Multiple sequence alignment - TraesCS7A01G100700

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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 TraesCS7A01G100700 chr7A 100.000 4145 0 0 1523 5667 61819705 61815561 0.000000e+00 7655.0
1 TraesCS7A01G100700 chr7A 91.287 2525 129 34 1525 4009 62083469 62085942 0.000000e+00 3360.0
2 TraesCS7A01G100700 chr7A 100.000 1216 0 0 1 1216 61821227 61820012 0.000000e+00 2246.0
3 TraesCS7A01G100700 chr7A 91.321 1302 105 2 3430 4731 61887265 61888558 0.000000e+00 1772.0
4 TraesCS7A01G100700 chr7A 89.737 838 64 14 1944 2765 61882612 61883443 0.000000e+00 1051.0
5 TraesCS7A01G100700 chr7A 86.297 686 72 12 2762 3434 61883601 61884277 0.000000e+00 726.0
6 TraesCS7A01G100700 chr7A 75.684 987 168 49 2339 3305 62743432 62742498 1.460000e-115 427.0
7 TraesCS7A01G100700 chr7A 81.323 514 76 8 3566 4077 62738862 62738367 3.180000e-107 399.0
8 TraesCS7A01G100700 chr7A 86.908 359 23 11 859 1216 62083087 62083422 1.150000e-101 381.0
9 TraesCS7A01G100700 chr7A 80.887 293 32 14 863 1153 61882291 61882561 5.750000e-50 209.0
10 TraesCS7A01G100700 chr7A 94.167 120 5 1 5413 5532 700603605 700603722 1.250000e-41 182.0
11 TraesCS7A01G100700 chr7A 92.623 122 7 1 5413 5534 90780689 90780808 2.100000e-39 174.0
12 TraesCS7A01G100700 chr4A 94.839 3333 145 14 1890 5211 673957489 673960805 0.000000e+00 5177.0
13 TraesCS7A01G100700 chr4A 84.301 637 71 21 109 731 637817866 637818487 3.780000e-166 595.0
14 TraesCS7A01G100700 chr4A 94.659 337 12 6 1562 1895 673957120 673957453 8.420000e-143 518.0
15 TraesCS7A01G100700 chr4A 88.547 358 32 6 859 1216 673956689 673957037 5.250000e-115 425.0
16 TraesCS7A01G100700 chr4A 99.153 118 1 0 5305 5422 673960804 673960921 4.450000e-51 213.0
17 TraesCS7A01G100700 chr4A 83.663 202 25 7 1 201 530820523 530820717 3.490000e-42 183.0
18 TraesCS7A01G100700 chr4A 94.690 113 6 0 5423 5535 64574132 64574020 5.840000e-40 176.0
19 TraesCS7A01G100700 chr4A 91.870 123 9 1 5423 5544 75836017 75835895 2.710000e-38 171.0
20 TraesCS7A01G100700 chr4A 82.840 169 24 3 2041 2204 674743962 674743794 4.580000e-31 147.0
21 TraesCS7A01G100700 chr4A 81.022 137 13 10 5531 5667 673960952 673961075 4.670000e-16 97.1
22 TraesCS7A01G100700 chr4A 90.164 61 4 2 3561 3620 674620948 674620889 1.690000e-10 78.7
23 TraesCS7A01G100700 chr4A 86.364 66 9 0 1010 1075 674744515 674744450 7.880000e-09 73.1
24 TraesCS7A01G100700 chr3D 94.770 3327 155 12 1893 5209 545261247 545257930 0.000000e+00 5162.0
25 TraesCS7A01G100700 chr3D 93.280 372 17 3 1525 1895 545261651 545261287 4.990000e-150 542.0
26 TraesCS7A01G100700 chr3D 87.793 426 25 8 791 1216 545262099 545261701 1.850000e-129 473.0
27 TraesCS7A01G100700 chr3D 99.153 118 1 0 5305 5422 545257926 545257809 4.450000e-51 213.0
28 TraesCS7A01G100700 chr3D 95.000 120 4 1 5413 5532 404384339 404384456 2.700000e-43 187.0
29 TraesCS7A01G100700 chr3D 92.913 127 8 1 1 126 504420160 504420286 3.490000e-42 183.0
30 TraesCS7A01G100700 chr7D 94.381 3328 171 12 1893 5211 57093143 57089823 0.000000e+00 5096.0
31 TraesCS7A01G100700 chr7D 92.003 1213 79 10 2819 4018 57793943 57795150 0.000000e+00 1687.0
32 TraesCS7A01G100700 chr7D 83.281 640 68 30 115 737 56394935 56394318 2.310000e-153 553.0
33 TraesCS7A01G100700 chr7D 92.072 391 11 4 1525 1895 57093572 57093182 3.010000e-147 532.0
34 TraesCS7A01G100700 chr7D 87.982 441 30 8 776 1216 57094038 57093621 3.050000e-137 499.0
35 TraesCS7A01G100700 chr7D 79.741 696 104 29 1 679 602825479 602824804 2.390000e-128 470.0
36 TraesCS7A01G100700 chr7D 86.253 371 29 13 859 1216 57777868 57778229 3.200000e-102 383.0
37 TraesCS7A01G100700 chr7D 90.580 138 13 0 5530 5667 57089668 57089531 3.490000e-42 183.0
38 TraesCS7A01G100700 chr7D 94.624 93 5 0 5330 5422 57089781 57089689 1.650000e-30 145.0
39 TraesCS7A01G100700 chr7D 88.350 103 12 0 4123 4225 57536851 57536953 2.140000e-24 124.0
40 TraesCS7A01G100700 chr7D 97.222 36 1 0 1812 1847 57791573 57791608 1.700000e-05 62.1
41 TraesCS7A01G100700 chr6D 83.830 637 74 24 113 730 333806911 333806285 3.810000e-161 579.0
42 TraesCS7A01G100700 chr6D 96.330 109 4 0 5423 5531 95293798 95293690 4.510000e-41 180.0
43 TraesCS7A01G100700 chr7B 83.178 642 72 32 109 735 34844545 34845165 6.420000e-154 555.0
44 TraesCS7A01G100700 chr7B 92.982 114 7 1 5197 5309 34327090 34326977 1.260000e-36 165.0
45 TraesCS7A01G100700 chr3B 82.527 641 83 21 109 731 676916659 676916030 2.320000e-148 536.0
46 TraesCS7A01G100700 chr3B 92.241 116 6 3 5210 5325 487221376 487221488 1.630000e-35 161.0
47 TraesCS7A01G100700 chr5A 82.059 641 75 26 117 735 85296256 85295634 1.410000e-140 510.0
48 TraesCS7A01G100700 chr5A 88.532 218 21 4 1 215 14132693 14132909 1.570000e-65 261.0
49 TraesCS7A01G100700 chr2A 81.875 640 83 25 109 731 678958142 678958765 5.070000e-140 508.0
50 TraesCS7A01G100700 chr2A 97.248 109 3 0 5423 5531 13832627 13832519 9.700000e-43 185.0
51 TraesCS7A01G100700 chr6A 81.424 646 79 29 109 737 414258290 414257669 1.830000e-134 490.0
52 TraesCS7A01G100700 chrUn 79.830 704 115 24 2413 3107 91222796 91223481 6.600000e-134 488.0
53 TraesCS7A01G100700 chrUn 81.188 505 62 17 3567 4062 91224372 91224852 5.360000e-100 375.0
54 TraesCS7A01G100700 chrUn 79.688 256 44 5 1957 2204 91222226 91222481 1.620000e-40 178.0
