Multiple sequence alignment - TraesCS5D01G247700

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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 TraesCS5D01G247700 chr5D 100.000 3158 0 0 1 3158 354940100 354943257 0.000000e+00 5832
1 TraesCS5D01G247700 chr5D 84.328 938 121 10 1240 2158 355797804 355796874 0.000000e+00 894
2 TraesCS5D01G247700 chr5D 83.967 736 85 16 1252 1963 355076716 355077442 0.000000e+00 675
3 TraesCS5D01G247700 chr5D 73.993 919 183 42 1282 2160 355796488 355795586 3.930000e-84 322
4 TraesCS5D01G247700 chr5B 93.987 1347 65 9 821 2167 419727085 419728415 0.000000e+00 2025
5 TraesCS5D01G247700 chr5B 84.026 939 122 12 1240 2158 420732961 420732031 0.000000e+00 878
6 TraesCS5D01G247700 chr5B 81.828 941 134 21 1252 2163 419947718 419948650 0.000000e+00 756
7 TraesCS5D01G247700 chr5B 93.114 334 18 3 2 334 419725608 419725937 4.740000e-133 484
8 TraesCS5D01G247700 chr5B 92.212 321 25 0 2833 3153 419760858 419761178 3.710000e-124 455
9 TraesCS5D01G247700 chr5B 88.068 352 32 6 2487 2834 419760472 419760817 2.930000e-110 409
10 TraesCS5D01G247700 chr5B 89.310 290 25 1 2864 3153 419841965 419842248 2.990000e-95 359
11 TraesCS5D01G247700 chr5B 74.046 917 188 33 1282 2160 420716168 420715264 2.350000e-86 329
12 TraesCS5D01G247700 chr5B 75.990 404 75 13 1352 1738 83677546 83677148 4.160000e-44 189
13 TraesCS5D01G247700 chr5B 87.288 118 10 3 2063 2178 419832602 419832716 2.560000e-26 130
14 TraesCS5D01G247700 chr5B 88.235 102 12 0 1830 1931 419832441 419832542 4.280000e-24 122
15 TraesCS5D01G247700 chr5A 94.588 1312 63 4 870 2178 457085957 457087263 0.000000e+00 2023
16 TraesCS5D01G247700 chr5A 84.968 938 115 12 1240 2158 457511592 457512522 0.000000e+00 928
17 TraesCS5D01G247700 chr5A 82.359 941 129 22 1252 2163 457380353 457381285 0.000000e+00 784
18 TraesCS5D01G247700 chr5A 92.414 290 22 0 2864 3153 457088336 457088625 6.300000e-112 414
19 TraesCS5D01G247700 chr5A 89.053 338 24 10 2 331 457081665 457081997 1.050000e-109 407
20 TraesCS5D01G247700 chr5A 73.885 919 190 34 1279 2160 457514832 457515737 3.930000e-84 322
21 TraesCS5D01G247700 chr5A 80.277 289 50 6 1353 1639 457516715 457516432 8.870000e-51 211


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 TraesCS5D01G247700 chr5D 354940100 354943257 3157 False 5832.0 5832 100.000000 1 3158 1 chr5D.!!$F1 3157
1 TraesCS5D01G247700 chr5D 355076716 355077442 726 False 675.0 675 83.967000 1252 1963 1 chr5D.!!$F2 711
2 TraesCS5D01G247700 chr5D 355795586 355797804 2218 True 608.0 894 79.160500 1240 2160 2 chr5D.!!$R1 920
3 TraesCS5D01G247700 chr5B 419725608 419728415 2807 False 1254.5 2025 93.550500 2 2167 2 chr5B.!!$F3 2165
4 TraesCS5D01G247700 chr5B 420732031 420732961 930 True 878.0 878 84.026000 1240 2158 1 chr5B.!!$R3 918
5 TraesCS5D01G247700 chr5B 419947718 419948650 932 False 756.0 756 81.828000 1252 2163 1 chr5B.!!$F2 911
6 TraesCS5D01G247700 chr5B 419760472 419761178 706 False 432.0 455 90.140000 2487 3153 2 chr5B.!!$F4 666
7 TraesCS5D01G247700 chr5B 420715264 420716168 904 True 329.0 329 74.046000 1282 2160 1 chr5B.!!$R2 878
8 TraesCS5D01G247700 chr5A 457081665 457088625 6960 False 948.0 2023 92.018333 2 3153 3 chr5A.!!$F2 3151
9 TraesCS5D01G247700 chr5A 457380353 457381285 932 False 784.0 784 82.359000 1252 2163 1 chr5A.!!$F1 911
10 TraesCS5D01G247700 chr5A 457511592 457515737 4145 False 625.0 928 79.426500 1240 2160 2 chr5A.!!$F3 920

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
682 4012 0.024619 GGCGTACGCGATCTTTTGAC 59.975 55.0 31.78 11.77 43.06 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2296 7785 0.108138 GCGGTGCTGACCAAGTCTAT 60.108 55.0 0.0 0.0 43.33 1.98 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
63 64 2.682856 GCAAAGCTAAATCCATCCGTGA 59.317 45.455 0.00 0.00 0.00 4.35
77 78 5.775195 TCCATCCGTGACATATAACTCTGAT 59.225 40.000 0.00 0.00 0.00 2.90
181 187 5.163405 CGGTCCAATAGGGGATATATGACTG 60.163 48.000 0.00 0.00 39.62 3.51
185 191 5.045651 CCAATAGGGGATATATGACTGTGCA 60.046 44.000 0.00 0.00 0.00 4.57
205 211 3.058016 GCAGAGAGCAATTTTGTGTAGCA 60.058 43.478 0.00 0.00 44.79 3.49
206 212 4.470462 CAGAGAGCAATTTTGTGTAGCAC 58.530 43.478 0.00 0.00 34.56 4.40
210 219 3.716601 AGCAATTTTGTGTAGCACCAAC 58.283 40.909 0.00 0.00 32.73 3.77
214 223 0.660488 TTTGTGTAGCACCAACGCAG 59.340 50.000 0.00 0.00 38.48 5.18
222 231 1.639298 GCACCAACGCAGTCATCTCC 61.639 60.000 0.00 0.00 45.00 3.71
252 261 3.074412 ACAGTAAAGAGGCATTGTTCGG 58.926 45.455 0.00 0.00 0.00 4.30
261 270 1.394697 GCATTGTTCGGTCGTGTTTG 58.605 50.000 0.00 0.00 0.00 2.93
314 324 2.032290 GGGTTTATGCGCTTCGGTTATC 60.032 50.000 9.73 0.00 0.00 1.75
315 325 2.610374 GGTTTATGCGCTTCGGTTATCA 59.390 45.455 9.73 0.00 0.00 2.15
334 344 3.449632 TCAAAAAGTGTAAAAAGGCGCC 58.550 40.909 21.89 21.89 0.00 6.53
335 345 3.119101 TCAAAAAGTGTAAAAAGGCGCCA 60.119 39.130 31.54 3.61 0.00 5.69
336 346 3.528597 AAAAGTGTAAAAAGGCGCCAA 57.471 38.095 31.54 5.16 0.00 4.52
337 347 2.793278 AAGTGTAAAAAGGCGCCAAG 57.207 45.000 31.54 0.00 0.00 3.61
338 348 1.687563 AGTGTAAAAAGGCGCCAAGT 58.312 45.000 31.54 10.81 0.00 3.16
339 349 2.853705 AGTGTAAAAAGGCGCCAAGTA 58.146 42.857 31.54 12.17 0.00 2.24
340 350 3.215975 AGTGTAAAAAGGCGCCAAGTAA 58.784 40.909 31.54 8.10 0.00 2.24
341 351 3.633065 AGTGTAAAAAGGCGCCAAGTAAA 59.367 39.130 31.54 7.23 0.00 2.01
342 352 3.732219 GTGTAAAAAGGCGCCAAGTAAAC 59.268 43.478 31.54 18.85 0.00 2.01
