Multiple sequence alignment - TraesCS1B01G072600

Loading Multiple Alignment...

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 TraesCS1B01G072600 chr1B 100.000 8653 0 0 1 8653 57052132 57043480 0.000000e+00 15980.0
1 TraesCS1B01G072600 chr1B 97.887 5112 82 12 1621 6728 628612360 628607271 0.000000e+00 8818.0
2 TraesCS1B01G072600 chr1B 87.893 4898 545 36 1595 6471 636471004 636466134 0.000000e+00 5716.0
3 TraesCS1B01G072600 chr1B 97.318 1939 39 8 6727 8653 57070654 57068717 0.000000e+00 3280.0
4 TraesCS1B01G072600 chr1B 98.999 1499 15 0 1 1499 57025462 57023964 0.000000e+00 2686.0
5 TraesCS1B01G072600 chr1B 90.135 963 56 8 6727 7686 57023968 57023042 0.000000e+00 1216.0
6 TraesCS1B01G072600 chr1B 85.135 814 93 15 1 796 57071994 57071191 0.000000e+00 808.0
7 TraesCS1B01G072600 chr1B 97.744 266 6 0 6461 6726 57050633 57050368 7.920000e-125 459.0
8 TraesCS1B01G072600 chr1B 95.918 196 8 0 8153 8348 637295673 637295478 1.400000e-82 318.0
9 TraesCS1B01G072600 chr1B 93.596 203 13 0 8153 8355 69144627 69144425 3.930000e-78 303.0
10 TraesCS1B01G072600 chr1B 93.939 198 12 0 1302 1499 57070847 57070650 5.080000e-77 300.0
11 TraesCS1B01G072600 chr1B 83.280 311 33 11 868 1161 57071152 57070844 1.430000e-67 268.0
12 TraesCS1B01G072600 chr1B 99.180 122 1 0 1500 1621 628614894 628614773 4.070000e-53 220.0
13 TraesCS1B01G072600 chr1B 82.326 215 23 9 7908 8120 117212761 117212560 1.150000e-38 172.0
14 TraesCS1B01G072600 chr4A 97.839 5229 106 5 1499 6724 725872996 725878220 0.000000e+00 9023.0
15 TraesCS1B01G072600 chr4A 93.953 5209 244 22 1541 6726 741573378 741568218 0.000000e+00 7808.0
16 TraesCS1B01G072600 chr4A 92.325 4078 275 16 1566 5623 93506481 93502422 0.000000e+00 5762.0
17 TraesCS1B01G072600 chr4A 98.120 266 5 0 6461 6726 725872997 725873262 1.700000e-126 464.0
18 TraesCS1B01G072600 chr4A 90.050 201 17 2 6527 6726 93488927 93488729 3.100000e-64 257.0
19 TraesCS1B01G072600 chr4B 95.523 5227 190 18 1524 6726 564655557 564660763 0.000000e+00 8316.0
20 TraesCS1B01G072600 chr4B 95.102 245 9 2 6485 6726 564655557 564655801 4.900000e-102 383.0
21 TraesCS1B01G072600 chr4B 86.301 219 27 3 4 221 424746866 424746650 1.450000e-57 235.0
22 TraesCS1B01G072600 chr4B 88.485 165 14 4 6564 6726 636499394 636499555 2.460000e-45 195.0
23 TraesCS1B01G072600 chr2A 93.650 5181 275 26 1566 6726 35387346 35392492 0.000000e+00 7696.0
24 TraesCS1B01G072600 chr2A 75.525 1524 337 34 4996 6500 385701142 385699636 0.000000e+00 715.0
25 TraesCS1B01G072600 chr2A 93.035 201 11 3 6527 6726 35387346 35387544 3.060000e-74 291.0
26 TraesCS1B01G072600 chr2B 93.458 5197 255 32 1541 6726 729637703 729642825 0.000000e+00 7635.0
