Multiple sequence alignment - TraesCS1D01G102800

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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 TraesCS1D01G102800 chr1D 100.000 2267 0 0 1 2267 92054256 92056522 0.000000e+00 4187.0
1 TraesCS1D01G102800 chr1D 88.948 2063 169 22 1 2056 392033405 392035415 0.000000e+00 2492.0
2 TraesCS1D01G102800 chr1D 81.716 268 30 12 2009 2264 427305662 427305922 2.950000e-49 206.0
3 TraesCS1D01G102800 chr5D 89.609 2300 182 37 1 2261 522787161 522789442 0.000000e+00 2870.0
4 TraesCS1D01G102800 chr5D 88.756 2259 191 22 3 2235 517099000 517101221 0.000000e+00 2706.0
5 TraesCS1D01G102800 chr5D 92.301 1221 88 5 445 1660 46684446 46683227 0.000000e+00 1729.0
6 TraesCS1D01G102800 chr5D 82.157 510 65 16 1656 2157 508239999 508240490 4.510000e-112 414.0
7 TraesCS1D01G102800 chr5D 80.905 199 25 7 1982 2169 452399441 452399245 6.530000e-31 145.0
8 TraesCS1D01G102800 chr5D 80.000 155 20 3 1985 2129 517101064 517101217 1.110000e-18 104.0
9 TraesCS1D01G102800 chr3D 90.052 2111 174 23 53 2151 445802580 445804666 0.000000e+00 2702.0
10 TraesCS1D01G102800 chr3D 83.070 443 60 11 1734 2165 416000235 416000673 2.730000e-104 388.0
11 TraesCS1D01G102800 chr3D 100.000 28 0 0 2142 2169 16220264 16220237 4.000000e-03 52.8
12 TraesCS1D01G102800 chr3B 88.305 2283 223 21 3 2257 213720117 213717851 0.000000e+00 2697.0
13 TraesCS1D01G102800 chr7D 91.748 1951 132 13 3 1937 411315782 411313845 0.000000e+00 2684.0
14 TraesCS1D01G102800 chr7D 86.592 179 22 2 2080 2256 411313411 411313233 1.780000e-46 196.0
15 TraesCS1D01G102800 chr7D 82.418 91 10 6 2013 2101 226109583 226109669 8.680000e-10 75.0
16 TraesCS1D01G102800 chr2B 90.852 1913 151 10 3 1899 747523235 747525139 0.000000e+00 2542.0
17 TraesCS1D01G102800 chr5B 92.282 1788 123 10 1 1786 586297991 586296217 0.000000e+00 2523.0
18 TraesCS1D01G102800 chr5B 89.161 286 25 6 1688 1971 539159447 539159166 3.580000e-93 351.0
19 TraesCS1D01G102800 chr5B 92.188 64 5 0 2074 2137 595179975 595179912 8.620000e-15 91.6
20 TraesCS1D01G102800 chr5A 86.849 2304 216 43 1 2264 602717949 602720205 0.000000e+00 2495.0
21 TraesCS1D01G102800 chr5A 93.108 798 45 8 2 797 353196027 353196816 0.000000e+00 1160.0
22 TraesCS1D01G102800 chr7B 89.401 1821 161 15 3 1819 122756894 122758686 0.000000e+00 2265.0
23 TraesCS1D01G102800 chr1B 92.234 1249 88 4 3 1249 425364736 425365977 0.000000e+00 1760.0
24 TraesCS1D01G102800 chr1B 83.333 156 23 2 2109 2264 425601384 425601536 8.440000e-30 141.0
25 TraesCS1D01G102800 chr4A 91.658 959 74 4 2 960 692682096 692681144 0.000000e+00 1323.0
26 TraesCS1D01G102800 chr2D 88.718 780 62 15 1299 2054 586863410 586862633 0.000000e+00 929.0
27 TraesCS1D01G102800 chr2D 87.048 332 26 7 1711 2039 12846092 12846409 2.140000e-95 359.0
28 TraesCS1D01G102800 chr2D 86.111 144 17 3 2013 2154 314478175 314478033 3.900000e-33 152.0
