Multiple sequence alignment - TraesCS1B01G122900

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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 TraesCS1B01G122900 chr1B 100.000 2789 0 0 1 2789 148433763 148436551 0.000000e+00 5151.0
1 TraesCS1B01G122900 chr1D 92.089 2326 133 25 489 2789 93111956 93114255 0.000000e+00 3229.0
2 TraesCS1B01G122900 chr1D 97.760 491 8 2 1 489 93111350 93111839 0.000000e+00 843.0
3 TraesCS1B01G122900 chr1D 83.146 178 27 3 499 674 466375352 466375176 2.880000e-35 159.0
4 TraesCS1B01G122900 chr1A 92.724 2144 97 21 697 2789 91060143 91058008 0.000000e+00 3040.0
5 TraesCS1B01G122900 chr1A 94.737 437 15 5 1 433 91060638 91060206 0.000000e+00 673.0
6 TraesCS1B01G122900 chr1A 95.455 44 1 1 447 489 91060223 91060180 4.980000e-08 69.4
7 TraesCS1B01G122900 chr5A 84.699 183 25 3 488 667 281143836 281144018 2.210000e-41 180.0
8 TraesCS1B01G122900 chr6D 84.916 179 24 2 498 673 12058707 12058529 7.940000e-41 178.0
9 TraesCS1B01G122900 chr2B 84.916 179 22 5 499 674 784765796 784765972 2.860000e-40 176.0
10 TraesCS1B01G122900 chr2B 83.146 178 27 3 499 674 758362592 758362416 2.880000e-35 159.0
11 TraesCS1B01G122900 chr3B 84.153 183 26 2 488 667 776993540 776993722 1.030000e-39 174.0
12 TraesCS1B01G122900 chr7A 84.971 173 23 3 498 667 632669158 632668986 3.690000e-39 172.0
13 TraesCS1B01G122900 chr5B 83.516 182 24 5 498 674 678906091 678906271 6.180000e-37 165.0


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 TraesCS1B01G122900 chr1B 148433763 148436551 2788 False 5151.0 5151 100.000000 1 2789 1 chr1B.!!$F1 2788
1 TraesCS1B01G122900 chr1D 93111350 93114255 2905 False 2036.0 3229 94.924500 1 2789 2 chr1D.!!$F1 2788
2 TraesCS1B01G122900 chr1A 91058008 91060638 2630 True 1260.8 3040 94.305333 1 2789 3 chr1A.!!$R1 2788

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
575 702 0.66102 CGAGGCGTTTTTGGTGACTT 59.339 50.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2198 2381 0.823356 ACTGACAATGGCGCAAACCT 60.823 50.0 10.83 0.0 0.0 3.5 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
251 255 7.143340 CAGTATCATTTGTATCTGGCCATTTG 58.857 38.462 5.51 0.00 0.00 2.32
575 702 0.661020 CGAGGCGTTTTTGGTGACTT 59.339 50.000 0.00 0.00 0.00 3.01
585 712 5.578776 GTTTTTGGTGACTTCGTCAATCTT 58.421 37.500 0.00 0.00 44.49 2.40
600 727 7.084486 TCGTCAATCTTAAGATGATATGTCGG 58.916 38.462 18.61 7.26 34.49 4.79
604 731 5.048153 TCTTAAGATGATATGTCGGCTCG 57.952 43.478 0.00 0.00 0.00 5.03
