Multiple sequence alignment - TraesCS7D01G292600

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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 TraesCS7D01G292600 chr7D 100.000 2294 0 0 1 2294 358720021 358717728 0.000000e+00 4237.0
1 TraesCS7D01G292600 chr7D 90.537 391 30 6 1549 1932 358546583 358546193 5.650000e-141 510.0
2 TraesCS7D01G292600 chr7A 94.974 1512 38 19 1 1504 347095272 347096753 0.000000e+00 2337.0
3 TraesCS7D01G292600 chr7A 90.145 761 56 8 1543 2289 369682823 369683578 0.000000e+00 972.0
4 TraesCS7D01G292600 chr7A 93.043 345 24 0 1950 2294 370799564 370799908 2.630000e-139 505.0
5 TraesCS7D01G292600 chr7A 84.211 342 37 2 1543 1867 370790858 370791199 1.320000e-82 316.0
6 TraesCS7D01G292600 chr7B 96.684 1327 29 8 194 1514 312345399 312346716 0.000000e+00 2193.0
7 TraesCS7D01G292600 chr7B 97.531 81 1 1 1 81 312345319 312345398 1.110000e-28 137.0
8 TraesCS7D01G292600 chr7B 88.889 54 5 1 1549 1601 93461815 93461762 5.290000e-07 65.8
9 TraesCS7D01G292600 chr7B 91.111 45 4 0 1549 1593 12274726 12274682 6.840000e-06 62.1
10 TraesCS7D01G292600 chr7B 87.037 54 6 1 1549 1601 93444777 93444830 2.460000e-05 60.2
11 TraesCS7D01G292600 chr7B 88.889 45 5 0 1549 1593 93452457 93452413 3.180000e-04 56.5
12 TraesCS7D01G292600 chr7B 88.889 45 5 0 1549 1593 652115799 652115755 3.180000e-04 56.5
13 TraesCS7D01G292600 chr4A 87.481 655 66 10 1648 2294 625388448 625387802 0.000000e+00 741.0
14 TraesCS7D01G292600 chr4A 87.179 312 39 1 1983 2294 240410491 240410801 1.010000e-93 353.0
15 TraesCS7D01G292600 chr5D 85.246 427 48 6 1798 2214 543743539 543743960 2.110000e-115 425.0
16 TraesCS7D01G292600 chr5D 90.576 191 14 3 1603 1793 543723338 543723524 1.360000e-62 250.0
17 TraesCS7D01G292600 chr4D 88.782 312 35 0 1983 2294 206036334 206036023 1.290000e-102 383.0
18 TraesCS7D01G292600 chr2D 81.857 474 65 11 1832 2289 125453113 125453581 1.660000e-101 379.0
19 TraesCS7D01G292600 chr4B 85.897 312 44 0 1983 2294 252899053 252898742 1.310000e-87 333.0
20 TraesCS7D01G292600 chr4B 86.538 52 7 0 1549 1600 363713290 363713341 8.850000e-05 58.4
21 TraesCS7D01G292600 chr6B 86.824 296 30 5 1951 2241 71117732 71118023 2.840000e-84 322.0
22 TraesCS7D01G292600 chr6B 88.889 54 5 1 1549 1601 31025187 31025240 5.290000e-07 65.8
23 TraesCS7D01G292600 chr6A 84.039 307 35 11 1993 2294 531362097 531361800 1.340000e-72 283.0


