Multiple sequence alignment - TraesCS6B01G406500

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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 TraesCS6B01G406500 chr6B 100.000 6795 0 0 1 6795 680930352 680937146 0.000000e+00 12549.0
1 TraesCS6B01G406500 chr6B 89.087 1961 170 24 901 2833 680737350 680735406 0.000000e+00 2396.0
2 TraesCS6B01G406500 chr6B 83.071 1778 226 21 810 2562 680988691 680990418 0.000000e+00 1546.0
3 TraesCS6B01G406500 chr6B 87.929 903 67 13 5466 6342 680732604 680731718 0.000000e+00 1026.0
4 TraesCS6B01G406500 chr6B 93.524 664 41 2 901 1564 680738627 680737966 0.000000e+00 987.0
5 TraesCS6B01G406500 chr6B 81.853 1058 130 31 5466 6510 680992411 680993419 0.000000e+00 833.0
6 TraesCS6B01G406500 chr6B 83.253 830 90 22 3022 3825 680735329 680734523 0.000000e+00 717.0
7 TraesCS6B01G406500 chr6B 98.127 267 5 0 486 752 531000005 530999739 3.710000e-127 466.0
8 TraesCS6B01G406500 chr6B 84.698 281 32 5 6185 6464 681370273 681370543 3.120000e-68 270.0
9 TraesCS6B01G406500 chr6B 76.908 524 72 27 4524 5017 680733583 680733079 1.130000e-62 252.0
10 TraesCS6B01G406500 chr6B 80.000 350 40 12 5114 5460 680992033 680992355 1.470000e-56 231.0
11 TraesCS6B01G406500 chr6B 89.286 84 7 2 6655 6737 681014616 681014698 3.350000e-18 104.0
12 TraesCS6B01G406500 chr6B 97.778 45 1 0 4461 4505 680934765 680934809 2.030000e-10 78.7
13 TraesCS6B01G406500 chr6B 97.778 45 1 0 4414 4458 680934812 680934856 2.030000e-10 78.7
14 TraesCS6B01G406500 chrUn 93.890 5941 266 31 901 6795 214051013 214045124 0.000000e+00 8870.0
15 TraesCS6B01G406500 chrUn 93.890 5941 266 31 901 6795 240294072 240299961 0.000000e+00 8870.0
16 TraesCS6B01G406500 chrUn 97.013 1942 57 1 956 2897 263804628 263806568 0.000000e+00 3264.0
17 TraesCS6B01G406500 chrUn 97.155 1933 54 1 965 2897 289985326 289983395 0.000000e+00 3264.0
18 TraesCS6B01G406500 chrUn 93.524 664 41 2 901 1564 79443669 79444330 0.000000e+00 987.0
19 TraesCS6B01G406500 chrUn 97.778 45 1 0 4414 4458 214047456 214047412 2.030000e-10 78.7
20 TraesCS6B01G406500 chrUn 97.778 45 1 0 4461 4505 214047503 214047459 2.030000e-10 78.7
21 TraesCS6B01G406500 chrUn 97.778 45 1 0 4461 4505 240297582 240297626 2.030000e-10 78.7
22 TraesCS6B01G406500 chrUn 97.778 45 1 0 4414 4458 240297629 240297673 2.030000e-10 78.7
23 TraesCS6B01G406500 chr6A 92.101 4355 265 26 916 5235 594990258 594985948 0.000000e+00 6063.0
24 TraesCS6B01G406500 chr6A 92.092 784 41 5 5301 6077 594985949 594985180 0.000000e+00 1085.0
25 TraesCS6B01G406500 chr6A 83.133 1079 157 12 1507 2562 595162902 595163978 0.000000e+00 961.0
26 TraesCS6B01G406500 chr6A 78.699 1061 162 25 3060 4083 101297470 101298503 0.000000e+00 649.0
27 TraesCS6B01G406500 chr6A 80.606 825 143 9 1070 1893 595328663 595329471 7.480000e-174 621.0
28 TraesCS6B01G406500 chr6A 82.956 663 76 19 5503 6153 595164701 595165338 1.280000e-156 564.0
29 TraesCS6B01G406500 chr6A 84.749 518 42 18 1 482 141368474 141368990 1.020000e-132 484.0
30 TraesCS6B01G406500 chr6A 79.036 768 98 29 5533 6286 602749640 602748922 1.030000e-127 468.0
31 TraesCS6B01G406500 chr6A 92.509 267 19 1 217 482 50183932 50184198 1.380000e-101 381.0
