Multiple sequence alignment - TraesCS4D01G256000

Loading Multiple Alignment...

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 TraesCS4D01G256000 chr4D 100.000 4377 0 0 1 4377 425223394 425227770 0.000000e+00 8083.0
1 TraesCS4D01G256000 chr4D 88.333 420 31 5 1030 1449 425212331 425212732 5.090000e-134 488.0
2 TraesCS4D01G256000 chr4A 94.488 2649 111 19 1753 4377 39544521 39541884 0.000000e+00 4050.0
3 TraesCS4D01G256000 chr4A 93.273 773 46 1 983 1755 39545353 39544587 0.000000e+00 1134.0
4 TraesCS4D01G256000 chr4B 94.345 2635 88 22 1758 4377 520888118 520890706 0.000000e+00 3984.0
5 TraesCS4D01G256000 chr4B 94.545 880 40 3 878 1755 520887176 520888049 0.000000e+00 1352.0
6 TraesCS4D01G256000 chr4B 88.507 844 68 12 2 826 520886332 520887165 0.000000e+00 994.0
7 TraesCS4D01G256000 chr3D 78.378 148 22 5 162 307 301778634 301778773 2.170000e-13 87.9
8 TraesCS4D01G256000 chr3B 77.703 148 23 5 162 307 419156897 419156758 1.010000e-11 82.4


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 TraesCS4D01G256000 chr4D 425223394 425227770 4376 False 8083 8083 100.000000 1 4377 1 chr4D.!!$F2 4376
1 TraesCS4D01G256000 chr4A 39541884 39545353 3469 True 2592 4050 93.880500 983 4377 2 chr4A.!!$R1 3394
2 TraesCS4D01G256000 chr4B 520886332 520890706 4374 False 2110 3984 92.465667 2 4377 3 chr4B.!!$F1 4375

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
845 864 0.390209 GCAAGCCCATGATTTTGCGT 60.390 50.0 10.69 0.0 36.89 5.24 F
1663 1683 0.398318 AAGCAGGACAGGGAACTCAC 59.602 55.0 0.00 0.0 40.21 3.51 F
2941 3048 0.467804 GATCCCAGGCTGAGTTCTCC 59.532 60.0 17.94 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2563 2670 0.868406 CGAGCAGGTGTGGAAAGTTC 59.132 55.0 0.00 0.0 0.0 3.01 R
3201 3312 1.189524 AAGAATGGTCCCGTCGGTGA 61.190 55.0 11.06 4.4 0.0 4.02 R
3948 4073 0.829602 TGCAGGAAAAATGGCCGGAA 60.830 50.0 5.05 0.0 0.0 4.30 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
27 28 5.616270 ACCACCAATGTGAATTTTTAACCC 58.384 37.500 0.00 0.00 45.76 4.11
30 31 6.714356 CCACCAATGTGAATTTTTAACCCATT 59.286 34.615 0.00 0.00 45.76 3.16
55 56 3.894427 TGGCCATTATTTCACACACTTGT 59.106 39.130 0.00 0.00 35.84 3.16
60 61 6.801862 GCCATTATTTCACACACTTGTAGTTC 59.198 38.462 0.00 0.00 33.30 3.01
64 65 9.730420 ATTATTTCACACACTTGTAGTTCAAAC 57.270 29.630 0.00 0.00 35.48 2.93
65 66 5.554822 TTCACACACTTGTAGTTCAAACC 57.445 39.130 0.00 0.00 35.48 3.27
72 82 6.692681 CACACTTGTAGTTCAAACCTTCATTG 59.307 38.462 0.00 0.00 35.48 2.82
77 87 6.446318 TGTAGTTCAAACCTTCATTGAATGC 58.554 36.000 0.00 1.09 45.50 3.56
111 121 8.469309 ACACTTAATGGCTTGAATATAGCAAT 57.531 30.769 0.00 0.00 40.42 3.56
121 131 7.041107 GCTTGAATATAGCAATCAAACCCAAA 58.959 34.615 0.00 0.00 38.51 3.28
178 189 7.280876 TGGTGTATGATCAAGTTGAAAGCTATC 59.719 37.037 10.14 2.31 0.00 2.08
209 220 1.269778 GCTGAAACTTGAAAGCCCCAC 60.270 52.381 0.00 0.00 0.00 4.61
276 287 9.276590 GGGAATTTGAAAGTGAAAAGATGAAAT 57.723 29.630 0.00 0.00 0.00 2.17
288 299 1.284785 AGATGAAATTGGGGAGGCGAA 59.715 47.619 0.00 0.00 0.00 4.70
343 354 6.410540 ACCAATAGAGAAGATTGTCCACTTC 58.589 40.000 0.00 0.00 41.64 3.01
347 358 8.786898 CAATAGAGAAGATTGTCCACTTCAAAA 58.213 33.333 0.00 0.00 43.13 2.44
348 359 6.874288 AGAGAAGATTGTCCACTTCAAAAG 57.126 37.500 0.00 0.00 43.13 2.27
349 360 6.595682 AGAGAAGATTGTCCACTTCAAAAGA 58.404 36.000 0.00 0.00 43.13 2.52
352 363 8.066612 AGAAGATTGTCCACTTCAAAAGAAAA 57.933 30.769 0.00 0.00 43.13 2.29
