Multiple sequence alignment - TraesCS1A01G032400

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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 TraesCS1A01G032400 chr1A 100.000 3496 0 0 1 3496 14859349 14855854 0.000000e+00 6457
1 TraesCS1A01G032400 chr1A 88.450 1723 133 25 674 2359 14800898 14799205 0.000000e+00 2019
2 TraesCS1A01G032400 chr1A 91.629 657 46 4 1 650 254173027 254173681 0.000000e+00 900
3 TraesCS1A01G032400 chr1D 89.371 2211 169 29 973 3158 14188339 14186170 0.000000e+00 2721
4 TraesCS1A01G032400 chr1D 87.052 1730 144 40 674 2359 13853622 13851929 0.000000e+00 1881
5 TraesCS1A01G032400 chr1D 92.117 647 42 7 1 645 192886759 192886120 0.000000e+00 904
6 TraesCS1A01G032400 chr1D 91.509 424 31 3 1937 2359 13970053 13969634 2.340000e-161 579
7 TraesCS1A01G032400 chr1D 88.827 358 25 11 3147 3496 14180866 14180516 3.230000e-115 425
8 TraesCS1A01G032400 chr1D 86.386 404 28 2 1956 2359 14001333 14000957 1.940000e-112 416
9 TraesCS1A01G032400 chr1D 81.441 458 53 16 674 1114 14001794 14001352 2.580000e-91 346
10 TraesCS1A01G032400 chr1D 81.046 459 53 21 674 1114 13970495 13970053 5.590000e-88 335
11 TraesCS1A01G032400 chr1B 86.494 1777 172 41 674 2409 20292576 20294325 0.000000e+00 1890
12 TraesCS1A01G032400 chr1B 85.780 1751 167 48 700 2409 20061452 20059743 0.000000e+00 1779
13 TraesCS1A01G032400 chr1B 88.437 934 77 15 973 1891 20127543 20126626 0.000000e+00 1098
14 TraesCS1A01G032400 chr1B 86.261 1019 79 26 1899 2906 20102666 20101698 0.000000e+00 1050
15 TraesCS1A01G032400 chr6A 91.454 667 46 5 1 659 410979862 410979199 0.000000e+00 905
16 TraesCS1A01G032400 chr4D 91.781 657 45 4 1 649 385881016 385880361 0.000000e+00 905
17 TraesCS1A01G032400 chr6D 91.871 652 44 4 1 645 115276515 115275866 0.000000e+00 902
18 TraesCS1A01G032400 chr6D 91.871 652 44 4 1 645 115283268 115282619 0.000000e+00 902
19 TraesCS1A01G032400 chr3D 91.938 645 48 4 3 645 44021824 44021182 0.000000e+00 900
20 TraesCS1A01G032400 chr3D 91.603 655 46 5 3 650 378867682 378867030 0.000000e+00 896
21 TraesCS1A01G032400 chr5A 90.991 666 52 4 1 659 402778936 402778272 0.000000e+00 891


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 TraesCS1A01G032400 chr1A 14855854 14859349 3495 True 6457 6457 100.0000 1 3496 1 chr1A.!!$R2 3495
1 TraesCS1A01G032400 chr1A 14799205 14800898 1693 True 2019 2019 88.4500 674 2359 1 chr1A.!!$R1 1685
2 TraesCS1A01G032400 chr1A 254173027 254173681 654 False 900 900 91.6290 1 650 1 chr1A.!!$F1 649
3 TraesCS1A01G032400 chr1D 14186170 14188339 2169 True 2721 2721 89.3710 973 3158 1 chr1D.!!$R3 2185
4 TraesCS1A01G032400 chr1D 13851929 13853622 1693 True 1881 1881 87.0520 674 2359 1 chr1D.!!$R1 1685
5 TraesCS1A01G032400 chr1D 192886120 192886759 639 True 904 904 92.1170 1 645 1 chr1D.!!$R4 644
6 TraesCS1A01G032400 chr1D 13969634 13970495 861 True 457 579 86.2775 674 2359 2 chr1D.!!$R5 1685
7 TraesCS1A01G032400 chr1D 14000957 14001794 837 True 381 416 83.9135 674 2359 2 chr1D.!!$R6 1685
8 TraesCS1A01G032400 chr1B 20292576 20294325 1749 False 1890 1890 86.4940 674 2409 1 chr1B.!!$F1 1735
9 TraesCS1A01G032400 chr1B 20059743 20061452 1709 True 1779 1779 85.7800 700 2409 1 chr1B.!!$R1 1709
