Multiple sequence alignment - TraesCS4B01G076600

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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 TraesCS4B01G076600 chr4B 100.000 2518 0 0 1 2518 73288290 73290807 0.000000e+00 4650
1 TraesCS4B01G076600 chr4B 95.747 2469 76 4 79 2518 66837481 66835013 0.000000e+00 3951
2 TraesCS4B01G076600 chr4B 94.120 2466 110 18 79 2515 403111603 403114062 0.000000e+00 3718
3 TraesCS4B01G076600 chr4B 93.700 2381 106 12 79 2448 5269323 5266976 0.000000e+00 3526
4 TraesCS4B01G076600 chr4B 94.721 2273 105 12 79 2347 657444002 657446263 0.000000e+00 3518
5 TraesCS4B01G076600 chr4B 96.386 83 3 0 1 83 5269762 5269680 1.210000e-28 137
6 TraesCS4B01G076600 chr4B 96.386 83 3 0 1 83 403111163 403111245 1.210000e-28 137
7 TraesCS4B01G076600 chr4B 96.386 83 2 1 1 83 66838538 66838457 4.370000e-28 135
8 TraesCS4B01G076600 chr4B 93.023 86 5 1 2431 2515 657446237 657446322 9.460000e-25 124
9 TraesCS4B01G076600 chr2B 94.596 2461 95 8 79 2509 393866618 393864166 0.000000e+00 3773
10 TraesCS4B01G076600 chr2B 93.920 2385 109 19 79 2436 665888666 665886291 0.000000e+00 3568
11 TraesCS4B01G076600 chr2B 97.500 80 2 0 4 83 665889102 665889023 1.210000e-28 137
12 TraesCS4B01G076600 chr3B 94.519 2445 118 14 79 2515 543548337 543550773 0.000000e+00 3759
13 TraesCS4B01G076600 chr3B 86.503 163 20 2 2274 2436 726414202 726414042 7.160000e-41 178
14 TraesCS4B01G076600 chr3B 84.868 152 21 2 2285 2436 85422314 85422463 4.340000e-33 152
15 TraesCS4B01G076600 chr3B 97.590 83 2 0 1 83 698401408 698401326 2.610000e-30 143
16 TraesCS4B01G076600 chr3B 91.667 84 6 1 2433 2515 543550766 543550849 5.690000e-22 115
17 TraesCS4B01G076600 chr1B 93.972 2472 114 8 79 2518 549436568 549434100 0.000000e+00 3707
18 TraesCS4B01G076600 chr1B 94.684 2295 112 10 79 2367 667334245 667331955 0.000000e+00 3554
19 TraesCS4B01G076600 chr1B 97.590 83 2 0 1 83 667334684 667334602 2.610000e-30 143
20 TraesCS4B01G076600 chr1B 95.181 83 4 0 1 83 549437009 549436927 5.650000e-27 132
21 TraesCS4B01G076600 chr7B 97.590 83 2 0 1 83 637742112 637742194 2.610000e-30 143
22 TraesCS4B01G076600 chr7B 95.181 83 4 0 1 83 549387548 549387466 5.650000e-27 132


