Multiple sequence alignment - TraesCS2D01G515600

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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 TraesCS2D01G515600 chr2D 100.000 2946 0 0 1 2946 606708268 606711213 0.000000e+00 5441.0
1 TraesCS2D01G515600 chr2D 85.294 102 15 0 1475 1576 590146506 590146607 4.020000e-19 106.0
2 TraesCS2D01G515600 chr2A 90.715 1594 94 22 546 2129 738371302 738372851 0.000000e+00 2074.0
3 TraesCS2D01G515600 chr2A 92.308 520 25 10 2240 2752 738372850 738373361 0.000000e+00 725.0
4 TraesCS2D01G515600 chr2A 88.249 417 48 1 124 540 738369352 738369767 5.670000e-137 497.0
5 TraesCS2D01G515600 chr2A 92.308 208 8 3 2747 2946 738373453 738373660 3.710000e-74 289.0
6 TraesCS2D01G515600 chr2B 88.758 1103 58 25 637 1693 740321871 740320789 0.000000e+00 1290.0
7 TraesCS2D01G515600 chr2B 86.058 416 37 9 1730 2137 740320605 740320203 7.550000e-116 427.0
8 TraesCS2D01G515600 chr1A 83.770 191 29 2 1388 1577 33398711 33398522 2.330000e-41 180.0
9 TraesCS2D01G515600 chr1D 83.246 191 30 2 1388 1577 35060893 35060704 1.090000e-39 174.0
10 TraesCS2D01G515600 chr1B 83.158 190 32 0 1388 1577 53365663 53365474 1.090000e-39 174.0
11 TraesCS2D01G515600 chr3D 82.877 146 19 6 384 527 522957611 522957470 3.080000e-25 126.0
12 TraesCS2D01G515600 chr5D 78.689 183 37 2 1392 1573 254023397 254023578 1.430000e-23 121.0
13 TraesCS2D01G515600 chr5A 78.689 183 37 2 1392 1573 336950088 336950269 1.430000e-23 121.0
14 TraesCS2D01G515600 chr5A 100.000 31 0 0 484 514 398721407 398721377 1.140000e-04 58.4
15 TraesCS2D01G515600 chr5B 78.142 183 38 2 1392 1573 288892889 288892708 6.670000e-22 115.0
16 TraesCS2D01G515600 chr4D 85.135 74 9 2 453 526 466381908 466381837 1.130000e-09 75.0


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 TraesCS2D01G515600 chr2D 606708268 606711213 2945 False 5441.00 5441 100.000 1 2946 1 chr2D.!!$F2 2945
1 TraesCS2D01G515600 chr2A 738369352 738373660 4308 False 896.25 2074 90.895 124 2946 4 chr2A.!!$F1 2822
2 TraesCS2D01G515600 chr2B 740320203 740321871 1668 True 858.50 1290 87.408 637 2137 2 chr2B.!!$R1 1500

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
675 2209 0.094046 GCGTACGTCGTGAATTTGGG 59.906 55.0 17.9 0.0 42.13 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2000 3741 0.03467 GGCTCCATCCAGGCATATCC 60.035 60.0 0.0 0.0 38.83 2.59 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
42 43 6.573617 AAAAAGTTTGTCGAATTCTTGCTG 57.426 33.333 3.52 0.00 0.00 4.41
43 44 3.904136 AGTTTGTCGAATTCTTGCTGG 57.096 42.857 3.52 0.00 0.00 4.85
44 45 3.476552 AGTTTGTCGAATTCTTGCTGGA 58.523 40.909 3.52 0.00 0.00 3.86
45 46 3.882888 AGTTTGTCGAATTCTTGCTGGAA 59.117 39.130 3.52 0.00 0.00 3.53
46 47 4.520492 AGTTTGTCGAATTCTTGCTGGAAT 59.480 37.500 3.52 0.17 37.51 3.01
47 48 5.010012 AGTTTGTCGAATTCTTGCTGGAATT 59.990 36.000 14.13 14.13 45.19 2.17
48 49 5.452078 TTGTCGAATTCTTGCTGGAATTT 57.548 34.783 14.96 4.03 43.36 1.82
49 50 4.797471 TGTCGAATTCTTGCTGGAATTTG 58.203 39.130 17.99 17.99 43.36 2.32
50 51 4.168760 GTCGAATTCTTGCTGGAATTTGG 58.831 43.478 21.03 14.89 43.36 3.28
51 52 2.925563 CGAATTCTTGCTGGAATTTGGC 59.074 45.455 17.06 7.57 43.36 4.52
52 53 2.660189 ATTCTTGCTGGAATTTGGCG 57.340 45.000 0.17 0.00 32.69 5.69
53 54 0.602562 TTCTTGCTGGAATTTGGCGG 59.397 50.000 0.00 0.00 0.00 6.13
54 55 1.446618 CTTGCTGGAATTTGGCGGC 60.447 57.895 0.00 0.00 0.00 6.53
55 56 3.279974 TTGCTGGAATTTGGCGGCG 62.280 57.895 0.51 0.51 0.00 6.46
56 57 4.496927 GCTGGAATTTGGCGGCGG 62.497 66.667 9.78 0.00 0.00 6.13
57 58 3.825611 CTGGAATTTGGCGGCGGG 61.826 66.667 9.78 0.00 0.00 6.13
58 59 4.352607 TGGAATTTGGCGGCGGGA 62.353 61.111 9.78 0.00 0.00 5.14
59 60 3.822192 GGAATTTGGCGGCGGGAC 61.822 66.667 9.78 0.00 0.00 4.46
103 104 2.380081 CGGAGGTACGGAATGTTGC 58.620 57.895 0.00 0.00 0.00 4.17
105 106 1.087771 GGAGGTACGGAATGTTGCGG 61.088 60.000 11.20 0.00 46.70 5.69
106 107 1.078708 AGGTACGGAATGTTGCGGG 60.079 57.895 11.20 0.00 46.70 6.13
107 108 2.110352 GGTACGGAATGTTGCGGGG 61.110 63.158 11.20 0.00 46.70 5.73
108 109 2.110352 GTACGGAATGTTGCGGGGG 61.110 63.158 11.20 0.00 46.70 5.40
139 140 1.370900 GCAAGCAACCGAGCAACAG 60.371 57.895 0.00 0.00 36.85 3.16
181 182 3.843027 AGAGAGGGAATCTTTTGCTGAGA 59.157 43.478 0.00 0.00 38.84 3.27
215 216 0.173481 TCATCTTTGAGAGGCGGTCG 59.827 55.000 0.00 0.00 0.00 4.79
218 219 1.758936 TCTTTGAGAGGCGGTCGATA 58.241 50.000 0.00 0.00 0.00 2.92
232 233 5.048507 GCGGTCGATACTTCTCCTAAATTT 58.951 41.667 0.00 0.00 0.00 1.82
258 259 4.708177 TGAGGAGTTCAAGGTTTTGAGAG 58.292 43.478 0.00 0.00 43.76 3.20
260 261 5.117406 AGGAGTTCAAGGTTTTGAGAGTT 57.883 39.130 0.00 0.00 43.76 3.01
