Multiple sequence alignment - TraesCS7A01G411600

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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 TraesCS7A01G411600 chr7A 100.000 2468 0 0 1 2468 602659703 602657236 0.000000e+00 4558.0
1 TraesCS7A01G411600 chr7A 77.386 482 54 25 668 1103 602098799 602099271 4.100000e-58 235.0
2 TraesCS7A01G411600 chr7A 100.000 92 0 0 2235 2326 602657189 602657280 1.170000e-38 171.0
3 TraesCS7A01G411600 chr7A 96.078 51 2 0 2418 2468 602657372 602657422 1.570000e-12 84.2
4 TraesCS7A01G411600 chr7D 92.573 1737 73 20 723 2410 522154981 522153252 0.000000e+00 2442.0
5 TraesCS7A01G411600 chr7D 92.297 688 38 7 1 687 522155650 522154977 0.000000e+00 963.0
6 TraesCS7A01G411600 chr7D 88.626 422 33 6 1781 2187 422617416 422616995 1.320000e-137 499.0
7 TraesCS7A01G411600 chr7D 78.151 476 57 20 668 1103 521763467 521763935 2.430000e-65 259.0
8 TraesCS7A01G411600 chr7D 100.000 51 0 0 2418 2468 522153329 522153379 7.270000e-16 95.3
9 TraesCS7A01G411600 chr7B 94.147 1589 59 13 207 1766 556334145 556332562 0.000000e+00 2388.0
10 TraesCS7A01G411600 chr7B 79.229 597 68 25 1209 1758 555656084 555656671 5.020000e-97 364.0
11 TraesCS7A01G411600 chr7B 91.781 219 8 5 1 213 556335829 556335615 1.860000e-76 296.0
12 TraesCS7A01G411600 chr7B 78.497 479 54 20 668 1103 555655513 555655985 4.050000e-68 268.0
13 TraesCS7A01G411600 chr7B 86.036 222 26 4 2190 2410 556332229 556332012 1.480000e-57 233.0
14 TraesCS7A01G411600 chr7B 93.023 43 1 1 2370 2410 512684979 512685021 7.370000e-06 62.1
15 TraesCS7A01G411600 chr1D 89.095 431 32 7 1771 2186 460919094 460919524 2.810000e-144 521.0
16 TraesCS7A01G411600 chr1D 74.089 494 69 33 996 1467 37517704 37517248 5.500000e-32 148.0
17 TraesCS7A01G411600 chr6D 88.647 414 39 7 1780 2186 123124340 123124752 4.740000e-137 497.0
18 TraesCS7A01G411600 chr2B 88.078 411 41 8 1782 2186 170995201 170994793 4.770000e-132 481.0
19 TraesCS7A01G411600 chr2A 87.591 411 46 5 1777 2185 75050278 75050685 2.870000e-129 472.0
20 TraesCS7A01G411600 chr2A 89.136 359 32 6 1832 2186 757931942 757931587 8.100000e-120 440.0
21 TraesCS7A01G411600 chr3D 87.651 413 36 11 1780 2186 360579809 360579406 1.340000e-127 466.0
22 TraesCS7A01G411600 chr5D 86.779 416 45 5 1780 2186 224321747 224321333 2.890000e-124 455.0
23 TraesCS7A01G411600 chr4D 85.476 420 47 11 1780 2186 126895961 126895543 2.270000e-115 425.0
24 TraesCS7A01G411600 chr4B 84.578 415 42 8 1780 2180 13083302 13083708 2.300000e-105 392.0
25 TraesCS7A01G411600 chr4A 81.690 426 51 10 1777 2186 673737181 673736767 1.830000e-86 329.0
