Multiple sequence alignment - TraesCS4A01G108800

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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 TraesCS4A01G108800 chr4A 100.000 6313 0 0 1 6313 127482185 127488497 0.000000e+00 11659.0
1 TraesCS4A01G108800 chr4A 98.189 2319 38 4 735 3052 127289830 127287515 0.000000e+00 4047.0
2 TraesCS4A01G108800 chr4A 98.570 1189 14 3 3051 4237 127287257 127286070 0.000000e+00 2098.0
3 TraesCS4A01G108800 chr4A 93.775 755 29 8 1 743 127330787 127330039 0.000000e+00 1118.0
4 TraesCS4A01G108800 chr4A 95.468 662 26 2 4884 5542 127281559 127280899 0.000000e+00 1053.0
5 TraesCS4A01G108800 chr4A 91.667 72 3 2 5374 5444 127281131 127281062 5.210000e-16 97.1
6 TraesCS4A01G108800 chr4A 93.846 65 3 1 5374 5437 127487496 127487560 5.210000e-16 97.1
7 TraesCS4A01G108800 chr4A 97.727 44 0 1 5499 5542 127487722 127487764 2.440000e-09 75.0
8 TraesCS4A01G108800 chr4D 96.142 2592 82 8 138 2716 340553827 340551241 0.000000e+00 4217.0
9 TraesCS4A01G108800 chr4D 96.888 2153 31 8 2729 4878 340551257 340549138 0.000000e+00 3572.0
10 TraesCS4A01G108800 chr4D 96.847 666 13 4 4884 5542 340549097 340548433 0.000000e+00 1107.0
11 TraesCS4A01G108800 chr4D 100.000 83 0 0 5538 5620 340548475 340548393 3.050000e-33 154.0
12 TraesCS4A01G108800 chr4D 91.429 105 3 1 1 105 340553910 340553812 8.530000e-29 139.0
13 TraesCS4A01G108800 chr4D 91.667 72 3 2 5374 5444 340548662 340548593 5.210000e-16 97.1
14 TraesCS4A01G108800 chr4B 97.350 2151 34 3 2729 4878 422032875 422030747 0.000000e+00 3635.0
15 TraesCS4A01G108800 chr4B 96.661 2186 69 4 533 2716 422035042 422032859 0.000000e+00 3629.0
16 TraesCS4A01G108800 chr4B 94.061 623 11 14 4921 5542 422030544 422029947 0.000000e+00 922.0
17 TraesCS4A01G108800 chr4B 88.715 319 27 5 138 454 422035488 422035177 1.280000e-101 381.0
18 TraesCS4A01G108800 chr4B 100.000 82 0 0 5538 5619 422029989 422029908 1.100000e-32 152.0
19 TraesCS4A01G108800 chr4B 95.181 83 2 2 472 554 422035133 422035053 5.140000e-26 130.0
20 TraesCS4A01G108800 chr4B 91.667 72 3 2 5374 5444 422030177 422030108 5.210000e-16 97.1
21 TraesCS4A01G108800 chr4B 96.552 58 1 1 49 105 422035530 422035473 1.870000e-15 95.3
22 TraesCS4A01G108800 chr7A 99.410 678 4 0 5636 6313 157170335 157171012 0.000000e+00 1230.0
23 TraesCS4A01G108800 chr7A 98.212 671 7 3 5647 6313 115322765 115323434 0.000000e+00 1168.0
24 TraesCS4A01G108800 chr6B 99.409 677 4 0 5637 6313 383569863 383569187 0.000000e+00 1229.0
25 TraesCS4A01G108800 chr6B 99.028 617 6 0 5697 6313 494090246 494090862 0.000000e+00 1107.0
26 TraesCS4A01G108800 chr3D 89.501 981 88 10 3904 4873 585711341 585710365 0.000000e+00 1227.0
27 TraesCS4A01G108800 chr3D 86.531 980 113 14 3907 4876 585433070 585432100 0.000000e+00 1061.0
28 TraesCS4A01G108800 chr3D 86.032 988 109 20 3904 4873 585652807 585653783 0.000000e+00 1033.0
29 TraesCS4A01G108800 chr3D 87.247 839 100 6 1838 2674 585712615 585711782 0.000000e+00 950.0
30 TraesCS4A01G108800 chr3D 86.874 838 96 6 1838 2674 585912161 585911337 0.000000e+00 926.0
31 TraesCS4A01G108800 chr3D 83.315 911 112 21 940 1830 585631374 585632264 0.000000e+00 804.0
