Multiple sequence alignment - TraesCS7D01G521300

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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 TraesCS7D01G521300 chr7D 100.000 2372 0 0 1 2372 618660266 618662637 0.000000e+00 4381.0
1 TraesCS7D01G521300 chr7D 90.813 283 25 1 135 417 415928333 415928614 6.190000e-101 377.0
2 TraesCS7D01G521300 chr7D 86.742 264 28 6 512 769 618678330 618678068 1.070000e-73 287.0
3 TraesCS7D01G521300 chr7A 97.062 1940 51 4 1 1940 712271678 712273611 0.000000e+00 3262.0
4 TraesCS7D01G521300 chr7A 88.372 301 32 3 103 402 634652696 634652994 2.240000e-95 359.0
5 TraesCS7D01G521300 chr7A 84.211 114 10 8 400 512 641446404 641446298 1.160000e-18 104.0
6 TraesCS7D01G521300 chr3B 89.046 1698 165 12 512 2200 625596481 625594796 0.000000e+00 2085.0
7 TraesCS7D01G521300 chr3B 86.719 256 27 6 513 763 625423293 625423546 6.460000e-71 278.0
8 TraesCS7D01G521300 chr3B 95.276 127 6 0 2246 2372 625594693 625594567 4.000000e-48 202.0
9 TraesCS7D01G521300 chr6B 85.895 1893 193 37 511 2372 260210066 260208217 0.000000e+00 1949.0
10 TraesCS7D01G521300 chr6B 85.660 265 30 5 511 769 260143056 260143318 3.000000e-69 272.0
11 TraesCS7D01G521300 chr1D 91.048 1240 108 3 635 1871 325554191 325555430 0.000000e+00 1672.0
12 TraesCS7D01G521300 chr1D 91.691 337 22 3 1870 2200 325565772 325566108 1.660000e-126 462.0
13 TraesCS7D01G521300 chr1D 96.875 128 3 1 2246 2372 325566211 325566338 1.850000e-51 213.0
14 TraesCS7D01G521300 chr5B 82.368 1571 234 29 512 2063 11286996 11285450 0.000000e+00 1327.0
15 TraesCS7D01G521300 chr2A 84.693 1287 171 20 499 1771 771874088 771875362 0.000000e+00 1262.0
16 TraesCS7D01G521300 chr1B 90.437 962 82 5 971 1930 437870907 437871860 0.000000e+00 1258.0
17 TraesCS7D01G521300 chr6A 81.623 1306 202 33 513 1802 596355514 596356797 0.000000e+00 1048.0
18 TraesCS7D01G521300 chr6A 92.164 268 21 0 135 402 105506432 105506699 1.720000e-101 379.0
19 TraesCS7D01G521300 chr6A 87.313 134 14 3 1 134 7901169 7901299 1.470000e-32 150.0
20 TraesCS7D01G521300 chr6A 86.567 134 16 2 1 134 7866420 7866551 1.900000e-31 147.0
21 TraesCS7D01G521300 chr6A 86.567 134 16 2 1 134 7968271 7968402 1.900000e-31 147.0
22 TraesCS7D01G521300 chr6A 85.821 134 16 3 1 134 7832461 7832591 3.180000e-29 139.0
23 TraesCS7D01G521300 chr6A 85.821 134 16 3 1 134 7933282 7933412 3.180000e-29 139.0
24 TraesCS7D01G521300 chr6A 89.706 68 5 2 440 506 85283917 85283851 4.200000e-13 86.1
