Multiple sequence alignment - TraesCS5B01G024700

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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 TraesCS5B01G024700 chr5B 100.000 6012 0 0 1 6012 23553333 23547322 0.000000e+00 11103.0
1 TraesCS5B01G024700 chr5B 84.615 273 36 3 343 614 659705546 659705279 3.570000e-67 267.0
2 TraesCS5B01G024700 chr5D 96.109 4549 124 22 582 5098 31275466 31270939 0.000000e+00 7371.0
3 TraesCS5B01G024700 chr5D 90.177 621 26 12 1 586 31298638 31298018 0.000000e+00 776.0
4 TraesCS5B01G024700 chr5D 96.501 343 9 2 5096 5436 31270854 31270513 1.130000e-156 564.0
5 TraesCS5B01G024700 chr5D 82.127 677 89 14 1 645 528136587 528137263 8.810000e-153 551.0
6 TraesCS5B01G024700 chr5D 78.491 530 73 24 137 645 486478207 486478716 5.850000e-80 309.0
7 TraesCS5B01G024700 chr5D 76.000 475 98 13 175 643 560005604 560005140 1.300000e-56 231.0
8 TraesCS5B01G024700 chr3B 92.188 576 41 4 5438 6011 689994446 689993873 0.000000e+00 811.0
9 TraesCS5B01G024700 chr3B 90.909 572 46 6 5442 6011 515250121 515250688 0.000000e+00 763.0
10 TraesCS5B01G024700 chr3B 90.718 571 50 3 5443 6011 98019522 98018953 0.000000e+00 758.0
11 TraesCS5B01G024700 chr4A 92.281 570 40 4 5444 6011 658408005 658408572 0.000000e+00 806.0
12 TraesCS5B01G024700 chr7D 91.289 574 44 6 5442 6012 403098090 403098660 0.000000e+00 778.0
13 TraesCS5B01G024700 chr7D 91.274 573 43 7 5444 6012 566012064 566012633 0.000000e+00 774.0
14 TraesCS5B01G024700 chr7D 82.344 674 81 20 1 643 159709432 159710098 8.810000e-153 551.0
15 TraesCS5B01G024700 chr2B 91.228 570 45 5 5444 6011 67031522 67032088 0.000000e+00 771.0
16 TraesCS5B01G024700 chr4B 90.909 572 49 3 5443 6012 34778323 34777753 0.000000e+00 765.0
17 TraesCS5B01G024700 chr4B 90.718 571 47 6 5444 6011 637986883 637987450 0.000000e+00 756.0
18 TraesCS5B01G024700 chr4D 81.916 741 95 20 1 719 13046168 13045445 1.870000e-164 590.0
19 TraesCS5B01G024700 chr2D 81.481 729 107 17 1 711 535583095 535583813 1.880000e-159 573.0
20 TraesCS5B01G024700 chr6D 82.036 668 84 16 1 641 157154410 157155068 2.470000e-148 536.0
21 TraesCS5B01G024700 chr6B 83.333 576 70 12 1 552 671018281 671018854 5.380000e-140 508.0
22 TraesCS5B01G024700 chr6B 83.299 479 49 17 2 457 484998448 484998918 4.340000e-111 412.0
23 TraesCS5B01G024700 chr3D 79.454 769 95 27 2 721 25385144 25385898 2.520000e-133 486.0
24 TraesCS5B01G024700 chr7B 80.975 636 97 16 100 719 243868374 243867747 3.260000e-132 483.0
25 TraesCS5B01G024700 chr6A 80.305 655 94 24 3 643 569429949 569430582 4.240000e-126 462.0
26 TraesCS5B01G024700 chr7A 83.599 439 49 12 2 418 485494840 485495277 2.030000e-104 390.0
27 TraesCS5B01G024700 chr5A 88.426 216 24 1 335 549 74707138 74706923 5.980000e-65 259.0
28 TraesCS5B01G024700 chr3A 79.758 331 54 9 398 723 644782323 644782645 1.690000e-55 228.0
29 TraesCS5B01G024700 chr2A 79.331 329 59 5 398 723 42477993 42478315 7.840000e-54 222.0
