Multiple sequence alignment - TraesCS4A01G488000

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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 TraesCS4A01G488000 chr4A 100.000 6909 0 0 1 6909 739904701 739911609 0.000000e+00 12759.0
1 TraesCS4A01G488000 chr4A 97.873 4419 69 6 374 4767 742143343 742147761 0.000000e+00 7616.0
2 TraesCS4A01G488000 chr4A 96.792 4489 96 17 1092 5540 733872383 733867903 0.000000e+00 7448.0
3 TraesCS4A01G488000 chr4A 91.932 2107 141 11 2405 4494 741864795 741866889 0.000000e+00 2922.0
4 TraesCS4A01G488000 chr4A 92.268 1927 110 15 499 2407 741849940 741851845 0.000000e+00 2697.0
5 TraesCS4A01G488000 chr4A 86.064 2203 295 11 1583 3779 733991009 733993205 0.000000e+00 2357.0
6 TraesCS4A01G488000 chr4A 85.922 2202 300 9 1583 3779 741159951 741162147 0.000000e+00 2340.0
7 TraesCS4A01G488000 chr4A 88.933 1265 78 11 5310 6526 741184891 741186141 0.000000e+00 1504.0
8 TraesCS4A01G488000 chr4A 90.518 791 28 16 4789 5540 733899922 733899140 0.000000e+00 1002.0
9 TraesCS4A01G488000 chr4A 88.564 787 51 14 5409 6170 740201223 740201995 0.000000e+00 918.0
10 TraesCS4A01G488000 chr4A 87.977 682 32 21 4743 5406 742147674 742148323 0.000000e+00 760.0
11 TraesCS4A01G488000 chr4A 95.745 376 15 1 1 375 742142937 742143312 7.670000e-169 604.0
12 TraesCS4A01G488000 chr4A 91.076 381 26 5 1 375 733878580 733878202 6.180000e-140 508.0
13 TraesCS4A01G488000 chr4A 93.939 231 14 0 145 375 741266647 741266877 3.970000e-92 350.0
14 TraesCS4A01G488000 chr4A 90.370 270 11 7 108 374 741849348 741849605 2.390000e-89 340.0
15 TraesCS4A01G488000 chr4A 92.735 234 16 1 506 739 741266913 741267145 3.090000e-88 337.0
16 TraesCS4A01G488000 chr4A 84.638 345 35 8 4877 5219 741870061 741870389 1.860000e-85 327.0
17 TraesCS4A01G488000 chr4A 80.000 380 69 5 3850 4227 741162641 741163015 2.460000e-69 274.0
18 TraesCS4A01G488000 chr4A 96.875 160 5 0 4720 4879 741869868 741870027 1.140000e-67 268.0
19 TraesCS4A01G488000 chr4A 93.056 144 10 0 4736 4879 741281446 741281589 1.950000e-50 211.0
20 TraesCS4A01G488000 chr4A 77.647 340 72 4 1726 2063 739740684 739741021 3.270000e-48 204.0
21 TraesCS4A01G488000 chr4A 88.000 150 14 2 4877 5025 741281623 741281769 2.560000e-39 174.0
22 TraesCS4A01G488000 chr4A 88.000 150 14 2 4877 5025 741293382 741293528 2.560000e-39 174.0
23 TraesCS4A01G488000 chr4A 88.079 151 11 4 3 147 741265657 741265806 9.210000e-39 172.0
24 TraesCS4A01G488000 chr4A 97.938 97 2 0 5310 5406 740201097 740201193 1.190000e-37 169.0
25 TraesCS4A01G488000 chr4A 75.000 332 77 3 1096 1421 741780524 741780193 1.550000e-31 148.0
26 TraesCS4A01G488000 chr4A 88.000 100 8 1 5311 5406 741282751 741282850 1.570000e-21 115.0
27 TraesCS4A01G488000 chr4A 88.000 100 8 1 5311 5406 741294510 741294609 1.570000e-21 115.0
28 TraesCS4A01G488000 chr4A 94.030 67 3 1 54 120 741847571 741847636 4.410000e-17 100.0
29 TraesCS4A01G488000 chr4A 96.491 57 2 0 5765 5821 741879135 741879191 2.050000e-15 95.3
30 TraesCS4A01G488000 chr4A 96.429 56 2 0 5766 5821 741477926 741477981 7.380000e-15 93.5
31 TraesCS4A01G488000 chr4A 97.059 34 0 1 454 487 741849909 741849941 1.000000e-03 56.5
