Multiple sequence alignment - TraesCS3B01G391200

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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 TraesCS3B01G391200 chr3B 100.000 4659 0 0 1 4659 616648900 616644242 0.000000e+00 8604.0
1 TraesCS3B01G391200 chr3B 92.238 889 61 5 1 888 616685666 616684785 0.000000e+00 1253.0
2 TraesCS3B01G391200 chr3B 83.186 791 76 23 962 1717 616427080 616426312 0.000000e+00 671.0
3 TraesCS3B01G391200 chr3B 87.500 392 45 4 268 655 616685025 616684634 2.560000e-122 449.0
4 TraesCS3B01G391200 chr3B 89.776 313 32 0 900 1212 616684710 616684398 7.260000e-108 401.0
5 TraesCS3B01G391200 chr3D 93.637 1933 102 14 2111 4037 463260359 463258442 0.000000e+00 2868.0
6 TraesCS3B01G391200 chr3D 93.533 1933 105 13 2111 4037 463228947 463227029 0.000000e+00 2859.0
7 TraesCS3B01G391200 chr3D 88.009 1693 153 19 2359 4037 463379555 463377899 0.000000e+00 1956.0
8 TraesCS3B01G391200 chr3D 92.774 941 42 15 894 1814 463381987 463381053 0.000000e+00 1338.0
9 TraesCS3B01G391200 chr3D 91.277 940 48 20 894 1814 463261953 463261029 0.000000e+00 1251.0
10 TraesCS3B01G391200 chr3D 91.020 735 43 10 160 888 463382773 463382056 0.000000e+00 970.0
11 TraesCS3B01G391200 chr3D 83.963 873 93 20 973 1814 463230555 463229699 0.000000e+00 793.0
12 TraesCS3B01G391200 chr3D 84.157 789 84 24 957 1717 463199352 463198577 0.000000e+00 726.0
13 TraesCS3B01G391200 chr3D 87.626 396 41 7 268 656 463382297 463381903 1.980000e-123 453.0
14 TraesCS3B01G391200 chr3D 89.494 257 25 2 2114 2368 463380213 463379957 1.620000e-84 324.0
15 TraesCS3B01G391200 chr3D 90.286 175 10 1 1864 2038 463229698 463229531 6.070000e-54 222.0
16 TraesCS3B01G391200 chr3D 87.283 173 21 1 188 359 463262298 463262126 3.680000e-46 196.0
17 TraesCS3B01G391200 chr3D 89.474 133 7 1 1864 1996 463381052 463380927 1.340000e-35 161.0
18 TraesCS3B01G391200 chr3D 88.806 134 10 4 2 135 463398476 463398348 4.830000e-35 159.0
19 TraesCS3B01G391200 chr3D 88.776 98 11 0 6 103 463405117 463405020 2.280000e-23 121.0
20 TraesCS3B01G391200 chr3D 95.652 69 3 0 1970 2038 463261014 463260946 1.370000e-20 111.0
21 TraesCS3B01G391200 chr3D 87.500 96 11 1 4 99 591585420 591585326 4.930000e-20 110.0
22 TraesCS3B01G391200 chr3D 89.286 56 6 0 1983 2038 463380822 463380767 2.330000e-08 71.3
23 TraesCS3B01G391200 chr3D 100.000 28 0 0 126 153 463398343 463398316 8.000000e-03 52.8
24 TraesCS3B01G391200 chr3A 93.401 1773 97 11 2271 4037 606517251 606515493 0.000000e+00 2608.0
25 TraesCS3B01G391200 chr3A 87.044 1397 137 13 2238 3622 606574694 606573330 0.000000e+00 1537.0
26 TraesCS3B01G391200 chr3A 92.025 953 52 15 885 1814 606576351 606575400 0.000000e+00 1317.0
27 TraesCS3B01G391200 chr3A 89.613 905 65 11 2 888 606577292 606576399 0.000000e+00 1123.0
28 TraesCS3B01G391200 chr3A 87.764 899 69 17 1053 1922 606519180 606518294 0.000000e+00 1013.0
29 TraesCS3B01G391200 chr3A 82.248 783 93 20 957 1706 606446894 606446125 6.580000e-178 634.0
30 TraesCS3B01G391200 chr3A 87.500 392 38 6 268 656 606576639 606576256 4.280000e-120 442.0
31 TraesCS3B01G391200 chr3A 89.457 313 28 5 3633 3942 606572029 606571719 1.570000e-104 390.0
32 TraesCS3B01G391200 chr3A 89.634 164 14 3 3876 4037 606571718 606571556 6.110000e-49 206.0
