Multiple sequence alignment - TraesCS4B01G299200

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 TraesCS4B01G299200 chr4B 100.000 5003 0 0 1 5003 585469993 585464991 0.000000e+00 9239
1 TraesCS4B01G299200 chr4B 96.830 757 24 0 3 759 434847182 434847938 0.000000e+00 1266
2 TraesCS4B01G299200 chr4B 93.617 94 4 2 751 843 666599934 666599842 6.750000e-29 139
3 TraesCS4B01G299200 chr4D 92.364 2737 147 32 1632 4324 467441422 467438704 0.000000e+00 3840
4 TraesCS4B01G299200 chr4D 89.925 804 57 14 841 1634 467442239 467441450 0.000000e+00 1014
5 TraesCS4B01G299200 chr4D 94.236 399 11 3 4615 5003 467438211 467437815 2.580000e-167 599
6 TraesCS4B01G299200 chr4A 92.389 2641 141 26 1632 4237 3442844 3445459 0.000000e+00 3709
7 TraesCS4B01G299200 chr4A 91.650 503 26 6 4516 5003 3445815 3446316 0.000000e+00 682
8 TraesCS4B01G299200 chr4A 92.708 384 20 4 841 1220 3442017 3442396 9.470000e-152 547
9 TraesCS4B01G299200 chr4A 92.308 234 14 1 1221 1450 3442429 3442662 3.730000e-86 329
10 TraesCS4B01G299200 chr4A 93.421 152 6 2 1485 1634 3442665 3442814 6.520000e-54 222
11 TraesCS4B01G299200 chr1B 97.124 765 17 5 1 763 372696286 372695525 0.000000e+00 1286
12 TraesCS4B01G299200 chr3A 96.706 759 25 0 1 759 281431556 281430798 0.000000e+00 1264
13 TraesCS4B01G299200 chr3A 93.617 94 4 2 751 843 728326312 728326220 6.750000e-29 139
14 TraesCS4B01G299200 chr2A 96.697 757 23 2 1 757 438818784 438819538 0.000000e+00 1258
15 TraesCS4B01G299200 chr2A 96.574 759 24 2 1 759 245805403 245804647 0.000000e+00 1256
16 TraesCS4B01G299200 chr2A 96.570 758 24 2 1 757 769854850 769855606 0.000000e+00 1254
17 TraesCS4B01G299200 chr2A 92.903 155 11 0 4849 5003 231290835 231290989 5.040000e-55 226
18 TraesCS4B01G299200 chr2A 94.068 118 7 0 4886 5003 121215763 121215880 3.980000e-41 180
19 TraesCS4B01G299200 chr2B 96.570 758 25 1 1 757 265337904 265337147 0.000000e+00 1254
20 TraesCS4B01G299200 chr2B 96.204 764 26 2 1 762 575301849 575301087 0.000000e+00 1247
21 TraesCS4B01G299200 chr2B 94.068 118 7 0 4886 5003 171453266 171453383 3.980000e-41 180
22 TraesCS4B01G299200 chr5B 96.073 764 27 3 1 763 674036737 674035976 0.000000e+00 1242
23 TraesCS4B01G299200 chr5B 93.548 93 5 1 751 843 874157 874066 2.430000e-28 137
24 TraesCS4B01G299200 chr5B 92.708 96 5 2 751 846 508800900 508800807 2.430000e-28 137
25 TraesCS4B01G299200 chr6D 96.129 155 6 0 4849 5003 450739114 450739268 2.310000e-63 254
26 TraesCS4B01G299200 chr7A 95.484 155 7 0 4849 5003 641827478 641827324 1.080000e-61 248
27 TraesCS4B01G299200 chr7B 93.464 153 10 0 4849 5001 707684876 707684724 1.400000e-55 228
28 TraesCS4B01G299200 chr2D 94.068 118 7 0 4886 5003 119263196 119263313 3.980000e-41 180
29 TraesCS4B01G299200 chr2D 91.919 99 7 1 751 848 14756697 14756599 2.430000e-28 137
30 TraesCS4B01G299200 chr2D 92.632 95 7 0 751 845 558189855 558189949 2.430000e-28 137
31 TraesCS4B01G299200 chrUn 94.565 92 4 1 751 842 15545192 15545282 1.880000e-29 141
32 TraesCS4B01G299200 chr3D 94.505 91 4 1 751 841 43660517 43660606 6.750000e-29 139
33 TraesCS4B01G299200 chr1A 93.617 94 5 1 751 844 561376672 561376580 6.750000e-29 139


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 TraesCS4B01G299200 chr4B 585464991 585469993 5002 True 9239.000000 9239 100.0000 1 5003 1 chr4B.!!$R1 5002
1 TraesCS4B01G299200 chr4B 434847182 434847938 756 False 1266.000000 1266 96.8300 3 759 1 chr4B.!!$F1 756
2 TraesCS4B01G299200 chr4D 467437815 467442239 4424 True 1817.666667 3840 92.1750 841 5003 3 chr4D.!!$R1 4162
3 TraesCS4B01G299200 chr4A 3442017 3446316 4299 False 1097.800000 3709 92.4952 841 5003 5 chr4A.!!$F1 4162
4 TraesCS4B01G299200 chr1B 372695525 372696286 761 True 1286.000000 1286 97.1240 1 763 1 chr1B.!!$R1 762
5 TraesCS4B01G299200 chr3A 281430798 281431556 758 True 1264.000000 1264 96.7060 1 759 1 chr3A.!!$R1 758
6 TraesCS4B01G299200 chr2A 438818784 438819538 754 False 1258.000000 1258 96.6970 1 757 1 chr2A.!!$F3 756
7 TraesCS4B01G299200 chr2A 245804647 245805403 756 True 1256.000000 1256 96.5740 1 759 1 chr2A.!!$R1 758
8 TraesCS4B01G299200 chr2A 769854850 769855606 756 False 1254.000000 1254 96.5700 1 757 1 chr2A.!!$F4 756