32 TraesCS4A01G488000 chr7D 92.602 4136 264 18 374 4494 2444181 2440073 0.000000e+00 5904.0
33 TraesCS4A01G488000 chr7D 93.200 2103 120 12 2159 4248 3847396 3845304 0.000000e+00 3070.0
34 TraesCS4A01G488000 chr7D 81.252 2683 441 44 1582 4246 19050640 19053278 0.000000e+00 2111.0
35 TraesCS4A01G488000 chr7D 93.775 1269 69 6 5591 6853 3208004 3209268 0.000000e+00 1897.0
36 TraesCS4A01G488000 chr7D 93.931 379 17 5 1 375 2444588 2444212 1.010000e-157 568.0
37 TraesCS4A01G488000 chr7D 84.314 357 34 8 6575 6909 3692263 3691907 5.170000e-86 329.0
38 TraesCS4A01G488000 chr7D 85.583 326 25 8 5095 5406 3207593 3207910 8.640000e-84 322.0
39 TraesCS4A01G488000 chr7D 95.625 160 7 0 4720 4879 2438645 2438486 2.470000e-64 257.0
40 TraesCS4A01G488000 chr7D 73.993 596 149 6 1442 2034 19050212 19050804 3.220000e-58 237.0
41 TraesCS4A01G488000 chr7D 95.804 143 6 0 4737 4879 3207406 3207548 1.500000e-56 231.0
42 TraesCS4A01G488000 chr7D 73.746 339 80 6 1091 1421 2885240 2884903 2.620000e-24 124.0
43 TraesCS4A01G488000 chr7D 94.643 56 3 0 5766 5821 3758378 3758323 3.430000e-13 87.9
44 TraesCS4A01G488000 chr7D 94.643 56 3 0 5766 5821 3780665 3780720 3.430000e-13 87.9
45 TraesCS4A01G488000 chr7D 100.000 34 0 0 5435 5468 3207975 3208008 5.790000e-06 63.9
46 TraesCS4A01G488000 chr7A 94.171 1441 82 2 2159 3597 3827920 3826480 0.000000e+00 2194.0
47 TraesCS4A01G488000 chr7A 86.720 625 57 12 3985 4609 3594904 3594306 0.000000e+00 671.0
48 TraesCS4A01G488000 chr7A 81.840 413 60 12 3834 4236 3141180 3141587 3.990000e-87 333.0
49 TraesCS4A01G488000 chr7A 89.720 107 11 0 5827 5933 3625802 3625908 3.360000e-28 137.0
50 TraesCS4A01G488000 chr7A 96.429 56 2 0 5766 5821 1990149 1990204 7.380000e-15 93.5
51 TraesCS4A01G488000 chr7A 92.727 55 4 0 5767 5821 3625351 3625405 5.740000e-11 80.5
52 TraesCS4A01G488000 chrUn 93.967 1094 64 2 819 1911 221199409 221198317 0.000000e+00 1653.0
53 TraesCS4A01G488000 chrUn 93.962 1093 64 2 820 1911 318474338 318475429 0.000000e+00 1652.0
54 TraesCS4A01G488000 chrUn 93.074 231 16 0 145 375 221205127 221204897 8.580000e-89 339.0
55 TraesCS4A01G488000 chrUn 93.074 231 16 0 145 375 232064931 232065161 8.580000e-89 339.0
56 TraesCS4A01G488000 chrUn 92.735 234 17 0 506 739 232065197 232065430 8.580000e-89 339.0
57 TraesCS4A01G488000 chrUn 92.735 234 16 1 506 739 221204861 221204629 3.090000e-88 337.0
58 TraesCS4A01G488000 chrUn 93.056 144 10 0 4736 4879 339257989 339257846 1.950000e-50 211.0
59 TraesCS4A01G488000 chrUn 93.056 144 10 0 4736 4879 352851635 352851492 1.950000e-50 211.0
60 TraesCS4A01G488000 chrUn 88.435 147 13 2 4880 5025 339257809 339257666 2.560000e-39 174.0
61 TraesCS4A01G488000 chrUn 88.435 147 13 2 4880 5025 352851455 352851312 2.560000e-39 174.0
62 TraesCS4A01G488000 chrUn 88.079 151 11 4 3 147 221206132 221205983 9.210000e-39 172.0
63 TraesCS4A01G488000 chrUn 88.079 151 11 4 3 147 232063926 232064075 9.210000e-39 172.0
64 TraesCS4A01G488000 chrUn 88.079 151 11 4 3 147 441409062 441408913 9.210000e-39 172.0
65 TraesCS4A01G488000 chrUn 88.000 100 8 1 5311 5406 339256685 339256586 1.570000e-21 115.0
66 TraesCS4A01G488000 chrUn 88.000 100 8 1 5311 5406 455665609 455665510 1.570000e-21 115.0
