Multiple sequence alignment - TraesCS7B01G414700

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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 TraesCS7B01G414700 chr7B 100.000 2912 0 0 1 2912 682742684 682745595 0.000000e+00 5378
1 TraesCS7B01G414700 chr7B 95.751 706 26 4 1 704 361211468 361212171 0.000000e+00 1134
2 TraesCS7B01G414700 chr7B 83.944 1065 116 34 705 1738 681790272 681789232 0.000000e+00 968
3 TraesCS7B01G414700 chrUn 92.527 1298 74 10 705 1999 87249192 87250469 0.000000e+00 1838
4 TraesCS7B01G414700 chrUn 92.527 1298 74 10 705 1999 235065051 235066328 0.000000e+00 1838
5 TraesCS7B01G414700 chrUn 92.389 1235 68 8 780 1999 87255461 87256684 0.000000e+00 1736
6 TraesCS7B01G414700 chrUn 92.389 1235 68 8 780 1999 235071320 235072543 0.000000e+00 1736
7 TraesCS7B01G414700 chrUn 94.507 710 32 5 1 704 126293281 126292573 0.000000e+00 1088
8 TraesCS7B01G414700 chrUn 92.624 705 46 6 1 702 405486125 405485424 0.000000e+00 1009
9 TraesCS7B01G414700 chrUn 92.199 705 49 6 1 702 356041745 356041044 0.000000e+00 992
10 TraesCS7B01G414700 chrUn 91.437 654 49 5 1 649 352095221 352094570 0.000000e+00 891
11 TraesCS7B01G414700 chr7D 87.602 1226 111 22 705 1918 602076219 602075023 0.000000e+00 1384
12 TraesCS7B01G414700 chr7D 90.570 912 79 7 1999 2907 88024562 88025469 0.000000e+00 1201
13 TraesCS7B01G414700 chr7D 90.667 900 79 5 2014 2910 144150685 144149788 0.000000e+00 1192
14 TraesCS7B01G414700 chr7D 81.410 936 121 26 974 1884 602262507 602263414 0.000000e+00 715
15 TraesCS7B01G414700 chr7A 87.378 1228 101 24 705 1918 693841665 693840478 0.000000e+00 1360
16 TraesCS7B01G414700 chr7A 82.724 492 71 7 1403 1884 694036928 694037415 2.680000e-115 425
17 TraesCS7B01G414700 chr7A 82.299 435 51 12 974 1407 694036484 694036893 1.280000e-93 353
18 TraesCS7B01G414700 chr2D 91.357 914 74 5 2000 2910 627628365 627627454 0.000000e+00 1245
19 TraesCS7B01G414700 chr3A 90.578 934 84 4 1980 2910 364194168 364193236 0.000000e+00 1234
20 TraesCS7B01G414700 chr2B 90.581 913 81 5 2000 2910 756219377 756220286 0.000000e+00 1205
21 TraesCS7B01G414700 chr2B 96.181 707 22 5 1 704 78863709 78864413 0.000000e+00 1151
22 TraesCS7B01G414700 chr2B 95.198 708 29 5 1 705 33538077 33538782 0.000000e+00 1114
23 TraesCS7B01G414700 chr5D 90.361 913 84 4 1998 2907 546071165 546070254 0.000000e+00 1195
24 TraesCS7B01G414700 chr6D 90.142 913 86 4 2000 2910 107936487 107935577 0.000000e+00 1184