269 270 2.994578 GGTTTTGAGAGTTCGACTAGGC 59.005 50.000 0.00 0.00 0.00 3.93
277 278 1.076332 GTTCGACTAGGCGCAACATT 58.924 50.000 14.83 0.00 0.00 2.71
309 310 8.992835 CCTAAAAAGGGATCAAAGAAAATCTG 57.007 34.615 0.00 0.00 0.00 2.90
311 312 9.987272 CTAAAAAGGGATCAAAGAAAATCTGTT 57.013 29.630 0.00 0.00 0.00 3.16
312 313 8.667076 AAAAAGGGATCAAAGAAAATCTGTTG 57.333 30.769 0.00 0.00 0.00 3.33
333 334 8.404107 TGTTGAGAATTAAACCCTTTTAGGAG 57.596 34.615 0.00 0.00 37.67 3.69
349 350 8.361889 CCTTTTAGGAGTTTAGCTAGAGATACC 58.638 40.741 0.00 0.00 37.67 2.73
353 354 5.836358 AGGAGTTTAGCTAGAGATACCCTTG 59.164 44.000 0.00 0.00 0.00 3.61
356 357 5.599242 AGTTTAGCTAGAGATACCCTTGGAC 59.401 44.000 0.00 0.00 0.00 4.02
365 366 4.897051 AGATACCCTTGGACAACCTCTAT 58.103 43.478 0.00 0.00 37.04 1.98
375 376 7.093289 CCTTGGACAACCTCTATTCTTCTAAGA 60.093 40.741 0.00 0.00 37.04 2.10
378 379 7.455008 TGGACAACCTCTATTCTTCTAAGAAGT 59.545 37.037 10.64 1.44 41.40 3.01
404 405 3.209091 GCTAGCTCAGTGGTAGGGA 57.791 57.895 7.70 0.00 44.48 4.20
416 417 1.691976 TGGTAGGGACACTGTCTTGTG 59.308 52.381 9.08 0.00 43.07 3.33
436 437 4.113815 CCAGGCCAGCCGGATTCA 62.114 66.667 5.05 0.00 41.95 2.57
465 466 4.746535 TGTGGAGCGAATATTTCTACCA 57.253 40.909 0.00 0.00 0.00 3.25
470 471 5.758296 TGGAGCGAATATTTCTACCATGTTC 59.242 40.000 0.00 0.00 0.00 3.18
471 472 5.107453 GGAGCGAATATTTCTACCATGTTCG 60.107 44.000 7.25 7.25 43.94 3.95
474 475 5.609696 GCGAATATTTCTACCATGTTCGTCG 60.610 44.000 11.70 0.00 43.37 5.12
475 476 5.609696 CGAATATTTCTACCATGTTCGTCGC 60.610 44.000 4.26 0.00 39.24 5.19
481 482 0.389948 ACCATGTTCGTCGCTCCTTC 60.390 55.000 0.00 0.00 0.00 3.46
482 483 1.084370 CCATGTTCGTCGCTCCTTCC 61.084 60.000 0.00 0.00 0.00 3.46
496 497 4.613622 CGCTCCTTCCATAAAAATATGCCG 60.614 45.833 0.00 0.00 0.00 5.69
501 502 3.761897 TCCATAAAAATATGCCGAGGGG 58.238 45.455 0.00 0.00 0.00 4.79
525 526 3.643554 CCCCTCCGGTCCCGTTTT 61.644 66.667 0.00 0.00 37.81 2.43
535 536 3.373130 CCGGTCCCGTTTTTCTATTCTTC 59.627 47.826 4.84 0.00 37.81 2.87
540 541 6.183360 GGTCCCGTTTTTCTATTCTTCTAAGC 60.183 42.308 0.00 0.00 0.00 3.09
541 542 6.370718 GTCCCGTTTTTCTATTCTTCTAAGCA 59.629 38.462 0.00 0.00 0.00 3.91
542 543 7.065923 GTCCCGTTTTTCTATTCTTCTAAGCAT 59.934 37.037 0.00 0.00 0.00 3.79
556 2086 9.777297 TTCTTCTAAGCATATATACAATGTGCA 57.223 29.630 9.00 0.00 38.23 4.57
561 2091 4.012374 GCATATATACAATGTGCAGCCCT 58.988 43.478 0.00 0.00 35.93 5.19
571 2101 2.124778 GCAGCCCTCTCCAAGAGC 60.125 66.667 0.00 0.00 40.98 4.09
572 2102 2.588989 CAGCCCTCTCCAAGAGCC 59.411 66.667 0.00 0.00 40.98 4.70
577 2107 2.057408 CCTCTCCAAGAGCCGAGCT 61.057 63.158 0.00 0.00 40.98 4.09
579 2109 0.383949 CTCTCCAAGAGCCGAGCTAC 59.616 60.000 0.00 0.00 39.88 3.58
580 2110 0.323451 TCTCCAAGAGCCGAGCTACA 60.323 55.000 0.00 0.00 39.88 2.74
581 2111 0.532573 CTCCAAGAGCCGAGCTACAA 59.467 55.000 0.00 0.00 39.88 2.41
604 2134 8.462811 ACAACGTCCAATGCAAATATACATTTA 58.537 29.630 0.00 0.00 34.32 1.40
606 2136 8.220755 ACGTCCAATGCAAATATACATTTAGT 57.779 30.769 0.00 0.00 34.32 2.24
607 2137 8.682710 ACGTCCAATGCAAATATACATTTAGTT 58.317 29.630 0.00 0.00 34.32 2.24
608 2138 9.515020 CGTCCAATGCAAATATACATTTAGTTT 57.485 29.630 0.00 0.00 34.32 2.66
611 2141 9.814899 CCAATGCAAATATACATTTAGTTTGGA 57.185 29.630 0.00 0.00 34.32 3.53
615 2145 9.800433 TGCAAATATACATTTAGTTTGGACATG 57.200 29.630 0.00 0.00 32.96 3.21
628 2158 1.002430 TGGACATGTTGGCTCAGAGTC 59.998 52.381 0.00 0.00 0.00 3.36
634 2164 0.514691 GTTGGCTCAGAGTCGCTTTG 59.485 55.000 0.00 0.00 0.00 2.77
654 2188 6.662414 TTTGGTATTAGCTTGTCAATCGAG 57.338 37.500 0.00 0.00 0.00 4.04
655 2189 5.592104 TGGTATTAGCTTGTCAATCGAGA 57.408 39.130 0.00 0.00 0.00 4.04
656 2190 5.592054 TGGTATTAGCTTGTCAATCGAGAG 58.408 41.667 0.00 0.00 0.00 3.20
675 2209 0.094046 GCGTACGTCGTGAATTTGGG 59.906 55.000 17.90 0.00 42.13 4.12
799 2340 2.240667 CCAATCTCCACATTCCCTGTCT 59.759 50.000 0.00 0.00 35.29 3.41
934 2495 2.210711 CGATCTCCACCTAGCCCCC 61.211 68.421 0.00 0.00 0.00 5.40
962 2523 1.087501 GAGCCAAATCTTCGTCCCAC 58.912 55.000 0.00 0.00 0.00 4.61
1022 2591 0.609662 AGGGTTCACCATTTGCATGC 59.390 50.000 11.82 11.82 43.89 4.06
1026 2595 2.815825 TTCACCATTTGCATGCGCCG 62.816 55.000 14.09 0.00 37.32 6.46
1083 2655 2.809601 GCTACTGCACCGTCCACG 60.810 66.667 0.00 0.00 39.41 4.94
1251 2823 1.070914 TGCACCGTCAGAAACCATACA 59.929 47.619 0.00 0.00 0.00 2.29
1263 2836 5.061808 CAGAAACCATACAGTACGCACTTAC 59.938 44.000 0.00 0.00 30.46 2.34
1298 2871 8.332996 TGTCTAGTGAAGTGGTAGTTAAGTAG 57.667 38.462 0.00 0.00 0.00 2.57
1299 2872 7.094463 TGTCTAGTGAAGTGGTAGTTAAGTAGC 60.094 40.741 11.77 11.77 0.00 3.58