67 TraesCS4A01G488000 chr5B 78.604 444 77 9 3829 4272 280603543 280603118 1.900000e-70 278.0
68 TraesCS4A01G488000 chr5B 89.474 76 4 4 6121 6195 20732154 20732226 7.380000e-15 93.5
69 TraesCS4A01G488000 chr2D 92.647 68 4 1 6131 6197 324997902 324997835 5.700000e-16 97.1
70 TraesCS4A01G488000 chr1D 89.744 78 5 3 6121 6197 204510876 204510951 5.700000e-16 97.1
71 TraesCS4A01G488000 chr1B 92.537 67 5 0 6131 6197 97734641 97734707 5.700000e-16 97.1
72 TraesCS4A01G488000 chr3A 88.889 72 8 0 6131 6202 628642485 628642414 9.540000e-14 89.8
73 TraesCS4A01G488000 chr5A 87.500 80 4 6 6121 6197 476821995 476821919 3.430000e-13 87.9


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 TraesCS4A01G488000 chr4A 739904701 739911609 6908 False 12759.000000 12759 100.000000 1 6909 1 chr4A.!!$F3 6908
1 TraesCS4A01G488000 chr4A 733867903 733872383 4480 True 7448.000000 7448 96.792000 1092 5540 1 chr4A.!!$R1 4448
2 TraesCS4A01G488000 chr4A 742142937 742148323 5386 False 2993.333333 7616 93.865000 1 5406 3 chr4A.!!$F14 5405
3 TraesCS4A01G488000 chr4A 733991009 733993205 2196 False 2357.000000 2357 86.064000 1583 3779 1 chr4A.!!$F1 2196
4 TraesCS4A01G488000 chr4A 741184891 741186141 1250 False 1504.000000 1504 88.933000 5310 6526 1 chr4A.!!$F4 1216
5 TraesCS4A01G488000 chr4A 741159951 741163015 3064 False 1307.000000 2340 82.961000 1583 4227 2 chr4A.!!$F8 2644
6 TraesCS4A01G488000 chr4A 741864795 741870389 5594 False 1172.333333 2922 91.148333 2405 5219 3 chr4A.!!$F13 2814
7 TraesCS4A01G488000 chr4A 733899140 733899922 782 True 1002.000000 1002 90.518000 4789 5540 1 chr4A.!!$R3 751
8 TraesCS4A01G488000 chr4A 741847571 741851845 4274 False 798.375000 2697 93.431750 54 2407 4 chr4A.!!$F12 2353
9 TraesCS4A01G488000 chr4A 740201097 740201995 898 False 543.500000 918 93.251000 5310 6170 2 chr4A.!!$F7 860
10 TraesCS4A01G488000 chr4A 741265657 741267145 1488 False 286.333333 350 91.584333 3 739 3 chr4A.!!$F9 736
11 TraesCS4A01G488000 chr7D 3845304 3847396 2092 True 3070.000000 3070 93.200000 2159 4248 1 chr7D.!!$R4 2089
12 TraesCS4A01G488000 chr7D 2438486 2444588 6102 True 2243.000000 5904 94.052667 1 4879 3 chr7D.!!$R5 4878
13 TraesCS4A01G488000 chr7D 19050212 19053278 3066 False 1174.000000 2111 77.622500 1442 4246 2 chr7D.!!$F3 2804
14 TraesCS4A01G488000 chr7D 3207406 3209268 1862 False 628.475000 1897 93.790500 4737 6853 4 chr7D.!!$F2 2116
15 TraesCS4A01G488000 chr7A 3826480 3827920 1440 True 2194.000000 2194 94.171000 2159 3597 1 chr7A.!!$R2 1438
16 TraesCS4A01G488000 chr7A 3594306 3594904 598 True 671.000000 671 86.720000 3985 4609 1 chr7A.!!$R1 624
17 TraesCS4A01G488000 chrUn 221198317 221199409 1092 True 1653.000000 1653 93.967000 819 1911 1 chrUn.!!$R1 1092
18 TraesCS4A01G488000 chrUn 318474338 318475429 1091 False 1652.000000 1652 93.962000 820 1911 1 chrUn.!!$F1 1091
19 TraesCS4A01G488000 chrUn 232063926 232065430 1504 False 283.333333 339 91.296000 3 739 3 chrUn.!!$F2 736
20 TraesCS4A01G488000 chrUn 221204629 221206132 1503 True 282.666667 339 91.296000 3 739 3 chrUn.!!$R4 736

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
760 3584 1.134610 TGATCGTCATGCATGCAGACT 60.135 47.619 30.20 20.82 0.00 3.24 F
