Multiple sequence alignment - TraesCS5B01G182100

Loading Multiple Alignment...

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 TraesCS5B01G182100 chr5B 100.000 5433 0 0 1 5433 331656899 331651467 0.000000e+00 10033.0
1 TraesCS5B01G182100 chr5A 93.264 4528 221 35 934 5433 383466963 383462492 0.000000e+00 6595.0
2 TraesCS5B01G182100 chr5A 87.893 413 49 1 416 828 383467402 383466991 8.180000e-133 484.0
3 TraesCS5B01G182100 chr5A 88.672 256 17 4 1 250 383467646 383467397 8.840000e-78 302.0
4 TraesCS5B01G182100 chr5D 93.216 3405 172 21 416 3803 291253680 291250318 0.000000e+00 4953.0
5 TraesCS5B01G182100 chr5D 90.156 1280 81 19 3820 5094 291250255 291249016 0.000000e+00 1624.0
6 TraesCS5B01G182100 chr5D 88.446 251 22 4 1 250 291253919 291253675 4.110000e-76 296.0
7 TraesCS5B01G182100 chr5D 87.821 156 11 3 5286 5433 291248772 291248617 5.590000e-40 176.0
8 TraesCS5B01G182100 chr6D 94.875 761 33 1 2182 2936 415402286 415403046 0.000000e+00 1184.0
9 TraesCS5B01G182100 chr1B 92.513 187 11 3 230 415 668435283 668435467 1.160000e-66 265.0
10 TraesCS5B01G182100 chr1B 91.429 175 12 3 248 420 332091163 332091336 2.530000e-58 237.0
11 TraesCS5B01G182100 chr7D 91.061 179 13 3 248 423 87366530 87366352 7.030000e-59 239.0
12 TraesCS5B01G182100 chr7D 90.698 43 4 0 3898 3940 617641490 617641448 2.110000e-04 58.4
13 TraesCS5B01G182100 chr7B 92.169 166 12 1 251 415 680125161 680125326 3.270000e-57 233.0
14 TraesCS5B01G182100 chr3A 92.169 166 12 1 251 415 655726606 655726771 3.270000e-57 233.0
15 TraesCS5B01G182100 chr3D 88.485 165 16 3 252 415 96899797 96899635 4.290000e-46 196.0
16 TraesCS5B01G182100 chr2A 84.259 108 9 4 309 415 570185164 570185264 1.250000e-16 99.0
17 TraesCS5B01G182100 chr4B 84.946 93 11 3 3858 3948 489088145 489088054 2.080000e-14 91.6
18 TraesCS5B01G182100 chr4B 88.462 52 6 0 3898 3949 328329269 328329320 4.540000e-06 63.9
19 TraesCS5B01G182100 chr7A 83.333 66 10 1 3893 3957 55395634 55395569 5.880000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G182100 chr5B 331651467 331656899 5432 True 10033.000000 10033 100.00000 1 5433 1 chr5B.!!$R1 5432
1 TraesCS5B01G182100 chr5A 383462492 383467646 5154 True 2460.333333 6595 89.94300 1 5433 3 chr5A.!!$R1 5432
2 TraesCS5B01G182100 chr5D 291248617 291253919 5302 True 1762.250000 4953 89.90975 1 5433 4 chr5D.!!$R1 5432
3 TraesCS5B01G182100 chr6D 415402286 415403046 760 False 1184.000000 1184 94.87500 2182 2936 1 chr6D.!!$F1 754

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
275 283 0.034059 CGTAGCTAGGGATTGGCCAG 59.966 60.0 5.11 0.0 38.95 4.85 F
591 600 0.099968 CGCATTTGGCACCATCTGAG 59.900 55.0 0.00 0.0 45.17 3.35 F
867 876 0.375454 CGCCAACTTTCGACACAACA 59.625 50.0 0.00 0.0 0.00 3.33 F
1431 1440 0.677098 TCGACCTCTCCCAGAACGAG 60.677 60.0 0.00 0.0 0.00 4.18 F
2580 2589 0.768221 TTTCCCAGCTGGACCTGAGT 60.768 55.0 34.91 0.0 45.11 3.41 F
3208 3223 0.036022 GGCTGTCAAGAAGCTCTGGT 59.964 55.0 0.00 0.0 40.64 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1269 1278 0.985490 AGAGGGAATGGCTGGACTCC 60.985 60.0 0.00 0.0 0.00 3.85 R
2289 2298 0.318441 CAGAGAGGCGGTTGTTCTGA 59.682 55.0 0.00 0.0 37.96 3.27 R
2403 2412 0.817634 CGAACAGGTTCTTGGCACCA 60.818 55.0 10.17 0.0 36.67 4.17 R
2962 2977 0.321653 AAACCCATGAGCAGGACGAC 60.322 55.0 0.00 0.0 0.00 4.34 R
3921 4008 0.325933 CAAGCTCCAGGATGACCACA 59.674 55.0 0.00 0.0 39.69 4.17 R
4891 4985 0.610232 CAAGGGGAGGCCAAAGAGTG 60.610 60.0 5.01 0.0 0.00 3.51 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
21 22 3.393089 AATCTCCGTAATGGCTAGCTG 57.607 47.619 15.72 0.00 37.80 4.24
22 23 2.067365 TCTCCGTAATGGCTAGCTGA 57.933 50.000 15.72 1.67 37.80 4.26
100 101 1.655372 TGGCATGATCCCATCCGATA 58.345 50.000 0.00 0.00 0.00 2.92
102 103 2.290260 TGGCATGATCCCATCCGATAAC 60.290 50.000 0.00 0.00 0.00 1.89
103 104 2.290260 GGCATGATCCCATCCGATAACA 60.290 50.000 0.00 0.00 0.00 2.41
125 126 8.498054 AACATTACTCAATTCGAGATGAATGT 57.502 30.769 18.03 18.03 46.65 2.71
223 231 4.154176 TGGCCCTTGTAGCGTAGAATATA 58.846 43.478 0.00 0.00 0.00 0.86
224 232 4.775780 TGGCCCTTGTAGCGTAGAATATAT 59.224 41.667 0.00 0.00 0.00 0.86
225 233 5.247564 TGGCCCTTGTAGCGTAGAATATATT 59.752 40.000 0.00 0.00 0.00 1.28
226 234 6.438108 TGGCCCTTGTAGCGTAGAATATATTA 59.562 38.462 0.00 0.00 0.00 0.98
254 262 8.737168 TTTAAGAAATATCTGGATGGACAGTG 57.263 34.615 0.00 0.00 39.48 3.66
255 263 5.301835 AGAAATATCTGGATGGACAGTGG 57.698 43.478 0.00 0.00 39.48 4.00
256 264 3.498774 AATATCTGGATGGACAGTGGC 57.501 47.619 0.00 0.00 39.48 5.01
257 265 0.752658 TATCTGGATGGACAGTGGCG 59.247 55.000 0.00 0.00 39.48 5.69
258 266 1.267574 ATCTGGATGGACAGTGGCGT 61.268 55.000 0.00 0.00 39.48 5.68
