Multiple sequence alignment - TraesCS5B01G410400

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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 TraesCS5B01G410400 chr5B 100.000 5042 0 0 1 5042 585755921 585750880 0.000000e+00 9311.0
1 TraesCS5B01G410400 chr5B 88.235 85 10 0 3038 3122 582392059 582391975 8.930000e-18 102.0
2 TraesCS5B01G410400 chr5A 92.814 3618 153 38 439 4009 597293010 597289453 0.000000e+00 5142.0
3 TraesCS5B01G410400 chr5A 85.496 393 36 13 42 422 597293605 597293222 1.700000e-104 390.0
4 TraesCS5B01G410400 chr5A 87.868 272 19 5 4387 4650 597288033 597287768 1.760000e-79 307.0
5 TraesCS5B01G410400 chr5A 89.024 82 9 0 3038 3119 594323322 594323241 8.930000e-18 102.0
6 TraesCS5B01G410400 chr5A 98.077 52 1 0 4666 4717 597287650 597287599 1.930000e-14 91.6
7 TraesCS5B01G410400 chr5A 94.737 57 3 0 4009 4065 597288216 597288160 6.950000e-14 89.8
8 TraesCS5B01G410400 chr5D 95.302 2682 77 21 367 3022 478167012 478164354 0.000000e+00 4209.0
9 TraesCS5B01G410400 chr5D 91.722 1667 66 25 3031 4650 478164271 478162630 0.000000e+00 2248.0
10 TraesCS5B01G410400 chr5D 82.162 370 27 11 1 358 478169066 478168724 1.070000e-71 281.0
11 TraesCS5B01G410400 chr5D 87.597 129 5 6 4805 4933 478162313 478162196 6.810000e-29 139.0
12 TraesCS5B01G410400 chr1A 79.851 670 111 19 3316 3980 520573058 520573708 7.640000e-128 468.0
13 TraesCS5B01G410400 chr1A 74.641 418 66 25 1077 1490 520570323 520570704 1.130000e-31 148.0
14 TraesCS5B01G410400 chr1B 79.552 670 113 19 3316 3980 573861268 573861918 1.650000e-124 457.0
15 TraesCS5B01G410400 chr1B 74.163 418 68 25 1077 1490 573858704 573859085 2.450000e-28 137.0
16 TraesCS5B01G410400 chr1D 79.290 676 118 16 3309 3980 424730655 424731312 2.140000e-123 453.0
17 TraesCS5B01G410400 chr1D 74.751 301 61 12 1192 1490 424728141 424728428 2.470000e-23 121.0
18 TraesCS5B01G410400 chr1D 91.228 57 4 1 1077 1132 424728047 424728103 5.410000e-10 76.8
19 TraesCS5B01G410400 chr3B 84.488 361 56 0 3322 3682 543467857 543467497 1.730000e-94 357.0
20 TraesCS5B01G410400 chr3B 74.961 647 128 27 1171 1789 543470727 543470087 2.990000e-67 267.0
21 TraesCS5B01G410400 chr3B 89.474 95 6 4 3033 3125 181288899 181288807 3.190000e-22 117.0
22 TraesCS5B01G410400 chr3A 83.791 364 59 0 3319 3682 533661709 533662072 3.740000e-91 346.0
23 TraesCS5B01G410400 chr3A 76.392 521 81 33 1171 1662 533658664 533659171 5.040000e-60 243.0
24 TraesCS5B01G410400 chr3A 88.172 93 7 4 3033 3123 137579648 137579558 1.920000e-19 108.0
25 TraesCS5B01G410400 chr3D 83.862 347 56 0 3336 3682 417160796 417160450 1.050000e-86 331.0
26 TraesCS5B01G410400 chr3D 75.977 512 102 17 1171 1668 417163816 417163312 1.400000e-60 244.0
27 TraesCS5B01G410400 chr3D 89.474 95 6 4 3033 3125 126949134 126949042 3.190000e-22 117.0
28 TraesCS5B01G410400 chr4A 77.223 461 64 27 2550 2991 532222343 532221905 1.090000e-56 231.0
29 TraesCS5B01G410400 chr7D 90.000 90 7 1 3038 3125 237415166 237415077 1.150000e-21 115.0
30 TraesCS5B01G410400 chr7B 87.912 91 8 2 3038 3125 214074956 214074866 2.480000e-18 104.0
31 TraesCS5B01G410400 chr6D 86.022 93 13 0 3034 3126 78352685 78352777 3.210000e-17 100.0
32 TraesCS5B01G410400 chr4B 87.143 70 8 1 1192 1260 628227457 628227526 1.500000e-10 78.7
33 TraesCS5B01G410400 chr4B 91.228 57 4 1 1077 1132 628227381 628227437 5.410000e-10 76.8


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 TraesCS5B01G410400 chr5B 585750880 585755921 5041 True 9311.000000 9311 100.000000 1 5042 1 chr5B.!!$R2 5041
