Multiple sequence alignment - TraesCS6D01G098400

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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 TraesCS6D01G098400 chr6D 100.000 6367 0 0 1 6367 62104062 62110428 0.000000e+00 11758
1 TraesCS6D01G098400 chr6A 94.305 5057 184 36 638 5677 79259280 79264249 0.000000e+00 7648
2 TraesCS6D01G098400 chr6A 88.889 621 30 14 5767 6367 79264285 79264886 0.000000e+00 728
3 TraesCS6D01G098400 chr6A 86.918 558 43 20 19 570 79258724 79259257 3.290000e-167 599
4 TraesCS6D01G098400 chr6B 92.595 3538 144 52 19 3471 135841690 135845194 0.000000e+00 4974
5 TraesCS6D01G098400 chr6B 94.140 2321 74 29 3885 6182 135845494 135847775 0.000000e+00 3476
6 TraesCS6D01G098400 chr6B 91.798 317 19 6 3500 3812 135845184 135845497 9.800000e-118 435
7 TraesCS6D01G098400 chr6B 91.099 191 9 3 6179 6367 135847849 135848033 1.060000e-62 252
8 TraesCS6D01G098400 chr5D 91.083 157 11 2 2395 2548 446626791 446626635 6.470000e-50 209
9 TraesCS6D01G098400 chr1D 91.083 157 11 3 2395 2548 182245120 182245276 6.470000e-50 209
10 TraesCS6D01G098400 chr1D 89.809 157 13 3 2395 2548 394927540 394927696 1.400000e-46 198
11 TraesCS6D01G098400 chr4D 90.446 157 12 2 2395 2548 22737946 22737790 3.010000e-48 204
12 TraesCS6D01G098400 chr4D 90.446 157 12 3 2395 2548 75934254 75934410 3.010000e-48 204
13 TraesCS6D01G098400 chr4D 90.446 157 12 3 2395 2548 439487278 439487434 3.010000e-48 204
14 TraesCS6D01G098400 chr3D 89.809 157 13 3 2395 2548 463316668 463316824 1.400000e-46 198
15 TraesCS6D01G098400 chr5B 78.279 244 51 2 1112 1354 420984907 420984665 8.550000e-34 156
16 TraesCS6D01G098400 chr5A 78.571 238 49 2 1112 1348 457789097 457789333 8.550000e-34 156


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 TraesCS6D01G098400 chr6D 62104062 62110428 6366 False 11758.000000 11758 100.000000 1 6367 1 chr6D.!!$F1 6366
1 TraesCS6D01G098400 chr6A 79258724 79264886 6162 False 2991.666667 7648 90.037333 19 6367 3 chr6A.!!$F1 6348
2 TraesCS6D01G098400 chr6B 135841690 135848033 6343 False 2284.250000 4974 92.408000 19 6367 4 chr6B.!!$F1 6348

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
507 572 0.325484 ATCCCTCTGCTCTGCTCTGT 60.325 55.0 0.00 0.0 0.00 3.41 F
511 576 0.458197 CTCTGCTCTGCTCTGTTCGG 60.458 60.0 0.00 0.0 0.00 4.30 F
1570 1645 0.109086 CGATGTGTCTGTCTCGGCTT 60.109 55.0 0.00 0.0 0.00 4.35 F
3170 3257 0.397254 TCCCTTCGAAGCTCCTAGGG 60.397 60.0 19.99 14.4 45.71 3.53 F
4149 4242 1.760192 AGGCTCCATGTTCTCATTGC 58.240 50.0 0.00 0.0 31.15 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1570 1645 0.182537 AGCTACACTTGTTGGCCACA 59.817 50.0 3.88 4.06 0.00 4.17 R
2118 2200 0.509929 GAACGTACGCAAGGTTGGAC 59.490 55.0 16.72 0.00 46.39 4.02 R
3380 3469 0.969149 AAGAGAGATGCACGTCCACA 59.031 50.0 0.00 0.00 0.00 4.17 R
4862 4955 0.543277 TCCCTGGCTGTATGCTCTTG 59.457 55.0 0.00 0.00 42.39 3.02 R
5422 5515 0.338467 TACCCCTCTAAGCTGCCAGA 59.662 55.0 0.00 0.00 0.00 3.86 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
95 96 0.596082 AAAACCGTCCTGGATTTGCG 59.404 50.000 0.00 0.00 40.85 4.85
147 149 6.080009 TCTTTCTACTACCCTGTTTACCACT 58.920 40.000 0.00 0.00 0.00 4.00
150 152 1.274447 ACTACCCTGTTTACCACTCGC 59.726 52.381 0.00 0.00 0.00 5.03
209 215 3.077359 GTCTAACAAACCATGCTGCTCT 58.923 45.455 0.00 0.00 0.00 4.09
276 282 2.244651 AAGCGTGTGAGGCGTGAAC 61.245 57.895 0.00 0.00 33.62 3.18
290 299 2.066262 CGTGAACGCCATATCCCATAC 58.934 52.381 0.00 0.00 0.00 2.39
