Multiple sequence alignment - TraesCS2A01G153100

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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 TraesCS2A01G153100 chr2A 100.000 4339 0 0 992 5330 101130268 101125930 0.000000e+00 8013.0
1 TraesCS2A01G153100 chr2A 95.898 2511 86 7 2089 4592 715827555 715825055 0.000000e+00 4050.0
2 TraesCS2A01G153100 chr2A 95.575 1017 42 3 992 2008 715828578 715827565 0.000000e+00 1626.0
3 TraesCS2A01G153100 chr2A 95.553 787 33 1 3153 3937 484994028 484993242 0.000000e+00 1258.0
4 TraesCS2A01G153100 chr2A 100.000 566 0 0 1 566 101131259 101130694 0.000000e+00 1046.0
5 TraesCS2A01G153100 chr2A 95.053 566 18 5 2 563 715829675 715829116 0.000000e+00 881.0
6 TraesCS2A01G153100 chr2A 93.871 310 18 1 2844 3152 484995501 484995192 2.910000e-127 466.0
7 TraesCS2A01G153100 chr2A 88.806 134 14 1 2940 3072 537058247 537058380 4.270000e-36 163.0
8 TraesCS2A01G153100 chr2A 91.463 82 7 0 2841 2922 687921163 687921082 4.360000e-21 113.0
9 TraesCS2A01G153100 chr1A 96.045 3843 133 3 992 4815 525835163 525839005 0.000000e+00 6237.0
10 TraesCS2A01G153100 chr1A 96.699 515 17 0 4816 5330 197274648 197274134 0.000000e+00 857.0
11 TraesCS2A01G153100 chr1A 96.162 469 13 3 1 465 525834259 525834726 0.000000e+00 761.0
12 TraesCS2A01G153100 chr1A 86.608 687 64 16 3933 4597 562584095 562584775 0.000000e+00 734.0
13 TraesCS2A01G153100 chr1A 88.368 533 32 3 3435 3937 74242135 74242667 9.810000e-172 614.0
14 TraesCS2A01G153100 chr1A 89.831 118 12 0 3371 3488 399507578 399507461 9.250000e-33 152.0
15 TraesCS2A01G153100 chr4A 95.386 3858 128 17 992 4815 196782727 196786568 0.000000e+00 6093.0
16 TraesCS2A01G153100 chr4A 95.922 515 20 1 4816 5330 317840687 317840174 0.000000e+00 833.0
17 TraesCS2A01G153100 chr4A 95.728 515 22 0 4816 5330 284700677 284700163 0.000000e+00 830.0
18 TraesCS2A01G153100 chr4A 89.781 411 29 6 1283 1680 13266106 13266516 1.020000e-141 514.0
19 TraesCS2A01G153100 chr5A 95.792 2329 92 4 2494 4818 146516599 146514273 0.000000e+00 3753.0
20 TraesCS2A01G153100 chr5A 92.650 1551 69 15 992 2498 146519757 146518208 0.000000e+00 2191.0
21 TraesCS2A01G153100 chr5A 95.062 486 13 5 1 481 146520743 146520264 0.000000e+00 754.0
22 TraesCS2A01G153100 chr5A 84.766 663 70 20 4179 4818 626908999 626908345 2.090000e-178 636.0
23 TraesCS2A01G153100 chr5A 88.248 451 39 6 1 450 446314600 446314163 1.310000e-145 527.0
24 TraesCS2A01G153100 chr5A 86.737 475 39 13 1 471 635646878 635647332 1.710000e-139 507.0
25 TraesCS2A01G153100 chr5A 90.244 164 6 2 2943 3105 73207843 73207689 7.000000e-49 206.0
