Multiple sequence alignment - TraesCS4B01G388700

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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 TraesCS4B01G388700 chr4B 100.000 3543 0 0 1 3543 665819341 665822883 0.000000e+00 6543.0
1 TraesCS4B01G388700 chr4B 93.243 74 5 0 10 83 42938226 42938153 3.740000e-20 110.0
2 TraesCS4B01G388700 chr4B 86.275 102 9 4 358 456 283253506 283253605 4.840000e-19 106.0
3 TraesCS4B01G388700 chr5A 97.202 3002 18 26 5 2962 705781311 705784290 0.000000e+00 5018.0
4 TraesCS4B01G388700 chr5A 99.219 512 4 0 3032 3543 705784404 705784915 0.000000e+00 924.0
5 TraesCS4B01G388700 chr5A 77.477 1403 247 55 1011 2367 529080997 529079618 0.000000e+00 776.0
6 TraesCS4B01G388700 chrUn 94.347 1946 66 12 845 2757 108385389 108383455 0.000000e+00 2944.0
7 TraesCS4B01G388700 chrUn 85.389 527 68 8 238 763 108385929 108385411 4.020000e-149 538.0
8 TraesCS4B01G388700 chrUn 83.133 249 32 6 522 762 312499448 312499694 5.960000e-53 219.0
9 TraesCS4B01G388700 chrUn 87.097 93 11 1 358 449 240280148 240280056 1.740000e-18 104.0
10 TraesCS4B01G388700 chr2D 79.091 1540 246 52 1013 2497 12550679 12552197 0.000000e+00 990.0
11 TraesCS4B01G388700 chr2D 73.861 417 77 22 3136 3539 134480053 134479656 1.720000e-28 137.0
12 TraesCS4B01G388700 chr2D 91.667 72 6 0 10 81 20689645 20689574 2.250000e-17 100.0
13 TraesCS4B01G388700 chr2B 77.345 1567 294 44 1010 2530 19075088 19073537 0.000000e+00 870.0
14 TraesCS4B01G388700 chr2B 80.583 927 155 19 1588 2497 18954882 18953964 0.000000e+00 691.0
15 TraesCS4B01G388700 chr2B 79.415 957 160 23 1585 2515 18922762 18923707 2.980000e-180 641.0
16 TraesCS4B01G388700 chr2B 81.010 495 83 6 1013 1497 18955479 18954986 2.000000e-102 383.0
17 TraesCS4B01G388700 chr2B 84.375 224 30 5 534 754 614246092 614246313 7.700000e-52 215.0
18 TraesCS4B01G388700 chr2B 92.647 68 5 0 10 77 717691274 717691341 8.090000e-17 99.0
19 TraesCS4B01G388700 chr2B 90.541 74 7 0 10 83 779174899 779174972 8.090000e-17 99.0
20 TraesCS4B01G388700 chr2A 80.838 955 154 19 1587 2519 13013837 13014784 0.000000e+00 723.0
21 TraesCS4B01G388700 chr2A 80.797 953 154 19 1585 2515 13004112 13003167 0.000000e+00 719.0
22 TraesCS4B01G388700 chr2A 80.683 937 151 20 1585 2497 12990990 12991920 0.000000e+00 701.0
23 TraesCS4B01G388700 chr2A 81.584 505 78 9 1006 1497 13004702 13004200 1.530000e-108 403.0
24 TraesCS4B01G388700 chr2A 80.404 495 86 6 1013 1497 12990414 12990907 2.010000e-97 366.0
25 TraesCS4B01G388700 chr5D 89.356 404 39 2 3138 3538 297051506 297051908 4.080000e-139 505.0
