Multiple sequence alignment - TraesCS5D01G145300

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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 TraesCS5D01G145300 chr5D 100.000 2810 0 0 1 2810 232010275 232013084 0.000000e+00 5190.0
1 TraesCS5D01G145300 chr5D 89.565 115 9 2 269 380 526752614 526752500 2.920000e-30 143.0
2 TraesCS5D01G145300 chr5A 91.176 2176 94 33 558 2686 324404360 324402236 0.000000e+00 2865.0
3 TraesCS5D01G145300 chr5A 90.854 1815 100 30 426 2206 324481170 324479388 0.000000e+00 2372.0
4 TraesCS5D01G145300 chr5A 92.199 282 15 3 111 391 324481771 324481496 2.620000e-105 392.0
5 TraesCS5D01G145300 chr5A 90.517 116 9 2 426 540 324405251 324405137 4.850000e-33 152.0
6 TraesCS5D01G145300 chr5A 91.667 108 9 0 1 108 324489526 324489419 1.740000e-32 150.0
7 TraesCS5D01G145300 chr5B 93.657 1072 40 8 465 1518 273148335 273147274 0.000000e+00 1578.0
8 TraesCS5D01G145300 chr5B 89.759 830 40 15 1577 2380 273147280 273146470 0.000000e+00 1020.0
9 TraesCS5D01G145300 chr6A 88.235 119 12 1 264 380 615495306 615495188 1.050000e-29 141.0
10 TraesCS5D01G145300 chr4D 87.395 119 13 1 264 380 428988460 428988578 4.880000e-28 135.0
11 TraesCS5D01G145300 chr3D 88.496 113 10 3 270 380 1847366 1847477 1.760000e-27 134.0
12 TraesCS5D01G145300 chr3D 86.885 122 11 4 264 381 590073705 590073585 6.320000e-27 132.0
13 TraesCS5D01G145300 chr4B 86.667 120 13 2 264 380 28633115 28632996 2.270000e-26 130.0
14 TraesCS5D01G145300 chr4B 84.071 113 18 0 90 202 400382794 400382682 2.960000e-20 110.0
15 TraesCS5D01G145300 chr2B 86.667 120 13 2 264 380 363772768 363772887 2.270000e-26 130.0
16 TraesCS5D01G145300 chr7B 86.667 120 11 4 265 380 135391340 135391458 8.170000e-26 128.0
17 TraesCS5D01G145300 chr7B 84.112 107 17 0 90 196 476643705 476643811 1.380000e-18 104.0
18 TraesCS5D01G145300 chr7A 86.916 107 14 0 90 196 693063498 693063604 1.370000e-23 121.0
19 TraesCS5D01G145300 chr7A 85.981 107 14 1 90 196 592200509 592200614 2.290000e-21 113.0
20 TraesCS5D01G145300 chr7A 85.859 99 14 0 90 188 693090089 693090187 3.830000e-19 106.0
21 TraesCS5D01G145300 chr4A 85.981 107 13 2 90 196 498691080 498691184 2.290000e-21 113.0
22 TraesCS5D01G145300 chr2D 86.000 100 14 0 94 193 571009084 571008985 1.060000e-19 108.0
23 TraesCS5D01G145300 chr1A 80.702 114 22 0 90 203 576315395 576315282 3.860000e-14 89.8
24 TraesCS5D01G145300 chr1B 97.143 35 1 0 2772 2806 269314862 269314896 3.020000e-05 60.2


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 TraesCS5D01G145300 chr5D 232010275 232013084 2809 False 5190.0 5190 100.0000 1 2810 1 chr5D.!!$F1 2809
1 TraesCS5D01G145300 chr5A 324402236 324405251 3015 True 1508.5 2865 90.8465 426 2686 2 chr5A.!!$R2 2260
2 TraesCS5D01G145300 chr5A 324479388 324481771 2383 True 1382.0 2372 91.5265 111 2206 2 chr5A.!!$R3 2095
3 TraesCS5D01G145300 chr5B 273146470 273148335 1865 True 1299.0 1578 91.7080 465 2380 2 chr5B.!!$R1 1915

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
938 2015 0.036671 ACTAGCTTAACCACACCGCC 60.037 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2774 3929 0.106894 TCGTGCCATGTGTTGTACCA 59.893 50.0 0.0 0.0 0.0 3.25 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
18 19 2.334307 CCTTGCTATGGATTGGCCG 58.666 57.895 0.00 0.00 40.66 6.13
19 20 1.174712 CCTTGCTATGGATTGGCCGG 61.175 60.000 0.00 0.00 40.66 6.13
20 21 1.152777 TTGCTATGGATTGGCCGGG 60.153 57.895 2.18 0.00 40.66 5.73
21 22 1.640593 TTGCTATGGATTGGCCGGGA 61.641 55.000 2.18 0.00 40.66 5.14
22 23 1.150536 GCTATGGATTGGCCGGGAA 59.849 57.895 2.18 0.00 40.66 3.97
23 24 0.467290 GCTATGGATTGGCCGGGAAA 60.467 55.000 2.18 0.00 40.66 3.13
24 25 1.318576 CTATGGATTGGCCGGGAAAC 58.681 55.000 2.18 0.00 40.66 2.78
25 26 0.464735 TATGGATTGGCCGGGAAACG 60.465 55.000 2.18 0.00 40.66 3.60
34 35 2.109387 CGGGAAACGGACCACACA 59.891 61.111 0.00 0.00 39.42 3.72
35 36 1.959226 CGGGAAACGGACCACACAG 60.959 63.158 0.00 0.00 39.42 3.66
36 37 2.258726 GGGAAACGGACCACACAGC 61.259 63.158 0.00 0.00 0.00 4.40
37 38 2.258726 GGAAACGGACCACACAGCC 61.259 63.158 0.00 0.00 0.00 4.85
38 39 2.203294 AAACGGACCACACAGCCC 60.203 61.111 0.00 0.00 0.00 5.19
39 40 3.785122 AAACGGACCACACAGCCCC 62.785 63.158 0.00 0.00 0.00 5.80
42 43 4.699522 GGACCACACAGCCCCGAC 62.700 72.222 0.00 0.00 0.00 4.79
43 44 3.936203 GACCACACAGCCCCGACA 61.936 66.667 0.00 0.00 0.00 4.35
44 45 3.469863 GACCACACAGCCCCGACAA 62.470 63.158 0.00 0.00 0.00 3.18
45 46 2.034066 CCACACAGCCCCGACAAT 59.966 61.111 0.00 0.00 0.00 2.71
46 47 2.334946 CCACACAGCCCCGACAATG 61.335 63.158 0.00 0.00 0.00 2.82
47 48 2.672996 ACACAGCCCCGACAATGC 60.673 61.111 0.00 0.00 0.00 3.56
48 49 3.443045 CACAGCCCCGACAATGCC 61.443 66.667 0.00 0.00 0.00 4.40
49 50 3.650950 ACAGCCCCGACAATGCCT 61.651 61.111 0.00 0.00 0.00 4.75
50 51 2.825836 CAGCCCCGACAATGCCTC 60.826 66.667 0.00 0.00 0.00 4.70
51 52 4.115199 AGCCCCGACAATGCCTCC 62.115 66.667 0.00 0.00 0.00 4.30
69 70 3.585990 GCGCCGCATGCTGGTATT 61.586 61.111 23.32 0.00 38.05 1.89
70 71 2.328989 CGCCGCATGCTGGTATTG 59.671 61.111 23.32 11.68 38.05 1.90
71 72 2.179547 CGCCGCATGCTGGTATTGA 61.180 57.895 23.32 0.00 38.05 2.57