25 TraesCS7D01G521300 chr5D 83.588 1048 160 10 775 1817 26959674 26958634 0.000000e+00 972.0
26 TraesCS7D01G521300 chr5D 86.331 139 19 0 1 139 393985992 393986130 4.080000e-33 152.0
27 TraesCS7D01G521300 chr2D 83.512 1025 160 7 796 1817 35331638 35330620 0.000000e+00 948.0
28 TraesCS7D01G521300 chr2D 90.780 282 21 5 123 402 331660752 331661030 2.880000e-99 372.0
29 TraesCS7D01G521300 chr3D 92.647 272 18 2 136 407 346816139 346816408 7.950000e-105 390.0
30 TraesCS7D01G521300 chr5A 92.222 270 20 1 133 402 568181429 568181697 4.780000e-102 381.0
31 TraesCS7D01G521300 chr5A 84.286 140 19 3 1 139 597336682 597336545 1.480000e-27 134.0
32 TraesCS7D01G521300 chr2B 91.575 273 22 1 130 402 419338803 419338532 2.230000e-100 375.0
33 TraesCS7D01G521300 chr2B 85.294 136 20 0 1 136 145381488 145381623 8.840000e-30 141.0
34 TraesCS7D01G521300 chr2B 82.407 108 14 5 401 506 793382806 793382910 3.250000e-14 89.8
35 TraesCS7D01G521300 chr7B 90.175 285 25 3 124 407 631775313 631775595 3.720000e-98 368.0
36 TraesCS7D01G521300 chr7B 87.833 263 26 5 512 769 713071840 713071579 1.070000e-78 303.0
37 TraesCS7D01G521300 chr7B 89.899 198 17 3 511 705 202987001 202986804 3.910000e-63 252.0
38 TraesCS7D01G521300 chr7B 100.000 42 0 0 2331 2372 713069265 713069306 7.030000e-11 78.7


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 TraesCS7D01G521300 chr7D 618660266 618662637 2371 False 4381.0 4381 100.000 1 2372 1 chr7D.!!$F2 2371
1 TraesCS7D01G521300 chr7A 712271678 712273611 1933 False 3262.0 3262 97.062 1 1940 1 chr7A.!!$F2 1939
2 TraesCS7D01G521300 chr3B 625594567 625596481 1914 True 1143.5 2085 92.161 512 2372 2 chr3B.!!$R1 1860
3 TraesCS7D01G521300 chr6B 260208217 260210066 1849 True 1949.0 1949 85.895 511 2372 1 chr6B.!!$R1 1861
4 TraesCS7D01G521300 chr1D 325554191 325555430 1239 False 1672.0 1672 91.048 635 1871 1 chr1D.!!$F1 1236
5 TraesCS7D01G521300 chr1D 325565772 325566338 566 False 337.5 462 94.283 1870 2372 2 chr1D.!!$F2 502
6 TraesCS7D01G521300 chr5B 11285450 11286996 1546 True 1327.0 1327 82.368 512 2063 1 chr5B.!!$R1 1551
7 TraesCS7D01G521300 chr2A 771874088 771875362 1274 False 1262.0 1262 84.693 499 1771 1 chr2A.!!$F1 1272
8 TraesCS7D01G521300 chr1B 437870907 437871860 953 False 1258.0 1258 90.437 971 1930 1 chr1B.!!$F1 959
9 TraesCS7D01G521300 chr6A 596355514 596356797 1283 False 1048.0 1048 81.623 513 1802 1 chr6A.!!$F7 1289
10 TraesCS7D01G521300 chr5D 26958634 26959674 1040 True 972.0 972 83.588 775 1817 1 chr5D.!!$R1 1042
