Multiple sequence alignment - TraesCS1B01G312200

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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 TraesCS1B01G312200 chr1B 100.000 7013 0 0 1 7013 535916092 535909080 0.000000e+00 12951.0
1 TraesCS1B01G312200 chr1B 100.000 2017 0 0 7124 9140 535908969 535906953 0.000000e+00 3725.0
2 TraesCS1B01G312200 chr1B 98.181 2034 19 1 1 2034 535941203 535939188 0.000000e+00 3535.0
3 TraesCS1B01G312200 chr1B 94.334 1059 60 0 976 2034 535799451 535798393 0.000000e+00 1624.0
4 TraesCS1B01G312200 chr1B 91.852 1080 66 16 8069 9140 536121380 536120315 0.000000e+00 1487.0
5 TraesCS1B01G312200 chr1B 91.988 1036 80 1 1002 2034 536122917 536121882 0.000000e+00 1450.0
6 TraesCS1B01G312200 chr1B 91.418 839 48 8 1 815 535917581 535916743 0.000000e+00 1129.0
7 TraesCS1B01G312200 chr1B 98.058 515 5 1 2034 2548 535909589 535909080 0.000000e+00 891.0
8 TraesCS1B01G312200 chr1B 90.616 682 45 14 8473 9140 535923713 535923037 0.000000e+00 887.0
9 TraesCS1B01G312200 chr1B 96.667 510 15 2 7480 7989 536121884 536121377 0.000000e+00 846.0
10 TraesCS1B01G312200 chr1B 96.667 510 14 2 7480 7989 535939190 535938684 0.000000e+00 845.0
11 TraesCS1B01G312200 chr1B 94.231 416 21 3 8069 8483 535938687 535938274 4.660000e-177 632.0
12 TraesCS1B01G312200 chr1B 98.315 356 5 1 7124 7478 535913529 535913174 2.800000e-174 623.0
13 TraesCS1B01G312200 chr1B 90.316 475 39 4 7480 7951 535798395 535797925 4.690000e-172 616.0
14 TraesCS1B01G312200 chr1B 85.946 555 52 16 1 529 47711257 47711811 3.700000e-158 569.0
15 TraesCS1B01G312200 chr1B 92.488 213 9 3 783 988 535799678 535799466 1.930000e-76 298.0
16 TraesCS1B01G312200 chr1B 94.828 58 3 0 669 726 535799743 535799686 3.510000e-14 91.6
17 TraesCS1B01G312200 chr2B 95.811 4464 172 9 2539 6991 578315144 578310685 0.000000e+00 7193.0
18 TraesCS1B01G312200 chr2B 93.573 3750 200 18 2541 6276 96116994 96113272 0.000000e+00 5552.0
19 TraesCS1B01G312200 chr2B 84.428 2832 366 46 2621 5427 251109708 251112489 0.000000e+00 2717.0
20 TraesCS1B01G312200 chr2B 91.033 1026 77 9 2619 3634 213678166 213679186 0.000000e+00 1371.0
21 TraesCS1B01G312200 chr2B 92.166 868 41 4 2034 2898 578311176 578310333 0.000000e+00 1201.0
22 TraesCS1B01G312200 chr2B 95.606 660 23 2 6309 6963 96113275 96112617 0.000000e+00 1053.0
23 TraesCS1B01G312200 chr2B 96.767 464 15 0 2037 2500 578315598 578315135 0.000000e+00 774.0
24 TraesCS1B01G312200 chr2B 96.129 465 18 0 2034 2498 96113081 96112617 0.000000e+00 760.0
25 TraesCS1B01G312200 chr2B 95.905 464 14 1 6507 6965 578315598 578315135 0.000000e+00 747.0
26 TraesCS1B01G312200 chr2B 90.713 463 35 3 206 660 569075755 569076217 2.180000e-170 610.0
27 TraesCS1B01G312200 chr2B 92.458 358 24 1 7124 7478 578315119 578314762 8.190000e-140 508.0
28 TraesCS1B01G312200 chr2B 92.582 337 22 1 7124 7457 578310669 578310333 1.780000e-131 481.0
