Multiple sequence alignment - TraesCS2B01G018800

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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 TraesCS2B01G018800 chr2B 100.000 2627 0 0 1 2627 8669792 8672418 0.000000e+00 4852.0
1 TraesCS2B01G018800 chr2B 99.187 738 5 1 1 738 8632895 8632159 0.000000e+00 1328.0
2 TraesCS2B01G018800 chr2B 78.666 1814 247 69 578 2291 8536861 8538634 0.000000e+00 1077.0
3 TraesCS2B01G018800 chr2B 78.136 1738 310 36 84 1770 9097717 9095999 0.000000e+00 1040.0
4 TraesCS2B01G018800 chr2B 79.214 1323 190 39 591 1860 8997790 8999080 0.000000e+00 841.0
5 TraesCS2B01G018800 chr2B 78.282 1432 211 47 699 2071 8342733 8344123 0.000000e+00 830.0
6 TraesCS2B01G018800 chr2B 80.000 515 67 17 1881 2369 9122371 9121867 5.380000e-92 348.0
7 TraesCS2B01G018800 chr2B 82.197 264 37 8 1998 2255 8999269 8999528 4.400000e-53 219.0
8 TraesCS2B01G018800 chr2B 79.545 308 41 10 1696 2000 9095997 9095709 1.590000e-47 200.0
9 TraesCS2B01G018800 chr2B 100.000 40 0 0 1883 1922 667792284 667792323 1.010000e-09 75.0
10 TraesCS2B01G018800 chr2D 89.721 2403 154 29 1 2369 2732855 2730512 0.000000e+00 2983.0
11 TraesCS2B01G018800 chr2D 79.448 1849 287 54 89 1870 22568447 22566625 0.000000e+00 1223.0
12 TraesCS2B01G018800 chr2D 83.576 688 100 12 84 765 2678464 2677784 1.330000e-177 632.0
13 TraesCS2B01G018800 chr2D 80.383 627 93 20 1180 1782 1995317 1995937 1.430000e-122 449.0
14 TraesCS2B01G018800 chr2D 92.910 268 12 4 2367 2627 2730476 2730209 1.480000e-102 383.0
15 TraesCS2B01G018800 chr2D 79.883 512 73 14 1881 2369 2537749 2537245 5.380000e-92 348.0
16 TraesCS2B01G018800 chr2D 88.525 61 7 0 2540 2600 2344834 2344894 1.010000e-09 75.0
17 TraesCS2B01G018800 chrUn 79.818 1868 287 38 84 1885 15916472 15914629 0.000000e+00 1279.0
18 TraesCS2B01G018800 chrUn 80.100 1603 260 34 85 1643 15478927 15477340 0.000000e+00 1138.0
19 TraesCS2B01G018800 chrUn 78.947 1691 272 35 84 1721 15777396 15779055 0.000000e+00 1074.0
20 TraesCS2B01G018800 chrUn 78.247 1278 193 43 655 1861 15492153 15490890 0.000000e+00 741.0
21 TraesCS2B01G018800 chrUn 82.536 836 123 6 81 911 305055566 305056383 0.000000e+00 713.0
22 TraesCS2B01G018800 chrUn 80.515 621 91 19 1177 1772 305056513 305057128 1.430000e-122 449.0
23 TraesCS2B01G018800 chrUn 79.429 525 65 24 1878 2369 15914278 15913764 5.420000e-87 331.0
24 TraesCS2B01G018800 chrUn 86.747 83 11 0 2455 2537 15955072 15954990 2.780000e-15 93.5
