Multiple sequence alignment - TraesCS4A01G231500

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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 TraesCS4A01G231500 chr4A 100.000 2491 0 0 1 2491 541171421 541173911 0.000000e+00 4601.0
1 TraesCS4A01G231500 chr4A 87.352 253 28 4 1859 2109 694897475 694897725 1.130000e-73 287.0
2 TraesCS4A01G231500 chr4A 87.352 253 27 5 1860 2110 738092001 738091752 4.060000e-73 285.0
3 TraesCS4A01G231500 chr4A 90.244 164 15 1 1515 1678 541341287 541341449 1.940000e-51 213.0
4 TraesCS4A01G231500 chr4D 87.751 1445 108 23 959 2370 55645218 55643810 0.000000e+00 1624.0
5 TraesCS4A01G231500 chr4D 90.840 917 48 15 66 960 55646187 55645285 0.000000e+00 1195.0
6 TraesCS4A01G231500 chr4D 94.737 209 6 2 1463 1667 55597774 55597567 1.110000e-83 320.0
7 TraesCS4A01G231500 chr4D 96.825 63 1 1 1616 1678 55580960 55580899 1.220000e-18 104.0
8 TraesCS4A01G231500 chr4B 94.955 555 20 3 959 1513 82919003 82918457 0.000000e+00 863.0
9 TraesCS4A01G231500 chr4B 90.596 638 29 10 178 800 82919884 82919263 0.000000e+00 817.0
10 TraesCS4A01G231500 chr4B 97.945 146 3 0 796 941 82919236 82919091 1.140000e-63 254.0
11 TraesCS4A01G231500 chr4B 77.333 375 54 14 2141 2491 168186919 168186552 2.530000e-45 193.0
12 TraesCS4A01G231500 chr4B 81.897 232 36 4 2252 2483 625295969 625296194 9.090000e-45 191.0
13 TraesCS4A01G231500 chr4B 86.957 161 12 2 1515 1667 82918425 82918266 3.290000e-39 172.0
14 TraesCS4A01G231500 chr4B 86.928 153 12 4 1515 1667 82664755 82664611 5.510000e-37 165.0
15 TraesCS4A01G231500 chr7A 83.237 346 51 5 2140 2485 77591416 77591754 6.690000e-81 311.0
16 TraesCS4A01G231500 chr5B 88.583 254 25 4 1859 2110 578439656 578439907 3.110000e-79 305.0
17 TraesCS4A01G231500 chr5B 78.962 366 59 6 2140 2491 712876418 712876057 1.490000e-57 233.0
18 TraesCS4A01G231500 chr5B 79.397 199 26 9 2140 2324 595065968 595065771 2.600000e-25 126.0
19 TraesCS4A01G231500 chr1D 88.372 258 24 6 1859 2113 139116150 139115896 3.110000e-79 305.0
20 TraesCS4A01G231500 chr7B 87.795 254 27 4 1859 2110 480639966 480639715 6.740000e-76 294.0
21 TraesCS4A01G231500 chr1B 87.843 255 25 6 1859 2109 4088754 4088502 6.740000e-76 294.0
22 TraesCS4A01G231500 chr1B 87.795 254 27 4 1859 2109 4787551 4787803 6.740000e-76 294.0
23 TraesCS4A01G231500 chr2D 83.077 325 49 6 2146 2468 178610698 178610378 8.720000e-75 291.0
24 TraesCS4A01G231500 chr5D 87.209 258 27 6 1859 2113 459115679 459115425 3.130000e-74 289.0
25 TraesCS4A01G231500 chr5D 81.148 366 53 7 2139 2491 530732663 530732301 1.890000e-71 279.0
26 TraesCS4A01G231500 chr5D 80.278 360 46 12 2139 2485 544488212 544488559 5.320000e-62 248.0
27 TraesCS4A01G231500 chrUn 86.538 260 31 4 1859 2116 63609652 63609909 1.460000e-72 283.0
28 TraesCS4A01G231500 chr3A 79.888 358 54 6 2140 2483 26210254 26209901 1.910000e-61 246.0
29 TraesCS4A01G231500 chr2B 79.778 361 52 8 2146 2491 201768247 201767893 2.480000e-60 243.0
30 TraesCS4A01G231500 chr7D 80.363 331 49 8 2172 2488 72449614 72449942 1.150000e-58 237.0
31 TraesCS4A01G231500 chr1A 80.335 239 33 4 2140 2364 71300375 71300613 4.260000e-38 169.0
32 TraesCS4A01G231500 chr3B 100.000 30 0 0 589 618 671868484 671868513 3.460000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G231500 chr4A 541171421 541173911 2490 False 4601.0 4601 100.00000 1 2491 1 chr4A.!!$F1 2490
1 TraesCS4A01G231500 chr4D 55643810 55646187 2377 True 1409.5 1624 89.29550 66 2370 2 chr4D.!!$R3 2304
