Multiple sequence alignment - TraesCS4B01G368900

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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 TraesCS4B01G368900 chr4B 100.000 2753 0 0 1 2753 654794954 654792202 0.000000e+00 5084.0
1 TraesCS4B01G368900 chr4B 96.779 1459 30 7 1 1445 654677459 654676004 0.000000e+00 2418.0
2 TraesCS4B01G368900 chr4B 96.844 1014 27 5 1743 2753 654676008 654674997 0.000000e+00 1690.0
3 TraesCS4B01G368900 chr4B 96.076 943 30 6 1816 2753 343473656 343472716 0.000000e+00 1530.0
4 TraesCS4B01G368900 chr4B 88.505 983 85 18 851 1815 654720328 654719356 0.000000e+00 1164.0
5 TraesCS4B01G368900 chr4B 87.437 987 86 18 851 1815 654593235 654592265 0.000000e+00 1101.0
6 TraesCS4B01G368900 chr4B 82.318 673 94 14 851 1513 654752242 654751585 6.660000e-156 560.0
7 TraesCS4B01G368900 chr4B 82.021 673 96 14 851 1513 654762481 654761824 1.440000e-152 549.0
8 TraesCS4B01G368900 chr4B 81.872 673 97 14 851 1513 654774687 654774030 6.710000e-151 544.0
9 TraesCS4B01G368900 chr4B 81.387 548 71 19 294 838 654721011 654720492 4.240000e-113 418.0
10 TraesCS4B01G368900 chr4B 88.587 184 18 3 656 838 654593587 654593406 1.280000e-53 220.0
11 TraesCS4B01G368900 chr5B 97.237 941 21 5 1816 2753 641330891 641329953 0.000000e+00 1589.0
12 TraesCS4B01G368900 chr5B 94.737 38 2 0 111 148 688488530 688488567 2.960000e-05 60.2
13 TraesCS4B01G368900 chr1B 96.918 941 25 4 1816 2753 647584287 647583348 0.000000e+00 1574.0
14 TraesCS4B01G368900 chr1B 96.174 941 30 6 1816 2753 49134785 49133848 0.000000e+00 1533.0
15 TraesCS4B01G368900 chr1B 98.131 107 2 0 1 107 106939512 106939618 1.300000e-43 187.0
16 TraesCS4B01G368900 chr1B 78.986 138 20 8 690 820 65708914 65708779 4.880000e-13 86.1
17 TraesCS4B01G368900 chr7B 96.599 941 28 4 1816 2753 636504815 636503876 0.000000e+00 1557.0
18 TraesCS4B01G368900 chr7B 96.178 942 31 5 1816 2753 640242296 640241356 0.000000e+00 1535.0
19 TraesCS4B01G368900 chr7B 96.178 942 31 5 1815 2753 695650794 695651733 0.000000e+00 1535.0
20 TraesCS4B01G368900 chr7B 96.174 941 30 6 1816 2753 743567527 743568464 0.000000e+00 1533.0
21 TraesCS4B01G368900 chr7B 88.889 162 7 4 1 151 692159118 692158957 3.620000e-44 189.0
22 TraesCS4B01G368900 chr7B 87.283 173 7 5 1 162 388177126 388176958 1.680000e-42 183.0
23 TraesCS4B01G368900 chrUn 88.511 1001 70 32 851 1815 154586651 154587642 0.000000e+00 1170.0
24 TraesCS4B01G368900 chrUn 88.127 598 59 7 1055 1649 154617347 154617935 0.000000e+00 701.0
25 TraesCS4B01G368900 chrUn 83.151 730 78 27 144 839 154585766 154586484 2.330000e-175 625.0
