Multiple sequence alignment - TraesCS7A01G392100

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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 TraesCS7A01G392100 chr7A 100.000 2369 0 0 1 2369 568128834 568131202 0.000000e+00 4375.0
1 TraesCS7A01G392100 chr7A 96.119 773 24 4 1599 2369 568580409 568581177 0.000000e+00 1256.0
2 TraesCS7A01G392100 chr7A 87.429 883 78 25 735 1602 569112808 569111944 0.000000e+00 985.0
3 TraesCS7A01G392100 chr7A 94.208 518 23 3 975 1492 568579791 568580301 0.000000e+00 784.0
4 TraesCS7A01G392100 chr7A 87.722 562 50 14 807 1357 568695908 568695355 2.570000e-179 638.0
5 TraesCS7A01G392100 chr7A 87.528 449 35 9 1599 2030 569111917 569111473 1.260000e-137 499.0
6 TraesCS7A01G392100 chr7A 89.337 347 27 8 2025 2368 569076099 569075760 6.050000e-116 427.0
7 TraesCS7A01G392100 chr7A 81.542 493 40 17 6 474 568698191 568697726 2.240000e-95 359.0
8 TraesCS7A01G392100 chr7A 81.221 426 50 12 73 474 567727649 567728068 1.370000e-82 316.0
9 TraesCS7A01G392100 chr7A 83.516 364 28 15 97 457 569119542 569119208 6.360000e-81 311.0
10 TraesCS7A01G392100 chr7A 79.357 373 31 27 574 905 568579116 568579483 1.100000e-53 220.0
11 TraesCS7A01G392100 chr7A 98.077 52 1 0 6 57 567727535 567727586 9.020000e-15 91.6
12 TraesCS7A01G392100 chr7A 96.875 32 1 0 519 550 568696330 568696299 1.000000e-03 54.7
13 TraesCS7A01G392100 chr7D 88.902 856 47 16 764 1602 501599737 501600561 0.000000e+00 1011.0
14 TraesCS7A01G392100 chr7D 87.083 720 59 17 764 1475 501778102 501777409 0.000000e+00 784.0
15 TraesCS7A01G392100 chr7D 89.878 573 35 13 769 1331 501610256 501609697 0.000000e+00 715.0
16 TraesCS7A01G392100 chr7D 93.157 453 27 2 1920 2369 501776276 501775825 0.000000e+00 662.0
17 TraesCS7A01G392100 chr7D 90.632 427 25 6 1 427 501583985 501584396 9.570000e-154 553.0
18 TraesCS7A01G392100 chr7D 87.734 481 39 14 6 474 501613572 501613100 5.760000e-151 544.0
19 TraesCS7A01G392100 chr7D 83.682 478 47 20 6 476 501827337 501826884 2.820000e-114 422.0
20 TraesCS7A01G392100 chr7D 83.333 492 43 23 6 474 501402556 501403031 3.640000e-113 418.0
21 TraesCS7A01G392100 chr7D 91.589 214 9 6 1599 1811 501600588 501600793 1.070000e-73 287.0
22 TraesCS7A01G392100 chr7D 83.072 319 17 9 1626 1922 501776740 501776437 3.020000e-64 255.0
23 TraesCS7A01G392100 chr7D 87.179 117 12 3 1914 2028 501601051 501601166 1.910000e-26 130.0
24 TraesCS7A01G392100 chr7D 91.860 86 3 2 386 468 501584397 501584481 1.490000e-22 117.0
25 TraesCS7A01G392100 chr7D 91.765 85 6 1 1518 1602 501777401 501777318 1.490000e-22 117.0