2 TraesCS4A01G231500 chr4B 82918266 82919884 1618 True 526.5 863 92.61325 178 1667 4 chr4B.!!$R3 1489

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
309 320 0.178995 TGAACCAAGCAGCACATGGA 60.179 50.0 16.4 0.0 37.66 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 2339 0.236187 CTAGGATTCCGCTCGAGTCG 59.764 60.0 15.13 17.04 0.0 4.18 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
19 20 2.452600 AGGGAGAGCCTAGTTCTCAG 57.547 55.000 18.11 0.00 40.77 3.35
20 21 1.926665 AGGGAGAGCCTAGTTCTCAGA 59.073 52.381 18.11 0.00 40.77 3.27
21 22 2.517980 AGGGAGAGCCTAGTTCTCAGAT 59.482 50.000 18.11 5.64 40.77 2.90
22 23 3.724738 AGGGAGAGCCTAGTTCTCAGATA 59.275 47.826 18.11 0.00 40.77 1.98
23 24 3.824443 GGGAGAGCCTAGTTCTCAGATAC 59.176 52.174 18.11 5.52 40.77 2.24
24 25 4.465886 GGAGAGCCTAGTTCTCAGATACA 58.534 47.826 18.11 0.00 40.77 2.29
25 26 5.076873 GGAGAGCCTAGTTCTCAGATACAT 58.923 45.833 18.11 0.00 40.77 2.29
26 27 6.242396 GGAGAGCCTAGTTCTCAGATACATA 58.758 44.000 18.11 0.00 40.77 2.29
27 28 6.889722 GGAGAGCCTAGTTCTCAGATACATAT 59.110 42.308 18.11 0.00 40.77 1.78
28 29 8.050325 GGAGAGCCTAGTTCTCAGATACATATA 58.950 40.741 18.11 0.00 40.77 0.86
29 30 9.109393 GAGAGCCTAGTTCTCAGATACATATAG 57.891 40.741 13.74 0.00 39.23 1.31
30 31 7.556275 AGAGCCTAGTTCTCAGATACATATAGC 59.444 40.741 10.66 0.00 33.15 2.97
31 32 7.410174 AGCCTAGTTCTCAGATACATATAGCT 58.590 38.462 0.00 0.00 0.00 3.32
32 33 8.553153 AGCCTAGTTCTCAGATACATATAGCTA 58.447 37.037 0.00 0.00 0.00 3.32
33 34 9.349713 GCCTAGTTCTCAGATACATATAGCTAT 57.650 37.037 11.77 11.77 0.00 2.97
68 69 7.841956 AGTACCAAGATAAATATGATCCTCGG 58.158 38.462 0.00 0.00 0.00 4.63
92 93 1.698532 GGATCATGACTCCAGGAGCAT 59.301 52.381 17.31 16.83 40.80 3.79
97 98 3.507622 TCATGACTCCAGGAGCATATACG 59.492 47.826 17.31 8.91 32.04 3.06
109 112 3.940221 GAGCATATACGATACTCCCGAGT 59.060 47.826 2.41 2.41 45.02 4.18
127 130 2.664085 GAGTTCGACTAAGAGTTGCAGC 59.336 50.000 0.00 0.00 29.55 5.25
148 151 3.564644 GCTTACACGACTCCTGCTCTATA 59.435 47.826 0.00 0.00 0.00 1.31
163 166 7.234371 TCCTGCTCTATAACTGATTGATTAGCT 59.766 37.037 0.00 0.00 0.00 3.32
164 167 8.526978 CCTGCTCTATAACTGATTGATTAGCTA 58.473 37.037 0.00 0.00 0.00 3.32
165 168 9.571810 CTGCTCTATAACTGATTGATTAGCTAG 57.428 37.037 0.00 0.00 0.00 3.42
166 169 8.031864 TGCTCTATAACTGATTGATTAGCTAGC 58.968 37.037 6.62 6.62 0.00 3.42
222 226 2.618839 CGCGCGCGCTTAGTTTAT 59.381 55.556 45.97 0.00 39.32 1.40
223 227 1.012671 CGCGCGCGCTTAGTTTATT 60.013 52.632 45.97 0.00 39.32 1.40
287 298 0.322726 TGTCCATGCATGTGTGAGGG 60.323 55.000 24.58 8.25 0.00 4.30
309 320 0.178995 TGAACCAAGCAGCACATGGA 60.179 50.000 16.40 0.00 37.66 3.41
349 360 1.129326 CGATCAATCGGTACCTTCGC 58.871 55.000 10.90 0.00 45.93 4.70
381 399 1.686587 TCGATCGCCACATGGATTAGT 59.313 47.619 11.09 0.00 37.39 2.24
390 408 4.823989 GCCACATGGATTAGTTTGCTAGAT 59.176 41.667 0.87 0.00 37.39 1.98
398 416 7.727181 TGGATTAGTTTGCTAGATAGAGGAAC 58.273 38.462 0.00 0.00 0.00 3.62
432 450 2.202518 GCACATCCGCACATGCAC 60.203 61.111 4.49 0.00 42.21 4.57
462 480 4.084849 CGAGTGTCAAATCCGATTAGCATC 60.085 45.833 0.00 0.00 0.00 3.91
463 481 4.130118 AGTGTCAAATCCGATTAGCATCC 58.870 43.478 0.00 0.00 0.00 3.51
518 540 7.566879 ACTTGTGAGATAGGAAGATTGGATACT 59.433 37.037 0.00 0.00 37.61 2.12
760 785 5.043737 TCCTACATTAAGGCCAATGGTAC 57.956 43.478 17.54 0.00 39.71 3.34
869 926 1.935873 CTACCACGTGCATCTCCAATG 59.064 52.381 10.91 0.00 0.00 2.82
