Multiple sequence alignment - TraesCS3B01G580600

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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 TraesCS3B01G580600 chr3B 100.000 2264 0 0 1 2264 809559727 809557464 0.000000e+00 4181
1 TraesCS3B01G580600 chr6B 89.409 2200 170 29 2 2182 281223401 281221246 0.000000e+00 2713
2 TraesCS3B01G580600 chr6B 93.742 1582 83 7 695 2264 605817498 605819075 0.000000e+00 2359
3 TraesCS3B01G580600 chr2D 90.000 2130 155 29 1 2105 632766150 632768246 0.000000e+00 2700
4 TraesCS3B01G580600 chr2D 93.411 1548 82 4 1 1543 476789261 476790793 0.000000e+00 2276
5 TraesCS3B01G580600 chr1D 87.850 2288 217 31 1 2264 14674856 14672606 0.000000e+00 2628
6 TraesCS3B01G580600 chr5A 88.434 2196 173 43 1 2164 690039133 690041279 0.000000e+00 2573
7 TraesCS3B01G580600 chr5A 92.759 1160 71 4 1 1159 599230938 599232085 0.000000e+00 1664
8 TraesCS3B01G580600 chr4A 87.829 2243 204 38 45 2262 564697244 564699442 0.000000e+00 2566
9 TraesCS3B01G580600 chr5B 87.682 2200 198 46 1 2164 584816919 584814757 0.000000e+00 2494
10 TraesCS3B01G580600 chr5B 87.085 1595 126 41 694 2262 98046437 98047977 0.000000e+00 1731
11 TraesCS3B01G580600 chr1B 94.560 1581 74 4 696 2264 549918221 549916641 0.000000e+00 2433
12 TraesCS3B01G580600 chr1B 94.101 1407 68 8 694 2089 540299455 540298053 0.000000e+00 2124
13 TraesCS3B01G580600 chr1B 93.310 1405 82 7 694 2089 540289877 540288476 0.000000e+00 2063
14 TraesCS3B01G580600 chr1B 94.623 1246 59 3 693 1931 504247256 504246012 0.000000e+00 1923
15 TraesCS3B01G580600 chr1B 91.824 318 23 2 1950 2264 504245706 504245389 7.420000e-120 440
16 TraesCS3B01G580600 chr1B 81.377 247 35 11 2023 2262 504245373 504245615 8.250000e-45 191
17 TraesCS3B01G580600 chr2B 95.708 1468 53 4 1 1467 546619176 546620634 0.000000e+00 2353
18 TraesCS3B01G580600 chr2B 90.278 1584 104 20 694 2262 215847876 215849424 0.000000e+00 2026
19 TraesCS3B01G580600 chr2B 91.566 1411 78 11 703 2089 430231746 430230353 0.000000e+00 1908
20 TraesCS3B01G580600 chr2B 88.995 1463 96 37 694 2133 722906059 722904639 0.000000e+00 1749
21 TraesCS3B01G580600 chr2B 94.624 930 39 4 1346 2264 465663749 465662820 0.000000e+00 1430
22 TraesCS3B01G580600 chr2B 89.615 780 44 8 1498 2264 546620617 546621372 0.000000e+00 957
23 TraesCS3B01G580600 chr2B 83.468 248 29 10 2023 2262 465662804 465663047 1.050000e-53 220
24 TraesCS3B01G580600 chr4B 91.601 631 38 8 1567 2187 9634866 9635491 0.000000e+00 857
25 TraesCS3B01G580600 chr4B 88.158 152 11 6 2114 2262 9635491 9635344 8.310000e-40 174


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 TraesCS3B01G580600 chr3B 809557464 809559727 2263 True 4181.0 4181 100.0000 1 2264 1 chr3B.!!$R1 2263
1 TraesCS3B01G580600 chr6B 281221246 281223401 2155 True 2713.0 2713 89.4090 2 2182 1 chr6B.!!$R1 2180
