Multiple sequence alignment - TraesCS5B01G374500

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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 TraesCS5B01G374500 chr5B 100.000 2582 0 0 1 2582 551678366 551680947 0.000000e+00 4769.0
1 TraesCS5B01G374500 chr5A 90.483 1492 79 25 603 2036 570777989 570779475 0.000000e+00 1910.0
2 TraesCS5B01G374500 chr5A 85.412 425 55 5 2161 2582 570781287 570781707 3.950000e-118 435.0
3 TraesCS5B01G374500 chr5A 86.305 387 36 8 1 386 570777486 570777856 3.090000e-109 405.0
4 TraesCS5B01G374500 chr5A 93.878 49 3 0 424 472 570777876 570777924 9.910000e-10 75.0
5 TraesCS5B01G374500 chr5D 92.963 1080 46 9 570 1635 451908974 451910037 0.000000e+00 1546.0
6 TraesCS5B01G374500 chr5D 91.080 213 16 3 1 211 451908483 451908694 4.210000e-73 285.0
7 TraesCS5B01G374500 chr5D 91.912 136 11 0 249 384 451908758 451908893 9.430000e-45 191.0
8 TraesCS5B01G374500 chr5D 94.444 54 2 1 2064 2117 322375792 322375740 5.920000e-12 82.4
9 TraesCS5B01G374500 chr5D 97.872 47 1 0 2064 2110 438950157 438950203 5.920000e-12 82.4
10 TraesCS5B01G374500 chr5D 92.727 55 3 1 2064 2117 228556478 228556424 7.660000e-11 78.7
11 TraesCS5B01G374500 chr7D 84.954 545 69 8 1037 1580 362366821 362366289 8.130000e-150 540.0
12 TraesCS5B01G374500 chr7D 96.970 33 1 0 2031 2063 28347577 28347545 3.590000e-04 56.5
13 TraesCS5B01G374500 chr7B 85.915 142 10 3 766 904 324390438 324390572 2.680000e-30 143.0
14 TraesCS5B01G374500 chr6A 87.654 81 9 1 2031 2111 417623148 417623069 2.740000e-15 93.5
15 TraesCS5B01G374500 chr6A 96.000 50 2 0 2064 2113 540320395 540320444 5.920000e-12 82.4
16 TraesCS5B01G374500 chr3B 86.076 79 8 2 2033 2108 486803297 486803375 5.920000e-12 82.4
17 TraesCS5B01G374500 chr3B 94.340 53 2 1 2064 2115 593935172 593935224 2.130000e-11 80.5
18 TraesCS5B01G374500 chr1A 91.525 59 2 3 2064 2122 449853626 449853571 7.660000e-11 78.7
19 TraesCS5B01G374500 chr6D 91.228 57 3 2 2064 2120 456456129 456456075 2.760000e-10 76.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G374500 chr5B 551678366 551680947 2581 False 4769.00 4769 100.0000 1 2582 1 chr5B.!!$F1 2581
1 TraesCS5B01G374500 chr5A 570777486 570781707 4221 False 706.25 1910 89.0195 1 2582 4 chr5A.!!$F1 2581
2 TraesCS5B01G374500 chr5D 451908483 451910037 1554 False 674.00 1546 91.9850 1 1635 3 chr5D.!!$F2 1634
3 TraesCS5B01G374500 chr7D 362366289 362366821 532 True 540.00 540 84.9540 1037 1580 1 chr7D.!!$R2 543

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
505 559 0.251341 AGTTTTCTTGCGGGCCTCAT 60.251 50.0 0.84 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2404 4231 0.107993 TTCCTCTGCTTCCTCGCATG 60.108 55.0 0.0 0.0 39.52 4.06 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
41 42 2.927553 GCTGTTAGCAACTGGGATTG 57.072 50.000 0.00 0.00 41.89 2.67
79 80 3.117512 GGATCTAATCATGGTGGGGTGTT 60.118 47.826 0.00 0.00 0.00 3.32
83 84 0.323725 ATCATGGTGGGGTGTTGAGC 60.324 55.000 0.00 0.00 0.00 4.26
100 101 2.515523 CCTGGAGGGAATGCAGCG 60.516 66.667 0.00 0.00 45.53 5.18
103 104 2.899339 GGAGGGAATGCAGCGAGC 60.899 66.667 0.00 0.00 45.96 5.03
122 123 1.517242 CAAGGTGACCAAGTGCTCTC 58.483 55.000 3.63 0.00 0.00 3.20
125 126 0.321122 GGTGACCAAGTGCTCTCCAG 60.321 60.000 0.00 0.00 0.00 3.86
181 184 1.153756 AAGCTGGGGTTCACCAAGG 59.846 57.895 0.00 0.00 41.06 3.61
211 214 2.291741 CAGGCAAAACCAGACTCTGTTC 59.708 50.000 5.32 0.00 43.14 3.18
212 215 2.173569 AGGCAAAACCAGACTCTGTTCT 59.826 45.455 5.32 0.00 43.14 3.01
214 217 3.206150 GCAAAACCAGACTCTGTTCTCA 58.794 45.455 5.32 0.00 0.00 3.27
215 218 3.249559 GCAAAACCAGACTCTGTTCTCAG 59.750 47.826 5.32 0.00 42.54 3.35
217 220 4.329462 AAACCAGACTCTGTTCTCAGTC 57.671 45.455 5.32 0.00 41.91 3.51
219 222 1.548269 CCAGACTCTGTTCTCAGTCCC 59.452 57.143 5.32 0.00 41.91 4.46
220 223 2.242926 CAGACTCTGTTCTCAGTCCCA 58.757 52.381 0.00 0.00 41.91 4.37
221 224 2.630098 CAGACTCTGTTCTCAGTCCCAA 59.370 50.000 0.00 0.00 41.91 4.12
224 227 4.349342 AGACTCTGTTCTCAGTCCCAAAAT 59.651 41.667 0.00 0.00 41.91 1.82
225 228 5.544176 AGACTCTGTTCTCAGTCCCAAAATA 59.456 40.000 0.00 0.00 41.91 1.40
227 230 6.234177 ACTCTGTTCTCAGTCCCAAAATAAG 58.766 40.000 0.00 0.00 41.91 1.73
228 231 6.183361 ACTCTGTTCTCAGTCCCAAAATAAGT 60.183 38.462 0.00 0.00 41.91 2.24
229 232 5.997746 TCTGTTCTCAGTCCCAAAATAAGTG 59.002 40.000 0.00 0.00 41.91 3.16
230 233 5.690865 TGTTCTCAGTCCCAAAATAAGTGT 58.309 37.500 0.00 0.00 0.00 3.55
232 235 4.566004 TCTCAGTCCCAAAATAAGTGTCG 58.434 43.478 0.00 0.00 0.00 4.35
233 236 4.039973 TCTCAGTCCCAAAATAAGTGTCGT 59.960 41.667 0.00 0.00 0.00 4.34
234 237 4.710324 TCAGTCCCAAAATAAGTGTCGTT 58.290 39.130 0.00 0.00 0.00 3.85
235 238 4.513692 TCAGTCCCAAAATAAGTGTCGTTG 59.486 41.667 0.00 0.00 0.00 4.10
241 273 4.274950 CCAAAATAAGTGTCGTTGACAGGT 59.725 41.667 0.00 0.00 43.57 4.00