33 TraesCS3B01G391200 chr3A 95.146 103 5 0 1932 2034 606518125 606518023 3.730000e-36 163.0
34 TraesCS3B01G391200 chr3A 89.474 133 7 1 1864 1996 606575399 606575274 1.340000e-35 161.0
35 TraesCS3B01G391200 chr2D 94.652 617 29 2 4047 4659 631562634 631563250 0.000000e+00 953.0
36 TraesCS3B01G391200 chr2D 93.301 612 37 4 4050 4659 627153274 627152665 0.000000e+00 900.0
37 TraesCS3B01G391200 chr5B 94.435 611 31 3 4047 4655 642231238 642231847 0.000000e+00 937.0
38 TraesCS3B01G391200 chr7B 94.165 617 29 5 4047 4659 11194601 11195214 0.000000e+00 933.0
39 TraesCS3B01G391200 chr1B 93.679 617 33 4 4047 4659 666789974 666789360 0.000000e+00 918.0
40 TraesCS3B01G391200 chr1B 93.008 615 41 2 4047 4659 283913266 283912652 0.000000e+00 896.0
41 TraesCS3B01G391200 chr2B 93.496 615 38 2 4047 4659 8420649 8421263 0.000000e+00 913.0
42 TraesCS3B01G391200 chr6B 93.182 616 38 4 4047 4659 174589032 174588418 0.000000e+00 902.0
43 TraesCS3B01G391200 chr5D 93.008 615 40 3 4047 4659 393815071 393815684 0.000000e+00 894.0
44 TraesCS3B01G391200 chr6D 86.538 104 13 1 4 107 177831912 177831810 3.810000e-21 113.0
45 TraesCS3B01G391200 chr5A 85.000 100 15 0 4 103 401502914 401503013 8.250000e-18 102.0
46 TraesCS3B01G391200 chr5A 84.536 97 13 2 4 99 279075934 279076029 1.380000e-15 95.3
47 TraesCS3B01G391200 chr1A 89.744 78 8 0 4 81 445546366 445546443 2.970000e-17 100.0
48 TraesCS3B01G391200 chr7A 82.857 105 18 0 4 108 80161660 80161556 1.380000e-15 95.3


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 TraesCS3B01G391200 chr3B 616644242 616648900 4658 True 8604.000000 8604 100.000000 1 4659 1 chr3B.!!$R2 4658
1 TraesCS3B01G391200 chr3B 616684398 616685666 1268 True 701.000000 1253 89.838000 1 1212 3 chr3B.!!$R3 1211
2 TraesCS3B01G391200 chr3B 616426312 616427080 768 True 671.000000 671 83.186000 962 1717 1 chr3B.!!$R1 755
3 TraesCS3B01G391200 chr3D 463227029 463230555 3526 True 1291.333333 2859 89.260667 973 4037 3 chr3D.!!$R4 3064
4 TraesCS3B01G391200 chr3D 463258442 463262298 3856 True 1106.500000 2868 91.962250 188 4037 4 chr3D.!!$R5 3849
5 TraesCS3B01G391200 chr3D 463377899 463382773 4874 True 753.328571 1956 89.669000 160 4037 7 chr3D.!!$R6 3877
6 TraesCS3B01G391200 chr3D 463198577 463199352 775 True 726.000000 726 84.157000 957 1717 1 chr3D.!!$R1 760
7 TraesCS3B01G391200 chr3A 606515493 606519180 3687 True 1261.333333 2608 92.103667 1053 4037 3 chr3A.!!$R2 2984
8 TraesCS3B01G391200 chr3A 606571556 606577292 5736 True 739.428571 1537 89.249571 2 4037 7 chr3A.!!$R3 4035
9 TraesCS3B01G391200 chr3A 606446125 606446894 769 True 634.000000 634 82.248000 957 1706 1 chr3A.!!$R1 749
10 TraesCS3B01G391200 chr2D 631562634 631563250 616 False 953.000000 953 94.652000 4047 4659 1 chr2D.!!$F1 612
11 TraesCS3B01G391200 chr2D 627152665 627153274 609 True 900.000000 900 93.301000 4050 4659 1 chr2D.!!$R1 609
12 TraesCS3B01G391200 chr5B 642231238 642231847 609 False 937.000000 937 94.435000 4047 4655 1 chr5B.!!$F1 608
13 TraesCS3B01G391200 chr7B 11194601 11195214 613 False 933.000000 933 94.165000 4047 4659 1 chr7B.!!$F1 612
14 TraesCS3B01G391200 chr1B 666789360 666789974 614 True 918.000000 918 93.679000 4047 4659 1 chr1B.!!$R2 612
15 TraesCS3B01G391200 chr1B 283912652 283913266 614 True 896.000000 896 93.008000 4047 4659 1 chr1B.!!$R1 612
