Multiple sequence alignment - TraesCS6D01G135700

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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 TraesCS6D01G135700 chr6D 100.000 2417 0 0 1 2417 104063331 104065747 0.000000e+00 4464.0
1 TraesCS6D01G135700 chr6D 100.000 34 0 0 1157 1190 104064376 104064409 2.010000e-06 63.9
2 TraesCS6D01G135700 chr6D 100.000 34 0 0 1046 1079 104064487 104064520 2.010000e-06 63.9
3 TraesCS6D01G135700 chr6D 95.122 41 1 1 152 191 156809573 156809613 2.010000e-06 63.9
4 TraesCS6D01G135700 chr5D 97.977 2274 35 9 152 2417 445095999 445093729 0.000000e+00 3934.0
5 TraesCS6D01G135700 chr5D 82.739 1037 107 29 1187 2156 440774828 440773797 0.000000e+00 857.0
6 TraesCS6D01G135700 chr5D 95.000 40 1 1 151 189 437094312 437094351 7.220000e-06 62.1
7 TraesCS6D01G135700 chr7D 98.306 2243 35 3 178 2417 202027797 202030039 0.000000e+00 3928.0
8 TraesCS6D01G135700 chr7D 100.000 34 0 0 1157 1190 202028667 202028700 2.010000e-06 63.9
9 TraesCS6D01G135700 chr7D 100.000 34 0 0 1046 1079 202028778 202028811 2.010000e-06 63.9
10 TraesCS6D01G135700 chr7D 95.000 40 1 1 151 189 162189050 162189011 7.220000e-06 62.1
11 TraesCS6D01G135700 chr7D 95.000 40 1 1 151 189 511631846 511631807 7.220000e-06 62.1
12 TraesCS6D01G135700 chr3B 97.097 1447 17 6 891 2331 61992690 61991263 0.000000e+00 2416.0
13 TraesCS6D01G135700 chr3B 80.910 901 99 24 1322 2154 115403470 115404365 0.000000e+00 643.0
14 TraesCS6D01G135700 chr3B 93.365 422 27 1 335 756 793281384 793280964 7.340000e-175 623.0
15 TraesCS6D01G135700 chr3B 92.654 422 29 2 335 756 402456943 402457362 7.390000e-170 606.0
16 TraesCS6D01G135700 chr3B 100.000 99 0 0 2319 2417 61991239 61991141 1.480000e-42 183.0
17 TraesCS6D01G135700 chr2A 97.871 1362 24 2 751 2111 650612071 650613428 0.000000e+00 2350.0
18 TraesCS6D01G135700 chr2A 96.453 1043 17 6 1291 2331 575680394 575679370 0.000000e+00 1703.0
19 TraesCS6D01G135700 chr2A 99.094 552 5 0 754 1305 575683806 575683255 0.000000e+00 992.0
20 TraesCS6D01G135700 chr2A 90.722 582 35 7 179 756 650611361 650611927 0.000000e+00 758.0
21 TraesCS6D01G135700 chr2A 95.696 395 14 1 362 756 575684344 575683953 1.220000e-177 632.0
22 TraesCS6D01G135700 chr2A 90.873 252 7 2 2074 2324 650613784 650614020 8.330000e-85 324.0
23 TraesCS6D01G135700 chr2A 92.627 217 13 2 751 964 433420115 433420331 2.330000e-80 309.0
24 TraesCS6D01G135700 chr2A 98.990 99 1 0 2319 2417 575679346 575679248 6.870000e-41 178.0
25 TraesCS6D01G135700 chr2A 98.990 99 1 0 2319 2417 650614049 650614147 6.870000e-41 178.0
26 TraesCS6D01G135700 chr2A 87.248 149 11 8 195 339 777208712 777208568 1.920000e-36 163.0
27 TraesCS6D01G135700 chr4D 98.438 704 8 2 1712 2414 129516070 129516771 0.000000e+00 1236.0
28 TraesCS6D01G135700 chr1D 83.124 1037 103 26 1187 2156 355680780 355681811 0.000000e+00 880.0
29 TraesCS6D01G135700 chr1D 90.625 96 8 1 2319 2414 67943069 67942975 2.520000e-25 126.0
30 TraesCS6D01G135700 chr1D 97.368 38 1 0 152 189 375766186 375766223 5.580000e-07 65.8
31 TraesCS6D01G135700 chr3D 83.124 1037 102 26 1187 2156 461438436 461439466 0.000000e+00 878.0
32 TraesCS6D01G135700 chr3D 86.310 168 11 1 239 394 265482178 265482011 3.190000e-39 172.0