291 300 2.288825 CGTGAACGCCATATCCCATACT 60.289 50.000 0.00 0.00 0.00 2.12
293 302 4.495422 GTGAACGCCATATCCCATACTAG 58.505 47.826 0.00 0.00 0.00 2.57
295 304 5.184479 GTGAACGCCATATCCCATACTAGTA 59.816 44.000 4.77 4.77 0.00 1.82
296 305 5.417894 TGAACGCCATATCCCATACTAGTAG 59.582 44.000 8.85 0.00 0.00 2.57
297 306 5.188988 ACGCCATATCCCATACTAGTAGA 57.811 43.478 8.85 0.82 0.00 2.59
300 309 6.065374 CGCCATATCCCATACTAGTAGAGAT 58.935 44.000 8.85 11.76 0.00 2.75
325 342 3.272716 AGAGTCATAGCCCATCCATCT 57.727 47.619 0.00 0.00 0.00 2.90
348 365 8.519799 TCTATCAACAACTTTTGAGGTTTCTT 57.480 30.769 0.00 0.00 38.87 2.52
353 378 5.016831 ACAACTTTTGAGGTTTCTTGAGGT 58.983 37.500 0.00 0.00 0.00 3.85
356 381 5.449553 ACTTTTGAGGTTTCTTGAGGTGAT 58.550 37.500 0.00 0.00 0.00 3.06
357 382 5.893824 ACTTTTGAGGTTTCTTGAGGTGATT 59.106 36.000 0.00 0.00 0.00 2.57
402 438 4.990526 AGATCAAACACACCCATCTCTTT 58.009 39.130 0.00 0.00 0.00 2.52
444 480 1.925959 CAATCTTCCTTTCCCCCTCCT 59.074 52.381 0.00 0.00 0.00 3.69
507 572 0.325484 ATCCCTCTGCTCTGCTCTGT 60.325 55.000 0.00 0.00 0.00 3.41
511 576 0.458197 CTCTGCTCTGCTCTGTTCGG 60.458 60.000 0.00 0.00 0.00 4.30
516 581 2.031012 CTGCTCTGTTCGGTGCCA 59.969 61.111 3.75 0.00 0.00 4.92
606 675 2.108168 CTGGGTAGTACTTGCTGGCTA 58.892 52.381 0.00 0.00 0.00 3.93
712 781 3.734902 CGCCAGGGCTTCATTTATTGTTC 60.735 47.826 8.91 0.00 39.32 3.18
726 795 7.236432 TCATTTATTGTTCCCCCAAAAGATTCA 59.764 33.333 0.00 0.00 0.00 2.57
767 836 0.676736 CTCTGGTAGCTCGGGGATTC 59.323 60.000 0.00 0.00 0.00 2.52
862 931 1.656095 CCGAGCTTCGATTTCAGTGTC 59.344 52.381 7.07 0.00 43.74 3.67
878 947 1.420138 GTGTCTTCTTGGAGGTTCCCA 59.580 52.381 0.00 0.00 35.03 4.37
932 1001 2.092753 TGGTTCATCCAAGATCTGAGCC 60.093 50.000 0.00 1.71 44.12 4.70
1062 1131 4.069232 CTCTTCGTCCTGGCGGCA 62.069 66.667 12.58 12.58 0.00 5.69
1308 1377 2.282391 AACAGCATGAAGGCCGCA 60.282 55.556 0.00 0.00 39.69 5.69
1456 1526 9.534565 TGATTTGTAACTAGTTCATGCTATCTC 57.465 33.333 12.39 0.29 0.00 2.75
1482 1552 7.004555 AGTGTGGTCTCATTTGATTGTACTA 57.995 36.000 0.00 0.00 0.00 1.82
1549 1623 1.795962 GACATTTTTCGCGGTGCCG 60.796 57.895 6.13 6.22 43.09 5.69
1570 1645 0.109086 CGATGTGTCTGTCTCGGCTT 60.109 55.000 0.00 0.00 0.00 4.35
1648 1723 1.436195 TTGCGCTCGGTTCATATGGC 61.436 55.000 9.73 0.00 0.00 4.40
1763 1838 1.526575 ATGGTGCCTTCTGGTTTGCG 61.527 55.000 0.00 0.00 35.27 4.85
1830 1905 1.269723 GTTACCAAGCAGGGCACTTTC 59.730 52.381 0.00 0.00 43.89 2.62
1841 1916 4.261994 GCAGGGCACTTTCTGTTTTCATTA 60.262 41.667 0.00 0.00 33.81 1.90
1849 1924 7.358683 GCACTTTCTGTTTTCATTAAGCATCAC 60.359 37.037 0.00 0.00 0.00 3.06
1850 1925 7.648908 CACTTTCTGTTTTCATTAAGCATCACA 59.351 33.333 0.00 0.00 0.00 3.58
1851 1926 8.362639 ACTTTCTGTTTTCATTAAGCATCACAT 58.637 29.630 0.00 0.00 0.00 3.21
1852 1927 9.199982 CTTTCTGTTTTCATTAAGCATCACATT 57.800 29.630 0.00 0.00 0.00 2.71
1887 1962 3.683340 GGTGGTATCGGTTTGAAGACTTC 59.317 47.826 8.34 8.34 0.00 3.01
1916 1991 7.080353 TGCTCATCAATTCATACTGTTTCTG 57.920 36.000 0.00 0.00 0.00 3.02
1928 2003 7.735500 TCATACTGTTTCTGTAAATTACACGC 58.264 34.615 1.08 0.00 34.46 5.34
1929 2004 5.352643 ACTGTTTCTGTAAATTACACGCC 57.647 39.130 1.08 0.00 34.46 5.68
1931 2006 5.297278 ACTGTTTCTGTAAATTACACGCCAA 59.703 36.000 1.08 0.00 34.46 4.52
1967 2049 2.046285 CCATGGTTCCAGCCGGTTC 61.046 63.158 2.57 0.00 0.00 3.62
2118 2200 3.132139 TCGTCCGCTCCTCCTTCG 61.132 66.667 0.00 0.00 0.00 3.79
2128 2210 0.685097 TCCTCCTTCGTCCAACCTTG 59.315 55.000 0.00 0.00 0.00 3.61
2150 2232 2.177734 GTACGTTCTCCCCTCCTCTTT 58.822 52.381 0.00 0.00 0.00 2.52