32 TraesCS4A01G108800 chr3D 82.609 736 99 17 934 1650 585401562 585400837 1.930000e-174 623.0
33 TraesCS4A01G108800 chr3D 87.344 482 43 9 1359 1829 585713576 585713102 2.590000e-148 536.0
34 TraesCS4A01G108800 chr3D 90.633 395 36 1 2729 3123 585911336 585910943 2.020000e-144 523.0
35 TraesCS4A01G108800 chr3D 86.580 462 57 5 2729 3187 585616496 585616955 7.300000e-139 505.0
36 TraesCS4A01G108800 chr3D 86.237 465 57 4 2729 3187 585433555 585433092 1.220000e-136 497.0
37 TraesCS4A01G108800 chr3D 87.470 415 37 7 1386 1791 585914541 585914133 1.240000e-126 464.0
38 TraesCS4A01G108800 chr3D 85.323 402 44 10 934 1324 585713977 585713580 9.860000e-108 401.0
39 TraesCS4A01G108800 chr3D 88.261 230 21 3 5129 5357 585653973 585654197 2.900000e-68 270.0
40 TraesCS4A01G108800 chr3D 87.234 235 24 3 5129 5362 585431902 585431673 4.850000e-66 263.0
41 TraesCS4A01G108800 chr3D 88.235 221 19 4 5129 5348 585618463 585618677 2.260000e-64 257.0
42 TraesCS4A01G108800 chr3D 84.462 251 29 7 5113 5362 585710155 585709914 8.180000e-59 239.0
43 TraesCS4A01G108800 chr3D 82.673 202 19 8 700 886 585631087 585631287 1.410000e-36 165.0
44 TraesCS4A01G108800 chr3D 81.053 190 20 6 706 886 585714242 585714060 3.070000e-28 137.0
45 TraesCS4A01G108800 chr3D 82.237 152 15 5 770 911 585915172 585915023 3.090000e-23 121.0
46 TraesCS4A01G108800 chr3D 91.765 85 3 3 5538 5618 585655170 585655254 1.440000e-21 115.0
47 TraesCS4A01G108800 chr3D 90.588 85 4 3 5538 5618 585467245 585467161 6.690000e-20 110.0
48 TraesCS4A01G108800 chr3D 90.588 85 4 3 5538 5618 585618786 585618870 6.690000e-20 110.0
49 TraesCS4A01G108800 chr3D 90.588 85 4 3 5538 5618 585654306 585654390 6.690000e-20 110.0
50 TraesCS4A01G108800 chr3D 80.180 111 15 2 726 829 585456395 585456285 6.790000e-10 76.8
51 TraesCS4A01G108800 chr3D 86.364 66 1 7 395 459 585714324 585714266 1.470000e-06 65.8
52 TraesCS4A01G108800 chr3D 86.667 60 1 4 400 459 585460409 585460357 6.830000e-05 60.2
53 TraesCS4A01G108800 chr3D 84.615 65 3 5 395 459 585635792 585635849 2.460000e-04 58.4
54 TraesCS4A01G108800 chr3D 84.615 65 3 5 395 459 585664958 585665015 2.460000e-04 58.4
55 TraesCS4A01G108800 chr3A 98.951 667 7 0 5647 6313 25927552 25928218 0.000000e+00 1194.0
56 TraesCS4A01G108800 chr3B 88.697 982 94 12 3904 4873 782113543 782112567 0.000000e+00 1182.0
57 TraesCS4A01G108800 chr3B 88.830 940 92 10 3904 4834 781553490 781552555 0.000000e+00 1142.0
58 TraesCS4A01G108800 chr3B 87.245 980 107 13 3907 4876 781837035 781836064 0.000000e+00 1101.0
59 TraesCS4A01G108800 chr3B 87.041 980 107 14 3904 4871 782341675 782340704 0.000000e+00 1088.0
60 TraesCS4A01G108800 chr3B 87.933 837 100 1 1838 2674 782482995 782482160 0.000000e+00 985.0
61 TraesCS4A01G108800 chr3B 85.775 935 86 19 940 1845 782484530 782483614 0.000000e+00 946.0
62 TraesCS4A01G108800 chr3B 85.867 934 77 23 938 1835 781854192 781853278 0.000000e+00 942.0
63 TraesCS4A01G108800 chr3B 86.477 843 104 7 1838 2674 782114824 782113986 0.000000e+00 917.0
64 TraesCS4A01G108800 chr3B 86.158 838 113 3 1838 2674 781554767 781553932 0.000000e+00 902.0
