Multiple sequence alignment - TraesCS5D01G287700

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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 TraesCS5D01G287700 chr5D 100.000 3653 0 0 1 3653 387249257 387252909 0.000000e+00 6746.0
1 TraesCS5D01G287700 chr5D 92.098 367 28 1 2907 3273 387288100 387287735 1.940000e-142 516.0
2 TraesCS5D01G287700 chr5D 95.385 65 3 0 1010 1074 387097983 387098047 1.790000e-18 104.0
3 TraesCS5D01G287700 chr5D 100.000 28 0 0 2839 2866 230374125 230374152 7.000000e-03 52.8
4 TraesCS5D01G287700 chr5B 93.891 2079 87 15 775 2838 465823774 465825827 0.000000e+00 3099.0
5 TraesCS5D01G287700 chr5B 91.181 669 57 2 109 777 659546949 659547615 0.000000e+00 907.0
6 TraesCS5D01G287700 chr5A 95.385 1105 40 9 1721 2819 489933911 489935010 0.000000e+00 1748.0
7 TraesCS5D01G287700 chr5A 84.265 966 73 40 775 1694 489932885 489933817 0.000000e+00 869.0
8 TraesCS5D01G287700 chr5A 82.209 652 84 15 3007 3652 338527985 338528610 1.930000e-147 532.0
9 TraesCS5D01G287700 chr5A 85.128 195 17 8 896 1079 302989259 302989066 4.820000e-44 189.0
10 TraesCS5D01G287700 chr5A 95.312 64 3 0 1011 1074 489843382 489843445 6.450000e-18 102.0
11 TraesCS5D01G287700 chr5A 100.000 28 0 0 2839 2866 562386467 562386494 7.000000e-03 52.8
12 TraesCS5D01G287700 chr6A 93.348 917 56 3 1818 2731 36859263 36858349 0.000000e+00 1351.0
13 TraesCS5D01G287700 chr4D 95.262 781 33 4 1 777 473870765 473869985 0.000000e+00 1234.0
14 TraesCS5D01G287700 chr4D 86.420 648 75 9 3007 3653 34698506 34697871 0.000000e+00 697.0
15 TraesCS5D01G287700 chr6B 94.344 778 42 2 1 777 147888488 147887712 0.000000e+00 1192.0
16 TraesCS5D01G287700 chr6B 91.656 779 60 3 1 777 717737928 717738703 0.000000e+00 1074.0
17 TraesCS5D01G287700 chr6B 83.390 584 44 26 896 1458 389763603 389764154 3.280000e-135 492.0
18 TraesCS5D01G287700 chr6B 88.889 144 14 2 1584 1725 389771330 389771473 3.750000e-40 176.0
19 TraesCS5D01G287700 chr6B 88.158 76 9 0 1450 1525 389771259 389771334 1.400000e-14 91.6
20 TraesCS5D01G287700 chr6B 97.368 38 0 1 1721 1757 389771519 389771556 3.050000e-06 63.9
21 TraesCS5D01G287700 chr3B 94.118 782 41 4 1 780 10022625 10021847 0.000000e+00 1184.0
22 TraesCS5D01G287700 chr7B 92.811 779 51 5 1 777 36411531 36410756 0.000000e+00 1123.0
23 TraesCS5D01G287700 chr7B 85.538 650 80 8 3007 3652 593419093 593419732 0.000000e+00 667.0
24 TraesCS5D01G287700 chr4B 92.159 778 57 3 1 777 622484936 622484162 0.000000e+00 1096.0
25 TraesCS5D01G287700 chr2B 92.021 777 60 2 1 776 225310223 225309448 0.000000e+00 1090.0
26 TraesCS5D01G287700 chr2B 84.891 642 53 25 896 1525 391877668 391877059 3.120000e-170 608.0
27 TraesCS5D01G287700 chr2B 86.331 139 17 2 1584 1721 391877063 391876926 2.270000e-32 150.0
28 TraesCS5D01G287700 chr1B 93.171 659 42 2 1 657 359213479 359212822 0.000000e+00 965.0
29 TraesCS5D01G287700 chr6D 88.296 581 32 9 949 1525 162246603 162246055 0.000000e+00 664.0
30 TraesCS5D01G287700 chr6D 83.409 657 87 15 3001 3653 398167223 398166585 1.130000e-164 590.0
31 TraesCS5D01G287700 chr6D 94.118 34 2 0 2839 2872 79823935 79823902 7.000000e-03 52.8
32 TraesCS5D01G287700 chr1A 84.793 651 81 13 3007 3653 494096519 494095883 3.980000e-179 638.0
33 TraesCS5D01G287700 chr1A 82.198 646 84 18 3007 3651 539381724 539382339 8.980000e-146 527.0
34 TraesCS5D01G287700 chr1A 100.000 28 0 0 2839 2866 86576471 86576444 7.000000e-03 52.8
35 TraesCS5D01G287700 chr2A 84.227 653 83 14 3007 3653 700537491 700536853 5.180000e-173 617.0
36 TraesCS5D01G287700 chr2A 82.407 648 92 12 3007 3652 739883478 739884105 2.480000e-151 545.0
37 TraesCS5D01G287700 chr2A 94.595 148 8 0 1176 1323 239955012 239955159 2.840000e-56 230.0
38 TraesCS5D01G287700 chr2A 91.803 61 5 0 1465 1525 239955765 239955705 6.500000e-13 86.1
39 TraesCS5D01G287700 chr2D 86.090 532 59 9 3124 3653 61372028 61371510 3.190000e-155 558.0
40 TraesCS5D01G287700 chr7A 83.256 430 61 7 3225 3653 22389311 22389730 5.720000e-103 385.0
41 TraesCS5D01G287700 chr7A 87.302 189 12 8 896 1073 503326448 503326635 4.780000e-49 206.0
42 TraesCS5D01G287700 chr4A 87.245 196 11 10 896 1079 142903567 142903374 1.030000e-50 211.0
43 TraesCS5D01G287700 chr4A 100.000 28 0 0 2839 2866 593201860 593201887 7.000000e-03 52.8
