Multiple sequence alignment - TraesCS7A01G004400

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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 TraesCS7A01G004400 chr7A 100.000 3965 0 0 1 3965 2555208 2551244 0.000000e+00 7323.0
1 TraesCS7A01G004400 chr7A 95.385 2362 91 5 1612 3965 2850580 2848229 0.000000e+00 3742.0
2 TraesCS7A01G004400 chr7A 95.427 1640 36 11 1 1604 2852307 2850671 0.000000e+00 2577.0
3 TraesCS7A01G004400 chr7A 91.165 1562 97 17 2416 3965 3002374 3000842 0.000000e+00 2082.0
4 TraesCS7A01G004400 chr7A 87.861 1178 122 12 913 2080 3379514 3380680 0.000000e+00 1363.0
5 TraesCS7A01G004400 chr7A 89.796 1029 101 2 999 2027 3004358 3003334 0.000000e+00 1315.0
6 TraesCS7A01G004400 chr7A 88.620 413 45 2 2416 2827 3582923 3583334 5.920000e-138 501.0
7 TraesCS7A01G004400 chr7A 97.297 37 0 1 592 628 20613009 20613044 1.190000e-05 62.1
8 TraesCS7A01G004400 chr7A 90.000 40 4 0 611 650 650528647 650528608 7.000000e-03 52.8
9 TraesCS7A01G004400 chr7D 96.215 3989 108 12 1 3965 3732273 3728304 0.000000e+00 6490.0
10 TraesCS7A01G004400 chr7D 88.989 1553 141 8 2415 3965 2429640 2431164 0.000000e+00 1893.0
11 TraesCS7A01G004400 chr7D 94.123 1140 58 2 2826 3965 3440882 3442012 0.000000e+00 1725.0
12 TraesCS7A01G004400 chr7D 92.193 1140 78 4 2826 3965 3699766 3700894 0.000000e+00 1602.0
13 TraesCS7A01G004400 chr7D 89.469 1035 105 2 992 2026 3438501 3439531 0.000000e+00 1304.0
14 TraesCS7A01G004400 chr7D 88.592 412 45 2 2417 2827 3699324 3699734 2.130000e-137 499.0
15 TraesCS7A01G004400 chr4A 94.635 1137 52 2 2829 3965 740867714 740866587 0.000000e+00 1753.0
16 TraesCS7A01G004400 chr4A 93.755 1137 62 5 2829 3965 742269665 742268538 0.000000e+00 1698.0
17 TraesCS7A01G004400 chr4A 93.509 1140 65 2 2826 3965 739808621 739809751 0.000000e+00 1687.0
18 TraesCS7A01G004400 chr4A 93.580 1137 63 5 2829 3965 740061273 740060147 0.000000e+00 1687.0
19 TraesCS7A01G004400 chr4A 93.246 1140 68 5 2826 3965 739833335 739834465 0.000000e+00 1670.0
20 TraesCS7A01G004400 chr4A 92.964 1137 71 6 2829 3965 733927121 733925994 0.000000e+00 1648.0
21 TraesCS7A01G004400 chr4A 89.684 1202 109 7 965 2157 739831306 739832501 0.000000e+00 1519.0
22 TraesCS7A01G004400 chr4A 89.318 1217 108 17 952 2157 742271708 742270503 0.000000e+00 1507.0
23 TraesCS7A01G004400 chr4A 89.829 1170 105 9 965 2126 740063302 740062139 0.000000e+00 1489.0
24 TraesCS7A01G004400 chr4A 89.372 1035 106 2 993 2027 739806199 739807229 0.000000e+00 1299.0
25 TraesCS7A01G004400 chr4A 89.504 1029 104 2 999 2027 740869549 740868525 0.000000e+00 1299.0
26 TraesCS7A01G004400 chr4A 86.275 459 60 3 2370 2827 739832847 739833303 2.750000e-136 496.0
27 TraesCS7A01G004400 chr4A 86.275 459 58 4 2370 2827 740061762 740061308 9.900000e-136 494.0
28 TraesCS7A01G004400 chr4A 85.683 454 57 6 2370 2819 742270157 742269708 4.640000e-129 472.0
29 TraesCS7A01G004400 chr4A 88.740 373 40 2 2456 2827 740868120 740867749 4.670000e-124 455.0
30 TraesCS7A01G004400 chr1A 83.420 193 26 6 280 472 323632239 323632425 1.460000e-39 174.0