9 TraesCS4B01G299200 chr2B 265337147 265337904 757 True 1254.000000 1254 96.5700 1 757 1 chr2B.!!$R1 756
10 TraesCS4B01G299200 chr2B 575301087 575301849 762 True 1247.000000 1247 96.2040 1 762 1 chr2B.!!$R2 761
11 TraesCS4B01G299200 chr5B 674035976 674036737 761 True 1242.000000 1242 96.0730 1 763 1 chr5B.!!$R3 762

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
794 802 0.106149 GTACCCTAGCCGGTTGATGG 59.894 60.000 1.90 1.87 37.34 3.51 F
1265 1311 0.533308 TCCGTGGTTGGTTGTGCTAC 60.533 55.000 0.00 0.00 0.00 3.58 F
1452 1502 0.899720 TGCCCGGAGTAGTAAACCTG 59.100 55.000 0.73 0.00 0.00 4.00 F
2022 2109 1.616865 TCGCTAGCCGTATTATGCCTT 59.383 47.619 9.66 0.00 38.35 4.35 F
3835 3971 1.523758 GCAACGAGTTCAATCACCCT 58.476 50.000 0.00 0.00 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2703 2821 0.104487 TCCACGTAACGGCAGAACAA 59.896 50.000 0.0 0.0 0.00 2.83 R
2983 3101 0.037326 TACTGCCAACGAAGCTCCAG 60.037 55.000 0.0 0.0 0.00 3.86 R
3023 3141 2.093500 TCACCAGCACTTATACTGCCAG 60.093 50.000 0.0 0.0 35.01 4.85 R
3856 3992 0.033504 GCTCGAAGGGAACTGTGTCA 59.966 55.000 0.0 0.0 42.68 3.58 R
4660 5205 2.582978 GACCGGCCCAGGTTACTC 59.417 66.667 0.0 0.0 46.09 2.59 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
172 173 7.790823 TTAAACTACCCGAGGTAATTAATGC 57.209 36.000 4.63 0.00 37.76 3.56
529 537 4.942761 ACAATGCTTTTGTCCTGAATGT 57.057 36.364 0.47 0.00 0.00 2.71
707 715 5.357257 ACTGAGCAAGTTCGAAAAGTAAGA 58.643 37.500 0.00 0.00 34.57 2.10
763 771 7.606073 GGTAAAAATGCAATTGTCCCTTGTAAT 59.394 33.333 7.40 0.00 36.10 1.89
764 772 8.998377 GTAAAAATGCAATTGTCCCTTGTAATT 58.002 29.630 7.40 0.00 36.10 1.40
765 773 8.462589 AAAAATGCAATTGTCCCTTGTAATTT 57.537 26.923 7.40 0.00 36.10 1.82
766 774 9.566432 AAAAATGCAATTGTCCCTTGTAATTTA 57.434 25.926 7.40 0.00 36.10 1.40
767 775 8.776376 AAATGCAATTGTCCCTTGTAATTTAG 57.224 30.769 7.40 0.00 36.10 1.85
768 776 5.719173 TGCAATTGTCCCTTGTAATTTAGC 58.281 37.500 7.40 0.00 0.00 3.09
769 777 5.244851 TGCAATTGTCCCTTGTAATTTAGCA 59.755 36.000 7.40 0.00 0.00 3.49
770 778 5.576774 GCAATTGTCCCTTGTAATTTAGCAC 59.423 40.000 7.40 0.00 0.00 4.40
771 779 5.914898 ATTGTCCCTTGTAATTTAGCACC 57.085 39.130 0.00 0.00 0.00 5.01
772 780 4.374689 TGTCCCTTGTAATTTAGCACCA 57.625 40.909 0.00 0.00 0.00 4.17
773 781 4.929479 TGTCCCTTGTAATTTAGCACCAT 58.071 39.130 0.00 0.00 0.00 3.55
774 782 5.329399 TGTCCCTTGTAATTTAGCACCATT 58.671 37.500 0.00 0.00 0.00 3.16
775 783 5.184864 TGTCCCTTGTAATTTAGCACCATTG 59.815 40.000 0.00 0.00 0.00 2.82
776 784 5.185056 GTCCCTTGTAATTTAGCACCATTGT 59.815 40.000 0.00 0.00 0.00 2.71
777 785 6.376018 GTCCCTTGTAATTTAGCACCATTGTA 59.624 38.462 0.00 0.00 0.00 2.41
778 786 6.376018 TCCCTTGTAATTTAGCACCATTGTAC 59.624 38.462 0.00 0.00 0.00 2.90
779 787 6.405397 CCCTTGTAATTTAGCACCATTGTACC 60.405 42.308 0.00 0.00 0.00 3.34
780 788 6.405397 CCTTGTAATTTAGCACCATTGTACCC 60.405 42.308 0.00 0.00 0.00 3.69
781 789 5.822204 TGTAATTTAGCACCATTGTACCCT 58.178 37.500 0.00 0.00 0.00 4.34
782 790 6.959904 TGTAATTTAGCACCATTGTACCCTA 58.040 36.000 0.00 0.00 0.00 3.53
783 791 7.051623 TGTAATTTAGCACCATTGTACCCTAG 58.948 38.462 0.00 0.00 0.00 3.02
784 792 3.553828 TTAGCACCATTGTACCCTAGC 57.446 47.619 0.00 0.00 0.00 3.42
785 793 0.546598 AGCACCATTGTACCCTAGCC 59.453 55.000 0.00 0.00 0.00 3.93
786 794 0.814010 GCACCATTGTACCCTAGCCG 60.814 60.000 0.00 0.00 0.00 5.52
787 795 0.179056 CACCATTGTACCCTAGCCGG 60.179 60.000 0.00 0.00 0.00 6.13
788 796 0.619543 ACCATTGTACCCTAGCCGGT 60.620 55.000 1.90 0.00 40.13 5.28
789 797 0.544697 CCATTGTACCCTAGCCGGTT 59.455 55.000 1.90 0.00 37.34 4.44
790 798 1.663695 CATTGTACCCTAGCCGGTTG 58.336 55.000 1.90 0.00 37.34 3.77
791 799 1.208535 CATTGTACCCTAGCCGGTTGA 59.791 52.381 1.90 0.00 37.34 3.18
792 800 1.575419 TTGTACCCTAGCCGGTTGAT 58.425 50.000 1.90 0.00 37.34 2.57
793 801 0.828022 TGTACCCTAGCCGGTTGATG 59.172 55.000 1.90 0.00 37.34 3.07
794 802 0.106149 GTACCCTAGCCGGTTGATGG 59.894 60.000 1.90 1.87 37.34 3.51
805 813 4.654091 CCGGTTGATGGCTTCATTAATT 57.346 40.909 3.72 0.00 33.34 1.40
806 814 5.009854 CCGGTTGATGGCTTCATTAATTT 57.990 39.130 3.72 0.00 33.34 1.82
807 815 4.805192 CCGGTTGATGGCTTCATTAATTTG 59.195 41.667 3.72 0.00 33.34 2.32