11 TraesCS7D01G521300 chr2D 35330620 35331638 1018 True 948.0 948 83.512 796 1817 1 chr2D.!!$R1 1021

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
203 204 1.269166 ATTAAAGAGCGCACGTCGAG 58.731 50.0 11.47 0.0 41.67 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2200 2243 2.301346 AGTTTGGTTTGCTCAGACCTG 58.699 47.619 10.39 0.0 36.6 4.0 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
198 199 2.583801 CACGAAAATTAAAGAGCGCACG 59.416 45.455 11.47 0.00 0.00 5.34
200 201 2.832745 CGAAAATTAAAGAGCGCACGTC 59.167 45.455 11.47 0.00 0.00 4.34
203 204 1.269166 ATTAAAGAGCGCACGTCGAG 58.731 50.000 11.47 0.00 41.67 4.04
240 241 1.271856 TTGGGCGAGATTACACCTGA 58.728 50.000 0.00 0.00 0.00 3.86
252 253 7.043125 CGAGATTACACCTGACTAATTGACATG 60.043 40.741 0.00 0.00 0.00 3.21
438 439 7.754069 TTGTTTTCTAATGCTTGTTCAACAG 57.246 32.000 0.00 0.00 0.00 3.16
495 496 9.778993 CATAGTCAACATTTTCTCAAATACCTG 57.221 33.333 0.00 0.00 30.90 4.00
600 607 1.963515 CTTCTTCCACCCCCAAACAAG 59.036 52.381 0.00 0.00 0.00 3.16
704 714 2.659610 GGCGCTCTTGTCAGGTCT 59.340 61.111 7.64 0.00 0.00 3.85
786 811 4.540099 TCTCTCACAACCCAAATCCCTAAT 59.460 41.667 0.00 0.00 0.00 1.73
1105 1131 2.922503 TGCTGGCGACCTTGGAGA 60.923 61.111 0.00 0.00 0.00 3.71
1705 1732 1.183549 GAAGGCGAGGACCTAACTCA 58.816 55.000 0.00 0.00 39.93 3.41
1999 2035 3.010250 TCCAGCTCCTCTTCTGTGTACTA 59.990 47.826 0.00 0.00 0.00 1.82
2006 2042 6.095720 GCTCCTCTTCTGTGTACTACTGTTAT 59.904 42.308 0.00 0.00 0.00 1.89
2014 2055 8.288689 TCTGTGTACTACTGTTATCATTAGCA 57.711 34.615 0.00 0.00 32.39 3.49
2053 2095 6.090628 GTGACATTGCAAAAAGAACTGACAAA 59.909 34.615 1.71 0.00 0.00 2.83
2069 2111 7.535489 ACTGACAAAAGAAACTGTACAGTAC 57.465 36.000 28.13 22.84 41.58 2.73
2084 2126 4.640771 ACAGTACCATCATTTCCACAGT 57.359 40.909 0.00 0.00 0.00 3.55
2104 2146 5.047660 ACAGTTTGCAAACACCTTTCAACTA 60.048 36.000 36.46 0.00 41.30 2.24
2127 2169 7.770433 ACTAAATTCATAGTGAGCAAGCATACA 59.230 33.333 0.00 0.00 34.86 2.29
2128 2170 7.395190 AAATTCATAGTGAGCAAGCATACAA 57.605 32.000 0.00 0.00 0.00 2.41
2138 2180 4.813027 AGCAAGCATACAAAACATTCCAG 58.187 39.130 0.00 0.00 0.00 3.86
2154 2196 7.759489 ACATTCCAGCTTAATTAACAGTGAA 57.241 32.000 0.00 0.00 0.00 3.18
2178 2221 5.251237 ACCAATTCCATCATTCACCCAAAAT 59.749 36.000 0.00 0.00 0.00 1.82
2201 2244 9.877178 AAATAAATGTGACAAACCAAACTTACA 57.123 25.926 0.00 0.00 0.00 2.41
2202 2245 9.528018 AATAAATGTGACAAACCAAACTTACAG 57.472 29.630 0.00 0.00 0.00 2.74