259 267 0.613572 TCTGGATGGACAGTGGCGTA 60.614 55.000 0.00 0.00 39.48 4.42
260 268 0.179100 CTGGATGGACAGTGGCGTAG 60.179 60.000 0.00 0.00 33.81 3.51
274 282 2.133195 CGTAGCTAGGGATTGGCCA 58.867 57.895 0.00 0.00 38.95 5.36
275 283 0.034059 CGTAGCTAGGGATTGGCCAG 59.966 60.000 5.11 0.00 38.95 4.85
276 284 0.398318 GTAGCTAGGGATTGGCCAGG 59.602 60.000 5.11 0.00 38.95 4.45
277 285 0.768221 TAGCTAGGGATTGGCCAGGG 60.768 60.000 5.11 0.00 38.95 4.45
278 286 2.386935 GCTAGGGATTGGCCAGGGT 61.387 63.158 5.11 0.00 38.95 4.34
279 287 1.533711 CTAGGGATTGGCCAGGGTG 59.466 63.158 5.11 0.00 38.95 4.61
280 288 1.999634 CTAGGGATTGGCCAGGGTGG 62.000 65.000 5.11 0.00 41.55 4.61
281 289 2.798760 TAGGGATTGGCCAGGGTGGT 62.799 60.000 5.11 0.00 40.46 4.16
282 290 2.043953 GGATTGGCCAGGGTGGTC 60.044 66.667 5.11 0.00 43.98 4.02
283 291 2.043953 GATTGGCCAGGGTGGTCC 60.044 66.667 5.11 0.00 42.76 4.46
284 292 2.863484 ATTGGCCAGGGTGGTCCA 60.863 61.111 5.11 5.35 42.76 4.02
285 293 2.228841 GATTGGCCAGGGTGGTCCAT 62.229 60.000 5.11 0.00 42.76 3.41
286 294 2.519119 ATTGGCCAGGGTGGTCCATG 62.519 60.000 5.11 0.00 42.76 3.66
298 306 2.683916 GTCCATGGACCACTCTGGA 58.316 57.895 31.37 10.73 40.96 3.86
299 307 0.984230 GTCCATGGACCACTCTGGAA 59.016 55.000 31.37 0.00 40.96 3.53
300 308 1.561542 GTCCATGGACCACTCTGGAAT 59.438 52.381 31.37 0.00 40.96 3.01
301 309 2.025887 GTCCATGGACCACTCTGGAATT 60.026 50.000 31.37 0.00 40.96 2.17
302 310 2.649312 TCCATGGACCACTCTGGAATTT 59.351 45.455 11.44 0.00 40.96 1.82
303 311 3.019564 CCATGGACCACTCTGGAATTTC 58.980 50.000 5.56 0.00 40.96 2.17
304 312 2.879103 TGGACCACTCTGGAATTTCC 57.121 50.000 8.59 8.59 40.96 3.13
305 313 1.354368 TGGACCACTCTGGAATTTCCC 59.646 52.381 12.90 0.00 40.96 3.97
306 314 1.341089 GGACCACTCTGGAATTTCCCC 60.341 57.143 12.90 0.56 40.96 4.81
307 315 1.354368 GACCACTCTGGAATTTCCCCA 59.646 52.381 12.90 0.00 40.96 4.96
308 316 2.003072 ACCACTCTGGAATTTCCCCAT 58.997 47.619 12.90 0.00 40.96 4.00
309 317 3.197983 ACCACTCTGGAATTTCCCCATA 58.802 45.455 12.90 0.00 40.96 2.74
310 318 3.596046 ACCACTCTGGAATTTCCCCATAA 59.404 43.478 12.90 0.00 40.96 1.90
311 319 3.954258 CCACTCTGGAATTTCCCCATAAC 59.046 47.826 12.90 0.00 40.96 1.89
312 320 4.325344 CCACTCTGGAATTTCCCCATAACT 60.325 45.833 12.90 0.00 40.96 2.24
313 321 5.264395 CACTCTGGAATTTCCCCATAACTT 58.736 41.667 12.90 0.00 35.03 2.66
314 322 5.126061 CACTCTGGAATTTCCCCATAACTTG 59.874 44.000 12.90 0.00 35.03 3.16
315 323 5.222337 ACTCTGGAATTTCCCCATAACTTGT 60.222 40.000 12.90 0.00 35.03 3.16
316 324 6.011981 ACTCTGGAATTTCCCCATAACTTGTA 60.012 38.462 12.90 0.00 35.03 2.41
317 325 6.980577 TCTGGAATTTCCCCATAACTTGTAT 58.019 36.000 12.90 0.00 35.03 2.29
318 326 8.108378 TCTGGAATTTCCCCATAACTTGTATA 57.892 34.615 12.90 0.00 35.03 1.47
319 327 8.732854 TCTGGAATTTCCCCATAACTTGTATAT 58.267 33.333 12.90 0.00 35.03 0.86
327 335 9.664777 TTCCCCATAACTTGTATATAGTGTAGT 57.335 33.333 0.00 0.00 0.00 2.73
388 396 9.758651 GTAAATATTTTCATTAATGGACCACCC 57.241 33.333 15.36 0.00 34.81 4.61
389 397 8.622572 AAATATTTTCATTAATGGACCACCCT 57.377 30.769 15.36 0.00 35.38 4.34
390 398 5.937975 ATTTTCATTAATGGACCACCCTG 57.062 39.130 15.36 0.00 35.38 4.45
391 399 4.666412 TTTCATTAATGGACCACCCTGA 57.334 40.909 15.36 0.00 35.38 3.86
392 400 3.931907 TCATTAATGGACCACCCTGAG 57.068 47.619 15.36 0.00 35.38 3.35
393 401 3.189606 TCATTAATGGACCACCCTGAGT 58.810 45.455 15.36 0.00 35.38 3.41
394 402 4.367166 TCATTAATGGACCACCCTGAGTA 58.633 43.478 15.36 0.00 35.38 2.59
395 403 4.975147 TCATTAATGGACCACCCTGAGTAT 59.025 41.667 15.36 0.00 35.38 2.12
396 404 5.431731 TCATTAATGGACCACCCTGAGTATT 59.568 40.000 15.36 0.00 35.38 1.89
397 405 3.652057 AATGGACCACCCTGAGTATTG 57.348 47.619 0.00 0.00 35.38 1.90
398 406 1.285280 TGGACCACCCTGAGTATTGG 58.715 55.000 0.00 0.00 35.38 3.16
404 412 1.152881 CCCTGAGTATTGGGCTGGC 60.153 63.158 0.00 0.00 36.61 4.85
405 413 1.639635 CCCTGAGTATTGGGCTGGCT 61.640 60.000 0.00 0.00 36.61 4.75
406 414 1.131638 CCTGAGTATTGGGCTGGCTA 58.868 55.000 0.00 0.00 0.00 3.93
407 415 1.202698 CCTGAGTATTGGGCTGGCTAC 60.203 57.143 0.00 0.00 0.00 3.58
408 416 0.464036 TGAGTATTGGGCTGGCTACG 59.536 55.000 0.00 0.00 0.00 3.51
409 417 0.880718 GAGTATTGGGCTGGCTACGC 60.881 60.000 0.00 0.00 0.00 4.42
454 462 3.855689 GTCCTTTTGACATGTCCATGG 57.144 47.619 22.85 18.66 43.85 3.66
474 482 3.127895 TGGAACTCAACTTTTGTCAACCG 59.872 43.478 0.00 0.00 0.00 4.44
482 491 3.811083 ACTTTTGTCAACCGGTATGTCA 58.189 40.909 8.00 9.88 0.00 3.58
491 500 4.865925 TCAACCGGTATGTCAATAACTTCG 59.134 41.667 8.00 0.00 0.00 3.79
524 533 9.840427 CTTTAAAGAAGATATTGAAAGCCGAAA 57.160 29.630 9.77 0.00 0.00 3.46
528 537 6.789262 AGAAGATATTGAAAGCCGAAACATG 58.211 36.000 0.00 0.00 0.00 3.21