343 353 3.633065 TGTAAAAAGGCGCCAAGTAAACT 59.367 39.130 31.54 0.76 0.00 2.66
344 354 2.793278 AAAAGGCGCCAAGTAAACTG 57.207 45.000 31.54 0.00 0.00 3.16
345 355 1.687563 AAAGGCGCCAAGTAAACTGT 58.312 45.000 31.54 0.00 0.00 3.55
346 356 1.235724 AAGGCGCCAAGTAAACTGTC 58.764 50.000 31.54 0.00 0.00 3.51
347 357 0.107831 AGGCGCCAAGTAAACTGTCA 59.892 50.000 31.54 0.00 0.00 3.58
348 358 1.165270 GGCGCCAAGTAAACTGTCAT 58.835 50.000 24.80 0.00 0.00 3.06
349 359 1.539827 GGCGCCAAGTAAACTGTCATT 59.460 47.619 24.80 0.00 0.00 2.57
350 360 2.030274 GGCGCCAAGTAAACTGTCATTT 60.030 45.455 24.80 0.00 0.00 2.32
351 361 3.234386 GCGCCAAGTAAACTGTCATTTC 58.766 45.455 0.00 0.00 0.00 2.17
352 362 3.058224 GCGCCAAGTAAACTGTCATTTCT 60.058 43.478 0.00 0.00 0.00 2.52
353 363 4.466828 CGCCAAGTAAACTGTCATTTCTG 58.533 43.478 0.00 0.00 0.00 3.02
354 364 4.024048 CGCCAAGTAAACTGTCATTTCTGT 60.024 41.667 0.00 0.00 0.00 3.41
355 365 5.505654 CGCCAAGTAAACTGTCATTTCTGTT 60.506 40.000 0.00 0.00 0.00 3.16
356 366 5.687285 GCCAAGTAAACTGTCATTTCTGTTG 59.313 40.000 0.00 0.00 31.74 3.33
357 367 6.459573 GCCAAGTAAACTGTCATTTCTGTTGA 60.460 38.462 0.00 0.00 31.74 3.18
358 368 6.912591 CCAAGTAAACTGTCATTTCTGTTGAC 59.087 38.462 0.00 0.00 43.04 3.18
359 369 6.619801 AGTAAACTGTCATTTCTGTTGACC 57.380 37.500 1.73 0.00 42.25 4.02
360 370 6.119536 AGTAAACTGTCATTTCTGTTGACCA 58.880 36.000 1.73 0.00 42.25 4.02
361 371 5.913137 AAACTGTCATTTCTGTTGACCAA 57.087 34.783 1.73 0.00 42.25 3.67
362 372 5.505173 AACTGTCATTTCTGTTGACCAAG 57.495 39.130 1.73 0.00 42.25 3.61
363 373 4.526970 ACTGTCATTTCTGTTGACCAAGT 58.473 39.130 1.73 0.00 42.25 3.16
364 374 5.680619 ACTGTCATTTCTGTTGACCAAGTA 58.319 37.500 1.73 0.00 42.25 2.24
365 375 6.119536 ACTGTCATTTCTGTTGACCAAGTAA 58.880 36.000 1.73 0.00 42.25 2.24
366 376 6.601613 ACTGTCATTTCTGTTGACCAAGTAAA 59.398 34.615 1.73 0.00 42.25 2.01
367 377 6.791303 TGTCATTTCTGTTGACCAAGTAAAC 58.209 36.000 1.73 0.00 42.25 2.01
368 378 6.601613 TGTCATTTCTGTTGACCAAGTAAACT 59.398 34.615 1.73 0.00 42.25 2.66
369 379 6.912591 GTCATTTCTGTTGACCAAGTAAACTG 59.087 38.462 0.00 0.00 38.00 3.16
370 380 5.828299 TTTCTGTTGACCAAGTAAACTGG 57.172 39.130 3.00 0.00 30.14 4.00
371 381 4.497291 TCTGTTGACCAAGTAAACTGGT 57.503 40.909 0.00 0.00 38.87 4.00
378 388 5.419760 GACCAAGTAAACTGGTCTGTTTC 57.580 43.478 13.53 3.35 46.22 2.78
385 395 5.701290 AGTAAACTGGTCTGTTTCATGCTAC 59.299 40.000 8.79 2.79 40.23 3.58
391 3132 3.437049 GGTCTGTTTCATGCTACCTTGTC 59.563 47.826 0.00 0.00 0.00 3.18
399 3140 3.008923 TCATGCTACCTTGTCAACCATGA 59.991 43.478 0.00 0.00 36.30 3.07
409 3150 1.820519 GTCAACCATGATGTGCCATGT 59.179 47.619 0.00 0.00 41.65 3.21
421 3162 2.819019 TGTGCCATGTCAGTTTGGTATG 59.181 45.455 0.00 0.00 35.34 2.39
425 3166 3.119849 GCCATGTCAGTTTGGTATGTGTC 60.120 47.826 0.00 0.00 35.34 3.67
426 3167 3.125146 CCATGTCAGTTTGGTATGTGTCG 59.875 47.826 0.00 0.00 0.00 4.35
427 3168 3.462483 TGTCAGTTTGGTATGTGTCGT 57.538 42.857 0.00 0.00 0.00 4.34
428 3169 4.587584 TGTCAGTTTGGTATGTGTCGTA 57.412 40.909 0.00 0.00 0.00 3.43
429 3170 4.946445 TGTCAGTTTGGTATGTGTCGTAA 58.054 39.130 0.00 0.00 0.00 3.18
430 3171 5.358090 TGTCAGTTTGGTATGTGTCGTAAA 58.642 37.500 0.00 0.00 0.00 2.01
431 3172 5.234757 TGTCAGTTTGGTATGTGTCGTAAAC 59.765 40.000 0.00 0.00 0.00 2.01
434 3353 6.018588 TCAGTTTGGTATGTGTCGTAAACTTG 60.019 38.462 0.00 0.00 36.54 3.16
437 3356 4.309099 TGGTATGTGTCGTAAACTTGTCC 58.691 43.478 0.00 0.00 0.00 4.02
440 3359 2.891112 TGTGTCGTAAACTTGTCCGTT 58.109 42.857 0.00 0.00 0.00 4.44
442 3361 3.306703 TGTGTCGTAAACTTGTCCGTTTC 59.693 43.478 0.00 0.00 38.08 2.78
443 3362 3.306703 GTGTCGTAAACTTGTCCGTTTCA 59.693 43.478 0.00 0.00 38.08 2.69
448 3367 3.481112 AAACTTGTCCGTTTCACACAC 57.519 42.857 0.00 0.00 31.87 3.82
453 3372 4.659874 CCGTTTCACACACGCGCC 62.660 66.667 5.73 0.00 36.27 6.53
455 3374 4.659874 GTTTCACACACGCGCCGG 62.660 66.667 5.73 0.00 0.00 6.13
467 3386 2.433334 GCGCCGGCATTTTCGTTTC 61.433 57.895 28.98 0.00 39.62 2.78
469 3388 1.584495 GCCGGCATTTTCGTTTCCT 59.416 52.632 24.80 0.00 0.00 3.36
470 3389 0.038618 GCCGGCATTTTCGTTTCCTT 60.039 50.000 24.80 0.00 0.00 3.36
471 3390 1.696988 CCGGCATTTTCGTTTCCTTG 58.303 50.000 0.00 0.00 0.00 3.61
473 3392 2.050691 CGGCATTTTCGTTTCCTTGTG 58.949 47.619 0.00 0.00 0.00 3.33
476 3395 3.490078 GGCATTTTCGTTTCCTTGTGTCA 60.490 43.478 0.00 0.00 0.00 3.58
477 3396 4.298332 GCATTTTCGTTTCCTTGTGTCAT 58.702 39.130 0.00 0.00 0.00 3.06
478 3397 4.148696 GCATTTTCGTTTCCTTGTGTCATG 59.851 41.667 0.00 0.00 0.00 3.07
479 3398 5.518812 CATTTTCGTTTCCTTGTGTCATGA 58.481 37.500 0.00 0.00 0.00 3.07
480 3399 5.766150 TTTTCGTTTCCTTGTGTCATGAT 57.234 34.783 0.00 0.00 0.00 2.45
531 3830 1.514087 GTATCTGAACCCACGCCGA 59.486 57.895 0.00 0.00 0.00 5.54
542 3841 3.645975 ACGCCGAGCAAAACGTGG 61.646 61.111 0.00 0.00 37.37 4.94
610 3909 2.276680 GAAAATCGCGCGGACAGC 60.277 61.111 31.69 13.40 43.95 4.40
638 3941 4.308526 GGTACGGACAGACGGAGA 57.691 61.111 0.00 0.00 38.39 3.71
639 3942 2.791170 GGTACGGACAGACGGAGAT 58.209 57.895 0.00 0.00 38.39 2.75
640 3943 0.662085 GGTACGGACAGACGGAGATC 59.338 60.000 0.00 0.00 38.39 2.75
641 3944 1.666054 GTACGGACAGACGGAGATCT 58.334 55.000 0.00 0.00 38.39 2.75
643 3946 1.096416 ACGGACAGACGGAGATCTTC 58.904 55.000 0.00 0.00 38.39 2.87
644 3947 1.095600 CGGACAGACGGAGATCTTCA 58.904 55.000 0.96 0.00 0.00 3.02
647 3950 1.469308 GACAGACGGAGATCTTCACGT 59.531 52.381 17.25 17.25 42.88 4.49