609 736 0.952280 TGATATGTCGGCTCGGTCTC 59.048 55.000 0.00 0.00 0.00 3.36
619 746 2.750637 TCGGTCTCTCGGAGGTGC 60.751 66.667 4.96 0.00 0.00 5.01
625 752 2.025155 GTCTCTCGGAGGTGCTCATAA 58.975 52.381 4.96 0.00 31.08 1.90
628 755 1.063942 TCTCGGAGGTGCTCATAAGGA 60.064 52.381 4.96 0.00 31.08 3.36
631 758 3.572642 TCGGAGGTGCTCATAAGGATAA 58.427 45.455 0.00 0.00 31.08 1.75
632 759 3.574396 TCGGAGGTGCTCATAAGGATAAG 59.426 47.826 0.00 0.00 31.08 1.73
643 770 5.178061 TCATAAGGATAAGGCATGCGTATG 58.822 41.667 14.17 9.36 43.74 2.39
667 794 5.554070 CATTCATAGGGATGAGTGTATGCA 58.446 41.667 0.00 0.00 43.03 3.96
668 795 5.830799 TTCATAGGGATGAGTGTATGCAT 57.169 39.130 3.79 3.79 43.03 3.96
677 804 5.349817 GGATGAGTGTATGCATGTATAGTGC 59.650 44.000 10.16 3.62 42.81 4.40
762 889 1.149987 TTAACTCCGACGCGCAAAAT 58.850 45.000 5.73 0.00 0.00 1.82
804 955 9.249053 TCAGCAGTATCCATTAATTTACCAAAA 57.751 29.630 0.00 0.00 0.00 2.44
1038 1192 2.366435 GAGACCCCGGGATCCCAA 60.366 66.667 30.42 0.00 35.37 4.12
1292 1446 2.034879 AACGCAAGGTGATCGCTGG 61.035 57.895 6.18 0.00 46.39 4.85
1310 1470 2.801679 CTGGTCGACCGAGTAGATCTAC 59.198 54.545 28.70 22.97 39.43 2.59
1348 1519 7.795482 TTTTGGCTATTATACATTACACGCT 57.205 32.000 0.00 0.00 0.00 5.07
1792 1963 0.815734 CAACTCGTACCGATGACCCT 59.184 55.000 0.00 0.00 34.61 4.34
1793 1964 0.815734 AACTCGTACCGATGACCCTG 59.184 55.000 0.00 0.00 34.61 4.45
1814 1985 2.824041 CCGTCCAAATCGCCAGGG 60.824 66.667 0.00 0.00 0.00 4.45
1841 2012 7.337480 ACAAATGTTCATGCATATAGAAGCA 57.663 32.000 0.00 1.54 45.92 3.91
1853 2024 8.768957 TGCATATAGAAGCATCTAGAACATTC 57.231 34.615 4.80 1.36 41.36 2.67
1855 2026 7.821359 GCATATAGAAGCATCTAGAACATTCCA 59.179 37.037 4.80 0.00 41.36 3.53
1886 2060 0.743097 AGAAGCACGTCGGTATACCC 59.257 55.000 16.47 2.20 0.00 3.69
1893 2067 3.374745 CACGTCGGTATACCCATTGTAC 58.625 50.000 16.47 4.59 30.62 2.90
1991 2166 1.414919 TGCTGAAGTACTGAACGGGTT 59.585 47.619 0.00 0.00 0.00 4.11
1992 2167 2.067013 GCTGAAGTACTGAACGGGTTC 58.933 52.381 0.00 4.63 39.91 3.62
2096 2279 2.135139 CGTGCACATCACAACACTAGT 58.865 47.619 18.64 0.00 45.92 2.57
2103 2286 5.741425 CACATCACAACACTAGTCAAACAG 58.259 41.667 0.00 0.00 0.00 3.16
2198 2381 0.764890 CCTCCCCTTCTTGTGTGACA 59.235 55.000 0.00 0.00 0.00 3.58
2342 2525 0.108615 CACCCCTCGCAGTTGTCTAG 60.109 60.000 0.00 0.00 0.00 2.43
2380 2563 9.469097 AAATGTATTAAGTACAAGGGCAATACA 57.531 29.630 7.25 7.25 45.87 2.29
2381 2564 9.469097 AATGTATTAAGTACAAGGGCAATACAA 57.531 29.630 8.52 0.00 45.87 2.41
