Multiple sequence alignment - TraesCS6D01G126000

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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 TraesCS6D01G126000 chr6D 100.000 3433 0 0 1 3433 89728953 89732385 0.000000e+00 6340.0
1 TraesCS6D01G126000 chr6D 93.684 95 6 0 393 487 89729206 89729300 3.570000e-30 143.0
2 TraesCS6D01G126000 chr6D 93.684 95 6 0 254 348 89729345 89729439 3.570000e-30 143.0
3 TraesCS6D01G126000 chr6A 92.206 1437 56 26 2019 3433 108177008 108178410 0.000000e+00 1982.0
4 TraesCS6D01G126000 chr6A 92.496 693 45 7 1173 1860 108176269 108176959 0.000000e+00 985.0
5 TraesCS6D01G126000 chr6A 94.505 546 19 4 330 874 108175424 108175959 0.000000e+00 832.0
6 TraesCS6D01G126000 chr6A 92.749 331 20 3 1 329 108175011 108175339 3.100000e-130 475.0
7 TraesCS6D01G126000 chr6A 96.053 228 6 1 875 1102 108176014 108176238 5.410000e-98 368.0
8 TraesCS6D01G126000 chr6B 90.819 1416 68 37 2019 3404 172262702 172264085 0.000000e+00 1838.0
9 TraesCS6D01G126000 chr6B 92.785 887 38 11 1 875 172260777 172261649 0.000000e+00 1260.0
10 TraesCS6D01G126000 chr6B 93.487 783 44 5 1153 1934 172261925 172262701 0.000000e+00 1157.0
11 TraesCS6D01G126000 chr6B 96.043 278 9 2 875 1152 172261706 172261981 5.220000e-123 451.0
12 TraesCS6D01G126000 chr6B 93.750 96 5 1 392 487 172261029 172261123 3.570000e-30 143.0
13 TraesCS6D01G126000 chr5D 94.231 104 2 3 1176 1278 546684167 546684267 4.590000e-34 156.0
14 TraesCS6D01G126000 chr5D 93.204 103 3 3 1173 1274 546686470 546686569 7.680000e-32 148.0
15 TraesCS6D01G126000 chr5D 92.063 63 4 1 1960 2022 496327626 496327565 1.700000e-13 87.9
16 TraesCS6D01G126000 chr4A 95.000 100 3 2 1176 1275 622239359 622239262 4.590000e-34 156.0
17 TraesCS6D01G126000 chr3D 94.118 102 5 1 1181 1281 48419260 48419159 1.650000e-33 154.0
18 TraesCS6D01G126000 chr3D 88.372 129 10 5 1178 1305 48406989 48406865 2.130000e-32 150.0
19 TraesCS6D01G126000 chr3D 93.333 60 3 1 1960 2019 192151808 192151866 1.700000e-13 87.9
20 TraesCS6D01G126000 chr5B 94.949 99 2 2 1176 1274 689883574 689883669 5.930000e-33 152.0
21 TraesCS6D01G126000 chr5B 93.269 104 2 4 1176 1278 689892620 689892719 7.680000e-32 148.0
22 TraesCS6D01G126000 chr3A 94.915 59 2 1 1961 2019 724015784 724015727 1.310000e-14 91.6
23 TraesCS6D01G126000 chr1D 94.915 59 1 2 1960 2018 67387236 67387180 1.310000e-14 91.6
24 TraesCS6D01G126000 chr1D 93.443 61 2 2 1960 2019 391324205 391324146 4.720000e-14 89.8
25 TraesCS6D01G126000 chrUn 93.443 61 3 1 1960 2020 79956713 79956772 4.720000e-14 89.8
26 TraesCS6D01G126000 chr7B 93.333 60 2 2 1960 2019 570220354 570220411 1.700000e-13 87.9
27 TraesCS6D01G126000 chr5A 93.333 60 2 2 1960 2019 631207514 631207457 1.700000e-13 87.9
28 TraesCS6D01G126000 chr2D 93.333 60 3 1 1960 2019 571443345 571443287 1.700000e-13 87.9


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G126000 chr6D 89728953 89732385 3432 False 2208.666667 6340 95.789333 1 3433 3 chr6D.!!$F1 3432
1 TraesCS6D01G126000 chr6A 108175011 108178410 3399 False 928.400000 1982 93.601800 1 3433 5 chr6A.!!$F1 3432
