Multiple sequence alignment - TraesCS4D01G219800

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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 TraesCS4D01G219800 chr4D 100.000 3130 0 0 1 3130 375118024 375121153 0.000000e+00 5781
1 TraesCS4D01G219800 chr4B 92.657 2492 124 28 656 3130 462211271 462213720 0.000000e+00 3533
2 TraesCS4D01G219800 chr4A 92.960 1946 86 26 619 2540 89449553 89447635 0.000000e+00 2787
3 TraesCS4D01G219800 chr4A 88.156 591 12 13 2524 3084 89447585 89447023 0.000000e+00 651
4 TraesCS4D01G219800 chr3D 90.563 604 46 6 1 595 495167909 495167308 0.000000e+00 789
5 TraesCS4D01G219800 chr5D 90.280 607 46 8 1 596 385949770 385950374 0.000000e+00 782
6 TraesCS4D01G219800 chr5D 88.742 604 55 7 1 595 255084282 255083683 0.000000e+00 726
7 TraesCS4D01G219800 chr5D 88.342 609 59 5 1 598 545282740 545282133 0.000000e+00 721
8 TraesCS4D01G219800 chr5D 83.594 256 35 5 2872 3126 69100013 69099764 1.880000e-57 233
9 TraesCS4D01G219800 chr3A 89.439 606 53 6 1 596 523610620 523610016 0.000000e+00 754
10 TraesCS4D01G219800 chr1D 89.055 603 54 7 3 595 289773357 289773957 0.000000e+00 737
11 TraesCS4D01G219800 chr1D 88.487 608 56 9 1 596 37440310 37440915 0.000000e+00 723
12 TraesCS4D01G219800 chr6B 88.926 605 55 7 1 595 216349016 216348414 0.000000e+00 736
13 TraesCS4D01G219800 chr1B 88.614 606 57 6 1 595 216105102 216104498 0.000000e+00 726
14 TraesCS4D01G219800 chr5A 83.203 256 36 5 2872 3126 59704508 59704259 8.730000e-56 228


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 TraesCS4D01G219800 chr4D 375118024 375121153 3129 False 5781 5781 100.000 1 3130 1 chr4D.!!$F1 3129
1 TraesCS4D01G219800 chr4B 462211271 462213720 2449 False 3533 3533 92.657 656 3130 1 chr4B.!!$F1 2474
2 TraesCS4D01G219800 chr4A 89447023 89449553 2530 True 1719 2787 90.558 619 3084 2 chr4A.!!$R1 2465
3 TraesCS4D01G219800 chr3D 495167308 495167909 601 True 789 789 90.563 1 595 1 chr3D.!!$R1 594
4 TraesCS4D01G219800 chr5D 385949770 385950374 604 False 782 782 90.280 1 596 1 chr5D.!!$F1 595
5 TraesCS4D01G219800 chr5D 255083683 255084282 599 True 726 726 88.742 1 595 1 chr5D.!!$R2 594
6 TraesCS4D01G219800 chr5D 545282133 545282740 607 True 721 721 88.342 1 598 1 chr5D.!!$R3 597
7 TraesCS4D01G219800 chr3A 523610016 523610620 604 True 754 754 89.439 1 596 1 chr3A.!!$R1 595
8 TraesCS4D01G219800 chr1D 289773357 289773957 600 False 737 737 89.055 3 595 1 chr1D.!!$F2 592
9 TraesCS4D01G219800 chr1D 37440310 37440915 605 False 723 723 88.487 1 596 1 chr1D.!!$F1 595
