Multiple sequence alignment - TraesCS7D01G295500

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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 TraesCS7D01G295500 chr7D 100.000 3560 0 0 1 3560 370465155 370461596 0.000000e+00 6575
1 TraesCS7D01G295500 chr7D 96.386 1937 64 5 1622 3557 234395113 234397044 0.000000e+00 3184
2 TraesCS7D01G295500 chr7D 95.267 1669 73 4 1 1664 234393540 234395207 0.000000e+00 2639
3 TraesCS7D01G295500 chr1D 95.973 1937 74 4 1622 3557 238011787 238013720 0.000000e+00 3142
4 TraesCS7D01G295500 chr1D 91.557 1670 102 13 3 1664 371719924 371721562 0.000000e+00 2266
5 TraesCS7D01G295500 chr3D 95.121 1947 88 5 1618 3560 428373491 428375434 0.000000e+00 3062
6 TraesCS7D01G295500 chr3D 94.353 1948 98 8 1622 3560 323156010 323157954 0.000000e+00 2977
7 TraesCS7D01G295500 chr3D 93.875 1943 106 8 1622 3560 395863269 395865202 0.000000e+00 2916
8 TraesCS7D01G295500 chr3D 91.727 1644 100 11 3 1639 323154465 323156079 0.000000e+00 2250
9 TraesCS7D01G295500 chr3D 95.425 153 7 0 1487 1639 428373413 428373565 9.870000e-61 244
10 TraesCS7D01G295500 chr4D 94.289 1926 101 7 1637 3558 310013833 310015753 0.000000e+00 2939
11 TraesCS7D01G295500 chr4D 91.938 1625 106 17 3 1620 148264685 148266291 0.000000e+00 2252
12 TraesCS7D01G295500 chr6D 93.789 1948 107 11 1622 3560 256022246 256024188 0.000000e+00 2915
13 TraesCS7D01G295500 chr5D 93.686 1948 110 9 1622 3560 190779588 190777645 0.000000e+00 2904
14 TraesCS7D01G295500 chr5D 90.920 1674 112 12 3 1667 190781133 190779491 0.000000e+00 2213
15 TraesCS7D01G295500 chr7A 93.515 1943 118 7 1622 3560 315494234 315492296 0.000000e+00 2883
16 TraesCS7D01G295500 chr7A 92.648 1673 105 17 1 1667 315495798 315494138 0.000000e+00 2392
17 TraesCS7D01G295500 chr2D 93.337 1666 91 10 1 1664 273055759 273057406 0.000000e+00 2444
18 TraesCS7D01G295500 chr6A 91.801 1671 119 14 1 1664 446428187 446429846 0.000000e+00 2311
19 TraesCS7D01G295500 chr6A 91.061 179 13 3 1491 1667 590012388 590012211 4.590000e-59 239
20 TraesCS7D01G295500 chr3A 91.882 1626 116 11 1 1620 217243209 217241594 0.000000e+00 2257
21 TraesCS7D01G295500 chr2A 94.410 161 8 1 1480 1639 434157269 434157109 2.740000e-61 246


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 TraesCS7D01G295500 chr7D 370461596 370465155 3559 True 6575.0 6575 100.0000 1 3560 1 chr7D.!!$R1 3559
1 TraesCS7D01G295500 chr7D 234393540 234397044 3504 False 2911.5 3184 95.8265 1 3557 2 chr7D.!!$F1 3556
2 TraesCS7D01G295500 chr1D 238011787 238013720 1933 False 3142.0 3142 95.9730 1622 3557 1 chr1D.!!$F1 1935
3 TraesCS7D01G295500 chr1D 371719924 371721562 1638 False 2266.0 2266 91.5570 3 1664 1 chr1D.!!$F2 1661
4 TraesCS7D01G295500 chr3D 395863269 395865202 1933 False 2916.0 2916 93.8750 1622 3560 1 chr3D.!!$F1 1938
5 TraesCS7D01G295500 chr3D 323154465 323157954 3489 False 2613.5 2977 93.0400 3 3560 2 chr3D.!!$F2 3557
