Multiple sequence alignment - TraesCS2B01G416100

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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 TraesCS2B01G416100 chr2B 100.000 3911 0 0 1 3911 594848182 594844272 0.000000e+00 7223
1 TraesCS2B01G416100 chr2B 82.415 853 122 18 3084 3911 735521449 735520600 0.000000e+00 719
2 TraesCS2B01G416100 chr2D 95.209 3945 112 35 1 3911 506793966 506790065 0.000000e+00 6167
3 TraesCS2B01G416100 chr2D 82.532 853 122 13 3084 3911 605371402 605370552 0.000000e+00 725
4 TraesCS2B01G416100 chr2A 93.146 3954 151 45 1 3911 651611207 651607331 0.000000e+00 5690
5 TraesCS2B01G416100 chr2A 82.884 853 118 15 3084 3911 736549563 736548714 0.000000e+00 741
6 TraesCS2B01G416100 chr3D 73.974 780 164 35 1653 2415 310683051 310683808 2.980000e-71 279
7 TraesCS2B01G416100 chr3B 73.758 785 157 39 1653 2415 410774953 410774196 3.000000e-66 263
8 TraesCS2B01G416100 chr3A 73.631 785 158 42 1653 2415 421720831 421720074 1.390000e-64 257
9 TraesCS2B01G416100 chr1A 77.376 442 85 15 1856 2291 154700834 154701266 8.390000e-62 248


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 TraesCS2B01G416100 chr2B 594844272 594848182 3910 True 7223 7223 100.000 1 3911 1 chr2B.!!$R1 3910
1 TraesCS2B01G416100 chr2B 735520600 735521449 849 True 719 719 82.415 3084 3911 1 chr2B.!!$R2 827
2 TraesCS2B01G416100 chr2D 506790065 506793966 3901 True 6167 6167 95.209 1 3911 1 chr2D.!!$R1 3910
3 TraesCS2B01G416100 chr2D 605370552 605371402 850 True 725 725 82.532 3084 3911 1 chr2D.!!$R2 827
4 TraesCS2B01G416100 chr2A 651607331 651611207 3876 True 5690 5690 93.146 1 3911 1 chr2A.!!$R1 3910
5 TraesCS2B01G416100 chr2A 736548714 736549563 849 True 741 741 82.884 3084 3911 1 chr2A.!!$R2 827
6 TraesCS2B01G416100 chr3D 310683051 310683808 757 False 279 279 73.974 1653 2415 1 chr3D.!!$F1 762
7 TraesCS2B01G416100 chr3B 410774196 410774953 757 True 263 263 73.758 1653 2415 1 chr3B.!!$R1 762
8 TraesCS2B01G416100 chr3A 421720074 421720831 757 True 257 257 73.631 1653 2415 1 chr3A.!!$R1 762

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
588 618 0.038343 GCTTTTGCCGAAATGCCAGA 60.038 50.0 0.00 0.00 36.62 3.86 F
847 879 1.712018 CTCTCCGTGTGCATGCATGG 61.712 60.0 25.64 24.19 44.70 3.66 F
1580 1630 0.467384 CCATCCATCTTGTCCTCGCT 59.533 55.0 0.00 0.00 0.00 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1404 1448 0.469070 CCAGCTCCTCCTTGATCCTG 59.531 60.000 0.00 0.00 0.00 3.86 R
