Multiple sequence alignment - TraesCS7D01G192200

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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 TraesCS7D01G192200 chr7D 100.000 2650 0 0 561 3210 148128881 148131530 0.000000e+00 4894.0
1 TraesCS7D01G192200 chr7D 100.000 374 0 0 1 374 148128321 148128694 0.000000e+00 691.0
2 TraesCS7D01G192200 chr7D 95.122 246 6 4 577 822 112329281 112329042 1.810000e-102 383.0
3 TraesCS7D01G192200 chr7D 98.592 213 2 1 1 212 112329958 112329746 3.020000e-100 375.0
4 TraesCS7D01G192200 chr7A 95.324 1839 59 13 816 2641 149166643 149168467 0.000000e+00 2894.0
5 TraesCS7D01G192200 chr7A 90.351 570 27 13 2642 3206 149168987 149169533 0.000000e+00 723.0
6 TraesCS7D01G192200 chr7B 93.604 1579 46 25 816 2372 111268803 111270348 0.000000e+00 2305.0
7 TraesCS7D01G192200 chr7B 94.004 567 23 6 2653 3209 111272098 111272663 0.000000e+00 848.0
8 TraesCS7D01G192200 chr4B 91.155 554 27 15 1436 1974 20727967 20728513 0.000000e+00 732.0
9 TraesCS7D01G192200 chr4B 92.169 332 26 0 1010 1341 20727517 20727848 1.350000e-128 470.0
10 TraesCS7D01G192200 chr4B 83.594 128 19 2 2253 2380 20729010 20729135 5.630000e-23 119.0
11 TraesCS7D01G192200 chr4A 88.388 577 26 26 1436 1973 591862171 591862745 0.000000e+00 656.0
12 TraesCS7D01G192200 chr4A 92.486 346 26 0 996 1341 591861710 591862055 2.220000e-136 496.0
13 TraesCS7D01G192200 chr4A 89.937 159 15 1 2060 2217 591862810 591862968 1.510000e-48 204.0
14 TraesCS7D01G192200 chr4A 82.353 136 17 3 2253 2388 591863226 591863354 9.410000e-21 111.0
15 TraesCS7D01G192200 chr4D 96.257 374 9 1 1 374 405024905 405025273 2.740000e-170 608.0
16 TraesCS7D01G192200 chr6D 95.989 374 11 1 1 374 2295525 2295156 3.540000e-169 604.0
17 TraesCS7D01G192200 chr1A 92.533 375 18 2 1 374 584067189 584067554 2.190000e-146 529.0
18 TraesCS7D01G192200 chr1A 95.367 259 9 2 561 819 584067752 584068007 2.980000e-110 409.0
19 TraesCS7D01G192200 chr1A 88.424 311 36 0 1031 1341 22985367 22985057 3.020000e-100 375.0
20 TraesCS7D01G192200 chr1A 91.255 263 19 3 561 823 532365506 532365248 3.940000e-94 355.0
21 TraesCS7D01G192200 chr1A 90.494 263 22 2 561 823 508390107 508389848 8.530000e-91 344.0
22 TraesCS7D01G192200 chr1A 95.122 123 6 0 252 374 532366254 532366132 9.090000e-46 195.0
23 TraesCS7D01G192200 chr1A 97.403 77 2 0 1 77 508390820 508390744 7.230000e-27 132.0
24 TraesCS7D01G192200 chr1A 96.000 75 2 1 1 75 532366332 532366259 1.560000e-23 121.0
25 TraesCS7D01G192200 chr2B 93.485 307 13 4 42 347 481633687 481633987 1.760000e-122 449.0
