Multiple sequence alignment - TraesCS6B01G094600

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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 TraesCS6B01G094600 chr6B 100.000 4560 0 0 1 4560 71038852 71043411 0.000000e+00 8421.0
1 TraesCS6B01G094600 chr6D 97.152 1229 22 5 2002 3218 34344287 34345514 0.000000e+00 2063.0
2 TraesCS6B01G094600 chr6D 95.331 1285 42 9 3269 4548 34345510 34346781 0.000000e+00 2025.0
3 TraesCS6B01G094600 chr6D 88.012 1318 80 35 650 1916 34342984 34344274 0.000000e+00 1487.0
4 TraesCS6B01G094600 chr6D 92.661 109 7 1 33 141 34342813 34342920 6.110000e-34 156.0
5 TraesCS6B01G094600 chr6A 91.325 1487 90 27 442 1916 38471815 38473274 0.000000e+00 1995.0
6 TraesCS6B01G094600 chr6A 94.449 1207 44 14 3163 4358 38474344 38475538 0.000000e+00 1836.0
7 TraesCS6B01G094600 chr6A 97.368 950 18 5 2002 2948 38473287 38474232 0.000000e+00 1609.0
8 TraesCS6B01G094600 chr6A 90.361 249 21 2 33 281 38471468 38471713 1.580000e-84 324.0
9 TraesCS6B01G094600 chr6A 96.373 193 6 1 4356 4548 38475619 38475810 2.650000e-82 316.0
10 TraesCS6B01G094600 chr6A 89.855 138 11 2 2970 3106 38474224 38474359 1.690000e-39 174.0
11 TraesCS6B01G094600 chr6A 82.677 127 15 5 296 416 38471696 38471821 6.240000e-19 106.0
12 TraesCS6B01G094600 chr7A 97.674 86 2 0 1919 2004 168872333 168872248 1.020000e-31 148.0
13 TraesCS6B01G094600 chr7D 96.512 86 2 1 1919 2004 167359604 167359520 1.710000e-29 141.0
14 TraesCS6B01G094600 chr3D 92.857 98 6 1 1919 2016 66406688 66406784 1.710000e-29 141.0
15 TraesCS6B01G094600 chr5D 91.954 87 5 1 1918 2004 548634068 548633984 2.230000e-23 121.0
16 TraesCS6B01G094600 chr7B 91.860 86 5 2 1919 2003 588875323 588875239 8.010000e-23 119.0
17 TraesCS6B01G094600 chr7B 88.764 89 10 0 1918 2006 135404682 135404594 4.820000e-20 110.0
18 TraesCS6B01G094600 chr1D 88.889 81 8 1 1919 1998 479778420 479778340 1.040000e-16 99.0
19 TraesCS6B01G094600 chr3A 89.706 68 6 1 1919 1986 722388751 722388817 8.130000e-13 86.1


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 TraesCS6B01G094600 chr6B 71038852 71043411 4559 False 8421.000000 8421 100.000000 1 4560 1 chr6B.!!$F1 4559
1 TraesCS6B01G094600 chr6D 34342813 34346781 3968 False 1432.750000 2063 93.289000 33 4548 4 chr6D.!!$F1 4515
2 TraesCS6B01G094600 chr6A 38471468 38475810 4342 False 908.571429 1995 91.772571 33 4548 7 chr6A.!!$F1 4515

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
262 263 0.036164 AGCGTTGGTAGCATGGTTGA 59.964 50.0 1.12 0.0 37.01 3.18 F
867 913 0.107654 GGTTTAGGTCGCTGCTCCAT 60.108 55.0 11.93 0.0 0.00 3.41 F
1590 1660 0.465705 GATCGCCAGGATGAAGGACA 59.534 55.0 0.00 0.0 39.69 4.02 F
1960 2030 0.256464 TGTCGTTGGGGAAAACCAGT 59.744 50.0 0.00 0.0 42.47 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1529 1599 0.179078 TTTGCTTTGCCACCAGCTTG 60.179 50.0 0.00 0.0 44.23 4.01 R
1941 2011 0.256464 ACTGGTTTTCCCCAACGACA 59.744 50.0 0.00 0.0 39.73 4.35 R
2417 2498 0.552848 ATGGATCCCGACCTTGCATT 59.447 50.0 9.90 0.0 0.00 3.56 R
3639 3722 0.313672 GTCCAACAAAAGGCGCATCA 59.686 50.0 10.83 0.0 0.00 3.07 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
30 31 9.708092 GGAGGGACTACATAATAACATTTAGAC 57.292 37.037 0.00 0.00 40.63 2.59
53 54 8.446273 AGACATTTGCTTCATATATGAATACGC 58.554 33.333 24.77 23.32 44.92 4.42
74 75 7.372451 ACGCTAGTGTAAGCATTTGAAAATA 57.628 32.000 7.28 0.00 42.91 1.40
148 149 7.885399 GGCCAATCAAGATCCTATTATTGTAGT 59.115 37.037 0.00 0.00 0.00 2.73
190 191 9.979578 AGAATTACTGTTATTGCATGAAAAACA 57.020 25.926 0.00 5.54 0.00 2.83
193 194 5.911752 ACTGTTATTGCATGAAAAACACCA 58.088 33.333 0.00 0.00 0.00 4.17
209 210 0.108396 ACCATTTGTTTTGGGCAGCC 59.892 50.000 1.26 1.26 38.64 4.85
244 245 8.870160 TTTTTGTGATGGATTGTTTTAGTCAG 57.130 30.769 0.00 0.00 0.00 3.51
248 249 4.759693 TGATGGATTGTTTTAGTCAGCGTT 59.240 37.500 0.00 0.00 0.00 4.84
251 252 3.252458 GGATTGTTTTAGTCAGCGTTGGT 59.748 43.478 0.00 0.00 0.00 3.67
262 263 0.036164 AGCGTTGGTAGCATGGTTGA 59.964 50.000 1.12 0.00 37.01 3.18
263 264 0.447801 GCGTTGGTAGCATGGTTGAG 59.552 55.000 1.12 0.00 34.19 3.02
264 265 1.943968 GCGTTGGTAGCATGGTTGAGA 60.944 52.381 1.12 0.00 34.19 3.27
265 266 2.002586 CGTTGGTAGCATGGTTGAGAG 58.997 52.381 1.12 0.00 0.00 3.20
266 267 2.359900 GTTGGTAGCATGGTTGAGAGG 58.640 52.381 1.12 0.00 0.00 3.69
267 268 1.951209 TGGTAGCATGGTTGAGAGGA 58.049 50.000 1.12 0.00 0.00 3.71
268 269 2.481441 TGGTAGCATGGTTGAGAGGAT 58.519 47.619 1.12 0.00 0.00 3.24
269 270 2.846206 TGGTAGCATGGTTGAGAGGATT 59.154 45.455 1.12 0.00 0.00 3.01
270 271 3.118261 TGGTAGCATGGTTGAGAGGATTC 60.118 47.826 1.12 0.00 0.00 2.52
271 272 3.118261 GGTAGCATGGTTGAGAGGATTCA 60.118 47.826 1.12 0.00 0.00 2.57
272 273 3.947612 AGCATGGTTGAGAGGATTCAT 57.052 42.857 0.00 0.00 0.00 2.57
273 274 5.221722 GGTAGCATGGTTGAGAGGATTCATA 60.222 44.000 1.12 0.00 0.00 2.15
274 275 5.579753 AGCATGGTTGAGAGGATTCATAT 57.420 39.130 0.00 0.00 0.00 1.78
275 276 6.692849 AGCATGGTTGAGAGGATTCATATA 57.307 37.500 0.00 0.00 0.00 0.86
