Multiple sequence alignment - TraesCS4B01G257800

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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 TraesCS4B01G257800 chr4B 100.000 5757 0 0 1 5757 523454485 523448729 0.000000e+00 10632
1 TraesCS4B01G257800 chr4D 93.421 2903 118 36 2888 5757 427462783 427459921 0.000000e+00 4235
2 TraesCS4B01G257800 chr4D 92.914 2865 114 29 18 2838 427465615 427462796 0.000000e+00 4084
3 TraesCS4B01G257800 chr4A 91.757 2584 108 29 325 2843 38639352 38641895 0.000000e+00 3494
4 TraesCS4B01G257800 chr4A 92.459 1830 72 32 3879 5701 38642872 38644642 0.000000e+00 2555
5 TraesCS4B01G257800 chr4A 89.749 517 46 6 3330 3841 38642361 38642875 0.000000e+00 654
6 TraesCS4B01G257800 chr4A 87.375 301 26 6 2984 3280 38642063 38642355 9.240000e-88 335


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 TraesCS4B01G257800 chr4B 523448729 523454485 5756 True 10632.0 10632 100.0000 1 5757 1 chr4B.!!$R1 5756
1 TraesCS4B01G257800 chr4D 427459921 427465615 5694 True 4159.5 4235 93.1675 18 5757 2 chr4D.!!$R1 5739
2 TraesCS4B01G257800 chr4A 38639352 38644642 5290 False 1759.5 3494 90.3350 325 5701 4 chr4A.!!$F1 5376

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
737 794 0.093705 CGAAGCGCCGAAGAAAAGAG 59.906 55.0 2.29 0.0 0.0 2.85 F
1046 1137 0.313987 TCTTCTTCTTCTGCGTGCGA 59.686 50.0 0.00 0.0 0.0 5.10 F
2283 2404 0.541863 CGTCAACCAATAGCCTCCCT 59.458 55.0 0.00 0.0 0.0 4.20 F
2882 3005 0.593773 TTTTGCGCCGAGTCTTTTGC 60.594 50.0 4.18 0.0 0.0 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1620 1735 0.607217 TGCCGACGTAGAGGAAGTCA 60.607 55.0 8.21 0.0 36.44 3.41 R
2871 2994 0.385974 CAAAGGGCGCAAAAGACTCG 60.386 55.0 10.83 0.0 0.00 4.18 R
3598 3796 0.381089 GCTTCTCTAAGTCGCCGCTA 59.619 55.0 0.00 0.0 34.99 4.26 R
4833 5045 0.178926 TCCTAACCTTGGTCGTCCCA 60.179 55.0 0.00 0.0 43.27 4.37 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
39 40 6.879400 TCCTAGACTTTTGAAGGATAGCTTC 58.121 40.000 0.00 0.00 33.18 3.86
41 42 6.760770 CCTAGACTTTTGAAGGATAGCTTCTG 59.239 42.308 0.00 0.00 0.00 3.02
42 43 4.940654 AGACTTTTGAAGGATAGCTTCTGC 59.059 41.667 0.00 0.00 40.05 4.26
44 45 4.263683 ACTTTTGAAGGATAGCTTCTGCCT 60.264 41.667 0.00 0.00 40.80 4.75
46 47 4.307032 TTGAAGGATAGCTTCTGCCTTT 57.693 40.909 0.00 0.00 40.64 3.11
94 95 5.494724 TCTCATTCTTTGGATCAAGGACAG 58.505 41.667 0.00 0.00 29.47 3.51
168 170 9.023962 TGTTTCTTATGATCAATAAAGCTTGGT 57.976 29.630 0.00 0.00 30.24 3.67
177 179 8.677300 TGATCAATAAAGCTTGGTAGATTGTTC 58.323 33.333 0.00 10.03 28.73 3.18
181 183 9.994432 CAATAAAGCTTGGTAGATTGTTCTAAG 57.006 33.333 0.00 0.00 36.23 2.18
204 210 7.634671 AGAAAAACTAATACCATTAACGGGG 57.365 36.000 0.00 0.00 0.00 5.73
208 214 0.927767 AATACCATTAACGGGGGCCA 59.072 50.000 4.39 0.00 0.00 5.36
234 240 3.636764 TGGCAAGGAGGAAAAGAAACTTC 59.363 43.478 0.00 0.00 0.00 3.01
248 254 3.251972 AGAAACTTCACTAGCAAAGCAGC 59.748 43.478 4.95 0.00 0.00 5.25
284 290 4.643387 AACCTGACCCGGCACTGC 62.643 66.667 0.00 0.00 0.00 4.40
315 321 3.120095 GCATTTGCTGGAATCAAAAAGGC 60.120 43.478 0.00 0.00 37.04 4.35
330 336 1.915078 AAGGCCTCTCCGTCCATTGG 61.915 60.000 5.23 0.00 40.77 3.16
349 361 3.081061 TGGCAACGTTATGAATCAAGCT 58.919 40.909 0.00 0.00 42.51 3.74
350 362 4.257731 TGGCAACGTTATGAATCAAGCTA 58.742 39.130 0.00 0.00 42.51 3.32
351 363 4.697828 TGGCAACGTTATGAATCAAGCTAA 59.302 37.500 0.00 0.00 42.51 3.09
352 364 5.356751 TGGCAACGTTATGAATCAAGCTAAT 59.643 36.000 0.00 0.00 42.51 1.73
361 373 9.651718 GTTATGAATCAAGCTAATTAACGAAGG 57.348 33.333 0.00 0.00 0.00 3.46
375 387 1.604278 ACGAAGGCAGTCAAAAGAAGC 59.396 47.619 0.00 0.00 0.00 3.86
376 388 1.068954 CGAAGGCAGTCAAAAGAAGCC 60.069 52.381 0.00 0.00 45.54 4.35
490 525 3.920231 TTGTTGATGATAGAGCTGGCT 57.080 42.857 0.00 0.00 0.00 4.75
529 570 5.581126 ATCGTGCATGTGTGGAATATTTT 57.419 34.783 5.68 0.00 0.00 1.82
