Multiple sequence alignment - TraesCS5D01G566600

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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 TraesCS5D01G566600 chr5D 100.000 4904 0 0 1588 6491 564844997 564849900 0.000000e+00 9057.0
1 TraesCS5D01G566600 chr5D 100.000 1166 0 0 1 1166 564843410 564844575 0.000000e+00 2154.0
2 TraesCS5D01G566600 chr5D 83.721 172 14 9 5824 5992 564891789 564891949 4.050000e-32 150.0
3 TraesCS5D01G566600 chr4A 92.850 2098 92 22 4041 6132 606364473 606366518 0.000000e+00 2990.0
4 TraesCS5D01G566600 chr4A 90.187 1284 81 23 1669 2929 606361903 606363164 0.000000e+00 1631.0
5 TraesCS5D01G566600 chr4A 95.019 522 20 2 2960 3479 606363164 606363681 0.000000e+00 815.0
6 TraesCS5D01G566600 chr4A 92.844 545 26 1 3441 3985 606363680 606364211 0.000000e+00 778.0
7 TraesCS5D01G566600 chr4A 85.094 691 47 29 505 1166 606360806 606361469 0.000000e+00 654.0
8 TraesCS5D01G566600 chr4A 82.801 407 62 4 1 406 606360119 606360518 2.230000e-94 357.0
9 TraesCS5D01G566600 chr4A 90.968 155 11 1 6303 6454 606366885 606367039 8.530000e-49 206.0
10 TraesCS5D01G566600 chr4A 90.000 70 7 0 1 70 606359975 606360044 2.490000e-14 91.6
11 TraesCS5D01G566600 chr5B 93.260 1543 53 27 4653 6169 709006832 709008349 0.000000e+00 2226.0
12 TraesCS5D01G566600 chr5B 95.583 1064 26 9 2327 3381 709004620 709005671 0.000000e+00 1685.0
13 TraesCS5D01G566600 chr5B 92.044 1194 47 22 3412 4585 709005667 709006832 0.000000e+00 1635.0
14 TraesCS5D01G566600 chr5B 93.099 710 28 5 1601 2295 709003923 709004626 0.000000e+00 1020.0
15 TraesCS5D01G566600 chr5B 85.700 1014 64 33 1 968 709002547 709003525 0.000000e+00 994.0
16 TraesCS5D01G566600 chr4D 75.847 708 105 34 4675 5366 15250297 15250954 3.800000e-77 300.0
17 TraesCS5D01G566600 chr4B 75.421 712 108 36 4675 5366 25781444 25782108 3.830000e-72 283.0
18 TraesCS5D01G566600 chr2B 82.178 101 13 5 3911 4009 612085603 612085506 1.500000e-11 82.4


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 TraesCS5D01G566600 chr5D 564843410 564849900 6490 False 5605.500 9057 100.000000 1 6491 2 chr5D.!!$F2 6490
1 TraesCS5D01G566600 chr4A 606359975 606367039 7064 False 940.325 2990 89.970375 1 6454 8 chr4A.!!$F1 6453
2 TraesCS5D01G566600 chr5B 709002547 709008349 5802 False 1512.000 2226 91.937200 1 6169 5 chr5B.!!$F1 6168
3 TraesCS5D01G566600 chr4D 15250297 15250954 657 False 300.000 300 75.847000 4675 5366 1 chr4D.!!$F1 691
4 TraesCS5D01G566600 chr4B 25781444 25782108 664 False 283.000 283 75.421000 4675 5366 1 chr4B.!!$F1 691

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
855 1222 0.107459 CAGGGCTAAAGAGGAGGTGC 60.107 60.000 0.0 0.0 0.00 5.01 F
859 1226 0.741221 GCTAAAGAGGAGGTGCGTGG 60.741 60.000 0.0 0.0 0.00 4.94 F
1719 2113 0.317519 CTTCCCGCCGTTTGTTTGTC 60.318 55.000 0.0 0.0 0.00 3.18 F
1914 2308 1.075970 CGGGATCACCAGGAGAGGA 60.076 63.158 0.0 0.0 40.22 3.71 F
1917 2311 1.406860 GGATCACCAGGAGAGGAGCC 61.407 65.000 0.0 0.0 35.97 4.70 F
2299 2696 2.073056 TCGCATCGCTTCTGCTTTTAA 58.927 42.857 0.0 0.0 37.48 1.52 F
2321 2718 2.092807 TGCTGCTGATGTGGTGATGTAT 60.093 45.455 0.0 0.0 0.00 2.29 F
2384 2783 2.126057 TGTCCAGATATGCCATCACCA 58.874 47.619 0.0 0.0 0.00 4.17 F
4351 5033 1.135575 GCTGTGTGGATAGTTTGCTGC 60.136 52.381 0.0 0.0 0.00 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1716 2110 0.247735 CGCAAACAAACGAACGGACA 60.248 50.000 0.00 0.00 0.00 4.02 R
1762 2156 0.529378 CATGGCCTGGAAAGAGCAAC 59.471 55.000 3.32 0.00 0.00 4.17 R
3615 4091 1.605232 CTGACTTCAAGCATGCACACA 59.395 47.619 21.98 8.71 0.00 3.72 R
3746 4222 4.439563 GCTACTCACTACCTCTTCTCTTGC 60.440 50.000 0.00 0.00 0.00 4.01 R
3806 4282 4.817318 TGATAACATGGTACTGCACTCA 57.183 40.909 0.00 0.00 0.00 3.41 R
4066 4748 2.412870 TGTCTGGCTATTGTCACAACG 58.587 47.619 0.00 0.00 0.00 4.10 R
4079 4761 2.955660 AGCTGAGTCTACTATGTCTGGC 59.044 50.000 0.00 0.00 0.00 4.85 R
4354 5036 3.133362 CCGCTAACCTAATAGTTCCCACA 59.867 47.826 0.00 0.00 0.00 4.17 R
6018 6771 0.031178 GGAGCAACCAAACACAGCAG 59.969 55.000 0.00 0.00 38.79 4.24 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
54 55 6.141369 GCGCAACAGAATATTCTTGCTATTTC 59.859 38.462 27.49 14.52 36.67 2.17
183 328 8.643324 ACTACCATTACCTAAGCTCTTCTAATG 58.357 37.037 0.00 0.00 0.00 1.90
244 389 1.282157 GTAGGCCAATCAAGACCAGGT 59.718 52.381 5.01 0.00 0.00 4.00
245 390 1.668826 AGGCCAATCAAGACCAGGTA 58.331 50.000 5.01 0.00 0.00 3.08
246 391 1.992557 AGGCCAATCAAGACCAGGTAA 59.007 47.619 5.01 0.00 0.00 2.85
318 464 6.045318 TCAAAGTTGACATAGAGCATAGAGC 58.955 40.000 0.00 0.00 36.35 4.09
329 480 3.554342 ATAGAGCCCGCTGCCAGG 61.554 66.667 0.00 0.00 42.71 4.45
343 494 3.004106 GCTGCCAGGCATAATAAAGACAG 59.996 47.826 16.64 0.00 38.13 3.51
345 496 4.599041 TGCCAGGCATAATAAAGACAGTT 58.401 39.130 11.22 0.00 31.71 3.16
352 503 9.132521 CAGGCATAATAAAGACAGTTCAAAAAG 57.867 33.333 0.00 0.00 0.00 2.27