16 TraesCS3B01G391200 chr2B 8420649 8421263 614 False 913.000000 913 93.496000 4047 4659 1 chr2B.!!$F1 612
17 TraesCS3B01G391200 chr6B 174588418 174589032 614 True 902.000000 902 93.182000 4047 4659 1 chr6B.!!$R1 612
18 TraesCS3B01G391200 chr5D 393815071 393815684 613 False 894.000000 894 93.008000 4047 4659 1 chr5D.!!$F1 612

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
408 426 0.315886 ACACGAGTCACGCCACATTA 59.684 50.0 0.00 0.00 46.94 1.90 F
889 910 0.321122 CTGGCCAGAGTCACTTGACC 60.321 60.0 29.88 0.00 45.85 4.02 F
1610 1758 0.322456 AGCTTCCAAATGCGCCTGTA 60.322 50.0 4.18 0.00 0.00 2.74 F
2035 2483 0.036388 ACTATGTGTCAACCGGCTGG 60.036 55.0 11.02 11.02 42.84 4.85 F
2173 3171 0.249155 CTGCCTGCAACACAACCAAG 60.249 55.0 0.00 0.00 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1735 1896 0.031917 TTGCCCAGATGGATGCCATT 60.032 50.000 0.00 0.00 45.26 3.16 R
1928 2258 1.002468 GTGCACATCGTGAGCAAAACT 60.002 47.619 13.17 0.00 44.93 2.66 R
3218 5008 0.103937 CCAAGAGATCGACCCTGAGC 59.896 60.000 0.00 0.00 0.00 4.26 R
3376 5166 0.325933 TGGCTTGTCCATGAGACTGG 59.674 55.000 13.32 8.39 46.46 4.00 R
4126 7281 1.741028 TCCACCATGAGTTTGAGGGA 58.259 50.000 0.00 0.00 0.00 4.20 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
65 66 9.542462 GATTGCCATACTTACTGTTTACTCATA 57.458 33.333 0.00 0.00 0.00 2.15
94 95 5.931146 AGATTAATCAAAGAGGCGCTGATAG 59.069 40.000 17.56 0.00 0.00 2.08
353 368 6.396829 ACGTTACTATATGTGGGGTCTTAC 57.603 41.667 0.00 0.00 0.00 2.34
359 374 4.677673 ATATGTGGGGTCTTACCGTTAC 57.322 45.455 0.00 0.00 39.83 2.50
360 375 2.014010 TGTGGGGTCTTACCGTTACT 57.986 50.000 0.00 0.00 39.83 2.24
374 392 1.073177 GTTACTACAACGCGGTGCAT 58.927 50.000 26.87 12.63 0.00 3.96
408 426 0.315886 ACACGAGTCACGCCACATTA 59.684 50.000 0.00 0.00 46.94 1.90
533 551 2.273619 AGACAATTTGAGCCCCTCTCT 58.726 47.619 2.79 0.00 42.38 3.10
545 563 1.695597 CCTCTCTGCCCATCCCCTT 60.696 63.158 0.00 0.00 0.00 3.95
617 635 4.626081 GTGCACCCACTCCACGCT 62.626 66.667 5.22 0.00 38.93 5.07
644 662 1.431633 CCCCTTCAAACCCTTACCCTT 59.568 52.381 0.00 0.00 0.00 3.95
662 680 3.368323 CCCTTCATGCGCCTTTTATGTTT 60.368 43.478 4.18 0.00 0.00 2.83
663 681 4.244862 CCTTCATGCGCCTTTTATGTTTT 58.755 39.130 4.18 0.00 0.00 2.43
664 682 5.406649 CCTTCATGCGCCTTTTATGTTTTA 58.593 37.500 4.18 0.00 0.00 1.52
665 683 6.042143 CCTTCATGCGCCTTTTATGTTTTAT 58.958 36.000 4.18 0.00 0.00 1.40
666 684 7.199766 CCTTCATGCGCCTTTTATGTTTTATA 58.800 34.615 4.18 0.00 0.00 0.98
718 737 3.183775 GTGAACCAGCTTGTACGTTACTG 59.816 47.826 0.00 0.00 0.00 2.74
804 825 1.539388 CCACATTGCGGTGCTTCTTTA 59.461 47.619 0.00 0.00 37.46 1.85
805 826 2.414559 CCACATTGCGGTGCTTCTTTAG 60.415 50.000 0.00 0.00 37.46 1.85
873 894 1.601759 CTGGCCCACTTGTCACTGG 60.602 63.158 0.00 0.00 0.00 4.00
888 909 0.394565 ACTGGCCAGAGTCACTTGAC 59.605 55.000 39.19 0.77 45.08 3.18
889 910 0.321122 CTGGCCAGAGTCACTTGACC 60.321 60.000 29.88 0.00 45.85 4.02
890 911 1.374758 GGCCAGAGTCACTTGACCG 60.375 63.158 0.00 0.00 45.85 4.79
891 912 2.029844 GCCAGAGTCACTTGACCGC 61.030 63.158 5.73 0.00 45.85 5.68
892 913 1.734477 CCAGAGTCACTTGACCGCG 60.734 63.158 0.00 0.00 45.85 6.46
893 914 2.049063 AGAGTCACTTGACCGCGC 60.049 61.111 0.00 0.00 45.85 6.86