26 TraesCS7D01G192200 chr2B 91.054 313 16 5 42 353 393459940 393459639 2.300000e-111 412.0
27 TraesCS7D01G192200 chr2B 93.846 260 12 3 561 819 481636094 481636350 3.880000e-104 388.0
28 TraesCS7D01G192200 chr2B 91.892 259 16 4 561 818 393459099 393458845 1.100000e-94 357.0
29 TraesCS7D01G192200 chr5D 78.838 671 117 18 1080 1738 426639485 426640142 2.290000e-116 429.0
30 TraesCS7D01G192200 chr3D 96.525 259 6 2 561 819 275642637 275642892 2.960000e-115 425.0
31 TraesCS7D01G192200 chr3D 98.352 182 3 0 1 182 275641969 275642150 1.440000e-83 320.0
32 TraesCS7D01G192200 chr3B 89.521 334 23 6 42 374 592331193 592331515 2.300000e-111 412.0
33 TraesCS7D01G192200 chr3A 89.939 328 21 1 42 369 388411991 388412306 2.300000e-111 412.0
34 TraesCS7D01G192200 chr5A 78.443 668 112 23 1080 1738 540681664 540682308 1.070000e-109 407.0
35 TraesCS7D01G192200 chr5B 78.222 675 106 25 1080 1738 516537886 516538535 8.350000e-106 394.0
36 TraesCS7D01G192200 chr5B 90.385 260 20 5 561 819 87010570 87010315 1.430000e-88 337.0
37 TraesCS7D01G192200 chr6B 90.228 307 16 2 42 347 672728872 672728579 3.880000e-104 388.0
38 TraesCS7D01G192200 chr6B 82.812 128 22 0 1819 1946 709019973 709019846 7.280000e-22 115.0
39 TraesCS7D01G192200 chr6A 89.575 259 20 4 561 819 551183819 551184070 3.990000e-84 322.0
40 TraesCS7D01G192200 chr6A 100.000 34 0 0 1 34 551182303 551182336 2.670000e-06 63.9
41 TraesCS7D01G192200 chr2A 80.201 298 56 3 1443 1738 29721224 29720928 1.500000e-53 220.0
42 TraesCS7D01G192200 chr2D 78.912 294 60 2 1446 1738 27483185 27482893 7.020000e-47 198.0


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 TraesCS7D01G192200 chr7D 148128321 148131530 3209 False 2792.500000 4894 100.000000 1 3210 2 chr7D.!!$F1 3209
1 TraesCS7D01G192200 chr7D 112329042 112329958 916 True 379.000000 383 96.857000 1 822 2 chr7D.!!$R1 821
2 TraesCS7D01G192200 chr7A 149166643 149169533 2890 False 1808.500000 2894 92.837500 816 3206 2 chr7A.!!$F1 2390
3 TraesCS7D01G192200 chr7B 111268803 111272663 3860 False 1576.500000 2305 93.804000 816 3209 2 chr7B.!!$F1 2393
4 TraesCS7D01G192200 chr4B 20727517 20729135 1618 False 440.333333 732 88.972667 1010 2380 3 chr4B.!!$F1 1370
5 TraesCS7D01G192200 chr4A 591861710 591863354 1644 False 366.750000 656 88.291000 996 2388 4 chr4A.!!$F1 1392
6 TraesCS7D01G192200 chr1A 584067189 584068007 818 False 469.000000 529 93.950000 1 819 2 chr1A.!!$F1 818
7 TraesCS7D01G192200 chr1A 508389848 508390820 972 True 238.000000 344 93.948500 1 823 2 chr1A.!!$R2 822
8 TraesCS7D01G192200 chr1A 532365248 532366332 1084 True 223.666667 355 94.125667 1 823 3 chr1A.!!$R3 822
