Multiple sequence alignment - TraesCS5A01G156400

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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 TraesCS5A01G156400 chr5A 100.000 7622 0 0 1 7622 335289536 335297157 0.000000e+00 14076
1 TraesCS5A01G156400 chr5A 92.763 152 11 0 1899 2050 303399810 303399961 3.580000e-53 220
2 TraesCS5A01G156400 chr5A 83.721 215 31 4 4813 5024 220453683 220453470 4.660000e-47 200
3 TraesCS5A01G156400 chr5D 94.603 5744 215 45 1921 7618 252615781 252621475 0.000000e+00 8802
4 TraesCS5A01G156400 chr5D 93.920 1842 69 21 100 1922 252613882 252615699 0.000000e+00 2741
5 TraesCS5A01G156400 chr5D 94.156 154 9 0 1901 2054 256749952 256749799 1.280000e-57 235
6 TraesCS5A01G156400 chr5B 94.775 4593 136 46 97 4644 285036052 285040585 0.000000e+00 7057
7 TraesCS5A01G156400 chr5B 93.772 2264 79 31 4624 6873 285040642 285042857 0.000000e+00 3343
8 TraesCS5A01G156400 chr5B 95.507 690 18 6 6937 7621 285042860 285043541 0.000000e+00 1090
9 TraesCS5A01G156400 chr5B 91.772 158 12 1 1898 2054 288327652 288327809 1.290000e-52 219
10 TraesCS5A01G156400 chr1A 91.755 376 27 1 3099 3474 7517886 7517515 3.150000e-143 520
11 TraesCS5A01G156400 chr1A 92.742 124 7 2 3456 3579 7518771 7518650 2.190000e-40 178
12 TraesCS5A01G156400 chr7B 81.250 400 51 16 4637 5024 712489926 712490313 1.240000e-77 302
13 TraesCS5A01G156400 chr7B 90.476 168 13 3 1889 2055 700413942 700413777 1.290000e-52 219
14 TraesCS5A01G156400 chr6A 78.004 541 70 23 4636 5139 602228078 602227550 2.080000e-75 294
15 TraesCS5A01G156400 chr6A 85.185 216 21 8 4812 5024 200742836 200742629 2.150000e-50 211
16 TraesCS5A01G156400 chr6A 88.636 88 9 1 3678 3764 197863389 197863302 1.050000e-18 106
17 TraesCS5A01G156400 chr3B 82.721 272 28 5 3678 3944 397324900 397324643 2.770000e-54 224
18 TraesCS5A01G156400 chr4A 86.111 216 19 8 4812 5024 46504983 46504776 9.950000e-54 222
19 TraesCS5A01G156400 chr2B 91.875 160 12 1 1896 2054 602996294 602996453 9.950000e-54 222
20 TraesCS5A01G156400 chr2B 83.898 236 23 10 4792 5024 583405613 583405836 2.150000e-50 211
21 TraesCS5A01G156400 chr7A 82.528 269 30 9 3678 3944 38080903 38080650 3.580000e-53 220
22 TraesCS5A01G156400 chr7A 90.476 168 13 3 1889 2055 701301523 701301358 1.290000e-52 219
23 TraesCS5A01G156400 chr7A 78.552 373 47 16 4792 5136 558253325 558253692 1.670000e-51 215
24 TraesCS5A01G156400 chr2D 91.195 159 14 0 1896 2054 512769186 512769344 4.630000e-52 217
25 TraesCS5A01G156400 chr2A 90.385 156 13 1 1901 2056 19922655 19922502 3.610000e-48 204
26 TraesCS5A01G156400 chr2A 87.500 88 10 1 3678 3764 381734484 381734397 4.870000e-17 100
27 TraesCS5A01G156400 chr2A 87.500 88 10 1 3678 3764 381736573 381736486 4.870000e-17 100
28 TraesCS5A01G156400 chr7D 91.447 152 6 4 3298 3444 563292011 563291862 1.300000e-47 202
29 TraesCS5A01G156400 chr7D 94.615 130 6 1 3459 3588 563291815 563291687 4.660000e-47 200


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 TraesCS5A01G156400 chr5A 335289536 335297157 7621 False 14076.0 14076 100.000000 1 7622 1 chr5A.!!$F2 7621
1 TraesCS5A01G156400 chr5D 252613882 252621475 7593 False 5771.5 8802 94.261500 100 7618 2 chr5D.!!$F1 7518
2 TraesCS5A01G156400 chr5B 285036052 285043541 7489 False 3830.0 7057 94.684667 97 7621 3 chr5B.!!$F2 7524
