Multiple sequence alignment - TraesCS5D01G128000

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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 TraesCS5D01G128000 chr5D 100.000 2973 0 0 1 2973 199724697 199721725 0.000000e+00 5491.0
1 TraesCS5D01G128000 chr5B 89.961 1275 44 20 849 2096 210168245 210167028 0.000000e+00 1568.0
2 TraesCS5D01G128000 chr5B 91.579 570 26 5 2424 2973 210167036 210166469 0.000000e+00 767.0
3 TraesCS5D01G128000 chr5B 90.604 298 24 2 302 595 210168734 210168437 2.780000e-105 392.0
4 TraesCS5D01G128000 chr5B 86.391 338 34 5 2108 2441 636932408 636932079 2.820000e-95 359.0
5 TraesCS5D01G128000 chr5B 86.562 320 33 6 2108 2423 239702601 239702914 7.890000e-91 344.0
6 TraesCS5D01G128000 chr5B 95.192 208 9 1 611 817 210168453 210168246 7.950000e-86 327.0
7 TraesCS5D01G128000 chr5A 88.187 1219 36 22 908 2096 216961549 216960409 0.000000e+00 1354.0
8 TraesCS5D01G128000 chr5A 91.690 361 13 4 2568 2919 216960303 216959951 4.460000e-133 484.0
9 TraesCS5D01G128000 chr5A 92.446 278 21 0 4 281 216968695 216968418 5.970000e-107 398.0
10 TraesCS5D01G128000 chr5A 88.968 281 21 5 615 888 216968304 216968027 3.670000e-89 339.0
11 TraesCS5D01G128000 chr5A 94.828 116 6 0 2424 2539 216960417 216960302 6.550000e-42 182.0
12 TraesCS5D01G128000 chr5A 94.915 59 3 0 2915 2973 216954672 216954614 3.160000e-15 93.5
13 TraesCS5D01G128000 chr2D 87.578 322 28 4 2108 2423 3954501 3954186 2.180000e-96 363.0
14 TraesCS5D01G128000 chr2D 86.604 321 32 5 2108 2424 154390517 154390204 7.890000e-91 344.0
15 TraesCS5D01G128000 chr1B 87.500 320 30 5 2108 2423 120065372 120065685 7.830000e-96 361.0
16 TraesCS5D01G128000 chr3A 87.382 317 28 3 2108 2418 653328185 653327875 1.310000e-93 353.0
17 TraesCS5D01G128000 chr3A 86.562 320 31 5 2108 2423 555120718 555120407 2.840000e-90 342.0
18 TraesCS5D01G128000 chr7B 86.562 320 33 5 2108 2423 322396242 322395929 7.890000e-91 344.0
19 TraesCS5D01G128000 chr4A 86.562 320 33 4 2108 2423 5663600 5663287 7.890000e-91 344.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G128000 chr5D 199721725 199724697 2972 True 5491.000000 5491 100.000000 1 2973 1 chr5D.!!$R1 2972
1 TraesCS5D01G128000 chr5B 210166469 210168734 2265 True 763.500000 1568 91.834000 302 2973 4 chr5B.!!$R2 2671
2 TraesCS5D01G128000 chr5A 216959951 216961549 1598 True 673.333333 1354 91.568333 908 2919 3 chr5A.!!$R2 2011
3 TraesCS5D01G128000 chr5A 216968027 216968695 668 True 368.500000 398 90.707000 4 888 2 chr5A.!!$R3 884

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
845 857 0.108709 CCCAAAACACATGGCGATGG 60.109 55.0 13.62 4.82 36.58 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2408 2463 0.105039 GATGCGGAACCGAATCCTCT 59.895 55.0 20.04 0.0 45.95 3.69 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
23 24 3.955471 TCATGAGGTGGTGGATCTTTTC 58.045 45.455 0.00 0.00 0.00 2.29
73 74 7.126573 TGGCCTTATCCGATCCATAATTGTATA 59.873 37.037 3.32 0.00 0.00 1.47
93 94 8.454570 TGTATAATGATGTGACATTCTTGCAT 57.545 30.769 0.00 0.00 40.36 3.96
95 96 5.907866 AATGATGTGACATTCTTGCATGA 57.092 34.783 0.00 0.00 35.92 3.07
168 169 8.494016 AATCTTGTCTTTAAGTAATTCCCTCG 57.506 34.615 0.00 0.00 0.00 4.63
174 175 6.985059 GTCTTTAAGTAATTCCCTCGTATGCT 59.015 38.462 0.00 0.00 0.00 3.79
193 194 8.598924 CGTATGCTCATATTTCCTCATGAATAC 58.401 37.037 0.00 0.00 31.04 1.89
194 195 7.606858 ATGCTCATATTTCCTCATGAATACG 57.393 36.000 0.00 0.00 31.04 3.06
197 198 6.870965 GCTCATATTTCCTCATGAATACGTCT 59.129 38.462 0.00 0.00 31.04 4.18
200 201 9.860898 TCATATTTCCTCATGAATACGTCTATG 57.139 33.333 0.00 0.00 31.67 2.23
219 220 7.538575 GTCTATGTCTGCAACAAACCATTAAT 58.461 34.615 5.94 0.00 42.37 1.40
221 222 8.028354 TCTATGTCTGCAACAAACCATTAATTG 58.972 33.333 5.94 0.00 42.37 2.32
229 230 6.146021 GCAACAAACCATTAATTGAGACAAGG 59.854 38.462 0.00 0.00 0.00 3.61
249 250 4.401022 AGGAGATTTGCACATCTTTGTCA 58.599 39.130 16.24 0.00 33.36 3.58
250 251 4.828939 AGGAGATTTGCACATCTTTGTCAA 59.171 37.500 16.24 0.00 33.36 3.18
251 252 5.479375 AGGAGATTTGCACATCTTTGTCAAT 59.521 36.000 16.24 0.00 33.36 2.57
252 253 6.660521 AGGAGATTTGCACATCTTTGTCAATA 59.339 34.615 16.24 0.00 33.36 1.90
253 254 7.341256 AGGAGATTTGCACATCTTTGTCAATAT 59.659 33.333 16.24 0.00 33.36 1.28
254 255 7.977853 GGAGATTTGCACATCTTTGTCAATATT 59.022 33.333 16.24 0.00 33.36 1.28
259 260 9.791820 TTTGCACATCTTTGTCAATATTATGAG 57.208 29.630 0.00 0.00 32.34 2.90
260 261 7.420002 TGCACATCTTTGTCAATATTATGAGC 58.580 34.615 7.28 7.28 32.34 4.26
261 262 7.067251 TGCACATCTTTGTCAATATTATGAGCA 59.933 33.333 11.00 11.00 37.21 4.26
262 263 7.916977 GCACATCTTTGTCAATATTATGAGCAA 59.083 33.333 8.66 1.41 32.34 3.91
263 264 9.961265 CACATCTTTGTCAATATTATGAGCAAT 57.039 29.630 0.00 0.00 32.34 3.56
267 268 8.786898 TCTTTGTCAATATTATGAGCAATAGGC 58.213 33.333 0.00 0.00 45.30 3.93
278 279 1.900237 GCAATAGGCAAGTTGAAGCG 58.100 50.000 7.16 0.00 43.97 4.68