55 TraesCS7A01G100700 chr4D 78.003 741 106 29 1 726 472218112 472218810 4.090000e-111 412.0
56 TraesCS7A01G100700 chr4D 92.857 126 9 0 1 126 495992933 495992808 3.490000e-42 183.0
57 TraesCS7A01G100700 chr4D 96.078 102 4 0 5208 5309 323929571 323929672 3.510000e-37 167.0
58 TraesCS7A01G100700 chr4D 89.844 128 11 2 5196 5322 13198393 13198267 4.540000e-36 163.0
59 TraesCS7A01G100700 chr2B 80.245 572 82 22 184 735 679895373 679895933 8.840000e-108 401.0
60 TraesCS7A01G100700 chr2B 95.283 106 5 0 5208 5313 601206945 601206840 9.760000e-38 169.0
61 TraesCS7A01G100700 chr1B 87.209 172 20 2 1 171 548651180 548651350 1.610000e-45 195.0
62 TraesCS7A01G100700 chr1B 96.364 110 4 0 5423 5532 402109948 402109839 1.250000e-41 182.0
63 TraesCS7A01G100700 chr6B 89.362 141 15 0 31 171 662969068 662969208 1.620000e-40 178.0
64 TraesCS7A01G100700 chr5D 93.162 117 6 2 5201 5315 125803452 125803568 2.710000e-38 171.0
65 TraesCS7A01G100700 chr5D 97.030 101 3 0 5208 5308 205794744 205794644 2.710000e-38 171.0
66 TraesCS7A01G100700 chr5D 93.220 118 5 3 5205 5320 558970537 558970421 2.710000e-38 171.0
67 TraesCS7A01G100700 chr5B 90.299 134 8 2 5402 5532 577520455 577520586 2.710000e-38 171.0
68 TraesCS7A01G100700 chr5B 90.833 120 7 4 5188 5306 269976862 269976746 2.110000e-34 158.0
69 TraesCS7A01G100700 chr4B 93.220 118 5 3 5204 5320 664775721 664775606 2.710000e-38 171.0
70 TraesCS7A01G100700 chr3A 95.283 106 4 1 5208 5313 269394413 269394309 3.510000e-37 167.0
71 TraesCS7A01G100700 chr3A 86.331 139 13 5 5208 5344 12852622 12852488 4.580000e-31 147.0


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 TraesCS7A01G100700 chr7A 61815561 61821227 5666 True 4950.50 7655 100.000000 1 5667 2 chr7A.!!$R1 5666
1 TraesCS7A01G100700 chr7A 62083087 62085942 2855 False 1870.50 3360 89.097500 859 4009 2 chr7A.!!$F4 3150
2 TraesCS7A01G100700 chr7A 61882291 61888558 6267 False 939.50 1772 87.060500 863 4731 4 chr7A.!!$F3 3868
3 TraesCS7A01G100700 chr7A 62738367 62743432 5065 True 413.00 427 78.503500 2339 4077 2 chr7A.!!$R2 1738
4 TraesCS7A01G100700 chr4A 673956689 673961075 4386 False 1286.02 5177 91.644000 859 5667 5 chr4A.!!$F3 4808
5 TraesCS7A01G100700 chr4A 637817866 637818487 621 False 595.00 595 84.301000 109 731 1 chr4A.!!$F2 622
6 TraesCS7A01G100700 chr3D 545257809 545262099 4290 True 1597.50 5162 93.749000 791 5422 4 chr3D.!!$R1 4631
7 TraesCS7A01G100700 chr7D 57089531 57094038 4507 True 1291.00 5096 91.927800 776 5667 5 chr7D.!!$R3 4891
8 TraesCS7A01G100700 chr7D 57791573 57795150 3577 False 874.55 1687 94.612500 1812 4018 2 chr7D.!!$F3 2206
9 TraesCS7A01G100700 chr7D 56394318 56394935 617 True 553.00 553 83.281000 115 737 1 chr7D.!!$R1 622
10 TraesCS7A01G100700 chr7D 602824804 602825479 675 True 470.00 470 79.741000 1 679 1 chr7D.!!$R2 678
11 TraesCS7A01G100700 chr6D 333806285 333806911 626 True 579.00 579 83.830000 113 730 1 chr6D.!!$R2 617
12 TraesCS7A01G100700 chr7B 34844545 34845165 620 False 555.00 555 83.178000 109 735 1 chr7B.!!$F1 626
13 TraesCS7A01G100700 chr3B 676916030 676916659 629 True 536.00 536 82.527000 109 731 1 chr3B.!!$R1 622
14 TraesCS7A01G100700 chr5A 85295634 85296256 622 True 510.00 510 82.059000 117 735 1 chr5A.!!$R1 618
15 TraesCS7A01G100700 chr2A 678958142 678958765 623 False 508.00 508 81.875000 109 731 1 chr2A.!!$F1 622
16 TraesCS7A01G100700 chr6A 414257669 414258290 621 True 490.00 490 81.424000 109 737 1 chr6A.!!$R1 628
17 TraesCS7A01G100700 chrUn 91222226 91224852 2626 False 347.00 488 80.235333 1957 4062 3 chrUn.!!$F1 2105
18 TraesCS7A01G100700 chr4D 472218112 472218810 698 False 412.00 412 78.003000 1 726 1 chr4D.!!$F2 725
19 TraesCS7A01G100700 chr2B 679895373 679895933 560 False 401.00 401 80.245000 184 735 1 chr2B.!!$F1 551

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
107 109 0.106268 TGCCTCCCACAGAAGCAAAA 60.106 50.000 0.00 0.00 39.02 2.44 F
921 1070 0.179086 AAAAGCCCACTTTGCCGTTG 60.179 50.000 0.00 0.00 45.48 4.10 F
1904 2116 0.172803 CTTGCAATTCCTCAGGCTGC 59.827 55.000 10.34 5.52 0.00 5.25 F
1911 2123 0.324943 TTCCTCAGGCTGCAGGTTAC 59.675 55.000 23.46 0.00 0.00 2.50 F
2000 2216 0.809385 ATCTGTTGCATGCTGCTGTC 59.191 50.000 20.33 3.63 45.31 3.51 F
2001 2217 1.154282 CTGTTGCATGCTGCTGTCG 60.154 57.895 20.33 0.00 45.31 4.35 F
2617 3516 1.545582 GCAATCACAAGGCCTTTGCTA 59.454 47.619 25.29 9.81 40.59 3.49 F
4018 12889 1.171308 GACTGCGAGTACCCACAGTA 58.829 55.000 11.08 0.00 43.16 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1007 1157 0.179012 GTCGTCTAGGGGAGGAGGAG 60.179 65.000 0.00 0.0 39.16 3.69 R
2070 2288 1.090052 GTACCCATCTCGCAACTGCC 61.090 60.000 0.00 0.0 37.91 4.85 R
3145 5464 0.320683 TGCAGAACTGTGTGGATCCG 60.321 55.000 7.39 0.0 0.00 4.18 R
3327 9024 1.064463 CCATGGATATTCCCCATCCCG 60.064 57.143 5.56 0.0 42.18 5.14 R
3965 12836 0.535335 ACCGTACTGCTATGGTGTGG 59.465 55.000 0.00 0.0 40.33 4.17 R
3982 12853 2.108970 AGTCTCCTCCGGTGATTTACC 58.891 52.381 4.76 0.0 46.56 2.85 R
4092 12963 2.902484 GCAGTTATGCGACAAAACTTCG 59.098 45.455 0.00 0.0 43.87 3.79 R
5502 14391 0.035056 AACCCAGTGCATGTAGCTCC 60.035 55.000 0.00 0.0 45.94 4.70 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 1.859302 AAAACCAAACCAGGAGCACA 58.141 45.000 0.00 0.00 0.00 4.57
33 35 1.859302 AAACCAAACCAGGAGCACAA 58.141 45.000 0.00 0.00 0.00 3.33