30 TraesCS5B01G024700 chr1A 83.000 100 16 1 3844 3943 27511444 27511542 8.300000e-14 89.8


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 TraesCS5B01G024700 chr5B 23547322 23553333 6011 True 11103.0 11103 100.000 1 6012 1 chr5B.!!$R1 6011
1 TraesCS5B01G024700 chr5D 31270513 31275466 4953 True 3967.5 7371 96.305 582 5436 2 chr5D.!!$R3 4854
2 TraesCS5B01G024700 chr5D 31298018 31298638 620 True 776.0 776 90.177 1 586 1 chr5D.!!$R1 585
3 TraesCS5B01G024700 chr5D 528136587 528137263 676 False 551.0 551 82.127 1 645 1 chr5D.!!$F2 644
4 TraesCS5B01G024700 chr5D 486478207 486478716 509 False 309.0 309 78.491 137 645 1 chr5D.!!$F1 508
5 TraesCS5B01G024700 chr3B 689993873 689994446 573 True 811.0 811 92.188 5438 6011 1 chr3B.!!$R2 573
6 TraesCS5B01G024700 chr3B 515250121 515250688 567 False 763.0 763 90.909 5442 6011 1 chr3B.!!$F1 569
7 TraesCS5B01G024700 chr3B 98018953 98019522 569 True 758.0 758 90.718 5443 6011 1 chr3B.!!$R1 568
8 TraesCS5B01G024700 chr4A 658408005 658408572 567 False 806.0 806 92.281 5444 6011 1 chr4A.!!$F1 567
9 TraesCS5B01G024700 chr7D 403098090 403098660 570 False 778.0 778 91.289 5442 6012 1 chr7D.!!$F2 570
10 TraesCS5B01G024700 chr7D 566012064 566012633 569 False 774.0 774 91.274 5444 6012 1 chr7D.!!$F3 568
11 TraesCS5B01G024700 chr7D 159709432 159710098 666 False 551.0 551 82.344 1 643 1 chr7D.!!$F1 642
12 TraesCS5B01G024700 chr2B 67031522 67032088 566 False 771.0 771 91.228 5444 6011 1 chr2B.!!$F1 567
13 TraesCS5B01G024700 chr4B 34777753 34778323 570 True 765.0 765 90.909 5443 6012 1 chr4B.!!$R1 569
14 TraesCS5B01G024700 chr4B 637986883 637987450 567 False 756.0 756 90.718 5444 6011 1 chr4B.!!$F1 567
15 TraesCS5B01G024700 chr4D 13045445 13046168 723 True 590.0 590 81.916 1 719 1 chr4D.!!$R1 718
16 TraesCS5B01G024700 chr2D 535583095 535583813 718 False 573.0 573 81.481 1 711 1 chr2D.!!$F1 710
17 TraesCS5B01G024700 chr6D 157154410 157155068 658 False 536.0 536 82.036 1 641 1 chr6D.!!$F1 640
18 TraesCS5B01G024700 chr6B 671018281 671018854 573 False 508.0 508 83.333 1 552 1 chr6B.!!$F2 551
19 TraesCS5B01G024700 chr3D 25385144 25385898 754 False 486.0 486 79.454 2 721 1 chr3D.!!$F1 719
20 TraesCS5B01G024700 chr7B 243867747 243868374 627 True 483.0 483 80.975 100 719 1 chr7B.!!$R1 619
21 TraesCS5B01G024700 chr6A 569429949 569430582 633 False 462.0 462 80.305 3 643 1 chr6A.!!$F1 640

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
684 798 0.247145 GCGTTCGCGATCGTTTGAAT 60.247 50.0 32.46 0.0 44.71 2.57 F
1348 1474 0.108138 CTCAAGCTCAACCTACCGGG 60.108 60.0 6.32 0.0 41.89 5.73 F
2904 3035 0.105964 TCTGCCAGTAAACGTGCACT 59.894 50.0 16.19 0.0 0.00 4.40 F
3303 3436 0.179119 GCCATGCACCTTCAATGAGC 60.179 55.0 0.00 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2661 2790 0.393537 CACAGACATCCTTGCTCCCC 60.394 60.0 0.00 0.00 0.00 4.81 R