279 280 1.468520 GCAATAGGCAAGTTGAAGCGA 59.531 47.619 7.16 0.00 43.97 4.93
280 281 2.098117 GCAATAGGCAAGTTGAAGCGAT 59.902 45.455 7.16 0.00 43.97 4.58
281 282 3.312421 GCAATAGGCAAGTTGAAGCGATA 59.688 43.478 7.16 0.00 43.97 2.92
282 283 4.201910 GCAATAGGCAAGTTGAAGCGATAA 60.202 41.667 7.16 0.00 43.97 1.75
283 284 5.506317 GCAATAGGCAAGTTGAAGCGATAAT 60.506 40.000 7.16 0.00 43.97 1.28
284 285 6.293407 GCAATAGGCAAGTTGAAGCGATAATA 60.293 38.462 7.16 0.00 43.97 0.98
285 286 7.639039 CAATAGGCAAGTTGAAGCGATAATAA 58.361 34.615 7.16 0.00 0.00 1.40
286 287 5.485662 AGGCAAGTTGAAGCGATAATAAC 57.514 39.130 7.16 0.00 0.00 1.89
287 288 4.941263 AGGCAAGTTGAAGCGATAATAACA 59.059 37.500 7.16 0.00 0.00 2.41
288 289 5.065218 AGGCAAGTTGAAGCGATAATAACAG 59.935 40.000 7.16 0.00 0.00 3.16
289 290 5.064707 GGCAAGTTGAAGCGATAATAACAGA 59.935 40.000 7.16 0.00 0.00 3.41
290 291 6.403200 GGCAAGTTGAAGCGATAATAACAGAA 60.403 38.462 7.16 0.00 0.00 3.02
291 292 7.021196 GCAAGTTGAAGCGATAATAACAGAAA 58.979 34.615 7.16 0.00 0.00 2.52
292 293 7.537306 GCAAGTTGAAGCGATAATAACAGAAAA 59.463 33.333 7.16 0.00 0.00 2.29
293 294 9.559958 CAAGTTGAAGCGATAATAACAGAAAAT 57.440 29.630 0.00 0.00 0.00 1.82
343 344 6.039382 AGGGAAAGTATGAATATTCGGCAAAC 59.961 38.462 10.80 4.60 0.00 2.93
382 387 3.344515 GGGTAAAGTTAGGAAGGCTGTG 58.655 50.000 0.00 0.00 0.00 3.66
396 401 1.571919 GCTGTGTATGGCGAACCTAG 58.428 55.000 0.00 0.00 36.63 3.02
417 422 7.103641 CCTAGGTTTACACACAACATCTACAT 58.896 38.462 0.00 0.00 0.00 2.29
419 424 7.202016 AGGTTTACACACAACATCTACATTG 57.798 36.000 0.00 0.00 0.00 2.82
421 426 7.284489 AGGTTTACACACAACATCTACATTGTT 59.716 33.333 0.00 0.00 36.92 2.83
443 448 9.638239 TTGTTCAAAACATTATAGAAGCATTCC 57.362 29.630 0.00 0.00 43.51 3.01
456 461 4.701361 GAAGCATTCCGAAACAATTTTGC 58.299 39.130 0.00 0.00 39.83 3.68
476 481 2.868044 GCTTGCTACGGATCTACCATGG 60.868 54.545 11.19 11.19 38.90 3.66
495 500 0.239879 GTTGTTGTGGCATGTACCCG 59.760 55.000 0.00 0.00 0.00 5.28
510 515 1.971695 CCCGGCACACCCTTTTCTC 60.972 63.158 0.00 0.00 0.00 2.87
513 518 1.676014 CCGGCACACCCTTTTCTCTAG 60.676 57.143 0.00 0.00 0.00 2.43
705 711 8.376942 CGCCACAACATAATTTACCATAAAAAC 58.623 33.333 0.00 0.00 0.00 2.43
706 712 9.430623 GCCACAACATAATTTACCATAAAAACT 57.569 29.630 0.00 0.00 0.00 2.66
726 733 3.181493 ACTTTCGATTTGGCATGATCAGC 60.181 43.478 0.09 5.10 0.00 4.26
837 849 0.398381 AGTGCCCACCCAAAACACAT 60.398 50.000 0.00 0.00 33.69 3.21
838 850 0.249826 GTGCCCACCCAAAACACATG 60.250 55.000 0.00 0.00 0.00 3.21
840 852 1.370810 CCCACCCAAAACACATGGC 59.629 57.895 0.00 0.00 36.58 4.40
841 853 1.006337 CCACCCAAAACACATGGCG 60.006 57.895 0.00 0.00 36.58 5.69
843 855 0.602562 CACCCAAAACACATGGCGAT 59.397 50.000 0.00 0.00 36.58 4.58
844 856 0.602562 ACCCAAAACACATGGCGATG 59.397 50.000 7.21 7.21 36.58 3.84
845 857 0.108709 CCCAAAACACATGGCGATGG 60.109 55.000 13.62 4.82 36.58 3.51
921 933 1.983119 GCCCATTCCGATCCTGTCCA 61.983 60.000 0.00 0.00 0.00 4.02
922 934 0.546122 CCCATTCCGATCCTGTCCAA 59.454 55.000 0.00 0.00 0.00 3.53
923 935 1.475751 CCCATTCCGATCCTGTCCAAG 60.476 57.143 0.00 0.00 0.00 3.61
980 992 1.478105 GCAGCATAAAAAGGTGGGAGG 59.522 52.381 0.00 0.00 35.17 4.30
982 994 3.430453 CAGCATAAAAAGGTGGGAGGAA 58.570 45.455 0.00 0.00 0.00 3.36
983 995 4.026052 CAGCATAAAAAGGTGGGAGGAAT 58.974 43.478 0.00 0.00 0.00 3.01
984 996 4.098501 CAGCATAAAAAGGTGGGAGGAATC 59.901 45.833 0.00 0.00 0.00 2.52
985 997 4.023291 GCATAAAAAGGTGGGAGGAATCA 58.977 43.478 0.00 0.00 0.00 2.57
986 998 4.142160 GCATAAAAAGGTGGGAGGAATCAC 60.142 45.833 0.00 0.00 0.00 3.06
992 1004 3.492686 TGGGAGGAATCACCACTGA 57.507 52.632 0.00 0.00 42.04 3.41
993 1005 1.279496 TGGGAGGAATCACCACTGAG 58.721 55.000 0.00 0.00 42.04 3.35
994 1006 1.280457 GGGAGGAATCACCACTGAGT 58.720 55.000 0.00 0.00 42.04 3.41
995 1007 1.208293 GGGAGGAATCACCACTGAGTC 59.792 57.143 0.00 0.00 40.20 3.36
996 1008 1.134965 GGAGGAATCACCACTGAGTCG 60.135 57.143 0.00 0.00 41.56 4.18
997 1009 0.898320 AGGAATCACCACTGAGTCGG 59.102 55.000 0.00 0.00 41.56 4.79
998 1010 0.895530 GGAATCACCACTGAGTCGGA 59.104 55.000 5.81 0.00 41.56 4.55
1002 1014 1.006102 CACCACTGAGTCGGACACC 60.006 63.158 11.27 2.36 0.00 4.16
1112 1128 3.703052 CTCCTCCCATCCAAATTCCAAAG 59.297 47.826 0.00 0.00 0.00 2.77
1126 1142 1.068434 TCCAAAGAAGCAAAAAGGCGG 59.932 47.619 0.00 0.00 39.27 6.13
1127 1143 1.068434 CCAAAGAAGCAAAAAGGCGGA 59.932 47.619 0.00 0.00 39.27 5.54
1128 1144 2.397549 CAAAGAAGCAAAAAGGCGGAG 58.602 47.619 0.00 0.00 39.27 4.63
1459 1487 2.028130 CTGCAGAAGTACCTCGAGGAT 58.972 52.381 37.69 22.80 38.94 3.24
1516 1544 1.176619 TCCGCGACCTCAGACAAGAA 61.177 55.000 8.23 0.00 0.00 2.52
1517 1545 1.009389 CCGCGACCTCAGACAAGAAC 61.009 60.000 8.23 0.00 0.00 3.01
1528 1556 2.253452 CAAGAACAGTGCAGCGGC 59.747 61.111 0.31 0.31 41.68 6.53
1592 1620 5.278808 GGATGGCTAATGTGATACAGTACGA 60.279 44.000 0.00 0.00 0.00 3.43