2640 2707 1.139095 GGTCGTCGACATGAGGGAC 59.861 63.158 25.64 12.82 33.68 4.46 R
2969 3040 0.706433 ATCAAGCCATGGAACCCTGT 59.294 50.000 18.40 0.00 0.00 4.00 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
23 24 0.538057 CCCAGGCTGTTGCTCTTTCA 60.538 55.000 14.43 0.00 39.59 2.69
32 33 2.034939 TGTTGCTCTTTCAATGCAGGTG 59.965 45.455 0.00 0.00 38.01 4.00
72 73 5.126061 CCATCTTAGGCTTAGCACATGTTTT 59.874 40.000 6.53 0.00 0.00 2.43
74 75 4.458989 TCTTAGGCTTAGCACATGTTTTGG 59.541 41.667 6.53 0.00 0.00 3.28
102 104 3.554324 CCACACCGCACACATACTTATAC 59.446 47.826 0.00 0.00 0.00 1.47
105 107 4.081309 ACACCGCACACATACTTATACCTT 60.081 41.667 0.00 0.00 0.00 3.50
191 195 2.742372 GCGGAAAGAAGGCTCGCA 60.742 61.111 10.62 0.00 44.87 5.10
459 475 1.305381 AACTAGTCCGGAGCTGGCT 60.305 57.895 3.06 0.00 0.00 4.75
460 476 0.905337 AACTAGTCCGGAGCTGGCTT 60.905 55.000 3.06 2.52 0.00 4.35
501 518 3.215151 TGTTTTTACGCCATCTGAACCA 58.785 40.909 0.00 0.00 0.00 3.67
531 561 1.852157 AGGTCACATGCCAAGGGGA 60.852 57.895 0.00 0.00 35.59 4.81
532 562 1.379044 GGTCACATGCCAAGGGGAG 60.379 63.158 0.00 0.00 35.59 4.30
533 563 1.380302 GTCACATGCCAAGGGGAGT 59.620 57.895 0.00 0.00 35.59 3.85
534 564 0.251341 GTCACATGCCAAGGGGAGTT 60.251 55.000 0.00 0.00 35.59 3.01
535 565 0.482446 TCACATGCCAAGGGGAGTTT 59.518 50.000 0.00 0.00 35.59 2.66
548 578 1.368850 GAGTTTGTTCGTGCGTGGC 60.369 57.895 0.00 0.00 0.00 5.01
588 618 0.038343 GCTTTTGCCGAAATGCCAGA 60.038 50.000 0.00 0.00 36.62 3.86
780 812 2.335712 AAAAGGCGTGGCTAGCAGC 61.336 57.895 18.24 17.67 41.46 5.25
800 832 2.978452 GATCCATGGTGTCCTCGGCG 62.978 65.000 12.58 0.00 0.00 6.46
847 879 1.712018 CTCTCCGTGTGCATGCATGG 61.712 60.000 25.64 24.19 44.70 3.66
1404 1448 2.045926 AACTCCATGCTGCCGTCC 60.046 61.111 0.00 0.00 0.00 4.79
1422 1466 0.469070 CCAGGATCAAGGAGGAGCTG 59.531 60.000 0.00 0.00 0.00 4.24
1577 1627 3.390639 AGTCATCCATCCATCTTGTCCTC 59.609 47.826 0.00 0.00 0.00 3.71
1580 1630 0.467384 CCATCCATCTTGTCCTCGCT 59.533 55.000 0.00 0.00 0.00 4.93
1586 1636 2.471818 CATCTTGTCCTCGCTGATCAG 58.528 52.381 18.84 18.84 0.00 2.90
1629 1679 7.050970 TCATACTACTGACTGAACTGTTTGT 57.949 36.000 0.00 0.00 0.00 2.83
2232 2282 2.349580 CCACTACATCGTCGTCTTCGTA 59.650 50.000 0.00 0.00 38.33 3.43
2592 2659 1.153628 GCTGGCGACCGTCAAGTAT 60.154 57.895 0.00 0.00 0.00 2.12
2947 3018 5.182950 TGTGTGATTAAACAGCATTACAGGG 59.817 40.000 0.00 0.00 0.00 4.45