32 TraesCS6B01G406500 chr6A 89.015 264 22 3 6083 6342 594985148 594984888 3.060000e-83 320.0
33 TraesCS6B01G406500 chr6A 76.329 621 128 15 2938 3553 472356653 472356047 1.420000e-81 315.0
34 TraesCS6B01G406500 chr6A 88.889 216 17 2 4 212 50183684 50183899 6.760000e-65 259.0
35 TraesCS6B01G406500 chr6A 85.845 219 20 4 1 212 206362353 206362139 8.870000e-54 222.0
36 TraesCS6B01G406500 chr6A 84.186 215 20 6 5 212 485188188 485188395 5.380000e-46 196.0
37 TraesCS6B01G406500 chr6A 88.421 95 9 2 6655 6748 595167583 595167676 5.570000e-21 113.0
38 TraesCS6B01G406500 chr6A 94.030 67 4 0 6211 6277 595165403 595165337 1.210000e-17 102.0
39 TraesCS6B01G406500 chr6A 97.727 44 1 0 4414 4457 594986725 594986682 7.310000e-10 76.8
40 TraesCS6B01G406500 chr6D 90.893 1680 113 17 908 2562 449145291 449143627 0.000000e+00 2218.0
41 TraesCS6B01G406500 chr6D 83.586 1779 247 20 810 2562 449376545 449378304 0.000000e+00 1626.0
42 TraesCS6B01G406500 chr6D 96.016 979 30 4 3955 4927 448911020 448910045 0.000000e+00 1583.0
43 TraesCS6B01G406500 chr6D 92.251 942 44 7 4947 5866 448909785 448908851 0.000000e+00 1308.0
44 TraesCS6B01G406500 chr6D 87.466 726 54 14 5315 6022 449108536 449107830 0.000000e+00 802.0
45 TraesCS6B01G406500 chr6D 89.344 610 26 16 6148 6748 449107832 449107253 0.000000e+00 730.0
46 TraesCS6B01G406500 chr6D 79.981 1049 154 32 3060 4083 84073341 84074358 0.000000e+00 723.0
47 TraesCS6B01G406500 chr6D 81.956 859 149 6 1037 1893 449767601 449768455 0.000000e+00 723.0
48 TraesCS6B01G406500 chr6D 85.643 599 69 10 5587 6175 449141503 449140912 1.250000e-171 614.0
49 TraesCS6B01G406500 chr6D 89.340 394 37 3 2955 3345 449130837 449130446 2.200000e-134 490.0
50 TraesCS6B01G406500 chr6D 86.198 384 43 8 5831 6208 449378456 449378835 2.280000e-109 407.0
51 TraesCS6B01G406500 chr6D 82.895 456 45 7 2428 2867 449131277 449130839 4.970000e-101 379.0
52 TraesCS6B01G406500 chr6D 85.311 354 40 10 5114 5460 449143590 449143242 8.380000e-94 355.0
53 TraesCS6B01G406500 chr6D 83.611 360 28 15 5131 5460 449132492 449132134 6.620000e-80 309.0
54 TraesCS6B01G406500 chr6D 83.920 199 20 6 6276 6472 449378830 449379018 5.410000e-41 180.0
55 TraesCS6B01G406500 chr6D 97.778 45 1 0 4414 4458 448910511 448910467 2.030000e-10 78.7
56 TraesCS6B01G406500 chr6D 97.778 45 1 0 4461 4505 448910561 448910517 2.030000e-10 78.7
57 TraesCS6B01G406500 chr6D 92.453 53 3 1 6212 6263 449140487 449140539 2.630000e-09 75.0
58 TraesCS6B01G406500 chr6D 90.909 44 2 2 6147 6189 449285012 449285054 2.650000e-04 58.4
59 TraesCS6B01G406500 chr4A 99.753 809 2 0 1 809 624892020 624892828 0.000000e+00 1483.0
60 TraesCS6B01G406500 chr5B 99.383 486 3 0 1 486 447836979 447836494 0.000000e+00 881.0
61 TraesCS6B01G406500 chr5B 81.698 683 107 9 2957 3633 107209382 107210052 2.770000e-153 553.0
62 TraesCS6B01G406500 chr5B 98.485 264 4 0 486 749 355210869 355210606 3.710000e-127 466.0
63 TraesCS6B01G406500 chr5B 80.000 355 60 5 3703 4053 107211539 107211886 1.130000e-62 252.0
64 TraesCS6B01G406500 chr4D 79.377 771 98 27 3060 3793 75505022 75505768 2.850000e-133 486.0
65 TraesCS6B01G406500 chr4D 86.387 191 19 2 29 212 58950545 58950735 1.160000e-47 202.0