894 915 3.470567 GAGTCACTTGACCGCGCG 61.471 66.667 25.67 25.67 45.85 6.86
921 1006 4.281947 TGCCGTTCGGTGCGTGTA 62.282 61.111 12.81 0.00 0.00 2.90
948 1033 4.332543 TCCACGCCCCTTCTCCCT 62.333 66.667 0.00 0.00 0.00 4.20
1013 1100 4.081030 CCGACTGCAAGCGCACAG 62.081 66.667 19.59 19.59 45.36 3.66
1122 1210 3.646715 CCCGCCTGTCCCTTTCCA 61.647 66.667 0.00 0.00 0.00 3.53
1214 1324 2.435586 CCGACAAGGGAGCAGCTG 60.436 66.667 10.11 10.11 35.97 4.24
1526 1645 2.493501 GGAGAAGGTACGTCCGCC 59.506 66.667 0.00 0.00 37.62 6.13
1527 1646 2.050934 GGAGAAGGTACGTCCGCCT 61.051 63.158 0.00 0.00 37.62 5.52
1528 1647 1.602327 GGAGAAGGTACGTCCGCCTT 61.602 60.000 15.85 15.85 46.75 4.35
1587 1735 4.621068 ATTGGCATGTACGTCTTGATTG 57.379 40.909 0.00 0.00 0.00 2.67
1588 1736 3.326836 TGGCATGTACGTCTTGATTGA 57.673 42.857 0.00 0.00 0.00 2.57
1589 1737 3.872696 TGGCATGTACGTCTTGATTGAT 58.127 40.909 0.00 0.00 0.00 2.57
1590 1738 4.260985 TGGCATGTACGTCTTGATTGATT 58.739 39.130 0.00 0.00 0.00 2.57
1610 1758 0.322456 AGCTTCCAAATGCGCCTGTA 60.322 50.000 4.18 0.00 0.00 2.74
1639 1787 1.626825 AGCCTAGCTTTACGTTTGGGA 59.373 47.619 0.00 0.00 33.89 4.37
1666 1819 3.008375 GCTGGAAGGGATATGCATCTACA 59.992 47.826 0.19 0.00 0.00 2.74
1685 1840 1.055849 AACTTTCCATTGCAACCCCC 58.944 50.000 0.00 0.00 0.00 5.40
1735 1896 2.684630 GCTGGTCATGTGATTGGATGGA 60.685 50.000 0.00 0.00 0.00 3.41
1840 2004 4.461781 AGCACGTACCTGTACTATCTGTTT 59.538 41.667 5.95 0.00 34.04 2.83
1841 2005 5.047519 AGCACGTACCTGTACTATCTGTTTT 60.048 40.000 5.95 0.00 34.04 2.43
1872 2036 4.798882 TGTGATGTCCCTTTGGTAGTTTT 58.201 39.130 0.00 0.00 0.00 2.43
1923 2253 6.101997 GCTTTGCTTGCTTGGTTATATTCTT 58.898 36.000 0.00 0.00 0.00 2.52
1924 2254 7.093988 TGCTTTGCTTGCTTGGTTATATTCTTA 60.094 33.333 0.00 0.00 0.00 2.10
1925 2255 7.922811 GCTTTGCTTGCTTGGTTATATTCTTAT 59.077 33.333 0.00 0.00 0.00 1.73
1926 2256 9.241317 CTTTGCTTGCTTGGTTATATTCTTATG 57.759 33.333 0.00 0.00 0.00 1.90
1927 2257 6.738114 TGCTTGCTTGGTTATATTCTTATGC 58.262 36.000 0.00 0.00 0.00 3.14
1928 2258 6.320926 TGCTTGCTTGGTTATATTCTTATGCA 59.679 34.615 0.00 0.00 0.00 3.96
1929 2259 6.860023 GCTTGCTTGGTTATATTCTTATGCAG 59.140 38.462 0.00 0.00 0.00 4.41
2035 2483 0.036388 ACTATGTGTCAACCGGCTGG 60.036 55.000 11.02 11.02 42.84 4.85
2074 3072 2.032652 GCTGATTCGTAGTACGCGTAC 58.967 52.381 35.97 35.97 42.21 3.67
2116 3114 3.630148 CGCCCTGTATTGCGCTCG 61.630 66.667 9.73 0.00 44.64 5.03
2117 3115 3.272334 GCCCTGTATTGCGCTCGG 61.272 66.667 9.73 1.64 0.00 4.63
2118 3116 3.272334 CCCTGTATTGCGCTCGGC 61.272 66.667 9.73 0.00 43.96 5.54
2119 3117 2.202932 CCTGTATTGCGCTCGGCT 60.203 61.111 9.73 0.00 44.05 5.52
2120 3118 2.528743 CCTGTATTGCGCTCGGCTG 61.529 63.158 9.73 0.90 44.05 4.85
2121 3119 2.511373 TGTATTGCGCTCGGCTGG 60.511 61.111 9.73 0.00 44.05 4.85
2122 3120 2.511600 GTATTGCGCTCGGCTGGT 60.512 61.111 9.73 0.00 44.05 4.00
2146 3144 1.810441 CGCAACACGCCCCGTATTA 60.810 57.895 0.00 0.00 38.32 0.98
2167 3165 4.560743 TCGGCTGCCTGCAACACA 62.561 61.111 17.92 0.00 45.15 3.72
2173 3171 0.249155 CTGCCTGCAACACAACCAAG 60.249 55.000 0.00 0.00 0.00 3.61
2267 3357 3.961849 AGAAGCCTTTTCCTTCTCATCC 58.038 45.455 0.00 0.00 44.13 3.51
2273 3363 1.673767 TTTCCTTCTCATCCTGCCCT 58.326 50.000 0.00 0.00 0.00 5.19
2526 4307 4.162651 AGATGGAAAATTTCTTGTGGGCT 58.837 39.130 5.65 0.00 0.00 5.19
