Multiple sequence alignment - TraesCS4B01G116900

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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 TraesCS4B01G116900 chr4B 100.000 2777 0 0 1 2777 134992756 134989980 0.000000e+00 5129
1 TraesCS4B01G116900 chr4D 92.823 1254 52 17 606 1838 95503136 95501900 0.000000e+00 1783
2 TraesCS4B01G116900 chr4D 90.518 791 66 7 1928 2711 95501902 95501114 0.000000e+00 1037
3 TraesCS4B01G116900 chr4A 92.895 943 45 15 903 1825 484360004 484360944 0.000000e+00 1351
4 TraesCS4B01G116900 chr4A 96.169 522 19 1 1 522 709804902 709805422 0.000000e+00 852
5 TraesCS4B01G116900 chr4A 94.403 268 13 2 600 866 484359434 484359700 7.160000e-111 411
6 TraesCS4B01G116900 chr1B 97.670 515 12 0 1 515 592431055 592431569 0.000000e+00 885
7 TraesCS4B01G116900 chr1B 96.518 517 18 0 1 517 46166017 46165501 0.000000e+00 856
8 TraesCS4B01G116900 chr1B 84.135 769 104 13 2020 2777 683442046 683441285 0.000000e+00 728
9 TraesCS4B01G116900 chr2B 97.485 517 13 0 1 517 737001344 737000828 0.000000e+00 883
10 TraesCS4B01G116900 chr3B 97.292 517 14 0 1 517 656593046 656592530 0.000000e+00 878
11 TraesCS4B01G116900 chr3B 97.292 517 14 0 1 517 785521419 785520903 0.000000e+00 878
12 TraesCS4B01G116900 chr3B 96.905 517 15 1 1 517 785527016 785526501 0.000000e+00 865
13 TraesCS4B01G116900 chr3B 96.712 517 16 1 1 517 155632841 155633356 0.000000e+00 859
14 TraesCS4B01G116900 chr3B 96.518 517 18 0 1 517 780191826 780192342 0.000000e+00 856
15 TraesCS4B01G116900 chr3B 94.898 98 3 1 1837 1934 187150491 187150396 4.790000e-33 152
16 TraesCS4B01G116900 chr1D 86.280 758 90 13 2027 2774 137069110 137069863 0.000000e+00 811
17 TraesCS4B01G116900 chr7B 85.845 763 91 15 2019 2768 510188341 510189099 0.000000e+00 795
18 TraesCS4B01G116900 chr7B 93.333 105 4 2 1833 1934 244219303 244219407 4.790000e-33 152
19 TraesCS4B01G116900 chr7D 85.156 768 95 16 2024 2777 45431164 45430402 0.000000e+00 769
20 TraesCS4B01G116900 chr7D 84.987 766 92 16 2025 2777 525483554 525484309 0.000000e+00 756
21 TraesCS4B01G116900 chr7D 96.875 96 2 1 1837 1931 635688885 635688980 2.860000e-35 159
22 TraesCS4B01G116900 chr7D 96.875 96 2 1 1837 1931 636310252 636310157 2.860000e-35 159
23 TraesCS4B01G116900 chr7D 90.351 114 5 5 1834 1943 478082508 478082397 8.020000e-31 145
24 TraesCS4B01G116900 chr6A 84.797 763 99 12 2024 2774 287630612 287629855 0.000000e+00 750
25 TraesCS4B01G116900 chr6A 93.069 101 4 1 1834 1931 507081999 507082099 8.020000e-31 145
26 TraesCS4B01G116900 chr2A 84.881 754 101 10 2024 2768 478384725 478385474 0.000000e+00 749
27 TraesCS4B01G116900 chr2A 92.523 107 5 2 1835 1938 763199305 763199411 1.720000e-32 150
28 TraesCS4B01G116900 chr3D 84.881 754 95 13 2024 2768 221678689 221679432 0.000000e+00 743
29 TraesCS4B01G116900 chr5A 93.204 103 6 1 1831 1932 230755589 230755691 1.720000e-32 150
30 TraesCS4B01G116900 chr5D 91.743 109 6 2 1834 1939 343630505 343630397 6.200000e-32 148


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 TraesCS4B01G116900 chr4B 134989980 134992756 2776 True 5129 5129 100.0000 1 2777 1 chr4B.!!$R1 2776
1 TraesCS4B01G116900 chr4D 95501114 95503136 2022 True 1410 1783 91.6705 606 2711 2 chr4D.!!$R1 2105
2 TraesCS4B01G116900 chr4A 484359434 484360944 1510 False 881 1351 93.6490 600 1825 2 chr4A.!!$F2 1225
3 TraesCS4B01G116900 chr4A 709804902 709805422 520 False 852 852 96.1690 1 522 1 chr4A.!!$F1 521
