Multiple sequence alignment - TraesCS7A01G315000

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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 TraesCS7A01G315000 chr7A 100.000 2507 0 0 1 2507 448724788 448727294 0.000000e+00 4630
1 TraesCS7A01G315000 chr1B 93.043 1811 104 8 1 1790 418816783 418814974 0.000000e+00 2627
2 TraesCS7A01G315000 chr3B 95.607 1639 49 12 184 1801 4299133 4297497 0.000000e+00 2606
3 TraesCS7A01G315000 chr3B 91.944 1204 76 7 618 1800 803413028 803414231 0.000000e+00 1666
4 TraesCS7A01G315000 chr3B 94.819 193 6 3 1 193 4299971 4299783 5.240000e-77 298
5 TraesCS7A01G315000 chr6B 94.136 1569 92 0 1 1569 599764248 599762680 0.000000e+00 2388
6 TraesCS7A01G315000 chr6B 79.443 574 82 10 1248 1800 212165102 212164544 8.470000e-100 374
7 TraesCS7A01G315000 chr2B 92.731 1527 82 15 265 1775 766530678 766532191 0.000000e+00 2178
8 TraesCS7A01G315000 chr5B 90.436 1537 103 17 286 1799 529384330 529382815 0.000000e+00 1984
9 TraesCS7A01G315000 chr5B 81.209 612 106 7 1198 1800 419522160 419522771 3.750000e-133 484
10 TraesCS7A01G315000 chr7B 91.882 1318 79 9 505 1800 628753143 628754454 0.000000e+00 1816
11 TraesCS7A01G315000 chr7B 91.845 515 17 10 1996 2507 395243079 395243571 0.000000e+00 695
12 TraesCS7A01G315000 chr7B 96.212 264 10 0 117 380 628752878 628753141 1.380000e-117 433
13 TraesCS7A01G315000 chr7B 95.238 126 5 1 1798 1922 395242705 395242830 5.470000e-47 198
14 TraesCS7A01G315000 chrUn 92.359 1204 71 7 618 1800 291471280 291470077 0.000000e+00 1694
15 TraesCS7A01G315000 chrUn 92.276 1204 72 7 618 1800 291269647 291270850 0.000000e+00 1688
16 TraesCS7A01G315000 chr4D 84.848 1089 147 5 250 1326 494058877 494059959 0.000000e+00 1081
17 TraesCS7A01G315000 chr4D 80.456 614 83 24 1219 1810 51916715 51917313 3.830000e-118 435
18 TraesCS7A01G315000 chr4D 78.846 572 98 9 255 813 51915805 51916366 5.100000e-97 364
19 TraesCS7A01G315000 chr4D 91.716 169 13 1 1633 1800 75795458 75795290 1.500000e-57 233
20 TraesCS7A01G315000 chr7D 91.197 727 21 19 1798 2507 395601766 395602466 0.000000e+00 948
21 TraesCS7A01G315000 chr6A 82.185 842 113 20 303 1128 187976160 187976980 0.000000e+00 689
22 TraesCS7A01G315000 chr2D 81.209 612 106 7 1198 1800 617966887 617967498 3.750000e-133 484
23 TraesCS7A01G315000 chr6D 80.407 393 68 9 1417 1800 39090112 39090504 8.770000e-75 291


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 TraesCS7A01G315000 chr7A 448724788 448727294 2506 False 4630.0 4630 100.0000 1 2507 1 chr7A.!!$F1 2506