2746 4530 1.135489 TCCCGATATTATGCTCGACGC 60.135 52.381 0.00 0.58 37.05 5.19
2764 4548 1.202031 CGCTGAGCAAAATACGGGAAC 60.202 52.381 4.88 0.00 0.00 3.62
2793 4580 5.988310 AAAGATCTCAATCCAAACATGCA 57.012 34.783 0.00 0.00 31.78 3.96
2795 4582 6.540438 AAGATCTCAATCCAAACATGCATT 57.460 33.333 0.00 0.00 31.78 3.56
2796 4583 7.649533 AAGATCTCAATCCAAACATGCATTA 57.350 32.000 0.00 0.00 31.78 1.90
2797 4584 7.649533 AGATCTCAATCCAAACATGCATTAA 57.350 32.000 0.00 0.00 31.78 1.40
2798 4585 8.070034 AGATCTCAATCCAAACATGCATTAAA 57.930 30.769 0.00 0.00 31.78 1.52
2799 4586 8.533657 AGATCTCAATCCAAACATGCATTAAAA 58.466 29.630 0.00 0.00 31.78 1.52
2800 4587 9.153721 GATCTCAATCCAAACATGCATTAAAAA 57.846 29.630 0.00 0.00 0.00 1.94
2801 4588 9.675464 ATCTCAATCCAAACATGCATTAAAAAT 57.325 25.926 0.00 0.00 0.00 1.82
2802 4589 9.504708 TCTCAATCCAAACATGCATTAAAAATT 57.495 25.926 0.00 0.00 0.00 1.82
2838 4625 8.126700 GGTTATACTGACATATTTTTCGTTGGG 58.873 37.037 0.00 0.00 0.00 4.12
2947 4734 0.457443 CTACTCACAGATGCAGCCGA 59.543 55.000 0.00 0.00 0.00 5.54
2953 4740 2.133553 CACAGATGCAGCCGAAGATAG 58.866 52.381 0.00 0.00 0.00 2.08
3000 4787 3.233684 CATGGCAATGTACATGCACAA 57.766 42.857 22.92 13.27 45.60 3.33
3023 4810 2.279918 GGCCGCCATGTACTACCG 60.280 66.667 3.91 0.00 0.00 4.02
3032 4819 0.837272 ATGTACTACCGGGCAGCATT 59.163 50.000 6.32 0.00 0.00 3.56
3040 4827 1.511887 CGGGCAGCATTTTCGAACG 60.512 57.895 0.00 0.00 0.00 3.95
3051 4838 2.296831 TTTCGAACGACTCCAACACA 57.703 45.000 0.00 0.00 0.00 3.72
3074 4864 0.370273 CAAATGCGCGTACTCCAGTC 59.630 55.000 8.43 0.00 0.00 3.51
3076 4866 1.605058 AATGCGCGTACTCCAGTCCT 61.605 55.000 8.43 0.00 0.00 3.85
3083 4873 2.243888 TACTCCAGTCCTCCCCGGT 61.244 63.158 0.00 0.00 0.00 5.28
3141 4931 1.134699 CGCCCTGTGCTTCTGAATCTA 60.135 52.381 0.00 0.00 38.05 1.98
3153 4943 6.100279 TGCTTCTGAATCTATTCCCACAGTAT 59.900 38.462 0.41 0.00 35.97 2.12
3266 5056 0.698818 AGTCCCAAGATCCCCAACAC 59.301 55.000 0.00 0.00 0.00 3.32
3309 5099 2.441750 ACTTCTTTGGTGAAGGCCACTA 59.558 45.455 5.01 0.00 45.49 2.74
3343 5133 6.622245 GCATTATTGCTGATATGCTCGACAAT 60.622 38.462 2.33 0.00 45.77 2.71
3376 5166 9.810545 GTTGAAATCATATAGGCTACTATCTCC 57.189 37.037 0.00 0.00 40.35 3.71
3426 5216 4.846779 TGTACCAGTTTTCTTTCATGGC 57.153 40.909 0.00 0.00 34.24 4.40
3427 5217 3.252215 TGTACCAGTTTTCTTTCATGGCG 59.748 43.478 0.00 0.00 34.24 5.69
3509 5299 0.095935 CTTGAAGCGTGCATCGGAAG 59.904 55.000 10.02 0.00 40.26 3.46
3827 6910 4.322349 CCCTTAGAGAAACTCAGAGGTGTG 60.322 50.000 1.53 0.00 34.91 3.82
3843 6926 7.228706 TCAGAGGTGTGTAGAATTTTCTTTTCC 59.771 37.037 0.00 0.00 38.70 3.13
3849 6932 8.352942 GTGTGTAGAATTTTCTTTTCCTGTGAT 58.647 33.333 0.00 0.00 38.70 3.06
3891 6974 7.697352 TCGATTAGTTGTTTAAGTCACGAAA 57.303 32.000 0.00 0.00 0.00 3.46
3925 7008 4.647964 CACAAGCGTATCATGTGTAAACC 58.352 43.478 0.00 0.00 39.00 3.27
4038 7192 9.612066 AATTTCACAAATTTGACACCTTATTGT 57.388 25.926 24.64 0.00 37.84 2.71
4039 7193 9.612066 ATTTCACAAATTTGACACCTTATTGTT 57.388 25.926 24.64 0.00 0.00 2.83
4040 7194 8.641499 TTCACAAATTTGACACCTTATTGTTC 57.359 30.769 24.64 0.00 0.00 3.18
4041 7195 6.915300 TCACAAATTTGACACCTTATTGTTCG 59.085 34.615 24.64 0.00 0.00 3.95
4042 7196 6.915300 CACAAATTTGACACCTTATTGTTCGA 59.085 34.615 24.64 0.00 0.00 3.71
