGAGGAT 59.437 52.381 0.00 0.00 0.00 3.24
5308 5447 2.270986 GCTTGCCTCTGGTGTTGGG 61.271 63.158 0.00 0.00 0.00 4.12
5327 5466 2.327373 GGGACCTGGTAATCCTACCTC 58.673 57.143 0.00 0.00 46.97 3.85
5328 5467 2.090663 GGGACCTGGTAATCCTACCTCT 60.091 54.545 0.00 0.00 46.97 3.69
5329 5468 2.966516 GGACCTGGTAATCCTACCTCTG 59.033 54.545 0.00 0.00 46.97 3.35
5342 5481 2.486472 ACCTCTGAATTGACTGCCTG 57.514 50.000 0.00 0.00 0.00 4.85
5343 5482 1.701847 ACCTCTGAATTGACTGCCTGT 59.298 47.619 0.00 0.00 0.00 4.00
5360 5502 3.855895 GCCTGTTTAACCGCTTCTTTTCC 60.856 47.826 0.00 0.00 0.00 3.13
5371 5513 2.672195 GCTTCTTTTCCCCATTGCTTCG 60.672 50.000 0.00 0.00 0.00 3.79
5625 5787 7.868415 GGCGACAAAGTAGTAGATTTATCATCT 59.132 37.037 0.00 0.00 0.00 2.90
5684 5846 1.979855 TGTGGAGTGGTTCATTGGTG 58.020 50.000 0.00 0.00 0.00 4.17
5704 5867 5.221204 TGGTGGGTTAAACGTAAAATTGACC 60.221 40.000 3.66 3.66 35.17 4.02
5858 6036 0.455633 CCGTCTAACTCGAACCCGTG 60.456 60.000 0.00 0.00 37.05 4.94
5872 6060 1.623311 ACCCGTGTGATGAGTGAATGA 59.377 47.619 0.00 0.00 0.00 2.57
5880 6068 4.945543 TGTGATGAGTGAATGAGAATTGGG 59.054 41.667 0.00 0.00 0.00 4.12
5883 6071 3.765381 TGAGTGAATGAGAATTGGGCAA 58.235 40.909 0.00 0.00 0.00 4.52
5884 6072 4.346730 TGAGTGAATGAGAATTGGGCAAT 58.653 39.130 0.00 0.00 0.00 3.56
5886 6074 3.449737 AGTGAATGAGAATTGGGCAATGG 59.550 43.478 0.00 0.00 0.00 3.16
5889 6077 1.851304 TGAGAATTGGGCAATGGTCC 58.149 50.000 0.00 0.00 40.08 4.46
5890 6078 1.358787 TGAGAATTGGGCAATGGTCCT 59.641 47.619 0.00 0.00 40.42 3.85
5893 6081 1.205417 GAATTGGGCAATGGTCCTGTG 59.795 52.381 0.00 0.00 40.42 3.66
5894 6082 1.259840 ATTGGGCAATGGTCCTGTGC 61.260 55.000 8.42 8.42 40.42 4.57
6037 6237 2.277057 TCGACACGTATGCGCTCG 60.277 61.111 9.73 14.92 42.83 5.03
6076 6279 3.364964 GCGGTGGTCATAAAGTTGTCTTG 60.365 47.826 0.00 0.00 33.79 3.02
6240 6604 0.747283 GCAGCTCAGGTCCAATCAGG 60.747 60.000 0.00 0.00 39.47 3.86
6286 6650 3.228017 GGCCTAGCCTCCTCGTCC 61.228 72.222 0.00 0.00 46.69 4.79
6287 6651 2.123640 GCCTAGCCTCCTCGTCCT 60.124 66.667 0.00 0.00 0.00 3.85
6289 6653 1.174078 GCCTAGCCTCCTCGTCCTAC 61.174 65.000 0.00 0.00 0.00 3.18
6290 6654 0.885596 CCTAGCCTCCTCGTCCTACG 60.886 65.000 0.00 0.00 44.19 3.51
6317 6692 3.560105 GATGGAATCTTGGGGAAGAAGG 58.440 50.000 0.00 0.00 41.17 3.46
6325 6700 3.584848 TCTTGGGGAAGAAGGAGAAGAAG 59.415 47.826 0.00 0.00 0.00 2.85
6326 6701 3.275848 TGGGGAAGAAGGAGAAGAAGA 57.724 47.619 0.00 0.00 0.00 2.87
