Multiple sequence alignment - TraesCS5B01G461700

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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 TraesCS5B01G461700 chr5B 100.000 2445 0 0 1 2445 637163145 637165589 0.000000e+00 4516.0
1 TraesCS5B01G461700 chr3B 88.360 2268 194 27 190 2443 59642097 59639886 0.000000e+00 2662.0
2 TraesCS5B01G461700 chr3B 87.844 2287 191 34 191 2445 786869736 786871967 0.000000e+00 2603.0
3 TraesCS5B01G461700 chr3B 89.100 422 41 4 191 611 677945804 677945387 1.000000e-143 520.0
4 TraesCS5B01G461700 chr3B 83.750 160 26 0 32 191 411275949 411276108 4.210000e-33 152.0
5 TraesCS5B01G461700 chr5D 88.983 2115 193 29 193 2286 414157952 414155857 0.000000e+00 2579.0
6 TraesCS5B01G461700 chr5D 94.764 191 10 0 1 191 506302661 506302851 5.110000e-77 298.0
7 TraesCS5B01G461700 chr7D 89.607 2059 161 30 408 2445 55090946 55092972 0.000000e+00 2567.0
8 TraesCS5B01G461700 chr7D 91.509 106 9 0 86 191 59290966 59290861 1.960000e-31 147.0
9 TraesCS5B01G461700 chr7D 87.000 100 13 0 86 185 321389236 321389137 1.990000e-21 113.0
10 TraesCS5B01G461700 chr7D 87.000 100 13 0 86 185 321397906 321397807 1.990000e-21 113.0
11 TraesCS5B01G461700 chr7D 86.000 100 11 2 86 185 45124878 45124974 1.200000e-18 104.0
12 TraesCS5B01G461700 chr6B 87.473 2283 196 42 192 2443 143410495 143408272 0.000000e+00 2549.0
13 TraesCS5B01G461700 chr6B 87.703 2220 205 31 192 2383 20876885 20874706 0.000000e+00 2525.0
14 TraesCS5B01G461700 chr6B 88.194 1999 187 29 469 2445 243795715 243793744 0.000000e+00 2338.0
15 TraesCS5B01G461700 chr6B 84.631 1939 204 44 179 2085 34705673 34703797 0.000000e+00 1844.0
16 TraesCS5B01G461700 chr6B 87.224 1628 141 19 192 1801 157159433 157161011 0.000000e+00 1792.0
17 TraesCS5B01G461700 chr6B 89.787 235 21 2 276 510 650682287 650682518 5.110000e-77 298.0
18 TraesCS5B01G461700 chr6B 77.055 292 53 5 192 482 44789956 44789678 3.260000e-34 156.0
19 TraesCS5B01G461700 chr6B 88.571 70 8 0 192 261 701432714 701432783 4.330000e-13 86.1
20 TraesCS5B01G461700 chr4B 89.827 2025 152 30 442 2445 17116853 17118844 0.000000e+00 2549.0
21 TraesCS5B01G461700 chr2B 89.650 2000 158 30 469 2445 727143732 727141759 0.000000e+00 2501.0
22 TraesCS5B01G461700 chr2B 89.361 2002 157 31 469 2445 612395192 612393222 0.000000e+00 2466.0
23 TraesCS5B01G461700 chr2B 86.571 700 65 21 195 893 97333667 97332996 0.000000e+00 745.0
24 TraesCS5B01G461700 chr2B 83.232 328 53 2 192 517 57128387 57128714 1.420000e-77 300.0
25 TraesCS5B01G461700 chr2B 77.931 290 53 5 192 481 574005858 574005580 1.160000e-38 171.0
26 TraesCS5B01G461700 chr2B 90.476 126 12 0 192 317 4511416 4511291 1.500000e-37 167.0
27 TraesCS5B01G461700 chr6A 89.318 2022 172 27 442 2445 91685193 91683198 0.000000e+00 2497.0
28 TraesCS5B01G461700 chr6A 88.889 90 10 0 86 175 66437086 66437175 7.150000e-21 111.0
29 TraesCS5B01G461700 chr4A 89.540 1998 166 22 469 2445 214310845 214308870 0.000000e+00 2492.0
30 TraesCS5B01G461700 chr4A 88.679 106 12 0 86 191 180449495 180449600 1.970000e-26 130.0