9 TraesCS7D01G192200 chr2B 481633687 481636350 2663 False 418.500000 449 93.665500 42 819 2 chr2B.!!$F1 777
10 TraesCS7D01G192200 chr2B 393458845 393459940 1095 True 384.500000 412 91.473000 42 818 2 chr2B.!!$R1 776
11 TraesCS7D01G192200 chr5D 426639485 426640142 657 False 429.000000 429 78.838000 1080 1738 1 chr5D.!!$F1 658
12 TraesCS7D01G192200 chr3D 275641969 275642892 923 False 372.500000 425 97.438500 1 819 2 chr3D.!!$F1 818
13 TraesCS7D01G192200 chr5A 540681664 540682308 644 False 407.000000 407 78.443000 1080 1738 1 chr5A.!!$F1 658
14 TraesCS7D01G192200 chr5B 516537886 516538535 649 False 394.000000 394 78.222000 1080 1738 1 chr5B.!!$F1 658

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
250 251 0.314302 CTTCACAGTTCGAGTCCGGT 59.686 55.000 0.0 0.00 36.24 5.28 F
931 3579 1.153289 CTTCCTCTCATGGCGTGGG 60.153 63.158 6.9 2.88 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 4573 1.430632 CGCCACCAGCTGCAATTAG 59.569 57.895 8.66 0.0 40.39 1.73 R
2779 7908 0.251787 GAAGGGTGGATGCAAGGGTT 60.252 55.000 0.00 0.0 0.00 4.11 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
69 70 4.032703 CAGCTAGTGCAACAAAAACAGT 57.967 40.909 0.00 0.00 41.43 3.55
202 203 7.864108 AAACATGAACACTAGCTGCATATAA 57.136 32.000 0.00 0.00 0.00 0.98
203 204 7.488187 AACATGAACACTAGCTGCATATAAG 57.512 36.000 0.00 0.00 0.00 1.73
204 205 5.994054 ACATGAACACTAGCTGCATATAAGG 59.006 40.000 0.00 0.00 0.00 2.69
205 206 4.960938 TGAACACTAGCTGCATATAAGGG 58.039 43.478 1.02 0.00 0.00 3.95
206 207 4.202357 TGAACACTAGCTGCATATAAGGGG 60.202 45.833 1.02 0.00 0.00 4.79
207 208 2.639839 ACACTAGCTGCATATAAGGGGG 59.360 50.000 1.02 0.00 0.00 5.40
250 251 0.314302 CTTCACAGTTCGAGTCCGGT 59.686 55.000 0.00 0.00 36.24 5.28
280 281 1.294780 CGCTGCTTGGAGTCCTTCT 59.705 57.895 11.33 0.00 0.00 2.85
313 314 5.293079 GCTGCAAAACGATAGAGAAAGAGAT 59.707 40.000 0.00 0.00 41.38 2.75
347 348 2.045340 AAGGGATGAAACGGCCGG 60.045 61.111 31.76 11.88 0.00 6.13
690 3338 4.357142 GGTATGACTTCGTTTCGCATCTA 58.643 43.478 0.00 0.00 0.00 1.98
691 3339 4.441415 GGTATGACTTCGTTTCGCATCTAG 59.559 45.833 0.00 0.00 0.00 2.43
692 3340 2.876091 TGACTTCGTTTCGCATCTAGG 58.124 47.619 0.00 0.00 0.00 3.02
693 3341 1.588861 GACTTCGTTTCGCATCTAGGC 59.411 52.381 0.00 0.00 0.00 3.93
901 3549 1.163420 TGCAAACACTTCACCGCGAT 61.163 50.000 8.23 0.00 0.00 4.58
931 3579 1.153289 CTTCCTCTCATGGCGTGGG 60.153 63.158 6.90 2.88 0.00 4.61
934 3582 2.513204 CTCTCATGGCGTGGGCAG 60.513 66.667 6.90 0.00 42.43 4.85
964 3613 3.850173 ACCCAGGAACCAAGCTAGATAAA 59.150 43.478 0.00 0.00 0.00 1.40
