Multiple sequence alignment - TraesCS7D01G031700

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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 TraesCS7D01G031700 chr7D 100.000 2855 0 0 1 2855 16692963 16690109 0.000000e+00 5273
1 TraesCS7D01G031700 chr7D 81.593 1494 212 24 607 2084 16705489 16704043 0.000000e+00 1177
2 TraesCS7D01G031700 chr7D 87.705 122 10 4 622 739 16705697 16705577 1.380000e-28 137
3 TraesCS7D01G031700 chr4A 93.010 2718 153 17 1 2683 718032153 718034868 0.000000e+00 3932
4 TraesCS7D01G031700 chr4A 80.904 1482 215 28 607 2072 717971485 717972914 0.000000e+00 1107
5 TraesCS7D01G031700 chr4A 87.705 122 11 3 622 739 717971275 717971396 3.840000e-29 139
6 TraesCS7D01G031700 chr7A 90.128 2897 224 22 1 2855 15640869 15637993 0.000000e+00 3709
7 TraesCS7D01G031700 chr7A 82.343 1127 159 25 960 2072 15689612 15688512 0.000000e+00 942
8 TraesCS7D01G031700 chr7A 80.363 331 56 6 1466 1796 15639743 15639422 2.840000e-60 243
9 TraesCS7D01G031700 chr7A 78.344 314 37 12 607 913 15690157 15689868 1.050000e-39 174


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 TraesCS7D01G031700 chr7D 16690109 16692963 2854 True 5273 5273 100.0000 1 2855 1 chr7D.!!$R1 2854
1 TraesCS7D01G031700 chr7D 16704043 16705697 1654 True 657 1177 84.6490 607 2084 2 chr7D.!!$R2 1477
2 TraesCS7D01G031700 chr4A 718032153 718034868 2715 False 3932 3932 93.0100 1 2683 1 chr4A.!!$F1 2682
3 TraesCS7D01G031700 chr4A 717971275 717972914 1639 False 623 1107 84.3045 607 2072 2 chr4A.!!$F2 1465
4 TraesCS7D01G031700 chr7A 15637993 15640869 2876 True 1976 3709 85.2455 1 2855 2 chr7A.!!$R1 2854
5 TraesCS7D01G031700 chr7A 15688512 15690157 1645 True 558 942 80.3435 607 2072 2 chr7A.!!$R2 1465

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
451 480 0.179076 CCTATGAGTCATGCCGTGCA 60.179 55.0 16.15 1.01 44.86 4.57 F
702 740 0.180406 AAGATATGCCGCCCGAACTT 59.820 50.0 0.00 0.00 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1497 1954 0.110056 GCTGTTGCAGGAATGTCGTG 60.110 55.0 0.00 0.0 39.41 4.35 R
2504 2975 0.942962 GCTTCGCTCTGCTGCATAAT 59.057 50.0 1.31 0.0 0.00 1.28 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
128 129 5.163804 GCATGGTTTGATTACACGTGACATA 60.164 40.000 25.01 0.55 0.00 2.29
247 274 4.709886 ACTAAATATGGTTTGGACAAGGGC 59.290 41.667 0.00 0.00 0.00 5.19
286 315 3.137385 TATGGATGGGCCTGGCAGC 62.137 63.158 22.05 2.98 37.63 5.25