564 605 1.678724 GGGCGTACCAACCTACCAA 59.321 57.895 0.00 0.00 39.85 3.67
567 608 1.673923 GGCGTACCAACCTACCAAGAC 60.674 57.143 0.00 0.00 35.26 3.01
573 614 1.835531 CCAACCTACCAAGACCCGTAT 59.164 52.381 0.00 0.00 0.00 3.06
574 615 2.237893 CCAACCTACCAAGACCCGTATT 59.762 50.000 0.00 0.00 0.00 1.89
581 622 7.275183 ACCTACCAAGACCCGTATTTTATAAC 58.725 38.462 0.00 0.00 0.00 1.89
586 627 5.963214 AGACCCGTATTTTATAACCCACT 57.037 39.130 0.00 0.00 0.00 4.00
632 673 6.403636 CGAAATCTCCATTCCGATCAAAGTTT 60.404 38.462 0.00 0.00 0.00 2.66
686 732 3.623510 GGCAGGAAAAAGAGGTTAGATCG 59.376 47.826 0.00 0.00 0.00 3.69
692 744 5.120363 GGAAAAAGAGGTTAGATCGACACAC 59.880 44.000 0.00 0.00 0.00 3.82
694 746 6.585695 AAAAGAGGTTAGATCGACACACTA 57.414 37.500 0.00 0.00 0.00 2.74
695 747 6.585695 AAAGAGGTTAGATCGACACACTAA 57.414 37.500 0.00 0.00 0.00 2.24
697 749 6.380095 AGAGGTTAGATCGACACACTAATC 57.620 41.667 0.00 0.00 0.00 1.75
701 758 6.377429 AGGTTAGATCGACACACTAATCTTCA 59.623 38.462 9.13 0.00 35.04 3.02
720 777 0.546122 ATAGTGGGATGCCAAAGCGA 59.454 50.000 7.86 0.00 44.31 4.93
735 792 4.725758 CGAAGCGCCGAAGAAAAG 57.274 55.556 2.29 0.00 0.00 2.27
736 793 2.150424 CGAAGCGCCGAAGAAAAGA 58.850 52.632 2.29 0.00 0.00 2.52
737 794 0.093705 CGAAGCGCCGAAGAAAAGAG 59.906 55.000 2.29 0.00 0.00 2.85
738 795 1.429463 GAAGCGCCGAAGAAAAGAGA 58.571 50.000 2.29 0.00 0.00 3.10
805 872 4.508128 GCAGATTCGGGCCGTCGA 62.508 66.667 27.32 13.70 37.38 4.20
818 891 2.202703 GTCGAAGGCGCCACGTAT 60.203 61.111 32.76 15.21 37.46 3.06
877 959 0.389817 TGGCGATCGCATATGGTAGC 60.390 55.000 38.00 19.51 44.11 3.58
893 975 1.035385 TAGCACATCTCCGAAGCCGA 61.035 55.000 0.00 0.00 38.22 5.54
894 976 1.447838 GCACATCTCCGAAGCCGAA 60.448 57.895 0.00 0.00 38.22 4.30
895 977 1.424493 GCACATCTCCGAAGCCGAAG 61.424 60.000 0.00 0.00 38.22 3.79
943 1025 3.356290 GTCTTCTCTCTCCTCTCAGCTT 58.644 50.000 0.00 0.00 0.00 3.74
1017 1099 2.745492 GAAGCTGCGCTCTGGCTT 60.745 61.111 22.40 22.40 46.99 4.35
1025 1107 1.662044 CGCTCTGGCTTTGGCTTTT 59.338 52.632 0.00 0.00 38.73 2.27
1026 1108 0.881118 CGCTCTGGCTTTGGCTTTTA 59.119 50.000 0.00 0.00 38.73 1.52
1037 1128 6.096036 GGCTTTGGCTTTTATCTTCTTCTTC 58.904 40.000 0.00 0.00 38.73 2.87
1046 1137 0.313987 TCTTCTTCTTCTGCGTGCGA 59.686 50.000 0.00 0.00 0.00 5.10
1185 1276 3.123620 CTGCACCAGCCGCTCTTC 61.124 66.667 0.00 0.00 41.13 2.87
1254 1345 3.316573 CTTCACCTCCGACCCCAGC 62.317 68.421 0.00 0.00 0.00 4.85
1356 1471 1.675641 GTCCAGTGATGGTGGTGGC 60.676 63.158 0.00 0.00 36.37 5.01
2152 2273 1.541672 CAACCCTCCAACCCACCTT 59.458 57.895 0.00 0.00 0.00 3.50
2160 2281 3.494254 AACCCACCTTCACGGCCA 61.494 61.111 2.24 0.00 35.61 5.36
2161 2282 3.785122 AACCCACCTTCACGGCCAC 62.785 63.158 2.24 0.00 35.61 5.01
2271 2392 3.124921 CCACCGATGGCGTCAACC 61.125 66.667 7.60 0.00 39.82 3.77
2274 2395 1.002624 ACCGATGGCGTCAACCAAT 60.003 52.632 7.60 0.00 44.65 3.16
2283 2404 0.541863 CGTCAACCAATAGCCTCCCT 59.458 55.000 0.00 0.00 0.00 4.20
2582 2705 3.014623 CTCTATCCGTATATGCCGGTGA 58.985 50.000 1.90 10.10 45.63 4.02
2583 2706 2.751259 TCTATCCGTATATGCCGGTGAC 59.249 50.000 1.90 0.00 45.63 3.67
2843 2966 1.534595 GGTGAGTGTTTGTGCTGCAAG 60.535 52.381 2.77 0.00 38.47 4.01
2868 2991 5.801947 CCTGCAACTACTGTCATAATTTTGC 59.198 40.000 0.00 0.00 38.83 3.68
2869 2992 5.389778 TGCAACTACTGTCATAATTTTGCG 58.610 37.500 0.00 0.00 40.76 4.85
2870 2993 4.262976 GCAACTACTGTCATAATTTTGCGC 59.737 41.667 0.00 0.00 0.00 6.09
2871 2994 4.616181 ACTACTGTCATAATTTTGCGCC 57.384 40.909 4.18 0.00 0.00 6.53
2872 2995 2.542766 ACTGTCATAATTTTGCGCCG 57.457 45.000 4.18 0.00 0.00 6.46
2873 2996 2.080693 ACTGTCATAATTTTGCGCCGA 58.919 42.857 4.18 0.00 0.00 5.54
2874 2997 2.095853 ACTGTCATAATTTTGCGCCGAG 59.904 45.455 4.18 0.00 0.00 4.63
2875 2998 2.080693 TGTCATAATTTTGCGCCGAGT 58.919 42.857 4.18 0.00 0.00 4.18