26 TraesCS4B01G388700 chr6A 75.371 674 137 24 1760 2417 592817754 592817094 7.440000e-77 298.0
27 TraesCS4B01G388700 chr6A 82.734 278 41 6 1012 1284 553913268 553912993 1.270000e-59 241.0
28 TraesCS4B01G388700 chr6A 83.505 194 22 7 2835 3027 60102148 60101964 4.700000e-39 172.0
29 TraesCS4B01G388700 chr6D 82.609 276 45 2 1012 1284 408157055 408156780 1.270000e-59 241.0
30 TraesCS4B01G388700 chr6B 81.754 285 49 2 1012 1293 612745121 612744837 5.910000e-58 235.0
31 TraesCS4B01G388700 chr7D 88.325 197 12 4 2835 3030 10466346 10466160 3.560000e-55 226.0
32 TraesCS4B01G388700 chr7D 82.661 248 37 3 521 762 600893513 600893760 7.700000e-52 215.0
33 TraesCS4B01G388700 chr7D 82.072 251 38 5 518 762 33204028 33204277 1.290000e-49 207.0
34 TraesCS4B01G388700 chr4D 83.401 247 34 5 523 763 120352147 120352392 4.600000e-54 222.0
35 TraesCS4B01G388700 chr4D 82.283 254 39 3 515 762 419245629 419245882 7.700000e-52 215.0
36 TraesCS4B01G388700 chr5B 81.496 254 41 2 515 762 430318792 430318539 1.670000e-48 204.0
37 TraesCS4B01G388700 chr3D 75.000 412 79 23 3140 3538 264591857 264592257 6.080000e-38 169.0
38 TraesCS4B01G388700 chr3D 85.859 99 13 1 359 456 400455402 400455500 1.740000e-18 104.0
39 TraesCS4B01G388700 chr4A 74.263 373 74 19 3139 3498 152611381 152611018 1.720000e-28 137.0
40 TraesCS4B01G388700 chr1B 86.000 100 13 1 358 456 281034861 281034762 4.840000e-19 106.0
41 TraesCS4B01G388700 chr1B 92.857 70 5 0 14 83 314731576 314731507 6.260000e-18 102.0
42 TraesCS4B01G388700 chr1B 92.647 68 5 0 14 81 17975813 17975746 8.090000e-17 99.0
43 TraesCS4B01G388700 chr1B 84.000 100 15 1 358 456 321029119 321029218 1.050000e-15 95.3
44 TraesCS4B01G388700 chr1B 84.000 100 15 1 358 456 321693376 321693277 1.050000e-15 95.3
45 TraesCS4B01G388700 chr3B 83.333 102 12 4 358 456 420655775 420655676 4.870000e-14 89.8
46 TraesCS4B01G388700 chr1D 90.625 64 6 0 10 73 438211137 438211200 6.300000e-13 86.1


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 TraesCS4B01G388700 chr4B 665819341 665822883 3542 False 6543.0 6543 100.0000 1 3543 1 chr4B.!!$F2 3542
1 TraesCS4B01G388700 chr5A 705781311 705784915 3604 False 2971.0 5018 98.2105 5 3543 2 chr5A.!!$F1 3538
2 TraesCS4B01G388700 chr5A 529079618 529080997 1379 True 776.0 776 77.4770 1011 2367 1 chr5A.!!$R1 1356
3 TraesCS4B01G388700 chrUn 108383455 108385929 2474 True 1741.0 2944 89.8680 238 2757 2 chrUn.!!$R2 2519
4 TraesCS4B01G388700 chr2D 12550679 12552197 1518 False 990.0 990 79.0910 1013 2497 1 chr2D.!!$F1 1484
5 TraesCS4B01G388700 chr2B 19073537 19075088 1551 True 870.0 870 77.3450 1010 2530 1 chr2B.!!$R1 1520