33 TraesCS6D01G135700 chr3D 88.679 53 3 2 140 191 54330852 54330902 7.220000e-06 62.1
34 TraesCS6D01G135700 chr3D 93.023 43 2 1 148 189 134599602 134599560 7.220000e-06 62.1
35 TraesCS6D01G135700 chr7B 82.642 1037 105 26 1187 2154 388877720 388878750 0.000000e+00 848.0
36 TraesCS6D01G135700 chr7A 99.085 437 4 0 754 1190 671523242 671522806 0.000000e+00 785.0
37 TraesCS6D01G135700 chr7A 88.909 559 40 12 216 753 671523928 671523371 0.000000e+00 669.0
38 TraesCS6D01G135700 chr7A 98.662 299 4 0 1046 1344 671522839 671522541 4.580000e-147 531.0
39 TraesCS6D01G135700 chr4A 96.413 446 15 1 311 756 615512324 615512768 0.000000e+00 734.0
40 TraesCS6D01G135700 chr4A 92.857 154 11 0 1 154 597663489 597663336 8.700000e-55 224.0
41 TraesCS6D01G135700 chr2B 89.138 580 45 13 178 756 528465941 528466503 0.000000e+00 706.0
42 TraesCS6D01G135700 chr2B 95.536 112 5 0 43 154 546823808 546823919 1.910000e-41 180.0
43 TraesCS6D01G135700 chr2D 83.026 760 85 18 1437 2156 14796701 14797456 0.000000e+00 649.0
44 TraesCS6D01G135700 chrUn 88.913 469 25 10 178 643 92586306 92585862 9.760000e-154 553.0
45 TraesCS6D01G135700 chrUn 95.181 83 4 0 2319 2401 50791886 50791968 5.420000e-27 132.0
46 TraesCS6D01G135700 chrUn 94.118 51 3 0 98 148 372351908 372351958 7.160000e-11 78.7
47 TraesCS6D01G135700 chr5A 92.991 214 15 0 751 964 548387282 548387495 1.800000e-81 313.0
48 TraesCS6D01G135700 chr6B 92.523 214 13 2 754 964 658609249 658609036 1.090000e-78 303.0
49 TraesCS6D01G135700 chr6B 92.056 214 14 2 754 964 652379003 652378790 5.050000e-77 298.0
50 TraesCS6D01G135700 chr6B 96.078 102 4 0 1 102 189131546 189131647 1.490000e-37 167.0
51 TraesCS6D01G135700 chr6B 96.667 60 2 0 95 154 189138372 189138431 1.530000e-17 100.0
52 TraesCS6D01G135700 chr6A 96.689 151 5 0 1 151 125486224 125486374 3.990000e-63 252.0
53 TraesCS6D01G135700 chr5B 84.211 114 11 6 37 148 548863815 548863923 1.180000e-18 104.0
54 TraesCS6D01G135700 chr5B 95.000 40 1 1 152 190 521783047 521783086 7.220000e-06 62.1
55 TraesCS6D01G135700 chr1A 93.103 58 2 2 72 128 364997515 364997459 1.540000e-12 84.2


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 TraesCS6D01G135700 chr6D 104063331 104065747 2416 False 1530.600000 4464 100.000000 1 2417 3 chr6D.!!$F2 2416
1 TraesCS6D01G135700 chr5D 445093729 445095999 2270 True 3934.000000 3934 97.977000 152 2417 1 chr5D.!!$R2 2265
2 TraesCS6D01G135700 chr5D 440773797 440774828 1031 True 857.000000 857 82.739000 1187 2156 1 chr5D.!!$R1 969
3 TraesCS6D01G135700 chr7D 202027797 202030039 2242 False 1351.933333 3928 99.435333 178 2417 3 chr7D.!!$F1 2239
4 TraesCS6D01G135700 chr3B 61991141 61992690 1549 True 1299.500000 2416 98.548500 891 2417 2 chr3B.!!$R2 1526
5 TraesCS6D01G135700 chr3B 115403470 115404365 895 False 643.000000 643 80.910000 1322 2154 1 chr3B.!!$F1 832
6 TraesCS6D01G135700 chr2A 650611361 650614147 2786 False 902.500000 2350 94.614000 179 2417 4 chr2A.!!$F2 2238
7 TraesCS6D01G135700 chr2A 575679248 575684344 5096 True 876.250000 1703 97.558250 362 2417 4 chr2A.!!$R2 2055
8 TraesCS6D01G135700 chr4D 129516070 129516771 701 False 1236.000000 1236 98.438000 1712 2414 1 chr4D.!!$F1 702
9 TraesCS6D01G135700 chr1D 355680780 355681811 1031 False 880.000000 880 83.124000 1187 2156 1 chr1D.!!$F1 969
