Multiple sequence alignment - TraesCS7B01G476600

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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 TraesCS7B01G476600 chr7B 100.000 2585 0 0 1 2585 732592628 732590044 0.000000e+00 4774
1 TraesCS7B01G476600 chr7B 95.500 1111 39 8 729 1830 732424635 732425743 0.000000e+00 1764
2 TraesCS7B01G476600 chr7B 87.075 441 46 9 266 698 113526273 113525836 2.990000e-134 488
3 TraesCS7B01G476600 chr7D 90.026 1163 81 12 696 1830 629630651 629629496 0.000000e+00 1472
4 TraesCS7B01G476600 chr7D 84.873 747 110 3 1840 2585 123413770 123413026 0.000000e+00 750
5 TraesCS7B01G476600 chr7D 81.542 428 44 19 720 1144 629792782 629792387 1.150000e-83 320
6 TraesCS7B01G476600 chr4B 93.173 747 49 2 1840 2585 581944589 581945334 0.000000e+00 1096
7 TraesCS7B01G476600 chr6B 92.476 731 52 3 1838 2567 94006444 94007172 0.000000e+00 1042
8 TraesCS7B01G476600 chr6B 91.176 748 50 4 1839 2585 659670731 659669999 0.000000e+00 1002
9 TraesCS7B01G476600 chr6B 83.949 704 90 13 1 686 37071932 37072630 0.000000e+00 652
10 TraesCS7B01G476600 chr2B 89.328 759 78 3 1828 2585 7581797 7582553 0.000000e+00 950
11 TraesCS7B01G476600 chr2B 88.770 748 82 2 1839 2585 705367815 705367069 0.000000e+00 915
12 TraesCS7B01G476600 chr3A 89.081 751 81 1 1836 2585 23296548 23297298 0.000000e+00 931
13 TraesCS7B01G476600 chr2D 89.023 747 80 2 1840 2585 442005453 442006198 0.000000e+00 924
14 TraesCS7B01G476600 chr5B 88.117 749 79 3 1838 2585 350410753 350410014 0.000000e+00 881
15 TraesCS7B01G476600 chr5B 87.322 631 68 11 1 621 611051150 611051778 0.000000e+00 712
16 TraesCS7B01G476600 chr5D 87.201 711 77 12 1 697 238777078 238777788 0.000000e+00 797
17 TraesCS7B01G476600 chr6D 86.827 706 83 9 1 697 367294331 367295035 0.000000e+00 780
18 TraesCS7B01G476600 chr1A 86.197 710 84 11 1 698 523110697 523111404 0.000000e+00 756
19 TraesCS7B01G476600 chr2A 85.955 712 87 12 1 702 715400217 715399509 0.000000e+00 749
20 TraesCS7B01G476600 chr4A 84.758 702 88 13 1 687 719550180 719549483 0.000000e+00 686
21 TraesCS7B01G476600 chr1D 85.307 667 84 13 40 696 423866783 423866121 0.000000e+00 676
22 TraesCS7B01G476600 chr3D 86.493 422 49 8 1 418 40993833 40994250 8.430000e-125 457
23 TraesCS7B01G476600 chr7A 92.281 285 20 2 705 988 725679085 725678802 1.110000e-108 403
24 TraesCS7B01G476600 chr7A 91.176 102 9 0 1687 1788 725678802 725678701 3.470000e-29 139
25 TraesCS7B01G476600 chr5A 81.772 395 67 5 3 393 548612098 548612491 2.480000e-85 326
26 TraesCS7B01G476600 chr5A 82.216 343 56 5 3 341 548618160 548618501 9.050000e-75 291
27 TraesCS7B01G476600 chr5A 82.216 343 56 5 3 341 548621760 548622101 9.050000e-75 291


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 TraesCS7B01G476600 chr7B 732590044 732592628 2584 True 4774 4774 100.000 1 2585 1 chr7B.!!$R2 2584
1 TraesCS7B01G476600 chr7B 732424635 732425743 1108 False 1764 1764 95.500 729 1830 1 chr7B.!!$F1 1101