2151 2233 1.730851 ACGTTCTCCCCTCCTCTTTT 58.269 50.000 0.00 0.00 0.00 2.27
2341 2423 7.888250 TTACACAATCACATAATATGGGCAA 57.112 32.000 5.16 0.00 32.41 4.52
2351 2433 2.071778 ATATGGGCAAGGCAAATCGT 57.928 45.000 0.00 0.00 0.00 3.73
2372 2454 4.319333 CGTGGGCTAACGTACTAGATACTG 60.319 50.000 0.00 0.00 38.74 2.74
2373 2455 4.023365 GTGGGCTAACGTACTAGATACTGG 60.023 50.000 0.00 0.00 0.00 4.00
2439 2521 4.184629 GTTAATTGTGTGTTTTGCCACCA 58.815 39.130 0.00 0.00 34.35 4.17
2663 2746 9.961265 GTAGGCCATTTTGTATTAAAAGTATCC 57.039 33.333 5.01 0.00 0.00 2.59
2683 2766 4.365723 TCCGTCTCTCACAAAAACTGTAC 58.634 43.478 0.00 0.00 36.10 2.90
2684 2767 3.493503 CCGTCTCTCACAAAAACTGTACC 59.506 47.826 0.00 0.00 36.10 3.34
2685 2768 4.116961 CGTCTCTCACAAAAACTGTACCA 58.883 43.478 0.00 0.00 36.10 3.25
2686 2769 4.209288 CGTCTCTCACAAAAACTGTACCAG 59.791 45.833 0.00 0.00 36.10 4.00
2687 2770 4.511826 GTCTCTCACAAAAACTGTACCAGG 59.488 45.833 0.00 0.00 36.10 4.45
2688 2771 3.815401 CTCTCACAAAAACTGTACCAGGG 59.185 47.826 0.00 0.00 36.10 4.45
2689 2772 3.201266 TCTCACAAAAACTGTACCAGGGT 59.799 43.478 0.00 0.00 36.10 4.34
3055 3142 3.658351 GTGCATTACGAGGTTCATGTC 57.342 47.619 0.00 0.00 0.00 3.06
3059 3146 4.868171 TGCATTACGAGGTTCATGTCTTAC 59.132 41.667 0.00 0.00 0.00 2.34
3127 3214 4.062293 TCAAACGGAACTGAACGATCAAT 58.938 39.130 0.00 0.00 34.49 2.57
3170 3257 0.397254 TCCCTTCGAAGCTCCTAGGG 60.397 60.000 19.99 14.40 45.71 3.53
3307 3394 8.798402 CCTTGAGTTATACCTCCTGTATAGAAG 58.202 40.741 0.00 0.00 42.05 2.85
3393 3482 4.693532 TCCTTGTGGACGTGCATC 57.306 55.556 14.45 7.84 37.46 3.91
3476 3565 9.346725 CTTTTTAGCACATTCTGAAAACCTATC 57.653 33.333 0.00 0.00 31.26 2.08
3477 3566 7.994425 TTTAGCACATTCTGAAAACCTATCA 57.006 32.000 0.00 0.00 0.00 2.15
3478 3567 7.615582 TTAGCACATTCTGAAAACCTATCAG 57.384 36.000 0.00 0.00 44.53 2.90
3479 3568 4.397417 AGCACATTCTGAAAACCTATCAGC 59.603 41.667 0.00 0.00 43.19 4.26
3480 3569 4.156556 GCACATTCTGAAAACCTATCAGCA 59.843 41.667 0.00 0.00 43.19 4.41
3481 3570 5.634896 CACATTCTGAAAACCTATCAGCAC 58.365 41.667 0.00 0.00 43.19 4.40
3482 3571 5.413833 CACATTCTGAAAACCTATCAGCACT 59.586 40.000 0.00 0.00 43.19 4.40
3483 3572 6.595326 CACATTCTGAAAACCTATCAGCACTA 59.405 38.462 0.00 0.00 43.19 2.74
3484 3573 6.595716 ACATTCTGAAAACCTATCAGCACTAC 59.404 38.462 0.00 0.00 43.19 2.73
3485 3574 5.086104 TCTGAAAACCTATCAGCACTACC 57.914 43.478 0.00 0.00 43.19 3.18
3486 3575 4.530553 TCTGAAAACCTATCAGCACTACCA 59.469 41.667 0.00 0.00 43.19 3.25
3487 3576 5.012664 TCTGAAAACCTATCAGCACTACCAA 59.987 40.000 0.00 0.00 43.19 3.67
3652 3745 9.135189 CAGATTATTATTCAACCTGGAAATCCA 57.865 33.333 0.00 1.53 45.30 3.41
3839 3932 9.933723 TTTAACCTAGTAATACAGAGTCAAACC 57.066 33.333 0.00 0.00 0.00 3.27
3840 3933 7.549147 AACCTAGTAATACAGAGTCAAACCA 57.451 36.000 0.00 0.00 0.00 3.67
3841 3934 6.932947 ACCTAGTAATACAGAGTCAAACCAC 58.067 40.000 0.00 0.00 0.00 4.16
3842 3935 6.495872 ACCTAGTAATACAGAGTCAAACCACA 59.504 38.462 0.00 0.00 0.00 4.17
3856 3949 5.351189 GTCAAACCACATCTGTTTTGCTTTT 59.649 36.000 3.63 0.00 33.82 2.27
3861 3954 5.049167 CCACATCTGTTTTGCTTTTTAGCA 58.951 37.500 0.00 0.00 43.81 3.49
3862 3955 5.176223 CCACATCTGTTTTGCTTTTTAGCAG 59.824 40.000 0.00 0.00 46.21 4.24
3863 3956 5.750067 CACATCTGTTTTGCTTTTTAGCAGT 59.250 36.000 0.00 0.00 46.21 4.40
3875 3968 4.706842 TTTTAGCAGTATCCCTCCATCC 57.293 45.455 0.00 0.00 0.00 3.51
3911 4004 9.722056 GTACTGGTAGCATTTATTTTGATGAAG 57.278 33.333 0.00 0.00 0.00 3.02