87 89 1.726791 CCTCTCACGAAATCACAACCG 59.273 52.381 0.00 0.00 0.00 4.44
94 96 0.521735 GAAATCACAACCGTGCCTCC 59.478 55.000 0.00 0.00 43.28 4.30
96 98 2.063015 AATCACAACCGTGCCTCCCA 62.063 55.000 0.00 0.00 43.28 4.37
97 99 2.748058 ATCACAACCGTGCCTCCCAC 62.748 60.000 0.00 0.00 43.28 4.61
98 100 3.484806 ACAACCGTGCCTCCCACA 61.485 61.111 0.00 0.00 44.91 4.17
107 109 0.106268 TGCCTCCCACAGAAGCAAAA 60.106 50.000 0.00 0.00 39.02 2.44
111 113 1.007387 CCCACAGAAGCAAAACCGC 60.007 57.895 0.00 0.00 0.00 5.68
165 191 1.531578 GAAGCAAAACCGTGACTCTCC 59.468 52.381 0.00 0.00 0.00 3.71
232 271 2.357034 GGCCGTGACTCTTGCGAA 60.357 61.111 0.00 0.00 0.00 4.70
233 272 1.959226 GGCCGTGACTCTTGCGAAA 60.959 57.895 0.00 0.00 0.00 3.46
234 273 1.493311 GCCGTGACTCTTGCGAAAG 59.507 57.895 0.00 0.00 0.00 2.62
315 376 1.944709 CTGGTTTTCTTCCGTTTCCGT 59.055 47.619 0.00 0.00 0.00 4.69
381 489 2.210116 GAAGCAAAACCGTGACTCTCA 58.790 47.619 0.00 0.00 0.00 3.27
480 616 7.216505 GTGACTCTCGTGAAAGAAAAAGAAAAC 59.783 37.037 0.00 0.00 0.00 2.43
485 621 6.144175 TCGTGAAAGAAAAAGAAAACACGTT 58.856 32.000 0.49 0.00 45.96 3.99
489 625 9.088059 GTGAAAGAAAAAGAAAACACGTTTTTC 57.912 29.630 19.45 19.45 44.82 2.29
490 626 8.818057 TGAAAGAAAAAGAAAACACGTTTTTCA 58.182 25.926 24.51 3.64 46.00 2.69
492 628 9.592720 AAAGAAAAAGAAAACACGTTTTTCATG 57.407 25.926 24.51 2.94 46.00 3.07
494 630 9.413048 AGAAAAAGAAAACACGTTTTTCATGTA 57.587 25.926 24.51 0.00 46.00 2.29
694 843 4.521075 GCTAAGTGGCGCTGATCA 57.479 55.556 7.64 0.00 0.00 2.92
731 880 3.012518 AGGAGCGCTCGTTAACTAGTTA 58.987 45.455 29.81 11.38 0.00 2.24
737 886 4.201802 GCGCTCGTTAACTAGTTACTCTCT 60.202 45.833 14.96 0.00 0.00 3.10
738 887 5.257108 CGCTCGTTAACTAGTTACTCTCTG 58.743 45.833 14.96 5.30 0.00 3.35
739 888 5.163874 CGCTCGTTAACTAGTTACTCTCTGT 60.164 44.000 14.96 0.00 0.00 3.41
740 889 6.610456 GCTCGTTAACTAGTTACTCTCTGTT 58.390 40.000 14.96 0.00 0.00 3.16
741 890 7.083230 GCTCGTTAACTAGTTACTCTCTGTTT 58.917 38.462 14.96 0.00 0.00 2.83
742 891 7.594386 GCTCGTTAACTAGTTACTCTCTGTTTT 59.406 37.037 14.96 0.00 0.00 2.43
743 892 9.460906 CTCGTTAACTAGTTACTCTCTGTTTTT 57.539 33.333 14.96 0.00 0.00 1.94
774 923 2.957491 CGAAGGATCAGTTGCTCTCT 57.043 50.000 0.00 0.00 0.00 3.10
824 973 4.382254 GGCAAATGATGAATTGGCTTGAGA 60.382 41.667 0.00 0.00 43.79 3.27
834 983 1.454663 GGCTTGAGAAGATGGCCCC 60.455 63.158 0.00 0.00 37.12 5.80
884 1033 0.536006 CGAATCCAAGCCCATCTCCC 60.536 60.000 0.00 0.00 0.00 4.30
890 1039 2.300967 AAGCCCATCTCCCGCTGAA 61.301 57.895 0.00 0.00 31.92 3.02
891 1040 2.514824 GCCCATCTCCCGCTGAAC 60.515 66.667 0.00 0.00 0.00 3.18
921 1070 0.179086 AAAAGCCCACTTTGCCGTTG 60.179 50.000 0.00 0.00 45.48 4.10
963 1112 2.511600 CCCTCTACCTTTGCGCGG 60.512 66.667 8.83 0.00 0.00 6.46
999 1148 2.747022 GGCGGCAAACCCCAAAAT 59.253 55.556 3.07 0.00 0.00 1.82
1032 1182 0.752376 CTCCCCTAGACGACCTCACC 60.752 65.000 0.00 0.00 0.00 4.02
1050 1200 3.449227 CACCTGCTCGCCGAGGTA 61.449 66.667 16.95 0.00 40.85 3.08
1191 1341 2.606519 TCCTCCGGAACCAGGGTG 60.607 66.667 5.23 0.00 0.00 4.61
1572 1722 0.783579 GTGCGTTCGCATTGCATTTT 59.216 45.000 21.98 0.00 43.37 1.82
1798 1949 1.074951 CCCCTTCCTTTGTTCGCCT 59.925 57.895 0.00 0.00 0.00 5.52
1860 2030 3.263261 GAACTTTAGGAGGCTGCTGTAC 58.737 50.000 19.68 0.74 0.00 2.90
1904 2116 0.172803 CTTGCAATTCCTCAGGCTGC 59.827 55.000 10.34 5.52 0.00 5.25
1911 2123 0.324943 TTCCTCAGGCTGCAGGTTAC 59.675 55.000 23.46 0.00 0.00 2.50
1954 2170 8.032952 TGATGTTCATGTATTGTGACTTTCTC 57.967 34.615 0.00 0.00 0.00 2.87
2000 2216 0.809385 ATCTGTTGCATGCTGCTGTC 59.191 50.000 20.33 3.63 45.31 3.51
2001 2217 1.154282 CTGTTGCATGCTGCTGTCG 60.154 57.895 20.33 0.00 45.31 4.35
2070 2288 6.873076 GCCATATTACAGAGAAGATGGAGAAG 59.127 42.308 12.72 0.00 46.69 2.85
2198 2422 8.421784 AGTTATACATGGACCAACATAGTACTG 58.578 37.037 5.39 0.00 0.00 2.74
2267 2537 5.246203 TGTCTTCTAGTAGTGATTTGGCTGT 59.754 40.000 0.00 0.00 0.00 4.40
2617 3516 1.545582 GCAATCACAAGGCCTTTGCTA 59.454 47.619 25.29 9.81 40.59 3.49
2646 3545 6.649155 TGAGAAAAGAATTACATGATCGGGA 58.351 36.000 0.00 0.00 0.00 5.14
2827 5127 4.826733 TGTGTTTATGTCAGTTGGCATCTT 59.173 37.500 1.95 0.00 39.96 2.40
2841 5147 4.735985 TGGCATCTTGAATCATTTTCACG 58.264 39.130 0.00 0.00 0.00 4.35
3076 5394 9.213777 TGTAGATGGAAACTCTATTAACCAGAT 57.786 33.333 0.00 0.00 0.00 2.90
3145 5464 5.540400 TGGTATACCCACAGCACTATTAC 57.460 43.478 19.42 0.00 38.72 1.89
3156 5475 2.764010 AGCACTATTACGGATCCACACA 59.236 45.455 13.41 0.00 0.00 3.72
3223 5551 9.612620 CTTGTTTGTGGATATCTCTTTTACAAC 57.387 33.333 2.05 0.00 0.00 3.32
3327 9024 9.169592 AGTATTAGATATTCTTCTCGAGCCTAC 57.830 37.037 7.81 0.00 0.00 3.18
3374 9155 7.699878 ACTAGGACAGAAATTTCCCTTTACAT 58.300 34.615 16.61 4.55 31.51 2.29
3424 9290 5.531287 GGATTTACTTGCCATACTAACTGGG 59.469 44.000 0.00 0.00 34.16 4.45
3828 12699 8.969260 ACTGCTGAATCAATAAGTGATATCAA 57.031 30.769 7.07 0.00 46.80 2.57
3882 12753 3.222603 GGGTGTTATGCCCTTCTAATGG 58.777 50.000 0.00 0.00 42.81 3.16
3965 12836 3.297830 ACAAAAAGCGCCCAAGTAATC 57.702 42.857 2.29 0.00 0.00 1.75
3982 12853 2.890808 ATCCACACCATAGCAGTACG 57.109 50.000 0.00 0.00 0.00 3.67
4018 12889 1.171308 GACTGCGAGTACCCACAGTA 58.829 55.000 11.08 0.00 43.16 2.74
4092 12963 3.687572 AGATTTTGATGATCGCTGTGC 57.312 42.857 0.00 0.00 0.00 4.57
4212 13083 0.755327 GGGGTGTTGCTTGTGTCCTT 60.755 55.000 0.00 0.00 0.00 3.36
