Multiple sequence alignment - TraesCS3B01G213300

Loading Multiple Alignment...

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 TraesCS3B01G213300 chr3B 100.000 2198 0 0 1 2198 252854942 252852745 0.000000e+00 4060
1 TraesCS3B01G213300 chr3B 90.725 345 30 1 1850 2192 109065750 109066094 1.990000e-125 459
2 TraesCS3B01G213300 chr3D 95.493 1664 72 3 1 1662 174073430 174071768 0.000000e+00 2654
3 TraesCS3B01G213300 chrUn 95.614 1596 67 3 69 1662 220605610 220604016 0.000000e+00 2556
4 TraesCS3B01G213300 chrUn 95.028 543 26 1 1121 1662 220587764 220587222 0.000000e+00 852
5 TraesCS3B01G213300 chr3A 92.137 1259 89 7 405 1662 212767282 212766033 0.000000e+00 1768
6 TraesCS3B01G213300 chr3A 90.262 267 21 5 1678 1942 710951379 710951116 5.810000e-91 344
7 TraesCS3B01G213300 chr3A 89.308 159 15 1 1932 2088 708691633 708691791 4.790000e-47 198
8 TraesCS3B01G213300 chr3A 87.850 107 13 0 2086 2192 708691863 708691969 2.290000e-25 126
9 TraesCS3B01G213300 chr5B 88.395 517 48 7 1677 2188 34913296 34913805 1.440000e-171 612
10 TraesCS3B01G213300 chr1B 88.193 415 43 4 1678 2088 410330682 410331094 7.050000e-135 490
11 TraesCS3B01G213300 chr1B 86.650 412 45 5 1678 2088 658356772 658357174 4.300000e-122 448
12 TraesCS3B01G213300 chr1B 80.831 313 41 10 910 1214 662031358 662031057 6.100000e-56 228
13 TraesCS3B01G213300 chr1B 89.720 107 11 0 2086 2192 410331145 410331251 1.060000e-28 137
14 TraesCS3B01G213300 chr1B 87.850 107 13 0 2086 2192 658357246 658357352 2.290000e-25 126
15 TraesCS3B01G213300 chr4D 87.065 402 39 11 1678 2075 337135042 337134650 2.000000e-120 442
16 TraesCS3B01G213300 chr4D 86.364 110 15 0 2086 2195 337134585 337134476 1.070000e-23 121
17 TraesCS3B01G213300 chr1A 83.934 361 45 12 1677 2028 426524319 426524675 1.260000e-87 333
18 TraesCS3B01G213300 chr1A 80.645 310 43 10 910 1214 571863239 571862942 7.900000e-55 224
19 TraesCS3B01G213300 chr5D 87.814 279 29 4 1678 1954 53873794 53873519 2.720000e-84 322
20 TraesCS3B01G213300 chr5D 90.254 236 18 5 1678 1911 431899682 431899914 9.860000e-79 303
21 TraesCS3B01G213300 chr5D 90.411 146 12 1 1945 2088 53873083 53872938 8.010000e-45 191
22 TraesCS3B01G213300 chr1D 78.585 509 80 14 744 1231 475967448 475966948 2.120000e-80 309
23 TraesCS3B01G213300 chr1D 93.458 107 7 0 2086 2192 473343530 473343636 2.260000e-35 159
24 TraesCS3B01G213300 chr6B 81.694 366 50 12 1677 2028 694109704 694110066 2.760000e-74 289
