Multiple sequence alignment - TraesCS6D01G057500

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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 TraesCS6D01G057500 chr6D 100.000 4347 0 0 1 4347 27330109 27325763 0.000000e+00 8028.0
1 TraesCS6D01G057500 chr6D 84.693 1692 215 28 1022 2686 27126923 27125249 0.000000e+00 1650.0
2 TraesCS6D01G057500 chr6D 83.590 1755 226 33 970 2686 27209709 27207979 0.000000e+00 1589.0
3 TraesCS6D01G057500 chr6D 81.992 1516 214 37 865 2361 27313958 27312483 0.000000e+00 1232.0
4 TraesCS6D01G057500 chr6D 78.422 621 103 18 139 737 381008058 381007447 4.100000e-100 375.0
5 TraesCS6D01G057500 chr6D 78.201 289 32 19 3140 3408 27312360 27312083 5.820000e-34 156.0
6 TraesCS6D01G057500 chr6A 92.926 3534 173 28 874 4347 31043963 31047479 0.000000e+00 5070.0
7 TraesCS6D01G057500 chr6A 83.577 1711 216 35 1022 2686 31159896 31161587 0.000000e+00 1543.0
8 TraesCS6D01G057500 chr6A 80.769 676 107 11 1616 2275 31108180 31108848 1.390000e-139 507.0
9 TraesCS6D01G057500 chr6A 81.184 659 97 15 961 1612 31092489 31093127 5.020000e-139 505.0
10 TraesCS6D01G057500 chr6A 72.131 1281 268 62 1056 2287 30041675 30040435 5.460000e-79 305.0
11 TraesCS6D01G057500 chrUn 94.696 1791 72 10 1651 3418 76751326 76749536 0.000000e+00 2760.0
12 TraesCS6D01G057500 chrUn 81.258 1478 220 28 919 2361 76831379 76832834 0.000000e+00 1142.0
13 TraesCS6D01G057500 chrUn 81.258 1478 220 28 919 2361 241635456 241636911 0.000000e+00 1142.0
14 TraesCS6D01G057500 chrUn 87.278 959 84 20 3413 4347 76767644 76768588 0.000000e+00 1061.0
15 TraesCS6D01G057500 chrUn 95.463 551 22 3 950 1497 76751871 76751321 0.000000e+00 876.0
16 TraesCS6D01G057500 chrUn 89.508 305 27 3 3999 4300 76787835 76788137 8.820000e-102 381.0
17 TraesCS6D01G057500 chr6B 83.604 1537 224 18 1166 2686 49701288 49699764 0.000000e+00 1417.0
18 TraesCS6D01G057500 chr6B 89.886 791 69 6 1 785 49947490 49946705 0.000000e+00 1007.0
19 TraesCS6D01G057500 chr6B 78.241 648 117 18 138 767 116328748 116328107 1.130000e-105 394.0
20 TraesCS6D01G057500 chr6B 72.811 651 141 26 1652 2287 51577037 51576408 5.740000e-44 189.0
21 TraesCS6D01G057500 chr6B 89.157 83 7 2 781 861 62005096 62005178 7.690000e-18 102.0
22 TraesCS6D01G057500 chr2A 80.032 616 105 11 139 737 765574506 765573892 1.430000e-119 440.0
23 TraesCS6D01G057500 chr7A 78.992 595 110 11 158 737 700652279 700651685 4.080000e-105 392.0
24 TraesCS6D01G057500 chr7A 79.537 562 100 11 191 737 700634622 700634061 1.900000e-103 387.0
25 TraesCS6D01G057500 chr7A 76.016 492 95 15 256 737 36355695 36355217 2.610000e-57 233.0
26 TraesCS6D01G057500 chr7A 100.000 57 0 0 781 837 36365062 36365118 5.950000e-19 106.0
27 TraesCS6D01G057500 chr4B 78.583 607 112 13 140 729 527122118 527122723 6.820000e-103 385.0
28 TraesCS6D01G057500 chr4B 89.333 75 7 1 784 857 272427624 272427550 4.630000e-15 93.5
29 TraesCS6D01G057500 chr7D 79.450 545 89 16 234 759 585416598 585417138 8.880000e-97 364.0
30 TraesCS6D01G057500 chr1B 77.304 586 113 14 192 763 355981976 355981397 1.170000e-85 327.0
31 TraesCS6D01G057500 chr1B 76.262 535 104 12 210 732 600981249 600980726 3.330000e-66 263.0