10 TraesCS4D01G219800 chr6B 216348414 216349016 602 True 736 736 88.926 1 595 1 chr6B.!!$R1 594
11 TraesCS4D01G219800 chr1B 216104498 216105102 604 True 726 726 88.614 1 595 1 chr1B.!!$R1 594

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
991 1026 0.038709 GGCCAACGTGCAAAAGCATA 60.039 50.000 0.00 0.0 0.0 3.14 F
1320 1359 1.743252 GCTCTACTGCAAGCGCCTT 60.743 57.895 2.29 0.0 37.6 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1913 1956 0.389166 GCTCCTGACTGTCTGGAACG 60.389 60.0 28.85 21.55 42.72 3.95 R
2325 2377 0.536006 GGCCATGGGATACAGCTGAC 60.536 60.0 23.35 11.02 39.74 3.51 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
95 96 2.580589 GCGTGATTTTGTGTTATGCGT 58.419 42.857 0.00 0.00 0.00 5.24
121 122 7.687941 AATCAACTCATACTTTTGTGGGTAG 57.312 36.000 0.00 0.00 0.00 3.18
267 272 8.538856 GTGTTGATTGATTTGAAAAATCGTTGA 58.461 29.630 7.90 0.00 33.83 3.18
270 276 7.432869 TGATTGATTTGAAAAATCGTTGACCT 58.567 30.769 7.90 0.00 33.83 3.85
275 281 4.661993 TGAAAAATCGTTGACCTGATCG 57.338 40.909 0.00 0.00 0.00 3.69
391 400 8.210265 GGAGAGATCCTTGAGAAATTATTGACT 58.790 37.037 0.00 0.00 0.00 3.41
428 444 5.593095 GGTGACCAAGTTCTAAAAAGACCTT 59.407 40.000 0.00 0.00 0.00 3.50
509 531 7.322664 AGAGCTTTGAAAAATTGTTGACTTGA 58.677 30.769 0.00 0.00 0.00 3.02
570 594 4.046286 TGATTGTGAGGCATTTTACCCT 57.954 40.909 0.00 0.00 0.00 4.34
572 596 4.462483 TGATTGTGAGGCATTTTACCCTTC 59.538 41.667 0.00 0.00 0.00 3.46
598 623 7.362142 CGGAGCTTAGTGATATAGTAGATGCAA 60.362 40.741 0.00 0.00 0.00 4.08
599 624 8.474025 GGAGCTTAGTGATATAGTAGATGCAAT 58.526 37.037 0.00 0.00 0.00 3.56
600 625 9.299963 GAGCTTAGTGATATAGTAGATGCAATG 57.700 37.037 0.00 0.00 0.00 2.82
601 626 8.256605 AGCTTAGTGATATAGTAGATGCAATGG 58.743 37.037 0.00 0.00 0.00 3.16
602 627 8.253810 GCTTAGTGATATAGTAGATGCAATGGA 58.746 37.037 0.00 0.00 0.00 3.41
603 628 9.800433 CTTAGTGATATAGTAGATGCAATGGAG 57.200 37.037 0.00 0.00 0.00 3.86
604 629 6.638610 AGTGATATAGTAGATGCAATGGAGC 58.361 40.000 0.00 0.00 0.00 4.70
605 630 5.814705 GTGATATAGTAGATGCAATGGAGCC 59.185 44.000 0.00 0.00 0.00 4.70
606 631 2.820059 TAGTAGATGCAATGGAGCCG 57.180 50.000 0.00 0.00 0.00 5.52
607 632 0.107456 AGTAGATGCAATGGAGCCGG 59.893 55.000 0.00 0.00 0.00 6.13
608 633 0.886490 GTAGATGCAATGGAGCCGGG 60.886 60.000 2.18 0.00 0.00 5.73
609 634 2.055689 TAGATGCAATGGAGCCGGGG 62.056 60.000 2.18 0.00 0.00 5.73
707 732 9.804547 TTTGCTCGCAATATTTTAAAAACATTC 57.195 25.926 4.44 2.74 35.70 2.67
795 820 2.484264 ACACGAGCCTACAAATTCTTGC 59.516 45.455 0.00 0.00 35.84 4.01
991 1026 0.038709 GGCCAACGTGCAAAAGCATA 60.039 50.000 0.00 0.00 0.00 3.14
