Multiple sequence alignment - TraesCS4B01G186600

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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 TraesCS4B01G186600 chr4B 100.000 2714 0 0 1 2714 406466555 406463842 0.000000e+00 5012.0
1 TraesCS4B01G186600 chr4A 94.141 1758 65 17 941 2684 144356367 144358100 0.000000e+00 2641.0
2 TraesCS4B01G186600 chr4A 86.556 662 57 10 1 632 144023720 144024379 0.000000e+00 701.0
3 TraesCS4B01G186600 chr4A 88.415 328 17 12 626 947 144355610 144355922 2.550000e-100 375.0
4 TraesCS4B01G186600 chr4A 100.000 30 0 0 2681 2710 678341627 678341598 3.780000e-04 56.5
5 TraesCS4B01G186600 chr5B 91.557 1374 75 17 1004 2357 700924388 700923036 0.000000e+00 1857.0
6 TraesCS4B01G186600 chr5B 86.930 329 23 1 2351 2679 700922922 700922614 4.300000e-93 351.0
7 TraesCS4B01G186600 chr5B 75.706 177 41 2 1316 1492 534639932 534640106 1.340000e-13 87.9
8 TraesCS4B01G186600 chr5B 75.141 177 42 2 1316 1492 534600493 534600667 6.230000e-12 82.4
9 TraesCS4B01G186600 chr4D 95.381 1169 25 8 799 1967 326981578 326980439 0.000000e+00 1832.0
10 TraesCS4B01G186600 chr4D 95.266 676 32 0 2009 2684 326980440 326979765 0.000000e+00 1072.0
11 TraesCS4B01G186600 chr4D 92.147 624 42 5 125 744 326983375 326982755 0.000000e+00 874.0
12 TraesCS4B01G186600 chr4D 94.059 101 6 0 1 101 327278068 327277968 1.300000e-33 154.0
13 TraesCS4B01G186600 chr4D 98.611 72 1 0 744 815 326981665 326981594 7.890000e-26 128.0
14 TraesCS4B01G186600 chr2A 91.095 1370 79 21 1004 2357 582969299 582967957 0.000000e+00 1814.0
15 TraesCS4B01G186600 chr2A 88.615 325 24 2 2355 2679 582967839 582967528 1.520000e-102 383.0
16 TraesCS4B01G186600 chr5D 73.091 275 59 12 1220 1492 439734018 439734279 1.730000e-12 84.2


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 TraesCS4B01G186600 chr4B 406463842 406466555 2713 True 5012.0 5012 100.00000 1 2714 1 chr4B.!!$R1 2713
1 TraesCS4B01G186600 chr4A 144355610 144358100 2490 False 1508.0 2641 91.27800 626 2684 2 chr4A.!!$F2 2058
2 TraesCS4B01G186600 chr4A 144023720 144024379 659 False 701.0 701 86.55600 1 632 1 chr4A.!!$F1 631
3 TraesCS4B01G186600 chr5B 700922614 700924388 1774 True 1104.0 1857 89.24350 1004 2679 2 chr5B.!!$R1 1675
4 TraesCS4B01G186600 chr4D 326979765 326983375 3610 True 976.5 1832 95.35125 125 2684 4 chr4D.!!$R2 2559
5 TraesCS4B01G186600 chr2A 582967528 582969299 1771 True 1098.5 1814 89.85500 1004 2679 2 chr2A.!!$R1 1675

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