368 379 7.339212 TCAAAAGAAAAACAGAGAAGATGGTCA 59.661 33.333 0.00 0.00 0.00 4.02
370 381 5.066593 AGAAAAACAGAGAAGATGGTCACC 58.933 41.667 0.00 0.00 0.00 4.02
392 411 0.405973 AAAGGAAGGGAGAAGGTGGC 59.594 55.000 0.00 0.00 0.00 5.01
395 414 3.978571 GAAGGGAGAAGGTGGCGGC 62.979 68.421 0.00 0.00 0.00 6.53
446 465 2.434185 GAGGATGCAACGGCGACA 60.434 61.111 16.62 9.40 45.35 4.35
451 470 3.620419 ATGCAACGGCGACATGGGA 62.620 57.895 16.62 0.00 45.35 4.37
461 480 2.627945 GCGACATGGGAGTATGAACAA 58.372 47.619 0.00 0.00 0.00 2.83
516 535 0.991920 GGGGGAAGGAAGACACATGA 59.008 55.000 0.00 0.00 0.00 3.07
524 543 4.013267 AGGAAGACACATGAAGGAACAG 57.987 45.455 0.00 0.00 0.00 3.16
526 545 3.748568 GGAAGACACATGAAGGAACAGAC 59.251 47.826 0.00 0.00 0.00 3.51
527 546 3.032017 AGACACATGAAGGAACAGACG 57.968 47.619 0.00 0.00 0.00 4.18
529 548 2.731976 GACACATGAAGGAACAGACGAC 59.268 50.000 0.00 0.00 0.00 4.34
578 597 8.425703 TGTTTAAGGACTTAAATGAAAAAGGGG 58.574 33.333 17.33 0.00 44.01 4.79
582 601 7.303182 AGGACTTAAATGAAAAAGGGGAAAG 57.697 36.000 0.00 0.00 0.00 2.62
584 603 5.538118 ACTTAAATGAAAAAGGGGAAAGCG 58.462 37.500 0.00 0.00 0.00 4.68
591 610 0.479378 AAAGGGGAAAGCGGTAACCA 59.521 50.000 11.11 0.00 0.00 3.67
604 623 6.096673 AGCGGTAACCAAGAAAATGAAAAT 57.903 33.333 0.00 0.00 0.00 1.82
605 624 6.156519 AGCGGTAACCAAGAAAATGAAAATC 58.843 36.000 0.00 0.00 0.00 2.17
606 625 5.060446 GCGGTAACCAAGAAAATGAAAATCG 59.940 40.000 0.00 0.00 0.00 3.34
610 629 9.036671 GGTAACCAAGAAAATGAAAATCGAAAA 57.963 29.630 0.00 0.00 0.00 2.29
613 632 8.130307 ACCAAGAAAATGAAAATCGAAAACTG 57.870 30.769 0.00 0.00 0.00 3.16
627 646 2.331019 AAACTGGGAAACACGCACGC 62.331 55.000 0.00 0.00 37.33 5.34
629 648 2.954753 CTGGGAAACACGCACGCTC 61.955 63.158 0.00 0.00 37.33 5.03
643 662 1.248785 ACGCTCGCCTCTCCTTACAA 61.249 55.000 0.00 0.00 0.00 2.41
646 665 1.134670 GCTCGCCTCTCCTTACAACAT 60.135 52.381 0.00 0.00 0.00 2.71
681 700 1.449601 GCGGCGAAAGAATCCCTCA 60.450 57.895 12.98 0.00 0.00 3.86
701 720 1.958715 CCCATGACAACGCGACACA 60.959 57.895 15.93 7.84 0.00 3.72
760 779 8.432805 CCACAAGATATCCCTTAACTAGTGATT 58.567 37.037 0.00 0.00 0.00 2.57
761 780 9.838339 CACAAGATATCCCTTAACTAGTGATTT 57.162 33.333 0.00 0.00 0.00 2.17
766 785 4.901868 TCCCTTAACTAGTGATTTTGCGT 58.098 39.130 0.00 0.00 0.00 5.24
769 788 5.640357 CCCTTAACTAGTGATTTTGCGTGTA 59.360 40.000 0.00 0.00 0.00 2.90
770 789 6.183360 CCCTTAACTAGTGATTTTGCGTGTAG 60.183 42.308 0.00 0.00 0.00 2.74
772 791 5.840940 AACTAGTGATTTTGCGTGTAGAC 57.159 39.130 0.00 0.00 0.00 2.59
773 792 5.135508 ACTAGTGATTTTGCGTGTAGACT 57.864 39.130 0.00 0.00 0.00 3.24
774 793 4.923871 ACTAGTGATTTTGCGTGTAGACTG 59.076 41.667 0.00 0.00 0.00 3.51
777 796 4.814234 AGTGATTTTGCGTGTAGACTGAAA 59.186 37.500 0.00 0.00 0.00 2.69
778 797 5.295787 AGTGATTTTGCGTGTAGACTGAAAA 59.704 36.000 0.00 0.00 0.00 2.29
779 798 5.395486 GTGATTTTGCGTGTAGACTGAAAAC 59.605 40.000 0.00 0.00 0.00 2.43
780 799 4.948608 TTTTGCGTGTAGACTGAAAACA 57.051 36.364 0.00 0.00 0.00 2.83
781 800 4.948608 TTTGCGTGTAGACTGAAAACAA 57.051 36.364 0.00 0.00 0.00 2.83
782 801 4.948608 TTGCGTGTAGACTGAAAACAAA 57.051 36.364 0.00 0.00 0.00 2.83
783 802 4.948608 TGCGTGTAGACTGAAAACAAAA 57.051 36.364 0.00 0.00 0.00 2.44
784 803 5.493133 TGCGTGTAGACTGAAAACAAAAT 57.507 34.783 0.00 0.00 0.00 1.82
785 804 5.507077 TGCGTGTAGACTGAAAACAAAATC 58.493 37.500 0.00 0.00 0.00 2.17
826 845 2.870411 GGAATTGACGATAACCTTCCCG 59.130 50.000 0.00 0.00 0.00 5.14
829 848 0.609151 TGACGATAACCTTCCCGCAA 59.391 50.000 0.00 0.00 0.00 4.85
