Multiple sequence alignment - TraesCS4B01G158200

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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 TraesCS4B01G158200 chr4B 100.000 5106 0 0 1 5106 305477130 305482235 0.000000e+00 9430.0
1 TraesCS4B01G158200 chr4B 89.685 921 70 12 1 898 79740569 79739651 0.000000e+00 1151.0
2 TraesCS4B01G158200 chr4B 92.683 41 2 1 2242 2282 187905959 187905998 1.990000e-04 58.4
3 TraesCS4B01G158200 chr4A 94.393 4209 126 41 937 5092 302721251 302717100 0.000000e+00 6364.0
4 TraesCS4B01G158200 chr4D 97.739 2344 44 5 935 3277 202762733 202760398 0.000000e+00 4026.0
5 TraesCS4B01G158200 chr4D 96.249 1013 30 4 3324 4329 202759835 202758824 0.000000e+00 1653.0
6 TraesCS4B01G158200 chr4D 84.979 719 60 18 199 901 58947942 58948628 0.000000e+00 686.0
7 TraesCS4B01G158200 chr4D 97.531 81 1 1 4332 4411 202758702 202758622 2.480000e-28 137.0
8 TraesCS4B01G158200 chr4D 98.276 58 1 0 3276 3333 202760064 202760007 9.040000e-18 102.0
9 TraesCS4B01G158200 chr4D 100.000 29 0 0 2216 2244 93339455 93339427 3.000000e-03 54.7
10 TraesCS4B01G158200 chr4D 94.286 35 2 0 2210 2244 274741052 274741018 3.000000e-03 54.7
11 TraesCS4B01G158200 chr4D 100.000 29 0 0 2242 2270 473133518 473133546 3.000000e-03 54.7
12 TraesCS4B01G158200 chr4D 100.000 28 0 0 2217 2244 9314141 9314114 9.000000e-03 52.8
13 TraesCS4B01G158200 chr4D 100.000 28 0 0 2217 2244 9327257 9327284 9.000000e-03 52.8
14 TraesCS4B01G158200 chr4D 100.000 28 0 0 2217 2244 94883331 94883358 9.000000e-03 52.8
15 TraesCS4B01G158200 chr4D 100.000 28 0 0 2215 2242 108302675 108302702 9.000000e-03 52.8
16 TraesCS4B01G158200 chr4D 94.118 34 2 0 2242 2275 179707461 179707428 9.000000e-03 52.8
17 TraesCS4B01G158200 chr5D 90.435 920 64 11 1 898 543276609 543275692 0.000000e+00 1190.0
18 TraesCS4B01G158200 chr5D 95.238 42 2 0 2234 2275 297981362 297981403 3.300000e-07 67.6
19 TraesCS4B01G158200 chr5D 97.297 37 1 0 2242 2278 322958612 322958576 4.270000e-06 63.9
20 TraesCS4B01G158200 chr5D 92.500 40 2 1 2232 2271 35348131 35348093 7.140000e-04 56.5
21 TraesCS4B01G158200 chr5D 85.455 55 6 2 2216 2268 45263713 45263767 7.140000e-04 56.5
22 TraesCS4B01G158200 chr5D 100.000 29 0 0 2216 2244 384468863 384468891 3.000000e-03 54.7
23 TraesCS4B01G158200 chr1B 90.231 911 75 9 1 898 573868085 573867176 0.000000e+00 1177.0
24 TraesCS4B01G158200 chr1B 88.453 918 83 14 1 898 61012108 61013022 0.000000e+00 1086.0
25 TraesCS4B01G158200 chr1B 82.569 327 26 8 584 898 117463989 117464296 5.070000e-65 259.0
26 TraesCS4B01G158200 chr1B 91.071 56 3 2 2215 2268 9984934 9984989 1.970000e-09 75.0
27 TraesCS4B01G158200 chr7B 89.640 917 78 9 1 900 139506273 139507189 0.000000e+00 1151.0
28 TraesCS4B01G158200 chr7B 88.865 916 72 18 1 900 109198770 109199671 0.000000e+00 1099.0
29 TraesCS4B01G158200 chr7B 91.525 59 0 1 2215 2268 119736370 119736312 5.480000e-10 76.8
30 TraesCS4B01G158200 chr7B 90.698 43 3 1 2203 2244 129190511 129190469 7.140000e-04 56.5
31 TraesCS4B01G158200 chr3B 89.617 915 75 8 1 900 680415654 680416563 0.000000e+00 1146.0
32 TraesCS4B01G158200 chr3B 83.929 336 32 6 584 898 580807981 580808315 8.310000e-78 302.0
33 TraesCS4B01G158200 chr3B 88.889 54 5 1 2218 2271 4625045 4624993 1.190000e-06 65.8