26 TraesCS2A01G153100 chr6A 94.767 1395 57 1 1522 2900 576846051 576844657 0.000000e+00 2158.0
27 TraesCS2A01G153100 chr6A 91.879 1490 76 16 992 2444 132411312 132412793 0.000000e+00 2039.0
28 TraesCS2A01G153100 chr6A 96.030 529 12 5 1 526 132410478 132411000 0.000000e+00 852.0
29 TraesCS2A01G153100 chr6A 95.922 515 21 0 4816 5330 264899729 264899215 0.000000e+00 835.0
30 TraesCS2A01G153100 chr6A 86.266 466 49 9 4362 4815 138424015 138424477 4.800000e-135 492.0
31 TraesCS2A01G153100 chr6A 85.684 468 53 10 4362 4817 437537127 437536662 1.040000e-131 481.0
32 TraesCS2A01G153100 chr6A 82.031 128 5 2 2945 3072 82805074 82804965 5.680000e-15 93.5
33 TraesCS2A01G153100 chr4B 94.480 1395 61 1 1522 2900 669672306 669670912 0.000000e+00 2135.0
34 TraesCS2A01G153100 chr4B 88.382 482 41 7 1237 1710 567470398 567469924 2.790000e-157 566.0
35 TraesCS2A01G153100 chr4B 86.567 134 8 2 2940 3072 101813039 101813163 7.200000e-29 139.0
36 TraesCS2A01G153100 chr4B 95.775 71 3 0 2841 2911 69134164 69134094 1.210000e-21 115.0
37 TraesCS2A01G153100 chr3A 93.462 1086 53 3 992 2060 706365486 706364402 0.000000e+00 1596.0
38 TraesCS2A01G153100 chr3A 95.388 954 39 4 3865 4815 242901168 242900217 0.000000e+00 1513.0
39 TraesCS2A01G153100 chr3A 94.035 570 24 4 1 566 706366123 706365560 0.000000e+00 856.0
40 TraesCS2A01G153100 chr3A 96.311 515 19 0 4816 5330 75213766 75213252 0.000000e+00 846.0
41 TraesCS2A01G153100 chr3A 96.117 515 20 0 4816 5330 75359612 75360126 0.000000e+00 841.0
42 TraesCS2A01G153100 chr3A 83.406 916 95 33 3933 4816 606612772 606611882 0.000000e+00 797.0
43 TraesCS2A01G153100 chr7A 94.130 920 33 5 1546 2447 650073062 650072146 0.000000e+00 1380.0
44 TraesCS2A01G153100 chr7A 88.555 533 31 5 3435 3937 205894865 205895397 2.110000e-173 619.0
45 TraesCS2A01G153100 chr7A 83.934 666 77 19 4179 4821 623773993 623773335 1.270000e-170 610.0
46 TraesCS2A01G153100 chr7A 79.231 650 80 34 2117 2738 670237033 670236411 8.310000e-108 401.0
47 TraesCS2A01G153100 chr7A 91.882 271 20 2 992 1261 650073306 650073037 1.400000e-100 377.0
48 TraesCS2A01G153100 chr7A 78.532 545 85 17 2199 2738 670567449 670567966 3.980000e-86 329.0
49 TraesCS2A01G153100 chr5D 87.253 910 74 18 3933 4816 27185653 27184760 0.000000e+00 1000.0
50 TraesCS2A01G153100 chr5D 87.267 911 73 22 3933 4816 27230689 27229795 0.000000e+00 1000.0
51 TraesCS2A01G153100 chr5D 95.728 515 22 0 4816 5330 187774881 187774367 0.000000e+00 830.0
52 TraesCS2A01G153100 chr5D 93.519 108 6 1 3000 3106 339384577 339384684 5.530000e-35 159.0
