Multiple sequence alignment - TraesCS6A01G366600

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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 TraesCS6A01G366600 chr6A 100.000 2255 0 0 1 2255 594278366 594280620 0.000000e+00 4165
1 TraesCS6A01G366600 chr5A 97.606 1504 30 2 1 1498 552382462 552380959 0.000000e+00 2573
2 TraesCS6A01G366600 chr3A 97.403 1502 33 5 1 1499 479688738 479690236 0.000000e+00 2553
3 TraesCS6A01G366600 chr7A 97.342 1505 32 4 1 1498 32948565 32947062 0.000000e+00 2551
4 TraesCS6A01G366600 chr7A 86.259 1259 96 26 248 1503 17458535 17459719 0.000000e+00 1295
5 TraesCS6A01G366600 chr6D 92.876 1151 57 11 350 1498 25493859 25494986 0.000000e+00 1648
6 TraesCS6A01G366600 chr6D 92.702 1151 59 11 350 1498 413024132 413025259 0.000000e+00 1637
7 TraesCS6A01G366600 chr6D 88.898 1279 84 24 2 1269 462350982 462352213 0.000000e+00 1522
8 TraesCS6A01G366600 chr6D 93.860 342 11 5 1 332 25493368 25493709 7.190000e-140 507
9 TraesCS6A01G366600 chr6D 94.048 336 16 3 1 332 413023651 413023986 7.190000e-140 507
10 TraesCS6A01G366600 chr5D 92.801 1153 58 11 350 1500 485921523 485920394 0.000000e+00 1646
11 TraesCS6A01G366600 chr5D 86.540 1263 93 26 247 1506 450171090 450169902 0.000000e+00 1319
12 TraesCS6A01G366600 chr4D 92.580 1159 60 12 350 1506 506094805 506095939 0.000000e+00 1640
13 TraesCS6A01G366600 chr4D 93.860 342 11 5 1 332 506094315 506094656 7.190000e-140 507
14 TraesCS6A01G366600 chr1A 86.328 1258 94 28 248 1502 249376329 249375147 0.000000e+00 1299
15 TraesCS6A01G366600 chr1A 90.795 239 22 0 2 240 249376737 249376499 1.000000e-83 320
16 TraesCS6A01G366600 chr6B 88.296 769 53 21 1499 2253 676871283 676872028 0.000000e+00 887
17 TraesCS6A01G366600 chr6B 87.632 663 38 18 1608 2255 677090710 677091343 0.000000e+00 730
18 TraesCS6A01G366600 chr6B 86.723 595 61 14 1664 2251 677646271 677646854 0.000000e+00 645
19 TraesCS6A01G366600 chr6B 90.777 412 20 10 1 409 124059570 124059966 3.300000e-148 534
20 TraesCS6A01G366600 chr4A 91.199 659 46 4 839 1494 648995966 648996615 0.000000e+00 885
21 TraesCS6A01G366600 chr4A 91.505 412 24 9 1 409 648979524 648979927 7.040000e-155 556
22 TraesCS6A01G366600 chr4B 87.037 216 28 0 1283 1498 650581125 650580910 6.220000e-61 244


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 TraesCS6A01G366600 chr6A 594278366 594280620 2254 False 4165.0 4165 100.0000 1 2255 1 chr6A.!!$F1 2254
1 TraesCS6A01G366600 chr5A 552380959 552382462 1503 True 2573.0 2573 97.6060 1 1498 1 chr5A.!!$R1 1497
2 TraesCS6A01G366600 chr3A 479688738 479690236 1498 False 2553.0 2553 97.4030 1 1499 1 chr3A.!!$F1 1498
3 TraesCS6A01G366600 chr7A 32947062 32948565 1503 True 2551.0 2551 97.3420 1 1498 1 chr7A.!!$R1 1497
4 TraesCS6A01G366600 chr7A 17458535 17459719 1184 False 1295.0 1295 86.2590 248 1503 1 chr7A.!!$F1 1255
5 TraesCS6A01G366600 chr6D 462350982 462352213 1231 False 1522.0 1522 88.8980 2 1269 1 chr6D.!!$F1 1267
6 TraesCS6A01G366600 chr6D 25493368 25494986 1618 False 1077.5 1648 93.3680 1 1498 2 chr6D.!!$F2 1497
7 TraesCS6A01G366600 chr6D 413023651 413025259 1608 False 1072.0 1637 93.3750 1 1498 2 chr6D.!!$F3 1497