2392 5530 7.170998 GTGAGTGCTACAAACTTACTGTGTTAT 59.829 37.037 0.00 0.00 32.85 1.89 F
3282 6428 0.464373 TTTGCATCGGATCTGGAGGC 60.464 55.000 14.21 14.21 41.27 4.70 F
4105 7723 0.107456 CCGGTGCATAGAGCCTGATT 59.893 55.000 0.00 0.00 44.83 2.57 F
5287 11842 0.675633 GCACCAAACCACAGCTTCAT 59.324 50.000 0.00 0.00 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 4866 2.548480 GCGTAAGAAAGTGAGCTTGGTT 59.452 45.455 0.00 0.0 43.02 3.67 R
4105 7723 0.606096 ATCGTTGGACGGTGTGATGA 59.394 50.000 0.27 0.0 42.81 2.92 R
4942 11478 1.322338 CGTCGGGCACTAAACAATACG 59.678 52.381 0.00 0.0 0.00 3.06 R
5512 12130 0.036952 AAGTGGCGAGACCTGACATG 60.037 55.000 0.00 0.0 40.22 3.21 R
6702 13349 0.109342 AGAGCTGGGGTGTGTTTCAG 59.891 55.000 0.00 0.0 0.00 3.02 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
223 2812 6.560253 AGTGAATGGTCAAGTGTTCATTAC 57.440 37.500 0.00 0.00 34.87 1.89
342 2934 7.523293 AAATGTAGTCACCATCATCAACAAA 57.477 32.000 0.00 0.00 0.00 2.83
445 3070 5.670097 CACTTGTGTCAATAGTCTTTGTCG 58.330 41.667 0.00 0.00 0.00 4.35
535 3350 2.607750 ATGGACGTCCTGGGCTGT 60.608 61.111 33.39 9.41 36.82 4.40
760 3584 1.134610 TGATCGTCATGCATGCAGACT 60.135 47.619 30.20 20.82 0.00 3.24
2392 5530 7.170998 GTGAGTGCTACAAACTTACTGTGTTAT 59.829 37.037 0.00 0.00 32.85 1.89
2413 5551 9.786105 TGTTATGTGCATCAAACAACAATATAG 57.214 29.630 7.88 0.00 30.49 1.31
2847 5986 6.149973 CCTTGAATCTTTCTCACAATGCACTA 59.850 38.462 0.00 0.00 0.00 2.74
2916 6055 4.629634 TCGATGGATGTGTCATACAACAAC 59.370 41.667 0.00 0.00 43.77 3.32
3049 6188 2.167900 CCTCGAGGTAGTAAACAAGGGG 59.832 54.545 24.04 0.00 0.00 4.79
3222 6367 5.456921 ACTTTGATGGGGAAGATGTGTAT 57.543 39.130 0.00 0.00 0.00 2.29
3282 6428 0.464373 TTTGCATCGGATCTGGAGGC 60.464 55.000 14.21 14.21 41.27 4.70
3862 7472 5.297547 AGCAAAACTGACTCTCGAATGTTA 58.702 37.500 0.00 0.00 0.00 2.41
3864 7474 5.846473 GCAAAACTGACTCTCGAATGTTAAC 59.154 40.000 0.00 0.00 0.00 2.01
3954 7564 3.650942 TGGTTCTAGAGTTGTTCATGGGT 59.349 43.478 0.00 0.00 0.00 4.51
3987 7597 7.775093 CCAGGTGATTTCCTTTCATCTATTGTA 59.225 37.037 0.00 0.00 32.81 2.41
4073 7691 3.057596 GCGGGTGAGATGTTTCAAATGAA 60.058 43.478 0.00 0.00 0.00 2.57
4105 7723 0.107456 CCGGTGCATAGAGCCTGATT 59.893 55.000 0.00 0.00 44.83 2.57
4926 11462 4.181578 CCACGTCAGTAATTAGAACCTGG 58.818 47.826 0.00 0.00 0.00 4.45
4942 11478 4.078639 ACCTGGCTTATAGAGTTGATGC 57.921 45.455 0.00 0.00 0.00 3.91
5013 11549 8.088365 AGTTTAGTGCCAAATAAGGATGAAAAC 58.912 33.333 0.00 0.00 0.00 2.43
5120 11660 3.709987 GCATTTGCTGAGTGTCAAAAGT 58.290 40.909 0.00 0.00 36.02 2.66
5255 11810 7.327275 GTGAACAACAACAAAAATATCGCCATA 59.673 33.333 0.00 0.00 0.00 2.74
5284 11839 2.489275 CGGCACCAAACCACAGCTT 61.489 57.895 0.00 0.00 0.00 3.74
5285 11840 1.363807 GGCACCAAACCACAGCTTC 59.636 57.895 0.00 0.00 0.00 3.86
5286 11841 1.391157 GGCACCAAACCACAGCTTCA 61.391 55.000 0.00 0.00 0.00 3.02
5287 11842 0.675633 GCACCAAACCACAGCTTCAT 59.324 50.000 0.00 0.00 0.00 2.57
5288 11843 1.603678 GCACCAAACCACAGCTTCATG 60.604 52.381 0.00 0.00 0.00 3.07
5289 11844 1.955778 CACCAAACCACAGCTTCATGA 59.044 47.619 0.00 0.00 0.00 3.07
5290 11845 2.361757 CACCAAACCACAGCTTCATGAA 59.638 45.455 8.12 8.12 0.00 2.57
5352 11907 2.601067 CCACCATGGCCTGCAACA 60.601 61.111 13.04 0.00 0.00 3.33
