Multiple sequence alignment - TraesCS2A01G403400

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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 TraesCS2A01G403400 chr2A 100.000 6084 0 0 1 6084 658905350 658911433 0.000000e+00 11236.0
1 TraesCS2A01G403400 chr2A 95.067 669 32 1 1 668 753032154 753032822 0.000000e+00 1051.0
2 TraesCS2A01G403400 chr2A 94.760 668 34 1 1 667 688432616 688431949 0.000000e+00 1038.0
3 TraesCS2A01G403400 chr2A 76.481 591 127 11 4399 4983 20561283 20561867 1.650000e-80 311.0
4 TraesCS2A01G403400 chr2A 75.974 154 34 2 2029 2182 759149528 759149678 6.540000e-10 76.8
5 TraesCS2A01G403400 chr2A 89.831 59 3 1 5692 5750 765790515 765790460 8.460000e-09 73.1
6 TraesCS2A01G403400 chr2A 90.566 53 5 0 6032 6084 7412356 7412304 3.040000e-08 71.3
7 TraesCS2A01G403400 chr2A 96.774 31 1 0 4061 4091 523873101 523873131 1.100000e-02 52.8
8 TraesCS2A01G403400 chr2B 92.150 2586 164 22 2762 5332 606614102 606616663 0.000000e+00 3615.0
9 TraesCS2A01G403400 chr2B 93.826 2057 75 14 703 2713 606612048 606614098 0.000000e+00 3048.0
10 TraesCS2A01G403400 chr2B 92.169 332 23 3 5723 6052 606616934 606617264 3.320000e-127 466.0
11 TraesCS2A01G403400 chr2B 93.286 283 14 5 5344 5623 606616647 606616927 4.390000e-111 412.0
12 TraesCS2A01G403400 chr2B 82.812 128 22 0 2142 2269 780015944 780015817 1.390000e-21 115.0
13 TraesCS2A01G403400 chr2B 75.000 160 37 1 2028 2187 655598242 655598398 3.040000e-08 71.3
14 TraesCS2A01G403400 chr2D 92.471 2125 133 17 3224 5332 514947942 514950055 0.000000e+00 3013.0
15 TraesCS2A01G403400 chr2D 94.764 1776 56 5 947 2704 514945734 514947490 0.000000e+00 2730.0
16 TraesCS2A01G403400 chr2D 93.834 746 37 9 5344 6084 514950039 514950780 0.000000e+00 1114.0
17 TraesCS2A01G403400 chr2D 91.781 438 25 6 2762 3197 514947515 514947943 3.140000e-167 599.0
18 TraesCS2A01G403400 chr2D 94.760 229 11 1 699 927 514945458 514945685 7.500000e-94 355.0
19 TraesCS2A01G403400 chr2D 74.532 695 158 16 4399 5082 19643999 19643313 9.980000e-73 285.0
20 TraesCS2A01G403400 chr2D 83.333 132 22 0 2127 2258 651070923 651070792 8.280000e-24 122.0
21 TraesCS2A01G403400 chr2D 91.525 59 4 1 2704 2762 23725398 23725341 5.060000e-11 80.5
22 TraesCS2A01G403400 chr2D 94.000 50 3 0 6032 6081 8375480 8375431 6.540000e-10 76.8
23 TraesCS2A01G403400 chr7A 95.509 668 28 2 1 667 734548243 734548909 0.000000e+00 1066.0
24 TraesCS2A01G403400 chr7A 95.045 666 32 1 1 665 63321896 63322561 0.000000e+00 1046.0
25 TraesCS2A01G403400 chr7A 94.745 666 34 1 1 665 668039014 668039679 0.000000e+00 1035.0
26 TraesCS2A01G403400 chr7A 94.595 666 35 1 1 665 686010188 686010853 0.000000e+00 1029.0
27 TraesCS2A01G403400 chr7A 79.365 189 22 3 5583 5757 500133190 500133375 3.850000e-22 117.0
28 TraesCS2A01G403400 chr3A 95.359 668 28 3 1 667 477984279 477984944 0.000000e+00 1059.0
29 TraesCS2A01G403400 chr3A 79.452 146 29 1 2126 2271 17332556 17332700 1.080000e-17 102.0
30 TraesCS2A01G403400 chr3A 86.207 87 12 0 2603 2689 17378257 17378171 1.810000e-15 95.3
31 TraesCS2A01G403400 chr3A 78.082 146 31 1 2126 2271 16233526 16233382 2.340000e-14 91.6
32 TraesCS2A01G403400 chr4A 95.045 666 32 1 1 665 603415172 603414507 0.000000e+00 1046.0
33 TraesCS2A01G403400 chr4A 90.196 51 5 0 6033 6083 638216716 638216766 3.940000e-07 67.6
34 TraesCS2A01G403400 chr6A 94.682 677 28 7 1 671 21310948 21310274 0.000000e+00 1044.0
35 TraesCS2A01G403400 chrUn 73.730 689 168 11 4399 5079 272323786 272324469 2.180000e-64 257.0
36 TraesCS2A01G403400 chrUn 74.787 587 137 10 4399 4980 16721838 16722418 2.810000e-63 254.0
37 TraesCS2A01G403400 chr7D 79.720 286 44 9 5416 5689 1751473 1751190 1.730000e-45 195.0
38 TraesCS2A01G403400 chr7D 88.776 98 10 1 3148 3245 167548504 167548408 1.070000e-22 119.0
39 TraesCS2A01G403400 chr7D 89.247 93 9 1 3141 3232 54564563 54564655 1.390000e-21 115.0
40 TraesCS2A01G403400 chr7D 94.915 59 2 1 2704 2762 368587322 368587379 2.340000e-14 91.6
41 TraesCS2A01G403400 chr7D 100.000 42 0 0 6032 6073 274858010 274858051 1.820000e-10 78.7
42 TraesCS2A01G403400 chr1A 77.465 284 38 9 5489 5749 372531759 372532039 4.910000e-31 147.0
43 TraesCS2A01G403400 chr1A 88.776 98 11 0 3135 3232 320485576 320485673 2.980000e-23 121.0
44 TraesCS2A01G403400 chr1A 89.362 47 4 1 5357 5402 30319394 30319440 2.370000e-04 58.4
45 TraesCS2A01G403400 chr1D 76.056 284 41 9 5489 5749 298636934 298637213 8.280000e-24 122.0
46 TraesCS2A01G403400 chr3B 91.765 85 7 0 3148 3232 284678843 284678927 1.070000e-22 119.0
