Multiple sequence alignment - TraesCS4A01G138500

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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 TraesCS4A01G138500 chr4A 100.000 2429 0 0 1 2429 204985680 204983252 0 4486
1 TraesCS4A01G138500 chr6D 95.390 2408 100 5 33 2429 389247244 389244837 0 3821
2 TraesCS4A01G138500 chr3A 95.388 2407 101 5 33 2429 66006554 66004148 0 3821
3 TraesCS4A01G138500 chr3A 94.601 2408 118 6 33 2429 695638966 695641372 0 3716
4 TraesCS4A01G138500 chr3A 94.599 2407 118 5 33 2429 650015934 650013530 0 3714
5 TraesCS4A01G138500 chr5D 95.307 2408 102 5 33 2429 503243850 503246257 0 3810
6 TraesCS4A01G138500 chr2A 95.307 2408 102 5 33 2429 726907877 726905470 0 3810
7 TraesCS4A01G138500 chr3D 95.262 2406 104 6 33 2429 589264945 589262541 0 3803
8 TraesCS4A01G138500 chr7B 95.224 2408 104 5 33 2429 663100847 663098440 0 3799
9 TraesCS4A01G138500 chr7B 95.100 2408 107 5 33 2429 662724982 662727389 0 3783


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 TraesCS4A01G138500 chr4A 204983252 204985680 2428 True 4486 4486 100.000 1 2429 1 chr4A.!!$R1 2428
1 TraesCS4A01G138500 chr6D 389244837 389247244 2407 True 3821 3821 95.390 33 2429 1 chr6D.!!$R1 2396
2 TraesCS4A01G138500 chr3A 66004148 66006554 2406 True 3821 3821 95.388 33 2429 1 chr3A.!!$R1 2396
3 TraesCS4A01G138500 chr3A 695638966 695641372 2406 False 3716 3716 94.601 33 2429 1 chr3A.!!$F1 2396
4 TraesCS4A01G138500 chr3A 650013530 650015934 2404 True 3714 3714 94.599 33 2429 1 chr3A.!!$R2 2396
5 TraesCS4A01G138500 chr5D 503243850 503246257 2407 False 3810 3810 95.307 33 2429 1 chr5D.!!$F1 2396
6 TraesCS4A01G138500 chr2A 726905470 726907877 2407 True 3810 3810 95.307 33 2429 1 chr2A.!!$R1 2396
7 TraesCS4A01G138500 chr3D 589262541 589264945 2404 True 3803 3803 95.262 33 2429 1 chr3D.!!$R1 2396
8 TraesCS4A01G138500 chr7B 663098440 663100847 2407 True 3799 3799 95.224 33 2429 1 chr7B.!!$R1 2396
9 TraesCS4A01G138500 chr7B 662724982 662727389 2407 False 3783 3783 95.100 33 2429 1 chr7B.!!$F1 2396

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
379 380 0.107214 CACCGGTCAGCCATATGGTT 60.107 55.0 22.79 14.79 37.57 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1695 1705 0.105194 TGAACCAGAGACCTCACCCA 60.105 55.0 0.0 0.0 0.0 4.51 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
