Multiple sequence alignment - TraesCS7D01G270200

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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 TraesCS7D01G270200 chr7D 100.000 2559 0 0 1 2559 255967998 255970556 0.000000e+00 4726
1 TraesCS7D01G270200 chr7D 84.848 594 70 8 1 578 363901746 363901157 4.750000e-162 580
2 TraesCS7D01G270200 chr7B 93.483 1872 77 17 707 2559 234590026 234591871 0.000000e+00 2739
3 TraesCS7D01G270200 chr7B 86.050 595 64 7 1 578 234520567 234521159 2.800000e-174 621
4 TraesCS7D01G270200 chr7B 83.866 595 75 6 1 578 323413772 323413182 4.810000e-152 547
5 TraesCS7D01G270200 chr7B 84.553 492 61 7 101 578 323445527 323445037 8.290000e-130 473
6 TraesCS7D01G270200 chr7A 94.190 1136 50 10 611 1739 275915759 275916885 0.000000e+00 1718
7 TraesCS7D01G270200 chr7A 92.737 537 37 2 1986 2522 275917046 275917580 0.000000e+00 774
8 TraesCS7D01G270200 chr7A 86.097 597 62 3 3 578 275914801 275915397 7.780000e-175 623
9 TraesCS7D01G270200 chr7A 85.520 587 69 2 1 571 275848753 275849339 1.310000e-167 599
10 TraesCS7D01G270200 chr7A 84.304 395 40 7 1 376 393487668 393488059 1.450000e-97 366
11 TraesCS7D01G270200 chr5B 84.808 599 70 11 1 578 197206919 197206321 1.320000e-162 582
12 TraesCS7D01G270200 chr5D 84.281 598 70 8 1 578 192534485 192535078 1.720000e-156 562
13 TraesCS7D01G270200 chr5D 81.538 585 92 2 3 571 155807665 155807081 3.860000e-128 468
14 TraesCS7D01G270200 chr5D 82.992 488 62 10 3 472 415311898 415312382 3.040000e-114 422
15 TraesCS7D01G270200 chr3D 83.959 586 74 9 10 578 133220355 133219773 6.230000e-151 544
16 TraesCS7D01G270200 chr1B 83.305 593 72 13 3 578 422976143 422975561 2.920000e-144 521
17 TraesCS7D01G270200 chr4D 81.664 589 74 19 3 571 224238956 224238382 2.320000e-125 459
18 TraesCS7D01G270200 chr3B 79.417 583 92 20 6 572 339828522 339829092 1.110000e-103 387


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 TraesCS7D01G270200 chr7D 255967998 255970556 2558 False 4726.000000 4726 100.000 1 2559 1 chr7D.!!$F1 2558
1 TraesCS7D01G270200 chr7D 363901157 363901746 589 True 580.000000 580 84.848 1 578 1 chr7D.!!$R1 577
2 TraesCS7D01G270200 chr7B 234590026 234591871 1845 False 2739.000000 2739 93.483 707 2559 1 chr7B.!!$F2 1852
3 TraesCS7D01G270200 chr7B 234520567 234521159 592 False 621.000000 621 86.050 1 578 1 chr7B.!!$F1 577
4 TraesCS7D01G270200 chr7B 323413182 323413772 590 True 547.000000 547 83.866 1 578 1 chr7B.!!$R1 577