1300 2873 7.121020 GTCTAGTGAAGTGGTAGTTAAGTAGCT 59.879 40.741 17.90 0.00 0.00 3.32
1301 2874 8.324306 TCTAGTGAAGTGGTAGTTAAGTAGCTA 58.676 37.037 17.90 0.00 0.00 3.32
1302 2875 7.393841 AGTGAAGTGGTAGTTAAGTAGCTAG 57.606 40.000 17.90 0.00 0.00 3.42
1303 2876 6.035217 GTGAAGTGGTAGTTAAGTAGCTAGC 58.965 44.000 17.90 6.62 37.80 3.42
1304 2877 5.950549 TGAAGTGGTAGTTAAGTAGCTAGCT 59.049 40.000 23.12 23.12 38.03 3.32
1305 2878 7.066766 GTGAAGTGGTAGTTAAGTAGCTAGCTA 59.933 40.741 20.67 20.67 38.03 3.32
1306 2879 7.282675 TGAAGTGGTAGTTAAGTAGCTAGCTAG 59.717 40.741 24.78 16.84 38.03 3.42
1363 2943 9.590451 AAGTGACATTGAAAATAAATATGCAGG 57.410 29.630 0.00 0.00 0.00 4.85
1364 2944 8.752187 AGTGACATTGAAAATAAATATGCAGGT 58.248 29.630 0.00 0.00 0.00 4.00
1560 3140 3.109847 GTTCCAGAACCACAAGGCA 57.890 52.632 0.00 0.00 39.06 4.75
1657 3240 4.124970 GGCGACCAAGGTACCTAATTAAG 58.875 47.826 16.67 6.83 0.00 1.85
1659 3243 3.800506 CGACCAAGGTACCTAATTAAGCG 59.199 47.826 16.67 9.18 0.00 4.68
1665 3249 6.338937 CAAGGTACCTAATTAAGCGAGAACT 58.661 40.000 16.67 0.00 0.00 3.01
1677 3261 0.782384 CGAGAACTACACGGTGCAAC 59.218 55.000 8.30 0.00 0.00 4.17
1693 3279 5.747197 CGGTGCAACTAATGGTTACTACTAG 59.253 44.000 0.00 0.00 36.23 2.57
1694 3280 6.626623 CGGTGCAACTAATGGTTACTACTAGT 60.627 42.308 0.00 0.00 36.23 2.57
1697 3283 9.298774 GTGCAACTAATGGTTACTACTAGTTAG 57.701 37.037 0.00 0.00 36.23 2.34
1760 3494 5.126067 ACAGCTACAATGTGTTTGTCTCTT 58.874 37.500 0.00 0.00 45.55 2.85
1791 3528 2.431057 GAGCCGGTGATAAGAAGGAAGA 59.569 50.000 1.90 0.00 0.00 2.87
1798 3535 5.059833 GGTGATAAGAAGGAAGATTGCGAT 58.940 41.667 0.00 0.00 0.00 4.58
1801 3538 5.987953 TGATAAGAAGGAAGATTGCGATGAG 59.012 40.000 0.00 0.00 0.00 2.90
1809 3546 1.145759 GATTGCGATGAGGCGACGAA 61.146 55.000 0.00 0.00 35.06 3.85
1810 3547 1.421410 ATTGCGATGAGGCGACGAAC 61.421 55.000 0.00 0.00 35.06 3.95
1819 3556 2.631428 GCGACGAACAGCTGCAAA 59.369 55.556 15.27 0.00 0.00 3.68
1834 3571 2.593148 AAACGGCGGTGCATGACA 60.593 55.556 13.24 0.00 0.00 3.58
1838 3575 2.438254 GGCGGTGCATGACATGGA 60.438 61.111 17.03 11.71 0.00 3.41
1840 3577 1.746615 GCGGTGCATGACATGGAGT 60.747 57.895 17.03 0.00 0.00 3.85
1842 3579 1.805254 GGTGCATGACATGGAGTGC 59.195 57.895 17.03 4.32 38.05 4.40
1843 3580 1.660560 GGTGCATGACATGGAGTGCC 61.661 60.000 17.03 8.27 36.79 5.01
1846 3583 2.124570 ATGACATGGAGTGCCGGC 60.125 61.111 22.73 22.73 36.79 6.13
1927 3664 2.342279 CTCTTCCCGTTGCGTCCA 59.658 61.111 0.00 0.00 0.00 4.02
1964 3701 2.378806 AGTTGTTGACTTCGTCGTACG 58.621 47.619 9.53 9.53 44.19 3.67
1998 3739 1.066215 ACTCCGTCTAACATGCATGCA 60.066 47.619 26.53 25.04 0.00 3.96
1999 3740 2.216046 CTCCGTCTAACATGCATGCAT 58.784 47.619 27.46 27.46 37.08 3.96
2099 3844 2.660189 AAAGCATGCATAGTTGTGGC 57.340 45.000 21.98 0.00 0.00 5.01
2127 3872 4.523173 TCAGTTTCCTACTAGTGGAGTGTG 59.477 45.833 7.98 9.25 39.39 3.82
2128 3873 4.281182 CAGTTTCCTACTAGTGGAGTGTGT 59.719 45.833 7.98 0.00 39.39 3.72
2129 3874 5.475909 CAGTTTCCTACTAGTGGAGTGTGTA 59.524 44.000 7.98 0.00 39.39 2.90
2130 3875 5.711036 AGTTTCCTACTAGTGGAGTGTGTAG 59.289 44.000 7.98 0.00 39.39 2.74
2131 3876 3.618351 TCCTACTAGTGGAGTGTGTAGC 58.382 50.000 7.98 0.00 39.39 3.58
2132 3877 3.009805 TCCTACTAGTGGAGTGTGTAGCA 59.990 47.826 7.98 0.00 39.39 3.49
2133 3878 3.954904 CCTACTAGTGGAGTGTGTAGCAT 59.045 47.826 7.98 0.00 39.39 3.79
2134 3879 4.402793 CCTACTAGTGGAGTGTGTAGCATT 59.597 45.833 7.98 0.00 39.39 3.56
2135 3880 4.457834 ACTAGTGGAGTGTGTAGCATTC 57.542 45.455 0.00 0.00 36.87 2.67
2136 3881 3.832490 ACTAGTGGAGTGTGTAGCATTCA 59.168 43.478 0.00 0.00 36.87 2.57
2137 3882 3.325293 AGTGGAGTGTGTAGCATTCAG 57.675 47.619 0.00 0.00 35.77 3.02
2138 3883 2.899900 AGTGGAGTGTGTAGCATTCAGA 59.100 45.455 0.00 0.00 35.77 3.27
2139 3884 3.517100 AGTGGAGTGTGTAGCATTCAGAT 59.483 43.478 0.00 0.00 35.77 2.90
2140 3885 3.620374 GTGGAGTGTGTAGCATTCAGATG 59.380 47.826 0.00 0.00 35.77 2.90
2141 3886 3.201290 GGAGTGTGTAGCATTCAGATGG 58.799 50.000 0.00 0.00 35.77 3.51
2142 3887 3.201290 GAGTGTGTAGCATTCAGATGGG 58.799 50.000 0.00 0.00 34.43 4.00
2143 3888 2.840038 AGTGTGTAGCATTCAGATGGGA 59.160 45.455 0.00 0.00 33.72 4.37
2144 3889 3.118482 AGTGTGTAGCATTCAGATGGGAG 60.118 47.826 0.00 0.00 33.72 4.30
2145 3890 2.171237 TGTGTAGCATTCAGATGGGAGG 59.829 50.000 0.00 0.00 33.72 4.30
2146 3891 2.435805 GTGTAGCATTCAGATGGGAGGA 59.564 50.000 0.00 0.00 33.72 3.71
2147 3892 3.114606 TGTAGCATTCAGATGGGAGGAA 58.885 45.455 0.00 0.00 33.72 3.36
2148 3893 2.725221 AGCATTCAGATGGGAGGAAC 57.275 50.000 0.00 0.00 33.72 3.62
2149 3894 2.203584 AGCATTCAGATGGGAGGAACT 58.796 47.619 0.00 0.00 35.74 3.01