25 26 5.635549 AAAATTGAAACTACTGCGTTTGC 57.364 34.783 1.13 0.00 37.24 3.68
26 27 2.766970 TTGAAACTACTGCGTTTGCC 57.233 45.000 1.13 0.00 41.78 4.52
27 28 1.669604 TGAAACTACTGCGTTTGCCA 58.330 45.000 1.13 0.00 41.78 4.92
28 29 2.017782 TGAAACTACTGCGTTTGCCAA 58.982 42.857 1.13 0.00 41.78 4.52
29 30 2.223386 TGAAACTACTGCGTTTGCCAAC 60.223 45.455 1.13 0.00 41.78 3.77
30 31 1.384525 AACTACTGCGTTTGCCAACA 58.615 45.000 1.21 0.00 41.78 3.33
31 32 1.384525 ACTACTGCGTTTGCCAACAA 58.615 45.000 1.21 0.00 41.78 2.83
71 72 3.326578 ACGGGTGGTGCATGGCTA 61.327 61.111 0.00 0.00 0.00 3.93
73 74 1.453745 CGGGTGGTGCATGGCTATT 60.454 57.895 0.00 0.00 0.00 1.73
85 86 0.608130 TGGCTATTGTCAGCTCGTGT 59.392 50.000 0.00 0.00 41.50 4.49
88 89 0.917259 CTATTGTCAGCTCGTGTCGC 59.083 55.000 0.00 0.00 0.00 5.19
131 132 0.320771 ACGAGCACAACCCTCATGTC 60.321 55.000 0.00 0.00 0.00 3.06
168 169 1.217916 TTGGAACCCTGAACAGACCA 58.782 50.000 3.19 5.04 0.00 4.02
170 171 0.765510 GGAACCCTGAACAGACCACT 59.234 55.000 3.19 0.00 0.00 4.00
171 172 1.975680 GGAACCCTGAACAGACCACTA 59.024 52.381 3.19 0.00 0.00 2.74
226 227 0.852155 TCATCATGCCCCTTATGCCA 59.148 50.000 0.00 0.00 0.00 4.92
299 300 3.138468 AGGGTGAGCTAACTCCAAAAACT 59.862 43.478 0.00 0.00 42.74 2.66
300 301 4.349930 AGGGTGAGCTAACTCCAAAAACTA 59.650 41.667 0.00 0.00 42.74 2.24
312 313 5.130477 ACTCCAAAAACTAGTCCTCAGTTCA 59.870 40.000 0.00 0.00 35.19 3.18
322 323 1.980765 TCCTCAGTTCAGATTGCAGGT 59.019 47.619 0.00 0.00 0.00 4.00
375 376 2.972713 AGTAATCACCGGTCAGCCATAT 59.027 45.455 2.59 0.00 34.09 1.78
378 379 0.980754 TCACCGGTCAGCCATATGGT 60.981 55.000 22.79 7.28 37.57 3.55
379 380 0.107214 CACCGGTCAGCCATATGGTT 60.107 55.000 22.79 14.79 37.57 3.67
396 397 1.271163 GGTTGTGAATCAGTTCCCGGA 60.271 52.381 0.73 0.00 33.26 5.14
463 464 6.549433 TGAAGTCATTACCCTTAACCGTAT 57.451 37.500 0.00 0.00 0.00 3.06
521 522 2.629137 TGAAGTCGTAACAAGGTAGCCA 59.371 45.455 0.00 0.00 0.00 4.75
524 525 5.047164 TGAAGTCGTAACAAGGTAGCCATAA 60.047 40.000 0.00 0.00 0.00 1.90
539 540 1.202758 CCATAATGGAAGGTGCGGCTA 60.203 52.381 0.00 0.00 40.96 3.93
605 606 5.983118 GGGTATTTTGGTTTGACACTTCTTG 59.017 40.000 0.00 0.00 0.00 3.02
607 608 7.433680 GGTATTTTGGTTTGACACTTCTTGAT 58.566 34.615 0.00 0.00 0.00 2.57
628 629 1.827344 GCCCAAAAAGAAGGCAGCTAT 59.173 47.619 0.00 0.00 46.34 2.97