29 TraesCS1D01G102800 chr6D 83.273 275 29 10 1911 2172 421612598 421612868 1.050000e-58 237.0
30 TraesCS1D01G102800 chr6D 78.138 247 39 12 2013 2255 364527521 364527756 2.350000e-30 143.0


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 TraesCS1D01G102800 chr1D 92054256 92056522 2266 False 4187 4187 100.000 1 2267 1 chr1D.!!$F1 2266
1 TraesCS1D01G102800 chr1D 392033405 392035415 2010 False 2492 2492 88.948 1 2056 1 chr1D.!!$F2 2055
2 TraesCS1D01G102800 chr5D 522787161 522789442 2281 False 2870 2870 89.609 1 2261 1 chr5D.!!$F2 2260
3 TraesCS1D01G102800 chr5D 46683227 46684446 1219 True 1729 1729 92.301 445 1660 1 chr5D.!!$R1 1215
4 TraesCS1D01G102800 chr5D 517099000 517101221 2221 False 1405 2706 84.378 3 2235 2 chr5D.!!$F3 2232
5 TraesCS1D01G102800 chr3D 445802580 445804666 2086 False 2702 2702 90.052 53 2151 1 chr3D.!!$F2 2098
6 TraesCS1D01G102800 chr3B 213717851 213720117 2266 True 2697 2697 88.305 3 2257 1 chr3B.!!$R1 2254
7 TraesCS1D01G102800 chr7D 411313233 411315782 2549 True 1440 2684 89.170 3 2256 2 chr7D.!!$R1 2253
8 TraesCS1D01G102800 chr2B 747523235 747525139 1904 False 2542 2542 90.852 3 1899 1 chr2B.!!$F1 1896
9 TraesCS1D01G102800 chr5B 586296217 586297991 1774 True 2523 2523 92.282 1 1786 1 chr5B.!!$R2 1785
10 TraesCS1D01G102800 chr5A 602717949 602720205 2256 False 2495 2495 86.849 1 2264 1 chr5A.!!$F2 2263
11 TraesCS1D01G102800 chr5A 353196027 353196816 789 False 1160 1160 93.108 2 797 1 chr5A.!!$F1 795
12 TraesCS1D01G102800 chr7B 122756894 122758686 1792 False 2265 2265 89.401 3 1819 1 chr7B.!!$F1 1816
13 TraesCS1D01G102800 chr1B 425364736 425365977 1241 False 1760 1760 92.234 3 1249 1 chr1B.!!$F1 1246
14 TraesCS1D01G102800 chr4A 692681144 692682096 952 True 1323 1323 91.658 2 960 1 chr4A.!!$R1 958
15 TraesCS1D01G102800 chr2D 586862633 586863410 777 True 929 929 88.718 1299 2054 1 chr2D.!!$R2 755

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
305 306 0.685131 ATCCGATGGTACCACCGTGA 60.685 55.0 26.83 22.2 42.58 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2062 2414 0.035881 TGAGAGGCAGCAGAACAAGG 59.964 55.0 0.0 0.0 0.0 3.61 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
21 22 2.576615 GGCCAAATGGATAGGTGAGAC 58.423 52.381 2.98 0.00 37.39 3.36
100 101 5.753744 TCGCGTCAACAAATCATTAGTTTT 58.246 33.333 5.77 0.00 0.00 2.43
158 159 2.258726 GGCACAACAAGGGACGACC 61.259 63.158 0.00 0.00 40.67 4.79
305 306 0.685131 ATCCGATGGTACCACCGTGA 60.685 55.000 26.83 22.20 42.58 4.35
499 503 4.482990 TGGATGATCTAGCTGGATACACA 58.517 43.478 13.16 7.45 46.17 3.72
552 556 1.072331 GGAGGCACCGGACATCAATAT 59.928 52.381 9.46 0.00 0.00 1.28
594 598 3.761752 CCGGGACACAATGTTAGGAAATT 59.238 43.478 0.00 0.00 0.00 1.82
631 635 1.021390 CCGATGCCAACACTCCAGAC 61.021 60.000 0.00 0.00 0.00 3.51
779 789 2.026262 GGACAAGGAGGCACTATTGGAA 60.026 50.000 0.00 0.00 41.55 3.53
928 939 9.581099 ACTTAAATTTATTGGCTTAATTCGGTG 57.419 29.630 0.00 0.00 0.00 4.94