25 TraesCS3B01G213300 chr6B 80.618 356 37 16 1733 2088 18125375 18125698 1.690000e-61 246
26 TraesCS3B01G213300 chr7B 79.722 360 61 9 1678 2028 91966327 91966683 1.300000e-62 250
27 TraesCS3B01G213300 chr2B 90.265 113 11 0 2086 2198 717870080 717869968 4.890000e-32 148


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 TraesCS3B01G213300 chr3B 252852745 252854942 2197 True 4060.0 4060 100.0000 1 2198 1 chr3B.!!$R1 2197
1 TraesCS3B01G213300 chr3D 174071768 174073430 1662 True 2654.0 2654 95.4930 1 1662 1 chr3D.!!$R1 1661
2 TraesCS3B01G213300 chrUn 220604016 220605610 1594 True 2556.0 2556 95.6140 69 1662 1 chrUn.!!$R2 1593
3 TraesCS3B01G213300 chrUn 220587222 220587764 542 True 852.0 852 95.0280 1121 1662 1 chrUn.!!$R1 541
4 TraesCS3B01G213300 chr3A 212766033 212767282 1249 True 1768.0 1768 92.1370 405 1662 1 chr3A.!!$R1 1257
5 TraesCS3B01G213300 chr5B 34913296 34913805 509 False 612.0 612 88.3950 1677 2188 1 chr5B.!!$F1 511
6 TraesCS3B01G213300 chr1B 410330682 410331251 569 False 313.5 490 88.9565 1678 2192 2 chr1B.!!$F1 514
7 TraesCS3B01G213300 chr1B 658356772 658357352 580 False 287.0 448 87.2500 1678 2192 2 chr1B.!!$F2 514
8 TraesCS3B01G213300 chr4D 337134476 337135042 566 True 281.5 442 86.7145 1678 2195 2 chr4D.!!$R1 517
9 TraesCS3B01G213300 chr5D 53872938 53873794 856 True 256.5 322 89.1125 1678 2088 2 chr5D.!!$R1 410
10 TraesCS3B01G213300 chr1D 475966948 475967448 500 True 309.0 309 78.5850 744 1231 1 chr1D.!!$R1 487

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
243 245 0.108585 AAACGGTCCTGCATGAGTGT 59.891 50.0 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1663 1685 0.034896 AAGAGCAACCGATCCACGTT 59.965 50.0 0.0 0.0 40.78 3.99 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
155 157 2.094762 AACACATGTTCTACCTCGGC 57.905 50.000 0.00 0.00 31.64 5.54
159 161 1.346395 ACATGTTCTACCTCGGCACAA 59.654 47.619 0.00 0.00 0.00 3.33
196 198 0.830648 CCGGATGGACCAAAGCTCTA 59.169 55.000 0.00 0.00 38.90 2.43
243 245 0.108585 AAACGGTCCTGCATGAGTGT 59.891 50.000 0.00 0.00 0.00 3.55
303 305 2.560504 CTATTGCGGGCTGTTGATACA 58.439 47.619 0.00 0.00 0.00 2.29
338 340 5.821204 ACCAGAGAAAACATTTCAACTTCG 58.179 37.500 5.71 0.00 0.00 3.79
341 343 5.909610 CAGAGAAAACATTTCAACTTCGGAC 59.090 40.000 5.71 0.00 0.00 4.79
499 501 1.531149 CTTCCCACTAGTTGCAACGTG 59.469 52.381 23.21 23.15 0.00 4.49
624 626 6.594937 TCATTTTCAAATTTTCTAGCCCATGC 59.405 34.615 0.00 0.00 37.95 4.06
