Multiple sequence alignment - TraesCS4D01G196100

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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 TraesCS4D01G196100 chr4D 100.000 6295 0 0 1 6295 340553955 340547661 0.000000e+00 11625.0
1 TraesCS4D01G196100 chr4D 91.667 72 3 2 5356 5426 340548662 340548593 5.190000e-16 97.1
2 TraesCS4D01G196100 chr4B 98.221 4385 55 10 534 4904 422035042 422030667 0.000000e+00 7644.0
3 TraesCS4D01G196100 chr4B 97.320 597 13 3 4984 5579 422030485 422029891 0.000000e+00 1011.0
4 TraesCS4D01G196100 chr4B 88.377 456 17 20 1 455 422035597 422035177 3.360000e-142 516.0
5 TraesCS4D01G196100 chr4B 89.796 392 28 6 5845 6229 621680954 621681340 5.670000e-135 492.0
6 TraesCS4D01G196100 chr4B 93.156 263 17 1 5586 5848 621680206 621680467 9.900000e-103 385.0
7 TraesCS4D01G196100 chr4B 97.727 88 1 1 465 551 422035141 422035054 3.930000e-32 150.0
8 TraesCS4D01G196100 chr4B 94.444 72 1 2 5356 5426 422030177 422030108 2.400000e-19 108.0
9 TraesCS4D01G196100 chr4B 96.552 58 2 0 4902 4959 422030544 422030487 5.190000e-16 97.1
10 TraesCS4D01G196100 chr4A 96.142 2592 82 8 129 2715 127482322 127484900 0.000000e+00 4217.0
11 TraesCS4D01G196100 chr4A 96.888 2153 31 8 2699 4818 127484913 127487062 0.000000e+00 3572.0
12 TraesCS4D01G196100 chr4A 95.968 1984 73 7 736 2715 127289830 127287850 0.000000e+00 3214.0
13 TraesCS4D01G196100 chr4A 96.170 1410 42 6 4171 5577 127282245 127280845 0.000000e+00 2294.0
14 TraesCS4D01G196100 chr4A 94.794 1191 25 9 3021 4177 127287257 127286070 0.000000e+00 1821.0
15 TraesCS4D01G196100 chr4A 96.847 666 13 4 4859 5523 127487068 127487726 0.000000e+00 1107.0
16 TraesCS4D01G196100 chr4A 94.984 618 28 2 129 744 127330655 127330039 0.000000e+00 966.0
17 TraesCS4D01G196100 chr4A 91.411 652 48 5 5578 6229 725934073 725933430 0.000000e+00 887.0
18 TraesCS4D01G196100 chr4A 93.333 150 4 1 1 144 127482140 127482289 3.820000e-52 217.0
19 TraesCS4D01G196100 chr4A 92.466 146 9 1 1 144 127330834 127330689 2.300000e-49 207.0
20 TraesCS4D01G196100 chr4A 96.923 65 1 1 5356 5419 127487496 127487560 2.400000e-19 108.0
21 TraesCS4D01G196100 chr4A 93.056 72 2 2 5356 5426 127281131 127281062 1.120000e-17 102.0
22 TraesCS4D01G196100 chr3B 87.343 1193 132 14 1945 3127 782342894 782341711 0.000000e+00 1349.0
23 TraesCS4D01G196100 chr3B 86.754 1223 142 14 1943 3152 781838274 781837059 0.000000e+00 1343.0
24 TraesCS4D01G196100 chr3B 86.032 1260 142 8 1838 3093 782482994 782481765 0.000000e+00 1321.0
25 TraesCS4D01G196100 chr3B 89.184 1017 94 11 3850 4856 782113534 782112524 0.000000e+00 1254.0
26 TraesCS4D01G196100 chr3B 86.832 1086 109 18 3850 4909 781553481 781552404 0.000000e+00 1182.0
27 TraesCS4D01G196100 chr3B 87.464 1029 112 12 3845 4865 781837034 781836015 0.000000e+00 1170.0
28 TraesCS4D01G196100 chr3B 87.150 1035 113 14 3841 4864 782341675 782340650 0.000000e+00 1157.0
29 TraesCS4D01G196100 chr3B 86.120 915 85 14 941 1829 782484530 782483632 0.000000e+00 948.0