4072 4165 8.471609 TGATAAGCACATGATGAAATGAAATGT 58.528 29.630 0.00 0.00 31.79 2.71
4147 4240 4.946157 CAGTTTAGGCTCCATGTTCTCATT 59.054 41.667 0.00 0.00 31.15 2.57
4148 4241 4.946157 AGTTTAGGCTCCATGTTCTCATTG 59.054 41.667 0.00 0.00 31.15 2.82
4149 4242 1.760192 AGGCTCCATGTTCTCATTGC 58.240 50.000 0.00 0.00 31.15 3.56
4202 4295 3.441572 CCTTCTTGATGTTGATCCACCAC 59.558 47.826 0.00 0.00 0.00 4.16
4259 4352 6.095440 CCTGTTATTTTGCTAGGTATGTTGCT 59.905 38.462 0.00 0.00 0.00 3.91
4292 4385 2.415512 GCCTTTCCTGTCGACATACAAC 59.584 50.000 20.40 2.13 0.00 3.32
4346 4439 5.334414 CCTCAAGAACATACAAAGTGCACTC 60.334 44.000 21.95 4.18 0.00 3.51
4781 4874 2.655090 TCAACCAAGGCTTCATGACA 57.345 45.000 0.00 0.00 0.00 3.58
4862 4955 3.567585 TCAGTCTGATCGATGAGGATGAC 59.432 47.826 12.13 3.13 0.00 3.06
4937 5030 2.225467 GGCATCCCAAAGTATCAGCTC 58.775 52.381 0.00 0.00 0.00 4.09
4964 5057 0.026803 GTGTGCCGAATTCGCAGATC 59.973 55.000 22.36 11.90 38.18 2.75
5006 5099 3.821033 AGTACCTTGACAAGAAATGGTGC 59.179 43.478 16.99 9.76 0.00 5.01
5048 5141 2.380410 CGACGACCCAAAGCTTCCG 61.380 63.158 0.00 1.61 0.00 4.30
5105 5198 1.448540 CAGCCTTGGCTACAGGACG 60.449 63.158 14.35 0.00 0.00 4.79
5367 5460 3.492309 CCTCTGTGTGTCATCCTCATAGC 60.492 52.174 0.00 0.00 0.00 2.97
5422 5515 1.171308 GCCATGACAGCATCAACAGT 58.829 50.000 0.00 0.00 41.93 3.55
5541 5639 2.368655 AGCCGCATGGTTGAAAATTC 57.631 45.000 0.00 0.00 37.67 2.17
5542 5640 1.617850 AGCCGCATGGTTGAAAATTCA 59.382 42.857 0.00 0.00 37.67 2.57
5546 5644 4.107622 CCGCATGGTTGAAAATTCATCTC 58.892 43.478 0.00 0.00 37.00 2.75
5646 5744 3.713764 ACTGAGGGCATAGCTATCAAACT 59.286 43.478 2.34 0.00 0.00 2.66
5707 5820 4.981806 CTCTAGACTTAGAGCTGTGCTT 57.018 45.455 0.00 0.00 44.65 3.91
5708 5821 4.920376 CTCTAGACTTAGAGCTGTGCTTC 58.080 47.826 0.00 0.00 44.65 3.86
5709 5822 4.336280 TCTAGACTTAGAGCTGTGCTTCA 58.664 43.478 0.00 0.00 39.88 3.02
5710 5823 4.952957 TCTAGACTTAGAGCTGTGCTTCAT 59.047 41.667 0.00 0.00 39.88 2.57
5711 5824 6.122964 TCTAGACTTAGAGCTGTGCTTCATA 58.877 40.000 0.00 0.00 39.88 2.15
5712 5825 5.667539 AGACTTAGAGCTGTGCTTCATAA 57.332 39.130 0.00 0.00 39.88 1.90
5713 5826 5.415221 AGACTTAGAGCTGTGCTTCATAAC 58.585 41.667 0.00 0.00 39.88 1.89
5714 5827 5.047021 AGACTTAGAGCTGTGCTTCATAACA 60.047 40.000 0.00 0.00 39.88 2.41
5715 5828 5.551233 ACTTAGAGCTGTGCTTCATAACAA 58.449 37.500 0.00 0.00 39.88 2.83
5716 5829 5.409826 ACTTAGAGCTGTGCTTCATAACAAC 59.590 40.000 0.00 0.00 39.88 3.32
5717 5830 3.077359 AGAGCTGTGCTTCATAACAACC 58.923 45.455 0.00 0.00 39.88 3.77
5718 5831 3.077359 GAGCTGTGCTTCATAACAACCT 58.923 45.455 0.00 0.00 39.88 3.50
5719 5832 3.490348 AGCTGTGCTTCATAACAACCTT 58.510 40.909 0.00 0.00 33.89 3.50
5742 5855 3.417690 TTTTTGCATGCCAAACAAAGC 57.582 38.095 15.90 0.00 42.81 3.51
5765 5878 6.642683 CATTTCTGAATGCATTTTCACTCC 57.357 37.500 14.33 0.00 36.54 3.85
5866 5998 1.931841 CACTGGCAATCTGAGTCGATG 59.068 52.381 0.00 0.00 0.00 3.84
5880 6012 5.838529 TGAGTCGATGTACTGAAAACTTGA 58.161 37.500 0.00 0.00 0.00 3.02
5896 6028 3.412386 ACTTGAGACCAATTGCCTGTAC 58.588 45.455 0.00 0.00 0.00 2.90
5900 6032 3.244875 TGAGACCAATTGCCTGTACACAT 60.245 43.478 0.00 0.00 0.00 3.21
5908 6040 1.338105 TGCCTGTACACATCTGCACTC 60.338 52.381 0.00 0.00 0.00 3.51
6038 6176 0.668706 AGCTATGTCGGCATCATCGC 60.669 55.000 5.39 5.56 36.58 4.58
6045 6183 2.890474 GGCATCATCGCCGTCGTT 60.890 61.111 0.00 0.00 43.52 3.85
6046 6184 2.321060 GCATCATCGCCGTCGTTG 59.679 61.111 0.00 0.00 36.90 4.10
6047 6185 2.452813 GCATCATCGCCGTCGTTGT 61.453 57.895 0.00 0.00 36.90 3.32