625 627 4.470334 TTCAAATTTTCTAGCCCATGCC 57.530 40.909 0.00 0.00 38.69 4.40
630 632 2.530460 TTTCTAGCCCATGCCAATGT 57.470 45.000 0.00 0.00 38.69 2.71
632 634 0.625316 TCTAGCCCATGCCAATGTGT 59.375 50.000 0.00 0.00 38.69 3.72
633 635 1.005805 TCTAGCCCATGCCAATGTGTT 59.994 47.619 0.00 0.00 38.69 3.32
774 776 4.508551 TGGAAACTGCCTATCATCACAT 57.491 40.909 0.00 0.00 0.00 3.21
862 864 8.946935 CAAACATAAACATAATCTACATGCACG 58.053 33.333 0.00 0.00 0.00 5.34
954 959 3.256631 CCAGCAAGTAGGAAATTGTGCTT 59.743 43.478 0.00 0.00 40.22 3.91
979 984 2.759191 TCCATCTCGCATTATCTGTGC 58.241 47.619 0.00 0.00 39.18 4.57
1074 1092 2.730090 GCTGTTCTTGATGATGGTTGCG 60.730 50.000 0.00 0.00 0.00 4.85
1241 1262 1.687493 CACTCTCCCCTCTGTCCCC 60.687 68.421 0.00 0.00 0.00 4.81
1251 1272 1.072965 CCTCTGTCCCCATGATTAGCC 59.927 57.143 0.00 0.00 0.00 3.93
1256 1277 2.174639 TGTCCCCATGATTAGCCGAATT 59.825 45.455 0.00 0.00 0.00 2.17
1278 1299 0.179137 CGTGAGCGCTCATTCCACTA 60.179 55.000 39.91 14.61 42.18 2.74
1293 1314 1.672737 CCACTAGTTCTGCATGCGTCA 60.673 52.381 14.09 0.00 0.00 4.35
1303 1324 1.132834 TGCATGCGTCAATGTGATTCC 59.867 47.619 14.09 0.00 0.00 3.01
1393 1414 5.597182 GTGGATGAGAGTATAACTGTACCCA 59.403 44.000 0.00 0.00 0.00 4.51
1408 1429 7.691993 ACTGTACCCATGATAAGGAAGTATT 57.308 36.000 0.00 0.00 0.00 1.89
1565 1587 6.900568 TGCAAAAGAACATTTTGTAACCAG 57.099 33.333 12.99 0.00 40.47 4.00
1590 1612 1.538204 CGGTCGTCCCTATTCCACATG 60.538 57.143 0.00 0.00 0.00 3.21
1621 1643 6.870965 GGTAGGAGATATAACAGTGAGCAATG 59.129 42.308 0.00 0.00 0.00 2.82
1622 1644 6.737720 AGGAGATATAACAGTGAGCAATGA 57.262 37.500 4.83 0.00 0.00 2.57
1662 1684 5.237127 AGCCATATCACATGTGTTTGATACG 59.763 40.000 24.63 8.32 37.50 3.06
1663 1685 5.236263 GCCATATCACATGTGTTTGATACGA 59.764 40.000 24.63 3.11 37.50 3.43
1664 1686 6.238347 GCCATATCACATGTGTTTGATACGAA 60.238 38.462 24.63 2.35 37.50 3.85
1665 1687 7.125755 CCATATCACATGTGTTTGATACGAAC 58.874 38.462 24.63 0.00 37.50 3.95
1666 1688 4.639189 TCACATGTGTTTGATACGAACG 57.361 40.909 24.63 0.00 0.00 3.95
1667 1689 4.052608 TCACATGTGTTTGATACGAACGT 58.947 39.130 24.63 5.03 0.00 3.99
1668 1690 4.084797 TCACATGTGTTTGATACGAACGTG 60.085 41.667 24.63 0.00 0.00 4.49
1669 1691 3.185594 ACATGTGTTTGATACGAACGTGG 59.814 43.478 10.14 0.00 0.00 4.94
1670 1692 3.095102 TGTGTTTGATACGAACGTGGA 57.905 42.857 10.14 0.00 0.00 4.02
1671 1693 3.655486 TGTGTTTGATACGAACGTGGAT 58.345 40.909 10.14 0.00 0.00 3.41
1672 1694 3.676172 TGTGTTTGATACGAACGTGGATC 59.324 43.478 10.14 6.63 0.00 3.36