30 TraesCS4D01G196100 chr3B 93.066 649 39 3 5581 6229 588159661 588159019 0.000000e+00 944.0
31 TraesCS4D01G196100 chr3B 85.730 932 80 16 939 1834 781854192 781853278 0.000000e+00 935.0
32 TraesCS4D01G196100 chr3B 82.198 910 99 25 935 1829 782343938 782343077 0.000000e+00 725.0
33 TraesCS4D01G196100 chr3B 82.787 732 99 16 935 1647 781809798 781809075 4.140000e-176 628.0
34 TraesCS4D01G196100 chr3B 86.307 482 49 7 1359 1829 782115813 782115338 5.630000e-140 508.0
35 TraesCS4D01G196100 chr3B 91.288 264 18 4 935 1196 782116296 782116036 7.760000e-94 355.0
36 TraesCS4D01G196100 chr3B 88.202 178 9 8 5411 5577 781669617 781669441 1.070000e-47 202.0
37 TraesCS4D01G196100 chr3B 82.286 175 19 5 707 876 782116561 782116394 2.370000e-29 141.0
38 TraesCS4D01G196100 chr3B 84.138 145 15 7 775 913 781854444 781854302 3.960000e-27 134.0
39 TraesCS4D01G196100 chr3D 90.019 1042 90 9 3850 4882 585711332 585710296 0.000000e+00 1336.0
40 TraesCS4D01G196100 chr3D 86.122 1225 146 19 1944 3157 585651581 585652792 0.000000e+00 1299.0
41 TraesCS4D01G196100 chr3D 85.972 1219 155 15 1943 3154 585632396 585633605 0.000000e+00 1290.0
42 TraesCS4D01G196100 chr3D 86.075 1149 125 15 1838 2982 585712614 585711497 0.000000e+00 1203.0
43 TraesCS4D01G196100 chr3D 86.880 1029 117 13 3845 4865 585433069 585432051 0.000000e+00 1136.0
44 TraesCS4D01G196100 chr3D 85.821 804 99 10 2361 3154 585616157 585616955 0.000000e+00 839.0
45 TraesCS4D01G196100 chr3D 83.499 903 116 13 941 1828 585650562 585651446 0.000000e+00 811.0
46 TraesCS4D01G196100 chr3D 85.437 721 90 9 2445 3154 585433808 585433092 0.000000e+00 736.0
47 TraesCS4D01G196100 chr3D 83.243 740 92 23 935 1656 585435240 585434515 0.000000e+00 651.0
48 TraesCS4D01G196100 chr3D 84.220 583 66 10 1257 1829 585615140 585615706 1.540000e-150 544.0
49 TraesCS4D01G196100 chr3D 87.526 481 43 8 1359 1828 585713576 585713102 2.000000e-149 540.0
50 TraesCS4D01G196100 chr3D 88.452 407 34 4 1393 1790 585914535 585914133 4.410000e-131 479.0
51 TraesCS4D01G196100 chr3D 85.396 404 43 9 935 1326 585713977 585713578 7.600000e-109 405.0
52 TraesCS4D01G196100 chr3D 86.809 235 25 4 5111 5344 585653973 585654202 2.250000e-64 257.0
53 TraesCS4D01G196100 chr3D 86.383 235 26 4 5111 5344 585431902 585431673 1.050000e-62 252.0
54 TraesCS4D01G196100 chr3D 87.330 221 21 5 5111 5330 585618463 585618677 4.870000e-61 246.0
55 TraesCS4D01G196100 chr3D 84.064 251 30 9 5095 5344 585710155 585709914 3.790000e-57 233.0
56 TraesCS4D01G196100 chr3D 87.912 182 12 6 5405 5577 585618706 585618886 8.270000e-49 206.0
57 TraesCS4D01G196100 chr3D 87.912 182 12 6 5405 5577 585654226 585654406 8.270000e-49 206.0
58 TraesCS4D01G196100 chr3D 87.293 181 11 8 5408 5577 585467324 585467145 4.980000e-46 196.0
59 TraesCS4D01G196100 chr3D 85.484 186 16 7 701 876 585613267 585613451 3.880000e-42 183.0
60 TraesCS4D01G196100 chr3D 85.027 187 16 7 701 876 585631087 585631272 5.010000e-41 180.0