44 TraesCS5D01G287700 chr3D 100.000 28 0 0 2839 2866 396215535 396215562 7.000000e-03 52.8
45 TraesCS5D01G287700 chr1D 100.000 28 0 0 2839 2866 25839375 25839348 7.000000e-03 52.8
46 TraesCS5D01G287700 chr1D 85.185 54 4 3 2839 2890 90577398 90577347 7.000000e-03 52.8
47 TraesCS5D01G287700 chr1D 100.000 28 0 0 2839 2866 450144976 450144949 7.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G287700 chr5D 387249257 387252909 3652 False 6746.0 6746 100.000 1 3653 1 chr5D.!!$F3 3652
1 TraesCS5D01G287700 chr5B 465823774 465825827 2053 False 3099.0 3099 93.891 775 2838 1 chr5B.!!$F1 2063
2 TraesCS5D01G287700 chr5B 659546949 659547615 666 False 907.0 907 91.181 109 777 1 chr5B.!!$F2 668
3 TraesCS5D01G287700 chr5A 489932885 489935010 2125 False 1308.5 1748 89.825 775 2819 2 chr5A.!!$F4 2044
4 TraesCS5D01G287700 chr5A 338527985 338528610 625 False 532.0 532 82.209 3007 3652 1 chr5A.!!$F1 645
5 TraesCS5D01G287700 chr6A 36858349 36859263 914 True 1351.0 1351 93.348 1818 2731 1 chr6A.!!$R1 913
6 TraesCS5D01G287700 chr4D 473869985 473870765 780 True 1234.0 1234 95.262 1 777 1 chr4D.!!$R2 776
7 TraesCS5D01G287700 chr4D 34697871 34698506 635 True 697.0 697 86.420 3007 3653 1 chr4D.!!$R1 646
8 TraesCS5D01G287700 chr6B 147887712 147888488 776 True 1192.0 1192 94.344 1 777 1 chr6B.!!$R1 776
9 TraesCS5D01G287700 chr6B 717737928 717738703 775 False 1074.0 1074 91.656 1 777 1 chr6B.!!$F2 776
10 TraesCS5D01G287700 chr6B 389763603 389764154 551 False 492.0 492 83.390 896 1458 1 chr6B.!!$F1 562
11 TraesCS5D01G287700 chr3B 10021847 10022625 778 True 1184.0 1184 94.118 1 780 1 chr3B.!!$R1 779
12 TraesCS5D01G287700 chr7B 36410756 36411531 775 True 1123.0 1123 92.811 1 777 1 chr7B.!!$R1 776
13 TraesCS5D01G287700 chr7B 593419093 593419732 639 False 667.0 667 85.538 3007 3652 1 chr7B.!!$F1 645
14 TraesCS5D01G287700 chr4B 622484162 622484936 774 True 1096.0 1096 92.159 1 777 1 chr4B.!!$R1 776
15 TraesCS5D01G287700 chr2B 225309448 225310223 775 True 1090.0 1090 92.021 1 776 1 chr2B.!!$R1 775
16 TraesCS5D01G287700 chr2B 391876926 391877668 742 True 379.0 608 85.611 896 1721 2 chr2B.!!$R2 825
17 TraesCS5D01G287700 chr1B 359212822 359213479 657 True 965.0 965 93.171 1 657 1 chr1B.!!$R1 656
18 TraesCS5D01G287700 chr6D 162246055 162246603 548 True 664.0 664 88.296 949 1525 1 chr6D.!!$R2 576
19 TraesCS5D01G287700 chr6D 398166585 398167223 638 True 590.0 590 83.409 3001 3653 1 chr6D.!!$R3 652
20 TraesCS5D01G287700 chr1A 494095883 494096519 636 True 638.0 638 84.793 3007 3653 1 chr1A.!!$R2 646
21 TraesCS5D01G287700 chr1A 539381724 539382339 615 False 527.0 527 82.198 3007 3651 1 chr1A.!!$F1 644
22 TraesCS5D01G287700 chr2A 700536853 700537491 638 True 617.0 617 84.227 3007 3653 1 chr2A.!!$R2 646
23 TraesCS5D01G287700 chr2A 739883478 739884105 627 False 545.0 545 82.407 3007 3652 1 chr2A.!!$F2 645
24 TraesCS5D01G287700 chr2D 61371510 61372028 518 True 558.0 558 86.090 3124 3653 1 chr2D.!!$R1 529

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
821 832 0.107081 ATCCGGACACGTTGGACAAA 59.893 50.0 6.12 0.0 38.78 2.83 F
822 833 0.107800 TCCGGACACGTTGGACAAAA 60.108 50.0 0.00 0.0 38.78 2.44 F
947 969 0.402504 ACCAGTCTCTCACTCGTCCT 59.597 55.0 0.00 0.0 30.26 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1823 1969 0.165944 CGGTGAATGCGTTGTCCTTC 59.834 55.0 0.00 0.0 0.0 3.46 R
1900 2048 0.238553 CTCGAGCGTGTCAGAAGTCA 59.761 55.0 0.00 0.0 0.0 3.41 R
2936 3091 0.098728 GCAAATGGATCGGGTTGACG 59.901 55.0 5.37 0.0 0.0 4.35 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
331 339 3.372440 AACTGATTGGAGGGAATGGAC 57.628 47.619 0.00 0.00 0.00 4.02
396 404 2.200955 GGTGAAGGGAAGAGGGAGATT 58.799 52.381 0.00 0.00 0.00 2.40
470 478 2.585153 GGAGGAGGAAGAACGGGC 59.415 66.667 0.00 0.00 0.00 6.13
486 494 2.609610 GCTGGTGGGTGGGGTAGA 60.610 66.667 0.00 0.00 0.00 2.59
675 684 1.143401 GTGTTCTAGCCTACCGCCC 59.857 63.158 0.00 0.00 38.78 6.13
697 706 0.108963 TCGGGTGACGGTTGGAAAAT 59.891 50.000 0.00 0.00 44.45 1.82
706 715 3.496331 ACGGTTGGAAAATGGTCAGATT 58.504 40.909 0.00 0.00 0.00 2.40
749 760 3.903783 ATGCGGCTAAACGTGCAT 58.096 50.000 0.00 3.19 42.84 3.96
820 831 0.601576 CATCCGGACACGTTGGACAA 60.602 55.000 6.12 0.00 38.78 3.18
