Multiple sequence alignment - TraesCS5A01G019300

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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 TraesCS5A01G019300 chr5A 100.000 3347 0 0 1 3347 14924291 14920945 0.000000e+00 6181.0
1 TraesCS5A01G019300 chr5A 94.915 59 3 0 2938 2996 14915759 14915701 3.560000e-15 93.5
2 TraesCS5A01G019300 chr5D 87.741 1452 80 35 702 2091 21559406 21557991 0.000000e+00 1605.0
3 TraesCS5A01G019300 chr5D 86.050 767 52 28 2184 2900 21557816 21557055 0.000000e+00 773.0
4 TraesCS5A01G019300 chr5D 86.182 550 41 11 155 698 21560785 21560265 2.250000e-156 562.0
5 TraesCS5A01G019300 chr5D 90.268 298 11 3 3068 3347 21556874 21556577 1.130000e-99 374.0
6 TraesCS5A01G019300 chr5D 92.670 191 13 1 485 675 21559852 21559663 1.180000e-69 274.0
7 TraesCS5A01G019300 chr5D 90.303 165 9 3 2899 3056 21557018 21556854 3.380000e-50 209.0
8 TraesCS5A01G019300 chr5D 96.364 55 2 0 2091 2145 21557936 21557882 1.280000e-14 91.6
9 TraesCS5A01G019300 chr5D 97.222 36 1 0 3193 3228 21557643 21557608 1.000000e-05 62.1
10 TraesCS5A01G019300 chr5B 87.948 1087 66 32 851 1915 15338344 15337301 0.000000e+00 1221.0
11 TraesCS5A01G019300 chr5B 87.370 863 51 20 699 1540 15270918 15271743 0.000000e+00 937.0
12 TraesCS5A01G019300 chr5B 84.005 744 45 23 1568 2270 15271739 15272449 0.000000e+00 647.0
13 TraesCS5A01G019300 chr5B 85.072 556 50 14 155 698 15339246 15338712 1.370000e-148 536.0
14 TraesCS5A01G019300 chr5B 84.532 556 52 15 155 698 15270126 15270659 1.380000e-143 520.0
15 TraesCS5A01G019300 chr5B 96.154 156 5 1 1 155 416592028 416591873 1.540000e-63 254.0
16 TraesCS5A01G019300 chr5B 92.308 91 6 1 1956 2045 15337306 15337216 9.750000e-26 128.0
17 TraesCS5A01G019300 chr5B 98.387 62 1 0 2801 2862 15272480 15272541 3.530000e-20 110.0
18 TraesCS5A01G019300 chr4A 96.795 156 4 1 1 155 514634558 514634403 3.310000e-65 259.0
19 TraesCS5A01G019300 chr4A 90.625 96 8 1 1108 1203 596571775 596571681 3.510000e-25 126.0
20 TraesCS5A01G019300 chr1A 96.774 155 4 1 1 154 350489745 350489591 1.190000e-64 257.0
21 TraesCS5A01G019300 chr1A 96.154 156 5 1 1 155 363450909 363450754 1.540000e-63 254.0
22 TraesCS5A01G019300 chr1A 93.865 163 9 1 1 162 578265110 578265272 9.280000e-61 244.0
23 TraesCS5A01G019300 chr3A 96.154 156 5 1 1 155 363316133 363315978 1.540000e-63 254.0
24 TraesCS5A01G019300 chr3A 95.625 160 4 3 1 158 638931514 638931356 1.540000e-63 254.0
25 TraesCS5A01G019300 chr2A 93.023 172 10 2 1 171 30311797 30311627 1.990000e-62 250.0
26 TraesCS5A01G019300 chr7A 93.452 168 9 2 1 167 40456727 40456561 7.170000e-62 248.0
27 TraesCS5A01G019300 chr4D 91.667 96 7 1 1108 1203 6969474 6969568 7.530000e-27 132.0
28 TraesCS5A01G019300 chr4B 91.667 96 7 1 1108 1203 12251716 12251810 7.530000e-27 132.0


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 TraesCS5A01G019300 chr5A 14920945 14924291 3346 True 6181.000000 6181 100.000000 1 3347 1 chr5A.!!$R2 3346
1 TraesCS5A01G019300 chr5D 21556577 21560785 4208 True 493.837500 1605 90.850000 155 3347 8 chr5D.!!$R1 3192
2 TraesCS5A01G019300 chr5B 15337216 15339246 2030 True 628.333333 1221 88.442667 155 2045 3 chr5B.!!$R2 1890
3 TraesCS5A01G019300 chr5B 15270126 15272541 2415 False 553.500000 937 88.573500 155 2862 4 chr5B.!!$F1 2707

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
328 329 0.032403 CGGTCGTTAGTGAACCCACA 59.968 55.0 0.0 0.0 45.54 4.17 F
1012 1930 0.035056 CCATCCCACTTCACACTCCC 60.035 60.0 0.0 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2214 3289 0.109365 TTTCAATCCAACATGCCGCG 60.109 50.0 0.0 0.0 0.00 6.46 R
2484 3580 0.179004 TCTCCTCTCCTCTCGGATGC 60.179 60.0 0.0 0.0 39.01 3.91 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
24 25 4.908601 TGAGCCTAGACTCAATGGAAAA 57.091 40.909 6.25 0.00 43.59 2.29
25 26 5.441718 TGAGCCTAGACTCAATGGAAAAT 57.558 39.130 6.25 0.00 43.59 1.82
26 27 5.819991 TGAGCCTAGACTCAATGGAAAATT 58.180 37.500 6.25 0.00 43.59 1.82
27 28 6.248433 TGAGCCTAGACTCAATGGAAAATTT 58.752 36.000 6.25 0.00 43.59 1.82
28 29 6.721208 TGAGCCTAGACTCAATGGAAAATTTT 59.279 34.615 6.25 2.28 43.59 1.82
29 30 7.094205 TGAGCCTAGACTCAATGGAAAATTTTC 60.094 37.037 20.51 20.51 43.59 2.29
30 31 6.950619 AGCCTAGACTCAATGGAAAATTTTCT 59.049 34.615 25.86 8.60 37.35 2.52
31 32 7.452813 AGCCTAGACTCAATGGAAAATTTTCTT 59.547 33.333 25.86 13.61 37.35 2.52
32 33 8.090831 GCCTAGACTCAATGGAAAATTTTCTTT 58.909 33.333 25.86 18.05 37.35 2.52
33 34 9.415544 CCTAGACTCAATGGAAAATTTTCTTTG 57.584 33.333 25.86 25.46 37.35 2.77
34 35 9.415544 CTAGACTCAATGGAAAATTTTCTTTGG 57.584 33.333 27.64 23.19 37.35 3.28
35 36 7.795047 AGACTCAATGGAAAATTTTCTTTGGT 58.205 30.769 27.64 24.84 37.35 3.67
