Multiple sequence alignment - TraesCS7D01G336400

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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 TraesCS7D01G336400 chr7D 100.000 3644 0 0 1 3644 428950801 428954444 0.000000e+00 6730.0
1 TraesCS7D01G336400 chr7B 95.071 2617 65 34 620 3199 446664267 446666856 0.000000e+00 4060.0
2 TraesCS7D01G336400 chr7B 91.480 446 33 4 1 443 446660824 446661267 3.110000e-170 608.0
3 TraesCS7D01G336400 chr7B 86.517 445 46 8 3211 3644 446667076 446667517 9.150000e-131 477.0
4 TraesCS7D01G336400 chr7B 79.690 581 92 19 102 666 446660624 446661194 2.640000e-106 396.0
5 TraesCS7D01G336400 chr7B 80.313 447 70 10 203 636 446660624 446661065 4.540000e-84 322.0
6 TraesCS7D01G336400 chr7A 93.770 2456 91 30 758 3180 503053348 503050922 0.000000e+00 3631.0
7 TraesCS7D01G336400 chr7A 84.006 669 90 9 10 666 503055005 503054342 8.590000e-176 627.0
8 TraesCS7D01G336400 chr7A 88.235 476 53 3 10 483 503054803 503054329 1.900000e-157 566.0
9 TraesCS7D01G336400 chr7A 89.381 452 40 5 3198 3644 503049209 503048761 2.460000e-156 562.0
10 TraesCS7D01G336400 chr7A 80.615 650 102 12 34 670 503055178 503054540 7.080000e-132 481.0
11 TraesCS7D01G336400 chr7A 73.602 644 122 28 34 666 503055554 503054948 1.720000e-48 204.0
12 TraesCS7D01G336400 chr1D 81.690 213 32 6 1795 2005 283617780 283617987 1.740000e-38 171.0
13 TraesCS7D01G336400 chr1A 81.690 213 32 6 1795 2005 355343664 355343871 1.740000e-38 171.0
14 TraesCS7D01G336400 chr1A 91.071 56 5 0 1800 1855 578299977 578300032 3.900000e-10 76.8
15 TraesCS7D01G336400 chr1B 81.731 208 31 6 1800 2005 385296737 385296939 2.250000e-37 167.0
16 TraesCS7D01G336400 chr5D 82.069 145 22 4 1810 1952 452365184 452365326 1.780000e-23 121.0
17 TraesCS7D01G336400 chr5B 82.069 145 22 4 1810 1952 552564877 552565019 1.780000e-23 121.0
18 TraesCS7D01G336400 chr5A 83.740 123 18 2 1810 1931 571305210 571305331 8.270000e-22 115.0


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 TraesCS7D01G336400 chr7D 428950801 428954444 3643 False 6730.000000 6730 100.000000 1 3644 1 chr7D.!!$F1 3643
1 TraesCS7D01G336400 chr7B 446660624 446667517 6893 False 1172.600000 4060 86.614200 1 3644 5 chr7B.!!$F1 3643
2 TraesCS7D01G336400 chr7A 503048761 503055554 6793 True 1011.833333 3631 84.934833 10 3644 6 chr7A.!!$R1 3634