830 849 1.287425 GACGATAACCTTCCCGCAAG 58.713 55.000 0.00 0.00 0.00 4.01
831 850 0.743345 ACGATAACCTTCCCGCAAGC 60.743 55.000 0.00 0.00 0.00 4.01
832 851 1.436983 CGATAACCTTCCCGCAAGCC 61.437 60.000 0.00 0.00 0.00 4.35
833 852 1.076995 ATAACCTTCCCGCAAGCCC 60.077 57.895 0.00 0.00 0.00 5.19
835 854 1.858739 TAACCTTCCCGCAAGCCCAT 61.859 55.000 0.00 0.00 0.00 4.00
836 855 3.142838 CCTTCCCGCAAGCCCATG 61.143 66.667 0.00 0.00 0.00 3.66
837 856 2.045045 CTTCCCGCAAGCCCATGA 60.045 61.111 0.00 0.00 0.00 3.07
838 857 1.454479 CTTCCCGCAAGCCCATGAT 60.454 57.895 0.00 0.00 0.00 2.45
839 858 1.000233 TTCCCGCAAGCCCATGATT 60.000 52.632 0.00 0.00 0.00 2.57
840 859 0.614415 TTCCCGCAAGCCCATGATTT 60.614 50.000 0.00 0.00 0.00 2.17
841 860 0.614415 TCCCGCAAGCCCATGATTTT 60.614 50.000 0.00 0.00 0.00 1.82
842 861 0.460635 CCCGCAAGCCCATGATTTTG 60.461 55.000 0.00 0.00 0.00 2.44
843 862 1.085501 CCGCAAGCCCATGATTTTGC 61.086 55.000 14.24 14.24 41.76 3.68
844 863 2.375981 GCAAGCCCATGATTTTGCG 58.624 52.632 10.69 0.00 36.89 4.85
845 864 0.390209 GCAAGCCCATGATTTTGCGT 60.390 50.000 10.69 0.00 36.89 5.24
846 865 1.352114 CAAGCCCATGATTTTGCGTG 58.648 50.000 0.00 0.00 0.00 5.34
847 866 0.968405 AAGCCCATGATTTTGCGTGT 59.032 45.000 0.00 0.00 0.00 4.49
848 867 1.832883 AGCCCATGATTTTGCGTGTA 58.167 45.000 0.00 0.00 0.00 2.90
849 868 1.745087 AGCCCATGATTTTGCGTGTAG 59.255 47.619 0.00 0.00 0.00 2.74
850 869 1.742831 GCCCATGATTTTGCGTGTAGA 59.257 47.619 0.00 0.00 0.00 2.59
851 870 2.477863 GCCCATGATTTTGCGTGTAGAC 60.478 50.000 0.00 0.00 0.00 2.59
852 871 3.009723 CCCATGATTTTGCGTGTAGACT 58.990 45.455 0.00 0.00 0.00 3.24
853 872 3.181507 CCCATGATTTTGCGTGTAGACTG 60.182 47.826 0.00 0.00 0.00 3.51
854 873 3.684305 CCATGATTTTGCGTGTAGACTGA 59.316 43.478 0.00 0.00 0.00 3.41
855 874 4.154015 CCATGATTTTGCGTGTAGACTGAA 59.846 41.667 0.00 0.00 0.00 3.02
856 875 5.334802 CCATGATTTTGCGTGTAGACTGAAA 60.335 40.000 0.00 0.00 0.00 2.69
857 876 5.743026 TGATTTTGCGTGTAGACTGAAAA 57.257 34.783 0.00 0.00 0.00 2.29
858 877 6.125327 TGATTTTGCGTGTAGACTGAAAAA 57.875 33.333 4.19 4.19 0.00 1.94
971 990 2.631428 CCACACCGTTTCTGCGTG 59.369 61.111 0.00 0.00 0.00 5.34
1136 1155 2.015726 TCTCCCTCTCCCTCTCCCC 61.016 68.421 0.00 0.00 0.00 4.81
1137 1156 3.036959 TCCCTCTCCCTCTCCCCC 61.037 72.222 0.00 0.00 0.00 5.40
1216 1235 2.103934 CTCTCTCGCCGCTTCCTG 59.896 66.667 0.00 0.00 0.00 3.86
1379 1398 1.134965 CCCTCTTTACTGGCTCTGTCG 60.135 57.143 0.00 0.00 0.00 4.35
1386 1405 1.185618 ACTGGCTCTGTCGGTAGCAA 61.186 55.000 0.00 0.00 40.61 3.91
1503 1522 8.084214 GCATTTTGCGTTTATTGATCAATTTG 57.916 30.769 25.26 13.65 31.71 2.32
1570 1590 1.547372 CCATTTGCTGCCAGCTTACTT 59.453 47.619 18.96 0.00 42.97 2.24
1663 1683 0.398318 AAGCAGGACAGGGAACTCAC 59.602 55.000 0.00 0.00 40.21 3.51
1708 1728 5.643777 GGGTGATGCATAGGTGTATTGTATC 59.356 44.000 0.00 0.00 30.30 2.24
1718 1739 9.371136 CATAGGTGTATTGTATCGCATAATCTT 57.629 33.333 0.00 0.00 0.00 2.40
1735 1756 8.668353 GCATAATCTTCATATCTTGCGGAATTA 58.332 33.333 0.00 0.00 0.00 1.40
1737 1758 9.725019 ATAATCTTCATATCTTGCGGAATTACA 57.275 29.630 0.00 0.00 0.00 2.41
1755 1776 8.078596 GGAATTACAATCTTGGAAGATGTATGC 58.921 37.037 2.62 0.00 44.67 3.14
1756 1777 8.757982 AATTACAATCTTGGAAGATGTATGCT 57.242 30.769 2.62 0.00 44.67 3.79
1757 1778 8.757982 ATTACAATCTTGGAAGATGTATGCTT 57.242 30.769 2.62 0.00 44.67 3.91
1787 1879 8.657387 TTATATAGGCTTAGCTTGAGATCTGT 57.343 34.615 0.00 0.00 0.00 3.41
