Multiple sequence alignment - TraesCS7D01G279600

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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 TraesCS7D01G279600 chr7D 100.000 2949 0 0 1 2949 271508337 271505389 0.000000e+00 5446
1 TraesCS7D01G279600 chr7B 92.949 3021 58 37 1 2929 268453110 268456067 0.000000e+00 4255
2 TraesCS7D01G279600 chr7A 92.578 2587 57 34 446 2938 303103096 303100551 0.000000e+00 3589
3 TraesCS7D01G279600 chr7A 91.975 324 10 2 1 308 303103985 303103662 9.700000e-120 440
4 TraesCS7D01G279600 chr7A 97.810 137 3 0 287 423 303103590 303103454 1.370000e-58 237


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 TraesCS7D01G279600 chr7D 271505389 271508337 2948 True 5446 5446 100.000 1 2949 1 chr7D.!!$R1 2948
1 TraesCS7D01G279600 chr7B 268453110 268456067 2957 False 4255 4255 92.949 1 2929 1 chr7B.!!$F1 2928
2 TraesCS7D01G279600 chr7A 303100551 303103985 3434 True 1422 3589 94.121 1 2938 3 chr7A.!!$R1 2937

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
662 1131 0.178921 ACCTCAGCTTCACCTCCTCA 60.179 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2170 2709 0.419459 AGGGGGAGAGGTTGAGATGT 59.581 55.0 0.0 0.0 0.0 3.06 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
92 95 5.176590 CAAGTTGTTGAAGAGACAGCTAGTC 59.823 44.000 7.88 7.88 40.81 2.59
180 183 0.670546 CCGTCAAGGATGAGCAACGT 60.671 55.000 0.00 0.00 45.00 3.99
208 211 5.009631 TGTGGAATGTGATTACTGGAAAGG 58.990 41.667 0.00 0.00 0.00 3.11
265 284 2.877786 TCGTTCCGTTTCCTTTTAACCC 59.122 45.455 0.00 0.00 0.00 4.11
269 288 3.075884 TCCGTTTCCTTTTAACCCGATG 58.924 45.455 0.00 0.00 0.00 3.84
313 425 4.637534 TGCTTAGCTGAATGAAGGAATGAC 59.362 41.667 5.60 0.00 0.00 3.06
402 514 2.745884 CGAAGCGGTCCATGCCAA 60.746 61.111 0.00 0.00 0.00 4.52
403 515 2.877691 GAAGCGGTCCATGCCAAC 59.122 61.111 0.00 0.00 0.00 3.77
404 516 1.971167 GAAGCGGTCCATGCCAACA 60.971 57.895 0.00 0.00 0.00 3.33
405 517 1.523154 GAAGCGGTCCATGCCAACAA 61.523 55.000 0.00 0.00 0.00 2.83
406 518 1.805428 AAGCGGTCCATGCCAACAAC 61.805 55.000 0.00 0.00 0.00 3.32
407 519 2.560119 GCGGTCCATGCCAACAACA 61.560 57.895 0.00 0.00 0.00 3.33
448 904 3.675698 GTCAGATTGTCACTCGAAACCTC 59.324 47.826 0.00 0.00 0.00 3.85
450 906 3.923461 CAGATTGTCACTCGAAACCTCTC 59.077 47.826 0.00 0.00 0.00 3.20
452 910 3.644884 TTGTCACTCGAAACCTCTCTC 57.355 47.619 0.00 0.00 0.00 3.20
469 927 1.275010 TCTCTGTGTGTGTGTGTGTGT 59.725 47.619 0.00 0.00 0.00 3.72
558 1017 2.187946 CCTCGACCATGACCTGCC 59.812 66.667 0.00 0.00 0.00 4.85
662 1131 0.178921 ACCTCAGCTTCACCTCCTCA 60.179 55.000 0.00 0.00 0.00 3.86