10 TraesCS1A01G032400 chr1B 20126626 20127543 917 True 1098 1098 88.4370 973 1891 1 chr1B.!!$R3 918
11 TraesCS1A01G032400 chr1B 20101698 20102666 968 True 1050 1050 86.2610 1899 2906 1 chr1B.!!$R2 1007
12 TraesCS1A01G032400 chr6A 410979199 410979862 663 True 905 905 91.4540 1 659 1 chr6A.!!$R1 658
13 TraesCS1A01G032400 chr4D 385880361 385881016 655 True 905 905 91.7810 1 649 1 chr4D.!!$R1 648
14 TraesCS1A01G032400 chr6D 115275866 115276515 649 True 902 902 91.8710 1 645 1 chr6D.!!$R1 644
15 TraesCS1A01G032400 chr6D 115282619 115283268 649 True 902 902 91.8710 1 645 1 chr6D.!!$R2 644
16 TraesCS1A01G032400 chr3D 44021182 44021824 642 True 900 900 91.9380 3 645 1 chr3D.!!$R1 642
17 TraesCS1A01G032400 chr3D 378867030 378867682 652 True 896 896 91.6030 3 650 1 chr3D.!!$R2 647
18 TraesCS1A01G032400 chr5A 402778272 402778936 664 True 891 891 90.9910 1 659 1 chr5A.!!$R1 658

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
904 922 0.038983 TTGTCAAGCGTACGCAGCTA 60.039 50.0 38.58 19.91 45.31 3.32 F
1204 1246 0.035439 TCGTGAAGCTTGGAATCCCC 60.035 55.0 2.10 0.00 0.00 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2265 2370 0.240945 GCATTCCCAAGACGTTGTGG 59.759 55.0 10.69 10.69 34.44 4.17 R
2661 2786 0.883833 AAATCAAAGACGCCCTGCAG 59.116 50.0 6.78 6.78 0.00 4.41 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
132 133 4.755629 GGAGACAACCCAGAAGTTTTAGAC 59.244 45.833 0.00 0.00 0.00 2.59
153 154 5.238214 AGACAGTCATTTCTTTCTGTTGAGC 59.762 40.000 2.66 0.00 40.53 4.26
158 159 4.754618 TCATTTCTTTCTGTTGAGCGCTTA 59.245 37.500 13.26 3.74 0.00 3.09
390 398 9.294614 AGATTTGCCTTTAGGATGATTAGATTC 57.705 33.333 0.00 0.00 37.39 2.52
410 418 0.453793 CTTGTTGGTTTGTGCGGTGA 59.546 50.000 0.00 0.00 0.00 4.02
421 429 3.791973 TGTGCGGTGAAAAACAGAAAT 57.208 38.095 0.00 0.00 0.00 2.17
448 458 4.332819 GGCTGTAGTGCTCGATTTTACATT 59.667 41.667 0.00 0.00 0.00 2.71
449 459 5.163754 GGCTGTAGTGCTCGATTTTACATTT 60.164 40.000 0.00 0.00 0.00 2.32
595 606 5.353394 ACAGACTGTCCTGTTTAAGACAA 57.647 39.130 1.07 0.00 44.32 3.18
604 615 7.703328 TGTCCTGTTTAAGACAAATTCTGTTC 58.297 34.615 0.00 0.00 39.96 3.18
617 628 6.643770 ACAAATTCTGTTCTTGATGCATTGTC 59.356 34.615 0.00 0.00 32.99 3.18
636 647 7.519328 GCATTGTCTTGCTTGTTTTGATGAAAT 60.519 33.333 0.00 0.00 39.57 2.17
665 676 9.839817 TCGATTTTTATTGATAGTATGGGTTCA 57.160 29.630 0.00 0.00 0.00 3.18
729 743 6.927416 TCTACTACTTAAGATTTTCCGTGCA 58.073 36.000 10.09 0.00 0.00 4.57
743 759 1.522676 CCGTGCACATTATAGTCGCTG 59.477 52.381 18.64 0.00 0.00 5.18
776 793 4.096003 ACAACGGGAGGGGCATCG 62.096 66.667 0.00 0.00 0.00 3.84
839 857 5.531122 TCTAGTAGGTGAATACATGTGCC 57.469 43.478 9.11 3.05 0.00 5.01
874 892 3.058293 TCGAAAAGAACATGTGTCATGGC 60.058 43.478 0.00 0.00 0.00 4.40
879 897 3.276857 AGAACATGTGTCATGGCTCATC 58.723 45.455 11.76 2.94 0.00 2.92
892 910 0.445436 GCTCATCGCCACTTGTCAAG 59.555 55.000 11.17 11.17 0.00 3.02
896 914 3.945436 CGCCACTTGTCAAGCGTA 58.055 55.556 12.66 0.00 43.45 4.42
897 915 1.491563 CGCCACTTGTCAAGCGTAC 59.508 57.895 12.66 0.00 43.45 3.67
904 922 0.038983 TTGTCAAGCGTACGCAGCTA 60.039 50.000 38.58 19.91 45.31 3.32
905 923 0.731514 TGTCAAGCGTACGCAGCTAC 60.732 55.000 38.58 28.46 45.31 3.58