4669 13540 4.450305 AATTCAGCCCTCTTCATAGCAT 57.550 40.909 0.00 0.00 0.00 3.79
4716 13587 1.131303 TGTGTCCGGATGGGTTCCTT 61.131 55.000 7.81 0.00 42.99 3.36
4936 13807 3.931578 AGTAACATCTGTCAGGTCTTGC 58.068 45.455 0.00 0.00 0.00 4.01
4990 13861 3.461831 TGGGCCAGGCAAAGTAGTAATAT 59.538 43.478 15.19 0.00 0.00 1.28
5001 13872 8.511465 GCAAAGTAGTAATATTGCATTCATGG 57.489 34.615 6.31 0.00 45.61 3.66
5015 13886 2.965572 TCATGGGCAAATTTAGCTGC 57.034 45.000 0.00 0.00 37.86 5.25
5028 13899 2.439156 GCTGCCGGCTCCATTCTT 60.439 61.111 29.70 0.00 38.06 2.52
5050 13921 8.690203 TCTTGATGTTTCCAGTTCATTTCTTA 57.310 30.769 0.00 0.00 0.00 2.10
5083 13954 9.722056 GGCTAAATATAGATTGTTGTGTTTGAG 57.278 33.333 0.00 0.00 0.00 3.02
5130 14001 8.617290 AGTCACCAGTTTATGTTTAGTAAAGG 57.383 34.615 0.00 0.00 0.00 3.11
5164 14035 7.781693 AGTTACTATCAATTTCCTACCCGTCTA 59.218 37.037 0.00 0.00 0.00 2.59
5166 14037 6.134754 ACTATCAATTTCCTACCCGTCTACT 58.865 40.000 0.00 0.00 0.00 2.57
5175 14046 4.019501 TCCTACCCGTCTACTGGAGATATC 60.020 50.000 0.00 0.00 36.29 1.63
5203 14074 9.456147 GATATTTCTATCTAGACTGAGCCACTA 57.544 37.037 0.00 0.00 32.51 2.74
5209 14080 8.387039 TCTATCTAGACTGAGCCACTAATGTAT 58.613 37.037 0.00 0.00 0.00 2.29
5210 14081 9.674068 CTATCTAGACTGAGCCACTAATGTATA 57.326 37.037 0.00 0.00 0.00 1.47
5211 14082 7.747155 TCTAGACTGAGCCACTAATGTATAC 57.253 40.000 0.00 0.00 0.00 1.47
5212 14083 7.519057 TCTAGACTGAGCCACTAATGTATACT 58.481 38.462 4.17 0.00 0.00 2.12
5213 14084 6.642707 AGACTGAGCCACTAATGTATACTC 57.357 41.667 4.17 0.00 0.00 2.59
5214 14085 5.536916 AGACTGAGCCACTAATGTATACTCC 59.463 44.000 4.17 0.00 0.00 3.85
5215 14086 4.589374 ACTGAGCCACTAATGTATACTCCC 59.411 45.833 4.17 0.00 0.00 4.30
5216 14087 4.816126 TGAGCCACTAATGTATACTCCCT 58.184 43.478 4.17 0.00 0.00 4.20
5217 14088 4.833380 TGAGCCACTAATGTATACTCCCTC 59.167 45.833 4.17 0.54 0.00 4.30
5218 14089 5.081032 GAGCCACTAATGTATACTCCCTCT 58.919 45.833 4.17 0.00 0.00 3.69
5219 14090 4.835615 AGCCACTAATGTATACTCCCTCTG 59.164 45.833 4.17 0.00 0.00 3.35
5220 14091 4.589374 GCCACTAATGTATACTCCCTCTGT 59.411 45.833 4.17 0.00 0.00 3.41
5221 14092 5.279056 GCCACTAATGTATACTCCCTCTGTC 60.279 48.000 4.17 0.00 0.00 3.51
5222 14093 5.244178 CCACTAATGTATACTCCCTCTGTCC 59.756 48.000 4.17 0.00 0.00 4.02
5223 14094 5.244178 CACTAATGTATACTCCCTCTGTCCC 59.756 48.000 4.17 0.00 0.00 4.46
5224 14095 3.993658 ATGTATACTCCCTCTGTCCCA 57.006 47.619 4.17 0.00 0.00 4.37
5225 14096 3.769189 TGTATACTCCCTCTGTCCCAA 57.231 47.619 4.17 0.00 0.00 4.12
5226 14097 4.069312 TGTATACTCCCTCTGTCCCAAA 57.931 45.455 4.17 0.00 0.00 3.28
5227 14098 4.431378 TGTATACTCCCTCTGTCCCAAAA 58.569 43.478 4.17 0.00 0.00 2.44
5228 14099 5.036916 TGTATACTCCCTCTGTCCCAAAAT 58.963 41.667 4.17 0.00 0.00 1.82
5229 14100 6.206787 TGTATACTCCCTCTGTCCCAAAATA 58.793 40.000 4.17 0.00 0.00 1.40
5230 14101 6.674861 TGTATACTCCCTCTGTCCCAAAATAA 59.325 38.462 4.17 0.00 0.00 1.40
5231 14102 4.576330 ACTCCCTCTGTCCCAAAATAAG 57.424 45.455 0.00 0.00 0.00 1.73
5232 14103 3.916989 ACTCCCTCTGTCCCAAAATAAGT 59.083 43.478 0.00 0.00 0.00 2.24
5233 14104 4.263506 ACTCCCTCTGTCCCAAAATAAGTG 60.264 45.833 0.00 0.00 0.00 3.16
5234 14105 3.655777 TCCCTCTGTCCCAAAATAAGTGT 59.344 43.478 0.00 0.00 0.00 3.55
5235 14106 4.010349 CCCTCTGTCCCAAAATAAGTGTC 58.990 47.826 0.00 0.00 0.00 3.67
5236 14107 4.263506 CCCTCTGTCCCAAAATAAGTGTCT 60.264 45.833 0.00 0.00 0.00 3.41
5237 14108 4.938226 CCTCTGTCCCAAAATAAGTGTCTC 59.062 45.833 0.00 0.00 0.00 3.36
5238 14109 5.513094 CCTCTGTCCCAAAATAAGTGTCTCA 60.513 44.000 0.00 0.00 0.00 3.27
5239 14110 5.935945 TCTGTCCCAAAATAAGTGTCTCAA 58.064 37.500 0.00 0.00 0.00 3.02
5240 14111 5.763204 TCTGTCCCAAAATAAGTGTCTCAAC 59.237 40.000 0.00 0.00 0.00 3.18
5241 14112 4.825085 TGTCCCAAAATAAGTGTCTCAACC 59.175 41.667 0.00 0.00 0.00 3.77
5242 14113 5.070685 GTCCCAAAATAAGTGTCTCAACCT 58.929 41.667 0.00 0.00 0.00 3.50
5243 14114 5.535030 GTCCCAAAATAAGTGTCTCAACCTT 59.465 40.000 0.00 0.00 0.00 3.50
5244 14115 6.713450 GTCCCAAAATAAGTGTCTCAACCTTA 59.287 38.462 0.00 0.00 0.00 2.69
5245 14116 6.940298 TCCCAAAATAAGTGTCTCAACCTTAG 59.060 38.462 0.00 0.00 0.00 2.18
5246 14117 6.715264 CCCAAAATAAGTGTCTCAACCTTAGT 59.285 38.462 0.00 0.00 0.00 2.24
5247 14118 7.881232 CCCAAAATAAGTGTCTCAACCTTAGTA 59.119 37.037 0.00 0.00 0.00 1.82
5248 14119 8.718734 CCAAAATAAGTGTCTCAACCTTAGTAC 58.281 37.037 0.00 0.00 0.00 2.73
5249 14120 9.268268 CAAAATAAGTGTCTCAACCTTAGTACA 57.732 33.333 0.00 0.00 0.00 2.90
5250 14121 9.841295 AAAATAAGTGTCTCAACCTTAGTACAA 57.159 29.630 0.00 0.00 0.00 2.41
5251 14122 8.828688 AATAAGTGTCTCAACCTTAGTACAAC 57.171 34.615 0.00 0.00 0.00 3.32
5252 14123 6.481434 AAGTGTCTCAACCTTAGTACAACT 57.519 37.500 0.00 0.00 0.00 3.16
5253 14124 6.481434 AGTGTCTCAACCTTAGTACAACTT 57.519 37.500 0.00 0.00 0.00 2.66
5254 14125 6.885922 AGTGTCTCAACCTTAGTACAACTTT 58.114 36.000 0.00 0.00 0.00 2.66
5255 14126 6.761714 AGTGTCTCAACCTTAGTACAACTTTG 59.238 38.462 0.00 0.00 0.00 2.77
5256 14127 6.537660 GTGTCTCAACCTTAGTACAACTTTGT 59.462 38.462 0.00 0.00 44.86 2.83
5257 14128 7.707893 GTGTCTCAACCTTAGTACAACTTTGTA 59.292 37.037 0.00 0.00 42.35 2.41
5282 14153 7.553334 ACTGAAGTTAGTACAAAGTTGAGACA 58.447 34.615 0.00 0.00 30.41 3.41
5283 14154 7.491696 ACTGAAGTTAGTACAAAGTTGAGACAC 59.508 37.037 0.00 0.00 30.41 3.67