4 TraesCS4B01G116900 chr1B 592431055 592431569 514 False 885 885 97.6700 1 515 1 chr1B.!!$F1 514
5 TraesCS4B01G116900 chr1B 46165501 46166017 516 True 856 856 96.5180 1 517 1 chr1B.!!$R1 516
6 TraesCS4B01G116900 chr1B 683441285 683442046 761 True 728 728 84.1350 2020 2777 1 chr1B.!!$R2 757
7 TraesCS4B01G116900 chr2B 737000828 737001344 516 True 883 883 97.4850 1 517 1 chr2B.!!$R1 516
8 TraesCS4B01G116900 chr3B 656592530 656593046 516 True 878 878 97.2920 1 517 1 chr3B.!!$R2 516
9 TraesCS4B01G116900 chr3B 785520903 785521419 516 True 878 878 97.2920 1 517 1 chr3B.!!$R3 516
10 TraesCS4B01G116900 chr3B 785526501 785527016 515 True 865 865 96.9050 1 517 1 chr3B.!!$R4 516
11 TraesCS4B01G116900 chr3B 155632841 155633356 515 False 859 859 96.7120 1 517 1 chr3B.!!$F1 516
12 TraesCS4B01G116900 chr3B 780191826 780192342 516 False 856 856 96.5180 1 517 1 chr3B.!!$F2 516
13 TraesCS4B01G116900 chr1D 137069110 137069863 753 False 811 811 86.2800 2027 2774 1 chr1D.!!$F1 747
14 TraesCS4B01G116900 chr7B 510188341 510189099 758 False 795 795 85.8450 2019 2768 1 chr7B.!!$F2 749
15 TraesCS4B01G116900 chr7D 45430402 45431164 762 True 769 769 85.1560 2024 2777 1 chr7D.!!$R1 753
16 TraesCS4B01G116900 chr7D 525483554 525484309 755 False 756 756 84.9870 2025 2777 1 chr7D.!!$F1 752
17 TraesCS4B01G116900 chr6A 287629855 287630612 757 True 750 750 84.7970 2024 2774 1 chr6A.!!$R1 750
18 TraesCS4B01G116900 chr2A 478384725 478385474 749 False 749 749 84.8810 2024 2768 1 chr2A.!!$F1 744
19 TraesCS4B01G116900 chr3D 221678689 221679432 743 False 743 743 84.8810 2024 2768 1 chr3D.!!$F1 744

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
549 550 0.035630 GCAGTCCACTTCCAGCAGAT 60.036 55.0 0.00 0.0 0.0 2.9 F
1293 1566 0.036388 ACGGCGGTCATGTTGAAGAT 60.036 50.0 13.24 0.0 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1508 1781 0.321653 CCTCCTTTACTGGCGCTTGT 60.322 55.000 7.64 9.28 0.00 3.16 R
2231 2520 3.523157 TGAATAACTCATGGCCTTCTCCA 59.477 43.478 3.32 0.00 40.97 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
285 286 6.328148 TCTTGTTTTTCCTGTTAGAGGTCCTA 59.672 38.462 0.00 0.00 43.37 2.94
365 366 4.441217 GCATCTTGATCTACTGTCTGCTCA 60.441 45.833 0.00 0.00 0.00 4.26
376 377 3.768215 ACTGTCTGCTCAAGAGATGATCA 59.232 43.478 0.00 0.00 37.44 2.92
517 518 8.344831 TCGATAAATTGCTCATATTTCCAACAG 58.655 33.333 0.00 0.00 0.00 3.16
518 519 8.131100 CGATAAATTGCTCATATTTCCAACAGT 58.869 33.333 0.00 0.00 0.00 3.55
522 523 5.818136 TGCTCATATTTCCAACAGTAAGC 57.182 39.130 0.00 0.00 0.00 3.09
523 524 5.252547 TGCTCATATTTCCAACAGTAAGCA 58.747 37.500 0.00 0.00 33.97 3.91
524 525 5.123820 TGCTCATATTTCCAACAGTAAGCAC 59.876 40.000 0.00 0.00 31.63 4.40
525 526 5.449177 GCTCATATTTCCAACAGTAAGCACC 60.449 44.000 0.00 0.00 0.00 5.01
526 527 5.565509 TCATATTTCCAACAGTAAGCACCA 58.434 37.500 0.00 0.00 0.00 4.17
527 528 5.414454 TCATATTTCCAACAGTAAGCACCAC 59.586 40.000 0.00 0.00 0.00 4.16
528 529 3.290948 TTTCCAACAGTAAGCACCACT 57.709 42.857 0.00 0.00 0.00 4.00
529 530 2.543777 TCCAACAGTAAGCACCACTC 57.456 50.000 0.00 0.00 0.00 3.51
530 531 1.148310 CCAACAGTAAGCACCACTCG 58.852 55.000 0.00 0.00 0.00 4.18
531 532 0.512952 CAACAGTAAGCACCACTCGC 59.487 55.000 0.00 0.00 0.00 5.03
532 533 0.105964 AACAGTAAGCACCACTCGCA 59.894 50.000 0.00 0.00 0.00 5.10
533 534 0.319900 ACAGTAAGCACCACTCGCAG 60.320 55.000 0.00 0.00 0.00 5.18
534 535 0.319900 CAGTAAGCACCACTCGCAGT 60.320 55.000 0.00 0.00 0.00 4.40
535 536 0.038159 AGTAAGCACCACTCGCAGTC 60.038 55.000 0.00 0.00 0.00 3.51