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 TraesCS7D01G292600 chr7D 358717728 358720021 2293 True 4237 4237 100.0000 1 2294 1 chr7D.!!$R2 2293
1 TraesCS7D01G292600 chr7A 347095272 347096753 1481 False 2337 2337 94.9740 1 1504 1 chr7A.!!$F1 1503
2 TraesCS7D01G292600 chr7A 369682823 369683578 755 False 972 972 90.1450 1543 2289 1 chr7A.!!$F2 746
3 TraesCS7D01G292600 chr7B 312345319 312346716 1397 False 1165 2193 97.1075 1 1514 2 chr7B.!!$F2 1513
4 TraesCS7D01G292600 chr4A 625387802 625388448 646 True 741 741 87.4810 1648 2294 1 chr4A.!!$R1 646

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
893 905 1.348696 GTACTCCCTCCGTCCCAAAAA 59.651 52.381 0.0 0.0 0.0 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 1979 0.179113 GCTCTTCTTGCTCGAGGGAG 60.179 60.0 15.58 1.56 43.46 4.3 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
332 337 3.820467 TGGCAGTTAAGAGTGGAATTGTG 59.180 43.478 0.00 0.0 0.00 3.33
441 449 6.753279 TCATTGTTCTGCTTTCTTTCTTGTTG 59.247 34.615 0.00 0.0 0.00 3.33
442 450 5.643379 TGTTCTGCTTTCTTTCTTGTTGT 57.357 34.783 0.00 0.0 0.00 3.32
443 451 6.024552 TGTTCTGCTTTCTTTCTTGTTGTT 57.975 33.333 0.00 0.0 0.00 2.83
550 558 3.684305 TGTCTCACTCGCAAAACATATGG 59.316 43.478 7.80 0.0 0.00 2.74
702 711 5.321927 TCTAGACCTGTGTGTGATTACTGA 58.678 41.667 0.00 0.0 0.00 3.41
818 830 8.729756 CACATCATTAAGGTTTGTATTGTGAGA 58.270 33.333 0.00 0.0 34.22 3.27
893 905 1.348696 GTACTCCCTCCGTCCCAAAAA 59.651 52.381 0.00 0.0 0.00 1.94
1225 1237 0.825010 ACAAGCTTGCTCAGGGTTGG 60.825 55.000 26.27 0.0 46.03 3.77
1348 1360 9.675464 TGGTCCAAATTCGTATATTCTTTAGTT 57.325 29.630 0.00 0.0 0.00 2.24
1380 1392 1.396653 AGGGCTTGTATTGATGCTGC 58.603 50.000 0.00 0.0 0.00 5.25
1414 1426 4.552883 TGGAGTGATAGAGGGGATTGTA 57.447 45.455 0.00 0.0 0.00 2.41
1422 1434 2.769209 AGAGGGGATTGTATGTGCTCT 58.231 47.619 0.00 0.0 0.00 4.09
1423 1435 2.437281 AGAGGGGATTGTATGTGCTCTG 59.563 50.000 0.00 0.0 0.00 3.35
1424 1436 2.435805 GAGGGGATTGTATGTGCTCTGA 59.564 50.000 0.00 0.0 0.00 3.27
1504 1516 3.202818 TCATGGCACTAATTCATCCTGGT 59.797 43.478 0.00 0.0 0.00 4.00
1514 1526 8.152898 CACTAATTCATCCTGGTGATTCTGATA 58.847 37.037 0.00 0.0 0.00 2.15
1515 1527 8.888419 ACTAATTCATCCTGGTGATTCTGATAT 58.112 33.333 0.00 0.0 0.00 1.63
1516 1528 9.736414 CTAATTCATCCTGGTGATTCTGATATT 57.264 33.333 0.00 0.0 0.00 1.28
