Multiple sequence alignment - TraesCS5A01G089900

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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 TraesCS5A01G089900 chr5A 100.000 6799 0 0 2499 9297 120747128 120753926 0.000000e+00 12556.0
1 TraesCS5A01G089900 chr5A 100.000 2223 0 0 1 2223 120744630 120746852 0.000000e+00 4106.0
2 TraesCS5A01G089900 chr5A 80.000 485 71 14 8809 9271 121113342 121113822 1.500000e-87 335.0
3 TraesCS5A01G089900 chr5A 80.244 410 76 5 1 408 573814865 573815271 4.220000e-78 303.0
4 TraesCS5A01G089900 chr5D 97.290 3469 76 15 5818 9274 114894088 114897550 0.000000e+00 5869.0
5 TraesCS5A01G089900 chr5D 98.054 3289 45 7 2543 5818 114890753 114894035 0.000000e+00 5701.0
6 TraesCS5A01G089900 chr5D 94.182 1564 51 17 689 2223 114888846 114890398 0.000000e+00 2348.0
7 TraesCS5A01G089900 chr5D 79.806 515 80 14 8773 9267 115021021 115021531 4.130000e-93 353.0
8 TraesCS5A01G089900 chr5B 97.925 3325 57 8 2499 5818 126240761 126244078 0.000000e+00 5747.0
9 TraesCS5A01G089900 chr5B 97.563 2503 52 9 6777 9274 126245266 126247764 0.000000e+00 4276.0
10 TraesCS5A01G089900 chr5B 90.612 2141 141 24 118 2223 126238598 126240713 0.000000e+00 2785.0
11 TraesCS5A01G089900 chr5B 97.718 964 15 4 5818 6780 126244131 126245088 0.000000e+00 1652.0
12 TraesCS5A01G089900 chr5B 79.435 496 78 15 8773 9248 126294341 126294832 6.960000e-86 329.0
13 TraesCS5A01G089900 chr5B 94.030 67 3 1 5752 5818 155715225 155715160 5.940000e-17 100.0
14 TraesCS5A01G089900 chr3D 83.415 410 65 3 1 408 5358671 5359079 2.450000e-100 377.0
15 TraesCS5A01G089900 chr4A 83.627 397 60 5 1 393 537537424 537537819 1.470000e-97 368.0
16 TraesCS5A01G089900 chr1D 81.752 411 72 3 1 408 347408165 347407755 3.220000e-89 340.0
17 TraesCS5A01G089900 chr1D 80.241 415 78 4 1 413 218683874 218684286 9.070000e-80 309.0
18 TraesCS5A01G089900 chr1D 90.541 74 6 1 5746 5819 471593844 471593772 7.680000e-16 97.1
19 TraesCS5A01G089900 chr1B 80.488 410 77 3 1 408 312554972 312555380 2.520000e-80 311.0
20 TraesCS5A01G089900 chr4D 80.296 406 76 4 1 404 8155096 8154693 4.220000e-78 303.0
21 TraesCS5A01G089900 chr7B 79.854 412 75 7 1 408 464533884 464534291 2.540000e-75 294.0
22 TraesCS5A01G089900 chr6A 96.825 63 2 0 5756 5818 27188894 27188956 1.280000e-18 106.0
23 TraesCS5A01G089900 chr6A 91.549 71 4 2 5745 5815 118284192 118284260 7.680000e-16 97.1
24 TraesCS5A01G089900 chr2A 96.875 64 1 1 5756 5818 446072051 446072114 1.280000e-18 106.0
25 TraesCS5A01G089900 chr2A 90.541 74 5 2 5743 5816 604860646 604860717 7.680000e-16 97.1
26 TraesCS5A01G089900 chr2A 100.000 29 0 0 9269 9297 706926133 706926105 5.000000e-03 54.7
27 TraesCS5A01G089900 chrUn 95.385 65 3 0 5754 5818 96471025 96471089 4.590000e-18 104.0


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 TraesCS5A01G089900 chr5A 120744630 120753926 9296 False 8331.000000 12556 100.000000 1 9297 2 chr5A.!!$F3 9296
1 TraesCS5A01G089900 chr5D 114888846 114897550 8704 False 4639.333333 5869 96.508667 689 9274 3 chr5D.!!$F2 8585
2 TraesCS5A01G089900 chr5D 115021021 115021531 510 False 353.000000 353 79.806000 8773 9267 1 chr5D.!!$F1 494
3 TraesCS5A01G089900 chr5B 126238598 126247764 9166 False 3615.000000 5747 95.954500 118 9274 4 chr5B.!!$F2 9156

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
366 368 0.107654 AAGTCCATAGGCTTGCCGAC 60.108 55.000 5.95 7.53 0.00 4.79 F
593 597 0.514255 CGTATCCGCGGATTCGTCTA 59.486 55.000 41.47 25.73 39.44 2.59 F
1391 1449 0.881118 TGAAATTGCGCTTCCCTGAC 59.119 50.000 9.73 0.00 0.00 3.51 F
2666 2786 1.267806 GGGATGCCAAATATGACAGCG 59.732 52.381 0.00 0.00 0.00 5.18 F
3766 3898 1.714794 GGACATGTCACTCGTCCTTG 58.285 55.000 26.47 0.00 44.82 3.61 F
5260 5393 0.611896 CGGCTGGACTTCCCCATTTT 60.612 55.000 0.00 0.00 35.33 1.82 F
5532 5665 1.651987 ATGCGATGGGAAAGTGTACG 58.348 50.000 0.00 0.00 0.00 3.67 F
6543 6729 1.747444 ACCCTTCCTTGGACACTGAT 58.253 50.000 0.00 0.00 0.00 2.90 F
6624 6810 3.316308 GCAGGCGGAATATTCATTGTTCT 59.684 43.478 17.07 5.99 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1370 1428 0.597568 CAGGGAAGCGCAATTTCACA 59.402 50.000 11.47 0.0 30.28 3.58 R
1804 1883 2.612721 CCACATTTGGCCCAAAAGCTAC 60.613 50.000 13.87 0.0 36.90 3.58 R
3135 3255 0.112412 AAGTCCAACCCCACATGACC 59.888 55.000 0.00 0.0 0.00 4.02 R
3777 3909 1.400142 CCTCGACAAAACACTGCAACA 59.600 47.619 0.00 0.0 0.00 3.33 R
5722 5855 0.392998 ACCACACATTCTCCCGATGC 60.393 55.000 0.00 0.0 0.00 3.91 R
6543 6729 1.380246 GCTCACATGGCCATTCCCA 60.380 57.895 17.92 0.0 39.65 4.37 R
7497 7869 5.862924 TTAACACACTAGCATTCAGAAGC 57.137 39.130 0.00 0.0 0.00 3.86 R
7729 8101 1.069022 CAACAGTCATGGCAAACCTCG 60.069 52.381 0.00 0.0 36.63 4.63 R
8359 8731 1.276622 ACGGATGGGCATAGGTATCC 58.723 55.000 0.00 0.0 36.56 2.59 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
37 38 4.704833 GCCTTGGAGCCGCAGTCA 62.705 66.667 0.00 0.00 0.00 3.41
38 39 2.270205 CCTTGGAGCCGCAGTCAT 59.730 61.111 0.00 0.00 0.00 3.06
39 40 1.817099 CCTTGGAGCCGCAGTCATC 60.817 63.158 0.00 0.00 0.00 2.92
40 41 2.125552 TTGGAGCCGCAGTCATCG 60.126 61.111 0.00 0.00 0.00 3.84