53 TraesCS2A01G153100 chr5D 96.491 57 2 0 2858 2914 123298343 123298287 1.580000e-15 95.3
54 TraesCS2A01G153100 chr5D 81.250 128 6 2 2945 3072 112833058 112832949 2.640000e-13 87.9
55 TraesCS2A01G153100 chr5D 81.250 128 6 2 2945 3072 395207004 395207113 2.640000e-13 87.9
56 TraesCS2A01G153100 chr7B 88.589 815 56 7 3155 3937 684163964 684164773 0.000000e+00 955.0
57 TraesCS2A01G153100 chr1B 85.479 909 95 24 3933 4815 81011952 81011055 0.000000e+00 913.0
58 TraesCS2A01G153100 chr1B 90.200 449 29 7 3501 3937 293862210 293862655 5.990000e-159 571.0
59 TraesCS2A01G153100 chr1B 86.867 533 40 5 3435 3937 31634355 31633823 2.150000e-158 569.0
60 TraesCS2A01G153100 chr1B 89.030 474 29 3 3434 3885 626334588 626334116 2.790000e-157 566.0
61 TraesCS2A01G153100 chr1B 84.490 490 58 14 1 487 576784529 576785003 8.080000e-128 468.0
62 TraesCS2A01G153100 chr1B 86.441 354 25 3 3423 3753 558598118 558597765 3.030000e-97 366.0
63 TraesCS2A01G153100 chr1B 86.080 352 25 6 3422 3750 44353283 44353633 1.830000e-94 357.0
64 TraesCS2A01G153100 chr1B 92.135 89 7 0 3222 3310 389736031 389736119 5.600000e-25 126.0
65 TraesCS2A01G153100 chr1D 96.484 512 18 0 4816 5327 151791145 151791656 0.000000e+00 846.0
66 TraesCS2A01G153100 chr1D 84.091 660 75 18 4179 4815 66932776 66933428 1.270000e-170 610.0
67 TraesCS2A01G153100 chr1D 84.308 650 73 17 4189 4815 424017651 424017008 4.560000e-170 608.0
68 TraesCS2A01G153100 chr1D 89.444 180 18 1 3310 3488 318384421 318384242 5.370000e-55 226.0
69 TraesCS2A01G153100 chr1D 86.567 134 8 2 2940 3072 473554848 473554972 7.200000e-29 139.0
70 TraesCS2A01G153100 chr1D 91.398 93 7 1 3222 3313 288148381 288148473 5.600000e-25 126.0
71 TraesCS2A01G153100 chr1D 94.737 57 3 0 2858 2914 12789654 12789598 7.350000e-14 89.8
72 TraesCS2A01G153100 chr1D 79.508 122 7 2 2945 3066 82434921 82434818 2.660000e-08 71.3
73 TraesCS2A01G153100 chr1D 100.000 28 0 0 3501 3528 318384198 318384171 1.000000e-02 52.8
74 TraesCS2A01G153100 chr2D 94.981 538 25 1 3402 3937 576107658 576108195 0.000000e+00 843.0
75 TraesCS2A01G153100 chr2D 91.106 461 29 7 1 457 576104415 576104867 9.810000e-172 614.0
76 TraesCS2A01G153100 chr2D 95.192 312 15 0 2841 3152 576106535 576106846 1.330000e-135 494.0
77 TraesCS2A01G153100 chr2D 91.304 138 10 2 992 1129 576105507 576105642 2.530000e-43 187.0
78 TraesCS2A01G153100 chr4D 96.289 512 19 0 4816 5327 404193963 404194474 0.000000e+00 841.0
79 TraesCS2A01G153100 chr4D 92.029 414 30 2 1218 1628 455017476 455017063 3.580000e-161 579.0