1806 1898 9.926158 AGATCTGTACATGCTTTGATAAGATAG 57.074 33.333 0.00 0.00 32.92 2.08
1821 1913 3.644884 AGATAGCCTGTAACGGATTCG 57.355 47.619 0.00 0.00 43.02 3.34
1947 2039 1.135689 GCAAAACTACTGGGACATGCG 60.136 52.381 0.00 0.00 38.20 4.73
1971 2063 9.649024 GCGATATTATAGACTTACCGATAACTC 57.351 37.037 0.00 0.00 0.00 3.01
1978 2070 6.439675 AGACTTACCGATAACTCTTCTGTC 57.560 41.667 0.00 0.00 0.00 3.51
2103 2195 8.008513 TGACTACCACTTAATCTATCTGGAAC 57.991 38.462 0.00 0.00 0.00 3.62
2121 2213 9.965902 ATCTGGAACATCAGTAGAAATTAGTTT 57.034 29.630 0.00 0.00 38.20 2.66
2122 2214 9.219603 TCTGGAACATCAGTAGAAATTAGTTTG 57.780 33.333 0.00 0.00 38.20 2.93
2123 2215 8.918202 TGGAACATCAGTAGAAATTAGTTTGT 57.082 30.769 0.00 0.00 0.00 2.83
2124 2216 9.349713 TGGAACATCAGTAGAAATTAGTTTGTT 57.650 29.630 0.00 0.00 0.00 2.83
2125 2217 9.827411 GGAACATCAGTAGAAATTAGTTTGTTC 57.173 33.333 0.00 0.00 0.00 3.18
2166 2270 2.978978 TCCTGAAGATTTCCCTGTCACA 59.021 45.455 0.00 0.00 0.00 3.58
2342 2446 5.070001 TCCGGCCTCTTGGATAAATTATTG 58.930 41.667 0.00 0.00 34.57 1.90
2513 2620 6.151312 CCTATGCGTATAGTGTCAGATTACCT 59.849 42.308 17.72 0.00 35.51 3.08
2563 2670 7.177407 GCACAATCTGCAACATTTTATGATTG 58.823 34.615 14.46 14.46 46.29 2.67
2575 2682 8.816640 ACATTTTATGATTGAACTTTCCACAC 57.183 30.769 0.00 0.00 0.00 3.82
2601 2708 1.264288 CGGTTCTTCACAGAAACCAGC 59.736 52.381 4.56 0.00 43.10 4.85
2722 2829 2.774234 TGGCCATTTGGGTTCTTGAAAA 59.226 40.909 0.00 0.00 39.65 2.29
2755 2862 3.469008 AGAACACTTCATCGTTGTGGA 57.531 42.857 0.00 0.00 36.16 4.02
2756 2863 3.131396 AGAACACTTCATCGTTGTGGAC 58.869 45.455 0.00 0.00 36.16 4.02
2757 2864 2.910688 ACACTTCATCGTTGTGGACT 57.089 45.000 0.00 0.00 36.16 3.85
2758 2865 3.194005 ACACTTCATCGTTGTGGACTT 57.806 42.857 0.00 0.00 36.16 3.01
2759 2866 2.872245 ACACTTCATCGTTGTGGACTTG 59.128 45.455 0.00 0.00 36.16 3.16
2760 2867 2.872245 CACTTCATCGTTGTGGACTTGT 59.128 45.455 0.00 0.00 0.00 3.16
2761 2868 2.872245 ACTTCATCGTTGTGGACTTGTG 59.128 45.455 0.00 0.00 0.00 3.33
2762 2869 1.877637 TCATCGTTGTGGACTTGTGG 58.122 50.000 0.00 0.00 0.00 4.17
2833 2940 5.079406 CGATCACCTTTTTGTGTTATGTCG 58.921 41.667 0.00 0.00 37.51 4.35
2893 3000 8.506168 TGTTAAACTGACTTCATTATGATCCC 57.494 34.615 0.00 0.00 0.00 3.85
2941 3048 0.467804 GATCCCAGGCTGAGTTCTCC 59.532 60.000 17.94 0.00 0.00 3.71
3013 3120 5.437263 ACGAGCAACTTTGTAATGTTTACG 58.563 37.500 0.00 0.00 0.00 3.18
3025 3132 1.739196 GTTTACGCGGTGGTCCCTC 60.739 63.158 12.47 0.00 0.00 4.30
3084 3192 4.894784 TCTGTTGTCACTGGAAAGATACC 58.105 43.478 0.00 0.00 0.00 2.73
3085 3193 4.346709 TCTGTTGTCACTGGAAAGATACCA 59.653 41.667 0.00 0.00 35.96 3.25
3094 3202 2.846206 TGGAAAGATACCATCTGCAGGT 59.154 45.455 15.13 2.68 40.13 4.00
3111 3219 3.820557 CAGGTCAAAAAGAGGAGAACCA 58.179 45.455 0.00 0.00 38.94 3.67
3201 3312 6.646267 TGACTTTACAGAATATTAGGCCGTT 58.354 36.000 0.00 0.00 0.00 4.44
3331 3442 2.505982 CTGGATTGCCCGGATCGT 59.494 61.111 0.73 0.00 44.44 3.73
3429 3540 4.499019 CGCCAGTAACAAATTTGAACCACT 60.499 41.667 24.64 16.23 0.00 4.00
3454 3565 0.846693 ATGGGCAATACCAGGAGGAC 59.153 55.000 0.00 0.00 45.20 3.85
3522 3633 2.111613 CTCCTCCATCCTCTATCCCTGT 59.888 54.545 0.00 0.00 0.00 4.00
3660 3782 5.071250 TGGGTGAAGTTGTATCAGTTACACT 59.929 40.000 0.00 0.00 40.53 3.55
3679 3803 6.942532 ACACTGATTTACTGCTTTCTGAAA 57.057 33.333 2.44 2.44 0.00 2.69
3687 3811 6.560253 TTACTGCTTTCTGAAATCTGAACC 57.440 37.500 14.89 0.00 34.31 3.62
3828 3953 1.000843 GGAAAAAGAGGCGGCAAATGT 59.999 47.619 13.08 0.00 0.00 2.71