1599 1627 4.182693 TGTGATACAGTACGAGTTTGGG 57.817 45.455 0.00 0.00 0.00 4.12
1644 1672 4.267452 CGTGTTTTGTTCTTGGTGAAATGG 59.733 41.667 0.00 0.00 36.30 3.16
1674 1710 8.358582 TCGAGAAATTAGGGACTACTACTTTT 57.641 34.615 0.00 0.00 42.67 2.27
1705 1741 6.980978 TGCGAAATTAGAGGAATTAGAGACTG 59.019 38.462 0.00 0.00 36.71 3.51
1770 1806 6.334202 AGAAAGAGATCGGCTACTAAACTTG 58.666 40.000 0.00 0.00 0.00 3.16
1771 1807 5.662674 AAGAGATCGGCTACTAAACTTGT 57.337 39.130 0.00 0.00 0.00 3.16
1772 1808 5.000012 AGAGATCGGCTACTAAACTTGTG 58.000 43.478 0.00 0.00 0.00 3.33
1773 1809 4.463186 AGAGATCGGCTACTAAACTTGTGT 59.537 41.667 0.00 0.00 0.00 3.72
1774 1810 4.745649 AGATCGGCTACTAAACTTGTGTC 58.254 43.478 0.00 0.00 0.00 3.67
1775 1811 3.308438 TCGGCTACTAAACTTGTGTCC 57.692 47.619 0.00 0.00 0.00 4.02
1776 1812 2.895404 TCGGCTACTAAACTTGTGTCCT 59.105 45.455 0.00 0.00 0.00 3.85
1777 1813 3.322828 TCGGCTACTAAACTTGTGTCCTT 59.677 43.478 0.00 0.00 0.00 3.36
1778 1814 4.062991 CGGCTACTAAACTTGTGTCCTTT 58.937 43.478 0.00 0.00 0.00 3.11
1779 1815 4.151867 CGGCTACTAAACTTGTGTCCTTTC 59.848 45.833 0.00 0.00 0.00 2.62
1780 1816 4.454847 GGCTACTAAACTTGTGTCCTTTCC 59.545 45.833 0.00 0.00 0.00 3.13
1781 1817 5.306394 GCTACTAAACTTGTGTCCTTTCCT 58.694 41.667 0.00 0.00 0.00 3.36
1782 1818 6.461640 GCTACTAAACTTGTGTCCTTTCCTA 58.538 40.000 0.00 0.00 0.00 2.94
1783 1819 6.932960 GCTACTAAACTTGTGTCCTTTCCTAA 59.067 38.462 0.00 0.00 0.00 2.69
1784 1820 7.443272 GCTACTAAACTTGTGTCCTTTCCTAAA 59.557 37.037 0.00 0.00 0.00 1.85
1785 1821 9.333724 CTACTAAACTTGTGTCCTTTCCTAAAA 57.666 33.333 0.00 0.00 0.00 1.52
1786 1822 8.584063 ACTAAACTTGTGTCCTTTCCTAAAAA 57.416 30.769 0.00 0.00 0.00 1.94
1787 1823 8.464404 ACTAAACTTGTGTCCTTTCCTAAAAAC 58.536 33.333 0.00 0.00 0.00 2.43
1788 1824 7.476540 AAACTTGTGTCCTTTCCTAAAAACT 57.523 32.000 0.00 0.00 0.00 2.66
1789 1825 8.584063 AAACTTGTGTCCTTTCCTAAAAACTA 57.416 30.769 0.00 0.00 0.00 2.24
1790 1826 8.584063 AACTTGTGTCCTTTCCTAAAAACTAA 57.416 30.769 0.00 0.00 0.00 2.24
1791 1827 8.584063 ACTTGTGTCCTTTCCTAAAAACTAAA 57.416 30.769 0.00 0.00 0.00 1.85
1792 1828 8.464404 ACTTGTGTCCTTTCCTAAAAACTAAAC 58.536 33.333 0.00 0.00 0.00 2.01
1793 1829 8.584063 TTGTGTCCTTTCCTAAAAACTAAACT 57.416 30.769 0.00 0.00 0.00 2.66
1794 1830 8.584063 TGTGTCCTTTCCTAAAAACTAAACTT 57.416 30.769 0.00 0.00 0.00 2.66
1795 1831 8.463607 TGTGTCCTTTCCTAAAAACTAAACTTG 58.536 33.333 0.00 0.00 0.00 3.16
1869 1907 3.779759 TGTGCCACTTGCTTTGTTAAAG 58.220 40.909 0.00 0.00 42.00 1.85
1915 1962 2.393989 TAGCCGCATCGCTTCTCTCG 62.394 60.000 0.00 0.00 40.39 4.04
1918 1965 1.475441 CCGCATCGCTTCTCTCGAAC 61.475 60.000 0.00 0.00 39.54 3.95
1956 2003 6.076981 AGACATTTCTTTTGTAACAGCTGG 57.923 37.500 19.93 0.00 0.00 4.85
2096 2151 0.389556 ATCGCAGGCAGCATCTATCG 60.390 55.000 1.96 0.00 46.13 2.92
2097 2152 2.025969 CGCAGGCAGCATCTATCGG 61.026 63.158 1.96 0.00 46.13 4.18
2098 2153 1.368950 GCAGGCAGCATCTATCGGA 59.631 57.895 0.00 0.00 44.79 4.55
2099 2154 0.250038 GCAGGCAGCATCTATCGGAA 60.250 55.000 0.00 0.00 44.79 4.30
2100 2155 1.506493 CAGGCAGCATCTATCGGAAC 58.494 55.000 0.00 0.00 0.00 3.62
2101 2156 1.069823 CAGGCAGCATCTATCGGAACT 59.930 52.381 0.00 0.00 0.00 3.01
2102 2157 1.342819 AGGCAGCATCTATCGGAACTC 59.657 52.381 0.00 0.00 0.00 3.01
2103 2158 1.342819 GGCAGCATCTATCGGAACTCT 59.657 52.381 0.00 0.00 0.00 3.24
2104 2159 2.558795 GGCAGCATCTATCGGAACTCTA 59.441 50.000 0.00 0.00 0.00 2.43
2105 2160 3.005897 GGCAGCATCTATCGGAACTCTAA 59.994 47.826 0.00 0.00 0.00 2.10
2106 2161 3.984633 GCAGCATCTATCGGAACTCTAAC 59.015 47.826 0.00 0.00 0.00 2.34
2107 2162 4.551388 CAGCATCTATCGGAACTCTAACC 58.449 47.826 0.00 0.00 0.00 2.85
2108 2163 4.279671 CAGCATCTATCGGAACTCTAACCT 59.720 45.833 0.00 0.00 0.00 3.50
2109 2164 5.473846 CAGCATCTATCGGAACTCTAACCTA 59.526 44.000 0.00 0.00 0.00 3.08
2110 2165 6.016192 CAGCATCTATCGGAACTCTAACCTAA 60.016 42.308 0.00 0.00 0.00 2.69
2111 2166 6.016108 AGCATCTATCGGAACTCTAACCTAAC 60.016 42.308 0.00 0.00 0.00 2.34
2112 2167 6.238953 GCATCTATCGGAACTCTAACCTAACA 60.239 42.308 0.00 0.00 0.00 2.41
2113 2168 7.524038 GCATCTATCGGAACTCTAACCTAACAT 60.524 40.741 0.00 0.00 0.00 2.71
2114 2169 7.273320 TCTATCGGAACTCTAACCTAACATG 57.727 40.000 0.00 0.00 0.00 3.21
2115 2170 4.730949 TCGGAACTCTAACCTAACATGG 57.269 45.455 0.00 0.00 0.00 3.66
2116 2171 4.091549 TCGGAACTCTAACCTAACATGGT 58.908 43.478 0.00 0.00 43.11 3.55
2117 2172 4.081862 TCGGAACTCTAACCTAACATGGTG 60.082 45.833 0.00 0.00 40.73 4.17
2118 2173 4.081862 CGGAACTCTAACCTAACATGGTGA 60.082 45.833 0.00 0.00 40.73 4.02
2119 2174 5.568023 CGGAACTCTAACCTAACATGGTGAA 60.568 44.000 0.00 0.00 40.73 3.18
2120 2175 5.875359 GGAACTCTAACCTAACATGGTGAAG 59.125 44.000 0.00 0.00 40.73 3.02
2121 2176 5.422214 ACTCTAACCTAACATGGTGAAGG 57.578 43.478 0.00 0.00 40.73 3.46
2122 2177 5.091552 ACTCTAACCTAACATGGTGAAGGA 58.908 41.667 6.57 0.00 40.73 3.36
2123 2178 5.546499 ACTCTAACCTAACATGGTGAAGGAA 59.454 40.000 6.57 0.00 40.73 3.36