5406 11965 1.203994 CTTCCGTTCCGTGTACATCCT 59.796 52.381 0.00 0.00 0.00 3.24
5580 12204 1.612950 TGGCACACCAACATGCTTTAG 59.387 47.619 0.00 0.00 45.37 1.85
5633 12257 9.123709 GATTCTCTTCGATCATACAGTACATTC 57.876 37.037 0.00 0.00 0.00 2.67
5645 12269 3.242936 ACAGTACATTCGTTGTTGCCAAC 60.243 43.478 0.00 0.00 46.09 3.77
5764 12403 3.307339 GCTGGAGATCAACAGAGTTTCCT 60.307 47.826 17.70 0.00 36.86 3.36
5771 12410 5.902431 AGATCAACAGAGTTTCCTAGCCTAT 59.098 40.000 0.00 0.00 0.00 2.57
5836 12475 5.449041 CGATCCATTCAAACAACCTGTATGG 60.449 44.000 0.00 0.00 40.97 2.74
5869 12508 1.124780 TGTCCTTTTCGACTGACCCA 58.875 50.000 0.00 0.00 33.70 4.51
5965 12604 5.435686 AAAGGTAGCATCTACCATTGACA 57.564 39.130 21.16 0.00 39.99 3.58
5972 12611 3.448686 CATCTACCATTGACACGAGGAC 58.551 50.000 0.00 0.00 0.00 3.85
6028 12667 3.206150 GTTGTTCAGGAGCTTCAGTTGA 58.794 45.455 0.00 0.00 0.00 3.18
6041 12680 4.934602 GCTTCAGTTGAATAGCAGAGAAGT 59.065 41.667 0.00 0.00 35.11 3.01
6108 12747 4.086457 GGAGAATGGGGAAACTTGCTTTA 58.914 43.478 0.00 0.00 0.00 1.85
6175 12814 3.412624 GATGCAGAGGCCAGGGGAC 62.413 68.421 5.01 0.00 40.13 4.46
6178 12817 2.988839 GCAGAGGCCAGGGGACATT 61.989 63.158 5.01 0.00 29.21 2.71
6278 12919 9.620259 GTGCAATCCCCCAAATTATTATTTTTA 57.380 29.630 0.00 0.00 31.63 1.52
6314 12956 4.867047 TGTTTGGTGTAAAGTGCAACATTG 59.133 37.500 0.00 0.00 41.43 2.82
6509 13156 5.300034 TGAGAAACAAACTCATGTGCATTCT 59.700 36.000 0.00 0.00 39.10 2.40
6529 13176 5.227569 TCTGGACAAACTTATGAGAAGCA 57.772 39.130 0.00 0.00 0.00 3.91
6533 13180 5.827797 TGGACAAACTTATGAGAAGCACTTT 59.172 36.000 0.00 0.00 0.00 2.66
6534 13181 6.995686 TGGACAAACTTATGAGAAGCACTTTA 59.004 34.615 0.00 0.00 0.00 1.85
6573 13220 0.605589 GTCCCCATAACCATAGCGGC 60.606 60.000 0.00 0.00 39.03 6.53
6604 13251 4.627741 GCACCTAAGAATCCACCATTACCA 60.628 45.833 0.00 0.00 0.00 3.25
6608 13255 6.388689 ACCTAAGAATCCACCATTACCACATA 59.611 38.462 0.00 0.00 0.00 2.29
6654 13301 1.351350 GGCTAGAAAGGACAACCCAGT 59.649 52.381 0.00 0.00 37.41 4.00
6673 13320 0.179059 TTGTCGAGGCAACAGAAGCA 60.179 50.000 0.00 0.00 41.41 3.91
6677 13324 1.509644 CGAGGCAACAGAAGCAGCAA 61.510 55.000 0.00 0.00 41.41 3.91
6702 13349 5.914898 ACTTAAAATGCCAACCTGATACC 57.085 39.130 0.00 0.00 0.00 2.73
6712 13359 3.502211 CCAACCTGATACCTGAAACACAC 59.498 47.826 0.00 0.00 0.00 3.82
6786 13433 2.099098 CGAAAGTGAAAACACCAGGCTT 59.901 45.455 0.00 0.00 0.00 4.35
6793 13440 0.468226 AAACACCAGGCTTGAGACGA 59.532 50.000 0.00 0.00 0.00 4.20
6796 13443 2.125350 CCAGGCTTGAGACGAGGC 60.125 66.667 0.00 0.00 39.76 4.70
6798 13445 1.220206 CAGGCTTGAGACGAGGCAT 59.780 57.895 13.52 0.00 41.73 4.40
6799 13446 0.392193 CAGGCTTGAGACGAGGCATT 60.392 55.000 13.52 0.00 41.73 3.56
6815 13462 1.406539 GCATTTGCAATCCACCGATCT 59.593 47.619 0.00 0.00 41.59 2.75
6816 13463 2.797087 GCATTTGCAATCCACCGATCTG 60.797 50.000 0.00 0.00 41.59 2.90
6856 13503 9.847224 ATAATTTATGTATGAAAGTTCCGACCT 57.153 29.630 0.00 0.00 0.00 3.85
6857 13504 7.787725 ATTTATGTATGAAAGTTCCGACCTC 57.212 36.000 0.00 0.00 0.00 3.85
6858 13505 3.226346 TGTATGAAAGTTCCGACCTCG 57.774 47.619 0.00 0.00 39.44 4.63
6859 13506 1.925185 GTATGAAAGTTCCGACCTCGC 59.075 52.381 0.00 0.00 38.18 5.03