34 TraesCS4B01G158200 chr6D 89.149 940 62 10 1 902 358398671 358399608 0.000000e+00 1134.0
35 TraesCS4B01G158200 chr6D 97.059 34 1 0 2242 2275 14520539 14520506 1.990000e-04 58.4
36 TraesCS4B01G158200 chr6D 100.000 30 0 0 2215 2244 106978865 106978836 7.140000e-04 56.5
37 TraesCS4B01G158200 chr6D 94.286 35 2 0 2242 2276 6967993 6968027 3.000000e-03 54.7
38 TraesCS4B01G158200 chr6D 92.105 38 3 0 2242 2279 33898429 33898392 3.000000e-03 54.7
39 TraesCS4B01G158200 chr6D 100.000 28 0 0 2244 2271 2278329 2278356 9.000000e-03 52.8
40 TraesCS4B01G158200 chr6D 100.000 28 0 0 2242 2269 34947150 34947177 9.000000e-03 52.8
41 TraesCS4B01G158200 chr6D 100.000 28 0 0 2242 2269 53670110 53670083 9.000000e-03 52.8
42 TraesCS4B01G158200 chr6D 100.000 28 0 0 2242 2269 97573803 97573776 9.000000e-03 52.8
43 TraesCS4B01G158200 chr6D 100.000 28 0 0 2242 2269 144591534 144591561 9.000000e-03 52.8
44 TraesCS4B01G158200 chr6A 88.147 928 85 14 1 905 371067148 371066223 0.000000e+00 1081.0
45 TraesCS4B01G158200 chr7D 92.254 723 49 4 1 716 292229401 292228679 0.000000e+00 1018.0
46 TraesCS4B01G158200 chr7D 89.516 124 12 1 782 904 397173290 397173167 6.850000e-34 156.0
47 TraesCS4B01G158200 chr7D 90.517 116 10 1 786 900 159898778 159898663 8.850000e-33 152.0
48 TraesCS4B01G158200 chr7D 94.737 38 2 0 2215 2252 71362849 71362886 5.520000e-05 60.2
49 TraesCS4B01G158200 chr7D 94.595 37 2 0 2215 2251 50723156 50723192 1.990000e-04 58.4
50 TraesCS4B01G158200 chr7D 97.059 34 1 0 2219 2252 71362973 71362940 1.990000e-04 58.4
51 TraesCS4B01G158200 chr7D 94.595 37 2 0 2216 2252 413545690 413545654 1.990000e-04 58.4
52 TraesCS4B01G158200 chr2D 84.914 464 30 15 475 898 180179484 180179947 2.820000e-117 433.0
53 TraesCS4B01G158200 chr2D 89.744 117 11 1 783 898 623306001 623306117 1.150000e-31 148.0
54 TraesCS4B01G158200 chr2D 96.970 33 1 0 2212 2244 317345738 317345706 7.140000e-04 56.5
55 TraesCS4B01G158200 chr2D 92.500 40 2 1 2215 2254 392090559 392090521 7.140000e-04 56.5
56 TraesCS4B01G158200 chr2D 92.105 38 2 1 2208 2245 586771120 586771156 9.000000e-03 52.8
57 TraesCS4B01G158200 chr5B 90.517 116 10 1 786 900 442745235 442745350 8.850000e-33 152.0
58 TraesCS4B01G158200 chr5B 92.727 55 0 1 2218 2268 250605929 250605875 5.480000e-10 76.8
59 TraesCS4B01G158200 chr5B 87.692 65 7 1 2212 2275 338716755 338716819 1.970000e-09 75.0
60 TraesCS4B01G158200 chr2B 84.000 150 19 5 752 900 739551974 739552119 6.890000e-29 139.0
61 TraesCS4B01G158200 chr2A 82.877 146 14 6 650 788 751895214 751895355 2.500000e-23 121.0
62 TraesCS4B01G158200 chr1A 94.643 56 3 0 2216 2271 495446311 495446256 2.530000e-13 87.9
63 TraesCS4B01G158200 chr1A 100.000 32 0 0 2242 2273 464800390 464800421 5.520000e-05 60.2
64 TraesCS4B01G158200 chr1A 90.698 43 4 0 2210 2252 281892574 281892532 1.990000e-04 58.4
65 TraesCS4B01G158200 chr1A 90.476 42 4 0 2234 2275 143815880 143815839 7.140000e-04 56.5
66 TraesCS4B01G158200 chr5A 97.297 37 1 0 2242 2278 419685310 419685274 4.270000e-06 63.9
67 TraesCS4B01G158200 chr5A 92.857 42 3 0 2234 2275 401142982 401142941 1.540000e-05 62.1
68 TraesCS4B01G158200 chrUn 94.444 36 2 0 2242 2277 77980115 77980080 7.140000e-04 56.5
69 TraesCS4B01G158200 chrUn 94.444 36 2 0 2242 2277 170445203 170445168 7.140000e-04 56.5
