Multiple sequence alignment - TraesCS7A01G040300

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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 TraesCS7A01G040300 chr7A 100.000 5767 0 0 1 5767 18574778 18569012 0.000000e+00 10650.0
1 TraesCS7A01G040300 chr7A 96.255 1335 30 5 4433 5767 17835756 17837070 0.000000e+00 2170.0
2 TraesCS7A01G040300 chr7A 82.265 874 147 4 3230 4096 17337204 17338076 0.000000e+00 749.0
3 TraesCS7A01G040300 chr7A 86.621 441 50 2 4212 4643 17338261 17338701 4.040000e-131 479.0
4 TraesCS7A01G040300 chr7A 83.033 389 64 2 1113 1500 17335407 17335794 9.190000e-93 351.0
5 TraesCS7A01G040300 chr7A 80.178 338 59 5 1895 2228 17328327 17328660 4.460000e-61 246.0
6 TraesCS7A01G040300 chr7A 91.489 94 7 1 2518 2610 213151264 213151357 1.690000e-25 128.0
7 TraesCS7A01G040300 chr4A 93.015 3221 123 24 4 3193 714746963 714743814 0.000000e+00 4608.0
8 TraesCS7A01G040300 chr4A 92.512 2377 140 14 3284 5654 714743300 714740956 0.000000e+00 3369.0
9 TraesCS7A01G040300 chr4A 83.222 900 141 7 3228 4122 715745377 715744483 0.000000e+00 817.0
10 TraesCS7A01G040300 chr4A 84.116 831 132 0 3266 4096 715809474 715810304 0.000000e+00 804.0
11 TraesCS7A01G040300 chr4A 83.468 865 139 4 3254 4116 715817715 715818577 0.000000e+00 802.0
12 TraesCS7A01G040300 chr4A 79.243 713 119 17 4211 4899 714917841 714917134 2.430000e-128 470.0
13 TraesCS7A01G040300 chr4A 84.715 386 55 2 1117 1500 715754223 715753840 3.260000e-102 383.0
14 TraesCS7A01G040300 chr4A 81.797 434 76 2 4206 4636 715744279 715743846 1.530000e-95 361.0
15 TraesCS7A01G040300 chr4A 79.060 468 93 4 1106 1572 715746985 715746522 3.350000e-82 316.0
16 TraesCS7A01G040300 chr4A 79.832 357 72 0 1895 2251 715816833 715817189 1.590000e-65 261.0
17 TraesCS7A01G040300 chr4A 97.895 95 2 0 3192 3286 714743732 714743638 1.290000e-36 165.0
18 TraesCS7A01G040300 chr7D 95.524 2748 96 14 3038 5767 18096128 18098866 0.000000e+00 4368.0
19 TraesCS7A01G040300 chr7D 95.136 1953 79 8 583 2520 18093780 18095731 0.000000e+00 3066.0
20 TraesCS7A01G040300 chr7D 83.514 831 137 0 3266 4096 17830582 17831412 0.000000e+00 776.0
21 TraesCS7A01G040300 chr7D 82.927 861 142 3 3266 4122 17859588 17860447 0.000000e+00 771.0
22 TraesCS7A01G040300 chr7D 88.288 444 20 13 1 415 18093344 18093784 2.400000e-138 503.0
23 TraesCS7A01G040300 chr7D 85.714 406 38 8 2602 2988 18095730 18096134 1.500000e-110 411.0