259 291 1.594331 GTGTTCTCCTCGCCTTTTGT 58.406 50.000 0.00 0.00 0.00 2.83
276 308 5.402270 CCTTTTGTGTGCATAGTTAGTTTGC 59.598 40.000 0.00 0.00 36.91 3.68
310 342 7.875041 TCAGTCTCAAGTCTGAATTTTAGGAAG 59.125 37.037 4.77 0.00 37.30 3.46
311 343 7.659390 CAGTCTCAAGTCTGAATTTTAGGAAGT 59.341 37.037 0.00 0.00 33.96 3.01
387 419 6.903883 AATTCTCATTTTGCATGATGAAGC 57.096 33.333 12.04 0.00 32.33 3.86
388 420 4.023739 TCTCATTTTGCATGATGAAGCG 57.976 40.909 12.04 3.71 32.33 4.68
389 421 2.532235 TCATTTTGCATGATGAAGCGC 58.468 42.857 0.00 0.00 29.82 5.92
390 422 1.591158 CATTTTGCATGATGAAGCGCC 59.409 47.619 2.29 0.00 0.00 6.53
391 423 0.889994 TTTTGCATGATGAAGCGCCT 59.110 45.000 2.29 0.00 0.00 5.52
393 425 0.961857 TTGCATGATGAAGCGCCTGT 60.962 50.000 2.29 0.00 0.00 4.00
394 426 1.063649 GCATGATGAAGCGCCTGTG 59.936 57.895 2.29 0.00 0.00 3.66
395 427 1.063649 CATGATGAAGCGCCTGTGC 59.936 57.895 2.29 0.00 0.00 4.57
397 429 1.374343 ATGATGAAGCGCCTGTGCTG 61.374 55.000 2.29 0.00 46.60 4.41
398 430 3.392595 GATGAAGCGCCTGTGCTGC 62.393 63.158 2.29 4.72 46.60 5.25
407 461 2.345244 CTGTGCTGCCGAAGAGGT 59.655 61.111 0.00 0.00 43.70 3.85
472 526 9.126151 CTCACAGAAGGTAAGATCAAGATAGTA 57.874 37.037 0.00 0.00 0.00 1.82
473 527 8.904834 TCACAGAAGGTAAGATCAAGATAGTAC 58.095 37.037 0.00 0.00 0.00 2.73
474 528 8.908903 CACAGAAGGTAAGATCAAGATAGTACT 58.091 37.037 0.00 0.00 0.00 2.73
475 529 8.908903 ACAGAAGGTAAGATCAAGATAGTACTG 58.091 37.037 5.39 0.00 0.00 2.74
476 530 8.908903 CAGAAGGTAAGATCAAGATAGTACTGT 58.091 37.037 5.39 0.00 0.00 3.55
477 531 9.482175 AGAAGGTAAGATCAAGATAGTACTGTT 57.518 33.333 5.39 0.00 0.00 3.16
479 533 9.877178 AAGGTAAGATCAAGATAGTACTGTTTG 57.123 33.333 5.39 7.48 0.00 2.93
490 544 7.897864 AGATAGTACTGTTTGCTACTGAGTTT 58.102 34.615 5.39 0.00 0.00 2.66
496 550 4.920376 TGTTTGCTACTGAGTTTTCTTGC 58.080 39.130 0.00 0.00 0.00 4.01
499 553 1.464997 GCTACTGAGTTTTCTTGCGGG 59.535 52.381 0.00 0.00 0.00 6.13
504 558 0.889186 GAGTTTTCTTGCGGGCCTCA 60.889 55.000 0.84 0.00 0.00 3.86
505 559 0.251341 AGTTTTCTTGCGGGCCTCAT 60.251 50.000 0.84 0.00 0.00 2.90
506 560 0.603065 GTTTTCTTGCGGGCCTCATT 59.397 50.000 0.84 0.00 0.00 2.57
507 561 1.816224 GTTTTCTTGCGGGCCTCATTA 59.184 47.619 0.84 0.00 0.00 1.90
508 562 2.427095 GTTTTCTTGCGGGCCTCATTAT 59.573 45.455 0.84 0.00 0.00 1.28
509 563 3.569194 TTTCTTGCGGGCCTCATTATA 57.431 42.857 0.84 0.00 0.00 0.98
510 564 3.788227 TTCTTGCGGGCCTCATTATAT 57.212 42.857 0.84 0.00 0.00 0.86
511 565 3.788227 TCTTGCGGGCCTCATTATATT 57.212 42.857 0.84 0.00 0.00 1.28
512 566 3.674997 TCTTGCGGGCCTCATTATATTC 58.325 45.455 0.84 0.00 0.00 1.75
513 567 2.093306 TGCGGGCCTCATTATATTCG 57.907 50.000 0.84 0.00 0.00 3.34
514 568 1.346395 TGCGGGCCTCATTATATTCGT 59.654 47.619 0.84 0.00 0.00 3.85
515 569 2.000447 GCGGGCCTCATTATATTCGTC 59.000 52.381 0.84 0.00 0.00 4.20
516 570 2.259618 CGGGCCTCATTATATTCGTCG 58.740 52.381 0.84 0.00 0.00 5.12
517 571 2.094906 CGGGCCTCATTATATTCGTCGA 60.095 50.000 0.84 0.00 0.00 4.20
518 572 3.428999 CGGGCCTCATTATATTCGTCGAT 60.429 47.826 0.84 0.00 0.00 3.59
519 573 4.201980 CGGGCCTCATTATATTCGTCGATA 60.202 45.833 0.84 0.00 0.00 2.92
520 574 5.657474 GGGCCTCATTATATTCGTCGATAA 58.343 41.667 0.84 0.00 0.00 1.75
521 575 5.519206 GGGCCTCATTATATTCGTCGATAAC 59.481 44.000 0.84 0.00 0.00 1.89
522 576 6.097356 GGCCTCATTATATTCGTCGATAACA 58.903 40.000 0.00 0.00 0.00 2.41
523 577 6.757010 GGCCTCATTATATTCGTCGATAACAT 59.243 38.462 0.00 0.00 0.00 2.71
524 578 7.254117 GGCCTCATTATATTCGTCGATAACATG 60.254 40.741 0.00 0.00 0.00 3.21
525 579 7.613146 CCTCATTATATTCGTCGATAACATGC 58.387 38.462 0.00 0.00 0.00 4.06
526 580 7.254117 CCTCATTATATTCGTCGATAACATGCC 60.254 40.741 0.00 0.00 0.00 4.40
527 581 7.093992 TCATTATATTCGTCGATAACATGCCA 58.906 34.615 0.00 0.00 0.00 4.92
528 582 7.763985 TCATTATATTCGTCGATAACATGCCAT 59.236 33.333 0.00 0.00 0.00 4.40
529 583 5.784750 ATATTCGTCGATAACATGCCATG 57.215 39.130 2.40 2.40 0.00 3.66
548 602 4.384537 CCATGTTCAATCTTCCAGGCTAGA 60.385 45.833 0.00 0.00 0.00 2.43
628 682 7.122650 TGAGACATGTTTTCCCTTAATTCCATC 59.877 37.037 0.00 0.00 0.00 3.51
698 760 3.003793 GCCGATTTTCTCATTCTTAGCCC 59.996 47.826 0.00 0.00 0.00 5.19
808 870 3.971971 TCTACCAGATTAAAGTAGGCCCC 59.028 47.826 0.00 0.00 35.30 5.80
843 905 3.987745 ACTCCAGGACAGTAGACATCAT 58.012 45.455 0.00 0.00 0.00 2.45
846 908 3.701542 TCCAGGACAGTAGACATCATCAC 59.298 47.826 0.00 0.00 0.00 3.06
847 909 3.448660 CCAGGACAGTAGACATCATCACA 59.551 47.826 0.00 0.00 0.00 3.58
864 928 4.617253 TCACACACAAGCAGGTAGTTAT 57.383 40.909 0.00 0.00 0.00 1.89
897 961 4.363991 ACCAGAAGAAGCTGATGAAACT 57.636 40.909 0.00 0.00 38.14 2.66
978 1047 4.460263 AGATCAGAAGCGACATAGAGAGT 58.540 43.478 0.00 0.00 0.00 3.24
1114 1183 0.537188 CATCTACAACGAGGCCCTGT 59.463 55.000 0.00 0.20 0.00 4.00