530 539 6.515272 AGATATTGAAAGCCGAAACATGTT 57.485 33.333 4.92 4.92 0.00 2.71
555 564 6.827762 TGCCAACACATATCATCTTCATAACA 59.172 34.615 0.00 0.00 0.00 2.41
556 565 7.338957 TGCCAACACATATCATCTTCATAACAA 59.661 33.333 0.00 0.00 0.00 2.83
566 575 7.878547 TCATCTTCATAACAACATGCCAATA 57.121 32.000 0.00 0.00 0.00 1.90
567 576 8.291191 TCATCTTCATAACAACATGCCAATAA 57.709 30.769 0.00 0.00 0.00 1.40
591 600 0.099968 CGCATTTGGCACCATCTGAG 59.900 55.000 0.00 0.00 45.17 3.35
602 611 4.142093 GGCACCATCTGAGCACAATAAAAT 60.142 41.667 0.00 0.00 0.00 1.82
612 621 9.013229 TCTGAGCACAATAAAATACAATGACTT 57.987 29.630 0.00 0.00 0.00 3.01
613 622 8.969121 TGAGCACAATAAAATACAATGACTTG 57.031 30.769 0.00 0.00 38.39 3.16
637 646 5.775686 CAAAGAGTTGAAGCCAATCAATGA 58.224 37.500 1.16 0.00 41.09 2.57
644 653 3.890756 TGAAGCCAATCAATGACACAACT 59.109 39.130 0.00 0.00 0.00 3.16
647 656 3.256631 AGCCAATCAATGACACAACTTCC 59.743 43.478 0.00 0.00 0.00 3.46
660 669 1.341209 CAACTTCCTTTTGCTCCCCAC 59.659 52.381 0.00 0.00 0.00 4.61
663 672 2.319844 CTTCCTTTTGCTCCCCACTTT 58.680 47.619 0.00 0.00 0.00 2.66
664 673 1.703411 TCCTTTTGCTCCCCACTTTG 58.297 50.000 0.00 0.00 0.00 2.77
676 685 2.422803 CCCCACTTTGTTGGAACAGAGA 60.423 50.000 15.01 0.00 42.04 3.10
680 689 4.023707 CCACTTTGTTGGAACAGAGACATC 60.024 45.833 15.01 0.00 42.04 3.06
684 693 7.012327 CACTTTGTTGGAACAGAGACATCTAAA 59.988 37.037 15.01 0.00 42.04 1.85
691 700 5.447818 GGAACAGAGACATCTAAAATTGCCG 60.448 44.000 0.00 0.00 33.22 5.69
698 707 3.880490 ACATCTAAAATTGCCGCCGATAA 59.120 39.130 0.00 0.00 0.00 1.75
723 732 7.765695 ATGTTACTCAATTCCACTTGAACAT 57.234 32.000 0.00 0.00 34.86 2.71
787 796 3.308705 GAACCCCCTCCGACACGT 61.309 66.667 0.00 0.00 0.00 4.49
798 807 0.793861 CCGACACGTGTTACCCAATG 59.206 55.000 24.26 5.54 0.00 2.82
802 811 2.873472 GACACGTGTTACCCAATGTGAA 59.127 45.455 24.26 0.00 36.00 3.18
846 855 1.973281 ACCACATGCTTCGCCCTTG 60.973 57.895 0.00 0.00 0.00 3.61
862 871 1.781025 CTTGGCGCCAACTTTCGACA 61.781 55.000 37.30 14.85 42.60 4.35
864 873 2.539338 GGCGCCAACTTTCGACACA 61.539 57.895 24.80 0.00 33.16 3.72
865 874 1.353804 GCGCCAACTTTCGACACAA 59.646 52.632 0.00 0.00 0.00 3.33
866 875 0.928451 GCGCCAACTTTCGACACAAC 60.928 55.000 0.00 0.00 0.00 3.32
867 876 0.375454 CGCCAACTTTCGACACAACA 59.625 50.000 0.00 0.00 0.00 3.33
868 877 1.002900 CGCCAACTTTCGACACAACAT 60.003 47.619 0.00 0.00 0.00 2.71
869 878 2.384382 GCCAACTTTCGACACAACATG 58.616 47.619 0.00 0.00 0.00 3.21
870 879 2.384382 CCAACTTTCGACACAACATGC 58.616 47.619 0.00 0.00 0.00 4.06
871 880 2.223456 CCAACTTTCGACACAACATGCA 60.223 45.455 0.00 0.00 0.00 3.96
872 881 3.433709 CAACTTTCGACACAACATGCAA 58.566 40.909 0.00 0.00 0.00 4.08
873 882 3.065019 ACTTTCGACACAACATGCAAC 57.935 42.857 0.00 0.00 0.00 4.17
874 883 2.223479 ACTTTCGACACAACATGCAACC 60.223 45.455 0.00 0.00 0.00 3.77
875 884 1.674359 TTCGACACAACATGCAACCT 58.326 45.000 0.00 0.00 0.00 3.50
876 885 1.225855 TCGACACAACATGCAACCTC 58.774 50.000 0.00 0.00 0.00 3.85
885 894 2.350522 ACATGCAACCTCTCGTCAATC 58.649 47.619 0.00 0.00 0.00 2.67
889 898 1.671850 GCAACCTCTCGTCAATCGGAA 60.672 52.381 0.00 0.00 40.32 4.30
973 982 2.158798 GGTACCCTTAGCCAAGATCCAC 60.159 54.545 0.00 0.00 33.20 4.02
974 983 1.668826 ACCCTTAGCCAAGATCCACA 58.331 50.000 0.00 0.00 33.20 4.17
975 984 1.992557 ACCCTTAGCCAAGATCCACAA 59.007 47.619 0.00 0.00 33.20 3.33
992 1001 1.355720 ACAACTCTCCTTCCCCAATGG 59.644 52.381 0.00 0.00 0.00 3.16
994 1003 2.576191 CAACTCTCCTTCCCCAATGGTA 59.424 50.000 0.00 0.00 34.77 3.25
998 1007 2.777692 TCTCCTTCCCCAATGGTATCAC 59.222 50.000 0.00 0.00 34.77 3.06
999 1008 2.780010 CTCCTTCCCCAATGGTATCACT 59.220 50.000 0.00 0.00 34.77 3.41
1000 1009 3.973973 CTCCTTCCCCAATGGTATCACTA 59.026 47.826 0.00 0.00 34.77 2.74
1001 1010 3.714798 TCCTTCCCCAATGGTATCACTAC 59.285 47.826 0.00 0.00 34.77 2.73
1002 1011 3.181443 CCTTCCCCAATGGTATCACTACC 60.181 52.174 0.00 0.00 46.65 3.18
1033 1042 1.237285 CGCTGACAAAACCAGGGAGG 61.237 60.000 0.00 0.00 44.33 4.30
1068 1077 2.727024 ACTCCCTCCTTAAAACCCCTT 58.273 47.619 0.00 0.00 0.00 3.95
1105 1114 4.366684 CTCCACCCACCAAGCCCC 62.367 72.222 0.00 0.00 0.00 5.80
1195 1204 1.201429 ACTCCCAATTGTCGCCTCCT 61.201 55.000 4.43 0.00 0.00 3.69
1206 1215 4.208686 GCCTCCTACGACGCCAGG 62.209 72.222 9.32 9.32 0.00 4.45
1327 1336 4.849310 GCGCCGGGCAATCTACCA 62.849 66.667 20.71 0.00 42.87 3.25
1353 1362 2.987125 GGGCTCTACCTCGGCAAA 59.013 61.111 0.00 0.00 39.10 3.68
1431 1440 0.677098 TCGACCTCTCCCAGAACGAG 60.677 60.000 0.00 0.00 0.00 4.18
1596 1605 3.528370 ATCTCCGGCGAGTTCCCG 61.528 66.667 9.30 0.00 45.17 5.14
1603 1612 2.342648 GCGAGTTCCCGTGGTTCT 59.657 61.111 0.00 0.00 0.00 3.01
