Multiple sequence alignment - TraesCS7D01G030900

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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 TraesCS7D01G030900 chr7D 100.000 5407 0 0 623 6029 16219707 16225113 0.000000e+00 9985
1 TraesCS7D01G030900 chr7D 100.000 379 0 0 1 379 16219085 16219463 0.000000e+00 701
2 TraesCS7D01G030900 chr7D 75.381 853 183 23 2738 3570 20327683 20328528 2.640000e-103 387
3 TraesCS7D01G030900 chr7D 84.307 274 31 6 5153 5417 26459700 26459970 2.160000e-64 257
4 TraesCS7D01G030900 chr7D 82.540 315 27 9 89 379 26458541 26458851 1.000000e-62 252
5 TraesCS7D01G030900 chr7D 100.000 59 0 0 2089 2147 26459114 26459172 6.390000e-20 110
6 TraesCS7D01G030900 chr7A 95.389 5010 138 36 802 5747 15035658 15040638 0.000000e+00 7886
7 TraesCS7D01G030900 chr7A 91.811 403 9 2 1 379 15034735 15035137 1.910000e-149 540
8 TraesCS7D01G030900 chr7A 75.781 640 133 17 1129 1751 716233138 716233772 2.730000e-78 303
9 TraesCS7D01G030900 chr7A 71.429 1162 275 42 2762 3893 19019286 19018152 2.790000e-63 254
10 TraesCS7D01G030900 chr7A 95.833 144 3 1 666 809 15035480 15035620 4.700000e-56 230
11 TraesCS7D01G030900 chr7A 97.170 106 2 1 5924 6029 15040814 15040918 1.730000e-40 178
12 TraesCS7D01G030900 chr7A 92.857 112 6 2 5810 5919 15040659 15040770 1.740000e-35 161
13 TraesCS7D01G030900 chr4A 95.635 4422 150 16 927 5311 718855044 718859459 0.000000e+00 7057
14 TraesCS7D01G030900 chr4A 80.828 1763 286 36 3124 4860 714339620 714341356 0.000000e+00 1336
15 TraesCS7D01G030900 chr4A 79.462 930 149 27 1027 1939 714330249 714331153 6.640000e-174 621
16 TraesCS7D01G030900 chr4A 85.677 384 36 11 5362 5742 718859457 718859824 2.640000e-103 387
17 TraesCS7D01G030900 chr4A 77.804 428 44 22 1 379 718853942 718854367 3.660000e-52 217
18 TraesCS7D01G030900 chr4A 84.332 217 9 5 5798 5989 718859837 718860053 7.980000e-44 189
19 TraesCS7D01G030900 chr3D 98.141 2905 34 4 3133 6029 585379338 585376446 0.000000e+00 5048
20 TraesCS7D01G030900 chr3D 81.405 1253 206 22 3629 4861 23615676 23616921 0.000000e+00 998
21 TraesCS7D01G030900 chr3D 81.235 842 140 9 2739 3565 23614822 23615660 0.000000e+00 664
22 TraesCS7D01G030900 chr3D 78.112 932 157 29 1027 1939 23612419 23613322 1.140000e-151 547
23 TraesCS7D01G030900 chr3A 89.276 1091 113 4 2716 3804 7498607 7497519 0.000000e+00 1363
24 TraesCS7D01G030900 chr3A 84.501 1142 153 16 3797 4925 7487592 7486462 0.000000e+00 1107
25 TraesCS7D01G030900 chr3A 88.110 471 51 3 1015 1480 7500154 7499684 6.830000e-154 555
26 TraesCS7D01G030900 chr3A 88.511 235 27 0 1706 1940 7499683 7499449 9.890000e-73 285
27 TraesCS7D01G030900 chr7B 77.328 816 148 29 1052 1852 740995128 740994335 1.190000e-121 448
28 TraesCS7D01G030900 chr7B 75.898 668 130 23 1129 1776 719097422 719096766 4.540000e-81 313