3 TraesCS5A01G156400 chr1A 7517515 7518771 1256 True 349.0 520 92.248500 3099 3579 2 chr1A.!!$R1 480
4 TraesCS5A01G156400 chr6A 602227550 602228078 528 True 294.0 294 78.004000 4636 5139 1 chr6A.!!$R3 503

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
322 328 0.109723 GGTAGCACCCACCACAAGAA 59.890 55.000 0.00 0.0 36.01 2.52 F
889 903 0.669077 CCTTGATACTCGGGAGTCGG 59.331 60.000 4.30 0.0 42.54 4.79 F
1575 1612 1.136984 GACACGCTACCTCGTCAGG 59.863 63.158 0.00 0.0 46.87 3.86 F
1848 1885 1.876156 CAGTTCTTCCTTGCACTGTCC 59.124 52.381 0.00 0.0 33.35 4.02 F
2162 2289 4.158764 GCAGTTACCACTAGAGTGTCTGAT 59.841 45.833 17.37 0.0 44.21 2.90 F
3518 3665 1.600058 TGCCATCCTCTTTGGGAGAT 58.400 50.000 0.00 0.0 44.45 2.75 F
3988 4136 0.804989 GAGCAACAATGGTCCTTCGG 59.195 55.000 0.00 0.0 46.07 4.30 F
4243 4393 1.024271 TGTGTTCTTTGGCTCAGTGC 58.976 50.000 0.00 0.0 41.94 4.40 F
5672 5948 1.023513 AGATGCTGCGAAAGGTCTGC 61.024 55.000 0.00 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1404 1441 0.617413 CAGAAGTCCACTGGATGCCT 59.383 55.000 0.0 0.0 32.73 4.75 R
1824 1861 1.133976 AGTGCAAGGAAGAACTGTGCT 60.134 47.619 0.0 0.0 36.18 4.40 R
2647 2774 1.608025 GCATTCTCCTCCACGTCAACA 60.608 52.381 0.0 0.0 0.00 3.33 R
2823 2950 2.744202 GTGGTCAACTGCTTACCATCTG 59.256 50.000 0.0 0.0 44.69 2.90 R
3987 4135 0.400594 AATACTATCGCTTGGCCCCC 59.599 55.000 0.0 0.0 0.00 5.40 R
4677 4906 0.550914 TTCTTGCTCCACAACAGGGT 59.449 50.000 0.0 0.0 33.68 4.34 R
5586 5861 2.030027 AGGTCCTCCTGTGAACATCA 57.970 50.000 0.0 0.0 43.33 3.07 R
6051 6327 2.289195 ACCTACTCGTCGCCATCAAAAA 60.289 45.455 0.0 0.0 0.00 1.94 R
6897 7179 0.313672 TTTGAGTGCAAACCCGCATC 59.686 50.000 0.0 0.0 45.26 3.91 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
69 70 2.052782 AAAATGGTCCGGTATGCCTC 57.947 50.000 0.00 0.00 0.00 4.70
70 71 1.213296 AAATGGTCCGGTATGCCTCT 58.787 50.000 0.00 0.00 0.00 3.69
71 72 2.097110 AATGGTCCGGTATGCCTCTA 57.903 50.000 0.00 0.00 0.00 2.43
72 73 1.633774 ATGGTCCGGTATGCCTCTAG 58.366 55.000 0.00 0.00 0.00 2.43
73 74 0.554305 TGGTCCGGTATGCCTCTAGA 59.446 55.000 0.00 0.00 0.00 2.43
74 75 1.063492 TGGTCCGGTATGCCTCTAGAA 60.063 52.381 0.00 0.00 0.00 2.10
76 77 2.633481 GGTCCGGTATGCCTCTAGAAAT 59.367 50.000 0.00 0.00 0.00 2.17
77 78 3.555168 GGTCCGGTATGCCTCTAGAAATG 60.555 52.174 0.00 0.00 0.00 2.32
78 79 3.321111 GTCCGGTATGCCTCTAGAAATGA 59.679 47.826 0.00 0.00 0.00 2.57
79 80 3.574396 TCCGGTATGCCTCTAGAAATGAG 59.426 47.826 0.00 0.00 0.00 2.90
80 81 3.322254 CCGGTATGCCTCTAGAAATGAGT 59.678 47.826 0.00 0.00 0.00 3.41
81 82 4.523173 CCGGTATGCCTCTAGAAATGAGTA 59.477 45.833 0.00 0.00 0.00 2.59
82 83 5.462405 CGGTATGCCTCTAGAAATGAGTAC 58.538 45.833 0.00 0.00 0.00 2.73
83 84 5.565045 CGGTATGCCTCTAGAAATGAGTACC 60.565 48.000 0.00 1.93 32.20 3.34
84 85 5.540719 GGTATGCCTCTAGAAATGAGTACCT 59.459 44.000 0.00 0.00 32.52 3.08
86 87 7.397761 GGTATGCCTCTAGAAATGAGTACCTAT 59.602 40.741 0.00 0.00 32.52 2.57
87 88 6.656632 TGCCTCTAGAAATGAGTACCTATG 57.343 41.667 0.00 0.00 0.00 2.23
88 89 6.373759 TGCCTCTAGAAATGAGTACCTATGA 58.626 40.000 0.00 0.00 0.00 2.15
89 90 6.491745 TGCCTCTAGAAATGAGTACCTATGAG 59.508 42.308 0.00 0.00 0.00 2.90
90 91 6.717540 GCCTCTAGAAATGAGTACCTATGAGA 59.282 42.308 0.00 0.00 0.00 3.27
93 94 8.554835 TCTAGAAATGAGTACCTATGAGATCG 57.445 38.462 0.00 0.00 0.00 3.69
95 96 7.589958 AGAAATGAGTACCTATGAGATCGTT 57.410 36.000 0.00 0.00 0.00 3.85
