Multiple sequence alignment - TraesCS7A01G532000

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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 TraesCS7A01G532000 chr7A 100.000 4942 0 0 1 4942 710836842 710831901 0.000000e+00 9127.0
1 TraesCS7A01G532000 chr7A 96.011 2507 80 12 553 3050 707111302 707113797 0.000000e+00 4058.0
2 TraesCS7A01G532000 chr7A 94.917 1082 19 10 3864 4942 707123420 707124468 0.000000e+00 1661.0
3 TraesCS7A01G532000 chr7A 98.293 820 14 0 3045 3864 707122441 707123260 0.000000e+00 1437.0
4 TraesCS7A01G532000 chr7A 93.696 349 19 1 1 349 707110597 707110942 2.040000e-143 520.0
5 TraesCS7A01G532000 chr7A 92.593 216 14 2 350 565 707111064 707111277 4.800000e-80 309.0
6 TraesCS7A01G532000 chr7D 96.491 4617 109 20 356 4942 614680806 614676213 0.000000e+00 7579.0
7 TraesCS7A01G532000 chr7D 93.983 349 16 2 1 349 614681277 614680934 1.580000e-144 523.0
8 TraesCS7A01G532000 chr7D 92.063 63 2 3 1259 1318 614928562 614928624 8.810000e-13 86.1
9 TraesCS7A01G532000 chr4D 74.763 1902 348 80 2417 4258 323116913 323115084 0.000000e+00 732.0
10 TraesCS7A01G532000 chr4D 73.068 427 93 13 907 1319 323118821 323118403 1.120000e-26 132.0
11 TraesCS7A01G532000 chr4A 76.101 1272 225 49 2417 3641 149029698 149030937 4.260000e-165 592.0
12 TraesCS7A01G532000 chr4A 72.834 427 94 13 907 1319 149027792 149028210 5.190000e-25 126.0
13 TraesCS7A01G532000 chr4B 75.268 1399 238 58 2417 3756 403273135 403271786 7.180000e-158 568.0
14 TraesCS7A01G532000 chr4B 72.770 426 94 13 908 1319 403275077 403274660 1.870000e-24 124.0
15 TraesCS7A01G532000 chr6B 92.000 50 3 1 1253 1302 30354973 30355021 8.880000e-08 69.4
16 TraesCS7A01G532000 chr6B 95.122 41 2 0 1253 1293 30465066 30465106 1.150000e-06 65.8
17 TraesCS7A01G532000 chr6A 92.683 41 3 0 1253 1293 18080918 18080958 5.340000e-05 60.2


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 TraesCS7A01G532000 chr7A 710831901 710836842 4941 True 9127 9127 100.0000 1 4942 1 chr7A.!!$R1 4941
1 TraesCS7A01G532000 chr7A 707110597 707113797 3200 False 1629 4058 94.1000 1 3050 3 chr7A.!!$F1 3049
2 TraesCS7A01G532000 chr7A 707122441 707124468 2027 False 1549 1661 96.6050 3045 4942 2 chr7A.!!$F2 1897
3 TraesCS7A01G532000 chr7D 614676213 614681277 5064 True 4051 7579 95.2370 1 4942 2 chr7D.!!$R1 4941
4 TraesCS7A01G532000 chr4D 323115084 323118821 3737 True 432 732 73.9155 907 4258 2 chr4D.!!$R1 3351
5 TraesCS7A01G532000 chr4A 149027792 149030937 3145 False 359 592 74.4675 907 3641 2 chr4A.!!$F1 2734
6 TraesCS7A01G532000 chr4B 403271786 403275077 3291 True 346 568 74.0190 908 3756 2 chr4B.!!$R1 2848