25 TraesCS2B01G018800 chr5A 78.967 1878 274 68 199 1995 599780717 599778880 0.000000e+00 1168.0
26 TraesCS2B01G018800 chr2A 80.451 1596 245 39 84 1643 2492315 2490751 0.000000e+00 1157.0
27 TraesCS2B01G018800 chr2A 79.041 1627 248 44 321 1885 2381062 2382657 0.000000e+00 1029.0
28 TraesCS2B01G018800 chr2A 77.148 1816 330 49 81 1863 2883901 2885664 0.000000e+00 976.0
29 TraesCS2B01G018800 chr2A 83.212 822 129 6 81 895 2324081 2324900 0.000000e+00 745.0
30 TraesCS2B01G018800 chr2A 78.653 1143 187 30 771 1878 2918889 2920009 0.000000e+00 706.0
31 TraesCS2B01G018800 chr2A 77.695 937 122 39 997 1878 2324918 2325822 2.350000e-135 492.0
32 TraesCS2B01G018800 chr2A 81.303 476 61 12 1917 2369 2490027 2489557 6.910000e-96 361.0
33 TraesCS2B01G018800 chr5D 78.587 1868 282 63 199 1995 480602076 480600256 0.000000e+00 1125.0
34 TraesCS2B01G018800 chr3B 77.253 1587 237 58 747 2255 52917286 52915746 0.000000e+00 817.0
35 TraesCS2B01G018800 chr4B 83.439 471 71 6 1177 1641 634317144 634317613 5.190000e-117 431.0
36 TraesCS2B01G018800 chr4B 84.195 348 39 10 1669 2006 634317725 634318066 9.070000e-85 324.0
37 TraesCS2B01G018800 chr4B 86.550 171 17 6 2367 2536 634318441 634318606 1.610000e-42 183.0
38 TraesCS2B01G018800 chr7A 87.952 83 9 1 1561 1643 48064942 48064861 2.150000e-16 97.1


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 TraesCS2B01G018800 chr2B 8669792 8672418 2626 False 4852.000000 4852 100.0000 1 2627 1 chr2B.!!$F3 2626
1 TraesCS2B01G018800 chr2B 8632159 8632895 736 True 1328.000000 1328 99.1870 1 738 1 chr2B.!!$R1 737
2 TraesCS2B01G018800 chr2B 8536861 8538634 1773 False 1077.000000 1077 78.6660 578 2291 1 chr2B.!!$F2 1713
3 TraesCS2B01G018800 chr2B 8342733 8344123 1390 False 830.000000 830 78.2820 699 2071 1 chr2B.!!$F1 1372
4 TraesCS2B01G018800 chr2B 9095709 9097717 2008 True 620.000000 1040 78.8405 84 2000 2 chr2B.!!$R3 1916
5 TraesCS2B01G018800 chr2B 8997790 8999528 1738 False 530.000000 841 80.7055 591 2255 2 chr2B.!!$F5 1664
6 TraesCS2B01G018800 chr2B 9121867 9122371 504 True 348.000000 348 80.0000 1881 2369 1 chr2B.!!$R2 488
7 TraesCS2B01G018800 chr2D 2730209 2732855 2646 True 1683.000000 2983 91.3155 1 2627 2 chr2D.!!$R4 2626
8 TraesCS2B01G018800 chr2D 22566625 22568447 1822 True 1223.000000 1223 79.4480 89 1870 1 chr2D.!!$R3 1781
9 TraesCS2B01G018800 chr2D 2677784 2678464 680 True 632.000000 632 83.5760 84 765 1 chr2D.!!$R2 681
10 TraesCS2B01G018800 chr2D 1995317 1995937 620 False 449.000000 449 80.3830 1180 1782 1 chr2D.!!$F1 602