29 TraesCS1B01G312200 chr2B 88.089 361 35 8 7124 7478 96112601 96112243 1.100000e-113 422.0
30 TraesCS1B01G312200 chr2B 94.444 90 5 0 7985 8074 49649220 49649131 1.240000e-28 139.0
31 TraesCS1B01G312200 chr3D 95.333 4435 193 7 2541 6963 375577520 375581952 0.000000e+00 7031.0
32 TraesCS1B01G312200 chr3D 95.196 4434 198 8 2541 6963 375581945 375586374 0.000000e+00 6994.0
33 TraesCS1B01G312200 chr3D 94.759 4446 204 16 2541 6963 504469231 504473670 0.000000e+00 6892.0
34 TraesCS1B01G312200 chr3D 95.923 466 19 0 2033 2498 504468773 504469238 0.000000e+00 756.0
35 TraesCS1B01G312200 chr3D 95.484 465 21 0 2034 2498 375577063 375577527 0.000000e+00 743.0
36 TraesCS1B01G312200 chr3D 85.303 694 55 18 1 664 6449343 6448667 0.000000e+00 673.0
37 TraesCS1B01G312200 chr3D 89.972 359 32 3 7124 7478 375581968 375582326 2.330000e-125 460.0
38 TraesCS1B01G312200 chr3D 89.136 359 35 3 7124 7478 375577543 375577901 2.340000e-120 444.0
39 TraesCS1B01G312200 chr3D 88.611 360 35 5 7124 7479 375586390 375586747 5.070000e-117 433.0
40 TraesCS1B01G312200 chr1D 93.892 4453 234 24 2541 6963 61431697 61436141 0.000000e+00 6682.0
41 TraesCS1B01G312200 chr1D 91.384 1207 85 10 839 2034 399394959 399393761 0.000000e+00 1635.0
42 TraesCS1B01G312200 chr1D 90.068 1168 100 12 876 2034 399415368 399414208 0.000000e+00 1500.0
43 TraesCS1B01G312200 chr1D 96.983 464 14 0 2035 2498 61431241 61431704 0.000000e+00 780.0
44 TraesCS1B01G312200 chr1D 96.559 465 16 0 2034 2498 61435677 61436141 0.000000e+00 771.0
45 TraesCS1B01G312200 chr1D 93.517 509 27 3 7480 7988 399414210 399413708 0.000000e+00 752.0
46 TraesCS1B01G312200 chr1D 87.590 556 37 16 8069 8598 399413710 399413161 4.690000e-172 616.0
47 TraesCS1B01G312200 chr1D 88.958 480 41 7 7480 7951 399393763 399393288 4.760000e-162 582.0
48 TraesCS1B01G312200 chr1D 82.723 382 37 14 669 1049 399411321 399410968 6.890000e-81 313.0
49 TraesCS1B01G312200 chr1D 91.176 102 9 0 8433 8534 399547332 399547231 1.240000e-28 139.0
50 TraesCS1B01G312200 chr1D 90.000 60 4 2 653 711 399395615 399395557 9.840000e-10 76.8
51 TraesCS1B01G312200 chr1D 92.453 53 4 0 8384 8436 399547452 399547400 9.840000e-10 76.8
52 TraesCS1B01G312200 chr5D 92.909 4442 268 25 2541 6963 337365857 337361444 0.000000e+00 6414.0
53 TraesCS1B01G312200 chr5D 87.920 654 55 16 1 633 373957591 373956941 0.000000e+00 749.0
54 TraesCS1B01G312200 chr5D 87.812 361 34 7 7124 7478 337365834 337365478 1.840000e-111 414.0
55 TraesCS1B01G312200 chr5D 83.654 104 17 0 8680 8783 119492074 119492177 2.100000e-16 99.0
56 TraesCS1B01G312200 chr3B 93.484 3990 232 9 2621 6605 803195061 803191095 0.000000e+00 5903.0
57 TraesCS1B01G312200 chr3B 89.390 688 48 4 1 663 503771390 503772077 0.000000e+00 843.0
58 TraesCS1B01G312200 chr3B 92.784 97 6 1 7986 8082 117602004 117601909 1.240000e-28 139.0