807 809 2.888212 TGTCAAAAGGAAAGGGATGGG 58.112 47.619 0.00 0.00 0.00 4.00
816 818 3.116356 AGGAAAGGGATGGGGTTTTTCTT 60.116 43.478 0.00 0.00 0.00 2.52
960 962 5.121811 GGATAGTTCAATGTGCTCATCAGT 58.878 41.667 1.01 0.00 32.56 3.41
1025 1027 3.616560 GCGTACTCCTCCTGTTTGAATCA 60.617 47.826 0.00 0.00 0.00 2.57
1028 1030 4.278975 ACTCCTCCTGTTTGAATCAGAC 57.721 45.455 4.89 0.00 35.20 3.51
1030 1032 5.087323 ACTCCTCCTGTTTGAATCAGACTA 58.913 41.667 5.52 0.00 35.20 2.59
1077 1079 2.303022 GAGGATAGATGGGGCGATTCAA 59.697 50.000 0.00 0.00 0.00 2.69
1118 1120 6.585695 TCTAACTTTCTATTCACTCGTGGT 57.414 37.500 0.00 0.00 0.00 4.16
1122 1124 6.777213 ACTTTCTATTCACTCGTGGTATCT 57.223 37.500 0.00 0.00 0.00 1.98
1351 1361 5.736951 TTTTCATGATTTTCCCATCGGTT 57.263 34.783 0.00 0.00 0.00 4.44
1442 1452 1.134401 TCCTTAAATGGGAGCAGAGCG 60.134 52.381 0.00 0.00 0.00 5.03
1456 1466 1.681264 CAGAGCGGGTTTGAAAAAGGT 59.319 47.619 0.00 0.00 0.00 3.50
1467 1477 6.320418 GGGTTTGAAAAAGGTTCTTAGAGTGA 59.680 38.462 0.00 0.00 0.00 3.41
1468 1478 7.147966 GGGTTTGAAAAAGGTTCTTAGAGTGAA 60.148 37.037 0.00 0.00 0.00 3.18
1582 1592 3.471680 GGAAGAAGCACACTTGAAGAGT 58.528 45.455 0.00 0.00 39.89 3.24
1583 1593 4.503296 GGGAAGAAGCACACTTGAAGAGTA 60.503 45.833 0.00 0.00 36.65 2.59
1584 1594 5.241662 GGAAGAAGCACACTTGAAGAGTAT 58.758 41.667 0.00 0.00 36.65 2.12
1585 1595 5.121454 GGAAGAAGCACACTTGAAGAGTATG 59.879 44.000 0.00 0.00 36.65 2.39
1596 1606 6.518369 CACTTGAAGAGTATGGTACAACAGGA 60.518 42.308 0.00 0.00 38.31 3.86
1635 1645 0.601311 GAAGGATGAATCGCTCCCGG 60.601 60.000 0.00 0.00 34.56 5.73
1680 1690 1.887797 ATTGGTTGGATCGTAGGGGA 58.112 50.000 0.00 0.00 0.00 4.81
1695 1705 5.839063 TCGTAGGGGAGATGATTTACTTCAT 59.161 40.000 0.00 0.00 39.04 2.57
1699 1709 4.141158 GGGGAGATGATTTACTTCATGGGT 60.141 45.833 0.00 0.00 36.48 4.51
1736 1746 4.124943 CAGGATGGCCCAGCTGCT 62.125 66.667 8.66 0.00 37.41 4.24
1762 1772 6.379417 CCAGGGAAAAGAATAGAAGAAGCATT 59.621 38.462 0.00 0.00 0.00 3.56
1845 1855 1.608590 CTCTTGCAATTGGGTCGTTGT 59.391 47.619 7.72 0.00 0.00 3.32
1859 1869 1.070445 TCGTTGTGATTACGGGTTGGT 59.930 47.619 0.00 0.00 39.38 3.67
1874 1884 3.892588 GGGTTGGTTGTCTAATTGTCCAA 59.107 43.478 0.00 0.00 33.42 3.53
1945 1955 5.959583 AGTAATGGGGAAGAGGACTAAAG 57.040 43.478 0.00 0.00 0.00 1.85
2095 2109 3.254217 CCTCATCTGGGATCCCTGT 57.746 57.895 31.05 17.55 36.57 4.00