1250 1319 3.717294 GGTGGTCCTGGTGCCGAT 61.717 66.667 0.00 0.00 0.00 4.18
1296 1365 2.254546 TCCAGAACATCGTTGTTGCT 57.745 45.000 16.24 10.13 46.01 3.91
1599 1680 0.179001 AACCCTTGTGTTCTTCGGGG 60.179 55.000 0.00 0.00 39.27 5.73
1623 1704 5.639506 GCAGAGCTTAGTTATTGTTGTCTCA 59.360 40.000 0.00 0.00 0.00 3.27
1666 1763 5.219739 TCCCTCCTTAGATTTGTCTGCTAT 58.780 41.667 0.00 0.00 0.00 2.97
1725 1822 1.252904 GCCCTGCTGCAAGGATTTGA 61.253 55.000 21.15 0.00 40.02 2.69
1769 1867 1.049855 TCCCATGCATCCCATTTGGC 61.050 55.000 0.00 0.00 29.71 4.52
1800 1898 1.293498 GCTGGGTCGAGCTTCAGAA 59.707 57.895 20.51 0.00 35.95 3.02
1811 1909 6.401581 GGTCGAGCTTCAGAAGATTAAAACAG 60.402 42.308 14.86 0.00 0.00 3.16
1812 1910 6.366332 GTCGAGCTTCAGAAGATTAAAACAGA 59.634 38.462 14.86 0.00 0.00 3.41
1815 1913 6.773638 AGCTTCAGAAGATTAAAACAGAGGA 58.226 36.000 14.86 0.00 0.00 3.71
1818 1916 7.805542 GCTTCAGAAGATTAAAACAGAGGAAAC 59.194 37.037 14.86 0.00 0.00 2.78
1819 1917 7.421530 TCAGAAGATTAAAACAGAGGAAACG 57.578 36.000 0.00 0.00 0.00 3.60
1821 1919 5.181433 AGAAGATTAAAACAGAGGAAACGGC 59.819 40.000 0.00 0.00 0.00 5.68
1825 1923 1.534729 AAACAGAGGAAACGGCCATC 58.465 50.000 2.24 0.00 0.00 3.51
1826 1924 0.400213 AACAGAGGAAACGGCCATCA 59.600 50.000 2.24 0.00 0.00 3.07
1827 1925 0.620556 ACAGAGGAAACGGCCATCAT 59.379 50.000 2.24 0.00 0.00 2.45
1828 1926 1.004745 ACAGAGGAAACGGCCATCATT 59.995 47.619 2.24 0.00 0.00 2.57
1829 1927 2.238646 ACAGAGGAAACGGCCATCATTA 59.761 45.455 2.24 0.00 0.00 1.90
1830 1928 3.278574 CAGAGGAAACGGCCATCATTAA 58.721 45.455 2.24 0.00 0.00 1.40
1831 1929 3.065371 CAGAGGAAACGGCCATCATTAAC 59.935 47.826 2.24 0.00 0.00 2.01
1833 1931 2.752903 AGGAAACGGCCATCATTAACAC 59.247 45.455 2.24 0.00 0.00 3.32
1834 1932 2.477189 GGAAACGGCCATCATTAACACG 60.477 50.000 2.24 0.00 0.00 4.49
1835 1933 2.102070 AACGGCCATCATTAACACGA 57.898 45.000 2.24 0.00 0.00 4.35
1837 1935 2.428491 ACGGCCATCATTAACACGAAA 58.572 42.857 2.24 0.00 0.00 3.46
1841 1939 3.057876 GGCCATCATTAACACGAAACACA 60.058 43.478 0.00 0.00 0.00 3.72
1842 1940 4.380444 GGCCATCATTAACACGAAACACAT 60.380 41.667 0.00 0.00 0.00 3.21
1843 1941 5.163703 GGCCATCATTAACACGAAACACATA 60.164 40.000 0.00 0.00 0.00 2.29
1846 1944 7.471721 CCATCATTAACACGAAACACATACAT 58.528 34.615 0.00 0.00 0.00 2.29
1849 1947 8.089115 TCATTAACACGAAACACATACATCAA 57.911 30.769 0.00 0.00 0.00 2.57
1850 1948 8.560374 TCATTAACACGAAACACATACATCAAA 58.440 29.630 0.00 0.00 0.00 2.69
1851 1949 8.839914 CATTAACACGAAACACATACATCAAAG 58.160 33.333 0.00 0.00 0.00 2.77
1852 1950 6.612247 AACACGAAACACATACATCAAAGA 57.388 33.333 0.00 0.00 0.00 2.52
1853 1951 6.228273 ACACGAAACACATACATCAAAGAG 57.772 37.500 0.00 0.00 0.00 2.85
1854 1952 5.989168 ACACGAAACACATACATCAAAGAGA 59.011 36.000 0.00 0.00 0.00 3.10
1855 1953 6.481976 ACACGAAACACATACATCAAAGAGAA 59.518 34.615 0.00 0.00 0.00 2.87
1856 1954 7.011950 ACACGAAACACATACATCAAAGAGAAA 59.988 33.333 0.00 0.00 0.00 2.52
1857 1955 8.017373 CACGAAACACATACATCAAAGAGAAAT 58.983 33.333 0.00 0.00 0.00 2.17
1859 1957 7.007725 CGAAACACATACATCAAAGAGAAATGC 59.992 37.037 0.00 0.00 0.00 3.56
1867 1989 9.842775 ATACATCAAAGAGAAATGCTAAGATGA 57.157 29.630 0.00 0.00 34.04 2.92
1872 1994 5.307544 AGAGAAATGCTAAGATGAGCCAT 57.692 39.130 0.00 0.00 42.11 4.40
1882 2004 5.163913 GCTAAGATGAGCCATTAATAGCACG 60.164 44.000 8.59 0.00 36.38 5.34
1886 2008 2.863740 TGAGCCATTAATAGCACGTTCG 59.136 45.455 8.59 0.00 0.00 3.95
1902 2024 3.005050 ACGTTCGTATGTGGAGTTTCAGA 59.995 43.478 0.00 0.00 0.00 3.27
1906 2028 5.907866 TCGTATGTGGAGTTTCAGACATA 57.092 39.130 0.00 0.00 31.56 2.29
1907 2029 5.891451 TCGTATGTGGAGTTTCAGACATAG 58.109 41.667 0.00 0.00 33.13 2.23
1908 2030 4.504461 CGTATGTGGAGTTTCAGACATAGC 59.496 45.833 0.00 0.00 33.13 2.97
1921 2043 5.470368 TCAGACATAGCACAACTGAACTAC 58.530 41.667 0.00 0.00 35.20 2.73
1931 2053 5.116180 CACAACTGAACTACCACTCTCAAA 58.884 41.667 0.00 0.00 0.00 2.69
1965 2087 6.166279 CAAGTCTATCTGCAGGTGAAGTTTA 58.834 40.000 15.13 0.00 0.00 2.01
1969 2091 4.623932 ATCTGCAGGTGAAGTTTACTCA 57.376 40.909 15.13 0.00 0.00 3.41
1979 2101 1.053424 AGTTTACTCACGCCCAAGGA 58.947 50.000 0.00 0.00 0.00 3.36
1993 2115 3.923017 CCAAGGATAATCGATTTGGGC 57.077 47.619 17.19 3.55 35.71 5.36
1994 2116 2.558359 CCAAGGATAATCGATTTGGGCC 59.442 50.000 17.19 12.18 35.71 5.80
1998 2120 2.550208 GGATAATCGATTTGGGCCGTCT 60.550 50.000 17.19 0.00 0.00 4.18
2007 2129 1.040339 TTGGGCCGTCTTTGCACTTT 61.040 50.000 0.00 0.00 31.89 2.66
2008 2130 1.007387 GGGCCGTCTTTGCACTTTG 60.007 57.895 0.00 0.00 0.00 2.77
2009 2131 1.733526 GGCCGTCTTTGCACTTTGT 59.266 52.632 0.00 0.00 0.00 2.83
2013 2135 2.602217 GCCGTCTTTGCACTTTGTGTAG 60.602 50.000 0.00 0.00 35.75 2.74
2027 2149 7.820872 GCACTTTGTGTAGGGTAAATAACTCTA 59.179 37.037 0.00 0.00 34.69 2.43
2037 2159 8.303780 AGGGTAAATAACTCTACCAAGTACTC 57.696 38.462 0.00 0.00 37.05 2.59