65 TraesCS4A01G108800 chr3B 81.372 1181 142 41 706 1830 781839557 781838399 0.000000e+00 891.0
66 TraesCS4A01G108800 chr3B 88.267 750 78 8 1972 2716 782342869 782342125 0.000000e+00 889.0
67 TraesCS4A01G108800 chr3B 83.647 850 83 24 934 1769 782343938 782343131 0.000000e+00 749.0
68 TraesCS4A01G108800 chr3B 83.356 733 95 15 934 1648 781809798 781809075 0.000000e+00 652.0
69 TraesCS4A01G108800 chr3B 89.107 459 46 4 2729 3185 781837515 781837059 9.180000e-158 568.0
70 TraesCS4A01G108800 chr3B 87.164 483 45 8 1359 1830 781555730 781555254 3.350000e-147 532.0
71 TraesCS4A01G108800 chr3B 86.028 501 49 10 1359 1845 782115813 782115320 9.380000e-143 518.0
72 TraesCS4A01G108800 chr3B 89.698 398 38 3 2729 3126 782482159 782481765 7.300000e-139 505.0
73 TraesCS4A01G108800 chr3B 84.483 406 42 14 934 1322 781556137 781555736 1.280000e-101 381.0
74 TraesCS4A01G108800 chr3B 90.406 271 21 4 934 1203 782116296 782116030 1.010000e-92 351.0
75 TraesCS4A01G108800 chr3B 80.000 190 22 6 706 886 782116561 782116379 6.640000e-25 126.0
76 TraesCS4A01G108800 chr3B 87.387 111 9 2 5436 5542 781552037 781551928 8.590000e-24 122.0
77 TraesCS4A01G108800 chr3B 82.313 147 18 6 771 911 781854447 781854303 3.090000e-23 121.0
78 TraesCS4A01G108800 chr3B 91.765 85 3 3 5538 5618 781669541 781669457 1.440000e-21 115.0
79 TraesCS4A01G108800 chr3B 100.000 34 0 0 426 459 782116701 782116668 5.280000e-06 63.9
80 TraesCS4A01G108800 chr3B 86.667 60 1 5 400 459 781681545 781681493 6.830000e-05 60.2
81 TraesCS4A01G108800 chr2B 98.227 677 9 3 5638 6313 790107331 790108005 0.000000e+00 1181.0
82 TraesCS4A01G108800 chr2B 99.837 614 1 0 5697 6310 753935805 753936418 0.000000e+00 1129.0
83 TraesCS4A01G108800 chr2B 96.875 32 0 1 653 684 761720187 761720217 1.100000e-02 52.8
84 TraesCS4A01G108800 chr1B 99.838 617 1 0 5697 6313 546702658 546703274 0.000000e+00 1134.0
85 TraesCS4A01G108800 chr5B 99.676 617 2 0 5697 6313 613640297 613640913 0.000000e+00 1129.0
86 TraesCS4A01G108800 chrUn 100.000 405 0 0 1402 1806 478229411 478229815 0.000000e+00 749.0
87 TraesCS4A01G108800 chrUn 84.075 584 66 12 1257 1830 358608502 358609068 7.200000e-149 538.0
88 TraesCS4A01G108800 chrUn 86.797 462 56 5 2729 3187 358609858 358610317 1.570000e-140 510.0
89 TraesCS4A01G108800 chrUn 87.406 397 46 4 2794 3187 321263238 321263633 2.680000e-123 453.0
90 TraesCS4A01G108800 chrUn 88.235 221 19 4 5129 5348 300191703 300191917 2.260000e-64 257.0
91 TraesCS4A01G108800 chrUn 88.235 221 19 4 5129 5348 321265141 321265355 2.260000e-64 257.0
92 TraesCS4A01G108800 chrUn 90.588 85 4 3 5538 5618 300192026 300192110 6.690000e-20 110.0
93 TraesCS4A01G108800 chrUn 90.588 85 4 3 5538 5618 321265464 321265548 6.690000e-20 110.0
94 TraesCS4A01G108800 chr6D 82.119 151 24 2 246 393 16850362 16850512 6.640000e-25 126.0
95 TraesCS4A01G108800 chr5A 88.060 67 8 0 3397 3463 700438329 700438395 5.250000e-11 80.5


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 TraesCS4A01G108800 chr4A 127482185 127488497 6312 False 3943.700000 11659 97.191000 1 6313 3 chr4A.!!$F1 6312