536 537 1.014564 GTAAGCACCACTCGCAGTCC 61.015 60.000 0.00 0.00 0.00 3.85
537 538 1.468506 TAAGCACCACTCGCAGTCCA 61.469 55.000 0.00 0.00 0.00 4.02
538 539 2.996168 AAGCACCACTCGCAGTCCAC 62.996 60.000 0.00 0.00 0.00 4.02
539 540 2.737180 CACCACTCGCAGTCCACT 59.263 61.111 0.00 0.00 0.00 4.00
540 541 1.069765 CACCACTCGCAGTCCACTT 59.930 57.895 0.00 0.00 0.00 3.16
541 542 0.946221 CACCACTCGCAGTCCACTTC 60.946 60.000 0.00 0.00 0.00 3.01
542 543 1.374758 CCACTCGCAGTCCACTTCC 60.375 63.158 0.00 0.00 0.00 3.46
543 544 1.367471 CACTCGCAGTCCACTTCCA 59.633 57.895 0.00 0.00 0.00 3.53
544 545 0.668706 CACTCGCAGTCCACTTCCAG 60.669 60.000 0.00 0.00 0.00 3.86
545 546 1.739562 CTCGCAGTCCACTTCCAGC 60.740 63.158 0.00 0.00 0.00 4.85
546 547 2.031012 CGCAGTCCACTTCCAGCA 59.969 61.111 0.00 0.00 0.00 4.41
547 548 2.031516 CGCAGTCCACTTCCAGCAG 61.032 63.158 0.00 0.00 0.00 4.24
548 549 1.372683 GCAGTCCACTTCCAGCAGA 59.627 57.895 0.00 0.00 0.00 4.26
549 550 0.035630 GCAGTCCACTTCCAGCAGAT 60.036 55.000 0.00 0.00 0.00 2.90
550 551 1.612726 GCAGTCCACTTCCAGCAGATT 60.613 52.381 0.00 0.00 0.00 2.40
551 552 2.787994 CAGTCCACTTCCAGCAGATTT 58.212 47.619 0.00 0.00 0.00 2.17
552 553 3.152341 CAGTCCACTTCCAGCAGATTTT 58.848 45.455 0.00 0.00 0.00 1.82
553 554 3.057736 CAGTCCACTTCCAGCAGATTTTG 60.058 47.826 0.00 0.00 0.00 2.44
554 555 2.887152 GTCCACTTCCAGCAGATTTTGT 59.113 45.455 0.00 0.00 0.00 2.83
555 556 3.057946 GTCCACTTCCAGCAGATTTTGTC 60.058 47.826 0.00 0.00 0.00 3.18
556 557 2.095567 CCACTTCCAGCAGATTTTGTCG 60.096 50.000 0.00 0.00 0.00 4.35
557 558 2.095567 CACTTCCAGCAGATTTTGTCGG 60.096 50.000 0.00 0.00 0.00 4.79
558 559 1.470098 CTTCCAGCAGATTTTGTCGGG 59.530 52.381 0.00 0.00 0.00 5.14
559 560 0.400213 TCCAGCAGATTTTGTCGGGT 59.600 50.000 0.00 0.00 32.90 5.28
560 561 0.523072 CCAGCAGATTTTGTCGGGTG 59.477 55.000 1.36 1.36 45.95 4.61
562 563 1.813513 AGCAGATTTTGTCGGGTGAG 58.186 50.000 0.00 0.00 31.49 3.51
563 564 1.072331 AGCAGATTTTGTCGGGTGAGT 59.928 47.619 0.00 0.00 31.49 3.41
564 565 1.880027 GCAGATTTTGTCGGGTGAGTT 59.120 47.619 0.00 0.00 0.00 3.01
565 566 3.071479 GCAGATTTTGTCGGGTGAGTTA 58.929 45.455 0.00 0.00 0.00 2.24
566 567 3.120304 GCAGATTTTGTCGGGTGAGTTAC 60.120 47.826 0.00 0.00 0.00 2.50
577 578 2.618053 GGTGAGTTACCGAGTTGGATG 58.382 52.381 2.42 0.00 40.26 3.51
578 579 2.028385 GGTGAGTTACCGAGTTGGATGT 60.028 50.000 2.42 0.00 40.26 3.06
579 580 3.194116 GGTGAGTTACCGAGTTGGATGTA 59.806 47.826 2.42 0.00 40.26 2.29
580 581 4.421948 GTGAGTTACCGAGTTGGATGTAG 58.578 47.826 2.42 0.00 42.00 2.74
581 582 3.119245 TGAGTTACCGAGTTGGATGTAGC 60.119 47.826 2.42 0.00 42.00 3.58
582 583 3.097614 AGTTACCGAGTTGGATGTAGCT 58.902 45.455 2.42 0.00 42.00 3.32
583 584 3.514309 AGTTACCGAGTTGGATGTAGCTT 59.486 43.478 2.42 0.00 42.00 3.74
584 585 2.674796 ACCGAGTTGGATGTAGCTTC 57.325 50.000 2.42 0.00 42.00 3.86
585 586 2.180276 ACCGAGTTGGATGTAGCTTCT 58.820 47.619 2.42 0.00 42.00 2.85
586 587 2.567615 ACCGAGTTGGATGTAGCTTCTT 59.432 45.455 2.42 0.00 42.00 2.52
587 588 3.190874 CCGAGTTGGATGTAGCTTCTTC 58.809 50.000 0.00 0.00 42.00 2.87
588 589 3.368427 CCGAGTTGGATGTAGCTTCTTCA 60.368 47.826 8.22 0.00 42.00 3.02
589 590 3.862267 CGAGTTGGATGTAGCTTCTTCAG 59.138 47.826 8.22 0.00 0.00 3.02
613 614 3.112075 CACGGCGGTGCTACACAG 61.112 66.667 13.24 0.00 37.35 3.66
631 633 6.721571 ACACAGTTGAGTATTGTAATTCCG 57.278 37.500 0.00 0.00 0.00 4.30
655 657 6.371389 GGTGAGAGTAATTTTGTTCTTTCCG 58.629 40.000 0.00 0.00 0.00 4.30
