Multiple sequence alignment - TraesCS4B01G133000

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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 TraesCS4B01G133000 chr4B 100.000 2441 0 0 1 2441 172735837 172733397 0.000000e+00 4508.0
1 TraesCS4B01G133000 chr4D 96.828 2459 54 11 3 2441 112074332 112071878 0.000000e+00 4087.0
2 TraesCS4B01G133000 chr4D 89.720 107 10 1 243 348 484462820 484462714 4.230000e-28 135.0
3 TraesCS4B01G133000 chr4A 93.417 1200 73 2 407 1605 465227877 465229071 0.000000e+00 1773.0
4 TraesCS4B01G133000 chr4A 93.662 426 19 3 1609 2028 465229130 465229553 4.430000e-177 630.0
5 TraesCS4B01G133000 chr4A 90.116 172 15 2 70 240 465227679 465227849 3.160000e-54 222.0
6 TraesCS4B01G133000 chr4A 96.124 129 3 1 2313 2441 465259490 465259616 2.460000e-50 209.0
7 TraesCS4B01G133000 chr4A 89.873 79 6 2 2021 2097 585545674 585545596 1.540000e-17 100.0
8 TraesCS4B01G133000 chr7B 91.509 106 7 2 249 352 376359551 376359656 7.030000e-31 145.0
9 TraesCS4B01G133000 chr7B 100.000 43 0 0 29 71 540049007 540048965 2.010000e-11 80.5
10 TraesCS4B01G133000 chr5B 90.741 108 8 2 243 348 296853887 296853994 2.530000e-30 143.0
11 TraesCS4B01G133000 chr5A 92.157 102 6 2 245 345 524052482 524052582 2.530000e-30 143.0
12 TraesCS4B01G133000 chr7D 90.566 106 8 2 241 345 135974782 135974678 3.270000e-29 139.0
13 TraesCS4B01G133000 chr7D 100.000 41 0 0 31 71 511224103 511224063 2.600000e-10 76.8
14 TraesCS4B01G133000 chr7A 92.000 100 7 1 249 347 406995313 406995412 3.270000e-29 139.0
15 TraesCS4B01G133000 chr7A 92.500 80 5 1 2020 2098 335980734 335980813 1.980000e-21 113.0
16 TraesCS4B01G133000 chr7A 91.892 74 6 0 2025 2098 639290035 639289962 1.190000e-18 104.0
17 TraesCS4B01G133000 chr7A 97.561 41 1 0 31 71 583164407 583164367 1.210000e-08 71.3
18 TraesCS4B01G133000 chr5D 92.784 97 6 1 249 344 384468961 384468865 3.270000e-29 139.0
19 TraesCS4B01G133000 chr2B 88.393 112 10 3 237 345 556697794 556697683 5.480000e-27 132.0
20 TraesCS4B01G133000 chr2B 92.105 76 5 1 2023 2097 37357069 37357144 3.320000e-19 106.0
21 TraesCS4B01G133000 chr2D 95.652 69 3 0 2029 2097 555946543 555946475 7.130000e-21 111.0
22 TraesCS4B01G133000 chr6A 93.333 75 4 1 2024 2098 146554490 146554563 2.570000e-20 110.0
23 TraesCS4B01G133000 chr6A 93.151 73 5 0 2025 2097 23679308 23679380 9.230000e-20 108.0
24 TraesCS4B01G133000 chr6D 88.372 86 10 0 2012 2097 20107169 20107084 1.190000e-18 104.0
25 TraesCS4B01G133000 chr4B 100.000 2441 0 0 1 2441 172735837 172733397 0.000000e+00 4508.0
26 TraesCS4B01G133000 chr4D 96.828 2459 54 11 3 2441 112074332 112071878 0.000000e+00 4087.0
27 TraesCS4B01G133000 chr4D 89.720 107 10 1 243 348 484462820 484462714 4.230000e-28 135.0