821 832 0.107081 ATCCGGACACGTTGGACAAA 59.893 50.000 6.12 0.00 38.78 2.83
822 833 0.107800 TCCGGACACGTTGGACAAAA 60.108 50.000 0.00 0.00 38.78 2.44
823 834 0.733729 CCGGACACGTTGGACAAAAA 59.266 50.000 0.00 0.00 38.78 1.94
856 867 1.279271 GTGATGGTTCAGGCAGGTACT 59.721 52.381 0.00 0.00 31.89 2.73
939 961 1.121407 CACCACCCACCAGTCTCTCA 61.121 60.000 0.00 0.00 0.00 3.27
944 966 0.896019 CCCACCAGTCTCTCACTCGT 60.896 60.000 0.00 0.00 30.26 4.18
945 967 0.523966 CCACCAGTCTCTCACTCGTC 59.476 60.000 0.00 0.00 30.26 4.20
946 968 0.523966 CACCAGTCTCTCACTCGTCC 59.476 60.000 0.00 0.00 30.26 4.79
947 969 0.402504 ACCAGTCTCTCACTCGTCCT 59.597 55.000 0.00 0.00 30.26 3.85
948 970 1.202952 ACCAGTCTCTCACTCGTCCTT 60.203 52.381 0.00 0.00 30.26 3.36
949 971 1.470890 CCAGTCTCTCACTCGTCCTTC 59.529 57.143 0.00 0.00 30.26 3.46
950 972 1.470890 CAGTCTCTCACTCGTCCTTCC 59.529 57.143 0.00 0.00 30.26 3.46
951 973 1.353022 AGTCTCTCACTCGTCCTTCCT 59.647 52.381 0.00 0.00 0.00 3.36
1082 1120 3.478509 GCCTCAAGGTACGATCTCTCTA 58.521 50.000 0.00 0.00 37.57 2.43
1088 1126 3.150767 AGGTACGATCTCTCTATGTGCC 58.849 50.000 0.00 0.00 35.81 5.01
1150 1189 2.476619 GTGTTCACTGATGGAACTGACG 59.523 50.000 6.80 0.00 43.84 4.35
1153 1196 3.303881 TCACTGATGGAACTGACGAAG 57.696 47.619 0.00 0.00 0.00 3.79
1332 1378 0.808755 CGCCAGGTAATTGAACCACC 59.191 55.000 0.31 0.00 42.40 4.61
1339 1385 2.412770 GGTAATTGAACCACCACGTACG 59.587 50.000 15.01 15.01 39.50 3.67
1417 1465 7.020010 GCAATATTCGCCAAAATAGAGATGAG 58.980 38.462 0.00 0.00 0.00 2.90
1459 1507 6.163159 GGCTTGATAGCTGATAAAATCTCG 57.837 41.667 0.00 0.00 46.90 4.04
1564 1641 0.601046 TGTTCGTTCTCTGCTGCTGG 60.601 55.000 6.69 0.00 0.00 4.85
1805 1951 1.186200 CGGGAGACAAGGTCATCTCA 58.814 55.000 3.84 0.00 42.73 3.27
1823 1969 1.209504 TCAATCAGCTTCCCGGTAAGG 59.790 52.381 9.04 0.00 40.63 2.69
1848 1994 1.673993 AACGCATTCACCGCCATGA 60.674 52.632 0.00 0.00 0.00 3.07
1900 2048 5.765182 CCCAACAGTCAAAATCTAGTGTTCT 59.235 40.000 0.00 0.00 37.19 3.01
2172 2320 2.400798 CATTACGCCGTGCAGCTG 59.599 61.111 10.11 10.11 0.00 4.24
2675 2824 7.766283 TGAACATGAAACTGTTGATGTGTTTA 58.234 30.769 15.37 9.18 40.22 2.01
2845 3000 5.447624 AAAAAGGGTTGGAGTTGATAACG 57.552 39.130 0.00 0.00 36.23 3.18
2846 3001 2.109425 AGGGTTGGAGTTGATAACGC 57.891 50.000 0.00 0.00 37.48 4.84
2851 3006 3.543884 GGAGTTGATAACGCCCACA 57.456 52.632 3.46 0.00 44.50 4.17
2852 3007 1.084289 GGAGTTGATAACGCCCACAC 58.916 55.000 3.46 0.00 44.50 3.82
2853 3008 0.719465 GAGTTGATAACGCCCACACG 59.281 55.000 0.00 0.00 36.23 4.49
2873 3028 3.933155 GTGTGGCACGAAGATATTCAG 57.067 47.619 13.77 0.00 0.00 3.02
2874 3029 3.262420 GTGTGGCACGAAGATATTCAGT 58.738 45.455 13.77 0.00 0.00 3.41
2875 3030 3.307242 GTGTGGCACGAAGATATTCAGTC 59.693 47.826 13.77 0.00 0.00 3.51
2876 3031 2.866762 GTGGCACGAAGATATTCAGTCC 59.133 50.000 0.00 0.00 0.00 3.85
2877 3032 2.128035 GGCACGAAGATATTCAGTCCG 58.872 52.381 0.35 0.00 0.00 4.79
2878 3033 2.223735 GGCACGAAGATATTCAGTCCGA 60.224 50.000 0.35 0.00 0.00 4.55
2879 3034 3.444916 GCACGAAGATATTCAGTCCGAA 58.555 45.455 0.35 0.00 38.22 4.30
2880 3035 3.243177 GCACGAAGATATTCAGTCCGAAC 59.757 47.826 0.35 0.00 36.12 3.95
2881 3036 3.482472 CACGAAGATATTCAGTCCGAACG 59.518 47.826 0.35 0.00 36.12 3.95
2882 3037 2.468040 CGAAGATATTCAGTCCGAACGC 59.532 50.000 0.35 0.00 36.12 4.84
2883 3038 2.510768 AGATATTCAGTCCGAACGCC 57.489 50.000 0.00 0.00 36.12 5.68
2884 3039 1.068741 AGATATTCAGTCCGAACGCCC 59.931 52.381 0.00 0.00 36.12 6.13
2885 3040 1.068741 GATATTCAGTCCGAACGCCCT 59.931 52.381 0.00 0.00 36.12 5.19
2886 3041 0.899720 TATTCAGTCCGAACGCCCTT 59.100 50.000 0.00 0.00 36.12 3.95
2887 3042 0.899720 ATTCAGTCCGAACGCCCTTA 59.100 50.000 0.00 0.00 36.12 2.69
2888 3043 0.899720 TTCAGTCCGAACGCCCTTAT 59.100 50.000 0.00 0.00 0.00 1.73
2889 3044 0.899720 TCAGTCCGAACGCCCTTATT 59.100 50.000 0.00 0.00 0.00 1.40
2890 3045 1.006832 CAGTCCGAACGCCCTTATTG 58.993 55.000 0.00 0.00 0.00 1.90
2891 3046 0.743345 AGTCCGAACGCCCTTATTGC 60.743 55.000 0.00 0.00 0.00 3.56
2892 3047 1.450669 TCCGAACGCCCTTATTGCC 60.451 57.895 0.00 0.00 0.00 4.52
2893 3048 2.707039 CGAACGCCCTTATTGCCG 59.293 61.111 0.00 0.00 0.00 5.69
2894 3049 2.104253 CGAACGCCCTTATTGCCGT 61.104 57.895 0.00 0.00 35.14 5.68
