Multiple sequence alignment - TraesCS7D01G143800

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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 TraesCS7D01G143800 chr7D 100.000 3101 0 0 1 3101 91990452 91993552 0.000000e+00 5727.0
1 TraesCS7D01G143800 chr7D 75.318 1888 382 49 271 2101 59163135 59161275 0.000000e+00 828.0
2 TraesCS7D01G143800 chr7A 95.964 2973 97 10 141 3100 94130709 94133671 0.000000e+00 4804.0
3 TraesCS7D01G143800 chr7A 95.254 2697 93 12 141 2804 93897861 93900555 0.000000e+00 4239.0
4 TraesCS7D01G143800 chr7A 82.579 2365 318 38 322 2632 94186025 94188349 0.000000e+00 1999.0
5 TraesCS7D01G143800 chr7A 82.199 2365 326 38 322 2632 94217234 94219557 0.000000e+00 1947.0
6 TraesCS7D01G143800 chr7A 94.286 175 7 2 2860 3034 93900554 93900725 6.590000e-67 265.0
7 TraesCS7D01G143800 chr7A 96.479 142 5 0 1 142 93897685 93897826 5.170000e-58 235.0
8 TraesCS7D01G143800 chr7A 96.479 142 5 0 1 142 94130533 94130674 5.170000e-58 235.0
9 TraesCS7D01G143800 chr7B 94.624 2976 136 13 141 3101 42178465 42175499 0.000000e+00 4588.0
10 TraesCS7D01G143800 chr7B 83.108 2368 318 32 322 2635 42139948 42137609 0.000000e+00 2082.0
11 TraesCS7D01G143800 chr7B 92.958 142 10 0 1 142 42178641 42178500 1.130000e-49 207.0
12 TraesCS7D01G143800 chr7B 96.825 63 1 1 2630 2691 448003488 448003426 1.520000e-18 104.0
13 TraesCS7D01G143800 chr4B 79.882 169 25 6 2629 2794 47379502 47379340 7.030000e-22 115.0
14 TraesCS7D01G143800 chr2D 95.385 65 2 1 2630 2693 1634470 1634534 5.470000e-18 102.0
15 TraesCS7D01G143800 chr5B 95.082 61 3 0 2633 2693 203440204 203440144 2.550000e-16 97.1
16 TraesCS7D01G143800 chr4A 95.082 61 3 0 2633 2693 655050942 655050882 2.550000e-16 97.1
17 TraesCS7D01G143800 chrUn 88.608 79 6 3 2633 2708 34811531 34811453 3.290000e-15 93.5


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 TraesCS7D01G143800 chr7D 91990452 91993552 3100 False 5727.000000 5727 100.000000 1 3101 1 chr7D.!!$F1 3100
1 TraesCS7D01G143800 chr7D 59161275 59163135 1860 True 828.000000 828 75.318000 271 2101 1 chr7D.!!$R1 1830
2 TraesCS7D01G143800 chr7A 94130533 94133671 3138 False 2519.500000 4804 96.221500 1 3100 2 chr7A.!!$F4 3099
3 TraesCS7D01G143800 chr7A 94186025 94188349 2324 False 1999.000000 1999 82.579000 322 2632 1 chr7A.!!$F1 2310
4 TraesCS7D01G143800 chr7A 94217234 94219557 2323 False 1947.000000 1947 82.199000 322 2632 1 chr7A.!!$F2 2310
5 TraesCS7D01G143800 chr7A 93897685 93900725 3040 False 1579.666667 4239 95.339667 1 3034 3 chr7A.!!$F3 3033
6 TraesCS7D01G143800 chr7B 42175499 42178641 3142 True 2397.500000 4588 93.791000 1 3101 2 chr7B.!!$R3 3100
7 TraesCS7D01G143800 chr7B 42137609 42139948 2339 True 2082.000000 2082 83.108000 322 2635 1 chr7B.!!$R1 2313

