Multiple sequence alignment - TraesCS7D01G146800

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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 TraesCS7D01G146800 chr7D 100.000 3236 0 0 1 3236 93788153 93791388 0.000000e+00 5976.0
1 TraesCS7D01G146800 chr7D 84.987 1512 197 29 1369 2868 606637652 606636159 0.000000e+00 1507.0
2 TraesCS7D01G146800 chr7D 82.891 339 44 12 1026 1357 606638105 606637774 3.160000e-75 292.0
3 TraesCS7D01G146800 chr7D 82.639 144 23 2 633 775 606638404 606638262 3.390000e-25 126.0
4 TraesCS7D01G146800 chr7B 95.231 3292 87 17 1 3236 47000083 47003360 0.000000e+00 5145.0
5 TraesCS7D01G146800 chr7B 85.545 1515 187 30 1369 2870 690753422 690754917 0.000000e+00 1555.0
6 TraesCS7D01G146800 chr7B 85.559 367 51 2 2871 3236 690755027 690755392 1.820000e-102 383.0
7 TraesCS7D01G146800 chr7B 83.776 339 41 12 1026 1357 690752954 690753285 3.140000e-80 309.0
8 TraesCS7D01G146800 chr7B 83.951 162 21 4 609 768 690752632 690752790 2.010000e-32 150.0
9 TraesCS7D01G146800 chr7A 97.024 2890 49 16 362 3236 96567357 96570224 0.000000e+00 4826.0
10 TraesCS7D01G146800 chr7A 85.461 1520 189 28 1369 2875 698677882 698679382 0.000000e+00 1554.0
11 TraesCS7D01G146800 chr7A 93.537 294 14 3 78 366 96566230 96566523 1.780000e-117 433.0
12 TraesCS7D01G146800 chr7A 84.524 336 44 7 1026 1357 698677422 698677753 3.110000e-85 326.0
13 TraesCS7D01G146800 chr7A 83.333 144 22 2 633 775 698677123 698677265 7.280000e-27 132.0
14 TraesCS7D01G146800 chr7A 97.619 42 1 0 1 42 96565677 96565718 4.480000e-09 73.1
15 TraesCS7D01G146800 chr6A 91.098 1876 151 16 1369 3236 591437877 591439744 0.000000e+00 2525.0
16 TraesCS7D01G146800 chr6A 86.501 363 47 2 1009 1370 591437416 591437777 6.510000e-107 398.0
17 TraesCS7D01G146800 chr6A 78.893 289 49 8 632 908 591437049 591437337 5.510000e-43 185.0
18 TraesCS7D01G146800 chr6A 73.834 493 93 23 632 1110 591436032 591436502 2.580000e-36 163.0
19 TraesCS7D01G146800 chr6A 91.954 87 5 1 287 373 190660436 190660352 1.580000e-23 121.0
20 TraesCS7D01G146800 chr6A 91.954 87 5 1 287 373 190738359 190738275 1.580000e-23 121.0
21 TraesCS7D01G146800 chr6D 90.938 1876 154 16 1369 3236 443847809 443849676 0.000000e+00 2508.0
22 TraesCS7D01G146800 chr6D 87.017 362 45 2 1010 1370 443847362 443847722 1.080000e-109 407.0
23 TraesCS7D01G146800 chr6D 80.000 290 44 8 632 908 443846995 443847283 5.470000e-48 202.0
24 TraesCS7D01G146800 chr6B 90.710 1873 164 10 1369 3236 668248469 668250336 0.000000e+00 2486.0
25 TraesCS7D01G146800 chr6B 85.984 371 50 2 1001 1370 668247983 668248352 2.340000e-106 396.0
26 TraesCS7D01G146800 chr6B 78.746 287 49 8 632 906 668247617 668247903 7.130000e-42 182.0
27 TraesCS7D01G146800 chr1D 83.302 1593 227 34 1646 3214 349792857 349794434 0.000000e+00 1432.0
28 TraesCS7D01G146800 chr1D 92.857 84 6 0 290 373 489299983 489300066 4.380000e-24 122.0
29 TraesCS7D01G146800 chr1D 92.857 84 6 0 290 373 489432871 489432954 4.380000e-24 122.0
30 TraesCS7D01G146800 chr1B 82.852 1592 236 32 1646 3214 471761605 471763182 0.000000e+00 1393.0
31 TraesCS7D01G146800 chr1A 82.652 1591 241 30 1646 3214 450094613 450096190 0.000000e+00 1376.0
32 TraesCS7D01G146800 chr1A 89.583 96 8 1 278 373 518662856 518662763 1.580000e-23 121.0
33 TraesCS7D01G146800 chr4B 80.639 563 91 14 1647 2194 586466727 586467286 1.390000e-113 420.0
34 TraesCS7D01G146800 chr3B 91.111 90 7 1 285 373 429973520 429973609 1.580000e-23 121.0
35 TraesCS7D01G146800 chr2B 88.542 96 9 2 285 380 483453041 483452948 7.340000e-22 115.0