1673 1695 2.918600 TGTTTGATACGAACGTGGATCG 59.081 45.455 10.14 6.58 45.47 3.69
1674 1696 2.197792 TTGATACGAACGTGGATCGG 57.802 50.000 12.32 0.00 44.32 4.18
1675 1697 1.097232 TGATACGAACGTGGATCGGT 58.903 50.000 12.32 1.24 44.32 4.69
1682 1704 0.034896 AACGTGGATCGGTTGCTCTT 59.965 50.000 0.00 0.00 44.69 2.85
1684 1706 1.361668 CGTGGATCGGTTGCTCTTGG 61.362 60.000 0.00 0.00 35.71 3.61
1760 1785 1.004891 ACCATCCTTCTCCTCCCCC 59.995 63.158 0.00 0.00 0.00 5.40
1838 1865 1.918800 CTTCCCCCTTCCGTCCAGT 60.919 63.158 0.00 0.00 0.00 4.00
2097 2647 2.752358 CTGGAGGCTGGAGTTGCA 59.248 61.111 0.00 0.00 0.00 4.08
2156 2706 4.443934 CGAGAGGTGGAGGAAGGT 57.556 61.111 0.00 0.00 0.00 3.50
2167 2717 2.116983 GAGGAAGGTGTGGAGCTGCA 62.117 60.000 2.72 2.72 0.00 4.41
2195 2745 2.107750 CAGATCTGGCGCGGATGT 59.892 61.111 15.38 11.49 28.51 3.06
2196 2746 1.953138 CAGATCTGGCGCGGATGTC 60.953 63.158 15.38 6.81 28.51 3.06
2197 2747 3.032609 GATCTGGCGCGGATGTCG 61.033 66.667 17.07 0.00 42.76 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 9.226606 CAGAATACCCTTTGTTACTGTTATGAA 57.773 33.333 0.00 0.00 0.00 2.57
55 56 8.561738 ACAGAATACCCTTTGTTACTGTTATG 57.438 34.615 0.00 0.00 33.15 1.90
58 59 7.891498 AAACAGAATACCCTTTGTTACTGTT 57.109 32.000 0.00 0.00 40.97 3.16
136 138 1.346395 TGCCGAGGTAGAACATGTGTT 59.654 47.619 0.00 0.00 41.64 3.32
155 157 6.146898 CGGGTTAACAAATAAGAACCTTGTG 58.853 40.000 8.10 0.00 41.00 3.33
159 161 5.245584 TCCGGGTTAACAAATAAGAACCT 57.754 39.130 8.10 0.00 41.00 3.50
243 245 3.922171 ACATTGGGGCACTTTTCAAAA 57.078 38.095 0.00 0.00 0.00 2.44
303 305 7.027874 TGTTTTCTCTGGTTATCACCCTAAT 57.972 36.000 0.00 0.00 43.49 1.73
338 340 2.361438 CACTTGGACCTAGTATCCGTCC 59.639 54.545 8.34 7.88 45.30 4.79
341 343 1.687123 CCCACTTGGACCTAGTATCCG 59.313 57.143 8.34 0.00 39.30 4.18
379 381 6.745116 ACGAACGATTGACATATATCTTGGA 58.255 36.000 0.14 0.00 0.00 3.53
481 483 0.882927 GCACGTTGCAACTAGTGGGA 60.883 55.000 27.81 0.00 44.26 4.37
499 501 1.290203 CACATGATCCAGGTACACGC 58.710 55.000 0.00 0.00 0.00 5.34
624 626 4.545823 AGTCGTAAACACAACACATTGG 57.454 40.909 0.00 0.00 40.42 3.16
625 627 6.281848 ACTAGTCGTAAACACAACACATTG 57.718 37.500 0.00 0.00 41.98 2.82
633 635 8.137437 GCCCTATAATAACTAGTCGTAAACACA 58.863 37.037 0.00 0.00 0.00 3.72
862 864 6.746104 CTCTATATATAGAGCAATGCACGC 57.254 41.667 28.53 1.65 46.80 5.34
954 959 5.525012 CACAGATAATGCGAGATGGAAAGAA 59.475 40.000 0.00 0.00 0.00 2.52