6048 6186 1.631072 CATCATCGCCGTCGTTGTC 59.369 57.895 0.00 0.00 36.90 3.18
6089 6230 7.360575 TCGTCTTCTTAAATTTTGTAGCTCC 57.639 36.000 0.00 0.00 0.00 4.70
6167 6310 7.883311 CCTTATTTTCCTCACCATCCGTATAAT 59.117 37.037 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.681982 CAGATATCGAAACTACTTCACGGAC 59.318 44.000 0.00 0.00 33.17 4.79
1 2 5.356190 ACAGATATCGAAACTACTTCACGGA 59.644 40.000 0.00 0.00 33.17 4.69
2 3 5.579718 ACAGATATCGAAACTACTTCACGG 58.420 41.667 0.00 0.00 33.17 4.94
3 4 6.357503 GCTACAGATATCGAAACTACTTCACG 59.642 42.308 0.00 0.00 33.17 4.35
4 5 6.637658 GGCTACAGATATCGAAACTACTTCAC 59.362 42.308 0.00 0.00 33.17 3.18
5 6 6.546403 AGGCTACAGATATCGAAACTACTTCA 59.454 38.462 0.00 0.00 33.17 3.02
6 7 6.972722 AGGCTACAGATATCGAAACTACTTC 58.027 40.000 0.00 0.00 0.00 3.01
7 8 6.963083 AGGCTACAGATATCGAAACTACTT 57.037 37.500 0.00 0.00 0.00 2.24
8 9 6.963083 AAGGCTACAGATATCGAAACTACT 57.037 37.500 0.00 0.00 0.00 2.57
9 10 6.641723 GGAAAGGCTACAGATATCGAAACTAC 59.358 42.308 0.00 0.00 0.00 2.73
10 11 6.239232 GGGAAAGGCTACAGATATCGAAACTA 60.239 42.308 0.00 0.00 0.00 2.24
11 12 5.453480 GGGAAAGGCTACAGATATCGAAACT 60.453 44.000 0.00 0.00 0.00 2.66
12 13 4.750598 GGGAAAGGCTACAGATATCGAAAC 59.249 45.833 0.00 0.00 0.00 2.78
13 14 4.202326 GGGGAAAGGCTACAGATATCGAAA 60.202 45.833 0.00 0.00 0.00 3.46
14 15 3.323979 GGGGAAAGGCTACAGATATCGAA 59.676 47.826 0.00 0.00 0.00 3.71
15 16 2.897969 GGGGAAAGGCTACAGATATCGA 59.102 50.000 0.00 0.00 0.00 3.59
16 17 2.028020 GGGGGAAAGGCTACAGATATCG 60.028 54.545 0.00 0.00 0.00 2.92
17 18 2.979678 TGGGGGAAAGGCTACAGATATC 59.020 50.000 0.00 0.00 0.00 1.63
110 112 5.118729 AGTAGAAAGATTCCTCCTCTCGA 57.881 43.478 0.00 0.00 0.00 4.04
168 172 2.095567 ACGCTTTTCACTGTCATGATGC 60.096 45.455 0.00 0.00 0.00 3.91
209 215 2.297033 GGAGTGCAAGCAAAAGGAATCA 59.703 45.455 0.00 0.00 0.00 2.57
276 282 5.437946 TCTCTACTAGTATGGGATATGGCG 58.562 45.833 2.33 0.00 0.00 5.69
290 299 9.982651 GGCTATGACTCTATCTATCTCTACTAG 57.017 40.741 0.00 0.00 0.00 2.57
291 300 8.930527 GGGCTATGACTCTATCTATCTCTACTA 58.069 40.741 0.00 0.00 0.00 1.82
293 302 7.570132 TGGGCTATGACTCTATCTATCTCTAC 58.430 42.308 0.00 0.00 0.00 2.59
295 304 6.650622 TGGGCTATGACTCTATCTATCTCT 57.349 41.667 0.00 0.00 0.00 3.10
296 305 6.490040 GGATGGGCTATGACTCTATCTATCTC 59.510 46.154 0.00 0.00 0.00 2.75
297 306 6.068557 TGGATGGGCTATGACTCTATCTATCT 60.069 42.308 0.00 0.00 0.00 1.98
300 309 5.536497 TGGATGGGCTATGACTCTATCTA 57.464 43.478 0.00 0.00 0.00 1.98
309 322 4.845796 TGTTGATAGATGGATGGGCTATGA 59.154 41.667 0.00 0.00 0.00 2.15
325 342 8.287439 TCAAGAAACCTCAAAAGTTGTTGATA 57.713 30.769 0.00 0.00 36.92 2.15
348 365 1.957668 CGGCATGATCAATCACCTCA 58.042 50.000 0.00 0.00 40.03 3.86
353 378 1.202325 GCAAAGCGGCATGATCAATCA 60.202 47.619 0.00 0.00 41.70 2.57
356 381 1.672363 CTAGCAAAGCGGCATGATCAA 59.328 47.619 0.00 0.00 35.83 2.57
357 382 1.134431 TCTAGCAAAGCGGCATGATCA 60.134 47.619 1.45 0.00 35.83 2.92
402 438 2.091610 TGATTTGAGTGTGGGGTTGGAA 60.092 45.455 0.00 0.00 0.00 3.53
444 480 5.509498 AGATTAGCCTTTCCAAGTAATGCA 58.491 37.500 0.00 0.00 0.00 3.96
511 576 2.337532 CAAAGCTGGCAGTGGCAC 59.662 61.111 16.56 10.29 43.71 5.01
570 635 0.965866 CCAGGCGAGGTGAGTACTGA 60.966 60.000 0.00 0.00 0.00 3.41
678 747 2.584608 CTGGCGAACCCCACCTAG 59.415 66.667 0.00 0.00 33.59 3.02
712 781 1.827344 GGAGCTTGAATCTTTTGGGGG 59.173 52.381 0.00 0.00 0.00 5.40
767 836 0.389166 ACTCAAGAAGAAGGCGCTCG 60.389 55.000 7.64 0.00 0.00 5.03
771 840 2.481952 CCAAGAACTCAAGAAGAAGGCG 59.518 50.000 0.00 0.00 0.00 5.52