6327 6702 3.598264 TGGGGAAGAAGGAGAAGAAGAA 58.402 45.455 0.00 0.00 0.00 2.52
6332 6707 6.007076 GGGAAGAAGGAGAAGAAGAAAATGT 58.993 40.000 0.00 0.00 0.00 2.71
6442 6817 9.927668 TCTTCAATTTTTCTTTAATGGATCCAC 57.072 29.630 18.99 0.00 0.00 4.02
6444 6819 9.709495 TTCAATTTTTCTTTAATGGATCCACAG 57.291 29.630 18.99 10.95 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.449095 GATTACTTTGGGCGCGGCG 62.449 63.158 27.12 19.62 0.00 6.46
8 9 2.407616 GATTACTTTGGGCGCGGC 59.592 61.111 26.39 26.39 0.00 6.53
9 10 1.309499 TTGGATTACTTTGGGCGCGG 61.309 55.000 8.83 0.00 0.00 6.46
10 11 0.179174 GTTGGATTACTTTGGGCGCG 60.179 55.000 0.00 0.00 0.00 6.86
11 12 0.172578 GGTTGGATTACTTTGGGCGC 59.827 55.000 0.00 0.00 0.00 6.53
12 13 1.540267 TGGTTGGATTACTTTGGGCG 58.460 50.000 0.00 0.00 0.00 6.13
13 14 2.418609 GCATGGTTGGATTACTTTGGGC 60.419 50.000 0.00 0.00 0.00 5.36
14 15 2.830923 TGCATGGTTGGATTACTTTGGG 59.169 45.455 0.00 0.00 0.00 4.12
15 16 3.763360 TCTGCATGGTTGGATTACTTTGG 59.237 43.478 0.00 0.00 0.00 3.28
16 17 4.672542 CGTCTGCATGGTTGGATTACTTTG 60.673 45.833 0.00 0.00 0.00 2.77
17 18 3.440173 CGTCTGCATGGTTGGATTACTTT 59.560 43.478 0.00 0.00 0.00 2.66
18 19 3.009723 CGTCTGCATGGTTGGATTACTT 58.990 45.455 0.00 0.00 0.00 2.24
19 20 2.027192 ACGTCTGCATGGTTGGATTACT 60.027 45.455 0.00 0.00 0.00 2.24
20 21 2.356135 ACGTCTGCATGGTTGGATTAC 58.644 47.619 0.00 0.00 0.00 1.89
21 22 2.779755 ACGTCTGCATGGTTGGATTA 57.220 45.000 0.00 0.00 0.00 1.75
22 23 2.779755 TACGTCTGCATGGTTGGATT 57.220 45.000 0.00 0.00 0.00 3.01
23 24 4.623932 ATATACGTCTGCATGGTTGGAT 57.376 40.909 0.00 0.00 0.00 3.41
24 25 5.245075 TGATATATACGTCTGCATGGTTGGA 59.755 40.000 0.00 0.00 0.00 3.53
25 26 5.348724 GTGATATATACGTCTGCATGGTTGG 59.651 44.000 0.00 0.00 0.00 3.77
26 27 5.060940 CGTGATATATACGTCTGCATGGTTG 59.939 44.000 0.00 0.00 36.83 3.77
27 28 5.161358 CGTGATATATACGTCTGCATGGTT 58.839 41.667 0.00 0.00 36.83 3.67
28 29 4.733850 CGTGATATATACGTCTGCATGGT 58.266 43.478 0.00 0.00 36.83 3.55
39 40 1.571840 CGTGCGTCGCGTGATATATAC 59.428 52.381 13.38 0.48 32.40 1.47
64 65 1.222115 GCCTCGTGTCGCTTGTTTCT 61.222 55.000 0.00 0.00 0.00 2.52
69 70 2.049156 TGAGCCTCGTGTCGCTTG 60.049 61.111 0.00 0.00 34.84 4.01
72 73 2.505118 GAGTGAGCCTCGTGTCGC 60.505 66.667 0.00 0.00 0.00 5.19
92 93 3.008049 GGGTTGTATATCCAGGCCTACAG 59.992 52.174 3.98 0.00 0.00 2.74
136 142 4.700213 AGGGAAACTAAATTCGTGGTCATG 59.300 41.667 0.00 0.00 0.00 3.07
137 143 4.918588 AGGGAAACTAAATTCGTGGTCAT 58.081 39.130 0.00 0.00 0.00 3.06