2179 2193 4.160736 ACGAAATGTAGCAAAAGGAAGC 57.839 40.909 0.00 0.00 0.00 3.86
2282 2296 5.741011 GTCACAAACCAATCATAGACCCTA 58.259 41.667 0.00 0.00 0.00 3.53
2327 2341 4.473520 CGCTCTCCGGTTGGGCAT 62.474 66.667 18.83 0.00 35.24 4.40
2389 2403 6.596888 CCAGCATTCTTAAGATCAAAGAGTCA 59.403 38.462 5.89 0.00 34.59 3.41
2391 2405 7.548427 CAGCATTCTTAAGATCAAAGAGTCAGA 59.452 37.037 5.89 0.00 34.59 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.006261 GGCAAACGCAGTAGTTTCAATTTTT 59.994 36.000 0.00 0.00 45.00 1.94
3 4 4.506288 GGCAAACGCAGTAGTTTCAATTTT 59.494 37.500 0.00 0.00 45.00 1.82
4 5 4.048504 GGCAAACGCAGTAGTTTCAATTT 58.951 39.130 0.00 0.00 45.00 1.82
5 6 3.067461 TGGCAAACGCAGTAGTTTCAATT 59.933 39.130 0.00 0.00 45.00 2.32
6 7 2.621055 TGGCAAACGCAGTAGTTTCAAT 59.379 40.909 0.00 0.00 45.00 2.57
7 8 2.017782 TGGCAAACGCAGTAGTTTCAA 58.982 42.857 0.00 0.00 45.00 2.69
8 9 1.669604 TGGCAAACGCAGTAGTTTCA 58.330 45.000 0.00 0.00 45.00 2.69
9 10 2.223386 TGTTGGCAAACGCAGTAGTTTC 60.223 45.455 0.00 0.00 45.00 2.78
10 11 1.746220 TGTTGGCAAACGCAGTAGTTT 59.254 42.857 0.00 0.00 45.00 2.66
11 12 1.384525 TGTTGGCAAACGCAGTAGTT 58.615 45.000 0.00 0.00 45.00 2.24
12 13 1.333619 CTTGTTGGCAAACGCAGTAGT 59.666 47.619 0.00 0.00 45.00 2.73
13 14 1.334960 CCTTGTTGGCAAACGCAGTAG 60.335 52.381 0.00 0.00 45.00 2.57
14 15 0.665835 CCTTGTTGGCAAACGCAGTA 59.334 50.000 0.00 0.00 45.00 2.74
16 17 1.300080 CCCTTGTTGGCAAACGCAG 60.300 57.895 0.00 0.00 39.30 5.18
17 18 2.055042 ACCCTTGTTGGCAAACGCA 61.055 52.632 0.00 0.00 39.30 5.24
18 19 1.591327 CACCCTTGTTGGCAAACGC 60.591 57.895 0.00 0.00 39.30 4.84
19 20 1.591327 GCACCCTTGTTGGCAAACG 60.591 57.895 0.00 0.00 39.30 3.60
20 21 1.227527 GGCACCCTTGTTGGCAAAC 60.228 57.895 0.00 0.00 33.73 2.93
21 22 3.225235 GGCACCCTTGTTGGCAAA 58.775 55.556 0.00 0.00 33.73 3.68
56 57 0.684153 ACAATAGCCATGCACCACCC 60.684 55.000 0.00 0.00 0.00 4.61
71 72 0.599991 TTGCGACACGAGCTGACAAT 60.600 50.000 0.00 0.00 35.28 2.71
73 74 1.661509 CTTGCGACACGAGCTGACA 60.662 57.895 0.00 0.00 35.28 3.58
85 86 1.134037 ACTTAACCCAACACCTTGCGA 60.134 47.619 0.00 0.00 0.00 5.10
88 89 2.806244 CGAGACTTAACCCAACACCTTG 59.194 50.000 0.00 0.00 0.00 3.61
118 119 2.290323 GGCAACTAGACATGAGGGTTGT 60.290 50.000 18.39 0.00 39.28 3.32
131 132 4.832248 TCCAAACTCATAGTGGCAACTAG 58.168 43.478 7.15 0.00 42.16 2.57