361 512 1.946768 CAGTTCAAAAAGCCAGACCGA 59.053 47.619 0.00 0.00 0.00 4.69
382 533 4.022935 CGACAGGTAAGGTATACCGCATAA 60.023 45.833 16.31 0.00 42.26 1.90
384 535 6.429521 ACAGGTAAGGTATACCGCATAAAT 57.570 37.500 16.31 0.00 42.26 1.40
450 775 2.891580 ACTCGCGTGATACCCTAATGAT 59.108 45.455 16.04 0.00 0.00 2.45
529 874 1.196130 GGATTTCAAATGCTCGCGCG 61.196 55.000 26.76 26.76 39.65 6.86
541 886 2.303452 TCGCGCGAGAAAAACTTGT 58.697 47.368 31.40 0.00 32.82 3.16
574 920 1.201343 GCCTTTCGACGTCTGCTATC 58.799 55.000 14.70 0.00 0.00 2.08
580 926 0.294887 CGACGTCTGCTATCAAACGC 59.705 55.000 14.70 0.00 38.64 4.84
606 952 3.565764 TTAGGATCCTTGAGTGCATGG 57.434 47.619 22.03 0.00 39.92 3.66
625 971 2.111384 GGAGAGGCTCATACTGGTCAA 58.889 52.381 18.26 0.00 31.08 3.18
626 972 2.501723 GGAGAGGCTCATACTGGTCAAA 59.498 50.000 18.26 0.00 31.08 2.69
627 973 3.135530 GGAGAGGCTCATACTGGTCAAAT 59.864 47.826 18.26 0.00 31.08 2.32
629 975 5.283457 AGAGGCTCATACTGGTCAAATAC 57.717 43.478 18.26 0.00 0.00 1.89
630 976 4.051922 GAGGCTCATACTGGTCAAATACG 58.948 47.826 10.25 0.00 0.00 3.06
631 977 3.451178 AGGCTCATACTGGTCAAATACGT 59.549 43.478 0.00 0.00 0.00 3.57
632 978 4.647853 AGGCTCATACTGGTCAAATACGTA 59.352 41.667 0.00 0.00 0.00 3.57
655 1006 8.021396 CGTAATGTTCCGAGTATCTTCATATGA 58.979 37.037 0.00 0.00 0.00 2.15
673 1024 9.557061 TTCATATGATCCTCTCAAATCTCAAAG 57.443 33.333 6.17 0.00 37.44 2.77
683 1034 5.877012 TCTCAAATCTCAAAGGAAAGGATCG 59.123 40.000 0.00 0.00 0.00 3.69
684 1035 4.943705 TCAAATCTCAAAGGAAAGGATCGG 59.056 41.667 0.00 0.00 0.00 4.18
705 1056 1.133884 CATGAGCCACTCACCCATCAT 60.134 52.381 0.00 0.00 43.63 2.45
706 1057 0.543277 TGAGCCACTCACCCATCATC 59.457 55.000 0.00 0.00 35.39 2.92
712 1063 3.828921 CCACTCACCCATCATCATCAAT 58.171 45.455 0.00 0.00 0.00 2.57
713 1064 3.819337 CCACTCACCCATCATCATCAATC 59.181 47.826 0.00 0.00 0.00 2.67
714 1065 4.457466 CACTCACCCATCATCATCAATCA 58.543 43.478 0.00 0.00 0.00 2.57
789 1150 8.774546 AAAGAAAGAAAGAAAGAAGGAATCCT 57.225 30.769 0.00 0.00 33.87 3.24
790 1151 9.868160 AAAGAAAGAAAGAAAGAAGGAATCCTA 57.132 29.630 0.46 0.00 31.13 2.94
792 1153 8.440771 AGAAAGAAAGAAAGAAGGAATCCTACA 58.559 33.333 0.46 0.00 31.13 2.74
793 1154 9.237187 GAAAGAAAGAAAGAAGGAATCCTACAT 57.763 33.333 0.46 0.00 31.13 2.29
827 1194 2.046285 CCAAGCAAACCCCTAGCCG 61.046 63.158 0.00 0.00 0.00 5.52
853 1220 0.621862 CCCAGGGCTAAAGAGGAGGT 60.622 60.000 0.00 0.00 0.00 3.85
855 1222 0.107459 CAGGGCTAAAGAGGAGGTGC 60.107 60.000 0.00 0.00 0.00 5.01
857 1224 1.597461 GGCTAAAGAGGAGGTGCGT 59.403 57.895 0.00 0.00 0.00 5.24
859 1226 0.741221 GCTAAAGAGGAGGTGCGTGG 60.741 60.000 0.00 0.00 0.00 4.94
861 1228 1.550130 TAAAGAGGAGGTGCGTGGGG 61.550 60.000 0.00 0.00 0.00 4.96
1716 2110 2.852180 GCCTTCCCGCCGTTTGTTT 61.852 57.895 0.00 0.00 0.00 2.83
1719 2113 0.317519 CTTCCCGCCGTTTGTTTGTC 60.318 55.000 0.00 0.00 0.00 3.18
1721 2115 2.051703 CCGCCGTTTGTTTGTCCG 60.052 61.111 0.00 0.00 0.00 4.79
1761 2155 2.094390 TGATTCGGTAGCTGTGTGGTAC 60.094 50.000 0.00 0.00 45.87 3.34
1914 2308 1.075970 CGGGATCACCAGGAGAGGA 60.076 63.158 0.00 0.00 40.22 3.71
1917 2311 1.406860 GGATCACCAGGAGAGGAGCC 61.407 65.000 0.00 0.00 35.97 4.70
2195 2592 3.704231 CTTCATGGGCCACCCTCCG 62.704 68.421 9.28 0.00 45.70 4.63
2257 2654 2.554893 TGGCGTTTCATGGTAAGGTTTC 59.445 45.455 0.00 0.00 0.00 2.78
2285 2682 4.498241 TCTGGTATTGCAGATATCGCATC 58.502 43.478 18.41 13.15 39.58 3.91
2288 2685 2.090400 ATTGCAGATATCGCATCGCT 57.910 45.000 18.41 6.09 39.58 4.93
2299 2696 2.073056 TCGCATCGCTTCTGCTTTTAA 58.927 42.857 0.00 0.00 37.48 1.52
2312 2709 3.840468 TGCTTTTAATGCTGCTGATGTG 58.160 40.909 0.00 0.00 0.00 3.21
2321 2718 2.092807 TGCTGCTGATGTGGTGATGTAT 60.093 45.455 0.00 0.00 0.00 2.29
2322 2719 3.134442 TGCTGCTGATGTGGTGATGTATA 59.866 43.478 0.00 0.00 0.00 1.47
2348 2747 3.273434 TCTGCTGGTATTGATCAGTTGC 58.727 45.455 0.00 0.00 33.81 4.17
2361 2760 3.222173 TCAGTTGCCACTATGGTTTGT 57.778 42.857 0.00 0.00 40.46 2.83
2362 2761 3.561143 TCAGTTGCCACTATGGTTTGTT 58.439 40.909 0.00 0.00 40.46 2.83
2381 2780 5.565455 TGTTATGTCCAGATATGCCATCA 57.435 39.130 0.00 0.00 0.00 3.07
2384 2783 2.126057 TGTCCAGATATGCCATCACCA 58.874 47.619 0.00 0.00 0.00 4.17
2537 2936 4.173924 GAGCCTGAGCCTGAGCCC 62.174 72.222 0.00 0.00 41.25 5.19
2540 2939 3.847602 CCTGAGCCTGAGCCCGAG 61.848 72.222 0.00 0.00 41.25 4.63
2541 2940 2.757508 CTGAGCCTGAGCCCGAGA 60.758 66.667 0.00 0.00 41.25 4.04
2631 3039 5.710984 AGTTCTACTTCAGGTCATTACACG 58.289 41.667 0.00 0.00 0.00 4.49
2834 3254 7.193377 TCGTGTTTACTGATTTTCCTTAACC 57.807 36.000 0.00 0.00 0.00 2.85
2958 3378 6.817765 TGTGGTTACTTCATTGGAATCTTC 57.182 37.500 0.00 0.00 31.34 2.87
3142 3565 7.665559 TCTGGCTTGATGTTAAAGTAGTGATTT 59.334 33.333 0.00 0.00 0.00 2.17
3143 3566 8.177119 TGGCTTGATGTTAAAGTAGTGATTTT 57.823 30.769 0.00 0.00 0.00 1.82
3144 3567 8.637986 TGGCTTGATGTTAAAGTAGTGATTTTT 58.362 29.630 0.00 0.00 0.00 1.94