26 TraesCS4B01G368900 chrUn 87.273 55 3 3 111 165 340113166 340113116 2.960000e-05 60.2
27 TraesCS4B01G368900 chr5A 87.992 1016 69 27 851 1815 692180022 692179009 0.000000e+00 1151.0
28 TraesCS4B01G368900 chr5A 84.872 509 42 15 152 645 692181208 692180720 5.330000e-132 481.0
29 TraesCS4B01G368900 chr5A 77.157 197 29 9 841 1036 692206009 692205828 1.740000e-17 100.0
30 TraesCS4B01G368900 chr1D 88.571 175 8 3 1 164 271285391 271285564 4.650000e-48 202.0
31 TraesCS4B01G368900 chr5D 89.506 162 6 3 1 151 408304788 408304627 7.780000e-46 195.0
32 TraesCS4B01G368900 chr5D 98.131 107 2 0 1 107 115404155 115404261 1.300000e-43 187.0
33 TraesCS4B01G368900 chr2A 88.889 162 7 7 1 151 585707753 585707914 3.620000e-44 189.0
34 TraesCS4B01G368900 chr6D 98.131 107 2 0 1 107 68083178 68083072 1.300000e-43 187.0
35 TraesCS4B01G368900 chr6D 98.131 107 2 0 1 107 272401838 272401944 1.300000e-43 187.0
36 TraesCS4B01G368900 chr6D 87.037 54 3 4 109 162 464848735 464848784 1.060000e-04 58.4
37 TraesCS4B01G368900 chr2D 98.131 107 2 0 1 107 293525003 293524897 1.300000e-43 187.0
38 TraesCS4B01G368900 chr3A 83.420 193 14 13 1 179 573109531 573109719 2.190000e-36 163.0
39 TraesCS4B01G368900 chr4D 88.889 54 2 3 109 162 504065054 504065005 2.290000e-06 63.9
40 TraesCS4B01G368900 chr6B 92.500 40 3 0 109 148 12748797 12748836 1.060000e-04 58.4


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 TraesCS4B01G368900 chr4B 654792202 654794954 2752 True 5084.0 5084 100.0000 1 2753 1 chr4B.!!$R5 2752
1 TraesCS4B01G368900 chr4B 654674997 654677459 2462 True 2054.0 2418 96.8115 1 2753 2 chr4B.!!$R7 2752
2 TraesCS4B01G368900 chr4B 343472716 343473656 940 True 1530.0 1530 96.0760 1816 2753 1 chr4B.!!$R1 937
3 TraesCS4B01G368900 chr4B 654719356 654721011 1655 True 791.0 1164 84.9460 294 1815 2 chr4B.!!$R8 1521
4 TraesCS4B01G368900 chr4B 654592265 654593587 1322 True 660.5 1101 88.0120 656 1815 2 chr4B.!!$R6 1159
5 TraesCS4B01G368900 chr4B 654751585 654752242 657 True 560.0 560 82.3180 851 1513 1 chr4B.!!$R2 662
6 TraesCS4B01G368900 chr4B 654761824 654762481 657 True 549.0 549 82.0210 851 1513 1 chr4B.!!$R3 662
7 TraesCS4B01G368900 chr4B 654774030 654774687 657 True 544.0 544 81.8720 851 1513 1 chr4B.!!$R4 662
8 TraesCS4B01G368900 chr5B 641329953 641330891 938 True 1589.0 1589 97.2370 1816 2753 1 chr5B.!!$R1 937
9 TraesCS4B01G368900 chr1B 647583348 647584287 939 True 1574.0 1574 96.9180 1816 2753 1 chr1B.!!$R3 937
10 TraesCS4B01G368900 chr1B 49133848 49134785 937 True 1533.0 1533 96.1740 1816 2753 1 chr1B.!!$R1 937
11 TraesCS4B01G368900 chr7B 636503876 636504815 939 True 1557.0 1557 96.5990 1816 2753 1 chr7B.!!$R2 937
