Multiple sequence alignment - TraesCS7B01G096800

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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 TraesCS7B01G096800 chr7B 100.000 3417 0 0 1 3417 111366672 111370088 0.000000e+00 6311.0
1 TraesCS7B01G096800 chr7B 84.932 219 28 5 419 635 573930546 573930331 2.060000e-52 217.0
2 TraesCS7B01G096800 chr7B 84.466 206 29 2 432 635 303164432 303164636 2.080000e-47 200.0
3 TraesCS7B01G096800 chr7B 86.842 76 10 0 23 98 146888928 146888853 6.080000e-13 86.1
4 TraesCS7B01G096800 chr7B 97.500 40 1 0 670 709 16932857 16932818 6.120000e-08 69.4
5 TraesCS7B01G096800 chr7D 92.284 1607 86 18 835 2431 149528626 149527048 0.000000e+00 2246.0
6 TraesCS7B01G096800 chr7D 91.325 1660 49 20 837 2437 148296864 148298487 0.000000e+00 2180.0
7 TraesCS7B01G096800 chr7D 84.977 659 79 7 1 651 149529791 149529145 0.000000e+00 651.0
8 TraesCS7B01G096800 chr7D 82.008 239 35 5 405 635 633524965 633525203 2.690000e-46 196.0
9 TraesCS7B01G096800 chr7D 96.364 110 2 2 2627 2734 148298483 148298592 2.710000e-41 180.0
10 TraesCS7B01G096800 chr7D 98.611 72 1 0 2660 2731 149527047 149526976 9.950000e-26 128.0
11 TraesCS7B01G096800 chr7D 95.062 81 4 0 737 817 149528693 149528613 9.950000e-26 128.0
12 TraesCS7B01G096800 chr7A 90.018 1683 57 30 837 2437 149601264 149602917 0.000000e+00 2074.0
13 TraesCS7B01G096800 chr7A 96.190 105 3 1 2627 2730 149602913 149603017 1.630000e-38 171.0
14 TraesCS7B01G096800 chr7A 86.747 83 10 1 6 88 612031201 612031120 1.310000e-14 91.6
15 TraesCS7B01G096800 chr7A 100.000 37 0 0 670 706 266637320 266637284 6.120000e-08 69.4
16 TraesCS7B01G096800 chr4A 96.616 591 17 3 2816 3404 731688036 731688625 0.000000e+00 977.0
17 TraesCS7B01G096800 chr4A 82.979 235 34 3 406 635 121480430 121480197 1.240000e-49 207.0
18 TraesCS7B01G096800 chr4A 97.297 74 2 0 2737 2810 731687926 731687999 3.580000e-25 126.0
19 TraesCS7B01G096800 chr4A 88.462 52 6 0 673 724 564950919 564950868 2.850000e-06 63.9
20 TraesCS7B01G096800 chr4B 95.710 606 24 2 2814 3417 67493536 67492931 0.000000e+00 974.0
21 TraesCS7B01G096800 chr4B 83.898 236 32 4 404 635 62974340 62974573 1.600000e-53 220.0
22 TraesCS7B01G096800 chr4B 97.436 78 2 0 2733 2810 67493648 67493571 2.140000e-27 134.0
23 TraesCS7B01G096800 chr1B 95.868 605 20 4 2816 3417 683095124 683094522 0.000000e+00 974.0
24 TraesCS7B01G096800 chr1B 89.362 141 15 0 2441 2581 646542088 646541948 9.740000e-41 178.0
25 TraesCS7B01G096800 chr1B 96.203 79 3 0 2732 2810 683095239 683095161 2.770000e-26 130.0
26 TraesCS7B01G096800 chr6A 86.819 698 44 16 2732 3404 34570698 34570024 0.000000e+00 736.0
27 TraesCS7B01G096800 chr1D 89.447 597 39 10 2814 3405 435530211 435530788 0.000000e+00 732.0
28 TraesCS7B01G096800 chr1D 88.739 595 43 6 2816 3405 26149835 26150410 0.000000e+00 706.0
29 TraesCS7B01G096800 chr1D 83.475 236 31 6 405 635 409313347 409313579 2.670000e-51 213.0
30 TraesCS7B01G096800 chr1D 96.203 79 3 0 2732 2810 435530097 435530175 2.770000e-26 130.0
31 TraesCS7B01G096800 chr1D 96.154 78 3 0 2733 2810 26149719 26149796 9.950000e-26 128.0
32 TraesCS7B01G096800 chr1D 91.304 46 4 0 670 715 347215352 347215307 2.850000e-06 63.9
33 TraesCS7B01G096800 chr6D 85.735 687 61 15 2729 3379 16746523 16747208 0.000000e+00 691.0
34 TraesCS7B01G096800 chr6D 82.051 234 36 4 408 635 38894811 38895044 9.680000e-46 195.0
35 TraesCS7B01G096800 chr6D 82.251 231 35 4 409 635 178861602 178861374 9.680000e-46 195.0
36 TraesCS7B01G096800 chr1A 86.655 592 74 5 2815 3405 582745559 582746146 0.000000e+00 651.0
37 TraesCS7B01G096800 chr3A 86.509 593 73 6 2815 3404 677839465 677838877 0.000000e+00 645.0
38 TraesCS7B01G096800 chr3A 89.286 84 7 2 1 83 691295182 691295264 1.680000e-18 104.0
39 TraesCS7B01G096800 chr3A 83.824 68 10 1 112 178 451154875 451154808 2.850000e-06 63.9
40 TraesCS7B01G096800 chr5D 87.027 555 66 6 2815 3367 21215933 21215383 3.750000e-174 621.0
41 TraesCS7B01G096800 chr5D 89.362 141 15 0 2441 2581 563730867 563730727 9.740000e-41 178.0
42 TraesCS7B01G096800 chr5D 88.811 143 16 0 2439 2581 513013983 513013841 3.500000e-40 176.0
43 TraesCS7B01G096800 chr5D 97.297 37 1 0 673 709 42955291 42955255 2.850000e-06 63.9
44 TraesCS7B01G096800 chrUn 84.100 239 28 6 400 630 93157201 93156965 4.440000e-54 222.0
45 TraesCS7B01G096800 chr3B 92.424 132 9 1 2440 2571 821035038 821034908 1.620000e-43 187.0
46 TraesCS7B01G096800 chr2D 81.513 238 34 6 404 633 181304343 181304108 1.620000e-43 187.0
47 TraesCS7B01G096800 chr2D 93.750 48 3 0 670 717 60191709 60191756 4.730000e-09 73.1
48 TraesCS7B01G096800 chr2B 90.141 142 14 0 2440 2581 686054381 686054240 5.820000e-43 185.0
49 TraesCS7B01G096800 chr5B 91.729 133 10 1 2439 2571 15328085 15327954 2.090000e-42 183.0
50 TraesCS7B01G096800 chr5B 88.435 147 15 2 2435 2581 622082208 622082352 3.500000e-40 176.0
