Multiple sequence alignment - TraesCS5B01G350000

Loading Multiple Alignment...

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 TraesCS5B01G350000 chr5B 100.000 5102 0 0 1 5102 531149572 531154673 0.000000e+00 9422.0
1 TraesCS5B01G350000 chr5B 92.149 242 15 4 2955 3194 531152481 531152720 6.330000e-89 339.0
2 TraesCS5B01G350000 chr5B 92.149 242 15 4 2910 3149 531152526 531152765 6.330000e-89 339.0
3 TraesCS5B01G350000 chr5B 77.812 320 52 11 1148 1455 364974126 364973814 4.060000e-41 180.0
4 TraesCS5B01G350000 chr5B 89.286 84 8 1 8 90 474466626 474466709 2.510000e-18 104.0
5 TraesCS5B01G350000 chr5D 94.649 3345 128 18 1249 4551 436948959 436952294 0.000000e+00 5138.0
6 TraesCS5B01G350000 chr5D 86.122 490 44 15 334 819 436947900 436948369 1.640000e-139 507.0
7 TraesCS5B01G350000 chr5D 97.585 207 5 0 864 1070 436948367 436948573 6.280000e-94 355.0
8 TraesCS5B01G350000 chr5D 92.531 241 16 2 2955 3194 436950642 436950881 1.360000e-90 344.0
9 TraesCS5B01G350000 chr5D 86.469 303 38 3 4799 5101 436953174 436953473 3.810000e-86 329.0
10 TraesCS5B01G350000 chr5D 90.871 241 20 2 2910 3149 436950687 436950926 6.370000e-84 322.0
11 TraesCS5B01G350000 chr5D 92.857 84 5 1 8 90 443258116 443258199 2.500000e-23 121.0
12 TraesCS5B01G350000 chr5A 91.915 1645 126 5 2910 4551 552161204 552162844 0.000000e+00 2294.0
13 TraesCS5B01G350000 chr5A 92.208 1309 92 8 1894 3194 552160137 552161443 0.000000e+00 1844.0
14 TraesCS5B01G350000 chr5A 85.783 837 83 19 1 819 552156459 552157277 0.000000e+00 854.0
15 TraesCS5B01G350000 chr5A 89.748 556 48 7 4551 5101 552162888 552163439 0.000000e+00 702.0
16 TraesCS5B01G350000 chr5A 90.575 435 26 4 915 1335 552157287 552157720 3.450000e-156 562.0
17 TraesCS5B01G350000 chr5A 91.185 363 26 5 1517 1877 552159796 552160154 5.940000e-134 488.0
18 TraesCS5B01G350000 chr5A 91.949 236 19 0 2914 3149 552161253 552161488 1.060000e-86 331.0
19 TraesCS5B01G350000 chr5A 90.295 237 23 0 2958 3194 552161162 552161398 1.380000e-80 311.0
20 TraesCS5B01G350000 chr5A 95.283 106 5 0 1356 1461 552159472 552159577 8.790000e-38 169.0
21 TraesCS5B01G350000 chr7D 79.632 761 139 13 3309 4060 619993595 619994348 2.700000e-147 532.0
22 TraesCS5B01G350000 chr7D 85.417 144 17 2 4401 4543 34756878 34757018 4.120000e-31 147.0
23 TraesCS5B01G350000 chr7B 79.245 742 135 16 3329 4060 716539286 716538554 2.740000e-137 499.0
24 TraesCS5B01G350000 chr7B 79.051 253 46 5 2486 2733 716595399 716595149 3.160000e-37 167.0
25 TraesCS5B01G350000 chr7B 95.238 42 2 0 814 855 53250574 53250615 3.300000e-07 67.6
26 TraesCS5B01G350000 chr2B 79.421 311 47 11 1148 1455 120177926 120178222 2.410000e-48 204.0
27 TraesCS5B01G350000 chr1B 78.457 311 49 12 1148 1455 113650595 113650300 2.430000e-43 187.0
28 TraesCS5B01G350000 chr1B 86.066 122 13 2 4404 4524 156850560 156850442 1.490000e-25 128.0
29 TraesCS5B01G350000 chr6A 86.620 142 13 3 4410 4549 430338887 430338750 8.850000e-33 152.0
30 TraesCS5B01G350000 chr6A 87.952 83 9 1 8 89 613108043 613107961 4.200000e-16 97.1
31 TraesCS5B01G350000 chr1A 84.722 144 20 2 4401 4543 91162191 91162333 5.320000e-30 143.0
32 TraesCS5B01G350000 chr1A 89.412 85 6 3 8 91 460934490 460934572 2.510000e-18 104.0
33 TraesCS5B01G350000 chr4A 85.106 141 16 2 4404 4543 690411426 690411290 6.890000e-29 139.0
34 TraesCS5B01G350000 chr4A 90.000 50 4 1 801 849 210167630 210167679 4.260000e-06 63.9
35 TraesCS5B01G350000 chr1D 86.154 130 12 3 4404 4532 289395155 289395031 8.910000e-28 135.0
36 TraesCS5B01G350000 chr1D 86.400 125 13 2 4401 4524 95869016 95869137 3.200000e-27 134.0
37 TraesCS5B01G350000 chr2D 85.156 128 15 2 4401 4527 302250103 302250227 1.490000e-25 128.0
38 TraesCS5B01G350000 chr2D 93.023 86 5 1 8 92 290738959 290739044 1.930000e-24 124.0
39 TraesCS5B01G350000 chr2A 90.698 86 5 2 8 92 315038066 315037983 1.500000e-20 111.0
40 TraesCS5B01G350000 chr2A 94.203 69 3 1 8 75 724414346 724414414 2.510000e-18 104.0
41 TraesCS5B01G350000 chr3D 92.857 70 4 1 8 76 135385394 135385463 3.250000e-17 100.0
42 TraesCS5B01G350000 chr7A 95.349 43 2 0 813 855 37273055 37273097 9.170000e-08 69.4
43 TraesCS5B01G350000 chr3B 95.349 43 2 0 814 856 5175531 5175489 9.170000e-08 69.4
44 TraesCS5B01G350000 chr3B 95.238 42 2 0 814 855 3660768 3660809 3.300000e-07 67.6
45 TraesCS5B01G350000 chr4D 97.436 39 1 0 817 855 499510316 499510354 3.300000e-07 67.6
46 TraesCS5B01G350000 chr4D 97.436 39 1 0 817 855 499510402 499510364 3.300000e-07 67.6
47 TraesCS5B01G350000 chr4D 88.889 54 5 1 801 853 275757680 275757627 1.190000e-06 65.8
48 TraesCS5B01G350000 chr4B 88.889 54 5 1 801 853 273246511 273246564 1.190000e-06 65.8


