Multiple sequence alignment - TraesCS3D01G366900

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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 TraesCS3D01G366900 chr3D 100.000 2357 0 0 1 2357 481071276 481068920 0.000000e+00 4353.0
1 TraesCS3D01G366900 chr3B 94.977 1553 63 8 806 2357 641988271 641986733 0.000000e+00 2422.0
2 TraesCS3D01G366900 chr3B 91.052 827 49 8 1 805 731352633 731353456 0.000000e+00 1094.0
3 TraesCS3D01G366900 chr3B 85.039 381 54 2 1 380 563463487 563463109 3.670000e-103 385.0
4 TraesCS3D01G366900 chr3B 76.799 681 118 22 1 658 713122526 713123189 1.730000e-91 346.0
5 TraesCS3D01G366900 chr5A 94.907 805 38 1 1 805 702021479 702020678 0.000000e+00 1256.0
6 TraesCS3D01G366900 chr2D 93.750 816 47 2 1 816 247404857 247404046 0.000000e+00 1221.0
7 TraesCS3D01G366900 chr5D 93.665 805 38 5 1 805 43138724 43137933 0.000000e+00 1192.0
8 TraesCS3D01G366900 chr3A 92.279 803 32 12 805 1588 623822996 623822205 0.000000e+00 1112.0
9 TraesCS3D01G366900 chr3A 89.179 767 37 13 1615 2357 623822208 623821464 0.000000e+00 915.0
10 TraesCS3D01G366900 chr3A 87.043 301 33 4 80 380 604497680 604497386 3.750000e-88 335.0
11 TraesCS3D01G366900 chr7A 94.907 648 29 2 1 648 672182024 672182667 0.000000e+00 1011.0
12 TraesCS3D01G366900 chr7A 96.774 124 4 0 682 805 672182672 672182795 8.540000e-50 207.0
13 TraesCS3D01G366900 chr4A 87.561 820 77 10 1 805 694665738 694666547 0.000000e+00 926.0
14 TraesCS3D01G366900 chr6B 85.752 379 48 2 2 380 251111770 251111398 1.700000e-106 396.0
15 TraesCS3D01G366900 chr6B 97.222 36 1 0 775 810 247051444 247051409 7.030000e-06 62.1
16 TraesCS3D01G366900 chr7B 95.238 42 1 1 775 816 451953319 451953359 5.440000e-07 65.8
17 TraesCS3D01G366900 chr1B 97.143 35 1 0 775 809 66195980 66196014 2.530000e-05 60.2


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 TraesCS3D01G366900 chr3D 481068920 481071276 2356 True 4353.0 4353 100.0000 1 2357 1 chr3D.!!$R1 2356
1 TraesCS3D01G366900 chr3B 641986733 641988271 1538 True 2422.0 2422 94.9770 806 2357 1 chr3B.!!$R2 1551
2 TraesCS3D01G366900 chr3B 731352633 731353456 823 False 1094.0 1094 91.0520 1 805 1 chr3B.!!$F2 804
3 TraesCS3D01G366900 chr3B 713122526 713123189 663 False 346.0 346 76.7990 1 658 1 chr3B.!!$F1 657
4 TraesCS3D01G366900 chr5A 702020678 702021479 801 True 1256.0 1256 94.9070 1 805 1 chr5A.!!$R1 804
5 TraesCS3D01G366900 chr2D 247404046 247404857 811 True 1221.0 1221 93.7500 1 816 1 chr2D.!!$R1 815
6 TraesCS3D01G366900 chr5D 43137933 43138724 791 True 1192.0 1192 93.6650 1 805 1 chr5D.!!$R1 804
7 TraesCS3D01G366900 chr3A 623821464 623822996 1532 True 1013.5 1112 90.7290 805 2357 2 chr3A.!!$R2 1552
8 TraesCS3D01G366900 chr7A 672182024 672182795 771 False 609.0 1011 95.8405 1 805 2 chr7A.!!$F1 804
9 TraesCS3D01G366900 chr4A 694665738 694666547 809 False 926.0 926 87.5610 1 805 1 chr4A.!!$F1 804

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
961 1009 0.684153 ACCAATTCGGCCATTCCCAG 60.684 55.0 2.24 0.0 39.03 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 1931 2.802057 GCTATACTACCCCAACAGTGCG 60.802 54.545 0.0 0.0 0.0 5.34 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