977 3626 7.220030 CAAGCTAGATAAAAATCCTCTGCCTA 58.780 38.462 0.00 0.00 0.00 3.93
1387 4074 3.186909 CGTGACCACATACATACAGGTG 58.813 50.000 0.85 0.00 31.57 4.00
1431 4133 1.338107 TTATCATCGCCTCCCGTGAT 58.662 50.000 0.00 0.00 42.62 3.06
1434 4136 2.501128 ATCGCCTCCCGTGATGTG 59.499 61.111 0.00 0.00 40.29 3.21
1743 4445 2.099062 CTTCGTCCCCGTACGTCG 59.901 66.667 15.21 12.76 43.31 5.12
1816 4573 1.146637 GGCATCTGATGATCTGTCGC 58.853 55.000 21.30 2.96 0.00 5.19
2223 5135 0.892063 GCTTGAAGGTCGAGAGAGGT 59.108 55.000 0.00 0.00 43.49 3.85
2234 5146 2.230994 GAGAGAGGTGACCATGCGCA 62.231 60.000 14.96 14.96 0.00 6.09
2278 5422 3.315470 TCATCGGTGTAAAGAGGATCGAG 59.685 47.826 0.00 0.00 42.67 4.04
2296 5440 3.759618 TCGAGAAGTTGTTGGTTGGTTTT 59.240 39.130 0.00 0.00 0.00 2.43
2398 5584 0.247814 GCCGTTCGTCATGATGCTTG 60.248 55.000 10.24 2.06 0.00 4.01
2407 5593 3.184541 GTCATGATGCTTGTCAATTGGC 58.815 45.455 2.20 2.20 0.00 4.52
2418 5604 2.911636 TGTCAATTGGCCCATTTGGAAT 59.088 40.909 16.18 0.00 37.39 3.01
2458 5644 9.144298 AGATCTTTATGAAGAAATCAATGCCAT 57.856 29.630 3.79 0.00 44.61 4.40
2609 5805 8.928733 TCAAAACATTGTCGTACTATCCTTAAC 58.071 33.333 0.00 0.00 0.00 2.01
2661 6376 5.968848 TCTTTAACACAAGATTCGTGCAAAC 59.031 36.000 0.00 0.00 37.93 2.93
2664 6379 3.952535 ACACAAGATTCGTGCAAACTTC 58.047 40.909 0.00 0.00 37.93 3.01
2669 6384 5.700832 ACAAGATTCGTGCAAACTTCTATGA 59.299 36.000 0.00 0.00 0.00 2.15
2670 6385 6.128445 ACAAGATTCGTGCAAACTTCTATGAG 60.128 38.462 0.00 0.00 0.00 2.90
2671 6386 4.872691 AGATTCGTGCAAACTTCTATGAGG 59.127 41.667 0.00 0.00 0.00 3.86
2677 7804 3.814842 TGCAAACTTCTATGAGGTGTGTG 59.185 43.478 2.75 0.00 30.82 3.82
2720 7849 6.942532 ACATGATGTATACCGAAGCAAAAT 57.057 33.333 0.00 0.00 0.00 1.82
2748 7877 3.397849 ACCCGTTAGACTTTGAAGGTC 57.602 47.619 0.00 0.00 0.00 3.85
2779 7908 0.756294 TGGACGTTGAAAGCCTCTCA 59.244 50.000 0.00 0.00 0.00 3.27
2810 7939 5.639082 GCATCCACCCTTCATTTTGTTTTAG 59.361 40.000 0.00 0.00 0.00 1.85
2853 7982 9.301897 TGACCATATATATCTATATGCGCTCTT 57.698 33.333 9.73 0.00 42.96 2.85
2887 8016 6.424812 GCCAATGCTTAAACTCAAAGACAAAT 59.575 34.615 0.00 0.00 33.53 2.32
2979 8108 5.063312 AGTGTTTTGCCAACAAGAATTTTCG 59.937 36.000 0.32 0.00 37.04 3.46
3209 8344 9.372369 GTATGTGAAACTCTTCTAAACTAGCAT 57.628 33.333 0.00 0.00 38.04 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
280 281 1.648720 GTTTTGCAGCAGCTCGACA 59.351 52.632 1.76 0.00 42.74 4.35
313 314 2.571653 CCCTTCCGGATGCCTGATAATA 59.428 50.000 4.15 0.00 0.00 0.98
336 337 3.636929 ATCCATGCCGGCCGTTTCA 62.637 57.895 26.77 18.75 33.14 2.69