325 354 6.989169 GGAAGATTACAGACTCATAGCACATT 59.011 38.462 0.00 0.00 0.00 2.71
335 364 4.077108 CTCATAGCACATTACCCATGCAT 58.923 43.478 0.00 0.00 41.97 3.96
337 366 5.818887 TCATAGCACATTACCCATGCATAT 58.181 37.500 0.00 0.00 41.97 1.78
338 367 5.648960 TCATAGCACATTACCCATGCATATG 59.351 40.000 0.00 1.37 41.97 1.78
445 474 1.350351 AGGGCATCCTATGAGTCATGC 59.650 52.381 16.15 11.25 42.75 4.06
451 480 0.179076 CCTATGAGTCATGCCGTGCA 60.179 55.000 16.15 1.01 44.86 4.57
461 490 1.599071 CATGCCGTGCACTACTAATGG 59.401 52.381 16.19 7.81 43.04 3.16
590 620 7.938140 ACCTAAACAGCTAATGCAAGATTAA 57.062 32.000 0.00 0.00 42.74 1.40
693 728 4.804108 TGGTTTCACAAAAAGATATGCCG 58.196 39.130 0.00 0.00 0.00 5.69
702 740 0.180406 AAGATATGCCGCCCGAACTT 59.820 50.000 0.00 0.00 0.00 2.66
752 790 8.152246 TGAGTCATATGCATTATCAATCTCACA 58.848 33.333 3.54 0.00 0.00 3.58
775 1015 1.210478 ACAGTCAGGTGATATGTGCCC 59.790 52.381 1.26 0.00 0.00 5.36
782 1022 3.511146 CAGGTGATATGTGCCCAAAAGTT 59.489 43.478 0.00 0.00 0.00 2.66
784 1024 4.021192 AGGTGATATGTGCCCAAAAGTTTG 60.021 41.667 0.00 0.00 37.90 2.93
832 1073 0.382515 GCGCCACCTAACACAACAAA 59.617 50.000 0.00 0.00 0.00 2.83
1026 1480 1.836802 GTCTTCATCCTGGCTCTCCTT 59.163 52.381 0.00 0.00 0.00 3.36
1091 1545 1.893062 GCCAGGGCTTTGGACAATC 59.107 57.895 11.87 0.00 40.87 2.67
1113 1567 2.028567 CCAACAACAACAACAACCTGGT 60.029 45.455 0.00 0.00 0.00 4.00
1203 1657 0.770499 TGCCATTCCTCCAGACACAA 59.230 50.000 0.00 0.00 0.00 3.33
1206 1660 2.704572 CCATTCCTCCAGACACAAGTC 58.295 52.381 0.00 0.00 45.31 3.01
1298 1752 1.759299 GGTGCCATGCCATCCACAT 60.759 57.895 7.16 0.00 0.00 3.21
1497 1954 2.607892 GGAGCAGTTGACACCGTGC 61.608 63.158 0.00 0.00 36.10 5.34
1498 1955 1.887242 GAGCAGTTGACACCGTGCA 60.887 57.895 0.00 0.00 38.44 4.57
1821 2284 1.074727 CCCACCACCTACAACATTCCA 59.925 52.381 0.00 0.00 0.00 3.53
1822 2285 2.291540 CCCACCACCTACAACATTCCAT 60.292 50.000 0.00 0.00 0.00 3.41
1861 2324 1.114627 TGGTGCGTGCTAGATGATCT 58.885 50.000 0.00 0.00 0.00 2.75
2098 2565 3.530265 ACAAAGTTGGTACACACGAGA 57.470 42.857 0.00 0.00 39.29 4.04
2265 2734 6.178607 AGCCCATCAAATCAAAAGAAGTTT 57.821 33.333 0.00 0.00 0.00 2.66
2326 2796 2.364632 CTGGTGAAGGAACACACAACA 58.635 47.619 0.00 0.00 41.88 3.33
2341 2811 7.094508 ACACACAACAAGAACATGTATGAAA 57.905 32.000 0.00 0.00 32.02 2.69
2462 2932 3.808728 TCACTGAGCCATAGTTATTGCC 58.191 45.455 0.00 0.00 0.00 4.52