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
946 5195 0.106918 ACCCCTTTGACTTTGTCGCA 60.107 50.0 0.0 0.0 34.95 5.10 F
1189 5452 0.402121 AGCAAGAACCAACTCTCCCC 59.598 55.0 0.0 0.0 0.00 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2422 6691 3.814842 TGCAACGAGCCAGGATTATAATG 59.185 43.478 1.78 0.0 44.83 1.90 R
3170 7461 2.403259 CACATTCAACCGAAAAAGGCC 58.597 47.619 0.00 0.0 34.01 5.19 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
53 595 3.956199 ACTGTTATCAATGGCCAATGAGG 59.044 43.478 26.79 16.09 41.84 3.86
88 630 1.005037 TGGACGCCATCATATCGGC 60.005 57.895 0.00 0.00 45.28 5.54
114 656 5.113529 GCGTTATACGAATGCATTAAGTTGC 59.886 40.000 20.54 14.37 46.05 4.17
153 695 4.591498 ACAATGCTATCAATGGCCAATGAT 59.409 37.500 33.19 33.19 39.50 2.45
171 713 4.067972 TGATCGGCCTACAAATTCTACC 57.932 45.455 0.00 0.00 0.00 3.18
186 829 4.955811 TTCTACCTGACGCCATCATATT 57.044 40.909 0.00 0.00 36.48 1.28
187 830 4.955811 TCTACCTGACGCCATCATATTT 57.044 40.909 0.00 0.00 36.48 1.40
252 998 3.993736 CACAGTGTTATCAATGGACGACA 59.006 43.478 6.23 0.00 42.88 4.35
294 1040 1.344942 GACGCCATCATATCGGTCGC 61.345 60.000 0.00 0.00 0.00 5.19
361 1107 1.226859 CAATGGCCAATGAGCAGCG 60.227 57.895 16.27 0.00 0.00 5.18
370 1116 3.312421 GCCAATGAGCAGCGTAGAAATTA 59.688 43.478 0.00 0.00 0.00 1.40
402 1148 4.391830 ACCATCATATTTGCCGCGTTATAG 59.608 41.667 4.92 0.00 0.00 1.31
458 3941 3.261580 TGTTATCAATGGTCACTGAGCG 58.738 45.455 3.84 0.00 32.15 5.03
475 3958 3.196901 TGAGCGGCTTAGAAATTCTACCA 59.803 43.478 2.97 0.00 0.00 3.25
483 3966 3.695830 AGAAATTCTACCAGACGCCAA 57.304 42.857 0.00 0.00 0.00 4.52
484 3967 3.600388 AGAAATTCTACCAGACGCCAAG 58.400 45.455 0.00 0.00 0.00 3.61
518 4063 4.657055 TGCATTGCGTTGATGTAATGTAC 58.343 39.130 13.18 0.00 41.97 2.90
547 4092 4.036734 ACGATGTTATCAATGGCCAATGAC 59.963 41.667 25.68 14.25 0.00 3.06
548 4093 4.276678 CGATGTTATCAATGGCCAATGACT 59.723 41.667 25.68 16.27 0.00 3.41
567 4160 5.978814 TGACTGGCTTAGAGAAATTCTACC 58.021 41.667 0.00 0.00 38.12 3.18
604 4202 4.921515 TCTGGCGCTTTATACGAATGTATC 59.078 41.667 7.64 0.00 41.50 2.24
673 4902 6.955963 GCGCATCCTATAGAAATTAAACATCG 59.044 38.462 0.30 0.00 0.00 3.84
760 4992 7.187244 CTCATTGCCATATGAGTACTGAAAG 57.813 40.000 0.00 0.00 44.16 2.62
763 4995 7.828717 TCATTGCCATATGAGTACTGAAAGAAA 59.171 33.333 0.00 0.00 32.04 2.52