2 TraesCS6D01G126000 chr6B 172260777 172264085 3308 False 969.800000 1838 93.376800 1 3404 5 chr6B.!!$F1 3403

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
887 1042 1.000955 ACACGTCGAGCTGAATTTCCT 59.999 47.619 0.00 0.0 0.00 3.36 F
1969 2146 0.106569 TAAGACCATGGGGCTGCATG 60.107 55.000 18.09 0.0 42.44 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2327 2505 0.118346 TTGCAGAGGAGGTAGGGGAA 59.882 55.0 0.0 0.0 0.00 3.97 R
3048 3245 0.318614 CGCAATGTTTTGGCGAGGTT 60.319 50.0 0.0 0.0 35.68 3.50 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
191 192 3.305720 ACAGTGGAGAGGTCAAGTTGTA 58.694 45.455 2.11 0.00 0.00 2.41
196 197 5.721960 AGTGGAGAGGTCAAGTTGTATGTAT 59.278 40.000 2.11 0.00 0.00 2.29
197 198 6.895756 AGTGGAGAGGTCAAGTTGTATGTATA 59.104 38.462 2.11 0.00 0.00 1.47
198 199 7.068839 AGTGGAGAGGTCAAGTTGTATGTATAG 59.931 40.741 2.11 0.00 0.00 1.31
199 200 6.895756 TGGAGAGGTCAAGTTGTATGTATAGT 59.104 38.462 2.11 0.00 0.00 2.12
222 223 2.310538 ACAACCAGCCTTTTTCCAGAG 58.689 47.619 0.00 0.00 0.00 3.35
270 271 6.566197 ACTGAGAAACTAATGCAGGAAAAG 57.434 37.500 0.00 0.00 0.00 2.27
756 854 4.256920 TGCTTTCTTGATTCCTCTACAGC 58.743 43.478 0.00 0.00 0.00 4.40
803 901 1.435577 TAAAGTCGGCTTTTCGGAGC 58.564 50.000 21.66 0.00 41.78 4.70
858 956 5.955355 AGTCTTGAGGTAAGCTATCTTCTGT 59.045 40.000 0.00 0.00 36.31 3.41
887 1042 1.000955 ACACGTCGAGCTGAATTTCCT 59.999 47.619 0.00 0.00 0.00 3.36
943 1098 4.214971 ACAGTTGTTCTGAATGCATCTGTC 59.785 41.667 14.23 0.00 46.27 3.51
1105 1260 0.618458 TTCCTCGGTCCTCCCATTTG 59.382 55.000 0.00 0.00 0.00 2.32
1150 1322 2.928801 AAAAACAATCAGGGCCCAAC 57.071 45.000 27.56 0.00 0.00 3.77
1151 1323 1.055849 AAAACAATCAGGGCCCAACC 58.944 50.000 27.56 0.00 37.93 3.77
1160 1332 3.683518 GGCCCAACCCCTCCCATT 61.684 66.667 0.00 0.00 0.00 3.16
1161 1333 2.449777 GCCCAACCCCTCCCATTT 59.550 61.111 0.00 0.00 0.00 2.32
1162 1334 1.989508 GCCCAACCCCTCCCATTTG 60.990 63.158 0.00 0.00 0.00 2.32
1163 1335 1.780327 CCCAACCCCTCCCATTTGA 59.220 57.895 0.00 0.00 0.00 2.69
1164 1336 0.116143 CCCAACCCCTCCCATTTGAA 59.884 55.000 0.00 0.00 0.00 2.69
1165 1337 1.560505 CCAACCCCTCCCATTTGAAG 58.439 55.000 0.00 0.00 0.00 3.02
1166 1338 1.077005 CCAACCCCTCCCATTTGAAGA 59.923 52.381 0.00 0.00 0.00 2.87
1167 1339 2.492567 CCAACCCCTCCCATTTGAAGAA 60.493 50.000 0.00 0.00 0.00 2.52
1168 1340 2.562738 CAACCCCTCCCATTTGAAGAAC 59.437 50.000 0.00 0.00 0.00 3.01
1169 1341 1.786441 ACCCCTCCCATTTGAAGAACA 59.214 47.619 0.00 0.00 0.00 3.18
1170 1342 2.178984 ACCCCTCCCATTTGAAGAACAA 59.821 45.455 0.00 0.00 36.65 2.83
1171 1343 2.562738 CCCCTCCCATTTGAAGAACAAC 59.437 50.000 0.00 0.00 38.29 3.32
1172 1344 3.500343 CCCTCCCATTTGAAGAACAACT 58.500 45.455 0.00 0.00 38.29 3.16
1173 1345 3.897505 CCCTCCCATTTGAAGAACAACTT 59.102 43.478 0.00 0.00 42.03 2.66
1282 1458 6.491062 TGAGCTATGGACCCATTTTATGAATG 59.509 38.462 6.88 0.00 37.82 2.67
1284 1460 7.068702 AGCTATGGACCCATTTTATGAATGAA 58.931 34.615 6.88 0.00 37.82 2.57
1378 1555 3.187227 CCTACTCACACATGAACTGTTGC 59.813 47.826 0.00 0.00 35.29 4.17
1382 1559 3.133691 TCACACATGAACTGTTGCTCTC 58.866 45.455 0.00 0.00 35.29 3.20
1399 1576 1.421268 TCTCCTGCAGCTCAAAAGGAA 59.579 47.619 8.66 0.00 38.34 3.36