28 TraesCS4B01G133000 chr4A 93.417 1200 73 2 407 1605 465227877 465229071 0.000000e+00 1773.0
29 TraesCS4B01G133000 chr4A 93.662 426 19 3 1609 2028 465229130 465229553 4.430000e-177 630.0
30 TraesCS4B01G133000 chr4A 90.116 172 15 2 70 240 465227679 465227849 3.160000e-54 222.0
31 TraesCS4B01G133000 chr4A 96.124 129 3 1 2313 2441 465259490 465259616 2.460000e-50 209.0
32 TraesCS4B01G133000 chr4A 89.873 79 6 2 2021 2097 585545674 585545596 1.540000e-17 100.0
33 TraesCS4B01G133000 chr7B 91.509 106 7 2 249 352 376359551 376359656 7.030000e-31 145.0
34 TraesCS4B01G133000 chr7B 100.000 43 0 0 29 71 540049007 540048965 2.010000e-11 80.5
35 TraesCS4B01G133000 chr5B 90.741 108 8 2 243 348 296853887 296853994 2.530000e-30 143.0
36 TraesCS4B01G133000 chr5A 92.157 102 6 2 245 345 524052482 524052582 2.530000e-30 143.0
37 TraesCS4B01G133000 chr7D 90.566 106 8 2 241 345 135974782 135974678 3.270000e-29 139.0
38 TraesCS4B01G133000 chr7D 100.000 41 0 0 31 71 511224103 511224063 2.600000e-10 76.8
39 TraesCS4B01G133000 chr7A 92.000 100 7 1 249 347 406995313 406995412 3.270000e-29 139.0
40 TraesCS4B01G133000 chr7A 92.500 80 5 1 2020 2098 335980734 335980813 1.980000e-21 113.0
41 TraesCS4B01G133000 chr7A 91.892 74 6 0 2025 2098 639290035 639289962 1.190000e-18 104.0
42 TraesCS4B01G133000 chr7A 97.561 41 1 0 31 71 583164407 583164367 1.210000e-08 71.3
43 TraesCS4B01G133000 chr5D 92.784 97 6 1 249 344 384468961 384468865 3.270000e-29 139.0
44 TraesCS4B01G133000 chr2B 88.393 112 10 3 237 345 556697794 556697683 5.480000e-27 132.0
45 TraesCS4B01G133000 chr2B 92.105 76 5 1 2023 2097 37357069 37357144 3.320000e-19 106.0
46 TraesCS4B01G133000 chr2D 95.652 69 3 0 2029 2097 555946543 555946475 7.130000e-21 111.0
47 TraesCS4B01G133000 chr6A 93.333 75 4 1 2024 2098 146554490 146554563 2.570000e-20 110.0
48 TraesCS4B01G133000 chr6A 93.151 73 5 0 2025 2097 23679308 23679380 9.230000e-20 108.0
49 TraesCS4B01G133000 chr6D 88.372 86 10 0 2012 2097 20107169 20107084 1.190000e-18 104.0


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 TraesCS4B01G133000 chr4B 172733397 172735837 2440 True 4508 4508 100.000000 1 2441 2 chr4B.!!$R1 2440
1 TraesCS4B01G133000 chr4D 112071878 112074332 2454 True 4087 4087 96.828000 3 2441 2 chr4D.!!$R1 2438
2 TraesCS4B01G133000 chr4A 465227679 465229553 1874 False 875 1773 92.398333 70 2028 6 chr4A.!!$F1 1958

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
723 726 0.391661 TGGACTTCAGCAATCTCCGC 60.392 55.0 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 2026 0.690762 AACGGCAGGTGATACCAAGT 59.309 50.0 0.28 0.0 41.95 3.16 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