70 TraesCS4B01G158200 chrUn 94.444 36 2 0 2242 2277 287034396 287034431 7.140000e-04 56.5
71 TraesCS4B01G158200 chrUn 100.000 30 0 0 2242 2271 296736952 296736923 7.140000e-04 56.5
72 TraesCS4B01G158200 chrUn 100.000 30 0 0 2242 2271 307808448 307808477 7.140000e-04 56.5
73 TraesCS4B01G158200 chrUn 100.000 30 0 0 2215 2244 352578916 352578945 7.140000e-04 56.5
74 TraesCS4B01G158200 chrUn 94.286 35 2 0 2242 2276 15984496 15984462 3.000000e-03 54.7
75 TraesCS4B01G158200 chrUn 94.118 34 2 0 2212 2245 11035640 11035673 9.000000e-03 52.8
76 TraesCS4B01G158200 chr1D 90.476 42 4 0 2234 2275 145938639 145938598 7.140000e-04 56.5
77 TraesCS4B01G158200 chr1D 100.000 30 0 0 2215 2244 315816904 315816933 7.140000e-04 56.5
78 TraesCS4B01G158200 chr1D 94.286 35 2 0 2218 2252 332603107 332603073 3.000000e-03 54.7
79 TraesCS4B01G158200 chr1D 92.308 39 2 1 2242 2280 367413207 367413170 3.000000e-03 54.7
80 TraesCS4B01G158200 chr6B 96.875 32 1 0 2244 2275 609842155 609842186 3.000000e-03 54.7


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 TraesCS4B01G158200 chr4B 305477130 305482235 5105 False 9430.0 9430 100.00000 1 5106 1 chr4B.!!$F2 5105
1 TraesCS4B01G158200 chr4B 79739651 79740569 918 True 1151.0 1151 89.68500 1 898 1 chr4B.!!$R1 897
2 TraesCS4B01G158200 chr4A 302717100 302721251 4151 True 6364.0 6364 94.39300 937 5092 1 chr4A.!!$R1 4155
3 TraesCS4B01G158200 chr4D 202758622 202762733 4111 True 1479.5 4026 97.44875 935 4411 4 chr4D.!!$R5 3476
4 TraesCS4B01G158200 chr4D 58947942 58948628 686 False 686.0 686 84.97900 199 901 1 chr4D.!!$F2 702
5 TraesCS4B01G158200 chr5D 543275692 543276609 917 True 1190.0 1190 90.43500 1 898 1 chr5D.!!$R3 897
6 TraesCS4B01G158200 chr1B 573867176 573868085 909 True 1177.0 1177 90.23100 1 898 1 chr1B.!!$R1 897
7 TraesCS4B01G158200 chr1B 61012108 61013022 914 False 1086.0 1086 88.45300 1 898 1 chr1B.!!$F2 897
8 TraesCS4B01G158200 chr7B 139506273 139507189 916 False 1151.0 1151 89.64000 1 900 1 chr7B.!!$F2 899
9 TraesCS4B01G158200 chr7B 109198770 109199671 901 False 1099.0 1099 88.86500 1 900 1 chr7B.!!$F1 899
10 TraesCS4B01G158200 chr3B 680415654 680416563 909 False 1146.0 1146 89.61700 1 900 1 chr3B.!!$F2 899
11 TraesCS4B01G158200 chr6D 358398671 358399608 937 False 1134.0 1134 89.14900 1 902 1 chr6D.!!$F5 901
12 TraesCS4B01G158200 chr6A 371066223 371067148 925 True 1081.0 1081 88.14700 1 905 1 chr6A.!!$R1 904
13 TraesCS4B01G158200 chr7D 292228679 292229401 722 True 1018.0 1018 92.25400 1 716 1 chr7D.!!$R3 715

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
728 784 0.961857 TGGCGTGAACTAGGTCGCTA 60.962 55.000 18.77 7.77 46.37 4.26 F
845 920 1.342672 ATCGCCCTACCCAAACGGAT 61.343 55.000 0.00 0.00 34.64 4.18 F
1736 1812 1.538512 CTGCAACTGGGTGATTCTGTG 59.461 52.381 0.00 0.00 0.00 3.66 F
1820 1896 3.462021 GTGAGATGGTATCTGAACTGCC 58.538 50.000 0.00 0.00 40.38 4.85 F
3663 4273 3.924918 TCTTCCTTGTCGACAGAGAAG 57.075 47.619 32.93 32.93 44.57 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1758 1834 2.034939 CAGGCACATCTGCTCACAAAAA 59.965 45.455 0.00 0.00 43.66 1.94 R
2744 2838 0.244994 CAGTGGTCTTGGACTCTCCG 59.755 60.000 0.00 0.00 40.17 4.63 R
3663 4273 1.160137 AATTGACCAGAAGCTCGTGC 58.840 50.000 0.07 0.07 40.05 5.34 R
3929 4540 6.405731 GCAATGCATACCTTTCCTATCACAAA 60.406 38.462 0.00 0.00 0.00 2.83 R