2 TraesCS3B01G580600 chr6B 605817498 605819075 1577 False 2359.0 2359 93.7420 695 2264 1 chr6B.!!$F1 1569
3 TraesCS3B01G580600 chr2D 632766150 632768246 2096 False 2700.0 2700 90.0000 1 2105 1 chr2D.!!$F2 2104
4 TraesCS3B01G580600 chr2D 476789261 476790793 1532 False 2276.0 2276 93.4110 1 1543 1 chr2D.!!$F1 1542
5 TraesCS3B01G580600 chr1D 14672606 14674856 2250 True 2628.0 2628 87.8500 1 2264 1 chr1D.!!$R1 2263
6 TraesCS3B01G580600 chr5A 690039133 690041279 2146 False 2573.0 2573 88.4340 1 2164 1 chr5A.!!$F2 2163
7 TraesCS3B01G580600 chr5A 599230938 599232085 1147 False 1664.0 1664 92.7590 1 1159 1 chr5A.!!$F1 1158
8 TraesCS3B01G580600 chr4A 564697244 564699442 2198 False 2566.0 2566 87.8290 45 2262 1 chr4A.!!$F1 2217
9 TraesCS3B01G580600 chr5B 584814757 584816919 2162 True 2494.0 2494 87.6820 1 2164 1 chr5B.!!$R1 2163
10 TraesCS3B01G580600 chr5B 98046437 98047977 1540 False 1731.0 1731 87.0850 694 2262 1 chr5B.!!$F1 1568
11 TraesCS3B01G580600 chr1B 549916641 549918221 1580 True 2433.0 2433 94.5600 696 2264 1 chr1B.!!$R3 1568
12 TraesCS3B01G580600 chr1B 540298053 540299455 1402 True 2124.0 2124 94.1010 694 2089 1 chr1B.!!$R2 1395
13 TraesCS3B01G580600 chr1B 540288476 540289877 1401 True 2063.0 2063 93.3100 694 2089 1 chr1B.!!$R1 1395
14 TraesCS3B01G580600 chr1B 504245389 504247256 1867 True 1181.5 1923 93.2235 693 2264 2 chr1B.!!$R4 1571
15 TraesCS3B01G580600 chr2B 215847876 215849424 1548 False 2026.0 2026 90.2780 694 2262 1 chr2B.!!$F1 1568
16 TraesCS3B01G580600 chr2B 430230353 430231746 1393 True 1908.0 1908 91.5660 703 2089 1 chr2B.!!$R1 1386
17 TraesCS3B01G580600 chr2B 722904639 722906059 1420 True 1749.0 1749 88.9950 694 2133 1 chr2B.!!$R3 1439
18 TraesCS3B01G580600 chr2B 546619176 546621372 2196 False 1655.0 2353 92.6615 1 2264 2 chr2B.!!$F3 2263
19 TraesCS3B01G580600 chr2B 465662820 465663749 929 True 1430.0 1430 94.6240 1346 2264 1 chr2B.!!$R2 918
20 TraesCS3B01G580600 chr4B 9634866 9635491 625 False 857.0 857 91.6010 1567 2187 1 chr4B.!!$F1 620

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
491 492 0.994247 TGCCAGATCCCACACTCATT 59.006 50.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2111 2605 0.107654 CTTACCTCCAAGGCTTCCGG 60.108 60.0 0.0 0.0 39.63 5.14 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
119 120 6.968263 TTCAAGGTTCATGATTGGTTGTTA 57.032 33.333 0.00 0.00 0.00 2.41
254 255 2.028476 AGTTGCTTACGAGGTGCACATA 60.028 45.455 20.43 2.15 36.37 2.29
321 322 1.469703 CTTGCTCGCATTTGATGACCA 59.530 47.619 0.00 0.00 0.00 4.02
353 354 1.004595 GAAACTTGCCCGTATCCGAC 58.995 55.000 0.00 0.00 35.63 4.79
408 409 3.826157 GGAATGAACAAGGTTGATGTGGA 59.174 43.478 0.00 0.00 0.00 4.02
491 492 0.994247 TGCCAGATCCCACACTCATT 59.006 50.000 0.00 0.00 0.00 2.57
558 559 8.976353 GTGATATGGATGATCTAGTTGGATACT 58.024 37.037 0.00 0.00 41.04 2.12
