Multiple sequence alignment - TraesCS4B01G153000

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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 TraesCS4B01G153000 chr4B 100.000 2423 0 0 1 2423 259079342 259076920 0.000000e+00 4475
1 TraesCS4B01G153000 chr4B 96.685 1478 44 3 1 1473 654022309 654020832 0.000000e+00 2453
2 TraesCS4B01G153000 chr4B 96.622 1480 42 5 1 1473 659610782 659612260 0.000000e+00 2449
3 TraesCS4B01G153000 chrUn 96.820 1478 42 3 1 1473 304964331 304965808 0.000000e+00 2464
4 TraesCS4B01G153000 chr3B 96.820 1478 42 3 1 1473 788712697 788714174 0.000000e+00 2464
5 TraesCS4B01G153000 chr3B 90.526 190 16 2 2235 2423 788961326 788961514 1.440000e-62 250
6 TraesCS4B01G153000 chr3B 90.164 183 16 2 2235 2416 788903817 788903998 1.120000e-58 237
7 TraesCS4B01G153000 chr3B 88.360 189 21 1 2235 2423 199684755 199684942 2.420000e-55 226
8 TraesCS4B01G153000 chr2B 96.631 1484 44 4 1 1480 704736844 704738325 0.000000e+00 2459
9 TraesCS4B01G153000 chr2B 96.617 1478 42 4 1 1473 750327818 750329292 0.000000e+00 2446
10 TraesCS4B01G153000 chr5A 96.685 1478 44 3 1 1473 423144507 423145984 0.000000e+00 2453
11 TraesCS4B01G153000 chr2A 96.429 1484 48 3 1 1479 40336557 40335074 0.000000e+00 2442
12 TraesCS4B01G153000 chr2A 86.047 989 97 14 1466 2423 352377228 352378206 0.000000e+00 1024
13 TraesCS4B01G153000 chr7B 96.606 1473 46 2 1 1469 304999950 305001422 0.000000e+00 2440
14 TraesCS4B01G153000 chr5B 91.457 714 50 6 1715 2423 605808111 605807404 0.000000e+00 970
15 TraesCS4B01G153000 chr5B 82.404 574 74 19 1863 2423 224002268 224001709 2.180000e-130 475
16 TraesCS4B01G153000 chr2D 89.608 664 58 8 1472 2128 506287907 506288566 0.000000e+00 833
17 TraesCS4B01G153000 chr2D 87.407 675 69 13 1466 2128 53766682 53767352 0.000000e+00 761
18 TraesCS4B01G153000 chr2D 91.005 189 16 1 2235 2423 506288572 506288759 1.110000e-63 254
19 TraesCS4B01G153000 chr2D 88.482 191 19 3 2235 2423 53767358 53767547 6.740000e-56 228
20 TraesCS4B01G153000 chr3D 87.722 676 66 14 1466 2128 581963992 581964663 0.000000e+00 773
21 TraesCS4B01G153000 chr7D 87.426 676 68 14 1466 2128 511207781 511208452 0.000000e+00 761
22 TraesCS4B01G153000 chr7D 89.474 190 18 2 2235 2423 511208458 511208646 3.110000e-59 239
23 TraesCS4B01G153000 chr6A 87.168 678 69 15 1466 2128 135578321 135578995 0.000000e+00 754
24 TraesCS4B01G153000 chr6D 87.001 677 70 13 1465 2128 25525328 25525999 0.000000e+00 747
25 TraesCS4B01G153000 chr4A 87.126 668 72 10 1472 2128 183159370 183158706 0.000000e+00 745


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 TraesCS4B01G153000 chr4B 259076920 259079342 2422 True 4475.0 4475 100.0000 1 2423 1 chr4B.!!$R1 2422
1 TraesCS4B01G153000 chr4B 654020832 654022309 1477 True 2453.0 2453 96.6850 1 1473 1 chr4B.!!$R2 1472
2 TraesCS4B01G153000 chr4B 659610782 659612260 1478 False 2449.0 2449 96.6220 1 1473 1 chr4B.!!$F1 1472
