Multiple sequence alignment - TraesCS2D01G223300

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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 TraesCS2D01G223300 chr2D 100.000 3604 0 0 1 3604 190353636 190350033 0.000000e+00 6656.0
1 TraesCS2D01G223300 chr2D 94.175 103 6 0 2185 2287 305515034 305514932 1.340000e-34 158.0
2 TraesCS2D01G223300 chr2B 93.685 2312 117 13 1 2287 247388840 247386533 0.000000e+00 3434.0
3 TraesCS2D01G223300 chr2B 98.109 1322 24 1 2283 3604 247386492 247385172 0.000000e+00 2302.0
4 TraesCS2D01G223300 chr2A 95.104 1777 79 4 1 1769 204884883 204883107 0.000000e+00 2793.0
5 TraesCS2D01G223300 chr2A 95.315 1238 45 5 2370 3604 204873921 204872694 0.000000e+00 1953.0
6 TraesCS2D01G223300 chr2A 92.000 775 52 8 1418 2190 204654491 204653725 0.000000e+00 1079.0
7 TraesCS2D01G223300 chr3D 96.040 101 4 0 2187 2287 410670226 410670126 8.010000e-37 165.0
8 TraesCS2D01G223300 chr1B 96.040 101 4 0 2187 2287 488538936 488539036 8.010000e-37 165.0
9 TraesCS2D01G223300 chr7D 96.000 100 4 0 2188 2287 414094934 414094835 2.880000e-36 163.0
10 TraesCS2D01G223300 chr4D 96.040 101 3 1 2187 2287 58643755 58643854 2.880000e-36 163.0
11 TraesCS2D01G223300 chr3B 95.960 99 4 0 2189 2287 540175090 540174992 1.040000e-35 161.0
12 TraesCS2D01G223300 chr3B 92.035 113 8 1 2176 2287 622764135 622764023 1.340000e-34 158.0
13 TraesCS2D01G223300 chr6B 90.756 119 8 2 2188 2305 561700717 561700601 4.820000e-34 156.0
14 TraesCS2D01G223300 chr6D 96.774 31 1 0 2283 2313 18879696 18879666 7.000000e-03 52.8


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 TraesCS2D01G223300 chr2D 190350033 190353636 3603 True 6656 6656 100.000 1 3604 1 chr2D.!!$R1 3603
1 TraesCS2D01G223300 chr2B 247385172 247388840 3668 True 2868 3434 95.897 1 3604 2 chr2B.!!$R1 3603
2 TraesCS2D01G223300 chr2A 204883107 204884883 1776 True 2793 2793 95.104 1 1769 1 chr2A.!!$R3 1768
3 TraesCS2D01G223300 chr2A 204872694 204873921 1227 True 1953 1953 95.315 2370 3604 1 chr2A.!!$R2 1234
4 TraesCS2D01G223300 chr2A 204653725 204654491 766 True 1079 1079 92.000 1418 2190 1 chr2A.!!$R1 772

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
961 984 2.939103 GCTTCATGAGTACTTCCGCAAT 59.061 45.455 0.00 0.0 0.00 3.56 F
1138 1164 0.393077 CCTTGTATCCCTCGCCGAAT 59.607 55.000 0.00 0.0 0.00 3.34 F
1159 1185 0.901124 ACTGTTTGCCAAAGCCACAA 59.099 45.000 0.00 0.0 38.69 3.33 F
1729 1755 1.658596 GCACATTGCGTTATGAGACGA 59.341 47.619 1.15 0.0 45.47 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2227 2255 3.057456 GCTCCGTATGTAGTCCATAGTGG 60.057 52.174 0.00 0.0 36.71 4.00 R