5284 14155 7.553334 TGAAGTTAGTACAAAGTTGAGACACT 58.447 34.615 0.00 0.00 0.00 3.55
5285 14156 8.038944 TGAAGTTAGTACAAAGTTGAGACACTT 58.961 33.333 0.00 3.16 38.74 3.16
5286 14157 9.525409 GAAGTTAGTACAAAGTTGAGACACTTA 57.475 33.333 0.00 0.00 35.87 2.24
5292 14163 8.621286 AGTACAAAGTTGAGACACTTATTTTGG 58.379 33.333 0.00 0.00 35.87 3.28
5293 14164 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
5294 14165 6.605594 ACAAAGTTGAGACACTTATTTTGGGA 59.394 34.615 0.00 0.00 35.87 4.37
5295 14166 6.635030 AAGTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
5296 14167 4.755123 AGTTGAGACACTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
5297 14168 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
5298 14169 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
5299 14170 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
5300 14171 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
5301 14172 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
5302 14173 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
5303 14174 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
5422 14311 2.101249 ACCAGTTCCAGTGCAAACATTG 59.899 45.455 2.09 0.00 33.51 2.82
5441 14330 8.682936 AACATTGCCTCTTACAGAAATATAGG 57.317 34.615 0.00 0.00 0.00 2.57
5442 14331 7.227156 ACATTGCCTCTTACAGAAATATAGGG 58.773 38.462 0.00 0.00 0.00 3.53
5443 14332 7.072454 ACATTGCCTCTTACAGAAATATAGGGA 59.928 37.037 0.00 0.00 0.00 4.20
5444 14333 7.446106 TTGCCTCTTACAGAAATATAGGGAA 57.554 36.000 0.00 0.00 31.58 3.97
5445 14334 7.446106 TGCCTCTTACAGAAATATAGGGAAA 57.554 36.000 0.00 0.00 0.00 3.13
5446 14335 7.509546 TGCCTCTTACAGAAATATAGGGAAAG 58.490 38.462 0.00 0.00 0.00 2.62
5447 14336 6.937465 GCCTCTTACAGAAATATAGGGAAAGG 59.063 42.308 0.00 0.00 0.00 3.11
5448 14337 6.937465 CCTCTTACAGAAATATAGGGAAAGGC 59.063 42.308 0.00 0.00 0.00 4.35
5449 14338 7.202139 CCTCTTACAGAAATATAGGGAAAGGCT 60.202 40.741 0.00 0.00 0.00 4.58
5450 14339 7.509546 TCTTACAGAAATATAGGGAAAGGCTG 58.490 38.462 0.00 0.00 0.00 4.85
5451 14340 4.464947 ACAGAAATATAGGGAAAGGCTGC 58.535 43.478 0.00 0.00 0.00 5.25
5452 14341 3.499918 CAGAAATATAGGGAAAGGCTGCG 59.500 47.826 0.00 0.00 0.00 5.18
5453 14342 3.136626 AGAAATATAGGGAAAGGCTGCGT 59.863 43.478 0.00 0.00 0.00 5.24
5454 14343 4.347000 AGAAATATAGGGAAAGGCTGCGTA 59.653 41.667 0.00 0.00 0.00 4.42
5455 14344 3.679824 ATATAGGGAAAGGCTGCGTAC 57.320 47.619 0.00 0.00 0.00 3.67
5456 14345 1.200519 ATAGGGAAAGGCTGCGTACA 58.799 50.000 0.00 0.00 0.00 2.90
5457 14346 0.978151 TAGGGAAAGGCTGCGTACAA 59.022 50.000 0.00 0.00 0.00 2.41
5458 14347 0.328258 AGGGAAAGGCTGCGTACAAT 59.672 50.000 0.00 0.00 0.00 2.71
5459 14348 1.557832 AGGGAAAGGCTGCGTACAATA 59.442 47.619 0.00 0.00 0.00 1.90
5460 14349 2.026636 AGGGAAAGGCTGCGTACAATAA 60.027 45.455 0.00 0.00 0.00 1.40
5461 14350 2.750712 GGGAAAGGCTGCGTACAATAAA 59.249 45.455 0.00 0.00 0.00 1.40
5462 14351 3.427098 GGGAAAGGCTGCGTACAATAAAC 60.427 47.826 0.00 0.00 0.00 2.01
5463 14352 3.427098 GGAAAGGCTGCGTACAATAAACC 60.427 47.826 0.00 0.00 0.00 3.27
5464 14353 1.746470 AGGCTGCGTACAATAAACCC 58.254 50.000 0.00 0.00 0.00 4.11
5465 14354 1.003812 AGGCTGCGTACAATAAACCCA 59.996 47.619 0.00 0.00 0.00 4.51
5466 14355 1.813786 GGCTGCGTACAATAAACCCAA 59.186 47.619 0.00 0.00 0.00 4.12
5467 14356 2.229302 GGCTGCGTACAATAAACCCAAA 59.771 45.455 0.00 0.00 0.00 3.28
5468 14357 3.498082 GCTGCGTACAATAAACCCAAAG 58.502 45.455 0.00 0.00 0.00 2.77
5469 14358 3.057806 GCTGCGTACAATAAACCCAAAGT 60.058 43.478 0.00 0.00 0.00 2.66
5470 14359 4.472286 CTGCGTACAATAAACCCAAAGTG 58.528 43.478 0.00 0.00 0.00 3.16
5471 14360 3.253677 TGCGTACAATAAACCCAAAGTGG 59.746 43.478 0.00 0.00 37.25 4.00
5472 14361 3.253921 GCGTACAATAAACCCAAAGTGGT 59.746 43.478 0.00 0.00 41.55 4.16
5473 14362 4.614306 GCGTACAATAAACCCAAAGTGGTC 60.614 45.833 0.00 0.00 37.76 4.02
5474 14363 4.377635 CGTACAATAAACCCAAAGTGGTCG 60.378 45.833 0.00 0.00 37.76 4.79
5475 14364 2.888414 ACAATAAACCCAAAGTGGTCGG 59.112 45.455 0.00 0.00 37.76 4.79
5476 14365 3.150767 CAATAAACCCAAAGTGGTCGGA 58.849 45.455 0.00 0.00 37.76 4.55
5477 14366 2.259266 TAAACCCAAAGTGGTCGGAC 57.741 50.000 0.00 0.00 37.76 4.79
5478 14367 0.466739 AAACCCAAAGTGGTCGGACC 60.467 55.000 20.36 20.36 37.76 4.46
5479 14368 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
5480 14369 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
5481 14370 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
5482 14371 0.179001 CCAAAGTGGTCGGACCCTTT 60.179 55.000 25.31 25.31 38.45 3.11
5483 14372 1.235724 CAAAGTGGTCGGACCCTTTC 58.764 55.000 26.88 15.90 36.95 2.62
5484 14373 0.109913 AAAGTGGTCGGACCCTTTCC 59.890 55.000 25.31 11.54 35.36 3.13
5485 14374 1.775934 AAGTGGTCGGACCCTTTCCC 61.776 60.000 23.81 5.51 42.27 3.97
5486 14375 3.315949 TGGTCGGACCCTTTCCCG 61.316 66.667 23.81 0.00 42.27 5.14
5487 14376 4.091939 GGTCGGACCCTTTCCCGG 62.092 72.222 16.55 0.00 45.36 5.73
5488 14377 2.999063 GTCGGACCCTTTCCCGGA 60.999 66.667 0.73 0.00 45.36 5.14
5489 14378 2.999063 TCGGACCCTTTCCCGGAC 60.999 66.667 0.73 0.00 45.36 4.79
5490 14379 4.091939 CGGACCCTTTCCCGGACC 62.092 72.222 0.73 0.00 42.27 4.46
5491 14380 3.725032 GGACCCTTTCCCGGACCC 61.725 72.222 0.73 0.00 38.70 4.46
5492 14381 2.609921 GACCCTTTCCCGGACCCT 60.610 66.667 0.73 0.00 0.00 4.34
5493 14382 2.933834 ACCCTTTCCCGGACCCTG 60.934 66.667 0.73 0.00 0.00 4.45