2150 3895 2.092538 AGCATTCAGATGGGAGGAACTG 60.093 50.000 0.00 0.00 33.84 3.16
2151 3896 2.928334 CATTCAGATGGGAGGAACTGG 58.072 52.381 0.00 0.00 41.55 4.00
2152 3897 0.620556 TTCAGATGGGAGGAACTGGC 59.379 55.000 0.00 0.00 41.55 4.85
2153 3898 0.252881 TCAGATGGGAGGAACTGGCT 60.253 55.000 0.00 0.00 41.55 4.75
2154 3899 0.622665 CAGATGGGAGGAACTGGCTT 59.377 55.000 0.00 0.00 41.55 4.35
2155 3900 0.915364 AGATGGGAGGAACTGGCTTC 59.085 55.000 0.00 0.00 41.55 3.86
2161 3906 3.758172 GGAACTGGCTTCCGCAAA 58.242 55.556 0.00 0.00 39.36 3.68
2162 3907 2.037871 GGAACTGGCTTCCGCAAAA 58.962 52.632 0.00 0.00 39.36 2.44
2163 3908 0.387565 GGAACTGGCTTCCGCAAAAA 59.612 50.000 0.00 0.00 39.36 1.94
2200 3945 7.981475 AAAAAGAGGAACTAGCTAGGAGTAT 57.019 36.000 24.35 6.58 41.55 2.12
2201 3946 7.591421 AAAAGAGGAACTAGCTAGGAGTATC 57.409 40.000 24.35 14.50 41.55 2.24
2219 3964 6.063496 AGTATCCCCTAGACAAGTTTTTCC 57.937 41.667 0.00 0.00 0.00 3.13
2220 3965 5.791141 AGTATCCCCTAGACAAGTTTTTCCT 59.209 40.000 0.00 0.00 0.00 3.36
2221 3966 5.600669 ATCCCCTAGACAAGTTTTTCCTT 57.399 39.130 0.00 0.00 0.00 3.36
2222 3967 4.981812 TCCCCTAGACAAGTTTTTCCTTC 58.018 43.478 0.00 0.00 0.00 3.46
2223 3968 4.414182 TCCCCTAGACAAGTTTTTCCTTCA 59.586 41.667 0.00 0.00 0.00 3.02
2224 3969 4.519350 CCCCTAGACAAGTTTTTCCTTCAC 59.481 45.833 0.00 0.00 0.00 3.18
2225 3970 5.377478 CCCTAGACAAGTTTTTCCTTCACT 58.623 41.667 0.00 0.00 0.00 3.41
2226 3971 5.828328 CCCTAGACAAGTTTTTCCTTCACTT 59.172 40.000 0.00 0.00 0.00 3.16
2230 3975 3.769536 CAAGTTTTTCCTTCACTTGCGT 58.230 40.909 0.00 0.00 40.63 5.24
2231 3976 4.173256 CAAGTTTTTCCTTCACTTGCGTT 58.827 39.130 0.00 0.00 40.63 4.84
2232 3977 4.450082 AGTTTTTCCTTCACTTGCGTTT 57.550 36.364 0.00 0.00 0.00 3.60
2233 3978 5.570234 AGTTTTTCCTTCACTTGCGTTTA 57.430 34.783 0.00 0.00 0.00 2.01
2234 3979 6.144078 AGTTTTTCCTTCACTTGCGTTTAT 57.856 33.333 0.00 0.00 0.00 1.40
2235 3980 6.569780 AGTTTTTCCTTCACTTGCGTTTATT 58.430 32.000 0.00 0.00 0.00 1.40
2236 3981 7.708998 AGTTTTTCCTTCACTTGCGTTTATTA 58.291 30.769 0.00 0.00 0.00 0.98
2237 3982 7.860872 AGTTTTTCCTTCACTTGCGTTTATTAG 59.139 33.333 0.00 0.00 0.00 1.73
2238 3983 7.499321 TTTTCCTTCACTTGCGTTTATTAGA 57.501 32.000 0.00 0.00 0.00 2.10
2269 4014 8.270744 AGAGCTTGATCATTATTAGGTTCTTGT 58.729 33.333 0.00 0.00 0.00 3.16
2392 4138 0.392461 ACACGTGGAAGCAAGTGTGT 60.392 50.000 21.57 0.00 43.86 3.72
2422 4168 2.097541 GTCGCGTGTTACAAGAACAGTC 60.098 50.000 5.77 0.00 0.00 3.51
2423 4169 1.136992 CGCGTGTTACAAGAACAGTCG 60.137 52.381 1.88 0.00 0.00 4.18
2424 4170 2.121786 GCGTGTTACAAGAACAGTCGA 58.878 47.619 1.88 0.00 0.00 4.20
2425 4171 2.729882 GCGTGTTACAAGAACAGTCGAT 59.270 45.455 1.88 0.00 0.00 3.59
2426 4172 3.421826 GCGTGTTACAAGAACAGTCGATG 60.422 47.826 1.88 0.00 0.00 3.84
2427 4173 3.734231 CGTGTTACAAGAACAGTCGATGT 59.266 43.478 0.00 0.00 46.97 3.06
2438 4184 2.753452 ACAGTCGATGTGGTACGATCTT 59.247 45.455 0.00 0.00 41.91 2.40
2439 4185 3.943381 ACAGTCGATGTGGTACGATCTTA 59.057 43.478 0.00 0.00 41.91 2.10
2440 4186 4.201891 ACAGTCGATGTGGTACGATCTTAC 60.202 45.833 0.76 0.76 41.91 2.34
2441 4187 4.035324 CAGTCGATGTGGTACGATCTTACT 59.965 45.833 9.04 0.00 40.50 2.24
2442 4188 4.272991 AGTCGATGTGGTACGATCTTACTC 59.727 45.833 9.04 4.38 40.50 2.59
2523 4269 0.179073 CCGGGTCACATGAGTCATCC 60.179 60.000 1.56 1.11 0.00 3.51
2524 4270 0.826715 CGGGTCACATGAGTCATCCT 59.173 55.000 1.56 0.00 0.00 3.24
2532 4278 4.276926 TCACATGAGTCATCCTGTCGATAG 59.723 45.833 1.56 1.54 32.64 2.08
2536 4282 3.815962 TGAGTCATCCTGTCGATAGTAGC 59.184 47.826 8.47 0.00 37.40 3.58
2538 4284 4.402829 AGTCATCCTGTCGATAGTAGCAT 58.597 43.478 8.47 0.00 37.40 3.79
2539 4285 4.217334 AGTCATCCTGTCGATAGTAGCATG 59.783 45.833 8.47 5.18 37.40 4.06
2548 4294 4.026475 GTCGATAGTAGCATGCTTTCACAC 60.026 45.833 28.02 17.47 28.88 3.82
2555 4301 2.038952 AGCATGCTTTCACACTAGTGGA 59.961 45.455 26.12 17.05 45.91 4.02
2588 4334 3.340814 AATCTACACCAACCAGAGCTG 57.659 47.619 0.00 0.00 0.00 4.24
2599 4347 4.701651 CCAACCAGAGCTGAAATATCAACA 59.298 41.667 0.00 0.00 34.49 3.33
2610 4358 6.325919 TGAAATATCAACAAAGTGGTGGTC 57.674 37.500 0.00 0.00 35.34 4.02
2614 4362 1.032014 CAACAAAGTGGTGGTCTGGG 58.968 55.000 0.00 0.00 29.70 4.45
2628 4376 6.435904 TGGTGGTCTGGGAAATAAATTAAGTG 59.564 38.462 0.00 0.00 0.00 3.16
2636 4384 5.291858 GGGAAATAAATTAAGTGCTTGCTGC 59.708 40.000 0.00 0.00 43.25 5.25
2660 4408 8.530311 TGCAACTAACCATGAATGAAATTATGT 58.470 29.630 0.00 0.00 36.07 2.29
2710 4458 2.724977 TAAGAACGAGGCTGTGTCTG 57.275 50.000 0.00 0.00 0.00 3.51
2720 4468 3.206150 AGGCTGTGTCTGTTACAACTTG 58.794 45.455 0.00 0.00 40.63 3.16