31 TraesCS5B01G461700 chr6D 88.878 2023 177 30 442 2439 18719208 18721207 0.000000e+00 2446.0
32 TraesCS5B01G461700 chr6D 88.423 2004 154 43 469 2445 446081826 446079874 0.000000e+00 2344.0
33 TraesCS5B01G461700 chr6D 88.112 2044 151 46 442 2445 463524142 463522151 0.000000e+00 2344.0
34 TraesCS5B01G461700 chr6D 89.247 93 10 0 86 178 48166159 48166067 1.540000e-22 117.0
35 TraesCS5B01G461700 chr6D 87.255 102 10 2 80 180 337681540 337681441 1.990000e-21 113.0
36 TraesCS5B01G461700 chrUn 87.123 2058 187 34 442 2445 82253295 82251262 0.000000e+00 2261.0
37 TraesCS5B01G461700 chrUn 87.029 2043 173 46 442 2445 190729755 190731744 0.000000e+00 2220.0
38 TraesCS5B01G461700 chrUn 87.166 1348 110 32 1111 2445 189428449 189429746 0.000000e+00 1472.0
39 TraesCS5B01G461700 chrUn 87.166 1348 110 32 1111 2445 237250723 237252020 0.000000e+00 1472.0
40 TraesCS5B01G461700 chrUn 90.032 933 82 2 1514 2445 349288743 349289665 0.000000e+00 1197.0
41 TraesCS5B01G461700 chrUn 89.925 933 83 2 1514 2445 349286435 349287357 0.000000e+00 1192.0
42 TraesCS5B01G461700 chrUn 87.162 148 9 4 2298 2445 114873822 114873959 2.520000e-35 159.0
43 TraesCS5B01G461700 chr1B 89.354 263 26 2 263 524 640016702 640016441 1.810000e-86 329.0
44 TraesCS5B01G461700 chr1B 86.111 108 15 0 84 191 272354375 272354268 1.540000e-22 117.0
45 TraesCS5B01G461700 chr5A 92.670 191 14 0 1 191 634091074 634091264 2.390000e-70 276.0
46 TraesCS5B01G461700 chr7A 85.542 166 20 4 23 186 561366875 561367038 1.160000e-38 171.0
47 TraesCS5B01G461700 chr3A 85.827 127 16 2 32 157 422337369 422337494 1.530000e-27 134.0
48 TraesCS5B01G461700 chr2A 88.679 106 12 0 86 191 425930592 425930697 1.970000e-26 130.0
49 TraesCS5B01G461700 chr1D 85.217 115 17 0 77 191 269979674 269979560 4.270000e-23 119.0
50 TraesCS5B01G461700 chr1D 86.364 88 12 0 104 191 257347479 257347392 2.000000e-16 97.1
51 TraesCS5B01G461700 chr1A 85.185 108 16 0 84 191 331229013 331228906 7.150000e-21 111.0
52 TraesCS5B01G461700 chr2D 84.466 103 14 2 88 189 60303021 60303122 1.550000e-17 100.0
53 TraesCS5B01G461700 chr4D 84.946 93 14 0 86 178 301244685 301244593 7.200000e-16 95.3
54 TraesCS5B01G461700 chr4D 89.655 58 6 0 97 154 15514374 15514317 9.380000e-10 75.0


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 TraesCS5B01G461700 chr5B 637163145 637165589 2444 False 4516.0 4516 100.0000 1 2445 1 chr5B.!!$F1 2444
1 TraesCS5B01G461700 chr3B 59639886 59642097 2211 True 2662.0 2662 88.3600 190 2443 1 chr3B.!!$R1 2253
2 TraesCS5B01G461700 chr3B 786869736 786871967 2231 False 2603.0 2603 87.8440 191 2445 1 chr3B.!!$F2 2254
3 TraesCS5B01G461700 chr5D 414155857 414157952 2095 True 2579.0 2579 88.9830 193 2286 1 chr5D.!!$R1 2093
4 TraesCS5B01G461700 chr7D 55090946 55092972 2026 False 2567.0 2567 89.6070 408 2445 1 chr7D.!!$F2 2037
5 TraesCS5B01G461700 chr6B 143408272 143410495 2223 True 2549.0 2549 87.4730 192 2443 1 chr6B.!!$R4 2251
6 TraesCS5B01G461700 chr6B 20874706 20876885 2179 True 2525.0 2525 87.7030 192 2383 1 chr6B.!!$R1 2191
7 TraesCS5B01G461700 chr6B 243793744 243795715 1971 True 2338.0 2338 88.1940 469 2445 1 chr6B.!!$R5 1976