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 TraesCS5B01G350000 chr5B 531149572 531154673 5101 False 3366.666667 9422 94.766000 1 5102 3 chr5B.!!$F2 5101
1 TraesCS5B01G350000 chr5D 436947900 436953473 5573 False 1165.833333 5138 91.371167 334 5101 6 chr5D.!!$F2 4767
2 TraesCS5B01G350000 chr5A 552156459 552163439 6980 False 839.444444 2294 90.993444 1 5101 9 chr5A.!!$F1 5100
3 TraesCS5B01G350000 chr7D 619993595 619994348 753 False 532.000000 532 79.632000 3309 4060 1 chr7D.!!$F2 751
4 TraesCS5B01G350000 chr7B 716538554 716539286 732 True 499.000000 499 79.245000 3329 4060 1 chr7B.!!$R1 731

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
600 618 0.033504 ACAGGCACAGTTACTGTCCG 59.966 55.000 15.79 15.77 43.43 4.79 F
867 890 0.034767 TCGACACGGAGGGAGTACAT 60.035 55.000 0.00 0.00 0.00 2.29 F
1774 3912 0.106708 TCCATCTCAATACGCAGCCC 59.893 55.000 0.00 0.00 0.00 5.19 F
2874 5021 3.454447 TCTTCGTGTCATATGGGTTGGAT 59.546 43.478 2.13 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1885 4025 1.946768 CCTCTTGCAAAGTCCGTTTCA 59.053 47.619 0.00 0.00 46.34 2.69 R
2770 4917 1.271597 CCTGCCTTCTACCCCATATGC 60.272 57.143 0.00 0.00 0.00 3.14 R
3363 5556 0.179234 TGTTCCCGTGCTTGTGAGAA 59.821 50.000 0.00 0.00 0.00 2.87 R
4460 6671 0.593773 ACATGTTTTGGTGCGTTCGC 60.594 50.000 10.34 10.34 0.00 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
23 24 5.106442 TGTACGGCATAATAAGTGTCACAG 58.894 41.667 5.62 0.00 0.00 3.66
31 32 7.326063 GGCATAATAAGTGTCACAGTTTTGAAC 59.674 37.037 2.42 0.00 0.00 3.18
45 46 8.215132 CACAGTTTTGAACTAAGATCGAACTAC 58.785 37.037 0.00 0.00 40.46 2.73
46 47 7.384387 ACAGTTTTGAACTAAGATCGAACTACC 59.616 37.037 0.00 0.00 40.46 3.18
58 60 8.768957 AAGATCGAACTACCCTTAGTTAAAAC 57.231 34.615 0.00 0.00 46.67 2.43
63 65 5.473066 ACTACCCTTAGTTAAAACTGCGA 57.527 39.130 5.62 0.00 40.07 5.10
75 77 7.699566 AGTTAAAACTGCGACACTTATTTTGA 58.300 30.769 0.00 0.00 37.98 2.69
76 78 8.185505 AGTTAAAACTGCGACACTTATTTTGAA 58.814 29.630 0.00 0.00 37.98 2.69
94 96 5.576563 TTGAATTGGAGGGAGTAGTTCAA 57.423 39.130 0.00 0.00 33.30 2.69
102 104 4.141914 GGAGGGAGTAGTTCAATCGTGATT 60.142 45.833 0.00 0.00 32.48 2.57
132 134 2.108168 ACATGTACGATAGGGTGCAGT 58.892 47.619 0.00 0.00 43.77 4.40
138 140 1.337823 ACGATAGGGTGCAGTGTGTTC 60.338 52.381 0.00 0.00 43.77 3.18
150 152 3.600388 CAGTGTGTTCCAGATCCTAACC 58.400 50.000 0.00 0.00 0.00 2.85
153 155 0.539986 TGTTCCAGATCCTAACCGGC 59.460 55.000 0.00 0.00 0.00 6.13
172 174 0.383949 CCCGGGTTTGCAATATTCCG 59.616 55.000 14.18 17.56 37.50 4.30
174 176 1.202245 CCGGGTTTGCAATATTCCGTG 60.202 52.381 20.62 12.80 36.19 4.94
175 177 1.470890 CGGGTTTGCAATATTCCGTGT 59.529 47.619 16.75 0.00 33.63 4.49
176 178 2.094957 CGGGTTTGCAATATTCCGTGTT 60.095 45.455 16.75 0.00 33.63 3.32
177 179 3.612955 CGGGTTTGCAATATTCCGTGTTT 60.613 43.478 16.75 0.00 33.63 2.83
262 266 3.384146 TCAAACAACGGGCGGTATAGATA 59.616 43.478 0.00 0.00 0.00 1.98
292 296 6.005583 TGAGCAGAAAATTGTGTTGAGATC 57.994 37.500 0.00 0.00 0.00 2.75
298 302 5.474876 AGAAAATTGTGTTGAGATCAGGACC 59.525 40.000 0.00 0.00 0.00 4.46
301 305 1.280457 GTGTTGAGATCAGGACCCCT 58.720 55.000 0.00 0.00 0.00 4.79
304 308 3.107601 TGTTGAGATCAGGACCCCTAAG 58.892 50.000 0.00 0.00 29.64 2.18
307 311 4.074799 TGAGATCAGGACCCCTAAGAAA 57.925 45.455 0.00 0.00 29.64 2.52
318 322 5.230323 ACCCCTAAGAAACAGAGTTCTTC 57.770 43.478 3.57 0.00 42.88 2.87
319 323 4.041815 ACCCCTAAGAAACAGAGTTCTTCC 59.958 45.833 3.57 0.00 42.88 3.46
342 347 8.348285 TCCAAGAACAAATAAAATAGACCCAG 57.652 34.615 0.00 0.00 0.00 4.45
352 357 8.469309 AATAAAATAGACCCAGTTGATGATGG 57.531 34.615 0.00 0.00 36.27 3.51
395 400 2.174639 TGTTGTCACCTGGATTTGGTCT 59.825 45.455 0.00 0.00 35.28 3.85
396 401 2.814336 GTTGTCACCTGGATTTGGTCTC 59.186 50.000 0.00 0.00 35.28 3.36
410 422 1.207791 GGTCTCATCACTCATGGGGT 58.792 55.000 0.00 0.00 33.07 4.95
411 423 1.134280 GGTCTCATCACTCATGGGGTG 60.134 57.143 0.00 5.49 33.07 4.61
414 426 0.620030 TCATCACTCATGGGGTGGTG 59.380 55.000 19.71 19.71 44.43 4.17
432 444 3.194968 TGGTGCGGTCTTTTGGTTAAAAA 59.805 39.130 0.00 0.00 35.50 1.94
456 473 9.862149 AAAAGAAGAAGGATAAAACCAGTTCTA 57.138 29.630 0.00 0.00 30.70 2.10
470 487 7.713734 AACCAGTTCTACTATGCTTGTACTA 57.286 36.000 0.00 0.00 0.00 1.82
476 493 7.774157 AGTTCTACTATGCTTGTACTACAGCTA 59.226 37.037 11.84 2.18 0.00 3.32
477 494 7.731882 TCTACTATGCTTGTACTACAGCTAG 57.268 40.000 11.84 11.97 0.00 3.42
487 504 5.651530 TGTACTACAGCTAGTGAATCTTGC 58.348 41.667 0.00 0.00 43.27 4.01
521 538 3.244770 GGAAATGTAACACACTCCCTCCA 60.245 47.826 0.00 0.00 30.84 3.86
539 557 0.109597 CAGTCGGAATTGCAAGGTGC 60.110 55.000 4.94 0.00 45.29 5.01