347 348 1.526917 CGGTTCCTCCCATCCATGC 60.527 63.158 0.00 0.00 0.00 4.06
690 3338 2.665185 GCGAATATTCCGCCGCCT 60.665 61.111 16.50 0.00 46.22 5.52
901 3549 5.072329 CCATGAGAGGAAGCTTAAATAGGGA 59.928 44.000 0.00 0.00 0.00 4.20
931 3579 2.125512 CCTGGGTGCTACGACTGC 60.126 66.667 0.00 0.00 0.00 4.40
934 3582 1.079336 GGTTCCTGGGTGCTACGAC 60.079 63.158 0.00 0.00 0.00 4.34
964 3613 1.213926 CCAAGGCTAGGCAGAGGATTT 59.786 52.381 19.70 0.00 0.00 2.17
1743 4445 4.577246 AGGAGAAGGCGCGCGATC 62.577 66.667 37.18 26.32 0.00 3.69
1816 4573 1.430632 CGCCACCAGCTGCAATTAG 59.569 57.895 8.66 0.00 40.39 1.73
1843 4604 1.847890 CGAACACCGCCAAACCGATT 61.848 55.000 0.00 0.00 0.00 3.34
2234 5146 7.258022 TGAAAAATACTGTATATGCATGCGT 57.742 32.000 18.07 18.07 0.00 5.24
2278 5422 6.627243 AGACTAAAAACCAACCAACAACTTC 58.373 36.000 0.00 0.00 0.00 3.01
2296 5440 5.476614 GGCCGAGAGAAGTAAAAAGACTAA 58.523 41.667 0.00 0.00 0.00 2.24
2398 5584 3.055240 TCATTCCAAATGGGCCAATTGAC 60.055 43.478 31.12 0.00 36.21 3.18
2407 5593 3.450578 CATTTCGCTCATTCCAAATGGG 58.549 45.455 0.00 0.00 34.10 4.00
2430 5616 8.627403 GGCATTGATTTCTTCATAAAGATCTGA 58.373 33.333 0.00 0.00 41.12 3.27
2436 5622 7.866393 GGAGATGGCATTGATTTCTTCATAAAG 59.134 37.037 0.00 0.00 33.34 1.85
2440 5626 5.205821 TGGAGATGGCATTGATTTCTTCAT 58.794 37.500 0.00 0.00 33.34 2.57
2441 5627 4.602107 TGGAGATGGCATTGATTTCTTCA 58.398 39.130 0.00 0.00 0.00 3.02
2458 5644 5.704978 TGATGTTTTCAACGATGATTGGAGA 59.295 36.000 0.00 0.00 34.96 3.71
2494 5680 3.193479 GCTCCCGTGATTTTCCAAAGATT 59.807 43.478 0.00 0.00 0.00 2.40
2661 6376 3.442625 TCGGTACACACACCTCATAGAAG 59.557 47.826 0.00 0.00 36.35 2.85
2664 6379 3.770666 CTTCGGTACACACACCTCATAG 58.229 50.000 0.00 0.00 36.35 2.23
2669 6384 0.466543 TTGCTTCGGTACACACACCT 59.533 50.000 0.00 0.00 36.35 4.00
2670 6385 1.301423 TTTGCTTCGGTACACACACC 58.699 50.000 0.00 0.00 35.04 4.16
2671 6386 2.353579 AGTTTTGCTTCGGTACACACAC 59.646 45.455 0.00 0.00 0.00 3.82
2677 7804 5.600908 TGTTATGAGTTTTGCTTCGGTAC 57.399 39.130 0.00 0.00 0.00 3.34
2720 7849 9.603921 CCTTCAAAGTCTAACGGGTAAAATATA 57.396 33.333 0.00 0.00 0.00 0.86
2779 7908 0.251787 GAAGGGTGGATGCAAGGGTT 60.252 55.000 0.00 0.00 0.00 4.11
2810 7939 4.894784 TGGTCACTAAGATTGTCCAAGTC 58.105 43.478 0.00 0.00 30.45 3.01
2875 8004 5.784750 TCGTCTGCATATTTGTCTTTGAG 57.215 39.130 0.00 0.00 0.00 3.02
2906 8035 5.772825 ATTTATTGTGTCCCGGATCATTG 57.227 39.130 0.73 0.00 0.00 2.82
2917 8046 7.763528 TGGAATTGGTTGCATATTTATTGTGTC 59.236 33.333 0.00 0.00 30.10 3.67
2963 8092 2.971261 GTCGACGAAAATTCTTGTTGGC 59.029 45.455 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.