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
235 236 0.251916 CAACCCCTGTTCCTATCGCA 59.748 55.000 0.00 0.00 30.42 5.10 F
531 653 0.787787 GGCCAAAAATCGCGGTTTTC 59.212 50.000 28.58 16.83 31.29 2.29 F
1922 2244 0.738762 CGATATCGGCAGAGGCATGG 60.739 60.000 17.51 0.00 43.71 3.66 F
2104 2434 1.674322 GGTGGACGGGACAATGTGG 60.674 63.158 0.00 0.00 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1794 2111 0.168788 ACACATTCTTCAATGCGCCG 59.831 50.000 4.18 0.0 43.03 6.46 R
2445 3142 1.565759 CATCAGGGAGGGAATTGGTCA 59.434 52.381 0.00 0.0 0.00 4.02 R
3821 4570 5.239359 AGTACGAAACAAGGGAACAAAAC 57.761 39.130 0.00 0.0 0.00 2.43 R
4309 5224 1.687612 CTTCAGCTCCACCATGGGT 59.312 57.895 18.09 0.0 38.32 4.51 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
93 94 3.077391 ACCAATCCCCAGAGAAATCCAAA 59.923 43.478 0.00 0.00 0.00 3.28
98 99 0.811281 CCAGAGAAATCCAAACGCCC 59.189 55.000 0.00 0.00 0.00 6.13
107 108 1.941377 TCCAAACGCCCTAGGTAAGA 58.059 50.000 8.29 0.00 0.00 2.10
116 117 2.559231 GCCCTAGGTAAGAATCTCCTCG 59.441 54.545 8.29 0.00 33.34 4.63
117 118 3.834938 CCCTAGGTAAGAATCTCCTCGT 58.165 50.000 8.29 0.00 33.34 4.18
177 178 2.584970 CCGCGCGCCTTCAATCTA 60.585 61.111 27.36 0.00 0.00 1.98
178 179 2.589492 CCGCGCGCCTTCAATCTAG 61.589 63.158 27.36 6.94 0.00 2.43
209 210 7.716612 TCTTGTTTTCTTTTTCCCTCAAGATC 58.283 34.615 0.00 0.00 36.31 2.75
210 211 6.072112 TGTTTTCTTTTTCCCTCAAGATCG 57.928 37.500 0.00 0.00 0.00 3.69
211 212 5.009610 TGTTTTCTTTTTCCCTCAAGATCGG 59.990 40.000 0.00 0.00 0.00 4.18
235 236 0.251916 CAACCCCTGTTCCTATCGCA 59.748 55.000 0.00 0.00 30.42 5.10
273 274 4.180817 GTCAACCTTTTCAAGTTTGTGGG 58.819 43.478 0.00 0.00 33.23 4.61
315 316 1.971357 AGACTCCGTGGTGATTTCTGT 59.029 47.619 0.00 0.00 0.00 3.41
335 336 9.745018 TTTCTGTTCAATCTCTTCCATTCTATT 57.255 29.630 0.00 0.00 0.00 1.73
363 485 9.278978 AGTTCCTTTTTGATCTTCTCTTAGTTC 57.721 33.333 0.00 0.00 0.00 3.01
405 527 2.814336 GGGTTCATTGTTGGAGTCTCAC 59.186 50.000 1.47 0.00 0.00 3.51
432 554 1.777941 ACGGGGATCTCTGTTCCTAC 58.222 55.000 0.00 0.00 33.53 3.18
487 609 1.654137 CTGTTGCCGTTGTTCGTGC 60.654 57.895 0.00 0.00 37.94 5.34
513 635 3.131396 GGCAACTCGACTATTATGGTGG 58.869 50.000 0.00 0.00 0.00 4.61
531 653 0.787787 GGCCAAAAATCGCGGTTTTC 59.212 50.000 28.58 16.83 31.29 2.29
532 654 0.787787 GCCAAAAATCGCGGTTTTCC 59.212 50.000 28.58 16.59 31.29 3.13
587 744 2.506438 CGTTCGTCCTTCCGCTCC 60.506 66.667 0.00 0.00 0.00 4.70
610 767 5.235186 CCCATACTGCTAATTGAAGTTCTCG 59.765 44.000 4.17 0.00 35.75 4.04
659 816 3.396560 TGCTCTTCAATATGCCTGATCG 58.603 45.455 0.00 0.00 0.00 3.69