75 76 0.250234 TTCAGGGCGGTGATGAAGAG 59.75 55.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2067 3708 0.460811 TGCTCTTGTAGGCATGCTCG 60.461 55.0 18.92 0.14 33.23 5.03 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
38 39 1.424493 CGAGGAAGACATCGCCTTGC 61.424 60.000 0.00 0.00 42.84 4.01
51 52 1.687612 CCTTGCTGGTCATCCCACT 59.312 57.895 0.00 0.00 38.72 4.00
53 54 1.171308 CTTGCTGGTCATCCCACTTG 58.829 55.000 0.00 0.00 38.72 3.16
75 76 0.250234 TTCAGGGCGGTGATGAAGAG 59.750 55.000 0.00 0.00 0.00 2.85
84 85 2.625314 CGGTGATGAAGAGATGGCTAGA 59.375 50.000 0.00 0.00 0.00 2.43
99 100 1.394618 CTAGACCTCAACCCTCCTCG 58.605 60.000 0.00 0.00 0.00 4.63
104 105 2.282958 TCAACCCTCCTCGCGTCT 60.283 61.111 5.77 0.00 0.00 4.18
105 106 1.878656 CTCAACCCTCCTCGCGTCTT 61.879 60.000 5.77 0.00 0.00 3.01
108 109 1.469335 AACCCTCCTCGCGTCTTCAA 61.469 55.000 5.77 0.00 0.00 2.69
174 188 3.650950 GTGCTTGGGAGGGGCTGA 61.651 66.667 0.00 0.00 0.00 4.26
201 215 1.153647 CTGGCGGCGTCACAAGATA 60.154 57.895 11.51 0.00 0.00 1.98
220 234 3.399181 CCCCTGGCGACCTGCTTA 61.399 66.667 0.00 0.00 45.43 3.09
375 389 5.513495 GTCTAGTCTGAACTTGTTAGCATCG 59.487 44.000 0.00 0.00 36.92 3.84
404 418 7.518370 CGTCTAAACTTGCTGTGAAACTGTATT 60.518 37.037 0.00 0.00 38.15 1.89
437 452 1.416243 TCAACACCCTAAGGTCGTGT 58.584 50.000 0.00 0.00 46.45 4.49
475 490 5.177696 GCCCTGCAGTCTTAAACTTATATCG 59.822 44.000 13.81 0.00 35.45 2.92
531 561 2.874086 TGACTGTTGCTCTTGTGTGATG 59.126 45.455 0.00 0.00 0.00 3.07
572 604 6.774656 TCTGATATGAAGTGCTACATCTGAGA 59.225 38.462 0.00 0.00 0.00 3.27
573 605 7.286316 TCTGATATGAAGTGCTACATCTGAGAA 59.714 37.037 0.00 0.00 0.00 2.87
602 634 4.148838 CCACTACATTTGAAAGGGGTGAA 58.851 43.478 15.39 0.00 0.00 3.18
661 693 6.128090 TGCTTTACATCTGCTCATTTCTGAAG 60.128 38.462 0.00 0.00 0.00 3.02
669 701 5.706833 TCTGCTCATTTCTGAAGCACAAATA 59.293 36.000 0.00 0.00 34.24 1.40
670 702 6.376299 TCTGCTCATTTCTGAAGCACAAATAT 59.624 34.615 0.00 0.00 34.24 1.28
855 2018 3.068873 GCTAGTCCAATGATTCGTCCTCT 59.931 47.826 0.00 0.00 0.00 3.69
859 2022 4.116238 GTCCAATGATTCGTCCTCTTCTC 58.884 47.826 0.00 0.00 0.00 2.87
860 2023 3.133003 TCCAATGATTCGTCCTCTTCTCC 59.867 47.826 0.00 0.00 0.00 3.71
861 2024 3.133721 CCAATGATTCGTCCTCTTCTCCT 59.866 47.826 0.00 0.00 0.00 3.69
862 2025 4.367450 CAATGATTCGTCCTCTTCTCCTC 58.633 47.826 0.00 0.00 0.00 3.71
863 2026 3.374042 TGATTCGTCCTCTTCTCCTCT 57.626 47.619 0.00 0.00 0.00 3.69
864 2027 3.283751 TGATTCGTCCTCTTCTCCTCTC 58.716 50.000 0.00 0.00 0.00 3.20
