Multiple sequence alignment - TraesCS2A01G138800

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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 TraesCS2A01G138800 chr2A 100.000 3242 0 0 1 3242 84142694 84145935 0.000000e+00 5987.0
1 TraesCS2A01G138800 chr2A 91.023 1994 121 28 925 2882 83990102 83992073 0.000000e+00 2638.0
2 TraesCS2A01G138800 chr2A 92.861 1821 98 20 932 2736 84228305 84230109 0.000000e+00 2614.0
3 TraesCS2A01G138800 chr2A 88.906 1965 145 37 932 2873 86062003 86060089 0.000000e+00 2353.0
4 TraesCS2A01G138800 chr2A 93.995 383 15 5 2865 3242 83991817 83992196 1.010000e-159 573.0
5 TraesCS2A01G138800 chr2A 85.593 236 28 6 2864 3097 134865783 134865552 3.230000e-60 243.0
6 TraesCS2A01G138800 chr2A 96.667 60 2 0 791 850 134867641 134867582 2.060000e-17 100.0
7 TraesCS2A01G138800 chr2A 98.246 57 1 0 793 849 733423534 733423478 2.060000e-17 100.0
8 TraesCS2A01G138800 chr2A 93.333 60 3 1 791 850 83989986 83990044 1.600000e-13 87.9
9 TraesCS2A01G138800 chr2B 89.956 2519 136 39 802 3229 135463517 135466009 0.000000e+00 3142.0
10 TraesCS2A01G138800 chr2B 87.455 2200 149 65 738 2833 135357740 135359916 0.000000e+00 2416.0
11 TraesCS2A01G138800 chr2B 90.156 1859 131 23 932 2744 137814521 137812669 0.000000e+00 2372.0
12 TraesCS2A01G138800 chr2B 90.290 1792 122 24 949 2699 137349335 137347555 0.000000e+00 2298.0
13 TraesCS2A01G138800 chr2B 86.082 2177 155 64 791 2882 135126554 135128667 0.000000e+00 2206.0
14 TraesCS2A01G138800 chr2B 95.199 1354 52 10 1882 3229 182132983 182131637 0.000000e+00 2128.0
15 TraesCS2A01G138800 chr2B 91.339 1374 53 22 1817 3154 135513480 135514823 0.000000e+00 1818.0
16 TraesCS2A01G138800 chr2B 91.615 966 65 12 1930 2887 136813863 136812906 0.000000e+00 1321.0
17 TraesCS2A01G138800 chr2B 90.122 901 77 7 949 1839 137622519 137621621 0.000000e+00 1160.0
18 TraesCS2A01G138800 chr2B 89.900 901 79 7 949 1839 136639002 136638104 0.000000e+00 1149.0
19 TraesCS2A01G138800 chr2B 89.157 498 44 6 2549 3044 135516610 135517099 2.140000e-171 612.0
20 TraesCS2A01G138800 chr2B 92.055 365 20 3 2884 3241 135128429 135128791 3.730000e-139 505.0
21 TraesCS2A01G138800 chr2B 92.135 267 9 3 2988 3242 135516444 135516710 1.840000e-97 366.0
22 TraesCS2A01G138800 chr2B 86.982 169 17 4 2718 2886 136635989 136635826 5.520000e-43 185.0
23 TraesCS2A01G138800 chr2B 91.579 95 8 0 3047 3141 137812665 137812571 7.300000e-27 132.0
24 TraesCS2A01G138800 chr2B 88.182 110 9 3 3137 3242 135128328 135128437 9.440000e-26 128.0
25 TraesCS2A01G138800 chr2B 87.273 110 10 3 3137 3242 182132326 182132217 4.390000e-24 122.0
26 TraesCS2A01G138800 chr2D 92.384 1812 97 22 1078 2874 85703670 85701885 0.000000e+00 2543.0
27 TraesCS2A01G138800 chr2D 89.368 1947 127 27 949 2887 85251880 85250006 0.000000e+00 2375.0
28 TraesCS2A01G138800 chr2D 87.190 2139 140 64 793 2833 83225057 83227159 0.000000e+00 2309.0
29 TraesCS2A01G138800 chr2D 86.533 2146 144 72 793 2833 83188238 83190343 0.000000e+00 2228.0
30 TraesCS2A01G138800 chr2D 90.576 902 71 8 949 1839 84938016 84937118 0.000000e+00 1182.0