168 169 4.876107 CGATGGTTAACCCTGCATATATCC 59.124 45.833 21.97 0.00 34.29 2.59
200 201 7.513371 AGAGGAAGTCAGTAAATCTATACGG 57.487 40.000 0.00 0.00 0.00 4.02
210 211 8.689061 TCAGTAAATCTATACGGCAAAGACTTA 58.311 33.333 0.00 0.00 0.00 2.24
300 301 6.507900 ACTATCTCATGTCGGTAACTCAATG 58.492 40.000 0.00 0.00 0.00 2.82
358 359 4.956085 TGATGGTTAATGTCCTGGTATCG 58.044 43.478 0.00 0.00 0.00 2.92
370 371 4.680110 GTCCTGGTATCGTATGATTTGTCG 59.320 45.833 2.02 0.00 35.99 4.35
564 607 2.608623 CAACCCTCCTTCCACCATTTT 58.391 47.619 0.00 0.00 0.00 1.82
599 642 5.592282 TCAAAAACTCTTCCATGCACAACTA 59.408 36.000 0.00 0.00 0.00 2.24
640 683 0.768221 AGGAGTTGAAGGAGGCACCA 60.768 55.000 3.18 0.00 42.04 4.17
795 838 4.706608 TGGCAACGCACGGGCATA 62.707 61.111 11.77 0.00 41.24 3.14
840 887 8.966069 ATATTCTGAGAATATCATGGATGCAG 57.034 34.615 19.28 0.00 37.28 4.41
860 907 4.617223 GCAGTATTTTCCGCAAGAAGTTTC 59.383 41.667 0.00 0.00 43.02 2.78
867 914 0.883833 CGCAAGAAGTTTCAGCCCAT 59.116 50.000 0.00 0.00 43.02 4.00
875 922 3.287867 AGTTTCAGCCCATGATGTAGG 57.712 47.619 0.00 0.00 37.89 3.18
961 1009 0.684153 ACCAATTCGGCCATTCCCAG 60.684 55.000 2.24 0.00 39.03 4.45
1084 1134 2.705826 GCAGCTTGATCGCGAAGG 59.294 61.111 15.24 0.00 34.40 3.46
1167 1217 3.593794 ATCCTCGTCTACGGCGGC 61.594 66.667 13.24 0.00 40.29 6.53
1539 1601 6.312426 CAGAATTCTGTGTTCATACTGGAGAC 59.688 42.308 24.65 0.00 39.09 3.36
1590 1652 9.411189 TGTTATTAATGTATGTTTACCCTTCCC 57.589 33.333 0.00 0.00 0.00 3.97
1591 1653 8.562052 GTTATTAATGTATGTTTACCCTTCCCG 58.438 37.037 0.00 0.00 0.00 5.14
1592 1654 2.406596 TGTATGTTTACCCTTCCCGC 57.593 50.000 0.00 0.00 0.00 6.13
1593 1655 1.910671 TGTATGTTTACCCTTCCCGCT 59.089 47.619 0.00 0.00 0.00 5.52
1594 1656 3.106054 TGTATGTTTACCCTTCCCGCTA 58.894 45.455 0.00 0.00 0.00 4.26
1595 1657 3.133362 TGTATGTTTACCCTTCCCGCTAG 59.867 47.826 0.00 0.00 0.00 3.42
1596 1658 0.906775 TGTTTACCCTTCCCGCTAGG 59.093 55.000 0.00 0.00 37.24 3.02
1609 1671 1.743394 CCGCTAGGGAATTTTGTCACC 59.257 52.381 8.65 0.00 38.47 4.02
1610 1672 1.396996 CGCTAGGGAATTTTGTCACCG 59.603 52.381 0.00 0.00 0.00 4.94
1611 1673 2.433436 GCTAGGGAATTTTGTCACCGT 58.567 47.619 0.00 0.00 0.00 4.83
1612 1674 2.161609 GCTAGGGAATTTTGTCACCGTG 59.838 50.000 0.00 0.00 0.00 4.94
1613 1675 2.649531 AGGGAATTTTGTCACCGTGA 57.350 45.000 0.00 0.00 0.00 4.35
1689 1780 9.559958 GTCTAAACAGATACAATGTTTCATTGG 57.440 33.333 21.18 9.52 45.33 3.16
1708 1799 6.367695 TCATTGGTTTAGTTCATGTACTCGTG 59.632 38.462 8.41 0.00 0.00 4.35
1785 1876 3.396260 CCGTTGGGGTAGTATGGTATG 57.604 52.381 0.00 0.00 0.00 2.39
1837 1931 5.577164 AGTCTGAACGAACATGCTGTATTAC 59.423 40.000 0.00 0.00 0.00 1.89
2096 2190 9.983024 TTATCAAACATCCCTTACCTTATTTCA 57.017 29.630 0.00 0.00 0.00 2.69
2135 2229 7.872138 TCCCAAAATTCCTGATCTGTTATAGT 58.128 34.615 0.00 0.00 0.00 2.12
2298 2414 3.889196 TTTCGACCGGAAACATCAAAG 57.111 42.857 9.46 0.00 39.67 2.77
2331 2447 7.712639 GTGTATATGTCATGATCAACAGTTCCT 59.287 37.037 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 9.961265 CATATTTCTGTCTTTGTCATGCATATT 57.039 29.630 0.00 0.00 0.00 1.28