648 3951 2.676839 GACAGACGGAGATCTTCACGTA 59.323 50.000 17.24 0.00 39.95 3.57
652 3955 4.272748 CAGACGGAGATCTTCACGTACATA 59.727 45.833 17.24 0.00 39.95 2.29
654 3957 5.049336 AGACGGAGATCTTCACGTACATATG 60.049 44.000 17.24 0.00 39.95 1.78
655 3958 4.579340 ACGGAGATCTTCACGTACATATGT 59.421 41.667 13.93 13.93 37.85 2.29
656 3959 5.147865 CGGAGATCTTCACGTACATATGTC 58.852 45.833 12.68 3.54 0.00 3.06
657 3960 5.049336 CGGAGATCTTCACGTACATATGTCT 60.049 44.000 12.68 0.00 0.00 3.41
658 3961 6.375377 GGAGATCTTCACGTACATATGTCTC 58.625 44.000 12.68 8.30 0.00 3.36
659 3962 6.320494 AGATCTTCACGTACATATGTCTCC 57.680 41.667 12.68 0.85 0.00 3.71
660 3963 4.913335 TCTTCACGTACATATGTCTCCC 57.087 45.455 12.68 0.00 0.00 4.30
661 3964 4.533815 TCTTCACGTACATATGTCTCCCT 58.466 43.478 12.68 0.00 0.00 4.20
662 3965 4.579340 TCTTCACGTACATATGTCTCCCTC 59.421 45.833 12.68 0.00 0.00 4.30
663 3966 2.876550 TCACGTACATATGTCTCCCTCG 59.123 50.000 12.68 10.82 0.00 4.63
664 3967 2.031069 CACGTACATATGTCTCCCTCGG 60.031 54.545 12.68 0.00 0.00 4.63
668 3998 1.244816 CATATGTCTCCCTCGGCGTA 58.755 55.000 6.85 0.00 0.00 4.42
670 4000 1.162181 TATGTCTCCCTCGGCGTACG 61.162 60.000 11.84 11.84 46.11 3.67
682 4012 0.024619 GGCGTACGCGATCTTTTGAC 59.975 55.000 31.78 11.77 43.06 3.18
692 4022 3.720051 GCGATCTTTTGACGTAACGTTCC 60.720 47.826 2.82 0.00 41.37 3.62
694 4024 2.126467 TCTTTTGACGTAACGTTCCCG 58.874 47.619 2.82 11.51 41.37 5.14
709 4039 2.443887 TCCCGACGTGTCCTTTTTAG 57.556 50.000 0.00 0.00 0.00 1.85
719 4049 3.872771 GTGTCCTTTTTAGAACGTGACCA 59.127 43.478 0.00 0.00 0.00 4.02
720 4050 4.514066 GTGTCCTTTTTAGAACGTGACCAT 59.486 41.667 0.00 0.00 0.00 3.55
722 4052 6.203338 GTGTCCTTTTTAGAACGTGACCATTA 59.797 38.462 0.00 0.00 0.00 1.90
723 4053 6.425721 TGTCCTTTTTAGAACGTGACCATTAG 59.574 38.462 0.00 0.00 0.00 1.73
724 4054 5.935789 TCCTTTTTAGAACGTGACCATTAGG 59.064 40.000 0.00 0.00 42.21 2.69
771 4101 4.939509 CCGTTAGGTTATGTTTGTCCTG 57.060 45.455 0.00 0.00 0.00 3.86
778 4108 3.758554 GGTTATGTTTGTCCTGAGCACAT 59.241 43.478 0.00 0.00 32.80 3.21
800 4130 1.741770 GTCGGTCAGGTCCATGCAC 60.742 63.158 0.00 0.00 0.00 4.57
802 4132 2.347490 GGTCAGGTCCATGCACGT 59.653 61.111 0.00 0.00 0.00 4.49
803 4133 1.594833 GGTCAGGTCCATGCACGTA 59.405 57.895 0.00 0.00 0.00 3.57
804 4134 0.739813 GGTCAGGTCCATGCACGTAC 60.740 60.000 0.00 0.00 0.00 3.67
809 4145 2.159627 CAGGTCCATGCACGTACTTTTC 59.840 50.000 0.00 0.00 0.00 2.29
838 4660 2.437413 CTGCATGATGATGATCCTGGG 58.563 52.381 0.00 0.00 0.00 4.45
980 5037 1.138069 TCTGAGCAAACACTCGGACAA 59.862 47.619 0.00 0.00 45.14 3.18
1031 5088 0.689080 ATCAGGAGCGGAGTCACCAT 60.689 55.000 0.00 0.00 38.90 3.55
1032 5089 1.142748 CAGGAGCGGAGTCACCATC 59.857 63.158 0.00 0.00 38.90 3.51
1033 5090 1.305297 AGGAGCGGAGTCACCATCA 60.305 57.895 0.00 0.00 38.90 3.07
1058 5115 2.678934 CACTGCTTGGGCTGCCAT 60.679 61.111 22.05 0.00 40.37 4.40
1103 5160 4.283722 ACTTGATCGGACAAGAAGGTTACT 59.716 41.667 22.10 2.45 46.85 2.24
1115 5172 3.072622 AGAAGGTTACTCCAACTCCAACC 59.927 47.826 0.00 0.00 39.15 3.77
1116 5173 2.414612 AGGTTACTCCAACTCCAACCA 58.585 47.619 4.75 0.00 40.92 3.67
1119 5176 1.809133 TACTCCAACTCCAACCACCA 58.191 50.000 0.00 0.00 0.00 4.17
1121 5178 2.344592 ACTCCAACTCCAACCACCATA 58.655 47.619 0.00 0.00 0.00 2.74
1128 5185 2.039879 ACTCCAACCACCATACTTGTCC 59.960 50.000 0.00 0.00 0.00 4.02
1132 5189 0.323629 ACCACCATACTTGTCCACCG 59.676 55.000 0.00 0.00 0.00 4.94
1139 5196 2.380084 TACTTGTCCACCGCATTCTC 57.620 50.000 0.00 0.00 0.00 2.87
1147 5204 1.448540 ACCGCATTCTCGCCTCAAG 60.449 57.895 0.00 0.00 0.00 3.02
1155 5212 4.437239 CATTCTCGCCTCAAGTAAGATGT 58.563 43.478 0.00 0.00 0.00 3.06
1158 5215 3.509967 TCTCGCCTCAAGTAAGATGTCAA 59.490 43.478 0.00 0.00 0.00 3.18
1184 5241 1.586564 GGCGATCGAGAGTCCGTTG 60.587 63.158 21.57 0.00 0.00 4.10
1267 5327 2.601666 ACGAGGTGCTGCTGGAGA 60.602 61.111 0.00 0.00 0.00 3.71
2178 7632 0.456653 CTGCTTGTTGTATTGCCCGC 60.457 55.000 0.00 0.00 0.00 6.13
2179 7633 1.153842 GCTTGTTGTATTGCCCGCC 60.154 57.895 0.00 0.00 0.00 6.13
2180 7634 1.872197 GCTTGTTGTATTGCCCGCCA 61.872 55.000 0.00 0.00 0.00 5.69
2181 7635 0.600557 CTTGTTGTATTGCCCGCCAA 59.399 50.000 0.00 0.00 37.94 4.52
2184 7673 1.067283 TGTTGTATTGCCCGCCAAATG 60.067 47.619 0.00 0.00 36.92 2.32
2197 7686 0.890683 CCAAATGTGGTTCTGAGGCC 59.109 55.000 0.00 0.00 40.42 5.19
2204 7693 0.842030 TGGTTCTGAGGCCCATGTCT 60.842 55.000 0.00 0.00 0.00 3.41
2205 7694 0.107459 GGTTCTGAGGCCCATGTCTC 60.107 60.000 0.00 0.00 43.79 3.36
2241 7730 1.122019 GGATCCCACCTATCACGCCT 61.122 60.000 0.00 0.00 0.00 5.52
2243 7732 2.180276 GATCCCACCTATCACGCCTAT 58.820 52.381 0.00 0.00 0.00 2.57
2247 7736 3.968649 TCCCACCTATCACGCCTATAAAA 59.031 43.478 0.00 0.00 0.00 1.52
2270 7759 0.606401 ACGCTGACCATTCCCAACTG 60.606 55.000 0.00 0.00 0.00 3.16
2275 7764 3.012518 CTGACCATTCCCAACTGTGATC 58.987 50.000 0.00 0.00 0.00 2.92
2278 7767 4.082125 GACCATTCCCAACTGTGATCTTT 58.918 43.478 0.00 0.00 0.00 2.52
2279 7768 4.082125 ACCATTCCCAACTGTGATCTTTC 58.918 43.478 0.00 0.00 0.00 2.62
2280 7769 4.202609 ACCATTCCCAACTGTGATCTTTCT 60.203 41.667 0.00 0.00 0.00 2.52
2281 7770 4.768968 CCATTCCCAACTGTGATCTTTCTT 59.231 41.667 0.00 0.00 0.00 2.52
2284 7773 6.877611 TTCCCAACTGTGATCTTTCTTAAC 57.122 37.500 0.00 0.00 0.00 2.01
2287 7776 5.711976 CCCAACTGTGATCTTTCTTAACCAT 59.288 40.000 0.00 0.00 0.00 3.55
2289 7778 6.349611 CCAACTGTGATCTTTCTTAACCATGG 60.350 42.308 11.19 11.19 0.00 3.66