96 97 8.012957 AGAAATGAGTACCTATGAGATCGTTT 57.987 34.615 0.00 0.00 0.00 3.60
98 99 8.425577 AAATGAGTACCTATGAGATCGTTTTG 57.574 34.615 0.00 0.00 0.00 2.44
146 147 1.309950 CGACGGCAGATAGAGGAAGA 58.690 55.000 0.00 0.00 0.00 2.87
200 201 7.121168 CCATTTGATACTTTGCTCACTAAAGGA 59.879 37.037 0.00 0.00 38.99 3.36
264 265 7.861629 TCCCATTGAAGACTATGAAAGTATGT 58.138 34.615 0.00 0.00 39.07 2.29
265 266 8.988060 TCCCATTGAAGACTATGAAAGTATGTA 58.012 33.333 0.00 0.00 39.07 2.29
266 267 9.784531 CCCATTGAAGACTATGAAAGTATGTAT 57.215 33.333 0.00 0.00 39.07 2.29
321 327 1.057275 TGGTAGCACCCACCACAAGA 61.057 55.000 0.00 0.00 41.17 3.02
322 328 0.109723 GGTAGCACCCACCACAAGAA 59.890 55.000 0.00 0.00 36.01 2.52
587 593 1.215382 GAACAATCAAAGCGCCCCC 59.785 57.895 2.29 0.00 0.00 5.40
589 595 1.535204 AACAATCAAAGCGCCCCCAG 61.535 55.000 2.29 0.00 0.00 4.45
712 720 2.748058 CTTCCCACACCCGGAACCAG 62.748 65.000 0.73 0.00 34.40 4.00
877 891 3.062122 GTCGGTTTTGACCCCTTGATA 57.938 47.619 0.00 0.00 32.61 2.15
881 895 3.007635 GGTTTTGACCCCTTGATACTCG 58.992 50.000 0.00 0.00 0.00 4.18
882 896 3.007635 GTTTTGACCCCTTGATACTCGG 58.992 50.000 0.00 0.00 0.00 4.63
889 903 0.669077 CCTTGATACTCGGGAGTCGG 59.331 60.000 4.30 0.00 42.54 4.79
1133 1158 2.044946 GGAGGATTGGCGCACCTT 60.045 61.111 10.83 0.00 36.63 3.50
1218 1243 5.449304 CAGCATATGCATGTTCATGTACTG 58.551 41.667 28.62 10.04 45.16 2.74
1231 1256 6.597672 TGTTCATGTACTGGTTGATAATCCAC 59.402 38.462 4.01 0.00 0.00 4.02
1275 1300 8.675705 TTATGCAACACATGTATGCTATACTT 57.324 30.769 26.68 13.06 40.06 2.24
1283 1311 7.653713 ACACATGTATGCTATACTTGCTAAGTC 59.346 37.037 0.00 0.00 41.77 3.01
1318 1349 5.695424 ATACTTTCTAAGTTCAGGGGACC 57.305 43.478 0.00 0.00 46.68 4.46
1404 1441 4.999311 GCTGATGATTACACAGATGGCATA 59.001 41.667 0.00 0.00 34.07 3.14
1575 1612 1.136984 GACACGCTACCTCGTCAGG 59.863 63.158 0.00 0.00 46.87 3.86
1824 1861 9.339850 GGTTCACTCTACTATACTGACTATGAA 57.660 37.037 0.00 0.00 0.00 2.57
1848 1885 1.876156 CAGTTCTTCCTTGCACTGTCC 59.124 52.381 0.00 0.00 33.35 4.02
2162 2289 4.158764 GCAGTTACCACTAGAGTGTCTGAT 59.841 45.833 17.37 0.00 44.21 2.90
2226 2353 6.480320 AGGATACATAACAAAGTTCTGATCGC 59.520 38.462 2.83 0.00 41.41 4.58
2647 2774 6.627953 GCATGCCATTATTCAGTAAACCAACT 60.628 38.462 6.36 0.00 0.00 3.16
2803 2930 8.931385 ATGCTATGGAAATTTACAAACATGTC 57.069 30.769 7.30 0.00 0.00 3.06
2823 2950 3.008485 GTCCAGATTACCATGGGATCTCC 59.992 52.174 22.93 13.76 37.19 3.71
2836 2963 2.038295 GGGATCTCCAGATGGTAAGCAG 59.962 54.545 0.00 0.00 37.91 4.24
2840 2967 3.173151 TCTCCAGATGGTAAGCAGTTGA 58.827 45.455 0.00 0.00 36.34 3.18
2851 2978 4.517453 GGTAAGCAGTTGACCACATTGTTA 59.483 41.667 0.00 0.00 33.16 2.41
2853 2980 5.376854 AAGCAGTTGACCACATTGTTATC 57.623 39.130 0.00 0.00 0.00 1.75
2856 2983 6.179756 AGCAGTTGACCACATTGTTATCATA 58.820 36.000 1.58 0.00 0.00 2.15
2857 2984 6.830324 AGCAGTTGACCACATTGTTATCATAT 59.170 34.615 1.58 0.00 0.00 1.78
2858 2985 6.914215 GCAGTTGACCACATTGTTATCATATG 59.086 38.462 0.00 0.00 0.00 1.78
2993 3129 1.792757 ATCCTCAAGCAGGTTGGGCA 61.793 55.000 12.42 0.00 43.95 5.36
3121 3257 4.589216 TTCTGCCTTCACTTTGGATTTG 57.411 40.909 0.00 0.00 0.00 2.32
3128 3264 5.759763 GCCTTCACTTTGGATTTGTTGATTT 59.240 36.000 0.00 0.00 0.00 2.17
3518 3665 1.600058 TGCCATCCTCTTTGGGAGAT 58.400 50.000 0.00 0.00 44.45 2.75