59 TraesCS1B01G312200 chr3B 88.462 104 12 0 8679 8782 421903055 421902952 9.630000e-25 126.0
60 TraesCS1B01G312200 chr3B 84.545 110 17 0 8679 8788 58678329 58678438 9.700000e-20 110.0
61 TraesCS1B01G312200 chr7D 94.963 3772 174 10 2621 6381 61146651 61150417 0.000000e+00 5899.0
62 TraesCS1B01G312200 chr7D 88.605 860 65 12 2541 3381 51840990 51840145 0.000000e+00 1014.0
63 TraesCS1B01G312200 chr7D 84.593 1032 143 13 1006 2034 154935832 154934814 0.000000e+00 1011.0
64 TraesCS1B01G312200 chr7D 71.256 908 210 35 1072 1970 178475050 178475915 5.640000e-42 183.0
65 TraesCS1B01G312200 chr7D 92.000 100 7 1 7987 8086 34845557 34845655 1.240000e-28 139.0
66 TraesCS1B01G312200 chr7D 85.149 101 13 2 8676 8776 554683945 554684043 1.620000e-17 102.0
67 TraesCS1B01G312200 chr6B 95.492 3305 139 5 3667 6963 204630922 204634224 0.000000e+00 5269.0
68 TraesCS1B01G312200 chr3A 91.638 3803 290 13 2621 6398 750626471 750630270 0.000000e+00 5236.0
69 TraesCS1B01G312200 chr4A 91.971 2242 154 9 4729 6959 718111164 718108938 0.000000e+00 3120.0
70 TraesCS1B01G312200 chr4A 91.618 2243 161 10 4729 6959 718210417 718208190 0.000000e+00 3075.0
71 TraesCS1B01G312200 chr1A 93.514 1033 67 0 1002 2034 496143396 496142364 0.000000e+00 1537.0
72 TraesCS1B01G312200 chr1A 88.150 481 44 8 7480 7952 496142366 496141891 2.230000e-155 560.0
73 TraesCS1B01G312200 chr7B 92.146 904 49 12 2034 2919 712121689 712120790 0.000000e+00 1256.0
74 TraesCS1B01G312200 chr7B 83.932 1058 151 15 983 2034 116753282 116754326 0.000000e+00 994.0
75 TraesCS1B01G312200 chr7B 82.932 996 142 18 1062 2034 45052424 45051434 0.000000e+00 872.0
76 TraesCS1B01G312200 chr7B 87.945 365 31 9 7124 7478 712125589 712125228 1.420000e-112 418.0
77 TraesCS1B01G312200 chr7B 84.652 417 59 3 7478 7893 45051438 45051026 2.380000e-110 411.0
78 TraesCS1B01G312200 chr7B 82.009 428 59 13 7480 7895 116754324 116754745 1.890000e-91 348.0
79 TraesCS1B01G312200 chr7B 84.685 111 9 7 8680 8785 237489312 237489419 4.510000e-18 104.0
80 TraesCS1B01G312200 chr7A 85.352 1024 134 12 1016 2034 156549129 156550141 0.000000e+00 1046.0
81 TraesCS1B01G312200 chr7A 82.599 431 54 13 7480 7895 156550139 156550563 2.430000e-95 361.0
82 TraesCS1B01G312200 chr5B 88.953 688 49 7 1 663 345852540 345853225 0.000000e+00 824.0
83 TraesCS1B01G312200 chr5B 88.679 689 51 8 1 663 478551506 478550819 0.000000e+00 815.0
84 TraesCS1B01G312200 chr5B 87.941 680 59 7 1 663 530260056 530260729 0.000000e+00 780.0
85 TraesCS1B01G312200 chr5B 87.663 689 47 15 1 663 514923914 514924590 0.000000e+00 767.0
86 TraesCS1B01G312200 chr5B 86.861 685 63 14 1 659 653225310 653225993 0.000000e+00 741.0
87 TraesCS1B01G312200 chr5B 85.839 685 73 14 1 663 486089663 486088981 0.000000e+00 706.0
88 TraesCS1B01G312200 chr5B 89.815 108 10 1 7984 8091 432174789 432174683 4.450000e-28 137.0