6 TraesCS7D01G295500 chr3D 428373413 428375434 2021 False 1653.0 3062 95.2730 1487 3560 2 chr3D.!!$F3 2073
7 TraesCS7D01G295500 chr4D 310013833 310015753 1920 False 2939.0 2939 94.2890 1637 3558 1 chr4D.!!$F2 1921
8 TraesCS7D01G295500 chr4D 148264685 148266291 1606 False 2252.0 2252 91.9380 3 1620 1 chr4D.!!$F1 1617
9 TraesCS7D01G295500 chr6D 256022246 256024188 1942 False 2915.0 2915 93.7890 1622 3560 1 chr6D.!!$F1 1938
10 TraesCS7D01G295500 chr5D 190777645 190781133 3488 True 2558.5 2904 92.3030 3 3560 2 chr5D.!!$R1 3557
11 TraesCS7D01G295500 chr7A 315492296 315495798 3502 True 2637.5 2883 93.0815 1 3560 2 chr7A.!!$R1 3559
12 TraesCS7D01G295500 chr2D 273055759 273057406 1647 False 2444.0 2444 93.3370 1 1664 1 chr2D.!!$F1 1663
13 TraesCS7D01G295500 chr6A 446428187 446429846 1659 False 2311.0 2311 91.8010 1 1664 1 chr6A.!!$F1 1663
14 TraesCS7D01G295500 chr3A 217241594 217243209 1615 True 2257.0 2257 91.8820 1 1620 1 chr3A.!!$R1 1619

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
761 772 0.739813 CGGTTAGTTCTTCCAGGCCG 60.740 60.0 0.0 0.0 0.00 6.13 F
2169 2195 0.312102 GCCTCAAACAGTTCCTGCAC 59.688 55.0 0.0 0.0 34.37 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2543 2575 0.320374 TCTTCATCCCGCGAAGTTGT 59.680 50.000 8.23 0.0 40.63 3.32 R
3304 3350 1.876156 CTGTGGTTCTTCTCAAGGCAC 59.124 52.381 0.00 0.0 0.00 5.01 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
83 84 8.205131 TGACAAGTTCAACTACTAAAAGGAAC 57.795 34.615 0.00 0.00 35.95 3.62
234 235 6.959639 ATTTGTACAAAATCTGTCCACACT 57.040 33.333 23.97 0.97 39.64 3.55
448 458 9.632638 ACCATAAGTGCACTAAAATGAGAATAT 57.367 29.630 26.39 13.69 0.00 1.28
485 495 5.290493 CCTAACATAGGTTGGCACAGATA 57.710 43.478 2.37 0.00 41.18 1.98
521 531 3.356290 ACCAGTTTTGAGCAACAACTCT 58.644 40.909 0.00 0.00 38.29 3.24
698 708 8.307483 GGATTTAGCAGATCATAAGTACAGCTA 58.693 37.037 0.00 0.00 32.70 3.32
734 745 5.652891 TCAGTGCAACAGTAAAAACCCTTTA 59.347 36.000 0.00 0.00 41.43 1.85
761 772 0.739813 CGGTTAGTTCTTCCAGGCCG 60.740 60.000 0.00 0.00 0.00 6.13
992 1005 4.681978 AGCCCACAGTCGCCGAAC 62.682 66.667 0.00 0.00 0.00 3.95
1048 1061 1.153823 CATGGTGAGACGTCGGACC 60.154 63.158 24.43 24.43 0.00 4.46
1075 1088 0.593008 CAACCTCGTCGACGTTCACA 60.593 55.000 34.40 16.33 40.80 3.58
1125 1138 1.763770 CCTCACAGGGGTTGAGCTT 59.236 57.895 0.00 0.00 0.00 3.74
1177 1190 2.281484 GCGAACCAGACAAGGCCA 60.281 61.111 5.01 0.00 0.00 5.36
1603 1624 7.887996 TGATGCACCAAATTAATTTCTGAAC 57.112 32.000 10.53 1.40 0.00 3.18
1604 1625 7.669427 TGATGCACCAAATTAATTTCTGAACT 58.331 30.769 10.53 0.00 0.00 3.01
1605 1626 8.149647 TGATGCACCAAATTAATTTCTGAACTT 58.850 29.630 10.53 0.00 0.00 2.66
1606 1627 7.712264 TGCACCAAATTAATTTCTGAACTTG 57.288 32.000 10.53 0.00 0.00 3.16
1607 1628 7.495901 TGCACCAAATTAATTTCTGAACTTGA 58.504 30.769 10.53 0.00 0.00 3.02
1608 1629 8.149647 TGCACCAAATTAATTTCTGAACTTGAT 58.850 29.630 10.53 0.00 0.00 2.57