8 TraesCS5B01G461700 chr6B 34703797 34705673 1876 True 1844.0 1844 84.6310 179 2085 1 chr6B.!!$R2 1906
9 TraesCS5B01G461700 chr6B 157159433 157161011 1578 False 1792.0 1792 87.2240 192 1801 1 chr6B.!!$F1 1609
10 TraesCS5B01G461700 chr4B 17116853 17118844 1991 False 2549.0 2549 89.8270 442 2445 1 chr4B.!!$F1 2003
11 TraesCS5B01G461700 chr2B 727141759 727143732 1973 True 2501.0 2501 89.6500 469 2445 1 chr2B.!!$R5 1976
12 TraesCS5B01G461700 chr2B 612393222 612395192 1970 True 2466.0 2466 89.3610 469 2445 1 chr2B.!!$R4 1976
13 TraesCS5B01G461700 chr2B 97332996 97333667 671 True 745.0 745 86.5710 195 893 1 chr2B.!!$R2 698
14 TraesCS5B01G461700 chr6A 91683198 91685193 1995 True 2497.0 2497 89.3180 442 2445 1 chr6A.!!$R1 2003
15 TraesCS5B01G461700 chr4A 214308870 214310845 1975 True 2492.0 2492 89.5400 469 2445 1 chr4A.!!$R1 1976
16 TraesCS5B01G461700 chr6D 18719208 18721207 1999 False 2446.0 2446 88.8780 442 2439 1 chr6D.!!$F1 1997
17 TraesCS5B01G461700 chr6D 446079874 446081826 1952 True 2344.0 2344 88.4230 469 2445 1 chr6D.!!$R3 1976
18 TraesCS5B01G461700 chr6D 463522151 463524142 1991 True 2344.0 2344 88.1120 442 2445 1 chr6D.!!$R4 2003
19 TraesCS5B01G461700 chrUn 82251262 82253295 2033 True 2261.0 2261 87.1230 442 2445 1 chrUn.!!$R1 2003
20 TraesCS5B01G461700 chrUn 190729755 190731744 1989 False 2220.0 2220 87.0290 442 2445 1 chrUn.!!$F3 2003
21 TraesCS5B01G461700 chrUn 189428449 189429746 1297 False 1472.0 1472 87.1660 1111 2445 1 chrUn.!!$F2 1334
22 TraesCS5B01G461700 chrUn 237250723 237252020 1297 False 1472.0 1472 87.1660 1111 2445 1 chrUn.!!$F4 1334
23 TraesCS5B01G461700 chrUn 349286435 349289665 3230 False 1194.5 1197 89.9785 1514 2445 2 chrUn.!!$F5 931

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
44 45 0.038892 GTGTGCAGGCACCTGATTTG 60.039 55.0 20.92 0.0 46.3 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1985 2858 0.889994 TGCGATGCAATTTCAGCCTT 59.11 45.0 0.0 0.0 34.76 4.35 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
32 33 8.756376 CAAACAAATAAGAATTTTGTGTGCAG 57.244 30.769 6.54 0.00 44.32 4.41
34 35 5.466393 ACAAATAAGAATTTTGTGTGCAGGC 59.534 36.000 1.32 0.00 43.65 4.85
35 36 4.870123 ATAAGAATTTTGTGTGCAGGCA 57.130 36.364 0.00 0.00 0.00 4.75
36 37 2.514205 AGAATTTTGTGTGCAGGCAC 57.486 45.000 17.11 17.11 46.33 5.01
37 38 1.069049 AGAATTTTGTGTGCAGGCACC 59.931 47.619 20.60 12.69 45.63 5.01
38 39 1.069049 GAATTTTGTGTGCAGGCACCT 59.931 47.619 20.60 0.00 45.63 4.00
39 40 0.390124 ATTTTGTGTGCAGGCACCTG 59.610 50.000 20.60 12.54 45.63 4.00
40 41 0.682532 TTTTGTGTGCAGGCACCTGA 60.683 50.000 20.92 2.96 46.30 3.86
41 42 0.467844 TTTGTGTGCAGGCACCTGAT 60.468 50.000 20.92 0.00 46.30 2.90
43 44 0.467844 TGTGTGCAGGCACCTGATTT 60.468 50.000 20.92 0.00 46.30 2.17
44 45 0.038892 GTGTGCAGGCACCTGATTTG 60.039 55.000 20.92 0.00 46.30 2.32
45 46 1.180456 TGTGCAGGCACCTGATTTGG 61.180 55.000 20.92 0.00 46.30 3.28
46 47 1.153524 TGCAGGCACCTGATTTGGT 59.846 52.632 20.92 0.00 46.30 3.67
