Multiple sequence alignment - TraesCS5B01G521600

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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 TraesCS5B01G521600 chr5B 100.000 2654 0 0 1 2654 683581784 683579131 0 4902
1 TraesCS5B01G521600 chr5B 94.587 1127 57 1 998 2120 143302232 143303358 0 1740
2 TraesCS5B01G521600 chr5B 94.106 1001 54 5 1 998 636691500 636690502 0 1517
3 TraesCS5B01G521600 chr5B 93.148 540 28 7 2122 2654 591499823 591499286 0 784
4 TraesCS5B01G521600 chr6D 95.741 1127 44 1 998 2120 224420213 224419087 0 1812
5 TraesCS5B01G521600 chr2D 95.652 1127 45 1 998 2120 2075546 2076672 0 1807
6 TraesCS5B01G521600 chr2D 94.106 1001 55 4 1 998 16527013 16528012 0 1519
7 TraesCS5B01G521600 chr1D 95.386 1127 48 1 998 2120 361394810 361395936 0 1790
8 TraesCS5B01G521600 chr1D 93.407 546 32 4 2112 2654 303074539 303073995 0 806
9 TraesCS5B01G521600 chr1A 95.386 1127 48 1 998 2120 369589776 369588650 0 1790
10 TraesCS5B01G521600 chr1A 94.321 1127 60 1 998 2120 30755191 30754065 0 1724
11 TraesCS5B01G521600 chr6A 94.902 1118 52 2 1007 2120 277539872 277538756 0 1744
12 TraesCS5B01G521600 chr7B 94.321 1127 60 3 998 2120 706524305 706525431 0 1724
13 TraesCS5B01G521600 chr7B 93.800 1000 56 5 1 997 380388346 380387350 0 1498
14 TraesCS5B01G521600 chr6B 93.268 1129 68 5 998 2120 290851861 290852987 0 1657
15 TraesCS5B01G521600 chr6B 94.311 1002 52 5 1 998 290169059 290168059 0 1530
16 TraesCS5B01G521600 chr1B 94.800 1000 48 4 1 997 608514716 608513718 0 1555
17 TraesCS5B01G521600 chr7D 94.257 1010 51 7 1 1005 2963946 2964953 0 1537
18 TraesCS5B01G521600 chr7D 93.135 539 32 3 2120 2654 169776600 169776063 0 785
19 TraesCS5B01G521600 chr7D 92.844 545 32 4 2114 2654 540724809 540725350 0 784
20 TraesCS5B01G521600 chrUn 94.306 1001 53 4 1 998 126500011 126499012 0 1530
21 TraesCS5B01G521600 chr4B 94.217 1003 50 7 1 998 130664358 130663359 0 1524
22 TraesCS5B01G521600 chr4B 92.976 541 30 7 2119 2654 300804371 300804908 0 782
23 TraesCS5B01G521600 chr2B 93.906 1001 55 5 1 998 476627681 476628678 0 1506
24 TraesCS5B01G521600 chr2A 93.506 539 28 5 2121 2654 92426974 92427510 0 795
25 TraesCS5B01G521600 chr2A 92.857 546 28 9 2118 2654 1947036 1947579 0 782
26 TraesCS5B01G521600 chr4A 93.173 542 27 7 2121 2654 507568655 507568116 0 787
27 TraesCS5B01G521600 chr4A 92.818 543 32 6 2119 2654 238503533 238504075 0 780