168 169 2.226962 TCCTCCGGCTTAACACTAGT 57.773 50.000 0.00 0.00 0.00 2.57
170 171 3.167485 TCTTTCCTCCGGCTTAACACTA 58.833 45.455 0.00 0.00 0.00 2.74
171 172 1.975680 TCTTTCCTCCGGCTTAACACT 59.024 47.619 0.00 0.00 0.00 3.55
189 190 1.273495 TGACTTGGCCTCATCCTCTCT 60.273 52.381 3.32 0.00 0.00 3.10
226 227 0.320421 GTAGCACGTGTGTCACCCAT 60.320 55.000 18.38 0.00 0.00 4.00
299 300 3.196469 CCTGCAATCTGAACTGAGGACTA 59.804 47.826 0.00 0.00 0.00 2.59
300 301 2.027377 CCTGCAATCTGAACTGAGGACT 60.027 50.000 0.00 0.00 0.00 3.85
375 376 1.544537 CCGGGAACTGATTCACAACCA 60.545 52.381 0.00 0.00 38.24 3.67
378 379 1.271163 GGTCCGGGAACTGATTCACAA 60.271 52.381 4.39 0.00 38.24 3.33
379 380 0.323629 GGTCCGGGAACTGATTCACA 59.676 55.000 4.39 0.00 38.24 3.58
396 397 2.428622 GGGCGGTGTGTACAAGGT 59.571 61.111 0.00 0.00 0.00 3.50
463 464 1.385915 CCTTAGGCATCCCCCTCCA 60.386 63.158 0.00 0.00 36.41 3.86
521 522 2.047061 TCTAGCCGCACCTTCCATTAT 58.953 47.619 0.00 0.00 0.00 1.28
524 525 0.394565 GATCTAGCCGCACCTTCCAT 59.605 55.000 0.00 0.00 0.00 3.41
539 540 2.843113 CTCCCTGAAAAGGAGGTGATCT 59.157 50.000 0.00 0.00 46.14 2.75
569 570 9.612066 CAAACCAAAATACCCAATAAGCATAAT 57.388 29.630 0.00 0.00 0.00 1.28
628 629 5.425217 TCCATATCCAAGTTTAGCTCAGACA 59.575 40.000 0.00 0.00 0.00 3.41
778 780 3.541242 TTCCTTTTGACATCCCCATGT 57.459 42.857 0.00 0.00 46.64 3.21
807 809 2.276201 ACGCCAAAAGCAAGAAAAACC 58.724 42.857 0.00 0.00 44.04 3.27
816 818 2.625823 GCCTGCTACGCCAAAAGCA 61.626 57.895 0.00 0.00 46.11 3.91
859 861 4.148838 CTCTACCACTGAGCTAATAGCCT 58.851 47.826 8.88 0.00 43.77 4.58
960 962 1.296392 CACATCTTCGGGTCAGGCA 59.704 57.895 0.00 0.00 0.00 4.75
1025 1027 7.013369 GGAGAAGTTTGTTTGGTTTCATAGTCT 59.987 37.037 0.00 0.00 0.00 3.24
1028 1030 7.013274 TGAGGAGAAGTTTGTTTGGTTTCATAG 59.987 37.037 0.00 0.00 0.00 2.23
1030 1032 5.656416 TGAGGAGAAGTTTGTTTGGTTTCAT 59.344 36.000 0.00 0.00 0.00 2.57
1077 1079 7.682787 AGTTAGATTTACATGGGATCTCACT 57.317 36.000 0.00 12.50 32.40 3.41
1118 1120 2.520982 CTCCGGACCGCCCAGATA 60.521 66.667 8.86 0.00 34.14 1.98
1337 1347 3.449746 TCTCCAAACCGATGGGAAAAT 57.550 42.857 0.00 0.00 41.05 1.82
1345 1355 1.168714 GCTGCTTTCTCCAAACCGAT 58.831 50.000 0.00 0.00 0.00 4.18
1346 1356 0.179032 TGCTGCTTTCTCCAAACCGA 60.179 50.000 0.00 0.00 0.00 4.69