3 TraesCS4B01G153000 chrUn 304964331 304965808 1477 False 2464.0 2464 96.8200 1 1473 1 chrUn.!!$F1 1472
4 TraesCS4B01G153000 chr3B 788712697 788714174 1477 False 2464.0 2464 96.8200 1 1473 1 chr3B.!!$F2 1472
5 TraesCS4B01G153000 chr2B 704736844 704738325 1481 False 2459.0 2459 96.6310 1 1480 1 chr2B.!!$F1 1479
6 TraesCS4B01G153000 chr2B 750327818 750329292 1474 False 2446.0 2446 96.6170 1 1473 1 chr2B.!!$F2 1472
7 TraesCS4B01G153000 chr5A 423144507 423145984 1477 False 2453.0 2453 96.6850 1 1473 1 chr5A.!!$F1 1472
8 TraesCS4B01G153000 chr2A 40335074 40336557 1483 True 2442.0 2442 96.4290 1 1479 1 chr2A.!!$R1 1478
9 TraesCS4B01G153000 chr2A 352377228 352378206 978 False 1024.0 1024 86.0470 1466 2423 1 chr2A.!!$F1 957
10 TraesCS4B01G153000 chr7B 304999950 305001422 1472 False 2440.0 2440 96.6060 1 1469 1 chr7B.!!$F1 1468
11 TraesCS4B01G153000 chr5B 605807404 605808111 707 True 970.0 970 91.4570 1715 2423 1 chr5B.!!$R2 708
12 TraesCS4B01G153000 chr5B 224001709 224002268 559 True 475.0 475 82.4040 1863 2423 1 chr5B.!!$R1 560
13 TraesCS4B01G153000 chr2D 506287907 506288759 852 False 543.5 833 90.3065 1472 2423 2 chr2D.!!$F2 951
14 TraesCS4B01G153000 chr2D 53766682 53767547 865 False 494.5 761 87.9445 1466 2423 2 chr2D.!!$F1 957
15 TraesCS4B01G153000 chr3D 581963992 581964663 671 False 773.0 773 87.7220 1466 2128 1 chr3D.!!$F1 662
16 TraesCS4B01G153000 chr7D 511207781 511208646 865 False 500.0 761 88.4500 1466 2423 2 chr7D.!!$F1 957
17 TraesCS4B01G153000 chr6A 135578321 135578995 674 False 754.0 754 87.1680 1466 2128 1 chr6A.!!$F1 662
18 TraesCS4B01G153000 chr6D 25525328 25525999 671 False 747.0 747 87.0010 1465 2128 1 chr6D.!!$F1 663
19 TraesCS4B01G153000 chr4A 183158706 183159370 664 True 745.0 745 87.1260 1472 2128 1 chr4A.!!$R1 656

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
941 949 3.454812 GTGACTGGGTATGGTGGTAATCT 59.545 47.826 0.0 0.0 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1999 2050 3.437049 GCTATTTTCTGTGAGCTTTCGGT 59.563 43.478 0.0 0.0 32.04 4.69 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
467 468 7.536159 ACATGCTCTAGATGTGATTCAGATA 57.464 36.000 0.00 0.00 32.68 1.98
613 618 7.316544 GTTCTAATTAACATGAACCATCCGT 57.683 36.000 0.00 0.00 34.47 4.69
668 676 4.270808 GTGTTTGTGGAAAGCAAGAAATGG 59.729 41.667 0.00 0.00 0.00 3.16
840 848 4.074970 CTCAAGGGCAAGAACAAGTACAT 58.925 43.478 0.00 0.00 0.00 2.29
941 949 3.454812 GTGACTGGGTATGGTGGTAATCT 59.545 47.826 0.00 0.00 0.00 2.40
1117 1125 5.290493 TCAGCAAGGTTCTTTTCTCACTA 57.710 39.130 0.00 0.00 0.00 2.74
1144 1152 6.786967 ATCTTTCATTAGCAAAGATGGCTT 57.213 33.333 7.87 0.00 45.08 4.35
1206 1214 3.682858 GCAGACAACCAATTAGCGAGTTA 59.317 43.478 0.00 0.00 0.00 2.24
1340 1348 3.809832 AGTTGTTCACGTTCTTCTCATGG 59.190 43.478 0.00 0.00 0.00 3.66
1352 1360 4.922206 TCTTCTCATGGCAATGTACCTTT 58.078 39.130 0.00 0.00 35.15 3.11
1365 1373 3.904717 TGTACCTTTCCCTTTTCTGCAA 58.095 40.909 0.00 0.00 0.00 4.08