41 42 4.819761 TGGAGCCGCAGTCATCGC 62.820 66.667 0.00 0.00 0.00 4.58
48 49 2.815211 GCAGTCATCGCCGCTGAA 60.815 61.111 0.00 0.00 32.39 3.02
49 50 3.084579 CAGTCATCGCCGCTGAAC 58.915 61.111 0.00 0.00 32.39 3.18
50 51 2.125512 AGTCATCGCCGCTGAACC 60.126 61.111 0.00 0.00 0.00 3.62
51 52 3.195698 GTCATCGCCGCTGAACCC 61.196 66.667 0.00 0.00 0.00 4.11
52 53 3.390521 TCATCGCCGCTGAACCCT 61.391 61.111 0.00 0.00 0.00 4.34
53 54 2.436646 CATCGCCGCTGAACCCTT 60.437 61.111 0.00 0.00 0.00 3.95
54 55 2.436646 ATCGCCGCTGAACCCTTG 60.437 61.111 0.00 0.00 0.00 3.61
57 58 3.064324 GCCGCTGAACCCTTGCAT 61.064 61.111 0.00 0.00 0.00 3.96
58 59 1.748879 GCCGCTGAACCCTTGCATA 60.749 57.895 0.00 0.00 0.00 3.14
59 60 1.718757 GCCGCTGAACCCTTGCATAG 61.719 60.000 0.00 0.00 0.00 2.23
60 61 0.107703 CCGCTGAACCCTTGCATAGA 60.108 55.000 0.00 0.00 0.00 1.98
61 62 1.475751 CCGCTGAACCCTTGCATAGAT 60.476 52.381 0.00 0.00 0.00 1.98
62 63 1.869767 CGCTGAACCCTTGCATAGATC 59.130 52.381 0.00 0.00 0.00 2.75
63 64 2.484417 CGCTGAACCCTTGCATAGATCT 60.484 50.000 0.00 0.00 0.00 2.75
64 65 2.877168 GCTGAACCCTTGCATAGATCTG 59.123 50.000 5.18 0.00 0.00 2.90
65 66 3.432749 GCTGAACCCTTGCATAGATCTGA 60.433 47.826 5.18 0.00 0.00 3.27
66 67 4.774124 CTGAACCCTTGCATAGATCTGAA 58.226 43.478 5.18 0.00 0.00 3.02
67 68 5.178096 TGAACCCTTGCATAGATCTGAAA 57.822 39.130 5.18 0.00 0.00 2.69
68 69 4.943705 TGAACCCTTGCATAGATCTGAAAC 59.056 41.667 5.18 0.00 0.00 2.78
69 70 4.574674 ACCCTTGCATAGATCTGAAACA 57.425 40.909 5.18 0.00 0.00 2.83
70 71 4.265073 ACCCTTGCATAGATCTGAAACAC 58.735 43.478 5.18 0.00 0.00 3.32
71 72 3.629398 CCCTTGCATAGATCTGAAACACC 59.371 47.826 5.18 0.00 0.00 4.16
72 73 4.521146 CCTTGCATAGATCTGAAACACCT 58.479 43.478 5.18 0.00 0.00 4.00
73 74 4.334759 CCTTGCATAGATCTGAAACACCTG 59.665 45.833 5.18 0.00 0.00 4.00
74 75 4.824479 TGCATAGATCTGAAACACCTGA 57.176 40.909 5.18 0.00 0.00 3.86
75 76 4.507710 TGCATAGATCTGAAACACCTGAC 58.492 43.478 5.18 0.00 0.00 3.51
76 77 4.020307 TGCATAGATCTGAAACACCTGACA 60.020 41.667 5.18 0.00 0.00 3.58
77 78 4.331168 GCATAGATCTGAAACACCTGACAC 59.669 45.833 5.18 0.00 0.00 3.67
78 79 3.409026 AGATCTGAAACACCTGACACC 57.591 47.619 0.00 0.00 0.00 4.16
79 80 2.705658 AGATCTGAAACACCTGACACCA 59.294 45.455 0.00 0.00 0.00 4.17
80 81 3.136443 AGATCTGAAACACCTGACACCAA 59.864 43.478 0.00 0.00 0.00 3.67
81 82 3.358111 TCTGAAACACCTGACACCAAA 57.642 42.857 0.00 0.00 0.00 3.28
82 83 3.897239 TCTGAAACACCTGACACCAAAT 58.103 40.909 0.00 0.00 0.00 2.32
83 84 5.042463 TCTGAAACACCTGACACCAAATA 57.958 39.130 0.00 0.00 0.00 1.40
84 85 5.630121 TCTGAAACACCTGACACCAAATAT 58.370 37.500 0.00 0.00 0.00 1.28
85 86 6.068010 TCTGAAACACCTGACACCAAATATT 58.932 36.000 0.00 0.00 0.00 1.28
86 87 6.016360 TCTGAAACACCTGACACCAAATATTG 60.016 38.462 0.00 0.00 0.00 1.90
87 88 4.519540 AACACCTGACACCAAATATTGC 57.480 40.909 0.00 0.00 0.00 3.56
88 89 2.825532 ACACCTGACACCAAATATTGCC 59.174 45.455 0.00 0.00 0.00 4.52
89 90 2.824936 CACCTGACACCAAATATTGCCA 59.175 45.455 0.00 0.00 0.00 4.92
90 91 2.825532 ACCTGACACCAAATATTGCCAC 59.174 45.455 0.00 0.00 0.00 5.01
91 92 2.159393 CCTGACACCAAATATTGCCACG 60.159 50.000 0.00 0.00 0.00 4.94
92 93 2.746904 CTGACACCAAATATTGCCACGA 59.253 45.455 0.00 0.00 0.00 4.35
93 94 2.746904 TGACACCAAATATTGCCACGAG 59.253 45.455 0.00 0.00 0.00 4.18
94 95 3.006940 GACACCAAATATTGCCACGAGA 58.993 45.455 0.00 0.00 0.00 4.04
95 96 2.747446 ACACCAAATATTGCCACGAGAC 59.253 45.455 0.00 0.00 0.00 3.36
96 97 2.006888 ACCAAATATTGCCACGAGACG 58.993 47.619 0.00 0.00 0.00 4.18
97 98 2.276201 CCAAATATTGCCACGAGACGA 58.724 47.619 0.00 0.00 0.00 4.20
98 99 2.285220 CCAAATATTGCCACGAGACGAG 59.715 50.000 0.00 0.00 0.00 4.18
99 100 3.186909 CAAATATTGCCACGAGACGAGA 58.813 45.455 0.00 0.00 0.00 4.04
100 101 3.520290 AATATTGCCACGAGACGAGAA 57.480 42.857 0.00 0.00 0.00 2.87
101 102 3.520290 ATATTGCCACGAGACGAGAAA 57.480 42.857 0.00 0.00 0.00 2.52
102 103 1.429463 ATTGCCACGAGACGAGAAAC 58.571 50.000 0.00 0.00 0.00 2.78
103 104 0.599204 TTGCCACGAGACGAGAAACC 60.599 55.000 0.00 0.00 0.00 3.27
104 105 1.737008 GCCACGAGACGAGAAACCC 60.737 63.158 0.00 0.00 0.00 4.11
105 106 1.965219 CCACGAGACGAGAAACCCT 59.035 57.895 0.00 0.00 0.00 4.34
106 107 1.171308 CCACGAGACGAGAAACCCTA 58.829 55.000 0.00 0.00 0.00 3.53
107 108 1.542915 CCACGAGACGAGAAACCCTAA 59.457 52.381 0.00 0.00 0.00 2.69
108 109 2.593257 CACGAGACGAGAAACCCTAAC 58.407 52.381 0.00 0.00 0.00 2.34
109 110 1.543358 ACGAGACGAGAAACCCTAACC 59.457 52.381 0.00 0.00 0.00 2.85
110 111 1.817447 CGAGACGAGAAACCCTAACCT 59.183 52.381 0.00 0.00 0.00 3.50
111 112 2.230750 CGAGACGAGAAACCCTAACCTT 59.769 50.000 0.00 0.00 0.00 3.50
112 113 3.441572 CGAGACGAGAAACCCTAACCTTA 59.558 47.826 0.00 0.00 0.00 2.69
113 114 4.673841 CGAGACGAGAAACCCTAACCTTAC 60.674 50.000 0.00 0.00 0.00 2.34
114 115 3.513119 AGACGAGAAACCCTAACCTTACC 59.487 47.826 0.00 0.00 0.00 2.85
115 116 3.242011 ACGAGAAACCCTAACCTTACCA 58.758 45.455 0.00 0.00 0.00 3.25
116 117 3.842436 ACGAGAAACCCTAACCTTACCAT 59.158 43.478 0.00 0.00 0.00 3.55
127 128 4.302559 AACCTTACCATCCCAAAGAGAC 57.697 45.455 0.00 0.00 0.00 3.36
