Multiple sequence alignment - TraesCS6D01G162600

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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 TraesCS6D01G162600 chr6D 100.000 2183 0 0 1 2183 141139153 141136971 0 4032
1 TraesCS6D01G162600 chr6A 92.485 2209 99 23 1 2183 185322836 185320669 0 3097
2 TraesCS6D01G162600 chr6B 91.190 1782 89 29 1 1752 240404564 240402821 0 2359
3 TraesCS6D01G162600 chr6B 94.896 431 10 3 1754 2183 240402781 240402362 0 664


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 TraesCS6D01G162600 chr6D 141136971 141139153 2182 True 4032.0 4032 100.000 1 2183 1 chr6D.!!$R1 2182
1 TraesCS6D01G162600 chr6A 185320669 185322836 2167 True 3097.0 3097 92.485 1 2183 1 chr6A.!!$R1 2182
2 TraesCS6D01G162600 chr6B 240402362 240404564 2202 True 1511.5 2359 93.043 1 2183 2 chr6B.!!$R1 2182

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
246 248 1.074084 AGGAACAGACAGACTCTCGGA 59.926 52.381 0.0 0.0 0.00 4.55 F
1014 1039 1.038130 AGAGGATGGCGAGCTTACGT 61.038 55.000 0.0 0.0 35.59 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1122 1147 0.316689 CGACAAACACCGGCAAGTTC 60.317 55.000 0.00 0.0 0.0 3.01 R
1892 1980 3.118186 CCCGGAGTAAATGATACCCAACA 60.118 47.826 0.73 0.0 0.0 3.33 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
47 48 1.376086 CCGGCCAGATGGATATGCA 59.624 57.895 2.24 0.00 37.39 3.96
73 74 1.135721 GCTAAATCCAGTACCGACCGT 59.864 52.381 0.00 0.00 0.00 4.83
246 248 1.074084 AGGAACAGACAGACTCTCGGA 59.926 52.381 0.00 0.00 0.00 4.55
284 286 7.876582 GTGGGTTTTACTACTACACATTCTCTT 59.123 37.037 0.00 0.00 0.00 2.85
285 287 9.092338 TGGGTTTTACTACTACACATTCTCTTA 57.908 33.333 0.00 0.00 0.00 2.10
286 288 9.933723 GGGTTTTACTACTACACATTCTCTTAA 57.066 33.333 0.00 0.00 0.00 1.85
378 389 7.950684 AGTACTATATCTCCTGCCAGTAATCAA 59.049 37.037 0.00 0.00 0.00 2.57
412 423 7.851508 TCAGAAAAGCGCATACATAAACTATC 58.148 34.615 11.47 0.00 0.00 2.08
413 424 7.710907 TCAGAAAAGCGCATACATAAACTATCT 59.289 33.333 11.47 0.00 0.00 1.98
414 425 8.978539 CAGAAAAGCGCATACATAAACTATCTA 58.021 33.333 11.47 0.00 0.00 1.98
415 426 9.197694 AGAAAAGCGCATACATAAACTATCTAG 57.802 33.333 11.47 0.00 0.00 2.43
416 427 6.952935 AAGCGCATACATAAACTATCTAGC 57.047 37.500 11.47 0.00 0.00 3.42
459 470 5.488919 ACCAGATAGAGAACCTGAATTTCCA 59.511 40.000 0.00 0.00 0.00 3.53
460 471 6.054295 CCAGATAGAGAACCTGAATTTCCAG 58.946 44.000 0.00 0.00 0.00 3.86
461 472 6.126940 CCAGATAGAGAACCTGAATTTCCAGA 60.127 42.308 0.00 0.00 36.29 3.86
462 473 7.419981 CCAGATAGAGAACCTGAATTTCCAGAT 60.420 40.741 0.00 0.00 36.29 2.90
463 474 8.646004 CAGATAGAGAACCTGAATTTCCAGATA 58.354 37.037 0.00 0.00 36.29 1.98