89 TraesCS1B01G312200 chr6D 86.637 681 53 12 1 663 36286202 36286862 0.000000e+00 719.0
90 TraesCS1B01G312200 chr6D 91.837 98 8 0 7978 8075 443958613 443958516 4.450000e-28 137.0
91 TraesCS1B01G312200 chrUn 85.735 680 56 22 1 655 42149456 42150119 0.000000e+00 680.0
92 TraesCS1B01G312200 chr2D 84.840 686 62 16 1 663 538072179 538072845 0.000000e+00 652.0
93 TraesCS1B01G312200 chr2D 86.667 90 12 0 8695 8784 317345717 317345628 5.840000e-17 100.0
94 TraesCS1B01G312200 chr6A 94.845 97 4 1 7976 8071 125259996 125260092 5.720000e-32 150.0
95 TraesCS1B01G312200 chr6A 93.617 94 6 0 7982 8075 108175336 108175429 3.440000e-29 141.0
96 TraesCS1B01G312200 chr6A 93.548 93 6 0 7980 8072 617249290 617249198 1.240000e-28 139.0
97 TraesCS1B01G312200 chr5A 97.701 87 2 0 7986 8072 496022124 496022210 5.720000e-32 150.0
98 TraesCS1B01G312200 chr2A 86.139 101 14 0 8679 8779 77795174 77795274 9.700000e-20 110.0


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 TraesCS1B01G312200 chr1B 535906953 535916092 9139 True 8338.000000 12951 100.000000 1 9140 2 chr1B.!!$R3 9139
1 TraesCS1B01G312200 chr1B 535938274 535941203 2929 True 1670.666667 3535 96.359667 1 8483 3 chr1B.!!$R5 8482
2 TraesCS1B01G312200 chr1B 536120315 536122917 2602 True 1261.000000 1487 93.502333 1002 9140 3 chr1B.!!$R6 8138
3 TraesCS1B01G312200 chr1B 535923037 535923713 676 True 887.000000 887 90.616000 8473 9140 1 chr1B.!!$R1 667
4 TraesCS1B01G312200 chr1B 535909080 535917581 8501 True 881.000000 1129 95.930333 1 7478 3 chr1B.!!$R4 7477
5 TraesCS1B01G312200 chr1B 535797925 535799743 1818 True 657.400000 1624 92.991500 669 7951 4 chr1B.!!$R2 7282
6 TraesCS1B01G312200 chr1B 47711257 47711811 554 False 569.000000 569 85.946000 1 529 1 chr1B.!!$F1 528
7 TraesCS1B01G312200 chr2B 251109708 251112489 2781 False 2717.000000 2717 84.428000 2621 5427 1 chr2B.!!$F2 2806
8 TraesCS1B01G312200 chr2B 96112243 96116994 4751 True 1946.750000 5552 93.349250 2034 7478 4 chr2B.!!$R2 5444
9 TraesCS1B01G312200 chr2B 578310333 578315598 5265 True 1817.333333 7193 94.281500 2034 7478 6 chr2B.!!$R3 5444
10 TraesCS1B01G312200 chr2B 213678166 213679186 1020 False 1371.000000 1371 91.033000 2619 3634 1 chr2B.!!$F1 1015
11 TraesCS1B01G312200 chr3D 375581945 375586374 4429 False 6994.000000 6994 95.196000 2541 6963 1 chr3D.!!$F2 4422
12 TraesCS1B01G312200 chr3D 375577063 375581952 4889 False 3887.000000 7031 95.408500 2034 6963 2 chr3D.!!$F5 4929
13 TraesCS1B01G312200 chr3D 504468773 504473670 4897 False 3824.000000 6892 95.341000 2033 6963 2 chr3D.!!$F6 4930
14 TraesCS1B01G312200 chr3D 6448667 6449343 676 True 673.000000 673 85.303000 1 664 1 chr3D.!!$R1 663
15 TraesCS1B01G312200 chr1D 61431241 61436141 4900 False 2744.333333 6682 95.811333 2034 6963 3 chr1D.!!$F1 4929
16 TraesCS1B01G312200 chr1D 399410968 399415368 4400 True 795.250000 1500 88.474500 669 8598 4 chr1D.!!$R2 7929