2019 2028 4.821805 CACATTTACCAGAACAACCTGACT 59.178 41.667 0.00 0.00 36.29 3.41
2289 2298 3.382832 CTGACGAGGGTCCGGCTT 61.383 66.667 0.00 0.00 42.73 4.35
2403 2412 1.224592 GGTCGATCCTGCCATTGGT 59.775 57.895 4.26 0.00 0.00 3.67
2451 2460 1.416243 TACAGGACAACCGGTTCACT 58.584 50.000 19.24 12.91 41.49 3.41
2495 2504 2.288152 GGAATTTGTCCTTGCTGCGAAA 60.288 45.455 0.00 0.00 43.98 3.46
2520 2529 2.945008 TCTTGCCTCAGACAACAACTTG 59.055 45.455 0.00 0.00 0.00 3.16
2556 2565 2.564975 TCGGTCGTCGAGCTTTCC 59.435 61.111 21.01 5.86 43.74 3.13
2580 2589 0.768221 TTTCCCAGCTGGACCTGAGT 60.768 55.000 34.91 0.00 45.11 3.41
2583 2592 1.207791 CCCAGCTGGACCTGAGTAAT 58.792 55.000 34.91 0.00 37.39 1.89
2807 2816 4.530710 ACCTGTCGTATAACAAGCTCAA 57.469 40.909 0.00 0.00 0.00 3.02
2813 2822 4.868171 GTCGTATAACAAGCTCAATGGACA 59.132 41.667 0.00 0.00 0.00 4.02
3036 3051 4.520846 CGTGCCGCCGAAATCAGC 62.521 66.667 0.00 0.00 0.00 4.26
3165 3180 3.113043 AGGGAAGGTATACAAGGTGGTC 58.887 50.000 5.01 0.00 0.00 4.02
3178 3193 4.077184 TGGTCGTTGGGCCTAGCG 62.077 66.667 19.32 19.32 0.00 4.26
3208 3223 0.036022 GGCTGTCAAGAAGCTCTGGT 59.964 55.000 0.00 0.00 40.64 4.00
3271 3286 2.033141 CTGAGGTGGCCACACTGG 59.967 66.667 35.78 19.05 46.85 4.00
3294 3309 1.967319 ACGTCAGGCACAAGAACATT 58.033 45.000 0.00 0.00 0.00 2.71
3322 3337 1.153269 TTCTGCTGCGTGACCAACA 60.153 52.632 0.00 0.00 0.00 3.33
3339 3354 4.711949 AGCTCCTGCCGGTTGCTG 62.712 66.667 14.06 0.00 42.00 4.41
3484 3499 4.457496 ATGACTGCGTGCCCTCGG 62.457 66.667 0.00 0.00 0.00 4.63
3523 3538 4.095632 TCAAGTCGAACAACATTTTGCTCA 59.904 37.500 0.00 0.00 36.00 4.26
3706 3721 2.159430 TGTTGCACGCTTTATACTGCTG 59.841 45.455 0.00 0.00 0.00 4.41
3708 3723 1.731709 TGCACGCTTTATACTGCTGTG 59.268 47.619 6.48 12.30 37.06 3.66
3709 3724 1.062587 GCACGCTTTATACTGCTGTGG 59.937 52.381 6.48 0.00 35.74 4.17
3710 3725 2.346803 CACGCTTTATACTGCTGTGGT 58.653 47.619 6.48 0.00 33.57 4.16
3716 3732 5.445939 CGCTTTATACTGCTGTGGTTTGTAG 60.446 44.000 6.48 0.00 0.00 2.74
3720 3736 2.222027 ACTGCTGTGGTTTGTAGAAGC 58.778 47.619 0.00 0.00 0.00 3.86
3724 3740 2.618709 GCTGTGGTTTGTAGAAGCTTGT 59.381 45.455 2.10 1.06 0.00 3.16
3725 3741 3.304057 GCTGTGGTTTGTAGAAGCTTGTC 60.304 47.826 2.10 0.00 0.00 3.18
3796 3829 5.724328 TGTGGTAATTTTGTTCTTGTGCAA 58.276 33.333 0.00 0.00 0.00 4.08
3815 3855 1.609208 ACTGGTGCCACTGCTAAAAG 58.391 50.000 0.00 0.00 38.71 2.27
3854 3941 4.024048 GGATCGTGTGTGTGATTTTGTTCT 60.024 41.667 0.00 0.00 0.00 3.01
3894 3981 3.169908 TGCCTACACTCTCCATGTAACA 58.830 45.455 0.00 0.00 32.27 2.41
3921 4008 1.081641 CGACGTGTACAGCTTCGGT 60.082 57.895 11.21 0.00 0.00 4.69
3930 4017 0.320771 ACAGCTTCGGTGTGGTCATC 60.321 55.000 0.00 0.00 42.86 2.92
3939 4026 0.326264 GTGTGGTCATCCTGGAGCTT 59.674 55.000 1.52 0.00 36.30 3.74
4002 4089 1.076339 CCTGGTGGTGTGGGTTTGT 60.076 57.895 0.00 0.00 0.00 2.83
4011 4098 2.167487 GGTGTGGGTTTGTGACAATGTT 59.833 45.455 0.00 0.00 0.00 2.71
4014 4101 3.119316 TGTGGGTTTGTGACAATGTTGAC 60.119 43.478 0.00 0.00 0.00 3.18
4168 4255 1.908619 TGAAGATGCTGCAGGAGGTTA 59.091 47.619 17.12 0.00 0.00 2.85
4256 4343 7.260603 AGGAATAATGCTAATTTTGTGCACTC 58.739 34.615 19.41 0.61 39.63 3.51
4274 4362 5.045942 TGCACTCCTTGGATCATGTACTTAA 60.046 40.000 0.00 0.00 0.00 1.85
4292 4380 9.243105 TGTACTTAATACCGTTAACTAGGAGTT 57.757 33.333 3.71 0.00 36.26 3.01
4411 4499 5.048434 AGCTAACCTTTTGCTCTGAATGAAC 60.048 40.000 0.00 0.00 30.41 3.18
4449 4537 1.195448 GCTGTCAACCAATCTGTGACG 59.805 52.381 0.00 0.00 32.68 4.35
4526 4614 3.454082 ACTTTTGTTGCCTCCATTTCCAA 59.546 39.130 0.00 0.00 0.00 3.53
4535 4623 3.069443 GCCTCCATTTCCAACACTGAAAA 59.931 43.478 0.00 0.00 35.52 2.29
4536 4624 4.442753 GCCTCCATTTCCAACACTGAAAAA 60.443 41.667 0.00 0.00 35.52 1.94
4550 4638 5.351189 ACACTGAAAAATGCACTTTGTTTCC 59.649 36.000 0.00 0.00 0.00 3.13
4575 4664 1.157870 ACACAGCCTTTTCGACGTGG 61.158 55.000 0.00 0.00 0.00 4.94
4641 4730 3.380637 GGCTGAATGAAGCACTCATGAAT 59.619 43.478 0.00 0.00 44.43 2.57
4644 4733 5.730847 GCTGAATGAAGCACTCATGAATCAG 60.731 44.000 16.92 16.92 44.43 2.90
4670 4759 5.252164 ACAGGAGTAGAAGTCTAGAAGTCCT 59.748 44.000 10.75 10.75 31.17 3.85
4760 4851 1.961277 CGGTGTCCCTGTTGACTGC 60.961 63.158 0.00 0.00 36.21 4.40
4831 4924 1.470632 GCAACCTCTGATCAGTCTCCG 60.471 57.143 21.92 10.50 0.00 4.63
4861 4954 4.250464 TGGCTGCTGTAGTAACAACATAC 58.750 43.478 0.00 0.00 34.49 2.39
4885 4979 1.825622 GCTGGAGGTAGCATTGCCC 60.826 63.158 4.70 0.00 43.17 5.36
4891 4985 1.882623 GAGGTAGCATTGCCCTTATGC 59.117 52.381 4.70 0.00 46.78 3.14
4964 5058 2.349817 GCTCATAAATCATTGGTCGCCG 60.350 50.000 0.00 0.00 0.00 6.46
4986 5080 3.753774 CAGGTAAACTGCGCACAAG 57.246 52.632 5.66 0.00 40.97 3.16