1526 1703 6.935167 TGAAGGCCTTTTCAAATTATCTTCC 58.065 36.000 21.54 0.77 34.32 3.46
1528 1705 7.235399 TGAAGGCCTTTTCAAATTATCTTCCTT 59.765 33.333 21.54 0.00 34.32 3.36
1590 1767 8.527810 AGTCTATCTATTGCCTTCTAGTATTGC 58.472 37.037 0.00 0.00 0.00 3.56
1592 1769 4.883083 TCTATTGCCTTCTAGTATTGCCG 58.117 43.478 0.00 0.00 0.00 5.69
1641 1818 9.770503 CATTTTAGATGAATGAGTTCAAGTCAG 57.229 33.333 0.53 0.00 46.67 3.51
1691 1868 0.887836 CAGCTGAGCAGTCAAGGCAA 60.888 55.000 8.42 0.00 30.14 4.52
1814 1991 5.494706 AGGGATAAAGTTTCATTCAGGGGTA 59.505 40.000 0.00 0.00 0.00 3.69
1831 2008 3.451402 GGTAATCCCTGGTTTTCCACT 57.549 47.619 0.00 0.00 46.22 4.00
1858 2035 6.575162 AAAGTTTCACATCCCTTGTATGTC 57.425 37.500 0.00 0.00 36.57 3.06
1958 2135 8.645814 TCGACACATTACCTATATAAGACCAT 57.354 34.615 0.00 0.00 0.00 3.55
1959 2136 8.520351 TCGACACATTACCTATATAAGACCATG 58.480 37.037 0.00 0.00 0.00 3.66
1960 2137 7.759886 CGACACATTACCTATATAAGACCATGG 59.240 40.741 11.19 11.19 0.00 3.66
1961 2138 7.918076 ACACATTACCTATATAAGACCATGGG 58.082 38.462 18.09 0.00 0.00 4.00
1962 2139 7.037586 ACACATTACCTATATAAGACCATGGGG 60.038 40.741 18.09 6.52 41.29 4.96
1963 2140 6.069615 ACATTACCTATATAAGACCATGGGGC 60.070 42.308 18.09 7.79 37.90 5.80
1965 2142 3.846588 ACCTATATAAGACCATGGGGCTG 59.153 47.826 18.09 2.06 42.44 4.85
1966 2143 2.887151 ATATAAGACCATGGGGCTGC 57.113 50.000 18.09 0.00 42.44 5.25
1967 2144 1.517238 TATAAGACCATGGGGCTGCA 58.483 50.000 18.09 5.42 42.44 4.41
1968 2145 0.855598 ATAAGACCATGGGGCTGCAT 59.144 50.000 18.09 7.43 42.44 3.96
1969 2146 0.106569 TAAGACCATGGGGCTGCATG 60.107 55.000 18.09 0.00 42.44 4.06
1970 2147 3.534056 GACCATGGGGCTGCATGC 61.534 66.667 18.09 11.82 37.90 4.06
1971 2148 4.385740 ACCATGGGGCTGCATGCA 62.386 61.111 21.29 21.29 45.15 3.96
1972 2149 2.842462 CCATGGGGCTGCATGCAT 60.842 61.111 22.97 1.24 45.15 3.96
1973 2150 2.734591 CATGGGGCTGCATGCATC 59.265 61.111 22.97 17.75 45.15 3.91
1974 2151 2.131067 CATGGGGCTGCATGCATCA 61.131 57.895 22.97 16.82 45.15 3.07
1975 2152 2.131709 ATGGGGCTGCATGCATCAC 61.132 57.895 22.97 18.98 45.15 3.06
1976 2153 2.441532 GGGGCTGCATGCATCACT 60.442 61.111 22.97 0.00 45.15 3.41
1977 2154 2.487532 GGGGCTGCATGCATCACTC 61.488 63.158 22.97 13.64 45.15 3.51
1978 2155 1.453379 GGGCTGCATGCATCACTCT 60.453 57.895 22.97 0.00 45.15 3.24
1979 2156 1.725557 GGGCTGCATGCATCACTCTG 61.726 60.000 22.97 8.76 45.15 3.35
1980 2157 0.746923 GGCTGCATGCATCACTCTGA 60.747 55.000 22.97 0.00 45.15 3.27
1981 2158 1.309950 GCTGCATGCATCACTCTGAT 58.690 50.000 22.97 0.00 42.31 2.90
1993 2170 3.473647 TCTGATGCAGAGGCCCGG 61.474 66.667 0.00 0.00 35.39 5.73
1994 2171 4.559063 CTGATGCAGAGGCCCGGG 62.559 72.222 19.09 19.09 40.13 5.73
1996 2173 4.247380 GATGCAGAGGCCCGGGAG 62.247 72.222 29.31 8.93 40.13 4.30
1998 2175 3.696518 ATGCAGAGGCCCGGGAGTA 62.697 63.158 29.31 7.67 40.13 2.59
1999 2176 3.081409 GCAGAGGCCCGGGAGTAA 61.081 66.667 29.31 0.00 0.00 2.24
2000 2177 2.444256 GCAGAGGCCCGGGAGTAAT 61.444 63.158 29.31 3.37 0.00 1.89
2001 2178 1.749033 CAGAGGCCCGGGAGTAATC 59.251 63.158 29.31 13.64 0.00 1.75
2002 2179 1.459730 AGAGGCCCGGGAGTAATCC 60.460 63.158 29.31 15.45 0.00 3.01