17 TraesCS1B01G312200 chr1D 399393288 399395615 2327 True 764.600000 1635 90.114000 653 7951 3 chr1D.!!$R1 7298
18 TraesCS1B01G312200 chr5D 337361444 337365857 4413 True 3414.000000 6414 90.360500 2541 7478 2 chr5D.!!$R2 4937
19 TraesCS1B01G312200 chr5D 373956941 373957591 650 True 749.000000 749 87.920000 1 633 1 chr5D.!!$R1 632
20 TraesCS1B01G312200 chr3B 803191095 803195061 3966 True 5903.000000 5903 93.484000 2621 6605 1 chr3B.!!$R3 3984
21 TraesCS1B01G312200 chr3B 503771390 503772077 687 False 843.000000 843 89.390000 1 663 1 chr3B.!!$F2 662
22 TraesCS1B01G312200 chr7D 61146651 61150417 3766 False 5899.000000 5899 94.963000 2621 6381 1 chr7D.!!$F2 3760
23 TraesCS1B01G312200 chr7D 51840145 51840990 845 True 1014.000000 1014 88.605000 2541 3381 1 chr7D.!!$R1 840
24 TraesCS1B01G312200 chr7D 154934814 154935832 1018 True 1011.000000 1011 84.593000 1006 2034 1 chr7D.!!$R2 1028
25 TraesCS1B01G312200 chr6B 204630922 204634224 3302 False 5269.000000 5269 95.492000 3667 6963 1 chr6B.!!$F1 3296
26 TraesCS1B01G312200 chr3A 750626471 750630270 3799 False 5236.000000 5236 91.638000 2621 6398 1 chr3A.!!$F1 3777
27 TraesCS1B01G312200 chr4A 718108938 718111164 2226 True 3120.000000 3120 91.971000 4729 6959 1 chr4A.!!$R1 2230
28 TraesCS1B01G312200 chr4A 718208190 718210417 2227 True 3075.000000 3075 91.618000 4729 6959 1 chr4A.!!$R2 2230
29 TraesCS1B01G312200 chr1A 496141891 496143396 1505 True 1048.500000 1537 90.832000 1002 7952 2 chr1A.!!$R1 6950
30 TraesCS1B01G312200 chr7B 712120790 712125589 4799 True 837.000000 1256 90.045500 2034 7478 2 chr7B.!!$R2 5444
31 TraesCS1B01G312200 chr7B 116753282 116754745 1463 False 671.000000 994 82.970500 983 7895 2 chr7B.!!$F2 6912
32 TraesCS1B01G312200 chr7B 45051026 45052424 1398 True 641.500000 872 83.792000 1062 7893 2 chr7B.!!$R1 6831
33 TraesCS1B01G312200 chr7A 156549129 156550563 1434 False 703.500000 1046 83.975500 1016 7895 2 chr7A.!!$F1 6879
34 TraesCS1B01G312200 chr5B 345852540 345853225 685 False 824.000000 824 88.953000 1 663 1 chr5B.!!$F1 662
35 TraesCS1B01G312200 chr5B 478550819 478551506 687 True 815.000000 815 88.679000 1 663 1 chr5B.!!$R2 662
36 TraesCS1B01G312200 chr5B 530260056 530260729 673 False 780.000000 780 87.941000 1 663 1 chr5B.!!$F3 662
37 TraesCS1B01G312200 chr5B 514923914 514924590 676 False 767.000000 767 87.663000 1 663 1 chr5B.!!$F2 662
38 TraesCS1B01G312200 chr5B 653225310 653225993 683 False 741.000000 741 86.861000 1 659 1 chr5B.!!$F4 658
39 TraesCS1B01G312200 chr5B 486088981 486089663 682 True 706.000000 706 85.839000 1 663 1 chr5B.!!$R3 662
40 TraesCS1B01G312200 chr6D 36286202 36286862 660 False 719.000000 719 86.637000 1 663 1 chr6D.!!$F1 662
41 TraesCS1B01G312200 chrUn 42149456 42150119 663 False 680.000000 680 85.735000 1 655 1 chrUn.!!$F1 654
42 TraesCS1B01G312200 chr2D 538072179 538072845 666 False 652.000000 652 84.840000 1 663 1 chr2D.!!$F1 662

