Multiple sequence alignment - TraesCS7A01G135000

Loading Multiple Alignment...

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 TraesCS7A01G135000 chr7A 100.000 4098 0 0 1 4098 87457620 87453523 0.000000e+00 7568
1 TraesCS7A01G135000 chr7A 90.569 3425 237 38 702 4098 88014072 88010706 0.000000e+00 4457
2 TraesCS7A01G135000 chr7A 90.327 3422 246 35 704 4098 88127349 88123986 0.000000e+00 4407
3 TraesCS7A01G135000 chr7A 90.213 3423 251 37 702 4093 88441589 88438220 0.000000e+00 4388
4 TraesCS7A01G135000 chr7A 89.398 3424 257 38 702 4098 88178098 88174754 0.000000e+00 4215
5 TraesCS7A01G135000 chr7A 89.522 1842 163 18 702 2533 88323392 88321571 0.000000e+00 2305
6 TraesCS7A01G135000 chr7A 88.301 718 58 11 1 705 88442321 88441617 0.000000e+00 837
7 TraesCS7A01G135000 chr7A 87.989 716 59 11 1 705 88324119 88323420 0.000000e+00 821
8 TraesCS7A01G135000 chr7A 87.291 716 68 14 1 700 88014810 88014102 0.000000e+00 797
9 TraesCS7A01G135000 chr7A 86.319 709 64 17 2 700 88128066 88127381 0.000000e+00 741
10 TraesCS7A01G135000 chr7B 92.330 3416 204 28 702 4096 35313283 35309905 0.000000e+00 4804
11 TraesCS7A01G135000 chr7B 90.354 3442 261 35 704 4098 35512988 35509571 0.000000e+00 4451
12 TraesCS7A01G135000 chr7B 88.640 713 47 16 1 705 35513704 35513018 0.000000e+00 837
13 TraesCS7A01G135000 chr7B 90.476 168 12 4 2 169 35314478 35314315 6.900000e-53 219
14 TraesCS7A01G135000 chr7D 92.126 3429 193 36 702 4098 86924250 86920867 0.000000e+00 4765
15 TraesCS7A01G135000 chr7D 91.956 3307 195 31 702 3982 86768222 86764961 0.000000e+00 4567
16 TraesCS7A01G135000 chr7D 90.930 3429 230 38 702 4098 87212159 87208780 0.000000e+00 4534
17 TraesCS7A01G135000 chr7D 95.289 2547 96 5 702 3244 86800663 86798137 0.000000e+00 4017
18 TraesCS7A01G135000 chr7D 90.058 1720 129 21 702 2398 86927000 86925300 0.000000e+00 2191
19 TraesCS7A01G135000 chr7D 95.894 828 29 2 3274 4098 86798137 86797312 0.000000e+00 1336
20 TraesCS7A01G135000 chr7D 89.554 718 48 16 1 705 87212890 87212187 0.000000e+00 885
21 TraesCS7A01G135000 chr7D 88.640 713 54 11 1 705 86768943 86768250 0.000000e+00 843
22 TraesCS7A01G135000 chr7D 87.377 713 56 19 1 705 86927714 86927028 0.000000e+00 787
23 TraesCS7A01G135000 chr7D 87.439 613 47 12 112 703 86298641 86298038 0.000000e+00 678
24 TraesCS7A01G135000 chr7D 91.509 106 9 0 6 111 86298784 86298679 3.300000e-31 147


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 TraesCS7A01G135000 chr7A 87453523 87457620 4097 True 7568.0 7568 100.000000 1 4098 1 chr7A.!!$R1 4097
1 TraesCS7A01G135000 chr7A 88174754 88178098 3344 True 4215.0 4215 89.398000 702 4098 1 chr7A.!!$R2 3396