72 73 1.356624 GCCGCATGCTGGTATTGAC 59.643 57.895 23.32 7.74 36.87 3.18
73 74 1.097547 GCCGCATGCTGGTATTGACT 61.098 55.000 23.32 0.00 36.87 3.41
74 75 0.940126 CCGCATGCTGGTATTGACTC 59.060 55.000 17.13 0.00 0.00 3.36
75 76 0.940126 CGCATGCTGGTATTGACTCC 59.060 55.000 17.13 0.00 0.00 3.85
76 77 0.940126 GCATGCTGGTATTGACTCCG 59.060 55.000 11.37 0.00 0.00 4.63
77 78 0.940126 CATGCTGGTATTGACTCCGC 59.060 55.000 0.00 0.00 0.00 5.54
78 79 0.179045 ATGCTGGTATTGACTCCGCC 60.179 55.000 0.00 0.00 0.00 6.13
79 80 1.264749 TGCTGGTATTGACTCCGCCT 61.265 55.000 0.00 0.00 0.00 5.52
80 81 0.530870 GCTGGTATTGACTCCGCCTC 60.531 60.000 0.00 0.00 0.00 4.70
81 82 1.115467 CTGGTATTGACTCCGCCTCT 58.885 55.000 0.00 0.00 0.00 3.69
82 83 2.307768 CTGGTATTGACTCCGCCTCTA 58.692 52.381 0.00 0.00 0.00 2.43
83 84 2.294791 CTGGTATTGACTCCGCCTCTAG 59.705 54.545 0.00 0.00 0.00 2.43
84 85 1.000052 GGTATTGACTCCGCCTCTAGC 60.000 57.143 0.00 0.00 38.52 3.42
85 86 1.000052 GTATTGACTCCGCCTCTAGCC 60.000 57.143 0.00 0.00 38.78 3.93
86 87 0.687757 ATTGACTCCGCCTCTAGCCA 60.688 55.000 0.00 0.00 38.78 4.75
87 88 1.323271 TTGACTCCGCCTCTAGCCAG 61.323 60.000 0.00 0.00 38.78 4.85
88 89 1.454111 GACTCCGCCTCTAGCCAGA 60.454 63.158 0.00 0.00 38.78 3.86
89 90 0.825840 GACTCCGCCTCTAGCCAGAT 60.826 60.000 0.00 0.00 38.78 2.90
90 91 0.478942 ACTCCGCCTCTAGCCAGATA 59.521 55.000 0.00 0.00 38.78 1.98
91 92 1.076350 ACTCCGCCTCTAGCCAGATAT 59.924 52.381 0.00 0.00 38.78 1.63
92 93 2.309162 ACTCCGCCTCTAGCCAGATATA 59.691 50.000 0.00 0.00 38.78 0.86
93 94 3.053245 ACTCCGCCTCTAGCCAGATATAT 60.053 47.826 0.00 0.00 38.78 0.86
94 95 4.166337 ACTCCGCCTCTAGCCAGATATATA 59.834 45.833 0.00 0.00 38.78 0.86
95 96 5.163034 ACTCCGCCTCTAGCCAGATATATAT 60.163 44.000 0.00 0.00 38.78 0.86
96 97 6.044520 ACTCCGCCTCTAGCCAGATATATATA 59.955 42.308 0.00 0.00 38.78 0.86
97 98 6.477253 TCCGCCTCTAGCCAGATATATATAG 58.523 44.000 0.00 0.00 38.78 1.31
98 99 5.650266 CCGCCTCTAGCCAGATATATATAGG 59.350 48.000 8.64 8.64 38.78 2.57
99 100 5.650266 CGCCTCTAGCCAGATATATATAGGG 59.350 48.000 13.04 10.36 38.78 3.53
100 101 5.955355 GCCTCTAGCCAGATATATATAGGGG 59.045 48.000 13.04 8.50 34.57 4.79
101 102 6.240615 GCCTCTAGCCAGATATATATAGGGGA 60.241 46.154 10.03 2.11 33.47 4.81
102 103 7.533865 GCCTCTAGCCAGATATATATAGGGGAT 60.534 44.444 10.03 6.83 33.47 3.85
103 104 8.405850 CCTCTAGCCAGATATATATAGGGGATT 58.594 40.741 13.04 4.01 33.47 3.01
104 105 9.253832 CTCTAGCCAGATATATATAGGGGATTG 57.746 40.741 13.04 7.55 0.00 2.67
105 106 8.180165 TCTAGCCAGATATATATAGGGGATTGG 58.820 40.741 13.04 6.84 0.00 3.16
106 107 6.949997 AGCCAGATATATATAGGGGATTGGA 58.050 40.000 13.04 0.00 0.00 3.53
107 108 7.560926 AGCCAGATATATATAGGGGATTGGAT 58.439 38.462 13.04 3.10 0.00 3.41
108 109 8.027521 AGCCAGATATATATAGGGGATTGGATT 58.972 37.037 13.04 0.00 0.00 3.01
109 110 8.105829 GCCAGATATATATAGGGGATTGGATTG 58.894 40.741 13.04 0.00 0.00 2.67
132 133 2.912956 TCCAGCCAAATCTTAGTGGAGT 59.087 45.455 0.00 0.00 37.03 3.85
133 134 4.081087 GTCCAGCCAAATCTTAGTGGAGTA 60.081 45.833 0.00 0.00 37.03 2.59
134 135 4.534500 TCCAGCCAAATCTTAGTGGAGTAA 59.466 41.667 0.00 0.00 37.03 2.24
135 136 5.013704 TCCAGCCAAATCTTAGTGGAGTAAA 59.986 40.000 0.00 0.00 37.03 2.01
136 137 5.710099 CCAGCCAAATCTTAGTGGAGTAAAA 59.290 40.000 0.00 0.00 37.03 1.52
137 138 6.208599 CCAGCCAAATCTTAGTGGAGTAAAAA 59.791 38.462 0.00 0.00 37.03 1.94
138 139 7.093771 CCAGCCAAATCTTAGTGGAGTAAAAAT 60.094 37.037 0.00 0.00 37.03 1.82
188 189 7.073725 TGGATACTCAGCTATTTTTAGGGGATT 59.926 37.037 0.00 0.00 37.61 3.01
202 203 2.587307 AGGGGATTGGTTAGAAATGCCT 59.413 45.455 6.64 0.00 43.13 4.75
268 269 1.226746 GCACCCTGACACAACAGTAC 58.773 55.000 0.00 0.00 36.30 2.73
293 294 1.669779 AGTCGTCGCTATGTGGTCTAC 59.330 52.381 0.00 0.00 0.00 2.59
294 295 1.019673 TCGTCGCTATGTGGTCTACC 58.980 55.000 0.00 0.00 0.00 3.18
338 339 4.725556 TTTCTGATGTTCGTTGTACTGC 57.274 40.909 0.00 0.00 0.00 4.40
375 377 9.631452 GGAATAGATTGGAAGTTTTCTTGAAAG 57.369 33.333 0.00 0.00 40.61 2.62
391 393 5.927689 TCTTGAAAGAAAACGACGGCTATAA 59.072 36.000 0.00 0.00 30.73 0.98
392 394 5.520022 TGAAAGAAAACGACGGCTATAAC 57.480 39.130 0.00 0.00 0.00 1.89
393 395 4.389687 TGAAAGAAAACGACGGCTATAACC 59.610 41.667 0.00 0.00 0.00 2.85
394 396 3.881937 AGAAAACGACGGCTATAACCT 57.118 42.857 0.00 0.00 0.00 3.50
395 397 3.778618 AGAAAACGACGGCTATAACCTC 58.221 45.455 0.00 0.00 0.00 3.85
396 398 2.199291 AAACGACGGCTATAACCTCG 57.801 50.000 0.00 10.54 36.81 4.63
397 399 0.383231 AACGACGGCTATAACCTCGG 59.617 55.000 14.40 0.00 35.79 4.63
398 400 1.285023 CGACGGCTATAACCTCGGG 59.715 63.158 0.00 0.00 31.13 5.14
417 691 3.462982 GGGAAAACAATGGACCAAACAC 58.537 45.455 0.00 0.00 0.00 3.32
420 694 1.036707 AACAATGGACCAAACACGGG 58.963 50.000 0.00 0.00 0.00 5.28
421 695 0.183971 ACAATGGACCAAACACGGGA 59.816 50.000 0.00 0.00 0.00 5.14
422 696 1.323412 CAATGGACCAAACACGGGAA 58.677 50.000 0.00 0.00 0.00 3.97
434 727 3.059352 ACACGGGAAGAAAAGATCCAG 57.941 47.619 0.00 0.00 37.46 3.86
437 730 2.025887 ACGGGAAGAAAAGATCCAGCAT 60.026 45.455 0.00 0.00 37.46 3.79
463 756 6.642430 TGCTGGCTTTTTATTGATTTAGCAT 58.358 32.000 0.00 0.00 33.10 3.79
529 1068 5.083533 ACAGAGGCAACAGAGATAGAAAG 57.916 43.478 0.00 0.00 41.41 2.62