663 665 6.763303 AATTTTGTTCTTTCCGAATTTCCG 57.237 33.333 0.00 0.00 33.45 4.30
752 754 5.885912 GGTGAAATAAAGTTGCCTCCATAGA 59.114 40.000 0.00 0.00 0.00 1.98
872 874 0.179092 TGCATGATCGCAGAGAGTGG 60.179 55.000 0.00 0.00 43.63 4.00
950 1220 1.534729 AAAAACGCATGGACCTCTCC 58.465 50.000 0.00 0.00 37.04 3.71
977 1247 2.625639 CACCTCCCTATATGAAGCCCT 58.374 52.381 0.00 0.00 0.00 5.19
991 1261 2.596851 GCCCTTCAGAGCCCTCACA 61.597 63.158 0.00 0.00 0.00 3.58
1151 1424 0.391528 TGCATCATGTCCGTGTCCAG 60.392 55.000 0.00 0.00 0.00 3.86
1286 1559 4.388499 GGTGGACGGCGGTCATGT 62.388 66.667 23.82 0.00 45.28 3.21
1293 1566 0.036388 ACGGCGGTCATGTTGAAGAT 60.036 50.000 13.24 0.00 0.00 2.40
1358 1631 0.038251 TCGTCGGATGATAGCCATGC 60.038 55.000 0.00 0.00 39.85 4.06
1508 1781 1.014044 GGCGACGACAAGAAGCATGA 61.014 55.000 0.00 0.00 0.00 3.07
1612 1891 4.838152 GATCTTGGCGCGGGCTGA 62.838 66.667 24.48 18.72 39.81 4.26
1723 2009 5.117287 GTCTGTGTTAATCAGTGTCTTCGAC 59.883 44.000 9.38 0.00 34.86 4.20
1764 2052 6.391227 AGGCAGCGCTTTTATATGTAAAAT 57.609 33.333 7.50 0.00 38.66 1.82
1841 2130 7.681939 TTTTGTGGATGATAGTTTGTACTCC 57.318 36.000 0.00 0.00 35.78 3.85
1842 2131 5.353394 TGTGGATGATAGTTTGTACTCCC 57.647 43.478 0.00 0.00 35.78 4.30
1843 2132 5.030147 TGTGGATGATAGTTTGTACTCCCT 58.970 41.667 0.00 0.00 35.78 4.20
1844 2133 5.128827 TGTGGATGATAGTTTGTACTCCCTC 59.871 44.000 0.00 0.00 35.78 4.30
1845 2134 4.654262 TGGATGATAGTTTGTACTCCCTCC 59.346 45.833 0.00 0.00 35.78 4.30
1846 2135 4.262079 GGATGATAGTTTGTACTCCCTCCG 60.262 50.000 0.00 0.00 35.78 4.63
1847 2136 3.705051 TGATAGTTTGTACTCCCTCCGT 58.295 45.455 0.00 0.00 35.78 4.69
1848 2137 4.091549 TGATAGTTTGTACTCCCTCCGTT 58.908 43.478 0.00 0.00 35.78 4.44
1849 2138 4.529377 TGATAGTTTGTACTCCCTCCGTTT 59.471 41.667 0.00 0.00 35.78 3.60
1850 2139 3.397849 AGTTTGTACTCCCTCCGTTTC 57.602 47.619 0.00 0.00 0.00 2.78
1851 2140 2.701951 AGTTTGTACTCCCTCCGTTTCA 59.298 45.455 0.00 0.00 0.00 2.69
1852 2141 3.135167 AGTTTGTACTCCCTCCGTTTCAA 59.865 43.478 0.00 0.00 0.00 2.69
1853 2142 3.842007 TTGTACTCCCTCCGTTTCAAA 57.158 42.857 0.00 0.00 0.00 2.69
1854 2143 3.842007 TGTACTCCCTCCGTTTCAAAA 57.158 42.857 0.00 0.00 0.00 2.44
1855 2144 4.360951 TGTACTCCCTCCGTTTCAAAAT 57.639 40.909 0.00 0.00 0.00 1.82
1856 2145 5.486735 TGTACTCCCTCCGTTTCAAAATA 57.513 39.130 0.00 0.00 0.00 1.40
1857 2146 5.484715 TGTACTCCCTCCGTTTCAAAATAG 58.515 41.667 0.00 0.00 0.00 1.73
1858 2147 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
1859 2148 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
1860 2149 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
1861 2150 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
1862 2151 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
1863 2152 5.045869 TCCCTCCGTTTCAAAATAGATGACT 60.046 40.000 0.00 0.00 0.00 3.41
1864 2153 5.294552 CCCTCCGTTTCAAAATAGATGACTC 59.705 44.000 0.00 0.00 0.00 3.36
1865 2154 5.874810 CCTCCGTTTCAAAATAGATGACTCA 59.125 40.000 0.00 0.00 0.00 3.41
1866 2155 6.371548 CCTCCGTTTCAAAATAGATGACTCAA 59.628 38.462 0.00 0.00 0.00 3.02
1867 2156 7.129109 TCCGTTTCAAAATAGATGACTCAAC 57.871 36.000 0.00 0.00 0.00 3.18
1868 2157 6.934645 TCCGTTTCAAAATAGATGACTCAACT 59.065 34.615 0.00 0.00 0.00 3.16
1869 2158 7.444183 TCCGTTTCAAAATAGATGACTCAACTT 59.556 33.333 0.00 0.00 0.00 2.66
1870 2159 8.076178 CCGTTTCAAAATAGATGACTCAACTTT 58.924 33.333 0.00 0.00 0.00 2.66
1871 2160 8.895845 CGTTTCAAAATAGATGACTCAACTTTG 58.104 33.333 0.00 0.00 0.00 2.77
