Multiple sequence alignment - TraesCS3B01G177300

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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 TraesCS3B01G177300 chr3B 100.000 9265 0 0 1 9265 181283164 181292428 0.000000e+00 17110.0
1 TraesCS3B01G177300 chr3B 93.453 611 21 11 8674 9265 8791258 8790648 0.000000e+00 889.0
2 TraesCS3B01G177300 chr3B 95.074 406 14 5 8673 9077 744208209 744207809 1.310000e-177 634.0
3 TraesCS3B01G177300 chr3B 81.746 378 57 10 4 373 109921171 109920798 1.170000e-78 305.0
4 TraesCS3B01G177300 chr3B 92.222 90 7 0 5647 5736 456554365 456554454 2.720000e-25 128.0
5 TraesCS3B01G177300 chr3D 95.987 7799 219 31 905 8674 126944331 126952064 0.000000e+00 12582.0
6 TraesCS3B01G177300 chr3D 90.559 286 14 8 481 755 126943716 126943999 5.290000e-97 366.0
7 TraesCS3B01G177300 chr3D 89.716 282 25 4 1 281 126940926 126941204 3.180000e-94 357.0
8 TraesCS3B01G177300 chr3D 88.186 237 27 1 3572 3807 540237422 540237186 1.970000e-71 281.0
9 TraesCS3B01G177300 chr3D 89.655 174 16 1 275 448 126942190 126942361 4.360000e-53 220.0
10 TraesCS3B01G177300 chr3D 89.320 103 7 3 5645 5743 79508468 79508366 9.770000e-25 126.0
11 TraesCS3B01G177300 chr3A 94.327 4319 155 32 4386 8674 137578288 137582546 0.000000e+00 6536.0
12 TraesCS3B01G177300 chr3A 91.943 3624 208 33 1 3574 137573186 137576775 0.000000e+00 4998.0
13 TraesCS3B01G177300 chr3A 93.322 614 20 9 8673 9265 66352251 66351638 0.000000e+00 887.0
14 TraesCS3B01G177300 chr3A 93.500 600 20 8 3794 4391 137577658 137578240 0.000000e+00 874.0
15 TraesCS3B01G177300 chr3A 92.985 613 22 13 8674 9265 474444425 474445037 0.000000e+00 874.0
16 TraesCS3B01G177300 chr2B 93.617 611 20 9 8674 9265 73114674 73114064 0.000000e+00 894.0
17 TraesCS3B01G177300 chr2B 94.595 74 4 0 3570 3643 583158063 583157990 2.110000e-21 115.0
18 TraesCS3B01G177300 chr4B 93.596 609 22 12 8674 9265 660132144 660131536 0.000000e+00 893.0
19 TraesCS3B01G177300 chr4B 92.157 102 8 0 3832 3933 32489985 32490086 2.700000e-30 145.0
20 TraesCS3B01G177300 chr4B 88.764 89 10 0 5646 5734 14016277 14016189 9.840000e-20 110.0
21 TraesCS3B01G177300 chrUn 93.312 613 20 13 8674 9265 53744971 53744359 0.000000e+00 885.0
22 TraesCS3B01G177300 chrUn 86.905 84 11 0 5647 5730 50872366 50872449 2.750000e-15 95.3
23 TraesCS3B01G177300 chrUn 86.905 84 11 0 5647 5730 50890278 50890361 2.750000e-15 95.3
24 TraesCS3B01G177300 chrUn 84.706 85 13 0 5647 5731 96589117 96589201 1.660000e-12 86.1
25 TraesCS3B01G177300 chr7B 92.985 613 22 9 8674 9265 54778022 54777410 0.000000e+00 874.0
26 TraesCS3B01G177300 chr7B 81.768 362 53 8 1 352 158013973 158013615 3.270000e-74 291.0
27 TraesCS3B01G177300 chr7B 92.473 93 5 2 5643 5734 142285349 142285258 2.100000e-26 132.0
28 TraesCS3B01G177300 chr7B 84.167 120 9 9 5618 5731 214074841 214074956 3.540000e-19 108.0
29 TraesCS3B01G177300 chr5B 96.018 452 17 1 8814 9265 163987575 163987125 0.000000e+00 734.0
30 TraesCS3B01G177300 chr5B 88.679 106 10 2 3833 3936 673768010 673767905 2.720000e-25 128.0
31 TraesCS3B01G177300 chr6B 94.194 465 24 3 8804 9265 711655670 711656134 0.000000e+00 706.0
32 TraesCS3B01G177300 chr6B 88.973 263 26 2 8674 8936 634497824 634498083 1.160000e-83 322.0
33 TraesCS3B01G177300 chr6B 81.117 376 60 9 3 369 678533345 678532972 3.270000e-74 291.0
34 TraesCS3B01G177300 chr6B 84.496 129 17 2 3029 3155 669079432 669079559 3.510000e-24 124.0
35 TraesCS3B01G177300 chr6B 83.721 129 18 2 3029 3155 669078010 669078137 1.630000e-22 119.0
36 TraesCS3B01G177300 chr1B 94.363 408 19 4 8668 9072 529704424 529704018 2.840000e-174 623.0
37 TraesCS3B01G177300 chr1B 76.914 810 97 41 7772 8537 540140444 540139681 2.440000e-100 377.0
38 TraesCS3B01G177300 chr1B 85.946 185 21 5 3667 3849 237010170 237010351 9.490000e-45 193.0
39 TraesCS3B01G177300 chr7D 91.698 265 13 4 8674 8938 603496304 603496559 8.850000e-95 359.0
40 TraesCS3B01G177300 chr7D 90.769 130 6 3 3572 3696 484423865 484423993 1.600000e-37 169.0
41 TraesCS3B01G177300 chr7D 96.000 75 3 0 3572 3646 25045023 25045097 1.260000e-23 122.0
42 TraesCS3B01G177300 chr7D 85.714 119 8 8 5618 5731 237415052 237415166 5.880000e-22 117.0
43 TraesCS3B01G177300 chr7D 89.888 89 7 2 5643 5731 8546687 8546773 7.600000e-21 113.0
44 TraesCS3B01G177300 chr7D 87.500 96 11 1 5642 5737 206988873 206988779 9.840000e-20 110.0
45 TraesCS3B01G177300 chr7D 88.764 89 5 5 5645 5731 190083217 190083302 4.580000e-18 104.0