27 TraesCS1B01G072600 chr2B 95.855 193 8 0 8153 8345 705937315 705937123 6.520000e-81 313.0
28 TraesCS1B01G072600 chr2B 89.140 221 23 1 1 221 793384241 793384460 3.080000e-69 274.0
29 TraesCS1B01G072600 chr6A 92.771 5229 283 48 1529 6726 5690310 5695474 0.000000e+00 7474.0
30 TraesCS1B01G072600 chr6A 80.911 461 41 24 7684 8120 73657720 73657283 3.900000e-83 320.0
31 TraesCS1B01G072600 chr6A 95.855 193 8 0 8153 8345 31010175 31010367 6.520000e-81 313.0
32 TraesCS1B01G072600 chr6A 95.855 193 8 0 8153 8345 35333594 35333402 6.520000e-81 313.0
33 TraesCS1B01G072600 chr3A 92.697 5231 274 41 1524 6727 221273284 221268135 0.000000e+00 7444.0
34 TraesCS1B01G072600 chr3A 92.593 135 10 0 87 221 54446609 54446475 2.460000e-45 195.0
35 TraesCS1B01G072600 chr3A 93.182 44 2 1 360 402 522265506 522265463 7.250000e-06 63.9
36 TraesCS1B01G072600 chr7B 98.002 2703 50 4 4026 6726 611481576 611484276 0.000000e+00 4689.0
37 TraesCS1B01G072600 chr7B 97.316 2534 62 4 1500 4032 611436763 611439291 0.000000e+00 4298.0
38 TraesCS1B01G072600 chr7B 97.744 266 6 0 6461 6726 611436763 611437028 7.920000e-125 459.0
39 TraesCS1B01G072600 chr7B 78.788 132 19 8 7682 7808 730056071 730055944 7.200000e-11 80.5
40 TraesCS1B01G072600 chr3B 98.445 2508 37 2 3646 6151 744335438 744337945 0.000000e+00 4414.0
41 TraesCS1B01G072600 chr3B 97.630 2152 36 3 1500 3650 744325042 744327179 0.000000e+00 3677.0
42 TraesCS1B01G072600 chr3B 94.224 277 5 1 6451 6727 744337945 744338210 6.250000e-111 412.0
43 TraesCS1B01G072600 chr3B 93.985 266 5 1 1500 1765 744337955 744338209 8.140000e-105 392.0
44 TraesCS1B01G072600 chr3B 86.885 305 38 2 8349 8653 757723503 757723201 2.990000e-89 340.0
45 TraesCS1B01G072600 chr3B 85.479 303 42 2 8351 8653 757718514 757718214 1.810000e-81 315.0
46 TraesCS1B01G072600 chr3B 84.516 310 41 4 8348 8651 167864967 167864659 5.080000e-77 300.0
47 TraesCS1B01G072600 chr3B 90.654 214 16 4 9 221 614249461 614249251 1.840000e-71 281.0
48 TraesCS1B01G072600 chr3B 78.834 463 50 24 7686 8120 787813381 787813823 1.430000e-67 268.0
49 TraesCS1B01G072600 chr3B 80.696 316 47 9 8349 8651 370036456 370036142 5.220000e-57 233.0
50 TraesCS1B01G072600 chr3B 79.751 321 34 13 8346 8653 20380428 20380730 4.100000e-48 204.0
51 TraesCS1B01G072600 chr3B 78.125 320 49 8 8346 8653 790390282 790389972 5.340000e-42 183.0
52 TraesCS1B01G072600 chr3B 85.549 173 14 6 8480 8651 604772892 604773054 4.150000e-38 171.0
53 TraesCS1B01G072600 chr3B 97.368 38 1 0 357 394 486597332 486597295 2.020000e-06 65.8
54 TraesCS1B01G072600 chr1A 84.425 2992 439 24 1699 4679 552883467 552880492 0.000000e+00 2918.0