3298 3431 0.739813 GACGGCCGTTTAGTGCTCAT 60.740 55.0 34.65 3.67 0.00 2.90 R
4118 4259 1.067295 AGGGGTTCTGCAAGATGTCA 58.933 50.0 0.00 0.00 46.36 3.58 R
5195 5426 0.885879 TCAGCTGCCATTTTGCTCAG 59.114 50.0 9.47 0.00 34.51 3.35 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
66 73 1.279271 CATTTTCCTCCTCCTGTCCGT 59.721 52.381 0.00 0.00 0.00 4.69
96 103 0.763223 ACTTTCCACTCCACCCGTCT 60.763 55.000 0.00 0.00 0.00 4.18
463 565 3.767268 AGGGGGAGGATGAGCCGA 61.767 66.667 0.00 0.00 43.43 5.54
482 585 3.400054 GGCCTCCTACTGCCCGTT 61.400 66.667 0.00 0.00 41.97 4.44
645 759 2.209690 TGAGACATGACCGGTCACTA 57.790 50.000 38.46 17.91 43.11 2.74
684 798 0.247145 GCGTTCGCGATCGTTTGAAT 60.247 50.000 32.46 0.00 44.71 2.57
690 804 0.719465 GCGATCGTTTGAATGACCGT 59.281 50.000 17.81 0.00 0.00 4.83
702 816 7.588488 CGTTTGAATGACCGTATTTGTAAAGTT 59.412 33.333 0.00 0.00 0.00 2.66
711 825 5.120519 CCGTATTTGTAAAGTTCGGCTGTAA 59.879 40.000 0.00 0.00 0.00 2.41
765 882 4.704833 TGAGGGAGCAAGCCGCAC 62.705 66.667 0.00 0.00 46.13 5.34
769 886 3.426568 GGAGCAAGCCGCACTGTC 61.427 66.667 0.00 0.00 46.13 3.51
803 920 2.278857 AGCAAGCCGTATCGCTCG 60.279 61.111 0.00 0.00 38.44 5.03
820 937 1.486726 CTCGGGCTCAACCTTATCCTT 59.513 52.381 0.00 0.00 39.10 3.36
821 938 2.698797 CTCGGGCTCAACCTTATCCTTA 59.301 50.000 0.00 0.00 39.10 2.69
822 939 3.314693 TCGGGCTCAACCTTATCCTTAT 58.685 45.455 0.00 0.00 39.10 1.73
823 940 4.485875 TCGGGCTCAACCTTATCCTTATA 58.514 43.478 0.00 0.00 39.10 0.98
909 1026 2.094762 AAACCCTCAAATCGACTCCG 57.905 50.000 0.00 0.00 37.07 4.63
1116 1242 5.121611 CAGATTGTTTGTGGCGTCTGTTATA 59.878 40.000 0.00 0.00 0.00 0.98
1151 1277 6.155737 GTGTAAGTATTCCTTTCCTCCCAGTA 59.844 42.308 0.00 0.00 34.46 2.74
1152 1278 5.695424 AAGTATTCCTTTCCTCCCAGTAC 57.305 43.478 0.00 0.00 0.00 2.73
1153 1279 4.695606 AGTATTCCTTTCCTCCCAGTACA 58.304 43.478 0.00 0.00 0.00 2.90
1154 1280 4.470304 AGTATTCCTTTCCTCCCAGTACAC 59.530 45.833 0.00 0.00 0.00 2.90
1155 1281 1.263356 TCCTTTCCTCCCAGTACACG 58.737 55.000 0.00 0.00 0.00 4.49
1156 1282 1.203087 TCCTTTCCTCCCAGTACACGA 60.203 52.381 0.00 0.00 0.00 4.35
1157 1283 1.067071 CCTTTCCTCCCAGTACACGAC 60.067 57.143 0.00 0.00 0.00 4.34
1158 1284 0.599558 TTTCCTCCCAGTACACGACG 59.400 55.000 0.00 0.00 0.00 5.12
1159 1285 0.250858 TTCCTCCCAGTACACGACGA 60.251 55.000 0.00 0.00 0.00 4.20
1160 1286 0.250858 TCCTCCCAGTACACGACGAA 60.251 55.000 0.00 0.00 0.00 3.85
1161 1287 0.815734 CCTCCCAGTACACGACGAAT 59.184 55.000 0.00 0.00 0.00 3.34
1162 1288 1.469251 CCTCCCAGTACACGACGAATG 60.469 57.143 0.00 0.00 0.00 2.67
1163 1289 1.201647 CTCCCAGTACACGACGAATGT 59.798 52.381 0.00 0.00 0.00 2.71
1205 1331 9.720769 CTATTTGTATACATATTTTCCCCTCGT 57.279 33.333 13.10 0.00 0.00 4.18
1206 1332 8.990163 ATTTGTATACATATTTTCCCCTCGTT 57.010 30.769 6.36 0.00 0.00 3.85
1246 1372 4.142491 TGTTTGCTTCTTTTCTTCGCAGAA 60.142 37.500 0.00 0.00 45.90 3.02
1348 1474 0.108138 CTCAAGCTCAACCTACCGGG 60.108 60.000 6.32 0.00 41.89 5.73