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 TraesCS7D01G146800 chr7D 93788153 93791388 3235 False 5976.000000 5976 100.000000 1 3236 1 chr7D.!!$F1 3235
1 TraesCS7D01G146800 chr7D 606636159 606638404 2245 True 641.666667 1507 83.505667 633 2868 3 chr7D.!!$R1 2235
2 TraesCS7D01G146800 chr7B 47000083 47003360 3277 False 5145.000000 5145 95.231000 1 3236 1 chr7B.!!$F1 3235
3 TraesCS7D01G146800 chr7B 690752632 690755392 2760 False 599.250000 1555 84.707750 609 3236 4 chr7B.!!$F2 2627
4 TraesCS7D01G146800 chr7A 96565677 96570224 4547 False 1777.366667 4826 96.060000 1 3236 3 chr7A.!!$F1 3235
5 TraesCS7D01G146800 chr7A 698677123 698679382 2259 False 670.666667 1554 84.439333 633 2875 3 chr7A.!!$F2 2242
6 TraesCS7D01G146800 chr6A 591436032 591439744 3712 False 817.750000 2525 82.581500 632 3236 4 chr6A.!!$F1 2604
7 TraesCS7D01G146800 chr6D 443846995 443849676 2681 False 1039.000000 2508 85.985000 632 3236 3 chr6D.!!$F1 2604
8 TraesCS7D01G146800 chr6B 668247617 668250336 2719 False 1021.333333 2486 85.146667 632 3236 3 chr6B.!!$F1 2604
9 TraesCS7D01G146800 chr1D 349792857 349794434 1577 False 1432.000000 1432 83.302000 1646 3214 1 chr1D.!!$F1 1568
10 TraesCS7D01G146800 chr1B 471761605 471763182 1577 False 1393.000000 1393 82.852000 1646 3214 1 chr1B.!!$F1 1568
11 TraesCS7D01G146800 chr1A 450094613 450096190 1577 False 1376.000000 1376 82.652000 1646 3214 1 chr1A.!!$F1 1568
12 TraesCS7D01G146800 chr4B 586466727 586467286 559 False 420.000000 420 80.639000 1647 2194 1 chr4B.!!$F1 547