55 TraesCS1B01G072600 chr1A 89.938 974 63 14 6727 7686 36620852 36619900 0.000000e+00 1223.0
56 TraesCS1B01G072600 chr1A 89.979 948 53 14 6727 7672 31895361 31896268 0.000000e+00 1186.0
57 TraesCS1B01G072600 chr1A 96.917 519 16 0 981 1499 31894847 31895365 0.000000e+00 870.0
58 TraesCS1B01G072600 chr1A 95.817 502 21 0 998 1499 36621349 36620848 0.000000e+00 811.0
59 TraesCS1B01G072600 chr6D 89.070 1473 122 23 5259 6727 12089926 12088489 0.000000e+00 1792.0
60 TraesCS1B01G072600 chr6D 81.457 453 56 19 7686 8120 456116410 456115968 6.430000e-91 346.0
61 TraesCS1B01G072600 chr6D 89.157 166 12 5 6564 6726 12097332 12097170 1.470000e-47 202.0
62 TraesCS1B01G072600 chr3D 81.675 1910 295 45 4823 6719 105187779 105189646 0.000000e+00 1537.0
63 TraesCS1B01G072600 chr3D 81.663 409 52 17 7721 8120 12885712 12886106 1.400000e-82 318.0
64 TraesCS1B01G072600 chr3D 91.781 219 15 3 4 221 462452984 462452768 1.410000e-77 302.0
65 TraesCS1B01G072600 chr3D 84.568 162 14 9 6561 6719 105212972 105213125 5.410000e-32 150.0
66 TraesCS1B01G072600 chr1D 81.774 1838 282 44 4895 6719 474135350 474137147 0.000000e+00 1489.0
67 TraesCS1B01G072600 chr1D 92.835 963 53 4 6727 7686 37438288 37437339 0.000000e+00 1382.0
68 TraesCS1B01G072600 chr1D 96.532 519 18 0 981 1499 37438802 37438284 0.000000e+00 859.0
69 TraesCS1B01G072600 chr1D 88.328 317 25 2 8349 8653 480795451 480795135 3.820000e-98 370.0
70 TraesCS1B01G072600 chr1D 95.855 193 8 0 8153 8345 29234201 29234009 6.520000e-81 313.0
71 TraesCS1B01G072600 chr1D 83.432 338 31 12 6391 6726 319593275 319593589 3.060000e-74 291.0
72 TraesCS1B01G072600 chr1D 89.109 202 18 2 6527 6726 319570204 319570403 1.870000e-61 248.0
73 TraesCS1B01G072600 chr1D 83.007 153 19 6 6571 6718 352959646 352959796 1.960000e-26 132.0
74 TraesCS1B01G072600 chr5B 88.562 306 34 1 8348 8653 666365553 666365249 3.820000e-98 370.0
75 TraesCS1B01G072600 chr2D 96.373 193 6 1 8153 8345 25731347 25731156 5.040000e-82 316.0
76 TraesCS1B01G072600 chr2D 85.342 307 37 2 8348 8653 88311055 88310756 2.350000e-80 311.0
77 TraesCS1B01G072600 chr2D 84.641 306 47 0 8348 8653 429375917 429375612 1.090000e-78 305.0
78 TraesCS1B01G072600 chr2D 79.808 416 47 25 7713 8120 88311451 88311065 1.430000e-67 268.0
79 TraesCS1B01G072600 chr2D 89.344 122 10 1 7999 8120 385158061 385157943 5.410000e-32 150.0
80 TraesCS1B01G072600 chr4D 85.113 309 44 2 8346 8653 117605898 117606205 1.810000e-81 315.0
81 TraesCS1B01G072600 chr4D 93.785 177 8 3 6552 6726 63790242 63790417 6.660000e-66 263.0
82 TraesCS1B01G072600 chr4D 92.655 177 10 3 6552 6726 63803818 63803993 1.440000e-62 252.0
83 TraesCS1B01G072600 chr4D 89.781 137 10 4 6587 6722 297357178 297357045 1.150000e-38 172.0