2038 2160 7.344093 AGGGTAAATAACTCTACCAAGTACTCC 59.656 40.741 0.00 0.00 37.05 3.85
2040 2162 6.847421 AAATAACTCTACCAAGTACTCCGT 57.153 37.500 0.00 0.00 0.00 4.69
2041 2163 6.448207 AATAACTCTACCAAGTACTCCGTC 57.552 41.667 0.00 0.00 0.00 4.79
2042 2164 2.720915 ACTCTACCAAGTACTCCGTCC 58.279 52.381 0.00 0.00 0.00 4.79
2043 2165 1.669779 CTCTACCAAGTACTCCGTCCG 59.330 57.143 0.00 0.00 0.00 4.79
2044 2166 1.003580 TCTACCAAGTACTCCGTCCGT 59.996 52.381 0.00 0.00 0.00 4.69
2045 2167 2.236146 TCTACCAAGTACTCCGTCCGTA 59.764 50.000 0.00 0.00 0.00 4.02
2048 2170 2.029918 ACCAAGTACTCCGTCCGTAAAC 60.030 50.000 0.00 0.00 0.00 2.01
2049 2171 2.229784 CCAAGTACTCCGTCCGTAAACT 59.770 50.000 0.00 0.00 0.00 2.66
2050 2172 3.440173 CCAAGTACTCCGTCCGTAAACTA 59.560 47.826 0.00 0.00 0.00 2.24
2054 2176 7.420800 CAAGTACTCCGTCCGTAAACTAATAT 58.579 38.462 0.00 0.00 0.00 1.28
2055 2177 8.559536 CAAGTACTCCGTCCGTAAACTAATATA 58.440 37.037 0.00 0.00 0.00 0.86
2056 2178 8.677148 AGTACTCCGTCCGTAAACTAATATAA 57.323 34.615 0.00 0.00 0.00 0.98
2057 2179 8.778358 AGTACTCCGTCCGTAAACTAATATAAG 58.222 37.037 0.00 0.00 0.00 1.73
2058 2180 6.974965 ACTCCGTCCGTAAACTAATATAAGG 58.025 40.000 0.00 0.00 0.00 2.69
2060 2182 4.925646 CCGTCCGTAAACTAATATAAGGGC 59.074 45.833 0.00 0.00 0.00 5.19
2063 2185 6.567701 CGTCCGTAAACTAATATAAGGGCGTA 60.568 42.308 4.08 0.00 41.65 4.42
2066 2188 7.014230 TCCGTAAACTAATATAAGGGCGTAAGT 59.986 37.037 0.00 0.00 41.68 2.24
2068 2190 9.334693 CGTAAACTAATATAAGGGCGTAAGTAG 57.665 37.037 0.00 0.00 41.68 2.57
2071 2193 8.469309 AACTAATATAAGGGCGTAAGTAGTGA 57.531 34.615 0.00 0.00 41.68 3.41
2072 2194 8.647256 ACTAATATAAGGGCGTAAGTAGTGAT 57.353 34.615 0.00 0.00 41.68 3.06
2075 2197 8.874744 AATATAAGGGCGTAAGTAGTGATCTA 57.125 34.615 0.00 0.00 41.68 1.98
2077 2199 5.927281 AAGGGCGTAAGTAGTGATCTAAA 57.073 39.130 0.00 0.00 41.68 1.85
2078 2200 5.259832 AGGGCGTAAGTAGTGATCTAAAC 57.740 43.478 0.00 0.00 41.68 2.01
2079 2201 4.040376 GGGCGTAAGTAGTGATCTAAACG 58.960 47.826 0.00 0.00 41.68 3.60
2082 2204 4.437171 GCGTAAGTAGTGATCTAAACGCTC 59.563 45.833 9.04 0.00 43.50 5.03
2083 2205 5.730010 GCGTAAGTAGTGATCTAAACGCTCT 60.730 44.000 9.04 0.00 43.50 4.09
2084 2206 6.256686 CGTAAGTAGTGATCTAAACGCTCTT 58.743 40.000 0.00 0.00 0.00 2.85
2085 2207 7.404985 CGTAAGTAGTGATCTAAACGCTCTTA 58.595 38.462 0.00 0.00 0.00 2.10
2086 2208 8.068977 CGTAAGTAGTGATCTAAACGCTCTTAT 58.931 37.037 0.00 0.00 0.00 1.73
2101 2223 9.530633 AAACGCTCTTATATTAACTTACAGAGG 57.469 33.333 0.00 0.00 0.00 3.69
2102 2224 7.659186 ACGCTCTTATATTAACTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2105 3932 8.862085 GCTCTTATATTAACTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
2117 3944 7.720515 ACTTACAGAGGGAGTACATACTGTATC 59.279 40.741 0.00 0.00 39.44 2.24
2143 3970 5.179452 GAGCATCTCTAGTCCTCTATCCT 57.821 47.826 0.00 0.00 0.00 3.24
2144 3971 5.570320 GAGCATCTCTAGTCCTCTATCCTT 58.430 45.833 0.00 0.00 0.00 3.36
2145 3972 5.964288 AGCATCTCTAGTCCTCTATCCTTT 58.036 41.667 0.00 0.00 0.00 3.11
2146 3973 7.097623 AGCATCTCTAGTCCTCTATCCTTTA 57.902 40.000 0.00 0.00 0.00 1.85
2147 3974 7.531317 AGCATCTCTAGTCCTCTATCCTTTAA 58.469 38.462 0.00 0.00 0.00 1.52
2148 3975 8.176780 AGCATCTCTAGTCCTCTATCCTTTAAT 58.823 37.037 0.00 0.00 0.00 1.40
2149 3976 8.466798 GCATCTCTAGTCCTCTATCCTTTAATC 58.533 40.741 0.00 0.00 0.00 1.75
2150 3977 8.966868 CATCTCTAGTCCTCTATCCTTTAATCC 58.033 40.741 0.00 0.00 0.00 3.01
2151 3978 8.295597 TCTCTAGTCCTCTATCCTTTAATCCT 57.704 38.462 0.00 0.00 0.00 3.24
2152 3979 8.387813 TCTCTAGTCCTCTATCCTTTAATCCTC 58.612 40.741 0.00 0.00 0.00 3.71
2153 3980 8.295597 TCTAGTCCTCTATCCTTTAATCCTCT 57.704 38.462 0.00 0.00 0.00 3.69
2154 3981 9.407957 TCTAGTCCTCTATCCTTTAATCCTCTA 57.592 37.037 0.00 0.00 0.00 2.43
2157 3984 9.150028 AGTCCTCTATCCTTTAATCCTCTAAAC 57.850 37.037 0.00 0.00 0.00 2.01
2158 3985 9.150028 GTCCTCTATCCTTTAATCCTCTAAACT 57.850 37.037 0.00 0.00 0.00 2.66
2159 3986 9.731001 TCCTCTATCCTTTAATCCTCTAAACTT 57.269 33.333 0.00 0.00 0.00 2.66
2190 4017 8.964420 TTAATCTCCTAAAACTTGAATTTGCG 57.036 30.769 0.00 0.00 0.00 4.85
2191 4018 5.371115 TCTCCTAAAACTTGAATTTGCGG 57.629 39.130 0.00 0.00 0.00 5.69
2192 4019 4.217550 TCTCCTAAAACTTGAATTTGCGGG 59.782 41.667 0.00 0.00 0.00 6.13
2222 4049 4.404715 GCCTTTTCCCTAAACTTAATCCCC 59.595 45.833 0.00 0.00 0.00 4.81
2228 4055 5.823312 TCCCTAAACTTAATCCCCTCAAAC 58.177 41.667 0.00 0.00 0.00 2.93
2229 4056 5.313772 TCCCTAAACTTAATCCCCTCAAACA 59.686 40.000 0.00 0.00 0.00 2.83
2231 4058 6.495526 CCCTAAACTTAATCCCCTCAAACAAA 59.504 38.462 0.00 0.00 0.00 2.83
2235 4062 4.760204 ACTTAATCCCCTCAAACAAACTCG 59.240 41.667 0.00 0.00 0.00 4.18
2240 4067 1.235724 CCTCAAACAAACTCGACCCC 58.764 55.000 0.00 0.00 0.00 4.95
2253 4080 0.035439 CGACCCCACATGTAAGCCTT 60.035 55.000 0.00 0.00 0.00 4.35