923 959 7.128976 GCAGCTACTAGCAAATGAGTATTTTC 58.871 38.462 10.73 0.00 45.56 2.29
924 960 7.011857 GCAGCTACTAGCAAATGAGTATTTTCT 59.988 37.037 10.73 0.00 45.56 2.52
983 1022 3.160269 CCATTTGCCCCTCTTATGATCC 58.840 50.000 0.00 0.00 0.00 3.36
1016 1055 5.707242 TCAGTCCTATAAATCAGCCGTAG 57.293 43.478 0.00 0.00 0.00 3.51
1049 1088 5.239525 GCAGATGTCCATTCCTAATACCAAC 59.760 44.000 0.00 0.00 0.00 3.77
1053 1092 4.018870 TGTCCATTCCTAATACCAACAGCA 60.019 41.667 0.00 0.00 0.00 4.41
1168 1210 1.068474 CCTTTGCGTACCTCAAGTCG 58.932 55.000 0.00 0.00 0.00 4.18
1185 1227 1.806542 GTCGATGGCATTGAACAGTGT 59.193 47.619 18.84 0.00 0.00 3.55
1204 1246 0.035439 TCGTGAAGCTTGGAATCCCC 60.035 55.000 2.10 0.00 0.00 4.81
1256 1298 2.177594 CTTGCCCGAGTTGCTCTCCT 62.178 60.000 4.44 0.00 39.84 3.69
1321 1363 4.421515 AAGATGCTGGCTGCGGCT 62.422 61.111 18.85 8.26 46.63 5.52
1343 1385 1.964223 GGATCTTCACGGCTGAGGATA 59.036 52.381 0.00 0.00 41.96 2.59
1418 1478 2.567049 GTCTCCTGGTGGACGACG 59.433 66.667 0.00 0.00 37.46 5.12
1419 1479 3.371063 TCTCCTGGTGGACGACGC 61.371 66.667 0.00 0.00 37.46 5.19
1518 1578 2.359230 GCACCAGTGGCTCCTGAC 60.359 66.667 9.78 0.00 34.23 3.51
1615 1678 2.542824 CCCAGAATTCAACGCGTTGTTT 60.543 45.455 41.16 34.62 39.29 2.83
1618 1681 4.915085 CCAGAATTCAACGCGTTGTTTAAT 59.085 37.500 41.16 32.03 39.29 1.40
1624 1687 1.173444 ACGCGTTGTTTAATGGGGCA 61.173 50.000 5.58 0.00 39.36 5.36
1678 1741 1.089112 CTGTCCATGAATGCAGCGAA 58.911 50.000 0.00 0.00 0.00 4.70
1765 1828 2.317609 CGAGGCTTTCCCACGTGTG 61.318 63.158 15.65 2.45 41.93 3.82
1813 1876 2.128035 GTGATACAAGGAATCTCGCCG 58.872 52.381 0.00 0.00 0.00 6.46
1864 1927 1.296715 GATGGAGTTCGTGCCACCT 59.703 57.895 0.00 0.00 36.92 4.00
1877 1940 1.530013 GCCACCTGCTGATGCTGTTT 61.530 55.000 0.00 0.00 40.48 2.83
1889 1952 5.627499 TGATGCTGTTTTGCTTAAGGTAG 57.373 39.130 4.29 0.00 0.00 3.18
1891 1954 5.412594 TGATGCTGTTTTGCTTAAGGTAGAG 59.587 40.000 4.29 0.00 0.00 2.43
1892 1955 4.714632 TGCTGTTTTGCTTAAGGTAGAGT 58.285 39.130 4.29 0.00 0.00 3.24
1897 1960 7.063191 GCTGTTTTGCTTAAGGTAGAGTAGTAC 59.937 40.741 4.29 0.00 0.00 2.73
1941 2017 7.819415 TCTTACTAATGGCATCATCTAATTCCG 59.181 37.037 0.00 0.00 32.24 4.30
1945 2021 4.422073 TGGCATCATCTAATTCCGACTT 57.578 40.909 0.00 0.00 0.00 3.01
1949 2025 5.529060 GGCATCATCTAATTCCGACTTTCTT 59.471 40.000 0.00 0.00 0.00 2.52
1961 2037 7.843490 TTCCGACTTTCTTCGATTCATAATT 57.157 32.000 0.00 0.00 41.78 1.40
1989 2070 6.077838 GTCGCAGTTTTGAACTAAGGTTATG 58.922 40.000 0.00 0.00 40.46 1.90
1991 2072 6.483974 TCGCAGTTTTGAACTAAGGTTATGAA 59.516 34.615 0.00 0.00 40.46 2.57
2001 2082 9.104965 TGAACTAAGGTTATGAATTATGGTTCG 57.895 33.333 0.00 0.00 35.58 3.95
2265 2370 5.585047 AGCCGGATTTAGTCACTACAAAATC 59.415 40.000 5.05 3.70 37.52 2.17
2314 2419 0.037605 CGAAGTCCACCCGTAGCTTT 60.038 55.000 0.00 0.00 0.00 3.51
2315 2420 1.607251 CGAAGTCCACCCGTAGCTTTT 60.607 52.381 0.00 0.00 0.00 2.27
2349 2460 9.345517 ACAATATTTATTATTCATCGCATGTGC 57.654 29.630 0.00 0.00 37.78 4.57
2394 2505 3.838244 ATGTACGTGGGTGATGCTTAT 57.162 42.857 0.00 0.00 0.00 1.73
2404 2515 6.073765 CGTGGGTGATGCTTATAGTTTGTATC 60.074 42.308 0.00 0.00 0.00 2.24
2416 2527 2.761208 AGTTTGTATCGTCTGCTAGCCT 59.239 45.455 13.29 0.00 0.00 4.58