2003 2180 1.459730 GAGGCCCGGGAGTAATCCT 60.460 63.158 29.31 20.77 0.00 3.24
2004 2181 1.004361 AGGCCCGGGAGTAATCCTT 59.996 57.895 29.31 0.00 0.00 3.36
2005 2182 1.054978 AGGCCCGGGAGTAATCCTTC 61.055 60.000 29.31 0.76 0.00 3.46
2006 2183 1.054978 GGCCCGGGAGTAATCCTTCT 61.055 60.000 29.31 0.00 0.00 2.85
2007 2184 0.837940 GCCCGGGAGTAATCCTTCTT 59.162 55.000 29.31 0.00 0.00 2.52
2008 2185 1.212195 GCCCGGGAGTAATCCTTCTTT 59.788 52.381 29.31 0.00 0.00 2.52
2009 2186 2.356844 GCCCGGGAGTAATCCTTCTTTT 60.357 50.000 29.31 0.00 0.00 2.27
2010 2187 3.542648 CCCGGGAGTAATCCTTCTTTTC 58.457 50.000 18.48 0.00 0.00 2.29
2011 2188 3.200165 CCCGGGAGTAATCCTTCTTTTCT 59.800 47.826 18.48 0.00 0.00 2.52
2012 2189 4.407945 CCCGGGAGTAATCCTTCTTTTCTA 59.592 45.833 18.48 0.00 0.00 2.10
2013 2190 5.104652 CCCGGGAGTAATCCTTCTTTTCTAA 60.105 44.000 18.48 0.00 0.00 2.10
2014 2191 6.412214 CCGGGAGTAATCCTTCTTTTCTAAA 58.588 40.000 9.45 0.00 0.00 1.85
2015 2192 6.882678 CCGGGAGTAATCCTTCTTTTCTAAAA 59.117 38.462 9.45 0.00 0.00 1.52
2016 2193 7.392393 CCGGGAGTAATCCTTCTTTTCTAAAAA 59.608 37.037 9.45 0.00 0.00 1.94
2148 2326 2.288579 CGTAGCACTACACAGTTTCCCA 60.289 50.000 8.45 0.00 35.87 4.37
2264 2442 1.053835 TCCCAGACAGACCAGCACAA 61.054 55.000 0.00 0.00 0.00 3.33
2327 2505 3.103742 GAGGAAGAAGACCAGGACATCT 58.896 50.000 0.00 0.00 0.00 2.90
2432 2610 2.183555 GGGCTTCGGGTCGTGTAG 59.816 66.667 0.00 0.00 0.00 2.74
2438 2618 1.271656 CTTCGGGTCGTGTAGAAACCT 59.728 52.381 0.00 0.00 33.42 3.50
2464 2644 5.820423 GTGTGACCACCTTGCATATAATACA 59.180 40.000 0.00 0.00 35.44 2.29
2472 2652 8.632679 CCACCTTGCATATAATACAATGTTTCT 58.367 33.333 0.00 0.00 0.00 2.52
2526 2707 7.136119 TGCTTTATTCTTTGTCCAGTTTAACG 58.864 34.615 0.00 0.00 0.00 3.18
2564 2753 6.096141 TGCAAAAGTAAGTTGGAAGTTGATCA 59.904 34.615 0.00 0.00 0.00 2.92
2809 3004 1.202734 AGAGATGGTTCATCATGCCCG 60.203 52.381 10.08 0.00 42.72 6.13
2887 3082 1.376543 CTGCCACATTGGTCAGCTAG 58.623 55.000 0.00 0.00 40.46 3.42
2893 3088 2.163010 CACATTGGTCAGCTAGCTTTGG 59.837 50.000 16.46 4.07 0.00 3.28
2936 3131 3.058016 CAGTAACAATCTGCCTGTTGTGG 60.058 47.826 0.00 0.00 38.47 4.17
2942 3137 2.949177 TCTGCCTGTTGTGGTTATGT 57.051 45.000 0.00 0.00 0.00 2.29
3033 3230 2.634815 ATAAGGTCAGGCAGATGCAG 57.365 50.000 7.19 0.00 44.36 4.41
3034 3231 0.543277 TAAGGTCAGGCAGATGCAGG 59.457 55.000 7.19 0.00 44.36 4.85
3046 3243 3.071602 GCAGATGCAGGGAAGATAGGTAA 59.928 47.826 0.00 0.00 41.59 2.85
3047 3244 4.263243 GCAGATGCAGGGAAGATAGGTAAT 60.263 45.833 0.00 0.00 41.59 1.89
3048 3245 5.046304 GCAGATGCAGGGAAGATAGGTAATA 60.046 44.000 0.00 0.00 41.59 0.98
3049 3246 6.520742 GCAGATGCAGGGAAGATAGGTAATAA 60.521 42.308 0.00 0.00 41.59 1.40
3078 3275 5.456822 GCCAAAACATTGCGAGAATCTTATC 59.543 40.000 0.00 0.00 0.00 1.75
3079 3276 6.554419 CCAAAACATTGCGAGAATCTTATCA 58.446 36.000 0.00 0.00 0.00 2.15
3080 3277 7.198390 CCAAAACATTGCGAGAATCTTATCAT 58.802 34.615 0.00 0.00 0.00 2.45
3081 3278 7.377928 CCAAAACATTGCGAGAATCTTATCATC 59.622 37.037 0.00 0.00 0.00 2.92
3082 3279 5.835911 ACATTGCGAGAATCTTATCATCG 57.164 39.130 0.00 0.00 36.51 3.84
3083 3280 4.687948 ACATTGCGAGAATCTTATCATCGG 59.312 41.667 0.00 0.00 34.11 4.18