6860 13507 0.608640 ATGAAAGTTCCGACCTCGCT 59.391 50.000 0.00 0.00 38.18 4.93
6861 13508 0.319555 TGAAAGTTCCGACCTCGCTG 60.320 55.000 0.00 0.00 38.18 5.18
6862 13509 0.038526 GAAAGTTCCGACCTCGCTGA 60.039 55.000 0.00 0.00 38.18 4.26
6863 13510 0.608640 AAAGTTCCGACCTCGCTGAT 59.391 50.000 0.00 0.00 38.18 2.90
6864 13511 0.608640 AAGTTCCGACCTCGCTGATT 59.391 50.000 0.00 0.00 38.18 2.57
6865 13512 0.173708 AGTTCCGACCTCGCTGATTC 59.826 55.000 0.00 0.00 38.18 2.52
6866 13513 0.108804 GTTCCGACCTCGCTGATTCA 60.109 55.000 0.00 0.00 38.18 2.57
6867 13514 0.606096 TTCCGACCTCGCTGATTCAA 59.394 50.000 0.00 0.00 38.18 2.69
6868 13515 0.824109 TCCGACCTCGCTGATTCAAT 59.176 50.000 0.00 0.00 38.18 2.57
6869 13516 1.202417 TCCGACCTCGCTGATTCAATC 60.202 52.381 0.00 0.00 38.18 2.67
6870 13517 0.848942 CGACCTCGCTGATTCAATCG 59.151 55.000 0.00 2.61 0.00 3.34
6871 13518 0.579156 GACCTCGCTGATTCAATCGC 59.421 55.000 4.66 4.66 0.00 4.58
6872 13519 0.176680 ACCTCGCTGATTCAATCGCT 59.823 50.000 10.94 0.00 0.00 4.93
6873 13520 0.857935 CCTCGCTGATTCAATCGCTC 59.142 55.000 10.94 0.00 0.00 5.03
6874 13521 1.564207 CTCGCTGATTCAATCGCTCA 58.436 50.000 10.94 0.20 0.00 4.26
6875 13522 2.133553 CTCGCTGATTCAATCGCTCAT 58.866 47.619 10.94 0.00 0.00 2.90
6876 13523 2.543012 CTCGCTGATTCAATCGCTCATT 59.457 45.455 10.94 0.00 0.00 2.57
6877 13524 2.541346 TCGCTGATTCAATCGCTCATTC 59.459 45.455 10.94 0.00 0.00 2.67
6878 13525 2.543012 CGCTGATTCAATCGCTCATTCT 59.457 45.455 10.94 0.00 0.00 2.40
6879 13526 3.002042 CGCTGATTCAATCGCTCATTCTT 59.998 43.478 10.94 0.00 0.00 2.52
6880 13527 4.495349 CGCTGATTCAATCGCTCATTCTTT 60.495 41.667 10.94 0.00 0.00 2.52
6881 13528 4.733887 GCTGATTCAATCGCTCATTCTTTG 59.266 41.667 6.88 0.00 0.00 2.77
6882 13529 5.239359 TGATTCAATCGCTCATTCTTTGG 57.761 39.130 0.00 0.00 0.00 3.28
6883 13530 4.943093 TGATTCAATCGCTCATTCTTTGGA 59.057 37.500 0.00 0.00 0.00 3.53
6884 13531 5.415389 TGATTCAATCGCTCATTCTTTGGAA 59.585 36.000 0.00 0.00 35.78 3.53
6885 13532 5.703978 TTCAATCGCTCATTCTTTGGAAA 57.296 34.783 0.00 0.00 34.90 3.13
6886 13533 5.902613 TCAATCGCTCATTCTTTGGAAAT 57.097 34.783 0.00 0.00 34.90 2.17
6887 13534 5.643664 TCAATCGCTCATTCTTTGGAAATG 58.356 37.500 0.00 0.00 34.90 2.32
6888 13535 5.415389 TCAATCGCTCATTCTTTGGAAATGA 59.585 36.000 0.00 0.00 34.90 2.57
6889 13536 5.902613 ATCGCTCATTCTTTGGAAATGAA 57.097 34.783 0.80 0.00 42.97 2.57
6890 13537 5.703978 TCGCTCATTCTTTGGAAATGAAA 57.296 34.783 0.80 0.00 42.25 2.69
6891 13538 6.083098 TCGCTCATTCTTTGGAAATGAAAA 57.917 33.333 0.80 0.00 42.25 2.29
6892 13539 6.690530 TCGCTCATTCTTTGGAAATGAAAAT 58.309 32.000 0.80 0.00 42.25 1.82
6893 13540 7.825681 TCGCTCATTCTTTGGAAATGAAAATA 58.174 30.769 0.80 0.00 42.25 1.40
6894 13541 8.303156 TCGCTCATTCTTTGGAAATGAAAATAA 58.697 29.630 0.80 0.00 42.25 1.40
6895 13542 8.375465 CGCTCATTCTTTGGAAATGAAAATAAC 58.625 33.333 0.80 0.00 42.25 1.89
6896 13543 9.428097 GCTCATTCTTTGGAAATGAAAATAACT 57.572 29.630 0.80 0.00 42.25 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 99 1.837439 TCCCTGCGTTCCTCACATATT 59.163 47.619 0.00 0.00 0.00 1.28
223 2812 4.092968 GGTTGACTTATAACGCTTGGTCAG 59.907 45.833 3.96 0.00 35.58 3.51
278 2870 6.006449 AGCCAATGTGAGAAAGTAATTGAGT 58.994 36.000 0.00 0.00 31.34 3.41