276 277 7.083062 AGCATGGTTGAGAGGATTCATATAA 57.917 36.000 0.00 0.00 0.00 0.98
277 278 7.520798 AGCATGGTTGAGAGGATTCATATAAA 58.479 34.615 0.00 0.00 0.00 1.40
278 279 7.446625 AGCATGGTTGAGAGGATTCATATAAAC 59.553 37.037 0.00 0.00 0.00 2.01
279 280 7.308830 GCATGGTTGAGAGGATTCATATAAACC 60.309 40.741 5.44 5.44 0.00 3.27
280 281 7.206789 TGGTTGAGAGGATTCATATAAACCA 57.793 36.000 10.21 10.21 33.04 3.67
281 282 7.054124 TGGTTGAGAGGATTCATATAAACCAC 58.946 38.462 10.21 0.00 31.42 4.16
282 283 6.486993 GGTTGAGAGGATTCATATAAACCACC 59.513 42.308 7.24 0.00 0.00 4.61
283 284 6.187727 TGAGAGGATTCATATAAACCACCC 57.812 41.667 0.00 0.00 0.00 4.61
284 285 5.221641 TGAGAGGATTCATATAAACCACCCG 60.222 44.000 0.00 0.00 0.00 5.28
285 286 3.751518 AGGATTCATATAAACCACCCGC 58.248 45.455 0.00 0.00 0.00 6.13
286 287 3.137544 AGGATTCATATAAACCACCCGCA 59.862 43.478 0.00 0.00 0.00 5.69
287 288 3.886505 GGATTCATATAAACCACCCGCAA 59.113 43.478 0.00 0.00 0.00 4.85
288 289 4.339814 GGATTCATATAAACCACCCGCAAA 59.660 41.667 0.00 0.00 0.00 3.68
289 290 5.163499 GGATTCATATAAACCACCCGCAAAA 60.163 40.000 0.00 0.00 0.00 2.44
290 291 5.723672 TTCATATAAACCACCCGCAAAAA 57.276 34.783 0.00 0.00 0.00 1.94
329 330 3.104843 ACCAGAGCTAGATTCAATCGC 57.895 47.619 0.00 0.00 0.00 4.58
334 335 3.067461 AGAGCTAGATTCAATCGCGAACT 59.933 43.478 15.24 8.55 0.00 3.01
361 365 4.389077 CGTAGCTCTAGTTTGGTTTCTTGG 59.611 45.833 0.00 0.00 0.00 3.61
365 369 3.821033 CTCTAGTTTGGTTTCTTGGTGGG 59.179 47.826 0.00 0.00 0.00 4.61
366 370 2.838637 AGTTTGGTTTCTTGGTGGGA 57.161 45.000 0.00 0.00 0.00 4.37
367 371 3.108847 AGTTTGGTTTCTTGGTGGGAA 57.891 42.857 0.00 0.00 0.00 3.97
368 372 2.764010 AGTTTGGTTTCTTGGTGGGAAC 59.236 45.455 0.00 0.00 0.00 3.62
370 374 2.065899 TGGTTTCTTGGTGGGAACAG 57.934 50.000 0.00 0.00 44.46 3.16
397 403 3.006537 TCAAGGTTCAAGTTCTAGACCGG 59.993 47.826 0.00 0.00 0.00 5.28
400 406 4.154942 AGGTTCAAGTTCTAGACCGGTAA 58.845 43.478 7.34 0.00 0.00 2.85
404 410 2.830321 CAAGTTCTAGACCGGTAAGGGT 59.170 50.000 7.34 0.00 46.96 4.34
416 422 1.408266 GGTAAGGGTAGGGTGTGCATG 60.408 57.143 0.00 0.00 0.00 4.06
417 423 0.254747 TAAGGGTAGGGTGTGCATGC 59.745 55.000 11.82 11.82 0.00 4.06
418 424 2.440247 GGGTAGGGTGTGCATGCC 60.440 66.667 16.68 7.25 0.00 4.40
419 425 2.677228 GGTAGGGTGTGCATGCCT 59.323 61.111 16.68 6.95 0.00 4.75
420 426 1.000896 GGTAGGGTGTGCATGCCTT 60.001 57.895 16.68 0.00 0.00 4.35
421 427 1.032114 GGTAGGGTGTGCATGCCTTC 61.032 60.000 16.68 6.46 0.00 3.46
422 428 0.322456 GTAGGGTGTGCATGCCTTCA 60.322 55.000 16.68 9.18 0.00 3.02
423 429 0.625316 TAGGGTGTGCATGCCTTCAT 59.375 50.000 16.68 2.59 0.00 2.57
424 430 0.251922 AGGGTGTGCATGCCTTCATT 60.252 50.000 16.68 0.00 0.00 2.57
425 431 0.174162 GGGTGTGCATGCCTTCATTC 59.826 55.000 16.68 8.36 0.00 2.67
426 432 0.889994 GGTGTGCATGCCTTCATTCA 59.110 50.000 16.68 0.39 0.00 2.57
427 433 1.403249 GGTGTGCATGCCTTCATTCAC 60.403 52.381 16.68 11.86 43.85 3.18
429 435 1.542472 TGTGCATGCCTTCATTCACAG 59.458 47.619 16.68 0.00 46.57 3.66
430 436 1.135199 GTGCATGCCTTCATTCACAGG 60.135 52.381 16.68 0.00 43.32 4.00
431 437 0.458669 GCATGCCTTCATTCACAGGG 59.541 55.000 6.36 0.00 0.00 4.45
432 438 1.108776 CATGCCTTCATTCACAGGGG 58.891 55.000 0.00 0.00 0.00 4.79
433 439 0.706433 ATGCCTTCATTCACAGGGGT 59.294 50.000 0.00 0.00 0.00 4.95
434 440 0.251297 TGCCTTCATTCACAGGGGTG 60.251 55.000 0.00 0.00 46.66 4.61
445 451 0.324943 ACAGGGGTGAGTGTATGTGC 59.675 55.000 0.00 0.00 0.00 4.57
446 452 0.324614 CAGGGGTGAGTGTATGTGCA 59.675 55.000 0.00 0.00 0.00 4.57
447 453 1.065199 CAGGGGTGAGTGTATGTGCAT 60.065 52.381 0.00 0.00 0.00 3.96
453 459 6.003950 GGGGTGAGTGTATGTGCATTTATAT 58.996 40.000 0.00 0.00 0.00 0.86
457 463 7.293745 GTGAGTGTATGTGCATTTATATGAGC 58.706 38.462 0.00 0.00 33.37 4.26
461 467 6.792250 GTGTATGTGCATTTATATGAGCGTTC 59.208 38.462 0.00 0.00 33.37 3.95
466 472 3.603857 GCATTTATATGAGCGTTCGCGTT 60.604 43.478 5.77 3.64 37.12 4.84
473 479 1.136474 TGAGCGTTCGCGTTTGTATTG 60.136 47.619 5.77 0.00 43.62 1.90
475 481 2.060284 AGCGTTCGCGTTTGTATTGTA 58.940 42.857 5.77 0.00 43.62 2.41
477 483 3.123959 AGCGTTCGCGTTTGTATTGTATT 59.876 39.130 5.77 0.00 43.62 1.89
478 484 4.326817 AGCGTTCGCGTTTGTATTGTATTA 59.673 37.500 5.77 0.00 43.62 0.98
479 485 4.658723 GCGTTCGCGTTTGTATTGTATTAG 59.341 41.667 5.77 0.00 43.62 1.73
529 535 3.454447 ACCCCGATATGACTCACATTTGA 59.546 43.478 0.00 0.00 40.07 2.69
542 548 6.314917 ACTCACATTTGAAAGGAACCCTAAT 58.685 36.000 0.00 0.00 31.13 1.73
587 594 3.968265 ACAAGATTCCGGGAATTCATGT 58.032 40.909 22.53 21.51 31.89 3.21
630 637 9.754382 AAAAAGTAGACAAGTACTATTTCACGA 57.246 29.630 0.00 0.00 32.69 4.35
645 652 2.385803 TCACGATCCCCTACTCTTTCC 58.614 52.381 0.00 0.00 0.00 3.13
662 669 3.810310 TTCCTGCGGTTTGTGAATTTT 57.190 38.095 0.00 0.00 0.00 1.82
667 674 3.304257 TGCGGTTTGTGAATTTTCATCG 58.696 40.909 0.00 0.00 39.73 3.84
683 690 7.617041 TTTTCATCGGTCCAAATTTTGTTTT 57.383 28.000 8.26 0.00 0.00 2.43
787 830 1.102978 ACAGGCAATTACCATTCGCC 58.897 50.000 0.00 0.00 43.31 5.54
788 831 0.385390 CAGGCAATTACCATTCGCCC 59.615 55.000 0.00 0.00 44.06 6.13