3084 3281 2.677199 TGCGAGAATCTTATCATCGGC 58.323 47.619 0.00 0.00 34.11 5.54
3085 3282 1.996191 GCGAGAATCTTATCATCGGCC 59.004 52.381 0.00 0.00 34.11 6.13
3086 3283 2.353208 GCGAGAATCTTATCATCGGCCT 60.353 50.000 0.00 0.00 34.11 5.19
3087 3284 3.506810 CGAGAATCTTATCATCGGCCTC 58.493 50.000 0.00 0.00 0.00 4.70
3088 3285 3.057245 CGAGAATCTTATCATCGGCCTCA 60.057 47.826 0.00 0.00 0.00 3.86
3089 3286 4.381398 CGAGAATCTTATCATCGGCCTCAT 60.381 45.833 0.00 0.00 0.00 2.90
3090 3287 5.486526 GAGAATCTTATCATCGGCCTCATT 58.513 41.667 0.00 0.00 0.00 2.57
3091 3288 5.243981 AGAATCTTATCATCGGCCTCATTG 58.756 41.667 0.00 0.00 0.00 2.82
3092 3289 3.407424 TCTTATCATCGGCCTCATTGG 57.593 47.619 0.00 0.00 39.35 3.16
3093 3290 2.972021 TCTTATCATCGGCCTCATTGGA 59.028 45.455 0.00 0.00 38.35 3.53
3094 3291 2.839486 TATCATCGGCCTCATTGGAC 57.161 50.000 0.00 0.00 41.70 4.02
3095 3292 0.109342 ATCATCGGCCTCATTGGACC 59.891 55.000 0.00 0.00 42.31 4.46
3096 3293 0.982852 TCATCGGCCTCATTGGACCT 60.983 55.000 0.00 0.00 42.31 3.85
3097 3294 0.758734 CATCGGCCTCATTGGACCTA 59.241 55.000 0.00 0.00 42.31 3.08
3098 3295 1.349026 CATCGGCCTCATTGGACCTAT 59.651 52.381 0.00 0.00 42.31 2.57
3099 3296 0.758734 TCGGCCTCATTGGACCTATG 59.241 55.000 9.42 9.42 42.31 2.23
3100 3297 0.758734 CGGCCTCATTGGACCTATGA 59.241 55.000 16.38 16.38 42.31 2.15
3101 3298 1.270518 CGGCCTCATTGGACCTATGAG 60.271 57.143 28.91 28.91 45.49 2.90
3206 3431 1.835483 GAATCCTGTGCTATGCGGCG 61.835 60.000 0.51 0.51 34.52 6.46
3228 3453 3.125487 GCTTACCGAAAAGAAGAGCCTTC 59.875 47.826 6.79 6.79 0.00 3.46
3229 3454 4.570930 CTTACCGAAAAGAAGAGCCTTCT 58.429 43.478 10.59 10.59 34.29 2.85
3230 3455 3.493767 ACCGAAAAGAAGAGCCTTCTT 57.506 42.857 18.80 18.80 46.22 2.52
3232 3457 4.316645 ACCGAAAAGAAGAGCCTTCTTAC 58.683 43.478 22.51 18.74 43.63 2.34
3233 3458 4.202326 ACCGAAAAGAAGAGCCTTCTTACA 60.202 41.667 22.51 0.00 43.63 2.41
3235 3460 5.106908 CCGAAAAGAAGAGCCTTCTTACAAG 60.107 44.000 22.51 16.10 43.63 3.16
3248 3473 6.601217 GCCTTCTTACAAGGAGATCAAAAGAT 59.399 38.462 4.49 0.00 39.81 2.40
3377 3609 5.105310 TGAGCCTTCTAGTCTTTATGACCAC 60.105 44.000 0.00 0.00 46.46 4.16
3384 3616 1.661112 GTCTTTATGACCACGCTCTGC 59.339 52.381 0.00 0.00 39.69 4.26
3419 3651 7.344871 GCTAGGAGGCTTTATTACCTGGATATA 59.655 40.741 0.00 0.00 36.05 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.618709 AGTTAAGAGCACAACAGCAACC 59.381 45.455 0.00 0.00 36.85 3.77
191 192 8.417273 AAAAAGGCTGGTTGTTTACTATACAT 57.583 30.769 0.00 0.00 0.00 2.29
196 197 5.202004 TGGAAAAAGGCTGGTTGTTTACTA 58.798 37.500 0.00 0.00 0.00 1.82
197 198 4.027437 TGGAAAAAGGCTGGTTGTTTACT 58.973 39.130 0.00 0.00 0.00 2.24
198 199 4.098807 TCTGGAAAAAGGCTGGTTGTTTAC 59.901 41.667 0.00 0.00 0.00 2.01
199 200 4.282496 TCTGGAAAAAGGCTGGTTGTTTA 58.718 39.130 0.00 0.00 0.00 2.01
205 206 0.185901 TGCTCTGGAAAAAGGCTGGT 59.814 50.000 0.00 0.00 0.00 4.00
222 223 5.266336 AACTGAATGTTTTGCAGAGCTTGC 61.266 41.667 12.25 12.25 44.11 4.01
250 251 9.481340 AATTTTCTTTTCCTGCATTAGTTTCTC 57.519 29.630 0.00 0.00 0.00 2.87
256 257 8.822652 AGTTGAATTTTCTTTTCCTGCATTAG 57.177 30.769 0.00 0.00 0.00 1.73