2876 2999 2.095213 TGTCATAATTTTGCGCCGAGTC 59.905 45.455 4.18 0.00 0.00 3.36
2877 3000 2.351726 GTCATAATTTTGCGCCGAGTCT 59.648 45.455 4.18 0.00 0.00 3.24
2878 3001 3.006940 TCATAATTTTGCGCCGAGTCTT 58.993 40.909 4.18 0.00 0.00 3.01
2879 3002 3.438781 TCATAATTTTGCGCCGAGTCTTT 59.561 39.130 4.18 0.00 0.00 2.52
2880 3003 2.793278 AATTTTGCGCCGAGTCTTTT 57.207 40.000 4.18 0.00 0.00 2.27
2881 3004 2.050477 ATTTTGCGCCGAGTCTTTTG 57.950 45.000 4.18 0.00 0.00 2.44
2882 3005 0.593773 TTTTGCGCCGAGTCTTTTGC 60.594 50.000 4.18 0.00 0.00 3.68
2885 3008 4.445545 CGCCGAGTCTTTTGCGCC 62.446 66.667 4.18 0.00 40.58 6.53
2886 3009 4.103103 GCCGAGTCTTTTGCGCCC 62.103 66.667 4.18 0.00 0.00 6.13
2893 3016 1.270550 AGTCTTTTGCGCCCTTTGATG 59.729 47.619 4.18 0.00 0.00 3.07
2900 3023 2.958213 TGCGCCCTTTGATGAAATTTC 58.042 42.857 11.41 11.41 0.00 2.17
2942 3065 3.726607 AGCATTCGCAAAATTGAACCAA 58.273 36.364 0.00 0.00 42.27 3.67
2948 3074 4.116238 TCGCAAAATTGAACCAACTTTCC 58.884 39.130 0.00 0.00 0.00 3.13
2982 3108 8.736097 TTAGCTAAGAAATATGATACTCCCCA 57.264 34.615 0.86 0.00 0.00 4.96
2986 3177 8.951243 GCTAAGAAATATGATACTCCCCAATTC 58.049 37.037 0.00 0.00 0.00 2.17
3000 3191 3.392882 CCCAATTCTGTTTGCAAACCTC 58.607 45.455 33.33 14.55 38.11 3.85
3293 3491 4.860907 GTGAACATCCAGCAATTGATGAAC 59.139 41.667 24.73 10.73 40.64 3.18
3373 3571 6.238621 CCAAAGTCCAAAACCTAAAATTTGCC 60.239 38.462 0.00 0.00 35.66 4.52
3377 3575 4.041075 TCCAAAACCTAAAATTTGCCCTCC 59.959 41.667 0.00 0.00 35.66 4.30
3404 3602 5.556915 TCAAACGTTCACCCTGATTTCTAT 58.443 37.500 0.00 0.00 0.00 1.98
3410 3608 7.963532 ACGTTCACCCTGATTTCTATACATAT 58.036 34.615 0.00 0.00 0.00 1.78
3457 3655 4.444056 GCGTTGTGCTGTTTACATCATTTT 59.556 37.500 0.00 0.00 41.73 1.82
3464 3662 7.860373 TGTGCTGTTTACATCATTTTTCTGTAC 59.140 33.333 0.00 0.00 0.00 2.90
3492 3690 6.769512 AGTGTCCACTGACTACATTATTTGT 58.230 36.000 0.00 0.00 42.28 2.83
3498 3696 6.316390 CCACTGACTACATTATTTGTTCTCCC 59.684 42.308 0.00 0.00 39.87 4.30
3523 3721 1.067425 TGAACAGGCAATGCTGAATGC 60.067 47.619 4.82 0.00 41.82 3.56
3560 3758 7.014615 AGCTTTTGGAAACATTAGTCAAGATGT 59.985 33.333 0.00 0.00 42.32 3.06
3598 3796 5.302313 GGAGGAGGTCAAACTACGAGATTAT 59.698 44.000 0.00 0.00 0.00 1.28
3612 3810 3.124806 CGAGATTATAGCGGCGACTTAGA 59.875 47.826 12.98 0.00 0.00 2.10
3758 3956 3.603158 TTGAAACGCTAGAGGTATGCA 57.397 42.857 0.00 0.00 0.00 3.96
3759 3957 2.888594 TGAAACGCTAGAGGTATGCAC 58.111 47.619 0.00 0.00 0.00 4.57
3760 3958 2.496070 TGAAACGCTAGAGGTATGCACT 59.504 45.455 0.00 0.00 0.00 4.40
3761 3959 3.697542 TGAAACGCTAGAGGTATGCACTA 59.302 43.478 0.00 0.00 0.00 2.74
3766 3964 5.671493 ACGCTAGAGGTATGCACTATTTTT 58.329 37.500 0.00 0.00 0.00 1.94
3769 3967 7.767198 ACGCTAGAGGTATGCACTATTTTTAAA 59.233 33.333 0.00 0.00 0.00 1.52
3770 3968 8.609176 CGCTAGAGGTATGCACTATTTTTAAAA 58.391 33.333 0.00 0.00 0.00 1.52
3797 3996 2.509569 TGTCATTTTGGTACCGCACAT 58.490 42.857 7.57 0.00 0.00 3.21
3807 4008 2.093869 GGTACCGCACATCCTTGACTTA 60.094 50.000 0.00 0.00 0.00 2.24
3808 4009 2.094762 ACCGCACATCCTTGACTTAC 57.905 50.000 0.00 0.00 0.00 2.34
3843 4044 5.717178 TCAATATCCATACTCAGCTACTCCC 59.283 44.000 0.00 0.00 0.00 4.30
3848 4049 1.475403 TACTCAGCTACTCCCACTGC 58.525 55.000 0.00 0.00 0.00 4.40
3851 4052 1.140589 CAGCTACTCCCACTGCTCG 59.859 63.158 0.00 0.00 33.03 5.03
3859 4060 2.766263 ACTCCCACTGCTCGATAATTCA 59.234 45.455 0.00 0.00 0.00 2.57
3861 4062 4.141620 ACTCCCACTGCTCGATAATTCATT 60.142 41.667 0.00 0.00 0.00 2.57
3863 4064 5.192927 TCCCACTGCTCGATAATTCATTTT 58.807 37.500 0.00 0.00 0.00 1.82
3870 4082 6.027131 TGCTCGATAATTCATTTTTGGAACG 58.973 36.000 0.00 0.00 0.00 3.95
3882 4094 5.502089 TTTTTGGAACGGAGGGAGTATTA 57.498 39.130 0.00 0.00 0.00 0.98
3883 4095 4.748277 TTTGGAACGGAGGGAGTATTAG 57.252 45.455 0.00 0.00 0.00 1.73
3944 4156 2.092699 AGCTTGTGAAGATCTTAGGGGC 60.093 50.000 8.25 9.45 0.00 5.80