2203 2246 4.974368 TGTGACAAACCAAACTTACAGG 57.026 40.909 0.00 0.00 0.00 4.00
2205 2248 4.396790 TGTGACAAACCAAACTTACAGGTC 59.603 41.667 0.00 0.00 33.74 3.85
2207 2250 4.638421 TGACAAACCAAACTTACAGGTCTG 59.362 41.667 0.00 0.00 33.74 3.51
2208 2251 4.850680 ACAAACCAAACTTACAGGTCTGA 58.149 39.130 4.84 0.00 33.74 3.27
2210 2253 3.127425 ACCAAACTTACAGGTCTGAGC 57.873 47.619 4.84 0.00 0.00 4.26
2211 2254 2.438021 ACCAAACTTACAGGTCTGAGCA 59.562 45.455 9.78 0.00 0.00 4.26
2212 2255 3.118038 ACCAAACTTACAGGTCTGAGCAA 60.118 43.478 9.78 0.00 0.00 3.91
2214 2257 4.261197 CCAAACTTACAGGTCTGAGCAAAC 60.261 45.833 9.78 0.00 0.00 2.93
2215 2258 3.127425 ACTTACAGGTCTGAGCAAACC 57.873 47.619 9.78 0.00 35.69 3.27
2216 2259 2.438021 ACTTACAGGTCTGAGCAAACCA 59.562 45.455 9.78 0.00 38.06 3.67
2221 2264 2.689983 CAGGTCTGAGCAAACCAAACTT 59.310 45.455 9.78 0.00 38.06 2.66
2229 2300 5.406649 TGAGCAAACCAAACTTACAAACAG 58.593 37.500 0.00 0.00 0.00 3.16
2230 2301 5.184096 TGAGCAAACCAAACTTACAAACAGA 59.816 36.000 0.00 0.00 0.00 3.41
2232 2303 5.867174 AGCAAACCAAACTTACAAACAGAAC 59.133 36.000 0.00 0.00 0.00 3.01
2234 2305 6.034577 GCAAACCAAACTTACAAACAGAACTC 59.965 38.462 0.00 0.00 0.00 3.01
2253 2353 4.297299 CTCACAGTGAGCAAACAACAAT 57.703 40.909 17.77 0.00 37.72 2.71
2318 2418 4.541705 TCCTTGTAGATCTCCTCCTTCTG 58.458 47.826 0.00 0.00 0.00 3.02
2344 2444 2.093106 AGTACTAGCTCCAGGTGTTCG 58.907 52.381 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
198 199 4.830826 ACTTGTGAAATTTTCCCTCGAC 57.169 40.909 6.68 0.00 0.00 4.20
200 201 5.234116 CCAAAACTTGTGAAATTTTCCCTCG 59.766 40.000 6.68 0.00 0.00 4.63
203 204 4.036262 GCCCAAAACTTGTGAAATTTTCCC 59.964 41.667 6.68 0.00 0.00 3.97
240 241 6.389869 TCCTCTATTTCCCCATGTCAATTAGT 59.610 38.462 0.00 0.00 0.00 2.24
252 253 1.477740 GGCAAGCTCCTCTATTTCCCC 60.478 57.143 0.00 0.00 0.00 4.81
704 714 1.889170 CACCGCATCTCTATCCAGCTA 59.111 52.381 0.00 0.00 0.00 3.32
763 787 2.348472 AGGGATTTGGGTTGTGAGAGA 58.652 47.619 0.00 0.00 0.00 3.10
809 834 2.125106 GGTGGTGGATCTCACGCC 60.125 66.667 7.85 8.59 46.96 5.68
880 905 4.680237 CTCGGTTGGACTGCGGCA 62.680 66.667 1.29 1.29 0.00 5.69
1341 1368 3.411351 CACCGAAGCCGTTGTCCG 61.411 66.667 0.00 0.00 0.00 4.79
1705 1732 4.394300 GCATAGTCTTGAAGATGTGCTTGT 59.606 41.667 16.70 0.00 36.83 3.16
1999 2035 8.306038 TGCTTTCAAAATGCTAATGATAACAGT 58.694 29.630 0.00 0.00 0.00 3.55
2006 2042 7.116662 GTCACATTGCTTTCAAAATGCTAATGA 59.883 33.333 18.21 9.85 37.30 2.57