5494 14383 4.426313 CCCTTTCCCGGACCCTGC 62.426 72.222 0.73 0.00 0.00 4.85
5495 14384 4.778143 CCTTTCCCGGACCCTGCG 62.778 72.222 0.73 0.00 0.00 5.18
5517 14406 4.115279 CGGGAGCTACATGCACTG 57.885 61.111 0.00 0.00 45.94 3.66
5518 14407 1.522355 CGGGAGCTACATGCACTGG 60.522 63.158 0.00 0.00 45.94 4.00
5519 14408 1.153086 GGGAGCTACATGCACTGGG 60.153 63.158 0.00 0.00 45.94 4.45
5520 14409 1.604378 GGAGCTACATGCACTGGGT 59.396 57.895 0.00 0.00 45.94 4.51
5521 14410 0.035056 GGAGCTACATGCACTGGGTT 60.035 55.000 0.00 0.00 45.94 4.11
5522 14411 1.089920 GAGCTACATGCACTGGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
5523 14412 0.962356 AGCTACATGCACTGGGTTGC 60.962 55.000 0.00 0.00 45.94 4.17
5524 14413 1.937546 GCTACATGCACTGGGTTGCC 61.938 60.000 0.00 0.00 42.25 4.52
5525 14414 1.304052 TACATGCACTGGGTTGCCC 60.304 57.895 0.00 0.00 45.71 5.36
5526 14415 1.788518 TACATGCACTGGGTTGCCCT 61.789 55.000 5.73 0.00 45.70 5.19
5527 14416 1.909781 CATGCACTGGGTTGCCCTT 60.910 57.895 5.73 0.00 45.70 3.95
5528 14417 1.152269 ATGCACTGGGTTGCCCTTT 60.152 52.632 5.73 0.00 45.70 3.11
5611 14512 8.651589 TCCTATTTTACTCTTCTCTTCTCACA 57.348 34.615 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 96 1.370414 CGCGGTTTTGCTTCTGTGG 60.370 57.895 0.00 0.00 0.00 4.17
96 98 0.814010 AGTCGCGGTTTTGCTTCTGT 60.814 50.000 6.13 0.00 0.00 3.41
97 99 0.110644 GAGTCGCGGTTTTGCTTCTG 60.111 55.000 6.13 0.00 0.00 3.02
98 100 0.249911 AGAGTCGCGGTTTTGCTTCT 60.250 50.000 6.13 0.00 0.00 2.85
111 113 1.275471 TTGTGCTTTCGCGAGAGTCG 61.275 55.000 25.34 4.35 43.69 4.18
229 268 2.631428 CACGGGTGTGTGCTTTCG 59.369 61.111 0.00 0.00 41.34 3.46
292 341 4.380841 GGAAACGGAAGAAAACCAGTTT 57.619 40.909 0.00 0.00 37.10 2.66
315 376 3.695606 GAGTCACGGCCTGCCTCA 61.696 66.667 6.60 0.00 0.00 3.86
520 663 6.316390 CCGGTCTTTCTTAGCTGTTCAATAAT 59.684 38.462 0.00 0.00 0.00 1.28
529 672 2.743636 TCACCGGTCTTTCTTAGCTG 57.256 50.000 2.59 0.00 0.00 4.24
577 720 5.699438 TTCGGCTTTTTAAACGGTTTTTC 57.301 34.783 11.87 0.00 0.00 2.29
624 768 2.979813 CTGGCGTTTCCTTCGAATTTTG 59.020 45.455 0.00 0.00 35.26 2.44
628 772 1.726853 CTCTGGCGTTTCCTTCGAAT 58.273 50.000 0.00 0.00 35.26 3.34
629 773 0.949105 GCTCTGGCGTTTCCTTCGAA 60.949 55.000 0.00 0.00 35.26 3.71
631 775 3.169198 GCTCTGGCGTTTCCTTCG 58.831 61.111 0.00 0.00 35.26 3.79
668 817 2.951745 CCACTTAGCGCGCTCTCG 60.952 66.667 40.23 27.41 39.07 4.04
679 828 1.016627 GCAATGATCAGCGCCACTTA 58.983 50.000 2.29 0.00 0.00 2.24
753 902 0.539051 AGAGCAACTGATCCTTCGGG 59.461 55.000 0.00 0.00 32.05 5.14
754 903 1.480137 AGAGAGCAACTGATCCTTCGG 59.520 52.381 0.00 0.00 0.00 4.30
755 904 2.538437 CAGAGAGCAACTGATCCTTCG 58.462 52.381 0.00 0.00 37.54 3.79
756 905 2.278854 GCAGAGAGCAACTGATCCTTC 58.721 52.381 8.56 0.00 44.79 3.46
757 906 2.399916 GCAGAGAGCAACTGATCCTT 57.600 50.000 8.56 0.00 44.79 3.36
820 969 3.797353 GCGGGGGCCATCTTCTCA 61.797 66.667 4.39 0.00 0.00 3.27
834 983 2.669569 CCAACTGTCCAGGTGCGG 60.670 66.667 6.82 0.00 44.57 5.69
884 1033 1.771073 TTGTGCTTCGGTGTTCAGCG 61.771 55.000 16.52 16.52 36.24 5.18
890 1039 1.733526 GGCTTTTGTGCTTCGGTGT 59.266 52.632 0.00 0.00 0.00 4.16
891 1040 1.007387 GGGCTTTTGTGCTTCGGTG 60.007 57.895 0.00 0.00 0.00 4.94
921 1070 1.219393 CCGAAGCCTGGGAAGAGAC 59.781 63.158 0.00 0.00 0.00 3.36
999 1148 2.524394 GGAGGAGGAGGCGCCATA 60.524 66.667 31.54 0.00 40.02 2.74
1007 1157 0.179012 GTCGTCTAGGGGAGGAGGAG 60.179 65.000 0.00 0.00 39.16 3.69
1008 1158 1.643475 GGTCGTCTAGGGGAGGAGGA 61.643 65.000 0.00 0.00 39.16 3.71
1009 1159 1.152715 GGTCGTCTAGGGGAGGAGG 60.153 68.421 0.00 0.00 39.16 4.30
1081 1231 4.423209 GGAGGAGGGGCCCAGACT 62.423 72.222 27.72 19.37 37.37 3.24
1522 1672 3.394836 AAGGCTCGCAGGGAGGAC 61.395 66.667 15.92 0.45 43.36 3.85
1523 1673 3.393970 CAAGGCTCGCAGGGAGGA 61.394 66.667 15.92 0.00 43.36 3.71
1572 1722 2.134287 GCGAGCCCTATCCACCTGA 61.134 63.158 0.00 0.00 0.00 3.86
1904 2116 5.298276 ACACCAACAAGTAACATGTAACCTG 59.702 40.000 0.00 0.00 0.00 4.00
1911 2123 5.830912 ACATCAACACCAACAAGTAACATG 58.169 37.500 0.00 0.00 0.00 3.21
1954 2170 4.347453 GCCCCGCAACTGCACAAG 62.347 66.667 2.12 0.00 42.21 3.16
2070 2288 1.090052 GTACCCATCTCGCAACTGCC 61.090 60.000 0.00 0.00 37.91 4.85
2105 2328 5.297776 CACTTGATAAGATGGATGGGTTGTC 59.702 44.000 0.00 0.00 0.00 3.18
2198 2422 9.066892 TCATACAACATCCTTAAATCTAATGCC 57.933 33.333 0.00 0.00 0.00 4.40
2290 2561 6.828273 TCCAGTTGCACTTTAGCATATATTGT 59.172 34.615 0.00 0.00 45.19 2.71
2617 3516 8.824781 CGATCATGTAATTCTTTTCTCAGACAT 58.175 33.333 0.00 0.00 0.00 3.06
2646 3545 1.819928 TACAATCACACGCCATGCTT 58.180 45.000 0.00 0.00 0.00 3.91
2778 4267 6.640907 ACAAACTCAGAGTCACAAACAAAAAC 59.359 34.615 2.72 0.00 0.00 2.43
2779 4268 6.744112 ACAAACTCAGAGTCACAAACAAAAA 58.256 32.000 2.72 0.00 0.00 1.94
2827 5127 3.639716 TGCAAGCGTGAAAATGATTCA 57.360 38.095 2.99 0.00 0.00 2.57
2927 5235 0.975040 TTGGCCATGCACATTACCCC 60.975 55.000 6.09 0.00 0.00 4.95
3145 5464 0.320683 TGCAGAACTGTGTGGATCCG 60.321 55.000 7.39 0.00 0.00 4.18
3156 5475 3.057736 GCATTCAGACAACATGCAGAACT 60.058 43.478 0.00 0.00 42.49 3.01
3327 9024 1.064463 CCATGGATATTCCCCATCCCG 60.064 57.143 5.56 0.00 42.18 5.14
3424 9290 2.105006 ATCGTCTGCATGATATGGGC 57.895 50.000 0.00 0.00 0.00 5.36
3828 12699 1.224039 GCTGCCCTCTGAGCAAGAT 59.776 57.895 0.00 0.00 40.35 2.40