2 TraesCS7A01G135000 chr7A 88010706 88014810 4104 True 2627.0 4457 88.930000 1 4098 2 chr7A.!!$R3 4097
3 TraesCS7A01G135000 chr7A 88438220 88442321 4101 True 2612.5 4388 89.257000 1 4093 2 chr7A.!!$R6 4092
4 TraesCS7A01G135000 chr7A 88123986 88128066 4080 True 2574.0 4407 88.323000 2 4098 2 chr7A.!!$R4 4096
5 TraesCS7A01G135000 chr7A 88321571 88324119 2548 True 1563.0 2305 88.755500 1 2533 2 chr7A.!!$R5 2532
6 TraesCS7A01G135000 chr7B 35509571 35513704 4133 True 2644.0 4451 89.497000 1 4098 2 chr7B.!!$R2 4097
7 TraesCS7A01G135000 chr7B 35309905 35314478 4573 True 2511.5 4804 91.403000 2 4096 2 chr7B.!!$R1 4094
8 TraesCS7A01G135000 chr7D 87208780 87212890 4110 True 2709.5 4534 90.242000 1 4098 2 chr7D.!!$R5 4097
9 TraesCS7A01G135000 chr7D 86764961 86768943 3982 True 2705.0 4567 90.298000 1 3982 2 chr7D.!!$R2 3981
10 TraesCS7A01G135000 chr7D 86797312 86800663 3351 True 2676.5 4017 95.591500 702 4098 2 chr7D.!!$R3 3396
11 TraesCS7A01G135000 chr7D 86920867 86927714 6847 True 2581.0 4765 89.853667 1 4098 3 chr7D.!!$R4 4097
12 TraesCS7A01G135000 chr7D 86298038 86298784 746 True 412.5 678 89.474000 6 703 2 chr7D.!!$R1 697

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
531 1077 0.678950 AGCAACCAAAACCGAATGGG 59.321 50.000 0.00 0.0 41.17 4.00 F
792 1405 1.961793 CGTGTTCCTCAAAGGGTCAA 58.038 50.000 0.00 0.0 35.59 3.18 F
1826 5213 1.207791 GAGGAGGTGACCATGGATGT 58.792 55.000 21.47 0.0 0.00 3.06 F
2348 5784 4.789012 ACTTTGATGATTGCCGTTTCAT 57.211 36.364 0.00 0.0 35.33 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1565 4952 0.608130 CCTGTGTTCCTCATCGGTCA 59.392 55.000 0.00 0.0 0.00 4.02 R
2446 5882 0.963962 GGGTACGGGATAGATCGCAA 59.036 55.000 7.28 0.0 39.45 4.85 R
2990 6426 0.107361 CCCATCATCTGCTGCTCACA 60.107 55.000 0.00 0.0 0.00 3.58 R
3633 7106 1.381327 TCTAGGGGCTCTTGGACGG 60.381 63.158 0.00 0.0 0.00 4.79 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
55 56 4.080919 TGCACATAGTCCCATATGATAGCC 60.081 45.833 3.65 0.00 36.76 3.93
166 305 4.525996 TGAACATGAGAGAGAGAGAGAGG 58.474 47.826 0.00 0.00 0.00 3.69
177 316 3.392616 GAGAGAGAGAGGGAGAGAGATGT 59.607 52.174 0.00 0.00 0.00 3.06
284 811 7.860649 ATTGATTGGCCCATGTATTAAATCT 57.139 32.000 0.00 0.00 0.00 2.40
351 878 4.202357 TGCCTATAGATGGAATTTCGTGCT 60.202 41.667 0.00 0.00 0.00 4.40
356 883 1.594862 GATGGAATTTCGTGCTCTCGG 59.405 52.381 0.00 0.00 0.00 4.63
389 916 8.115490 AGAATGGTCACCAAAATTAAGAGAAG 57.885 34.615 0.00 0.00 36.95 2.85
424 958 2.418368 TGCTGGTAATGTGTGGATCC 57.582 50.000 4.20 4.20 0.00 3.36