47 48 0.403655 TGCAGGCACCTGATTTGGTA 59.596 50.000 20.92 0.00 46.30 3.25
48 49 1.098050 GCAGGCACCTGATTTGGTAG 58.902 55.000 20.92 0.00 46.30 3.18
49 50 1.614317 GCAGGCACCTGATTTGGTAGT 60.614 52.381 20.92 0.00 46.30 2.73
50 51 2.795329 CAGGCACCTGATTTGGTAGTT 58.205 47.619 11.43 0.00 46.30 2.24
52 53 2.108250 AGGCACCTGATTTGGTAGTTGT 59.892 45.455 0.00 0.00 38.45 3.32
53 54 2.890945 GGCACCTGATTTGGTAGTTGTT 59.109 45.455 0.00 0.00 38.45 2.83
54 55 3.305335 GGCACCTGATTTGGTAGTTGTTG 60.305 47.826 0.00 0.00 38.45 3.33
55 56 3.568007 GCACCTGATTTGGTAGTTGTTGA 59.432 43.478 0.00 0.00 38.45 3.18
57 58 4.821805 CACCTGATTTGGTAGTTGTTGACT 59.178 41.667 0.00 0.00 42.55 3.41
58 59 5.049405 CACCTGATTTGGTAGTTGTTGACTC 60.049 44.000 0.00 0.00 39.86 3.36
60 61 5.409826 CCTGATTTGGTAGTTGTTGACTCTC 59.590 44.000 0.00 0.00 39.86 3.20
61 62 5.305585 TGATTTGGTAGTTGTTGACTCTCC 58.694 41.667 0.00 0.00 39.86 3.71
62 63 3.380479 TTGGTAGTTGTTGACTCTCCG 57.620 47.619 0.00 0.00 39.86 4.63
64 65 1.672145 GGTAGTTGTTGACTCTCCGGC 60.672 57.143 0.00 0.00 39.86 6.13
65 66 1.000506 GTAGTTGTTGACTCTCCGGCA 59.999 52.381 0.00 0.00 39.86 5.69
66 67 0.468226 AGTTGTTGACTCTCCGGCAA 59.532 50.000 0.00 0.00 31.20 4.52
67 68 0.586802 GTTGTTGACTCTCCGGCAAC 59.413 55.000 13.17 13.17 41.57 4.17
85 86 3.112580 CAACGACGCCAAAAATTCTTGT 58.887 40.909 0.00 0.00 0.00 3.16
87 88 1.451651 CGACGCCAAAAATTCTTGTGC 59.548 47.619 0.00 0.00 0.00 4.57
88 89 2.742774 GACGCCAAAAATTCTTGTGCT 58.257 42.857 4.27 0.00 0.00 4.40
89 90 3.608241 CGACGCCAAAAATTCTTGTGCTA 60.608 43.478 4.27 0.00 0.00 3.49
90 91 3.638484 ACGCCAAAAATTCTTGTGCTAC 58.362 40.909 4.27 0.00 0.00 3.58
91 92 3.317993 ACGCCAAAAATTCTTGTGCTACT 59.682 39.130 4.27 0.00 0.00 2.57
92 93 3.914364 CGCCAAAAATTCTTGTGCTACTC 59.086 43.478 4.27 0.00 0.00 2.59
93 94 4.556501 CGCCAAAAATTCTTGTGCTACTCA 60.557 41.667 4.27 0.00 0.00 3.41
103 104 2.511659 TGTGCTACTCACGTAGGAGTT 58.488 47.619 13.13 0.00 45.59 3.01
105 106 2.228343 GTGCTACTCACGTAGGAGTTGT 59.772 50.000 13.13 0.00 45.59 3.32
106 107 2.889045 TGCTACTCACGTAGGAGTTGTT 59.111 45.455 13.13 0.00 45.59 2.83
107 108 4.074259 TGCTACTCACGTAGGAGTTGTTA 58.926 43.478 13.13 3.99 45.59 2.41
111 112 5.979288 ACTCACGTAGGAGTTGTTAGATT 57.021 39.130 2.84 0.00 45.59 2.40
112 113 5.952033 ACTCACGTAGGAGTTGTTAGATTC 58.048 41.667 2.84 0.00 45.59 2.52
113 114 5.105837 ACTCACGTAGGAGTTGTTAGATTCC 60.106 44.000 2.84 0.00 45.59 3.01
114 115 4.159135 TCACGTAGGAGTTGTTAGATTCCC 59.841 45.833 0.00 0.00 0.00 3.97
115 116 3.450096 ACGTAGGAGTTGTTAGATTCCCC 59.550 47.826 0.00 0.00 0.00 4.81
116 117 3.490419 CGTAGGAGTTGTTAGATTCCCCG 60.490 52.174 0.00 0.00 0.00 5.73
118 119 3.178865 AGGAGTTGTTAGATTCCCCGAA 58.821 45.455 0.00 0.00 0.00 4.30
120 121 3.197116 GGAGTTGTTAGATTCCCCGAAGA 59.803 47.826 0.00 0.00 0.00 2.87
121 122 4.434520 GAGTTGTTAGATTCCCCGAAGAG 58.565 47.826 0.00 0.00 0.00 2.85
122 123 3.197983 AGTTGTTAGATTCCCCGAAGAGG 59.802 47.826 0.00 0.00 40.63 3.69
123 124 3.110293 TGTTAGATTCCCCGAAGAGGA 57.890 47.619 0.00 0.00 45.00 3.71
128 129 3.175498 TTCCCCGAAGAGGAAAGGT 57.825 52.632 0.00 0.00 42.95 3.50