1 TraesCS5B01G410400 chr5A 597287599 597293605 6006 True 1204.080000 5142 91.798400 42 4717 5 chr5A.!!$R2 4675
2 TraesCS5B01G410400 chr5D 478162196 478169066 6870 True 1719.250000 4209 89.195750 1 4933 4 chr5D.!!$R1 4932
3 TraesCS5B01G410400 chr1A 520570323 520573708 3385 False 308.000000 468 77.246000 1077 3980 2 chr1A.!!$F1 2903
4 TraesCS5B01G410400 chr1B 573858704 573861918 3214 False 297.000000 457 76.857500 1077 3980 2 chr1B.!!$F1 2903
5 TraesCS5B01G410400 chr1D 424728047 424731312 3265 False 216.933333 453 81.756333 1077 3980 3 chr1D.!!$F1 2903
6 TraesCS5B01G410400 chr3B 543467497 543470727 3230 True 312.000000 357 79.724500 1171 3682 2 chr3B.!!$R2 2511
7 TraesCS5B01G410400 chr3A 533658664 533662072 3408 False 294.500000 346 80.091500 1171 3682 2 chr3A.!!$F1 2511
8 TraesCS5B01G410400 chr3D 417160450 417163816 3366 True 287.500000 331 79.919500 1171 3682 2 chr3D.!!$R2 2511

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
427 2149 0.888619 GGGCCAAAGTGTAAAGCCTC 59.111 55.000 4.39 0.0 43.36 4.70 F
428 2150 1.547901 GGGCCAAAGTGTAAAGCCTCT 60.548 52.381 4.39 0.0 43.36 3.69 F
881 2832 2.309504 GGGTGGAAAGGAGGGAGGG 61.310 68.421 0.00 0.0 0.00 4.30 F
2409 5716 2.227388 GCAGGTGAATGGAGTGTTCTTG 59.773 50.000 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1501 3505 1.127567 CGATAATGGGGAGGGCCAGA 61.128 60.000 6.18 0.0 35.15 3.86 R
2260 5554 1.963515 GTTGTCCTGAAAACAGCCCAT 59.036 47.619 0.00 0.0 0.00 4.00 R
2442 5749 1.078214 CAGCGCCTTGATCCTCCAA 60.078 57.895 2.29 0.0 0.00 3.53 R
4363 9434 1.073177 ATGAGTTTTTACGGACGGCG 58.927 50.000 4.80 4.8 0.00 6.46 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
25 26 5.349543 AGCGGCATCAATTGAAAATTTTCTC 59.650 36.000 26.73 7.60 38.02 2.87
26 27 5.446340 GCGGCATCAATTGAAAATTTTCTCC 60.446 40.000 26.73 14.86 38.02 3.71
35 36 6.443934 TTGAAAATTTTCTCCGACAAGTCA 57.556 33.333 26.73 4.84 38.02 3.41
40 41 0.902531 TTCTCCGACAAGTCATCCCC 59.097 55.000 0.72 0.00 0.00 4.81
52 54 6.074648 ACAAGTCATCCCCAAAAATACTCAA 58.925 36.000 0.00 0.00 0.00 3.02
54 56 6.139679 AGTCATCCCCAAAAATACTCAAGA 57.860 37.500 0.00 0.00 0.00 3.02
61 63 7.242359 TCCCCAAAAATACTCAAGAACCATTA 58.758 34.615 0.00 0.00 0.00 1.90
129 133 2.594303 TGCCCGGAAAGCACACTG 60.594 61.111 0.73 0.00 34.69 3.66
184 188 5.523588 AGAGAGAGAGAGAGAGAGAGAGAA 58.476 45.833 0.00 0.00 0.00 2.87
231 245 4.471386 TCTTTTCACCAAATCCAACCCAAA 59.529 37.500 0.00 0.00 0.00 3.28
245 261 9.762381 AATCCAACCCAAATTTAGTATCTTACA 57.238 29.630 0.00 0.00 0.00 2.41
247 263 8.164733 TCCAACCCAAATTTAGTATCTTACACA 58.835 33.333 0.00 0.00 0.00 3.72
312 331 5.690865 TGTGGTTACTCTGGAAACTTGAAT 58.309 37.500 0.00 0.00 0.00 2.57
319 338 9.880064 GTTACTCTGGAAACTTGAATAAAGAAC 57.120 33.333 0.00 0.00 39.38 3.01
345 364 6.201044 CGAGCATAATGGACGATAAGACTTTT 59.799 38.462 0.00 0.00 0.00 2.27
346 365 7.381408 CGAGCATAATGGACGATAAGACTTTTA 59.619 37.037 0.00 0.00 0.00 1.52
347 366 8.366671 AGCATAATGGACGATAAGACTTTTAC 57.633 34.615 0.00 0.00 0.00 2.01
349 368 7.568861 GCATAATGGACGATAAGACTTTTACGG 60.569 40.741 0.00 0.00 0.00 4.02
350 369 4.114058 TGGACGATAAGACTTTTACGGG 57.886 45.455 0.00 0.00 0.00 5.28
351 370 2.862536 GGACGATAAGACTTTTACGGGC 59.137 50.000 0.00 0.00 0.00 6.13
352 371 3.514645 GACGATAAGACTTTTACGGGCA 58.485 45.455 0.00 0.00 0.00 5.36
353 372 3.928375 GACGATAAGACTTTTACGGGCAA 59.072 43.478 0.00 0.00 0.00 4.52
354 373 3.930848 ACGATAAGACTTTTACGGGCAAG 59.069 43.478 0.00 0.00 0.00 4.01