141 147 3.254657 TGCAAGGGAAACTAAATTCGTGG 59.745 43.478 0.00 0.00 0.00 4.94
186 192 4.646040 TCCACGATTTCCCGTATTTAGAGA 59.354 41.667 0.00 0.00 41.29 3.10
206 212 7.654568 CAATTATAGCAATGCATTTCTCTCCA 58.345 34.615 15.06 0.00 0.00 3.86
260 266 2.671070 CGGCTTGGGTTATCAGCAAAAC 60.671 50.000 0.00 0.00 0.00 2.43
282 291 0.837691 ACAGTCATCCTGCCAGGTGA 60.838 55.000 11.27 10.93 45.68 4.02
354 373 2.238521 GCCTTGTTCCATCCAAGTGAA 58.761 47.619 0.00 0.00 38.07 3.18
647 691 2.824388 AAAGACCGGGGAGGAGGAGG 62.824 65.000 6.32 0.00 45.00 4.30
648 692 0.032416 TAAAGACCGGGGAGGAGGAG 60.032 60.000 6.32 0.00 45.00 3.69
649 693 0.640495 ATAAAGACCGGGGAGGAGGA 59.360 55.000 6.32 0.00 45.00 3.71
688 733 3.427193 CGGGACAAAATTTTAACTTGCGG 59.573 43.478 2.44 0.00 0.00 5.69
1167 1265 4.803426 GAGCTCTCACCGCCACCG 62.803 72.222 6.43 0.00 0.00 4.94
1168 1266 4.459089 GGAGCTCTCACCGCCACC 62.459 72.222 14.64 0.00 0.00 4.61
1169 1267 4.803426 CGGAGCTCTCACCGCCAC 62.803 72.222 14.64 0.00 42.55 5.01
1288 1390 0.391661 GAATCTGCAGAGCCCGTGAA 60.392 55.000 22.96 0.00 0.00 3.18
1348 1450 2.396955 CCTGCTTCTGCTGCTTCCG 61.397 63.158 0.00 0.00 40.48 4.30
1349 1451 1.002868 TCCTGCTTCTGCTGCTTCC 60.003 57.895 0.00 0.00 40.48 3.46
1351 1453 1.002379 CCTCCTGCTTCTGCTGCTT 60.002 57.895 0.00 0.00 40.48 3.91
1360 1462 1.220206 CGTGCTCATCCTCCTGCTT 59.780 57.895 0.00 0.00 0.00 3.91
1368 1470 1.522580 GCCTTCCTCGTGCTCATCC 60.523 63.158 0.00 0.00 0.00 3.51
1369 1471 1.880340 CGCCTTCCTCGTGCTCATC 60.880 63.158 0.00 0.00 0.00 2.92
1370 1472 2.185350 CGCCTTCCTCGTGCTCAT 59.815 61.111 0.00 0.00 0.00 2.90
1371 1473 4.069232 CCGCCTTCCTCGTGCTCA 62.069 66.667 0.00 0.00 0.00 4.26
1497 1599 3.878667 GAGATGGGAAGGGGCGGG 61.879 72.222 0.00 0.00 0.00 6.13
1498 1600 3.878667 GGAGATGGGAAGGGGCGG 61.879 72.222 0.00 0.00 0.00 6.13
1499 1601 2.770048 AGGAGATGGGAAGGGGCG 60.770 66.667 0.00 0.00 0.00 6.13
1600 1705 3.138798 CCGACGATGACCTCCGGT 61.139 66.667 0.00 0.00 39.44 5.28
1952 2057 1.536907 TCCGGGGTAACAGCTTGGA 60.537 57.895 0.00 0.00 39.74 3.53
2045 2151 1.722751 CGCACACGATTCAGAAGCAAC 60.723 52.381 0.00 0.00 43.93 4.17
2103 2209 3.445008 TCATTCAGAAGGTCAGGCTAGT 58.555 45.455 0.00 0.00 0.00 2.57
2137 2243 2.262915 GGAGCTCACACGGGTCTG 59.737 66.667 17.19 0.00 0.00 3.51
2257 2363 4.142609 TCCACTGGAAGATCTTACATGC 57.857 45.455 20.79 1.62 37.43 4.06
2273 2379 5.827797 TGCTACAAAACTGAGAAAATCCACT 59.172 36.000 0.00 0.00 0.00 4.00
