Multiple sequence alignment - TraesCS1B01G197400
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 pairsThese primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible. |
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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 primersListed 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. |
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Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.