969 1102 2.110901 ATCTGCAACTTCTCTGCCTG 57.889 50.000 0.00 0.00 39.13 4.85
976 1109 2.540265 ACTTCTCTGCCTGTGTCTTG 57.460 50.000 0.00 0.00 0.00 3.02
1053 1186 4.434195 AGAAGAGTTCCCAGGAAGAAGAT 58.566 43.478 0.00 0.00 34.49 2.40
1155 1288 2.911928 GGCTACTTGGGCCTCTCC 59.088 66.667 4.53 0.00 45.57 3.71
1243 1376 0.663688 CCAGCTGCATGATGAAGAGC 59.336 55.000 8.66 4.09 33.12 4.09
1251 1384 0.467384 ATGATGAAGAGCCCGGAGTG 59.533 55.000 0.73 0.00 0.00 3.51
1285 1418 1.201647 ACGCTGCAGATGTAAGTACGT 59.798 47.619 20.43 11.22 0.00 3.57
1287 1420 2.731027 CGCTGCAGATGTAAGTACGTCA 60.731 50.000 20.43 0.00 43.07 4.35
1288 1421 3.448686 GCTGCAGATGTAAGTACGTCAT 58.551 45.455 20.43 0.00 43.07 3.06
1289 1422 3.243877 GCTGCAGATGTAAGTACGTCATG 59.756 47.826 20.43 8.70 43.07 3.07
1290 1423 4.672409 CTGCAGATGTAAGTACGTCATGA 58.328 43.478 8.42 0.00 43.07 3.07
1291 1424 5.262588 TGCAGATGTAAGTACGTCATGAT 57.737 39.130 12.12 0.00 43.07 2.45
1292 1425 5.281727 TGCAGATGTAAGTACGTCATGATC 58.718 41.667 12.12 0.00 43.07 2.92
1293 1426 5.163561 TGCAGATGTAAGTACGTCATGATCA 60.164 40.000 12.12 0.00 43.07 2.92
1294 1427 5.400782 GCAGATGTAAGTACGTCATGATCAG 59.599 44.000 12.12 0.00 43.07 2.90
1322 1458 7.334421 TGATCTACCTTGTTATTTGCTCTGTTC 59.666 37.037 0.00 0.00 0.00 3.18
1364 1500 4.318332 ACTTCTGATTCAATCTCGTTGCA 58.682 39.130 0.00 0.00 37.74 4.08
1392 1528 5.906113 ATATGTCTATGATCGGTCAGGAC 57.094 43.478 20.71 20.71 39.43 3.85
1560 1734 3.756117 TCAGAGTCTTAGAGTGAGTGCA 58.244 45.455 0.00 0.00 0.00 4.57
1573 1747 1.487976 TGAGTGCATCCATCTCTTCCC 59.512 52.381 0.00 0.00 0.00 3.97
1578 1752 3.114606 TGCATCCATCTCTTCCCTGTTA 58.885 45.455 0.00 0.00 0.00 2.41
1678 1852 4.730487 CTGGGTGGAAGCAAGGAG 57.270 61.111 0.00 0.00 29.69 3.69
1680 1854 0.111253 CTGGGTGGAAGCAAGGAGTT 59.889 55.000 0.00 0.00 29.69 3.01
1681 1855 0.178992 TGGGTGGAAGCAAGGAGTTG 60.179 55.000 0.00 0.00 34.77 3.16
1684 1858 2.031870 GGTGGAAGCAAGGAGTTGTTT 58.968 47.619 0.00 0.00 39.57 2.83
1731 1905 4.067896 CACATCTTACTTGTGAGCTTGGT 58.932 43.478 0.00 0.00 45.83 3.67
1734 1908 5.012148 ACATCTTACTTGTGAGCTTGGTACT 59.988 40.000 0.00 0.00 0.00 2.73
1735 1909 4.883083 TCTTACTTGTGAGCTTGGTACTG 58.117 43.478 0.00 0.00 0.00 2.74
1754 1928 8.003044 TGGTACTGTATTACACTAGGCTTCTAT 58.997 37.037 0.00 0.00 0.00 1.98
1776 1950 9.026121 TCTATGGAGTAAAGAGTATGCTAATCC 57.974 37.037 0.00 0.00 0.00 3.01
1791 1965 5.138276 TGCTAATCCGTATAGAGGACACTT 58.862 41.667 0.00 0.00 41.10 3.16
1796 1970 4.597004 TCCGTATAGAGGACACTTTGTCT 58.403 43.478 6.29 0.00 46.19 3.41
1797 1971 5.014858 TCCGTATAGAGGACACTTTGTCTT 58.985 41.667 6.29 0.00 46.19 3.01
1808 1982 6.486993 AGGACACTTTGTCTTATTGTTTCCTC 59.513 38.462 6.29 0.00 46.19 3.71
1811 1985 6.263168 ACACTTTGTCTTATTGTTTCCTCCAG 59.737 38.462 0.00 0.00 0.00 3.86
1831 2005 4.459337 CCAGTGTTATTTCCTCCTTTCCAC 59.541 45.833 0.00 0.00 0.00 4.02
1833 2007 6.472887 CAGTGTTATTTCCTCCTTTCCACTA 58.527 40.000 0.00 0.00 0.00 2.74
1843 2017 5.729229 TCCTCCTTTCCACTACCATTTATCA 59.271 40.000 0.00 0.00 0.00 2.15
1849 2023 8.244113 CCTTTCCACTACCATTTATCAGTTTTC 58.756 37.037 0.00 0.00 0.00 2.29
1851 2025 5.878116 TCCACTACCATTTATCAGTTTTCGG 59.122 40.000 0.00 0.00 0.00 4.30
1886 2060 2.667874 TGCGATTGTGCAGCCGAA 60.668 55.556 0.00 0.00 40.62 4.30
1887 2061 2.039974 TGCGATTGTGCAGCCGAAT 61.040 52.632 0.00 0.00 40.62 3.34
1888 2062 1.584483 GCGATTGTGCAGCCGAATG 60.584 57.895 0.00 0.00 34.15 2.67
