Multiple sequence alignment - TraesCS7D01G237800

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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 TraesCS7D01G237800 chr7D 100.000 3986 0 0 1 3986 202059504 202055519 0.000000e+00 7361
1 TraesCS7D01G237800 chr7D 84.923 325 23 18 3681 3985 201979194 201978876 5.000000e-79 305
2 TraesCS7D01G237800 chr7B 95.712 3661 91 27 17 3665 165533252 165529646 0.000000e+00 5830
3 TraesCS7D01G237800 chr7B 92.604 338 15 6 3649 3986 165529630 165529303 1.000000e-130 477
4 TraesCS7D01G237800 chr7A 96.404 3476 103 9 20 3479 214436489 214433020 0.000000e+00 5707
5 TraesCS7D01G237800 chr7A 92.521 468 27 5 3520 3986 214433058 214432598 0.000000e+00 664
6 TraesCS7D01G237800 chr6D 76.155 1862 389 45 1138 2979 375028608 375030434 0.000000e+00 928
7 TraesCS7D01G237800 chr6B 75.483 1917 417 41 1082 2979 561701016 561702898 0.000000e+00 887


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 TraesCS7D01G237800 chr7D 202055519 202059504 3985 True 7361.0 7361 100.0000 1 3986 1 chr7D.!!$R2 3985
1 TraesCS7D01G237800 chr7B 165529303 165533252 3949 True 3153.5 5830 94.1580 17 3986 2 chr7B.!!$R1 3969
2 TraesCS7D01G237800 chr7A 214432598 214436489 3891 True 3185.5 5707 94.4625 20 3986 2 chr7A.!!$R1 3966
3 TraesCS7D01G237800 chr6D 375028608 375030434 1826 False 928.0 928 76.1550 1138 2979 1 chr6D.!!$F1 1841
4 TraesCS7D01G237800 chr6B 561701016 561702898 1882 False 887.0 887 75.4830 1082 2979 1 chr6B.!!$F1 1897

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
270 276 0.456995 CTGGAACCTTCTCGACGCTC 60.457 60.000 0.00 0.00 0.00 5.03 F
477 483 0.729116 CTGCCATCGATGTGTCAACC 59.271 55.000 23.27 4.16 0.00 3.77 F
515 521 0.793104 GCCGAACGCTTCCGATTTTG 60.793 55.000 0.00 0.00 38.29 2.44 F
1031 1040 1.858091 CTGCACAGTTCTCGTTGTCT 58.142 50.000 0.00 0.00 0.00 3.41 F
1386 1395 3.536917 CAGCGGGCCCGTGATCTA 61.537 66.667 42.53 0.00 42.09 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1572 1581 3.024547 TCCTTCTTCTCCAGTACCGATG 58.975 50.0 0.0 0.0 0.00 3.84 R
2362 2380 0.823356 GTGCTCTTGCTTCCCCACAA 60.823 55.0 0.0 0.0 40.48 3.33 R
2493 2511 0.030235 GGTTGGTGCGAACAGGAAAC 59.970 55.0 0.0 0.0 0.00 2.78 R
2964 2982 0.172578 AATCGATCTTCACGGACGCA 59.827 50.0 0.0 0.0 0.00 5.24 R
3265 3291 0.035152 CTACCATGCCTTGCCACTCA 60.035 55.0 0.0 0.0 0.00 3.41 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
253 257 0.895530 TACCTTCCTCCGCAGTTCTG 59.104 55.000 0.00 0.00 0.00 3.02
270 276 0.456995 CTGGAACCTTCTCGACGCTC 60.457 60.000 0.00 0.00 0.00 5.03
274 280 2.156051 AACCTTCTCGACGCTCCCAC 62.156 60.000 0.00 0.00 0.00 4.61