791 834 1.205893 GGCAATTACCATTCGCCCAAA 59.794 47.619 0.00 0.00 36.73 3.28
867 913 0.107654 GGTTTAGGTCGCTGCTCCAT 60.108 55.000 11.93 0.00 0.00 3.41
909 955 3.431725 CCCGACCGCTCCTTTTGC 61.432 66.667 0.00 0.00 0.00 3.68
1234 1283 3.354678 GTGTGCGCACCCATTTCT 58.645 55.556 35.72 0.00 39.61 2.52
1340 1389 6.869206 AAAGCACAACCTTAGATAGTCCTA 57.131 37.500 0.00 0.00 0.00 2.94
1386 1438 2.799126 AGCAACGGATGAATTACCCA 57.201 45.000 0.00 0.00 0.00 4.51
1414 1484 4.320491 GCTTGTTAGTTGTTACATACGCG 58.680 43.478 3.53 3.53 0.00 6.01
1479 1549 5.565455 AATTGTGTTGATGGATGGGTTTT 57.435 34.783 0.00 0.00 0.00 2.43
1508 1578 0.675083 CCACTGTTTTGGCTGATGCA 59.325 50.000 0.00 0.00 41.91 3.96
1529 1599 1.493950 CTGCCAAGATCATCGACGGC 61.494 60.000 7.81 7.81 40.02 5.68
1590 1660 0.465705 GATCGCCAGGATGAAGGACA 59.534 55.000 0.00 0.00 39.69 4.02
1598 1668 0.744874 GGATGAAGGACACGATCGGA 59.255 55.000 20.98 0.00 0.00 4.55
1709 1779 3.949754 TCGGTATCAAGTCGTATGAGGTT 59.050 43.478 0.00 0.00 0.00 3.50
1713 1783 6.921857 CGGTATCAAGTCGTATGAGGTTAATT 59.078 38.462 0.00 0.00 0.00 1.40
1830 1900 1.849219 CTCGCGTGAGTTCTCAATAGC 59.151 52.381 17.90 9.35 37.46 2.97
1831 1901 0.924090 CGCGTGAGTTCTCAATAGCC 59.076 55.000 0.00 0.00 0.00 3.93
1832 1902 0.924090 GCGTGAGTTCTCAATAGCCG 59.076 55.000 3.99 5.02 0.00 5.52
1835 1905 2.223502 CGTGAGTTCTCAATAGCCGCTA 60.224 50.000 1.73 1.73 0.00 4.26
1836 1906 3.117046 GTGAGTTCTCAATAGCCGCTAC 58.883 50.000 1.14 0.00 0.00 3.58
1837 1907 3.024547 TGAGTTCTCAATAGCCGCTACT 58.975 45.455 1.14 0.00 0.00 2.57
1838 1908 3.066900 TGAGTTCTCAATAGCCGCTACTC 59.933 47.826 1.14 6.28 33.25 2.59
1839 1909 3.024547 AGTTCTCAATAGCCGCTACTCA 58.975 45.455 1.14 0.00 0.00 3.41
1840 1910 3.447586 AGTTCTCAATAGCCGCTACTCAA 59.552 43.478 1.14 0.00 0.00 3.02
1841 1911 4.100189 AGTTCTCAATAGCCGCTACTCAAT 59.900 41.667 1.14 0.00 0.00 2.57
1889 1959 3.879892 GCCTGAAGGGACTGTCATATTTC 59.120 47.826 10.38 7.75 40.86 2.17
1896 1966 7.987458 TGAAGGGACTGTCATATTTCATCTTAC 59.013 37.037 10.38 0.00 40.86 2.34
1924 1994 3.975168 TTTGTTGTCTAGCCTACTCCC 57.025 47.619 0.00 0.00 0.00 4.30
1925 1995 2.921834 TGTTGTCTAGCCTACTCCCT 57.078 50.000 0.00 0.00 0.00 4.20
1927 1997 2.312140 TGTTGTCTAGCCTACTCCCTCT 59.688 50.000 0.00 0.00 0.00 3.69
1928 1998 3.526430 TGTTGTCTAGCCTACTCCCTCTA 59.474 47.826 0.00 0.00 0.00 2.43
1929 1999 4.168283 TGTTGTCTAGCCTACTCCCTCTAT 59.832 45.833 0.00 0.00 0.00 1.98
1930 2000 5.371769 TGTTGTCTAGCCTACTCCCTCTATA 59.628 44.000 0.00 0.00 0.00 1.31
1931 2001 5.502089 TGTCTAGCCTACTCCCTCTATAC 57.498 47.826 0.00 0.00 0.00 1.47
1932 2002 4.289148 TGTCTAGCCTACTCCCTCTATACC 59.711 50.000 0.00 0.00 0.00 2.73
1933 2003 2.883122 AGCCTACTCCCTCTATACCG 57.117 55.000 0.00 0.00 0.00 4.02
1934 2004 2.346529 AGCCTACTCCCTCTATACCGA 58.653 52.381 0.00 0.00 0.00 4.69
1935 2005 2.715336 AGCCTACTCCCTCTATACCGAA 59.285 50.000 0.00 0.00 0.00 4.30
1936 2006 3.139770 AGCCTACTCCCTCTATACCGAAA 59.860 47.826 0.00 0.00 0.00 3.46
1937 2007 4.087907 GCCTACTCCCTCTATACCGAAAT 58.912 47.826 0.00 0.00 0.00 2.17
1938 2008 5.014966 AGCCTACTCCCTCTATACCGAAATA 59.985 44.000 0.00 0.00 0.00 1.40
1939 2009 5.125257 GCCTACTCCCTCTATACCGAAATAC 59.875 48.000 0.00 0.00 0.00 1.89
1940 2010 6.483405 CCTACTCCCTCTATACCGAAATACT 58.517 44.000 0.00 0.00 0.00 2.12
1941 2011 6.947158 CCTACTCCCTCTATACCGAAATACTT 59.053 42.308 0.00 0.00 0.00 2.24
1942 2012 6.651975 ACTCCCTCTATACCGAAATACTTG 57.348 41.667 0.00 0.00 0.00 3.16
1943 2013 6.134754 ACTCCCTCTATACCGAAATACTTGT 58.865 40.000 0.00 0.00 0.00 3.16
1944 2014 6.264970 ACTCCCTCTATACCGAAATACTTGTC 59.735 42.308 0.00 0.00 0.00 3.18
1945 2015 5.240183 TCCCTCTATACCGAAATACTTGTCG 59.760 44.000 0.00 0.00 37.01 4.35
1946 2016 5.009410 CCCTCTATACCGAAATACTTGTCGT 59.991 44.000 0.00 0.00 35.48 4.34
1947 2017 6.460676 CCCTCTATACCGAAATACTTGTCGTT 60.461 42.308 0.00 0.00 35.48 3.85
1948 2018 6.417044 CCTCTATACCGAAATACTTGTCGTTG 59.583 42.308 0.00 0.00 35.48 4.10
1949 2019 6.267817 TCTATACCGAAATACTTGTCGTTGG 58.732 40.000 0.00 0.00 35.48 3.77
1950 2020 2.419667 ACCGAAATACTTGTCGTTGGG 58.580 47.619 0.00 0.00 35.48 4.12
1951 2021 1.735571 CCGAAATACTTGTCGTTGGGG 59.264 52.381 0.00 0.00 35.48 4.96
1952 2022 2.613474 CCGAAATACTTGTCGTTGGGGA 60.613 50.000 0.00 0.00 35.48 4.81
1953 2023 3.068560 CGAAATACTTGTCGTTGGGGAA 58.931 45.455 0.00 0.00 32.61 3.97
1954 2024 3.499157 CGAAATACTTGTCGTTGGGGAAA 59.501 43.478 0.00 0.00 32.61 3.13
1955 2025 4.023878 CGAAATACTTGTCGTTGGGGAAAA 60.024 41.667 0.00 0.00 32.61 2.29
1956 2026 4.841443 AATACTTGTCGTTGGGGAAAAC 57.159 40.909 0.00 0.00 0.00 2.43
1957 2027 1.395635 ACTTGTCGTTGGGGAAAACC 58.604 50.000 0.00 0.00 39.11 3.27
1958 2028 1.341187 ACTTGTCGTTGGGGAAAACCA 60.341 47.619 0.00 0.00 42.91 3.67
1959 2029 1.336755 CTTGTCGTTGGGGAAAACCAG 59.663 52.381 0.00 0.00 42.47 4.00
1960 2030 0.256464 TGTCGTTGGGGAAAACCAGT 59.744 50.000 0.00 0.00 42.47 4.00
1961 2031 1.489649 TGTCGTTGGGGAAAACCAGTA 59.510 47.619 0.00 0.00 42.47 2.74
1962 2032 1.875514 GTCGTTGGGGAAAACCAGTAC 59.124 52.381 0.00 0.00 42.47 2.73