701 1170 7.753309 ATAGATAGCACCACTACTTCTACAG 57.247 40.000 0.00 0.00 29.37 2.74
702 1171 5.511363 AGATAGCACCACTACTTCTACAGT 58.489 41.667 0.00 0.00 39.87 3.55
703 1172 3.944055 AGCACCACTACTTCTACAGTG 57.056 47.619 0.00 0.00 41.51 3.66
704 1173 2.338500 GCACCACTACTTCTACAGTGC 58.662 52.381 0.00 0.00 40.69 4.40
705 1174 2.028930 GCACCACTACTTCTACAGTGCT 60.029 50.000 5.05 0.00 44.29 4.40
706 1175 3.579709 CACCACTACTTCTACAGTGCTG 58.420 50.000 0.00 0.00 40.69 4.41
782 1254 1.819632 GCACGTGACCATCCATCCC 60.820 63.158 22.23 0.00 0.00 3.85
809 1285 5.391312 AGAAAGAGAGAGAAACAGAGAGC 57.609 43.478 0.00 0.00 0.00 4.09
810 1286 3.848272 AAGAGAGAGAAACAGAGAGCG 57.152 47.619 0.00 0.00 0.00 5.03
811 1287 3.066291 AGAGAGAGAAACAGAGAGCGA 57.934 47.619 0.00 0.00 0.00 4.93
812 1288 3.009723 AGAGAGAGAAACAGAGAGCGAG 58.990 50.000 0.00 0.00 0.00 5.03
853 1329 1.511043 CACGCCAATTAACACGCCG 60.511 57.895 0.00 0.00 0.00 6.46
854 1330 2.575789 CGCCAATTAACACGCCGC 60.576 61.111 0.00 0.00 0.00 6.53
855 1331 2.202557 GCCAATTAACACGCCGCC 60.203 61.111 0.00 0.00 0.00 6.13
856 1332 2.487892 CCAATTAACACGCCGCCC 59.512 61.111 0.00 0.00 0.00 6.13
857 1333 2.099446 CAATTAACACGCCGCCCG 59.901 61.111 0.00 0.00 44.21 6.13
924 1413 1.040339 CGCTACTCCTGCTTCTCCCT 61.040 60.000 0.00 0.00 0.00 4.20
926 1415 1.687996 GCTACTCCTGCTTCTCCCTCT 60.688 57.143 0.00 0.00 0.00 3.69
927 1416 2.745968 CTACTCCTGCTTCTCCCTCTT 58.254 52.381 0.00 0.00 0.00 2.85
928 1417 1.567357 ACTCCTGCTTCTCCCTCTTC 58.433 55.000 0.00 0.00 0.00 2.87
983 1483 4.052229 CGGGTCGCTCTTGGTCGT 62.052 66.667 0.00 0.00 0.00 4.34
984 1484 2.432628 GGGTCGCTCTTGGTCGTG 60.433 66.667 0.00 0.00 0.00 4.35
985 1485 2.432628 GGTCGCTCTTGGTCGTGG 60.433 66.667 0.00 0.00 0.00 4.94
1269 1774 6.659242 TCCTTCTCTTCTCTTCTCTTCTCTTC 59.341 42.308 0.00 0.00 0.00 2.87
1274 1779 7.607991 TCTCTTCTCTTCTCTTCTCTTCTCTTC 59.392 40.741 0.00 0.00 0.00 2.87
1594 2103 2.943978 CGACCCCTTCCGCTTCTGT 61.944 63.158 0.00 0.00 0.00 3.41
1754 2282 1.263356 AATCCGTTTCTCCTCCGTGA 58.737 50.000 0.00 0.00 0.00 4.35
2076 2613 7.106239 TCCTCACATATCAAGAAAGGAAAGAC 58.894 38.462 0.00 0.00 0.00 3.01
2117 2656 0.037590 AAAGATAGCACCGCCCAACA 59.962 50.000 0.00 0.00 0.00 3.33
2170 2709 3.093814 TGGAAGGAGTAAGCGACATGTA 58.906 45.455 0.00 0.00 0.00 2.29
2198 2737 0.859760 CCTCTCCCCCTCATCTCTCT 59.140 60.000 0.00 0.00 0.00 3.10
2199 2738 1.203050 CCTCTCCCCCTCATCTCTCTC 60.203 61.905 0.00 0.00 0.00 3.20
2200 2739 1.782752 CTCTCCCCCTCATCTCTCTCT 59.217 57.143 0.00 0.00 0.00 3.10
2201 2740 1.780309 TCTCCCCCTCATCTCTCTCTC 59.220 57.143 0.00 0.00 0.00 3.20