358 377 6.347888 CGATAAGACTTTTACGGGCAAGAAAA 60.348 38.462 0.00 0.00 0.00 2.29
364 2086 8.364894 AGACTTTTACGGGCAAGAAAAATAAAT 58.635 29.630 0.00 0.00 0.00 1.40
365 2087 8.305441 ACTTTTACGGGCAAGAAAAATAAATG 57.695 30.769 0.00 0.00 0.00 2.32
370 2092 6.754193 ACGGGCAAGAAAAATAAATGAAAGA 58.246 32.000 0.00 0.00 0.00 2.52
386 2108 4.198530 TGAAAGAGTGAAACATGCACAGA 58.801 39.130 0.00 0.00 41.43 3.41
427 2149 0.888619 GGGCCAAAGTGTAAAGCCTC 59.111 55.000 4.39 0.00 43.36 4.70
428 2150 1.547901 GGGCCAAAGTGTAAAGCCTCT 60.548 52.381 4.39 0.00 43.36 3.69
513 2430 6.990349 TGAATTTCTCACCGTAATTATCTCCC 59.010 38.462 0.00 0.00 0.00 4.30
516 2433 4.717877 TCTCACCGTAATTATCTCCCGTA 58.282 43.478 0.00 0.00 0.00 4.02
517 2434 4.758674 TCTCACCGTAATTATCTCCCGTAG 59.241 45.833 0.00 0.00 0.00 3.51
518 2435 3.254166 TCACCGTAATTATCTCCCGTAGC 59.746 47.826 0.00 0.00 0.00 3.58
560 2482 8.546322 AGGAGTACGAAGGAAGGTAAATAAATT 58.454 33.333 0.00 0.00 0.00 1.82
563 2485 9.828039 AGTACGAAGGAAGGTAAATAAATTAGG 57.172 33.333 0.00 0.00 0.00 2.69
564 2486 9.822185 GTACGAAGGAAGGTAAATAAATTAGGA 57.178 33.333 0.00 0.00 0.00 2.94
688 2634 2.913617 TCCCTCTGTCTGTCTGTCTCTA 59.086 50.000 0.00 0.00 0.00 2.43
881 2832 2.309504 GGGTGGAAAGGAGGGAGGG 61.310 68.421 0.00 0.00 0.00 4.30
910 2862 2.772622 CCGGGGGCCAGGAATAGT 60.773 66.667 11.39 0.00 0.00 2.12
1689 3696 2.334946 TGAAGCGCATCAAGCCCAC 61.335 57.895 13.73 0.00 41.38 4.61
2237 5530 6.072728 TGTTATCAATCGGCTATGGTTTATGC 60.073 38.462 0.00 0.00 0.00 3.14
2260 5554 6.489700 TGCTTCCAGTTCTGATTTGTCAATTA 59.510 34.615 1.00 0.00 0.00 1.40
2409 5716 2.227388 GCAGGTGAATGGAGTGTTCTTG 59.773 50.000 0.00 0.00 0.00 3.02
2573 5880 2.030893 TGAACGACGTCGAGGTATTGTT 60.031 45.455 41.52 23.54 43.02 2.83
2651 5972 6.671190 TGAGCTGAAATGTTGTCTTAATGTG 58.329 36.000 0.00 0.00 0.00 3.21
2741 6062 3.555966 GGTCCAATGCAGCTATTTAGGT 58.444 45.455 0.00 0.00 33.70 3.08
2743 6064 5.130350 GGTCCAATGCAGCTATTTAGGTTA 58.870 41.667 0.00 0.00 30.45 2.85
2755 6076 6.070194 AGCTATTTAGGTTATGCATACCGGAT 60.070 38.462 9.46 9.90 40.69 4.18
2801 6288 7.719633 TGTTCTGCTCTTTTTCTTGTACCTAAT 59.280 33.333 0.00 0.00 0.00 1.73
2876 6363 5.292834 CGTGAGACGTTCTCCAGTAATACTA 59.707 44.000 11.01 0.00 42.73 1.82
3019 6597 3.676646 GCTTTGTCATCATTTGCCTTCAC 59.323 43.478 0.00 0.00 0.00 3.18
3022 6600 3.229293 TGTCATCATTTGCCTTCACCAA 58.771 40.909 0.00 0.00 0.00 3.67
3029 6674 1.999648 TTGCCTTCACCAATTCAGCT 58.000 45.000 0.00 0.00 0.00 4.24
3042 6694 7.124298 TCACCAATTCAGCTATACAAGTACTCT 59.876 37.037 0.00 0.00 0.00 3.24
3053 6705 8.339714 GCTATACAAGTACTCTCTCTGTAACTG 58.660 40.741 8.12 4.11 0.00 3.16
3097 6749 7.422179 CAGTTCAAATTAAACTGCAAAAACGTG 59.578 33.333 16.36 0.00 44.94 4.49
3119 6771 7.809806 ACGTGTTACATTAAGTTACAGAGGTAC 59.190 37.037 0.00 0.00 40.11 3.34
3445 7237 0.247262 CGATGACGATGTTTGTGCCG 60.247 55.000 0.00 0.00 42.66 5.69
3545 7337 1.025041 GTTCCCTTTCATCATCCCGC 58.975 55.000 0.00 0.00 0.00 6.13
3613 7405 3.965539 CTCGGGCCTGTTCCAGCTG 62.966 68.421 12.43 6.78 0.00 4.24
3616 7408 3.650950 GGCCTGTTCCAGCTGGGA 61.651 66.667 32.23 23.18 46.61 4.37
3862 7657 2.508887 CTGTCGCTGCTCCTGCTC 60.509 66.667 0.00 0.00 40.48 4.26
4069 9102 1.078497 TGATGTCCCGTGATGGTGC 60.078 57.895 0.00 0.00 35.15 5.01
4095 9128 4.778143 CTCGGCCGGGGTTCCAAG 62.778 72.222 27.83 8.77 0.00 3.61
4169 9202 2.583593 GCGAGCATGGTCGGAGTC 60.584 66.667 38.86 23.61 40.44 3.36
4210 9243 1.002011 GAGGCTTGGTTCTGGTCCC 60.002 63.158 0.00 0.00 0.00 4.46
4272 9305 0.963856 CTTGCAAGCAGGCATCTCCA 60.964 55.000 14.65 0.00 44.48 3.86