2124 2179 6.043938 ACTCTAACCTAACATGGTGAAGGAAA 59.956 38.462 6.57 0.00 40.73 3.13
2125 2180 6.472887 TCTAACCTAACATGGTGAAGGAAAG 58.527 40.000 6.57 3.64 40.73 2.62
2126 2181 4.724279 ACCTAACATGGTGAAGGAAAGT 57.276 40.909 6.57 0.00 39.17 2.66
2127 2182 4.652822 ACCTAACATGGTGAAGGAAAGTC 58.347 43.478 6.57 0.00 39.17 3.01
2128 2183 4.104102 ACCTAACATGGTGAAGGAAAGTCA 59.896 41.667 6.57 0.00 39.17 3.41
2129 2184 4.455877 CCTAACATGGTGAAGGAAAGTCAC 59.544 45.833 0.00 0.00 43.87 3.67
2134 2189 0.586802 GTGAAGGAAAGTCACCGTGC 59.413 55.000 0.00 0.00 39.62 5.34
2135 2190 0.468226 TGAAGGAAAGTCACCGTGCT 59.532 50.000 0.00 0.00 0.00 4.40
2136 2191 1.689813 TGAAGGAAAGTCACCGTGCTA 59.310 47.619 0.00 0.00 0.00 3.49
2137 2192 2.301870 TGAAGGAAAGTCACCGTGCTAT 59.698 45.455 0.00 0.00 0.00 2.97
2138 2193 3.512329 TGAAGGAAAGTCACCGTGCTATA 59.488 43.478 0.00 0.00 0.00 1.31
2139 2194 3.802948 AGGAAAGTCACCGTGCTATAG 57.197 47.619 0.00 0.00 0.00 1.31
2140 2195 3.097614 AGGAAAGTCACCGTGCTATAGT 58.902 45.455 0.84 0.00 0.00 2.12
2141 2196 3.119101 AGGAAAGTCACCGTGCTATAGTG 60.119 47.826 0.84 0.00 0.00 2.74
2142 2197 3.368116 GGAAAGTCACCGTGCTATAGTGT 60.368 47.826 0.84 0.00 33.21 3.55
2143 2198 3.955650 AAGTCACCGTGCTATAGTGTT 57.044 42.857 0.84 0.00 33.21 3.32
2144 2199 3.955650 AGTCACCGTGCTATAGTGTTT 57.044 42.857 0.84 0.00 33.21 2.83
2145 2200 5.395682 AAGTCACCGTGCTATAGTGTTTA 57.604 39.130 0.84 0.00 33.21 2.01
2146 2201 4.995124 AGTCACCGTGCTATAGTGTTTAG 58.005 43.478 0.84 0.00 33.21 1.85
2147 2202 4.461781 AGTCACCGTGCTATAGTGTTTAGT 59.538 41.667 0.84 0.00 33.21 2.24
2148 2203 4.561606 GTCACCGTGCTATAGTGTTTAGTG 59.438 45.833 0.84 3.10 33.21 2.74
2149 2204 4.219070 TCACCGTGCTATAGTGTTTAGTGT 59.781 41.667 0.84 0.00 33.21 3.55
2150 2205 5.415389 TCACCGTGCTATAGTGTTTAGTGTA 59.585 40.000 0.84 0.00 33.21 2.90
2151 2206 6.072008 TCACCGTGCTATAGTGTTTAGTGTAA 60.072 38.462 0.84 0.00 33.21 2.41
2152 2207 6.587226 CACCGTGCTATAGTGTTTAGTGTAAA 59.413 38.462 0.84 0.00 0.00 2.01
2153 2208 7.116662 CACCGTGCTATAGTGTTTAGTGTAAAA 59.883 37.037 0.84 0.00 0.00 1.52
2154 2209 7.820872 ACCGTGCTATAGTGTTTAGTGTAAAAT 59.179 33.333 0.84 0.00 0.00 1.82
2155 2210 8.114290 CCGTGCTATAGTGTTTAGTGTAAAATG 58.886 37.037 0.84 0.00 0.00 2.32
2156 2211 8.865978 CGTGCTATAGTGTTTAGTGTAAAATGA 58.134 33.333 0.84 0.00 0.00 2.57
2163 2218 8.974060 AGTGTTTAGTGTAAAATGAAGAAGGA 57.026 30.769 0.00 0.00 0.00 3.36
2164 2219 9.403583 AGTGTTTAGTGTAAAATGAAGAAGGAA 57.596 29.630 0.00 0.00 0.00 3.36
2171 2226 9.067986 AGTGTAAAATGAAGAAGGAAAGTTAGG 57.932 33.333 0.00 0.00 0.00 2.69
2172 2227 8.297426 GTGTAAAATGAAGAAGGAAAGTTAGGG 58.703 37.037 0.00 0.00 0.00 3.53
2173 2228 8.002459 TGTAAAATGAAGAAGGAAAGTTAGGGT 58.998 33.333 0.00 0.00 0.00 4.34
2174 2229 7.526142 AAAATGAAGAAGGAAAGTTAGGGTC 57.474 36.000 0.00 0.00 0.00 4.46
2175 2230 6.455690 AATGAAGAAGGAAAGTTAGGGTCT 57.544 37.500 0.00 0.00 0.00 3.85
2176 2231 5.228945 TGAAGAAGGAAAGTTAGGGTCTG 57.771 43.478 0.00 0.00 0.00 3.51
2177 2232 4.658901 TGAAGAAGGAAAGTTAGGGTCTGT 59.341 41.667 0.00 0.00 0.00 3.41
2178 2233 5.132144 TGAAGAAGGAAAGTTAGGGTCTGTT 59.868 40.000 0.00 0.00 0.00 3.16
2179 2234 6.328148 TGAAGAAGGAAAGTTAGGGTCTGTTA 59.672 38.462 0.00 0.00 0.00 2.41
2180 2235 6.361768 AGAAGGAAAGTTAGGGTCTGTTAG 57.638 41.667 0.00 0.00 0.00 2.34
2181 2236 5.845065 AGAAGGAAAGTTAGGGTCTGTTAGT 59.155 40.000 0.00 0.00 0.00 2.24
2182 2237 7.015064 AGAAGGAAAGTTAGGGTCTGTTAGTA 58.985 38.462 0.00 0.00 0.00 1.82
2183 2238 6.854091 AGGAAAGTTAGGGTCTGTTAGTAG 57.146 41.667 0.00 0.00 0.00 2.57
2184 2239 6.559429 AGGAAAGTTAGGGTCTGTTAGTAGA 58.441 40.000 0.00 0.00 0.00 2.59
2185 2240 7.190501 AGGAAAGTTAGGGTCTGTTAGTAGAT 58.809 38.462 0.00 0.00 0.00 1.98
2186 2241 8.342270 AGGAAAGTTAGGGTCTGTTAGTAGATA 58.658 37.037 0.00 0.00 0.00 1.98
2187 2242 8.975295 GGAAAGTTAGGGTCTGTTAGTAGATAA 58.025 37.037 0.00 0.00 0.00 1.75
2195 2250 9.357161 AGGGTCTGTTAGTAGATAATTAGTCAG 57.643 37.037 0.00 0.00 0.00 3.51
2196 2251 9.134055 GGGTCTGTTAGTAGATAATTAGTCAGT 57.866 37.037 0.00 0.00 0.00 3.41
2278 2333 9.761504 TGTTTCATCATCAATTTGTTTGTATGT 57.238 25.926 0.00 0.00 36.65 2.29
2317 2372 9.936759 TGTACACAGTAGATCATCAATTTACAA 57.063 29.630 0.00 0.00 29.35 2.41
2405 2460 8.159344 AGTTTCTCTAACTTTCCTTCACAATG 57.841 34.615 0.00 0.00 44.73 2.82
2406 2461 7.775561 AGTTTCTCTAACTTTCCTTCACAATGT 59.224 33.333 0.00 0.00 44.73 2.71
2407 2462 8.406297 GTTTCTCTAACTTTCCTTCACAATGTT 58.594 33.333 0.00 0.00 33.79 2.71
2408 2463 9.621629 TTTCTCTAACTTTCCTTCACAATGTTA 57.378 29.630 0.00 0.00 0.00 2.41
2409 2464 8.833231 TCTCTAACTTTCCTTCACAATGTTAG 57.167 34.615 0.00 0.00 40.02 2.34
2410 2465 8.647796 TCTCTAACTTTCCTTCACAATGTTAGA 58.352 33.333 14.95 14.95 42.45 2.10
2411 2466 8.833231 TCTAACTTTCCTTCACAATGTTAGAG 57.167 34.615 13.06 0.00 41.22 2.43
2412 2467 6.884280 AACTTTCCTTCACAATGTTAGAGG 57.116 37.500 1.31 1.31 0.00 3.69
