Multiple sequence alignment - TraesCS1B01G250900

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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 TraesCS1B01G250900 chr1B 100.000 2570 0 0 1 2570 442971964 442969395 0.000000e+00 4747
1 TraesCS1B01G250900 chr1D 88.146 2033 93 68 1 1915 328799299 328797297 0.000000e+00 2283
2 TraesCS1B01G250900 chr1D 91.364 220 8 7 1916 2133 328797260 328797050 9.000000e-75 291
3 TraesCS1B01G250900 chr1D 86.792 212 17 6 2368 2570 328796953 328796744 2.570000e-55 226
4 TraesCS1B01G250900 chr1A 85.876 2032 83 83 1 1894 425682832 425680867 0.000000e+00 1975
5 TraesCS1B01G250900 chr1A 91.403 221 15 4 1916 2133 425680815 425680596 1.490000e-77 300
6 TraesCS1B01G250900 chr3D 85.194 412 55 3 1117 1525 580713774 580714182 3.960000e-113 418
7 TraesCS1B01G250900 chr3D 84.487 419 57 5 1117 1531 581834193 581833779 8.560000e-110 407
8 TraesCS1B01G250900 chr3B 84.878 410 60 2 1117 1525 776195217 776195625 1.840000e-111 412
9 TraesCS1B01G250900 chr3B 84.135 416 64 2 1117 1531 777997583 777997169 3.980000e-108 401
10 TraesCS1B01G250900 chr3A 84.466 412 58 4 1117 1525 716258966 716259374 3.980000e-108 401


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 TraesCS1B01G250900 chr1B 442969395 442971964 2569 True 4747.000000 4747 100.000000 1 2570 1 chr1B.!!$R1 2569
1 TraesCS1B01G250900 chr1D 328796744 328799299 2555 True 933.333333 2283 88.767333 1 2570 3 chr1D.!!$R1 2569
2 TraesCS1B01G250900 chr1A 425680596 425682832 2236 True 1137.500000 1975 88.639500 1 2133 2 chr1A.!!$R1 2132

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
996 1151 0.471617 CCACCACATCCATCTCCCTC 59.528 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2278 2518 0.027455 CTGTTCGACAAGCACGCAAA 59.973 50.0 0.0 0.0 0.0 3.68 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
17 18 2.358615 ATGCTCGCCACGCAAAGA 60.359 55.556 0.00 0.00 41.26 2.52
18 19 1.965930 ATGCTCGCCACGCAAAGAA 60.966 52.632 0.00 0.00 41.26 2.52
108 109 1.807165 CCCGTGCAGTCATGTCTCG 60.807 63.158 0.00 0.00 0.00 4.04
234 280 1.616327 CCACAGATCCCAGACCCCA 60.616 63.158 0.00 0.00 0.00 4.96
235 281 1.207488 CCACAGATCCCAGACCCCAA 61.207 60.000 0.00 0.00 0.00 4.12
341 400 1.896694 GACAGAGAGAGCCCTGGTG 59.103 63.158 0.00 0.00 34.85 4.17
389 491 1.883084 GATCATGGCCACGTCGGTC 60.883 63.158 8.16 0.00 41.21 4.79
427 530 3.701532 TTTTTCACCGCTTGATTCGTT 57.298 38.095 0.00 0.00 32.84 3.85
429 532 2.961522 TTCACCGCTTGATTCGTTTC 57.038 45.000 0.00 0.00 32.84 2.78
476 580 0.525242 GCTTTGCTGCGTGTGACAAA 60.525 50.000 0.00 0.00 0.00 2.83
477 581 1.191096 CTTTGCTGCGTGTGACAAAC 58.809 50.000 0.00 0.00 0.00 2.93
478 582 0.522286 TTTGCTGCGTGTGACAAACG 60.522 50.000 13.99 13.99 43.81 3.60
487 591 0.596600 TGTGACAAACGACGAGGCTC 60.597 55.000 3.87 3.87 0.00 4.70
550 658 5.620011 CGCGGTAAAGAAAGAAAGAAAGAAC 59.380 40.000 0.00 0.00 0.00 3.01
552 660 6.970613 GCGGTAAAGAAAGAAAGAAAGAACAA 59.029 34.615 0.00 0.00 0.00 2.83
554 662 9.349145 CGGTAAAGAAAGAAAGAAAGAACAAAA 57.651 29.630 0.00 0.00 0.00 2.44
593 702 2.760799 ATAGGTACCGCCACCGCA 60.761 61.111 6.18 0.00 43.84 5.69
826 977 2.813908 ACGCGCAACCGAATCCTC 60.814 61.111 5.73 0.00 36.29 3.71
840 991 0.957395 ATCCTCAACGGCAGCAACAG 60.957 55.000 0.00 0.00 0.00 3.16
861 1013 1.170290 CCAAAAACCGCGTCCTCCTT 61.170 55.000 4.92 0.00 0.00 3.36
889 1041 1.291272 CTATAAGTACGCCCCGCCC 59.709 63.158 0.00 0.00 0.00 6.13