4283 9316 3.318275 CAGGCATCTCCATTCCATTCTTG 59.682 47.826 0.00 0.00 37.29 3.02
4286 9319 3.067742 GCATCTCCATTCCATTCTTGTGG 59.932 47.826 0.00 0.00 40.76 4.17
4287 9320 2.726821 TCTCCATTCCATTCTTGTGGC 58.273 47.619 0.00 0.00 39.19 5.01
4334 9405 1.071385 GATCATGTCCCAGGATCGCTT 59.929 52.381 3.48 0.00 40.79 4.68
4363 9434 0.529378 CAGAAGGTGGCTGATTTGGC 59.471 55.000 0.00 0.00 35.39 4.52
4444 9515 1.741706 GTGCATGGTTGATCTGGTCAG 59.258 52.381 0.00 0.00 38.29 3.51
4451 9522 2.808543 GGTTGATCTGGTCAGTGTGTTC 59.191 50.000 0.00 0.00 38.29 3.18
4530 9612 5.493133 TTCGTGTGTATGAGCAAAAGTTT 57.507 34.783 0.00 0.00 0.00 2.66
4667 9803 4.141459 TGGTACAACTGGACACCATGTAAA 60.141 41.667 6.01 0.00 36.15 2.01
4669 9805 2.875933 ACAACTGGACACCATGTAAACG 59.124 45.455 0.00 0.00 30.82 3.60
4670 9806 3.135225 CAACTGGACACCATGTAAACGA 58.865 45.455 0.00 0.00 30.82 3.85
4673 9809 3.181458 ACTGGACACCATGTAAACGACTT 60.181 43.478 0.00 0.00 30.82 3.01
4717 9910 4.695455 CGAGGTGTCATTTCCAAGTATTGT 59.305 41.667 0.00 0.00 46.99 2.71
4719 9912 5.010282 AGGTGTCATTTCCAAGTATTGTCC 58.990 41.667 0.00 0.00 46.99 4.02
4720 9913 4.157840 GGTGTCATTTCCAAGTATTGTCCC 59.842 45.833 0.00 0.00 46.99 4.46
4722 9915 6.177610 GTGTCATTTCCAAGTATTGTCCCTA 58.822 40.000 0.00 0.00 46.99 3.53
4723 9916 6.828785 GTGTCATTTCCAAGTATTGTCCCTAT 59.171 38.462 0.00 0.00 46.99 2.57
4741 9955 4.846367 CCCTATCCTATCCAGTCCATTCAA 59.154 45.833 0.00 0.00 0.00 2.69
4746 9960 6.823286 TCCTATCCAGTCCATTCAATACAA 57.177 37.500 0.00 0.00 0.00 2.41
4750 9964 5.715439 TCCAGTCCATTCAATACAAGGAT 57.285 39.130 0.00 0.00 0.00 3.24
4751 9965 6.823286 TCCAGTCCATTCAATACAAGGATA 57.177 37.500 0.00 0.00 0.00 2.59
4753 9967 7.638444 TCCAGTCCATTCAATACAAGGATAAA 58.362 34.615 0.00 0.00 0.00 1.40
4754 9968 8.281531 TCCAGTCCATTCAATACAAGGATAAAT 58.718 33.333 0.00 0.00 0.00 1.40
4755 9969 9.573166 CCAGTCCATTCAATACAAGGATAAATA 57.427 33.333 0.00 0.00 0.00 1.40
4757 9971 9.574516 AGTCCATTCAATACAAGGATAAATACC 57.425 33.333 0.00 0.00 0.00 2.73
4758 9972 8.793592 GTCCATTCAATACAAGGATAAATACCC 58.206 37.037 0.00 0.00 0.00 3.69
4759 9973 7.947890 TCCATTCAATACAAGGATAAATACCCC 59.052 37.037 0.00 0.00 0.00 4.95
4761 9975 6.750660 TCAATACAAGGATAAATACCCCGA 57.249 37.500 0.00 0.00 0.00 5.14
4762 9976 6.765403 TCAATACAAGGATAAATACCCCGAG 58.235 40.000 0.00 0.00 0.00 4.63
4763 9977 6.555738 TCAATACAAGGATAAATACCCCGAGA 59.444 38.462 0.00 0.00 0.00 4.04
4764 9978 4.684484 ACAAGGATAAATACCCCGAGAC 57.316 45.455 0.00 0.00 0.00 3.36
4765 9979 3.069158 ACAAGGATAAATACCCCGAGACG 59.931 47.826 0.00 0.00 0.00 4.18
4787 10002 0.095762 GACGTAAAATGAACCGGCCG 59.904 55.000 21.04 21.04 0.00 6.13
4789 10004 1.138036 GTAAAATGAACCGGCCGGC 59.862 57.895 43.58 28.55 39.32 6.13
4822 10074 1.375268 GACTGGAGGTGAGCTGTGC 60.375 63.158 0.00 0.00 0.00 4.57
4832 10084 1.457303 GTGAGCTGTGCGTAACTGAAG 59.543 52.381 0.00 0.00 0.00 3.02
4841 10093 1.544691 GCGTAACTGAAGGAGGAGTGA 59.455 52.381 0.00 0.00 0.00 3.41
4843 10095 2.414293 CGTAACTGAAGGAGGAGTGACG 60.414 54.545 0.00 0.00 39.94 4.35
4849 10101 3.775654 GGAGGAGTGACGGGCAGG 61.776 72.222 0.00 0.00 0.00 4.85
4850 10102 4.459089 GAGGAGTGACGGGCAGGC 62.459 72.222 0.00 0.00 0.00 4.85
4852 10104 4.767255 GGAGTGACGGGCAGGCAG 62.767 72.222 0.00 0.00 39.56 4.85
4867 10119 3.123620 CAGCGGGCTGAACTGAGC 61.124 66.667 15.38 0.00 46.30 4.26
4933 10185 0.955428 ATTTCTGCATCGCGTGTGGT 60.955 50.000 5.77 0.00 0.00 4.16
4934 10186 1.840630 TTTCTGCATCGCGTGTGGTG 61.841 55.000 5.77 0.00 0.00 4.17