47 TraesCS2A01G403400 chr3B 86.364 88 12 0 2602 2689 12841463 12841376 5.020000e-16 97.1
48 TraesCS2A01G403400 chr3B 74.561 228 55 1 2029 2256 13413888 13414112 5.020000e-16 97.1
49 TraesCS2A01G403400 chr3B 85.227 88 13 0 2602 2689 13247725 13247812 2.340000e-14 91.6
50 TraesCS2A01G403400 chr3B 96.226 53 2 0 6032 6084 739228820 739228872 3.020000e-13 87.9
51 TraesCS2A01G403400 chr1B 90.909 88 7 1 3148 3234 476018791 476018878 3.850000e-22 117.0
52 TraesCS2A01G403400 chr1B 91.525 59 4 1 2704 2762 302244508 302244565 5.060000e-11 80.5
53 TraesCS2A01G403400 chr1B 90.000 40 4 0 5299 5338 399329025 399328986 1.100000e-02 52.8
54 TraesCS2A01G403400 chr4D 90.000 90 7 2 3148 3236 19442563 19442651 1.390000e-21 115.0
55 TraesCS2A01G403400 chr3D 89.130 92 10 0 3141 3232 302930478 302930387 1.390000e-21 115.0
56 TraesCS2A01G403400 chr3D 74.494 247 58 3 2028 2273 5375526 5375284 1.080000e-17 102.0
57 TraesCS2A01G403400 chr3D 74.486 243 57 3 2016 2257 5329653 5329891 3.880000e-17 100.0
58 TraesCS2A01G403400 chr3D 86.364 88 12 0 2602 2689 41595111 41595024 5.020000e-16 97.1
59 TraesCS2A01G403400 chr3D 86.207 87 12 0 2603 2689 5330270 5330356 1.810000e-15 95.3
60 TraesCS2A01G403400 chr3D 86.207 87 12 0 2603 2689 5374921 5374835 1.810000e-15 95.3
61 TraesCS2A01G403400 chr3D 85.057 87 13 0 2603 2689 41425392 41425306 8.400000e-14 89.8
62 TraesCS2A01G403400 chr5B 82.069 145 8 13 5556 5685 232589849 232589708 2.320000e-19 108.0
63 TraesCS2A01G403400 chr7B 94.340 53 3 0 6032 6084 261999995 261999943 1.410000e-11 82.4
64 TraesCS2A01G403400 chr7B 90.566 53 5 0 6032 6084 261999938 261999990 3.040000e-08 71.3
65 TraesCS2A01G403400 chr5D 90.385 52 5 0 6033 6084 533641695 533641644 1.090000e-07 69.4
66 TraesCS2A01G403400 chr6B 100.000 28 0 0 5300 5327 205013721 205013748 1.100000e-02 52.8
67 TraesCS2A01G403400 chr6B 96.774 31 1 0 4061 4091 653010257 653010287 1.100000e-02 52.8
68 TraesCS2A01G403400 chr5A 96.774 31 1 0 4061 4091 668889898 668889928 1.100000e-02 52.8


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 TraesCS2A01G403400 chr2A 658905350 658911433 6083 False 11236.00 11236 100.00000 1 6084 1 chr2A.!!$F3 6083
1 TraesCS2A01G403400 chr2A 753032154 753032822 668 False 1051.00 1051 95.06700 1 668 1 chr2A.!!$F4 667
2 TraesCS2A01G403400 chr2A 688431949 688432616 667 True 1038.00 1038 94.76000 1 667 1 chr2A.!!$R2 666
3 TraesCS2A01G403400 chr2A 20561283 20561867 584 False 311.00 311 76.48100 4399 4983 1 chr2A.!!$F1 584
4 TraesCS2A01G403400 chr2B 606612048 606617264 5216 False 1885.25 3615 92.85775 703 6052 4 chr2B.!!$F2 5349
5 TraesCS2A01G403400 chr2D 514945458 514950780 5322 False 1562.20 3013 93.52200 699 6084 5 chr2D.!!$F1 5385
6 TraesCS2A01G403400 chr2D 19643313 19643999 686 True 285.00 285 74.53200 4399 5082 1 chr2D.!!$R2 683
7 TraesCS2A01G403400 chr7A 734548243 734548909 666 False 1066.00 1066 95.50900 1 667 1 chr7A.!!$F5 666
8 TraesCS2A01G403400 chr7A 63321896 63322561 665 False 1046.00 1046 95.04500 1 665 1 chr7A.!!$F1 664
9 TraesCS2A01G403400 chr7A 668039014 668039679 665 False 1035.00 1035 94.74500 1 665 1 chr7A.!!$F3 664
10 TraesCS2A01G403400 chr7A 686010188 686010853 665 False 1029.00 1029 94.59500 1 665 1 chr7A.!!$F4 664
11 TraesCS2A01G403400 chr3A 477984279 477984944 665 False 1059.00 1059 95.35900 1 667 1 chr3A.!!$F2 666
12 TraesCS2A01G403400 chr4A 603414507 603415172 665 True 1046.00 1046 95.04500 1 665 1 chr4A.!!$R1 664
13 TraesCS2A01G403400 chr6A 21310274 21310948 674 True 1044.00 1044 94.68200 1 671 1 chr6A.!!$R1 670
14 TraesCS2A01G403400 chrUn 272323786 272324469 683 False 257.00 257 73.73000 4399 5079 1 chrUn.!!$F2 680
15 TraesCS2A01G403400 chrUn 16721838 16722418 580 False 254.00 254 74.78700 4399 4980 1 chrUn.!!$F1 581

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
940 946 0.092519 GCTTTTCGCGAACCGTCTAC 59.907 55.0 23.33 3.27 38.35 2.59 F
2686 2749 0.039256 TGGTAGCACGTCAACGGTAC 60.039 55.0 7.53 4.82 44.95 3.34 F
2756 2831 0.179134 GCTGTTCGTAGACGGAGCAT 60.179 55.0 13.32 0.00 40.29 3.79 F
3511 3593 0.322546 GATTGGTCTTGGTCGCCCTT 60.323 55.0 0.00 0.00 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2737 2812 0.179134 ATGCTCCGTCTACGAACAGC 60.179 55.0 3.65 8.75 43.02 4.40 R
3704 3786 0.179006 GGTGATCCAGAGGGCAATCC 60.179 60.0 0.00 0.00 0.00 3.01 R
4483 4581 0.243907 CGAAGAAGAAGAGCCCGTCA 59.756 55.0 0.00 0.00 0.00 4.35 R
5197 5298 0.179018 GCCACCATGTCTCCCATACC 60.179 60.0 0.00 0.00 30.71 2.73 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