573 1626 4.727507 AGCTACTCAGTCATGGTTACAG 57.272 45.455 0.00 0.00 0.00 2.74
744 1818 2.199291 GCCAATTGCAAAGAGATCGG 57.801 50.000 1.71 0.00 40.77 4.18
828 1902 4.681978 AACGACCTGGCAGCGACC 62.682 66.667 19.10 3.15 0.00 4.79
862 1939 4.202121 GCTCAATCAATCCTGCATGTTCAT 60.202 41.667 0.00 0.00 0.00 2.57
865 1942 1.672363 TCAATCCTGCATGTTCATCGC 59.328 47.619 0.00 0.00 0.00 4.58
884 1961 2.165845 CGCTCCCCTATTTATACCCTCG 59.834 54.545 0.00 0.00 0.00 4.63
886 1963 3.836562 GCTCCCCTATTTATACCCTCGAA 59.163 47.826 0.00 0.00 0.00 3.71
887 1964 4.285260 GCTCCCCTATTTATACCCTCGAAA 59.715 45.833 0.00 0.00 0.00 3.46
921 1998 0.397941 CCACACCATCACACTCCACT 59.602 55.000 0.00 0.00 0.00 4.00
931 2008 3.236047 TCACACTCCACTAGCTTAACCA 58.764 45.455 0.00 0.00 0.00 3.67
932 2009 3.006537 TCACACTCCACTAGCTTAACCAC 59.993 47.826 0.00 0.00 0.00 4.16
933 2010 2.969950 ACACTCCACTAGCTTAACCACA 59.030 45.455 0.00 0.00 0.00 4.17
934 2011 3.244112 ACACTCCACTAGCTTAACCACAC 60.244 47.826 0.00 0.00 0.00 3.82
935 2012 2.302157 ACTCCACTAGCTTAACCACACC 59.698 50.000 0.00 0.00 0.00 4.16
936 2013 1.274167 TCCACTAGCTTAACCACACCG 59.726 52.381 0.00 0.00 0.00 4.94
937 2014 1.076332 CACTAGCTTAACCACACCGC 58.924 55.000 0.00 0.00 0.00 5.68
938 2015 0.036671 ACTAGCTTAACCACACCGCC 60.037 55.000 0.00 0.00 0.00 6.13
939 2016 1.079681 TAGCTTAACCACACCGCCG 60.080 57.895 0.00 0.00 0.00 6.46
1413 2502 2.076100 TGCATTTTCATCTTCTCGCGT 58.924 42.857 5.77 0.00 0.00 6.01
1448 2537 6.712095 GTCCAGATCTTGTGCATATTTCCATA 59.288 38.462 0.00 0.00 0.00 2.74
1450 2539 7.609146 TCCAGATCTTGTGCATATTTCCATATC 59.391 37.037 0.00 0.00 0.00 1.63
1521 2610 3.579534 TTACACCAGGCCAAACAGTTA 57.420 42.857 5.01 0.00 0.00 2.24
1522 2611 1.687563 ACACCAGGCCAAACAGTTAC 58.312 50.000 5.01 0.00 0.00 2.50
1523 2612 1.214424 ACACCAGGCCAAACAGTTACT 59.786 47.619 5.01 0.00 0.00 2.24
1524 2613 1.608590 CACCAGGCCAAACAGTTACTG 59.391 52.381 11.21 11.21 37.52 2.74
1526 2615 2.440253 ACCAGGCCAAACAGTTACTGTA 59.560 45.455 18.93 0.00 44.62 2.74
1550 2639 3.386768 TTAATCCAGCATCCGAGCTAC 57.613 47.619 0.00 0.00 44.54 3.58
1551 2640 1.418334 AATCCAGCATCCGAGCTACT 58.582 50.000 0.00 0.00 44.54 2.57
1552 2641 2.294449 ATCCAGCATCCGAGCTACTA 57.706 50.000 0.00 0.00 44.54 1.82
1676 2772 7.875554 AGTTTTTCTTAAGAGCTAGGAAGTGAG 59.124 37.037 5.12 0.00 28.26 3.51
1730 2827 7.000575 TCATATTGAAGAAAAACGGTCGATC 57.999 36.000 0.00 0.00 0.00 3.69
1735 2832 3.287312 AGAAAAACGGTCGATCGTGTA 57.713 42.857 26.49 0.00 43.07 2.90
1754 2852 9.758651 ATCGTGTATTTTAGCATGTTACATCTA 57.241 29.630 0.00 0.00 0.00 1.98
1755 2853 9.589111 TCGTGTATTTTAGCATGTTACATCTAA 57.411 29.630 0.00 4.35 0.00 2.10
1946 3069 4.084013 GCTTGCGTGTGTTATTTCAGTACT 60.084 41.667 0.00 0.00 0.00 2.73
1947 3070 4.983215 TGCGTGTGTTATTTCAGTACTG 57.017 40.909 17.17 17.17 0.00 2.74
1948 3071 4.373527 TGCGTGTGTTATTTCAGTACTGT 58.626 39.130 21.99 6.25 0.00 3.55
1949 3072 4.210328 TGCGTGTGTTATTTCAGTACTGTG 59.790 41.667 21.99 0.00 0.00 3.66
1950 3073 4.210537 GCGTGTGTTATTTCAGTACTGTGT 59.789 41.667 21.99 11.71 0.00 3.72
1951 3074 5.611844 GCGTGTGTTATTTCAGTACTGTGTC 60.612 44.000 21.99 8.91 0.00 3.67
1952 3075 5.460748 CGTGTGTTATTTCAGTACTGTGTCA 59.539 40.000 21.99 11.06 0.00 3.58
1953 3076 6.561533 CGTGTGTTATTTCAGTACTGTGTCAC 60.562 42.308 21.99 19.90 0.00 3.67
1954 3077 6.479001 GTGTGTTATTTCAGTACTGTGTCACT 59.521 38.462 21.99 5.74 0.00 3.41
1955 3078 6.478673 TGTGTTATTTCAGTACTGTGTCACTG 59.521 38.462 21.99 8.21 42.88 3.66
1956 3079 6.479001 GTGTTATTTCAGTACTGTGTCACTGT 59.521 38.462 21.99 18.15 42.28 3.55
1957 3080 6.478673 TGTTATTTCAGTACTGTGTCACTGTG 59.521 38.462 21.99 0.17 42.28 3.66
1958 3081 4.465632 TTTCAGTACTGTGTCACTGTGT 57.534 40.909 21.99 12.21 42.28 3.72
1959 3082 3.436700 TCAGTACTGTGTCACTGTGTG 57.563 47.619 21.99 18.25 42.28 3.82
1960 3083 2.758423 TCAGTACTGTGTCACTGTGTGT 59.242 45.455 21.99 6.73 42.28 3.72
1961 3084 3.116300 CAGTACTGTGTCACTGTGTGTC 58.884 50.000 21.87 11.41 37.87 3.67
1968 3091 1.134818 TGTCACTGTGTGTCTGTGTCC 60.135 52.381 7.79 0.00 43.39 4.02
1984 3107 1.337728 TGTCCATGTCTGTACCTTGCG 60.338 52.381 0.00 0.00 0.00 4.85
2059 3185 2.799917 GCGTGAGTGAACTGTCAACTCT 60.800 50.000 18.16 4.82 34.87 3.24
2071 3197 4.100189 ACTGTCAACTCTTTGCTGTACTCT 59.900 41.667 0.00 0.00 32.17 3.24
2075 3201 5.631512 GTCAACTCTTTGCTGTACTCTAGTG 59.368 44.000 0.00 0.00 32.17 2.74
2168 3297 4.818534 ATTATTGACGTGCATGGATGTC 57.181 40.909 27.34 27.34 33.18 3.06
2206 3353 3.572632 AGCAGTATGATGGAGCATTGT 57.427 42.857 0.00 0.00 39.69 2.71
2207 3354 3.211865 AGCAGTATGATGGAGCATTGTG 58.788 45.455 0.00 0.00 39.69 3.33
2315 3462 4.209288 CACTAGTTTGGACTTTCTGTGTCG 59.791 45.833 0.00 0.00 37.33 4.35
2382 3529 4.106197 CGAGACGTTTTCCTTCTGATAGG 58.894 47.826 0.00 0.00 36.59 2.57
2384 3531 4.094476 AGACGTTTTCCTTCTGATAGGGA 58.906 43.478 0.00 0.00 35.90 4.20
2462 3610 9.434420 AAGAAACAAAGAATGAAAACACATGAA 57.566 25.926 0.00 0.00 0.00 2.57
2527 3680 3.243101 ACTGTGAAGTGTGAGTACAGTCG 60.243 47.826 0.00 0.00 46.34 4.18
2549 3702 4.659088 GAAGACATGACACGTCGAATCTA 58.341 43.478 0.00 0.00 38.46 1.98
2596 3751 7.921214 ACCTATAAACATATCACAGTCGTTCAG 59.079 37.037 0.00 0.00 0.00 3.02