24 TraesCS7A01G040300 chr7D 85.233 386 53 2 1117 1500 17847869 17848252 1.510000e-105 394.0
25 TraesCS7A01G040300 chr7D 82.176 432 74 3 4213 4642 17860712 17861142 9.130000e-98 368.0
26 TraesCS7A01G040300 chr7D 90.135 223 22 0 4228 4450 17831535 17831757 2.030000e-74 291.0
27 TraesCS7A01G040300 chr7D 75.814 215 42 6 1143 1352 94116015 94115806 3.680000e-17 100.0
28 TraesCS7A01G040300 chrUn 92.512 2377 140 14 3284 5654 321395162 321392818 0.000000e+00 3369.0
29 TraesCS7A01G040300 chrUn 92.808 1321 49 4 456 1775 417025470 417024195 0.000000e+00 1871.0
30 TraesCS7A01G040300 chrUn 88.372 473 32 13 4 454 463779340 463778869 1.090000e-151 547.0
31 TraesCS7A01G040300 chrUn 79.161 715 116 20 4211 4899 277338861 277339568 1.130000e-126 464.0
32 TraesCS7A01G040300 chrUn 97.895 95 2 0 3192 3286 461112367 461112461 1.290000e-36 165.0
33 TraesCS7A01G040300 chr1A 92.473 93 7 0 2518 2610 409786917 409787009 3.630000e-27 134.0
34 TraesCS7A01G040300 chr2A 91.579 95 7 1 2519 2612 41474164 41474258 4.690000e-26 130.0
35 TraesCS7A01G040300 chr2A 89.216 102 10 1 2506 2606 667105325 667105426 6.070000e-25 126.0
36 TraesCS7A01G040300 chr4B 90.625 96 9 0 2519 2614 548118340 548118245 1.690000e-25 128.0
37 TraesCS7A01G040300 chr3B 91.398 93 8 0 2511 2603 188484170 188484078 1.690000e-25 128.0
38 TraesCS7A01G040300 chr3B 91.398 93 8 0 2511 2603 818896581 818896673 1.690000e-25 128.0
39 TraesCS7A01G040300 chr1B 89.000 100 11 0 2504 2603 449749175 449749076 2.180000e-24 124.0
40 TraesCS7A01G040300 chr7B 85.507 69 10 0 1245 1313 48052845 48052777 8.020000e-09 73.1


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 TraesCS7A01G040300 chr7A 18569012 18574778 5766 True 10650.000000 10650 100.000000 1 5767 1 chr7A.!!$R1 5766
1 TraesCS7A01G040300 chr7A 17835756 17837070 1314 False 2170.000000 2170 96.255000 4433 5767 1 chr7A.!!$F2 1334
2 TraesCS7A01G040300 chr7A 17335407 17338701 3294 False 526.333333 749 83.973000 1113 4643 3 chr7A.!!$F4 3530
3 TraesCS7A01G040300 chr4A 714740956 714746963 6007 True 2714.000000 4608 94.474000 4 5654 3 chr4A.!!$R3 5650
4 TraesCS7A01G040300 chr4A 715809474 715810304 830 False 804.000000 804 84.116000 3266 4096 1 chr4A.!!$F1 830
5 TraesCS7A01G040300 chr4A 715816833 715818577 1744 False 531.500000 802 81.650000 1895 4116 2 chr4A.!!$F2 2221
6 TraesCS7A01G040300 chr4A 715743846 715746985 3139 True 498.000000 817 81.359667 1106 4636 3 chr4A.!!$R4 3530