8 TraesCS6A01G366600 chr5D 485920394 485921523 1129 True 1646.0 1646 92.8010 350 1500 1 chr5D.!!$R2 1150
9 TraesCS6A01G366600 chr5D 450169902 450171090 1188 True 1319.0 1319 86.5400 247 1506 1 chr5D.!!$R1 1259
10 TraesCS6A01G366600 chr4D 506094315 506095939 1624 False 1073.5 1640 93.2200 1 1506 2 chr4D.!!$F1 1505
11 TraesCS6A01G366600 chr1A 249375147 249376737 1590 True 809.5 1299 88.5615 2 1502 2 chr1A.!!$R1 1500
12 TraesCS6A01G366600 chr6B 676871283 676872028 745 False 887.0 887 88.2960 1499 2253 1 chr6B.!!$F2 754
13 TraesCS6A01G366600 chr6B 677090710 677091343 633 False 730.0 730 87.6320 1608 2255 1 chr6B.!!$F3 647
14 TraesCS6A01G366600 chr6B 677646271 677646854 583 False 645.0 645 86.7230 1664 2251 1 chr6B.!!$F4 587
15 TraesCS6A01G366600 chr4A 648995966 648996615 649 False 885.0 885 91.1990 839 1494 1 chr4A.!!$F2 655

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
208 220 1.408702 ACACCGCAATGCAGAAAGTTT 59.591 42.857 5.91 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1695 2033 0.467384 CCATGAAGCTCGTCCTCCAT 59.533 55.0 0.0 0.0 0.0 3.41 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
192 204 3.119137 GGAATTTAGTTGGGCATGACACC 60.119 47.826 0.00 0.00 0.00 4.16
208 220 1.408702 ACACCGCAATGCAGAAAGTTT 59.591 42.857 5.91 0.00 0.00 2.66
224 236 3.915437 AGTTTAGGTTGGTTGCAATCG 57.085 42.857 0.59 0.00 0.00 3.34
545 858 5.510520 CCTCTTGTATCTCCTGTTATCTGGC 60.511 48.000 0.00 0.00 33.50 4.85
704 1017 8.961092 CAAATGAAAATATTGCATCCTACTTCG 58.039 33.333 4.96 0.00 0.00 3.79
1461 1797 1.615883 CGTCAGATCAGGGTGGATAGG 59.384 57.143 0.00 0.00 0.00 2.57
1469 1805 2.109181 GGTGGATAGGCGGCTCAC 59.891 66.667 17.67 17.72 0.00 3.51
1519 1855 9.670442 TTGTAATAATTGTATACTCTCCTCCCT 57.330 33.333 4.17 0.00 0.00 4.20
1526 1862 0.478942 TACTCTCCTCCCTCATCCCG 59.521 60.000 0.00 0.00 0.00 5.14
1528 1864 3.237741 CTCCTCCCTCATCCCGCC 61.238 72.222 0.00 0.00 0.00 6.13
1578 1914 1.816074 TGTTTTCAGCGGGTATGACC 58.184 50.000 0.00 0.00 37.60 4.02
1617 1953 8.899427 TGAGAGAAGATACCATTTCATCATTC 57.101 34.615 0.00 0.00 0.00 2.67
1628 1964 3.301794 TTCATCATTCAGGTGGATGGG 57.698 47.619 0.00 0.00 39.07 4.00
1655 1991 5.183331 CGCCTACACATAAGCTCTATTCCTA 59.817 44.000 0.00 0.00 0.00 2.94
1656 1992 6.391537 GCCTACACATAAGCTCTATTCCTAC 58.608 44.000 0.00 0.00 0.00 3.18
1657 1993 6.613233 CCTACACATAAGCTCTATTCCTACG 58.387 44.000 0.00 0.00 0.00 3.51
1695 2033 6.326375 ACAAGTCACGTCAAAAATGCTAAAA 58.674 32.000 0.00 0.00 0.00 1.52
1718 2056 1.522580 GGACGAGCTTCATGGAGCC 60.523 63.158 22.85 12.83 43.74 4.70
1764 2105 8.689972 AGAAATCAGACTGTGAAGTTTCAAAAT 58.310 29.630 1.59 0.00 36.92 1.82
1766 2107 8.862550 AATCAGACTGTGAAGTTTCAAAATTC 57.137 30.769 3.30 3.30 39.19 2.17
1831 2172 7.443218 TGTGTGTAAAATTTGAACATGTTCG 57.557 32.000 28.55 0.00 42.28 3.95
1856 2197 5.174035 TGTTTTGAAAATGGCGAACAATACG 59.826 36.000 0.00 0.00 0.00 3.06
1858 2199 5.608676 TTGAAAATGGCGAACAATACGTA 57.391 34.783 0.00 0.00 0.00 3.57
2090 2433 5.055642 CTCAGGTCACATTGAGTACGTAA 57.944 43.478 0.00 0.00 36.82 3.18
2140 2483 5.784177 ACTTGAATCTCTAACGACACACAT 58.216 37.500 0.00 0.00 0.00 3.21
2159 2526 2.821810 CACGCACACACACCCACA 60.822 61.111 0.00 0.00 0.00 4.17
2222 2591 1.132500 GATCCCTAGTGAGTTGGGGG 58.868 60.000 6.96 0.00 41.22 5.40
