Multiple sequence alignment - TraesCS7B01G316300

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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 TraesCS7B01G316300 chr7B 100.000 2753 0 0 1 2753 565744424 565741672 0.000000e+00 5084
1 TraesCS7B01G316300 chr7B 98.141 1775 30 1 85 1856 565789421 565787647 0.000000e+00 3092
2 TraesCS7B01G316300 chr7B 98.331 899 15 0 1855 2753 565787496 565786598 0.000000e+00 1578
3 TraesCS7B01G316300 chr4D 92.030 1606 75 20 981 2555 133609540 133611123 0.000000e+00 2207
4 TraesCS7B01G316300 chr4D 94.366 284 16 0 699 982 133609223 133609506 1.170000e-118 436
5 TraesCS7B01G316300 chr4D 81.122 392 61 13 175 560 12500939 12500555 4.460000e-78 302
6 TraesCS7B01G316300 chr4D 87.264 212 13 6 2545 2753 133611145 133611345 2.130000e-56 230
7 TraesCS7B01G316300 chr4A 90.671 1222 65 17 981 2187 427883950 427882763 0.000000e+00 1580
8 TraesCS7B01G316300 chr4A 91.477 352 16 4 638 982 427884328 427883984 3.210000e-129 472
9 TraesCS7B01G316300 chr4A 97.753 89 2 0 1 89 688917134 688917046 1.320000e-33 154
10 TraesCS7B01G316300 chr4A 96.739 92 2 1 1 91 195630230 195630321 4.750000e-33 152
11 TraesCS7B01G316300 chr4A 93.939 99 5 1 1 98 672583904 672584002 6.140000e-32 148
12 TraesCS7B01G316300 chr4A 93.069 101 5 2 1 101 566405074 566404976 2.210000e-31 147
13 TraesCS7B01G316300 chr5D 80.055 366 51 15 229 588 271459922 271460271 4.550000e-63 252
14 TraesCS7B01G316300 chr6B 97.753 89 2 0 1 89 441513513 441513601 1.320000e-33 154
15 TraesCS7B01G316300 chr2B 96.703 91 3 0 1 91 123459601 123459691 4.750000e-33 152
16 TraesCS7B01G316300 chr5B 93.939 99 4 2 1 97 37896317 37896219 6.140000e-32 148
17 TraesCS7B01G316300 chr1D 94.792 96 4 1 1 96 52108334 52108428 6.140000e-32 148
18 TraesCS7B01G316300 chr2A 92.308 104 4 3 1 102 435604624 435604523 7.950000e-31 145


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 TraesCS7B01G316300 chr7B 565741672 565744424 2752 True 5084.000000 5084 100.000 1 2753 1 chr7B.!!$R1 2752
1 TraesCS7B01G316300 chr7B 565786598 565789421 2823 True 2335.000000 3092 98.236 85 2753 2 chr7B.!!$R2 2668
2 TraesCS7B01G316300 chr4D 133609223 133611345 2122 False 957.666667 2207 91.220 699 2753 3 chr4D.!!$F1 2054
3 TraesCS7B01G316300 chr4A 427882763 427884328 1565 True 1026.000000 1580 91.074 638 2187 2 chr4A.!!$R3 1549

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
144 145 0.396435 TGTGCCCTAGGACACAAGTG 59.604 55.0 26.68 0.58 43.48 3.16 F
256 257 0.953471 CTTTCGATTGCACCCCACGA 60.953 55.0 0.00 0.00 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1270 1323 0.822532 CACCGGTAGAGGTATCCGCT 60.823 60.000 6.87 0.0 43.89 5.52 R
2207 2429 1.683365 GCATGTGAAGGGGGCATGT 60.683 57.895 0.00 0.0 41.27 3.21 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