2727 4475 6.607689 TGTGTCTGTTACAACTTGTTTTCAG 58.392 36.000 0.00 6.95 40.63 3.02
2732 4480 7.913297 GTCTGTTACAACTTGTTTTCAGCATAA 59.087 33.333 0.00 0.00 0.00 1.90
2734 4482 8.401046 TGTTACAACTTGTTTTCAGCATAAAC 57.599 30.769 0.00 0.00 36.32 2.01
2780 4628 0.251698 TGAGTTTGGGGCATGCATGA 60.252 50.000 30.64 6.27 0.00 3.07
2796 4652 6.527023 GCATGCATGATACTATTTTCAGCATC 59.473 38.462 30.64 1.71 35.99 3.91
2858 4714 1.303561 ATTCAGGCTTTCTGCGGCA 60.304 52.632 1.29 1.29 43.06 5.69
2878 4734 3.654414 CAATTATACCGAGACCTGAGCC 58.346 50.000 0.00 0.00 0.00 4.70
2933 4789 7.873739 ACATTGCTTTGCTTTAAACATCTAC 57.126 32.000 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 5.519927 CCAGCAAGAATTCGACAAACTTTTT 59.480 36.000 0.00 0.00 0.00 1.94
20 21 5.043248 CCAGCAAGAATTCGACAAACTTTT 58.957 37.500 0.00 0.00 0.00 2.27
21 22 4.338118 TCCAGCAAGAATTCGACAAACTTT 59.662 37.500 0.00 0.00 0.00 2.66
22 23 3.882888 TCCAGCAAGAATTCGACAAACTT 59.117 39.130 0.00 0.00 0.00 2.66
23 24 3.476552 TCCAGCAAGAATTCGACAAACT 58.523 40.909 0.00 0.00 0.00 2.66
24 25 3.896648 TCCAGCAAGAATTCGACAAAC 57.103 42.857 0.00 0.00 0.00 2.93
25 26 5.452078 AATTCCAGCAAGAATTCGACAAA 57.548 34.783 7.86 0.00 41.54 2.83
26 27 5.221880 CAAATTCCAGCAAGAATTCGACAA 58.778 37.500 12.67 0.00 43.90 3.18
27 28 4.321156 CCAAATTCCAGCAAGAATTCGACA 60.321 41.667 12.67 0.00 43.90 4.35
28 29 4.168760 CCAAATTCCAGCAAGAATTCGAC 58.831 43.478 12.67 0.00 43.90 4.20
29 30 3.367292 GCCAAATTCCAGCAAGAATTCGA 60.367 43.478 12.67 0.00 43.90 3.71
30 31 2.925563 GCCAAATTCCAGCAAGAATTCG 59.074 45.455 12.67 4.05 43.90 3.34
31 32 2.925563 CGCCAAATTCCAGCAAGAATTC 59.074 45.455 12.67 0.00 43.90 2.17
32 33 2.354003 CCGCCAAATTCCAGCAAGAATT 60.354 45.455 7.86 7.86 46.04 2.17
33 34 1.205417 CCGCCAAATTCCAGCAAGAAT 59.795 47.619 0.00 0.00 38.11 2.40
34 35 0.602562 CCGCCAAATTCCAGCAAGAA 59.397 50.000 0.00 0.00 0.00 2.52
35 36 1.876497 GCCGCCAAATTCCAGCAAGA 61.876 55.000 0.00 0.00 0.00 3.02
36 37 1.446618 GCCGCCAAATTCCAGCAAG 60.447 57.895 0.00 0.00 0.00 4.01
37 38 2.656055 GCCGCCAAATTCCAGCAA 59.344 55.556 0.00 0.00 0.00 3.91
38 39 3.746889 CGCCGCCAAATTCCAGCA 61.747 61.111 0.00 0.00 0.00 4.41
39 40 4.496927 CCGCCGCCAAATTCCAGC 62.497 66.667 0.00 0.00 0.00 4.85
40 41 3.825611 CCCGCCGCCAAATTCCAG 61.826 66.667 0.00 0.00 0.00 3.86
41 42 4.352607 TCCCGCCGCCAAATTCCA 62.353 61.111 0.00 0.00 0.00 3.53
42 43 3.822192 GTCCCGCCGCCAAATTCC 61.822 66.667 0.00 0.00 0.00 3.01
43 44 4.174129 CGTCCCGCCGCCAAATTC 62.174 66.667 0.00 0.00 0.00 2.17
76 77 4.139234 GTACCTCCGGCGACCACC 62.139 72.222 9.30 0.00 0.00 4.61
77 78 4.487412 CGTACCTCCGGCGACCAC 62.487 72.222 9.30 0.00 0.00 4.16
85 86 1.418342 CGCAACATTCCGTACCTCCG 61.418 60.000 0.00 0.00 0.00 4.63
86 87 1.087771 CCGCAACATTCCGTACCTCC 61.088 60.000 0.00 0.00 0.00 4.30
87 88 1.087771 CCCGCAACATTCCGTACCTC 61.088 60.000 0.00 0.00 0.00 3.85
88 89 1.078708 CCCGCAACATTCCGTACCT 60.079 57.895 0.00 0.00 0.00 3.08
89 90 2.110352 CCCCGCAACATTCCGTACC 61.110 63.158 0.00 0.00 0.00 3.34
90 91 2.110352 CCCCCGCAACATTCCGTAC 61.110 63.158 0.00 0.00 0.00 3.67
91 92 2.269562 CCCCCGCAACATTCCGTA 59.730 61.111 0.00 0.00 0.00 4.02
113 114 4.683334 GGTTGCTTGCACGCCGAC 62.683 66.667 13.19 11.00 0.00 4.79
116 117 4.389576 CTCGGTTGCTTGCACGCC 62.390 66.667 13.19 0.00 0.00 5.68
118 119 3.179869 TTGCTCGGTTGCTTGCACG 62.180 57.895 0.00 0.00 35.01 5.34
119 120 1.658409 GTTGCTCGGTTGCTTGCAC 60.658 57.895 0.00 0.00 35.01 4.57
120 121 2.062361 CTGTTGCTCGGTTGCTTGCA 62.062 55.000 0.00 0.00 0.00 4.08
121 122 1.370900 CTGTTGCTCGGTTGCTTGC 60.371 57.895 0.00 0.00 0.00 4.01
122 123 0.236711 CTCTGTTGCTCGGTTGCTTG 59.763 55.000 0.00 0.00 0.00 4.01
139 140 1.381872 TCACTAGGCTGCCTCCCTC 60.382 63.158 27.16 0.00 34.61 4.30
181 182 6.000219 TCAAAGATGAGAAGCTAAAGCAAGT 59.000 36.000 4.54 0.00 45.16 3.16
232 233 6.435904 TCTCAAAACCTTGAACTCCTCAAAAA 59.564 34.615 0.00 0.00 43.54 1.94
245 246 4.686554 CCTAGTCGAACTCTCAAAACCTTG 59.313 45.833 0.00 0.00 0.00 3.61
254 255 0.170561 TTGCGCCTAGTCGAACTCTC 59.829 55.000 4.18 0.00 0.00 3.20
258 259 1.076332 AATGTTGCGCCTAGTCGAAC 58.924 50.000 4.18 0.49 0.00 3.95
260 261 2.658373 TAAATGTTGCGCCTAGTCGA 57.342 45.000 4.18 0.00 0.00 4.20
269 270 5.861787 CCTTTTTAGGGAGTTAAATGTTGCG 59.138 40.000 0.00 0.00 0.00 4.85
307 308 8.404107 TCCTAAAAGGGTTTAATTCTCAACAG 57.596 34.615 0.00 0.00 35.59 3.16
309 310 8.405418 ACTCCTAAAAGGGTTTAATTCTCAAC 57.595 34.615 0.00 0.00 35.59 3.18
333 334 5.363005 TGTCCAAGGGTATCTCTAGCTAAAC 59.637 44.000 0.00 0.00 0.00 2.01
349 350 5.428184 AGAAGAATAGAGGTTGTCCAAGG 57.572 43.478 0.00 0.00 35.89 3.61
353 354 7.842982 ACTTCTTAGAAGAATAGAGGTTGTCC 58.157 38.462 26.49 0.00 43.52 4.02