1891 2065 0.099436 GATTGTGCAGCCGAATGACC 59.901 55.000 0.00 0.00 0.00 4.02
1895 2069 2.435938 GCAGCCGAATGACCCGAA 60.436 61.111 0.00 0.00 0.00 4.30
1898 2072 0.657840 CAGCCGAATGACCCGAATTC 59.342 55.000 0.00 0.00 0.00 2.17
1901 2075 1.676006 GCCGAATGACCCGAATTCAAT 59.324 47.619 6.22 0.00 34.34 2.57
1907 2081 6.183360 CCGAATGACCCGAATTCAATTTCTAA 60.183 38.462 6.22 0.00 34.34 2.10
1916 2090 8.863049 CCCGAATTCAATTTCTAAAATTGACAG 58.137 33.333 21.34 14.44 43.81 3.51
1917 2091 9.624697 CCGAATTCAATTTCTAAAATTGACAGA 57.375 29.630 21.34 11.75 43.81 3.41
1938 2113 8.095452 ACAGATGATGTATAGGGAGTTTTCTT 57.905 34.615 0.00 0.00 41.60 2.52
1941 2116 8.428063 AGATGATGTATAGGGAGTTTTCTTCTG 58.572 37.037 0.00 0.00 0.00 3.02
1951 2126 6.717084 AGGGAGTTTTCTTCTGTTTATTGAGG 59.283 38.462 0.00 0.00 0.00 3.86
1972 2147 3.884774 AAGCTTGGTGTGGGGCGA 61.885 61.111 0.00 0.00 0.00 5.54
2035 2210 7.771927 AAATTCTGAGAACCATGTTCATCTT 57.228 32.000 0.00 0.00 0.00 2.40
2037 2212 8.503458 AATTCTGAGAACCATGTTCATCTTAG 57.497 34.615 0.00 5.67 0.00 2.18
2074 2249 2.364324 GGTCGTATGCATCCCTAGTTGA 59.636 50.000 0.19 0.00 0.00 3.18
2082 2257 3.834489 CATCCCTAGTTGATGCAGAGT 57.166 47.619 6.57 0.00 33.81 3.24
2083 2258 3.726607 CATCCCTAGTTGATGCAGAGTC 58.273 50.000 6.57 0.00 33.81 3.36
2085 2260 1.751351 CCCTAGTTGATGCAGAGTCGA 59.249 52.381 0.00 0.00 0.00 4.20
2097 2272 3.742882 TGCAGAGTCGAGAAGTGAAAATG 59.257 43.478 0.00 0.00 0.00 2.32
2119 2295 5.902681 TGTCTCCCATTTTATGAGAGTACG 58.097 41.667 0.00 0.00 36.60 3.67
2130 2306 4.974368 ATGAGAGTACGTTGGAAGAGAG 57.026 45.455 0.00 0.00 0.00 3.20
2177 2353 2.202623 GTGCGACTCGAGCGGAAT 60.203 61.111 23.77 2.04 37.44 3.01
2186 2362 0.827925 TCGAGCGGAATCCTAGCCAT 60.828 55.000 0.00 0.00 0.00 4.40
2286 2462 0.114560 AACTCCGGTTCTCCCTCTCA 59.885 55.000 0.00 0.00 0.00 3.27
2307 2483 4.821589 GGCTCGGGAGTTGCGGAG 62.822 72.222 4.25 4.25 0.00 4.63
2357 2534 2.361610 AAGCTTGCATCGGGTGGG 60.362 61.111 0.00 0.00 0.00 4.61
2414 2591 3.423154 GCGGACGCAAGGAAGGTG 61.423 66.667 12.31 0.00 46.39 4.00
2415 2592 2.742372 CGGACGCAAGGAAGGTGG 60.742 66.667 0.00 0.00 46.39 4.61
2416 2593 2.359975 GGACGCAAGGAAGGTGGG 60.360 66.667 0.00 0.00 46.39 4.61
2417 2594 3.056328 GACGCAAGGAAGGTGGGC 61.056 66.667 0.00 0.00 46.39 5.36
2418 2595 3.553095 GACGCAAGGAAGGTGGGCT 62.553 63.158 0.00 0.00 46.39 5.19
2419 2596 2.747855 CGCAAGGAAGGTGGGCTC 60.748 66.667 0.00 0.00 0.00 4.70
2420 2597 2.759795 GCAAGGAAGGTGGGCTCT 59.240 61.111 0.00 0.00 0.00 4.09
2421 2598 1.676967 GCAAGGAAGGTGGGCTCTG 60.677 63.158 0.00 0.00 0.00 3.35
2422 2599 1.001641 CAAGGAAGGTGGGCTCTGG 60.002 63.158 0.00 0.00 0.00 3.86
2423 2600 2.911926 AAGGAAGGTGGGCTCTGGC 61.912 63.158 0.00 0.00 37.82 4.85
2424 2601 3.334054 GGAAGGTGGGCTCTGGCT 61.334 66.667 0.00 0.00 38.73 4.75
2425 2602 2.270527 GAAGGTGGGCTCTGGCTC 59.729 66.667 0.00 0.00 39.89 4.70
2426 2603 2.204059 AAGGTGGGCTCTGGCTCT 60.204 61.111 0.00 0.00 40.19 4.09
2427 2604 2.250741 GAAGGTGGGCTCTGGCTCTC 62.251 65.000 0.00 0.00 40.19 3.20
2428 2605 3.005539 GGTGGGCTCTGGCTCTCA 61.006 66.667 0.00 0.00 40.19 3.27
2429 2606 2.373707 GGTGGGCTCTGGCTCTCAT 61.374 63.158 0.00 0.00 40.19 2.90
2430 2607 1.153208 GTGGGCTCTGGCTCTCATG 60.153 63.158 0.00 0.00 40.19 3.07
2431 2608 2.372890 TGGGCTCTGGCTCTCATGG 61.373 63.158 0.00 0.00 40.19 3.66
2432 2609 2.203181 GGCTCTGGCTCTCATGGC 60.203 66.667 0.00 0.00 38.73 4.40
2433 2610 2.588439 GCTCTGGCTCTCATGGCA 59.412 61.111 0.00 0.00 40.25 4.92