26 TraesCS7A01G411600 chr1A 74.377 281 49 17 1209 1471 36768108 36767833 5.620000e-17 99.0
27 TraesCS7A01G411600 chr1B 97.297 37 0 1 1502 1538 57430689 57430654 7.370000e-06 62.1


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 TraesCS7A01G411600 chr7A 602657236 602659703 2467 True 4558.000000 4558 100.000000 1 2468 1 chr7A.!!$R1 2467
1 TraesCS7A01G411600 chr7D 522153252 522155650 2398 True 1702.500000 2442 92.435000 1 2410 2 chr7D.!!$R2 2409
2 TraesCS7A01G411600 chr7B 556332012 556335829 3817 True 972.333333 2388 90.654667 1 2410 3 chr7B.!!$R1 2409
3 TraesCS7A01G411600 chr7B 555655513 555656671 1158 False 316.000000 364 78.863000 668 1758 2 chr7B.!!$F2 1090

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
53 54 0.770499 TGACAGCACCAATTCCCAGA 59.23 50.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1672 3288 1.864565 TCCACGCATATTGTCGATGG 58.135 50.0 0.0 0.0 0.0 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
47 48 6.160576 ACTAACAAATTGACAGCACCAATT 57.839 33.333 0.00 0.00 43.66 2.32
53 54 0.770499 TGACAGCACCAATTCCCAGA 59.230 50.000 0.00 0.00 0.00 3.86
87 88 7.210174 TCCATCTAGTACATCTTATGCAACAC 58.790 38.462 0.00 0.00 0.00 3.32
104 105 5.298276 TGCAACACGAAAAGAAATACTCCTT 59.702 36.000 0.00 0.00 0.00 3.36
147 148 7.891498 TGTAGCACAGTAATAGAATCCACTA 57.109 36.000 0.00 0.00 0.00 2.74
149 150 8.195436 TGTAGCACAGTAATAGAATCCACTAAC 58.805 37.037 0.00 0.00 0.00 2.34
213 220 2.570302 GAGGGCACTACCTTTCCAGTTA 59.430 50.000 0.00 0.00 42.10 2.24
216 223 4.141111 AGGGCACTACCTTTCCAGTTAAAA 60.141 41.667 0.00 0.00 37.69 1.52
217 1699 4.585581 GGGCACTACCTTTCCAGTTAAAAA 59.414 41.667 0.00 0.00 39.10 1.94
280 1764 6.544197 TGTTGTCCTTGCTATTTTGTACTGAA 59.456 34.615 0.00 0.00 0.00 3.02
283 1767 8.856153 TGTCCTTGCTATTTTGTACTGAAATA 57.144 30.769 11.75 11.75 0.00 1.40
364 1849 1.393539 CGGCTAAAACGACATCACAGG 59.606 52.381 0.00 0.00 0.00 4.00
478 1963 6.951062 TTTCAATGGAATTATACGCATCCA 57.049 33.333 0.00 0.00 45.42 3.41
481 1966 3.769739 TGGAATTATACGCATCCAGCT 57.230 42.857 0.00 0.00 42.61 4.24
574 2059 2.225547 ACTCCTAGGCAACAGTTCCCTA 60.226 50.000 2.96 2.78 41.41 3.53
652 2137 2.911509 TGTGCCACCACATGTGCC 60.912 61.111 20.81 8.46 46.51 5.01
658 2143 1.531365 CACCACATGTGCCCCTTGT 60.531 57.895 20.81 8.77 38.34 3.16
737 2223 5.613358 AGTAGCACTGTAACAAAAGCATC 57.387 39.130 0.00 0.00 0.00 3.91
798 2284 5.182380 CCAGGAAGATTATCGGAGAGTACTC 59.818 48.000 15.41 15.41 43.63 2.59
808 2294 4.138290 TCGGAGAGTACTCATCCTGATTC 58.862 47.826 24.44 10.33 44.22 2.52
978 2504 1.301716 GCACACACTCCACATCGGT 60.302 57.895 0.00 0.00 35.57 4.69
