Multiple sequence alignment - TraesCS1B01G197400

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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 TraesCS1B01G197400 chr1B 100.000 8073 0 0 1 8073 354990241 354982169 0.000000e+00 14909.0
1 TraesCS1B01G197400 chr1B 99.371 1750 11 0 3753 5502 655771256 655769507 0.000000e+00 3171.0
2 TraesCS1B01G197400 chr1B 99.257 1750 13 0 3753 5502 152830390 152832139 0.000000e+00 3160.0
3 TraesCS1B01G197400 chr1B 91.060 1868 105 16 869 2709 355107603 355105771 0.000000e+00 2468.0
4 TraesCS1B01G197400 chr1B 88.954 1023 84 15 6413 7416 355104121 355103109 0.000000e+00 1236.0
5 TraesCS1B01G197400 chr1B 93.702 778 39 6 5501 6273 355104873 355104101 0.000000e+00 1157.0
6 TraesCS1B01G197400 chr1B 89.053 813 63 16 2948 3750 355105652 355104856 0.000000e+00 985.0
7 TraesCS1B01G197400 chr1B 89.767 772 70 9 1 764 355108588 355107818 0.000000e+00 979.0
8 TraesCS1B01G197400 chr1B 81.203 665 113 5 978 1638 354930191 354929535 7.180000e-145 525.0
9 TraesCS1B01G197400 chr1B 84.244 311 44 5 5501 5809 354925819 354925512 1.700000e-76 298.0
10 TraesCS1B01G197400 chr1B 95.333 150 4 3 6270 6418 39380620 39380767 1.350000e-57 235.0
11 TraesCS1B01G197400 chr1B 87.273 110 14 0 6676 6785 354922639 354922530 8.510000e-25 126.0
12 TraesCS1B01G197400 chr1B 85.586 111 16 0 2701 2811 188263551 188263441 5.120000e-22 117.0
13 TraesCS1B01G197400 chr1D 96.046 2883 91 8 869 3750 258090132 258092992 0.000000e+00 4671.0
14 TraesCS1B01G197400 chr1D 98.068 1139 15 5 5501 6634 258092975 258094111 0.000000e+00 1975.0
15 TraesCS1B01G197400 chr1D 89.617 809 59 12 6627 7416 258094364 258095166 0.000000e+00 1005.0
16 TraesCS1B01G197400 chr1D 89.146 691 58 11 1 676 445316418 445317106 0.000000e+00 845.0
17 TraesCS1B01G197400 chr1D 86.416 692 70 13 6 676 378109543 378108855 0.000000e+00 736.0
18 TraesCS1B01G197400 chr1D 80.931 666 114 7 978 1638 258332306 258332963 1.550000e-141 514.0
19 TraesCS1B01G197400 chr1D 83.654 312 44 7 5501 5809 258339008 258339315 3.690000e-73 287.0
20 TraesCS1B01G197400 chr1D 95.833 144 3 3 6276 6418 193964353 193964212 6.300000e-56 230.0
21 TraesCS1B01G197400 chr1D 94.000 150 7 2 6270 6417 225419440 225419589 8.150000e-55 226.0
22 TraesCS1B01G197400 chr1D 91.975 162 10 3 6270 6430 160525228 160525069 2.930000e-54 224.0
23 TraesCS1B01G197400 chr1D 92.357 157 10 2 6270 6424 138276247 138276403 1.050000e-53 222.0
24 TraesCS1B01G197400 chr1D 88.679 106 12 0 6678 6783 258341978 258342083 6.580000e-26 130.0
25 TraesCS1B01G197400 chr5A 99.371 1750 11 0 3753 5502 259067967 259069716 0.000000e+00 3171.0
26 TraesCS1B01G197400 chr5B 99.204 1758 12 2 3753 5509 138781076 138779320 0.000000e+00 3168.0
27 TraesCS1B01G197400 chr3A 99.314 1750 11 1 3753 5502 11466366 11468114 0.000000e+00 3164.0
28 TraesCS1B01G197400 chr3A 85.882 85 9 3 717 800 691993857 691993775 4.010000e-13 87.9
29 TraesCS1B01G197400 chr3A 84.722 72 10 1 609 679 509113866 509113795 4.040000e-08 71.3
30 TraesCS1B01G197400 chr4B 99.201 1753 14 0 3753 5505 90725471 90723719 0.000000e+00 3160.0