46 TraesCS3B01G177300 chr1D 89.964 279 18 7 3573 3844 211688916 211688641 1.480000e-92 351.0
47 TraesCS3B01G177300 chr1D 76.173 810 94 35 7772 8537 402151692 402150938 1.490000e-87 335.0
48 TraesCS3B01G177300 chr1D 82.873 362 49 8 1 352 224573409 224573767 6.980000e-81 313.0
49 TraesCS3B01G177300 chr1D 94.118 85 5 0 5647 5731 33988079 33987995 7.550000e-26 130.0
50 TraesCS3B01G177300 chr1D 89.412 85 4 5 5644 5726 410795902 410795983 1.650000e-17 102.0
51 TraesCS3B01G177300 chr1D 97.674 43 0 1 5643 5685 303325649 303325608 1.290000e-08 73.1
52 TraesCS3B01G177300 chr1D 85.714 70 6 4 5636 5703 53260503 53260570 4.640000e-08 71.3
53 TraesCS3B01G177300 chr1D 85.294 68 9 1 5664 5731 393747474 393747540 1.670000e-07 69.4
54 TraesCS3B01G177300 chr1D 90.698 43 4 0 5652 5694 122974476 122974434 3.610000e-04 58.4
55 TraesCS3B01G177300 chr6A 89.744 273 20 6 8668 8938 521439631 521439897 8.910000e-90 342.0
56 TraesCS3B01G177300 chr6A 91.489 141 12 0 3701 3841 370677374 370677514 2.640000e-45 195.0
57 TraesCS3B01G177300 chr6A 86.517 89 6 6 5647 5732 101930579 101930664 9.910000e-15 93.5
58 TraesCS3B01G177300 chr5A 89.130 276 19 9 8674 8938 653938339 653938064 5.360000e-87 333.0
59 TraesCS3B01G177300 chr5A 85.091 275 27 13 8673 8938 679668519 679668788 1.530000e-67 268.0
60 TraesCS3B01G177300 chr4D 88.087 277 19 11 8674 8938 214997885 214997611 5.400000e-82 316.0
61 TraesCS3B01G177300 chr4D 82.320 362 51 8 1 352 346204045 346203687 1.510000e-77 302.0
62 TraesCS3B01G177300 chr4D 87.209 258 25 8 3577 3830 507718560 507718307 4.230000e-73 287.0
63 TraesCS3B01G177300 chr4D 88.496 113 7 6 3826 3933 451152138 451152249 2.100000e-26 132.0
64 TraesCS3B01G177300 chr4D 86.364 88 11 1 5645 5732 20114853 20114939 2.750000e-15 95.3
65 TraesCS3B01G177300 chr4D 85.882 85 11 1 5647 5731 509646357 509646440 1.280000e-13 89.8
66 TraesCS3B01G177300 chr1A 88.433 268 21 6 8674 8938 25677757 25677497 1.940000e-81 315.0
67 TraesCS3B01G177300 chr1A 77.295 414 48 18 8131 8537 497754215 497753841 1.580000e-47 202.0
68 TraesCS3B01G177300 chr1A 89.524 105 9 2 3838 3941 181775586 181775689 2.100000e-26 132.0
69 TraesCS3B01G177300 chr1A 91.860 86 6 1 5647 5731 2945671 2945586 1.630000e-22 119.0
70 TraesCS3B01G177300 chr6D 81.894 359 52 8 4 352 448654623 448654268 3.270000e-74 291.0
71 TraesCS3B01G177300 chr6D 81.492 362 54 7 1 352 460866046 460866404 1.520000e-72 285.0
72 TraesCS3B01G177300 chr6D 91.275 149 13 0 3691 3839 260022707 260022559 4.390000e-48 204.0
73 TraesCS3B01G177300 chr6D 83.721 86 14 0 5647 5732 343295805 343295720 2.140000e-11 82.4
74 TraesCS3B01G177300 chr6D 85.000 80 12 0 5652 5731 438915044 438914965 2.140000e-11 82.4
75 TraesCS3B01G177300 chr7A 91.892 185 14 1 3660 3844 126583789 126583606 3.320000e-64 257.0
76 TraesCS3B01G177300 chr7A 89.706 136 12 2 3707 3841 25930750 25930884 1.240000e-38 172.0
77 TraesCS3B01G177300 chr7A 91.089 101 7 2 3843 3942 82204210 82204111 1.620000e-27 135.0
78 TraesCS3B01G177300 chr7A 97.260 73 2 0 3573 3645 25930819 25930891 3.510000e-24 124.0
79 TraesCS3B01G177300 chr5D 77.673 318 54 6 3029 3331 42520107 42519792 2.660000e-40 178.0
80 TraesCS3B01G177300 chr5D 89.623 106 9 2 3833 3936 533662944 533662839 5.840000e-27 134.0
81 TraesCS3B01G177300 chr5D 93.103 87 2 4 5652 5736 478164185 478164269 3.510000e-24 124.0
82 TraesCS3B01G177300 chr5D 89.655 87 5 4 5646 5731 5804063 5804146 3.540000e-19 108.0
83 TraesCS3B01G177300 chr5D 88.889 90 6 4 5648 5735 456063615 456063702 3.540000e-19 108.0
84 TraesCS3B01G177300 chr5D 85.057 87 13 0 5645 5731 324374996 324375082 1.280000e-13 89.8
85 TraesCS3B01G177300 chr4A 83.957 187 19 4 3571 3751 204963608 204963789 1.600000e-37 169.0
86 TraesCS3B01G177300 chr4A 88.000 100 9 3 5642 5739 662286508 662286410 2.110000e-21 115.0
87 TraesCS3B01G177300 chr2D 93.333 105 5 1 3835 3937 473091647 473091543 4.480000e-33 154.0
88 TraesCS3B01G177300 chr2D 93.750 96 6 0 5644 5739 172409663 172409758 2.700000e-30 145.0
89 TraesCS3B01G177300 chr2D 93.182 88 6 0 5644 5731 569193723 569193636 7.550000e-26 130.0
90 TraesCS3B01G177300 chr2D 93.103 87 6 0 5646 5732 2608238 2608152 2.720000e-25 128.0
91 TraesCS3B01G177300 chr2A 94.624 93 5 0 5647 5739 177658409 177658317 2.700000e-30 145.0


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 TraesCS3B01G177300 chr3B 181283164 181292428 9264 False 17110.00 17110 100.000000 1 9265 1 chr3B.!!$F1 9264