1872 2161 9.736023 GTTTCAAAATAGATGACTCAACTTTGT 57.264 29.630 0.00 0.00 0.00 2.83
1875 2164 9.778741 TCAAAATAGATGACTCAACTTTGTACT 57.221 29.630 0.00 0.00 0.00 2.73
1884 2173 9.826574 ATGACTCAACTTTGTACTAACTTTACA 57.173 29.630 0.00 0.00 0.00 2.41
1885 2174 9.656040 TGACTCAACTTTGTACTAACTTTACAA 57.344 29.630 0.00 0.00 37.60 2.41
1906 2195 9.656040 TTACAAAGTTAGTACAAAGTTGAGTCA 57.344 29.630 0.00 0.00 0.00 3.41
1907 2196 8.732746 ACAAAGTTAGTACAAAGTTGAGTCAT 57.267 30.769 0.00 0.00 0.00 3.06
1908 2197 8.827677 ACAAAGTTAGTACAAAGTTGAGTCATC 58.172 33.333 0.00 0.00 0.00 2.92
1909 2198 9.046296 CAAAGTTAGTACAAAGTTGAGTCATCT 57.954 33.333 0.00 0.00 0.00 2.90
1919 2208 9.736023 ACAAAGTTGAGTCATCTATTTTTGAAC 57.264 29.630 15.48 0.00 30.22 3.18
1920 2209 8.895845 CAAAGTTGAGTCATCTATTTTTGAACG 58.104 33.333 4.14 0.00 0.00 3.95
1921 2210 7.133891 AGTTGAGTCATCTATTTTTGAACGG 57.866 36.000 1.70 0.00 0.00 4.44
1922 2211 6.934645 AGTTGAGTCATCTATTTTTGAACGGA 59.065 34.615 1.70 0.00 0.00 4.69
1923 2212 7.444183 AGTTGAGTCATCTATTTTTGAACGGAA 59.556 33.333 1.70 0.00 0.00 4.30
1924 2213 7.364522 TGAGTCATCTATTTTTGAACGGAAG 57.635 36.000 0.00 0.00 0.00 3.46
1925 2214 6.371548 TGAGTCATCTATTTTTGAACGGAAGG 59.628 38.462 0.00 0.00 0.00 3.46
1926 2215 6.472887 AGTCATCTATTTTTGAACGGAAGGA 58.527 36.000 0.00 0.00 0.00 3.36
2051 2340 1.431488 ATATGCTCGTGCGTGGCAAG 61.431 55.000 14.18 0.00 41.47 4.01
2052 2341 2.499756 TATGCTCGTGCGTGGCAAGA 62.500 55.000 14.18 6.11 43.82 3.02
2054 2343 2.892334 GCTCGTGCGTGGCAAGAAA 61.892 57.895 4.11 0.00 45.08 2.52
2120 2409 2.315176 AGCAAAACCCTATGTGCACAA 58.685 42.857 25.72 12.25 39.50 3.33
2163 2452 1.433837 GGTTTCGCCGTGTGTGAAGT 61.434 55.000 0.00 0.00 43.90 3.01
2231 2520 7.548097 AGAGTTTTATCACGTCATCATACACT 58.452 34.615 0.00 0.00 0.00 3.55
2259 2549 7.753630 AGAAGGCCATGAGTTATTCAATCTAT 58.246 34.615 5.01 0.00 39.77 1.98
2288 2578 5.979517 CCTTTTAATCATTTCAATCGAGGGC 59.020 40.000 0.00 0.00 0.00 5.19
2661 2969 8.716646 AGAAACCTCGAACAATTTTGAAAAAT 57.283 26.923 0.00 0.00 40.15 1.82
2711 3022 7.896811 ACCTTTTGGAAGTCCTGAATATTTTC 58.103 34.615 0.00 0.00 44.07 2.29
2715 3026 9.762933 TTTTGGAAGTCCTGAATATTTTCAAAG 57.237 29.630 0.20 0.00 41.22 2.77
2716 3027 8.477419 TTGGAAGTCCTGAATATTTTCAAAGT 57.523 30.769 0.20 0.00 41.22 2.66
2717 3028 9.581289 TTGGAAGTCCTGAATATTTTCAAAGTA 57.419 29.630 0.20 0.00 41.22 2.24
2719 3030 8.184848 GGAAGTCCTGAATATTTTCAAAGTAGC 58.815 37.037 0.20 0.00 41.22 3.58
2720 3031 8.635765 AAGTCCTGAATATTTTCAAAGTAGCA 57.364 30.769 0.20 0.00 41.22 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
285 286 9.708092 GTAAACACTAGAAGAAAGAACTATGGT 57.292 33.333 0.00 0.00 0.00 3.55
517 518 1.014564 GGACTGCGAGTGGTGCTTAC 61.015 60.000 0.00 0.00 0.00 2.34
518 519 1.292223 GGACTGCGAGTGGTGCTTA 59.708 57.895 0.00 0.00 0.00 3.09
520 521 3.233980 TGGACTGCGAGTGGTGCT 61.234 61.111 0.00 0.00 0.00 4.40
521 522 2.996168 AAGTGGACTGCGAGTGGTGC 62.996 60.000 0.00 0.00 0.00 5.01
522 523 0.946221 GAAGTGGACTGCGAGTGGTG 60.946 60.000 0.00 0.00 0.00 4.17
523 524 1.367840 GAAGTGGACTGCGAGTGGT 59.632 57.895 0.00 0.00 0.00 4.16
524 525 1.374758 GGAAGTGGACTGCGAGTGG 60.375 63.158 0.00 0.00 0.00 4.00
525 526 0.668706 CTGGAAGTGGACTGCGAGTG 60.669 60.000 0.00 0.00 0.00 3.51
526 527 1.668294 CTGGAAGTGGACTGCGAGT 59.332 57.895 0.00 0.00 0.00 4.18
527 528 1.739562 GCTGGAAGTGGACTGCGAG 60.740 63.158 0.00 0.00 35.30 5.03
528 529 2.343758 GCTGGAAGTGGACTGCGA 59.656 61.111 0.00 0.00 35.30 5.10
529 530 2.031012 TGCTGGAAGTGGACTGCG 59.969 61.111 0.00 0.00 35.30 5.18