2304 2410 1.207329 GCTCCCAATACAGACGAAGGT 59.793 52.381 0.00 0.00 0.00 3.50
2550 2657 6.565623 GCGAGAAAAGATTCATAGAAGCATCC 60.566 42.308 0.00 0.00 38.06 3.51
2692 2805 4.098501 GGATCAAAGGGGATCAAATGTGAC 59.901 45.833 5.63 0.00 44.38 3.67
2724 2837 7.221838 CGTGGTCAACAAAAACAATGTCTAAAT 59.778 33.333 0.00 0.00 0.00 1.40
2726 2839 6.030849 CGTGGTCAACAAAAACAATGTCTAA 58.969 36.000 0.00 0.00 0.00 2.10
2733 2846 4.563184 GCAATACGTGGTCAACAAAAACAA 59.437 37.500 0.00 0.00 0.00 2.83
2750 2863 5.633182 ACAAAATCCAAACGACATGCAATAC 59.367 36.000 0.00 0.00 0.00 1.89
2756 2869 7.060979 CAGTATCAACAAAATCCAAACGACATG 59.939 37.037 0.00 0.00 0.00 3.21
2806 2919 6.150809 GGCAGAAGAAGAGTTGATTTGATTCT 59.849 38.462 0.00 0.00 0.00 2.40
2844 2957 3.066760 GGGACAACTTGAACACTGGAAAG 59.933 47.826 0.00 0.00 0.00 2.62
2890 3003 2.983192 TGGGACTACAGGAAACAATGGA 59.017 45.455 0.00 0.00 0.00 3.41
2893 3006 3.394606 ACAGTGGGACTACAGGAAACAAT 59.605 43.478 0.00 0.00 0.00 2.71
2970 3083 3.758023 CACAGAAGTGTTCCATGGCATTA 59.242 43.478 6.96 0.00 40.92 1.90
2971 3084 2.559668 CACAGAAGTGTTCCATGGCATT 59.440 45.455 6.96 0.00 40.92 3.56
3045 3158 5.677178 CAGTTTCGCTAACAAGAAAGTCAAC 59.323 40.000 3.61 0.00 37.77 3.18
3109 3222 6.149474 CCTTCCGTATATCCATCAATTTCACC 59.851 42.308 0.00 0.00 0.00 4.02
3428 3546 8.239314 GCAAATTCTCAGATATCACAGTTTGAA 58.761 33.333 5.32 0.56 37.92 2.69
3976 4095 0.033503 TCCCGCCAGACATAGACAGA 60.034 55.000 0.00 0.00 0.00 3.41
3991 4111 3.891366 AGGGCAGATAATTTCATTTCCCG 59.109 43.478 0.00 0.00 36.40 5.14
3994 4114 5.360714 TGACCAGGGCAGATAATTTCATTTC 59.639 40.000 0.00 0.00 0.00 2.17
3995 4115 5.271598 TGACCAGGGCAGATAATTTCATTT 58.728 37.500 0.00 0.00 0.00 2.32
3996 4116 4.870636 TGACCAGGGCAGATAATTTCATT 58.129 39.130 0.00 0.00 0.00 2.57
3997 4117 4.524802 TGACCAGGGCAGATAATTTCAT 57.475 40.909 0.00 0.00 0.00 2.57
3998 4118 4.524802 ATGACCAGGGCAGATAATTTCA 57.475 40.909 0.00 0.00 0.00 2.69
3999 4119 4.279420 GGAATGACCAGGGCAGATAATTTC 59.721 45.833 0.00 0.00 38.79 2.17
4021 4141 5.907391 GTCAACAACAAGAAGACAAATACGG 59.093 40.000 0.00 0.00 0.00 4.02
4022 4142 6.482835 TGTCAACAACAAGAAGACAAATACG 58.517 36.000 0.00 0.00 36.39 3.06
4040 4160 7.307694 TCATGAGAAATACAGCAAATGTCAAC 58.692 34.615 0.00 0.00 42.70 3.18
4203 4323 2.441001 AGTTGGGGCATTATCAGGAGAG 59.559 50.000 0.00 0.00 0.00 3.20
4361 4481 3.567164 GCTGCTATCAACACTGCCAATAT 59.433 43.478 0.00 0.00 0.00 1.28
4482 4603 1.511850 CACTGCCATGTCGAGTTTGA 58.488 50.000 0.00 0.00 0.00 2.69