103 104 0.809385 GTCGACCGATGAGGAAGACA 59.191 55.000 3.51 0.00 45.00 3.41
107 108 0.898789 ACCGATGAGGAAGACACCGT 60.899 55.000 0.00 0.00 45.00 4.83
358 360 3.647771 GAGCGGGAGGGGTTTGGT 61.648 66.667 0.00 0.00 0.00 3.67
591 593 1.654954 GCCTTCTGAGGACGCGACTA 61.655 60.000 15.93 0.00 46.74 2.59
625 630 4.474846 CCGGCGTGGCAAAATCGG 62.475 66.667 6.01 0.00 0.00 4.18
633 638 1.981853 GGCAAAATCGGCTGGGGAA 60.982 57.895 0.00 0.00 0.00 3.97
644 650 2.451493 TGGGGAAGCCCTGTTGGA 60.451 61.111 2.01 0.00 44.66 3.53
689 695 4.210304 GCAGCGAGCGCCGTTTAG 62.210 66.667 17.38 4.64 43.17 1.85
690 696 2.506217 CAGCGAGCGCCGTTTAGA 60.506 61.111 17.38 0.00 43.17 2.10
691 697 2.092291 CAGCGAGCGCCGTTTAGAA 61.092 57.895 17.38 0.00 43.17 2.10
692 698 1.153628 AGCGAGCGCCGTTTAGAAT 60.154 52.632 17.38 0.00 43.17 2.40
693 699 0.739813 AGCGAGCGCCGTTTAGAATT 60.740 50.000 17.38 0.00 43.17 2.17
694 700 0.096454 GCGAGCGCCGTTTAGAATTT 59.904 50.000 17.38 0.00 41.15 1.82
695 701 1.797964 CGAGCGCCGTTTAGAATTTG 58.202 50.000 2.29 0.00 0.00 2.32
696 702 1.535088 GAGCGCCGTTTAGAATTTGC 58.465 50.000 2.29 0.00 0.00 3.68
697 703 0.170339 AGCGCCGTTTAGAATTTGCC 59.830 50.000 2.29 0.00 0.00 4.52
698 704 1.131618 GCGCCGTTTAGAATTTGCCG 61.132 55.000 0.00 0.00 0.00 5.69
699 705 0.522495 CGCCGTTTAGAATTTGCCGG 60.522 55.000 0.00 0.00 38.45 6.13
700 706 0.524414 GCCGTTTAGAATTTGCCGGT 59.476 50.000 1.90 0.00 37.76 5.28
701 707 1.731098 GCCGTTTAGAATTTGCCGGTG 60.731 52.381 1.90 0.00 37.76 4.94
704 710 2.224549 CGTTTAGAATTTGCCGGTGTGA 59.775 45.455 1.90 0.00 0.00 3.58
716 722 3.357079 GTGTGAGGCGCCAACCAG 61.357 66.667 31.54 0.00 0.00 4.00
795 801 3.244561 TGGAGACAACCTCAACTTGGATC 60.245 47.826 0.00 0.00 43.76 3.36
825 831 5.393866 TGGAGGCTTACTTTTCAAGGAAAT 58.606 37.500 0.00 0.00 31.34 2.17
893 899 3.901844 TCCTTACCCGATATAAAGCAGCT 59.098 43.478 0.00 0.00 0.00 4.24
927 933 4.464112 GGTCGAGTTGTATTGTGCTTTTC 58.536 43.478 0.00 0.00 0.00 2.29
928 934 4.141680 GTCGAGTTGTATTGTGCTTTTCG 58.858 43.478 0.00 0.00 0.00 3.46
931 937 2.546368 AGTTGTATTGTGCTTTTCGCGA 59.454 40.909 3.71 3.71 43.27 5.87
932 938 3.002862 AGTTGTATTGTGCTTTTCGCGAA 59.997 39.130 19.38 19.38 43.27 4.70
933 939 2.911120 TGTATTGTGCTTTTCGCGAAC 58.089 42.857 23.33 11.30 43.27 3.95
934 940 2.239201 GTATTGTGCTTTTCGCGAACC 58.761 47.619 23.33 13.34 43.27 3.62
936 942 1.707239 TTGTGCTTTTCGCGAACCGT 61.707 50.000 23.33 0.00 43.27 4.83
939 945 0.318869 TGCTTTTCGCGAACCGTCTA 60.319 50.000 23.33 2.12 43.27 2.59
940 946 0.092519 GCTTTTCGCGAACCGTCTAC 59.907 55.000 23.33 3.27 38.35 2.59
942 948 1.385743 CTTTTCGCGAACCGTCTACAG 59.614 52.381 23.33 0.00 38.35 2.74
945 951 2.152699 CGCGAACCGTCTACAGCAG 61.153 63.158 0.00 0.00 0.00 4.24
975 1010 3.552294 GCAGATCTAGTCGGTAACTTTGC 59.448 47.826 0.00 0.00 39.55 3.68
1184 1223 0.690762 GTGGTGACCAGGAAAGCCTA 59.309 55.000 3.58 0.00 44.80 3.93
1216 1255 1.467734 TCGTCGACAGAAGCTACTTCC 59.532 52.381 17.16 0.00 40.98 3.46
1266 1305 2.125673 CTCGGCGGTCAAATCGGT 60.126 61.111 7.21 0.00 0.00 4.69
1753 1792 0.321122 CGTTCAAGAGCTTGCTCCCT 60.321 55.000 17.78 4.24 40.24 4.20
1766 1805 1.531739 GCTCCCTCGGCCTATCAGAG 61.532 65.000 0.00 0.00 36.86 3.35
1803 1842 0.667487 TCTTTTGCTCCGCGTCTGAG 60.667 55.000 4.92 5.87 0.00 3.35
1847 1886 2.727777 GTGCTTCCTTCGAAAAACCAC 58.272 47.619 0.00 1.43 0.00 4.16
1973 2030 2.223829 ACAGTGACACGACAGAAGAAGG 60.224 50.000 0.00 0.00 0.00 3.46
1986 2043 0.247736 AAGAAGGTGAGCGCGAATCT 59.752 50.000 12.10 0.00 0.00 2.40
1996 2053 1.712081 CGCGAATCTCCAAGCACAG 59.288 57.895 0.00 0.00 0.00 3.66
2006 2063 1.293498 CAAGCACAGCTACGGTCCT 59.707 57.895 0.00 0.00 38.25 3.85
2007 2064 1.016130 CAAGCACAGCTACGGTCCTG 61.016 60.000 7.06 7.06 38.25 3.86
2136 2193 3.506096 CAGCTGCCCATGAGCGTG 61.506 66.667 0.00 0.00 41.61 5.34
2260 2317 0.696501 GTTCCTCCCAGGGCAGTTTA 59.303 55.000 0.00 0.00 35.59 2.01
2529 2592 4.504461 GCTTACTATGGAGATGTCGTTGTG 59.496 45.833 0.00 0.00 0.00 3.33
2544 2607 3.264897 GTGCGCCTGCTACCATCG 61.265 66.667 4.18 0.00 43.34 3.84
2616 2679 4.398319 AGAAACACGATCTTTCATGGGTT 58.602 39.130 8.21 0.00 31.12 4.11
2628 2691 4.885270 TGGGTTGGGCGTGTGGTG 62.885 66.667 0.00 0.00 0.00 4.17
2683 2746 0.389296 TGATGGTAGCACGTCAACGG 60.389 55.000 7.53 0.00 44.95 4.44
2684 2747 0.389426 GATGGTAGCACGTCAACGGT 60.389 55.000 7.53 0.00 44.95 4.83
2685 2748 0.889994 ATGGTAGCACGTCAACGGTA 59.110 50.000 7.53 0.00 44.95 4.02
2686 2749 0.039256 TGGTAGCACGTCAACGGTAC 60.039 55.000 7.53 4.82 44.95 3.34
2715 2790 7.584122 TGCTATCTTCTGTTACTACTTAGGG 57.416 40.000 0.00 0.00 0.00 3.53