31 TraesCS2A01G138800 chr2D 90.344 901 75 6 949 1839 85408813 85407915 0.000000e+00 1171.0
32 TraesCS2A01G138800 chr2D 85.841 226 24 8 2864 3086 127819681 127819461 1.940000e-57 233.0
33 TraesCS2A01G138800 chr2D 100.000 60 0 0 791 850 127821527 127821468 9.510000e-21 111.0
34 TraesCS2A01G138800 chr2D 100.000 34 0 0 743 776 83529746 83529779 2.700000e-06 63.9
35 TraesCS2A01G138800 chr7A 91.249 1817 115 28 949 2733 618195365 618193561 0.000000e+00 2435.0
36 TraesCS2A01G138800 chr5D 92.126 1651 87 17 1048 2661 283110283 283108639 0.000000e+00 2289.0
37 TraesCS2A01G138800 chr5D 86.364 110 11 3 3137 3242 283108760 283108651 2.040000e-22 117.0
38 TraesCS2A01G138800 chr5B 98.780 738 7 2 1 737 319314618 319315354 0.000000e+00 1312.0
39 TraesCS2A01G138800 chr5B 87.273 110 10 3 3137 3242 321476677 321476568 4.390000e-24 122.0
40 TraesCS2A01G138800 chrUn 87.769 1161 90 24 743 1866 25419891 25418746 0.000000e+00 1310.0
41 TraesCS2A01G138800 chrUn 89.391 575 31 15 793 1350 362506273 362506834 0.000000e+00 697.0
42 TraesCS2A01G138800 chr4A 98.509 738 10 1 1 737 34862609 34861872 0.000000e+00 1301.0
43 TraesCS2A01G138800 chr1B 98.509 738 10 1 1 737 466928083 466928820 0.000000e+00 1301.0
44 TraesCS2A01G138800 chr1B 94.986 738 35 2 1 737 95488779 95489515 0.000000e+00 1157.0
45 TraesCS2A01G138800 chr6A 95.799 738 25 2 1 737 34970295 34971027 0.000000e+00 1186.0
46 TraesCS2A01G138800 chr6A 95.122 738 35 1 1 737 1951788 1951051 0.000000e+00 1162.0
47 TraesCS2A01G138800 chr6B 94.986 738 35 2 1 737 145016314 145017050 0.000000e+00 1157.0
48 TraesCS2A01G138800 chr3B 94.715 738 37 2 1 737 581683088 581683824 0.000000e+00 1146.0
49 TraesCS2A01G138800 chr1A 94.723 739 36 3 1 737 589034864 589034127 0.000000e+00 1146.0


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 TraesCS2A01G138800 chr2A 84142694 84145935 3241 False 5987.000000 5987 100.000000 1 3242 1 chr2A.!!$F1 3241
1 TraesCS2A01G138800 chr2A 84228305 84230109 1804 False 2614.000000 2614 92.861000 932 2736 1 chr2A.!!$F2 1804
2 TraesCS2A01G138800 chr2A 86060089 86062003 1914 True 2353.000000 2353 88.906000 932 2873 1 chr2A.!!$R1 1941
3 TraesCS2A01G138800 chr2A 83989986 83992196 2210 False 1099.633333 2638 92.783667 791 3242 3 chr2A.!!$F3 2451
4 TraesCS2A01G138800 chr2B 135463517 135466009 2492 False 3142.000000 3142 89.956000 802 3229 1 chr2B.!!$F2 2427
5 TraesCS2A01G138800 chr2B 135357740 135359916 2176 False 2416.000000 2416 87.455000 738 2833 1 chr2B.!!$F1 2095
6 TraesCS2A01G138800 chr2B 137347555 137349335 1780 True 2298.000000 2298 90.290000 949 2699 1 chr2B.!!$R2 1750
7 TraesCS2A01G138800 chr2B 136812906 136813863 957 True 1321.000000 1321 91.615000 1930 2887 1 chr2B.!!$R1 957
8 TraesCS2A01G138800 chr2B 137812571 137814521 1950 True 1252.000000 2372 90.867500 932 3141 2 chr2B.!!$R5 2209
9 TraesCS2A01G138800 chr2B 137621621 137622519 898 True 1160.000000 1160 90.122000 949 1839 1 chr2B.!!$R3 890
10 TraesCS2A01G138800 chr2B 182131637 182132983 1346 True 1125.000000 2128 91.236000 1882 3242 2 chr2B.!!$R6 1360