6 TraesCS4B01G388700 chr2B 18922762 18923707 945 False 641.0 641 79.4150 1585 2515 1 chr2B.!!$F1 930
7 TraesCS4B01G388700 chr2B 18953964 18955479 1515 True 537.0 691 80.7965 1013 2497 2 chr2B.!!$R2 1484
8 TraesCS4B01G388700 chr2A 13013837 13014784 947 False 723.0 723 80.8380 1587 2519 1 chr2A.!!$F1 932
9 TraesCS4B01G388700 chr2A 13003167 13004702 1535 True 561.0 719 81.1905 1006 2515 2 chr2A.!!$R1 1509
10 TraesCS4B01G388700 chr2A 12990414 12991920 1506 False 533.5 701 80.5435 1013 2497 2 chr2A.!!$F2 1484
11 TraesCS4B01G388700 chr6A 592817094 592817754 660 True 298.0 298 75.3710 1760 2417 1 chr6A.!!$R3 657

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
440 472 3.648339 AACTCGCGTGAGGTTAACTAA 57.352 42.857 28.30 0.00 39.90 2.24 F
820 852 6.491062 ACATCAAAGTCTGTCCATCAATTTGA 59.509 34.615 0.75 0.75 37.41 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1724 1827 2.031012 CTCCGAGTGGTGCAGCAA 59.969 61.111 22.04 3.29 36.3 3.91 R
2914 3056 7.161773 ACGCCTAACTAGTGTGTAAATTAGA 57.838 36.000 0.00 0.00 0.0 2.10 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
440 472 3.648339 AACTCGCGTGAGGTTAACTAA 57.352 42.857 28.30 0.00 39.90 2.24
820 852 6.491062 ACATCAAAGTCTGTCCATCAATTTGA 59.509 34.615 0.75 0.75 37.41 2.69
867 900 9.007901 AGAGTCTGTCTATCAATTTGAAAAAGG 57.992 33.333 2.68 0.00 31.71 3.11
1724 1827 1.000163 ACGACGTGATGCTCAACTTCT 60.000 47.619 0.00 0.00 0.00 2.85
2653 2792 4.457257 GCTTTCCTATGCCTGTAATCCATC 59.543 45.833 0.00 0.00 0.00 3.51
2913 3055 6.775234 TTAATAGGGAAGGAGGGGTTAATC 57.225 41.667 0.00 0.00 0.00 1.75
2914 3056 2.993604 AGGGAAGGAGGGGTTAATCT 57.006 50.000 0.00 0.00 0.00 2.40
2915 3057 2.777913 AGGGAAGGAGGGGTTAATCTC 58.222 52.381 0.00 0.00 0.00 2.75
2916 3058 2.322543 AGGGAAGGAGGGGTTAATCTCT 59.677 50.000 0.00 0.00 0.00 3.10
2917 3059 3.540687 AGGGAAGGAGGGGTTAATCTCTA 59.459 47.826 0.00 0.00 0.00 2.43
2918 3060 4.014593 AGGGAAGGAGGGGTTAATCTCTAA 60.015 45.833 0.00 0.00 0.00 2.10
2919 3061 4.914581 GGGAAGGAGGGGTTAATCTCTAAT 59.085 45.833 0.00 0.00 0.00 1.73
2920 3062 5.372959 GGGAAGGAGGGGTTAATCTCTAATT 59.627 44.000 0.00 0.00 0.00 1.40
2921 3063 6.126156 GGGAAGGAGGGGTTAATCTCTAATTT 60.126 42.308 0.00 0.00 0.00 1.82
2922 3064 7.073343 GGGAAGGAGGGGTTAATCTCTAATTTA 59.927 40.741 0.00 0.00 0.00 1.40
2923 3065 7.937942 GGAAGGAGGGGTTAATCTCTAATTTAC 59.062 40.741 0.00 0.00 0.00 2.01
2942 3084 8.606040 AATTTACACACTAGTTAGGCGTAAAA 57.394 30.769 0.00 2.67 33.36 1.52
2979 3121 8.862085 TCTTTAATGGTTGTAAAAGTTAAGGGG 58.138 33.333 0.00 0.00 32.15 4.79
2980 3122 7.541916 TTAATGGTTGTAAAAGTTAAGGGGG 57.458 36.000 0.00 0.00 0.00 5.40