577 595 5.376625 AGTCAAGATTTTCACCAGCAGTTA 58.623 37.500 0.00 0.00 0.00 2.24
578 596 5.239525 AGTCAAGATTTTCACCAGCAGTTAC 59.760 40.000 0.00 0.00 0.00 2.50
579 597 4.213270 TCAAGATTTTCACCAGCAGTTACG 59.787 41.667 0.00 0.00 0.00 3.18
580 598 3.074412 AGATTTTCACCAGCAGTTACGG 58.926 45.455 0.00 0.00 0.00 4.02
581 599 2.623878 TTTTCACCAGCAGTTACGGA 57.376 45.000 0.00 0.00 0.00 4.69
582 600 1.873698 TTTCACCAGCAGTTACGGAC 58.126 50.000 0.00 0.00 0.00 4.79
583 601 0.753867 TTCACCAGCAGTTACGGACA 59.246 50.000 0.00 0.00 0.00 4.02
586 604 1.741770 CCAGCAGTTACGGACAGGC 60.742 63.158 0.00 0.00 0.00 4.85
600 618 0.033504 ACAGGCACAGTTACTGTCCG 59.966 55.000 15.79 15.77 43.43 4.79
603 621 1.004918 GCACAGTTACTGTCCGCCT 60.005 57.895 15.79 0.00 43.43 5.52
604 622 1.291877 GCACAGTTACTGTCCGCCTG 61.292 60.000 15.79 4.58 43.43 4.85
607 625 0.389948 CAGTTACTGTCCGCCTGTCC 60.390 60.000 3.88 0.00 0.00 4.02
609 627 2.288025 TTACTGTCCGCCTGTCCCC 61.288 63.158 0.00 0.00 0.00 4.81
617 636 4.530857 GCCTGTCCCCCGATCGTG 62.531 72.222 15.09 1.60 0.00 4.35
618 637 4.530857 CCTGTCCCCCGATCGTGC 62.531 72.222 15.09 0.00 0.00 5.34
638 657 3.574396 TGCCACAGCTCTAGTATATCCAC 59.426 47.826 0.00 0.00 40.80 4.02
648 669 9.084533 AGCTCTAGTATATCCACTAAAGAAAGG 57.915 37.037 0.00 0.00 30.77 3.11
657 678 4.100498 TCCACTAAAGAAAGGAACACGAGT 59.900 41.667 0.00 0.00 0.00 4.18
659 680 5.404667 CCACTAAAGAAAGGAACACGAGTAC 59.595 44.000 0.00 0.00 0.00 2.73
698 719 6.812656 TCTTAACTACGAGTTGTTGTGTGAAA 59.187 34.615 12.02 0.00 39.11 2.69
721 742 3.185246 CTGAGTGGTCAGTGTCAAGTT 57.815 47.619 0.00 0.00 44.72 2.66
804 827 6.855763 ATCTTGAATATTCAACCTGGCAAA 57.144 33.333 23.86 3.99 41.88 3.68
819 842 2.093500 TGGCAAATGACGAGCATCTACT 60.093 45.455 0.00 0.00 35.78 2.57
820 843 2.541762 GGCAAATGACGAGCATCTACTC 59.458 50.000 0.00 0.00 35.78 2.59
821 844 2.541762 GCAAATGACGAGCATCTACTCC 59.458 50.000 0.00 0.00 35.78 3.85
822 845 3.126831 CAAATGACGAGCATCTACTCCC 58.873 50.000 0.00 0.00 35.78 4.30
823 846 2.373335 ATGACGAGCATCTACTCCCT 57.627 50.000 0.00 0.00 32.79 4.20
824 847 1.681538 TGACGAGCATCTACTCCCTC 58.318 55.000 0.00 0.00 32.79 4.30
825 848 1.213182 TGACGAGCATCTACTCCCTCT 59.787 52.381 0.00 0.00 32.79 3.69
826 849 1.606668 GACGAGCATCTACTCCCTCTG 59.393 57.143 0.00 0.00 32.79 3.35
827 850 1.064314 ACGAGCATCTACTCCCTCTGT 60.064 52.381 0.00 0.00 32.79 3.41
828 851 1.606668 CGAGCATCTACTCCCTCTGTC 59.393 57.143 0.00 0.00 32.79 3.51
829 852 1.960689 GAGCATCTACTCCCTCTGTCC 59.039 57.143 0.00 0.00 0.00 4.02
830 853 1.044611 GCATCTACTCCCTCTGTCCC 58.955 60.000 0.00 0.00 0.00 4.46
831 854 1.689575 GCATCTACTCCCTCTGTCCCA 60.690 57.143 0.00 0.00 0.00 4.37
832 855 2.969628 CATCTACTCCCTCTGTCCCAT 58.030 52.381 0.00 0.00 0.00 4.00
833 856 3.755483 GCATCTACTCCCTCTGTCCCATA 60.755 52.174 0.00 0.00 0.00 2.74
834 857 4.483950 CATCTACTCCCTCTGTCCCATAA 58.516 47.826 0.00 0.00 0.00 1.90
835 858 4.834406 TCTACTCCCTCTGTCCCATAAT 57.166 45.455 0.00 0.00 0.00 1.28
836 859 4.483950 TCTACTCCCTCTGTCCCATAATG 58.516 47.826 0.00 0.00 0.00 1.90
837 860 3.136641 ACTCCCTCTGTCCCATAATGT 57.863 47.619 0.00 0.00 0.00 2.71
838 861 4.280789 ACTCCCTCTGTCCCATAATGTA 57.719 45.455 0.00 0.00 0.00 2.29
839 862 4.631234 ACTCCCTCTGTCCCATAATGTAA 58.369 43.478 0.00 0.00 0.00 2.41
840 863 4.656112 ACTCCCTCTGTCCCATAATGTAAG 59.344 45.833 0.00 0.00 0.00 2.34
841 864 3.973973 TCCCTCTGTCCCATAATGTAAGG 59.026 47.826 0.00 0.00 0.00 2.69
842 865 3.496870 CCCTCTGTCCCATAATGTAAGGC 60.497 52.174 0.00 0.00 0.00 4.35
843 866 3.393800 CTCTGTCCCATAATGTAAGGCG 58.606 50.000 0.00 0.00 0.00 5.52
844 867 2.769663 TCTGTCCCATAATGTAAGGCGT 59.230 45.455 0.00 0.00 0.00 5.68
845 868 3.199071 TCTGTCCCATAATGTAAGGCGTT 59.801 43.478 0.00 0.00 0.00 4.84
846 869 3.945285 CTGTCCCATAATGTAAGGCGTTT 59.055 43.478 0.00 0.00 0.00 3.60
847 870 4.337145 TGTCCCATAATGTAAGGCGTTTT 58.663 39.130 0.00 0.00 0.00 2.43
848 871 4.767928 TGTCCCATAATGTAAGGCGTTTTT 59.232 37.500 0.00 0.00 0.00 1.94
849 872 5.106078 TGTCCCATAATGTAAGGCGTTTTTC 60.106 40.000 0.00 0.00 0.00 2.29
850 873 4.095185 TCCCATAATGTAAGGCGTTTTTCG 59.905 41.667 0.00 0.00 43.12 3.46
851 874 4.095185 CCCATAATGTAAGGCGTTTTTCGA 59.905 41.667 0.00 0.00 42.86 3.71
858 881 4.792125 GCGTTTTTCGACACGGAG 57.208 55.556 11.69 0.00 42.86 4.63
859 882 1.203313 GCGTTTTTCGACACGGAGG 59.797 57.895 11.69 0.00 42.86 4.30
860 883 1.857364 CGTTTTTCGACACGGAGGG 59.143 57.895 3.57 0.00 42.86 4.30
861 884 0.598158 CGTTTTTCGACACGGAGGGA 60.598 55.000 3.57 0.00 42.86 4.20
862 885 1.145803 GTTTTTCGACACGGAGGGAG 58.854 55.000 0.00 0.00 0.00 4.30
863 886 0.754472 TTTTTCGACACGGAGGGAGT 59.246 50.000 0.00 0.00 0.00 3.85
