Multiple sequence alignment - TraesCS3B01G181800

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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 TraesCS3B01G181800 chr3B 100.000 2632 0 0 1 2632 190889985 190887354 0.000000e+00 4861.0
1 TraesCS3B01G181800 chr3B 99.517 621 3 0 1 621 771437882 771438502 0.000000e+00 1131.0
2 TraesCS3B01G181800 chr5D 96.335 2019 47 6 621 2632 60243557 60241559 0.000000e+00 3293.0
3 TraesCS3B01G181800 chr5D 94.301 193 10 1 430 621 484995959 484995767 7.120000e-76 294.0
4 TraesCS3B01G181800 chr4B 98.712 621 8 0 1 621 77011726 77011106 0.000000e+00 1103.0
5 TraesCS3B01G181800 chr3D 82.609 1150 162 18 777 1894 331001091 331002234 0.000000e+00 981.0
6 TraesCS3B01G181800 chr3D 95.642 413 18 0 18 430 424222577 424222989 0.000000e+00 664.0
7 TraesCS3B01G181800 chr3D 84.314 102 16 0 659 760 569067854 569067955 1.670000e-17 100.0
8 TraesCS3B01G181800 chr7B 95.008 621 28 1 1 621 599105229 599105846 0.000000e+00 972.0
9 TraesCS3B01G181800 chrUn 100.000 390 0 0 196 585 479942914 479943303 0.000000e+00 721.0
10 TraesCS3B01G181800 chrUn 92.157 51 4 0 1821 1871 82409567 82409517 3.630000e-09 73.1
11 TraesCS3B01G181800 chr7D 96.126 413 15 1 18 430 638153066 638153477 0.000000e+00 673.0
12 TraesCS3B01G181800 chr1B 95.884 413 17 0 18 430 667635116 667635528 0.000000e+00 669.0
13 TraesCS3B01G181800 chr1B 89.956 229 16 5 397 621 13340869 13340644 3.310000e-74 289.0
14 TraesCS3B01G181800 chr1B 89.083 229 18 5 397 621 13300233 13300008 7.170000e-71 278.0
15 TraesCS3B01G181800 chr5A 95.652 414 17 1 18 430 326654919 326654506 0.000000e+00 664.0
16 TraesCS3B01G181800 chr5A 77.489 693 142 12 775 1463 6175945 6175263 1.130000e-108 403.0
17 TraesCS3B01G181800 chr1D 80.427 889 145 18 1187 2061 295856348 295855475 0.000000e+00 651.0
18 TraesCS3B01G181800 chr1D 75.982 1120 227 35 777 1878 229965352 229964257 8.290000e-150 540.0
19 TraesCS3B01G181800 chr1D 81.388 317 52 7 878 1191 295858260 295857948 4.350000e-63 252.0
20 TraesCS3B01G181800 chr4D 93.779 434 22 4 1 429 418512168 418512601 0.000000e+00 647.0
21 TraesCS3B01G181800 chr4D 75.603 1119 235 31 777 1878 428939014 428937917 1.080000e-143 520.0
22 TraesCS3B01G181800 chr1A 74.950 994 222 25 775 1754 50932357 50931377 5.200000e-117 431.0
23 TraesCS3B01G181800 chr1A 78.383 643 119 16 830 1464 426923930 426924560 1.470000e-107 399.0
24 TraesCS3B01G181800 chr6B 90.393 229 16 4 397 621 395689346 395689572 1.980000e-76 296.0
25 TraesCS3B01G181800 chr6B 78.355 231 49 1 799 1028 221421257 221421487 5.870000e-32 148.0
26 TraesCS3B01G181800 chr6D 90.000 230 17 4 397 622 58108556 58108329 2.560000e-75 292.0
27 TraesCS3B01G181800 chr5B 78.846 260 48 4 774 1032 526651928 526652181 4.510000e-38 169.0