2603 3758 6.650807 ACATATCACAGTCGTTCAGAAAATGT 59.349 34.615 0.00 0.00 0.00 2.71
2604 3759 7.817478 ACATATCACAGTCGTTCAGAAAATGTA 59.183 33.333 0.00 0.00 0.00 2.29
2605 3760 8.820933 CATATCACAGTCGTTCAGAAAATGTAT 58.179 33.333 0.00 0.00 0.00 2.29
2606 3761 7.672983 ATCACAGTCGTTCAGAAAATGTATT 57.327 32.000 0.00 0.00 0.00 1.89
2607 3762 7.490962 TCACAGTCGTTCAGAAAATGTATTT 57.509 32.000 0.00 0.00 0.00 1.40
2608 3763 7.572759 TCACAGTCGTTCAGAAAATGTATTTC 58.427 34.615 0.00 0.00 0.00 2.17
2609 3764 6.516355 CACAGTCGTTCAGAAAATGTATTTCG 59.484 38.462 0.00 0.00 33.86 3.46
2610 3765 6.202188 ACAGTCGTTCAGAAAATGTATTTCGT 59.798 34.615 0.00 0.00 33.86 3.85
2611 3766 7.069569 CAGTCGTTCAGAAAATGTATTTCGTT 58.930 34.615 0.00 0.00 33.86 3.85
2612 3767 7.058354 CAGTCGTTCAGAAAATGTATTTCGTTG 59.942 37.037 0.00 0.00 33.86 4.10
2613 3768 6.849305 GTCGTTCAGAAAATGTATTTCGTTGT 59.151 34.615 0.00 0.00 33.86 3.32
2614 3769 6.848800 TCGTTCAGAAAATGTATTTCGTTGTG 59.151 34.615 0.00 0.00 33.86 3.33
2615 3770 6.086241 CGTTCAGAAAATGTATTTCGTTGTGG 59.914 38.462 0.00 0.00 33.86 4.17
2616 3771 6.869315 TCAGAAAATGTATTTCGTTGTGGA 57.131 33.333 0.00 0.00 33.86 4.02
2617 3772 7.265647 TCAGAAAATGTATTTCGTTGTGGAA 57.734 32.000 0.00 0.00 33.86 3.53
2618 3773 7.881142 TCAGAAAATGTATTTCGTTGTGGAAT 58.119 30.769 0.00 0.00 33.86 3.01
2651 3806 8.766000 ATGTATTACGATGTGAACAGTTGTAA 57.234 30.769 0.00 7.14 0.00 2.41
2686 3841 5.462398 AGTTTTAAATAGCGTGCTATCTCGG 59.538 40.000 14.32 0.00 38.20 4.63
2687 3842 4.579454 TTAAATAGCGTGCTATCTCGGT 57.421 40.909 14.32 0.00 38.20 4.69
2688 3843 2.708386 AATAGCGTGCTATCTCGGTC 57.292 50.000 14.32 0.00 38.20 4.79
2689 3844 0.882474 ATAGCGTGCTATCTCGGTCC 59.118 55.000 8.54 0.00 39.95 4.46
2690 3845 0.179026 TAGCGTGCTATCTCGGTCCT 60.179 55.000 0.00 0.00 39.95 3.85
2691 3846 0.179026 AGCGTGCTATCTCGGTCCTA 60.179 55.000 0.00 0.00 35.38 2.94
2692 3847 0.882474 GCGTGCTATCTCGGTCCTAT 59.118 55.000 0.00 0.00 0.00 2.57
2693 3848 2.082231 GCGTGCTATCTCGGTCCTATA 58.918 52.381 0.00 0.00 0.00 1.31
2694 3849 2.486982 GCGTGCTATCTCGGTCCTATAA 59.513 50.000 0.00 0.00 0.00 0.98
2695 3850 3.670091 GCGTGCTATCTCGGTCCTATAAC 60.670 52.174 0.00 0.00 0.00 1.89
2696 3851 3.501062 CGTGCTATCTCGGTCCTATAACA 59.499 47.826 0.00 0.00 0.00 2.41
2697 3852 4.156190 CGTGCTATCTCGGTCCTATAACAT 59.844 45.833 0.00 0.00 0.00 2.71
2698 3853 5.335740 CGTGCTATCTCGGTCCTATAACATT 60.336 44.000 0.00 0.00 0.00 2.71
2699 3854 6.456501 GTGCTATCTCGGTCCTATAACATTT 58.543 40.000 0.00 0.00 0.00 2.32
2700 3855 6.366332 GTGCTATCTCGGTCCTATAACATTTG 59.634 42.308 0.00 0.00 0.00 2.32
2701 3856 5.348997 GCTATCTCGGTCCTATAACATTTGC 59.651 44.000 0.00 0.00 0.00 3.68
2702 3857 4.746535 TCTCGGTCCTATAACATTTGCA 57.253 40.909 0.00 0.00 0.00 4.08
2703 3858 4.693283 TCTCGGTCCTATAACATTTGCAG 58.307 43.478 0.00 0.00 0.00 4.41
2704 3859 3.804036 TCGGTCCTATAACATTTGCAGG 58.196 45.455 0.00 0.00 0.00 4.85
2705 3860 2.878406 CGGTCCTATAACATTTGCAGGG 59.122 50.000 0.00 0.00 0.00 4.45
2706 3861 2.623416 GGTCCTATAACATTTGCAGGGC 59.377 50.000 0.00 0.00 0.00 5.19
2707 3862 2.290641 GTCCTATAACATTTGCAGGGCG 59.709 50.000 0.00 0.00 0.00 6.13
2708 3863 2.092646 TCCTATAACATTTGCAGGGCGT 60.093 45.455 0.00 0.00 0.00 5.68
2709 3864 2.290641 CCTATAACATTTGCAGGGCGTC 59.709 50.000 0.00 0.00 0.00 5.19
2710 3865 1.832883 ATAACATTTGCAGGGCGTCA 58.167 45.000 0.00 0.00 0.00 4.35
2711 3866 1.832883 TAACATTTGCAGGGCGTCAT 58.167 45.000 0.00 0.00 0.00 3.06
2712 3867 0.244450 AACATTTGCAGGGCGTCATG 59.756 50.000 0.00 0.00 0.00 3.07
2717 3872 3.414272 GCAGGGCGTCATGCTAAG 58.586 61.111 20.84 0.00 46.01 2.18
2718 3873 2.828128 GCAGGGCGTCATGCTAAGC 61.828 63.158 20.84 0.00 46.01 3.09
2723 3878 3.833706 GCGTCATGCTAAGCCATTC 57.166 52.632 0.00 0.00 41.73 2.67
2724 3879 1.016627 GCGTCATGCTAAGCCATTCA 58.983 50.000 0.00 0.00 41.73 2.57
2725 3880 1.003116 GCGTCATGCTAAGCCATTCAG 60.003 52.381 0.00 0.00 41.73 3.02
2726 3881 2.283298 CGTCATGCTAAGCCATTCAGT 58.717 47.619 0.00 0.00 0.00 3.41
2727 3882 3.457234 CGTCATGCTAAGCCATTCAGTA 58.543 45.455 0.00 0.00 0.00 2.74
2728 3883 3.492383 CGTCATGCTAAGCCATTCAGTAG 59.508 47.826 0.00 0.00 0.00 2.57
2729 3884 4.697514 GTCATGCTAAGCCATTCAGTAGA 58.302 43.478 0.00 0.00 0.00 2.59
2730 3885 5.118990 GTCATGCTAAGCCATTCAGTAGAA 58.881 41.667 0.00 0.00 38.31 2.10
2731 3886 5.762218 GTCATGCTAAGCCATTCAGTAGAAT 59.238 40.000 0.00 0.00 45.16 2.40
2732 3887 6.261826 GTCATGCTAAGCCATTCAGTAGAATT 59.738 38.462 0.00 0.00 42.46 2.17
2733 3888 6.830324 TCATGCTAAGCCATTCAGTAGAATTT 59.170 34.615 0.00 0.00 42.46 1.82
2734 3889 7.992608 TCATGCTAAGCCATTCAGTAGAATTTA 59.007 33.333 0.00 0.00 42.46 1.40
2735 3890 7.792374 TGCTAAGCCATTCAGTAGAATTTAG 57.208 36.000 0.00 0.00 42.46 1.85
2736 3891 6.260936 TGCTAAGCCATTCAGTAGAATTTAGC 59.739 38.462 17.68 17.68 46.30 3.09
2737 3892 5.741388 AAGCCATTCAGTAGAATTTAGCG 57.259 39.130 0.00 0.00 42.46 4.26
2738 3893 4.770795 AGCCATTCAGTAGAATTTAGCGT 58.229 39.130 0.00 0.00 42.46 5.07
2739 3894 4.572389 AGCCATTCAGTAGAATTTAGCGTG 59.428 41.667 0.00 0.00 42.46 5.34
2740 3895 4.332819 GCCATTCAGTAGAATTTAGCGTGT 59.667 41.667 0.00 0.00 42.46 4.49
2741 3896 5.163754 GCCATTCAGTAGAATTTAGCGTGTT 60.164 40.000 0.00 0.00 42.46 3.32