2424 2535 2.764010 TCGTCTGCTAGCCTTATTTCCA 59.236 45.455 13.29 0.00 0.00 3.53
2441 2552 2.487775 TCCAGTAATGTGTATGCCCCT 58.512 47.619 0.00 0.00 0.00 4.79
2445 2556 5.847265 TCCAGTAATGTGTATGCCCCTAATA 59.153 40.000 0.00 0.00 0.00 0.98
2453 2564 7.011499 TGTGTATGCCCCTAATATTATCGTT 57.989 36.000 0.00 0.00 0.00 3.85
2455 2566 6.255020 GTGTATGCCCCTAATATTATCGTTCG 59.745 42.308 0.00 0.00 0.00 3.95
2485 2596 1.135689 GTGTCCATAGTTTGGCGCAAG 60.136 52.381 10.83 0.00 46.01 4.01
2519 2630 9.284968 AGAATAAATTATACCTTGATGGAACGG 57.715 33.333 0.00 0.00 39.71 4.44
2529 2640 5.305902 ACCTTGATGGAACGGGTTTATTTTT 59.694 36.000 0.00 0.00 39.71 1.94
2533 2644 9.430623 CTTGATGGAACGGGTTTATTTTTAATT 57.569 29.630 0.00 0.00 0.00 1.40
2574 2697 3.816523 CCAATGTACAACCACGGTTACTT 59.183 43.478 0.00 0.00 36.46 2.24
2620 2743 7.534085 TCTGACACATTTTACCGATTGATAC 57.466 36.000 0.00 0.00 0.00 2.24
2660 2785 9.573166 TTTATCATATGGACAAATCCTAGGTTG 57.427 33.333 9.08 9.59 46.43 3.77
2661 2786 5.376625 TCATATGGACAAATCCTAGGTTGC 58.623 41.667 9.08 3.75 46.43 4.17
2670 2795 2.821366 CTAGGTTGCTGCAGGGCG 60.821 66.667 17.12 0.00 34.52 6.13
2695 2820 9.632807 CGTCTTTGATTTATGGGATTGTAAAAA 57.367 29.630 0.00 0.00 0.00 1.94
2699 2824 7.164230 TGATTTATGGGATTGTAAAAACGCT 57.836 32.000 0.00 0.00 0.00 5.07
2711 2836 6.004408 TGTAAAAACGCTGGAATAGGAAAC 57.996 37.500 0.00 0.00 0.00 2.78
2718 2843 4.188462 CGCTGGAATAGGAAACACACATA 58.812 43.478 0.00 0.00 0.00 2.29
2734 2859 5.045215 CACACATAATTGGAATGTCATGCC 58.955 41.667 2.34 2.34 35.39 4.40
2735 2860 4.957954 ACACATAATTGGAATGTCATGCCT 59.042 37.500 11.41 0.00 35.39 4.75
2737 2862 6.039717 ACACATAATTGGAATGTCATGCCTAC 59.960 38.462 11.41 0.00 35.39 3.18
2744 2869 5.263599 TGGAATGTCATGCCTACTCAAATT 58.736 37.500 11.41 0.00 0.00 1.82
2776 2901 9.243637 TGTGTTTGTTTGATTTAGCATAAGAAC 57.756 29.630 0.00 0.00 0.00 3.01
2781 2906 9.462174 TTGTTTGATTTAGCATAAGAACAACAG 57.538 29.630 0.00 0.00 32.67 3.16
2783 2908 9.334693 GTTTGATTTAGCATAAGAACAACAGAG 57.665 33.333 0.00 0.00 0.00 3.35
2786 2911 8.049117 TGATTTAGCATAAGAACAACAGAGGAT 58.951 33.333 0.00 0.00 0.00 3.24
2863 2991 8.515414 CGATCAGAAGTATACTTGATATCACCA 58.485 37.037 22.68 0.00 36.11 4.17
2876 3004 5.825532 TGATATCACCAAAGGTTCATGGAA 58.174 37.500 0.00 0.00 39.12 3.53
2939 3068 7.497595 AGACGTAATATCACATGCCTTTAAGA 58.502 34.615 0.00 0.00 0.00 2.10
2951 3080 5.880054 TGCCTTTAAGATCTGCAACTAAC 57.120 39.130 0.00 0.00 0.00 2.34
2954 3083 5.183140 GCCTTTAAGATCTGCAACTAACCAA 59.817 40.000 0.00 0.00 0.00 3.67
2984 3113 3.923017 AAGTTTGAGCTGTTATGCCAC 57.077 42.857 0.00 0.00 0.00 5.01
2989 3118 3.643199 TGAGCTGTTATGCCACCATTA 57.357 42.857 0.00 0.00 32.85 1.90
2998 3127 8.792633 GCTGTTATGCCACCATTATTATTTCTA 58.207 33.333 0.00 0.00 32.85 2.10
3046 3175 7.872993 TCTCTTATTCAGAAATATAACCAGCCG 59.127 37.037 0.00 0.00 0.00 5.52
3048 3177 2.479837 TCAGAAATATAACCAGCCGCG 58.520 47.619 0.00 0.00 0.00 6.46
3052 3181 1.808411 AATATAACCAGCCGCGGATG 58.192 50.000 35.49 35.49 0.00 3.51
3055 3184 2.996168 ATAACCAGCCGCGGATGCTC 62.996 60.000 36.87 15.13 36.81 4.26
3127 3257 7.481798 GTGAATTTGTACTTATTCGCCTGAAAG 59.518 37.037 16.57 0.00 37.71 2.62
3145 3275 8.072567 GCCTGAAAGACACATATCAATATCAAC 58.927 37.037 0.00 0.00 34.07 3.18