4043 7197 7.594758 CACAAATTTGACACCTTATTGTTCGAT 59.405 33.333 24.64 0.00 0.00 3.59
4044 7198 8.788806 ACAAATTTGACACCTTATTGTTCGATA 58.211 29.630 24.64 0.00 0.00 2.92
4045 7199 9.619316 CAAATTTGACACCTTATTGTTCGATAA 57.381 29.630 13.08 0.00 0.00 1.75
4071 7226 0.602905 ACGGAGTGGTAAAGTGCAGC 60.603 55.000 0.00 0.00 42.51 5.25
4075 7230 2.360801 GGAGTGGTAAAGTGCAGCAAAA 59.639 45.455 0.00 0.00 0.00 2.44
4092 7247 4.027437 GCAAAACCCCTTATACAATGGGA 58.973 43.478 0.49 0.00 41.03 4.37
4126 7281 7.691993 AGGAAATATACACATCTAACACCCT 57.308 36.000 0.00 0.00 0.00 4.34
4332 7490 0.107508 CTCATGCTTCACCGGGTCAT 60.108 55.000 6.32 0.00 0.00 3.06
4335 7493 2.359850 GCTTCACCGGGTCATGCA 60.360 61.111 6.32 0.00 0.00 3.96
4395 7555 2.163815 GTCGAGGTAGTAGCACACACAT 59.836 50.000 1.58 0.00 0.00 3.21
4438 7598 2.202987 CCAGATCACCTCAGCCGC 60.203 66.667 0.00 0.00 0.00 6.53
4475 7635 1.337260 CGCAACTCAGCCTCTGTACTT 60.337 52.381 0.00 0.00 32.61 2.24
4563 7723 2.623718 CAAACAGCGTGCGTCGAA 59.376 55.556 0.00 0.00 42.86 3.71
4655 7816 1.067084 CGCTGAGAGATCGTGCCAT 59.933 57.895 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 6.017605 CAGCGCCTCTTTGATTAATCTAATGT 60.018 38.462 16.24 0.00 0.00 2.71
81 82 2.028112 TGTTGAAACTATCAGCGCCTCT 60.028 45.455 2.29 0.00 41.77 3.69
94 95 9.535878 TTTTTGGTTCCAAGTATATGTTGAAAC 57.464 29.630 4.44 0.00 0.00 2.78
166 181 4.450976 AGCGCAATCATGTAGGACAAATA 58.549 39.130 11.47 0.00 0.00 1.40
359 374 1.288419 TGTCATGCACCGCGTTGTAG 61.288 55.000 5.30 0.00 0.00 2.74
360 375 1.301009 TGTCATGCACCGCGTTGTA 60.301 52.632 5.30 0.00 0.00 2.41
374 392 1.300620 GTGTGCCAGCTACGTGTCA 60.301 57.895 0.00 0.00 0.00 3.58
408 426 6.128363 GCTAACATAAGTTAAAGAAGCACCGT 60.128 38.462 0.00 0.00 39.58 4.83
533 551 2.283821 GTGCAAAGGGGATGGGCA 60.284 61.111 0.00 0.00 0.00 5.36
545 563 2.718731 CGCGGTCAAAAGGTGCAA 59.281 55.556 0.00 0.00 0.00 4.08
573 591 2.123897 AAACAACGCCAGGCTGGT 60.124 55.556 32.80 13.33 40.46 4.00
583 601 2.353376 CACAGGCGCCAAACAACG 60.353 61.111 31.54 9.83 0.00 4.10
585 603 2.804167 CACACAGGCGCCAAACAA 59.196 55.556 31.54 0.00 0.00 2.83
617 635 1.073098 GGGTTTGAAGGGGAGAAGGA 58.927 55.000 0.00 0.00 0.00 3.36
684 702 5.108385 AGCTGGTTCACTACGAAAAATTG 57.892 39.130 0.00 0.00 34.69 2.32
691 709 2.351060 CGTACAAGCTGGTTCACTACGA 60.351 50.000 7.58 0.00 0.00 3.43
696 714 3.183775 CAGTAACGTACAAGCTGGTTCAC 59.816 47.826 0.00 0.00 0.00 3.18
718 737 5.924825 GTGATAACGATAAGACCCCACATAC 59.075 44.000 0.00 0.00 0.00 2.39
804 825 7.928706 CCACTATAAAGTCAGCTAACATAAGCT 59.071 37.037 0.00 0.00 43.46 3.74
805 826 7.307455 GCCACTATAAAGTCAGCTAACATAAGC 60.307 40.741 0.00 0.00 36.93 3.09
873 894 2.029844 GCGGTCAAGTGACTCTGGC 61.030 63.158 11.07 6.51 44.20 4.85
917 1002 2.813474 TGGAGCGCGTGCATACAC 60.813 61.111 24.79 8.46 46.23 2.90
948 1033 1.835895 TGGAGGGTAAGGGTTTGGAA 58.164 50.000 0.00 0.00 0.00 3.53
1013 1100 0.596082 TTGGCTAGCCTTTGCGTTTC 59.404 50.000 33.07 4.32 44.33 2.78
1257 1367 1.080434 GATGTATCTCCTCGGCGGC 60.080 63.158 7.21 0.00 0.00 6.53
1448 1567 3.918328 GACCGGGGAGAAGGGGTGA 62.918 68.421 6.32 0.00 31.66 4.02
1526 1645 0.171007 AATTGAATGGCGTGCCGAAG 59.829 50.000 6.37 0.00 39.42 3.79
1527 1646 1.454201 TAATTGAATGGCGTGCCGAA 58.546 45.000 6.37 0.00 39.42 4.30