7 TraesCS7A01G040300 chr4A 714917134 714917841 707 True 470.000000 470 79.243000 4211 4899 1 chr4A.!!$R1 688
8 TraesCS7A01G040300 chr7D 18093344 18098866 5522 False 2087.000000 4368 91.165500 1 5767 4 chr7D.!!$F4 5766
9 TraesCS7A01G040300 chr7D 17859588 17861142 1554 False 569.500000 771 82.551500 3266 4642 2 chr7D.!!$F3 1376
10 TraesCS7A01G040300 chr7D 17830582 17831757 1175 False 533.500000 776 86.824500 3266 4450 2 chr7D.!!$F2 1184
11 TraesCS7A01G040300 chrUn 321392818 321395162 2344 True 3369.000000 3369 92.512000 3284 5654 1 chrUn.!!$R1 2370
12 TraesCS7A01G040300 chrUn 417024195 417025470 1275 True 1871.000000 1871 92.808000 456 1775 1 chrUn.!!$R2 1319
13 TraesCS7A01G040300 chrUn 277338861 277339568 707 False 464.000000 464 79.161000 4211 4899 1 chrUn.!!$F1 688

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
354 383 0.238553 GGCCGAGTTTTGTCTTGCTC 59.761 55.000 0.00 0.0 0.0 4.26 F
537 567 1.144057 GGTGGTCCTGACGCCTATG 59.856 63.158 0.00 0.0 0.0 2.23 F
1686 1731 0.178068 ATCCAATCCGACTCCAACCG 59.822 55.000 0.00 0.0 0.0 4.44 F
2044 2410 0.753867 TGTTACAAGCACGTGGGAGA 59.246 50.000 18.88 0.0 0.0 3.71 F
2829 3420 1.004745 CCAAAGTACCACAGCCCAGAT 59.995 52.381 0.00 0.0 0.0 2.90 F
3401 4531 0.253044 GCCATCCAGTGCTCCAACTA 59.747 55.000 0.00 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 1731 0.534873 AAAACCAATGGGGCGTATGC 59.465 50.000 3.55 0.00 42.05 3.14 R
2438 2929 1.067283 CGCATGCCAATACCCAAAACA 60.067 47.619 13.15 0.00 0.00 2.83 R
2825 3416 0.247537 GCGTCGGCCGTAAAAATCTG 60.248 55.000 27.15 6.49 39.32 2.90 R
2940 3531 2.698855 AGCGGAATAGCTTCACACAT 57.301 45.000 0.00 0.00 46.80 3.21 R
4163 5351 1.202687 TCACCTTGTCTGAGTTGCCTG 60.203 52.381 0.00 0.00 0.00 4.85 R
5301 6672 0.606604 GGTATCACCACGACACTGGT 59.393 55.000 0.00 0.00 46.18 4.00 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
294 322 5.437289 TGCAAGTTGGATTTAGTTGACTG 57.563 39.130 4.75 0.00 0.00 3.51
332 361 4.996758 TCAAGCGAATCAGATTGAAAGTCA 59.003 37.500 0.00 0.00 42.58 3.41
352 381 1.082104 CGGCCGAGTTTTGTCTTGC 60.082 57.895 24.07 0.00 0.00 4.01
354 383 0.238553 GGCCGAGTTTTGTCTTGCTC 59.761 55.000 0.00 0.00 0.00 4.26
465 495 7.509141 GGTCTAACCTATAGAGTTACTGGTC 57.491 44.000 0.00 0.00 34.73 4.02
471 501 4.455190 CCTATAGAGTTACTGGTCGTAGCC 59.545 50.000 0.00 0.00 30.39 3.93
497 527 8.603181 CAAAATAACTATACAAAATTGGCAGGC 58.397 33.333 0.00 0.00 0.00 4.85
537 567 1.144057 GGTGGTCCTGACGCCTATG 59.856 63.158 0.00 0.00 0.00 2.23
