Multiple sequence alignment - TraesCS7B01G213500

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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 TraesCS7B01G213500 chr7B 100.000 2462 0 0 1 2462 392025647 392023186 0.000000e+00 4547
1 TraesCS7B01G213500 chr4B 95.194 2476 102 7 1 2462 141019345 141021817 0.000000e+00 3897
2 TraesCS7B01G213500 chr4B 81.557 732 109 15 1737 2462 488105094 488105805 4.560000e-162 580
3 TraesCS7B01G213500 chr1D 91.360 1632 94 22 4 1626 406719455 406717862 0.000000e+00 2189
4 TraesCS7B01G213500 chr1D 91.208 853 52 8 1626 2462 406717755 406716910 0.000000e+00 1138
5 TraesCS7B01G213500 chr2D 93.630 1193 67 6 421 1607 557120723 557119534 0.000000e+00 1773
6 TraesCS7B01G213500 chr2D 90.522 1245 89 13 386 1626 373385372 373386591 0.000000e+00 1618
7 TraesCS7B01G213500 chr2D 89.918 853 65 7 1626 2462 633361501 633362348 0.000000e+00 1079
8 TraesCS7B01G213500 chr2D 93.963 646 36 2 593 1235 633360608 633361253 0.000000e+00 974
9 TraesCS7B01G213500 chr2D 89.723 759 58 6 1626 2368 557119414 557118660 0.000000e+00 952
10 TraesCS7B01G213500 chr2D 90.215 511 31 5 1648 2142 373386712 373387219 0.000000e+00 649
11 TraesCS7B01G213500 chr2D 90.212 378 32 3 1 375 557121110 557120735 2.850000e-134 488
12 TraesCS7B01G213500 chr2D 91.054 313 27 1 2150 2462 373390367 373390678 2.930000e-114 422
13 TraesCS7B01G213500 chr5D 93.456 1192 71 5 421 1607 448518704 448517515 0.000000e+00 1762
14 TraesCS7B01G213500 chr5D 88.202 873 63 7 1626 2462 448517391 448516523 0.000000e+00 1005
15 TraesCS7B01G213500 chr7A 90.281 1245 92 7 386 1626 609997994 609999213 0.000000e+00 1602
16 TraesCS7B01G213500 chr7A 88.672 512 37 6 1648 2142 609999334 609999841 2.710000e-169 604
17 TraesCS7B01G213500 chr3D 90.661 1210 89 9 420 1626 387337115 387335927 0.000000e+00 1587
18 TraesCS7B01G213500 chr3D 89.449 853 66 10 1626 2462 534038438 534039282 0.000000e+00 1055
19 TraesCS7B01G213500 chr3D 94.058 690 38 2 940 1626 534037597 534038286 0.000000e+00 1044
20 TraesCS7B01G213500 chr3D 89.669 513 32 6 1648 2142 387335806 387335297 3.450000e-178 634
21 TraesCS7B01G213500 chr2B 84.674 1442 138 44 940 2317 747620202 747621624 0.000000e+00 1362
22 TraesCS7B01G213500 chrUn 92.115 799 55 6 434 1226 429716678 429717474 0.000000e+00 1120
23 TraesCS7B01G213500 chrUn 91.990 799 56 6 434 1226 31833026 31833822 0.000000e+00 1114
24 TraesCS7B01G213500 chrUn 89.474 855 67 14 1626 2462 253773747 253774596 0.000000e+00 1059
25 TraesCS7B01G213500 chrUn 90.212 378 32 3 1 375 31832641 31833016 2.850000e-134 488
26 TraesCS7B01G213500 chr4A 95.693 534 23 0 4 537 733226733 733226200 0.000000e+00 859
27 TraesCS7B01G213500 chr4A 95.506 534 24 0 4 537 733176138 733175605 0.000000e+00 854
28 TraesCS7B01G213500 chr4A 95.506 534 24 0 4 537 733201945 733201412 0.000000e+00 854