2254 4081 1.613255 CGACCCCACATGTAAGCCTTT 60.613 52.381 0.00 0.00 0.00 3.11
2257 4084 2.110011 ACCCCACATGTAAGCCTTTCTT 59.890 45.455 0.00 0.00 38.79 2.52
2258 4085 2.755103 CCCCACATGTAAGCCTTTCTTC 59.245 50.000 0.00 0.00 36.25 2.87
2259 4086 3.420893 CCCACATGTAAGCCTTTCTTCA 58.579 45.455 0.00 0.00 36.25 3.02
2282 4109 6.443206 TCATCATCTTCTTCCTTCTTCCTCTT 59.557 38.462 0.00 0.00 0.00 2.85
2286 4113 6.107901 TCTTCTTCCTTCTTCCTCTTCTTG 57.892 41.667 0.00 0.00 0.00 3.02
2290 4117 4.713792 TCCTTCTTCCTCTTCTTGCTTT 57.286 40.909 0.00 0.00 0.00 3.51
2293 4120 5.008980 CCTTCTTCCTCTTCTTGCTTTCAT 58.991 41.667 0.00 0.00 0.00 2.57
2295 4122 4.978099 TCTTCCTCTTCTTGCTTTCATGT 58.022 39.130 0.00 0.00 0.00 3.21
2297 4124 3.415212 TCCTCTTCTTGCTTTCATGTGG 58.585 45.455 0.00 0.00 0.00 4.17
2301 4128 1.250328 TCTTGCTTTCATGTGGCCAG 58.750 50.000 5.11 0.00 0.00 4.85
2306 4133 0.675083 CTTTCATGTGGCCAGCAACA 59.325 50.000 5.11 1.58 33.96 3.33
2313 4140 0.312102 GTGGCCAGCAACAACTTCTC 59.688 55.000 5.11 0.00 0.00 2.87
2323 4150 3.589988 CAACAACTTCTCGCCAGTAGAT 58.410 45.455 0.00 0.00 0.00 1.98
2325 4152 2.826128 ACAACTTCTCGCCAGTAGATGA 59.174 45.455 2.70 0.00 0.00 2.92
2334 4161 2.036346 CGCCAGTAGATGATGTCCATGA 59.964 50.000 0.00 0.00 35.17 3.07
2403 4230 1.601162 GCTCACCGAACACGAAGTACA 60.601 52.381 0.00 0.00 41.61 2.90
2404 4231 2.049228 CTCACCGAACACGAAGTACAC 58.951 52.381 0.00 0.00 41.61 2.90
2412 4239 0.992072 CACGAAGTACACATGCGAGG 59.008 55.000 0.00 0.00 41.61 4.63
2416 4243 1.661112 GAAGTACACATGCGAGGAAGC 59.339 52.381 0.00 0.00 37.71 3.86
2424 4251 2.057830 TGCGAGGAAGCAGAGGAAA 58.942 52.632 0.00 0.00 42.92 3.13
2441 4268 0.112412 AAATTTGTCCTCCACGGGCT 59.888 50.000 0.00 0.00 38.58 5.19
2460 4287 2.419990 GCTTTGGTTTGGGCAGTTCTTT 60.420 45.455 0.00 0.00 0.00 2.52
2463 4290 1.754226 TGGTTTGGGCAGTTCTTTGTC 59.246 47.619 0.00 0.00 0.00 3.18
2470 4297 2.229784 GGGCAGTTCTTTGTCTGAATGG 59.770 50.000 0.00 0.00 34.02 3.16
2471 4298 2.229784 GGCAGTTCTTTGTCTGAATGGG 59.770 50.000 0.00 0.00 34.02 4.00
2484 4311 5.129485 TGTCTGAATGGGTTCTTATCCTCTC 59.871 44.000 0.00 0.00 35.33 3.20
2501 4331 0.827368 CTCCCTTCTCCTAGTGGCAC 59.173 60.000 10.29 10.29 0.00 5.01
2505 4335 0.888619 CTTCTCCTAGTGGCACGACA 59.111 55.000 12.71 0.54 0.00 4.35
2542 4372 5.011451 GGAACGATTTATCAGAATCTGCG 57.989 43.478 5.18 4.84 34.58 5.18
2569 4399 3.050275 GGCGGCCAGTGTGTTCTC 61.050 66.667 15.62 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 5.279406 CCAATTTCAATCCCAGTTGCTAACA 60.279 40.000 0.00 0.00 0.00 2.41
41 42 4.890158 AGATCCCAAACCAACCAATTTC 57.110 40.909 0.00 0.00 0.00 2.17
79 80 1.918467 CTGCATTCCCTCCAGGCTCA 61.918 60.000 0.00 0.00 34.51 4.26
83 84 2.515523 CGCTGCATTCCCTCCAGG 60.516 66.667 0.00 0.00 0.00 4.45
100 101 0.536006 AGCACTTGGTCACCTTGCTC 60.536 55.000 11.29 0.00 39.32 4.26
103 104 1.517242 GAGAGCACTTGGTCACCTTG 58.483 55.000 10.86 0.00 44.42 3.61
104 105 0.398318 GGAGAGCACTTGGTCACCTT 59.602 55.000 15.22 0.00 45.57 3.50
125 126 1.462670 CGTCTCCAAAGAAGCTGCTTC 59.537 52.381 30.02 30.02 40.45 3.86
198 201 2.243810 GGACTGAGAACAGAGTCTGGT 58.756 52.381 23.79 18.55 46.03 4.00
211 214 4.315803 ACGACACTTATTTTGGGACTGAG 58.684 43.478 0.00 0.00 0.00 3.35
212 215 4.345859 ACGACACTTATTTTGGGACTGA 57.654 40.909 0.00 0.00 0.00 3.41
214 217 4.514066 GTCAACGACACTTATTTTGGGACT 59.486 41.667 0.00 0.00 32.09 3.85
215 218 4.273969 TGTCAACGACACTTATTTTGGGAC 59.726 41.667 0.00 0.00 37.67 4.46
217 220 4.320202 CCTGTCAACGACACTTATTTTGGG 60.320 45.833 0.00 0.00 37.67 4.12
219 222 5.204833 CACCTGTCAACGACACTTATTTTG 58.795 41.667 0.00 0.00 37.67 2.44
220 223 4.879545 ACACCTGTCAACGACACTTATTTT 59.120 37.500 0.00 0.00 37.67 1.82
221 224 4.448210 ACACCTGTCAACGACACTTATTT 58.552 39.130 0.00 0.00 37.67 1.40
224 227 3.131577 AGAACACCTGTCAACGACACTTA 59.868 43.478 0.00 0.00 37.67 2.24
225 228 2.093658 AGAACACCTGTCAACGACACTT 60.094 45.455 0.00 0.00 37.67 3.16
227 230 1.859080 GAGAACACCTGTCAACGACAC 59.141 52.381 0.00 0.00 37.67 3.67
228 231 1.202486 GGAGAACACCTGTCAACGACA 60.202 52.381 0.00 0.00 40.50 4.35
229 232 1.068741 AGGAGAACACCTGTCAACGAC 59.931 52.381 0.00 0.00 39.01 4.34
230 233 1.340248 GAGGAGAACACCTGTCAACGA 59.660 52.381 0.00 0.00 40.73 3.85
232 235 1.784525 CGAGGAGAACACCTGTCAAC 58.215 55.000 0.00 0.00 40.73 3.18
233 236 0.033504 GCGAGGAGAACACCTGTCAA 59.966 55.000 0.00 0.00 40.73 3.18
234 237 1.666011 GCGAGGAGAACACCTGTCA 59.334 57.895 0.00 0.00 40.73 3.58
235 238 1.079750 GGCGAGGAGAACACCTGTC 60.080 63.158 0.00 0.00 40.73 3.51
241 273 1.134220 ACACAAAAGGCGAGGAGAACA 60.134 47.619 0.00 0.00 0.00 3.18
259 291 4.893608 TCTGAGCAAACTAACTATGCACA 58.106 39.130 0.00 0.00 42.45 4.57
310 342 6.318900 CCACTCCATCTTACAGGGAAATTAAC 59.681 42.308 0.00 0.00 0.00 2.01
311 343 6.423182 CCACTCCATCTTACAGGGAAATTAA 58.577 40.000 0.00 0.00 0.00 1.40
388 420 3.123620 CTCTTCGGCAGCACAGGC 61.124 66.667 0.00 0.00 41.61 4.85