31 TraesCS1B01G197400 chr4B 99.201 1753 13 1 3753 5505 371973455 371971704 0.000000e+00 3158.0
32 TraesCS1B01G197400 chr4B 100.000 37 0 0 3715 3751 420223724 420223688 1.450000e-07 69.4
33 TraesCS1B01G197400 chr4A 99.257 1750 13 0 3753 5502 97256496 97258245 0.000000e+00 3160.0
34 TraesCS1B01G197400 chr4A 91.074 661 43 8 7416 8073 395091497 395090850 0.000000e+00 880.0
35 TraesCS1B01G197400 chr4A 92.147 382 26 4 7415 7796 124011120 124010743 3.320000e-148 536.0
36 TraesCS1B01G197400 chr4A 90.000 280 19 1 7794 8073 123956964 123956694 3.580000e-93 353.0
37 TraesCS1B01G197400 chr4A 91.026 234 21 0 5501 5734 573697579 573697346 4.700000e-82 316.0
38 TraesCS1B01G197400 chr4A 88.393 224 25 1 7416 7638 744303470 744303247 1.340000e-67 268.0
39 TraesCS1B01G197400 chr4A 83.275 287 32 8 7681 7965 744302376 744302104 4.840000e-62 250.0
40 TraesCS1B01G197400 chr4A 90.099 101 8 2 2712 2811 699792032 699791933 6.580000e-26 130.0
41 TraesCS1B01G197400 chr4A 100.000 37 0 0 3715 3751 573697597 573697561 1.450000e-07 69.4
42 TraesCS1B01G197400 chr3B 99.143 1751 14 1 3753 5502 583366321 583368071 0.000000e+00 3149.0
43 TraesCS1B01G197400 chr3B 80.684 673 63 28 7416 8073 803383223 803383843 2.050000e-125 460.0
44 TraesCS1B01G197400 chr3B 79.732 671 72 24 7416 8073 803387727 803388346 2.080000e-115 427.0
45 TraesCS1B01G197400 chr1A 97.676 1420 32 1 1477 2895 343422778 343421359 0.000000e+00 2438.0
46 TraesCS1B01G197400 chr1A 97.896 808 11 4 2948 3750 343421338 343420532 0.000000e+00 1393.0
47 TraesCS1B01G197400 chr1A 90.341 1025 67 18 6413 7416 343419796 343418783 0.000000e+00 1315.0
48 TraesCS1B01G197400 chr1A 97.283 773 19 1 5501 6271 343420549 343419777 0.000000e+00 1310.0
49 TraesCS1B01G197400 chr1A 93.617 658 38 2 7416 8073 442916021 442916674 0.000000e+00 979.0
50 TraesCS1B01G197400 chr1A 94.364 621 25 4 869 1488 343424849 343424238 0.000000e+00 944.0
51 TraesCS1B01G197400 chr1A 82.577 551 64 11 7416 7965 66657419 66656900 2.660000e-124 457.0
52 TraesCS1B01G197400 chr1A 90.606 330 26 3 7090 7416 343416596 343416269 4.480000e-117 433.0
53 TraesCS1B01G197400 chr1A 83.923 311 45 5 5501 5809 343399289 343398982 7.920000e-75 292.0
54 TraesCS1B01G197400 chr1A 96.000 150 3 3 6270 6418 24135797 24135944 2.910000e-59 241.0
55 TraesCS1B01G197400 chr1A 94.667 150 6 2 6270 6418 382127554 382127406 1.750000e-56 231.0
56 TraesCS1B01G197400 chr1A 92.079 101 7 1 2708 2808 489238919 489239018 3.040000e-29 141.0
57 TraesCS1B01G197400 chr1A 91.753 97 8 0 2712 2808 385896054 385895958 1.410000e-27 135.0
58 TraesCS1B01G197400 chr1A 88.182 110 13 0 6676 6785 343396039 343395930 1.830000e-26 132.0
59 TraesCS1B01G197400 chr1A 89.655 87 8 1 7981 8066 66656921 66656835 8.570000e-20 110.0
60 TraesCS1B01G197400 chr6B 87.299 685 75 10 1 678 514658892 514658213 0.000000e+00 773.0
61 TraesCS1B01G197400 chr7B 86.752 702 71 10 1 682 68533181 68533880 0.000000e+00 761.0
62 TraesCS1B01G197400 chr7B 92.941 170 7 4 6270 6438 511856747 511856912 8.090000e-60 243.0
63 TraesCS1B01G197400 chr7B 92.353 170 8 4 6270 6438 511815882 511816047 3.770000e-58 237.0