1963 2033 1.489649 TCGTTGGGGAAAACCAGTACA 59.510 47.619 0.00 0.00 42.47 2.90
1964 2034 2.092538 TCGTTGGGGAAAACCAGTACAA 60.093 45.455 0.00 0.00 42.47 2.41
1965 2035 2.292292 CGTTGGGGAAAACCAGTACAAG 59.708 50.000 0.00 0.00 42.47 3.16
1966 2036 3.293337 GTTGGGGAAAACCAGTACAAGT 58.707 45.455 0.00 0.00 42.47 3.16
1967 2037 3.673543 TGGGGAAAACCAGTACAAGTT 57.326 42.857 0.00 0.00 42.91 2.66
1968 2038 3.558033 TGGGGAAAACCAGTACAAGTTC 58.442 45.455 0.00 0.00 42.91 3.01
1969 2039 2.889045 GGGGAAAACCAGTACAAGTTCC 59.111 50.000 0.00 0.73 42.91 3.62
1970 2040 2.889045 GGGAAAACCAGTACAAGTTCCC 59.111 50.000 13.69 13.69 45.45 3.97
1971 2041 2.889045 GGAAAACCAGTACAAGTTCCCC 59.111 50.000 0.00 0.07 0.00 4.81
1972 2042 2.670019 AAACCAGTACAAGTTCCCCC 57.330 50.000 0.00 0.00 0.00 5.40
1973 2043 1.525175 AACCAGTACAAGTTCCCCCA 58.475 50.000 0.00 0.00 0.00 4.96
1974 2044 1.064825 ACCAGTACAAGTTCCCCCAG 58.935 55.000 0.00 0.00 0.00 4.45
1975 2045 0.322546 CCAGTACAAGTTCCCCCAGC 60.323 60.000 0.00 0.00 0.00 4.85
1976 2046 0.673644 CAGTACAAGTTCCCCCAGCG 60.674 60.000 0.00 0.00 0.00 5.18
1977 2047 0.834687 AGTACAAGTTCCCCCAGCGA 60.835 55.000 0.00 0.00 0.00 4.93
1978 2048 0.672711 GTACAAGTTCCCCCAGCGAC 60.673 60.000 0.00 0.00 0.00 5.19
1979 2049 1.122632 TACAAGTTCCCCCAGCGACA 61.123 55.000 0.00 0.00 0.00 4.35
1980 2050 1.966451 CAAGTTCCCCCAGCGACAC 60.966 63.158 0.00 0.00 0.00 3.67
1981 2051 3.530910 AAGTTCCCCCAGCGACACG 62.531 63.158 0.00 0.00 0.00 4.49
1982 2052 4.309950 GTTCCCCCAGCGACACGT 62.310 66.667 0.00 0.00 0.00 4.49
1983 2053 2.601067 TTCCCCCAGCGACACGTA 60.601 61.111 0.00 0.00 0.00 3.57
1984 2054 1.985662 TTCCCCCAGCGACACGTAT 60.986 57.895 0.00 0.00 0.00 3.06
1985 2055 1.546589 TTCCCCCAGCGACACGTATT 61.547 55.000 0.00 0.00 0.00 1.89
1986 2056 1.813753 CCCCCAGCGACACGTATTG 60.814 63.158 0.00 0.00 0.00 1.90
1987 2057 1.079405 CCCCAGCGACACGTATTGT 60.079 57.895 0.00 0.00 43.10 2.71
1998 2068 2.888594 CACGTATTGTGGTACAGAGGG 58.111 52.381 0.00 0.00 45.21 4.30
1999 2069 2.494471 CACGTATTGTGGTACAGAGGGA 59.506 50.000 0.00 0.00 45.21 4.20
2000 2070 2.758979 ACGTATTGTGGTACAGAGGGAG 59.241 50.000 0.00 0.00 41.80 4.30
2034 2104 2.936498 AGCGTGCCACTGAAATATGTAC 59.064 45.455 0.00 0.00 0.00 2.90
2173 2243 6.352516 AGCCATCTGGTTACATTCTTTAGAG 58.647 40.000 0.00 0.00 37.57 2.43
2189 2260 9.956640 ATTCTTTAGAGCTCATGGATAATAAGG 57.043 33.333 17.77 3.88 0.00 2.69
2417 2498 1.601903 GTGAACATTGGACGACTTGCA 59.398 47.619 0.00 0.00 0.00 4.08
2659 2740 9.656040 AATGATTATTAGAAAGCAAATGCAACA 57.344 25.926 8.28 0.00 45.16 3.33
2884 2965 6.204108 TCCCGTTCTTTTCTTTTTAGTGCTAG 59.796 38.462 0.00 0.00 0.00 3.42
2941 3023 7.765307 TCTCAATGGAAAAGCTTGATAATGTC 58.235 34.615 0.00 0.00 0.00 3.06
3002 3084 7.475771 TGTTTTGGTTCAGATAATGCAAAAC 57.524 32.000 4.05 4.05 42.98 2.43
3014 3096 9.844790 CAGATAATGCAAAACTTTGACAATCTA 57.155 29.630 6.37 0.15 40.55 1.98
3226 3309 5.054390 TCTTATTTTAAGTTTGGGCAGCG 57.946 39.130 0.00 0.00 0.00 5.18
3232 3315 4.347453 GTTTGGGCAGCGCAGTGG 62.347 66.667 11.47 0.00 0.00 4.00
3243 3326 3.429085 CAGCGCAGTGGTCAATTAATTC 58.571 45.455 11.47 0.00 0.00 2.17
3253 3336 9.388506 CAGTGGTCAATTAATTCAGAACTCTAT 57.611 33.333 0.00 0.00 0.00 1.98
3254 3337 9.965902 AGTGGTCAATTAATTCAGAACTCTATT 57.034 29.630 0.00 0.00 0.00 1.73
3315 3398 8.044060 TCCAGTGTATATTTTCTCTTTTGCTG 57.956 34.615 0.00 0.00 0.00 4.41
3400 3483 0.750546 TGCATCAGGATCCAGCAAGC 60.751 55.000 15.82 11.52 31.42 4.01
3575 3658 1.620323 AGTAACCGGACAACCCTGTAC 59.380 52.381 9.46 0.00 35.30 2.90
3585 3668 4.058817 GACAACCCTGTACTCAGAACTTG 58.941 47.826 0.00 0.00 43.76 3.16
3592 3675 2.563179 TGTACTCAGAACTTGGGAGAGC 59.437 50.000 0.00 0.00 33.00 4.09
3600 3683 0.036294 ACTTGGGAGAGCGCTTAACC 60.036 55.000 13.26 14.80 0.00 2.85
3694 3778 7.708752 TCAACAAGAGCCGTGAAATAAATTTTT 59.291 29.630 0.00 0.00 0.00 1.94
3813 3897 5.078411 TGAGATCTCAGTTAAGCTTGGAC 57.922 43.478 21.67 7.94 34.14 4.02
3965 4052 8.275040 AGTTGGATACTGGATTTTATTAGCTGT 58.725 33.333 0.00 0.00 35.19 4.40
3966 4053 8.560374 GTTGGATACTGGATTTTATTAGCTGTC 58.440 37.037 0.00 0.00 37.61 3.51
3967 4054 7.224297 TGGATACTGGATTTTATTAGCTGTCC 58.776 38.462 0.00 0.00 37.61 4.02
3968 4055 6.655425 GGATACTGGATTTTATTAGCTGTCCC 59.345 42.308 0.00 0.00 0.00 4.46
3969 4056 5.450818 ACTGGATTTTATTAGCTGTCCCA 57.549 39.130 0.00 0.00 0.00 4.37
3970 4057 5.826643 ACTGGATTTTATTAGCTGTCCCAA 58.173 37.500 0.00 0.00 0.00 4.12
4129 4217 8.870116 TGCAGTTTCTAGACCACATACATATAT 58.130 33.333 0.00 0.00 0.00 0.86
4267 4360 5.774690 TGCAGGAATTGGAGTGTTTTCTTAT 59.225 36.000 0.00 0.00 0.00 1.73
4268 4361 6.095377 GCAGGAATTGGAGTGTTTTCTTATG 58.905 40.000 0.00 0.00 0.00 1.90
4283 4376 4.439305 TCTTATGGAAATGTTGCTGCAC 57.561 40.909 0.00 0.00 0.00 4.57
4342 4435 3.882888 CAGAGGTGTGCAAAAGGTTTCTA 59.117 43.478 0.00 0.00 0.00 2.10
4385 4561 3.216800 TGCACATCTGAAAGGATATGGC 58.783 45.455 0.00 0.00 0.00 4.40
4423 4599 3.405831 CCTGTGCACTTCTGAATCTTGA 58.594 45.455 19.41 0.00 0.00 3.02