2895 3050 1.641123 CGAACGCCCTTATTGCCGTT 61.641 55.000 0.00 0.00 45.31 4.44
2896 3051 0.179174 GAACGCCCTTATTGCCGTTG 60.179 55.000 1.81 0.00 43.05 4.10
2897 3052 1.591504 AACGCCCTTATTGCCGTTGG 61.592 55.000 0.00 0.00 41.67 3.77
2898 3053 1.747367 CGCCCTTATTGCCGTTGGA 60.747 57.895 0.00 0.00 0.00 3.53
2899 3054 1.101049 CGCCCTTATTGCCGTTGGAT 61.101 55.000 0.00 0.00 0.00 3.41
2900 3055 0.668535 GCCCTTATTGCCGTTGGATC 59.331 55.000 0.00 0.00 0.00 3.36
2901 3056 0.944386 CCCTTATTGCCGTTGGATCG 59.056 55.000 0.00 0.00 0.00 3.69
2908 3063 4.120085 CCGTTGGATCGGGCTAAC 57.880 61.111 0.00 0.00 45.88 2.34
2909 3064 1.523032 CCGTTGGATCGGGCTAACC 60.523 63.158 0.00 0.00 45.88 2.85
2910 3065 1.219664 CGTTGGATCGGGCTAACCA 59.780 57.895 0.00 0.00 40.22 3.67
2911 3066 1.087771 CGTTGGATCGGGCTAACCAC 61.088 60.000 0.00 0.00 40.22 4.16
2912 3067 0.746923 GTTGGATCGGGCTAACCACC 60.747 60.000 0.00 0.00 40.22 4.61
2913 3068 0.912487 TTGGATCGGGCTAACCACCT 60.912 55.000 0.00 0.00 40.22 4.00
2914 3069 1.335132 TGGATCGGGCTAACCACCTC 61.335 60.000 0.00 0.00 40.22 3.85
2915 3070 1.446366 GATCGGGCTAACCACCTCC 59.554 63.158 0.00 0.00 40.22 4.30
2916 3071 1.003051 ATCGGGCTAACCACCTCCT 59.997 57.895 0.00 0.00 40.22 3.69
2917 3072 1.049289 ATCGGGCTAACCACCTCCTC 61.049 60.000 0.00 0.00 40.22 3.71
2918 3073 2.732619 CGGGCTAACCACCTCCTCC 61.733 68.421 0.00 0.00 40.22 4.30
2919 3074 2.732619 GGGCTAACCACCTCCTCCG 61.733 68.421 0.00 0.00 39.85 4.63
2920 3075 2.187163 GCTAACCACCTCCTCCGC 59.813 66.667 0.00 0.00 0.00 5.54
2921 3076 2.359967 GCTAACCACCTCCTCCGCT 61.360 63.158 0.00 0.00 0.00 5.52
2922 3077 1.041447 GCTAACCACCTCCTCCGCTA 61.041 60.000 0.00 0.00 0.00 4.26
2923 3078 1.481871 CTAACCACCTCCTCCGCTAA 58.518 55.000 0.00 0.00 0.00 3.09
2924 3079 1.409427 CTAACCACCTCCTCCGCTAAG 59.591 57.143 0.00 0.00 0.00 2.18
2925 3080 1.900545 AACCACCTCCTCCGCTAAGC 61.901 60.000 0.00 0.00 0.00 3.09
2926 3081 2.359169 CCACCTCCTCCGCTAAGCA 61.359 63.158 0.00 0.00 0.00 3.91
2927 3082 1.690219 CCACCTCCTCCGCTAAGCAT 61.690 60.000 0.00 0.00 0.00 3.79
2928 3083 0.179000 CACCTCCTCCGCTAAGCATT 59.821 55.000 0.00 0.00 0.00 3.56
2929 3084 0.466124 ACCTCCTCCGCTAAGCATTC 59.534 55.000 0.00 0.00 0.00 2.67
2930 3085 0.250081 CCTCCTCCGCTAAGCATTCC 60.250 60.000 0.00 0.00 0.00 3.01
2931 3086 0.250081 CTCCTCCGCTAAGCATTCCC 60.250 60.000 0.00 0.00 0.00 3.97
2932 3087 0.691078 TCCTCCGCTAAGCATTCCCT 60.691 55.000 0.00 0.00 0.00 4.20
2933 3088 0.250081 CCTCCGCTAAGCATTCCCTC 60.250 60.000 0.00 0.00 0.00 4.30
2934 3089 0.598680 CTCCGCTAAGCATTCCCTCG 60.599 60.000 0.00 0.00 0.00 4.63
2935 3090 2.247437 CCGCTAAGCATTCCCTCGC 61.247 63.158 0.00 0.00 0.00 5.03
2936 3091 2.247437 CGCTAAGCATTCCCTCGCC 61.247 63.158 0.00 0.00 0.00 5.54
2937 3092 2.247437 GCTAAGCATTCCCTCGCCG 61.247 63.158 0.00 0.00 0.00 6.46
2938 3093 1.144057 CTAAGCATTCCCTCGCCGT 59.856 57.895 0.00 0.00 0.00 5.68
2939 3094 0.876342 CTAAGCATTCCCTCGCCGTC 60.876 60.000 0.00 0.00 0.00 4.79
2940 3095 1.609635 TAAGCATTCCCTCGCCGTCA 61.610 55.000 0.00 0.00 0.00 4.35
2941 3096 2.435938 GCATTCCCTCGCCGTCAA 60.436 61.111 0.00 0.00 0.00 3.18
2942 3097 2.750888 GCATTCCCTCGCCGTCAAC 61.751 63.158 0.00 0.00 0.00 3.18
2943 3098 2.106683 CATTCCCTCGCCGTCAACC 61.107 63.158 0.00 0.00 0.00 3.77
2944 3099 3.325201 ATTCCCTCGCCGTCAACCC 62.325 63.158 0.00 0.00 0.00 4.11
2947 3102 4.143333 CCTCGCCGTCAACCCGAT 62.143 66.667 0.00 0.00 0.00 4.18
2948 3103 2.582498 CTCGCCGTCAACCCGATC 60.582 66.667 0.00 0.00 0.00 3.69
2949 3104 4.137872 TCGCCGTCAACCCGATCC 62.138 66.667 0.00 0.00 0.00 3.36
2950 3105 4.444838 CGCCGTCAACCCGATCCA 62.445 66.667 0.00 0.00 0.00 3.41
2951 3106 2.189521 GCCGTCAACCCGATCCAT 59.810 61.111 0.00 0.00 0.00 3.41
2952 3107 1.451387 GCCGTCAACCCGATCCATT 60.451 57.895 0.00 0.00 0.00 3.16
2953 3108 1.029947 GCCGTCAACCCGATCCATTT 61.030 55.000 0.00 0.00 0.00 2.32
2954 3109 0.732571 CCGTCAACCCGATCCATTTG 59.267 55.000 0.00 0.00 0.00 2.32
2955 3110 0.098728 CGTCAACCCGATCCATTTGC 59.901 55.000 0.00 0.00 0.00 3.68
2956 3111 1.463674 GTCAACCCGATCCATTTGCT 58.536 50.000 0.00 0.00 0.00 3.91
2957 3112 1.133025 GTCAACCCGATCCATTTGCTG 59.867 52.381 0.00 0.00 0.00 4.41
2958 3113 1.176527 CAACCCGATCCATTTGCTGT 58.823 50.000 0.00 0.00 0.00 4.40