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 TraesCS3B01G181800 chr3B 190887354 190889985 2631 True 4861.0 4861 100.0000 1 2632 1 chr3B.!!$R1 2631
1 TraesCS3B01G181800 chr3B 771437882 771438502 620 False 1131.0 1131 99.5170 1 621 1 chr3B.!!$F1 620
2 TraesCS3B01G181800 chr5D 60241559 60243557 1998 True 3293.0 3293 96.3350 621 2632 1 chr5D.!!$R1 2011
3 TraesCS3B01G181800 chr4B 77011106 77011726 620 True 1103.0 1103 98.7120 1 621 1 chr4B.!!$R1 620
4 TraesCS3B01G181800 chr3D 331001091 331002234 1143 False 981.0 981 82.6090 777 1894 1 chr3D.!!$F1 1117
5 TraesCS3B01G181800 chr7B 599105229 599105846 617 False 972.0 972 95.0080 1 621 1 chr7B.!!$F1 620
6 TraesCS3B01G181800 chr5A 6175263 6175945 682 True 403.0 403 77.4890 775 1463 1 chr5A.!!$R1 688
7 TraesCS3B01G181800 chr1D 229964257 229965352 1095 True 540.0 540 75.9820 777 1878 1 chr1D.!!$R1 1101
8 TraesCS3B01G181800 chr1D 295855475 295858260 2785 True 451.5 651 80.9075 878 2061 2 chr1D.!!$R2 1183
9 TraesCS3B01G181800 chr4D 428937917 428939014 1097 True 520.0 520 75.6030 777 1878 1 chr4D.!!$R1 1101
10 TraesCS3B01G181800 chr1A 50931377 50932357 980 True 431.0 431 74.9500 775 1754 1 chr1A.!!$R1 979
11 TraesCS3B01G181800 chr1A 426923930 426924560 630 False 399.0 399 78.3830 830 1464 1 chr1A.!!$F1 634