10 TraesCS6D01G135700 chr3D 461438436 461439466 1030 False 878.000000 878 83.124000 1187 2156 1 chr3D.!!$F2 969
11 TraesCS6D01G135700 chr7B 388877720 388878750 1030 False 848.000000 848 82.642000 1187 2154 1 chr7B.!!$F1 967
12 TraesCS6D01G135700 chr7A 671522541 671523928 1387 True 661.666667 785 95.552000 216 1344 3 chr7A.!!$R1 1128
13 TraesCS6D01G135700 chr2B 528465941 528466503 562 False 706.000000 706 89.138000 178 756 1 chr2B.!!$F1 578
14 TraesCS6D01G135700 chr2D 14796701 14797456 755 False 649.000000 649 83.026000 1437 2156 1 chr2D.!!$F1 719

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
31 32 0.037326 GCCGCGGATGGATTGATCTA 60.037 55.0 33.48 0.0 0.0 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1435 4614 3.254166 GGAGCTTCTTCTGTTGCATTTCA 59.746 43.478 0.0 0.0 0.0 2.69 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
17 18 4.027755 ACTATCAAATCCGCCGCG 57.972 55.556 5.59 5.59 0.00 6.46
28 29 2.666190 CGCCGCGGATGGATTGAT 60.666 61.111 33.48 0.00 0.00 2.57
29 30 2.671177 CGCCGCGGATGGATTGATC 61.671 63.158 33.48 5.54 0.00 2.92
30 31 1.302033 GCCGCGGATGGATTGATCT 60.302 57.895 33.48 0.00 0.00 2.75
31 32 0.037326 GCCGCGGATGGATTGATCTA 60.037 55.000 33.48 0.00 0.00 1.98
32 33 1.714794 CCGCGGATGGATTGATCTAC 58.285 55.000 24.07 0.00 0.00 2.59
33 34 1.340658 CGCGGATGGATTGATCTACG 58.659 55.000 0.00 0.00 0.00 3.51
34 35 1.335964 CGCGGATGGATTGATCTACGT 60.336 52.381 0.00 0.00 0.00 3.57
35 36 2.755650 GCGGATGGATTGATCTACGTT 58.244 47.619 0.00 0.00 0.00 3.99
36 37 3.610821 CGCGGATGGATTGATCTACGTTA 60.611 47.826 0.00 0.00 0.00 3.18
37 38 4.304110 GCGGATGGATTGATCTACGTTAA 58.696 43.478 0.00 0.00 0.00 2.01
38 39 4.929808 GCGGATGGATTGATCTACGTTAAT 59.070 41.667 0.00 0.00 0.00 1.40
39 40 5.062308 GCGGATGGATTGATCTACGTTAATC 59.938 44.000 0.00 0.00 0.00 1.75
40 41 6.156519 CGGATGGATTGATCTACGTTAATCA 58.843 40.000 0.00 0.12 32.57 2.57
41 42 6.309009 CGGATGGATTGATCTACGTTAATCAG 59.691 42.308 11.06 0.00 33.66 2.90
42 43 6.091441 GGATGGATTGATCTACGTTAATCAGC 59.909 42.308 11.06 8.49 33.66 4.26
43 44 5.912892 TGGATTGATCTACGTTAATCAGCA 58.087 37.500 11.06 1.33 33.66 4.41
44 45 6.524734 TGGATTGATCTACGTTAATCAGCAT 58.475 36.000 11.06 5.22 33.66 3.79
45 46 7.666623 TGGATTGATCTACGTTAATCAGCATA 58.333 34.615 11.06 0.49 33.66 3.14
46 47 7.598869 TGGATTGATCTACGTTAATCAGCATAC 59.401 37.037 11.06 6.34 33.66 2.39
47 48 7.063544 GGATTGATCTACGTTAATCAGCATACC 59.936 40.741 11.06 8.62 33.66 2.73
48 49 6.399639 TGATCTACGTTAATCAGCATACCA 57.600 37.500 0.00 0.00 0.00 3.25
49 50 6.993079 TGATCTACGTTAATCAGCATACCAT 58.007 36.000 0.00 0.00 0.00 3.55
50 51 7.441836 TGATCTACGTTAATCAGCATACCATT 58.558 34.615 0.00 0.00 0.00 3.16
51 52 8.581578 TGATCTACGTTAATCAGCATACCATTA 58.418 33.333 0.00 0.00 0.00 1.90
52 53 8.758633 ATCTACGTTAATCAGCATACCATTAC 57.241 34.615 0.00 0.00 0.00 1.89
53 54 7.948357 TCTACGTTAATCAGCATACCATTACT 58.052 34.615 0.00 0.00 0.00 2.24
54 55 8.080417 TCTACGTTAATCAGCATACCATTACTC 58.920 37.037 0.00 0.00 0.00 2.59
55 56 6.578944 ACGTTAATCAGCATACCATTACTCA 58.421 36.000 0.00 0.00 0.00 3.41
56 57 7.045416 ACGTTAATCAGCATACCATTACTCAA 58.955 34.615 0.00 0.00 0.00 3.02
57 58 7.715249 ACGTTAATCAGCATACCATTACTCAAT 59.285 33.333 0.00 0.00 0.00 2.57
58 59 8.223769 CGTTAATCAGCATACCATTACTCAATC 58.776 37.037 0.00 0.00 0.00 2.67