2 TraesCS7B01G476600 chr7D 629629496 629630651 1155 True 1472 1472 90.026 696 1830 1 chr7D.!!$R2 1134
3 TraesCS7B01G476600 chr7D 123413026 123413770 744 True 750 750 84.873 1840 2585 1 chr7D.!!$R1 745
4 TraesCS7B01G476600 chr4B 581944589 581945334 745 False 1096 1096 93.173 1840 2585 1 chr4B.!!$F1 745
5 TraesCS7B01G476600 chr6B 94006444 94007172 728 False 1042 1042 92.476 1838 2567 1 chr6B.!!$F2 729
6 TraesCS7B01G476600 chr6B 659669999 659670731 732 True 1002 1002 91.176 1839 2585 1 chr6B.!!$R1 746
7 TraesCS7B01G476600 chr6B 37071932 37072630 698 False 652 652 83.949 1 686 1 chr6B.!!$F1 685
8 TraesCS7B01G476600 chr2B 7581797 7582553 756 False 950 950 89.328 1828 2585 1 chr2B.!!$F1 757
9 TraesCS7B01G476600 chr2B 705367069 705367815 746 True 915 915 88.770 1839 2585 1 chr2B.!!$R1 746
10 TraesCS7B01G476600 chr3A 23296548 23297298 750 False 931 931 89.081 1836 2585 1 chr3A.!!$F1 749
11 TraesCS7B01G476600 chr2D 442005453 442006198 745 False 924 924 89.023 1840 2585 1 chr2D.!!$F1 745
12 TraesCS7B01G476600 chr5B 350410014 350410753 739 True 881 881 88.117 1838 2585 1 chr5B.!!$R1 747
13 TraesCS7B01G476600 chr5B 611051150 611051778 628 False 712 712 87.322 1 621 1 chr5B.!!$F1 620
14 TraesCS7B01G476600 chr5D 238777078 238777788 710 False 797 797 87.201 1 697 1 chr5D.!!$F1 696
15 TraesCS7B01G476600 chr6D 367294331 367295035 704 False 780 780 86.827 1 697 1 chr6D.!!$F1 696
16 TraesCS7B01G476600 chr1A 523110697 523111404 707 False 756 756 86.197 1 698 1 chr1A.!!$F1 697
17 TraesCS7B01G476600 chr2A 715399509 715400217 708 True 749 749 85.955 1 702 1 chr2A.!!$R1 701
18 TraesCS7B01G476600 chr4A 719549483 719550180 697 True 686 686 84.758 1 687 1 chr4A.!!$R1 686
19 TraesCS7B01G476600 chr1D 423866121 423866783 662 True 676 676 85.307 40 696 1 chr1D.!!$R1 656
20 TraesCS7B01G476600 chr5A 548618160 548622101 3941 False 291 291 82.216 3 341 2 chr5A.!!$F2 338

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
421 860 0.034337 GAGTGGCGGTCAGTTTGGTA 59.966 55.0 0.00 0.0 0.0 3.25 F
1021 1686 0.745845 GAGACAGAACGGCATGGCAT 60.746 55.0 20.37 7.2 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1407 2442 0.601311 GCTTGCTCGAGTCAACCACT 60.601 55.0 15.13 0.0 38.45 4.00 R
2550 4673 0.950555 TCATGTTGCTGTGGCGTCTC 60.951 55.0 0.00 0.0 42.25 3.36 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
48 49 1.672356 CAACCTCTGCTTGGGACCG 60.672 63.158 0.00 0.00 0.00 4.79
49 50 1.841556 AACCTCTGCTTGGGACCGA 60.842 57.895 0.00 0.00 0.00 4.69
71 72 0.038166 TGCCTTCACATGGGGAGAAC 59.962 55.000 4.23 0.00 0.00 3.01
140 141 0.904649 ACATCCTGACATCCAAGCGA 59.095 50.000 0.00 0.00 0.00 4.93
146 147 1.536766 CTGACATCCAAGCGAGCAAAA 59.463 47.619 0.00 0.00 0.00 2.44
155 156 6.109156 TCCAAGCGAGCAAAATATAGGATA 57.891 37.500 0.00 0.00 0.00 2.59
170 171 3.319031 AGGATATTGGAGGCTTTTGGG 57.681 47.619 0.00 0.00 0.00 4.12
214 215 1.349357 AGAGGGTCCAGAGCAAAAGAC 59.651 52.381 0.00 0.00 0.00 3.01
225 226 1.879380 AGCAAAAGACGCAAGCATACA 59.121 42.857 0.00 0.00 45.62 2.29