2202 2741 1.782752 CTCCCCCTCATCTCTCTCTCT 59.217 57.143 0.00 0.00 0.00 3.10
2203 2742 1.780309 TCCCCCTCATCTCTCTCTCTC 59.220 57.143 0.00 0.00 0.00 3.20
2204 2743 1.782752 CCCCCTCATCTCTCTCTCTCT 59.217 57.143 0.00 0.00 0.00 3.10
2205 2744 2.224867 CCCCCTCATCTCTCTCTCTCTC 60.225 59.091 0.00 0.00 0.00 3.20
2206 2745 2.713167 CCCCTCATCTCTCTCTCTCTCT 59.287 54.545 0.00 0.00 0.00 3.10
2207 2746 3.244700 CCCCTCATCTCTCTCTCTCTCTC 60.245 56.522 0.00 0.00 0.00 3.20
2208 2747 3.649981 CCCTCATCTCTCTCTCTCTCTCT 59.350 52.174 0.00 0.00 0.00 3.10
2209 2748 4.262808 CCCTCATCTCTCTCTCTCTCTCTC 60.263 54.167 0.00 0.00 0.00 3.20
2610 3201 3.949113 TGCTGCTGCTTCATTTCATCATA 59.051 39.130 17.00 0.00 40.48 2.15
2796 3391 2.027100 CCCTACACTTGTTCCTTCCTCC 60.027 54.545 0.00 0.00 0.00 4.30
2812 3407 6.098982 TCCTTCCTCCTCAATTCTCTTATGTC 59.901 42.308 0.00 0.00 0.00 3.06
2819 3414 6.765036 TCCTCAATTCTCTTATGTCATCAAGC 59.235 38.462 0.00 0.00 0.00 4.01
2820 3415 6.766944 CCTCAATTCTCTTATGTCATCAAGCT 59.233 38.462 0.00 0.00 0.00 3.74
2821 3416 7.254829 CCTCAATTCTCTTATGTCATCAAGCTG 60.255 40.741 0.00 0.00 0.00 4.24
2822 3417 6.541278 TCAATTCTCTTATGTCATCAAGCTGG 59.459 38.462 0.00 0.00 0.00 4.85
2823 3418 5.426689 TTCTCTTATGTCATCAAGCTGGT 57.573 39.130 0.00 0.00 0.00 4.00
2824 3419 5.426689 TCTCTTATGTCATCAAGCTGGTT 57.573 39.130 0.00 0.00 0.00 3.67
2825 3420 6.544928 TCTCTTATGTCATCAAGCTGGTTA 57.455 37.500 0.00 0.00 0.00 2.85
2826 3421 6.946340 TCTCTTATGTCATCAAGCTGGTTAA 58.054 36.000 0.00 0.00 0.00 2.01
2827 3422 7.568349 TCTCTTATGTCATCAAGCTGGTTAAT 58.432 34.615 0.00 0.00 0.00 1.40
2828 3423 7.712639 TCTCTTATGTCATCAAGCTGGTTAATC 59.287 37.037 0.00 0.00 0.00 1.75
2829 3424 7.337938 TCTTATGTCATCAAGCTGGTTAATCA 58.662 34.615 0.00 0.00 0.00 2.57
2830 3425 7.496920 TCTTATGTCATCAAGCTGGTTAATCAG 59.503 37.037 11.61 11.61 37.79 2.90
2920 3528 9.821662 GACAACATTTAGTTACCAATAAGTGTC 57.178 33.333 0.00 0.00 38.74 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 95 1.379044 ATGCCTGCCTTCCTTTCGG 60.379 57.895 0.00 0.00 0.00 4.30
180 183 5.104569 TCCAGTAATCACATTCCACATGCTA 60.105 40.000 0.00 0.00 0.00 3.49
208 211 2.747989 GGAGGATTTGTCGGGTTTCTTC 59.252 50.000 0.00 0.00 0.00 2.87
265 284 4.876125 AGCCAAGATACATACAGTCATCG 58.124 43.478 0.00 0.00 0.00 3.84
269 288 5.355350 AGCAAAAGCCAAGATACATACAGTC 59.645 40.000 0.00 0.00 0.00 3.51
313 425 2.583593 GCGAGCTAGCGGTTCCAG 60.584 66.667 9.55 0.00 0.00 3.86
401 513 2.760092 AGATGCAGTTGGTGTTGTTGTT 59.240 40.909 0.00 0.00 0.00 2.83
402 514 2.378038 AGATGCAGTTGGTGTTGTTGT 58.622 42.857 0.00 0.00 0.00 3.32
403 515 3.067180 AGAAGATGCAGTTGGTGTTGTTG 59.933 43.478 0.00 0.00 0.00 3.33