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 TraesCS5B01G521600 chr5B 683579131 683581784 2653 True 4902 4902 100.000 1 2654 1 chr5B.!!$R3 2653
1 TraesCS5B01G521600 chr5B 143302232 143303358 1126 False 1740 1740 94.587 998 2120 1 chr5B.!!$F1 1122
2 TraesCS5B01G521600 chr5B 636690502 636691500 998 True 1517 1517 94.106 1 998 1 chr5B.!!$R2 997
3 TraesCS5B01G521600 chr5B 591499286 591499823 537 True 784 784 93.148 2122 2654 1 chr5B.!!$R1 532
4 TraesCS5B01G521600 chr6D 224419087 224420213 1126 True 1812 1812 95.741 998 2120 1 chr6D.!!$R1 1122
5 TraesCS5B01G521600 chr2D 2075546 2076672 1126 False 1807 1807 95.652 998 2120 1 chr2D.!!$F1 1122
6 TraesCS5B01G521600 chr2D 16527013 16528012 999 False 1519 1519 94.106 1 998 1 chr2D.!!$F2 997
7 TraesCS5B01G521600 chr1D 361394810 361395936 1126 False 1790 1790 95.386 998 2120 1 chr1D.!!$F1 1122
8 TraesCS5B01G521600 chr1D 303073995 303074539 544 True 806 806 93.407 2112 2654 1 chr1D.!!$R1 542
9 TraesCS5B01G521600 chr1A 369588650 369589776 1126 True 1790 1790 95.386 998 2120 1 chr1A.!!$R2 1122
10 TraesCS5B01G521600 chr1A 30754065 30755191 1126 True 1724 1724 94.321 998 2120 1 chr1A.!!$R1 1122
11 TraesCS5B01G521600 chr6A 277538756 277539872 1116 True 1744 1744 94.902 1007 2120 1 chr6A.!!$R1 1113
12 TraesCS5B01G521600 chr7B 706524305 706525431 1126 False 1724 1724 94.321 998 2120 1 chr7B.!!$F1 1122
13 TraesCS5B01G521600 chr7B 380387350 380388346 996 True 1498 1498 93.800 1 997 1 chr7B.!!$R1 996
14 TraesCS5B01G521600 chr6B 290851861 290852987 1126 False 1657 1657 93.268 998 2120 1 chr6B.!!$F1 1122
15 TraesCS5B01G521600 chr6B 290168059 290169059 1000 True 1530 1530 94.311 1 998 1 chr6B.!!$R1 997
16 TraesCS5B01G521600 chr1B 608513718 608514716 998 True 1555 1555 94.800 1 997 1 chr1B.!!$R1 996
17 TraesCS5B01G521600 chr7D 2963946 2964953 1007 False 1537 1537 94.257 1 1005 1 chr7D.!!$F1 1004
18 TraesCS5B01G521600 chr7D 169776063 169776600 537 True 785 785 93.135 2120 2654 1 chr7D.!!$R1 534
19 TraesCS5B01G521600 chr7D 540724809 540725350 541 False 784 784 92.844 2114 2654 1 chr7D.!!$F2 540
20 TraesCS5B01G521600 chrUn 126499012 126500011 999 True 1530 1530 94.306 1 998 1 chrUn.!!$R1 997
21 TraesCS5B01G521600 chr4B 130663359 130664358 999 True 1524 1524 94.217 1 998 1 chr4B.!!$R1 997
22 TraesCS5B01G521600 chr4B 300804371 300804908 537 False 782 782 92.976 2119 2654 1 chr4B.!!$F1 535
23 TraesCS5B01G521600 chr2B 476627681 476628678 997 False 1506 1506 93.906 1 998 1 chr2B.!!$F1 997