80 TraesCS2A01G153100 chr4D 93.519 108 6 1 3000 3106 332131857 332131964 5.530000e-35 159.0
81 TraesCS2A01G153100 chr7D 87.040 571 50 15 2051 2599 578136465 578137033 1.630000e-174 623.0
82 TraesCS2A01G153100 chr7D 77.231 549 75 25 2199 2727 578484703 578485221 5.260000e-70 276.0
83 TraesCS2A01G153100 chrUn 88.555 533 31 5 3435 3937 766959 766427 2.110000e-173 619.0
84 TraesCS2A01G153100 chrUn 88.555 533 31 5 3435 3937 71270287 71270819 2.110000e-173 619.0
85 TraesCS2A01G153100 chrUn 88.555 533 31 5 3435 3937 370168874 370168342 2.110000e-173 619.0
86 TraesCS2A01G153100 chrUn 92.683 82 6 0 2841 2922 117190041 117189960 9.380000e-23 119.0
87 TraesCS2A01G153100 chr2B 88.555 533 31 3 3435 3937 88447893 88447361 2.110000e-173 619.0
88 TraesCS2A01G153100 chr2B 84.274 585 63 12 2041 2606 756118405 756117831 1.310000e-150 544.0
89 TraesCS2A01G153100 chr2B 94.488 127 6 1 2980 3105 752988171 752988045 1.510000e-45 195.0
90 TraesCS2A01G153100 chr2B 93.902 82 5 0 2841 2922 93478568 93478487 2.020000e-24 124.0
91 TraesCS2A01G153100 chr5B 87.992 533 33 5 3435 3937 564298642 564299173 7.640000e-168 601.0
92 TraesCS2A01G153100 chr5B 87.805 533 35 3 3435 3937 36572567 36572035 9.880000e-167 597.0
93 TraesCS2A01G153100 chr5B 87.242 533 37 4 3435 3937 564357027 564357558 3.580000e-161 579.0
94 TraesCS2A01G153100 chr5B 87.054 533 38 4 3435 3937 564419618 564420149 1.670000e-159 573.0
95 TraesCS2A01G153100 chr5B 94.488 127 6 1 2980 3105 665599628 665599502 1.510000e-45 195.0
96 TraesCS2A01G153100 chr6D 83.448 580 66 16 4014 4571 242421858 242421287 3.680000e-141 512.0
97 TraesCS2A01G153100 chr6D 90.184 163 6 4 2943 3104 172926591 172926438 2.520000e-48 204.0
98 TraesCS2A01G153100 chr6D 89.024 164 8 2 2943 3105 440890323 440890169 1.510000e-45 195.0
99 TraesCS2A01G153100 chr6D 92.593 108 7 1 3000 3106 73252258 73252151 2.570000e-33 154.0
100 TraesCS2A01G153100 chr3D 89.820 167 7 3 2940 3105 480723412 480723569 7.000000e-49 206.0
101 TraesCS2A01G153100 chr3D 90.226 133 12 1 992 1124 33178880 33178749 7.100000e-39 172.0


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 TraesCS2A01G153100 chr2A 101125930 101131259 5329 True 4529.500000 8013 100.000000 1 5330 2 chr2A.!!$R2 5329
1 TraesCS2A01G153100 chr2A 715825055 715829675 4620 True 2185.666667 4050 95.508667 2 4592 3 chr2A.!!$R4 4590
2 TraesCS2A01G153100 chr2A 484993242 484995501 2259 True 862.000000 1258 94.712000 2844 3937 2 chr2A.!!$R3 1093
3 TraesCS2A01G153100 chr1A 525834259 525839005 4746 False 3499.000000 6237 96.103500 1 4815 2 chr1A.!!$F3 4814