29 TraesCS7B01G213500 chr4A 95.560 518 23 0 4 521 733044200 733043683 0.000000e+00 830
30 TraesCS7B01G213500 chr4A 93.633 534 25 2 4 537 733103762 733103238 0.000000e+00 789


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 TraesCS7B01G213500 chr7B 392023186 392025647 2461 True 4547.000000 4547 100.000000 1 2462 1 chr7B.!!$R1 2461
1 TraesCS7B01G213500 chr4B 141019345 141021817 2472 False 3897.000000 3897 95.194000 1 2462 1 chr4B.!!$F1 2461
2 TraesCS7B01G213500 chr4B 488105094 488105805 711 False 580.000000 580 81.557000 1737 2462 1 chr4B.!!$F2 725
3 TraesCS7B01G213500 chr1D 406716910 406719455 2545 True 1663.500000 2189 91.284000 4 2462 2 chr1D.!!$R1 2458
4 TraesCS7B01G213500 chr2D 557118660 557121110 2450 True 1071.000000 1773 91.188333 1 2368 3 chr2D.!!$R1 2367
5 TraesCS7B01G213500 chr2D 633360608 633362348 1740 False 1026.500000 1079 91.940500 593 2462 2 chr2D.!!$F2 1869
6 TraesCS7B01G213500 chr2D 373385372 373390678 5306 False 896.333333 1618 90.597000 386 2462 3 chr2D.!!$F1 2076
7 TraesCS7B01G213500 chr5D 448516523 448518704 2181 True 1383.500000 1762 90.829000 421 2462 2 chr5D.!!$R1 2041
8 TraesCS7B01G213500 chr7A 609997994 609999841 1847 False 1103.000000 1602 89.476500 386 2142 2 chr7A.!!$F1 1756
9 TraesCS7B01G213500 chr3D 387335297 387337115 1818 True 1110.500000 1587 90.165000 420 2142 2 chr3D.!!$R1 1722
10 TraesCS7B01G213500 chr3D 534037597 534039282 1685 False 1049.500000 1055 91.753500 940 2462 2 chr3D.!!$F1 1522
11 TraesCS7B01G213500 chr2B 747620202 747621624 1422 False 1362.000000 1362 84.674000 940 2317 1 chr2B.!!$F1 1377
12 TraesCS7B01G213500 chrUn 429716678 429717474 796 False 1120.000000 1120 92.115000 434 1226 1 chrUn.!!$F2 792
13 TraesCS7B01G213500 chrUn 253773747 253774596 849 False 1059.000000 1059 89.474000 1626 2462 1 chrUn.!!$F1 836
14 TraesCS7B01G213500 chrUn 31832641 31833822 1181 False 801.000000 1114 91.101000 1 1226 2 chrUn.!!$F3 1225
15 TraesCS7B01G213500 chr4A 733226200 733226733 533 True 859.000000 859 95.693000 4 537 1 chr4A.!!$R5 533
16 TraesCS7B01G213500 chr4A 733175605 733176138 533 True 854.000000 854 95.506000 4 537 1 chr4A.!!$R3 533
17 TraesCS7B01G213500 chr4A 733201412 733201945 533 True 854.000000 854 95.506000 4 537 1 chr4A.!!$R4 533
18 TraesCS7B01G213500 chr4A 733043683 733044200 517 True 830.000000 830 95.560000 4 521 1 chr4A.!!$R1 517
19 TraesCS7B01G213500 chr4A 733103238 733103762 524 True 789.000000 789 93.633000 4 537 1 chr4A.!!$R2 533

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
391 393 0.391661 ACGCCATCTTGACGCTCAAT 60.392 50.0 1.76 0.0 35.59 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 2197 1.078759 GCAACATCTCTCGGTCACGG 61.079 60.0 0.0 0.0 41.39 4.94 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
71 72 8.815565 TTTGTTCCATCCAGTTTTATATGCTA 57.184 30.769 0.00 0.00 0.00 3.49
173 174 5.582665 CCCTTGAGCTTTATGAGTGTCTAAC 59.417 44.000 0.00 0.00 0.00 2.34