2293 7782 7.505585 ACTGTGATCTTTCTTAACCATGGAAAA 59.494 33.333 21.47 10.94 0.00 2.29
2294 7783 8.243961 TGTGATCTTTCTTAACCATGGAAAAA 57.756 30.769 21.47 8.32 0.00 1.94
2295 7784 8.869109 TGTGATCTTTCTTAACCATGGAAAAAT 58.131 29.630 21.47 0.00 0.00 1.82
2306 7795 9.762381 TTAACCATGGAAAAATATAGACTTGGT 57.238 29.630 21.47 0.00 35.36 3.67
2307 7796 7.881775 ACCATGGAAAAATATAGACTTGGTC 57.118 36.000 21.47 0.00 0.00 4.02
2308 7797 7.410174 ACCATGGAAAAATATAGACTTGGTCA 58.590 34.615 21.47 0.00 34.60 4.02
2309 7798 7.557719 ACCATGGAAAAATATAGACTTGGTCAG 59.442 37.037 21.47 0.00 34.60 3.51
2310 7799 7.420800 CATGGAAAAATATAGACTTGGTCAGC 58.579 38.462 0.52 0.00 34.60 4.26
2311 7800 6.480763 TGGAAAAATATAGACTTGGTCAGCA 58.519 36.000 0.52 0.00 34.60 4.41
2312 7801 6.374333 TGGAAAAATATAGACTTGGTCAGCAC 59.626 38.462 0.52 0.00 34.60 4.40
2313 7802 6.183360 GGAAAAATATAGACTTGGTCAGCACC 60.183 42.308 0.52 0.00 44.10 5.01
2322 7811 4.980805 GTCAGCACCGCGACCCAA 62.981 66.667 8.23 0.00 0.00 4.12
2323 7812 4.680237 TCAGCACCGCGACCCAAG 62.680 66.667 8.23 0.00 0.00 3.61
2324 7813 4.988598 CAGCACCGCGACCCAAGT 62.989 66.667 8.23 0.00 0.00 3.16
2325 7814 4.250305 AGCACCGCGACCCAAGTT 62.250 61.111 8.23 0.00 0.00 2.66
2326 7815 4.025401 GCACCGCGACCCAAGTTG 62.025 66.667 8.23 0.00 0.00 3.16
2331 7820 3.670377 GCGACCCAAGTTGCCACC 61.670 66.667 0.00 0.00 46.27 4.61
2332 7821 2.113139 CGACCCAAGTTGCCACCT 59.887 61.111 0.00 0.00 0.00 4.00
2333 7822 2.260869 CGACCCAAGTTGCCACCTG 61.261 63.158 0.00 0.00 0.00 4.00
2334 7823 2.521708 ACCCAAGTTGCCACCTGC 60.522 61.111 0.00 0.00 41.77 4.85
2353 7842 1.207488 CCCAGGGAACTCCATGTCCA 61.207 60.000 0.00 0.00 45.66 4.02
2391 7880 4.060900 GCGAGATTGCATTATCCTCTTGA 58.939 43.478 0.00 0.00 34.15 3.02
2393 7882 4.152045 CGAGATTGCATTATCCTCTTGAGC 59.848 45.833 0.00 0.00 0.00 4.26
2395 7884 5.307204 AGATTGCATTATCCTCTTGAGCTC 58.693 41.667 6.82 6.82 0.00 4.09
2396 7885 4.492494 TTGCATTATCCTCTTGAGCTCA 57.508 40.909 13.74 13.74 0.00 4.26
2401 7890 6.877855 TGCATTATCCTCTTGAGCTCATAATC 59.122 38.462 19.04 11.10 0.00 1.75
2413 7902 9.512435 CTTGAGCTCATAATCCAACAATAAAAG 57.488 33.333 19.04 1.27 0.00 2.27
2416 7905 8.230472 AGCTCATAATCCAACAATAAAAGAGG 57.770 34.615 0.00 0.00 0.00 3.69
2433 7922 3.243359 GAGGATCCTCTCTCCATCTGT 57.757 52.381 31.11 0.00 39.80 3.41
2435 7924 4.735369 GAGGATCCTCTCTCCATCTGTTA 58.265 47.826 31.11 0.00 39.80 2.41
2436 7925 5.144100 GAGGATCCTCTCTCCATCTGTTAA 58.856 45.833 31.11 0.00 39.80 2.01
2438 7927 5.543405 AGGATCCTCTCTCCATCTGTTAATG 59.457 44.000 9.02 0.00 35.08 1.90
2439 7928 5.541868 GGATCCTCTCTCCATCTGTTAATGA 59.458 44.000 3.84 0.00 32.72 2.57
2441 7930 6.662865 TCCTCTCTCCATCTGTTAATGATC 57.337 41.667 0.00 0.00 0.00 2.92
2442 7931 6.380414 TCCTCTCTCCATCTGTTAATGATCT 58.620 40.000 0.00 0.00 0.00 2.75
2443 7932 6.843333 TCCTCTCTCCATCTGTTAATGATCTT 59.157 38.462 0.00 0.00 0.00 2.40
2444 7933 6.930164 CCTCTCTCCATCTGTTAATGATCTTG 59.070 42.308 0.00 0.00 0.00 3.02
2445 7934 7.201983 CCTCTCTCCATCTGTTAATGATCTTGA 60.202 40.741 0.00 0.00 0.00 3.02
2446 7935 7.495901 TCTCTCCATCTGTTAATGATCTTGAC 58.504 38.462 0.00 0.00 0.00 3.18
2447 7936 7.344093 TCTCTCCATCTGTTAATGATCTTGACT 59.656 37.037 0.00 0.00 0.00 3.41
2448 7937 7.855375 TCTCCATCTGTTAATGATCTTGACTT 58.145 34.615 0.00 0.00 0.00 3.01
2449 7938 7.984050 TCTCCATCTGTTAATGATCTTGACTTC 59.016 37.037 0.00 0.00 0.00 3.01
2450 7939 7.855375 TCCATCTGTTAATGATCTTGACTTCT 58.145 34.615 0.00 0.00 0.00 2.85
2451 7940 8.981659 TCCATCTGTTAATGATCTTGACTTCTA 58.018 33.333 0.00 0.00 0.00 2.10
2452 7941 9.775854 CCATCTGTTAATGATCTTGACTTCTAT 57.224 33.333 0.00 0.00 0.00 1.98
2466 7955 8.319146 TCTTGACTTCTATAAACTGGTAAAGGG 58.681 37.037 0.00 0.00 0.00 3.95
2468 7957 8.669055 TGACTTCTATAAACTGGTAAAGGGTA 57.331 34.615 0.00 0.00 0.00 3.69
2470 7959 8.906238 ACTTCTATAAACTGGTAAAGGGTAGA 57.094 34.615 0.00 0.00 0.00 2.59
2471 7960 8.756927 ACTTCTATAAACTGGTAAAGGGTAGAC 58.243 37.037 0.00 0.00 0.00 2.59
2485 7974 4.461198 AGGGTAGACAACAGGTTTTTCAG 58.539 43.478 0.00 0.00 0.00 3.02
2506 8003 9.554724 TTTCAGTTTCGTTGCTATTATGAAATC 57.445 29.630 0.00 0.00 34.20 2.17
2546 8043 0.464013 TGTTTTCTCCGAACCCGCAA 60.464 50.000 0.00 0.00 0.00 4.85
2569 8066 2.838736 AGCTCTTGTGTGTGGTTGTAG 58.161 47.619 0.00 0.00 0.00 2.74
2572 8069 4.040461 AGCTCTTGTGTGTGGTTGTAGTAT 59.960 41.667 0.00 0.00 0.00 2.12
2573 8070 4.755123 GCTCTTGTGTGTGGTTGTAGTATT 59.245 41.667 0.00 0.00 0.00 1.89
2574 8071 5.929992 GCTCTTGTGTGTGGTTGTAGTATTA 59.070 40.000 0.00 0.00 0.00 0.98
2575 8072 6.090898 GCTCTTGTGTGTGGTTGTAGTATTAG 59.909 42.308 0.00 0.00 0.00 1.73
2576 8073 7.292713 TCTTGTGTGTGGTTGTAGTATTAGA 57.707 36.000 0.00 0.00 0.00 2.10
2579 8076 7.292713 TGTGTGTGGTTGTAGTATTAGAGAA 57.707 36.000 0.00 0.00 0.00 2.87
2582 8079 8.086522 GTGTGTGGTTGTAGTATTAGAGAAGAA 58.913 37.037 0.00 0.00 0.00 2.52
2591 8088 9.961264 TGTAGTATTAGAGAAGAAGAAGACAGA 57.039 33.333 0.00 0.00 0.00 3.41
2596 8093 8.821686 ATTAGAGAAGAAGAAGACAGAGATGA 57.178 34.615 0.00 0.00 0.00 2.92
2603 8100 0.467384 AAGACAGAGATGATGGGCGG 59.533 55.000 0.00 0.00 0.00 6.13
2604 8101 0.397675 AGACAGAGATGATGGGCGGA 60.398 55.000 0.00 0.00 0.00 5.54
2605 8102 0.033228 GACAGAGATGATGGGCGGAG 59.967 60.000 0.00 0.00 0.00 4.63
2606 8103 0.397675 ACAGAGATGATGGGCGGAGA 60.398 55.000 0.00 0.00 0.00 3.71
2607 8104 0.755079 CAGAGATGATGGGCGGAGAA 59.245 55.000 0.00 0.00 0.00 2.87
2608 8105 1.347050 CAGAGATGATGGGCGGAGAAT 59.653 52.381 0.00 0.00 0.00 2.40