2382 2565 9.640952 ATGTATTAAGTACAAGGGCAATACAAT 57.359 29.630 8.52 0.00 45.87 2.71
2389 2572 8.029782 AGTACAAGGGCAATACAATGTCTATA 57.970 34.615 0.00 0.00 0.00 1.31
2394 2577 9.725019 CAAGGGCAATACAATGTCTATAGATAA 57.275 33.333 5.57 0.00 0.00 1.75
2439 2622 5.994668 AGAGCTTACCTCAAAGAAAGAGTTG 59.005 40.000 0.00 0.00 43.31 3.16
2445 2628 8.575649 TTACCTCAAAGAAAGAGTTGAAGTTT 57.424 30.769 0.00 0.00 33.52 2.66
2490 2673 1.722034 AAGGTGCTCTCTGACTTCCA 58.278 50.000 0.00 0.00 0.00 3.53
2514 2697 4.498345 GCAAGTCGACTACTCCTTAGGATG 60.498 50.000 20.39 9.71 37.50 3.51
2556 2739 6.968131 TTCTTGTTGAACTCCTGAATATCG 57.032 37.500 0.00 0.00 0.00 2.92
2644 2832 0.098200 CATGAGTGATGTGCCAAGCG 59.902 55.000 0.00 0.00 0.00 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 132 3.381272 CCGTGGATGTATTTCTTTGCCAT 59.619 43.478 0.00 0.00 0.00 4.40
268 272 5.845985 TTCTCTAGCTTTGACAATTGACG 57.154 39.130 13.59 0.00 0.00 4.35
499 626 5.448089 GCGTCGCCAGAAATCCTAAAATAAA 60.448 40.000 5.75 0.00 0.00 1.40
503 630 1.735571 GCGTCGCCAGAAATCCTAAAA 59.264 47.619 5.75 0.00 0.00 1.52
527 654 0.832135 AGGCGTCTCTTCCCACTGAA 60.832 55.000 0.00 0.00 0.00 3.02
531 658 2.182030 CGAGGCGTCTCTTCCCAC 59.818 66.667 16.21 0.00 37.86 4.61
556 683 0.661020 AAGTCACCAAAAACGCCTCG 59.339 50.000 0.00 0.00 0.00 4.63
575 702 7.084486 CCGACATATCATCTTAAGATTGACGA 58.916 38.462 26.53 17.88 31.33 4.20
585 712 3.154710 ACCGAGCCGACATATCATCTTA 58.845 45.455 0.00 0.00 0.00 2.10
600 727 2.438795 ACCTCCGAGAGACCGAGC 60.439 66.667 0.00 0.00 0.00 5.03
604 731 1.040339 ATGAGCACCTCCGAGAGACC 61.040 60.000 0.00 0.00 0.00 3.85
609 736 1.403814 TCCTTATGAGCACCTCCGAG 58.596 55.000 0.00 0.00 0.00 4.63
619 746 3.668447 ACGCATGCCTTATCCTTATGAG 58.332 45.455 13.15 0.00 0.00 2.90
643 770 4.394300 GCATACACTCATCCCTATGAATGC 59.606 45.833 6.88 6.88 41.91 3.56
644 771 5.554070 TGCATACACTCATCCCTATGAATG 58.446 41.667 0.00 0.00 43.41 2.67
645 772 5.830799 TGCATACACTCATCCCTATGAAT 57.169 39.130 0.00 0.00 41.57 2.57
648 775 4.903054 ACATGCATACACTCATCCCTATG 58.097 43.478 0.00 0.00 0.00 2.23
654 781 5.349817 GGCACTATACATGCATACACTCATC 59.650 44.000 0.00 0.00 45.27 2.92
762 889 4.263905 ACTGCTGATTCTTTGGGACCATAA 60.264 41.667 0.00 0.00 0.00 1.90
857 1009 9.766277 GATTGCTCGATTTTTATTATCAGATCC 57.234 33.333 0.00 0.00 0.00 3.36
858 1010 9.766277 GGATTGCTCGATTTTTATTATCAGATC 57.234 33.333 0.00 0.00 0.00 2.75
875 1027 2.807967 TGTTTTGACTCTGGATTGCTCG 59.192 45.455 0.00 0.00 0.00 5.03
1030 1184 2.513897 CGACGGCCTTTGGGATCC 60.514 66.667 1.92 1.92 33.58 3.36