230 233 9.499479 ACTCTCTTATATGCAATATTGGTTCTG 57.501 33.333 17.02 0.00 40.66 3.02
279 282 4.700213 CCGTCCCAAAATAAGTGTCTCAAT 59.300 41.667 0.00 0.00 0.00 2.57
723 726 0.391661 TGGACTTCAGCAATCTCCGC 60.392 55.000 0.00 0.00 0.00 5.54
768 771 1.672356 GGCGGTTGTGATCAGCTGT 60.672 57.895 14.67 0.42 34.39 4.40
891 894 3.927548 TGCTCAGCGTGCAGTCCA 61.928 61.111 0.00 0.00 35.31 4.02
913 916 2.479730 GCATCGACACTGAACTATCCGT 60.480 50.000 0.00 0.00 0.00 4.69
984 987 3.134127 GCCATCCGTGCCCTTGAC 61.134 66.667 0.00 0.00 0.00 3.18
1027 1030 1.594293 CAAGACGCGGACCACAACT 60.594 57.895 12.47 0.00 0.00 3.16
1173 1176 6.295575 GGGAGGAGATCAAGAATATACTGGTG 60.296 46.154 0.00 0.00 0.00 4.17
1176 1179 6.613271 AGGAGATCAAGAATATACTGGTGTGT 59.387 38.462 0.00 0.00 0.00 3.72
1179 1182 7.268586 AGATCAAGAATATACTGGTGTGTGAC 58.731 38.462 0.00 0.00 0.00 3.67
1188 1191 2.280592 GTGTGTGACGGGGTCCAC 60.281 66.667 9.15 9.15 35.70 4.02
1189 1192 3.552384 TGTGTGACGGGGTCCACC 61.552 66.667 11.91 0.00 34.92 4.61
1366 1369 1.679311 CTTCTGCTGTGCTGGGGTA 59.321 57.895 0.00 0.00 0.00 3.69
1503 1506 4.326278 CGAATAAGACGCTGTTGCTTAAGA 59.674 41.667 6.67 0.00 36.97 2.10
1542 1550 1.928503 CAAATTGATTGGTGCGATGCC 59.071 47.619 0.00 0.00 35.27 4.40
1619 1683 4.260194 CGAACTGATCTCGTCGTACTTTTC 59.740 45.833 0.00 0.00 0.00 2.29
1646 1710 3.069443 TGCCTTCATCAAAGTTGGGTTTC 59.931 43.478 0.00 0.00 32.69 2.78
1676 1740 9.807921 ATTAGGATATGGTTTAGGGTGTATTTG 57.192 33.333 0.00 0.00 0.00 2.32
1716 1780 2.154462 CTTCAGTTGACCGGCTGAAAT 58.846 47.619 18.88 0.07 46.82 2.17
1729 1793 3.677148 CGGCTGAAATAGAGCAGAGTTGA 60.677 47.826 0.00 0.00 38.27 3.18
1763 1833 4.553547 GCAAAGAAGCATAGTAAGATGGCG 60.554 45.833 0.00 0.00 0.00 5.69
1791 1861 1.089112 TGTGATTGCCTGCTTCGATG 58.911 50.000 0.00 0.00 0.00 3.84
1843 1913 1.352352 CCCAGTGTGATCCTCCTTGTT 59.648 52.381 0.00 0.00 0.00 2.83
1956 2026 1.211703 TGAGCACTCCAAGAACACCAA 59.788 47.619 0.00 0.00 0.00 3.67
2062 2132 3.902515 CATCTAGATGTGCCCCGAG 57.097 57.895 22.42 0.00 34.23 4.63
2067 2137 4.108501 TCTAGATGTGCCCCGAGTATTA 57.891 45.455 0.00 0.00 0.00 0.98
2125 2195 7.947782 AAATCCCAAGTGTATCCCTAGATTA 57.052 36.000 0.00 0.00 33.67 1.75
2270 2353 5.876357 TGGATACATATGGGCCTTCTAAAC 58.124 41.667 4.53 0.00 46.17 2.01
2276 2359 0.326927 TGGGCCTTCTAAACCGGAAG 59.673 55.000 9.46 0.00 39.65 3.46
2314 2397 8.578308 AACAACATGAATTGTGATGTTAACTG 57.422 30.769 7.22 0.00 42.01 3.16
2329 2412 4.215109 GTTAACTGGTGGGCCATGATTAT 58.785 43.478 10.70 0.00 45.05 1.28
2419 2502 6.373779 ACTAGAAAACATTGTTTGCTGATCG 58.626 36.000 26.48 16.32 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.598924 CATGATGTTACTATTGATAATCCTCGC 58.401 37.037 0.00 0.00 0.00 5.03