36 37 7.712205 AGACTCAATGGAAAATTTTCTTTGGTG 59.288 33.333 27.64 24.10 37.35 4.17
37 38 7.337938 ACTCAATGGAAAATTTTCTTTGGTGT 58.662 30.769 27.64 24.46 37.35 4.16
38 39 7.280652 ACTCAATGGAAAATTTTCTTTGGTGTG 59.719 33.333 27.64 20.85 37.35 3.82
39 40 7.334090 TCAATGGAAAATTTTCTTTGGTGTGA 58.666 30.769 27.64 19.65 37.35 3.58
40 41 7.826252 TCAATGGAAAATTTTCTTTGGTGTGAA 59.174 29.630 27.64 15.87 37.35 3.18
41 42 6.976636 TGGAAAATTTTCTTTGGTGTGAAC 57.023 33.333 25.86 9.01 37.35 3.18
42 43 5.877564 TGGAAAATTTTCTTTGGTGTGAACC 59.122 36.000 25.86 9.51 37.35 3.62
43 44 5.877564 GGAAAATTTTCTTTGGTGTGAACCA 59.122 36.000 25.86 0.00 37.35 3.67
44 45 6.372937 GGAAAATTTTCTTTGGTGTGAACCAA 59.627 34.615 25.86 6.23 40.72 3.67
52 53 4.582701 TTGGTGTGAACCAAATGACATC 57.417 40.909 7.85 0.00 45.79 3.06
53 54 3.831323 TGGTGTGAACCAAATGACATCT 58.169 40.909 0.00 0.00 36.74 2.90
54 55 4.214310 TGGTGTGAACCAAATGACATCTT 58.786 39.130 0.00 0.00 36.74 2.40
55 56 4.037803 TGGTGTGAACCAAATGACATCTTG 59.962 41.667 0.00 0.00 36.74 3.02
56 57 4.037923 GGTGTGAACCAAATGACATCTTGT 59.962 41.667 0.00 0.00 0.00 3.16
57 58 5.451798 GGTGTGAACCAAATGACATCTTGTT 60.452 40.000 0.00 0.00 0.00 2.83
58 59 6.042143 GTGTGAACCAAATGACATCTTGTTT 58.958 36.000 0.00 0.00 0.00 2.83
59 60 6.198966 GTGTGAACCAAATGACATCTTGTTTC 59.801 38.462 10.70 10.70 0.00 2.78
60 61 5.691754 GTGAACCAAATGACATCTTGTTTCC 59.308 40.000 13.07 6.15 0.00 3.13
61 62 5.598005 TGAACCAAATGACATCTTGTTTCCT 59.402 36.000 13.07 0.00 0.00 3.36
62 63 6.775142 TGAACCAAATGACATCTTGTTTCCTA 59.225 34.615 13.07 1.13 0.00 2.94
63 64 7.451255 TGAACCAAATGACATCTTGTTTCCTAT 59.549 33.333 13.07 0.00 0.00 2.57
64 65 7.781324 ACCAAATGACATCTTGTTTCCTATT 57.219 32.000 0.00 0.00 0.00 1.73
65 66 7.830739 ACCAAATGACATCTTGTTTCCTATTC 58.169 34.615 0.00 0.00 0.00 1.75
66 67 7.093771 ACCAAATGACATCTTGTTTCCTATTCC 60.094 37.037 0.00 0.00 0.00 3.01
67 68 7.123247 CCAAATGACATCTTGTTTCCTATTCCT 59.877 37.037 0.00 0.00 0.00 3.36
68 69 9.177608 CAAATGACATCTTGTTTCCTATTCCTA 57.822 33.333 0.00 0.00 0.00 2.94
69 70 9.927081 AAATGACATCTTGTTTCCTATTCCTAT 57.073 29.630 0.00 0.00 0.00 2.57
70 71 9.927081 AATGACATCTTGTTTCCTATTCCTATT 57.073 29.630 0.00 0.00 0.00 1.73
71 72 8.964476 TGACATCTTGTTTCCTATTCCTATTC 57.036 34.615 0.00 0.00 0.00 1.75
72 73 8.548025 TGACATCTTGTTTCCTATTCCTATTCA 58.452 33.333 0.00 0.00 0.00 2.57
73 74 9.566432 GACATCTTGTTTCCTATTCCTATTCAT 57.434 33.333 0.00 0.00 0.00 2.57
95 96 9.716531 TTCATAGGATTTGAGATACATGTCATC 57.283 33.333 0.00 4.47 29.66 2.92
96 97 9.097946 TCATAGGATTTGAGATACATGTCATCT 57.902 33.333 0.00 9.42 35.43 2.90
97 98 9.368674 CATAGGATTTGAGATACATGTCATCTC 57.631 37.037 24.04 24.04 45.76 2.75
106 107 7.846101 AGATACATGTCATCTCATTCCTACA 57.154 36.000 0.00 0.00 0.00 2.74
107 108 8.255111 AGATACATGTCATCTCATTCCTACAA 57.745 34.615 0.00 0.00 0.00 2.41
108 109 8.708378 AGATACATGTCATCTCATTCCTACAAA 58.292 33.333 0.00 0.00 0.00 2.83
109 110 9.499479 GATACATGTCATCTCATTCCTACAAAT 57.501 33.333 0.00 0.00 0.00 2.32
110 111 9.857656 ATACATGTCATCTCATTCCTACAAATT 57.142 29.630 0.00 0.00 0.00 1.82
111 112 8.585471 ACATGTCATCTCATTCCTACAAATTT 57.415 30.769 0.00 0.00 0.00 1.82
112 113 8.680903 ACATGTCATCTCATTCCTACAAATTTC 58.319 33.333 0.00 0.00 0.00 2.17
113 114 7.630242 TGTCATCTCATTCCTACAAATTTCC 57.370 36.000 0.00 0.00 0.00 3.13
114 115 7.405292 TGTCATCTCATTCCTACAAATTTCCT 58.595 34.615 0.00 0.00 0.00 3.36
115 116 8.548025 TGTCATCTCATTCCTACAAATTTCCTA 58.452 33.333 0.00 0.00 0.00 2.94
116 117 9.566432 GTCATCTCATTCCTACAAATTTCCTAT 57.434 33.333 0.00 0.00 0.00 2.57
119 120 8.980481 TCTCATTCCTACAAATTTCCTATTCC 57.020 34.615 0.00 0.00 0.00 3.01
120 121 8.781951 TCTCATTCCTACAAATTTCCTATTCCT 58.218 33.333 0.00 0.00 0.00 3.36
143 144 9.661954 TCCTATGATAATCCTATCCTATGAACC 57.338 37.037 0.00 0.00 34.10 3.62
144 145 9.439461 CCTATGATAATCCTATCCTATGAACCA 57.561 37.037 0.00 0.00 34.10 3.67
151 152 6.500589 TCCTATCCTATGAACCAAAAGAGG 57.499 41.667 0.00 0.00 0.00 3.69
152 153 5.066593 CCTATCCTATGAACCAAAAGAGGC 58.933 45.833 0.00 0.00 0.00 4.70
153 154 3.366052 TCCTATGAACCAAAAGAGGCC 57.634 47.619 0.00 0.00 0.00 5.19
162 163 2.242043 CCAAAAGAGGCCTCACATTGT 58.758 47.619 33.90 12.73 0.00 2.71
267 268 6.403866 AAAGTAGATGCATTTTGTGTCCAA 57.596 33.333 0.00 0.00 0.00 3.53
328 329 0.032403 CGGTCGTTAGTGAACCCACA 59.968 55.000 0.00 0.00 45.54 4.17
376 377 3.744660 CAAGGGATGGCCTGTCTTATAC 58.255 50.000 3.32 0.00 0.00 1.47
379 380 3.584848 AGGGATGGCCTGTCTTATACATC 59.415 47.826 3.32 0.00 37.50 3.06
382 383 3.475566 TGGCCTGTCTTATACATCTGC 57.524 47.619 3.32 0.00 37.50 4.26
404 405 6.743110 TGCGGCAAAATTTTCATGCTATATA 58.257 32.000 11.92 0.00 39.94 0.86
405 406 6.862608 TGCGGCAAAATTTTCATGCTATATAG 59.137 34.615 11.92 5.30 39.94 1.31