26 TraesCS7A01G392100 chr7D 93.478 46 3 0 505 550 501508200 501508245 4.220000e-08 69.4
27 TraesCS7A01G392100 chr7D 92.857 42 0 3 724 765 501599685 501599723 9.150000e-05 58.4
28 TraesCS7A01G392100 chr7B 85.482 861 55 25 764 1602 531179923 531180735 0.000000e+00 833.0
29 TraesCS7A01G392100 chr7B 89.310 580 49 8 763 1335 531222604 531222031 0.000000e+00 715.0
30 TraesCS7A01G392100 chr7B 82.390 636 67 27 814 1421 530869717 530870335 1.620000e-141 512.0
31 TraesCS7A01G392100 chr7B 86.975 476 28 14 13 468 531233611 531233150 2.720000e-139 505.0
32 TraesCS7A01G392100 chr7B 83.918 485 40 16 11 471 531177800 531178270 1.680000e-116 429.0
33 TraesCS7A01G392100 chr7B 83.374 409 47 14 73 472 530864420 530864816 2.240000e-95 359.0


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 TraesCS7A01G392100 chr7A 568128834 568131202 2368 False 4375.000000 4375 100.000000 1 2369 1 chr7A.!!$F1 2368
1 TraesCS7A01G392100 chr7A 568579116 568581177 2061 False 753.333333 1256 89.894667 574 2369 3 chr7A.!!$F3 1795
2 TraesCS7A01G392100 chr7A 569111473 569112808 1335 True 742.000000 985 87.478500 735 2030 2 chr7A.!!$R4 1295
3 TraesCS7A01G392100 chr7A 568695355 568698191 2836 True 350.566667 638 88.713000 6 1357 3 chr7A.!!$R3 1351
4 TraesCS7A01G392100 chr7A 567727535 567728068 533 False 203.800000 316 89.649000 6 474 2 chr7A.!!$F2 468
5 TraesCS7A01G392100 chr7D 501609697 501613572 3875 True 629.500000 715 88.806000 6 1331 2 chr7D.!!$R2 1325
6 TraesCS7A01G392100 chr7D 501775825 501778102 2277 True 454.500000 784 88.769250 764 2369 4 chr7D.!!$R3 1605
7 TraesCS7A01G392100 chr7D 501599685 501601166 1481 False 371.600000 1011 90.131750 724 2028 4 chr7D.!!$F4 1304
8 TraesCS7A01G392100 chr7B 531222031 531222604 573 True 715.000000 715 89.310000 763 1335 1 chr7B.!!$R1 572
9 TraesCS7A01G392100 chr7B 531177800 531180735 2935 False 631.000000 833 84.700000 11 1602 2 chr7B.!!$F3 1591
10 TraesCS7A01G392100 chr7B 530869717 530870335 618 False 512.000000 512 82.390000 814 1421 1 chr7B.!!$F2 607

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
391 476 0.249447 TCGGCCGTAGCATGAAGATG 60.249 55.0 27.15 0.0 42.56 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 5035 1.143183 GCCGGCTATTTCCTCGACA 59.857 57.895 22.15 0.0 0.0 4.35 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
57 66 2.802816 GCGCCATCACCAAGTAATCTAG 59.197 50.000 0.00 0.00 0.00 2.43
59 68 4.442706 CGCCATCACCAAGTAATCTAGTT 58.557 43.478 0.00 0.00 0.00 2.24
60 69 4.271049 CGCCATCACCAAGTAATCTAGTTG 59.729 45.833 0.00 0.00 38.52 3.16
62 71 6.346096 GCCATCACCAAGTAATCTAGTTGTA 58.654 40.000 0.00 0.00 37.39 2.41