32 TraesCS6D01G057500 chr5A 76.923 533 104 12 252 767 25751686 25752216 7.120000e-73 285.0
33 TraesCS6D01G057500 chr4A 77.861 402 74 11 197 591 628628587 628628980 7.270000e-58 235.0
34 TraesCS6D01G057500 chr2B 77.872 235 43 5 518 748 563313980 563314209 2.110000e-28 137.0
35 TraesCS6D01G057500 chr7B 100.000 57 0 0 781 837 534830180 534830236 5.950000e-19 106.0
36 TraesCS6D01G057500 chr1A 96.774 62 2 0 781 842 1209585 1209524 2.140000e-18 104.0
37 TraesCS6D01G057500 chr5B 96.774 62 1 1 781 841 24807219 24807280 7.690000e-18 102.0
38 TraesCS6D01G057500 chr5B 91.026 78 1 6 781 855 24673767 24673841 2.770000e-17 100.0
39 TraesCS6D01G057500 chr5B 92.857 70 2 3 781 848 704989324 704989256 9.950000e-17 99.0
40 TraesCS6D01G057500 chr3A 96.721 61 2 0 781 841 692954372 692954432 7.690000e-18 102.0


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 TraesCS6D01G057500 chr6D 27325763 27330109 4346 True 8028 8028 100.0000 1 4347 1 chr6D.!!$R3 4346
1 TraesCS6D01G057500 chr6D 27125249 27126923 1674 True 1650 1650 84.6930 1022 2686 1 chr6D.!!$R1 1664
2 TraesCS6D01G057500 chr6D 27207979 27209709 1730 True 1589 1589 83.5900 970 2686 1 chr6D.!!$R2 1716
3 TraesCS6D01G057500 chr6D 27312083 27313958 1875 True 694 1232 80.0965 865 3408 2 chr6D.!!$R5 2543
4 TraesCS6D01G057500 chr6D 381007447 381008058 611 True 375 375 78.4220 139 737 1 chr6D.!!$R4 598
5 TraesCS6D01G057500 chr6A 31043963 31047479 3516 False 5070 5070 92.9260 874 4347 1 chr6A.!!$F1 3473
6 TraesCS6D01G057500 chr6A 31159896 31161587 1691 False 1543 1543 83.5770 1022 2686 1 chr6A.!!$F4 1664
7 TraesCS6D01G057500 chr6A 31108180 31108848 668 False 507 507 80.7690 1616 2275 1 chr6A.!!$F3 659
8 TraesCS6D01G057500 chr6A 31092489 31093127 638 False 505 505 81.1840 961 1612 1 chr6A.!!$F2 651
9 TraesCS6D01G057500 chr6A 30040435 30041675 1240 True 305 305 72.1310 1056 2287 1 chr6A.!!$R1 1231
10 TraesCS6D01G057500 chrUn 76749536 76751871 2335 True 1818 2760 95.0795 950 3418 2 chrUn.!!$R1 2468
11 TraesCS6D01G057500 chrUn 76831379 76832834 1455 False 1142 1142 81.2580 919 2361 1 chrUn.!!$F3 1442
12 TraesCS6D01G057500 chrUn 241635456 241636911 1455 False 1142 1142 81.2580 919 2361 1 chrUn.!!$F4 1442
13 TraesCS6D01G057500 chrUn 76767644 76768588 944 False 1061 1061 87.2780 3413 4347 1 chrUn.!!$F1 934
14 TraesCS6D01G057500 chr6B 49699764 49701288 1524 True 1417 1417 83.6040 1166 2686 1 chr6B.!!$R1 1520
15 TraesCS6D01G057500 chr6B 49946705 49947490 785 True 1007 1007 89.8860 1 785 1 chr6B.!!$R2 784
16 TraesCS6D01G057500 chr6B 116328107 116328748 641 True 394 394 78.2410 138 767 1 chr6B.!!$R4 629
17 TraesCS6D01G057500 chr2A 765573892 765574506 614 True 440 440 80.0320 139 737 1 chr2A.!!$R1 598
18 TraesCS6D01G057500 chr7A 700651685 700652279 594 True 392 392 78.9920 158 737 1 chr7A.!!$R3 579
19 TraesCS6D01G057500 chr7A 700634061 700634622 561 True 387 387 79.5370 191 737 1 chr7A.!!$R2 546
20 TraesCS6D01G057500 chr4B 527122118 527122723 605 False 385 385 78.5830 140 729 1 chr4B.!!$F1 589
21 TraesCS6D01G057500 chr7D 585416598 585417138 540 False 364 364 79.4500 234 759 1 chr7D.!!$F1 525
