Multiple sequence alignment - TraesCS7A01G332100

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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 TraesCS7A01G332100 chr7A 100.000 3683 0 0 1 3683 485609362 485605680 0.000000e+00 6802.0
1 TraesCS7A01G332100 chr7A 97.792 951 18 3 93 1043 705505263 705506210 0.000000e+00 1637.0
2 TraesCS7A01G332100 chr7D 97.351 2643 67 2 1044 3683 436951373 436954015 0.000000e+00 4490.0
3 TraesCS7A01G332100 chr7D 96.703 91 3 0 2 92 436951290 436951380 6.370000e-33 152.0
4 TraesCS7A01G332100 chr7D 82.759 87 15 0 950 1036 469896566 469896652 1.100000e-10 78.7
5 TraesCS7A01G332100 chr7B 97.124 2643 73 2 1044 3683 453446756 453449398 0.000000e+00 4457.0
6 TraesCS7A01G332100 chr7B 97.802 91 2 0 2 92 453446673 453446763 1.370000e-34 158.0
7 TraesCS7A01G332100 chrUn 97.059 952 27 1 93 1043 63606294 63607245 0.000000e+00 1602.0
8 TraesCS7A01G332100 chr5A 97.062 953 22 3 92 1043 689692436 689693383 0.000000e+00 1600.0
9 TraesCS7A01G332100 chr5A 96.534 952 32 1 93 1044 319239711 319238761 0.000000e+00 1574.0
10 TraesCS7A01G332100 chr5A 96.324 952 33 2 90 1040 366251854 366252804 0.000000e+00 1563.0
11 TraesCS7A01G332100 chr5A 96.126 955 20 2 91 1044 689704883 689705821 0.000000e+00 1543.0
12 TraesCS7A01G332100 chr5A 95.846 650 25 1 93 742 689691789 689692436 0.000000e+00 1050.0
13 TraesCS7A01G332100 chr5A 96.308 325 8 4 719 1043 689705807 689706127 7.000000e-147 531.0
14 TraesCS7A01G332100 chr1B 96.414 948 32 2 93 1040 189327207 189328152 0.000000e+00 1561.0
15 TraesCS7A01G332100 chr4B 89.418 189 19 1 90 278 114485107 114485294 1.710000e-58 237.0
16 TraesCS7A01G332100 chr4A 90.000 100 2 2 275 374 618241921 618242012 4.990000e-24 122.0
17 TraesCS7A01G332100 chr2A 87.209 86 11 0 958 1043 335679159 335679074 8.420000e-17 99.0


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 TraesCS7A01G332100 chr7A 485605680 485609362 3682 True 6802.0 6802 100.000 1 3683 1 chr7A.!!$R1 3682
1 TraesCS7A01G332100 chr7A 705505263 705506210 947 False 1637.0 1637 97.792 93 1043 1 chr7A.!!$F1 950
2 TraesCS7A01G332100 chr7D 436951290 436954015 2725 False 2321.0 4490 97.027 2 3683 2 chr7D.!!$F2 3681
3 TraesCS7A01G332100 chr7B 453446673 453449398 2725 False 2307.5 4457 97.463 2 3683 2 chr7B.!!$F1 3681
4 TraesCS7A01G332100 chrUn 63606294 63607245 951 False 1602.0 1602 97.059 93 1043 1 chrUn.!!$F1 950