66 TraesCS6B01G406500 chr3B 98.141 269 5 0 484 752 678683016 678682748 2.870000e-128 470.0
67 TraesCS6B01G406500 chr3B 98.491 265 4 0 486 750 754259545 754259809 1.030000e-127 468.0
68 TraesCS6B01G406500 chr3B 97.070 273 7 1 486 757 256788125 256788397 6.210000e-125 459.0
69 TraesCS6B01G406500 chr3B 92.279 272 20 1 212 482 734739421 734739150 1.070000e-102 385.0
70 TraesCS6B01G406500 chr3B 92.509 267 19 1 217 482 754222973 754223239 1.380000e-101 381.0
71 TraesCS6B01G406500 chr3B 92.509 267 19 1 220 485 754286103 754285837 1.380000e-101 381.0
72 TraesCS6B01G406500 chr3B 78.500 400 59 11 9 382 436704399 436704797 3.170000e-58 237.0
73 TraesCS6B01G406500 chr1B 98.491 265 4 0 486 750 358062001 358061737 1.030000e-127 468.0
74 TraesCS6B01G406500 chr1B 81.905 105 16 3 4087 4190 31292286 31292388 1.210000e-12 86.1
75 TraesCS6B01G406500 chr5A 98.485 264 4 0 486 749 382088617 382088354 3.710000e-127 466.0
76 TraesCS6B01G406500 chr5A 79.112 383 60 11 3698 4072 105462493 105462123 5.260000e-61 246.0
77 TraesCS6B01G406500 chr5A 80.415 337 54 6 2957 3290 105606772 105606445 5.260000e-61 246.0
78 TraesCS6B01G406500 chr5A 94.382 89 5 0 2874 2962 370102434 370102522 3.310000e-28 137.0
79 TraesCS6B01G406500 chr4B 97.770 269 6 0 485 753 25394539 25394271 1.330000e-126 464.0
80 TraesCS6B01G406500 chr4B 96.552 87 2 1 2872 2958 132053330 132053245 7.100000e-30 143.0
81 TraesCS6B01G406500 chr4B 79.096 177 31 6 2702 2875 666597416 666597243 4.310000e-22 117.0
82 TraesCS6B01G406500 chr5D 84.024 507 43 22 12 482 365131330 365131834 2.890000e-123 453.0
83 TraesCS6B01G406500 chr5D 83.301 521 49 16 1 485 558024791 558024273 4.830000e-121 446.0
84 TraesCS6B01G406500 chr2B 80.155 645 81 26 3465 4073 386305266 386304633 8.090000e-119 438.0
85 TraesCS6B01G406500 chr2B 81.493 335 46 11 3706 4032 549040672 549040998 1.880000e-65 261.0
86 TraesCS6B01G406500 chr2B 85.116 215 18 6 5 212 171708851 171708644 2.480000e-49 207.0
87 TraesCS6B01G406500 chr2D 78.947 665 95 18 3450 4078 318328047 318327392 1.760000e-110 411.0
88 TraesCS6B01G406500 chr7A 92.884 267 18 1 217 482 668709444 668709710 2.970000e-103 387.0
89 TraesCS6B01G406500 chr1D 75.784 574 104 22 3140 3686 195160785 195160220 2.430000e-64 257.0
90 TraesCS6B01G406500 chr1D 81.461 178 30 2 2701 2877 449332965 449332790 7.100000e-30 143.0
91 TraesCS6B01G406500 chr1D 93.548 93 5 1 2874 2966 449276308 449276399 3.310000e-28 137.0
92 TraesCS6B01G406500 chr3D 89.637 193 13 2 25 210 200434565 200434373 8.810000e-59 239.0
93 TraesCS6B01G406500 chr3D 75.102 245 46 11 3030 3267 355326644 355326880 4.340000e-17 100.0
94 TraesCS6B01G406500 chr3A 87.500 184 16 1 36 212 432399720 432399537 8.930000e-49 206.0
95 TraesCS6B01G406500 chr7D 81.148 244 35 6 2962 3202 488791507 488791742 1.160000e-42 185.0
96 TraesCS6B01G406500 chr1A 91.919 99 7 1 2868 2966 80687849 80687946 3.310000e-28 137.0
97 TraesCS6B01G406500 chr7B 92.553 94 5 2 2877 2969 471435368 471435460 4.280000e-27 134.0
98 TraesCS6B01G406500 chr7B 78.673 211 35 8 3071 3276 53245712 53245917 1.540000e-26 132.0
99 TraesCS6B01G406500 chr7B 90.566 53 5 0 2821 2873 749505938 749505990 3.400000e-08 71.3