864 887 1.619654 TTTTCGACACGGAGGGAGTA 58.380 50.000 0.00 0.00 0.00 2.59
865 888 0.883833 TTTCGACACGGAGGGAGTAC 59.116 55.000 0.00 0.00 0.00 2.73
866 889 0.250858 TTCGACACGGAGGGAGTACA 60.251 55.000 0.00 0.00 0.00 2.90
867 890 0.034767 TCGACACGGAGGGAGTACAT 60.035 55.000 0.00 0.00 0.00 2.29
875 898 3.637229 ACGGAGGGAGTACATGATTACTG 59.363 47.826 0.00 0.00 32.17 2.74
905 928 2.014068 GCCGAGCATCTACAAGGCTTT 61.014 52.381 0.00 0.00 41.21 3.51
1083 1106 3.081061 AGATTTGTGTGTGTGTGTGTGT 58.919 40.909 0.00 0.00 0.00 3.72
1085 1108 1.598882 TTGTGTGTGTGTGTGTGTGT 58.401 45.000 0.00 0.00 0.00 3.72
1087 1110 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1089 1112 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1091 1114 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1093 1116 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1095 1118 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1099 1136 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1103 1140 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1107 1144 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1111 1148 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1137 1174 5.929415 TGTGTGTGTGTTACGATCATTATGT 59.071 36.000 0.00 0.00 0.00 2.29
1202 1239 3.277211 TTGGGAGCTTCGTCGACGG 62.277 63.158 35.05 22.18 40.29 4.79
1411 3372 1.134694 GCGCACATTTCCCTCGTTC 59.865 57.895 0.30 0.00 0.00 3.95
1461 3422 3.146066 TGGTTTGCAGTCCATCACTAAC 58.854 45.455 7.68 0.00 32.21 2.34
1464 3425 4.218417 GGTTTGCAGTCCATCACTAACATT 59.782 41.667 4.67 0.00 32.21 2.71
1511 3648 7.309316 GGCTAGTGAATGATACTCCCTTAGTAC 60.309 44.444 0.00 0.00 43.47 2.73
1525 3662 8.554011 ACTCCCTTAGTACAAAAATATAAGGCA 58.446 33.333 8.60 0.00 40.68 4.75
1657 3794 4.836825 AGAAGCATAGTACTTGTGCATGT 58.163 39.130 25.50 15.11 41.19 3.21
1720 3858 9.841295 AAATACAAAAGTCGTATGTATATGGGT 57.159 29.630 0.00 0.00 38.85 4.51
1737 3875 2.496871 TGGGTGTCATCAATCAAATGGC 59.503 45.455 0.00 0.00 0.00 4.40
1741 3879 2.164017 TGTCATCAATCAAATGGCACGG 59.836 45.455 0.00 0.00 33.98 4.94
1745 3883 1.959985 TCAATCAAATGGCACGGTTGT 59.040 42.857 0.00 0.00 0.00 3.32
1774 3912 0.106708 TCCATCTCAATACGCAGCCC 59.893 55.000 0.00 0.00 0.00 5.19
1956 4096 5.509605 AAATTTAAATGGTTTCGAAGCGC 57.490 34.783 0.00 0.00 0.00 5.92
2122 4264 4.083110 GCCCTTTGATTGACATGGATATCG 60.083 45.833 0.00 0.00 0.00 2.92
2135 4277 9.559732 TGACATGGATATCGACAATTATTTTCT 57.440 29.630 0.00 0.00 0.00 2.52
2192 4336 7.546667 GTGAATGAGGAACAATGTATGCATTTT 59.453 33.333 3.54 5.20 42.91 1.82
2193 4337 7.760794 TGAATGAGGAACAATGTATGCATTTTC 59.239 33.333 3.54 12.62 42.91 2.29
2194 4338 6.587206 TGAGGAACAATGTATGCATTTTCA 57.413 33.333 21.03 2.80 42.91 2.69
2237 4381 3.673338 TGTTGTGATTGTCTCGTCGATTC 59.327 43.478 0.00 0.00 0.00 2.52
2271 4415 5.655532 TGTCCTCACCACTATTAACCTACTC 59.344 44.000 0.00 0.00 0.00 2.59
2416 4560 7.996644 ACTATGAAAAACTCAAGTTGGAACCTA 59.003 33.333 2.34 0.00 37.67 3.08
2432 4576 4.445879 GGAACCTACCCATGAGGATAAACC 60.446 50.000 5.96 0.00 39.89 3.27
2505 4649 5.728471 ACACATAGAACAGACATGGAAGAG 58.272 41.667 0.00 0.00 0.00 2.85
2535 4679 7.516198 AAAGGAAATATCAGTGTCATATGGC 57.484 36.000 0.00 0.00 0.00 4.40
2574 4718 7.287696 ACATACTCAAACAAAGTTCTCCCAAAT 59.712 33.333 0.00 0.00 0.00 2.32
2577 4721 6.818142 ACTCAAACAAAGTTCTCCCAAATTTG 59.182 34.615 11.40 11.40 37.00 2.32
2719 4866 7.941919 AGGTGAAAAGGAGTTGAAAGAAATAC 58.058 34.615 0.00 0.00 0.00 1.89
2847 4994 6.918569 GGAAAGAACAAGAAGGAAAGCTAAAC 59.081 38.462 0.00 0.00 0.00 2.01
2855 5002 7.013369 ACAAGAAGGAAAGCTAAACGAAATCTT 59.987 33.333 0.00 0.00 0.00 2.40
2874 5021 3.454447 TCTTCGTGTCATATGGGTTGGAT 59.546 43.478 2.13 0.00 0.00 3.41
2901 5048 7.296628 AGGCAAAGGTGAACACAATAAATTA 57.703 32.000 7.25 0.00 0.00 1.40
2999 5146 5.802465 AGCTACAATGTCATATGGATCTGG 58.198 41.667 2.13 0.00 0.00 3.86
3126 5318 9.224267 GATCCACATAAAGCTACAATGTCATAT 57.776 33.333 5.73 1.72 31.60 1.78
3129 5321 9.494271 CCACATAAAGCTACAATGTCATATAGT 57.506 33.333 5.73 0.26 31.60 2.12
3218 5410 9.567776 TCTAAAGACATTTTTAACAGGACATGA 57.432 29.630 0.00 0.00 0.00 3.07
3363 5556 0.622738 AGGGGAGTCACCATGCTCAT 60.623 55.000 15.52 0.00 41.20 2.90
3395 5588 0.033920 GGGAACAAAAAGCAGGCAGG 59.966 55.000 0.00 0.00 0.00 4.85
3425 5618 3.049674 CCACGACATGTTGCGGCT 61.050 61.111 13.30 0.00 0.00 5.52
3534 5727 3.433319 GAGCGCCTCTCCGACATA 58.567 61.111 2.29 0.00 35.77 2.29
3591 5784 2.147958 AGAGAGATACGATGGACGCTC 58.852 52.381 0.00 0.00 46.94 5.03
3600 5793 0.458543 GATGGACGCTCGACACATGT 60.459 55.000 0.00 0.00 0.00 3.21
3663 5856 0.252467 CCTCCCTTGAGTCCCTCACT 60.252 60.000 0.00 0.00 40.46 3.41
3769 5962 1.739929 CTGCGCGGGATGTACAACA 60.740 57.895 8.83 0.00 0.00 3.33