1 TraesCS4A01G108800 chr4A 127286070 127289830 3760 True 3072.500000 4047 98.379500 735 4237 2 chr4A.!!$R3 3502
2 TraesCS4A01G108800 chr4A 127330039 127330787 748 True 1118.000000 1118 93.775000 1 743 1 chr4A.!!$R1 742
3 TraesCS4A01G108800 chr4A 127280899 127281559 660 True 575.050000 1053 93.567500 4884 5542 2 chr4A.!!$R2 658
4 TraesCS4A01G108800 chr4D 340548393 340553910 5517 True 1547.683333 4217 95.495500 1 5620 6 chr4D.!!$R1 5619
5 TraesCS4A01G108800 chr4B 422029908 422035530 5622 True 1130.175000 3635 95.023375 49 5619 8 chr4B.!!$R1 5570
6 TraesCS4A01G108800 chr7A 157170335 157171012 677 False 1230.000000 1230 99.410000 5636 6313 1 chr7A.!!$F2 677
7 TraesCS4A01G108800 chr7A 115322765 115323434 669 False 1168.000000 1168 98.212000 5647 6313 1 chr7A.!!$F1 666
8 TraesCS4A01G108800 chr6B 383569187 383569863 676 True 1229.000000 1229 99.409000 5637 6313 1 chr6B.!!$R1 676
9 TraesCS4A01G108800 chr6B 494090246 494090862 616 False 1107.000000 1107 99.028000 5697 6313 1 chr6B.!!$F1 616
10 TraesCS4A01G108800 chr3D 585400837 585401562 725 True 623.000000 623 82.609000 934 1650 1 chr3D.!!$R1 716
11 TraesCS4A01G108800 chr3D 585431673 585433555 1882 True 607.000000 1061 86.667333 2729 5362 3 chr3D.!!$R3 2633
12 TraesCS4A01G108800 chr3D 585910943 585915172 4229 True 508.500000 926 86.803500 770 3123 4 chr3D.!!$R6 2353
13 TraesCS4A01G108800 chr3D 585709914 585714324 4410 True 507.971429 1227 85.899143 395 5362 7 chr3D.!!$R5 4967
14 TraesCS4A01G108800 chr3D 585652807 585655254 2447 False 382.000000 1033 89.161500 3904 5618 4 chr3D.!!$F4 1714
15 TraesCS4A01G108800 chr3D 585631087 585635849 4762 False 342.466667 804 83.534333 395 1830 3 chr3D.!!$F3 1435
16 TraesCS4A01G108800 chr3D 585616496 585618870 2374 False 290.666667 505 88.467667 2729 5618 3 chr3D.!!$F2 2889
17 TraesCS4A01G108800 chr3A 25927552 25928218 666 False 1194.000000 1194 98.951000 5647 6313 1 chr3A.!!$F1 666
18 TraesCS4A01G108800 chr3B 782340704 782343938 3234 True 908.666667 1088 86.318333 934 4871 3 chr3B.!!$R8 3937
19 TraesCS4A01G108800 chr3B 781836064 781839557 3493 True 853.333333 1101 85.908000 706 4876 3 chr3B.!!$R5 4170
20 TraesCS4A01G108800 chr3B 782481765 782484530 2765 True 812.000000 985 87.802000 940 3126 3 chr3B.!!$R9 2186
21 TraesCS4A01G108800 chr3B 781809075 781809798 723 True 652.000000 652 83.356000 934 1648 1 chr3B.!!$R3 714
22 TraesCS4A01G108800 chr3B 781551928 781556137 4209 True 615.800000 1142 86.804400 934 5542 5 chr3B.!!$R4 4608
23 TraesCS4A01G108800 chr3B 781853278 781854447 1169 True 531.500000 942 84.090000 771 1835 2 chr3B.!!$R6 1064
24 TraesCS4A01G108800 chr3B 782112567 782116701 4134 True 526.316667 1182 88.601333 426 4873 6 chr3B.!!$R7 4447
25 TraesCS4A01G108800 chr2B 790107331 790108005 674 False 1181.000000 1181 98.227000 5638 6313 1 chr2B.!!$F3 675
26 TraesCS4A01G108800 chr2B 753935805 753936418 613 False 1129.000000 1129 99.837000 5697 6310 1 chr2B.!!$F1 613
27 TraesCS4A01G108800 chr1B 546702658 546703274 616 False 1134.000000 1134 99.838000 5697 6313 1 chr1B.!!$F1 616
28 TraesCS4A01G108800 chr5B 613640297 613640913 616 False 1129.000000 1129 99.676000 5697 6313 1 chr5B.!!$F1 616