51 TraesCS7B01G096800 chr5B 85.882 85 12 0 2 86 241975280 241975364 1.310000e-14 91.6
52 TraesCS7B01G096800 chr5B 82.222 90 12 3 1 89 473781294 473781208 1.320000e-09 75.0
53 TraesCS7B01G096800 chr5B 94.737 38 2 0 18 55 678334866 678334829 3.680000e-05 60.2
54 TraesCS7B01G096800 chr3D 89.928 139 14 0 2443 2581 540258371 540258233 2.710000e-41 180.0
55 TraesCS7B01G096800 chr3D 89.362 141 14 1 2441 2581 574731623 574731762 3.500000e-40 176.0
56 TraesCS7B01G096800 chr3D 83.505 97 16 0 2 98 104031526 104031430 1.310000e-14 91.6
57 TraesCS7B01G096800 chr6B 97.500 40 1 0 670 709 22895387 22895426 6.120000e-08 69.4
58 TraesCS7B01G096800 chr6B 84.483 58 6 3 678 734 2307758 2307703 2.000000e-03 54.7
59 TraesCS7B01G096800 chr2A 95.349 43 1 1 670 711 726228668 726228710 2.200000e-07 67.6


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 TraesCS7B01G096800 chr7B 111366672 111370088 3416 False 6311.00 6311 100.0000 1 3417 1 chr7B.!!$F1 3416
1 TraesCS7B01G096800 chr7D 148296864 148298592 1728 False 1180.00 2180 93.8445 837 2734 2 chr7D.!!$F2 1897
2 TraesCS7B01G096800 chr7D 149526976 149529791 2815 True 788.25 2246 92.7335 1 2731 4 chr7D.!!$R1 2730
3 TraesCS7B01G096800 chr7A 149601264 149603017 1753 False 1122.50 2074 93.1040 837 2730 2 chr7A.!!$F1 1893
4 TraesCS7B01G096800 chr4A 731687926 731688625 699 False 551.50 977 96.9565 2737 3404 2 chr4A.!!$F1 667
5 TraesCS7B01G096800 chr4B 67492931 67493648 717 True 554.00 974 96.5730 2733 3417 2 chr4B.!!$R1 684
6 TraesCS7B01G096800 chr1B 683094522 683095239 717 True 552.00 974 96.0355 2732 3417 2 chr1B.!!$R2 685
7 TraesCS7B01G096800 chr6A 34570024 34570698 674 True 736.00 736 86.8190 2732 3404 1 chr6A.!!$R1 672
8 TraesCS7B01G096800 chr1D 435530097 435530788 691 False 431.00 732 92.8250 2732 3405 2 chr1D.!!$F3 673
9 TraesCS7B01G096800 chr1D 26149719 26150410 691 False 417.00 706 92.4465 2733 3405 2 chr1D.!!$F2 672
10 TraesCS7B01G096800 chr6D 16746523 16747208 685 False 691.00 691 85.7350 2729 3379 1 chr6D.!!$F1 650
11 TraesCS7B01G096800 chr1A 582745559 582746146 587 False 651.00 651 86.6550 2815 3405 1 chr1A.!!$F1 590
12 TraesCS7B01G096800 chr3A 677838877 677839465 588 True 645.00 645 86.5090 2815 3404 1 chr3A.!!$R2 589
13 TraesCS7B01G096800 chr5D 21215383 21215933 550 True 621.00 621 87.0270 2815 3367 1 chr5D.!!$R1 552

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
895 1293 0.861837 GGCGCTCAAACTCCGATATG 59.138 55.0 7.64 0.0 0.0 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2599 3094 0.10412 GCTTTGCCCCGAGTGTTTTT 59.896 50.0 0.0 0.0 0.0 1.94 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
35 36 5.814188 GTCATAGACTTGACATTGATGCTCA 59.186 40.000 10.87 0.00 44.38 4.26
66 67 1.839424 ATTTCTTTCAGGCCTTCCGG 58.161 50.000 0.00 0.00 37.47 5.14
75 76 1.961277 GGCCTTCCGGTGATATGCG 60.961 63.158 0.00 0.00 0.00 4.73
83 84 1.470805 CCGGTGATATGCGTTCAGTGA 60.471 52.381 0.00 0.00 0.00 3.41
89 90 5.340803 GTGATATGCGTTCAGTGAGAAGTA 58.659 41.667 0.00 0.00 36.78 2.24
95 96 4.447724 TGCGTTCAGTGAGAAGTAACATTC 59.552 41.667 0.00 0.00 36.78 2.67
110 111 7.781324 AGTAACATTCCCAAAGATGATGTTT 57.219 32.000 5.49 0.00 33.52 2.83
113 114 4.158394 ACATTCCCAAAGATGATGTTTCGG 59.842 41.667 0.00 0.00 0.00 4.30
115 116 1.134946 CCCAAAGATGATGTTTCGGCC 59.865 52.381 0.00 0.00 0.00 6.13
126 127 1.605451 TTTCGGCCCAGTCTCTCGA 60.605 57.895 0.00 0.00 0.00 4.04
129 130 1.227089 CGGCCCAGTCTCTCGAATG 60.227 63.158 0.00 0.00 35.13 2.67
130 131 1.901085 GGCCCAGTCTCTCGAATGT 59.099 57.895 0.00 0.00 33.59 2.71
131 132 1.112113 GGCCCAGTCTCTCGAATGTA 58.888 55.000 0.00 0.00 33.59 2.29
132 133 1.689273 GGCCCAGTCTCTCGAATGTAT 59.311 52.381 0.00 0.00 33.59 2.29
133 134 2.103263 GGCCCAGTCTCTCGAATGTATT 59.897 50.000 0.00 0.00 33.59 1.89
137 138 5.605534 CCCAGTCTCTCGAATGTATTCATT 58.394 41.667 0.00 0.00 45.57 2.57
166 167 2.166270 TGCGTGCGTGCATTCATAA 58.834 47.368 0.00 0.00 40.62 1.90
178 179 6.643845 CGTGCATTCATAAAGATGAGTGTAG 58.356 40.000 10.81 1.94 46.40 2.74
179 180 6.476706 CGTGCATTCATAAAGATGAGTGTAGA 59.523 38.462 10.81 0.00 46.40 2.59
188 189 9.433153 CATAAAGATGAGTGTAGATGCATATGT 57.567 33.333 3.54 0.00 34.73 2.29
191 192 8.999220 AAGATGAGTGTAGATGCATATGTATG 57.001 34.615 11.33 0.00 36.78 2.39
194 195 7.530426 TGAGTGTAGATGCATATGTATGAGT 57.470 36.000 11.33 0.00 35.75 3.41
195 196 8.635765 TGAGTGTAGATGCATATGTATGAGTA 57.364 34.615 11.33 0.00 35.75 2.59
206 207 7.761249 TGCATATGTATGAGTATATGTGTCTGC 59.239 37.037 4.29 0.00 38.76 4.26
211 212 3.785486 TGAGTATATGTGTCTGCACTGC 58.215 45.455 0.00 0.00 45.44 4.40
212 213 3.195396 TGAGTATATGTGTCTGCACTGCA 59.805 43.478 3.11 3.11 45.44 4.41
214 215 5.068987 TGAGTATATGTGTCTGCACTGCATA 59.931 40.000 3.64 0.00 45.44 3.14
246 248 9.902684 AGATGATTAAAGGATATTATCAGCCAG 57.097 33.333 6.04 0.00 0.00 4.85