2617 8114 1.003233 GGCGGAGAATAGATGCCCC 60.003 63.158 0.00 0.00 39.83 5.80
2619 8116 0.108585 GCGGAGAATAGATGCCCCAA 59.891 55.000 0.00 0.00 0.00 4.12
2636 8133 2.134346 CCAAAAATGAAACCTGCCACG 58.866 47.619 0.00 0.00 0.00 4.94
2742 8240 8.138074 GGTAAAATCCTGCCTAATTCTGAATTC 58.862 37.037 18.22 6.19 32.38 2.17
2757 8255 2.009774 GAATTCTGAGGCGCTTTAGCA 58.990 47.619 7.64 0.00 42.21 3.49
2764 8268 1.132640 GGCGCTTTAGCAGTCAACG 59.867 57.895 7.64 0.00 42.21 4.10
2770 8274 3.122948 CGCTTTAGCAGTCAACGTTACAT 59.877 43.478 0.00 0.00 42.21 2.29
2780 8284 4.023450 AGTCAACGTTACATCTTCGAGACA 60.023 41.667 0.00 0.00 36.52 3.41
2804 8724 5.247564 AGTGTCCAGTGTTTAATAGCCTGTA 59.752 40.000 0.00 0.00 0.00 2.74
2809 8729 5.237344 CCAGTGTTTAATAGCCTGTAGATGC 59.763 44.000 0.00 0.00 0.00 3.91
2828 8761 4.724074 TGCCTTCATAATTTTGAGCCTG 57.276 40.909 7.38 0.00 0.00 4.85
2830 8763 3.119029 GCCTTCATAATTTTGAGCCTGCA 60.119 43.478 0.00 0.00 0.00 4.41
2977 8971 2.230994 CTGGTGCTCCGCTGCTTCTA 62.231 60.000 0.00 0.00 36.30 2.10
3008 9776 4.468153 GTCTTCCTGAACACCTTCTAGGAT 59.532 45.833 0.00 0.00 37.67 3.24
3088 9930 1.768684 AAGGGCAGCGAGTTTCTGGA 61.769 55.000 0.00 0.00 32.41 3.86
3122 9964 0.330604 TACAGACCGCCTAGACTGGT 59.669 55.000 0.00 0.00 39.12 4.00
3153 10363 4.334443 CACAACGTATCTTGTGCTTATGC 58.666 43.478 5.25 0.00 43.38 3.14
3154 10364 3.374058 ACAACGTATCTTGTGCTTATGCC 59.626 43.478 0.00 0.00 38.71 4.40
3155 10365 3.543680 ACGTATCTTGTGCTTATGCCT 57.456 42.857 0.00 0.00 38.71 4.75
3156 10366 3.198068 ACGTATCTTGTGCTTATGCCTG 58.802 45.455 0.00 0.00 38.71 4.85
3157 10367 3.118775 ACGTATCTTGTGCTTATGCCTGA 60.119 43.478 0.00 0.00 38.71 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.821160 TGCAGGTTCAGACGAAAATGATATTA 59.179 34.615 0.00 0.00 31.43 0.98
63 64 6.014156 GGAGCAGGGTTATCAGAGTTATATGT 60.014 42.308 0.00 0.00 0.00 2.29
77 78 2.365105 CCTCCGGGAGCAGGGTTA 60.365 66.667 18.91 0.00 33.58 2.85
110 111 0.453793 CCTCGAAGCTCACGTCATCT 59.546 55.000 11.82 0.00 0.00 2.90
185 191 3.503748 GGTGCTACACAAAATTGCTCTCT 59.496 43.478 0.00 0.00 35.86 3.10
201 207 0.608130 AGATGACTGCGTTGGTGCTA 59.392 50.000 0.00 0.00 35.36 3.49
202 208 0.671781 GAGATGACTGCGTTGGTGCT 60.672 55.000 0.00 0.00 35.36 4.40
203 209 1.639298 GGAGATGACTGCGTTGGTGC 61.639 60.000 0.00 0.00 0.00 5.01
205 211 0.036952 CAGGAGATGACTGCGTTGGT 60.037 55.000 0.00 0.00 39.46 3.67
206 212 0.036952 ACAGGAGATGACTGCGTTGG 60.037 55.000 0.00 0.00 39.55 3.77
210 219 0.738762 CACCACAGGAGATGACTGCG 60.739 60.000 0.00 0.00 39.55 5.18
252 261 3.944422 ACAAGACATGACAAACACGAC 57.056 42.857 0.00 0.00 0.00 4.34
261 270 8.342634 ACACAATACAAAGTAACAAGACATGAC 58.657 33.333 0.00 0.00 0.00 3.06
292 301 0.606944 AACCGAAGCGCATAAACCCA 60.607 50.000 11.47 0.00 0.00 4.51
314 324 3.190874 TGGCGCCTTTTTACACTTTTTG 58.809 40.909 29.70 0.00 0.00 2.44
315 325 3.528597 TGGCGCCTTTTTACACTTTTT 57.471 38.095 29.70 0.00 0.00 1.94
334 344 7.898725 GTCAACAGAAATGACAGTTTACTTG 57.101 36.000 2.01 0.00 45.13 3.16
344 354 6.912591 CAGTTTACTTGGTCAACAGAAATGAC 59.087 38.462 0.00 0.00 45.08 3.06
345 355 6.039270 CCAGTTTACTTGGTCAACAGAAATGA 59.961 38.462 0.00 0.00 0.00 2.57
346 356 6.183360 ACCAGTTTACTTGGTCAACAGAAATG 60.183 38.462 0.00 0.00 0.00 2.32
347 357 5.891551 ACCAGTTTACTTGGTCAACAGAAAT 59.108 36.000 0.00 0.00 0.00 2.17
348 358 5.258051 ACCAGTTTACTTGGTCAACAGAAA 58.742 37.500 0.00 0.00 0.00 2.52
349 359 4.850680 ACCAGTTTACTTGGTCAACAGAA 58.149 39.130 0.00 0.00 0.00 3.02
350 360 4.497291 ACCAGTTTACTTGGTCAACAGA 57.503 40.909 0.00 0.00 0.00 3.41
357 367 4.850680 TGAAACAGACCAGTTTACTTGGT 58.149 39.130 0.00 0.00 41.48 3.67
358 368 5.762045 CATGAAACAGACCAGTTTACTTGG 58.238 41.667 0.00 0.00 41.48 3.61
359 369 5.009010 AGCATGAAACAGACCAGTTTACTTG 59.991 40.000 0.00 0.00 41.48 3.16
360 370 5.133221 AGCATGAAACAGACCAGTTTACTT 58.867 37.500 0.00 0.00 41.48 2.24
361 371 4.718961 AGCATGAAACAGACCAGTTTACT 58.281 39.130 0.00 0.00 41.48 2.24
362 372 5.106673 GGTAGCATGAAACAGACCAGTTTAC 60.107 44.000 0.00 0.00 41.48 2.01
363 373 5.001232 GGTAGCATGAAACAGACCAGTTTA 58.999 41.667 0.00 0.00 41.48 2.01
364 374 3.821033 GGTAGCATGAAACAGACCAGTTT 59.179 43.478 0.00 0.00 43.90 2.66
365 375 3.073062 AGGTAGCATGAAACAGACCAGTT 59.927 43.478 0.00 0.00 0.00 3.16
366 376 2.639839 AGGTAGCATGAAACAGACCAGT 59.360 45.455 0.00 0.00 0.00 4.00
367 377 3.340814 AGGTAGCATGAAACAGACCAG 57.659 47.619 0.00 0.00 0.00 4.00
368 378 3.181445 ACAAGGTAGCATGAAACAGACCA 60.181 43.478 3.86 0.00 0.00 4.02
369 379 3.412386 ACAAGGTAGCATGAAACAGACC 58.588 45.455 3.86 0.00 0.00 3.85
370 380 4.065088 TGACAAGGTAGCATGAAACAGAC 58.935 43.478 3.86 0.00 0.00 3.51
371 381 4.350368 TGACAAGGTAGCATGAAACAGA 57.650 40.909 3.86 0.00 0.00 3.41
372 382 4.320494 GGTTGACAAGGTAGCATGAAACAG 60.320 45.833 16.27 0.00 0.00 3.16
373 383 3.568007 GGTTGACAAGGTAGCATGAAACA 59.432 43.478 16.27 7.25 0.00 2.83
374 384 3.568007 TGGTTGACAAGGTAGCATGAAAC 59.432 43.478 3.86 7.79 0.00 2.78
375 385 3.826524 TGGTTGACAAGGTAGCATGAAA 58.173 40.909 3.86 0.00 0.00 2.69
376 386 3.500448 TGGTTGACAAGGTAGCATGAA 57.500 42.857 3.86 0.00 0.00 2.57
377 387 3.346315 CATGGTTGACAAGGTAGCATGA 58.654 45.455 10.23 0.00 45.69 3.07
378 388 3.346315 TCATGGTTGACAAGGTAGCATG 58.654 45.455 9.70 9.70 44.75 4.06
385 395 1.203052 GGCACATCATGGTTGACAAGG 59.797 52.381 0.00 0.00 33.85 3.61
409 3150 5.603596 AGTTTACGACACATACCAAACTGA 58.396 37.500 0.00 0.00 35.51 3.41