1 2 9.645059 ACATGATGTTACTATTGATAATCCTCG 57.355 33.333 0.00 0.00 0.00 4.63
20 21 7.243487 ACGTTTAAGCAGTTCAATACATGATG 58.757 34.615 0.00 0.00 38.03 3.07
169 172 2.753452 AGTCAAGCTTGGATGCAGATTG 59.247 45.455 25.73 7.85 38.71 2.67
230 233 3.610911 AGTAGTAATTGACCTTGCTGGC 58.389 45.455 0.00 0.00 40.22 4.85
723 726 6.418226 CACCGAAGTTTATCTTAAGGATCTCG 59.582 42.308 1.85 3.06 37.43 4.04
768 771 0.249615 GGCGATGCATCTGTAGAGCA 60.250 55.000 23.73 7.94 43.14 4.26
891 894 2.223595 CGGATAGTTCAGTGTCGATGCT 60.224 50.000 0.00 0.00 0.00 3.79
913 916 1.191535 CGTTGAGGGGATGGTGTCTA 58.808 55.000 0.00 0.00 0.00 2.59
1027 1030 3.000819 ATCGTGGAACAGCGGGGA 61.001 61.111 0.00 0.00 41.80 4.81
1173 1176 4.675029 CGGTGGACCCCGTCACAC 62.675 72.222 11.95 0.00 43.07 3.82
1366 1369 4.038763 TGAAATGGAGTACAGACGAGTTGT 59.961 41.667 0.00 0.00 0.00 3.32
1503 1506 5.664294 TTTGAGTTGCCATTCAAGCATAT 57.336 34.783 0.00 0.00 40.59 1.78
1542 1550 8.200792 ACTTTCATCTCTACATACCTAAGCTTG 58.799 37.037 9.86 0.00 0.00 4.01
1619 1683 1.915141 ACTTTGATGAAGGCAGGGTG 58.085 50.000 0.00 0.00 39.79 4.61
1646 1710 4.534897 ACCCTAAACCATATCCTAATCGGG 59.465 45.833 0.00 0.00 0.00 5.14
1716 1780 5.489792 ACTCCAAAATCAACTCTGCTCTA 57.510 39.130 0.00 0.00 0.00 2.43
1729 1793 4.405116 TGCTTCTTTGCAACTCCAAAAT 57.595 36.364 0.00 0.00 40.29 1.82
1763 1833 3.441572 AGCAGGCAATCACAAGAATGTAC 59.558 43.478 0.00 0.00 37.82 2.90
1791 1861 6.980397 CCTAATTCAAGGAAAACATATGGCAC 59.020 38.462 7.80 0.00 39.15 5.01
1843 1913 8.851145 TGCACACATACTTTTATACAGGAAAAA 58.149 29.630 0.00 0.00 0.00 1.94
1956 2026 0.690762 AACGGCAGGTGATACCAAGT 59.309 50.000 0.28 0.00 41.95 3.16
2111 2181 6.183360 GGTCAAGCTGTTAATCTAGGGATACA 60.183 42.308 0.00 0.00 39.74 2.29
2125 2195 5.590530 TGTGTTAAATTGGTCAAGCTGTT 57.409 34.783 0.00 0.00 0.00 3.16
2168 2238 8.507470 AGAAAATCTAACATTTGAAGTTTCGC 57.493 30.769 0.00 0.00 31.71 4.70
2221 2298 5.333111 GGCTCGACAATTTGACCGTAATATC 60.333 44.000 2.79 0.00 0.00 1.63
2223 2300 3.866910 GGCTCGACAATTTGACCGTAATA 59.133 43.478 2.79 0.00 0.00 0.98
2224 2301 2.676342 GGCTCGACAATTTGACCGTAAT 59.324 45.455 2.79 0.00 0.00 1.89
2225 2302 2.070783 GGCTCGACAATTTGACCGTAA 58.929 47.619 2.79 0.00 0.00 3.18
2228 2305 1.086696 ATGGCTCGACAATTTGACCG 58.913 50.000 2.79 6.52 0.00 4.79
2270 2353 3.952323 TGTTAGATACTCACTCCTTCCGG 59.048 47.826 0.00 0.00 0.00 5.14
2276 2359 8.607459 CAATTCATGTTGTTAGATACTCACTCC 58.393 37.037 0.00 0.00 0.00 3.85
2314 2397 4.101430 ACATTGAAATAATCATGGCCCACC 59.899 41.667 0.00 0.00 38.03 4.61
2419 2502 1.164411 TTCACGCATCAATGGTGACC 58.836 50.000 0.00 0.00 37.55 4.02


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

AutoCloner maintained by Alex Coulton.