22 TraesCS6D01G057500 chr1B 355981397 355981976 579 True 327 327 77.3040 192 763 1 chr1B.!!$R1 571
23 TraesCS6D01G057500 chr1B 600980726 600981249 523 True 263 263 76.2620 210 732 1 chr1B.!!$R2 522
24 TraesCS6D01G057500 chr5A 25751686 25752216 530 False 285 285 76.9230 252 767 1 chr5A.!!$F1 515

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
947 989 0.031857 CCCACATTTGCGCTTTCACA 59.968 50.000 9.73 0.00 0.00 3.58 F
948 990 1.537776 CCCACATTTGCGCTTTCACAA 60.538 47.619 9.73 0.00 0.00 3.33 F
1656 1746 3.064324 GAAGGCATGCCCGCTGTT 61.064 61.111 33.14 20.24 39.21 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1873 1972 1.203052 CCATGAAGCAACACCATCACC 59.797 52.381 0.00 0.00 0.0 4.02 R
1949 2048 2.670414 GCTAGCATCGATATGTGGCTTC 59.330 50.000 10.63 2.69 36.1 3.86 R
3632 3825 0.915364 AGGAAGGGATGAGGAAGCAC 59.085 55.000 0.00 0.00 0.0 4.40 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
33 34 5.237815 TGTGTCTAGGCTGAACAATTACAG 58.762 41.667 0.00 0.00 37.22 2.74
45 46 7.055667 TGAACAATTACAGCCAATTTGGTAA 57.944 32.000 16.62 8.13 40.46 2.85
47 48 7.816995 TGAACAATTACAGCCAATTTGGTAATC 59.183 33.333 16.62 0.25 40.46 1.75
58 59 6.926272 GCCAATTTGGTAATCAGTGTTTTACA 59.074 34.615 16.62 4.49 40.46 2.41
92 93 3.756082 TTTGGCCTGGGATTGTAATCT 57.244 42.857 3.32 0.00 35.73 2.40
102 103 8.311109 GCCTGGGATTGTAATCTTAAAGAAAAA 58.689 33.333 4.75 0.00 35.73 1.94
130 131 4.381718 GGAACGAGTAGTTGGTCTAAGCAT 60.382 45.833 2.80 0.00 44.35 3.79
136 137 5.833082 AGTAGTTGGTCTAAGCATACATCG 58.167 41.667 0.00 0.00 0.00 3.84
164 166 6.570680 TCCTCCCCAAGAAAAATTAGGATTT 58.429 36.000 0.00 0.00 37.06 2.17
205 207 0.179040 TCGTTGGTCCGCCTCTTTTT 60.179 50.000 0.00 0.00 35.27 1.94
301 304 8.691661 ATTTCTTTGAGTCTTGTTAGGCTTTA 57.308 30.769 0.00 0.00 36.18 1.85
314 317 2.716217 AGGCTTTATGTCCTGCTCAAC 58.284 47.619 0.00 0.00 0.00 3.18
424 429 0.387929 GTGTGGAGGTGTGTCTTCGA 59.612 55.000 0.00 0.00 0.00 3.71
454 469 2.831526 TCTTTGATGGATCTGGTCGTCA 59.168 45.455 0.00 0.00 0.00 4.35
472 487 3.907788 CGTCATTTGTCTACGTTCGTGTA 59.092 43.478 8.14 0.00 32.16 2.90
513 532 3.567797 GCCACTCTTCATCGGCGC 61.568 66.667 0.00 0.00 34.26 6.53
541 561 3.889134 TTCTGCTGCGCTGGTCCTG 62.889 63.158 16.47 3.98 0.00 3.86
696 725 5.125417 ACGGGTCTGGATGTAATTTTCATTG 59.875 40.000 0.00 0.00 0.00 2.82
701 730 8.087750 GGTCTGGATGTAATTTTCATTGTTTCA 58.912 33.333 0.00 0.00 0.00 2.69
737 766 8.197439 TGTACTGTCACGATTGAAGATGAATAT 58.803 33.333 0.00 0.00 31.90 1.28
751 780 9.770097 TGAAGATGAATATGTCAGAAGTTATCC 57.230 33.333 0.00 0.00 40.43 2.59
752 781 9.770097 GAAGATGAATATGTCAGAAGTTATCCA 57.230 33.333 0.00 0.00 40.43 3.41
808 837 9.716531 ATACTAAAGTTAGTACAAAGTTGGGTC 57.283 33.333 12.07 0.00 45.86 4.46
809 838 7.567458 ACTAAAGTTAGTACAAAGTTGGGTCA 58.433 34.615 1.81 0.00 41.92 4.02
810 839 8.215736 ACTAAAGTTAGTACAAAGTTGGGTCAT 58.784 33.333 1.81 0.00 41.92 3.06
811 840 7.506328 AAAGTTAGTACAAAGTTGGGTCATC 57.494 36.000 0.00 0.00 0.00 2.92
812 841 6.435292 AGTTAGTACAAAGTTGGGTCATCT 57.565 37.500 0.00 0.00 0.00 2.90
813 842 7.549147 AGTTAGTACAAAGTTGGGTCATCTA 57.451 36.000 0.00 0.00 0.00 1.98