5024 5118 9.507329 AAAGAACTTTATTGAGATGCAGTTCTA 57.493 29.630 11.69 0.15 46.19 2.10
5025 5119 8.715191 AGAACTTTATTGAGATGCAGTTCTAG 57.285 34.615 10.00 0.00 45.46 2.43
5078 5172 5.008217 TGTTTAGTTTCACAGTGGCACATAC 59.992 40.000 21.41 4.36 44.52 2.39
5079 5173 3.492102 AGTTTCACAGTGGCACATACT 57.508 42.857 21.41 6.68 44.52 2.12
5080 5174 4.617253 AGTTTCACAGTGGCACATACTA 57.383 40.909 21.41 0.00 44.52 1.82
5081 5175 4.569943 AGTTTCACAGTGGCACATACTAG 58.430 43.478 21.41 4.67 44.52 2.57
5105 5203 1.885157 TGGTAGGACCAGCGTAACG 59.115 57.895 0.00 0.00 44.79 3.18
5122 5221 5.220416 GCGTAACGAGATCTAATTTGCAACT 60.220 40.000 0.00 0.00 0.00 3.16
5124 5223 6.895040 CGTAACGAGATCTAATTTGCAACTTC 59.105 38.462 5.18 0.00 0.00 3.01
5134 5233 8.806429 TCTAATTTGCAACTTCTCATTGGATA 57.194 30.769 5.18 0.00 0.00 2.59
5136 5235 9.859427 CTAATTTGCAACTTCTCATTGGATAAA 57.141 29.630 5.18 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.657634 ACATCATCAGCTAGCCATTACG 58.342 45.455 12.13 0.00 0.00 3.18
19 20 6.147581 GCCAAATGCTATTGTACATCATCAG 58.852 40.000 0.00 0.00 36.87 2.90
20 21 5.277925 CGCCAAATGCTATTGTACATCATCA 60.278 40.000 0.00 0.00 38.05 3.07
21 22 5.149273 CGCCAAATGCTATTGTACATCATC 58.851 41.667 0.00 0.00 38.05 2.92
22 23 4.557296 GCGCCAAATGCTATTGTACATCAT 60.557 41.667 0.00 0.00 38.05 2.45
91 92 6.645003 TCGAATTGAGTAATGTTATCGGATGG 59.355 38.462 0.00 0.00 0.00 3.51
100 101 8.393366 CACATTCATCTCGAATTGAGTAATGTT 58.607 33.333 17.54 7.97 41.83 2.71
102 103 8.134905 TCACATTCATCTCGAATTGAGTAATG 57.865 34.615 15.03 15.03 41.83 1.90
103 104 8.200120 TCTCACATTCATCTCGAATTGAGTAAT 58.800 33.333 17.04 0.00 41.83 1.89
179 181 7.600375 GGCCATCATATAGTGACCATATTATCG 59.400 40.741 0.00 0.00 40.28 2.92
188 190 3.073062 ACAAGGGCCATCATATAGTGACC 59.927 47.826 6.18 0.00 40.28 4.02
243 251 1.521681 GCTACGCCACTGTCCATCC 60.522 63.158 0.00 0.00 0.00 3.51
244 252 0.744874 TAGCTACGCCACTGTCCATC 59.255 55.000 0.00 0.00 0.00 3.51
245 253 0.747255 CTAGCTACGCCACTGTCCAT 59.253 55.000 0.00 0.00 0.00 3.41
246 254 1.320344 CCTAGCTACGCCACTGTCCA 61.320 60.000 0.00 0.00 0.00 4.02
247 255 1.437986 CCTAGCTACGCCACTGTCC 59.562 63.158 0.00 0.00 0.00 4.02
248 256 1.035932 TCCCTAGCTACGCCACTGTC 61.036 60.000 0.00 0.00 0.00 3.51
249 257 0.397254 ATCCCTAGCTACGCCACTGT 60.397 55.000 0.00 0.00 0.00 3.55
250 258 0.753262 AATCCCTAGCTACGCCACTG 59.247 55.000 0.00 0.00 0.00 3.66
251 259 0.753262 CAATCCCTAGCTACGCCACT 59.247 55.000 0.00 0.00 0.00 4.00
252 260 0.249911 CCAATCCCTAGCTACGCCAC 60.250 60.000 0.00 0.00 0.00 5.01
253 261 2.040009 GCCAATCCCTAGCTACGCCA 62.040 60.000 0.00 0.00 0.00 5.69
254 262 1.301795 GCCAATCCCTAGCTACGCC 60.302 63.158 0.00 0.00 0.00 5.68
255 263 1.301795 GGCCAATCCCTAGCTACGC 60.302 63.158 0.00 0.00 0.00 4.42
256 264 0.034059 CTGGCCAATCCCTAGCTACG 59.966 60.000 7.01 0.00 0.00 3.51
257 265 0.398318 CCTGGCCAATCCCTAGCTAC 59.602 60.000 7.01 0.00 0.00 3.58
258 266 0.768221 CCCTGGCCAATCCCTAGCTA 60.768 60.000 7.01 0.00 0.00 3.32
259 267 2.081161 CCCTGGCCAATCCCTAGCT 61.081 63.158 7.01 0.00 0.00 3.32
260 268 2.386935 ACCCTGGCCAATCCCTAGC 61.387 63.158 7.01 0.00 0.00 3.42
261 269 1.533711 CACCCTGGCCAATCCCTAG 59.466 63.158 7.01 0.00 0.00 3.02
262 270 2.006415 CCACCCTGGCCAATCCCTA 61.006 63.158 7.01 0.00 0.00 3.53
263 271 3.350163 CCACCCTGGCCAATCCCT 61.350 66.667 7.01 0.00 0.00 4.20
264 272 3.662117 GACCACCCTGGCCAATCCC 62.662 68.421 7.01 0.00 42.67 3.85
265 273 2.043953 GACCACCCTGGCCAATCC 60.044 66.667 7.01 0.00 42.67 3.01
266 274 2.043953 GGACCACCCTGGCCAATC 60.044 66.667 7.01 0.00 42.67 2.67
267 275 2.248374 ATGGACCACCCTGGCCAAT 61.248 57.895 7.01 0.00 43.41 3.16
268 276 2.863484 ATGGACCACCCTGGCCAA 60.863 61.111 7.01 0.00 43.41 4.52
269 277 3.660571 CATGGACCACCCTGGCCA 61.661 66.667 4.71 4.71 43.97 5.36
270 278 4.447342 CCATGGACCACCCTGGCC 62.447 72.222 5.56 0.00 43.04 5.36
271 279 3.338250 TCCATGGACCACCCTGGC 61.338 66.667 11.44 0.00 46.80 4.85
280 288 0.984230 TTCCAGAGTGGTCCATGGAC 59.016 55.000 33.14 33.14 41.45 4.02
281 289 1.971149 ATTCCAGAGTGGTCCATGGA 58.029 50.000 11.44 11.44 40.04 3.41
282 290 2.814805 AATTCCAGAGTGGTCCATGG 57.185 50.000 4.97 4.97 39.03 3.66
283 291 3.019564 GGAAATTCCAGAGTGGTCCATG 58.980 50.000 7.23 0.00 39.03 3.66
284 292 2.024941 GGGAAATTCCAGAGTGGTCCAT 60.025 50.000 14.68 0.00 38.64 3.41
285 293 1.354368 GGGAAATTCCAGAGTGGTCCA 59.646 52.381 14.68 0.00 38.64 4.02
286 294 1.341089 GGGGAAATTCCAGAGTGGTCC 60.341 57.143 14.68 0.00 38.64 4.46
287 295 1.354368 TGGGGAAATTCCAGAGTGGTC 59.646 52.381 14.68 0.00 38.64 4.02
288 296 1.455822 TGGGGAAATTCCAGAGTGGT 58.544 50.000 14.68 0.00 38.64 4.16
289 297 2.834638 ATGGGGAAATTCCAGAGTGG 57.165 50.000 14.68 0.00 38.64 4.00