3257 3682 3.622206 GCCATCAGTTGTGTTGGGAGATA 60.622 47.826 4.97 0.00 42.02 1.98
3269 3694 6.156256 TGTGTTGGGAGATAGTGCTTTATAGT 59.844 38.462 0.00 0.00 0.00 2.12
3400 3825 5.907197 AGTATGACGGAATATTTTCTGCG 57.093 39.130 4.79 0.00 41.22 5.18
3416 3841 2.182842 GCGCATCCCAGATGTGGTC 61.183 63.158 17.25 1.30 43.23 4.02
3549 4025 5.476599 TGGCTGCACTTAGATTGTGTTTTAT 59.523 36.000 0.50 0.00 37.70 1.40
3550 4026 6.657117 TGGCTGCACTTAGATTGTGTTTTATA 59.343 34.615 0.50 0.00 37.70 0.98
3551 4027 7.339212 TGGCTGCACTTAGATTGTGTTTTATAT 59.661 33.333 0.50 0.00 37.70 0.86
3552 4028 8.836413 GGCTGCACTTAGATTGTGTTTTATATA 58.164 33.333 0.50 0.00 37.70 0.86
3615 4091 4.623932 ATGAGTGGTAGTGACATTGTGT 57.376 40.909 0.00 0.00 0.00 3.72
3654 4130 3.252215 TCAGTTTAACATGCCTTCGTTGG 59.748 43.478 0.00 0.00 0.00 3.77
3746 4222 8.292448 GCAGGTTGAGTATATTACATTGATTGG 58.708 37.037 0.00 0.00 0.00 3.16
3773 4249 4.924625 AGAAGAGGTAGTGAGTAGCAAGA 58.075 43.478 0.00 0.00 0.00 3.02
3988 4530 4.737855 TGGCTGTAAGATAGGAGTTCAC 57.262 45.455 0.00 0.00 34.07 3.18
4019 4561 8.153550 AGCAGTATTGAATATTCCCTCTGTAAG 58.846 37.037 12.90 0.00 0.00 2.34
4020 4562 8.150945 GCAGTATTGAATATTCCCTCTGTAAGA 58.849 37.037 12.90 0.00 43.69 2.10
4026 4568 8.657387 TGAATATTCCCTCTGTAAGATAGGAG 57.343 38.462 12.90 0.00 45.62 3.69
4028 4570 9.095700 GAATATTCCCTCTGTAAGATAGGAGTT 57.904 37.037 3.92 0.00 45.62 3.01
4031 4573 5.838955 TCCCTCTGTAAGATAGGAGTTCAA 58.161 41.667 0.00 0.00 45.62 2.69
4034 4576 6.834451 CCCTCTGTAAGATAGGAGTTCAAGTA 59.166 42.308 0.00 0.00 45.62 2.24
4036 4578 9.575868 CCTCTGTAAGATAGGAGTTCAAGTATA 57.424 37.037 0.00 0.00 45.62 1.47
4066 4748 5.008118 GGGACTATCTAAAGAACATTGCAGC 59.992 44.000 0.00 0.00 0.00 5.25
4079 4761 2.967459 TTGCAGCGTTGTGACAATAG 57.033 45.000 0.00 0.10 0.00 1.73
4221 4903 9.971922 CATTTCTTTGGTTGTTTATTTCTCTCT 57.028 29.630 0.00 0.00 0.00 3.10
4258 4940 6.207928 TGTGCTCAAATACACTCAAATGTTG 58.792 36.000 0.00 0.00 37.68 3.33
4262 4944 6.086765 GCTCAAATACACTCAAATGTTGTTCG 59.913 38.462 0.00 0.00 33.85 3.95
4348 5030 1.879380 TGTGCTGTGTGGATAGTTTGC 59.121 47.619 0.00 0.00 0.00 3.68
4349 5031 2.154462 GTGCTGTGTGGATAGTTTGCT 58.846 47.619 0.00 0.00 0.00 3.91
4350 5032 2.095567 GTGCTGTGTGGATAGTTTGCTG 60.096 50.000 0.00 0.00 0.00 4.41
4351 5033 1.135575 GCTGTGTGGATAGTTTGCTGC 60.136 52.381 0.00 0.00 0.00 5.25
4352 5034 2.430465 CTGTGTGGATAGTTTGCTGCT 58.570 47.619 0.00 0.00 0.00 4.24
4353 5035 3.599343 CTGTGTGGATAGTTTGCTGCTA 58.401 45.455 0.00 0.00 0.00 3.49
4354 5036 4.194640 CTGTGTGGATAGTTTGCTGCTAT 58.805 43.478 0.00 0.00 32.38 2.97
4355 5037 3.940852 TGTGTGGATAGTTTGCTGCTATG 59.059 43.478 0.00 0.00 30.09 2.23
4356 5038 3.941483 GTGTGGATAGTTTGCTGCTATGT 59.059 43.478 0.00 0.00 30.09 2.29
4357 5039 3.940852 TGTGGATAGTTTGCTGCTATGTG 59.059 43.478 0.00 0.00 30.09 3.21
4358 5040 3.313526 GTGGATAGTTTGCTGCTATGTGG 59.686 47.826 0.00 0.00 30.09 4.17
4359 5041 2.880890 GGATAGTTTGCTGCTATGTGGG 59.119 50.000 0.00 0.00 30.09 4.61
4360 5042 3.433598 GGATAGTTTGCTGCTATGTGGGA 60.434 47.826 0.00 0.00 30.09 4.37
4361 5043 2.584835 AGTTTGCTGCTATGTGGGAA 57.415 45.000 0.00 0.00 0.00 3.97
4362 5044 2.162681 AGTTTGCTGCTATGTGGGAAC 58.837 47.619 0.00 0.00 0.00 3.62
4363 5045 2.162681 GTTTGCTGCTATGTGGGAACT 58.837 47.619 0.00 0.00 0.00 3.01
4364 5046 3.009033 AGTTTGCTGCTATGTGGGAACTA 59.991 43.478 0.00 0.00 0.00 2.24
4365 5047 3.931907 TTGCTGCTATGTGGGAACTAT 57.068 42.857 0.00 0.00 0.00 2.12
4489 5171 4.923893 TGCTGTAATGTTTCTGCATATGC 58.076 39.130 21.09 21.09 42.50 3.14
4535 5217 6.472016 TGTCCTTTAGTTGATCATGCACTAA 58.528 36.000 12.45 12.45 0.00 2.24
4596 5279 1.524776 CCGTTGTTGCCAATTTTTCCG 59.475 47.619 0.00 0.00 32.11 4.30
4598 5281 2.470999 CGTTGTTGCCAATTTTTCCGAG 59.529 45.455 0.00 0.00 32.11 4.63
4607 5290 5.095490 GCCAATTTTTCCGAGTCACTATTG 58.905 41.667 0.00 0.00 0.00 1.90
4625 5308 0.309302 TGTTATTTGCGCGCTTGTGT 59.691 45.000 33.29 15.59 0.00 3.72
4730 5414 5.871396 AAAGGAGGTTCGAGCTGAATATA 57.129 39.130 0.00 0.00 39.21 0.86
4924 5615 1.086696 GTGGTGTGCACTATCGCATT 58.913 50.000 19.41 0.00 45.26 3.56
5044 5744 1.202651 AGTTGGTTTGGACTCGACCAG 60.203 52.381 0.00 0.00 43.72 4.00
5135 5864 4.370776 TCCATTCCCTTCTCTAATGACCA 58.629 43.478 0.00 0.00 33.38 4.02
5199 5929 1.173043 TTTTCCACTAATGCAGGGCG 58.827 50.000 0.00 0.00 0.00 6.13
5421 6154 2.636830 GACCAGAACCATCATGAGGTG 58.363 52.381 15.00 3.81 39.86 4.00
5617 6359 1.809207 CTTGCGGGGTTGCATTAGG 59.191 57.895 0.00 0.00 45.78 2.69
5712 6455 1.467374 CGATAGGCGGCCAAACAAAAG 60.467 52.381 23.09 0.00 36.03 2.27
5720 6463 3.734463 CGGCCAAACAAAAGGGTTTATT 58.266 40.909 2.24 0.00 38.86 1.40
5748 6491 1.369091 GGGCATCAAACGCGATGAGT 61.369 55.000 15.93 4.64 44.67 3.41
5772 6515 2.428890 GAGAAGCCGAAGAAGAGGATGA 59.571 50.000 0.00 0.00 0.00 2.92
5776 6519 4.021102 AGCCGAAGAAGAGGATGAAAAA 57.979 40.909 0.00 0.00 0.00 1.94
5814 6559 1.225376 TTGCTTAGTGTGCGGTTCCG 61.225 55.000 6.90 6.90 0.00 4.30