4449 4625 5.183904 GTCTTGCCTTTCAACCAACATATCT 59.816 40.000 0.00 0.00 0.00 1.98
4453 4629 4.142381 GCCTTTCAACCAACATATCTCACC 60.142 45.833 0.00 0.00 0.00 4.02
4463 4639 5.716703 CCAACATATCTCACCTTTCCCTTTT 59.283 40.000 0.00 0.00 0.00 2.27
4548 4724 2.756400 GTGGTGTGGGCAGATGGA 59.244 61.111 0.00 0.00 0.00 3.41
4549 4725 1.074775 GTGGTGTGGGCAGATGGAA 59.925 57.895 0.00 0.00 0.00 3.53
4550 4726 1.074775 TGGTGTGGGCAGATGGAAC 59.925 57.895 0.00 0.00 0.00 3.62
4551 4727 2.040544 GGTGTGGGCAGATGGAACG 61.041 63.158 0.00 0.00 0.00 3.95
4552 4728 2.359850 TGTGGGCAGATGGAACGC 60.360 61.111 0.00 0.00 0.00 4.84
4553 4729 2.359850 GTGGGCAGATGGAACGCA 60.360 61.111 0.00 0.00 0.00 5.24
4554 4730 1.750399 GTGGGCAGATGGAACGCAT 60.750 57.895 0.00 0.00 0.00 4.73
4555 4731 0.463654 GTGGGCAGATGGAACGCATA 60.464 55.000 0.00 0.00 0.00 3.14
4556 4732 0.254462 TGGGCAGATGGAACGCATAA 59.746 50.000 0.00 0.00 0.00 1.90
4557 4733 1.133823 TGGGCAGATGGAACGCATAAT 60.134 47.619 0.00 0.00 0.00 1.28
4558 4734 2.105649 TGGGCAGATGGAACGCATAATA 59.894 45.455 0.00 0.00 0.00 0.98
4559 4735 3.146066 GGGCAGATGGAACGCATAATAA 58.854 45.455 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.574516 AAATGTTATTATGTAGTCCCTCCATTC 57.425 33.333 0.00 0.00 0.00 2.67
3 4 9.442062 TCTAAATGTTATTATGTAGTCCCTCCA 57.558 33.333 0.00 0.00 0.00 3.86
4 5 9.708092 GTCTAAATGTTATTATGTAGTCCCTCC 57.292 37.037 0.00 0.00 0.00 4.30
148 149 9.515226 ACAGTAATTCTCTTGTTATGGCTAAAA 57.485 29.630 0.00 0.00 0.00 1.52
190 191 0.108396 GGCTGCCCAAAACAAATGGT 59.892 50.000 7.66 0.00 36.14 3.55
193 194 3.295585 AAAAGGCTGCCCAAAACAAAT 57.704 38.095 16.57 0.00 0.00 2.32
222 223 5.334802 CGCTGACTAAAACAATCCATCACAA 60.335 40.000 0.00 0.00 0.00 3.33
223 224 4.154015 CGCTGACTAAAACAATCCATCACA 59.846 41.667 0.00 0.00 0.00 3.58
224 225 4.154195 ACGCTGACTAAAACAATCCATCAC 59.846 41.667 0.00 0.00 0.00 3.06
225 226 4.323417 ACGCTGACTAAAACAATCCATCA 58.677 39.130 0.00 0.00 0.00 3.07
230 231 4.483476 ACCAACGCTGACTAAAACAATC 57.517 40.909 0.00 0.00 0.00 2.67
232 233 3.249080 GCTACCAACGCTGACTAAAACAA 59.751 43.478 0.00 0.00 0.00 2.83
239 240 0.391661 CCATGCTACCAACGCTGACT 60.392 55.000 0.00 0.00 0.00 3.41
241 242 0.036164 AACCATGCTACCAACGCTGA 59.964 50.000 0.00 0.00 0.00 4.26
244 245 0.447801 CTCAACCATGCTACCAACGC 59.552 55.000 0.00 0.00 0.00 4.84
248 249 1.951209 TCCTCTCAACCATGCTACCA 58.049 50.000 0.00 0.00 0.00 3.25
251 252 6.692849 ATATGAATCCTCTCAACCATGCTA 57.307 37.500 0.00 0.00 0.00 3.49
262 263 4.505039 GCGGGTGGTTTATATGAATCCTCT 60.505 45.833 0.00 0.00 0.00 3.69
263 264 3.751698 GCGGGTGGTTTATATGAATCCTC 59.248 47.826 0.00 0.00 0.00 3.71
264 265 3.137544 TGCGGGTGGTTTATATGAATCCT 59.862 43.478 0.00 0.00 0.00 3.24
265 266 3.482436 TGCGGGTGGTTTATATGAATCC 58.518 45.455 0.00 0.00 0.00 3.01
266 267 5.508200 TTTGCGGGTGGTTTATATGAATC 57.492 39.130 0.00 0.00 0.00 2.52
267 268 5.923733 TTTTGCGGGTGGTTTATATGAAT 57.076 34.783 0.00 0.00 0.00 2.57
268 269 5.723672 TTTTTGCGGGTGGTTTATATGAA 57.276 34.783 0.00 0.00 0.00 2.57
289 290 9.844257 CTCTGGTTTATATGAATCCTCTCTTTT 57.156 33.333 0.00 0.00 0.00 2.27
290 291 7.936301 GCTCTGGTTTATATGAATCCTCTCTTT 59.064 37.037 0.00 0.00 0.00 2.52
291 292 7.292120 AGCTCTGGTTTATATGAATCCTCTCTT 59.708 37.037 0.00 0.00 0.00 2.85
292 293 6.786959 AGCTCTGGTTTATATGAATCCTCTCT 59.213 38.462 0.00 0.00 0.00 3.10
293 294 7.003402 AGCTCTGGTTTATATGAATCCTCTC 57.997 40.000 0.00 0.00 0.00 3.20
294 295 7.952930 TCTAGCTCTGGTTTATATGAATCCTCT 59.047 37.037 0.00 0.00 0.00 3.69
340 341 5.305585 CACCAAGAAACCAAACTAGAGCTA 58.694 41.667 0.00 0.00 0.00 3.32
341 342 4.137543 CACCAAGAAACCAAACTAGAGCT 58.862 43.478 0.00 0.00 0.00 4.09
342 343 3.253432 CCACCAAGAAACCAAACTAGAGC 59.747 47.826 0.00 0.00 0.00 4.09
347 351 2.764010 GTTCCCACCAAGAAACCAAACT 59.236 45.455 0.00 0.00 0.00 2.66
351 355 2.026905 GCTGTTCCCACCAAGAAACCA 61.027 52.381 0.00 0.00 0.00 3.67
361 365 1.282157 ACCTTGATAGGCTGTTCCCAC 59.718 52.381 0.00 0.00 46.22 4.61
365 369 4.327680 ACTTGAACCTTGATAGGCTGTTC 58.672 43.478 0.00 1.42 46.22 3.18
366 370 4.373156 ACTTGAACCTTGATAGGCTGTT 57.627 40.909 0.00 0.00 46.22 3.16
367 371 4.042187 AGAACTTGAACCTTGATAGGCTGT 59.958 41.667 0.00 0.00 46.22 4.40
368 372 4.583871 AGAACTTGAACCTTGATAGGCTG 58.416 43.478 0.00 0.00 46.22 4.85
370 374 5.813157 GTCTAGAACTTGAACCTTGATAGGC 59.187 44.000 0.00 0.00 46.22 3.93
372 376 6.037098 CGGTCTAGAACTTGAACCTTGATAG 58.963 44.000 6.16 0.00 0.00 2.08
373 377 5.105473 CCGGTCTAGAACTTGAACCTTGATA 60.105 44.000 6.16 0.00 0.00 2.15
374 378 4.322801 CCGGTCTAGAACTTGAACCTTGAT 60.323 45.833 6.16 0.00 0.00 2.57
375 379 3.006537 CCGGTCTAGAACTTGAACCTTGA 59.993 47.826 6.16 0.00 0.00 3.02
397 403 2.017113 GCATGCACACCCTACCCTTAC 61.017 57.143 14.21 0.00 0.00 2.34
400 406 2.677228 GCATGCACACCCTACCCT 59.323 61.111 14.21 0.00 0.00 4.34
402 408 1.000896 AAGGCATGCACACCCTACC 60.001 57.895 21.36 0.00 0.00 3.18
404 410 0.625316 ATGAAGGCATGCACACCCTA 59.375 50.000 21.36 0.00 32.31 3.53
416 422 2.571548 CACCCCTGTGAATGAAGGC 58.428 57.895 0.00 0.00 45.76 4.35
425 431 1.945819 GCACATACACTCACCCCTGTG 60.946 57.143 0.00 0.00 44.18 3.66
