Multiple sequence alignment - TraesCS5B01G338400

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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 TraesCS5B01G338400 chr5B 100.000 3067 0 0 504 3570 522407942 522411008 0.000000e+00 5664.0
1 TraesCS5B01G338400 chr5B 93.954 2944 118 21 504 3414 522862152 522859236 0.000000e+00 4396.0
2 TraesCS5B01G338400 chr5B 100.000 198 0 0 1 198 522407439 522407636 2.030000e-97 366.0
3 TraesCS5B01G338400 chr5B 95.175 228 9 2 510 737 522931485 522931260 3.390000e-95 359.0
4 TraesCS5B01G338400 chr5B 92.195 205 15 1 2532 2736 521276716 521276513 4.510000e-74 289.0
5 TraesCS5B01G338400 chr5B 89.565 115 12 0 2 116 55544154 55544040 2.870000e-31 147.0
6 TraesCS5B01G338400 chr5B 92.647 68 5 0 1 68 94148206 94148273 8.160000e-17 99.0
7 TraesCS5B01G338400 chr5A 95.342 2941 97 17 504 3416 546771206 546768278 0.000000e+00 4636.0
8 TraesCS5B01G338400 chr5A 96.970 198 6 0 1 198 546771432 546771235 2.050000e-87 333.0
9 TraesCS5B01G338400 chr5A 95.122 123 6 0 3448 3570 546767572 546767450 1.010000e-45 195.0
10 TraesCS5B01G338400 chr5D 94.040 2936 120 20 504 3414 513307652 513310557 0.000000e+00 4401.0
11 TraesCS5B01G338400 chr5D 93.759 2868 126 20 571 3414 431780586 431783424 0.000000e+00 4255.0
12 TraesCS5B01G338400 chr5D 92.830 2929 133 25 511 3414 433685235 433682359 0.000000e+00 4174.0
13 TraesCS5B01G338400 chr5D 91.870 123 10 0 3448 3570 431783719 431783841 4.740000e-39 172.0
14 TraesCS5B01G338400 chr5D 91.870 123 6 2 3448 3570 513310992 513311110 6.130000e-38 169.0
15 TraesCS5B01G338400 chr5D 91.057 123 11 0 3448 3570 433682058 433681936 2.200000e-37 167.0
16 TraesCS5B01G338400 chr5D 88.889 126 11 3 4 127 52394027 52393903 6.170000e-33 152.0
17 TraesCS5B01G338400 chr5D 77.003 287 45 14 2757 3036 431790660 431790932 1.030000e-30 145.0
18 TraesCS5B01G338400 chr5D 77.113 284 44 14 2760 3036 431792667 431792936 1.030000e-30 145.0
19 TraesCS5B01G338400 chr5D 77.113 284 44 14 2760 3036 431796042 431796311 1.030000e-30 145.0
20 TraesCS5B01G338400 chr5D 77.113 284 44 14 2760 3036 431801423 431801692 1.030000e-30 145.0
21 TraesCS5B01G338400 chr5D 76.761 284 45 14 2760 3036 431799418 431799687 4.810000e-29 139.0
22 TraesCS5B01G338400 chr2A 83.441 1697 165 51 1030 2678 27956706 27958334 0.000000e+00 1471.0
23 TraesCS5B01G338400 chr2A 84.901 1318 136 33 1319 2592 27952723 27954021 0.000000e+00 1273.0