814 843 8.147244 AGTTAGTACAAAGTTGGGTCATCTAT 57.853 34.615 0.00 0.00 0.00 1.98
815 844 8.603304 AGTTAGTACAAAGTTGGGTCATCTATT 58.397 33.333 0.00 0.00 0.00 1.73
816 845 9.227777 GTTAGTACAAAGTTGGGTCATCTATTT 57.772 33.333 0.00 0.00 0.00 1.40
817 846 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
818 847 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
819 848 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
820 849 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
821 850 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
822 851 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
823 852 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
824 853 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
825 854 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
826 855 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
827 856 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
828 857 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
829 858 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
830 859 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
831 860 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
832 861 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
833 862 4.966805 TCTATTTTGGAACGGAGGGAGTAT 59.033 41.667 0.00 0.00 0.00 2.12
834 863 6.138263 TCTATTTTGGAACGGAGGGAGTATA 58.862 40.000 0.00 0.00 0.00 1.47
835 864 5.906772 ATTTTGGAACGGAGGGAGTATAT 57.093 39.130 0.00 0.00 0.00 0.86
836 865 4.682778 TTTGGAACGGAGGGAGTATATG 57.317 45.455 0.00 0.00 0.00 1.78
837 866 3.323774 TGGAACGGAGGGAGTATATGT 57.676 47.619 0.00 0.00 0.00 2.29
838 867 3.649843 TGGAACGGAGGGAGTATATGTT 58.350 45.455 0.00 0.00 0.00 2.71
839 868 4.035112 TGGAACGGAGGGAGTATATGTTT 58.965 43.478 0.00 0.00 0.00 2.83
840 869 4.141801 TGGAACGGAGGGAGTATATGTTTG 60.142 45.833 0.00 0.00 0.00 2.93
841 870 3.470645 ACGGAGGGAGTATATGTTTGC 57.529 47.619 0.00 0.00 0.00 3.68
842 871 2.769663 ACGGAGGGAGTATATGTTTGCA 59.230 45.455 0.00 0.00 0.00 4.08
843 872 3.391296 ACGGAGGGAGTATATGTTTGCAT 59.609 43.478 0.00 0.00 39.03 3.96
844 873 4.141482 ACGGAGGGAGTATATGTTTGCATT 60.141 41.667 0.00 0.00 36.58 3.56
845 874 4.821805 CGGAGGGAGTATATGTTTGCATTT 59.178 41.667 0.00 0.00 36.58 2.32
846 875 5.299279 CGGAGGGAGTATATGTTTGCATTTT 59.701 40.000 0.00 0.00 36.58 1.82
847 876 6.183360 CGGAGGGAGTATATGTTTGCATTTTT 60.183 38.462 0.00 0.00 36.58 1.94
848 877 7.012894 CGGAGGGAGTATATGTTTGCATTTTTA 59.987 37.037 0.00 0.00 36.58 1.52
849 878 8.691797 GGAGGGAGTATATGTTTGCATTTTTAA 58.308 33.333 0.00 0.00 36.58 1.52
929 967 0.332972 AGTTCTGGGGGCTTCAATCC 59.667 55.000 0.00 0.00 0.00 3.01
935 977 0.325577 GGGGGCTTCAATCCCACATT 60.326 55.000 0.00 0.00 46.62 2.71
939 981 1.632422 GCTTCAATCCCACATTTGCG 58.368 50.000 0.00 0.00 0.00 4.85
947 989 0.031857 CCCACATTTGCGCTTTCACA 59.968 50.000 9.73 0.00 0.00 3.58
948 990 1.537776 CCCACATTTGCGCTTTCACAA 60.538 47.619 9.73 0.00 0.00 3.33
1656 1746 3.064324 GAAGGCATGCCCGCTGTT 61.064 61.111 33.14 20.24 39.21 3.16
1873 1972 4.037684 AGTTATGGAAGAGGAATACCGACG 59.962 45.833 0.00 0.00 41.83 5.12
1949 2048 4.714308 ACTTCCCCTGTCTTCAGATAAGAG 59.286 45.833 0.00 0.00 43.76 2.85