938 1093 4.000325 TGTTAACCTCACAACATCATCCG 59.000 43.478 2.48 0.00 29.93 4.18
984 1139 4.927782 GACAGCACCGCCACCACA 62.928 66.667 0.00 0.00 0.00 4.17
985 1140 4.269523 ACAGCACCGCCACCACAT 62.270 61.111 0.00 0.00 0.00 3.21
986 1141 3.434319 CAGCACCGCCACCACATC 61.434 66.667 0.00 0.00 0.00 3.06
989 1144 2.045045 CACCGCCACCACATCCAT 60.045 61.111 0.00 0.00 0.00 3.41
991 1146 2.300967 ACCGCCACCACATCCATCT 61.301 57.895 0.00 0.00 0.00 2.90
992 1147 1.524621 CCGCCACCACATCCATCTC 60.525 63.158 0.00 0.00 0.00 2.75
993 1148 1.524621 CGCCACCACATCCATCTCC 60.525 63.158 0.00 0.00 0.00 3.71
994 1149 1.152881 GCCACCACATCCATCTCCC 60.153 63.158 0.00 0.00 0.00 4.30
995 1150 1.639635 GCCACCACATCCATCTCCCT 61.640 60.000 0.00 0.00 0.00 4.20
996 1151 0.471617 CCACCACATCCATCTCCCTC 59.528 60.000 0.00 0.00 0.00 4.30
1578 1737 3.121030 CGCGCCTGAACCTCAAGG 61.121 66.667 0.00 0.00 42.17 3.61
1667 1831 3.181483 CCCACCGCGAAATACTTACTACT 60.181 47.826 8.23 0.00 0.00 2.57
1668 1832 4.040376 CCACCGCGAAATACTTACTACTC 58.960 47.826 8.23 0.00 0.00 2.59
1669 1833 4.201990 CCACCGCGAAATACTTACTACTCT 60.202 45.833 8.23 0.00 0.00 3.24
1670 1834 5.008019 CCACCGCGAAATACTTACTACTCTA 59.992 44.000 8.23 0.00 0.00 2.43
1671 1835 5.906285 CACCGCGAAATACTTACTACTCTAC 59.094 44.000 8.23 0.00 0.00 2.59
1672 1836 5.136020 CCGCGAAATACTTACTACTCTACG 58.864 45.833 8.23 0.00 0.00 3.51
1705 1879 3.551485 TCGCAGATCACACGAACATTATG 59.449 43.478 0.00 0.00 31.97 1.90
1717 1891 3.629855 CGAACATTATGGGTGTGCCATTA 59.370 43.478 0.00 0.00 36.17 1.90
1744 1925 7.827819 TTTGCTGTATATATATCGGAACTGC 57.172 36.000 13.96 13.96 33.88 4.40
1745 1926 6.775594 TGCTGTATATATATCGGAACTGCT 57.224 37.500 18.38 0.00 34.24 4.24
1747 1928 5.460419 GCTGTATATATATCGGAACTGCTGC 59.540 44.000 13.73 0.00 0.00 5.25
1760 1941 1.150827 CTGCTGCATCGACACTGAAA 58.849 50.000 1.31 0.00 0.00 2.69
1763 1944 2.286950 TGCTGCATCGACACTGAAAAAC 60.287 45.455 0.00 0.00 0.00 2.43
1764 1945 2.918131 GCTGCATCGACACTGAAAAACC 60.918 50.000 0.00 0.00 0.00 3.27
1766 1947 2.290367 TGCATCGACACTGAAAAACCAG 59.710 45.455 0.00 0.00 39.93 4.00
1768 1949 2.325583 TCGACACTGAAAAACCAGCT 57.674 45.000 0.00 0.00 37.68 4.24
1769 1950 2.210116 TCGACACTGAAAAACCAGCTC 58.790 47.619 0.00 0.00 37.68 4.09
1771 1952 2.297701 GACACTGAAAAACCAGCTCCA 58.702 47.619 0.00 0.00 37.68 3.86
1772 1953 2.887152 GACACTGAAAAACCAGCTCCAT 59.113 45.455 0.00 0.00 37.68 3.41
1773 1954 2.624838 ACACTGAAAAACCAGCTCCATG 59.375 45.455 0.00 0.00 37.68 3.66
1774 1955 2.624838 CACTGAAAAACCAGCTCCATGT 59.375 45.455 0.00 0.00 37.68 3.21
1775 1956 2.887152 ACTGAAAAACCAGCTCCATGTC 59.113 45.455 0.00 0.00 37.68 3.06
1776 1957 2.886523 CTGAAAAACCAGCTCCATGTCA 59.113 45.455 0.00 0.00 0.00 3.58
1836 2021 5.410746 TCAGATTTTCACTTCTGCTCATCAC 59.589 40.000 0.00 0.00 39.36 3.06
1846 2031 5.104610 ACTTCTGCTCATCACATAATGTCCT 60.105 40.000 0.00 0.00 0.00 3.85
1870 2071 7.255312 CCTTGAGTCTCGTAGTATAATGCTTCT 60.255 40.741 0.00 0.00 0.00 2.85
1894 2095 5.947443 GCTTTCTGCAGTTCTATGTCAAAT 58.053 37.500 14.67 0.00 42.31 2.32
1896 2097 7.530010 GCTTTCTGCAGTTCTATGTCAAATTA 58.470 34.615 14.67 0.00 42.31 1.40
1897 2098 8.186821 GCTTTCTGCAGTTCTATGTCAAATTAT 58.813 33.333 14.67 0.00 42.31 1.28
1932 2170 4.245660 CGGCCTCATGTGAATATACGAAT 58.754 43.478 0.00 0.00 0.00 3.34
1938 2176 7.761704 GCCTCATGTGAATATACGAATCTGTAT 59.238 37.037 0.00 3.97 38.54 2.29
1969 2208 2.662596 GTCGATGTGACCCAGGCA 59.337 61.111 0.00 0.00 42.04 4.75