29 TraesCS7D01G030900 chr7B 74.156 770 162 25 1100 1852 717167611 717166862 9.890000e-73 285
30 TraesCS7D01G030900 chr7B 81.169 154 27 2 2758 2910 717154752 717154600 8.210000e-24 122
31 TraesCS7D01G030900 chr7B 81.169 154 27 2 2758 2910 717230224 717230072 8.210000e-24 122
32 TraesCS7D01G030900 chr6D 73.938 1224 266 43 2766 3970 440644823 440646012 1.540000e-120 444
33 TraesCS7D01G030900 chr2B 73.241 1222 276 44 2761 3952 778469051 778467851 1.220000e-106 398
34 TraesCS7D01G030900 chr2A 73.167 1159 268 36 2761 3893 778586802 778587943 1.590000e-100 377
35 TraesCS7D01G030900 chr5D 73.179 1167 250 52 2765 3895 35963030 35961891 4.440000e-96 363
36 TraesCS7D01G030900 chr5B 72.915 1067 251 33 2848 3895 26875581 26874534 9.680000e-88 335


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 TraesCS7D01G030900 chr7D 16219085 16225113 6028 False 5343.000000 9985 100.000000 1 6029 2 chr7D.!!$F2 6028
1 TraesCS7D01G030900 chr7D 20327683 20328528 845 False 387.000000 387 75.381000 2738 3570 1 chr7D.!!$F1 832
2 TraesCS7D01G030900 chr7D 26458541 26459970 1429 False 206.333333 257 88.949000 89 5417 3 chr7D.!!$F3 5328
3 TraesCS7D01G030900 chr7A 15034735 15040918 6183 False 1799.000000 7886 94.612000 1 6029 5 chr7A.!!$F2 6028
4 TraesCS7D01G030900 chr7A 716233138 716233772 634 False 303.000000 303 75.781000 1129 1751 1 chr7A.!!$F1 622
5 TraesCS7D01G030900 chr7A 19018152 19019286 1134 True 254.000000 254 71.429000 2762 3893 1 chr7A.!!$R1 1131
6 TraesCS7D01G030900 chr4A 718853942 718860053 6111 False 1962.500000 7057 85.862000 1 5989 4 chr4A.!!$F3 5988
7 TraesCS7D01G030900 chr4A 714339620 714341356 1736 False 1336.000000 1336 80.828000 3124 4860 1 chr4A.!!$F2 1736
8 TraesCS7D01G030900 chr4A 714330249 714331153 904 False 621.000000 621 79.462000 1027 1939 1 chr4A.!!$F1 912
9 TraesCS7D01G030900 chr3D 585376446 585379338 2892 True 5048.000000 5048 98.141000 3133 6029 1 chr3D.!!$R1 2896
10 TraesCS7D01G030900 chr3D 23612419 23616921 4502 False 736.333333 998 80.250667 1027 4861 3 chr3D.!!$F1 3834
11 TraesCS7D01G030900 chr3A 7486462 7487592 1130 True 1107.000000 1107 84.501000 3797 4925 1 chr3A.!!$R1 1128
12 TraesCS7D01G030900 chr3A 7497519 7500154 2635 True 734.333333 1363 88.632333 1015 3804 3 chr3A.!!$R2 2789
13 TraesCS7D01G030900 chr7B 740994335 740995128 793 True 448.000000 448 77.328000 1052 1852 1 chr7B.!!$R5 800
14 TraesCS7D01G030900 chr7B 719096766 719097422 656 True 313.000000 313 75.898000 1129 1776 1 chr7B.!!$R4 647
15 TraesCS7D01G030900 chr7B 717166862 717167611 749 True 285.000000 285 74.156000 1100 1852 1 chr7B.!!$R2 752
16 TraesCS7D01G030900 chr6D 440644823 440646012 1189 False 444.000000 444 73.938000 2766 3970 1 chr6D.!!$F1 1204