808 816 5.394005 CCGGTTGATGGCTTCATTAATTTGA 60.394 40.000 3.72 0.00 33.34 2.69
809 817 6.098679 CGGTTGATGGCTTCATTAATTTGAA 58.901 36.000 3.72 0.00 33.34 2.69
818 826 6.743575 CTTCATTAATTTGAAGTCGGACCT 57.256 37.500 10.51 0.00 44.90 3.85
819 827 7.145932 CTTCATTAATTTGAAGTCGGACCTT 57.854 36.000 10.51 0.00 44.90 3.50
820 828 6.737254 TCATTAATTTGAAGTCGGACCTTC 57.263 37.500 4.14 8.61 41.01 3.46
821 829 5.350365 TCATTAATTTGAAGTCGGACCTTCG 59.650 40.000 4.14 0.00 43.06 3.79
822 830 2.833631 ATTTGAAGTCGGACCTTCGT 57.166 45.000 4.14 0.00 43.06 3.85
823 831 1.860676 TTTGAAGTCGGACCTTCGTG 58.139 50.000 4.14 0.00 43.06 4.35
824 832 0.599204 TTGAAGTCGGACCTTCGTGC 60.599 55.000 4.14 0.00 43.06 5.34
825 833 1.737008 GAAGTCGGACCTTCGTGCC 60.737 63.158 4.14 0.00 32.23 5.01
826 834 2.156051 GAAGTCGGACCTTCGTGCCT 62.156 60.000 4.14 0.00 32.23 4.75
827 835 1.755393 AAGTCGGACCTTCGTGCCTT 61.755 55.000 4.14 0.00 0.00 4.35
828 836 1.301479 GTCGGACCTTCGTGCCTTT 60.301 57.895 0.00 0.00 0.00 3.11
829 837 0.883370 GTCGGACCTTCGTGCCTTTT 60.883 55.000 0.00 0.00 0.00 2.27
830 838 0.601841 TCGGACCTTCGTGCCTTTTC 60.602 55.000 0.00 0.00 0.00 2.29
831 839 0.602905 CGGACCTTCGTGCCTTTTCT 60.603 55.000 0.00 0.00 0.00 2.52
832 840 1.157585 GGACCTTCGTGCCTTTTCTC 58.842 55.000 0.00 0.00 0.00 2.87
833 841 1.270893 GGACCTTCGTGCCTTTTCTCT 60.271 52.381 0.00 0.00 0.00 3.10
834 842 2.028385 GGACCTTCGTGCCTTTTCTCTA 60.028 50.000 0.00 0.00 0.00 2.43
835 843 3.556423 GGACCTTCGTGCCTTTTCTCTAA 60.556 47.826 0.00 0.00 0.00 2.10
836 844 4.062991 GACCTTCGTGCCTTTTCTCTAAA 58.937 43.478 0.00 0.00 0.00 1.85
837 845 4.457466 ACCTTCGTGCCTTTTCTCTAAAA 58.543 39.130 0.00 0.00 33.58 1.52
838 846 4.885325 ACCTTCGTGCCTTTTCTCTAAAAA 59.115 37.500 0.00 0.00 34.26 1.94
885 893 8.583296 GGGGTATATGTATTATATCGGAACCTC 58.417 40.741 0.00 0.00 0.00 3.85
886 894 9.139734 GGGTATATGTATTATATCGGAACCTCA 57.860 37.037 0.00 0.00 0.00 3.86
891 899 6.631016 TGTATTATATCGGAACCTCATGAGC 58.369 40.000 17.76 3.70 0.00 4.26
908 916 1.591059 GCACACCAACGCATTTGCA 60.591 52.632 3.13 0.00 42.21 4.08
1023 1032 2.896443 GCCACTTCTCTCCCCTCG 59.104 66.667 0.00 0.00 0.00 4.63
1026 1035 2.035940 ACTTCTCTCCCCTCGCGT 59.964 61.111 5.77 0.00 0.00 6.01
1260 1306 2.551504 GGTAGATTCCGTGGTTGGTTGT 60.552 50.000 0.00 0.00 0.00 3.32
1265 1311 0.533308 TCCGTGGTTGGTTGTGCTAC 60.533 55.000 0.00 0.00 0.00 3.58
1268 1314 1.540363 CGTGGTTGGTTGTGCTACTCT 60.540 52.381 0.00 0.00 0.00 3.24
1324 1374 1.684450 GAAATCGGTTGGTTGGTTGGT 59.316 47.619 0.00 0.00 0.00 3.67
1450 1500 1.277273 AGTTGCCCGGAGTAGTAAACC 59.723 52.381 0.73 0.00 0.00 3.27
1452 1502 0.899720 TGCCCGGAGTAGTAAACCTG 59.100 55.000 0.73 0.00 0.00 4.00
1456 1506 2.173519 CCGGAGTAGTAAACCTGGTGA 58.826 52.381 0.00 0.00 0.00 4.02
1458 1508 3.956199 CCGGAGTAGTAAACCTGGTGATA 59.044 47.826 0.00 0.00 0.00 2.15
1506 1556 5.463392 GCTTATCAGTTAATCATCAGCGTGA 59.537 40.000 0.00 0.00 0.00 4.35
1507 1557 6.018751 GCTTATCAGTTAATCATCAGCGTGAA 60.019 38.462 0.00 0.00 0.00 3.18
1547 1599 5.105635 CGTACTTTGTAGTCTGGGGTCATAA 60.106 44.000 0.00 0.00 35.78 1.90
1740 1825 4.122046 GCAGATGATACACATACAGCACA 58.878 43.478 0.00 0.00 39.56 4.57
1803 1888 9.118236 GTTAAATCTACAGAAACATGCTTGAAC 57.882 33.333 6.60 0.00 0.00 3.18
1983 2070 5.807909 TCTACGCCTTTACCAGGTAAAATT 58.192 37.500 22.70 11.33 46.07 1.82
2022 2109 1.616865 TCGCTAGCCGTATTATGCCTT 59.383 47.619 9.66 0.00 38.35 4.35
2029 2116 6.238211 GCTAGCCGTATTATGCCTTGATTATG 60.238 42.308 2.29 0.00 0.00 1.90
2137 2225 9.614792 GGTCAGAGAACAACTAATGGTTATAAT 57.385 33.333 0.00 0.00 36.23 1.28
2267 2363 3.513912 TCCTGAACACGTGGTATGAGAAT 59.486 43.478 21.57 0.00 0.00 2.40
2364 2460 7.384115 GCAAATGCTATTGAACATGCATCTTAT 59.616 33.333 0.00 0.00 44.15 1.73
2378 2474 8.454106 ACATGCATCTTATGAGTGTCTAAAAAC 58.546 33.333 0.00 0.00 0.00 2.43
2412 2508 9.844790 TTGATTTAGATGTGAATGTTCATTGAC 57.155 29.630 7.88 7.88 39.73 3.18
2419 2515 5.655488 TGTGAATGTTCATTGACCGTTTTT 58.345 33.333 11.27 0.00 39.73 1.94
2484 2581 1.960040 TAGGCCTGGAGATGCACACG 61.960 60.000 17.99 0.00 0.00 4.49
2521 2623 4.047822 CGGACTTCTAGTTGATGAGCATC 58.952 47.826 3.55 3.55 38.29 3.91
2557 2668 4.707030 AAGCTCATTTCGATTTCATGCA 57.293 36.364 0.00 0.00 0.00 3.96