2037 2277 2.851824 CGTGAACAACAAAACCTCAAGC 59.148 45.455 0.00 0.00 0.00 4.01
2078 2318 7.678218 GCAATACCTCTGATGAAATTGACAGTC 60.678 40.741 12.80 0.00 0.00 3.51
2087 2327 5.845985 TGAAATTGACAGTCGAGCTAAAG 57.154 39.130 0.00 0.00 0.00 1.85
2128 2368 2.029739 TGACACGACGCCAAGAATCTAA 60.030 45.455 0.00 0.00 0.00 2.10
2129 2369 3.187700 GACACGACGCCAAGAATCTAAT 58.812 45.455 0.00 0.00 0.00 1.73
2131 2371 3.617263 ACACGACGCCAAGAATCTAATTC 59.383 43.478 0.00 0.00 39.56 2.17
2133 2373 3.194861 CGACGCCAAGAATCTAATTCCA 58.805 45.455 0.00 0.00 40.13 3.53
2134 2374 3.809832 CGACGCCAAGAATCTAATTCCAT 59.190 43.478 0.00 0.00 40.13 3.41
2135 2375 4.319046 CGACGCCAAGAATCTAATTCCATG 60.319 45.833 0.00 0.00 40.13 3.66
2137 2377 4.949856 ACGCCAAGAATCTAATTCCATGTT 59.050 37.500 0.00 0.00 40.13 2.71
2138 2378 5.163622 ACGCCAAGAATCTAATTCCATGTTG 60.164 40.000 0.00 0.00 40.13 3.33
2139 2379 5.045872 GCCAAGAATCTAATTCCATGTTGC 58.954 41.667 0.00 0.00 40.13 4.17
2140 2380 5.276270 CCAAGAATCTAATTCCATGTTGCG 58.724 41.667 0.00 0.00 40.13 4.85
2141 2381 4.558538 AGAATCTAATTCCATGTTGCGC 57.441 40.909 0.00 0.00 40.13 6.09
2142 2382 3.947196 AGAATCTAATTCCATGTTGCGCA 59.053 39.130 5.66 5.66 40.13 6.09
2143 2383 4.398988 AGAATCTAATTCCATGTTGCGCAA 59.601 37.500 21.02 21.02 40.13 4.85
2144 2384 4.717233 ATCTAATTCCATGTTGCGCAAA 57.283 36.364 26.87 15.55 0.00 3.68
2145 2385 4.511617 TCTAATTCCATGTTGCGCAAAA 57.488 36.364 26.87 21.87 0.00 2.44
2146 2386 4.233789 TCTAATTCCATGTTGCGCAAAAC 58.766 39.130 26.87 15.44 0.00 2.43
2147 2387 2.522836 ATTCCATGTTGCGCAAAACA 57.477 40.000 26.87 21.24 43.82 2.83
2148 2388 1.850377 TTCCATGTTGCGCAAAACAG 58.150 45.000 26.87 15.68 42.99 3.16
2149 2389 1.028130 TCCATGTTGCGCAAAACAGA 58.972 45.000 26.87 16.89 42.99 3.41
2150 2390 1.406898 TCCATGTTGCGCAAAACAGAA 59.593 42.857 26.87 7.11 42.99 3.02
2151 2391 1.522258 CCATGTTGCGCAAAACAGAAC 59.478 47.619 26.87 12.11 42.99 3.01
2152 2392 2.191802 CATGTTGCGCAAAACAGAACA 58.808 42.857 26.87 18.00 42.99 3.18
2153 2393 2.354109 TGTTGCGCAAAACAGAACAA 57.646 40.000 26.87 0.00 35.16 2.83
2154 2394 2.677199 TGTTGCGCAAAACAGAACAAA 58.323 38.095 26.87 0.00 35.16 2.83
2155 2395 3.059884 TGTTGCGCAAAACAGAACAAAA 58.940 36.364 26.87 0.00 35.16 2.44
2156 2396 3.494626 TGTTGCGCAAAACAGAACAAAAA 59.505 34.783 26.87 0.00 35.16 1.94
2195 2435 8.751335 CCATGTATTGTTTATAATCCGTTTTGC 58.249 33.333 0.00 0.00 0.00 3.68
2196 2436 9.515020 CATGTATTGTTTATAATCCGTTTTGCT 57.485 29.630 0.00 0.00 0.00 3.91
2203 2443 9.615295 TGTTTATAATCCGTTTTGCTAAAGAAC 57.385 29.630 0.00 0.00 0.00 3.01
2204 2444 9.615295 GTTTATAATCCGTTTTGCTAAAGAACA 57.385 29.630 0.00 0.00 0.00 3.18
2206 2446 9.997482 TTATAATCCGTTTTGCTAAAGAACATC 57.003 29.630 0.00 0.00 0.00 3.06
2207 2447 6.575162 AATCCGTTTTGCTAAAGAACATCT 57.425 33.333 0.00 0.00 0.00 2.90
2208 2448 7.681939 AATCCGTTTTGCTAAAGAACATCTA 57.318 32.000 0.00 0.00 0.00 1.98
2209 2449 6.721571 TCCGTTTTGCTAAAGAACATCTAG 57.278 37.500 0.00 0.00 0.00 2.43
2210 2450 6.460781 TCCGTTTTGCTAAAGAACATCTAGA 58.539 36.000 0.00 0.00 0.00 2.43
2211 2451 7.103641 TCCGTTTTGCTAAAGAACATCTAGAT 58.896 34.615 0.00 0.00 0.00 1.98
2212 2452 7.606456 TCCGTTTTGCTAAAGAACATCTAGATT 59.394 33.333 1.33 0.00 0.00 2.40
2213 2453 8.879759 CCGTTTTGCTAAAGAACATCTAGATTA 58.120 33.333 1.33 0.00 0.00 1.75
2243 2483 8.814733 TGTTTATTCGTAACATAAGATTTGCG 57.185 30.769 0.00 0.00 30.96 4.85
2244 2484 8.444715 TGTTTATTCGTAACATAAGATTTGCGT 58.555 29.630 0.00 0.00 33.24 5.24