2540 3011 3.632189 GAAGCAACTCAAGCAAATCGTT 58.368 40.909 0.00 0.00 0.00 3.85
2544 3015 3.365364 GCAACTCAAGCAAATCGTTAGCT 60.365 43.478 0.00 0.00 41.03 3.32
2549 3020 3.004210 TCAAGCAAATCGTTAGCTGCAAA 59.996 39.130 1.02 0.00 38.86 3.68
2574 3045 5.070446 TCCATCGGATAGTATCAAAACTGCT 59.930 40.000 12.19 0.00 0.00 4.24
2581 3052 6.818644 GGATAGTATCAAAACTGCTGTGAAGA 59.181 38.462 12.19 0.00 0.00 2.87
2586 3057 4.985413 TCAAAACTGCTGTGAAGAAACTG 58.015 39.130 0.00 0.00 0.00 3.16
2590 3061 3.878778 ACTGCTGTGAAGAAACTGAAGT 58.121 40.909 0.00 0.00 34.10 3.01
2620 3091 1.135915 CAGCCGCAATCTCACTCTAGT 59.864 52.381 0.00 0.00 0.00 2.57
2623 3094 1.751351 CCGCAATCTCACTCTAGTCCA 59.249 52.381 0.00 0.00 0.00 4.02
2625 3096 3.181471 CCGCAATCTCACTCTAGTCCAAT 60.181 47.826 0.00 0.00 0.00 3.16
2642 3113 5.049167 GTCCAATGAGCAAACAATCAAACA 58.951 37.500 0.00 0.00 0.00 2.83
2685 3162 7.759886 TGCTCATACTATACAGTTCAGTTTGAC 59.240 37.037 4.33 3.78 36.14 3.18
2729 3207 3.196469 CCACTGACTAGCTTGGATTGAGA 59.804 47.826 0.00 0.00 0.00 3.27
2732 3210 4.961730 ACTGACTAGCTTGGATTGAGAGAT 59.038 41.667 0.00 0.00 0.00 2.75
2743 3221 4.161189 TGGATTGAGAGATGGAAGAGACAC 59.839 45.833 0.00 0.00 0.00 3.67
2744 3222 3.857549 TTGAGAGATGGAAGAGACACG 57.142 47.619 0.00 0.00 0.00 4.49
2749 3227 1.895798 AGATGGAAGAGACACGCAAGA 59.104 47.619 0.00 0.00 43.62 3.02
2755 3233 2.969628 AGAGACACGCAAGATTAGGG 57.030 50.000 0.00 0.00 43.62 3.53
2766 3244 0.395311 AGATTAGGGTGAGCGTCCGA 60.395 55.000 0.00 0.00 0.00 4.55
2781 3259 0.320374 TCCGAACCTGACGCAAAGAT 59.680 50.000 0.00 0.00 0.00 2.40
2784 3262 1.798223 CGAACCTGACGCAAAGATTCA 59.202 47.619 0.00 0.00 0.00 2.57
2787 3265 3.678056 ACCTGACGCAAAGATTCACTA 57.322 42.857 0.00 0.00 0.00 2.74
2794 3272 2.346803 GCAAAGATTCACTAGTGCGGA 58.653 47.619 18.45 6.92 32.70 5.54
2795 3273 2.939103 GCAAAGATTCACTAGTGCGGAT 59.061 45.455 18.45 11.35 32.70 4.18
2808 3288 4.552365 CGGATGGCGGCATGGAGT 62.552 66.667 30.87 5.20 0.00 3.85
2851 3335 3.864686 CGATTTCGGCGGTGGCAG 61.865 66.667 7.21 0.00 42.47 4.85
2852 3336 4.179579 GATTTCGGCGGTGGCAGC 62.180 66.667 7.21 6.62 42.47 5.25
2853 3337 4.722700 ATTTCGGCGGTGGCAGCT 62.723 61.111 15.48 0.00 42.47 4.24
2854 3338 4.947147 TTTCGGCGGTGGCAGCTT 62.947 61.111 15.48 0.00 42.47 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.733227 CGCTACTTTGTCGGTCGGTAAT 60.733 50.000 0.00 0.00 0.00 1.89