1351 1361 4.400251 CCTATTGATTGCTGCTTTCTCCAA 59.600 41.667 0.00 0.00 0.00 3.53
1417 1427 5.105187 GCTCTGCTCCCATTTAAGGAAAAAT 60.105 40.000 0.00 0.00 31.49 1.82
1442 1452 6.320418 TCACTCTAAGAACCTTTTTCAAACCC 59.680 38.462 0.00 0.00 0.00 4.11
1456 1466 4.080526 GCCCAACCCTATTCACTCTAAGAA 60.081 45.833 0.00 0.00 0.00 2.52
1467 1477 1.289244 CCTCCTGGCCCAACCCTATT 61.289 60.000 0.00 0.00 37.83 1.73
1468 1478 1.697754 CCTCCTGGCCCAACCCTAT 60.698 63.158 0.00 0.00 37.83 2.57
1596 1606 0.796312 CCGAACGCAGCATACAACTT 59.204 50.000 0.00 0.00 0.00 2.66
1635 1645 6.098982 TGGGAGAGAATCAATAGACTCCTTTC 59.901 42.308 0.00 0.00 42.17 2.62
1680 1690 5.192522 ACCTCACCCATGAAGTAAATCATCT 59.807 40.000 0.00 0.00 37.96 2.90
1695 1705 0.105194 TGAACCAGAGACCTCACCCA 60.105 55.000 0.00 0.00 0.00 4.51
1699 1709 1.971357 GGACTTGAACCAGAGACCTCA 59.029 52.381 0.00 0.00 0.00 3.86
1736 1746 5.014123 TGCTTCTTCTATTCTTTTCCCTGGA 59.986 40.000 0.00 0.00 0.00 3.86
1762 1772 4.937620 GTGGAGTATGCATGAAAGAGTCAA 59.062 41.667 10.16 0.00 39.99 3.18
1822 1832 1.298157 CGACCCAATTGCAAGAGCGA 61.298 55.000 4.94 0.00 46.23 4.93
1845 1855 4.620589 TTAGACAACCAACCCGTAATCA 57.379 40.909 0.00 0.00 0.00 2.57
1859 1869 3.134574 ACCGCTTGGACAATTAGACAA 57.865 42.857 0.00 0.00 36.26 3.18
1874 1884 6.720288 AGGTACAAGATACTATCATTACCGCT 59.280 38.462 0.00 0.00 36.28 5.52
1945 1955 4.331168 CAGTAGAGTCTTTTAGTGGCATGC 59.669 45.833 9.90 9.90 0.00 4.06
2095 2109 1.004745 GGCCAACTTGATCCTCTTCCA 59.995 52.381 0.00 0.00 0.00 3.53
2158 2172 3.568007 TGCTTCCTTTTGCTACATTTCGT 59.432 39.130 0.00 0.00 0.00 3.85
2179 2193 1.102978 GGGTCGGTCCATGGATTTTG 58.897 55.000 19.62 8.37 38.11 2.44
2225 2239 1.299976 GCGTCCTTGGGGTGATCTT 59.700 57.895 0.00 0.00 0.00 2.40
2271 2285 9.793259 GTTCCATTTATTGAATAGGGTCTATGA 57.207 33.333 0.00 0.00 0.00 2.15
2282 2296 8.956426 ACGACTAATGTGTTCCATTTATTGAAT 58.044 29.630 0.00 0.00 41.01 2.57
2291 2305 2.888594 CGGACGACTAATGTGTTCCAT 58.111 47.619 0.00 0.00 34.36 3.41
2305 2319 3.744719 CAACCGGAGAGCGGACGA 61.745 66.667 9.46 0.00 0.00 4.20
2327 2341 0.545787 TGCCCTTCTCCGACCCTTAA 60.546 55.000 0.00 0.00 0.00 1.85
2389 2403 0.325272 GCTCTCCCCTTTTTCCGTCT 59.675 55.000 0.00 0.00 0.00 4.18
2391 2405 0.325272 GAGCTCTCCCCTTTTTCCGT 59.675 55.000 6.43 0.00 0.00 4.69


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

AutoCloner maintained by Alex Coulton.