Multiple sequence alignment - TraesCS5D01G162300

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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 TraesCS5D01G162300 chr5D 100.000 4225 0 0 1 4225 253203295 253199071 0.000000e+00 7803.0
1 TraesCS5D01G162300 chr5B 93.675 1992 59 28 841 2784 285627209 285625237 0.000000e+00 2918.0
2 TraesCS5D01G162300 chr5B 97.721 746 15 2 2776 3521 285623702 285622959 0.000000e+00 1282.0
3 TraesCS5D01G162300 chr5B 87.402 127 16 0 666 792 635809748 635809622 3.400000e-31 147.0
4 TraesCS5D01G162300 chr5B 98.684 76 0 1 2776 2851 285623960 285623886 2.650000e-27 134.0
5 TraesCS5D01G162300 chr5A 92.225 1865 99 18 2209 4047 335684680 335682836 0.000000e+00 2599.0
6 TraesCS5D01G162300 chr5A 95.743 1245 40 6 989 2221 335685944 335684701 0.000000e+00 1993.0
7 TraesCS5D01G162300 chr5A 95.918 49 1 1 895 942 335686373 335686325 1.260000e-10 78.7
8 TraesCS5D01G162300 chr4D 97.033 674 20 0 1 674 437459293 437459966 0.000000e+00 1134.0
9 TraesCS5D01G162300 chr4D 97.173 672 16 2 1 672 153849017 153848349 0.000000e+00 1133.0
10 TraesCS5D01G162300 chr4D 86.441 118 13 2 3877 3993 259497365 259497250 4.430000e-25 126.0
11 TraesCS5D01G162300 chr4D 78.261 138 20 6 674 805 108229727 108229860 3.500000e-11 80.5
12 TraesCS5D01G162300 chr2D 97.024 672 20 0 1 672 183871405 183872076 0.000000e+00 1131.0
13 TraesCS5D01G162300 chr2D 96.884 674 21 0 1 674 577397144 577397817 0.000000e+00 1129.0
14 TraesCS5D01G162300 chr7D 97.024 672 19 1 1 672 559561137 559561807 0.000000e+00 1129.0
15 TraesCS5D01G162300 chr7D 96.880 673 18 3 1 672 559542490 559543160 0.000000e+00 1123.0
16 TraesCS5D01G162300 chr7D 88.889 108 9 2 3878 3984 566782912 566783017 3.430000e-26 130.0
17 TraesCS5D01G162300 chr7D 87.179 117 9 6 3873 3986 514658917 514658804 1.230000e-25 128.0
18 TraesCS5D01G162300 chr7D 85.124 121 14 4 3877 3995 79629834 79629952 2.060000e-23 121.0
19 TraesCS5D01G162300 chr6D 96.750 677 21 1 1 677 451973043 451972368 0.000000e+00 1127.0
20 TraesCS5D01G162300 chr6D 96.731 673 21 1 1 673 441598708 441598037 0.000000e+00 1120.0
21 TraesCS5D01G162300 chr6D 96.726 672 20 2 1 672 8220001 8219332 0.000000e+00 1118.0
22 TraesCS5D01G162300 chr6B 87.500 128 16 0 666 793 154404339 154404212 9.460000e-32 148.0
23 TraesCS5D01G162300 chr6B 85.833 120 13 4 3877 3994 507471655 507471538 1.600000e-24 124.0
24 TraesCS5D01G162300 chr4B 88.991 109 9 2 3877 3984 255388174 255388280 9.530000e-27 132.0
25 TraesCS5D01G162300 chr2B 87.288 118 9 5 3877 3991 51645326 51645212 3.430000e-26 130.0
26 TraesCS5D01G162300 chr6A 86.842 114 12 2 3873 3985 222554895 222555006 1.600000e-24 124.0


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 TraesCS5D01G162300 chr5D 253199071 253203295 4224 True 7803.000000 7803 100.000000 1 4225 1 chr5D.!!$R1 4224
1 TraesCS5D01G162300 chr5B 285622959 285627209 4250 True 1444.666667 2918 96.693333 841 3521 3 chr5B.!!$R2 2680
2 TraesCS5D01G162300 chr5A 335682836 335686373 3537 True 1556.900000 2599 94.628667 895 4047 3 chr5A.!!$R1 3152
3 TraesCS5D01G162300 chr4D 437459293 437459966 673 False 1134.000000 1134 97.033000 1 674 1 chr4D.!!$F2 673
4 TraesCS5D01G162300 chr4D 153848349 153849017 668 True 1133.000000 1133 97.173000 1 672 1 chr4D.!!$R1 671
5 TraesCS5D01G162300 chr2D 183871405 183872076 671 False 1131.000000 1131 97.024000 1 672 1 chr2D.!!$F1 671
6 TraesCS5D01G162300 chr2D 577397144 577397817 673 False 1129.000000 1129 96.884000 1 674 1 chr2D.!!$F2 673
7 TraesCS5D01G162300 chr7D 559561137 559561807 670 False 1129.000000 1129 97.024000 1 672 1 chr7D.!!$F3 671
8 TraesCS5D01G162300 chr7D 559542490 559543160 670 False 1123.000000 1123 96.880000 1 672 1 chr7D.!!$F2 671
9 TraesCS5D01G162300 chr6D 451972368 451973043 675 True 1127.000000 1127 96.750000 1 677 1 chr6D.!!$R3 676
10 TraesCS5D01G162300 chr6D 441598037 441598708 671 True 1120.000000 1120 96.731000 1 673 1 chr6D.!!$R2 672
11 TraesCS5D01G162300 chr6D 8219332 8220001 669 True 1118.000000 1118 96.726000 1 672 1 chr6D.!!$R1 671

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
743 744 0.109532 TTTTCACCCTGCATGACGGA 59.890 50.0 0.0 0.0 0.0 4.69 F
1504 1852 0.109342 CCTGTCCTGCCTCACTTTGT 59.891 55.0 0.0 0.0 0.0 2.83 F
2197 2563 1.542492 CAGCCTGCATTTCTCACCTT 58.458 50.0 0.0 0.0 0.0 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1811 2167 1.006571 TCGAGCCGTTCTGGACAAC 60.007 57.895 0.0 0.0 42.00 3.32 R
3160 5121 0.957362 GGCCTTATCAAGAGCCATGC 59.043 55.000 0.0 0.0 41.58 4.06 R
4141 6119 0.035820 TACAACCAATCCACCGAGCC 60.036 55.000 0.0 0.0 0.00 4.70 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
349 350 1.802880 CGATGACCAGGGAGCTTAACG 60.803 57.143 0.00 0.00 0.00 3.18
379 380 2.812591 TGGCTCTCGACGATATCTTACC 59.187 50.000 0.00 0.00 0.00 2.85