1 TraesCS7A01G315000 chr1B 418814974 418816783 1809 True 2627.0 2627 93.0430 1 1790 1 chr1B.!!$R1 1789
2 TraesCS7A01G315000 chr3B 803413028 803414231 1203 False 1666.0 1666 91.9440 618 1800 1 chr3B.!!$F1 1182
3 TraesCS7A01G315000 chr3B 4297497 4299971 2474 True 1452.0 2606 95.2130 1 1801 2 chr3B.!!$R1 1800
4 TraesCS7A01G315000 chr6B 599762680 599764248 1568 True 2388.0 2388 94.1360 1 1569 1 chr6B.!!$R2 1568
5 TraesCS7A01G315000 chr6B 212164544 212165102 558 True 374.0 374 79.4430 1248 1800 1 chr6B.!!$R1 552
6 TraesCS7A01G315000 chr2B 766530678 766532191 1513 False 2178.0 2178 92.7310 265 1775 1 chr2B.!!$F1 1510
7 TraesCS7A01G315000 chr5B 529382815 529384330 1515 True 1984.0 1984 90.4360 286 1799 1 chr5B.!!$R1 1513
8 TraesCS7A01G315000 chr5B 419522160 419522771 611 False 484.0 484 81.2090 1198 1800 1 chr5B.!!$F1 602
9 TraesCS7A01G315000 chr7B 628752878 628754454 1576 False 1124.5 1816 94.0470 117 1800 2 chr7B.!!$F2 1683
10 TraesCS7A01G315000 chr7B 395242705 395243571 866 False 446.5 695 93.5415 1798 2507 2 chr7B.!!$F1 709
11 TraesCS7A01G315000 chrUn 291470077 291471280 1203 True 1694.0 1694 92.3590 618 1800 1 chrUn.!!$R1 1182
12 TraesCS7A01G315000 chrUn 291269647 291270850 1203 False 1688.0 1688 92.2760 618 1800 1 chrUn.!!$F1 1182
13 TraesCS7A01G315000 chr4D 494058877 494059959 1082 False 1081.0 1081 84.8480 250 1326 1 chr4D.!!$F1 1076
14 TraesCS7A01G315000 chr4D 51915805 51917313 1508 False 399.5 435 79.6510 255 1810 2 chr4D.!!$F2 1555
15 TraesCS7A01G315000 chr7D 395601766 395602466 700 False 948.0 948 91.1970 1798 2507 1 chr7D.!!$F1 709
16 TraesCS7A01G315000 chr6A 187976160 187976980 820 False 689.0 689 82.1850 303 1128 1 chr6A.!!$F1 825
17 TraesCS7A01G315000 chr2D 617966887 617967498 611 False 484.0 484 81.2090 1198 1800 1 chr2D.!!$F1 602

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 1626 0.029567 CTGTCGTCGAGGCCTATGTC 59.97 60.0 4.42 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2054 3083 0.515564 ATTCGAAAACTGCCGTTCGG 59.484 50.0 0.0 6.9 45.16 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
186 192 2.280797 GAGTTGGCACCGCAGACA 60.281 61.111 0.00 0.00 0.00 3.41
547 1214 1.134367 GTCTTCGATCCGGTCACATCA 59.866 52.381 0.00 0.00 0.00 3.07
632 1299 1.601759 CTGCACCCACCAGTGAAGG 60.602 63.158 0.00 0.00 39.44 3.46
889 1622 0.393944 ATGTCTGTCGTCGAGGCCTA 60.394 55.000 4.42 0.00 0.00 3.93
893 1626 0.029567 CTGTCGTCGAGGCCTATGTC 59.970 60.000 4.42 0.00 0.00 3.06