4 TraesCS2A01G153100 chr1A 197274134 197274648 514 True 857.000000 857 96.699000 4816 5330 1 chr1A.!!$R1 514
5 TraesCS2A01G153100 chr1A 562584095 562584775 680 False 734.000000 734 86.608000 3933 4597 1 chr1A.!!$F2 664
6 TraesCS2A01G153100 chr1A 74242135 74242667 532 False 614.000000 614 88.368000 3435 3937 1 chr1A.!!$F1 502
7 TraesCS2A01G153100 chr4A 196782727 196786568 3841 False 6093.000000 6093 95.386000 992 4815 1 chr4A.!!$F2 3823
8 TraesCS2A01G153100 chr4A 317840174 317840687 513 True 833.000000 833 95.922000 4816 5330 1 chr4A.!!$R2 514
9 TraesCS2A01G153100 chr4A 284700163 284700677 514 True 830.000000 830 95.728000 4816 5330 1 chr4A.!!$R1 514
10 TraesCS2A01G153100 chr5A 146514273 146520743 6470 True 2232.666667 3753 94.501333 1 4818 3 chr5A.!!$R4 4817
11 TraesCS2A01G153100 chr5A 626908345 626908999 654 True 636.000000 636 84.766000 4179 4818 1 chr5A.!!$R3 639
12 TraesCS2A01G153100 chr6A 576844657 576846051 1394 True 2158.000000 2158 94.767000 1522 2900 1 chr6A.!!$R4 1378
13 TraesCS2A01G153100 chr6A 132410478 132412793 2315 False 1445.500000 2039 93.954500 1 2444 2 chr6A.!!$F2 2443
14 TraesCS2A01G153100 chr6A 264899215 264899729 514 True 835.000000 835 95.922000 4816 5330 1 chr6A.!!$R2 514
15 TraesCS2A01G153100 chr4B 669670912 669672306 1394 True 2135.000000 2135 94.480000 1522 2900 1 chr4B.!!$R3 1378
16 TraesCS2A01G153100 chr3A 242900217 242901168 951 True 1513.000000 1513 95.388000 3865 4815 1 chr3A.!!$R2 950
17 TraesCS2A01G153100 chr3A 706364402 706366123 1721 True 1226.000000 1596 93.748500 1 2060 2 chr3A.!!$R4 2059
18 TraesCS2A01G153100 chr3A 75213252 75213766 514 True 846.000000 846 96.311000 4816 5330 1 chr3A.!!$R1 514
19 TraesCS2A01G153100 chr3A 75359612 75360126 514 False 841.000000 841 96.117000 4816 5330 1 chr3A.!!$F1 514
20 TraesCS2A01G153100 chr3A 606611882 606612772 890 True 797.000000 797 83.406000 3933 4816 1 chr3A.!!$R3 883
21 TraesCS2A01G153100 chr7A 650072146 650073306 1160 True 878.500000 1380 93.006000 992 2447 2 chr7A.!!$R3 1455
22 TraesCS2A01G153100 chr7A 205894865 205895397 532 False 619.000000 619 88.555000 3435 3937 1 chr7A.!!$F1 502
23 TraesCS2A01G153100 chr7A 623773335 623773993 658 True 610.000000 610 83.934000 4179 4821 1 chr7A.!!$R1 642
24 TraesCS2A01G153100 chr7A 670236411 670237033 622 True 401.000000 401 79.231000 2117 2738 1 chr7A.!!$R2 621
25 TraesCS2A01G153100 chr7A 670567449 670567966 517 False 329.000000 329 78.532000 2199 2738 1 chr7A.!!$F2 539
26 TraesCS2A01G153100 chr5D 27184760 27185653 893 True 1000.000000 1000 87.253000 3933 4816 1 chr5D.!!$R1 883