2245 2485 8.721476 GTTTATTCGTAACATAAGATTTGCGTG 58.279 33.333 0.00 0.00 33.24 5.34
2246 2486 4.253352 TCGTAACATAAGATTTGCGTGC 57.747 40.909 0.00 0.00 33.24 5.34
2247 2487 3.680458 TCGTAACATAAGATTTGCGTGCA 59.320 39.130 0.00 0.00 33.24 4.57
2248 2488 4.331443 TCGTAACATAAGATTTGCGTGCAT 59.669 37.500 0.00 0.00 33.24 3.96
2249 2489 4.666176 CGTAACATAAGATTTGCGTGCATC 59.334 41.667 0.00 0.00 0.00 3.91
2250 2490 3.323729 ACATAAGATTTGCGTGCATCG 57.676 42.857 0.00 0.00 43.12 3.84
2251 2491 2.032054 ACATAAGATTTGCGTGCATCGG 59.968 45.455 10.02 0.00 40.26 4.18
2252 2492 1.732941 TAAGATTTGCGTGCATCGGT 58.267 45.000 10.02 0.00 40.26 4.69
2253 2493 0.881118 AAGATTTGCGTGCATCGGTT 59.119 45.000 10.02 0.00 40.26 4.44
2254 2494 0.881118 AGATTTGCGTGCATCGGTTT 59.119 45.000 10.02 0.00 40.26 3.27
2255 2495 1.269448 AGATTTGCGTGCATCGGTTTT 59.731 42.857 10.02 0.00 40.26 2.43
2256 2496 2.058057 GATTTGCGTGCATCGGTTTTT 58.942 42.857 10.02 0.00 40.26 1.94
2257 2497 1.203928 TTTGCGTGCATCGGTTTTTG 58.796 45.000 10.02 0.00 40.26 2.44
2258 2498 1.211818 TTGCGTGCATCGGTTTTTGC 61.212 50.000 10.02 0.00 40.26 3.68
2259 2499 2.371923 GCGTGCATCGGTTTTTGCC 61.372 57.895 10.02 0.00 38.08 4.52
2260 2500 1.732683 CGTGCATCGGTTTTTGCCC 60.733 57.895 0.00 0.00 38.08 5.36
2261 2501 1.732683 GTGCATCGGTTTTTGCCCG 60.733 57.895 0.00 0.00 46.83 6.13
2262 2502 2.126110 GCATCGGTTTTTGCCCGG 60.126 61.111 0.00 0.00 45.51 5.73
2263 2503 2.926420 GCATCGGTTTTTGCCCGGT 61.926 57.895 0.00 0.00 45.51 5.28
2264 2504 1.663173 CATCGGTTTTTGCCCGGTT 59.337 52.632 0.00 0.00 45.51 4.44
2265 2505 0.032815 CATCGGTTTTTGCCCGGTTT 59.967 50.000 0.00 0.00 45.51 3.27
2266 2506 0.753867 ATCGGTTTTTGCCCGGTTTT 59.246 45.000 0.00 0.00 45.51 2.43
2267 2507 0.102663 TCGGTTTTTGCCCGGTTTTC 59.897 50.000 0.00 0.00 45.51 2.29
2268 2508 1.209910 CGGTTTTTGCCCGGTTTTCG 61.210 55.000 0.00 0.00 41.78 3.46
2269 2509 0.102663 GGTTTTTGCCCGGTTTTCGA 59.897 50.000 0.00 0.00 42.43 3.71
2270 2510 1.471153 GGTTTTTGCCCGGTTTTCGAA 60.471 47.619 0.00 0.00 42.43 3.71
2271 2511 2.269172 GTTTTTGCCCGGTTTTCGAAA 58.731 42.857 6.47 6.47 42.43 3.46
2272 2512 2.667473 TTTTGCCCGGTTTTCGAAAA 57.333 40.000 19.08 19.08 42.43 2.29
2273 2513 2.667473 TTTGCCCGGTTTTCGAAAAA 57.333 40.000 24.04 5.64 42.43 1.94
2310 2550 3.890756 TGTCGAACAGGTGGAGTTTACTA 59.109 43.478 0.00 0.00 0.00 1.82
2311 2551 4.022589 TGTCGAACAGGTGGAGTTTACTAG 60.023 45.833 0.00 0.00 0.00 2.57
2317 2557 4.466726 ACAGGTGGAGTTTACTAGTGGATC 59.533 45.833 5.39 0.00 0.00 3.36
2323 2563 5.419155 TGGAGTTTACTAGTGGATCTGAGTG 59.581 44.000 5.39 0.00 0.00 3.51
2324 2564 5.652891 GGAGTTTACTAGTGGATCTGAGTGA 59.347 44.000 5.39 0.00 0.00 3.41
2328 2568 6.701145 TTACTAGTGGATCTGAGTGATGAC 57.299 41.667 5.39 0.00 35.14 3.06
2331 2571 2.765135 AGTGGATCTGAGTGATGACTGG 59.235 50.000 0.00 0.00 35.14 4.00
2332 2572 2.113807 TGGATCTGAGTGATGACTGGG 58.886 52.381 0.00 0.00 35.14 4.45
2333 2573 1.202627 GGATCTGAGTGATGACTGGGC 60.203 57.143 0.00 0.00 35.14 5.36
2334 2574 0.463204 ATCTGAGTGATGACTGGGCG 59.537 55.000 0.00 0.00 33.43 6.13
2335 2575 1.153489 CTGAGTGATGACTGGGCGG 60.153 63.158 0.00 0.00 30.16 6.13
2336 2576 1.892819 CTGAGTGATGACTGGGCGGT 61.893 60.000 0.00 0.00 30.16 5.68
2337 2577 1.448540 GAGTGATGACTGGGCGGTG 60.449 63.158 0.00 0.00 30.16 4.94
2338 2578 1.888436 GAGTGATGACTGGGCGGTGA 61.888 60.000 0.00 0.00 30.16 4.02
2339 2579 1.003839 GTGATGACTGGGCGGTGAA 60.004 57.895 0.00 0.00 0.00 3.18