3582 3729 3.494223 GCACTTTGTTTATGCACCCCTTT 60.494 43.478 0.00 0.00 39.23 3.11
3649 3796 5.411053 CCTCTCTTTGTTTCCTGATGTTCTC 59.589 44.000 0.00 0.00 0.00 2.87
3656 3803 4.260170 GTTTCCTGATGTTCTCTGCTCAT 58.740 43.478 0.00 0.00 0.00 2.90
3657 3804 5.046376 TGTTTCCTGATGTTCTCTGCTCATA 60.046 40.000 0.00 0.00 0.00 2.15
3756 3903 8.854614 ACTTCTGCATTTACTTATTCTCAACT 57.145 30.769 0.00 0.00 0.00 3.16
3988 4136 0.804989 GAGCAACAATGGTCCTTCGG 59.195 55.000 0.00 0.00 46.07 4.30
4168 4318 1.135689 GCCATCTTGTTACTTGCGGTG 60.136 52.381 0.00 0.00 0.00 4.94
4243 4393 1.024271 TGTGTTCTTTGGCTCAGTGC 58.976 50.000 0.00 0.00 41.94 4.40
4273 4423 4.062293 TGGTACTGTGTAAGAACATGCAC 58.938 43.478 0.00 0.00 38.08 4.57
4279 4429 6.230472 ACTGTGTAAGAACATGCACTGATTA 58.770 36.000 10.98 0.00 38.08 1.75
4323 4473 1.036481 TTGTTCTTGCAGCACCAGCA 61.036 50.000 0.00 0.00 45.49 4.41
4407 4557 9.842775 TTATCAGAAATTGAAGATGCTACTGAT 57.157 29.630 0.00 0.00 42.49 2.90
4455 4605 6.088819 TGGAGGGTTTGGCATAGTATACTAT 58.911 40.000 18.01 18.01 39.61 2.12
4677 4906 3.296854 AGTATGGCTTGGTAGATCGACA 58.703 45.455 8.30 0.00 0.00 4.35
4712 4946 3.220110 CAAGAACCTGATATGCCATGCT 58.780 45.455 0.00 0.00 0.00 3.79
4714 4948 2.174210 AGAACCTGATATGCCATGCTGT 59.826 45.455 0.00 0.00 0.00 4.40
4749 4983 3.855689 AATGACCTGTTAATGTGCTGC 57.144 42.857 0.00 0.00 0.00 5.25
4762 4996 3.396751 GCTGCGAGCATGAGACAG 58.603 61.111 0.00 0.00 41.89 3.51
4868 5102 3.510719 GCGCTTGCCTTTTGAAATATCA 58.489 40.909 0.00 0.00 0.00 2.15
4878 5115 8.476447 TGCCTTTTGAAATATCATTGCATTCTA 58.524 29.630 0.00 0.00 34.96 2.10
4993 5230 4.813027 TGCTCATGCATTTCTTTTCTTCC 58.187 39.130 0.00 0.00 45.31 3.46
4994 5231 4.281435 TGCTCATGCATTTCTTTTCTTCCA 59.719 37.500 0.00 0.00 45.31 3.53
5025 5287 4.039730 TCCTGATGAGTTAGCTGGCTTATC 59.960 45.833 13.50 13.50 34.17 1.75
5146 5410 3.628032 TCATGCACAACGGAACACTAAAA 59.372 39.130 0.00 0.00 0.00 1.52
5184 5448 4.261801 GAGTGCCCTTAGCTGATGTTAAA 58.738 43.478 0.00 0.00 44.23 1.52
5193 5457 7.148590 CCCTTAGCTGATGTTAAATTTGTTTGC 60.149 37.037 0.00 0.00 0.00 3.68
5262 5531 1.538849 GGCAAAACTTTGTCTGGGCAG 60.539 52.381 4.23 0.00 39.57 4.85
5275 5544 2.170607 TCTGGGCAGCTGTATTTAGGAC 59.829 50.000 16.64 0.00 0.00 3.85
5279 5548 3.621558 GGCAGCTGTATTTAGGACCTTT 58.378 45.455 16.64 0.00 0.00 3.11
5283 5552 5.066117 GCAGCTGTATTTAGGACCTTTTACC 59.934 44.000 16.64 0.00 0.00 2.85
5317 5586 4.448210 TGGTTGACCTCAAACTTGTACTC 58.552 43.478 4.75 0.00 43.65 2.59
5320 5589 2.036733 TGACCTCAAACTTGTACTCGGG 59.963 50.000 0.00 0.00 0.00 5.14
5417 5686 2.158885 GCCCTTAAACCAAAAGTTGCCA 60.159 45.455 0.00 0.00 39.19 4.92
5459 5728 9.485206 TTCCAGTAGTACACAGAAAATTTAGTC 57.515 33.333 2.52 0.00 0.00 2.59
5495 5770 8.783833 TCTGAATTTCTATTCTTCACTCTTGG 57.216 34.615 0.00 0.00 40.68 3.61
5496 5771 8.378565 TCTGAATTTCTATTCTTCACTCTTGGT 58.621 33.333 0.00 0.00 40.68 3.67
5500 5775 2.100605 ATTCTTCACTCTTGGTCCGC 57.899 50.000 0.00 0.00 0.00 5.54
5530 5805 7.277981 ACCGACATGAACTGTTAGATTAATGTC 59.722 37.037 0.00 4.88 38.54 3.06
5534 5809 8.543774 ACATGAACTGTTAGATTAATGTCCTCT 58.456 33.333 0.00 0.00 32.90 3.69
5543 5818 9.315525 GTTAGATTAATGTCCTCTTTACTCCAC 57.684 37.037 0.00 0.00 0.00 4.02
5672 5948 1.023513 AGATGCTGCGAAAGGTCTGC 61.024 55.000 0.00 0.00 0.00 4.26
5701 5977 6.218107 AGTTTCCCTCCTACTCTTCTACTAGT 59.782 42.308 0.00 0.00 0.00 2.57