3947 4159 2.551270 TGTGAAGATCTTAGGGGCAGT 58.449 47.619 8.25 0.00 0.00 4.40
4127 4339 4.486125 TGTCCAAGAAATGATCCGATCA 57.514 40.909 13.46 13.46 44.55 2.92
4140 4352 0.640768 CCGATCAGAAGACGCGAAAC 59.359 55.000 15.93 3.56 0.00 2.78
4160 4372 6.460399 CGAAACCTGAAAAGGAAAATACCACA 60.460 38.462 0.00 0.00 0.00 4.17
4286 4498 0.529773 ACGTCAGCAAGCTCGAAACA 60.530 50.000 9.68 0.00 0.00 2.83
4499 4711 2.586792 GCGCACCCTCTGAGGATT 59.413 61.111 25.18 8.58 37.67 3.01
4685 4897 2.480802 CTCCGACGACGATGATGATAGT 59.519 50.000 9.28 0.00 42.66 2.12
4705 4917 0.255318 ATGTCGTCGTAGGAGAGGGT 59.745 55.000 0.00 0.00 0.00 4.34
4707 4919 0.392193 GTCGTCGTAGGAGAGGGTGA 60.392 60.000 0.00 0.00 0.00 4.02
4708 4920 0.107800 TCGTCGTAGGAGAGGGTGAG 60.108 60.000 0.00 0.00 0.00 3.51
4711 4923 1.212934 TCGTAGGAGAGGGTGAGGGT 61.213 60.000 0.00 0.00 0.00 4.34
4714 4926 1.153695 TAGGAGAGGGTGAGGGTGGT 61.154 60.000 0.00 0.00 0.00 4.16
4717 4929 2.529389 GAGGGTGAGGGTGGTGGT 60.529 66.667 0.00 0.00 0.00 4.16
4965 5177 2.362736 TGCAATGCTGAGGCTTAGAAG 58.637 47.619 10.92 0.00 39.59 2.85
4989 5204 5.523438 AGGCTGCTTCACTAGTTATCTAC 57.477 43.478 0.00 0.00 0.00 2.59
4990 5205 5.205056 AGGCTGCTTCACTAGTTATCTACT 58.795 41.667 0.00 0.00 41.04 2.57
4991 5206 5.300792 AGGCTGCTTCACTAGTTATCTACTC 59.699 44.000 0.00 0.00 38.33 2.59
4999 5214 2.500509 AGTTATCTACTCGCAGCAGC 57.499 50.000 0.00 0.00 28.23 5.25
5013 5228 0.686789 AGCAGCTACACATGGTCACA 59.313 50.000 0.00 0.00 0.00 3.58
5014 5229 1.081892 GCAGCTACACATGGTCACAG 58.918 55.000 0.00 0.00 0.00 3.66
5015 5230 1.730501 CAGCTACACATGGTCACAGG 58.269 55.000 0.00 0.00 0.00 4.00
5016 5231 1.276138 CAGCTACACATGGTCACAGGA 59.724 52.381 0.00 0.00 31.68 3.86
5144 5362 4.227197 TCAGGAACCAGCCCAAAATTAAA 58.773 39.130 0.00 0.00 0.00 1.52
5179 5397 7.908827 TCAGAACAACTGTAAACAACTTACA 57.091 32.000 0.00 0.00 46.16 2.41
5182 5400 9.221775 CAGAACAACTGTAAACAACTTACATTC 57.778 33.333 0.00 0.80 46.88 2.67
5197 5415 5.938125 ACTTACATTCACCCACTGTACAATC 59.062 40.000 0.00 0.00 0.00 2.67
5228 5446 1.909700 ATTTCTCCTGCGCTTGGAAA 58.090 45.000 19.87 17.73 32.61 3.13
5233 5451 0.667993 TCCTGCGCTTGGAAAAACAG 59.332 50.000 17.84 0.00 0.00 3.16
5338 5556 7.070447 TCCAGATATCTCTGCAAGTAACAGAAT 59.930 37.037 1.03 0.00 46.39 2.40
5341 5559 4.623932 TCTCTGCAAGTAACAGAATGGT 57.376 40.909 0.00 0.00 43.30 3.55
5365 5583 3.652057 AAGGGGAACCATCACTATGTG 57.348 47.619 0.00 0.00 40.34 3.21
5366 5584 2.562296 AGGGGAACCATCACTATGTGT 58.438 47.619 0.00 0.00 40.34 3.72
5367 5585 2.919602 AGGGGAACCATCACTATGTGTT 59.080 45.455 0.00 0.00 40.34 3.32
5368 5586 4.108570 AGGGGAACCATCACTATGTGTTA 58.891 43.478 0.00 0.00 40.34 2.41
5369 5587 4.164221 AGGGGAACCATCACTATGTGTTAG 59.836 45.833 0.00 0.00 40.34 2.34
5417 5635 3.935828 GTCAAGGTAAAGGATGAGAGCAC 59.064 47.826 0.00 0.00 0.00 4.40
5534 5769 3.740452 CGATGGAGATCACTTGAGCATGT 60.740 47.826 0.00 0.00 31.88 3.21
5565 5800 4.669318 CGTAGAGATAAAGAAAGCACCGA 58.331 43.478 0.00 0.00 0.00 4.69
5647 5882 1.004560 CTTCACGAGCCTGCCTTCA 60.005 57.895 0.00 0.00 0.00 3.02
5651 5886 1.078143 ACGAGCCTGCCTTCATTCC 60.078 57.895 0.00 0.00 0.00 3.01
5657 5892 1.760192 CCTGCCTTCATTCCTTCCTG 58.240 55.000 0.00 0.00 0.00 3.86
5658 5893 1.005215 CCTGCCTTCATTCCTTCCTGT 59.995 52.381 0.00 0.00 0.00 4.00
5659 5894 2.239654 CCTGCCTTCATTCCTTCCTGTA 59.760 50.000 0.00 0.00 0.00 2.74
5660 5895 3.539604 CTGCCTTCATTCCTTCCTGTAG 58.460 50.000 0.00 0.00 0.00 2.74
5661 5896 2.912956 TGCCTTCATTCCTTCCTGTAGT 59.087 45.455 0.00 0.00 0.00 2.73
5689 5924 2.695666 AGTAGAATGGAGACGTGATGGG 59.304 50.000 0.00 0.00 0.00 4.00
5715 5950 1.138883 GAGCCGCTATCGTGTGTGA 59.861 57.895 0.00 0.00 0.00 3.58
5717 5952 1.153823 GCCGCTATCGTGTGTGAGT 60.154 57.895 0.00 0.00 0.00 3.41
5718 5953 0.099968 GCCGCTATCGTGTGTGAGTA 59.900 55.000 0.00 0.00 0.00 2.59
5721 5956 2.852413 CCGCTATCGTGTGTGAGTAAAG 59.148 50.000 0.00 0.00 0.00 1.85