2416 2489 4.852134 AGTTATGTGCTGCATTGTTGAA 57.148 36.364 5.27 0.0 38.94 2.69 R
2579 2652 5.418524 TCATTGTGTTTTGACCCAGATATGG 59.581 40.000 0.00 0.0 0.00 2.74 R
3339 3416 6.250819 CACATCAAAACTAGAAATGCTACCG 58.749 40.000 0.00 0.0 0.00 4.02 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
253 264 7.432252 CAGAAACTTTGGAACTTTGTGACATAC 59.568 37.037 0.00 0.00 0.00 2.39
595 615 5.014755 TGTCCCAACCCAAATAGATAGTGTT 59.985 40.000 0.00 0.00 0.00 3.32
687 709 7.827236 AGATAACGGGATTGAAAAGTATGACAA 59.173 33.333 0.00 0.00 0.00 3.18
822 845 4.946157 ACCATCAGTCATCCTGTCAATTTC 59.054 41.667 0.00 0.00 42.19 2.17
931 954 5.645497 AGAGAAGATGTTATTTGCCACTCAC 59.355 40.000 0.00 0.00 0.00 3.51
956 979 6.341316 TCATTACAGCTTCATGAGTACTTCC 58.659 40.000 0.00 0.00 0.00 3.46
961 984 2.939103 GCTTCATGAGTACTTCCGCAAT 59.061 45.455 0.00 0.00 0.00 3.56
1004 1030 6.959639 TTTTCTGAAGTAAACAAGGATGCT 57.040 33.333 0.00 0.00 0.00 3.79
1006 1032 8.635765 TTTTCTGAAGTAAACAAGGATGCTAT 57.364 30.769 0.00 0.00 0.00 2.97
1037 1063 5.258051 TCTCTTAGTTCTCTTCCTCACCTC 58.742 45.833 0.00 0.00 0.00 3.85
1039 1065 1.945580 AGTTCTCTTCCTCACCTCCC 58.054 55.000 0.00 0.00 0.00 4.30
1065 1091 1.371558 GTCGGAAGGTCAGGCACTT 59.628 57.895 0.00 0.00 34.60 3.16
1134 1160 0.463833 CCAACCTTGTATCCCTCGCC 60.464 60.000 0.00 0.00 0.00 5.54
1138 1164 0.393077 CCTTGTATCCCTCGCCGAAT 59.607 55.000 0.00 0.00 0.00 3.34
1159 1185 0.901124 ACTGTTTGCCAAAGCCACAA 59.099 45.000 0.00 0.00 38.69 3.33
1239 1265 2.941415 GCTTTGTCGGGGTGATTCTGAT 60.941 50.000 0.00 0.00 0.00 2.90
1264 1290 3.127352 GACTGTCGGGAGCGCCTAG 62.127 68.421 2.29 0.94 0.00 3.02
1439 1465 5.813672 GCACCGTGAATACTAACCTGAATTA 59.186 40.000 1.65 0.00 0.00 1.40
1528 1554 1.891919 GTTGTGGTGAGCCGAGCAA 60.892 57.895 0.00 0.00 37.67 3.91
1619 1645 1.908619 ACGGGATATGCCATATGAGCA 59.091 47.619 14.28 17.54 45.94 4.26
1729 1755 1.658596 GCACATTGCGTTATGAGACGA 59.341 47.619 1.15 0.00 45.47 4.20
1735 1761 2.745102 TGCGTTATGAGACGAACACAA 58.255 42.857 1.15 0.00 45.47 3.33
1760 1786 6.711277 AGTTCTTTACTGATACCAAGATGCA 58.289 36.000 0.00 0.00 35.19 3.96
1796 1822 5.642063 CGCTCCCAAGAAGTATGTTTTCTTA 59.358 40.000 0.43 0.00 41.60 2.10
1865 1891 6.935208 ACCATTCCAGTAGAACAGAAGTAAAC 59.065 38.462 0.00 0.00 37.29 2.01
1912 1939 5.153950 AGTAATTTCGACTTTGAGCCTCT 57.846 39.130 0.00 0.00 0.00 3.69
2102 2130 4.102367 AGCCTCCAATTTGCCTTTTTACAA 59.898 37.500 0.00 0.00 0.00 2.41
2212 2240 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2414 2487 6.511416 CACTAGTCATAGCAAAGACATAGCT 58.489 40.000 0.00 0.00 42.14 3.32
2416 2489 7.493971 CACTAGTCATAGCAAAGACATAGCTTT 59.506 37.037 0.00 0.00 39.68 3.51