2948 3019 5.183140 GTGTGATTAAACAGCATTACAGGGT 59.817 40.000 0.00 0.00 0.00 4.34
2950 3021 6.072175 TGTGATTAAACAGCATTACAGGGTTC 60.072 38.462 0.00 0.00 0.00 3.62
2951 3022 5.417580 TGATTAAACAGCATTACAGGGTTCC 59.582 40.000 0.00 0.00 0.00 3.62
2952 3023 2.969821 AACAGCATTACAGGGTTCCA 57.030 45.000 0.00 0.00 0.00 3.53
2953 3024 3.456380 AACAGCATTACAGGGTTCCAT 57.544 42.857 0.00 0.00 0.00 3.41
2954 3025 2.726821 ACAGCATTACAGGGTTCCATG 58.273 47.619 1.81 1.81 0.00 3.66
2955 3026 2.026641 CAGCATTACAGGGTTCCATGG 58.973 52.381 4.97 4.97 0.00 3.66
2956 3027 0.746659 GCATTACAGGGTTCCATGGC 59.253 55.000 6.96 0.00 0.00 4.40
2957 3028 1.686115 GCATTACAGGGTTCCATGGCT 60.686 52.381 6.96 0.00 0.00 4.75
2958 3029 2.738743 CATTACAGGGTTCCATGGCTT 58.261 47.619 6.96 0.00 0.00 4.35
2959 3030 2.214376 TTACAGGGTTCCATGGCTTG 57.786 50.000 6.96 2.42 0.00 4.01
2960 3031 1.367346 TACAGGGTTCCATGGCTTGA 58.633 50.000 6.96 0.00 0.00 3.02
2961 3032 0.706433 ACAGGGTTCCATGGCTTGAT 59.294 50.000 6.96 0.00 0.00 2.57
2962 3033 1.341383 ACAGGGTTCCATGGCTTGATC 60.341 52.381 6.96 0.00 0.00 2.92
2963 3034 1.002069 AGGGTTCCATGGCTTGATCA 58.998 50.000 6.96 0.00 0.00 2.92
2964 3035 1.064166 AGGGTTCCATGGCTTGATCAG 60.064 52.381 6.96 0.00 0.00 2.90
3060 3131 9.223099 GTAACCTAGAGCTAGAAGGAATACTAG 57.777 40.741 13.89 4.14 39.05 2.57
3454 3550 1.599606 CTACACCGAGCTGAGCCAGT 61.600 60.000 0.00 0.00 33.43 4.00
3465 3561 0.815213 TGAGCCAGTGCAGTGTTGAC 60.815 55.000 19.93 9.03 41.13 3.18
3478 3574 3.915437 GTGTTGACACCAATCGGATTT 57.085 42.857 0.00 0.00 40.85 2.17
3565 3661 4.850822 ATGAGACTGCGCATGAGG 57.149 55.556 12.24 0.40 33.06 3.86
3612 3708 2.996249 ATGACTCCAGTAGCACCATG 57.004 50.000 0.00 0.00 0.00 3.66
3760 3856 1.001764 TGCCTCAATGACTGCAGGG 60.002 57.895 19.93 8.64 0.00 4.45
3766 3862 2.705658 CTCAATGACTGCAGGGGGTATA 59.294 50.000 19.93 0.00 0.00 1.47
3792 3896 1.742761 CCAGTCCTGGCACATTGTAG 58.257 55.000 0.00 0.00 44.73 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.157087 CCCTTTAGAACACACCTGCATT 58.843 45.455 0.00 0.00 0.00 3.56
32 33 3.421844 AGATGGTTGCCCTTTAGAACAC 58.578 45.455 0.00 0.00 0.00 3.32
74 75 1.231221 TGTGTGCGGTGTGGAAATAC 58.769 50.000 0.00 0.00 0.00 1.89
87 89 9.326413 AGTAAATCAAGGTATAAGTATGTGTGC 57.674 33.333 0.00 0.00 0.00 4.57
102 104 5.648092 CCTCCTGGTTAACAGTAAATCAAGG 59.352 44.000 8.10 0.58 46.06 3.61
105 107 6.235664 GTTCCTCCTGGTTAACAGTAAATCA 58.764 40.000 8.10 0.00 46.06 2.57
119 123 2.711922 CCGGTCTCGTTCCTCCTGG 61.712 68.421 0.00 0.00 33.95 4.45