979 984 0.872388 GGTCGGTTGTTGTTGGCTAG 59.128 55.000 0.00 0.00 0.00 3.42
1241 1262 3.740832 TCACGCTAATTCGGCTAATCATG 59.259 43.478 0.00 0.00 0.00 3.07
1278 1299 1.198408 CACATTGACGCATGCAGAACT 59.802 47.619 19.57 0.00 0.00 3.01
1293 1314 2.557924 TGAAAAGCAGCGGAATCACATT 59.442 40.909 0.00 0.00 0.00 2.71
1303 1324 6.865726 AGTATATAGAGACATGAAAAGCAGCG 59.134 38.462 0.00 0.00 0.00 5.18
1433 1454 8.791327 TGTAGCAATTGAAGATAAATCTGTGA 57.209 30.769 10.34 0.00 37.19 3.58
1565 1587 2.973180 GAATAGGGACGACCGCCTGC 62.973 65.000 0.00 0.00 46.96 4.85
1590 1612 6.097839 TCACTGTTATATCTCCTACCACCAAC 59.902 42.308 0.00 0.00 0.00 3.77
1621 1643 5.897377 ATGGCTACACAATTACCAAGTTC 57.103 39.130 0.00 0.00 33.30 3.01
1622 1644 7.067008 GTGATATGGCTACACAATTACCAAGTT 59.933 37.037 0.00 0.00 33.30 2.66
1662 1684 0.389948 AGAGCAACCGATCCACGTTC 60.390 55.000 0.00 0.00 40.78 3.95
1663 1685 0.034896 AAGAGCAACCGATCCACGTT 59.965 50.000 0.00 0.00 40.78 3.99
1664 1686 0.670546 CAAGAGCAACCGATCCACGT 60.671 55.000 0.00 0.00 40.78 4.49
1665 1687 1.361668 CCAAGAGCAACCGATCCACG 61.362 60.000 0.00 0.00 42.18 4.94
1666 1688 1.026718 CCCAAGAGCAACCGATCCAC 61.027 60.000 0.00 0.00 0.00 4.02
1667 1689 1.299648 CCCAAGAGCAACCGATCCA 59.700 57.895 0.00 0.00 0.00 3.41
1668 1690 0.744771 GACCCAAGAGCAACCGATCC 60.745 60.000 0.00 0.00 0.00 3.36
1669 1691 1.084370 CGACCCAAGAGCAACCGATC 61.084 60.000 0.00 0.00 0.00 3.69
1670 1692 1.079127 CGACCCAAGAGCAACCGAT 60.079 57.895 0.00 0.00 0.00 4.18
1671 1693 2.342279 CGACCCAAGAGCAACCGA 59.658 61.111 0.00 0.00 0.00 4.69
1672 1694 3.423154 GCGACCCAAGAGCAACCG 61.423 66.667 0.00 0.00 0.00 4.44
1673 1695 2.032681 AGCGACCCAAGAGCAACC 59.967 61.111 0.00 0.00 0.00 3.77
1674 1696 2.035442 GGAGCGACCCAAGAGCAAC 61.035 63.158 0.00 0.00 0.00 4.17
1675 1697 2.347490 GGAGCGACCCAAGAGCAA 59.653 61.111 0.00 0.00 0.00 3.91
1726 1749 2.123468 GTGGGTGGGTTGTTGGCT 60.123 61.111 0.00 0.00 0.00 4.75
1731 1756 1.368268 AAGGATGGTGGGTGGGTTGT 61.368 55.000 0.00 0.00 0.00 3.32
1734 1759 1.151587 AGAAGGATGGTGGGTGGGT 60.152 57.895 0.00 0.00 0.00 4.51
1915 1942 4.643387 GCCTTCGTGCACCACCCT 62.643 66.667 12.15 0.00 0.00 4.34
2001 2477 4.828925 GCAGAGGAGCTCCACCGC 62.829 72.222 33.90 26.94 38.89 5.68
2138 2688 1.305381 ACCTTCCTCCACCTCTCGG 60.305 63.158 0.00 0.00 0.00 4.63
2152 2702 2.281070 CGTGCAGCTCCACACCTT 60.281 61.111 8.83 0.00 35.47 3.50


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

AutoCloner maintained by Alex Coulton.