2601 2674 5.579047 TCCATATCTGGGTCAAAACACAAT 58.421 37.500 0.00 0.00 38.65 2.71
2994 3067 9.777297 ACTGCTTTTGTTTGAATACCATATTTT 57.223 25.926 0.00 0.00 0.00 1.82
3339 3416 7.100409 ACAAAAGCCTAGACTACTTCATCTTC 58.900 38.462 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
214 217 6.772716 TCCAAAGTTTCTGTAGCTCAAGAAAT 59.227 34.615 20.60 8.44 33.63 2.17
324 336 1.204146 GAATACTCCCAGTGCTCCCA 58.796 55.000 0.00 0.00 0.00 4.37
493 505 4.627467 CACTGTTGTAGCATGTCCTAGTTC 59.373 45.833 0.00 0.00 0.00 3.01
745 767 1.198759 AACATGCCTACTGGACGGGT 61.199 55.000 0.00 0.00 34.57 5.28
889 912 7.434492 TCTTCTCTTTGTGTACAAGAGGTAAG 58.566 38.462 18.60 15.75 37.15 2.34
956 979 4.319333 GGTCTTTGATCTATCTGCATTGCG 60.319 45.833 3.84 0.00 0.00 4.85
961 984 7.066645 CAGAAAATGGTCTTTGATCTATCTGCA 59.933 37.037 0.00 0.00 0.00 4.41
1037 1063 4.814294 CTTCCGACGAAGCCGGGG 62.814 72.222 2.18 0.00 46.47 5.73
1039 1065 3.984200 GACCTTCCGACGAAGCCGG 62.984 68.421 0.00 0.00 43.66 6.13
1050 1076 0.823356 TGCAAAGTGCCTGACCTTCC 60.823 55.000 0.00 0.00 44.23 3.46
1065 1091 0.098552 CGCCATTATTGTCGCTGCAA 59.901 50.000 0.00 0.00 0.00 4.08
1103 1129 4.178956 ACAAGGTTGGATTTGTAGGTGT 57.821 40.909 0.00 0.00 35.86 4.16
1134 1160 2.986479 GGCTTTGGCAAACAGTAATTCG 59.014 45.455 8.93 0.00 40.87 3.34
1138 1164 2.103373 TGTGGCTTTGGCAAACAGTAA 58.897 42.857 8.93 0.00 40.46 2.24
1264 1290 1.755783 CTTCATCAAGGGCCCTGGC 60.756 63.158 29.50 0.00 41.06 4.85
1326 1352 4.181578 GGTCGTAGTAGTAGGTCACGTTA 58.818 47.826 0.00 0.00 34.39 3.18
1693 1719 1.152777 TGCACCACACCCCAAGAAG 60.153 57.895 0.00 0.00 0.00 2.85
1729 1755 8.514330 TTGGTATCAGTAAAGAACTTTGTGTT 57.486 30.769 9.66 5.59 42.38 3.32
1735 1761 7.168219 TGCATCTTGGTATCAGTAAAGAACTT 58.832 34.615 0.00 0.00 35.76 2.66
1912 1939 9.790297 ATCTATGCCCTCTTAGGATAAGATAAA 57.210 33.333 0.00 0.00 37.67 1.40
2212 2240 4.096382 CCATAGTGGAATGCCTACAAACAC 59.904 45.833 0.00 0.00 40.96 3.32
2227 2255 3.057456 GCTCCGTATGTAGTCCATAGTGG 60.057 52.174 0.00 0.00 36.71 4.00
2275 2303 5.869888 CCTCCGTTCCTAAATATAGATGCAC 59.130 44.000 0.00 0.00 0.00 4.57
2414 2487 5.599732 AGTTATGTGCTGCATTGTTGAAAA 58.400 33.333 5.27 0.00 38.94 2.29
2416 2489 4.852134 AGTTATGTGCTGCATTGTTGAA 57.148 36.364 5.27 0.00 38.94 2.69
2579 2652 5.418524 TCATTGTGTTTTGACCCAGATATGG 59.581 40.000 0.00 0.00 0.00 2.74
2601 2674 6.546034 TGATGAGAATACATACCTCTTCGTCA 59.454 38.462 0.00 0.00 35.27 4.35
3068 3141 6.826231 TGTATACAGTGTATCATGTTTTGGGG 59.174 38.462 19.01 0.00 0.00 4.96
3204 3281 8.021396 ACCTTTGCTATAAGTTGAATTTCGTTC 58.979 33.333 0.00 0.00 37.35 3.95
3339 3416 6.250819 CACATCAAAACTAGAAATGCTACCG 58.749 40.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.