247 249 9.118300 GATGATTAAAGGATATTATCAGCCAGG 57.882 37.037 6.04 0.00 0.00 4.45
251 253 2.915604 AGGATATTATCAGCCAGGTGGG 59.084 50.000 6.04 0.00 40.85 4.61
255 257 5.222048 GGATATTATCAGCCAGGTGGGTAAA 60.222 44.000 0.00 0.00 45.47 2.01
257 259 1.668826 ATCAGCCAGGTGGGTAAAGA 58.331 50.000 0.00 0.00 45.47 2.52
267 270 2.492088 GGTGGGTAAAGATCAAAGGCAC 59.508 50.000 0.00 0.00 0.00 5.01
289 292 4.469586 ACCACAAAAGAATGACCAACCTTT 59.530 37.500 0.00 0.00 0.00 3.11
295 298 4.982241 AGAATGACCAACCTTTGAGAGA 57.018 40.909 0.00 0.00 0.00 3.10
354 358 1.078214 CGCCTCCACCATCACATGT 60.078 57.895 0.00 0.00 0.00 3.21
387 391 6.980593 AGCAACATCAAAATAAAGTAGTGCA 58.019 32.000 0.00 0.00 0.00 4.57
390 394 8.798153 GCAACATCAAAATAAAGTAGTGCATAC 58.202 33.333 0.00 0.00 34.30 2.39
429 436 6.797748 TATCCAAATGATAACCACACGTGTGA 60.798 38.462 42.33 27.13 39.36 3.58
443 450 3.060761 CACGTGTGACATGAAGTAATCCG 59.939 47.826 12.40 0.00 0.00 4.18
446 453 4.000988 GTGTGACATGAAGTAATCCGGTT 58.999 43.478 0.00 0.00 0.00 4.44
447 454 4.092968 GTGTGACATGAAGTAATCCGGTTC 59.907 45.833 0.00 0.00 0.00 3.62
448 455 3.621715 GTGACATGAAGTAATCCGGTTCC 59.378 47.826 0.00 0.00 0.00 3.62
515 522 4.093743 ACCCCAAAAGAACTGAAACTTGT 58.906 39.130 0.00 0.00 0.00 3.16
521 528 6.405731 CCAAAAGAACTGAAACTTGTCATCCA 60.406 38.462 0.00 0.00 0.00 3.41
524 531 6.966534 AGAACTGAAACTTGTCATCCAAAT 57.033 33.333 0.00 0.00 31.20 2.32
525 532 6.974965 AGAACTGAAACTTGTCATCCAAATC 58.025 36.000 0.00 0.00 31.20 2.17
526 533 6.547141 AGAACTGAAACTTGTCATCCAAATCA 59.453 34.615 0.00 0.00 31.20 2.57
528 535 6.742109 ACTGAAACTTGTCATCCAAATCAAG 58.258 36.000 0.00 0.00 41.74 3.02
564 573 1.003118 ACTAAAGTTGCCATCCTCGCA 59.997 47.619 0.00 0.00 0.00 5.10
577 586 3.678056 TCCTCGCATCACTAAACTTGT 57.322 42.857 0.00 0.00 0.00 3.16
581 590 5.105513 TCCTCGCATCACTAAACTTGTCATA 60.106 40.000 0.00 0.00 0.00 2.15
612 621 3.311871 TCAAAATTGCCATGTGTTTGTGC 59.688 39.130 0.00 0.00 32.34 4.57
613 622 1.881591 AATTGCCATGTGTTTGTGCC 58.118 45.000 0.00 0.00 0.00 5.01
633 642 1.003972 CACACGTGTGGCACTTAACAG 60.004 52.381 35.65 10.09 42.10 3.16
637 646 2.151202 CGTGTGGCACTTAACAGGATT 58.849 47.619 19.83 0.00 34.84 3.01
642 651 5.648092 GTGTGGCACTTAACAGGATTCTATT 59.352 40.000 19.83 0.00 0.00 1.73
654 663 7.939784 ACAGGATTCTATTTTTGTTACTCCC 57.060 36.000 0.00 0.00 0.00 4.30
655 664 7.699878 ACAGGATTCTATTTTTGTTACTCCCT 58.300 34.615 0.00 0.00 0.00 4.20
657 666 8.678199 CAGGATTCTATTTTTGTTACTCCCTTC 58.322 37.037 0.00 0.00 0.00 3.46
658 667 8.390921 AGGATTCTATTTTTGTTACTCCCTTCA 58.609 33.333 0.00 0.00 0.00 3.02
659 668 9.190317 GGATTCTATTTTTGTTACTCCCTTCAT 57.810 33.333 0.00 0.00 0.00 2.57
669 678 9.802039 TTTGTTACTCCCTTCATAAACTAATGT 57.198 29.630 0.00 0.00 0.00 2.71
671 680 9.880157 TGTTACTCCCTTCATAAACTAATGTAC 57.120 33.333 0.00 0.00 0.00 2.90
735 888 8.426569 AAATACAAGGGTAGTACTAACAGTCA 57.573 34.615 19.43 1.12 31.88 3.41
798 1194 6.738114 CAAGTATTTCTTGGTTTCTGCAAGA 58.262 36.000 0.00 0.00 46.85 3.02
805 1201 5.132502 TCTTGGTTTCTGCAAGATCTCAAA 58.867 37.500 0.00 0.00 46.36 2.69
806 1202 5.771666 TCTTGGTTTCTGCAAGATCTCAAAT 59.228 36.000 0.00 0.00 46.36 2.32
807 1203 6.266103 TCTTGGTTTCTGCAAGATCTCAAATT 59.734 34.615 0.00 0.00 46.36 1.82
808 1204 5.775686 TGGTTTCTGCAAGATCTCAAATTG 58.224 37.500 0.00 0.00 46.36 2.32
809 1205 5.302568 TGGTTTCTGCAAGATCTCAAATTGT 59.697 36.000 0.00 0.00 46.36 2.71
810 1206 5.860716 GGTTTCTGCAAGATCTCAAATTGTC 59.139 40.000 0.00 0.00 46.36 3.18
811 1207 4.934075 TCTGCAAGATCTCAAATTGTCG 57.066 40.909 0.00 0.00 38.67 4.35
812 1208 3.686241 TCTGCAAGATCTCAAATTGTCGG 59.314 43.478 0.00 0.00 38.67 4.79
813 1209 2.162208 TGCAAGATCTCAAATTGTCGGC 59.838 45.455 0.00 0.00 0.00 5.54
814 1210 2.789092 GCAAGATCTCAAATTGTCGGCG 60.789 50.000 0.00 0.00 0.00 6.46
815 1211 2.386661 AGATCTCAAATTGTCGGCGT 57.613 45.000 6.85 0.00 0.00 5.68
816 1212 2.699954 AGATCTCAAATTGTCGGCGTT 58.300 42.857 6.85 0.00 0.00 4.84
817 1213 3.074412 AGATCTCAAATTGTCGGCGTTT 58.926 40.909 6.85 0.00 0.00 3.60
818 1214 3.502211 AGATCTCAAATTGTCGGCGTTTT 59.498 39.130 6.85 0.44 0.00 2.43
819 1215 3.701532 TCTCAAATTGTCGGCGTTTTT 57.298 38.095 6.85 0.07 0.00 1.94
895 1293 0.861837 GGCGCTCAAACTCCGATATG 59.138 55.000 7.64 0.00 0.00 1.78
939 1344 6.879276 AGATTCCAATCTCTACATGCATTG 57.121 37.500 0.00 0.00 41.82 2.82
993 1424 4.439057 GGTACAAGGCTTCATATCGTTCA 58.561 43.478 0.00 0.00 0.00 3.18
1056 1493 4.905456 TGTTCCTTCCTCAAGAACTTCCTA 59.095 41.667 0.00 0.00 0.00 2.94
1105 1542 1.776662 TTACATCCTCCTCCACTCCG 58.223 55.000 0.00 0.00 0.00 4.63
1164 1607 2.126734 GCACATCGCACAAGCACC 60.127 61.111 0.00 0.00 42.27 5.01
1174 1620 2.045536 CAAGCACCAGCCCTCCTC 60.046 66.667 0.00 0.00 43.56 3.71
1175 1621 3.334054 AAGCACCAGCCCTCCTCC 61.334 66.667 0.00 0.00 43.56 4.30
1176 1622 3.880033 AAGCACCAGCCCTCCTCCT 62.880 63.158 0.00 0.00 43.56 3.69