2586 2701 9.502145 GAAATGTGCATTTCGATTTGAAGTATA 57.498 29.630 18.16 0.00 44.68 1.47
2588 2703 7.371126 TGTGCATTTCGATTTGAAGTATACA 57.629 32.000 5.50 0.00 37.99 2.29
2676 2792 7.379529 GTGAGATGTTTGTATTTGTGACCTTTG 59.620 37.037 0.00 0.00 0.00 2.77
2702 2820 6.748333 TGTGCATCTTTTAAATCTCCTGAG 57.252 37.500 0.00 0.00 0.00 3.35
2703 2821 6.240894 TGTGCATCTTTTAAATCTCCTGAGT 58.759 36.000 0.00 0.00 0.00 3.41
2736 2854 5.176223 CGTTACGTGGAGTTGACTTTTATGT 59.824 40.000 0.00 0.00 0.00 2.29
2873 2991 4.512944 AGCCTGTATTGATTATTGACTGCG 59.487 41.667 0.00 0.00 0.00 5.18
2888 3006 4.832248 TGACTGCGAACCTTGATTAATCT 58.168 39.130 16.24 0.00 0.00 2.40
2977 3095 6.694447 TGTTGTACCAGGTATACACTTCTTC 58.306 40.000 1.54 0.00 32.30 2.87
2983 3101 5.047235 ACCAGGTATACACTTCTTCAGACAC 60.047 44.000 5.01 0.00 0.00 3.67
3023 3141 2.302157 ACTAGTGCTTGTTGGTAGGACC 59.698 50.000 0.00 0.00 39.22 4.46
3033 3151 3.036091 GTTGGTAGGACCTGGCAGTATA 58.964 50.000 14.43 0.00 39.58 1.47
3040 3158 2.555199 GACCTGGCAGTATAAGTGCTG 58.445 52.381 14.43 0.00 43.82 4.41
3066 3184 7.264221 GTGAATGAATGTTAATGCCCACATAA 58.736 34.615 0.00 0.00 34.62 1.90
3080 3198 5.045213 TGCCCACATAAGATTCCTGAGTTTA 60.045 40.000 0.00 0.00 0.00 2.01
3091 3209 5.825593 TTCCTGAGTTTAGAACCATGTCT 57.174 39.130 0.00 0.00 0.00 3.41
3093 3211 4.593206 TCCTGAGTTTAGAACCATGTCTGT 59.407 41.667 0.00 0.00 0.00 3.41
3095 3213 5.290493 TGAGTTTAGAACCATGTCTGTGT 57.710 39.130 0.00 0.00 0.00 3.72
3150 3269 2.693797 CGCAAGTGCAGATTTTCTGT 57.306 45.000 3.87 0.00 45.94 3.41
3153 3272 4.536065 CGCAAGTGCAGATTTTCTGTTTA 58.464 39.130 3.87 0.00 45.94 2.01
3154 3273 4.379793 CGCAAGTGCAGATTTTCTGTTTAC 59.620 41.667 3.87 4.20 45.94 2.01
3155 3274 5.523369 GCAAGTGCAGATTTTCTGTTTACT 58.477 37.500 6.40 6.06 45.94 2.24
3156 3275 5.400485 GCAAGTGCAGATTTTCTGTTTACTG 59.600 40.000 6.40 0.00 45.94 2.74
3157 3276 6.498304 CAAGTGCAGATTTTCTGTTTACTGT 58.502 36.000 6.40 0.00 45.94 3.55
3158 3277 7.639039 CAAGTGCAGATTTTCTGTTTACTGTA 58.361 34.615 6.40 0.00 45.94 2.74
3259 3394 8.359642 TGGCATATTTATTTCAAATAGCTGACC 58.640 33.333 0.00 0.00 0.00 4.02
3369 3504 6.599638 ACTGCTACAGAGTTCTTTGTCTTTTT 59.400 34.615 0.78 0.00 35.18 1.94
3403 3539 8.534333 TGAAGTGTTACTGATATTGTGAGTTC 57.466 34.615 0.00 0.00 0.00 3.01
3534 3670 7.973402 TCCTTATTATGCTGTATAGGCTTTCA 58.027 34.615 0.00 0.00 0.00 2.69
3835 3971 1.523758 GCAACGAGTTCAATCACCCT 58.476 50.000 0.00 0.00 0.00 4.34
3856 3992 4.125703 CTGAACTCAAGAAGAACACAGCT 58.874 43.478 0.00 0.00 0.00 4.24
3862 3998 2.938451 CAAGAAGAACACAGCTGACACA 59.062 45.455 23.35 0.00 0.00 3.72
3868 4004 0.179045 ACACAGCTGACACAGTTCCC 60.179 55.000 23.35 0.00 33.43 3.97
3899 4035 0.693049 GACCCGCATATTCCCCATCT 59.307 55.000 0.00 0.00 0.00 2.90
3948 4084 5.533903 AGATTGACATCAAGCACTTTTGTCT 59.466 36.000 12.07 0.00 44.03 3.41
4153 4290 2.738314 GTTGCAATTGCCTGACATTTCC 59.262 45.455 26.94 0.00 41.18 3.13
4158 4295 1.538047 TTGCCTGACATTTCCTGAGC 58.462 50.000 0.00 0.00 0.00 4.26
4173 4310 1.301716 GAGCGCACCTTTCCTGTCA 60.302 57.895 11.47 0.00 0.00 3.58
4185 4322 4.687483 CCTTTCCTGTCAAATGTTGCAATC 59.313 41.667 0.59 0.00 0.00 2.67
4195 4332 4.717233 AATGTTGCAATCGCCTGAAATA 57.283 36.364 0.59 0.00 37.32 1.40
4201 4338 3.884693 TGCAATCGCCTGAAATATCATGT 59.115 39.130 0.00 0.00 37.32 3.21
4202 4339 4.338964 TGCAATCGCCTGAAATATCATGTT 59.661 37.500 0.00 0.00 37.32 2.71
4206 4343 3.038017 CGCCTGAAATATCATGTTTGCG 58.962 45.455 0.00 0.00 34.37 4.85
4259 4550 3.441572 CCCAGCACAAGTTTATCTTCCAG 59.558 47.826 0.00 0.00 33.63 3.86
4308 4599 7.493499 AGATATGAGAATGCTAGCTGGTATT 57.507 36.000 17.23 13.06 0.00 1.89
4311 4602 5.102953 TGAGAATGCTAGCTGGTATTGTT 57.897 39.130 17.72 6.22 0.00 2.83
4312 4603 6.233905 TGAGAATGCTAGCTGGTATTGTTA 57.766 37.500 17.72 8.16 0.00 2.41
4319 4610 4.267928 GCTAGCTGGTATTGTTAGTGTTCG 59.732 45.833 7.70 0.00 0.00 3.95
4327 4618 6.146510 TGGTATTGTTAGTGTTCGCTTGTTAG 59.853 38.462 0.00 0.00 0.00 2.34
4329 4620 6.613755 ATTGTTAGTGTTCGCTTGTTAGTT 57.386 33.333 0.00 0.00 0.00 2.24
4330 4621 5.646467 TGTTAGTGTTCGCTTGTTAGTTC 57.354 39.130 0.00 0.00 0.00 3.01
4334 4625 7.438757 TGTTAGTGTTCGCTTGTTAGTTCATTA 59.561 33.333 0.00 0.00 0.00 1.90
4336 4627 6.656003 AGTGTTCGCTTGTTAGTTCATTAAC 58.344 36.000 0.00 0.00 34.78 2.01