64 TraesCS1B01G197400 chr3D 88.871 620 60 6 1 614 446704547 446705163 0.000000e+00 754.0
65 TraesCS1B01G197400 chr3D 85.362 690 82 18 1 676 363255373 363254689 0.000000e+00 697.0
66 TraesCS1B01G197400 chr3D 83.871 279 28 7 195 465 15386005 15386274 4.840000e-62 250.0
67 TraesCS1B01G197400 chr3D 94.667 150 6 2 6270 6418 422743000 422743148 1.750000e-56 231.0
68 TraesCS1B01G197400 chr3D 89.899 99 10 0 2710 2808 513951644 513951742 2.360000e-25 128.0
69 TraesCS1B01G197400 chr3D 86.957 115 9 6 2700 2811 1887692 1887581 3.060000e-24 124.0
70 TraesCS1B01G197400 chr3D 100.000 37 0 0 3715 3751 549728816 549728780 1.450000e-07 69.4
71 TraesCS1B01G197400 chr3D 78.000 100 20 2 701 799 17746008 17745910 2.430000e-05 62.1
72 TraesCS1B01G197400 chr4D 92.621 515 36 2 1 513 363692081 363691567 0.000000e+00 739.0
73 TraesCS1B01G197400 chr4D 95.973 149 4 2 6270 6418 325107965 325108111 2.910000e-59 241.0
74 TraesCS1B01G197400 chr4D 94.631 149 6 2 6270 6417 48073484 48073631 6.300000e-56 230.0
75 TraesCS1B01G197400 chr4D 93.506 154 7 3 6270 6420 164880451 164880604 8.150000e-55 226.0
76 TraesCS1B01G197400 chr4D 92.949 156 7 4 6270 6423 331642840 331642993 2.930000e-54 224.0
77 TraesCS1B01G197400 chr4D 89.691 97 9 1 7978 8073 344878071 344878167 1.100000e-23 122.0
78 TraesCS1B01G197400 chr4D 92.308 65 4 1 7901 7965 344878032 344878095 3.100000e-14 91.6
79 TraesCS1B01G197400 chr4D 100.000 37 0 0 3715 3751 443715613 443715577 1.450000e-07 69.4
80 TraesCS1B01G197400 chr6A 86.377 690 72 12 7 676 550622031 550622718 0.000000e+00 734.0
81 TraesCS1B01G197400 chr6A 97.931 145 1 2 6270 6413 381088847 381088704 4.840000e-62 250.0
82 TraesCS1B01G197400 chr6A 93.506 154 8 2 6272 6423 352633648 352633801 2.270000e-55 228.0
83 TraesCS1B01G197400 chr2A 83.485 551 56 13 7416 7965 157499883 157499367 1.580000e-131 481.0
84 TraesCS1B01G197400 chr2A 89.655 87 8 1 7981 8066 157499388 157499302 8.570000e-20 110.0
85 TraesCS1B01G197400 chr2D 91.453 234 20 0 5501 5734 356538173 356537940 1.010000e-83 322.0
86 TraesCS1B01G197400 chr2D 97.297 37 1 0 3715 3751 356538191 356538155 6.760000e-06 63.9
87 TraesCS1B01G197400 chrUn 81.454 399 41 13 7676 8073 354127315 354127681 6.130000e-76 296.0
88 TraesCS1B01G197400 chrUn 85.000 160 23 1 7416 7575 342332686 342332844 2.330000e-35 161.0
89 TraesCS1B01G197400 chrUn 100.000 30 0 0 7653 7682 354127280 354127309 1.000000e-03 56.5
90 TraesCS1B01G197400 chr7A 96.667 150 2 3 6270 6418 552975388 552975535 6.260000e-61 246.0
91 TraesCS1B01G197400 chr6D 96.667 150 2 3 6270 6418 267532954 267532807 6.260000e-61 246.0
92 TraesCS1B01G197400 chr6D 95.333 150 4 3 6270 6418 269703946 269703799 1.350000e-57 235.0
93 TraesCS1B01G197400 chr6D 93.506 154 6 4 6270 6421 391746455 391746304 8.150000e-55 226.0
94 TraesCS1B01G197400 chr6D 94.558 147 6 2 6270 6415 469750527 469750672 8.150000e-55 226.0
95 TraesCS1B01G197400 chr6D 94.000 150 6 3 6270 6418 115323724 115323577 2.930000e-54 224.0
96 TraesCS1B01G197400 chr6D 95.714 140 4 2 6275 6413 126434345 126434207 2.930000e-54 224.0
97 TraesCS1B01G197400 chr6D 94.000 150 6 3 6270 6418 153190921 153190774 2.930000e-54 224.0