23 24 6.566079 TTGGTCTGAAATGGTCATAGATCT 57.434 37.500 0.00 0.00 35.07 2.75
24 25 7.675161 TTGGTCTGAAATGGTCATAGATCTA 57.325 36.000 4.57 4.57 35.07 1.98
25 26 7.862274 TGGTCTGAAATGGTCATAGATCTAT 57.138 36.000 9.57 9.57 35.07 1.98
26 27 7.674120 TGGTCTGAAATGGTCATAGATCTATG 58.326 38.462 29.54 29.54 43.16 2.23
27 28 7.510343 TGGTCTGAAATGGTCATAGATCTATGA 59.490 37.037 32.49 32.49 46.81 2.15
41 42 9.650539 CATAGATCTATGACCAATTCTTACAGG 57.349 37.037 31.04 4.05 44.22 4.00
42 43 7.072263 AGATCTATGACCAATTCTTACAGGG 57.928 40.000 0.00 0.00 0.00 4.45
43 44 6.617371 AGATCTATGACCAATTCTTACAGGGT 59.383 38.462 0.00 0.00 33.78 4.34
44 45 6.235231 TCTATGACCAATTCTTACAGGGTC 57.765 41.667 0.00 0.00 46.40 4.46
47 48 4.287766 GACCAATTCTTACAGGGTCACT 57.712 45.455 0.00 0.00 45.70 3.41
48 49 4.652822 GACCAATTCTTACAGGGTCACTT 58.347 43.478 0.00 0.00 45.70 3.16
49 50 5.801380 GACCAATTCTTACAGGGTCACTTA 58.199 41.667 0.00 0.00 45.70 2.24
50 51 5.557866 ACCAATTCTTACAGGGTCACTTAC 58.442 41.667 0.00 0.00 0.00 2.34
51 52 5.072600 ACCAATTCTTACAGGGTCACTTACA 59.927 40.000 0.00 0.00 0.00 2.41
52 53 5.643777 CCAATTCTTACAGGGTCACTTACAG 59.356 44.000 0.00 0.00 0.00 2.74
53 54 6.464222 CAATTCTTACAGGGTCACTTACAGA 58.536 40.000 0.00 0.00 0.00 3.41
54 55 6.681729 ATTCTTACAGGGTCACTTACAGAA 57.318 37.500 0.00 0.00 0.00 3.02
55 56 5.723672 TCTTACAGGGTCACTTACAGAAG 57.276 43.478 0.00 0.00 38.76 2.85
56 57 4.527038 TCTTACAGGGTCACTTACAGAAGG 59.473 45.833 0.00 0.00 36.95 3.46
57 58 2.690840 ACAGGGTCACTTACAGAAGGT 58.309 47.619 0.00 0.00 36.95 3.50
58 59 2.633481 ACAGGGTCACTTACAGAAGGTC 59.367 50.000 0.00 0.00 36.95 3.85
59 60 2.632996 CAGGGTCACTTACAGAAGGTCA 59.367 50.000 0.00 0.00 36.95 4.02
60 61 2.633481 AGGGTCACTTACAGAAGGTCAC 59.367 50.000 0.00 0.00 36.95 3.67
61 62 2.633481 GGGTCACTTACAGAAGGTCACT 59.367 50.000 0.00 0.00 36.95 3.41
62 63 3.830755 GGGTCACTTACAGAAGGTCACTA 59.169 47.826 0.00 0.00 36.95 2.74
63 64 4.082136 GGGTCACTTACAGAAGGTCACTAG 60.082 50.000 0.00 0.00 36.95 2.57
64 65 4.523558 GGTCACTTACAGAAGGTCACTAGT 59.476 45.833 0.00 0.00 36.95 2.57
65 66 5.010820 GGTCACTTACAGAAGGTCACTAGTT 59.989 44.000 0.00 0.00 36.95 2.24
66 67 5.921408 GTCACTTACAGAAGGTCACTAGTTG 59.079 44.000 0.00 0.00 36.95 3.16
67 68 5.831525 TCACTTACAGAAGGTCACTAGTTGA 59.168 40.000 0.00 0.00 36.95 3.18
83 84 9.639601 TCACTAGTTGACATATTTCTTGTAGTG 57.360 33.333 13.42 13.42 33.23 2.74
96 97 0.533978 TGTAGTGCATGCGTTGTGGT 60.534 50.000 14.09 0.00 0.00 4.16
99 100 1.065600 GTGCATGCGTTGTGGTGTT 59.934 52.632 14.09 0.00 0.00 3.32
100 101 1.065436 TGCATGCGTTGTGGTGTTG 59.935 52.632 14.09 0.00 0.00 3.33
112 113 1.593209 GGTGTTGTCTCGGTTCGCA 60.593 57.895 0.00 0.00 0.00 5.10
132 133 2.380064 TGACCTTTCAATTGTGCCCT 57.620 45.000 5.13 0.00 0.00 5.19