421 3162 3.306703 TGAAACGGACAAGTTTACGACAC 59.693 43.478 0.00 0.00 43.54 3.67
425 3166 3.062369 TGTGTGAAACGGACAAGTTTACG 59.938 43.478 0.00 0.00 43.54 3.18
426 3167 4.336932 GTGTGTGAAACGGACAAGTTTAC 58.663 43.478 0.00 0.00 43.54 2.01
427 3168 3.062369 CGTGTGTGAAACGGACAAGTTTA 59.938 43.478 0.00 0.00 43.54 2.01
428 3169 2.159626 CGTGTGTGAAACGGACAAGTTT 60.160 45.455 0.00 0.00 45.85 2.66
429 3170 1.395608 CGTGTGTGAAACGGACAAGTT 59.604 47.619 0.00 0.00 42.39 2.66
430 3171 1.003851 CGTGTGTGAAACGGACAAGT 58.996 50.000 0.00 0.00 42.39 3.16
431 3172 0.315869 GCGTGTGTGAAACGGACAAG 60.316 55.000 0.00 0.00 42.39 3.16
434 3353 2.244382 CGCGTGTGTGAAACGGAC 59.756 61.111 0.00 0.00 42.39 4.79
437 3356 4.986531 CGGCGCGTGTGTGAAACG 62.987 66.667 8.43 0.00 42.39 3.60
448 3367 4.752142 AACGAAAATGCCGGCGCG 62.752 61.111 23.90 20.93 38.08 6.86
453 3372 2.050691 CACAAGGAAACGAAAATGCCG 58.949 47.619 0.00 0.00 0.00 5.69
455 3374 3.701241 TGACACAAGGAAACGAAAATGC 58.299 40.909 0.00 0.00 0.00 3.56
467 3386 9.778993 CTATTTTCAGTTAATCATGACACAAGG 57.221 33.333 0.00 0.00 0.00 3.61
507 3464 2.588034 GGGTTCAGATACGCCGGC 60.588 66.667 19.07 19.07 0.00 6.13
531 3830 2.255252 GCGATGCCACGTTTTGCT 59.745 55.556 0.00 0.00 35.59 3.91
570 3869 3.961414 TCCCCGGTTGAACAGCCC 61.961 66.667 0.00 0.00 0.00 5.19
571 3870 2.671963 GTCCCCGGTTGAACAGCC 60.672 66.667 0.00 0.00 0.00 4.85
594 3893 3.047280 TGCTGTCCGCGCGATTTT 61.047 55.556 34.63 0.00 43.27 1.82
610 3909 3.773630 CCGTACCGCGCAACTGTG 61.774 66.667 8.75 0.00 39.71 3.66
611 3910 3.980989 TCCGTACCGCGCAACTGT 61.981 61.111 8.75 0.62 39.71 3.55
625 3928 1.095600 TGAAGATCTCCGTCTGTCCG 58.904 55.000 0.00 0.00 0.00 4.79
637 3940 5.241949 AGGGAGACATATGTACGTGAAGATC 59.758 44.000 8.71 0.00 0.00 2.75
638 3941 5.141182 AGGGAGACATATGTACGTGAAGAT 58.859 41.667 8.71 0.00 0.00 2.40
639 3942 4.533815 AGGGAGACATATGTACGTGAAGA 58.466 43.478 8.71 0.00 0.00 2.87
640 3943 4.554919 CGAGGGAGACATATGTACGTGAAG 60.555 50.000 8.71 0.00 0.00 3.02
641 3944 3.314357 CGAGGGAGACATATGTACGTGAA 59.686 47.826 8.71 0.00 0.00 3.18
643 3946 2.031069 CCGAGGGAGACATATGTACGTG 60.031 54.545 8.71 0.00 0.00 4.49
644 3947 2.228059 CCGAGGGAGACATATGTACGT 58.772 52.381 8.71 4.08 0.00 3.57
647 3950 1.244816 CGCCGAGGGAGACATATGTA 58.755 55.000 8.71 0.00 0.00 2.29
648 3951 0.755698 ACGCCGAGGGAGACATATGT 60.756 55.000 8.43 8.43 0.00 2.29
652 3955 2.478890 CGTACGCCGAGGGAGACAT 61.479 63.158 0.52 0.00 39.56 3.06
654 3957 4.549516 GCGTACGCCGAGGGAGAC 62.550 72.222 29.51 0.00 39.56 3.36
658 3961 4.977126 GATCGCGTACGCCGAGGG 62.977 72.222 32.64 19.08 39.56 4.30
659 3962 2.931713 AAAGATCGCGTACGCCGAGG 62.932 60.000 32.64 19.46 39.56 4.63
660 3963 1.138047 AAAAGATCGCGTACGCCGAG 61.138 55.000 32.64 19.82 39.56 4.63
661 3964 1.153978 AAAAGATCGCGTACGCCGA 60.154 52.632 32.64 29.75 39.56 5.54
662 3965 1.013755 CAAAAGATCGCGTACGCCG 60.014 57.895 32.64 26.04 39.84 6.46
663 3966 0.024619 GTCAAAAGATCGCGTACGCC 59.975 55.000 32.64 19.68 39.84 5.68
664 3967 0.313233 CGTCAAAAGATCGCGTACGC 60.313 55.000 29.83 29.83 39.84 4.42
668 3998 1.384409 CGTTACGTCAAAAGATCGCGT 59.616 47.619 5.77 0.00 39.23 6.01
670 4000 3.393022 GAACGTTACGTCAAAAGATCGC 58.607 45.455 11.79 0.00 39.99 4.58
692 4022 2.154389 CGTTCTAAAAAGGACACGTCGG 59.846 50.000 0.00 0.00 0.00 4.79
694 4024 3.798337 TCACGTTCTAAAAAGGACACGTC 59.202 43.478 0.00 0.00 38.75 4.34
734 4064 2.619362 CGGTGTAGTCCCGCAAAAA 58.381 52.632 0.00 0.00 38.85 1.94
735 4065 4.364817 CGGTGTAGTCCCGCAAAA 57.635 55.556 0.00 0.00 38.85 2.44
741 4071 3.448660 ACATAACCTAACGGTGTAGTCCC 59.551 47.826 0.00 0.00 44.73 4.46
742 4072 4.725790 ACATAACCTAACGGTGTAGTCC 57.274 45.455 0.00 0.00 44.73 3.85
743 4073 5.928264 ACAAACATAACCTAACGGTGTAGTC 59.072 40.000 0.00 0.00 44.73 2.59
744 4074 5.857268 ACAAACATAACCTAACGGTGTAGT 58.143 37.500 0.00 0.00 44.73 2.73
745 4075 5.349543 GGACAAACATAACCTAACGGTGTAG 59.650 44.000 0.00 0.00 44.73 2.74
746 4076 5.011943 AGGACAAACATAACCTAACGGTGTA 59.988 40.000 0.00 0.00 44.73 2.90
747 4077 4.067192 GGACAAACATAACCTAACGGTGT 58.933 43.478 0.00 0.00 44.73 4.16
748 4078 4.153475 CAGGACAAACATAACCTAACGGTG 59.847 45.833 0.00 0.00 44.73 4.94
750 4080 4.571919 TCAGGACAAACATAACCTAACGG 58.428 43.478 0.00 0.00 0.00 4.44
751 4081 4.092968 GCTCAGGACAAACATAACCTAACG 59.907 45.833 0.00 0.00 0.00 3.18
752 4082 5.001232 TGCTCAGGACAAACATAACCTAAC 58.999 41.667 0.00 0.00 0.00 2.34
753 4083 5.001232 GTGCTCAGGACAAACATAACCTAA 58.999 41.667 0.00 0.00 0.00 2.69
754 4084 4.041075 TGTGCTCAGGACAAACATAACCTA 59.959 41.667 0.00 0.00 0.00 3.08
755 4085 3.181445 TGTGCTCAGGACAAACATAACCT 60.181 43.478 0.00 0.00 0.00 3.50
756 4086 3.146066 TGTGCTCAGGACAAACATAACC 58.854 45.455 0.00 0.00 0.00 2.85
757 4087 4.726416 CATGTGCTCAGGACAAACATAAC 58.274 43.478 1.88 0.00 30.55 1.89
758 4088 3.191162 GCATGTGCTCAGGACAAACATAA 59.809 43.478 1.88 0.00 38.21 1.90
759 4089 2.749076 GCATGTGCTCAGGACAAACATA 59.251 45.455 1.88 0.00 38.21 2.29
760 4090 1.542915 GCATGTGCTCAGGACAAACAT 59.457 47.619 1.88 0.00 38.21 2.71
761 4091 0.953727 GCATGTGCTCAGGACAAACA 59.046 50.000 1.88 0.00 38.21 2.83
762 4092 0.110056 CGCATGTGCTCAGGACAAAC 60.110 55.000 1.88 0.00 39.32 2.93
763 4093 1.236616 CCGCATGTGCTCAGGACAAA 61.237 55.000 1.88 0.00 39.32 2.83
764 4094 1.672030 CCGCATGTGCTCAGGACAA 60.672 57.895 1.88 0.00 39.32 3.18
765 4095 2.046988 CCGCATGTGCTCAGGACA 60.047 61.111 0.00 0.00 39.32 4.02
766 4096 2.046892 ACCGCATGTGCTCAGGAC 60.047 61.111 4.36 0.00 39.32 3.85