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 TraesCS4B01G076600 chr4B 73288290 73290807 2517 False 4650.0 4650 100.0000 1 2518 1 chr4B.!!$F1 2517
1 TraesCS4B01G076600 chr4B 66835013 66838538 3525 True 2043.0 3951 96.0665 1 2518 2 chr4B.!!$R2 2517
2 TraesCS4B01G076600 chr4B 403111163 403114062 2899 False 1927.5 3718 95.2530 1 2515 2 chr4B.!!$F2 2514
3 TraesCS4B01G076600 chr4B 5266976 5269762 2786 True 1831.5 3526 95.0430 1 2448 2 chr4B.!!$R1 2447
4 TraesCS4B01G076600 chr4B 657444002 657446322 2320 False 1821.0 3518 93.8720 79 2515 2 chr4B.!!$F3 2436
5 TraesCS4B01G076600 chr2B 393864166 393866618 2452 True 3773.0 3773 94.5960 79 2509 1 chr2B.!!$R1 2430
6 TraesCS4B01G076600 chr2B 665886291 665889102 2811 True 1852.5 3568 95.7100 4 2436 2 chr2B.!!$R2 2432
7 TraesCS4B01G076600 chr3B 543548337 543550849 2512 False 1937.0 3759 93.0930 79 2515 2 chr3B.!!$F2 2436
8 TraesCS4B01G076600 chr1B 549434100 549437009 2909 True 1919.5 3707 94.5765 1 2518 2 chr1B.!!$R1 2517
9 TraesCS4B01G076600 chr1B 667331955 667334684 2729 True 1848.5 3554 96.1370 1 2367 2 chr1B.!!$R2 2366