5 TraesCS7D01G270200 chr7A 275914801 275917580 2779 False 1038.333333 1718 91.008 3 2522 3 chr7A.!!$F3 2519
6 TraesCS7D01G270200 chr7A 275848753 275849339 586 False 599.000000 599 85.520 1 571 1 chr7A.!!$F1 570
7 TraesCS7D01G270200 chr5B 197206321 197206919 598 True 582.000000 582 84.808 1 578 1 chr5B.!!$R1 577
8 TraesCS7D01G270200 chr5D 192534485 192535078 593 False 562.000000 562 84.281 1 578 1 chr5D.!!$F1 577
9 TraesCS7D01G270200 chr5D 155807081 155807665 584 True 468.000000 468 81.538 3 571 1 chr5D.!!$R1 568
10 TraesCS7D01G270200 chr3D 133219773 133220355 582 True 544.000000 544 83.959 10 578 1 chr3D.!!$R1 568
11 TraesCS7D01G270200 chr1B 422975561 422976143 582 True 521.000000 521 83.305 3 578 1 chr1B.!!$R1 575
12 TraesCS7D01G270200 chr4D 224238382 224238956 574 True 459.000000 459 81.664 3 571 1 chr4D.!!$R1 568
13 TraesCS7D01G270200 chr3B 339828522 339829092 570 False 387.000000 387 79.417 6 572 1 chr3B.!!$F1 566

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
361 389 1.948834 CCTTTGTATGCGCCATCATCA 59.051 47.619 4.18 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1760 2146 0.245539 TAGTGCTGGAAGGTGCGTAC 59.754 55.0 0.0 0.0 0.0 3.67 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
234 247 1.993956 AAATAAGGTGGTGCAGCACA 58.006 45.000 40.33 26.19 35.86 4.57
301 329 2.291735 TGGATGTCATCATGGTGGCTTT 60.292 45.455 12.63 0.00 34.06 3.51
347 375 4.146745 ACTACGTTCTTGTTCCCTTTGT 57.853 40.909 0.00 0.00 0.00 2.83
361 389 1.948834 CCTTTGTATGCGCCATCATCA 59.051 47.619 4.18 0.00 0.00 3.07
376 404 5.007682 CCATCATCACCATGCTTGATCATA 58.992 41.667 0.00 0.00 30.98 2.15
380 408 3.721035 TCACCATGCTTGATCATACTCG 58.279 45.455 0.00 0.00 0.00 4.18
403 431 5.817296 CGAATGTTCATCCTTCTTGTCCATA 59.183 40.000 0.00 0.00 0.00 2.74
434 462 8.553459 TCCTTCATTTGTAAGCAAAACAAAAA 57.447 26.923 13.10 5.80 46.59 1.94
551 596 7.002879 TCTAGTAGTTGGTCCAGTATGTATCC 58.997 42.308 0.00 0.00 0.00 2.59
578 623 4.146564 GGGTTGTGGGTGTAATTGTAGTT 58.853 43.478 0.00 0.00 0.00 2.24
580 625 4.022676 GGTTGTGGGTGTAATTGTAGTTGG 60.023 45.833 0.00 0.00 0.00 3.77
582 627 3.138653 TGTGGGTGTAATTGTAGTTGGGT 59.861 43.478 0.00 0.00 0.00 4.51
583 628 3.504520 GTGGGTGTAATTGTAGTTGGGTG 59.495 47.826 0.00 0.00 0.00 4.61
584 629 3.138653 TGGGTGTAATTGTAGTTGGGTGT 59.861 43.478 0.00 0.00 0.00 4.16
585 630 4.350225 TGGGTGTAATTGTAGTTGGGTGTA 59.650 41.667 0.00 0.00 0.00 2.90