59 60 8.507249 GTTAATCAGCATACCATTACTCAATCC 58.493 37.037 0.00 0.00 0.00 3.01
60 61 4.973168 TCAGCATACCATTACTCAATCCC 58.027 43.478 0.00 0.00 0.00 3.85
61 62 4.411869 TCAGCATACCATTACTCAATCCCA 59.588 41.667 0.00 0.00 0.00 4.37
62 63 4.516698 CAGCATACCATTACTCAATCCCAC 59.483 45.833 0.00 0.00 0.00 4.61
63 64 3.821033 GCATACCATTACTCAATCCCACC 59.179 47.826 0.00 0.00 0.00 4.61
64 65 4.398319 CATACCATTACTCAATCCCACCC 58.602 47.826 0.00 0.00 0.00 4.61
65 66 2.283834 ACCATTACTCAATCCCACCCA 58.716 47.619 0.00 0.00 0.00 4.51
66 67 2.858768 ACCATTACTCAATCCCACCCAT 59.141 45.455 0.00 0.00 0.00 4.00
67 68 3.225104 CCATTACTCAATCCCACCCATG 58.775 50.000 0.00 0.00 0.00 3.66
68 69 3.225104 CATTACTCAATCCCACCCATGG 58.775 50.000 4.14 4.14 46.81 3.66
85 86 3.891817 GGGCATGGCTCCTAGCTA 58.108 61.111 19.78 0.00 41.99 3.32
86 87 2.145865 GGGCATGGCTCCTAGCTAA 58.854 57.895 19.78 0.00 41.99 3.09
87 88 0.250510 GGGCATGGCTCCTAGCTAAC 60.251 60.000 19.78 0.00 41.99 2.34
88 89 0.601311 GGCATGGCTCCTAGCTAACG 60.601 60.000 12.86 0.00 41.99 3.18
89 90 0.105039 GCATGGCTCCTAGCTAACGT 59.895 55.000 0.00 0.00 41.99 3.99
90 91 1.340248 GCATGGCTCCTAGCTAACGTA 59.660 52.381 0.00 0.00 41.99 3.57
91 92 2.223971 GCATGGCTCCTAGCTAACGTAA 60.224 50.000 0.00 0.00 41.99 3.18
92 93 3.381949 CATGGCTCCTAGCTAACGTAAC 58.618 50.000 0.00 0.00 41.99 2.50
93 94 1.753073 TGGCTCCTAGCTAACGTAACC 59.247 52.381 0.00 0.00 41.99 2.85
94 95 1.753073 GGCTCCTAGCTAACGTAACCA 59.247 52.381 0.00 0.00 41.99 3.67
95 96 2.167075 GGCTCCTAGCTAACGTAACCAA 59.833 50.000 0.00 0.00 41.99 3.67
96 97 3.368739 GGCTCCTAGCTAACGTAACCAAA 60.369 47.826 0.00 0.00 41.99 3.28
97 98 4.439968 GCTCCTAGCTAACGTAACCAAAT 58.560 43.478 0.00 0.00 38.45 2.32
98 99 4.507021 GCTCCTAGCTAACGTAACCAAATC 59.493 45.833 0.00 0.00 38.45 2.17
99 100 5.657474 CTCCTAGCTAACGTAACCAAATCA 58.343 41.667 0.00 0.00 0.00 2.57
100 101 6.040209 TCCTAGCTAACGTAACCAAATCAA 57.960 37.500 0.00 0.00 0.00 2.57
101 102 6.465948 TCCTAGCTAACGTAACCAAATCAAA 58.534 36.000 0.00 0.00 0.00 2.69
102 103 7.107542 TCCTAGCTAACGTAACCAAATCAAAT 58.892 34.615 0.00 0.00 0.00 2.32
103 104 7.279313 TCCTAGCTAACGTAACCAAATCAAATC 59.721 37.037 0.00 0.00 0.00 2.17
104 105 6.811253 AGCTAACGTAACCAAATCAAATCA 57.189 33.333 0.00 0.00 0.00 2.57
105 106 6.842163 AGCTAACGTAACCAAATCAAATCAG 58.158 36.000 0.00 0.00 0.00 2.90
106 107 5.511729 GCTAACGTAACCAAATCAAATCAGC 59.488 40.000 0.00 0.00 0.00 4.26
107 108 5.446143 AACGTAACCAAATCAAATCAGCA 57.554 34.783 0.00 0.00 0.00 4.41
108 109 5.643379 ACGTAACCAAATCAAATCAGCAT 57.357 34.783 0.00 0.00 0.00 3.79
109 110 6.751514 ACGTAACCAAATCAAATCAGCATA 57.248 33.333 0.00 0.00 0.00 3.14
110 111 6.551736 ACGTAACCAAATCAAATCAGCATAC 58.448 36.000 0.00 0.00 0.00 2.39
111 112 5.971202 CGTAACCAAATCAAATCAGCATACC 59.029 40.000 0.00 0.00 0.00 2.73
112 113 6.183360 CGTAACCAAATCAAATCAGCATACCT 60.183 38.462 0.00 0.00 0.00 3.08
113 114 6.610075 AACCAAATCAAATCAGCATACCTT 57.390 33.333 0.00 0.00 0.00 3.50
114 115 7.716799 AACCAAATCAAATCAGCATACCTTA 57.283 32.000 0.00 0.00 0.00 2.69
115 116 7.716799 ACCAAATCAAATCAGCATACCTTAA 57.283 32.000 0.00 0.00 0.00 1.85
116 117 7.547227 ACCAAATCAAATCAGCATACCTTAAC 58.453 34.615 0.00 0.00 0.00 2.01