2959 3114 1.545582 CAACCCGATCCATTTGCTGTT 59.454 47.619 0.00 0.00 0.00 3.16
2960 3115 1.463674 ACCCGATCCATTTGCTGTTC 58.536 50.000 0.00 0.00 0.00 3.18
2961 3116 1.271871 ACCCGATCCATTTGCTGTTCA 60.272 47.619 0.00 0.00 0.00 3.18
2962 3117 1.133025 CCCGATCCATTTGCTGTTCAC 59.867 52.381 0.00 0.00 0.00 3.18
2963 3118 1.133025 CCGATCCATTTGCTGTTCACC 59.867 52.381 0.00 0.00 0.00 4.02
2964 3119 1.202065 CGATCCATTTGCTGTTCACCG 60.202 52.381 0.00 0.00 0.00 4.94
2965 3120 0.527565 ATCCATTTGCTGTTCACCGC 59.472 50.000 0.00 0.00 0.00 5.68
2966 3121 1.080569 CCATTTGCTGTTCACCGCC 60.081 57.895 0.00 0.00 0.00 6.13
2967 3122 1.442520 CATTTGCTGTTCACCGCCG 60.443 57.895 0.00 0.00 0.00 6.46
2968 3123 3.267597 ATTTGCTGTTCACCGCCGC 62.268 57.895 0.00 0.00 0.00 6.53
2997 3152 4.162690 CCTGCCACCGCCTACCTC 62.163 72.222 0.00 0.00 0.00 3.85
2998 3153 3.390521 CTGCCACCGCCTACCTCA 61.391 66.667 0.00 0.00 0.00 3.86
2999 3154 3.665675 CTGCCACCGCCTACCTCAC 62.666 68.421 0.00 0.00 0.00 3.51
3003 3158 1.982395 CACCGCCTACCTCACCAGA 60.982 63.158 0.00 0.00 0.00 3.86
3034 3189 5.841957 ATTGCAAGGAGATACCACATTTC 57.158 39.130 4.94 0.00 42.04 2.17
3037 3192 4.263462 TGCAAGGAGATACCACATTTCAGT 60.263 41.667 0.00 0.00 42.04 3.41
3040 3195 5.615925 AGGAGATACCACATTTCAGTACC 57.384 43.478 0.00 0.00 42.04 3.34
3041 3196 5.030147 AGGAGATACCACATTTCAGTACCA 58.970 41.667 0.00 0.00 42.04 3.25
3060 3215 3.057033 ACCATGTAACGAGTCAGTACCAC 60.057 47.826 0.00 0.00 0.00 4.16
3061 3219 3.057104 CCATGTAACGAGTCAGTACCACA 60.057 47.826 0.00 0.00 0.00 4.17
3062 3220 3.631145 TGTAACGAGTCAGTACCACAC 57.369 47.619 0.00 0.00 0.00 3.82
3063 3221 3.216800 TGTAACGAGTCAGTACCACACT 58.783 45.455 0.00 0.00 38.32 3.55
3078 3236 1.330213 CACACTTCGTGCATGTCACAA 59.670 47.619 16.80 10.68 45.92 3.33
3081 3239 3.066621 ACACTTCGTGCATGTCACAATTT 59.933 39.130 16.80 0.59 45.92 1.82
3098 3256 5.815740 CACAATTTAGTACCACTATTCGGCT 59.184 40.000 0.00 0.00 29.64 5.52
3133 3291 6.673154 AAAAATACTGACAGCCGTATAACC 57.327 37.500 1.25 0.00 0.00 2.85
3227 3386 0.328592 TGCTGACTAGGACGAGGTCT 59.671 55.000 0.00 0.00 32.47 3.85
3293 3461 1.465387 ACCCCCACAAACCCTAGCT 60.465 57.895 0.00 0.00 0.00 3.32
3297 3465 1.165270 CCCACAAACCCTAGCTTTCG 58.835 55.000 0.00 0.00 0.00 3.46
3311 3479 0.537653 CTTTCGTTCTCCCCTCTCCC 59.462 60.000 0.00 0.00 0.00 4.30
3327 3495 1.457455 CCCTCTCCTCTCTCCCTGC 60.457 68.421 0.00 0.00 0.00 4.85
3329 3497 1.225983 CTCTCCTCTCTCCCTGCGA 59.774 63.158 0.00 0.00 0.00 5.10
3344 3512 1.685517 CTGCGAATCTCAGGAGATGGA 59.314 52.381 12.27 2.26 46.75 3.41
3405 3576 4.475135 GGCGACCTTCCTGGCCTC 62.475 72.222 3.32 0.00 42.29 4.70
3445 3616 4.373116 TGGACGGCTCCAGTTCGC 62.373 66.667 0.00 0.00 42.15 4.70
3456 3627 1.071471 CAGTTCGCCCAACTCCACT 59.929 57.895 0.00 0.00 44.14 4.00
3470 3641 2.125912 CACTGGCGACGAGGAAGG 60.126 66.667 0.00 0.00 0.00 3.46
3498 3672 4.424711 GCGCCCCTGTCCATGGAA 62.425 66.667 18.20 6.23 0.00 3.53
3586 3760 2.354403 GCGGGTGGAGTGTTGTAAGTAT 60.354 50.000 0.00 0.00 0.00 2.12
3588 3762 3.056393 CGGGTGGAGTGTTGTAAGTATCA 60.056 47.826 0.00 0.00 0.00 2.15
3591 3765 4.262721 GGTGGAGTGTTGTAAGTATCACCA 60.263 45.833 0.00 0.00 41.05 4.17
3592 3766 5.488341 GTGGAGTGTTGTAAGTATCACCAT 58.512 41.667 0.00 0.00 0.00 3.55
3593 3767 5.938125 GTGGAGTGTTGTAAGTATCACCATT 59.062 40.000 0.00 0.00 0.00 3.16
3631 3806 2.119495 TCAAATCAGAGGGCTAGGGTC 58.881 52.381 0.00 0.00 0.00 4.46
3640 3815 0.250513 GGGCTAGGGTCAGTGTTCTG 59.749 60.000 0.00 0.00 42.54 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
244 248 3.320826 GCAACCTAGGTTTTGGTGTTGAT 59.679 43.478 24.99 0.00 36.15 2.57
350 358 0.536724 GCGGATCTTTGGGGCAAATT 59.463 50.000 0.00 0.00 32.70 1.82
396 404 3.033773 TCCCGATCCCCTCCCTCA 61.034 66.667 0.00 0.00 0.00 3.86
470 478 2.670148 GCTCTACCCCACCCACCAG 61.670 68.421 0.00 0.00 0.00 4.00
496 504 0.605319 CCTTTCGTGCTTGGTGGCTA 60.605 55.000 0.00 0.00 0.00 3.93
587 595 4.007644 TCTGCCTGCTGACGTGGG 62.008 66.667 0.00 0.00 0.00 4.61
690 699 5.534654 AGTTTTCGAATCTGACCATTTTCCA 59.465 36.000 0.00 0.00 0.00 3.53
697 706 6.443934 TTGAAAAGTTTTCGAATCTGACCA 57.556 33.333 20.51 0.31 0.00 4.02
706 715 5.047235 TGACCCCTTTTTGAAAAGTTTTCGA 60.047 36.000 20.51 17.10 42.92 3.71
749 760 7.044798 CCAAATTCACTGTTTTGACCCTTTTA 58.955 34.615 5.29 0.00 35.34 1.52