27 TraesCS2A01G153100 chr5D 27229795 27230689 894 True 1000.000000 1000 87.267000 3933 4816 1 chr5D.!!$R2 883
28 TraesCS2A01G153100 chr5D 187774367 187774881 514 True 830.000000 830 95.728000 4816 5330 1 chr5D.!!$R5 514
29 TraesCS2A01G153100 chr7B 684163964 684164773 809 False 955.000000 955 88.589000 3155 3937 1 chr7B.!!$F1 782
30 TraesCS2A01G153100 chr1B 81011055 81011952 897 True 913.000000 913 85.479000 3933 4815 1 chr1B.!!$R2 882
31 TraesCS2A01G153100 chr1B 31633823 31634355 532 True 569.000000 569 86.867000 3435 3937 1 chr1B.!!$R1 502
32 TraesCS2A01G153100 chr1D 151791145 151791656 511 False 846.000000 846 96.484000 4816 5327 1 chr1D.!!$F2 511
33 TraesCS2A01G153100 chr1D 66932776 66933428 652 False 610.000000 610 84.091000 4179 4815 1 chr1D.!!$F1 636
34 TraesCS2A01G153100 chr1D 424017008 424017651 643 True 608.000000 608 84.308000 4189 4815 1 chr1D.!!$R3 626
35 TraesCS2A01G153100 chr2D 576104415 576108195 3780 False 534.500000 843 93.145750 1 3937 4 chr2D.!!$F1 3936
36 TraesCS2A01G153100 chr4D 404193963 404194474 511 False 841.000000 841 96.289000 4816 5327 1 chr4D.!!$F2 511
37 TraesCS2A01G153100 chr7D 578136465 578137033 568 False 623.000000 623 87.040000 2051 2599 1 chr7D.!!$F1 548
38 TraesCS2A01G153100 chr7D 578484703 578485221 518 False 276.000000 276 77.231000 2199 2727 1 chr7D.!!$F2 528
39 TraesCS2A01G153100 chrUn 766427 766959 532 True 619.000000 619 88.555000 3435 3937 1 chrUn.!!$R1 502
40 TraesCS2A01G153100 chrUn 71270287 71270819 532 False 619.000000 619 88.555000 3435 3937 1 chrUn.!!$F1 502
41 TraesCS2A01G153100 chrUn 370168342 370168874 532 True 619.000000 619 88.555000 3435 3937 1 chrUn.!!$R3 502
42 TraesCS2A01G153100 chr2B 88447361 88447893 532 True 619.000000 619 88.555000 3435 3937 1 chr2B.!!$R1 502
43 TraesCS2A01G153100 chr2B 756117831 756118405 574 True 544.000000 544 84.274000 2041 2606 1 chr2B.!!$R4 565
44 TraesCS2A01G153100 chr5B 564298642 564299173 531 False 601.000000 601 87.992000 3435 3937 1 chr5B.!!$F1 502
45 TraesCS2A01G153100 chr5B 36572035 36572567 532 True 597.000000 597 87.805000 3435 3937 1 chr5B.!!$R1 502
46 TraesCS2A01G153100 chr5B 564357027 564357558 531 False 579.000000 579 87.242000 3435 3937 1 chr5B.!!$F2 502
47 TraesCS2A01G153100 chr5B 564419618 564420149 531 False 573.000000 573 87.054000 3435 3937 1 chr5B.!!$F3 502
48 TraesCS2A01G153100 chr6D 242421287 242421858 571 True 512.000000 512 83.448000 4014 4571 1 chr6D.!!$R3 557

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
382 388 2.358247 AACCGCAGCCCAACTACG 60.358 61.111 0.00 0.00 34.76 3.51 F