3007 3149 3.758931 GCATTGCCCCCGTTGGTC 61.759 66.667 0.00 0.00 0.00 4.02
3008 3150 2.035626 CATTGCCCCCGTTGGTCT 59.964 61.111 0.00 0.00 0.00 3.85
3009 3151 1.301623 CATTGCCCCCGTTGGTCTA 59.698 57.895 0.00 0.00 0.00 2.59
3010 3152 0.106719 CATTGCCCCCGTTGGTCTAT 60.107 55.000 0.00 0.00 0.00 1.98
3011 3153 1.142060 CATTGCCCCCGTTGGTCTATA 59.858 52.381 0.00 0.00 0.00 1.31
3012 3154 0.542805 TTGCCCCCGTTGGTCTATAC 59.457 55.000 0.00 0.00 0.00 1.47
3013 3155 0.618107 TGCCCCCGTTGGTCTATACA 60.618 55.000 0.00 0.00 0.00 2.29
3014 3156 0.179065 GCCCCCGTTGGTCTATACAC 60.179 60.000 0.00 0.00 0.00 2.90
3015 3157 0.103572 CCCCCGTTGGTCTATACACG 59.896 60.000 0.00 0.00 0.00 4.49
3016 3158 1.105457 CCCCGTTGGTCTATACACGA 58.895 55.000 0.00 0.00 0.00 4.35
3017 3159 1.477700 CCCCGTTGGTCTATACACGAA 59.522 52.381 0.00 0.00 0.00 3.85
3018 3160 2.480759 CCCCGTTGGTCTATACACGAAG 60.481 54.545 0.00 0.00 0.00 3.79
3019 3161 2.190981 CCGTTGGTCTATACACGAAGC 58.809 52.381 0.00 0.00 0.00 3.86
3020 3162 2.159282 CCGTTGGTCTATACACGAAGCT 60.159 50.000 0.00 0.00 0.00 3.74
3021 3163 3.106672 CGTTGGTCTATACACGAAGCTC 58.893 50.000 0.00 0.00 0.00 4.09
3022 3164 3.445857 GTTGGTCTATACACGAAGCTCC 58.554 50.000 0.00 0.00 0.00 4.70
3023 3165 1.674441 TGGTCTATACACGAAGCTCCG 59.326 52.381 0.00 0.00 0.00 4.63
3024 3166 1.599916 GGTCTATACACGAAGCTCCGC 60.600 57.143 0.00 0.00 0.00 5.54
3025 3167 0.666913 TCTATACACGAAGCTCCGCC 59.333 55.000 0.00 0.00 0.00 6.13
3026 3168 0.384309 CTATACACGAAGCTCCGCCA 59.616 55.000 0.00 0.00 0.00 5.69
3027 3169 0.101759 TATACACGAAGCTCCGCCAC 59.898 55.000 0.00 0.00 0.00 5.01
3028 3170 1.605058 ATACACGAAGCTCCGCCACT 61.605 55.000 0.00 0.00 0.00 4.00
3029 3171 2.486636 TACACGAAGCTCCGCCACTG 62.487 60.000 0.00 0.00 0.00 3.66
3291 3477 8.504812 ACACTTTATTTTTGCAAAATCAACCT 57.495 26.923 24.39 8.63 0.00 3.50
3303 3489 6.017109 TGCAAAATCAACCTAGTTCAACTCTC 60.017 38.462 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.042684 AGGTGAGAGAAATCAAGAAGGCTT 59.957 41.667 0.00 0.00 33.74 4.35
2 3 3.938334 GAGGTGAGAGAAATCAAGAAGGC 59.062 47.826 0.00 0.00 0.00 4.35
6 7 3.261897 GGTGGAGGTGAGAGAAATCAAGA 59.738 47.826 0.00 0.00 0.00 3.02
7 8 3.262915 AGGTGGAGGTGAGAGAAATCAAG 59.737 47.826 0.00 0.00 0.00 3.02
8 9 3.251484 AGGTGGAGGTGAGAGAAATCAA 58.749 45.455 0.00 0.00 0.00 2.57
655 687 7.102847 ACAACCCCAAACATATAAAATACGG 57.897 36.000 0.00 0.00 0.00 4.02
941 979 9.878737 GAGGACCCCTTACTGCTTATATATATA 57.121 37.037 0.00 0.00 31.76 0.86
942 980 8.352181 TGAGGACCCCTTACTGCTTATATATAT 58.648 37.037 0.00 0.00 31.76 0.86