823 834 4.223923 TGAACCATCACCAACAACCTTTTT 59.776 37.500 0.00 0.00 0.00 1.94
824 835 3.772025 TGAACCATCACCAACAACCTTTT 59.228 39.130 0.00 0.00 0.00 2.27
825 836 3.370104 TGAACCATCACCAACAACCTTT 58.630 40.909 0.00 0.00 0.00 3.11
826 837 2.958355 CTGAACCATCACCAACAACCTT 59.042 45.455 0.00 0.00 0.00 3.50
939 961 2.307686 AGAGAGAGAAGGAAGGACGAGT 59.692 50.000 0.00 0.00 0.00 4.18
944 966 4.111577 AGAGAGAGAGAGAGAAGGAAGGA 58.888 47.826 0.00 0.00 0.00 3.36
945 967 4.164988 AGAGAGAGAGAGAGAGAAGGAAGG 59.835 50.000 0.00 0.00 0.00 3.46
946 968 5.130145 AGAGAGAGAGAGAGAGAGAAGGAAG 59.870 48.000 0.00 0.00 0.00 3.46
947 969 5.032846 AGAGAGAGAGAGAGAGAGAAGGAA 58.967 45.833 0.00 0.00 0.00 3.36
948 970 4.624913 AGAGAGAGAGAGAGAGAGAAGGA 58.375 47.826 0.00 0.00 0.00 3.36
949 971 4.653341 AGAGAGAGAGAGAGAGAGAGAAGG 59.347 50.000 0.00 0.00 0.00 3.46
950 972 5.598005 AGAGAGAGAGAGAGAGAGAGAGAAG 59.402 48.000 0.00 0.00 0.00 2.85
951 973 5.523588 AGAGAGAGAGAGAGAGAGAGAGAA 58.476 45.833 0.00 0.00 0.00 2.87
1005 1043 1.000019 TCTCATCGTCCTCGGGGTT 60.000 57.895 0.00 0.00 37.69 4.11
1082 1120 2.363306 TTCAGTTCAGTTGGGCACAT 57.637 45.000 0.00 0.00 0.00 3.21
1088 1126 6.814506 AGAGATGATTTTCAGTTCAGTTGG 57.185 37.500 0.00 0.00 0.00 3.77
1157 1203 0.798776 CTGCGAGTGAAATCCACCAC 59.201 55.000 0.00 0.00 46.87 4.16
1339 1385 1.912110 CAGTCTGAAGCTACGCGTAAC 59.088 52.381 20.97 16.25 0.00 2.50
1346 1392 2.419297 CCATGTCCCAGTCTGAAGCTAC 60.419 54.545 0.00 0.00 0.00 3.58
1429 1477 2.505982 GCTATCAAGCCGGCCAGA 59.494 61.111 26.15 22.19 43.40 3.86
1459 1507 3.521560 TCACTAGCCAAATGACATCGAC 58.478 45.455 0.00 0.00 0.00 4.20
1564 1641 5.349824 AGAAGCTTGTTTCGTTTCTGATC 57.650 39.130 2.10 0.00 31.93 2.92
1805 1951 1.580059 TCCTTACCGGGAAGCTGATT 58.420 50.000 22.03 0.00 31.67 2.57
1823 1969 0.165944 CGGTGAATGCGTTGTCCTTC 59.834 55.000 0.00 0.00 0.00 3.46
1848 1994 2.125269 GGAATGGTAGCGTGGCGT 60.125 61.111 0.00 0.00 0.00 5.68
1900 2048 0.238553 CTCGAGCGTGTCAGAAGTCA 59.761 55.000 0.00 0.00 0.00 3.41
2214 2362 2.660552 ACGAAGTCCACGTTGCGG 60.661 61.111 0.00 0.00 41.18 5.69
2301 2449 3.755628 GCGTCGTACCTCCTGCCA 61.756 66.667 0.00 0.00 0.00 4.92
2675 2824 5.981088 TTCTCAAATTGCCACACATACAT 57.019 34.783 0.00 0.00 0.00 2.29
2718 2867 5.737860 TGCACTGCATATAGCTAGCATATT 58.262 37.500 18.83 0.00 45.94 1.28
2828 2983 1.092348 GGCGTTATCAACTCCAACCC 58.908 55.000 0.00 0.00 36.30 4.11
2838 2993 0.946700 CACACGTGTGGGCGTTATCA 60.947 55.000 35.65 0.00 43.83 2.15
2839 2994 1.785321 CACACGTGTGGGCGTTATC 59.215 57.895 35.65 0.00 43.83 1.75
2840 2995 3.960237 CACACGTGTGGGCGTTAT 58.040 55.556 35.65 1.93 43.83 1.89
2853 3008 3.262420 ACTGAATATCTTCGTGCCACAC 58.738 45.455 0.00 0.00 33.86 3.82
2854 3009 3.521560 GACTGAATATCTTCGTGCCACA 58.478 45.455 0.00 0.00 33.86 4.17
2855 3010 2.866762 GGACTGAATATCTTCGTGCCAC 59.133 50.000 0.00 0.00 33.86 5.01
2856 3011 2.481276 CGGACTGAATATCTTCGTGCCA 60.481 50.000 0.00 0.00 33.86 4.92
2857 3012 2.128035 CGGACTGAATATCTTCGTGCC 58.872 52.381 0.00 0.00 33.86 5.01
2858 3013 3.079960 TCGGACTGAATATCTTCGTGC 57.920 47.619 0.00 0.00 33.86 5.34
2859 3014 3.482472 CGTTCGGACTGAATATCTTCGTG 59.518 47.826 0.00 0.00 39.21 4.35
2860 3015 3.692576 CGTTCGGACTGAATATCTTCGT 58.307 45.455 0.00 0.00 39.21 3.85
2861 3016 2.468040 GCGTTCGGACTGAATATCTTCG 59.532 50.000 0.00 0.00 39.21 3.79
2862 3017 2.795470 GGCGTTCGGACTGAATATCTTC 59.205 50.000 0.00 0.00 39.21 2.87
2863 3018 2.483188 GGGCGTTCGGACTGAATATCTT 60.483 50.000 0.00 0.00 39.21 2.40
2864 3019 1.068741 GGGCGTTCGGACTGAATATCT 59.931 52.381 0.00 0.00 39.21 1.98
2865 3020 1.068741 AGGGCGTTCGGACTGAATATC 59.931 52.381 0.00 0.00 39.21 1.63
2866 3021 1.120530 AGGGCGTTCGGACTGAATAT 58.879 50.000 0.00 0.00 39.21 1.28
2867 3022 0.899720 AAGGGCGTTCGGACTGAATA 59.100 50.000 0.00 0.00 39.21 1.75
2868 3023 0.899720 TAAGGGCGTTCGGACTGAAT 59.100 50.000 0.00 0.00 39.21 2.57
2869 3024 0.899720 ATAAGGGCGTTCGGACTGAA 59.100 50.000 0.00 0.00 0.00 3.02
2870 3025 0.899720 AATAAGGGCGTTCGGACTGA 59.100 50.000 0.00 0.00 0.00 3.41
2871 3026 1.006832 CAATAAGGGCGTTCGGACTG 58.993 55.000 0.00 0.00 0.00 3.51
2872 3027 0.743345 GCAATAAGGGCGTTCGGACT 60.743 55.000 0.00 0.00 0.00 3.85
2873 3028 1.712018 GGCAATAAGGGCGTTCGGAC 61.712 60.000 0.00 0.00 0.00 4.79