563 593 4.329545 GACTGGCTGTGGCGGGAA 62.330 66.667 0.29 0.00 38.89 3.97
564 594 3.628646 GACTGGCTGTGGCGGGAAT 62.629 63.158 0.29 0.00 38.89 3.01
565 595 2.361610 CTGGCTGTGGCGGGAATT 60.362 61.111 0.00 0.00 39.81 2.17
689 719 9.196552 CTCGTCATTAACTATTCAGCAATGATA 57.803 33.333 0.00 0.00 38.13 2.15
691 721 9.750882 CGTCATTAACTATTCAGCAATGATATG 57.249 33.333 0.00 0.00 38.13 1.78
800 833 5.346181 ACAACTAAGCAAGAGGATAGGTC 57.654 43.478 0.00 0.00 0.00 3.85
844 888 2.100087 GACCTAGCTAGTCTTGTCTGGC 59.900 54.545 19.31 0.00 41.21 4.85
847 891 1.352083 AGCTAGTCTTGTCTGGCCAA 58.648 50.000 7.01 0.00 41.71 4.52
1138 1183 4.573201 CCAAAACTGTACGAGTTCAAGGAA 59.427 41.667 9.99 0.00 44.68 3.36
1525 1570 1.911057 TCCTCGCTGTCTTCTTCTCA 58.089 50.000 0.00 0.00 0.00 3.27
1686 1731 0.178068 ATCCAATCCGACTCCAACCG 59.822 55.000 0.00 0.00 0.00 4.44
1692 1737 1.876714 CCGACTCCAACCGCATACG 60.877 63.158 0.00 0.00 39.67 3.06
2044 2410 0.753867 TGTTACAAGCACGTGGGAGA 59.246 50.000 18.88 0.00 0.00 3.71
2438 2929 7.330700 CCATTTACAAATGCTTACCGTTTTCAT 59.669 33.333 8.83 0.00 43.38 2.57
2463 2970 1.356624 GGTATTGGCATGCGAGCAC 59.643 57.895 12.44 9.21 35.83 4.40
2466 2973 1.016627 TATTGGCATGCGAGCACTTC 58.983 50.000 12.44 0.00 35.83 3.01
2526 3036 8.686334 TCTTTTGGCATTAATTTCTACTCCATC 58.314 33.333 0.00 0.00 0.00 3.51
2528 3038 9.693739 TTTTGGCATTAATTTCTACTCCATCTA 57.306 29.630 0.00 0.00 0.00 1.98
2639 3211 9.982651 TTAATAGAACTATGTGCATAGAAGTCC 57.017 33.333 21.81 8.62 42.55 3.85
2825 3416 2.801077 ATACCAAAGTACCACAGCCC 57.199 50.000 0.00 0.00 0.00 5.19
2829 3420 1.004745 CCAAAGTACCACAGCCCAGAT 59.995 52.381 0.00 0.00 0.00 2.90
2866 3457 3.586100 TGCACGACACTAGCTAATCAA 57.414 42.857 0.00 0.00 0.00 2.57
2867 3458 4.123497 TGCACGACACTAGCTAATCAAT 57.877 40.909 0.00 0.00 0.00 2.57
2940 3531 3.884895 ACATGCCGTCCAGAAAATATCA 58.115 40.909 0.00 0.00 0.00 2.15
2991 3582 3.807209 GCCAAAACTAGGAGCTCACTTGA 60.807 47.826 17.19 0.00 0.00 3.02
2998 3589 6.566197 ACTAGGAGCTCACTTGAAATTTTG 57.434 37.500 17.19 0.00 0.00 2.44
3118 3716 9.357652 AGTGAAATTTTCATGTGTATATTGTGC 57.642 29.630 14.54 0.00 42.47 4.57
3290 4420 4.759782 ACACTCGCTATCTTGTTATGCTT 58.240 39.130 0.00 0.00 0.00 3.91
3401 4531 0.253044 GCCATCCAGTGCTCCAACTA 59.747 55.000 0.00 0.00 0.00 2.24
3953 5089 1.482593 CCGAAGCTATATAGGCCAGGG 59.517 57.143 5.01 2.49 0.00 4.45
4145 5333 2.002586 CATAACCAAGCTGACTCACCG 58.997 52.381 0.00 0.00 0.00 4.94