1062 1131 2.367202 CCAGGATACCACCACCGCT 61.367 63.158 0.00 0.00 37.17 5.52
1064 1133 1.520666 GACCAGGATACCACCACCG 59.479 63.158 0.00 0.00 37.17 4.94
1098 1167 2.589540 CAGTTGGCCCCTATCGCA 59.410 61.111 0.00 0.00 0.00 5.10
1155 1224 3.141398 GTTGTCCTTGAGCATCTTCACA 58.859 45.455 0.00 0.00 34.92 3.58
1158 1227 1.734465 CCGTTGTCCTTGAGCATCTTC 59.266 52.381 0.00 0.00 34.92 2.87
1308 1377 1.996798 TCTTCTCGACCCACTTGTCT 58.003 50.000 0.00 0.00 32.97 3.41
1440 1509 5.211454 CACACTCGAGATAGCATGAACTAG 58.789 45.833 21.68 0.00 0.00 2.57
1456 1526 3.748048 ACAATCAAATGAGACCACACTCG 59.252 43.478 0.00 0.00 39.49 4.18
1546 1620 0.798771 GAGACAGACACATCGACGGC 60.799 60.000 0.00 0.00 0.00 5.68
1549 1623 0.798771 GCCGAGACAGACACATCGAC 60.799 60.000 0.00 0.00 37.35 4.20
1555 1629 0.946221 CCACAAGCCGAGACAGACAC 60.946 60.000 0.00 0.00 0.00 3.67
1570 1645 0.182537 AGCTACACTTGTTGGCCACA 59.817 50.000 3.88 4.06 0.00 4.17
1648 1723 7.010923 GCTAATTCTAGATTTGTCACTGTCCAG 59.989 40.741 9.62 0.00 0.00 3.86
1727 1802 1.021390 CATGGAAAGCGCCGAGAAGT 61.021 55.000 2.29 0.00 0.00 3.01
1774 1849 4.517285 AGGAATACATGTAACCAGTGCAG 58.483 43.478 24.47 0.00 0.00 4.41
1779 1854 5.110814 TCCCAAGGAATACATGTAACCAG 57.889 43.478 24.47 18.47 0.00 4.00
1830 1905 7.595875 TGTGAATGTGATGCTTAATGAAAACAG 59.404 33.333 0.00 0.00 0.00 3.16
1841 1916 5.907866 TCAATCATGTGAATGTGATGCTT 57.092 34.783 0.00 0.00 0.00 3.91
1849 1924 4.994907 ACCACCATCAATCATGTGAATG 57.005 40.909 0.00 0.00 0.00 2.67
1850 1925 5.471116 CGATACCACCATCAATCATGTGAAT 59.529 40.000 0.00 0.00 0.00 2.57
1851 1926 4.815846 CGATACCACCATCAATCATGTGAA 59.184 41.667 0.00 0.00 0.00 3.18
1852 1927 4.379652 CGATACCACCATCAATCATGTGA 58.620 43.478 0.00 0.00 0.00 3.58
1887 1962 6.849502 ACAGTATGAATTGATGAGCAAAGTG 58.150 36.000 0.00 0.00 38.17 3.16
1916 1991 5.754778 ACTTCTTGTTGGCGTGTAATTTAC 58.245 37.500 0.00 0.00 0.00 2.01
1928 2003 3.004734 GGACATGGTGAACTTCTTGTTGG 59.995 47.826 0.00 0.00 39.30 3.77
1929 2004 3.631686 TGGACATGGTGAACTTCTTGTTG 59.368 43.478 0.00 0.00 39.30 3.33
1931 2006 3.576078 TGGACATGGTGAACTTCTTGT 57.424 42.857 0.00 0.00 0.00 3.16
1967 2049 3.443099 TGATGAGAATCCAGTAGTGCG 57.557 47.619 0.00 0.00 0.00 5.34
2086 2168 1.282930 GACGACAGAACCTTGCGTCC 61.283 60.000 0.00 0.00 39.45 4.79
2118 2200 0.509929 GAACGTACGCAAGGTTGGAC 59.490 55.000 16.72 0.00 46.39 4.02
2128 2210 2.002509 GAGGAGGGGAGAACGTACGC 62.003 65.000 16.72 0.00 0.00 4.42
2150 2232 5.301835 TGGGAGCAAAAATTCCAAATGAA 57.698 34.783 0.00 0.00 37.38 2.57
2151 2233 4.970860 TGGGAGCAAAAATTCCAAATGA 57.029 36.364 0.00 0.00 35.09 2.57
2267 2349 8.443937 CACTTACTATTTGGAAAGCACTTACTC 58.556 37.037 0.00 0.00 0.00 2.59
2341 2423 1.024579 CGTTAGCCCACGATTTGCCT 61.025 55.000 0.00 0.00 43.15 4.75
2351 2433 4.139786 CCAGTATCTAGTACGTTAGCCCA 58.860 47.826 0.00 0.00 38.38 5.36
2372 2454 1.134946 GTGCATTGCAACAGGGTATCC 59.865 52.381 13.94 0.00 41.47 2.59
2373 2455 1.202177 CGTGCATTGCAACAGGGTATC 60.202 52.381 13.94 0.00 41.47 2.24
2663 2746 4.116961 TGGTACAGTTTTTGTGAGAGACG 58.883 43.478 0.00 0.00 41.10 4.18
2683 2766 1.765314 CTAGATGTTCCTGGACCCTGG 59.235 57.143 0.00 5.69 36.53 4.45
2684 2767 2.472029 ACTAGATGTTCCTGGACCCTG 58.528 52.381 0.00 0.00 0.00 4.45
2685 2768 2.950990 ACTAGATGTTCCTGGACCCT 57.049 50.000 0.00 0.00 0.00 4.34
2686 2769 5.431179 TTTTACTAGATGTTCCTGGACCC 57.569 43.478 0.00 0.00 0.00 4.46
2687 2770 5.354513 GCTTTTTACTAGATGTTCCTGGACC 59.645 44.000 0.00 0.00 0.00 4.46
2688 2771 5.938125 TGCTTTTTACTAGATGTTCCTGGAC 59.062 40.000 0.00 0.00 0.00 4.02