129 130 0.690762 TTCCCCGAAGAGGAAAGGTG 59.309 55.000 0.00 0.00 42.95 4.00
130 131 0.178915 TCCCCGAAGAGGAAAGGTGA 60.179 55.000 0.00 0.00 45.00 4.02
133 134 1.279271 CCCGAAGAGGAAAGGTGATGT 59.721 52.381 0.00 0.00 45.00 3.06
134 135 2.500098 CCCGAAGAGGAAAGGTGATGTA 59.500 50.000 0.00 0.00 45.00 2.29
136 137 3.190874 CGAAGAGGAAAGGTGATGTAGC 58.809 50.000 0.00 0.00 0.00 3.58
137 138 3.368427 CGAAGAGGAAAGGTGATGTAGCA 60.368 47.826 0.00 0.00 0.00 3.49
138 139 3.618690 AGAGGAAAGGTGATGTAGCAC 57.381 47.619 0.00 0.00 38.05 4.40
139 140 2.906389 AGAGGAAAGGTGATGTAGCACA 59.094 45.455 2.51 0.00 40.52 4.57
140 141 3.327757 AGAGGAAAGGTGATGTAGCACAA 59.672 43.478 2.51 0.00 40.52 3.33
141 142 3.412386 AGGAAAGGTGATGTAGCACAAC 58.588 45.455 2.51 0.00 40.52 3.32
143 144 3.758554 GGAAAGGTGATGTAGCACAACAT 59.241 43.478 2.51 0.00 42.75 2.71
154 155 7.928307 ATGTAGCACAACATCAGAAAGTATT 57.072 32.000 0.00 0.00 35.08 1.89
156 157 8.454106 ATGTAGCACAACATCAGAAAGTATTTC 58.546 33.333 0.00 0.00 44.71 2.17
226 227 2.360165 GGGCCTAATGTTCAGCTCATTG 59.640 50.000 0.84 1.13 36.92 2.82
261 262 3.040147 CCGAACCGGCACTAATATGAT 57.960 47.619 0.00 0.00 41.17 2.45
277 278 8.861086 ACTAATATGATCATTAGTGACGGTTCT 58.139 33.333 14.65 0.00 45.60 3.01
304 305 1.748879 GGCGGGCTGTGCTCATTAA 60.749 57.895 0.00 0.00 0.00 1.40
336 337 2.002509 GCGAACCTCTAGTCCCGGTC 62.003 65.000 0.00 0.00 0.00 4.79
456 458 1.480954 GAGATGCACCTTTAGTCCCGA 59.519 52.381 0.00 0.00 0.00 5.14
463 465 5.071370 TGCACCTTTAGTCCCGATTTTTAA 58.929 37.500 0.00 0.00 0.00 1.52
553 571 4.227073 CCTTTCATTCCTTCCTCTCCTCTT 59.773 45.833 0.00 0.00 0.00 2.85
912 1019 7.336931 TGGTGAGCCTCTTGTTCTTATATTTTC 59.663 37.037 0.00 0.00 35.27 2.29
1003 1130 6.130298 TGTTTGTTATACATAGTGCCATGC 57.870 37.500 0.00 0.00 0.00 4.06
1018 1145 2.880890 GCCATGCTTTTGATATCCGTCT 59.119 45.455 0.00 0.00 0.00 4.18
1155 1282 3.643237 TCTAGGAGGTATGTGAACCAGG 58.357 50.000 0.00 0.00 42.40 4.45
1178 1305 0.906775 TCCAACCGACCCTATTGTCC 59.093 55.000 0.00 0.00 31.35 4.02
1314 1444 4.354893 AGATCAAGATGGAGAAGATGCC 57.645 45.455 0.00 0.00 0.00 4.40
1334 1473 6.764308 TGCCCTTGAAGATTAGAAAGATTG 57.236 37.500 0.00 0.00 0.00 2.67
1404 1544 5.600908 TCAATTGTTACCTTAGTTGCGAC 57.399 39.130 5.13 0.00 0.00 5.19
1420 1560 2.442189 CGACCTTGATCGCATTTGTC 57.558 50.000 0.00 0.00 34.90 3.18
1457 1601 5.812642 TGCTTTAGCTAGAGAGTTTGTATGC 59.187 40.000 15.20 1.24 42.66 3.14
1570 2366 1.144936 CGATGCTCTCCCCAGTTCC 59.855 63.158 0.00 0.00 0.00 3.62
1702 2498 2.690778 GCCATTCACGTCCACCTGC 61.691 63.158 0.00 0.00 0.00 4.85
1763 2559 1.002773 GCACGGAGAAAGAGGGGTTAA 59.997 52.381 0.00 0.00 0.00 2.01
1795 2591 3.878160 ATGAAGAAGAAGAGGACGACC 57.122 47.619 0.00 0.00 0.00 4.79
1876 2721 2.040544 CGGCAATGCGGGAAGAAGT 61.041 57.895 4.78 0.00 0.00 3.01
1922 2793 6.897986 AGTTAAAGAAGAGGCATCAGATGAT 58.102 36.000 15.12 1.22 34.56 2.45
1979 2852 1.506493 AGAGAAACTGCGCAAGTGAG 58.494 50.000 13.05 0.79 39.81 3.51
1985 2858 0.106708 ACTGCGCAAGTGAGAAGGAA 59.893 50.000 13.05 0.00 37.88 3.36
2000 2873 3.836562 AGAAGGAAAGGCTGAAATTGCAT 59.163 39.130 0.00 0.00 0.00 3.96