117 118 6.980397 CCAAATCAAATCAGCATACCTTAACC 59.020 38.462 0.00 0.00 0.00 2.85
118 119 7.363705 CCAAATCAAATCAGCATACCTTAACCA 60.364 37.037 0.00 0.00 0.00 3.67
119 120 6.699575 ATCAAATCAGCATACCTTAACCAC 57.300 37.500 0.00 0.00 0.00 4.16
120 121 5.815581 TCAAATCAGCATACCTTAACCACT 58.184 37.500 0.00 0.00 0.00 4.00
121 122 6.953101 TCAAATCAGCATACCTTAACCACTA 58.047 36.000 0.00 0.00 0.00 2.74
122 123 7.573710 TCAAATCAGCATACCTTAACCACTAT 58.426 34.615 0.00 0.00 0.00 2.12
123 124 7.715249 TCAAATCAGCATACCTTAACCACTATC 59.285 37.037 0.00 0.00 0.00 2.08
124 125 6.747414 ATCAGCATACCTTAACCACTATCA 57.253 37.500 0.00 0.00 0.00 2.15
125 126 6.553953 TCAGCATACCTTAACCACTATCAA 57.446 37.500 0.00 0.00 0.00 2.57
126 127 6.953101 TCAGCATACCTTAACCACTATCAAA 58.047 36.000 0.00 0.00 0.00 2.69
127 128 7.573710 TCAGCATACCTTAACCACTATCAAAT 58.426 34.615 0.00 0.00 0.00 2.32
128 129 7.715249 TCAGCATACCTTAACCACTATCAAATC 59.285 37.037 0.00 0.00 0.00 2.17
129 130 6.998673 AGCATACCTTAACCACTATCAAATCC 59.001 38.462 0.00 0.00 0.00 3.01
130 131 6.770785 GCATACCTTAACCACTATCAAATCCA 59.229 38.462 0.00 0.00 0.00 3.41
131 132 7.284489 GCATACCTTAACCACTATCAAATCCAA 59.716 37.037 0.00 0.00 0.00 3.53
132 133 8.621286 CATACCTTAACCACTATCAAATCCAAC 58.379 37.037 0.00 0.00 0.00 3.77
133 134 6.790319 ACCTTAACCACTATCAAATCCAACT 58.210 36.000 0.00 0.00 0.00 3.16
134 135 7.924541 ACCTTAACCACTATCAAATCCAACTA 58.075 34.615 0.00 0.00 0.00 2.24
135 136 8.557450 ACCTTAACCACTATCAAATCCAACTAT 58.443 33.333 0.00 0.00 0.00 2.12
138 139 9.537192 TTAACCACTATCAAATCCAACTATACG 57.463 33.333 0.00 0.00 0.00 3.06
139 140 7.356089 ACCACTATCAAATCCAACTATACGA 57.644 36.000 0.00 0.00 0.00 3.43
140 141 7.788026 ACCACTATCAAATCCAACTATACGAA 58.212 34.615 0.00 0.00 0.00 3.85
141 142 8.429641 ACCACTATCAAATCCAACTATACGAAT 58.570 33.333 0.00 0.00 0.00 3.34
142 143 9.923143 CCACTATCAAATCCAACTATACGAATA 57.077 33.333 0.00 0.00 0.00 1.75
148 149 9.476202 TCAAATCCAACTATACGAATATGACTG 57.524 33.333 0.00 0.00 0.00 3.51
149 150 8.712363 CAAATCCAACTATACGAATATGACTGG 58.288 37.037 0.00 0.00 0.00 4.00
150 151 7.776618 ATCCAACTATACGAATATGACTGGA 57.223 36.000 0.00 0.00 32.12 3.86
160 161 7.209471 ACGAATATGACTGGAATCTCTACTC 57.791 40.000 0.00 0.00 0.00 2.59
170 171 6.775629 ACTGGAATCTCTACTCCTAATGTCTC 59.224 42.308 0.00 0.00 32.51 3.36
176 177 5.888724 TCTCTACTCCTAATGTCTCAGTTGG 59.111 44.000 0.00 0.00 0.00 3.77
203 208 0.531311 GTTCCACCACTTTCGTCCGT 60.531 55.000 0.00 0.00 0.00 4.69
242 251 1.609501 TCCTCTTCTCACACCCCGG 60.610 63.158 0.00 0.00 0.00 5.73
438 475 2.927856 TTCTTCCCTGGAGCGCCA 60.928 61.111 9.48 9.48 43.47 5.69
594 631 2.039624 ACCGGATCCTGCCTCACT 59.960 61.111 9.46 0.00 0.00 3.41
1435 4614 7.397761 GCAGGTAGATTATCTTATAGGACAGGT 59.602 40.741 0.00 0.00 0.00 4.00
2104 5724 2.609747 TGGTCCTCTGAGTAAGCACTT 58.390 47.619 3.66 0.00 34.21 3.16
2218 5854 2.368439 GCAGCTGGTCCAATTACATGA 58.632 47.619 17.12 0.00 0.00 3.07
2226 5862 6.513806 TGGTCCAATTACATGATCTTTGTG 57.486 37.500 0.00 0.65 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.027755 CGCGGCGGATTTGATAGT 57.972 55.556 15.84 0.00 0.00 2.12
11 12 2.666190 ATCAATCCATCCGCGGCG 60.666 61.111 23.51 16.78 0.00 6.46
12 13 0.037326 TAGATCAATCCATCCGCGGC 60.037 55.000 23.51 1.36 0.00 6.53
13 14 1.714794 GTAGATCAATCCATCCGCGG 58.285 55.000 22.12 22.12 0.00 6.46