2742 3897 6.036735 GCCATTCAGTAGAATTTAGCGTGTTA 59.963 38.462 0.00 0.00 42.46 2.41
2743 3898 7.254795 GCCATTCAGTAGAATTTAGCGTGTTAT 60.255 37.037 0.00 0.00 42.46 1.89
2744 3899 9.256477 CCATTCAGTAGAATTTAGCGTGTTATA 57.744 33.333 0.00 0.00 42.46 0.98
2770 3925 9.880157 ATATTTTTCACAAATATGCAGAGCTTT 57.120 25.926 0.00 0.00 33.08 3.51
2772 3927 8.746922 TTTTTCACAAATATGCAGAGCTTTAG 57.253 30.769 0.00 0.00 0.00 1.85
2773 3928 6.441093 TTCACAAATATGCAGAGCTTTAGG 57.559 37.500 0.00 0.00 0.00 2.69
2774 3929 5.500234 TCACAAATATGCAGAGCTTTAGGT 58.500 37.500 0.00 0.00 0.00 3.08
2775 3930 5.355071 TCACAAATATGCAGAGCTTTAGGTG 59.645 40.000 0.00 0.00 0.00 4.00
2776 3931 4.641989 ACAAATATGCAGAGCTTTAGGTGG 59.358 41.667 0.00 0.00 0.00 4.61
2777 3932 4.510167 AATATGCAGAGCTTTAGGTGGT 57.490 40.909 0.00 0.00 0.00 4.16
2778 3933 5.630415 AATATGCAGAGCTTTAGGTGGTA 57.370 39.130 0.00 0.00 0.00 3.25
2779 3934 2.762535 TGCAGAGCTTTAGGTGGTAC 57.237 50.000 0.00 0.00 0.00 3.34
2780 3935 1.974957 TGCAGAGCTTTAGGTGGTACA 59.025 47.619 0.00 0.00 0.00 2.90
2781 3936 2.370519 TGCAGAGCTTTAGGTGGTACAA 59.629 45.455 0.00 0.00 44.16 2.41
2792 3947 0.237235 GTGGTACAACACATGGCACG 59.763 55.000 0.00 0.00 44.16 5.34
2793 3948 0.106894 TGGTACAACACATGGCACGA 59.893 50.000 0.00 0.00 31.92 4.35
2794 3949 1.231221 GGTACAACACATGGCACGAA 58.769 50.000 0.00 0.00 0.00 3.85
2795 3950 1.069500 GGTACAACACATGGCACGAAC 60.069 52.381 0.00 0.00 0.00 3.95
2796 3951 0.862490 TACAACACATGGCACGAACG 59.138 50.000 0.00 0.00 0.00 3.95
2797 3952 1.725625 CAACACATGGCACGAACGC 60.726 57.895 0.00 0.00 0.00 4.84
2798 3953 2.183504 AACACATGGCACGAACGCA 61.184 52.632 0.00 0.00 0.00 5.24
2799 3954 1.719725 AACACATGGCACGAACGCAA 61.720 50.000 0.00 0.00 0.00 4.85
2801 3956 1.596752 ACATGGCACGAACGCAAGA 60.597 52.632 0.00 0.00 43.62 3.02
2802 3957 1.133253 CATGGCACGAACGCAAGAG 59.867 57.895 0.00 0.00 43.62 2.85
2803 3958 2.034879 ATGGCACGAACGCAAGAGG 61.035 57.895 0.00 0.00 43.62 3.69
2804 3959 4.090057 GGCACGAACGCAAGAGGC 62.090 66.667 0.00 0.00 43.62 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.174712 CCGGCCAATCCATAGCAAGG 61.175 60.000 2.24 0.00 34.01 3.61
1 2 1.174712 CCCGGCCAATCCATAGCAAG 61.175 60.000 2.24 0.00 34.01 4.01
2 3 1.152777 CCCGGCCAATCCATAGCAA 60.153 57.895 2.24 0.00 34.01 3.91
3 4 1.640593 TTCCCGGCCAATCCATAGCA 61.641 55.000 2.24 0.00 34.01 3.49
4 5 0.467290 TTTCCCGGCCAATCCATAGC 60.467 55.000 2.24 0.00 34.01 2.97
5 6 1.318576 GTTTCCCGGCCAATCCATAG 58.681 55.000 2.24 0.00 34.01 2.23
6 7 0.464735 CGTTTCCCGGCCAATCCATA 60.465 55.000 2.24 0.00 34.01 2.74
7 8 1.752694 CGTTTCCCGGCCAATCCAT 60.753 57.895 2.24 0.00 34.01 3.41
8 9 2.360600 CGTTTCCCGGCCAATCCA 60.361 61.111 2.24 0.00 34.01 3.41
17 18 1.959226 CTGTGTGGTCCGTTTCCCG 60.959 63.158 0.00 0.00 0.00 5.14
18 19 2.258726 GCTGTGTGGTCCGTTTCCC 61.259 63.158 0.00 0.00 0.00 3.97
19 20 2.258726 GGCTGTGTGGTCCGTTTCC 61.259 63.158 0.00 0.00 0.00 3.13
20 21 2.258726 GGGCTGTGTGGTCCGTTTC 61.259 63.158 0.00 0.00 0.00 2.78
21 22 2.203294 GGGCTGTGTGGTCCGTTT 60.203 61.111 0.00 0.00 0.00 3.60
22 23 4.265056 GGGGCTGTGTGGTCCGTT 62.265 66.667 0.00 0.00 0.00 4.44
25 26 4.699522 GTCGGGGCTGTGTGGTCC 62.700 72.222 0.00 0.00 0.00 4.46
26 27 2.748058 ATTGTCGGGGCTGTGTGGTC 62.748 60.000 0.00 0.00 0.00 4.02
27 28 2.829384 ATTGTCGGGGCTGTGTGGT 61.829 57.895 0.00 0.00 0.00 4.16
28 29 2.034066 ATTGTCGGGGCTGTGTGG 59.966 61.111 0.00 0.00 0.00 4.17
29 30 2.981560 GCATTGTCGGGGCTGTGTG 61.982 63.158 0.00 0.00 0.00 3.82
30 31 2.672996 GCATTGTCGGGGCTGTGT 60.673 61.111 0.00 0.00 0.00 3.72
31 32 3.443045 GGCATTGTCGGGGCTGTG 61.443 66.667 0.00 0.00 0.00 3.66
32 33 3.628646 GAGGCATTGTCGGGGCTGT 62.629 63.158 0.00 0.00 40.34 4.40
33 34 2.825836 GAGGCATTGTCGGGGCTG 60.826 66.667 0.00 0.00 40.34 4.85
34 35 4.115199 GGAGGCATTGTCGGGGCT 62.115 66.667 0.00 0.00 43.26 5.19
54 55 1.097547 AGTCAATACCAGCATGCGGC 61.098 55.000 22.90 5.83 45.30 6.53
55 56 0.940126 GAGTCAATACCAGCATGCGG 59.060 55.000 21.83 21.83 31.97 5.69
56 57 0.940126 GGAGTCAATACCAGCATGCG 59.060 55.000 13.01 7.31 31.97 4.73
57 58 0.940126 CGGAGTCAATACCAGCATGC 59.060 55.000 10.51 10.51 31.97 4.06
58 59 0.940126 GCGGAGTCAATACCAGCATG 59.060 55.000 0.00 0.00 0.00 4.06
59 60 0.179045 GGCGGAGTCAATACCAGCAT 60.179 55.000 0.00 0.00 0.00 3.79
60 61 1.220749 GGCGGAGTCAATACCAGCA 59.779 57.895 0.00 0.00 0.00 4.41
61 62 0.530870 GAGGCGGAGTCAATACCAGC 60.531 60.000 0.00 0.00 0.00 4.85
62 63 1.115467 AGAGGCGGAGTCAATACCAG 58.885 55.000 0.00 0.00 0.00 4.00
63 64 2.307768 CTAGAGGCGGAGTCAATACCA 58.692 52.381 0.00 0.00 0.00 3.25
64 65 1.000052 GCTAGAGGCGGAGTCAATACC 60.000 57.143 0.00 0.00 0.00 2.73
65 66 1.000052 GGCTAGAGGCGGAGTCAATAC 60.000 57.143 0.00 0.00 42.94 1.89
66 67 1.329256 GGCTAGAGGCGGAGTCAATA 58.671 55.000 0.00 0.00 42.94 1.90
67 68 0.687757 TGGCTAGAGGCGGAGTCAAT 60.688 55.000 0.00 0.00 44.42 2.57
68 69 1.304962 TGGCTAGAGGCGGAGTCAA 60.305 57.895 0.00 0.00 44.42 3.18
69 70 2.359011 TGGCTAGAGGCGGAGTCA 59.641 61.111 0.00 0.00 44.42 3.41
75 76 5.650266 CCCTATATATATCTGGCTAGAGGCG 59.350 48.000 5.82 0.00 44.42 5.52
76 77 5.955355 CCCCTATATATATCTGGCTAGAGGC 59.045 48.000 5.82 0.00 36.14 4.70
77 78 7.350044 TCCCCTATATATATCTGGCTAGAGG 57.650 44.000 5.82 0.00 36.14 3.69