381 382 3.125658 GGCTCTCGACGATATCTTACCTC 59.874 52.174 0.00 0.00 0.00 3.85
617 618 1.598701 GGGCTTCTGGCAATGACCAC 61.599 60.000 1.62 0.00 44.01 4.16
674 675 9.440761 ACTCTAAGGTCTATATCCTCAACAAAT 57.559 33.333 0.00 0.00 33.76 2.32
677 678 9.646427 CTAAGGTCTATATCCTCAACAAATAGC 57.354 37.037 0.00 0.00 33.76 2.97
678 679 6.692486 AGGTCTATATCCTCAACAAATAGCG 58.308 40.000 0.00 0.00 0.00 4.26
679 680 6.493802 AGGTCTATATCCTCAACAAATAGCGA 59.506 38.462 0.00 0.00 0.00 4.93
680 681 7.015292 AGGTCTATATCCTCAACAAATAGCGAA 59.985 37.037 0.00 0.00 0.00 4.70
681 682 7.329717 GGTCTATATCCTCAACAAATAGCGAAG 59.670 40.741 0.00 0.00 0.00 3.79
682 683 7.868415 GTCTATATCCTCAACAAATAGCGAAGT 59.132 37.037 0.00 0.00 0.00 3.01
683 684 8.421784 TCTATATCCTCAACAAATAGCGAAGTT 58.578 33.333 0.00 0.00 0.00 2.66
684 685 7.865706 ATATCCTCAACAAATAGCGAAGTTT 57.134 32.000 0.00 0.00 0.00 2.66
685 686 8.958119 ATATCCTCAACAAATAGCGAAGTTTA 57.042 30.769 0.00 0.00 0.00 2.01
686 687 6.721571 TCCTCAACAAATAGCGAAGTTTAG 57.278 37.500 0.00 0.00 0.00 1.85
687 688 6.228258 TCCTCAACAAATAGCGAAGTTTAGT 58.772 36.000 0.00 0.00 0.00 2.24
688 689 6.708949 TCCTCAACAAATAGCGAAGTTTAGTT 59.291 34.615 0.00 0.00 0.00 2.24
689 690 7.227910 TCCTCAACAAATAGCGAAGTTTAGTTT 59.772 33.333 0.00 0.00 0.00 2.66
690 691 7.860872 CCTCAACAAATAGCGAAGTTTAGTTTT 59.139 33.333 0.00 0.00 0.00 2.43
691 692 8.555166 TCAACAAATAGCGAAGTTTAGTTTTG 57.445 30.769 0.00 0.00 0.00 2.44
692 693 8.399425 TCAACAAATAGCGAAGTTTAGTTTTGA 58.601 29.630 0.00 0.00 0.00 2.69
693 694 9.180678 CAACAAATAGCGAAGTTTAGTTTTGAT 57.819 29.630 0.00 0.00 0.00 2.57
700 701 8.788325 AGCGAAGTTTAGTTTTGATAATAGGT 57.212 30.769 0.00 0.00 0.00 3.08
701 702 8.880750 AGCGAAGTTTAGTTTTGATAATAGGTC 58.119 33.333 0.00 0.00 0.00 3.85
702 703 8.662141 GCGAAGTTTAGTTTTGATAATAGGTCA 58.338 33.333 0.00 0.00 0.00 4.02
723 724 9.574516 AGGTCAGATGTTTTTCTTTGTAATAGT 57.425 29.630 0.00 0.00 0.00 2.12
734 735 9.810545 TTTTCTTTGTAATAGTTTTTCACCCTG 57.189 29.630 0.00 0.00 0.00 4.45
735 736 6.977213 TCTTTGTAATAGTTTTTCACCCTGC 58.023 36.000 0.00 0.00 0.00 4.85
736 737 6.547880 TCTTTGTAATAGTTTTTCACCCTGCA 59.452 34.615 0.00 0.00 0.00 4.41
737 738 6.909550 TTGTAATAGTTTTTCACCCTGCAT 57.090 33.333 0.00 0.00 0.00 3.96
738 739 6.266168 TGTAATAGTTTTTCACCCTGCATG 57.734 37.500 0.00 0.00 0.00 4.06
739 740 6.007076 TGTAATAGTTTTTCACCCTGCATGA 58.993 36.000 0.00 0.00 0.00 3.07
740 741 5.391312 AATAGTTTTTCACCCTGCATGAC 57.609 39.130 0.00 0.00 0.00 3.06
741 742 1.608590 AGTTTTTCACCCTGCATGACG 59.391 47.619 0.00 0.00 0.00 4.35
742 743 0.958091 TTTTTCACCCTGCATGACGG 59.042 50.000 0.00 0.00 0.00 4.79
743 744 0.109532 TTTTCACCCTGCATGACGGA 59.890 50.000 0.00 0.00 0.00 4.69
744 745 0.327924 TTTCACCCTGCATGACGGAT 59.672 50.000 0.00 0.00 0.00 4.18
745 746 1.199615 TTCACCCTGCATGACGGATA 58.800 50.000 0.00 0.00 0.00 2.59
746 747 0.464036 TCACCCTGCATGACGGATAC 59.536 55.000 0.00 0.00 0.00 2.24
747 748 0.465705 CACCCTGCATGACGGATACT 59.534 55.000 0.00 0.00 0.00 2.12
748 749 0.465705 ACCCTGCATGACGGATACTG 59.534 55.000 0.00 0.00 0.00 2.74
749 750 0.465705 CCCTGCATGACGGATACTGT 59.534 55.000 0.00 0.00 0.00 3.55
750 751 1.686587 CCCTGCATGACGGATACTGTA 59.313 52.381 0.00 0.00 0.00 2.74
751 752 2.102420 CCCTGCATGACGGATACTGTAA 59.898 50.000 0.00 0.00 0.00 2.41
752 753 3.384668 CCTGCATGACGGATACTGTAAG 58.615 50.000 0.00 0.00 42.29 2.34
753 754 3.068165 CCTGCATGACGGATACTGTAAGA 59.932 47.826 0.00 0.00 37.43 2.10
754 755 4.441495 CCTGCATGACGGATACTGTAAGAA 60.441 45.833 0.00 0.00 37.43 2.52
755 756 5.079689 TGCATGACGGATACTGTAAGAAA 57.920 39.130 0.00 0.00 37.43 2.52
756 757 5.670485 TGCATGACGGATACTGTAAGAAAT 58.330 37.500 0.00 0.00 37.43 2.17
757 758 5.523552 TGCATGACGGATACTGTAAGAAATG 59.476 40.000 0.00 0.00 37.43 2.32
758 759 5.753438 GCATGACGGATACTGTAAGAAATGA 59.247 40.000 0.00 0.00 37.43 2.57
759 760 6.425114 GCATGACGGATACTGTAAGAAATGAT 59.575 38.462 0.00 0.00 37.43 2.45
760 761 7.041780 GCATGACGGATACTGTAAGAAATGATT 60.042 37.037 0.00 0.00 37.43 2.57
761 762 7.770801 TGACGGATACTGTAAGAAATGATTG 57.229 36.000 0.00 0.00 37.43 2.67
762 763 7.327975 TGACGGATACTGTAAGAAATGATTGT 58.672 34.615 0.00 0.00 37.43 2.71
763 764 8.471609 TGACGGATACTGTAAGAAATGATTGTA 58.528 33.333 0.00 0.00 37.43 2.41
764 765 9.477484 GACGGATACTGTAAGAAATGATTGTAT 57.523 33.333 0.00 0.00 37.43 2.29
765 766 9.832445 ACGGATACTGTAAGAAATGATTGTATT 57.168 29.630 0.00 0.00 37.43 1.89
852 856 8.974060 AGTTCTTTTTAGGTGTCAGATTTGTA 57.026 30.769 0.00 0.00 0.00 2.41
880 884 6.428083 TTTAGGTGTCAGATTTGTAGTGGA 57.572 37.500 0.00 0.00 0.00 4.02
881 885 4.974645 AGGTGTCAGATTTGTAGTGGAA 57.025 40.909 0.00 0.00 0.00 3.53
943 956 4.619320 TTGGGTTGGGCTGGGCTG 62.619 66.667 0.00 0.00 0.00 4.85
958 986 1.700955 GGCTGGGCATGATTGAGATT 58.299 50.000 0.00 0.00 0.00 2.40