406 407 7.083858 GCGGCAAAATTTTCATGCTATATAGA 58.916 34.615 14.16 0.00 39.94 1.98
407 408 7.272084 GCGGCAAAATTTTCATGCTATATAGAG 59.728 37.037 14.16 2.80 39.94 2.43
408 409 7.752239 CGGCAAAATTTTCATGCTATATAGAGG 59.248 37.037 14.16 2.07 39.94 3.69
409 410 8.796475 GGCAAAATTTTCATGCTATATAGAGGA 58.204 33.333 14.16 4.38 39.94 3.71
418 419 8.247666 TCATGCTATATAGAGGATCAATCAGG 57.752 38.462 14.16 0.92 37.82 3.86
419 420 7.289549 TCATGCTATATAGAGGATCAATCAGGG 59.710 40.741 14.16 0.00 37.82 4.45
420 421 5.901853 TGCTATATAGAGGATCAATCAGGGG 59.098 44.000 14.16 0.00 37.82 4.79
421 422 5.902431 GCTATATAGAGGATCAATCAGGGGT 59.098 44.000 14.16 0.00 37.82 4.95
422 423 6.041523 GCTATATAGAGGATCAATCAGGGGTC 59.958 46.154 14.16 0.00 37.82 4.46
423 424 2.885388 AGAGGATCAATCAGGGGTCT 57.115 50.000 0.00 0.00 37.82 3.85
438 439 2.509166 GGTCTCCCCTTTTCCGAAAT 57.491 50.000 0.00 0.00 0.00 2.17
439 440 2.803956 GGTCTCCCCTTTTCCGAAATT 58.196 47.619 0.00 0.00 0.00 1.82
440 441 3.162666 GGTCTCCCCTTTTCCGAAATTT 58.837 45.455 0.00 0.00 0.00 1.82
441 442 3.576982 GGTCTCCCCTTTTCCGAAATTTT 59.423 43.478 0.00 0.00 0.00 1.82
442 443 4.039973 GGTCTCCCCTTTTCCGAAATTTTT 59.960 41.667 0.00 0.00 0.00 1.94
541 558 6.434340 AGGAGCCTTTTATTTCTTAAGTGTGG 59.566 38.462 1.63 0.00 0.00 4.17
567 584 6.207417 CCTGTTAATCTTATCCCGCATCAATT 59.793 38.462 0.00 0.00 0.00 2.32
576 593 9.349713 TCTTATCCCGCATCAATTAATTAAAGT 57.650 29.630 1.21 0.00 0.00 2.66
581 598 9.126151 TCCCGCATCAATTAATTAAAGTGAATA 57.874 29.630 15.17 0.00 44.63 1.75
595 612 8.942338 TTAAAGTGAATATGACGTAATCAGCT 57.058 30.769 0.00 0.00 41.91 4.24
597 614 7.932120 AAGTGAATATGACGTAATCAGCTAC 57.068 36.000 0.00 0.00 41.91 3.58
615 632 5.624081 CAGCTACGTGACTATGGTATAAACG 59.376 44.000 0.00 5.18 0.00 3.60
617 634 3.709987 ACGTGACTATGGTATAAACGCC 58.290 45.455 0.00 0.00 0.00 5.68
618 635 2.722629 CGTGACTATGGTATAAACGCCG 59.277 50.000 0.00 0.00 0.00 6.46
620 637 3.979495 GTGACTATGGTATAAACGCCGAG 59.021 47.826 0.00 0.00 0.00 4.63
727 1007 9.545105 TGTTCAAAAATCTAATGCTCAATTTGT 57.455 25.926 0.00 0.00 0.00 2.83
809 1700 6.857777 TTGGGCATAATTTTGTTTGTCAAG 57.142 33.333 0.00 0.00 37.35 3.02
849 1745 3.132925 AGCAAATGCACACAAAATCCAC 58.867 40.909 8.28 0.00 45.16 4.02
901 1806 9.587772 CTAGAGTATGTAGTAAATGTTTGCACT 57.412 33.333 0.00 0.00 0.00 4.40
924 1829 0.382515 CGGCGGTTTCCTTGTTTTCA 59.617 50.000 0.00 0.00 0.00 2.69
951 1868 3.634448 TCACGAAATCCAAAGCAAAGGAA 59.366 39.130 0.00 0.00 37.48 3.36
959 1876 3.132111 TCCAAAGCAAAGGAAACAAGGAC 59.868 43.478 0.00 0.00 0.00 3.85
963 1880 0.313987 CAAAGGAAACAAGGACGCCC 59.686 55.000 0.00 0.00 0.00 6.13
964 1881 0.106419 AAAGGAAACAAGGACGCCCA 60.106 50.000 0.00 0.00 33.88 5.36
1012 1930 0.035056 CCATCCCACTTCACACTCCC 60.035 60.000 0.00 0.00 0.00 4.30
1047 1965 1.042559 CCTGTCCTCTCCTCTCCTGC 61.043 65.000 0.00 0.00 0.00 4.85
1278 2199 2.413142 CGGTGGACGTAGGGGAGAC 61.413 68.421 0.00 0.00 37.93 3.36
1330 2251 3.760035 CCGGTGGTCGTGGAGGAG 61.760 72.222 0.00 0.00 37.11 3.69
1490 2411 4.498520 CCATCGCCTCGCTGTCGT 62.499 66.667 0.00 0.00 36.96 4.34
1690 2641 4.191015 GAAGATCCGGCCACCCCC 62.191 72.222 2.24 0.00 0.00 5.40
1700 2651 1.606601 GCCACCCCCAAGAGGAAAC 60.607 63.158 0.00 0.00 38.24 2.78
1776 2727 2.765122 GAAGGATGCCTCATGCTCTAC 58.235 52.381 1.42 0.00 41.50 2.59
1875 2838 2.317609 CGTCGGAACCAAGCACAGG 61.318 63.158 0.00 0.00 0.00 4.00
1876 2839 1.070786 GTCGGAACCAAGCACAGGA 59.929 57.895 0.00 0.00 0.00 3.86
1902 2865 2.632028 CGGTGGAGATGAAGATGGAGAT 59.368 50.000 0.00 0.00 0.00 2.75
1921 2884 3.717294 GAAAGGCGAGGGGGCAGA 61.717 66.667 0.00 0.00 45.36 4.26
1957 2920 4.570663 GTCCCGGTCATCCTCGCG 62.571 72.222 0.00 0.00 0.00 5.87
2045 3008 1.488261 CCGTCGAGCGAATTTAGGCC 61.488 60.000 0.00 0.00 44.77 5.19
2052 3020 0.812412 GCGAATTTAGGCCGCCAGTA 60.812 55.000 13.15 0.00 42.77 2.74
2056 3024 0.106868 ATTTAGGCCGCCAGTAACCC 60.107 55.000 13.15 0.00 0.00 4.11
2071 3045 2.438614 CCCGCCGAGTGAGAGAGA 60.439 66.667 0.00 0.00 0.00 3.10
2127 3168 7.961325 AAATCAGAGACAGAAGAAGAAGAAC 57.039 36.000 0.00 0.00 0.00 3.01
2172 3213 1.731093 CGGCTTTTCCACCGTTTGT 59.269 52.632 0.00 0.00 44.46 2.83
2173 3214 0.945813 CGGCTTTTCCACCGTTTGTA 59.054 50.000 0.00 0.00 44.46 2.41
2201 3276 2.751259 TGCTGTCATGCCTGAATTTCTC 59.249 45.455 0.00 0.00 31.85 2.87
2205 3280 2.948315 GTCATGCCTGAATTTCTCTCCC 59.052 50.000 0.00 0.00 31.85 4.30
2214 3289 0.674895 ATTTCTCTCCCGTGTGCAGC 60.675 55.000 0.00 0.00 0.00 5.25
2230 3305 2.580326 GCGCGGCATGTTGGATTG 60.580 61.111 8.83 0.00 0.00 2.67
2236 3314 2.598589 CGGCATGTTGGATTGAAACAG 58.401 47.619 0.00 0.00 40.64 3.16
2283 3361 2.716828 CGTTAGCGCGTGACCACAG 61.717 63.158 8.43 0.00 0.00 3.66
2284 3362 2.736995 TTAGCGCGTGACCACAGC 60.737 61.111 8.43 8.80 35.68 4.40