1390 1516 6.886178 ACATGTACTTATCCCAACCTTACT 57.114 37.500 0.00 0.00 0.00 2.24
1481 1607 7.165485 ACACTTAATGTCTAATTGGTGCACTA 58.835 34.615 17.98 8.10 36.54 2.74
1519 1645 5.588648 CGGTTGTTGGTGATCCATATAGTTT 59.411 40.000 0.00 0.00 43.91 2.66
1575 1701 2.806945 TATCTGTGCTGAAAAGGGGG 57.193 50.000 0.00 0.00 0.00 5.40
1577 1703 0.110486 TCTGTGCTGAAAAGGGGGTC 59.890 55.000 0.00 0.00 0.00 4.46
1629 1755 4.816925 GTGTCATTAGCCCATCTTTCTACC 59.183 45.833 0.00 0.00 0.00 3.18
1801 1929 4.243270 GCGTACTGTTCTTGAGGTAATGT 58.757 43.478 0.00 0.00 0.00 2.71
1819 1947 8.532819 AGGTAATGTTCTTCTCCTACTTACTTG 58.467 37.037 0.00 0.00 0.00 3.16
1848 1976 1.181786 GTGTGTCTGCTCTCTAGGCT 58.818 55.000 0.00 0.00 0.00 4.58
1883 2011 9.914923 GTTACAACTCCATTTCAAATTTTCAAC 57.085 29.630 0.00 0.00 0.00 3.18
1953 2081 3.721706 GGCACCCCAGGACTCAGG 61.722 72.222 0.00 0.00 0.00 3.86
2018 2147 6.211587 TGAAACAACATCCATTGATCCATC 57.788 37.500 0.00 0.00 33.57 3.51
2155 2284 3.372897 AGAGTTCATGATCTGCTCCTCA 58.627 45.455 11.04 0.00 0.00 3.86
2164 2293 6.496218 TCATGATCTGCTCCTCACTTGTATAT 59.504 38.462 0.00 0.00 0.00 0.86
2391 2520 3.251571 GCGACAGTCTTACCGAATCTTT 58.748 45.455 0.00 0.00 0.00 2.52
2661 2790 1.325640 CAGAAGGTCATCATTGCGACG 59.674 52.381 0.00 0.00 32.74 5.12
2675 2804 2.990479 GACGGGGAGCAAGGATGT 59.010 61.111 0.00 0.00 0.00 3.06
2676 2805 1.153349 GACGGGGAGCAAGGATGTC 60.153 63.158 0.00 0.00 0.00 3.06
2758 2887 2.969821 TGCCTGGAGCCTCTTTAAAA 57.030 45.000 0.00 0.00 42.71 1.52
2846 2975 5.452636 GCCCACCAAAATGTTGTTTCTAAGA 60.453 40.000 0.00 0.00 32.40 2.10
2872 3001 1.825090 CATGCCAGCACTTCCTGTTA 58.175 50.000 0.00 0.00 0.00 2.41
2904 3035 0.105964 TCTGCCAGTAAACGTGCACT 59.894 50.000 16.19 0.00 0.00 4.40
2961 3092 8.281212 CCTAGTTATTAGGCAATTGTTCAAGT 57.719 34.615 7.40 0.00 42.50 3.16
2962 3093 8.184192 CCTAGTTATTAGGCAATTGTTCAAGTG 58.816 37.037 7.40 8.34 42.50 3.16
2963 3094 7.759489 AGTTATTAGGCAATTGTTCAAGTGA 57.241 32.000 15.45 0.00 0.00 3.41
2966 3097 9.423061 GTTATTAGGCAATTGTTCAAGTGAAAT 57.577 29.630 15.45 12.58 35.58 2.17
2967 3098 9.638239 TTATTAGGCAATTGTTCAAGTGAAATC 57.362 29.630 15.45 3.60 35.58 2.17
2968 3099 5.534207 AGGCAATTGTTCAAGTGAAATCA 57.466 34.783 15.45 0.00 35.58 2.57
2969 3100 5.916318 AGGCAATTGTTCAAGTGAAATCAA 58.084 33.333 15.45 0.00 35.58 2.57
3225 3358 2.550830 AACCTTCTCATCACAAGCGT 57.449 45.000 0.00 0.00 0.00 5.07
3245 3378 3.551890 CGTTATCACTCCCTCAATTCGTG 59.448 47.826 0.00 0.00 0.00 4.35
3252 3385 3.118592 ACTCCCTCAATTCGTGGATTCTC 60.119 47.826 0.00 0.00 0.00 2.87
3292 3425 1.935199 GTATTGCCAATTGCCATGCAC 59.065 47.619 6.60 0.00 38.71 4.57
3298 3431 1.002201 CCAATTGCCATGCACCTTCAA 59.998 47.619 0.00 0.00 38.71 2.69
3303 3436 0.179119 GCCATGCACCTTCAATGAGC 60.179 55.000 0.00 0.00 0.00 4.26
3447 3580 9.807921 AAGGTTTTCTTCAAGATAGTTAATGGA 57.192 29.630 0.00 0.00 0.00 3.41
3463 3596 2.380064 TGGAGCCAACAAGGAAACAT 57.620 45.000 0.00 0.00 41.22 2.71