765 4997 8.579850 TTGCCATATGAGTACTGAAAGAAAAT 57.420 30.769 0.00 0.00 37.43 1.82
831 5074 1.028905 CCTCCAGCAACGGTGAAAAA 58.971 50.000 3.55 0.00 32.22 1.94
944 5193 1.873591 CTCACCCCTTTGACTTTGTCG 59.126 52.381 0.00 0.00 34.95 4.35
946 5195 0.106918 ACCCCTTTGACTTTGTCGCA 60.107 50.000 0.00 0.00 34.95 5.10
1179 5438 1.673168 CTCCATAGCCAGCAAGAACC 58.327 55.000 0.00 0.00 0.00 3.62
1185 5448 0.475906 AGCCAGCAAGAACCAACTCT 59.524 50.000 0.00 0.00 0.00 3.24
1186 5449 0.877743 GCCAGCAAGAACCAACTCTC 59.122 55.000 0.00 0.00 0.00 3.20
1187 5450 1.528129 CCAGCAAGAACCAACTCTCC 58.472 55.000 0.00 0.00 0.00 3.71
1188 5451 1.528129 CAGCAAGAACCAACTCTCCC 58.472 55.000 0.00 0.00 0.00 4.30
1189 5452 0.402121 AGCAAGAACCAACTCTCCCC 59.598 55.000 0.00 0.00 0.00 4.81
1190 5453 0.955919 GCAAGAACCAACTCTCCCCG 60.956 60.000 0.00 0.00 0.00 5.73
1191 5454 0.955919 CAAGAACCAACTCTCCCCGC 60.956 60.000 0.00 0.00 0.00 6.13
1192 5455 2.434359 GAACCAACTCTCCCCGCG 60.434 66.667 0.00 0.00 0.00 6.46
1193 5456 4.699522 AACCAACTCTCCCCGCGC 62.700 66.667 0.00 0.00 0.00 6.86
1406 5669 2.586792 GCGTTGCTCCCTGATCCT 59.413 61.111 0.00 0.00 0.00 3.24
1659 5928 2.030451 AGAAAGTACGTCCCGAACACTC 60.030 50.000 0.00 0.00 0.00 3.51
1660 5929 1.613836 AAGTACGTCCCGAACACTCT 58.386 50.000 0.00 0.00 0.00 3.24
2087 6356 1.179814 AGCCAAGGAAGAGTCGTCGT 61.180 55.000 0.00 0.00 0.00 4.34
2671 6950 5.182487 ACCAAACCCAAAGACAATGTTTTC 58.818 37.500 0.00 0.00 0.00 2.29
2757 7038 0.590682 TGGTGCTACATTTGTGCGTG 59.409 50.000 0.00 0.00 0.00 5.34
3038 7329 3.905968 TCTCGGTCCTATGTGTATTGGA 58.094 45.455 0.00 0.00 36.13 3.53
3065 7356 1.798735 CTGCTGCAACCAATCCTCG 59.201 57.895 3.02 0.00 0.00 4.63
3069 7360 1.810151 GCTGCAACCAATCCTCGTTTA 59.190 47.619 0.00 0.00 0.00 2.01
3170 7461 8.349245 TGGCGTGTAAATCCTTATGAAAATATG 58.651 33.333 0.00 0.00 0.00 1.78
3183 7474 5.476091 TGAAAATATGGCCTTTTTCGGTT 57.524 34.783 22.57 6.04 42.19 4.44
3209 9195 5.152623 TGTGGATGTATAAGAGCCATAGC 57.847 43.478 0.00 0.00 40.32 2.97
3222 9415 1.032014 CCATAGCACATTTTCCCCCG 58.968 55.000 0.00 0.00 0.00 5.73
3230 9423 1.203125 ACATTTTCCCCCGAACCATGT 60.203 47.619 0.00 0.00 31.48 3.21
3257 9453 7.596749 AAGAGTTAGGTGTCAATTCATTACG 57.403 36.000 0.00 0.00 0.00 3.18
3322 9518 0.984230 AGAGGCATGACCCGAAAAGA 59.016 50.000 0.00 0.00 40.58 2.52
3353 9550 7.349859 ACCTAAATGACCTAAGATCAATACCCA 59.650 37.037 0.00 0.00 0.00 4.51