571 572 2.398588 TGGATACTCCGGAATGAAGCT 58.601 47.619 5.23 0.00 40.17 3.74
741 742 4.410400 GTGGCCGTGGAGGAAGGG 62.410 72.222 0.00 0.00 45.00 3.95
764 765 2.516888 CCTTGGAGGTGGTCGTGGT 61.517 63.158 0.00 0.00 0.00 4.16
870 872 1.282248 CGACGTGTTGCTCAATCCGT 61.282 55.000 0.00 8.52 34.04 4.69
885 888 5.406649 TCAATCCGTTGGTTGAAATAATGC 58.593 37.500 0.00 0.00 35.99 3.56
892 895 3.779759 TGGTTGAAATAATGCGAATGGC 58.220 40.909 0.00 0.00 43.96 4.40
916 923 8.458843 GGCACTACTTTTAATATGTTCATGTGT 58.541 33.333 0.00 0.00 0.00 3.72
917 924 9.840427 GCACTACTTTTAATATGTTCATGTGTT 57.160 29.630 0.00 0.00 0.00 3.32
1069 1093 3.555324 TGCCGCACAAGTGGGAGA 61.555 61.111 17.50 2.11 45.77 3.71
1111 1137 7.038017 AGGTGAAGGAGAAAGATGTGAAGATTA 60.038 37.037 0.00 0.00 0.00 1.75
1118 1144 5.882557 AGAAAGATGTGAAGATTACGCCATT 59.117 36.000 0.00 0.00 0.00 3.16
1544 1576 1.610327 CTCGTGAGGAGGAGAGGGA 59.390 63.158 0.00 0.00 39.22 4.20
1548 1580 1.199615 GTGAGGAGGAGAGGGAAAGG 58.800 60.000 0.00 0.00 0.00 3.11
1745 1790 5.182950 ACTTGTCGTGAATGAATTTGCCATA 59.817 36.000 0.00 0.00 0.00 2.74
1870 1962 2.039084 GAGAAGAGGGGCAAAACAGAGA 59.961 50.000 0.00 0.00 0.00 3.10
1892 1997 3.836949 ACAACTCTGTTTTGCACTGTTG 58.163 40.909 0.00 0.00 39.23 3.33
1917 2120 4.123545 GGCACCCCTTACCGCCAT 62.124 66.667 0.00 0.00 44.25 4.40
2035 2529 3.324108 GGGACCCTACCGCCACAA 61.324 66.667 2.09 0.00 0.00 3.33
2042 2536 0.673644 CCTACCGCCACAACTTCTGG 60.674 60.000 0.00 0.00 0.00 3.86
2046 2540 2.594592 GCCACAACTTCTGGCGGT 60.595 61.111 0.00 0.00 44.78 5.68
2047 2541 1.302192 GCCACAACTTCTGGCGGTA 60.302 57.895 0.00 0.00 44.78 4.02
2048 2542 1.298859 GCCACAACTTCTGGCGGTAG 61.299 60.000 0.00 0.00 44.78 3.18
2049 2543 0.673644 CCACAACTTCTGGCGGTAGG 60.674 60.000 4.91 0.00 0.00 3.18
2050 2544 0.034896 CACAACTTCTGGCGGTAGGT 59.965 55.000 4.91 0.00 0.00 3.08
2051 2545 0.320697 ACAACTTCTGGCGGTAGGTC 59.679 55.000 4.91 0.00 0.00 3.85
2052 2546 0.320374 CAACTTCTGGCGGTAGGTCA 59.680 55.000 4.91 0.00 0.00 4.02
2053 2547 1.066143 CAACTTCTGGCGGTAGGTCAT 60.066 52.381 4.91 0.00 0.00 3.06
2054 2548 0.537188 ACTTCTGGCGGTAGGTCATG 59.463 55.000 4.91 0.00 0.00 3.07
2055 2549 0.824109 CTTCTGGCGGTAGGTCATGA 59.176 55.000 0.00 0.00 0.00 3.07
2056 2550 0.535335 TTCTGGCGGTAGGTCATGAC 59.465 55.000 17.91 17.91 0.00 3.06
2065 2559 4.456806 GGTCATGACCCATACCGC 57.543 61.111 31.37 6.18 45.68 5.68
2066 2560 1.830145 GGTCATGACCCATACCGCT 59.170 57.895 31.37 0.00 45.68 5.52
2067 2561 1.045407 GGTCATGACCCATACCGCTA 58.955 55.000 31.37 0.00 45.68 4.26
2068 2562 1.000955 GGTCATGACCCATACCGCTAG 59.999 57.143 31.37 0.00 45.68 3.42
2069 2563 1.687123 GTCATGACCCATACCGCTAGT 59.313 52.381 15.31 0.00 0.00 2.57
2070 2564 1.686587 TCATGACCCATACCGCTAGTG 59.313 52.381 0.00 0.00 0.00 2.74
2071 2565 0.393077 ATGACCCATACCGCTAGTGC 59.607 55.000 0.00 0.00 0.00 4.40