84 TraesCS1B01G072600 chr6B 95.855 193 8 0 8153 8345 638375096 638374904 6.520000e-81 313.0
85 TraesCS1B01G072600 chr6B 79.126 206 24 7 7367 7572 543080197 543080383 3.280000e-24 124.0
86 TraesCS1B01G072600 chr7A 90.594 202 11 6 6527 6726 117281316 117281511 2.400000e-65 261.0
87 TraesCS1B01G072600 chr7A 88.298 188 18 3 7479 7666 465753347 465753164 1.130000e-53 222.0
88 TraesCS1B01G072600 chr7A 86.957 184 16 5 7937 8120 608983013 608983188 5.300000e-47 200.0
89 TraesCS1B01G072600 chr7D 92.655 177 10 3 6552 6726 101284963 101284788 1.440000e-62 252.0
90 TraesCS1B01G072600 chr5A 78.261 207 25 8 7367 7572 66827414 66827227 1.970000e-21 115.0
91 TraesCS1B01G072600 chr5A 87.500 64 7 1 360 422 378503240 378503303 1.200000e-08 73.1


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 TraesCS1B01G072600 chr1B 57043480 57052132 8652 True 8219.500000 15980 98.872000 1 8653 2 chr1B.!!$R6 8652
1 TraesCS1B01G072600 chr1B 636466134 636471004 4870 True 5716.000000 5716 87.893000 1595 6471 1 chr1B.!!$R3 4876
2 TraesCS1B01G072600 chr1B 628607271 628614894 7623 True 4519.000000 8818 98.533500 1500 6728 2 chr1B.!!$R8 5228
3 TraesCS1B01G072600 chr1B 57023042 57025462 2420 True 1951.000000 2686 94.567000 1 7686 2 chr1B.!!$R5 7685
4 TraesCS1B01G072600 chr1B 57068717 57071994 3277 True 1164.000000 3280 89.918000 1 8653 4 chr1B.!!$R7 8652
5 TraesCS1B01G072600 chr4A 725872996 725878220 5224 False 9023.000000 9023 97.839000 1499 6724 1 chr4A.!!$F1 5225
6 TraesCS1B01G072600 chr4A 741568218 741573378 5160 True 7808.000000 7808 93.953000 1541 6726 1 chr4A.!!$R3 5185
7 TraesCS1B01G072600 chr4A 93502422 93506481 4059 True 5762.000000 5762 92.325000 1566 5623 1 chr4A.!!$R2 4057
8 TraesCS1B01G072600 chr4B 564655557 564660763 5206 False 8316.000000 8316 95.523000 1524 6726 1 chr4B.!!$F1 5202
9 TraesCS1B01G072600 chr2A 35387346 35392492 5146 False 7696.000000 7696 93.650000 1566 6726 1 chr2A.!!$F1 5160
10 TraesCS1B01G072600 chr2A 385699636 385701142 1506 True 715.000000 715 75.525000 4996 6500 1 chr2A.!!$R1 1504
11 TraesCS1B01G072600 chr2B 729637703 729642825 5122 False 7635.000000 7635 93.458000 1541 6726 1 chr2B.!!$F1 5185
12 TraesCS1B01G072600 chr6A 5690310 5695474 5164 False 7474.000000 7474 92.771000 1529 6726 1 chr6A.!!$F1 5197
13 TraesCS1B01G072600 chr3A 221268135 221273284 5149 True 7444.000000 7444 92.697000 1524 6727 1 chr3A.!!$R2 5203
14 TraesCS1B01G072600 chr7B 611481576 611484276 2700 False 4689.000000 4689 98.002000 4026 6726 1 chr7B.!!$F1 2700
15 TraesCS1B01G072600 chr7B 611436763 611439291 2528 False 2378.500000 4298 97.530000 1500 6726 2 chr7B.!!$F2 5226