228 229 3.825308 CAAAAGACGCAAGCATACATGT 58.175 40.909 2.69 2.69 45.62 3.21
347 353 8.800370 TTTCCACAAGATAATGTTAGCACATA 57.200 30.769 0.00 0.00 43.34 2.29
367 559 6.368791 CACATAATTCTTTGAGACCGAGACAA 59.631 38.462 0.00 0.00 0.00 3.18
398 590 2.502538 TCGATATGGACGGTTTCCCTTT 59.497 45.455 0.00 0.00 45.17 3.11
401 667 0.481128 ATGGACGGTTTCCCTTTGGT 59.519 50.000 0.00 0.00 45.17 3.67
421 860 0.034337 GAGTGGCGGTCAGTTTGGTA 59.966 55.000 0.00 0.00 0.00 3.25
430 869 2.548480 GGTCAGTTTGGTAGCACTTGAC 59.452 50.000 17.68 17.68 0.00 3.18
436 875 0.830444 TGGTAGCACTTGACCCTCGT 60.830 55.000 0.00 0.00 34.58 4.18
505 973 2.798976 TGCTGCATTTTGTCTTGTCC 57.201 45.000 0.00 0.00 0.00 4.02
507 975 1.615392 GCTGCATTTTGTCTTGTCCCT 59.385 47.619 0.00 0.00 0.00 4.20
509 989 3.445096 GCTGCATTTTGTCTTGTCCCTAT 59.555 43.478 0.00 0.00 0.00 2.57
569 1053 6.850752 TCTTTCTTTTTGGGTTTTCACTCT 57.149 33.333 0.00 0.00 0.00 3.24
609 1093 5.701290 CCGAGAATGTTAGGTTTTCTTGTCT 59.299 40.000 0.00 0.00 31.60 3.41
659 1143 8.099537 ACTCTCTTCTTCTTAATGAAATGCAGA 58.900 33.333 0.00 0.00 33.79 4.26
717 1203 6.942532 AAATCATGCGTAATCATGTAAGGT 57.057 33.333 4.01 0.00 43.18 3.50
767 1253 9.130661 TCACCCAATCCAATTACTAAATATGTG 57.869 33.333 0.00 0.00 0.00 3.21
911 1568 1.881973 GTGATGCAGTGATGGTTGTGT 59.118 47.619 0.00 0.00 0.00 3.72
1021 1686 0.745845 GAGACAGAACGGCATGGCAT 60.746 55.000 20.37 7.20 0.00 4.40
1209 2115 8.319143 TCTAAAACATGCTTAAACCAGTCTAC 57.681 34.615 0.00 0.00 0.00 2.59
1229 2157 7.386025 AGTCTACGTACCTAACAAAATGGAAAC 59.614 37.037 0.00 0.00 0.00 2.78
1282 2286 5.829924 ACTGCCAAAATCGGATCTTATGATT 59.170 36.000 0.00 0.00 33.94 2.57
1397 2432 3.003897 GGGCTTACAAACACAAATGACGA 59.996 43.478 0.00 0.00 0.00 4.20
1586 3248 6.428159 CCCAAGTGCACATCCTATAATTAGTC 59.572 42.308 21.04 0.00 0.00 2.59
1804 3478 0.250209 TACCTCTACCGAGCTAGGCG 60.250 60.000 13.48 4.60 35.90 5.52
2002 3676 4.690748 TCTGCTATCCTATTTTGCATACGC 59.309 41.667 0.00 0.00 39.24 4.42
2089 3763 5.012561 CCCATAGGCAGATCTAGTTAAGCTT 59.987 44.000 3.48 3.48 0.00 3.74
2167 3841 3.136763 CTCACAATGCTGGATCGCTATT 58.863 45.455 0.00 0.00 0.00 1.73
2208 4143 1.292223 GTAGTTCCGCCTGAGTGCA 59.708 57.895 0.00 0.00 0.00 4.57
2212 4147 1.375908 TTCCGCCTGAGTGCATCAC 60.376 57.895 0.00 0.00 33.22 3.06
2231 4166 7.260558 CATCACTGCAATTGAAGATGTATCT 57.739 36.000 20.85 0.00 39.22 1.98
2512 4635 1.588139 GTAGACGGAATCGGTGGCG 60.588 63.158 0.00 0.00 41.39 5.69
2550 4673 2.558554 AATCGTTCCGGAGCGACCAG 62.559 60.000 39.91 14.21 46.11 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 1.379044 CCCCATGTGAAGGCACCTC 60.379 63.158 0.00 0.00 44.51 3.85
49 50 1.852157 TCCCCATGTGAAGGCACCT 60.852 57.895 0.00 0.00 44.51 4.00
71 72 2.179018 CTTTGCCGCCCGTCATTG 59.821 61.111 0.00 0.00 0.00 2.82
94 95 5.997746 CACACCTTGTTCTTCTTATCCAGAA 59.002 40.000 0.00 0.00 39.39 3.02
140 141 7.037342 AGCCTCCAATATCCTATATTTTGCT 57.963 36.000 0.00 0.00 0.00 3.91
146 147 6.297830 CCCCAAAAGCCTCCAATATCCTATAT 60.298 42.308 0.00 0.00 0.00 0.86
