Multiple sequence alignment - TraesCS2D01G345200

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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 TraesCS2D01G345200 chr2D 100.000 4821 0 0 1 4821 441525171 441529991 0.000000e+00 8903
1 TraesCS2D01G345200 chr2A 96.463 4835 117 30 2 4821 585135418 585140213 0.000000e+00 7932
2 TraesCS2D01G345200 chr2B 95.917 4286 106 23 336 4568 519014105 519018374 0.000000e+00 6881
3 TraesCS2D01G345200 chr2B 95.349 258 8 4 131 387 519013867 519014121 1.620000e-109 407
4 TraesCS2D01G345200 chr2B 94.410 161 6 2 4662 4821 519018621 519018779 1.340000e-60 244
5 TraesCS2D01G345200 chr2B 94.118 119 7 0 4535 4653 519018377 519018495 1.070000e-41 182
6 TraesCS2D01G345200 chr2B 98.413 63 1 0 1 63 519013805 519013867 1.420000e-20 111
7 TraesCS2D01G345200 chr3B 91.370 1066 57 14 654 1709 75589829 75588789 0.000000e+00 1426
8 TraesCS2D01G345200 chr6B 80.030 671 109 20 2099 2761 435305938 435306591 1.570000e-129 473
9 TraesCS2D01G345200 chr6A 80.000 670 111 18 2099 2761 390732440 390733093 1.570000e-129 473
10 TraesCS2D01G345200 chr6D 79.732 671 111 20 2099 2761 273089087 273089740 3.400000e-126 462


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 TraesCS2D01G345200 chr2D 441525171 441529991 4820 False 8903 8903 100.0000 1 4821 1 chr2D.!!$F1 4820
1 TraesCS2D01G345200 chr2A 585135418 585140213 4795 False 7932 7932 96.4630 2 4821 1 chr2A.!!$F1 4819
2 TraesCS2D01G345200 chr2B 519013805 519018779 4974 False 1565 6881 95.6414 1 4821 5 chr2B.!!$F1 4820
3 TraesCS2D01G345200 chr3B 75588789 75589829 1040 True 1426 1426 91.3700 654 1709 1 chr3B.!!$R1 1055
4 TraesCS2D01G345200 chr6B 435305938 435306591 653 False 473 473 80.0300 2099 2761 1 chr6B.!!$F1 662
5 TraesCS2D01G345200 chr6A 390732440 390733093 653 False 473 473 80.0000 2099 2761 1 chr6A.!!$F1 662
6 TraesCS2D01G345200 chr6D 273089087 273089740 653 False 462 462 79.7320 2099 2761 1 chr6D.!!$F1 662