1 TraesCS3B01G177300 chr3B 8790648 8791258 610 True 889.00 889 93.453000 8674 9265 1 chr3B.!!$R1 591
2 TraesCS3B01G177300 chr3D 126940926 126952064 11138 False 3381.25 12582 91.479250 1 8674 4 chr3D.!!$F1 8673
3 TraesCS3B01G177300 chr3A 137573186 137582546 9360 False 4136.00 6536 93.256667 1 8674 3 chr3A.!!$F2 8673
4 TraesCS3B01G177300 chr3A 66351638 66352251 613 True 887.00 887 93.322000 8673 9265 1 chr3A.!!$R1 592
5 TraesCS3B01G177300 chr3A 474444425 474445037 612 False 874.00 874 92.985000 8674 9265 1 chr3A.!!$F1 591
6 TraesCS3B01G177300 chr2B 73114064 73114674 610 True 894.00 894 93.617000 8674 9265 1 chr2B.!!$R1 591
7 TraesCS3B01G177300 chr4B 660131536 660132144 608 True 893.00 893 93.596000 8674 9265 1 chr4B.!!$R2 591
8 TraesCS3B01G177300 chrUn 53744359 53744971 612 True 885.00 885 93.312000 8674 9265 1 chrUn.!!$R1 591
9 TraesCS3B01G177300 chr7B 54777410 54778022 612 True 874.00 874 92.985000 8674 9265 1 chr7B.!!$R1 591
10 TraesCS3B01G177300 chr1B 540139681 540140444 763 True 377.00 377 76.914000 7772 8537 1 chr1B.!!$R2 765
11 TraesCS3B01G177300 chr1D 402150938 402151692 754 True 335.00 335 76.173000 7772 8537 1 chr1D.!!$R5 765

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
477 2812 0.036105 CAAATGCTTTTCCCTGCCCC 60.036 55.000 0.00 0.0 0.00 5.80 F
1986 4517 0.112412 AGGGAGTTCCACGGCATTTT 59.888 50.000 0.00 0.0 38.24 1.82 F
1987 4518 0.966179 GGGAGTTCCACGGCATTTTT 59.034 50.000 0.00 0.0 37.91 1.94 F
2729 5271 1.362224 AAGGAGGTTGCTGCCTAGAA 58.638 50.000 0.00 0.0 39.34 2.10 F
3992 7203 0.042731 TAGTTGAGGAGGGGTGAGGG 59.957 60.000 0.00 0.0 0.00 4.30 F
3994 7205 1.538876 TTGAGGAGGGGTGAGGGTG 60.539 63.158 0.00 0.0 0.00 4.61 F
3995 7206 2.689034 GAGGAGGGGTGAGGGTGG 60.689 72.222 0.00 0.0 0.00 4.61 F
4177 7390 3.128764 GGTAGGTTTGGCTCTTTACATGC 59.871 47.826 0.00 0.0 0.00 4.06 F
5169 8455 3.243336 GTCTGTGCTAGTCCACTAAACG 58.757 50.000 2.73 0.0 36.68 3.60 F
6327 9619 1.350193 CAACACCGTCTCCAAGATCG 58.650 55.000 0.00 0.0 0.00 3.69 F
7910 11233 2.205022 TGAACCCTCCTCAATTGCAG 57.795 50.000 0.00 0.0 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2094 4625 0.034477 CCCCCGCTCACTAAATGGTT 60.034 55.000 0.00 0.0 0.00 3.67 R
3531 6079 1.064060 CGGATGATTTTCGGTGCCTTC 59.936 52.381 0.00 0.0 0.00 3.46 R
3660 6466 1.920574 GATCATTCCATATCCGCGTCG 59.079 52.381 4.92 0.0 0.00 5.12 R
4394 7608 0.452987 TGCCATTCGATGCAAAGAGC 59.547 50.000 0.00 0.0 45.96 4.09 R
4892 8174 0.696501 TGGCCAGTAAGAAGGGGTTC 59.303 55.000 0.00 0.0 0.00 3.62 R
5407 8693 1.808945 GCAACACATTAGACAGCTGCT 59.191 47.619 15.27 14.4 0.00 4.24 R
5489 8779 2.351418 TGCGTACATAGCATCTTTGTGC 59.649 45.455 0.00 0.0 45.38 4.57 R
5507 8797 6.527722 AGCTACAAACAAAAATATGACATGCG 59.472 34.615 0.00 0.0 0.00 4.73 R
6429 9721 1.436600 ATGACTGCAGCTTCTTCACG 58.563 50.000 15.27 0.0 0.00 4.35 R
8263 11612 0.108756 ACGAGGCGAGGCTTTAACTC 60.109 55.000 0.00 0.0 0.00 3.01 R
8820 12174 0.047176 AGAGAGAGGGAGGAGGGAGA 59.953 60.000 0.00 0.0 0.00 3.71 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
32 34 0.892755 CGTGTAGGAGTGTTGCCCTA 59.107 55.000 0.00 0.00 34.11 3.53
49 51 2.422479 CCCTAGTCTGATTCGTTCGACA 59.578 50.000 0.00 0.00 33.27 4.35
87 89 1.473434 GGGAGCCACATTAGAGGTTCG 60.473 57.143 0.00 0.00 36.76 3.95
113 115 3.139850 GCTGCATATCAGTGATTGAGCT 58.860 45.455 11.68 0.00 44.66 4.09
115 117 4.377897 CTGCATATCAGTGATTGAGCTGA 58.622 43.478 11.68 0.00 44.55 4.26
125 127 2.558359 TGATTGAGCTGAGTCGAGTTCA 59.442 45.455 0.00 0.00 31.98 3.18
271 278 2.891112 TGTTCTTTTGTGCAAAGGCTG 58.109 42.857 0.00 0.00 42.18 4.85
272 279 2.495270 TGTTCTTTTGTGCAAAGGCTGA 59.505 40.909 0.00 0.00 42.18 4.26
273 280 2.860136 GTTCTTTTGTGCAAAGGCTGAC 59.140 45.455 0.00 0.00 42.18 3.51
287 1286 3.391049 AGGCTGACGTTTTACTGTCTTC 58.609 45.455 0.00 0.00 36.10 2.87
305 1304 3.990469 TCTTCTCAGTTTTGTCAGATCGC 59.010 43.478 0.00 0.00 0.00 4.58
310 1309 0.452784 GTTTTGTCAGATCGCCGTGC 60.453 55.000 0.00 0.00 0.00 5.34
325 1324 0.502695 CGTGCACGTGACTTGTACTG 59.497 55.000 30.50 0.00 34.11 2.74
327 1326 1.257936 GTGCACGTGACTTGTACTGTG 59.742 52.381 22.23 0.00 0.00 3.66
331 1330 3.985279 GCACGTGACTTGTACTGTGATTA 59.015 43.478 22.23 0.00 0.00 1.75
360 1361 0.586319 AAATGAGACACACGTTGCCG 59.414 50.000 0.00 0.00 40.83 5.69
449 2784 6.474751 TCGATATATACTGACCGATCGTACTG 59.525 42.308 15.09 13.00 37.88 2.74
451 2786 7.433425 CGATATATACTGACCGATCGTACTGTA 59.567 40.741 15.09 18.82 33.33 2.74
455 2790 1.739466 TGACCGATCGTACTGTACCAC 59.261 52.381 15.09 3.60 0.00 4.16