155 156 0.615827 GCTCCCCAAAAGCCTCCAAT 60.616 55.000 0.00 0.00 33.53 3.16
170 171 4.154347 CTGACCTCCGGCAGCTCC 62.154 72.222 0.00 0.00 0.00 4.70
225 226 2.350498 GCGGCTTTTCGTACATGTACAT 59.650 45.455 30.17 1.41 35.87 2.29
228 229 2.094390 AGAGCGGCTTTTCGTACATGTA 60.094 45.455 2.97 0.08 0.00 2.29
237 240 1.349973 GCGATGAGAGCGGCTTTTC 59.650 57.895 2.97 6.23 0.00 2.29
242 245 2.510238 ACTTGCGATGAGAGCGGC 60.510 61.111 0.00 0.00 37.44 6.53
347 353 6.055588 TCTTTTGTCTCGGTCTCAAAGAATT 58.944 36.000 0.00 0.00 33.61 2.17
367 559 4.099573 ACCGTCCATATCGAATGACTCTTT 59.900 41.667 8.56 0.00 0.00 2.52
398 590 1.978455 AAACTGACCGCCACTCACCA 61.978 55.000 0.00 0.00 0.00 4.17
401 667 1.227823 CCAAACTGACCGCCACTCA 60.228 57.895 0.00 0.00 0.00 3.41
421 860 1.272769 GTTAGACGAGGGTCAAGTGCT 59.727 52.381 0.00 0.00 45.92 4.40
430 869 1.676014 CCCAAAGCAGTTAGACGAGGG 60.676 57.143 0.00 0.00 0.00 4.30
436 875 1.559682 CCTAGGCCCAAAGCAGTTAGA 59.440 52.381 0.00 0.00 46.50 2.10
505 973 3.041946 AGGCACTAGAACTTGGGATAGG 58.958 50.000 0.00 0.00 36.02 2.57
507 975 3.995636 AGAGGCACTAGAACTTGGGATA 58.004 45.455 0.00 0.00 41.55 2.59
509 989 2.327325 AGAGGCACTAGAACTTGGGA 57.673 50.000 0.00 0.00 41.55 4.37
569 1053 4.627284 TCTCGGTTAATCAGGGAAAACA 57.373 40.909 0.00 0.00 0.00 2.83
609 1093 5.954757 TGGTCCAGTTTATAAGGAAAACCA 58.045 37.500 6.89 6.89 37.51 3.67
659 1143 2.941583 GAGAGGGGCAGGGGGTTT 60.942 66.667 0.00 0.00 0.00 3.27
767 1253 5.643777 AGGCATACAATCTGCGTAATATTCC 59.356 40.000 0.00 0.00 40.59 3.01
824 1477 6.318144 AGAAAGATTGCATGATCTGAACGAAT 59.682 34.615 1.64 0.00 36.53 3.34
911 1568 5.939764 ATAGAGGATTGACTGTAGCACAA 57.060 39.130 0.00 0.00 0.00 3.33
985 1650 5.840693 TCTGTCTCATATTATCCTGGCTTCA 59.159 40.000 0.00 0.00 0.00 3.02
993 1658 4.883083 TGCCGTTCTGTCTCATATTATCC 58.117 43.478 0.00 0.00 0.00 2.59
1209 2115 4.213906 ACGGTTTCCATTTTGTTAGGTACG 59.786 41.667 0.00 0.00 0.00 3.67
1247 2251 5.460646 CGATTTTGGCAGTTGTATCACTTT 58.539 37.500 0.00 0.00 0.00 2.66
1282 2286 8.183104 TGTAAACACACATATGGATGGAAAAA 57.817 30.769 7.80 0.00 37.39 1.94
1397 2432 3.740115 GAGTCAACCACTGTACCATTGT 58.260 45.455 0.00 0.00 34.41 2.71
1407 2442 0.601311 GCTTGCTCGAGTCAACCACT 60.601 55.000 15.13 0.00 38.45 4.00
1586 3248 1.567504 CGCTATTTCCACTGGTACCG 58.432 55.000 7.57 4.79 0.00 4.02
1751 3425 9.796120 TGTTATAAATGGTGCTTAATTTAGTGC 57.204 29.630 0.00 0.00 0.00 4.40
2027 3701 9.467796 TGAGATTCGTCATCTTATGGTAGATAT 57.532 33.333 2.08 0.00 42.92 1.63
2089 3763 4.693283 CTCTTTCCGCATTATCTGGTACA 58.307 43.478 0.00 0.00 0.00 2.90
2212 4147 8.996271 TGCTTATAGATACATCTTCAATTGCAG 58.004 33.333 0.00 0.00 38.32 4.41
2231 4166 7.109501 TGGAAGTGTTATCTTTGCTGCTTATA 58.890 34.615 0.00 0.00 0.00 0.98
2512 4635 2.862674 TTAACGCATGGGACGGAGGC 62.863 60.000 17.76 0.00 34.00 4.70
2550 4673 0.950555 TCATGTTGCTGTGGCGTCTC 60.951 55.000 0.00 0.00 42.25 3.36


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

AutoCloner maintained by Alex Coulton.