3948 4073 1.603739 GGCCACCTTCCTCGCTTTT 60.604 57.895 0.00 0.00 0.00 2.27
3949 4074 1.179174 GGCCACCTTCCTCGCTTTTT 61.179 55.000 0.00 0.00 0.00 1.94
4086 4211 1.586028 GTTGCATCACCCGTTGCAT 59.414 52.632 0.00 0.00 44.99 3.96
4112 4237 4.551702 TGCACTGCCTGTCTTTATCTTA 57.448 40.909 0.00 0.00 0.00 2.10
4145 4270 1.609072 GGTCTCAAGGAAGCAAACCAC 59.391 52.381 0.00 0.00 0.00 4.16
4169 4294 2.972505 CAACGCCGGTGCTGAAGT 60.973 61.111 16.69 0.00 34.43 3.01
4171 4303 2.542907 AACGCCGGTGCTGAAGTTG 61.543 57.895 16.69 0.00 34.43 3.16
4174 4306 1.282875 GCCGGTGCTGAAGTTGAAC 59.717 57.895 1.90 0.00 33.53 3.18
4194 4326 1.671261 CCGTCTCACCTTCTGAGCTTG 60.671 57.143 0.00 0.00 45.64 4.01
4195 4327 1.671261 CGTCTCACCTTCTGAGCTTGG 60.671 57.143 0.00 0.00 45.64 3.61
4196 4328 1.620819 GTCTCACCTTCTGAGCTTGGA 59.379 52.381 0.00 0.00 45.64 3.53
4218 4354 2.032528 TTGCAAGCGGTGGAGAGG 59.967 61.111 0.00 0.00 0.00 3.69
4263 4399 2.856032 CTGGCTTTGCTCGTCGTG 59.144 61.111 0.00 0.00 0.00 4.35
4266 4402 4.430423 GCTTTGCTCGTCGTGGCG 62.430 66.667 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.170828 GGTTAAAAATTCACATTGGTGGTCTTC 59.829 37.037 0.00 0.00 45.32 2.87
13 14 5.411361 GGCCAGAAATGGGTTAAAAATTCAC 59.589 40.000 0.00 0.00 0.00 3.18
21 22 6.441924 TGAAATAATGGCCAGAAATGGGTTAA 59.558 34.615 13.05 0.00 0.00 2.01
27 28 5.577945 GTGTGTGAAATAATGGCCAGAAATG 59.422 40.000 13.05 0.00 0.00 2.32
30 31 4.406456 AGTGTGTGAAATAATGGCCAGAA 58.594 39.130 13.05 0.91 0.00 3.02
55 56 5.774690 AGGCATTCAATGAAGGTTTGAACTA 59.225 36.000 9.43 0.00 43.65 2.24
64 65 9.071276 AGTGTATTTATAGGCATTCAATGAAGG 57.929 33.333 0.00 2.96 0.00 3.46
72 82 9.014297 AGCCATTAAGTGTATTTATAGGCATTC 57.986 33.333 0.00 0.00 36.27 2.67
91 101 8.359642 GGTTTGATTGCTATATTCAAGCCATTA 58.640 33.333 12.54 0.00 43.62 1.90
134 145 5.242434 ACACCATTACATGTTACGTGTCAT 58.758 37.500 13.91 6.03 29.83 3.06
143 154 8.461222 CAACTTGATCATACACCATTACATGTT 58.539 33.333 2.30 0.00 0.00 2.71
178 189 7.272948 GCTTTCAAGTTTCAGCTCTATCAAATG 59.727 37.037 0.00 0.00 0.00 2.32
192 203 0.679505 GGGTGGGGCTTTCAAGTTTC 59.320 55.000 0.00 0.00 0.00 2.78
209 220 6.214177 AGGAGTTTTATGGGGTAATATGGG 57.786 41.667 0.00 0.00 0.00 4.00
270 281 2.230130 TTTCGCCTCCCCAATTTCAT 57.770 45.000 0.00 0.00 0.00 2.57
271 282 2.002505 TTTTCGCCTCCCCAATTTCA 57.997 45.000 0.00 0.00 0.00 2.69
276 287 2.232399 GTTAGTTTTTCGCCTCCCCAA 58.768 47.619 0.00 0.00 0.00 4.12
288 299 4.477780 CGTTGTGTGTTGTGGTTAGTTTT 58.522 39.130 0.00 0.00 0.00 2.43
324 335 7.735917 TCTTTTGAAGTGGACAATCTTCTCTA 58.264 34.615 0.00 0.00 40.20 2.43
334 345 6.432783 TCTCTGTTTTTCTTTTGAAGTGGACA 59.567 34.615 0.00 0.00 39.88 4.02
343 354 7.433425 GTGACCATCTTCTCTGTTTTTCTTTTG 59.567 37.037 0.00 0.00 0.00 2.44
347 358 5.066593 GGTGACCATCTTCTCTGTTTTTCT 58.933 41.667 0.00 0.00 0.00 2.52
348 359 5.363979 GGTGACCATCTTCTCTGTTTTTC 57.636 43.478 0.00 0.00 0.00 2.29
368 379 1.076438 CTTCTCCCTTCCTTTGGGGT 58.924 55.000 0.00 0.00 44.67 4.95
370 381 1.076438 ACCTTCTCCCTTCCTTTGGG 58.924 55.000 0.00 0.00 45.90 4.12
407 426 2.729028 ATTATTGTTCCTCCACCCCG 57.271 50.000 0.00 0.00 0.00 5.73
418 437 4.821805 CCGTTGCATCCTCCTATTATTGTT 59.178 41.667 0.00 0.00 0.00 2.83
446 465 2.632377 CAGCGTTGTTCATACTCCCAT 58.368 47.619 0.00 0.00 0.00 4.00
451 470 1.019278 CCGCCAGCGTTGTTCATACT 61.019 55.000 11.55 0.00 37.81 2.12
461 480 3.030652 CTTGTTTTCCGCCAGCGT 58.969 55.556 11.55 0.00 37.81 5.07
498 517 2.619074 CCTTCATGTGTCTTCCTTCCCC 60.619 54.545 0.00 0.00 0.00 4.81