24 TraesCS5B01G338400 chr2A 84.500 1129 119 37 1030 2122 27963001 27964109 0.000000e+00 1064.0
25 TraesCS5B01G338400 chr2A 77.519 129 24 4 1 127 42941225 42941350 4.940000e-09 73.1
26 TraesCS5B01G338400 chr2A 89.091 55 1 1 913 967 27952322 27952371 2.980000e-06 63.9
27 TraesCS5B01G338400 chr2D 83.960 1409 147 40 1376 2738 25339354 25340729 0.000000e+00 1277.0
28 TraesCS5B01G338400 chr2D 85.231 1124 110 36 1030 2118 25347630 25348732 0.000000e+00 1105.0
29 TraesCS5B01G338400 chr2D 83.275 568 62 16 2191 2735 25348727 25349284 3.200000e-135 492.0
30 TraesCS5B01G338400 chr2D 90.323 217 9 5 1030 1238 25339017 25339229 1.260000e-69 274.0
31 TraesCS5B01G338400 chr2D 81.364 220 23 13 590 805 25338448 25338653 2.850000e-36 163.0
32 TraesCS5B01G338400 chr2D 85.938 128 15 2 1 128 596567632 596567756 2.240000e-27 134.0
33 TraesCS5B01G338400 chr2D 97.297 37 1 0 931 967 25338888 25338924 2.980000e-06 63.9
34 TraesCS5B01G338400 chr2B 84.796 1322 134 33 1319 2591 41132976 41134279 0.000000e+00 1266.0
35 TraesCS5B01G338400 chr2B 82.847 548 58 19 2191 2715 41142041 41142575 3.250000e-125 459.0
36 TraesCS5B01G338400 chr2B 86.099 223 27 4 1030 1250 41141186 41141406 1.660000e-58 237.0
37 TraesCS5B01G338400 chr2B 84.158 202 17 4 596 796 41140622 41140809 7.870000e-42 182.0
38 TraesCS5B01G338400 chr2B 82.840 169 19 8 629 797 41132173 41132331 3.720000e-30 143.0
39 TraesCS5B01G338400 chr2B 83.810 105 10 7 25 125 464027381 464027280 3.790000e-15 93.5
40 TraesCS5B01G338400 chr2B 90.566 53 0 2 915 967 41141059 41141106 8.270000e-07 65.8
41 TraesCS5B01G338400 chr2B 89.091 55 1 1 913 967 41132574 41132623 2.980000e-06 63.9
42 TraesCS5B01G338400 chr7B 85.424 295 31 10 3122 3412 2938615 2938329 2.690000e-76 296.0
43 TraesCS5B01G338400 chr7A 85.324 293 35 6 3122 3412 64715281 64714995 2.690000e-76 296.0
44 TraesCS5B01G338400 chr7A 93.023 43 2 1 10 51 649128000 649127958 1.070000e-05 62.1
45 TraesCS5B01G338400 chr7D 85.560 277 33 5 3122 3396 60435883 60435612 2.100000e-72 283.0
46 TraesCS5B01G338400 chr7D 87.879 66 3 4 56 118 462279332 462279395 4.940000e-09 73.1
47 TraesCS5B01G338400 chr1D 84.158 101 13 3 29 127 478341698 478341599 1.060000e-15 95.3
48 TraesCS5B01G338400 chr1A 84.615 78 8 3 51 127 437592600 437592526 1.370000e-09 75.0


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 TraesCS5B01G338400 chr5B 522407439 522411008 3569 False 3015.000000 5664 100.000000 1 3570 2 chr5B.!!$F2 3569