5006 5772 0.179081 GTAGGAGTGTCCGGAATGCC 60.179 60.000 5.23 5.68 42.75 4.40 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
157 160 5.675575 GCATGATGTCTCAAAAGGATGTGAC 60.676 44.000 0.00 3.32 41.73 3.67
210 213 5.128919 AGCAAATGAAGCAATACCTAGAGG 58.871 41.667 0.00 0.00 42.17 3.69
225 228 4.605183 CCTAGAGGTTCAGAGGAAGAAGA 58.395 47.826 0.00 0.00 32.62 2.87
274 277 2.035632 GAAGATCGACATGGAGGAGGT 58.964 52.381 0.00 0.00 0.00 3.85
324 328 1.607467 GCCAATGTCAAGGCCAGGT 60.607 57.895 5.01 0.00 45.18 4.00
365 369 1.292860 CACCAATGCCGCAACCAAT 59.707 52.632 0.00 0.00 0.00 3.16
389 393 2.044946 GAGGTGGCCCTTGCGATT 60.045 61.111 0.00 0.00 42.86 3.34
514 521 2.026522 CCGTGGCCGTTCTTTTTGA 58.973 52.632 0.00 0.00 0.00 2.69
523 530 1.770957 GTTCTTTTTGAAGGCTGGCG 58.229 50.000 0.00 0.00 35.01 5.69
723 779 2.261671 CGCTGGCGTGAACTAGGT 59.738 61.111 6.83 0.00 34.35 3.08
728 784 0.961857 TGGCGTGAACTAGGTCGCTA 60.962 55.000 18.77 7.77 46.37 4.26
748 806 6.007677 CGCTAGTATTTGAAACGTTGTTCTC 58.992 40.000 0.00 0.00 0.00 2.87
818 893 3.723235 CTCATGACAGGCCCGGACG 62.723 68.421 0.73 0.00 0.00 4.79
845 920 1.342672 ATCGCCCTACCCAAACGGAT 61.343 55.000 0.00 0.00 34.64 4.18
902 977 2.514803 GCGGTGGAATTGGCCTAATAT 58.485 47.619 3.32 0.00 0.00 1.28
903 978 3.681593 GCGGTGGAATTGGCCTAATATA 58.318 45.455 3.32 0.00 0.00 0.86
904 979 3.439129 GCGGTGGAATTGGCCTAATATAC 59.561 47.826 3.32 0.00 0.00 1.47
906 981 4.341487 GGTGGAATTGGCCTAATATACCC 58.659 47.826 3.32 3.62 0.00 3.69
907 982 4.202631 GGTGGAATTGGCCTAATATACCCA 60.203 45.833 3.32 5.89 0.00 4.51
908 983 5.010282 GTGGAATTGGCCTAATATACCCAG 58.990 45.833 3.32 0.00 0.00 4.45
909 984 4.044065 TGGAATTGGCCTAATATACCCAGG 59.956 45.833 3.32 0.00 0.00 4.45
910 985 4.044191 GGAATTGGCCTAATATACCCAGGT 59.956 45.833 3.32 0.00 0.00 4.00
911 986 5.252164 GGAATTGGCCTAATATACCCAGGTA 59.748 44.000 3.32 0.00 34.87 3.08
912 987 5.774102 ATTGGCCTAATATACCCAGGTAC 57.226 43.478 3.32 0.00 33.01 3.34
913 988 4.497100 TGGCCTAATATACCCAGGTACT 57.503 45.455 3.32 0.00 43.88 2.73
914 989 4.422984 TGGCCTAATATACCCAGGTACTC 58.577 47.826 3.32 0.00 34.60 2.59
915 990 4.109106 TGGCCTAATATACCCAGGTACTCT 59.891 45.833 3.32 0.00 34.60 3.24
916 991 5.092259 GGCCTAATATACCCAGGTACTCTT 58.908 45.833 0.00 0.00 34.60 2.85
917 992 5.546887 GGCCTAATATACCCAGGTACTCTTT 59.453 44.000 0.00 0.00 34.60 2.52
918 993 6.044054 GGCCTAATATACCCAGGTACTCTTTT 59.956 42.308 0.00 0.00 34.60 2.27
919 994 7.421030 GGCCTAATATACCCAGGTACTCTTTTT 60.421 40.741 0.00 0.00 34.60 1.94
971 1047 9.947669 CTGGATTGAGATAAAGCTTAAATGAAG 57.052 33.333 0.00 0.00 38.30 3.02
1123 1199 2.936032 GTCCCCTGCCACCTCCTT 60.936 66.667 0.00 0.00 0.00 3.36
1189 1265 3.055819 GTCACTGTAGATGCCTCCTTTCA 60.056 47.826 0.00 0.00 0.00 2.69
1275 1351 3.636043 CACGTGCGCGGTTGTTCT 61.636 61.111 25.20 0.00 43.45 3.01
1418 1494 2.932234 CGTCCTCGACAAGGCCACT 61.932 63.158 5.01 0.00 45.78 4.00
1443 1519 3.203040 CACCCTTAAGATTGTCCCCATCT 59.797 47.826 3.36 0.00 0.00 2.90
1517 1593 9.290988 TGGTCTTGTTTAAGCAATTCTACATAA 57.709 29.630 5.13 0.00 33.82 1.90
1552 1628 8.832521 TGTTCTTAGTTGACGTGAAATGTTATT 58.167 29.630 0.00 0.00 35.18 1.40
1559 1635 4.331443 TGACGTGAAATGTTATTGATCCCG 59.669 41.667 0.00 0.00 35.18 5.14
1736 1812 1.538512 CTGCAACTGGGTGATTCTGTG 59.461 52.381 0.00 0.00 0.00 3.66