5979 6255 6.109156 TCCTGAGCTCATAGTGTTTGTTTA 57.891 37.500 18.63 0.00 0.00 2.01
5984 6260 7.861630 TGAGCTCATAGTGTTTGTTTACTTTC 58.138 34.615 13.74 0.00 0.00 2.62
6032 6308 2.896685 GCTATCCTGGTAGCATCTGAGT 59.103 50.000 17.71 0.00 45.03 3.41
6043 6319 8.677148 TGGTAGCATCTGAGTTATAATTTTCC 57.323 34.615 0.00 0.00 0.00 3.13
6095 6371 0.543749 ACATCTCCCAGCAGCTAACC 59.456 55.000 0.00 0.00 0.00 2.85
6220 6496 1.406341 GGCGTGGGTAAGTATCTTGCA 60.406 52.381 0.00 0.00 0.00 4.08
6238 6514 3.148412 TGCAATCTGTTAGCTTTCTGCA 58.852 40.909 0.00 0.00 45.94 4.41
6645 6924 2.360483 TCAGGATTCATCAGAGACGCTC 59.640 50.000 0.00 0.00 0.00 5.03
6663 6942 2.352814 GCTCTTCGTGTAAGCAAGGAGA 60.353 50.000 0.00 0.00 36.58 3.71
6676 6955 2.363683 CAAGGAGAAGGCAAGGATCAC 58.636 52.381 0.00 0.00 0.00 3.06
6795 7074 1.896220 TGGTGATCTGGAACTGTTGC 58.104 50.000 4.98 4.98 0.00 4.17
6806 7088 3.130340 TGGAACTGTTGCTTTCCTTGTTC 59.870 43.478 13.23 0.00 41.76 3.18
6807 7089 3.381590 GGAACTGTTGCTTTCCTTGTTCT 59.618 43.478 4.68 0.00 38.65 3.01
6808 7090 4.142160 GGAACTGTTGCTTTCCTTGTTCTT 60.142 41.667 4.68 0.00 38.65 2.52
6890 7172 4.017130 AGGAGATGGGGCAAATAGAAAACT 60.017 41.667 0.00 0.00 0.00 2.66
6891 7173 5.193728 AGGAGATGGGGCAAATAGAAAACTA 59.806 40.000 0.00 0.00 0.00 2.24
6897 7179 4.640647 GGGGCAAATAGAAAACTAGACAGG 59.359 45.833 0.00 0.00 0.00 4.00
6901 7183 6.458888 GGCAAATAGAAAACTAGACAGGATGC 60.459 42.308 0.00 0.00 42.53 3.91
6963 7245 3.758023 TGCTGGATTCAATTTCATGACGT 59.242 39.130 0.00 0.00 0.00 4.34
7043 7336 4.045636 TCCAAAAAGCTTGCTTGAGAAC 57.954 40.909 18.60 0.00 0.00 3.01
7055 7348 6.389830 TTGCTTGAGAACAACACATTACAT 57.610 33.333 0.00 0.00 32.27 2.29
7087 7380 8.419076 ACAAACATCAAATGTAGTCAAAAACC 57.581 30.769 0.00 0.00 44.07 3.27
7088 7381 8.257306 ACAAACATCAAATGTAGTCAAAAACCT 58.743 29.630 0.00 0.00 44.07 3.50
7089 7382 9.097257 CAAACATCAAATGTAGTCAAAAACCTT 57.903 29.630 0.00 0.00 44.07 3.50
7205 7502 3.485394 TGAGCTTTCTATGCACCACAAA 58.515 40.909 0.00 0.00 0.00 2.83
7206 7503 3.888323 TGAGCTTTCTATGCACCACAAAA 59.112 39.130 0.00 0.00 0.00 2.44
7231 7528 1.394618 ACCAGCGGCAAGTTACAAAA 58.605 45.000 1.45 0.00 0.00 2.44
7241 7538 5.794945 CGGCAAGTTACAAAATCATGTACAG 59.205 40.000 0.33 0.00 35.60 2.74
7288 7585 5.339611 GCAAGAAAACATTTACACAGCTACG 59.660 40.000 0.00 0.00 0.00 3.51
7441 7743 1.398692 TGACCAAGCAAGGGAACAAC 58.601 50.000 0.00 0.00 0.00 3.32
7442 7745 1.341482 TGACCAAGCAAGGGAACAACA 60.341 47.619 0.00 0.00 0.00 3.33
7491 7794 1.202245 GCAACGTTCACAACACCACAT 60.202 47.619 0.00 0.00 0.00 3.21
7565 7870 9.979578 GTATATCAAATTGGTGGATAAAATGCA 57.020 29.630 0.00 0.00 0.00 3.96
7613 7918 7.364232 GGAAGATCTAGTTCAAACTCAGGATCA 60.364 40.741 21.52 0.40 39.40 2.92
7621 7926 0.904649 AACTCAGGATCATGTCGGCA 59.095 50.000 7.33 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 2.025321 AGAGGCATACCGGACCATTTTT 60.025 45.455 9.46 0.00 42.76 1.94
50 51 1.564348 AGAGGCATACCGGACCATTTT 59.436 47.619 9.46 0.00 42.76 1.82
51 52 1.213296 AGAGGCATACCGGACCATTT 58.787 50.000 9.46 0.00 42.76 2.32
52 53 1.971357 CTAGAGGCATACCGGACCATT 59.029 52.381 9.46 0.00 42.76 3.16
53 54 1.147191 TCTAGAGGCATACCGGACCAT 59.853 52.381 9.46 0.00 42.76 3.55
55 56 1.700955 TTCTAGAGGCATACCGGACC 58.299 55.000 9.46 3.61 42.76 4.46
57 58 3.572642 TCATTTCTAGAGGCATACCGGA 58.427 45.455 9.46 0.00 42.76 5.14