16 TraesCS1B01G072600 chr3B 744325042 744327179 2137 False 3677.000000 3677 97.630000 1500 3650 1 chr3B.!!$F3 2150
17 TraesCS1B01G072600 chr3B 744335438 744338210 2772 False 1739.333333 4414 95.551333 1500 6727 3 chr3B.!!$F5 5227
18 TraesCS1B01G072600 chr1A 552880492 552883467 2975 True 2918.000000 2918 84.425000 1699 4679 1 chr1A.!!$R1 2980
19 TraesCS1B01G072600 chr1A 31894847 31896268 1421 False 1028.000000 1186 93.448000 981 7672 2 chr1A.!!$F1 6691
20 TraesCS1B01G072600 chr1A 36619900 36621349 1449 True 1017.000000 1223 92.877500 998 7686 2 chr1A.!!$R2 6688
21 TraesCS1B01G072600 chr6D 12088489 12089926 1437 True 1792.000000 1792 89.070000 5259 6727 1 chr6D.!!$R1 1468
22 TraesCS1B01G072600 chr3D 105187779 105189646 1867 False 1537.000000 1537 81.675000 4823 6719 1 chr3D.!!$F2 1896
23 TraesCS1B01G072600 chr1D 474135350 474137147 1797 False 1489.000000 1489 81.774000 4895 6719 1 chr1D.!!$F4 1824
24 TraesCS1B01G072600 chr1D 37437339 37438802 1463 True 1120.500000 1382 94.683500 981 7686 2 chr1D.!!$R3 6705
25 TraesCS1B01G072600 chr2D 88310756 88311451 695 True 289.500000 311 82.575000 7713 8653 2 chr2D.!!$R4 940

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
714 736 1.277739 GATGCGCGTGATGGATGTG 59.722 57.895 6.97 0.00 0.00 3.21 F
761 783 2.390599 TGTTTGCTGCGATCGAGCC 61.391 57.895 25.96 16.43 35.43 4.70 F
2575 5054 0.882927 CCGAAACCAGAAGAACGGCA 60.883 55.000 0.00 0.00 34.36 5.69 F
4163 6653 0.249120 CTTGATGTAGCCACGGGACA 59.751 55.000 0.00 0.00 0.00 4.02 F
4303 6794 1.069823 CGTTGATCATGGGGGAGAGAG 59.930 57.143 0.00 0.00 0.00 3.20 F
6339 8898 3.060607 CGTGTTGCCAATAAACAACTTGC 60.061 43.478 7.32 0.00 45.07 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1657 4129 7.378181 CAAAGGCATACAAGATTAGGTTGTTT 58.622 34.615 0.00 0.00 38.98 2.83 R
2781 5267 1.349973 GAAGCGAGCGCCTTGATTC 59.650 57.895 11.66 4.94 43.17 2.52 R
4555 7057 0.460284 GCCGTCGTTGTCCTGATCAT 60.460 55.000 0.00 0.00 0.00 2.45 R
6339 8898 9.884465 GATTTTTGGAAGGTATAAATCTGATCG 57.116 33.333 0.00 0.00 34.18 3.69 R
6430 8989 7.773224 CCCCATAATCACAACTATGACAAGTTA 59.227 37.037 3.67 0.00 37.61 2.24 R
8060 10724 0.448990 CGACGATCGGTACCTTGACA 59.551 55.000 20.98 0.00 36.00 3.58 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
336 340 7.603180 TTGATGATATAGTTGCACTCCTACT 57.397 36.000 0.00 0.00 34.00 2.57
504 521 3.314541 AACCTAGCAACGGTTCTACAG 57.685 47.619 0.00 0.00 40.63 2.74
662 684 5.827568 AATTTCAACATTGTTGCGATGTC 57.172 34.783 22.02 0.00 37.48 3.06
714 736 1.277739 GATGCGCGTGATGGATGTG 59.722 57.895 6.97 0.00 0.00 3.21
761 783 2.390599 TGTTTGCTGCGATCGAGCC 61.391 57.895 25.96 16.43 35.43 4.70
1430 1481 2.738139 CAGTGCATCCACGACGCA 60.738 61.111 0.00 0.00 46.62 5.24