3191 3321 9.596308 ACTTTTGGTCCCTTAACTATTTAATGT 57.404 29.630 0.00 0.00 0.00 2.71
3245 3375 8.365399 GCAATGAGCATACTAATAACAGTACA 57.635 34.615 0.00 0.00 44.79 2.90
3246 3376 8.993121 GCAATGAGCATACTAATAACAGTACAT 58.007 33.333 0.00 0.00 44.79 2.29
3250 3380 9.884636 TGAGCATACTAATAACAGTACATTTGT 57.115 29.630 0.00 0.00 33.94 2.83
3262 3392 4.202245 GTACATTTGTACCCTCAGAGCA 57.798 45.455 9.27 0.00 43.73 4.26
3263 3393 3.340814 ACATTTGTACCCTCAGAGCAG 57.659 47.619 0.00 0.00 0.00 4.24
3264 3394 2.639839 ACATTTGTACCCTCAGAGCAGT 59.360 45.455 0.00 0.00 0.00 4.40
3265 3395 3.073062 ACATTTGTACCCTCAGAGCAGTT 59.927 43.478 0.00 0.00 0.00 3.16
3266 3396 3.857157 TTTGTACCCTCAGAGCAGTTT 57.143 42.857 0.00 0.00 0.00 2.66
3267 3397 3.857157 TTGTACCCTCAGAGCAGTTTT 57.143 42.857 0.00 0.00 0.00 2.43
3268 3398 3.857157 TGTACCCTCAGAGCAGTTTTT 57.143 42.857 0.00 0.00 0.00 1.94
3269 3399 4.967084 TGTACCCTCAGAGCAGTTTTTA 57.033 40.909 0.00 0.00 0.00 1.52
3270 3400 4.638304 TGTACCCTCAGAGCAGTTTTTAC 58.362 43.478 0.00 0.00 0.00 2.01
3271 3401 3.857157 ACCCTCAGAGCAGTTTTTACA 57.143 42.857 0.00 0.00 0.00 2.41
3272 3402 3.477530 ACCCTCAGAGCAGTTTTTACAC 58.522 45.455 0.00 0.00 0.00 2.90
3273 3403 3.118038 ACCCTCAGAGCAGTTTTTACACA 60.118 43.478 0.00 0.00 0.00 3.72
3274 3404 3.882888 CCCTCAGAGCAGTTTTTACACAA 59.117 43.478 0.00 0.00 0.00 3.33
3275 3405 4.338118 CCCTCAGAGCAGTTTTTACACAAA 59.662 41.667 0.00 0.00 0.00 2.83
3276 3406 5.163561 CCCTCAGAGCAGTTTTTACACAAAA 60.164 40.000 0.00 0.00 31.76 2.44
3277 3407 6.329496 CCTCAGAGCAGTTTTTACACAAAAA 58.671 36.000 0.00 0.00 40.47 1.94
3448 3578 8.948631 TTTTACATATTTTGTCCTTTTGCACA 57.051 26.923 0.00 0.00 39.87 4.57
3449 3579 7.938563 TTACATATTTTGTCCTTTTGCACAC 57.061 32.000 0.00 0.00 39.87 3.82
3450 3580 5.911752 ACATATTTTGTCCTTTTGCACACA 58.088 33.333 0.00 0.00 30.89 3.72
3451 3581 6.523840 ACATATTTTGTCCTTTTGCACACAT 58.476 32.000 0.00 0.00 30.89 3.21
3452 3582 6.991531 ACATATTTTGTCCTTTTGCACACATT 59.008 30.769 0.00 0.00 30.89 2.71
3453 3583 5.738118 ATTTTGTCCTTTTGCACACATTG 57.262 34.783 0.00 0.00 0.00 2.82
3487 3617 8.433421 TTTCCAGCGATTTAAGTAATCTAAGG 57.567 34.615 0.00 0.00 40.46 2.69
3488 3618 7.356089 TCCAGCGATTTAAGTAATCTAAGGA 57.644 36.000 0.00 0.00 40.46 3.36
3489 3619 7.208080 TCCAGCGATTTAAGTAATCTAAGGAC 58.792 38.462 0.00 0.00 40.46 3.85
3490 3620 7.069578 TCCAGCGATTTAAGTAATCTAAGGACT 59.930 37.037 0.00 0.00 40.46 3.85
3491 3621 8.358148 CCAGCGATTTAAGTAATCTAAGGACTA 58.642 37.037 0.00 0.00 40.46 2.59
3492 3622 9.915629 CAGCGATTTAAGTAATCTAAGGACTAT 57.084 33.333 0.00 0.00 40.46 2.12
3494 3624 9.356433 GCGATTTAAGTAATCTAAGGACTATCC 57.644 37.037 0.00 0.00 40.46 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.532834 TCCCAAGGTATATCAAAGCCAAC 58.467 43.478 0.00 0.00 0.00 3.77
105 106 2.408565 ACTTCTGGGTTGTCTCCTTGA 58.591 47.619 0.00 0.00 0.00 3.02
108 109 3.953542 AAAACTTCTGGGTTGTCTCCT 57.046 42.857 0.00 0.00 0.00 3.69
132 133 4.461405 CGCTCAACAGAAAGAAATGACTG 58.539 43.478 0.00 0.00 36.58 3.51
390 398 0.527385 CACCGCACAAACCAACAAGG 60.527 55.000 0.00 0.00 45.67 3.61
410 418 6.037062 GCACTACAGCCAAAATTTCTGTTTTT 59.963 34.615 14.17 0.50 40.96 1.94