530 531 0.035630 ATCTGCTGGAAGTGGACTGC 60.036 55.000 0.00 0.00 35.30 4.40
531 532 2.486472 AATCTGCTGGAAGTGGACTG 57.514 50.000 0.00 0.00 35.30 3.51
532 533 3.152341 CAAAATCTGCTGGAAGTGGACT 58.848 45.455 0.00 0.00 35.30 3.85
533 534 2.887152 ACAAAATCTGCTGGAAGTGGAC 59.113 45.455 0.00 0.00 35.30 4.02
534 535 3.149196 GACAAAATCTGCTGGAAGTGGA 58.851 45.455 0.00 0.00 35.30 4.02
535 536 2.095567 CGACAAAATCTGCTGGAAGTGG 60.096 50.000 0.00 0.00 35.30 4.00
536 537 2.095567 CCGACAAAATCTGCTGGAAGTG 60.096 50.000 0.00 0.00 35.30 3.16
537 538 2.154462 CCGACAAAATCTGCTGGAAGT 58.846 47.619 0.00 0.00 35.30 3.01
538 539 1.470098 CCCGACAAAATCTGCTGGAAG 59.530 52.381 0.00 0.00 0.00 3.46
539 540 1.202879 ACCCGACAAAATCTGCTGGAA 60.203 47.619 0.00 0.00 0.00 3.53
540 541 0.400213 ACCCGACAAAATCTGCTGGA 59.600 50.000 0.00 0.00 0.00 3.86
541 542 0.523072 CACCCGACAAAATCTGCTGG 59.477 55.000 0.00 0.00 0.00 4.85
542 543 1.466167 CTCACCCGACAAAATCTGCTG 59.534 52.381 0.00 0.00 0.00 4.41
543 544 1.072331 ACTCACCCGACAAAATCTGCT 59.928 47.619 0.00 0.00 0.00 4.24
544 545 1.523758 ACTCACCCGACAAAATCTGC 58.476 50.000 0.00 0.00 0.00 4.26
545 546 3.435671 GGTAACTCACCCGACAAAATCTG 59.564 47.826 0.00 0.00 42.07 2.90
546 547 3.671716 GGTAACTCACCCGACAAAATCT 58.328 45.455 0.00 0.00 42.07 2.40
555 556 0.389426 CCAACTCGGTAACTCACCCG 60.389 60.000 0.00 0.00 45.52 5.28
556 557 0.971386 TCCAACTCGGTAACTCACCC 59.029 55.000 0.00 0.00 45.52 4.61
557 558 2.028385 ACATCCAACTCGGTAACTCACC 60.028 50.000 0.00 0.00 44.75 4.02
558 559 3.314541 ACATCCAACTCGGTAACTCAC 57.685 47.619 0.00 0.00 35.57 3.51
559 560 3.119245 GCTACATCCAACTCGGTAACTCA 60.119 47.826 0.00 0.00 35.57 3.41
560 561 3.130693 AGCTACATCCAACTCGGTAACTC 59.869 47.826 0.00 0.00 35.57 3.01
561 562 3.097614 AGCTACATCCAACTCGGTAACT 58.902 45.455 0.00 0.00 35.57 2.24
562 563 3.521947 AGCTACATCCAACTCGGTAAC 57.478 47.619 0.00 0.00 35.57 2.50
563 564 3.767673 AGAAGCTACATCCAACTCGGTAA 59.232 43.478 0.00 0.00 35.57 2.85
564 565 3.362706 AGAAGCTACATCCAACTCGGTA 58.637 45.455 0.00 0.00 35.57 4.02
565 566 2.180276 AGAAGCTACATCCAACTCGGT 58.820 47.619 0.00 0.00 35.57 4.69
566 567 2.969628 AGAAGCTACATCCAACTCGG 57.030 50.000 0.00 0.00 0.00 4.63
567 568 3.849911 TGAAGAAGCTACATCCAACTCG 58.150 45.455 0.00 0.00 0.00 4.18
581 582 1.572085 CCGTGCCTGTGCTGAAGAAG 61.572 60.000 0.00 0.00 38.71 2.85
582 583 1.597854 CCGTGCCTGTGCTGAAGAA 60.598 57.895 0.00 0.00 38.71 2.52
583 584 2.031012 CCGTGCCTGTGCTGAAGA 59.969 61.111 0.00 0.00 38.71 2.87
584 585 3.730761 GCCGTGCCTGTGCTGAAG 61.731 66.667 0.00 0.00 38.71 3.02
596 597 3.112075 CTGTGTAGCACCGCCGTG 61.112 66.667 0.34 0.34 43.35 4.94
597 598 3.159858 AACTGTGTAGCACCGCCGT 62.160 57.895 0.00 0.00 32.73 5.68
598 599 2.357034 AACTGTGTAGCACCGCCG 60.357 61.111 0.00 0.00 32.73 6.46
604 605 7.333423 GGAATTACAATACTCAACTGTGTAGCA 59.667 37.037 0.00 0.00 0.00 3.49
613 614 6.103997 TCTCACCGGAATTACAATACTCAAC 58.896 40.000 9.46 0.00 0.00 3.18
631 633 6.204108 TCGGAAAGAACAAAATTACTCTCACC 59.796 38.462 0.00 0.00 0.00 4.02
752 754 4.317488 TCGTTTTTATTACGGAAGCAGGT 58.683 39.130 0.00 0.00 39.38 4.00
872 874 2.663826 AGTCTCTCTTCGTCAATGCC 57.336 50.000 0.00 0.00 0.00 4.40
894 911 9.206870 AGTATTGATGCGAAATCAAACAAATTT 57.793 25.926 15.28 3.43 40.84 1.82
950 1220 4.133526 TCATATAGGGAGGTGGAGGAAG 57.866 50.000 0.00 0.00 0.00 3.46
977 1247 1.418097 TTGGCTGTGAGGGCTCTGAA 61.418 55.000 0.00 0.00 0.00 3.02
991 1261 1.272147 GGGAAGGAGTGTGATTTGGCT 60.272 52.381 0.00 0.00 0.00 4.75