5722 5957 2.852413 CGCTATCGTGTGTGAGTAAAGG 59.148 50.000 0.00 0.00 0.00 3.11
5723 5958 3.672511 CGCTATCGTGTGTGAGTAAAGGT 60.673 47.826 0.00 0.00 0.00 3.50
5724 5959 4.437794 CGCTATCGTGTGTGAGTAAAGGTA 60.438 45.833 0.00 0.00 0.00 3.08
5734 5970 7.065443 GTGTGTGAGTAAAGGTAAAAACAGAGT 59.935 37.037 0.00 0.00 0.00 3.24
5747 5983 3.857157 AACAGAGTGAAGCAAAGGGTA 57.143 42.857 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.549347 AGTCTAGGATAGCTGCAATCAATG 58.451 41.667 1.02 0.00 38.99 2.82
1 2 5.822132 AGTCTAGGATAGCTGCAATCAAT 57.178 39.130 1.02 0.00 38.99 2.57
2 3 5.620738 AAGTCTAGGATAGCTGCAATCAA 57.379 39.130 1.02 0.00 38.99 2.57
3 4 5.620738 AAAGTCTAGGATAGCTGCAATCA 57.379 39.130 1.02 0.00 38.99 2.57
4 5 6.051717 TCAAAAGTCTAGGATAGCTGCAATC 58.948 40.000 1.02 0.00 38.99 2.67
5 6 5.994250 TCAAAAGTCTAGGATAGCTGCAAT 58.006 37.500 1.02 0.00 38.99 3.56
6 7 5.420725 TCAAAAGTCTAGGATAGCTGCAA 57.579 39.130 1.02 0.00 38.99 4.08
7 8 5.420725 TTCAAAAGTCTAGGATAGCTGCA 57.579 39.130 1.02 0.00 38.99 4.41
8 9 4.813697 CCTTCAAAAGTCTAGGATAGCTGC 59.186 45.833 0.00 0.00 38.99 5.25
9 10 6.227298 TCCTTCAAAAGTCTAGGATAGCTG 57.773 41.667 0.00 0.00 38.99 4.24
13 14 8.554490 AAGCTATCCTTCAAAAGTCTAGGATA 57.446 34.615 0.00 0.00 43.83 2.59
14 15 7.444703 AAGCTATCCTTCAAAAGTCTAGGAT 57.555 36.000 0.00 0.00 46.49 3.24
15 16 6.875972 AAGCTATCCTTCAAAAGTCTAGGA 57.124 37.500 0.00 0.00 40.82 2.94
39 40 0.947244 AGCGTGAGTTTCAAAGGCAG 59.053 50.000 0.00 0.00 0.00 4.85
41 42 1.069636 CAGAGCGTGAGTTTCAAAGGC 60.070 52.381 0.00 0.00 0.00 4.35
42 43 1.532868 CCAGAGCGTGAGTTTCAAAGG 59.467 52.381 0.00 0.00 0.00 3.11
44 45 0.944386 GCCAGAGCGTGAGTTTCAAA 59.056 50.000 0.00 0.00 0.00 2.69
46 47 1.301716 GGCCAGAGCGTGAGTTTCA 60.302 57.895 0.00 0.00 41.24 2.69
107 109 2.812836 ATGTGATCATGAGGTTGGCA 57.187 45.000 0.00 0.00 32.51 4.92
181 183 6.681120 GCCCCCGTTAATGGTATTAGTTTTTC 60.681 42.308 12.77 0.00 0.00 2.29
194 196 0.530288 CAAGTTGGCCCCCGTTAATG 59.470 55.000 0.00 0.00 0.00 1.90
208 214 3.312736 TCTTTTCCTCCTTGCCAAGTT 57.687 42.857 3.37 0.00 0.00 2.66
234 240 1.337703 TGGTTTGCTGCTTTGCTAGTG 59.662 47.619 0.00 0.00 0.00 2.74
248 254 2.859981 GCCACCCTGCACTGGTTTG 61.860 63.158 0.28 0.00 32.46 2.93
315 321 1.026718 GTTGCCAATGGACGGAGAGG 61.027 60.000 2.05 0.00 0.00 3.69
330 336 8.734030 GTTAATTAGCTTGATTCATAACGTTGC 58.266 33.333 11.99 1.89 0.00 4.17
349 361 7.499321 TTCTTTTGACTGCCTTCGTTAATTA 57.501 32.000 0.00 0.00 0.00 1.40
350 362 6.385649 TTCTTTTGACTGCCTTCGTTAATT 57.614 33.333 0.00 0.00 0.00 1.40
351 363 5.562890 GCTTCTTTTGACTGCCTTCGTTAAT 60.563 40.000 0.00 0.00 0.00 1.40
352 364 4.261031 GCTTCTTTTGACTGCCTTCGTTAA 60.261 41.667 0.00 0.00 0.00 2.01
361 373 4.773323 ATTAGTGGCTTCTTTTGACTGC 57.227 40.909 0.00 0.00 0.00 4.40
375 387 3.105203 CGCACCGCATTTTAATTAGTGG 58.895 45.455 1.55 1.55 37.65 4.00
490 525 2.252747 CGATACTTTGCGTACCGACAA 58.747 47.619 0.00 0.00 37.28 3.18
529 570 3.115892 CGCCGCGCAAGGTAAAGA 61.116 61.111 8.75 0.00 38.28 2.52
564 605 5.963214 AGTGGGTTATAAAATACGGGTCT 57.037 39.130 0.00 0.00 0.00 3.85
567 608 7.557358 AGGTTTTAGTGGGTTATAAAATACGGG 59.443 37.037 0.00 0.00 34.41 5.28
574 615 9.519191 GTTTAGGAGGTTTTAGTGGGTTATAAA 57.481 33.333 0.00 0.00 0.00 1.40
581 622 2.745821 GCGTTTAGGAGGTTTTAGTGGG 59.254 50.000 0.00 0.00 0.00 4.61
586 627 2.809696 GTGCTGCGTTTAGGAGGTTTTA 59.190 45.455 0.00 0.00 38.88 1.52
614 655 5.782893 ACAAAAACTTTGATCGGAATGGA 57.217 34.783 6.15 0.00 0.00 3.41
632 673 3.252215 GTGTGCAGGTGCTAATGTACAAA 59.748 43.478 0.00 0.00 42.41 2.83
686 732 6.222038 TCCCACTATGAAGATTAGTGTGTC 57.778 41.667 9.31 0.00 43.21 3.67
692 744 5.233083 TGGCATCCCACTATGAAGATTAG 57.767 43.478 0.00 0.00 35.79 1.73
694 746 4.524802 TTGGCATCCCACTATGAAGATT 57.475 40.909 0.00 0.00 41.97 2.40
695 747 4.467769 CTTTGGCATCCCACTATGAAGAT 58.532 43.478 0.00 0.00 41.97 2.40