2434 2611 1.818785 GCTCTGGCTCTCATGGCAC 60.819 63.158 0.00 0.00 37.59 5.01
2435 2612 1.153208 CTCTGGCTCTCATGGCACC 60.153 63.158 0.00 0.00 37.59 5.01
2436 2613 2.513204 CTGGCTCTCATGGCACCG 60.513 66.667 0.00 0.00 37.59 4.94
2437 2614 4.783621 TGGCTCTCATGGCACCGC 62.784 66.667 0.00 0.00 37.59 5.68
2456 2633 4.615815 GCGGCTGGCAGATCGGAT 62.616 66.667 20.86 0.00 42.87 4.18
2457 2634 2.356793 CGGCTGGCAGATCGGATC 60.357 66.667 20.86 10.02 0.00 3.36
2458 2635 2.865598 CGGCTGGCAGATCGGATCT 61.866 63.158 20.86 14.68 41.15 2.75
2459 2636 1.005156 GGCTGGCAGATCGGATCTC 60.005 63.158 20.86 11.97 37.58 2.75
2460 2637 1.372748 GCTGGCAGATCGGATCTCG 60.373 63.158 20.86 13.57 37.58 4.04
2461 2638 1.288439 CTGGCAGATCGGATCTCGG 59.712 63.158 17.41 9.01 37.58 4.63
2462 2639 2.152297 CTGGCAGATCGGATCTCGGG 62.152 65.000 17.41 8.31 37.58 5.14
2463 2640 2.653702 GCAGATCGGATCTCGGGG 59.346 66.667 17.41 7.96 37.58 5.73
2464 2641 2.653702 CAGATCGGATCTCGGGGC 59.346 66.667 17.41 0.00 37.58 5.80
2465 2642 2.986413 AGATCGGATCTCGGGGCG 60.986 66.667 14.68 0.00 39.77 6.13
2466 2643 4.057428 GATCGGATCTCGGGGCGG 62.057 72.222 10.73 0.00 39.77 6.13
2480 2657 4.814294 GCGGCAACCTCGATCGGT 62.814 66.667 16.41 2.86 39.48 4.69
2481 2658 2.885644 CGGCAACCTCGATCGGTG 60.886 66.667 16.41 9.22 37.36 4.94
2482 2659 2.511600 GGCAACCTCGATCGGTGG 60.512 66.667 16.41 19.15 37.36 4.61
2483 2660 3.195698 GCAACCTCGATCGGTGGC 61.196 66.667 21.93 15.59 46.07 5.01
2484 2661 2.885644 CAACCTCGATCGGTGGCG 60.886 66.667 21.93 13.07 37.36 5.69
2485 2662 3.379445 AACCTCGATCGGTGGCGT 61.379 61.111 21.93 11.56 37.36 5.68
2486 2663 3.642778 AACCTCGATCGGTGGCGTG 62.643 63.158 21.93 5.32 37.36 5.34
2488 2665 4.794439 CTCGATCGGTGGCGTGCA 62.794 66.667 16.41 0.00 0.00 4.57
2489 2666 4.794439 TCGATCGGTGGCGTGCAG 62.794 66.667 16.41 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.445682 TCTGAGAACTAGGCTCTCCC 57.554 55.000 17.08 0.67 38.89 4.30
2 3 4.465886 TGTATCTGAGAACTAGGCTCTCC 58.534 47.826 17.08 6.20 38.89 3.71
3 4 7.938140 ATATGTATCTGAGAACTAGGCTCTC 57.062 40.000 14.29 14.29 39.89 3.20
4 5 7.556275 GCTATATGTATCTGAGAACTAGGCTCT 59.444 40.741 13.80 6.42 33.57 4.09
5 6 7.556275 AGCTATATGTATCTGAGAACTAGGCTC 59.444 40.741 0.00 7.68 0.00 4.70
6 7 7.410174 AGCTATATGTATCTGAGAACTAGGCT 58.590 38.462 0.00 0.00 0.00 4.58
7 8 7.639113 AGCTATATGTATCTGAGAACTAGGC 57.361 40.000 0.00 0.00 0.00 3.93
41 42 9.144747 CGAGGATCATATTTATCTTGGTACTTG 57.855 37.037 0.00 0.00 33.17 3.16
42 43 8.314751 CCGAGGATCATATTTATCTTGGTACTT 58.685 37.037 0.00 0.00 33.17 2.24
43 44 7.579723 GCCGAGGATCATATTTATCTTGGTACT 60.580 40.741 0.00 0.00 33.17 2.73
44 45 6.535508 GCCGAGGATCATATTTATCTTGGTAC 59.464 42.308 0.00 0.00 33.17 3.34
45 46 6.351881 GGCCGAGGATCATATTTATCTTGGTA 60.352 42.308 0.00 0.00 33.17 3.25
46 47 5.491982 GCCGAGGATCATATTTATCTTGGT 58.508 41.667 0.00 0.00 33.17 3.67
47 48 4.878397 GGCCGAGGATCATATTTATCTTGG 59.122 45.833 0.00 0.00 33.17 3.61
48 49 5.491070 TGGCCGAGGATCATATTTATCTTG 58.509 41.667 0.00 0.00 33.17 3.02
49 50 5.338708 CCTGGCCGAGGATCATATTTATCTT 60.339 44.000 14.21 0.00 46.33 2.40
50 51 4.163078 CCTGGCCGAGGATCATATTTATCT 59.837 45.833 14.21 0.00 46.33 1.98
51 52 4.162320 TCCTGGCCGAGGATCATATTTATC 59.838 45.833 17.12 0.00 46.96 1.75
52 53 4.104086 TCCTGGCCGAGGATCATATTTAT 58.896 43.478 17.12 0.00 46.96 1.40
53 54 3.516586 TCCTGGCCGAGGATCATATTTA 58.483 45.455 17.12 0.00 46.96 1.40