959 987 2.037144 GGCTGGGCATGATTGAGATTT 58.963 47.619 0.00 0.00 0.00 2.17
960 988 2.223971 GGCTGGGCATGATTGAGATTTG 60.224 50.000 0.00 0.00 0.00 2.32
961 989 2.802057 GCTGGGCATGATTGAGATTTGC 60.802 50.000 0.00 0.00 0.00 3.68
962 990 2.693591 CTGGGCATGATTGAGATTTGCT 59.306 45.455 0.00 0.00 33.86 3.91
966 1309 5.163488 TGGGCATGATTGAGATTTGCTTTAG 60.163 40.000 0.00 0.00 33.86 1.85
1063 1411 4.083862 GCTTTCGTCCCCGCCTCT 62.084 66.667 0.00 0.00 0.00 3.69
1066 1414 1.889530 CTTTCGTCCCCGCCTCTCTT 61.890 60.000 0.00 0.00 0.00 2.85
1071 1419 1.078528 TCCCCGCCTCTCTTTCTCA 59.921 57.895 0.00 0.00 0.00 3.27
1083 1431 2.215478 CTTTCTCAACCGCTGCGTCG 62.215 60.000 21.59 9.06 0.00 5.12
1195 1543 0.529773 GATCACCATACGCCGAGCAA 60.530 55.000 0.00 0.00 0.00 3.91
1202 1550 1.800586 CATACGCCGAGCAATAGCATT 59.199 47.619 0.00 0.00 45.49 3.56
1251 1599 1.852157 AAGGGTGGAGGATGTGCCA 60.852 57.895 0.00 0.00 40.02 4.92
1291 1639 1.738099 GGCGTCTGCGTGAAGATGT 60.738 57.895 0.00 0.00 44.10 3.06
1504 1852 0.109342 CCTGTCCTGCCTCACTTTGT 59.891 55.000 0.00 0.00 0.00 2.83
1653 2002 3.044305 GCTGCCACTGTCACGGTC 61.044 66.667 0.00 0.00 0.00 4.79
1811 2167 9.999009 CATTATTTGCTATATTAGGTGATGCTG 57.001 33.333 0.00 0.00 0.00 4.41
2197 2563 1.542492 CAGCCTGCATTTCTCACCTT 58.458 50.000 0.00 0.00 0.00 3.50
2704 3118 2.239907 GTCAGCCCATCCTTTCCTACTT 59.760 50.000 0.00 0.00 0.00 2.24
2705 3119 3.454812 GTCAGCCCATCCTTTCCTACTTA 59.545 47.826 0.00 0.00 0.00 2.24
2706 3120 4.103311 GTCAGCCCATCCTTTCCTACTTAT 59.897 45.833 0.00 0.00 0.00 1.73
2707 3121 4.103153 TCAGCCCATCCTTTCCTACTTATG 59.897 45.833 0.00 0.00 0.00 1.90
2708 3122 4.103153 CAGCCCATCCTTTCCTACTTATGA 59.897 45.833 0.00 0.00 0.00 2.15
2709 3123 4.103311 AGCCCATCCTTTCCTACTTATGAC 59.897 45.833 0.00 0.00 0.00 3.06
2710 3124 4.103311 GCCCATCCTTTCCTACTTATGACT 59.897 45.833 0.00 0.00 0.00 3.41
2711 3125 5.743422 GCCCATCCTTTCCTACTTATGACTC 60.743 48.000 0.00 0.00 0.00 3.36
2712 3126 5.604650 CCCATCCTTTCCTACTTATGACTCT 59.395 44.000 0.00 0.00 0.00 3.24
2713 3127 6.782988 CCCATCCTTTCCTACTTATGACTCTA 59.217 42.308 0.00 0.00 0.00 2.43
2714 3128 7.256012 CCCATCCTTTCCTACTTATGACTCTAC 60.256 44.444 0.00 0.00 0.00 2.59
2715 3129 7.287927 CCATCCTTTCCTACTTATGACTCTACA 59.712 40.741 0.00 0.00 0.00 2.74
2745 3159 3.242518 GTTTGGCGGCTCTAAACATTTC 58.757 45.455 11.43 0.00 43.20 2.17
2780 3199 8.773404 AGAATTACTTTGTGCGTTAGAAGTAT 57.227 30.769 0.00 0.00 35.31 2.12
3160 5121 1.078848 CCCCCTTCAGCGAGTTCAG 60.079 63.158 0.00 0.00 0.00 3.02
3236 5203 9.255304 GTTCTTAGGTTCTGATAAGATGATGAC 57.745 37.037 1.30 0.00 37.73 3.06
3588 5557 5.067413 CAGCAGTAGGTTTTAGAGGTATCGA 59.933 44.000 0.00 0.00 0.00 3.59
3605 5574 4.627611 ATCGATTTGCTTGAACCATCAG 57.372 40.909 0.00 0.00 36.78 2.90
3612 5581 7.541783 CGATTTGCTTGAACCATCAGAAAAATA 59.458 33.333 0.00 0.00 36.78 1.40
3619 5588 9.695526 CTTGAACCATCAGAAAAATAATTGTGA 57.304 29.630 0.00 0.00 37.06 3.58
3659 5628 7.791766 ACATTCTTATCTTCCAAGAGAGGGATA 59.208 37.037 0.00 0.00 38.66 2.59
3669 5638 5.104360 TCCAAGAGAGGGATATTTGGAGTTG 60.104 44.000 0.39 0.00 41.60 3.16
3701 5670 6.564557 TTTTCCCCTCTACCACGTTTATAT 57.435 37.500 0.00 0.00 0.00 0.86
3702 5671 5.540400 TTCCCCTCTACCACGTTTATATG 57.460 43.478 0.00 0.00 0.00 1.78
3709 5678 7.144000 CCTCTACCACGTTTATATGTACCTTC 58.856 42.308 0.00 0.00 0.00 3.46
3734 5703 0.250684 TCATGGGAAGTCAAGCGCAA 60.251 50.000 11.47 0.00 0.00 4.85
3738 5707 0.109132 GGGAAGTCAAGCGCAAATGG 60.109 55.000 11.47 0.00 0.00 3.16
3767 5736 1.005512 TGTGCGGCTATGTGTTCGT 60.006 52.632 0.00 0.00 0.00 3.85
3807 5776 4.021192 ACCTTCGTCCGGTTTATTAGTTCA 60.021 41.667 0.00 0.00 0.00 3.18
3828 5802 9.463443 AGTTCATATTTTGTGCTAAACTTTGAC 57.537 29.630 0.00 0.00 0.00 3.18
3832 5806 9.906660 CATATTTTGTGCTAAACTTTGACCTTA 57.093 29.630 0.00 0.00 0.00 2.69
3901 5876 4.144297 TCCCTCCAATGCATATTACTTGC 58.856 43.478 0.00 0.00 40.55 4.01
3910 5886 3.029074 GCATATTACTTGCGCTCAAACG 58.971 45.455 9.73 0.00 0.00 3.60
3919 5895 3.660501 TGCGCTCAAACGGATATATCT 57.339 42.857 9.73 0.00 0.00 1.98
3925 5901 5.620205 CGCTCAAACGGATATATCTAGCACT 60.620 44.000 12.42 0.00 0.00 4.40
3927 5903 6.570571 GCTCAAACGGATATATCTAGCACTGA 60.571 42.308 12.42 7.38 0.00 3.41
3928 5904 7.284919 TCAAACGGATATATCTAGCACTGAA 57.715 36.000 12.42 0.00 0.00 3.02
3931 5907 9.639601 CAAACGGATATATCTAGCACTGAAATA 57.360 33.333 12.42 0.00 0.00 1.40
3935 5911 7.640630 CGGATATATCTAGCACTGAAATACGTC 59.359 40.741 12.42 0.00 0.00 4.34
3945 5921 7.364200 AGCACTGAAATACGTCTAGATACATC 58.636 38.462 0.00 0.00 0.00 3.06
3946 5922 6.583050 GCACTGAAATACGTCTAGATACATCC 59.417 42.308 0.00 0.00 0.00 3.51
3948 5924 6.072618 ACTGAAATACGTCTAGATACATCCGG 60.073 42.308 0.00 0.00 0.00 5.14
3951 5927 6.645790 AATACGTCTAGATACATCCGGTTT 57.354 37.500 0.00 0.00 0.00 3.27
3954 5930 5.825507 ACGTCTAGATACATCCGGTTTAAC 58.174 41.667 0.00 0.00 0.00 2.01