1758 1834 6.761242 TGTGACATCGCTAGCATAATTTAAGT 59.239 34.615 16.45 0.00 0.00 2.24
1820 1896 3.462021 GTGAGATGGTATCTGAACTGCC 58.538 50.000 0.00 0.00 40.38 4.85
2398 2492 7.872483 AGTTTTGTGCATTTAGATAAACTTGGG 59.128 33.333 0.00 0.00 32.24 4.12
2582 2676 9.719355 GACTATTTTTCTTCTTCTCCTCTTCTT 57.281 33.333 0.00 0.00 0.00 2.52
2596 2690 7.182760 TCTCCTCTTCTTCCATCTTAACAGTA 58.817 38.462 0.00 0.00 0.00 2.74
2744 2838 5.431765 TCTGCTTATTTGGACCTTGATCTC 58.568 41.667 0.00 0.00 0.00 2.75
3131 3225 4.202398 ACTTGAGCAGGATTGTTGAGAAGA 60.202 41.667 0.00 0.00 0.00 2.87
3135 3229 5.009010 TGAGCAGGATTGTTGAGAAGAAAAC 59.991 40.000 0.00 0.00 0.00 2.43
3367 3977 6.599638 AGTTAATGATGGAAAACTAGCTGTCC 59.400 38.462 0.00 0.00 30.62 4.02
3411 4021 7.719633 ACTTAATTTAGAAGGAGTTGCTTCACA 59.280 33.333 14.52 0.94 32.44 3.58
3663 4273 3.924918 TCTTCCTTGTCGACAGAGAAG 57.075 47.619 32.93 32.93 44.57 2.85
3929 4540 7.838696 TCAGTATTGGTTTCCATTTGATATGGT 59.161 33.333 1.87 0.00 40.06 3.55
3968 4583 1.671054 ATTGCCACCGTCGAACCTG 60.671 57.895 0.00 0.00 0.00 4.00
3992 4607 0.671781 CCCTCAGCTCAGTTTCACCG 60.672 60.000 0.00 0.00 0.00 4.94
4227 4853 2.128290 CTGTGATGGTCACCTGCCCA 62.128 60.000 7.55 0.00 46.40 5.36
4228 4854 1.304282 GTGATGGTCACCTGCCCAT 59.696 57.895 0.00 0.00 44.11 4.00
4259 4888 0.251209 AGGTGGATAGCCGAGCGATA 60.251 55.000 0.00 0.00 36.79 2.92
4312 4941 0.328258 ACCTCAGGGCCACATGTAAC 59.672 55.000 6.18 0.00 35.63 2.50
4386 5134 5.819901 CAGGTAGAAGGTGAATTCTGAATCC 59.180 44.000 7.05 1.07 39.81 3.01
4411 5160 3.430497 TCTCTCCCCCTCCCTCCG 61.430 72.222 0.00 0.00 0.00 4.63
4412 5161 3.756783 CTCTCCCCCTCCCTCCGT 61.757 72.222 0.00 0.00 0.00 4.69
4413 5162 3.742248 CTCTCCCCCTCCCTCCGTC 62.742 73.684 0.00 0.00 0.00 4.79
4414 5163 4.862823 CTCCCCCTCCCTCCGTCC 62.863 77.778 0.00 0.00 0.00 4.79
4417 5166 4.862823 CCCCTCCCTCCGTCCCTC 62.863 77.778 0.00 0.00 0.00 4.30
4418 5167 4.862823 CCCTCCCTCCGTCCCTCC 62.863 77.778 0.00 0.00 0.00 4.30
4445 5194 1.944024 TGAAGTGGAAAACGACGCATT 59.056 42.857 0.00 0.00 0.00 3.56
4460 5209 1.536766 CGCATTCAACACTGGTGTGAT 59.463 47.619 7.16 0.45 46.55 3.06
4468 5217 0.535780 CACTGGTGTGATGGCTGTGT 60.536 55.000 0.00 0.00 46.55 3.72
4479 5228 3.256936 GCTGTGTTCATGCAGCGA 58.743 55.556 7.20 0.00 46.67 4.93
4539 5288 4.270566 GTCATGAACTGCAAGCTCTCTATG 59.729 45.833 0.00 0.00 37.60 2.23
4542 5291 5.604758 TGAACTGCAAGCTCTCTATGTAT 57.395 39.130 0.00 0.00 37.60 2.29
4543 5292 5.354767 TGAACTGCAAGCTCTCTATGTATG 58.645 41.667 0.00 0.00 37.60 2.39
4544 5293 5.127682 TGAACTGCAAGCTCTCTATGTATGA 59.872 40.000 0.00 0.00 37.60 2.15
4554 5303 8.540507 AGCTCTCTATGTATGAAAAGGAGTTA 57.459 34.615 0.00 0.00 0.00 2.24
4606 5355 2.763448 AGACAATACCTGCAGAGAGGTC 59.237 50.000 17.39 15.11 43.33 3.85
4630 5379 5.939883 CCTTTCACTATTTGGACTGATCACA 59.060 40.000 0.00 0.00 0.00 3.58
4634 5383 6.533730 TCACTATTTGGACTGATCACAAGTT 58.466 36.000 0.00 0.00 0.00 2.66
4658 5407 2.093606 TGCTCTCTTTCTGATCAGCAGG 60.094 50.000 18.36 8.06 44.98 4.85
4666 5415 1.690283 CTGATCAGCAGGCGACAACG 61.690 60.000 10.38 0.00 41.07 4.10
4692 5441 4.887290 GCGCAAAGCTATGGCAAA 57.113 50.000 0.30 0.00 44.04 3.68
4693 5442 2.657336 GCGCAAAGCTATGGCAAAG 58.343 52.632 0.30 0.00 44.04 2.77
4694 5443 0.109132 GCGCAAAGCTATGGCAAAGT 60.109 50.000 0.30 0.00 44.04 2.66