1609 1630 8.437742 GCACCAAATTAATTTCTGAACTTGATG 58.562 33.333 10.53 0.00 0.00 3.07
1610 1631 9.480053 CACCAAATTAATTTCTGAACTTGATGT 57.520 29.630 10.53 0.00 0.00 3.06
1617 1638 9.719355 TTAATTTCTGAACTTGATGTACTAGCA 57.281 29.630 3.54 0.00 0.00 3.49
1618 1639 8.798859 AATTTCTGAACTTGATGTACTAGCAT 57.201 30.769 0.00 0.00 0.00 3.79
1619 1640 9.890629 AATTTCTGAACTTGATGTACTAGCATA 57.109 29.630 0.00 0.00 0.00 3.14
1846 1867 7.335924 GCACTGGTATAGGTCTTTTATTCAACA 59.664 37.037 0.00 0.00 0.00 3.33
1912 1934 7.672983 TGACTCTGGTAAAATGATTCTTCAC 57.327 36.000 0.00 0.00 33.85 3.18
1917 1939 7.370383 TCTGGTAAAATGATTCTTCACTTTGC 58.630 34.615 0.00 0.00 32.73 3.68
1940 1963 0.963962 AGCATTTGGTGAAGCACTGG 59.036 50.000 0.00 0.00 34.40 4.00
2022 2046 9.639601 TGTACTAGTTTCTGAACTACATTCATG 57.360 33.333 0.00 0.00 46.37 3.07
2074 2098 7.888021 ACCTCATGGATTATCACTTGTAAAACA 59.112 33.333 0.00 0.00 37.04 2.83
2169 2195 0.312102 GCCTCAAACAGTTCCTGCAC 59.688 55.000 0.00 0.00 34.37 4.57
2236 2262 3.107402 AGAGGATGCTGGACAAGTCTA 57.893 47.619 0.00 0.00 0.00 2.59
2265 2291 5.253330 GAGATCAACCCCAACAACTTCATA 58.747 41.667 0.00 0.00 0.00 2.15
2481 2513 5.179368 CACGTACAAGTCATGGAAGACAATT 59.821 40.000 0.00 0.00 40.98 2.32
2513 2545 5.637810 TCGTGACAGGTTCAGATATTTCAAC 59.362 40.000 0.00 0.00 33.71 3.18
2543 2575 2.861317 AGGCTAACCCCTACTACCACTA 59.139 50.000 0.00 0.00 36.11 2.74
2642 2674 7.542890 TGTTTCAGATTTGTAGTTTGCTTTCA 58.457 30.769 0.00 0.00 0.00 2.69
2666 2698 7.715249 TCATTATGTTGAACCAGCTACCTTATC 59.285 37.037 0.00 0.00 0.00 1.75
2686 2718 3.146066 TCTTATGTGTGTCAGGGTTTGC 58.854 45.455 0.00 0.00 0.00 3.68
2696 2728 2.094234 GTCAGGGTTTGCACAAGTTTGT 60.094 45.455 0.00 0.00 43.36 2.83
2782 2814 6.680810 TGTTGATCCATCATTTGAAGTTGAC 58.319 36.000 0.00 0.00 36.56 3.18
2788 2820 4.437390 CCATCATTTGAAGTTGACGTAGGC 60.437 45.833 0.00 0.00 0.00 3.93
2942 2984 6.908216 GTACAGCTTATACATGTACGCTAC 57.092 41.667 19.63 14.10 39.73 3.58
3286 3332 6.793349 ACAACTTAGTCTATACGGCAAGTAG 58.207 40.000 0.00 0.00 38.94 2.57
3304 3350 7.041780 GGCAAGTAGTATGATCATACCAAACAG 60.042 40.741 32.70 24.44 43.51 3.16
3358 3404 7.786178 AAGAAGGCCAAAACTAAATCAAAAC 57.214 32.000 5.01 0.00 0.00 2.43
3432 3480 0.962356 CCACATTGACCAGTGAGGCC 60.962 60.000 0.00 0.00 43.14 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 8.647143 ACAAACATTGTCTATTTTGAACTTGG 57.353 30.769 5.42 0.00 40.56 3.61
148 149 9.463443 GAACTTGTTGCATTTTAGTACTTGAAT 57.537 29.630 0.00 0.00 0.00 2.57
215 216 6.371809 TTGAAGTGTGGACAGATTTTGTAC 57.628 37.500 0.00 0.00 41.05 2.90
218 219 6.075762 TCATTGAAGTGTGGACAGATTTTG 57.924 37.500 0.00 0.00 0.00 2.44
340 350 1.130054 AGTGGTGTGAGTGGCCTGAT 61.130 55.000 3.32 0.00 0.00 2.90
521 531 4.161189 TCAAAACATTTTTCAGTGCCCTGA 59.839 37.500 0.00 0.00 45.95 3.86
698 708 3.384789 TGTTGCACTGAGTAGTCTTGTCT 59.615 43.478 0.00 0.00 34.07 3.41
734 745 3.581332 TGGAAGAACTAACCGTCCAAGAT 59.419 43.478 0.00 0.00 38.80 2.40
