Multiple sequence alignment - TraesCS7B01G470000

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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 TraesCS7B01G470000 chr7B 100.000 2294 0 0 1 2294 726364932 726362639 0.000000e+00 4237
1 TraesCS7B01G470000 chr7B 79.535 430 65 9 1665 2093 713513959 713513552 3.730000e-73 285
2 TraesCS7B01G470000 chrUn 99.284 1536 10 1 759 2294 330580603 330579069 0.000000e+00 2774
3 TraesCS7B01G470000 chrUn 98.907 366 3 1 1 365 388972092 388971727 0.000000e+00 652
4 TraesCS7B01G470000 chrUn 99.167 360 3 0 4 363 308512985 308512626 0.000000e+00 649
5 TraesCS7B01G470000 chr5A 96.705 607 13 2 951 1550 608438998 608438392 0.000000e+00 1003
6 TraesCS7B01G470000 chr5A 95.580 543 16 1 411 953 608441620 608441086 0.000000e+00 863
7 TraesCS7B01G470000 chr7A 94.144 666 16 7 302 953 690016979 690017635 0.000000e+00 992
8 TraesCS7B01G470000 chr7A 94.911 393 13 2 1162 1547 578060984 578061376 1.950000e-170 608
9 TraesCS7B01G470000 chr7A 90.805 435 17 8 295 719 578060556 578060977 5.530000e-156 560
10 TraesCS7B01G470000 chr7A 77.090 598 99 20 1618 2207 712467611 712467044 6.150000e-81 311
11 TraesCS7B01G470000 chr5B 93.355 602 23 6 302 894 458622867 458623460 0.000000e+00 874
12 TraesCS7B01G470000 chr5B 93.642 173 7 1 1379 1547 458623457 458623629 2.920000e-64 255
13 TraesCS7B01G470000 chr3A 95.345 537 15 3 302 837 658046711 658046184 0.000000e+00 845
14 TraesCS7B01G470000 chr3A 93.863 277 9 3 1279 1547 658046177 658045901 5.900000e-111 411
15 TraesCS7B01G470000 chr3A 94.215 242 7 2 1313 1547 655805542 655805783 1.680000e-96 363
16 TraesCS7B01G470000 chr6B 87.003 754 65 13 1549 2290 718480214 718479482 0.000000e+00 819
17 TraesCS7B01G470000 chr6B 79.690 581 99 10 1712 2290 718591611 718591048 3.550000e-108 401
18 TraesCS7B01G470000 chr6B 88.312 308 23 9 4 301 718480511 718480207 7.790000e-95 357
19 TraesCS7B01G470000 chr6B 75.552 634 123 23 1678 2290 718597892 718597270 1.340000e-72 283
20 TraesCS7B01G470000 chr6B 71.971 421 94 17 1785 2185 718231113 718231529 4.030000e-18 102
21 TraesCS7B01G470000 chr4A 91.002 489 22 3 302 781 702011110 702010635 6.910000e-180 640
22 TraesCS7B01G470000 chr6A 91.026 468 21 3 300 758 577694689 577695144 1.510000e-171 612
23 TraesCS7B01G470000 chr6A 91.026 468 21 3 300 758 577712263 577712718 1.510000e-171 612
24 TraesCS7B01G470000 chr6A 94.340 265 7 3 1290 1547 577695140 577695403 1.280000e-107 399
25 TraesCS7B01G470000 chr6A 94.340 265 7 3 1290 1547 577712714 577712977 1.280000e-107 399
26 TraesCS7B01G470000 chr6A 83.990 406 39 9 1908 2294 616794230 616794628 1.290000e-97 366
27 TraesCS7B01G470000 chr3B 91.126 462 17 8 302 753 590445549 590445102 2.520000e-169 604
28 TraesCS7B01G470000 chr3B 96.353 329 6 2 1223 1547 590445109 590444783 9.330000e-149 536
29 TraesCS7B01G470000 chr2A 92.288 389 12 4 385 763 762725382 762725762 9.330000e-149 536
30 TraesCS7B01G470000 chr7D 89.189 407 41 3 951 1354 126610089 126609683 2.630000e-139 505
31 TraesCS7B01G470000 chr7D 88.780 410 43 2 948 1354 612425885 612426294 1.220000e-137 499
32 TraesCS7B01G470000 chr7D 88.725 408 42 4 951 1354 8440541 8440134 1.580000e-136 496
33 TraesCS7B01G470000 chr7D 88.321 411 44 3 948 1354 180788424 180788834 7.360000e-135 490
34 TraesCS7B01G470000 chr6D 89.189 407 41 3 951 1354 395320191 395319785 2.630000e-139 505
35 TraesCS7B01G470000 chr6D 88.537 410 44 2 948 1354 465190510 465190919 5.690000e-136 494
36 TraesCS7B01G470000 chr3D 89.303 402 40 3 951 1349 573154676 573154275 3.400000e-138 501