2652 2815 3.600388 ACTGGTAGCATTAGTTCTGTGC 58.400 45.455 0.00 0.00 39.10 4.57
2862 3026 4.750021 TCATCTCATCTCTTGTTGGAGG 57.250 45.455 0.00 0.00 34.39 4.30
2863 3027 4.356436 TCATCTCATCTCTTGTTGGAGGA 58.644 43.478 0.00 0.00 34.39 3.71
2902 3067 4.032960 AGTCCATTGTACCAATGAAGCA 57.967 40.909 16.42 0.00 0.00 3.91
3020 3188 9.461312 TGGTATGAGCATATTTTACTGTTTCTT 57.539 29.630 0.00 0.00 0.00 2.52
3211 3385 5.768164 TGAGAACTGAGTTATTTTCCCCAAC 59.232 40.000 0.00 0.00 0.00 3.77
3353 3545 5.279708 GCCATGGAGCTAGTATGATGTACTT 60.280 44.000 18.40 0.00 0.00 2.24
3632 3825 7.102346 ACATCTTGTTTCTTATCTCCAGACAG 58.898 38.462 0.00 0.00 0.00 3.51
3688 3881 0.254747 TTTCCTCATGCCCTAACCCG 59.745 55.000 0.00 0.00 0.00 5.28
3703 3896 4.995487 CCTAACCCGCCTACATTATCTTTC 59.005 45.833 0.00 0.00 0.00 2.62
3746 3939 0.397941 CCACTGGAGGTGCTCTTTCA 59.602 55.000 0.00 0.00 44.08 2.69
3752 3945 1.544314 GGAGGTGCTCTTTCACTTGCT 60.544 52.381 0.00 0.00 37.16 3.91
3768 3961 4.952335 CACTTGCTTTTCCCTTCTATCCAT 59.048 41.667 0.00 0.00 0.00 3.41
3798 3991 2.452600 TTCAGTTTGCCACCTCCTTT 57.547 45.000 0.00 0.00 0.00 3.11
3799 3992 1.981256 TCAGTTTGCCACCTCCTTTC 58.019 50.000 0.00 0.00 0.00 2.62
3849 4042 2.624557 GGTTCTTCTCCTCTAGCTCCCA 60.625 54.545 0.00 0.00 0.00 4.37
3857 4050 1.339610 CCTCTAGCTCCCAAGATGACG 59.660 57.143 0.00 0.00 0.00 4.35
3858 4051 0.747255 TCTAGCTCCCAAGATGACGC 59.253 55.000 0.00 0.00 0.00 5.19
3859 4052 0.749649 CTAGCTCCCAAGATGACGCT 59.250 55.000 0.00 0.00 0.00 5.07
3860 4053 1.957177 CTAGCTCCCAAGATGACGCTA 59.043 52.381 0.00 0.00 0.00 4.26
3910 4104 4.752101 AGAAGTTTGTTCCAACTCGATCAG 59.248 41.667 0.00 0.00 0.00 2.90
3950 4165 6.428385 AAATACATCCTCTTTCTTGCTTCG 57.572 37.500 0.00 0.00 0.00 3.79
3996 4212 5.378230 TGCTCTTATGGATCAATCAGGTT 57.622 39.130 0.00 0.00 0.00 3.50
4014 4230 6.399743 TCAGGTTGCAGTGTAATTTATACGA 58.600 36.000 0.00 0.00 0.00 3.43
4023 4239 7.307811 GCAGTGTAATTTATACGATTTCCCCTC 60.308 40.741 0.00 0.00 0.00 4.30
4036 4252 1.276622 TCCCCTCTTAAGTGACTGCC 58.723 55.000 6.11 0.00 0.00 4.85
4037 4253 0.108138 CCCCTCTTAAGTGACTGCCG 60.108 60.000 6.11 0.00 0.00 5.69
4045 4261 2.386661 AAGTGACTGCCGACTAATGG 57.613 50.000 0.00 0.00 0.00 3.16
4146 4362 8.554835 TGGACTGATAATCGTGACAATTTTTA 57.445 30.769 0.00 0.00 0.00 1.52
4175 4391 3.206964 TGCCTTCGTGAATTGTTGTACA 58.793 40.909 0.00 0.00 0.00 2.90
4210 4427 7.801315 TCGTTTTGCTTGCAGTTAAGTTATTAG 59.199 33.333 0.00 0.00 0.00 1.73
4288 4505 8.089597 CAGCATATCTCTCATTGTCAGTCTAAT 58.910 37.037 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 7.816995 TGATTACCAAATTGGCTGTAATTGTTC 59.183 33.333 12.67 0.00 42.67 3.18
33 34 6.926272 TGTAAAACACTGATTACCAAATTGGC 59.074 34.615 12.67 0.00 42.67 4.52
34 35 8.879342 TTGTAAAACACTGATTACCAAATTGG 57.121 30.769 11.02 11.02 45.02 3.16
45 46 4.814234 TCGCACTCTTTGTAAAACACTGAT 59.186 37.500 0.00 0.00 0.00 2.90
47 48 4.530094 TCGCACTCTTTGTAAAACACTG 57.470 40.909 0.00 0.00 0.00 3.66
58 59 1.000274 GGCCAAAACATCGCACTCTTT 60.000 47.619 0.00 0.00 0.00 2.52
92 93 7.872483 ACTACTCGTTCCCGTATTTTTCTTTAA 59.128 33.333 0.00 0.00 35.01 1.52
102 103 2.424956 GACCAACTACTCGTTCCCGTAT 59.575 50.000 0.00 0.00 32.27 3.06