389 421 2.435586 CCTCTTCGGCAGCACAGG 60.436 66.667 0.00 0.00 0.00 4.00
390 422 1.739562 GACCTCTTCGGCAGCACAG 60.740 63.158 0.00 0.00 35.61 3.66
391 423 2.343758 GACCTCTTCGGCAGCACA 59.656 61.111 0.00 0.00 35.61 4.57
415 469 3.901797 CTTTCGCCCAAGCCGAGGT 62.902 63.158 0.00 0.00 34.57 3.85
427 481 3.494626 TGAGTGAATCAGTCAACTTTCGC 59.505 43.478 17.57 0.00 40.33 4.70
472 526 5.449177 GCAAGAAAACTCAGTAGCAAACAGT 60.449 40.000 0.00 0.00 0.00 3.55
473 527 4.972440 GCAAGAAAACTCAGTAGCAAACAG 59.028 41.667 0.00 0.00 0.00 3.16
474 528 4.495679 CGCAAGAAAACTCAGTAGCAAACA 60.496 41.667 0.00 0.00 43.02 2.83
475 529 3.968724 CGCAAGAAAACTCAGTAGCAAAC 59.031 43.478 0.00 0.00 43.02 2.93
476 530 3.003275 CCGCAAGAAAACTCAGTAGCAAA 59.997 43.478 0.00 0.00 43.02 3.68
477 531 2.548057 CCGCAAGAAAACTCAGTAGCAA 59.452 45.455 0.00 0.00 43.02 3.91
478 532 2.143122 CCGCAAGAAAACTCAGTAGCA 58.857 47.619 0.00 0.00 43.02 3.49
479 533 1.464997 CCCGCAAGAAAACTCAGTAGC 59.535 52.381 0.00 0.00 43.02 3.58
490 544 3.788227 ATATAATGAGGCCCGCAAGAA 57.212 42.857 0.00 0.00 43.02 2.52
496 550 2.094906 TCGACGAATATAATGAGGCCCG 60.095 50.000 0.00 0.00 0.00 6.13
499 553 7.613146 CATGTTATCGACGAATATAATGAGGC 58.387 38.462 0.00 0.00 0.00 4.70
504 558 7.549134 ACATGGCATGTTATCGACGAATATAAT 59.451 33.333 26.78 0.00 41.63 1.28
505 559 6.871492 ACATGGCATGTTATCGACGAATATAA 59.129 34.615 26.78 0.00 41.63 0.98
506 560 6.394809 ACATGGCATGTTATCGACGAATATA 58.605 36.000 26.78 0.00 41.63 0.86
507 561 5.237815 ACATGGCATGTTATCGACGAATAT 58.762 37.500 26.78 0.00 41.63 1.28
508 562 4.627058 ACATGGCATGTTATCGACGAATA 58.373 39.130 26.78 0.00 41.63 1.75
509 563 3.466836 ACATGGCATGTTATCGACGAAT 58.533 40.909 26.78 0.00 41.63 3.34
510 564 2.899976 ACATGGCATGTTATCGACGAA 58.100 42.857 26.78 0.00 41.63 3.85
511 565 2.595124 ACATGGCATGTTATCGACGA 57.405 45.000 26.78 0.00 41.63 4.20
516 570 7.946187 CTGGAAGATTGAACATGGCATGTTATC 60.946 40.741 37.77 33.83 45.74 1.75
517 571 6.183360 CTGGAAGATTGAACATGGCATGTTAT 60.183 38.462 37.77 29.71 45.74 1.89
518 572 5.125900 CTGGAAGATTGAACATGGCATGTTA 59.874 40.000 37.77 26.88 45.74 2.41
520 574 3.446161 CTGGAAGATTGAACATGGCATGT 59.554 43.478 26.78 26.78 40.80 3.21
521 575 3.181479 CCTGGAAGATTGAACATGGCATG 60.181 47.826 25.31 25.31 34.07 4.06
522 576 3.028850 CCTGGAAGATTGAACATGGCAT 58.971 45.455 0.00 0.00 34.07 4.40
523 577 2.449464 CCTGGAAGATTGAACATGGCA 58.551 47.619 0.00 0.00 34.07 4.92
524 578 1.135721 GCCTGGAAGATTGAACATGGC 59.864 52.381 0.00 0.00 34.07 4.40
525 579 2.731572 AGCCTGGAAGATTGAACATGG 58.268 47.619 0.00 0.00 34.07 3.66
526 580 4.774124 TCTAGCCTGGAAGATTGAACATG 58.226 43.478 0.00 0.00 34.07 3.21
527 581 5.643421 ATCTAGCCTGGAAGATTGAACAT 57.357 39.130 0.00 0.00 34.07 2.71
528 582 5.441718 AATCTAGCCTGGAAGATTGAACA 57.558 39.130 18.48 0.00 40.17 3.18
548 602 6.003950 GCAAGTACCCATATGTATCCACAAT 58.996 40.000 1.24 0.00 38.42 2.71
628 682 3.318839 TGTGGAAAAGTTGATTCCTGCTG 59.681 43.478 7.65 0.00 45.40 4.41
640 694 4.644685 AGCAAACTACACATGTGGAAAAGT 59.355 37.500 28.64 21.09 34.19 2.66
698 760 5.463499 TTTACGACACCATTCAATCATCG 57.537 39.130 0.00 0.00 0.00 3.84
766 828 7.890127 TGGTAGATGAACAAATCCAAGAGAAAT 59.110 33.333 0.00 0.00 0.00 2.17
773 835 9.527157 TTTAATCTGGTAGATGAACAAATCCAA 57.473 29.630 0.00 0.00 34.65 3.53
774 836 9.177608 CTTTAATCTGGTAGATGAACAAATCCA 57.822 33.333 0.00 0.00 34.65 3.41
808 870 1.967066 CTGGAGTATAGTGGAGGCAGG 59.033 57.143 0.00 0.00 0.00 4.85
843 905 4.617253 ATAACTACCTGCTTGTGTGTGA 57.383 40.909 0.00 0.00 0.00 3.58
846 908 8.718102 ACTAATTATAACTACCTGCTTGTGTG 57.282 34.615 0.00 0.00 0.00 3.82
847 909 9.162764 CAACTAATTATAACTACCTGCTTGTGT 57.837 33.333 0.00 0.00 0.00 3.72
864 928 6.003950 AGCTTCTTCTGGTTGCAACTAATTA 58.996 36.000 27.64 8.67 0.00 1.40
978 1047 1.673033 GCAGCCTCTTCGTTCAGCTTA 60.673 52.381 0.00 0.00 0.00 3.09
1114 1183 1.290955 CCCGCTCGTAACACTCCAA 59.709 57.895 0.00 0.00 0.00 3.53
1250 1319 2.832778 ATGACCAGCACCAGCACCA 61.833 57.895 0.00 0.00 45.49 4.17
1599 1680 5.639506 TGAGACAACAATAACTAAGCTCTGC 59.360 40.000 0.00 0.00 0.00 4.26
1623 1704 1.174712 GCCATGAGCGGTAATGCCAT 61.175 55.000 6.42 0.00 36.97 4.40
1666 1763 6.292328 CGCGTCTGCTAAAATTCTTATGATGA 60.292 38.462 0.00 0.00 39.65 2.92
1708 1805 2.298163 ACTTTCAAATCCTTGCAGCAGG 59.702 45.455 0.00 0.00 34.86 4.85
1725 1822 6.040054 ACGCTGTTAAAGGTCCATTTTACTTT 59.960 34.615 0.00 0.00 37.05 2.66
1784 1882 1.561643 ATCTTCTGAAGCTCGACCCA 58.438 50.000 12.54 0.00 0.00 4.51
1800 1898 3.756963 GGCCGTTTCCTCTGTTTTAATCT 59.243 43.478 0.00 0.00 0.00 2.40
1811 1909 3.013921 TGTTAATGATGGCCGTTTCCTC 58.986 45.455 0.00 0.00 0.00 3.71
1812 1910 2.752903 GTGTTAATGATGGCCGTTTCCT 59.247 45.455 0.00 0.00 0.00 3.36
1815 1913 2.428491 TCGTGTTAATGATGGCCGTTT 58.572 42.857 0.00 0.00 0.00 3.60