678 835 1.740025 CGTTCTCATCCAAAAGAGGGC 59.260 52.381 0.00 0.00 32.76 5.19
806 963 7.558161 TGTATTAGTTTGATTCAGCTGGATG 57.442 36.000 13.71 0.00 0.00 3.51
882 1040 3.060479 AGCATACCTTATCCACCCAGA 57.940 47.619 0.00 0.00 0.00 3.86
946 1104 9.431887 ACAAGTAATTAGTTTTCGCTGATAAGA 57.568 29.630 2.65 0.00 0.00 2.10
996 1155 1.227823 TTTCAGCAGTGTGACCCGG 60.228 57.895 0.00 0.00 0.00 5.73
1196 1367 8.121305 TGCCATTACAGTACTGAATTTGATTT 57.879 30.769 29.30 5.99 0.00 2.17
1220 1391 2.023673 CCTGTCTTGTTTGCAGTGGAA 58.976 47.619 0.00 0.00 0.00 3.53
1244 1415 7.993821 AATCTCACGTACATCTACTTGATTG 57.006 36.000 0.00 0.00 32.33 2.67
1247 1418 6.150474 TCTCACGTACATCTACTTGATTGTGA 59.850 38.462 0.00 0.00 32.33 3.58
1248 1419 6.683715 TCACGTACATCTACTTGATTGTGAA 58.316 36.000 0.00 0.00 32.49 3.18
1251 1422 5.867174 CGTACATCTACTTGATTGTGAACCA 59.133 40.000 0.00 0.00 32.05 3.67
1500 1801 9.384682 CAAACATTTATTTGATCTGTTTTTGGC 57.615 29.630 4.71 0.00 41.28 4.52
1501 1802 7.350110 ACATTTATTTGATCTGTTTTTGGCG 57.650 32.000 0.00 0.00 0.00 5.69
1627 1932 7.649306 AGCTTGTGATGATTTTTACACTGTTTC 59.351 33.333 0.00 0.00 34.81 2.78
1794 2111 1.419387 AGCTATGTCCTCAATCTGCCC 59.581 52.381 0.00 0.00 0.00 5.36
1922 2244 0.738762 CGATATCGGCAGAGGCATGG 60.739 60.000 17.51 0.00 43.71 3.66
2003 2327 8.166061 ACACAATATGATCAAATATGGCCTACT 58.834 33.333 3.32 0.00 0.00 2.57
2014 2340 6.506538 AATATGGCCTACTCAAGAGACATT 57.493 37.500 3.32 0.00 29.84 2.71
2104 2434 1.674322 GGTGGACGGGACAATGTGG 60.674 63.158 0.00 0.00 0.00 4.17
2136 2466 4.320870 AGAAAGTACCAATGTTGTACCCG 58.679 43.478 0.00 0.00 0.00 5.28
2248 2695 6.617879 CATTGATGAGAAGTTGCAAGAATCA 58.382 36.000 0.00 2.53 0.00 2.57
2367 2814 9.927668 CAAGGTGATACTGGATGTTTTTAAAAT 57.072 29.630 0.55 0.00 0.00 1.82
2414 3098 6.112058 CCCTTTTCCTGTGTTTGATTTTGAA 58.888 36.000 0.00 0.00 0.00 2.69
2526 3227 5.358442 TCCATTCGGTTTTGACTCTTTTTCA 59.642 36.000 0.00 0.00 0.00 2.69
2534 3235 7.797123 CGGTTTTGACTCTTTTTCATAGTGTAC 59.203 37.037 0.00 0.00 0.00 2.90
2718 3428 5.304778 TGTGGCGCAATACTATTATGTCAT 58.695 37.500 10.83 0.00 0.00 3.06
2850 3560 3.075134 AGAATTGAAAAGGCAGGAGGACT 59.925 43.478 0.00 0.00 34.99 3.85
2981 3703 6.746104 TTTTATTTCGCTGACATTTGTGTG 57.254 33.333 0.00 0.00 0.00 3.82
3102 3824 4.937620 GTGACATGTTGTCCAGACATATGT 59.062 41.667 21.42 21.42 46.40 2.29
3169 3891 7.727578 TGTTTCTGATAGGTGTGGTCTTATA 57.272 36.000 0.00 0.00 0.00 0.98
3245 3977 6.724893 TGTTATAGCAAGTGCAGGTATCTA 57.275 37.500 6.00 0.00 45.16 1.98
3471 4212 3.996363 TGAGTTTCTTCATCGTGATGTGG 59.004 43.478 9.51 4.60 39.72 4.17
3473 4214 4.248859 AGTTTCTTCATCGTGATGTGGAG 58.751 43.478 9.51 6.93 39.72 3.86