456 2791 1.064654 GACCGATCGTACTGTACCACC 59.935 57.143 15.09 1.13 0.00 4.61
458 2793 1.332997 CCGATCGTACTGTACCACCTC 59.667 57.143 15.09 3.71 0.00 3.85
459 2794 2.011947 CGATCGTACTGTACCACCTCA 58.988 52.381 7.03 0.00 0.00 3.86
465 2800 3.616560 CGTACTGTACCACCTCAAATGCT 60.617 47.826 12.08 0.00 0.00 3.79
475 2810 1.066645 CCTCAAATGCTTTTCCCTGCC 60.067 52.381 0.00 0.00 0.00 4.85
476 2811 0.975887 TCAAATGCTTTTCCCTGCCC 59.024 50.000 0.00 0.00 0.00 5.36
477 2812 0.036105 CAAATGCTTTTCCCTGCCCC 60.036 55.000 0.00 0.00 0.00 5.80
478 2813 1.200760 AAATGCTTTTCCCTGCCCCC 61.201 55.000 0.00 0.00 0.00 5.40
479 2814 3.963124 ATGCTTTTCCCTGCCCCCG 62.963 63.158 0.00 0.00 0.00 5.73
497 2832 4.161295 CCCCCTCGCTCGCAATCA 62.161 66.667 0.00 0.00 0.00 2.57
499 2834 2.125552 CCCTCGCTCGCAATCACA 60.126 61.111 0.00 0.00 0.00 3.58
511 2846 6.304445 CGCTCGCAATCACAGTTTAAATAAAA 59.696 34.615 0.00 0.00 0.00 1.52
512 2847 7.008266 CGCTCGCAATCACAGTTTAAATAAAAT 59.992 33.333 0.00 0.00 0.00 1.82
645 2980 2.127708 GACCCCATCCACCAGTCTAAT 58.872 52.381 0.00 0.00 0.00 1.73
723 3067 2.443016 CCCCTCCTCTCCTCACCG 60.443 72.222 0.00 0.00 0.00 4.94
724 3068 3.151022 CCCTCCTCTCCTCACCGC 61.151 72.222 0.00 0.00 0.00 5.68
726 3070 2.363018 CTCCTCTCCTCACCGCCA 60.363 66.667 0.00 0.00 0.00 5.69
749 3093 1.742761 GCACCTACAGCATGACATGT 58.257 50.000 16.62 0.00 39.69 3.21
757 3101 2.114670 GCATGACATGTGGGACCCG 61.115 63.158 16.62 0.00 0.00 5.28
803 3147 2.356794 GCGTAGTATATTCCGCCGC 58.643 57.895 0.00 0.00 40.25 6.53
804 3148 1.400990 GCGTAGTATATTCCGCCGCG 61.401 60.000 5.59 5.59 40.25 6.46
844 3188 3.733960 TCCACCGCGTGACTCGAG 61.734 66.667 11.84 11.84 42.86 4.04
880 3224 1.681486 CCGCCTTCTTCCTCCTCCTC 61.681 65.000 0.00 0.00 0.00 3.71
882 3226 0.326143 GCCTTCTTCCTCCTCCTCCT 60.326 60.000 0.00 0.00 0.00 3.69
884 3228 1.691163 CCTTCTTCCTCCTCCTCCTCC 60.691 61.905 0.00 0.00 0.00 4.30
886 3230 1.074850 CTTCCTCCTCCTCCTCCCC 60.075 68.421 0.00 0.00 0.00 4.81
887 3231 1.550374 TTCCTCCTCCTCCTCCCCT 60.550 63.158 0.00 0.00 0.00 4.79
890 3234 1.456705 CTCCTCCTCCTCCCCTTCG 60.457 68.421 0.00 0.00 0.00 3.79
892 3236 3.157949 CTCCTCCTCCCCTTCGCC 61.158 72.222 0.00 0.00 0.00 5.54
991 3517 3.662117 GAGGGGAAAAGGCGGCCAT 62.662 63.158 23.09 6.30 0.00 4.40
1496 4022 2.066393 CCGGATCTGCTGGGAGGAA 61.066 63.158 0.00 0.00 39.56 3.36
1680 4206 2.611292 CGGCTGGAATGATGAGAGAAAC 59.389 50.000 0.00 0.00 0.00 2.78
1685 4211 2.565841 GAATGATGAGAGAAACGGGGG 58.434 52.381 0.00 0.00 0.00 5.40
1815 4341 1.045407 TGCTGGGTGAGTCGTTTAGT 58.955 50.000 0.00 0.00 0.00 2.24
1869 4395 1.905637 ACCTGGGATCGTTTGTTTCC 58.094 50.000 0.00 0.00 0.00 3.13
1986 4517 0.112412 AGGGAGTTCCACGGCATTTT 59.888 50.000 0.00 0.00 38.24 1.82
1987 4518 0.966179 GGGAGTTCCACGGCATTTTT 59.034 50.000 0.00 0.00 37.91 1.94
2037 4568 8.200120 ACTATATACTAAACCTTCCCAACGAAC 58.800 37.037 0.00 0.00 0.00 3.95
2135 4669 3.245990 GCATGTTTTGGCACTTTGACTTC 59.754 43.478 0.00 0.00 0.00 3.01
2136 4670 4.685924 CATGTTTTGGCACTTTGACTTCT 58.314 39.130 0.00 0.00 0.00 2.85
2137 4671 4.799564 TGTTTTGGCACTTTGACTTCTT 57.200 36.364 0.00 0.00 0.00 2.52
2321 4855 2.303022 TCCTTGCTACTCCAGTTTCCTG 59.697 50.000 0.00 0.00 38.50 3.86
2352 4886 6.823689 ACCTGCAGATATCGAAGTAATTTTGT 59.176 34.615 17.39 0.00 0.00 2.83
2393 4927 7.120873 GCTGGCATCTGATCTGTTGATATTATT 59.879 37.037 13.19 0.00 32.19 1.40
2502 5036 6.040278 TGTGATTTTGATTTGTAGTGCTTCCA 59.960 34.615 0.00 0.00 0.00 3.53
2672 5214 4.685169 ATGTCTGTTAAGGCATTTCACG 57.315 40.909 0.00 0.00 46.83 4.35
2716 5258 8.428186 TGCGTAAATATTAAGTGTTAAGGAGG 57.572 34.615 0.00 0.00 0.00 4.30
2727 5269 2.027192 TGTTAAGGAGGTTGCTGCCTAG 60.027 50.000 0.00 0.00 39.34 3.02
2729 5271 1.362224 AAGGAGGTTGCTGCCTAGAA 58.638 50.000 0.00 0.00 39.34 2.10
2787 5329 8.692110 ACTACAAATTGCACAATATCACATTG 57.308 30.769 0.00 0.00 35.29 2.82
2882 5424 8.612619 CACAATTCTTCTAGTGTTGTACAGTTT 58.387 33.333 0.00 0.00 33.15 2.66
2895 5437 6.943146 TGTTGTACAGTTTAAGCCAATCCATA 59.057 34.615 0.00 0.00 0.00 2.74
3006 5548 8.311120 GCAACACGTCTAATTATTAAATGCAAC 58.689 33.333 0.00 0.00 0.00 4.17
3531 6079 2.205074 GCCGTGGTTATCAGATCTGTG 58.795 52.381 21.92 0.00 0.00 3.66
3567 6115 2.260869 CCGGGTGCTTGTGAGGTTG 61.261 63.158 0.00 0.00 0.00 3.77
3597 6402 9.832445 TTGTTAGATATTCCTATCAACCAACTC 57.168 33.333 0.00 0.00 36.90 3.01
3660 6466 0.393820 TAACACCCCACTTCACGTCC 59.606 55.000 0.00 0.00 0.00 4.79
3663 6469 2.048503 CCCCACTTCACGTCCGAC 60.049 66.667 0.00 0.00 0.00 4.79