25 TraesCS7B01G414700 chr1B 89.869 918 91 2 1994 2910 567690391 567691307 0.000000e+00 1179
26 TraesCS7B01G414700 chr5A 89.570 930 89 7 1987 2910 664255770 664256697 0.000000e+00 1173
27 TraesCS7B01G414700 chr6B 95.556 720 28 4 1 717 88447059 88447777 0.000000e+00 1149
28 TraesCS7B01G414700 chr2A 94.184 705 38 3 1 704 39741467 39742169 0.000000e+00 1072


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 TraesCS7B01G414700 chr7B 682742684 682745595 2911 False 5378 5378 100.0000 1 2912 1 chr7B.!!$F2 2911
1 TraesCS7B01G414700 chr7B 361211468 361212171 703 False 1134 1134 95.7510 1 704 1 chr7B.!!$F1 703
2 TraesCS7B01G414700 chr7B 681789232 681790272 1040 True 968 968 83.9440 705 1738 1 chr7B.!!$R1 1033
3 TraesCS7B01G414700 chrUn 87249192 87250469 1277 False 1838 1838 92.5270 705 1999 1 chrUn.!!$F1 1294
4 TraesCS7B01G414700 chrUn 235065051 235066328 1277 False 1838 1838 92.5270 705 1999 1 chrUn.!!$F3 1294
5 TraesCS7B01G414700 chrUn 87255461 87256684 1223 False 1736 1736 92.3890 780 1999 1 chrUn.!!$F2 1219
6 TraesCS7B01G414700 chrUn 235071320 235072543 1223 False 1736 1736 92.3890 780 1999 1 chrUn.!!$F4 1219
7 TraesCS7B01G414700 chrUn 126292573 126293281 708 True 1088 1088 94.5070 1 704 1 chrUn.!!$R1 703
8 TraesCS7B01G414700 chrUn 405485424 405486125 701 True 1009 1009 92.6240 1 702 1 chrUn.!!$R4 701
9 TraesCS7B01G414700 chrUn 356041044 356041745 701 True 992 992 92.1990 1 702 1 chrUn.!!$R3 701
10 TraesCS7B01G414700 chrUn 352094570 352095221 651 True 891 891 91.4370 1 649 1 chrUn.!!$R2 648
11 TraesCS7B01G414700 chr7D 602075023 602076219 1196 True 1384 1384 87.6020 705 1918 1 chr7D.!!$R2 1213
12 TraesCS7B01G414700 chr7D 88024562 88025469 907 False 1201 1201 90.5700 1999 2907 1 chr7D.!!$F1 908
13 TraesCS7B01G414700 chr7D 144149788 144150685 897 True 1192 1192 90.6670 2014 2910 1 chr7D.!!$R1 896
14 TraesCS7B01G414700 chr7D 602262507 602263414 907 False 715 715 81.4100 974 1884 1 chr7D.!!$F2 910
15 TraesCS7B01G414700 chr7A 693840478 693841665 1187 True 1360 1360 87.3780 705 1918 1 chr7A.!!$R1 1213
16 TraesCS7B01G414700 chr7A 694036484 694037415 931 False 389 425 82.5115 974 1884 2 chr7A.!!$F1 910
17 TraesCS7B01G414700 chr2D 627627454 627628365 911 True 1245 1245 91.3570 2000 2910 1 chr2D.!!$R1 910
18 TraesCS7B01G414700 chr3A 364193236 364194168 932 True 1234 1234 90.5780 1980 2910 1 chr3A.!!$R1 930