586 631 5.163120 TGGGTGTAATTGTAGTTGGGTGTAA 60.163 40.000 0.00 0.00 0.00 2.41
587 632 5.769162 GGGTGTAATTGTAGTTGGGTGTAAA 59.231 40.000 0.00 0.00 0.00 2.01
588 633 6.434965 GGGTGTAATTGTAGTTGGGTGTAAAT 59.565 38.462 0.00 0.00 0.00 1.40
589 634 7.039574 GGGTGTAATTGTAGTTGGGTGTAAATT 60.040 37.037 0.00 0.00 0.00 1.82
590 635 8.361889 GGTGTAATTGTAGTTGGGTGTAAATTT 58.638 33.333 0.00 0.00 0.00 1.82
991 1367 4.081365 GCCTTCCAAGTTCTACTAGCTCTT 60.081 45.833 0.00 0.00 0.00 2.85
1410 1786 2.361610 CCCTCCCGCTGCAACATT 60.362 61.111 0.00 0.00 0.00 2.71
1442 1820 3.981308 CTGTAAGCCCACAACCCG 58.019 61.111 0.00 0.00 0.00 5.28
1495 1881 4.021104 TCACTACTACTGCTTGTTCATGCT 60.021 41.667 10.95 0.00 0.00 3.79
1531 1917 8.316640 TCTAAGCTTGATTCTGTCTCTTTTTC 57.683 34.615 9.86 0.00 0.00 2.29
1560 1946 4.626081 AACGGCAGCGGCTTGAGT 62.626 61.111 9.17 0.00 40.87 3.41
1584 1970 2.833631 ACGAAGAAACGATCCAGGTT 57.166 45.000 0.00 0.00 37.03 3.50
1611 1997 6.536582 CAGAGTGACTAATAATGAAGGTGGTG 59.463 42.308 0.00 0.00 0.00 4.17
1654 2040 2.992689 TGCCTCTTCACCGCCGTA 60.993 61.111 0.00 0.00 0.00 4.02
1658 2044 1.472026 GCCTCTTCACCGCCGTATTAA 60.472 52.381 0.00 0.00 0.00 1.40
1691 2077 1.109920 AGTCTGTCGTGTCCTGCTGT 61.110 55.000 0.00 0.00 0.00 4.40
1697 2083 2.641559 GTGTCCTGCTGTTGCTGC 59.358 61.111 0.00 0.00 40.48 5.25
1760 2146 1.933853 CGCTACCGATTTCCTTCCTTG 59.066 52.381 0.00 0.00 36.29 3.61
1763 2149 3.869832 GCTACCGATTTCCTTCCTTGTAC 59.130 47.826 0.00 0.00 0.00 2.90
1772 2158 1.439679 CTTCCTTGTACGCACCTTCC 58.560 55.000 0.00 0.00 0.00 3.46
1780 2166 1.134788 GTACGCACCTTCCAGCACTAT 60.135 52.381 0.00 0.00 0.00 2.12
1785 2171 2.540515 CACCTTCCAGCACTATGTACG 58.459 52.381 0.00 0.00 0.00 3.67
1835 2223 6.875948 TTTCTTCATTCAAACTCGATGGAA 57.124 33.333 0.00 0.00 0.00 3.53
1836 2224 7.452880 TTTCTTCATTCAAACTCGATGGAAT 57.547 32.000 0.00 0.00 0.00 3.01
1923 2328 5.885912 AGGTTGCCGTGTAGAAATATCAATT 59.114 36.000 0.00 0.00 0.00 2.32
2103 2511 9.739276 ATATCTCACAAAGAACCTTAACATGAA 57.261 29.630 0.00 0.00 37.61 2.57
2107 2515 6.262273 TCACAAAGAACCTTAACATGAAGTCC 59.738 38.462 0.00 0.00 0.00 3.85
2120 2528 1.864711 TGAAGTCCGCAAACTCGAAAG 59.135 47.619 0.00 0.00 0.00 2.62
2160 2568 6.417327 CATTAGCTTAGATCACAAAAGAGCG 58.583 40.000 0.00 0.00 34.09 5.03
2202 2615 2.300956 TGCCTAAAGTGGGATTTGCA 57.699 45.000 0.00 0.00 0.00 4.08
2261 2674 9.468532 GGATCATAAAACAAAAGAGGATAATGC 57.531 33.333 0.00 0.00 0.00 3.56