356 357 9.796120 CAGTACTTCTTAGAAGAATAGAGGTTG 57.204 37.037 26.49 8.76 43.52 3.77
365 366 4.459685 AGCGCTCAGTACTTCTTAGAAGAA 59.540 41.667 26.49 9.13 42.41 2.52
409 410 1.518903 GCTGGCCTGGAACACAAGAC 61.519 60.000 12.06 0.00 0.00 3.01
416 417 3.645268 AATCCGGCTGGCCTGGAAC 62.645 63.158 21.69 0.00 40.28 3.62
419 420 2.916527 ATTGAATCCGGCTGGCCTGG 62.917 60.000 6.73 12.05 34.14 4.45
420 421 1.450531 GATTGAATCCGGCTGGCCTG 61.451 60.000 6.73 4.26 34.14 4.85
432 433 2.171237 TCGCTCCACATGAGGATTGAAT 59.829 45.455 12.62 0.00 41.73 2.57
436 437 4.630644 ATATTCGCTCCACATGAGGATT 57.369 40.909 12.62 0.00 41.73 3.01
442 443 5.056480 TGGTAGAAATATTCGCTCCACATG 58.944 41.667 0.00 0.00 34.02 3.21
443 444 5.290493 TGGTAGAAATATTCGCTCCACAT 57.710 39.130 0.00 0.00 34.02 3.21
446 447 5.290493 ACATGGTAGAAATATTCGCTCCA 57.710 39.130 0.00 0.00 34.88 3.86
447 448 5.107453 CGAACATGGTAGAAATATTCGCTCC 60.107 44.000 0.00 0.00 32.18 4.70
465 466 0.537188 ATGGAAGGAGCGACGAACAT 59.463 50.000 0.00 0.00 0.00 2.71
470 471 5.679906 CATATTTTTATGGAAGGAGCGACG 58.320 41.667 0.00 0.00 0.00 5.12
471 472 5.452777 GCATATTTTTATGGAAGGAGCGAC 58.547 41.667 0.00 0.00 0.00 5.19
474 475 4.518970 TCGGCATATTTTTATGGAAGGAGC 59.481 41.667 0.00 0.00 0.00 4.70
475 476 5.182001 CCTCGGCATATTTTTATGGAAGGAG 59.818 44.000 0.00 0.00 0.00 3.69
481 482 3.255642 CACCCCTCGGCATATTTTTATGG 59.744 47.826 0.00 0.00 0.00 2.74
482 483 3.305335 GCACCCCTCGGCATATTTTTATG 60.305 47.826 0.00 0.00 0.00 1.90
513 514 2.981898 AGAATAGAAAAACGGGACCGG 58.018 47.619 15.92 0.00 44.69 5.28
514 515 4.251268 AGAAGAATAGAAAAACGGGACCG 58.749 43.478 9.56 9.56 46.03 4.79
535 536 6.183360 GGGCTGCACATTGTATATATGCTTAG 60.183 42.308 0.50 0.00 37.20 2.18
540 541 5.494724 AGAGGGCTGCACATTGTATATATG 58.505 41.667 4.01 0.00 0.00 1.78
541 542 5.338708 GGAGAGGGCTGCACATTGTATATAT 60.339 44.000 4.01 0.00 31.98 0.86
542 543 4.020218 GGAGAGGGCTGCACATTGTATATA 60.020 45.833 4.01 0.00 31.98 0.86
561 2091 0.323451 TGTAGCTCGGCTCTTGGAGA 60.323 55.000 1.46 0.00 40.44 3.71
571 2101 0.999406 CATTGGACGTTGTAGCTCGG 59.001 55.000 0.00 0.00 0.00 4.63
572 2102 0.370273 GCATTGGACGTTGTAGCTCG 59.630 55.000 0.00 0.00 0.00 5.03
577 2107 6.986904 TGTATATTTGCATTGGACGTTGTA 57.013 33.333 0.00 0.00 0.00 2.41
579 2109 7.754069 AAATGTATATTTGCATTGGACGTTG 57.246 32.000 0.61 0.00 38.07 4.10
580 2110 8.682710 ACTAAATGTATATTTGCATTGGACGTT 58.317 29.630 7.63 0.00 38.07 3.99
581 2111 8.220755 ACTAAATGTATATTTGCATTGGACGT 57.779 30.769 7.63 0.00 38.07 4.34
604 2134 2.158623 TCTGAGCCAACATGTCCAAACT 60.159 45.455 0.00 0.00 0.00 2.66
606 2136 2.158623 ACTCTGAGCCAACATGTCCAAA 60.159 45.455 4.19 0.00 0.00 3.28
607 2137 1.421268 ACTCTGAGCCAACATGTCCAA 59.579 47.619 4.19 0.00 0.00 3.53
608 2138 1.002430 GACTCTGAGCCAACATGTCCA 59.998 52.381 4.19 0.00 0.00 4.02
609 2139 1.731720 GACTCTGAGCCAACATGTCC 58.268 55.000 4.19 0.00 0.00 4.02
611 2141 0.671781 GCGACTCTGAGCCAACATGT 60.672 55.000 4.19 0.00 0.00 3.21
612 2142 0.390866 AGCGACTCTGAGCCAACATG 60.391 55.000 4.19 0.00 0.00 3.21
613 2143 0.322975 AAGCGACTCTGAGCCAACAT 59.677 50.000 4.19 0.00 0.00 2.71
614 2144 0.106708 AAAGCGACTCTGAGCCAACA 59.893 50.000 4.19 0.00 0.00 3.33
615 2145 0.514691 CAAAGCGACTCTGAGCCAAC 59.485 55.000 4.19 0.00 0.00 3.77
619 2149 2.301577 ATACCAAAGCGACTCTGAGC 57.698 50.000 4.19 0.00 0.00 4.26
628 2158 4.678509 TTGACAAGCTAATACCAAAGCG 57.321 40.909 0.00 0.00 43.63 4.68
634 2164 4.446051 GCTCTCGATTGACAAGCTAATACC 59.554 45.833 1.44 0.00 0.00 2.73
654 2188 1.058695 CCAAATTCACGACGTACGCTC 59.941 52.381 16.72 11.14 46.94 5.03
655 2189 1.065358 CCAAATTCACGACGTACGCT 58.935 50.000 16.72 2.20 46.94 5.07
656 2190 0.094046 CCCAAATTCACGACGTACGC 59.906 55.000 16.72 7.41 46.94 4.42
675 2209 3.304996 GCTCTCTTTTCACCTTTTCCTGC 60.305 47.826 0.00 0.00 0.00 4.85
709 2243 3.124806 GGCGCTCTAGTAAAGGTGAAAAC 59.875 47.826 7.64 0.00 0.00 2.43
934 2495 0.842635 AGATTTGGCTCAGGGCTAGG 59.157 55.000 0.00 0.00 41.46 3.02
962 2523 0.320073 TGCAAAGTTCGTACGGGGAG 60.320 55.000 16.52 2.40 0.00 4.30
998 2567 1.895131 GCAAATGGTGAACCCTCATGT 59.105 47.619 0.00 0.00 33.05 3.21
1022 2591 1.601419 TTTCTCCAGGTAGGACGGCG 61.601 60.000 4.80 4.80 43.07 6.46
1026 2595 0.175989 CCGCTTTCTCCAGGTAGGAC 59.824 60.000 0.00 0.00 43.07 3.85
1083 2655 4.467107 AGGGCCGAGGGAGGAGAC 62.467 72.222 0.00 0.00 0.00 3.36
1251 2823 2.944349 GAGCTAGAGGTAAGTGCGTACT 59.056 50.000 0.00 0.00 39.32 2.73
1263 2836 4.335315 CACTTCACTAGACAGAGCTAGAGG 59.665 50.000 0.00 0.00 40.20 3.69
1299 2872 1.863267 GGACATGCACAGCTAGCTAG 58.137 55.000 18.86 16.84 0.00 3.42
1300 2873 0.103026 CGGACATGCACAGCTAGCTA 59.897 55.000 18.86 1.28 0.00 3.32