2340 2580 1.021390 GTGATGACTGGGCGGTGAAG 61.021 60.000 0.00 0.00 0.00 3.02
2341 2581 1.191489 TGATGACTGGGCGGTGAAGA 61.191 55.000 0.00 0.00 0.00 2.87
2342 2582 0.179000 GATGACTGGGCGGTGAAGAT 59.821 55.000 0.00 0.00 0.00 2.40
2343 2583 0.107508 ATGACTGGGCGGTGAAGATG 60.108 55.000 0.00 0.00 0.00 2.90
2345 2585 0.179000 GACTGGGCGGTGAAGATGAT 59.821 55.000 0.00 0.00 0.00 2.45
2346 2586 0.179000 ACTGGGCGGTGAAGATGATC 59.821 55.000 0.00 0.00 0.00 2.92
2347 2587 0.877649 CTGGGCGGTGAAGATGATCG 60.878 60.000 0.00 0.00 0.00 3.69
2348 2588 1.144057 GGGCGGTGAAGATGATCGT 59.856 57.895 0.00 0.00 0.00 3.73
2349 2589 0.387929 GGGCGGTGAAGATGATCGTA 59.612 55.000 0.00 0.00 0.00 3.43
2350 2590 1.000955 GGGCGGTGAAGATGATCGTAT 59.999 52.381 0.00 0.00 0.00 3.06
2351 2591 2.061773 GGCGGTGAAGATGATCGTATG 58.938 52.381 0.00 0.00 0.00 2.39
2352 2592 2.061773 GCGGTGAAGATGATCGTATGG 58.938 52.381 0.00 0.00 0.00 2.74
2353 2593 2.288213 GCGGTGAAGATGATCGTATGGA 60.288 50.000 0.00 0.00 0.00 3.41
2354 2594 3.798889 GCGGTGAAGATGATCGTATGGAA 60.799 47.826 0.00 0.00 0.00 3.53
2355 2595 4.560128 CGGTGAAGATGATCGTATGGAAT 58.440 43.478 0.00 0.00 0.00 3.01
2356 2596 5.709966 CGGTGAAGATGATCGTATGGAATA 58.290 41.667 0.00 0.00 0.00 1.75
2357 2597 5.573282 CGGTGAAGATGATCGTATGGAATAC 59.427 44.000 0.00 0.00 46.27 1.89
2395 2635 9.906660 TTTTTACTATGAAAAATGTAGGTGCTG 57.093 29.630 0.00 0.00 34.23 4.41
2439 2685 2.173996 AGTACCCCCGACAATTAATGGG 59.826 50.000 5.02 5.02 41.56 4.00
2443 2689 2.424234 CCCCCGACAATTAATGGGTCAT 60.424 50.000 16.40 0.00 40.20 3.06
2453 2699 0.032813 AATGGGTCATTGGCCCTGAG 60.033 55.000 26.24 0.00 46.22 3.35
2457 2703 1.034292 GGTCATTGGCCCTGAGCTTC 61.034 60.000 21.23 5.21 43.05 3.86
2460 2706 3.350031 ATTGGCCCTGAGCTTCCGG 62.350 63.158 0.00 0.00 43.05 5.14
2463 2709 3.394836 GCCCTGAGCTTCCGGAGT 61.395 66.667 3.34 0.00 38.99 3.85
2469 2715 1.550976 CTGAGCTTCCGGAGTTTACCT 59.449 52.381 3.34 0.00 0.00 3.08
2472 2718 1.697982 AGCTTCCGGAGTTTACCTGTT 59.302 47.619 3.34 0.00 0.00 3.16
2489 2738 4.261801 CCTGTTTGGATAGACGGTTTGAT 58.738 43.478 0.00 0.00 38.35 2.57
2490 2739 4.094887 CCTGTTTGGATAGACGGTTTGATG 59.905 45.833 0.00 0.00 38.35 3.07
2541 2790 2.660189 ACCAACAATACCGGAGTACG 57.340 50.000 9.46 0.00 43.80 3.67
2563 2812 1.352114 TGATACCGCGTCCGAAAAAG 58.648 50.000 4.92 0.00 36.29 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 109 0.096976 CGTCGTCATGGATTGGTTGC 59.903 55.000 0.00 0.00 0.00 4.17
427 530 1.003262 CCGCGACGACCTTTTACGAA 61.003 55.000 8.23 0.00 0.00 3.85
429 532 3.063052 GCCGCGACGACCTTTTACG 62.063 63.158 8.23 0.00 0.00 3.18
478 582 1.512310 CAAGTCGTCGAGCCTCGTC 60.512 63.158 14.64 7.71 41.35 4.20
487 591 2.551270 GTGCAAGCCAAGTCGTCG 59.449 61.111 0.00 0.00 0.00 5.12
552 660 1.056660 TCGGGACTCCTCTGCTTTTT 58.943 50.000 0.00 0.00 0.00 1.94
554 662 2.035632 CTATCGGGACTCCTCTGCTTT 58.964 52.381 0.00 0.00 0.00 3.51
556 664 0.178975 CCTATCGGGACTCCTCTGCT 60.179 60.000 0.00 0.00 37.23 4.24
557 665 0.178987 TCCTATCGGGACTCCTCTGC 60.179 60.000 0.00 0.00 39.58 4.26
673 809 1.061905 TAGGGACAGGGATGCCATGG 61.062 60.000 7.63 7.63 39.88 3.66
680 816 2.559931 CCATACGGATAGGGACAGGGAT 60.560 54.545 0.00 0.00 33.84 3.85
681 817 1.203137 CCATACGGATAGGGACAGGGA 60.203 57.143 0.00 0.00 33.84 4.20
686 822 0.896226 GCTCCCATACGGATAGGGAC 59.104 60.000 12.37 7.49 46.42 4.46
840 991 3.263503 GAGGACGCGGTTTTTGGGC 62.264 63.158 12.47 0.00 0.00 5.36
861 1013 2.224967 GCGTACTTATAGGAGGGAGGGA 60.225 54.545 0.00 0.00 0.00 4.20