2265 2678 5.957842 AAACAAAAGAGGATAATGCGACA 57.042 34.783 0.00 0.00 0.00 4.35
2289 2702 2.181021 GACGCGGAGGTTCACGAT 59.819 61.111 12.47 0.00 0.00 3.73
2306 2719 6.476243 TCACGATAAACCTTGCTAACTTTC 57.524 37.500 0.00 0.00 0.00 2.62
2359 2772 0.740737 GAATCCCCAGTTGAATGCCG 59.259 55.000 0.00 0.00 0.00 5.69
2522 2935 8.508875 TGCACATCATAGATTTGCATTAGTATG 58.491 33.333 14.70 0.00 38.25 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 47 5.048294 CCCTTAAGGCAACGTTTAGATTTGT 60.048 40.000 16.70 0.00 46.39 2.83
49 51 4.296621 ACCCTTAAGGCAACGTTTAGAT 57.703 40.909 16.70 0.00 46.39 1.98
211 224 2.697751 TGCTGCACCACCTTATTTTTGT 59.302 40.909 0.00 0.00 0.00 2.83
301 329 8.823818 GTTACTAGTGAAGTTTTCAGCACTTTA 58.176 33.333 5.39 0.00 41.01 1.85
347 375 1.525941 CATGGTGATGATGGCGCATA 58.474 50.000 10.83 0.00 0.00 3.14
361 389 4.406648 TTCGAGTATGATCAAGCATGGT 57.593 40.909 0.00 0.00 0.00 3.55
376 404 4.899502 ACAAGAAGGATGAACATTCGAGT 58.100 39.130 0.00 0.00 43.00 4.18
380 408 6.825721 AGTATGGACAAGAAGGATGAACATTC 59.174 38.462 0.00 0.00 39.25 2.67
403 431 4.922206 TGCTTACAAATGAAGGATCCAGT 58.078 39.130 15.82 0.04 0.00 4.00
477 505 8.164070 ACCAGATACTTTCATTTCTTGGTAACT 58.836 33.333 0.00 0.00 37.61 2.24
498 534 2.745281 GCACGCCAACTAAATTACCAGA 59.255 45.455 0.00 0.00 0.00 3.86
533 574 2.159014 TGCGGATACATACTGGACCAAC 60.159 50.000 0.00 0.00 0.00 3.77
551 596 2.684192 TTACACCCACAACCCCTGCG 62.684 60.000 0.00 0.00 0.00 5.18
589 634 8.483758 TGGCCAGGTAATTTAGTTGTTTAAAAA 58.516 29.630 0.00 0.00 0.00 1.94
590 635 8.019656 TGGCCAGGTAATTTAGTTGTTTAAAA 57.980 30.769 0.00 0.00 0.00 1.52
592 637 7.784470 ATGGCCAGGTAATTTAGTTGTTTAA 57.216 32.000 13.05 0.00 0.00 1.52
593 638 7.784470 AATGGCCAGGTAATTTAGTTGTTTA 57.216 32.000 13.05 0.00 0.00 2.01
594 639 6.680148 AATGGCCAGGTAATTTAGTTGTTT 57.320 33.333 13.05 0.00 0.00 2.83
596 641 6.680148 AAAATGGCCAGGTAATTTAGTTGT 57.320 33.333 13.05 0.00 0.00 3.32
648 1023 6.141211 CAGTCTTGAAAAATGTTCATCACGTG 59.859 38.462 9.94 9.94 0.00 4.49
1029 1405 7.596248 GCTATGGTATTTATACGGAGTTTTCGA 59.404 37.037 0.00 0.00 37.78 3.71
1069 1445 3.379445 GCTGGCTGGCTGTTGCAT 61.379 61.111 9.69 0.00 41.91 3.96
1098 1474 0.685097 TCAAACGCTGGAGTAGGCTT 59.315 50.000 0.00 0.00 0.00 4.35
1103 1479 1.544691 GTCCTCTCAAACGCTGGAGTA 59.455 52.381 0.00 0.00 32.93 2.59
1106 1482 0.756294 TTGTCCTCTCAAACGCTGGA 59.244 50.000 0.00 0.00 0.00 3.86
1410 1786 3.466836 CTTACAGCAGTTGACTTGTCCA 58.533 45.455 0.00 0.00 0.00 4.02