63 72 6.821665 GCCATCACCAAGTAATCTAGTTGTAA 59.178 38.462 0.00 0.00 37.39 2.41
64 73 7.499232 GCCATCACCAAGTAATCTAGTTGTAAT 59.501 37.037 0.00 0.00 37.39 1.89
65 74 9.046296 CCATCACCAAGTAATCTAGTTGTAATC 57.954 37.037 0.00 0.00 37.39 1.75
89 145 4.545706 TCGCCGGCCACATCATCC 62.546 66.667 23.46 0.00 0.00 3.51
106 162 2.753966 CCCGCGAGTGGATTTGCAG 61.754 63.158 8.23 0.00 0.00 4.41
107 163 2.034879 CCGCGAGTGGATTTGCAGT 61.035 57.895 8.23 0.00 0.00 4.40
217 280 1.234821 TGTGTGCGAAAGGAATGGAC 58.765 50.000 0.00 0.00 0.00 4.02
282 355 2.099263 ACCTGATCGTCAATTCGTCGAT 59.901 45.455 0.00 8.13 46.37 3.59
368 449 2.329379 CCCGTCTTTCTCGTCTCTTTG 58.671 52.381 0.00 0.00 0.00 2.77
369 450 1.721926 CCGTCTTTCTCGTCTCTTTGC 59.278 52.381 0.00 0.00 0.00 3.68
374 455 1.996292 TTCTCGTCTCTTTGCCATCG 58.004 50.000 0.00 0.00 0.00 3.84
391 476 0.249447 TCGGCCGTAGCATGAAGATG 60.249 55.000 27.15 0.00 42.56 2.90
463 565 5.118990 GGTCGATTTCTCATGAGAATCCAA 58.881 41.667 33.02 21.29 45.78 3.53
497 2517 3.181487 GCACTGTCTTCTTTTCTTTGCCA 60.181 43.478 0.00 0.00 0.00 4.92
501 2521 6.368516 CACTGTCTTCTTTTCTTTGCCAAAAA 59.631 34.615 0.00 0.00 0.00 1.94
609 2699 0.605589 TCTCGAGTGTCCGCTTCTCA 60.606 55.000 13.13 0.00 0.00 3.27
635 2725 4.344679 TCACCCACAGATTTTTGCAGAAAT 59.655 37.500 14.55 14.55 32.16 2.17
640 2730 5.107375 CCACAGATTTTTGCAGAAATTTCCG 60.107 40.000 15.62 5.78 29.75 4.30
722 2859 0.776080 AAACCAGGTCCCACCATCCT 60.776 55.000 0.00 0.00 41.95 3.24
837 4036 2.423577 GCCACCTATAAATACCGCCTG 58.576 52.381 0.00 0.00 0.00 4.85
929 4160 1.375268 GCCCACACACAGAGAGAGC 60.375 63.158 0.00 0.00 0.00 4.09
934 4165 2.224137 CCACACACAGAGAGAGCAAGAA 60.224 50.000 0.00 0.00 0.00 2.52
935 4166 3.461061 CACACACAGAGAGAGCAAGAAA 58.539 45.455 0.00 0.00 0.00 2.52
936 4167 3.247173 CACACACAGAGAGAGCAAGAAAC 59.753 47.826 0.00 0.00 0.00 2.78
938 4169 3.873361 CACACAGAGAGAGCAAGAAACAA 59.127 43.478 0.00 0.00 0.00 2.83
1012 4530 1.143305 GTTCATCATGAGGCCGATCG 58.857 55.000 8.51 8.51 0.00 3.69
1088 4621 4.778143 GCACCCGGCGTTCTGGAT 62.778 66.667 6.01 0.00 41.45 3.41
1095 4628 2.434185 GCGTTCTGGATGACGCCA 60.434 61.111 9.47 0.00 44.62 5.69
1271 4804 2.432628 GCCCAAGGTCGTCGTCAG 60.433 66.667 0.00 0.00 0.00 3.51
1334 4876 2.355481 GTTCGCGTTCCCTGACGT 60.355 61.111 5.77 0.00 44.50 4.34
1492 5044 7.790027 ACTAGTAGTAGTATCTTGTCGAGGAA 58.210 38.462 8.55 0.00 37.76 3.36
1532 5144 3.366781 CGTGAGCTGAGATCTGTGAAAGA 60.367 47.826 0.00 0.00 39.94 2.52
1538 5150 4.571580 GCTGAGATCTGTGAAAGAGAATGG 59.428 45.833 0.00 0.00 40.81 3.16
1548 5160 3.244561 TGAAAGAGAATGGAGTTTCGGCT 60.245 43.478 0.00 0.00 32.58 5.52
1578 5193 1.181098 TTGCTTTTGCCTGCTCTCCC 61.181 55.000 0.00 0.00 46.87 4.30