1517 1529 7.997773 ATTCATCCTGGTGATTCTGATATTG 57.002 36.000 0.00 0.0 0.00 1.90
1518 1530 6.505048 TCATCCTGGTGATTCTGATATTGT 57.495 37.500 0.00 0.0 0.00 2.71
1519 1531 6.903516 TCATCCTGGTGATTCTGATATTGTT 58.096 36.000 0.00 0.0 0.00 2.83
1520 1532 8.033178 TCATCCTGGTGATTCTGATATTGTTA 57.967 34.615 0.00 0.0 0.00 2.41
1521 1533 8.663167 TCATCCTGGTGATTCTGATATTGTTAT 58.337 33.333 0.00 0.0 0.00 1.89
1522 1534 9.948964 CATCCTGGTGATTCTGATATTGTTATA 57.051 33.333 0.00 0.0 0.00 0.98
1632 1647 2.205307 GCAAGAAGCAAGCATCATCC 57.795 50.000 0.00 0.0 44.79 3.51
1633 1648 1.475280 GCAAGAAGCAAGCATCATCCA 59.525 47.619 0.00 0.0 44.79 3.41
1695 1721 0.392193 ACATCGCAGAAGAAGGCAGG 60.392 55.000 0.00 0.0 43.58 4.85
1739 1765 1.896465 AGTAACGAAGCTGAGAAGGCT 59.104 47.619 0.00 0.0 42.31 4.58
1765 1791 1.737363 GCAAGTAACGAGGAGCTGAGG 60.737 57.143 0.00 0.0 0.00 3.86
1794 1820 2.900122 TGCAAATAACGAGAAGCTGC 57.100 45.000 0.00 0.0 0.00 5.25
1796 1822 1.468520 GCAAATAACGAGAAGCTGCCA 59.531 47.619 0.00 0.0 0.00 4.92
1932 1966 2.063541 AACGGAGCAGCAACACAAGC 62.064 55.000 0.00 0.0 0.00 4.01
1939 1973 1.150081 AGCAACACAAGCAGAGCCT 59.850 52.632 0.00 0.0 0.00 4.58
1944 1978 2.880890 CAACACAAGCAGAGCCTAAAGT 59.119 45.455 0.00 0.0 0.00 2.66
1945 1979 2.772287 ACACAAGCAGAGCCTAAAGTC 58.228 47.619 0.00 0.0 0.00 3.01
1946 1980 2.370189 ACACAAGCAGAGCCTAAAGTCT 59.630 45.455 0.00 0.0 0.00 3.24
1947 1981 2.999355 CACAAGCAGAGCCTAAAGTCTC 59.001 50.000 0.00 0.0 0.00 3.36
2024 2061 3.503827 TGTAGAATAGCCGCCATATCG 57.496 47.619 0.00 0.0 0.00 2.92
2194 2231 7.994425 TTTGTTGGATGAGTTCTTATGCTAA 57.006 32.000 0.00 0.0 0.00 3.09
2268 2305 3.064820 GCGTTTGAAAGAGAACCTTGTGA 59.935 43.478 0.00 0.0 34.79 3.58
2269 2306 4.261197 GCGTTTGAAAGAGAACCTTGTGAT 60.261 41.667 0.00 0.0 34.79 3.06
2289 2326 4.527038 TGATCGTAGAGAAGTGTTCCCTTT 59.473 41.667 0.00 0.0 43.63 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
332 337 2.489722 GTCCAAGATGCCTGTTCTTTCC 59.510 50.000 0.00 0.00 31.11 3.13
407 413 3.679389 AGCAGAACAATGAGTAGGGTTG 58.321 45.455 0.00 0.00 0.00 3.77
702 711 7.989416 TTTTATCAAATAGACCTTTGACCGT 57.011 32.000 1.68 0.00 45.21 4.83
893 905 7.230849 TGTTCATAAGCAAGAACCATGATTT 57.769 32.000 0.00 0.00 42.57 2.17
969 981 1.067000 CGGGCAAATTTGAATCCTGCA 60.067 47.619 22.31 0.00 34.66 4.41
1225 1237 2.715624 GGTCATTTCATCGCCCGC 59.284 61.111 0.00 0.00 0.00 6.13