112 113 5.915758 CGATGTATGCTTAGACCAACTACTC 59.084 44.000 0.00 0.00 0.00 2.59
130 131 0.337082 TTGGGGAGGAGGACGATGTA 59.663 55.000 0.00 0.00 0.00 2.29
136 137 2.971901 TTTTTCTTGGGGAGGAGGAC 57.028 50.000 0.00 0.00 0.00 3.85
164 166 2.852075 ACCGGTGGGAGGCAAAGA 60.852 61.111 6.12 0.00 36.97 2.52
243 245 2.115266 CCTCCCGTTGGCAAAGGT 59.885 61.111 26.73 0.00 0.00 3.50
301 304 0.957395 CGCCTTGTTGAGCAGGACAT 60.957 55.000 0.00 0.00 0.00 3.06
424 429 6.504634 ACCAGATCCATCAAAGATAGATCCAT 59.495 38.462 10.43 0.00 35.08 3.41
454 469 8.437742 CCTAAAAATACACGAACGTAGACAAAT 58.562 33.333 0.00 0.00 0.00 2.32
513 532 0.453282 CGCAGCAGAACAACAATCGG 60.453 55.000 0.00 0.00 0.00 4.18
541 561 0.038892 TCGTCGTGCTAAAGACCCAC 60.039 55.000 0.00 0.00 31.80 4.61
670 699 5.180271 TGAAAATTACATCCAGACCCGTAC 58.820 41.667 0.00 0.00 0.00 3.67
696 725 5.106475 TGACAGTACAACAAACACCTGAAAC 60.106 40.000 0.00 0.00 0.00 2.78
701 730 2.933906 CGTGACAGTACAACAAACACCT 59.066 45.455 0.00 0.00 0.00 4.00
785 814 8.617290 ATGACCCAACTTTGTACTAACTTTAG 57.383 34.615 0.00 0.00 36.82 1.85
786 815 8.434392 AGATGACCCAACTTTGTACTAACTTTA 58.566 33.333 0.00 0.00 0.00 1.85
787 816 7.287810 AGATGACCCAACTTTGTACTAACTTT 58.712 34.615 0.00 0.00 0.00 2.66
788 817 6.838382 AGATGACCCAACTTTGTACTAACTT 58.162 36.000 0.00 0.00 0.00 2.66
789 818 6.435292 AGATGACCCAACTTTGTACTAACT 57.565 37.500 0.00 0.00 0.00 2.24
790 819 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
791 820 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
792 821 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
793 822 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
794 823 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
795 824 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
796 825 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
797 826 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
798 827 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
799 828 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
800 829 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
801 830 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
802 831 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
803 832 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
804 833 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
805 834 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
806 835 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
807 836 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
808 837 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
809 838 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
810 839 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
811 840 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
812 841 6.328148 ACATATACTCCCTCCGTTCCAAAATA 59.672 38.462 0.00 0.00 0.00 1.40
813 842 5.132144 ACATATACTCCCTCCGTTCCAAAAT 59.868 40.000 0.00 0.00 0.00 1.82
814 843 4.472108 ACATATACTCCCTCCGTTCCAAAA 59.528 41.667 0.00 0.00 0.00 2.44
815 844 4.035112 ACATATACTCCCTCCGTTCCAAA 58.965 43.478 0.00 0.00 0.00 3.28
816 845 3.649843 ACATATACTCCCTCCGTTCCAA 58.350 45.455 0.00 0.00 0.00 3.53