1271 1751 5.885230 TGGCTTGATTGCATGCTATATAC 57.115 39.130 20.33 5.83 42.84 1.47
1287 1767 6.669591 TGCTATATACTATGCTGACCTCCATT 59.330 38.462 0.00 0.00 0.00 3.16
1288 1768 7.839200 TGCTATATACTATGCTGACCTCCATTA 59.161 37.037 0.00 0.00 0.00 1.90
1313 1793 0.391130 TCTTGCGTTCCTGATTCCCG 60.391 55.000 0.00 0.00 0.00 5.14
1315 1795 3.202706 GCGTTCCTGATTCCCGGC 61.203 66.667 0.00 0.00 0.00 6.13
1316 1796 2.513897 CGTTCCTGATTCCCGGCC 60.514 66.667 0.00 0.00 0.00 6.13
1317 1797 2.124278 GTTCCTGATTCCCGGCCC 60.124 66.667 0.00 0.00 0.00 5.80
1318 1798 3.792736 TTCCTGATTCCCGGCCCG 61.793 66.667 0.00 0.00 0.00 6.13
1319 1799 4.789173 TCCTGATTCCCGGCCCGA 62.789 66.667 3.71 0.00 0.00 5.14
1320 1800 4.241555 CCTGATTCCCGGCCCGAG 62.242 72.222 3.71 0.00 0.00 4.63
1379 1859 4.147449 TCTGGGATGGCAGCGTCG 62.147 66.667 0.00 0.00 0.00 5.12
1544 2024 4.785453 GGGCAGTCCGAGGCAAGG 62.785 72.222 0.00 0.00 0.00 3.61
1603 2083 1.878656 CGGAGTCCCTCGTCTGCTTT 61.879 60.000 2.80 0.00 0.00 3.51
2302 2797 1.445582 CGTGAAGGACAGGTACGGC 60.446 63.158 0.00 0.00 0.00 5.68
2420 2915 3.359523 CTGCAAGCGGCTGAAGCA 61.360 61.111 19.39 19.39 43.53 3.91
2432 2927 1.537202 GCTGAAGCAATTGTTCGGAGT 59.463 47.619 22.83 0.00 41.59 3.85
2433 2928 2.742053 GCTGAAGCAATTGTTCGGAGTA 59.258 45.455 22.83 6.01 41.59 2.59
2434 2929 3.181516 GCTGAAGCAATTGTTCGGAGTAG 60.182 47.826 22.83 12.92 41.59 2.57
2435 2930 3.997021 CTGAAGCAATTGTTCGGAGTAGT 59.003 43.478 17.62 0.00 32.79 2.73
2436 2931 5.142061 TGAAGCAATTGTTCGGAGTAGTA 57.858 39.130 7.40 0.00 0.00 1.82
2437 2932 4.927425 TGAAGCAATTGTTCGGAGTAGTAC 59.073 41.667 7.40 0.00 0.00 2.73
2438 2933 4.803098 AGCAATTGTTCGGAGTAGTACT 57.197 40.909 1.37 1.37 0.00 2.73
2439 2934 5.148651 AGCAATTGTTCGGAGTAGTACTT 57.851 39.130 7.40 0.00 0.00 2.24
2440 2935 5.548406 AGCAATTGTTCGGAGTAGTACTTT 58.452 37.500 7.40 0.00 0.00 2.66
2441 2936 5.995897 AGCAATTGTTCGGAGTAGTACTTTT 59.004 36.000 7.40 0.00 0.00 2.27
2442 2937 6.485648 AGCAATTGTTCGGAGTAGTACTTTTT 59.514 34.615 7.40 0.00 0.00 1.94
2466 2961 6.907206 TTTTCAAAACTGAGGCAAAGATTG 57.093 33.333 0.00 0.00 0.00 2.67
2484 2979 9.956720 CAAAGATTGCCTCACCTATTAAATAAG 57.043 33.333 0.00 0.00 0.00 1.73
2485 2980 7.751768 AGATTGCCTCACCTATTAAATAAGC 57.248 36.000 0.00 0.00 0.00 3.09
2486 2981 7.290061 AGATTGCCTCACCTATTAAATAAGCA 58.710 34.615 0.00 0.00 0.00 3.91
2487 2982 6.942532 TTGCCTCACCTATTAAATAAGCAG 57.057 37.500 0.00 0.00 0.00 4.24
2488 2983 6.247229 TGCCTCACCTATTAAATAAGCAGA 57.753 37.500 0.00 0.00 0.00 4.26
2489 2984 6.658849 TGCCTCACCTATTAAATAAGCAGAA 58.341 36.000 0.00 0.00 0.00 3.02
2490 2985 6.767902 TGCCTCACCTATTAAATAAGCAGAAG 59.232 38.462 0.00 0.00 0.00 2.85
2491 2986 6.992715 GCCTCACCTATTAAATAAGCAGAAGA 59.007 38.462 0.00 0.00 0.00 2.87
2492 2987 7.172361 GCCTCACCTATTAAATAAGCAGAAGAG 59.828 40.741 0.00 0.00 0.00 2.85
2493 2988 8.424918 CCTCACCTATTAAATAAGCAGAAGAGA 58.575 37.037 0.00 0.00 0.00 3.10
2494 2989 9.823647 CTCACCTATTAAATAAGCAGAAGAGAA 57.176 33.333 0.00 0.00 0.00 2.87
2501 2996 8.862325 TTAAATAAGCAGAAGAGAATTGTCCA 57.138 30.769 0.00 0.00 0.00 4.02
2502 2997 6.998968 AATAAGCAGAAGAGAATTGTCCAG 57.001 37.500 0.00 0.00 0.00 3.86
2503 2998 4.363991 AAGCAGAAGAGAATTGTCCAGT 57.636 40.909 0.00 0.00 0.00 4.00
2504 2999 4.363991 AGCAGAAGAGAATTGTCCAGTT 57.636 40.909 0.00 0.00 0.00 3.16
2505 3000 5.489792 AGCAGAAGAGAATTGTCCAGTTA 57.510 39.130 0.00 0.00 0.00 2.24
2506 3001 5.869579 AGCAGAAGAGAATTGTCCAGTTAA 58.130 37.500 0.00 0.00 0.00 2.01
2507 3002 6.479884 AGCAGAAGAGAATTGTCCAGTTAAT 58.520 36.000 0.00 0.00 0.00 1.40
2508 3003 6.944862 AGCAGAAGAGAATTGTCCAGTTAATT 59.055 34.615 0.00 0.00 0.00 1.40
2509 3004 8.103305 AGCAGAAGAGAATTGTCCAGTTAATTA 58.897 33.333 0.00 0.00 0.00 1.40
2510 3005 8.178313 GCAGAAGAGAATTGTCCAGTTAATTAC 58.822 37.037 0.00 0.00 0.00 1.89
2511 3006 9.219603 CAGAAGAGAATTGTCCAGTTAATTACA 57.780 33.333 0.00 0.00 0.00 2.41
2512 3007 9.793259 AGAAGAGAATTGTCCAGTTAATTACAA 57.207 29.630 0.00 0.00 36.37 2.41
2535 3030 4.993029 AAATCAGACAAAAACCGGAACA 57.007 36.364 9.46 0.00 0.00 3.18
2536 3031 4.993029 AATCAGACAAAAACCGGAACAA 57.007 36.364 9.46 0.00 0.00 2.83
2537 3032 3.768468 TCAGACAAAAACCGGAACAAC 57.232 42.857 9.46 0.00 0.00 3.32
2538 3033 3.082548 TCAGACAAAAACCGGAACAACA 58.917 40.909 9.46 0.00 0.00 3.33
2539 3034 3.506455 TCAGACAAAAACCGGAACAACAA 59.494 39.130 9.46 0.00 0.00 2.83
2540 3035 4.022242 TCAGACAAAAACCGGAACAACAAA 60.022 37.500 9.46 0.00 0.00 2.83
2541 3036 4.326009 CAGACAAAAACCGGAACAACAAAG 59.674 41.667 9.46 0.00 0.00 2.77
2542 3037 4.218852 AGACAAAAACCGGAACAACAAAGA 59.781 37.500 9.46 0.00 0.00 2.52
2543 3038 4.239304 ACAAAAACCGGAACAACAAAGAC 58.761 39.130 9.46 0.00 0.00 3.01
2544 3039 3.513680 AAAACCGGAACAACAAAGACC 57.486 42.857 9.46 0.00 0.00 3.85
2545 3040 2.131776 AACCGGAACAACAAAGACCA 57.868 45.000 9.46 0.00 0.00 4.02