4695 5444 1.669795 GCGCAAAGCTATGGCAAAGTT 60.670 47.619 0.30 0.00 44.04 2.66
4696 5445 2.415357 GCGCAAAGCTATGGCAAAGTTA 60.415 45.455 0.30 0.00 44.04 2.24
4697 5446 3.429085 CGCAAAGCTATGGCAAAGTTAG 58.571 45.455 3.10 0.00 41.70 2.34
4698 5447 3.119849 CGCAAAGCTATGGCAAAGTTAGT 60.120 43.478 3.10 0.00 41.70 2.24
4699 5448 4.615912 CGCAAAGCTATGGCAAAGTTAGTT 60.616 41.667 3.10 0.00 41.70 2.24
4700 5449 5.230182 GCAAAGCTATGGCAAAGTTAGTTT 58.770 37.500 3.10 0.00 41.70 2.66
4814 5563 1.267806 CAGGCCATGTCTGTTTGTCAC 59.732 52.381 5.01 0.00 29.72 3.67
4914 5680 5.105635 GCCATTCATTCTCTTTGGAACATGA 60.106 40.000 0.00 0.00 39.30 3.07
4915 5681 6.561614 CCATTCATTCTCTTTGGAACATGAG 58.438 40.000 0.00 0.00 39.30 2.90
4978 5744 5.938438 TGGCTTTGCAAACCAAATTAATC 57.062 34.783 22.92 0.35 42.22 1.75
4992 5758 1.643868 TTAATCGCTGCCTTGCACGG 61.644 55.000 4.51 4.51 35.24 4.94
5001 5767 2.819595 CTTGCACGGCACCGCTAT 60.820 61.111 9.43 0.00 44.19 2.97
5003 5769 2.582202 CTTGCACGGCACCGCTATTG 62.582 60.000 9.43 0.72 44.19 1.90
5004 5770 3.876198 GCACGGCACCGCTATTGG 61.876 66.667 9.43 0.00 44.19 3.16
5005 5771 3.202001 CACGGCACCGCTATTGGG 61.202 66.667 9.43 0.00 44.19 4.12
5012 5778 3.763671 CCGCTATTGGGGGCATTC 58.236 61.111 2.17 0.00 41.97 2.67
5013 5779 1.903404 CCGCTATTGGGGGCATTCC 60.903 63.158 2.17 0.00 41.97 3.01
5014 5780 2.260869 CGCTATTGGGGGCATTCCG 61.261 63.158 0.00 0.00 36.01 4.30
5015 5781 1.903404 GCTATTGGGGGCATTCCGG 60.903 63.158 0.00 0.00 36.01 5.14
5016 5782 1.843421 CTATTGGGGGCATTCCGGA 59.157 57.895 0.00 0.00 36.01 5.14
5033 5799 2.619849 CCGGACACTCCTACTTACCAGA 60.620 54.545 0.00 0.00 33.30 3.86
5059 5825 0.036875 AGAAGTTGCACTAGTGGCCC 59.963 55.000 23.95 8.41 0.00 5.80
5073 5839 2.269241 GCCCGGCTTGAAGCTAGT 59.731 61.111 17.59 0.00 41.99 2.57
5075 5841 1.648467 GCCCGGCTTGAAGCTAGTTG 61.648 60.000 17.59 6.41 41.99 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
157 160 2.881352 GCCGCTTCTTCTCGTCCG 60.881 66.667 0.00 0.00 0.00 4.79
210 213 5.816777 CCATCTCAATCTTCTTCCTCTGAAC 59.183 44.000 0.00 0.00 0.00 3.18
215 218 4.653341 TCCTCCATCTCAATCTTCTTCCTC 59.347 45.833 0.00 0.00 0.00 3.71
225 228 0.473326 GCTGCCTCCTCCATCTCAAT 59.527 55.000 0.00 0.00 0.00 2.57
274 277 2.909965 GTTGCCTTTGCCGGGACA 60.910 61.111 2.18 0.00 36.33 4.02
324 328 0.463833 TCGATGTCGAGCTGCCTCTA 60.464 55.000 0.21 0.00 44.22 2.43
365 369 3.185203 AGGGCCACCTCCTTTGCA 61.185 61.111 6.18 0.00 46.95 4.08
389 393 5.692115 TCTTGGTCAAGTCCATGCTTATA 57.308 39.130 10.10 0.00 39.38 0.98
659 694 1.227380 GCGGCCTACATGTCCTCAG 60.227 63.158 0.00 0.00 0.00 3.35
723 779 5.693104 AGAACAACGTTTCAAATACTAGCGA 59.307 36.000 0.00 0.00 0.00 4.93
728 784 7.066525 TCCAAAGAGAACAACGTTTCAAATACT 59.933 33.333 0.00 0.00 0.00 2.12
748 806 2.089980 CCATCTTGTCTGCCTCCAAAG 58.910 52.381 0.00 0.00 0.00 2.77
825 900 0.687098 TCCGTTTGGGTAGGGCGATA 60.687 55.000 0.00 0.00 37.00 2.92
845 920 1.200484 GTCCGCTTTGCCCGAATTTTA 59.800 47.619 0.00 0.00 0.00 1.52
890 965 5.421356 AGTACCTGGGTATATTAGGCCAAT 58.579 41.667 5.01 5.55 34.93 3.16
921 996 3.716872 ACCTGGGTTCTCTCTCTCAAAAA 59.283 43.478 0.00 0.00 0.00 1.94
922 997 3.318313 ACCTGGGTTCTCTCTCTCAAAA 58.682 45.455 0.00 0.00 0.00 2.44
923 998 2.977808 ACCTGGGTTCTCTCTCTCAAA 58.022 47.619 0.00 0.00 0.00 2.69
924 999 2.704190 ACCTGGGTTCTCTCTCTCAA 57.296 50.000 0.00 0.00 0.00 3.02