12 TraesCS4B01G368900 chr7B 640241356 640242296 940 True 1535.0 1535 96.1780 1816 2753 1 chr7B.!!$R3 937
13 TraesCS4B01G368900 chr7B 695650794 695651733 939 False 1535.0 1535 96.1780 1815 2753 1 chr7B.!!$F1 938
14 TraesCS4B01G368900 chr7B 743567527 743568464 937 False 1533.0 1533 96.1740 1816 2753 1 chr7B.!!$F2 937
15 TraesCS4B01G368900 chrUn 154585766 154587642 1876 False 897.5 1170 85.8310 144 1815 2 chrUn.!!$F2 1671
16 TraesCS4B01G368900 chrUn 154617347 154617935 588 False 701.0 701 88.1270 1055 1649 1 chrUn.!!$F1 594
17 TraesCS4B01G368900 chr5A 692179009 692181208 2199 True 816.0 1151 86.4320 152 1815 2 chr5A.!!$R2 1663

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
530 568 3.063180 CGTCCATGTCTTGCTTTGAGATC 59.937 47.826 0.0 0.0 0.00 2.75 F
1430 2054 0.796312 CGGCATCAAGCTTAACGTGT 59.204 50.000 0.0 0.0 44.79 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1532 2158 0.598419 ATGACGATGACGCGATGCAT 60.598 50.000 15.93 13.51 43.96 3.96 R
2260 2932 3.748863 GCTTGGAGATCGAGCTTGA 57.251 52.632 3.92 6.01 46.85 3.02 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
132 133 3.901290 CGATCTAGAACTACGCGAATGAC 59.099 47.826 15.93 0.66 0.00 3.06
530 568 3.063180 CGTCCATGTCTTGCTTTGAGATC 59.937 47.826 0.00 0.00 0.00 2.75
1006 1614 2.449137 AGCATCCCAAGCTAGCAAAT 57.551 45.000 18.83 0.00 41.32 2.32
1281 1905 1.740380 GCTGAAGCTGAAGGTATGCGA 60.740 52.381 0.00 0.00 38.21 5.10
1423 2047 1.448540 CGTCCTCGGCATCAAGCTT 60.449 57.895 0.00 0.00 44.79 3.74
1430 2054 0.796312 CGGCATCAAGCTTAACGTGT 59.204 50.000 0.00 0.00 44.79 4.49
1532 2158 7.040494 CCATCACAAACCATGCATTTTATACA 58.960 34.615 0.00 0.00 0.00 2.29
1552 2181 0.805711 TGCATCGCGTCATCGTCATT 60.806 50.000 5.77 0.00 39.49 2.57
1568 2197 5.023920 TCGTCATTGTCGTACTCGTAATTC 58.976 41.667 3.38 0.00 38.33 2.17
1569 2198 4.789629 CGTCATTGTCGTACTCGTAATTCA 59.210 41.667 0.00 0.00 38.33 2.57
1606 2237 8.055986 CGTATACGCATGCACCTATATATTTTG 58.944 37.037 19.57 0.00 0.00 2.44
1677 2343 6.579865 AGTTAGTCATTTCCCGTTATGGTAG 58.420 40.000 0.00 0.00 35.15 3.18
1688 2354 4.154195 CCCGTTATGGTAGCTAAATGCATC 59.846 45.833 0.00 0.00 39.41 3.91
1802 2473 2.358125 CGGTCCGTGATGTGCCAA 60.358 61.111 2.08 0.00 0.00 4.52
1850 2522 1.926489 TATTGGTCCAGGCCGGGTT 60.926 57.895 22.25 5.68 34.36 4.11
1891 2563 2.480555 CAGAACCGCGACCAATGC 59.519 61.111 8.23 0.00 0.00 3.56
1950 2622 3.372730 CCACGTGGGCCATTGGTG 61.373 66.667 27.57 22.19 0.00 4.17
2128 2800 1.476477 TGCCTATATATACGCCCGCA 58.524 50.000 10.15 2.02 0.00 5.69
2133 2805 2.691409 ATATATACGCCCGCAAGCAT 57.309 45.000 0.00 0.00 0.00 3.79