1 TraesCS5B01G338400 chr5B 522859236 522862152 2916 True 4396.000000 4396 93.954000 504 3414 1 chr5B.!!$R3 2910
2 TraesCS5B01G338400 chr5A 546767450 546771432 3982 True 1721.333333 4636 95.811333 1 3570 3 chr5A.!!$R1 3569
3 TraesCS5B01G338400 chr5D 513307652 513311110 3458 False 2285.000000 4401 92.955000 504 3570 2 chr5D.!!$F3 3066
4 TraesCS5B01G338400 chr5D 431780586 431783841 3255 False 2213.500000 4255 92.814500 571 3570 2 chr5D.!!$F1 2999
5 TraesCS5B01G338400 chr5D 433681936 433685235 3299 True 2170.500000 4174 91.943500 511 3570 2 chr5D.!!$R2 3059
6 TraesCS5B01G338400 chr2A 27963001 27964109 1108 False 1064.000000 1064 84.500000 1030 2122 1 chr2A.!!$F1 1092
7 TraesCS5B01G338400 chr2A 27952322 27958334 6012 False 935.966667 1471 85.811000 913 2678 3 chr2A.!!$F3 1765
8 TraesCS5B01G338400 chr2D 25347630 25349284 1654 False 798.500000 1105 84.253000 1030 2735 2 chr2D.!!$F3 1705
9 TraesCS5B01G338400 chr2D 25338448 25340729 2281 False 444.475000 1277 88.236000 590 2738 4 chr2D.!!$F2 2148
10 TraesCS5B01G338400 chr2B 41132173 41134279 2106 False 490.966667 1266 85.575667 629 2591 3 chr2B.!!$F1 1962
11 TraesCS5B01G338400 chr2B 41140622 41142575 1953 False 235.950000 459 85.917500 596 2715 4 chr2B.!!$F2 2119

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
99 100 0.529337 ATCGCTTGATGCAGAGGTCG 60.529 55.000 0.0 0.0 43.06 4.79 F
885 991 2.430610 GGCCTCATCCAGTCGCTCT 61.431 63.158 0.0 0.0 0.00 4.09 F
2089 2385 1.147824 CTCCTCCCGCTCATTGCAT 59.852 57.895 0.0 0.0 43.06 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1371 1615 0.742281 CAGTGAACGGATGAGCCCAG 60.742 60.0 0.00 0.00 0.00 4.45 R
2314 2634 1.262640 TGATCTGCTGCTCAGGCTGA 61.263 55.0 17.68 17.68 43.06 4.26 R
3426 5204 0.261696 AACTGACCCCAAGGCAAACT 59.738 50.0 0.00 0.00 36.11 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
52 53 9.341899 GATGTATTACTTTGTAAGGCTTTGTTG 57.658 33.333 4.45 0.00 0.00 3.33
99 100 0.529337 ATCGCTTGATGCAGAGGTCG 60.529 55.000 0.00 0.00 43.06 4.79
158 159 4.397420 ACCATTAGCACTCACATGAAACA 58.603 39.130 0.00 0.00 0.00 2.83
180 181 7.365840 ACAGAGAATTTTCGTTTCAGGTATC 57.634 36.000 0.00 0.00 0.00 2.24
181 182 6.934645 ACAGAGAATTTTCGTTTCAGGTATCA 59.065 34.615 0.00 0.00 0.00 2.15
545 546 5.098211 GGTGCTCAATAAAGAGTTGCATTC 58.902 41.667 0.00 0.00 37.94 2.67
625 626 5.891551 TGGGGAGGCTAATAAAAGATGAAAC 59.108 40.000 0.00 0.00 0.00 2.78