3465 3598 2.364970 TGGAGCCAACAAGGAAACATTG 59.635 45.455 0.00 0.00 41.22 2.82
3522 3655 7.896811 AGTATCTGTAAAGTTGATCTGTGTCA 58.103 34.615 0.00 0.00 0.00 3.58
3525 3658 6.582636 TCTGTAAAGTTGATCTGTGTCAGTT 58.417 36.000 0.00 0.00 32.61 3.16
3662 3795 4.622220 GCTTTCACAATGGATGGATTGCTT 60.622 41.667 0.00 0.00 36.89 3.91
3666 3799 3.635373 CACAATGGATGGATTGCTTAGCT 59.365 43.478 5.60 0.00 36.89 3.32
3675 3808 6.183360 GGATGGATTGCTTAGCTGAAAGATTT 60.183 38.462 5.60 0.00 34.07 2.17
3682 3815 4.488879 CTTAGCTGAAAGATTTTGGGCAC 58.511 43.478 0.00 0.00 34.07 5.01
3700 3833 4.041723 GGCACATACAATCGGTAAATTGC 58.958 43.478 0.00 0.00 39.72 3.56
3703 3836 6.459024 GGCACATACAATCGGTAAATTGCTTA 60.459 38.462 0.00 0.00 39.72 3.09
3738 3871 4.104831 ACAAGCTAACCTTAGGGACTGAT 58.895 43.478 2.32 0.00 41.52 2.90
3751 3884 3.010200 GGACTGATTCCAAGGCATCTT 57.990 47.619 0.68 0.00 45.10 2.40
3789 3922 1.420430 ACCAGACTCCGGAAACTTCA 58.580 50.000 5.23 0.00 0.00 3.02
3840 3973 0.883833 AGTGAGAAAATGGCTTGCGG 59.116 50.000 0.00 0.00 0.00 5.69
3902 4035 8.547069 GCTAATTTATGAGACAGAAAGCTACTG 58.453 37.037 16.08 16.08 40.68 2.74
3912 4045 3.196469 CAGAAAGCTACTGATGGAGACCA 59.804 47.826 13.44 0.00 37.54 4.02
3959 4092 5.648092 CCCAGATTTGTAACTTGGGACTTAG 59.352 44.000 1.59 0.00 37.29 2.18
3960 4093 5.648092 CCAGATTTGTAACTTGGGACTTAGG 59.352 44.000 0.00 0.00 0.00 2.69
3965 4106 5.416271 TGTAACTTGGGACTTAGGCTTAG 57.584 43.478 0.00 0.00 0.00 2.18
3970 4111 4.536489 ACTTGGGACTTAGGCTTAGACAAT 59.464 41.667 7.64 0.00 0.00 2.71
4118 4259 5.053978 AGTTTTCCATCTTCAGTGACCTT 57.946 39.130 0.00 0.00 0.00 3.50
4152 4293 1.145738 ACCCCTTCTGAAGCACACATT 59.854 47.619 11.93 0.00 0.00 2.71
4156 4297 4.463891 CCCCTTCTGAAGCACACATTAAAT 59.536 41.667 11.93 0.00 0.00 1.40
4186 4327 5.607939 TGTACCAAGTACCATAGTCCATG 57.392 43.478 2.63 0.00 38.14 3.66
4406 4549 4.936396 GTTGAAGAAAACAACTGATGCG 57.064 40.909 0.00 0.00 42.63 4.73
4413 4556 5.591099 AGAAAACAACTGATGCGTTTGAAT 58.409 33.333 0.00 0.00 33.33 2.57
4425 4568 5.351233 TGCGTTTGAATTATCGTTGACTT 57.649 34.783 0.00 0.00 0.00 3.01
4645 4788 1.005450 GACCCCATAGCCCAACTTGAA 59.995 52.381 0.00 0.00 0.00 2.69
4671 4814 6.982899 AGAGTTCAGGTTCTAGGGTTATAGA 58.017 40.000 0.00 0.00 0.00 1.98
4796 4939 3.005791 GTGGCTAAATTTCAACCTGCTGT 59.994 43.478 0.00 0.00 0.00 4.40
4835 4978 7.824289 AGCTGCTTAACTTGATTGACTGTTATA 59.176 33.333 0.00 0.00 0.00 0.98
4882 5025 2.293627 GCCGATAGCACTACGCACG 61.294 63.158 0.00 0.00 46.13 5.34
4920 5063 2.486918 TGCGATACAAGATGCAGATGG 58.513 47.619 0.00 0.00 32.73 3.51
5098 5329 6.575162 AATTGTCCTTGCCTAGTAAAAGTG 57.425 37.500 0.00 0.00 0.00 3.16
5190 5421 6.775594 AATAATTCTAACAGCCCCAACTTC 57.224 37.500 0.00 0.00 0.00 3.01
5195 5426 0.178961 AACAGCCCCAACTTCCCTTC 60.179 55.000 0.00 0.00 0.00 3.46
5297 5528 9.455847 GGCATACAAATTCTTATTTCAGCTTAG 57.544 33.333 0.00 0.00 31.63 2.18