925 1000 2.650322 AGTACCTGGGTTCTCTCTCTCA 59.350 50.000 0.00 0.00 0.00 3.27
926 1001 3.020984 CAGTACCTGGGTTCTCTCTCTC 58.979 54.545 0.00 0.00 0.00 3.20
927 1002 3.094484 CAGTACCTGGGTTCTCTCTCT 57.906 52.381 0.00 0.00 0.00 3.10
928 1003 3.628769 ATCCAGTACCTGGGTTCTCTCTC 60.629 52.174 10.26 0.00 43.31 3.20
929 1004 2.316372 ATCCAGTACCTGGGTTCTCTCT 59.684 50.000 10.26 0.00 43.31 3.10
930 1005 2.753247 ATCCAGTACCTGGGTTCTCTC 58.247 52.381 10.26 0.00 43.31 3.20
931 1006 2.950990 ATCCAGTACCTGGGTTCTCT 57.049 50.000 10.26 0.00 43.31 3.10
971 1047 1.214373 CCACAACCACAACATTGCGC 61.214 55.000 0.00 0.00 0.00 6.09
1100 1176 4.717313 GTGGCAGGGGACGGGTTC 62.717 72.222 0.00 0.00 0.00 3.62
1123 1199 5.394738 TGGAGTACCTCTTCTTCTTCTTGA 58.605 41.667 0.00 0.00 37.04 3.02
1140 1216 0.673644 GCCTTGCGCTTCTTGGAGTA 60.674 55.000 9.73 0.00 0.00 2.59
1275 1351 0.323302 TTATGGTGCTTCTCGTGGCA 59.677 50.000 0.00 0.00 36.01 4.92
1418 1494 1.005450 GGGACAATCTTAAGGGTGCCA 59.995 52.381 20.28 0.00 40.93 4.92
1443 1519 0.108585 GTGCTCACCTTGTTGGAGGA 59.891 55.000 0.00 0.00 39.25 3.71
1517 1593 8.355169 TCACGTCAACTAAGAACAATACTACTT 58.645 33.333 0.00 0.00 0.00 2.24
1552 1628 9.787435 AACTGCTTATAAATATAAACGGGATCA 57.213 29.630 0.00 0.00 29.27 2.92
1736 1812 9.503427 AAAAACTTAAATTATGCTAGCGATGTC 57.497 29.630 10.77 0.00 0.00 3.06
1758 1834 2.034939 CAGGCACATCTGCTCACAAAAA 59.965 45.455 0.00 0.00 43.66 1.94
1820 1896 4.022849 ACTGAGAAAGAAAATTCCCTTGCG 60.023 41.667 0.00 0.00 0.00 4.85
2398 2492 6.483640 TCACACTAAAAAGAGAGAGGAAAAGC 59.516 38.462 0.00 0.00 0.00 3.51
2596 2690 4.833478 AGTGTTAAGCATGTCAGAGGAT 57.167 40.909 0.00 0.00 0.00 3.24
2744 2838 0.244994 CAGTGGTCTTGGACTCTCCG 59.755 60.000 0.00 0.00 40.17 4.63
3622 4232 2.358737 CCCTGGCTCCGTGAACAC 60.359 66.667 0.00 0.00 0.00 3.32
3663 4273 1.160137 AATTGACCAGAAGCTCGTGC 58.840 50.000 0.07 0.07 40.05 5.34
3929 4540 6.405731 GCAATGCATACCTTTCCTATCACAAA 60.406 38.462 0.00 0.00 0.00 2.83
3968 4583 0.536006 AAACTGAGCTGAGGGCACAC 60.536 55.000 4.85 0.00 44.79 3.82
3992 4607 6.825721 ACCTTCATCATTTTCTCCACTACATC 59.174 38.462 0.00 0.00 0.00 3.06
4132 4747 3.895232 ACTCACAGCAAGGTGGTATAG 57.105 47.619 4.16 0.00 39.27 1.31
4227 4853 0.994247 TCCACCTGCTGGTTCATCAT 59.006 50.000 13.36 0.00 46.05 2.45
4228 4854 0.994247 ATCCACCTGCTGGTTCATCA 59.006 50.000 13.36 0.00 46.05 3.07
4259 4888 2.437897 CAGACAGCTGGGCCCTTT 59.562 61.111 25.70 5.24 38.51 3.11
4312 4941 2.320587 GCAGGCAGAGAACACACGG 61.321 63.158 0.00 0.00 0.00 4.94
4386 5134 0.478507 GAGGGGGAGAGAGAGAGAGG 59.521 65.000 0.00 0.00 0.00 3.69
4411 5160 0.547954 ACTTCAAGGGAGGGAGGGAC 60.548 60.000 0.00 0.00 0.00 4.46
4412 5161 0.547712 CACTTCAAGGGAGGGAGGGA 60.548 60.000 0.00 0.00 0.00 4.20
4413 5162 1.566298 CCACTTCAAGGGAGGGAGGG 61.566 65.000 0.00 0.00 0.00 4.30
4414 5163 0.547712 TCCACTTCAAGGGAGGGAGG 60.548 60.000 0.00 0.00 0.00 4.30
4415 5164 1.362224 TTCCACTTCAAGGGAGGGAG 58.638 55.000 0.00 0.00 34.02 4.30
4416 5165 1.827792 TTTCCACTTCAAGGGAGGGA 58.172 50.000 0.00 0.00 34.02 4.20
4417 5166 2.239400 GTTTTCCACTTCAAGGGAGGG 58.761 52.381 0.00 0.00 34.02 4.30
4418 5167 1.880027 CGTTTTCCACTTCAAGGGAGG 59.120 52.381 0.00 0.00 34.02 4.30
4445 5194 0.473755 AGCCATCACACCAGTGTTGA 59.526 50.000 0.00 3.42 44.48 3.18
4468 5217 1.820906 GATGGCCTCGCTGCATGAA 60.821 57.895 3.32 0.00 0.00 2.57