3755 6561 1.002544 GGGACTGAGACTTGAACCCAG 59.997 57.143 0.00 0.00 36.27 4.45
3988 7199 5.437191 AACTAAATAGTTGAGGAGGGGTG 57.563 43.478 5.07 0.00 44.30 4.61
3989 7200 4.695606 ACTAAATAGTTGAGGAGGGGTGA 58.304 43.478 0.00 0.00 31.13 4.02
3990 7201 4.717280 ACTAAATAGTTGAGGAGGGGTGAG 59.283 45.833 0.00 0.00 31.13 3.51
3991 7202 2.182516 ATAGTTGAGGAGGGGTGAGG 57.817 55.000 0.00 0.00 0.00 3.86
3992 7203 0.042731 TAGTTGAGGAGGGGTGAGGG 59.957 60.000 0.00 0.00 0.00 4.30
3993 7204 1.539124 GTTGAGGAGGGGTGAGGGT 60.539 63.158 0.00 0.00 0.00 4.34
3994 7205 1.538876 TTGAGGAGGGGTGAGGGTG 60.539 63.158 0.00 0.00 0.00 4.61
3995 7206 2.689034 GAGGAGGGGTGAGGGTGG 60.689 72.222 0.00 0.00 0.00 4.61
3996 7207 4.354943 AGGAGGGGTGAGGGTGGG 62.355 72.222 0.00 0.00 0.00 4.61
3997 7208 4.677151 GGAGGGGTGAGGGTGGGT 62.677 72.222 0.00 0.00 0.00 4.51
4130 7342 7.337184 GGAGGAAGGTAAGAAAATTTAGAGTGG 59.663 40.741 0.00 0.00 0.00 4.00
4135 7347 5.479027 GGTAAGAAAATTTAGAGTGGCCCAA 59.521 40.000 0.00 0.00 0.00 4.12
4177 7390 3.128764 GGTAGGTTTGGCTCTTTACATGC 59.871 47.826 0.00 0.00 0.00 4.06
4394 7608 4.803613 GGTGTGAAACCTAAAAAGCTTGTG 59.196 41.667 0.00 0.00 46.55 3.33
4817 8098 7.926555 TCCTGCATACATTAAAGCTACTAAGTC 59.073 37.037 0.00 0.00 0.00 3.01
4928 8210 5.221843 ACTGGCCAACATGTTATATCCGTAT 60.222 40.000 11.53 0.00 0.00 3.06
4931 8213 5.351465 GGCCAACATGTTATATCCGTATGAG 59.649 44.000 11.53 0.00 0.00 2.90
5169 8455 3.243336 GTCTGTGCTAGTCCACTAAACG 58.757 50.000 2.73 0.00 36.68 3.60
5217 8503 7.607607 TCTTTGACACAATAGAATGCATGTAGT 59.392 33.333 0.00 0.00 0.00 2.73
5239 8525 3.735591 ACTTTGTAAGCGCTTCCTTGTA 58.264 40.909 28.82 4.62 0.00 2.41
5450 8739 5.182001 GCTTGGTGAACTTGATACTTCATGT 59.818 40.000 0.00 0.00 40.79 3.21
5482 8772 3.938334 TGACACGCACATACTTAATGCAT 59.062 39.130 0.00 0.00 39.39 3.96
5483 8773 5.112686 TGACACGCACATACTTAATGCATA 58.887 37.500 0.00 0.00 39.39 3.14
5484 8774 5.006261 TGACACGCACATACTTAATGCATAC 59.994 40.000 0.00 0.00 39.39 2.39
5485 8775 5.116180 ACACGCACATACTTAATGCATACT 58.884 37.500 0.00 0.00 39.39 2.12
5486 8776 5.584649 ACACGCACATACTTAATGCATACTT 59.415 36.000 0.00 0.00 39.39 2.24
5487 8777 6.759356 ACACGCACATACTTAATGCATACTTA 59.241 34.615 0.00 0.00 39.39 2.24
5488 8778 7.441157 ACACGCACATACTTAATGCATACTTAT 59.559 33.333 0.00 0.00 39.39 1.73
5489 8779 7.741652 CACGCACATACTTAATGCATACTTATG 59.258 37.037 0.00 7.68 39.39 1.90
5507 8797 7.251704 ACTTATGCACAAAGATGCTATGTAC 57.748 36.000 15.62 0.00 46.28 2.90
5622 8913 3.503363 CACATTTGGCAGCTCAGAAGTTA 59.497 43.478 0.00 0.00 0.00 2.24
5795 9087 4.505922 GCATCCTTGATCGTCTAGACAAAG 59.494 45.833 22.37 17.21 0.00 2.77
5861 9153 4.214971 CACATGCTAGCAATGTATTCCTCC 59.785 45.833 23.54 0.00 0.00 4.30
5876 9168 8.721133 TGTATTCCTCCAAGATAGCTTATACA 57.279 34.615 7.39 7.39 31.03 2.29
5877 9169 8.807118 TGTATTCCTCCAAGATAGCTTATACAG 58.193 37.037 7.39 0.00 30.48 2.74
5965 9257 4.156922 CCTTAGTCATCTGTCGACTTCAGT 59.843 45.833 17.92 2.07 40.89 3.41
5966 9258 5.354513 CCTTAGTCATCTGTCGACTTCAGTA 59.645 44.000 17.92 1.15 40.89 2.74
5967 9259 4.955925 AGTCATCTGTCGACTTCAGTAG 57.044 45.455 17.92 4.48 40.89 2.57
5968 9260 4.328536 AGTCATCTGTCGACTTCAGTAGT 58.671 43.478 17.92 0.00 40.89 2.73
5969 9261 5.489249 AGTCATCTGTCGACTTCAGTAGTA 58.511 41.667 17.92 0.00 40.89 1.82
5970 9262 5.352016 AGTCATCTGTCGACTTCAGTAGTAC 59.648 44.000 17.92 5.40 40.89 2.73
5971 9263 5.121925 GTCATCTGTCGACTTCAGTAGTACA 59.878 44.000 17.92 0.00 37.17 2.90
5972 9264 5.121925 TCATCTGTCGACTTCAGTAGTACAC 59.878 44.000 17.92 0.00 37.17 2.90
6002 9294 3.532542 GCTGTACAGGTTGTTATCTCCC 58.467 50.000 23.95 0.00 0.00 4.30
6298 9590 1.856265 GAAGGCTGTTTGCGAGGTGG 61.856 60.000 0.00 0.00 44.05 4.61
6327 9619 1.350193 CAACACCGTCTCCAAGATCG 58.650 55.000 0.00 0.00 0.00 3.69
6429 9721 5.561679 AGTAAAATGGACTGGAAGAAGGTC 58.438 41.667 0.00 0.00 37.43 3.85
6450 9742 3.118992 TCGTGAAGAAGCTGCAGTCATAT 60.119 43.478 16.64 0.00 0.00 1.78
6621 9913 8.305317 ACTCTATAGGTTTCTGTTGTTAGTGTC 58.695 37.037 0.00 0.00 0.00 3.67
6651 9943 3.895656 CCATGAGGTCGATAACTCCCTTA 59.104 47.826 10.83 0.00 32.80 2.69
6743 10035 5.839262 TTTGACACGTAGACATTCACATC 57.161 39.130 0.00 0.00 0.00 3.06
6751 10043 5.923114 ACGTAGACATTCACATCAGATATGC 59.077 40.000 0.00 0.00 0.00 3.14
6836 10128 5.708948 TCACTTATGGTGCTTTGTAATTGC 58.291 37.500 0.00 0.00 44.98 3.56
6983 10275 3.120649 AGACGCTATTTTTGTCGCAGTTC 60.121 43.478 0.00 0.00 37.69 3.01