58 59 3.322254 ACTCATTTCTAGAGGCATACCGG 59.678 47.826 0.00 0.00 42.76 5.28
59 60 4.592485 ACTCATTTCTAGAGGCATACCG 57.408 45.455 0.00 0.00 42.76 4.02
61 62 6.658188 AGGTACTCATTTCTAGAGGCATAC 57.342 41.667 0.00 0.00 37.43 2.39
63 64 7.013220 TCATAGGTACTCATTTCTAGAGGCAT 58.987 38.462 0.00 0.00 41.75 4.40
65 66 6.717540 TCTCATAGGTACTCATTTCTAGAGGC 59.282 42.308 0.00 0.00 41.75 4.70
69 70 8.330466 ACGATCTCATAGGTACTCATTTCTAG 57.670 38.462 0.00 0.00 41.75 2.43
70 71 8.693120 AACGATCTCATAGGTACTCATTTCTA 57.307 34.615 0.00 0.00 41.75 2.10
71 72 7.589958 AACGATCTCATAGGTACTCATTTCT 57.410 36.000 0.00 0.00 41.75 2.52
72 73 8.543774 CAAAACGATCTCATAGGTACTCATTTC 58.456 37.037 0.00 0.00 41.75 2.17
73 74 8.041323 ACAAAACGATCTCATAGGTACTCATTT 58.959 33.333 0.00 0.00 41.75 2.32
74 75 7.492669 CACAAAACGATCTCATAGGTACTCATT 59.507 37.037 0.00 0.00 41.75 2.57
76 77 6.330278 CACAAAACGATCTCATAGGTACTCA 58.670 40.000 0.00 0.00 41.75 3.41
77 78 5.232414 GCACAAAACGATCTCATAGGTACTC 59.768 44.000 0.00 0.00 41.75 2.59
78 79 5.109903 GCACAAAACGATCTCATAGGTACT 58.890 41.667 0.00 0.00 46.37 2.73
79 80 4.868171 TGCACAAAACGATCTCATAGGTAC 59.132 41.667 0.00 0.00 0.00 3.34
80 81 4.868171 GTGCACAAAACGATCTCATAGGTA 59.132 41.667 13.17 0.00 0.00 3.08
81 82 3.684788 GTGCACAAAACGATCTCATAGGT 59.315 43.478 13.17 0.00 0.00 3.08
82 83 3.935203 AGTGCACAAAACGATCTCATAGG 59.065 43.478 21.04 0.00 0.00 2.57
83 84 6.643845 CATAGTGCACAAAACGATCTCATAG 58.356 40.000 21.04 0.00 0.00 2.23
84 85 5.006649 GCATAGTGCACAAAACGATCTCATA 59.993 40.000 21.04 0.00 44.26 2.15
86 87 3.125146 GCATAGTGCACAAAACGATCTCA 59.875 43.478 21.04 0.00 44.26 3.27
87 88 3.674423 GCATAGTGCACAAAACGATCTC 58.326 45.455 21.04 0.00 44.26 2.75
88 89 3.747099 GCATAGTGCACAAAACGATCT 57.253 42.857 21.04 0.00 44.26 2.75
128 129 3.648009 CAATCTTCCTCTATCTGCCGTC 58.352 50.000 0.00 0.00 0.00 4.79
146 147 4.020839 CCACAAGAATCCCTCAAAAGCAAT 60.021 41.667 0.00 0.00 0.00 3.56
321 327 2.430367 GACCGTCTTGTGGCCCTT 59.570 61.111 0.00 0.00 0.00 3.95
322 328 3.637273 GGACCGTCTTGTGGCCCT 61.637 66.667 0.00 0.00 0.00 5.19
360 366 3.190874 GGCGACACTAATTCTCTTGGAG 58.809 50.000 0.00 0.00 0.00 3.86
587 593 2.924290 GGAGAAAGAAATCGACGGACTG 59.076 50.000 0.00 0.00 0.00 3.51
589 595 2.269172 GGGAGAAAGAAATCGACGGAC 58.731 52.381 0.00 0.00 0.00 4.79
595 603 2.012673 CTGCTGGGGAGAAAGAAATCG 58.987 52.381 0.00 0.00 0.00 3.34
712 720 3.077556 TTGCGGCTCCTCCTCCTC 61.078 66.667 0.00 0.00 0.00 3.71
877 891 4.444081 CCCTCCCGACTCCCGAGT 62.444 72.222 0.00 0.00 45.84 4.18
881 895 3.075641 GACACCCTCCCGACTCCC 61.076 72.222 0.00 0.00 0.00 4.30
882 896 2.037527 AGACACCCTCCCGACTCC 59.962 66.667 0.00 0.00 0.00 3.85
889 903 0.908198 ATCTTGAGCAGACACCCTCC 59.092 55.000 0.00 0.00 32.83 4.30
935 952 0.746204 GAGAAGCAGCTAGGCAACCC 60.746 60.000 0.00 0.00 35.83 4.11
1133 1158 8.232412 TCTAAGGCTATGGATTCTAACCTAAGA 58.768 37.037 0.00 0.00 0.00 2.10
1218 1243 7.814264 ATGAAATCTGAGTGGATTATCAACC 57.186 36.000 0.00 0.00 35.19 3.77
1310 1341 4.615588 TTTTTATTTTGCTGGTCCCCTG 57.384 40.909 0.00 0.00 0.00 4.45
1318 1349 7.485595 GCCCAATTTGCTATTTTTATTTTGCTG 59.514 33.333 0.00 0.00 0.00 4.41
1404 1441 0.617413 CAGAAGTCCACTGGATGCCT 59.383 55.000 0.00 0.00 32.73 4.75
1689 1726 3.056465 CCAAGATAATCGCCTCCTCTACC 60.056 52.174 0.00 0.00 0.00 3.18
1824 1861 1.133976 AGTGCAAGGAAGAACTGTGCT 60.134 47.619 0.00 0.00 36.18 4.40