2413 2468 6.187727 ACTTTCCTTCACAATGTTAGAGGA 57.812 37.500 5.38 5.38 0.00 3.71
2414 2469 6.784031 ACTTTCCTTCACAATGTTAGAGGAT 58.216 36.000 9.15 0.00 0.00 3.24
2415 2470 7.234355 ACTTTCCTTCACAATGTTAGAGGATT 58.766 34.615 9.15 0.00 0.00 3.01
2416 2471 7.391833 ACTTTCCTTCACAATGTTAGAGGATTC 59.608 37.037 9.15 0.00 0.00 2.52
2417 2472 5.419542 TCCTTCACAATGTTAGAGGATTCG 58.580 41.667 5.38 0.00 0.00 3.34
2418 2473 4.572389 CCTTCACAATGTTAGAGGATTCGG 59.428 45.833 1.46 0.00 0.00 4.30
2419 2474 4.819105 TCACAATGTTAGAGGATTCGGT 57.181 40.909 0.00 0.00 0.00 4.69
2420 2475 5.160607 TCACAATGTTAGAGGATTCGGTT 57.839 39.130 0.00 0.00 0.00 4.44
2421 2476 5.175859 TCACAATGTTAGAGGATTCGGTTC 58.824 41.667 0.00 0.00 0.00 3.62
2422 2477 4.332819 CACAATGTTAGAGGATTCGGTTCC 59.667 45.833 0.00 0.00 35.90 3.62
2423 2478 2.953466 TGTTAGAGGATTCGGTTCCG 57.047 50.000 4.74 4.74 40.94 4.30
2424 2479 1.134907 TGTTAGAGGATTCGGTTCCGC 60.135 52.381 6.35 1.11 40.94 5.54
2425 2480 1.134907 GTTAGAGGATTCGGTTCCGCA 60.135 52.381 6.35 0.00 40.94 5.69
2426 2481 1.410004 TAGAGGATTCGGTTCCGCAT 58.590 50.000 6.35 0.76 40.94 4.73
2427 2482 0.105039 AGAGGATTCGGTTCCGCATC 59.895 55.000 13.66 13.66 40.94 3.91
2428 2483 0.105039 GAGGATTCGGTTCCGCATCT 59.895 55.000 19.23 8.84 40.94 2.90
2429 2484 1.340248 GAGGATTCGGTTCCGCATCTA 59.660 52.381 19.23 0.00 40.94 1.98
2430 2485 1.971357 AGGATTCGGTTCCGCATCTAT 59.029 47.619 19.23 9.12 40.94 1.98
2431 2486 2.368875 AGGATTCGGTTCCGCATCTATT 59.631 45.455 19.23 6.92 40.94 1.73
2488 2543 1.573829 TTTGCGCGCTGGGTTTAGAG 61.574 55.000 33.29 0.00 0.00 2.43
2573 2633 2.625737 CGACATGACTGGAATCAGCTT 58.374 47.619 0.00 0.00 44.59 3.74
2629 2689 1.486211 CACTCGGATAGAACCAGGGT 58.514 55.000 0.00 0.00 0.00 4.34
2659 2720 1.766494 AAATTCCATGGATGCGCTCA 58.234 45.000 17.06 4.92 0.00 4.26
2701 2762 9.915629 CTGTCCAGAATAATCCTACACTAATAC 57.084 37.037 0.00 0.00 0.00 1.89
2718 2779 4.829872 AATACCAGGGTCGTATTTGACA 57.170 40.909 0.00 0.00 40.72 3.58
2864 2938 5.122239 CGACAAATCAGGATTCAACTAAGCA 59.878 40.000 0.00 0.00 0.00 3.91
2901 2975 9.959749 TTTTCTTGTTTCTAAAATAGACGCAAT 57.040 25.926 0.00 0.00 33.84 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.387026 AAAGATCCACCACCTCATGAAA 57.613 40.909 0.00 0.00 0.00 2.69
1 2 4.335416 GAAAAGATCCACCACCTCATGAA 58.665 43.478 0.00 0.00 0.00 2.57
2 3 3.955471 GAAAAGATCCACCACCTCATGA 58.045 45.455 0.00 0.00 0.00 3.07
14 15 7.148120 CATGCTATCATGTATGGGAAAAGATCC 60.148 40.741 0.00 0.00 44.59 3.36
16 17 7.698506 CATGCTATCATGTATGGGAAAAGAT 57.301 36.000 0.00 0.00 43.85 2.40
42 43 1.543429 GGATCGGATAAGGCCACCTTG 60.543 57.143 5.01 0.00 44.44 3.61
73 74 5.907866 TCATGCAAGAATGTCACATCATT 57.092 34.783 0.00 0.00 40.20 2.57
160 161 5.249393 AGGAAATATGAGCATACGAGGGAAT 59.751 40.000 0.00 0.00 0.00 3.01
167 168 7.606858 ATTCATGAGGAAATATGAGCATACG 57.393 36.000 0.00 0.00 39.39 3.06
168 169 8.598924 CGTATTCATGAGGAAATATGAGCATAC 58.401 37.037 0.00 0.00 39.39 2.39
174 175 9.860898 CATAGACGTATTCATGAGGAAATATGA 57.139 33.333 10.12 0.00 39.39 2.15
193 194 2.805671 TGGTTTGTTGCAGACATAGACG 59.194 45.455 3.15 0.00 38.26 4.18
194 195 5.376854 AATGGTTTGTTGCAGACATAGAC 57.623 39.130 3.15 3.67 38.26 2.59
197 198 7.890515 TCAATTAATGGTTTGTTGCAGACATA 58.109 30.769 3.15 0.00 38.26 2.29
200 201 6.363357 GTCTCAATTAATGGTTTGTTGCAGAC 59.637 38.462 0.00 0.00 0.00 3.51
219 220 3.819368 TGTGCAAATCTCCTTGTCTCAA 58.181 40.909 0.00 0.00 0.00 3.02
221 222 4.260170 AGATGTGCAAATCTCCTTGTCTC 58.740 43.478 14.00 0.00 30.91 3.36
229 230 8.922058 AATATTGACAAAGATGTGCAAATCTC 57.078 30.769 19.84 8.24 40.74 2.75
249 250 8.696043 TCAACTTGCCTATTGCTCATAATATT 57.304 30.769 0.00 0.00 42.00 1.28
250 251 8.696043 TTCAACTTGCCTATTGCTCATAATAT 57.304 30.769 0.00 0.00 42.00 1.28
251 252 7.255242 GCTTCAACTTGCCTATTGCTCATAATA 60.255 37.037 0.00 0.00 42.00 0.98
252 253 6.460676 GCTTCAACTTGCCTATTGCTCATAAT 60.461 38.462 0.00 0.00 42.00 1.28
253 254 5.163622 GCTTCAACTTGCCTATTGCTCATAA 60.164 40.000 0.00 0.00 42.00 1.90
254 255 4.336433 GCTTCAACTTGCCTATTGCTCATA 59.664 41.667 0.00 0.00 42.00 2.15
255 256 3.129988 GCTTCAACTTGCCTATTGCTCAT 59.870 43.478 0.00 0.00 42.00 2.90
256 257 2.489329 GCTTCAACTTGCCTATTGCTCA 59.511 45.455 0.00 0.00 42.00 4.26
257 258 2.476854 CGCTTCAACTTGCCTATTGCTC 60.477 50.000 0.00 0.00 42.00 4.26
258 259 1.470098 CGCTTCAACTTGCCTATTGCT 59.530 47.619 0.00 0.00 42.00 3.91
259 260 1.468520 TCGCTTCAACTTGCCTATTGC 59.531 47.619 0.00 0.00 41.77 3.56
260 261 5.484173 TTATCGCTTCAACTTGCCTATTG 57.516 39.130 0.00 0.00 0.00 1.90
261 262 7.282224 TGTTATTATCGCTTCAACTTGCCTATT 59.718 33.333 0.00 0.00 0.00 1.73
262 263 6.765989 TGTTATTATCGCTTCAACTTGCCTAT 59.234 34.615 0.00 0.00 0.00 2.57
263 264 6.110033 TGTTATTATCGCTTCAACTTGCCTA 58.890 36.000 0.00 0.00 0.00 3.93
264 265 4.941263 TGTTATTATCGCTTCAACTTGCCT 59.059 37.500 0.00 0.00 0.00 4.75
265 266 5.064707 TCTGTTATTATCGCTTCAACTTGCC 59.935 40.000 0.00 0.00 0.00 4.52