2072 2566 1.069258 GACCCATACCGCTAGTGCC 59.931 63.158 0.00 0.00 35.36 5.01
2073 2567 1.382695 ACCCATACCGCTAGTGCCT 60.383 57.895 0.00 0.00 35.36 4.75
2074 2568 1.069765 CCCATACCGCTAGTGCCTG 59.930 63.158 0.00 0.00 35.36 4.85
2075 2569 1.686325 CCCATACCGCTAGTGCCTGT 61.686 60.000 0.00 0.00 35.36 4.00
2076 2570 0.530650 CCATACCGCTAGTGCCTGTG 60.531 60.000 0.00 0.00 35.36 3.66
2077 2571 0.530650 CATACCGCTAGTGCCTGTGG 60.531 60.000 0.00 0.00 39.53 4.17
2102 2596 3.757836 GGGGGCAAACCTACTTTGA 57.242 52.632 0.00 0.00 41.81 2.69
2103 2597 1.254026 GGGGGCAAACCTACTTTGAC 58.746 55.000 0.00 0.00 46.18 3.18
2106 2600 1.601166 GGCAAACCTACTTTGACGGT 58.399 50.000 0.00 0.00 41.81 4.83
2107 2601 1.265905 GGCAAACCTACTTTGACGGTG 59.734 52.381 0.00 0.00 41.81 4.94
2108 2602 2.215196 GCAAACCTACTTTGACGGTGA 58.785 47.619 0.00 0.00 41.81 4.02
2109 2603 2.614983 GCAAACCTACTTTGACGGTGAA 59.385 45.455 0.00 0.00 41.81 3.18
2110 2604 3.065648 GCAAACCTACTTTGACGGTGAAA 59.934 43.478 0.00 0.00 41.81 2.69
2111 2605 4.594136 CAAACCTACTTTGACGGTGAAAC 58.406 43.478 0.00 0.00 41.81 2.78
2123 2617 1.956802 GTGAAACCGGAAGCCTTGG 59.043 57.895 9.46 0.00 0.00 3.61
2124 2618 0.536460 GTGAAACCGGAAGCCTTGGA 60.536 55.000 9.46 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 1.669115 AGACTTGCGCGCTTGATGT 60.669 52.632 33.29 19.61 0.00 3.06
321 322 1.608590 CAAGTTTCTCGCCCATGTTGT 59.391 47.619 0.00 0.00 0.00 3.32
408 409 0.036306 AAAGGATTGAACCGAGGCGT 59.964 50.000 0.00 0.00 34.73 5.68
448 449 1.702401 TGTCTGGCCCAACATACTCAA 59.298 47.619 0.00 0.00 0.00 3.02
491 492 1.839994 CTTCTTCCCCTCATAGGCACA 59.160 52.381 0.00 0.00 32.73 4.57
558 559 3.644966 ACCAAATAGCTTCATTCCGGA 57.355 42.857 0.00 0.00 0.00 5.14
741 742 1.222113 GACCACCTCCAAGGCTAGC 59.778 63.158 6.04 6.04 39.63 3.42
764 765 0.683504 GGCTAGTCCTTCCTCCACGA 60.684 60.000 0.00 0.00 0.00 4.35
870 872 4.180057 GCCATTCGCATTATTTCAACCAA 58.820 39.130 0.00 0.00 37.47 3.67
885 888 8.394877 TGAACATATTAAAAGTAGTGCCATTCG 58.605 33.333 0.00 0.00 0.00 3.34
1069 1093 3.897239 TCACCTTGTCCAAAGATGTGTT 58.103 40.909 0.00 0.00 0.00 3.32
1111 1137 0.179004 TCTCCACACCAAAATGGCGT 60.179 50.000 0.00 0.00 42.67 5.68
1118 1144 2.382882 TGCAAACATCTCCACACCAAA 58.617 42.857 0.00 0.00 0.00 3.28
1544 1576 1.342496 GAGCCTTTGCAAGCTTCCTTT 59.658 47.619 13.77 0.00 40.11 3.11
1548 1580 1.242076 TGAGAGCCTTTGCAAGCTTC 58.758 50.000 13.77 12.73 40.11 3.86
1745 1790 6.599244 ACATCTCGACACCAAATTCAATACAT 59.401 34.615 0.00 0.00 0.00 2.29
2035 2529 0.537188 CATGACCTACCGCCAGAAGT 59.463 55.000 0.00 0.00 0.00 3.01
2049 2543 1.687123 ACTAGCGGTATGGGTCATGAC 59.313 52.381 17.91 17.91 0.00 3.06
2050 2544 1.686587 CACTAGCGGTATGGGTCATGA 59.313 52.381 0.00 0.00 0.00 3.07
2051 2545 1.873903 GCACTAGCGGTATGGGTCATG 60.874 57.143 0.00 0.00 0.00 3.07