6018 6771 6.903883 TTTTACAGATATTTCCTCTCGTGC 57.096 37.500 0.00 0.00 0.00 5.34
6040 6793 1.402787 CTGTGTTTGGTTGCTCCCTT 58.597 50.000 0.00 0.00 34.77 3.95
6041 6794 1.067516 CTGTGTTTGGTTGCTCCCTTG 59.932 52.381 0.00 0.00 34.77 3.61
6042 6795 0.249447 GTGTTTGGTTGCTCCCTTGC 60.249 55.000 0.00 0.00 34.77 4.01
6043 6796 1.367471 GTTTGGTTGCTCCCTTGCC 59.633 57.895 0.00 0.00 34.77 4.52
6044 6797 1.075674 TTTGGTTGCTCCCTTGCCA 60.076 52.632 0.00 0.00 34.77 4.92
6045 6798 0.471591 TTTGGTTGCTCCCTTGCCAT 60.472 50.000 0.00 0.00 34.77 4.40
6046 6799 1.186917 TTGGTTGCTCCCTTGCCATG 61.187 55.000 0.00 0.00 34.77 3.66
6047 6800 1.607467 GGTTGCTCCCTTGCCATGT 60.607 57.895 0.00 0.00 0.00 3.21
6048 6801 1.187567 GGTTGCTCCCTTGCCATGTT 61.188 55.000 0.00 0.00 0.00 2.71
6049 6802 0.037975 GTTGCTCCCTTGCCATGTTG 60.038 55.000 0.00 0.00 0.00 3.33
6050 6803 0.469705 TTGCTCCCTTGCCATGTTGT 60.470 50.000 0.00 0.00 0.00 3.32
6051 6804 0.469705 TGCTCCCTTGCCATGTTGTT 60.470 50.000 0.00 0.00 0.00 2.83
6052 6805 0.037975 GCTCCCTTGCCATGTTGTTG 60.038 55.000 0.00 0.00 0.00 3.33
6053 6806 0.037975 CTCCCTTGCCATGTTGTTGC 60.038 55.000 0.00 0.00 0.00 4.17
6054 6807 0.469705 TCCCTTGCCATGTTGTTGCT 60.470 50.000 0.00 0.00 0.00 3.91
6055 6808 0.393820 CCCTTGCCATGTTGTTGCTT 59.606 50.000 0.00 0.00 0.00 3.91
6057 6810 1.606224 CCTTGCCATGTTGTTGCTTCC 60.606 52.381 0.00 0.00 0.00 3.46
6058 6811 0.031857 TTGCCATGTTGTTGCTTCCG 59.968 50.000 0.00 0.00 0.00 4.30
6080 6849 2.113139 CTGTGGGAGCCGTTGGTT 59.887 61.111 0.00 0.00 0.00 3.67
6083 6852 2.203280 TGGGAGCCGTTGGTTGTG 60.203 61.111 0.00 0.00 0.00 3.33
6084 6853 2.203294 GGGAGCCGTTGGTTGTGT 60.203 61.111 0.00 0.00 0.00 3.72
6086 6855 1.388837 GGGAGCCGTTGGTTGTGTTT 61.389 55.000 0.00 0.00 0.00 2.83
6087 6856 0.248866 GGAGCCGTTGGTTGTGTTTG 60.249 55.000 0.00 0.00 0.00 2.93
6091 6860 1.670380 GCCGTTGGTTGTGTTTGTGTT 60.670 47.619 0.00 0.00 0.00 3.32
6092 6861 1.989165 CCGTTGGTTGTGTTTGTGTTG 59.011 47.619 0.00 0.00 0.00 3.33
6136 6907 4.470462 GCATTGTTGCTCTAGTTTCTGTG 58.530 43.478 0.00 0.00 45.77 3.66
6151 6922 5.883673 AGTTTCTGTGGCTGTAGTTTTTGTA 59.116 36.000 0.00 0.00 0.00 2.41
6153 6924 6.554334 TTCTGTGGCTGTAGTTTTTGTATC 57.446 37.500 0.00 0.00 0.00 2.24
6169 6940 5.590530 TTGTATCCAATTGGTTATGGTGC 57.409 39.130 23.76 8.43 37.94 5.01
6170 6941 4.865905 TGTATCCAATTGGTTATGGTGCT 58.134 39.130 23.76 2.33 37.94 4.40
6171 6942 6.007485 TGTATCCAATTGGTTATGGTGCTA 57.993 37.500 23.76 0.83 37.94 3.49
6173 6944 7.066142 TGTATCCAATTGGTTATGGTGCTAAT 58.934 34.615 23.76 8.08 37.94 1.73
6174 6945 5.850557 TCCAATTGGTTATGGTGCTAATG 57.149 39.130 23.76 0.00 37.94 1.90
6175 6946 4.099266 TCCAATTGGTTATGGTGCTAATGC 59.901 41.667 23.76 0.00 37.94 3.56
6176 6947 4.099881 CCAATTGGTTATGGTGCTAATGCT 59.900 41.667 16.90 0.00 40.48 3.79
6177 6948 4.924305 ATTGGTTATGGTGCTAATGCTG 57.076 40.909 0.00 0.00 40.48 4.41
6178 6949 3.643199 TGGTTATGGTGCTAATGCTGA 57.357 42.857 0.00 0.00 40.48 4.26
6181 6952 4.338964 TGGTTATGGTGCTAATGCTGATTG 59.661 41.667 0.00 0.00 40.48 2.67
6182 6953 4.580167 GGTTATGGTGCTAATGCTGATTGA 59.420 41.667 0.00 0.00 40.48 2.57
6188 6959 4.261489 GGTGCTAATGCTGATTGATTCTGG 60.261 45.833 0.00 0.00 40.48 3.86
6192 7149 5.066893 GCTAATGCTGATTGATTCTGGTGAA 59.933 40.000 0.00 0.00 34.85 3.18
6199 7156 1.661463 TGATTCTGGTGAAGGAGGCT 58.339 50.000 0.00 0.00 35.44 4.58
6206 7163 2.048222 TGAAGGAGGCTTCGTGCG 60.048 61.111 0.00 0.00 44.05 5.34
6207 7164 3.491652 GAAGGAGGCTTCGTGCGC 61.492 66.667 0.00 0.00 44.05 6.09
6211 7168 1.740296 GGAGGCTTCGTGCGCTTAA 60.740 57.895 9.73 0.00 44.05 1.85
6227 7184 4.963237 GCTTAAGATGAGCGTCTACATG 57.037 45.455 6.67 0.00 0.00 3.21
6228 7185 4.363999 GCTTAAGATGAGCGTCTACATGT 58.636 43.478 6.67 2.69 0.00 3.21
6229 7186 5.520632 GCTTAAGATGAGCGTCTACATGTA 58.479 41.667 6.67 5.25 0.00 2.29
6230 7187 5.627367 GCTTAAGATGAGCGTCTACATGTAG 59.373 44.000 24.37 24.37 34.56 2.74
6231 7188 6.694877 TTAAGATGAGCGTCTACATGTAGT 57.305 37.500 27.83 12.37 34.84 2.73
6232 7189 4.560136 AGATGAGCGTCTACATGTAGTG 57.440 45.455 27.83 22.34 34.84 2.74
6233 7190 3.316588 AGATGAGCGTCTACATGTAGTGG 59.683 47.826 27.83 21.59 34.84 4.00
6234 7191 2.443416 TGAGCGTCTACATGTAGTGGT 58.557 47.619 27.83 25.16 34.84 4.16
6235 7192 2.163613 TGAGCGTCTACATGTAGTGGTG 59.836 50.000 27.83 17.98 34.84 4.17
6236 7193 1.135083 AGCGTCTACATGTAGTGGTGC 60.135 52.381 27.83 24.47 34.84 5.01
6237 7194 1.545759 CGTCTACATGTAGTGGTGCG 58.454 55.000 27.83 20.64 34.84 5.34
6238 7195 1.278238 GTCTACATGTAGTGGTGCGC 58.722 55.000 27.83 0.00 34.84 6.09
6239 7196 0.179148 TCTACATGTAGTGGTGCGCG 60.179 55.000 27.83 0.00 34.84 6.86
6240 7197 0.457853 CTACATGTAGTGGTGCGCGT 60.458 55.000 22.48 0.00 0.00 6.01
6241 7198 0.457166 TACATGTAGTGGTGCGCGTC 60.457 55.000 8.43 0.00 0.00 5.19
6258 7215 1.661178 CGTCGCAATGCTGGCAATATC 60.661 52.381 2.94 0.00 0.00 1.63
6357 7358 0.447801 CAACAGAGGAATTTCGGCGG 59.552 55.000 7.21 0.00 0.00 6.13