11 TraesCS2B01G018800 chr2D 2537245 2537749 504 True 348.000000 348 79.8830 1881 2369 1 chr2D.!!$R1 488
12 TraesCS2B01G018800 chrUn 15477340 15478927 1587 True 1138.000000 1138 80.1000 85 1643 1 chrUn.!!$R1 1558
13 TraesCS2B01G018800 chrUn 15777396 15779055 1659 False 1074.000000 1074 78.9470 84 1721 1 chrUn.!!$F1 1637
14 TraesCS2B01G018800 chrUn 15913764 15916472 2708 True 805.000000 1279 79.6235 84 2369 2 chrUn.!!$R4 2285
15 TraesCS2B01G018800 chrUn 15490890 15492153 1263 True 741.000000 741 78.2470 655 1861 1 chrUn.!!$R2 1206
16 TraesCS2B01G018800 chrUn 305055566 305057128 1562 False 581.000000 713 81.5255 81 1772 2 chrUn.!!$F2 1691
17 TraesCS2B01G018800 chr5A 599778880 599780717 1837 True 1168.000000 1168 78.9670 199 1995 1 chr5A.!!$R1 1796
18 TraesCS2B01G018800 chr2A 2381062 2382657 1595 False 1029.000000 1029 79.0410 321 1885 1 chr2A.!!$F1 1564
19 TraesCS2B01G018800 chr2A 2883901 2885664 1763 False 976.000000 976 77.1480 81 1863 1 chr2A.!!$F2 1782
20 TraesCS2B01G018800 chr2A 2489557 2492315 2758 True 759.000000 1157 80.8770 84 2369 2 chr2A.!!$R1 2285
21 TraesCS2B01G018800 chr2A 2918889 2920009 1120 False 706.000000 706 78.6530 771 1878 1 chr2A.!!$F3 1107
22 TraesCS2B01G018800 chr2A 2324081 2325822 1741 False 618.500000 745 80.4535 81 1878 2 chr2A.!!$F4 1797
23 TraesCS2B01G018800 chr5D 480600256 480602076 1820 True 1125.000000 1125 78.5870 199 1995 1 chr5D.!!$R1 1796
24 TraesCS2B01G018800 chr3B 52915746 52917286 1540 True 817.000000 817 77.2530 747 2255 1 chr3B.!!$R1 1508
25 TraesCS2B01G018800 chr4B 634317144 634318606 1462 False 312.666667 431 84.7280 1177 2536 3 chr4B.!!$F1 1359

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
744 790 0.025001 CGCGAGGTGAAATAACAGCG 59.975 55.0 0.0 0.0 42.15 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1793 2158 0.678048 GGCCACAAGACCCTCATGTC 60.678 60.0 0.0 0.0 35.43 3.06 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
725 759 1.140452 TCAGAAGCATCAGAGATGGGC 59.860 52.381 8.87 0.00 0.00 5.36
744 790 0.025001 CGCGAGGTGAAATAACAGCG 59.975 55.000 0.00 0.00 42.15 5.18
772 823 1.216990 GGAAGAGGATGATGGGGTGT 58.783 55.000 0.00 0.00 0.00 4.16
775 826 1.673767 AGAGGATGATGGGGTGTTGT 58.326 50.000 0.00 0.00 0.00 3.32
806 857 3.694072 GCTCATCTCTGTGACTCACTACT 59.306 47.826 10.54 0.00 35.11 2.57
813 864 4.215908 TCTGTGACTCACTACTGGAGTTT 58.784 43.478 10.54 0.00 45.21 2.66
834 885 0.247736 AGTTCGATGACTGCCCAGAC 59.752 55.000 1.69 0.00 0.00 3.51