17 TraesCS7D01G030900 chr2B 778467851 778469051 1200 True 398.000000 398 73.241000 2761 3952 1 chr2B.!!$R1 1191
18 TraesCS7D01G030900 chr2A 778586802 778587943 1141 False 377.000000 377 73.167000 2761 3893 1 chr2A.!!$F1 1132
19 TraesCS7D01G030900 chr5D 35961891 35963030 1139 True 363.000000 363 73.179000 2765 3895 1 chr5D.!!$R1 1130
20 TraesCS7D01G030900 chr5B 26874534 26875581 1047 True 335.000000 335 72.915000 2848 3895 1 chr5B.!!$R1 1047

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
895 1324 0.806884 TATGGCCGGCGAGTAAAACG 60.807 55.000 22.54 0.0 0.00 3.60 F
916 1345 1.006998 AGGATGCAGACTGAGGAGAGT 59.993 52.381 6.65 0.0 0.00 3.24 F
917 1346 1.830477 GGATGCAGACTGAGGAGAGTT 59.170 52.381 6.65 0.0 0.00 3.01 F
1048 1479 2.851263 AAATCCACACAGTAGCGGAA 57.149 45.000 0.00 0.0 0.00 4.30 F
1897 2369 2.912295 TGACAGAATGGATGTGGAGGAA 59.088 45.455 0.00 0.0 43.62 3.36 F
2567 3478 4.095782 TCTCAGCTGTTGTTACACCAAAAC 59.904 41.667 14.67 0.0 0.00 2.43 F
2611 3969 4.770795 ACCTGTCTTATAACCATCAGTGC 58.229 43.478 0.00 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1862 2334 1.695242 TCTGTCAATGTTACCCACGGT 59.305 47.619 0.00 0.00 40.16 4.83 R
2169 2681 2.103432 TGGGTTTGTTAGTTCTCGCTCA 59.897 45.455 0.00 0.00 0.00 4.26 R
2507 3418 5.047872 TCAAGGGAATGTTGTGAATGATGTG 60.048 40.000 0.00 0.00 0.00 3.21 R
2611 3969 5.527214 TGAAACTGAACCATGTGTTAGTCAG 59.473 40.000 10.49 10.49 37.29 3.51 R
2704 4392 9.442047 AAAGCTAGCACTATAAGCAATTATAGG 57.558 33.333 18.83 8.52 40.22 2.57 R
4003 5801 6.015918 TGCCTTCATTTTTGAGATCCCTTTA 58.984 36.000 0.00 0.00 0.00 1.85 R
5577 7436 4.098196 AGAACTAGAGACCCGAATAAGTGC 59.902 45.833 0.00 0.00 0.00 4.40 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
75 81 9.784531 CCTATTGTACTTGATCAAACATAGGAT 57.215 33.333 24.09 15.08 31.66 3.24
79 85 9.739276 TTGTACTTGATCAAACATAGGATTTCT 57.261 29.630 12.55 0.00 0.00 2.52
80 86 9.166173 TGTACTTGATCAAACATAGGATTTCTG 57.834 33.333 9.88 0.00 0.00 3.02
81 87 7.636150 ACTTGATCAAACATAGGATTTCTGG 57.364 36.000 9.88 0.00 0.00 3.86
84 90 3.631250 TCAAACATAGGATTTCTGGGCC 58.369 45.455 0.00 0.00 0.00 5.80
85 91 3.011144 TCAAACATAGGATTTCTGGGCCA 59.989 43.478 5.85 5.85 0.00 5.36
86 92 3.962718 CAAACATAGGATTTCTGGGCCAT 59.037 43.478 6.72 0.00 0.00 4.40
87 93 5.103728 TCAAACATAGGATTTCTGGGCCATA 60.104 40.000 6.72 0.00 0.00 2.74
89 95 5.184892 ACATAGGATTTCTGGGCCATATC 57.815 43.478 6.72 10.62 0.00 1.63
90 96 4.854436 ACATAGGATTTCTGGGCCATATCT 59.146 41.667 6.72 1.97 0.00 1.98
91 97 5.045286 ACATAGGATTTCTGGGCCATATCTC 60.045 44.000 6.72 1.98 0.00 2.75
92 98 3.606972 AGGATTTCTGGGCCATATCTCT 58.393 45.455 6.72 7.47 0.00 3.10
244 317 6.116126 GCACAGACCTAAAGGATTTGATACT 58.884 40.000 2.23 0.00 39.63 2.12
254 327 6.986904 AAGGATTTGATACTCTTCCGTTTC 57.013 37.500 0.00 0.00 0.00 2.78
776 1158 8.705134 CCCGGAGTTAAAATTTTGATGTTTAAC 58.295 33.333 13.76 7.84 43.35 2.01