19 TraesCS7B01G414700 chr2B 756219377 756220286 909 False 1205 1205 90.5810 2000 2910 1 chr2B.!!$F3 910
20 TraesCS7B01G414700 chr2B 78863709 78864413 704 False 1151 1151 96.1810 1 704 1 chr2B.!!$F2 703
21 TraesCS7B01G414700 chr2B 33538077 33538782 705 False 1114 1114 95.1980 1 705 1 chr2B.!!$F1 704
22 TraesCS7B01G414700 chr5D 546070254 546071165 911 True 1195 1195 90.3610 1998 2907 1 chr5D.!!$R1 909
23 TraesCS7B01G414700 chr6D 107935577 107936487 910 True 1184 1184 90.1420 2000 2910 1 chr6D.!!$R1 910
24 TraesCS7B01G414700 chr1B 567690391 567691307 916 False 1179 1179 89.8690 1994 2910 1 chr1B.!!$F1 916
25 TraesCS7B01G414700 chr5A 664255770 664256697 927 False 1173 1173 89.5700 1987 2910 1 chr5A.!!$F1 923
26 TraesCS7B01G414700 chr6B 88447059 88447777 718 False 1149 1149 95.5560 1 717 1 chr6B.!!$F1 716
27 TraesCS7B01G414700 chr2A 39741467 39742169 702 False 1072 1072 94.1840 1 704 1 chr2A.!!$F1 703

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
154 156 0.787787 CGAAGTTTTCACCGCGATGA 59.212 50.0 8.23 1.53 0.00 2.92 F
1447 1533 0.107508 CCTCAACCATGTCGGCATCT 60.108 55.0 0.00 0.00 39.03 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1886 2005 0.609662 TAGCCAAGGTAACACGACCC 59.390 55.0 0.0 0.0 40.74 4.46 R
2312 2437 0.105964 TGCACCCAAAGTTGCCCTTA 60.106 50.0 0.0 0.0 31.48 2.69 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
146 148 7.639162 TGAGATCTAGTTTCGAAGTTTTCAC 57.361 36.000 0.00 0.00 0.00 3.18
154 156 0.787787 CGAAGTTTTCACCGCGATGA 59.212 50.000 8.23 1.53 0.00 2.92
197 200 9.640974 CAATTTTTCAATCAAACATGTCAGTTC 57.359 29.630 0.00 0.00 0.00 3.01
223 226 8.067784 CGAGCTCTAAAACATTTTACAGTTTCA 58.932 33.333 12.85 0.00 36.98 2.69
474 479 5.783654 CGTCGTGACAAATCTTTTATGTGAC 59.216 40.000 0.41 0.00 0.00 3.67
491 496 5.060662 TGTGACAACGGTTTTTCAATCAA 57.939 34.783 4.02 0.00 0.00 2.57
550 555 4.453478 TGAATTCGATGGAATCTATGCTGC 59.547 41.667 3.21 0.00 41.99 5.25
600 606 4.933400 GCATGCAACAATTGAGGAAAAGAT 59.067 37.500 14.21 0.00 0.00 2.40
660 671 1.797537 GCATGCAAAACTCGTCCGC 60.798 57.895 14.21 0.00 0.00 5.54
686 697 2.172851 TGCTAATGTTCCGAACGGTT 57.827 45.000 12.93 6.82 36.47 4.44
768 779 4.142902 CGCTTTGTTGAACGACCATTAGAT 60.143 41.667 0.00 0.00 0.00 1.98
772 783 7.358352 GCTTTGTTGAACGACCATTAGATTTTG 60.358 37.037 0.00 0.00 0.00 2.44
776 787 5.698832 TGAACGACCATTAGATTTTGCTTG 58.301 37.500 0.00 0.00 0.00 4.01
878 896 2.835156 GTGGGCTCTCTAGTTCCTTTCT 59.165 50.000 0.00 0.00 0.00 2.52