1194 2002 1.296715 GGCGGTGTCTGTGAGGAAT 59.703 57.895 0.00 0.00 0.00 3.01
1328 2136 0.108615 ATTGACGAGGCGGTCTTCAG 60.109 55.000 11.91 0.00 35.05 3.02
1559 2383 1.511305 GATTGGCTCGTCTCCGTGA 59.489 57.895 0.00 0.00 35.01 4.35
1641 2471 4.222124 AGTGTGAGGGATTATGGTTGTC 57.778 45.455 0.00 0.00 0.00 3.18
1749 2602 9.471084 CCGTTAATTAACTGGACAATTCTTTTT 57.529 29.630 23.47 0.00 34.24 1.94
1852 2705 2.257207 TCCCCTTTCACTCCACTGTAG 58.743 52.381 0.00 0.00 0.00 2.74
1869 2722 3.165875 TGTAGAGTCTGTCCCCTTTGAG 58.834 50.000 1.86 0.00 0.00 3.02
1929 2782 4.666253 CCAGCCCACACCCACAGG 62.666 72.222 0.00 0.00 40.04 4.00
1949 2802 1.317431 GGCACACCCGTAAATTCCCC 61.317 60.000 0.00 0.00 0.00 4.81
1967 2820 2.359975 CCCAGAACCACGCCCTTC 60.360 66.667 0.00 0.00 0.00 3.46
1992 3008 1.534729 CCCCTAATCCCGCATTTAGC 58.465 55.000 0.00 0.00 40.87 3.09
1993 3009 1.202879 CCCCTAATCCCGCATTTAGCA 60.203 52.381 0.00 0.00 46.13 3.49
1994 3010 2.555227 CCCCTAATCCCGCATTTAGCAT 60.555 50.000 0.00 0.00 46.13 3.79
2053 3082 3.787001 CCGTTCTGCCCCTCCCTC 61.787 72.222 0.00 0.00 0.00 4.30
2054 3083 3.787001 CGTTCTGCCCCTCCCTCC 61.787 72.222 0.00 0.00 0.00 4.30
2055 3084 3.412408 GTTCTGCCCCTCCCTCCC 61.412 72.222 0.00 0.00 0.00 4.30
2064 3093 4.148825 CTCCCTCCCGAACGGCAG 62.149 72.222 7.80 2.13 0.00 4.85
2094 3123 1.154035 CGCATTGAAAACTCGGCCC 60.154 57.895 0.00 0.00 0.00 5.80
2135 3164 6.592798 ATTTCGCGTCCGATTTCTTTATTA 57.407 33.333 5.77 0.00 43.97 0.98
2138 3167 5.969741 TCGCGTCCGATTTCTTTATTATTG 58.030 37.500 5.77 0.00 38.82 1.90
2140 3169 6.036300 TCGCGTCCGATTTCTTTATTATTGTT 59.964 34.615 5.77 0.00 38.82 2.83
2141 3170 7.222417 TCGCGTCCGATTTCTTTATTATTGTTA 59.778 33.333 5.77 0.00 38.82 2.41
2142 3171 8.007716 CGCGTCCGATTTCTTTATTATTGTTAT 58.992 33.333 0.00 0.00 36.29 1.89
2143 3172 9.314501 GCGTCCGATTTCTTTATTATTGTTATC 57.685 33.333 0.00 0.00 0.00 1.75
2144 3173 9.512287 CGTCCGATTTCTTTATTATTGTTATCG 57.488 33.333 0.00 0.00 33.98 2.92
2145 3174 9.314501 GTCCGATTTCTTTATTATTGTTATCGC 57.685 33.333 0.00 0.00 33.14 4.58
2340 3375 2.436115 CGCTCCCGGTTTCTTCCC 60.436 66.667 0.00 0.00 0.00 3.97
2376 3411 2.892425 CGGCGCAGGGATTCTGTC 60.892 66.667 10.83 0.00 45.08 3.51
2409 3445 5.237815 GTTCCTGGGATTTGTGGATTTTTC 58.762 41.667 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
199 855 2.666190 CTCCACACACGCCACTGG 60.666 66.667 0.00 0.00 0.00 4.00
439 1106 1.895798 CCTATCTCTTAGCCATGCCGA 59.104 52.381 0.00 0.00 0.00 5.54
889 1622 1.273606 CCCAGAGACAGACAACGACAT 59.726 52.381 0.00 0.00 0.00 3.06