144 145 0.396435 TGTGCCCTAGGACACAAGTG 59.604 55.000 26.68 0.58 43.48 3.16
168 169 3.071459 GCGACATTGTGCGGTCTCG 62.071 63.158 0.00 0.00 39.81 4.04
179 180 2.497092 CGGTCTCGAACACGCGATG 61.497 63.158 15.93 10.38 39.85 3.84
219 220 3.659092 CACATGTGCCGTGGCGTT 61.659 61.111 13.94 0.00 45.51 4.84
255 256 1.501741 CTTTCGATTGCACCCCACG 59.498 57.895 0.00 0.00 0.00 4.94
256 257 0.953471 CTTTCGATTGCACCCCACGA 60.953 55.000 0.00 0.00 0.00 4.35
437 438 3.243367 CCCCTGTTATGTGTGTTGTTGTG 60.243 47.826 0.00 0.00 0.00 3.33
445 446 2.816672 TGTGTGTTGTTGTGTGTGTCAT 59.183 40.909 0.00 0.00 0.00 3.06
477 478 5.906772 TTTCTTCTCCTTACATATCCCCC 57.093 43.478 0.00 0.00 0.00 5.40
508 509 7.921786 TTCGGTTCATTTGAATCTATCTTGT 57.078 32.000 2.36 0.00 36.33 3.16
675 679 4.016629 CGTGTCACGTCGGACCGA 62.017 66.667 13.88 13.88 36.74 4.69
845 860 2.102420 TGAACGGTAGGAGCATATGGTG 59.898 50.000 13.10 0.00 0.00 4.17
1270 1323 4.980592 TCAGGTCCTGCCAGGGCA 62.981 66.667 18.72 13.18 43.30 5.36
1765 1830 4.445385 GCAGGAGTTAAAATTGTTGTGCAG 59.555 41.667 0.00 0.00 0.00 4.41
1907 2126 2.682836 GTGCTCTTGTCTCTGGAGAAC 58.317 52.381 1.56 0.00 39.48 3.01
1956 2175 1.219664 CCCGATCCAAACCGCAGTA 59.780 57.895 0.00 0.00 0.00 2.74
2043 2263 8.481492 AGATCAGATCATAGTTGAGAACTGAT 57.519 34.615 13.14 12.87 44.35 2.90
2207 2429 8.938906 GTTGGATAATCGGTGTAAAGAAACTTA 58.061 33.333 0.00 0.00 0.00 2.24
2312 2540 7.365473 GGCCCTCTCTCATCTATATAAGCAAAT 60.365 40.741 0.00 0.00 0.00 2.32
2439 2678 1.376942 CACCAGCTTCAGCCTCAGG 60.377 63.158 0.00 0.00 43.38 3.86
2516 2755 3.346315 CACTGTACAATTGATCCAGGCA 58.654 45.455 13.59 0.00 0.00 4.75
2589 2863 5.460091 GCAAAACTTGTCTCATTCAACTTCC 59.540 40.000 0.00 0.00 0.00 3.46
2618 2892 2.350192 CCAAAGAAACCCGTTTTGCAAC 59.650 45.455 0.00 0.00 32.11 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.566079 AGATCTATGACCATTTCAGACCAA 57.434 37.500 0.00 0.00 37.77 3.67
1 2 7.510343 TCATAGATCTATGACCATTTCAGACCA 59.490 37.037 32.49 12.46 44.87 4.02
2 3 7.901029 TCATAGATCTATGACCATTTCAGACC 58.099 38.462 32.49 0.00 44.87 3.85
15 16 9.650539 CCTGTAAGAATTGGTCATAGATCTATG 57.349 37.037 29.54 29.54 39.58 2.23
16 17 8.820831 CCCTGTAAGAATTGGTCATAGATCTAT 58.179 37.037 9.57 9.57 34.07 1.98
17 18 7.789831 ACCCTGTAAGAATTGGTCATAGATCTA 59.210 37.037 4.57 4.57 34.07 1.98
18 19 6.617371 ACCCTGTAAGAATTGGTCATAGATCT 59.383 38.462 0.00 0.00 34.07 2.75
19 20 6.831976 ACCCTGTAAGAATTGGTCATAGATC 58.168 40.000 0.00 0.00 34.07 2.75
20 21 6.386927 TGACCCTGTAAGAATTGGTCATAGAT 59.613 38.462 5.61 0.00 43.56 1.98
21 22 5.724370 TGACCCTGTAAGAATTGGTCATAGA 59.276 40.000 5.61 0.00 43.56 1.98
22 23 5.989477 TGACCCTGTAAGAATTGGTCATAG 58.011 41.667 5.61 0.00 43.56 2.23
24 25 4.927267 TGACCCTGTAAGAATTGGTCAT 57.073 40.909 5.61 0.00 43.56 3.06