14 15 1.335964 ACGTAGATCAATCCATCCGCG 60.336 52.381 0.00 0.00 0.00 6.46
15 16 2.440539 ACGTAGATCAATCCATCCGC 57.559 50.000 0.00 0.00 0.00 5.54
16 17 6.156519 TGATTAACGTAGATCAATCCATCCG 58.843 40.000 10.36 0.00 29.82 4.18
17 18 6.091441 GCTGATTAACGTAGATCAATCCATCC 59.909 42.308 12.93 0.00 32.33 3.51
18 19 6.646653 TGCTGATTAACGTAGATCAATCCATC 59.353 38.462 12.93 0.00 32.33 3.51
19 20 6.524734 TGCTGATTAACGTAGATCAATCCAT 58.475 36.000 12.93 0.00 32.33 3.41
20 21 5.912892 TGCTGATTAACGTAGATCAATCCA 58.087 37.500 12.93 8.79 32.33 3.41
21 22 7.063544 GGTATGCTGATTAACGTAGATCAATCC 59.936 40.741 12.93 8.45 32.33 3.01
22 23 7.598869 TGGTATGCTGATTAACGTAGATCAATC 59.401 37.037 12.93 9.27 32.33 2.67
23 24 7.441836 TGGTATGCTGATTAACGTAGATCAAT 58.558 34.615 12.93 8.49 32.33 2.57
24 25 6.811954 TGGTATGCTGATTAACGTAGATCAA 58.188 36.000 12.93 2.79 32.33 2.57
25 26 6.399639 TGGTATGCTGATTAACGTAGATCA 57.600 37.500 11.77 11.77 0.00 2.92
26 27 7.891183 AATGGTATGCTGATTAACGTAGATC 57.109 36.000 0.00 0.00 0.00 2.75
27 28 8.585881 AGTAATGGTATGCTGATTAACGTAGAT 58.414 33.333 0.00 0.00 0.00 1.98
28 29 7.948357 AGTAATGGTATGCTGATTAACGTAGA 58.052 34.615 0.00 0.00 0.00 2.59
29 30 7.865889 TGAGTAATGGTATGCTGATTAACGTAG 59.134 37.037 0.00 0.00 0.00 3.51
30 31 7.718525 TGAGTAATGGTATGCTGATTAACGTA 58.281 34.615 0.00 0.00 0.00 3.57
31 32 6.578944 TGAGTAATGGTATGCTGATTAACGT 58.421 36.000 0.00 0.00 0.00 3.99
32 33 7.477144 TTGAGTAATGGTATGCTGATTAACG 57.523 36.000 0.00 0.00 0.00 3.18
33 34 8.507249 GGATTGAGTAATGGTATGCTGATTAAC 58.493 37.037 0.00 0.00 0.00 2.01
34 35 7.665559 GGGATTGAGTAATGGTATGCTGATTAA 59.334 37.037 0.00 0.00 0.00 1.40
35 36 7.168219 GGGATTGAGTAATGGTATGCTGATTA 58.832 38.462 0.00 0.00 0.00 1.75
36 37 6.006449 GGGATTGAGTAATGGTATGCTGATT 58.994 40.000 0.00 0.00 0.00 2.57
37 38 5.073554 TGGGATTGAGTAATGGTATGCTGAT 59.926 40.000 0.00 0.00 0.00 2.90
38 39 4.411869 TGGGATTGAGTAATGGTATGCTGA 59.588 41.667 0.00 0.00 0.00 4.26
39 40 4.516698 GTGGGATTGAGTAATGGTATGCTG 59.483 45.833 0.00 0.00 0.00 4.41
40 41 4.446311 GGTGGGATTGAGTAATGGTATGCT 60.446 45.833 0.00 0.00 0.00 3.79
41 42 3.821033 GGTGGGATTGAGTAATGGTATGC 59.179 47.826 0.00 0.00 0.00 3.14
42 43 4.141274 TGGGTGGGATTGAGTAATGGTATG 60.141 45.833 0.00 0.00 0.00 2.39
43 44 4.051478 TGGGTGGGATTGAGTAATGGTAT 58.949 43.478 0.00 0.00 0.00 2.73
44 45 3.465832 TGGGTGGGATTGAGTAATGGTA 58.534 45.455 0.00 0.00 0.00 3.25
45 46 2.283834 TGGGTGGGATTGAGTAATGGT 58.716 47.619 0.00 0.00 0.00 3.55
46 47 3.225104 CATGGGTGGGATTGAGTAATGG 58.775 50.000 0.00 0.00 0.00 3.16
47 48 3.225104 CCATGGGTGGGATTGAGTAATG 58.775 50.000 2.85 0.00 42.11 1.90
48 49 3.600448 CCATGGGTGGGATTGAGTAAT 57.400 47.619 2.85 0.00 42.11 1.89
64 65 1.074423 CTAGGAGCCATGCCCCATG 59.926 63.158 0.00 0.00 41.10 3.66
65 66 2.838467 GCTAGGAGCCATGCCCCAT 61.838 63.158 0.00 0.00 34.48 4.00
66 67 2.620048 TAGCTAGGAGCCATGCCCCA 62.620 60.000 0.00 0.00 43.77 4.96
67 68 1.418908 TTAGCTAGGAGCCATGCCCC 61.419 60.000 0.00 0.00 43.77 5.80
68 69 0.250510 GTTAGCTAGGAGCCATGCCC 60.251 60.000 0.00 0.00 43.77 5.36
69 70 0.601311 CGTTAGCTAGGAGCCATGCC 60.601 60.000 0.00 0.00 43.77 4.40
70 71 0.105039 ACGTTAGCTAGGAGCCATGC 59.895 55.000 0.00 0.00 43.77 4.06
71 72 3.381949 GTTACGTTAGCTAGGAGCCATG 58.618 50.000 0.00 0.00 43.77 3.66