4163 5351 1.565305 CGCAAGCTGATCTACCAGAC 58.435 55.000 0.00 0.00 36.29 3.51
4956 6327 7.330946 TCCGTGAACTAATATTGAGAACAACTG 59.669 37.037 0.00 0.00 38.90 3.16
4985 6356 6.071391 AGTGACATTTGCCCATAACCTAAAAG 60.071 38.462 0.00 0.00 0.00 2.27
5035 6406 6.382570 TGAAAGAAACCAGAAAAATCCAGGAA 59.617 34.615 0.00 0.00 0.00 3.36
5243 6614 3.268603 CGACGTGCTGTTGTGGCA 61.269 61.111 0.00 0.00 37.36 4.92
5301 6672 0.991146 TGGCCTGGATGCAGAGTTTA 59.009 50.000 16.85 0.00 0.00 2.01
5465 6839 3.507162 AGTGGATGTGGATGTCAAACA 57.493 42.857 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.101249 ACTCCATTGTGCCTTGTTTGTG 59.899 45.455 0.00 0.00 0.00 3.33
32 33 4.022068 ACATACTCCATTGTGCCTTGTTTG 60.022 41.667 0.00 0.00 0.00 2.93
33 34 4.151883 ACATACTCCATTGTGCCTTGTTT 58.848 39.130 0.00 0.00 0.00 2.83
44 56 9.775854 CAAGAGATTCATCTTACATACTCCATT 57.224 33.333 0.00 0.00 37.43 3.16
246 273 6.455360 AGAAATGCACAACCACCTTATATG 57.545 37.500 0.00 0.00 0.00 1.78
262 290 6.973229 AAATCCAACTTGCATTAGAAATGC 57.027 33.333 15.88 15.88 44.76 3.56
294 322 9.929722 TGATTCGCTTGATACATAATTAAACAC 57.070 29.630 0.00 0.00 0.00 3.32
312 341 4.269603 CGATGACTTTCAATCTGATTCGCT 59.730 41.667 0.00 0.00 0.00 4.93
321 350 1.594862 CTCGGCCGATGACTTTCAATC 59.405 52.381 31.19 0.00 0.00 2.67
332 361 1.156736 CAAGACAAAACTCGGCCGAT 58.843 50.000 31.19 13.32 0.00 4.18
352 381 3.547868 CACATATTCGACACCAGTTCGAG 59.452 47.826 0.00 0.00 37.20 4.04
354 383 2.029244 GCACATATTCGACACCAGTTCG 59.971 50.000 0.00 0.00 0.00 3.95
471 501 8.603181 GCCTGCCAATTTTGTATAGTTATTTTG 58.397 33.333 0.00 0.00 0.00 2.44
497 527 2.563976 CGCTCGTGATTTTGTGTCTTG 58.436 47.619 0.00 0.00 0.00 3.02
537 567 2.124403 CAGCCAGTCATCCCTGCC 60.124 66.667 0.00 0.00 0.00 4.85
800 833 1.540267 TGCCCGGTGGTCAATTTAAG 58.460 50.000 0.00 0.00 0.00 1.85
844 888 6.404293 CGGTTCCATTCCTATAGTTTGTTTGG 60.404 42.308 0.00 0.00 0.00 3.28
847 891 6.057321 TCGGTTCCATTCCTATAGTTTGTT 57.943 37.500 0.00 0.00 0.00 2.83
957 1001 7.361885 GCTCTGGCTTCAATTTATATCATCCAG 60.362 40.741 0.00 0.00 38.85 3.86
989 1033 2.472695 TGCTACTTTGCCATCGAACT 57.527 45.000 0.00 0.00 0.00 3.01
990 1034 3.552604 TTTGCTACTTTGCCATCGAAC 57.447 42.857 0.00 0.00 0.00 3.95
993 1037 2.801063 CCATTTGCTACTTTGCCATCG 58.199 47.619 0.00 0.00 0.00 3.84
1057 1102 2.283173 TGGCTCTCCAGACGCTCA 60.283 61.111 0.00 0.00 37.47 4.26
1557 1602 5.291971 GGGAATTATCATCACCATTGTTGC 58.708 41.667 0.00 0.00 0.00 4.17