3370 9567 1.539065 CCCAAGAGAATCGGATCCACG 60.539 57.143 13.41 0.00 42.67 4.94
3399 9596 2.362717 GACGAGCAATCCTAGCTTAGGT 59.637 50.000 0.00 0.00 46.32 3.08
3412 9609 4.137116 AGCTTAGGTTGCATCATACGAA 57.863 40.909 0.00 0.00 0.00 3.85
3422 9619 5.895636 TGCATCATACGAAATGAAAAGGT 57.104 34.783 8.81 0.00 0.00 3.50
3434 9631 7.444183 ACGAAATGAAAAGGTGAGAAACATCTA 59.556 33.333 0.00 0.00 39.27 1.98
3447 9644 4.467795 AGAAACATCTACTGCAAGAGCCTA 59.532 41.667 0.00 0.00 41.13 3.93
3469 9666 3.527533 GACACCAGTCAACTGTAACACA 58.472 45.455 9.19 0.00 44.34 3.72
3520 9723 1.808512 CGACTAACACACAAGCACCCA 60.809 52.381 0.00 0.00 0.00 4.51
3521 9724 1.873591 GACTAACACACAAGCACCCAG 59.126 52.381 0.00 0.00 0.00 4.45
3524 9727 0.034574 AACACACAAGCACCCAGTGA 60.035 50.000 0.00 0.00 35.23 3.41
3525 9728 0.748005 ACACACAAGCACCCAGTGAC 60.748 55.000 0.00 0.00 35.23 3.67
3563 9769 9.950680 CAAACATAAAGACAACACTACTTGAAT 57.049 29.630 0.00 0.00 0.00 2.57
3566 9772 8.774586 ACATAAAGACAACACTACTTGAATGAC 58.225 33.333 0.00 0.00 0.00 3.06
3613 9819 1.082117 CGCCACCGTTCCATCACTAC 61.082 60.000 0.00 0.00 0.00 2.73
3621 9827 2.028476 CGTTCCATCACTACCAGACCAA 60.028 50.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 574 3.319972 CCCTCATTGGCCATTGATAACAG 59.680 47.826 26.25 15.96 0.00 3.16
53 595 1.485066 TCCAGTCGAATTTCTAGGCCC 59.515 52.381 0.00 0.00 0.00 5.80
88 630 2.941891 AATGCATTCGTATAACGCGG 57.058 45.000 12.47 0.00 42.21 6.46
124 666 5.009911 TGGCCATTGATAGCATTGTGTAATC 59.990 40.000 0.00 0.00 0.00 1.75
153 695 3.101437 TCAGGTAGAATTTGTAGGCCGA 58.899 45.455 0.00 0.00 0.00 5.54
161 703 3.270027 TGATGGCGTCAGGTAGAATTTG 58.730 45.455 5.03 0.00 31.80 2.32
171 713 3.510251 CGACAAATATGATGGCGTCAG 57.490 47.619 15.57 3.55 44.19 3.51
186 829 2.260481 TGCATTCGTATAACGCGACAA 58.740 42.857 15.93 0.00 42.21 3.18
187 830 1.910688 TGCATTCGTATAACGCGACA 58.089 45.000 15.93 0.00 42.21 4.35
247 993 0.034337 TTTCTAGGCCGCTTTGTCGT 59.966 50.000 0.00 0.00 0.00 4.34
252 998 0.690762 TCCAGTTTCTAGGCCGCTTT 59.309 50.000 0.00 0.00 0.00 3.51
370 1116 5.239306 CGGCAAATATGATGGTGTCAAGTAT 59.761 40.000 0.00 0.00 40.97 2.12
449 3932 3.055819 AGAATTTCTAAGCCGCTCAGTGA 60.056 43.478 0.00 0.00 0.00 3.41
452 3935 3.804873 GGTAGAATTTCTAAGCCGCTCAG 59.195 47.826 7.70 0.00 29.58 3.35
458 3941 3.556365 GCGTCTGGTAGAATTTCTAAGCC 59.444 47.826 7.70 6.87 29.58 4.35