72 73 2.364647 GGTTACGTTAGCTAGGAGCCAT 59.635 50.000 0.00 0.00 43.77 4.40
73 74 1.753073 GGTTACGTTAGCTAGGAGCCA 59.247 52.381 0.00 0.00 43.77 4.75
74 75 1.753073 TGGTTACGTTAGCTAGGAGCC 59.247 52.381 5.29 0.00 43.77 4.70
75 76 3.515330 TTGGTTACGTTAGCTAGGAGC 57.485 47.619 5.29 0.00 42.84 4.70
76 77 5.657474 TGATTTGGTTACGTTAGCTAGGAG 58.343 41.667 5.29 0.00 0.00 3.69
77 78 5.664294 TGATTTGGTTACGTTAGCTAGGA 57.336 39.130 5.29 0.00 0.00 2.94
78 79 6.730960 TTTGATTTGGTTACGTTAGCTAGG 57.269 37.500 5.29 0.00 0.00 3.02
79 80 7.970384 TGATTTGATTTGGTTACGTTAGCTAG 58.030 34.615 5.29 0.00 0.00 3.42
80 81 7.413657 GCTGATTTGATTTGGTTACGTTAGCTA 60.414 37.037 5.29 0.00 0.00 3.32
81 82 6.622896 GCTGATTTGATTTGGTTACGTTAGCT 60.623 38.462 5.29 0.00 0.00 3.32
82 83 5.511729 GCTGATTTGATTTGGTTACGTTAGC 59.488 40.000 0.00 0.00 0.00 3.09
83 84 6.607689 TGCTGATTTGATTTGGTTACGTTAG 58.392 36.000 0.00 0.00 0.00 2.34
84 85 6.561737 TGCTGATTTGATTTGGTTACGTTA 57.438 33.333 0.00 0.00 0.00 3.18
85 86 5.446143 TGCTGATTTGATTTGGTTACGTT 57.554 34.783 0.00 0.00 0.00 3.99
86 87 5.643379 ATGCTGATTTGATTTGGTTACGT 57.357 34.783 0.00 0.00 0.00 3.57
87 88 5.971202 GGTATGCTGATTTGATTTGGTTACG 59.029 40.000 0.00 0.00 0.00 3.18
88 89 7.100458 AGGTATGCTGATTTGATTTGGTTAC 57.900 36.000 0.00 0.00 0.00 2.50
89 90 7.716799 AAGGTATGCTGATTTGATTTGGTTA 57.283 32.000 0.00 0.00 0.00 2.85
90 91 6.610075 AAGGTATGCTGATTTGATTTGGTT 57.390 33.333 0.00 0.00 0.00 3.67
91 92 7.363793 GGTTAAGGTATGCTGATTTGATTTGGT 60.364 37.037 0.00 0.00 0.00 3.67
92 93 6.980397 GGTTAAGGTATGCTGATTTGATTTGG 59.020 38.462 0.00 0.00 0.00 3.28
93 94 7.489113 GTGGTTAAGGTATGCTGATTTGATTTG 59.511 37.037 0.00 0.00 0.00 2.32
94 95 7.397192 AGTGGTTAAGGTATGCTGATTTGATTT 59.603 33.333 0.00 0.00 0.00 2.17
95 96 6.891908 AGTGGTTAAGGTATGCTGATTTGATT 59.108 34.615 0.00 0.00 0.00 2.57
96 97 6.426587 AGTGGTTAAGGTATGCTGATTTGAT 58.573 36.000 0.00 0.00 0.00 2.57
97 98 5.815581 AGTGGTTAAGGTATGCTGATTTGA 58.184 37.500 0.00 0.00 0.00 2.69
98 99 7.498900 TGATAGTGGTTAAGGTATGCTGATTTG 59.501 37.037 0.00 0.00 0.00 2.32
99 100 7.573710 TGATAGTGGTTAAGGTATGCTGATTT 58.426 34.615 0.00 0.00 0.00 2.17
100 101 7.136822 TGATAGTGGTTAAGGTATGCTGATT 57.863 36.000 0.00 0.00 0.00 2.57
101 102 6.747414 TGATAGTGGTTAAGGTATGCTGAT 57.253 37.500 0.00 0.00 0.00 2.90
102 103 6.553953 TTGATAGTGGTTAAGGTATGCTGA 57.446 37.500 0.00 0.00 0.00 4.26
103 104 7.041098 GGATTTGATAGTGGTTAAGGTATGCTG 60.041 40.741 0.00 0.00 0.00 4.41
104 105 6.998673 GGATTTGATAGTGGTTAAGGTATGCT 59.001 38.462 0.00 0.00 0.00 3.79
105 106 6.770785 TGGATTTGATAGTGGTTAAGGTATGC 59.229 38.462 0.00 0.00 0.00 3.14
106 107 8.621286 GTTGGATTTGATAGTGGTTAAGGTATG 58.379 37.037 0.00 0.00 0.00 2.39
107 108 8.557450 AGTTGGATTTGATAGTGGTTAAGGTAT 58.443 33.333 0.00 0.00 0.00 2.73
108 109 7.924541 AGTTGGATTTGATAGTGGTTAAGGTA 58.075 34.615 0.00 0.00 0.00 3.08
109 110 6.790319 AGTTGGATTTGATAGTGGTTAAGGT 58.210 36.000 0.00 0.00 0.00 3.50
110 111 8.980481 ATAGTTGGATTTGATAGTGGTTAAGG 57.020 34.615 0.00 0.00 0.00 2.69
112 113 9.537192 CGTATAGTTGGATTTGATAGTGGTTAA 57.463 33.333 0.00 0.00 0.00 2.01
113 114 8.916062 TCGTATAGTTGGATTTGATAGTGGTTA 58.084 33.333 0.00 0.00 0.00 2.85
114 115 7.788026 TCGTATAGTTGGATTTGATAGTGGTT 58.212 34.615 0.00 0.00 0.00 3.67