626 627 5.891551 GGGGAGGCTAATAAAAGATGAAACA 59.108 40.000 0.00 0.00 0.00 2.83
627 628 6.039829 GGGGAGGCTAATAAAAGATGAAACAG 59.960 42.308 0.00 0.00 0.00 3.16
885 991 2.430610 GGCCTCATCCAGTCGCTCT 61.431 63.158 0.00 0.00 0.00 4.09
980 1171 3.319137 TTCACTACTGCACAAGCTAGG 57.681 47.619 0.00 0.00 42.74 3.02
1304 1533 6.712276 AGATTGTACTAGTTTCTTCCAAGGG 58.288 40.000 0.00 0.00 0.00 3.95
1734 1987 2.165998 GCAGCAAGAGGGATCAAAACT 58.834 47.619 0.00 0.00 0.00 2.66
1797 2053 1.630369 CCATCACTTCCCAAGAGACCA 59.370 52.381 0.00 0.00 30.95 4.02
1803 2059 2.840651 ACTTCCCAAGAGACCAATCGAT 59.159 45.455 0.00 0.00 0.00 3.59
1841 2102 7.484641 GCTCAACGTAAGCATTTCAATTCATAA 59.515 33.333 15.78 0.00 45.62 1.90
1875 2141 9.787532 TTACAGAGCTAAATTCAAATGTTATGC 57.212 29.630 0.00 0.00 0.00 3.14
1990 2259 1.968540 GCTGTCTCACACTTGGGGC 60.969 63.158 0.00 0.00 0.00 5.80
2029 2325 4.527816 ACAACTGAGCAAGATCTCTTCTCT 59.472 41.667 15.43 6.17 34.36 3.10
2089 2385 1.147824 CTCCTCCCGCTCATTGCAT 59.852 57.895 0.00 0.00 43.06 3.96
2314 2634 2.035066 GCTCTTCAACATGCAGTTTGGT 59.965 45.455 9.56 0.00 38.74 3.67
2463 2795 0.035915 GAGGCTCCAGGGAAACTCAC 60.036 60.000 2.15 0.00 31.47 3.51
2464 2796 0.474660 AGGCTCCAGGGAAACTCACT 60.475 55.000 0.00 0.00 0.00 3.41
2642 2978 6.690194 AGCATTTCTGTTAGCAAAGATAGG 57.310 37.500 0.00 0.00 0.00 2.57
2842 3199 4.927267 AGAAGTTACAACATGGATGGGA 57.073 40.909 0.00 0.00 0.00 4.37
2937 3815 6.808008 TCCTGTTTCTGAATTCATGTCTTC 57.192 37.500 8.96 0.00 0.00 2.87
2956 3855 6.370442 TGTCTTCATTACCCTTATCAAACACG 59.630 38.462 0.00 0.00 0.00 4.49
2958 3857 7.280205 GTCTTCATTACCCTTATCAAACACGAT 59.720 37.037 0.00 0.00 0.00 3.73
2972 3871 7.795482 TCAAACACGATCTCTTTCCTTTAAA 57.205 32.000 0.00 0.00 0.00 1.52
2979 3878 5.163754 CGATCTCTTTCCTTTAAACCGCAAT 60.164 40.000 0.00 0.00 0.00 3.56
2996 3895 7.875327 ACCGCAATTACCAACTAAGAATATT 57.125 32.000 0.00 0.00 0.00 1.28
3008 3915 7.255104 CCAACTAAGAATATTCGCAGCCAATAA 60.255 37.037 9.78 0.00 0.00 1.40
3263 4174 5.574188 AGCAAAGGTCTTGGATTCATAAGT 58.426 37.500 0.00 0.00 0.00 2.24
3346 4664 8.370940 AGAACATCTCAGTAAGATTCAGAACAA 58.629 33.333 0.00 0.00 42.30 2.83
3347 4665 9.160496 GAACATCTCAGTAAGATTCAGAACAAT 57.840 33.333 0.00 0.00 42.30 2.71
3424 5202 6.542852 CCATAAGTGGCATATACGTATTTGC 58.457 40.000 31.02 31.02 39.01 3.68
3433 5211 3.775661 ATACGTATTTGCCAGTTTGCC 57.224 42.857 1.14 0.00 0.00 4.52