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
7159 9337 5.193679 TCAAGATGGACAGATTCTAGTCGA 58.806 41.667 8.94 6.74 35.63 4.20 F
7880 10080 0.101759 CATGCAGGAATTCCTTGCCG 59.898 55.000 29.90 22.29 46.09 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
8070 10275 1.200252 CAACTCAGTCGAGACGATGGT 59.80 52.381 0.0 0.00 42.34 3.55 R
8804 11080 1.349542 ATACATGGGCCGGCCTAACA 61.35 55.000 42.7 32.47 36.10 2.41 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
7159 9337 5.193679 TCAAGATGGACAGATTCTAGTCGA 58.806 41.667 8.94 6.74 35.63 4.20
7170 9348 7.548097 ACAGATTCTAGTCGATTTAGCTTTGA 58.452 34.615 0.00 0.00 0.00 2.69
7180 9358 9.313118 AGTCGATTTAGCTTTGAAATTGTTTTT 57.687 25.926 0.00 0.00 31.93 1.94
7346 9533 4.812091 GGTTTGGTAATCTTTGCCGTTTTT 59.188 37.500 0.00 0.00 38.38 1.94
7459 9647 1.302383 TTATCTTGGTGTTGCGCGGG 61.302 55.000 8.83 0.00 0.00 6.13
7465 9653 2.648454 GTGTTGCGCGGGGATTTT 59.352 55.556 8.83 0.00 0.00 1.82
7466 9654 1.443702 GTGTTGCGCGGGGATTTTC 60.444 57.895 8.83 0.00 0.00 2.29
7478 9666 2.553685 GGGGATTTTCCGTACCAACACT 60.554 50.000 0.00 0.00 37.43 3.55
7880 10080 0.101759 CATGCAGGAATTCCTTGCCG 59.898 55.000 29.90 22.29 46.09 5.69
7909 10114 2.509336 CTGCTCTGTTACCGGCCG 60.509 66.667 21.04 21.04 0.00 6.13
7989 10194 7.883311 ACTATCCTGTTGCACTTATTTTGTACT 59.117 33.333 0.00 0.00 0.00 2.73
7990 10195 6.952773 TCCTGTTGCACTTATTTTGTACTT 57.047 33.333 0.00 0.00 0.00 2.24
7991 10196 6.966021 TCCTGTTGCACTTATTTTGTACTTC 58.034 36.000 0.00 0.00 0.00 3.01
7992 10197 6.016610 TCCTGTTGCACTTATTTTGTACTTCC 60.017 38.462 0.00 0.00 0.00 3.46
7993 10198 6.016276 CCTGTTGCACTTATTTTGTACTTCCT 60.016 38.462 0.00 0.00 0.00 3.36
7994 10199 6.966021 TGTTGCACTTATTTTGTACTTCCTC 58.034 36.000 0.00 0.00 0.00 3.71
7995 10200 6.770785 TGTTGCACTTATTTTGTACTTCCTCT 59.229 34.615 0.00 0.00 0.00 3.69
7996 10201 6.801539 TGCACTTATTTTGTACTTCCTCTG 57.198 37.500 0.00 0.00 0.00 3.35
7997 10202 6.296026 TGCACTTATTTTGTACTTCCTCTGT 58.704 36.000 0.00 0.00 0.00 3.41
7998 10203 7.446769 TGCACTTATTTTGTACTTCCTCTGTA 58.553 34.615 0.00 0.00 0.00 2.74
7999 10204 7.934665 TGCACTTATTTTGTACTTCCTCTGTAA 59.065 33.333 0.00 0.00 0.00 2.41
8000 10205 8.780249 GCACTTATTTTGTACTTCCTCTGTAAA 58.220 33.333 0.00 0.00 0.00 2.01
8014 10219 9.400638 CTTCCTCTGTAAACTAATATAAGAGCG 57.599 37.037 0.00 0.00 0.00 5.03
8015 10220 8.461249 TCCTCTGTAAACTAATATAAGAGCGT 57.539 34.615 0.00 0.00 0.00 5.07
8016 10221 8.910944 TCCTCTGTAAACTAATATAAGAGCGTT 58.089 33.333 0.00 0.00 0.00 4.84
8017 10222 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
8032 10237 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
8033 10238 7.393841 AGAGCGTTTAGATCACTAAAGTAGT 57.606 36.000 0.00 0.00 45.42 2.73
8066 10271 9.727627 AACGTTCTTATATTAGTTAACGGAGAG 57.272 33.333 15.64 0.00 42.79 3.20