25 26 3.650942 AGTGACCCTGTAAGAATTGGTCA 59.349 43.478 5.61 5.61 45.33 4.02
26 27 4.287766 AGTGACCCTGTAAGAATTGGTC 57.712 45.455 0.00 0.00 40.60 4.02
27 28 4.724279 AAGTGACCCTGTAAGAATTGGT 57.276 40.909 0.00 0.00 34.07 3.67
28 29 5.556915 TGTAAGTGACCCTGTAAGAATTGG 58.443 41.667 0.00 0.00 34.07 3.16
29 30 6.464222 TCTGTAAGTGACCCTGTAAGAATTG 58.536 40.000 0.00 0.00 31.25 2.32
30 31 6.681729 TCTGTAAGTGACCCTGTAAGAATT 57.318 37.500 0.00 0.00 31.25 2.17
31 32 6.295916 CCTTCTGTAAGTGACCCTGTAAGAAT 60.296 42.308 0.00 0.00 31.25 2.40
32 33 5.011738 CCTTCTGTAAGTGACCCTGTAAGAA 59.988 44.000 0.00 0.00 31.25 2.52
33 34 4.527038 CCTTCTGTAAGTGACCCTGTAAGA 59.473 45.833 0.00 0.00 31.25 2.10
34 35 4.283722 ACCTTCTGTAAGTGACCCTGTAAG 59.716 45.833 0.00 0.00 33.76 2.34
35 36 4.228824 ACCTTCTGTAAGTGACCCTGTAA 58.771 43.478 0.00 0.00 33.76 2.41
36 37 3.830755 GACCTTCTGTAAGTGACCCTGTA 59.169 47.826 0.00 0.00 33.76 2.74
37 38 2.633481 GACCTTCTGTAAGTGACCCTGT 59.367 50.000 0.00 0.00 33.76 4.00
38 39 2.632996 TGACCTTCTGTAAGTGACCCTG 59.367 50.000 0.00 0.00 33.76 4.45
39 40 2.633481 GTGACCTTCTGTAAGTGACCCT 59.367 50.000 0.00 0.00 33.76 4.34
40 41 2.633481 AGTGACCTTCTGTAAGTGACCC 59.367 50.000 0.00 0.00 33.76 4.46
41 42 4.523558 ACTAGTGACCTTCTGTAAGTGACC 59.476 45.833 0.00 0.00 33.76 4.02
42 43 5.708877 ACTAGTGACCTTCTGTAAGTGAC 57.291 43.478 0.00 0.00 33.76 3.67
43 44 5.831525 TCAACTAGTGACCTTCTGTAAGTGA 59.168 40.000 0.00 0.00 33.76 3.41
44 45 6.085555 TCAACTAGTGACCTTCTGTAAGTG 57.914 41.667 0.00 0.00 33.76 3.16
57 58 9.639601 CACTACAAGAAATATGTCAACTAGTGA 57.360 33.333 13.66 0.00 35.72 3.41
58 59 8.383619 GCACTACAAGAAATATGTCAACTAGTG 58.616 37.037 14.17 14.17 36.31 2.74
59 60 8.094548 TGCACTACAAGAAATATGTCAACTAGT 58.905 33.333 0.00 0.00 32.27 2.57
60 61 8.479313 TGCACTACAAGAAATATGTCAACTAG 57.521 34.615 0.00 0.00 32.27 2.57
61 62 8.882736 CATGCACTACAAGAAATATGTCAACTA 58.117 33.333 0.00 0.00 32.27 2.24
62 63 7.627088 GCATGCACTACAAGAAATATGTCAACT 60.627 37.037 14.21 0.00 32.27 3.16
63 64 6.470235 GCATGCACTACAAGAAATATGTCAAC 59.530 38.462 14.21 0.00 32.27 3.18
64 65 6.554419 GCATGCACTACAAGAAATATGTCAA 58.446 36.000 14.21 0.00 32.27 3.18
65 66 5.220643 CGCATGCACTACAAGAAATATGTCA 60.221 40.000 19.57 0.00 32.27 3.58
66 67 5.200454 CGCATGCACTACAAGAAATATGTC 58.800 41.667 19.57 0.00 32.27 3.06
67 68 4.635765 ACGCATGCACTACAAGAAATATGT 59.364 37.500 19.57 0.00 34.81 2.29
68 69 5.160699 ACGCATGCACTACAAGAAATATG 57.839 39.130 19.57 0.00 0.00 1.78
69 70 5.123820 ACAACGCATGCACTACAAGAAATAT 59.876 36.000 19.57 0.00 0.00 1.28
70 71 4.454161 ACAACGCATGCACTACAAGAAATA 59.546 37.500 19.57 0.00 0.00 1.40
71 72 3.253188 ACAACGCATGCACTACAAGAAAT 59.747 39.130 19.57 0.00 0.00 2.17