5 TraesCS7A01G332100 chr5A 319238761 319239711 950 True 1574.0 1574 96.534 93 1044 1 chr5A.!!$R1 951
6 TraesCS7A01G332100 chr5A 366251854 366252804 950 False 1563.0 1563 96.324 90 1040 1 chr5A.!!$F1 950
7 TraesCS7A01G332100 chr5A 689691789 689693383 1594 False 1325.0 1600 96.454 92 1043 2 chr5A.!!$F2 951
8 TraesCS7A01G332100 chr5A 689704883 689706127 1244 False 1037.0 1543 96.217 91 1044 2 chr5A.!!$F3 953
9 TraesCS7A01G332100 chr1B 189327207 189328152 945 False 1561.0 1561 96.414 93 1040 1 chr1B.!!$F1 947

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
538 1185 0.179468 ATTCGTACACCGGGGAATGG 59.821 55.0 12.96 0.0 37.11 3.16 F
1188 2146 1.023513 AGAGCTTCTGTCAATGGCGC 61.024 55.0 0.00 0.0 0.00 6.53 F
1872 2830 0.106335 CCTTCGCTCATGCATCCTCT 59.894 55.0 0.00 0.0 39.64 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1411 2369 0.107456 GACAGTGCATCGGGGATCAT 59.893 55.000 0.0 0.0 0.00 2.45 R
2278 3236 3.142579 AGACCCCAGAGAAGGAATGAT 57.857 47.619 0.0 0.0 0.00 2.45 R
3399 4360 0.618981 ATCTTTTCCACCCCTCGGAC 59.381 55.000 0.0 0.0 30.29 4.79 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
43 44 3.259374 TCCCTACACTGCTTCTTTCTCTG 59.741 47.826 0.00 0.00 0.00 3.35
84 85 2.731691 TTCTTCCCCTGCACGCACTC 62.732 60.000 0.00 0.00 0.00 3.51
85 86 4.329545 TTCCCCTGCACGCACTCC 62.330 66.667 0.00 0.00 0.00 3.85
88 89 4.767255 CCCTGCACGCACTCCCTC 62.767 72.222 0.00 0.00 0.00 4.30
188 835 7.724305 AAGAGTCAATACACATTACAAACGT 57.276 32.000 0.00 0.00 0.00 3.99
189 836 7.724305 AGAGTCAATACACATTACAAACGTT 57.276 32.000 0.00 0.00 0.00 3.99
401 1048 7.504238 ACAAACTTTCCACCATATTGTACAAGA 59.496 33.333 14.65 10.17 0.00 3.02
538 1185 0.179468 ATTCGTACACCGGGGAATGG 59.821 55.000 12.96 0.00 37.11 3.16
626 1273 2.359107 CCTTCGCTGGAGCTTGCA 60.359 61.111 7.80 0.00 39.32 4.08
1088 2046 2.023414 AACAACTCTGACGCCGACCA 62.023 55.000 0.00 0.00 0.00 4.02
1188 2146 1.023513 AGAGCTTCTGTCAATGGCGC 61.024 55.000 0.00 0.00 0.00 6.53
1233 2191 2.534019 CGCAGCACCTCGTGTTGTT 61.534 57.895 9.82 0.00 44.49 2.83
1383 2341 2.224281 CCTGGCACAACTCAGACAACTA 60.224 50.000 0.00 0.00 38.70 2.24
1411 2369 0.179048 CATCAACTCCATAGGCGGCA 60.179 55.000 13.08 0.00 0.00 5.69
1518 2476 3.679389 TCTTGCTCAAAGTTCATCCCTC 58.321 45.455 0.00 0.00 37.18 4.30
1521 2479 2.038426 TGCTCAAAGTTCATCCCTCGAA 59.962 45.455 0.00 0.00 0.00 3.71
1530 2488 1.066858 TCATCCCTCGAACAGCTTGTC 60.067 52.381 0.00 0.00 0.00 3.18