849 900 1.479709 CAGACCTAGTCCTGGTGGAG 58.520 60.000 0.00 0.00 44.16 3.86
900 954 0.398381 TCCAAGCCTTGCAAACCCTT 60.398 50.000 0.00 0.27 0.00 3.95
917 973 4.967036 ACCCTTCAGAGATTAAGCATAGC 58.033 43.478 0.00 0.00 0.00 2.97
924 980 2.408050 AGATTAAGCATAGCGCCTTCG 58.592 47.619 2.29 0.00 44.04 3.79
934 990 2.983592 CGCCTTCGCCCAGGTTTT 60.984 61.111 0.00 0.00 36.15 2.43
1085 1141 3.146104 ACTGTTGAATTGTGGAGAGGG 57.854 47.619 0.00 0.00 0.00 4.30
1097 1153 0.457851 GGAGAGGGTCTGACATGTCG 59.542 60.000 20.54 14.91 0.00 4.35
1147 1203 3.129462 GGGCCAGCTCAAAGAATTAAGAC 59.871 47.826 4.39 0.00 0.00 3.01
1163 1219 6.875972 ATTAAGACTCTCTTTCAGCCCTAA 57.124 37.500 0.00 0.00 37.89 2.69
1199 1279 0.533032 GAGGACGTTGAAGGAGGAGG 59.467 60.000 0.00 0.00 0.00 4.30
1215 1295 0.536260 GAGGAGAGCAGCAGACACAT 59.464 55.000 0.00 0.00 0.00 3.21
1216 1296 0.982704 AGGAGAGCAGCAGACACATT 59.017 50.000 0.00 0.00 0.00 2.71
1440 1535 2.106338 TCACAATCTTCAGCAACTCCCA 59.894 45.455 0.00 0.00 0.00 4.37
1517 1615 0.321210 TCGTCATTGCCCAACGATGT 60.321 50.000 0.00 0.00 40.21 3.06
1643 1774 5.197451 ACACTGATCCAAGGTAACACAAAA 58.803 37.500 0.00 0.00 41.41 2.44
1655 1880 4.208253 GGTAACACAAAATTCCACTTTGCG 59.792 41.667 0.00 0.00 37.29 4.85
1775 2139 3.006430 TGTTCTGCTCTTTCCATACGACA 59.994 43.478 0.00 0.00 0.00 4.35
1776 2140 3.232213 TCTGCTCTTTCCATACGACAC 57.768 47.619 0.00 0.00 0.00 3.67
1777 2141 2.826128 TCTGCTCTTTCCATACGACACT 59.174 45.455 0.00 0.00 0.00 3.55
1974 3115 4.906747 TTTCCATTTTCTTCCCAATGGG 57.093 40.909 13.28 13.28 46.65 4.00
2178 3363 7.725844 GGGTTATTGTCATCCCTTCATTAAGAT 59.274 37.037 0.00 0.00 37.18 2.40
2316 3505 4.266265 CCATATACTGCTATGTTGCGATCG 59.734 45.833 11.69 11.69 35.36 3.69
2321 3510 1.135333 TGCTATGTTGCGATCGGTACA 59.865 47.619 18.30 3.25 35.36 2.90
2365 3554 0.459489 TGTTGGCTTGTTGTTCAGGC 59.541 50.000 0.00 0.00 46.37 4.85
2501 3736 6.770785 AGTGTTTTGCTACTGATAAGGTTTGA 59.229 34.615 0.00 0.00 0.00 2.69
2539 3774 5.652891 AGTTGACATTCTACTGATACCTCGT 59.347 40.000 0.00 0.00 31.55 4.18
2545 3780 8.101654 ACATTCTACTGATACCTCGTATTCTC 57.898 38.462 0.00 0.00 0.00 2.87
2553 3788 3.892918 ACCTCGTATTCTCGTATTCGG 57.107 47.619 0.00 0.00 37.69 4.30
2554 3789 3.209410 ACCTCGTATTCTCGTATTCGGT 58.791 45.455 0.00 0.00 37.69 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 2.092375 TGAGTCGGAGAGATAAGCTGGA 60.092 50.000 0.00 0.0 36.95 3.86
725 759 0.025001 CGCTGTTATTTCACCTCGCG 59.975 55.000 0.00 0.0 0.00 5.87