100 TraesCS6B01G406500 chr2A 89.216 102 9 2 2868 2969 627615680 627615779 7.150000e-25 126.0


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 TraesCS6B01G406500 chr6B 680930352 680937146 6794 False 4235.466667 12549 98.518667 1 6795 3 chr6B.!!$F3 6794
1 TraesCS6B01G406500 chr6B 680731718 680738627 6909 True 1075.600000 2396 86.140200 901 6342 5 chr6B.!!$R2 5441
2 TraesCS6B01G406500 chr6B 680988691 680993419 4728 False 870.000000 1546 81.641333 810 6510 3 chr6B.!!$F4 5700
3 TraesCS6B01G406500 chrUn 263804628 263806568 1940 False 3264.000000 3264 97.013000 956 2897 1 chrUn.!!$F2 1941
4 TraesCS6B01G406500 chrUn 289983395 289985326 1931 True 3264.000000 3264 97.155000 965 2897 1 chrUn.!!$R1 1932
5 TraesCS6B01G406500 chrUn 214045124 214051013 5889 True 3009.133333 8870 96.482000 901 6795 3 chrUn.!!$R2 5894
6 TraesCS6B01G406500 chrUn 240294072 240299961 5889 False 3009.133333 8870 96.482000 901 6795 3 chrUn.!!$F3 5894
7 TraesCS6B01G406500 chrUn 79443669 79444330 661 False 987.000000 987 93.524000 901 1564 1 chrUn.!!$F1 663
8 TraesCS6B01G406500 chr6A 594984888 594990258 5370 True 1886.200000 6063 92.733750 916 6342 4 chr6A.!!$R5 5426
9 TraesCS6B01G406500 chr6A 101297470 101298503 1033 False 649.000000 649 78.699000 3060 4083 1 chr6A.!!$F1 1023
10 TraesCS6B01G406500 chr6A 595328663 595329471 808 False 621.000000 621 80.606000 1070 1893 1 chr6A.!!$F4 823
11 TraesCS6B01G406500 chr6A 595162902 595167676 4774 False 546.000000 961 84.836667 1507 6748 3 chr6A.!!$F6 5241
12 TraesCS6B01G406500 chr6A 141368474 141368990 516 False 484.000000 484 84.749000 1 482 1 chr6A.!!$F2 481
13 TraesCS6B01G406500 chr6A 602748922 602749640 718 True 468.000000 468 79.036000 5533 6286 1 chr6A.!!$R4 753
14 TraesCS6B01G406500 chr6A 50183684 50184198 514 False 320.000000 381 90.699000 4 482 2 chr6A.!!$F5 478
15 TraesCS6B01G406500 chr6A 472356047 472356653 606 True 315.000000 315 76.329000 2938 3553 1 chr6A.!!$R2 615
16 TraesCS6B01G406500 chr6D 449140912 449145291 4379 True 1062.333333 2218 87.282333 908 6175 3 chr6D.!!$R4 5267
17 TraesCS6B01G406500 chr6D 449107253 449108536 1283 True 766.000000 802 88.405000 5315 6748 2 chr6D.!!$R2 1433
18 TraesCS6B01G406500 chr6D 448908851 448911020 2169 True 762.100000 1583 95.955750 3955 5866 4 chr6D.!!$R1 1911
19 TraesCS6B01G406500 chr6D 449376545 449379018 2473 False 737.666667 1626 84.568000 810 6472 3 chr6D.!!$F5 5662
20 TraesCS6B01G406500 chr6D 84073341 84074358 1017 False 723.000000 723 79.981000 3060 4083 1 chr6D.!!$F1 1023
21 TraesCS6B01G406500 chr6D 449767601 449768455 854 False 723.000000 723 81.956000 1037 1893 1 chr6D.!!$F4 856
22 TraesCS6B01G406500 chr6D 449130446 449132492 2046 True 392.666667 490 85.282000 2428 5460 3 chr6D.!!$R3 3032
23 TraesCS6B01G406500 chr4A 624892020 624892828 808 False 1483.000000 1483 99.753000 1 809 1 chr4A.!!$F1 808
24 TraesCS6B01G406500 chr5B 107209382 107211886 2504 False 402.500000 553 80.849000 2957 4053 2 chr5B.!!$F1 1096
25 TraesCS6B01G406500 chr4D 75505022 75505768 746 False 486.000000 486 79.377000 3060 3793 1 chr4D.!!$F2 733