882 900 4.263112 GGGCTCTCTAGTTCCTTTCTTGTT 60.263 45.833 0.00 0.00 0.00 2.83
884 902 5.511545 GGCTCTCTAGTTCCTTTCTTGTTCA 60.512 44.000 0.00 0.00 0.00 3.18
885 903 5.407084 GCTCTCTAGTTCCTTTCTTGTTCAC 59.593 44.000 0.00 0.00 0.00 3.18
886 904 6.732896 TCTCTAGTTCCTTTCTTGTTCACT 57.267 37.500 0.00 0.00 0.00 3.41
889 907 8.871125 TCTCTAGTTCCTTTCTTGTTCACTATT 58.129 33.333 0.00 0.00 0.00 1.73
890 908 9.495572 CTCTAGTTCCTTTCTTGTTCACTATTT 57.504 33.333 0.00 0.00 0.00 1.40
926 953 6.721571 ATTTGACCATGACAACTAACTACG 57.278 37.500 0.00 0.00 0.00 3.51
1068 1106 1.081108 GCTATGCCTCTACCTCGCG 60.081 63.158 0.00 0.00 0.00 5.87
1069 1107 1.081108 CTATGCCTCTACCTCGCGC 60.081 63.158 0.00 0.00 0.00 6.86
1070 1108 1.796190 CTATGCCTCTACCTCGCGCA 61.796 60.000 8.75 0.00 0.00 6.09
1447 1533 0.107508 CCTCAACCATGTCGGCATCT 60.108 55.000 0.00 0.00 39.03 2.90
1464 1550 1.123077 TCTACATCAGCTCCGGCAAT 58.877 50.000 0.00 0.00 41.70 3.56
1470 1556 1.675310 CAGCTCCGGCAATTCCACA 60.675 57.895 0.00 0.00 41.70 4.17
1516 1605 2.742372 CGGGCAAGAACCTCACGG 60.742 66.667 0.00 0.00 0.00 4.94
1597 1686 3.120979 CTACTCATCGACGGCGCCA 62.121 63.158 28.98 7.02 37.46 5.69
1599 1688 1.167781 TACTCATCGACGGCGCCATA 61.168 55.000 28.98 8.49 37.46 2.74
1665 1754 4.117661 GTCGCGGTCGGCTTCTCT 62.118 66.667 6.13 0.00 40.44 3.10
1724 1837 1.006102 CGTTCGGTTCCACTCTGCT 60.006 57.895 0.00 0.00 0.00 4.24
1824 1943 6.257586 AGCATTAGTCCTACTATTCCTAGGG 58.742 44.000 9.46 0.00 32.79 3.53
1884 2003 0.462047 GATTCAAGACATCGCCGGGT 60.462 55.000 2.18 0.00 0.00 5.28
1885 2004 0.462047 ATTCAAGACATCGCCGGGTC 60.462 55.000 2.18 1.28 0.00 4.46
1886 2005 2.829043 TTCAAGACATCGCCGGGTCG 62.829 60.000 2.18 0.00 39.01 4.79
1905 2024 0.609662 GGGTCGTGTTACCTTGGCTA 59.390 55.000 0.00 0.00 39.65 3.93
2009 2128 1.308998 AAGAAACAAGGACGTGGCTG 58.691 50.000 0.00 0.00 0.00 4.85
2064 2184 6.199043 GCGCATAGCCGTATATAGTAATTG 57.801 41.667 0.30 0.00 40.81 2.32
2066 2186 5.977725 CGCATAGCCGTATATAGTAATTGCT 59.022 40.000 0.56 0.56 0.00 3.91
2132 2252 0.320334 CACACCCTGTACGCACATGA 60.320 55.000 0.00 0.00 33.14 3.07
2182 2304 4.075682 TCTCACGTGCATTTATTTTGGGA 58.924 39.130 11.67 0.00 0.00 4.37
2183 2305 4.083003 TCTCACGTGCATTTATTTTGGGAC 60.083 41.667 11.67 0.00 0.00 4.46
2186 2309 3.249917 CGTGCATTTATTTTGGGACCAC 58.750 45.455 0.00 0.00 0.00 4.16
2190 2313 5.049749 GTGCATTTATTTTGGGACCACAAAC 60.050 40.000 7.42 0.00 39.82 2.93
2200 2323 4.345854 TGGGACCACAAACTTGTAAAAGT 58.654 39.130 0.00 0.00 39.91 2.66