290 298 4.860022 AGTTATGGGGAAATTCCAGAGTG 58.140 43.478 14.68 0.00 38.64 3.51
291 299 5.222337 ACAAGTTATGGGGAAATTCCAGAGT 60.222 40.000 14.68 0.00 38.64 3.24
292 300 5.264395 ACAAGTTATGGGGAAATTCCAGAG 58.736 41.667 14.68 0.00 38.64 3.35
293 301 5.269554 ACAAGTTATGGGGAAATTCCAGA 57.730 39.130 14.68 0.00 38.64 3.86
294 302 8.940397 ATATACAAGTTATGGGGAAATTCCAG 57.060 34.615 14.68 0.00 38.64 3.86
301 309 9.664777 ACTACACTATATACAAGTTATGGGGAA 57.335 33.333 0.00 0.00 0.00 3.97
362 370 9.758651 GGGTGGTCCATTAATGAAAATATTTAC 57.241 33.333 17.23 3.69 35.00 2.01
363 371 9.722317 AGGGTGGTCCATTAATGAAAATATTTA 57.278 29.630 17.23 0.00 38.24 1.40
364 372 8.485392 CAGGGTGGTCCATTAATGAAAATATTT 58.515 33.333 17.23 0.00 38.24 1.40
365 373 7.843760 TCAGGGTGGTCCATTAATGAAAATATT 59.156 33.333 17.23 0.00 38.24 1.28
366 374 7.361438 TCAGGGTGGTCCATTAATGAAAATAT 58.639 34.615 17.23 0.00 38.24 1.28
367 375 6.736581 TCAGGGTGGTCCATTAATGAAAATA 58.263 36.000 17.23 0.00 38.24 1.40
368 376 5.588845 TCAGGGTGGTCCATTAATGAAAAT 58.411 37.500 17.23 0.00 38.24 1.82
369 377 5.004361 TCAGGGTGGTCCATTAATGAAAA 57.996 39.130 17.23 0.00 38.24 2.29
370 378 4.044065 ACTCAGGGTGGTCCATTAATGAAA 59.956 41.667 17.23 1.81 38.24 2.69
371 379 3.591527 ACTCAGGGTGGTCCATTAATGAA 59.408 43.478 17.23 0.00 38.24 2.57
372 380 3.189606 ACTCAGGGTGGTCCATTAATGA 58.810 45.455 17.23 0.46 38.24 2.57
373 381 3.652057 ACTCAGGGTGGTCCATTAATG 57.348 47.619 8.58 8.58 38.24 1.90
374 382 5.399038 CCAATACTCAGGGTGGTCCATTAAT 60.399 44.000 0.00 0.00 38.24 1.40
375 383 4.080015 CCAATACTCAGGGTGGTCCATTAA 60.080 45.833 0.00 0.00 38.24 1.40
376 384 3.458118 CCAATACTCAGGGTGGTCCATTA 59.542 47.826 0.00 0.00 38.24 1.90
377 385 2.242196 CCAATACTCAGGGTGGTCCATT 59.758 50.000 0.00 0.00 38.24 3.16
378 386 1.846439 CCAATACTCAGGGTGGTCCAT 59.154 52.381 0.00 0.00 38.24 3.41
379 387 1.285280 CCAATACTCAGGGTGGTCCA 58.715 55.000 0.00 0.00 38.24 4.02
380 388 0.546598 CCCAATACTCAGGGTGGTCC 59.453 60.000 0.00 0.00 40.34 4.46
387 395 1.131638 TAGCCAGCCCAATACTCAGG 58.868 55.000 0.00 0.00 0.00 3.86
388 396 1.539065 CGTAGCCAGCCCAATACTCAG 60.539 57.143 0.00 0.00 0.00 3.35
389 397 0.464036 CGTAGCCAGCCCAATACTCA 59.536 55.000 0.00 0.00 0.00 3.41
390 398 3.290776 CGTAGCCAGCCCAATACTC 57.709 57.895 0.00 0.00 0.00 2.59
437 445 4.520111 TGAGTTCCATGGACATGTCAAAAG 59.480 41.667 26.47 12.80 37.11 2.27
454 462 3.128068 ACCGGTTGACAAAAGTTGAGTTC 59.872 43.478 0.00 0.00 0.00 3.01
482 491 9.946165 CTTCTTTAAAGAACCAACGAAGTTATT 57.054 29.630 23.65 0.00 44.25 1.40
514 523 1.269517 TGGCAACATGTTTCGGCTTTC 60.270 47.619 19.07 5.86 46.17 2.62
528 537 5.565592 TGAAGATGATATGTGTTGGCAAC 57.434 39.130 23.12 23.12 0.00 4.17
530 539 6.827762 TGTTATGAAGATGATATGTGTTGGCA 59.172 34.615 0.00 0.00 0.00 4.92
555 564 1.204231 TGCGCACATTATTGGCATGTT 59.796 42.857 5.66 0.00 32.25 2.71
556 565 0.816373 TGCGCACATTATTGGCATGT 59.184 45.000 5.66 0.00 35.10 3.21
559 568 2.269172 CAAATGCGCACATTATTGGCA 58.731 42.857 14.90 0.00 45.90 4.92
591 600 7.579589 TGCAAGTCATTGTATTTTATTGTGC 57.420 32.000 0.00 0.00 38.76 4.57
602 611 6.691754 TTCAACTCTTTGCAAGTCATTGTA 57.308 33.333 0.00 0.00 38.76 2.41
612 621 2.957680 TGATTGGCTTCAACTCTTTGCA 59.042 40.909 0.00 0.00 32.63 4.08
613 622 3.648339 TGATTGGCTTCAACTCTTTGC 57.352 42.857 0.00 0.00 32.63 3.68
631 640 4.402155 AGCAAAAGGAAGTTGTGTCATTGA 59.598 37.500 0.00 0.00 0.00 2.57
637 646 2.031870 GGGAGCAAAAGGAAGTTGTGT 58.968 47.619 0.00 0.00 0.00 3.72
644 653 2.038659 CAAAGTGGGGAGCAAAAGGAA 58.961 47.619 0.00 0.00 0.00 3.36
647 656 2.483538 CCAACAAAGTGGGGAGCAAAAG 60.484 50.000 0.00 0.00 34.77 2.27
660 669 7.496529 TTTAGATGTCTCTGTTCCAACAAAG 57.503 36.000 0.00 0.00 38.66 2.77
663 672 7.522073 GCAATTTTAGATGTCTCTGTTCCAACA 60.522 37.037 0.00 0.00 37.37 3.33
664 673 6.803807 GCAATTTTAGATGTCTCTGTTCCAAC 59.196 38.462 0.00 0.00 32.66 3.77
676 685 1.745232 TCGGCGGCAATTTTAGATGT 58.255 45.000 10.53 0.00 0.00 3.06
680 689 4.606961 ACATTTATCGGCGGCAATTTTAG 58.393 39.130 10.53 0.00 0.00 1.85
684 693 3.630312 AGTAACATTTATCGGCGGCAATT 59.370 39.130 10.53 0.00 0.00 2.32
691 700 6.038271 AGTGGAATTGAGTAACATTTATCGGC 59.962 38.462 0.00 0.00 0.00 5.54
698 707 7.581213 TGTTCAAGTGGAATTGAGTAACATT 57.419 32.000 0.00 0.00 40.16 2.71
723 732 6.491745 TCCTTGTGAGCCAATGTATTTTGTTA 59.508 34.615 0.00 0.00 31.20 2.41
734 743 2.957402 TGAACTCCTTGTGAGCCAAT 57.043 45.000 0.00 0.00 45.61 3.16
787 796 4.158025 ACGTGTTTTTCACATTGGGTAACA 59.842 37.500 0.00 0.00 46.44 2.41
798 807 4.087930 CACACTTTGACACGTGTTTTTCAC 59.912 41.667 24.26 9.32 42.05 3.18
802 811 2.030717 TGCACACTTTGACACGTGTTTT 60.031 40.909 24.26 0.00 42.05 2.43
846 855 2.054140 TTGTGTCGAAAGTTGGCGCC 62.054 55.000 22.73 22.73 0.00 6.53