2139 2811 3.892581 GCCCGCAAGCATAGCACC 61.893 66.667 0.00 0.00 0.00 5.01
2140 2812 3.576356 CCCGCAAGCATAGCACCG 61.576 66.667 0.00 0.00 0.00 4.94
2260 2932 6.459923 CACACTACTTAAGCTTTCTCCTCTT 58.540 40.000 3.20 0.00 0.00 2.85
2287 2959 3.944015 CTCGATCTCCAAGCTCCATTTTT 59.056 43.478 0.00 0.00 0.00 1.94
2561 3238 8.466798 TGTCTATGATTCGGTGTGGTATATATG 58.533 37.037 0.00 0.00 0.00 1.78
2615 3292 6.096141 TGTTTATGACAATTATGCCGACCAAT 59.904 34.615 0.00 0.00 34.69 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 114 4.959596 AAGTCATTCGCGTAGTTCTAGA 57.040 40.909 5.77 0.00 0.00 2.43
116 117 5.515626 GTGAATAAGTCATTCGCGTAGTTCT 59.484 40.000 5.77 0.00 45.25 3.01
117 118 5.715264 GTGAATAAGTCATTCGCGTAGTTC 58.285 41.667 5.77 0.29 45.25 3.01
132 133 7.380065 GCTACCTTCTTCGTCTATGTGAATAAG 59.620 40.741 0.00 0.00 31.68 1.73
398 409 4.026744 CCTGATCTTGAGGGTCACTAGAA 58.973 47.826 0.00 0.00 0.00 2.10
1006 1614 3.461773 GCTGAGCGCTAGGTGGGA 61.462 66.667 11.50 0.00 35.14 4.37
1137 1755 2.029369 GTGTTACCGCACGACCCA 59.971 61.111 0.00 0.00 0.00 4.51
1212 1836 4.194720 CCGGTCGAAGGCGGAGAG 62.195 72.222 0.00 0.00 38.28 3.20
1281 1905 0.732571 CAGCAGGTTCAACACGTTGT 59.267 50.000 9.60 0.00 41.16 3.32
1430 2054 3.429141 GAGCACGAGGTCGACGGA 61.429 66.667 9.92 0.00 43.02 4.69
1532 2158 0.598419 ATGACGATGACGCGATGCAT 60.598 50.000 15.93 13.51 43.96 3.96
1541 2167 2.776765 CGAGTACGACAATGACGATGAC 59.223 50.000 12.41 6.76 42.66 3.06
1568 2197 7.058354 GTGCATGCGTATACGAGAAAATATTTG 59.942 37.037 28.66 8.29 43.02 2.32
1569 2198 7.069569 GTGCATGCGTATACGAGAAAATATTT 58.930 34.615 28.66 0.00 43.02 1.40
1616 2247 4.158949 ACGCGGCTGACATATACCATATTA 59.841 41.667 12.47 0.00 0.00 0.98
1652 2318 5.425630 ACCATAACGGGAAATGACTAACTC 58.574 41.667 0.00 0.00 40.22 3.01
1677 2343 8.638685 ACAAATACTTGAATGATGCATTTAGC 57.361 30.769 0.00 0.00 38.88 3.09
1719 2385 7.763985 ACAACCTGAACAAACTTTTTATTCCAG 59.236 33.333 0.00 0.00 0.00 3.86
1827 2499 2.006991 GGCCTGGACCAATACCCCT 61.007 63.158 0.00 0.00 0.00 4.79
1850 2522 1.125633 GAACCGGGACTAATGGGCTA 58.874 55.000 6.32 0.00 0.00 3.93
1950 2622 2.726822 AAAGGTCCAGACGAACCGGC 62.727 60.000 0.00 0.00 40.63 6.13
2128 2800 3.143675 CACTGACGGTGCTATGCTT 57.856 52.632 0.43 0.00 39.22 3.91
2139 2811 1.593006 ACGAAAAACAGAGCACTGACG 59.407 47.619 18.54 15.14 46.03 4.35
2140 2812 2.286418 CCACGAAAAACAGAGCACTGAC 60.286 50.000 18.54 3.24 46.03 3.51
2260 2932 3.748863 GCTTGGAGATCGAGCTTGA 57.251 52.632 3.92 6.01 46.85 3.02
2287 2959 7.929785 CCGCTAAACCTAGACAAATATTAAGGA 59.070 37.037 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.