61 TraesCS4D01G196100 chr3D 83.429 175 17 5 707 876 585714242 585714075 1.090000e-32 152.0
62 TraesCS4D01G196100 chr3D 83.660 153 13 8 771 913 585915172 585915022 3.960000e-27 134.0
63 TraesCS4D01G196100 chr3D 100.000 71 0 0 6225 6295 121560713 121560643 1.420000e-26 132.0
64 TraesCS4D01G196100 chr3D 100.000 67 0 0 6229 6295 379748534 379748468 2.380000e-24 124.0
65 TraesCS4D01G196100 chr3D 90.909 88 8 0 6208 6295 375741055 375741142 1.110000e-22 119.0
66 TraesCS4D01G196100 chr3D 86.420 81 8 1 727 804 585478047 585477967 1.120000e-12 86.1
67 TraesCS4D01G196100 chr1D 98.560 625 9 0 5605 6229 469529644 469530268 0.000000e+00 1105.0
68 TraesCS4D01G196100 chr2D 97.077 650 18 1 5580 6229 484360431 484359783 0.000000e+00 1094.0
69 TraesCS4D01G196100 chr2D 95.000 80 2 2 6217 6295 22890415 22890337 2.380000e-24 124.0
70 TraesCS4D01G196100 chr1B 93.538 650 33 4 5580 6229 57703796 57704436 0.000000e+00 959.0
71 TraesCS4D01G196100 chr1B 94.790 499 25 1 5580 6077 629319598 629320096 0.000000e+00 776.0
72 TraesCS4D01G196100 chrUn 85.945 804 98 10 2361 3154 358609519 358610317 0.000000e+00 845.0
73 TraesCS4D01G196100 chrUn 97.284 405 10 1 1402 1805 478229411 478229815 0.000000e+00 686.0
74 TraesCS4D01G196100 chrUn 84.220 583 66 10 1257 1829 358608502 358609068 1.540000e-150 544.0
75 TraesCS4D01G196100 chrUn 86.398 397 47 5 2764 3154 321263238 321263633 1.620000e-115 427.0
76 TraesCS4D01G196100 chrUn 86.478 318 36 5 5575 5887 23401255 23400940 6.040000e-90 342.0
77 TraesCS4D01G196100 chrUn 87.330 221 21 5 5111 5330 300191703 300191917 4.870000e-61 246.0
78 TraesCS4D01G196100 chrUn 87.330 221 21 5 5111 5330 321265141 321265355 4.870000e-61 246.0
79 TraesCS4D01G196100 chrUn 87.912 182 12 6 5405 5577 300191946 300192126 8.270000e-49 206.0
80 TraesCS4D01G196100 chrUn 87.912 182 12 6 5405 5577 321265384 321265564 8.270000e-49 206.0
81 TraesCS4D01G196100 chr7D 97.368 76 1 1 6221 6295 458217873 458217948 1.840000e-25 128.0
82 TraesCS4D01G196100 chr7D 96.154 78 2 1 6219 6295 84216113 84216190 6.630000e-25 126.0
83 TraesCS4D01G196100 chr7D 100.000 68 0 0 6228 6295 223145368 223145301 6.630000e-25 126.0
84 TraesCS4D01G196100 chr6D 100.000 67 0 0 6229 6295 52922262 52922196 2.380000e-24 124.0
85 TraesCS4D01G196100 chr6D 93.902 82 5 0 6214 6295 146662362 146662443 2.380000e-24 124.0
86 TraesCS4D01G196100 chr5A 97.778 45 1 0 3359 3403 700438353 700438397 1.880000e-10 78.7


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 TraesCS4D01G196100 chr4D 340547661 340553955 6294 True 11625.000000 11625 100.000000 1 6295 1 chr4D.!!$R1 6294
1 TraesCS4D01G196100 chr4B 422029891 422035597 5706 True 1587.683333 7644 95.440167 1 5579 6 chr4B.!!$R1 5578
2 TraesCS4D01G196100 chr4B 621680206 621681340 1134 False 438.500000 492 91.476000 5586 6229 2 chr4B.!!$F1 643
3 TraesCS4D01G196100 chr4A 127286070 127289830 3760 True 2517.500000 3214 95.381000 736 4177 2 chr4A.!!$R3 3441
4 TraesCS4D01G196100 chr4A 127482140 127487726 5586 False 1844.200000 4217 96.026600 1 5523 5 chr4A.!!$F1 5522