2015 2888 1.939974 TGCATCGCATGTTAGAGGAC 58.060 50.000 0.00 0.00 31.71 3.85
2051 2924 7.723838 GTTGTACCCAAATTGCGAAGCTGAA 62.724 44.000 0.00 0.00 43.84 3.02
2097 2970 1.200519 ATTGCTGCAATGGAAGGCAT 58.799 45.000 25.76 0.06 39.65 4.40
2099 2972 1.849977 TGCTGCAATGGAAGGCATAA 58.150 45.000 0.00 0.00 39.65 1.90
2114 2987 6.491403 GGAAGGCATAAAATGGTGTATCTGAT 59.509 38.462 0.00 0.00 0.00 2.90
2178 3051 5.269554 TCCAAAGGACAATGAATTACCCT 57.730 39.130 0.00 0.00 0.00 4.34
2194 3067 2.911484 ACCCTAGAGTACGTACGAAGG 58.089 52.381 24.41 25.13 0.00 3.46
2223 3096 4.550076 GCTGTCTGCCCTCTATGATTAT 57.450 45.455 0.00 0.00 35.15 1.28
2263 3138 0.183492 TGCCCTAATGACTGCATCCC 59.817 55.000 0.00 0.00 32.35 3.85
2292 3167 3.613193 CGGTGAGTACGAGGATTTGAACA 60.613 47.826 0.00 0.00 0.00 3.18
2306 3181 0.615850 TGAACACATGCCCGGTATGA 59.384 50.000 21.13 0.00 30.48 2.15
2327 3202 3.480470 AGGTGCATTGCGCTATAAGATT 58.520 40.909 20.61 0.00 43.06 2.40
2336 3211 2.917971 GCGCTATAAGATTAGCCGTGAG 59.082 50.000 0.00 0.00 41.27 3.51
2352 3227 0.178906 TGAGGACCCTGGTGATGTCA 60.179 55.000 0.00 0.00 0.00 3.58
2374 3249 4.082523 CGAGCGCCCCAGGAAGAA 62.083 66.667 2.29 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.553418 GCACACAAAATTCTTATTTGTTTGTTT 57.447 25.926 15.48 0.00 45.97 2.83
7 8 7.851963 CCTGCACACAAAATTCTTATTTGTTTG 59.148 33.333 11.77 11.77 45.97 2.93
8 9 7.467131 GCCTGCACACAAAATTCTTATTTGTTT 60.467 33.333 2.14 0.00 45.97 2.83
11 12 5.466058 TGCCTGCACACAAAATTCTTATTTG 59.534 36.000 0.00 0.00 42.18 2.32
13 14 4.990426 GTGCCTGCACACAAAATTCTTATT 59.010 37.500 16.95 0.00 45.53 1.40
14 15 4.559153 GTGCCTGCACACAAAATTCTTAT 58.441 39.130 16.95 0.00 45.53 1.73
15 16 3.976169 GTGCCTGCACACAAAATTCTTA 58.024 40.909 16.95 0.00 45.53 2.10
16 17 2.825205 GTGCCTGCACACAAAATTCTT 58.175 42.857 16.95 0.00 45.53 2.52
17 18 2.514205 GTGCCTGCACACAAAATTCT 57.486 45.000 16.95 0.00 45.53 2.40
27 28 1.181098 ACCAAATCAGGTGCCTGCAC 61.181 55.000 13.75 13.75 43.31 4.57
30 31 2.489329 CAACTACCAAATCAGGTGCCTG 59.511 50.000 11.82 11.82 43.14 4.85
32 33 2.514803 ACAACTACCAAATCAGGTGCC 58.485 47.619 0.00 0.00 43.14 5.01
34 35 4.821805 AGTCAACAACTACCAAATCAGGTG 59.178 41.667 0.00 0.00 43.14 4.00
35 36 5.048846 AGTCAACAACTACCAAATCAGGT 57.951 39.130 0.00 0.00 45.72 4.00
36 37 5.308825 AGAGTCAACAACTACCAAATCAGG 58.691 41.667 0.00 0.00 38.74 3.86
37 38 5.409826 GGAGAGTCAACAACTACCAAATCAG 59.590 44.000 0.00 0.00 38.74 2.90
38 39 5.305585 GGAGAGTCAACAACTACCAAATCA 58.694 41.667 0.00 0.00 38.74 2.57
39 40 4.389077 CGGAGAGTCAACAACTACCAAATC 59.611 45.833 0.00 0.00 38.74 2.17
40 41 4.315803 CGGAGAGTCAACAACTACCAAAT 58.684 43.478 0.00 0.00 38.74 2.32
41 42 3.493699 CCGGAGAGTCAACAACTACCAAA 60.494 47.826 0.00 0.00 38.74 3.28
43 44 1.616865 CCGGAGAGTCAACAACTACCA 59.383 52.381 0.00 0.00 38.74 3.25
44 45 1.672145 GCCGGAGAGTCAACAACTACC 60.672 57.143 5.05 0.00 38.74 3.18
45 46 1.000506 TGCCGGAGAGTCAACAACTAC 59.999 52.381 5.05 0.00 38.74 2.73
46 47 1.334160 TGCCGGAGAGTCAACAACTA 58.666 50.000 5.05 0.00 38.74 2.24
47 48 0.468226 TTGCCGGAGAGTCAACAACT 59.532 50.000 5.05 0.00 42.42 3.16