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
530 591 0.459489 GAACAAAACCACCAGCAGCA 59.541 50.000 0.00 0.0 0.00 4.41 F
531 592 0.461135 AACAAAACCACCAGCAGCAG 59.539 50.000 0.00 0.0 0.00 4.24 F
868 945 0.613260 CCGAGGTCAGATCCAAACCA 59.387 55.000 10.43 0.0 35.43 3.67 F
1779 1883 1.550065 CAGGTGCTAACGATGACGAG 58.450 55.000 0.00 0.0 42.66 4.18 F
3354 3460 1.001706 GTCTTTTTCTGGGCGTCCAAC 60.002 52.381 11.40 0.0 43.51 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 1532 0.520404 CAGTCACTGCACCAGAATGC 59.480 55.000 0.00 0.00 46.32 3.56 R
1896 2000 0.544357 ACATGGTCCTCCGTCCAGAA 60.544 55.000 0.00 0.00 37.14 3.02 R
2559 2663 3.008049 ACATAGTCAACAGGAACCTGGTC 59.992 47.826 22.40 7.51 42.91 4.02 R
3450 3556 3.921119 AAATTGACAGCGCAAGATTCA 57.079 38.095 11.47 0.77 43.02 2.57 R
4437 4549 2.983898 ACTAAAACAGAGCCCTTGGGTA 59.016 45.455 7.61 0.00 31.55 3.69 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
64 65 1.802715 CTTTTGCGCATTGCCCTCG 60.803 57.895 12.75 0.0 45.60 4.63
66 67 2.745906 TTTTGCGCATTGCCCTCGTG 62.746 55.000 12.75 0.0 45.60 4.35
70 71 2.486966 GCATTGCCCTCGTGAAGC 59.513 61.111 0.00 0.0 0.00 3.86
72 73 0.744414 GCATTGCCCTCGTGAAGCTA 60.744 55.000 0.00 0.0 0.00 3.32
185 186 7.733402 TGCTTGTAACCGACTTACTTTTTAT 57.267 32.000 5.04 0.0 36.43 1.40
188 189 7.955864 GCTTGTAACCGACTTACTTTTTATCTG 59.044 37.037 5.04 0.0 36.43 2.90
189 190 9.199982 CTTGTAACCGACTTACTTTTTATCTGA 57.800 33.333 5.04 0.0 36.43 3.27
190 191 8.752766 TGTAACCGACTTACTTTTTATCTGAG 57.247 34.615 5.04 0.0 36.43 3.35
288 289 8.260818 ACGACCTGATCCCATAATAAATGATAG 58.739 37.037 0.00 0.0 0.00 2.08
358 361 3.189287 AGGTGTCAATCATTTCTTGTCGC 59.811 43.478 0.00 0.0 0.00 5.19
445 490 2.372172 AGATTCGAAGAAACCACCACCT 59.628 45.455 3.35 0.0 45.90 4.00
530 591 0.459489 GAACAAAACCACCAGCAGCA 59.541 50.000 0.00 0.0 0.00 4.41
531 592 0.461135 AACAAAACCACCAGCAGCAG 59.539 50.000 0.00 0.0 0.00 4.24
532 593 1.300388 CAAAACCACCAGCAGCAGC 60.300 57.895 0.00 0.0 42.56 5.25
533 594 2.501602 AAAACCACCAGCAGCAGCC 61.502 57.895 0.00 0.0 43.56 4.85
868 945 0.613260 CCGAGGTCAGATCCAAACCA 59.387 55.000 10.43 0.0 35.43 3.67
946 1023 4.770874 CCGTGGAATTCCGGGCGT 62.771 66.667 24.29 0.0 40.54 5.68
959 1036 3.370231 GGCGTGGGGCAATTCGTT 61.370 61.111 0.00 0.0 46.16 3.85
997 1074 3.564027 GCGGCTCGGATTTCGTGG 61.564 66.667 0.00 0.0 40.32 4.94
999 1076 1.740296 CGGCTCGGATTTCGTGGTT 60.740 57.895 0.00 0.0 40.32 3.67
1263 1367 3.071206 AGCGGGAGTGCGTCAGAT 61.071 61.111 0.00 0.0 40.67 2.90
1302 1406 4.717313 AGAGCGGCGGGGGAAAAC 62.717 66.667 9.78 0.0 0.00 2.43
1306 1410 4.653888 CGGCGGGGGAAAACACCT 62.654 66.667 0.00 0.0 42.11 4.00
1309 1413 2.570284 GCGGGGGAAAACACCTTGG 61.570 63.158 0.00 0.0 42.11 3.61
1536 1640 2.184631 TCAACTCCCTCCCCCTCCT 61.185 63.158 0.00 0.0 0.00 3.69
1608 1712 1.617804 CCAATGGATGTGGACCTTGCT 60.618 52.381 0.00 0.0 38.54 3.91
1619 1723 2.290260 TGGACCTTGCTGTTGATACTGG 60.290 50.000 0.00 0.0 0.00 4.00
1620 1724 2.359900 GACCTTGCTGTTGATACTGGG 58.640 52.381 0.00 0.0 0.00 4.45
1625 1729 3.500448 TGCTGTTGATACTGGGAACAA 57.500 42.857 0.00 0.0 42.06 2.83
1689 1793 7.654452 AGGTAGAGGAGAGTAAAGTAAAGGAT 58.346 38.462 0.00 0.0 0.00 3.24
1779 1883 1.550065 CAGGTGCTAACGATGACGAG 58.450 55.000 0.00 0.0 42.66 4.18
3354 3460 1.001706 GTCTTTTTCTGGGCGTCCAAC 60.002 52.381 11.40 0.0 43.51 3.77
3450 3556 3.096852 TCAATGGGACTCGTGACTACAT 58.903 45.455 0.00 0.0 0.00 2.29
3461 3567 2.285256 CGTGACTACATGAATCTTGCGC 60.285 50.000 0.00 0.0 35.25 6.09
3960 4067 2.682856 GGTGTCTTCAAGCAACTGACAA 59.317 45.455 0.00 0.0 39.01 3.18
4434 4546 7.525688 TGAATACGTGTTCTGAAAGATCATC 57.474 36.000 23.09 0.0 46.36 2.92