148 149 1.300233 CAGGAATCTACGCCGGAGC 60.300 63.158 5.05 0.00 0.00 4.70
151 152 1.007154 GAATCTACGCCGGAGCTCC 60.007 63.158 23.79 23.79 36.60 4.70
179 180 3.330766 GTCCAGACGGATGAACTCG 57.669 57.895 0.00 0.00 45.33 4.18
182 183 1.095600 CCAGACGGATGAACTCGAGA 58.904 55.000 21.68 0.00 0.00 4.04
209 210 3.933955 TCGAAGTCCGAAAAACAAACTCA 59.066 39.130 0.00 0.00 45.43 3.41
210 211 4.033587 TCGAAGTCCGAAAAACAAACTCAG 59.966 41.667 0.00 0.00 45.43 3.35
212 213 5.485662 AAGTCCGAAAAACAAACTCAGAG 57.514 39.130 0.00 0.00 0.00 3.35
282 283 8.924511 AAAAACCCTAACCTAAACTACTAACC 57.075 34.615 0.00 0.00 0.00 2.85
284 285 5.580022 ACCCTAACCTAAACTACTAACCGA 58.420 41.667 0.00 0.00 0.00 4.69
285 286 6.016555 ACCCTAACCTAAACTACTAACCGAA 58.983 40.000 0.00 0.00 0.00 4.30
286 287 6.669591 ACCCTAACCTAAACTACTAACCGAAT 59.330 38.462 0.00 0.00 0.00 3.34
306 307 0.818296 CGGAGACACGAGAATTCCCT 59.182 55.000 0.65 0.00 35.47 4.20
317 318 2.573915 GAGAATTCCCTTCCCTGTCACT 59.426 50.000 0.65 0.00 34.11 3.41
318 319 3.775316 GAGAATTCCCTTCCCTGTCACTA 59.225 47.826 0.65 0.00 34.11 2.74
319 320 4.175962 AGAATTCCCTTCCCTGTCACTAA 58.824 43.478 0.65 0.00 34.11 2.24
330 331 2.992689 TCACTAACCGCCGGAGCA 60.993 61.111 11.71 0.00 39.83 4.26
354 356 0.622665 CAGAGGGAAGGCAAGTCCAT 59.377 55.000 4.56 0.00 36.83 3.41
366 368 0.107654 AAGTCCATAGGCTTGCCGAC 60.108 55.000 5.95 7.53 0.00 4.79
396 398 2.579410 GGGAAGAGTTTGCCTAACCA 57.421 50.000 0.00 0.00 41.28 3.67
397 399 2.160205 GGGAAGAGTTTGCCTAACCAC 58.840 52.381 0.00 0.00 41.28 4.16
420 423 6.944862 CACCTAGGGTTAGAGGTATTATACGT 59.055 42.308 14.81 0.00 44.54 3.57
427 430 7.168135 GGGTTAGAGGTATTATACGTTTTGACG 59.832 40.741 0.00 0.00 39.31 4.35
437 440 2.170770 ACGTTTTGACGTGCTTTTTCG 58.829 42.857 3.57 0.00 45.30 3.46
439 442 2.590712 CGTTTTGACGTGCTTTTTCGTT 59.409 40.909 0.00 0.00 40.39 3.85
447 450 3.242641 ACGTGCTTTTTCGTTTCTTCCTC 60.243 43.478 0.00 0.00 36.93 3.71
449 452 3.066203 GTGCTTTTTCGTTTCTTCCTCCA 59.934 43.478 0.00 0.00 0.00 3.86
452 455 4.554919 GCTTTTTCGTTTCTTCCTCCACTC 60.555 45.833 0.00 0.00 0.00 3.51
454 457 1.612676 TCGTTTCTTCCTCCACTCGA 58.387 50.000 0.00 0.00 0.00 4.04
459 462 2.125773 TCTTCCTCCACTCGACCTAC 57.874 55.000 0.00 0.00 0.00 3.18
461 464 2.842496 TCTTCCTCCACTCGACCTACTA 59.158 50.000 0.00 0.00 0.00 1.82
464 467 4.038271 TCCTCCACTCGACCTACTAAAA 57.962 45.455 0.00 0.00 0.00 1.52
467 470 6.189859 TCCTCCACTCGACCTACTAAAATTA 58.810 40.000 0.00 0.00 0.00 1.40
468 471 6.837568 TCCTCCACTCGACCTACTAAAATTAT 59.162 38.462 0.00 0.00 0.00 1.28
480 483 5.353394 ACTAAAATTATGCTCACCCGAGA 57.647 39.130 0.00 0.00 42.34 4.04
573 577 8.870075 AAGGTATAGGATTGAATGCTAATTCC 57.130 34.615 10.44 12.04 41.40 3.01
574 578 7.406104 AGGTATAGGATTGAATGCTAATTCCC 58.594 38.462 10.44 7.98 41.40 3.97
577 581 5.304686 AGGATTGAATGCTAATTCCCGTA 57.695 39.130 0.00 0.00 41.40 4.02
582 586 2.094762 ATGCTAATTCCCGTATCCGC 57.905 50.000 0.00 0.00 0.00 5.54
592 596 1.281960 CGTATCCGCGGATTCGTCT 59.718 57.895 41.47 25.80 39.44 4.18
593 597 0.514255 CGTATCCGCGGATTCGTCTA 59.486 55.000 41.47 25.73 39.44 2.59
596 600 1.849097 ATCCGCGGATTCGTCTAAAC 58.151 50.000 34.60 0.00 38.89 2.01
600 604 1.257936 CGCGGATTCGTCTAAACATGG 59.742 52.381 0.00 0.00 38.89 3.66
615 619 1.548719 ACATGGTCGGATCGTTTCAGA 59.451 47.619 0.00 0.00 0.00 3.27
616 620 2.168521 ACATGGTCGGATCGTTTCAGAT 59.831 45.455 0.00 0.00 31.01 2.90
617 621 2.579207 TGGTCGGATCGTTTCAGATC 57.421 50.000 0.00 0.00 44.62 2.75
624 628 3.641439 GATCGTTTCAGATCCGTGTTG 57.359 47.619 0.00 0.00 40.73 3.33
625 629 2.804697 TCGTTTCAGATCCGTGTTGA 57.195 45.000 0.00 0.00 0.00 3.18
626 630 3.100658 TCGTTTCAGATCCGTGTTGAA 57.899 42.857 0.00 0.00 0.00 2.69
627 631 3.057019 TCGTTTCAGATCCGTGTTGAAG 58.943 45.455 0.00 0.00 32.92 3.02
628 632 3.057019 CGTTTCAGATCCGTGTTGAAGA 58.943 45.455 0.00 0.00 32.92 2.87
629 633 3.679980 CGTTTCAGATCCGTGTTGAAGAT 59.320 43.478 0.00 0.00 32.92 2.40
630 634 4.152402 CGTTTCAGATCCGTGTTGAAGATT 59.848 41.667 0.00 0.00 32.92 2.40
631 635 5.334105 CGTTTCAGATCCGTGTTGAAGATTT 60.334 40.000 0.00 0.00 32.92 2.17
632 636 5.611796 TTCAGATCCGTGTTGAAGATTTG 57.388 39.130 0.00 0.00 0.00 2.32
633 637 3.436704 TCAGATCCGTGTTGAAGATTTGC 59.563 43.478 0.00 0.00 0.00 3.68
634 638 2.416547 AGATCCGTGTTGAAGATTTGCG 59.583 45.455 0.00 0.00 0.00 4.85
635 639 1.872388 TCCGTGTTGAAGATTTGCGA 58.128 45.000 0.00 0.00 0.00 5.10
636 640 2.214347 TCCGTGTTGAAGATTTGCGAA 58.786 42.857 0.00 0.00 0.00 4.70
637 641 2.614520 TCCGTGTTGAAGATTTGCGAAA 59.385 40.909 0.00 0.00 0.00 3.46
638 642 2.973224 CCGTGTTGAAGATTTGCGAAAG 59.027 45.455 0.00 0.00 0.00 2.62
639 643 3.303725 CCGTGTTGAAGATTTGCGAAAGA 60.304 43.478 0.00 0.00 0.00 2.52
640 644 4.278858 CGTGTTGAAGATTTGCGAAAGAA 58.721 39.130 0.00 0.00 0.00 2.52
641 645 4.732923 CGTGTTGAAGATTTGCGAAAGAAA 59.267 37.500 0.00 0.00 0.00 2.52
642 646 5.229052 CGTGTTGAAGATTTGCGAAAGAAAA 59.771 36.000 0.00 0.00 44.16 2.29
643 647 6.237437 CGTGTTGAAGATTTGCGAAAGAAAAA 60.237 34.615 0.00 0.00 43.06 1.94
660 664 3.915437 AAAAATGTCCGCGTTGAAGAT 57.085 38.095 4.92 0.00 0.00 2.40
704 734 1.072331 ACCCTACTTGTCCACTTGCAG 59.928 52.381 0.00 0.00 0.00 4.41