266 267 6.106877 TCTGTTATTATCGCTTCAACTTGC 57.893 37.500 0.00 0.00 0.00 4.01
267 268 8.948853 TTTTCTGTTATTATCGCTTCAACTTG 57.051 30.769 0.00 0.00 0.00 3.16
295 296 9.542462 CCCTCGTTAAAACTTGATATTCTATGA 57.458 33.333 0.00 0.00 0.00 2.15
296 297 9.542462 TCCCTCGTTAAAACTTGATATTCTATG 57.458 33.333 0.00 0.00 0.00 2.23
298 299 9.947433 TTTCCCTCGTTAAAACTTGATATTCTA 57.053 29.630 0.00 0.00 0.00 2.10
299 300 8.857694 TTTCCCTCGTTAAAACTTGATATTCT 57.142 30.769 0.00 0.00 0.00 2.40
300 301 8.727910 ACTTTCCCTCGTTAAAACTTGATATTC 58.272 33.333 0.00 0.00 0.00 1.75
313 314 7.149973 CCGAATATTCATACTTTCCCTCGTTA 58.850 38.462 15.57 0.00 0.00 3.18
358 359 3.053619 CAGCCTTCCTAACTTTACCCCAT 60.054 47.826 0.00 0.00 0.00 4.00
359 360 2.307686 CAGCCTTCCTAACTTTACCCCA 59.692 50.000 0.00 0.00 0.00 4.96
372 377 0.392461 TTCGCCATACACAGCCTTCC 60.392 55.000 0.00 0.00 0.00 3.46
373 378 0.727398 GTTCGCCATACACAGCCTTC 59.273 55.000 0.00 0.00 0.00 3.46
382 387 3.867493 GTGTAAACCTAGGTTCGCCATAC 59.133 47.826 27.24 22.88 40.60 2.39
396 401 6.966021 ACAATGTAGATGTTGTGTGTAAACC 58.034 36.000 0.00 0.00 37.19 3.27
417 422 9.638239 GGAATGCTTCTATAATGTTTTGAACAA 57.362 29.630 0.00 0.00 45.86 2.83
419 424 8.181573 TCGGAATGCTTCTATAATGTTTTGAAC 58.818 33.333 0.00 0.00 0.00 3.18
421 426 7.857734 TCGGAATGCTTCTATAATGTTTTGA 57.142 32.000 0.00 0.00 0.00 2.69
440 445 3.791245 AGCAAGCAAAATTGTTTCGGAA 58.209 36.364 0.00 0.00 32.56 4.30
443 448 3.119463 CCGTAGCAAGCAAAATTGTTTCG 59.881 43.478 0.00 0.00 35.20 3.46
450 455 3.877508 GGTAGATCCGTAGCAAGCAAAAT 59.122 43.478 0.00 0.00 0.00 1.82
456 461 2.365617 ACCATGGTAGATCCGTAGCAAG 59.634 50.000 18.10 0.00 39.52 4.01
476 481 0.239879 CGGGTACATGCCACAACAAC 59.760 55.000 0.00 0.00 0.00 3.32
495 500 3.418684 TTCTAGAGAAAAGGGTGTGCC 57.581 47.619 0.00 0.00 0.00 5.01
598 603 4.389992 TGACAATTTTCTGTTGCGCAAAAA 59.610 33.333 26.87 21.21 0.00 1.94
599 604 3.928992 TGACAATTTTCTGTTGCGCAAAA 59.071 34.783 26.87 20.01 0.00 2.44
600 605 3.515630 TGACAATTTTCTGTTGCGCAAA 58.484 36.364 26.87 14.12 0.00 3.68
601 606 3.156511 TGACAATTTTCTGTTGCGCAA 57.843 38.095 21.02 21.02 0.00 4.85
602 607 2.859526 TGACAATTTTCTGTTGCGCA 57.140 40.000 5.66 5.66 0.00 6.09
603 608 3.983344 AGAATGACAATTTTCTGTTGCGC 59.017 39.130 0.00 0.00 31.15 6.09
604 609 4.319115 CGAGAATGACAATTTTCTGTTGCG 59.681 41.667 0.00 0.00 32.46 4.85
605 610 5.116074 CACGAGAATGACAATTTTCTGTTGC 59.884 40.000 0.00 0.00 32.46 4.17
606 611 6.358030 GTCACGAGAATGACAATTTTCTGTTG 59.642 38.462 1.08 0.00 46.89 3.33
607 612 6.430451 GTCACGAGAATGACAATTTTCTGTT 58.570 36.000 1.08 0.00 46.89 3.16
608 613 5.990408 GTCACGAGAATGACAATTTTCTGT 58.010 37.500 1.08 0.00 46.89 3.41
652 657 9.822185 AGACAATTTTCTTTAGCAAATCAAACT 57.178 25.926 0.00 0.00 0.00 2.66
705 711 3.181494 TGCTGATCATGCCAAATCGAAAG 60.181 43.478 12.62 0.00 0.00 2.62
706 712 2.754002 TGCTGATCATGCCAAATCGAAA 59.246 40.909 12.62 0.00 0.00 3.46
709 716 2.855660 TTGCTGATCATGCCAAATCG 57.144 45.000 12.62 0.00 0.00 3.34
841 853 2.830186 TTTAGCGCCCCACCACCATC 62.830 60.000 2.29 0.00 0.00 3.51
843 855 3.134703 TTTTAGCGCCCCACCACCA 62.135 57.895 2.29 0.00 0.00 4.17
844 856 2.282603 TTTTAGCGCCCCACCACC 60.283 61.111 2.29 0.00 0.00 4.61
845 857 0.891904 TTCTTTTAGCGCCCCACCAC 60.892 55.000 2.29 0.00 0.00 4.16
921 933 5.470047 TCGCCTTTCTCTTACTTCTTCTT 57.530 39.130 0.00 0.00 0.00 2.52
922 934 5.656480 GATCGCCTTTCTCTTACTTCTTCT 58.344 41.667 0.00 0.00 0.00 2.85
923 935 4.501198 CGATCGCCTTTCTCTTACTTCTTC 59.499 45.833 0.26 0.00 0.00 2.87
980 992 1.272490 TGTCCGACTCAGTGGTGATTC 59.728 52.381 0.00 0.00 30.18 2.52
982 994 0.603569 GTGTCCGACTCAGTGGTGAT 59.396 55.000 0.00 0.00 30.18 3.06
983 995 1.461091 GGTGTCCGACTCAGTGGTGA 61.461 60.000 0.00 0.00 0.00 4.02
984 996 1.006102 GGTGTCCGACTCAGTGGTG 60.006 63.158 0.00 0.00 0.00 4.17
985 997 3.456317 GGTGTCCGACTCAGTGGT 58.544 61.111 0.00 0.00 0.00 4.16
1002 1014 3.103911 GTTGGCGTGTCCGAGTCG 61.104 66.667 5.29 5.29 37.80 4.18
1112 1128 0.387750 CTGCTCCGCCTTTTTGCTTC 60.388 55.000 0.00 0.00 0.00 3.86
1126 1142 0.520847 GCTTTGGTCTTGCTCTGCTC 59.479 55.000 0.00 0.00 0.00 4.26
1127 1143 1.233285 CGCTTTGGTCTTGCTCTGCT 61.233 55.000 0.00 0.00 0.00 4.24
1128 1144 1.208614 CGCTTTGGTCTTGCTCTGC 59.791 57.895 0.00 0.00 0.00 4.26
1129 1145 1.871772 CCGCTTTGGTCTTGCTCTG 59.128 57.895 0.00 0.00 0.00 3.35
1130 1146 1.968540 GCCGCTTTGGTCTTGCTCT 60.969 57.895 0.00 0.00 41.21 4.09
1540 1568 5.719563 AGACCTCCAAAAAGAACAAGGAAAA 59.280 36.000 0.00 0.00 0.00 2.29
1592 1620 1.229209 TCTCGGCCTCTCCCAAACT 60.229 57.895 0.00 0.00 0.00 2.66
1599 1627 1.281899 CAAAATCGTCTCGGCCTCTC 58.718 55.000 0.00 0.00 0.00 3.20
1631 1659 4.002982 CTCGATGTTCCATTTCACCAAGA 58.997 43.478 0.00 0.00 0.00 3.02
1644 1672 6.807789 AGTAGTCCCTAATTTCTCGATGTTC 58.192 40.000 0.00 0.00 0.00 3.18
1661 1689 6.051646 TCGCAAAAACAAAAGTAGTAGTCC 57.948 37.500 0.00 0.00 0.00 3.85
1674 1710 8.788806 TCTAATTCCTCTAATTTCGCAAAAACA 58.211 29.630 0.00 0.00 38.71 2.83