24 TraesCS5B01G521600 chr2A 92426974 92427510 536 False 795 795 93.506 2121 2654 1 chr2A.!!$F2 533
25 TraesCS5B01G521600 chr2A 1947036 1947579 543 False 782 782 92.857 2118 2654 1 chr2A.!!$F1 536
26 TraesCS5B01G521600 chr4A 507568116 507568655 539 True 787 787 93.173 2121 2654 1 chr4A.!!$R1 533
27 TraesCS5B01G521600 chr4A 238503533 238504075 542 False 780 780 92.818 2119 2654 1 chr4A.!!$F1 535

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
966 979 2.500504 GCTACTAGTGGGCACTAAACCT 59.499 50.0 5.39 0.0 42.72 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2286 2308 1.282157 AGGACTCTTATGTGTTGGCCC 59.718 52.381 0.0 0.0 0.0 5.8 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
60 61 4.338879 GGCCAAGATATCCTACAATGCAT 58.661 43.478 0.00 0.00 0.00 3.96
91 92 6.015434 TGCATACAGGATTTCTAATAGCGAGA 60.015 38.462 0.00 0.00 0.00 4.04
114 115 9.155975 GAGAAATGCTTAATAGTGAAAGACTGA 57.844 33.333 0.00 0.00 35.96 3.41
116 117 9.548208 GAAATGCTTAATAGTGAAAGACTGAAC 57.452 33.333 0.00 0.00 35.96 3.18
189 190 3.005897 GCAGCCCACGATTAGAAGATAGA 59.994 47.826 0.00 0.00 0.00 1.98
217 218 2.892215 TGCATGCTCCAACTTGATGAAA 59.108 40.909 20.33 0.00 0.00 2.69
220 221 4.796946 GCATGCTCCAACTTGATGAAACAA 60.797 41.667 11.37 0.00 0.00 2.83
288 294 7.015682 AGCAGGAGTGATTAATTAGCTAGCTAA 59.984 37.037 33.35 33.35 41.95 3.09
369 376 5.234329 GTGTTCGTGGTAATGACTATGATGG 59.766 44.000 0.00 0.00 32.66 3.51
433 440 5.453339 GCAGCTAGTATTGGTGGTGATTAGA 60.453 44.000 0.00 0.00 33.98 2.10
446 453 7.093992 GGTGGTGATTAGATAGCTAGAATGAC 58.906 42.308 0.00 3.58 0.00 3.06
486 493 7.373493 TGTGCTACACTATGACTATGATGATG 58.627 38.462 0.00 0.00 35.11 3.07
561 569 3.197766 TGCGGATTAGATTCAAGTGGAGT 59.802 43.478 0.00 0.00 0.00 3.85
702 710 9.679661 ATTTGACACACTGTTATGGACATAATA 57.320 29.630 7.90 4.95 37.69 0.98
966 979 2.500504 GCTACTAGTGGGCACTAAACCT 59.499 50.000 5.39 0.00 42.72 3.50
1090 1103 3.461773 CATGGACCCTCGTCGCCT 61.462 66.667 0.00 0.00 40.17 5.52
1221 1234 6.152379 GCTTCGATTTCCAAATGAGAAAAGT 58.848 36.000 0.00 0.00 36.83 2.66
1222 1235 6.642540 GCTTCGATTTCCAAATGAGAAAAGTT 59.357 34.615 0.00 0.00 36.83 2.66
1334 1347 3.038280 TCACTTGGGAGAACAGTCTTCA 58.962 45.455 0.00 0.00 32.80 3.02
1406 1419 7.418378 TGGGAATCTAAATTTCCTATGGTGTT 58.582 34.615 0.00 0.00 40.79 3.32
1559 1576 0.696143 TGGTCAAGGAGGTGTGGGAA 60.696 55.000 0.00 0.00 0.00 3.97
1564 1581 2.243736 TCAAGGAGGTGTGGGAAAAACT 59.756 45.455 0.00 0.00 0.00 2.66