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 TraesCS7B01G470000 chr7B 726362639 726364932 2293 True 4237.0 4237 100.0000 1 2294 1 chr7B.!!$R2 2293
1 TraesCS7B01G470000 chrUn 330579069 330580603 1534 True 2774.0 2774 99.2840 759 2294 1 chrUn.!!$R2 1535
2 TraesCS7B01G470000 chr5A 608438392 608441620 3228 True 933.0 1003 96.1425 411 1550 2 chr5A.!!$R1 1139
3 TraesCS7B01G470000 chr7A 690016979 690017635 656 False 992.0 992 94.1440 302 953 1 chr7A.!!$F1 651
4 TraesCS7B01G470000 chr7A 578060556 578061376 820 False 584.0 608 92.8580 295 1547 2 chr7A.!!$F2 1252
5 TraesCS7B01G470000 chr7A 712467044 712467611 567 True 311.0 311 77.0900 1618 2207 1 chr7A.!!$R1 589
6 TraesCS7B01G470000 chr5B 458622867 458623629 762 False 564.5 874 93.4985 302 1547 2 chr5B.!!$F1 1245
7 TraesCS7B01G470000 chr3A 658045901 658046711 810 True 628.0 845 94.6040 302 1547 2 chr3A.!!$R1 1245
8 TraesCS7B01G470000 chr6B 718479482 718480511 1029 True 588.0 819 87.6575 4 2290 2 chr6B.!!$R3 2286
9 TraesCS7B01G470000 chr6B 718591048 718591611 563 True 401.0 401 79.6900 1712 2290 1 chr6B.!!$R1 578
10 TraesCS7B01G470000 chr6B 718597270 718597892 622 True 283.0 283 75.5520 1678 2290 1 chr6B.!!$R2 612
11 TraesCS7B01G470000 chr6A 577694689 577695403 714 False 505.5 612 92.6830 300 1547 2 chr6A.!!$F2 1247
12 TraesCS7B01G470000 chr6A 577712263 577712977 714 False 505.5 612 92.6830 300 1547 2 chr6A.!!$F3 1247
13 TraesCS7B01G470000 chr3B 590444783 590445549 766 True 570.0 604 93.7395 302 1547 2 chr3B.!!$R1 1245