599 697 3.030668 GCAAGTTAGTTGGCTGCATTT 57.969 42.857 0.50 0.00 36.56 2.32
600 698 2.730550 GCAAGTTAGTTGGCTGCATT 57.269 45.000 0.50 0.00 36.56 3.56
756 854 4.511454 TGAATCTTCAGAACCAGTTTCACG 59.489 41.667 0.00 0.00 36.57 4.35
803 901 3.780925 CTTTCAAGCTGCCCGAAAG 57.219 52.632 20.24 20.24 39.59 2.62
822 920 3.065655 CCTCAAGACTCAAGAGCAAGTG 58.934 50.000 0.00 0.00 0.00 3.16
829 927 6.191315 AGATAGCTTACCTCAAGACTCAAGA 58.809 40.000 0.00 0.00 36.22 3.02
830 928 6.463995 AGATAGCTTACCTCAAGACTCAAG 57.536 41.667 0.00 0.00 36.22 3.02
831 929 6.665680 AGAAGATAGCTTACCTCAAGACTCAA 59.334 38.462 0.00 0.00 36.22 3.02
832 930 6.096141 CAGAAGATAGCTTACCTCAAGACTCA 59.904 42.308 0.00 0.00 36.22 3.41
833 931 6.096282 ACAGAAGATAGCTTACCTCAAGACTC 59.904 42.308 0.00 0.00 36.22 3.36
834 932 5.955355 ACAGAAGATAGCTTACCTCAAGACT 59.045 40.000 0.00 0.00 36.22 3.24
835 933 6.215495 ACAGAAGATAGCTTACCTCAAGAC 57.785 41.667 0.00 0.00 36.22 3.01
858 956 1.878088 AGCTCGACGTGTACAGAAGAA 59.122 47.619 0.00 0.00 0.00 2.52
887 1042 1.967319 AGCTGTTTTTCGCCTTCTCA 58.033 45.000 0.00 0.00 0.00 3.27
1134 1306 4.539235 GGTTGGGCCCTGATTGTT 57.461 55.556 25.70 0.00 0.00 2.83
1143 1315 3.252585 AAATGGGAGGGGTTGGGCC 62.253 63.158 0.00 0.00 0.00 5.80
1144 1316 1.989508 CAAATGGGAGGGGTTGGGC 60.990 63.158 0.00 0.00 0.00 5.36
1145 1317 0.116143 TTCAAATGGGAGGGGTTGGG 59.884 55.000 0.00 0.00 0.00 4.12
1146 1318 1.077005 TCTTCAAATGGGAGGGGTTGG 59.923 52.381 0.00 0.00 0.00 3.77
1147 1319 2.562738 GTTCTTCAAATGGGAGGGGTTG 59.437 50.000 0.00 0.00 0.00 3.77
1148 1320 2.178984 TGTTCTTCAAATGGGAGGGGTT 59.821 45.455 0.00 0.00 0.00 4.11
1149 1321 1.786441 TGTTCTTCAAATGGGAGGGGT 59.214 47.619 0.00 0.00 0.00 4.95
1150 1322 2.562738 GTTGTTCTTCAAATGGGAGGGG 59.437 50.000 0.00 0.00 37.81 4.79
1151 1323 3.500343 AGTTGTTCTTCAAATGGGAGGG 58.500 45.455 0.00 0.00 37.81 4.30
1189 1361 2.037902 CGGTTGGGCCCTAATTGTTTTT 59.962 45.455 25.70 0.00 0.00 1.94
1190 1362 1.621317 CGGTTGGGCCCTAATTGTTTT 59.379 47.619 25.70 0.00 0.00 2.43
1191 1363 1.262417 CGGTTGGGCCCTAATTGTTT 58.738 50.000 25.70 0.00 0.00 2.83
1192 1364 0.613572 CCGGTTGGGCCCTAATTGTT 60.614 55.000 25.70 0.00 0.00 2.83
1294 1470 9.926751 CATAAGCACAATACTTTGAGTAGAATG 57.073 33.333 0.00 0.00 33.66 2.67
1356 1532 3.187227 GCAACAGTTCATGTGTGAGTAGG 59.813 47.826 0.00 0.00 43.00 3.18
1362 1538 2.225019 GGAGAGCAACAGTTCATGTGTG 59.775 50.000 0.00 0.00 43.00 3.82
1378 1555 1.002888 TCCTTTTGAGCTGCAGGAGAG 59.997 52.381 17.12 0.00 31.45 3.20
1382 1559 1.321474 TGTTCCTTTTGAGCTGCAGG 58.679 50.000 17.12 0.00 0.00 4.85
1399 1576 4.026052 GGAACCCAATTTCCATCTCATGT 58.974 43.478 0.00 0.00 44.14 3.21
1577 1754 2.890808 TCAGCGGCAATACTAGAAGG 57.109 50.000 1.45 0.00 0.00 3.46
1590 1767 0.747644 TGCACATTACCCATCAGCGG 60.748 55.000 0.00 0.00 0.00 5.52
1592 1769 2.428171 ACAATGCACATTACCCATCAGC 59.572 45.455 0.00 0.00 0.00 4.26
1791 1968 4.610333 ACCCCTGAATGAAACTTTATCCC 58.390 43.478 0.00 0.00 0.00 3.85
1814 1991 4.463050 TTACAGTGGAAAACCAGGGATT 57.537 40.909 0.00 0.00 0.00 3.01
1822 1999 7.222031 GGATGTGAAACTTTTACAGTGGAAAAC 59.778 37.037 9.29 0.36 38.04 2.43
1831 2008 7.504238 ACATACAAGGGATGTGAAACTTTTACA 59.496 33.333 1.91 1.91 43.77 2.41