3774 5967 1.732941 GCGGGATGTACAACATGACA 58.267 50.000 0.00 0.00 39.27 3.58
3783 5976 2.030412 AACATGACAGCCGTGCGA 59.970 55.556 0.00 0.00 35.17 5.10
3870 6066 2.747686 CACACCGCCAACCCTACT 59.252 61.111 0.00 0.00 0.00 2.57
3897 6093 0.759436 ACACGGTCACCCTTGAGAGT 60.759 55.000 0.00 0.00 34.20 3.24
3914 6110 1.896660 GTGTGGATGGTGCAACGGT 60.897 57.895 0.00 0.00 38.12 4.83
4113 6309 0.460311 CCCGTTAGAAGAGGACGCAT 59.540 55.000 0.00 0.00 35.60 4.73
4125 6321 2.969806 GACGCATGTGCACCTGTGG 61.970 63.158 30.56 21.04 42.21 4.17
4126 6322 2.979676 CGCATGTGCACCTGTGGT 60.980 61.111 23.21 0.00 42.21 4.16
4144 6340 1.001974 GGTGTCTGTATGTGTGAGCCA 59.998 52.381 0.00 0.00 0.00 4.75
4187 6383 9.233649 ACATTATGTGGGTAAATCTTCGTAAAA 57.766 29.630 0.00 0.00 0.00 1.52
4219 6415 6.393990 TGGTGTTATGAAATAAATGGTGTGC 58.606 36.000 0.00 0.00 41.12 4.57
4220 6416 6.015095 TGGTGTTATGAAATAAATGGTGTGCA 60.015 34.615 0.00 0.00 41.12 4.57
4227 6425 5.534278 TGAAATAAATGGTGTGCAGAAGTCA 59.466 36.000 0.00 0.00 0.00 3.41
4272 6470 5.793457 GTGAGTAAAATATTTGTGGCGTGTC 59.207 40.000 0.39 0.00 0.00 3.67
4460 6671 4.748892 ACATACGGACTGAAATGAGTGAG 58.251 43.478 7.93 0.00 0.00 3.51
4466 6677 2.061773 ACTGAAATGAGTGAGCGAACG 58.938 47.619 0.00 0.00 0.00 3.95
4468 6679 0.790207 GAAATGAGTGAGCGAACGCA 59.210 50.000 20.66 1.21 44.88 5.24
4551 6762 9.866655 TTTTGAATGCAGGGAGTATATTCTAAT 57.133 29.630 0.00 0.00 0.00 1.73
4561 6818 7.345914 AGGGAGTATATTCTAATATGCCCTGTC 59.654 40.741 20.42 8.99 41.77 3.51
4620 6878 8.821894 GTCTTCACTATATCCAACTTTCATCAC 58.178 37.037 0.00 0.00 0.00 3.06
4714 7395 5.644977 ATTGACTACACATTCTGAGTCGA 57.355 39.130 0.00 0.00 41.02 4.20
4720 7401 1.991264 CACATTCTGAGTCGACTGCAG 59.009 52.381 25.58 25.93 0.00 4.41
4721 7402 1.067283 ACATTCTGAGTCGACTGCAGG 60.067 52.381 28.78 20.83 0.00 4.85
4722 7403 0.108424 ATTCTGAGTCGACTGCAGGC 60.108 55.000 28.78 15.62 0.00 4.85
4737 7418 2.032620 GCAGGCTAGCTTACTAGGACA 58.967 52.381 15.72 0.00 45.25 4.02
4789 7471 5.680594 ATATTTTCCATGCTTCTTGCCAA 57.319 34.783 0.00 0.00 42.00 4.52
4794 7476 2.494471 TCCATGCTTCTTGCCAAATCTG 59.506 45.455 0.00 0.00 42.00 2.90
4803 7650 6.128742 GCTTCTTGCCAAATCTGTTTGTAATG 60.129 38.462 0.88 0.00 42.50 1.90
4807 7654 5.527951 TGCCAAATCTGTTTGTAATGTGTC 58.472 37.500 0.88 0.00 42.50 3.67
4895 7742 4.235939 TGTTCCATGACAAATTTCACCG 57.764 40.909 0.00 0.00 0.00 4.94
4935 7784 1.094785 ATATTGAGTTGGCGTGGTGC 58.905 50.000 0.00 0.00 45.38 5.01
4952 7801 1.301716 GCTTCGTGCTCCTGGTTCA 60.302 57.895 0.00 0.00 38.95 3.18
4959 7808 2.205074 GTGCTCCTGGTTCATCGTATG 58.795 52.381 0.00 0.00 0.00 2.39
4989 7838 1.165270 GTTCGATGTGGGGAAACAGG 58.835 55.000 0.00 0.00 32.52 4.00
4994 7843 0.409092 ATGTGGGGAAACAGGCATCA 59.591 50.000 0.00 0.00 32.52 3.07
5008 7857 4.263462 ACAGGCATCACAACTCCTATTTGA 60.263 41.667 0.00 0.00 0.00 2.69
5011 7860 4.641989 GGCATCACAACTCCTATTTGACAT 59.358 41.667 0.00 0.00 0.00 3.06
5095 7944 2.224670 CCCAAGTAGGCTGGTACAACAA 60.225 50.000 0.00 0.00 32.89 2.83
5101 7950 1.774856 AGGCTGGTACAACAAACTCCT 59.225 47.619 0.00 0.00 38.70 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.545658 AAACTGTGACACTTATTATGCCG 57.454 39.130 7.20 0.00 0.00 5.69
23 24 6.872547 AGGGTAGTTCGATCTTAGTTCAAAAC 59.127 38.462 0.48 0.00 0.00 2.43
45 46 4.062991 AGTGTCGCAGTTTTAACTAAGGG 58.937 43.478 0.00 0.00 37.08 3.95
46 47 5.668558 AAGTGTCGCAGTTTTAACTAAGG 57.331 39.130 0.00 0.00 37.08 2.69
54 55 7.042791 CCAATTCAAAATAAGTGTCGCAGTTTT 60.043 33.333 5.46 0.00 0.00 2.43
58 60 5.698832 TCCAATTCAAAATAAGTGTCGCAG 58.301 37.500 0.00 0.00 0.00 5.18
63 65 6.314917 ACTCCCTCCAATTCAAAATAAGTGT 58.685 36.000 0.00 0.00 0.00 3.55
75 77 4.225267 ACGATTGAACTACTCCCTCCAATT 59.775 41.667 0.00 0.00 0.00 2.32
76 78 3.775316 ACGATTGAACTACTCCCTCCAAT 59.225 43.478 0.00 0.00 0.00 3.16
115 117 1.203758 CACACTGCACCCTATCGTACA 59.796 52.381 0.00 0.00 0.00 2.90
132 134 1.553248 CCGGTTAGGATCTGGAACACA 59.447 52.381 0.00 0.00 45.00 3.72
138 140 2.829592 GGGCCGGTTAGGATCTGG 59.170 66.667 1.90 0.00 45.00 3.86
150 152 1.671901 AATATTGCAAACCCGGGCCG 61.672 55.000 24.08 21.46 0.00 6.13
153 155 0.383949 CGGAATATTGCAAACCCGGG 59.616 55.000 22.25 22.25 33.94 5.73
194 196 2.159627 CACCATGTGGAACTCGCTTTAC 59.840 50.000 5.96 0.00 38.04 2.01
262 266 4.634199 CACAATTTTCTGCTCAATTGGGT 58.366 39.130 7.27 0.00 42.40 4.51
264 268 5.754406 TCAACACAATTTTCTGCTCAATTGG 59.246 36.000 5.42 0.00 42.40 3.16
272 276 5.048504 TCCTGATCTCAACACAATTTTCTGC 60.049 40.000 0.00 0.00 0.00 4.26
273 277 6.376978 GTCCTGATCTCAACACAATTTTCTG 58.623 40.000 0.00 0.00 0.00 3.02
275 279 5.335976 GGGTCCTGATCTCAACACAATTTTC 60.336 44.000 0.00 0.00 0.00 2.29