1639 5809 1.793353 CGTCATGCTGAGACTCTGTCG 60.793 57.143 10.64 3.56 37.67 4.35
1640 5810 1.470494 GTCATGCTGAGACTCTGTCGA 59.530 52.381 10.64 3.17 37.67 4.20
1702 5872 6.870965 GCATTAACCACAAACCATCAACAATA 59.129 34.615 0.00 0.00 0.00 1.90
1704 5874 9.434420 CATTAACCACAAACCATCAACAATAAT 57.566 29.630 0.00 0.00 0.00 1.28
1751 5921 1.609072 CAGATTGATCTGCTGGCATGG 59.391 52.381 7.97 0.00 46.63 3.66
1752 5922 0.314302 GATTGATCTGCTGGCATGGC 59.686 55.000 13.29 13.29 0.00 4.40
1753 5923 0.396556 ATTGATCTGCTGGCATGGCA 60.397 50.000 21.97 21.97 38.10 4.92
1786 5964 4.390603 AGCATTACGAGTTTGTGCGAAATA 59.609 37.500 0.00 0.00 40.54 1.40
2282 6802 4.407296 AGAGGTGTTCTTCTGTTCTTGACT 59.593 41.667 0.00 0.00 29.61 3.41
2350 6870 3.141398 GTGAGACATGCTTGAGACCAAA 58.859 45.455 6.60 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 66 4.142966 GGCCGGCGAAATATAGATTACAAC 60.143 45.833 22.54 0.00 0.00 3.32
59 68 3.007074 TGGCCGGCGAAATATAGATTACA 59.993 43.478 22.54 4.02 0.00 2.41
60 69 3.370061 GTGGCCGGCGAAATATAGATTAC 59.630 47.826 22.54 0.89 0.00 1.89
62 71 2.224426 TGTGGCCGGCGAAATATAGATT 60.224 45.455 22.54 0.00 0.00 2.40
63 72 1.346395 TGTGGCCGGCGAAATATAGAT 59.654 47.619 22.54 0.00 0.00 1.98
64 73 0.753867 TGTGGCCGGCGAAATATAGA 59.246 50.000 22.54 0.00 0.00 1.98
65 74 1.732259 GATGTGGCCGGCGAAATATAG 59.268 52.381 22.54 0.00 0.00 1.31
68 77 0.179032 ATGATGTGGCCGGCGAAATA 60.179 50.000 22.54 7.37 0.00 1.40
69 78 1.447317 GATGATGTGGCCGGCGAAAT 61.447 55.000 22.54 18.62 0.00 2.17
71 80 2.513666 GATGATGTGGCCGGCGAA 60.514 61.111 22.54 8.64 0.00 4.70
89 145 2.034879 ACTGCAAATCCACTCGCGG 61.035 57.895 6.13 0.00 36.79 6.46
106 162 2.030805 GTCCAGCTTTTGACATGACCAC 60.031 50.000 0.00 0.00 0.00 4.16
107 163 2.229792 GTCCAGCTTTTGACATGACCA 58.770 47.619 0.00 0.00 0.00 4.02
169 227 8.402472 CGAAATATAGAAGGCTAGAGATCGATT 58.598 37.037 0.00 0.00 34.49 3.34
204 267 1.519408 AACACCGTCCATTCCTTTCG 58.481 50.000 0.00 0.00 0.00 3.46
206 269 2.884639 CAGAAACACCGTCCATTCCTTT 59.115 45.455 0.00 0.00 0.00 3.11
217 280 1.948104 TGGTCAAGTCAGAAACACCG 58.052 50.000 0.00 0.00 0.00 4.94
330 411 1.267121 GGGAAAAGGGAGAAAAGGGC 58.733 55.000 0.00 0.00 0.00 5.19
331 412 1.891011 CGGGGAAAAGGGAGAAAAGGG 60.891 57.143 0.00 0.00 0.00 3.95
369 450 1.224069 CTTCATGCTACGGCCGATGG 61.224 60.000 35.90 21.14 37.74 3.51
374 455 0.940126 CACATCTTCATGCTACGGCC 59.060 55.000 0.00 0.00 37.74 6.13
478 2498 6.966435 TTTTTGGCAAAGAAAAGAAGACAG 57.034 33.333 13.04 0.00 0.00 3.51
501 2521 8.310671 GCCATATGCAAATCAAACGCATGTTT 62.311 38.462 6.37 0.00 45.58 2.83
502 2522 4.567558 CCATATGCAAATCAAACGCATGTT 59.432 37.500 6.37 0.00 45.58 2.71