1156 1191 4.671590 TCGTCCTCGGCCACCTCA 62.672 66.667 2.24 0.00 37.69 3.86
1320 1359 1.743252 GCTCTACTGCAAGCGCCTT 60.743 57.895 2.29 0.00 37.60 4.35
1357 1396 4.466370 AGCAGTTAGACAAGCCACAGTATA 59.534 41.667 0.00 0.00 0.00 1.47
1361 1400 6.818644 CAGTTAGACAAGCCACAGTATATTGT 59.181 38.462 0.00 0.00 36.83 2.71
1653 1695 3.194861 TGATCATTTTTAGCGGGTCTCG 58.805 45.455 0.00 0.00 42.76 4.04
1665 1707 2.167861 GGTCTCGTTGATCCGCAGC 61.168 63.158 0.00 0.00 0.00 5.25
1913 1956 0.310854 CCGAGGAAGGCAACAACAAC 59.689 55.000 0.00 0.00 41.41 3.32
1999 2042 1.207089 GTCGGACAATGACCATCCTCA 59.793 52.381 2.62 0.00 0.00 3.86
2086 2132 6.752285 TGATGGATCAGATGATGAGGTTAA 57.248 37.500 0.00 0.00 42.53 2.01
2090 2136 5.429762 TGGATCAGATGATGAGGTTAAAGGT 59.570 40.000 0.00 0.00 42.53 3.50
2096 2142 0.743345 ATGAGGTTAAAGGTCGGCGC 60.743 55.000 0.00 0.00 0.00 6.53
2181 2227 5.010314 TCCGGCTAGAAATGTAACGATATGT 59.990 40.000 0.00 0.00 0.00 2.29
2194 2240 0.383231 GATATGTGCAGCAGGGCAAC 59.617 55.000 0.00 0.00 46.93 4.17
2265 2312 7.435068 ACACATGTGTACTTTCAAACTATCC 57.565 36.000 29.66 0.00 42.90 2.59
2277 2326 9.295825 ACTTTCAAACTATCCAACAATATGTCA 57.704 29.630 0.00 0.00 0.00 3.58
2289 2338 9.725019 TCCAACAATATGTCAATATCCATCTAC 57.275 33.333 0.00 0.00 0.00 2.59
2298 2347 6.266330 TGTCAATATCCATCTACTCCAGTCAG 59.734 42.308 0.00 0.00 0.00 3.51
2313 2365 4.645136 TCCAGTCAGCTGTATCGTCTAAAT 59.355 41.667 14.67 0.00 41.02 1.40
2321 2373 6.258727 CAGCTGTATCGTCTAAATGGAAATGT 59.741 38.462 5.25 0.00 0.00 2.71
2337 2389 5.880332 TGGAAATGTTAAGTCAGCTGTATCC 59.120 40.000 14.67 3.39 0.00 2.59
2440 2492 1.449601 GGTCACCGCCGTTCATCAT 60.450 57.895 0.00 0.00 0.00 2.45
2483 2536 7.181485 AGTTTACAGTAACCACCATACCACTAT 59.819 37.037 0.00 0.00 0.00 2.12
2509 2562 9.391006 TGTTATCCAACCTATCTTTAATGTCAC 57.609 33.333 0.00 0.00 33.41 3.67
2581 2700 7.488150 GCTAGCAAACCAACAAATATTTACTCC 59.512 37.037 10.63 0.00 0.00 3.85
2601 2720 5.209818 TCCACGAGATCAGTACAAAAACT 57.790 39.130 0.00 0.00 0.00 2.66
2610 2729 8.045176 AGATCAGTACAAAAACTAAAGATGGC 57.955 34.615 0.00 0.00 0.00 4.40
2705 2852 4.877378 AAGATCATGGCAAGAAAAAGCA 57.123 36.364 0.00 0.00 0.00 3.91
2760 2908 6.928492 GGGTGATTTTGAATTTTCTTGCTACA 59.072 34.615 0.00 0.00 0.00 2.74
3067 3216 5.006386 CAGTCTAAGGCCTCAAGTCAAATT 58.994 41.667 5.23 0.00 0.00 1.82
3070 3219 2.222227 AGGCCTCAAGTCAAATTCCC 57.778 50.000 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.134287 CATCGTCTCCCCCATCCGT 61.134 63.158 0.00 0.00 0.00 4.69
76 77 6.521477 TGATTAACGCATAACACAAAATCACG 59.479 34.615 0.00 0.00 29.67 4.35