1138 2635 1.227704 TCCGTCCGCAACATGTTGT 60.228 52.632 33.01 1.99 42.31 3.32 F
1342 2882 0.835941 ATCGGAGCTGCTTGATTCCT 59.164 50.000 2.53 0.00 0.00 3.36 F
2304 4123 1.743321 GCTAGCGTGAGGAGGCAGAT 61.743 60.000 0.00 0.00 35.31 2.90 F
3984 8760 2.428171 CCATGCATGTTTCTTTCCGGAT 59.572 45.455 24.58 0.00 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1295 2835 0.902531 CTCCAGCCTCGGGTCTTTAA 59.097 55.000 0.00 0.0 0.00 1.52 R
2632 6111 0.672889 ATTGCATCACACGCCAACAA 59.327 45.000 0.00 0.0 0.00 2.83 R
3116 6596 0.742281 ACTCAGCTGTAGCCAATGCG 60.742 55.000 14.67 0.0 44.33 4.73 R
4000 8780 2.036256 AGCAAGTGATGGGGTGCC 59.964 61.111 0.00 0.0 0.00 5.01 R
4980 9812 3.813529 ATCTTGTGCTAACTTTCACGC 57.186 42.857 0.00 0.0 36.06 5.34 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
382 388 2.358247 AACCGCAGCCCAACTACG 60.358 61.111 0.00 0.00 34.76 3.51
1138 2635 1.227704 TCCGTCCGCAACATGTTGT 60.228 52.632 33.01 1.99 42.31 3.32
1235 2754 2.281070 CGTGGCACAGACCTTGCT 60.281 61.111 19.09 0.00 41.80 3.91
1295 2835 1.513158 CGTCAGAGCCACCGATTCT 59.487 57.895 0.00 0.00 0.00 2.40
1342 2882 0.835941 ATCGGAGCTGCTTGATTCCT 59.164 50.000 2.53 0.00 0.00 3.36
1766 3520 5.180271 AGAATAAACTTTGGCATGCCATTG 58.820 37.500 38.78 32.16 46.64 2.82
2115 3904 2.422479 AGTGACTTAATCGAGCGCTACA 59.578 45.455 11.50 0.00 0.00 2.74
2251 4070 3.440173 CACAGAAACTGTTGGCGGATATT 59.560 43.478 1.46 0.00 42.59 1.28
2304 4123 1.743321 GCTAGCGTGAGGAGGCAGAT 61.743 60.000 0.00 0.00 35.31 2.90
2444 4276 2.749076 GCACTGCACAATATTCACCTCA 59.251 45.455 0.00 0.00 0.00 3.86
2479 4333 6.447162 CACTCGCAGTACAGGATAATCAATA 58.553 40.000 0.00 0.00 0.00 1.90
2632 6111 3.251729 GTGATTGATCGTGCATATGGCTT 59.748 43.478 4.56 0.00 45.15 4.35
2915 6394 5.911752 TGGTTAGACGGTAAACTTGTTGTA 58.088 37.500 5.99 0.00 0.00 2.41
3116 6596 4.156455 TCTTTTAGGCTCCCATCATGTC 57.844 45.455 0.00 0.00 0.00 3.06
3213 7857 8.712228 ACTAATTTCTTCTTCTTCCCAAACAT 57.288 30.769 0.00 0.00 0.00 2.71
3253 7955 3.822940 CACAACCTTTGTACCCAACCTA 58.177 45.455 0.00 0.00 43.23 3.08
3367 8083 5.721480 CCCCCTTTTCTCTGGTTTATGATTT 59.279 40.000 0.00 0.00 0.00 2.17
3741 8508 9.707957 AATTTATTACATAAACATGTGGAGGGA 57.292 29.630 0.00 0.00 37.53 4.20
3791 8558 8.960591 CATATGGTACTGATTCCTTTCTTGTTT 58.039 33.333 0.00 0.00 0.00 2.83
3940 8716 3.838244 ATACGGCAACCACATGTAGAT 57.162 42.857 0.00 0.00 0.00 1.98
3984 8760 2.428171 CCATGCATGTTTCTTTCCGGAT 59.572 45.455 24.58 0.00 0.00 4.18
4386 9193 0.770557 AACCTGACTAGTGGGGCCAA 60.771 55.000 4.39 0.00 0.00 4.52
4827 9659 7.451731 TTTCCTGTAGTGAATCTATGGGATT 57.548 36.000 0.00 0.00 46.24 3.01