2546 3041 2.131776 ACCGGAACAACAAAGACCAA 57.868 45.000 9.46 0.00 0.00 3.67
2547 3042 2.021457 ACCGGAACAACAAAGACCAAG 58.979 47.619 9.46 0.00 0.00 3.61
2548 3043 1.269051 CCGGAACAACAAAGACCAAGC 60.269 52.381 0.00 0.00 0.00 4.01
2549 3044 1.269051 CGGAACAACAAAGACCAAGCC 60.269 52.381 0.00 0.00 0.00 4.35
2550 3045 1.068588 GGAACAACAAAGACCAAGCCC 59.931 52.381 0.00 0.00 0.00 5.19
2551 3046 1.754226 GAACAACAAAGACCAAGCCCA 59.246 47.619 0.00 0.00 0.00 5.36
2552 3047 1.111277 ACAACAAAGACCAAGCCCAC 58.889 50.000 0.00 0.00 0.00 4.61
2553 3048 1.341976 ACAACAAAGACCAAGCCCACT 60.342 47.619 0.00 0.00 0.00 4.00
2554 3049 1.338020 CAACAAAGACCAAGCCCACTC 59.662 52.381 0.00 0.00 0.00 3.51
2555 3050 0.178990 ACAAAGACCAAGCCCACTCC 60.179 55.000 0.00 0.00 0.00 3.85
2556 3051 0.895559 CAAAGACCAAGCCCACTCCC 60.896 60.000 0.00 0.00 0.00 4.30
2557 3052 1.360393 AAAGACCAAGCCCACTCCCA 61.360 55.000 0.00 0.00 0.00 4.37
2558 3053 1.142688 AAGACCAAGCCCACTCCCAT 61.143 55.000 0.00 0.00 0.00 4.00
2559 3054 0.253160 AGACCAAGCCCACTCCCATA 60.253 55.000 0.00 0.00 0.00 2.74
2560 3055 0.181350 GACCAAGCCCACTCCCATAG 59.819 60.000 0.00 0.00 0.00 2.23
2561 3056 0.253160 ACCAAGCCCACTCCCATAGA 60.253 55.000 0.00 0.00 0.00 1.98
2562 3057 0.181350 CCAAGCCCACTCCCATAGAC 59.819 60.000 0.00 0.00 0.00 2.59
2563 3058 1.207791 CAAGCCCACTCCCATAGACT 58.792 55.000 0.00 0.00 0.00 3.24
2564 3059 1.134280 CAAGCCCACTCCCATAGACTG 60.134 57.143 0.00 0.00 0.00 3.51
2565 3060 0.339859 AGCCCACTCCCATAGACTGA 59.660 55.000 0.00 0.00 0.00 3.41
2566 3061 1.204146 GCCCACTCCCATAGACTGAA 58.796 55.000 0.00 0.00 0.00 3.02
2567 3062 1.559682 GCCCACTCCCATAGACTGAAA 59.440 52.381 0.00 0.00 0.00 2.69
2568 3063 2.681097 GCCCACTCCCATAGACTGAAAC 60.681 54.545 0.00 0.00 0.00 2.78
2569 3064 2.571653 CCCACTCCCATAGACTGAAACA 59.428 50.000 0.00 0.00 0.00 2.83
2570 3065 3.600388 CCACTCCCATAGACTGAAACAC 58.400 50.000 0.00 0.00 0.00 3.32
2571 3066 3.600388 CACTCCCATAGACTGAAACACC 58.400 50.000 0.00 0.00 0.00 4.16
2572 3067 2.572104 ACTCCCATAGACTGAAACACCC 59.428 50.000 0.00 0.00 0.00 4.61
2573 3068 1.553248 TCCCATAGACTGAAACACCCG 59.447 52.381 0.00 0.00 0.00 5.28
2574 3069 1.406887 CCCATAGACTGAAACACCCGG 60.407 57.143 0.00 0.00 0.00 5.73
2575 3070 1.406887 CCATAGACTGAAACACCCGGG 60.407 57.143 22.25 22.25 0.00 5.73
2576 3071 1.553248 CATAGACTGAAACACCCGGGA 59.447 52.381 32.02 1.10 0.00 5.14
2577 3072 0.971386 TAGACTGAAACACCCGGGAC 59.029 55.000 32.02 13.07 0.00 4.46
2578 3073 1.052124 AGACTGAAACACCCGGGACA 61.052 55.000 32.02 16.89 0.00 4.02
2579 3074 0.179040 GACTGAAACACCCGGGACAA 60.179 55.000 32.02 5.13 0.00 3.18
2580 3075 0.256464 ACTGAAACACCCGGGACAAA 59.744 50.000 32.02 6.32 0.00 2.83
2581 3076 0.666374 CTGAAACACCCGGGACAAAC 59.334 55.000 32.02 15.68 0.00 2.93
2582 3077 0.256464 TGAAACACCCGGGACAAACT 59.744 50.000 32.02 5.80 0.00 2.66
2583 3078 0.949397 GAAACACCCGGGACAAACTC 59.051 55.000 32.02 11.80 0.00 3.01
2584 3079 0.466739 AAACACCCGGGACAAACTCC 60.467 55.000 32.02 0.00 38.55 3.85
2618 3113 0.104120 AAAAACACTCGGGGCAAAGC 59.896 50.000 0.00 0.00 0.00 3.51
2633 3128 2.355716 GCAAAGCCCACACCTAGTATGA 60.356 50.000 0.00 0.00 0.00 2.15
2676 3172 0.462581 ACTCATCGTGCATTCGCCAT 60.463 50.000 0.00 0.00 37.32 4.40
2945 3477 3.690460 AGAATCCACACCAAATCCTCAC 58.310 45.455 0.00 0.00 0.00 3.51
3100 3637 5.290493 TGAGGTTGAGTTCAAGTACATGT 57.710 39.130 2.69 2.69 36.39 3.21
3282 3839 1.271325 ACATGACGATGCTGGAACCAA 60.271 47.619 0.00 0.00 32.14 3.67
3326 3883 0.753262 GCGTCCTGGATAGGTGACAT 59.247 55.000 0.00 0.00 44.88 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 9.415544 GAAAGAAATACAGAAAAATGTGAGCAT 57.584 29.630 0.00 0.00 36.80 3.79
35 36 7.015584 AGGCCTGAAAGAAATACAGAAAAATGT 59.984 33.333 3.11 0.00 34.07 2.71
66 67 4.177026 ACTTCTCACTGAACGCATATCAC 58.823 43.478 0.00 0.00 0.00 3.06
75 76 5.305585 TGGGAATGTTACTTCTCACTGAAC 58.694 41.667 0.00 0.00 30.67 3.18
83 84 7.177878 ACATCATCTTTGGGAATGTTACTTCT 58.822 34.615 0.00 0.00 0.00 2.85
89 90 5.336690 CCGAAACATCATCTTTGGGAATGTT 60.337 40.000 0.00 0.00 30.15 2.71
95 96 1.134946 GGCCGAAACATCATCTTTGGG 59.865 52.381 0.00 0.00 31.46 4.12
110 111 1.379977 ATTCGAGAGACTGGGCCGA 60.380 57.895 0.00 0.00 41.84 5.54
113 114 3.181475 TGAATACATTCGAGAGACTGGGC 60.181 47.826 0.00 0.00 44.16 5.36
115 116 5.464722 CCAATGAATACATTCGAGAGACTGG 59.535 44.000 0.00 0.00 44.16 4.00
126 127 5.590259 GCACACTCTACCCAATGAATACATT 59.410 40.000 0.00 0.00 46.10 2.71
129 130 3.555956 CGCACACTCTACCCAATGAATAC 59.444 47.826 0.00 0.00 0.00 1.89
130 131 3.196901 ACGCACACTCTACCCAATGAATA 59.803 43.478 0.00 0.00 0.00 1.75
131 132 2.027192 ACGCACACTCTACCCAATGAAT 60.027 45.455 0.00 0.00 0.00 2.57
132 133 1.346395 ACGCACACTCTACCCAATGAA 59.654 47.619 0.00 0.00 0.00 2.57
133 134 0.973632 ACGCACACTCTACCCAATGA 59.026 50.000 0.00 0.00 0.00 2.57