4935 10187 2.987282 TTCTGCATCGCGTGTGGTGT 62.987 55.000 5.77 0.00 0.00 4.16
4936 10188 3.299304 CTGCATCGCGTGTGGTGTG 62.299 63.158 5.77 0.00 0.00 3.82
4937 10189 4.088762 GCATCGCGTGTGGTGTGG 62.089 66.667 5.77 0.00 0.00 4.17
4938 10190 3.422303 CATCGCGTGTGGTGTGGG 61.422 66.667 5.77 0.00 0.00 4.61
4939 10191 3.936203 ATCGCGTGTGGTGTGGGT 61.936 61.111 5.77 0.00 0.00 4.51
4940 10192 4.901123 TCGCGTGTGGTGTGGGTG 62.901 66.667 5.77 0.00 0.00 4.61
4942 10194 3.582120 GCGTGTGGTGTGGGTGTG 61.582 66.667 0.00 0.00 0.00 3.82
4943 10195 2.899838 CGTGTGGTGTGGGTGTGG 60.900 66.667 0.00 0.00 0.00 4.17
4944 10196 3.216292 GTGTGGTGTGGGTGTGGC 61.216 66.667 0.00 0.00 0.00 5.01
4945 10197 3.415983 TGTGGTGTGGGTGTGGCT 61.416 61.111 0.00 0.00 0.00 4.75
4946 10198 2.906897 GTGGTGTGGGTGTGGCTG 60.907 66.667 0.00 0.00 0.00 4.85
4947 10199 4.892965 TGGTGTGGGTGTGGCTGC 62.893 66.667 0.00 0.00 0.00 5.25
4949 10201 4.927782 GTGTGGGTGTGGCTGCGA 62.928 66.667 0.00 0.00 0.00 5.10
4950 10202 4.624364 TGTGGGTGTGGCTGCGAG 62.624 66.667 0.00 0.00 0.00 5.03
4955 10207 3.702048 GTGTGGCTGCGAGGGGTA 61.702 66.667 0.00 0.00 0.00 3.69
4956 10208 3.702048 TGTGGCTGCGAGGGGTAC 61.702 66.667 0.00 0.00 0.00 3.34
4957 10209 3.702048 GTGGCTGCGAGGGGTACA 61.702 66.667 0.00 0.00 0.00 2.90
4958 10210 3.390521 TGGCTGCGAGGGGTACAG 61.391 66.667 0.00 0.00 34.48 2.74
4961 10213 2.185350 CTGCGAGGGGTACAGCTG 59.815 66.667 13.48 13.48 0.00 4.24
4962 10214 2.603473 TGCGAGGGGTACAGCTGT 60.603 61.111 25.12 25.12 0.00 4.40
4963 10215 2.125512 GCGAGGGGTACAGCTGTG 60.126 66.667 29.57 11.60 0.00 3.66
4964 10216 2.125512 CGAGGGGTACAGCTGTGC 60.126 66.667 29.57 27.19 0.00 4.57
4965 10217 2.125512 GAGGGGTACAGCTGTGCG 60.126 66.667 29.57 0.00 0.00 5.34
4966 10218 3.665675 GAGGGGTACAGCTGTGCGG 62.666 68.421 29.57 0.00 0.00 5.69
5027 10279 2.403586 GCGGTAAGCGCATTCCAC 59.596 61.111 11.47 0.00 35.41 4.02
5028 10280 2.395360 GCGGTAAGCGCATTCCACA 61.395 57.895 11.47 0.00 35.41 4.17
5029 10281 1.423845 CGGTAAGCGCATTCCACAC 59.576 57.895 11.47 0.00 0.00 3.82
5030 10282 1.423845 GGTAAGCGCATTCCACACG 59.576 57.895 11.47 0.00 0.00 4.49
5031 10283 1.296056 GGTAAGCGCATTCCACACGT 61.296 55.000 11.47 0.00 0.00 4.49
5032 10284 0.094730 GTAAGCGCATTCCACACGTC 59.905 55.000 11.47 0.00 0.00 4.34
5033 10285 1.348538 TAAGCGCATTCCACACGTCG 61.349 55.000 11.47 0.00 0.00 5.12
5034 10286 3.411351 GCGCATTCCACACGTCGT 61.411 61.111 0.30 0.00 0.00 4.34
5035 10287 2.950172 GCGCATTCCACACGTCGTT 61.950 57.895 0.30 0.00 0.00 3.85
5036 10288 1.154672 CGCATTCCACACGTCGTTG 60.155 57.895 0.00 0.00 0.00 4.10
5037 10289 1.206578 GCATTCCACACGTCGTTGG 59.793 57.895 16.02 16.02 0.00 3.77
5038 10290 1.206578 CATTCCACACGTCGTTGGC 59.793 57.895 16.87 0.00 0.00 4.52
5039 10291 2.314647 ATTCCACACGTCGTTGGCG 61.315 57.895 16.87 1.21 39.92 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.904287 TTTTGGGGATGACTTGTCGG 58.096 50.000 0.00 0.00 0.00 4.79
26 27 4.700213 AGTATTTTTGGGGATGACTTGTCG 59.300 41.667 0.00 0.00 0.00 4.35
35 36 5.650283 TGGTTCTTGAGTATTTTTGGGGAT 58.350 37.500 0.00 0.00 0.00 3.85
78 82 0.832135 TCTGGCAAGAACGTCCCTCT 60.832 55.000 0.00 0.00 0.00 3.69
117 121 1.064060 GTGTGACACAGTGTGCTTTCC 59.936 52.381 23.21 7.51 36.98 3.13
118 122 2.009774 AGTGTGACACAGTGTGCTTTC 58.990 47.619 23.21 13.62 36.98 2.62
129 133 1.933853 GGAACAGTGTGAGTGTGACAC 59.066 52.381 7.83 7.83 43.45 3.67
184 188 3.119849 GGCAATGACTGTATTTGCTCGTT 60.120 43.478 20.00 0.00 0.00 3.85
277 296 9.362151 TCCAGAGTAACCACAGATTTTATTTTT 57.638 29.630 0.00 0.00 0.00 1.94