292 296 2.907042 ACTCTGTTTCTTAGGGGTCCTG 59.093 50.000 0.00 0.00 34.61 3.86
298 302 5.228945 TGGAAGAACTCTGTTTCTTAGGG 57.771 43.478 6.90 0.00 44.27 3.53
318 322 8.122472 ACTGGGTCTATTTTATTTGTTCTTGG 57.878 34.615 0.00 0.00 0.00 3.61
319 323 9.410556 CAACTGGGTCTATTTTATTTGTTCTTG 57.589 33.333 0.00 0.00 0.00 3.02
358 363 1.738908 CAACACGTCCATCATGCATGA 59.261 47.619 30.47 30.47 41.70 3.07
383 388 4.212143 TGAGTGATGAGACCAAATCCAG 57.788 45.455 0.00 0.00 0.00 3.86
385 390 3.881688 CCATGAGTGATGAGACCAAATCC 59.118 47.826 0.00 0.00 33.31 3.01
387 392 3.372349 CCCCATGAGTGATGAGACCAAAT 60.372 47.826 0.00 0.00 33.31 2.32
388 393 2.025981 CCCCATGAGTGATGAGACCAAA 60.026 50.000 0.00 0.00 33.31 3.28
395 400 0.620030 CACCACCCCATGAGTGATGA 59.380 55.000 15.14 0.00 37.42 2.92
396 401 1.033746 GCACCACCCCATGAGTGATG 61.034 60.000 15.14 10.67 37.42 3.07
410 422 2.054232 TTAACCAAAAGACCGCACCA 57.946 45.000 0.00 0.00 0.00 4.17
411 423 3.439895 TTTTAACCAAAAGACCGCACC 57.560 42.857 0.00 0.00 0.00 5.01
432 444 8.661345 AGTAGAACTGGTTTTATCCTTCTTCTT 58.339 33.333 0.00 0.00 0.00 2.52
433 445 8.208575 AGTAGAACTGGTTTTATCCTTCTTCT 57.791 34.615 0.00 0.00 0.00 2.85
456 473 5.886474 TCACTAGCTGTAGTACAAGCATAGT 59.114 40.000 19.92 18.81 37.40 2.12
470 487 4.582869 TGAATGCAAGATTCACTAGCTGT 58.417 39.130 0.00 0.00 33.55 4.40
476 493 3.944015 GGTAGCTGAATGCAAGATTCACT 59.056 43.478 0.00 0.12 45.94 3.41
477 494 3.242543 CGGTAGCTGAATGCAAGATTCAC 60.243 47.826 0.00 0.00 45.94 3.18
487 504 4.634004 TGTTACATTTCCGGTAGCTGAATG 59.366 41.667 0.00 6.61 0.00 2.67
521 538 2.257353 GCACCTTGCAATTCCGACT 58.743 52.632 0.00 0.00 44.26 4.18
539 557 8.574196 AAATCTTGACTTAACCGAACAAAATG 57.426 30.769 0.00 0.00 0.00 2.32
548 566 5.682943 TGGTGAAAATCTTGACTTAACCG 57.317 39.130 0.00 0.00 0.00 4.44
577 595 0.033504 CAGTAACTGTGCCTGTCCGT 59.966 55.000 0.00 0.00 0.00 4.69
578 596 0.033504 ACAGTAACTGTGCCTGTCCG 59.966 55.000 0.00 0.00 43.63 4.79
579 597 1.797025 GACAGTAACTGTGCCTGTCC 58.203 55.000 20.84 9.58 45.44 4.02
586 604 0.033504 ACAGGCGGACAGTAACTGTG 59.966 55.000 0.00 0.00 45.44 3.66
600 618 4.530857 CACGATCGGGGGACAGGC 62.531 72.222 20.98 0.00 0.00 4.85
604 622 4.832608 GTGGCACGATCGGGGGAC 62.833 72.222 20.80 11.03 0.00 4.46
609 627 2.004808 TAGAGCTGTGGCACGATCGG 62.005 60.000 20.98 9.59 41.70 4.18
611 630 0.457851 ACTAGAGCTGTGGCACGATC 59.542 55.000 13.77 15.19 41.70 3.69
612 631 1.763968 TACTAGAGCTGTGGCACGAT 58.236 50.000 13.77 6.54 41.70 3.73
613 632 1.763968 ATACTAGAGCTGTGGCACGA 58.236 50.000 13.77 1.31 41.70 4.35
614 633 3.366476 GGATATACTAGAGCTGTGGCACG 60.366 52.174 13.77 9.03 41.70 5.34
615 634 3.574396 TGGATATACTAGAGCTGTGGCAC 59.426 47.826 11.55 11.55 41.70 5.01
616 635 3.574396 GTGGATATACTAGAGCTGTGGCA 59.426 47.826 0.00 0.00 41.70 4.92
617 636 3.829601 AGTGGATATACTAGAGCTGTGGC 59.170 47.826 0.00 0.00 39.06 5.01
618 637 7.448777 TCTTTAGTGGATATACTAGAGCTGTGG 59.551 40.741 0.00 0.00 36.09 4.17
638 657 4.620184 CGGTACTCGTGTTCCTTTCTTTAG 59.380 45.833 10.89 0.00 32.30 1.85
648 669 0.389426 ACCATGCGGTACTCGTGTTC 60.389 55.000 0.00 0.00 46.71 3.18
657 678 4.221262 AGTTAAGAACTACACCATGCGGTA 59.779 41.667 0.00 0.00 41.63 4.02
659 680 3.596214 AGTTAAGAACTACACCATGCGG 58.404 45.455 0.00 0.00 40.69 5.69
671 692 6.254157 TCACACAACAACTCGTAGTTAAGAAC 59.746 38.462 0.87 0.00 36.03 3.01
686 707 2.423185 CACTCAGCCTTTCACACAACAA 59.577 45.455 0.00 0.00 0.00 2.83
691 712 1.230324 GACCACTCAGCCTTTCACAC 58.770 55.000 0.00 0.00 0.00 3.82
717 738 3.686016 AGGCCAACGTATGATGAAACTT 58.314 40.909 5.01 0.00 0.00 2.66
721 742 2.752354 CCAAAGGCCAACGTATGATGAA 59.248 45.455 5.01 0.00 0.00 2.57
748 771 5.545723 AGAACAATCTGGCCTAGCTATACAT 59.454 40.000 3.32 0.00 33.59 2.29
804 827 2.158534 AGAGGGAGTAGATGCTCGTCAT 60.159 50.000 0.00 0.00 38.32 3.06
824 847 9.927304 CGAAAAACGCCTTACATTATGGGACAG 62.927 44.444 0.00 0.00 37.07 3.51
825 848 8.269095 CGAAAAACGCCTTACATTATGGGACA 62.269 42.308 0.00 0.00 37.89 4.02
826 849 4.976224 AAAACGCCTTACATTATGGGAC 57.024 40.909 0.00 0.00 0.00 4.46
827 850 4.095185 CGAAAAACGCCTTACATTATGGGA 59.905 41.667 0.00 0.00 34.51 4.37
828 851 4.095185 TCGAAAAACGCCTTACATTATGGG 59.905 41.667 0.00 0.00 42.26 4.00
829 852 5.025826 GTCGAAAAACGCCTTACATTATGG 58.974 41.667 0.00 0.00 42.26 2.74
830 853 5.506832 GTGTCGAAAAACGCCTTACATTATG 59.493 40.000 0.00 0.00 42.26 1.90
831 854 5.624292 GTGTCGAAAAACGCCTTACATTAT 58.376 37.500 0.00 0.00 42.26 1.28
832 855 4.376210 CGTGTCGAAAAACGCCTTACATTA 60.376 41.667 3.96 0.00 42.26 1.90
833 856 3.605231 CGTGTCGAAAAACGCCTTACATT 60.605 43.478 3.96 0.00 42.26 2.71
834 857 2.096614 CGTGTCGAAAAACGCCTTACAT 60.097 45.455 3.96 0.00 42.26 2.29