137 138 2.342279 GCACGCACACTCTACCCA 59.658 61.111 0.00 0.00 0.00 4.51
166 167 8.810041 TCATACATATGCATCTACACTCATCTT 58.190 33.333 0.19 0.00 33.76 2.40
179 180 9.813446 CAGACACATATACTCATACATATGCAT 57.187 33.333 3.79 3.79 38.25 3.96
226 228 6.467194 CCCACCTGGCTGATAATATCCTTTAA 60.467 42.308 0.00 0.00 0.00 1.52
231 233 2.644798 ACCCACCTGGCTGATAATATCC 59.355 50.000 0.00 0.00 37.83 2.59
243 245 3.356290 CCTTTGATCTTTACCCACCTGG 58.644 50.000 0.00 0.00 41.37 4.45
246 248 2.492088 GTGCCTTTGATCTTTACCCACC 59.508 50.000 0.00 0.00 0.00 4.61
247 249 2.492088 GGTGCCTTTGATCTTTACCCAC 59.508 50.000 0.00 0.00 0.00 4.61
251 253 4.846779 TTGTGGTGCCTTTGATCTTTAC 57.153 40.909 0.00 0.00 0.00 2.01
255 257 3.565307 TCTTTTGTGGTGCCTTTGATCT 58.435 40.909 0.00 0.00 0.00 2.75
257 259 4.344679 TCATTCTTTTGTGGTGCCTTTGAT 59.655 37.500 0.00 0.00 0.00 2.57
267 270 4.670896 AAGGTTGGTCATTCTTTTGTGG 57.329 40.909 0.00 0.00 0.00 4.17
317 321 6.428159 GGAGGCGATCACATGATTAATAAAGT 59.572 38.462 0.00 0.00 34.37 2.66
322 326 4.067896 GTGGAGGCGATCACATGATTAAT 58.932 43.478 0.00 0.00 34.37 1.40
376 380 5.333299 ACGGATGTGTATGCACTACTTTA 57.667 39.130 15.25 0.00 45.44 1.85
413 417 3.322369 TCATGTCACACGTGTGGTTATC 58.678 45.455 39.88 26.13 45.65 1.75
418 422 1.581934 ACTTCATGTCACACGTGTGG 58.418 50.000 39.88 27.09 45.65 4.17
429 436 2.901249 CGGAACCGGATTACTTCATGT 58.099 47.619 9.46 0.00 35.56 3.21
489 496 5.023452 AGTTTCAGTTCTTTTGGGGTTTCT 58.977 37.500 0.00 0.00 0.00 2.52
490 497 5.339008 AGTTTCAGTTCTTTTGGGGTTTC 57.661 39.130 0.00 0.00 0.00 2.78
491 498 5.012664 ACAAGTTTCAGTTCTTTTGGGGTTT 59.987 36.000 0.00 0.00 0.00 3.27
492 499 4.530553 ACAAGTTTCAGTTCTTTTGGGGTT 59.469 37.500 0.00 0.00 0.00 4.11
493 500 4.093743 ACAAGTTTCAGTTCTTTTGGGGT 58.906 39.130 0.00 0.00 0.00 4.95
494 501 4.159506 TGACAAGTTTCAGTTCTTTTGGGG 59.840 41.667 0.00 0.00 0.00 4.96
495 502 5.323371 TGACAAGTTTCAGTTCTTTTGGG 57.677 39.130 0.00 0.00 0.00 4.12
496 503 5.979517 GGATGACAAGTTTCAGTTCTTTTGG 59.020 40.000 0.00 0.00 0.00 3.28
497 504 6.563422 TGGATGACAAGTTTCAGTTCTTTTG 58.437 36.000 0.00 0.00 0.00 2.44
498 505 6.773976 TGGATGACAAGTTTCAGTTCTTTT 57.226 33.333 0.00 0.00 0.00 2.27
499 506 6.773976 TTGGATGACAAGTTTCAGTTCTTT 57.226 33.333 0.00 0.00 33.18 2.52
500 507 6.773976 TTTGGATGACAAGTTTCAGTTCTT 57.226 33.333 0.00 0.00 40.82 2.52
501 508 6.547141 TGATTTGGATGACAAGTTTCAGTTCT 59.453 34.615 0.00 0.00 40.82 3.01
502 509 6.738114 TGATTTGGATGACAAGTTTCAGTTC 58.262 36.000 0.00 0.00 40.82 3.01
515 522 3.368635 GCATGGCAACTTGATTTGGATGA 60.369 43.478 0.00 0.00 44.16 2.92
524 531 2.030371 TTGTCAAGCATGGCAACTTGA 58.970 42.857 24.28 24.28 45.79 3.02
525 532 2.512485 TTGTCAAGCATGGCAACTTG 57.488 45.000 21.31 21.31 45.79 3.16
592 601 2.617774 GGCACAAACACATGGCAATTTT 59.382 40.909 0.00 0.00 40.91 1.82
593 602 2.220313 GGCACAAACACATGGCAATTT 58.780 42.857 0.00 0.00 40.91 1.82
613 622 1.003972 CTGTTAAGTGCCACACGTGTG 60.004 52.381 36.13 36.13 45.23 3.82
630 639 7.699878 AGGGAGTAACAAAAATAGAATCCTGT 58.300 34.615 0.00 0.00 0.00 4.00
633 642 8.575649 TGAAGGGAGTAACAAAAATAGAATCC 57.424 34.615 0.00 0.00 0.00 3.01
706 859 9.939802 CTGTTAGTACTACCCTTGTATTTTCTT 57.060 33.333 0.91 0.00 0.00 2.52
707 860 9.097946 ACTGTTAGTACTACCCTTGTATTTTCT 57.902 33.333 0.91 0.00 0.00 2.52
708 861 9.363763 GACTGTTAGTACTACCCTTGTATTTTC 57.636 37.037 0.91 0.00 0.00 2.29
709 862 8.873144 TGACTGTTAGTACTACCCTTGTATTTT 58.127 33.333 0.91 0.00 0.00 1.82
710 863 8.426569 TGACTGTTAGTACTACCCTTGTATTT 57.573 34.615 0.91 0.00 0.00 1.40
711 864 8.426569 TTGACTGTTAGTACTACCCTTGTATT 57.573 34.615 0.91 0.00 0.00 1.89
712 865 7.673082 ACTTGACTGTTAGTACTACCCTTGTAT 59.327 37.037 0.91 0.00 0.00 2.29
713 866 7.006509 ACTTGACTGTTAGTACTACCCTTGTA 58.993 38.462 0.91 0.00 0.00 2.41
714 867 5.837438 ACTTGACTGTTAGTACTACCCTTGT 59.163 40.000 0.91 0.00 0.00 3.16
715 868 6.342338 ACTTGACTGTTAGTACTACCCTTG 57.658 41.667 0.91 0.00 0.00 3.61
716 869 9.933240 ATATACTTGACTGTTAGTACTACCCTT 57.067 33.333 0.91 0.00 30.24 3.95
735 888 7.658261 TGCAAAGTGAGCGATAGTATATACTT 58.342 34.615 20.21 8.68 34.69 2.24
795 1191 2.699954 ACGCCGACAATTTGAGATCTT 58.300 42.857 2.79 0.00 0.00 2.40
798 1194 3.915437 AAAACGCCGACAATTTGAGAT 57.085 38.095 2.79 0.00 0.00 2.75
822 1218 3.372954 CCGACAATTTACCACGCAAAAA 58.627 40.909 0.00 0.00 0.00 1.94
823 1219 2.859032 GCCGACAATTTACCACGCAAAA 60.859 45.455 0.00 0.00 0.00 2.44
824 1220 1.335142 GCCGACAATTTACCACGCAAA 60.335 47.619 0.00 0.00 0.00 3.68
825 1221 0.238817 GCCGACAATTTACCACGCAA 59.761 50.000 0.00 0.00 0.00 4.85
826 1222 1.870383 GCCGACAATTTACCACGCA 59.130 52.632 0.00 0.00 0.00 5.24
827 1223 1.225908 CGCCGACAATTTACCACGC 60.226 57.895 0.00 0.00 0.00 5.34
828 1224 0.513820 AACGCCGACAATTTACCACG 59.486 50.000 0.00 0.00 0.00 4.94
829 1225 1.532007 TCAACGCCGACAATTTACCAC 59.468 47.619 0.00 0.00 0.00 4.16