867 2030 1.065053 TCGTCCTCTTCTCCTCTCCTG 60.065 57.143 0.00 0.00 0.00 3.86
882 2045 2.651361 CTGCCTTGGTCGTCGACT 59.349 61.111 23.69 0.00 32.47 4.18
883 2046 1.444553 CTGCCTTGGTCGTCGACTC 60.445 63.158 23.69 14.63 32.47 3.36
884 2047 2.126031 GCCTTGGTCGTCGACTCC 60.126 66.667 23.69 15.67 32.47 3.85
885 2048 2.927580 GCCTTGGTCGTCGACTCCA 61.928 63.158 23.69 20.22 32.47 3.86
886 2049 1.663739 CCTTGGTCGTCGACTCCAA 59.336 57.895 27.71 27.71 38.65 3.53
888 2051 2.422303 TTGGTCGTCGACTCCAAGT 58.578 52.632 26.68 0.00 36.48 3.16
889 2052 0.313043 TTGGTCGTCGACTCCAAGTC 59.687 55.000 26.68 6.93 41.71 3.01
902 2065 0.460284 CCAAGTCTCCAACCGATCCG 60.460 60.000 0.00 0.00 0.00 4.18
946 2561 0.439985 CCGCATCATACACGCATAGC 59.560 55.000 0.00 0.00 0.00 2.97
1024 2639 4.069232 CGGAGGCTCGCAAGACCA 62.069 66.667 8.69 0.00 45.01 4.02
1994 3635 3.564225 CGTATTGGGATAAGGGTTTGCTC 59.436 47.826 0.00 0.00 0.00 4.26
2000 3641 3.201045 GGGATAAGGGTTTGCTCTCTTCT 59.799 47.826 0.00 0.00 0.00 2.85
2042 3683 3.817647 GACTTCAAAGATGAGTGCTTGGT 59.182 43.478 0.00 0.00 36.78 3.67
2070 3711 1.065401 TGCAAAAACAGAAGCACCGAG 59.935 47.619 0.00 0.00 31.05 4.63
2183 3825 4.942761 AGTTGAAACCAGCATCACAATT 57.057 36.364 0.00 0.00 0.00 2.32
2283 3928 4.311816 AGCACAAACTTTGGAACTGATG 57.688 40.909 6.47 0.00 34.12 3.07
2353 4120 4.898320 TGCAGAAGAAAGAATGCTGTCTA 58.102 39.130 0.00 0.00 37.75 2.59
2441 4220 5.692814 CAAATGCAGTTCATACATATCGGG 58.307 41.667 0.00 0.00 34.33 5.14
2462 4241 5.641209 CGGGCCAAAATATTGTTTCATTCAA 59.359 36.000 4.39 0.00 34.60 2.69
2634 4427 4.947388 TGCTGTGGGGTCAATATTAACTTC 59.053 41.667 0.00 0.00 0.00 3.01
2687 4480 9.349713 TGGATTAGCAGTACATAAAATTTAGGG 57.650 33.333 2.45 0.00 0.00 3.53
2688 4481 9.350951 GGATTAGCAGTACATAAAATTTAGGGT 57.649 33.333 2.45 1.05 0.00 4.34
2691 4484 7.865706 AGCAGTACATAAAATTTAGGGTCTG 57.134 36.000 14.49 14.49 0.00 3.51
2692 4485 7.402862 AGCAGTACATAAAATTTAGGGTCTGT 58.597 34.615 17.51 8.91 0.00 3.41
2693 4486 7.553044 AGCAGTACATAAAATTTAGGGTCTGTC 59.447 37.037 17.51 12.82 0.00 3.51
2694 4487 7.553044 GCAGTACATAAAATTTAGGGTCTGTCT 59.447 37.037 17.51 5.19 0.00 3.41
2697 4490 9.543783 GTACATAAAATTTAGGGTCTGTCTAGG 57.456 37.037 2.45 0.00 0.00 3.02
2698 4491 8.388656 ACATAAAATTTAGGGTCTGTCTAGGA 57.611 34.615 2.45 0.00 0.00 2.94
2699 4492 8.265764 ACATAAAATTTAGGGTCTGTCTAGGAC 58.734 37.037 2.45 0.00 0.00 3.85
2700 4493 6.697641 AAAATTTAGGGTCTGTCTAGGACA 57.302 37.500 0.00 0.43 40.50 4.02
2701 4494 5.678955 AATTTAGGGTCTGTCTAGGACAC 57.321 43.478 0.00 0.00 37.67 3.67