4587 4708 2.492881 TCGGCGATCTGTTGTTACCTTA 59.507 45.455 4.99 0.00 0.00 2.69
4602 4723 6.243811 ACTGTAAATTTAAAATGTCGGCGA 57.756 33.333 4.99 4.99 0.00 5.54
4605 4726 9.893305 AGAGAAACTGTAAATTTAAAATGTCGG 57.107 29.630 0.00 0.00 0.00 4.79
4688 4819 7.916914 TCCAGCCTTTTAGAATGTTTAGTAC 57.083 36.000 0.00 0.00 0.00 2.73
4691 4822 6.238484 CGGATCCAGCCTTTTAGAATGTTTAG 60.238 42.308 13.41 0.00 0.00 1.85
4714 4845 1.605710 ACGATACGGATAACAGGACGG 59.394 52.381 0.00 0.00 0.00 4.79
4724 4855 4.098960 ACACCAGAATAACACGATACGGAT 59.901 41.667 0.00 0.00 0.00 4.18
5042 5177 2.158957 TCGATCTATGCCCACCAAAGTC 60.159 50.000 0.00 0.00 0.00 3.01
5289 5428 1.228367 CCAACACCAGAGGCAAGCT 60.228 57.895 0.00 0.00 0.00 3.74
5293 5432 2.449518 TCCCCAACACCAGAGGCA 60.450 61.111 0.00 0.00 0.00 4.75
5320 5459 2.503356 AGGCAGTCAATTCAGAGGTAGG 59.497 50.000 0.00 0.00 0.00 3.18
5321 5460 3.055530 ACAGGCAGTCAATTCAGAGGTAG 60.056 47.826 0.00 0.00 0.00 3.18
5322 5461 2.906389 ACAGGCAGTCAATTCAGAGGTA 59.094 45.455 0.00 0.00 0.00 3.08
5323 5462 1.701847 ACAGGCAGTCAATTCAGAGGT 59.298 47.619 0.00 0.00 0.00 3.85
5324 5463 2.486472 ACAGGCAGTCAATTCAGAGG 57.514 50.000 0.00 0.00 0.00 3.69
5325 5464 5.335191 GGTTAAACAGGCAGTCAATTCAGAG 60.335 44.000 0.00 0.00 0.00 3.35
5327 5466 4.613622 CGGTTAAACAGGCAGTCAATTCAG 60.614 45.833 0.00 0.00 0.00 3.02
5328 5467 3.252215 CGGTTAAACAGGCAGTCAATTCA 59.748 43.478 0.00 0.00 0.00 2.57
5329 5468 3.821841 CGGTTAAACAGGCAGTCAATTC 58.178 45.455 0.00 0.00 0.00 2.17
5342 5481 2.624364 TGGGGAAAAGAAGCGGTTAAAC 59.376 45.455 0.00 0.00 0.00 2.01
5343 5482 2.946785 TGGGGAAAAGAAGCGGTTAAA 58.053 42.857 0.00 0.00 0.00 1.52
5371 5513 6.109359 GGTACATACAGATCATTAGGATGCC 58.891 44.000 0.00 0.00 36.00 4.40
5479 5621 4.898829 TCAATTTGACGGCCAAGATATG 57.101 40.909 2.24 0.00 35.94 1.78
5480 5622 4.279169 CCATCAATTTGACGGCCAAGATAT 59.721 41.667 2.24 0.00 35.94 1.63
5595 5756 1.192428 CTACTACTTTGTCGCCCCCT 58.808 55.000 0.00 0.00 0.00 4.79
5596 5757 1.188863 TCTACTACTTTGTCGCCCCC 58.811 55.000 0.00 0.00 0.00 5.40
5646 5808 7.665559 ACTCCACAAGATAACACACACATAAAT 59.334 33.333 0.00 0.00 0.00 1.40
5684 5846 6.075762 ACTGGTCAATTTTACGTTTAACCC 57.924 37.500 0.00 0.00 0.00 4.11
5704 5867 4.795795 CACTGCTACTCAATTCGACTACTG 59.204 45.833 0.00 0.00 0.00 2.74
5820 5997 3.581332 ACGGAGTCCAAGAAGAATTACCA 59.419 43.478 10.49 0.00 29.74 3.25
5858 6036 4.201990 GCCCAATTCTCATTCACTCATCAC 60.202 45.833 0.00 0.00 0.00 3.06