95 96 9.226606 CTACCCACAAAAGTATGAGTTGATTAA 57.773 33.333 0.00 0.00 0.00 1.40
121 122 2.457970 GTAGCCACCGACGTAGAAATC 58.542 52.381 0.00 0.00 0.00 2.17
198 202 0.617820 ACCCCGTGCATCCTCTTACT 60.618 55.000 0.00 0.00 0.00 2.24
207 211 2.435372 AACATATCAACCCCGTGCAT 57.565 45.000 0.00 0.00 0.00 3.96
267 272 4.196626 TGGTTTACGATTTCGATCAGGT 57.803 40.909 7.01 0.00 43.02 4.00
270 276 7.135089 TGAATTTGGTTTACGATTTCGATCA 57.865 32.000 7.01 0.00 43.02 2.92
320 326 6.049149 TCATACTCCCTAATTTTGAAGCTCG 58.951 40.000 0.00 0.00 0.00 5.03
391 400 3.694043 TGGTCACCTGATTTTGATCGA 57.306 42.857 0.00 0.00 0.00 3.59
453 469 9.862371 CCTTTATACTATACACTATGCTTCCTG 57.138 37.037 0.00 0.00 0.00 3.86
478 495 7.439056 TCAACAATTTTTCAAAGCTCTCATTCC 59.561 33.333 0.00 0.00 0.00 3.01
570 594 7.148222 GCATCTACTATATCACTAAGCTCCGAA 60.148 40.741 0.00 0.00 0.00 4.30
572 596 6.094186 TGCATCTACTATATCACTAAGCTCCG 59.906 42.308 0.00 0.00 0.00 4.63
601 626 3.987954 TTGATTTCGGCCCCGGCTC 62.988 63.158 6.90 2.55 41.60 4.70
602 627 3.995506 CTTGATTTCGGCCCCGGCT 62.996 63.158 6.90 0.00 41.60 5.52
603 628 2.879813 TACTTGATTTCGGCCCCGGC 62.880 60.000 6.90 0.00 40.25 6.13
604 629 1.093496 GTACTTGATTTCGGCCCCGG 61.093 60.000 6.90 0.00 40.25 5.73
605 630 0.107848 AGTACTTGATTTCGGCCCCG 60.108 55.000 0.00 0.00 41.35 5.73
606 631 2.169978 AGTAGTACTTGATTTCGGCCCC 59.830 50.000 0.00 0.00 0.00 5.80
607 632 3.118884 TGAGTAGTACTTGATTTCGGCCC 60.119 47.826 0.00 0.00 0.00 5.80
608 633 3.864003 GTGAGTAGTACTTGATTTCGGCC 59.136 47.826 0.00 0.00 0.00 6.13
609 634 4.745649 AGTGAGTAGTACTTGATTTCGGC 58.254 43.478 0.00 0.00 0.00 5.54
610 635 6.197364 AGAGTGAGTAGTACTTGATTTCGG 57.803 41.667 0.00 0.00 0.00 4.30
611 636 6.034044 GCAAGAGTGAGTAGTACTTGATTTCG 59.966 42.308 0.00 0.00 39.84 3.46
612 637 6.034044 CGCAAGAGTGAGTAGTACTTGATTTC 59.966 42.308 0.00 0.00 39.84 2.17
613 638 5.864474 CGCAAGAGTGAGTAGTACTTGATTT 59.136 40.000 0.00 0.00 39.84 2.17
614 639 5.047943 ACGCAAGAGTGAGTAGTACTTGATT 60.048 40.000 0.00 0.00 39.84 2.57
615 640 4.459685 ACGCAAGAGTGAGTAGTACTTGAT 59.540 41.667 0.00 0.00 39.84 2.57
616 641 3.819337 ACGCAAGAGTGAGTAGTACTTGA 59.181 43.478 0.00 0.00 39.84 3.02
617 642 3.914966 CACGCAAGAGTGAGTAGTACTTG 59.085 47.826 0.00 0.00 44.43 3.16
707 732 7.562640 TTATATGTCTTTCGCTAATGCTACG 57.437 36.000 0.00 0.00 36.97 3.51
777 802 1.401905 GGGCAAGAATTTGTAGGCTCG 59.598 52.381 0.00 0.00 36.65 5.03
983 1018 1.392589 CATGGCCGGACTATGCTTTT 58.607 50.000 9.82 0.00 29.73 2.27
991 1026 2.757124 GGAATCCCATGGCCGGACT 61.757 63.158 9.82 0.00 30.39 3.85
1320 1359 1.039785 ACTGCTCAGCCTGCTCGATA 61.040 55.000 0.00 0.00 0.00 2.92