1734 1751 3.181420 GGCAGAGGTTAGACCCCTATCTA 60.181 52.174 0.00 0.00 39.75 1.98
1737 1754 5.693321 GCAGAGGTTAGACCCCTATCTAAGA 60.693 48.000 0.00 0.00 40.92 2.10
1784 1802 6.084326 TCGAATGCACAGATAGCTAACATA 57.916 37.500 0.00 0.00 0.00 2.29
1787 1805 7.040686 TCGAATGCACAGATAGCTAACATACTA 60.041 37.037 0.00 0.00 0.00 1.82
1888 1906 1.021390 GGAGTCACCAATGGCAGACG 61.021 60.000 16.38 0.00 36.56 4.18
1952 1970 0.991146 TTGAGGGGCATGAGCAACTA 59.009 50.000 0.00 0.00 44.61 2.24
2107 2125 3.358118 ACTCGGAGGAGGAAGTTAGAAG 58.642 50.000 10.23 0.00 44.93 2.85
2160 2178 7.551585 AGAAATAAATGAGACACGAGAGACAT 58.448 34.615 0.00 0.00 0.00 3.06
2198 2219 1.376812 GCGGGAGAAAACCACGGAT 60.377 57.895 0.00 0.00 0.00 4.18
2243 2265 3.130693 AGGAGGAGTATTACAAGCACGAC 59.869 47.826 0.00 0.00 0.00 4.34
2269 2291 1.478510 AGACCATCTTAGGTGCGACTG 59.521 52.381 0.00 0.00 43.38 3.51
2286 2308 4.686972 CGACTGCATGGGGTATATATGAG 58.313 47.826 0.00 0.00 0.00 2.90
2289 2311 2.509548 TGCATGGGGTATATATGAGGGC 59.490 50.000 0.00 0.00 0.00 5.19
2346 2369 0.310543 TGTACTTGTACGCGTCGGTT 59.689 50.000 18.63 0.00 0.00 4.44
2350 2373 1.611592 CTTGTACGCGTCGGTTCCAC 61.612 60.000 18.63 7.15 0.00 4.02
2378 2403 2.764572 GGCCCACACTGTATGTACTACT 59.235 50.000 0.00 0.00 40.64 2.57
2538 2570 9.478768 GACTAATAGAAATACCAACTAAGCCTC 57.521 37.037 0.00 0.00 0.00 4.70
2550 2582 2.008329 CTAAGCCTCAGCAAAGCTCAG 58.992 52.381 0.00 0.00 43.56 3.35
2595 2627 7.572724 GCTTTGTCATCATATCAGCAGGATTAC 60.573 40.741 0.00 0.00 37.44 1.89
2598 2630 5.873712 GTCATCATATCAGCAGGATTACCAG 59.126 44.000 0.00 0.00 37.44 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.050769 CGTAAGCTAACAATTCTCATGCGAT 60.051 40.000 0.00 0.00 0.00 4.58
91 92 8.515414 GGTTCAGTCTTTCACTATTAAGCATTT 58.485 33.333 0.00 0.00 32.21 2.32
114 115 3.243234 TGCGATCGTTCACAATTTTGGTT 60.243 39.130 17.81 0.00 0.00 3.67
116 117 2.910482 CTGCGATCGTTCACAATTTTGG 59.090 45.455 17.81 0.00 0.00 3.28
182 183 5.221864 TGGAGCATGCAGATGAATCTATCTT 60.222 40.000 21.98 0.00 35.28 2.40
189 190 3.014304 AGTTGGAGCATGCAGATGAAT 57.986 42.857 21.98 0.00 38.09 2.57
217 218 7.038154 ACATAAAACATGTGTAGCACTTTGT 57.962 32.000 0.00 2.56 34.67 2.83
257 261 2.698855 TTAATCACTCCTGCTGCTCC 57.301 50.000 0.00 0.00 0.00 4.70
288 294 7.544566 GCACATCATCATCTTCAAACTCATTTT 59.455 33.333 0.00 0.00 0.00 1.82
350 357 7.962964 AATAACCATCATAGTCATTACCACG 57.037 36.000 0.00 0.00 0.00 4.94