4515 5264 1.392853 GAGAGCTTGCAGTTCATGACG 59.607 52.381 0.00 0.00 0.00 4.35
4539 5288 8.547967 TGACTGACATTAACTCCTTTTCATAC 57.452 34.615 0.00 0.00 0.00 2.39
4542 5291 7.223584 TCATGACTGACATTAACTCCTTTTCA 58.776 34.615 0.00 0.00 37.07 2.69
4543 5292 7.672983 TCATGACTGACATTAACTCCTTTTC 57.327 36.000 0.00 0.00 37.07 2.29
4544 5293 7.121759 CCATCATGACTGACATTAACTCCTTTT 59.878 37.037 0.00 0.00 37.07 2.27
4554 5303 1.065199 ACCGCCATCATGACTGACATT 60.065 47.619 0.00 0.00 37.07 2.71
4558 5307 1.221566 CCACCGCCATCATGACTGA 59.778 57.895 0.00 0.00 35.41 3.41
4561 5310 2.254546 TTATCCACCGCCATCATGAC 57.745 50.000 0.00 0.00 0.00 3.06
4596 5345 4.479786 AATAGTGAAAGGACCTCTCTGC 57.520 45.455 0.00 0.00 0.00 4.26
4606 5355 5.939883 TGTGATCAGTCCAAATAGTGAAAGG 59.060 40.000 0.00 0.00 32.71 3.11
4630 5379 5.371526 TGATCAGAAAGAGAGCACAAACTT 58.628 37.500 0.00 0.00 0.00 2.66
4634 5383 3.244318 TGCTGATCAGAAAGAGAGCACAA 60.244 43.478 27.04 0.00 39.48 3.33
4658 5407 1.655697 CGCTGCAAATTCGTTGTCGC 61.656 55.000 0.00 0.00 39.63 5.19
4814 5563 3.713764 ACCTCTTGTATCCAATCTCAGGG 59.286 47.826 0.00 0.00 0.00 4.45
4914 5680 5.353394 TCGTCCTTGGTATTTTATCAGCT 57.647 39.130 0.00 0.00 0.00 4.24
4915 5681 6.430451 CAATCGTCCTTGGTATTTTATCAGC 58.570 40.000 0.00 0.00 0.00 4.26
4992 5758 4.813235 TGCCCCCAATAGCGGTGC 62.813 66.667 0.00 0.00 0.00 5.01
4993 5759 1.455383 GAATGCCCCCAATAGCGGTG 61.455 60.000 0.00 0.00 0.00 4.94
4994 5760 1.152756 GAATGCCCCCAATAGCGGT 60.153 57.895 0.00 0.00 0.00 5.68
4995 5761 1.903404 GGAATGCCCCCAATAGCGG 60.903 63.158 0.00 0.00 0.00 5.52
4997 5763 1.903404 CCGGAATGCCCCCAATAGC 60.903 63.158 0.00 0.00 0.00 2.97
4998 5764 0.537371 GTCCGGAATGCCCCCAATAG 60.537 60.000 5.23 0.00 0.00 1.73
4999 5765 1.282653 TGTCCGGAATGCCCCCAATA 61.283 55.000 5.23 0.00 0.00 1.90
5001 5767 3.260888 TGTCCGGAATGCCCCCAA 61.261 61.111 5.23 0.00 0.00 4.12
5003 5769 3.699134 GAGTGTCCGGAATGCCCCC 62.699 68.421 5.23 0.00 0.00 5.40
5004 5770 2.124695 GAGTGTCCGGAATGCCCC 60.125 66.667 5.23 0.00 0.00 5.80
5005 5771 1.335132 TAGGAGTGTCCGGAATGCCC 61.335 60.000 5.23 5.86 42.75 5.36
5006 5772 0.179081 GTAGGAGTGTCCGGAATGCC 60.179 60.000 5.23 5.68 42.75 4.40
5007 5773 0.824759 AGTAGGAGTGTCCGGAATGC 59.175 55.000 5.23 0.00 42.75 3.56
5008 5774 3.181478 GGTAAGTAGGAGTGTCCGGAATG 60.181 52.174 5.23 0.00 42.75 2.67
5009 5775 3.029570 GGTAAGTAGGAGTGTCCGGAAT 58.970 50.000 5.23 0.00 42.75 3.01
5010 5776 2.225091 TGGTAAGTAGGAGTGTCCGGAA 60.225 50.000 5.23 0.00 42.75 4.30
5011 5777 1.355381 TGGTAAGTAGGAGTGTCCGGA 59.645 52.381 0.00 0.00 42.75 5.14
5012 5778 1.749634 CTGGTAAGTAGGAGTGTCCGG 59.250 57.143 0.00 0.00 42.75 5.14
5013 5779 2.683867 CTCTGGTAAGTAGGAGTGTCCG 59.316 54.545 0.00 0.00 42.75 4.79
5014 5780 3.949113 CTCTCTGGTAAGTAGGAGTGTCC 59.051 52.174 0.00 0.00 36.58 4.02
5015 5781 3.379057 GCTCTCTGGTAAGTAGGAGTGTC 59.621 52.174 0.00 0.00 0.00 3.67
5016 5782 3.245300 TGCTCTCTGGTAAGTAGGAGTGT 60.245 47.826 0.00 0.00 0.00 3.55
5048 5814 2.436646 CAAGCCGGGCCACTAGTG 60.437 66.667 17.02 16.34 0.00 2.74
5053 5819 3.622060 TAGCTTCAAGCCGGGCCAC 62.622 63.158 17.02 0.00 43.77 5.01
5059 5825 0.798776 CCACAACTAGCTTCAAGCCG 59.201 55.000 5.53 0.00 43.77 5.52


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

AutoCloner maintained by Alex Coulton.