1528 1647 1.454201 TTAATTGAATGGCGTGCCGA 58.546 45.000 6.37 0.00 39.42 5.54
1531 1650 7.698836 AGATTTAATTAATTGAATGGCGTGC 57.301 32.000 19.57 7.14 0.00 5.34
1532 1651 9.950680 AGTAGATTTAATTAATTGAATGGCGTG 57.049 29.630 19.57 0.00 0.00 5.34
1587 1735 1.678101 AGGCGCATTTGGAAGCTAATC 59.322 47.619 10.83 0.00 0.00 1.75
1588 1736 1.406539 CAGGCGCATTTGGAAGCTAAT 59.593 47.619 10.83 0.00 0.00 1.73
1589 1737 0.810648 CAGGCGCATTTGGAAGCTAA 59.189 50.000 10.83 0.00 0.00 3.09
1590 1738 0.322456 ACAGGCGCATTTGGAAGCTA 60.322 50.000 10.83 0.00 0.00 3.32
1610 1758 4.171754 CGTAAAGCTAGGCTAAGAAACGT 58.828 43.478 0.00 0.00 38.25 3.99
1639 1787 4.729552 TGCATATCCCTTCCAGCTAAAT 57.270 40.909 0.00 0.00 0.00 1.40
1666 1819 1.055849 GGGGGTTGCAATGGAAAGTT 58.944 50.000 0.59 0.00 0.00 2.66
1685 1840 2.025156 GATGCATGAAAGCCGCGG 59.975 61.111 24.05 24.05 0.00 6.46
1700 1855 0.403271 ACCAGCTTTGACCAGCAGAT 59.597 50.000 0.00 0.00 42.84 2.90
1735 1896 0.031917 TTGCCCAGATGGATGCCATT 60.032 50.000 0.00 0.00 45.26 3.16
1840 2004 3.897239 AGGGACATCACAAAACAGACAA 58.103 40.909 0.00 0.00 0.00 3.18
1841 2005 3.576078 AGGGACATCACAAAACAGACA 57.424 42.857 0.00 0.00 0.00 3.41
1923 2253 3.073678 ACATCGTGAGCAAAACTGCATA 58.926 40.909 0.00 0.00 37.25 3.14
1924 2254 1.881973 ACATCGTGAGCAAAACTGCAT 59.118 42.857 0.00 0.00 37.25 3.96
1925 2255 1.002576 CACATCGTGAGCAAAACTGCA 60.003 47.619 0.00 0.00 35.23 4.41
1926 2256 1.678360 CACATCGTGAGCAAAACTGC 58.322 50.000 0.00 0.00 35.23 4.40
1927 2257 1.002576 TGCACATCGTGAGCAAAACTG 60.003 47.619 7.41 0.00 40.81 3.16
1928 2258 1.002468 GTGCACATCGTGAGCAAAACT 60.002 47.619 13.17 0.00 44.93 2.66
1929 2259 1.398595 GTGCACATCGTGAGCAAAAC 58.601 50.000 13.17 0.00 44.93 2.43
2035 2483 1.204062 CACACACGCACGGATTGAC 59.796 57.895 0.00 0.00 0.00 3.18
2038 2486 3.353836 GCCACACACGCACGGATT 61.354 61.111 0.00 0.00 0.00 3.01
2042 2490 2.498761 GAATCAGCCACACACGCACG 62.499 60.000 0.00 0.00 0.00 5.34
2043 2491 1.207593 GAATCAGCCACACACGCAC 59.792 57.895 0.00 0.00 0.00 5.34
2104 3102 2.511373 CCAGCCGAGCGCAATACA 60.511 61.111 11.47 0.00 41.38 2.29
2116 3114 1.971167 TGTTGCGGATTGACCAGCC 60.971 57.895 0.00 0.00 38.90 4.85
2117 3115 1.210155 GTGTTGCGGATTGACCAGC 59.790 57.895 0.00 0.00 38.90 4.85
2118 3116 1.497278 CGTGTTGCGGATTGACCAG 59.503 57.895 0.00 0.00 38.90 4.00
2119 3117 2.612567 GCGTGTTGCGGATTGACCA 61.613 57.895 0.00 0.00 41.69 4.02
2120 3118 2.175811 GCGTGTTGCGGATTGACC 59.824 61.111 0.00 0.00 41.69 4.02
2167 3165 3.299503 AGAGGTGTTTGCAATCTTGGTT 58.700 40.909 0.00 0.00 0.00 3.67
2173 3171 2.229784 CCAGGAAGAGGTGTTTGCAATC 59.770 50.000 0.00 0.00 0.00 2.67
2526 4307 1.947146 CGCGTCGTTCCACTGTCAA 60.947 57.895 0.00 0.00 0.00 3.18
2623 4404 8.515414 ACTCAAAGAAACAGGAGCAATATAAAC 58.485 33.333 0.00 0.00 0.00 2.01
2746 4530 2.161609 GTGGTTCCCGTATTTTGCTCAG 59.838 50.000 0.00 0.00 0.00 3.35
2764 4548 5.710513 TTGGATTGAGATCTTTTGTGTGG 57.289 39.130 0.00 0.00 32.66 4.17
2838 4625 5.105063 GCTGCAAGAAAAAGGAATATGGAC 58.895 41.667 0.00 0.00 34.07 4.02
2947 4734 3.627732 CGCACTCGGATACACTATCTT 57.372 47.619 0.00 0.00 35.52 2.40
3000 4787 3.716195 TACATGGCGGCCTGTGCT 61.716 61.111 26.23 14.99 37.74 4.40
3003 4790 1.520666 GTAGTACATGGCGGCCTGT 59.479 57.895 22.45 22.45 0.00 4.00
3023 4810 0.454452 GTCGTTCGAAAATGCTGCCC 60.454 55.000 0.00 0.00 0.00 5.36