31 TraesCS7A01G004400 chr5B 82.564 195 25 9 282 475 579517262 579517076 3.170000e-36 163.0
32 TraesCS7A01G004400 chr5B 74.051 316 69 11 282 593 421995453 421995147 2.500000e-22 117.0
33 TraesCS7A01G004400 chr5D 74.684 316 67 12 282 594 357156674 357156369 1.160000e-25 128.0
34 TraesCS7A01G004400 chr5D 97.368 38 1 0 601 638 242117133 242117170 9.200000e-07 65.8
35 TraesCS7A01G004400 chr5D 85.714 63 6 3 591 651 255943013 255943074 3.310000e-06 63.9
36 TraesCS7A01G004400 chr1B 78.610 187 34 6 284 470 2280341 2280521 6.960000e-23 119.0
37 TraesCS7A01G004400 chrUn 92.308 52 3 1 592 643 27363069 27363119 5.500000e-09 73.1
38 TraesCS7A01G004400 chrUn 94.444 36 1 1 593 628 42252696 42252730 2.000000e-03 54.7
39 TraesCS7A01G004400 chr3A 88.333 60 4 3 592 650 457465193 457465250 7.110000e-08 69.4


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 TraesCS7A01G004400 chr7A 2551244 2555208 3964 True 7323.000000 7323 100.000000 1 3965 1 chr7A.!!$R1 3964
1 TraesCS7A01G004400 chr7A 2848229 2852307 4078 True 3159.500000 3742 95.406000 1 3965 2 chr7A.!!$R3 3964
2 TraesCS7A01G004400 chr7A 3000842 3004358 3516 True 1698.500000 2082 90.480500 999 3965 2 chr7A.!!$R4 2966
3 TraesCS7A01G004400 chr7A 3379514 3380680 1166 False 1363.000000 1363 87.861000 913 2080 1 chr7A.!!$F1 1167
4 TraesCS7A01G004400 chr7D 3728304 3732273 3969 True 6490.000000 6490 96.215000 1 3965 1 chr7D.!!$R1 3964
5 TraesCS7A01G004400 chr7D 2429640 2431164 1524 False 1893.000000 1893 88.989000 2415 3965 1 chr7D.!!$F1 1550
6 TraesCS7A01G004400 chr7D 3438501 3442012 3511 False 1514.500000 1725 91.796000 992 3965 2 chr7D.!!$F2 2973
7 TraesCS7A01G004400 chr7D 3699324 3700894 1570 False 1050.500000 1602 90.392500 2417 3965 2 chr7D.!!$F3 1548
8 TraesCS7A01G004400 chr4A 733925994 733927121 1127 True 1648.000000 1648 92.964000 2829 3965 1 chr4A.!!$R1 1136
9 TraesCS7A01G004400 chr4A 739806199 739809751 3552 False 1493.000000 1687 91.440500 993 3965 2 chr4A.!!$F1 2972
10 TraesCS7A01G004400 chr4A 739831306 739834465 3159 False 1228.333333 1670 89.735000 965 3965 3 chr4A.!!$F2 3000
11 TraesCS7A01G004400 chr4A 742268538 742271708 3170 True 1225.666667 1698 89.585333 952 3965 3 chr4A.!!$R4 3013
12 TraesCS7A01G004400 chr4A 740060147 740063302 3155 True 1223.333333 1687 89.894667 965 3965 3 chr4A.!!$R2 3000
13 TraesCS7A01G004400 chr4A 740866587 740869549 2962 True 1169.000000 1753 90.959667 999 3965 3 chr4A.!!$R3 2966

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
182 183 0.104934 AGTAGTGGGGATGGCCTAGG 60.105 60.0 3.67 3.67 0.00 3.02 F
419 437 0.251033 AAGCTTGGTGCATGCTGAGA 60.251 50.0 20.33 0.00 42.61 3.27 F
420 438 0.959372 AGCTTGGTGCATGCTGAGAC 60.959 55.0 20.33 8.36 42.01 3.36 F
1997 2124 0.251341 AAACGCCTGCTTGGAAGGAT 60.251 50.0 0.00 0.00 36.91 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1323 1367 0.036732 GCCTGAATGTCCACACCTCA 59.963 55.000 0.00 0.00 0.00 3.86 R
1892 2019 2.124109 TTTGCGGCCTGTGACCAA 60.124 55.556 0.00 0.00 0.00 3.67 R