502 521 4.103153 TCTGTTCCTTCATGTGTCTTCCTT 59.897 41.667 0.00 0.00 0.00 3.36
516 535 5.934402 ATATACCTTGTCGTCTGTTCCTT 57.066 39.130 0.00 0.00 0.00 3.36
524 543 9.807649 TTAGGTTTCTTAATATACCTTGTCGTC 57.192 33.333 8.02 0.00 41.16 4.20
561 580 5.510690 CCGCTTTCCCCTTTTTCATTTAAGT 60.511 40.000 0.00 0.00 0.00 2.24
564 583 3.898741 ACCGCTTTCCCCTTTTTCATTTA 59.101 39.130 0.00 0.00 0.00 1.40
572 591 0.479378 TGGTTACCGCTTTCCCCTTT 59.521 50.000 0.00 0.00 0.00 3.11
576 595 1.900245 TTCTTGGTTACCGCTTTCCC 58.100 50.000 0.00 0.00 0.00 3.97
578 597 5.116069 TCATTTTCTTGGTTACCGCTTTC 57.884 39.130 0.00 0.00 0.00 2.62
582 601 5.060446 CGATTTTCATTTTCTTGGTTACCGC 59.940 40.000 0.00 0.00 0.00 5.68
584 603 8.582433 TTTCGATTTTCATTTTCTTGGTTACC 57.418 30.769 0.00 0.00 0.00 2.85
591 610 7.496747 TCCCAGTTTTCGATTTTCATTTTCTT 58.503 30.769 0.00 0.00 0.00 2.52
604 623 0.658897 GCGTGTTTCCCAGTTTTCGA 59.341 50.000 0.00 0.00 0.00 3.71
605 624 0.378962 TGCGTGTTTCCCAGTTTTCG 59.621 50.000 0.00 0.00 0.00 3.46
606 625 1.835121 GTGCGTGTTTCCCAGTTTTC 58.165 50.000 0.00 0.00 0.00 2.29
610 629 3.276846 GCGTGCGTGTTTCCCAGT 61.277 61.111 0.00 0.00 0.00 4.00
613 632 4.072088 CGAGCGTGCGTGTTTCCC 62.072 66.667 0.00 0.00 0.00 3.97
627 646 2.969628 ATGTTGTAAGGAGAGGCGAG 57.030 50.000 0.00 0.00 0.00 5.03
629 648 4.051922 GACATATGTTGTAAGGAGAGGCG 58.948 47.826 10.30 0.00 39.18 5.52
643 662 2.864097 GCTCTCCGCATTCGACATATGT 60.864 50.000 8.43 8.43 38.92 2.29
646 665 0.317854 CGCTCTCCGCATTCGACATA 60.318 55.000 0.00 0.00 39.08 2.29
666 685 1.134098 TGGGATGAGGGATTCTTTCGC 60.134 52.381 0.00 0.00 37.56 4.70
672 691 3.217626 GTTGTCATGGGATGAGGGATTC 58.782 50.000 0.00 0.00 40.53 2.52
681 700 1.019278 GTGTCGCGTTGTCATGGGAT 61.019 55.000 5.77 0.00 33.68 3.85
701 720 1.376424 CAGAGTCCCAGCGCAACAT 60.376 57.895 11.47 0.00 0.00 2.71
746 765 5.607119 ACACGCAAAATCACTAGTTAAGG 57.393 39.130 0.00 0.00 0.00 2.69
760 779 4.948608 TTGTTTTCAGTCTACACGCAAA 57.051 36.364 0.00 0.00 0.00 3.68
761 780 4.948608 TTTGTTTTCAGTCTACACGCAA 57.051 36.364 0.00 0.00 0.00 4.85
762 781 4.948608 TTTTGTTTTCAGTCTACACGCA 57.051 36.364 0.00 0.00 0.00 5.24
763 782 5.507077 TGATTTTGTTTTCAGTCTACACGC 58.493 37.500 0.00 0.00 0.00 5.34
766 785 8.275015 TGAGTTGATTTTGTTTTCAGTCTACA 57.725 30.769 0.00 0.00 0.00 2.74
769 788 7.542130 GTGTTGAGTTGATTTTGTTTTCAGTCT 59.458 33.333 0.00 0.00 0.00 3.24
770 789 7.201435 GGTGTTGAGTTGATTTTGTTTTCAGTC 60.201 37.037 0.00 0.00 0.00 3.51
772 791 6.237542 CGGTGTTGAGTTGATTTTGTTTTCAG 60.238 38.462 0.00 0.00 0.00 3.02
773 792 5.574830 CGGTGTTGAGTTGATTTTGTTTTCA 59.425 36.000 0.00 0.00 0.00 2.69
774 793 5.005299 CCGGTGTTGAGTTGATTTTGTTTTC 59.995 40.000 0.00 0.00 0.00 2.29
777 796 3.697045 TCCGGTGTTGAGTTGATTTTGTT 59.303 39.130 0.00 0.00 0.00 2.83
778 797 3.283751 TCCGGTGTTGAGTTGATTTTGT 58.716 40.909 0.00 0.00 0.00 2.83
779 798 3.980646 TCCGGTGTTGAGTTGATTTTG 57.019 42.857 0.00 0.00 0.00 2.44
780 799 3.243401 GCTTCCGGTGTTGAGTTGATTTT 60.243 43.478 0.00 0.00 0.00 1.82
781 800 2.293399 GCTTCCGGTGTTGAGTTGATTT 59.707 45.455 0.00 0.00 0.00 2.17
782 801 1.880027 GCTTCCGGTGTTGAGTTGATT 59.120 47.619 0.00 0.00 0.00 2.57
783 802 1.523758 GCTTCCGGTGTTGAGTTGAT 58.476 50.000 0.00 0.00 0.00 2.57
784 803 0.534203 GGCTTCCGGTGTTGAGTTGA 60.534 55.000 0.00 0.00 0.00 3.18
785 804 0.535102 AGGCTTCCGGTGTTGAGTTG 60.535 55.000 0.00 0.00 0.00 3.16
826 845 0.390209 ACGCAAAATCATGGGCTTGC 60.390 50.000 13.35 13.35 40.58 4.01
829 848 1.745087 CTACACGCAAAATCATGGGCT 59.255 47.619 0.00 0.00 36.78 5.19