98 TraesCS1B01G197400 chr6D 94.000 150 6 3 6270 6418 422907580 422907433 2.930000e-54 224.0
99 TraesCS1B01G197400 chr6D 93.960 149 6 3 6271 6418 160204544 160204398 1.050000e-53 222.0
100 TraesCS1B01G197400 chr6D 92.308 156 8 4 6270 6423 34318514 34318667 1.360000e-52 219.0
101 TraesCS1B01G197400 chr7D 96.000 150 2 4 6266 6413 604292781 604292928 2.910000e-59 241.0
102 TraesCS1B01G197400 chr7D 97.122 139 3 1 6270 6407 605211855 605211993 4.870000e-57 233.0
103 TraesCS1B01G197400 chr7D 93.631 157 6 4 6270 6425 394066397 394066550 1.750000e-56 231.0
104 TraesCS1B01G197400 chr5D 90.654 107 9 1 2702 2808 553674719 553674824 3.040000e-29 141.0


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 TraesCS1B01G197400 chr1B 354982169 354990241 8072 True 14909.000000 14909 100.000000 1 8073 1 chr1B.!!$R2 8072
1 TraesCS1B01G197400 chr1B 655769507 655771256 1749 True 3171.000000 3171 99.371000 3753 5502 1 chr1B.!!$R3 1749
2 TraesCS1B01G197400 chr1B 152830390 152832139 1749 False 3160.000000 3160 99.257000 3753 5502 1 chr1B.!!$F2 1749
3 TraesCS1B01G197400 chr1B 355103109 355108588 5479 True 1365.000000 2468 90.507200 1 7416 5 chr1B.!!$R5 7415
4 TraesCS1B01G197400 chr1B 354922530 354930191 7661 True 316.333333 525 84.240000 978 6785 3 chr1B.!!$R4 5807
5 TraesCS1B01G197400 chr1D 258090132 258095166 5034 False 2550.333333 4671 94.577000 869 7416 3 chr1D.!!$F5 6547
6 TraesCS1B01G197400 chr1D 445316418 445317106 688 False 845.000000 845 89.146000 1 676 1 chr1D.!!$F4 675
7 TraesCS1B01G197400 chr1D 378108855 378109543 688 True 736.000000 736 86.416000 6 676 1 chr1D.!!$R3 670
8 TraesCS1B01G197400 chr1D 258332306 258332963 657 False 514.000000 514 80.931000 978 1638 1 chr1D.!!$F3 660
9 TraesCS1B01G197400 chr1D 258339008 258342083 3075 False 208.500000 287 86.166500 5501 6783 2 chr1D.!!$F6 1282
10 TraesCS1B01G197400 chr5A 259067967 259069716 1749 False 3171.000000 3171 99.371000 3753 5502 1 chr5A.!!$F1 1749
11 TraesCS1B01G197400 chr5B 138779320 138781076 1756 True 3168.000000 3168 99.204000 3753 5509 1 chr5B.!!$R1 1756
12 TraesCS1B01G197400 chr3A 11466366 11468114 1748 False 3164.000000 3164 99.314000 3753 5502 1 chr3A.!!$F1 1749
13 TraesCS1B01G197400 chr4B 90723719 90725471 1752 True 3160.000000 3160 99.201000 3753 5505 1 chr4B.!!$R1 1752
14 TraesCS1B01G197400 chr4B 371971704 371973455 1751 True 3158.000000 3158 99.201000 3753 5505 1 chr4B.!!$R2 1752
15 TraesCS1B01G197400 chr4A 97256496 97258245 1749 False 3160.000000 3160 99.257000 3753 5502 1 chr4A.!!$F1 1749
16 TraesCS1B01G197400 chr4A 395090850 395091497 647 True 880.000000 880 91.074000 7416 8073 1 chr4A.!!$R3 657
17 TraesCS1B01G197400 chr4A 744302104 744303470 1366 True 259.000000 268 85.834000 7416 7965 2 chr4A.!!$R6 549
18 TraesCS1B01G197400 chr3B 583366321 583368071 1750 False 3149.000000 3149 99.143000 3753 5502 1 chr3B.!!$F1 1749
19 TraesCS1B01G197400 chr3B 803383223 803388346 5123 False 443.500000 460 80.208000 7416 8073 2 chr3B.!!$F2 657
20 TraesCS1B01G197400 chr1A 343416269 343424849 8580 True 1305.500000 2438 94.694333 869 7416 6 chr1A.!!$R5 6547