26 TraesCS6B01G406500 chr5D 365131330 365131834 504 False 453.000000 453 84.024000 12 482 1 chr5D.!!$F1 470
27 TraesCS6B01G406500 chr5D 558024273 558024791 518 True 446.000000 446 83.301000 1 485 1 chr5D.!!$R1 484
28 TraesCS6B01G406500 chr2B 386304633 386305266 633 True 438.000000 438 80.155000 3465 4073 1 chr2B.!!$R2 608
29 TraesCS6B01G406500 chr2D 318327392 318328047 655 True 411.000000 411 78.947000 3450 4078 1 chr2D.!!$R1 628
30 TraesCS6B01G406500 chr1D 195160220 195160785 565 True 257.000000 257 75.784000 3140 3686 1 chr1D.!!$R1 546

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
961 1007 1.003866 CCGCGCCTAGTTTGCTAATTC 60.004 52.381 0.00 0.0 0.00 2.17 F
1015 1061 0.315251 CGGAATGCTCGAGATGGCTA 59.685 55.000 18.75 0.0 0.00 3.93 F
1093 1139 0.972983 CTCCTTCCTTCCGGCAGAGA 60.973 60.000 1.35 0.0 0.00 3.10 F
1315 1361 1.091537 CACGTTCACAAACACCAGGT 58.908 50.000 0.00 0.0 34.93 4.00 F
1464 1510 1.279271 CTTGAAGGGGTCAACCTCGAT 59.721 52.381 0.00 0.0 41.47 3.59 F
3631 5050 1.004628 TGCAAGCTCTAGGCATCCAAA 59.995 47.619 6.07 0.0 44.79 3.28 F
4130 7691 0.614812 GCACAATTCCCCCTTTGCAT 59.385 50.000 0.00 0.0 0.00 3.96 F
4808 8542 0.532862 CAGCAAGAACGGGTGTCAGT 60.533 55.000 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2004 3363 2.030457 GTGTTGTTAGCCATCGATTCGG 59.970 50.000 6.18 0.00 0.00 4.30 R
2972 4368 1.534729 GGGTTGTGGACTGATGAACC 58.465 55.000 0.00 0.00 36.18 3.62 R
3448 4848 0.971959 GTGATGCCATTTCCCAGCCA 60.972 55.000 0.00 0.00 0.00 4.75 R
3631 5050 2.481441 TGTAGATCAGGAGGCATGGTT 58.519 47.619 0.00 0.00 0.00 3.67 R
3638 5057 3.135348 TGAAGCCATTGTAGATCAGGAGG 59.865 47.826 0.00 0.00 0.00 4.30 R
4599 8301 0.663688 GAGCTCTCGATACAAGGCGA 59.336 55.000 6.43 0.00 35.01 5.54 R
5669 12286 0.745845 AAGGAACTATGCTGCAGCCG 60.746 55.000 34.64 24.09 38.49 5.52 R
6608 15061 0.447801 CGTGGCCAGCAATACAAGAC 59.552 55.000 5.11 0.00 0.00 3.01 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
292 328 4.312443 CAATTTGAAGCAGATTTGGCAGT 58.688 39.130 0.00 0.00 0.00 4.40
796 833 4.726825 AGAATACCCAGGAGCAATTTCCTA 59.273 41.667 0.00 0.00 45.86 2.94
889 935 4.358851 GTGAGCTGTCTGTGATGATACTC 58.641 47.826 0.00 0.00 0.00 2.59
890 936 3.382865 TGAGCTGTCTGTGATGATACTCC 59.617 47.826 0.00 0.00 0.00 3.85
891 937 3.369175 AGCTGTCTGTGATGATACTCCA 58.631 45.455 0.00 0.00 0.00 3.86
892 938 3.771479 AGCTGTCTGTGATGATACTCCAA 59.229 43.478 0.00 0.00 0.00 3.53
893 939 4.408270 AGCTGTCTGTGATGATACTCCAAT 59.592 41.667 0.00 0.00 0.00 3.16
894 940 4.510711 GCTGTCTGTGATGATACTCCAATG 59.489 45.833 0.00 0.00 0.00 2.82
896 942 6.053632 TGTCTGTGATGATACTCCAATGTT 57.946 37.500 0.00 0.00 0.00 2.71
897 943 5.876460 TGTCTGTGATGATACTCCAATGTTG 59.124 40.000 0.00 0.00 0.00 3.33
898 944 6.108687 GTCTGTGATGATACTCCAATGTTGA 58.891 40.000 0.00 0.00 0.00 3.18
947 993 3.941836 GCTGCATTAGACCGCGCC 61.942 66.667 0.00 0.00 0.00 6.53
949 995 1.067416 CTGCATTAGACCGCGCCTA 59.933 57.895 0.00 0.80 0.00 3.93
961 1007 1.003866 CCGCGCCTAGTTTGCTAATTC 60.004 52.381 0.00 0.00 0.00 2.17
1015 1061 0.315251 CGGAATGCTCGAGATGGCTA 59.685 55.000 18.75 0.00 0.00 3.93
1093 1139 0.972983 CTCCTTCCTTCCGGCAGAGA 60.973 60.000 1.35 0.00 0.00 3.10