830 849 1.742831 TCTACACGCAAAATCATGGGC 59.257 47.619 0.00 0.00 36.78 5.36
831 850 3.009723 AGTCTACACGCAAAATCATGGG 58.990 45.455 0.00 0.00 39.03 4.00
832 851 3.684305 TCAGTCTACACGCAAAATCATGG 59.316 43.478 0.00 0.00 0.00 3.66
833 852 4.926860 TCAGTCTACACGCAAAATCATG 57.073 40.909 0.00 0.00 0.00 3.07
835 854 5.743026 TTTTCAGTCTACACGCAAAATCA 57.257 34.783 0.00 0.00 0.00 2.57
859 878 6.923199 ATTCCTGTGGATGAGTTGATTTTT 57.077 33.333 0.00 0.00 0.00 1.94
860 879 6.494491 TCAATTCCTGTGGATGAGTTGATTTT 59.506 34.615 0.00 0.00 0.00 1.82
861 880 6.012113 TCAATTCCTGTGGATGAGTTGATTT 58.988 36.000 0.00 0.00 0.00 2.17
862 881 5.416952 GTCAATTCCTGTGGATGAGTTGATT 59.583 40.000 0.00 0.00 29.37 2.57
863 882 4.946157 GTCAATTCCTGTGGATGAGTTGAT 59.054 41.667 0.00 0.00 29.37 2.57
864 883 4.326826 GTCAATTCCTGTGGATGAGTTGA 58.673 43.478 0.00 0.00 0.00 3.18
865 884 3.125829 CGTCAATTCCTGTGGATGAGTTG 59.874 47.826 0.00 0.00 0.00 3.16
866 885 3.007940 TCGTCAATTCCTGTGGATGAGTT 59.992 43.478 0.00 0.00 0.00 3.01
867 886 2.567169 TCGTCAATTCCTGTGGATGAGT 59.433 45.455 0.00 0.00 0.00 3.41
868 887 3.251479 TCGTCAATTCCTGTGGATGAG 57.749 47.619 0.00 0.00 0.00 2.90
869 888 3.912496 ATCGTCAATTCCTGTGGATGA 57.088 42.857 0.00 0.00 0.00 2.92
870 889 4.273480 GGTTATCGTCAATTCCTGTGGATG 59.727 45.833 0.00 0.00 0.00 3.51
871 890 4.080582 TGGTTATCGTCAATTCCTGTGGAT 60.081 41.667 0.00 0.00 0.00 3.41
872 891 3.262151 TGGTTATCGTCAATTCCTGTGGA 59.738 43.478 0.00 0.00 0.00 4.02
873 892 3.605634 TGGTTATCGTCAATTCCTGTGG 58.394 45.455 0.00 0.00 0.00 4.17
874 893 3.623060 CCTGGTTATCGTCAATTCCTGTG 59.377 47.826 0.00 0.00 0.00 3.66
875 894 3.873910 CCTGGTTATCGTCAATTCCTGT 58.126 45.455 0.00 0.00 0.00 4.00
876 895 2.614057 GCCTGGTTATCGTCAATTCCTG 59.386 50.000 0.00 0.00 0.00 3.86
971 990 0.326143 AGGAGAGAGGGGAAGCTTCC 60.326 60.000 33.67 33.67 46.82 3.46
1237 1256 2.100989 CCGAACACCTTAGGAGTAGCT 58.899 52.381 4.77 0.00 0.00 3.32
1361 1380 1.546476 ACCGACAGAGCCAGTAAAGAG 59.454 52.381 0.00 0.00 0.00 2.85
1386 1405 2.369532 AGGCAATTGCTGAACATTGGTT 59.630 40.909 28.42 0.00 41.70 3.67
1503 1522 1.398390 CTCGTTGCCTTATCCACAAGC 59.602 52.381 0.00 0.00 0.00 4.01
1533 1552 6.753279 AGCAAATGGATTTAATGTGTCGATTG 59.247 34.615 0.00 0.00 0.00 2.67
1534 1553 6.753279 CAGCAAATGGATTTAATGTGTCGATT 59.247 34.615 0.00 0.00 0.00 3.34
1540 1559 4.505808 TGGCAGCAAATGGATTTAATGTG 58.494 39.130 0.00 0.00 0.00 3.21
1541 1560 4.761975 CTGGCAGCAAATGGATTTAATGT 58.238 39.130 0.00 0.00 0.00 2.71
1543 1562 3.453353 AGCTGGCAGCAAATGGATTTAAT 59.547 39.130 38.09 12.58 45.56 1.40
1570 1590 6.214399 ACTGAAACACGGTTAAACAAAACAA 58.786 32.000 0.00 0.00 33.91 2.83
1663 1683 5.719563 ACCCCCAAATGTAAAGAAATGTAGG 59.280 40.000 0.00 0.00 0.00 3.18
1718 1739 7.041167 CCAAGATTGTAATTCCGCAAGATATGA 60.041 37.037 0.00 0.00 43.02 2.15
1735 1756 7.472334 AAAAGCATACATCTTCCAAGATTGT 57.528 32.000 0.00 4.84 42.96 2.71
1785 1877 6.707608 CAGGCTATCTTATCAAAGCATGTACA 59.292 38.462 0.00 0.00 40.74 2.90
1971 2063 9.658799 TCAGAACTTATTAGAAATGGACAGAAG 57.341 33.333 0.00 0.00 0.00 2.85
1978 2070 9.383519 TGTAAGCTCAGAACTTATTAGAAATGG 57.616 33.333 0.00 0.00 32.53 3.16
2071 2163 9.828852 GATAGATTAAGTGGTAGTCAATAGTCG 57.171 37.037 0.00 0.00 0.00 4.18
2129 2221 7.938140 TCTTCAGGAAGAGAGAAAACAAAAA 57.062 32.000 7.62 0.00 42.06 1.94
2166 2270 8.416329 AGACAAGCAAAAGTTAAAATGAGATGT 58.584 29.630 0.00 0.00 0.00 3.06
2342 2446 4.091365 GCATCAAACCGCTTAAATGGAAAC 59.909 41.667 0.00 0.00 0.00 2.78