5310 5541 4.277515 TCAGCTTAGATTTCTGCACTGT 57.722 40.909 0.00 0.00 0.00 3.55
5325 5556 6.314018 TCTGCACTGTAAAAATAATTCAGCG 58.686 36.000 0.00 0.00 0.00 5.18
5404 5637 3.350219 AGTCAAAATCCGGCAGTGTAT 57.650 42.857 0.00 0.00 0.00 2.29
5419 5652 5.238583 GCAGTGTATGTGGAGTAACTTCTT 58.761 41.667 0.00 0.00 0.00 2.52
5482 5715 0.674895 GCCTCAACTTGTCCGATGCT 60.675 55.000 0.00 0.00 0.00 3.79
5561 5794 1.816074 GTTCAAATACGGTGCCTCCA 58.184 50.000 0.00 0.00 35.57 3.86
5564 5797 1.837439 TCAAATACGGTGCCTCCATCT 59.163 47.619 0.00 0.00 35.57 2.90
5574 5807 1.831652 GCCTCCATCTGTATCCGGGG 61.832 65.000 0.00 0.00 0.00 5.73
5701 5938 4.525912 ATTTTCGCAAAAGCTCCTGATT 57.474 36.364 0.00 0.00 33.22 2.57
5705 5942 5.446143 TTCGCAAAAGCTCCTGATTTTTA 57.554 34.783 0.00 0.00 39.41 1.52
5838 6076 3.937814 TGAATTCATTACCTCACGCACT 58.062 40.909 3.38 0.00 0.00 4.40
5890 6128 8.438513 CCAAGAACAATTATCTATGCACTATCG 58.561 37.037 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
226 233 2.187946 CCTCCGGATCCACTGCAC 59.812 66.667 13.41 0.00 0.00 4.57
552 655 4.574013 AGAAAGCATGCGAAGAAATCCTAG 59.426 41.667 13.01 0.00 0.00 3.02
564 676 5.455392 CCCTAATTTCATAGAAAGCATGCG 58.545 41.667 13.01 0.00 0.00 4.73
645 759 1.767289 GATCGCACGTGTCCGATAAT 58.233 50.000 24.54 9.70 43.48 1.28
669 783 0.996462 GGTCATTCAAACGATCGCGA 59.004 50.000 16.60 13.09 41.64 5.87
684 798 3.432933 GCCGAACTTTACAAATACGGTCA 59.567 43.478 0.00 0.00 40.76 4.02
690 804 9.439500 AGTATTTACAGCCGAACTTTACAAATA 57.561 29.630 0.00 0.00 0.00 1.40
737 851 1.984570 CTCCCTCACGGCTTCTCCA 60.985 63.158 0.00 0.00 34.01 3.86
803 920 6.779860 TGAATATAAGGATAAGGTTGAGCCC 58.220 40.000 0.00 0.00 38.26 5.19
820 937 5.130477 GGACTGGACCCTCTTGTTGAATATA 59.870 44.000 0.00 0.00 0.00 0.86
821 938 4.080299 GGACTGGACCCTCTTGTTGAATAT 60.080 45.833 0.00 0.00 0.00 1.28
822 939 3.263425 GGACTGGACCCTCTTGTTGAATA 59.737 47.826 0.00 0.00 0.00 1.75
823 940 2.040412 GGACTGGACCCTCTTGTTGAAT 59.960 50.000 0.00 0.00 0.00 2.57
963 1089 1.686355 CAGGAGCGAGTAGATCTGGT 58.314 55.000 5.18 0.00 35.20 4.00
1116 1242 4.347000 AGGAATACTTACACACACACCAGT 59.653 41.667 0.00 0.00 0.00 4.00
1152 1278 4.384547 TGAAACATCTACACATTCGTCGTG 59.615 41.667 0.00 0.00 40.32 4.35
1153 1279 4.552355 TGAAACATCTACACATTCGTCGT 58.448 39.130 0.00 0.00 0.00 4.34
1154 1280 5.702622 ATGAAACATCTACACATTCGTCG 57.297 39.130 0.00 0.00 0.00 5.12
1155 1281 6.313905 AGGAATGAAACATCTACACATTCGTC 59.686 38.462 0.00 0.00 44.05 4.20
1156 1282 6.173339 AGGAATGAAACATCTACACATTCGT 58.827 36.000 0.00 0.00 44.05 3.85
1157 1283 6.668541 AGGAATGAAACATCTACACATTCG 57.331 37.500 0.00 0.00 44.05 3.34
1160 1286 9.466497 ACAAATAGGAATGAAACATCTACACAT 57.534 29.630 0.00 0.00 0.00 3.21
1161 1287 8.862325 ACAAATAGGAATGAAACATCTACACA 57.138 30.769 0.00 0.00 0.00 3.72
1224 1350 3.952535 TCTGCGAAGAAAAGAAGCAAAC 58.047 40.909 0.00 0.00 37.38 2.93
1232 1358 3.482110 CCAAAACGTTCTGCGAAGAAAAG 59.518 43.478 7.62 7.86 44.77 2.27