48 49 0.586802 GTTGCCGGAGAGTCAACAAC 59.413 55.000 5.05 3.25 39.69 3.32
49 50 0.878523 CGTTGCCGGAGAGTCAACAA 60.879 55.000 18.16 3.25 39.84 2.83
50 51 1.300620 CGTTGCCGGAGAGTCAACA 60.301 57.895 18.16 0.00 39.84 3.33
52 53 1.006571 GTCGTTGCCGGAGAGTCAA 60.007 57.895 5.05 0.00 33.95 3.18
53 54 2.649034 GTCGTTGCCGGAGAGTCA 59.351 61.111 5.05 0.00 33.95 3.41
54 55 2.504244 CGTCGTTGCCGGAGAGTC 60.504 66.667 5.05 0.00 33.95 3.36
55 56 4.719369 GCGTCGTTGCCGGAGAGT 62.719 66.667 5.05 0.00 33.95 3.24
64 65 3.061271 CACAAGAATTTTTGGCGTCGTTG 60.061 43.478 12.83 0.00 32.32 4.10
65 66 3.112580 CACAAGAATTTTTGGCGTCGTT 58.887 40.909 12.83 0.00 32.32 3.85
66 67 2.726633 CACAAGAATTTTTGGCGTCGT 58.273 42.857 12.83 0.00 32.32 4.34
67 68 1.451651 GCACAAGAATTTTTGGCGTCG 59.548 47.619 12.83 0.00 32.32 5.12
69 70 2.888834 AGCACAAGAATTTTTGGCGT 57.111 40.000 12.83 2.54 32.82 5.68
70 71 3.900941 AGTAGCACAAGAATTTTTGGCG 58.099 40.909 12.83 5.14 32.82 5.69
71 72 4.681483 GTGAGTAGCACAAGAATTTTTGGC 59.319 41.667 12.83 12.17 46.91 4.52
88 89 6.094603 GGAATCTAACAACTCCTACGTGAGTA 59.905 42.308 8.79 0.00 44.68 2.59
90 91 5.341617 GGAATCTAACAACTCCTACGTGAG 58.658 45.833 0.00 0.00 38.37 3.51
91 92 4.159135 GGGAATCTAACAACTCCTACGTGA 59.841 45.833 0.00 0.00 0.00 4.35
92 93 4.430908 GGGAATCTAACAACTCCTACGTG 58.569 47.826 0.00 0.00 0.00 4.49
93 94 3.450096 GGGGAATCTAACAACTCCTACGT 59.550 47.826 0.00 0.00 0.00 3.57
95 96 3.703052 TCGGGGAATCTAACAACTCCTAC 59.297 47.826 0.00 0.00 0.00 3.18
96 97 3.985127 TCGGGGAATCTAACAACTCCTA 58.015 45.455 0.00 0.00 0.00 2.94
98 99 3.197116 TCTTCGGGGAATCTAACAACTCC 59.803 47.826 0.00 0.00 0.00 3.85
99 100 4.434520 CTCTTCGGGGAATCTAACAACTC 58.565 47.826 0.00 0.00 0.00 3.01
102 103 3.446968 TCCTCTTCGGGGAATCTAACAA 58.553 45.455 0.00 0.00 0.00 2.83
103 104 3.110293 TCCTCTTCGGGGAATCTAACA 57.890 47.619 0.00 0.00 0.00 2.41
105 106 3.454812 CCTTTCCTCTTCGGGGAATCTAA 59.545 47.826 0.00 0.00 41.72 2.10
106 107 3.039011 CCTTTCCTCTTCGGGGAATCTA 58.961 50.000 0.00 0.00 41.72 1.98
107 108 1.840635 CCTTTCCTCTTCGGGGAATCT 59.159 52.381 0.00 0.00 41.72 2.40
111 112 0.178915 TCACCTTTCCTCTTCGGGGA 60.179 55.000 0.00 0.00 0.00 4.81
112 113 0.912486 ATCACCTTTCCTCTTCGGGG 59.088 55.000 0.00 0.00 0.00 5.73
113 114 1.279271 ACATCACCTTTCCTCTTCGGG 59.721 52.381 0.00 0.00 0.00 5.14
114 115 2.770164 ACATCACCTTTCCTCTTCGG 57.230 50.000 0.00 0.00 0.00 4.30
115 116 3.190874 GCTACATCACCTTTCCTCTTCG 58.809 50.000 0.00 0.00 0.00 3.79
116 117 3.935828 GTGCTACATCACCTTTCCTCTTC 59.064 47.826 0.00 0.00 0.00 2.87
118 119 2.906389 TGTGCTACATCACCTTTCCTCT 59.094 45.455 0.00 0.00 36.17 3.69
120 121 3.181445 TGTTGTGCTACATCACCTTTCCT 60.181 43.478 0.00 0.00 36.17 3.36
121 122 3.146066 TGTTGTGCTACATCACCTTTCC 58.854 45.455 0.00 0.00 36.17 3.13
130 131 7.928307 AATACTTTCTGATGTTGTGCTACAT 57.072 32.000 0.00 0.00 41.30 2.29
170 171 9.653287 CTAGTGTACTGATTCAATAAACCTTGA 57.347 33.333 0.00 0.00 33.42 3.02
171 172 9.436957 ACTAGTGTACTGATTCAATAAACCTTG 57.563 33.333 0.00 0.00 0.00 3.61
180 181 9.706691 CCTTTTTCTACTAGTGTACTGATTCAA 57.293 33.333 5.39 0.00 0.00 2.69