6360 7361 1.276989 ACAGAGGAATTTCGGCGGTTA 59.723 47.619 7.21 0.00 0.00 2.85
6411 7412 6.323996 TGAAGCAGCTACACCTAACAGTATAT 59.676 38.462 0.00 0.00 0.00 0.86
6450 7454 4.641989 ACAGGCCATACTGATCAACAATTC 59.358 41.667 5.01 0.00 40.97 2.17
6454 7458 4.641989 GCCATACTGATCAACAATTCCAGT 59.358 41.667 0.00 0.00 40.66 4.00
6455 7459 5.822519 GCCATACTGATCAACAATTCCAGTA 59.177 40.000 0.00 0.00 42.32 2.74
6456 7460 6.017605 GCCATACTGATCAACAATTCCAGTAG 60.018 42.308 0.00 0.00 41.70 2.57
6457 7461 6.484643 CCATACTGATCAACAATTCCAGTAGG 59.515 42.308 0.00 0.00 41.70 3.18
6458 7462 4.265073 ACTGATCAACAATTCCAGTAGGC 58.735 43.478 0.00 0.00 36.44 3.93
6459 7463 4.263462 ACTGATCAACAATTCCAGTAGGCA 60.263 41.667 0.00 0.00 36.44 4.75
6460 7464 4.264253 TGATCAACAATTCCAGTAGGCAG 58.736 43.478 0.00 0.00 33.74 4.85
6461 7465 4.019411 TGATCAACAATTCCAGTAGGCAGA 60.019 41.667 0.00 0.00 33.74 4.26
6462 7466 3.942829 TCAACAATTCCAGTAGGCAGAG 58.057 45.455 0.00 0.00 33.74 3.35
6463 7467 3.012518 CAACAATTCCAGTAGGCAGAGG 58.987 50.000 0.00 0.00 33.74 3.69
6464 7468 2.551270 ACAATTCCAGTAGGCAGAGGA 58.449 47.619 0.00 0.00 33.74 3.71
6465 7469 2.503356 ACAATTCCAGTAGGCAGAGGAG 59.497 50.000 0.00 0.00 33.74 3.69
6466 7470 2.503356 CAATTCCAGTAGGCAGAGGAGT 59.497 50.000 0.00 0.00 33.74 3.85
6467 7471 1.561643 TTCCAGTAGGCAGAGGAGTG 58.438 55.000 0.00 0.00 33.74 3.51
6468 7472 0.409876 TCCAGTAGGCAGAGGAGTGT 59.590 55.000 0.00 0.00 33.74 3.55
6469 7473 1.203187 TCCAGTAGGCAGAGGAGTGTT 60.203 52.381 0.00 0.00 33.74 3.32
6470 7474 1.205893 CCAGTAGGCAGAGGAGTGTTC 59.794 57.143 0.00 0.00 0.00 3.18
6471 7475 1.895798 CAGTAGGCAGAGGAGTGTTCA 59.104 52.381 0.00 0.00 0.00 3.18
6472 7476 2.300152 CAGTAGGCAGAGGAGTGTTCAA 59.700 50.000 0.00 0.00 0.00 2.69
6473 7477 3.055530 CAGTAGGCAGAGGAGTGTTCAAT 60.056 47.826 0.00 0.00 0.00 2.57
6474 7478 2.486472 AGGCAGAGGAGTGTTCAATG 57.514 50.000 0.00 0.00 0.00 2.82
6475 7479 1.004044 AGGCAGAGGAGTGTTCAATGG 59.996 52.381 0.00 0.00 0.00 3.16
6476 7480 1.271597 GGCAGAGGAGTGTTCAATGGT 60.272 52.381 0.00 0.00 0.00 3.55
6477 7481 2.508526 GCAGAGGAGTGTTCAATGGTT 58.491 47.619 0.00 0.00 0.00 3.67
6478 7482 2.227388 GCAGAGGAGTGTTCAATGGTTG 59.773 50.000 0.00 0.00 0.00 3.77
6479 7483 3.480470 CAGAGGAGTGTTCAATGGTTGT 58.520 45.455 0.00 0.00 0.00 3.32
6480 7484 3.251729 CAGAGGAGTGTTCAATGGTTGTG 59.748 47.826 0.00 0.00 0.00 3.33
6481 7485 3.136443 AGAGGAGTGTTCAATGGTTGTGA 59.864 43.478 0.00 0.00 0.00 3.58
6482 7486 3.882888 GAGGAGTGTTCAATGGTTGTGAA 59.117 43.478 0.00 0.00 32.62 3.18
6490 7494 5.350504 TTCAATGGTTGTGAACACCAATT 57.649 34.783 8.25 0.00 37.07 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 224 8.875803 CATTTATTGGATCTTTGTGTTGGATTG 58.124 33.333 0.00 0.00 0.00 2.67
183 328 4.695217 TGCGGGTACTCATTTTTCATTC 57.305 40.909 0.00 0.00 0.00 2.67
263 408 2.416547 CGCTTTTTCCATCATCGTGTCT 59.583 45.455 0.00 0.00 0.00 3.41
272 417 3.171277 CCGTCATTTCGCTTTTTCCATC 58.829 45.455 0.00 0.00 0.00 3.51
318 464 0.537143 TTATTATGCCTGGCAGCGGG 60.537 55.000 27.20 0.00 43.65 6.13
329 480 7.598493 TGGCTTTTTGAACTGTCTTTATTATGC 59.402 33.333 0.00 0.00 0.00 3.14
343 494 1.673920 TGTCGGTCTGGCTTTTTGAAC 59.326 47.619 0.00 0.00 0.00 3.18
345 496 1.593196 CTGTCGGTCTGGCTTTTTGA 58.407 50.000 0.00 0.00 0.00 2.69
352 503 1.218316 CCTTACCTGTCGGTCTGGC 59.782 63.158 0.00 0.00 44.21 4.85
361 512 5.874897 TTTATGCGGTATACCTTACCTGT 57.125 39.130 19.68 1.95 35.49 4.00
375 526 7.377766 AGGCATATTAACACTATTTATGCGG 57.622 36.000 8.22 0.00 39.53 5.69
450 775 3.014623 CTGTAGAGATGACGTGGGTACA 58.985 50.000 0.00 0.00 0.00 2.90
502 846 4.171754 GAGCATTTGAAATCCTTGTCTGC 58.828 43.478 0.00 0.00 0.00 4.26
538 883 4.705337 AAGGCGACAAACTTACAAACAA 57.295 36.364 0.00 0.00 0.00 2.83
539 884 4.664188 GAAAGGCGACAAACTTACAAACA 58.336 39.130 0.00 0.00 0.00 2.83
540 885 3.722289 CGAAAGGCGACAAACTTACAAAC 59.278 43.478 0.00 0.00 44.57 2.93
541 886 3.622163 TCGAAAGGCGACAAACTTACAAA 59.378 39.130 0.00 0.00 45.59 2.83
574 920 3.480470 AGGATCCTAATCATGGCGTTTG 58.520 45.455 14.27 0.00 33.21 2.93
580 926 4.070716 GCACTCAAGGATCCTAATCATGG 58.929 47.826 16.55 6.07 33.21 3.66
606 952 3.895232 TTTGACCAGTATGAGCCTCTC 57.105 47.619 0.00 0.00 39.69 3.20
625 971 7.709947 TGAAGATACTCGGAACATTACGTATT 58.290 34.615 0.00 0.00 35.58 1.89
626 972 7.268199 TGAAGATACTCGGAACATTACGTAT 57.732 36.000 0.00 0.00 35.58 3.06
627 973 6.682423 TGAAGATACTCGGAACATTACGTA 57.318 37.500 0.00 0.00 35.58 3.57
629 975 8.021396 TCATATGAAGATACTCGGAACATTACG 58.979 37.037 1.98 0.00 35.34 3.18
630 976 9.862371 ATCATATGAAGATACTCGGAACATTAC 57.138 33.333 9.99 0.00 0.00 1.89
632 978 8.037758 GGATCATATGAAGATACTCGGAACATT 58.962 37.037 9.99 0.00 0.00 2.71
655 1006 6.012157 TCCTTTCCTTTGAGATTTGAGAGGAT 60.012 38.462 0.00 0.00 33.01 3.24
673 1024 2.325218 GCTCATGCCGATCCTTTCC 58.675 57.895 0.00 0.00 0.00 3.13
684 1035 1.077212 ATGGGTGAGTGGCTCATGC 60.077 57.895 1.99 0.00 42.73 4.06