191 195 1.649664 CTGATTGAACTGCTAGCGCT 58.350 50.000 17.26 17.26 36.97 5.92
459 475 6.588719 ACATAAGCAAAAACTGGCAGATAA 57.411 33.333 23.66 0.00 0.00 1.75
460 476 6.588719 AACATAAGCAAAAACTGGCAGATA 57.411 33.333 23.66 0.00 0.00 1.98
501 518 3.306364 GCATGTGACCTCAGAACACTACT 60.306 47.826 0.00 0.00 35.83 2.57
531 561 1.817941 AGCCACGCACGAACAAACT 60.818 52.632 0.00 0.00 0.00 2.66
532 562 1.654137 CAGCCACGCACGAACAAAC 60.654 57.895 0.00 0.00 0.00 2.93
533 563 2.712539 CAGCCACGCACGAACAAA 59.287 55.556 0.00 0.00 0.00 2.83
534 564 3.947841 GCAGCCACGCACGAACAA 61.948 61.111 0.00 0.00 0.00 2.83
535 565 4.908687 AGCAGCCACGCACGAACA 62.909 61.111 0.00 0.00 0.00 3.18
548 578 0.108804 CACGTGTAGGTACCCAGCAG 60.109 60.000 8.74 0.17 0.00 4.24
588 618 1.671742 CTGCCTAGTGTGTTCGGGT 59.328 57.895 0.00 0.00 0.00 5.28
754 785 1.739049 CCACGCCTTTTGCTCCAAA 59.261 52.632 0.00 0.00 38.05 3.28
759 791 2.335712 GCTAGCCACGCCTTTTGCT 61.336 57.895 2.29 0.00 38.05 3.91
775 807 1.153289 GACACCATGGATCGCTGCT 60.153 57.895 21.47 0.00 0.00 4.24
780 812 1.068083 CCGAGGACACCATGGATCG 59.932 63.158 21.47 17.74 0.00 3.69
1404 1448 0.469070 CCAGCTCCTCCTTGATCCTG 59.531 60.000 0.00 0.00 0.00 3.86
1577 1627 4.271776 TCAGCAAAATCATACTGATCAGCG 59.728 41.667 22.83 11.47 35.76 5.18
1592 1642 9.066892 AGTCAGTAGTATGATTTTTCAGCAAAA 57.933 29.630 0.00 0.00 38.76 2.44
1593 1643 8.506437 CAGTCAGTAGTATGATTTTTCAGCAAA 58.494 33.333 0.00 0.00 0.00 3.68
1594 1644 7.877612 TCAGTCAGTAGTATGATTTTTCAGCAA 59.122 33.333 0.00 0.00 0.00 3.91
1598 1648 9.208022 CAGTTCAGTCAGTAGTATGATTTTTCA 57.792 33.333 0.00 0.00 0.00 2.69
1599 1649 9.209175 ACAGTTCAGTCAGTAGTATGATTTTTC 57.791 33.333 0.00 0.00 0.00 2.29
1603 1653 8.150945 ACAAACAGTTCAGTCAGTAGTATGATT 58.849 33.333 0.00 0.00 0.00 2.57
1604 1654 7.671302 ACAAACAGTTCAGTCAGTAGTATGAT 58.329 34.615 0.00 0.00 0.00 2.45
1605 1655 7.050970 ACAAACAGTTCAGTCAGTAGTATGA 57.949 36.000 0.00 0.00 0.00 2.15
1606 1656 7.060748 CGTACAAACAGTTCAGTCAGTAGTATG 59.939 40.741 0.00 0.00 0.00 2.39
1607 1657 7.082602 CGTACAAACAGTTCAGTCAGTAGTAT 58.917 38.462 0.00 0.00 0.00 2.12
1608 1658 6.038603 ACGTACAAACAGTTCAGTCAGTAGTA 59.961 38.462 0.00 0.00 0.00 1.82
1609 1659 5.163581 ACGTACAAACAGTTCAGTCAGTAGT 60.164 40.000 0.00 0.00 0.00 2.73
1610 1660 5.279384 ACGTACAAACAGTTCAGTCAGTAG 58.721 41.667 0.00 0.00 0.00 2.57
1644 1694 1.302285 CTTGGGCAGCAGGATGTCT 59.698 57.895 0.00 0.00 39.31 3.41