2689 2772 6.121776 TGCTTTTTACTAGATGTTCCTGGA 57.878 37.500 0.00 0.00 0.00 3.86
2718 2801 1.613437 GCCAGCTTTCAACAAAGGCTA 59.387 47.619 0.00 0.00 39.69 3.93
2726 2809 1.662044 CCACAGGCCAGCTTTCAAC 59.338 57.895 5.01 0.00 0.00 3.18
3055 3142 4.256110 TGGCTGTGAACATCTCATGTAAG 58.744 43.478 0.00 0.00 44.07 2.34
3059 3146 2.163010 GGTTGGCTGTGAACATCTCATG 59.837 50.000 0.00 0.00 36.14 3.07
3127 3214 4.487948 GCAATTGAATGCTACTGCTCAAA 58.512 39.130 10.34 0.00 43.06 2.69
3190 3277 2.785269 AGGATGCATTTCCTCCATGGTA 59.215 45.455 12.58 0.00 42.71 3.25
3307 3394 5.105473 TGCAAGACAGTAGGTATGAGGTAAC 60.105 44.000 0.00 0.00 0.00 2.50
3380 3469 0.969149 AAGAGAGATGCACGTCCACA 59.031 50.000 0.00 0.00 0.00 4.17
3387 3476 7.959689 ATTATGACACATAAGAGAGATGCAC 57.040 36.000 9.47 0.00 0.00 4.57
3476 3565 1.001974 TGGTAGTGCTTGGTAGTGCTG 59.998 52.381 0.00 0.00 0.00 4.41
3477 3566 1.348064 TGGTAGTGCTTGGTAGTGCT 58.652 50.000 0.00 0.00 0.00 4.40
3478 3567 2.076863 CTTGGTAGTGCTTGGTAGTGC 58.923 52.381 0.00 0.00 0.00 4.40
3479 3568 2.076863 GCTTGGTAGTGCTTGGTAGTG 58.923 52.381 0.00 0.00 0.00 2.74
3480 3569 1.697432 TGCTTGGTAGTGCTTGGTAGT 59.303 47.619 0.00 0.00 0.00 2.73
3481 3570 2.472695 TGCTTGGTAGTGCTTGGTAG 57.527 50.000 0.00 0.00 0.00 3.18
3482 3571 3.433306 AATGCTTGGTAGTGCTTGGTA 57.567 42.857 0.00 0.00 0.00 3.25
3483 3572 2.292828 AATGCTTGGTAGTGCTTGGT 57.707 45.000 0.00 0.00 0.00 3.67
3484 3573 3.319755 CAAAATGCTTGGTAGTGCTTGG 58.680 45.455 0.00 0.00 0.00 3.61
3485 3574 2.733026 GCAAAATGCTTGGTAGTGCTTG 59.267 45.455 0.00 0.00 40.96 4.01
3486 3575 2.364970 TGCAAAATGCTTGGTAGTGCTT 59.635 40.909 3.78 0.00 45.31 3.91
3487 3576 1.962807 TGCAAAATGCTTGGTAGTGCT 59.037 42.857 3.78 0.00 45.31 4.40
3825 3918 5.489792 ACAGATGTGGTTTGACTCTGTAT 57.510 39.130 1.88 0.00 43.42 2.29
3826 3919 4.955811 ACAGATGTGGTTTGACTCTGTA 57.044 40.909 1.88 0.00 43.42 2.74
3827 3920 3.845781 ACAGATGTGGTTTGACTCTGT 57.154 42.857 0.00 0.00 41.17 3.41
3828 3921 5.505173 AAAACAGATGTGGTTTGACTCTG 57.495 39.130 4.86 0.00 42.27 3.35
3835 3928 6.037062 GCTAAAAAGCAAAACAGATGTGGTTT 59.963 34.615 0.00 0.00 44.88 3.27
3836 3929 5.523552 GCTAAAAAGCAAAACAGATGTGGTT 59.476 36.000 0.00 0.00 33.85 3.67
3837 3930 5.049828 GCTAAAAAGCAAAACAGATGTGGT 58.950 37.500 0.00 0.00 34.41 4.16
3838 3931 5.049167 TGCTAAAAAGCAAAACAGATGTGG 58.951 37.500 0.00 0.00 42.40 4.17
3839 3932 5.750067 ACTGCTAAAAAGCAAAACAGATGTG 59.250 36.000 1.28 0.00 44.88 3.21
3840 3933 5.906073 ACTGCTAAAAAGCAAAACAGATGT 58.094 33.333 1.28 0.00 44.88 3.06
3841 3934 7.274250 GGATACTGCTAAAAAGCAAAACAGATG 59.726 37.037 1.28 0.00 44.88 2.90
3842 3935 7.315890 GGATACTGCTAAAAAGCAAAACAGAT 58.684 34.615 1.28 0.00 44.88 2.90
3856 3949 3.637821 AGGATGGAGGGATACTGCTAA 57.362 47.619 0.00 0.00 38.54 3.09
3861 3954 6.019748 CAGTGTTATAGGATGGAGGGATACT 58.980 44.000 0.00 0.00 0.00 2.12
3862 3955 5.780793 ACAGTGTTATAGGATGGAGGGATAC 59.219 44.000 0.00 0.00 0.00 2.24
3863 3956 5.977533 ACAGTGTTATAGGATGGAGGGATA 58.022 41.667 0.00 0.00 0.00 2.59
3875 3968 9.982651 ATAAATGCTACCAGTACAGTGTTATAG 57.017 33.333 0.00 0.00 0.00 1.31
3928 4021 2.057137 TTTATCAGGGGCAGTGCATC 57.943 50.000 18.61 8.31 0.00 3.91
3937 4030 3.385433 TGCTGCATGAAATTTATCAGGGG 59.615 43.478 0.00 0.00 32.00 4.79
4072 4165 7.592938 CAACATATTGTGGAAGCAGTAAAGAA 58.407 34.615 0.00 0.00 0.00 2.52
4147 4240 3.584406 AGAATGAGATCGAATATGGGGCA 59.416 43.478 0.00 0.00 0.00 5.36
4148 4241 4.213564 AGAATGAGATCGAATATGGGGC 57.786 45.455 0.00 0.00 0.00 5.80