1060 1331 3.004944 GCAAGGGGAACACAAACGATAAA 59.995 43.478 0.00 0.00 0.00 1.40
1151 1424 2.583593 GCCACCTCGATCGCACTC 60.584 66.667 11.09 0.00 0.00 3.51
1220 1493 2.115291 GGAGGCGATTGGTTCAGGC 61.115 63.158 0.00 0.00 0.00 4.85
1286 1559 3.669824 GCTGTAGTCGTCGTCATCTTCAA 60.670 47.826 0.00 0.00 0.00 2.69
1293 1566 0.385098 CGTTGCTGTAGTCGTCGTCA 60.385 55.000 0.00 0.00 0.00 4.35
1320 1593 1.139734 CACACACGAGCTAGGCGAT 59.860 57.895 0.00 0.00 0.00 4.58
1508 1781 0.321653 CCTCCTTTACTGGCGCTTGT 60.322 55.000 7.64 9.28 0.00 3.16
1612 1891 0.905357 ATCTAACGGCTTGCAGTCCT 59.095 50.000 0.00 0.00 0.00 3.85
1619 1898 1.006832 CCGGACAATCTAACGGCTTG 58.993 55.000 0.00 0.00 39.85 4.01
1683 1969 4.471025 ACACAGACTGGGTCATGAATCATA 59.529 41.667 3.94 0.00 34.60 2.15
1694 1980 3.391296 ACACTGATTAACACAGACTGGGT 59.609 43.478 3.94 3.94 33.89 4.51
1723 2009 5.220931 GCTGCCTTATGACAGGAAATAACTG 60.221 44.000 0.00 0.00 41.64 3.16
1743 2029 6.675515 GGATTTTACATATAAAAGCGCTGC 57.324 37.500 12.58 0.00 44.21 5.25
1825 2114 4.287552 ACGGAGGGAGTACAAACTATCAT 58.712 43.478 0.00 0.00 35.56 2.45
1826 2115 3.705051 ACGGAGGGAGTACAAACTATCA 58.295 45.455 0.00 0.00 35.56 2.15
1827 2116 4.732672 AACGGAGGGAGTACAAACTATC 57.267 45.455 0.00 0.00 35.56 2.08
1828 2117 4.529377 TGAAACGGAGGGAGTACAAACTAT 59.471 41.667 0.00 0.00 35.56 2.12
1829 2118 3.896888 TGAAACGGAGGGAGTACAAACTA 59.103 43.478 0.00 0.00 35.56 2.24
1830 2119 2.701951 TGAAACGGAGGGAGTACAAACT 59.298 45.455 0.00 0.00 39.21 2.66
1831 2120 3.116079 TGAAACGGAGGGAGTACAAAC 57.884 47.619 0.00 0.00 0.00 2.93
1832 2121 3.842007 TTGAAACGGAGGGAGTACAAA 57.158 42.857 0.00 0.00 0.00 2.83
1835 2124 5.727434 TCTATTTTGAAACGGAGGGAGTAC 58.273 41.667 0.00 0.00 0.00 2.73
1836 2125 6.155565 TCATCTATTTTGAAACGGAGGGAGTA 59.844 38.462 0.00 0.00 0.00 2.59
1837 2126 4.903045 TCTATTTTGAAACGGAGGGAGT 57.097 40.909 0.00 0.00 0.00 3.85
1838 2127 5.294552 GTCATCTATTTTGAAACGGAGGGAG 59.705 44.000 0.00 0.00 0.00 4.30
1839 2128 5.045869 AGTCATCTATTTTGAAACGGAGGGA 60.046 40.000 0.00 0.00 0.00 4.20
1840 2129 5.186198 AGTCATCTATTTTGAAACGGAGGG 58.814 41.667 0.00 0.00 0.00 4.30
1841 2130 5.874810 TGAGTCATCTATTTTGAAACGGAGG 59.125 40.000 0.00 0.00 0.00 4.30
1842 2131 6.968131 TGAGTCATCTATTTTGAAACGGAG 57.032 37.500 0.00 0.00 0.00 4.63
1843 2132 6.934645 AGTTGAGTCATCTATTTTGAAACGGA 59.065 34.615 1.70 0.00 0.00 4.69
1844 2133 7.133891 AGTTGAGTCATCTATTTTGAAACGG 57.866 36.000 1.70 0.00 0.00 4.44
1845 2134 8.895845 CAAAGTTGAGTCATCTATTTTGAAACG 58.104 33.333 4.14 0.00 38.91 3.60
1846 2135 9.736023 ACAAAGTTGAGTCATCTATTTTGAAAC 57.264 29.630 15.99 0.00 38.91 2.78
1849 2138 9.778741 AGTACAAAGTTGAGTCATCTATTTTGA 57.221 29.630 15.99 3.46 38.91 2.69
1858 2147 9.826574 TGTAAAGTTAGTACAAAGTTGAGTCAT 57.173 29.630 0.00 0.00 0.00 3.06
1859 2148 9.656040 TTGTAAAGTTAGTACAAAGTTGAGTCA 57.344 29.630 0.00 0.00 38.25 3.41
1880 2169 9.656040 TGACTCAACTTTGTACTAACTTTGTAA 57.344 29.630 0.00 0.00 0.00 2.41
1881 2170 9.826574 ATGACTCAACTTTGTACTAACTTTGTA 57.173 29.630 0.00 0.00 0.00 2.41
1882 2171 8.732746 ATGACTCAACTTTGTACTAACTTTGT 57.267 30.769 0.00 0.00 0.00 2.83
1883 2172 9.046296 AGATGACTCAACTTTGTACTAACTTTG 57.954 33.333 0.00 0.00 0.00 2.77
1893 2182 9.736023 GTTCAAAAATAGATGACTCAACTTTGT 57.264 29.630 0.00 0.00 0.00 2.83
1894 2183 8.895845 CGTTCAAAAATAGATGACTCAACTTTG 58.104 33.333 0.00 0.00 0.00 2.77
1895 2184 8.076178 CCGTTCAAAAATAGATGACTCAACTTT 58.924 33.333 0.00 0.00 0.00 2.66
1896 2185 7.444183 TCCGTTCAAAAATAGATGACTCAACTT 59.556 33.333 0.00 0.00 0.00 2.66