291 297 0.995024 CACCCATTCCCACTCCTTCT 59.005 55.000 0.00 0.00 0.00 2.85
323 329 4.135153 CTCTACCAGCAGCGCGGT 62.135 66.667 4.23 4.23 38.49 5.68
414 420 0.830648 TTTCTGTAGATCTGCGGGGG 59.169 55.000 18.30 3.71 0.00 5.40
477 483 0.729116 CTGCCATCGATGTGTCAACC 59.271 55.000 23.27 4.16 0.00 3.77
515 521 0.793104 GCCGAACGCTTCCGATTTTG 60.793 55.000 0.00 0.00 38.29 2.44
531 537 2.110901 TTTGGGCGCGTAGGAAATAA 57.889 45.000 8.43 0.00 0.00 1.40
714 722 5.176223 TGCACTGCGTTAGTTACTTCTTAAC 59.824 40.000 0.00 0.00 40.57 2.01
752 761 6.609616 TGTTTATGGGAGGGGAATTAATGTTC 59.390 38.462 0.00 0.00 0.00 3.18
764 773 9.895138 GGGGAATTAATGTTCACTAGTAACTTA 57.105 33.333 0.00 0.77 32.10 2.24
810 819 3.135167 GGGAATGGATGGATTTTGCATGT 59.865 43.478 0.00 0.00 0.00 3.21
886 895 9.739276 AGATGTTGTTGTCCAGATAAAAAGATA 57.261 29.630 0.00 0.00 0.00 1.98
887 896 9.774742 GATGTTGTTGTCCAGATAAAAAGATAC 57.225 33.333 0.00 0.00 0.00 2.24
973 982 5.487488 ACAGGGTATTCCTCACATGTTCTAA 59.513 40.000 0.00 0.00 46.12 2.10
974 983 6.012858 ACAGGGTATTCCTCACATGTTCTAAA 60.013 38.462 0.00 0.00 46.12 1.85
976 985 7.557719 CAGGGTATTCCTCACATGTTCTAAATT 59.442 37.037 0.00 0.00 46.12 1.82
982 991 5.048083 TCCTCACATGTTCTAAATTGTTGGC 60.048 40.000 0.00 0.00 0.00 4.52
1031 1040 1.858091 CTGCACAGTTCTCGTTGTCT 58.142 50.000 0.00 0.00 0.00 3.41
1386 1395 3.536917 CAGCGGGCCCGTGATCTA 61.537 66.667 42.53 0.00 42.09 1.98
1572 1581 8.252964 AGTACGAAGGAACAAATGTAGAAATC 57.747 34.615 0.00 0.00 0.00 2.17
2362 2380 6.489022 GGTCCTTACCATCTTAAACTTTGTGT 59.511 38.462 0.00 0.00 45.98 3.72
2493 2511 4.142730 GGTACAAGAGCAGAGCAAATTGAG 60.143 45.833 0.00 0.00 0.00 3.02
2496 2514 4.340381 ACAAGAGCAGAGCAAATTGAGTTT 59.660 37.500 0.00 0.00 0.00 2.66
2964 2982 1.968493 TCCTTCGTGCACTACCTCTTT 59.032 47.619 16.19 0.00 0.00 2.52
3037 3055 7.434307 TCTGTATCTGTATTGCTAAAAGTACGC 59.566 37.037 0.00 0.00 0.00 4.42
3049 3067 0.595567 AAGTACGCGCGTGAGTTTCA 60.596 50.000 42.78 20.80 0.00 2.69
3052 3070 4.409588 CGCGCGTGAGTTTCACCG 62.410 66.667 24.19 12.53 44.20 4.94
3059 3077 2.881074 CGTGAGTTTCACCGATGAGAT 58.119 47.619 3.81 0.00 44.20 2.75
3112 3130 7.602517 ACTGCAGATGTTTTTAGTAGATGTC 57.397 36.000 23.35 0.00 0.00 3.06
3140 3158 6.150474 TGCAGTTTTTCCCTAGTAAATGTAGC 59.850 38.462 0.00 0.00 0.00 3.58
3141 3159 6.404403 GCAGTTTTTCCCTAGTAAATGTAGCC 60.404 42.308 0.00 0.00 0.00 3.93
3145 3163 2.044758 CCCTAGTAAATGTAGCCCCGT 58.955 52.381 0.00 0.00 0.00 5.28
3169 3187 6.691754 TGTTCAACTGCAGATGTTTTCTTA 57.308 33.333 23.35 0.00 29.93 2.10
3201 3219 2.860735 GGTCAGCTGCTACACTTATTCG 59.139 50.000 9.47 0.00 0.00 3.34