1315 1361 1.091537 CACGTTCACAAACACCAGGT 58.908 50.000 0.00 0.00 34.93 4.00
1464 1510 1.279271 CTTGAAGGGGTCAACCTCGAT 59.721 52.381 0.00 0.00 41.47 3.59
1538 2862 3.913548 ACTTTGCAACATTCGTGCATA 57.086 38.095 0.00 0.00 38.43 3.14
1970 3328 7.992180 AAGCAAGTTCTTTACTTTCATTGTG 57.008 32.000 0.00 0.00 44.73 3.33
2004 3363 8.940952 GGTACTTTATCTTCATCTAATGCATCC 58.059 37.037 0.00 0.00 0.00 3.51
2300 3670 9.582431 GGTATATGCTGTATATAACGATGTTGT 57.418 33.333 6.98 0.00 36.30 3.32
2578 3950 9.595823 TTGTAAGTTAGCTTTGTCCATATCTAC 57.404 33.333 0.00 0.00 36.22 2.59
2732 4111 8.053355 AGAGAAGGTTTTTGGTCTCTAGAAAAA 58.947 33.333 0.26 0.00 43.90 1.94
2737 4116 8.135529 AGGTTTTTGGTCTCTAGAAAAATTTCG 58.864 33.333 0.00 0.00 41.92 3.46
2972 4368 9.877178 ACAGAGGAAGTACTTCTTTATTACATG 57.123 33.333 29.66 18.26 39.45 3.21
3448 4848 4.606210 ACCAAGTTGTTTCTTACCTTGGT 58.394 39.130 14.79 14.79 45.40 3.67
3631 5050 1.004628 TGCAAGCTCTAGGCATCCAAA 59.995 47.619 6.07 0.00 44.79 3.28
3638 5057 2.360165 CTCTAGGCATCCAAAACCATGC 59.640 50.000 0.00 0.00 44.06 4.06
3968 7529 2.205022 TGCCAAAGTCATCTTCTGGG 57.795 50.000 0.00 0.00 32.90 4.45
4130 7691 0.614812 GCACAATTCCCCCTTTGCAT 59.385 50.000 0.00 0.00 0.00 3.96
4175 7737 2.886523 CAGAGTTGCAATGTGGAGGAAA 59.113 45.455 0.59 0.00 0.00 3.13
4519 8218 2.230940 CGGCCGATGTAGCTCGTTG 61.231 63.158 24.07 0.00 36.93 4.10
4808 8542 0.532862 CAGCAAGAACGGGTGTCAGT 60.533 55.000 0.00 0.00 0.00 3.41
4903 9139 3.239449 GAAATTTCAGGTTGGGGTTCCT 58.761 45.455 13.40 0.00 33.96 3.36
5057 9763 4.864704 TTTTGGCCTCAAAGACCATAAC 57.135 40.909 3.32 0.00 42.93 1.89
5058 9764 3.806949 TTGGCCTCAAAGACCATAACT 57.193 42.857 3.32 0.00 32.39 2.24
5222 9934 8.823220 AGTTTAGGTGGCTGTTATATTTCAAT 57.177 30.769 0.00 0.00 0.00 2.57
5263 9975 8.788806 TGTAATTGTTGGTGACACTAAAATAGG 58.211 33.333 5.89 0.00 42.67 2.57
5428 10333 8.980481 TTGAAATTCAGTTTAGGTCTTCTCTT 57.020 30.769 0.00 0.00 0.00 2.85
5468 10499 8.934697 AGAATACATATCACTAAGTTTAGGCCA 58.065 33.333 5.01 0.00 35.08 5.36
5669 12286 9.233232 CTGTTAACAACTACAGAAATTTTGTCC 57.767 33.333 10.03 0.00 43.45 4.02
5688 12313 0.745845 CGGCTGCAGCATAGTTCCTT 60.746 55.000 37.63 0.00 44.36 3.36
5729 12356 6.190587 CCAGGATATTTGAAGTTCCCTTCTT 58.809 40.000 0.00 0.00 46.07 2.52
5743 12370 4.207165 TCCCTTCTTTGTTTCTGACTTGG 58.793 43.478 0.00 0.00 0.00 3.61
5780 12407 1.959985 CATCCGCTGATAGTGACTCCT 59.040 52.381 0.00 0.00 0.00 3.69
5824 12451 2.698803 TCGGTCACATTGTTCATCTGG 58.301 47.619 0.00 0.00 0.00 3.86
5890 12524 2.767505 GCTGTTAGCCTGTAAGTGTGT 58.232 47.619 0.00 0.00 34.48 3.72
5935 12569 2.162681 CTTTGGTCTCTGCCGGAATTT 58.837 47.619 5.05 0.00 0.00 1.82
5953 12587 7.095816 CCGGAATTTTGTCTTTATGGTTTGTTC 60.096 37.037 0.00 0.00 0.00 3.18
5961 12595 4.098044 TCTTTATGGTTTGTTCGGTGCAAA 59.902 37.500 0.00 0.00 33.96 3.68
5990 12628 2.157668 CGTTCCACTTTGTCAGGAATCG 59.842 50.000 0.00 0.00 42.82 3.34
5991 12629 3.399330 GTTCCACTTTGTCAGGAATCGA 58.601 45.455 0.00 0.00 42.82 3.59
6006 12644 4.102681 AGGAATCGACCGGGAATCTAAATT 59.897 41.667 6.32 0.00 34.73 1.82
6542 13225 4.505566 GGATTGTTATGATCCTGGCTGCTA 60.506 45.833 0.00 0.00 39.97 3.49
6566 15019 3.693578 TGTTTGACAAGATGTGCACTTGA 59.306 39.130 20.46 1.05 44.92 3.02