1897 2186 6.934645 TCCGTTCAAAAATAGATGACTCAACT 59.065 34.615 0.00 0.00 0.00 3.16
1898 2187 7.129109 TCCGTTCAAAAATAGATGACTCAAC 57.871 36.000 0.00 0.00 0.00 3.18
1899 2188 7.094805 CCTTCCGTTCAAAAATAGATGACTCAA 60.095 37.037 0.00 0.00 0.00 3.02
1900 2189 6.371548 CCTTCCGTTCAAAAATAGATGACTCA 59.628 38.462 0.00 0.00 0.00 3.41
1901 2190 6.594159 TCCTTCCGTTCAAAAATAGATGACTC 59.406 38.462 0.00 0.00 0.00 3.36
1902 2191 6.472887 TCCTTCCGTTCAAAAATAGATGACT 58.527 36.000 0.00 0.00 0.00 3.41
1903 2192 6.371825 ACTCCTTCCGTTCAAAAATAGATGAC 59.628 38.462 0.00 0.00 0.00 3.06
1904 2193 6.472887 ACTCCTTCCGTTCAAAAATAGATGA 58.527 36.000 0.00 0.00 0.00 2.92
1905 2194 6.743575 ACTCCTTCCGTTCAAAAATAGATG 57.256 37.500 0.00 0.00 0.00 2.90
1911 2200 9.947433 TTAGAATATACTCCTTCCGTTCAAAAA 57.053 29.630 0.00 0.00 0.00 1.94
1912 2201 9.374838 GTTAGAATATACTCCTTCCGTTCAAAA 57.625 33.333 0.00 0.00 0.00 2.44
1913 2202 8.755977 AGTTAGAATATACTCCTTCCGTTCAAA 58.244 33.333 0.00 0.00 0.00 2.69
1914 2203 8.302515 AGTTAGAATATACTCCTTCCGTTCAA 57.697 34.615 0.00 0.00 0.00 2.69
1915 2204 7.893124 AGTTAGAATATACTCCTTCCGTTCA 57.107 36.000 0.00 0.00 0.00 3.18
1916 2205 8.022550 GCTAGTTAGAATATACTCCTTCCGTTC 58.977 40.741 0.00 0.00 0.00 3.95
1917 2206 7.039853 GGCTAGTTAGAATATACTCCTTCCGTT 60.040 40.741 0.00 0.00 0.00 4.44
1918 2207 6.433716 GGCTAGTTAGAATATACTCCTTCCGT 59.566 42.308 0.00 0.00 0.00 4.69
1919 2208 6.433404 TGGCTAGTTAGAATATACTCCTTCCG 59.567 42.308 0.00 0.00 0.00 4.30
1920 2209 7.577998 GCTGGCTAGTTAGAATATACTCCTTCC 60.578 44.444 0.00 0.00 0.00 3.46
1921 2210 7.177744 AGCTGGCTAGTTAGAATATACTCCTTC 59.822 40.741 0.00 0.00 0.00 3.46
1922 2211 7.013834 AGCTGGCTAGTTAGAATATACTCCTT 58.986 38.462 0.00 0.00 0.00 3.36
1923 2212 6.557568 AGCTGGCTAGTTAGAATATACTCCT 58.442 40.000 0.00 0.00 0.00 3.69
1924 2213 6.844097 AGCTGGCTAGTTAGAATATACTCC 57.156 41.667 0.00 0.00 0.00 3.85
1925 2214 7.465989 CGTAGCTGGCTAGTTAGAATATACTC 58.534 42.308 0.00 0.00 0.00 2.59
1926 2215 7.380431 CGTAGCTGGCTAGTTAGAATATACT 57.620 40.000 0.00 0.00 0.00 2.12
2038 2327 0.812014 TCTTTTCTTGCCACGCACGA 60.812 50.000 0.00 0.00 38.71 4.35
2046 2335 9.971922 ATGCATACTATTTTATCTTTTCTTGCC 57.028 29.630 0.00 0.00 0.00 4.52
2084 2373 6.762661 GGGTTTTGCTTGCACATATAATTCAT 59.237 34.615 0.00 0.00 0.00 2.57
2085 2374 6.070881 AGGGTTTTGCTTGCACATATAATTCA 60.071 34.615 0.00 0.00 0.00 2.57
2120 2409 6.072452 CCGAGAAGCTAAATGTTCCTTTTTCT 60.072 38.462 0.00 0.00 0.00 2.52
2183 2472 7.223584 TCTTAAATGCCCTCGATCAATGAATA 58.776 34.615 0.00 0.00 0.00 1.75
2231 2520 3.523157 TGAATAACTCATGGCCTTCTCCA 59.477 43.478 3.32 0.00 40.97 3.86
2269 2559 6.713762 AAATGCCCTCGATTGAAATGATTA 57.286 33.333 0.00 0.00 0.00 1.75
2440 2734 7.744087 TCAAGCTTTTATAAGAAAGTCAGCA 57.256 32.000 0.00 0.00 38.56 4.41
2441 2735 8.076178 TGTTCAAGCTTTTATAAGAAAGTCAGC 58.924 33.333 0.00 0.00 38.56 4.26
2500 2797 8.421249 TCTTATGAATTTTCAACCCATGTTCT 57.579 30.769 0.00 0.00 41.13 3.01
2684 2995 8.950007 AAATATTCAGGACTTCCAAAAGGTTA 57.050 30.769 0.00 0.00 38.89 2.85
2694 3005 8.730680 TGCTACTTTGAAAATATTCAGGACTTC 58.269 33.333 0.00 0.00 45.82 3.01
2726 3039 8.885494 TTTGGAAAATGTTCAGAATTCGAATT 57.115 26.923 22.93 22.93 35.25 2.17
2727 3040 8.885494 TTTTGGAAAATGTTCAGAATTCGAAT 57.115 26.923 4.39 4.39 35.25 3.34
2730 3043 9.372541 CAAATTTTGGAAAATGTTCAGAATTCG 57.627 29.630 0.00 0.00 38.53 3.34


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

AutoCloner maintained by Alex Coulton.