3255 3281 7.827729 AGTGTTAAGGGGTAATGACTATGAAAC 59.172 37.037 0.00 0.00 0.00 2.78
3386 3413 7.062488 GGAAAACGCTTTCTGTTTCTTTTACAA 59.938 33.333 10.85 0.00 40.76 2.41
3447 3474 5.028802 TGCCATATTCCTTGGGAAATTTCA 58.971 37.500 19.49 0.00 45.41 2.69
3484 3511 4.887071 ACAGAATGACACTTTGTTAGCCAA 59.113 37.500 0.00 0.00 39.69 4.52
3485 3512 5.359576 ACAGAATGACACTTTGTTAGCCAAA 59.640 36.000 0.00 0.00 39.69 3.28
3486 3513 6.040842 ACAGAATGACACTTTGTTAGCCAAAT 59.959 34.615 0.00 0.00 39.64 2.32
3487 3514 6.364165 CAGAATGACACTTTGTTAGCCAAATG 59.636 38.462 0.00 0.00 39.64 2.32
3488 3515 4.582701 TGACACTTTGTTAGCCAAATGG 57.417 40.909 0.00 0.00 42.02 3.16
3498 3525 4.023137 CCAAATGGCAGGGTCCTG 57.977 61.111 12.42 12.42 46.15 3.86
3517 3544 4.968719 TCCTGCCATATTCCTTCTACAAGA 59.031 41.667 0.00 0.00 0.00 3.02
3600 3628 4.081365 TCGAACAGCCATATTGGTCACTTA 60.081 41.667 0.00 0.00 40.46 2.24
3647 3675 0.250295 TGCTAGTGGTTCTGTGGCAC 60.250 55.000 11.55 11.55 0.00 5.01
3678 3736 8.413229 ACATGCAAAAGTACAGAGTTTTTGTAT 58.587 29.630 14.89 13.50 43.21 2.29
3789 3847 2.596346 TGGTGGCATGAACAACAGAAT 58.404 42.857 4.65 0.00 30.83 2.40
3799 3857 6.311935 GCATGAACAACAGAATACGTAGGTAA 59.688 38.462 0.08 0.00 31.15 2.85
3817 3875 9.539825 CGTAGGTAAGAAACAGATAGTAGTAGA 57.460 37.037 0.00 0.00 0.00 2.59
3824 3882 8.967664 AGAAACAGATAGTAGTAGACTAGTGG 57.032 38.462 0.00 0.00 43.99 4.00
3837 3898 5.759506 AGACTAGTGGTACATCGATCTTG 57.240 43.478 0.00 0.00 44.52 3.02
3839 3900 2.604046 AGTGGTACATCGATCTTGGC 57.396 50.000 0.00 0.00 44.52 4.52
3867 3928 4.020617 CAACAGAGCTGGCCGGGA 62.021 66.667 15.02 0.00 34.19 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.675317 CGACCGGCATCTTCTCTCTTTT 60.675 50.000 0.00 0.00 0.00 2.27
1 2 1.134965 CGACCGGCATCTTCTCTCTTT 60.135 52.381 0.00 0.00 0.00 2.52
2 3 0.457851 CGACCGGCATCTTCTCTCTT 59.542 55.000 0.00 0.00 0.00 2.85
3 4 0.394488 TCGACCGGCATCTTCTCTCT 60.394 55.000 0.00 0.00 0.00 3.10
4 5 0.456221 TTCGACCGGCATCTTCTCTC 59.544 55.000 0.00 0.00 0.00 3.20
5 6 0.895530 TTTCGACCGGCATCTTCTCT 59.104 50.000 0.00 0.00 0.00 3.10
6 7 1.000145 GTTTCGACCGGCATCTTCTC 59.000 55.000 0.00 0.00 0.00 2.87
7 8 0.736325 CGTTTCGACCGGCATCTTCT 60.736 55.000 0.00 0.00 0.00 2.85
8 9 1.693083 CCGTTTCGACCGGCATCTTC 61.693 60.000 0.00 0.00 38.85 2.87
9 10 1.740296 CCGTTTCGACCGGCATCTT 60.740 57.895 0.00 0.00 38.85 2.40
10 11 2.125673 CCGTTTCGACCGGCATCT 60.126 61.111 0.00 0.00 38.85 2.90
253 257 1.153804 GGAGCGTCGAGAAGGTTCC 60.154 63.158 0.00 0.00 36.23 3.62
270 276 1.509548 AAGGAGTGGGAATGGGTGGG 61.510 60.000 0.00 0.00 0.00 4.61
274 280 3.495100 CGAATAGAAGGAGTGGGAATGGG 60.495 52.174 0.00 0.00 0.00 4.00