3882 12753 3.881688 AGCTAACATCTGGCATTCATCAC 59.118 43.478 0.00 0.00 0.00 3.06
3965 12836 0.535335 ACCGTACTGCTATGGTGTGG 59.465 55.000 0.00 0.00 40.33 4.17
3982 12853 2.108970 AGTCTCCTCCGGTGATTTACC 58.891 52.381 4.76 0.00 46.56 2.85
4018 12889 6.215636 ACACATTAAGTTTCTCTGTATCCCCT 59.784 38.462 0.00 0.00 0.00 4.79
4092 12963 2.902484 GCAGTTATGCGACAAAACTTCG 59.098 45.455 0.00 0.00 43.87 3.79
4138 13009 3.964411 TGAGAGAGGGACGTCTAATTGA 58.036 45.455 16.46 0.00 0.00 2.57
4498 13369 9.409312 TCATTCAGCAATAAATTTACACACTTG 57.591 29.630 0.00 2.39 0.00 3.16
4669 13540 8.106462 TCACAGTTACATAAAATCCCTGATCAA 58.894 33.333 0.00 0.00 0.00 2.57
4716 13587 3.709653 AGTACAGTCACCAAAAGGAGACA 59.290 43.478 13.22 0.00 33.56 3.41
4878 13749 6.054860 ACCTGACAGATGCTACTTTACAAT 57.945 37.500 3.32 0.00 0.00 2.71
4936 13807 4.921547 TCGCAGATGCTACTTTACACTAG 58.078 43.478 2.95 0.00 39.32 2.57
4990 13861 3.940221 GCTAAATTTGCCCATGAATGCAA 59.060 39.130 11.59 11.59 45.12 4.08
5015 13886 1.755179 AACATCAAGAATGGAGCCGG 58.245 50.000 0.00 0.00 39.90 6.13
5028 13899 8.408043 ACATAAGAAATGAACTGGAAACATCA 57.592 30.769 0.00 0.00 41.51 3.07
5050 13921 9.578576 ACAACAATCTATATTTAGCCATGACAT 57.421 29.630 0.00 0.00 0.00 3.06
5175 14046 8.243426 GTGGCTCAGTCTAGATAGAAATATCAG 58.757 40.741 0.00 0.00 33.47 2.90
5203 14074 4.280789 TGGGACAGAGGGAGTATACATT 57.719 45.455 5.50 0.00 0.00 2.71
5209 14080 5.045869 CACTTATTTTGGGACAGAGGGAGTA 60.046 44.000 0.00 0.00 42.39 2.59
5210 14081 3.916989 ACTTATTTTGGGACAGAGGGAGT 59.083 43.478 0.00 0.00 42.39 3.85
5211 14082 4.263506 ACACTTATTTTGGGACAGAGGGAG 60.264 45.833 0.00 0.00 42.39 4.30
5212 14083 3.655777 ACACTTATTTTGGGACAGAGGGA 59.344 43.478 0.00 0.00 42.39 4.20
5213 14084 4.010349 GACACTTATTTTGGGACAGAGGG 58.990 47.826 0.00 0.00 42.39 4.30
5214 14085 4.911390 AGACACTTATTTTGGGACAGAGG 58.089 43.478 0.00 0.00 42.39 3.69
5215 14086 5.551233 TGAGACACTTATTTTGGGACAGAG 58.449 41.667 0.00 0.00 42.39 3.35
5216 14087 5.560722 TGAGACACTTATTTTGGGACAGA 57.439 39.130 0.00 0.00 42.39 3.41
5217 14088 5.048713 GGTTGAGACACTTATTTTGGGACAG 60.049 44.000 0.00 0.00 42.39 3.51
5218 14089 4.825085 GGTTGAGACACTTATTTTGGGACA 59.175 41.667 0.00 0.00 0.00 4.02
5219 14090 5.070685 AGGTTGAGACACTTATTTTGGGAC 58.929 41.667 0.00 0.00 0.00 4.46
5220 14091 5.319043 AGGTTGAGACACTTATTTTGGGA 57.681 39.130 0.00 0.00 0.00 4.37
5221 14092 6.715264 ACTAAGGTTGAGACACTTATTTTGGG 59.285 38.462 0.00 0.00 0.00 4.12
5222 14093 7.745620 ACTAAGGTTGAGACACTTATTTTGG 57.254 36.000 0.00 0.00 0.00 3.28
5223 14094 9.268268 TGTACTAAGGTTGAGACACTTATTTTG 57.732 33.333 0.00 0.00 0.00 2.44
5224 14095 9.841295 TTGTACTAAGGTTGAGACACTTATTTT 57.159 29.630 0.00 0.00 0.00 1.82
5225 14096 9.269453 GTTGTACTAAGGTTGAGACACTTATTT 57.731 33.333 0.00 0.00 0.00 1.40
5226 14097 8.648693 AGTTGTACTAAGGTTGAGACACTTATT 58.351 33.333 0.00 0.00 0.00 1.40
5227 14098 8.191534 AGTTGTACTAAGGTTGAGACACTTAT 57.808 34.615 0.00 0.00 0.00 1.73
5228 14099 7.592885 AGTTGTACTAAGGTTGAGACACTTA 57.407 36.000 0.00 0.00 0.00 2.24
5229 14100 6.481434 AGTTGTACTAAGGTTGAGACACTT 57.519 37.500 0.00 0.00 0.00 3.16
5230 14101 6.481434 AAGTTGTACTAAGGTTGAGACACT 57.519 37.500 0.00 0.00 0.00 3.55
5231 14102 6.537660 ACAAAGTTGTACTAAGGTTGAGACAC 59.462 38.462 0.00 0.00 40.16 3.67
5232 14103 6.646267 ACAAAGTTGTACTAAGGTTGAGACA 58.354 36.000 0.00 0.00 40.16 3.41
5256 14127 8.689061 TGTCTCAACTTTGTACTAACTTCAGTA 58.311 33.333 0.00 0.00 0.00 2.74
5257 14128 7.491696 GTGTCTCAACTTTGTACTAACTTCAGT 59.508 37.037 0.00 0.00 0.00 3.41
5258 14129 7.707035 AGTGTCTCAACTTTGTACTAACTTCAG 59.293 37.037 0.00 0.00 0.00 3.02
5259 14130 7.553334 AGTGTCTCAACTTTGTACTAACTTCA 58.447 34.615 0.00 0.00 0.00 3.02
5260 14131 8.421673 AAGTGTCTCAACTTTGTACTAACTTC 57.578 34.615 0.00 0.00 37.05 3.01
5266 14137 8.621286 CCAAAATAAGTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
5267 14138 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
5268 14139 7.776030 TCCCAAAATAAGTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
5269 14140 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
5270 14141 6.918022 GTCCCAAAATAAGTGTCTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
5271 14142 6.238648 CGTCCCAAAATAAGTGTCTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
5272 14143 5.238650 CGTCCCAAAATAAGTGTCTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
5273 14144 4.755123 CGTCCCAAAATAAGTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
5274 14145 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
5275 14146 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
5276 14147 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
5277 14148 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
5278 14149 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
5279 14150 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
5280 14151 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
5281 14152 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
5282 14153 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
5283 14154 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
5284 14155 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
5285 14156 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
5286 14157 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
5287 14158 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