464 475 8.869109 AGATAGAGAACCTGAATTTCCAGATAG 58.131 37.037 0.00 0.00 36.29 2.08
574 594 3.377485 TGTATCCGTTCACTACAGCTCTC 59.623 47.826 0.00 0.00 0.00 3.20
576 596 2.447443 TCCGTTCACTACAGCTCTCAT 58.553 47.619 0.00 0.00 0.00 2.90
671 691 3.894427 TGCAACCCAGAAAAGCAAAGATA 59.106 39.130 0.00 0.00 31.42 1.98
733 753 2.714808 ACCTACCACCTTCCTTTCCTT 58.285 47.619 0.00 0.00 0.00 3.36
734 754 3.061369 ACCTACCACCTTCCTTTCCTTT 58.939 45.455 0.00 0.00 0.00 3.11
735 755 3.074094 ACCTACCACCTTCCTTTCCTTTC 59.926 47.826 0.00 0.00 0.00 2.62
736 756 2.677542 ACCACCTTCCTTTCCTTTCC 57.322 50.000 0.00 0.00 0.00 3.13
737 757 2.144450 ACCACCTTCCTTTCCTTTCCT 58.856 47.619 0.00 0.00 0.00 3.36
940 964 1.748493 ACTCTCTCTTGCTGATCGACC 59.252 52.381 0.00 0.00 0.00 4.79
1014 1039 1.038130 AGAGGATGGCGAGCTTACGT 61.038 55.000 0.00 0.00 35.59 3.57
1211 1236 6.090898 CGGGTTCTCTATGTAAAGTTGTGAAG 59.909 42.308 0.00 0.00 0.00 3.02
1261 1286 5.820131 TCAGTAGTTTTTGCTGATGTTGTG 58.180 37.500 0.00 0.00 42.63 3.33
1264 1289 3.709987 AGTTTTTGCTGATGTTGTGCTC 58.290 40.909 0.00 0.00 0.00 4.26
1273 1298 1.237285 ATGTTGTGCTCCGGCTGTTC 61.237 55.000 0.00 0.00 39.59 3.18
1306 1331 2.563471 CGATAGGTATAGGCTTCGGC 57.437 55.000 0.00 0.00 40.88 5.54
1405 1430 4.082125 CAACCTAGCCCTCTTTTTCACAT 58.918 43.478 0.00 0.00 0.00 3.21
1438 1463 5.365619 GGGTTCGATTACATGTAAGATGGT 58.634 41.667 22.03 6.42 0.00 3.55
1439 1464 6.463331 GGGGTTCGATTACATGTAAGATGGTA 60.463 42.308 22.03 0.00 0.00 3.25
1483 1509 8.161699 AGGTGTTATGTTATCTTTTCGTTTGT 57.838 30.769 0.00 0.00 0.00 2.83
1513 1540 3.253188 TGCAGATGGAGTTTAACAGCAAC 59.747 43.478 0.00 0.00 0.00 4.17
1564 1606 4.260907 CCAGGTTTAATGCTCATGATCACG 60.261 45.833 0.42 0.00 0.00 4.35
1566 1608 3.876914 GGTTTAATGCTCATGATCACGGA 59.123 43.478 0.42 0.00 0.00 4.69
1568 1610 2.251409 AATGCTCATGATCACGGAGG 57.749 50.000 21.46 8.80 0.00 4.30
1570 1612 0.461548 TGCTCATGATCACGGAGGAC 59.538 55.000 21.46 10.73 0.00 3.85
1571 1613 0.461548 GCTCATGATCACGGAGGACA 59.538 55.000 21.46 0.00 0.00 4.02
1572 1614 1.134699 GCTCATGATCACGGAGGACAA 60.135 52.381 21.46 0.00 0.00 3.18
1573 1615 2.677902 GCTCATGATCACGGAGGACAAA 60.678 50.000 21.46 0.00 0.00 2.83
1574 1616 3.801698 CTCATGATCACGGAGGACAAAT 58.198 45.455 15.32 0.00 0.00 2.32
1575 1617 3.534554 TCATGATCACGGAGGACAAATG 58.465 45.455 0.00 0.00 0.00 2.32
1576 1618 3.197549 TCATGATCACGGAGGACAAATGA 59.802 43.478 0.00 0.00 0.00 2.57
1577 1619 3.694043 TGATCACGGAGGACAAATGAA 57.306 42.857 0.00 0.00 0.00 2.57
1578 1620 4.014569 TGATCACGGAGGACAAATGAAA 57.985 40.909 0.00 0.00 0.00 2.69