426 432 0.324943 GCACATACACTCACCCCTGT 59.675 55.000 0.00 0.00 0.00 4.00
427 433 0.324614 TGCACATACACTCACCCCTG 59.675 55.000 0.00 0.00 0.00 4.45
428 434 1.289160 ATGCACATACACTCACCCCT 58.711 50.000 0.00 0.00 0.00 4.79
429 435 2.128771 AATGCACATACACTCACCCC 57.871 50.000 0.00 0.00 0.00 4.95
430 436 6.710295 TCATATAAATGCACATACACTCACCC 59.290 38.462 0.00 0.00 32.76 4.61
431 437 7.571983 GCTCATATAAATGCACATACACTCACC 60.572 40.741 0.00 0.00 32.76 4.02
432 438 7.293745 GCTCATATAAATGCACATACACTCAC 58.706 38.462 0.00 0.00 32.76 3.51
433 439 6.146021 CGCTCATATAAATGCACATACACTCA 59.854 38.462 0.00 0.00 32.76 3.41
434 440 6.146184 ACGCTCATATAAATGCACATACACTC 59.854 38.462 0.00 0.00 32.76 3.51
435 441 5.991606 ACGCTCATATAAATGCACATACACT 59.008 36.000 0.00 0.00 32.76 3.55
436 442 6.228273 ACGCTCATATAAATGCACATACAC 57.772 37.500 0.00 0.00 32.76 2.90
437 443 6.346518 CGAACGCTCATATAAATGCACATACA 60.347 38.462 0.00 0.00 32.76 2.29
438 444 6.009474 CGAACGCTCATATAAATGCACATAC 58.991 40.000 0.00 0.00 32.76 2.39
439 445 5.389411 GCGAACGCTCATATAAATGCACATA 60.389 40.000 11.97 0.00 38.26 2.29
440 446 4.611355 GCGAACGCTCATATAAATGCACAT 60.611 41.667 11.97 0.00 38.26 3.21
441 447 3.303066 GCGAACGCTCATATAAATGCACA 60.303 43.478 11.97 0.00 38.26 4.57
442 448 3.218398 GCGAACGCTCATATAAATGCAC 58.782 45.455 11.97 0.00 38.26 4.57
443 449 2.096958 CGCGAACGCTCATATAAATGCA 60.097 45.455 16.66 0.00 39.32 3.96
444 450 2.096909 ACGCGAACGCTCATATAAATGC 60.097 45.455 15.93 0.00 45.53 3.56
445 451 3.770765 ACGCGAACGCTCATATAAATG 57.229 42.857 15.93 0.46 45.53 2.32
446 452 4.033587 ACAAACGCGAACGCTCATATAAAT 59.966 37.500 15.93 0.00 45.53 1.40
447 453 3.368539 ACAAACGCGAACGCTCATATAAA 59.631 39.130 15.93 0.00 45.53 1.40
453 459 1.136474 CAATACAAACGCGAACGCTCA 60.136 47.619 15.93 0.00 45.53 4.26
516 522 3.888930 GGGTTCCTTTCAAATGTGAGTCA 59.111 43.478 0.00 0.00 34.49 3.41
542 548 5.777449 TCCTTGTAGAATCTAGATGACCCA 58.223 41.667 5.86 0.00 0.00 4.51
550 556 7.436673 CGGAATCTTGTTCCTTGTAGAATCTAG 59.563 40.741 5.40 0.00 36.45 2.43
624 631 2.764572 GGAAAGAGTAGGGGATCGTGAA 59.235 50.000 0.00 0.00 0.00 3.18
625 632 2.024273 AGGAAAGAGTAGGGGATCGTGA 60.024 50.000 0.00 0.00 0.00 4.35
630 637 1.123928 CGCAGGAAAGAGTAGGGGAT 58.876 55.000 0.00 0.00 0.00 3.85
645 652 3.361644 CGATGAAAATTCACAAACCGCAG 59.638 43.478 0.00 0.00 40.49 5.18
662 669 8.030106 GGTATAAAACAAAATTTGGACCGATGA 58.970 33.333 10.71 0.00 34.12 2.92
667 674 8.097662 TCATGGGTATAAAACAAAATTTGGACC 58.902 33.333 10.71 7.04 32.09 4.46
762 769 4.821805 CGAATGGTAATTGCCTGTAGGATT 59.178 41.667 14.11 3.88 37.39 3.01
771 814 0.820871 TTGGGCGAATGGTAATTGCC 59.179 50.000 5.49 5.49 38.34 4.52
979 1025 1.833049 CCGCTCGGATTCTAGGGGT 60.833 63.158 1.35 0.00 40.12 4.95
1005 1051 2.226330 CAGTCGGAGAGTATGGAGGAG 58.774 57.143 0.00 0.00 38.70 3.69
1234 1283 2.291024 ACTAGTGAGGCGAGGAGAAGAA 60.291 50.000 0.00 0.00 0.00 2.52
1350 1399 4.733887 CGTTGCTACACTAGGATTAACTCG 59.266 45.833 0.00 0.00 0.00 4.18
1351 1400 5.041940 CCGTTGCTACACTAGGATTAACTC 58.958 45.833 0.00 0.00 0.00 3.01
1352 1401 4.708421 TCCGTTGCTACACTAGGATTAACT 59.292 41.667 0.00 0.00 0.00 2.24
1353 1402 5.002464 TCCGTTGCTACACTAGGATTAAC 57.998 43.478 0.00 0.00 0.00 2.01
1355 1404 4.891168 TCATCCGTTGCTACACTAGGATTA 59.109 41.667 0.00 0.00 36.45 1.75
1356 1405 3.704566 TCATCCGTTGCTACACTAGGATT 59.295 43.478 0.00 0.00 36.45 3.01
1357 1406 3.296854 TCATCCGTTGCTACACTAGGAT 58.703 45.455 0.00 0.00 38.87 3.24
1359 1408 3.520290 TTCATCCGTTGCTACACTAGG 57.480 47.619 0.00 0.00 0.00 3.02
1360 1409 5.462398 GGTAATTCATCCGTTGCTACACTAG 59.538 44.000 0.00 0.00 0.00 2.57
1361 1410 5.353938 GGTAATTCATCCGTTGCTACACTA 58.646 41.667 0.00 0.00 0.00 2.74
1386 1438 5.546621 TGTAACAACTAACAAGCCTCTCT 57.453 39.130 0.00 0.00 0.00 3.10
1414 1484 7.265673 TGATGTAGAACAGGATTTACAGCTAC 58.734 38.462 0.00 0.00 34.49 3.58
1479 1549 1.134753 CAAAACAGTGGCTGCACAAGA 59.865 47.619 0.50 0.00 34.37 3.02
1502 1572 2.721425 TGATCTTGGCAGATGCATCA 57.279 45.000 27.81 5.54 40.14 3.07
1508 1578 1.269988 CCGTCGATGATCTTGGCAGAT 60.270 52.381 6.11 0.00 43.03 2.90
1514 1584 0.302890 GCTTGCCGTCGATGATCTTG 59.697 55.000 6.11 0.00 0.00 3.02
1529 1599 0.179078 TTTGCTTTGCCACCAGCTTG 60.179 50.000 0.00 0.00 44.23 4.01
1541 1611 3.622455 CGACCTCCTCCCTTATTTGCTTT 60.622 47.826 0.00 0.00 0.00 3.51
1590 1660 2.680352 AGGCACCACTCCGATCGT 60.680 61.111 15.09 0.00 0.00 3.73
1709 1779 2.356135 GAAGCGTCCTCTGGCAAATTA 58.644 47.619 0.00 0.00 0.00 1.40
1713 1783 2.347490 GGAAGCGTCCTCTGGCAA 59.653 61.111 11.87 0.00 41.24 4.52
1830 1900 3.944055 ATACTAGCCATTGAGTAGCGG 57.056 47.619 0.00 0.00 31.87 5.52
1831 1901 6.868864 ACAATTATACTAGCCATTGAGTAGCG 59.131 38.462 9.56 0.00 31.87 4.26
1832 1902 8.499162 CAACAATTATACTAGCCATTGAGTAGC 58.501 37.037 9.56 0.00 31.87 3.58
1835 1905 8.893727 GTTCAACAATTATACTAGCCATTGAGT 58.106 33.333 9.56 0.00 32.07 3.41
1836 1906 8.345565 GGTTCAACAATTATACTAGCCATTGAG 58.654 37.037 9.56 4.12 32.07 3.02