817 846 3.323774 ACATATACTCCCTCCGTTCCA 57.676 47.619 0.00 0.00 0.00 3.53
818 847 4.377897 CAAACATATACTCCCTCCGTTCC 58.622 47.826 0.00 0.00 0.00 3.62
819 848 3.808174 GCAAACATATACTCCCTCCGTTC 59.192 47.826 0.00 0.00 0.00 3.95
820 849 3.199071 TGCAAACATATACTCCCTCCGTT 59.801 43.478 0.00 0.00 0.00 4.44
821 850 2.769663 TGCAAACATATACTCCCTCCGT 59.230 45.455 0.00 0.00 0.00 4.69
822 851 3.469008 TGCAAACATATACTCCCTCCG 57.531 47.619 0.00 0.00 0.00 4.63
823 852 6.715347 AAAATGCAAACATATACTCCCTCC 57.285 37.500 0.00 0.00 34.62 4.30
854 883 9.066892 TGCAGTGTGATTAAGTTCTCTTTATTT 57.933 29.630 0.00 0.00 35.36 1.40
855 884 8.621532 TGCAGTGTGATTAAGTTCTCTTTATT 57.378 30.769 0.00 0.00 35.36 1.40
856 885 7.148340 GCTGCAGTGTGATTAAGTTCTCTTTAT 60.148 37.037 16.64 0.00 35.36 1.40
857 886 6.147821 GCTGCAGTGTGATTAAGTTCTCTTTA 59.852 38.462 16.64 0.00 35.36 1.85
858 887 5.049129 GCTGCAGTGTGATTAAGTTCTCTTT 60.049 40.000 16.64 0.00 35.36 2.52
859 888 4.453819 GCTGCAGTGTGATTAAGTTCTCTT 59.546 41.667 16.64 0.00 37.65 2.85
860 889 3.999663 GCTGCAGTGTGATTAAGTTCTCT 59.000 43.478 16.64 0.00 0.00 3.10
861 890 3.999663 AGCTGCAGTGTGATTAAGTTCTC 59.000 43.478 16.64 0.00 0.00 2.87
862 891 4.013267 AGCTGCAGTGTGATTAAGTTCT 57.987 40.909 16.64 0.00 0.00 3.01
863 892 4.214119 TGAAGCTGCAGTGTGATTAAGTTC 59.786 41.667 16.64 4.11 0.00 3.01
864 893 4.136796 TGAAGCTGCAGTGTGATTAAGTT 58.863 39.130 16.64 0.00 0.00 2.66
865 894 3.743521 TGAAGCTGCAGTGTGATTAAGT 58.256 40.909 16.64 0.00 0.00 2.24
866 895 4.959596 ATGAAGCTGCAGTGTGATTAAG 57.040 40.909 16.64 0.00 0.00 1.85
867 896 5.710513 AAATGAAGCTGCAGTGTGATTAA 57.289 34.783 16.64 0.00 0.00 1.40
868 897 5.710513 AAAATGAAGCTGCAGTGTGATTA 57.289 34.783 16.64 0.00 0.00 1.75
897 926 5.891551 GCCCCCAGAACTATCATTTAGAAAA 59.108 40.000 0.00 0.00 0.00 2.29
901 930 4.713792 AGCCCCCAGAACTATCATTTAG 57.286 45.455 0.00 0.00 0.00 1.85
905 934 2.492025 TGAAGCCCCCAGAACTATCAT 58.508 47.619 0.00 0.00 0.00 2.45
906 935 1.965414 TGAAGCCCCCAGAACTATCA 58.035 50.000 0.00 0.00 0.00 2.15
907 936 3.481453 GATTGAAGCCCCCAGAACTATC 58.519 50.000 0.00 0.00 0.00 2.08
909 938 1.564348 GGATTGAAGCCCCCAGAACTA 59.436 52.381 0.00 0.00 0.00 2.24
911 940 0.684479 GGGATTGAAGCCCCCAGAAC 60.684 60.000 7.42 0.00 39.81 3.01
912 941 1.145900 TGGGATTGAAGCCCCCAGAA 61.146 55.000 17.04 0.00 44.67 3.02
913 942 1.543642 TGGGATTGAAGCCCCCAGA 60.544 57.895 17.04 0.00 44.67 3.86
914 943 3.099171 TGGGATTGAAGCCCCCAG 58.901 61.111 17.04 0.00 44.67 4.45
916 945 0.325577 AATGTGGGATTGAAGCCCCC 60.326 55.000 17.04 4.74 45.40 5.40
929 967 1.850377 TTGTGAAAGCGCAAATGTGG 58.150 45.000 11.47 0.00 41.22 4.17
939 981 1.736696 CGCAATGGGGATTGTGAAAGC 60.737 52.381 0.00 0.00 42.78 3.51
947 989 3.149648 GCAGCCGCAATGGGGATT 61.150 61.111 21.12 4.22 37.91 3.01
993 1044 4.408821 TGCGTGCTCATGGGGGAC 62.409 66.667 0.00 0.00 0.00 4.46
994 1045 4.100084 CTGCGTGCTCATGGGGGA 62.100 66.667 0.00 0.00 0.00 4.81
1420 1490 3.683937 GGCAATGCGGTGCTGGTT 61.684 61.111 10.83 0.00 44.31 3.67
1656 1746 0.331278 AAATGGAATGCCCGACCAGA 59.669 50.000 0.00 0.00 37.12 3.86
1873 1972 1.203052 CCATGAAGCAACACCATCACC 59.797 52.381 0.00 0.00 0.00 4.02