312 331 4.116961 CGTCCATTATGCTCGGTTCTTTA 58.883 43.478 0.00 0.00 0.00 1.85
319 338 3.921021 GTCTTATCGTCCATTATGCTCGG 59.079 47.826 7.20 0.00 0.00 4.63
345 364 7.887381 TCTTTCATTTATTTTTCTTGCCCGTA 58.113 30.769 0.00 0.00 0.00 4.02
346 365 6.754193 TCTTTCATTTATTTTTCTTGCCCGT 58.246 32.000 0.00 0.00 0.00 5.28
347 366 6.868339 ACTCTTTCATTTATTTTTCTTGCCCG 59.132 34.615 0.00 0.00 0.00 6.13
349 368 8.816640 TCACTCTTTCATTTATTTTTCTTGCC 57.183 30.769 0.00 0.00 0.00 4.52
358 377 8.143193 TGTGCATGTTTCACTCTTTCATTTATT 58.857 29.630 0.00 0.00 35.58 1.40
364 2086 4.035558 GTCTGTGCATGTTTCACTCTTTCA 59.964 41.667 0.00 0.00 35.58 2.69
365 2087 4.274459 AGTCTGTGCATGTTTCACTCTTTC 59.726 41.667 0.00 0.00 35.58 2.62
370 2092 6.639632 AATAAAGTCTGTGCATGTTTCACT 57.360 33.333 0.00 0.00 35.58 3.41
386 2108 4.973663 CCGTGCTTTCGAACAAAATAAAGT 59.026 37.500 0.00 0.00 32.70 2.66
427 2149 1.202177 GCAATTGCATGGTACCGACAG 60.202 52.381 25.36 0.00 41.59 3.51
428 2150 0.808125 GCAATTGCATGGTACCGACA 59.192 50.000 25.36 2.06 41.59 4.35
525 2442 2.507110 TTCGTACTCCTGCTGCTGCC 62.507 60.000 13.47 0.00 38.71 4.85
688 2634 2.515947 GAACAGCTCGACGCGTCTCT 62.516 60.000 33.94 24.32 45.59 3.10
745 2691 6.126652 TGCCATTAGAGCTTTAAGAAGAGGAT 60.127 38.462 2.88 0.00 34.71 3.24
910 2862 1.369692 CGCCCACTCTACCACACAA 59.630 57.895 0.00 0.00 0.00 3.33
949 2901 1.674651 GGGCCTGGACCTTTCGTTC 60.675 63.158 12.69 0.00 0.00 3.95
1501 3505 1.127567 CGATAATGGGGAGGGCCAGA 61.128 60.000 6.18 0.00 35.15 3.86
2070 5344 4.862447 TAGCTGCAGGCCATGGCG 62.862 66.667 29.90 18.44 43.05 5.69
2237 5530 7.972277 CCATAATTGACAAATCAGAACTGGAAG 59.028 37.037 1.93 0.00 35.83 3.46
2260 5554 1.963515 GTTGTCCTGAAAACAGCCCAT 59.036 47.619 0.00 0.00 0.00 4.00
2409 5716 3.069443 TGCCATTGAACCCAAAGAAGTTC 59.931 43.478 0.00 0.00 42.20 3.01
2442 5749 1.078214 CAGCGCCTTGATCCTCCAA 60.078 57.895 2.29 0.00 0.00 3.53
2651 5972 1.210155 GTTCGCATTGGCACTGTCC 59.790 57.895 6.71 0.00 41.24 4.02
2741 6062 6.946340 ACTTGATGATATCCGGTATGCATAA 58.054 36.000 8.28 0.00 0.00 1.90
2743 6064 5.423015 GACTTGATGATATCCGGTATGCAT 58.577 41.667 3.79 3.79 0.00 3.96
2755 6076 7.770433 CAGAACAATACCTTGGACTTGATGATA 59.230 37.037 10.95 0.00 36.64 2.15
2801 6288 7.819415 CACTGTCTAAATTGTAGTCCATTCTGA 59.181 37.037 0.00 0.00 0.00 3.27
2823 6310 4.179926 TCTCAGTTAGCTTGTAGCACTG 57.820 45.455 11.02 11.02 45.56 3.66
2876 6363 5.634859 CAGAGTTTTCGCCAGCAATTTTAAT 59.365 36.000 0.00 0.00 0.00 1.40
3019 6597 7.721402 AGAGAGTACTTGTATAGCTGAATTGG 58.279 38.462 0.00 0.00 0.00 3.16
3022 6600 7.777910 ACAGAGAGAGTACTTGTATAGCTGAAT 59.222 37.037 0.00 0.00 0.00 2.57
3029 6674 9.955102 TTCAGTTACAGAGAGAGTACTTGTATA 57.045 33.333 0.00 0.00 0.00 1.47
3053 6705 8.816144 TTTGAACTGCAAAAATGTCTTACATTC 58.184 29.630 5.79 0.00 41.68 2.67
3157 6826 4.555348 TGTAAACACCGTCACCAATTTC 57.445 40.909 0.00 0.00 0.00 2.17
3301 7059 8.654230 TCTGCAGCAAAATAAAACAATGTTAA 57.346 26.923 9.47 0.00 0.00 2.01
3305 7063 7.476183 CGAAATCTGCAGCAAAATAAAACAATG 59.524 33.333 9.47 0.00 0.00 2.82
3308 7066 5.404968 CCGAAATCTGCAGCAAAATAAAACA 59.595 36.000 9.47 0.00 0.00 2.83
3613 7405 2.202756 CACTCGTAGGCGCTTCCC 60.203 66.667 7.64 0.00 38.14 3.97
3616 7408 2.995574 ACCCACTCGTAGGCGCTT 60.996 61.111 7.64 0.52 38.14 4.68
3776 7571 1.153549 CTTCCTTCTTCGGGCTCGG 60.154 63.158 5.94 0.00 36.95 4.63
3985 7780 6.817765 ATCGTGTCCATGTTTACATTTTCT 57.182 33.333 0.00 0.00 33.61 2.52
4043 9076 1.535444 ACGGGACATCACACTCCCA 60.535 57.895 3.67 0.00 46.11 4.37