2206 2329 8.357402 GGACCACAAACTTGTAAAAGTCATAAT 58.643 33.333 0.00 0.00 39.91 1.28
2283 2406 6.097915 ACGAGTTCTTCAAAACTAGATCCA 57.902 37.500 0.00 0.00 39.55 3.41
2389 2514 5.578157 TTCTTTTTGGCCTAGTAGGACTT 57.422 39.130 23.02 0.00 46.32 3.01
2401 2526 7.176515 GGCCTAGTAGGACTTACTATTAGGTTC 59.823 44.444 21.02 7.45 46.78 3.62
2488 2615 5.334802 GCAATTTCACTGCACTGTGTGTATA 60.335 40.000 9.86 0.00 39.69 1.47
2494 2621 4.872124 CACTGCACTGTGTGTATATGTGAT 59.128 41.667 9.86 0.00 35.75 3.06
2495 2622 4.872124 ACTGCACTGTGTGTATATGTGATG 59.128 41.667 9.86 0.00 35.75 3.07
2504 2631 8.329203 TGTGTGTATATGTGATGTTTGCTAAA 57.671 30.769 0.00 0.00 0.00 1.85
2505 2632 8.233868 TGTGTGTATATGTGATGTTTGCTAAAC 58.766 33.333 5.22 5.22 41.73 2.01
2530 2657 1.670811 CCCAACTTGCGTATCATGACC 59.329 52.381 0.00 0.00 0.00 4.02
2540 2667 2.866156 CGTATCATGACCGCTCAATTGT 59.134 45.455 5.13 0.00 0.00 2.71
2545 2672 4.122046 TCATGACCGCTCAATTGTCTATG 58.878 43.478 5.13 3.13 0.00 2.23
2554 2681 4.498682 GCTCAATTGTCTATGGTTGATGGC 60.499 45.833 5.13 0.00 30.97 4.40
2580 2707 7.390440 CCAGTTCCTACACTTGATGTTCAATTA 59.610 37.037 0.00 0.00 43.19 1.40
2638 2767 9.325198 TGTATACTTGTCTGCTATTGGTAATTG 57.675 33.333 4.17 0.00 0.00 2.32
2771 2900 3.431856 CAAGATTCACCATCATGTTGCG 58.568 45.455 0.00 0.00 33.75 4.85
2774 2903 4.454678 AGATTCACCATCATGTTGCGTAT 58.545 39.130 0.00 0.00 33.75 3.06
2910 3039 4.468510 TGGCGAGGAAGTTAGGAGAAAATA 59.531 41.667 0.00 0.00 0.00 1.40
2911 3040 5.051153 GGCGAGGAAGTTAGGAGAAAATAG 58.949 45.833 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
197 200 8.067784 TGAAACTGTAAAATGTTTTAGAGCTCG 58.932 33.333 17.36 1.89 43.73 5.03
223 226 6.867816 TGTCATTGCAAAATCTCGCTATTTTT 59.132 30.769 1.71 0.00 37.03 1.94
408 413 4.511454 CCCATGTTGATATGTTTCGACGAT 59.489 41.667 0.00 0.00 33.42 3.73
474 479 5.477136 GTCGTTTTGATTGAAAAACCGTTG 58.523 37.500 6.89 0.00 43.86 4.10
491 496 3.648339 TTGTAGCTCTAACCGTCGTTT 57.352 42.857 0.00 0.00 33.17 3.60
600 606 2.702592 AACTGAGAACCCACACGAAA 57.297 45.000 0.00 0.00 0.00 3.46
628 639 0.108898 GCATGCATGCGGTTGGTTTA 60.109 50.000 33.99 0.00 44.67 2.01
660 671 4.651994 GTTCGGAACATTAGCAACAGATG 58.348 43.478 15.70 0.00 0.00 2.90
794 805 6.543831 GCCATTAGATTACACAGGATCAAGTT 59.456 38.462 0.00 0.00 0.00 2.66
926 953 1.712018 GAACGGGATTTAGTGGCGGC 61.712 60.000 0.00 0.00 0.00 6.53
1204 1242 2.961669 GCGGCACTTTGTACCGGTG 61.962 63.158 19.93 1.45 42.16 4.94