4338 4629 5.049267 TGTTCGCTTGTTAGTTCATTAACCC 60.049 40.000 0.00 0.00 36.15 4.11
4360 4651 5.308825 CCAACTCTTCACTCCAATGTAGTT 58.691 41.667 0.00 0.00 0.00 2.24
4380 4671 4.153256 GTTGAAAACGCTATTACCGGTTG 58.847 43.478 15.04 1.92 36.92 3.77
4381 4672 2.160022 TGAAAACGCTATTACCGGTTGC 59.840 45.455 15.04 11.89 35.54 4.17
4382 4673 1.089112 AAACGCTATTACCGGTTGCC 58.911 50.000 15.04 0.00 33.84 4.52
4386 4677 1.746470 GCTATTACCGGTTGCCACTT 58.254 50.000 15.04 0.00 0.00 3.16
4387 4678 1.400494 GCTATTACCGGTTGCCACTTG 59.600 52.381 15.04 0.00 0.00 3.16
4402 4693 5.629079 GCCACTTGCATATTCCCTATTAC 57.371 43.478 0.00 0.00 40.77 1.89
4403 4694 5.316987 GCCACTTGCATATTCCCTATTACT 58.683 41.667 0.00 0.00 40.77 2.24
4404 4695 5.412904 GCCACTTGCATATTCCCTATTACTC 59.587 44.000 0.00 0.00 40.77 2.59
4405 4696 6.745474 GCCACTTGCATATTCCCTATTACTCT 60.745 42.308 0.00 0.00 40.77 3.24
4406 4697 6.652481 CCACTTGCATATTCCCTATTACTCTG 59.348 42.308 0.00 0.00 0.00 3.35
4408 4699 8.099537 CACTTGCATATTCCCTATTACTCTGAT 58.900 37.037 0.00 0.00 0.00 2.90
4412 4703 8.708378 TGCATATTCCCTATTACTCTGATATGG 58.292 37.037 0.00 0.00 0.00 2.74
4413 4704 8.928448 GCATATTCCCTATTACTCTGATATGGA 58.072 37.037 0.00 0.00 0.00 3.41
4488 5000 5.704217 TTTCACCGTGTTACAAAAATTGC 57.296 34.783 0.00 0.00 0.00 3.56
4489 5001 3.707793 TCACCGTGTTACAAAAATTGCC 58.292 40.909 0.00 0.00 0.00 4.52
4490 5002 2.797719 CACCGTGTTACAAAAATTGCCC 59.202 45.455 0.00 0.00 0.00 5.36
4491 5003 2.224090 ACCGTGTTACAAAAATTGCCCC 60.224 45.455 0.00 0.00 0.00 5.80
4492 5004 2.055100 CGTGTTACAAAAATTGCCCCG 58.945 47.619 0.00 0.00 0.00 5.73
4493 5005 2.544069 CGTGTTACAAAAATTGCCCCGT 60.544 45.455 0.00 0.00 0.00 5.28
4494 5006 3.304525 CGTGTTACAAAAATTGCCCCGTA 60.305 43.478 0.00 0.00 0.00 4.02
4495 5007 4.616373 CGTGTTACAAAAATTGCCCCGTAT 60.616 41.667 0.00 0.00 0.00 3.06
4496 5008 5.231702 GTGTTACAAAAATTGCCCCGTATT 58.768 37.500 0.00 0.00 0.00 1.89
4497 5009 5.346551 GTGTTACAAAAATTGCCCCGTATTC 59.653 40.000 0.00 0.00 0.00 1.75
4498 5010 5.244178 TGTTACAAAAATTGCCCCGTATTCT 59.756 36.000 0.00 0.00 0.00 2.40
4499 5011 4.450082 ACAAAAATTGCCCCGTATTCTC 57.550 40.909 0.00 0.00 0.00 2.87
4500 5012 3.829601 ACAAAAATTGCCCCGTATTCTCA 59.170 39.130 0.00 0.00 0.00 3.27
4501 5013 4.173256 CAAAAATTGCCCCGTATTCTCAC 58.827 43.478 0.00 0.00 0.00 3.51
4502 5014 3.366052 AAATTGCCCCGTATTCTCACT 57.634 42.857 0.00 0.00 0.00 3.41
4503 5015 2.332063 ATTGCCCCGTATTCTCACTG 57.668 50.000 0.00 0.00 0.00 3.66
4504 5016 0.981183 TTGCCCCGTATTCTCACTGT 59.019 50.000 0.00 0.00 0.00 3.55
4505 5017 0.535335 TGCCCCGTATTCTCACTGTC 59.465 55.000 0.00 0.00 0.00 3.51
4506 5018 0.535335 GCCCCGTATTCTCACTGTCA 59.465 55.000 0.00 0.00 0.00 3.58
4507 5019 1.471676 GCCCCGTATTCTCACTGTCAG 60.472 57.143 0.00 0.00 0.00 3.51
4508 5020 1.137086 CCCCGTATTCTCACTGTCAGG 59.863 57.143 4.53 0.00 0.00 3.86
4509 5021 1.825474 CCCGTATTCTCACTGTCAGGT 59.175 52.381 4.53 0.00 0.00 4.00
4510 5022 3.021695 CCCGTATTCTCACTGTCAGGTA 58.978 50.000 4.53 0.00 0.00 3.08
4511 5023 3.637229 CCCGTATTCTCACTGTCAGGTAT 59.363 47.826 4.53 0.00 0.00 2.73
4512 5024 4.099573 CCCGTATTCTCACTGTCAGGTATT 59.900 45.833 4.53 0.00 0.00 1.89
4513 5025 5.301045 CCCGTATTCTCACTGTCAGGTATTA 59.699 44.000 4.53 0.00 0.00 0.98
4514 5026 6.015350 CCCGTATTCTCACTGTCAGGTATTAT 60.015 42.308 4.53 0.00 0.00 1.28
4541 5054 5.479124 AAAACTGACCCGTATACTTGTCT 57.521 39.130 17.36 2.18 0.00 3.41
4546 5059 5.011329 ACTGACCCGTATACTTGTCTTTGAA 59.989 40.000 17.36 2.66 0.00 2.69
4660 5205 3.072184 AGGAGAAAGCAGGCCATATGTAG 59.928 47.826 5.01 0.00 0.00 2.74
4664 5211 4.901849 AGAAAGCAGGCCATATGTAGAGTA 59.098 41.667 5.01 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 5.221481 TGCAAATGATATGCCCATAAAGGTG 60.221 40.000 0.00 0.00 43.16 4.00
497 505 6.981559 GGACAAAAGCATTGTTTAAACTACCA 59.018 34.615 18.72 1.82 31.96 3.25
529 537 9.821240 ACATTACCTTTATGGGCATATCATTTA 57.179 29.630 0.00 0.00 41.11 1.40
615 623 7.097834 ACCGTTTGACCAAAACTTTGAAAATA 58.902 30.769 3.72 0.00 45.10 1.40
763 771 3.371166 GGCTAGGGTACAATGGTGCTAAA 60.371 47.826 0.00 0.00 0.00 1.85
764 772 2.171870 GGCTAGGGTACAATGGTGCTAA 59.828 50.000 0.00 0.00 0.00 3.09
765 773 1.766496 GGCTAGGGTACAATGGTGCTA 59.234 52.381 0.00 0.00 0.00 3.49