697 749 2.360165 GCTTTGGCATCCCACTATGAAG 59.640 50.000 0.00 0.00 41.97 3.02
701 758 0.546122 TCGCTTTGGCATCCCACTAT 59.454 50.000 0.00 0.00 41.97 2.12
720 777 1.801178 CTTCTCTTTTCTTCGGCGCTT 59.199 47.619 7.64 0.00 0.00 4.68
734 791 2.224314 CGCCGCTTTTCTTTTCTTCTCT 59.776 45.455 0.00 0.00 0.00 3.10
735 792 2.223377 TCGCCGCTTTTCTTTTCTTCTC 59.777 45.455 0.00 0.00 0.00 2.87
736 793 2.218603 TCGCCGCTTTTCTTTTCTTCT 58.781 42.857 0.00 0.00 0.00 2.85
737 794 2.575363 CTCGCCGCTTTTCTTTTCTTC 58.425 47.619 0.00 0.00 0.00 2.87
738 795 1.266989 CCTCGCCGCTTTTCTTTTCTT 59.733 47.619 0.00 0.00 0.00 2.52
805 872 1.686325 ATCTCCATACGTGGCGCCTT 61.686 55.000 29.70 14.52 45.63 4.35
818 891 3.377253 ACGGTCTGGTAGTAATCTCCA 57.623 47.619 0.00 0.00 0.00 3.86
820 893 4.715527 ACAACGGTCTGGTAGTAATCTC 57.284 45.455 0.00 0.00 0.00 2.75
822 895 4.813027 TCAACAACGGTCTGGTAGTAATC 58.187 43.478 0.00 0.00 0.00 1.75
823 896 4.877378 TCAACAACGGTCTGGTAGTAAT 57.123 40.909 0.00 0.00 0.00 1.89
824 897 4.525487 AGATCAACAACGGTCTGGTAGTAA 59.475 41.667 0.00 0.00 0.00 2.24
825 898 4.084287 AGATCAACAACGGTCTGGTAGTA 58.916 43.478 0.00 0.00 0.00 1.82
826 899 2.897969 AGATCAACAACGGTCTGGTAGT 59.102 45.455 0.00 0.00 0.00 2.73
827 900 3.512680 GAGATCAACAACGGTCTGGTAG 58.487 50.000 0.00 0.00 0.00 3.18
877 959 1.424493 GCTTCGGCTTCGGAGATGTG 61.424 60.000 0.00 0.00 41.91 3.21
943 1025 3.375699 GGAGGGGAGAGAGTGTGAATTA 58.624 50.000 0.00 0.00 0.00 1.40
1017 1099 5.106555 CGCAGAAGAAGAAGATAAAAGCCAA 60.107 40.000 0.00 0.00 0.00 4.52
1025 1107 2.163613 TCGCACGCAGAAGAAGAAGATA 59.836 45.455 0.00 0.00 0.00 1.98
1026 1108 1.067565 TCGCACGCAGAAGAAGAAGAT 60.068 47.619 0.00 0.00 0.00 2.40
1371 1486 2.047560 GGAGGGGACGAAACCGTG 60.048 66.667 0.00 0.00 40.80 4.94
1376 1491 0.179012 GGTGTTTGGAGGGGACGAAA 60.179 55.000 0.00 0.00 0.00 3.46
1521 1636 2.267642 CGGCCGGTGATGAGGAAA 59.732 61.111 20.10 0.00 0.00 3.13
1620 1735 0.607217 TGCCGACGTAGAGGAAGTCA 60.607 55.000 8.21 0.00 36.44 3.41
2162 2283 3.775654 GAGGAGGAGGTGGTGGCG 61.776 72.222 0.00 0.00 0.00 5.69
2172 2293 1.230650 TGGAGGAGGAGGAGGAGGA 60.231 63.158 0.00 0.00 0.00 3.71
2221 2342 1.451936 GTGGTGGTCTTGGAGCTGT 59.548 57.895 0.00 0.00 0.00 4.40
2271 2392 2.743183 CGTCTTTGGAGGGAGGCTATTG 60.743 54.545 0.00 0.00 0.00 1.90
2274 2395 0.976073 CCGTCTTTGGAGGGAGGCTA 60.976 60.000 0.00 0.00 46.96 3.93
2283 2404 3.327404 GGCTCCCCCGTCTTTGGA 61.327 66.667 0.00 0.00 0.00 3.53
2582 2705 1.816863 ATCACGCACAGTTCGGAGGT 61.817 55.000 0.00 0.00 0.00 3.85
2583 2706 1.079819 ATCACGCACAGTTCGGAGG 60.080 57.895 0.00 0.00 0.00 4.30
2822 2945 0.679321 TGCAGCACAAACACTCACCA 60.679 50.000 0.00 0.00 0.00 4.17
2843 2966 5.567138 AAATTATGACAGTAGTTGCAGGC 57.433 39.130 0.00 0.00 0.00 4.85
2845 2968 5.509272 CGCAAAATTATGACAGTAGTTGCAG 59.491 40.000 0.00 0.00 40.00 4.41
2848 2971 4.793216 GGCGCAAAATTATGACAGTAGTTG 59.207 41.667 10.83 0.00 0.00 3.16
2849 2972 4.436852 CGGCGCAAAATTATGACAGTAGTT 60.437 41.667 10.83 0.00 0.00 2.24
2850 2973 3.063452 CGGCGCAAAATTATGACAGTAGT 59.937 43.478 10.83 0.00 0.00 2.73
2851 2974 3.308595 TCGGCGCAAAATTATGACAGTAG 59.691 43.478 10.83 0.00 0.00 2.57
2852 2975 3.263261 TCGGCGCAAAATTATGACAGTA 58.737 40.909 10.83 0.00 0.00 2.74
2853 2976 2.080693 TCGGCGCAAAATTATGACAGT 58.919 42.857 10.83 0.00 0.00 3.55
2854 2977 2.095853 ACTCGGCGCAAAATTATGACAG 59.904 45.455 10.83 0.00 0.00 3.51
2858 2981 3.405170 AAGACTCGGCGCAAAATTATG 57.595 42.857 10.83 0.00 0.00 1.90
2869 2992 4.103103 GGGCGCAAAAGACTCGGC 62.103 66.667 10.83 0.00 46.07 5.54
2870 2993 1.515521 AAAGGGCGCAAAAGACTCGG 61.516 55.000 10.83 0.00 0.00 4.63
2871 2994 0.385974 CAAAGGGCGCAAAAGACTCG 60.386 55.000 10.83 0.00 0.00 4.18
2872 2995 0.951558 TCAAAGGGCGCAAAAGACTC 59.048 50.000 10.83 0.00 0.00 3.36
2873 2996 1.270550 CATCAAAGGGCGCAAAAGACT 59.729 47.619 10.83 0.00 0.00 3.24
2874 2997 1.269448 TCATCAAAGGGCGCAAAAGAC 59.731 47.619 10.83 0.00 0.00 3.01