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
126 127 3.896272 TGGCACGGGGTACTTTAAAATTT 59.104 39.13 0.00 0.0 0.00 1.82 F
1140 1225 0.180406 CCCGTGCTAGGGTTGCTATT 59.820 55.00 8.66 0.0 46.38 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1188 1273 0.452987 CATCAACAATGGGGTCAGCG 59.547 55.0 0.0 0.0 0.00 5.18 R
3072 3230 0.107081 TGTCGGTGAAACATTCCGGT 59.893 50.0 0.0 0.0 43.75 5.28 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
84 85 6.127083 CCAATTTTGTAACCCCAATATGAGCT 60.127 38.462 0.00 0.00 0.00 4.09
126 127 3.896272 TGGCACGGGGTACTTTAAAATTT 59.104 39.130 0.00 0.00 0.00 1.82
225 262 9.666626 CTACTAGTAGAGATTTTGGATGTAACG 57.333 37.037 23.20 0.00 35.21 3.18
682 725 9.300681 TGGATGTATGGATTAGGATGAAATTTC 57.699 33.333 11.41 11.41 0.00 2.17
1039 1124 1.916394 GCTCAGCTATCACGTACGTCG 60.916 57.143 19.94 14.17 46.00 5.12
1123 1208 1.686052 CTGACCTCTCTGCTATCACCC 59.314 57.143 0.00 0.00 0.00 4.61
1140 1225 0.180406 CCCGTGCTAGGGTTGCTATT 59.820 55.000 8.66 0.00 46.38 1.73
1383 1468 1.057275 TGGAGCAACACCCAGGTACA 61.057 55.000 0.00 0.00 0.00 2.90
1546 1631 4.496360 TGGTGCAAGCATGATACAAAATG 58.504 39.130 0.00 0.00 40.88 2.32
1601 1686 2.568956 TGAAGACTGTCCCTTCATCAGG 59.431 50.000 3.76 0.00 43.39 3.86
1636 1733 0.606401 ACAACACCAGATGCCTTCGG 60.606 55.000 0.00 0.00 0.00 4.30
1687 1787 0.244721 GGCACCACATTTTCCTCAGC 59.755 55.000 0.00 0.00 0.00 4.26
1915 2016 0.400213 TTTGGTCAACTCTGGCGGAT 59.600 50.000 0.00 0.00 0.00 4.18
2102 2203 4.320935 GCCGGAATCTTCTTCTAGCTAGAG 60.321 50.000 22.19 16.28 33.21 2.43
2223 2324 6.530181 CGCTCGAGGCAATAATATACATGTTA 59.470 38.462 15.58 0.00 41.91 2.41
2683 2824 5.948162 ACCATATTTCTCTTGACATGCAACT 59.052 36.000 0.00 0.00 31.96 3.16
2795 2952 2.367241 TGGGTCGTTTGATCTTCTGACA 59.633 45.455 0.00 0.00 0.00 3.58
2865 3022 0.824109 TTGATCTACACGCCCTCCTG 59.176 55.000 0.00 0.00 0.00 3.86
2909 3066 3.057315 CCAAAATCAAGCTTCGATGTGGT 60.057 43.478 20.08 0.00 29.91 4.16
2913 3070 0.798776 CAAGCTTCGATGTGGTCCAC 59.201 55.000 15.64 15.64 34.56 4.02
2914 3071 0.687354 AAGCTTCGATGTGGTCCACT 59.313 50.000 22.56 8.50 35.11 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 9.343539 GGCCTACTAACTTTCTCAATTTCATAT 57.656 33.333 0.00 0.0 0.00 1.78
47 48 7.256048 GGGTTACAAAATTGGCCTACTAACTTT 60.256 37.037 3.32 0.0 0.00 2.66
126 127 8.934023 AATGGACTTTTGAGTTTATAGGTTCA 57.066 30.769 0.00 0.0 0.00 3.18
479 519 0.717224 TCTTTTGAATCGCCGCGTAC 59.283 50.000 13.39 6.2 0.00 3.67
572 613 9.976511 TCTGTAGTAGGCATTAACATATTACAC 57.023 33.333 0.00 0.0 0.00 2.90
877 952 8.975295 CATATTGGTGAGAGATATGTGGAGATA 58.025 37.037 0.00 0.0 31.99 1.98
1039 1124 1.698165 TCACGCTCTTTGTCGTCATC 58.302 50.000 0.00 0.0 36.73 2.92
1123 1208 1.933853 GACAATAGCAACCCTAGCACG 59.066 52.381 0.00 0.0 0.00 5.34
1140 1225 7.658261 TCTTCTCATTTTCTTTCTCTACGACA 58.342 34.615 0.00 0.0 0.00 4.35
1188 1273 0.452987 CATCAACAATGGGGTCAGCG 59.547 55.000 0.00 0.0 0.00 5.18
1383 1468 3.260884 TCGAGAAGATAAGGTTTGCCACT 59.739 43.478 0.00 0.0 37.19 4.00
1566 1651 4.081476 ACAGTCTTCATGTGATTCGATGGA 60.081 41.667 0.00 0.0 0.00 3.41
1607 1692 1.696884 TCTGGTGTTGTGGCAGATGTA 59.303 47.619 0.00 0.0 0.00 2.29
1636 1733 1.003718 GTGGTGGTGGTAGTGGAGC 60.004 63.158 0.00 0.0 0.00 4.70
1915 2016 2.948979 GGTCATTGGCGGTCAAATCATA 59.051 45.455 0.00 0.0 39.05 2.15
2102 2203 7.277174 ACTAAAATGGCAATGATAACTAGCC 57.723 36.000 0.00 0.0 45.41 3.93
2173 2274 7.095481 CGGACTCAGTAAATTGTCCATATGATG 60.095 40.741 3.65 0.0 46.65 3.07
2223 2324 1.600485 GGTCCAACACGTCGAACATTT 59.400 47.619 0.00 0.0 0.00 2.32
2683 2824 9.480861 TTTGTGGGATGTTTATTATGTGGATAA 57.519 29.630 0.00 0.0 0.00 1.75
2795 2952 1.270678 GGCTTCCTCGGCGGTTATATT 60.271 52.381 7.21 0.0 0.00 1.28
2865 3022 2.898705 AGTGATGGCTCGATTCAGAAC 58.101 47.619 0.00 0.0 0.00 3.01
2909 3066 4.603094 TGGTCCTAGTAATGAGAGTGGA 57.397 45.455 0.00 0.0 0.00 4.02
2913 3070 3.643320 TGGCATGGTCCTAGTAATGAGAG 59.357 47.826 0.00 0.0 0.00 3.20
2914 3071 3.653164 TGGCATGGTCCTAGTAATGAGA 58.347 45.455 0.00 0.0 0.00 3.27
2996 3154 4.269523 AGGGAAGCGTTGCTGGCA 62.270 61.111 0.00 0.0 39.62 4.92
3000 3158 2.281761 CACCAGGGAAGCGTTGCT 60.282 61.111 0.00 0.0 42.56 3.91
3072 3230 0.107081 TGTCGGTGAAACATTCCGGT 59.893 50.000 0.00 0.0 43.75 5.28


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

AutoCloner maintained by Alex Coulton.