835 858 1.258458 CGTGTCGAAAAACGCCTTACA 59.742 47.619 3.96 0.00 42.26 2.41
836 859 1.397567 CCGTGTCGAAAAACGCCTTAC 60.398 52.381 10.19 0.00 42.26 2.34
837 860 0.860533 CCGTGTCGAAAAACGCCTTA 59.139 50.000 10.19 0.00 42.26 2.69
838 861 0.810823 TCCGTGTCGAAAAACGCCTT 60.811 50.000 10.19 0.00 42.26 4.35
839 862 1.219522 CTCCGTGTCGAAAAACGCCT 61.220 55.000 10.19 0.00 42.26 5.52
840 863 1.203313 CTCCGTGTCGAAAAACGCC 59.797 57.895 10.19 0.00 42.26 5.68
841 864 1.203313 CCTCCGTGTCGAAAAACGC 59.797 57.895 10.19 0.00 42.26 4.84
842 865 0.598158 TCCCTCCGTGTCGAAAAACG 60.598 55.000 9.01 9.01 44.09 3.60
843 866 1.145803 CTCCCTCCGTGTCGAAAAAC 58.854 55.000 0.00 0.00 0.00 2.43
844 867 0.754472 ACTCCCTCCGTGTCGAAAAA 59.246 50.000 0.00 0.00 0.00 1.94
845 868 1.270550 GTACTCCCTCCGTGTCGAAAA 59.729 52.381 0.00 0.00 0.00 2.29
846 869 0.883833 GTACTCCCTCCGTGTCGAAA 59.116 55.000 0.00 0.00 0.00 3.46
847 870 0.250858 TGTACTCCCTCCGTGTCGAA 60.251 55.000 0.00 0.00 0.00 3.71
848 871 0.034767 ATGTACTCCCTCCGTGTCGA 60.035 55.000 0.00 0.00 0.00 4.20
849 872 0.100682 CATGTACTCCCTCCGTGTCG 59.899 60.000 0.00 0.00 0.00 4.35
850 873 1.471119 TCATGTACTCCCTCCGTGTC 58.529 55.000 0.00 0.00 0.00 3.67
851 874 2.160721 ATCATGTACTCCCTCCGTGT 57.839 50.000 0.00 0.00 0.00 4.49
852 875 3.637229 AGTAATCATGTACTCCCTCCGTG 59.363 47.826 0.00 0.00 27.56 4.94
853 876 3.637229 CAGTAATCATGTACTCCCTCCGT 59.363 47.826 0.00 0.00 31.78 4.69
854 877 3.637229 ACAGTAATCATGTACTCCCTCCG 59.363 47.826 0.00 0.00 31.78 4.63
855 878 5.615925 AACAGTAATCATGTACTCCCTCC 57.384 43.478 0.00 0.00 31.78 4.30
856 879 6.879400 AGAAACAGTAATCATGTACTCCCTC 58.121 40.000 0.00 0.00 31.78 4.30
857 880 6.875972 AGAAACAGTAATCATGTACTCCCT 57.124 37.500 0.00 0.00 31.78 4.20
858 881 6.879458 ACAAGAAACAGTAATCATGTACTCCC 59.121 38.462 0.00 0.00 31.78 4.30
859 882 7.148407 CCACAAGAAACAGTAATCATGTACTCC 60.148 40.741 0.00 0.00 31.78 3.85
860 883 7.624344 GCCACAAGAAACAGTAATCATGTACTC 60.624 40.741 0.00 0.00 31.78 2.59
861 884 6.149474 GCCACAAGAAACAGTAATCATGTACT 59.851 38.462 0.00 0.00 34.56 2.73
862 885 6.314784 GCCACAAGAAACAGTAATCATGTAC 58.685 40.000 0.00 0.00 0.00 2.90
863 886 5.414454 GGCCACAAGAAACAGTAATCATGTA 59.586 40.000 0.00 0.00 0.00 2.29
864 887 4.218417 GGCCACAAGAAACAGTAATCATGT 59.782 41.667 0.00 0.00 0.00 3.21
865 888 4.672542 CGGCCACAAGAAACAGTAATCATG 60.673 45.833 2.24 0.00 0.00 3.07
866 889 3.440173 CGGCCACAAGAAACAGTAATCAT 59.560 43.478 2.24 0.00 0.00 2.45
867 890 2.811431 CGGCCACAAGAAACAGTAATCA 59.189 45.455 2.24 0.00 0.00 2.57
875 898 0.169009 GATGCTCGGCCACAAGAAAC 59.831 55.000 2.24 0.00 0.00 2.78
929 952 7.044798 GGTCCTATTTATAGTCCAGATGCATC 58.955 42.308 19.37 19.37 0.00 3.91
931 954 5.248477 GGGTCCTATTTATAGTCCAGATGCA 59.752 44.000 0.00 0.00 0.00 3.96
1083 1106 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1085 1108 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1087 1110 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1089 1112 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1091 1114 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1093 1116 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1095 1118 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1099 1136 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1103 1140 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1107 1144 1.727335 CGTAACACACACACACACACA 59.273 47.619 0.00 0.00 0.00 3.72
1111 1148 3.166489 TGATCGTAACACACACACACA 57.834 42.857 0.00 0.00 0.00 3.72
1137 1174 1.569003 CGTGCATCACAACGAGCAA 59.431 52.632 0.00 0.00 38.91 3.91
1258 1488 1.425066 TGGAATTCCAGGAAGCACTGT 59.575 47.619 23.63 0.00 42.01 3.55
1438 3399 2.665165 AGTGATGGACTGCAAACCAAA 58.335 42.857 14.13 4.98 39.69 3.28
1485 3622 4.965200 AAGGGAGTATCATTCACTAGCC 57.035 45.455 0.00 0.00 36.25 3.93
1639 3776 3.270027 TCCACATGCACAAGTACTATGC 58.730 45.455 20.16 20.16 39.88 3.14
1657 3794 3.479489 GGTTTAGAAGGGTCGTTTTCCA 58.521 45.455 0.00 0.00 0.00 3.53
1720 3858 2.164017 CCGTGCCATTTGATTGATGACA 59.836 45.455 0.00 0.00 0.00 3.58
1737 3875 5.752955 AGATGGAAATTTTGAAACAACCGTG 59.247 36.000 0.00 0.00 0.00 4.94
1745 3883 7.374272 TGCGTATTGAGATGGAAATTTTGAAA 58.626 30.769 0.00 0.00 0.00 2.69
1884 4024 2.357637 CCTCTTGCAAAGTCCGTTTCAA 59.642 45.455 0.00 0.00 46.34 2.69
1885 4025 1.946768 CCTCTTGCAAAGTCCGTTTCA 59.053 47.619 0.00 0.00 46.34 2.69
1956 4096 5.384063 TGCATGGGTTAATTTACACACTG 57.616 39.130 0.86 3.78 33.54 3.66
2002 4143 9.696917 ATAATTCCTTCAAAAGAATGTCAACAC 57.303 29.630 0.00 0.00 0.00 3.32
2035 4177 6.408869 ACTAAGCATTGCCTTTAATTGCATT 58.591 32.000 4.70 0.00 37.33 3.56
2122 4264 9.406828 GTGGTTAACTTGGAGAAAATAATTGTC 57.593 33.333 5.42 0.00 0.00 3.18