404 516 3.067180 CAGAAGATGCAGTTGGTGTTGTT 59.933 43.478 0.00 0.00 0.00 2.83
405 517 2.620115 CAGAAGATGCAGTTGGTGTTGT 59.380 45.455 0.00 0.00 0.00 3.32
406 518 2.620115 ACAGAAGATGCAGTTGGTGTTG 59.380 45.455 0.00 0.00 0.00 3.33
407 519 2.880890 GACAGAAGATGCAGTTGGTGTT 59.119 45.455 0.00 0.00 0.00 3.32
448 904 1.929169 CACACACACACACACAGAGAG 59.071 52.381 0.00 0.00 0.00 3.20
450 906 1.725641 ACACACACACACACACAGAG 58.274 50.000 0.00 0.00 0.00 3.35
452 910 2.739379 TGTTACACACACACACACACAG 59.261 45.455 0.00 0.00 0.00 3.66
476 935 6.662865 TGCATCTTCTCCTCCTTCTAATAG 57.337 41.667 0.00 0.00 0.00 1.73
477 936 7.093552 GCTATGCATCTTCTCCTCCTTCTAATA 60.094 40.741 0.19 0.00 0.00 0.98
478 937 6.295802 GCTATGCATCTTCTCCTCCTTCTAAT 60.296 42.308 0.19 0.00 0.00 1.73
479 938 5.011533 GCTATGCATCTTCTCCTCCTTCTAA 59.988 44.000 0.19 0.00 0.00 2.10
480 939 4.526262 GCTATGCATCTTCTCCTCCTTCTA 59.474 45.833 0.19 0.00 0.00 2.10
558 1017 1.293924 CATCCTTCCTTGTAGCAGCG 58.706 55.000 0.00 0.00 0.00 5.18
662 1131 6.980978 GTGCTATCTATATATGCAATGTCGGT 59.019 38.462 0.00 0.00 35.34 4.69
698 1167 2.011122 ACTAGTACCACCAGCACTGT 57.989 50.000 0.00 0.00 0.00 3.55
700 1169 3.453059 AGTACTAGTACCACCAGCACT 57.547 47.619 25.97 6.39 36.75 4.40
701 1170 4.268359 AGTAGTACTAGTACCACCAGCAC 58.732 47.826 25.97 13.73 36.75 4.40
702 1171 4.581309 AGTAGTACTAGTACCACCAGCA 57.419 45.455 25.97 3.88 36.75 4.41
782 1254 6.015519 TCTCTGTTTCTCTCTCTTTCTTGGAG 60.016 42.308 0.00 0.00 0.00 3.86
810 1286 4.180946 TTCTCCGCTCGCTCGCTC 62.181 66.667 0.00 0.00 0.00 5.03
811 1287 4.186433 CTTCTCCGCTCGCTCGCT 62.186 66.667 0.00 0.00 0.00 4.93
854 1330 3.853698 TTCGTTTCCTTGGGCCGGG 62.854 63.158 2.18 8.82 0.00 5.73
855 1331 2.281900 TTCGTTTCCTTGGGCCGG 60.282 61.111 0.00 0.00 0.00 6.13
856 1332 1.448922 TTGTTCGTTTCCTTGGGCCG 61.449 55.000 0.00 0.00 0.00 6.13
857 1333 0.313987 CTTGTTCGTTTCCTTGGGCC 59.686 55.000 0.00 0.00 0.00 5.80
924 1413 3.105283 GCTAACTAACAGGGGGAGAAGA 58.895 50.000 0.00 0.00 0.00 2.87
926 1415 1.829222 CGCTAACTAACAGGGGGAGAA 59.171 52.381 0.00 0.00 0.00 2.87
927 1416 1.481871 CGCTAACTAACAGGGGGAGA 58.518 55.000 0.00 0.00 0.00 3.71
928 1417 0.179081 GCGCTAACTAACAGGGGGAG 60.179 60.000 0.00 0.00 0.00 4.30
1086 1586 1.228459 GGCCAGGAAGAAACGGGTT 60.228 57.895 0.00 0.00 0.00 4.11
1092 1592 2.672996 GCGCAGGCCAGGAAGAAA 60.673 61.111 5.01 0.00 0.00 2.52
1210 1710 4.430765 GATGACCCGGTGCGACGT 62.431 66.667 0.00 0.00 0.00 4.34
1269 1774 5.942236 TCCCAATCAATCAACAAGAGAAGAG 59.058 40.000 0.00 0.00 0.00 2.85
1274 1779 6.985117 TCTTTTCCCAATCAATCAACAAGAG 58.015 36.000 0.00 0.00 0.00 2.85