291 297 2.149578 GTAGAGCTAGGGACGCGAATA 58.850 52.381 15.93 0.00 0.00 1.75
477 483 2.384382 GCAACCATGAAACACTTCACG 58.616 47.619 0.00 0.00 44.28 4.35
515 521 0.105408 TCCTTATTTCCTACGCGCCC 59.895 55.000 5.73 0.00 0.00 6.13
542 548 7.162082 ACAACAAATCTTACCTCTAACCAGAG 58.838 38.462 0.00 0.00 46.85 3.35
575 581 8.863872 ATACTGCAAAAGGTTACTATGAAACT 57.136 30.769 0.00 0.00 0.00 2.66
714 722 7.041372 CCCTCCCATAAACAATAATTGACTACG 60.041 40.741 0.00 0.00 0.00 3.51
734 743 4.251103 AGTGAACATTAATTCCCCTCCC 57.749 45.455 0.00 0.00 0.00 4.30
752 761 9.862371 AGAACAATCACATCTAAGTTACTAGTG 57.138 33.333 5.39 0.00 0.00 2.74
764 773 8.373981 CCCTCATAATCTAGAACAATCACATCT 58.626 37.037 0.00 0.00 0.00 2.90
772 781 7.690454 TCCATTCCCTCATAATCTAGAACAA 57.310 36.000 0.00 0.00 0.00 2.83
784 793 3.644738 GCAAAATCCATCCATTCCCTCAT 59.355 43.478 0.00 0.00 0.00 2.90
810 819 4.765856 ACTAGTCGTTTCCTAGAGCAAGAA 59.234 41.667 0.00 0.00 36.29 2.52
886 895 8.740123 TTACATCCATCGTTATTTTGGTATGT 57.260 30.769 0.00 0.00 36.34 2.29
958 967 5.048083 GCCAACAATTTAGAACATGTGAGGA 60.048 40.000 0.00 0.00 0.00 3.71
973 982 2.543653 GCACAAACTCTCGCCAACAATT 60.544 45.455 0.00 0.00 0.00 2.32
974 983 1.001378 GCACAAACTCTCGCCAACAAT 60.001 47.619 0.00 0.00 0.00 2.71
976 985 0.463654 AGCACAAACTCTCGCCAACA 60.464 50.000 0.00 0.00 0.00 3.33
982 991 2.414481 CCATCTGAAGCACAAACTCTCG 59.586 50.000 0.00 0.00 0.00 4.04
1031 1040 2.161855 CAGCCAACAATAACAGAGCCA 58.838 47.619 0.00 0.00 0.00 4.75
1386 1395 4.103627 TCCAGCATCATGTTCACCTGATAT 59.896 41.667 0.00 0.00 31.49 1.63
1572 1581 3.024547 TCCTTCTTCTCCAGTACCGATG 58.975 50.000 0.00 0.00 0.00 3.84
2362 2380 0.823356 GTGCTCTTGCTTCCCCACAA 60.823 55.000 0.00 0.00 40.48 3.33
2493 2511 0.030235 GGTTGGTGCGAACAGGAAAC 59.970 55.000 0.00 0.00 0.00 2.78
2496 2514 1.227823 CTGGTTGGTGCGAACAGGA 60.228 57.895 0.00 0.00 0.00 3.86
2910 2928 4.517663 CCAATGGTTCCAGTGGCA 57.482 55.556 22.27 0.00 43.58 4.92
2964 2982 0.172578 AATCGATCTTCACGGACGCA 59.827 50.000 0.00 0.00 0.00 5.24
3049 3067 0.391661 AAACTGCGCATCTCATCGGT 60.392 50.000 12.24 0.00 0.00 4.69
3052 3070 4.319333 CCTCATTAAACTGCGCATCTCATC 60.319 45.833 12.24 0.00 0.00 2.92
3059 3077 2.177394 TCACCTCATTAAACTGCGCA 57.823 45.000 10.98 10.98 0.00 6.09
3112 3130 5.873179 TTTACTAGGGAAAAACTGCATCG 57.127 39.130 0.00 0.00 0.00 3.84
3140 3158 0.817634 TCTGCAGTTGAACAACGGGG 60.818 55.000 14.67 9.95 45.50 5.73
3141 3159 1.069022 CATCTGCAGTTGAACAACGGG 60.069 52.381 18.19 11.89 45.50 5.28
3145 3163 5.581126 AGAAAACATCTGCAGTTGAACAA 57.419 34.783 27.42 1.45 36.88 2.83
3169 3187 4.026356 AGCAGCTGACCAAAATCTACTT 57.974 40.909 20.43 0.00 0.00 2.24