29 TraesCS4A01G108800 chrUn 358608502 358610317 1815 False 524.000000 538 85.436000 1257 3187 2 chrUn.!!$F4 1930
30 TraesCS4A01G108800 chrUn 321263238 321265548 2310 False 273.333333 453 88.743000 2794 5618 3 chrUn.!!$F3 2824

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
106 107 0.174389 CCATGTGTGGTCTCTCTCCG 59.826 60.000 0.00 0.0 40.83 4.63 F
468 508 0.387929 TTATGATCCTCACCGTCGGC 59.612 55.000 12.28 0.0 0.00 5.54 F
669 739 1.268352 ACGGCATGTTTGTGCGTATTT 59.732 42.857 0.00 0.0 45.97 1.40 F
814 893 1.757682 TGACCTTTGAACCGCACTTT 58.242 45.000 0.00 0.0 0.00 2.66 F
1122 1372 2.374504 AGAGCATAAGCATACAGGGCAT 59.625 45.455 0.00 0.0 45.49 4.40 F
2712 5334 6.282199 ACGTTCATGTAGATTAGTTGGACT 57.718 37.500 0.00 0.0 0.00 3.85 F
3591 6479 2.263540 GCATGCCTTGCCAACAGG 59.736 61.111 6.36 0.0 46.15 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1961 4538 4.210331 AGGCATCAAAAGAACAAGACACT 58.790 39.130 0.00 0.0 0.00 3.55 R
2151 4736 4.508551 ACCTGAATATGCATCCAGTGAA 57.491 40.909 0.19 0.0 0.00 3.18 R
2726 5348 8.635765 TGAATGCTAAAGTCCAACTAATCTTT 57.364 30.769 0.00 0.0 34.98 2.52 R
2727 5349 8.814038 ATGAATGCTAAAGTCCAACTAATCTT 57.186 30.769 0.00 0.0 0.00 2.40 R
3591 6479 1.880340 CTGAGAACGGAGCATCGCC 60.880 63.158 0.00 0.0 34.37 5.54 R
3613 6501 5.059833 GGTTAGAAGAGCTATGAATGTGGG 58.940 45.833 0.00 0.0 0.00 4.61 R
5623 9379 0.751643 CGGGGGTATGGCTTCCTTTG 60.752 60.000 0.00 0.0 0.00 2.77 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
37 38 4.320057 GCACATGCCTAGTGATGCTATTTC 60.320 45.833 4.67 0.00 39.30 2.17
39 40 6.226052 CACATGCCTAGTGATGCTATTTCTA 58.774 40.000 0.00 0.00 39.30 2.10
40 41 6.877855 CACATGCCTAGTGATGCTATTTCTAT 59.122 38.462 0.00 0.00 39.30 1.98
42 43 7.941238 ACATGCCTAGTGATGCTATTTCTATTT 59.059 33.333 0.00 0.00 0.00 1.40
43 44 7.734924 TGCCTAGTGATGCTATTTCTATTTG 57.265 36.000 0.00 0.00 0.00 2.32
44 45 7.282585 TGCCTAGTGATGCTATTTCTATTTGT 58.717 34.615 0.00 0.00 0.00 2.83
45 46 7.227314 TGCCTAGTGATGCTATTTCTATTTGTG 59.773 37.037 0.00 0.00 0.00 3.33
46 47 7.442364 GCCTAGTGATGCTATTTCTATTTGTGA 59.558 37.037 0.00 0.00 0.00 3.58
47 48 9.330063 CCTAGTGATGCTATTTCTATTTGTGAA 57.670 33.333 0.00 0.00 0.00 3.18
106 107 0.174389 CCATGTGTGGTCTCTCTCCG 59.826 60.000 0.00 0.00 40.83 4.63
320 332 2.436646 CCGCTGAGCCATTTCCGT 60.437 61.111 0.00 0.00 0.00 4.69
335 348 2.732094 CGTCGGAAGCGAAACGGT 60.732 61.111 0.00 0.00 40.00 4.83
468 508 0.387929 TTATGATCCTCACCGTCGGC 59.612 55.000 12.28 0.00 0.00 5.54
599 669 6.829298 CCAGAGTGAGTAGTCCACTTTATAGA 59.171 42.308 0.00 0.00 44.14 1.98
669 739 1.268352 ACGGCATGTTTGTGCGTATTT 59.732 42.857 0.00 0.00 45.97 1.40
774 848 8.441311 AATATGTGTCTGTCCCTATATGACAT 57.559 34.615 5.88 0.00 41.58 3.06
814 893 1.757682 TGACCTTTGAACCGCACTTT 58.242 45.000 0.00 0.00 0.00 2.66
1122 1372 2.374504 AGAGCATAAGCATACAGGGCAT 59.625 45.455 0.00 0.00 45.49 4.40
1176 1426 7.466455 CGTCAAATGAGAACTATGGAAATGGAG 60.466 40.741 0.00 0.00 0.00 3.86
1961 4538 6.755141 GCGTCTATTGTTTTAGTATCACTCCA 59.245 38.462 0.00 0.00 0.00 3.86
2151 4736 8.655935 ATGTAATTTGAAGGGTTCTTTCAGAT 57.344 30.769 0.00 0.00 32.52 2.90