1594 2103 0.539986 GTACCTTGCATCCGAGGGAA 59.460 55.000 7.09 0.00 45.60 3.97
2010 2544 1.034292 GTGCTCTTCCTTCCCATGGC 61.034 60.000 6.09 0.00 0.00 4.40
2117 2656 2.091885 TGGTGGTTGGCTTCTCTTTCTT 60.092 45.455 0.00 0.00 0.00 2.52
2170 2709 0.419459 AGGGGGAGAGGTTGAGATGT 59.581 55.000 0.00 0.00 0.00 3.06
2198 2737 2.278657 TGGGAGGAGAGAGAGAGAGA 57.721 55.000 0.00 0.00 0.00 3.10
2199 2738 2.713167 AGATGGGAGGAGAGAGAGAGAG 59.287 54.545 0.00 0.00 0.00 3.20
2200 2739 2.711009 GAGATGGGAGGAGAGAGAGAGA 59.289 54.545 0.00 0.00 0.00 3.10
2201 2740 2.442878 TGAGATGGGAGGAGAGAGAGAG 59.557 54.545 0.00 0.00 0.00 3.20
2202 2741 2.174639 GTGAGATGGGAGGAGAGAGAGA 59.825 54.545 0.00 0.00 0.00 3.10
2203 2742 2.586425 GTGAGATGGGAGGAGAGAGAG 58.414 57.143 0.00 0.00 0.00 3.20
2204 2743 1.216678 GGTGAGATGGGAGGAGAGAGA 59.783 57.143 0.00 0.00 0.00 3.10
2205 2744 1.063341 TGGTGAGATGGGAGGAGAGAG 60.063 57.143 0.00 0.00 0.00 3.20
2206 2745 1.010795 TGGTGAGATGGGAGGAGAGA 58.989 55.000 0.00 0.00 0.00 3.10
2207 2746 2.100128 ATGGTGAGATGGGAGGAGAG 57.900 55.000 0.00 0.00 0.00 3.20
2208 2747 2.426414 GGTATGGTGAGATGGGAGGAGA 60.426 54.545 0.00 0.00 0.00 3.71
2209 2748 1.974236 GGTATGGTGAGATGGGAGGAG 59.026 57.143 0.00 0.00 0.00 3.69
2507 3098 0.548031 CATTCCTCCTAGGCCTGCAA 59.452 55.000 17.99 0.00 34.61 4.08
2796 3391 7.254829 CCAGCTTGATGACATAAGAGAATTGAG 60.255 40.741 8.13 0.00 0.00 3.02
2819 3414 2.158755 AGAATCCGGGCTGATTAACCAG 60.159 50.000 0.00 0.00 35.15 4.00
2820 3415 1.843851 AGAATCCGGGCTGATTAACCA 59.156 47.619 0.00 0.00 35.15 3.67
2821 3416 2.640316 AGAATCCGGGCTGATTAACC 57.360 50.000 0.00 0.00 35.15 2.85
2822 3417 6.465084 AGTAATAGAATCCGGGCTGATTAAC 58.535 40.000 0.00 0.00 35.15 2.01
2823 3418 6.681729 AGTAATAGAATCCGGGCTGATTAA 57.318 37.500 0.00 0.00 35.15 1.40
2824 3419 7.973048 ATAGTAATAGAATCCGGGCTGATTA 57.027 36.000 0.00 0.00 35.15 1.75
2825 3420 6.875972 ATAGTAATAGAATCCGGGCTGATT 57.124 37.500 0.00 0.00 37.66 2.57
2826 3421 7.472100 GCATATAGTAATAGAATCCGGGCTGAT 60.472 40.741 0.00 0.00 0.00 2.90
2827 3422 6.183360 GCATATAGTAATAGAATCCGGGCTGA 60.183 42.308 0.00 0.00 0.00 4.26
2828 3423 5.986135 GCATATAGTAATAGAATCCGGGCTG 59.014 44.000 0.00 0.00 0.00 4.85
2829 3424 5.900123 AGCATATAGTAATAGAATCCGGGCT 59.100 40.000 0.00 0.00 0.00 5.19
2830 3425 6.163135 AGCATATAGTAATAGAATCCGGGC 57.837 41.667 0.00 0.00 0.00 6.13
2831 3426 7.815068 GCATAGCATATAGTAATAGAATCCGGG 59.185 40.741 0.00 0.00 0.00 5.73
2895 3503 9.344772 TGACACTTATTGGTAACTAAATGTTGT 57.655 29.630 0.00 0.00 39.55 3.32


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

AutoCloner maintained by Alex Coulton.