1357 1396 1.180029 GTGATGAGGCAGGCAACAAT 58.820 50.000 0.00 0.00 41.41 2.71
1361 1400 2.747460 GCGTGATGAGGCAGGCAA 60.747 61.111 0.00 0.00 45.94 4.52
1417 1457 4.082026 AGCCCAAACAGAATAGCAATGTTC 60.082 41.667 0.00 0.00 36.18 3.18
1592 1632 3.080765 ATGGGGTCGACGATGCCA 61.081 61.111 9.92 0.00 0.00 4.92
1624 1664 7.781056 ACCCGCTAAAAATGATCAAATGTTAT 58.219 30.769 0.00 0.00 0.00 1.89
1625 1665 7.122055 AGACCCGCTAAAAATGATCAAATGTTA 59.878 33.333 0.00 0.00 0.00 2.41
1626 1666 6.036577 ACCCGCTAAAAATGATCAAATGTT 57.963 33.333 0.00 0.00 0.00 2.71
1641 1683 0.458669 GGATCAACGAGACCCGCTAA 59.541 55.000 0.00 0.00 43.32 3.09
1653 1695 2.440501 CATTTTACGCTGCGGATCAAC 58.559 47.619 26.95 0.00 0.00 3.18
1665 1707 3.125316 GCAGTTCCTCTGTCCATTTTACG 59.875 47.826 0.00 0.00 45.23 3.18
1862 1905 2.550180 GAGCTCAAAGAAGTCCACCAAC 59.450 50.000 9.40 0.00 0.00 3.77
1913 1956 0.389166 GCTCCTGACTGTCTGGAACG 60.389 60.000 28.85 21.55 42.72 3.95
1999 2042 4.079253 GGGTGTATTTGTTCCATGTGAGT 58.921 43.478 0.00 0.00 0.00 3.41
2096 2142 3.353836 CGCCACCACCTTCGGTTG 61.354 66.667 0.00 0.00 37.07 3.77
2194 2240 1.616620 GTGCACATGTACAAATGGCG 58.383 50.000 13.17 0.00 30.73 5.69
2276 2325 5.245751 AGCTGACTGGAGTAGATGGATATTG 59.754 44.000 0.00 0.00 0.00 1.90
2277 2326 5.245751 CAGCTGACTGGAGTAGATGGATATT 59.754 44.000 8.42 0.00 40.48 1.28
2298 2347 6.604735 ACATTTCCATTTAGACGATACAGC 57.395 37.500 0.00 0.00 0.00 4.40
2313 2365 5.880332 GGATACAGCTGACTTAACATTTCCA 59.120 40.000 23.35 0.00 0.00 3.53
2321 2373 3.433598 GCCATGGGATACAGCTGACTTAA 60.434 47.826 23.35 1.21 39.74 1.85
2325 2377 0.536006 GGCCATGGGATACAGCTGAC 60.536 60.000 23.35 11.02 39.74 3.51
2337 2389 1.227943 CACTATGGGTCGGCCATGG 60.228 63.158 9.07 7.63 36.17 3.66
2350 2402 6.659242 GGTTATATTGTAGCATTGGCCACTAT 59.341 38.462 3.88 0.00 42.56 2.12
2440 2492 9.725019 ACTGTAAACTACATCATCAAATCAAGA 57.275 29.630 0.00 0.00 38.15 3.02
2457 2509 5.308759 AGTGGTATGGTGGTTACTGTAAACT 59.691 40.000 15.93 3.34 0.00 2.66
2463 2516 5.353394 ACATAGTGGTATGGTGGTTACTG 57.647 43.478 0.00 0.00 40.53 2.74
2483 2536 9.391006 GTGACATTAAAGATAGGTTGGATAACA 57.609 33.333 0.00 0.00 38.58 2.41
2509 2562 5.457148 TGTTTACAAAAATACTTGCACAGCG 59.543 36.000 0.00 0.00 0.00 5.18
2581 2700 8.294341 TCTTTAGTTTTTGTACTGATCTCGTG 57.706 34.615 0.00 0.00 0.00 4.35
2621 2767 1.474855 GCCCCTGTGCATTTTTGTTGT 60.475 47.619 0.00 0.00 0.00 3.32
2705 2852 2.601367 AAATGCGGGCCTTGCAGT 60.601 55.556 23.83 20.06 46.98 4.40


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

AutoCloner maintained by Alex Coulton.