744 790 0.179051 CATCCTCTTCCTCTGCTGCC 60.179 60.000 0.00 0.0 0.00 4.85
772 823 2.909006 AGAGATGAGCTGGGAAGAACAA 59.091 45.455 0.00 0.0 0.00 2.83
775 826 2.235650 CACAGAGATGAGCTGGGAAGAA 59.764 50.000 0.00 0.0 39.11 2.52
806 857 3.653344 CAGTCATCGAACTCAAACTCCA 58.347 45.455 0.00 0.0 0.00 3.86
813 864 0.247460 CTGGGCAGTCATCGAACTCA 59.753 55.000 0.00 0.0 0.00 3.41
834 885 1.306141 TGGCTCCACCAGGACTAGG 60.306 63.158 0.00 0.0 46.36 3.02
849 900 0.954452 CAGGAACAAGAGTTGGTGGC 59.046 55.000 0.00 0.0 38.30 5.01
900 954 2.630098 AGGCGCTATGCTTAATCTCTGA 59.370 45.455 7.64 0.0 45.43 3.27
924 980 3.132824 CCAATCTGGATAAAAACCTGGGC 59.867 47.826 0.00 0.0 40.96 5.36
934 990 6.266131 AGGCACTATTTCCAATCTGGATAA 57.734 37.500 0.00 0.0 42.25 1.75
1085 1141 1.021390 CAAGCCCCGACATGTCAGAC 61.021 60.000 24.93 11.2 0.00 3.51
1147 1203 7.392953 AGAAAAGAATTTAGGGCTGAAAGAGAG 59.607 37.037 0.00 0.0 37.28 3.20
1163 1219 4.152647 GTCCTCCCAACCAGAAAAGAATT 58.847 43.478 0.00 0.0 0.00 2.17
1199 1279 2.551459 ACAAAATGTGTCTGCTGCTCTC 59.449 45.455 0.00 0.0 34.38 3.20
1215 1295 4.669206 ATGCAGTGTGGATGAAACAAAA 57.331 36.364 0.00 0.0 0.00 2.44
1517 1615 4.655963 CTTTTGAAGTGATTCAGGGAGGA 58.344 43.478 0.00 0.0 31.87 3.71
1643 1774 1.963515 AGGAAAAGCGCAAAGTGGAAT 59.036 42.857 11.47 0.0 0.00 3.01
1793 2158 0.678048 GGCCACAAGACCCTCATGTC 60.678 60.000 0.00 0.0 35.43 3.06
1967 3108 7.938140 TCTTAAATACTTTCACTCCCATTGG 57.062 36.000 0.00 0.0 0.00 3.16
2012 3171 6.357579 TGGCTGATATTGATGTTGGTTTTT 57.642 33.333 0.00 0.0 0.00 1.94
2026 3185 3.870538 TCAGAAGGCATTGGCTGATAT 57.129 42.857 14.12 0.0 38.81 1.63
2178 3363 7.732025 TCAAAATAGGAAAGTAGACTGACACA 58.268 34.615 0.00 0.0 0.00 3.72
2316 3505 2.200373 ATGCAAGAACACCCTGTACC 57.800 50.000 0.00 0.0 0.00 3.34
2321 3510 6.494835 AGAAATTAGAAATGCAAGAACACCCT 59.505 34.615 0.00 0.0 0.00 4.34
2365 3554 7.513190 TGAGTTTTTGGACAAAATGTAAACG 57.487 32.000 10.64 0.0 39.69 3.60
2465 3700 4.297299 AGCAAAACACTGACAACTCATG 57.703 40.909 0.00 0.0 0.00 3.07
2536 3771 5.294306 AGTTGTACCGAATACGAGAATACGA 59.706 40.000 0.00 0.0 42.66 3.43
2537 3772 5.394613 CAGTTGTACCGAATACGAGAATACG 59.605 44.000 0.00 0.0 42.66 3.06
2539 3774 6.441093 ACAGTTGTACCGAATACGAGAATA 57.559 37.500 0.00 0.0 42.66 1.75
2545 3780 4.694177 CAACAACAGTTGTACCGAATACG 58.306 43.478 19.45 0.0 44.59 3.06
2600 3835 5.582665 GCTATGGTATACAGGCTATTCTTGC 59.417 44.000 5.01 0.0 0.00 4.01


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

AutoCloner maintained by Alex Coulton.