785 826 9.683069 AGATCATACAAAACAAAAGAATCACAC 57.317 29.630 0.00 0.00 0.00 3.82
786 827 9.462174 GATCATACAAAACAAAAGAATCACACA 57.538 29.630 0.00 0.00 0.00 3.72
963 1019 1.826096 GGAATATACCTCCTCCGAGCC 59.174 57.143 0.00 0.00 34.49 4.70
964 1020 2.526432 GAATATACCTCCTCCGAGCCA 58.474 52.381 0.00 0.00 34.49 4.75
965 1021 2.696526 ATATACCTCCTCCGAGCCAA 57.303 50.000 0.00 0.00 34.49 4.52
966 1022 1.700955 TATACCTCCTCCGAGCCAAC 58.299 55.000 0.00 0.00 34.49 3.77
967 1023 1.049289 ATACCTCCTCCGAGCCAACC 61.049 60.000 0.00 0.00 34.49 3.77
1125 1183 1.957562 CGTCGTCCTCAAGTCCTGT 59.042 57.895 0.00 0.00 0.00 4.00
1165 1223 1.762460 AAGATCGGTCCGCATCCCT 60.762 57.895 6.34 0.00 0.00 4.20
1192 1250 2.044946 GCCCTTCCCGCTTCATGT 60.045 61.111 0.00 0.00 0.00 3.21
1370 1428 2.671070 CTTGCGACCCTGACCCAT 59.329 61.111 0.00 0.00 0.00 4.00
1371 1429 1.746615 CTTGCGACCCTGACCCATG 60.747 63.158 0.00 0.00 0.00 3.66
1372 1430 2.469465 CTTGCGACCCTGACCCATGT 62.469 60.000 0.00 0.00 0.00 3.21
1373 1431 2.436646 GCGACCCTGACCCATGTG 60.437 66.667 0.00 0.00 0.00 3.21
1391 1449 0.881118 TGAAATTGCGCTTCCCTGAC 59.119 50.000 9.73 0.00 0.00 3.51
1413 1471 2.238521 TCTTGGTCAGGTGAAAATGCC 58.761 47.619 0.00 0.00 0.00 4.40
1719 1795 4.510038 AATTGTCCAACTCATGTCAAGC 57.490 40.909 0.00 0.00 0.00 4.01
1743 1819 4.098044 TGCGGAGGTCTTTCATCTAACTAG 59.902 45.833 0.00 0.00 0.00 2.57
1845 1924 2.076100 GATGCTGTGTCGGAACATTGA 58.924 47.619 0.00 0.00 37.81 2.57
2541 2626 4.202461 TGAACTTCTAAACAGTGGATGCCT 60.202 41.667 0.00 0.00 0.00 4.75
2582 2702 2.045047 TGAGAAGGAGAGGAAGGGTGAT 59.955 50.000 0.00 0.00 0.00 3.06
2648 2768 2.224079 GCTATGTTCACATATGCACGGG 59.776 50.000 1.58 0.00 38.09 5.28
2666 2786 1.267806 GGGATGCCAAATATGACAGCG 59.732 52.381 0.00 0.00 0.00 5.18
2686 2806 6.090783 CAGCGTATGACACTCTTACAACTAA 58.909 40.000 0.00 0.00 30.19 2.24
2838 2958 4.887655 GGTAGGGTTTTGGGACATCTTATG 59.112 45.833 0.00 0.00 39.30 1.90
3043 3163 2.668457 GGCTTCTGTGTCTGTTGTATCG 59.332 50.000 0.00 0.00 0.00 2.92
3135 3255 6.489127 TTTTGTGATTAACTGGACATACCG 57.511 37.500 0.00 0.00 42.61 4.02
3260 3391 8.445588 AGGAGAGTTTGAATTAGGAAACCTTAA 58.554 33.333 0.00 0.00 34.61 1.85
3438 3570 6.233434 TCATGCACACTTCTTCTGTCTAATT 58.767 36.000 0.00 0.00 0.00 1.40
3766 3898 1.714794 GGACATGTCACTCGTCCTTG 58.285 55.000 26.47 0.00 44.82 3.61
3777 3909 7.778083 TGTCACTCGTCCTTGTATATTATTGT 58.222 34.615 0.00 0.00 0.00 2.71
3807 3939 2.742053 GTTTTGTCGAGGCAGCTAATCA 59.258 45.455 0.00 0.00 0.00 2.57
3841 3973 5.995446 ACCCTCATATTCTTGTCTCCTTTC 58.005 41.667 0.00 0.00 0.00 2.62
4120 4252 3.160269 AGTCCTTTTCCAGAAGCCATTG 58.840 45.455 0.00 0.00 0.00 2.82
4255 4387 7.777440 AGGAATTTGAAAAAGGCCATTTTGTTA 59.223 29.630 22.60 8.05 40.27 2.41
4542 4674 2.435069 TCCAGGTGAGTCAAACGGTTAA 59.565 45.455 0.00 0.00 0.00 2.01
4654 4786 2.589014 GGCGCTGCTGATATTTTATGC 58.411 47.619 7.64 0.00 0.00 3.14
4842 4974 3.543680 TTGGTCTTATAGGTCTGCTGC 57.456 47.619 0.00 0.00 0.00 5.25
4922 5054 5.934625 ACCTCTGTTAGCATTGTTCTACAAG 59.065 40.000 0.00 0.00 41.94 3.16
5156 5289 5.155278 TCAAGCTTGCCAATGATGAAAAT 57.845 34.783 21.99 0.00 0.00 1.82
5260 5393 0.611896 CGGCTGGACTTCCCCATTTT 60.612 55.000 0.00 0.00 35.33 1.82
5265 5398 3.430790 GCTGGACTTCCCCATTTTTATGC 60.431 47.826 0.00 0.00 35.33 3.14
5416 5549 3.073650 AGTGGGTTTCAGCTTCAGATCTT 59.926 43.478 0.00 0.00 0.00 2.40
5480 5613 8.158169 TGCTTTTCATAAGATATGTTGGCTAG 57.842 34.615 0.00 0.00 0.00 3.42
5532 5665 1.651987 ATGCGATGGGAAAGTGTACG 58.348 50.000 0.00 0.00 0.00 3.67
5722 5855 5.450965 CCAGGCTTTGCTTCCTTGTATTATG 60.451 44.000 0.00 0.00 0.00 1.90
5723 5856 4.098501 AGGCTTTGCTTCCTTGTATTATGC 59.901 41.667 0.00 0.00 0.00 3.14
5768 5901 8.239478 ACAATCCTAAGTTATATACTCCCTCCA 58.761 37.037 0.00 0.00 35.54 3.86
5782 5915 5.256474 ACTCCCTCCATTCACAAATACAAG 58.744 41.667 0.00 0.00 0.00 3.16
5855 6041 4.644103 TGTATTAGTGAACGTAGGGAGC 57.356 45.455 0.00 0.00 0.00 4.70
6030 6216 5.424252 TGTACGGATTATCCTCAGAGGTTTT 59.576 40.000 16.65 5.57 36.53 2.43
6182 6368 2.515398 CAGTGCACCCAACCTCCA 59.485 61.111 14.63 0.00 0.00 3.86
6239 6425 9.832445 ACGAAAAATAGATGGTATAGACACAAT 57.168 29.630 0.00 0.00 0.00 2.71
6340 6526 2.404215 CGATAATGGGTCGAATTCGCT 58.596 47.619 22.90 5.23 41.40 4.93
6390 6576 7.704047 GCAGAGAGATTTGTCTTTTTGTTTCTT 59.296 33.333 0.00 0.00 0.00 2.52
6429 6615 9.643693 AATTTTTATATTGGAACTTCACAGCTG 57.356 29.630 13.48 13.48 0.00 4.24
6430 6616 7.759489 TTTTATATTGGAACTTCACAGCTGT 57.241 32.000 15.25 15.25 0.00 4.40
6431 6617 7.759489 TTTATATTGGAACTTCACAGCTGTT 57.241 32.000 18.94 1.07 0.00 3.16
6432 6618 8.856153 TTTATATTGGAACTTCACAGCTGTTA 57.144 30.769 18.94 6.64 0.00 2.41
6435 6621 6.655078 ATTGGAACTTCACAGCTGTTAAAT 57.345 33.333 18.94 1.94 0.00 1.40
6543 6729 1.747444 ACCCTTCCTTGGACACTGAT 58.253 50.000 0.00 0.00 0.00 2.90
6624 6810 3.316308 GCAGGCGGAATATTCATTGTTCT 59.684 43.478 17.07 5.99 0.00 3.01
6700 6886 6.710744 TCTCAGTGCTGTAGATATCGATGTAA 59.289 38.462 8.54 0.00 0.00 2.41
6972 7344 6.852858 AAGCTCAGTCTTCTAAAAGTGTTC 57.147 37.500 0.00 0.00 33.95 3.18
7172 7544 9.556030 GTATGCTTCCTTTTATTACTTGTCAAC 57.444 33.333 0.00 0.00 0.00 3.18