5 TraesCS4D01G196100 chr4A 127280845 127282245 1400 True 1198.000000 2294 94.613000 4171 5577 2 chr4A.!!$R2 1406
6 TraesCS4D01G196100 chr4A 725933430 725934073 643 True 887.000000 887 91.411000 5578 6229 1 chr4A.!!$R1 651
7 TraesCS4D01G196100 chr4A 127330039 127330834 795 True 586.500000 966 93.725000 1 744 2 chr4A.!!$R4 743
8 TraesCS4D01G196100 chr3B 781836015 781838274 2259 True 1256.500000 1343 87.109000 1943 4865 2 chr3B.!!$R5 2922
9 TraesCS4D01G196100 chr3B 781552404 781553481 1077 True 1182.000000 1182 86.832000 3850 4909 1 chr3B.!!$R2 1059
10 TraesCS4D01G196100 chr3B 782481765 782484530 2765 True 1134.500000 1321 86.076000 941 3093 2 chr3B.!!$R9 2152
11 TraesCS4D01G196100 chr3B 782340650 782343938 3288 True 1077.000000 1349 85.563667 935 4864 3 chr3B.!!$R8 3929
12 TraesCS4D01G196100 chr3B 588159019 588159661 642 True 944.000000 944 93.066000 5581 6229 1 chr3B.!!$R1 648
13 TraesCS4D01G196100 chr3B 781809075 781809798 723 True 628.000000 628 82.787000 935 1647 1 chr3B.!!$R4 712
14 TraesCS4D01G196100 chr3B 782112524 782116561 4037 True 564.500000 1254 87.266250 707 4856 4 chr3B.!!$R7 4149
15 TraesCS4D01G196100 chr3B 781853278 781854444 1166 True 534.500000 935 84.934000 775 1834 2 chr3B.!!$R6 1059
16 TraesCS4D01G196100 chr3D 585631087 585633605 2518 False 735.000000 1290 85.499500 701 3154 2 chr3D.!!$F3 2453
17 TraesCS4D01G196100 chr3D 585431673 585435240 3567 True 693.750000 1136 85.485750 935 5344 4 chr3D.!!$R5 4409
18 TraesCS4D01G196100 chr3D 585709914 585714242 4328 True 644.833333 1336 86.084833 707 5344 6 chr3D.!!$R6 4637
19 TraesCS4D01G196100 chr3D 585650562 585654406 3844 False 643.250000 1299 86.085500 941 5577 4 chr3D.!!$F4 4636
20 TraesCS4D01G196100 chr3D 585613267 585618886 5619 False 403.600000 839 86.153400 701 5577 5 chr3D.!!$F2 4876
21 TraesCS4D01G196100 chr3D 585914133 585915172 1039 True 306.500000 479 86.056000 771 1790 2 chr3D.!!$R7 1019
22 TraesCS4D01G196100 chr1D 469529644 469530268 624 False 1105.000000 1105 98.560000 5605 6229 1 chr1D.!!$F1 624
23 TraesCS4D01G196100 chr2D 484359783 484360431 648 True 1094.000000 1094 97.077000 5580 6229 1 chr2D.!!$R2 649
24 TraesCS4D01G196100 chr1B 57703796 57704436 640 False 959.000000 959 93.538000 5580 6229 1 chr1B.!!$F1 649
25 TraesCS4D01G196100 chrUn 358608502 358610317 1815 False 694.500000 845 85.082500 1257 3154 2 chrUn.!!$F4 1897
26 TraesCS4D01G196100 chrUn 321263238 321265564 2326 False 293.000000 427 87.213333 2764 5577 3 chrUn.!!$F3 2813

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
155 213 0.038310 TCTCTCTCTTCGCACCAGGA 59.962 55.000 0.00 0.00 0.00 3.86 F
254 314 0.179000 CTAGGCCGTGCTTGGAATCT 59.821 55.000 0.00 0.00 0.00 2.40 F
324 384 2.513897 GAGCCATTTCCGGACGGG 60.514 66.667 1.83 7.33 35.59 5.28 F
1362 3008 4.610680 CGGCTTCCGTAAAGAAGAAAGTTG 60.611 45.833 5.50 0.00 45.08 3.16 F
2449 5059 0.746204 TTGTGCTTCCTGACACGCAA 60.746 50.000 0.00 0.00 39.71 4.85 F