1246 1372 2.756207 GCATAACATACCCCCAAAACGT 59.244 45.455 0.00 0.00 0.00 3.99
1327 1453 0.741221 CGGTAGGTTGAGCTTGAGCC 60.741 60.000 0.00 0.00 43.38 4.70
1348 1474 1.136500 GTACTCCATGAGGAACCGGAC 59.864 57.143 9.46 0.76 45.19 4.79
1452 1578 7.094805 TGCACCAATTAGACATTAAGTGTTCTC 60.095 37.037 0.00 0.00 42.36 2.87
1481 1607 1.227734 AACCGGCTTAACACAGCGT 60.228 52.632 0.00 0.00 41.12 5.07
1536 1662 7.040062 ACAGATATGTTCTCTGCTAGTACATCC 60.040 40.741 12.68 8.35 40.97 3.51
1603 1729 4.018050 AGAAAGATGGGCTAATGACACCTT 60.018 41.667 0.00 0.00 0.00 3.50
1629 1755 2.038557 CCTTATATCACCCAGTTCCCCG 59.961 54.545 0.00 0.00 0.00 5.73
1801 1929 4.426704 AGGCCAAGTAAGTAGGAGAAGAA 58.573 43.478 5.01 0.00 0.00 2.52
1819 1947 2.226674 GAGCAGACACACTTTTAAGGCC 59.773 50.000 0.00 0.00 0.00 5.19
1848 1976 6.488344 TGAAATGGAGTTGTAACATTACAGCA 59.512 34.615 17.47 1.79 44.25 4.41
1883 2011 4.119862 CGTAGTACAATGGAATCCTGTGG 58.880 47.826 0.00 0.00 0.00 4.17
2018 2147 3.565764 TCATGCTCATAAAGGGACCAG 57.434 47.619 0.00 0.00 0.00 4.00
2155 2284 1.340248 CGACCGGAGCCATATACAAGT 59.660 52.381 9.46 0.00 0.00 3.16
2466 2595 3.305094 CGTAGTTGTAGCCCAAACATACG 59.695 47.826 10.33 10.33 36.63 3.06
2661 2790 0.393537 CACAGACATCCTTGCTCCCC 60.394 60.000 0.00 0.00 0.00 4.81
2758 2887 2.225091 TGATTGCATCCCCAACTCTGTT 60.225 45.455 0.00 0.00 0.00 3.16
2805 2934 0.960861 GGCTGTGTACCTCTTTGGCC 60.961 60.000 0.00 0.00 40.22 5.36
2846 2975 1.136305 GAAGTGCTGGCATGCATGAAT 59.864 47.619 30.64 5.08 45.23 2.57
2896 3027 2.363038 TCCTACAGTTACAAGTGCACGT 59.637 45.455 12.01 5.01 32.54 4.49
3075 3208 5.047021 TGTTGTCTTGGATTTTGTTGTTGGA 60.047 36.000 0.00 0.00 0.00 3.53
3088 3221 8.482128 ACCAAAGATAAAAATTGTTGTCTTGGA 58.518 29.630 25.57 0.00 38.50 3.53
3168 3301 9.541143 ACGTGGATTTGTAAAATTTGAAATCTT 57.459 25.926 19.71 0.00 35.84 2.40
3188 3321 8.757982 AGAAGGTTAATATCTAACTACGTGGA 57.242 34.615 5.70 0.00 0.00 4.02
3218 3351 1.899814 TGAGGGAGTGATAACGCTTGT 59.100 47.619 0.00 0.00 36.96 3.16
3225 3358 3.772572 TCCACGAATTGAGGGAGTGATAA 59.227 43.478 0.00 0.00 35.03 1.75
3245 3378 4.027437 AGGGTGACTAGACTTGAGAATCC 58.973 47.826 0.00 0.00 0.00 3.01
3252 3385 4.608948 ACTGAAAGGGTGACTAGACTTG 57.391 45.455 0.00 0.00 39.30 3.16
3292 3425 2.159517 GCCGTTTAGTGCTCATTGAAGG 60.160 50.000 0.00 0.00 0.00 3.46
3298 3431 0.739813 GACGGCCGTTTAGTGCTCAT 60.740 55.000 34.65 3.67 0.00 2.90
3303 3436 0.788391 GTCTTGACGGCCGTTTAGTG 59.212 55.000 34.65 19.97 0.00 2.74
3350 3483 4.132336 TCAGATCATGCCTCTTATTGTGC 58.868 43.478 0.00 0.00 0.00 4.57
3447 3580 2.765699 ACACAATGTTTCCTTGTTGGCT 59.234 40.909 0.00 0.00 34.69 4.75
3463 3596 1.133407 GGTTTCTTGCGGAACACACAA 59.867 47.619 0.00 0.00 33.13 3.33
3465 3598 1.021968 AGGTTTCTTGCGGAACACAC 58.978 50.000 0.00 0.00 33.13 3.82
3548 3681 7.918076 AGTATTTGAGGTTAGGTTTCTGATGA 58.082 34.615 0.00 0.00 0.00 2.92
3662 3795 3.495331 TGTGCCCAAAATCTTTCAGCTA 58.505 40.909 0.00 0.00 0.00 3.32