21 TraesCS1B01G197400 chr1A 442916021 442916674 653 False 979.000000 979 93.617000 7416 8073 1 chr1A.!!$F2 657
22 TraesCS1B01G197400 chr1A 66656835 66657419 584 True 283.500000 457 86.116000 7416 8066 2 chr1A.!!$R3 650
23 TraesCS1B01G197400 chr1A 343395930 343399289 3359 True 212.000000 292 86.052500 5501 6785 2 chr1A.!!$R4 1284
24 TraesCS1B01G197400 chr6B 514658213 514658892 679 True 773.000000 773 87.299000 1 678 1 chr6B.!!$R1 677
25 TraesCS1B01G197400 chr7B 68533181 68533880 699 False 761.000000 761 86.752000 1 682 1 chr7B.!!$F1 681
26 TraesCS1B01G197400 chr3D 446704547 446705163 616 False 754.000000 754 88.871000 1 614 1 chr3D.!!$F3 613
27 TraesCS1B01G197400 chr3D 363254689 363255373 684 True 697.000000 697 85.362000 1 676 1 chr3D.!!$R3 675
28 TraesCS1B01G197400 chr4D 363691567 363692081 514 True 739.000000 739 92.621000 1 513 1 chr4D.!!$R1 512
29 TraesCS1B01G197400 chr6A 550622031 550622718 687 False 734.000000 734 86.377000 7 676 1 chr6A.!!$F2 669
30 TraesCS1B01G197400 chr2A 157499302 157499883 581 True 295.500000 481 86.570000 7416 8066 2 chr2A.!!$R1 650

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
822 823 0.247537 GGATTAGTTTTCGGCGTGCG 60.248 55.000 6.85 0.00 0.00 5.34 F
1101 1107 0.034059 CGTCACTCCCTCAACTGCTT 59.966 55.000 0.00 0.00 0.00 3.91 F
1576 1582 0.034476 TTGCTCTCTCCACAGTGCTG 59.966 55.000 0.00 0.00 34.58 4.41 F
2996 3002 0.031178 CTGCAACAAAGTGTGGAGCC 59.969 55.000 0.00 0.00 32.04 4.70 F
3560 3566 0.032540 CACAGGCTTGGTTTTCTGCC 59.967 55.000 0.00 0.00 45.21 4.85 F
3677 3683 0.036105 ATGCATCGCTTCTCACCACA 60.036 50.000 0.00 0.00 0.00 4.17 F
3679 3685 0.166814 GCATCGCTTCTCACCACAAC 59.833 55.000 0.00 0.00 0.00 3.32 F
3684 3690 0.179018 GCTTCTCACCACAACCACCT 60.179 55.000 0.00 0.00 0.00 4.00 F
3690 3696 1.283613 TCACCACAACCACCTTCTTGT 59.716 47.619 0.00 0.00 0.00 3.16 F
5705 12983 1.324736 GCTACAAAGTTCGAGATGCCG 59.675 52.381 0.00 0.00 0.00 5.69 F
6312 15200 0.105039 GGTGCGTGGAAGCTAGCTAT 59.895 55.000 19.70 8.44 38.13 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2680 2686 0.036875 AACTGGGTTGTCTGCTAGGC 59.963 55.000 0.00 0.00 0.00 3.93 R
2977 2983 0.031178 GGCTCCACACTTTGTTGCAG 59.969 55.000 0.00 0.00 0.00 4.41 R
3541 3547 0.032540 GGCAGAAAACCAAGCCTGTG 59.967 55.000 0.00 0.00 43.70 3.66 R
4920 5351 1.153369 CGCCACTTCATCCATCCGT 60.153 57.895 0.00 0.00 0.00 4.69 R
5222 12074 2.683572 TTCTGGAGGCCTGCGCTA 60.684 61.111 20.39 4.23 34.44 4.26 R
5532 12806 2.997463 TCCACCCCCTTTTAAAGATGGA 59.003 45.455 15.77 14.07 32.62 3.41 R
5559 12833 3.118738 GGGTCGTCAGATCAGTAAACCAT 60.119 47.826 0.00 0.00 0.00 3.55 R
5705 12983 8.911247 AAAAATAGTTGAAGGATGCGATAAAC 57.089 30.769 0.00 0.00 0.00 2.01 R
6133 15021 3.423539 TGCTCTCACAAACTGCCTTAT 57.576 42.857 0.00 0.00 0.00 1.73 R
6960 16976 0.034896 TTCTTTGACAGGAGACGGGC 59.965 55.000 0.00 0.00 0.00 6.13 R
7818 20757 0.037882 ATCAGGCAGTGACGACAGTG 60.038 55.000 16.83 16.83 46.64 3.66 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)


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AutoCloner maintained by Alex Coulton.