766 774 0.546598 GGCTAGGGTACAATGGTGCT 59.453 55.000 0.00 0.00 0.00 4.40
767 775 0.814010 CGGCTAGGGTACAATGGTGC 60.814 60.000 0.00 0.00 0.00 5.01
768 776 0.179056 CCGGCTAGGGTACAATGGTG 60.179 60.000 0.00 0.00 35.97 4.17
769 777 0.619543 ACCGGCTAGGGTACAATGGT 60.620 55.000 0.00 0.00 46.96 3.55
770 778 0.544697 AACCGGCTAGGGTACAATGG 59.455 55.000 0.00 0.00 46.96 3.16
771 779 1.208535 TCAACCGGCTAGGGTACAATG 59.791 52.381 0.00 0.00 46.96 2.82
772 780 1.575419 TCAACCGGCTAGGGTACAAT 58.425 50.000 0.00 0.00 46.96 2.71
773 781 1.208535 CATCAACCGGCTAGGGTACAA 59.791 52.381 0.00 0.00 46.96 2.41
774 782 0.828022 CATCAACCGGCTAGGGTACA 59.172 55.000 0.00 0.00 46.96 2.90
775 783 0.106149 CCATCAACCGGCTAGGGTAC 59.894 60.000 0.00 0.00 46.96 3.34
776 784 1.692173 GCCATCAACCGGCTAGGGTA 61.692 60.000 0.00 0.00 46.56 3.69
777 785 3.043999 GCCATCAACCGGCTAGGGT 62.044 63.158 0.00 0.00 46.56 4.34
778 786 2.203209 GCCATCAACCGGCTAGGG 60.203 66.667 0.00 0.00 46.56 3.53
784 792 4.654091 AATTAATGAAGCCATCAACCGG 57.346 40.909 0.00 0.00 42.54 5.28
785 793 5.649557 TCAAATTAATGAAGCCATCAACCG 58.350 37.500 0.00 0.00 42.54 4.44
786 794 7.529880 CTTCAAATTAATGAAGCCATCAACC 57.470 36.000 6.89 0.00 46.88 3.77
796 804 6.128391 CGAAGGTCCGACTTCAAATTAATGAA 60.128 38.462 12.63 0.00 45.54 2.57
797 805 5.350365 CGAAGGTCCGACTTCAAATTAATGA 59.650 40.000 12.63 0.00 45.54 2.57
798 806 5.121768 ACGAAGGTCCGACTTCAAATTAATG 59.878 40.000 12.63 0.00 45.54 1.90
799 807 5.121768 CACGAAGGTCCGACTTCAAATTAAT 59.878 40.000 12.63 0.00 45.54 1.40
800 808 4.449743 CACGAAGGTCCGACTTCAAATTAA 59.550 41.667 12.63 0.00 45.54 1.40
801 809 3.991773 CACGAAGGTCCGACTTCAAATTA 59.008 43.478 12.63 0.00 45.54 1.40
802 810 2.806244 CACGAAGGTCCGACTTCAAATT 59.194 45.455 12.63 0.00 45.54 1.82
803 811 2.413837 CACGAAGGTCCGACTTCAAAT 58.586 47.619 12.63 0.00 45.54 2.32
804 812 1.860676 CACGAAGGTCCGACTTCAAA 58.139 50.000 12.63 0.00 45.54 2.69
805 813 0.599204 GCACGAAGGTCCGACTTCAA 60.599 55.000 12.63 0.00 45.54 2.69
806 814 1.006571 GCACGAAGGTCCGACTTCA 60.007 57.895 12.63 0.00 45.54 3.02
807 815 1.737008 GGCACGAAGGTCCGACTTC 60.737 63.158 0.00 0.00 42.63 3.01
808 816 1.755393 AAGGCACGAAGGTCCGACTT 61.755 55.000 0.00 0.00 0.00 3.01
809 817 1.755393 AAAGGCACGAAGGTCCGACT 61.755 55.000 0.00 0.00 0.00 4.18
810 818 0.883370 AAAAGGCACGAAGGTCCGAC 60.883 55.000 0.00 0.00 0.00 4.79
811 819 0.601841 GAAAAGGCACGAAGGTCCGA 60.602 55.000 0.00 0.00 0.00 4.55
812 820 0.602905 AGAAAAGGCACGAAGGTCCG 60.603 55.000 0.00 0.00 0.00 4.79
813 821 1.157585 GAGAAAAGGCACGAAGGTCC 58.842 55.000 0.00 0.00 0.00 4.46
814 822 2.171341 AGAGAAAAGGCACGAAGGTC 57.829 50.000 0.00 0.00 0.00 3.85
815 823 3.764237 TTAGAGAAAAGGCACGAAGGT 57.236 42.857 0.00 0.00 0.00 3.50
816 824 5.432885 TTTTTAGAGAAAAGGCACGAAGG 57.567 39.130 0.00 0.00 35.96 3.46
855 863 8.935614 TCCGATATAATACATATACCCCTCAG 57.064 38.462 0.00 0.00 29.33 3.35
856 864 9.139734 GTTCCGATATAATACATATACCCCTCA 57.860 37.037 0.00 0.00 29.33 3.86
872 880 3.895041 TGTGCTCATGAGGTTCCGATATA 59.105 43.478 23.89 0.00 0.00 0.86
878 886 0.036732 TGGTGTGCTCATGAGGTTCC 59.963 55.000 23.89 7.91 0.00 3.62
885 893 0.241749 AATGCGTTGGTGTGCTCATG 59.758 50.000 0.00 0.00 0.00 3.07
886 894 0.961019 AAATGCGTTGGTGTGCTCAT 59.039 45.000 0.00 0.00 0.00 2.90
891 899 1.550659 GCTGCAAATGCGTTGGTGTG 61.551 55.000 0.35 0.00 45.83 3.82
1023 1032 1.966451 CAAACCCTGGGAGACACGC 60.966 63.158 22.23 0.00 0.00 5.34
1026 1035 2.843545 GGCAAACCCTGGGAGACA 59.156 61.111 22.23 0.00 0.00 3.41
1241 1287 2.773487 CACAACCAACCACGGAATCTA 58.227 47.619 0.00 0.00 0.00 1.98
1244 1290 0.467290 AGCACAACCAACCACGGAAT 60.467 50.000 0.00 0.00 0.00 3.01
1260 1306 1.148310 GACAGCGCAAAAGAGTAGCA 58.852 50.000 11.47 0.00 0.00 3.49
1265 1311 0.236711 CACCAGACAGCGCAAAAGAG 59.763 55.000 11.47 0.00 0.00 2.85
1268 1314 1.669604 TAACACCAGACAGCGCAAAA 58.330 45.000 11.47 0.00 0.00 2.44
1299 1345 1.269309 CCAACCAACCGATTTCGCAAA 60.269 47.619 0.00 0.00 38.18 3.68
1324 1374 2.603247 CGCCGCACAGTTTAGCACA 61.603 57.895 0.00 0.00 0.00 4.57
1450 1500 7.826252 CACCCTCAATCCTTAATATATCACCAG 59.174 40.741 0.00 0.00 0.00 4.00
1452 1502 7.112779 CCACCCTCAATCCTTAATATATCACC 58.887 42.308 0.00 0.00 0.00 4.02