1533 2491 0.390472 CCCTCGAACAGCTTGTCCTC 60.390 60.000 0.00 0.00 0.00 3.71
1539 2497 2.139118 GAACAGCTTGTCCTCAGTGAC 58.861 52.381 0.00 0.00 35.77 3.67
1560 2518 3.181434 ACAACTTTCTTCAGGGGCACATA 60.181 43.478 0.00 0.00 0.00 2.29
1583 2541 2.650778 CGGGTTTGCCTTGCTTCC 59.349 61.111 0.00 0.00 34.45 3.46
1637 2595 1.089920 CTTTCAGGCACCATTCCTCG 58.910 55.000 0.00 0.00 0.00 4.63
1718 2676 3.369576 GGAGAAATTCCACGCTTCCTAGT 60.370 47.826 0.00 0.00 46.01 2.57
1858 2816 4.515404 GGTCAATCCCGTCCTTCG 57.485 61.111 0.00 0.00 39.52 3.79
1872 2830 0.106335 CCTTCGCTCATGCATCCTCT 59.894 55.000 0.00 0.00 39.64 3.69
1893 2851 6.709846 CCTCTCCCTTGAAATATCTTAGCTTG 59.290 42.308 0.00 0.00 0.00 4.01
1959 2917 5.236425 ACTTTTCCTCCCTATCCTTCCTA 57.764 43.478 0.00 0.00 0.00 2.94
1980 2938 5.412594 CCTATTGCTTGCTCTGAACAACTTA 59.587 40.000 0.00 0.00 0.00 2.24
1988 2946 5.292765 TGCTCTGAACAACTTACAAGAGAG 58.707 41.667 1.80 0.00 0.00 3.20
2272 3230 1.013596 CCTCCGCAATAACGCATTCA 58.986 50.000 0.00 0.00 0.00 2.57
2278 3236 2.350192 CGCAATAACGCATTCAGTGGTA 59.650 45.455 0.00 0.00 33.76 3.25
2637 3595 7.106439 TGTCCTGAATTTAGCAGAAAACAAA 57.894 32.000 0.00 0.00 35.39 2.83
2907 3866 5.236047 AGCAGCTTAAATAATCTTGAGCTCG 59.764 40.000 9.64 0.00 44.03 5.03
3306 4267 5.680619 TCATATGTTCTAATGGTGGTGGTC 58.319 41.667 1.90 0.00 0.00 4.02
3344 4305 7.468141 TTGTTCTAGTCTCACTCATATGTGT 57.532 36.000 4.59 4.59 38.90 3.72
3399 4360 3.457610 AAACAACCAATCAACCAGCAG 57.542 42.857 0.00 0.00 0.00 4.24
3481 4442 4.755266 TCTATTAACCTGGTTGGAGAGC 57.245 45.455 22.04 0.00 39.71 4.09
3525 4486 2.092323 GGTACATTCTTGGCTGAACCC 58.908 52.381 0.00 0.00 37.83 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 2.281484 TGCGTGCAGGGGAAGAAC 60.281 61.111 8.72 0.00 0.00 3.01
86 87 1.527148 TCCTCCGCCTCTGATCGAG 60.527 63.158 7.37 7.37 39.57 4.04
87 88 1.824329 GTCCTCCGCCTCTGATCGA 60.824 63.158 0.00 0.00 0.00 3.59
88 89 2.725008 GTCCTCCGCCTCTGATCG 59.275 66.667 0.00 0.00 0.00 3.69
89 90 1.384989 TTCGTCCTCCGCCTCTGATC 61.385 60.000 0.00 0.00 36.19 2.92
188 835 8.754080 CCTACATTTTCATTGTATTGGGGTTAA 58.246 33.333 0.00 0.00 0.00 2.01
189 836 7.147811 GCCTACATTTTCATTGTATTGGGGTTA 60.148 37.037 0.00 0.00 0.00 2.85
538 1185 1.338105 GCAGTTGGGAATTTTCCTGGC 60.338 52.381 9.13 3.26 46.72 4.85
626 1273 2.427753 GCTTATAGGGCTGCCGCT 59.572 61.111 13.40 13.22 37.98 5.52