850 859 2.223456 TGCATGTTGTGTCGAAAGTTGG 60.223 45.455 0.00 0.00 0.00 3.77
855 864 2.020720 AGGTTGCATGTTGTGTCGAAA 58.979 42.857 0.00 0.00 0.00 3.46
862 871 1.202639 TGACGAGAGGTTGCATGTTGT 60.203 47.619 0.00 0.00 0.00 3.32
864 873 2.254546 TTGACGAGAGGTTGCATGTT 57.745 45.000 0.00 0.00 0.00 2.71
865 874 2.350522 GATTGACGAGAGGTTGCATGT 58.649 47.619 0.00 0.00 0.00 3.21
866 875 1.325640 CGATTGACGAGAGGTTGCATG 59.674 52.381 0.00 0.00 45.77 4.06
867 876 1.645034 CGATTGACGAGAGGTTGCAT 58.355 50.000 0.00 0.00 45.77 3.96
868 877 0.389817 CCGATTGACGAGAGGTTGCA 60.390 55.000 0.00 0.00 45.77 4.08
869 878 0.108804 TCCGATTGACGAGAGGTTGC 60.109 55.000 0.00 0.00 45.77 4.17
870 879 2.363788 TTCCGATTGACGAGAGGTTG 57.636 50.000 0.00 0.00 45.77 3.77
871 880 2.496070 TGATTCCGATTGACGAGAGGTT 59.504 45.455 0.00 0.00 45.77 3.50
872 881 2.099921 CTGATTCCGATTGACGAGAGGT 59.900 50.000 0.00 0.00 45.77 3.85
873 882 2.544694 CCTGATTCCGATTGACGAGAGG 60.545 54.545 0.00 0.00 45.77 3.69
874 883 2.544694 CCCTGATTCCGATTGACGAGAG 60.545 54.545 0.00 0.00 45.77 3.20
875 884 1.409064 CCCTGATTCCGATTGACGAGA 59.591 52.381 0.00 0.00 45.77 4.04
876 885 1.539065 CCCCTGATTCCGATTGACGAG 60.539 57.143 0.00 0.00 45.77 4.18
885 894 4.918201 GCCGAGCCCCTGATTCCG 62.918 72.222 0.00 0.00 0.00 4.30
889 898 4.804420 TGGAGCCGAGCCCCTGAT 62.804 66.667 0.00 0.00 0.00 2.90
907 916 2.660064 CGGAGGGGAGGAGTTGGTG 61.660 68.421 0.00 0.00 0.00 4.17
973 982 1.355720 ACCATTGGGGAAGGAGAGTTG 59.644 52.381 7.78 0.00 41.15 3.16
974 983 1.760405 ACCATTGGGGAAGGAGAGTT 58.240 50.000 7.78 0.00 41.15 3.01
975 984 2.661176 TACCATTGGGGAAGGAGAGT 57.339 50.000 7.78 0.00 41.15 3.24
992 1001 5.458891 CGCATTGTAGTAGGGTAGTGATAC 58.541 45.833 0.00 0.00 0.00 2.24
994 1003 3.243771 GCGCATTGTAGTAGGGTAGTGAT 60.244 47.826 0.30 0.00 0.00 3.06
998 1007 2.361119 TCAGCGCATTGTAGTAGGGTAG 59.639 50.000 11.47 0.00 0.00 3.18
999 1008 2.100252 GTCAGCGCATTGTAGTAGGGTA 59.900 50.000 11.47 0.00 0.00 3.69
1000 1009 1.134788 GTCAGCGCATTGTAGTAGGGT 60.135 52.381 11.47 0.00 0.00 4.34
1001 1010 1.134818 TGTCAGCGCATTGTAGTAGGG 60.135 52.381 11.47 0.00 0.00 3.53
1002 1011 2.293677 TGTCAGCGCATTGTAGTAGG 57.706 50.000 11.47 0.00 0.00 3.18
1033 1042 2.239907 AGGGAGTTACAGGATTGGAAGC 59.760 50.000 0.00 0.00 0.00 3.86
1068 1077 2.776526 AGTGGGGAGTGTGGGCAA 60.777 61.111 0.00 0.00 0.00 4.52
1195 1204 1.750399 GGAGGTACCTGGCGTCGTA 60.750 63.158 22.10 0.00 35.41 3.43
1206 1215 3.682292 CTTGGCGGCCAGGAGGTAC 62.682 68.421 25.42 0.00 31.89 3.34
1269 1278 0.985490 AGAGGGAATGGCTGGACTCC 60.985 60.000 0.00 0.00 0.00 3.85
1271 1280 1.919600 GCAGAGGGAATGGCTGGACT 61.920 60.000 0.00 0.00 0.00 3.85
1318 1327 4.104143 GGCGACGGTGGTAGATTG 57.896 61.111 0.00 0.00 0.00 2.67
1560 1569 2.409064 TGGAGTTCTGGACCAGGTTA 57.591 50.000 21.56 4.81 31.51 2.85
1596 1605 1.270550 CTGATGTTGGCCAAGAACCAC 59.729 52.381 21.21 7.32 36.76 4.16
1603 1612 1.907807 GGGTGCTGATGTTGGCCAA 60.908 57.895 16.05 16.05 0.00 4.52
1902 1911 1.274712 AGAACTGGAGCTTCCTGAGG 58.725 55.000 13.40 0.00 37.65 3.86
2050 2059 1.209275 CTTAGATCGGCAAGACGCGG 61.209 60.000 12.47 0.00 43.84 6.46
2289 2298 0.318441 CAGAGAGGCGGTTGTTCTGA 59.682 55.000 0.00 0.00 37.96 3.27
2333 2342 1.396653 CATCTGGACAAGGGGCAATC 58.603 55.000 0.00 0.00 0.00 2.67
2335 2344 1.304381 GCATCTGGACAAGGGGCAA 60.304 57.895 0.00 0.00 0.00 4.52
2403 2412 0.817634 CGAACAGGTTCTTGGCACCA 60.818 55.000 10.17 0.00 36.67 4.17
2438 2447 2.590575 CGCCAGTGAACCGGTTGT 60.591 61.111 27.87 0.00 0.00 3.32
2495 2504 1.141657 TGTTGTCTGAGGCAAGAAGCT 59.858 47.619 0.00 0.00 44.79 3.74
2542 2551 4.059136 CTCGGAAAGCTCGACGAC 57.941 61.111 0.00 0.00 32.86 4.34
2571 2580 5.012251 GGAGAGGGAATTATTACTCAGGTCC 59.988 48.000 10.38 6.22 32.52 4.46
2686 2695 0.933700 ATCCGGTGGATTTCCCCAAT 59.066 50.000 0.00 0.00 39.79 3.16
2807 2816 2.761809 AGAAGAGAGGCAGATGTCCAT 58.238 47.619 0.00 0.00 0.00 3.41
2813 2822 2.093553 GCACTGAAGAAGAGAGGCAGAT 60.094 50.000 0.00 0.00 0.00 2.90
2962 2977 0.321653 AAACCCATGAGCAGGACGAC 60.322 55.000 0.00 0.00 0.00 4.34
3027 3042 1.073216 ACTCGTCAGCGCTGATTTCG 61.073 55.000 39.91 35.16 42.18 3.46
3036 3051 1.284982 CCCAACTTGACTCGTCAGCG 61.285 60.000 0.00 0.00 41.13 5.18
3165 3180 4.077184 TCACCGCTAGGCCCAACG 62.077 66.667 0.00 0.00 42.76 4.10
3178 3193 2.439156 GACAGCCATGGCCTCACC 60.439 66.667 33.14 14.13 43.17 4.02
3208 3223 0.872451 TTGCTTTCGACGTCGCTTGA 60.872 50.000 32.19 13.26 39.60 3.02
3271 3286 1.444119 TTCTTGTGCCTGACGTTGCC 61.444 55.000 0.00 0.00 0.00 4.52
3276 3291 1.603802 ACAATGTTCTTGTGCCTGACG 59.396 47.619 0.00 0.00 0.00 4.35
3294 3309 0.947660 CGCAGCAGAAGAGCTTGACA 60.948 55.000 0.00 0.00 43.70 3.58