1348 1360 0.112995 AAGCCCTTTCAGCATCCACA 59.887 50.000 0.00 0.00 0.00 4.17
1380 1392 9.265901 CCTCTATCACTCCATTAAAATGTACAG 57.734 37.037 0.33 0.00 34.60 2.74
1414 1426 2.479566 ACGGTTTCATCAGAGCACAT 57.520 45.000 0.00 0.00 0.00 3.21
1422 1434 7.788026 ACCTATTCAGTTATACGGTTTCATCA 58.212 34.615 0.00 0.00 0.00 3.07
1423 1435 7.384387 GGACCTATTCAGTTATACGGTTTCATC 59.616 40.741 0.00 0.00 0.00 2.92
1424 1436 7.215085 GGACCTATTCAGTTATACGGTTTCAT 58.785 38.462 0.00 0.00 0.00 2.57
1466 1478 6.260050 AGTGCCATGATATTTTTAGTACACCG 59.740 38.462 0.00 0.00 0.00 4.94
1557 1569 7.505585 ACCCCGCCCATATTATTGATAATATTG 59.494 37.037 11.66 9.39 41.55 1.90
1640 1655 6.365970 TCAAGCTTGGTCTTCTTATCTTCT 57.634 37.500 25.73 0.00 0.00 2.85
1695 1721 4.447054 CACATTCTGTCTTGACTCAGACAC 59.553 45.833 0.00 0.00 46.76 3.67
1739 1765 2.076100 CTCCTCGTTACTTGCATTGCA 58.924 47.619 7.38 7.38 36.47 4.08
1765 1791 1.268539 CGTTATTTGCATTCCGGCCTC 60.269 52.381 0.00 0.00 0.00 4.70
1772 1798 3.788163 GCAGCTTCTCGTTATTTGCATTC 59.212 43.478 0.00 0.00 0.00 2.67
1794 1820 1.009389 GTCTTCACGAGAACGGCTGG 61.009 60.000 0.00 0.00 44.46 4.85
1796 1822 0.603569 ATGTCTTCACGAGAACGGCT 59.396 50.000 0.00 0.00 44.46 5.52
1855 1881 1.066071 GCGTTAGGGAGCCTTCTCTTT 60.066 52.381 0.00 0.00 39.31 2.52
1932 1966 1.407258 CGAGGGAGACTTTAGGCTCTG 59.593 57.143 12.17 0.00 0.00 3.35
1939 1973 2.803956 TCTTGCTCGAGGGAGACTTTA 58.196 47.619 15.58 0.00 43.27 1.85
1944 1978 1.468985 CTCTTCTTGCTCGAGGGAGA 58.531 55.000 15.58 6.29 43.27 3.71
1945 1979 0.179113 GCTCTTCTTGCTCGAGGGAG 60.179 60.000 15.58 1.56 43.46 4.30
1946 1980 0.900182 TGCTCTTCTTGCTCGAGGGA 60.900 55.000 15.58 0.00 0.00 4.20
1947 1981 0.459934 CTGCTCTTCTTGCTCGAGGG 60.460 60.000 15.58 0.00 0.00 4.30
2173 2210 6.349300 TCCTTAGCATAAGAACTCATCCAAC 58.651 40.000 0.00 0.00 0.00 3.77
2175 2212 6.239714 GGATCCTTAGCATAAGAACTCATCCA 60.240 42.308 3.84 0.00 0.00 3.41
2179 2216 9.249053 CTATAGGATCCTTAGCATAAGAACTCA 57.751 37.037 22.03 0.00 0.00 3.41
2219 2256 6.183360 ACACAAGGCTAAACAGAGAACTTCTA 60.183 38.462 0.00 0.00 33.83 2.10
2222 2259 4.576463 CACACAAGGCTAAACAGAGAACTT 59.424 41.667 0.00 0.00 0.00 2.66
2268 2305 4.322801 CCAAAGGGAACACTTCTCTACGAT 60.323 45.833 0.00 0.00 40.34 3.73
2269 2306 3.006537 CCAAAGGGAACACTTCTCTACGA 59.993 47.826 0.00 0.00 40.34 3.43


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

AutoCloner maintained by Alex Coulton.