2716 2791 7.351952 TGCTATCTTCTGTTACTACTTAGGGA 58.648 38.462 0.00 0.00 0.00 4.20
2717 2792 7.837689 TGCTATCTTCTGTTACTACTTAGGGAA 59.162 37.037 0.00 0.00 0.00 3.97
2718 2793 8.693625 GCTATCTTCTGTTACTACTTAGGGAAA 58.306 37.037 0.00 0.00 0.00 3.13
2723 2798 9.298774 CTTCTGTTACTACTTAGGGAAATTACG 57.701 37.037 0.00 0.00 0.00 3.18
2724 2799 8.353423 TCTGTTACTACTTAGGGAAATTACGT 57.647 34.615 0.00 0.00 0.00 3.57
2725 2800 8.806146 TCTGTTACTACTTAGGGAAATTACGTT 58.194 33.333 0.00 0.00 0.00 3.99
2727 2802 9.855021 TGTTACTACTTAGGGAAATTACGTTAC 57.145 33.333 0.00 0.00 0.00 2.50
2733 2808 8.466086 ACTTAGGGAAATTACGTTACTTTACG 57.534 34.615 0.00 0.00 46.52 3.18
2743 2818 4.812862 CGTTACTTTACGTAGGCTGTTC 57.187 45.455 0.00 0.00 36.80 3.18
2744 2819 3.299020 CGTTACTTTACGTAGGCTGTTCG 59.701 47.826 0.00 1.93 36.80 3.95
2745 2820 4.229876 GTTACTTTACGTAGGCTGTTCGT 58.770 43.478 15.59 15.59 40.78 3.85
2746 2821 5.390613 GTTACTTTACGTAGGCTGTTCGTA 58.609 41.667 14.03 14.03 38.69 3.43
2747 2822 4.088823 ACTTTACGTAGGCTGTTCGTAG 57.911 45.455 16.17 12.36 40.26 3.51
2748 2823 3.753272 ACTTTACGTAGGCTGTTCGTAGA 59.247 43.478 16.17 12.97 40.26 2.59
2749 2824 3.747099 TTACGTAGGCTGTTCGTAGAC 57.253 47.619 16.17 0.00 40.26 2.59
2750 2825 0.445436 ACGTAGGCTGTTCGTAGACG 59.555 55.000 11.20 6.54 34.32 4.18
2751 2826 0.247974 CGTAGGCTGTTCGTAGACGG 60.248 60.000 0.00 0.00 40.29 4.79
2752 2827 1.089920 GTAGGCTGTTCGTAGACGGA 58.910 55.000 0.00 0.00 40.29 4.69
2753 2828 1.063764 GTAGGCTGTTCGTAGACGGAG 59.936 57.143 0.00 0.00 40.29 4.63
2754 2829 1.516603 GGCTGTTCGTAGACGGAGC 60.517 63.158 1.67 7.50 40.29 4.70
2755 2830 1.211969 GCTGTTCGTAGACGGAGCA 59.788 57.895 13.32 5.74 40.29 4.26
2756 2831 0.179134 GCTGTTCGTAGACGGAGCAT 60.179 55.000 13.32 0.00 40.29 3.79
2757 2832 1.736032 GCTGTTCGTAGACGGAGCATT 60.736 52.381 13.32 0.00 40.29 3.56
2758 2833 2.479049 GCTGTTCGTAGACGGAGCATTA 60.479 50.000 13.32 0.00 40.29 1.90
2759 2834 3.795826 GCTGTTCGTAGACGGAGCATTAT 60.796 47.826 13.32 0.00 40.29 1.28
2760 2835 3.961182 TGTTCGTAGACGGAGCATTATC 58.039 45.455 1.67 0.00 40.29 1.75
2798 2873 2.001872 TGTACGTGCATGCATTCTCTG 58.998 47.619 25.64 11.91 0.00 3.35
2877 2952 4.051237 TCTGTGTCATCAACGAACAGAAG 58.949 43.478 1.52 0.00 30.98 2.85
2883 2958 4.857588 GTCATCAACGAACAGAAGTACGAT 59.142 41.667 0.00 0.00 0.00 3.73
2897 2972 2.359531 AGTACGATGAACTAGAGGCTGC 59.640 50.000 0.00 0.00 0.00 5.25
2935 3010 0.742990 GGACGACGGCATTGATCCAA 60.743 55.000 1.63 0.00 0.00 3.53
2947 3022 0.768622 TGATCCAACCCAAGAACCGT 59.231 50.000 0.00 0.00 0.00 4.83
2981 3060 5.163237 ACACGGTATCTACCCAGCATTAATT 60.163 40.000 0.82 0.00 43.51 1.40
3006 3087 4.150897 TCACTGTTAGCAAACAAGGACT 57.849 40.909 0.00 0.00 44.79 3.85
3007 3088 5.284861 TCACTGTTAGCAAACAAGGACTA 57.715 39.130 0.00 0.00 44.79 2.59
3010 3091 4.202182 ACTGTTAGCAAACAAGGACTACGA 60.202 41.667 0.00 0.00 44.79 3.43
3101 3182 2.755650 TGAACTCCTTGCTCTCGTTTC 58.244 47.619 0.00 0.00 0.00 2.78
3115 3196 7.429633 TGCTCTCGTTTCCATTTAATTGAAAA 58.570 30.769 5.89 0.00 30.47 2.29
3170 3252 8.677870 AATACTCCCTCTGCAGAGAAATATAT 57.322 34.615 39.34 25.61 44.74 0.86
3246 3328 6.490721 CCGAGGGAGTAGTTAACTGAATATCT 59.509 42.308 18.56 8.35 39.07 1.98
3329 3411 3.356529 AAAGTGATGGGCCTCTTACTG 57.643 47.619 4.53 0.00 0.00 2.74
3356 3438 2.880963 ATGTTCCACAAAACCCAACG 57.119 45.000 0.00 0.00 0.00 4.10
3436 3518 1.374758 GCCTGGGTTCTGTCGTCTG 60.375 63.158 0.00 0.00 0.00 3.51
3453 3535 1.905894 TCTGGTTTGTGATCGGATGGA 59.094 47.619 0.00 0.00 0.00 3.41
3502 3584 2.271800 GTGTCTAGCGGATTGGTCTTG 58.728 52.381 0.00 0.00 0.00 3.02
3504 3586 1.207329 GTCTAGCGGATTGGTCTTGGT 59.793 52.381 0.00 0.00 0.00 3.67
3507 3589 2.750888 GCGGATTGGTCTTGGTCGC 61.751 63.158 0.00 0.00 35.12 5.19
3509 3591 1.749258 GGATTGGTCTTGGTCGCCC 60.749 63.158 0.00 0.00 0.00 6.13
3511 3593 0.322546 GATTGGTCTTGGTCGCCCTT 60.323 55.000 0.00 0.00 0.00 3.95
3529 3611 3.325135 CCCTTATCAGGCTCCGAGTTATT 59.675 47.826 0.00 0.00 39.20 1.40
3554 3636 2.169789 CGCAGAGAATGTGGGAGCG 61.170 63.158 0.00 0.00 45.53 5.03
3557 3639 1.992277 AGAGAATGTGGGAGCGCCT 60.992 57.895 2.29 0.00 0.00 5.52
3652 3734 1.613630 GTGAGGGGAAGGAGGCTGA 60.614 63.158 0.00 0.00 0.00 4.26
3698 3780 4.931002 CCATTCCGTTTTCTGCATTTTGAT 59.069 37.500 0.00 0.00 0.00 2.57
3704 3786 4.320690 CGTTTTCTGCATTTTGATGTACGG 59.679 41.667 0.00 0.00 0.00 4.02
3708 3790 4.269183 TCTGCATTTTGATGTACGGGATT 58.731 39.130 0.00 0.00 0.00 3.01
3750 3832 2.918802 ACACCGCGGACCAGGTAA 60.919 61.111 35.90 0.00 39.00 2.85