342 2934 3.695830 TGCTTACGAGACCCATTTCTT 57.304 42.857 0.00 0.00 0.00 2.52
535 3350 1.344953 CCCACATGGAGATTCCCGGA 61.345 60.000 0.73 0.00 35.03 5.14
939 3788 0.106519 GCGGGAGGGGTACTAGTACA 60.107 60.000 29.38 0.00 37.78 2.90
1358 4207 3.309296 AGGCCCTCGAGAATCTTGATAA 58.691 45.455 15.71 0.00 0.00 1.75
1359 4208 2.894126 GAGGCCCTCGAGAATCTTGATA 59.106 50.000 15.71 0.00 0.00 2.15
1872 4866 2.548480 GCGTAAGAAAGTGAGCTTGGTT 59.452 45.455 0.00 0.00 43.02 3.67
2392 5530 6.324042 CAGCTATATTGTTGTTTGATGCACA 58.676 36.000 0.00 0.00 0.00 4.57
2413 5551 7.324178 CCTATACTTGATGGTATTACTCCAGC 58.676 42.308 0.00 0.00 41.14 4.85
2847 5986 1.812571 GATGGTGGAATGCTGTCGTTT 59.187 47.619 0.00 0.00 0.00 3.60
2916 6055 1.134699 TGCGGCACTGATCCTTCTAAG 60.135 52.381 0.00 0.00 0.00 2.18
3222 6367 5.798125 TTGTGGCATCAACAATTTTCCTA 57.202 34.783 0.00 0.00 0.00 2.94
3282 6428 4.529769 TGAGCCCTATAGACAGATCCATTG 59.470 45.833 0.00 0.00 0.00 2.82
3862 7472 5.474532 TGTATGCAAGCTCTGAAGAAATGTT 59.525 36.000 0.00 0.00 0.00 2.71
3864 7474 5.106436 TGTGTATGCAAGCTCTGAAGAAATG 60.106 40.000 0.00 0.00 0.00 2.32
3954 7564 4.868172 AAGGAAATCACCTGGATGATGA 57.132 40.909 0.00 0.00 39.32 2.92
4073 7691 3.908081 ACCGGACAGCGACAACGT 61.908 61.111 9.46 0.00 41.98 3.99
4105 7723 0.606096 ATCGTTGGACGGTGTGATGA 59.394 50.000 0.27 0.00 42.81 2.92
4926 11462 6.771188 ACAATACGCATCAACTCTATAAGC 57.229 37.500 0.00 0.00 0.00 3.09
4942 11478 1.322338 CGTCGGGCACTAAACAATACG 59.678 52.381 0.00 0.00 0.00 3.06
5013 11549 2.754472 GGCAAAGCCTTTACAAAGTGG 58.246 47.619 0.00 0.00 46.69 4.00
5246 11801 3.478780 GCCCCACCTATGGCGATA 58.521 61.111 0.00 0.00 45.76 2.92
5267 11822 1.363807 GAAGCTGTGGTTTGGTGCC 59.636 57.895 0.00 0.00 0.00 5.01
5274 11829 4.338012 TCATGATTCATGAAGCTGTGGTT 58.662 39.130 23.72 0.00 46.17 3.67
5284 11839 1.065564 TGTGGCGGTCATGATTCATGA 60.066 47.619 22.47 22.47 46.84 3.07
5285 11840 1.381522 TGTGGCGGTCATGATTCATG 58.618 50.000 18.71 18.71 42.60 3.07
5286 11841 2.224606 GATGTGGCGGTCATGATTCAT 58.775 47.619 0.00 0.00 0.00 2.57
5287 11842 1.667236 GATGTGGCGGTCATGATTCA 58.333 50.000 0.00 0.00 0.00 2.57
5288 11843 0.583438 CGATGTGGCGGTCATGATTC 59.417 55.000 0.00 0.00 0.00 2.52
5289 11844 1.439353 GCGATGTGGCGGTCATGATT 61.439 55.000 0.00 0.00 0.00 2.57
5290 11845 1.889105 GCGATGTGGCGGTCATGAT 60.889 57.895 0.00 0.00 0.00 2.45
5406 11965 4.738998 CCTTGTCGCCCCATGCCA 62.739 66.667 0.00 0.00 36.24 4.92
5512 12130 0.036952 AAGTGGCGAGACCTGACATG 60.037 55.000 0.00 0.00 40.22 3.21
5645 12269 9.255304 GCTCAGTATTCTGTAAATAAGAAGAGG 57.745 37.037 0.00 0.00 41.91 3.69
5764 12403 3.186283 TCCAAACAGACCCAATAGGCTA 58.814 45.455 0.00 0.00 40.58 3.93
5771 12410 0.178992 CCAGCTCCAAACAGACCCAA 60.179 55.000 0.00 0.00 0.00 4.12
5836 12475 6.150474 TCGAAAAGGACATGGAATTTTACTCC 59.850 38.462 0.00 0.00 0.00 3.85
5869 12508 7.309990 CCACCTGATACAAAATGAGGAAACAAT 60.310 37.037 0.00 0.00 0.00 2.71
5955 12594 1.548719 CCTGTCCTCGTGTCAATGGTA 59.451 52.381 0.00 0.00 0.00 3.25
5991 12630 2.509569 ACAACATGTTAATGGCGGACA 58.490 42.857 11.53 0.00 38.19 4.02
6028 12667 4.632153 ACGAACAACACTTCTCTGCTATT 58.368 39.130 0.00 0.00 0.00 1.73
6041 12680 2.223971 GGGACTCAAGAGACGAACAACA 60.224 50.000 3.73 0.00 0.00 3.33