1858 2035 1.676635 CCAGGCCCACATGTGAGTG 60.677 63.158 27.46 16.42 39.21 3.51
1883 2060 1.072173 TCATGACACTGACAAGGTGGG 59.928 52.381 0.00 0.00 38.83 4.61
1937 2114 7.338710 CCCCATGGTCTTATATAGGTAATGTG 58.661 42.308 11.73 0.00 0.00 3.21
1940 2117 6.158695 CAGCCCCATGGTCTTATATAGGTAAT 59.841 42.308 11.73 0.00 0.00 1.89
1953 2130 3.534056 GCATGCAGCCCCATGGTC 61.534 66.667 14.21 1.73 42.18 4.02
1958 2135 2.756691 GTGATGCATGCAGCCCCA 60.757 61.111 31.30 19.49 44.83 4.96
1959 2136 2.441532 AGTGATGCATGCAGCCCC 60.442 61.111 31.30 21.66 44.83 5.80
1960 2137 1.453379 AGAGTGATGCATGCAGCCC 60.453 57.895 31.30 21.81 44.83 5.19
1961 2138 0.746923 TCAGAGTGATGCATGCAGCC 60.747 55.000 31.30 22.08 44.83 4.85
1962 2139 1.002359 CATCAGAGTGATGCATGCAGC 60.002 52.381 28.44 28.44 46.37 5.25
1976 2153 3.473647 CCGGGCCTCTGCATCAGA 61.474 66.667 0.84 0.00 38.25 3.27
1977 2154 4.559063 CCCGGGCCTCTGCATCAG 62.559 72.222 8.08 0.00 40.13 2.90
1979 2156 4.247380 CTCCCGGGCCTCTGCATC 62.247 72.222 18.49 0.00 40.13 3.91
1980 2157 3.696518 TACTCCCGGGCCTCTGCAT 62.697 63.158 18.49 0.00 40.13 3.96
1981 2158 3.916438 TTACTCCCGGGCCTCTGCA 62.916 63.158 18.49 0.00 40.13 4.41
1982 2159 2.384653 GATTACTCCCGGGCCTCTGC 62.385 65.000 18.49 0.00 0.00 4.26
1983 2160 1.749033 GATTACTCCCGGGCCTCTG 59.251 63.158 18.49 5.65 0.00 3.35
1984 2161 1.459730 GGATTACTCCCGGGCCTCT 60.460 63.158 18.49 0.00 35.28 3.69
1985 2162 1.054978 AAGGATTACTCCCGGGCCTC 61.055 60.000 18.49 7.33 43.21 4.70
1986 2163 1.004361 AAGGATTACTCCCGGGCCT 59.996 57.895 18.49 13.08 43.21 5.19
1987 2164 1.054978 AGAAGGATTACTCCCGGGCC 61.055 60.000 18.49 10.50 43.21 5.80
1988 2165 0.837940 AAGAAGGATTACTCCCGGGC 59.162 55.000 18.49 0.00 43.21 6.13
1989 2166 3.200165 AGAAAAGAAGGATTACTCCCGGG 59.800 47.826 16.85 16.85 43.21 5.73
1990 2167 4.489306 AGAAAAGAAGGATTACTCCCGG 57.511 45.455 0.00 0.00 43.21 5.73
1991 2168 7.916914 TTTTAGAAAAGAAGGATTACTCCCG 57.083 36.000 0.00 0.00 43.21 5.14
2014 2191 8.598041 CAGAGGCATAGTCCTATATAGGTTTTT 58.402 37.037 25.06 13.21 44.02 1.94
2015 2192 7.735321 ACAGAGGCATAGTCCTATATAGGTTTT 59.265 37.037 25.06 15.25 44.02 2.43
2016 2193 7.249715 ACAGAGGCATAGTCCTATATAGGTTT 58.750 38.462 25.06 17.33 44.02 3.27
2017 2194 6.806217 ACAGAGGCATAGTCCTATATAGGTT 58.194 40.000 25.06 17.63 44.02 3.50
2027 2204 3.808728 TGCAATAACAGAGGCATAGTCC 58.191 45.455 0.00 0.00 0.00 3.85
2148 2326 4.159557 AGTAAACATGGAGGCAACCAATT 58.840 39.130 7.45 6.36 43.47 2.32
2264 2442 2.366570 GGGCAGGAGGAGGACTCT 59.633 66.667 0.00 0.00 45.83 3.24
2327 2505 0.118346 TTGCAGAGGAGGTAGGGGAA 59.882 55.000 0.00 0.00 0.00 3.97
2333 2511 3.921104 AGATGATCTTGCAGAGGAGGTA 58.079 45.455 0.00 0.00 0.00 3.08
2464 2644 3.660669 TCCCTCCCTAAACCAGAAACATT 59.339 43.478 0.00 0.00 0.00 2.71
2472 2652 0.494551 TCACCTCCCTCCCTAAACCA 59.505 55.000 0.00 0.00 0.00 3.67
2526 2707 4.006780 ACTTTTGCATTTCCAACCATCC 57.993 40.909 0.00 0.00 0.00 3.51
2564 2753 6.173427 ACCAAAGCTTTATGGACAAACATT 57.827 33.333 21.51 0.00 39.12 2.71
2667 2862 6.765036 GTCATGATCATTGACATTACTCTGGT 59.235 38.462 22.62 0.00 33.20 4.00