78 79 9.253832 CAATCCCCTATATATATCTGGCTAGAG 57.746 40.741 5.82 0.00 36.14 2.43
79 80 8.180165 CCAATCCCCTATATATATCTGGCTAGA 58.820 40.741 0.82 0.82 37.35 2.43
80 81 8.180165 TCCAATCCCCTATATATATCTGGCTAG 58.820 40.741 0.00 0.00 0.00 3.42
81 82 8.080658 TCCAATCCCCTATATATATCTGGCTA 57.919 38.462 0.00 0.00 0.00 3.93
82 83 6.949997 TCCAATCCCCTATATATATCTGGCT 58.050 40.000 0.00 0.00 0.00 4.75
83 84 7.821134 ATCCAATCCCCTATATATATCTGGC 57.179 40.000 0.00 0.00 0.00 4.85
84 85 8.609483 CCAATCCAATCCCCTATATATATCTGG 58.391 40.741 0.00 3.41 0.00 3.86
85 86 9.175577 ACCAATCCAATCCCCTATATATATCTG 57.824 37.037 0.00 0.00 0.00 2.90
86 87 9.398921 GACCAATCCAATCCCCTATATATATCT 57.601 37.037 0.00 0.00 0.00 1.98
87 88 8.606830 GGACCAATCCAATCCCCTATATATATC 58.393 40.741 0.00 0.00 45.47 1.63
88 89 8.525729 GGACCAATCCAATCCCCTATATATAT 57.474 38.462 0.00 0.00 45.47 0.86
89 90 7.947782 GGACCAATCCAATCCCCTATATATA 57.052 40.000 0.00 0.00 45.47 0.86
90 91 6.848562 GGACCAATCCAATCCCCTATATAT 57.151 41.667 0.00 0.00 45.47 0.86
109 110 2.026262 TCCACTAAGATTTGGCTGGACC 60.026 50.000 0.00 0.00 39.84 4.46
115 116 8.957466 AGTATTTTTACTCCACTAAGATTTGGC 58.043 33.333 0.00 0.00 32.37 4.52
133 134 8.418662 GGAGTAAAACCTTTGTGGAGTATTTTT 58.581 33.333 0.00 0.00 39.71 1.94
134 135 7.255346 CGGAGTAAAACCTTTGTGGAGTATTTT 60.255 37.037 0.00 0.00 39.71 1.82
135 136 6.206048 CGGAGTAAAACCTTTGTGGAGTATTT 59.794 38.462 0.00 0.00 39.71 1.40
136 137 5.704053 CGGAGTAAAACCTTTGTGGAGTATT 59.296 40.000 0.00 0.00 39.71 1.89
137 138 5.243207 CGGAGTAAAACCTTTGTGGAGTAT 58.757 41.667 0.00 0.00 39.71 2.12
138 139 4.634199 CGGAGTAAAACCTTTGTGGAGTA 58.366 43.478 0.00 0.00 39.71 2.59
145 146 2.500229 TCCAGCGGAGTAAAACCTTTG 58.500 47.619 0.00 0.00 0.00 2.77
149 150 3.118884 TGAGTATCCAGCGGAGTAAAACC 60.119 47.826 3.76 0.00 34.05 3.27
188 189 4.385199 CCCATCTACAGGCATTTCTAACCA 60.385 45.833 0.00 0.00 0.00 3.67
202 203 4.346709 TGTGAACTCTTGAACCCATCTACA 59.653 41.667 0.00 0.00 0.00 2.74
250 251 2.872245 CAAGTACTGTTGTGTCAGGGTG 59.128 50.000 0.00 0.00 39.48 4.61
268 269 2.159421 ACCACATAGCGACGACTACAAG 60.159 50.000 0.00 0.00 0.00 3.16
315 316 6.163476 AGCAGTACAACGAACATCAGAAATA 58.837 36.000 0.00 0.00 0.00 1.40
370 371 4.389687 GGTTATAGCCGTCGTTTTCTTTCA 59.610 41.667 0.00 0.00 0.00 2.69
375 377 2.533129 CGAGGTTATAGCCGTCGTTTTC 59.467 50.000 14.74 0.84 0.00 2.29
391 393 1.546998 GGTCCATTGTTTTCCCGAGGT 60.547 52.381 0.00 0.00 0.00 3.85
392 394 1.173913 GGTCCATTGTTTTCCCGAGG 58.826 55.000 0.00 0.00 0.00 4.63
393 395 1.904287 TGGTCCATTGTTTTCCCGAG 58.096 50.000 0.00 0.00 0.00 4.63
394 396 2.362717 GTTTGGTCCATTGTTTTCCCGA 59.637 45.455 0.00 0.00 0.00 5.14
395 397 2.101582 TGTTTGGTCCATTGTTTTCCCG 59.898 45.455 0.00 0.00 0.00 5.14
396 398 3.462982 GTGTTTGGTCCATTGTTTTCCC 58.537 45.455 0.00 0.00 0.00 3.97
397 399 3.120041 CGTGTTTGGTCCATTGTTTTCC 58.880 45.455 0.00 0.00 0.00 3.13
398 400 3.120041 CCGTGTTTGGTCCATTGTTTTC 58.880 45.455 0.00 0.00 0.00 2.29
417 691 2.113860 TGCTGGATCTTTTCTTCCCG 57.886 50.000 0.00 0.00 0.00 5.14
434 727 5.806366 ATCAATAAAAAGCCAGCAAATGC 57.194 34.783 0.00 0.00 42.49 3.56
437 730 6.933521 TGCTAAATCAATAAAAAGCCAGCAAA 59.066 30.769 0.00 0.00 32.77 3.68
450 743 7.910584 TCCATCTGCTCTATGCTAAATCAATA 58.089 34.615 0.00 0.00 43.37 1.90
463 756 3.264193 ACACCATGTTTCCATCTGCTCTA 59.736 43.478 0.00 0.00 0.00 2.43
573 1626 0.899717 TTTGGCTGCTCCCATGGAAC 60.900 55.000 15.22 2.12 34.21 3.62
744 1818 0.740737 TACCCGCTAGAAAGTACGCC 59.259 55.000 0.00 0.00 0.00 5.68
862 1939 3.438183 GAGGGTATAAATAGGGGAGCGA 58.562 50.000 0.00 0.00 0.00 4.93
865 1942 5.279859 GGTTTCGAGGGTATAAATAGGGGAG 60.280 48.000 0.00 0.00 0.00 4.30
884 1961 1.133606 TGGAGGAAAGGGTGTGGTTTC 60.134 52.381 0.00 0.00 32.79 2.78
886 1963 0.185175 GTGGAGGAAAGGGTGTGGTT 59.815 55.000 0.00 0.00 0.00 3.67
887 1964 0.991355 TGTGGAGGAAAGGGTGTGGT 60.991 55.000 0.00 0.00 0.00 4.16
921 1998 1.079681 CGGCGGTGTGGTTAAGCTA 60.080 57.895 6.19 0.00 0.00 3.32
931 2008 2.261671 GATGAGTGTCGGCGGTGT 59.738 61.111 7.21 0.00 0.00 4.16
932 2009 1.807165 CAGATGAGTGTCGGCGGTG 60.807 63.158 7.21 0.00 0.00 4.94
933 2010 1.323271 ATCAGATGAGTGTCGGCGGT 61.323 55.000 7.21 0.00 0.00 5.68
934 2011 0.596083 GATCAGATGAGTGTCGGCGG 60.596 60.000 7.21 0.00 0.00 6.13
935 2012 0.101219 TGATCAGATGAGTGTCGGCG 59.899 55.000 0.00 0.00 0.00 6.46
936 2013 1.565305 GTGATCAGATGAGTGTCGGC 58.435 55.000 0.00 0.00 0.00 5.54
937 2014 1.202463 GGGTGATCAGATGAGTGTCGG 60.202 57.143 0.00 0.00 0.00 4.79
938 2015 1.478105 TGGGTGATCAGATGAGTGTCG 59.522 52.381 0.00 0.00 0.00 4.35
939 2016 2.499289 AGTGGGTGATCAGATGAGTGTC 59.501 50.000 0.00 0.00 0.00 3.67
985 2066 1.959848 CCATCGATCGCTAGCTGGA 59.040 57.895 13.93 3.75 0.00 3.86
986 2067 1.735920 GCCATCGATCGCTAGCTGG 60.736 63.158 13.93 13.30 0.00 4.85
1059 2144 3.419580 TCCCTGCCGGCCATCATT 61.420 61.111 26.77 0.00 0.00 2.57
1150 2238 0.179089 CACTCCTTGCTGATCGAGGG 60.179 60.000 0.00 0.00 45.05 4.30
1179 2267 4.641645 CCGTTCAGCCCCTGCACA 62.642 66.667 0.00 0.00 41.13 4.57
1280 2368 4.681978 GCACGCCGGAGACCTTGT 62.682 66.667 13.83 0.00 0.00 3.16
1413 2502 3.215151 CAAGATCTGGACTAGACGGCTA 58.785 50.000 0.00 0.00 38.49 3.93