2208 2493 5.182570 TCTTTGATGAAACTTCCATCTGCAG 59.817 40.000 7.63 7.63 40.65 4.41 R
3705 4731 0.321653 GCACCCCGACATTTGTCTCT 60.322 55.000 8.91 0.00 42.66 3.10 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
33 34 2.684001 TTGCACTATGGTACTTCCCG 57.316 50.000 0.00 0.00 34.77 5.14
69 70 1.595382 GCCAAGTGACGACTGCAGT 60.595 57.895 21.88 21.88 30.61 4.40
182 183 0.104934 AGTAGTGGGGATGGCCTAGG 60.105 60.000 3.67 3.67 0.00 3.02
317 319 1.152589 TCAGTGGTTGGGCATGCAA 60.153 52.632 21.36 2.70 0.00 4.08
419 437 0.251033 AAGCTTGGTGCATGCTGAGA 60.251 50.000 20.33 0.00 42.61 3.27
420 438 0.959372 AGCTTGGTGCATGCTGAGAC 60.959 55.000 20.33 8.36 42.01 3.36
510 528 6.531948 GTGGTGAGACTACACATCAAGATAAC 59.468 42.308 0.00 0.00 41.88 1.89
533 551 5.957774 ACCCAAGTGCTCATAATAAAATGGT 59.042 36.000 0.00 0.00 0.00 3.55
844 881 5.754890 ACATTGTTTCATGTTCTGCCTTTTC 59.245 36.000 0.00 0.00 0.00 2.29
1217 1261 2.842496 AGAACTGGATGAAGCAGATCCA 59.158 45.455 10.08 10.08 45.90 3.41
1323 1367 2.180946 TCCTGGTGATGGCAGTCTAT 57.819 50.000 0.00 0.00 0.00 1.98
1709 1836 3.545124 ATTGCCGGGCGTCAGTCAA 62.545 57.895 15.40 0.90 0.00 3.18
1812 1939 4.095400 GAGGAGGGGCAGGAGGGA 62.095 72.222 0.00 0.00 0.00 4.20
1892 2019 1.027357 CAAGTTGTGCCACTGCTCTT 58.973 50.000 0.00 0.00 38.71 2.85
1997 2124 0.251341 AAACGCCTGCTTGGAAGGAT 60.251 50.000 0.00 0.00 36.91 3.24
2142 2340 7.864379 AGCAATTTCATTCTGAAGTTTGTACAG 59.136 33.333 0.00 0.00 37.70 2.74
2213 2498 9.294030 CCAAAAGATTAATAGTTAAAGCTGCAG 57.706 33.333 10.11 10.11 0.00 4.41
2470 3447 6.238049 GCTAGCACATTTCATCTCACTTGTAG 60.238 42.308 10.63 0.00 0.00 2.74
3272 4298 1.022735 GGATCACAGCAGCAATGGAG 58.977 55.000 0.00 0.00 0.00 3.86
3319 4345 8.601476 CATGACATGATCCTTGAATATATCGTG 58.399 37.037 10.03 0.00 39.93 4.35
3320 4346 7.670364 TGACATGATCCTTGAATATATCGTGT 58.330 34.615 0.00 8.36 46.20 4.49
3321 4347 7.599998 TGACATGATCCTTGAATATATCGTGTG 59.400 37.037 12.36 0.00 44.53 3.82
3322 4348 7.670364 ACATGATCCTTGAATATATCGTGTGA 58.330 34.615 0.00 0.00 43.48 3.58
3323 4349 8.316946 ACATGATCCTTGAATATATCGTGTGAT 58.683 33.333 0.00 0.00 43.48 3.06
3324 4350 8.815189 CATGATCCTTGAATATATCGTGTGATC 58.185 37.037 0.00 0.00 35.99 2.92
3325 4351 7.029563 TGATCCTTGAATATATCGTGTGATCG 58.970 38.462 0.00 0.00 35.99 3.69
3326 4352 6.327279 TCCTTGAATATATCGTGTGATCGT 57.673 37.500 0.00 0.00 35.99 3.73
3366 4392 8.842358 AAGAGAATTTTATTACTGTCGTTGGA 57.158 30.769 0.00 0.00 0.00 3.53
3434 4460 0.675633 ATGCAAAGCAGTGGTTCCAC 59.324 50.000 13.45 13.45 43.65 4.02
3566 4592 3.320610 AGTGCTAGATCTTGAGGGCTA 57.679 47.619 8.45 0.00 0.00 3.93
3650 4676 1.542915 CCTCCGACGAACAGAGGTTTA 59.457 52.381 9.09 0.00 41.96 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.941999 GCTGCAATGGTCTGGGAAGC 61.942 60.000 0.00 0.00 0.00 3.86
69 70 1.768684 AAGGGCGTTGAGAAGAGGCA 61.769 55.000 0.00 0.00 0.00 4.75
131 132 2.696707 CACCTTGCCATCCATTAGCATT 59.303 45.455 0.00 0.00 36.20 3.56
136 137 2.419990 CGTCTCACCTTGCCATCCATTA 60.420 50.000 0.00 0.00 0.00 1.90