27 28 7.067251 TGCATATTTCTGTCTTTGTCATGCATA 59.933 33.333 0.00 0.00 40.75 3.14
28 29 6.127563 TGCATATTTCTGTCTTTGTCATGCAT 60.128 34.615 0.00 0.00 40.75 3.96
33 34 9.791820 CATATTTGCATATTTCTGTCTTTGTCA 57.208 29.630 0.00 0.00 0.00 3.58
74 75 6.700352 TGCAATTTGCTTTATCCTAGCTTTT 58.300 32.000 21.19 0.00 45.31 2.27
168 169 3.760580 ACTGACTTCCTCTTCTGTTGG 57.239 47.619 0.00 0.00 0.00 3.77
200 201 5.371115 TGTGCTAACCATTAAGTCTTTGC 57.629 39.130 0.00 0.00 0.00 3.68
210 211 5.709631 TCATGTTGTGTATGTGCTAACCATT 59.290 36.000 0.00 0.00 0.00 3.16
289 290 1.826385 AGCACCTGCATTGAGTTACC 58.174 50.000 0.00 0.00 45.16 2.85
391 392 4.674211 GCCGACTTAACTATGACGATGTAC 59.326 45.833 0.00 0.00 0.00 2.90
476 519 9.744468 GCCTATTTTCTTGACTTTGAAGTAAAA 57.256 29.630 0.00 1.38 39.88 1.52
564 607 5.359860 GGAAGAGTTTTTGAGTGGGAGAAAA 59.640 40.000 0.00 0.00 0.00 2.29
599 642 2.025887 CAGTGCCCTAGGGTTGAAGATT 60.026 50.000 28.96 3.99 37.65 2.40
640 683 1.747355 ACGATACTCATTTCGTCCGGT 59.253 47.619 0.00 0.00 44.72 5.28
840 887 4.617223 GCTGAAACTTCTTGCGGAAAATAC 59.383 41.667 0.00 0.00 33.07 1.89
867 914 2.998097 GTGGGCTGGCCTACATCA 59.002 61.111 21.72 3.63 45.42 3.07
875 922 0.817634 TTGCATATACGTGGGCTGGC 60.818 55.000 0.00 0.00 0.00 4.85
961 1009 0.521735 CGCCTTGTTCTTAGGGCAAC 59.478 55.000 0.00 0.00 44.27 4.17
1167 1217 2.954868 GTGATGTACGCGCCGAGG 60.955 66.667 5.73 0.00 0.00 4.63
1514 1576 6.312426 GTCTCCAGTATGAACACAGAATTCTG 59.688 42.308 29.74 29.74 44.62 3.02
1589 1651 1.743394 GGTGACAAAATTCCCTAGCGG 59.257 52.381 0.00 0.00 0.00 5.52
1590 1652 1.396996 CGGTGACAAAATTCCCTAGCG 59.603 52.381 0.00 0.00 0.00 4.26
1591 1653 2.161609 CACGGTGACAAAATTCCCTAGC 59.838 50.000 0.74 0.00 0.00 3.42
1592 1654 3.435671 GTCACGGTGACAAAATTCCCTAG 59.564 47.826 30.78 0.00 46.22 3.02
1593 1655 3.404899 GTCACGGTGACAAAATTCCCTA 58.595 45.455 30.78 0.00 46.22 3.53
1594 1656 2.227194 GTCACGGTGACAAAATTCCCT 58.773 47.619 30.78 0.00 46.22 4.20
1595 1657 2.699251 GTCACGGTGACAAAATTCCC 57.301 50.000 30.78 5.25 46.22 3.97
1689 1780 8.186821 ACTATACCACGAGTACATGAACTAAAC 58.813 37.037 0.00 0.00 32.46 2.01
1745 1836 4.935808 ACGGTGATAGTTCAACAGATTTCC 59.064 41.667 0.00 0.00 39.72 3.13
1750 1841 3.556213 CCCAACGGTGATAGTTCAACAGA 60.556 47.826 0.00 0.00 39.72 3.41
1784 1875 3.693578 TCAAATTCTCACAACAGTGCACA 59.306 39.130 21.04 0.00 33.28 4.57
1785 1876 4.291540 TCAAATTCTCACAACAGTGCAC 57.708 40.909 9.40 9.40 33.28 4.57
1837 1931 2.802057 GCTATACTACCCCAACAGTGCG 60.802 54.545 0.00 0.00 0.00 5.34
1987 2081 7.888514 ATTCCTACCACCATCATTTAGGATA 57.111 36.000 0.00 0.00 38.47 2.59
2079 2173 6.824958 TGCTACTGAAATAAGGTAAGGGAT 57.175 37.500 0.00 0.00 0.00 3.85
2096 2190 3.806949 TTTGGGAGGAACAATGCTACT 57.193 42.857 0.00 0.00 0.00 2.57
2147 2241 9.390795 CAACACAAGATAATTGCATAGATAAGC 57.609 33.333 0.00 0.00 0.00 3.09
2317 2433 4.371624 AACATGGAGGAACTGTTGATCA 57.628 40.909 0.00 0.00 41.55 2.92
2331 2447 3.327757 ACCTGACAGAGCTAAAACATGGA 59.672 43.478 3.32 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.