3666 3799 5.798125 TTGTATGTGCCCAAAATCTTTCA 57.202 34.783 0.00 0.00 0.00 2.69
3675 3808 3.351794 TTACCGATTGTATGTGCCCAA 57.648 42.857 0.00 0.00 0.00 4.12
3710 3843 8.211629 CAGTCCCTAAGGTTAGCTTGTTAATAT 58.788 37.037 6.95 0.00 0.00 1.28
3789 3922 8.466798 TGATTTTTCTTCGAGAAGTTTTTCCTT 58.533 29.630 12.01 0.00 35.37 3.36
3840 3973 3.312697 GTCTTGTTATTCGAATCCCTGCC 59.687 47.826 15.25 0.00 0.00 4.85
3890 4023 3.196469 TGGTCTCCATCAGTAGCTTTCTG 59.804 47.826 10.97 10.97 0.00 3.02
3934 4067 3.397955 AGTCCCAAGTTACAAATCTGGGT 59.602 43.478 5.39 0.00 36.55 4.51
4118 4259 1.067295 AGGGGTTCTGCAAGATGTCA 58.933 50.000 0.00 0.00 46.36 3.58
4186 4327 8.231161 GTGACTGTTTTCTCTTAAAGATTAGCC 58.769 37.037 0.00 0.00 32.82 3.93
4406 4549 8.290325 AGGAAAGAAGTCAACGATAATTCAAAC 58.710 33.333 0.00 0.00 0.00 2.93
4413 4556 6.018262 CACACAAGGAAAGAAGTCAACGATAA 60.018 38.462 0.00 0.00 0.00 1.75
4425 4568 2.928801 TAGCAGCACACAAGGAAAGA 57.071 45.000 0.00 0.00 0.00 2.52
4485 4628 7.469537 TGTTGTTCTTTTGGGAGTTTTTAGA 57.530 32.000 0.00 0.00 0.00 2.10
4518 4661 8.734386 ACAGAATATGAATTGTCAACTTCCTTC 58.266 33.333 0.00 0.00 37.30 3.46
4645 4788 6.954352 ATAACCCTAGAACCTGAACTCTTT 57.046 37.500 0.00 0.00 0.00 2.52
4671 4814 4.219288 GGCTGGAACAAATCATCTCAACTT 59.781 41.667 0.00 0.00 38.70 2.66
4796 4939 5.588648 AGTTAAGCAGCTGTTGTGAAAGTAA 59.411 36.000 16.64 0.00 0.00 2.24
5094 5237 3.766591 TGGTTGGACATTCAAACACACTT 59.233 39.130 0.00 0.00 39.17 3.16
5169 5400 4.569015 GGGAAGTTGGGGCTGTTAGAATTA 60.569 45.833 0.00 0.00 0.00 1.40
5190 5421 1.203994 CTGCCATTTTGCTCAGAAGGG 59.796 52.381 0.21 0.21 30.63 3.95
5195 5426 0.885879 TCAGCTGCCATTTTGCTCAG 59.114 50.000 9.47 0.00 34.51 3.35
5310 5541 6.449635 AGGCATGACGCTGAATTATTTTTA 57.550 33.333 0.00 0.00 41.91 1.52
5325 5556 8.143835 ACTTATGGCAAATAATAAAGGCATGAC 58.856 33.333 10.08 0.00 45.29 3.06
5404 5637 5.180271 ACAAAACGAAGAAGTTACTCCACA 58.820 37.500 0.00 0.00 33.41 4.17
5436 5669 8.320617 ACCCGTGGTGTATTTAACTCTATTTAA 58.679 33.333 0.00 0.00 32.98 1.52
5437 5670 7.850193 ACCCGTGGTGTATTTAACTCTATTTA 58.150 34.615 0.00 0.00 32.98 1.40
5438 5671 6.714278 ACCCGTGGTGTATTTAACTCTATTT 58.286 36.000 0.00 0.00 32.98 1.40
5439 5672 6.303903 ACCCGTGGTGTATTTAACTCTATT 57.696 37.500 0.00 0.00 32.98 1.73
5440 5673 5.945144 ACCCGTGGTGTATTTAACTCTAT 57.055 39.130 0.00 0.00 32.98 1.98
5561 5794 2.501723 GTGCATATCCCCGGATACAGAT 59.498 50.000 0.73 0.00 39.56 2.90
5564 5797 1.623311 CTGTGCATATCCCCGGATACA 59.377 52.381 0.73 1.77 39.56 2.29
5574 5807 0.956633 CCATGTGGGCTGTGCATATC 59.043 55.000 0.00 0.00 0.00 1.63
5718 5955 6.839124 AACAGGTGAGATCAATGCAATTTA 57.161 33.333 0.00 0.00 31.22 1.40
5722 5959 5.164620 TCTAACAGGTGAGATCAATGCAA 57.835 39.130 0.00 0.00 0.00 4.08
5797 6034 1.754380 AATCCTGCCGGTGCGCTATA 61.754 55.000 9.73 0.00 41.78 1.31


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

AutoCloner maintained by Alex Coulton.