54 55 2.338809 TCCTGGCCGAGGATCATATTT 58.661 47.619 17.12 0.00 46.96 1.40
55 56 2.030027 TCCTGGCCGAGGATCATATT 57.970 50.000 17.12 0.00 46.96 1.28
56 57 3.794786 TCCTGGCCGAGGATCATAT 57.205 52.632 17.12 0.00 46.96 1.78
63 64 1.070445 GTCATGATCCTGGCCGAGG 59.930 63.158 13.43 13.43 44.45 4.63
64 65 0.033228 GAGTCATGATCCTGGCCGAG 59.967 60.000 0.00 0.00 0.00 4.63
68 69 0.108207 CCTGGAGTCATGATCCTGGC 59.892 60.000 23.95 0.00 45.50 4.85
74 75 4.159321 CGTATATGCTCCTGGAGTCATGAT 59.841 45.833 28.47 21.91 32.21 2.45
78 79 3.223674 TCGTATATGCTCCTGGAGTCA 57.776 47.619 23.92 20.94 31.39 3.41
92 93 3.990469 GTCGAACTCGGGAGTATCGTATA 59.010 47.826 21.29 9.33 41.58 1.47
97 98 4.125703 TCTTAGTCGAACTCGGGAGTATC 58.874 47.826 1.08 2.15 41.58 2.24
109 112 3.386768 AAGCTGCAACTCTTAGTCGAA 57.613 42.857 1.02 0.00 0.00 3.71
127 130 5.297278 AGTTATAGAGCAGGAGTCGTGTAAG 59.703 44.000 13.97 0.00 0.00 2.34
148 151 5.365021 ACAGGCTAGCTAATCAATCAGTT 57.635 39.130 15.72 0.00 0.00 3.16
216 220 6.952773 TTGACAGCCAACACTAAATAAACT 57.047 33.333 0.00 0.00 0.00 2.66
287 298 1.068748 CATGTGCTGCTTGGTTCACTC 60.069 52.381 0.00 0.00 0.00 3.51
335 346 1.606885 TTCCCGCGAAGGTACCGATT 61.607 55.000 8.23 0.00 38.74 3.34
340 351 1.005867 TGTGTTCCCGCGAAGGTAC 60.006 57.895 8.23 5.89 38.74 3.34
349 360 1.683790 GCGATCGAAGTGTGTTCCCG 61.684 60.000 21.57 0.00 0.00 5.14
381 399 6.173339 CAAAGTGGTTCCTCTATCTAGCAAA 58.827 40.000 0.00 0.00 0.00 3.68
398 416 1.362355 GCCGGTGGAAACAAAGTGG 59.638 57.895 1.90 0.00 46.06 4.00
462 480 2.223923 CCTGATCTGAAACTAGGAGCGG 60.224 54.545 0.38 0.00 0.00 5.52
463 481 2.428890 ACCTGATCTGAAACTAGGAGCG 59.571 50.000 0.38 0.00 32.86 5.03
518 540 4.480115 TCTCTGAACCTGAGTACAAAGGA 58.520 43.478 18.05 0.00 37.01 3.36
641 663 5.437060 TCCCATATGGCAGTAAGTTCTTTC 58.563 41.667 16.97 0.00 0.00 2.62
645 670 6.715347 AAATTCCCATATGGCAGTAAGTTC 57.285 37.500 16.97 0.00 0.00 3.01
684 709 5.122519 GGAGAGAGGAACCATTGATTTCTC 58.877 45.833 0.00 0.00 0.00 2.87
760 785 6.055231 TGTTTTGTTTCTTCAGACGTATGG 57.945 37.500 10.78 0.00 0.00 2.74
869 926 3.247563 GAGAGTGACTCGTCATCGATC 57.752 52.381 6.99 0.00 45.21 3.69
901 958 1.374758 CAGTTGCGAGGACTGTCCC 60.375 63.158 22.81 13.28 39.66 4.46
969 1102 2.365617 TGGAGTTCAGAGACCAAGACAC 59.634 50.000 0.00 0.00 0.00 3.67
976 1109 0.534873 GAGGCTGGAGTTCAGAGACC 59.465 60.000 1.33 0.00 46.18 3.85
1071 1204 1.205055 GGAAGAAGGAAGGGGACGAT 58.795 55.000 0.00 0.00 0.00 3.73
1200 1333 2.184579 GTAGCTGCGGGAGGTGAC 59.815 66.667 11.66 2.58 33.31 3.67
1290 1423 8.216423 AGCAAATAACAAGGTAGATCATCTGAT 58.784 33.333 0.00 0.00 37.51 2.90
1291 1424 7.568349 AGCAAATAACAAGGTAGATCATCTGA 58.432 34.615 0.00 0.00 0.00 3.27
1292 1425 7.714377 AGAGCAAATAACAAGGTAGATCATCTG 59.286 37.037 0.00 0.00 0.00 2.90
1293 1426 7.714377 CAGAGCAAATAACAAGGTAGATCATCT 59.286 37.037 0.00 0.00 0.00 2.90
1294 1427 7.497249 ACAGAGCAAATAACAAGGTAGATCATC 59.503 37.037 0.00 0.00 0.00 2.92
1322 1458 1.000843 TCAGTCCACCACATGAACTCG 59.999 52.381 0.00 0.00 0.00 4.18
1364 1500 8.690884 CCTGACCGATCATAGACATATTAGATT 58.309 37.037 0.00 0.00 33.22 2.40
1407 1543 2.202676 CCTCTCGAGCGCACTTCC 60.203 66.667 11.47 0.00 0.00 3.46
1560 1734 5.983333 AACATAACAGGGAAGAGATGGAT 57.017 39.130 0.00 0.00 0.00 3.41
1671 1845 4.110036 ACAAACAGAAACAACTCCTTGC 57.890 40.909 0.00 0.00 0.00 4.01
1678 1852 6.533367 TCTTGGCAAATACAAACAGAAACAAC 59.467 34.615 0.00 0.00 0.00 3.32
1680 1854 6.214191 TCTTGGCAAATACAAACAGAAACA 57.786 33.333 0.00 0.00 0.00 2.83