2710 5332 7.972832 AAAACGTTCATGTAGATTAGTTGGA 57.027 32.000 0.00 0.00 0.00 3.53
2711 5333 6.963049 AACGTTCATGTAGATTAGTTGGAC 57.037 37.500 0.00 0.00 0.00 4.02
2712 5334 6.282199 ACGTTCATGTAGATTAGTTGGACT 57.718 37.500 0.00 0.00 0.00 3.85
2713 5335 6.698380 ACGTTCATGTAGATTAGTTGGACTT 58.302 36.000 0.00 0.00 0.00 3.01
2714 5336 7.159372 ACGTTCATGTAGATTAGTTGGACTTT 58.841 34.615 0.00 0.00 0.00 2.66
2715 5337 8.308931 ACGTTCATGTAGATTAGTTGGACTTTA 58.691 33.333 0.00 0.00 0.00 1.85
2716 5338 9.314321 CGTTCATGTAGATTAGTTGGACTTTAT 57.686 33.333 0.00 0.00 0.00 1.40
3591 6479 2.263540 GCATGCCTTGCCAACAGG 59.736 61.111 6.36 0.00 46.15 4.00
3613 6501 2.656085 CGATGCTCCGTTCTCAGATAC 58.344 52.381 0.00 0.00 0.00 2.24
3618 6506 2.100197 CTCCGTTCTCAGATACCCACA 58.900 52.381 0.00 0.00 0.00 4.17
3934 6824 1.138247 CTCCTTGCAATGCCGCTTC 59.862 57.895 1.53 0.00 0.00 3.86
4537 7759 4.972201 ACTTTGCTTTGTTTTGCACATTG 58.028 34.783 0.00 0.00 39.05 2.82
4807 8275 3.636300 TCAAGTTTGAAATCCAGGTGTGG 59.364 43.478 0.00 0.00 38.64 4.17
4881 8371 8.595362 TGGATTTTCTACTCAATCTCACTAGA 57.405 34.615 0.00 0.00 35.80 2.43
4882 8372 9.206690 TGGATTTTCTACTCAATCTCACTAGAT 57.793 33.333 0.00 0.00 44.67 1.98
4905 8434 3.582714 GCAAAGGCTGGCCAATATATC 57.417 47.619 7.01 0.00 38.92 1.63
5358 9083 7.665690 AGTGATGAATAGTGAGACATATGACC 58.334 38.462 10.38 0.64 0.00 4.02
5414 9163 6.257411 GGTTGAGTGATGAATAGTGAGACATG 59.743 42.308 0.00 0.00 0.00 3.21
5425 9174 3.225940 AGTGAGACATGTGACTGTCAGA 58.774 45.455 11.41 10.79 46.45 3.27
5502 9255 1.594293 CCTGACAGCGAACCGTGTT 60.594 57.895 0.00 0.00 0.00 3.32
5503 9256 1.564622 CTGACAGCGAACCGTGTTG 59.435 57.895 0.00 0.00 0.00 3.33
5504 9257 1.151777 CTGACAGCGAACCGTGTTGT 61.152 55.000 0.00 0.00 0.00 3.32
5505 9258 0.741574 TGACAGCGAACCGTGTTGTT 60.742 50.000 0.00 0.00 0.00 2.83
5506 9259 0.375803 GACAGCGAACCGTGTTGTTT 59.624 50.000 0.00 0.00 0.00 2.83
5507 9260 0.098025 ACAGCGAACCGTGTTGTTTG 59.902 50.000 0.00 0.00 33.53 2.93
5508 9261 0.591236 CAGCGAACCGTGTTGTTTGG 60.591 55.000 0.00 0.00 31.46 3.28
5509 9262 1.298788 GCGAACCGTGTTGTTTGGG 60.299 57.895 0.00 0.00 31.46 4.12
5510 9263 1.995646 GCGAACCGTGTTGTTTGGGT 61.996 55.000 0.00 0.00 31.46 4.51
5511 9264 0.248296 CGAACCGTGTTGTTTGGGTG 60.248 55.000 0.00 0.00 31.96 4.61
5512 9265 1.096416 GAACCGTGTTGTTTGGGTGA 58.904 50.000 0.00 0.00 31.96 4.02
5513 9266 0.812549 AACCGTGTTGTTTGGGTGAC 59.187 50.000 0.00 0.00 31.96 3.67
5514 9267 0.034863 ACCGTGTTGTTTGGGTGACT 60.035 50.000 0.00 0.00 0.00 3.41
5515 9268 1.209990 ACCGTGTTGTTTGGGTGACTA 59.790 47.619 0.00 0.00 0.00 2.59
5516 9269 1.871039 CCGTGTTGTTTGGGTGACTAG 59.129 52.381 0.00 0.00 0.00 2.57
5517 9270 2.557317 CGTGTTGTTTGGGTGACTAGT 58.443 47.619 0.00 0.00 0.00 2.57
5518 9271 2.542595 CGTGTTGTTTGGGTGACTAGTC 59.457 50.000 16.32 16.32 0.00 2.59
5519 9272 2.876550 GTGTTGTTTGGGTGACTAGTCC 59.123 50.000 20.11 11.08 0.00 3.85
5520 9273 2.775384 TGTTGTTTGGGTGACTAGTCCT 59.225 45.455 20.11 0.00 0.00 3.85
5521 9274 3.139077 GTTGTTTGGGTGACTAGTCCTG 58.861 50.000 20.11 0.00 0.00 3.86
5522 9275 2.404559 TGTTTGGGTGACTAGTCCTGT 58.595 47.619 20.11 0.00 0.00 4.00