483 3966 2.160219 CGCAATGCATCCATATAACGCT 59.840 45.455 5.91 0.00 0.00 5.07
484 3967 2.095768 ACGCAATGCATCCATATAACGC 60.096 45.455 5.91 0.00 0.00 4.84
494 4039 4.353737 ACATTACATCAACGCAATGCATC 58.646 39.130 5.91 0.00 32.76 3.91
518 4063 5.008514 TGGCCATTGATAACATCGTGTAATG 59.991 40.000 0.00 0.00 0.00 1.90
527 4072 4.342951 CCAGTCATTGGCCATTGATAACAT 59.657 41.667 28.08 12.79 40.87 2.71
547 4092 6.045955 GTCAGGTAGAATTTCTCTAAGCCAG 58.954 44.000 1.27 0.00 38.41 4.85
548 4093 5.394224 CGTCAGGTAGAATTTCTCTAAGCCA 60.394 44.000 1.27 0.00 38.41 4.75
557 4102 3.531538 TGATGGCGTCAGGTAGAATTTC 58.468 45.455 5.03 0.00 31.80 2.17
625 4684 5.064707 GCATTGGTCATTCGTAACACTATGT 59.935 40.000 0.00 0.00 0.00 2.29
636 4695 0.317269 GGATGCGCATTGGTCATTCG 60.317 55.000 26.12 0.00 0.00 3.34
638 4697 2.346766 TAGGATGCGCATTGGTCATT 57.653 45.000 26.12 7.23 0.00 2.57
639 4698 2.574006 ATAGGATGCGCATTGGTCAT 57.426 45.000 26.12 12.92 0.00 3.06
673 4902 8.200364 TCTACCGTGTAAATTATTTGCTTACC 57.800 34.615 7.25 0.00 0.00 2.85
787 5020 0.722469 GAGCGCAACACATGTGAACG 60.722 55.000 31.94 27.65 42.32 3.95
854 5103 4.170256 TGTTTTCACCGTTGCTTTCTTTC 58.830 39.130 0.00 0.00 0.00 2.62
857 5106 5.705609 ATATGTTTTCACCGTTGCTTTCT 57.294 34.783 0.00 0.00 0.00 2.52
866 5115 6.700081 TCGATTCTAGGAATATGTTTTCACCG 59.300 38.462 0.00 0.00 0.00 4.94
944 5193 0.673985 GGTCCCCACTTGACTTTTGC 59.326 55.000 0.00 0.00 33.22 3.68
946 5195 2.666317 CAAGGTCCCCACTTGACTTTT 58.334 47.619 0.00 0.00 46.27 2.27
1192 5455 4.451150 TGTCCATGGTCGGCTCGC 62.451 66.667 12.58 0.00 0.00 5.03
1193 5456 2.202797 CTGTCCATGGTCGGCTCG 60.203 66.667 12.58 0.00 0.00 5.03
1194 5457 2.187946 CCTGTCCATGGTCGGCTC 59.812 66.667 12.58 0.00 0.00 4.70
1195 5458 3.402681 CCCTGTCCATGGTCGGCT 61.403 66.667 12.58 0.00 0.00 5.52
1319 5582 0.043485 AGAAGGAGGAGAAGGGGTCC 59.957 60.000 0.00 0.00 0.00 4.46
1550 5819 2.125552 TCGTCTTGCTGCATCGGG 60.126 61.111 1.84 0.00 0.00 5.14
1613 5882 3.744719 CTCGACCCTTCGCCGACA 61.745 66.667 0.00 0.00 45.46 4.35
1687 5956 2.286418 GCACAAGCATACACGATAAGCC 60.286 50.000 0.00 0.00 41.58 4.35
1728 5997 1.845809 CTTCCTGCACAGACGCCAAC 61.846 60.000 0.00 0.00 0.00 3.77
2421 6690 4.065088 GCAACGAGCCAGGATTATAATGA 58.935 43.478 1.78 0.00 37.23 2.57
2422 6691 3.814842 TGCAACGAGCCAGGATTATAATG 59.185 43.478 1.78 0.00 44.83 1.90