3538 4280 4.342951 TCCCGAGTTCAAGTTAGTGAAAGA 59.657 41.667 0.00 0.00 39.18 2.52
3735 4484 5.728471 TGTGCCAAGTTTTCTTTTCATTCA 58.272 33.333 0.00 0.00 38.17 2.57
3821 4570 5.760253 CAGCCACTATTACAAAGGGACATAG 59.240 44.000 0.00 0.00 0.00 2.23
4309 5224 1.337118 GGTTCAATTCAAGGCCACCA 58.663 50.000 5.01 0.00 0.00 4.17
4586 5503 4.694509 CCACAGTTTGATCAAGAAGAGAGG 59.305 45.833 8.41 3.10 0.00 3.69
4657 5575 6.377429 TCGGAGACAGAATTATGTGTTAGACT 59.623 38.462 11.08 0.00 32.34 3.24
4693 5611 3.622459 GCAGTTGCTTCGTTGTGTT 57.378 47.368 0.00 0.00 38.21 3.32
4743 5661 7.040892 TGGATTCACTCTCTTGTTCTGATTTTG 60.041 37.037 0.00 0.00 0.00 2.44
4894 5812 7.388776 ACAGTAATCGGCAGTATATAACGACTA 59.611 37.037 0.00 0.00 36.32 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 2.091222 AGGAGATTCTTACCTAGGGCGT 60.091 50.000 14.81 0.00 31.78 5.68
98 99 3.058777 GCGACGAGGAGATTCTTACCTAG 60.059 52.174 0.00 0.00 33.89 3.02
166 167 8.499403 AAACAAGAATCTACTAGATTGAAGGC 57.501 34.615 14.89 2.11 44.41 4.35
176 177 9.862149 AGGGAAAAAGAAAACAAGAATCTACTA 57.138 29.630 0.00 0.00 0.00 1.82
177 178 8.768501 AGGGAAAAAGAAAACAAGAATCTACT 57.231 30.769 0.00 0.00 0.00 2.57
178 179 8.630037 TGAGGGAAAAAGAAAACAAGAATCTAC 58.370 33.333 0.00 0.00 0.00 2.59
200 201 0.107654 GTTGGACCCCGATCTTGAGG 60.108 60.000 0.00 0.00 0.00 3.86
273 274 2.824489 GCTGTTTAGCCTCCCCGC 60.824 66.667 0.00 0.00 44.33 6.13
353 475 0.895530 CCGCCACAGGAACTAAGAGA 59.104 55.000 0.00 0.00 36.02 3.10
354 476 0.741221 GCCGCCACAGGAACTAAGAG 60.741 60.000 0.00 0.00 36.02 2.85
405 527 1.519455 GAGATCCCCGTTGTGCTCG 60.519 63.158 0.00 0.00 0.00 5.03
432 554 2.202743 TTCCGATGGAGAAGCGCG 60.203 61.111 0.00 0.00 31.21 6.86
487 609 2.403252 AATAGTCGAGTTGCCCTTGG 57.597 50.000 0.00 0.00 0.00 3.61
513 635 0.787787 GGAAAACCGCGATTTTTGGC 59.212 50.000 13.40 0.00 31.90 4.52
532 654 3.673484 CACACGCTGCAAAGGGGG 61.673 66.667 0.00 0.00 0.00 5.40
587 744 6.042777 TCGAGAACTTCAATTAGCAGTATGG 58.957 40.000 0.00 0.00 35.86 2.74
630 787 4.641989 GGCATATTGAAGAGCAAGAGGAAA 59.358 41.667 0.00 0.00 40.42 3.13
634 791 4.449131 TCAGGCATATTGAAGAGCAAGAG 58.551 43.478 0.00 0.00 40.42 2.85
640 797 5.295950 AGAACGATCAGGCATATTGAAGAG 58.704 41.667 0.00 0.00 0.00 2.85
659 816 3.013219 GAGCCCTCTTTTGGATGAGAAC 58.987 50.000 0.00 0.00 32.44 3.01
678 835 9.454859 AGAAGAAACCAATATAGAACAAAGGAG 57.545 33.333 0.00 0.00 0.00 3.69
806 963 3.194005 TCAGGGCTTTCACCGAATATC 57.806 47.619 0.00 0.00 0.00 1.63
882 1040 4.729868 ACACAACTTGGATTTAAGAGCCT 58.270 39.130 0.00 0.00 0.00 4.58
996 1155 1.138859 GTTATTGCCTTCCCCATTGCC 59.861 52.381 0.00 0.00 0.00 4.52