3436 5214 2.288152 ACGTATTTGCCAGTTTGCCTTG 60.288 45.455 0.00 0.00 0.00 3.61
3545 7866 1.383803 CTCCCTCCCCTTCCTCCTG 60.384 68.421 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 8.905702 CACGCAGCCATTCTTTATTAATTATTC 58.094 33.333 0.00 0.00 0.00 1.75
99 100 1.841919 TCGAAAAGGAGGATAACCCCC 59.158 52.381 0.00 0.00 36.73 5.40
158 159 7.979444 TTGATACCTGAAACGAAAATTCTCT 57.021 32.000 0.00 0.00 0.00 3.10
545 546 3.001939 GGCAATAACCGACCGAAACTATG 59.998 47.826 0.00 0.00 0.00 2.23
633 641 8.739972 ACACTTGCCTTATAGATTTACTTTTGG 58.260 33.333 0.00 0.00 0.00 3.28
885 991 7.769507 CCGAGAGATGTACTTATATGCTACCTA 59.230 40.741 0.00 0.00 0.00 3.08
980 1171 7.970614 CCTCCATTGTAAGTAATCTCAAAAAGC 59.029 37.037 0.00 0.00 0.00 3.51
985 1176 5.045213 TGCCCTCCATTGTAAGTAATCTCAA 60.045 40.000 0.00 0.00 0.00 3.02
1293 1522 1.080498 TCCTAGCTCCCCTTGGAAGAA 59.920 52.381 0.00 0.00 41.56 2.52
1304 1533 3.580458 TCAGCATCCTAATTCCTAGCTCC 59.420 47.826 0.00 0.00 0.00 4.70
1364 1595 1.051812 CGGATGAGCCCAGGACTTAT 58.948 55.000 0.00 0.00 0.00 1.73
1371 1615 0.742281 CAGTGAACGGATGAGCCCAG 60.742 60.000 0.00 0.00 0.00 4.45
1734 1987 3.054948 TGAACTCATGCATCATCCAGTCA 60.055 43.478 0.00 0.00 0.00 3.41
1797 2053 3.069586 TGAGCGGGATGTTCTTATCGATT 59.930 43.478 1.71 0.00 0.00 3.34
1803 2059 1.274167 ACGTTGAGCGGGATGTTCTTA 59.726 47.619 0.00 0.00 46.52 2.10
1875 2141 7.716612 ACAGAAAAGTGACCTTAAGAATTTGG 58.283 34.615 3.36 0.00 0.00 3.28
2314 2634 1.262640 TGATCTGCTGCTCAGGCTGA 61.263 55.000 17.68 17.68 43.06 4.26
2457 2789 5.648092 CCTAAATCGAATGGGAAAGTGAGTT 59.352 40.000 0.00 0.00 0.00 3.01
2463 2795 4.199310 TGCTCCTAAATCGAATGGGAAAG 58.801 43.478 7.84 0.28 0.00 2.62
2464 2796 4.080582 TCTGCTCCTAAATCGAATGGGAAA 60.081 41.667 7.84 0.49 0.00 3.13
2515 2847 2.690497 GCTAAGAAAGGATTCCCAAGGC 59.310 50.000 0.00 0.00 36.12 4.35
2642 2978 3.240069 CTGAACAAACAATAGCTGCTGC 58.760 45.455 13.43 7.62 40.05 5.25
2826 3183 3.737559 AGCTTCCCATCCATGTTGTAA 57.262 42.857 0.00 0.00 0.00 2.41
2828 3185 2.225091 TGAAGCTTCCCATCCATGTTGT 60.225 45.455 23.42 0.00 0.00 3.32
2829 3186 2.165030 GTGAAGCTTCCCATCCATGTTG 59.835 50.000 23.42 0.00 0.00 3.33
2830 3187 2.225091 TGTGAAGCTTCCCATCCATGTT 60.225 45.455 23.42 0.00 0.00 2.71
2832 3189 2.133281 TGTGAAGCTTCCCATCCATG 57.867 50.000 23.42 0.00 0.00 3.66
2833 3190 2.827921 GTTTGTGAAGCTTCCCATCCAT 59.172 45.455 23.42 0.00 0.00 3.41