1371 1379 2.514458 TCCCTTTTCTGCAATCCCTC 57.486 50.000 0.00 0.00 0.00 4.30
1450 1458 1.202114 GAAATTGTGGCGCTTGATGGA 59.798 47.619 7.64 0.00 0.00 3.41
1556 1565 4.626042 CATAGATCTAGCACACAACCTCC 58.374 47.826 8.70 0.00 0.00 4.30
1566 1575 2.742053 CACACAACCTCCTTATTCACCG 59.258 50.000 0.00 0.00 0.00 4.94
1581 1590 3.057969 TCACCGAATGAACAATGCTCT 57.942 42.857 0.00 0.00 33.02 4.09
1600 1609 2.092429 TCTAAAGGAGCGGGCATTCAAT 60.092 45.455 0.00 0.00 0.00 2.57
1617 1626 3.565307 TCAATGAAGAGTTGGTGGCTTT 58.435 40.909 0.00 0.00 0.00 3.51
1623 1632 6.478512 TGAAGAGTTGGTGGCTTTATTTTT 57.521 33.333 0.00 0.00 0.00 1.94
1649 1658 1.149148 GTTCAAGACGGACAAGCTCC 58.851 55.000 0.00 0.00 35.33 4.70
1666 1676 5.979288 AGCTCCTTTCTTCGTTAGTCTAA 57.021 39.130 0.00 0.00 0.00 2.10
1686 1696 5.958380 TCTAAATCATGTCTGAGGTGGTAGT 59.042 40.000 0.00 0.00 34.12 2.73
1695 1705 3.511540 TCTGAGGTGGTAGTGTTCTGATG 59.488 47.826 0.00 0.00 0.00 3.07
1771 1781 9.077885 ACAGATGTGTTCTTTTGGTATGTAAAT 57.922 29.630 0.00 0.00 30.30 1.40
1798 1832 8.781196 CGATGATAACTTGATCTTTGGATGAAT 58.219 33.333 0.00 0.00 31.46 2.57
1800 1834 8.146479 TGATAACTTGATCTTTGGATGAATCG 57.854 34.615 0.00 0.00 31.46 3.34
1849 1884 4.583907 TCTTCTGTTTGCCAACATGATCAA 59.416 37.500 3.52 0.00 42.21 2.57
1937 1980 5.138125 TCAAGGGAATCTTTGTGCATTTC 57.862 39.130 0.00 0.00 32.41 2.17
1999 2050 8.615878 AATGCTACACTGTCACACTTAAATTA 57.384 30.769 0.00 0.00 0.00 1.40
2001 2052 6.425721 TGCTACACTGTCACACTTAAATTACC 59.574 38.462 0.00 0.00 0.00 2.85
2031 2082 6.594159 GCTCACAGAAAATAGCTACAACCTTA 59.406 38.462 0.00 0.00 32.18 2.69
2046 2097 8.512138 GCTACAACCTTATGTTAGATTTGTTGT 58.488 33.333 9.30 9.30 44.87 3.32
2081 2135 5.144692 TGCATTTTACCTGCAAATTAGCA 57.855 34.783 0.00 0.00 46.06 3.49
2083 2137 6.171921 TGCATTTTACCTGCAAATTAGCAAT 58.828 32.000 0.00 0.00 46.06 3.56
2088 2142 2.164219 ACCTGCAAATTAGCAATGTCCG 59.836 45.455 0.00 0.00 45.13 4.79
2107 2161 5.106475 TGTCCGTACAATATTTTTGCTGGAC 60.106 40.000 13.72 13.72 38.07 4.02
2263 2331 3.447918 GCTGCATAGCCAAATCAACAT 57.552 42.857 0.00 0.00 44.33 2.71
2282 2351 8.537049 TCAACATTTTAAATCATTCAAGGCTG 57.463 30.769 0.00 0.00 0.00 4.85
2306 2375 7.556844 TGTTCCTTTGCCAACTTGTTATTTTA 58.443 30.769 0.00 0.00 0.00 1.52
2345 2415 6.042143 TCAAGAAGCTTCAACCATGTTTTTC 58.958 36.000 27.57 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
685 693 6.157820 TGAACCTGATGGGAATGTGATACTTA 59.842 38.462 0.00 0.00 38.76 2.24
689 697 4.385199 GGTGAACCTGATGGGAATGTGATA 60.385 45.833 0.00 0.00 38.76 2.15
697 705 0.038166 GCTTGGTGAACCTGATGGGA 59.962 55.000 0.37 0.00 38.76 4.37
840 848 1.004745 GATTTGAGGGTGGAGCCTTGA 59.995 52.381 0.00 0.00 37.43 3.02
905 913 4.018960 ACCCAGTCACATTCTTCTTATGCT 60.019 41.667 0.00 0.00 0.00 3.79
922 930 2.777692 CCAGATTACCACCATACCCAGT 59.222 50.000 0.00 0.00 0.00 4.00
941 949 2.640332 TGAACACCAATACCAGTAGCCA 59.360 45.455 0.00 0.00 0.00 4.75