1848 1885 3.613737 CAGCACCAAAATTTATCCTTGCG 59.386 43.478 0.00 0.00 33.90 4.85
1954 2074 5.944049 ACACACTAAAACGCGTCTATATG 57.056 39.130 14.44 11.70 0.00 1.78
2226 2353 6.408858 AAACACATGATACTAAGTGAAGCG 57.591 37.500 0.00 0.00 35.97 4.68
2486 2613 3.452878 TCAAGGATCCATTTTGGCCAAT 58.547 40.909 21.26 2.03 37.47 3.16
2647 2774 1.608025 GCATTCTCCTCCACGTCAACA 60.608 52.381 0.00 0.00 0.00 3.33
2803 2930 2.981784 TGGAGATCCCATGGTAATCTGG 59.018 50.000 24.38 3.92 40.82 3.86
2823 2950 2.744202 GTGGTCAACTGCTTACCATCTG 59.256 50.000 0.00 0.00 44.69 2.90
2836 2963 9.638239 AAAACATATGATAACAATGTGGTCAAC 57.362 29.630 10.38 0.00 34.20 3.18
2840 2967 9.859427 CTGAAAAACATATGATAACAATGTGGT 57.141 29.630 10.38 0.00 34.20 4.16
2853 2980 9.499585 CAGTTAGCTTGATCTGAAAAACATATG 57.500 33.333 0.00 0.00 0.00 1.78
2856 2983 7.013655 ACACAGTTAGCTTGATCTGAAAAACAT 59.986 33.333 0.00 0.00 0.00 2.71
2857 2984 6.318648 ACACAGTTAGCTTGATCTGAAAAACA 59.681 34.615 0.00 0.00 0.00 2.83
2858 2985 6.729187 ACACAGTTAGCTTGATCTGAAAAAC 58.271 36.000 0.00 0.00 0.00 2.43
2927 3062 6.098679 GGTGTTTGCTGTCAATATTATGCAA 58.901 36.000 0.00 10.46 38.41 4.08
2929 3064 5.649557 TGGTGTTTGCTGTCAATATTATGC 58.350 37.500 0.00 0.00 31.33 3.14
2993 3129 3.180449 TGGATCACCACCCTCTTGT 57.820 52.632 0.00 0.00 41.77 3.16
3518 3665 4.417437 ACAGCTCTTTGAGGTTAGGTAGA 58.583 43.478 0.00 0.00 38.40 2.59
3582 3729 7.345653 ACTGTATCAACTTCCATTCTCCATAGA 59.654 37.037 0.00 0.00 0.00 1.98
3622 3769 5.885465 ACATCAGGAAACAAAGAGAGGAAT 58.115 37.500 0.00 0.00 0.00 3.01
3751 3898 8.264347 TGTTCTGAATATACCTGCAATAGTTGA 58.736 33.333 0.00 0.00 0.00 3.18
3756 3903 9.725019 CCTATTGTTCTGAATATACCTGCAATA 57.275 33.333 0.00 0.40 0.00 1.90
3894 4042 4.060900 CACAGTAGTGTTCTCAAGCACAT 58.939 43.478 0.00 0.00 40.92 3.21
3987 4135 0.400594 AATACTATCGCTTGGCCCCC 59.599 55.000 0.00 0.00 0.00 5.40
3988 4136 2.935676 GCTAATACTATCGCTTGGCCCC 60.936 54.545 0.00 0.00 0.00 5.80
4168 4318 2.493278 ACACAAACAGCATCCAATAGCC 59.507 45.455 0.00 0.00 0.00 3.93
4243 4393 6.481976 TGTTCTTACACAGTACCAGAAACATG 59.518 38.462 0.00 0.00 0.00 3.21
4279 4429 8.504812 ACAGTTTCTACAAAATGGCAAAAATT 57.495 26.923 0.00 0.00 41.06 1.82
4338 4488 8.648968 GTTTCTGTAGCTACTTCACTGAAATAC 58.351 37.037 23.84 8.36 40.14 1.89
4407 4557 3.711704 AGCCGATCCTCCTCTCAAATTTA 59.288 43.478 0.00 0.00 0.00 1.40
4455 4605 1.000521 CCCATCTGCCAGCTTTCCA 60.001 57.895 0.00 0.00 0.00 3.53
4647 4874 6.055588 TCTACCAAGCCATACTAAAATCAGC 58.944 40.000 0.00 0.00 0.00 4.26
4651 4878 6.929606 GTCGATCTACCAAGCCATACTAAAAT 59.070 38.462 0.00 0.00 0.00 1.82
4677 4906 0.550914 TTCTTGCTCCACAACAGGGT 59.449 50.000 0.00 0.00 33.68 4.34
4749 4983 2.578495 GCAAAAACTGTCTCATGCTCG 58.422 47.619 0.00 0.00 0.00 5.03
4757 4991 8.409358 AAGTATAATTGAGGCAAAAACTGTCT 57.591 30.769 0.00 0.00 44.95 3.41
4810 5044 9.638176 AATTGCAGAAACATAGAGAAGGATTAT 57.362 29.630 0.00 0.00 0.00 1.28
4868 5102 6.000219 GGGATGTGTAGACATAGAATGCAAT 59.000 40.000 5.33 0.00 43.22 3.56
4878 5115 5.273208 ACTACAAGAGGGATGTGTAGACAT 58.727 41.667 15.06 4.97 44.94 3.06
4993 5230 4.569966 GCTAACTCATCAGGACAACATCTG 59.430 45.833 0.00 0.00 0.00 2.90
4994 5231 4.469227 AGCTAACTCATCAGGACAACATCT 59.531 41.667 0.00 0.00 0.00 2.90
5025 5287 2.051345 GCAACGCCACCTGAAACG 60.051 61.111 0.00 0.00 0.00 3.60
5184 5448 4.261578 CTGTTGATCCCAGCAAACAAAT 57.738 40.909 0.00 0.00 33.11 2.32