2458 2508 5.160607 TGAATCGAAAGGTGGTACAAGAT 57.839 39.130 0.00 0.00 44.16 2.40
2508 2574 1.374125 CCTGTTCGTCGTCATGGCA 60.374 57.895 0.00 0.00 0.00 4.92
2640 2707 1.139095 GGTCGTCGACATGAGGGAC 59.861 63.158 25.64 12.82 33.68 4.46
2956 3027 3.629398 GGAACCCTGTAATGCTGATCAAG 59.371 47.826 0.00 0.00 0.00 3.02
2957 3028 3.010027 TGGAACCCTGTAATGCTGATCAA 59.990 43.478 0.00 0.00 0.00 2.57
2958 3029 2.575735 TGGAACCCTGTAATGCTGATCA 59.424 45.455 0.00 0.00 0.00 2.92
2959 3030 3.281727 TGGAACCCTGTAATGCTGATC 57.718 47.619 0.00 0.00 0.00 2.92
2960 3031 3.559069 CATGGAACCCTGTAATGCTGAT 58.441 45.455 0.00 0.00 0.00 2.90
2961 3032 2.357050 CCATGGAACCCTGTAATGCTGA 60.357 50.000 5.56 0.00 0.00 4.26
2962 3033 2.026641 CCATGGAACCCTGTAATGCTG 58.973 52.381 5.56 0.00 0.00 4.41
2963 3034 1.686115 GCCATGGAACCCTGTAATGCT 60.686 52.381 18.40 0.00 0.00 3.79
2964 3035 0.746659 GCCATGGAACCCTGTAATGC 59.253 55.000 18.40 0.00 0.00 3.56
2965 3036 2.428171 CAAGCCATGGAACCCTGTAATG 59.572 50.000 18.40 0.00 0.00 1.90
2966 3037 2.311542 TCAAGCCATGGAACCCTGTAAT 59.688 45.455 18.40 0.00 0.00 1.89
2967 3038 1.707989 TCAAGCCATGGAACCCTGTAA 59.292 47.619 18.40 0.00 0.00 2.41
2968 3039 1.367346 TCAAGCCATGGAACCCTGTA 58.633 50.000 18.40 0.00 0.00 2.74
2969 3040 0.706433 ATCAAGCCATGGAACCCTGT 59.294 50.000 18.40 0.00 0.00 4.00
2970 3041 1.341285 TGATCAAGCCATGGAACCCTG 60.341 52.381 18.40 4.28 0.00 4.45
2971 3042 1.002069 TGATCAAGCCATGGAACCCT 58.998 50.000 18.40 0.00 0.00 4.34
2972 3043 1.396653 CTGATCAAGCCATGGAACCC 58.603 55.000 18.40 0.00 0.00 4.11
3019 3090 9.245481 GCTCTAGGTTACTACAATCCATATAGT 57.755 37.037 0.00 0.00 33.73 2.12
3027 3098 7.720515 TCCTTCTAGCTCTAGGTTACTACAATC 59.279 40.741 0.00 0.00 34.06 2.67
3038 3109 9.969001 ATAACTAGTATTCCTTCTAGCTCTAGG 57.031 37.037 0.00 0.00 37.67 3.02
3060 3131 6.018098 CAGCTCTCTTGTGATCAATCCATAAC 60.018 42.308 0.00 0.00 32.82 1.89
3207 3280 6.992063 TCTCCTTTTAGACATTTCATCAGC 57.008 37.500 0.00 0.00 0.00 4.26
3454 3550 0.943673 CGATTGGTGTCAACACTGCA 59.056 50.000 12.65 1.22 45.73 4.41
3478 3574 6.436847 TGATGAAATGGTTATTTTCTGAGCCA 59.563 34.615 0.00 0.00 36.66 4.75
3565 3661 1.168714 CTAGCAACCTTGTTCCTGGC 58.831 55.000 0.00 0.00 0.00 4.85
3612 3708 2.562298 TGCCATGATTCAAGGTGGAAAC 59.438 45.455 9.52 0.00 33.53 2.78
3760 3856 2.900546 CAGGACTGGTCAGGATATACCC 59.099 54.545 2.87 0.00 40.05 3.69
3792 3896 1.949525 CCGATGGGTCCAACAATCATC 59.050 52.381 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.