889 1041 0.984961 TGAGGATCTGGAGCTTGGGG 60.985 60.000 0.00 0.00 34.92 4.96
892 1044 1.407989 GGGTTGAGGATCTGGAGCTTG 60.408 57.143 0.00 0.00 34.92 4.01
894 1046 1.333636 CGGGTTGAGGATCTGGAGCT 61.334 60.000 0.00 0.00 34.92 4.09
895 1047 1.144936 CGGGTTGAGGATCTGGAGC 59.855 63.158 0.00 0.00 34.92 4.70
938 1093 2.879103 TCAAGTGGGAGGTTTGGATC 57.121 50.000 0.00 0.00 0.00 3.36
978 1133 1.415659 GAGAGGGAGATGGATGTGGTG 59.584 57.143 0.00 0.00 0.00 4.17
980 1135 1.055040 GGAGAGGGAGATGGATGTGG 58.945 60.000 0.00 0.00 0.00 4.17
981 1136 1.798626 TGGAGAGGGAGATGGATGTG 58.201 55.000 0.00 0.00 0.00 3.21
982 1137 2.336891 CATGGAGAGGGAGATGGATGT 58.663 52.381 0.00 0.00 0.00 3.06
984 1139 2.041824 CCATGGAGAGGGAGATGGAT 57.958 55.000 5.56 0.00 38.10 3.41
985 1140 3.565979 CCATGGAGAGGGAGATGGA 57.434 57.895 5.56 0.00 38.10 3.41
993 1148 0.822532 GCATCTTGCCCATGGAGAGG 60.823 60.000 15.22 11.30 37.42 3.69
994 1149 1.164662 CGCATCTTGCCCATGGAGAG 61.165 60.000 15.22 7.97 41.12 3.20
995 1150 1.153107 CGCATCTTGCCCATGGAGA 60.153 57.895 15.22 8.90 41.12 3.71
996 1151 2.842256 GCGCATCTTGCCCATGGAG 61.842 63.158 15.22 2.37 41.12 3.86
1053 1208 3.077556 TTGGAGGAGGAGGAGCGC 61.078 66.667 0.00 0.00 0.00 5.92
1197 1352 4.069232 TGGCCCACGCTCTCGAAG 62.069 66.667 0.00 0.00 39.41 3.79
1497 1652 2.502213 TGAGCTTGAACTCGTCGAAA 57.498 45.000 0.00 0.00 39.68 3.46
1554 1709 3.774702 GTTCAGGCGCGGACGTTC 61.775 66.667 8.83 0.00 42.83 3.95
1596 1755 4.858935 TCGCAAAAGAATGAAGGAACAAG 58.141 39.130 0.00 0.00 0.00 3.16
1744 1925 2.290367 TGGTTTTTCAGTGTCGATGCAG 59.710 45.455 0.00 0.00 0.00 4.41
1745 1926 2.290367 CTGGTTTTTCAGTGTCGATGCA 59.710 45.455 0.00 0.00 0.00 3.96
1747 1928 2.549754 AGCTGGTTTTTCAGTGTCGATG 59.450 45.455 0.00 0.00 37.12 3.84
1760 1941 2.165167 CATGTGACATGGAGCTGGTTT 58.835 47.619 17.51 0.00 0.00 3.27
1763 1944 1.376543 GACATGTGACATGGAGCTGG 58.623 55.000 27.23 3.02 0.00 4.85
1764 1945 1.004595 CGACATGTGACATGGAGCTG 58.995 55.000 27.23 9.80 0.00 4.24
1766 1947 1.945387 ATCGACATGTGACATGGAGC 58.055 50.000 27.23 15.67 0.00 4.70
1768 1949 6.374053 ACATAAAAATCGACATGTGACATGGA 59.626 34.615 27.23 16.88 30.64 3.41
1769 1950 6.554419 ACATAAAAATCGACATGTGACATGG 58.446 36.000 27.23 12.28 30.64 3.66
1771 1952 7.376435 TGACATAAAAATCGACATGTGACAT 57.624 32.000 1.15 0.00 31.94 3.06
1772 1953 6.620518 GCTGACATAAAAATCGACATGTGACA 60.621 38.462 1.15 0.00 31.94 3.58
1773 1954 5.734498 GCTGACATAAAAATCGACATGTGAC 59.266 40.000 1.15 0.00 31.94 3.67
1774 1955 5.643348 AGCTGACATAAAAATCGACATGTGA 59.357 36.000 1.15 1.26 31.94 3.58
1775 1956 5.872635 AGCTGACATAAAAATCGACATGTG 58.127 37.500 1.15 0.00 31.94 3.21
1776 1957 6.072508 ACAAGCTGACATAAAAATCGACATGT 60.073 34.615 0.00 0.00 34.41 3.21
1836 2021 6.137794 ACTACGAGACTCAAGGACATTATG 57.862 41.667 2.82 0.00 0.00 1.90
1846 2031 7.418408 CAGAAGCATTATACTACGAGACTCAA 58.582 38.462 2.82 0.00 0.00 3.02
1894 2095 2.775384 AGGCCGGGTGTTGAAGATATAA 59.225 45.455 2.18 0.00 0.00 0.98
1896 2097 1.141053 GAGGCCGGGTGTTGAAGATAT 59.859 52.381 2.18 0.00 0.00 1.63
1897 2098 0.539986 GAGGCCGGGTGTTGAAGATA 59.460 55.000 2.18 0.00 0.00 1.98
1898 2099 1.299976 GAGGCCGGGTGTTGAAGAT 59.700 57.895 2.18 0.00 0.00 2.40
1899 2100 1.488705 ATGAGGCCGGGTGTTGAAGA 61.489 55.000 2.18 0.00 0.00 2.87
1900 2101 1.002134 ATGAGGCCGGGTGTTGAAG 60.002 57.895 2.18 0.00 0.00 3.02
1902 2103 2.350895 CATGAGGCCGGGTGTTGA 59.649 61.111 2.18 0.00 0.00 3.18