705 1056 8.640063 TTTCTCCTCTTTGATTTGATTGATGA 57.360 30.769 0.00 0.00 0.00 2.92
706 1057 9.701098 TTTTTCTCCTCTTTGATTTGATTGATG 57.299 29.630 0.00 0.00 0.00 3.07
712 1063 7.039504 CCCATCTTTTTCTCCTCTTTGATTTGA 60.040 37.037 0.00 0.00 0.00 2.69
713 1064 7.095270 CCCATCTTTTTCTCCTCTTTGATTTG 58.905 38.462 0.00 0.00 0.00 2.32
714 1065 6.784473 ACCCATCTTTTTCTCCTCTTTGATTT 59.216 34.615 0.00 0.00 0.00 2.17
797 1158 1.494960 TTGCTTGGGTTCAGGCTTTT 58.505 45.000 2.46 0.00 44.97 2.27
801 1162 1.367471 GGTTTGCTTGGGTTCAGGC 59.633 57.895 0.00 0.00 44.95 4.85
802 1163 1.471829 GGGGTTTGCTTGGGTTCAGG 61.472 60.000 0.00 0.00 0.00 3.86
805 1166 1.545841 CTAGGGGTTTGCTTGGGTTC 58.454 55.000 0.00 0.00 0.00 3.62
806 1167 0.541998 GCTAGGGGTTTGCTTGGGTT 60.542 55.000 0.00 0.00 0.00 4.11
839 1206 0.741221 CACGCACCTCCTCTTTAGCC 60.741 60.000 0.00 0.00 0.00 3.93
840 1207 0.741221 CCACGCACCTCCTCTTTAGC 60.741 60.000 0.00 0.00 0.00 3.09
842 1209 1.550130 CCCCACGCACCTCCTCTTTA 61.550 60.000 0.00 0.00 0.00 1.85
844 1211 3.322466 CCCCACGCACCTCCTCTT 61.322 66.667 0.00 0.00 0.00 2.85
1590 1962 4.733725 TTGGGGGAGTCGGAGGGG 62.734 72.222 0.00 0.00 0.00 4.79
1591 1963 3.083997 CTTGGGGGAGTCGGAGGG 61.084 72.222 0.00 0.00 0.00 4.30
1592 1964 3.787001 GCTTGGGGGAGTCGGAGG 61.787 72.222 0.00 0.00 0.00 4.30
1593 1965 3.787001 GGCTTGGGGGAGTCGGAG 61.787 72.222 0.00 0.00 0.00 4.63
1594 1966 4.332543 AGGCTTGGGGGAGTCGGA 62.333 66.667 0.00 0.00 0.00 4.55
1595 1967 3.787001 GAGGCTTGGGGGAGTCGG 61.787 72.222 0.00 0.00 0.00 4.79
1596 1968 3.787001 GGAGGCTTGGGGGAGTCG 61.787 72.222 0.00 0.00 0.00 4.18
1597 1969 3.412408 GGGAGGCTTGGGGGAGTC 61.412 72.222 0.00 0.00 0.00 3.36
1648 2020 3.380142 GAAAGAGAGATCTGACCGATGC 58.620 50.000 0.00 0.00 30.84 3.91
1716 2110 0.247735 CGCAAACAAACGAACGGACA 60.248 50.000 0.00 0.00 0.00 4.02
1719 2113 2.622522 CGCGCAAACAAACGAACGG 61.623 57.895 8.75 0.00 0.00 4.44
1721 2115 1.117234 AATCGCGCAAACAAACGAAC 58.883 45.000 8.75 0.00 38.15 3.95
1761 2155 0.962356 ATGGCCTGGAAAGAGCAACG 60.962 55.000 3.32 0.00 0.00 4.10
1762 2156 0.529378 CATGGCCTGGAAAGAGCAAC 59.471 55.000 3.32 0.00 0.00 4.17
2257 2654 5.632764 CGATATCTGCAATACCAGAGAAGTG 59.367 44.000 0.34 0.00 44.37 3.16
2288 2685 4.219070 ACATCAGCAGCATTAAAAGCAGAA 59.781 37.500 0.00 0.00 0.00 3.02
2299 2696 1.340697 ACATCACCACATCAGCAGCAT 60.341 47.619 0.00 0.00 0.00 3.79
2312 2709 9.672673 AATACCAGCAGATTATTATACATCACC 57.327 33.333 0.00 0.00 0.00 4.02
2321 2718 9.276590 CAACTGATCAATACCAGCAGATTATTA 57.723 33.333 0.00 0.00 33.90 0.98
2322 2719 7.255381 GCAACTGATCAATACCAGCAGATTATT 60.255 37.037 0.00 0.00 33.90 1.40
2343 2742 5.076873 ACATAACAAACCATAGTGGCAACT 58.923 37.500 0.00 0.00 42.67 3.16
2344 2743 5.385509 ACATAACAAACCATAGTGGCAAC 57.614 39.130 0.00 0.00 42.67 4.17
2348 2747 5.496556 TCTGGACATAACAAACCATAGTGG 58.503 41.667 0.00 0.00 45.02 4.00
2361 2760 4.350520 TGGTGATGGCATATCTGGACATAA 59.649 41.667 0.00 0.00 0.00 1.90
2362 2761 3.909364 TGGTGATGGCATATCTGGACATA 59.091 43.478 0.00 0.00 0.00 2.29
2381 2780 0.765510 GGGAAACAGGAGACACTGGT 59.234 55.000 0.00 0.00 40.93 4.00
2384 2783 1.518367 TTGGGGAAACAGGAGACACT 58.482 50.000 0.00 0.00 0.00 3.55
2537 2936 2.493973 GGCTCAGGCTCAGTCTCG 59.506 66.667 0.00 0.00 38.73 4.04
2540 2939 3.386237 ACGGGCTCAGGCTCAGTC 61.386 66.667 0.00 0.00 39.29 3.51
2541 2940 3.699894 CACGGGCTCAGGCTCAGT 61.700 66.667 0.00 0.00 39.29 3.41
2834 3254 2.658538 CGACAGTCTCGAATGGCAG 58.341 57.895 0.93 0.00 46.14 4.85
2958 3378 7.137490 TCATGCACAGTAAAGATCAAAAGAG 57.863 36.000 0.00 0.00 0.00 2.85
3142 3565 7.814264 ATTGCAAATATCCAACCAAAACAAA 57.186 28.000 1.71 0.00 0.00 2.83
3143 3566 7.814264 AATTGCAAATATCCAACCAAAACAA 57.186 28.000 1.71 0.00 0.00 2.83
3144 3567 7.814264 AAATTGCAAATATCCAACCAAAACA 57.186 28.000 1.71 0.00 0.00 2.83
3176 3599 8.543071 GGAAATATTCCGTCATTCTAAAAACG 57.457 34.615 0.00 0.00 40.59 3.60
3269 3694 6.951198 TGGTCCAGGAAGAATAAAGCAATTTA 59.049 34.615 0.00 0.00 0.00 1.40
3314 3739 7.121759 CACAATCTACCAGAAAAGGACATGAAT 59.878 37.037 0.00 0.00 0.00 2.57
3552 4028 9.193806 AGGAGATGTATTCATGCTAAAAACAAT 57.806 29.630 0.00 0.00 34.06 2.71
3553 4029 8.579850 AGGAGATGTATTCATGCTAAAAACAA 57.420 30.769 0.00 0.00 34.06 2.83
3554 4030 8.579850 AAGGAGATGTATTCATGCTAAAAACA 57.420 30.769 0.00 0.00 34.06 2.83
3555 4031 9.860898 AAAAGGAGATGTATTCATGCTAAAAAC 57.139 29.630 0.00 0.00 34.06 2.43
3615 4091 1.605232 CTGACTTCAAGCATGCACACA 59.395 47.619 21.98 8.71 0.00 3.72
3746 4222 4.439563 GCTACTCACTACCTCTTCTCTTGC 60.440 50.000 0.00 0.00 0.00 4.01
3806 4282 4.817318 TGATAACATGGTACTGCACTCA 57.183 40.909 0.00 0.00 0.00 3.41
3965 4507 5.675538 GTGAACTCCTATCTTACAGCCAAT 58.324 41.667 0.00 0.00 0.00 3.16
3988 4530 8.470805 AGAGGGAATATTCAATACTGCTATACG 58.529 37.037 17.07 0.00 0.00 3.06
4019 4561 6.071616 CCCTCTGCTATACTTGAACTCCTATC 60.072 46.154 0.00 0.00 0.00 2.08