8067 10272 9.113838 ACGTTCTTATATTAGTTAACGGAGAGA 57.886 33.333 15.64 0.00 42.79 3.10
8068 10273 9.596677 CGTTCTTATATTAGTTAACGGAGAGAG 57.403 37.037 0.00 0.00 36.86 3.20
8089 10294 1.535833 ACCATCGTCTCGACTGAGTT 58.464 50.000 0.00 0.00 43.09 3.01
8156 10361 7.546667 CAGCTATGTGTTAATTGCTTGGAAAAT 59.453 33.333 0.00 0.00 36.66 1.82
8157 10362 8.096414 AGCTATGTGTTAATTGCTTGGAAAATT 58.904 29.630 0.00 0.00 35.50 1.82
8407 10638 7.226128 TGAATGCATGCACAATTTTAAAACTCA 59.774 29.630 25.37 3.27 0.00 3.41
8551 10782 6.293081 CGTATGTCTCCATTTAGCCAAATCTG 60.293 42.308 0.00 0.00 31.82 2.90
8559 10791 6.485313 TCCATTTAGCCAAATCTGTATAACGG 59.515 38.462 0.00 0.00 31.82 4.44
8689 10955 5.658190 TGTGTCATGAATGATACTCTCTCCA 59.342 40.000 17.58 0.00 45.56 3.86
8693 10959 7.234988 TGTCATGAATGATACTCTCTCCATCAT 59.765 37.037 0.00 0.00 40.31 2.45
8749 11020 9.953565 TGGTGCTAAAACTAGTATAAAGTTGAT 57.046 29.630 0.00 0.18 37.26 2.57
8797 11068 8.015185 AGTAATAAATAAGGTACTCGGAGCAA 57.985 34.615 4.58 0.00 38.49 3.91
8798 11069 8.648693 AGTAATAAATAAGGTACTCGGAGCAAT 58.351 33.333 4.58 0.00 38.49 3.56
8804 11080 4.947449 AAGGTACTCGGAGCAATGAAGCT 61.947 47.826 4.58 0.00 44.54 3.74
8888 11188 6.288941 TCCATCATTCTGCATCATGTTTTT 57.711 33.333 5.42 0.00 0.00 1.94
8936 11236 6.015772 TCCTTATTCTTTTCACCCTTTTTCCG 60.016 38.462 0.00 0.00 0.00 4.30
8941 11245 0.878416 TTCACCCTTTTTCCGATGCG 59.122 50.000 0.00 0.00 0.00 4.73
9120 11424 9.143631 CACCTACAATTTTCAAATTCAGAATCC 57.856 33.333 0.00 0.00 36.52 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7170 9348 6.643360 GGACTTGGCGTATACAAAAACAATTT 59.357 34.615 3.32 0.00 0.00 1.82
7180 9358 0.179121 CGCTGGACTTGGCGTATACA 60.179 55.000 3.32 0.00 45.34 2.29
7270 9455 8.671921 AGAACGATAGAGAAAAAGACATACGTA 58.328 33.333 0.00 0.00 41.38 3.57
7317 9503 4.569015 GGCAAAGATTACCAAACCCTAGGA 60.569 45.833 11.48 0.00 0.00 2.94
7459 9647 3.057806 CCAAGTGTTGGTACGGAAAATCC 60.058 47.826 0.00 0.00 45.93 3.01
7740 9940 1.455032 TTCTCCGCTATCTCCGCCA 60.455 57.895 0.00 0.00 0.00 5.69
7880 10080 2.813042 GAGCAGTCACCTGAGCGC 60.813 66.667 0.00 0.00 41.50 5.92
7909 10114 0.690762 TCAGTAACCAACAGCTCCCC 59.309 55.000 0.00 0.00 0.00 4.81
7966 10171 7.309194 GGAAGTACAAAATAAGTGCAACAGGAT 60.309 37.037 0.00 0.00 41.43 3.24
7989 10194 8.910944 ACGCTCTTATATTAGTTTACAGAGGAA 58.089 33.333 0.00 0.00 0.00 3.36
7990 10195 8.461249 ACGCTCTTATATTAGTTTACAGAGGA 57.539 34.615 0.00 0.00 0.00 3.71
7991 10196 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
8006 10211 9.953697 CTACTTTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 40.05 1.73
8007 10212 8.954350 ACTACTTTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 40.05 2.10
8008 10213 7.828712 ACTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
8009 10214 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
8040 10245 9.727627 CTCTCCGTTAACTAATATAAGAACGTT 57.272 33.333 0.00 0.00 38.32 3.99