2053 2095 7.390718 GGAAATGATGGTACTGTACAGTTTCTT 59.609 37.037 32.15 20.79 42.54 2.52
2069 2111 3.663995 TGCAAACTGTGGAAATGATGG 57.336 42.857 0.00 0.00 0.00 3.51
2084 2126 7.604164 TGAATTTAGTTGAAAGGTGTTTGCAAA 59.396 29.630 8.05 8.05 0.00 3.68
2104 2146 7.395190 TTGTATGCTTGCTCACTATGAATTT 57.605 32.000 0.00 0.00 0.00 1.82
2127 2169 8.637986 TCACTGTTAATTAAGCTGGAATGTTTT 58.362 29.630 0.00 0.00 0.00 2.43
2128 2170 8.177119 TCACTGTTAATTAAGCTGGAATGTTT 57.823 30.769 0.00 0.00 0.00 2.83
2138 2180 7.375053 TGGAATTGGTTCACTGTTAATTAAGC 58.625 34.615 0.00 0.00 36.01 3.09
2154 2196 3.471430 TGGGTGAATGATGGAATTGGT 57.529 42.857 0.00 0.00 0.00 3.67
2178 2221 7.122948 ACCTGTAAGTTTGGTTTGTCACATTTA 59.877 33.333 0.00 0.00 0.00 1.40
2200 2243 2.301346 AGTTTGGTTTGCTCAGACCTG 58.699 47.619 10.39 0.00 36.60 4.00
2201 2244 2.736670 AGTTTGGTTTGCTCAGACCT 57.263 45.000 10.39 0.00 36.60 3.85
2202 2245 3.630312 TGTAAGTTTGGTTTGCTCAGACC 59.370 43.478 2.90 2.90 36.23 3.85
2203 2246 4.893424 TGTAAGTTTGGTTTGCTCAGAC 57.107 40.909 0.00 0.00 0.00 3.51
2205 2248 5.406649 TGTTTGTAAGTTTGGTTTGCTCAG 58.593 37.500 0.00 0.00 0.00 3.35
2207 2250 5.646606 TCTGTTTGTAAGTTTGGTTTGCTC 58.353 37.500 0.00 0.00 0.00 4.26
2208 2251 5.652994 TCTGTTTGTAAGTTTGGTTTGCT 57.347 34.783 0.00 0.00 0.00 3.91
2210 2253 7.061789 GTGAGTTCTGTTTGTAAGTTTGGTTTG 59.938 37.037 0.00 0.00 0.00 2.93
2211 2254 7.088272 GTGAGTTCTGTTTGTAAGTTTGGTTT 58.912 34.615 0.00 0.00 0.00 3.27
2212 2255 6.207810 TGTGAGTTCTGTTTGTAAGTTTGGTT 59.792 34.615 0.00 0.00 0.00 3.67
2214 2257 6.128007 ACTGTGAGTTCTGTTTGTAAGTTTGG 60.128 38.462 0.00 0.00 0.00 3.28
2215 2258 6.742718 CACTGTGAGTTCTGTTTGTAAGTTTG 59.257 38.462 0.32 0.00 0.00 2.93
2216 2259 6.653320 TCACTGTGAGTTCTGTTTGTAAGTTT 59.347 34.615 6.36 0.00 0.00 2.66
2221 2264 4.119862 GCTCACTGTGAGTTCTGTTTGTA 58.880 43.478 31.76 0.00 45.94 2.41
2229 2300 3.126858 TGTTGTTTGCTCACTGTGAGTTC 59.873 43.478 31.76 20.04 45.94 3.01
2230 2301 3.081061 TGTTGTTTGCTCACTGTGAGTT 58.919 40.909 31.76 0.00 45.94 3.01
2232 2303 3.763097 TTGTTGTTTGCTCACTGTGAG 57.237 42.857 28.91 28.91 46.90 3.51
2234 2305 5.173774 ACTATTGTTGTTTGCTCACTGTG 57.826 39.130 0.17 0.17 0.00 3.66
2246 2317 9.569122 AGGAGTTAAACATGTAACTATTGTTGT 57.431 29.630 12.86 0.00 42.94 3.32
2318 2418 3.628487 CACCTGGAGCTAGTACTAGTCAC 59.372 52.174 26.76 17.94 35.65 3.67
2344 2444 1.667722 CCTCCAAAACAAGCCAGCC 59.332 57.895 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.