2702 4495 3.820195 TTAGGGTCTGTCTAGGACACA 57.180 47.619 3.18 0.00 39.36 3.72
2703 4496 2.930109 AGGGTCTGTCTAGGACACAT 57.070 50.000 3.18 0.00 39.36 3.21
2704 4497 2.741145 AGGGTCTGTCTAGGACACATC 58.259 52.381 3.18 0.00 39.36 3.06
2705 4498 1.757699 GGGTCTGTCTAGGACACATCC 59.242 57.143 0.00 0.00 46.69 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.417288 TCCTCGTCCATGATCTGCAT 58.583 50.000 0.00 0.00 37.85 3.96
8 9 2.428530 TGTCTTCCTCGTCCATGATCTG 59.571 50.000 0.00 0.00 0.00 2.90
15 16 1.511305 GCGATGTCTTCCTCGTCCA 59.489 57.895 0.00 0.00 37.23 4.02
75 76 1.414550 GAGGGTTGAGGTCTAGCCATC 59.585 57.143 11.41 3.84 40.76 3.51
84 85 3.382832 CGCGAGGAGGGTTGAGGT 61.383 66.667 0.00 0.00 0.00 3.85
99 100 2.755650 TGGAAGAGAAGTTGAAGACGC 58.244 47.619 0.00 0.00 0.00 5.19
104 105 4.584325 CCCATTGTTGGAAGAGAAGTTGAA 59.416 41.667 0.00 0.00 46.92 2.69
105 106 4.144297 CCCATTGTTGGAAGAGAAGTTGA 58.856 43.478 0.00 0.00 46.92 3.18
108 109 3.490348 CACCCATTGTTGGAAGAGAAGT 58.510 45.455 0.00 0.00 46.92 3.01
174 188 1.935327 GACGCCGCCAGAAGTAGTCT 61.935 60.000 0.00 0.00 36.88 3.24
375 389 2.750948 TCACAGCAAGTTTAGACGACC 58.249 47.619 0.00 0.00 0.00 4.79
404 418 1.208293 GTGTTGAACCCTGGGCAAAAA 59.792 47.619 14.08 0.00 0.00 1.94
427 441 6.152323 GCATCTAATATCCCTACACGACCTTA 59.848 42.308 0.00 0.00 0.00 2.69
437 452 3.776969 CTGCAGGGCATCTAATATCCCTA 59.223 47.826 5.57 0.00 46.89 3.53
553 585 8.481314 TCTTATTTCTCAGATGTAGCACTTCAT 58.519 33.333 0.00 0.00 0.00 2.57
563 595 7.482169 TGTAGTGGTCTTATTTCTCAGATGT 57.518 36.000 0.00 0.00 0.00 3.06
572 604 7.178451 CCCCTTTCAAATGTAGTGGTCTTATTT 59.822 37.037 0.00 0.00 0.00 1.40
573 605 6.663523 CCCCTTTCAAATGTAGTGGTCTTATT 59.336 38.462 0.00 0.00 0.00 1.40
602 634 3.605634 TGTGTGCAAGTAGTTGTTCTGT 58.394 40.909 11.85 0.00 35.92 3.41
661 693 6.036517 TGTTGTTTGGTTGTTCATATTTGTGC 59.963 34.615 0.00 0.00 0.00 4.57
669 701 6.036577 AGAACTTGTTGTTTGGTTGTTCAT 57.963 33.333 0.00 0.00 39.30 2.57
670 702 5.461032 AGAACTTGTTGTTTGGTTGTTCA 57.539 34.783 0.00 0.00 39.30 3.18
801 1932 1.330779 CGTGTCAGCGTGAGAACTCG 61.331 60.000 0.00 0.00 36.33 4.18
855 2018 0.178891 ACCAAGGCAGGAGAGGAGAA 60.179 55.000 2.81 0.00 0.00 2.87
859 2022 2.232298 GACGACCAAGGCAGGAGAGG 62.232 65.000 2.81 0.00 0.00 3.69
860 2023 1.216710 GACGACCAAGGCAGGAGAG 59.783 63.158 2.81 0.00 0.00 3.20
861 2024 2.636412 CGACGACCAAGGCAGGAGA 61.636 63.158 2.81 0.00 0.00 3.71
862 2025 2.125912 CGACGACCAAGGCAGGAG 60.126 66.667 2.81 0.00 0.00 3.69