893 1626 0.962489 ACTCCCAGAGACAGACAACG 59.038 55.000 0.00 0.00 33.32 4.10
1194 2002 1.968017 ACCGACAGACGCGACCTTA 60.968 57.895 15.93 0.00 41.07 2.69
1328 2136 2.360475 AGCCGCCAAGCTTCTTCC 60.360 61.111 0.00 0.00 41.41 3.46
1461 2270 1.301716 GGCGTCACTCTTCTTGCCA 60.302 57.895 0.00 0.00 42.03 4.92
1559 2383 2.940410 AGACAACGAACGACACCAAATT 59.060 40.909 0.14 0.00 0.00 1.82
1641 2471 2.423373 CCCCTAACCCATGATCAACCTG 60.423 54.545 0.00 0.00 0.00 4.00
1749 2602 6.971527 TTGCCTCGTCGATTAATTAAGAAA 57.028 33.333 3.94 0.00 0.00 2.52
1776 2629 3.817148 TTTTTCGAAACGGAGGCATAC 57.183 42.857 10.79 0.00 0.00 2.39
1852 2705 1.067495 CGACTCAAAGGGGACAGACTC 60.067 57.143 0.00 0.00 0.00 3.36
1949 2802 3.920093 GAAGGGCGTGGTTCTGGGG 62.920 68.421 0.00 0.00 0.00 4.96
1954 2807 4.735358 GGGGGAAGGGCGTGGTTC 62.735 72.222 0.00 0.00 0.00 3.62
2015 3044 3.554960 GGGAAGTGGAAAATGTTTGGCTC 60.555 47.826 0.00 0.00 0.00 4.70
2052 3081 1.957186 CGAAAACTGCCGTTCGGGA 60.957 57.895 13.16 9.31 42.21 5.14
2053 3082 1.500512 TTCGAAAACTGCCGTTCGGG 61.501 55.000 13.16 0.00 45.16 5.14
2054 3083 0.515564 ATTCGAAAACTGCCGTTCGG 59.484 50.000 0.00 6.90 45.16 4.30
2055 3084 2.230864 GAATTCGAAAACTGCCGTTCG 58.769 47.619 0.00 0.00 46.17 3.95
2064 3093 5.174943 AGTTTTCAATGCGGAATTCGAAAAC 59.825 36.000 24.51 24.51 42.43 2.43
2094 3123 2.852495 ATTGTCGCTGTACGCCCCAG 62.852 60.000 4.51 0.00 43.23 4.45
2320 3355 2.047179 AAGAAACCGGGAGCGAGC 60.047 61.111 6.32 0.00 0.00 5.03
2321 3356 1.448013 GGAAGAAACCGGGAGCGAG 60.448 63.158 6.32 0.00 0.00 5.03
2322 3357 2.660802 GGAAGAAACCGGGAGCGA 59.339 61.111 6.32 0.00 0.00 4.93
2323 3358 2.436115 GGGAAGAAACCGGGAGCG 60.436 66.667 6.32 0.00 0.00 5.03
2324 3359 2.045242 GGGGAAGAAACCGGGAGC 60.045 66.667 6.32 0.00 0.00 4.70
2325 3360 1.911702 GAGGGGGAAGAAACCGGGAG 61.912 65.000 6.32 0.00 0.00 4.30
2326 3361 1.921857 GAGGGGGAAGAAACCGGGA 60.922 63.158 6.32 0.00 0.00 5.14
2327 3362 1.911702 GAGAGGGGGAAGAAACCGGG 61.912 65.000 6.32 0.00 0.00 5.73
2360 3395 1.078143 AAGACAGAATCCCTGCGCC 60.078 57.895 4.18 0.00 46.81 6.53
2368 3403 5.979517 CAGGAACCAAAAACAAGACAGAATC 59.020 40.000 0.00 0.00 0.00 2.52
2374 3409 3.028130 TCCCAGGAACCAAAAACAAGAC 58.972 45.455 0.00 0.00 0.00 3.01
2375 3410 3.390175 TCCCAGGAACCAAAAACAAGA 57.610 42.857 0.00 0.00 0.00 3.02
2376 3411 4.687901 AATCCCAGGAACCAAAAACAAG 57.312 40.909 0.00 0.00 0.00 3.16
2467 3506 0.843343 TCCCTCCTTAAAACCCGCCT 60.843 55.000 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.