1705 1741 3.307242 CGGTGACAAGAAATACTAGCAGC 59.693 47.826 0.00 0.00 0.00 5.25
1770 1806 8.464404 ACAAGTTTAGTTTTTAGGAAAGGACAC 58.536 33.333 0.00 0.00 0.00 3.67
1771 1807 8.463607 CACAAGTTTAGTTTTTAGGAAAGGACA 58.536 33.333 0.00 0.00 0.00 4.02
1772 1808 8.464404 ACACAAGTTTAGTTTTTAGGAAAGGAC 58.536 33.333 0.00 0.00 0.00 3.85
1773 1809 8.584063 ACACAAGTTTAGTTTTTAGGAAAGGA 57.416 30.769 0.00 0.00 0.00 3.36
1774 1810 9.297586 GAACACAAGTTTAGTTTTTAGGAAAGG 57.702 33.333 0.00 0.00 38.30 3.11
1784 1820 8.708742 GCAAAAGAAAGAACACAAGTTTAGTTT 58.291 29.630 0.00 0.00 38.30 2.66
1785 1821 8.088365 AGCAAAAGAAAGAACACAAGTTTAGTT 58.912 29.630 0.00 0.00 38.30 2.24
1786 1822 7.542130 CAGCAAAAGAAAGAACACAAGTTTAGT 59.458 33.333 0.00 0.00 38.30 2.24
1787 1823 7.754924 TCAGCAAAAGAAAGAACACAAGTTTAG 59.245 33.333 0.00 0.00 38.30 1.85
1788 1824 7.598278 TCAGCAAAAGAAAGAACACAAGTTTA 58.402 30.769 0.00 0.00 38.30 2.01
1789 1825 6.454795 TCAGCAAAAGAAAGAACACAAGTTT 58.545 32.000 0.00 0.00 38.30 2.66
1790 1826 6.024552 TCAGCAAAAGAAAGAACACAAGTT 57.975 33.333 0.00 0.00 41.64 2.66
1791 1827 5.643379 TCAGCAAAAGAAAGAACACAAGT 57.357 34.783 0.00 0.00 0.00 3.16
1792 1828 6.949578 TTTCAGCAAAAGAAAGAACACAAG 57.050 33.333 0.00 0.00 31.79 3.16
1793 1829 7.903995 AATTTCAGCAAAAGAAAGAACACAA 57.096 28.000 0.00 0.00 38.27 3.33
1794 1830 7.148440 CCAAATTTCAGCAAAAGAAAGAACACA 60.148 33.333 0.00 0.00 38.27 3.72
1795 1831 7.182089 CCAAATTTCAGCAAAAGAAAGAACAC 58.818 34.615 0.00 0.00 38.27 3.32
1915 1962 2.987821 GTCTCCGTGTAGCTTCAAGTTC 59.012 50.000 5.63 0.00 0.00 3.01
1918 1965 2.724977 TGTCTCCGTGTAGCTTCAAG 57.275 50.000 0.00 0.00 0.00 3.02
1956 2003 5.741388 ATTCACTTTAATCGCATCTGGAC 57.259 39.130 0.00 0.00 0.00 4.02
1999 2046 5.423886 TGTTTCAGGGGAAAACAAATGTTC 58.576 37.500 0.00 0.00 44.18 3.18
2035 2090 1.382522 ATGTGCCAAGAAGCGTATGG 58.617 50.000 0.33 0.33 37.29 2.74
2096 2151 5.416271 TCACCATGTTAGGTTAGAGTTCC 57.584 43.478 0.00 0.00 40.77 3.62
2097 2152 5.875359 CCTTCACCATGTTAGGTTAGAGTTC 59.125 44.000 0.00 0.00 40.77 3.01
2098 2153 5.546499 TCCTTCACCATGTTAGGTTAGAGTT 59.454 40.000 0.00 0.00 40.77 3.01
2099 2154 5.091552 TCCTTCACCATGTTAGGTTAGAGT 58.908 41.667 0.00 0.00 40.77 3.24
2100 2155 5.677319 TCCTTCACCATGTTAGGTTAGAG 57.323 43.478 0.00 0.00 40.77 2.43
2101 2156 6.043938 ACTTTCCTTCACCATGTTAGGTTAGA 59.956 38.462 0.00 0.00 40.77 2.10
2102 2157 6.238648 ACTTTCCTTCACCATGTTAGGTTAG 58.761 40.000 0.00 0.00 40.77 2.34
2103 2158 6.183361 TGACTTTCCTTCACCATGTTAGGTTA 60.183 38.462 0.00 0.00 40.77 2.85
2104 2159 5.061721 ACTTTCCTTCACCATGTTAGGTT 57.938 39.130 0.00 0.00 40.77 3.50
2105 2160 4.104102 TGACTTTCCTTCACCATGTTAGGT 59.896 41.667 0.00 0.00 44.48 3.08
2106 2161 4.455877 GTGACTTTCCTTCACCATGTTAGG 59.544 45.833 0.00 0.00 37.93 2.69
2107 2162 5.613358 GTGACTTTCCTTCACCATGTTAG 57.387 43.478 0.00 0.00 37.93 2.34
2115 2170 0.586802 GCACGGTGACTTTCCTTCAC 59.413 55.000 13.29 0.00 42.35 3.18
2116 2171 0.468226 AGCACGGTGACTTTCCTTCA 59.532 50.000 13.29 0.00 0.00 3.02
2117 2172 2.450609 TAGCACGGTGACTTTCCTTC 57.549 50.000 13.29 0.00 0.00 3.46
2118 2173 3.514309 ACTATAGCACGGTGACTTTCCTT 59.486 43.478 13.29 0.00 0.00 3.36
2119 2174 3.097614 ACTATAGCACGGTGACTTTCCT 58.902 45.455 13.29 0.48 0.00 3.36
2120 2175 3.187700 CACTATAGCACGGTGACTTTCC 58.812 50.000 13.29 0.00 33.32 3.13
2121 2176 3.846360 ACACTATAGCACGGTGACTTTC 58.154 45.455 13.29 0.00 35.28 2.62
2122 2177 3.955650 ACACTATAGCACGGTGACTTT 57.044 42.857 13.29 6.55 35.28 2.66
2123 2178 3.955650 AACACTATAGCACGGTGACTT 57.044 42.857 13.29 0.00 35.28 3.01
2124 2179 3.955650 AAACACTATAGCACGGTGACT 57.044 42.857 13.29 10.94 35.28 3.41
2125 2180 4.561606 CACTAAACACTATAGCACGGTGAC 59.438 45.833 13.29 3.33 35.28 3.67
2126 2181 4.219070 ACACTAAACACTATAGCACGGTGA 59.781 41.667 13.29 0.00 35.28 4.02
2127 2182 4.491676 ACACTAAACACTATAGCACGGTG 58.508 43.478 3.15 3.15 37.05 4.94
2128 2183 4.796038 ACACTAAACACTATAGCACGGT 57.204 40.909 0.00 0.00 0.00 4.83
2129 2184 7.585286 TTTTACACTAAACACTATAGCACGG 57.415 36.000 0.00 0.00 0.00 4.94
2130 2185 8.865978 TCATTTTACACTAAACACTATAGCACG 58.134 33.333 0.00 0.00 0.00 5.34
2138 2193 8.974060 TCCTTCTTCATTTTACACTAAACACT 57.026 30.769 0.00 0.00 0.00 3.55
2145 2200 9.067986 CCTAACTTTCCTTCTTCATTTTACACT 57.932 33.333 0.00 0.00 0.00 3.55
2146 2201 8.297426 CCCTAACTTTCCTTCTTCATTTTACAC 58.703 37.037 0.00 0.00 0.00 2.90
2147 2202 8.002459 ACCCTAACTTTCCTTCTTCATTTTACA 58.998 33.333 0.00 0.00 0.00 2.41
2148 2203 8.405418 ACCCTAACTTTCCTTCTTCATTTTAC 57.595 34.615 0.00 0.00 0.00 2.01
2149 2204 8.445588 AGACCCTAACTTTCCTTCTTCATTTTA 58.554 33.333 0.00 0.00 0.00 1.52
2150 2205 7.231519 CAGACCCTAACTTTCCTTCTTCATTTT 59.768 37.037 0.00 0.00 0.00 1.82
2151 2206 6.717084 CAGACCCTAACTTTCCTTCTTCATTT 59.283 38.462 0.00 0.00 0.00 2.32
2152 2207 6.183361 ACAGACCCTAACTTTCCTTCTTCATT 60.183 38.462 0.00 0.00 0.00 2.57