6985 10277 3.120649 ACGCTATTTTTGTCGCAGTTCTC 60.121 43.478 0.00 0.00 0.00 2.87
7140 10438 9.515226 TTAAGATGTTAAGGCTGACAAAAGTAT 57.485 29.630 7.88 0.00 0.00 2.12
7458 10762 4.755266 AGCCAGGTAAACCACTGTATAG 57.245 45.455 1.26 0.00 38.89 1.31
7482 10786 6.437162 AGCTTCTGATAGTCAGGGAGATATTC 59.563 42.308 7.08 0.00 44.39 1.75
7507 10811 4.023279 CCGATCTCAGACTCTGGTATCTTG 60.023 50.000 6.20 1.62 31.51 3.02
7509 10813 4.323569 TCTCAGACTCTGGTATCTTGGT 57.676 45.455 6.20 0.00 31.51 3.67
7651 10955 6.985117 AGTGTTCACATACAATTTGATGCTT 58.015 32.000 2.79 0.00 0.00 3.91
7685 10989 4.521146 CTCCATTGGTCTTGACTAATGCT 58.479 43.478 24.76 1.28 37.29 3.79
7841 11145 6.409704 TCTTGTCACTTCTATATGCTGCTTT 58.590 36.000 0.00 0.00 0.00 3.51
7869 11190 9.640963 AAGTATAGTGACTGCAGTAGTTTTAAG 57.359 33.333 21.73 0.00 40.53 1.85
7896 11217 7.306866 GCATCGTCTTCATACTCTAAATGAACC 60.307 40.741 0.00 0.00 38.19 3.62
7910 11233 2.205022 TGAACCCTCCTCAATTGCAG 57.795 50.000 0.00 0.00 0.00 4.41
7968 11293 4.889409 ACATTTAGTCTTGTGGCCATATGG 59.111 41.667 18.07 18.07 38.53 2.74
7985 11310 7.268586 GCCATATGGTCCAGTATAGTAGAATG 58.731 42.308 22.79 0.00 37.57 2.67
8001 11326 2.954318 AGAATGTTGTTGTGCAGCTCTT 59.046 40.909 0.00 0.00 0.00 2.85
8029 11354 7.920682 GTGGGGTTTGTAATGCTGATATTTTAG 59.079 37.037 0.00 0.00 0.00 1.85
8263 11612 1.326852 GCATGACAGCGATTCTGACTG 59.673 52.381 0.00 0.00 45.72 3.51
8430 11779 3.982058 CGAGGTAGTTTCTGACACAGTTC 59.018 47.826 0.00 0.00 32.61 3.01
8464 11813 0.595310 GAAGATAGGCGCCGTCTGAC 60.595 60.000 29.77 23.37 0.00 3.51
8785 12139 4.454678 ACATATCAAGTGACATTGGCGAT 58.545 39.130 0.00 0.00 0.00 4.58
8820 12174 5.069648 TCAAATTCTCACACACACTCTCTCT 59.930 40.000 0.00 0.00 0.00 3.10
8840 12215 0.933700 CTCCCTCCTCCCTCTCTCTT 59.066 60.000 0.00 0.00 0.00 2.85
8847 12222 2.092646 TCCTCCCTCTCTCTTTCTCTCG 60.093 54.545 0.00 0.00 0.00 4.04
8873 12248 9.325198 GAACACACACACATATCCATCTTATTA 57.675 33.333 0.00 0.00 0.00 0.98
8882 12257 6.383147 ACATATCCATCTTATTAGGTACGGGG 59.617 42.308 0.00 0.00 0.00 5.73
8894 12269 1.074889 GGTACGGGGCCATAATCCATT 59.925 52.381 4.39 0.00 0.00 3.16
8911 12286 3.565902 TCCATTTATTTCACACGCACACA 59.434 39.130 0.00 0.00 0.00 3.72
9008 12383 6.348621 ACAAATGTTTTGCATTGAAGACAC 57.651 33.333 2.61 0.00 46.29 3.67
9127 12502 6.096141 AGAGCCAACATATATCATCCTAGACG 59.904 42.308 0.00 0.00 0.00 4.18
9150 12525 2.095466 ACGCAACATCAACCATTTACCG 60.095 45.455 0.00 0.00 0.00 4.02
9169 12544 1.753073 CGTGGTACTTTAGGGACCGAT 59.247 52.381 0.00 0.00 35.91 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.609491 GCAACACTCCTACACGTCATCA 60.609 50.000 0.00 0.00 0.00 3.07
18 19 1.203187 TCAGACTAGGGCAACACTCCT 60.203 52.381 0.00 0.00 39.74 3.69
19 20 1.267121 TCAGACTAGGGCAACACTCC 58.733 55.000 0.00 0.00 39.74 3.85
32 34 5.520288 CCATTATTGTCGAACGAATCAGACT 59.480 40.000 0.00 0.00 34.66 3.24
108 110 1.897560 TCTGAACTCGACTCAGCTCA 58.102 50.000 12.90 0.00 40.18 4.26
113 115 3.013219 CTCCTCATCTGAACTCGACTCA 58.987 50.000 0.00 0.00 0.00 3.41
115 117 2.291282 ACCTCCTCATCTGAACTCGACT 60.291 50.000 0.00 0.00 0.00 4.18
125 127 1.063642 TGACGGATCACCTCCTCATCT 60.064 52.381 0.00 0.00 42.47 2.90
256 263 0.814457 ACGTCAGCCTTTGCACAAAA 59.186 45.000 0.00 0.00 41.13 2.44
287 1286 1.391485 CGGCGATCTGACAAAACTGAG 59.609 52.381 0.00 0.00 0.00 3.35
305 1304 0.596600 AGTACAAGTCACGTGCACGG 60.597 55.000 39.21 28.05 44.95 4.94
310 1309 6.706055 AATAATCACAGTACAAGTCACGTG 57.294 37.500 9.94 9.94 0.00 4.49
449 2784 3.056821 GGGAAAAGCATTTGAGGTGGTAC 60.057 47.826 0.00 0.00 39.02 3.34
451 2786 1.970640 GGGAAAAGCATTTGAGGTGGT 59.029 47.619 0.00 0.00 39.02 4.16
455 2790 1.066645 GGCAGGGAAAAGCATTTGAGG 60.067 52.381 0.00 0.00 39.02 3.86
456 2791 1.066645 GGGCAGGGAAAAGCATTTGAG 60.067 52.381 0.00 0.00 39.02 3.02
458 2793 0.036105 GGGGCAGGGAAAAGCATTTG 60.036 55.000 0.00 0.00 39.02 2.32
459 2794 1.200760 GGGGGCAGGGAAAAGCATTT 61.201 55.000 0.00 0.00 42.41 2.32
645 2980 1.063070 TGGACTGCTGGTTTACCCCA 61.063 55.000 0.00 0.00 34.29 4.96
686 3021 2.127065 TGGATGGAAGGGGGCTGA 59.873 61.111 0.00 0.00 0.00 4.26
689 3024 4.143301 GGGTGGATGGAAGGGGGC 62.143 72.222 0.00 0.00 0.00 5.80
724 3068 3.687321 ATGCTGTAGGTGCGGCTGG 62.687 63.158 0.00 0.00 41.12 4.85
726 3070 2.124983 CATGCTGTAGGTGCGGCT 60.125 61.111 0.00 0.00 41.12 5.52
732 3076 1.065199 CCCACATGTCATGCTGTAGGT 60.065 52.381 12.91 0.00 0.00 3.08
737 3081 1.033746 GGGTCCCACATGTCATGCTG 61.034 60.000 12.91 9.91 0.00 4.41