7497 7869 9.599866 TTGTTTGTTAGACAGATATATGTGAGG 57.400 33.333 16.26 0.00 32.25 3.86
7729 8101 0.249073 AGCGCCATCGTCACAGATAC 60.249 55.000 2.29 0.00 38.14 2.24
7821 8193 7.122650 CCTTATGCTCCTTGGAAGTGATAAAAA 59.877 37.037 0.00 0.00 0.00 1.94
8177 8549 2.101415 GCCATAATTTGCCCCTGTTCTC 59.899 50.000 0.00 0.00 0.00 2.87
8196 8568 7.136772 TGTTCTCGTTTATCACCGTGATATAG 58.863 38.462 19.60 14.60 38.94 1.31
8359 8731 0.322187 ATCCCCGAACGTTTTCCTGG 60.322 55.000 0.46 0.00 0.00 4.45
8444 8816 2.121786 CAATGTGTGTGCAGTTCAAGC 58.878 47.619 0.00 0.00 0.00 4.01
8557 8929 4.814234 GTGGCTTAACCGATCATCATACAA 59.186 41.667 0.00 0.00 43.94 2.41
8579 8951 1.158434 GGGTCGTAATTTCGTTGGCA 58.842 50.000 4.34 0.00 0.00 4.92
8580 8952 1.135888 GGGTCGTAATTTCGTTGGCAC 60.136 52.381 4.34 0.00 0.00 5.01
8583 8955 3.223157 GTCGTAATTTCGTTGGCACTTG 58.777 45.455 4.34 0.00 0.00 3.16
8585 8957 3.059461 TCGTAATTTCGTTGGCACTTGTC 60.059 43.478 4.34 0.00 0.00 3.18
8672 9045 8.853077 ATGATCATGTAAAGAGTTCTTTGACA 57.147 30.769 7.59 14.53 45.01 3.58
9002 9379 5.989168 TGTGTCCAAACATACAGTCTACAAG 59.011 40.000 0.00 0.00 37.81 3.16
9035 9421 5.683681 TGCACATCATATATCACAACCTGT 58.316 37.500 0.00 0.00 0.00 4.00
9052 9438 7.065803 CACAACCTGTCACCTAAGTTATAATGG 59.934 40.741 0.00 0.00 0.00 3.16
9075 9468 4.555708 GCACAAAACCATGATGTTACACGA 60.556 41.667 0.00 0.00 0.00 4.35
9112 9505 1.322538 AATGGGCCCGCTTGCTAAAG 61.323 55.000 19.37 0.00 36.41 1.85
9132 9525 1.412074 GGTTTCCATGATCCAGCCCAT 60.412 52.381 0.00 0.00 0.00 4.00
9146 9539 3.245016 CCAGCCCATGATAAGGATAAGCA 60.245 47.826 0.00 0.00 0.00 3.91
9248 9642 1.217244 CCCAGGCATGCTTTCTTGC 59.783 57.895 18.92 0.00 41.18 4.01
9255 9649 3.068560 GGCATGCTTTCTTGCAATTGAA 58.931 40.909 18.92 0.00 46.61 2.69
9271 9665 5.063817 GCAATTGAATAGGCACAAATGGTTC 59.936 40.000 10.34 0.00 30.55 3.62
9272 9666 4.433186 TTGAATAGGCACAAATGGTTCG 57.567 40.909 0.00 0.00 0.00 3.95
9274 9668 2.799126 ATAGGCACAAATGGTTCGGA 57.201 45.000 0.00 0.00 0.00 4.55
9275 9669 2.570415 TAGGCACAAATGGTTCGGAA 57.430 45.000 0.00 0.00 0.00 4.30
9276 9670 1.698506 AGGCACAAATGGTTCGGAAA 58.301 45.000 0.00 0.00 0.00 3.13
9277 9671 2.035632 AGGCACAAATGGTTCGGAAAA 58.964 42.857 0.00 0.00 0.00 2.29
9278 9672 2.632512 AGGCACAAATGGTTCGGAAAAT 59.367 40.909 0.00 0.00 0.00 1.82
9279 9673 2.736192 GGCACAAATGGTTCGGAAAATG 59.264 45.455 0.00 0.00 0.00 2.32
9280 9674 2.157474 GCACAAATGGTTCGGAAAATGC 59.843 45.455 0.00 0.00 0.00 3.56
9281 9675 2.736192 CACAAATGGTTCGGAAAATGCC 59.264 45.455 0.00 0.00 0.00 4.40
9282 9676 2.366916 ACAAATGGTTCGGAAAATGCCA 59.633 40.909 0.89 0.89 0.00 4.92
9283 9677 3.181461 ACAAATGGTTCGGAAAATGCCAA 60.181 39.130 2.39 0.00 32.54 4.52
9284 9678 2.741759 ATGGTTCGGAAAATGCCAAC 57.258 45.000 2.39 0.00 32.54 3.77
9285 9679 0.312416 TGGTTCGGAAAATGCCAACG 59.688 50.000 0.00 0.00 0.00 4.10
9286 9680 0.388006 GGTTCGGAAAATGCCAACGG 60.388 55.000 0.00 0.00 0.00 4.44
9287 9681 0.594110 GTTCGGAAAATGCCAACGGA 59.406 50.000 0.00 0.00 0.00 4.69
9288 9682 0.878416 TTCGGAAAATGCCAACGGAG 59.122 50.000 0.00 0.00 0.00 4.63
9289 9683 0.958382 TCGGAAAATGCCAACGGAGG 60.958 55.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.984193 ATGACTGCGGCTCCAAGGC 62.984 63.158 0.00 0.00 37.44 4.35
21 22 1.817099 GATGACTGCGGCTCCAAGG 60.817 63.158 0.00 0.00 0.00 3.61
22 23 2.169789 CGATGACTGCGGCTCCAAG 61.170 63.158 0.00 0.00 0.00 3.61
23 24 2.125552 CGATGACTGCGGCTCCAA 60.126 61.111 0.00 0.00 0.00 3.53
24 25 4.819761 GCGATGACTGCGGCTCCA 62.820 66.667 0.00 0.00 0.00 3.86
31 32 2.815211 TTCAGCGGCGATGACTGC 60.815 61.111 28.87 0.00 42.55 4.40
32 33 2.456119 GGTTCAGCGGCGATGACTG 61.456 63.158 28.87 16.39 0.00 3.51
33 34 2.125512 GGTTCAGCGGCGATGACT 60.126 61.111 28.87 2.53 0.00 3.41
34 35 3.195698 GGGTTCAGCGGCGATGAC 61.196 66.667 28.87 21.07 0.00 3.06
35 36 2.954684 AAGGGTTCAGCGGCGATGA 61.955 57.895 25.30 25.30 0.00 2.92
36 37 2.436646 AAGGGTTCAGCGGCGATG 60.437 61.111 20.57 20.57 0.00 3.84
37 38 2.436646 CAAGGGTTCAGCGGCGAT 60.437 61.111 12.98 0.00 0.00 4.58
40 41 1.718757 CTATGCAAGGGTTCAGCGGC 61.719 60.000 0.00 0.00 0.00 6.53
41 42 0.107703 TCTATGCAAGGGTTCAGCGG 60.108 55.000 0.00 0.00 0.00 5.52
42 43 1.869767 GATCTATGCAAGGGTTCAGCG 59.130 52.381 0.00 0.00 0.00 5.18
43 44 2.877168 CAGATCTATGCAAGGGTTCAGC 59.123 50.000 0.00 0.00 0.00 4.26
44 45 4.412796 TCAGATCTATGCAAGGGTTCAG 57.587 45.455 0.00 0.00 0.00 3.02
45 46 4.842531 TTCAGATCTATGCAAGGGTTCA 57.157 40.909 0.00 0.00 0.00 3.18
46 47 4.943705 TGTTTCAGATCTATGCAAGGGTTC 59.056 41.667 0.00 0.00 0.00 3.62
47 48 4.702131 GTGTTTCAGATCTATGCAAGGGTT 59.298 41.667 0.00 0.00 0.00 4.11
48 49 4.265073 GTGTTTCAGATCTATGCAAGGGT 58.735 43.478 0.00 0.00 0.00 4.34
49 50 3.629398 GGTGTTTCAGATCTATGCAAGGG 59.371 47.826 0.00 0.00 0.00 3.95
50 51 4.334759 CAGGTGTTTCAGATCTATGCAAGG 59.665 45.833 0.00 0.00 0.00 3.61
51 52 5.064452 GTCAGGTGTTTCAGATCTATGCAAG 59.936 44.000 0.00 0.00 0.00 4.01
52 53 4.937620 GTCAGGTGTTTCAGATCTATGCAA 59.062 41.667 0.00 0.00 0.00 4.08
53 54 4.020307 TGTCAGGTGTTTCAGATCTATGCA 60.020 41.667 0.00 0.00 0.00 3.96
54 55 4.331168 GTGTCAGGTGTTTCAGATCTATGC 59.669 45.833 0.00 0.00 0.00 3.14