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
479 1468 1.596934 GGTGATCTTGCCGAGTCCA 59.403 57.895 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2408 3521 0.915364 GAGAATGGCTCTTGAGGGGT 59.085 55.0 0.0 0.0 40.61 4.95 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
164 1148 1.750399 CCCGAATTCAGGGCCACAG 60.750 63.158 18.34 0.0 42.77 3.66
181 1165 2.300152 CACAGAGGAACAGAACCAGCTA 59.700 50.000 0.00 0.0 0.00 3.32
337 1323 9.639601 CATACTTTCTATACATGATCCGCTTAA 57.360 33.333 0.00 0.0 0.00 1.85
391 1380 2.534150 GGCATGATTCGTTCGTGTTACG 60.534 50.000 0.00 0.0 42.42 3.18
420 1409 4.650734 TCATACAGCTCATGTTTGGACAA 58.349 39.130 5.05 0.0 39.96 3.18
479 1468 1.596934 GGTGATCTTGCCGAGTCCA 59.403 57.895 0.00 0.0 0.00 4.02
625 1614 5.453198 GGATGGTGACTTCAACCACAAAATT 60.453 40.000 0.00 0.0 36.24 1.82
944 1941 5.313712 ACGTGATTCTACATTTTTGTCCCT 58.686 37.500 0.00 0.0 0.00 4.20
968 1965 5.614308 TGATGTTCTTCATGTGAACTCTGT 58.386 37.500 23.68 13.6 42.86 3.41
979 1977 6.767423 TCATGTGAACTCTGTTTCTCATTTCA 59.233 34.615 0.00 0.0 37.52 2.69
1027 2025 1.471119 CATGTTCCAGGAGCTTGCAT 58.529 50.000 4.73 0.0 0.00 3.96
1385 2396 1.946768 TCTTTTTGCGAGTTCACCTGG 59.053 47.619 0.00 0.0 0.00 4.45
1436 2447 3.123959 GCTTTCACGCGTTGGAATACTTA 59.876 43.478 10.22 0.0 0.00 2.24
1516 2527 5.188163 TCCGGAAAATCTACACATGGAACTA 59.812 40.000 0.00 0.0 0.00 2.24
1604 2615 6.708054 AGAAAGTCATCAAGAAGTACAAGTGG 59.292 38.462 0.00 0.0 0.00 4.00
1758 2770 1.210722 TGTAGTGGTGGTTTGTGAGCA 59.789 47.619 0.00 0.0 0.00 4.26
1815 2828 3.065648 GTGAACCTTTTTAGGCGTGACAA 59.934 43.478 0.00 0.0 0.00 3.18
1888 2904 4.791411 GCACCAGTTTTGCTGTTTCGAATA 60.791 41.667 0.00 0.0 43.55 1.75
1893 2909 6.597099 CAGTTTTGCTGTTTCGAATACGTCG 61.597 44.000 0.00 0.0 44.41 5.12
2051 3068 4.174305 AACCTTTCCTGCGGTTGG 57.826 55.556 0.00 0.0 41.71 3.77
2130 3148 4.609708 GTGTTACTAAACCGCGTTGAATTG 59.390 41.667 4.92 0.0 34.49 2.32
2199 3217 9.665719 TCATATTTTTCAGTACAGCTAACATGA 57.334 29.630 0.00 0.0 0.00 3.07
2202 3220 7.744087 TTTTTCAGTACAGCTAACATGACAT 57.256 32.000 0.00 0.0 0.00 3.06
2251 3269 7.041635 TCCAATACAATTAACATGGCAGATG 57.958 36.000 0.00 0.0 0.00 2.90
2337 3403 8.514594 GCATGGCAAATTTAGTATAAGATAGCA 58.485 33.333 0.00 0.0 0.00 3.49
2408 3521 6.419484 TGTATTCTCCTTCAACTTCTGACA 57.581 37.500 0.00 0.0 32.21 3.58
2420 3533 0.687354 TTCTGACACCCCTCAAGAGC 59.313 55.000 0.00 0.0 0.00 4.09
2450 3639 9.967451 TCTCCCAATTTAGTACAAATAACATGA 57.033 29.630 0.00 0.0 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.614903 CAAATGCAGGTGACATGGTGT 59.385 47.619 0.00 0.00 0.00 4.16
164 1148 3.380637 TCGTATAGCTGGTTCTGTTCCTC 59.619 47.826 0.00 0.00 0.00 3.71
181 1165 4.272504 CCAAACCGCTTGACAATATCGTAT 59.727 41.667 0.00 0.00 37.17 3.06
391 1380 6.529125 CCAAACATGAGCTGTATGAAAATGAC 59.471 38.462 13.05 0.00 36.98 3.06
420 1409 2.029110 CCGCATTGAATGACCTTGGTTT 60.029 45.455 9.76 0.00 0.00 3.27
479 1468 4.142182 CGACATTTTACCATTTGGCCTCAT 60.142 41.667 3.32 0.00 39.32 2.90
625 1614 1.628340 TGGGCGAAATTCTTCCTCAGA 59.372 47.619 0.00 0.00 0.00 3.27
944 1941 6.057533 ACAGAGTTCACATGAAGAACATCAA 58.942 36.000 25.92 0.00 45.93 2.57
968 1965 9.195411 GCATGTAAAAGTGATTGAAATGAGAAA 57.805 29.630 0.00 0.00 0.00 2.52
1027 2025 1.946475 TTGTCGTGTGGGTCGTGTGA 61.946 55.000 0.00 0.00 0.00 3.58
1436 2447 2.339769 AGTCTACCTTCCCACTTTGCT 58.660 47.619 0.00 0.00 0.00 3.91
1516 2527 6.618287 TGTTGAAATCTTCATTCGTCAACT 57.382 33.333 13.61 0.00 38.98 3.16
1604 2615 1.523934 CCGGTTGTAACTTCACGTGAC 59.476 52.381 19.90 7.63 0.00 3.67
1888 2904 4.775440 TGTTTTAAAACATCGTCGACGT 57.225 36.364 34.40 20.51 43.45 4.34
2130 3148 7.389884 ACTCAGCATCACATATATTTCCATGAC 59.610 37.037 0.00 0.00 0.00 3.06
2199 3217 5.334569 GCCGTGTTGTTTGTACTGAATATGT 60.335 40.000 0.00 0.00 0.00 2.29
2202 3220 4.127907 TGCCGTGTTGTTTGTACTGAATA 58.872 39.130 0.00 0.00 0.00 1.75
2251 3269 9.620660 CCAAATTTTCCATGTTAGTTGTACTAC 57.379 33.333 0.00 0.00 28.93 2.73
2337 3403 8.571461 CATGTTATGGATACTTAATCTGCCAT 57.429 34.615 0.00 0.00 38.33 4.40
2408 3521 0.915364 GAGAATGGCTCTTGAGGGGT 59.085 55.000 0.00 0.00 40.61 4.95


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

AutoCloner maintained by Alex Coulton.