863 2026 2.599281 TCGACGACCAAGGCAGGA 60.599 61.111 2.81 0.00 0.00 3.86
864 2027 2.432628 GTCGACGACCAAGGCAGG 60.433 66.667 17.25 0.00 0.00 4.85
867 2030 2.126031 GGAGTCGACGACCAAGGC 60.126 66.667 23.76 8.77 32.18 4.35
882 2045 0.902531 GGATCGGTTGGAGACTTGGA 59.097 55.000 0.00 0.00 0.00 3.53
883 2046 0.460284 CGGATCGGTTGGAGACTTGG 60.460 60.000 0.00 0.00 0.00 3.61
884 2047 0.460284 CCGGATCGGTTGGAGACTTG 60.460 60.000 0.00 0.00 42.73 3.16
885 2048 1.898154 CCGGATCGGTTGGAGACTT 59.102 57.895 0.00 0.00 42.73 3.01
886 2049 3.617368 CCGGATCGGTTGGAGACT 58.383 61.111 0.00 0.00 42.73 3.24
946 2561 3.419759 GGGCTGTGGTTGCGTACG 61.420 66.667 11.84 11.84 0.00 3.67
947 2562 2.281208 TGGGCTGTGGTTGCGTAC 60.281 61.111 0.00 0.00 0.00 3.67
1008 2623 2.435059 GTGGTCTTGCGAGCCTCC 60.435 66.667 13.52 8.65 36.84 4.30
1041 2656 4.377760 AGGAAGTCGCGGGGAGGA 62.378 66.667 6.13 0.00 0.00 3.71
1433 3056 0.816825 CTTGATGGTGATGGAGCCGG 60.817 60.000 0.00 0.00 0.00 6.13
1954 3594 6.205464 CCAATACGACCATAATGAAGCATCTT 59.795 38.462 0.00 0.00 0.00 2.40
1994 3635 4.391216 CCATAAGCAACACAGTCAGAAGAG 59.609 45.833 0.00 0.00 0.00 2.85
2042 3683 4.340666 TGCTTCTGTTTTTGCACTATGGAA 59.659 37.500 0.00 0.00 0.00 3.53
2067 3708 0.460811 TGCTCTTGTAGGCATGCTCG 60.461 55.000 18.92 0.14 33.23 5.03
2070 3711 2.030007 TGTTTTGCTCTTGTAGGCATGC 60.030 45.455 9.90 9.90 38.30 4.06
2183 3825 4.042311 TCCAGCAGGAAAACTATACACCAA 59.958 41.667 0.00 0.00 42.23 3.67
2353 4120 7.408756 ACATTGTAGCATGTGGTAATCAAAT 57.591 32.000 0.00 0.00 0.00 2.32
2441 4220 9.949174 AAACTTTGAATGAAACAATATTTTGGC 57.051 25.926 0.89 0.00 37.15 4.52
2480 4266 3.610114 GCATTGCAGTTTACAGGTGACAG 60.610 47.826 3.15 0.00 0.00 3.51
2653 4446 8.574251 TTATGTACTGCTAATCCAAACAATGT 57.426 30.769 0.00 0.00 0.00 2.71
2684 4477 2.624557 GGATGTGTCCTAGACAGACCCT 60.625 54.545 0.00 0.00 43.57 4.34
2685 4478 1.757699 GGATGTGTCCTAGACAGACCC 59.242 57.143 0.00 0.00 43.57 4.46
2686 4479 2.428890 CTGGATGTGTCCTAGACAGACC 59.571 54.545 0.00 3.31 43.57 3.85
2687 4480 3.357203 TCTGGATGTGTCCTAGACAGAC 58.643 50.000 0.00 0.00 43.57 3.51
2688 4481 3.739401 TCTGGATGTGTCCTAGACAGA 57.261 47.619 0.00 0.00 43.57 3.41
2689 4482 4.161189 ACAATCTGGATGTGTCCTAGACAG 59.839 45.833 0.00 0.00 43.57 3.51
2690 4483 4.096681 ACAATCTGGATGTGTCCTAGACA 58.903 43.478 0.00 0.00 45.32 3.41
2691 4484 4.744795 ACAATCTGGATGTGTCCTAGAC 57.255 45.455 0.00 0.00 45.32 2.59


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

AutoCloner maintained by Alex Coulton.