6608 15061 5.046663 AGGCTTCTTCTGTTCCTCTAAAGAG 60.047 44.000 0.00 0.00 41.71 2.85
6626 15079 1.740025 GAGTCTTGTATTGCTGGCCAC 59.260 52.381 0.00 0.00 0.00 5.01
6717 15213 2.300956 TTAATGGCAGTTGGGAAGCA 57.699 45.000 0.00 0.00 0.00 3.91
6733 15229 5.948758 TGGGAAGCACATTGATATGTTTGTA 59.051 36.000 0.00 0.00 42.29 2.41
6749 15245 5.481105 TGTTTGTATTAGTGGTAACGGAGG 58.519 41.667 0.00 0.00 42.51 4.30
6758 15255 3.945285 AGTGGTAACGGAGGCATATTTTG 59.055 43.478 0.00 0.00 42.51 2.44
6766 15263 4.336433 ACGGAGGCATATTTTGTTGATGAG 59.664 41.667 0.00 0.00 0.00 2.90
6767 15264 4.261322 CGGAGGCATATTTTGTTGATGAGG 60.261 45.833 0.00 0.00 0.00 3.86
6780 15277 7.750229 TTGTTGATGAGGAATATATTCTGGC 57.250 36.000 21.80 13.16 37.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
292 328 1.071542 TGCCAGGATCACGTTTCAGAA 59.928 47.619 0.00 0.00 0.00 3.02
889 935 8.997323 GGAAATCATCTACTAGATCAACATTGG 58.003 37.037 0.00 0.00 31.32 3.16
890 936 8.997323 GGGAAATCATCTACTAGATCAACATTG 58.003 37.037 0.00 0.00 31.32 2.82
891 937 8.160106 GGGGAAATCATCTACTAGATCAACATT 58.840 37.037 0.00 0.00 31.32 2.71
892 938 7.256835 GGGGGAAATCATCTACTAGATCAACAT 60.257 40.741 0.00 0.00 31.32 2.71
893 939 6.043243 GGGGGAAATCATCTACTAGATCAACA 59.957 42.308 0.00 0.00 31.32 3.33
894 940 6.468543 GGGGGAAATCATCTACTAGATCAAC 58.531 44.000 0.00 0.00 31.32 3.18
896 942 4.772624 CGGGGGAAATCATCTACTAGATCA 59.227 45.833 0.00 0.00 31.32 2.92
897 943 5.017490 TCGGGGGAAATCATCTACTAGATC 58.983 45.833 0.00 0.00 31.32 2.75
898 944 5.011982 TCGGGGGAAATCATCTACTAGAT 57.988 43.478 0.00 0.00 34.74 1.98
947 993 3.309954 GCGGAGTGGAATTAGCAAACTAG 59.690 47.826 0.00 0.00 0.00 2.57
949 995 2.084546 GCGGAGTGGAATTAGCAAACT 58.915 47.619 0.00 0.00 0.00 2.66
1015 1061 1.364171 GGTCACTGTCACTCGCAGT 59.636 57.895 0.00 0.00 46.86 4.40
1093 1139 1.968017 CACAGGTCTGCACGGCATT 60.968 57.895 0.00 0.00 38.13 3.56
1099 1145 2.313172 CGAGCACACAGGTCTGCAC 61.313 63.158 2.62 0.00 42.56 4.57
1315 1361 3.325870 CCAGAGCGTAGTCAATCAACAA 58.674 45.455 0.00 0.00 0.00 2.83
1464 1510 4.375272 CTGAGAAGTTCAAAGCAGAGTGA 58.625 43.478 5.50 0.00 34.81 3.41
1538 2862 7.823310 GCTTTAGTGACATGGATGATATCTCAT 59.177 37.037 3.98 0.00 44.93 2.90
1928 3282 5.862924 TGCTTATCTGCAGTTCTAACAAC 57.137 39.130 14.67 2.65 38.12 3.32
2004 3363 2.030457 GTGTTGTTAGCCATCGATTCGG 59.970 50.000 6.18 0.00 0.00 4.30
2725 4104 5.596845 ACTGCAAAAGCCGAAATTTTTCTA 58.403 33.333 0.00 0.00 35.07 2.10
2732 4111 2.488153 GGTCTACTGCAAAAGCCGAAAT 59.512 45.455 0.00 0.00 0.00 2.17
2737 4116 3.726291 TTTTGGTCTACTGCAAAAGCC 57.274 42.857 0.00 0.00 0.00 4.35
2848 4237 6.866248 ACTATTTGTGCTTTATTTGTTTCGGG 59.134 34.615 0.00 0.00 0.00 5.14
2972 4368 1.534729 GGGTTGTGGACTGATGAACC 58.465 55.000 0.00 0.00 36.18 3.62
3448 4848 0.971959 GTGATGCCATTTCCCAGCCA 60.972 55.000 0.00 0.00 0.00 4.75
3631 5050 2.481441 TGTAGATCAGGAGGCATGGTT 58.519 47.619 0.00 0.00 0.00 3.67
3638 5057 3.135348 TGAAGCCATTGTAGATCAGGAGG 59.865 47.826 0.00 0.00 0.00 4.30
3968 7529 7.142680 GCCTGAGATCTTAGACACAATACTAC 58.857 42.308 15.79 0.00 0.00 2.73
4085 7646 4.780815 AGATCTTGGACACAACACTTTCA 58.219 39.130 0.00 0.00 32.14 2.69
4130 7691 5.048504 GTCAAAGAGCATGACCAATTCTTCA 60.049 40.000 0.00 0.00 41.02 3.02