2294 3372 1.300931 GACCACAGCTCGCAAGTCA 60.301 57.895 0.00 0.00 39.48 3.41
2317 3412 4.420143 GACGGTGTCGATGGATGG 57.580 61.111 0.00 0.00 40.11 3.51
2320 3415 0.104855 ACGGTGTCGATGGATGGATG 59.895 55.000 0.00 0.00 40.11 3.51
2327 3422 5.403246 GTGTCGATGGATGGATGTATCTAC 58.597 45.833 0.00 0.00 0.00 2.59
2329 3424 3.694566 TCGATGGATGGATGTATCTACGG 59.305 47.826 0.00 0.00 0.00 4.02
2338 3433 5.793817 TGGATGTATCTACGGGATGAAATG 58.206 41.667 3.86 0.00 35.98 2.32
2354 3450 9.671279 GGGATGAAATGGAATTAAACTGAAATT 57.329 29.630 0.00 0.00 33.67 1.82
2382 3478 0.036388 GTCAGGCATTCAACCCTCGA 60.036 55.000 0.00 0.00 0.00 4.04
2398 3494 1.070445 CGAGGGAGCCCACATCATC 59.930 63.158 8.53 0.00 38.92 2.92
2415 3511 4.597404 TCATCATGCTATCTGAGTGGAC 57.403 45.455 0.00 0.00 0.00 4.02
2427 3523 3.070159 TCTGAGTGGACTGGTCTTTTCTG 59.930 47.826 0.67 1.75 0.00 3.02
2432 3528 1.597742 GACTGGTCTTTTCTGCAGCA 58.402 50.000 9.47 0.00 0.00 4.41
2433 3529 1.534595 GACTGGTCTTTTCTGCAGCAG 59.465 52.381 17.10 17.10 40.71 4.24
2452 3548 6.292596 GCAGCAGAGTGATTAATTGTACTAGC 60.293 42.308 0.00 12.39 0.00 3.42
2454 3550 7.278646 CAGCAGAGTGATTAATTGTACTAGCAA 59.721 37.037 17.47 0.00 30.97 3.91
2483 3579 6.828273 TCATCAGACGGATCAACCAATAATTT 59.172 34.615 0.00 0.00 38.90 1.82
2484 3580 6.435430 TCAGACGGATCAACCAATAATTTG 57.565 37.500 0.00 0.00 38.90 2.32
2485 3581 5.036737 CAGACGGATCAACCAATAATTTGC 58.963 41.667 0.00 0.00 38.90 3.68
2486 3582 4.704540 AGACGGATCAACCAATAATTTGCA 59.295 37.500 0.00 0.00 38.90 4.08
2487 3583 5.360714 AGACGGATCAACCAATAATTTGCAT 59.639 36.000 0.00 0.00 38.90 3.96
2489 3585 4.984161 CGGATCAACCAATAATTTGCATCC 59.016 41.667 0.00 0.00 38.90 3.51
2513 3618 4.434195 AGAGGAGAGGAGAGGAAACAAAT 58.566 43.478 0.00 0.00 0.00 2.32
2540 3645 2.081425 TTTTCCATGTGCGTGGTGGC 62.081 55.000 9.94 0.00 40.27 5.01
2568 3673 1.217585 CCACAGCACGACAGACACAG 61.218 60.000 0.00 0.00 0.00 3.66
2569 3674 1.592669 ACAGCACGACAGACACAGC 60.593 57.895 0.00 0.00 0.00 4.40
2570 3675 1.592400 CAGCACGACAGACACAGCA 60.592 57.895 0.00 0.00 0.00 4.41
2603 3708 3.891049 AGCAAGTTCTTGGTGAGAAACT 58.109 40.909 14.98 0.00 45.59 2.66
2604 3709 3.629398 AGCAAGTTCTTGGTGAGAAACTG 59.371 43.478 14.98 0.00 45.59 3.16
2605 3710 3.378427 GCAAGTTCTTGGTGAGAAACTGT 59.622 43.478 13.35 0.00 45.59 3.55
2606 3711 4.731773 GCAAGTTCTTGGTGAGAAACTGTG 60.732 45.833 13.35 0.00 45.59 3.66
2608 3713 4.192317 AGTTCTTGGTGAGAAACTGTGTC 58.808 43.478 0.00 0.00 45.59 3.67
2609 3714 3.194005 TCTTGGTGAGAAACTGTGTCC 57.806 47.619 0.00 0.00 0.00 4.02
2647 3758 4.017877 GCGTGCTGTGGTCTGTGC 62.018 66.667 0.00 0.00 0.00 4.57
2667 3778 2.069273 CCTGTCGGCTACAAGTTCTTG 58.931 52.381 10.50 10.50 37.74 3.02
2679 3797 6.092807 GCTACAAGTTCTTGGTGATAAAGGAG 59.907 42.308 15.51 0.00 0.00 3.69
2681 3799 4.576330 AGTTCTTGGTGATAAAGGAGGG 57.424 45.455 0.00 0.00 0.00 4.30
2718 3836 6.749139 TGAGGTACAAGTATGTAGATCATGC 58.251 40.000 0.00 0.00 42.54 4.06
2719 3837 6.102897 AGGTACAAGTATGTAGATCATGCC 57.897 41.667 0.00 0.00 42.54 4.40
2720 3838 5.841237 AGGTACAAGTATGTAGATCATGCCT 59.159 40.000 0.00 0.00 42.54 4.75
2724 3842 5.129320 ACAAGTATGTAGATCATGCCTGTCA 59.871 40.000 0.00 0.00 38.70 3.58
2740 3858 1.318576 GTCAGTGGTTGGGTTTCAGG 58.681 55.000 0.00 0.00 0.00 3.86
2770 3888 4.424626 TCTGCAAGATCGTGATGAACTAC 58.575 43.478 13.18 0.00 38.67 2.73
2777 3899 5.547465 AGATCGTGATGAACTACCAAACAA 58.453 37.500 0.00 0.00 0.00 2.83
2886 4011 3.878160 TGTGGGGAAAACAACTTGAAC 57.122 42.857 0.00 0.00 0.00 3.18
2916 4079 8.248945 AGAATGAACATCAACCAATCATCTTTC 58.751 33.333 0.00 0.00 30.76 2.62
2924 4091 7.615582 TCAACCAATCATCTTTCTCATGTAC 57.384 36.000 0.00 0.00 0.00 2.90
2934 4101 4.868171 TCTTTCTCATGTACATTACGGTGC 59.132 41.667 5.37 0.00 0.00 5.01
2935 4102 3.878160 TCTCATGTACATTACGGTGCA 57.122 42.857 5.37 0.00 37.78 4.57
2944 4111 2.143122 CATTACGGTGCACTGACTTGT 58.857 47.619 31.98 11.75 0.00 3.16
2946 4113 0.462375 TACGGTGCACTGACTTGTGT 59.538 50.000 31.98 10.24 39.89 3.72
2996 4163 8.095792 AGATGATTGCTGAGGTAAGAGATAATG 58.904 37.037 0.00 0.00 0.00 1.90
3000 4167 7.618019 TTGCTGAGGTAAGAGATAATGGTAT 57.382 36.000 0.00 0.00 0.00 2.73
3034 4201 8.030106 AGCTTGTCACACTTAAGATAAGAGTAC 58.970 37.037 10.09 0.00 35.70 2.73
3035 4202 7.813148 GCTTGTCACACTTAAGATAAGAGTACA 59.187 37.037 10.09 0.08 35.70 2.90
3037 4204 9.692749 TTGTCACACTTAAGATAAGAGTACAAG 57.307 33.333 10.09 0.00 0.00 3.16
3038 4205 9.074576 TGTCACACTTAAGATAAGAGTACAAGA 57.925 33.333 10.09 0.00 0.00 3.02
3039 4206 9.344309 GTCACACTTAAGATAAGAGTACAAGAC 57.656 37.037 10.09 3.25 0.00 3.01
3040 4207 9.074576 TCACACTTAAGATAAGAGTACAAGACA 57.925 33.333 10.09 0.00 0.00 3.41
3041 4208 9.862371 CACACTTAAGATAAGAGTACAAGACAT 57.138 33.333 10.09 0.00 0.00 3.06