809 1191 1.607148 CCCTCCGGCCGAAAATATTTC 59.393 52.381 30.73 0.00 0.00 2.17
812 1194 3.837669 CGGCCGAAAATATTTCCGG 57.162 52.632 24.07 20.40 44.34 5.14
870 1299 7.255451 GGTCAGGAGAGAGAGTATGTAATTGAG 60.255 44.444 0.00 0.00 0.00 3.02
892 1321 2.110901 TTTTATGGCCGGCGAGTAAA 57.889 45.000 22.54 20.51 0.00 2.01
895 1324 0.806884 TATGGCCGGCGAGTAAAACG 60.807 55.000 22.54 0.00 0.00 3.60
910 1339 2.376808 AAACGAGGATGCAGACTGAG 57.623 50.000 6.65 0.00 0.00 3.35
916 1345 1.006998 AGGATGCAGACTGAGGAGAGT 59.993 52.381 6.65 0.00 0.00 3.24
917 1346 1.830477 GGATGCAGACTGAGGAGAGTT 59.170 52.381 6.65 0.00 0.00 3.01
959 1390 6.932947 AGAGTACACCAATAACTCTGGTTAC 58.067 40.000 3.55 0.35 45.13 2.50
1048 1479 2.851263 AAATCCACACAGTAGCGGAA 57.149 45.000 0.00 0.00 0.00 4.30
1058 1494 3.013921 ACAGTAGCGGAAAGAGAGAGAG 58.986 50.000 0.00 0.00 0.00 3.20
1629 2098 4.240881 TGATGGAGAAGGAAAAGGATGG 57.759 45.455 0.00 0.00 0.00 3.51
1716 2188 3.790437 CCGGCAGCTGGAGACCAT 61.790 66.667 16.28 0.00 30.82 3.55
1862 2334 5.280499 TCATGGAAGAAGAGGAACAGGATA 58.720 41.667 0.00 0.00 0.00 2.59
1897 2369 2.912295 TGACAGAATGGATGTGGAGGAA 59.088 45.455 0.00 0.00 43.62 3.36
1951 2426 5.126061 AGGCAAGAGGTATGCAAACATAAAG 59.874 40.000 0.00 0.00 45.60 1.85
2169 2681 5.130145 TGGGTTTTGATGGTTTGTGAATTCT 59.870 36.000 7.05 0.00 0.00 2.40
2521 3432 5.700832 TGGAGTAACTCACATCATTCACAAC 59.299 40.000 0.00 0.00 31.08 3.32
2537 3448 4.645535 TCACAACATTCCCTTGAGAAGAG 58.354 43.478 0.00 0.00 0.00 2.85
2567 3478 4.095782 TCTCAGCTGTTGTTACACCAAAAC 59.904 41.667 14.67 0.00 0.00 2.43
2611 3969 4.770795 ACCTGTCTTATAACCATCAGTGC 58.229 43.478 0.00 0.00 0.00 4.40
4003 5801 0.184451 CTGCCCTATGGACATTGCCT 59.816 55.000 0.00 0.00 0.00 4.75
5519 7366 6.521162 TCAACAACAGTCAGTCTATTAGCAA 58.479 36.000 0.00 0.00 0.00 3.91
5520 7367 6.989759 TCAACAACAGTCAGTCTATTAGCAAA 59.010 34.615 0.00 0.00 0.00 3.68
5594 7453 2.358267 CGTAGCACTTATTCGGGTCTCT 59.642 50.000 0.00 0.00 0.00 3.10
5595 7454 3.562973 CGTAGCACTTATTCGGGTCTCTA 59.437 47.826 0.00 0.00 0.00 2.43
6001 7912 6.826893 AAATACAAAGACATGCACAACAAC 57.173 33.333 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 81 3.900601 GAGAGAGAGATATGGCCCAGAAA 59.099 47.826 0.00 0.00 0.00 2.52
76 82 3.141838 AGAGAGAGAGATATGGCCCAGAA 59.858 47.826 0.00 0.00 0.00 3.02
78 84 3.091545 GAGAGAGAGAGATATGGCCCAG 58.908 54.545 0.00 0.00 0.00 4.45
79 85 2.721355 AGAGAGAGAGAGATATGGCCCA 59.279 50.000 0.00 0.00 0.00 5.36
80 86 3.010584 AGAGAGAGAGAGAGATATGGCCC 59.989 52.174 0.00 0.00 0.00 5.80
81 87 4.018960 AGAGAGAGAGAGAGAGATATGGCC 60.019 50.000 0.00 0.00 0.00 5.36
84 90 7.396907 AGAGAGAGAGAGAGAGAGAGAGATATG 59.603 44.444 0.00 0.00 0.00 1.78
85 91 7.477864 AGAGAGAGAGAGAGAGAGAGAGATAT 58.522 42.308 0.00 0.00 0.00 1.63