943 981 7.715482 TGAGGACCCCTTACTGCTTATATATA 58.285 38.462 0.00 0.00 31.76 0.86
945 983 5.972698 TGAGGACCCCTTACTGCTTATATA 58.027 41.667 0.00 0.00 31.76 0.86
946 984 4.827789 TGAGGACCCCTTACTGCTTATAT 58.172 43.478 0.00 0.00 31.76 0.86
947 985 4.274794 TGAGGACCCCTTACTGCTTATA 57.725 45.455 0.00 0.00 31.76 0.98
948 986 3.130734 TGAGGACCCCTTACTGCTTAT 57.869 47.619 0.00 0.00 31.76 1.73
995 1033 4.670765 AGGCTTCTTCATCTCCATGTTTT 58.329 39.130 0.00 0.00 0.00 2.43
996 1034 4.263639 TGAGGCTTCTTCATCTCCATGTTT 60.264 41.667 0.00 0.00 0.00 2.83
1724 1827 2.031012 CTCCGAGTGGTGCAGCAA 59.969 61.111 22.04 3.29 36.30 3.91
2913 3055 7.256286 ACGCCTAACTAGTGTGTAAATTAGAG 58.744 38.462 0.00 0.00 0.00 2.43
2914 3056 7.161773 ACGCCTAACTAGTGTGTAAATTAGA 57.838 36.000 0.00 0.00 0.00 2.10
2915 3057 8.915871 TTACGCCTAACTAGTGTGTAAATTAG 57.084 34.615 12.80 2.33 0.00 1.73
2916 3058 9.703892 TTTTACGCCTAACTAGTGTGTAAATTA 57.296 29.630 21.59 11.68 32.38 1.40
2917 3059 8.606040 TTTTACGCCTAACTAGTGTGTAAATT 57.394 30.769 21.59 0.00 32.38 1.82
2918 3060 8.782339 ATTTTACGCCTAACTAGTGTGTAAAT 57.218 30.769 21.59 13.72 32.38 1.40
2919 3061 9.703892 TTATTTTACGCCTAACTAGTGTGTAAA 57.296 29.630 19.02 19.02 0.00 2.01
2920 3062 9.703892 TTTATTTTACGCCTAACTAGTGTGTAA 57.296 29.630 11.68 11.68 0.00 2.41
2921 3063 9.357652 CTTTATTTTACGCCTAACTAGTGTGTA 57.642 33.333 0.00 0.00 0.00 2.90
2922 3064 7.148523 GCTTTATTTTACGCCTAACTAGTGTGT 60.149 37.037 0.00 0.00 0.00 3.72
2923 3065 7.148540 TGCTTTATTTTACGCCTAACTAGTGTG 60.149 37.037 0.00 0.00 0.00 3.82
2996 3138 0.103572 CGTGTATAGACCAACGGGGG 59.896 60.000 0.26 0.00 42.91 5.40
2997 3139 1.105457 TCGTGTATAGACCAACGGGG 58.895 55.000 1.23 0.00 44.81 5.73
2998 3140 2.805845 CTTCGTGTATAGACCAACGGG 58.194 52.381 1.23 0.00 36.70 5.28
2999 3141 2.159282 AGCTTCGTGTATAGACCAACGG 60.159 50.000 1.23 0.00 36.70 4.44
3000 3142 3.106672 GAGCTTCGTGTATAGACCAACG 58.893 50.000 0.00 0.00 37.38 4.10
3001 3143 3.445857 GGAGCTTCGTGTATAGACCAAC 58.554 50.000 0.00 0.00 0.00 3.77
3002 3144 2.098607 CGGAGCTTCGTGTATAGACCAA 59.901 50.000 6.14 0.00 0.00 3.67
3003 3145 1.674441 CGGAGCTTCGTGTATAGACCA 59.326 52.381 6.14 0.00 0.00 4.02
3004 3146 2.402640 CGGAGCTTCGTGTATAGACC 57.597 55.000 6.14 0.00 0.00 3.85
3140 3326 4.209703 TCGTTTGTTTCACAGGATACGTTC 59.790 41.667 0.00 0.00 46.39 3.95
3291 3477 0.879090 TCGCAGCGAGAGTTGAACTA 59.121 50.000 15.11 0.00 46.01 2.24
3303 3489 1.004610 CACTGTATGGAAATCGCAGCG 60.005 52.381 9.06 9.06 0.00 5.18
3411 3597 1.203812 GGCGCATTTGCAAAAACGG 59.796 52.632 27.74 15.56 42.21 4.44


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

AutoCloner maintained by Alex Coulton.