3781 3866 5.289193 CCAAATGTTAATTGCGTTCCTGATG 59.711 40.000 0.00 0.00 0.00 3.07
3847 3932 9.330063 CTATAACTGAACTGCATATTCTTTCCA 57.670 33.333 11.07 0.00 0.00 3.53
3851 3936 5.508567 TGAACTGCATATTCTTTCCATGGA 58.491 37.500 11.44 11.44 0.00 3.41
3868 3953 2.853705 TGGAAAAAGAACCTACACCCG 58.146 47.619 0.00 0.00 0.00 5.28
4027 4115 4.917906 ACAGAGGGAGTAGCTGATTTTT 57.082 40.909 0.00 0.00 33.94 1.94
4064 4152 9.777297 ATTGTTTTAACTAAAATCATGGCAACT 57.223 25.926 0.00 0.00 37.48 3.16
4095 4183 3.139077 CGGAGGGAGTATTATTTGTGGC 58.861 50.000 0.00 0.00 0.00 5.01
4345 4440 5.254115 GGAGCTACCTTTTATGGTTTCACT 58.746 41.667 0.00 0.00 41.22 3.41
4376 4471 2.351835 CGAGCATACCCTATGAACCGAG 60.352 54.545 0.00 0.00 38.45 4.63
4439 4537 2.802816 GCATTCGAGAACCGCATAGATT 59.197 45.455 4.73 0.00 38.37 2.40
4507 4605 2.610727 CGGGCTCTTCTTCTTCGACTTT 60.611 50.000 0.00 0.00 0.00 2.66
4528 4626 4.143333 CTGCCACCGTCCTACCCG 62.143 72.222 0.00 0.00 0.00 5.28
4873 4971 1.343465 GGGTTCGAGGAGTTTGTCAGA 59.657 52.381 0.00 0.00 0.00 3.27
4879 4977 2.232452 CGAGGAGTTTGTCAGAGACCAT 59.768 50.000 0.00 0.00 0.00 3.55
4888 4986 1.079127 CAGAGACCATTTCCGCCGT 60.079 57.895 0.00 0.00 0.00 5.68
4906 5004 0.179119 GTCGGGGGACGTTCATACTG 60.179 60.000 0.00 0.00 44.69 2.74
4911 5009 1.481871 GGGACGTTCATACTGAGGGA 58.518 55.000 0.00 0.00 0.00 4.20
4912 5010 2.040178 GGGACGTTCATACTGAGGGAT 58.960 52.381 0.00 0.00 0.00 3.85
4921 5019 0.824109 TACTGAGGGATTGTGAGGCG 59.176 55.000 0.00 0.00 0.00 5.52
4923 5021 0.742281 CTGAGGGATTGTGAGGCGTG 60.742 60.000 0.00 0.00 0.00 5.34
4930 5028 1.728971 GATTGTGAGGCGTGTCTTCAG 59.271 52.381 0.00 0.00 0.00 3.02
5054 5155 3.430862 GGCTCGTTGCGGCATTCA 61.431 61.111 2.28 0.00 44.05 2.57
5067 5168 0.460284 GCATTCACGGAGATCGGTGT 60.460 55.000 16.96 0.46 44.41 4.16
5135 5236 6.639563 AGGATAAACAAAATGGTATTGTGCC 58.360 36.000 0.00 0.00 39.98 5.01
5157 5258 5.588648 GCCTTTGCTACTATATGTCCAAACA 59.411 40.000 0.00 0.00 35.45 2.83
5197 5298 6.300354 AGTGTTTTAGTTCAGATCAAACCG 57.700 37.500 7.22 0.00 0.00 4.44
5201 5302 6.938030 TGTTTTAGTTCAGATCAAACCGGTAT 59.062 34.615 8.00 0.00 0.00 2.73
5222 5323 0.393537 GGAGACATGGTGGCAAGGAG 60.394 60.000 0.00 0.00 0.00 3.69
5223 5324 0.615331 GAGACATGGTGGCAAGGAGA 59.385 55.000 0.00 0.00 0.00 3.71
5316 5418 8.783660 TTATGTCAGAAATATGTCCTAGAGGT 57.216 34.615 0.00 0.00 36.34 3.85
5317 5419 9.877222 TTATGTCAGAAATATGTCCTAGAGGTA 57.123 33.333 0.00 0.00 36.34 3.08
5318 5420 8.783660 ATGTCAGAAATATGTCCTAGAGGTAA 57.216 34.615 0.00 0.00 36.34 2.85
5319 5421 8.783660 TGTCAGAAATATGTCCTAGAGGTAAT 57.216 34.615 0.00 0.00 36.34 1.89
5320 5422 9.877222 TGTCAGAAATATGTCCTAGAGGTAATA 57.123 33.333 0.00 0.00 36.34 0.98
5384 5487 5.046520 ACTCCCTTCGGCCATAATATAAGAC 60.047 44.000 2.24 0.00 0.00 3.01
5385 5488 4.841813 TCCCTTCGGCCATAATATAAGACA 59.158 41.667 2.24 0.00 0.00 3.41
5487 5592 8.709272 TGCATTGATTCTTGAATATGGGATTA 57.291 30.769 7.70 0.00 0.00 1.75
5531 5636 8.623903 CATGTGTAGAAACATAAGCACCAATAT 58.376 33.333 0.00 0.00 38.75 1.28
5623 5728 7.173218 ACATTGTTAGGACGCTATCAATAATGG 59.827 37.037 0.00 0.00 31.70 3.16
5682 5787 5.679638 GCCCCAACTTATGAATTACTGCAAG 60.680 44.000 0.00 0.00 42.29 4.01
5738 5844 8.175925 ACGTTTACTTAGTTCTTCCTTAGACT 57.824 34.615 0.00 0.00 30.90 3.24
5756 5862 9.221933 CCTTAGACTATGAGAATATCGTACACT 57.778 37.037 0.00 0.00 0.00 3.55
5762 5868 7.878644 ACTATGAGAATATCGTACACTGAGCTA 59.121 37.037 0.00 0.00 0.00 3.32
5797 5903 7.119699 AGGATGTGTGTAGTGTTGATATTTGTG 59.880 37.037 0.00 0.00 0.00 3.33
5870 5977 7.382110 ACTATGTCCAAAATCATCTCCTATCG 58.618 38.462 0.00 0.00 0.00 2.92
5874 5981 5.872070 GTCCAAAATCATCTCCTATCGGATC 59.128 44.000 0.00 0.00 39.01 3.36
5881 5988 4.840680 TCATCTCCTATCGGATCAAACCAT 59.159 41.667 0.00 0.00 39.01 3.55
5882 5989 4.607293 TCTCCTATCGGATCAAACCATG 57.393 45.455 0.00 0.00 39.01 3.66
5915 6024 3.993920 GTCCTGACCAACATGCATTTTT 58.006 40.909 0.00 0.00 0.00 1.94
5943 6052 9.490663 CATTAGATCGGTGATTTTCTTAAACAC 57.509 33.333 0.00 0.00 0.00 3.32
5948 6057 6.853720 TCGGTGATTTTCTTAAACACAAACA 58.146 32.000 0.00 0.00 32.11 2.83
5950 6059 7.273815 TCGGTGATTTTCTTAAACACAAACAAC 59.726 33.333 0.00 0.00 32.11 3.32
5960 6069 9.575783 TCTTAAACACAAACAACTTTATGTTCC 57.424 29.630 0.00 0.00 42.49 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
358 360 1.298953 CATTCTCCCCCTTTCTCCCA 58.701 55.000 0.00 0.00 0.00 4.37
517 519 3.467226 GATCCAGGCCGAACCCGA 61.467 66.667 0.00 0.00 40.58 5.14
558 560 4.941309 AGGCCGTTTTTCGCCGGT 62.941 61.111 1.90 0.00 45.91 5.28