509 2566 5.520376 ACCTAGCCATATGCAAATCAAAC 57.480 39.130 0.00 0.00 44.83 2.93
521 2578 4.345257 GGAGATTCAGTGAACCTAGCCATA 59.655 45.833 7.96 0.00 0.00 2.74
609 2699 4.344679 TCTGCAAAAATCTGTGGGTGAAAT 59.655 37.500 0.00 0.00 0.00 2.17
635 2725 5.246656 TGTGACTTATCTAAGGTTCCGGAAA 59.753 40.000 20.79 1.68 37.62 3.13
640 2730 8.794335 AATTTCTGTGACTTATCTAAGGTTCC 57.206 34.615 2.29 0.00 37.62 3.62
837 4036 2.851588 GGAGAGGATGGGGGAGGC 60.852 72.222 0.00 0.00 0.00 4.70
846 4045 1.643286 TCTGACTGAGTGGGAGAGGAT 59.357 52.381 0.00 0.00 0.00 3.24
929 4160 7.559590 TCTCTTCCTCTTTCTTTGTTTCTTG 57.440 36.000 0.00 0.00 0.00 3.02
934 4165 8.581253 TTTCTTTCTCTTCCTCTTTCTTTGTT 57.419 30.769 0.00 0.00 0.00 2.83
935 4166 8.049721 TCTTTCTTTCTCTTCCTCTTTCTTTGT 58.950 33.333 0.00 0.00 0.00 2.83
936 4167 8.443953 TCTTTCTTTCTCTTCCTCTTTCTTTG 57.556 34.615 0.00 0.00 0.00 2.77
938 4169 7.223584 CCTCTTTCTTTCTCTTCCTCTTTCTT 58.776 38.462 0.00 0.00 0.00 2.52
1095 4628 1.556564 CGATGAAGATGTACGGCGTT 58.443 50.000 21.24 0.00 0.00 4.84
1415 4965 9.565213 CCTAGAAATCTGATTGATGAACAAAAC 57.435 33.333 3.22 0.00 42.03 2.43
1468 5020 8.659925 TTTCCTCGACAAGATACTACTACTAG 57.340 38.462 0.00 0.00 0.00 2.57
1483 5035 1.143183 GCCGGCTATTTCCTCGACA 59.857 57.895 22.15 0.00 0.00 4.35
1532 5144 2.029918 GCAAAAGCCGAAACTCCATTCT 60.030 45.455 0.00 0.00 0.00 2.40
1538 5150 1.456923 GCAATGCAAAAGCCGAAACTC 59.543 47.619 0.00 0.00 0.00 3.01
1578 5193 3.680642 ATGCGAGTGGAAAATCGAATG 57.319 42.857 0.00 0.00 41.40 2.67
1640 5810 8.755977 ATCGTTGAGATTTACCACTACGAGAGT 61.756 40.741 0.00 0.00 41.47 3.24
1749 5919 4.697828 TCGTAATGCTTATCACTTTTGCCA 59.302 37.500 0.00 0.00 0.00 4.92
1750 5920 5.163754 ACTCGTAATGCTTATCACTTTTGCC 60.164 40.000 0.00 0.00 0.00 4.52
1751 5921 5.869350 ACTCGTAATGCTTATCACTTTTGC 58.131 37.500 0.00 0.00 0.00 3.68
1752 5922 7.803189 ACAAACTCGTAATGCTTATCACTTTTG 59.197 33.333 0.00 0.00 0.00 2.44
1753 5923 7.803189 CACAAACTCGTAATGCTTATCACTTTT 59.197 33.333 0.00 0.00 0.00 2.27
1786 5964 3.127548 CAGCAATCATGTAAAGCTCCGTT 59.872 43.478 0.00 0.00 32.35 4.44
2049 6568 5.060506 CAGTGGTAATCCAAGTACAACACA 58.939 41.667 0.00 0.00 46.15 3.72
2128 6647 4.350368 TTGACTGGAGTGCTAATCAACA 57.650 40.909 0.00 0.00 0.00 3.33
2190 6709 9.467258 GTAATTTCCCACTAAGTTAACCAAAAC 57.533 33.333 0.88 0.00 0.00 2.43
2234 6753 9.971922 CTGAAAATATGATATGGGAGGTTTTTC 57.028 33.333 0.00 0.00 33.42 2.29
2282 6802 9.342308 GGTCATGAAAGGATTAATGATCTTGTA 57.658 33.333 0.00 0.00 34.90 2.41
2350 6870 1.608336 TGTGTCCGAGACCCCGAAT 60.608 57.895 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.