1949 2048 2.670414 GCTAGCATCGATATGTGGCTTC 59.330 50.000 10.63 2.69 36.10 3.86
2672 2835 7.632721 AGCTAATTTTTCATGCAGTTGTTTTG 58.367 30.769 0.00 0.00 0.00 2.44
2803 2967 9.978044 TTCATTTACAACAAATTCATCATGACA 57.022 25.926 0.00 0.00 0.00 3.58
2806 2970 9.697250 GCATTCATTTACAACAAATTCATCATG 57.303 29.630 0.00 0.00 0.00 3.07
2862 3026 2.894387 GCCACTCGCAGCAGGATC 60.894 66.667 0.00 0.00 37.47 3.36
2863 3027 3.709633 TGCCACTCGCAGCAGGAT 61.710 61.111 0.00 0.00 44.64 3.24
3134 3302 9.777297 AACACAGCCTGTCAAATTTAAAATTAT 57.223 25.926 0.00 0.00 30.29 1.28
3188 3362 6.004574 AGTTGGGGAAAATAACTCAGTTCTC 58.995 40.000 0.00 0.00 29.12 2.87
3353 3545 2.086869 GATAAGCTTGCCTGCTCAACA 58.913 47.619 9.86 0.00 43.24 3.33
3418 3611 5.123979 GGCAGTACAAAGGAAAGGAATACAG 59.876 44.000 0.00 0.00 0.00 2.74
3423 3616 3.586470 TGGCAGTACAAAGGAAAGGAA 57.414 42.857 0.00 0.00 0.00 3.36
3425 3618 3.193479 GGAATGGCAGTACAAAGGAAAGG 59.807 47.826 0.00 0.00 0.00 3.11
3632 3825 0.915364 AGGAAGGGATGAGGAAGCAC 59.085 55.000 0.00 0.00 0.00 4.40
3688 3881 5.994054 TCAGCTGATGAAAGATAATGTAGGC 59.006 40.000 13.74 0.00 34.02 3.93
3746 3939 4.657814 TGGATAGAAGGGAAAAGCAAGT 57.342 40.909 0.00 0.00 0.00 3.16
3752 3945 3.788142 AGGCAGATGGATAGAAGGGAAAA 59.212 43.478 0.00 0.00 0.00 2.29
3768 3961 2.362077 GGCAAACTGAAAGAAAGGCAGA 59.638 45.455 0.00 0.00 37.43 4.26
3798 3991 3.702792 CAGAGGGAACTTGGAGAGTAGA 58.297 50.000 0.00 0.00 44.43 2.59
3799 3992 2.167487 GCAGAGGGAACTTGGAGAGTAG 59.833 54.545 0.00 0.00 44.43 2.57
3849 4042 3.251571 GGTTTCGAGTTAGCGTCATCTT 58.748 45.455 0.00 0.00 0.00 2.40
3857 4050 1.678123 GGGGAAGGGTTTCGAGTTAGC 60.678 57.143 0.00 0.00 33.98 3.09
3858 4051 1.065636 GGGGGAAGGGTTTCGAGTTAG 60.066 57.143 0.00 0.00 33.98 2.34
3859 4052 0.986527 GGGGGAAGGGTTTCGAGTTA 59.013 55.000 0.00 0.00 33.98 2.24
3860 4053 0.770948 AGGGGGAAGGGTTTCGAGTT 60.771 55.000 0.00 0.00 33.98 3.01
3978 4194 4.885907 ACTGCAACCTGATTGATCCATAAG 59.114 41.667 0.00 0.00 41.23 1.73
3988 4204 7.551262 TCGTATAAATTACACTGCAACCTGATT 59.449 33.333 0.00 0.00 0.00 2.57
3996 4212 6.261381 GGGGAAATCGTATAAATTACACTGCA 59.739 38.462 0.00 0.00 0.00 4.41
4014 4230 3.308473 GGCAGTCACTTAAGAGGGGAAAT 60.308 47.826 10.09 0.00 0.00 2.17
4023 4239 3.865745 CCATTAGTCGGCAGTCACTTAAG 59.134 47.826 0.00 0.00 0.00 1.85
4036 4252 3.735237 ATGCTCAGGTACCATTAGTCG 57.265 47.619 15.94 0.00 0.00 4.18
4037 4253 5.186198 ACAAATGCTCAGGTACCATTAGTC 58.814 41.667 15.94 5.40 0.00 2.59
4094 4310 3.239587 TCAGCAATGTGAAATGGCATG 57.760 42.857 0.00 0.00 0.00 4.06
4133 4349 5.164061 GGCATGCTCTTTAAAAATTGTCACG 60.164 40.000 18.92 0.00 0.00 4.35
4146 4362 1.896220 TTCACGAAGGCATGCTCTTT 58.104 45.000 18.92 9.87 0.00 2.52
4175 4391 5.119931 TGCAAGCAAAACGATGAATAGTT 57.880 34.783 0.00 0.00 0.00 2.24
4210 4427 9.668497 AACCTAGACTAATTGTCCATAAAACTC 57.332 33.333 0.00 0.00 46.46 3.01
4234 4451 7.026562 ACAATTTTTAAGCAAACTGCCAAAAC 58.973 30.769 7.76 0.00 46.52 2.43
4238 4455 5.669477 AGACAATTTTTAAGCAAACTGCCA 58.331 33.333 0.00 0.00 46.52 4.92
4288 4505 3.977134 ATGGCCAATTACATGTGCAAA 57.023 38.095 10.96 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.