4896 9728 3.734463 TGCGAGGTTGACAAGTATTCAA 58.266 40.909 0.00 0.00 0.00 2.69
4980 9812 3.132925 TCCATCATGATGTGTATGTGCG 58.867 45.455 29.23 13.89 37.11 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
212 218 7.444183 ACCATATAAATTGGTCGTGATCGATTT 59.556 33.333 11.90 11.90 44.15 2.17
382 388 2.644676 GGGATCTGAGTTAGGGTTTGC 58.355 52.381 0.00 0.00 0.00 3.68
1129 2416 3.214328 GAACTCTCCACCACAACATGTT 58.786 45.455 4.92 4.92 0.00 2.71
1220 2718 2.113774 CCAGCAAGGTCTGTGCCA 59.886 61.111 0.00 0.00 43.27 4.92
1224 2722 2.753029 GGCTCCAGCAAGGTCTGT 59.247 61.111 0.03 0.00 44.36 3.41
1295 2835 0.902531 CTCCAGCCTCGGGTCTTTAA 59.097 55.000 0.00 0.00 0.00 1.52
1571 3325 3.691342 CGAGGTTGGGCTCCACGA 61.691 66.667 0.00 0.00 40.40 4.35
1766 3520 2.748532 ACTGTAGCTACGTCTGAAGTCC 59.251 50.000 18.74 0.00 0.00 3.85
2115 3904 7.177921 CAGATATTCACCATGATTTATGCCCTT 59.822 37.037 0.00 0.00 35.37 3.95
2251 4070 1.855213 GCTCATGCCTCAACGTTGCA 61.855 55.000 23.47 18.09 39.68 4.08
2304 4123 1.760192 GGACGGCAGGTCTTCTACTA 58.240 55.000 7.04 0.00 45.35 1.82
2444 4276 2.435586 GCGAGTGGCATGTGAGCT 60.436 61.111 0.00 0.00 42.87 4.09
2479 4333 6.428159 CCTGCACATAAGAAAGTCAAGTAACT 59.572 38.462 0.00 0.00 0.00 2.24
2632 6111 0.672889 ATTGCATCACACGCCAACAA 59.327 45.000 0.00 0.00 0.00 2.83
2915 6394 9.219603 CCATCGTAGATTCATACCAATATTTGT 57.780 33.333 0.00 0.00 45.12 2.83
3116 6596 0.742281 ACTCAGCTGTAGCCAATGCG 60.742 55.000 14.67 0.00 44.33 4.73
3213 7857 7.232534 AGGTTGTGCTTCAATACCTTCAAAATA 59.767 33.333 0.00 0.00 38.38 1.40
3367 8083 2.638325 TGGGAGGTAGGAAATGTTGGA 58.362 47.619 0.00 0.00 0.00 3.53
3741 8508 6.770785 TGACCAACTCTGCTAAAGTTACAATT 59.229 34.615 0.00 0.00 35.25 2.32
3940 8716 7.168219 TGGAAATTAAGAAGAGCTAGAGCAAA 58.832 34.615 4.01 0.00 45.16 3.68
3984 8760 6.494952 TGGGGTGCCATTTAGTAAGATTAAA 58.505 36.000 0.00 0.00 0.00 1.52
4000 8780 2.036256 AGCAAGTGATGGGGTGCC 59.964 61.111 0.00 0.00 0.00 5.01
4277 9061 4.989797 TCATGTTTCCATTGCACACATTTC 59.010 37.500 0.00 0.00 0.00 2.17
4526 9350 0.968901 ACGTTCTACATGGGCCGAGA 60.969 55.000 0.00 0.00 0.00 4.04
4610 9436 3.118038 TGTTTTGGTCACTAGCAACCTCT 60.118 43.478 13.64 0.00 42.54 3.69
4827 9659 4.958581 TCTAGAGAGCAATGATGACTTGGA 59.041 41.667 0.00 0.00 0.00 3.53
4896 9728 5.128205 GTGTTTCTTTTGTGTAGGTACCCT 58.872 41.667 8.74 0.00 37.71 4.34
4980 9812 3.813529 ATCTTGTGCTAACTTTCACGC 57.186 42.857 0.00 0.00 36.06 5.34
5083 9915 5.421693 ACTTGTATGCTAAATTTGCATCCCA 59.578 36.000 22.74 18.78 46.80 4.37


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

AutoCloner maintained by Alex Coulton.