2228 2597 3.385115 CCTAGTGAGTTGGGGGTAAGAT 58.615 50.000 0.00 0.00 0.00 2.40
2231 2600 3.464828 AGTGAGTTGGGGGTAAGATCAT 58.535 45.455 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
192 204 3.559238 ACCTAAACTTTCTGCATTGCG 57.441 42.857 3.84 0.00 0.00 4.85
208 220 1.001068 TCGTCGATTGCAACCAACCTA 59.999 47.619 0.00 0.00 32.95 3.08
224 236 5.647589 TCATGTACCTGTTTGTCTATCGTC 58.352 41.667 0.00 0.00 0.00 4.20
748 1061 9.821662 GCTTCGAGTAAAAAGTATAAACACATT 57.178 29.630 0.00 0.00 0.00 2.71
764 1083 0.966179 TGGTCTGCAGCTTCGAGTAA 59.034 50.000 9.47 0.00 0.00 2.24
882 1212 2.481854 GATGATTGCAGCGTCAGAGAT 58.518 47.619 6.47 0.00 0.00 2.75
1272 1608 1.615883 CTCACGTATCTGCCTAGCCAT 59.384 52.381 0.00 0.00 0.00 4.40
1350 1686 7.778382 GGACCATTACAATATTTTAGTGGGACT 59.222 37.037 20.88 6.38 0.00 3.85
1461 1797 2.202479 GGCGATTTTGTGAGCCGC 60.202 61.111 0.00 0.00 44.45 6.53
1469 1805 3.168193 GTTACGGTGATTGGCGATTTTG 58.832 45.455 0.00 0.00 0.00 2.44
1508 1844 1.231641 CGGGATGAGGGAGGAGAGT 59.768 63.158 0.00 0.00 0.00 3.24
1509 1845 2.206536 GCGGGATGAGGGAGGAGAG 61.207 68.421 0.00 0.00 0.00 3.20
1589 1925 9.690913 ATGATGAAATGGTATCTTCTCTCAAAA 57.309 29.630 0.00 0.00 0.00 2.44
1593 1929 8.899427 TGAATGATGAAATGGTATCTTCTCTC 57.101 34.615 0.00 0.00 0.00 3.20
1596 1932 7.501559 CACCTGAATGATGAAATGGTATCTTCT 59.498 37.037 0.00 0.00 0.00 2.85
1604 1940 4.038763 CCATCCACCTGAATGATGAAATGG 59.961 45.833 0.00 0.00 38.49 3.16
1617 1953 4.489771 GGCGGACCCATCCACCTG 62.490 72.222 0.00 0.00 46.67 4.00
1628 1964 1.409427 AGAGCTTATGTGTAGGCGGAC 59.591 52.381 0.00 0.00 37.92 4.79
1637 1973 6.804295 GTGATCGTAGGAATAGAGCTTATGTG 59.196 42.308 0.00 0.00 0.00 3.21
1655 1991 7.440556 ACGTGACTTGTAGTATATAGTGATCGT 59.559 37.037 0.00 0.00 0.00 3.73
1656 1992 7.794880 ACGTGACTTGTAGTATATAGTGATCG 58.205 38.462 0.00 0.00 0.00 3.69
1657 1993 8.771766 TGACGTGACTTGTAGTATATAGTGATC 58.228 37.037 0.00 0.00 0.00 2.92
1695 2033 0.467384 CCATGAAGCTCGTCCTCCAT 59.533 55.000 0.00 0.00 0.00 3.41
1736 2077 7.630242 TGAAACTTCACAGTCTGATTTCTTT 57.370 32.000 6.91 0.00 32.42 2.52
1739 2080 8.862550 ATTTTGAAACTTCACAGTCTGATTTC 57.137 30.769 6.91 8.58 36.83 2.17
1764 2105 5.850557 ACATGTGTGATTGTTTTCAGGAA 57.149 34.783 0.00 0.00 0.00 3.36
1766 2107 5.590145 TGAACATGTGTGATTGTTTTCAGG 58.410 37.500 0.00 0.00 36.25 3.86
1831 2172 4.849111 TTGTTCGCCATTTTCAAAACAC 57.151 36.364 0.00 0.00 0.00 3.32
1890 2231 5.452078 TGATGAAAGCTACACAAAAAGGG 57.548 39.130 0.00 0.00 0.00 3.95
2023 2364 5.345202 GCTCAATGAAGCATGTTTCTTTCAG 59.655 40.000 21.00 17.38 42.05 3.02
2029 2372 3.120060 ACGAGCTCAATGAAGCATGTTTC 60.120 43.478 15.40 14.76 45.00 2.78
2043 2386 0.820226 CATCTTGGAGGACGAGCTCA 59.180 55.000 15.40 0.00 0.00 4.26
2124 2467 2.672714 GTGCATGTGTGTCGTTAGAGA 58.327 47.619 0.00 0.00 0.00 3.10
2140 2483 4.785453 TGGGTGTGTGTGCGTGCA 62.785 61.111 0.00 0.00 0.00 4.57
2159 2526 5.453339 CCCGTATGTCTCATGAAGGTTGTAT 60.453 44.000 0.00 0.00 0.00 2.29
2222 2591 7.382759 GTCGAATGGTTAGAAGGATGATCTTAC 59.617 40.741 0.00 0.00 0.00 2.34
2228 2597 5.655090 TGTAGTCGAATGGTTAGAAGGATGA 59.345 40.000 0.00 0.00 0.00 2.92
2231 2600 4.401519 CCTGTAGTCGAATGGTTAGAAGGA 59.598 45.833 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.