421 429 2.472695 ATCGAGCACTACAGCCAAAA 57.527 45.000 0.00 0.00 34.23 2.44
564 575 9.524496 TTAAACAGGACAGTCTGTAGTAATCTA 57.476 33.333 5.21 0.00 46.17 1.98
595 606 6.585695 AGACAATGCATCAAGAACAGAATT 57.414 33.333 0.00 0.00 0.00 2.17
617 628 8.451687 TCGATAATTTCATCAAAACAAGCAAG 57.548 30.769 0.00 0.00 0.00 4.01
650 661 7.914427 AACTAGTCATGAACCCATACTATCA 57.086 36.000 0.00 0.00 0.00 2.15
652 663 9.614792 GAAAAACTAGTCATGAACCCATACTAT 57.385 33.333 0.00 0.00 0.00 2.12
705 719 6.810182 GTGCACGGAAAATCTTAAGTAGTAGA 59.190 38.462 0.00 0.00 0.00 2.59
708 722 5.302360 TGTGCACGGAAAATCTTAAGTAGT 58.698 37.500 13.13 0.00 0.00 2.73
729 743 7.438459 GGAATTTGTAGACAGCGACTATAATGT 59.562 37.037 0.00 0.00 0.00 2.71
743 759 2.412325 CGTTGTGGCGGAATTTGTAGAC 60.412 50.000 0.00 0.00 0.00 2.59
765 782 3.487120 AAAACTATACGATGCCCCTCC 57.513 47.619 0.00 0.00 0.00 4.30
839 857 6.548171 TGTTCTTTTCGAAACAACAACTAGG 58.452 36.000 23.17 0.00 32.41 3.02
874 892 0.445436 GCTTGACAAGTGGCGATGAG 59.555 55.000 16.39 0.00 0.00 2.90
892 910 0.524816 TTGCTAGTAGCTGCGTACGC 60.525 55.000 32.49 32.49 42.97 4.42
896 914 2.093973 ACTCATTTGCTAGTAGCTGCGT 60.094 45.455 22.34 11.02 42.97 5.24
897 915 2.544685 ACTCATTTGCTAGTAGCTGCG 58.455 47.619 22.34 10.41 42.97 5.18
923 959 5.932883 GGAGGGAGCGACCTAATAATTAAAG 59.067 44.000 2.01 0.00 42.10 1.85
924 960 5.221783 GGGAGGGAGCGACCTAATAATTAAA 60.222 44.000 2.01 0.00 42.10 1.52
983 1022 5.791336 TTATAGGACTGATAGCACCACAG 57.209 43.478 0.00 0.00 37.62 3.66
1016 1055 2.680312 TGGACATCTGCAGTTAGAGC 57.320 50.000 14.67 0.00 0.00 4.09
1018 1057 3.776969 AGGAATGGACATCTGCAGTTAGA 59.223 43.478 14.67 0.00 0.00 2.10
1021 1060 4.574674 TTAGGAATGGACATCTGCAGTT 57.425 40.909 14.67 1.65 0.00 3.16
1049 1088 7.104939 TGATCCATTTCCCTTAATTTTTGCTG 58.895 34.615 0.00 0.00 0.00 4.41
1053 1092 7.457535 TGGTCTGATCCATTTCCCTTAATTTTT 59.542 33.333 0.00 0.00 31.96 1.94
1168 1210 1.806542 ACGACACTGTTCAATGCCATC 59.193 47.619 0.00 0.00 0.00 3.51
1185 1227 0.035439 GGGGATTCCAAGCTTCACGA 60.035 55.000 4.80 0.00 35.00 4.35
1247 1289 2.683933 GGGGACGGAGGAGAGCAA 60.684 66.667 0.00 0.00 0.00 3.91
1256 1298 3.261315 TTGGATGGAGGGGGACGGA 62.261 63.158 0.00 0.00 0.00 4.69
1321 1363 1.617018 CCTCAGCCGTGAAGATCCCA 61.617 60.000 0.00 0.00 30.14 4.37
1336 1378 1.227943 GCCGGCAGCAATATCCTCA 60.228 57.895 24.80 0.00 42.97 3.86
1424 1484 4.487412 GCATGAGCTGCGGTTGGC 62.487 66.667 0.00 0.00 41.97 4.52
1472 1532 2.039879 AGGAGGCCGACACAAATAAGTT 59.960 45.455 0.00 0.00 0.00 2.66
1477 1537 1.674817 CGTAAGGAGGCCGACACAAAT 60.675 52.381 0.00 0.00 0.00 2.32
1480 1540 2.967397 CGTAAGGAGGCCGACACA 59.033 61.111 0.00 0.00 0.00 3.72
1539 1602 2.024918 GCCATCATGAACGGCGAAT 58.975 52.632 20.20 0.54 35.79 3.34
1615 1678 4.371699 GCACCCATTGCCCCATTA 57.628 55.556 0.00 0.00 46.63 1.90
1624 1687 3.925630 CTCGCTGGTGGCACCCATT 62.926 63.158 32.61 0.00 41.91 3.16
1665 1728 1.129251 CGAACACTTCGCTGCATTCAT 59.871 47.619 0.00 0.00 46.97 2.57
1678 1741 1.153706 CGTTATCCCGGCGAACACT 60.154 57.895 9.30 0.00 0.00 3.55
1765 1828 1.228657 GGTCCAACACCGAGCACTTC 61.229 60.000 0.00 0.00 34.56 3.01
1813 1876 1.675641 AAGCTCAACCGTGCCATCC 60.676 57.895 0.00 0.00 31.86 3.51
1864 1927 3.305539 CCTTAAGCAAAACAGCATCAGCA 60.306 43.478 0.00 0.00 45.49 4.41