2834 3191 2.158475 AGTTTGTGAAGCTTCCCATCCA 60.158 45.455 23.42 9.43 0.00 3.41
2835 3192 2.519013 AGTTTGTGAAGCTTCCCATCC 58.481 47.619 23.42 11.35 0.00 3.51
2836 3193 3.858503 GCAAGTTTGTGAAGCTTCCCATC 60.859 47.826 23.42 13.71 0.00 3.51
2842 3199 3.132646 TCCATTGCAAGTTTGTGAAGCTT 59.867 39.130 4.94 0.00 0.00 3.74
2923 3801 9.342308 GATAAGGGTAATGAAGACATGAATTCA 57.658 33.333 11.26 11.26 39.59 2.57
2924 3802 9.342308 TGATAAGGGTAATGAAGACATGAATTC 57.658 33.333 0.00 0.00 36.79 2.17
2937 3815 6.986817 AGAGATCGTGTTTGATAAGGGTAATG 59.013 38.462 0.00 0.00 0.00 1.90
2956 3855 5.622770 TTGCGGTTTAAAGGAAAGAGATC 57.377 39.130 0.00 0.00 0.00 2.75
2958 3857 6.072342 GGTAATTGCGGTTTAAAGGAAAGAGA 60.072 38.462 0.00 0.00 0.00 3.10
2972 3871 7.254658 CGAATATTCTTAGTTGGTAATTGCGGT 60.255 37.037 13.45 0.00 0.00 5.68
2979 3878 5.526111 GGCTGCGAATATTCTTAGTTGGTAA 59.474 40.000 13.45 0.00 0.00 2.85
3008 3915 4.734398 TTTTCTGCTTTGTGTGACCATT 57.266 36.364 0.00 0.00 0.00 3.16
3074 3981 5.009911 TCCATCTTTCATTGCATTTATCGGG 59.990 40.000 0.00 0.00 0.00 5.14
3219 4130 6.999950 TGCTATTGAAGTTCAGGTACTACAA 58.000 36.000 5.56 0.00 36.02 2.41
3263 4174 2.151202 GGCTTGCTGTAGCTGTTGTTA 58.849 47.619 5.38 0.00 40.99 2.41
3346 4664 4.669206 TGTCAGAATTTGGTGTGCAAAT 57.331 36.364 0.00 0.00 34.11 2.32
3347 4665 4.669206 ATGTCAGAATTTGGTGTGCAAA 57.331 36.364 0.00 0.00 0.00 3.68
3416 5194 2.327568 CAAGGCAAACTGGCAAATACG 58.672 47.619 2.87 0.00 46.46 3.06
3418 5196 1.622811 CCCAAGGCAAACTGGCAAATA 59.377 47.619 2.87 0.00 46.46 1.40
3420 5198 1.694133 CCCCAAGGCAAACTGGCAAA 61.694 55.000 2.87 0.00 46.46 3.68
3421 5199 2.139484 CCCCAAGGCAAACTGGCAA 61.139 57.895 2.87 0.00 46.46 4.52
3424 5202 1.152567 TGACCCCAAGGCAAACTGG 60.153 57.895 0.00 0.00 36.11 4.00
3425 5203 0.468029 ACTGACCCCAAGGCAAACTG 60.468 55.000 0.00 0.00 36.11 3.16
3426 5204 0.261696 AACTGACCCCAAGGCAAACT 59.738 50.000 0.00 0.00 36.11 2.66
3427 5205 1.119684 AAACTGACCCCAAGGCAAAC 58.880 50.000 0.00 0.00 36.11 2.93
3433 5211 1.463553 GGCCACAAACTGACCCCAAG 61.464 60.000 0.00 0.00 0.00 3.61
3436 5214 2.197324 TGGCCACAAACTGACCCC 59.803 61.111 0.00 0.00 0.00 4.95
3525 7846 2.788589 GAGGAAGGGGAGGGAGGT 59.211 66.667 0.00 0.00 0.00 3.85
3537 7858 1.403814 CGACCAGATAGCAGGAGGAA 58.596 55.000 0.00 0.00 0.00 3.36
3545 7866 3.850095 GAGCCGGCGACCAGATAGC 62.850 68.421 23.20 0.00 0.00 2.97


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

AutoCloner maintained by Alex Coulton.