4175 7737 4.399303 CGATCCAAAATGGCTCCTAACTTT 59.601 41.667 0.00 0.00 37.47 2.66
4404 8100 7.760340 GTGTTCGATGGAAGTTCTCTAAGTTAT 59.240 37.037 2.25 0.00 31.49 1.89
4470 8169 1.358759 GTGCCCACAAAGTGTTCGG 59.641 57.895 0.00 0.00 0.00 4.30
4599 8301 0.663688 GAGCTCTCGATACAAGGCGA 59.336 55.000 6.43 0.00 35.01 5.54
4678 8393 1.134995 GCCGATGGATGATATGCTCGA 60.135 52.381 0.00 0.00 0.00 4.04
4741 8456 2.510238 GCCGCAGAAGCTCGACAT 60.510 61.111 0.00 0.00 39.10 3.06
4794 8528 1.367840 GAGCACTGACACCCGTTCT 59.632 57.895 0.00 0.00 0.00 3.01
4846 8580 2.813474 CATCTCGTTGCCGCCGAA 60.813 61.111 0.00 0.00 33.34 4.30
4903 9139 3.840890 AAAACGCAAAACACTCTGACA 57.159 38.095 0.00 0.00 0.00 3.58
5167 9875 6.800408 CAGCATGCAGATACAATTTATACTGC 59.200 38.462 21.98 0.00 46.91 4.40
5263 9975 3.753272 AGTACATCAGAAATGTGTGCCAC 59.247 43.478 0.00 0.00 33.76 5.01
5374 10098 7.877612 TGAGAACAGCTACTATTTTCATCACAA 59.122 33.333 0.00 0.00 0.00 3.33
5468 10499 6.003950 ACAACAGTAAATACAGTGAGGCAAT 58.996 36.000 0.00 0.00 0.00 3.56
5669 12286 0.745845 AAGGAACTATGCTGCAGCCG 60.746 55.000 34.64 24.09 38.49 5.52
5729 12356 4.021544 ACAAACAAGCCAAGTCAGAAACAA 60.022 37.500 0.00 0.00 0.00 2.83
5743 12370 3.248266 GGATGAATCTGCACAAACAAGC 58.752 45.455 0.00 0.00 0.00 4.01
5780 12407 4.881850 TCACACATCTTAGTCGCTATCAGA 59.118 41.667 0.00 0.00 0.00 3.27
5824 12451 9.139174 CAGATTCTTTAGAGAAACAGAAGTCTC 57.861 37.037 0.00 0.00 44.61 3.36
5885 12519 4.811557 AGCAGAAACAGAAGAACTACACAC 59.188 41.667 0.00 0.00 0.00 3.82
5890 12524 4.102524 TGGGAAGCAGAAACAGAAGAACTA 59.897 41.667 0.00 0.00 0.00 2.24
5935 12569 4.498345 GCACCGAACAAACCATAAAGACAA 60.498 41.667 0.00 0.00 0.00 3.18
5961 12595 2.290641 GACAAAGTGGAACGTCTTGCAT 59.709 45.455 0.00 0.00 45.86 3.96
5990 12628 6.993902 TGTAACCATAATTTAGATTCCCGGTC 59.006 38.462 0.00 0.00 0.00 4.79
5991 12629 6.902408 TGTAACCATAATTTAGATTCCCGGT 58.098 36.000 0.00 0.00 0.00 5.28
6006 12644 8.630054 AGAAACATAGCAAAGTTGTAACCATA 57.370 30.769 0.00 0.00 0.00 2.74
6081 12747 8.926710 GCATGTACTGTTCCTGTATATATTGAC 58.073 37.037 0.00 0.00 0.00 3.18
6093 12764 4.469227 AGAAGAGATGCATGTACTGTTCCT 59.531 41.667 15.84 0.32 35.50 3.36
6542 13225 4.924305 AGTGCACATCTTGTCAAACATT 57.076 36.364 21.04 0.00 0.00 2.71
6566 15019 6.944862 AGAAGCCTTTAGACAAACATCAAGAT 59.055 34.615 0.00 0.00 0.00 2.40
6608 15061 0.447801 CGTGGCCAGCAATACAAGAC 59.552 55.000 5.11 0.00 0.00 3.01
6626 15079 1.998315 CAGATTTCCAGCAGAGTCACG 59.002 52.381 0.00 0.00 0.00 4.35
6667 15163 3.488721 GCAATGTTCTGACAGGCATCATC 60.489 47.826 1.81 0.00 39.58 2.92
6733 15229 5.562298 AATATGCCTCCGTTACCACTAAT 57.438 39.130 0.00 0.00 0.00 1.73
6738 15234 3.958018 ACAAAATATGCCTCCGTTACCA 58.042 40.909 0.00 0.00 0.00 3.25
6758 15255 6.939163 ACTGCCAGAATATATTCCTCATCAAC 59.061 38.462 19.67 4.49 37.51 3.18
6766 15263 4.999950 CAGGACACTGCCAGAATATATTCC 59.000 45.833 19.67 7.39 38.01 3.01
6767 15264 4.999950 CCAGGACACTGCCAGAATATATTC 59.000 45.833 16.35 16.35 43.53 1.75
6776 15273 3.419793 TTTTCCAGGACACTGCCAG 57.580 52.632 0.00 0.00 43.53 4.85


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

AutoCloner maintained by Alex Coulton.