431 967 5.804639 TGGTAATGTGTGGATCCTATATGC 58.195 41.667 14.23 3.68 0.00 3.14
461 998 9.191479 CTAGTTATCGTGGGGAGATATTAATCT 57.809 37.037 0.00 0.00 45.46 2.40
495 1041 7.379529 GCACATATGTATGCAATAAAACTCCAC 59.620 37.037 8.32 0.00 41.65 4.02
505 1051 5.345702 CAATAAAACTCCACTGATGCATGG 58.654 41.667 2.46 0.00 37.32 3.66
516 1062 1.281577 TGATGCATGGGTCACTAGCAA 59.718 47.619 2.46 0.00 38.85 3.91
531 1077 0.678950 AGCAACCAAAACCGAATGGG 59.321 50.000 0.00 0.00 41.17 4.00
678 1229 4.102996 TGATCAATACTCAATAGGCCTGCA 59.897 41.667 17.99 0.00 0.00 4.41
748 1361 9.874205 AATCTTTTTCAAAGAAAGACACAATGA 57.126 25.926 3.13 0.00 43.58 2.57
774 1387 4.935808 AGGTCAACTTAGAATAGTTTGGCG 59.064 41.667 0.00 0.00 36.24 5.69
792 1405 1.961793 CGTGTTCCTCAAAGGGTCAA 58.038 50.000 0.00 0.00 35.59 3.18
794 1407 2.032924 CGTGTTCCTCAAAGGGTCAAAC 59.967 50.000 0.00 0.00 35.59 2.93
805 1422 6.908825 TCAAAGGGTCAAACGATTTATCTTG 58.091 36.000 0.00 0.00 0.00 3.02
1013 1635 4.563168 CCACTCTCTCATGGATCCAATAGC 60.563 50.000 20.67 0.00 38.34 2.97
1107 1732 2.905959 TGTACGACGACGATGACAAT 57.094 45.000 15.32 0.00 42.66 2.71
1325 1953 3.768633 CGAAGGAGGAGAATGGTGG 57.231 57.895 0.00 0.00 0.00 4.61
1386 2014 4.303282 CAAATGAAAACTTTGGGGTACGG 58.697 43.478 0.00 0.00 31.43 4.02
1813 5200 2.962421 GAGGTACAAGAGGATGAGGAGG 59.038 54.545 0.00 0.00 0.00 4.30
1826 5213 1.207791 GAGGAGGTGACCATGGATGT 58.792 55.000 21.47 0.00 0.00 3.06
2005 5410 5.123227 CCAAAGAGGAACACAAGTTAGTCA 58.877 41.667 0.00 0.00 41.22 3.41
2015 5420 7.201617 GGAACACAAGTTAGTCAATGCCTATAC 60.202 40.741 0.00 0.00 38.30 1.47
2023 5428 5.189659 AGTCAATGCCTATACTCTTCGTC 57.810 43.478 0.00 0.00 0.00 4.20
2042 5448 6.680055 TCGTCGTCATTAGTTTTAGTTGTC 57.320 37.500 0.00 0.00 0.00 3.18
2116 5523 8.925161 TTATGAGGCAAGTATGTTAAATTTGC 57.075 30.769 0.00 0.00 42.43 3.68
2117 5524 6.338214 TGAGGCAAGTATGTTAAATTTGCA 57.662 33.333 0.00 0.28 44.33 4.08
2118 5525 6.753180 TGAGGCAAGTATGTTAAATTTGCAA 58.247 32.000 0.00 0.00 44.33 4.08
2208 5621 8.765488 TCCCTGCAAATTAGATATTGATGAAA 57.235 30.769 0.00 0.00 0.00 2.69
2332 5768 8.928733 CCCAATCAAACAGATCAATAAACTTTG 58.071 33.333 0.00 0.00 35.39 2.77
2348 5784 4.789012 ACTTTGATGATTGCCGTTTCAT 57.211 36.364 0.00 0.00 35.33 2.57
2432 5868 8.613482 TGTTACAAAATGTTCGTTCACTTATGA 58.387 29.630 0.00 0.00 0.00 2.15
2450 5886 9.803130 CACTTATGAATTTCTGATATACTTGCG 57.197 33.333 0.00 0.00 0.00 4.85
3086 6522 9.528489 AACAAGGGTCAGCTTATTTTTATCTTA 57.472 29.630 0.00 0.00 0.00 2.10
3157 6594 1.489481 TGCTAGCTAGGCATGTGTCT 58.511 50.000 22.10 0.00 34.56 3.41
3223 6660 0.596082 AGCCGGCATGTGTGTTTAAC 59.404 50.000 31.54 0.00 0.00 2.01