5872 6060 1.077663 ACAGGACCATTGCCCAATTCT 59.922 47.619 0.00 0.00 0.00 2.40
5880 6068 0.681175 AAAAGGCACAGGACCATTGC 59.319 50.000 8.51 8.51 35.40 3.56
5883 6071 1.133513 TGTCAAAAGGCACAGGACCAT 60.134 47.619 0.00 0.00 0.00 3.55
5884 6072 0.257328 TGTCAAAAGGCACAGGACCA 59.743 50.000 0.00 0.00 0.00 4.02
5886 6074 0.312102 GCTGTCAAAAGGCACAGGAC 59.688 55.000 4.37 0.00 40.45 3.85
5889 6077 1.269413 CCAAGCTGTCAAAAGGCACAG 60.269 52.381 0.00 0.00 42.61 3.66
5890 6078 0.746063 CCAAGCTGTCAAAAGGCACA 59.254 50.000 0.00 0.00 0.00 4.57
5893 6081 1.005748 GGCCAAGCTGTCAAAAGGC 60.006 57.895 0.00 0.00 41.29 4.35
5894 6082 0.316204 CTGGCCAAGCTGTCAAAAGG 59.684 55.000 7.01 0.00 0.00 3.11
5939 6127 2.338785 GCACTTGAGGCTGCCTTCC 61.339 63.158 24.26 11.70 31.76 3.46
5944 6132 3.730761 CACCGCACTTGAGGCTGC 61.731 66.667 0.00 0.00 38.67 5.25
5980 6180 1.284408 GCATCGCGGTTGGTCAAAA 59.716 52.632 6.13 0.00 0.00 2.44
6006 6206 1.329292 GTGTCGAGATCTCAGACTCCG 59.671 57.143 30.10 16.28 35.63 4.63
6037 6237 1.269309 CCGCTGTAGATACTGTGAGGC 60.269 57.143 10.82 0.00 37.70 4.70
6091 6294 4.803426 GTCGGCTCCGCTGGTCAG 62.803 72.222 2.96 0.00 39.59 3.51
6145 6381 4.554363 CCGTCACGAGCTAGCGGG 62.554 72.222 9.55 7.82 38.86 6.13
6221 6585 0.747283 CCTGATTGGACCTGAGCTGC 60.747 60.000 0.00 0.00 38.35 5.25
6229 6593 2.758979 TCTTCGTACTCCTGATTGGACC 59.241 50.000 0.00 0.00 40.56 4.46
6240 6604 4.555906 GCCTAGAGAAGCATCTTCGTACTC 60.556 50.000 0.00 0.00 35.54 2.59
6286 6650 2.810274 CAAGATTCCATCCATGCCGTAG 59.190 50.000 0.00 0.00 0.00 3.51
6287 6651 2.487086 CCAAGATTCCATCCATGCCGTA 60.487 50.000 0.00 0.00 0.00 4.02
6289 6653 0.956633 CCAAGATTCCATCCATGCCG 59.043 55.000 0.00 0.00 0.00 5.69
6290 6654 1.335145 CCCAAGATTCCATCCATGCC 58.665 55.000 0.00 0.00 0.00 4.40
6317 6692 4.691216 AGTACGGCACATTTTCTTCTTCTC 59.309 41.667 0.00 0.00 0.00 2.87
6325 6700 3.844099 CGCTTTTAGTACGGCACATTTTC 59.156 43.478 0.00 0.00 0.00 2.29
6326 6701 3.365565 CCGCTTTTAGTACGGCACATTTT 60.366 43.478 0.00 0.00 40.55 1.82
6327 6702 2.160813 CCGCTTTTAGTACGGCACATTT 59.839 45.455 0.00 0.00 40.55 2.32
6369 6744 3.184683 CTTCACTCGCTCGCTGCC 61.185 66.667 0.00 0.00 38.78 4.85
6374 6749 1.488957 GTGCAACTTCACTCGCTCG 59.511 57.895 0.00 0.00 34.29 5.03
6420 6795 9.143631 GACTGTGGATCCATTAAAGAAAAATTG 57.856 33.333 19.62 0.00 0.00 2.32
6422 6797 8.526147 CAGACTGTGGATCCATTAAAGAAAAAT 58.474 33.333 19.62 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.