369 376 7.767198 TCACCACCAACACTAGCTAATAATAAC 59.233 37.037 0.00 0.00 0.00 1.89
418 425 7.618019 TTCTAGCTATCTAATCACCACCAAT 57.382 36.000 0.00 0.00 0.00 3.16
446 453 8.206325 AGTGTAGCACATCATTATCTTCAAAG 57.794 34.615 2.01 0.00 36.74 2.77
456 463 7.955918 TCATAGTCATAGTGTAGCACATCATT 58.044 34.615 2.01 0.00 36.74 2.57
486 493 8.448615 GTCATTACCACCAACAGTAGTTATTTC 58.551 37.037 0.00 0.00 35.85 2.17
539 547 3.197766 ACTCCACTTGAATCTAATCCGCA 59.802 43.478 0.00 0.00 0.00 5.69
638 646 2.684881 CAAGTGGAGGCAATATGTGGTC 59.315 50.000 0.00 0.00 0.00 4.02
966 979 2.167075 GGAAAACCCTAGTAGTAGCGCA 59.833 50.000 11.47 0.00 0.00 6.09
1039 1052 3.487544 GCCTTGTTGCGAATATGGAGTTC 60.488 47.826 0.00 0.00 0.00 3.01
1221 1234 6.127479 GCCAATGATTATCAAACCTACCACAA 60.127 38.462 0.00 0.00 0.00 3.33
1222 1235 5.359576 GCCAATGATTATCAAACCTACCACA 59.640 40.000 0.00 0.00 0.00 4.17
1311 1324 4.103153 TGAAGACTGTTCTCCCAAGTGAAT 59.897 41.667 0.00 0.00 0.00 2.57
1334 1347 5.892119 TCTAGTTTCTCATATGTCGGTTCCT 59.108 40.000 1.90 0.00 0.00 3.36
1406 1419 2.902705 ACGAGGTAGAGCACAAACAA 57.097 45.000 0.00 0.00 0.00 2.83
1411 1424 2.320745 TCGATACGAGGTAGAGCACA 57.679 50.000 0.00 0.00 0.00 4.57
1441 1454 1.303317 GGAGAATGGGTGCGTGGTT 60.303 57.895 0.00 0.00 0.00 3.67
1784 1802 6.164176 CCATTTAAGTTCCTCTTCACGTAGT 58.836 40.000 0.00 0.00 38.42 2.73
1787 1805 4.969484 ACCATTTAAGTTCCTCTTCACGT 58.031 39.130 0.00 0.00 37.56 4.49
1888 1906 7.117285 AGGGAATGAATAATTTTCTTCCTGC 57.883 36.000 17.82 0.00 34.06 4.85
2107 2125 9.569167 GTTATTATCTAACAAGAAAAACTGCCC 57.431 33.333 0.00 0.00 0.00 5.36
2243 2265 2.881074 CACCTAAGATGGTCTGTCGTG 58.119 52.381 0.00 0.00 38.45 4.35
2269 2291 2.158608 GGCCCTCATATATACCCCATGC 60.159 54.545 0.00 0.00 0.00 4.06
2286 2308 1.282157 AGGACTCTTATGTGTTGGCCC 59.718 52.381 0.00 0.00 0.00 5.80
2289 2311 5.046591 TCCTACAAGGACTCTTATGTGTTGG 60.047 44.000 0.00 0.00 40.06 3.77
2333 2356 2.050168 GTGGAACCGACGCGTACA 60.050 61.111 13.97 1.58 0.00 2.90
2346 2369 4.966787 GTGGGCCTTTGCGGTGGA 62.967 66.667 4.53 0.00 38.85 4.02
2350 2373 3.673484 CAGTGTGGGCCTTTGCGG 61.673 66.667 4.53 0.00 38.85 5.69
2538 2570 3.755378 ACCAATAAGTCTGAGCTTTGCTG 59.245 43.478 0.00 0.00 39.88 4.41
2550 2582 2.007608 GCCAGTTCCGACCAATAAGTC 58.992 52.381 0.00 0.00 0.00 3.01
2595 2627 5.305644 AGGTATGCAAGATAAGTACTCCTGG 59.694 44.000 0.00 0.00 0.00 4.45
2598 2630 6.817184 TGAAGGTATGCAAGATAAGTACTCC 58.183 40.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.