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
190 192 1.269448 CAATTTTGCAGCCCGTGTACT 59.731 47.619 0.0 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1775 4021 0.755698 ATGGTATCCGCAGACCTCGT 60.756 55.0 0.0 0.0 34.64 4.18 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
95 97 2.041485 TCACCAATCTGCATCCCTGAAA 59.959 45.455 0.00 0.0 0.00 2.69
190 192 1.269448 CAATTTTGCAGCCCGTGTACT 59.731 47.619 0.00 0.0 0.00 2.73
197 199 1.399714 CAGCCCGTGTACTATGAGGA 58.600 55.000 0.00 0.0 0.00 3.71
232 244 2.119495 ACATGGTAACCCTCTAGGCAG 58.881 52.381 0.00 0.0 40.58 4.85
260 282 3.108289 CCGCGCTCACAGACACTG 61.108 66.667 5.56 0.0 37.52 3.66
261 283 2.355126 CGCGCTCACAGACACTGT 60.355 61.111 5.56 0.0 46.51 3.55
290 312 3.115892 GATCGTGGACGGCGCAAA 61.116 61.111 10.83 0.0 40.29 3.68
298 320 3.919973 GACGGCGCAAACCCTCGTA 62.920 63.158 10.83 0.0 34.06 3.43
527 575 2.203788 TCTGGTCCTGGTCGCCTT 60.204 61.111 0.00 0.0 0.00 4.35
535 583 3.503839 TGGTCGCCTTGGGGGTTT 61.504 61.111 3.89 0.0 36.95 3.27
648 697 3.774766 GGTGGCCCTTTAATCCTTGATTT 59.225 43.478 0.00 0.0 33.95 2.17
651 700 3.490933 GGCCCTTTAATCCTTGATTTCGC 60.491 47.826 0.00 0.0 33.95 4.70
691 740 5.934935 TCTTGGTACGGTTGATTTTCTTC 57.065 39.130 0.00 0.0 0.00 2.87
814 863 2.297033 ACGAAACCTAAGTTCGGTGCTA 59.703 45.455 10.85 0.0 34.19 3.49
1036 3175 5.551233 AGATTCTGCAGTTTGTTACAGCTA 58.449 37.500 14.67 0.0 39.76 3.32
1203 3342 2.440517 TGGCCATGTGCTGTATTGAT 57.559 45.000 0.00 0.0 40.92 2.57
1775 4021 4.651008 GTCGACCGTCGGCACCAA 62.651 66.667 20.27 0.0 45.01 3.67
1778 4024 4.651008 GACCGTCGGCACCAACGA 62.651 66.667 12.28 0.0 41.29 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 42 3.699067 GCACGCCTCTTACGAATAGTAA 58.301 45.455 0.00 0.00 42.56 2.24
95 97 7.556733 TTACGACAGTAAAATTGAACCACTT 57.443 32.000 0.00 0.00 39.64 3.16
167 169 1.139163 CACGGGCTGCAAAATTGTTC 58.861 50.000 0.50 0.00 0.00 3.18
190 192 1.965414 TGGGCTTTGAGGTCCTCATA 58.035 50.000 22.45 16.35 40.39 2.15
197 199 1.693606 CCATGTTTTGGGCTTTGAGGT 59.306 47.619 0.00 0.00 42.33 3.85
255 277 1.908793 CCTCCCGGAGACACAGTGT 60.909 63.158 16.69 5.68 0.00 3.55
256 278 0.972983 ATCCTCCCGGAGACACAGTG 60.973 60.000 16.69 0.00 44.06 3.66
257 279 0.684805 GATCCTCCCGGAGACACAGT 60.685 60.000 16.69 0.00 44.06 3.55
258 280 1.729470 CGATCCTCCCGGAGACACAG 61.729 65.000 16.69 0.00 44.06 3.66
259 281 1.753078 CGATCCTCCCGGAGACACA 60.753 63.158 16.69 0.00 44.06 3.72
260 282 1.753463 ACGATCCTCCCGGAGACAC 60.753 63.158 16.69 5.47 44.06 3.67
261 283 1.753078 CACGATCCTCCCGGAGACA 60.753 63.158 16.69 2.17 44.06 3.41
262 284 2.491022 CCACGATCCTCCCGGAGAC 61.491 68.421 16.69 6.15 44.06 3.36
293 315 1.716826 GAGCCGACCCTGACTACGAG 61.717 65.000 0.00 0.00 0.00 4.18
294 316 1.748122 GAGCCGACCCTGACTACGA 60.748 63.158 0.00 0.00 0.00 3.43
295 317 1.749638 AGAGCCGACCCTGACTACG 60.750 63.158 0.00 0.00 0.00 3.51
296 318 1.668101 CCAGAGCCGACCCTGACTAC 61.668 65.000 0.00 0.00 32.37 2.73
297 319 1.379977 CCAGAGCCGACCCTGACTA 60.380 63.158 0.00 0.00 32.37 2.59
298 320 2.681778 CCAGAGCCGACCCTGACT 60.682 66.667 0.00 0.00 32.37 3.41
362 387 4.785346 ATATGTATCTGATGATGCCCCC 57.215 45.455 0.00 0.00 34.94 5.40
363 388 6.989169 GTCTTATATGTATCTGATGATGCCCC 59.011 42.308 0.00 0.00 34.94 5.80
364 389 7.790027 AGTCTTATATGTATCTGATGATGCCC 58.210 38.462 0.00 0.00 34.94 5.36
527 575 3.961414 GAGGCGGACAAACCCCCA 61.961 66.667 0.00 0.00 38.99 4.96
648 697 0.174845 AATCAAGACGGGAATCGCGA 59.825 50.000 25.89 13.09 42.31 5.87
651 700 4.437390 CCAAGAAAATCAAGACGGGAATCG 60.437 45.833 0.00 0.00 45.88 3.34
691 740 4.673534 AATACGTTTACGCCAAGAAAGG 57.326 40.909 0.00 0.00 44.43 3.11
1036 3175 7.285566 ACTGACACATTTGGATAGCAATCTAT 58.714 34.615 0.00 0.00 38.19 1.98
1203 3342 8.717717 AGATCAATGTTGTCCAAGATATCCTTA 58.282 33.333 0.00 0.00 32.86 2.69
1775 4021 0.755698 ATGGTATCCGCAGACCTCGT 60.756 55.000 0.00 0.00 34.64 4.18
1778 4024 1.043816 CAGATGGTATCCGCAGACCT 58.956 55.000 0.00 0.00 34.64 3.85


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

AutoCloner maintained by Alex Coulton.