202 203 5.221244 GGTTTGCTCCAATCAGTGTTAAACT 60.221 40.000 0.00 0.00 40.93 2.66
215 216 8.106247 TCAGTGTTAAACTCTGTTCAGTTTTT 57.894 30.769 4.03 3.95 42.81 1.94
232 234 6.809689 TCAGTTTTTAGCATTGATGAAGCATG 59.190 34.615 0.00 0.00 0.00 4.06
234 236 4.722361 TTTAGCATTGATGAAGCATGCA 57.278 36.364 21.98 0.00 40.41 3.96
248 250 2.835764 AGCATGCAGGGTCATGAAAATT 59.164 40.909 21.98 0.00 44.94 1.82
328 330 7.985184 GTGTATGAGTGTCTAATATTTGTCCCA 59.015 37.037 0.00 0.00 0.00 4.37
336 338 7.012421 GTGTCTAATATTTGTCCCACATCTTCC 59.988 40.741 0.00 0.00 0.00 3.46
391 393 0.391661 ACGCCATCTTGACGCTCAAT 60.392 50.000 1.76 0.00 35.59 2.57
605 616 9.857345 AATGACCAAAATCCCCCATATAATATT 57.143 29.630 0.00 0.00 0.00 1.28
609 620 6.323739 CCAAAATCCCCCATATAATATTCGGG 59.676 42.308 0.00 0.00 36.59 5.14
694 705 6.578944 ACGTGTATCATCAGCCTTAAATGTA 58.421 36.000 0.00 0.00 0.00 2.29
699 710 9.851686 TGTATCATCAGCCTTAAATGTATTTCT 57.148 29.630 0.00 0.00 0.00 2.52
1057 1072 5.391312 TGATCAAGAAGACACGAATCAGA 57.609 39.130 0.00 0.00 0.00 3.27
1353 1368 5.238624 ACTATGATATTCTGCAGGCACAT 57.761 39.130 15.13 14.13 0.00 3.21
1417 1432 1.052617 TCATTTGACGGAGGTGGTCA 58.947 50.000 0.00 0.00 42.31 4.02
1458 1476 1.152777 CAAGAAGCCACCACCACCA 60.153 57.895 0.00 0.00 0.00 4.17
1497 1515 5.505780 TGAGGGGGTCTACATTGTTATTTG 58.494 41.667 0.00 0.00 0.00 2.32
1630 1804 5.583854 GTGCTTGATGTCAATGTGATACTCT 59.416 40.000 0.00 0.00 35.02 3.24
1635 1809 8.797350 TTGATGTCAATGTGATACTCTCAAAT 57.203 30.769 0.00 0.00 35.07 2.32
1700 1889 3.393941 CCTCTCCTATCTTTGGGATGCTT 59.606 47.826 0.00 0.00 35.98 3.91
1702 1891 4.785301 TCTCCTATCTTTGGGATGCTTTG 58.215 43.478 0.00 0.00 35.98 2.77
1742 1931 3.254060 CTCATTACCAGTGTGTTCTCCG 58.746 50.000 0.00 0.00 0.00 4.63
1743 1954 1.732259 CATTACCAGTGTGTTCTCCGC 59.268 52.381 0.00 0.00 0.00 5.54
1772 1983 2.188994 GATGGCTTCCGCTGCTCT 59.811 61.111 0.00 0.00 36.09 4.09
1842 2054 1.757699 AGTTTTACCCAGGCGCAAAAA 59.242 42.857 10.83 2.96 0.00 1.94
1852 2064 2.481185 CAGGCGCAAAAATTTTGATGCT 59.519 40.909 24.48 14.19 36.67 3.79
1870 2082 3.426568 GACGAGCAGCAGCAACCC 61.427 66.667 3.17 0.00 45.49 4.11
1883 2095 3.181510 GCAGCAACCCGAGTACTTATTTG 60.182 47.826 0.00 0.19 0.00 2.32
1945 2187 3.648067 AGAGAGAGAGAGAGATGGATCGT 59.352 47.826 0.00 0.00 0.00 3.73
1949 2191 6.542821 AGAGAGAGAGAGATGGATCGTTTAT 58.457 40.000 0.00 0.00 0.00 1.40
1990 2232 2.079158 GTTGCTGATGTGCTGCTTCTA 58.921 47.619 0.00 0.00 41.53 2.10
1992 2234 1.002315 TGCTGATGTGCTGCTTCTACA 59.998 47.619 0.00 0.00 41.53 2.74
2005 2247 5.619757 GCTGCTTCTACAAATGCATACACAA 60.620 40.000 0.00 0.00 34.79 3.33
2007 2249 6.923012 TGCTTCTACAAATGCATACACAAAT 58.077 32.000 0.00 0.00 0.00 2.32
2012 2254 7.342581 TCTACAAATGCATACACAAATAGGGA 58.657 34.615 0.00 0.00 0.00 4.20
2031 2273 5.978814 AGGGACATGTGTCTAATACAGTTC 58.021 41.667 1.15 0.00 44.20 3.01