1041 1056 3.015145 AGGCCCCCGTGTGCTAAT 61.015 61.111 0.00 0.00 0.00 1.73
1071 1086 3.213506 CATGTTGGACAAGTGGACAGAA 58.786 45.455 0.00 0.00 0.00 3.02
1136 1151 4.979335 TCATGTTGGTGTGGAGATGTTTA 58.021 39.130 0.00 0.00 0.00 2.01
1214 1230 2.513753 TGTTTGTCCCAACTATGCCTG 58.486 47.619 0.00 0.00 0.00 4.85
1296 1312 3.997021 AGAGTATTCAACCGTTGCTTCAG 59.003 43.478 6.37 0.00 0.00 3.02
1359 1378 4.509737 GTAGTCGCCGCCTCCACC 62.510 72.222 0.00 0.00 0.00 4.61
1384 1403 8.258007 CCTTGTAAGTACTTCACATGGATAGAA 58.742 37.037 25.74 9.73 38.92 2.10
1508 1527 3.832490 TCGTGAAAAGGAGAAGATGGAGA 59.168 43.478 0.00 0.00 0.00 3.71
1518 1537 4.081198 GGAGAAGATGGAGAGAAAGAAGCA 60.081 45.833 0.00 0.00 0.00 3.91
1523 1542 4.715792 AGATGGAGAGAAAGAAGCATGAGA 59.284 41.667 0.00 0.00 0.00 3.27
1533 1554 1.344191 AAGCATGAGAGGAGAGGGCC 61.344 60.000 0.00 0.00 0.00 5.80
1539 1560 3.717294 GAGGAGAGGGCCCGCAAA 61.717 66.667 28.68 0.00 0.00 3.68
1558 1579 4.805192 GCAAACAGAAGATTGCTTGTGAAA 59.195 37.500 9.38 0.00 45.48 2.69
1575 1598 5.192927 TGTGAAAAGGAGAGAGCAAGAAAA 58.807 37.500 0.00 0.00 0.00 2.29
1594 1617 0.250901 ACTTGCAAGGGCTCGTGAAT 60.251 50.000 29.18 2.15 41.91 2.57
1598 1621 1.815421 CAAGGGCTCGTGAATCCCG 60.815 63.158 0.00 0.00 44.70 5.14
1628 1651 0.512952 GATGCACGCGACAAGAAAGT 59.487 50.000 15.93 0.00 0.00 2.66
1660 1683 2.158385 TGTGTGACCCAATAAGGCCTTT 60.158 45.455 26.08 8.91 35.39 3.11
1824 1933 8.394971 ACTTGTGATGAAACTATGTCATGAAA 57.605 30.769 0.00 0.00 35.84 2.69
1841 1961 7.975058 TGTCATGAAATATATTTGTTGTGCTGG 59.025 33.333 15.39 0.00 0.00 4.85
1888 2021 9.123902 TGAAATGATGAAGAAGAAAAACAGAGA 57.876 29.630 0.00 0.00 0.00 3.10
1926 2064 3.834799 CCCTACCGCCAGACGTCC 61.835 72.222 13.01 0.00 41.42 4.79
1944 2082 1.968493 TCCTGGCGGTAGGATATGAAC 59.032 52.381 0.00 0.00 41.85 3.18
1946 2084 1.691976 CTGGCGGTAGGATATGAACCA 59.308 52.381 0.00 0.00 32.55 3.67
1983 2121 0.685458 GGCGGTAGGGTGGAGAACTA 60.685 60.000 0.00 0.00 0.00 2.24
2040 2280 4.123545 GGCCACCCTACCGCCAAT 62.124 66.667 0.00 0.00 42.52 3.16
2081 2433 0.035881 CCTTGTTCTGCTGCCTCTCA 59.964 55.000 0.00 0.00 0.00 3.27
2123 2475 3.976701 CTGCGGTAGGGTTGGCCAG 62.977 68.421 5.11 0.00 36.17 4.85
2170 2522 2.160171 TTGGCCACCCTACTGCCTT 61.160 57.895 3.88 0.00 45.56 4.35
2173 2525 1.250840 GGCCACCCTACTGCCTTTTG 61.251 60.000 0.00 0.00 42.01 2.44
2185 2650 1.423541 TGCCTTTTGTTGCCTCTCCTA 59.576 47.619 0.00 0.00 0.00 2.94
2224 2689 2.046314 CTGTGGTAGGGTTGGCCG 60.046 66.667 0.00 0.00 34.97 6.13
2225 2690 2.850130 TGTGGTAGGGTTGGCCGT 60.850 61.111 0.00 0.00 36.71 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 6.523840 TCAACTTTGAAGGGAAATTCCATTG 58.476 36.000 17.16 4.87 41.11 2.82
158 159 2.753452 ACACTACTCCACCGTATGTCAG 59.247 50.000 0.00 0.00 0.00 3.51
227 228 1.869767 CGAGCAAGGCCAATGATACTC 59.130 52.381 5.01 5.18 0.00 2.59
305 306 2.559668 CCAATGTGAACTCATGCAACCT 59.440 45.455 0.00 0.00 0.00 3.50