1818 1916 2.160615 TGTTTCGTGTTAATGATGGCCG 59.839 45.455 0.00 0.00 0.00 6.13
1819 1917 3.057876 TGTGTTTCGTGTTAATGATGGCC 60.058 43.478 0.00 0.00 0.00 5.36
1821 1919 6.836953 TGTATGTGTTTCGTGTTAATGATGG 58.163 36.000 0.00 0.00 0.00 3.51
1825 1923 8.720909 TTTGATGTATGTGTTTCGTGTTAATG 57.279 30.769 0.00 0.00 0.00 1.90
1826 1924 8.779303 TCTTTGATGTATGTGTTTCGTGTTAAT 58.221 29.630 0.00 0.00 0.00 1.40
1827 1925 8.144155 TCTTTGATGTATGTGTTTCGTGTTAA 57.856 30.769 0.00 0.00 0.00 2.01
1828 1926 7.654116 TCTCTTTGATGTATGTGTTTCGTGTTA 59.346 33.333 0.00 0.00 0.00 2.41
1829 1927 6.481976 TCTCTTTGATGTATGTGTTTCGTGTT 59.518 34.615 0.00 0.00 0.00 3.32
1830 1928 5.989168 TCTCTTTGATGTATGTGTTTCGTGT 59.011 36.000 0.00 0.00 0.00 4.49
1831 1929 6.466308 TCTCTTTGATGTATGTGTTTCGTG 57.534 37.500 0.00 0.00 0.00 4.35
1833 1931 7.007725 GCATTTCTCTTTGATGTATGTGTTTCG 59.992 37.037 0.00 0.00 0.00 3.46
1834 1932 8.025445 AGCATTTCTCTTTGATGTATGTGTTTC 58.975 33.333 0.00 0.00 0.00 2.78
1835 1933 7.889469 AGCATTTCTCTTTGATGTATGTGTTT 58.111 30.769 0.00 0.00 0.00 2.83
1837 1935 8.565896 TTAGCATTTCTCTTTGATGTATGTGT 57.434 30.769 0.00 0.00 0.00 3.72
1841 1939 9.842775 TCATCTTAGCATTTCTCTTTGATGTAT 57.157 29.630 0.00 0.00 32.99 2.29
1842 1940 9.322773 CTCATCTTAGCATTTCTCTTTGATGTA 57.677 33.333 0.00 0.00 32.99 2.29
1843 1941 7.201714 GCTCATCTTAGCATTTCTCTTTGATGT 60.202 37.037 0.00 0.00 42.30 3.06
1846 1944 5.587844 GGCTCATCTTAGCATTTCTCTTTGA 59.412 40.000 0.00 0.00 44.64 2.69
1849 1947 5.108187 TGGCTCATCTTAGCATTTCTCTT 57.892 39.130 0.00 0.00 44.64 2.85
1850 1948 4.767578 TGGCTCATCTTAGCATTTCTCT 57.232 40.909 0.00 0.00 44.64 3.10
1851 1949 7.502120 TTAATGGCTCATCTTAGCATTTCTC 57.498 36.000 0.00 0.00 44.64 2.87
1852 1950 9.228949 CTATTAATGGCTCATCTTAGCATTTCT 57.771 33.333 0.00 0.00 44.64 2.52
1853 1951 7.967303 GCTATTAATGGCTCATCTTAGCATTTC 59.033 37.037 15.90 0.00 44.64 2.17
1854 1952 7.449395 TGCTATTAATGGCTCATCTTAGCATTT 59.551 33.333 22.40 0.00 44.64 2.32
1855 1953 6.944290 TGCTATTAATGGCTCATCTTAGCATT 59.056 34.615 22.40 0.00 44.64 3.56
1856 1954 6.373774 GTGCTATTAATGGCTCATCTTAGCAT 59.626 38.462 22.40 0.00 44.64 3.79
1857 1955 5.702670 GTGCTATTAATGGCTCATCTTAGCA 59.297 40.000 22.40 10.94 44.64 3.49
1859 1957 5.928839 ACGTGCTATTAATGGCTCATCTTAG 59.071 40.000 22.40 9.23 35.09 2.18
1867 1989 2.901249 ACGAACGTGCTATTAATGGCT 58.099 42.857 22.40 4.31 35.09 4.75
1872 1994 4.996344 TCCACATACGAACGTGCTATTAA 58.004 39.130 10.14 0.00 0.00 1.40
1882 2004 4.304110 TGTCTGAAACTCCACATACGAAC 58.696 43.478 0.00 0.00 0.00 3.95
1886 2008 5.292101 GTGCTATGTCTGAAACTCCACATAC 59.708 44.000 0.00 0.00 31.83 2.39
1902 2024 4.040461 AGTGGTAGTTCAGTTGTGCTATGT 59.960 41.667 0.00 0.00 0.00 2.29
1906 2028 2.700897 AGAGTGGTAGTTCAGTTGTGCT 59.299 45.455 0.00 0.00 0.00 4.40
1907 2029 3.060602 GAGAGTGGTAGTTCAGTTGTGC 58.939 50.000 0.00 0.00 0.00 4.57
1908 2030 4.322080 TGAGAGTGGTAGTTCAGTTGTG 57.678 45.455 0.00 0.00 0.00 3.33
1921 2043 2.749076 TGCCGAATCATTTTGAGAGTGG 59.251 45.455 0.00 0.00 0.00 4.00
1931 2053 3.812053 GCAGATAGACTTGCCGAATCATT 59.188 43.478 0.00 0.00 0.00 2.57
1965 2087 1.202533 CGATTATCCTTGGGCGTGAGT 60.203 52.381 0.00 0.00 0.00 3.41
1969 2091 2.878406 CAAATCGATTATCCTTGGGCGT 59.122 45.455 11.83 0.00 0.00 5.68
1979 2101 2.930826 AGACGGCCCAAATCGATTAT 57.069 45.000 11.83 0.00 0.00 1.28
1993 2115 2.032030 CCTACACAAAGTGCAAAGACGG 60.032 50.000 0.00 0.00 36.98 4.79
1994 2116 2.032030 CCCTACACAAAGTGCAAAGACG 60.032 50.000 0.00 0.00 36.98 4.18
1998 2120 7.285858 AGTTATTTACCCTACACAAAGTGCAAA 59.714 33.333 0.00 0.00 36.98 3.68
2007 2129 7.455638 ACTTGGTAGAGTTATTTACCCTACACA 59.544 37.037 0.00 0.00 39.21 3.72
2008 2130 7.845037 ACTTGGTAGAGTTATTTACCCTACAC 58.155 38.462 0.00 0.00 39.21 2.90
2009 2131 8.971073 GTACTTGGTAGAGTTATTTACCCTACA 58.029 37.037 0.00 0.00 39.21 2.74
2013 2135 7.495901 GGAGTACTTGGTAGAGTTATTTACCC 58.504 42.308 0.00 0.00 38.84 3.69
2035 2157 6.385033 CCCTTATATTAGTTTACGGACGGAG 58.615 44.000 0.00 0.00 0.00 4.63
2036 2158 5.278957 GCCCTTATATTAGTTTACGGACGGA 60.279 44.000 0.00 0.00 0.00 4.69
2037 2159 4.925646 GCCCTTATATTAGTTTACGGACGG 59.074 45.833 0.00 0.00 0.00 4.79
2038 2160 4.618489 CGCCCTTATATTAGTTTACGGACG 59.382 45.833 0.00 0.00 0.00 4.79
2040 2162 5.789643 ACGCCCTTATATTAGTTTACGGA 57.210 39.130 0.00 0.00 0.00 4.69
2041 2163 7.147976 ACTTACGCCCTTATATTAGTTTACGG 58.852 38.462 0.00 0.00 0.00 4.02
2042 2164 9.334693 CTACTTACGCCCTTATATTAGTTTACG 57.665 37.037 0.00 0.00 0.00 3.18
2045 2167 8.917088 TCACTACTTACGCCCTTATATTAGTTT 58.083 33.333 0.00 0.00 0.00 2.66
2048 2170 8.958506 AGATCACTACTTACGCCCTTATATTAG 58.041 37.037 0.00 0.00 0.00 1.73
2049 2171 8.874744 AGATCACTACTTACGCCCTTATATTA 57.125 34.615 0.00 0.00 0.00 0.98
2050 2172 7.778185 AGATCACTACTTACGCCCTTATATT 57.222 36.000 0.00 0.00 0.00 1.28
2054 2176 6.458751 CGTTTAGATCACTACTTACGCCCTTA 60.459 42.308 0.00 0.00 0.00 2.69