5288 14159 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
5289 14160 1.961133 AAATACTCCCTCCGTCCCAA 58.039 50.000 0.00 0.00 0.00 4.12
5290 14161 1.961133 AAAATACTCCCTCCGTCCCA 58.039 50.000 0.00 0.00 0.00 4.37
5291 14162 2.767960 TGTAAAATACTCCCTCCGTCCC 59.232 50.000 0.00 0.00 0.00 4.46
5292 14163 4.100498 TCATGTAAAATACTCCCTCCGTCC 59.900 45.833 0.00 0.00 0.00 4.79
5293 14164 5.048507 GTCATGTAAAATACTCCCTCCGTC 58.951 45.833 0.00 0.00 0.00 4.79
5294 14165 4.468510 TGTCATGTAAAATACTCCCTCCGT 59.531 41.667 0.00 0.00 0.00 4.69
5295 14166 5.018539 TGTCATGTAAAATACTCCCTCCG 57.981 43.478 0.00 0.00 0.00 4.63
5296 14167 5.239525 GCATGTCATGTAAAATACTCCCTCC 59.760 44.000 14.26 0.00 0.00 4.30
5297 14168 5.822519 TGCATGTCATGTAAAATACTCCCTC 59.177 40.000 14.26 0.00 0.00 4.30
5298 14169 5.590259 GTGCATGTCATGTAAAATACTCCCT 59.410 40.000 14.26 0.00 0.00 4.20
5299 14170 5.356751 TGTGCATGTCATGTAAAATACTCCC 59.643 40.000 14.26 0.00 0.00 4.30
5300 14171 6.435430 TGTGCATGTCATGTAAAATACTCC 57.565 37.500 14.26 0.00 0.00 3.85
5301 14172 7.903452 CATGTGCATGTCATGTAAAATACTC 57.097 36.000 14.26 0.00 38.17 2.59
5426 14315 6.205658 GCAGCCTTTCCCTATATTTCTGTAAG 59.794 42.308 0.00 0.00 0.00 2.34
5429 14318 4.464947 GCAGCCTTTCCCTATATTTCTGT 58.535 43.478 0.00 0.00 0.00 3.41
5432 14321 3.477530 ACGCAGCCTTTCCCTATATTTC 58.522 45.455 0.00 0.00 0.00 2.17
5433 14322 3.577805 ACGCAGCCTTTCCCTATATTT 57.422 42.857 0.00 0.00 0.00 1.40
5435 14324 2.969950 TGTACGCAGCCTTTCCCTATAT 59.030 45.455 0.00 0.00 0.00 0.86
5437 14326 1.200519 TGTACGCAGCCTTTCCCTAT 58.799 50.000 0.00 0.00 0.00 2.57
5438 14327 0.978151 TTGTACGCAGCCTTTCCCTA 59.022 50.000 0.00 0.00 0.00 3.53
5441 14330 3.427098 GGTTTATTGTACGCAGCCTTTCC 60.427 47.826 0.00 0.00 0.00 3.13
5442 14331 3.427098 GGGTTTATTGTACGCAGCCTTTC 60.427 47.826 0.00 0.00 0.00 2.62
5443 14332 2.490509 GGGTTTATTGTACGCAGCCTTT 59.509 45.455 0.00 0.00 0.00 3.11
5444 14333 2.089201 GGGTTTATTGTACGCAGCCTT 58.911 47.619 0.00 0.00 0.00 4.35
5445 14334 1.003812 TGGGTTTATTGTACGCAGCCT 59.996 47.619 0.00 0.00 34.09 4.58
5446 14335 1.455248 TGGGTTTATTGTACGCAGCC 58.545 50.000 0.00 0.00 34.09 4.85
5447 14336 3.057806 ACTTTGGGTTTATTGTACGCAGC 60.058 43.478 0.00 0.00 39.24 5.25
5448 14337 4.472286 CACTTTGGGTTTATTGTACGCAG 58.528 43.478 0.00 0.00 39.24 5.18
5449 14338 3.253677 CCACTTTGGGTTTATTGTACGCA 59.746 43.478 0.00 0.00 36.77 5.24
5450 14339 3.253921 ACCACTTTGGGTTTATTGTACGC 59.746 43.478 0.00 0.00 43.37 4.42
5451 14340 4.377635 CGACCACTTTGGGTTTATTGTACG 60.378 45.833 0.00 0.00 43.37 3.67
5452 14341 4.083164 CCGACCACTTTGGGTTTATTGTAC 60.083 45.833 0.00 0.00 43.37 2.90
5453 14342 4.073549 CCGACCACTTTGGGTTTATTGTA 58.926 43.478 0.00 0.00 43.37 2.41
5454 14343 2.888414 CCGACCACTTTGGGTTTATTGT 59.112 45.455 0.00 0.00 43.37 2.71
5455 14344 3.057806 GTCCGACCACTTTGGGTTTATTG 60.058 47.826 0.00 0.00 43.37 1.90
5456 14345 3.151554 GTCCGACCACTTTGGGTTTATT 58.848 45.455 0.00 0.00 43.37 1.40
5457 14346 2.553685 GGTCCGACCACTTTGGGTTTAT 60.554 50.000 13.05 0.00 43.37 1.40
5458 14347 1.202794 GGTCCGACCACTTTGGGTTTA 60.203 52.381 13.05 0.00 43.37 2.01
5459 14348 0.466739 GGTCCGACCACTTTGGGTTT 60.467 55.000 13.05 0.00 43.37 3.27
5460 14349 1.149854 GGTCCGACCACTTTGGGTT 59.850 57.895 13.05 0.00 43.37 4.11
5461 14350 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
5462 14351 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
5463 14352 0.179001 AAAGGGTCCGACCACTTTGG 60.179 55.000 22.93 0.00 41.02 3.28
5464 14353 1.235724 GAAAGGGTCCGACCACTTTG 58.764 55.000 26.16 0.00 41.02 2.77
5465 14354 0.109913 GGAAAGGGTCCGACCACTTT 59.890 55.000 23.42 23.42 41.02 2.66
5466 14355 1.759236 GGAAAGGGTCCGACCACTT 59.241 57.895 19.43 15.68 41.02 3.16
5467 14356 3.479979 GGAAAGGGTCCGACCACT 58.520 61.111 19.43 10.80 41.02 4.00
5475 14364 2.609921 AGGGTCCGGGAAAGGGTC 60.610 66.667 0.00 0.00 0.00 4.46
5476 14365 2.933834 CAGGGTCCGGGAAAGGGT 60.934 66.667 0.00 0.00 0.00 4.34
5477 14366 4.426313 GCAGGGTCCGGGAAAGGG 62.426 72.222 0.00 0.00 0.00 3.95
5478 14367 4.778143 CGCAGGGTCCGGGAAAGG 62.778 72.222 0.00 0.00 0.00 3.11
5491 14380 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
5494 14383 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
5495 14384 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
5496 14385 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
5497 14386 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
5499 14388 2.176273 CAGTGCATGTAGCTCCCGC 61.176 63.158 0.00 0.00 45.94 6.13
5500 14389 1.522355 CCAGTGCATGTAGCTCCCG 60.522 63.158 0.00 0.00 45.94 5.14
5501 14390 1.153086 CCCAGTGCATGTAGCTCCC 60.153 63.158 0.00 0.00 45.94 4.30
5502 14391 0.035056 AACCCAGTGCATGTAGCTCC 60.035 55.000 0.00 0.00 45.94 4.70
5503 14392 1.089920 CAACCCAGTGCATGTAGCTC 58.910 55.000 0.00 0.00 45.94 4.09
5504 14393 0.962356 GCAACCCAGTGCATGTAGCT 60.962 55.000 0.00 0.00 44.29 3.32
5505 14394 1.508088 GCAACCCAGTGCATGTAGC 59.492 57.895 0.00 0.00 44.29 3.58
5506 14395 2.183409 GGCAACCCAGTGCATGTAG 58.817 57.895 0.00 0.00 46.81 2.74
5507 14396 4.413928 GGCAACCCAGTGCATGTA 57.586 55.556 0.00 0.00 46.81 2.29
5527 14416 1.774110 TCACCCAAGCAGCTCAAAAA 58.226 45.000 0.00 0.00 0.00 1.94
5528 14417 1.888512 GATCACCCAAGCAGCTCAAAA 59.111 47.619 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.