2874 3029 1.450669 GGCAATAAGGGCGTTCGGA 60.451 57.895 0.00 0.00 0.00 4.55
2875 3030 3.107447 GGCAATAAGGGCGTTCGG 58.893 61.111 0.00 0.00 0.00 4.30
2881 3036 0.668535 GATCCAACGGCAATAAGGGC 59.331 55.000 0.00 0.00 0.00 5.19
2882 3037 0.944386 CGATCCAACGGCAATAAGGG 59.056 55.000 0.00 0.00 0.00 3.95
2883 3038 0.944386 CCGATCCAACGGCAATAAGG 59.056 55.000 0.00 0.00 46.20 2.69
2892 3047 1.087771 GTGGTTAGCCCGATCCAACG 61.088 60.000 0.00 0.00 35.15 4.10
2893 3048 0.746923 GGTGGTTAGCCCGATCCAAC 60.747 60.000 0.00 0.00 35.15 3.77
2894 3049 0.912487 AGGTGGTTAGCCCGATCCAA 60.912 55.000 0.00 0.00 35.15 3.53
2895 3050 1.306654 AGGTGGTTAGCCCGATCCA 60.307 57.895 0.00 0.00 35.15 3.41
2896 3051 1.446366 GAGGTGGTTAGCCCGATCC 59.554 63.158 0.00 0.00 35.15 3.36
2897 3052 1.049289 AGGAGGTGGTTAGCCCGATC 61.049 60.000 0.00 0.00 35.15 3.69
2898 3053 1.003051 AGGAGGTGGTTAGCCCGAT 59.997 57.895 0.00 0.00 35.15 4.18
2899 3054 1.684734 GAGGAGGTGGTTAGCCCGA 60.685 63.158 0.00 0.00 35.15 5.14
2900 3055 2.732619 GGAGGAGGTGGTTAGCCCG 61.733 68.421 0.00 0.00 35.15 6.13
2901 3056 2.732619 CGGAGGAGGTGGTTAGCCC 61.733 68.421 0.00 0.00 0.00 5.19
2902 3057 2.901042 CGGAGGAGGTGGTTAGCC 59.099 66.667 0.00 0.00 0.00 3.93
2903 3058 1.041447 TAGCGGAGGAGGTGGTTAGC 61.041 60.000 0.00 0.00 0.00 3.09
2904 3059 1.409427 CTTAGCGGAGGAGGTGGTTAG 59.591 57.143 0.00 0.00 0.00 2.34
2905 3060 1.481871 CTTAGCGGAGGAGGTGGTTA 58.518 55.000 0.00 0.00 0.00 2.85
2906 3061 1.900545 GCTTAGCGGAGGAGGTGGTT 61.901 60.000 0.00 0.00 0.00 3.67
2907 3062 2.359967 GCTTAGCGGAGGAGGTGGT 61.360 63.158 0.00 0.00 0.00 4.16
2908 3063 1.690219 ATGCTTAGCGGAGGAGGTGG 61.690 60.000 0.00 0.00 0.00 4.61
2909 3064 0.179000 AATGCTTAGCGGAGGAGGTG 59.821 55.000 0.00 0.00 0.00 4.00
2910 3065 0.466124 GAATGCTTAGCGGAGGAGGT 59.534 55.000 0.00 0.00 0.00 3.85
2911 3066 0.250081 GGAATGCTTAGCGGAGGAGG 60.250 60.000 0.00 0.00 0.00 4.30
2912 3067 0.250081 GGGAATGCTTAGCGGAGGAG 60.250 60.000 0.00 0.00 0.00 3.69
2913 3068 0.691078 AGGGAATGCTTAGCGGAGGA 60.691 55.000 0.00 0.00 0.00 3.71
2914 3069 0.250081 GAGGGAATGCTTAGCGGAGG 60.250 60.000 0.00 0.00 0.00 4.30
2915 3070 0.598680 CGAGGGAATGCTTAGCGGAG 60.599 60.000 0.00 0.00 0.00 4.63
2916 3071 1.441729 CGAGGGAATGCTTAGCGGA 59.558 57.895 0.00 0.00 0.00 5.54
2917 3072 2.247437 GCGAGGGAATGCTTAGCGG 61.247 63.158 0.00 0.00 0.00 5.52
2918 3073 2.247437 GGCGAGGGAATGCTTAGCG 61.247 63.158 0.00 0.00 0.00 4.26
2919 3074 2.247437 CGGCGAGGGAATGCTTAGC 61.247 63.158 0.00 0.00 0.00 3.09
2920 3075 0.876342 GACGGCGAGGGAATGCTTAG 60.876 60.000 16.62 0.00 0.00 2.18
2921 3076 1.143183 GACGGCGAGGGAATGCTTA 59.857 57.895 16.62 0.00 0.00 3.09
2922 3077 2.125106 GACGGCGAGGGAATGCTT 60.125 61.111 16.62 0.00 0.00 3.91
2923 3078 2.954684 TTGACGGCGAGGGAATGCT 61.955 57.895 16.62 0.00 0.00 3.79
2924 3079 2.435938 TTGACGGCGAGGGAATGC 60.436 61.111 16.62 0.00 0.00 3.56
2925 3080 2.106683 GGTTGACGGCGAGGGAATG 61.107 63.158 16.62 0.00 0.00 2.67
2926 3081 2.267961 GGTTGACGGCGAGGGAAT 59.732 61.111 16.62 0.00 0.00 3.01
2927 3082 4.011517 GGGTTGACGGCGAGGGAA 62.012 66.667 16.62 0.00 0.00 3.97
2930 3085 4.143333 ATCGGGTTGACGGCGAGG 62.143 66.667 16.62 0.00 0.00 4.63
2931 3086 2.582498 GATCGGGTTGACGGCGAG 60.582 66.667 16.62 0.00 0.00 5.03
2932 3087 4.137872 GGATCGGGTTGACGGCGA 62.138 66.667 16.62 0.00 0.00 5.54
2933 3088 3.733344 ATGGATCGGGTTGACGGCG 62.733 63.158 4.80 4.80 0.00 6.46
2934 3089 1.029947 AAATGGATCGGGTTGACGGC 61.030 55.000 0.00 0.00 0.00 5.68
2935 3090 0.732571 CAAATGGATCGGGTTGACGG 59.267 55.000 0.00 0.00 0.00 4.79
2936 3091 0.098728 GCAAATGGATCGGGTTGACG 59.901 55.000 5.37 0.00 0.00 4.35
2937 3092 1.133025 CAGCAAATGGATCGGGTTGAC 59.867 52.381 5.37 0.00 0.00 3.18
2938 3093 1.271871 ACAGCAAATGGATCGGGTTGA 60.272 47.619 5.37 0.00 0.00 3.18
2939 3094 1.176527 ACAGCAAATGGATCGGGTTG 58.823 50.000 0.00 0.00 0.00 3.77
2940 3095 1.818674 GAACAGCAAATGGATCGGGTT 59.181 47.619 0.00 0.00 0.00 4.11
2941 3096 1.271871 TGAACAGCAAATGGATCGGGT 60.272 47.619 0.00 0.00 0.00 5.28
2942 3097 1.133025 GTGAACAGCAAATGGATCGGG 59.867 52.381 0.00 0.00 0.00 5.14
2943 3098 1.133025 GGTGAACAGCAAATGGATCGG 59.867 52.381 0.00 0.00 0.00 4.18
2944 3099 1.202065 CGGTGAACAGCAAATGGATCG 60.202 52.381 4.94 0.00 0.00 3.69