614 616 2.679642 CCCCAGCCGATTTTGCCA 60.680 61.111 0.00 0.00 0.00 4.92
674 680 0.739813 AATTCTAAACGGCGCTCGCT 60.740 50.000 16.48 3.50 43.89 4.93
675 681 0.096454 AAATTCTAAACGGCGCTCGC 59.904 50.000 16.48 5.60 43.89 5.03
676 682 1.797964 CAAATTCTAAACGGCGCTCG 58.202 50.000 6.90 12.33 45.88 5.03
677 683 1.535088 GCAAATTCTAAACGGCGCTC 58.465 50.000 6.90 0.00 0.00 5.03
678 684 0.170339 GGCAAATTCTAAACGGCGCT 59.830 50.000 6.90 0.00 0.00 5.92
679 685 1.131618 CGGCAAATTCTAAACGGCGC 61.132 55.000 6.90 0.00 38.81 6.53
680 686 0.522495 CCGGCAAATTCTAAACGGCG 60.522 55.000 4.80 4.80 44.26 6.46
681 687 0.524414 ACCGGCAAATTCTAAACGGC 59.476 50.000 0.00 0.00 44.73 5.68
682 688 1.538075 ACACCGGCAAATTCTAAACGG 59.462 47.619 0.00 0.00 46.16 4.44
683 689 2.224549 TCACACCGGCAAATTCTAAACG 59.775 45.455 0.00 0.00 0.00 3.60
684 690 3.365969 CCTCACACCGGCAAATTCTAAAC 60.366 47.826 0.00 0.00 0.00 2.01
685 691 2.817258 CCTCACACCGGCAAATTCTAAA 59.183 45.455 0.00 0.00 0.00 1.85
686 692 2.432444 CCTCACACCGGCAAATTCTAA 58.568 47.619 0.00 0.00 0.00 2.10
687 693 1.948611 GCCTCACACCGGCAAATTCTA 60.949 52.381 0.00 0.00 46.77 2.10
688 694 1.244019 GCCTCACACCGGCAAATTCT 61.244 55.000 0.00 0.00 46.77 2.40
689 695 1.212751 GCCTCACACCGGCAAATTC 59.787 57.895 0.00 0.00 46.77 2.17
690 696 3.365535 GCCTCACACCGGCAAATT 58.634 55.556 0.00 0.00 46.77 1.82
698 704 4.947147 TGGTTGGCGCCTCACACC 62.947 66.667 29.70 25.67 0.00 4.16
699 705 3.357079 CTGGTTGGCGCCTCACAC 61.357 66.667 29.70 17.97 0.00 3.82
700 706 4.641645 CCTGGTTGGCGCCTCACA 62.642 66.667 29.70 21.06 0.00 3.58
701 707 4.329545 TCCTGGTTGGCGCCTCAC 62.330 66.667 29.70 23.15 35.26 3.51
729 735 1.784358 CCTATACACAAGGACCCGGA 58.216 55.000 0.73 0.00 36.08 5.14
777 783 3.140325 TGGATCCAAGTTGAGGTTGTC 57.860 47.619 13.46 0.00 0.00 3.18
795 801 6.956371 CTTGAAAAGTAAGCCTCCAAGTTTGG 60.956 42.308 4.48 4.48 43.89 3.28
825 831 6.141560 TCTTCGTATACTAGACAGACTCGA 57.858 41.667 0.00 0.00 0.00 4.04
893 899 3.016997 CTCGACCCGAGCATACCTA 57.983 57.895 3.34 0.00 46.75 3.08
927 933 2.126618 TGCTGTAGACGGTTCGCG 60.127 61.111 0.00 0.00 0.00 5.87
928 934 1.805945 CCTGCTGTAGACGGTTCGC 60.806 63.158 0.00 0.00 0.00 4.70
931 937 1.817447 GTAGACCTGCTGTAGACGGTT 59.183 52.381 0.00 0.00 0.00 4.44
932 938 1.271762 TGTAGACCTGCTGTAGACGGT 60.272 52.381 0.00 0.00 0.00 4.83
933 939 1.402259 CTGTAGACCTGCTGTAGACGG 59.598 57.143 0.00 0.00 0.00 4.79
934 940 1.202200 GCTGTAGACCTGCTGTAGACG 60.202 57.143 0.00 0.00 35.32 4.18
936 942 2.095461 CTGCTGTAGACCTGCTGTAGA 58.905 52.381 0.00 0.00 38.70 2.59
939 945 1.480137 GATCTGCTGTAGACCTGCTGT 59.520 52.381 0.00 0.00 38.49 4.40
940 946 1.755959 AGATCTGCTGTAGACCTGCTG 59.244 52.381 0.00 0.00 38.49 4.41
942 948 2.955660 ACTAGATCTGCTGTAGACCTGC 59.044 50.000 5.18 0.00 38.49 4.85
945 951 2.550606 CCGACTAGATCTGCTGTAGACC 59.449 54.545 5.18 0.00 38.49 3.85
975 1010 4.943705 TCTTTTGGATCGAATTCCTCCTTG 59.056 41.667 17.99 8.96 36.68 3.61
1141 1180 1.226046 CGTCGACGCAGAGAATCGT 60.226 57.895 26.59 0.00 42.67 3.73
1417 1456 4.367023 CTCGACGACCCGGCCAAA 62.367 66.667 2.24 0.00 0.00 3.28
1532 1571 0.830648 CATCTCAGGGCGGTAAAGGA 59.169 55.000 0.00 0.00 0.00 3.36
1744 1783 1.369321 GATAGGCCGAGGGAGCAAG 59.631 63.158 0.00 0.00 0.00 4.01
1766 1805 1.000396 AAGGTCAGATTGCCAGGGC 60.000 57.895 2.62 2.62 42.35 5.19
1847 1886 1.444553 GCGGGAAGTGAGTCGTCAG 60.445 63.158 0.00 0.00 31.53 3.51
1875 1914 0.883833 CATGAGCACCCTTGTTGGTC 59.116 55.000 0.00 0.00 36.12 4.02
1973 2030 2.002127 CTTGGAGATTCGCGCTCAC 58.998 57.895 5.56 6.09 34.07 3.51
1986 2043 1.292223 GACCGTAGCTGTGCTTGGA 59.708 57.895 14.50 0.00 40.44 3.53
1996 2053 0.320421 TGCTTTGTCAGGACCGTAGC 60.320 55.000 9.29 9.29 0.00 3.58
2006 2063 0.887836 CTCCTGCTGCTGCTTTGTCA 60.888 55.000 17.00 0.00 40.48 3.58
2007 2064 0.604780 TCTCCTGCTGCTGCTTTGTC 60.605 55.000 17.00 0.00 40.48 3.18
2193 2250 4.129737 AGGGACGTCGATGGTGCG 62.130 66.667 9.92 0.00 0.00 5.34
2205 2262 1.295746 GTTGAAGGGGACGAGGGAC 59.704 63.158 0.00 0.00 0.00 4.46
2544 2607 2.124695 GGGCCGTCAGTTGATCCC 60.125 66.667 0.00 2.71 0.00 3.85
2599 2662 1.745087 CCCAACCCATGAAAGATCGTG 59.255 52.381 0.00 0.00 41.42 4.35
2600 2663 1.955208 GCCCAACCCATGAAAGATCGT 60.955 52.381 0.00 0.00 0.00 3.73
2683 2746 9.379811 GTAGTAACAGAAGATAGCATTACGTAC 57.620 37.037 0.00 0.00 0.00 3.67
2684 2747 9.334947 AGTAGTAACAGAAGATAGCATTACGTA 57.665 33.333 0.00 0.00 0.00 3.57
2685 2748 8.223177 AGTAGTAACAGAAGATAGCATTACGT 57.777 34.615 0.00 0.00 0.00 3.57
2723 2798 4.229876 ACGAACAGCCTACGTAAAGTAAC 58.770 43.478 0.00 0.00 38.47 2.50