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
752 753 1.321743 CGATTCACAAGTACGCAGAGC 59.678 52.381 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2279 3965 0.03601 AACTTGCTGATCCCCGACAG 60.036 55.0 0.0 0.0 37.22 3.51 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
670 671 3.614870 GCCTGTGGTTTTGCAGATTAAGG 60.615 47.826 0.00 0.00 34.87 2.69
752 753 1.321743 CGATTCACAAGTACGCAGAGC 59.678 52.381 0.00 0.00 0.00 4.09
1138 1166 3.576861 TGGAGATACTACATGTGGAGGG 58.423 50.000 16.98 0.08 0.00 4.30
1203 2836 4.572389 CGAGGGACATACTTCCAAAAGATG 59.428 45.833 0.00 0.00 37.40 2.90
1389 3030 0.177141 CGGAAAGCGAAGGGATGGTA 59.823 55.000 0.00 0.00 0.00 3.25
1527 3168 0.694771 TGTCAATGCTCTCCTTGGCT 59.305 50.000 0.00 0.00 0.00 4.75
1596 3243 0.172803 GGAGAACGCACCATACGAGT 59.827 55.000 0.00 0.00 0.00 4.18
1889 3574 3.325870 CTCAATTTCGTGTGGCACTCTA 58.674 45.455 19.83 4.35 31.34 2.43
1890 3575 3.935203 CTCAATTTCGTGTGGCACTCTAT 59.065 43.478 19.83 6.16 31.34 1.98
1918 3603 4.685628 GTGCGAAAACCATGTTTCATGAAT 59.314 37.500 9.40 0.00 37.35 2.57
2020 3706 3.777106 TCTTGTTTCTGCTGGAGTCAT 57.223 42.857 0.00 0.00 0.00 3.06
2024 3710 3.405831 TGTTTCTGCTGGAGTCATTCAG 58.594 45.455 0.00 0.00 0.00 3.02
2026 3712 4.260170 GTTTCTGCTGGAGTCATTCAGAT 58.740 43.478 7.85 0.00 34.62 2.90
2210 3896 9.559958 CAAACATTTTTGAAGCTATAGTGGTAG 57.440 33.333 0.84 0.00 44.38 3.18
2229 3915 1.152984 TACCAATGGCGCCATCCTG 60.153 57.895 40.38 33.09 35.31 3.86
2279 3965 1.402613 GAGGTCTGAAGGTAGTCGCTC 59.597 57.143 0.00 0.00 0.00 5.03
2339 4025 5.064834 GCTGTTTGTACCTATCTTTGGCTAC 59.935 44.000 0.00 0.00 0.00 3.58
2340 4026 5.172934 TGTTTGTACCTATCTTTGGCTACG 58.827 41.667 0.00 0.00 0.00 3.51
2487 4180 3.898123 ACGAGGTATAGGTGCATCTTCAT 59.102 43.478 3.93 0.00 0.00 2.57
2494 4187 6.656693 GGTATAGGTGCATCTTCATTTAGCAT 59.343 38.462 3.93 0.00 37.56 3.79
2495 4188 7.175641 GGTATAGGTGCATCTTCATTTAGCATT 59.824 37.037 3.93 0.00 37.56 3.56
2519 4212 0.755686 TTTGGTGGTGGGTTGAATGC 59.244 50.000 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
670 671 2.985847 GGTGGTGCACTTCCCAGC 60.986 66.667 17.98 12.14 41.51 4.85
752 753 4.984161 CCTTATCACACTTTTTGTTGGCTG 59.016 41.667 0.00 0.00 35.67 4.85
848 851 5.126869 TCATCTTCTCCTTCTCTGTGACATC 59.873 44.000 0.00 0.00 0.00 3.06
1138 1166 7.281999 GCTTCAATATATGCTTAGAAGGGATCC 59.718 40.741 1.92 1.92 34.57 3.36
1146 1174 5.011635 TCCACCGCTTCAATATATGCTTAGA 59.988 40.000 0.00 0.00 0.00 2.10
1389 3030 0.541764 ATGCGGTCCACAAAACCCAT 60.542 50.000 0.00 0.00 32.89 4.00
1527 3168 5.711976 CCCTTTTCTTTTCTGGAGCTATGAA 59.288 40.000 0.00 0.00 0.00 2.57
1596 3243 1.339929 TCTTGTGCGCTTACTCAGACA 59.660 47.619 9.73 0.00 0.00 3.41
1738 3385 3.124921 GGCTTGTGCGCGTGGTAT 61.125 61.111 8.43 0.00 40.82 2.73
1820 3502 7.773224 TCACAGAAAAACACTAGAAAATCCTCA 59.227 33.333 0.00 0.00 0.00 3.86
2020 3706 4.262635 GCCGAAATCCTCATCCTATCTGAA 60.263 45.833 0.00 0.00 0.00 3.02
2024 3710 3.594134 CAGCCGAAATCCTCATCCTATC 58.406 50.000 0.00 0.00 0.00 2.08
2026 3712 1.694150 CCAGCCGAAATCCTCATCCTA 59.306 52.381 0.00 0.00 0.00 2.94
2210 3896 1.152963 AGGATGGCGCCATTGGTAC 60.153 57.895 40.56 27.16 36.70 3.34
2229 3915 0.235665 CACTCATGCGGTGTCAACAC 59.764 55.000 4.67 4.67 45.72 3.32
2279 3965 0.036010 AACTTGCTGATCCCCGACAG 60.036 55.000 0.00 0.00 37.22 3.51
2339 4025 7.110179 ACGATTTCTCTGCATCATTATTACG 57.890 36.000 0.00 0.00 0.00 3.18
2519 4212 4.042062 TGGATTCACCTATCCCTGCTAATG 59.958 45.833 0.00 0.00 42.91 1.90
2531 4224 5.674525 CTCATTGCTAGTTGGATTCACCTA 58.325 41.667 0.00 0.00 39.86 3.08


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

AutoCloner maintained by Alex Coulton.