3355 6293 2.930562 AGGCTGCCCCTCGAACTT 60.931 61.111 16.57 0.00 41.21 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1362 3008 1.742831 TCACAGCAACAACACAAGGTC 59.257 47.619 0.0 0.0 0.00 3.85 R
1921 4275 5.578727 ACAATAGACGCATCAAGAAGAAGTC 59.421 40.000 0.0 0.0 32.75 3.01 R
1924 4278 6.801539 AAACAATAGACGCATCAAGAAGAA 57.198 33.333 0.0 0.0 0.00 2.52 R
3267 6205 1.196127 CTTCCCGCTTTAACCACGTTC 59.804 52.381 0.0 0.0 0.00 3.95 R
3446 6401 3.066760 GGGTGTCAAGGTTGTTTCTTCTG 59.933 47.826 0.0 0.0 0.00 3.02 R
5299 8829 1.345741 TCACTCAACCAGAAGAGGCAG 59.654 52.381 0.0 0.0 36.20 4.85 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
117 126 5.869649 AGAAAACTTTGCATGTTAACCCT 57.130 34.783 2.48 0.00 0.00 4.34
155 213 0.038310 TCTCTCTCTTCGCACCAGGA 59.962 55.000 0.00 0.00 0.00 3.86
254 314 0.179000 CTAGGCCGTGCTTGGAATCT 59.821 55.000 0.00 0.00 0.00 2.40
324 384 2.513897 GAGCCATTTCCGGACGGG 60.514 66.667 1.83 7.33 35.59 5.28
1362 3008 4.610680 CGGCTTCCGTAAAGAAGAAAGTTG 60.611 45.833 5.50 0.00 45.08 3.16
1836 4190 6.127810 TGCTCAGTTTGCATTCATCTAATC 57.872 37.500 0.00 0.00 35.31 1.75
2060 4414 7.898014 TCTCTATGCCTTGATTGTCTTAGTA 57.102 36.000 0.00 0.00 0.00 1.82
2449 5059 0.746204 TTGTGCTTCCTGACACGCAA 60.746 50.000 0.00 0.00 39.71 4.85
2967 5619 6.461509 GCCAAAATGGTACCCATCTATTTCAG 60.462 42.308 10.07 4.83 44.40 3.02
3336 6274 3.117776 AGGTAGAAATGAGGCATCATGCA 60.118 43.478 15.62 0.00 45.67 3.96
3355 6293 2.930562 AGGCTGCCCCTCGAACTT 60.931 61.111 16.57 0.00 41.21 2.66
3446 6401 5.713389 ACTAGCCCTTGGTGGTATTTTTAAC 59.287 40.000 0.00 0.00 31.35 2.01
3676 6631 1.550524 CACTGCTCCTGCTGGTTACTA 59.449 52.381 9.73 0.00 41.57 1.82
4012 7289 5.376625 TGTCAACCTGGGATATGATAAAGC 58.623 41.667 0.00 0.00 0.00 3.51
4881 8222 3.917988 GCAAAGGCTGGCCAATATATTC 58.082 45.455 7.01 0.00 38.92 1.75
4882 8223 3.575687 GCAAAGGCTGGCCAATATATTCT 59.424 43.478 7.01 0.00 38.92 2.40
4883 8224 4.039609 GCAAAGGCTGGCCAATATATTCTT 59.960 41.667 7.01 0.09 38.92 2.52
4884 8225 5.243730 GCAAAGGCTGGCCAATATATTCTTA 59.756 40.000 7.01 0.00 38.92 2.10
4885 8226 6.071165 GCAAAGGCTGGCCAATATATTCTTAT 60.071 38.462 7.01 0.00 38.92 1.73
4886 8227 7.526025 GCAAAGGCTGGCCAATATATTCTTATT 60.526 37.037 7.01 0.00 38.92 1.40
4931 8397 1.875514 TGTCTGCATGTGTCTGCTTTC 59.124 47.619 0.00 0.00 42.75 2.62
4998 8464 4.785301 AGTATTGTCTGCTGTTGCCATAT 58.215 39.130 0.00 0.00 38.71 1.78
5249 8718 1.274712 CTGGACCTCAGCTCCTCTTT 58.725 55.000 0.00 0.00 36.60 2.52
5305 8835 3.835395 AGGGTTCTATAGTATGCTGCCTC 59.165 47.826 0.00 0.00 0.00 4.70
5335 8865 6.257411 GGTTGAGTGATGAATAGTGAGACATG 59.743 42.308 0.00 0.00 0.00 3.21
5645 9199 1.960689 CGAAATCAAAGGGTGGTGGTT 59.039 47.619 0.00 0.00 0.00 3.67
5869 9915 1.299850 CGTCGCCTTCACACTGTCA 60.300 57.895 0.00 0.00 0.00 3.58
5950 10000 2.194271 CTCACGGCCTAAATCGTCTTC 58.806 52.381 0.00 0.00 37.53 2.87
5951 10001 1.134907 TCACGGCCTAAATCGTCTTCC 60.135 52.381 0.00 0.00 37.53 3.46
5953 10003 1.553704 ACGGCCTAAATCGTCTTCCTT 59.446 47.619 0.00 0.00 34.20 3.36