3042 4209 9.862371 ACACTTAAGATAAGAGTACAAGACATG 57.138 33.333 10.09 0.00 0.00 3.21
3043 4210 9.862371 CACTTAAGATAAGAGTACAAGACATGT 57.138 33.333 10.09 0.00 46.36 3.21
3048 4215 9.646427 AAGATAAGAGTACAAGACATGTTTCTC 57.354 33.333 0.00 0.00 43.63 2.87
3049 4216 9.030452 AGATAAGAGTACAAGACATGTTTCTCT 57.970 33.333 0.00 0.00 45.39 3.10
3050 4217 8.994429 ATAAGAGTACAAGACATGTTTCTCTG 57.006 34.615 14.39 0.00 44.09 3.35
3051 4218 6.412362 AGAGTACAAGACATGTTTCTCTGT 57.588 37.500 0.00 0.00 43.67 3.41
3052 4219 6.821388 AGAGTACAAGACATGTTTCTCTGTT 58.179 36.000 0.00 0.00 43.67 3.16
3053 4220 7.275920 AGAGTACAAGACATGTTTCTCTGTTT 58.724 34.615 0.00 0.00 43.67 2.83
3054 4221 8.421784 AGAGTACAAGACATGTTTCTCTGTTTA 58.578 33.333 0.00 0.00 43.67 2.01
3055 4222 9.209175 GAGTACAAGACATGTTTCTCTGTTTAT 57.791 33.333 0.00 0.00 43.63 1.40
3056 4223 9.561069 AGTACAAGACATGTTTCTCTGTTTATT 57.439 29.630 0.00 0.00 43.63 1.40
3113 4280 5.590663 ACGACATGTCAGCTCTTATTCTCTA 59.409 40.000 24.93 0.00 0.00 2.43
3114 4281 6.095580 ACGACATGTCAGCTCTTATTCTCTAA 59.904 38.462 24.93 0.00 0.00 2.10
3151 4322 4.522114 TGACAAGTCACAAGGAACATCAA 58.478 39.130 0.00 0.00 34.14 2.57
3192 4363 8.567104 TCCATGATATGAAATGAAACGTAATGG 58.433 33.333 0.00 0.00 0.00 3.16
3228 4399 0.172578 TGTCGGCGTCAGGTATTCAG 59.827 55.000 6.85 0.00 0.00 3.02
3284 4469 7.352739 GTCTCTCGTTTTTCTTGCTTTCATTA 58.647 34.615 0.00 0.00 0.00 1.90
3293 4478 0.657312 TGCTTTCATTAGGCGATGCG 59.343 50.000 0.00 0.00 0.00 4.73
3295 4480 1.595489 GCTTTCATTAGGCGATGCGTG 60.595 52.381 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.441718 TTCCATTGAGTCTAGGCTCATTT 57.558 39.130 26.91 15.12 43.99 2.32
1 2 5.441718 TTTCCATTGAGTCTAGGCTCATT 57.558 39.130 26.91 20.33 43.99 2.57
2 3 5.441718 TTTTCCATTGAGTCTAGGCTCAT 57.558 39.130 26.91 14.39 43.99 2.90
3 4 4.908601 TTTTCCATTGAGTCTAGGCTCA 57.091 40.909 23.07 23.07 43.03 4.26
4 5 6.765915 AAATTTTCCATTGAGTCTAGGCTC 57.234 37.500 17.74 17.74 36.12 4.70
5 6 6.950619 AGAAAATTTTCCATTGAGTCTAGGCT 59.049 34.615 24.01 0.00 37.92 4.58
6 7 7.163001 AGAAAATTTTCCATTGAGTCTAGGC 57.837 36.000 24.01 0.00 37.92 3.93
7 8 9.415544 CAAAGAAAATTTTCCATTGAGTCTAGG 57.584 33.333 27.15 9.86 36.99 3.02
8 9 9.415544 CCAAAGAAAATTTTCCATTGAGTCTAG 57.584 33.333 30.07 17.83 36.99 2.43
9 10 8.923270 ACCAAAGAAAATTTTCCATTGAGTCTA 58.077 29.630 30.07 0.00 36.99 2.59
10 11 7.712205 CACCAAAGAAAATTTTCCATTGAGTCT 59.288 33.333 30.07 16.51 36.99 3.24
11 12 7.495606 ACACCAAAGAAAATTTTCCATTGAGTC 59.504 33.333 30.07 9.55 36.99 3.36
12 13 7.280652 CACACCAAAGAAAATTTTCCATTGAGT 59.719 33.333 30.07 25.82 36.99 3.41
13 14 7.495279 TCACACCAAAGAAAATTTTCCATTGAG 59.505 33.333 30.07 25.43 36.99 3.02
14 15 7.334090 TCACACCAAAGAAAATTTTCCATTGA 58.666 30.769 30.07 19.62 36.99 2.57
15 16 7.551035 TCACACCAAAGAAAATTTTCCATTG 57.449 32.000 25.64 25.64 37.92 2.82
16 17 7.066887 GGTTCACACCAAAGAAAATTTTCCATT 59.933 33.333 24.01 17.38 43.61 3.16
17 18 6.542005 GGTTCACACCAAAGAAAATTTTCCAT 59.458 34.615 24.01 12.92 43.61 3.41
18 19 5.877564 GGTTCACACCAAAGAAAATTTTCCA 59.122 36.000 24.01 0.00 43.61 3.53
19 20 6.358118 GGTTCACACCAAAGAAAATTTTCC 57.642 37.500 24.01 9.23 43.61 3.13
33 34 4.037923 ACAAGATGTCATTTGGTTCACACC 59.962 41.667 10.50 0.00 44.56 4.16
34 35 5.186996 ACAAGATGTCATTTGGTTCACAC 57.813 39.130 10.50 0.00 0.00 3.82
35 36 5.850557 AACAAGATGTCATTTGGTTCACA 57.149 34.783 10.50 0.00 0.00 3.58
36 37 6.753897 GAAACAAGATGTCATTTGGTTCAC 57.246 37.500 21.24 8.30 45.69 3.18
38 39 6.089249 AGGAAACAAGATGTCATTTGGTTC 57.911 37.500 19.58 19.58 45.67 3.62
39 40 7.781324 ATAGGAAACAAGATGTCATTTGGTT 57.219 32.000 9.41 9.41 36.95 3.67
40 41 7.093771 GGAATAGGAAACAAGATGTCATTTGGT 60.094 37.037 10.50 3.75 0.00 3.67
41 42 7.123247 AGGAATAGGAAACAAGATGTCATTTGG 59.877 37.037 10.50 0.00 0.00 3.28
42 43 8.059798 AGGAATAGGAAACAAGATGTCATTTG 57.940 34.615 0.00 0.00 0.00 2.32
43 44 9.927081 ATAGGAATAGGAAACAAGATGTCATTT 57.073 29.630 0.00 0.00 0.00 2.32
44 45 9.927081 AATAGGAATAGGAAACAAGATGTCATT 57.073 29.630 0.00 0.00 0.00 2.57
45 46 9.566432 GAATAGGAATAGGAAACAAGATGTCAT 57.434 33.333 0.00 0.00 0.00 3.06
46 47 8.548025 TGAATAGGAATAGGAAACAAGATGTCA 58.452 33.333 0.00 0.00 0.00 3.58
47 48 8.964476 TGAATAGGAATAGGAAACAAGATGTC 57.036 34.615 0.00 0.00 0.00 3.06
69 70 9.716531 GATGACATGTATCTCAAATCCTATGAA 57.283 33.333 0.00 0.00 0.00 2.57
70 71 9.097946 AGATGACATGTATCTCAAATCCTATGA 57.902 33.333 0.00 0.00 29.05 2.15
71 72 9.368674 GAGATGACATGTATCTCAAATCCTATG 57.631 37.037 24.95 0.00 46.22 2.23
81 82 7.890515 TGTAGGAATGAGATGACATGTATCTC 58.109 38.462 24.04 24.04 46.82 2.75
82 83 7.846101 TGTAGGAATGAGATGACATGTATCT 57.154 36.000 14.05 14.05 37.59 1.98
83 84 8.893219 TTTGTAGGAATGAGATGACATGTATC 57.107 34.615 0.00 2.87 0.00 2.24