1657 4129 6.194967 TCTCCATGTATCTCTCTGGTTGTTA 58.805 40.000 0.00 0.00 0.00 2.41
1680 4153 8.520351 GTTAAACAACCTAATCTTGTATGCCTT 58.480 33.333 0.00 0.00 31.43 4.35
2575 5054 0.882927 CCGAAACCAGAAGAACGGCA 60.883 55.000 0.00 0.00 34.36 5.69
2752 5237 2.487625 GGGGGCTACTACAACAACAACA 60.488 50.000 0.00 0.00 0.00 3.33
2753 5238 3.215975 GGGGCTACTACAACAACAACAA 58.784 45.455 0.00 0.00 0.00 2.83
2754 5239 3.004002 GGGGCTACTACAACAACAACAAC 59.996 47.826 0.00 0.00 0.00 3.32
2755 5240 3.628487 GGGCTACTACAACAACAACAACA 59.372 43.478 0.00 0.00 0.00 3.33
2756 5241 4.096682 GGGCTACTACAACAACAACAACAA 59.903 41.667 0.00 0.00 0.00 2.83
2781 5267 2.607187 CCTCGCCACTACTACAACAAG 58.393 52.381 0.00 0.00 0.00 3.16
2837 5323 8.250332 GGAGTATGAAAACAAATGCCAAATCTA 58.750 33.333 0.00 0.00 0.00 1.98
3061 5547 1.238439 CACTGCTGAAAACGGTCCAT 58.762 50.000 0.00 0.00 0.00 3.41
3107 5593 5.448632 GCAAGTCTATTATTCAAACCCCACG 60.449 44.000 0.00 0.00 0.00 4.94
3560 6047 6.575244 TGTATTTTCTGATGTATGGGGACT 57.425 37.500 0.00 0.00 0.00 3.85
3607 6094 5.867174 CACACCTATTACGTGAGTTTCATCA 59.133 40.000 0.00 0.00 46.40 3.07
3826 6315 2.811431 CCTCACGCTCACCAACAAAATA 59.189 45.455 0.00 0.00 0.00 1.40
4163 6653 0.249120 CTTGATGTAGCCACGGGACA 59.751 55.000 0.00 0.00 0.00 4.02
4176 6666 3.565516 CACGGGACATGTGTATATCTCG 58.434 50.000 1.15 1.10 40.91 4.04
4303 6794 1.069823 CGTTGATCATGGGGGAGAGAG 59.930 57.143 0.00 0.00 0.00 3.20
4415 6906 7.041712 TGCAGTTCAAACAGACGTGATTTTATA 60.042 33.333 0.00 0.00 0.00 0.98
4420 6912 5.751243 AACAGACGTGATTTTATATGCCC 57.249 39.130 0.00 0.00 0.00 5.36
6339 8898 3.060607 CGTGTTGCCAATAAACAACTTGC 60.061 43.478 7.32 0.00 45.07 4.01
6687 9284 1.552578 ATATATACCACGCGGGCTCA 58.447 50.000 12.47 0.00 42.05 4.26
6728 9325 2.159517 CGCTTCTACAATTTCCACAGCC 60.160 50.000 0.00 0.00 0.00 4.85
6729 9326 2.819608 GCTTCTACAATTTCCACAGCCA 59.180 45.455 0.00 0.00 0.00 4.75
6730 9327 3.366374 GCTTCTACAATTTCCACAGCCAC 60.366 47.826 0.00 0.00 0.00 5.01
6760 9357 2.050350 CCTCGTCGGCCTACTTCCA 61.050 63.158 5.79 0.00 0.00 3.53
7359 9990 4.770874 AAGCATTACCGGCGGCGT 62.771 61.111 30.09 19.58 36.08 5.68
7360 9991 4.770874 AGCATTACCGGCGGCGTT 62.771 61.111 30.09 19.77 36.08 4.84
7665 10306 5.596836 TGCTTGATCCAAAACTCTGTTTT 57.403 34.783 2.97 2.97 0.00 2.43
7761 10405 1.407437 CCTCGGTAGCCAGATTTTGCT 60.407 52.381 0.00 0.00 41.57 3.91
7878 10523 0.892755 ACACATTCCGCTCCGACTTA 59.107 50.000 0.00 0.00 0.00 2.24
8060 10724 1.202582 CTCCGACGTCTGAATGAAGGT 59.797 52.381 14.70 0.00 0.00 3.50
8280 10947 1.067776 GGTATAGCCGGATCGTCAAGG 60.068 57.143 5.05 0.00 0.00 3.61
8289 10956 2.351726 CGGATCGTCAAGGTCAAAATCC 59.648 50.000 0.00 0.00 0.00 3.01