5954 10004 1.933853 CGGCCTAAATCGTCTTCCTTG 59.066 52.381 0.00 0.00 0.00 3.61
5955 10005 2.418197 CGGCCTAAATCGTCTTCCTTGA 60.418 50.000 0.00 0.00 0.00 3.02
5956 10006 2.937149 GGCCTAAATCGTCTTCCTTGAC 59.063 50.000 0.00 0.00 0.00 3.18
5957 10007 3.596214 GCCTAAATCGTCTTCCTTGACA 58.404 45.455 0.00 0.00 36.82 3.58
6229 10286 1.597663 CAACCAGAGCGAAAAGAACGT 59.402 47.619 0.00 0.00 0.00 3.99
6230 10287 1.217882 ACCAGAGCGAAAAGAACGTG 58.782 50.000 0.00 0.00 0.00 4.49
6231 10288 1.217882 CCAGAGCGAAAAGAACGTGT 58.782 50.000 0.00 0.00 0.00 4.49
6232 10289 2.223876 ACCAGAGCGAAAAGAACGTGTA 60.224 45.455 0.00 0.00 0.00 2.90
6233 10290 2.408704 CCAGAGCGAAAAGAACGTGTAG 59.591 50.000 0.00 0.00 0.00 2.74
6234 10291 2.059541 AGAGCGAAAAGAACGTGTAGC 58.940 47.619 0.00 0.00 0.00 3.58
6236 10293 0.780002 GCGAAAAGAACGTGTAGCGA 59.220 50.000 0.00 0.00 44.77 4.93
6237 10294 1.459784 GCGAAAAGAACGTGTAGCGAC 60.460 52.381 0.00 0.00 44.77 5.19
6238 10295 1.123756 CGAAAAGAACGTGTAGCGACC 59.876 52.381 0.00 0.00 44.77 4.79
6239 10296 2.129607 GAAAAGAACGTGTAGCGACCA 58.870 47.619 0.00 0.00 44.77 4.02
6240 10297 1.779569 AAAGAACGTGTAGCGACCAG 58.220 50.000 0.00 0.00 44.77 4.00
6241 10298 0.956633 AAGAACGTGTAGCGACCAGA 59.043 50.000 0.00 0.00 44.77 3.86
6242 10299 0.240411 AGAACGTGTAGCGACCAGAC 59.760 55.000 0.00 0.00 44.77 3.51
6243 10300 0.731855 GAACGTGTAGCGACCAGACC 60.732 60.000 0.00 0.00 44.77 3.85
6244 10301 1.177256 AACGTGTAGCGACCAGACCT 61.177 55.000 0.00 0.00 44.77 3.85
6245 10302 1.136984 CGTGTAGCGACCAGACCTC 59.863 63.158 0.00 0.00 44.77 3.85
6246 10303 1.583495 CGTGTAGCGACCAGACCTCA 61.583 60.000 0.00 0.00 44.77 3.86
6247 10304 0.601558 GTGTAGCGACCAGACCTCAA 59.398 55.000 0.00 0.00 0.00 3.02
6248 10305 1.000506 GTGTAGCGACCAGACCTCAAA 59.999 52.381 0.00 0.00 0.00 2.69
6249 10306 1.899814 TGTAGCGACCAGACCTCAAAT 59.100 47.619 0.00 0.00 0.00 2.32
6250 10307 2.271800 GTAGCGACCAGACCTCAAATG 58.728 52.381 0.00 0.00 0.00 2.32
6251 10308 0.036010 AGCGACCAGACCTCAAATGG 60.036 55.000 0.00 0.00 40.10 3.16
6260 10317 1.901591 ACCTCAAATGGTCTGTGCTG 58.098 50.000 0.00 0.00 34.86 4.41
6261 10318 0.524862 CCTCAAATGGTCTGTGCTGC 59.475 55.000 0.00 0.00 0.00 5.25
6262 10319 1.531423 CTCAAATGGTCTGTGCTGCT 58.469 50.000 0.00 0.00 0.00 4.24
6263 10320 1.199327 CTCAAATGGTCTGTGCTGCTG 59.801 52.381 0.00 0.00 0.00 4.41
6264 10321 0.956633 CAAATGGTCTGTGCTGCTGT 59.043 50.000 0.00 0.00 0.00 4.40
6265 10322 0.956633 AAATGGTCTGTGCTGCTGTG 59.043 50.000 0.00 0.00 0.00 3.66
6266 10323 1.521450 AATGGTCTGTGCTGCTGTGC 61.521 55.000 0.00 0.00 0.00 4.57
6267 10324 2.592574 GGTCTGTGCTGCTGTGCA 60.593 61.111 0.00 0.00 41.05 4.57
6273 10330 2.903350 TGCTGCTGTGCACCAGTG 60.903 61.111 19.98 12.80 43.55 3.66
6274 10331 2.903855 GCTGCTGTGCACCAGTGT 60.904 61.111 19.98 0.00 43.55 3.55
6275 10332 2.901292 GCTGCTGTGCACCAGTGTC 61.901 63.158 19.98 4.77 43.55 3.67
6276 10333 1.524393 CTGCTGTGCACCAGTGTCA 60.524 57.895 15.69 4.95 43.55 3.58
