Multiple sequence alignment - TraesCS7A01G092400

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 TraesCS7A01G092400 chr7A 100.000 3545 0 0 1 3545 56203978 56207522 0.000000e+00 6547
1 TraesCS7A01G092400 chr7A 85.397 2698 348 26 869 3543 8634262 8636936 0.000000e+00 2758
2 TraesCS7A01G092400 chr7A 81.784 269 43 6 1 265 8587822 8588088 1.660000e-53 220
3 TraesCS7A01G092400 chr4A 92.998 3556 206 18 1 3545 731852334 731848811 0.000000e+00 5147
4 TraesCS7A01G092400 chr4A 94.503 3220 151 15 344 3545 732354229 732357440 0.000000e+00 4942
5 TraesCS7A01G092400 chr4A 82.540 2669 413 43 915 3545 731875436 731872783 0.000000e+00 2298
6 TraesCS7A01G092400 chr4A 86.359 1818 212 13 895 2681 731664164 731662352 0.000000e+00 1951
7 TraesCS7A01G092400 chr4A 87.013 1617 183 15 853 2446 731616944 731615332 0.000000e+00 1797
8 TraesCS7A01G092400 chr4A 85.169 1780 233 19 904 2662 732378026 732379795 0.000000e+00 1796
9 TraesCS7A01G092400 chr4A 88.082 881 102 3 2667 3545 731615054 731614175 0.000000e+00 1042
10 TraesCS7A01G092400 chr4A 82.981 1087 171 10 2465 3545 732060150 732061228 0.000000e+00 970
11 TraesCS7A01G092400 chr4A 94.613 297 10 4 419 709 732395490 732395786 4.170000e-124 455
12 TraesCS7A01G092400 chr4A 82.883 555 42 13 344 894 731664820 731664315 1.940000e-122 449
13 TraesCS7A01G092400 chr4A 85.756 344 30 11 1 340 731665196 731664868 2.620000e-91 346
14 TraesCS7A01G092400 chr4A 80.802 349 42 16 1 345 732353851 732354178 2.110000e-62 250
15 TraesCS7A01G092400 chr4A 87.417 151 15 1 1 147 731606702 731606552 1.690000e-38 171
16 TraesCS7A01G092400 chr4A 82.249 169 24 5 344 510 732361343 732361507 1.330000e-29 141
17 TraesCS7A01G092400 chr7D 85.505 2656 352 24 915 3545 7749985 7752632 0.000000e+00 2741
18 TraesCS7A01G092400 chr7D 84.074 2656 386 28 915 3544 7712568 7715212 0.000000e+00 2527
19 TraesCS7A01G092400 chr7D 85.032 2492 338 27 1077 3542 7606298 7608780 0.000000e+00 2503
20 TraesCS7A01G092400 chr7D 85.490 1785 230 18 904 2668 8030614 8032389 0.000000e+00 1834
21 TraesCS7A01G092400 chr7D 84.986 1785 225 24 915 2666 7548372 7550146 0.000000e+00 1772
22 TraesCS7A01G092400 chr7D 86.871 1531 197 3 915 2443 7561060 7562588 0.000000e+00 1711
23 TraesCS7A01G092400 chr7D 86.976 883 112 3 2665 3545 7562867 7563748 0.000000e+00 990
24 TraesCS7A01G092400 chr7D 84.262 413 39 11 344 752 8222838 8223228 2.580000e-101 379
25 TraesCS7A01G092400 chr7D 83.954 349 37 8 1 345 8222462 8222795 2.050000e-82 316