1456 1506 6.297243 CCAGCCACCCTCAATCCTTAATATAT 60.297 42.308 0.00 0.00 0.00 0.86
1458 1508 4.202609 CCAGCCACCCTCAATCCTTAATAT 60.203 45.833 0.00 0.00 0.00 1.28
1547 1599 0.991920 TTTCCTCGGCAATCCCTCTT 59.008 50.000 0.00 0.00 0.00 2.85
1761 1846 2.719531 TAACAGGCTGAACAACCACA 57.280 45.000 23.66 0.00 0.00 4.17
1803 1888 5.248870 ACACAGAGCCTAAAAACAGTTTG 57.751 39.130 0.00 0.00 0.00 2.93
1836 1921 4.168760 GTGACACAAAAGAATAGCATGCC 58.831 43.478 15.66 0.00 0.00 4.40
2003 2090 1.726791 CAAGGCATAATACGGCTAGCG 59.273 52.381 9.00 6.83 38.52 4.26
2152 2240 6.605594 AGTTGAGAATGAACCAACAAAAGGTA 59.394 34.615 0.00 0.00 38.76 3.08
2215 2311 1.522569 GCATAGGCTGAAGTCGGGT 59.477 57.895 0.00 0.00 36.96 5.28
2267 2363 2.452600 AACAGGGAAGCAGGACAAAA 57.547 45.000 0.00 0.00 0.00 2.44
2387 2483 8.461222 GGTCAATGAACATTCACATCTAAATCA 58.539 33.333 4.23 0.00 40.49 2.57
2419 2515 7.201696 GGCCAAAGTAAAATCATCTACGATGAA 60.202 37.037 10.24 0.00 0.00 2.57
2484 2581 7.868415 ACTAGAAGTCCGCAAGTAATTATGATC 59.132 37.037 0.00 0.00 0.00 2.92
2546 2648 4.386350 TGCACATTTCTTTGCATGAAATCG 59.614 37.500 19.07 16.82 43.79 3.34
2547 2649 5.849357 TGCACATTTCTTTGCATGAAATC 57.151 34.783 19.07 12.24 43.79 2.17
2586 2701 8.918202 TTTAGATGTTTAAGTGACCAGAATGT 57.082 30.769 0.00 0.00 0.00 2.71
2631 2746 9.211485 CATCTCACATCTTATACATATGTGCAA 57.789 33.333 18.81 10.57 46.43 4.08
2633 2748 8.768957 ACATCTCACATCTTATACATATGTGC 57.231 34.615 18.81 0.00 46.43 4.57
2676 2792 7.765307 TCAGGAGATTTAAAAGATGCACAATC 58.235 34.615 0.00 0.00 35.29 2.67
2702 2820 0.233848 CCACGTAACGGCAGAACAAC 59.766 55.000 0.00 0.00 0.00 3.32
2703 2821 0.104487 TCCACGTAACGGCAGAACAA 59.896 50.000 0.00 0.00 0.00 2.83
2736 2854 7.255590 GCTCCTCCATTTGCTATAATAAAAGCA 60.256 37.037 0.00 0.00 46.59 3.91
2873 2991 7.849804 TCTGTAAGCAGATTAATCAAGGTTC 57.150 36.000 21.12 15.48 45.94 3.62
2888 3006 2.565834 GGAACCTACCAGTCTGTAAGCA 59.434 50.000 0.00 0.00 0.00 3.91
2977 3095 1.143305 CAACGAAGCTCCAGTGTCTG 58.857 55.000 0.00 0.00 0.00 3.51
2983 3101 0.037326 TACTGCCAACGAAGCTCCAG 60.037 55.000 0.00 0.00 0.00 3.86
3023 3141 2.093500 TCACCAGCACTTATACTGCCAG 60.093 50.000 0.00 0.00 35.01 4.85
3033 3151 6.392354 CATTAACATTCATTCACCAGCACTT 58.608 36.000 0.00 0.00 0.00 3.16
3040 3158 4.081752 TGTGGGCATTAACATTCATTCACC 60.082 41.667 0.00 0.00 0.00 4.02
3066 3184 6.214412 AGACATGGTTCTAAACTCAGGAATCT 59.786 38.462 0.00 0.00 0.00 2.40
3080 3198 6.152661 TGAAAGAAAAACACAGACATGGTTCT 59.847 34.615 0.00 0.00 0.00 3.01
3534 3670 5.010719 CCTTGAATTGCCATGAGCTCATAAT 59.989 40.000 28.27 20.65 44.23 1.28
3583 3719 7.321908 GCCTTAGGCTGGTATAAATAGTACTC 58.678 42.308 17.16 0.00 46.69 2.59
3835 3971 3.873361 CAGCTGTGTTCTTCTTGAGTTCA 59.127 43.478 5.25 0.00 0.00 3.18
3856 3992 0.033504 GCTCGAAGGGAACTGTGTCA 59.966 55.000 0.00 0.00 42.68 3.58
3862 3998 1.006102 CACGTGCTCGAAGGGAACT 60.006 57.895 16.04 0.00 41.26 3.01
3868 4004 2.805353 CGGGTCACGTGCTCGAAG 60.805 66.667 22.26 7.09 40.62 3.79
3948 4084 4.007644 CTGGGTGCAGCCGAGACA 62.008 66.667 28.67 10.99 44.79 3.41
3969 4105 7.974504 TCAAGTTCTATTAAACCTCCTCAGTT 58.025 34.615 0.00 0.00 0.00 3.16
3977 4113 5.940470 CACTGGCTCAAGTTCTATTAAACCT 59.060 40.000 0.00 0.00 0.00 3.50
4117 4254 1.885233 TGCAACATTCGGCAGAAATGA 59.115 42.857 2.68 0.00 40.15 2.57
4153 4290 1.294659 GACAGGAAAGGTGCGCTCAG 61.295 60.000 9.73 0.00 0.00 3.35
4158 4295 1.608590 ACATTTGACAGGAAAGGTGCG 59.391 47.619 0.00 0.00 29.10 5.34
4173 4310 3.383620 TTTCAGGCGATTGCAACATTT 57.616 38.095 0.00 0.00 45.35 2.32
4185 4322 3.038017 CGCAAACATGATATTTCAGGCG 58.962 45.455 0.00 0.00 37.15 5.52
4216 4354 4.155644 GGGAGCAAAATAGATAGCAGATGC 59.844 45.833 0.00 0.00 42.49 3.91
4247 4538 4.732938 GCAAGCATGCTCTGGAAGATAAAC 60.733 45.833 22.93 2.36 45.62 2.01
4280 4571 5.106634 CCAGCTAGCATTCTCATATCTTTGC 60.107 44.000 18.83 0.00 0.00 3.68
4308 4599 5.110598 TGAACTAACAAGCGAACACTAACA 58.889 37.500 0.00 0.00 0.00 2.41
4311 4602 7.095523 GGTTAATGAACTAACAAGCGAACACTA 60.096 37.037 0.00 0.00 35.74 2.74
4312 4603 6.293244 GGTTAATGAACTAACAAGCGAACACT 60.293 38.462 0.00 0.00 35.74 3.55
4319 4610 6.206829 AGAGTTGGGTTAATGAACTAACAAGC 59.793 38.462 12.90 5.45 36.21 4.01
4327 4618 5.181433 GGAGTGAAGAGTTGGGTTAATGAAC 59.819 44.000 0.00 0.00 34.56 3.18