1301 2874 1.153489 CGGACATGCACAGCTAGCT 60.153 57.895 12.68 12.68 0.00 3.32
1302 2875 1.448540 ACGGACATGCACAGCTAGC 60.449 57.895 6.62 6.62 0.00 3.42
1303 2876 0.390340 ACACGGACATGCACAGCTAG 60.390 55.000 0.00 0.00 0.00 3.42
1304 2877 0.670239 CACACGGACATGCACAGCTA 60.670 55.000 0.00 0.00 0.00 3.32
1305 2878 1.962822 CACACGGACATGCACAGCT 60.963 57.895 0.00 0.00 0.00 4.24
1306 2879 1.506309 TTCACACGGACATGCACAGC 61.506 55.000 0.00 0.00 0.00 4.40
1307 2880 0.943673 TTTCACACGGACATGCACAG 59.056 50.000 0.00 0.00 0.00 3.66
1308 2881 1.266446 CATTTCACACGGACATGCACA 59.734 47.619 0.00 0.00 27.76 4.57
1309 2882 1.967762 CATTTCACACGGACATGCAC 58.032 50.000 0.00 0.00 27.76 4.57
1368 2948 4.954970 CCCACCGGCACTTGCACT 62.955 66.667 0.00 0.00 44.36 4.40
1521 3101 2.028930 CCAGTAGAAGACGTTCTTGCCT 60.029 50.000 5.20 1.31 40.35 4.75
1657 3240 0.942410 TTGCACCGTGTAGTTCTCGC 60.942 55.000 0.00 0.00 0.00 5.03
1659 3243 2.150397 AGTTGCACCGTGTAGTTCTC 57.850 50.000 0.00 0.00 0.00 2.87
1665 3249 2.843401 ACCATTAGTTGCACCGTGTA 57.157 45.000 0.00 0.00 0.00 2.90
1693 3279 7.067008 TCCGTGTAGGTGGTAGTAATTACTAAC 59.933 40.741 27.06 27.06 41.52 2.34
1694 3280 7.116075 TCCGTGTAGGTGGTAGTAATTACTAA 58.884 38.462 23.66 9.47 39.65 2.24
1697 3283 5.734503 GCTCCGTGTAGGTGGTAGTAATTAC 60.735 48.000 7.57 7.57 41.99 1.89
1699 3285 3.131755 GCTCCGTGTAGGTGGTAGTAATT 59.868 47.826 0.00 0.00 41.99 1.40
1701 3287 2.094675 GCTCCGTGTAGGTGGTAGTAA 58.905 52.381 0.00 0.00 41.99 2.24
1702 3288 1.283029 AGCTCCGTGTAGGTGGTAGTA 59.717 52.381 0.00 0.00 41.82 1.82
1760 3494 0.616395 TCACCGGCTCCATCCTACAA 60.616 55.000 0.00 0.00 0.00 2.41
1791 3528 1.153647 TTCGTCGCCTCATCGCAAT 60.154 52.632 0.00 0.00 0.00 3.56
1798 3535 2.049156 CAGCTGTTCGTCGCCTCA 60.049 61.111 5.25 0.00 0.00 3.86
1801 3538 2.892334 TTTGCAGCTGTTCGTCGCC 61.892 57.895 16.64 0.00 0.00 5.54
1810 3547 4.688419 CACCGCCGTTTGCAGCTG 62.688 66.667 10.11 10.11 41.33 4.24
1819 3556 3.126879 CATGTCATGCACCGCCGT 61.127 61.111 0.00 0.00 0.00 5.68
1830 3567 4.408821 GGCCGGCACTCCATGTCA 62.409 66.667 30.85 0.00 29.41 3.58
1834 3571 4.511246 CCATGGCCGGCACTCCAT 62.511 66.667 30.85 19.38 43.45 3.41
1878 3615 3.709880 TTATCCGTGCAGCCGTCGG 62.710 63.158 6.99 6.99 44.76 4.79
1879 3616 2.202690 TTATCCGTGCAGCCGTCG 60.203 61.111 0.00 0.00 0.00 5.12
1927 3664 1.296715 CTACGCAGCTTTCCCCTGT 59.703 57.895 0.00 0.00 32.93 4.00
1998 3739 1.284198 GCTCCATCCAGGCATATCCAT 59.716 52.381 0.00 0.00 37.29 3.41
1999 3740 0.694771 GCTCCATCCAGGCATATCCA 59.305 55.000 0.00 0.00 37.29 3.41
2000 3741 0.034670 GGCTCCATCCAGGCATATCC 60.035 60.000 0.00 0.00 38.83 2.59
2001 3742 0.392193 CGGCTCCATCCAGGCATATC 60.392 60.000 0.00 0.00 38.92 1.63
2002 3743 1.681666 CGGCTCCATCCAGGCATAT 59.318 57.895 0.00 0.00 38.92 1.78
2003 3744 2.519622 CCGGCTCCATCCAGGCATA 61.520 63.158 0.00 0.00 38.92 3.14
2004 3745 3.882326 CCGGCTCCATCCAGGCAT 61.882 66.667 0.00 0.00 38.92 4.40
2006 3747 3.645268 AAACCGGCTCCATCCAGGC 62.645 63.158 0.00 0.00 37.29 4.85
2007 3748 1.000896 AAAACCGGCTCCATCCAGG 60.001 57.895 0.00 0.00 39.47 4.45
2008 3749 0.322456 TGAAAACCGGCTCCATCCAG 60.322 55.000 0.00 0.00 0.00 3.86
2009 3750 0.331278 ATGAAAACCGGCTCCATCCA 59.669 50.000 0.00 0.00 0.00 3.41
2010 3751 1.134946 CAATGAAAACCGGCTCCATCC 59.865 52.381 0.00 0.00 0.00 3.51
2011 3752 1.134946 CCAATGAAAACCGGCTCCATC 59.865 52.381 0.00 0.00 0.00 3.51
2036 3777 4.370364 AACACACGCAAAAATCAGAAGT 57.630 36.364 0.00 0.00 0.00 3.01
2099 3844 4.398358 TCCACTAGTAGGAAACTGATCACG 59.602 45.833 10.51 0.00 43.88 4.35
2127 3872 3.135530 AGTTCCTCCCATCTGAATGCTAC 59.864 47.826 0.00 0.00 0.00 3.58
2128 3873 3.135348 CAGTTCCTCCCATCTGAATGCTA 59.865 47.826 0.00 0.00 0.00 3.49
2129 3874 2.092538 CAGTTCCTCCCATCTGAATGCT 60.093 50.000 0.00 0.00 0.00 3.79
2130 3875 2.295885 CAGTTCCTCCCATCTGAATGC 58.704 52.381 0.00 0.00 0.00 3.56
2131 3876 2.928334 CCAGTTCCTCCCATCTGAATG 58.072 52.381 0.00 0.00 0.00 2.67
2132 3877 1.213926 GCCAGTTCCTCCCATCTGAAT 59.786 52.381 0.00 0.00 0.00 2.57
2133 3878 0.620556 GCCAGTTCCTCCCATCTGAA 59.379 55.000 0.00 0.00 0.00 3.02
2134 3879 0.252881 AGCCAGTTCCTCCCATCTGA 60.253 55.000 0.00 0.00 0.00 3.27
2135 3880 0.622665 AAGCCAGTTCCTCCCATCTG 59.377 55.000 0.00 0.00 0.00 2.90
2136 3881 0.915364 GAAGCCAGTTCCTCCCATCT 59.085 55.000 0.00 0.00 0.00 2.90
2137 3882 3.485764 GAAGCCAGTTCCTCCCATC 57.514 57.895 0.00 0.00 0.00 3.51
2176 3921 7.070198 GGATACTCCTAGCTAGTTCCTCTTTTT 59.930 40.741 19.31 0.00 32.53 1.94
2177 3922 6.551975 GGATACTCCTAGCTAGTTCCTCTTTT 59.448 42.308 19.31 0.00 32.53 2.27
2178 3923 6.072649 GGATACTCCTAGCTAGTTCCTCTTT 58.927 44.000 19.31 0.00 32.53 2.52