11 TraesCS2A01G138800 chr2B 135126554 135128791 2237 False 946.333333 2206 88.773000 791 3242 3 chr2B.!!$F3 2451
12 TraesCS2A01G138800 chr2B 135513480 135517099 3619 False 932.000000 1818 90.877000 1817 3242 3 chr2B.!!$F4 1425
13 TraesCS2A01G138800 chr2B 136635826 136639002 3176 True 667.000000 1149 88.441000 949 2886 2 chr2B.!!$R4 1937
14 TraesCS2A01G138800 chr2D 85701885 85703670 1785 True 2543.000000 2543 92.384000 1078 2874 1 chr2D.!!$R4 1796
15 TraesCS2A01G138800 chr2D 85250006 85251880 1874 True 2375.000000 2375 89.368000 949 2887 1 chr2D.!!$R2 1938
16 TraesCS2A01G138800 chr2D 83225057 83227159 2102 False 2309.000000 2309 87.190000 793 2833 1 chr2D.!!$F2 2040
17 TraesCS2A01G138800 chr2D 83188238 83190343 2105 False 2228.000000 2228 86.533000 793 2833 1 chr2D.!!$F1 2040
18 TraesCS2A01G138800 chr2D 84937118 84938016 898 True 1182.000000 1182 90.576000 949 1839 1 chr2D.!!$R1 890
19 TraesCS2A01G138800 chr2D 85407915 85408813 898 True 1171.000000 1171 90.344000 949 1839 1 chr2D.!!$R3 890
20 TraesCS2A01G138800 chr7A 618193561 618195365 1804 True 2435.000000 2435 91.249000 949 2733 1 chr7A.!!$R1 1784
21 TraesCS2A01G138800 chr5D 283108639 283110283 1644 True 1203.000000 2289 89.245000 1048 3242 2 chr5D.!!$R1 2194
22 TraesCS2A01G138800 chr5B 319314618 319315354 736 False 1312.000000 1312 98.780000 1 737 1 chr5B.!!$F1 736
23 TraesCS2A01G138800 chrUn 25418746 25419891 1145 True 1310.000000 1310 87.769000 743 1866 1 chrUn.!!$R1 1123
24 TraesCS2A01G138800 chrUn 362506273 362506834 561 False 697.000000 697 89.391000 793 1350 1 chrUn.!!$F1 557
25 TraesCS2A01G138800 chr4A 34861872 34862609 737 True 1301.000000 1301 98.509000 1 737 1 chr4A.!!$R1 736
26 TraesCS2A01G138800 chr1B 466928083 466928820 737 False 1301.000000 1301 98.509000 1 737 1 chr1B.!!$F2 736
27 TraesCS2A01G138800 chr1B 95488779 95489515 736 False 1157.000000 1157 94.986000 1 737 1 chr1B.!!$F1 736
28 TraesCS2A01G138800 chr6A 34970295 34971027 732 False 1186.000000 1186 95.799000 1 737 1 chr6A.!!$F1 736
29 TraesCS2A01G138800 chr6A 1951051 1951788 737 True 1162.000000 1162 95.122000 1 737 1 chr6A.!!$R1 736
30 TraesCS2A01G138800 chr6B 145016314 145017050 736 False 1157.000000 1157 94.986000 1 737 1 chr6B.!!$F1 736
31 TraesCS2A01G138800 chr3B 581683088 581683824 736 False 1146.000000 1146 94.715000 1 737 1 chr3B.!!$F1 736
32 TraesCS2A01G138800 chr1A 589034127 589034864 737 True 1146.000000 1146 94.723000 1 737 1 chr1A.!!$R1 736

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
946 983 4.435436 AGCGCGTGAGATTGCCGA 62.435 61.111 8.43 0.00 0.00 5.54 F
1507 1677 0.179094 GTCTGGTGTGTCAACCACGA 60.179 55.000 0.00 3.89 45.43 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 1987 0.877071 CAGTGACTGGCAATGGTGTC 59.123 55.000 4.28 0.0 38.85 3.67 R
2506 3025 1.597663 CTCGTCGGAAACTGCAACTTT 59.402 47.619 0.00 0.0 0.00 2.66 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
698 701 6.953520 TGAAAGAATTAGGACCCAATCAACAT 59.046 34.615 0.00 0.00 0.00 2.71
778 781 8.508800 TTAATATTGCTTTTTGTACCAACACG 57.491 30.769 0.00 0.00 34.61 4.49
781 784 4.959596 TGCTTTTTGTACCAACACGTTA 57.040 36.364 0.00 0.00 34.61 3.18