6208 12849 1.005450 GTTCCCCTGCTTGGTAATGGA 59.995 52.381 0.00 0.00 0.00 3.41
6290 12931 4.727507 TGTTGCACTTTACACCAAACAT 57.272 36.364 0.00 0.00 0.00 2.71
6333 12975 8.547894 CGTGCTAATTGTGCATACTAATCTTAA 58.452 33.333 10.38 0.00 42.69 1.85
6509 13156 4.973168 AGTGCTTCTCATAAGTTTGTCCA 58.027 39.130 0.00 0.00 0.00 4.02
6551 13198 1.336887 CGCTATGGTTATGGGGACTCG 60.337 57.143 0.00 0.00 30.64 4.18
6573 13220 3.209410 GGATTCTTAGGTGCTGGATGTG 58.791 50.000 0.00 0.00 0.00 3.21
6604 13251 7.205297 GGCATTGTGCTATCAATTTCTTATGT 58.795 34.615 1.64 0.00 44.28 2.29
6608 13255 4.467082 TGGGCATTGTGCTATCAATTTCTT 59.533 37.500 1.64 0.00 44.28 2.52
6654 13301 0.179059 TGCTTCTGTTGCCTCGACAA 60.179 50.000 0.00 0.00 0.00 3.18
6673 13320 4.832823 AGGTTGGCATTTTAAGTAGTTGCT 59.167 37.500 0.00 0.00 33.86 3.91
6677 13324 6.602009 GGTATCAGGTTGGCATTTTAAGTAGT 59.398 38.462 0.00 0.00 0.00 2.73
6702 13349 0.109342 AGAGCTGGGGTGTGTTTCAG 59.891 55.000 0.00 0.00 0.00 3.02
6712 13359 3.205395 CTCGAGACAGAGCTGGGG 58.795 66.667 6.58 0.00 34.19 4.96
6731 13378 3.742983 GACAGGGTCGGTGAATCTC 57.257 57.895 0.00 0.00 0.00 2.75
6786 13433 1.739466 GATTGCAAATGCCTCGTCTCA 59.261 47.619 1.71 0.00 41.18 3.27
6793 13440 0.611618 TCGGTGGATTGCAAATGCCT 60.612 50.000 1.71 0.00 41.18 4.75
6796 13443 2.424601 ACAGATCGGTGGATTGCAAATG 59.575 45.455 1.71 0.00 31.51 2.32
6798 13445 2.198827 ACAGATCGGTGGATTGCAAA 57.801 45.000 1.71 0.00 31.51 3.68
6799 13446 2.198827 AACAGATCGGTGGATTGCAA 57.801 45.000 0.00 0.00 31.51 4.08
6838 13485 2.673043 GCGAGGTCGGAACTTTCATACA 60.673 50.000 0.00 0.00 40.23 2.29
6840 13487 1.822990 AGCGAGGTCGGAACTTTCATA 59.177 47.619 0.00 0.00 40.23 2.15
6853 13500 0.176680 AGCGATTGAATCAGCGAGGT 59.823 50.000 5.95 0.00 35.20 3.85
6854 13501 0.857935 GAGCGATTGAATCAGCGAGG 59.142 55.000 5.95 0.00 35.20 4.63
6855 13502 1.564207 TGAGCGATTGAATCAGCGAG 58.436 50.000 5.95 0.00 35.20 5.03
6856 13503 2.229675 ATGAGCGATTGAATCAGCGA 57.770 45.000 5.95 3.39 35.20 4.93
6857 13504 2.543012 AGAATGAGCGATTGAATCAGCG 59.457 45.455 5.95 3.74 35.20 5.18
6858 13505 4.548991 AAGAATGAGCGATTGAATCAGC 57.451 40.909 5.95 9.49 0.00 4.26
6859 13506 5.065602 TCCAAAGAATGAGCGATTGAATCAG 59.934 40.000 5.95 0.00 0.00 2.90
6860 13507 4.943093 TCCAAAGAATGAGCGATTGAATCA 59.057 37.500 5.95 0.00 0.00 2.57
6861 13508 5.490139 TCCAAAGAATGAGCGATTGAATC 57.510 39.130 0.00 0.00 0.00 2.52
6862 13509 5.902613 TTCCAAAGAATGAGCGATTGAAT 57.097 34.783 0.00 0.00 0.00 2.57
6863 13510 5.703978 TTTCCAAAGAATGAGCGATTGAA 57.296 34.783 0.00 0.00 0.00 2.69
6864 13511 5.415389 TCATTTCCAAAGAATGAGCGATTGA 59.585 36.000 0.00 0.00 38.29 2.57
6865 13512 5.643664 TCATTTCCAAAGAATGAGCGATTG 58.356 37.500 0.00 0.00 38.29 2.67
6866 13513 5.902613 TCATTTCCAAAGAATGAGCGATT 57.097 34.783 0.00 0.00 38.29 3.34
6867 13514 5.902613 TTCATTTCCAAAGAATGAGCGAT 57.097 34.783 0.00 0.00 42.54 4.58
6868 13515 5.703978 TTTCATTTCCAAAGAATGAGCGA 57.296 34.783 0.00 0.00 42.54 4.93
6869 13516 6.956299 ATTTTCATTTCCAAAGAATGAGCG 57.044 33.333 0.00 0.00 42.54 5.03
6870 13517 9.428097 AGTTATTTTCATTTCCAAAGAATGAGC 57.572 29.630 0.00 0.00 42.54 4.26


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

AutoCloner maintained by Alex Coulton.