2671 6950 8.152309 ACATGTCAAGAAAGAAGAAGAAGAAG 57.848 34.615 0.00 0.00 0.00 2.85
2757 7038 4.844998 TGATGATCAGTCTAGCTAGTGC 57.155 45.455 20.10 13.92 40.05 4.40
3065 7356 6.223120 AGAGCAACATGAAAATTGGGTAAAC 58.777 36.000 0.00 0.00 0.00 2.01
3069 7360 4.590222 AGAAGAGCAACATGAAAATTGGGT 59.410 37.500 0.00 0.00 0.00 4.51
3170 7461 2.403259 CACATTCAACCGAAAAAGGCC 58.597 47.619 0.00 0.00 34.01 5.19
3183 7474 5.628797 TGGCTCTTATACATCCACATTCA 57.371 39.130 0.00 0.00 0.00 2.57
3209 9195 1.204467 CATGGTTCGGGGGAAAATGTG 59.796 52.381 0.00 0.00 0.00 3.21
3222 9415 7.553334 TGACACCTAACTCTTATACATGGTTC 58.447 38.462 0.00 0.00 0.00 3.62
3255 9451 4.113354 GGCGATGTATCTTTTTCTCTCGT 58.887 43.478 0.00 0.00 0.00 4.18
3256 9452 4.112634 TGGCGATGTATCTTTTTCTCTCG 58.887 43.478 0.00 0.00 0.00 4.04
3257 9453 6.422776 TTTGGCGATGTATCTTTTTCTCTC 57.577 37.500 0.00 0.00 0.00 3.20
3322 9518 9.981460 ATTGATCTTAGGTCATTTAGGTTCTTT 57.019 29.630 0.00 0.00 0.00 2.52
3353 9550 2.379972 ACTCGTGGATCCGATTCTCTT 58.620 47.619 7.39 0.00 36.08 2.85
3370 9567 1.205893 AGGATTGCTCGTCTCCAACTC 59.794 52.381 0.00 0.00 0.00 3.01
3371 9568 1.270907 AGGATTGCTCGTCTCCAACT 58.729 50.000 0.00 0.00 0.00 3.16
3372 9569 2.815478 CTAGGATTGCTCGTCTCCAAC 58.185 52.381 0.00 0.00 0.00 3.77
3373 9570 1.137086 GCTAGGATTGCTCGTCTCCAA 59.863 52.381 0.00 0.00 0.00 3.53
3374 9571 0.747255 GCTAGGATTGCTCGTCTCCA 59.253 55.000 0.00 0.00 0.00 3.86
3399 9596 6.072230 TCACCTTTTCATTTCGTATGATGCAA 60.072 34.615 0.00 0.00 0.00 4.08
3412 9609 7.308830 GCAGTAGATGTTTCTCACCTTTTCATT 60.309 37.037 0.00 0.00 33.17 2.57
3422 9619 4.248859 GCTCTTGCAGTAGATGTTTCTCA 58.751 43.478 1.80 0.00 39.41 3.27
3434 9631 0.610687 GGTGTCTAGGCTCTTGCAGT 59.389 55.000 0.00 0.00 41.91 4.40
3469 9666 0.110486 ATGGCTGTCGAGTTTGGGTT 59.890 50.000 0.00 0.00 0.00 4.11
3524 9727 8.037758 TGTCTTTATGTTTGGTTGTGATTTTGT 58.962 29.630 0.00 0.00 0.00 2.83
3525 9728 8.417780 TGTCTTTATGTTTGGTTGTGATTTTG 57.582 30.769 0.00 0.00 0.00 2.44
3563 9769 1.220749 GATGTTGCGCCTAGGGTCA 59.779 57.895 11.72 1.18 0.00 4.02
3587 9793 2.474612 GGAACGGTGGCGTTGTTGT 61.475 57.895 0.00 0.00 31.71 3.32
3613 9819 0.682852 TTAGGTGACGGTTGGTCTGG 59.317 55.000 0.00 0.00 46.24 3.86
3621 9827 0.322816 TCTACGGCTTAGGTGACGGT 60.323 55.000 0.00 0.00 0.00 4.83


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

AutoCloner maintained by Alex Coulton.