1907 2108 1.140312 ATATTCACATGAGGCCGGGT 58.860 50.000 2.18 0.00 0.00 5.28
1932 2170 5.596772 TCGACATGTCCCTTTCATATACAGA 59.403 40.000 20.03 3.46 0.00 3.41
1938 2176 4.161377 TCACATCGACATGTCCCTTTCATA 59.839 41.667 20.03 0.00 41.69 2.15
1985 2224 4.095483 GGCAGAATGATTGTCTTGACGAAT 59.905 41.667 0.00 0.00 39.69 3.34
2037 2277 3.119495 GGTATTGCAAGTTTGGGCTACAG 60.119 47.826 4.94 0.00 0.00 2.74
2087 2327 5.123820 TGTCATTGTTTATAGAACTGCAGCC 59.876 40.000 15.27 6.07 0.00 4.85
2100 2340 1.867166 TGGCGTCGTGTCATTGTTTA 58.133 45.000 0.00 0.00 0.00 2.01
2128 2368 2.035704 TCTGTTTTGCGCAACATGGAAT 59.964 40.909 24.99 0.00 36.08 3.01
2129 2369 1.406898 TCTGTTTTGCGCAACATGGAA 59.593 42.857 24.99 11.54 36.08 3.53
2131 2371 1.522258 GTTCTGTTTTGCGCAACATGG 59.478 47.619 24.99 13.62 36.08 3.66
2133 2373 2.575694 TGTTCTGTTTTGCGCAACAT 57.424 40.000 24.99 0.00 36.08 2.71
2134 2374 2.354109 TTGTTCTGTTTTGCGCAACA 57.646 40.000 24.99 18.69 35.33 3.33
2135 2375 3.713889 TTTTGTTCTGTTTTGCGCAAC 57.286 38.095 24.99 14.42 0.00 4.17
2169 2409 8.751335 GCAAAACGGATTATAAACAATACATGG 58.249 33.333 0.00 0.00 0.00 3.66
2170 2410 9.515020 AGCAAAACGGATTATAAACAATACATG 57.485 29.630 0.00 0.00 0.00 3.21
2177 2417 9.615295 GTTCTTTAGCAAAACGGATTATAAACA 57.385 29.630 0.00 0.00 0.00 2.83
2178 2418 9.615295 TGTTCTTTAGCAAAACGGATTATAAAC 57.385 29.630 0.00 0.00 0.00 2.01
2180 2420 9.997482 GATGTTCTTTAGCAAAACGGATTATAA 57.003 29.630 0.00 0.00 0.00 0.98
2181 2421 9.391006 AGATGTTCTTTAGCAAAACGGATTATA 57.609 29.630 0.00 0.00 0.00 0.98
2182 2422 8.281212 AGATGTTCTTTAGCAAAACGGATTAT 57.719 30.769 0.00 0.00 0.00 1.28
2183 2423 7.681939 AGATGTTCTTTAGCAAAACGGATTA 57.318 32.000 0.00 0.00 0.00 1.75
2184 2424 6.575162 AGATGTTCTTTAGCAAAACGGATT 57.425 33.333 0.00 0.00 0.00 3.01
2185 2425 7.103641 TCTAGATGTTCTTTAGCAAAACGGAT 58.896 34.615 0.00 0.00 0.00 4.18
2186 2426 6.460781 TCTAGATGTTCTTTAGCAAAACGGA 58.539 36.000 0.00 0.00 0.00 4.69
2187 2427 6.721571 TCTAGATGTTCTTTAGCAAAACGG 57.278 37.500 0.00 0.00 0.00 4.44
2219 2459 8.721476 CACGCAAATCTTATGTTACGAATAAAC 58.279 33.333 0.00 0.00 0.00 2.01
2221 2461 6.902948 GCACGCAAATCTTATGTTACGAATAA 59.097 34.615 0.00 0.00 0.00 1.40
2224 2464 4.152580 TGCACGCAAATCTTATGTTACGAA 59.847 37.500 0.00 0.00 0.00 3.85
2230 2470 2.032054 CCGATGCACGCAAATCTTATGT 59.968 45.455 0.00 0.00 41.07 2.29
2237 2477 1.791785 CAAAAACCGATGCACGCAAAT 59.208 42.857 0.00 0.00 41.07 2.32
2241 2481 2.371923 GGCAAAAACCGATGCACGC 61.372 57.895 0.00 0.00 44.32 5.34
2242 2482 1.732683 GGGCAAAAACCGATGCACG 60.733 57.895 0.00 0.00 44.32 5.34
2243 2483 4.260194 GGGCAAAAACCGATGCAC 57.740 55.556 0.00 0.00 44.32 4.57
2250 2490 0.102663 TCGAAAACCGGGCAAAAACC 59.897 50.000 6.32 0.00 39.14 3.27
2251 2491 1.923899 TTCGAAAACCGGGCAAAAAC 58.076 45.000 6.32 0.00 39.14 2.43
2252 2492 2.667473 TTTCGAAAACCGGGCAAAAA 57.333 40.000 8.44 0.00 39.14 1.94
2253 2493 2.667473 TTTTCGAAAACCGGGCAAAA 57.333 40.000 19.08 0.00 39.14 2.44
2254 2494 2.667473 TTTTTCGAAAACCGGGCAAA 57.333 40.000 22.41 3.11 39.14 3.68
2271 2511 2.788786 CGACAAGCACGCAAATCTTTTT 59.211 40.909 0.00 0.00 0.00 1.94
2272 2512 2.032799 TCGACAAGCACGCAAATCTTTT 59.967 40.909 0.00 0.00 0.00 2.27
2273 2513 1.601903 TCGACAAGCACGCAAATCTTT 59.398 42.857 0.00 0.00 0.00 2.52
2274 2514 1.225855 TCGACAAGCACGCAAATCTT 58.774 45.000 0.00 0.00 0.00 2.40
2275 2515 1.069906 GTTCGACAAGCACGCAAATCT 60.070 47.619 0.00 0.00 0.00 2.40
2276 2516 1.318251 GTTCGACAAGCACGCAAATC 58.682 50.000 0.00 0.00 0.00 2.17