3964 5940 4.336153 ACATCCGGTTTAACGAAACAACTT 59.664 37.500 0.00 0.00 45.78 2.66
3991 5967 5.455872 TGAATCGGAGGGAGTAGTAGATTT 58.544 41.667 0.00 0.00 0.00 2.17
3992 5968 6.607970 TGAATCGGAGGGAGTAGTAGATTTA 58.392 40.000 0.00 0.00 0.00 1.40
4021 5999 8.970691 AAGAAGTTTCCAATGATACATTTTCG 57.029 30.769 0.00 0.00 0.00 3.46
4025 6003 8.343168 AGTTTCCAATGATACATTTTCGGTTA 57.657 30.769 0.00 0.00 0.00 2.85
4026 6004 8.798402 AGTTTCCAATGATACATTTTCGGTTAA 58.202 29.630 0.00 0.00 0.00 2.01
4078 6056 7.671495 ATGATCAAACTTTAACCCAAAATGC 57.329 32.000 0.00 0.00 0.00 3.56
4079 6057 5.694006 TGATCAAACTTTAACCCAAAATGCG 59.306 36.000 0.00 0.00 0.00 4.73
4080 6058 5.263968 TCAAACTTTAACCCAAAATGCGA 57.736 34.783 0.00 0.00 0.00 5.10
4081 6059 5.285651 TCAAACTTTAACCCAAAATGCGAG 58.714 37.500 0.00 0.00 0.00 5.03
4082 6060 5.067936 TCAAACTTTAACCCAAAATGCGAGA 59.932 36.000 0.00 0.00 0.00 4.04
4083 6061 4.766404 ACTTTAACCCAAAATGCGAGAG 57.234 40.909 0.00 0.00 0.00 3.20
4084 6062 4.394729 ACTTTAACCCAAAATGCGAGAGA 58.605 39.130 0.00 0.00 0.00 3.10
4085 6063 4.455877 ACTTTAACCCAAAATGCGAGAGAG 59.544 41.667 0.00 0.00 0.00 3.20
4086 6064 2.859165 AACCCAAAATGCGAGAGAGA 57.141 45.000 0.00 0.00 0.00 3.10
4087 6065 2.100605 ACCCAAAATGCGAGAGAGAC 57.899 50.000 0.00 0.00 0.00 3.36
4088 6066 1.625818 ACCCAAAATGCGAGAGAGACT 59.374 47.619 0.00 0.00 0.00 3.24
4089 6067 2.832129 ACCCAAAATGCGAGAGAGACTA 59.168 45.455 0.00 0.00 0.00 2.59
4090 6068 3.260884 ACCCAAAATGCGAGAGAGACTAA 59.739 43.478 0.00 0.00 0.00 2.24
4091 6069 4.080863 ACCCAAAATGCGAGAGAGACTAAT 60.081 41.667 0.00 0.00 0.00 1.73
4092 6070 5.128827 ACCCAAAATGCGAGAGAGACTAATA 59.871 40.000 0.00 0.00 0.00 0.98
4093 6071 6.049149 CCCAAAATGCGAGAGAGACTAATAA 58.951 40.000 0.00 0.00 0.00 1.40
4094 6072 6.538742 CCCAAAATGCGAGAGAGACTAATAAA 59.461 38.462 0.00 0.00 0.00 1.40
4095 6073 7.402640 CCAAAATGCGAGAGAGACTAATAAAC 58.597 38.462 0.00 0.00 0.00 2.01
4096 6074 7.402640 CAAAATGCGAGAGAGACTAATAAACC 58.597 38.462 0.00 0.00 0.00 3.27
4097 6075 4.650754 TGCGAGAGAGACTAATAAACCC 57.349 45.455 0.00 0.00 0.00 4.11
4098 6076 3.066342 TGCGAGAGAGACTAATAAACCCG 59.934 47.826 0.00 0.00 0.00 5.28
4099 6077 3.550436 GCGAGAGAGACTAATAAACCCGG 60.550 52.174 0.00 0.00 0.00 5.73
4100 6078 3.004524 CGAGAGAGACTAATAAACCCGGG 59.995 52.174 22.25 22.25 0.00 5.73
4101 6079 2.699321 AGAGAGACTAATAAACCCGGGC 59.301 50.000 24.08 0.00 0.00 6.13
4102 6080 1.411612 AGAGACTAATAAACCCGGGCG 59.588 52.381 24.08 0.00 0.00 6.13
4103 6081 1.137675 GAGACTAATAAACCCGGGCGT 59.862 52.381 24.08 11.72 0.00 5.68
4104 6082 2.362077 GAGACTAATAAACCCGGGCGTA 59.638 50.000 24.08 13.93 0.00 4.42
4105 6083 2.363359 AGACTAATAAACCCGGGCGTAG 59.637 50.000 24.08 16.67 0.00 3.51
4106 6084 1.413812 ACTAATAAACCCGGGCGTAGG 59.586 52.381 24.08 7.69 0.00 3.18
4107 6085 1.413812 CTAATAAACCCGGGCGTAGGT 59.586 52.381 24.08 7.75 38.27 3.08
4108 6086 1.494960 AATAAACCCGGGCGTAGGTA 58.505 50.000 24.08 3.98 34.45 3.08
4109 6087 1.043022 ATAAACCCGGGCGTAGGTAG 58.957 55.000 24.08 0.00 34.45 3.18
4110 6088 0.324275 TAAACCCGGGCGTAGGTAGT 60.324 55.000 24.08 0.00 34.45 2.73
4111 6089 0.324275 AAACCCGGGCGTAGGTAGTA 60.324 55.000 24.08 0.00 34.45 1.82
4112 6090 0.106015 AACCCGGGCGTAGGTAGTAT 60.106 55.000 24.08 0.00 34.45 2.12
4113 6091 0.771127 ACCCGGGCGTAGGTAGTATA 59.229 55.000 24.08 0.00 33.52 1.47
4114 6092 1.144913 ACCCGGGCGTAGGTAGTATAA 59.855 52.381 24.08 0.00 33.52 0.98
4115 6093 2.238521 CCCGGGCGTAGGTAGTATAAA 58.761 52.381 8.08 0.00 0.00 1.40
4116 6094 2.029918 CCCGGGCGTAGGTAGTATAAAC 60.030 54.545 8.08 0.00 0.00 2.01
4117 6095 2.887152 CCGGGCGTAGGTAGTATAAACT 59.113 50.000 0.00 0.00 39.91 2.66
4118 6096 3.319122 CCGGGCGTAGGTAGTATAAACTT 59.681 47.826 0.00 0.00 37.15 2.66
4119 6097 4.540824 CGGGCGTAGGTAGTATAAACTTC 58.459 47.826 0.00 0.00 37.15 3.01
4120 6098 4.557496 CGGGCGTAGGTAGTATAAACTTCC 60.557 50.000 0.00 0.00 42.10 3.46
4140 6118 9.793259 AACTTCCTTCTTATGAACTTATGTTGA 57.207 29.630 0.00 0.00 36.39 3.18
4141 6119 9.442047 ACTTCCTTCTTATGAACTTATGTTGAG 57.558 33.333 0.00 0.00 36.39 3.02
4142 6120 8.792830 TTCCTTCTTATGAACTTATGTTGAGG 57.207 34.615 0.00 0.00 36.39 3.86
4143 6121 6.823689 TCCTTCTTATGAACTTATGTTGAGGC 59.176 38.462 0.00 0.00 36.39 4.70
4144 6122 6.825721 CCTTCTTATGAACTTATGTTGAGGCT 59.174 38.462 0.00 0.00 36.39 4.58
4145 6123 7.011857 CCTTCTTATGAACTTATGTTGAGGCTC 59.988 40.741 7.79 7.79 36.39 4.70
4146 6124 6.042777 TCTTATGAACTTATGTTGAGGCTCG 58.957 40.000 10.42 0.00 36.39 5.03
4147 6125 2.972625 TGAACTTATGTTGAGGCTCGG 58.027 47.619 10.42 0.00 36.39 4.63
4148 6126 2.301870 TGAACTTATGTTGAGGCTCGGT 59.698 45.455 10.42 0.00 36.39 4.69
4149 6127 2.386661 ACTTATGTTGAGGCTCGGTG 57.613 50.000 10.42 0.00 0.00 4.94
4150 6128 1.066143 ACTTATGTTGAGGCTCGGTGG 60.066 52.381 10.42 0.00 0.00 4.61