6277 10334 0.887836 CTGCTGTGCACCAGTGTCAT 60.888 55.000 15.69 0.00 43.55 3.06
6278 10335 0.886043 TGCTGTGCACCAGTGTCATC 60.886 55.000 15.69 0.00 43.55 2.92
6279 10336 1.580845 GCTGTGCACCAGTGTCATCC 61.581 60.000 15.69 0.00 43.55 3.51
6280 10337 0.957395 CTGTGCACCAGTGTCATCCC 60.957 60.000 15.69 0.00 36.37 3.85
6281 10338 1.376466 GTGCACCAGTGTCATCCCT 59.624 57.895 5.22 0.00 0.00 4.20
6282 10339 0.957395 GTGCACCAGTGTCATCCCTG 60.957 60.000 5.22 0.00 0.00 4.45
6288 10345 2.616634 CAGTGTCATCCCTGGATCAG 57.383 55.000 0.00 0.00 31.62 2.90
6289 10346 1.836166 CAGTGTCATCCCTGGATCAGT 59.164 52.381 0.00 0.00 31.62 3.41
6290 10347 3.033909 CAGTGTCATCCCTGGATCAGTA 58.966 50.000 0.00 0.00 31.62 2.74
6291 10348 3.452264 CAGTGTCATCCCTGGATCAGTAA 59.548 47.826 0.00 0.00 31.62 2.24
6292 10349 4.102210 CAGTGTCATCCCTGGATCAGTAAT 59.898 45.833 0.00 0.00 31.62 1.89
6293 10350 4.102210 AGTGTCATCCCTGGATCAGTAATG 59.898 45.833 0.00 0.00 31.62 1.90
6294 10351 3.181451 TGTCATCCCTGGATCAGTAATGC 60.181 47.826 0.00 0.00 31.62 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 5.028549 AGACATACTACAAGGAATGCAGG 57.971 43.478 0.00 0.00 0.00 4.85
155 213 4.032960 TCATGTTGGTACTTTGGATGCT 57.967 40.909 0.00 0.00 0.00 3.79
254 314 5.155278 ACACCTCCGTATTGAATTACACA 57.845 39.130 0.00 0.00 0.00 3.72
377 437 2.297880 GGGCTTGTTTGGATTACCGTTT 59.702 45.455 0.00 0.00 39.42 3.60
450 510 6.151144 TGACGTATCGATGGTGAAGATCATAT 59.849 38.462 8.54 0.00 0.00 1.78
458 518 3.129638 TGACATGACGTATCGATGGTGAA 59.870 43.478 8.54 0.00 0.00 3.18
693 810 3.955650 ACCAACAATGTCTAGTAGCGT 57.044 42.857 0.00 0.00 0.00 5.07
1362 3008 1.742831 TCACAGCAACAACACAAGGTC 59.257 47.619 0.00 0.00 0.00 3.85
1836 4190 6.208988 TGTAGTACAGGTCATGAGCTAAAG 57.791 41.667 26.06 16.67 37.39 1.85
1921 4275 5.578727 ACAATAGACGCATCAAGAAGAAGTC 59.421 40.000 0.00 0.00 32.75 3.01
1924 4278 6.801539 AAACAATAGACGCATCAAGAAGAA 57.198 33.333 0.00 0.00 0.00 2.52
2060 4414 7.391148 AGCACAATTTGATTTAAGTACCGAT 57.609 32.000 2.79 0.00 0.00 4.18
2449 5059 6.594159 ACTCACTAAGCTATTAACGCAAACAT 59.406 34.615 0.00 0.00 0.00 2.71
2967 5619 6.073058 TGCACACAAGATAGTCACTTGAAATC 60.073 38.462 13.34 0.00 44.92 2.17
2986 5638 4.875544 TGAGAAGTTTTACTGTGCACAC 57.124 40.909 17.42 4.95 0.00 3.82
3267 6205 1.196127 CTTCCCGCTTTAACCACGTTC 59.804 52.381 0.00 0.00 0.00 3.95
3336 6274 3.394836 GTTCGAGGGGCAGCCTCT 61.395 66.667 16.14 16.14 36.82 3.69
3355 6293 4.007644 CACAGGCCCGTGAGCTCA 62.008 66.667 14.31 13.74 39.34 4.26
3446 6401 3.066760 GGGTGTCAAGGTTGTTTCTTCTG 59.933 47.826 0.00 0.00 0.00 3.02
3695 6650 3.891366 ACAGCTGCTGGATAGTTTTGTTT 59.109 39.130 31.00 4.73 35.51 2.83
3929 7206 9.511272 AATGAACATAGAGCAAATCAGCATATA 57.489 29.630 0.00 0.00 36.85 0.86
4012 7289 3.840468 CACAATGATTCACACACATGGG 58.160 45.455 0.00 0.00 0.00 4.00
4492 7774 2.159043 AGACTGGTGGATAAGTGATGCG 60.159 50.000 0.00 0.00 0.00 4.73
4881 8222 8.868744 TTTGTAACAATTACGAAGCGAATAAG 57.131 30.769 0.00 0.00 38.98 1.73
4882 8223 8.868744 CTTTGTAACAATTACGAAGCGAATAA 57.131 30.769 13.27 0.00 45.56 1.40