830 1226 1.532007 GTCAACGCCGACAATTTACCA 59.468 47.619 0.00 0.00 35.88 3.25
831 1227 1.802365 AGTCAACGCCGACAATTTACC 59.198 47.619 7.48 0.00 38.43 2.85
832 1228 2.159747 GGAGTCAACGCCGACAATTTAC 60.160 50.000 7.48 0.00 38.43 2.01
833 1229 2.070783 GGAGTCAACGCCGACAATTTA 58.929 47.619 7.48 0.00 38.43 1.40
834 1230 0.872388 GGAGTCAACGCCGACAATTT 59.128 50.000 7.48 0.00 38.43 1.82
835 1231 0.034896 AGGAGTCAACGCCGACAATT 59.965 50.000 7.48 0.00 40.98 2.32
841 1237 0.661020 AAAACAAGGAGTCAACGCCG 59.339 50.000 0.00 0.00 40.98 6.46
993 1424 1.322538 GCATTCCTCCCATTTGGCGT 61.323 55.000 0.00 0.00 0.00 5.68
1105 1542 5.247110 TGGTATATGAGAGGAAAGATGGAGC 59.753 44.000 0.00 0.00 0.00 4.70
1164 1607 2.445654 GGGAGAGGAGGAGGGCTG 60.446 72.222 0.00 0.00 0.00 4.85
1174 1620 0.980231 CCTTGAGGAGGTGGGAGAGG 60.980 65.000 0.00 0.00 40.95 3.69
1175 1621 2.601664 CCTTGAGGAGGTGGGAGAG 58.398 63.158 0.00 0.00 40.95 3.20
1176 1622 4.896979 CCTTGAGGAGGTGGGAGA 57.103 61.111 0.00 0.00 40.95 3.71
1424 1904 3.935133 CGTTGATGACGCACTTCTG 57.065 52.632 0.00 0.00 45.86 3.02
1537 2017 1.075659 GAAAGCCAGGACCTTGCCT 59.924 57.895 13.81 0.00 39.37 4.75
1544 2024 3.119096 GCCGACGAAAGCCAGGAC 61.119 66.667 0.00 0.00 0.00 3.85
1603 2083 3.733960 CGCGACACCGTGGAGAGA 61.734 66.667 0.00 0.00 42.13 3.10
2442 2937 7.306205 CAATCTTTGCCTCAGTTTTGAAAAA 57.694 32.000 0.00 0.00 31.69 1.94
2443 2938 6.907206 CAATCTTTGCCTCAGTTTTGAAAA 57.093 33.333 0.00 0.00 31.69 2.29
2458 2953 9.956720 CTTATTTAATAGGTGAGGCAATCTTTG 57.043 33.333 0.00 0.00 0.00 2.77
2459 2954 8.633561 GCTTATTTAATAGGTGAGGCAATCTTT 58.366 33.333 0.00 0.00 0.00 2.52
2460 2955 7.779798 TGCTTATTTAATAGGTGAGGCAATCTT 59.220 33.333 0.00 0.00 0.00 2.40
2461 2956 7.290061 TGCTTATTTAATAGGTGAGGCAATCT 58.710 34.615 0.00 0.00 0.00 2.40
2462 2957 7.445402 TCTGCTTATTTAATAGGTGAGGCAATC 59.555 37.037 0.00 0.00 0.00 2.67
2463 2958 7.290061 TCTGCTTATTTAATAGGTGAGGCAAT 58.710 34.615 0.00 0.00 0.00 3.56
2464 2959 6.658849 TCTGCTTATTTAATAGGTGAGGCAA 58.341 36.000 0.00 0.00 0.00 4.52
2465 2960 6.247229 TCTGCTTATTTAATAGGTGAGGCA 57.753 37.500 0.00 0.00 0.00 4.75
2466 2961 6.992715 TCTTCTGCTTATTTAATAGGTGAGGC 59.007 38.462 0.00 0.00 0.00 4.70
2467 2962 8.424918 TCTCTTCTGCTTATTTAATAGGTGAGG 58.575 37.037 0.00 0.00 0.00 3.86
2468 2963 9.823647 TTCTCTTCTGCTTATTTAATAGGTGAG 57.176 33.333 0.00 0.00 0.00 3.51
2475 2970 9.466497 TGGACAATTCTCTTCTGCTTATTTAAT 57.534 29.630 0.00 0.00 0.00 1.40
2476 2971 8.862325 TGGACAATTCTCTTCTGCTTATTTAA 57.138 30.769 0.00 0.00 0.00 1.52
2477 2972 8.103305 ACTGGACAATTCTCTTCTGCTTATTTA 58.897 33.333 0.00 0.00 0.00 1.40
2478 2973 6.944862 ACTGGACAATTCTCTTCTGCTTATTT 59.055 34.615 0.00 0.00 0.00 1.40
2479 2974 6.479884 ACTGGACAATTCTCTTCTGCTTATT 58.520 36.000 0.00 0.00 0.00 1.40
2480 2975 6.059787 ACTGGACAATTCTCTTCTGCTTAT 57.940 37.500 0.00 0.00 0.00 1.73
2481 2976 5.489792 ACTGGACAATTCTCTTCTGCTTA 57.510 39.130 0.00 0.00 0.00 3.09
2482 2977 4.363991 ACTGGACAATTCTCTTCTGCTT 57.636 40.909 0.00 0.00 0.00 3.91
2483 2978 4.363991 AACTGGACAATTCTCTTCTGCT 57.636 40.909 0.00 0.00 0.00 4.24
2484 2979 6.749923 ATTAACTGGACAATTCTCTTCTGC 57.250 37.500 0.00 0.00 0.00 4.26
2485 2980 9.219603 TGTAATTAACTGGACAATTCTCTTCTG 57.780 33.333 0.00 0.00 0.00 3.02
2486 2981 9.793259 TTGTAATTAACTGGACAATTCTCTTCT 57.207 29.630 0.00 0.00 0.00 2.85
2512 3007 5.725362 TGTTCCGGTTTTTGTCTGATTTTT 58.275 33.333 0.00 0.00 0.00 1.94
2513 3008 5.331876 TGTTCCGGTTTTTGTCTGATTTT 57.668 34.783 0.00 0.00 0.00 1.82
2514 3009 4.993029 TGTTCCGGTTTTTGTCTGATTT 57.007 36.364 0.00 0.00 0.00 2.17
2515 3010 4.158764 TGTTGTTCCGGTTTTTGTCTGATT 59.841 37.500 0.00 0.00 0.00 2.57
2516 3011 3.697045 TGTTGTTCCGGTTTTTGTCTGAT 59.303 39.130 0.00 0.00 0.00 2.90
2517 3012 3.082548 TGTTGTTCCGGTTTTTGTCTGA 58.917 40.909 0.00 0.00 0.00 3.27
2518 3013 3.495670 TGTTGTTCCGGTTTTTGTCTG 57.504 42.857 0.00 0.00 0.00 3.51
2519 3014 4.218852 TCTTTGTTGTTCCGGTTTTTGTCT 59.781 37.500 0.00 0.00 0.00 3.41
2520 3015 4.325204 GTCTTTGTTGTTCCGGTTTTTGTC 59.675 41.667 0.00 0.00 0.00 3.18
2521 3016 4.239304 GTCTTTGTTGTTCCGGTTTTTGT 58.761 39.130 0.00 0.00 0.00 2.83
2522 3017 3.615056 GGTCTTTGTTGTTCCGGTTTTTG 59.385 43.478 0.00 0.00 0.00 2.44
2523 3018 3.258622 TGGTCTTTGTTGTTCCGGTTTTT 59.741 39.130 0.00 0.00 0.00 1.94
2524 3019 2.826725 TGGTCTTTGTTGTTCCGGTTTT 59.173 40.909 0.00 0.00 0.00 2.43
2525 3020 2.448453 TGGTCTTTGTTGTTCCGGTTT 58.552 42.857 0.00 0.00 0.00 3.27
2526 3021 2.131776 TGGTCTTTGTTGTTCCGGTT 57.868 45.000 0.00 0.00 0.00 4.44
2527 3022 2.021457 CTTGGTCTTTGTTGTTCCGGT 58.979 47.619 0.00 0.00 0.00 5.28
2528 3023 1.269051 GCTTGGTCTTTGTTGTTCCGG 60.269 52.381 0.00 0.00 0.00 5.14
2529 3024 1.269051 GGCTTGGTCTTTGTTGTTCCG 60.269 52.381 0.00 0.00 0.00 4.30
2530 3025 1.068588 GGGCTTGGTCTTTGTTGTTCC 59.931 52.381 0.00 0.00 0.00 3.62
2531 3026 1.754226 TGGGCTTGGTCTTTGTTGTTC 59.246 47.619 0.00 0.00 0.00 3.18