3032 4819 1.928503 GTGTGTTGGAGTCGTTCGAAA 59.071 47.619 0.00 0.00 0.00 3.46
3040 4827 3.115554 GCATTTGTTGTGTGTTGGAGTC 58.884 45.455 0.00 0.00 0.00 3.36
3051 4838 0.515564 GGAGTACGCGCATTTGTTGT 59.484 50.000 5.73 0.00 0.00 3.32
3103 4893 1.681327 GGTGGGAGTAGGCGTCAGA 60.681 63.158 0.00 0.00 0.00 3.27
3126 4916 4.019411 TGTGGGAATAGATTCAGAAGCACA 60.019 41.667 0.31 0.00 38.53 4.57
3141 4931 2.286935 AGGTGGGATACTGTGGGAAT 57.713 50.000 0.00 0.00 0.00 3.01
3153 4943 1.963679 GCGATTTGCAAAGGTGGGA 59.036 52.632 18.19 0.00 45.45 4.37
3218 5008 0.103937 CCAAGAGATCGACCCTGAGC 59.896 60.000 0.00 0.00 0.00 4.26
3266 5056 5.578336 AGTCATAGATCGACAACAATGTGTG 59.422 40.000 0.00 0.00 40.74 3.82
3322 5112 7.154656 AGTAATTGTCGAGCATATCAGCAATA 58.845 34.615 0.00 0.00 36.85 1.90
3369 5159 3.570540 TGTCCATGAGACTGGGAGATAG 58.429 50.000 13.32 0.00 46.46 2.08
3370 5160 3.688049 TGTCCATGAGACTGGGAGATA 57.312 47.619 13.32 0.00 46.46 1.98
3371 5161 2.557555 TGTCCATGAGACTGGGAGAT 57.442 50.000 13.32 0.00 46.46 2.75
3372 5162 2.182827 CTTGTCCATGAGACTGGGAGA 58.817 52.381 13.32 0.00 46.46 3.71
3373 5163 1.406614 GCTTGTCCATGAGACTGGGAG 60.407 57.143 13.32 8.46 46.46 4.30
3374 5164 0.615331 GCTTGTCCATGAGACTGGGA 59.385 55.000 13.32 0.00 46.46 4.37
3375 5165 0.393537 GGCTTGTCCATGAGACTGGG 60.394 60.000 13.32 6.63 46.46 4.45
3376 5166 0.325933 TGGCTTGTCCATGAGACTGG 59.674 55.000 13.32 8.39 46.46 4.00
3426 5216 9.849166 AGTAAACCAACATTCCAAATAAATACG 57.151 29.630 0.00 0.00 0.00 3.06
3509 5299 9.129209 GACTAACTCAATGAAATTTAACAAGGC 57.871 33.333 0.00 0.00 31.22 4.35
3559 5350 6.092748 AGCTAAAACCAAAATAGAACATGCG 58.907 36.000 0.00 0.00 0.00 4.73
3925 7008 7.173390 TGACCATGATACTTATCTCGTCTACAG 59.827 40.741 0.00 0.00 33.88 2.74
4037 7191 6.211515 ACCACTCCGTATATGTTTATCGAAC 58.788 40.000 0.00 0.00 38.78 3.95
4038 7192 6.395426 ACCACTCCGTATATGTTTATCGAA 57.605 37.500 0.00 0.00 0.00 3.71
4039 7193 7.509141 TTACCACTCCGTATATGTTTATCGA 57.491 36.000 0.00 0.00 0.00 3.59
4040 7194 7.864379 ACTTTACCACTCCGTATATGTTTATCG 59.136 37.037 0.00 0.00 0.00 2.92
4041 7195 8.975439 CACTTTACCACTCCGTATATGTTTATC 58.025 37.037 0.00 0.00 0.00 1.75
4042 7196 7.440255 GCACTTTACCACTCCGTATATGTTTAT 59.560 37.037 0.00 0.00 0.00 1.40
4043 7197 6.757947 GCACTTTACCACTCCGTATATGTTTA 59.242 38.462 0.00 0.00 0.00 2.01
4044 7198 5.583457 GCACTTTACCACTCCGTATATGTTT 59.417 40.000 0.00 0.00 0.00 2.83
4045 7199 5.114081 GCACTTTACCACTCCGTATATGTT 58.886 41.667 0.00 0.00 0.00 2.71
4092 7247 9.905713 AGATGTGTATATTTCCTTGTGTACATT 57.094 29.630 0.00 0.00 0.00 2.71
4126 7281 1.741028 TCCACCATGAGTTTGAGGGA 58.259 50.000 0.00 0.00 0.00 4.20
4215 7373 1.348036 GCCCTCTGAGTTACAGTTGGT 59.652 52.381 3.66 0.00 45.86 3.67
4332 7490 1.754226 TGGTGCTATCAGTATCGTGCA 59.246 47.619 0.00 0.00 0.00 4.57
4335 7493 4.276183 CAGTACTGGTGCTATCAGTATCGT 59.724 45.833 15.49 4.26 45.70 3.73
4395 7555 3.493699 CGGTGGTTACTTGAGGACTTTGA 60.494 47.826 0.00 0.00 0.00 2.69
4475 7635 0.676184 AGACTGCAGTTTCTCGCTCA 59.324 50.000 22.65 0.00 0.00 4.26
4555 7715 0.108804 GTGATCCCTCTTTCGACGCA 60.109 55.000 0.00 0.00 0.00 5.24
4563 7723 1.694048 CCTGGGCTAGTGATCCCTCTT 60.694 57.143 4.94 0.00 43.04 2.85
4626 7787 2.851195 TCTCTCAGCGCCTTTTCTTTT 58.149 42.857 2.29 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.