499 503 3.071312 TGCTGCCAAATTGTTTCATTCCT 59.929 39.130 0.00 0.00 0.00 3.36
552 556 2.557924 GGCTCATCACATTGACCACAAA 59.442 45.455 0.00 0.00 39.54 2.83
594 598 1.104577 GGTCCGTGGCTTTTTGGTGA 61.105 55.000 0.00 0.00 0.00 4.02
779 789 1.078528 TCGACCATCCTCCACACCT 59.921 57.895 0.00 0.00 0.00 4.00
838 848 4.039245 TCAATAGGCCTTCCTCTATCAACG 59.961 45.833 12.58 0.00 43.06 4.10
1041 1056 1.080093 GTCCAACATGTCCTCGCGA 60.080 57.895 9.26 9.26 0.00 5.87
1071 1086 3.562176 CCTTCACCTTATCCAACTTGGCT 60.562 47.826 2.52 0.00 37.47 4.75
1214 1230 0.526662 AGTTGGACGAGGACGATCAC 59.473 55.000 0.00 0.00 42.66 3.06
1296 1312 7.272978 TGGTCATTAGTAAGATAGGTTCAAGC 58.727 38.462 0.00 0.00 0.00 4.01
1359 1378 9.088512 GTTCTATCCATGTGAAGTACTTACAAG 57.911 37.037 8.42 9.96 0.00 3.16
1384 1403 3.430042 ACATCTTCTGGCACATCTTGT 57.570 42.857 0.00 0.00 38.20 3.16
1474 1493 1.336877 TTTCACGACGCTCTTCATCG 58.663 50.000 0.00 0.00 41.60 3.84
1508 1527 3.451902 CCTCTCCTCTCATGCTTCTTTCT 59.548 47.826 0.00 0.00 0.00 2.52
1518 1537 2.123077 CGGGCCCTCTCCTCTCAT 60.123 66.667 22.43 0.00 0.00 2.90
1523 1542 4.035102 GTTTGCGGGCCCTCTCCT 62.035 66.667 22.43 0.00 0.00 3.69
1539 1560 4.889409 TCCTTTTCACAAGCAATCTTCTGT 59.111 37.500 0.00 0.00 0.00 3.41
1552 1573 4.422073 TTCTTGCTCTCTCCTTTTCACA 57.578 40.909 0.00 0.00 0.00 3.58
1575 1598 0.250901 ATTCACGAGCCCTTGCAAGT 60.251 50.000 24.35 6.74 41.13 3.16
1594 1617 0.829602 GCATCATCCTCCTCTCGGGA 60.830 60.000 0.00 0.00 42.77 5.14
1598 1621 0.599728 GCGTGCATCATCCTCCTCTC 60.600 60.000 0.00 0.00 0.00 3.20
1611 1634 1.573026 TTACTTTCTTGTCGCGTGCA 58.427 45.000 5.77 3.73 0.00 4.57
1628 1651 2.243810 GGGTCACACAAGGCCATTTTA 58.756 47.619 5.01 0.00 0.00 1.52
1660 1683 7.548196 AGTTCATGACTAGTTTTTCGAAACA 57.452 32.000 10.79 0.25 36.65 2.83
1824 1933 6.208402 TCACAACACCAGCACAACAAATATAT 59.792 34.615 0.00 0.00 0.00 0.86
1841 1961 4.391830 TCAAGACAAGTCAAGTCACAACAC 59.608 41.667 2.72 0.00 38.46 3.32
1900 2038 3.799755 GCGGTAGGGTGCAAAGCG 61.800 66.667 0.00 0.00 37.20 4.68
1926 2064 1.691976 TGGTTCATATCCTACCGCCAG 59.308 52.381 0.00 0.00 34.62 4.85
1944 2082 1.201429 AAGGCCTCTGGTGGTAGTGG 61.201 60.000 5.23 0.00 35.07 4.00
1946 2084 1.201429 CCAAGGCCTCTGGTGGTAGT 61.201 60.000 20.06 0.00 0.00 2.73
1983 2121 1.671742 AGCGTTTCGGTCACAGGAT 59.328 52.632 0.00 0.00 29.31 3.24
2062 2414 0.035881 TGAGAGGCAGCAGAACAAGG 59.964 55.000 0.00 0.00 0.00 3.61
2064 2416 1.072806 ACATGAGAGGCAGCAGAACAA 59.927 47.619 0.00 0.00 0.00 2.83
2123 2475 0.394352 CATGTCCCTTGGTGGTAGGC 60.394 60.000 0.00 0.00 0.00 3.93
2165 2517 0.185901 AGGAGAGGCAACAAAAGGCA 59.814 50.000 0.00 0.00 41.41 4.75
2170 2522 2.642311 TGGTCATAGGAGAGGCAACAAA 59.358 45.455 0.00 0.00 41.41 2.83
2173 2525 3.567478 ATTGGTCATAGGAGAGGCAAC 57.433 47.619 0.00 0.00 0.00 4.17
2235 2700 2.192175 CCTACCGCCATGAACCCC 59.808 66.667 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.