2809 3004 3.316308 ACATGGCTCTTGAACAAAGTGAC 59.684 43.478 0.00 0.00 37.82 3.67
2887 3082 1.868469 TGCAAAATGCTGACCAAAGC 58.132 45.000 3.78 0.00 45.31 3.51
2893 3088 3.248266 GACCTGATTGCAAAATGCTGAC 58.752 45.455 1.71 0.00 45.31 3.51
2909 3104 3.005554 CAGGCAGATTGTTACTGACCTG 58.994 50.000 16.82 16.82 43.67 4.00
2936 3131 1.936547 GACAGGCTGCAGCTACATAAC 59.063 52.381 35.82 18.70 41.70 1.89
2942 3137 0.906756 AGGAAGACAGGCTGCAGCTA 60.907 55.000 35.82 0.00 41.70 3.32
3003 3200 4.721776 TGCCTGACCTTATAAACCATCTCT 59.278 41.667 0.00 0.00 0.00 3.10
3046 3243 2.415357 CGCAATGTTTTGGCGAGGTTAT 60.415 45.455 0.00 0.00 35.68 1.89
3047 3244 1.068885 CGCAATGTTTTGGCGAGGTTA 60.069 47.619 0.00 0.00 35.68 2.85
3048 3245 0.318614 CGCAATGTTTTGGCGAGGTT 60.319 50.000 0.00 0.00 35.68 3.50
3049 3246 1.169661 TCGCAATGTTTTGGCGAGGT 61.170 50.000 3.63 0.00 36.87 3.85
3078 3275 0.758734 TAGGTCCAATGAGGCCGATG 59.241 55.000 0.00 0.00 38.25 3.84
3079 3276 1.349026 CATAGGTCCAATGAGGCCGAT 59.651 52.381 0.00 0.00 38.25 4.18
3080 3277 0.758734 CATAGGTCCAATGAGGCCGA 59.241 55.000 0.00 0.00 38.25 5.54
3081 3278 0.758734 TCATAGGTCCAATGAGGCCG 59.241 55.000 0.00 0.00 38.25 6.13
3082 3279 2.557920 CTCATAGGTCCAATGAGGCC 57.442 55.000 0.00 0.00 44.34 5.19
3086 3283 3.197766 GGTCACACTCATAGGTCCAATGA 59.802 47.826 0.00 0.00 32.56 2.57
3087 3284 3.055167 TGGTCACACTCATAGGTCCAATG 60.055 47.826 0.00 0.00 0.00 2.82
3088 3285 3.181329 TGGTCACACTCATAGGTCCAAT 58.819 45.455 0.00 0.00 0.00 3.16
3089 3286 2.615391 TGGTCACACTCATAGGTCCAA 58.385 47.619 0.00 0.00 0.00 3.53
3090 3287 2.319025 TGGTCACACTCATAGGTCCA 57.681 50.000 0.00 0.00 0.00 4.02
3091 3288 4.202264 CCTTATGGTCACACTCATAGGTCC 60.202 50.000 0.00 0.00 0.00 4.46
3092 3289 4.406003 ACCTTATGGTCACACTCATAGGTC 59.594 45.833 0.00 0.00 44.78 3.85
3093 3290 4.362677 ACCTTATGGTCACACTCATAGGT 58.637 43.478 0.00 0.00 44.78 3.08
3094 3291 6.479972 TTACCTTATGGTCACACTCATAGG 57.520 41.667 3.06 0.00 44.78 2.57
3095 3292 7.492669 CACTTTACCTTATGGTCACACTCATAG 59.507 40.741 3.06 0.00 44.78 2.23
3096 3293 7.179516 TCACTTTACCTTATGGTCACACTCATA 59.820 37.037 3.06 0.00 44.78 2.15
3097 3294 6.013725 TCACTTTACCTTATGGTCACACTCAT 60.014 38.462 3.06 0.00 44.78 2.90
3098 3295 5.305902 TCACTTTACCTTATGGTCACACTCA 59.694 40.000 3.06 0.00 44.78 3.41
3099 3296 5.790593 TCACTTTACCTTATGGTCACACTC 58.209 41.667 3.06 0.00 44.78 3.51
3100 3297 5.280011 CCTCACTTTACCTTATGGTCACACT 60.280 44.000 3.06 0.00 44.78 3.55
3101 3298 4.935808 CCTCACTTTACCTTATGGTCACAC 59.064 45.833 3.06 0.00 44.78 3.82
3206 3431 2.701107 AGGCTCTTCTTTTCGGTAAGC 58.299 47.619 0.00 0.00 0.00 3.09
3228 3453 8.558973 AAGTCATCTTTTGATCTCCTTGTAAG 57.441 34.615 0.00 0.00 36.97 2.34
3229 3454 8.924511 AAAGTCATCTTTTGATCTCCTTGTAA 57.075 30.769 0.00 0.00 40.50 2.41
3255 3480 6.745794 ATGGTGAAAAAGGAATCCTTCAAA 57.254 33.333 15.81 2.20 43.92 2.69
3256 3481 8.434589 AATATGGTGAAAAAGGAATCCTTCAA 57.565 30.769 15.81 0.00 43.92 2.69
3377 3609 0.457853 TAGCTAAACGTGGCAGAGCG 60.458 55.000 10.26 0.00 38.20 5.03
3384 3616 0.824759 AGCCTCCTAGCTAAACGTGG 59.175 55.000 0.00 0.00 42.70 4.94


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

AutoCloner maintained by Alex Coulton.