4020 4562 5.777732 CCCTCTGCTATACTTGAACTCCTAT 59.222 44.000 0.00 0.00 0.00 2.57
4021 4563 5.103643 TCCCTCTGCTATACTTGAACTCCTA 60.104 44.000 0.00 0.00 0.00 2.94
4023 4565 3.961408 TCCCTCTGCTATACTTGAACTCC 59.039 47.826 0.00 0.00 0.00 3.85
4024 4566 4.647399 AGTCCCTCTGCTATACTTGAACTC 59.353 45.833 0.00 0.00 0.00 3.01
4026 4568 6.492087 AGATAGTCCCTCTGCTATACTTGAAC 59.508 42.308 0.00 0.00 0.00 3.18
4028 4570 6.207509 AGATAGTCCCTCTGCTATACTTGA 57.792 41.667 0.00 0.00 0.00 3.02
4031 4573 7.991174 TCTTTAGATAGTCCCTCTGCTATACT 58.009 38.462 0.00 0.00 0.00 2.12
4034 4576 7.069986 TGTTCTTTAGATAGTCCCTCTGCTAT 58.930 38.462 0.00 0.00 0.00 2.97
4036 4578 5.273208 TGTTCTTTAGATAGTCCCTCTGCT 58.727 41.667 0.00 0.00 0.00 4.24
4037 4579 5.599999 TGTTCTTTAGATAGTCCCTCTGC 57.400 43.478 0.00 0.00 0.00 4.26
4066 4748 2.412870 TGTCTGGCTATTGTCACAACG 58.587 47.619 0.00 0.00 0.00 4.10
4079 4761 2.955660 AGCTGAGTCTACTATGTCTGGC 59.044 50.000 0.00 0.00 0.00 4.85
4221 4903 4.350368 TTGAGCACAGTGATACCTCAAA 57.650 40.909 15.23 4.01 38.98 2.69
4258 4940 6.750501 TCTCACAAGTATATTGCAGTACGAAC 59.249 38.462 0.00 0.00 0.00 3.95
4262 4944 6.697892 GGAGTCTCACAAGTATATTGCAGTAC 59.302 42.308 1.47 0.00 0.00 2.73
4348 5030 5.552870 ACCTAATAGTTCCCACATAGCAG 57.447 43.478 0.00 0.00 0.00 4.24
4349 5031 5.968676 AACCTAATAGTTCCCACATAGCA 57.031 39.130 0.00 0.00 0.00 3.49
4350 5032 5.932883 GCTAACCTAATAGTTCCCACATAGC 59.067 44.000 0.00 0.00 0.00 2.97
4351 5033 6.157211 CGCTAACCTAATAGTTCCCACATAG 58.843 44.000 0.00 0.00 0.00 2.23
4352 5034 5.011329 CCGCTAACCTAATAGTTCCCACATA 59.989 44.000 0.00 0.00 0.00 2.29
4353 5035 4.202326 CCGCTAACCTAATAGTTCCCACAT 60.202 45.833 0.00 0.00 0.00 3.21
4354 5036 3.133362 CCGCTAACCTAATAGTTCCCACA 59.867 47.826 0.00 0.00 0.00 4.17
4355 5037 3.133542 ACCGCTAACCTAATAGTTCCCAC 59.866 47.826 0.00 0.00 0.00 4.61
4356 5038 3.377573 ACCGCTAACCTAATAGTTCCCA 58.622 45.455 0.00 0.00 0.00 4.37
4357 5039 3.244009 GGACCGCTAACCTAATAGTTCCC 60.244 52.174 0.00 0.00 0.00 3.97
4358 5040 3.640498 AGGACCGCTAACCTAATAGTTCC 59.360 47.826 0.00 0.00 34.47 3.62
4359 5041 4.933505 AGGACCGCTAACCTAATAGTTC 57.066 45.455 0.00 0.00 34.47 3.01
4360 5042 4.713321 TGAAGGACCGCTAACCTAATAGTT 59.287 41.667 0.00 0.00 35.25 2.24
4361 5043 4.284178 TGAAGGACCGCTAACCTAATAGT 58.716 43.478 0.00 0.00 35.25 2.12
4362 5044 4.931661 TGAAGGACCGCTAACCTAATAG 57.068 45.455 0.00 0.00 35.25 1.73
4363 5045 5.601313 AGAATGAAGGACCGCTAACCTAATA 59.399 40.000 0.00 0.00 35.25 0.98
4364 5046 4.409247 AGAATGAAGGACCGCTAACCTAAT 59.591 41.667 0.00 0.00 35.25 1.73
4365 5047 3.773119 AGAATGAAGGACCGCTAACCTAA 59.227 43.478 0.00 0.00 35.25 2.69
4489 5171 0.881118 ACCAAAAGTATGCAGTGCCG 59.119 50.000 13.72 0.00 0.00 5.69
4491 5173 4.119136 ACAAAACCAAAAGTATGCAGTGC 58.881 39.130 8.58 8.58 0.00 4.40
4543 5225 6.711277 AGCAACAAGGTTGACTAGATTCATA 58.289 36.000 12.90 0.00 0.00 2.15
4596 5279 4.263800 CGCGCAAATAACAATAGTGACTC 58.736 43.478 8.75 0.00 0.00 3.36
4598 5281 2.776225 GCGCGCAAATAACAATAGTGAC 59.224 45.455 29.10 0.00 0.00 3.67
4607 5290 2.235238 TACACAAGCGCGCAAATAAC 57.765 45.000 35.10 0.72 0.00 1.89
4625 5308 5.777732 AGTACCTTGCCAATTTTTGTGGATA 59.222 36.000 0.00 0.00 38.54 2.59
4637 5320 1.145571 AGGACCAAGTACCTTGCCAA 58.854 50.000 0.00 0.00 39.85 4.52
4730 5414 4.392138 GCACGGTTAGCAGACTTCTTAAAT 59.608 41.667 0.00 0.00 0.00 1.40
4924 5615 6.850263 TGAAGGAACCCCCATAACATATAA 57.150 37.500 0.00 0.00 37.41 0.98
5001 5700 8.565896 ACTCTAGTTGAATGTTTATGAATGCA 57.434 30.769 0.00 0.00 0.00 3.96
5044 5744 8.292448 CCAATGGTCATGAATGCTATTAACTAC 58.708 37.037 0.00 0.00 0.00 2.73
5199 5929 1.601903 TGCATCAACACAGAAACCGAC 59.398 47.619 0.00 0.00 0.00 4.79
5617 6359 1.782028 AAACGAACCCGCTTGTCAGC 61.782 55.000 0.00 0.00 43.41 4.26
5654 6397 5.183140 ACCGATTTTCACCAATAACCAGAAG 59.817 40.000 0.00 0.00 0.00 2.85
5748 6491 0.898320 CTCTTCTTCGGCTTCTCCCA 59.102 55.000 0.00 0.00 0.00 4.37
5772 6515 3.073274 AGCCCTAATCAGCGTCTTTTT 57.927 42.857 0.00 0.00 0.00 1.94
5776 6519 2.074729 ACTAGCCCTAATCAGCGTCT 57.925 50.000 0.00 0.00 0.00 4.18
5992 6745 8.488764 GCACGAGAGGAAATATCTGTAAAATAC 58.511 37.037 0.00 0.00 0.00 1.89
6018 6771 0.031178 GGAGCAACCAAACACAGCAG 59.969 55.000 0.00 0.00 38.79 4.24
6040 6793 1.659233 CGGAAGCAACAACATGGCA 59.341 52.632 0.00 0.00 0.00 4.92
6041 6794 1.080569 CCGGAAGCAACAACATGGC 60.081 57.895 0.00 0.00 0.00 4.40
6042 6795 0.039256 CACCGGAAGCAACAACATGG 60.039 55.000 9.46 0.00 0.00 3.66
6043 6796 0.039256 CCACCGGAAGCAACAACATG 60.039 55.000 9.46 0.00 0.00 3.21
6044 6797 1.805428 GCCACCGGAAGCAACAACAT 61.805 55.000 9.46 0.00 0.00 2.71
6045 6798 2.485795 GCCACCGGAAGCAACAACA 61.486 57.895 9.46 0.00 0.00 3.33
6046 6799 2.193536 AGCCACCGGAAGCAACAAC 61.194 57.895 9.46 0.00 0.00 3.32
6047 6800 2.192861 CAGCCACCGGAAGCAACAA 61.193 57.895 9.46 0.00 0.00 2.83
6048 6801 2.594303 CAGCCACCGGAAGCAACA 60.594 61.111 9.46 0.00 0.00 3.33