782 785 5.306532 TGCTTTTTGTACCAACACGTTAA 57.693 34.783 0.00 0.00 34.61 2.01
784 787 5.972382 TGCTTTTTGTACCAACACGTTAATC 59.028 36.000 0.00 0.00 34.61 1.75
787 790 7.520292 GCTTTTTGTACCAACACGTTAATCCTA 60.520 37.037 0.00 0.00 34.61 2.94
788 791 7.424227 TTTTGTACCAACACGTTAATCCTAG 57.576 36.000 0.00 0.00 34.61 3.02
789 792 4.497300 TGTACCAACACGTTAATCCTAGC 58.503 43.478 0.00 0.00 0.00 3.42
862 891 7.969536 TTTAACTGAAGATGGTCTGAGAAAG 57.030 36.000 0.00 0.00 0.00 2.62
946 983 4.435436 AGCGCGTGAGATTGCCGA 62.435 61.111 8.43 0.00 0.00 5.54
1507 1677 0.179094 GTCTGGTGTGTCAACCACGA 60.179 55.000 0.00 3.89 45.43 4.35
1733 1918 4.031129 CCACTCTGCCTGCCTGCT 62.031 66.667 0.00 0.00 0.00 4.24
1802 1987 3.241059 CGCTCTTTCGTCGGCTCG 61.241 66.667 0.00 0.00 0.00 5.03
2194 2705 4.513442 GACATAGTTACCACTGCATCCAA 58.487 43.478 0.00 0.00 34.06 3.53
2294 2809 5.627499 TTGGAAACTCATGTACTGCAATC 57.373 39.130 0.00 0.00 0.00 2.67
2506 3025 2.422597 CATTGGCGTCTTGGTGAGTTA 58.577 47.619 0.00 0.00 0.00 2.24
2782 3357 3.873952 GGCACTGATCCAATAGAACTCAC 59.126 47.826 0.00 0.00 0.00 3.51
2906 3485 1.236616 TGTTGGCCTGAATCTGTGCG 61.237 55.000 3.32 0.00 0.00 5.34
2974 3559 7.148000 GCTTCTATGGCTTCTTAAAACATTCCT 60.148 37.037 0.00 0.00 0.00 3.36
3207 6539 8.673711 TCAATGTACCAAATATCAAGTTGTAGC 58.326 33.333 2.11 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
187 188 3.203487 ACCACAAGAGGAGGTTTTTACCA 59.797 43.478 0.00 0.00 29.58 3.25
377 379 2.816958 CATCGCAGGCGCTTGTCT 60.817 61.111 21.36 0.00 39.59 3.41
698 701 4.021807 GCGGTCCTAATTCTTTCCCAAAAA 60.022 41.667 0.00 0.00 0.00 1.94
862 891 6.696148 TGAAGAAAGAAGTAGAACGTCTTCAC 59.304 38.462 14.85 7.56 44.11 3.18
946 983 2.187958 TGGAACTGGGATCGAACTCAT 58.812 47.619 0.00 0.00 0.00 2.90
1084 1177 1.115467 CGTGCCTAGGTCTGGAGATT 58.885 55.000 11.31 0.00 0.00 2.40
1542 1712 1.599542 GGCAATATCAGAGGCAACGAC 59.400 52.381 0.00 0.00 46.39 4.34
1733 1918 4.308458 ACGGGCGCAACAGCAGTA 62.308 61.111 10.83 0.00 39.27 2.74
1802 1987 0.877071 CAGTGACTGGCAATGGTGTC 59.123 55.000 4.28 0.00 38.85 3.67
1880 2277 3.004951 CAGCTGAGCTCCCCCATT 58.995 61.111 8.42 0.00 36.40 3.16
2194 2705 5.658198 AAACCTTAACTTAGGACCAGGTT 57.342 39.130 4.67 4.67 44.79 3.50
2294 2809 4.803426 GCTCTGTCTCGTGCCGGG 62.803 72.222 2.18 0.00 0.00 5.73
2506 3025 1.597663 CTCGTCGGAAACTGCAACTTT 59.402 47.619 0.00 0.00 0.00 2.66
2765 3340 5.272402 TCAGAGGTGAGTTCTATTGGATCA 58.728 41.667 0.00 0.00 0.00 2.92
2782 3357 7.331934 TCAAACGAAGTATTGAGAAATCAGAGG 59.668 37.037 0.00 0.00 45.00 3.69
2857 3436 9.653287 TCAGATTACAGTATCTCAAACGAAAAT 57.347 29.630 0.00 0.00 32.60 1.82
2862 3441 9.694520 CAAATTCAGATTACAGTATCTCAAACG 57.305 33.333 0.00 0.00 32.60 3.60
2906 3485 9.508567 GATACAAAAAGATTACTCAAATGCTCC 57.491 33.333 0.00 0.00 0.00 4.70
2936 3515 7.877097 AGAAGCCATAGAAGCATACAAGAATAG 59.123 37.037 0.00 0.00 0.00 1.73
2974 3559 2.238646 ACACTTCTCCAACCAGAACACA 59.761 45.455 0.00 0.00 0.00 3.72
3207 6539 9.940166 TTTCATTCATATCTGAAATTGATCACG 57.060 29.630 0.00 0.00 44.29 4.35


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

AutoCloner maintained by Alex Coulton.