1640 1682 9.696917 AGACCACAAAATGTTTTCTGAAATATC 57.303 29.630 3.31 0.00 0.00 1.63
1679 1728 5.885465 AGATCATCAACTTTGGAAGGAGTT 58.115 37.500 0.00 0.00 36.58 3.01
1682 1731 6.877611 TCATCAACTTTGGAAGGAGTTAAC 57.122 37.500 0.00 0.00 34.52 2.01
1741 1790 7.781324 AGACCATCAAATTTGTAAGGAACAT 57.219 32.000 23.32 6.23 38.10 2.71
1892 1980 3.443329 CAGCAGATGTCCGATAGATAGCT 59.557 47.826 0.00 0.00 31.76 3.32
2049 2137 0.250124 TGAGAACCAACCGCGAACAT 60.250 50.000 8.23 0.00 0.00 2.71
2174 2262 1.852633 TCTCGCCCTCATCTTCTTCA 58.147 50.000 0.00 0.00 0.00 3.02
2180 2268 3.212685 GCCCTCATCTTCTTCAATCAGG 58.787 50.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.367840 GGCCGGATCGTGCTATTCT 59.632 57.895 5.05 0.00 0.00 2.40
47 48 5.010820 GGTCGGTACTGGATTTAGCTATCTT 59.989 44.000 0.85 0.00 0.00 2.40
73 74 0.753479 TCTTTCACCAAAAGCGCCCA 60.753 50.000 2.29 0.00 43.48 5.36
171 173 2.027561 CGGTAATCCTGGTTGGTCAGAA 60.028 50.000 0.00 0.00 36.93 3.02
176 178 0.248289 CGTCGGTAATCCTGGTTGGT 59.752 55.000 0.00 0.00 37.07 3.67
221 223 1.346068 GAGTCTGTCTGTTCCTTGGCT 59.654 52.381 0.00 0.00 0.00 4.75
284 286 7.547019 TGTCAATTTGTTTCACACTGCAAATTA 59.453 29.630 11.93 0.00 44.59 1.40
285 287 6.370994 TGTCAATTTGTTTCACACTGCAAATT 59.629 30.769 7.89 7.89 46.18 1.82
286 288 5.873712 TGTCAATTTGTTTCACACTGCAAAT 59.126 32.000 0.00 0.00 41.52 2.32
287 289 5.119898 GTGTCAATTTGTTTCACACTGCAAA 59.880 36.000 10.31 0.00 35.50 3.68
396 407 7.253917 GCTCATGCTAGATAGTTTATGTATGCG 60.254 40.741 0.00 0.00 36.03 4.73
412 423 2.544694 CGTAGGTGAAGGCTCATGCTAG 60.545 54.545 0.00 0.00 39.59 3.42
413 424 1.409064 CGTAGGTGAAGGCTCATGCTA 59.591 52.381 0.00 0.00 39.59 3.49
414 425 0.176680 CGTAGGTGAAGGCTCATGCT 59.823 55.000 0.00 0.00 39.59 3.79
415 426 0.108138 ACGTAGGTGAAGGCTCATGC 60.108 55.000 0.00 0.00 33.05 4.06
416 427 2.481449 GGTACGTAGGTGAAGGCTCATG 60.481 54.545 0.00 0.00 33.05 3.07
459 470 5.538433 GCAAGTTCAGTCCCTATCTCTATCT 59.462 44.000 0.00 0.00 0.00 1.98
460 471 5.303078 TGCAAGTTCAGTCCCTATCTCTATC 59.697 44.000 0.00 0.00 0.00 2.08
461 472 5.069781 GTGCAAGTTCAGTCCCTATCTCTAT 59.930 44.000 0.00 0.00 0.00 1.98
462 473 4.402793 GTGCAAGTTCAGTCCCTATCTCTA 59.597 45.833 0.00 0.00 0.00 2.43
463 474 3.196685 GTGCAAGTTCAGTCCCTATCTCT 59.803 47.826 0.00 0.00 0.00 3.10
464 475 3.196685 AGTGCAAGTTCAGTCCCTATCTC 59.803 47.826 0.00 0.00 0.00 2.75
505 522 3.853671 ACTCCGCGTTACAGTATAAAACG 59.146 43.478 4.92 2.50 46.50 3.60
559 579 8.934507 AAATAGTAATGAGAGCTGTAGTGAAC 57.065 34.615 0.00 0.00 0.00 3.18
574 594 8.272173 TGGAGAGGGGTTCTTAAAATAGTAATG 58.728 37.037 0.00 0.00 35.87 1.90
576 596 7.238096 TGTGGAGAGGGGTTCTTAAAATAGTAA 59.762 37.037 0.00 0.00 35.87 2.24