8553 11220 0.658829 GTCGCGACGATCCTCATCAG 60.659 60.000 25.19 0.00 38.42 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.642848 AGGCAACAAAGGTGATGTCAATT 59.357 39.130 0.00 0.00 34.75 2.32
504 521 4.034394 TCATCGATTGCATGCACTAAGAAC 59.966 41.667 22.58 2.94 0.00 3.01
662 684 1.009903 TCGTGGTATTTGTGCCGACG 61.010 55.000 0.00 0.00 33.72 5.12
714 736 3.771577 TGTTTTTCCTCCTCTGGTCTC 57.228 47.619 0.00 0.00 0.00 3.36
1657 4129 7.378181 CAAAGGCATACAAGATTAGGTTGTTT 58.622 34.615 0.00 0.00 38.98 2.83
2781 5267 1.349973 GAAGCGAGCGCCTTGATTC 59.650 57.895 11.66 4.94 43.17 2.52
2884 5370 2.291217 GCCTCCTTCTGGAATTGTCCTT 60.291 50.000 0.00 0.00 45.22 3.36
3061 5547 6.355747 TGCCAACATGACTTATCATCATACA 58.644 36.000 0.00 0.00 44.13 2.29
3107 5593 8.526218 AACATCATCTACATGAATATCACGAC 57.474 34.615 0.00 0.00 42.53 4.34
3560 6047 1.360393 ACCAACAGAGAAAGGGGCCA 61.360 55.000 4.39 0.00 0.00 5.36
3569 6056 1.069090 GTGTGCCGACCAACAGAGA 59.931 57.895 0.00 0.00 0.00 3.10
4163 6653 5.157067 CAACATCTCGCGAGATATACACAT 58.843 41.667 42.05 22.72 45.78 3.21
4176 6666 4.398247 GTTTCATCAAGACAACATCTCGC 58.602 43.478 0.00 0.00 36.27 5.03
4303 6794 5.731591 AGGCAAGTTGGTCAGTACTATTAC 58.268 41.667 4.75 0.00 0.00 1.89
4420 6912 4.742201 CCGTGTCGCCAGTCAGGG 62.742 72.222 0.00 0.00 38.09 4.45
4555 7057 0.460284 GCCGTCGTTGTCCTGATCAT 60.460 55.000 0.00 0.00 0.00 2.45
6339 8898 9.884465 GATTTTTGGAAGGTATAAATCTGATCG 57.116 33.333 0.00 0.00 34.18 3.69
6430 8989 7.773224 CCCCATAATCACAACTATGACAAGTTA 59.227 37.037 3.67 0.00 37.61 2.24
6687 9284 2.352421 CGTCTCAACTCCCGTAACATGT 60.352 50.000 0.00 0.00 0.00 3.21
6728 9325 3.155167 GAGGGCGGGTAGGAGGTG 61.155 72.222 0.00 0.00 0.00 4.00
6729 9326 4.835891 CGAGGGCGGGTAGGAGGT 62.836 72.222 0.00 0.00 0.00 3.85
6730 9327 4.835891 ACGAGGGCGGGTAGGAGG 62.836 72.222 0.00 0.00 43.17 4.30
6829 9426 0.900421 GAAGTAGGGGTAGGCGTTGT 59.100 55.000 0.00 0.00 0.00 3.32
7359 9990 1.072332 TTGTTCTGCGGCCTGCTAA 59.928 52.632 18.14 10.95 46.63 3.09
7360 9991 1.671054 GTTGTTCTGCGGCCTGCTA 60.671 57.895 18.14 6.21 46.63 3.49
7693 10337 2.712539 CGTTGCGTGCTTGTTGGA 59.287 55.556 0.00 0.00 0.00 3.53
7730 10374 1.138047 CTACCGAGGCGCTGTAAACG 61.138 60.000 7.64 4.50 0.00 3.60
7789 10433 3.071751 GCGCGCGATTTTTGCAAT 58.928 50.000 37.18 0.00 0.00 3.56
8060 10724 0.448990 CGACGATCGGTACCTTGACA 59.551 55.000 20.98 0.00 36.00 3.58
8150 10817 1.165907 TGAGTTCCTGCAAGCAACGG 61.166 55.000 0.00 0.00 0.00 4.44
8233 10900 0.736636 ACGATACGGCTCGACAATCA 59.263 50.000 14.63 0.00 41.12 2.57
8280 10947 5.528870 ACTTTCGATTTGGTGGATTTTGAC 58.471 37.500 0.00 0.00 0.00 3.18
8289 10956 4.013728 TGGGGATAACTTTCGATTTGGTG 58.986 43.478 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.