7 8 0.168788 CGCTACTTTGTCGGTCGGTA 59.831 55.000 0.00 0.00 0.00 4.02
266 295 2.116125 GCCAGGCCCATCCATACC 59.884 66.667 0.00 0.00 37.29 2.73
286 315 6.057533 TGTAATCTTCCATGGTTGCTATCTG 58.942 40.000 12.58 0.00 0.00 2.90
325 354 4.488770 TCTACAGGACATATGCATGGGTA 58.511 43.478 10.16 0.80 36.39 3.69
335 364 9.793259 AATTTGTTCTTTCTTCTACAGGACATA 57.207 29.630 0.00 0.00 0.00 2.29
337 366 7.773224 TGAATTTGTTCTTTCTTCTACAGGACA 59.227 33.333 0.00 0.00 0.00 4.02
338 367 8.154649 TGAATTTGTTCTTTCTTCTACAGGAC 57.845 34.615 0.00 0.00 0.00 3.85
445 474 3.179443 ACATCCATTAGTAGTGCACGG 57.821 47.619 12.01 4.68 0.00 4.94
504 533 4.700213 CCACACTCGATTAATTGTTCCCTT 59.300 41.667 2.57 0.00 0.00 3.95
506 535 4.258543 TCCACACTCGATTAATTGTTCCC 58.741 43.478 2.57 0.00 0.00 3.97
693 728 3.907894 TTACATGTCAAAAGTTCGGGC 57.092 42.857 0.00 0.00 0.00 6.13
702 740 9.012161 TCATCAATCATCACTTTACATGTCAAA 57.988 29.630 0.00 1.08 0.00 2.69
752 790 3.432749 GGCACATATCACCTGACTGTCAT 60.433 47.826 11.45 0.00 0.00 3.06
775 1015 5.296283 TCAATGGCCATCAAACAAACTTTTG 59.704 36.000 21.08 9.64 43.62 2.44
782 1022 5.486735 AATCTTCAATGGCCATCAAACAA 57.513 34.783 21.08 6.65 0.00 2.83
784 1024 6.096001 AGTCTAATCTTCAATGGCCATCAAAC 59.904 38.462 21.08 8.78 0.00 2.93
832 1073 4.154918 GCTTTCCAAACTGATCATCTCGTT 59.845 41.667 0.00 0.00 0.00 3.85
1091 1545 2.615869 CAGGTTGTTGTTGTTGTTGGG 58.384 47.619 0.00 0.00 0.00 4.12
1203 1657 0.605589 AGCTGCTAAGTTGCTCGACT 59.394 50.000 0.00 0.00 30.41 4.18
1255 1709 2.586245 CTCTGGGATCTGCGCCAA 59.414 61.111 4.18 0.00 0.00 4.52
1298 1752 3.562182 TGAATGATAGCCTCTACCACGA 58.438 45.455 0.00 0.00 0.00 4.35
1497 1954 0.110056 GCTGTTGCAGGAATGTCGTG 60.110 55.000 0.00 0.00 39.41 4.35
1498 1955 0.534877 TGCTGTTGCAGGAATGTCGT 60.535 50.000 0.00 0.00 45.31 4.34
1578 2035 2.485903 CAACATTGGTGCTGCACATTT 58.514 42.857 31.35 13.93 35.86 2.32
1656 2113 1.340017 TGTTGTTGCCTGATAGCCTCC 60.340 52.381 0.00 0.00 0.00 4.30
1785 2242 4.123545 GGGGCGGGGCATTGTACT 62.124 66.667 0.00 0.00 0.00 2.73
1861 2324 5.899120 TTTTATTTTGCCACCGCTACATA 57.101 34.783 0.00 0.00 35.36 2.29
1999 2464 9.750125 GTTAAGTTCAACCAGAAGATTCAAAAT 57.250 29.630 0.00 0.00 36.78 1.82
2205 2674 6.306987 AGTGATGGTTCAGTTTGGTAAGATT 58.693 36.000 0.00 0.00 31.17 2.40
2301 2771 1.843851 TGTGTTCCTTCACCAGGTCTT 59.156 47.619 0.00 0.00 44.37 3.01
2350 2820 6.155827 ACATGTGTTTCAAATCCGGTAATTG 58.844 36.000 0.00 5.82 0.00 2.32