4151 6129 1.207089 CTTATGTTGAGGCTCGGTGGA 59.793 52.381 10.42 0.00 0.00 4.02
4152 6130 1.496060 TATGTTGAGGCTCGGTGGAT 58.504 50.000 10.42 0.20 0.00 3.41
4153 6131 0.620556 ATGTTGAGGCTCGGTGGATT 59.379 50.000 10.42 0.00 0.00 3.01
4154 6132 0.321564 TGTTGAGGCTCGGTGGATTG 60.322 55.000 10.42 0.00 0.00 2.67
4155 6133 1.026718 GTTGAGGCTCGGTGGATTGG 61.027 60.000 10.42 0.00 0.00 3.16
4156 6134 1.488705 TTGAGGCTCGGTGGATTGGT 61.489 55.000 10.42 0.00 0.00 3.67
4157 6135 1.299976 GAGGCTCGGTGGATTGGTT 59.700 57.895 0.00 0.00 0.00 3.67
4158 6136 1.002134 AGGCTCGGTGGATTGGTTG 60.002 57.895 0.00 0.00 0.00 3.77
4159 6137 1.303317 GGCTCGGTGGATTGGTTGT 60.303 57.895 0.00 0.00 0.00 3.32
4160 6138 0.035820 GGCTCGGTGGATTGGTTGTA 60.036 55.000 0.00 0.00 0.00 2.41
4161 6139 1.612199 GGCTCGGTGGATTGGTTGTAA 60.612 52.381 0.00 0.00 0.00 2.41
4162 6140 2.365582 GCTCGGTGGATTGGTTGTAAT 58.634 47.619 0.00 0.00 0.00 1.89
4163 6141 2.752903 GCTCGGTGGATTGGTTGTAATT 59.247 45.455 0.00 0.00 0.00 1.40
4164 6142 3.192633 GCTCGGTGGATTGGTTGTAATTT 59.807 43.478 0.00 0.00 0.00 1.82
4165 6143 4.674362 GCTCGGTGGATTGGTTGTAATTTC 60.674 45.833 0.00 0.00 0.00 2.17
4166 6144 4.658063 TCGGTGGATTGGTTGTAATTTCT 58.342 39.130 0.00 0.00 0.00 2.52
4167 6145 5.074115 TCGGTGGATTGGTTGTAATTTCTT 58.926 37.500 0.00 0.00 0.00 2.52
4168 6146 5.536916 TCGGTGGATTGGTTGTAATTTCTTT 59.463 36.000 0.00 0.00 0.00 2.52
4169 6147 6.041069 TCGGTGGATTGGTTGTAATTTCTTTT 59.959 34.615 0.00 0.00 0.00 2.27
4170 6148 7.230913 TCGGTGGATTGGTTGTAATTTCTTTTA 59.769 33.333 0.00 0.00 0.00 1.52
4171 6149 8.032451 CGGTGGATTGGTTGTAATTTCTTTTAT 58.968 33.333 0.00 0.00 0.00 1.40
4172 6150 9.719355 GGTGGATTGGTTGTAATTTCTTTTATT 57.281 29.630 0.00 0.00 0.00 1.40
4197 6175 9.892130 TTTTAAAGTTGTTTCCATGGTTATGTT 57.108 25.926 12.58 0.31 32.21 2.71
4198 6176 9.892130 TTTAAAGTTGTTTCCATGGTTATGTTT 57.108 25.926 12.58 7.00 32.21 2.83
4200 6178 8.880878 AAAGTTGTTTCCATGGTTATGTTTAC 57.119 30.769 12.58 1.71 32.21 2.01
4201 6179 7.589958 AGTTGTTTCCATGGTTATGTTTACA 57.410 32.000 12.58 3.21 32.21 2.41
4202 6180 8.012957 AGTTGTTTCCATGGTTATGTTTACAA 57.987 30.769 12.58 8.67 32.21 2.41
4203 6181 8.141268 AGTTGTTTCCATGGTTATGTTTACAAG 58.859 33.333 12.58 0.00 31.93 3.16
4204 6182 7.589958 TGTTTCCATGGTTATGTTTACAAGT 57.410 32.000 12.58 0.00 32.21 3.16
4205 6183 8.012957 TGTTTCCATGGTTATGTTTACAAGTT 57.987 30.769 12.58 0.00 32.21 2.66
4206 6184 8.478877 TGTTTCCATGGTTATGTTTACAAGTTT 58.521 29.630 12.58 0.00 32.21 2.66
4207 6185 9.320352 GTTTCCATGGTTATGTTTACAAGTTTT 57.680 29.630 12.58 0.00 32.21 2.43
4208 6186 9.892130 TTTCCATGGTTATGTTTACAAGTTTTT 57.108 25.926 12.58 0.00 32.21 1.94
4209 6187 9.535878 TTCCATGGTTATGTTTACAAGTTTTTC 57.464 29.630 12.58 0.00 32.21 2.29
4210 6188 8.919145 TCCATGGTTATGTTTACAAGTTTTTCT 58.081 29.630 12.58 0.00 32.21 2.52
4223 6201 6.712549 ACAAGTTTTTCTAGAAGTACAACGC 58.287 36.000 16.65 2.72 0.00 4.84
4224 6202 5.571778 AGTTTTTCTAGAAGTACAACGCG 57.428 39.130 3.53 3.53 0.00 6.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
379 380 1.153349 GGCAGCGGTTTAGGGAGAG 60.153 63.158 0.00 0.00 0.00 3.20
381 382 2.511600 CGGCAGCGGTTTAGGGAG 60.512 66.667 0.00 0.00 0.00 4.30
617 618 0.763223 AGGGGCCGGGTTACTCATAG 60.763 60.000 2.18 0.00 0.00 2.23
674 675 9.880157 ACCTATTATCAAAACTAAACTTCGCTA 57.120 29.630 0.00 0.00 0.00 4.26
697 698 9.574516 ACTATTACAAAGAAAAACATCTGACCT 57.425 29.630 0.00 0.00 0.00 3.85
708 709 9.810545 CAGGGTGAAAAACTATTACAAAGAAAA 57.189 29.630 0.00 0.00 0.00 2.29
709 710 7.923878 GCAGGGTGAAAAACTATTACAAAGAAA 59.076 33.333 0.00 0.00 0.00 2.52
710 711 7.068839 TGCAGGGTGAAAAACTATTACAAAGAA 59.931 33.333 0.00 0.00 0.00 2.52
711 712 6.547880 TGCAGGGTGAAAAACTATTACAAAGA 59.452 34.615 0.00 0.00 0.00 2.52
712 713 6.744112 TGCAGGGTGAAAAACTATTACAAAG 58.256 36.000 0.00 0.00 0.00 2.77
713 714 6.716934 TGCAGGGTGAAAAACTATTACAAA 57.283 33.333 0.00 0.00 0.00 2.83
714 715 6.491745 TCATGCAGGGTGAAAAACTATTACAA 59.508 34.615 0.00 0.00 0.00 2.41
715 716 6.007076 TCATGCAGGGTGAAAAACTATTACA 58.993 36.000 0.00 0.00 0.00 2.41
716 717 6.322491 GTCATGCAGGGTGAAAAACTATTAC 58.678 40.000 0.00 0.00 0.00 1.89
717 718 5.123186 CGTCATGCAGGGTGAAAAACTATTA 59.877 40.000 0.00 0.00 0.00 0.98
718 719 4.082787 CGTCATGCAGGGTGAAAAACTATT 60.083 41.667 0.00 0.00 0.00 1.73
719 720 3.440173 CGTCATGCAGGGTGAAAAACTAT 59.560 43.478 0.00 0.00 0.00 2.12
720 721 2.811431 CGTCATGCAGGGTGAAAAACTA 59.189 45.455 0.00 0.00 0.00 2.24
721 722 1.608590 CGTCATGCAGGGTGAAAAACT 59.391 47.619 0.00 0.00 0.00 2.66
722 723 1.335872 CCGTCATGCAGGGTGAAAAAC 60.336 52.381 0.00 0.00 0.00 2.43
723 724 0.958091 CCGTCATGCAGGGTGAAAAA 59.042 50.000 0.00 0.00 0.00 1.94
724 725 0.109532 TCCGTCATGCAGGGTGAAAA 59.890 50.000 0.00 0.00 0.00 2.29
725 726 0.327924 ATCCGTCATGCAGGGTGAAA 59.672 50.000 0.00 0.00 0.00 2.69