1011 1019 6.533730 AGGTGAACAAACATCATGAGTAGAA 58.466 36.000 0.09 0.00 0.00 2.10
1117 1125 6.815142 GCCATCTTTGCTAATGAAAGATTGTT 59.185 34.615 6.30 0.00 44.26 2.83
1144 1152 9.383519 GTTGGTGTTATTGATATCTCTTGAAGA 57.616 33.333 3.98 0.00 38.72 2.87
1206 1214 9.484806 ACATTAAGAGAATGGGAGATTTGAAAT 57.515 29.630 0.00 0.00 32.14 2.17
1340 1348 4.809673 CAGAAAAGGGAAAGGTACATTGC 58.190 43.478 0.00 0.00 0.00 3.56
1352 1360 1.005924 GGAGGGATTGCAGAAAAGGGA 59.994 52.381 0.00 0.00 0.00 4.20
1365 1373 5.644188 TGAACTTGAAAATTGAGGAGGGAT 58.356 37.500 0.00 0.00 0.00 3.85
1371 1379 3.575687 AGCCCTGAACTTGAAAATTGAGG 59.424 43.478 0.00 0.00 0.00 3.86
1537 1546 2.826488 AGGAGGTTGTGTGCTAGATCT 58.174 47.619 0.00 0.00 0.00 2.75
1541 1550 4.631813 GTGAATAAGGAGGTTGTGTGCTAG 59.368 45.833 0.00 0.00 0.00 3.42
1543 1552 3.412386 GTGAATAAGGAGGTTGTGTGCT 58.588 45.455 0.00 0.00 0.00 4.40
1556 1565 5.883661 AGCATTGTTCATTCGGTGAATAAG 58.116 37.500 14.86 10.22 46.57 1.73
1579 1588 0.908910 TGAATGCCCGCTCCTTTAGA 59.091 50.000 0.00 0.00 0.00 2.10
1581 1590 2.023673 CATTGAATGCCCGCTCCTTTA 58.976 47.619 0.00 0.00 0.00 1.85
1600 1609 6.478512 AAAAATAAAGCCACCAACTCTTCA 57.521 33.333 0.00 0.00 0.00 3.02
1623 1632 1.487142 TGTCCGTCTTGAACCTTCCAA 59.513 47.619 0.00 0.00 0.00 3.53
1640 1649 4.308265 ACTAACGAAGAAAGGAGCTTGTC 58.692 43.478 0.00 0.00 0.00 3.18
1649 1658 9.360093 AGACATGATTTAGACTAACGAAGAAAG 57.640 33.333 0.00 0.00 0.00 2.62
1666 1676 3.840666 ACACTACCACCTCAGACATGATT 59.159 43.478 0.00 0.00 34.12 2.57
1686 1696 5.163405 GCACTACTCTAATCCCATCAGAACA 60.163 44.000 0.00 0.00 0.00 3.18
1695 1705 3.521947 AACACGCACTACTCTAATCCC 57.478 47.619 0.00 0.00 0.00 3.85
1771 1781 7.500141 TCATCCAAAGATCAAGTTATCATCGA 58.500 34.615 0.00 0.00 0.00 3.59
1798 1832 7.168972 CACATCCATTAAAAACAAAAGAAGCGA 59.831 33.333 0.00 0.00 0.00 4.93
1800 1834 8.141835 ACACATCCATTAAAAACAAAAGAAGC 57.858 30.769 0.00 0.00 0.00 3.86
1999 2050 3.437049 GCTATTTTCTGTGAGCTTTCGGT 59.563 43.478 0.00 0.00 32.04 4.69
2001 2052 4.935885 AGCTATTTTCTGTGAGCTTTCG 57.064 40.909 0.00 0.00 42.59 3.46
2031 2082 7.759489 TTTGGCTCTACAACAAATCTAACAT 57.241 32.000 0.00 0.00 0.00 2.71
2046 2097 7.684187 GCAGGTAAAATGCATATTTTGGCTCTA 60.684 37.037 0.00 0.00 44.12 2.43
2060 2112 6.092533 ACATTGCTAATTTGCAGGTAAAATGC 59.907 34.615 14.07 0.00 44.27 3.56
2081 2135 6.151985 TCCAGCAAAAATATTGTACGGACATT 59.848 34.615 0.00 0.00 34.86 2.71
2083 2137 5.004448 TCCAGCAAAAATATTGTACGGACA 58.996 37.500 0.00 0.00 0.00 4.02
2210 2278 9.806448 TGGCTATACATGTTTCCATTATATGTT 57.194 29.630 2.30 0.00 34.22 2.71
2282 2351 6.918892 AAAATAACAAGTTGGCAAAGGAAC 57.081 33.333 7.96 0.00 0.00 3.62
2290 2359 6.981559 TGGTTGAAGTAAAATAACAAGTTGGC 59.018 34.615 7.96 0.00 0.00 4.52
2306 2375 5.127682 AGCTTCTTGAAAACATGGTTGAAGT 59.872 36.000 17.70 6.78 34.12 3.01
2345 2415 4.696455 AGGAAACATGGTTGAAGCTTTTG 58.304 39.130 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.