2277 2517 0.660488 TGTTCGACAAGCACGCAAAT 59.340 45.000 0.00 0.00 0.00 2.32
2278 2518 0.027455 CTGTTCGACAAGCACGCAAA 59.973 50.000 0.00 0.00 0.00 3.68
2279 2519 1.641140 CTGTTCGACAAGCACGCAA 59.359 52.632 0.00 0.00 0.00 4.85
2280 2520 2.243957 CCTGTTCGACAAGCACGCA 61.244 57.895 0.00 0.00 0.00 5.24
2281 2521 2.244651 ACCTGTTCGACAAGCACGC 61.245 57.895 0.00 0.00 0.00 5.34
2282 2522 1.564622 CACCTGTTCGACAAGCACG 59.435 57.895 0.00 0.00 0.00 5.34
2283 2523 0.531974 TCCACCTGTTCGACAAGCAC 60.532 55.000 0.00 0.00 0.00 4.40
2286 2526 2.240493 AACTCCACCTGTTCGACAAG 57.760 50.000 0.00 0.00 0.00 3.16
2289 2529 3.382048 AGTAAACTCCACCTGTTCGAC 57.618 47.619 0.00 0.00 0.00 4.20
2291 2531 4.235360 CACTAGTAAACTCCACCTGTTCG 58.765 47.826 0.00 0.00 0.00 3.95
2310 2550 2.765135 CCAGTCATCACTCAGATCCACT 59.235 50.000 0.00 0.00 33.72 4.00
2311 2551 2.158986 CCCAGTCATCACTCAGATCCAC 60.159 54.545 0.00 0.00 33.72 4.02
2317 2557 1.153489 CCGCCCAGTCATCACTCAG 60.153 63.158 0.00 0.00 0.00 3.35
2323 2563 0.179000 ATCTTCACCGCCCAGTCATC 59.821 55.000 0.00 0.00 0.00 2.92
2324 2564 0.107508 CATCTTCACCGCCCAGTCAT 60.108 55.000 0.00 0.00 0.00 3.06
2328 2568 0.877649 CGATCATCTTCACCGCCCAG 60.878 60.000 0.00 0.00 0.00 4.45
2331 2571 2.061773 CATACGATCATCTTCACCGCC 58.938 52.381 0.00 0.00 0.00 6.13
2332 2572 2.061773 CCATACGATCATCTTCACCGC 58.938 52.381 0.00 0.00 0.00 5.68
2333 2573 3.643159 TCCATACGATCATCTTCACCG 57.357 47.619 0.00 0.00 0.00 4.94
2334 2574 6.366332 GTGTATTCCATACGATCATCTTCACC 59.634 42.308 0.00 0.00 38.59 4.02
2335 2575 6.088217 CGTGTATTCCATACGATCATCTTCAC 59.912 42.308 0.00 0.00 43.78 3.18
2336 2576 6.016610 TCGTGTATTCCATACGATCATCTTCA 60.017 38.462 0.00 0.00 44.59 3.02
2337 2577 6.379386 TCGTGTATTCCATACGATCATCTTC 58.621 40.000 0.00 0.00 44.59 2.87
2338 2578 6.327279 TCGTGTATTCCATACGATCATCTT 57.673 37.500 0.00 0.00 44.59 2.40
2339 2579 5.959618 TCGTGTATTCCATACGATCATCT 57.040 39.130 0.00 0.00 44.59 2.90
2346 2586 6.525121 AATCATGTTCGTGTATTCCATACG 57.475 37.500 0.00 0.00 42.56 3.06
2377 2617 4.022068 CACCACAGCACCTACATTTTTCAT 60.022 41.667 0.00 0.00 0.00 2.57
2379 2619 3.857010 GCACCACAGCACCTACATTTTTC 60.857 47.826 0.00 0.00 0.00 2.29
2386 2626 1.237285 CCTTGCACCACAGCACCTAC 61.237 60.000 0.00 0.00 45.61 3.18
2387 2627 1.073025 CCTTGCACCACAGCACCTA 59.927 57.895 0.00 0.00 45.61 3.08
2394 2634 1.488812 AGTCTACAACCTTGCACCACA 59.511 47.619 0.00 0.00 0.00 4.17
2395 2635 2.256117 AGTCTACAACCTTGCACCAC 57.744 50.000 0.00 0.00 0.00 4.16
2439 2685 1.034292 GGAAGCTCAGGGCCAATGAC 61.034 60.000 6.18 3.62 43.05 3.06
2443 2689 4.033776 CCGGAAGCTCAGGGCCAA 62.034 66.667 6.18 0.00 43.05 4.52
2453 2699 2.180432 AACAGGTAAACTCCGGAAGC 57.820 50.000 5.23 0.00 0.00 3.86
2457 2703 2.554370 TCCAAACAGGTAAACTCCGG 57.446 50.000 0.00 0.00 39.02 5.14
2460 2706 4.868734 CCGTCTATCCAAACAGGTAAACTC 59.131 45.833 0.00 0.00 39.02 3.01
2463 2709 4.895668 ACCGTCTATCCAAACAGGTAAA 57.104 40.909 0.00 0.00 39.02 2.01
2469 2715 3.438781 GCATCAAACCGTCTATCCAAACA 59.561 43.478 0.00 0.00 0.00 2.83
2472 2718 3.055458 TCAGCATCAAACCGTCTATCCAA 60.055 43.478 0.00 0.00 0.00 3.53
2505 2754 5.477510 TGTTGGTATCCATCAATTTGTTGC 58.522 37.500 2.50 0.00 31.25 4.17
2533 2782 1.002250 GCGGTATCATGCGTACTCCG 61.002 60.000 0.00 0.00 39.52 4.63
2541 2790 1.149361 TTTCGGACGCGGTATCATGC 61.149 55.000 12.47 0.00 0.00 4.06


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

AutoCloner maintained by Alex Coulton.