726 727 1.134521 GTATCCGTCATGCAGGGTGAA 60.135 52.381 0.00 0.00 0.00 3.18
727 728 0.464036 GTATCCGTCATGCAGGGTGA 59.536 55.000 0.00 0.00 0.00 4.02
728 729 0.465705 AGTATCCGTCATGCAGGGTG 59.534 55.000 0.00 0.00 0.00 4.61
729 730 0.465705 CAGTATCCGTCATGCAGGGT 59.534 55.000 0.00 2.42 0.00 4.34
730 731 0.465705 ACAGTATCCGTCATGCAGGG 59.534 55.000 0.00 0.00 0.00 4.45
731 732 3.068165 TCTTACAGTATCCGTCATGCAGG 59.932 47.826 0.00 0.00 0.00 4.85
732 733 4.307443 TCTTACAGTATCCGTCATGCAG 57.693 45.455 0.00 0.00 0.00 4.41
733 734 4.729227 TTCTTACAGTATCCGTCATGCA 57.271 40.909 0.00 0.00 0.00 3.96
734 735 5.753438 TCATTTCTTACAGTATCCGTCATGC 59.247 40.000 0.00 0.00 0.00 4.06
735 736 7.953158 ATCATTTCTTACAGTATCCGTCATG 57.047 36.000 0.00 0.00 0.00 3.07
736 737 7.987458 ACAATCATTTCTTACAGTATCCGTCAT 59.013 33.333 0.00 0.00 0.00 3.06
737 738 7.327975 ACAATCATTTCTTACAGTATCCGTCA 58.672 34.615 0.00 0.00 0.00 4.35
738 739 7.772332 ACAATCATTTCTTACAGTATCCGTC 57.228 36.000 0.00 0.00 0.00 4.79
739 740 9.832445 AATACAATCATTTCTTACAGTATCCGT 57.168 29.630 0.00 0.00 0.00 4.69
825 826 9.403583 ACAAATCTGACACCTAAAAAGAACTAA 57.596 29.630 0.00 0.00 0.00 2.24
826 827 8.974060 ACAAATCTGACACCTAAAAAGAACTA 57.026 30.769 0.00 0.00 0.00 2.24
827 828 7.881775 ACAAATCTGACACCTAAAAAGAACT 57.118 32.000 0.00 0.00 0.00 3.01
860 864 4.974645 TTCCACTACAAATCTGACACCT 57.025 40.909 0.00 0.00 0.00 4.00
890 894 3.939066 ACAGTAATACACTTGCTGGTCC 58.061 45.455 7.74 0.00 36.62 4.46
943 956 3.814005 AAGCAAATCTCAATCATGCCC 57.186 42.857 0.00 0.00 37.73 5.36
950 978 6.956497 AGAGGTCTCTAAAGCAAATCTCAAT 58.044 36.000 0.00 0.00 38.35 2.57
958 986 6.071278 GGTTTCTCTAGAGGTCTCTAAAGCAA 60.071 42.308 19.67 0.00 41.22 3.91
959 987 5.419471 GGTTTCTCTAGAGGTCTCTAAAGCA 59.581 44.000 19.67 0.00 41.22 3.91
960 988 5.163488 GGGTTTCTCTAGAGGTCTCTAAAGC 60.163 48.000 19.67 18.06 41.22 3.51
961 989 5.361571 GGGGTTTCTCTAGAGGTCTCTAAAG 59.638 48.000 19.67 5.74 41.22 1.85
962 990 5.270794 GGGGTTTCTCTAGAGGTCTCTAAA 58.729 45.833 19.67 8.70 41.22 1.85
966 1309 2.025898 CGGGGTTTCTCTAGAGGTCTC 58.974 57.143 19.67 9.89 0.00 3.36
1063 1411 0.944311 GACGCAGCGGTTGAGAAAGA 60.944 55.000 21.15 0.00 0.00 2.52
1066 1414 2.733218 CGACGCAGCGGTTGAGAA 60.733 61.111 21.15 0.00 0.00 2.87
1071 1419 4.664677 AAGAGCGACGCAGCGGTT 62.665 61.111 23.70 0.00 42.62 4.44
1083 1431 2.185608 GAGGGCGGTGAGAAGAGC 59.814 66.667 0.00 0.00 0.00 4.09
1195 1543 7.309194 GGCGTTAAATTGGAGGATTAATGCTAT 60.309 37.037 9.72 0.00 44.80 2.97
1202 1550 4.590918 TGTGGCGTTAAATTGGAGGATTA 58.409 39.130 0.00 0.00 0.00 1.75
1251 1599 4.626402 TCCCCGAGTTCCACCGGT 62.626 66.667 0.00 0.00 43.93 5.28
1291 1639 1.377987 GGTTGATGGGTGCGGCTAA 60.378 57.895 0.00 0.00 0.00 3.09
1504 1852 1.375523 GAGCGAGCCCGAGGAAAAA 60.376 57.895 0.00 0.00 38.22 1.94
1653 2002 2.281761 AGCGCTGTCAAGGGGTTG 60.282 61.111 10.39 0.00 43.86 3.77
1811 2167 1.006571 TCGAGCCGTTCTGGACAAC 60.007 57.895 0.00 0.00 42.00 3.32
2305 2707 3.190874 CGATTTGAGTTCTGTAGGGCTC 58.809 50.000 0.00 0.00 0.00 4.70
2338 2740 6.127897 GCACCTCAGCATAAACAATAACTTCT 60.128 38.462 0.00 0.00 0.00 2.85
2596 2998 1.064389 GGTGCCTCCTTGCCTAAAGAT 60.064 52.381 0.00 0.00 38.24 2.40
2705 3119 9.371136 CGCCAAACATATTATATGTAGAGTCAT 57.629 33.333 17.00 0.00 0.00 3.06
2706 3120 7.817478 CCGCCAAACATATTATATGTAGAGTCA 59.183 37.037 17.00 0.00 0.00 3.41
2707 3121 7.201530 GCCGCCAAACATATTATATGTAGAGTC 60.202 40.741 17.00 6.44 0.00 3.36
2708 3122 6.594159 GCCGCCAAACATATTATATGTAGAGT 59.406 38.462 17.00 0.40 0.00 3.24
2709 3123 6.818644 AGCCGCCAAACATATTATATGTAGAG 59.181 38.462 17.00 10.96 0.00 2.43
2710 3124 6.707290 AGCCGCCAAACATATTATATGTAGA 58.293 36.000 17.00 0.00 0.00 2.59
2711 3125 6.818644 AGAGCCGCCAAACATATTATATGTAG 59.181 38.462 17.00 12.68 0.00 2.74
2712 3126 6.707290 AGAGCCGCCAAACATATTATATGTA 58.293 36.000 17.00 0.00 0.00 2.29
2713 3127 5.560724 AGAGCCGCCAAACATATTATATGT 58.439 37.500 11.68 11.68 0.00 2.29
2714 3128 7.609760 TTAGAGCCGCCAAACATATTATATG 57.390 36.000 10.37 10.37 0.00 1.78
2715 3129 7.663905 TGTTTAGAGCCGCCAAACATATTATAT 59.336 33.333 10.06 0.00 37.27 0.86
2745 3159 6.797033 CGCACAAAGTAATTCTCAAAAGGTAG 59.203 38.462 0.00 0.00 0.00 3.18
2780 3199 4.222145 ACTTTACGAGGCATTCCAGACTAA 59.778 41.667 0.00 0.00 33.74 2.24
3160 5121 0.957362 GGCCTTATCAAGAGCCATGC 59.043 55.000 0.00 0.00 41.58 4.06
3236 5203 4.360563 CCAACACAATACTAGCTACCTCG 58.639 47.826 0.00 0.00 0.00 4.63
3550 5518 1.965643 ACTGCTGGCACAAAATGATGT 59.034 42.857 0.00 0.00 38.70 3.06
3588 5557 9.729281 ATTATTTTTCTGATGGTTCAAGCAAAT 57.271 25.926 0.00 0.00 0.00 2.32
3612 5581 5.655488 TGTGATTCCGTTTGTTTCACAATT 58.345 33.333 1.84 0.00 42.53 2.32
3619 5588 8.110860 AGATAAGAATGTGATTCCGTTTGTTT 57.889 30.769 0.00 0.00 40.13 2.83