4095 9128 2.358510 GGTTAACCCCATAAACCCTCCC 60.359 54.545 14.16 0.00 37.31 4.30
4096 9129 2.684630 CGGTTAACCCCATAAACCCTCC 60.685 54.545 19.09 0.00 39.63 4.30
4097 9130 2.646930 CGGTTAACCCCATAAACCCTC 58.353 52.381 19.09 0.00 39.63 4.30
4188 9221 2.356667 CAGAACCAAGCCTCCCCC 59.643 66.667 0.00 0.00 0.00 5.40
4193 9226 3.171348 GGGACCAGAACCAAGCCT 58.829 61.111 0.00 0.00 0.00 4.58
4210 9243 7.159322 AGGCTATATCTACACATTCTTACGG 57.841 40.000 0.00 0.00 0.00 4.02
4272 9305 5.750352 ATTTCTTGCCACAAGAATGGAAT 57.250 34.783 20.09 10.25 43.02 3.01
4283 9316 6.258507 AGACAACATCAAAAATTTCTTGCCAC 59.741 34.615 0.00 0.00 0.00 5.01
4286 9319 7.121272 CACAGACAACATCAAAAATTTCTTGC 58.879 34.615 0.00 0.00 0.00 4.01
4287 9320 7.254522 CCCACAGACAACATCAAAAATTTCTTG 60.255 37.037 0.00 0.00 0.00 3.02
4343 9414 1.915141 CCAAATCAGCCACCTTCTGT 58.085 50.000 0.00 0.00 33.48 3.41
4360 9431 2.280660 TTTTTACGGACGGCGCCA 60.281 55.556 28.98 1.46 0.00 5.69
4363 9434 1.073177 ATGAGTTTTTACGGACGGCG 58.927 50.000 4.80 4.80 0.00 6.46
4444 9515 2.719354 GTGCCAACCCGAACACAC 59.281 61.111 0.00 0.00 33.23 3.82
4530 9612 2.103094 CCGGATCTACTCCAAGATGCAA 59.897 50.000 0.00 0.00 45.24 4.08
4538 9620 2.820728 TCTTGACCGGATCTACTCCA 57.179 50.000 9.46 0.00 45.24 3.86
4651 9787 2.367567 AGTCGTTTACATGGTGTCCAGT 59.632 45.455 0.00 0.00 36.75 4.00
4667 9803 4.569943 TGGAGACTACGTACTTAAGTCGT 58.430 43.478 25.40 25.40 43.51 4.34
4669 9805 4.940654 ACCTGGAGACTACGTACTTAAGTC 59.059 45.833 12.39 7.23 39.95 3.01
4670 9806 4.699257 CACCTGGAGACTACGTACTTAAGT 59.301 45.833 13.68 13.68 0.00 2.24
4673 9809 3.012518 GCACCTGGAGACTACGTACTTA 58.987 50.000 0.00 0.00 0.00 2.24
4717 9910 4.109600 TGAATGGACTGGATAGGATAGGGA 59.890 45.833 0.00 0.00 0.00 4.20
4719 9912 6.633325 ATTGAATGGACTGGATAGGATAGG 57.367 41.667 0.00 0.00 0.00 2.57
4720 9913 8.138928 TGTATTGAATGGACTGGATAGGATAG 57.861 38.462 0.00 0.00 0.00 2.08
4722 9915 7.392766 TTGTATTGAATGGACTGGATAGGAT 57.607 36.000 0.00 0.00 0.00 3.24
4723 9916 6.183361 CCTTGTATTGAATGGACTGGATAGGA 60.183 42.308 0.00 0.00 0.00 2.94
4741 9955 5.047519 CGTCTCGGGGTATTTATCCTTGTAT 60.048 44.000 0.00 0.00 0.00 2.29
4746 9960 2.245582 CCGTCTCGGGGTATTTATCCT 58.754 52.381 0.00 0.00 44.15 3.24
4758 9972 0.174162 ATTTTACGTCCCCGTCTCGG 59.826 55.000 0.00 0.85 46.28 4.63
4759 9973 1.135315 TCATTTTACGTCCCCGTCTCG 60.135 52.381 0.00 0.00 46.28 4.04
4761 9975 2.613725 GGTTCATTTTACGTCCCCGTCT 60.614 50.000 0.00 0.00 46.28 4.18
4762 9976 1.733912 GGTTCATTTTACGTCCCCGTC 59.266 52.381 0.00 0.00 46.28 4.79
4764 9978 0.722848 CGGTTCATTTTACGTCCCCG 59.277 55.000 0.00 0.00 40.83 5.73
4765 9979 1.089112 CCGGTTCATTTTACGTCCCC 58.911 55.000 0.00 0.00 0.00 4.81
4767 9981 0.448990 GGCCGGTTCATTTTACGTCC 59.551 55.000 1.90 0.00 0.00 4.79
4768 9982 0.095762 CGGCCGGTTCATTTTACGTC 59.904 55.000 20.10 0.00 0.00 4.34
4769 9983 1.300266 CCGGCCGGTTCATTTTACGT 61.300 55.000 36.64 0.00 0.00 3.57
4770 9984 1.426223 CCGGCCGGTTCATTTTACG 59.574 57.895 36.64 5.51 0.00 3.18
4771 9985 1.138036 GCCGGCCGGTTCATTTTAC 59.862 57.895 42.53 20.88 37.65 2.01
4772 9986 1.001887 AGCCGGCCGGTTCATTTTA 60.002 52.632 42.53 0.00 37.65 1.52
4789 10004 2.357517 GTCCAGTGCACCCGACAG 60.358 66.667 22.58 4.50 0.00 3.51
4822 10074 2.414293 CGTCACTCCTCCTTCAGTTACG 60.414 54.545 0.00 0.00 34.83 3.18
4832 10084 3.775654 CCTGCCCGTCACTCCTCC 61.776 72.222 0.00 0.00 0.00 4.30
4849 10101 3.123620 CTCAGTTCAGCCCGCTGC 61.124 66.667 11.92 0.00 43.31 5.25
4850 10102 3.123620 GCTCAGTTCAGCCCGCTG 61.124 66.667 10.52 10.52 44.86 5.18