1405 1491 1.135083 AGCGTCAAATCCTACCGTCAG 60.135 52.381 0.00 0.00 0.00 3.51
1416 1502 2.582052 TGGTTGAGGAAAGCGTCAAAT 58.418 42.857 0.00 0.00 46.66 2.32
1447 1533 1.475034 GGAATTGCCGGAGCTGATGTA 60.475 52.381 5.05 0.00 40.80 2.29
1516 1605 1.448540 CCTCCATGACACTGGACGC 60.449 63.158 0.00 0.00 40.43 5.19
1597 1686 2.597455 GGTTGCATTGGCCTGGTATAT 58.403 47.619 3.32 0.00 40.13 0.86
1599 1688 1.037030 CGGTTGCATTGGCCTGGTAT 61.037 55.000 3.32 0.00 40.13 2.73
1724 1837 3.003173 CCTCCCGCTTGGACTCCA 61.003 66.667 0.00 0.00 38.61 3.86
1824 1943 0.793478 CACACCTCGTCGTGATCGTC 60.793 60.000 10.82 0.00 37.20 4.20
1884 2003 1.667151 CCAAGGTAACACGACCCGA 59.333 57.895 0.00 0.00 40.74 5.14
1885 2004 2.030958 GCCAAGGTAACACGACCCG 61.031 63.158 0.00 0.00 40.74 5.28
1886 2005 0.609662 TAGCCAAGGTAACACGACCC 59.390 55.000 0.00 0.00 40.74 4.46
1887 2006 2.547826 GATAGCCAAGGTAACACGACC 58.452 52.381 0.00 0.00 40.08 4.79
1888 2007 2.167900 AGGATAGCCAAGGTAACACGAC 59.832 50.000 0.00 0.00 35.89 4.34
1931 2050 9.893305 ACTGAAATCCAATTAAAGTTCTTTACG 57.107 29.630 4.74 0.00 0.00 3.18
1986 2105 2.357952 GCCACGTCCTTGTTTCTTTCTT 59.642 45.455 0.00 0.00 0.00 2.52
2029 2149 1.709147 CTATGCGCTCCAGGCAACAC 61.709 60.000 9.73 0.00 44.66 3.32
2064 2184 2.423538 ACAGTTGAACACAAGGACAAGC 59.576 45.455 0.00 0.00 0.00 4.01
2066 2186 3.950397 AGACAGTTGAACACAAGGACAA 58.050 40.909 0.00 0.00 0.00 3.18
2111 2231 1.764571 ATGTGCGTACAGGGTGTGGT 61.765 55.000 12.93 0.00 40.79 4.16
2132 2252 5.808366 TTTAGGCTGATTCCATCGATAGT 57.192 39.130 0.00 0.00 37.40 2.12
2312 2437 0.105964 TGCACCCAAAGTTGCCCTTA 60.106 50.000 0.00 0.00 31.48 2.69
2488 2615 6.663093 TGGGATAAGTTTAGCAAACATCACAT 59.337 34.615 12.28 1.48 43.79 3.21
2494 2621 6.737346 GCAAGTTGGGATAAGTTTAGCAAACA 60.737 38.462 4.75 0.00 43.79 2.83
2495 2622 5.633601 GCAAGTTGGGATAAGTTTAGCAAAC 59.366 40.000 4.75 4.26 41.69 2.93
2530 2657 4.260907 CCATCAACCATAGACAATTGAGCG 60.261 45.833 13.59 0.00 34.71 5.03
2540 2667 2.092429 GGAACTGGCCATCAACCATAGA 60.092 50.000 5.51 0.00 36.36 1.98
2545 2672 1.004277 TGTAGGAACTGGCCATCAACC 59.996 52.381 5.51 8.13 41.52 3.77
2554 2681 4.641396 TGAACATCAAGTGTAGGAACTGG 58.359 43.478 0.00 0.00 41.14 4.00
2618 2747 6.324819 CAACCAATTACCAATAGCAGACAAG 58.675 40.000 0.00 0.00 0.00 3.16
2638 2767 2.403259 GTGCAACAATTGTAGGCAACC 58.597 47.619 28.79 18.66 39.20 3.77


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

AutoCloner maintained by Alex Coulton.