3201 3219 6.552445 AGATATGGGTTGCAGTATCTATCC 57.448 41.667 0.00 0.00 33.40 2.59
3255 3281 3.529533 CCTTGCCACTCACAGATTAGAG 58.470 50.000 0.00 0.00 37.87 2.43
3265 3291 0.035152 CTACCATGCCTTGCCACTCA 60.035 55.000 0.00 0.00 0.00 3.41
3386 3413 3.292460 TGGTTGGAAGGAAAAACGACAT 58.708 40.909 0.00 0.00 0.00 3.06
3489 3516 1.143813 AGGAATATGGCAGGACCCTG 58.856 55.000 11.59 11.59 46.15 4.45
3490 3517 1.777272 GAAGGAATATGGCAGGACCCT 59.223 52.381 0.00 0.00 37.83 4.34
3491 3518 1.777272 AGAAGGAATATGGCAGGACCC 59.223 52.381 0.00 0.00 37.83 4.46
3492 3519 3.391296 TGTAGAAGGAATATGGCAGGACC 59.609 47.826 0.00 0.00 39.84 4.46
3493 3520 4.689612 TGTAGAAGGAATATGGCAGGAC 57.310 45.455 0.00 0.00 0.00 3.85
3494 3521 4.968719 TCTTGTAGAAGGAATATGGCAGGA 59.031 41.667 0.00 0.00 0.00 3.86
3495 3522 5.296151 TCTTGTAGAAGGAATATGGCAGG 57.704 43.478 0.00 0.00 0.00 4.85
3496 3523 7.630242 TTTTCTTGTAGAAGGAATATGGCAG 57.370 36.000 0.00 0.00 35.37 4.85
3543 3570 7.174946 TCTTGTAGAAGAACAAATGGGACATTC 59.825 37.037 0.00 0.00 38.11 2.67
3575 3602 3.006940 TGACCAATATGGCTGTTCGAAC 58.993 45.455 21.42 21.42 42.67 3.95
3600 3628 2.142292 AATGGCTTCCTGGACCGCTT 62.142 55.000 14.58 2.63 0.00 4.68
3647 3675 4.512944 ACTCTGTACTTTTGCATGTCACTG 59.487 41.667 0.00 0.00 0.00 3.66
3678 3736 4.495911 TTGCAATTCGTATTCAACTGCA 57.504 36.364 0.00 0.00 34.72 4.41
3775 3833 7.758076 TCTTACCTACGTATTCTGTTGTTCATG 59.242 37.037 0.00 0.00 0.00 3.07
3799 3857 8.550585 ACCACTAGTCTACTACTATCTGTTTCT 58.449 37.037 0.00 0.00 39.96 2.52
3817 3875 3.068307 GCCAAGATCGATGTACCACTAGT 59.932 47.826 0.54 0.00 0.00 2.57
3818 3876 3.319405 AGCCAAGATCGATGTACCACTAG 59.681 47.826 0.54 0.00 0.00 2.57
3819 3877 3.296854 AGCCAAGATCGATGTACCACTA 58.703 45.455 0.54 0.00 0.00 2.74
3820 3878 2.101582 GAGCCAAGATCGATGTACCACT 59.898 50.000 0.54 0.00 0.00 4.00
3821 3879 2.474816 GAGCCAAGATCGATGTACCAC 58.525 52.381 0.54 0.00 0.00 4.16
3822 3880 1.412710 GGAGCCAAGATCGATGTACCA 59.587 52.381 0.54 0.00 0.00 3.25
3823 3881 1.603172 CGGAGCCAAGATCGATGTACC 60.603 57.143 0.54 0.00 0.00 3.34
3824 3882 1.603172 CCGGAGCCAAGATCGATGTAC 60.603 57.143 0.54 0.00 0.00 2.90
3837 3898 4.373116 TGTTGTCTCGCCGGAGCC 62.373 66.667 5.05 0.00 40.26 4.70
3839 3900 1.153939 CTCTGTTGTCTCGCCGGAG 60.154 63.158 5.05 0.00 41.89 4.63
3851 3912 4.021925 GTCCCGGCCAGCTCTGTT 62.022 66.667 2.24 0.00 0.00 3.16
3877 3938 1.729838 GAACGTGAAGCGCTCGACT 60.730 57.895 21.90 9.48 46.11 4.18
3879 3940 1.007734 AAGAACGTGAAGCGCTCGA 60.008 52.632 21.90 4.05 46.11 4.04
3964 4025 0.320247 AGCACGTCTCCTTCAAGCTG 60.320 55.000 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.