5523 9276 2.104111 TGTTTGGGTGACTAGTCCTGTG 59.896 50.000 20.11 0.00 0.00 3.66
5524 9277 2.097110 TTGGGTGACTAGTCCTGTGT 57.903 50.000 20.11 0.00 0.00 3.72
5525 9278 1.338107 TGGGTGACTAGTCCTGTGTG 58.662 55.000 20.11 0.00 0.00 3.82
5526 9279 1.133294 TGGGTGACTAGTCCTGTGTGA 60.133 52.381 20.11 0.00 0.00 3.58
5527 9280 1.968493 GGGTGACTAGTCCTGTGTGAA 59.032 52.381 20.11 0.00 0.00 3.18
5528 9281 2.028930 GGGTGACTAGTCCTGTGTGAAG 60.029 54.545 20.11 0.00 0.00 3.02
5529 9282 2.610727 GGTGACTAGTCCTGTGTGAAGC 60.611 54.545 20.11 4.84 0.00 3.86
5530 9283 2.035961 GTGACTAGTCCTGTGTGAAGCA 59.964 50.000 20.11 0.00 0.00 3.91
5623 9379 5.243207 ACTTATATGGTAAATAGGCGGTGC 58.757 41.667 0.00 0.00 0.00 5.01
5624 9380 3.780804 ATATGGTAAATAGGCGGTGCA 57.219 42.857 0.00 0.00 0.00 4.57
5625 9381 2.428544 ATGGTAAATAGGCGGTGCAA 57.571 45.000 0.00 0.00 0.00 4.08
5627 9383 2.088423 TGGTAAATAGGCGGTGCAAAG 58.912 47.619 0.00 0.00 0.00 2.77
5628 9384 1.404035 GGTAAATAGGCGGTGCAAAGG 59.596 52.381 0.00 0.00 0.00 3.11
5629 9385 2.361789 GTAAATAGGCGGTGCAAAGGA 58.638 47.619 0.00 0.00 0.00 3.36
5630 9386 1.917872 AAATAGGCGGTGCAAAGGAA 58.082 45.000 0.00 0.00 0.00 3.36
5631 9387 1.463674 AATAGGCGGTGCAAAGGAAG 58.536 50.000 0.00 0.00 0.00 3.46
5632 9388 1.032114 ATAGGCGGTGCAAAGGAAGC 61.032 55.000 0.00 0.00 0.00 3.86
5633 9389 4.056125 GGCGGTGCAAAGGAAGCC 62.056 66.667 0.00 0.00 37.61 4.35
5634 9390 3.294493 GCGGTGCAAAGGAAGCCA 61.294 61.111 0.00 0.00 0.00 4.75
6294 10782 4.386711 CTTCTCGGGTGAAAACCTAACTT 58.613 43.478 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 7.657761 TGCAAAGTTTTCTTAAAAAGGTTCACA 59.342 29.630 0.00 0.00 39.48 3.58
43 44 8.024146 TGCAAAGTTTTCTTAAAAAGGTTCAC 57.976 30.769 0.00 0.00 39.48 3.18
44 45 8.663911 CATGCAAAGTTTTCTTAAAAAGGTTCA 58.336 29.630 0.00 0.00 39.48 3.18
45 46 8.664798 ACATGCAAAGTTTTCTTAAAAAGGTTC 58.335 29.630 0.00 0.00 39.48 3.62
46 47 8.560355 ACATGCAAAGTTTTCTTAAAAAGGTT 57.440 26.923 0.00 0.00 39.48 3.50
47 48 8.560355 AACATGCAAAGTTTTCTTAAAAAGGT 57.440 26.923 0.00 0.00 39.48 3.50
320 332 2.356553 CCACCGTTTCGCTTCCGA 60.357 61.111 0.00 0.00 42.66 4.55
335 348 0.968901 AGAATACACGTCTCGGCCCA 60.969 55.000 0.00 0.00 0.00 5.36
545 615 0.822121 GTCAACGCCCCAAAGAAGGT 60.822 55.000 0.00 0.00 0.00 3.50
599 669 1.925455 CCTCCACCACCACCCTCAT 60.925 63.158 0.00 0.00 0.00 2.90
680 751 6.399743 TGTCTAGTAGCGAGTAGGATCATAG 58.600 44.000 8.61 0.00 30.49 2.23
814 893 2.359169 GGACATGAGTGGCGAGGGA 61.359 63.158 0.00 0.00 32.55 4.20
1122 1372 8.879759 CGGTTCAGAATCTTTATAGCAACTTTA 58.120 33.333 0.00 0.00 0.00 1.85
1961 4538 4.210331 AGGCATCAAAAGAACAAGACACT 58.790 39.130 0.00 0.00 0.00 3.55
2151 4736 4.508551 ACCTGAATATGCATCCAGTGAA 57.491 40.909 0.19 0.00 0.00 3.18
2724 5346 9.914131 GAATGCTAAAGTCCAACTAATCTTTTT 57.086 29.630 0.00 0.00 33.22 1.94
2725 5347 9.077885 TGAATGCTAAAGTCCAACTAATCTTTT 57.922 29.630 0.00 0.00 33.22 2.27
2726 5348 8.635765 TGAATGCTAAAGTCCAACTAATCTTT 57.364 30.769 0.00 0.00 34.98 2.52
2727 5349 8.814038 ATGAATGCTAAAGTCCAACTAATCTT 57.186 30.769 0.00 0.00 0.00 2.40
3591 6479 1.880340 CTGAGAACGGAGCATCGCC 60.880 63.158 0.00 0.00 34.37 5.54