767 4097 2.265739 GACCGCATGTGCTCAGGA 59.734 61.111 4.36 0.00 39.32 3.86
768 4098 3.190849 CGACCGCATGTGCTCAGG 61.191 66.667 0.00 0.00 39.32 3.86
769 4099 3.190849 CCGACCGCATGTGCTCAG 61.191 66.667 0.00 0.00 39.32 3.35
770 4100 3.932580 GACCGACCGCATGTGCTCA 62.933 63.158 0.00 0.00 39.32 4.26
771 4101 3.188786 GACCGACCGCATGTGCTC 61.189 66.667 0.00 0.00 39.32 4.26
788 4118 1.808411 AAAGTACGTGCATGGACCTG 58.192 50.000 17.98 1.05 0.00 4.00
800 4130 1.131126 CAGCATGCCAGGAAAAGTACG 59.869 52.381 15.66 0.00 0.00 3.67
980 5037 1.133915 TGGAGGCCGAGTGTTCTTTTT 60.134 47.619 0.00 0.00 0.00 1.94
1031 5088 0.607217 CCAAGCAGTGCAGATGGTGA 60.607 55.000 19.20 0.00 0.00 4.02
1032 5089 1.592400 CCCAAGCAGTGCAGATGGTG 61.592 60.000 24.33 15.95 30.72 4.17
1033 5090 1.303888 CCCAAGCAGTGCAGATGGT 60.304 57.895 24.33 0.00 30.72 3.55
1053 5110 4.776322 CGGCAAGGTCGGATGGCA 62.776 66.667 0.00 0.00 41.79 4.92
1103 5160 2.344592 AGTATGGTGGTTGGAGTTGGA 58.655 47.619 0.00 0.00 0.00 3.53
1115 5172 0.321210 TGCGGTGGACAAGTATGGTG 60.321 55.000 0.00 0.00 0.00 4.17
1116 5173 0.618458 ATGCGGTGGACAAGTATGGT 59.382 50.000 0.00 0.00 0.00 3.55
1119 5176 2.738643 CGAGAATGCGGTGGACAAGTAT 60.739 50.000 0.00 0.00 0.00 2.12
1121 5178 0.670546 CGAGAATGCGGTGGACAAGT 60.671 55.000 0.00 0.00 0.00 3.16
1128 5185 1.699656 CTTGAGGCGAGAATGCGGTG 61.700 60.000 0.00 0.00 35.06 4.94
1132 5189 2.893637 TCTTACTTGAGGCGAGAATGC 58.106 47.619 0.00 0.00 0.00 3.56
1139 5196 2.932614 CCTTGACATCTTACTTGAGGCG 59.067 50.000 0.00 0.00 0.00 5.52
1147 5204 1.732259 CCACACGCCTTGACATCTTAC 59.268 52.381 0.00 0.00 0.00 2.34
1155 5212 2.434185 GATCGCCACACGCCTTGA 60.434 61.111 0.00 0.00 43.23 3.02
1158 5215 4.498520 CTCGATCGCCACACGCCT 62.499 66.667 11.09 0.00 43.23 5.52
1184 5241 1.373497 CCACTCGTGTCTGAGGTGC 60.373 63.158 0.00 0.00 40.39 5.01
1363 5423 2.126031 GACGACGTCCTTGGAGGC 60.126 66.667 17.25 0.00 34.61 4.70
1608 5668 2.488820 GCCCAGGAGTCGTCGTAC 59.511 66.667 0.00 0.00 0.00 3.67
2163 6262 1.040646 TTTGGCGGGCAATACAACAA 58.959 45.000 18.14 0.00 0.00 2.83
2164 7618 1.067283 CATTTGGCGGGCAATACAACA 60.067 47.619 18.14 2.04 0.00 3.33
2179 7633 0.890683 GGGCCTCAGAACCACATTTG 59.109 55.000 0.84 0.00 0.00 2.32
2180 7634 0.482446 TGGGCCTCAGAACCACATTT 59.518 50.000 4.53 0.00 0.00 2.32
2181 7635 0.706433 ATGGGCCTCAGAACCACATT 59.294 50.000 4.53 0.00 37.05 2.71
2184 7673 0.678048 GACATGGGCCTCAGAACCAC 60.678 60.000 4.53 0.00 37.05 4.16
2195 7684 0.322816 TTTCTGCTGGAGACATGGGC 60.323 55.000 0.00 0.00 41.51 5.36
2217 7706 1.701847 GTGATAGGTGGGATCCATGCT 59.298 52.381 15.23 0.00 35.28 3.79
2218 7707 1.609061 CGTGATAGGTGGGATCCATGC 60.609 57.143 15.23 2.35 35.28 4.06
2219 7708 1.609061 GCGTGATAGGTGGGATCCATG 60.609 57.143 15.23 0.00 35.28 3.66
2220 7709 0.687354 GCGTGATAGGTGGGATCCAT 59.313 55.000 15.23 0.00 35.28 3.41
2221 7710 1.407656 GGCGTGATAGGTGGGATCCA 61.408 60.000 15.23 0.00 0.00 3.41
2224 7713 2.327325 ATAGGCGTGATAGGTGGGAT 57.673 50.000 0.00 0.00 0.00 3.85
2225 7714 2.984435 TATAGGCGTGATAGGTGGGA 57.016 50.000 0.00 0.00 0.00 4.37
2247 7736 0.179004 TGGGAATGGTCAGCGTGTTT 60.179 50.000 0.00 0.00 0.00 2.83
2280 7769 9.762381 ACCAAGTCTATATTTTTCCATGGTTAA 57.238 29.630 12.58 4.77 33.92 2.01
2281 7770 9.403583 GACCAAGTCTATATTTTTCCATGGTTA 57.596 33.333 12.58 0.00 37.56 2.85
2284 7773 7.469181 GCTGACCAAGTCTATATTTTTCCATGG 60.469 40.741 4.97 4.97 33.15 3.66
2287 7776 6.374333 GTGCTGACCAAGTCTATATTTTTCCA 59.626 38.462 0.00 0.00 33.15 3.53
2289 7778 6.456988 CGGTGCTGACCAAGTCTATATTTTTC 60.457 42.308 0.00 0.00 43.33 2.29
2293 7782 3.741388 GCGGTGCTGACCAAGTCTATATT 60.741 47.826 0.00 0.00 43.33 1.28
2294 7783 2.224066 GCGGTGCTGACCAAGTCTATAT 60.224 50.000 0.00 0.00 43.33 0.86
2295 7784 1.136305 GCGGTGCTGACCAAGTCTATA 59.864 52.381 0.00 0.00 43.33 1.31
2296 7785 0.108138 GCGGTGCTGACCAAGTCTAT 60.108 55.000 0.00 0.00 43.33 1.98
2297 7786 1.292223 GCGGTGCTGACCAAGTCTA 59.708 57.895 0.00 0.00 43.33 2.59
2298 7787 2.031163 GCGGTGCTGACCAAGTCT 59.969 61.111 0.00 0.00 43.33 3.24
2299 7788 3.414700 CGCGGTGCTGACCAAGTC 61.415 66.667 0.00 0.00 43.33 3.01
2302 7791 4.980805 GGTCGCGGTGCTGACCAA 62.981 66.667 20.13 0.00 44.78 3.67
2306 7795 4.680237 CTTGGGTCGCGGTGCTGA 62.680 66.667 6.13 0.00 0.00 4.26
2307 7796 4.988598 ACTTGGGTCGCGGTGCTG 62.989 66.667 6.13 0.00 0.00 4.41
2308 7797 4.250305 AACTTGGGTCGCGGTGCT 62.250 61.111 6.13 0.00 0.00 4.40
2309 7798 4.025401 CAACTTGGGTCGCGGTGC 62.025 66.667 6.13 0.00 0.00 5.01
2310 7799 4.025401 GCAACTTGGGTCGCGGTG 62.025 66.667 6.13 0.00 0.00 4.94
2313 7802 4.025401 GTGGCAACTTGGGTCGCG 62.025 66.667 0.00 0.00 37.61 5.87
2314 7803 3.670377 GGTGGCAACTTGGGTCGC 61.670 66.667 0.00 0.00 37.61 5.19
2315 7804 2.113139 AGGTGGCAACTTGGGTCG 59.887 61.111 0.00 0.00 37.61 4.79
2316 7805 2.564721 GCAGGTGGCAACTTGGGTC 61.565 63.158 0.00 0.00 43.97 4.46
2317 7806 2.521708 GCAGGTGGCAACTTGGGT 60.522 61.111 0.00 0.00 43.97 4.51
2331 7820 1.077212 CATGGAGTTCCCTGGGCAG 60.077 63.158 8.22 0.00 35.38 4.85
2332 7821 1.852157 ACATGGAGTTCCCTGGGCA 60.852 57.895 8.22 0.00 36.17 5.36
2333 7822 1.077429 GACATGGAGTTCCCTGGGC 60.077 63.158 8.22 0.00 36.17 5.36
2334 7823 1.207488 TGGACATGGAGTTCCCTGGG 61.207 60.000 6.33 6.33 36.17 4.45
2370 7859 4.152045 GCTCAAGAGGATAATGCAATCTCG 59.848 45.833 0.00 0.00 0.00 4.04
2381 7870 6.327365 TGTTGGATTATGAGCTCAAGAGGATA 59.673 38.462 22.50 4.25 0.00 2.59
2391 7880 8.055181 TCCTCTTTTATTGTTGGATTATGAGCT 58.945 33.333 0.00 0.00 0.00 4.09