3351 6818 9.546428 AAAAATAAGTTTTTGTCATCTCCCTTG 57.454 29.630 0.00 0.00 43.82 3.61
3475 6946 3.237746 TGCAATCACCCCATGAAAAAGA 58.762 40.909 0.00 0.00 41.93 2.52
3500 6971 7.215719 ACAGGAATCTTAGCAAAAGGTTAAC 57.784 36.000 0.00 0.00 0.00 2.01
3578 7049 6.123651 ACGTTCTACTTGATAGTCAGATCCT 58.876 40.000 0.00 0.00 35.78 3.24
3579 7050 7.281098 ACGTTCTACTTGATAGTCAGATCCTA 58.719 38.462 0.00 0.00 35.78 2.94
3633 7106 4.158394 TGCATATTGGCTCTTCCTGTTTTC 59.842 41.667 0.00 0.00 35.26 2.29
3652 7125 1.395826 CCGTCCAAGAGCCCCTAGAG 61.396 65.000 0.00 0.00 0.00 2.43
3657 7131 3.967987 GTCCAAGAGCCCCTAGAGATTAA 59.032 47.826 0.00 0.00 0.00 1.40
3676 7150 9.988350 GAGATTAAATATTGTGTGGTGTTACTG 57.012 33.333 0.00 0.00 0.00 2.74
3814 7299 3.055021 GGGGGTCAAACAAAGAAACCAAA 60.055 43.478 0.00 0.00 0.00 3.28
3964 7449 6.452242 TCATGTTACGTTCTTCTTGCTCTAA 58.548 36.000 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 3.058224 AGAGGTTGCAAAACGAACATAGC 60.058 43.478 0.00 0.00 39.71 2.97
166 305 7.067615 TGACACACTTATCTTACATCTCTCTCC 59.932 40.741 0.00 0.00 0.00 3.71
204 343 8.915057 AGAGATACAAATTAATGACCCATGAG 57.085 34.615 0.00 0.00 0.00 2.90
245 772 6.073765 GGCCAATCAATTGTGTACGTATCTAG 60.074 42.308 5.13 0.00 36.06 2.43
351 878 0.613260 CCATTCTTCCCACACCGAGA 59.387 55.000 0.00 0.00 0.00 4.04
356 883 1.202879 TGGTGACCATTCTTCCCACAC 60.203 52.381 0.00 0.00 0.00 3.82
389 916 7.496529 TTACCAGCAAATGTAAGCATATCTC 57.503 36.000 0.00 0.00 34.39 2.75
402 934 3.701040 GGATCCACACATTACCAGCAAAT 59.299 43.478 6.95 0.00 0.00 2.32
424 958 5.344066 CCACGATAACTAGGCTGCATATAG 58.656 45.833 0.50 3.19 0.00 1.31
431 967 1.341531 CTCCCCACGATAACTAGGCTG 59.658 57.143 0.00 0.00 0.00 4.85
495 1041 1.134310 TGCTAGTGACCCATGCATCAG 60.134 52.381 0.00 0.00 0.00 2.90
505 1051 1.265905 CGGTTTTGGTTGCTAGTGACC 59.734 52.381 9.07 9.07 36.45 4.02
516 1062 4.167307 AGGATATACCCATTCGGTTTTGGT 59.833 41.667 0.00 0.00 45.36 3.67
678 1229 7.365741 CAAGAAGATTGCTAGAAACAACACAT 58.634 34.615 0.00 0.00 0.00 3.21
748 1361 6.164176 CCAAACTATTCTAAGTTGACCTCGT 58.836 40.000 0.00 0.00 39.62 4.18
774 1387 2.032924 CGTTTGACCCTTTGAGGAACAC 59.967 50.000 0.00 0.00 37.67 3.32
916 1534 1.969240 GCTTGGGGATGGAGAGACTCT 60.969 57.143 4.14 4.14 0.00 3.24
917 1535 0.467804 GCTTGGGGATGGAGAGACTC 59.532 60.000 0.00 0.00 0.00 3.36
918 1536 0.043940 AGCTTGGGGATGGAGAGACT 59.956 55.000 0.00 0.00 0.00 3.24
919 1537 1.794714 TAGCTTGGGGATGGAGAGAC 58.205 55.000 0.00 0.00 0.00 3.36
920 1538 2.803285 ATAGCTTGGGGATGGAGAGA 57.197 50.000 0.00 0.00 0.00 3.10
1013 1635 2.858974 AGGTCCACCCCTGGTTGG 60.859 66.667 5.41 5.41 38.90 3.77
1038 1660 0.826715 GTGAGCATGCCTCCTCTACA 59.173 55.000 15.66 0.00 39.98 2.74