2055 2177 5.658468 GTTTAGATCACTACTTACGCCCTT 58.342 41.667 0.00 0.00 0.00 3.95
2056 2178 4.201990 CGTTTAGATCACTACTTACGCCCT 60.202 45.833 0.00 0.00 0.00 5.19
2057 2179 4.040376 CGTTTAGATCACTACTTACGCCC 58.960 47.826 0.00 0.00 0.00 6.13
2058 2180 3.485013 GCGTTTAGATCACTACTTACGCC 59.515 47.826 0.00 0.00 42.03 5.68
2060 2182 5.808403 AGAGCGTTTAGATCACTACTTACG 58.192 41.667 0.00 0.00 37.82 3.18
2075 2197 9.530633 CCTCTGTAAGTTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 33.76 3.60
2077 2199 7.504911 TCCCTCTGTAAGTTAATATAAGAGCGT 59.495 37.037 0.00 0.00 33.76 5.07
2078 2200 7.883217 TCCCTCTGTAAGTTAATATAAGAGCG 58.117 38.462 0.00 0.00 33.76 5.03
2079 2201 8.862085 ACTCCCTCTGTAAGTTAATATAAGAGC 58.138 37.037 0.00 0.00 33.76 4.09
2087 2209 8.915036 CAGTATGTACTCCCTCTGTAAGTTAAT 58.085 37.037 0.00 0.00 33.46 1.40
2088 2210 8.289939 CAGTATGTACTCCCTCTGTAAGTTAA 57.710 38.462 0.00 0.00 33.46 2.01
2089 2211 7.876936 CAGTATGTACTCCCTCTGTAAGTTA 57.123 40.000 0.00 0.00 33.46 2.24
2111 3938 7.168219 AGGACTAGAGATGCTCTTAGATACAG 58.832 42.308 1.88 0.00 41.50 2.74
2117 3944 6.823689 GGATAGAGGACTAGAGATGCTCTTAG 59.176 46.154 7.95 1.86 41.63 2.18
2166 3993 7.362574 CCCGCAAATTCAAGTTTTAGGAGATTA 60.363 37.037 0.00 0.00 0.00 1.75
2170 3997 4.485163 CCCGCAAATTCAAGTTTTAGGAG 58.515 43.478 0.00 0.00 0.00 3.69
2172 3999 2.993220 GCCCGCAAATTCAAGTTTTAGG 59.007 45.455 0.00 0.00 0.00 2.69
2179 4006 1.133025 CTAGGTGCCCGCAAATTCAAG 59.867 52.381 0.00 0.00 0.00 3.02
2192 4019 2.753452 GTTTAGGGAAAAGGCTAGGTGC 59.247 50.000 0.00 0.00 41.94 5.01
2199 4026 4.404715 GGGGATTAAGTTTAGGGAAAAGGC 59.595 45.833 0.00 0.00 0.00 4.35
2200 4027 5.838955 AGGGGATTAAGTTTAGGGAAAAGG 58.161 41.667 0.00 0.00 0.00 3.11
2222 4049 1.602377 GTGGGGTCGAGTTTGTTTGAG 59.398 52.381 0.00 0.00 0.00 3.02
2228 4055 2.465860 TACATGTGGGGTCGAGTTTG 57.534 50.000 9.11 0.00 0.00 2.93
2229 4056 2.874457 GCTTACATGTGGGGTCGAGTTT 60.874 50.000 9.11 0.00 0.00 2.66
2231 4058 0.249398 GCTTACATGTGGGGTCGAGT 59.751 55.000 9.11 0.00 0.00 4.18
2235 4062 2.092323 GAAAGGCTTACATGTGGGGTC 58.908 52.381 9.11 0.00 0.00 4.46
2240 4067 5.885230 TGATGAAGAAAGGCTTACATGTG 57.115 39.130 9.11 0.00 36.83 3.21
2253 4080 7.037730 AGGAAGAAGGAAGAAGATGATGAAGAA 60.038 37.037 0.00 0.00 0.00 2.52
2254 4081 6.443206 AGGAAGAAGGAAGAAGATGATGAAGA 59.557 38.462 0.00 0.00 0.00 2.87
2257 4084 5.963253 AGAGGAAGAAGGAAGAAGATGATGA 59.037 40.000 0.00 0.00 0.00 2.92
2258 4085 6.237887 AGAGGAAGAAGGAAGAAGATGATG 57.762 41.667 0.00 0.00 0.00 3.07
2259 4086 6.673537 AGAAGAGGAAGAAGGAAGAAGATGAT 59.326 38.462 0.00 0.00 0.00 2.45
2282 4109 1.250328 CTGGCCACATGAAAGCAAGA 58.750 50.000 0.00 0.00 28.21 3.02
2286 4113 0.668401 GTTGCTGGCCACATGAAAGC 60.668 55.000 0.00 1.74 0.00 3.51
2290 4117 0.467844 AGTTGTTGCTGGCCACATGA 60.468 50.000 0.00 0.00 0.00 3.07
2293 4120 0.395586 AGAAGTTGTTGCTGGCCACA 60.396 50.000 0.00 1.92 0.00 4.17
2295 4122 1.165907 CGAGAAGTTGTTGCTGGCCA 61.166 55.000 4.71 4.71 0.00 5.36
2297 4124 1.081840 GCGAGAAGTTGTTGCTGGC 60.082 57.895 4.99 0.00 0.00 4.85
2301 4128 1.461127 CTACTGGCGAGAAGTTGTTGC 59.539 52.381 1.44 3.59 0.00 4.17
2306 4133 3.449018 ACATCATCTACTGGCGAGAAGTT 59.551 43.478 1.44 0.00 0.00 2.66
2313 4140 2.036346 TCATGGACATCATCTACTGGCG 59.964 50.000 0.00 0.00 32.92 5.69
2323 4150 3.121738 CATGCTAGCTCATGGACATCA 57.878 47.619 17.23 0.00 39.98 3.07
2334 4161 3.496160 CCCAGGCCCATGCTAGCT 61.496 66.667 17.23 0.00 37.74 3.32
2376 4203 1.534175 CGTGTTCGGTGAGCCTCTATC 60.534 57.143 0.00 0.00 0.00 2.08
2380 4207 1.006571 TTCGTGTTCGGTGAGCCTC 60.007 57.895 0.00 0.00 37.69 4.70
2403 4230 1.220206 CCTCTGCTTCCTCGCATGT 59.780 57.895 0.00 0.00 39.52 3.21
2404 4231 0.107993 TTCCTCTGCTTCCTCGCATG 60.108 55.000 0.00 0.00 39.52 4.06
2424 4251 0.112412 AAAGCCCGTGGAGGACAAAT 59.888 50.000 0.00 0.00 45.00 2.32
2436 4263 3.225069 CTGCCCAAACCAAAGCCCG 62.225 63.158 0.00 0.00 0.00 6.13
2441 4268 2.569404 ACAAAGAACTGCCCAAACCAAA 59.431 40.909 0.00 0.00 0.00 3.28
2460 4287 5.032846 AGAGGATAAGAACCCATTCAGACA 58.967 41.667 0.00 0.00 37.29 3.41
2463 4290 4.202409 GGGAGAGGATAAGAACCCATTCAG 60.202 50.000 0.00 0.00 37.29 3.02
2470 4297 3.644265 GGAGAAGGGAGAGGATAAGAACC 59.356 52.174 0.00 0.00 0.00 3.62
2471 4298 4.552674 AGGAGAAGGGAGAGGATAAGAAC 58.447 47.826 0.00 0.00 0.00 3.01
2484 4311 0.970937 TCGTGCCACTAGGAGAAGGG 60.971 60.000 0.00 0.00 36.89 3.95
2515 4345 7.119997 CAGATTCTGATAAATCGTTCCGTTTC 58.880 38.462 8.00 0.00 40.00 2.78
2519 4349 4.375405 CGCAGATTCTGATAAATCGTTCCG 60.375 45.833 17.87 3.06 40.00 4.30
2520 4350 4.745125 TCGCAGATTCTGATAAATCGTTCC 59.255 41.667 17.87 0.00 40.00 3.62
2553 4383 3.050275 GGAGAACACACTGGCCGC 61.050 66.667 0.00 0.00 0.00 6.53
2554 4384 0.535102 AAAGGAGAACACACTGGCCG 60.535 55.000 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.