1837 1907 7.284489 GGGTTCAACAATTATACTAGCCATTGA 59.716 37.037 9.56 0.00 32.07 2.57
1838 1908 7.068103 TGGGTTCAACAATTATACTAGCCATTG 59.932 37.037 0.00 0.00 33.58 2.82
1839 1909 7.122715 TGGGTTCAACAATTATACTAGCCATT 58.877 34.615 0.00 0.00 0.00 3.16
1840 1910 6.668645 TGGGTTCAACAATTATACTAGCCAT 58.331 36.000 0.00 0.00 0.00 4.40
1841 1911 6.068461 TGGGTTCAACAATTATACTAGCCA 57.932 37.500 0.00 0.00 0.00 4.75
1916 1986 6.483405 AGTATTTCGGTATAGAGGGAGTAGG 58.517 44.000 0.00 0.00 0.00 3.18
1917 1987 7.447853 ACAAGTATTTCGGTATAGAGGGAGTAG 59.552 40.741 0.00 0.00 0.00 2.57
1918 1988 7.293073 ACAAGTATTTCGGTATAGAGGGAGTA 58.707 38.462 0.00 0.00 0.00 2.59
1919 1989 6.134754 ACAAGTATTTCGGTATAGAGGGAGT 58.865 40.000 0.00 0.00 0.00 3.85
1920 1990 6.568081 CGACAAGTATTTCGGTATAGAGGGAG 60.568 46.154 0.00 0.00 0.00 4.30
1921 1991 5.240183 CGACAAGTATTTCGGTATAGAGGGA 59.760 44.000 0.00 0.00 0.00 4.20
1923 1993 6.069684 ACGACAAGTATTTCGGTATAGAGG 57.930 41.667 0.00 0.00 39.63 3.69
1924 1994 6.417044 CCAACGACAAGTATTTCGGTATAGAG 59.583 42.308 0.00 0.00 39.63 2.43
1925 1995 6.267817 CCAACGACAAGTATTTCGGTATAGA 58.732 40.000 0.00 0.00 39.63 1.98
1927 1997 5.350633 CCCAACGACAAGTATTTCGGTATA 58.649 41.667 0.00 0.00 39.63 1.47
1928 1998 4.186159 CCCAACGACAAGTATTTCGGTAT 58.814 43.478 0.00 0.00 39.63 2.73
1929 1999 3.587923 CCCAACGACAAGTATTTCGGTA 58.412 45.455 0.00 0.00 39.63 4.02
1930 2000 2.419667 CCCAACGACAAGTATTTCGGT 58.580 47.619 0.00 0.00 39.63 4.69
1931 2001 1.735571 CCCCAACGACAAGTATTTCGG 59.264 52.381 0.00 0.00 39.63 4.30
1932 2002 2.690786 TCCCCAACGACAAGTATTTCG 58.309 47.619 0.00 0.00 41.14 3.46
1933 2003 5.217393 GTTTTCCCCAACGACAAGTATTTC 58.783 41.667 0.00 0.00 0.00 2.17
1934 2004 4.038282 GGTTTTCCCCAACGACAAGTATTT 59.962 41.667 0.00 0.00 0.00 1.40
1935 2005 3.570975 GGTTTTCCCCAACGACAAGTATT 59.429 43.478 0.00 0.00 0.00 1.89
1936 2006 3.151554 GGTTTTCCCCAACGACAAGTAT 58.848 45.455 0.00 0.00 0.00 2.12
1937 2007 2.092538 TGGTTTTCCCCAACGACAAGTA 60.093 45.455 0.00 0.00 39.73 2.24
1938 2008 1.341187 TGGTTTTCCCCAACGACAAGT 60.341 47.619 0.00 0.00 39.73 3.16
1939 2009 1.336755 CTGGTTTTCCCCAACGACAAG 59.663 52.381 0.00 0.00 39.73 3.16
1940 2010 1.341187 ACTGGTTTTCCCCAACGACAA 60.341 47.619 0.00 0.00 39.73 3.18
1941 2011 0.256464 ACTGGTTTTCCCCAACGACA 59.744 50.000 0.00 0.00 39.73 4.35
1942 2012 1.875514 GTACTGGTTTTCCCCAACGAC 59.124 52.381 0.00 0.00 39.73 4.34
1943 2013 1.489649 TGTACTGGTTTTCCCCAACGA 59.510 47.619 0.00 0.00 39.73 3.85
1944 2014 1.970092 TGTACTGGTTTTCCCCAACG 58.030 50.000 0.00 0.00 39.73 4.10
1945 2015 3.293337 ACTTGTACTGGTTTTCCCCAAC 58.707 45.455 0.00 0.00 39.73 3.77
1946 2016 3.673543 ACTTGTACTGGTTTTCCCCAA 57.326 42.857 0.00 0.00 39.73 4.12
1947 2017 3.558033 GAACTTGTACTGGTTTTCCCCA 58.442 45.455 0.00 0.00 39.73 4.96
1948 2018 2.889045 GGAACTTGTACTGGTTTTCCCC 59.111 50.000 0.00 0.00 39.73 4.81
1949 2019 2.889045 GGGAACTTGTACTGGTTTTCCC 59.111 50.000 12.54 12.54 44.11 3.97
1950 2020 2.889045 GGGGAACTTGTACTGGTTTTCC 59.111 50.000 0.00 5.64 41.14 3.13
1951 2021 2.889045 GGGGGAACTTGTACTGGTTTTC 59.111 50.000 0.00 0.00 0.00 2.29
1952 2022 2.245287 TGGGGGAACTTGTACTGGTTTT 59.755 45.455 0.00 0.00 0.00 2.43
1953 2023 1.854280 TGGGGGAACTTGTACTGGTTT 59.146 47.619 0.00 0.00 0.00 3.27
1954 2024 1.423921 CTGGGGGAACTTGTACTGGTT 59.576 52.381 0.00 0.00 0.00 3.67
1955 2025 1.064825 CTGGGGGAACTTGTACTGGT 58.935 55.000 0.00 0.00 0.00 4.00
1956 2026 0.322546 GCTGGGGGAACTTGTACTGG 60.323 60.000 0.00 0.00 0.00 4.00
1957 2027 0.673644 CGCTGGGGGAACTTGTACTG 60.674 60.000 0.00 0.00 0.00 2.74
1958 2028 0.834687 TCGCTGGGGGAACTTGTACT 60.835 55.000 0.00 0.00 0.00 2.73
1959 2029 0.672711 GTCGCTGGGGGAACTTGTAC 60.673 60.000 0.00 0.00 0.00 2.90
1960 2030 1.122632 TGTCGCTGGGGGAACTTGTA 61.123 55.000 0.00 0.00 0.00 2.41
1961 2031 2.430367 GTCGCTGGGGGAACTTGT 59.570 61.111 0.00 0.00 0.00 3.16
1962 2032 1.966451 GTGTCGCTGGGGGAACTTG 60.966 63.158 0.00 0.00 0.00 3.16
1963 2033 2.430367 GTGTCGCTGGGGGAACTT 59.570 61.111 0.00 0.00 0.00 2.66
1964 2034 4.003788 CGTGTCGCTGGGGGAACT 62.004 66.667 0.00 0.00 0.00 3.01
1965 2035 2.234913 ATACGTGTCGCTGGGGGAAC 62.235 60.000 0.00 0.00 0.00 3.62
1966 2036 1.546589 AATACGTGTCGCTGGGGGAA 61.547 55.000 0.00 0.00 0.00 3.97
1967 2037 1.985662 AATACGTGTCGCTGGGGGA 60.986 57.895 0.00 0.00 0.00 4.81
1968 2038 1.813753 CAATACGTGTCGCTGGGGG 60.814 63.158 0.00 0.00 0.00 5.40
1969 2039 1.079405 ACAATACGTGTCGCTGGGG 60.079 57.895 0.00 0.00 34.38 4.96
1970 2040 1.358725 CCACAATACGTGTCGCTGGG 61.359 60.000 0.00 0.00 44.78 4.45
1971 2041 0.669318 ACCACAATACGTGTCGCTGG 60.669 55.000 0.00 0.00 44.78 4.85
1972 2042 1.652124 GTACCACAATACGTGTCGCTG 59.348 52.381 0.00 0.00 44.78 5.18
1973 2043 1.270274 TGTACCACAATACGTGTCGCT 59.730 47.619 0.00 0.00 44.78 4.93
1974 2044 1.652124 CTGTACCACAATACGTGTCGC 59.348 52.381 0.00 0.00 44.78 5.19
1975 2045 3.168963 CTCTGTACCACAATACGTGTCG 58.831 50.000 0.00 0.00 44.78 4.35
1976 2046 3.508762 CCTCTGTACCACAATACGTGTC 58.491 50.000 0.00 0.00 44.78 3.67
1977 2047 2.232941 CCCTCTGTACCACAATACGTGT 59.767 50.000 0.00 0.00 44.78 4.49