872 883 4.220602 AGACAATGGGGTATTTTTGCAGTC 59.779 41.667 0.00 0.00 0.00 3.51
1025 1038 1.067669 CCGACGTCTCACCATGATGAT 59.932 52.381 14.70 0.00 0.00 2.45
1048 1061 2.091112 CGACGAGGTTGCTGCTCTG 61.091 63.158 0.00 0.00 0.00 3.35
1125 1138 0.325933 CCAGTGTCTCCTTGCCATGA 59.674 55.000 0.00 0.00 0.00 3.07
1177 1190 1.078848 GCCTGCTCATCACCTCGTT 60.079 57.895 0.00 0.00 0.00 3.85
1303 1317 1.429463 GTACACCAAGCAGAGTTCCG 58.571 55.000 0.00 0.00 0.00 4.30
1611 1632 8.537858 TGCATCAAGATCAGAATATATGCTAGT 58.462 33.333 0.00 0.00 39.30 2.57
1612 1633 8.819015 GTGCATCAAGATCAGAATATATGCTAG 58.181 37.037 0.00 0.00 39.30 3.42
1613 1634 7.767659 GGTGCATCAAGATCAGAATATATGCTA 59.232 37.037 0.00 0.00 39.30 3.49
1614 1635 6.598457 GGTGCATCAAGATCAGAATATATGCT 59.402 38.462 0.00 0.00 39.30 3.79
1615 1636 6.373495 TGGTGCATCAAGATCAGAATATATGC 59.627 38.462 0.00 0.00 39.08 3.14
1616 1637 7.916914 TGGTGCATCAAGATCAGAATATATG 57.083 36.000 0.00 0.00 0.00 1.78
1617 1638 8.929260 TTTGGTGCATCAAGATCAGAATATAT 57.071 30.769 13.02 0.00 0.00 0.86
1618 1639 8.929260 ATTTGGTGCATCAAGATCAGAATATA 57.071 30.769 13.02 0.00 0.00 0.86
1619 1640 7.834881 ATTTGGTGCATCAAGATCAGAATAT 57.165 32.000 13.02 0.00 0.00 1.28
1620 1641 7.649533 AATTTGGTGCATCAAGATCAGAATA 57.350 32.000 13.02 0.00 0.00 1.75
1628 1649 7.894708 TCAGAAATTAATTTGGTGCATCAAGA 58.105 30.769 17.98 4.84 0.00 3.02
1917 1939 2.295349 AGTGCTTCACCAAATGCTTCAG 59.705 45.455 0.00 0.00 34.49 3.02
2169 2195 6.241207 ACAAATGTGTACAATTTCTCCTCG 57.759 37.500 0.00 0.00 35.72 4.63
2265 2291 2.330372 CCACTTGCGCTGCATGTCT 61.330 57.895 9.73 0.00 43.35 3.41
2339 2365 3.947834 GTCTTTGTAGAATGGGTGGATGG 59.052 47.826 0.00 0.00 30.65 3.51
2481 2513 2.159028 TGAACCTGTCACGATGTTGTCA 60.159 45.455 0.00 0.00 0.00 3.58
2543 2575 0.320374 TCTTCATCCCGCGAAGTTGT 59.680 50.000 8.23 0.00 40.63 3.32
2642 2674 7.806180 AGATAAGGTAGCTGGTTCAACATAAT 58.194 34.615 0.00 0.00 0.00 1.28
2666 2698 2.884012 TGCAAACCCTGACACACATAAG 59.116 45.455 0.00 0.00 0.00 1.73
2686 2718 8.539770 AGTTGATAGACATAGACAAACTTGTG 57.460 34.615 0.00 0.00 42.43 3.33
2696 2728 7.648112 GCAAACGATGTAGTTGATAGACATAGA 59.352 37.037 0.00 0.00 33.99 1.98
2782 2814 3.807622 TCAAGTTTCAACTTCAGCCTACG 59.192 43.478 1.76 0.00 45.65 3.51
2788 2820 4.543692 CAGCCATCAAGTTTCAACTTCAG 58.456 43.478 1.76 0.00 45.65 3.02
2824 2856 4.281435 TGTGTGATTTTGTTGCTCCATGAT 59.719 37.500 0.00 0.00 0.00 2.45
2868 2904 4.347000 TGTCCTTAGTTAGTCTGCCACTTT 59.653 41.667 0.00 0.00 36.43 2.66
3204 3249 5.751243 AGTGTGTCACTGTTTTATGGAAC 57.249 39.130 4.27 0.00 43.63 3.62
3286 3332 5.126067 AGGCACTGTTTGGTATGATCATAC 58.874 41.667 30.03 30.03 39.48 2.39
3304 3350 1.876156 CTGTGGTTCTTCTCAAGGCAC 59.124 52.381 0.00 0.00 0.00 5.01
3358 3404 3.315470 TCTCCTTGGTCGAACTGATATCG 59.685 47.826 0.33 0.00 41.53 2.92
3491 3539 9.695526 TTAGCGAATAAACTAAGTTGTACTGAA 57.304 29.630 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.