72 73 2.616376 ACAACGCATGCACTACAAGAAA 59.384 40.909 19.57 0.00 0.00 2.52
73 74 2.032117 CACAACGCATGCACTACAAGAA 60.032 45.455 19.57 0.00 0.00 2.52
74 75 1.530720 CACAACGCATGCACTACAAGA 59.469 47.619 19.57 0.00 0.00 3.02
75 76 1.400113 CCACAACGCATGCACTACAAG 60.400 52.381 19.57 1.32 0.00 3.16
76 77 0.590682 CCACAACGCATGCACTACAA 59.409 50.000 19.57 0.00 0.00 2.41
77 78 0.533978 ACCACAACGCATGCACTACA 60.534 50.000 19.57 0.00 0.00 2.74
78 79 0.110238 CACCACAACGCATGCACTAC 60.110 55.000 19.57 0.00 0.00 2.73
79 80 0.533978 ACACCACAACGCATGCACTA 60.534 50.000 19.57 0.00 0.00 2.74
80 81 1.383456 AACACCACAACGCATGCACT 61.383 50.000 19.57 0.00 0.00 4.40
81 82 1.065600 AACACCACAACGCATGCAC 59.934 52.632 19.57 0.00 0.00 4.57
82 83 1.065436 CAACACCACAACGCATGCA 59.935 52.632 19.57 0.00 0.00 3.96
83 84 0.934436 GACAACACCACAACGCATGC 60.934 55.000 7.91 7.91 0.00 4.06
96 97 0.032815 TCATGCGAACCGAGACAACA 59.967 50.000 0.00 0.00 0.00 3.33
99 100 1.080093 GGTCATGCGAACCGAGACA 60.080 57.895 0.00 0.00 0.00 3.41
100 101 0.389948 AAGGTCATGCGAACCGAGAC 60.390 55.000 0.00 0.00 41.89 3.36
112 113 2.893424 AGGGCACAATTGAAAGGTCAT 58.107 42.857 13.59 0.00 32.48 3.06
144 145 1.725625 CGCACAATGTCGCAACACC 60.726 57.895 8.13 0.00 38.48 4.16
153 154 0.249699 TGTTCGAGACCGCACAATGT 60.250 50.000 0.00 0.00 38.84 2.71
168 169 1.573829 TTGAAGGGCATCGCGTGTTC 61.574 55.000 5.77 5.01 0.00 3.18
179 180 3.365265 CCGGCACAGTTGAAGGGC 61.365 66.667 0.00 0.00 0.00 5.19
230 231 0.865769 GTGCAATCGAAAGGTCACGT 59.134 50.000 0.00 0.00 0.00 4.49
255 256 3.036084 CGTGACACCACCTGCGTC 61.036 66.667 0.00 0.00 40.12 5.19
256 257 4.602259 CCGTGACACCACCTGCGT 62.602 66.667 0.00 0.00 40.12 5.24
322 323 2.105821 CCAAGACCAAACCAGGACACTA 59.894 50.000 0.00 0.00 0.00 2.74
504 505 2.556534 GCTTTGCAGCCTATCACAAG 57.443 50.000 0.00 0.00 40.61 3.16
525 526 8.849168 CCTGAATTGTATTCATGTTGCCTATAA 58.151 33.333 2.84 0.00 0.00 0.98
845 860 1.287425 GACTAGCGTGGGCAATACAC 58.713 55.000 0.00 0.00 43.41 2.90
1270 1323 0.822532 CACCGGTAGAGGTATCCGCT 60.823 60.000 6.87 0.00 43.89 5.52
1765 1830 5.591099 TGAGAAAAGAAACAATTGGTCAGC 58.409 37.500 10.83 0.00 0.00 4.26
1907 2126 2.353357 TTCATTCTATGCCAGCCAGG 57.647 50.000 0.00 0.00 41.84 4.45
1956 2175 2.291741 ACGAACGAAAGACCGACTTACT 59.708 45.455 0.14 0.00 37.93 2.24
2043 2263 7.984422 ACAACAATACACAAGATTCTCATGA 57.016 32.000 0.00 0.00 0.00 3.07
2207 2429 1.683365 GCATGTGAAGGGGGCATGT 60.683 57.895 0.00 0.00 41.27 3.21
2337 2570 5.705441 TCGCTACAATGATTCTTTTTCCTGT 59.295 36.000 0.00 0.00 0.00 4.00
2439 2678 5.128008 AGCTCACCTCCTACTATTCAGAAAC 59.872 44.000 0.00 0.00 0.00 2.78
2556 2827 2.689983 AGACAAGTTTTGCTGGAACCAG 59.310 45.455 15.64 15.64 46.15 4.00


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

AutoCloner maintained by Alex Coulton.