671 691 2.780010 CCACCCCTAGATTCTGAACCAT 59.220 50.000 0.00 0.00 0.00 3.55
733 753 0.179012 GGGGTTGACAAACGGAGGAA 60.179 55.000 0.00 0.00 37.15 3.36
734 754 1.452801 GGGGTTGACAAACGGAGGA 59.547 57.895 0.00 0.00 37.15 3.71
735 755 1.602605 GGGGGTTGACAAACGGAGG 60.603 63.158 0.00 0.00 37.15 4.30
736 756 0.251165 ATGGGGGTTGACAAACGGAG 60.251 55.000 0.00 0.00 37.15 4.63
737 757 0.250989 GATGGGGGTTGACAAACGGA 60.251 55.000 0.00 0.00 37.15 4.69
995 1020 1.038130 ACGTAAGCTCGCCATCCTCT 61.038 55.000 0.00 0.00 45.62 3.69
996 1021 0.872021 CACGTAAGCTCGCCATCCTC 60.872 60.000 0.00 0.00 45.62 3.71
1122 1147 0.316689 CGACAAACACCGGCAAGTTC 60.317 55.000 0.00 0.00 0.00 3.01
1173 1198 0.459078 GAACCCGCTACTAGTGACCC 59.541 60.000 5.39 0.00 0.00 4.46
1211 1236 4.762765 AGAGAGACCGGTGATATGATACAC 59.237 45.833 14.63 0.00 36.44 2.90
1273 1298 3.886123 ACCTATCGGGAAGAACAAATGG 58.114 45.455 0.00 0.00 38.76 3.16
1438 1463 7.070629 ACACCTTTTTAGGGGAAAGTTCATTA 58.929 34.615 0.00 0.00 35.49 1.90
1439 1464 5.903010 ACACCTTTTTAGGGGAAAGTTCATT 59.097 36.000 0.00 0.00 35.49 2.57
1478 1504 1.203052 CATCTGCACATCCCCACAAAC 59.797 52.381 0.00 0.00 0.00 2.93
1483 1509 0.915872 ACTCCATCTGCACATCCCCA 60.916 55.000 0.00 0.00 0.00 4.96
1564 1606 3.058224 CGACAACCTTTCATTTGTCCTCC 60.058 47.826 8.48 0.00 45.93 4.30
1566 1608 2.884639 CCGACAACCTTTCATTTGTCCT 59.115 45.455 8.48 0.00 45.93 3.85
1568 1610 3.606153 CGACCGACAACCTTTCATTTGTC 60.606 47.826 4.69 4.69 45.45 3.18
1570 1612 2.350388 CCGACCGACAACCTTTCATTTG 60.350 50.000 0.00 0.00 0.00 2.32
1571 1613 1.877443 CCGACCGACAACCTTTCATTT 59.123 47.619 0.00 0.00 0.00 2.32
1572 1614 1.519408 CCGACCGACAACCTTTCATT 58.481 50.000 0.00 0.00 0.00 2.57
1573 1615 0.953960 GCCGACCGACAACCTTTCAT 60.954 55.000 0.00 0.00 0.00 2.57
1574 1616 1.595929 GCCGACCGACAACCTTTCA 60.596 57.895 0.00 0.00 0.00 2.69
1575 1617 1.301479 AGCCGACCGACAACCTTTC 60.301 57.895 0.00 0.00 0.00 2.62
1576 1618 1.597027 CAGCCGACCGACAACCTTT 60.597 57.895 0.00 0.00 0.00 3.11
1577 1619 2.030562 CAGCCGACCGACAACCTT 59.969 61.111 0.00 0.00 0.00 3.50
1578 1620 4.003788 CCAGCCGACCGACAACCT 62.004 66.667 0.00 0.00 0.00 3.50
1659 1701 6.262273 GTGTTAACTCCTTCCAAAGTTGATGA 59.738 38.462 7.22 0.00 36.44 2.92
1666 1708 4.757149 CCTCTGTGTTAACTCCTTCCAAAG 59.243 45.833 7.22 0.00 0.00 2.77
1679 1728 9.494271 GCAATCAGATATTTATCCTCTGTGTTA 57.506 33.333 0.00 0.00 38.05 2.41
1682 1731 7.660617 AGTGCAATCAGATATTTATCCTCTGTG 59.339 37.037 0.00 0.00 38.05 3.66
1892 1980 3.118186 CCCGGAGTAAATGATACCCAACA 60.118 47.826 0.73 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.