84 85 9.857656 AATTTGTAGGAATGAGATGACATGTAT 57.142 29.630 0.00 0.00 0.00 2.29
85 86 9.685276 AAATTTGTAGGAATGAGATGACATGTA 57.315 29.630 0.00 0.00 0.00 2.29
86 87 8.585471 AAATTTGTAGGAATGAGATGACATGT 57.415 30.769 0.00 0.00 0.00 3.21
87 88 8.133627 GGAAATTTGTAGGAATGAGATGACATG 58.866 37.037 0.00 0.00 0.00 3.21
88 89 8.057623 AGGAAATTTGTAGGAATGAGATGACAT 58.942 33.333 0.00 0.00 0.00 3.06
89 90 7.405292 AGGAAATTTGTAGGAATGAGATGACA 58.595 34.615 0.00 0.00 0.00 3.58
90 91 7.872113 AGGAAATTTGTAGGAATGAGATGAC 57.128 36.000 0.00 0.00 0.00 3.06
93 94 9.579932 GGAATAGGAAATTTGTAGGAATGAGAT 57.420 33.333 0.00 0.00 0.00 2.75
94 95 8.781951 AGGAATAGGAAATTTGTAGGAATGAGA 58.218 33.333 0.00 0.00 0.00 3.27
95 96 8.986929 AGGAATAGGAAATTTGTAGGAATGAG 57.013 34.615 0.00 0.00 0.00 2.90
117 118 9.661954 GGTTCATAGGATAGGATTATCATAGGA 57.338 37.037 0.00 1.09 39.88 2.94
118 119 9.439461 TGGTTCATAGGATAGGATTATCATAGG 57.561 37.037 0.00 0.00 36.37 2.57
125 126 8.660435 CCTCTTTTGGTTCATAGGATAGGATTA 58.340 37.037 0.00 0.00 28.27 1.75
126 127 7.521669 CCTCTTTTGGTTCATAGGATAGGATT 58.478 38.462 0.00 0.00 28.27 3.01
127 128 6.466470 GCCTCTTTTGGTTCATAGGATAGGAT 60.466 42.308 0.00 0.00 28.27 3.24
128 129 5.163195 GCCTCTTTTGGTTCATAGGATAGGA 60.163 44.000 0.00 0.00 0.00 2.94
129 130 5.066593 GCCTCTTTTGGTTCATAGGATAGG 58.933 45.833 0.00 0.00 0.00 2.57
130 131 5.066593 GGCCTCTTTTGGTTCATAGGATAG 58.933 45.833 0.00 0.00 0.00 2.08
131 132 4.726825 AGGCCTCTTTTGGTTCATAGGATA 59.273 41.667 0.00 0.00 0.00 2.59
132 133 3.529319 AGGCCTCTTTTGGTTCATAGGAT 59.471 43.478 0.00 0.00 0.00 3.24
133 134 2.919602 AGGCCTCTTTTGGTTCATAGGA 59.080 45.455 0.00 0.00 0.00 2.94
134 135 3.282885 GAGGCCTCTTTTGGTTCATAGG 58.717 50.000 26.25 0.00 0.00 2.57
135 136 3.691609 GTGAGGCCTCTTTTGGTTCATAG 59.308 47.826 32.28 0.00 0.00 2.23
136 137 3.073798 TGTGAGGCCTCTTTTGGTTCATA 59.926 43.478 32.28 6.26 0.00 2.15
137 138 2.158475 TGTGAGGCCTCTTTTGGTTCAT 60.158 45.455 32.28 0.00 0.00 2.57
138 139 1.214175 TGTGAGGCCTCTTTTGGTTCA 59.786 47.619 32.28 14.95 0.00 3.18
139 140 1.981256 TGTGAGGCCTCTTTTGGTTC 58.019 50.000 32.28 12.85 0.00 3.62
140 141 2.629617 CAATGTGAGGCCTCTTTTGGTT 59.370 45.455 32.28 15.50 0.00 3.67
141 142 2.242043 CAATGTGAGGCCTCTTTTGGT 58.758 47.619 32.28 10.95 0.00 3.67
142 143 2.242043 ACAATGTGAGGCCTCTTTTGG 58.758 47.619 32.28 20.58 0.00 3.28
143 144 5.649782 AATACAATGTGAGGCCTCTTTTG 57.350 39.130 32.28 29.13 0.00 2.44
144 145 6.670695 AAAATACAATGTGAGGCCTCTTTT 57.329 33.333 32.28 22.81 0.00 2.27
145 146 6.041979 ACAAAAATACAATGTGAGGCCTCTTT 59.958 34.615 32.28 18.64 0.00 2.52
146 147 5.539955 ACAAAAATACAATGTGAGGCCTCTT 59.460 36.000 32.28 16.70 0.00 2.85
147 148 5.079643 ACAAAAATACAATGTGAGGCCTCT 58.920 37.500 32.28 14.48 0.00 3.69
148 149 5.391312 ACAAAAATACAATGTGAGGCCTC 57.609 39.130 26.78 26.78 0.00 4.70
149 150 5.806654 AACAAAAATACAATGTGAGGCCT 57.193 34.783 3.86 3.86 0.00 5.19
150 151 5.988561 TCAAACAAAAATACAATGTGAGGCC 59.011 36.000 0.00 0.00 0.00 5.19
151 152 7.656707 ATCAAACAAAAATACAATGTGAGGC 57.343 32.000 0.00 0.00 0.00 4.70
244 245 6.403866 TTGGACACAAAATGCATCTACTTT 57.596 33.333 0.00 0.00 32.66 2.66
282 283 4.508124 AGAACGACTCACTTTTTACTGCAG 59.492 41.667 13.48 13.48 0.00 4.41
289 290 3.675467 GTGCAGAACGACTCACTTTTT 57.325 42.857 0.00 0.00 0.00 1.94
340 341 5.306160 CCATCCCTTGCCTATGAATTTCAAT 59.694 40.000 2.68 0.00 0.00 2.57
376 377 3.484557 GCATGAAAATTTTGCCGCAGATG 60.485 43.478 8.47 0.00 0.00 2.90
379 380 2.070783 AGCATGAAAATTTTGCCGCAG 58.929 42.857 8.47 0.00 37.07 5.18
382 383 7.752239 CCTCTATATAGCATGAAAATTTTGCCG 59.248 37.037 8.47 0.00 37.07 5.69
404 405 2.688477 GAGACCCCTGATTGATCCTCT 58.312 52.381 0.00 0.00 0.00 3.69
405 406 1.696884 GGAGACCCCTGATTGATCCTC 59.303 57.143 0.00 0.00 0.00 3.71
406 407 1.813102 GGAGACCCCTGATTGATCCT 58.187 55.000 0.00 0.00 0.00 3.24
420 421 4.866508 AAAATTTCGGAAAAGGGGAGAC 57.133 40.909 7.33 0.00 0.00 3.36
440 441 6.543465 AGATACGATGCATTGATCCTCAAAAA 59.457 34.615 21.12 0.00 40.12 1.94
441 442 6.057533 AGATACGATGCATTGATCCTCAAAA 58.942 36.000 21.12 0.00 40.12 2.44
442 443 5.614308 AGATACGATGCATTGATCCTCAAA 58.386 37.500 21.12 0.00 40.12 2.69
443 444 5.219343 AGATACGATGCATTGATCCTCAA 57.781 39.130 21.12 0.00 41.09 3.02
450 454 6.907741 TGTTGAAAAAGATACGATGCATTGA 58.092 32.000 21.12 4.83 0.00 2.57
541 558 2.846193 TGCGGGATAAGATTAACAGGC 58.154 47.619 0.00 0.00 0.00 4.85
586 603 5.184340 ACCATAGTCACGTAGCTGATTAC 57.816 43.478 0.00 0.00 0.00 1.89
595 612 4.554526 CGGCGTTTATACCATAGTCACGTA 60.555 45.833 0.00 0.00 0.00 3.57
597 614 2.722629 CGGCGTTTATACCATAGTCACG 59.277 50.000 0.00 0.00 0.00 4.35
628 646 5.008613 AGCAAGTCTAACAATTTTTCAGCGA 59.991 36.000 0.00 0.00 0.00 4.93