26 TraesCS7A01G092400 chr7D 76.330 545 79 27 1 521 8037375 8037893 2.730000e-61 246
27 TraesCS7A01G092400 chr3B 88.549 1537 167 8 915 2447 741463153 741464684 0.000000e+00 1855
28 TraesCS7A01G092400 chr3B 88.525 61 7 0 230 290 741456834 741456894 1.360000e-09 75
29 TraesCS7A01G092400 chr5B 82.208 1096 170 20 2463 3545 37483165 37484248 0.000000e+00 920


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 TraesCS7A01G092400 chr7A 56203978 56207522 3544 False 6547.000000 6547 100.000000 1 3545 1 chr7A.!!$F3 3544
1 TraesCS7A01G092400 chr7A 8634262 8636936 2674 False 2758.000000 2758 85.397000 869 3543 1 chr7A.!!$F2 2674
2 TraesCS7A01G092400 chr4A 731848811 731852334 3523 True 5147.000000 5147 92.998000 1 3545 1 chr4A.!!$R2 3544
3 TraesCS7A01G092400 chr4A 731872783 731875436 2653 True 2298.000000 2298 82.540000 915 3545 1 chr4A.!!$R3 2630
4 TraesCS7A01G092400 chr4A 732378026 732379795 1769 False 1796.000000 1796 85.169000 904 2662 1 chr4A.!!$F2 1758
5 TraesCS7A01G092400 chr4A 732353851 732361507 7656 False 1777.666667 4942 85.851333 1 3545 3 chr4A.!!$F4 3544
6 TraesCS7A01G092400 chr4A 731614175 731616944 2769 True 1419.500000 1797 87.547500 853 3545 2 chr4A.!!$R4 2692
7 TraesCS7A01G092400 chr4A 732060150 732061228 1078 False 970.000000 970 82.981000 2465 3545 1 chr4A.!!$F1 1080
8 TraesCS7A01G092400 chr4A 731662352 731665196 2844 True 915.333333 1951 84.999333 1 2681 3 chr4A.!!$R5 2680
9 TraesCS7A01G092400 chr7D 7749985 7752632 2647 False 2741.000000 2741 85.505000 915 3545 1 chr7D.!!$F4 2630
10 TraesCS7A01G092400 chr7D 7712568 7715212 2644 False 2527.000000 2527 84.074000 915 3544 1 chr7D.!!$F3 2629
11 TraesCS7A01G092400 chr7D 7606298 7608780 2482 False 2503.000000 2503 85.032000 1077 3542 1 chr7D.!!$F2 2465
12 TraesCS7A01G092400 chr7D 8030614 8032389 1775 False 1834.000000 1834 85.490000 904 2668 1 chr7D.!!$F5 1764
13 TraesCS7A01G092400 chr7D 7548372 7550146 1774 False 1772.000000 1772 84.986000 915 2666 1 chr7D.!!$F1 1751
14 TraesCS7A01G092400 chr7D 7561060 7563748 2688 False 1350.500000 1711 86.923500 915 3545 2 chr7D.!!$F7 2630
15 TraesCS7A01G092400 chr7D 8222462 8223228 766 False 347.500000 379 84.108000 1 752 2 chr7D.!!$F8 751
16 TraesCS7A01G092400 chr7D 8037375 8037893 518 False 246.000000 246 76.330000 1 521 1 chr7D.!!$F6 520
17 TraesCS7A01G092400 chr3B 741463153 741464684 1531 False 1855.000000 1855 88.549000 915 2447 1 chr3B.!!$F2 1532
18 TraesCS7A01G092400 chr5B 37483165 37484248 1083 False 920.000000 920 82.208000 2463 3545 1 chr5B.!!$F1 1082