1686 1731 0.534873 AAAACCAATGGGGCGTATGC 59.465 50.000 3.55 0.00 42.05 3.14
1692 1737 4.751767 TCATTATCAAAACCAATGGGGC 57.248 40.909 3.55 0.00 42.05 5.80
2044 2410 3.005684 TGCAAATGAAGAAAGCACGGAAT 59.994 39.130 0.00 0.00 0.00 3.01
2438 2929 1.067283 CGCATGCCAATACCCAAAACA 60.067 47.619 13.15 0.00 0.00 2.83
2463 2970 3.288809 TCGTGCATCTCCATATCGAAG 57.711 47.619 0.00 0.00 0.00 3.79
2466 2973 3.500558 AGATCGTGCATCTCCATATCG 57.499 47.619 0.00 0.00 37.24 2.92
2586 3096 9.720769 ATTTTATAAATACTCCCTCCATACACG 57.279 33.333 0.00 0.00 0.00 4.49
2639 3211 4.868067 ACTACAGACGACAGTGGTAAAAG 58.132 43.478 0.00 0.00 0.00 2.27
2769 3341 0.250424 TGTGACATGCCACCAGACAG 60.250 55.000 9.84 0.00 36.26 3.51
2825 3416 0.247537 GCGTCGGCCGTAAAAATCTG 60.248 55.000 27.15 6.49 39.32 2.90
2829 3420 1.498166 CATGCGTCGGCCGTAAAAA 59.502 52.632 27.15 8.93 38.85 1.94
2940 3531 2.698855 AGCGGAATAGCTTCACACAT 57.301 45.000 0.00 0.00 46.80 3.21
3096 3694 9.236691 GATCGCACAATATACACATGAAAATTT 57.763 29.630 0.00 0.00 0.00 1.82
3118 3716 7.850268 TTGTTACATTGTTTGAATGTGATCG 57.150 32.000 9.74 0.00 40.70 3.69
3290 4420 3.133901 TGGTCACAACAAGAGTAGCAAGA 59.866 43.478 0.00 0.00 0.00 3.02
3401 4531 6.100004 CACTCTATAACGAGTTGGATGTGTT 58.900 40.000 0.00 0.00 42.10 3.32
3953 5089 4.680110 ACATAGAGCGCATAACAACGTATC 59.320 41.667 11.47 0.00 0.00 2.24
4145 5333 2.548875 CTGTCTGGTAGATCAGCTTGC 58.451 52.381 0.00 0.00 34.91 4.01
4163 5351 1.202687 TCACCTTGTCTGAGTTGCCTG 60.203 52.381 0.00 0.00 0.00 4.85
4910 6281 4.337274 CGGATATGTCCATGCATGCAATAT 59.663 41.667 26.68 21.23 45.37 1.28
4956 6327 4.142469 GGTTATGGGCAAATGTCACTGTAC 60.142 45.833 0.00 0.00 0.00 2.90
5035 6406 5.394773 GGTGTGTTGTATTTGGGTTTCTGTT 60.395 40.000 0.00 0.00 0.00 3.16
5093 6464 0.656495 CGAAGCGACATCATGCATGC 60.656 55.000 22.25 11.82 35.65 4.06
5118 6489 2.499685 GAGCGGGAGTAACGGCAT 59.500 61.111 0.00 0.00 38.93 4.40
5301 6672 0.606604 GGTATCACCACGACACTGGT 59.393 55.000 0.00 0.00 46.18 4.00
5390 6764 7.936496 TGTAACAGCAATTGATCATTCCTTA 57.064 32.000 10.34 0.00 0.00 2.69
5391 6765 6.839124 TGTAACAGCAATTGATCATTCCTT 57.161 33.333 10.34 0.00 0.00 3.36
5392 6766 6.839124 TTGTAACAGCAATTGATCATTCCT 57.161 33.333 10.34 0.00 0.00 3.36
5446 6820 4.361451 GATGTTTGACATCCACATCCAC 57.639 45.455 9.38 0.00 46.99 4.02
5465 6839 4.150359 GAGGAATTGCTGGATCAATGGAT 58.850 43.478 3.35 0.00 36.83 3.41


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

AutoCloner maintained by Alex Coulton.