1107 1732 5.176774 CACGATGTAGTTGTGCTTCTTGTTA 59.823 40.000 0.00 0.00 35.50 2.41
1365 1993 3.322541 CCCGTACCCCAAAGTTTTCATTT 59.677 43.478 0.00 0.00 0.00 2.32
1386 2014 3.539604 CATGATTGTTGTCTCCTCCTCC 58.460 50.000 0.00 0.00 0.00 4.30
1565 4952 0.608130 CCTGTGTTCCTCATCGGTCA 59.392 55.000 0.00 0.00 0.00 4.02
1693 5080 8.284945 ACAATATCATCACAAACATAAGCTGT 57.715 30.769 0.00 0.00 40.84 4.40
1813 5200 3.627395 TCCACTAACATCCATGGTCAC 57.373 47.619 12.58 0.00 33.67 3.67
1850 5237 5.777449 TCCTGATTCTTGTATCCTCCAGTA 58.223 41.667 0.00 0.00 0.00 2.74
2005 5410 3.630769 TGACGACGAAGAGTATAGGCATT 59.369 43.478 0.00 0.00 0.00 3.56
2015 5420 7.114529 ACAACTAAAACTAATGACGACGAAGAG 59.885 37.037 0.00 0.00 0.00 2.85
2075 5481 9.638239 TTGCCTCATAAAATTAATTTCAGACAC 57.362 29.630 13.68 3.12 32.27 3.67
2115 5522 8.562892 ACATCTAGTAAAGTGCAATATCATTGC 58.437 33.333 15.28 15.28 45.11 3.56
2137 5550 7.766219 AACTGTAAACGTCCATGTATACATC 57.234 36.000 15.60 4.33 33.61 3.06
2218 5644 7.877612 GGTCCAATCACATCAAAAATTTAAGGT 59.122 33.333 0.00 0.00 0.00 3.50
2332 5768 9.515020 TTTTTCTATAATGAAACGGCAATCATC 57.485 29.630 0.00 0.00 35.29 2.92
2432 5868 9.593134 GGATAGATCGCAAGTATATCAGAAATT 57.407 33.333 0.00 0.00 39.48 1.82
2446 5882 0.963962 GGGTACGGGATAGATCGCAA 59.036 55.000 7.28 0.00 39.45 4.85
2450 5886 4.460382 TGATTTACGGGTACGGGATAGATC 59.540 45.833 0.00 0.00 46.48 2.75
2502 5938 6.295719 AGTACCTATTTGACAGGTTCGAAT 57.704 37.500 0.00 0.00 44.18 3.34
2990 6426 0.107361 CCCATCATCTGCTGCTCACA 60.107 55.000 0.00 0.00 0.00 3.58
3086 6522 8.478066 TCTACTACATCTTGTTCATACATTGCT 58.522 33.333 0.00 0.00 33.44 3.91
3157 6594 5.104527 AGGAGGACAATCCGTTTATTCATGA 60.105 40.000 0.00 0.00 44.65 3.07
3172 6609 3.073798 TGTTGCCATCTTTAGGAGGACAA 59.926 43.478 0.00 0.00 0.00 3.18
3279 6746 7.986320 AGATGATGAGACTATCAAAGGTGAAAG 59.014 37.037 0.00 0.00 42.53 2.62
3335 6802 5.930837 ACAAAACAAGGGAGATGACAAAA 57.069 34.783 0.00 0.00 0.00 2.44
3475 6946 7.505923 AGTTAACCTTTTGCTAAGATTCCTGTT 59.494 33.333 0.88 0.00 0.00 3.16
3633 7106 1.381327 TCTAGGGGCTCTTGGACGG 60.381 63.158 0.00 0.00 0.00 4.79
3652 7125 8.240682 TGCAGTAACACCACACAATATTTAATC 58.759 33.333 0.00 0.00 0.00 1.75
3657 7131 6.389091 CAATGCAGTAACACCACACAATATT 58.611 36.000 0.00 0.00 0.00 1.28
3814 7299 8.387813 TGGTGAGGGTAAGATTTTTATAACTGT 58.612 33.333 0.00 0.00 0.00 3.55
3964 7449 2.454538 CTACGTCCCAACCTAGGTCTT 58.545 52.381 16.64 0.00 0.00 3.01
4049 7534 7.870509 TCTTTATGAAATGACCCATTCTGAG 57.129 36.000 0.00 0.00 32.43 3.35


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

AutoCloner maintained by Alex Coulton.