2355 2459 1.202222 GGCATCTCAAGCATCAAACCG 60.202 52.381 0.00 0.00 0.00 4.44
2436 2540 2.760092 AGCAGCAAAAGGTCAAAGAACA 59.240 40.909 0.00 0.00 0.00 3.18
2513 2620 8.783093 GCCAGACAAGTGCATGTATATAAATTA 58.217 33.333 0.00 0.00 32.57 1.40
2563 2670 0.868406 CGAGCAGGTGTGGAAAGTTC 59.132 55.000 0.00 0.00 0.00 3.01
2722 2829 7.276658 CGATGAAGTGTTCTAATCTAAGCAAGT 59.723 37.037 0.00 0.00 0.00 3.16
2755 2862 6.547880 TGGTTTGAACATATTACACCACAAGT 59.452 34.615 0.00 0.00 0.00 3.16
2756 2863 6.976088 TGGTTTGAACATATTACACCACAAG 58.024 36.000 0.00 0.00 0.00 3.16
2757 2864 6.961360 TGGTTTGAACATATTACACCACAA 57.039 33.333 0.00 0.00 0.00 3.33
2758 2865 6.491745 ACATGGTTTGAACATATTACACCACA 59.508 34.615 0.00 0.00 0.00 4.17
2759 2866 6.806249 CACATGGTTTGAACATATTACACCAC 59.194 38.462 0.00 0.00 0.00 4.16
2760 2867 6.717084 TCACATGGTTTGAACATATTACACCA 59.283 34.615 0.00 0.00 0.00 4.17
2761 2868 7.151999 TCACATGGTTTGAACATATTACACC 57.848 36.000 0.00 0.00 0.00 4.16
2762 2869 8.458052 TGATCACATGGTTTGAACATATTACAC 58.542 33.333 0.00 0.00 0.00 2.90
2833 2940 5.300286 AGAACAGCCTATTTGCCATTATGTC 59.700 40.000 0.00 0.00 0.00 3.06
2893 3000 3.924686 GCACAGGATTTGCTCTGAAAATG 59.075 43.478 0.00 0.00 37.00 2.32
3013 3120 3.540367 TTTTCCGAGGGACCACCGC 62.540 63.158 0.00 0.00 46.96 5.68
3084 3192 3.415212 TCCTCTTTTTGACCTGCAGATG 58.585 45.455 17.39 1.02 0.00 2.90
3085 3193 3.328931 TCTCCTCTTTTTGACCTGCAGAT 59.671 43.478 17.39 0.00 0.00 2.90
3094 3202 4.277476 TGCTTTGGTTCTCCTCTTTTTGA 58.723 39.130 0.00 0.00 34.23 2.69
3111 3219 6.190954 GGAACCAAAACGATATACTGCTTT 57.809 37.500 0.00 0.00 0.00 3.51
3180 3291 6.018180 GGTGAACGGCCTAATATTCTGTAAAG 60.018 42.308 0.00 0.00 0.00 1.85
3201 3312 1.189524 AAGAATGGTCCCGTCGGTGA 61.190 55.000 11.06 4.40 0.00 4.02
3240 3351 4.057432 GCTGCAAAACACAACCACAATAT 58.943 39.130 0.00 0.00 0.00 1.28
3331 3442 2.571757 CCTTCTAGGTCGCACGCA 59.428 61.111 0.00 0.00 0.00 5.24
3429 3540 3.059853 TCCTGGTATTGCCCATCCAATA 58.940 45.455 0.00 0.00 36.80 1.90
3454 3565 8.624776 GGTATTGTCCTGAATTATCTTTCCTTG 58.375 37.037 0.00 0.00 0.00 3.61
3660 3782 7.984422 TCAGATTTCAGAAAGCAGTAAATCA 57.016 32.000 13.54 0.00 38.45 2.57
3672 3794 4.012374 GCATCAGGGTTCAGATTTCAGAA 58.988 43.478 0.00 0.00 0.00 3.02
3716 3840 3.735746 GCACAGAAACCTGTAATGTTTGC 59.264 43.478 0.00 0.00 42.60 3.68
3741 3865 2.027561 CCAGGGTTTTCGGTGATACAGA 60.028 50.000 0.00 0.00 0.00 3.41
3777 3901 5.619132 TCCTATGCAATCTCATGAACAGA 57.381 39.130 0.00 0.00 0.00 3.41
3869 3994 1.602311 CAAGCTCTTGCAGGTCTTGT 58.398 50.000 18.16 0.00 42.74 3.16
3948 4073 0.829602 TGCAGGAAAAATGGCCGGAA 60.830 50.000 5.05 0.00 0.00 4.30
3949 4074 1.228706 TGCAGGAAAAATGGCCGGA 60.229 52.632 5.05 0.00 0.00 5.14
4112 4237 1.979693 GAGACCGTCTCCTGGCTGT 60.980 63.158 16.58 0.00 37.55 4.40
4145 4270 2.637025 CACCGGCGTTGGTTCTTG 59.363 61.111 6.01 0.00 41.38 3.02
4169 4294 2.036387 TCAGAAGGTGAGACGGTTCAA 58.964 47.619 0.00 0.00 0.00 2.69
4194 4326 2.032681 ACCGCTTGCAAGGTCTCC 59.967 61.111 27.10 9.58 35.50 3.71
4195 4327 2.328099 CCACCGCTTGCAAGGTCTC 61.328 63.158 27.10 9.95 39.00 3.36
4196 4328 2.281761 CCACCGCTTGCAAGGTCT 60.282 61.111 27.10 3.13 39.00 3.85
4218 4354 2.923854 CGCTTCATCGCCATCGTC 59.076 61.111 0.00 0.00 36.96 4.20
4263 4399 4.060038 TTCCCTCCGACGAACGCC 62.060 66.667 0.00 0.00 41.07 5.68
4266 4402 1.080025 CAGGTTCCCTCCGACGAAC 60.080 63.158 0.00 0.00 38.10 3.95


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

AutoCloner maintained by Alex Coulton.