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
313 322 0.521291 TCACAGCAAATGCCGCTTAC 59.479 50.000 0.94 0.0 43.38 2.34 F
992 1274 1.203313 AGTCCTTGTTCCTCTGGCCTA 60.203 52.381 3.32 0.0 0.00 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1362 1644 0.522180 TCTCGAGGACGTTCTTGAGC 59.478 55.000 29.78 3.30 42.34 4.26 R
2860 3234 2.359107 CCGCAGCTCCTTGCAAGA 60.359 61.111 28.05 12.59 44.28 3.02 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
34 35 3.746045 AATCCTTTCCATGCATCATGC 57.254 42.857 1.35 1.35 45.29 4.06
97 98 0.972883 ACTCTGGGTTCACTGAGCTC 59.027 55.000 6.82 6.82 39.27 4.09
111 116 6.283694 TCACTGAGCTCACCATAATATGAAC 58.716 40.000 13.74 0.00 0.00 3.18
181 190 4.852697 AGGAGAAAAAGGATTACCAGGTCT 59.147 41.667 0.00 0.00 38.94 3.85
208 217 1.433879 CGCCTCCGGTCTAGTTCAG 59.566 63.158 0.00 0.00 0.00 3.02
297 306 7.489574 AGTGAGAAAAGTCTTCATTCTTCAC 57.510 36.000 14.25 14.25 33.73 3.18
302 311 6.319658 AGAAAAGTCTTCATTCTTCACAGCAA 59.680 34.615 0.00 0.00 29.35 3.91
313 322 0.521291 TCACAGCAAATGCCGCTTAC 59.479 50.000 0.94 0.00 43.38 2.34
341 350 8.358148 GTCCTATCTACGAGTTGGAAAATGATA 58.642 37.037 0.00 0.00 0.00 2.15
414 486 8.405531 AGAGCTTAGCTTGAATATCGATATCTC 58.594 37.037 18.01 16.25 39.88 2.75
568 642 5.858381 TCTTATCTCCATTTCCTTCCATCG 58.142 41.667 0.00 0.00 0.00 3.84
569 643 3.498774 ATCTCCATTTCCTTCCATCGG 57.501 47.619 0.00 0.00 0.00 4.18
742 820 1.801178 GCTCTTCTTCGGTTGTTCTGG 59.199 52.381 0.00 0.00 0.00 3.86
744 822 3.060602 CTCTTCTTCGGTTGTTCTGGTC 58.939 50.000 0.00 0.00 0.00 4.02
748 826 4.675976 TCTTCGGTTGTTCTGGTCTTTA 57.324 40.909 0.00 0.00 0.00 1.85
992 1274 1.203313 AGTCCTTGTTCCTCTGGCCTA 60.203 52.381 3.32 0.00 0.00 3.93
1362 1644 3.253188 TCCGTTTTGAAATGAGCAGGAAG 59.747 43.478 0.00 0.00 0.00 3.46
1472 1758 2.596851 ATCCTTGGCGGCAGACACT 61.597 57.895 12.87 0.00 33.22 3.55
1634 1920 6.146216 CGACTCTTGCTAAGATGGTGTATAG 58.854 44.000 0.00 0.00 36.82 1.31
1722 2009 4.939439 GCCATTGCTCTTTTGAAATCCATT 59.061 37.500 0.00 0.00 33.53 3.16
1755 2042 8.213518 TGGCTGTAAATAAAAGATGTGATCTC 57.786 34.615 0.00 0.00 39.08 2.75
1796 2083 2.130395 GCAAAAGCAACTTCAGGAAGC 58.870 47.619 8.89 0.00 41.99 3.86
1986 2273 3.718956 AGCCCCATGAGCTAGTATTTCTT 59.281 43.478 8.29 0.00 39.29 2.52
2112 2408 0.905357 GAGGGTTGCCTCTTGCTCTA 59.095 55.000 0.00 0.00 42.00 2.43
2542 2874 8.743085 ATGTGCAAGTATAGATGAACTGAATT 57.257 30.769 0.00 0.00 0.00 2.17
2860 3234 1.084370 GCAAACGCTGAGGCTCGTAT 61.084 55.000 10.42 0.00 38.03 3.06