5262 5531 5.941647 TGTGGTAAAAGGTCCTAAATACAGC 59.058 40.000 0.00 0.00 0.00 4.40
5275 5544 6.399639 ACCAACTAAACATGTGGTAAAAGG 57.600 37.500 0.00 0.00 0.00 3.11
5279 5548 5.299782 GGTCAACCAACTAAACATGTGGTAA 59.700 40.000 0.00 0.00 35.64 2.85
5283 5552 4.578516 TGAGGTCAACCAACTAAACATGTG 59.421 41.667 0.00 0.00 38.89 3.21
5317 5586 3.408634 TCCTTAAAAAGAAGCTGACCCG 58.591 45.455 0.00 0.00 0.00 5.28
5320 5589 8.723942 TGATCTATCCTTAAAAAGAAGCTGAC 57.276 34.615 0.00 0.00 0.00 3.51
5496 5771 2.279810 TTCATGTCGGTCCTGCGGA 61.280 57.895 0.00 0.00 0.00 5.54
5500 5775 2.169832 AACAGTTCATGTCGGTCCTG 57.830 50.000 0.00 0.00 43.00 3.86
5530 5805 9.535878 GTTATTCTATTCTGTGGAGTAAAGAGG 57.464 37.037 0.00 0.00 0.00 3.69
5586 5861 2.030027 AGGTCCTCCTGTGAACATCA 57.970 50.000 0.00 0.00 43.33 3.07
5672 5948 3.108847 AGAGTAGGAGGGAAACTGAGG 57.891 52.381 0.00 0.00 0.00 3.86
5979 6255 6.074648 TCAAATCACTAAACCATGGGAAAGT 58.925 36.000 18.09 12.66 0.00 2.66
5984 6260 5.243730 ACACTTCAAATCACTAAACCATGGG 59.756 40.000 18.09 0.00 0.00 4.00
6051 6327 2.289195 ACCTACTCGTCGCCATCAAAAA 60.289 45.455 0.00 0.00 0.00 1.94
6095 6371 7.009631 CCAAAACTGTATATGTCACTCTTCTCG 59.990 40.741 0.00 0.00 0.00 4.04
6220 6496 4.338879 ACCATGCAGAAAGCTAACAGATT 58.661 39.130 0.00 0.00 45.94 2.40
6238 6514 6.774170 TGCTCATCAATATCAGCTTAAACCAT 59.226 34.615 0.00 0.00 32.76 3.55
6272 6550 4.081309 CCTGCCAATTCCAGTTCATTCATT 60.081 41.667 2.87 0.00 0.00 2.57
6645 6924 2.996621 CCTTCTCCTTGCTTACACGAAG 59.003 50.000 0.00 0.00 38.30 3.79
6663 6942 2.038557 ACTAACACGTGATCCTTGCCTT 59.961 45.455 25.01 4.96 0.00 4.35
6676 6955 6.426025 AGGAAAAGTAAAGCCTAACTAACACG 59.574 38.462 0.00 0.00 0.00 4.49
6795 7074 4.637483 TGAAGCACAAGAACAAGGAAAG 57.363 40.909 0.00 0.00 0.00 2.62
6806 7088 6.925165 AGTTTGAAACCAATATGAAGCACAAG 59.075 34.615 4.14 0.00 0.00 3.16
6807 7089 6.700960 CAGTTTGAAACCAATATGAAGCACAA 59.299 34.615 4.14 0.00 0.00 3.33
6808 7090 6.183360 ACAGTTTGAAACCAATATGAAGCACA 60.183 34.615 4.14 0.00 0.00 4.57
6864 7146 2.852449 TCTATTTGCCCCATCTCCTTGT 59.148 45.455 0.00 0.00 0.00 3.16
6890 7172 0.392461 GCAAACCCGCATCCTGTCTA 60.392 55.000 0.00 0.00 0.00 2.59
6891 7173 1.675641 GCAAACCCGCATCCTGTCT 60.676 57.895 0.00 0.00 0.00 3.41
6897 7179 0.313672 TTTGAGTGCAAACCCGCATC 59.686 50.000 0.00 0.00 45.26 3.91
6901 7183 2.223688 TGTGATTTTGAGTGCAAACCCG 60.224 45.455 0.00 0.00 43.27 5.28
6911 7193 5.698832 TCTTATTTGGCGTGTGATTTTGAG 58.301 37.500 0.00 0.00 0.00 3.02
6963 7245 6.537355 AGTTTTGAGATGAACATTCCTCTGA 58.463 36.000 4.39 0.00 33.23 3.27
7055 7348 9.990360 TGACTACATTTGATGTTTGTTACTAGA 57.010 29.630 0.00 0.00 41.63 2.43
7086 7379 2.517959 TGGCATCAAACTGAAGGAAGG 58.482 47.619 0.00 0.00 0.00 3.46
7087 7380 4.589216 TTTGGCATCAAACTGAAGGAAG 57.411 40.909 0.00 0.00 37.89 3.46
7205 7502 1.296715 CTTGCCGCTGGTAGGTCTT 59.703 57.895 0.00 0.00 0.00 3.01
7206 7503 1.481056 AACTTGCCGCTGGTAGGTCT 61.481 55.000 1.81 0.00 26.43 3.85
7288 7585 4.608445 GCGTGTATGTTCTATTTCGCCATC 60.608 45.833 0.00 0.00 37.14 3.51
7320 7617 2.469952 AGCTGGCTTGAGAAGAGAGAT 58.530 47.619 0.00 0.00 0.00 2.75
7441 7743 2.602933 CCGGCACATTAATGATCGCTTG 60.603 50.000 22.16 9.47 0.00 4.01
7442 7745 1.603802 CCGGCACATTAATGATCGCTT 59.396 47.619 22.16 0.00 0.00 4.68


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

AutoCloner maintained by Alex Coulton.