115 116 7.356089 TCGTATAGTTGGATTTGATAGTGGT 57.644 36.000 0.00 0.00 0.00 4.16
116 117 8.833231 ATTCGTATAGTTGGATTTGATAGTGG 57.167 34.615 0.00 0.00 0.00 4.00
122 123 9.476202 CAGTCATATTCGTATAGTTGGATTTGA 57.524 33.333 0.00 0.00 0.00 2.69
123 124 8.712363 CCAGTCATATTCGTATAGTTGGATTTG 58.288 37.037 0.00 0.00 0.00 2.32
124 125 8.647796 TCCAGTCATATTCGTATAGTTGGATTT 58.352 33.333 0.00 0.00 0.00 2.17
125 126 8.190326 TCCAGTCATATTCGTATAGTTGGATT 57.810 34.615 0.00 0.00 0.00 3.01
126 127 7.776618 TCCAGTCATATTCGTATAGTTGGAT 57.223 36.000 0.00 0.00 0.00 3.41
127 128 7.591421 TTCCAGTCATATTCGTATAGTTGGA 57.409 36.000 0.00 0.00 0.00 3.53
128 129 8.307483 AGATTCCAGTCATATTCGTATAGTTGG 58.693 37.037 0.00 0.00 0.00 3.77
129 130 9.347934 GAGATTCCAGTCATATTCGTATAGTTG 57.652 37.037 0.00 0.00 0.00 3.16
130 131 9.303116 AGAGATTCCAGTCATATTCGTATAGTT 57.697 33.333 0.00 0.00 0.00 2.24
131 132 8.871629 AGAGATTCCAGTCATATTCGTATAGT 57.128 34.615 0.00 0.00 0.00 2.12
133 134 9.961264 AGTAGAGATTCCAGTCATATTCGTATA 57.039 33.333 0.00 0.00 0.00 1.47
134 135 8.871629 AGTAGAGATTCCAGTCATATTCGTAT 57.128 34.615 0.00 0.00 0.00 3.06
135 136 7.390996 GGAGTAGAGATTCCAGTCATATTCGTA 59.609 40.741 0.00 0.00 31.70 3.43
136 137 6.207810 GGAGTAGAGATTCCAGTCATATTCGT 59.792 42.308 0.00 0.00 31.70 3.85
137 138 6.432783 AGGAGTAGAGATTCCAGTCATATTCG 59.567 42.308 0.00 0.00 33.85 3.34
138 139 7.775053 AGGAGTAGAGATTCCAGTCATATTC 57.225 40.000 0.00 0.00 33.85 1.75
139 140 9.836179 ATTAGGAGTAGAGATTCCAGTCATATT 57.164 33.333 0.00 0.00 33.85 1.28
140 141 9.253832 CATTAGGAGTAGAGATTCCAGTCATAT 57.746 37.037 0.00 0.00 33.85 1.78
141 142 8.228206 ACATTAGGAGTAGAGATTCCAGTCATA 58.772 37.037 0.00 0.00 33.85 2.15
142 143 7.072562 ACATTAGGAGTAGAGATTCCAGTCAT 58.927 38.462 0.00 0.00 33.85 3.06
143 144 6.436027 ACATTAGGAGTAGAGATTCCAGTCA 58.564 40.000 0.00 0.00 33.85 3.41
144 145 6.775629 AGACATTAGGAGTAGAGATTCCAGTC 59.224 42.308 0.00 0.00 33.85 3.51
145 146 6.678547 AGACATTAGGAGTAGAGATTCCAGT 58.321 40.000 0.00 0.00 33.85 4.00
146 147 6.775142 TGAGACATTAGGAGTAGAGATTCCAG 59.225 42.308 0.00 0.00 33.85 3.86
147 148 6.673583 TGAGACATTAGGAGTAGAGATTCCA 58.326 40.000 0.00 0.00 33.85 3.53
148 149 6.775629 ACTGAGACATTAGGAGTAGAGATTCC 59.224 42.308 0.00 0.00 0.00 3.01
149 150 7.817418 ACTGAGACATTAGGAGTAGAGATTC 57.183 40.000 0.00 0.00 0.00 2.52
150 151 7.069331 CCAACTGAGACATTAGGAGTAGAGATT 59.931 40.741 0.00 0.00 0.00 2.40
160 161 6.594159 ACGAAAATACCAACTGAGACATTAGG 59.406 38.462 0.00 0.00 0.00 2.69
170 171 3.566322 TGGTGGAACGAAAATACCAACTG 59.434 43.478 0.00 0.00 40.35 3.16
176 177 4.024641 ACGAAAGTGGTGGAACGAAAATAC 60.025 41.667 0.00 0.00 46.97 1.89
227 236 0.613260 CAATCCGGGGTGTGAGAAGA 59.387 55.000 0.00 0.00 0.00 2.87
242 251 1.027792 TTTTAGCGGGTCGGGCAATC 61.028 55.000 0.00 0.00 0.00 2.67
555 592 2.370445 CCTCCGGCAGATCTGGGTT 61.370 63.158 23.89 0.00 41.78 4.11
797 983 2.725312 GGACGGGATCTGCAGCTCA 61.725 63.158 18.65 0.00 0.00 4.26
1435 4614 3.254166 GGAGCTTCTTCTGTTGCATTTCA 59.746 43.478 0.00 0.00 0.00 2.69
2104 5724 1.073284 GCCAGACCTAACAAGGAACCA 59.927 52.381 0.00 0.00 0.00 3.67
2226 5862 4.399618 TCAGCCATCTGAGTGTTAGTCTAC 59.600 45.833 0.00 0.00 43.95 2.59


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

AutoCloner maintained by Alex Coulton.