55 56 4.872691 GGTGTCAGGTGTTTCAGATCTATG 59.127 45.833 0.00 0.00 0.00 2.23
56 57 4.532126 TGGTGTCAGGTGTTTCAGATCTAT 59.468 41.667 0.00 0.00 0.00 1.98
57 58 3.901222 TGGTGTCAGGTGTTTCAGATCTA 59.099 43.478 0.00 0.00 0.00 1.98
58 59 2.705658 TGGTGTCAGGTGTTTCAGATCT 59.294 45.455 0.00 0.00 0.00 2.75
59 60 3.126001 TGGTGTCAGGTGTTTCAGATC 57.874 47.619 0.00 0.00 0.00 2.75
60 61 3.576078 TTGGTGTCAGGTGTTTCAGAT 57.424 42.857 0.00 0.00 0.00 2.90
61 62 3.358111 TTTGGTGTCAGGTGTTTCAGA 57.642 42.857 0.00 0.00 0.00 3.27
62 63 5.964958 ATATTTGGTGTCAGGTGTTTCAG 57.035 39.130 0.00 0.00 0.00 3.02
63 64 5.508825 GCAATATTTGGTGTCAGGTGTTTCA 60.509 40.000 0.00 0.00 0.00 2.69
64 65 4.923281 GCAATATTTGGTGTCAGGTGTTTC 59.077 41.667 0.00 0.00 0.00 2.78
65 66 4.262420 GGCAATATTTGGTGTCAGGTGTTT 60.262 41.667 0.00 0.00 0.00 2.83
66 67 3.258123 GGCAATATTTGGTGTCAGGTGTT 59.742 43.478 0.00 0.00 0.00 3.32
67 68 2.825532 GGCAATATTTGGTGTCAGGTGT 59.174 45.455 0.00 0.00 0.00 4.16
68 69 2.824936 TGGCAATATTTGGTGTCAGGTG 59.175 45.455 0.00 0.00 0.00 4.00
69 70 2.825532 GTGGCAATATTTGGTGTCAGGT 59.174 45.455 0.00 0.00 28.01 4.00
70 71 2.159393 CGTGGCAATATTTGGTGTCAGG 60.159 50.000 0.00 0.00 28.01 3.86
71 72 2.746904 TCGTGGCAATATTTGGTGTCAG 59.253 45.455 0.00 0.00 28.01 3.51
72 73 2.746904 CTCGTGGCAATATTTGGTGTCA 59.253 45.455 0.00 0.00 0.00 3.58
73 74 3.006940 TCTCGTGGCAATATTTGGTGTC 58.993 45.455 0.00 0.00 0.00 3.67
74 75 2.747446 GTCTCGTGGCAATATTTGGTGT 59.253 45.455 0.00 0.00 0.00 4.16
75 76 2.223021 CGTCTCGTGGCAATATTTGGTG 60.223 50.000 0.00 0.00 0.00 4.17
76 77 2.006888 CGTCTCGTGGCAATATTTGGT 58.993 47.619 0.00 0.00 0.00 3.67
77 78 2.276201 TCGTCTCGTGGCAATATTTGG 58.724 47.619 0.00 0.00 0.00 3.28
78 79 3.186909 TCTCGTCTCGTGGCAATATTTG 58.813 45.455 0.00 0.00 0.00 2.32
79 80 3.520290 TCTCGTCTCGTGGCAATATTT 57.480 42.857 0.00 0.00 0.00 1.40
80 81 3.520290 TTCTCGTCTCGTGGCAATATT 57.480 42.857 0.00 0.00 0.00 1.28
81 82 3.187700 GTTTCTCGTCTCGTGGCAATAT 58.812 45.455 0.00 0.00 0.00 1.28
82 83 2.602878 GTTTCTCGTCTCGTGGCAATA 58.397 47.619 0.00 0.00 0.00 1.90
83 84 1.429463 GTTTCTCGTCTCGTGGCAAT 58.571 50.000 0.00 0.00 0.00 3.56
84 85 0.599204 GGTTTCTCGTCTCGTGGCAA 60.599 55.000 0.00 0.00 0.00 4.52
85 86 1.006571 GGTTTCTCGTCTCGTGGCA 60.007 57.895 0.00 0.00 0.00 4.92
86 87 1.737008 GGGTTTCTCGTCTCGTGGC 60.737 63.158 0.00 0.00 0.00 5.01
87 88 1.171308 TAGGGTTTCTCGTCTCGTGG 58.829 55.000 0.00 0.00 0.00 4.94
88 89 2.593257 GTTAGGGTTTCTCGTCTCGTG 58.407 52.381 0.00 0.00 0.00 4.35
89 90 1.543358 GGTTAGGGTTTCTCGTCTCGT 59.457 52.381 0.00 0.00 0.00 4.18
90 91 1.817447 AGGTTAGGGTTTCTCGTCTCG 59.183 52.381 0.00 0.00 0.00 4.04
91 92 3.957591 AAGGTTAGGGTTTCTCGTCTC 57.042 47.619 0.00 0.00 0.00 3.36
92 93 3.513119 GGTAAGGTTAGGGTTTCTCGTCT 59.487 47.826 0.00 0.00 0.00 4.18
93 94 3.259123 TGGTAAGGTTAGGGTTTCTCGTC 59.741 47.826 0.00 0.00 0.00 4.20
94 95 3.242011 TGGTAAGGTTAGGGTTTCTCGT 58.758 45.455 0.00 0.00 0.00 4.18
95 96 3.967332 TGGTAAGGTTAGGGTTTCTCG 57.033 47.619 0.00 0.00 0.00 4.04
96 97 4.384978 GGGATGGTAAGGTTAGGGTTTCTC 60.385 50.000 0.00 0.00 0.00 2.87
97 98 3.526430 GGGATGGTAAGGTTAGGGTTTCT 59.474 47.826 0.00 0.00 0.00 2.52
98 99 3.267551 TGGGATGGTAAGGTTAGGGTTTC 59.732 47.826 0.00 0.00 0.00 2.78
99 100 3.270812 TGGGATGGTAAGGTTAGGGTTT 58.729 45.455 0.00 0.00 0.00 3.27
100 101 2.937442 TGGGATGGTAAGGTTAGGGTT 58.063 47.619 0.00 0.00 0.00 4.11
101 102 2.672703 TGGGATGGTAAGGTTAGGGT 57.327 50.000 0.00 0.00 0.00 4.34
102 103 3.526019 TCTTTGGGATGGTAAGGTTAGGG 59.474 47.826 0.00 0.00 0.00 3.53
103 104 4.473559 TCTCTTTGGGATGGTAAGGTTAGG 59.526 45.833 0.00 0.00 0.00 2.69
104 105 5.429130 GTCTCTTTGGGATGGTAAGGTTAG 58.571 45.833 0.00 0.00 0.00 2.34
105 106 4.081309 CGTCTCTTTGGGATGGTAAGGTTA 60.081 45.833 0.00 0.00 0.00 2.85
106 107 3.307480 CGTCTCTTTGGGATGGTAAGGTT 60.307 47.826 0.00 0.00 0.00 3.50
107 108 2.236395 CGTCTCTTTGGGATGGTAAGGT 59.764 50.000 0.00 0.00 0.00 3.50
108 109 2.420129 CCGTCTCTTTGGGATGGTAAGG 60.420 54.545 0.00 0.00 35.70 2.69
109 110 2.906354 CCGTCTCTTTGGGATGGTAAG 58.094 52.381 0.00 0.00 35.70 2.34
110 111 1.065709 GCCGTCTCTTTGGGATGGTAA 60.066 52.381 7.44 0.00 40.80 2.85
111 112 0.539986 GCCGTCTCTTTGGGATGGTA 59.460 55.000 7.44 0.00 40.80 3.25
112 113 1.299976 GCCGTCTCTTTGGGATGGT 59.700 57.895 7.44 0.00 40.80 3.55
113 114 0.745845 CTGCCGTCTCTTTGGGATGG 60.746 60.000 1.48 1.48 41.43 3.51
114 115 0.745845 CCTGCCGTCTCTTTGGGATG 60.746 60.000 0.00 0.00 0.00 3.51
115 116 0.909610 TCCTGCCGTCTCTTTGGGAT 60.910 55.000 0.00 0.00 0.00 3.85
116 117 1.125093 TTCCTGCCGTCTCTTTGGGA 61.125 55.000 0.00 0.00 0.00 4.37
190 191 5.183228 TCTCTGAGTTTGTTTTTCGGACTT 58.817 37.500 4.32 0.00 0.00 3.01
197 198 5.007724 CCGCTACTTCTCTGAGTTTGTTTTT 59.992 40.000 4.32 0.00 0.00 1.94
200 201 3.654414 CCGCTACTTCTCTGAGTTTGTT 58.346 45.455 4.32 0.00 0.00 2.83
201 202 2.610727 GCCGCTACTTCTCTGAGTTTGT 60.611 50.000 4.32 5.13 0.00 2.83
209 210 2.356818 GATGGCGCCGCTACTTCTCT 62.357 60.000 23.90 0.00 0.00 3.10
210 211 1.951631 GATGGCGCCGCTACTTCTC 60.952 63.158 23.90 4.24 0.00 2.87