182 183 1.161563 CGTCCTACTCTCGCCTCTCC 61.162 65.000 0.00 0.00 0.00 3.71
317 319 1.604593 GGTGGTCAGGCTGCACAAT 60.605 57.895 21.53 0.00 0.00 2.71
419 437 8.531146 CAAGATTTTTATCTTAATGGGTGGTGT 58.469 33.333 0.46 0.00 38.73 4.16
420 438 8.748412 TCAAGATTTTTATCTTAATGGGTGGTG 58.252 33.333 0.46 0.00 38.73 4.17
481 499 3.255888 TGATGTGTAGTCTCACCACTCAC 59.744 47.826 0.00 0.00 37.51 3.51
510 528 6.469782 ACCATTTTATTATGAGCACTTGGG 57.530 37.500 0.00 0.00 0.00 4.12
533 551 6.048732 TGAACCAACTAGAGATGCATACAA 57.951 37.500 0.00 0.00 0.00 2.41
844 881 3.260380 TGGTGGTGGCAAAATAATCTTGG 59.740 43.478 0.00 0.00 0.00 3.61
1217 1261 4.376225 TCCATGTCATATGCCATGTCAT 57.624 40.909 21.69 0.00 37.37 3.06
1323 1367 0.036732 GCCTGAATGTCCACACCTCA 59.963 55.000 0.00 0.00 0.00 3.86
1574 1618 4.096382 AGCCTTTATCATGTTTGGTTAGCG 59.904 41.667 0.00 0.00 0.00 4.26
1610 1737 3.573967 ACCAAATCCAATCAAGGACACAC 59.426 43.478 0.00 0.00 41.30 3.82
1709 1836 3.157881 TCATCGAAGTTCTGAGACACCT 58.842 45.455 0.56 0.00 0.00 4.00
1812 1939 7.060421 TCTTCTTCAACTTCCCTATGTTGTTT 58.940 34.615 0.00 0.00 42.71 2.83
1892 2019 2.124109 TTTGCGGCCTGTGACCAA 60.124 55.556 0.00 0.00 0.00 3.67
1997 2124 9.883142 AAACAAAAGAAATGATTTTGAGGTACA 57.117 25.926 15.77 0.00 46.01 2.90
2030 2158 6.665985 GCACAGTCGTTACTACACGTAATTTC 60.666 42.308 0.00 0.00 40.04 2.17
2142 2340 5.701290 ACTAGCTACATTTTTCAGTCACCAC 59.299 40.000 0.00 0.00 0.00 4.16
2208 2493 5.182570 TCTTTGATGAAACTTCCATCTGCAG 59.817 40.000 7.63 7.63 40.65 4.41
2213 2498 6.364435 GCAACTTCTTTGATGAAACTTCCATC 59.636 38.462 0.00 0.00 40.48 3.51
2263 2559 6.336842 TGTAACTAGTTGGAGGTCAGTTAC 57.663 41.667 18.56 13.38 46.00 2.50
2470 3447 4.808895 CCTGCCAAGAAAAAGGTAACAAAC 59.191 41.667 0.00 0.00 41.41 2.93
2958 3984 7.177216 TGCAAAATTTACTCCAATGATCACTCT 59.823 33.333 0.00 0.00 0.00 3.24
2978 4004 6.158598 GCTCTGGAAATAATGACTTGCAAAA 58.841 36.000 0.00 0.00 0.00 2.44
3272 4298 9.346725 GTCATGAACTTTAAATGATTTGACCTC 57.653 33.333 0.00 0.00 33.19 3.85
3319 4345 2.476619 CACTTGACTTGGACACGATCAC 59.523 50.000 0.00 0.00 0.00 3.06
3320 4346 2.364002 TCACTTGACTTGGACACGATCA 59.636 45.455 0.00 0.00 0.00 2.92
3321 4347 3.026630 TCACTTGACTTGGACACGATC 57.973 47.619 0.00 0.00 0.00 3.69
3322 4348 3.069586 TCTTCACTTGACTTGGACACGAT 59.930 43.478 0.00 0.00 0.00 3.73
3323 4349 2.429250 TCTTCACTTGACTTGGACACGA 59.571 45.455 0.00 0.00 0.00 4.35
3324 4350 2.797156 CTCTTCACTTGACTTGGACACG 59.203 50.000 0.00 0.00 0.00 4.49
3325 4351 4.060038 TCTCTTCACTTGACTTGGACAC 57.940 45.455 0.00 0.00 0.00 3.67
3326 4352 4.753516 TTCTCTTCACTTGACTTGGACA 57.246 40.909 0.00 0.00 0.00 4.02
3566 4592 7.615365 TCATATGCTTATTTGTCAAACCCTTCT 59.385 33.333 0.00 0.00 0.00 2.85
3603 4629 7.307694 TCAAATACTTCAGCACTAGCATTTTG 58.692 34.615 0.00 0.00 45.49 2.44
3650 4676 6.416631 TCTCGATCTTTGATGGAATCTCAT 57.583 37.500 0.00 0.00 45.81 2.90
3705 4731 0.321653 GCACCCCGACATTTGTCTCT 60.322 55.000 8.91 0.00 42.66 3.10
3807 4833 2.354103 CGGCTCCTTGTTCTTCTCATGA 60.354 50.000 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.