2875 2998 1.614996 TCATCAAAGGGCGCAAAAGA 58.385 45.000 10.83 0.00 0.00 2.52
2876 2999 2.437200 TTCATCAAAGGGCGCAAAAG 57.563 45.000 10.83 0.00 0.00 2.27
2877 3000 2.898729 TTTCATCAAAGGGCGCAAAA 57.101 40.000 10.83 0.00 0.00 2.44
2878 3001 3.399440 AATTTCATCAAAGGGCGCAAA 57.601 38.095 10.83 0.00 0.00 3.68
2879 3002 3.244009 TGAAATTTCATCAAAGGGCGCAA 60.244 39.130 16.91 0.00 31.01 4.85
2880 3003 2.298446 TGAAATTTCATCAAAGGGCGCA 59.702 40.909 16.91 0.00 31.01 6.09
2881 3004 2.925563 CTGAAATTTCATCAAAGGGCGC 59.074 45.455 20.76 0.00 36.46 6.53
2882 3005 2.925563 GCTGAAATTTCATCAAAGGGCG 59.074 45.455 20.76 7.51 36.46 6.13
2883 3006 4.179298 GAGCTGAAATTTCATCAAAGGGC 58.821 43.478 20.76 17.44 36.46 5.19
2884 3007 5.395682 TGAGCTGAAATTTCATCAAAGGG 57.604 39.130 20.76 8.87 36.46 3.95
2885 3008 7.900782 AAATGAGCTGAAATTTCATCAAAGG 57.099 32.000 22.07 11.88 36.46 3.11
2886 3009 9.807386 GAAAAATGAGCTGAAATTTCATCAAAG 57.193 29.630 22.07 12.47 36.46 2.77
2893 3016 6.925165 TCAGGTGAAAAATGAGCTGAAATTTC 59.075 34.615 11.41 11.41 42.27 2.17
2900 3023 5.106038 TGCTAATCAGGTGAAAAATGAGCTG 60.106 40.000 0.00 0.00 38.74 4.24
2942 3065 6.827727 TCTTAGCTAAAGAACAGTGGAAAGT 58.172 36.000 7.74 0.00 41.35 2.66
2976 3102 3.392882 GTTTGCAAACAGAATTGGGGAG 58.607 45.455 32.21 0.00 38.74 4.30
2977 3103 2.103941 GGTTTGCAAACAGAATTGGGGA 59.896 45.455 35.95 0.00 40.63 4.81
2978 3104 2.104622 AGGTTTGCAAACAGAATTGGGG 59.895 45.455 35.95 0.00 40.63 4.96
2979 3105 3.181467 TGAGGTTTGCAAACAGAATTGGG 60.181 43.478 35.95 0.00 40.63 4.12
2980 3106 4.057406 TGAGGTTTGCAAACAGAATTGG 57.943 40.909 35.95 0.00 40.63 3.16
2982 3108 6.822676 TCAATTTGAGGTTTGCAAACAGAATT 59.177 30.769 35.95 28.67 40.63 2.17
2986 3177 5.646467 CTCAATTTGAGGTTTGCAAACAG 57.354 39.130 35.95 21.03 40.71 3.16
3000 3191 8.918658 CACAATCAAACATAACTCCTCAATTTG 58.081 33.333 0.00 0.00 0.00 2.32
3054 3252 1.101331 GAGTGTCCTACCTACCACCG 58.899 60.000 0.00 0.00 0.00 4.94
3305 3503 6.296026 CCATCGGTTATAATGGAAGAAAGGA 58.704 40.000 0.00 0.00 44.37 3.36
3373 3571 1.463444 GGTGAACGTTTGATTCGGAGG 59.537 52.381 0.46 0.00 0.00 4.30
3377 3575 2.139917 TCAGGGTGAACGTTTGATTCG 58.860 47.619 0.46 0.00 0.00 3.34
3410 3608 7.361201 CGCTCCATTGAGAAGTATGAAAAAGAA 60.361 37.037 0.00 0.00 41.42 2.52
3413 3611 5.705441 ACGCTCCATTGAGAAGTATGAAAAA 59.295 36.000 0.00 0.00 41.42 1.94
3485 3683 6.014669 CCTGTTCAAATGGGGAGAACAAATAA 60.015 38.462 8.35 0.00 35.68 1.40
3492 3690 1.146774 TGCCTGTTCAAATGGGGAGAA 59.853 47.619 0.00 0.00 0.00 2.87
3498 3696 2.028839 TCAGCATTGCCTGTTCAAATGG 60.029 45.455 4.70 0.00 34.47 3.16
3523 3721 2.783135 TCCAAAAGCTCACTGCCTAAG 58.217 47.619 0.00 0.00 44.23 2.18
3560 3758 3.596956 ACCTCCTCCTCTTTAGTAGGTGA 59.403 47.826 0.00 0.00 34.64 4.02
3598 3796 0.381089 GCTTCTCTAAGTCGCCGCTA 59.619 55.000 0.00 0.00 34.99 4.26
3612 3810 1.192146 TTCTGCGGTACCCAGCTTCT 61.192 55.000 19.93 0.00 0.00 2.85
3766 3964 8.679100 CGGTACCAAAATGACAATAGGATTTTA 58.321 33.333 13.54 0.00 30.07 1.52
3769 3967 5.067283 GCGGTACCAAAATGACAATAGGATT 59.933 40.000 13.54 0.00 0.00 3.01
3770 3968 4.578928 GCGGTACCAAAATGACAATAGGAT 59.421 41.667 13.54 0.00 0.00 3.24
3771 3969 3.942748 GCGGTACCAAAATGACAATAGGA 59.057 43.478 13.54 0.00 0.00 2.94
3772 3970 3.692101 TGCGGTACCAAAATGACAATAGG 59.308 43.478 13.54 0.00 0.00 2.57
3831 4032 0.459489 GAGCAGTGGGAGTAGCTGAG 59.541 60.000 0.00 0.00 37.48 3.35
3843 4044 6.554419 TCCAAAAATGAATTATCGAGCAGTG 58.446 36.000 0.00 0.00 0.00 3.66
3848 4049 6.781138 TCCGTTCCAAAAATGAATTATCGAG 58.219 36.000 0.00 0.00 0.00 4.04
3851 4052 6.096282 TCCCTCCGTTCCAAAAATGAATTATC 59.904 38.462 0.00 0.00 0.00 1.75
3859 4060 2.971901 ACTCCCTCCGTTCCAAAAAT 57.028 45.000 0.00 0.00 0.00 1.82
3861 4062 4.778958 TCTAATACTCCCTCCGTTCCAAAA 59.221 41.667 0.00 0.00 0.00 2.44
3863 4064 3.703052 GTCTAATACTCCCTCCGTTCCAA 59.297 47.826 0.00 0.00 0.00 3.53