2179 3924 5.458508 GGGATACTCCTAGCTAGTTCCTCTT 60.459 48.000 19.31 0.00 36.57 2.85
2180 3925 4.043686 GGGATACTCCTAGCTAGTTCCTCT 59.956 50.000 19.31 0.00 36.57 3.69
2181 3926 4.338012 GGGATACTCCTAGCTAGTTCCTC 58.662 52.174 19.31 8.99 36.57 3.71
2182 3927 3.076333 GGGGATACTCCTAGCTAGTTCCT 59.924 52.174 19.31 0.26 36.57 3.36
2183 3928 3.076333 AGGGGATACTCCTAGCTAGTTCC 59.924 52.174 19.31 15.03 38.59 3.62
2184 3929 4.391683 AGGGGATACTCCTAGCTAGTTC 57.608 50.000 19.31 7.88 38.59 3.01
2185 3930 5.523883 CTAGGGGATACTCCTAGCTAGTT 57.476 47.826 19.31 6.06 44.94 2.24
2192 3937 5.745988 AACTTGTCTAGGGGATACTCCTA 57.254 43.478 0.00 0.00 38.59 2.94
2193 3938 4.628661 AACTTGTCTAGGGGATACTCCT 57.371 45.455 0.00 0.00 38.59 3.69
2194 3939 5.695424 AAAACTTGTCTAGGGGATACTCC 57.305 43.478 0.00 0.00 38.59 3.85
2195 3940 6.070136 AGGAAAAACTTGTCTAGGGGATACTC 60.070 42.308 0.00 0.00 37.29 2.59
2196 3941 5.791141 AGGAAAAACTTGTCTAGGGGATACT 59.209 40.000 0.00 0.00 0.00 2.12
2197 3942 6.063496 AGGAAAAACTTGTCTAGGGGATAC 57.937 41.667 0.00 0.00 0.00 2.24
2198 3943 6.273730 TGAAGGAAAAACTTGTCTAGGGGATA 59.726 38.462 0.00 0.00 0.00 2.59
2199 3944 5.074515 TGAAGGAAAAACTTGTCTAGGGGAT 59.925 40.000 0.00 0.00 0.00 3.85
2200 3945 4.414182 TGAAGGAAAAACTTGTCTAGGGGA 59.586 41.667 0.00 0.00 0.00 4.81
2201 3946 4.519350 GTGAAGGAAAAACTTGTCTAGGGG 59.481 45.833 0.00 0.00 0.00 4.79
2202 3947 5.377478 AGTGAAGGAAAAACTTGTCTAGGG 58.623 41.667 0.00 0.00 0.00 3.53
2203 3948 6.729187 CAAGTGAAGGAAAAACTTGTCTAGG 58.271 40.000 6.61 0.00 43.67 3.02
2225 3970 7.601130 TCAAGCTCTTAACTCTAATAAACGCAA 59.399 33.333 0.00 0.00 0.00 4.85
2226 3971 7.094631 TCAAGCTCTTAACTCTAATAAACGCA 58.905 34.615 0.00 0.00 0.00 5.24
2227 3972 7.521509 TCAAGCTCTTAACTCTAATAAACGC 57.478 36.000 0.00 0.00 0.00 4.84
2228 3973 9.302345 TGATCAAGCTCTTAACTCTAATAAACG 57.698 33.333 0.00 0.00 0.00 3.60
2236 3981 9.995003 CCTAATAATGATCAAGCTCTTAACTCT 57.005 33.333 0.00 0.00 0.00 3.24
2237 3982 9.771534 ACCTAATAATGATCAAGCTCTTAACTC 57.228 33.333 0.00 0.00 0.00 3.01
2258 4003 9.817809 GATGTAGTAATCATGACAAGAACCTAA 57.182 33.333 0.00 0.00 0.00 2.69
2259 4004 9.201989 AGATGTAGTAATCATGACAAGAACCTA 57.798 33.333 0.00 0.00 0.00 3.08
2260 4005 8.083828 AGATGTAGTAATCATGACAAGAACCT 57.916 34.615 0.00 0.00 0.00 3.50
2392 4138 2.030096 TGTAACACGCGACCTGATTACA 60.030 45.455 15.93 14.38 31.82 2.41
2422 4168 4.815040 AGAGTAAGATCGTACCACATCG 57.185 45.455 14.23 0.00 0.00 3.84
2423 4169 7.649973 ACATAAGAGTAAGATCGTACCACATC 58.350 38.462 14.23 6.46 0.00 3.06
2424 4170 7.584122 ACATAAGAGTAAGATCGTACCACAT 57.416 36.000 14.23 6.05 0.00 3.21
2425 4171 7.772292 ACTACATAAGAGTAAGATCGTACCACA 59.228 37.037 14.23 0.00 0.00 4.17
2426 4172 8.152309 ACTACATAAGAGTAAGATCGTACCAC 57.848 38.462 14.23 9.56 0.00 4.16
2523 4269 4.208047 GTGAAAGCATGCTACTATCGACAG 59.792 45.833 23.00 0.00 0.00 3.51
2524 4270 4.112634 GTGAAAGCATGCTACTATCGACA 58.887 43.478 23.00 9.39 0.00 4.35
2532 4278 3.372206 CCACTAGTGTGAAAGCATGCTAC 59.628 47.826 23.00 16.38 46.55 3.58
2536 4282 3.930336 TCTCCACTAGTGTGAAAGCATG 58.070 45.455 21.18 3.10 46.55 4.06
2538 4284 5.480422 TCTTATCTCCACTAGTGTGAAAGCA 59.520 40.000 21.18 11.10 46.55 3.91
2539 4285 5.967088 TCTTATCTCCACTAGTGTGAAAGC 58.033 41.667 21.18 0.00 46.55 3.51
2548 4294 9.959749 GTAGATTTGAACTCTTATCTCCACTAG 57.040 37.037 0.00 0.00 0.00 2.57
2555 4301 7.824779 GGTTGGTGTAGATTTGAACTCTTATCT 59.175 37.037 0.00 0.00 0.00 1.98
2588 4334 6.381801 CAGACCACCACTTTGTTGATATTTC 58.618 40.000 0.00 0.00 0.00 2.17
2599 4347 4.463050 TTATTTCCCAGACCACCACTTT 57.537 40.909 0.00 0.00 0.00 2.66
2610 4358 6.532657 CAGCAAGCACTTAATTTATTTCCCAG 59.467 38.462 0.00 0.00 0.00 4.45
2628 4376 1.541147 TCATGGTTAGTTGCAGCAAGC 59.459 47.619 8.49 3.83 45.96 4.01
2694 4442 2.059541 GTAACAGACACAGCCTCGTTC 58.940 52.381 0.00 0.00 0.00 3.95
2702 4450 6.607689 TGAAAACAAGTTGTAACAGACACAG 58.392 36.000 9.37 0.00 37.96 3.66
2710 4458 8.531530 CAGTTTATGCTGAAAACAAGTTGTAAC 58.468 33.333 9.37 5.95 38.92 2.50
2752 4503 1.480545 GCCCCAAACTCACAGTTTTGT 59.519 47.619 0.00 0.00 45.38 2.83
2780 4628 8.716674 ATGATTTGGGATGCTGAAAATAGTAT 57.283 30.769 0.00 0.00 0.00 2.12
2796 4652 7.119699 ACGCATATGTATACAGAATGATTTGGG 59.880 37.037 24.70 17.79 39.69 4.12
2858 4714 3.574826 GAGGCTCAGGTCTCGGTATAATT 59.425 47.826 10.25 0.00 34.33 1.40
2867 4723 0.969917 TGCTCAGAGGCTCAGGTCTC 60.970 60.000 18.26 1.15 43.94 3.36
2871 4727 1.221293 CCTTGCTCAGAGGCTCAGG 59.779 63.158 18.26 9.59 0.00 3.86
2878 4734 2.105466 GCCGAAGCCTTGCTCAGAG 61.105 63.158 0.00 0.00 38.25 3.35


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

AutoCloner maintained by Alex Coulton.