4329 4620 4.349636 TGGAGTGAAGAGTTGGGTTAATGA 59.650 41.667 0.00 0.00 0.00 2.57
4330 4621 4.651778 TGGAGTGAAGAGTTGGGTTAATG 58.348 43.478 0.00 0.00 0.00 1.90
4334 4625 3.117512 ACATTGGAGTGAAGAGTTGGGTT 60.118 43.478 0.00 0.00 0.00 4.11
4336 4627 3.146104 ACATTGGAGTGAAGAGTTGGG 57.854 47.619 0.00 0.00 0.00 4.12
4338 4629 5.991606 TCAACTACATTGGAGTGAAGAGTTG 59.008 40.000 1.30 0.00 42.37 3.16
4360 4651 2.160022 GCAACCGGTAATAGCGTTTTCA 59.840 45.455 8.00 0.00 37.40 2.69
4370 4661 2.263153 GCAAGTGGCAACCGGTAAT 58.737 52.632 8.00 0.00 43.97 1.89
4380 4671 5.316987 AGTAATAGGGAATATGCAAGTGGC 58.683 41.667 0.00 0.00 45.13 5.01
4381 4672 6.652481 CAGAGTAATAGGGAATATGCAAGTGG 59.348 42.308 0.00 0.00 0.00 4.00
4382 4673 7.445121 TCAGAGTAATAGGGAATATGCAAGTG 58.555 38.462 0.00 0.00 0.00 3.16
4386 4677 8.708378 CCATATCAGAGTAATAGGGAATATGCA 58.292 37.037 0.00 0.00 33.38 3.96
4387 4678 8.928448 TCCATATCAGAGTAATAGGGAATATGC 58.072 37.037 0.00 0.00 36.80 3.14
4403 4694 9.837681 TCCCTATGTTTTATACTCCATATCAGA 57.162 33.333 0.00 0.00 0.00 3.27
4405 4696 9.615660 ACTCCCTATGTTTTATACTCCATATCA 57.384 33.333 0.00 0.00 0.00 2.15
4467 4979 4.113354 GGCAATTTTTGTAACACGGTGAA 58.887 39.130 16.29 0.00 0.00 3.18
4468 4980 3.491104 GGGCAATTTTTGTAACACGGTGA 60.491 43.478 16.29 0.00 0.00 4.02
4471 4983 2.409012 GGGGCAATTTTTGTAACACGG 58.591 47.619 0.00 0.00 0.00 4.94
4473 4985 3.100658 ACGGGGCAATTTTTGTAACAC 57.899 42.857 0.00 0.00 0.00 3.32
4477 4989 5.010933 TGAGAATACGGGGCAATTTTTGTA 58.989 37.500 0.00 0.00 0.00 2.41
4480 4992 4.082245 CAGTGAGAATACGGGGCAATTTTT 60.082 41.667 0.00 0.00 0.00 1.94
4481 4993 3.443681 CAGTGAGAATACGGGGCAATTTT 59.556 43.478 0.00 0.00 0.00 1.82
4482 4994 3.016736 CAGTGAGAATACGGGGCAATTT 58.983 45.455 0.00 0.00 0.00 1.82
4483 4995 2.026262 ACAGTGAGAATACGGGGCAATT 60.026 45.455 0.00 0.00 0.00 2.32
4484 4996 1.559682 ACAGTGAGAATACGGGGCAAT 59.440 47.619 0.00 0.00 0.00 3.56
4485 4997 0.981183 ACAGTGAGAATACGGGGCAA 59.019 50.000 0.00 0.00 0.00 4.52
4486 4998 0.535335 GACAGTGAGAATACGGGGCA 59.465 55.000 0.00 0.00 0.00 5.36
4487 4999 0.535335 TGACAGTGAGAATACGGGGC 59.465 55.000 0.00 0.00 0.00 5.80
4488 5000 1.137086 CCTGACAGTGAGAATACGGGG 59.863 57.143 0.00 0.00 0.00 5.73
4489 5001 1.825474 ACCTGACAGTGAGAATACGGG 59.175 52.381 0.00 0.00 0.00 5.28
4490 5002 4.920640 ATACCTGACAGTGAGAATACGG 57.079 45.455 0.00 0.00 0.00 4.02
4491 5003 9.395707 GTAATAATACCTGACAGTGAGAATACG 57.604 37.037 0.00 0.00 0.00 3.06
4498 5010 9.787435 AGTTTTTGTAATAATACCTGACAGTGA 57.213 29.630 0.00 0.00 0.00 3.41
4499 5011 9.825972 CAGTTTTTGTAATAATACCTGACAGTG 57.174 33.333 0.93 0.00 0.00 3.66
4500 5012 9.787435 TCAGTTTTTGTAATAATACCTGACAGT 57.213 29.630 0.93 0.00 0.00 3.55
4502 5014 9.005777 GGTCAGTTTTTGTAATAATACCTGACA 57.994 33.333 18.20 0.00 42.23 3.58
4503 5015 8.456471 GGGTCAGTTTTTGTAATAATACCTGAC 58.544 37.037 12.37 12.37 41.09 3.51
4504 5016 7.334921 CGGGTCAGTTTTTGTAATAATACCTGA 59.665 37.037 0.00 0.00 32.51 3.86
4505 5017 7.120138 ACGGGTCAGTTTTTGTAATAATACCTG 59.880 37.037 0.00 0.00 36.06 4.00
4506 5018 7.170277 ACGGGTCAGTTTTTGTAATAATACCT 58.830 34.615 0.00 0.00 0.00 3.08
4507 5019 7.381766 ACGGGTCAGTTTTTGTAATAATACC 57.618 36.000 0.00 0.00 0.00 2.73
4510 5022 9.895138 AGTATACGGGTCAGTTTTTGTAATAAT 57.105 29.630 0.00 0.00 0.00 1.28
4511 5023 9.723601 AAGTATACGGGTCAGTTTTTGTAATAA 57.276 29.630 0.00 0.00 0.00 1.40
4512 5024 9.153721 CAAGTATACGGGTCAGTTTTTGTAATA 57.846 33.333 0.00 0.00 0.00 0.98
4513 5025 7.662669 ACAAGTATACGGGTCAGTTTTTGTAAT 59.337 33.333 0.00 0.00 0.00 1.89
4514 5026 6.991531 ACAAGTATACGGGTCAGTTTTTGTAA 59.008 34.615 0.00 0.00 0.00 2.41
4523 5036 5.068234 TCAAAGACAAGTATACGGGTCAG 57.932 43.478 23.16 15.70 32.79 3.51
4553 5066 5.902613 AAATCCAGATGAATTTTCGCAGA 57.097 34.783 0.00 0.00 0.00 4.26
4633 5178 0.393673 GGCCTGCTTTCTCCTTCTCC 60.394 60.000 0.00 0.00 0.00 3.71
4660 5205 2.582978 GACCGGCCCAGGTTACTC 59.417 66.667 0.00 0.00 46.09 2.59
4664 5211 3.264845 AATGGACCGGCCCAGGTT 61.265 61.111 16.91 2.15 46.09 3.50
4845 5400 4.041762 GCCATGGTTGGTCGGGGA 62.042 66.667 14.67 0.00 45.57 4.81


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

AutoCloner maintained by Alex Coulton.