6049 6802 2.594592 ACAGCCACCGGAAGCAAC 60.595 61.111 9.46 0.00 0.00 4.17
6050 6803 2.594303 CACAGCCACCGGAAGCAA 60.594 61.111 9.46 0.00 0.00 3.91
6051 6804 4.641645 CCACAGCCACCGGAAGCA 62.642 66.667 9.46 0.00 0.00 3.91
6053 6806 3.612247 CTCCCACAGCCACCGGAAG 62.612 68.421 9.46 0.00 0.00 3.46
6054 6807 3.636231 CTCCCACAGCCACCGGAA 61.636 66.667 9.46 0.00 0.00 4.30
6072 6841 1.989165 CAACACAAACACAACCAACGG 59.011 47.619 0.00 0.00 0.00 4.44
6080 6849 2.064762 GCAAGCAACAACACAAACACA 58.935 42.857 0.00 0.00 0.00 3.72
6083 6852 3.253230 AGAAGCAAGCAACAACACAAAC 58.747 40.909 0.00 0.00 0.00 2.93
6084 6853 3.510719 GAGAAGCAAGCAACAACACAAA 58.489 40.909 0.00 0.00 0.00 2.83
6086 6855 1.405105 GGAGAAGCAAGCAACAACACA 59.595 47.619 0.00 0.00 0.00 3.72
6087 6856 1.678101 AGGAGAAGCAAGCAACAACAC 59.322 47.619 0.00 0.00 0.00 3.32
6091 6860 1.677576 CAACAGGAGAAGCAAGCAACA 59.322 47.619 0.00 0.00 0.00 3.33
6092 6861 1.949525 TCAACAGGAGAAGCAAGCAAC 59.050 47.619 0.00 0.00 0.00 4.17
6132 6903 5.296813 GGATACAAAAACTACAGCCACAG 57.703 43.478 0.00 0.00 0.00 3.66
6151 6922 5.221501 GCATTAGCACCATAACCAATTGGAT 60.222 40.000 31.22 21.77 41.58 3.41
6153 6924 4.099881 AGCATTAGCACCATAACCAATTGG 59.900 41.667 23.31 23.31 45.49 3.16
6164 6935 4.337274 CAGAATCAATCAGCATTAGCACCA 59.663 41.667 0.00 0.00 45.49 4.17
6169 6940 6.238676 CCTTCACCAGAATCAATCAGCATTAG 60.239 42.308 0.00 0.00 32.31 1.73
6170 6941 5.591472 CCTTCACCAGAATCAATCAGCATTA 59.409 40.000 0.00 0.00 32.31 1.90
6171 6942 4.401519 CCTTCACCAGAATCAATCAGCATT 59.598 41.667 0.00 0.00 32.31 3.56
6173 6944 3.009363 TCCTTCACCAGAATCAATCAGCA 59.991 43.478 0.00 0.00 32.31 4.41
6174 6945 3.614092 TCCTTCACCAGAATCAATCAGC 58.386 45.455 0.00 0.00 32.31 4.26
6175 6946 4.197750 CCTCCTTCACCAGAATCAATCAG 58.802 47.826 0.00 0.00 32.31 2.90
6176 6947 3.623203 GCCTCCTTCACCAGAATCAATCA 60.623 47.826 0.00 0.00 32.31 2.57
6177 6948 2.948315 GCCTCCTTCACCAGAATCAATC 59.052 50.000 0.00 0.00 32.31 2.67
6178 6949 2.579860 AGCCTCCTTCACCAGAATCAAT 59.420 45.455 0.00 0.00 32.31 2.57
6181 6952 2.637947 GAAGCCTCCTTCACCAGAATC 58.362 52.381 0.00 0.00 45.44 2.52
6182 6953 1.065854 CGAAGCCTCCTTCACCAGAAT 60.066 52.381 4.55 0.00 46.25 2.40
6188 6959 2.383527 CGCACGAAGCCTCCTTCAC 61.384 63.158 0.00 0.00 46.25 3.18
6192 7149 2.167398 TTAAGCGCACGAAGCCTCCT 62.167 55.000 11.47 0.00 41.38 3.69
6199 7156 0.999406 GCTCATCTTAAGCGCACGAA 59.001 50.000 11.47 0.00 0.00 3.85
6206 7163 4.363999 ACATGTAGACGCTCATCTTAAGC 58.636 43.478 0.00 0.00 36.38 3.09
6207 7164 6.634837 CACTACATGTAGACGCTCATCTTAAG 59.365 42.308 34.16 9.43 36.97 1.85
6211 7168 3.316588 CCACTACATGTAGACGCTCATCT 59.683 47.826 34.16 10.05 36.97 2.90
6221 7178 0.457853 ACGCGCACCACTACATGTAG 60.458 55.000 27.66 27.66 39.04 2.74
6222 7179 0.457166 GACGCGCACCACTACATGTA 60.457 55.000 5.73 5.25 0.00 2.29
6223 7180 1.736645 GACGCGCACCACTACATGT 60.737 57.895 5.73 2.69 0.00 3.21
6224 7181 2.788176 CGACGCGCACCACTACATG 61.788 63.158 5.73 0.00 0.00 3.21
6225 7182 2.506217 CGACGCGCACCACTACAT 60.506 61.111 5.73 0.00 0.00 2.29
6237 7194 2.321668 TATTGCCAGCATTGCGACGC 62.322 55.000 14.19 14.19 0.00 5.19
6238 7195 0.308684 ATATTGCCAGCATTGCGACG 59.691 50.000 2.38 0.00 0.00 5.12
6239 7196 1.605710 AGATATTGCCAGCATTGCGAC 59.394 47.619 2.38 0.00 0.00 5.19
6240 7197 1.971481 AGATATTGCCAGCATTGCGA 58.029 45.000 2.38 0.00 0.00 5.10
6241 7198 3.754955 CATAGATATTGCCAGCATTGCG 58.245 45.455 2.38 0.00 0.00 4.85
6324 7325 8.954950 ATTCCTCTGTTGTTCAGTATCATTAG 57.045 34.615 0.00 0.00 43.97 1.73
6329 7330 6.183360 CCGAAATTCCTCTGTTGTTCAGTATC 60.183 42.308 0.00 0.00 43.97 2.24
6336 7337 1.535462 CGCCGAAATTCCTCTGTTGTT 59.465 47.619 0.00 0.00 0.00 2.83
6338 7339 0.447801 CCGCCGAAATTCCTCTGTTG 59.552 55.000 0.00 0.00 0.00 3.33
6341 7342 1.933853 CTAACCGCCGAAATTCCTCTG 59.066 52.381 0.00 0.00 0.00 3.35
6357 7358 4.122776 CACCACTGTATGCTCATCCTAAC 58.877 47.826 0.00 0.00 0.00 2.34
6360 7361 2.169352 GTCACCACTGTATGCTCATCCT 59.831 50.000 0.00 0.00 0.00 3.24
6411 7412 5.702266 TGGCCTGTAGCTAGATTCTAACTA 58.298 41.667 3.32 0.60 43.05 2.24
6450 7454 1.205893 GAACACTCCTCTGCCTACTGG 59.794 57.143 0.00 0.00 0.00 4.00
6454 7458 2.237143 CCATTGAACACTCCTCTGCCTA 59.763 50.000 0.00 0.00 0.00 3.93
6455 7459 1.004044 CCATTGAACACTCCTCTGCCT 59.996 52.381 0.00 0.00 0.00 4.75
6456 7460 1.271597 ACCATTGAACACTCCTCTGCC 60.272 52.381 0.00 0.00 0.00 4.85
6457 7461 2.191128 ACCATTGAACACTCCTCTGC 57.809 50.000 0.00 0.00 0.00 4.26
6458 7462 3.251729 CACAACCATTGAACACTCCTCTG 59.748 47.826 0.00 0.00 0.00 3.35
6459 7463 3.136443 TCACAACCATTGAACACTCCTCT 59.864 43.478 0.00 0.00 0.00 3.69
6460 7464 3.476552 TCACAACCATTGAACACTCCTC 58.523 45.455 0.00 0.00 0.00 3.71
6461 7465 3.576078 TCACAACCATTGAACACTCCT 57.424 42.857 0.00 0.00 0.00 3.69
6468 7472 5.350504 AATTGGTGTTCACAACCATTGAA 57.649 34.783 5.32 0.00 29.13 2.69


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

AutoCloner maintained by Alex Coulton.