4931 8397 5.174395 GCAGATGCAGGATATACTGGTTAG 58.826 45.833 16.91 0.00 41.59 2.34
4998 8464 6.702716 ACTTGGGAAGTTCGTTTTATCAAA 57.297 33.333 0.00 0.00 39.04 2.69
5249 8718 2.566010 GCCGCGCAAAAATCCAGA 59.434 55.556 8.75 0.00 0.00 3.86
5299 8829 1.345741 TCACTCAACCAGAAGAGGCAG 59.654 52.381 0.00 0.00 36.20 4.85
5305 8835 6.401394 TCACTATTCATCACTCAACCAGAAG 58.599 40.000 0.00 0.00 0.00 2.85
5335 8865 4.177026 ACTTATTCATCGCTGACAGTCAC 58.823 43.478 0.00 0.00 0.00 3.67
5592 9146 4.136796 GCTCATATTCATTGCAGGGTACA 58.863 43.478 0.00 0.00 0.00 2.90
5645 9199 3.070159 GCCCAGTTGAGCAGTATAGATCA 59.930 47.826 0.00 0.00 31.10 2.92
5869 9915 4.988598 CGGTCCACAAGCACGGCT 62.989 66.667 0.00 0.00 42.56 5.52
5950 10000 3.307059 AGGAAGACGAATCCTTGTCAAGG 60.307 47.826 23.69 23.69 45.06 3.61
5951 10001 3.931578 AGGAAGACGAATCCTTGTCAAG 58.068 45.455 5.53 5.53 45.06 3.02
6229 10286 1.334160 TTTGAGGTCTGGTCGCTACA 58.666 50.000 0.00 0.00 0.00 2.74
6230 10287 2.271800 CATTTGAGGTCTGGTCGCTAC 58.728 52.381 0.00 0.00 0.00 3.58
6231 10288 1.207089 CCATTTGAGGTCTGGTCGCTA 59.793 52.381 0.00 0.00 0.00 4.26
6232 10289 0.036010 CCATTTGAGGTCTGGTCGCT 60.036 55.000 0.00 0.00 0.00 4.93
6233 10290 0.321653 ACCATTTGAGGTCTGGTCGC 60.322 55.000 0.00 0.00 38.99 5.19
6234 10291 3.935993 ACCATTTGAGGTCTGGTCG 57.064 52.632 0.00 0.00 38.99 4.79
6241 10298 1.901591 CAGCACAGACCATTTGAGGT 58.098 50.000 0.00 0.00 46.82 3.85
6242 10299 0.524862 GCAGCACAGACCATTTGAGG 59.475 55.000 0.00 0.00 0.00 3.86
6243 10300 1.199327 CAGCAGCACAGACCATTTGAG 59.801 52.381 0.00 0.00 0.00 3.02
6244 10301 1.241165 CAGCAGCACAGACCATTTGA 58.759 50.000 0.00 0.00 0.00 2.69
6245 10302 0.956633 ACAGCAGCACAGACCATTTG 59.043 50.000 0.00 0.00 0.00 2.32
6246 10303 0.956633 CACAGCAGCACAGACCATTT 59.043 50.000 0.00 0.00 0.00 2.32
6247 10304 1.521450 GCACAGCAGCACAGACCATT 61.521 55.000 0.00 0.00 0.00 3.16
6248 10305 1.970114 GCACAGCAGCACAGACCAT 60.970 57.895 0.00 0.00 0.00 3.55
6249 10306 2.592574 GCACAGCAGCACAGACCA 60.593 61.111 0.00 0.00 0.00 4.02
6250 10307 2.592574 TGCACAGCAGCACAGACC 60.593 61.111 0.00 0.00 40.11 3.85
6262 10319 1.073025 GGGATGACACTGGTGCACA 59.927 57.895 20.43 3.92 0.00 4.57
6263 10320 0.957395 CAGGGATGACACTGGTGCAC 60.957 60.000 8.80 8.80 43.19 4.57
6264 10321 1.376086 CAGGGATGACACTGGTGCA 59.624 57.895 0.17 1.12 43.19 4.57
6265 10322 4.308526 CAGGGATGACACTGGTGC 57.691 61.111 0.17 0.00 43.19 5.01
6269 10326 1.836166 ACTGATCCAGGGATGACACTG 59.164 52.381 5.35 0.00 46.15 3.66
6270 10327 2.260639 ACTGATCCAGGGATGACACT 57.739 50.000 5.35 0.00 35.51 3.55
6271 10328 4.384056 CATTACTGATCCAGGGATGACAC 58.616 47.826 5.35 0.00 35.51 3.67
6272 10329 3.181451 GCATTACTGATCCAGGGATGACA 60.181 47.826 5.35 0.00 35.51 3.58
6273 10330 3.406764 GCATTACTGATCCAGGGATGAC 58.593 50.000 5.35 0.00 35.51 3.06
6274 10331 3.777106 GCATTACTGATCCAGGGATGA 57.223 47.619 5.35 0.00 35.51 2.92


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

AutoCloner maintained by Alex Coulton.