3613 6501 5.059833 GGTTAGAAGAGCTATGAATGTGGG 58.940 45.833 0.00 0.00 0.00 4.61
4905 8434 9.009327 CAATACTTTGTAACAATTATGAAGCGG 57.991 33.333 0.00 0.00 0.00 5.52
5100 8764 7.564793 ACATCTGAAGTATACAGGCATTAACA 58.435 34.615 5.50 0.00 36.22 2.41
5358 9083 2.930040 ACCAACTTATTCATCGCTGACG 59.070 45.455 0.00 0.00 42.01 4.35
5414 9163 6.625362 TCACTTATTCATCTCTGACAGTCAC 58.375 40.000 0.00 0.00 0.00 3.67
5502 9255 2.104111 CACAGGACTAGTCACCCAAACA 59.896 50.000 23.91 0.00 0.00 2.83
5503 9256 2.104281 ACACAGGACTAGTCACCCAAAC 59.896 50.000 23.91 5.15 0.00 2.93
5504 9257 2.104111 CACACAGGACTAGTCACCCAAA 59.896 50.000 23.91 0.00 0.00 3.28
5505 9258 1.691976 CACACAGGACTAGTCACCCAA 59.308 52.381 23.91 0.00 0.00 4.12
5506 9259 1.133294 TCACACAGGACTAGTCACCCA 60.133 52.381 23.91 0.00 0.00 4.51
5507 9260 1.629043 TCACACAGGACTAGTCACCC 58.371 55.000 23.91 8.09 0.00 4.61
5508 9261 2.610727 GCTTCACACAGGACTAGTCACC 60.611 54.545 23.91 8.85 0.00 4.02
5509 9262 2.035961 TGCTTCACACAGGACTAGTCAC 59.964 50.000 23.91 13.28 0.00 3.67
5510 9263 2.316108 TGCTTCACACAGGACTAGTCA 58.684 47.619 23.91 0.00 0.00 3.41
5521 9274 3.613910 ACAACACTTTTGGTGCTTCACAC 60.614 43.478 0.00 0.00 45.28 3.82
5522 9275 2.560542 ACAACACTTTTGGTGCTTCACA 59.439 40.909 0.00 0.00 45.28 3.58
5523 9276 3.230743 ACAACACTTTTGGTGCTTCAC 57.769 42.857 0.00 0.00 45.28 3.18
5524 9277 3.951775 AACAACACTTTTGGTGCTTCA 57.048 38.095 0.00 0.00 45.28 3.02
5525 9278 3.370672 CCAAACAACACTTTTGGTGCTTC 59.629 43.478 5.80 0.00 45.28 3.86
5526 9279 3.333804 CCAAACAACACTTTTGGTGCTT 58.666 40.909 5.80 0.00 45.28 3.91
5527 9280 2.971307 CCAAACAACACTTTTGGTGCT 58.029 42.857 5.80 0.00 45.28 4.40
5532 9285 4.186856 AGTCACCCAAACAACACTTTTG 57.813 40.909 0.00 0.00 34.31 2.44
5533 9286 5.014202 ACTAGTCACCCAAACAACACTTTT 58.986 37.500 0.00 0.00 0.00 2.27
5534 9287 4.595986 ACTAGTCACCCAAACAACACTTT 58.404 39.130 0.00 0.00 0.00 2.66
5535 9288 4.196971 GACTAGTCACCCAAACAACACTT 58.803 43.478 18.20 0.00 0.00 3.16
5536 9289 3.433173 GGACTAGTCACCCAAACAACACT 60.433 47.826 23.91 0.00 0.00 3.55
5537 9290 2.876550 GGACTAGTCACCCAAACAACAC 59.123 50.000 23.91 0.00 0.00 3.32
5538 9291 2.775384 AGGACTAGTCACCCAAACAACA 59.225 45.455 23.91 0.00 0.00 3.33
5539 9292 3.139077 CAGGACTAGTCACCCAAACAAC 58.861 50.000 23.91 3.00 0.00 3.32
5623 9379 0.751643 CGGGGGTATGGCTTCCTTTG 60.752 60.000 0.00 0.00 0.00 2.77
5624 9380 1.613061 CGGGGGTATGGCTTCCTTT 59.387 57.895 0.00 0.00 0.00 3.11
5625 9381 3.056754 GCGGGGGTATGGCTTCCTT 62.057 63.158 0.00 0.00 0.00 3.36
5627 9383 4.929707 CGCGGGGGTATGGCTTCC 62.930 72.222 0.00 0.00 0.00 3.46
5628 9384 2.799452 TACGCGGGGGTATGGCTTC 61.799 63.158 12.47 0.00 0.00 3.86
5629 9385 2.764967 TACGCGGGGGTATGGCTT 60.765 61.111 12.47 0.00 0.00 4.35
5630 9386 3.543641 GTACGCGGGGGTATGGCT 61.544 66.667 12.47 0.00 0.00 4.75
5631 9387 4.614112 GGTACGCGGGGGTATGGC 62.614 72.222 12.47 0.00 0.00 4.40
5632 9388 3.932483 GGGTACGCGGGGGTATGG 61.932 72.222 12.47 0.00 0.00 2.74
5633 9389 3.932483 GGGGTACGCGGGGGTATG 61.932 72.222 12.47 0.00 0.00 2.39


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

AutoCloner maintained by Alex Coulton.