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
580 1933 0.454196 AAACCACGCAACACAAGGAC 59.546 50.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2274 4887 1.47973 TCATCGAGCTCTGCAAGATGT 59.52 47.619 20.87 0.0 45.62 3.06 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
131 608 4.065789 GTGTTTCTGTAAACCTGAGGAGG 58.934 47.826 4.99 0.00 43.66 4.30
143 621 2.436173 CCTGAGGAGGGATGAGGTTTAC 59.564 54.545 0.00 0.00 35.40 2.01
250 729 9.617975 GTTCATTCATTTGAAAAGTAGAAGAGG 57.382 33.333 0.00 0.00 37.36 3.69
297 797 3.780850 CCAGTTTTCATAGTACCCCCTCT 59.219 47.826 0.00 0.00 0.00 3.69
304 804 5.476950 TCATAGTACCCCCTCTGTAAAGA 57.523 43.478 0.00 0.00 0.00 2.52
373 877 7.579916 GCTCTTATATTAGTTTAGGGAGGGAGC 60.580 44.444 0.00 0.00 33.61 4.70
460 1804 7.247456 TCCCACACACTTGTATTACAGATAA 57.753 36.000 0.00 0.00 33.30 1.75
483 1827 5.321959 TGTCAGATAGAGAGCACAAGAAG 57.678 43.478 0.00 0.00 0.00 2.85
578 1931 1.135257 TGAAAACCACGCAACACAAGG 60.135 47.619 0.00 0.00 0.00 3.61
579 1932 1.133407 GAAAACCACGCAACACAAGGA 59.867 47.619 0.00 0.00 0.00 3.36
580 1933 0.454196 AAACCACGCAACACAAGGAC 59.546 50.000 0.00 0.00 0.00 3.85
666 2019 1.299850 CTGCGGAATGGCGTCGATA 60.300 57.895 0.00 0.00 35.06 2.92
981 3412 3.418913 CAACAATGGCGACGGCGA 61.419 61.111 18.90 0.00 41.24 5.54
983 3414 2.255172 AACAATGGCGACGGCGAAA 61.255 52.632 18.90 0.00 41.24 3.46
984 3415 2.202298 CAATGGCGACGGCGAAAC 60.202 61.111 18.90 3.59 41.24 2.78
985 3416 3.428282 AATGGCGACGGCGAAACC 61.428 61.111 18.90 6.92 41.24 3.27
986 3417 4.690719 ATGGCGACGGCGAAACCA 62.691 61.111 18.90 14.20 41.24 3.67
987 3418 4.912485 TGGCGACGGCGAAACCAA 62.912 61.111 18.90 0.00 41.24 3.67
988 3419 4.379143 GGCGACGGCGAAACCAAC 62.379 66.667 18.90 0.00 41.24 3.77
1159 3618 1.198094 TCCCCTCCATGTCGCAGAAA 61.198 55.000 0.00 0.00 39.69 2.52
1618 4219 0.529773 GCATGAACCCGAGCACGATA 60.530 55.000 4.70 0.00 42.66 2.92
2524 5140 0.320771 GCACCATGTCCTTGTCGACT 60.321 55.000 17.92 0.00 33.70 4.18
2656 5272 2.044650 ATGCGCTTGGTGATGGCT 60.045 55.556 9.73 0.00 0.00 4.75
2974 5699 2.754254 TCGAGCTCGCCCTGCTTA 60.754 61.111 30.97 8.61 41.30 3.09
2983 5708 1.077716 GCCCTGCTTAACCGTGGAT 60.078 57.895 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 576 5.236911 GGTTTACAGAAACACGATGGTACAA 59.763 40.000 0.00 0.0 44.64 2.41
131 608 5.008316 ACACAAAAACTCGTAAACCTCATCC 59.992 40.000 0.00 0.0 0.00 3.51
143 621 5.924254 TCACATCTACCTACACAAAAACTCG 59.076 40.000 0.00 0.0 0.00 4.18
240 719 6.023603 TCCTACATCCAAAACCTCTTCTACT 58.976 40.000 0.00 0.0 0.00 2.57
250 729 2.790433 TGCACCTCCTACATCCAAAAC 58.210 47.619 0.00 0.0 0.00 2.43
343 847 7.813627 CCTCCCTAAACTAATATAAGAGCGTTC 59.186 40.741 0.00 0.0 0.00 3.95
358 862 0.547712 TGCTGCTCCCTCCCTAAACT 60.548 55.000 0.00 0.0 0.00 2.66
373 877 2.339418 CTCTTGCTTCTCTCACTGCTG 58.661 52.381 0.00 0.0 0.00 4.41
460 1804 5.655974 TCTTCTTGTGCTCTCTATCTGACAT 59.344 40.000 0.00 0.0 0.00 3.06
483 1827 3.218453 TCTCTCTACTGCTGCATAGGTC 58.782 50.000 1.31 0.0 0.00 3.85
605 1958 1.493950 GATCGATTGCTGCTCCGGTG 61.494 60.000 0.00 0.0 0.00 4.94
666 2019 0.543277 TCAAGCAGAAGGGCATCGAT 59.457 50.000 0.00 0.0 35.83 3.59
784 3154 2.125753 CGACCTCCTCAGCAGCAC 60.126 66.667 0.00 0.0 0.00 4.40
787 3166 3.074999 GCTCCGACCTCCTCAGCAG 62.075 68.421 0.00 0.0 0.00 4.24
1159 3618 2.890371 GTGTACGCCGACTGGGAT 59.110 61.111 0.00 0.0 38.47 3.85
2274 4887 1.479730 TCATCGAGCTCTGCAAGATGT 59.520 47.619 20.87 0.0 45.62 3.06
2524 5140 2.583441 CGAGGTGTGCTCCAAGGGA 61.583 63.158 0.00 0.0 0.00 4.20
2974 5699 0.613853 TCTTCTCGGGATCCACGGTT 60.614 55.000 15.23 0.0 0.00 4.44
2983 5708 1.682684 GCAGGAGGTCTTCTCGGGA 60.683 63.158 0.00 0.0 43.34 5.14


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

AutoCloner maintained by Alex Coulton.