2153 2208 5.310857 ACAGACCCTAACTTTCCTTCTTCAT 59.689 40.000 0.00 0.00 0.00 2.57
2154 2209 4.658901 ACAGACCCTAACTTTCCTTCTTCA 59.341 41.667 0.00 0.00 0.00 3.02
2155 2210 5.230323 ACAGACCCTAACTTTCCTTCTTC 57.770 43.478 0.00 0.00 0.00 2.87
2156 2211 5.648330 AACAGACCCTAACTTTCCTTCTT 57.352 39.130 0.00 0.00 0.00 2.52
2157 2212 5.845065 ACTAACAGACCCTAACTTTCCTTCT 59.155 40.000 0.00 0.00 0.00 2.85
2158 2213 6.111669 ACTAACAGACCCTAACTTTCCTTC 57.888 41.667 0.00 0.00 0.00 3.46
2159 2214 7.015064 TCTACTAACAGACCCTAACTTTCCTT 58.985 38.462 0.00 0.00 0.00 3.36
2160 2215 6.559429 TCTACTAACAGACCCTAACTTTCCT 58.441 40.000 0.00 0.00 0.00 3.36
2161 2216 6.847421 TCTACTAACAGACCCTAACTTTCC 57.153 41.667 0.00 0.00 0.00 3.13
2169 2224 9.357161 CTGACTAATTATCTACTAACAGACCCT 57.643 37.037 0.00 0.00 0.00 4.34
2170 2225 9.134055 ACTGACTAATTATCTACTAACAGACCC 57.866 37.037 0.00 0.00 0.00 4.46
2252 2307 9.761504 ACATACAAACAAATTGATGATGAAACA 57.238 25.926 0.00 0.00 41.85 2.83
2291 2346 9.936759 TTGTAAATTGATGATCTACTGTGTACA 57.063 29.630 0.00 0.00 0.00 2.90
2381 2436 7.931275 ACATTGTGAAGGAAAGTTAGAGAAAC 58.069 34.615 0.00 0.00 38.46 2.78
2382 2437 8.519799 AACATTGTGAAGGAAAGTTAGAGAAA 57.480 30.769 0.00 0.00 0.00 2.52
2383 2438 9.273016 CTAACATTGTGAAGGAAAGTTAGAGAA 57.727 33.333 0.00 0.00 39.29 2.87
2384 2439 8.647796 TCTAACATTGTGAAGGAAAGTTAGAGA 58.352 33.333 0.00 0.00 40.27 3.10
2385 2440 8.833231 TCTAACATTGTGAAGGAAAGTTAGAG 57.167 34.615 0.00 0.00 40.27 2.43
2386 2441 7.878127 CCTCTAACATTGTGAAGGAAAGTTAGA 59.122 37.037 0.00 0.00 41.85 2.10
2387 2442 7.878127 TCCTCTAACATTGTGAAGGAAAGTTAG 59.122 37.037 10.89 0.00 38.67 2.34
2388 2443 7.741785 TCCTCTAACATTGTGAAGGAAAGTTA 58.258 34.615 10.89 0.00 0.00 2.24
2389 2444 6.601332 TCCTCTAACATTGTGAAGGAAAGTT 58.399 36.000 10.89 0.00 0.00 2.66
2390 2445 6.187727 TCCTCTAACATTGTGAAGGAAAGT 57.812 37.500 10.89 0.00 0.00 2.66
2391 2446 7.413438 CGAATCCTCTAACATTGTGAAGGAAAG 60.413 40.741 15.19 8.67 0.00 2.62
2392 2447 6.371548 CGAATCCTCTAACATTGTGAAGGAAA 59.628 38.462 15.19 0.13 0.00 3.13
2393 2448 5.874810 CGAATCCTCTAACATTGTGAAGGAA 59.125 40.000 15.19 4.27 0.00 3.36
2394 2449 5.419542 CGAATCCTCTAACATTGTGAAGGA 58.580 41.667 14.12 14.12 0.00 3.36
2395 2450 4.572389 CCGAATCCTCTAACATTGTGAAGG 59.428 45.833 6.18 6.18 0.00 3.46
2396 2451 5.178797 ACCGAATCCTCTAACATTGTGAAG 58.821 41.667 0.00 0.00 0.00 3.02
2397 2452 5.160607 ACCGAATCCTCTAACATTGTGAA 57.839 39.130 0.00 0.00 0.00 3.18
2398 2453 4.819105 ACCGAATCCTCTAACATTGTGA 57.181 40.909 0.00 0.00 0.00 3.58
2399 2454 4.332819 GGAACCGAATCCTCTAACATTGTG 59.667 45.833 0.00 0.00 36.50 3.33
2400 2455 4.514401 GGAACCGAATCCTCTAACATTGT 58.486 43.478 0.00 0.00 36.50 2.71
2401 2456 3.555956 CGGAACCGAATCCTCTAACATTG 59.444 47.826 7.53 0.00 42.83 2.82
2402 2457 3.793559 CGGAACCGAATCCTCTAACATT 58.206 45.455 7.53 0.00 42.83 2.71
2403 2458 2.483188 GCGGAACCGAATCCTCTAACAT 60.483 50.000 17.63 0.00 42.83 2.71
2404 2459 1.134907 GCGGAACCGAATCCTCTAACA 60.135 52.381 17.63 0.00 42.83 2.41
2405 2460 1.134907 TGCGGAACCGAATCCTCTAAC 60.135 52.381 17.63 0.00 42.83 2.34
2406 2461 1.187974 TGCGGAACCGAATCCTCTAA 58.812 50.000 17.63 0.00 42.83 2.10
2407 2462 1.340248 GATGCGGAACCGAATCCTCTA 59.660 52.381 20.04 0.00 45.95 2.43
2408 2463 0.105039 GATGCGGAACCGAATCCTCT 59.895 55.000 20.04 0.00 45.95 3.69
2409 2464 2.606275 GATGCGGAACCGAATCCTC 58.394 57.895 20.04 0.74 45.95 3.71
2410 2465 4.857251 GATGCGGAACCGAATCCT 57.143 55.556 20.04 0.00 45.95 3.24
2413 2468 2.104111 TGGAATAGATGCGGAACCGAAT 59.896 45.455 17.63 12.22 40.96 3.34
2414 2469 1.483004 TGGAATAGATGCGGAACCGAA 59.517 47.619 17.63 6.95 42.83 4.30
2415 2470 1.116308 TGGAATAGATGCGGAACCGA 58.884 50.000 17.63 2.87 42.83 4.69
2416 2471 2.069273 GATGGAATAGATGCGGAACCG 58.931 52.381 9.00 9.00 43.09 4.44
2417 2472 2.039084 AGGATGGAATAGATGCGGAACC 59.961 50.000 0.00 0.00 0.00 3.62
2418 2473 3.070018 CAGGATGGAATAGATGCGGAAC 58.930 50.000 0.00 0.00 0.00 3.62
2419 2474 2.705658 ACAGGATGGAATAGATGCGGAA 59.294 45.455 0.00 0.00 43.62 4.30
2420 2475 2.329267 ACAGGATGGAATAGATGCGGA 58.671 47.619 0.00 0.00 43.62 5.54
2421 2476 2.847327 ACAGGATGGAATAGATGCGG 57.153 50.000 0.00 0.00 43.62 5.69
2488 2543 0.672711 GAAACCTGGCACCGGTAGAC 60.673 60.000 6.87 4.58 33.53 2.59
2532 2592 0.956410 CACTCTCCCTCACGAGACGT 60.956 60.000 0.00 0.00 42.36 4.34
2629 2689 6.680131 GCATCCATGGAATTTTCATTCACGTA 60.680 38.462 20.67 0.00 40.77 3.57
2641 2701 1.315690 CTGAGCGCATCCATGGAATT 58.684 50.000 20.67 0.00 0.00 2.17
2659 2720 3.064900 GACAGAAGATTTGTCCAGCCT 57.935 47.619 0.00 0.00 39.17 4.58
2701 2762 3.408634 AGTTTGTCAAATACGACCCTGG 58.591 45.455 0.40 0.00 34.88 4.45
2758 2819 3.560503 CAACCGAAAATGTACGTGCATT 58.439 40.909 23.86 23.86 40.43 3.56
2892 2966 6.834168 TCAGATGGACATATATTGCGTCTA 57.166 37.500 9.26 2.15 0.00 2.59
2950 3025 4.903054 TCAGTCGTACAAGGAGAGAGTAA 58.097 43.478 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.