182 183 7.278203 GCCCTTTTTCTACTAGTGTACTGATTC 59.722 40.741 5.39 0.00 0.00 2.52
183 184 7.104290 GCCCTTTTTCTACTAGTGTACTGATT 58.896 38.462 5.39 0.00 0.00 2.57
185 186 5.046807 GGCCCTTTTTCTACTAGTGTACTGA 60.047 44.000 5.39 0.00 0.00 3.41
261 262 3.674138 GCCGTTAGAACCGTCACTAATGA 60.674 47.826 14.18 0.00 37.63 2.57
270 271 1.514553 GCCTAGCCGTTAGAACCGT 59.485 57.895 0.00 0.00 0.00 4.83
277 278 3.845259 CAGCCCGCCTAGCCGTTA 61.845 66.667 0.00 0.00 0.00 3.18
304 305 1.969589 GTTCGCCACAAACCGGGAT 60.970 57.895 6.32 0.00 0.00 3.85
427 429 2.438800 AGGTGCATCTCTAGTACCGT 57.561 50.000 0.00 0.00 36.55 4.83
456 458 6.728089 TTAGTCCCGGTTGGTTTTAAAAAT 57.272 33.333 1.31 0.00 34.77 1.82
463 465 3.073356 TGATCTTTAGTCCCGGTTGGTTT 59.927 43.478 0.00 0.00 34.77 3.27
553 571 1.623811 CGAGGAAGAGGGGAAGAACAA 59.376 52.381 0.00 0.00 0.00 2.83
771 870 6.738649 GCAAACTAAGAGTTATTTTGAGCTCG 59.261 38.462 9.64 0.00 37.47 5.03
1018 1145 3.062466 CAGACGAGGGCCGACAGA 61.062 66.667 0.00 0.00 41.76 3.41
1088 1215 8.945481 TGATGGGCATAATTTTTCATAAACAG 57.055 30.769 0.00 0.00 0.00 3.16
1155 1282 3.617284 ACAATAGGGTCGGTTGGAATTC 58.383 45.455 0.00 0.00 0.00 2.17
1309 1439 7.424001 CAATCTTTCTAATCTTCAAGGGCATC 58.576 38.462 0.00 0.00 0.00 3.91
1334 1473 6.571150 GCCTCACTATCAATGGCATATTTTCC 60.571 42.308 0.00 0.00 42.79 3.13
1404 1544 2.855963 GCAATGACAAATGCGATCAAGG 59.144 45.455 1.38 0.00 32.17 3.61
1570 2366 3.124636 AGAAAAGTACGCACGCCATTAAG 59.875 43.478 0.00 0.00 0.00 1.85
1684 2480 2.690778 GCAGGTGGACGTGAATGGC 61.691 63.158 0.00 0.00 33.92 4.40
1702 2498 1.815003 GGGCATGAAACCAGACTCAAG 59.185 52.381 0.00 0.00 0.00 3.02
1738 2534 1.301677 CCTCTTTCTCCGTGCTTGGC 61.302 60.000 0.00 0.00 0.00 4.52
1763 2559 7.364939 CCTCTTCTTCTTCATTCTCTTCCATCT 60.365 40.741 0.00 0.00 0.00 2.90
1876 2721 3.063704 CCCGCATTGCTGGCTCAA 61.064 61.111 6.14 0.00 0.00 3.02
1922 2793 2.234143 CGACCTAGATCATCAGCAGGA 58.766 52.381 6.91 0.00 0.00 3.86
1979 2852 3.665745 TGCAATTTCAGCCTTTCCTTC 57.334 42.857 0.00 0.00 0.00 3.46
1985 2858 0.889994 TGCGATGCAATTTCAGCCTT 59.110 45.000 0.00 0.00 34.76 4.35
2000 2873 1.262417 TGTGGTCCTCTAACATGCGA 58.738 50.000 0.00 0.00 0.00 5.10
2015 2888 4.927978 TGGGTACAACAATTTCTTGTGG 57.072 40.909 8.07 0.00 44.83 4.17
2051 2924 2.569404 TGTGGTGCCCAACTTTTTCTTT 59.431 40.909 0.00 0.00 34.18 2.52
2099 2972 7.506938 CCAAATCCCTTATCAGATACACCATTT 59.493 37.037 0.00 0.00 0.00 2.32
2114 2987 4.735369 TCAGCAACTTTCCAAATCCCTTA 58.265 39.130 0.00 0.00 0.00 2.69
2178 3051 5.352569 CCTTCTTTCCTTCGTACGTACTCTA 59.647 44.000 22.55 6.20 0.00 2.43
2217 3090 6.875726 GCATGTATCTTCTGCACCTATAATCA 59.124 38.462 0.00 0.00 35.96 2.57
2263 3138 2.044832 CTCGTACTCACCGCGGTAGG 62.045 65.000 33.70 26.98 37.30 3.18
2292 3167 1.526887 CACCTCATACCGGGCATGT 59.473 57.895 6.32 0.00 0.00 3.21
2327 3202 2.363795 CCAGGGTCCTCACGGCTA 60.364 66.667 0.00 0.00 0.00 3.93
2336 3211 0.035056 CCTTGACATCACCAGGGTCC 60.035 60.000 0.00 0.00 0.00 4.46
2374 3249 2.848694 TGGCAGGAATCTTCAGGAATCT 59.151 45.455 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.