884 3228 4.521062 CAGAGAGCGGGCGAAGGG 62.521 72.222 0.00 0.00 0.00 3.95
894 3238 1.002868 TTTCAGCCTGGCAGAGAGC 60.003 57.895 22.65 11.29 44.65 4.09
908 3434 6.443934 TTTGACTTTTTCCTGATCGTTTCA 57.556 33.333 0.00 0.00 0.00 2.69
991 3517 2.437716 GGGCTTCATTTCGGGCGA 60.438 61.111 0.00 0.00 0.00 5.54
1593 4119 2.179517 CTTCTCTCGGTCGCGCTT 59.820 61.111 5.56 0.00 0.00 4.68
1659 4185 2.609427 TTCTCTCATCATTCCAGCCG 57.391 50.000 0.00 0.00 0.00 5.52
1685 4211 0.392327 GGCACCTCTGCTTTCTCTCC 60.392 60.000 0.00 0.00 43.66 3.71
1696 4222 3.461773 CGTGGGATCGGCACCTCT 61.462 66.667 0.00 0.00 0.00 3.69
1703 4229 1.330521 CAACATTAAGCGTGGGATCGG 59.669 52.381 0.00 0.00 0.00 4.18
1815 4341 7.505923 TGGATATGAAAAGTAGAGCAGCTAGTA 59.494 37.037 0.00 0.00 32.40 1.82
1869 4395 1.009829 GGTTATGACTTCTGGCAGCG 58.990 55.000 10.34 5.84 0.00 5.18
1922 4453 3.915437 ACCTTTTATCCAAACACGCAG 57.085 42.857 0.00 0.00 0.00 5.18
2037 4568 2.689983 GCCCTGGTTGGATGACATTTAG 59.310 50.000 0.00 0.00 38.35 1.85
2094 4625 0.034477 CCCCCGCTCACTAAATGGTT 60.034 55.000 0.00 0.00 0.00 3.67
2135 4669 7.149569 TGGCACATCAAATTTCTAAGAGAAG 57.850 36.000 0.00 0.00 35.37 2.85
2136 4670 7.523293 TTGGCACATCAAATTTCTAAGAGAA 57.477 32.000 0.00 0.00 39.30 2.87
2137 4671 7.523293 TTTGGCACATCAAATTTCTAAGAGA 57.477 32.000 0.00 0.00 39.30 3.10
2170 4704 1.170442 TGCATGCCTCATGTGTTCTG 58.830 50.000 16.68 0.00 43.10 3.02
2279 4813 7.617041 AGGAAATAGCACACAGAATTACTTC 57.383 36.000 0.00 0.00 0.00 3.01
2352 4886 0.676466 CCAGCGTGGAAATAGCACCA 60.676 55.000 0.00 0.00 40.96 4.17
2393 4927 3.510753 TGCTTAAAGAGAATGCAATGCCA 59.489 39.130 1.53 0.00 0.00 4.92
2451 4985 3.634568 TTTTGACGGTCGCAATTTGAT 57.365 38.095 3.34 0.00 0.00 2.57
2502 5036 6.375455 CCTTGCTAATTACAAACATCCACTCT 59.625 38.462 0.00 0.00 0.00 3.24
2576 5118 9.961265 CTTGCACATGATAAACTCAATAATCAT 57.039 29.630 0.00 0.00 39.14 2.45
2672 5214 0.915364 AGGGAGAACAAGGGAGCATC 59.085 55.000 0.00 0.00 0.00 3.91
2716 5258 6.037062 ACAAAACAAAAATTCTAGGCAGCAAC 59.963 34.615 0.00 0.00 0.00 4.17
2729 5271 8.806146 AGGTAGCTCATATCACAAAACAAAAAT 58.194 29.630 0.00 0.00 0.00 1.82
2882 5424 6.661377 TGCAACTAAAACTATGGATTGGCTTA 59.339 34.615 0.00 0.00 0.00 3.09
2895 5437 5.989777 CAGGTACTAGTGTGCAACTAAAACT 59.010 40.000 5.39 6.54 40.92 2.66
3006 5548 3.781079 TCCAGTTGTTGAAACAGCAAG 57.219 42.857 11.80 4.69 41.82 4.01
3051 5593 9.884636 TTACATTAAGCAGCTTCTTACAGAATA 57.115 29.630 12.07 0.00 33.13 1.75
3181 5724 3.937706 CCAGACTGACCTGCAAGAAATAG 59.062 47.826 3.32 0.00 34.07 1.73
3484 6032 1.903183 GAAGAGGAGGTAGGCAACACT 59.097 52.381 0.00 0.00 41.41 3.55
3531 6079 1.064060 CGGATGATTTTCGGTGCCTTC 59.936 52.381 0.00 0.00 0.00 3.46
3597 6402 3.550437 ATCAGATCGGTCTTTTGGGAG 57.450 47.619 0.00 0.00 30.42 4.30
3660 6466 1.920574 GATCATTCCATATCCGCGTCG 59.079 52.381 4.92 0.00 0.00 5.12
3663 6469 3.066380 TGTTGATCATTCCATATCCGCG 58.934 45.455 0.00 0.00 0.00 6.46
3909 7120 5.408824 ACTCCCTCCGTCCCATAATATAAA 58.591 41.667 0.00 0.00 0.00 1.40
3985 7196 3.966543 CACCCACCCACCCTCACC 61.967 72.222 0.00 0.00 0.00 4.02
3986 7197 2.852075 TCACCCACCCACCCTCAC 60.852 66.667 0.00 0.00 0.00 3.51
3987 7198 2.529136 CTCACCCACCCACCCTCA 60.529 66.667 0.00 0.00 0.00 3.86
3988 7199 3.330720 CCTCACCCACCCACCCTC 61.331 72.222 0.00 0.00 0.00 4.30
3991 7202 3.966543 CACCCTCACCCACCCACC 61.967 72.222 0.00 0.00 0.00 4.61
3992 7203 3.175710 ACACCCTCACCCACCCAC 61.176 66.667 0.00 0.00 0.00 4.61
3993 7204 3.174987 CACACCCTCACCCACCCA 61.175 66.667 0.00 0.00 0.00 4.51
3994 7205 3.966543 CCACACCCTCACCCACCC 61.967 72.222 0.00 0.00 0.00 4.61
3995 7206 3.966543 CCCACACCCTCACCCACC 61.967 72.222 0.00 0.00 0.00 4.61
3996 7207 2.852075 TCCCACACCCTCACCCAC 60.852 66.667 0.00 0.00 0.00 4.61
3997 7208 2.852075 GTCCCACACCCTCACCCA 60.852 66.667 0.00 0.00 0.00 4.51
4062 7273 8.120140 TCTTCTCTACTACTTTAAGTTCCCAC 57.880 38.462 1.94 0.00 0.00 4.61
4135 7347 3.271490 ACCTGTCATACCACCCTAGTACT 59.729 47.826 0.00 0.00 0.00 2.73
4145 7357 2.026636 GCCAAACCTACCTGTCATACCA 60.027 50.000 0.00 0.00 0.00 3.25
4177 7390 1.062587 GGCATCGACCAACAGAAATCG 59.937 52.381 0.00 0.00 35.91 3.34
4394 7608 0.452987 TGCCATTCGATGCAAAGAGC 59.547 50.000 0.00 0.00 45.96 4.09
4401 7668 5.821204 ACTTAAAAGTATGCCATTCGATGC 58.179 37.500 0.00 0.00 37.52 3.91
4455 7722 1.610522 CCAGAGCCTGAAAACACCTTG 59.389 52.381 4.00 0.00 32.44 3.61
4456 7723 1.494721 TCCAGAGCCTGAAAACACCTT 59.505 47.619 4.00 0.00 32.44 3.50
4749 8030 7.170965 TGAAATTTCTATGATCCCAGGCTATC 58.829 38.462 18.64 0.00 0.00 2.08