4435 4547 7.323420 TGAATACGTGTTCTGAAAGATCATCT 58.677 34.615 23.09 0.0 46.36 2.90
4436 4548 8.466798 TGAATACGTGTTCTGAAAGATCATCTA 58.533 33.333 23.09 0.0 46.36 1.98
4437 4549 9.469807 GAATACGTGTTCTGAAAGATCATCTAT 57.530 33.333 16.81 0.0 46.36 1.98
4593 4741 4.728772 ACATGACTTGAATGAAGACCCAA 58.271 39.130 0.00 0.0 35.42 4.12
4617 4765 4.641989 CCTGGATGGGTGTATTCTCTTTTG 59.358 45.833 0.00 0.0 0.00 2.44
4734 4999 1.066215 TGCCTGTGCGTCATATGTCTT 60.066 47.619 1.90 0.0 41.78 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 1.797025 AGCACCTCGTTTAGCTTCAC 58.203 50.000 0.00 0.00 32.52 3.18
66 67 3.505464 TCTAGCACCTCGTTTAGCTTC 57.495 47.619 0.00 0.00 38.47 3.86
70 71 5.446143 AGATGATCTAGCACCTCGTTTAG 57.554 43.478 0.00 0.00 0.00 1.85
72 73 4.437239 CAAGATGATCTAGCACCTCGTTT 58.563 43.478 0.00 0.00 0.00 3.60
288 289 5.888412 AAATTCACTGCAACATCGTTTTC 57.112 34.783 0.00 0.00 0.00 2.29
386 429 9.996554 ACTCCAAATACTTTCCCTAAAATTTTG 57.003 29.630 13.76 3.88 0.00 2.44
531 592 4.717313 GAGGTTGGTGGGTCCGGC 62.717 72.222 0.00 0.00 39.52 6.13
532 593 4.029809 GGAGGTTGGTGGGTCCGG 62.030 72.222 0.00 0.00 39.52 5.14
533 594 4.029809 GGGAGGTTGGTGGGTCCG 62.030 72.222 0.00 0.00 39.52 4.79
715 777 0.321996 GGAGCGAATAGGATGGGGAC 59.678 60.000 0.00 0.00 0.00 4.46
868 945 2.610859 ATTCGGACCTGGGGCTGT 60.611 61.111 0.76 0.00 0.00 4.40
944 1021 1.366111 ATCGAACGAATTGCCCCACG 61.366 55.000 0.12 0.00 0.00 4.94
946 1023 1.091537 GAATCGAACGAATTGCCCCA 58.908 50.000 0.12 0.00 0.00 4.96
1263 1367 0.542938 CTGACCTCCCACCAGAGTCA 60.543 60.000 0.00 0.00 31.53 3.41
1299 1403 2.863809 CTAGAACTGGCCAAGGTGTTT 58.136 47.619 7.01 1.72 0.00 2.83
1302 1406 0.036732 TGCTAGAACTGGCCAAGGTG 59.963 55.000 7.01 0.00 36.12 4.00
1306 1410 0.840288 TCCCTGCTAGAACTGGCCAA 60.840 55.000 7.01 0.00 36.12 4.52
1309 1413 1.524482 CCTCCCTGCTAGAACTGGC 59.476 63.158 3.29 3.29 37.60 4.85
1368 1472 5.793030 TGGGCGAAAATTTCCTCTTTTTA 57.207 34.783 0.00 0.00 0.00 1.52
1428 1532 0.520404 CAGTCACTGCACCAGAATGC 59.480 55.000 0.00 0.00 46.32 3.56
1492 1596 1.974236 AGAGGACTCCACCACTTTCTG 59.026 52.381 0.00 0.00 0.00 3.02
1569 1673 2.039746 TGGTGAATTCTCCACGACCAAT 59.960 45.455 22.34 0.00 34.88 3.16
1608 1712 4.009675 GCTCATTGTTCCCAGTATCAACA 58.990 43.478 0.00 0.00 0.00 3.33
1619 1723 1.664016 CGTGCAACTGCTCATTGTTCC 60.664 52.381 2.95 0.00 42.66 3.62
1620 1724 1.264020 TCGTGCAACTGCTCATTGTTC 59.736 47.619 2.95 0.00 42.66 3.18
1625 1729 1.004080 AGCTCGTGCAACTGCTCAT 60.004 52.632 12.58 0.00 39.42 2.90
1689 1793 6.437793 CCTCCTTTACTTTACTCTCCTCTTCA 59.562 42.308 0.00 0.00 0.00 3.02
1779 1883 1.550976 CTCAGTGTTACACCCTCCTCC 59.449 57.143 12.28 0.00 34.49 4.30
1896 2000 0.544357 ACATGGTCCTCCGTCCAGAA 60.544 55.000 0.00 0.00 37.14 3.02
2559 2663 3.008049 ACATAGTCAACAGGAACCTGGTC 59.992 47.826 22.40 7.51 42.91 4.02
3354 3460 3.955471 TCAAAACCAGCTTCAGATAGGG 58.045 45.455 0.00 0.00 0.00 3.53
3450 3556 3.921119 AAATTGACAGCGCAAGATTCA 57.079 38.095 11.47 0.77 43.02 2.57
3960 4067 2.290641 CACAAAGCCTGCTAAAGAACGT 59.709 45.455 0.00 0.00 0.00 3.99
4417 4525 7.500992 TGGGTATAGATGATCTTTCAGAACAC 58.499 38.462 0.00 0.00 34.73 3.32
4434 4546 3.933861 AAACAGAGCCCTTGGGTATAG 57.066 47.619 7.61 0.00 31.55 1.31
4435 4547 4.786454 ACTAAAACAGAGCCCTTGGGTATA 59.214 41.667 7.61 0.00 31.55 1.47
4436 4548 3.591977 ACTAAAACAGAGCCCTTGGGTAT 59.408 43.478 7.61 0.00 31.55 2.73
4437 4549 2.983898 ACTAAAACAGAGCCCTTGGGTA 59.016 45.455 7.61 0.00 31.55 3.69
4593 4741 3.136641 AGAGAATACACCCATCCAGGT 57.863 47.619 0.00 0.00 42.40 4.00
4617 4765 4.181578 ACTTGTATACATCGTCAAGGTGC 58.818 43.478 6.36 0.00 40.74 5.01


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

AutoCloner maintained by Alex Coulton.