1448 2537 2.029623 ACGGTTATGGAGTAGCACGAT 58.970 47.619 0.00 0.00 0.00 3.73
1450 2539 1.404391 AGACGGTTATGGAGTAGCACG 59.596 52.381 0.00 0.00 0.00 5.34
1521 2610 4.876107 CGGATGCTGGATTAAAACTACAGT 59.124 41.667 0.00 0.00 0.00 3.55
1522 2611 5.116180 TCGGATGCTGGATTAAAACTACAG 58.884 41.667 0.00 0.00 0.00 2.74
1523 2612 5.092554 TCGGATGCTGGATTAAAACTACA 57.907 39.130 0.00 0.00 0.00 2.74
1524 2613 4.024809 GCTCGGATGCTGGATTAAAACTAC 60.025 45.833 0.00 0.00 0.00 2.73
1525 2614 4.127171 GCTCGGATGCTGGATTAAAACTA 58.873 43.478 0.00 0.00 0.00 2.24
1526 2615 2.945668 GCTCGGATGCTGGATTAAAACT 59.054 45.455 0.00 0.00 0.00 2.66
1550 2639 6.588373 GCAGAACCTTTTCTCTTCTGTACTAG 59.412 42.308 8.10 0.00 40.34 2.57
1551 2640 6.456501 GCAGAACCTTTTCTCTTCTGTACTA 58.543 40.000 8.10 0.00 40.34 1.82
1552 2641 5.301555 GCAGAACCTTTTCTCTTCTGTACT 58.698 41.667 8.10 0.00 40.34 2.73
1575 2664 5.529581 GGGGGTCATATTGTTTGTATTGG 57.470 43.478 0.00 0.00 0.00 3.16
1730 2827 9.632969 GTTAGATGTAACATGCTAAAATACACG 57.367 33.333 7.83 0.00 38.78 4.49
1735 2832 8.487313 TCACGTTAGATGTAACATGCTAAAAT 57.513 30.769 12.72 0.00 38.86 1.82
1908 3010 6.362016 CACACGCAAGCAACTTCATTTTATTA 59.638 34.615 0.00 0.00 45.62 0.98
1925 3027 4.812091 ACAGTACTGAAATAACACACGCAA 59.188 37.500 29.30 0.00 0.00 4.85
1946 3069 1.275010 ACACAGACACACAGTGACACA 59.725 47.619 7.81 0.00 38.95 3.72
1947 3070 1.927174 GACACAGACACACAGTGACAC 59.073 52.381 7.81 0.00 38.95 3.67
1948 3071 1.134818 GGACACAGACACACAGTGACA 60.135 52.381 7.81 0.00 38.95 3.58
1949 3072 1.134818 TGGACACAGACACACAGTGAC 60.135 52.381 7.81 0.00 38.95 3.67
1950 3073 1.190643 TGGACACAGACACACAGTGA 58.809 50.000 7.81 0.00 38.95 3.41
1951 3074 1.869132 CATGGACACAGACACACAGTG 59.131 52.381 0.00 0.00 40.92 3.66
1952 3075 1.486310 ACATGGACACAGACACACAGT 59.514 47.619 0.00 0.00 0.00 3.55
1953 3076 2.138320 GACATGGACACAGACACACAG 58.862 52.381 0.00 0.00 0.00 3.66
1954 3077 1.762370 AGACATGGACACAGACACACA 59.238 47.619 0.00 0.00 0.00 3.72
1955 3078 2.138320 CAGACATGGACACAGACACAC 58.862 52.381 0.00 0.00 0.00 3.82
1956 3079 1.762370 ACAGACATGGACACAGACACA 59.238 47.619 0.00 0.00 0.00 3.72
1957 3080 2.533266 ACAGACATGGACACAGACAC 57.467 50.000 0.00 0.00 0.00 3.67
1958 3081 2.299013 GGTACAGACATGGACACAGACA 59.701 50.000 0.00 0.00 42.67 3.41
1959 3082 2.563179 AGGTACAGACATGGACACAGAC 59.437 50.000 0.00 0.00 42.67 3.51
1960 3083 2.889512 AGGTACAGACATGGACACAGA 58.110 47.619 0.00 0.00 42.67 3.41
1961 3084 3.329386 CAAGGTACAGACATGGACACAG 58.671 50.000 0.00 0.00 42.67 3.66
1968 3091 0.443869 GTGCGCAAGGTACAGACATG 59.556 55.000 14.00 0.00 38.28 3.21
2027 3153 2.202557 CTCACGCATACGGACGCA 60.203 61.111 0.00 0.00 46.04 5.24
2059 3185 3.119602 CGGCTACACTAGAGTACAGCAAA 60.120 47.826 14.49 0.00 36.38 3.68
2071 3197 2.096335 CACGTACACATCGGCTACACTA 59.904 50.000 0.00 0.00 0.00 2.74
2075 3201 1.135603 TCACACGTACACATCGGCTAC 60.136 52.381 0.00 0.00 0.00 3.58
2155 3284 0.179076 TAGCTGGACATCCATGCACG 60.179 55.000 18.50 3.32 46.46 5.34
2168 3297 2.149578 GCTGGATAGTGCAATAGCTGG 58.850 52.381 9.49 3.94 42.74 4.85
2206 3353 3.621268 GCTCAAAACATCCGTATAGTGCA 59.379 43.478 0.00 0.00 0.00 4.57
2207 3354 3.002348 GGCTCAAAACATCCGTATAGTGC 59.998 47.826 0.00 0.00 0.00 4.40
2273 3420 2.939103 GTGGAGATCTCGTTCATTTGGG 59.061 50.000 16.46 0.00 0.00 4.12
2382 3529 6.422400 TGTGTTTTTCTGTTTGAGTGTTTTCC 59.578 34.615 0.00 0.00 0.00 3.13
2384 3531 6.758886 TGTGTGTTTTTCTGTTTGAGTGTTTT 59.241 30.769 0.00 0.00 0.00 2.43
2388 3535 6.148948 TCTTGTGTGTTTTTCTGTTTGAGTG 58.851 36.000 0.00 0.00 0.00 3.51
2462 3610 7.230510 GGGTTCCCAATTCTGCTTTAAATTTTT 59.769 33.333 2.59 0.00 0.00 1.94
2482 3630 1.948721 ATACGGACGTTCGGGGTTCC 61.949 60.000 22.31 0.00 0.00 3.62
2487 3635 3.003689 ACAGTATTATACGGACGTTCGGG 59.996 47.826 22.31 0.00 0.00 5.14
2527 3680 3.502920 AGATTCGACGTGTCATGTCTTC 58.497 45.455 20.31 14.45 32.08 2.87
2549 3702 7.676683 AGGTTATTCCAGTCATATGTGTACT 57.323 36.000 1.90 0.00 39.02 2.73
2591 3746 7.136119 TCCACAACGAAATACATTTTCTGAAC 58.864 34.615 0.00 0.00 0.00 3.18
2627 3782 8.590719 TTTACAACTGTTCACATCGTAATACA 57.409 30.769 0.00 0.00 0.00 2.29
2657 3812 8.979574 AGATAGCACGCTATTTAAAACTATGAC 58.020 33.333 12.62 0.00 39.15 3.06
2659 3814 8.156553 CGAGATAGCACGCTATTTAAAACTATG 58.843 37.037 12.62 0.00 39.15 2.23
2663 3818 5.233689 ACCGAGATAGCACGCTATTTAAAAC 59.766 40.000 12.62 0.00 39.15 2.43
2686 3841 2.290641 CGCCCTGCAAATGTTATAGGAC 59.709 50.000 0.00 0.00 0.00 3.85
2687 3842 2.092646 ACGCCCTGCAAATGTTATAGGA 60.093 45.455 0.00 0.00 0.00 2.94
2688 3843 2.290641 GACGCCCTGCAAATGTTATAGG 59.709 50.000 0.00 0.00 0.00 2.57
2689 3844 2.942376 TGACGCCCTGCAAATGTTATAG 59.058 45.455 0.00 0.00 0.00 1.31
2690 3845 2.992593 TGACGCCCTGCAAATGTTATA 58.007 42.857 0.00 0.00 0.00 0.98
2691 3846 1.832883 TGACGCCCTGCAAATGTTAT 58.167 45.000 0.00 0.00 0.00 1.89
2692 3847 1.472082 CATGACGCCCTGCAAATGTTA 59.528 47.619 0.00 0.00 0.00 2.41
2693 3848 0.244450 CATGACGCCCTGCAAATGTT 59.756 50.000 0.00 0.00 0.00 2.71
2694 3849 1.885157 CATGACGCCCTGCAAATGT 59.115 52.632 0.00 0.00 0.00 2.71
2695 3850 1.517694 GCATGACGCCCTGCAAATG 60.518 57.895 0.00 0.00 38.28 2.32