1926 1989 6.563010 CGAAGAAAGTCGGAATTAGATGATGC 60.563 42.308 0.00 0.00 37.37 3.91
1945 2021 6.754675 TGCGACACTAATTATGAATCGAAGAA 59.245 34.615 10.83 0.00 43.58 2.52
1949 2025 5.588240 ACTGCGACACTAATTATGAATCGA 58.412 37.500 10.83 0.00 0.00 3.59
1961 2037 4.748102 CCTTAGTTCAAAACTGCGACACTA 59.252 41.667 2.65 0.00 42.84 2.74
1989 2070 3.303791 GCCAATCGGACGAACCATAATTC 60.304 47.826 0.00 0.00 38.90 2.17
1991 2072 2.218603 GCCAATCGGACGAACCATAAT 58.781 47.619 0.00 0.00 38.90 1.28
2001 2082 1.693083 GCACGTACTGCCAATCGGAC 61.693 60.000 6.14 0.00 40.42 4.79
2265 2370 0.240945 GCATTCCCAAGACGTTGTGG 59.759 55.000 10.69 10.69 34.44 4.17
2330 2435 4.786507 GCAGCACATGCGATGAATAATAA 58.213 39.130 2.57 0.00 46.99 1.40
2349 2460 2.161855 TGTGGGAAATGTAAGCAGCAG 58.838 47.619 0.00 0.00 0.00 4.24
2352 2463 6.263842 ACATATGATGTGGGAAATGTAAGCAG 59.736 38.462 10.38 0.00 43.01 4.24
2394 2505 3.952323 AGGCTAGCAGACGATACAAACTA 59.048 43.478 18.24 0.00 0.00 2.24
2404 2515 3.126831 CTGGAAATAAGGCTAGCAGACG 58.873 50.000 18.24 0.00 0.00 4.18
2416 2527 5.830991 GGGGCATACACATTACTGGAAATAA 59.169 40.000 0.00 0.00 0.00 1.40
2441 2552 7.853437 CACAACCAAATGCGAACGATAATATTA 59.147 33.333 0.00 0.00 0.00 0.98
2445 2556 4.083003 ACACAACCAAATGCGAACGATAAT 60.083 37.500 0.00 0.00 0.00 1.28
2453 2564 1.614996 ATGGACACAACCAAATGCGA 58.385 45.000 0.00 0.00 43.47 5.10
2455 2566 4.519540 AACTATGGACACAACCAAATGC 57.480 40.909 0.00 0.00 43.47 3.56
2556 2679 3.540314 ACAAGTAACCGTGGTTGTACA 57.460 42.857 14.45 0.00 38.92 2.90
2564 2687 8.488651 AAAATAGAGGATAACAAGTAACCGTG 57.511 34.615 0.00 0.00 29.89 4.94
2637 2760 6.006449 GCAACCTAGGATTTGTCCATATGAT 58.994 40.000 17.98 0.00 0.00 2.45
2638 2761 5.132648 AGCAACCTAGGATTTGTCCATATGA 59.867 40.000 17.98 0.00 0.00 2.15
2640 2763 5.380043 CAGCAACCTAGGATTTGTCCATAT 58.620 41.667 17.98 0.00 0.00 1.78
2641 2764 4.780815 CAGCAACCTAGGATTTGTCCATA 58.219 43.478 17.98 0.00 0.00 2.74
2642 2765 3.624777 CAGCAACCTAGGATTTGTCCAT 58.375 45.455 17.98 0.00 0.00 3.41
2643 2766 2.879756 GCAGCAACCTAGGATTTGTCCA 60.880 50.000 17.98 0.00 0.00 4.02
2644 2767 1.745653 GCAGCAACCTAGGATTTGTCC 59.254 52.381 17.98 0.00 0.00 4.02
2659 2784 2.753009 ATCAAAGACGCCCTGCAGCA 62.753 55.000 8.66 0.00 0.00 4.41
2660 2785 1.589716 AATCAAAGACGCCCTGCAGC 61.590 55.000 8.66 0.00 0.00 5.25
2661 2786 0.883833 AAATCAAAGACGCCCTGCAG 59.116 50.000 6.78 6.78 0.00 4.41
2695 2820 2.224426 TGTGTGTTTCCTATTCCAGCGT 60.224 45.455 0.00 0.00 0.00 5.07
2699 2824 7.178573 TCCAATTATGTGTGTTTCCTATTCCA 58.821 34.615 0.00 0.00 0.00 3.53
2711 2836 5.045215 GGCATGACATTCCAATTATGTGTG 58.955 41.667 0.00 0.00 36.41 3.82
2718 2843 4.858850 TGAGTAGGCATGACATTCCAATT 58.141 39.130 0.00 0.00 0.00 2.32
2744 2869 9.979578 ATGCTAAATCAAACAAACACAAATAGA 57.020 25.926 0.00 0.00 0.00 1.98
2809 2937 8.873215 ACTACTTGAAACATCTTATACCATCG 57.127 34.615 0.00 0.00 0.00 3.84
2818 2946 8.304596 TCTGATCGTAACTACTTGAAACATCTT 58.695 33.333 0.00 0.00 0.00 2.40
2837 2965 8.515414 TGGTGATATCAAGTATACTTCTGATCG 58.485 37.037 18.96 7.47 33.11 3.69
2861 2989 6.054295 TCAAATGTTTTCCATGAACCTTTGG 58.946 36.000 18.04 7.48 40.19 3.28
2863 2991 8.750515 AATTCAAATGTTTTCCATGAACCTTT 57.249 26.923 0.00 0.00 32.82 3.11