2952 3326 6.874134 TCTTTGGTTGTGATAGTCTTAGAAGC 59.126 38.462 0.00 0.00 0.00 3.86
3065 3439 2.498167 AGACTTGCAACACCTTAGCAG 58.502 47.619 0.00 0.00 39.72 4.24
3147 3524 7.042523 CCAACCTCAGTCAAAAGCAAAATTTAG 60.043 37.037 0.00 0.00 0.00 1.85
3188 3565 5.792741 TGGGACCAAAAATTTCATGATGAC 58.207 37.500 0.00 0.00 0.00 3.06
3231 3620 4.943705 TGCTCCAATGTTTAGAACCTCATC 59.056 41.667 0.00 0.00 0.00 2.92
3478 3871 5.701224 AGGACACATTACTCCTTTCCAAAA 58.299 37.500 0.00 0.00 32.53 2.44
3482 3875 7.931407 GGACACATTACTCCTTTCCAAAATTTT 59.069 33.333 0.00 0.00 0.00 1.82
3523 3916 2.035449 GGTTGTTTGAGTTACCAAGCCC 59.965 50.000 0.00 0.00 31.07 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
197 206 4.142049 ACTTGCTCTATGCTGAACTAGACC 60.142 45.833 0.00 0.00 43.37 3.85
208 217 2.275318 GACCTGTCACTTGCTCTATGC 58.725 52.381 0.00 0.00 43.25 3.14
302 311 2.700897 AGATAGGACAGTAAGCGGCATT 59.299 45.455 1.45 0.00 0.00 3.56
313 322 5.578005 TTTCCAACTCGTAGATAGGACAG 57.422 43.478 0.00 0.00 33.89 3.51
569 643 2.533391 GATTGCGTGGTTGCTGGAGC 62.533 60.000 0.00 0.00 42.50 4.70
839 949 3.742433 ATAGCTCTTGTTCATCCCTCG 57.258 47.619 0.00 0.00 0.00 4.63
992 1274 1.470098 GCGATTCTGCCATGTTCTTGT 59.530 47.619 0.00 0.00 0.00 3.16
1274 1556 2.871096 AGTGGACCTGCCGATTTTAA 57.129 45.000 0.00 0.00 40.66 1.52
1362 1644 0.522180 TCTCGAGGACGTTCTTGAGC 59.478 55.000 29.78 3.30 42.34 4.26
1472 1758 4.838423 TGGTAGAGTCATCCAGTTTTGAGA 59.162 41.667 2.76 0.00 0.00 3.27
1634 1920 8.170444 GAAATGTTTCTGGACCTCTTGGTCAC 62.170 46.154 15.84 6.61 46.61 3.67
1755 2042 2.864114 CAGCTCAATGGTGTCAGGG 58.136 57.895 0.00 0.00 39.17 4.45
1986 2273 3.713248 AGTCCCATGAATCATCTGCACTA 59.287 43.478 0.00 0.00 0.00 2.74
2112 2408 4.222336 TCAACAATCCACCCATTGTCTTT 58.778 39.130 0.00 0.00 44.62 2.52
2542 2874 6.434028 ACATCTTTTAACAATGCCTTCTGCTA 59.566 34.615 0.00 0.00 42.00 3.49
2860 3234 2.359107 CCGCAGCTCCTTGCAAGA 60.359 61.111 28.05 12.59 44.28 3.02
3065 3439 6.072783 GCTCAAATTCAATATCTCCAGCCTAC 60.073 42.308 0.00 0.00 0.00 3.18
3147 3524 2.291741 CCCAAGAGAACAACAACTCAGC 59.708 50.000 0.00 0.00 35.83 4.26
3188 3565 3.619038 GCACTTCTTCGACATCTTTAGGG 59.381 47.826 0.00 0.00 0.00 3.53
3259 3649 7.090319 TGTGATATTTCTAGGCCACCATATT 57.910 36.000 5.01 0.00 0.00 1.28
3397 3787 6.648725 GGTCAAGTTATCCATCTTCTCTATGC 59.351 42.308 0.00 0.00 0.00 3.14
3478 3871 5.644188 TCATCCTCTTCAACCTTGGAAAAT 58.356 37.500 0.00 0.00 0.00 1.82
3482 3875 2.573462 CCTCATCCTCTTCAACCTTGGA 59.427 50.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.