212 213 2.967615 GGATGGCGCCGCTACTTC 60.968 66.667 23.90 11.01 0.00 3.01
257 258 7.661437 CGGTTAGTAGTTTAGGTTAGGGTTTTT 59.339 37.037 0.00 0.00 0.00 1.94
282 283 2.476873 ATTCTCGTGTCTCCGATTCG 57.523 50.000 0.00 0.00 36.08 3.34
284 285 2.159085 GGGAATTCTCGTGTCTCCGATT 60.159 50.000 5.23 0.00 36.08 3.34
285 286 1.409427 GGGAATTCTCGTGTCTCCGAT 59.591 52.381 5.23 0.00 36.08 4.18
286 287 0.815734 GGGAATTCTCGTGTCTCCGA 59.184 55.000 5.23 0.00 35.22 4.55
294 295 1.555533 GACAGGGAAGGGAATTCTCGT 59.444 52.381 5.23 0.00 43.80 4.18
296 297 2.573915 AGTGACAGGGAAGGGAATTCTC 59.426 50.000 5.23 0.00 38.85 2.87
297 298 2.637165 AGTGACAGGGAAGGGAATTCT 58.363 47.619 5.23 0.00 38.07 2.40
299 300 3.010250 GGTTAGTGACAGGGAAGGGAATT 59.990 47.826 0.00 0.00 0.00 2.17
306 307 1.675219 GGCGGTTAGTGACAGGGAA 59.325 57.895 0.00 0.00 0.00 3.97
340 342 0.548510 AGCCTATGGACTTGCCTTCC 59.451 55.000 0.00 0.00 37.63 3.46
342 344 2.134789 CAAGCCTATGGACTTGCCTT 57.865 50.000 0.00 0.00 37.11 4.35
354 356 0.034337 AAACTTCGTCGGCAAGCCTA 59.966 50.000 9.73 0.00 0.00 3.93
366 368 1.884235 ACTCTTCCCTGCAAACTTCG 58.116 50.000 0.00 0.00 0.00 3.79
375 377 2.224769 TGGTTAGGCAAACTCTTCCCTG 60.225 50.000 1.75 0.00 38.23 4.45
377 379 2.160205 GTGGTTAGGCAAACTCTTCCC 58.840 52.381 1.75 0.00 38.23 3.97
379 381 3.141767 AGGTGGTTAGGCAAACTCTTC 57.858 47.619 1.75 0.00 38.23 2.87
391 393 5.756314 ATACCTCTAACCCTAGGTGGTTA 57.244 43.478 8.29 9.02 46.70 2.85
394 396 6.376581 CGTATAATACCTCTAACCCTAGGTGG 59.623 46.154 8.29 2.67 45.75 4.61
397 399 8.414629 AAACGTATAATACCTCTAACCCTAGG 57.585 38.462 0.06 0.06 38.93 3.02
420 423 4.477780 AGAAACGAAAAAGCACGTCAAAA 58.522 34.783 0.00 0.00 41.87 2.44
427 430 3.066203 TGGAGGAAGAAACGAAAAAGCAC 59.934 43.478 0.00 0.00 0.00 4.40
437 440 1.619332 AGGTCGAGTGGAGGAAGAAAC 59.381 52.381 0.00 0.00 0.00 2.78
439 442 2.041350 AGTAGGTCGAGTGGAGGAAGAA 59.959 50.000 0.00 0.00 0.00 2.52
447 450 6.281405 AGCATAATTTTAGTAGGTCGAGTGG 58.719 40.000 0.00 0.00 0.00 4.00
449 452 6.979238 GTGAGCATAATTTTAGTAGGTCGAGT 59.021 38.462 0.00 0.00 0.00 4.18
452 455 5.465724 GGGTGAGCATAATTTTAGTAGGTCG 59.534 44.000 0.00 0.00 0.00 4.79
454 457 5.129815 TCGGGTGAGCATAATTTTAGTAGGT 59.870 40.000 0.00 0.00 0.00 3.08
459 462 5.360591 AGTCTCGGGTGAGCATAATTTTAG 58.639 41.667 0.00 0.00 42.26 1.85
461 464 4.222124 AGTCTCGGGTGAGCATAATTTT 57.778 40.909 0.00 0.00 42.26 1.82
464 467 5.552870 AAATAGTCTCGGGTGAGCATAAT 57.447 39.130 0.00 0.00 42.26 1.28
467 470 3.243907 GCTAAATAGTCTCGGGTGAGCAT 60.244 47.826 0.00 0.00 42.26 3.79
468 471 2.100916 GCTAAATAGTCTCGGGTGAGCA 59.899 50.000 0.00 0.00 42.26 4.26
480 483 3.128589 CCGCCAAACATGTGCTAAATAGT 59.871 43.478 0.00 0.00 0.00 2.12
577 581 1.135527 TGTTTAGACGAATCCGCGGAT 59.864 47.619 34.60 34.60 39.95 4.18
582 586 2.534349 CGACCATGTTTAGACGAATCCG 59.466 50.000 0.00 0.00 42.50 4.18
587 591 2.223409 CGATCCGACCATGTTTAGACGA 60.223 50.000 0.00 0.00 0.00 4.20
592 596 3.927854 TGAAACGATCCGACCATGTTTA 58.072 40.909 0.00 0.00 33.27 2.01
593 597 2.742053 CTGAAACGATCCGACCATGTTT 59.258 45.455 0.00 0.00 35.61 2.83
596 600 2.293677 TCTGAAACGATCCGACCATG 57.706 50.000 0.00 0.00 0.00 3.66
615 619 2.422597 TCGCAAATCTTCAACACGGAT 58.577 42.857 0.00 0.00 0.00 4.18
616 620 1.872388 TCGCAAATCTTCAACACGGA 58.128 45.000 0.00 0.00 0.00 4.69
617 621 2.679355 TTCGCAAATCTTCAACACGG 57.321 45.000 0.00 0.00 0.00 4.94
618 622 3.872354 TCTTTCGCAAATCTTCAACACG 58.128 40.909 0.00 0.00 0.00 4.49
619 623 6.567769 TTTTCTTTCGCAAATCTTCAACAC 57.432 33.333 0.00 0.00 0.00 3.32
640 644 3.564511 CATCTTCAACGCGGACATTTTT 58.435 40.909 12.47 0.00 0.00 1.94
641 645 2.668279 GCATCTTCAACGCGGACATTTT 60.668 45.455 12.47 0.00 0.00 1.82
642 646 1.135689 GCATCTTCAACGCGGACATTT 60.136 47.619 12.47 0.00 0.00 2.32
643 647 0.447801 GCATCTTCAACGCGGACATT 59.552 50.000 12.47 0.00 0.00 2.71
644 648 1.369091 GGCATCTTCAACGCGGACAT 61.369 55.000 12.47 0.00 0.00 3.06
645 649 2.032634 GGCATCTTCAACGCGGACA 61.033 57.895 12.47 0.00 0.00 4.02
660 664 6.649141 GTGATGAATATTATGGAGTAACGGCA 59.351 38.462 0.00 0.00 0.00 5.69
785 826 0.234625 GTATGGTGCGTGTGTGTGTG 59.765 55.000 0.00 0.00 0.00 3.82
786 827 1.218875 CGTATGGTGCGTGTGTGTGT 61.219 55.000 0.00 0.00 0.00 3.72
922 973 4.150454 AGGGAGAGAGGCGGGGAG 62.150 72.222 0.00 0.00 0.00 4.30
1101 1159 3.263503 CTTGAGGACGACGCCGACA 62.264 63.158 0.00 1.48 39.50 4.35
1183 1241 4.665142 CGAGAAGTGAGAAAACATGAAGCG 60.665 45.833 0.00 0.00 0.00 4.68
1192 1250 1.416401 AGTGGGCGAGAAGTGAGAAAA 59.584 47.619 0.00 0.00 0.00 2.29
1370 1428 0.597568 CAGGGAAGCGCAATTTCACA 59.402 50.000 11.47 0.00 30.28 3.58
1371 1429 0.881118 TCAGGGAAGCGCAATTTCAC 59.119 50.000 11.47 6.02 0.00 3.18
1372 1430 0.881118 GTCAGGGAAGCGCAATTTCA 59.119 50.000 11.47 0.00 0.00 2.69
1373 1431 1.168714 AGTCAGGGAAGCGCAATTTC 58.831 50.000 11.47 4.49 0.00 2.17
1391 1449 3.305608 GGCATTTTCACCTGACCAAGAAG 60.306 47.826 0.00 0.00 0.00 2.85
1452 1510 8.882736 GCACCCAAAATTGAGGAAATAAATAAG 58.117 33.333 7.41 0.00 0.00 1.73
1485 1543 2.928731 GCATGCGATCTCCTTAGTAGCC 60.929 54.545 0.00 0.00 0.00 3.93
1490 1548 4.250116 ACTTAGCATGCGATCTCCTTAG 57.750 45.455 13.01 1.85 0.00 2.18