4844 8125 4.870021 AAAGAACTATGATCCCAGGCTT 57.130 40.909 0.00 0.00 0.00 4.35
4892 8174 0.696501 TGGCCAGTAAGAAGGGGTTC 59.303 55.000 0.00 0.00 0.00 3.62
4928 8210 4.968719 TGCAATCTAAACTATCCCCTCTCA 59.031 41.667 0.00 0.00 0.00 3.27
5169 8455 8.457238 AAGAAATAATAGGAAACTGGAGATGC 57.543 34.615 0.00 0.00 43.88 3.91
5217 8503 3.735591 ACAAGGAAGCGCTTACAAAGTA 58.264 40.909 32.97 0.00 0.00 2.24
5407 8693 1.808945 GCAACACATTAGACAGCTGCT 59.191 47.619 15.27 14.40 0.00 4.24
5408 8694 1.808945 AGCAACACATTAGACAGCTGC 59.191 47.619 15.27 6.85 0.00 5.25
5409 8695 3.365666 CCAAGCAACACATTAGACAGCTG 60.366 47.826 13.48 13.48 0.00 4.24
5489 8779 2.351418 TGCGTACATAGCATCTTTGTGC 59.649 45.455 0.00 0.00 45.38 4.57
5501 8791 9.283420 CAAACAAAAATATGACATGCGTACATA 57.717 29.630 0.00 7.22 33.67 2.29
5507 8797 6.527722 AGCTACAAACAAAAATATGACATGCG 59.472 34.615 0.00 0.00 0.00 4.73
6002 9294 7.468141 TGACTACTGATACCATTATGCCTAG 57.532 40.000 0.00 0.00 0.00 3.02
6327 9619 2.034999 TTGGAATCCACCACCGCC 59.965 61.111 0.00 0.00 39.85 6.13
6429 9721 1.436600 ATGACTGCAGCTTCTTCACG 58.563 50.000 15.27 0.00 0.00 4.35
6450 9742 3.216800 GCTTGCTGTGATGGGATGATTA 58.783 45.455 0.00 0.00 0.00 1.75
6559 9851 6.889301 AGTATGTAAATTGCCATGATGGAG 57.111 37.500 17.22 0.00 40.96 3.86
6743 10035 7.714377 AGAAGTTCCATTGTAAGAGCATATCTG 59.286 37.037 0.00 0.00 38.67 2.90
6751 10043 8.025445 CCATCAAAAGAAGTTCCATTGTAAGAG 58.975 37.037 14.48 5.41 0.00 2.85
6836 10128 3.708195 GCAGCAGTGCCAAATACAG 57.292 52.632 12.58 0.00 44.72 2.74
6983 10275 3.415457 AAGAAGAACTGGCTCAAGGAG 57.585 47.619 0.00 0.00 0.00 3.69
6985 10277 3.633986 ACAAAAGAAGAACTGGCTCAAGG 59.366 43.478 0.00 0.00 0.00 3.61
7029 10321 2.336945 CAGCAGCCTGTATGGAATCA 57.663 50.000 0.00 0.00 38.35 2.57
7150 10448 6.100859 TGAAAGATAAAGAGATCATGCCCTCT 59.899 38.462 9.88 9.88 41.17 3.69
7158 10456 9.618890 CATTAAGGGTGAAAGATAAAGAGATCA 57.381 33.333 0.00 0.00 0.00 2.92
7319 10620 9.760077 GATACTAAGGCACAAGTTAGCTATAAA 57.240 33.333 0.00 0.00 30.57 1.40
7329 10630 6.763610 GCTATTTGAGATACTAAGGCACAAGT 59.236 38.462 0.00 0.00 0.00 3.16
7330 10631 6.203723 GGCTATTTGAGATACTAAGGCACAAG 59.796 42.308 0.00 0.00 0.00 3.16
7458 10762 7.362920 GAGAATATCTCCCTGACTATCAGAAGC 60.363 44.444 7.41 0.00 40.91 3.86
7482 10786 2.051334 ACCAGAGTCTGAGATCGGAG 57.949 55.000 22.09 4.54 32.44 4.63
7507 10811 2.531522 ATGCTTGTTTCTGCCAAACC 57.468 45.000 6.04 0.00 0.00 3.27
7509 10813 6.338214 TGTTATATGCTTGTTTCTGCCAAA 57.662 33.333 0.00 0.00 0.00 3.28
7651 10955 9.693739 TCAAGACCAATGGAGCTAAATAATTAA 57.306 29.630 6.16 0.00 0.00 1.40
7685 10989 8.924511 AAGAGAAAGGAAGACATGACAATAAA 57.075 30.769 0.00 0.00 0.00 1.40
7869 11190 6.216569 TCATTTAGAGTATGAAGACGATGCC 58.783 40.000 0.00 0.00 0.00 4.40
7896 11217 1.915141 ACCAACTGCAATTGAGGAGG 58.085 50.000 9.94 11.58 0.00 4.30
7910 11233 1.895131 AGGATGCAACATCCAACCAAC 59.105 47.619 24.55 0.52 40.61 3.77
7968 11293 7.201530 GCACAACAACATTCTACTATACTGGAC 60.202 40.741 0.00 0.00 0.00 4.02
7985 11310 0.740737 ACCAAGAGCTGCACAACAAC 59.259 50.000 1.02 0.00 0.00 3.32
8001 11326 1.145945 TCAGCATTACAAACCCCACCA 59.854 47.619 0.00 0.00 0.00 4.17
8263 11612 0.108756 ACGAGGCGAGGCTTTAACTC 60.109 55.000 0.00 0.00 0.00 3.01
8430 11779 5.233988 CCTATCTTCTCTTTGCTATTCCCG 58.766 45.833 0.00 0.00 0.00 5.14
8464 11813 2.477825 CAGCCTAGAATGATGGTGACG 58.522 52.381 0.00 0.00 0.00 4.35
8571 11923 5.221925 ACTGCATAAACTAGATACATGGGGG 60.222 44.000 0.00 0.00 0.00 5.40
8572 11924 5.702670 CACTGCATAAACTAGATACATGGGG 59.297 44.000 0.00 0.00 0.00 4.96
8785 12139 8.134895 GTGTGTGAGAATTTGATGGTAAAAAGA 58.865 33.333 0.00 0.00 0.00 2.52
8820 12174 0.047176 AGAGAGAGGGAGGAGGGAGA 59.953 60.000 0.00 0.00 0.00 3.71
8847 12222 7.792374 ATAAGATGGATATGTGTGTGTGTTC 57.208 36.000 0.00 0.00 0.00 3.18
8873 12248 0.400815 TGGATTATGGCCCCGTACCT 60.401 55.000 0.00 0.00 0.00 3.08
8882 12257 5.402270 GCGTGTGAAATAAATGGATTATGGC 59.598 40.000 0.00 0.00 34.41 4.40
8894 12269 2.939756 AGTGTGTGTGCGTGTGAAATAA 59.060 40.909 0.00 0.00 0.00 1.40
8999 12374 5.765677 TGGGAATTGTTTATCGTGTCTTCAA 59.234 36.000 0.00 0.00 0.00 2.69
9008 12383 4.804108 TGCACTTTGGGAATTGTTTATCG 58.196 39.130 0.00 0.00 0.00 2.92
9127 12502 3.917985 GGTAAATGGTTGATGTTGCGTTC 59.082 43.478 0.00 0.00 0.00 3.95
9150 12525 3.320256 CCTATCGGTCCCTAAAGTACCAC 59.680 52.174 0.00 0.00 32.55 4.16
9169 12544 3.800261 GCGCTTCTACATGCATTCTCCTA 60.800 47.826 0.00 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.