2462 2932 1.136363 CAGGTTGTATTGCGACACGTG 60.136 52.381 15.48 15.48 33.06 4.49
2473 2943 7.441836 TCATCTATATCGTTTGCAGGTTGTAT 58.558 34.615 0.00 0.00 0.00 2.29
2474 2944 6.811954 TCATCTATATCGTTTGCAGGTTGTA 58.188 36.000 0.00 0.00 0.00 2.41
2504 2975 0.942962 GCTTCGCTCTGCTGCATAAT 59.057 50.000 1.31 0.00 0.00 1.28
2540 3011 2.936919 ATCCGATGGATTTGCAGCTA 57.063 45.000 0.00 0.00 39.79 3.32
2544 3015 5.482163 TGATACTATCCGATGGATTTGCA 57.518 39.130 3.27 0.00 39.79 4.08
2549 3020 5.934625 GCAGTTTTGATACTATCCGATGGAT 59.065 40.000 3.49 3.49 45.40 3.41
2574 3045 1.939934 CCGCACTTCAGTTTCTTCACA 59.060 47.619 0.00 0.00 0.00 3.58
2581 3052 3.005554 CTGATGATCCGCACTTCAGTTT 58.994 45.455 0.00 0.00 35.92 2.66
2586 3057 1.493950 CGGCTGATGATCCGCACTTC 61.494 60.000 10.91 0.00 39.14 3.01
2620 3091 5.273674 TGTTTGATTGTTTGCTCATTGGA 57.726 34.783 0.00 0.00 0.00 3.53
2623 3094 7.094975 CCATCATTGTTTGATTGTTTGCTCATT 60.095 33.333 0.00 0.00 42.62 2.57
2625 3096 5.697178 CCATCATTGTTTGATTGTTTGCTCA 59.303 36.000 0.00 0.00 42.62 4.26
2642 3113 3.012518 GAGCAGTGTTAGTGCCATCATT 58.987 45.455 5.09 0.00 45.41 2.57
2653 3130 8.288689 TGAACTGTATAGTATGAGCAGTGTTA 57.711 34.615 13.76 5.31 39.90 2.41
2702 3180 1.066573 CCAAGCTAGTCAGTGGACCAG 60.067 57.143 0.00 0.00 45.48 4.00
2729 3207 1.895798 TCTTGCGTGTCTCTTCCATCT 59.104 47.619 0.00 0.00 0.00 2.90
2732 3210 2.839486 AATCTTGCGTGTCTCTTCCA 57.161 45.000 0.00 0.00 0.00 3.53
2743 3221 0.460284 ACGCTCACCCTAATCTTGCG 60.460 55.000 0.00 0.00 46.02 4.85
2744 3222 1.291132 GACGCTCACCCTAATCTTGC 58.709 55.000 0.00 0.00 0.00 4.01
2749 3227 0.175073 GTTCGGACGCTCACCCTAAT 59.825 55.000 0.00 0.00 0.00 1.73
2755 3233 1.733399 GTCAGGTTCGGACGCTCAC 60.733 63.158 0.00 0.00 0.00 3.51
2766 3244 2.851195 AGTGAATCTTTGCGTCAGGTT 58.149 42.857 0.00 0.00 0.00 3.50
2776 3254 3.535561 CCATCCGCACTAGTGAATCTTT 58.464 45.455 27.08 2.55 0.00 2.52
2777 3255 2.743183 GCCATCCGCACTAGTGAATCTT 60.743 50.000 27.08 3.63 37.47 2.40
2781 3259 1.153647 CGCCATCCGCACTAGTGAA 60.154 57.895 27.08 11.00 37.30 3.18
2784 3262 4.530857 GCCGCCATCCGCACTAGT 62.531 66.667 0.00 0.00 37.30 2.57
2792 3270 2.903855 CACTCCATGCCGCCATCC 60.904 66.667 0.00 0.00 0.00 3.51
2802 3280 2.190578 GGCCGCTAAGCACTCCAT 59.809 61.111 0.00 0.00 0.00 3.41
2836 3316 4.722700 AGCTGCCACCGCCGAAAT 62.723 61.111 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.