4851 10103 3.308014 GAGCTCAGTTCAGCCCGCT 62.308 63.158 9.40 0.00 40.65 5.52
4852 10104 2.817396 GAGCTCAGTTCAGCCCGC 60.817 66.667 9.40 0.00 40.65 6.13
4853 10105 2.507992 CGAGCTCAGTTCAGCCCG 60.508 66.667 15.40 0.00 40.65 6.13
4854 10106 1.446966 GTCGAGCTCAGTTCAGCCC 60.447 63.158 15.40 0.00 40.65 5.19
4855 10107 1.446966 GGTCGAGCTCAGTTCAGCC 60.447 63.158 15.40 0.77 40.65 4.85
4856 10108 0.735632 CAGGTCGAGCTCAGTTCAGC 60.736 60.000 15.54 1.34 39.99 4.26
4857 10109 0.600557 ACAGGTCGAGCTCAGTTCAG 59.399 55.000 15.54 4.16 0.00 3.02
4858 10110 1.540267 GTACAGGTCGAGCTCAGTTCA 59.460 52.381 15.54 0.00 0.00 3.18
4859 10111 1.466024 CGTACAGGTCGAGCTCAGTTC 60.466 57.143 15.54 7.81 0.00 3.01
4860 10112 0.522180 CGTACAGGTCGAGCTCAGTT 59.478 55.000 15.54 2.01 0.00 3.16
4861 10113 0.605860 ACGTACAGGTCGAGCTCAGT 60.606 55.000 15.54 13.26 0.00 3.41
4867 10119 1.801913 GCTGCACGTACAGGTCGAG 60.802 63.158 17.32 0.00 38.16 4.04
4893 10145 0.105039 CAGATAAGGTGAGGCGGACC 59.895 60.000 0.04 0.04 0.00 4.46
4933 10185 4.624364 CTCGCAGCCACACCCACA 62.624 66.667 0.00 0.00 0.00 4.17
4938 10190 3.702048 TACCCCTCGCAGCCACAC 61.702 66.667 0.00 0.00 0.00 3.82
4939 10191 3.702048 GTACCCCTCGCAGCCACA 61.702 66.667 0.00 0.00 0.00 4.17
4940 10192 3.665675 CTGTACCCCTCGCAGCCAC 62.666 68.421 0.00 0.00 0.00 5.01
4941 10193 3.390521 CTGTACCCCTCGCAGCCA 61.391 66.667 0.00 0.00 0.00 4.75
4942 10194 4.840005 GCTGTACCCCTCGCAGCC 62.840 72.222 4.60 0.00 46.93 4.85
4944 10196 2.185350 CAGCTGTACCCCTCGCAG 59.815 66.667 5.25 0.00 0.00 5.18
4945 10197 2.603473 ACAGCTGTACCCCTCGCA 60.603 61.111 20.16 0.00 0.00 5.10
4946 10198 2.125512 CACAGCTGTACCCCTCGC 60.126 66.667 21.20 0.00 0.00 5.03
4947 10199 2.125512 GCACAGCTGTACCCCTCG 60.126 66.667 21.20 6.37 0.00 4.63
4948 10200 2.125512 CGCACAGCTGTACCCCTC 60.126 66.667 21.20 3.89 0.00 4.30
4949 10201 3.706373 CCGCACAGCTGTACCCCT 61.706 66.667 21.20 0.00 0.00 4.79
4964 10216 3.688475 CTTCCATTGCTTGGCGCCG 62.688 63.158 23.90 9.82 46.01 6.46
4965 10217 2.182537 CTTCCATTGCTTGGCGCC 59.817 61.111 22.73 22.73 46.01 6.53
4966 10218 2.182537 CCTTCCATTGCTTGGCGC 59.817 61.111 0.00 0.00 46.01 6.53
4967 10219 2.182537 GCCTTCCATTGCTTGGCG 59.817 61.111 1.73 0.00 46.01 5.69
4968 10220 2.182537 CGCCTTCCATTGCTTGGC 59.817 61.111 1.73 0.00 46.01 4.52
4969 10221 1.937546 GGACGCCTTCCATTGCTTGG 61.938 60.000 0.23 0.23 45.10 3.61
4970 10222 1.508088 GGACGCCTTCCATTGCTTG 59.492 57.895 0.00 0.00 45.10 4.01
4971 10223 4.002797 GGACGCCTTCCATTGCTT 57.997 55.556 0.00 0.00 45.10 3.91
5011 10263 1.423845 GTGTGGAATGCGCTTACCG 59.576 57.895 9.73 0.00 40.75 4.02
5012 10264 1.296056 ACGTGTGGAATGCGCTTACC 61.296 55.000 9.73 9.65 0.00 2.85
5013 10265 0.094730 GACGTGTGGAATGCGCTTAC 59.905 55.000 9.73 1.49 0.00 2.34
5014 10266 1.348538 CGACGTGTGGAATGCGCTTA 61.349 55.000 9.73 0.00 0.00 3.09
5015 10267 2.667318 CGACGTGTGGAATGCGCTT 61.667 57.895 9.73 0.00 0.00 4.68
5016 10268 3.112075 CGACGTGTGGAATGCGCT 61.112 61.111 9.73 0.00 0.00 5.92
5017 10269 2.950172 AACGACGTGTGGAATGCGC 61.950 57.895 0.00 0.00 0.00 6.09
5018 10270 1.154672 CAACGACGTGTGGAATGCG 60.155 57.895 0.00 0.00 0.00 4.73
5019 10271 1.206578 CCAACGACGTGTGGAATGC 59.793 57.895 18.55 0.00 0.00 3.56
5020 10272 1.206578 GCCAACGACGTGTGGAATG 59.793 57.895 24.21 9.92 0.00 2.67
5021 10273 2.314647 CGCCAACGACGTGTGGAAT 61.315 57.895 24.21 0.00 43.93 3.01
5022 10274 2.962786 CGCCAACGACGTGTGGAA 60.963 61.111 24.21 0.00 43.93 3.53


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

AutoCloner maintained by Alex Coulton.