3870 4082 3.967987 ACCACATGTCTAATACTCCCTCC 59.032 47.826 0.00 0.00 0.00 4.30
3882 4094 2.346766 TGTGAGCAAACCACATGTCT 57.653 45.000 0.00 0.00 39.36 3.41
3906 4118 2.590821 AGCTGCCTGAAAACAAGTGAT 58.409 42.857 0.00 0.00 0.00 3.06
4127 4339 2.234300 TTTCAGGTTTCGCGTCTTCT 57.766 45.000 5.77 0.00 0.00 2.85
4140 4352 4.321974 GGCTGTGGTATTTTCCTTTTCAGG 60.322 45.833 0.00 0.00 42.50 3.86
4286 4498 1.754226 GACTTGATCTTCTCGAGGCCT 59.246 52.381 3.86 3.86 37.43 5.19
4451 4663 2.658422 GCGTCCCCGTGGAAGTAA 59.342 61.111 1.52 0.00 44.07 2.24
4499 4711 1.444933 AGTCCCTCACCACCATGAAA 58.555 50.000 0.00 0.00 0.00 2.69
4685 4897 1.487976 ACCCTCTCCTACGACGACATA 59.512 52.381 0.00 0.00 0.00 2.29
4705 4917 3.174987 CCACCACCACCACCCTCA 61.175 66.667 0.00 0.00 0.00 3.86
4707 4919 3.498071 CACCACCACCACCACCCT 61.498 66.667 0.00 0.00 0.00 4.34
4708 4920 4.596585 CCACCACCACCACCACCC 62.597 72.222 0.00 0.00 0.00 4.61
4711 4923 2.277672 CTTCACCACCACCACCACCA 62.278 60.000 0.00 0.00 0.00 4.17
4714 4926 1.694525 TCCTTCACCACCACCACCA 60.695 57.895 0.00 0.00 0.00 4.17
4717 4929 2.055689 CTGCTCCTTCACCACCACCA 62.056 60.000 0.00 0.00 0.00 4.17
4833 5045 0.178926 TCCTAACCTTGGTCGTCCCA 60.179 55.000 0.00 0.00 43.27 4.37
4900 5112 9.388506 GGAAGATCTTCTTGTCATTATTCTTCA 57.611 33.333 29.64 0.00 36.73 3.02
4965 5177 5.523438 AGATAACTAGTGAAGCAGCCTAC 57.477 43.478 0.00 0.00 0.00 3.18
4989 5204 1.426816 CCATGTGTAGCTGCTGCGAG 61.427 60.000 13.43 2.21 45.42 5.03
4990 5205 1.448365 CCATGTGTAGCTGCTGCGA 60.448 57.895 13.43 1.51 45.42 5.10
4991 5206 1.699656 GACCATGTGTAGCTGCTGCG 61.700 60.000 13.43 0.00 45.42 5.18
4999 5214 2.303022 AGGTTCCTGTGACCATGTGTAG 59.697 50.000 0.00 0.00 39.71 2.74
5170 5388 4.164843 ACAGTGGGTGAATGTAAGTTGT 57.835 40.909 0.00 0.00 0.00 3.32
5179 5397 3.846588 AGGAGATTGTACAGTGGGTGAAT 59.153 43.478 0.00 0.00 0.00 2.57
5182 5400 2.834549 AGAGGAGATTGTACAGTGGGTG 59.165 50.000 0.00 0.00 0.00 4.61
5197 5415 4.142730 CGCAGGAGAAATTTGAAAGAGGAG 60.143 45.833 0.00 0.00 0.00 3.69
5228 5446 3.700538 TGGCTGATAGATTTGCCTGTTT 58.299 40.909 0.00 0.00 45.11 2.83
5233 5451 4.026356 AGGTATGGCTGATAGATTTGCC 57.974 45.455 0.00 0.00 45.10 4.52
5338 5556 1.501170 TGATGGTTCCCCTTTTCACCA 59.499 47.619 0.00 0.00 43.48 4.17
5341 5559 4.044065 ACATAGTGATGGTTCCCCTTTTCA 59.956 41.667 0.00 0.00 37.39 2.69
5534 5769 6.525578 TTCTTTATCTCTACGCAAAGAGGA 57.474 37.500 11.34 0.01 42.78 3.71
5565 5800 3.113043 ACTTTCGCCCTAGTTATTCCCT 58.887 45.455 0.00 0.00 0.00 4.20
5647 5882 5.833340 ACTCTACAGACTACAGGAAGGAAT 58.167 41.667 0.00 0.00 0.00 3.01
5651 5886 7.012894 CCATTCTACTCTACAGACTACAGGAAG 59.987 44.444 0.00 0.00 0.00 3.46
5657 5892 6.201425 CGTCTCCATTCTACTCTACAGACTAC 59.799 46.154 0.00 0.00 0.00 2.73
5658 5893 6.127111 ACGTCTCCATTCTACTCTACAGACTA 60.127 42.308 0.00 0.00 0.00 2.59
5659 5894 5.120399 CGTCTCCATTCTACTCTACAGACT 58.880 45.833 0.00 0.00 0.00 3.24
5660 5895 4.877251 ACGTCTCCATTCTACTCTACAGAC 59.123 45.833 0.00 0.00 0.00 3.51
5661 5896 4.876679 CACGTCTCCATTCTACTCTACAGA 59.123 45.833 0.00 0.00 0.00 3.41
5689 5924 1.269309 ACGATAGCGGCTCATTCACTC 60.269 52.381 5.39 0.00 43.17 3.51
5715 5950 6.826741 TGCTTCACTCTGTTTTTACCTTTACT 59.173 34.615 0.00 0.00 0.00 2.24
5717 5952 7.633193 TTGCTTCACTCTGTTTTTACCTTTA 57.367 32.000 0.00 0.00 0.00 1.85
5718 5953 6.524101 TTGCTTCACTCTGTTTTTACCTTT 57.476 33.333 0.00 0.00 0.00 3.11
5721 5956 5.281727 CCTTTGCTTCACTCTGTTTTTACC 58.718 41.667 0.00 0.00 0.00 2.85
5722 5957 5.163550 ACCCTTTGCTTCACTCTGTTTTTAC 60.164 40.000 0.00 0.00 0.00 2.01
5723 5958 4.953579 ACCCTTTGCTTCACTCTGTTTTTA 59.046 37.500 0.00 0.00 0.00 1.52
5724 5959 3.769300 ACCCTTTGCTTCACTCTGTTTTT 59.231 39.130 0.00 0.00 0.00 1.94
5734 5970 2.291475 TGATGCCATACCCTTTGCTTCA 60.291 45.455 0.00 0.00 36.09 3.02


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

AutoCloner maintained by Alex Coulton.