2034 2276 6.043411 GGACATGTGTCTAATACAGTTCCTC 58.957 44.000 1.15 0.00 44.20 3.71
2155 5539 7.485418 TCTCATTTGTAACGTATGTGTGTTT 57.515 32.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 9.193806 AGCTATCAATGTACATGAAAAAGGAAT 57.806 29.630 9.63 0.00 0.00 3.01
91 92 6.763610 ACTAACAACAAGCCTTGATAGCTATC 59.236 38.462 24.27 24.27 40.49 2.08
202 203 7.509141 TCATCAATGCTAAAAACTGAACAGA 57.491 32.000 8.87 0.00 0.00 3.41
215 216 2.621526 CCTGCATGCTTCATCAATGCTA 59.378 45.455 20.33 0.00 38.88 3.49
232 234 2.091541 TCGGAATTTTCATGACCCTGC 58.908 47.619 0.00 0.00 0.00 4.85
234 236 3.193479 GCTTTCGGAATTTTCATGACCCT 59.807 43.478 0.00 0.00 0.00 4.34
248 250 4.522114 TGAAATCCATGTATGCTTTCGGA 58.478 39.130 0.00 0.00 33.92 4.55
391 393 9.311916 GCACCAATATAATTTGAGCACATTAAA 57.688 29.630 0.00 0.00 31.80 1.52
605 616 5.775686 CCGTCATATACTATTTGTTCCCGA 58.224 41.667 0.00 0.00 0.00 5.14
609 620 7.223971 TCACTTGCCGTCATATACTATTTGTTC 59.776 37.037 0.00 0.00 0.00 3.18
694 705 7.226059 ACCCCTTTGGAGATATAACAGAAAT 57.774 36.000 0.00 0.00 38.00 2.17
1057 1072 4.560739 TGACCTAGATCATCAGGGTGAAT 58.439 43.478 6.32 0.00 36.15 2.57
1328 1343 5.887598 TGTGCCTGCAGAATATCATAGTTTT 59.112 36.000 17.39 0.00 0.00 2.43
1329 1344 5.439721 TGTGCCTGCAGAATATCATAGTTT 58.560 37.500 17.39 0.00 0.00 2.66
1353 1368 1.548719 ACCAACATGCTAGTACGCTGA 59.451 47.619 0.00 0.00 0.00 4.26
1417 1432 2.228103 CGCATGCTTGGATATGCTTCAT 59.772 45.455 17.13 0.00 45.64 2.57
1458 1476 3.028850 CCCTCATGCTTGGTCATTTCAT 58.971 45.455 0.00 0.00 0.00 2.57
1507 1525 5.476599 AGGAGCAATGCAACAACTAACATAA 59.523 36.000 8.35 0.00 0.00 1.90
1584 1602 6.138761 CACAAGTATGAGAGAACAAGCAAAC 58.861 40.000 0.00 0.00 0.00 2.93
1700 1889 3.650942 AGGTGACAATTGGAGGTAGACAA 59.349 43.478 10.83 0.00 0.00 3.18
1702 1891 3.260884 TGAGGTGACAATTGGAGGTAGAC 59.739 47.826 10.83 0.00 0.00 2.59
1772 1983 1.690893 GCATGCTCTCTCTCCCATACA 59.309 52.381 11.37 0.00 0.00 2.29
1852 2064 2.666190 GGTTGCTGCTGCTCGTCA 60.666 61.111 17.00 0.00 40.48 4.35
1870 2082 5.999361 CGAAACACGAACAAATAAGTACTCG 59.001 40.000 0.00 0.00 45.77 4.18
1883 2095 3.027029 GTTCTTCTTGCGAAACACGAAC 58.973 45.455 0.00 0.00 45.77 3.95
1955 2197 1.078759 GCAACATCTCTCGGTCACGG 61.079 60.000 0.00 0.00 41.39 4.94
1990 2232 5.714333 TGTCCCTATTTGTGTATGCATTTGT 59.286 36.000 3.54 0.00 0.00 2.83
1992 2234 6.380846 ACATGTCCCTATTTGTGTATGCATTT 59.619 34.615 3.54 0.00 0.00 2.32
2005 2247 7.676683 ACTGTATTAGACACATGTCCCTATT 57.323 36.000 8.41 0.09 45.85 1.73
2007 2249 6.097839 GGAACTGTATTAGACACATGTCCCTA 59.902 42.308 8.41 0.00 45.85 3.53
2012 2254 5.721960 AGGAGGAACTGTATTAGACACATGT 59.278 40.000 0.00 0.00 41.55 3.21
2142 2385 8.185505 ACAACAATCTTTAAAACACACATACGT 58.814 29.630 0.00 0.00 0.00 3.57
2348 5733 5.106475 GGTAATTGACCTTGCGTAAATCACA 60.106 40.000 0.19 0.00 45.89 3.58


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

AutoCloner maintained by Alex Coulton.