2052 2546 0.393077 GCACTAGCGGTATGGGTCAT 59.607 55.000 0.00 0.00 0.00 3.06
2053 2547 1.682451 GGCACTAGCGGTATGGGTCA 61.682 60.000 0.00 0.00 43.41 4.02
2054 2548 1.069258 GGCACTAGCGGTATGGGTC 59.931 63.158 0.00 0.00 43.41 4.46
2055 2549 1.382695 AGGCACTAGCGGTATGGGT 60.383 57.895 0.00 0.00 43.41 4.51
2056 2550 1.069765 CAGGCACTAGCGGTATGGG 59.930 63.158 0.00 0.00 43.41 4.00
2057 2551 0.530650 CACAGGCACTAGCGGTATGG 60.531 60.000 0.00 0.00 43.41 2.74
2058 2552 0.530650 CCACAGGCACTAGCGGTATG 60.531 60.000 0.00 0.00 43.41 2.39
2059 2553 1.823295 CCACAGGCACTAGCGGTAT 59.177 57.895 0.00 0.00 43.41 2.73
2060 2554 3.294750 CCACAGGCACTAGCGGTA 58.705 61.111 0.00 0.00 43.41 4.02
2084 2578 1.254026 GTCAAAGTAGGTTTGCCCCC 58.746 55.000 0.00 0.00 44.67 5.40
2085 2579 0.879090 CGTCAAAGTAGGTTTGCCCC 59.121 55.000 0.00 0.00 44.67 5.80
2086 2580 0.879090 CCGTCAAAGTAGGTTTGCCC 59.121 55.000 0.00 0.00 44.67 5.36
2087 2581 1.265905 CACCGTCAAAGTAGGTTTGCC 59.734 52.381 0.00 0.00 44.67 4.52
2088 2582 2.215196 TCACCGTCAAAGTAGGTTTGC 58.785 47.619 0.00 0.00 44.67 3.68
2089 2583 4.496840 GGTTTCACCGTCAAAGTAGGTTTG 60.497 45.833 0.00 0.00 46.17 2.93
2090 2584 3.628942 GGTTTCACCGTCAAAGTAGGTTT 59.371 43.478 0.00 0.00 35.85 3.27
2091 2585 3.208594 GGTTTCACCGTCAAAGTAGGTT 58.791 45.455 0.00 0.00 35.85 3.50
2092 2586 2.842457 GGTTTCACCGTCAAAGTAGGT 58.158 47.619 0.00 0.00 39.12 3.08
2104 2598 1.524008 CCAAGGCTTCCGGTTTCACC 61.524 60.000 0.00 0.00 34.05 4.02
2105 2599 0.536460 TCCAAGGCTTCCGGTTTCAC 60.536 55.000 0.00 0.00 0.00 3.18
2106 2600 0.250727 CTCCAAGGCTTCCGGTTTCA 60.251 55.000 0.00 0.00 0.00 2.69
2107 2601 0.960861 CCTCCAAGGCTTCCGGTTTC 60.961 60.000 0.00 0.00 0.00 2.78
2108 2602 1.074951 CCTCCAAGGCTTCCGGTTT 59.925 57.895 0.00 0.00 0.00 3.27
2109 2603 0.838987 TACCTCCAAGGCTTCCGGTT 60.839 55.000 14.51 0.00 39.63 4.44
2110 2604 0.838987 TTACCTCCAAGGCTTCCGGT 60.839 55.000 13.95 13.95 39.63 5.28
2111 2605 0.107654 CTTACCTCCAAGGCTTCCGG 60.108 60.000 0.00 0.00 39.63 5.14
2112 2606 0.107654 CCTTACCTCCAAGGCTTCCG 60.108 60.000 0.00 0.00 39.63 4.30
2113 2607 0.256177 CCCTTACCTCCAAGGCTTCC 59.744 60.000 0.00 0.00 43.30 3.46
2114 2608 0.256177 CCCCTTACCTCCAAGGCTTC 59.744 60.000 0.00 0.00 43.30 3.86
2115 2609 1.214992 CCCCCTTACCTCCAAGGCTT 61.215 60.000 0.00 0.00 43.30 4.35
2116 2610 1.619669 CCCCCTTACCTCCAAGGCT 60.620 63.158 0.00 0.00 43.30 4.58
2117 2611 1.618447 TCCCCCTTACCTCCAAGGC 60.618 63.158 0.00 0.00 43.30 4.35
2118 2612 1.279749 GGTCCCCCTTACCTCCAAGG 61.280 65.000 0.00 0.00 44.11 3.61
2119 2613 1.279749 GGGTCCCCCTTACCTCCAAG 61.280 65.000 0.00 0.00 41.34 3.61
2120 2614 1.230050 GGGTCCCCCTTACCTCCAA 60.230 63.158 0.00 0.00 41.34 3.53
2121 2615 2.457794 GGGTCCCCCTTACCTCCA 59.542 66.667 0.00 0.00 41.34 3.86
2201 2963 1.615116 GGTAGGGGGTGTAAACTTGCC 60.615 57.143 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.