633 651 8.634475 AACAAGAGCAAGTCTAACAATTTTTC 57.366 30.769 0.00 0.00 32.65 2.29
776 1056 8.098220 ACAAAATTATGCCCAAAATCTTGTTC 57.902 30.769 0.00 0.00 0.00 3.18
784 1064 7.554118 TCTTGACAAACAAAATTATGCCCAAAA 59.446 29.630 0.00 0.00 38.08 2.44
823 1714 4.645762 TTTTGTGTGCATTTGCTCTACA 57.354 36.364 3.94 3.97 42.66 2.74
829 1725 2.871022 TGTGGATTTTGTGTGCATTTGC 59.129 40.909 0.00 0.00 42.50 3.68
901 1806 0.535553 AACAAGGAAACCGCCGCTAA 60.536 50.000 0.00 0.00 0.00 3.09
951 1868 2.029380 GCTTTTATTGGGCGTCCTTGTT 60.029 45.455 7.97 0.00 0.00 2.83
959 1876 0.175531 CCCTTGGCTTTTATTGGGCG 59.824 55.000 0.00 0.00 0.00 6.13
963 1880 3.326297 TGGGTTTCCCTTGGCTTTTATTG 59.674 43.478 6.38 0.00 45.70 1.90
964 1881 3.592865 TGGGTTTCCCTTGGCTTTTATT 58.407 40.909 6.38 0.00 45.70 1.40
984 1901 3.503748 GTGAAGTGGGATGGTCTCTTTTG 59.496 47.826 0.00 0.00 0.00 2.44
1029 1947 0.324183 TGCAGGAGAGGAGAGGACAG 60.324 60.000 0.00 0.00 0.00 3.51
1030 1948 0.337773 ATGCAGGAGAGGAGAGGACA 59.662 55.000 0.00 0.00 0.00 4.02
1031 1949 0.752054 CATGCAGGAGAGGAGAGGAC 59.248 60.000 0.00 0.00 0.00 3.85
1278 2199 4.845580 ATGGCGGCAGCGAAGGAG 62.846 66.667 19.29 0.00 46.35 3.69
1490 2411 1.809869 CCGACTCGATCCAGAGCAA 59.190 57.895 0.00 0.00 41.77 3.91
1609 2539 2.955022 AATCGGAGCAGCTGGATGGC 62.955 60.000 17.12 0.00 0.00 4.40
1610 2540 0.883814 GAATCGGAGCAGCTGGATGG 60.884 60.000 17.12 0.00 0.00 3.51
1611 2541 0.883814 GGAATCGGAGCAGCTGGATG 60.884 60.000 17.12 0.00 0.00 3.51
1612 2542 1.449353 GGAATCGGAGCAGCTGGAT 59.551 57.895 17.12 6.61 0.00 3.41
1613 2543 2.903357 GGAATCGGAGCAGCTGGA 59.097 61.111 17.12 4.15 0.00 3.86
1614 2544 2.587194 CGGAATCGGAGCAGCTGG 60.587 66.667 17.12 0.00 0.00 4.85
1615 2545 1.880340 GTCGGAATCGGAGCAGCTG 60.880 63.158 10.11 10.11 36.95 4.24
1616 2546 2.290122 CTGTCGGAATCGGAGCAGCT 62.290 60.000 0.00 0.00 36.95 4.24
1617 2547 1.880340 CTGTCGGAATCGGAGCAGC 60.880 63.158 0.00 0.00 36.95 5.25
1690 2641 0.977395 ACCTCCTCGGTTTCCTCTTG 59.023 55.000 0.00 0.00 46.37 3.02
1700 2651 3.522731 CCTCAGCGACCTCCTCGG 61.523 72.222 0.00 0.00 43.18 4.63
1768 2719 2.827190 TCGCCGTCGGTAGAGCAT 60.827 61.111 13.94 0.00 36.13 3.79
1769 2720 3.506096 CTCGCCGTCGGTAGAGCA 61.506 66.667 20.35 0.00 36.13 4.26
1791 2742 3.003173 TAACTGGCTCCGGCTGCT 61.003 61.111 16.62 2.52 38.73 4.24
1875 2838 1.676529 TCTTCATCTCCACCGACGATC 59.323 52.381 0.00 0.00 0.00 3.69
1876 2839 1.763968 TCTTCATCTCCACCGACGAT 58.236 50.000 0.00 0.00 0.00 3.73
2052 3020 2.282958 TCTCTCACTCGGCGGGTT 60.283 61.111 11.11 0.00 0.00 4.11
2056 3024 1.652012 GGATCTCTCTCACTCGGCG 59.348 63.158 0.00 0.00 0.00 6.46
2127 3168 6.566141 TCAACATTCAGCATGTATGGATTTG 58.434 36.000 0.00 3.21 46.58 2.32
2155 3196 3.439895 TTTACAAACGGTGGAAAAGCC 57.560 42.857 0.00 0.00 37.09 4.35
2169 3210 4.523943 AGGCATGACAGCAGAATTTTACAA 59.476 37.500 0.00 0.00 35.83 2.41
2170 3211 4.081406 AGGCATGACAGCAGAATTTTACA 58.919 39.130 0.00 0.00 35.83 2.41
2172 3213 4.334552 TCAGGCATGACAGCAGAATTTTA 58.665 39.130 0.00 0.00 35.83 1.52
2173 3214 3.159472 TCAGGCATGACAGCAGAATTTT 58.841 40.909 0.00 0.00 35.83 1.82
2214 3289 0.109365 TTTCAATCCAACATGCCGCG 60.109 50.000 0.00 0.00 0.00 6.46
2226 3301 4.036734 TGTCAGCCAAGAACTGTTTCAATC 59.963 41.667 0.00 0.00 36.50 2.67
2230 3305 2.287248 GCTGTCAGCCAAGAACTGTTTC 60.287 50.000 14.27 0.00 34.48 2.78
2236 3314 0.723981 GATCGCTGTCAGCCAAGAAC 59.276 55.000 19.14 6.04 38.18 3.01
2287 3365 3.470567 CCGTCGCGTCTGACTTGC 61.471 66.667 5.77 2.00 36.71 4.01
2317 3412 6.037786 TCCATTTCATCCCGTAGATACATC 57.962 41.667 0.00 0.00 32.37 3.06
2320 3415 8.842358 TTAATTCCATTTCATCCCGTAGATAC 57.158 34.615 0.00 0.00 32.37 2.24
2327 3422 6.449635 TCAGTTTAATTCCATTTCATCCCG 57.550 37.500 0.00 0.00 0.00 5.14
2338 3433 5.800438 GCCGACAGAATTTCAGTTTAATTCC 59.200 40.000 0.00 0.00 40.98 3.01
2354 3450 2.835701 GAATGCCTGACGCCGACAGA 62.836 60.000 17.77 0.00 37.54 3.41
2382 3478 0.477204 CATGATGATGTGGGCTCCCT 59.523 55.000 6.50 0.00 36.94 4.20
2392 3488 4.930405 GTCCACTCAGATAGCATGATGATG 59.070 45.833 0.00 0.00 0.00 3.07
2398 3494 2.433604 ACCAGTCCACTCAGATAGCATG 59.566 50.000 0.00 0.00 0.00 4.06
2415 3511 1.805345 CTCTGCTGCAGAAAAGACCAG 59.195 52.381 30.00 13.20 40.18 4.00
2427 3523 6.292596 GCTAGTACAATTAATCACTCTGCTGC 60.293 42.308 0.00 0.00 0.00 5.25
2452 3548 5.759763 TGGTTGATCCGTCTGATGATATTTG 59.240 40.000 0.00 0.00 39.52 2.32
2454 3550 5.551305 TGGTTGATCCGTCTGATGATATT 57.449 39.130 0.00 0.00 39.52 1.28
2483 3579 0.467106 CTCCTCTCCTCTCGGATGCA 60.467 60.000 0.00 0.00 39.01 3.96
2484 3580 0.179004 TCTCCTCTCCTCTCGGATGC 60.179 60.000 0.00 0.00 39.01 3.91
2485 3581 1.545428 CCTCTCCTCTCCTCTCGGATG 60.545 61.905 0.00 0.00 39.01 3.51
2486 3582 0.771127 CCTCTCCTCTCCTCTCGGAT 59.229 60.000 0.00 0.00 39.01 4.18