1442 1820 2.691526 TGAAGAAGGAATGATGCATGGC 59.308 45.455 2.46 0.00 0.00 4.40
1473 1857 4.248859 AGCATGAACAAGCAGTAGTAGTG 58.751 43.478 0.00 0.17 0.00 2.74
1479 1863 3.138884 TGGAAGCATGAACAAGCAGTA 57.861 42.857 0.00 0.00 0.00 2.74
1490 1876 5.776744 AGCTTAGAAAACTTTGGAAGCATG 58.223 37.500 15.08 0.00 41.34 4.06
1495 1881 8.137437 CAGAATCAAGCTTAGAAAACTTTGGAA 58.863 33.333 0.00 0.00 0.00 3.53
1531 1917 3.443045 GCCGTTCATGCACAGGGG 61.443 66.667 0.00 0.00 0.00 4.79
1560 1946 1.270274 TGGATCGTTTCTTCGTTCCGA 59.730 47.619 10.23 0.00 46.40 4.55
1578 1964 7.782049 TCATTATTAGTCACTCTGTAACCTGG 58.218 38.462 0.00 0.00 0.00 4.45
1581 1967 8.258708 ACCTTCATTATTAGTCACTCTGTAACC 58.741 37.037 0.00 0.00 0.00 2.85
1584 1970 7.399191 ACCACCTTCATTATTAGTCACTCTGTA 59.601 37.037 0.00 0.00 0.00 2.74
1611 1997 2.712077 CGCAACAACGGCAGAAATC 58.288 52.632 0.00 0.00 0.00 2.17
1654 2040 7.272037 ACAGACTGGACAAACGAAAATTAAT 57.728 32.000 7.51 0.00 0.00 1.40
1658 2044 3.247648 CGACAGACTGGACAAACGAAAAT 59.752 43.478 7.51 0.00 0.00 1.82
1697 2083 5.937165 TTTTATTAACGTGTCGAGATCGG 57.063 39.130 1.91 0.00 40.29 4.18
1741 2127 2.987232 ACAAGGAAGGAAATCGGTAGC 58.013 47.619 0.00 0.00 0.00 3.58
1760 2146 0.245539 TAGTGCTGGAAGGTGCGTAC 59.754 55.000 0.00 0.00 0.00 3.67
1763 2149 0.391661 ACATAGTGCTGGAAGGTGCG 60.392 55.000 0.00 0.00 0.00 5.34
1780 2166 4.376615 GCTTAAAGTGAAATCGCACGTACA 60.377 41.667 0.00 0.00 43.42 2.90
1785 2171 3.408150 CGAGCTTAAAGTGAAATCGCAC 58.592 45.455 0.00 0.00 39.05 5.34
2005 2412 0.327924 CCCAACCTGATGTAGTGGCA 59.672 55.000 0.00 0.00 0.00 4.92
2103 2511 1.202486 TGTCTTTCGAGTTTGCGGACT 60.202 47.619 0.00 0.00 0.00 3.85
2107 2515 2.734606 TGGTATGTCTTTCGAGTTTGCG 59.265 45.455 0.00 0.00 0.00 4.85
2120 2528 4.763793 AGCTAATGGATTGCATGGTATGTC 59.236 41.667 0.00 0.00 0.00 3.06
2160 2568 5.139435 TGCAGTCAGGATGTATATACAGC 57.861 43.478 20.44 20.44 41.56 4.40
2202 2615 6.294508 GCAAGTTCCATTATGTACTTGGTGTT 60.295 38.462 24.96 1.42 44.66 3.32
2261 2674 1.464429 CTCCGCGTCGAGAAATGTCG 61.464 60.000 4.92 0.00 41.51 4.35
2265 2678 0.458025 GAACCTCCGCGTCGAGAAAT 60.458 55.000 13.15 0.25 30.97 2.17
2289 2702 6.547880 TGTTGATGGAAAGTTAGCAAGGTTTA 59.452 34.615 0.00 0.00 0.00 2.01
2306 2719 9.987272 TTACTTCTATCTGTCATATGTTGATGG 57.013 33.333 1.90 7.32 36.54 3.51
2359 2772 9.262358 GATAGTGTGAAGGATTTAGTAATGGAC 57.738 37.037 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.