3339 3354 1.019673 TCGGCATGTACTCGTAGACC 58.980 55.000 0.00 0.00 0.00 3.85
3501 3516 4.350346 TGAGCAAAATGTTGTTCGACTTG 58.650 39.130 7.83 0.00 45.25 3.16
3552 3567 6.096141 TCTCAATAGTCTTTGCAACACCAAAA 59.904 34.615 0.00 0.00 34.59 2.44
3603 3618 1.374947 GTAACCACAGGAGCCAGCA 59.625 57.895 0.00 0.00 0.00 4.41
3692 3707 3.188460 ACAAACCACAGCAGTATAAAGCG 59.812 43.478 0.00 0.00 35.48 4.68
3706 3721 2.870411 ACGACAAGCTTCTACAAACCAC 59.130 45.455 0.00 0.00 0.00 4.16
3708 3723 4.524749 GAAACGACAAGCTTCTACAAACC 58.475 43.478 0.00 0.00 0.00 3.27
3709 3724 4.272748 AGGAAACGACAAGCTTCTACAAAC 59.727 41.667 0.00 0.00 0.00 2.93
3710 3725 4.448210 AGGAAACGACAAGCTTCTACAAA 58.552 39.130 0.00 0.00 0.00 2.83
3716 3732 4.510340 TGAAGTTAGGAAACGACAAGCTTC 59.490 41.667 0.00 0.00 40.73 3.86
3720 3736 5.290386 AGACTGAAGTTAGGAAACGACAAG 58.710 41.667 0.00 0.00 40.73 3.16
3724 3740 6.585695 ATGTAGACTGAAGTTAGGAAACGA 57.414 37.500 0.00 0.00 40.73 3.85
3725 3741 7.653767 AAATGTAGACTGAAGTTAGGAAACG 57.346 36.000 0.00 0.00 40.73 3.60
3781 3814 3.583806 CACCAGTTGCACAAGAACAAAA 58.416 40.909 0.00 0.00 0.00 2.44
3796 3829 1.609208 CTTTTAGCAGTGGCACCAGT 58.391 50.000 15.27 0.85 44.61 4.00
3803 3836 7.816640 TCTAAAATACAAGCTTTTAGCAGTGG 58.183 34.615 0.00 0.00 45.56 4.00
3815 3855 5.585047 ACACGATCCCTTCTAAAATACAAGC 59.415 40.000 0.00 0.00 0.00 4.01
3830 3917 2.552315 ACAAAATCACACACACGATCCC 59.448 45.455 0.00 0.00 0.00 3.85
3882 3969 3.129462 CGCTCTTCTCTGTTACATGGAGA 59.871 47.826 0.00 0.93 34.77 3.71
3894 3981 1.465387 CTGTACACGTCGCTCTTCTCT 59.535 52.381 0.00 0.00 0.00 3.10
3921 4008 0.325933 CAAGCTCCAGGATGACCACA 59.674 55.000 0.00 0.00 39.69 4.17
3930 4017 2.046892 CCGGTGACAAGCTCCAGG 60.047 66.667 0.00 0.00 0.00 4.45
4002 4089 1.887854 CCATGCTGGTCAACATTGTCA 59.112 47.619 0.00 0.00 31.35 3.58
4014 4101 3.807538 GACTGCGCACCATGCTGG 61.808 66.667 5.66 0.00 42.25 4.85
4027 4114 2.740981 GCCTGTGATCAAGAACAGACTG 59.259 50.000 11.56 0.00 45.43 3.51
4168 4255 0.836400 TTCGGCTTGTTCTCTCCCCT 60.836 55.000 0.00 0.00 0.00 4.79
4190 4277 2.231380 GGGGCCACCTCCTTCTTCA 61.231 63.158 4.39 0.00 36.80 3.02
4256 4343 6.522054 ACGGTATTAAGTACATGATCCAAGG 58.478 40.000 0.00 0.00 34.87 3.61
4274 4362 9.507329 TCGAATATAACTCCTAGTTAACGGTAT 57.493 33.333 0.00 0.00 43.16 2.73
4292 4380 6.920210 CAGTGCACTTCTGAAGATCGAATATA 59.080 38.462 23.36 0.00 35.20 0.86
4297 4385 2.928301 GCAGTGCACTTCTGAAGATCGA 60.928 50.000 23.36 0.00 35.20 3.59
4411 4499 2.659757 CAGCAACTGCACATTTCATTCG 59.340 45.455 4.22 0.00 45.16 3.34
4449 4537 1.737838 TGCAACAACATCGGATCTCC 58.262 50.000 0.00 0.00 0.00 3.71
4526 4614 5.351189 GGAAACAAAGTGCATTTTTCAGTGT 59.649 36.000 4.19 0.00 0.00 3.55
4535 4623 5.351189 GTGTGAAAAGGAAACAAAGTGCATT 59.649 36.000 0.00 0.00 0.00 3.56
4536 4624 4.869861 GTGTGAAAAGGAAACAAAGTGCAT 59.130 37.500 0.00 0.00 0.00 3.96
4550 4638 3.363178 GTCGAAAAGGCTGTGTGAAAAG 58.637 45.455 0.00 0.00 0.00 2.27
4575 4664 5.415701 TCCATAAGTTGTTCCAAAGCATCTC 59.584 40.000 0.00 0.00 0.00 2.75
4641 4730 6.375830 TCTAGACTTCTACTCCTGTTCTGA 57.624 41.667 0.00 0.00 0.00 3.27
4644 4733 6.094464 GGACTTCTAGACTTCTACTCCTGTTC 59.906 46.154 0.00 0.00 0.00 3.18
4760 4851 5.485662 ACCAAAAGAAGAAACGAGAACAG 57.514 39.130 0.00 0.00 0.00 3.16
4815 4907 1.950909 GTACCGGAGACTGATCAGAGG 59.049 57.143 29.27 21.98 0.00 3.69
4880 4973 2.170166 CCAAAGAGTGCATAAGGGCAA 58.830 47.619 0.00 0.00 46.93 4.52
4885 4979 2.019984 GGAGGCCAAAGAGTGCATAAG 58.980 52.381 5.01 0.00 0.00 1.73
4891 4985 0.610232 CAAGGGGAGGCCAAAGAGTG 60.610 60.000 5.01 0.00 0.00 3.51
4964 5058 1.302192 TGCGCAGTTTACCTGTCCC 60.302 57.895 5.66 0.00 43.55 4.46
4970 5064 2.485266 AAACTTGTGCGCAGTTTACC 57.515 45.000 20.68 5.54 34.47 2.85
4979 5073 4.693566 TCTTTGTCCCTATAAACTTGTGCG 59.306 41.667 0.00 0.00 0.00 5.34
4980 5074 6.206829 AGTTCTTTGTCCCTATAAACTTGTGC 59.793 38.462 0.00 0.00 0.00 4.57
5055 5149 4.568152 ATGTGCCACTGTGAAACTAAAC 57.432 40.909 9.86 0.00 38.04 2.01
5056 5150 5.373222 AGTATGTGCCACTGTGAAACTAAA 58.627 37.500 9.86 0.00 38.04 1.85
5097 5195 4.430007 TGCAAATTAGATCTCGTTACGCT 58.570 39.130 0.00 0.00 0.00 5.07
5099 5197 6.332504 AGTTGCAAATTAGATCTCGTTACG 57.667 37.500 0.00 0.00 0.00 3.18
5103 5201 6.166279 TGAGAAGTTGCAAATTAGATCTCGT 58.834 36.000 12.76 0.00 35.88 4.18
5105 5203 7.914346 CCAATGAGAAGTTGCAAATTAGATCTC 59.086 37.037 12.76 14.63 34.19 2.75
5122 5221 7.631161 GCACCATGTCAATTTATCCAATGAGAA 60.631 37.037 0.00 0.00 0.00 2.87
5124 5223 5.981315 GCACCATGTCAATTTATCCAATGAG 59.019 40.000 0.00 0.00 0.00 2.90
5221 5326 1.434696 CCATGCATGGTCGGAAAGC 59.565 57.895 33.68 0.00 43.05 3.51


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

AutoCloner maintained by Alex Coulton.