1681 1855 7.713764 ATTCTTGGCAAATACAAACAGAAAC 57.286 32.000 0.00 0.00 0.00 2.78
1684 1858 7.446931 TGAGTATTCTTGGCAAATACAAACAGA 59.553 33.333 19.11 1.05 40.49 3.41
1731 1905 8.222637 TCCATAGAAGCCTAGTGTAATACAGTA 58.777 37.037 7.63 7.63 33.15 2.74
1734 1908 7.067421 ACTCCATAGAAGCCTAGTGTAATACA 58.933 38.462 0.00 0.00 0.00 2.29
1735 1909 7.527568 ACTCCATAGAAGCCTAGTGTAATAC 57.472 40.000 0.00 0.00 0.00 1.89
1754 1928 5.597182 ACGGATTAGCATACTCTTTACTCCA 59.403 40.000 0.00 0.00 0.00 3.86
1791 1965 5.690865 ACACTGGAGGAAACAATAAGACAA 58.309 37.500 0.00 0.00 0.00 3.18
1796 1970 7.947890 AGGAAATAACACTGGAGGAAACAATAA 59.052 33.333 0.00 0.00 0.00 1.40
1797 1971 7.466804 AGGAAATAACACTGGAGGAAACAATA 58.533 34.615 0.00 0.00 0.00 1.90
1808 1982 4.459337 GTGGAAAGGAGGAAATAACACTGG 59.541 45.833 0.00 0.00 0.00 4.00
1811 1985 5.646793 GGTAGTGGAAAGGAGGAAATAACAC 59.353 44.000 0.00 0.00 0.00 3.32
1831 2005 6.456449 CCGAACCGAAAACTGATAAATGGTAG 60.456 42.308 0.00 0.00 0.00 3.18
1833 2007 4.155280 CCGAACCGAAAACTGATAAATGGT 59.845 41.667 0.00 0.00 0.00 3.55
1843 2017 2.248835 CCACGCCGAACCGAAAACT 61.249 57.895 0.00 0.00 0.00 2.66
1873 2047 1.315257 GGGTCATTCGGCTGCACAAT 61.315 55.000 0.50 0.00 0.00 2.71
1882 2056 4.096382 AGAAATTGAATTCGGGTCATTCGG 59.904 41.667 0.04 0.00 33.91 4.30
1883 2057 5.235305 AGAAATTGAATTCGGGTCATTCG 57.765 39.130 0.04 0.00 33.91 3.34
1884 2058 8.980143 TTTTAGAAATTGAATTCGGGTCATTC 57.020 30.769 0.04 0.44 34.46 2.67
1885 2059 9.942850 AATTTTAGAAATTGAATTCGGGTCATT 57.057 25.926 0.04 0.00 34.46 2.57
1886 2060 9.369904 CAATTTTAGAAATTGAATTCGGGTCAT 57.630 29.630 17.02 0.00 39.36 3.06
1887 2061 8.580720 TCAATTTTAGAAATTGAATTCGGGTCA 58.419 29.630 20.46 1.40 41.92 4.02
1888 2062 8.860128 GTCAATTTTAGAAATTGAATTCGGGTC 58.140 33.333 22.98 10.14 45.06 4.46
1891 2065 9.624697 TCTGTCAATTTTAGAAATTGAATTCGG 57.375 29.630 22.98 17.43 45.06 4.30
1907 2081 8.038862 ACTCCCTATACATCATCTGTCAATTT 57.961 34.615 0.00 0.00 39.39 1.82
1916 2090 8.207545 ACAGAAGAAAACTCCCTATACATCATC 58.792 37.037 0.00 0.00 0.00 2.92
1917 2091 8.095452 ACAGAAGAAAACTCCCTATACATCAT 57.905 34.615 0.00 0.00 0.00 2.45
1930 2105 8.924511 TGATCCTCAATAAACAGAAGAAAACT 57.075 30.769 0.00 0.00 0.00 2.66
1938 2113 5.649395 CCAAGCTTGATCCTCAATAAACAGA 59.351 40.000 28.05 0.00 35.59 3.41
1941 2116 5.183904 ACACCAAGCTTGATCCTCAATAAAC 59.816 40.000 28.05 0.00 35.59 2.01
1951 2126 1.598701 GCCCCACACCAAGCTTGATC 61.599 60.000 28.05 0.00 0.00 2.92
2037 2212 7.650504 TGCATACGACCATTTTAGTATGAGTAC 59.349 37.037 15.84 0.00 45.38 2.73
2074 2249 3.667497 TTTCACTTCTCGACTCTGCAT 57.333 42.857 0.00 0.00 0.00 3.96
2079 2254 4.623595 GGAGACATTTTCACTTCTCGACTC 59.376 45.833 0.00 0.00 36.18 3.36
2082 2257 3.323691 TGGGAGACATTTTCACTTCTCGA 59.676 43.478 0.00 0.00 36.18 4.04
2083 2258 3.664107 TGGGAGACATTTTCACTTCTCG 58.336 45.455 0.00 0.00 36.18 4.04
2119 2295 2.356227 GGTCAATCCCCTCTCTTCCAAC 60.356 54.545 0.00 0.00 0.00 3.77
2161 2337 2.102357 GATTCCGCTCGAGTCGCA 59.898 61.111 15.13 1.17 0.00 5.10
2163 2339 0.236187 CTAGGATTCCGCTCGAGTCG 59.764 60.000 15.13 17.04 0.00 4.18
2167 2343 0.827925 ATGGCTAGGATTCCGCTCGA 60.828 55.000 0.00 0.00 0.00 4.04
2169 2345 0.681733 TGATGGCTAGGATTCCGCTC 59.318 55.000 0.00 0.00 0.00 5.03
2170 2346 0.683973 CTGATGGCTAGGATTCCGCT 59.316 55.000 0.00 0.00 0.00 5.52
2186 2362 1.682684 GAGGAGGGAGTTCGCCTGA 60.683 63.158 0.00 0.00 37.07 3.86