1719 1795 3.118956 AGTTAGATGAAAGACCTCCGCAG 60.119 47.826 0.00 0.00 0.00 5.18
1804 1883 2.612721 CCACATTTGGCCCAAAAGCTAC 60.613 50.000 13.87 0.00 36.90 3.58
1978 2063 6.366340 TGGGTCTGTAAAAACACAGGAAATA 58.634 36.000 3.61 0.00 44.98 1.40
2505 2590 3.070018 AGAAGTTCAAGCGACAATCAGG 58.930 45.455 5.50 0.00 0.00 3.86
2515 2600 5.693814 CATCCACTGTTTAGAAGTTCAAGC 58.306 41.667 5.50 0.98 0.00 4.01
2582 2702 3.055385 CCTGGACCGTCTTTCCAAGATAA 60.055 47.826 0.00 0.00 42.76 1.75
2648 2768 4.452114 TCATACGCTGTCATATTTGGCATC 59.548 41.667 0.00 0.00 36.73 3.91
3043 3163 8.770438 AATAGAGAAGAGAGACAATGTGAAAC 57.230 34.615 0.00 0.00 37.35 2.78
3135 3255 0.112412 AAGTCCAACCCCACATGACC 59.888 55.000 0.00 0.00 0.00 4.02
3137 3257 2.025416 CCATAAGTCCAACCCCACATGA 60.025 50.000 0.00 0.00 0.00 3.07
3260 3391 6.375455 ACTTTCGTGATGCAGATTCCTTAATT 59.625 34.615 0.00 0.00 0.00 1.40
3438 3570 0.107897 GTGCCGTGATCATGGTGGTA 60.108 55.000 30.22 14.78 39.68 3.25
3464 3596 0.912486 GGCACTACCAGGATGACCTT 59.088 55.000 0.00 0.00 45.36 3.50
3766 3898 9.405587 ACAAAACACTGCAACACAATAATATAC 57.594 29.630 0.00 0.00 0.00 1.47
3777 3909 1.400142 CCTCGACAAAACACTGCAACA 59.600 47.619 0.00 0.00 0.00 3.33
3841 3973 7.757624 TGTGTTGGCTTAGTTTTCTACAAAAAG 59.242 33.333 0.00 0.00 33.17 2.27
4120 4252 6.152831 ACATAGGAAAAACCAAGCCAGATTAC 59.847 38.462 0.00 0.00 42.04 1.89
4542 4674 9.941325 TTAACATTCATAAGCAATGGTTTTCAT 57.059 25.926 2.10 0.00 35.82 2.57
4690 4822 7.526608 TCTCTAACATTCATTAAAAGGCAACG 58.473 34.615 0.00 0.00 46.39 4.10
4922 5054 5.298777 AGCATGCAATCAATAAAGAGAGGAC 59.701 40.000 21.98 0.00 0.00 3.85
5079 5212 8.301730 TGTAATGTTTGTAACTAGGAAAGACG 57.698 34.615 0.00 0.00 0.00 4.18
5131 5264 4.811969 TCATCATTGGCAAGCTTGATTT 57.188 36.364 30.39 8.14 0.00 2.17
5156 5289 7.577303 AGCAGAAATCCTAGTTATTGGAATCA 58.423 34.615 0.00 0.00 35.81 2.57
5480 5613 2.613133 CGGGTCTACTGTGCTAGTACTC 59.387 54.545 12.42 0.00 40.89 2.59
5496 5629 4.304110 TCGCATATTAAGTTCATCGGGTC 58.696 43.478 0.00 0.00 0.00 4.46
5532 5665 3.753272 ACACCAACATGTCTATTGCTCAC 59.247 43.478 0.00 0.00 0.00 3.51
5722 5855 0.392998 ACCACACATTCTCCCGATGC 60.393 55.000 0.00 0.00 0.00 3.91
5723 5856 2.093711 TGTACCACACATTCTCCCGATG 60.094 50.000 0.00 0.00 30.04 3.84
5855 6041 6.708949 AGGGTTACAAGCGTATATAAATGGTG 59.291 38.462 0.00 0.00 0.00 4.17
5942 6128 2.567169 CCATGGAAGACTGTAGACCACA 59.433 50.000 5.56 0.00 33.38 4.17
6072 6258 8.630917 CATTTGCTCTGGAGAAATGATAAAGAT 58.369 33.333 18.97 0.00 37.70 2.40
6239 6425 7.497579 TGAAATTTTTAGACTGCAGTGTACTCA 59.502 33.333 27.27 15.35 0.00 3.41
6340 6526 6.590292 GCATAGTAGCTAATCTAAATTCGGCA 59.410 38.462 0.00 0.00 0.00 5.69
6390 6576 9.743057 CCAATATAAAAATTTGAATACGGCTCA 57.257 29.630 0.00 0.00 0.00 4.26
6432 6618 9.159364 CAGCATGCAGACACAGTATATATATTT 57.841 33.333 21.98 0.00 0.00 1.40
6435 6621 7.466746 TCAGCATGCAGACACAGTATATATA 57.533 36.000 21.98 0.00 34.76 0.86
6543 6729 1.380246 GCTCACATGGCCATTCCCA 60.380 57.895 17.92 0.00 39.65 4.37
7172 7544 8.525290 AAATCAGGGTCTACAAAGATAATTGG 57.475 34.615 0.00 0.00 34.56 3.16
7497 7869 5.862924 TTAACACACTAGCATTCAGAAGC 57.137 39.130 0.00 0.00 0.00 3.86
7729 8101 1.069022 CAACAGTCATGGCAAACCTCG 60.069 52.381 0.00 0.00 36.63 4.63
7973 8345 1.900016 TGCAAGCAGGTTCAGGCTG 60.900 57.895 8.58 8.58 40.93 4.85
8177 8549 4.090066 GCAGCTATATCACGGTGATAAACG 59.910 45.833 28.79 20.93 42.05 3.60
8196 8568 8.567285 ACCTTCATACCAAATTATATAGCAGC 57.433 34.615 0.00 0.00 0.00 5.25
8359 8731 1.276622 ACGGATGGGCATAGGTATCC 58.723 55.000 0.00 0.00 36.56 2.59
8370 8742 3.275617 TCCACTCATAAAACGGATGGG 57.724 47.619 0.00 0.00 0.00 4.00
8444 8816 1.532437 TGCTTTGACGACAAGCAGATG 59.468 47.619 15.95 0.00 36.27 2.90
8459 8831 4.520111 TGACTACATGATGCAAACTGCTTT 59.480 37.500 0.00 0.00 45.31 3.51
8557 8929 2.361789 CCAACGAAATTACGACCCCAT 58.638 47.619 0.00 0.00 37.03 4.00
8579 8951 3.909662 GCATGGCCATCGACAAGT 58.090 55.556 17.61 0.00 0.00 3.16
8672 9045 3.181418 CCATGGTAATAAAGAGGGGGCAT 60.181 47.826 2.57 0.00 0.00 4.40
8765 9141 9.297586 GTACTGTTCCGAAAAAGAAAGAAAATT 57.702 29.630 0.00 0.00 0.00 1.82
8766 9142 7.919091 GGTACTGTTCCGAAAAAGAAAGAAAAT 59.081 33.333 0.00 0.00 0.00 1.82
8782 9158 6.282199 TGAATAGAAGACTGGTACTGTTCC 57.718 41.667 0.00 0.00 41.64 3.62
8856 9232 3.349006 CTGCGTGCACCCACTGAC 61.349 66.667 12.15 0.00 39.86 3.51
9002 9379 2.267174 ATGATGTGCAGTATCAGGCC 57.733 50.000 16.14 0.00 37.91 5.19
9035 9421 7.094118 GGTTTTGTGCCATTATAACTTAGGTGA 60.094 37.037 0.00 0.00 0.00 4.02
9052 9438 3.668191 CGTGTAACATCATGGTTTTGTGC 59.332 43.478 0.00 0.00 35.74 4.57
9097 9490 1.532604 AAACCTTTAGCAAGCGGGCC 61.533 55.000 0.00 0.00 0.00 5.80
9112 9505 0.033208 TGGGCTGGATCATGGAAACC 60.033 55.000 0.00 0.00 0.00 3.27
9167 9560 3.340814 ACGATATGGCAAGATGATCCC 57.659 47.619 0.00 0.00 0.00 3.85
9176 9570 1.557371 TCTGGACCAACGATATGGCAA 59.443 47.619 0.00 0.00 44.75 4.52
9248 9642 5.289193 CGAACCATTTGTGCCTATTCAATTG 59.711 40.000 0.00 0.00 0.00 2.32
9255 9649 2.799126 TCCGAACCATTTGTGCCTAT 57.201 45.000 0.00 0.00 0.00 2.57
9271 9665 1.506262 CCTCCGTTGGCATTTTCCG 59.494 57.895 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.