1196 1367 2.942376 CACTGCAAACAAGACAGGTACA 59.058 45.455 0.00 0.00 35.70 2.90
1220 1391 7.489435 CACAATCAAGTAGATGTACGTGAGATT 59.511 37.037 20.09 10.54 46.53 2.40
1370 1587 1.069022 ACACAGATGCACATGAAACGC 60.069 47.619 0.00 0.00 0.00 4.84
1401 1618 3.493129 GCACATTCAAAGCATATGCATGG 59.507 43.478 28.62 15.61 45.16 3.66
1462 1763 1.047801 AATGTTTGGCCCCTCACAAC 58.952 50.000 0.00 0.00 0.00 3.32
1500 1801 1.296715 CCACCCTCCAACTCCTTCG 59.703 63.158 0.00 0.00 0.00 3.79
1501 1802 1.652947 TACCACCCTCCAACTCCTTC 58.347 55.000 0.00 0.00 0.00 3.46
1649 1954 5.413309 AACAAGGGTTGAATCAAACACAA 57.587 34.783 13.49 0.00 35.83 3.33
1794 2111 0.168788 ACACATTCTTCAATGCGCCG 59.831 50.000 4.18 0.00 43.03 6.46
2104 2434 5.067283 ACATTGGTACTTTCTCAAACACCAC 59.933 40.000 0.00 0.00 35.86 4.16
2136 2466 6.857777 AGCAATTGCATCTATGTAGAGAAC 57.142 37.500 30.89 0.00 45.16 3.01
2248 2695 2.776536 CAAGTCCCTCCTCCATTCATCT 59.223 50.000 0.00 0.00 0.00 2.90
2289 2736 6.897413 AGTCCATAGCCACCTTATCAAATTTT 59.103 34.615 0.00 0.00 0.00 1.82
2367 2814 6.119536 GGTTATTTGTCATGTGGTATCTCCA 58.880 40.000 0.00 0.00 45.01 3.86
2377 2824 5.838521 ACAGGAAAAGGGTTATTTGTCATGT 59.161 36.000 0.00 0.00 0.00 3.21
2427 3119 7.737972 TTGGTCAATGTTCGATAAAAGAAGA 57.262 32.000 0.00 0.00 0.00 2.87
2445 3142 1.565759 CATCAGGGAGGGAATTGGTCA 59.434 52.381 0.00 0.00 0.00 4.02
2526 3227 7.231467 ACAAATTCCAAACTGAGGTACACTAT 58.769 34.615 0.00 0.00 0.00 2.12
2534 3235 6.147864 TGAAGAACAAATTCCAAACTGAGG 57.852 37.500 0.00 0.00 35.18 3.86
2718 3428 4.321899 GCACCACTTGAATGCCTTCATTAA 60.322 41.667 5.20 0.00 42.60 1.40
2981 3703 6.569226 GCCCATCAGCAATGAATAGATTGTAC 60.569 42.308 0.96 0.00 37.59 2.90
3169 3891 9.971922 CACCTAGAAAAACAAAAGATCATTTCT 57.028 29.630 0.00 0.00 39.60 2.52
3471 4212 5.924475 TCGAGAAATGGAAAACTGAACTC 57.076 39.130 0.00 0.00 0.00 3.01
3473 4214 5.909610 CAGTTCGAGAAATGGAAAACTGAAC 59.090 40.000 7.14 0.00 43.85 3.18
3821 4570 5.239359 AGTACGAAACAAGGGAACAAAAC 57.761 39.130 0.00 0.00 0.00 2.43
4309 5224 1.687612 CTTCAGCTCCACCATGGGT 59.312 57.895 18.09 0.00 38.32 4.51
4586 5503 0.179936 CCTTCCCAGCTCAGGATCAC 59.820 60.000 2.82 0.00 32.10 3.06
4653 5571 3.779444 TCACACCCTATTGAGTGAGTCT 58.221 45.455 0.00 0.00 36.20 3.24
4657 5575 2.234661 CTGCTCACACCCTATTGAGTGA 59.765 50.000 0.00 0.00 41.24 3.41
4693 5611 0.527385 GCGCTCAAGCAAAACCAACA 60.527 50.000 0.00 0.00 42.21 3.33
4743 5661 6.012745 ACCCCATTAAGCATCTTCAATATCC 58.987 40.000 0.00 0.00 0.00 2.59
4889 5807 6.157211 AGTCAAGGCCGATTAATAATAGTCG 58.843 40.000 0.00 0.00 39.97 4.18
4894 5812 6.780706 CGTAAGTCAAGGCCGATTAATAAT 57.219 37.500 0.00 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.