2135 4277 4.069304 GCAGTACATGTGGTTAACTTGGA 58.931 43.478 9.11 0.00 38.07 3.53
2194 4338 9.964354 ACAACATATATCCTATGCACATTATGT 57.036 29.630 0.00 0.00 0.00 2.29
2237 4381 2.744202 GTGGTGAGGACAAGTTGCATAG 59.256 50.000 1.81 0.00 0.00 2.23
2416 4560 3.591527 TGAACAGGTTTATCCTCATGGGT 59.408 43.478 0.00 0.00 46.24 4.51
2535 4679 7.648142 TGTTTGAGTATGTTTTGCCTTCTAAG 58.352 34.615 0.00 0.00 0.00 2.18
2574 4718 5.717078 ATGCTGCAAAGATCTTCTTCAAA 57.283 34.783 8.78 0.00 35.27 2.69
2577 4721 7.859875 GGTTTATATGCTGCAAAGATCTTCTTC 59.140 37.037 8.78 1.74 35.27 2.87
2654 4798 4.290722 AGACTTCTGGTTCATCCTTTCCAT 59.709 41.667 0.00 0.00 37.07 3.41
2719 4866 4.781934 CCTTCTACCCCATAAGACAAAGG 58.218 47.826 0.00 0.00 0.00 3.11
2770 4917 1.271597 CCTGCCTTCTACCCCATATGC 60.272 57.143 0.00 0.00 0.00 3.14
2855 5002 2.769095 TCATCCAACCCATATGACACGA 59.231 45.455 3.65 0.00 0.00 4.35
2874 5021 2.136298 TGTGTTCACCTTTGCCTTCA 57.864 45.000 0.37 0.00 0.00 3.02
2901 5048 3.726557 TCCTCTGCATCTTGGTTGAAT 57.273 42.857 0.00 0.00 0.00 2.57
2999 5146 6.545298 AGCTTTATGTGGATCCTCTTCATTTC 59.455 38.462 14.23 0.00 0.00 2.17
3126 5318 5.721480 TGGATCCTCTTCATGTTCTGAACTA 59.279 40.000 20.18 8.31 38.97 2.24
3127 5319 4.533707 TGGATCCTCTTCATGTTCTGAACT 59.466 41.667 20.18 4.65 38.97 3.01
3129 5321 4.286808 TGTGGATCCTCTTCATGTTCTGAA 59.713 41.667 14.23 0.00 41.61 3.02
3363 5556 0.179234 TGTTCCCGTGCTTGTGAGAA 59.821 50.000 0.00 0.00 0.00 2.87
3395 5588 1.595794 TGTCGTGGAAGAAGAAAACGC 59.404 47.619 0.00 0.00 34.38 4.84
3425 5618 5.389520 TGGTTGGAATTATCACAGAACCAA 58.610 37.500 0.00 0.00 38.68 3.67
3534 5727 0.586319 CCGGTGCAAATATCGCGATT 59.414 50.000 28.81 8.25 0.00 3.34
3591 5784 2.027073 CGGGTGGTCACATGTGTCG 61.027 63.158 24.63 15.16 0.00 4.35
3663 5856 2.103771 GTGAAGGGATGATGCTAGCTCA 59.896 50.000 17.23 16.49 0.00 4.26
3769 5962 2.680913 GCTTTCGCACGGCTGTCAT 61.681 57.895 0.00 0.00 35.78 3.06
3774 5967 2.433318 GAGAGCTTTCGCACGGCT 60.433 61.111 0.00 0.00 39.10 5.52
3783 5976 2.562298 CTCCTGTGAGTCAGAGAGCTTT 59.438 50.000 18.49 0.00 46.27 3.51
3897 6093 1.896183 CACCGTTGCACCATCCACA 60.896 57.895 0.00 0.00 0.00 4.17
3914 6110 2.046023 CCTCCATCACTTGCGGCA 60.046 61.111 0.00 0.00 0.00 5.69
3919 6115 2.237393 GCTAGAGCCTCCATCACTTG 57.763 55.000 0.00 0.00 34.31 3.16
4125 6321 2.455674 TGGCTCACACATACAGACAC 57.544 50.000 0.00 0.00 0.00 3.67
4126 6322 2.566724 TCATGGCTCACACATACAGACA 59.433 45.455 0.00 0.00 0.00 3.41
4168 6364 5.945155 TGCATTTTACGAAGATTTACCCAC 58.055 37.500 0.00 0.00 0.00 4.61
4174 6370 6.753279 CACCATCATGCATTTTACGAAGATTT 59.247 34.615 0.00 0.00 0.00 2.17
4187 6383 9.483916 CATTTATTTCATAACACCATCATGCAT 57.516 29.630 0.00 0.00 0.00 3.96
4219 6415 8.634475 TTATGAAGTTCATACGATGACTTCTG 57.366 34.615 22.44 0.00 41.97 3.02
4272 6470 4.211389 GTGATGTTCTTACAACAACTGCG 58.789 43.478 0.00 0.00 38.56 5.18
4346 6544 8.408601 TCTTTATATACTGTACGGAAAGACACC 58.591 37.037 9.17 0.00 0.00 4.16
4433 6644 5.652891 ACTCATTTCAGTCCGTATGTAGTCT 59.347 40.000 0.00 0.00 0.00 3.24
4460 6671 0.593773 ACATGTTTTGGTGCGTTCGC 60.594 50.000 10.34 10.34 0.00 4.70
4551 6762 3.737559 AATTGTTCTGGACAGGGCATA 57.262 42.857 0.00 0.00 39.94 3.14
4552 6763 2.564062 CAAATTGTTCTGGACAGGGCAT 59.436 45.455 0.00 0.00 39.94 4.40
4553 6764 1.962807 CAAATTGTTCTGGACAGGGCA 59.037 47.619 0.00 0.00 39.94 5.36
4561 6818 4.297510 TGCAAATCGACAAATTGTTCTGG 58.702 39.130 0.00 0.00 0.00 3.86
4686 7367 9.371136 GACTCAGAATGTGTAGTCAATATTCAA 57.629 33.333 0.00 0.00 43.72 2.69
4714 7395 2.035632 CCTAGTAAGCTAGCCTGCAGT 58.964 52.381 12.13 0.00 42.51 4.40
4720 7401 3.955551 ACTCTTGTCCTAGTAAGCTAGCC 59.044 47.826 12.13 0.00 42.51 3.93
4721 7402 6.887626 ATACTCTTGTCCTAGTAAGCTAGC 57.112 41.667 6.62 6.62 42.51 3.42
4756 7437 8.953368 AAGCATGGAAAATATTCTTGGAATTC 57.047 30.769 0.00 0.00 35.79 2.17
4794 7476 9.632807 TGGCAAATATAAAGACACATTACAAAC 57.367 29.630 0.00 0.00 0.00 2.93
4803 7650 8.931385 AAACATGATGGCAAATATAAAGACAC 57.069 30.769 0.00 0.00 0.00 3.67
4875 7722 4.475944 CTCGGTGAAATTTGTCATGGAAC 58.524 43.478 0.00 0.00 0.00 3.62
4935 7784 1.363744 GATGAACCAGGAGCACGAAG 58.636 55.000 0.00 0.00 0.00 3.79
4965 7814 1.515081 TTCCCCACATCGAACGTTTC 58.485 50.000 0.46 0.00 0.00 2.78
4989 7838 5.124457 ACATGTCAAATAGGAGTTGTGATGC 59.876 40.000 0.00 0.00 0.00 3.91
4994 7843 6.013725 TGACCTACATGTCAAATAGGAGTTGT 60.014 38.462 16.83 0.00 42.06 3.32
5008 7857 2.290916 CGCTATCGAGTGACCTACATGT 59.709 50.000 2.69 2.69 38.10 3.21
5011 7860 2.320745 TCGCTATCGAGTGACCTACA 57.679 50.000 0.00 0.00 40.21 2.74


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

AutoCloner maintained by Alex Coulton.