8041 10246 9.113838 TCTCTCCGTTAACTAATATAAGAACGT 57.886 33.333 3.71 0.00 38.32 3.99
8042 10247 9.596677 CTCTCTCCGTTAACTAATATAAGAACG 57.403 37.037 3.71 0.00 39.38 3.95
8047 10252 9.851686 TGGTACTCTCTCCGTTAACTAATATAA 57.148 33.333 3.71 0.00 0.00 0.98
8049 10254 8.937207 ATGGTACTCTCTCCGTTAACTAATAT 57.063 34.615 3.71 0.00 0.00 1.28
8050 10255 7.172190 CGATGGTACTCTCTCCGTTAACTAATA 59.828 40.741 3.71 0.00 0.00 0.98
8051 10256 6.017275 CGATGGTACTCTCTCCGTTAACTAAT 60.017 42.308 3.71 0.00 0.00 1.73
8052 10257 5.295292 CGATGGTACTCTCTCCGTTAACTAA 59.705 44.000 3.71 0.00 0.00 2.24
8053 10258 4.813161 CGATGGTACTCTCTCCGTTAACTA 59.187 45.833 3.71 0.00 0.00 2.24
8054 10259 3.626670 CGATGGTACTCTCTCCGTTAACT 59.373 47.826 3.71 0.00 0.00 2.24
8055 10260 3.376546 ACGATGGTACTCTCTCCGTTAAC 59.623 47.826 0.00 0.00 0.00 2.01
8056 10261 3.614092 ACGATGGTACTCTCTCCGTTAA 58.386 45.455 0.00 0.00 0.00 2.01
8057 10262 3.118482 AGACGATGGTACTCTCTCCGTTA 60.118 47.826 0.00 0.00 0.00 3.18
8058 10263 2.015587 GACGATGGTACTCTCTCCGTT 58.984 52.381 0.00 0.00 0.00 4.44
8059 10264 1.209990 AGACGATGGTACTCTCTCCGT 59.790 52.381 0.00 0.00 0.00 4.69
8060 10265 1.868498 GAGACGATGGTACTCTCTCCG 59.132 57.143 0.00 0.00 0.00 4.63
8061 10266 1.868498 CGAGACGATGGTACTCTCTCC 59.132 57.143 7.30 0.00 0.00 3.71
8062 10267 2.540931 GTCGAGACGATGGTACTCTCTC 59.459 54.545 7.30 5.19 38.42 3.20
8063 10268 2.168936 AGTCGAGACGATGGTACTCTCT 59.831 50.000 7.30 0.00 38.42 3.10
8064 10269 2.285756 CAGTCGAGACGATGGTACTCTC 59.714 54.545 0.00 0.00 38.42 3.20
8065 10270 2.093606 TCAGTCGAGACGATGGTACTCT 60.094 50.000 0.00 0.00 38.42 3.24
8066 10271 2.277969 TCAGTCGAGACGATGGTACTC 58.722 52.381 0.00 0.00 38.42 2.59
8067 10272 2.281517 CTCAGTCGAGACGATGGTACT 58.718 52.381 0.00 0.00 42.34 2.73
8068 10273 2.008329 ACTCAGTCGAGACGATGGTAC 58.992 52.381 0.00 0.00 42.34 3.34
8069 10274 2.398252 ACTCAGTCGAGACGATGGTA 57.602 50.000 0.00 0.00 42.34 3.25
8070 10275 1.200252 CAACTCAGTCGAGACGATGGT 59.800 52.381 0.00 0.00 42.34 3.55
8071 10276 1.901538 CAACTCAGTCGAGACGATGG 58.098 55.000 0.00 0.00 42.34 3.51
8156 10361 4.205385 GCGCGAATTGACTTACAACAAAAA 59.795 37.500 12.10 0.00 41.52 1.94
8157 10362 3.726730 GCGCGAATTGACTTACAACAAAA 59.273 39.130 12.10 0.00 41.52 2.44
8368 10598 6.532302 GTGCATGCATTCAAGAAATATTCACA 59.468 34.615 25.64 0.00 0.00 3.58
8551 10782 3.806625 TGACCTGCCTAACCGTTATAC 57.193 47.619 0.00 0.00 0.00 1.47
8559 10791 4.327680 ACTCTCATTTTGACCTGCCTAAC 58.672 43.478 0.00 0.00 0.00 2.34
8749 11020 4.847512 TCCCTCTGTCCCAAAATAAGTGTA 59.152 41.667 0.00 0.00 0.00 2.90
8797 11068 1.452108 GCCGGCCTAACAGCTTCAT 60.452 57.895 18.11 0.00 0.00 2.57
8798 11069 2.046314 GCCGGCCTAACAGCTTCA 60.046 61.111 18.11 0.00 0.00 3.02
8804 11080 1.349542 ATACATGGGCCGGCCTAACA 61.350 55.000 42.70 32.47 36.10 2.41


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

AutoCloner maintained by Alex Coulton.