2395 7884 9.359653 AGGATCCTCTTTTATTGTTGGATTATG 57.640 33.333 9.02 0.00 34.82 1.90
2396 7885 9.579932 GAGGATCCTCTTTTATTGTTGGATTAT 57.420 33.333 31.11 0.00 39.80 1.28
2413 7902 3.243359 ACAGATGGAGAGAGGATCCTC 57.757 52.381 31.27 31.27 43.03 3.71
2416 7905 6.662865 TCATTAACAGATGGAGAGAGGATC 57.337 41.667 0.00 0.00 0.00 3.36
2419 7908 6.669125 AGATCATTAACAGATGGAGAGAGG 57.331 41.667 0.00 0.00 0.00 3.69
2425 7914 7.855375 AGAAGTCAAGATCATTAACAGATGGA 58.145 34.615 0.00 0.00 0.00 3.41
2426 7915 9.775854 ATAGAAGTCAAGATCATTAACAGATGG 57.224 33.333 0.00 0.00 0.00 3.51
2439 7928 9.892130 CCTTTACCAGTTTATAGAAGTCAAGAT 57.108 33.333 0.00 0.00 0.00 2.40
2441 7930 8.101419 ACCCTTTACCAGTTTATAGAAGTCAAG 58.899 37.037 0.00 0.00 0.00 3.02
2442 7931 7.981142 ACCCTTTACCAGTTTATAGAAGTCAA 58.019 34.615 0.00 0.00 0.00 3.18
2443 7932 7.563724 ACCCTTTACCAGTTTATAGAAGTCA 57.436 36.000 0.00 0.00 0.00 3.41
2444 7933 8.975295 TCTACCCTTTACCAGTTTATAGAAGTC 58.025 37.037 0.00 0.00 0.00 3.01
2445 7934 8.756927 GTCTACCCTTTACCAGTTTATAGAAGT 58.243 37.037 0.00 0.00 0.00 3.01
2446 7935 8.755977 TGTCTACCCTTTACCAGTTTATAGAAG 58.244 37.037 0.00 0.00 0.00 2.85
2447 7936 8.669055 TGTCTACCCTTTACCAGTTTATAGAA 57.331 34.615 0.00 0.00 0.00 2.10
2448 7937 8.534496 GTTGTCTACCCTTTACCAGTTTATAGA 58.466 37.037 0.00 0.00 0.00 1.98
2449 7938 8.316214 TGTTGTCTACCCTTTACCAGTTTATAG 58.684 37.037 0.00 0.00 0.00 1.31
2450 7939 8.204903 TGTTGTCTACCCTTTACCAGTTTATA 57.795 34.615 0.00 0.00 0.00 0.98
2451 7940 7.081857 TGTTGTCTACCCTTTACCAGTTTAT 57.918 36.000 0.00 0.00 0.00 1.40
2452 7941 6.464749 CCTGTTGTCTACCCTTTACCAGTTTA 60.465 42.308 0.00 0.00 0.00 2.01
2454 7943 4.202430 CCTGTTGTCTACCCTTTACCAGTT 60.202 45.833 0.00 0.00 0.00 3.16
2458 7947 4.362470 AACCTGTTGTCTACCCTTTACC 57.638 45.455 0.00 0.00 0.00 2.85
2460 7949 6.424883 TGAAAAACCTGTTGTCTACCCTTTA 58.575 36.000 0.00 0.00 0.00 1.85
2461 7950 5.265989 TGAAAAACCTGTTGTCTACCCTTT 58.734 37.500 0.00 0.00 0.00 3.11
2463 7952 4.079958 ACTGAAAAACCTGTTGTCTACCCT 60.080 41.667 0.00 0.00 0.00 4.34
2464 7953 4.204799 ACTGAAAAACCTGTTGTCTACCC 58.795 43.478 0.00 0.00 0.00 3.69
2466 7955 5.963586 CGAAACTGAAAAACCTGTTGTCTAC 59.036 40.000 0.00 0.00 0.00 2.59
2468 7957 4.457949 ACGAAACTGAAAAACCTGTTGTCT 59.542 37.500 0.00 0.00 0.00 3.41
2470 7959 4.776795 ACGAAACTGAAAAACCTGTTGT 57.223 36.364 0.00 0.00 0.00 3.32
2471 7960 4.201580 GCAACGAAACTGAAAAACCTGTTG 60.202 41.667 0.00 0.00 37.73 3.33
2485 7974 7.693952 TCTGGATTTCATAATAGCAACGAAAC 58.306 34.615 0.00 0.00 0.00 2.78
2506 8003 6.017400 ACATGCTTGAACTGTAATTTCTGG 57.983 37.500 6.60 0.00 0.00 3.86
2546 8043 2.292267 CAACCACACACAAGAGCTTCT 58.708 47.619 0.00 0.00 0.00 2.85
2557 8054 7.770366 TCTTCTCTAATACTACAACCACACA 57.230 36.000 0.00 0.00 0.00 3.72
2569 8066 9.950680 CATCTCTGTCTTCTTCTTCTCTAATAC 57.049 37.037 0.00 0.00 0.00 1.89
2572 8069 8.685427 CATCATCTCTGTCTTCTTCTTCTCTAA 58.315 37.037 0.00 0.00 0.00 2.10
2573 8070 7.285172 CCATCATCTCTGTCTTCTTCTTCTCTA 59.715 40.741 0.00 0.00 0.00 2.43
2574 8071 6.097270 CCATCATCTCTGTCTTCTTCTTCTCT 59.903 42.308 0.00 0.00 0.00 3.10
2575 8072 6.275335 CCATCATCTCTGTCTTCTTCTTCTC 58.725 44.000 0.00 0.00 0.00 2.87
2576 8073 5.129155 CCCATCATCTCTGTCTTCTTCTTCT 59.871 44.000 0.00 0.00 0.00 2.85
2579 8076 3.134442 GCCCATCATCTCTGTCTTCTTCT 59.866 47.826 0.00 0.00 0.00 2.85
2582 8079 1.411977 CGCCCATCATCTCTGTCTTCT 59.588 52.381 0.00 0.00 0.00 2.85
2591 8088 2.894731 TCTATTCTCCGCCCATCATCT 58.105 47.619 0.00 0.00 0.00 2.90
2596 8093 0.326264 GGCATCTATTCTCCGCCCAT 59.674 55.000 0.00 0.00 36.73 4.00
2603 8100 6.469782 TTCATTTTTGGGGCATCTATTCTC 57.530 37.500 0.00 0.00 0.00 2.87
2604 8101 6.352137 GGTTTCATTTTTGGGGCATCTATTCT 60.352 38.462 0.00 0.00 0.00 2.40
2605 8102 5.817296 GGTTTCATTTTTGGGGCATCTATTC 59.183 40.000 0.00 0.00 0.00 1.75
2606 8103 5.488561 AGGTTTCATTTTTGGGGCATCTATT 59.511 36.000 0.00 0.00 0.00 1.73
2607 8104 5.032170 AGGTTTCATTTTTGGGGCATCTAT 58.968 37.500 0.00 0.00 0.00 1.98
2608 8105 4.222588 CAGGTTTCATTTTTGGGGCATCTA 59.777 41.667 0.00 0.00 0.00 1.98
2617 8114 2.794350 GACGTGGCAGGTTTCATTTTTG 59.206 45.455 14.71 0.00 0.00 2.44
2619 8116 2.028130 TGACGTGGCAGGTTTCATTTT 58.972 42.857 14.71 0.00 0.00 1.82
2636 8133 7.851822 TTTGATTTTAGCTGACGAAATTGAC 57.148 32.000 0.00 0.00 0.00 3.18
2742 8240 0.390340 TGACTGCTAAAGCGCCTCAG 60.390 55.000 2.29 7.10 45.83 3.35
2757 8255 4.023450 TGTCTCGAAGATGTAACGTTGACT 60.023 41.667 11.99 1.93 33.89 3.41
2764 8268 4.167268 GGACACTGTCTCGAAGATGTAAC 58.833 47.826 9.08 0.00 33.89 2.50
2770 8274 1.609072 CACTGGACACTGTCTCGAAGA 59.391 52.381 9.08 0.00 32.47 2.87
2780 8284 4.041691 ACAGGCTATTAAACACTGGACACT 59.958 41.667 0.00 0.00 33.63 3.55
2804 8724 5.068723 CAGGCTCAAAATTATGAAGGCATCT 59.931 40.000 0.00 0.00 35.94 2.90
2809 8729 4.724074 TGCAGGCTCAAAATTATGAAGG 57.276 40.909 0.00 0.00 0.00 3.46
2828 8761 4.034510 CGGAACAGGTTTTATCTGAGATGC 59.965 45.833 4.96 0.00 36.22 3.91
2830 8763 4.770795 CCGGAACAGGTTTTATCTGAGAT 58.229 43.478 0.00 0.00 36.22 2.75
2977 8971 5.120172 GGTGTTCAGGAAGACGAGGAACT 62.120 52.174 0.00 0.00 38.82 3.01
3008 9776 1.685180 CCATGGACTCGGTGGTCTCTA 60.685 57.143 5.56 0.00 36.55 2.43
3080 9922 0.586802 GTTCAGTGCGGTCCAGAAAC 59.413 55.000 0.00 0.00 0.00 2.78
3088 9930 0.039437 CTGTACTCGTTCAGTGCGGT 60.039 55.000 0.00 0.00 40.53 5.68


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

AutoCloner maintained by Alex Coulton.