4149 4242 5.181748 GGAAGAATGAGATCGAATATGGGG 58.818 45.833 0.00 0.00 0.00 4.96
4202 4295 6.418585 AGATGCGACAATGATATATGCAAG 57.581 37.500 0.00 0.00 34.21 4.01
4259 4352 1.418637 AGGAAAGGCTCGTTACCAACA 59.581 47.619 0.00 0.00 0.00 3.33
4346 4439 2.919494 GCCCAAACCAGCCTTCACG 61.919 63.158 0.00 0.00 0.00 4.35
4862 4955 0.543277 TCCCTGGCTGTATGCTCTTG 59.457 55.000 0.00 0.00 42.39 3.02
4958 5051 1.467035 CCGCTTGCTCTTTTGATCTGC 60.467 52.381 0.00 0.00 0.00 4.26
4964 5057 1.727022 CACGCCGCTTGCTCTTTTG 60.727 57.895 0.00 0.00 38.05 2.44
5111 5204 3.716195 CGGGTGTCCAGCATCCCA 61.716 66.667 0.00 0.00 45.67 4.37
5376 5469 4.795962 GCCATCTTCCGCAAAGAAAAAGAA 60.796 41.667 2.92 0.00 46.85 2.52
5377 5470 3.305335 GCCATCTTCCGCAAAGAAAAAGA 60.305 43.478 2.92 0.00 46.85 2.52
5422 5515 0.338467 TACCCCTCTAAGCTGCCAGA 59.662 55.000 0.00 0.00 0.00 3.86
5484 5579 8.404107 TCCACCGAAATTAGAAGAAAAAGATT 57.596 30.769 0.00 0.00 0.00 2.40
5537 5635 4.308899 AGCTACGCTAACGAGATGAATT 57.691 40.909 0.00 0.00 43.93 2.17
5538 5636 3.992260 AGCTACGCTAACGAGATGAAT 57.008 42.857 0.00 0.00 43.93 2.57
5539 5637 3.777465 AAGCTACGCTAACGAGATGAA 57.223 42.857 0.00 0.00 43.93 2.57
5540 5638 3.128068 TCAAAGCTACGCTAACGAGATGA 59.872 43.478 0.00 0.00 43.93 2.92
5541 5639 3.435566 TCAAAGCTACGCTAACGAGATG 58.564 45.455 0.00 0.00 43.93 2.90
5542 5640 3.777465 TCAAAGCTACGCTAACGAGAT 57.223 42.857 0.00 0.00 43.93 2.75
5646 5744 1.955778 CTGGACTCACCACATTTGCAA 59.044 47.619 0.00 0.00 44.64 4.08
5697 5810 3.077359 AGGTTGTTATGAAGCACAGCTC 58.923 45.455 0.00 0.00 38.25 4.09
5698 5811 3.146104 AGGTTGTTATGAAGCACAGCT 57.854 42.857 0.00 0.00 42.56 4.24
5699 5812 3.923017 AAGGTTGTTATGAAGCACAGC 57.077 42.857 0.00 0.00 0.00 4.40
5730 5843 3.815856 TCAGAAATGCTTTGTTTGGCA 57.184 38.095 0.00 0.00 42.80 4.92
5742 5855 5.287752 CGGAGTGAAAATGCATTCAGAAATG 59.712 40.000 13.38 0.00 44.31 2.32
5759 5872 2.615240 CCAATGTGTTCCATCGGAGTGA 60.615 50.000 0.00 0.00 27.93 3.41
5765 5878 3.343617 AGGTTACCAATGTGTTCCATCG 58.656 45.455 3.51 0.00 31.75 3.84
5818 5938 1.270358 GCCTACTGCTAGTGTATGGCC 60.270 57.143 0.00 0.00 33.66 5.36
5819 5939 2.156343 GCCTACTGCTAGTGTATGGC 57.844 55.000 15.13 15.13 36.87 4.40
5846 5966 1.931841 CATCGACTCAGATTGCCAGTG 59.068 52.381 0.00 0.00 0.00 3.66
5851 5983 4.033990 TCAGTACATCGACTCAGATTGC 57.966 45.455 0.00 0.00 0.00 3.56
5866 5998 5.915196 GCAATTGGTCTCAAGTTTTCAGTAC 59.085 40.000 7.72 0.00 36.19 2.73
5880 6012 2.949177 TGTGTACAGGCAATTGGTCT 57.051 45.000 7.72 0.00 0.00 3.85
5896 6028 1.812922 GCTCCCGAGTGCAGATGTG 60.813 63.158 0.00 0.00 32.66 3.21
5908 6040 2.208431 GATCTGAAATGACTGCTCCCG 58.792 52.381 0.00 0.00 0.00 5.14
6040 6178 2.071526 GGACGACGACGACAACGAC 61.072 63.158 15.32 2.54 42.66 4.34
6041 6179 2.249309 GGACGACGACGACAACGA 59.751 61.111 15.32 0.00 42.66 3.85
6042 6180 2.798262 GGGACGACGACGACAACG 60.798 66.667 15.32 4.49 42.66 4.10
6043 6181 2.429739 GGGGACGACGACGACAAC 60.430 66.667 15.32 4.83 42.66 3.32
6044 6182 2.203972 GATGGGGACGACGACGACAA 62.204 60.000 15.32 0.00 42.66 3.18
6045 6183 2.674033 ATGGGGACGACGACGACA 60.674 61.111 15.32 7.63 42.66 4.35
6046 6184 2.001361 ATGATGGGGACGACGACGAC 62.001 60.000 15.32 7.84 42.66 4.34
6047 6185 1.721664 GATGATGGGGACGACGACGA 61.722 60.000 15.32 0.00 42.66 4.20
6048 6186 1.299165 GATGATGGGGACGACGACG 60.299 63.158 5.58 5.58 45.75 5.12
6089 6230 0.674581 TGCCTCTTCATTGCAGTCCG 60.675 55.000 0.00 0.00 0.00 4.79
6224 6444 4.306600 CCACAGGGTTTTAGTTCAATTGC 58.693 43.478 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.