638 1285 3.825623 GGCAGGCTGGGGGCTTAT 61.826 66.667 17.64 0.00 46.62 1.73
1088 2046 1.882989 GAGGCAGAGGAGCGTCTGTT 61.883 60.000 18.10 9.50 45.07 3.16
1188 2146 2.557805 GTGCTGCATGTCACACCG 59.442 61.111 5.27 0.00 33.63 4.94
1221 2179 0.944311 CTAGCGCAACAACACGAGGT 60.944 55.000 11.47 0.00 0.00 3.85
1233 2191 1.433471 CGACATGAGGTCTAGCGCA 59.567 57.895 11.47 0.00 44.68 6.09
1383 2341 2.957402 TGGAGTTGATGCTGAGGTTT 57.043 45.000 0.00 0.00 0.00 3.27
1411 2369 0.107456 GACAGTGCATCGGGGATCAT 59.893 55.000 0.00 0.00 0.00 2.45
1518 2476 1.143305 CACTGAGGACAAGCTGTTCG 58.857 55.000 0.00 0.00 29.06 3.95
1521 2479 1.123077 TGTCACTGAGGACAAGCTGT 58.877 50.000 2.01 0.00 44.34 4.40
1530 2488 3.812053 CCTGAAGAAAGTTGTCACTGAGG 59.188 47.826 0.00 0.00 31.60 3.86
1533 2491 2.880890 CCCCTGAAGAAAGTTGTCACTG 59.119 50.000 0.00 0.00 31.60 3.66
1539 2497 1.691196 TGTGCCCCTGAAGAAAGTTG 58.309 50.000 0.00 0.00 0.00 3.16
1583 2541 8.608844 AGCAAAGGATAATATAGAAAGGTTCG 57.391 34.615 0.00 0.00 34.02 3.95
1617 2575 0.813821 GAGGAATGGTGCCTGAAAGC 59.186 55.000 0.00 0.00 35.44 3.51
1637 2595 0.175989 CGAGTTGCCTCCTAGGAACC 59.824 60.000 13.77 7.15 37.67 3.62
1656 2614 0.444260 GAGCAAGCTTGGTAAGACGC 59.556 55.000 29.74 13.45 39.30 5.19
1718 2676 0.615331 AGCAAGCGAGGAGGAATTCA 59.385 50.000 7.93 0.00 0.00 2.57
1851 2809 0.179062 AGGATGCATGAGCGAAGGAC 60.179 55.000 2.46 0.00 46.23 3.85
1858 2816 0.473326 AAGGGAGAGGATGCATGAGC 59.527 55.000 2.46 0.00 42.57 4.26
1872 2830 7.200434 AGTCAAGCTAAGATATTTCAAGGGA 57.800 36.000 0.00 0.00 0.00 4.20
1953 2911 4.005650 TGTTCAGAGCAAGCAATAGGAAG 58.994 43.478 0.00 0.00 0.00 3.46
1959 2917 4.580167 TGTAAGTTGTTCAGAGCAAGCAAT 59.420 37.500 0.00 0.00 0.00 3.56
1980 2938 2.093553 GCTCTCTGGAATGCTCTCTTGT 60.094 50.000 0.00 0.00 0.00 3.16
1988 2946 2.998316 ACCTAAGCTCTCTGGAATGC 57.002 50.000 0.00 0.00 0.00 3.56
2162 3120 5.945191 TGCATTACCAACATCTGAATTCTCA 59.055 36.000 7.05 0.00 0.00 3.27
2272 3230 3.713764 CCCAGAGAAGGAATGATACCACT 59.286 47.826 0.00 0.00 0.00 4.00
2278 3236 3.142579 AGACCCCAGAGAAGGAATGAT 57.857 47.619 0.00 0.00 0.00 2.45
2907 3866 6.037610 CAGATAGCTGGTTGTTGGAGATTAAC 59.962 42.308 0.00 0.00 38.51 2.01
3344 4305 4.635765 GCTTTCTGTGTACAATGGCTATGA 59.364 41.667 0.00 0.00 0.00 2.15
3399 4360 0.618981 ATCTTTTCCACCCCTCGGAC 59.381 55.000 0.00 0.00 30.29 4.79
3481 4442 1.763968 TAGACAGATCCACACCCTCG 58.236 55.000 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.