2724 2799 4.503741 ACGAACAGCCTACGTAAAGTAA 57.496 40.909 0.00 0.00 38.47 2.24
2725 2800 4.935205 TCTACGAACAGCCTACGTAAAGTA 59.065 41.667 0.00 0.00 40.88 2.24
2726 2801 3.753272 TCTACGAACAGCCTACGTAAAGT 59.247 43.478 0.00 0.00 40.88 2.66
2727 2802 4.094212 GTCTACGAACAGCCTACGTAAAG 58.906 47.826 0.00 0.00 40.88 1.85
2728 2803 3.424829 CGTCTACGAACAGCCTACGTAAA 60.425 47.826 0.00 0.00 40.88 2.01
2729 2804 2.094258 CGTCTACGAACAGCCTACGTAA 59.906 50.000 0.00 0.00 40.88 3.18
2730 2805 1.660607 CGTCTACGAACAGCCTACGTA 59.339 52.381 0.00 0.00 43.02 3.57
2731 2806 0.445436 CGTCTACGAACAGCCTACGT 59.555 55.000 0.00 0.00 43.02 3.57
2732 2807 0.247974 CCGTCTACGAACAGCCTACG 60.248 60.000 3.65 0.00 43.02 3.51
2733 2808 1.063764 CTCCGTCTACGAACAGCCTAC 59.936 57.143 3.65 0.00 43.02 3.18
2734 2809 1.376543 CTCCGTCTACGAACAGCCTA 58.623 55.000 3.65 0.00 43.02 3.93
2735 2810 1.935327 GCTCCGTCTACGAACAGCCT 61.935 60.000 3.65 0.00 43.02 4.58
2736 2811 1.516603 GCTCCGTCTACGAACAGCC 60.517 63.158 3.65 0.00 43.02 4.85
2737 2812 0.179134 ATGCTCCGTCTACGAACAGC 60.179 55.000 3.65 8.75 43.02 4.40
2738 2813 2.279582 AATGCTCCGTCTACGAACAG 57.720 50.000 3.65 0.00 43.02 3.16
2739 2814 3.547413 CGATAATGCTCCGTCTACGAACA 60.547 47.826 3.65 0.00 43.02 3.18
2740 2815 2.971915 CGATAATGCTCCGTCTACGAAC 59.028 50.000 3.65 0.00 43.02 3.95
2741 2816 2.615447 ACGATAATGCTCCGTCTACGAA 59.385 45.455 3.65 0.00 43.02 3.85
2742 2817 2.216046 ACGATAATGCTCCGTCTACGA 58.784 47.619 3.65 0.00 43.02 3.43
2743 2818 2.682952 ACGATAATGCTCCGTCTACG 57.317 50.000 0.00 0.00 39.44 3.51
2744 2819 3.501445 AGGTACGATAATGCTCCGTCTAC 59.499 47.826 0.00 0.00 37.69 2.59
2745 2820 3.748083 AGGTACGATAATGCTCCGTCTA 58.252 45.455 0.00 0.00 37.69 2.59
2746 2821 2.584236 AGGTACGATAATGCTCCGTCT 58.416 47.619 0.00 0.00 37.69 4.18
2747 2822 3.306818 GAAGGTACGATAATGCTCCGTC 58.693 50.000 0.00 0.00 37.69 4.79
2748 2823 2.035576 GGAAGGTACGATAATGCTCCGT 59.964 50.000 0.00 0.00 39.94 4.69
2749 2824 2.673833 GGAAGGTACGATAATGCTCCG 58.326 52.381 0.00 0.00 0.00 4.63
2750 2825 2.673833 CGGAAGGTACGATAATGCTCC 58.326 52.381 0.00 0.00 0.00 4.70
2751 2826 2.059541 GCGGAAGGTACGATAATGCTC 58.940 52.381 0.00 0.00 0.00 4.26
2752 2827 1.687123 AGCGGAAGGTACGATAATGCT 59.313 47.619 0.00 0.00 41.99 3.79
2753 2828 2.150397 AGCGGAAGGTACGATAATGC 57.850 50.000 0.00 0.00 41.99 3.56
2798 2873 6.919662 TCAAAAGAACTGTGAATGAATTGAGC 59.080 34.615 0.00 0.00 0.00 4.26
2877 2952 2.099263 TGCAGCCTCTAGTTCATCGTAC 59.901 50.000 0.00 0.00 0.00 3.67
2883 2958 1.065199 CCCATTGCAGCCTCTAGTTCA 60.065 52.381 0.00 0.00 0.00 3.18
2897 2972 1.379710 TCCACCCATTCGCCCATTG 60.380 57.895 0.00 0.00 0.00 2.82
2907 2982 3.075005 CCGTCGTCCTCCACCCAT 61.075 66.667 0.00 0.00 0.00 4.00
2935 3010 0.540365 TCGGTAGACGGTTCTTGGGT 60.540 55.000 0.00 0.00 44.45 4.51
2981 3060 4.702612 TCCTTGTTTGCTAACAGTGAACAA 59.297 37.500 13.29 1.18 44.56 2.83
3006 3087 2.158856 TGAGAGAATAGAGCCGGTCGTA 60.159 50.000 1.90 0.00 0.00 3.43
3007 3088 1.310904 GAGAGAATAGAGCCGGTCGT 58.689 55.000 1.90 0.00 0.00 4.34
3010 3091 1.757699 GGTTGAGAGAATAGAGCCGGT 59.242 52.381 1.90 0.00 0.00 5.28
3072 3153 6.569226 CGAGAGCAAGGAGTTCATCAATTTTT 60.569 38.462 0.00 0.00 0.00 1.94
3073 3154 5.106396 CGAGAGCAAGGAGTTCATCAATTTT 60.106 40.000 0.00 0.00 0.00 1.82
3081 3162 2.548067 GGAAACGAGAGCAAGGAGTTCA 60.548 50.000 0.00 0.00 0.00 3.18
3101 3182 8.742188 CATCGTTATCGGTTTTCAATTAAATGG 58.258 33.333 0.00 0.00 37.69 3.16
3115 3196 2.688446 TGAGAAGCTCATCGTTATCGGT 59.312 45.455 0.00 0.00 35.39 4.69
3204 3286 9.557061 ACTCCCTCGGTAAAGAAATATAAAATC 57.443 33.333 0.00 0.00 0.00 2.17
3212 3294 7.179872 AGTTAACTACTCCCTCGGTAAAGAAAT 59.820 37.037 6.26 0.00 28.23 2.17
3259 3341 4.178545 AGAAAATGGAATTCTGCAACCG 57.821 40.909 5.23 0.00 33.67 4.44
3299 3381 5.388654 AGGCCCATCACTTTATTAATGGAG 58.611 41.667 0.00 0.00 40.98 3.86
3365 3447 3.838271 GCAGGATCCTCGTCGCCA 61.838 66.667 12.69 0.00 0.00 5.69
3430 3512 0.963225 TCCGATCACAAACCAGACGA 59.037 50.000 0.00 0.00 0.00 4.20
3436 3518 2.107950 TGTCCATCCGATCACAAACC 57.892 50.000 0.00 0.00 0.00 3.27
3453 3535 2.738846 CTCGAGCTAACACATTGCTTGT 59.261 45.455 0.00 0.00 38.82 3.16
3507 3589 1.123928 AACTCGGAGCCTGATAAGGG 58.876 55.000 4.58 0.00 0.00 3.95
3509 3591 4.212214 GCAAATAACTCGGAGCCTGATAAG 59.788 45.833 4.58 0.00 0.00 1.73
3511 3593 3.133901 TGCAAATAACTCGGAGCCTGATA 59.866 43.478 4.58 0.00 0.00 2.15
3554 3636 1.982938 ACCAGGTACCGTCTCAGGC 60.983 63.158 6.18 0.00 33.69 4.85
3557 3639 4.107029 CCACCAGGTACCGTCTCA 57.893 61.111 6.18 0.00 0.00 3.27