3624 5593 6.414732 TGGAAGATAAGAATGTGATTCCGTT 58.585 36.000 0.00 0.00 40.13 4.44
3630 5599 7.419981 CCCTCTCTTGGAAGATAAGAATGTGAT 60.420 40.741 0.00 0.00 34.07 3.06
3637 5606 8.654997 CAAATATCCCTCTCTTGGAAGATAAGA 58.345 37.037 0.00 0.00 35.03 2.10
3659 5628 2.014010 ATGGTGCCACAACTCCAAAT 57.986 45.000 0.00 0.00 36.82 2.32
3669 5638 0.251787 AGAGGGGAAAATGGTGCCAC 60.252 55.000 0.00 0.00 0.00 5.01
3701 5670 7.027874 ACTTCCCATGAATTTAGAAGGTACA 57.972 36.000 0.00 0.00 38.58 2.90
3702 5671 7.110155 TGACTTCCCATGAATTTAGAAGGTAC 58.890 38.462 0.00 0.00 38.58 3.34
3709 5678 4.731773 GCGCTTGACTTCCCATGAATTTAG 60.732 45.833 0.00 0.00 0.00 1.85
3734 5703 0.604578 GCACACTGCATCCAACCATT 59.395 50.000 0.00 0.00 44.26 3.16
3738 5707 2.562912 CCGCACACTGCATCCAAC 59.437 61.111 0.00 0.00 45.36 3.77
3767 5736 7.108841 ACGAAGGTAGTAATTCATAAGCAGA 57.891 36.000 0.00 0.00 0.00 4.26
3862 5836 9.768215 ATTGGAGGGAGTAAAATAATTTCTTGA 57.232 29.630 0.00 0.00 0.00 3.02
3865 5839 7.619302 TGCATTGGAGGGAGTAAAATAATTTCT 59.381 33.333 0.00 0.00 0.00 2.52
3871 5846 9.515226 GTAATATGCATTGGAGGGAGTAAAATA 57.485 33.333 3.54 0.00 0.00 1.40
3901 5876 4.559251 GTGCTAGATATATCCGTTTGAGCG 59.441 45.833 9.18 0.00 0.00 5.03
3910 5886 8.679100 AGACGTATTTCAGTGCTAGATATATCC 58.321 37.037 9.18 0.00 0.00 2.59
3919 5895 7.797038 TGTATCTAGACGTATTTCAGTGCTA 57.203 36.000 0.00 0.00 0.00 3.49
3925 5901 5.766670 ACCGGATGTATCTAGACGTATTTCA 59.233 40.000 9.46 0.00 0.00 2.69
3927 5903 6.645790 AACCGGATGTATCTAGACGTATTT 57.354 37.500 9.46 0.00 0.00 1.40
3928 5904 6.645790 AAACCGGATGTATCTAGACGTATT 57.354 37.500 9.46 0.00 0.00 1.89
3931 5907 5.504665 CGTTAAACCGGATGTATCTAGACGT 60.505 44.000 9.46 0.00 0.00 4.34
3935 5911 6.753279 TGTTTCGTTAAACCGGATGTATCTAG 59.247 38.462 9.46 0.00 43.66 2.43
3945 5921 7.741198 TCATATAAGTTGTTTCGTTAAACCGG 58.259 34.615 0.00 0.00 43.66 5.28
3946 5922 9.763465 ATTCATATAAGTTGTTTCGTTAAACCG 57.237 29.630 0.00 0.00 43.66 4.44
3951 5927 8.929827 TCCGATTCATATAAGTTGTTTCGTTA 57.070 30.769 0.00 0.00 0.00 3.18
3954 5930 6.073765 CCCTCCGATTCATATAAGTTGTTTCG 60.074 42.308 0.00 0.00 0.00 3.46
3964 5940 7.506361 TCTACTACTCCCTCCGATTCATATA 57.494 40.000 0.00 0.00 0.00 0.86
4000 5978 6.834168 ACCGAAAATGTATCATTGGAAACT 57.166 33.333 4.95 0.00 0.00 2.66
4052 6030 9.382275 GCATTTTGGGTTAAAGTTTGATCATAT 57.618 29.630 0.00 0.00 0.00 1.78
4053 6031 7.543868 CGCATTTTGGGTTAAAGTTTGATCATA 59.456 33.333 0.00 0.00 0.00 2.15
4054 6032 6.368516 CGCATTTTGGGTTAAAGTTTGATCAT 59.631 34.615 0.00 0.00 0.00 2.45
4055 6033 5.694006 CGCATTTTGGGTTAAAGTTTGATCA 59.306 36.000 0.00 0.00 0.00 2.92
4056 6034 5.923684 TCGCATTTTGGGTTAAAGTTTGATC 59.076 36.000 0.00 0.00 0.00 2.92
4057 6035 5.848406 TCGCATTTTGGGTTAAAGTTTGAT 58.152 33.333 0.00 0.00 0.00 2.57
4058 6036 5.067936 TCTCGCATTTTGGGTTAAAGTTTGA 59.932 36.000 0.00 0.00 0.00 2.69
4059 6037 5.285651 TCTCGCATTTTGGGTTAAAGTTTG 58.714 37.500 0.00 0.00 0.00 2.93
4060 6038 5.300792 TCTCTCGCATTTTGGGTTAAAGTTT 59.699 36.000 0.00 0.00 0.00 2.66
4061 6039 4.825085 TCTCTCGCATTTTGGGTTAAAGTT 59.175 37.500 0.00 0.00 0.00 2.66
4062 6040 4.394729 TCTCTCGCATTTTGGGTTAAAGT 58.605 39.130 0.00 0.00 0.00 2.66
4063 6041 4.695455 TCTCTCTCGCATTTTGGGTTAAAG 59.305 41.667 0.00 0.00 0.00 1.85
4064 6042 4.454504 GTCTCTCTCGCATTTTGGGTTAAA 59.545 41.667 0.00 0.00 0.00 1.52
4065 6043 4.000988 GTCTCTCTCGCATTTTGGGTTAA 58.999 43.478 0.00 0.00 0.00 2.01
4066 6044 3.260884 AGTCTCTCTCGCATTTTGGGTTA 59.739 43.478 0.00 0.00 0.00 2.85
4067 6045 2.039084 AGTCTCTCTCGCATTTTGGGTT 59.961 45.455 0.00 0.00 0.00 4.11
4068 6046 1.625818 AGTCTCTCTCGCATTTTGGGT 59.374 47.619 0.00 0.00 0.00 4.51
4069 6047 2.393271 AGTCTCTCTCGCATTTTGGG 57.607 50.000 0.00 0.00 0.00 4.12
4070 6048 7.402640 GTTTATTAGTCTCTCTCGCATTTTGG 58.597 38.462 0.00 0.00 0.00 3.28
4071 6049 7.402640 GGTTTATTAGTCTCTCTCGCATTTTG 58.597 38.462 0.00 0.00 0.00 2.44
4072 6050 6.539103 GGGTTTATTAGTCTCTCTCGCATTTT 59.461 38.462 0.00 0.00 0.00 1.82
4073 6051 6.049790 GGGTTTATTAGTCTCTCTCGCATTT 58.950 40.000 0.00 0.00 0.00 2.32
4074 6052 5.602628 GGGTTTATTAGTCTCTCTCGCATT 58.397 41.667 0.00 0.00 0.00 3.56
4075 6053 4.261656 CGGGTTTATTAGTCTCTCTCGCAT 60.262 45.833 0.00 0.00 0.00 4.73
4076 6054 3.066342 CGGGTTTATTAGTCTCTCTCGCA 59.934 47.826 0.00 0.00 0.00 5.10
4077 6055 3.550436 CCGGGTTTATTAGTCTCTCTCGC 60.550 52.174 0.00 0.00 0.00 5.03
4078 6056 3.004524 CCCGGGTTTATTAGTCTCTCTCG 59.995 52.174 14.18 0.00 0.00 4.04
4079 6057 3.243805 GCCCGGGTTTATTAGTCTCTCTC 60.244 52.174 24.63 0.00 0.00 3.20
4080 6058 2.699321 GCCCGGGTTTATTAGTCTCTCT 59.301 50.000 24.63 0.00 0.00 3.10
4081 6059 2.545322 CGCCCGGGTTTATTAGTCTCTC 60.545 54.545 24.63 0.00 0.00 3.20
4082 6060 1.411612 CGCCCGGGTTTATTAGTCTCT 59.588 52.381 24.63 0.00 0.00 3.10
4083 6061 1.137675 ACGCCCGGGTTTATTAGTCTC 59.862 52.381 24.63 0.00 0.00 3.36