2696 3851 0.394216 TAGCATGACGCCCTGCAAAT 60.394 50.000 1.47 0.00 44.04 2.32
2697 3852 0.607762 TTAGCATGACGCCCTGCAAA 60.608 50.000 1.47 0.00 44.04 3.68
2698 3853 1.002746 TTAGCATGACGCCCTGCAA 60.003 52.632 1.47 0.00 44.04 4.08
2699 3854 1.450134 CTTAGCATGACGCCCTGCA 60.450 57.895 1.47 0.00 44.04 4.41
2700 3855 2.828128 GCTTAGCATGACGCCCTGC 61.828 63.158 0.00 0.00 44.04 4.85
2701 3856 2.182842 GGCTTAGCATGACGCCCTG 61.183 63.158 6.53 0.00 44.04 4.45
2702 3857 1.987807 ATGGCTTAGCATGACGCCCT 61.988 55.000 6.53 0.00 44.04 5.19
2703 3858 1.103398 AATGGCTTAGCATGACGCCC 61.103 55.000 6.53 0.00 44.04 6.13
2704 3859 0.308993 GAATGGCTTAGCATGACGCC 59.691 55.000 6.53 2.27 44.04 5.68
2705 3860 1.003116 CTGAATGGCTTAGCATGACGC 60.003 52.381 6.53 0.00 42.91 5.19
2706 3861 2.283298 ACTGAATGGCTTAGCATGACG 58.717 47.619 6.53 0.00 0.00 4.35
2707 3862 4.697514 TCTACTGAATGGCTTAGCATGAC 58.302 43.478 6.53 0.00 0.00 3.06
2708 3863 5.357742 TTCTACTGAATGGCTTAGCATGA 57.642 39.130 6.53 0.00 0.00 3.07
2709 3864 6.630444 AATTCTACTGAATGGCTTAGCATG 57.370 37.500 6.53 0.00 41.62 4.06
2710 3865 7.040823 GCTAAATTCTACTGAATGGCTTAGCAT 60.041 37.037 18.65 0.00 45.02 3.79
2711 3866 6.260936 GCTAAATTCTACTGAATGGCTTAGCA 59.739 38.462 18.65 0.00 45.02 3.49
2712 3867 6.564873 CGCTAAATTCTACTGAATGGCTTAGC 60.565 42.308 16.03 16.03 43.86 3.09
2713 3868 6.480320 ACGCTAAATTCTACTGAATGGCTTAG 59.520 38.462 0.00 0.00 41.62 2.18
2714 3869 6.257849 CACGCTAAATTCTACTGAATGGCTTA 59.742 38.462 0.00 0.00 41.62 3.09
2715 3870 5.065218 CACGCTAAATTCTACTGAATGGCTT 59.935 40.000 0.00 0.00 41.62 4.35
2716 3871 4.572389 CACGCTAAATTCTACTGAATGGCT 59.428 41.667 0.00 0.00 41.62 4.75
2717 3872 4.332819 ACACGCTAAATTCTACTGAATGGC 59.667 41.667 0.00 0.00 41.62 4.40
2718 3873 6.422776 AACACGCTAAATTCTACTGAATGG 57.577 37.500 0.00 0.00 41.62 3.16
2744 3899 9.880157 AAAGCTCTGCATATTTGTGAAAAATAT 57.120 25.926 0.00 0.00 0.00 1.28
2746 3901 9.362539 CTAAAGCTCTGCATATTTGTGAAAAAT 57.637 29.630 0.00 0.00 0.00 1.82
2747 3902 7.814107 CCTAAAGCTCTGCATATTTGTGAAAAA 59.186 33.333 0.00 0.00 0.00 1.94
2748 3903 7.039784 ACCTAAAGCTCTGCATATTTGTGAAAA 60.040 33.333 0.00 0.00 0.00 2.29
2749 3904 6.434028 ACCTAAAGCTCTGCATATTTGTGAAA 59.566 34.615 0.00 0.00 0.00 2.69
2750 3905 5.945784 ACCTAAAGCTCTGCATATTTGTGAA 59.054 36.000 0.00 0.00 0.00 3.18
2751 3906 5.355071 CACCTAAAGCTCTGCATATTTGTGA 59.645 40.000 0.00 0.00 0.00 3.58
2752 3907 5.449588 CCACCTAAAGCTCTGCATATTTGTG 60.450 44.000 0.00 0.00 0.00 3.33
2753 3908 4.641989 CCACCTAAAGCTCTGCATATTTGT 59.358 41.667 0.00 0.00 0.00 2.83
2754 3909 4.641989 ACCACCTAAAGCTCTGCATATTTG 59.358 41.667 0.00 0.00 0.00 2.32
2755 3910 4.860022 ACCACCTAAAGCTCTGCATATTT 58.140 39.130 0.00 0.00 0.00 1.40
2756 3911 4.510167 ACCACCTAAAGCTCTGCATATT 57.490 40.909 0.00 0.00 0.00 1.28
2757 3912 4.408921 TGTACCACCTAAAGCTCTGCATAT 59.591 41.667 0.00 0.00 0.00 1.78
2758 3913 3.772572 TGTACCACCTAAAGCTCTGCATA 59.227 43.478 0.00 0.00 0.00 3.14
2759 3914 2.571653 TGTACCACCTAAAGCTCTGCAT 59.428 45.455 0.00 0.00 0.00 3.96
2760 3915 1.974957 TGTACCACCTAAAGCTCTGCA 59.025 47.619 0.00 0.00 0.00 4.41
2761 3916 2.742589 GTTGTACCACCTAAAGCTCTGC 59.257 50.000 0.00 0.00 0.00 4.26
2762 3917 3.746492 GTGTTGTACCACCTAAAGCTCTG 59.254 47.826 0.00 0.00 0.00 3.35
2763 3918 3.389983 TGTGTTGTACCACCTAAAGCTCT 59.610 43.478 0.00 0.00 34.35 4.09
2764 3919 3.735591 TGTGTTGTACCACCTAAAGCTC 58.264 45.455 0.00 0.00 34.35 4.09
2765 3920 3.849563 TGTGTTGTACCACCTAAAGCT 57.150 42.857 0.00 0.00 34.35 3.74
2766 3921 3.190535 CCATGTGTTGTACCACCTAAAGC 59.809 47.826 0.00 0.00 34.35 3.51
2767 3922 3.190535 GCCATGTGTTGTACCACCTAAAG 59.809 47.826 0.00 0.00 34.35 1.85
2768 3923 3.150767 GCCATGTGTTGTACCACCTAAA 58.849 45.455 0.00 0.00 34.35 1.85
2769 3924 2.106684 TGCCATGTGTTGTACCACCTAA 59.893 45.455 0.00 0.00 34.35 2.69
2770 3925 1.700186 TGCCATGTGTTGTACCACCTA 59.300 47.619 0.00 0.00 34.35 3.08
2771 3926 0.476338 TGCCATGTGTTGTACCACCT 59.524 50.000 0.00 0.00 34.35 4.00
2772 3927 0.596082 GTGCCATGTGTTGTACCACC 59.404 55.000 0.00 0.00 34.35 4.61
2773 3928 0.237235 CGTGCCATGTGTTGTACCAC 59.763 55.000 0.00 0.00 35.86 4.16
2774 3929 0.106894 TCGTGCCATGTGTTGTACCA 59.893 50.000 0.00 0.00 0.00 3.25
2775 3930 1.069500 GTTCGTGCCATGTGTTGTACC 60.069 52.381 0.00 0.00 0.00 3.34
2776 3931 1.397945 CGTTCGTGCCATGTGTTGTAC 60.398 52.381 0.00 0.00 0.00 2.90
2777 3932 0.862490 CGTTCGTGCCATGTGTTGTA 59.138 50.000 0.00 0.00 0.00 2.41
2778 3933 1.646540 CGTTCGTGCCATGTGTTGT 59.353 52.632 0.00 0.00 0.00 3.32
2779 3934 1.725625 GCGTTCGTGCCATGTGTTG 60.726 57.895 0.00 0.00 0.00 3.33
2780 3935 1.719725 TTGCGTTCGTGCCATGTGTT 61.720 50.000 0.00 0.00 0.00 3.32
2781 3936 2.116736 CTTGCGTTCGTGCCATGTGT 62.117 55.000 0.00 0.00 0.00 3.72
2782 3937 1.440850 CTTGCGTTCGTGCCATGTG 60.441 57.895 0.00 0.00 0.00 3.21
2783 3938 1.568612 CTCTTGCGTTCGTGCCATGT 61.569 55.000 0.00 0.00 0.00 3.21
2784 3939 1.133253 CTCTTGCGTTCGTGCCATG 59.867 57.895 0.00 0.00 0.00 3.66
2785 3940 2.034879 CCTCTTGCGTTCGTGCCAT 61.035 57.895 0.00 0.00 0.00 4.40
2786 3941 2.664851 CCTCTTGCGTTCGTGCCA 60.665 61.111 0.00 0.00 0.00 4.92
2787 3942 4.090057 GCCTCTTGCGTTCGTGCC 62.090 66.667 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.