2487 3583 0.326713 TCCTCTCCTCTCCTCTCGGA 60.327 60.000 0.00 0.00 37.82 4.55
2489 3585 2.021457 GTTTCCTCTCCTCTCCTCTCG 58.979 57.143 0.00 0.00 0.00 4.04
2499 3604 3.641436 ACACCCAAATTTGTTTCCTCTCC 59.359 43.478 16.73 0.00 0.00 3.71
2513 3618 1.202463 CGCACATGGAAAACACCCAAA 60.202 47.619 0.00 0.00 37.22 3.28
2540 3645 1.063972 CGTGCTGTGGTTGGTGTTG 59.936 57.895 0.00 0.00 0.00 3.33
2554 3659 2.947890 GCTGCTGTGTCTGTCGTGC 61.948 63.158 0.00 0.00 0.00 5.34
2568 3673 0.179161 CTTGCTGAATCTGCTGCTGC 60.179 55.000 13.10 8.89 40.20 5.25
2569 3674 1.166129 ACTTGCTGAATCTGCTGCTG 58.834 50.000 13.10 0.00 34.32 4.41
2570 3675 1.811359 GAACTTGCTGAATCTGCTGCT 59.189 47.619 13.10 0.00 34.32 4.24
2602 3707 4.929211 TGTTTATCAAGATGACGGACACAG 59.071 41.667 0.00 0.00 0.00 3.66
2603 3708 4.888917 TGTTTATCAAGATGACGGACACA 58.111 39.130 0.00 0.00 0.00 3.72
2604 3709 5.856126 TTGTTTATCAAGATGACGGACAC 57.144 39.130 0.00 0.00 0.00 3.67
2605 3710 5.163764 GCATTGTTTATCAAGATGACGGACA 60.164 40.000 0.00 0.00 39.55 4.02
2606 3711 5.266242 GCATTGTTTATCAAGATGACGGAC 58.734 41.667 0.00 0.00 39.55 4.79
2608 3713 4.274069 CGCATTGTTTATCAAGATGACGG 58.726 43.478 0.00 0.00 39.55 4.79
2609 3714 3.720818 GCGCATTGTTTATCAAGATGACG 59.279 43.478 0.30 0.00 39.55 4.35
2647 3758 2.069273 CAAGAACTTGTAGCCGACAGG 58.931 52.381 6.41 0.00 39.88 4.00
2659 3770 4.354087 ACCCTCCTTTATCACCAAGAACTT 59.646 41.667 0.00 0.00 0.00 2.66
2660 3771 3.916989 ACCCTCCTTTATCACCAAGAACT 59.083 43.478 0.00 0.00 0.00 3.01
2664 3775 2.846827 AGGACCCTCCTTTATCACCAAG 59.153 50.000 0.00 0.00 46.91 3.61
2679 3797 1.630878 ACCTCAGAATCACAAGGACCC 59.369 52.381 3.17 0.00 32.99 4.46
2681 3799 4.537135 TGTACCTCAGAATCACAAGGAC 57.463 45.455 3.17 0.00 32.99 3.85
2718 3836 1.318576 GAAACCCAACCACTGACAGG 58.681 55.000 7.51 0.00 0.00 4.00
2719 3837 1.949525 CTGAAACCCAACCACTGACAG 59.050 52.381 0.00 0.00 0.00 3.51
2720 3838 1.409521 CCTGAAACCCAACCACTGACA 60.410 52.381 0.00 0.00 0.00 3.58
2724 3842 0.188342 ATGCCTGAAACCCAACCACT 59.812 50.000 0.00 0.00 0.00 4.00
2740 3858 1.394917 ACGATCTTGCAGACGAAATGC 59.605 47.619 9.91 0.00 44.11 3.56
2770 3888 4.432712 CTGTTTCCAGGAAAGTTGTTTGG 58.567 43.478 15.49 0.00 34.90 3.28
2777 3899 1.683385 GCTTGCTGTTTCCAGGAAAGT 59.317 47.619 15.49 0.00 46.63 2.66
2886 4011 4.852134 TTGGTTGATGTTCATTCTGTGG 57.148 40.909 0.00 0.00 0.00 4.17
2916 4079 3.306973 CAGTGCACCGTAATGTACATGAG 59.693 47.826 14.63 3.92 37.63 2.90
2924 4091 2.096268 CACAAGTCAGTGCACCGTAATG 60.096 50.000 14.63 10.42 32.04 1.90
2934 4101 2.032054 ACATCGCAAACACAAGTCAGTG 59.968 45.455 0.00 0.00 44.93 3.66
2935 4102 2.287915 GACATCGCAAACACAAGTCAGT 59.712 45.455 0.00 0.00 0.00 3.41
2944 4111 1.889545 TGGACATGACATCGCAAACA 58.110 45.000 0.00 0.00 0.00 2.83
2946 4113 4.198530 ACATATGGACATGACATCGCAAA 58.801 39.130 7.80 0.00 0.00 3.68
2996 4163 7.611213 AGTGTGACAAGCTTAATTACATACC 57.389 36.000 0.00 0.00 0.00 2.73
3000 4167 8.896320 TCTTAAGTGTGACAAGCTTAATTACA 57.104 30.769 0.00 0.72 35.15 2.41
3057 4224 5.499139 AGAAACATGTCTTCTCGCAAAAA 57.501 34.783 13.96 0.00 0.00 1.94
3058 4225 5.095691 GAGAAACATGTCTTCTCGCAAAA 57.904 39.130 23.05 0.00 39.46 2.44
3059 4226 4.732285 GAGAAACATGTCTTCTCGCAAA 57.268 40.909 23.05 0.00 39.46 3.68
3065 4232 8.926710 CGTTATTAACAGAGAAACATGTCTTCT 58.073 33.333 17.61 17.61 35.82 2.85
3066 4233 8.922676 TCGTTATTAACAGAGAAACATGTCTTC 58.077 33.333 0.00 5.78 0.00 2.87
3113 4280 5.072741 ACTTGTCAACTGTGATGCCTTATT 58.927 37.500 0.00 0.00 35.80 1.40
3114 4281 4.655963 ACTTGTCAACTGTGATGCCTTAT 58.344 39.130 0.00 0.00 35.80 1.73
3118 4285 2.031682 GTGACTTGTCAACTGTGATGCC 60.032 50.000 4.93 0.00 35.80 4.40
3119 4286 2.613595 TGTGACTTGTCAACTGTGATGC 59.386 45.455 4.93 0.00 35.80 3.91
3120 4287 4.260907 CCTTGTGACTTGTCAACTGTGATG 60.261 45.833 4.93 0.00 35.80 3.07
3121 4288 3.879295 CCTTGTGACTTGTCAACTGTGAT 59.121 43.478 4.93 0.00 35.80 3.06
3122 4289 3.055458 TCCTTGTGACTTGTCAACTGTGA 60.055 43.478 4.93 0.00 0.00 3.58
3123 4290 3.270027 TCCTTGTGACTTGTCAACTGTG 58.730 45.455 4.93 0.00 0.00 3.66
3187 4358 7.967854 CGACAGCATTTCAGTTTAATTCCATTA 59.032 33.333 0.00 0.00 0.00 1.90
3192 4363 4.558860 GCCGACAGCATTTCAGTTTAATTC 59.441 41.667 0.00 0.00 42.97 2.17
3195 4366 2.095969 CGCCGACAGCATTTCAGTTTAA 60.096 45.455 0.00 0.00 44.04 1.52
3197 4368 0.238289 CGCCGACAGCATTTCAGTTT 59.762 50.000 0.00 0.00 44.04 2.66
3228 4399 5.010516 ACTCAGGTAGTATGATGATGTGAGC 59.989 44.000 0.00 0.00 36.36 4.26
3284 4469 2.525248 CGTAATGCACGCATCGCCT 61.525 57.895 4.73 0.00 45.03 5.52
3293 4478 4.614555 TGGTTGATTGATCGTAATGCAC 57.385 40.909 0.00 0.00 0.00 4.57
3295 4480 9.546909 CTATTATTGGTTGATTGATCGTAATGC 57.453 33.333 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.