2532 3027 1.480545 GTGGGCTTGGTCTTTGTTGTT 59.519 47.619 0.00 0.00 0.00 2.83
2533 3028 1.111277 GTGGGCTTGGTCTTTGTTGT 58.889 50.000 0.00 0.00 0.00 3.32
2534 3029 1.338020 GAGTGGGCTTGGTCTTTGTTG 59.662 52.381 0.00 0.00 0.00 3.33
2535 3030 1.692411 GAGTGGGCTTGGTCTTTGTT 58.308 50.000 0.00 0.00 0.00 2.83
2536 3031 0.178990 GGAGTGGGCTTGGTCTTTGT 60.179 55.000 0.00 0.00 0.00 2.83
2537 3032 0.895559 GGGAGTGGGCTTGGTCTTTG 60.896 60.000 0.00 0.00 0.00 2.77
2538 3033 1.360393 TGGGAGTGGGCTTGGTCTTT 61.360 55.000 0.00 0.00 0.00 2.52
2539 3034 1.142688 ATGGGAGTGGGCTTGGTCTT 61.143 55.000 0.00 0.00 0.00 3.01
2540 3035 0.253160 TATGGGAGTGGGCTTGGTCT 60.253 55.000 0.00 0.00 0.00 3.85
2541 3036 0.181350 CTATGGGAGTGGGCTTGGTC 59.819 60.000 0.00 0.00 0.00 4.02
2542 3037 0.253160 TCTATGGGAGTGGGCTTGGT 60.253 55.000 0.00 0.00 0.00 3.67
2543 3038 0.181350 GTCTATGGGAGTGGGCTTGG 59.819 60.000 0.00 0.00 0.00 3.61
2544 3039 1.134280 CAGTCTATGGGAGTGGGCTTG 60.134 57.143 0.00 0.00 40.65 4.01
2545 3040 1.207791 CAGTCTATGGGAGTGGGCTT 58.792 55.000 0.00 0.00 40.65 4.35
2546 3041 0.339859 TCAGTCTATGGGAGTGGGCT 59.660 55.000 0.00 0.00 43.58 5.19
2547 3042 1.204146 TTCAGTCTATGGGAGTGGGC 58.796 55.000 0.00 0.00 43.58 5.36
2548 3043 2.571653 TGTTTCAGTCTATGGGAGTGGG 59.428 50.000 0.00 0.00 43.58 4.61
2549 3044 3.600388 GTGTTTCAGTCTATGGGAGTGG 58.400 50.000 0.00 0.00 43.58 4.00
2550 3045 3.600388 GGTGTTTCAGTCTATGGGAGTG 58.400 50.000 0.00 0.00 44.47 3.51
2551 3046 2.572104 GGGTGTTTCAGTCTATGGGAGT 59.428 50.000 0.00 0.00 0.00 3.85
2552 3047 2.418746 CGGGTGTTTCAGTCTATGGGAG 60.419 54.545 0.00 0.00 0.00 4.30
2553 3048 1.553248 CGGGTGTTTCAGTCTATGGGA 59.447 52.381 0.00 0.00 0.00 4.37
2554 3049 1.406887 CCGGGTGTTTCAGTCTATGGG 60.407 57.143 0.00 0.00 0.00 4.00
2555 3050 1.406887 CCCGGGTGTTTCAGTCTATGG 60.407 57.143 14.18 0.00 0.00 2.74
2556 3051 1.553248 TCCCGGGTGTTTCAGTCTATG 59.447 52.381 22.86 0.00 0.00 2.23
2557 3052 1.553704 GTCCCGGGTGTTTCAGTCTAT 59.446 52.381 22.86 0.00 0.00 1.98
2558 3053 0.971386 GTCCCGGGTGTTTCAGTCTA 59.029 55.000 22.86 0.00 0.00 2.59
2559 3054 1.052124 TGTCCCGGGTGTTTCAGTCT 61.052 55.000 22.86 0.00 0.00 3.24
2560 3055 0.179040 TTGTCCCGGGTGTTTCAGTC 60.179 55.000 22.86 1.83 0.00 3.51
2561 3056 0.256464 TTTGTCCCGGGTGTTTCAGT 59.744 50.000 22.86 0.00 0.00 3.41
2562 3057 0.666374 GTTTGTCCCGGGTGTTTCAG 59.334 55.000 22.86 0.00 0.00 3.02
2563 3058 0.256464 AGTTTGTCCCGGGTGTTTCA 59.744 50.000 22.86 10.40 0.00 2.69
2564 3059 0.949397 GAGTTTGTCCCGGGTGTTTC 59.051 55.000 22.86 9.88 0.00 2.78
2565 3060 0.466739 GGAGTTTGTCCCGGGTGTTT 60.467 55.000 22.86 2.22 39.88 2.83
2566 3061 1.149854 GGAGTTTGTCCCGGGTGTT 59.850 57.895 22.86 1.01 39.88 3.32
2567 3062 2.833957 GGAGTTTGTCCCGGGTGT 59.166 61.111 22.86 0.00 39.88 4.16
2599 3094 0.104120 GCTTTGCCCCGAGTGTTTTT 59.896 50.000 0.00 0.00 0.00 1.94
2600 3095 1.739667 GCTTTGCCCCGAGTGTTTT 59.260 52.632 0.00 0.00 0.00 2.43
2601 3096 2.200337 GGCTTTGCCCCGAGTGTTT 61.200 57.895 0.00 0.00 44.06 2.83
2602 3097 2.597510 GGCTTTGCCCCGAGTGTT 60.598 61.111 0.00 0.00 44.06 3.32
2612 3107 2.017049 CATACTAGGTGTGGGCTTTGC 58.983 52.381 0.00 0.00 0.00 3.68
2613 3108 3.627395 TCATACTAGGTGTGGGCTTTG 57.373 47.619 0.00 0.00 0.00 2.77
2614 3109 3.618997 CGTTCATACTAGGTGTGGGCTTT 60.619 47.826 0.00 0.00 0.00 3.51
2615 3110 2.093658 CGTTCATACTAGGTGTGGGCTT 60.094 50.000 0.00 0.00 0.00 4.35
2616 3111 1.480954 CGTTCATACTAGGTGTGGGCT 59.519 52.381 0.00 0.00 0.00 5.19
2617 3112 1.479323 TCGTTCATACTAGGTGTGGGC 59.521 52.381 0.00 0.00 0.00 5.36
2618 3113 3.383505 TCATCGTTCATACTAGGTGTGGG 59.616 47.826 0.00 0.00 0.00 4.61
2619 3114 4.499865 CCTCATCGTTCATACTAGGTGTGG 60.500 50.000 0.00 0.00 0.00 4.17
2620 3115 4.098044 ACCTCATCGTTCATACTAGGTGTG 59.902 45.833 0.00 0.00 34.64 3.82
2621 3116 4.279145 ACCTCATCGTTCATACTAGGTGT 58.721 43.478 0.00 0.00 34.64 4.16
2622 3117 4.920640 ACCTCATCGTTCATACTAGGTG 57.079 45.455 0.00 0.00 34.64 4.00
2623 3118 5.692928 AGTACCTCATCGTTCATACTAGGT 58.307 41.667 0.00 0.00 39.19 3.08
2624 3119 6.039493 ACAAGTACCTCATCGTTCATACTAGG 59.961 42.308 0.00 0.00 0.00 3.02
2625 3120 6.913132 CACAAGTACCTCATCGTTCATACTAG 59.087 42.308 0.00 0.00 0.00 2.57
2633 3128 1.346395 TGGCACAAGTACCTCATCGTT 59.654 47.619 0.00 0.00 31.92 3.85
2812 3341 2.421529 GGATAAGATGAAAGCGGTGGGT 60.422 50.000 0.00 0.00 0.00 4.51
3002 3534 2.286121 TCACCCCCTCCCATGGAC 60.286 66.667 15.22 0.00 0.00 4.02
3088 3625 4.035091 GTGTGTGAGCAACATGTACTTGAA 59.965 41.667 15.13 0.00 41.97 2.69
3100 3637 2.661537 CCGAGCGTGTGTGAGCAA 60.662 61.111 0.00 0.00 35.48 3.91
3282 3839 0.257039 GTTCCAGCATCAGGGGACAT 59.743 55.000 0.00 0.00 0.00 3.06
3334 3892 4.082125 CAAAAATAGAGGCTGGTTCCAGT 58.918 43.478 18.42 1.55 36.52 4.00
3348 3906 4.766404 AAGACGGTTCCAGCAAAAATAG 57.234 40.909 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.