86 92 6.857848 AGAGAGAGAGAGAGAGAGAGAGATA 58.142 44.000 0.00 0.00 0.00 1.98
87 93 5.714863 AGAGAGAGAGAGAGAGAGAGAGAT 58.285 45.833 0.00 0.00 0.00 2.75
89 95 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
90 96 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
91 97 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
92 98 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
244 317 7.773224 ACATGTAAATCCATATGAAACGGAAGA 59.227 33.333 3.65 0.00 31.18 2.87
662 1044 8.349983 ACCTACAACTGTGTTGATAAATGTTTC 58.650 33.333 16.04 0.00 39.30 2.78
664 1046 7.817418 ACCTACAACTGTGTTGATAAATGTT 57.183 32.000 16.04 0.00 39.30 2.71
809 1191 0.105658 TTCAGATACTCCCTCCCCGG 60.106 60.000 0.00 0.00 0.00 5.73
812 1194 6.882768 ATATGATTTCAGATACTCCCTCCC 57.117 41.667 0.00 0.00 0.00 4.30
848 1277 9.432982 AAATCTCAATTACATACTCTCTCTCCT 57.567 33.333 0.00 0.00 0.00 3.69
870 1299 1.021968 ACTCGCCGGCCATAAAAATC 58.978 50.000 23.46 0.00 0.00 2.17
892 1321 0.534412 CCTCAGTCTGCATCCTCGTT 59.466 55.000 0.00 0.00 0.00 3.85
895 1324 1.682854 CTCTCCTCAGTCTGCATCCTC 59.317 57.143 0.00 0.00 0.00 3.71
959 1390 5.888161 AGCAAAGGTTGGACTTTATATCTGG 59.112 40.000 0.00 0.00 38.56 3.86
1048 1479 6.041979 GCTCCATTATTCTTCCTCTCTCTCTT 59.958 42.308 0.00 0.00 0.00 2.85
1058 1494 1.261619 CGTGCGCTCCATTATTCTTCC 59.738 52.381 9.73 0.00 0.00 3.46
1716 2188 2.435938 GGGCTTGGCGATCGAACA 60.436 61.111 21.57 14.16 0.00 3.18
1862 2334 1.695242 TCTGTCAATGTTACCCACGGT 59.305 47.619 0.00 0.00 40.16 4.83
2036 2547 7.472334 AGAATTTTAGATCAATGTGGTGCTT 57.528 32.000 0.00 0.00 0.00 3.91
2038 2549 7.761409 TGTAGAATTTTAGATCAATGTGGTGC 58.239 34.615 0.00 0.00 0.00 5.01
2148 2660 6.074142 GCTCAGAATTCACAAACCATCAAAAC 60.074 38.462 8.44 0.00 0.00 2.43
2169 2681 2.103432 TGGGTTTGTTAGTTCTCGCTCA 59.897 45.455 0.00 0.00 0.00 4.26
2507 3418 5.047872 TCAAGGGAATGTTGTGAATGATGTG 60.048 40.000 0.00 0.00 0.00 3.21
2521 3432 7.563906 AGATAGAAACTCTTCTCAAGGGAATG 58.436 38.462 0.00 0.00 41.19 2.67
2537 3448 6.128526 GGTGTAACAACAGCTGAGATAGAAAC 60.129 42.308 23.35 9.18 39.98 2.78
2611 3969 5.527214 TGAAACTGAACCATGTGTTAGTCAG 59.473 40.000 10.49 10.49 37.29 3.51
2649 4337 9.241317 CGTTAATTTATACGGACTCATTAGTGT 57.759 33.333 0.00 0.00 35.56 3.55
2692 4380 6.469782 AGCAATTATAGGTTCCATTTGTGG 57.530 37.500 0.00 0.00 0.00 4.17
2704 4392 9.442047 AAAGCTAGCACTATAAGCAATTATAGG 57.558 33.333 18.83 8.52 40.22 2.57
4003 5801 6.015918 TGCCTTCATTTTTGAGATCCCTTTA 58.984 36.000 0.00 0.00 0.00 1.85
5577 7436 4.098196 AGAACTAGAGACCCGAATAAGTGC 59.902 45.833 0.00 0.00 0.00 4.40
5594 7453 3.257375 TCACGCAAGAGCCTTTAGAACTA 59.743 43.478 0.00 0.00 43.62 2.24
5595 7454 2.037251 TCACGCAAGAGCCTTTAGAACT 59.963 45.455 0.00 0.00 43.62 3.01


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

AutoCloner maintained by Alex Coulton.