2191 2367 3.068691 TGGCGAGGAGGGAGTTCG 61.069 66.667 0.00 0.00 37.40 3.95
2295 2471 4.070552 AGACGCTCCGCAACTCCC 62.071 66.667 0.00 0.00 0.00 4.30
2397 2574 3.423154 CACCTTCCTTGCGTCCGC 61.423 66.667 4.42 4.42 42.35 5.54
2398 2575 2.742372 CCACCTTCCTTGCGTCCG 60.742 66.667 0.00 0.00 0.00 4.79
2399 2576 2.359975 CCCACCTTCCTTGCGTCC 60.360 66.667 0.00 0.00 0.00 4.79
2400 2577 3.056328 GCCCACCTTCCTTGCGTC 61.056 66.667 0.00 0.00 0.00 5.19
2401 2578 3.553095 GAGCCCACCTTCCTTGCGT 62.553 63.158 0.00 0.00 0.00 5.24
2402 2579 2.747855 GAGCCCACCTTCCTTGCG 60.748 66.667 0.00 0.00 0.00 4.85
2403 2580 1.676967 CAGAGCCCACCTTCCTTGC 60.677 63.158 0.00 0.00 0.00 4.01
2404 2581 1.001641 CCAGAGCCCACCTTCCTTG 60.002 63.158 0.00 0.00 0.00 3.61
2405 2582 2.911926 GCCAGAGCCCACCTTCCTT 61.912 63.158 0.00 0.00 0.00 3.36
2406 2583 3.334054 GCCAGAGCCCACCTTCCT 61.334 66.667 0.00 0.00 0.00 3.36
2407 2584 3.334054 AGCCAGAGCCCACCTTCC 61.334 66.667 0.00 0.00 41.25 3.46
2408 2585 2.250741 GAGAGCCAGAGCCCACCTTC 62.251 65.000 0.00 0.00 41.25 3.46
2409 2586 2.204059 AGAGCCAGAGCCCACCTT 60.204 61.111 0.00 0.00 41.25 3.50
2410 2587 2.686835 GAGAGCCAGAGCCCACCT 60.687 66.667 0.00 0.00 41.25 4.00
2411 2588 2.373707 ATGAGAGCCAGAGCCCACC 61.374 63.158 0.00 0.00 41.25 4.61
2412 2589 1.153208 CATGAGAGCCAGAGCCCAC 60.153 63.158 0.00 0.00 41.25 4.61
2413 2590 2.372890 CCATGAGAGCCAGAGCCCA 61.373 63.158 0.00 0.00 41.25 5.36
2414 2591 2.509916 CCATGAGAGCCAGAGCCC 59.490 66.667 0.00 0.00 41.25 5.19
2415 2592 2.203181 GCCATGAGAGCCAGAGCC 60.203 66.667 0.00 0.00 41.25 4.70
2416 2593 1.818785 GTGCCATGAGAGCCAGAGC 60.819 63.158 0.00 0.00 40.32 4.09
2417 2594 1.153208 GGTGCCATGAGAGCCAGAG 60.153 63.158 0.00 0.00 0.00 3.35
2418 2595 2.993008 GGTGCCATGAGAGCCAGA 59.007 61.111 0.00 0.00 0.00 3.86
2419 2596 2.513204 CGGTGCCATGAGAGCCAG 60.513 66.667 0.00 0.00 0.00 4.85
2420 2597 4.783621 GCGGTGCCATGAGAGCCA 62.784 66.667 0.00 0.00 0.00 4.75
2439 2616 4.615815 ATCCGATCTGCCAGCCGC 62.616 66.667 1.62 0.00 38.31 6.53
2440 2617 2.356793 GATCCGATCTGCCAGCCG 60.357 66.667 0.75 0.00 0.00 5.52
2441 2618 1.005156 GAGATCCGATCTGCCAGCC 60.005 63.158 15.85 0.00 40.38 4.85
2442 2619 1.372748 CGAGATCCGATCTGCCAGC 60.373 63.158 15.85 0.13 40.38 4.85
2443 2620 1.288439 CCGAGATCCGATCTGCCAG 59.712 63.158 15.85 4.58 40.38 4.85
2444 2621 2.203082 CCCGAGATCCGATCTGCCA 61.203 63.158 15.85 0.00 40.38 4.92
2445 2622 2.653702 CCCGAGATCCGATCTGCC 59.346 66.667 15.85 1.56 40.38 4.85
2446 2623 2.653702 CCCCGAGATCCGATCTGC 59.346 66.667 15.85 6.68 40.38 4.26
2447 2624 2.653702 GCCCCGAGATCCGATCTG 59.346 66.667 15.85 7.98 40.38 2.90
2448 2625 2.986413 CGCCCCGAGATCCGATCT 60.986 66.667 10.83 10.83 43.70 2.75
2449 2626 4.057428 CCGCCCCGAGATCCGATC 62.057 72.222 0.00 0.00 41.76 3.69
2463 2640 4.814294 ACCGATCGAGGTTGCCGC 62.814 66.667 18.66 0.00 43.00 6.53
2464 2641 2.885644 CACCGATCGAGGTTGCCG 60.886 66.667 18.66 0.00 43.00 5.69
2465 2642 2.511600 CCACCGATCGAGGTTGCC 60.512 66.667 18.66 0.00 43.00 4.52
2466 2643 3.195698 GCCACCGATCGAGGTTGC 61.196 66.667 18.66 10.62 43.00 4.17
2467 2644 2.885644 CGCCACCGATCGAGGTTG 60.886 66.667 18.66 10.91 43.00 3.77
2468 2645 3.379445 ACGCCACCGATCGAGGTT 61.379 61.111 18.66 6.82 43.00 3.50
2471 2648 4.794439 TGCACGCCACCGATCGAG 62.794 66.667 18.66 9.42 38.29 4.04
2472 2649 4.794439 CTGCACGCCACCGATCGA 62.794 66.667 18.66 0.00 38.29 3.59


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

AutoCloner maintained by Alex Coulton.