1288 1442 0.308376 GATCTACTCGGTCGACCAGC 59.692 60.000 32.80 12.52 35.14 4.85
1328 1492 6.387465 TCAGAGCGTGTAATGTATAATAGCC 58.613 40.000 0.00 0.00 0.00 3.93
1546 1717 3.672293 CTTGTCCACGGCAAGCAT 58.328 55.556 7.13 0.00 37.18 3.79
1561 1732 0.905337 AGGCGGTAGAGTTCTGGCTT 60.905 55.000 0.00 0.00 42.97 4.35
1636 1807 1.154016 CGGCGATGAGTGTCTCGTT 60.154 57.895 0.00 0.00 37.23 3.85
1800 1971 1.976474 GTTGCCCTGGCGATTTGGA 60.976 57.895 0.49 0.00 45.51 3.53
1803 1974 0.975887 ATTTGTTGCCCTGGCGATTT 59.024 45.000 0.49 0.00 45.51 2.17
1814 1985 7.306399 GCTTCTATATGCATGAACATTTGTTGC 60.306 37.037 10.16 0.00 38.56 4.17
1841 2012 6.897966 TCTACAACCTCTGGAATGTTCTAGAT 59.102 38.462 8.92 0.00 42.71 1.98
1853 2024 3.330267 GTGCTTCTTCTACAACCTCTGG 58.670 50.000 0.00 0.00 0.00 3.86
1855 2026 2.628657 ACGTGCTTCTTCTACAACCTCT 59.371 45.455 0.00 0.00 0.00 3.69
1886 2060 6.985117 CCAAAGAATATGGGGATGTACAATG 58.015 40.000 0.00 0.00 34.15 2.82
1911 2085 7.494625 AGGATGAATGCAACATTGAAATGAATC 59.505 33.333 9.94 0.00 39.67 2.52
1991 2166 3.494398 GGCCTTAGATGAAATGGTAGCGA 60.494 47.826 0.00 0.00 0.00 4.93
1992 2167 2.808543 GGCCTTAGATGAAATGGTAGCG 59.191 50.000 0.00 0.00 0.00 4.26
2096 2279 3.884895 ACACTTGGTGATGTCTGTTTGA 58.115 40.909 4.62 0.00 36.96 2.69
2103 2286 4.215613 GGGAAGTAAACACTTGGTGATGTC 59.784 45.833 4.62 0.00 36.96 3.06
2198 2381 0.823356 ACTGACAATGGCGCAAACCT 60.823 50.000 10.83 0.00 0.00 3.50
2394 2577 8.728098 AGCTCTTCCAATTAGGGATTAGTTAAT 58.272 33.333 0.00 0.00 36.67 1.40
2400 2583 6.619852 AGGTAAGCTCTTCCAATTAGGGATTA 59.380 38.462 0.00 0.00 36.67 1.75
2401 2584 5.433381 AGGTAAGCTCTTCCAATTAGGGATT 59.567 40.000 0.00 0.00 36.67 3.01
2439 2622 6.128418 GGCAGTTTCTGATGAGACTAAACTTC 60.128 42.308 0.66 0.00 35.76 3.01
2445 2628 4.089361 TGAGGCAGTTTCTGATGAGACTA 58.911 43.478 0.66 0.00 35.76 2.59
2490 2673 3.018149 CCTAAGGAGTAGTCGACTTGCT 58.982 50.000 25.44 21.18 39.06 3.91
2514 2697 5.296813 AGAAATCAAATTCGCTGTACACC 57.703 39.130 0.00 0.00 34.46 4.16
2556 2739 8.402472 TGTAGCATAAACTTACATACATTTGGC 58.598 33.333 0.00 0.00 0.00 4.52
2644 2832 1.156736 ACAAATAGTGACGTGCCAGC 58.843 50.000 0.00 0.00 0.00 4.85
2651 2839 4.377431 GCCTTCTGTGAACAAATAGTGACG 60.377 45.833 0.00 0.00 0.00 4.35
2655 2843 3.074412 CGGCCTTCTGTGAACAAATAGT 58.926 45.455 0.00 0.00 0.00 2.12
2731 2919 1.067142 TCGAGCAATACGAAACAGGCT 60.067 47.619 0.00 0.00 36.84 4.58


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

AutoCloner maintained by Alex Coulton.