3613 3695 0.882042 GGCAGAATCGTCCGCATCAT 60.882 55.000 0.00 0.00 0.00 2.45
3614 3696 1.521457 GGCAGAATCGTCCGCATCA 60.521 57.895 0.00 0.00 0.00 3.07
3704 3786 0.179006 GGTGATCCAGAGGGCAATCC 60.179 60.000 0.00 0.00 0.00 3.01
3750 3832 3.663025 GCAATTAACATTTGGTGGTGCT 58.337 40.909 0.00 0.00 0.00 4.40
3757 3842 4.804108 TCAGGAACGCAATTAACATTTGG 58.196 39.130 0.00 0.00 0.00 3.28
3781 3866 8.801913 GTGAATATCAAAGCTAATTTTCTGCAC 58.198 33.333 0.00 0.00 0.00 4.57
3797 3882 8.868522 AGAAGAACTGGATTTGTGAATATCAA 57.131 30.769 0.00 0.00 0.00 2.57
3826 3911 5.359009 CCATGGAAAGAATATGCAGTTCAGT 59.641 40.000 5.56 4.29 0.00 3.41
3829 3914 6.455360 TTCCATGGAAAGAATATGCAGTTC 57.545 37.500 25.13 6.53 0.00 3.01
3840 3925 6.264518 GTGTAGGTTCTTTTTCCATGGAAAGA 59.735 38.462 32.77 28.63 43.75 2.52
3841 3926 6.447162 GTGTAGGTTCTTTTTCCATGGAAAG 58.553 40.000 32.77 24.92 43.75 2.62
3847 3932 3.418047 CGGGTGTAGGTTCTTTTTCCAT 58.582 45.455 0.00 0.00 0.00 3.41
3851 3936 2.651382 AGCGGGTGTAGGTTCTTTTT 57.349 45.000 0.00 0.00 0.00 1.94
3868 3953 2.597748 GGTTTTCTCGACGTAGCTAAGC 59.402 50.000 6.59 0.00 0.00 3.09
3994 4082 9.160412 AGCTACTCCCTCTGTAAACAAATATAT 57.840 33.333 0.00 0.00 0.00 0.86
4038 4126 9.777297 AGTTGCCATGATTTTAGTTAAAACAAT 57.223 25.926 0.00 0.00 37.92 2.71
4059 4147 3.504520 TCCCTCCGTTTCAAAATAGTTGC 59.495 43.478 0.00 0.00 0.00 4.17
4064 4152 9.689501 AAATAATACTCCCTCCGTTTCAAAATA 57.310 29.630 0.00 0.00 0.00 1.40
4095 4183 7.298507 AGGAAAAATGATGCATTCAAAATCG 57.701 32.000 0.00 0.00 38.03 3.34
4204 4299 2.099921 TCACGGAGAGAAGAGCATTAGC 59.900 50.000 0.00 0.00 42.56 3.09
4209 4304 2.171003 TGAATCACGGAGAGAAGAGCA 58.829 47.619 0.00 0.00 0.00 4.26
4244 4339 0.329261 CCACCTCTTTCCATGGCAGA 59.671 55.000 6.96 10.00 0.00 4.26
4250 4345 2.348472 TCTTGACCCACCTCTTTCCAT 58.652 47.619 0.00 0.00 0.00 3.41
4322 4417 5.254115 AGTGAAACCATAAAAGGTAGCTCC 58.746 41.667 0.00 0.00 42.25 4.70
4323 4418 6.612306 CAAGTGAAACCATAAAAGGTAGCTC 58.388 40.000 0.00 0.00 42.25 4.09
4326 4421 5.390613 CGCAAGTGAAACCATAAAAGGTAG 58.609 41.667 0.00 0.00 42.25 3.18
4345 4440 1.352114 GGTATGCTCGTTACACGCAA 58.648 50.000 0.03 0.00 42.21 4.85
4362 4457 2.537143 AGTCAACTCGGTTCATAGGGT 58.463 47.619 0.00 0.00 0.00 4.34
4376 4471 7.359595 TCTGCATAATTACACACAAAGTCAAC 58.640 34.615 0.00 0.00 0.00 3.18
4483 4581 0.243907 CGAAGAAGAAGAGCCCGTCA 59.756 55.000 0.00 0.00 0.00 4.35
4507 4605 2.283604 TAGGACGGTGGCAGCAGA 60.284 61.111 17.80 0.00 0.00 4.26
4785 4883 3.097614 AGGTAGGCATTCTCGTTGTACT 58.902 45.455 0.00 0.00 0.00 2.73
4873 4971 2.125673 CGACGGCGGAAATGGTCT 60.126 61.111 13.24 0.00 0.00 3.85
4888 4986 0.323633 TCAGTATGAACGTCCCCCGA 60.324 55.000 0.00 0.00 45.97 5.14
4906 5004 0.741221 GACACGCCTCACAATCCCTC 60.741 60.000 0.00 0.00 0.00 4.30
4911 5009 1.609061 CCTGAAGACACGCCTCACAAT 60.609 52.381 0.00 0.00 0.00 2.71
4912 5010 0.249868 CCTGAAGACACGCCTCACAA 60.250 55.000 0.00 0.00 0.00 3.33
4921 5019 1.668151 GTCGCACCCCTGAAGACAC 60.668 63.158 0.00 0.00 30.99 3.67
4923 5021 2.432628 CGTCGCACCCCTGAAGAC 60.433 66.667 0.00 0.00 0.00 3.01
4930 5028 3.351416 GTTCCAACGTCGCACCCC 61.351 66.667 0.00 0.00 0.00 4.95
5017 5118 2.045926 GGCACCAGATTGGCGAGT 60.046 61.111 0.00 0.00 42.67 4.18
5054 5155 2.113433 CCTCGACACCGATCTCCGT 61.113 63.158 0.00 0.00 44.62 4.69
5067 5168 3.259625 TCAACATTACACACATCCCTCGA 59.740 43.478 0.00 0.00 0.00 4.04
5135 5236 6.312918 ACGTGTTTGGACATATAGTAGCAAAG 59.687 38.462 0.00 0.00 38.23 2.77
5157 5258 2.101917 ACACTAGTTTGGTAGCACACGT 59.898 45.455 5.62 0.00 0.00 4.49
5197 5298 0.179018 GCCACCATGTCTCCCATACC 60.179 60.000 0.00 0.00 30.71 2.73
5201 5302 1.379916 CTTGCCACCATGTCTCCCA 59.620 57.895 0.00 0.00 0.00 4.37
5281 5383 9.672673 ACATATTTCTGACATAAAAGCAGTAGT 57.327 29.630 0.00 0.00 0.00 2.73
5482 5587 7.404671 TGCAATTAAGTTTTCCTCCTAATCC 57.595 36.000 0.00 0.00 0.00 3.01
5487 5592 5.539955 ACACATGCAATTAAGTTTTCCTCCT 59.460 36.000 0.00 0.00 0.00 3.69
5531 5636 7.112122 AGTCTTAAAGGCATGACAACATATCA 58.888 34.615 0.00 0.00 35.09 2.15
5623 5728 9.832445 TCTATTGTTCTGATAATAAGGTGTTCC 57.168 33.333 0.00 0.00 0.00 3.62
5738 5844 8.669243 CATAGCTCAGTGTACGATATTCTCATA 58.331 37.037 0.00 0.00 0.00 2.15
5870 5977 1.752084 GCTCCTCCCATGGTTTGATCC 60.752 57.143 11.73 0.00 0.00 3.36
5874 5981 4.344237 GGCTCCTCCCATGGTTTG 57.656 61.111 11.73 0.00 0.00 2.93
5926 6035 8.474006 AGTTGTTTGTGTTTAAGAAAATCACC 57.526 30.769 0.00 0.00 31.34 4.02
6006 6115 9.953697 TGTAGTAAAGTTGCGTCAATTAATTTT 57.046 25.926 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.