4084 6062 1.197812 ACGCCCGGGTTTATTAGTCT 58.802 50.000 24.63 0.00 0.00 3.24
4085 6063 2.546584 CCTACGCCCGGGTTTATTAGTC 60.547 54.545 24.63 0.00 0.00 2.59
4086 6064 1.413812 CCTACGCCCGGGTTTATTAGT 59.586 52.381 24.63 12.94 0.00 2.24
4087 6065 1.413812 ACCTACGCCCGGGTTTATTAG 59.586 52.381 24.63 14.49 30.80 1.73
4088 6066 1.494960 ACCTACGCCCGGGTTTATTA 58.505 50.000 24.63 5.46 30.80 0.98
4089 6067 1.413812 CTACCTACGCCCGGGTTTATT 59.586 52.381 24.63 5.06 37.07 1.40
4090 6068 1.043022 CTACCTACGCCCGGGTTTAT 58.957 55.000 24.63 7.79 37.07 1.40
4091 6069 0.324275 ACTACCTACGCCCGGGTTTA 60.324 55.000 24.63 12.66 37.07 2.01
4092 6070 0.324275 TACTACCTACGCCCGGGTTT 60.324 55.000 24.63 12.11 37.07 3.27
4093 6071 0.106015 ATACTACCTACGCCCGGGTT 60.106 55.000 24.63 12.52 37.07 4.11
4094 6072 0.771127 TATACTACCTACGCCCGGGT 59.229 55.000 24.63 5.39 39.40 5.28
4095 6073 1.909700 TTATACTACCTACGCCCGGG 58.090 55.000 19.09 19.09 0.00 5.73
4096 6074 2.887152 AGTTTATACTACCTACGCCCGG 59.113 50.000 0.00 0.00 31.21 5.73
4097 6075 4.540824 GAAGTTTATACTACCTACGCCCG 58.459 47.826 0.00 0.00 33.17 6.13
4098 6076 4.586421 AGGAAGTTTATACTACCTACGCCC 59.414 45.833 0.00 0.00 33.17 6.13
4099 6077 5.781210 AGGAAGTTTATACTACCTACGCC 57.219 43.478 0.00 0.00 33.17 5.68
4100 6078 7.036996 AGAAGGAAGTTTATACTACCTACGC 57.963 40.000 0.00 0.00 33.17 4.42
4114 6092 9.793259 TCAACATAAGTTCATAAGAAGGAAGTT 57.207 29.630 0.00 0.00 40.91 2.66
4115 6093 9.442047 CTCAACATAAGTTCATAAGAAGGAAGT 57.558 33.333 0.00 0.00 35.28 3.01
4116 6094 8.887717 CCTCAACATAAGTTCATAAGAAGGAAG 58.112 37.037 0.00 0.00 35.28 3.46
4117 6095 7.336931 GCCTCAACATAAGTTCATAAGAAGGAA 59.663 37.037 0.00 0.00 35.28 3.36
4118 6096 6.823689 GCCTCAACATAAGTTCATAAGAAGGA 59.176 38.462 0.00 0.00 35.28 3.36
4119 6097 6.825721 AGCCTCAACATAAGTTCATAAGAAGG 59.174 38.462 0.00 0.00 35.28 3.46
4120 6098 7.254252 CGAGCCTCAACATAAGTTCATAAGAAG 60.254 40.741 0.00 0.00 35.28 2.85
4121 6099 6.535150 CGAGCCTCAACATAAGTTCATAAGAA 59.465 38.462 0.00 0.00 35.28 2.52
4122 6100 6.042777 CGAGCCTCAACATAAGTTCATAAGA 58.957 40.000 0.00 0.00 35.28 2.10
4123 6101 5.235186 CCGAGCCTCAACATAAGTTCATAAG 59.765 44.000 0.00 0.00 35.28 1.73
4124 6102 5.116180 CCGAGCCTCAACATAAGTTCATAA 58.884 41.667 0.00 0.00 35.28 1.90
4125 6103 4.161565 ACCGAGCCTCAACATAAGTTCATA 59.838 41.667 0.00 0.00 35.28 2.15
4126 6104 3.055094 ACCGAGCCTCAACATAAGTTCAT 60.055 43.478 0.00 0.00 35.28 2.57
4127 6105 2.301870 ACCGAGCCTCAACATAAGTTCA 59.698 45.455 0.00 0.00 35.28 3.18
4128 6106 2.673368 CACCGAGCCTCAACATAAGTTC 59.327 50.000 0.00 0.00 35.28 3.01
4129 6107 2.615493 CCACCGAGCCTCAACATAAGTT 60.615 50.000 0.00 0.00 38.88 2.66
4130 6108 1.066143 CCACCGAGCCTCAACATAAGT 60.066 52.381 0.00 0.00 0.00 2.24
4131 6109 1.207089 TCCACCGAGCCTCAACATAAG 59.793 52.381 0.00 0.00 0.00 1.73
4132 6110 1.271856 TCCACCGAGCCTCAACATAA 58.728 50.000 0.00 0.00 0.00 1.90
4133 6111 1.496060 ATCCACCGAGCCTCAACATA 58.504 50.000 0.00 0.00 0.00 2.29
4134 6112 0.620556 AATCCACCGAGCCTCAACAT 59.379 50.000 0.00 0.00 0.00 2.71
4135 6113 0.321564 CAATCCACCGAGCCTCAACA 60.322 55.000 0.00 0.00 0.00 3.33
4136 6114 1.026718 CCAATCCACCGAGCCTCAAC 61.027 60.000 0.00 0.00 0.00 3.18
4137 6115 1.299648 CCAATCCACCGAGCCTCAA 59.700 57.895 0.00 0.00 0.00 3.02
4138 6116 1.488705 AACCAATCCACCGAGCCTCA 61.489 55.000 0.00 0.00 0.00 3.86
4139 6117 1.026718 CAACCAATCCACCGAGCCTC 61.027 60.000 0.00 0.00 0.00 4.70
4140 6118 1.002134 CAACCAATCCACCGAGCCT 60.002 57.895 0.00 0.00 0.00 4.58
4141 6119 0.035820 TACAACCAATCCACCGAGCC 60.036 55.000 0.00 0.00 0.00 4.70
4142 6120 1.816074 TTACAACCAATCCACCGAGC 58.184 50.000 0.00 0.00 0.00 5.03
4143 6121 4.700213 AGAAATTACAACCAATCCACCGAG 59.300 41.667 0.00 0.00 0.00 4.63
4144 6122 4.658063 AGAAATTACAACCAATCCACCGA 58.342 39.130 0.00 0.00 0.00 4.69
4145 6123 5.385509 AAGAAATTACAACCAATCCACCG 57.614 39.130 0.00 0.00 0.00 4.94
4146 6124 9.719355 AATAAAAGAAATTACAACCAATCCACC 57.281 29.630 0.00 0.00 0.00 4.61
4181 6159 8.880878 AAACTTGTAAACATAACCATGGAAAC 57.119 30.769 21.47 4.85 36.39 2.78
4182 6160 9.892130 AAAAACTTGTAAACATAACCATGGAAA 57.108 25.926 21.47 5.93 36.39 3.13
4183 6161 9.535878 GAAAAACTTGTAAACATAACCATGGAA 57.464 29.630 21.47 6.36 36.39 3.53
4184 6162 8.919145 AGAAAAACTTGTAAACATAACCATGGA 58.081 29.630 21.47 0.00 36.39 3.41
4197 6175 8.330302 GCGTTGTACTTCTAGAAAAACTTGTAA 58.670 33.333 6.63 0.00 0.00 2.41
4198 6176 7.306167 CGCGTTGTACTTCTAGAAAAACTTGTA 60.306 37.037 6.63 1.55 0.00 2.41
4199 6177 6.509039 CGCGTTGTACTTCTAGAAAAACTTGT 60.509 38.462 6.63 2.52 0.00 3.16
4200 6178 5.839239 CGCGTTGTACTTCTAGAAAAACTTG 59.161 40.000 6.63 0.00 0.00 3.16
4201 6179 5.970879 CGCGTTGTACTTCTAGAAAAACTT 58.029 37.500 6.63 0.00 0.00 2.66
4202 6180 5.571778 CGCGTTGTACTTCTAGAAAAACT 57.428 39.130 6.63 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.