1124 2664 1.976404 TCATCATCTGAGGCCTCATCC 59.024 52.381 35.11 9.31 39.13 3.51
1473 3058 2.924290 GGTGCTCAGCTTCTAAAGTACG 59.076 50.000 0.00 0.00 0.00 3.67
1555 3144 1.662122 CCTAACGTTTGTGGGTATCGC 59.338 52.381 5.91 0.00 0.00 4.58
1559 3156 1.273048 ACGTTTGTGGGTATCGCACTA 59.727 47.619 15.57 7.52 45.53 2.74
1672 3288 8.553696 CGGGAAAATATAAGTATGTACACCAAC 58.446 37.037 0.00 0.00 0.00 3.77
1688 3306 1.939934 CCAACCATCGACAATATGCGT 59.060 47.619 0.00 0.00 0.00 5.24
1826 3444 3.243704 CCATGGAGCTCGGTTTTGAAAAA 60.244 43.478 5.56 0.00 0.00 1.94
1940 3559 1.722011 AGTACGTTGAAATGAGGGCG 58.278 50.000 0.00 0.00 0.00 6.13
1976 3597 6.872920 ACAAATCTGAGGCTTTTTAACACAA 58.127 32.000 0.00 0.00 0.00 3.33
1994 3615 4.080863 ACACAAGACACTATTCATCCTCCC 60.081 45.833 0.00 0.00 0.00 4.30
1997 3618 3.312890 AGACACTATTCATCCTCCCAGG 58.687 50.000 0.00 0.00 36.46 4.45
2046 3667 5.643348 GGTCCCATTTCAATGTTTTTCATCC 59.357 40.000 0.00 0.00 35.48 3.51
2089 3710 8.349983 ACACATAACATCCTTGTTTACTTTCAC 58.650 33.333 0.00 0.00 43.57 3.18
2278 3935 5.058490 CCATTTGGAAGCAAAACTGAACAT 58.942 37.500 0.00 0.00 37.39 2.71
2326 3983 7.050377 ACGAGTATGAAATCTGGATGTTGATT 58.950 34.615 0.00 0.00 34.75 2.57
2328 3985 8.400947 CGAGTATGAAATCTGGATGTTGATTTT 58.599 33.333 0.00 0.00 41.30 1.82
2413 4070 9.500701 AACCCATTTGTTATATCCAATAAAGGT 57.499 29.630 0.00 0.00 0.00 3.50
2414 4071 9.500701 ACCCATTTGTTATATCCAATAAAGGTT 57.499 29.630 0.00 0.00 0.00 3.50
2446 4103 8.768957 ATATCAACATCCAGATTTCATACTCG 57.231 34.615 0.00 0.00 0.00 4.18
2447 4104 5.977635 TCAACATCCAGATTTCATACTCGT 58.022 37.500 0.00 0.00 0.00 4.18
2448 4105 7.107639 TCAACATCCAGATTTCATACTCGTA 57.892 36.000 0.00 0.00 0.00 3.43
2449 4106 7.203218 TCAACATCCAGATTTCATACTCGTAG 58.797 38.462 0.00 0.00 0.00 3.51
2450 4107 6.090483 ACATCCAGATTTCATACTCGTAGG 57.910 41.667 0.00 0.00 0.00 3.18
2451 4108 5.833667 ACATCCAGATTTCATACTCGTAGGA 59.166 40.000 0.00 0.00 0.00 2.94
2452 4109 6.495181 ACATCCAGATTTCATACTCGTAGGAT 59.505 38.462 0.00 0.00 32.70 3.24
2453 4110 6.978674 TCCAGATTTCATACTCGTAGGATT 57.021 37.500 0.00 0.00 0.00 3.01
2454 4111 8.523658 CATCCAGATTTCATACTCGTAGGATTA 58.476 37.037 0.00 0.00 30.22 1.75
2455 4112 8.651589 TCCAGATTTCATACTCGTAGGATTAT 57.348 34.615 0.00 0.00 0.00 1.28
2456 4113 9.749340 TCCAGATTTCATACTCGTAGGATTATA 57.251 33.333 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.878477 TGTTAGTTTTAATAGTCTGGTGTCG 57.122 36.000 0.00 0.00 0.00 4.35
20 21 7.101652 TGGTGCTGTCAATTTGTTAGTTTTA 57.898 32.000 0.00 0.00 0.00 1.52
47 48 1.909302 GATGGAAAGACACCTCTGGGA 59.091 52.381 0.00 0.00 36.25 4.37
53 54 6.198639 AGATGTACTAGATGGAAAGACACCT 58.801 40.000 0.00 0.00 0.00 4.00