2917 3046 8.438513 CAGATCTTAAAGGCATGTGATATTACG 58.561 37.037 0.00 0.00 0.00 3.18
2925 3054 4.157289 AGTTGCAGATCTTAAAGGCATGTG 59.843 41.667 5.60 0.00 34.03 3.21
2929 3058 4.700213 GGTTAGTTGCAGATCTTAAAGGCA 59.300 41.667 0.77 0.77 0.00 4.75
2930 3059 4.700213 TGGTTAGTTGCAGATCTTAAAGGC 59.300 41.667 0.00 0.00 0.00 4.35
2931 3060 6.655003 TCTTGGTTAGTTGCAGATCTTAAAGG 59.345 38.462 0.00 0.00 0.00 3.11
2951 3080 5.979517 CAGCTCAAACTTTTAAACCTCTTGG 59.020 40.000 0.00 0.00 39.83 3.61
2954 3083 6.775594 AACAGCTCAAACTTTTAAACCTCT 57.224 33.333 0.00 0.00 0.00 3.69
2960 3089 6.212955 GTGGCATAACAGCTCAAACTTTTAA 58.787 36.000 0.00 0.00 34.17 1.52
2968 3097 2.512692 ATGGTGGCATAACAGCTCAA 57.487 45.000 0.00 0.00 39.48 3.02
3109 3239 4.927425 TGTGTCTTTCAGGCGAATAAGTAC 59.073 41.667 0.00 0.00 0.00 2.73
3110 3240 5.142061 TGTGTCTTTCAGGCGAATAAGTA 57.858 39.130 0.00 0.00 0.00 2.24
3165 3295 9.596308 ACATTAAATAGTTAAGGGACCAAAAGT 57.404 29.630 11.45 0.00 35.72 2.66
3217 3347 9.559732 TACTGTTATTAGTATGCTCATTGCAAT 57.440 29.630 5.99 5.99 42.42 3.56
3218 3348 8.826710 GTACTGTTATTAGTATGCTCATTGCAA 58.173 33.333 0.00 0.00 42.42 4.08
3219 3349 7.984617 TGTACTGTTATTAGTATGCTCATTGCA 59.015 33.333 0.00 0.00 42.89 4.08
3220 3350 8.365399 TGTACTGTTATTAGTATGCTCATTGC 57.635 34.615 0.00 0.00 35.75 3.56
3224 3354 9.884636 ACAAATGTACTGTTATTAGTATGCTCA 57.115 29.630 0.00 0.00 35.75 4.26
3242 3372 3.838317 ACTGCTCTGAGGGTACAAATGTA 59.162 43.478 6.83 0.00 0.00 2.29
3243 3373 2.639839 ACTGCTCTGAGGGTACAAATGT 59.360 45.455 6.83 0.00 0.00 2.71
3244 3374 3.340814 ACTGCTCTGAGGGTACAAATG 57.659 47.619 6.83 0.00 0.00 2.32
3245 3375 4.373156 AAACTGCTCTGAGGGTACAAAT 57.627 40.909 6.83 0.00 0.00 2.32
3246 3376 3.857157 AAACTGCTCTGAGGGTACAAA 57.143 42.857 6.83 0.00 0.00 2.83
3247 3377 3.857157 AAAACTGCTCTGAGGGTACAA 57.143 42.857 6.83 0.00 0.00 2.41
3248 3378 3.857157 AAAAACTGCTCTGAGGGTACA 57.143 42.857 6.83 0.00 0.00 2.90
3249 3379 4.451435 GTGTAAAAACTGCTCTGAGGGTAC 59.549 45.833 6.83 0.00 0.00 3.34
3250 3380 4.101898 TGTGTAAAAACTGCTCTGAGGGTA 59.898 41.667 6.83 0.00 0.00 3.69
3251 3381 3.118038 TGTGTAAAAACTGCTCTGAGGGT 60.118 43.478 6.83 0.00 0.00 4.34
3252 3382 3.476552 TGTGTAAAAACTGCTCTGAGGG 58.523 45.455 6.83 0.00 0.00 4.30
3253 3383 5.499139 TTTGTGTAAAAACTGCTCTGAGG 57.501 39.130 6.83 0.00 0.00 3.86
3422 3552 9.553064 TGTGCAAAAGGACAAAATATGTAAAAT 57.447 25.926 0.00 0.00 44.12 1.82
3423 3553 8.821894 GTGTGCAAAAGGACAAAATATGTAAAA 58.178 29.630 0.00 0.00 44.12 1.52
3424 3554 7.981789 TGTGTGCAAAAGGACAAAATATGTAAA 59.018 29.630 0.00 0.00 44.12 2.01
3425 3555 7.492524 TGTGTGCAAAAGGACAAAATATGTAA 58.507 30.769 0.00 0.00 44.12 2.41
3426 3556 7.043961 TGTGTGCAAAAGGACAAAATATGTA 57.956 32.000 0.00 0.00 44.12 2.29
3428 3558 7.292292 CAATGTGTGCAAAAGGACAAAATATG 58.708 34.615 0.00 0.00 0.00 1.78
3429 3559 7.424227 CAATGTGTGCAAAAGGACAAAATAT 57.576 32.000 0.00 0.00 0.00 1.28
3430 3560 6.841443 CAATGTGTGCAAAAGGACAAAATA 57.159 33.333 0.00 0.00 0.00 1.40
3431 3561 5.738118 CAATGTGTGCAAAAGGACAAAAT 57.262 34.783 0.00 0.00 0.00 1.82
3468 3598 9.356433 GGATAGTCCTTAGATTACTTAAATCGC 57.644 37.037 0.00 0.00 40.28 4.58


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

AutoCloner maintained by Alex Coulton.