1978 2048 2.494471 TCCCTCTGTACCACAATACGTG 59.506 50.000 0.00 0.00 45.92 4.49
1979 2049 2.758979 CTCCCTCTGTACCACAATACGT 59.241 50.000 0.00 0.00 0.00 3.57
1980 2050 2.758979 ACTCCCTCTGTACCACAATACG 59.241 50.000 0.00 0.00 0.00 3.06
1981 2051 5.198965 TCTACTCCCTCTGTACCACAATAC 58.801 45.833 0.00 0.00 0.00 1.89
1982 2052 5.461516 TCTACTCCCTCTGTACCACAATA 57.538 43.478 0.00 0.00 0.00 1.90
1983 2053 4.332683 TCTACTCCCTCTGTACCACAAT 57.667 45.455 0.00 0.00 0.00 2.71
1984 2054 3.820195 TCTACTCCCTCTGTACCACAA 57.180 47.619 0.00 0.00 0.00 3.33
1985 2055 5.664815 ATATCTACTCCCTCTGTACCACA 57.335 43.478 0.00 0.00 0.00 4.17
1986 2056 7.670559 ACATAATATCTACTCCCTCTGTACCAC 59.329 40.741 0.00 0.00 0.00 4.16
1987 2057 7.766628 ACATAATATCTACTCCCTCTGTACCA 58.233 38.462 0.00 0.00 0.00 3.25
1988 2058 9.398538 CTACATAATATCTACTCCCTCTGTACC 57.601 40.741 0.00 0.00 0.00 3.34
1989 2059 8.895737 GCTACATAATATCTACTCCCTCTGTAC 58.104 40.741 0.00 0.00 0.00 2.90
1990 2060 7.769507 CGCTACATAATATCTACTCCCTCTGTA 59.230 40.741 0.00 0.00 0.00 2.74
1991 2061 6.600032 CGCTACATAATATCTACTCCCTCTGT 59.400 42.308 0.00 0.00 0.00 3.41
1992 2062 6.600032 ACGCTACATAATATCTACTCCCTCTG 59.400 42.308 0.00 0.00 0.00 3.35
1993 2063 6.600032 CACGCTACATAATATCTACTCCCTCT 59.400 42.308 0.00 0.00 0.00 3.69
1994 2064 6.678409 GCACGCTACATAATATCTACTCCCTC 60.678 46.154 0.00 0.00 0.00 4.30
1995 2065 5.125739 GCACGCTACATAATATCTACTCCCT 59.874 44.000 0.00 0.00 0.00 4.20
1996 2066 5.341617 GCACGCTACATAATATCTACTCCC 58.658 45.833 0.00 0.00 0.00 4.30
1997 2067 5.105877 TGGCACGCTACATAATATCTACTCC 60.106 44.000 0.00 0.00 0.00 3.85
1998 2068 5.800941 GTGGCACGCTACATAATATCTACTC 59.199 44.000 0.00 0.00 35.02 2.59
1999 2069 5.710984 GTGGCACGCTACATAATATCTACT 58.289 41.667 0.00 0.00 35.02 2.57
2034 2104 6.265196 TGCCTTAACAGATTTATTATGCCTGG 59.735 38.462 0.00 0.00 0.00 4.45
2173 2243 5.822519 TGTGTTCACCTTATTATCCATGAGC 59.177 40.000 0.00 0.00 0.00 4.26
2417 2498 0.552848 ATGGATCCCGACCTTGCATT 59.447 50.000 9.90 0.00 0.00 3.56
2659 2740 8.458573 TGGTTTTTGAATGTACAATACTCACT 57.541 30.769 0.00 0.00 0.00 3.41
2884 2965 8.182227 GCTATGTTAAAAGTAAACAGATCACCC 58.818 37.037 0.00 0.00 40.00 4.61
3002 3084 8.432805 ACTCCCCATATACTTAGATTGTCAAAG 58.567 37.037 0.00 0.00 0.00 2.77
3014 3096 4.202503 CCATGCAGAACTCCCCATATACTT 60.203 45.833 0.00 0.00 0.00 2.24
3017 3099 3.326521 ACCATGCAGAACTCCCCATATA 58.673 45.455 0.00 0.00 0.00 0.86
3145 3228 9.608617 GGTGTTCATAAAAACTTAAGAAGCTAC 57.391 33.333 10.09 0.00 0.00 3.58
3226 3309 6.150140 AGAGTTCTGAATTAATTGACCACTGC 59.850 38.462 5.17 0.00 0.00 4.40
3243 3326 8.749026 TTCCAGGTACTACTAATAGAGTTCTG 57.251 38.462 0.00 5.51 39.81 3.02
3400 3483 1.453762 CTAGCCGGTAACCTCGAGGG 61.454 65.000 34.04 16.82 40.27 4.30
3550 3633 1.875514 GGGTTGTCCGGTTACTTGAAC 59.124 52.381 0.00 0.00 37.31 3.18
3575 3658 0.739112 GCGCTCTCCCAAGTTCTGAG 60.739 60.000 0.00 0.00 0.00 3.35
3585 3668 1.087501 CAAAGGTTAAGCGCTCTCCC 58.912 55.000 12.06 10.96 0.00 4.30
3592 3675 5.121298 GGTAGACTAAACCAAAGGTTAAGCG 59.879 44.000 1.26 0.00 46.20 4.68
3600 3683 4.015872 TGCCTGGTAGACTAAACCAAAG 57.984 45.455 0.00 0.00 46.14 2.77
3639 3722 0.313672 GTCCAACAAAAGGCGCATCA 59.686 50.000 10.83 0.00 0.00 3.07
3640 3723 0.388520 GGTCCAACAAAAGGCGCATC 60.389 55.000 10.83 0.00 0.00 3.91
3694 3778 3.245122 GGGTAAATTTCTCACCCCTGTCA 60.245 47.826 14.53 0.00 45.34 3.58
3813 3897 5.229887 GCAAACAAGCATAACATATGGTTCG 59.770 40.000 7.80 9.57 40.96 3.95
3856 3940 1.692749 GGGGAGCCCACCACTCATA 60.693 63.158 8.02 0.00 44.65 2.15
3947 4034 5.450818 TGGGACAGCTAATAAAATCCAGT 57.549 39.130 0.00 0.00 0.00 4.00
3965 4052 5.789574 ACATAAACTAGTTGGGATTGGGA 57.210 39.130 9.34 0.00 0.00 4.37
3966 4053 6.490040 CCATACATAAACTAGTTGGGATTGGG 59.510 42.308 9.34 3.48 0.00 4.12
3967 4054 7.060421 ACCATACATAAACTAGTTGGGATTGG 58.940 38.462 9.34 13.90 0.00 3.16
3968 4055 9.052759 GTACCATACATAAACTAGTTGGGATTG 57.947 37.037 9.34 5.57 0.00 2.67
3969 4056 8.774183 TGTACCATACATAAACTAGTTGGGATT 58.226 33.333 9.34 0.00 32.89 3.01
3970 4057 8.208903 GTGTACCATACATAAACTAGTTGGGAT 58.791 37.037 9.34 1.54 41.34 3.85
4130 4218 9.347240 ACTTAGAAGCAAAGCAATATCATACAT 57.653 29.630 0.00 0.00 0.00 2.29
4136 4224 7.254932 CCCTACACTTAGAAGCAAAGCAATATC 60.255 40.741 0.00 0.00 0.00 1.63
4185 4274 2.162608 TCATTTATTTGGCGGTTCCACG 59.837 45.455 0.00 0.00 46.55 4.94
4267 4360 1.962100 TCATGTGCAGCAACATTTCCA 59.038 42.857 0.00 0.00 38.75 3.53
4268 4361 2.728690 TCATGTGCAGCAACATTTCC 57.271 45.000 0.00 0.00 38.75 3.13
4370 4546 4.541250 AATTGGGCCATATCCTTTCAGA 57.459 40.909 7.26 0.00 0.00 3.27
4385 4561 4.157289 GCACAGGCATCTCATATAATTGGG 59.843 45.833 0.00 0.00 40.72 4.12
4423 4599 3.030291 TGTTGGTTGAAAGGCAAGACAT 58.970 40.909 0.00 0.00 37.12 3.06
4449 4625 1.216678 TGCCAGAAAAGGGAAAGGTGA 59.783 47.619 0.00 0.00 0.00 4.02
4453 4629 3.005155 CACTCTTGCCAGAAAAGGGAAAG 59.995 47.826 0.00 0.00 41.72 2.62
4463 4639 0.610174 CACTAGCCACTCTTGCCAGA 59.390 55.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.