58 59 8.250143 TGCATAAGATGTACTAGATGGAAAGA 57.750 34.615 0.00 0.00 0.00 2.52
104 105 7.820872 GTGCTACAAAACCACCTTCTATTACTA 59.179 37.037 0.00 0.00 0.00 1.82
147 148 2.716217 GCAGAAAGGCACTCATAGGTT 58.284 47.619 0.00 0.00 38.49 3.50
149 150 1.293924 CGCAGAAAGGCACTCATAGG 58.706 55.000 0.00 0.00 38.49 2.57
244 1726 2.656560 AGGACAACAGCTGTATCGAC 57.343 50.000 22.01 11.75 38.84 4.20
283 1767 7.121168 TGTGACATTTTCTTCAGAAGAACAGTT 59.879 33.333 22.97 9.41 46.53 3.16
309 1794 2.629617 CCTTTGAGCCCAAGTTTCACAT 59.370 45.455 0.00 0.00 33.23 3.21
311 1796 2.034685 GTCCTTTGAGCCCAAGTTTCAC 59.965 50.000 0.00 0.00 33.23 3.18
364 1849 8.709386 ATATATACGATGTGATCTTTGGCTTC 57.291 34.615 0.00 0.00 0.00 3.86
652 2137 0.532640 GCAAAAAGCCACCACAAGGG 60.533 55.000 0.00 0.00 39.26 3.95
737 2223 5.375417 TCCAAAACATGCAACAGTATCAG 57.625 39.130 0.00 0.00 0.00 2.90
798 2284 7.388224 CCTTTGATATCTCACAGAATCAGGATG 59.612 40.741 3.98 0.00 31.98 3.51
808 2294 6.462552 TCTCACTCCTTTGATATCTCACAG 57.537 41.667 3.98 0.00 0.00 3.66
978 2504 2.136298 TGGTTGCCAACAGAGAAACA 57.864 45.000 10.18 0.00 0.00 2.83
1672 3288 1.864565 TCCACGCATATTGTCGATGG 58.135 50.000 0.00 0.00 0.00 3.51
1688 3306 7.093421 TGCAATGTCTGAATTCCATTTTATCCA 60.093 33.333 2.27 0.00 0.00 3.41
1881 3500 4.707030 CACATGTGTGTTATGCCTTCAT 57.293 40.909 18.03 0.00 40.96 2.57
1913 3532 3.252215 TCATTTCAACGTACTTTGCCCTG 59.748 43.478 7.20 4.74 0.00 4.45
1976 3597 3.312890 CCTGGGAGGATGAATAGTGTCT 58.687 50.000 0.00 0.00 37.67 3.41
2347 4004 2.821969 GTTTGGTGCACCTCAGATGAAT 59.178 45.455 34.75 0.00 36.82 2.57
2356 4013 2.503775 CCAACAGTTTGGTGCACCT 58.496 52.632 34.75 13.76 46.63 4.00
2420 4077 9.860898 CGAGTATGAAATCTGGATGTTGATATA 57.139 33.333 0.00 0.00 0.00 0.86
2421 4078 8.370940 ACGAGTATGAAATCTGGATGTTGATAT 58.629 33.333 0.00 0.00 0.00 1.63
2422 4079 7.726216 ACGAGTATGAAATCTGGATGTTGATA 58.274 34.615 0.00 0.00 0.00 2.15
2423 4080 6.586344 ACGAGTATGAAATCTGGATGTTGAT 58.414 36.000 0.00 0.00 0.00 2.57
2424 4081 5.977635 ACGAGTATGAAATCTGGATGTTGA 58.022 37.500 0.00 0.00 0.00 3.18
2425 4082 6.422100 CCTACGAGTATGAAATCTGGATGTTG 59.578 42.308 0.00 0.00 0.00 3.33
2426 4083 6.323996 TCCTACGAGTATGAAATCTGGATGTT 59.676 38.462 0.00 0.00 0.00 2.71
2427 4084 5.833667 TCCTACGAGTATGAAATCTGGATGT 59.166 40.000 0.00 0.00 0.00 3.06
2428 4085 6.332735 TCCTACGAGTATGAAATCTGGATG 57.667 41.667 0.00 0.00 0.00 3.51
2429 4086 7.546250 AATCCTACGAGTATGAAATCTGGAT 57.454 36.000 0.00 0.00 32.68 3.41
2430 4087 6.978674 AATCCTACGAGTATGAAATCTGGA 57.021 37.500 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.