2945 3100 1.468054 GCGGTGAACAGCAAATGGATC 60.468 52.381 0.47 0.00 37.03 3.36
2946 3101 0.527565 GCGGTGAACAGCAAATGGAT 59.472 50.000 0.47 0.00 37.03 3.41
2947 3102 1.523154 GGCGGTGAACAGCAAATGGA 61.523 55.000 7.84 0.00 38.83 3.41
2948 3103 1.080569 GGCGGTGAACAGCAAATGG 60.081 57.895 7.84 0.00 38.83 3.16
2949 3104 1.442520 CGGCGGTGAACAGCAAATG 60.443 57.895 0.00 0.00 38.83 2.32
2950 3105 2.953821 CGGCGGTGAACAGCAAAT 59.046 55.556 0.00 0.00 38.83 2.32
2951 3106 3.959975 GCGGCGGTGAACAGCAAA 61.960 61.111 9.78 0.00 38.83 3.68
2980 3135 4.162690 GAGGTAGGCGGTGGCAGG 62.163 72.222 0.00 0.00 42.47 4.85
2981 3136 3.390521 TGAGGTAGGCGGTGGCAG 61.391 66.667 0.00 0.00 42.47 4.85
2982 3137 3.702048 GTGAGGTAGGCGGTGGCA 61.702 66.667 0.00 0.00 42.47 4.92
2983 3138 4.468689 GGTGAGGTAGGCGGTGGC 62.469 72.222 0.00 0.00 38.90 5.01
2984 3139 3.000819 TGGTGAGGTAGGCGGTGG 61.001 66.667 0.00 0.00 0.00 4.61
2985 3140 1.982395 TCTGGTGAGGTAGGCGGTG 60.982 63.158 0.00 0.00 0.00 4.94
2986 3141 1.982938 GTCTGGTGAGGTAGGCGGT 60.983 63.158 0.00 0.00 0.00 5.68
2987 3142 2.893398 GTCTGGTGAGGTAGGCGG 59.107 66.667 0.00 0.00 0.00 6.13
2988 3143 2.490217 CGTCTGGTGAGGTAGGCG 59.510 66.667 0.00 0.00 35.59 5.52
2989 3144 1.668101 CTCCGTCTGGTGAGGTAGGC 61.668 65.000 0.00 0.00 36.30 3.93
2990 3145 0.323542 ACTCCGTCTGGTGAGGTAGG 60.324 60.000 0.00 0.00 36.30 3.18
2991 3146 1.546961 AACTCCGTCTGGTGAGGTAG 58.453 55.000 0.00 0.00 36.30 3.18
2992 3147 2.885135 TAACTCCGTCTGGTGAGGTA 57.115 50.000 0.00 0.00 36.30 3.08
2993 3148 2.005370 TTAACTCCGTCTGGTGAGGT 57.995 50.000 0.00 0.00 36.30 3.85
2994 3149 3.262420 CAATTAACTCCGTCTGGTGAGG 58.738 50.000 0.00 0.00 36.30 3.86
2995 3150 2.673368 GCAATTAACTCCGTCTGGTGAG 59.327 50.000 0.00 0.00 36.30 3.51
2996 3151 2.037902 TGCAATTAACTCCGTCTGGTGA 59.962 45.455 0.00 0.00 36.30 4.02
2997 3152 2.422597 TGCAATTAACTCCGTCTGGTG 58.577 47.619 0.00 0.00 36.30 4.17
2998 3153 2.851263 TGCAATTAACTCCGTCTGGT 57.149 45.000 0.00 0.00 36.30 4.00
2999 3154 2.420022 CCTTGCAATTAACTCCGTCTGG 59.580 50.000 0.00 0.00 0.00 3.86
3003 3158 3.695830 TCTCCTTGCAATTAACTCCGT 57.304 42.857 0.00 0.00 0.00 4.69
3034 3189 4.436242 ACTGACTCGTTACATGGTACTG 57.564 45.455 0.00 0.00 0.00 2.74
3037 3192 4.156556 GTGGTACTGACTCGTTACATGGTA 59.843 45.833 0.00 0.00 0.00 3.25
3040 3195 3.918591 GTGTGGTACTGACTCGTTACATG 59.081 47.826 0.00 0.00 0.00 3.21
3041 3196 3.825014 AGTGTGGTACTGACTCGTTACAT 59.175 43.478 0.00 0.00 38.49 2.29
3078 3236 7.597743 CGATTAAGCCGAATAGTGGTACTAAAT 59.402 37.037 0.00 0.00 33.89 1.40
3081 3239 5.532406 ACGATTAAGCCGAATAGTGGTACTA 59.468 40.000 6.99 0.00 34.82 1.82
3115 3273 2.034124 GGGGTTATACGGCTGTCAGTA 58.966 52.381 0.00 0.00 0.00 2.74
3133 3291 4.307432 GTCAGATACATGGTCAATACGGG 58.693 47.826 0.00 0.00 0.00 5.28
3208 3367 0.328592 AGACCTCGTCCTAGTCAGCA 59.671 55.000 0.00 0.00 32.18 4.41
3227 3386 4.789075 GCTAAGACCGACCGCGCA 62.789 66.667 8.75 0.00 35.83 6.09
3274 3433 1.001269 GCTAGGGTTTGTGGGGGTC 60.001 63.158 0.00 0.00 0.00 4.46
3276 3435 0.114364 AAAGCTAGGGTTTGTGGGGG 59.886 55.000 0.00 0.00 31.83 5.40
3277 3436 1.545841 GAAAGCTAGGGTTTGTGGGG 58.454 55.000 0.00 0.00 33.25 4.96
3279 3438 1.892209 ACGAAAGCTAGGGTTTGTGG 58.108 50.000 0.00 0.00 33.25 4.17
3280 3439 3.139077 AGAACGAAAGCTAGGGTTTGTG 58.861 45.455 0.00 0.00 33.25 3.33
3283 3450 2.290134 GGGAGAACGAAAGCTAGGGTTT 60.290 50.000 0.00 0.00 35.90 3.27
3293 3461 0.116541 AGGGAGAGGGGAGAACGAAA 59.883 55.000 0.00 0.00 0.00 3.46
3297 3465 0.397957 GGAGAGGGAGAGGGGAGAAC 60.398 65.000 0.00 0.00 0.00 3.01
3311 3479 0.395036 TTCGCAGGGAGAGAGGAGAG 60.395 60.000 0.00 0.00 0.00 3.20
3327 3495 2.686235 GCATCCATCTCCTGAGATTCG 58.314 52.381 6.92 1.53 45.31 3.34
3329 3497 1.347050 CCGCATCCATCTCCTGAGATT 59.653 52.381 6.92 0.00 45.31 2.40
3338 3506 4.241555 GGGTCGCCGCATCCATCT 62.242 66.667 3.72 0.00 0.00 2.90
3370 3541 4.747529 GTACCCGCCCACGACACC 62.748 72.222 0.00 0.00 43.93 4.16
3384 3555 2.183555 CCAGGAAGGTCGCCGTAC 59.816 66.667 0.00 0.00 0.00 3.67
3405 3576 4.129737 ACGTGGTCATCGCTCCCG 62.130 66.667 0.00 0.00 0.00 5.14
3441 3612 2.429930 CCAGTGGAGTTGGGCGAA 59.570 61.111 1.68 0.00 31.87 4.70
3445 3616 2.358737 GTCGCCAGTGGAGTTGGG 60.359 66.667 15.20 0.00 36.19 4.12
3456 3627 4.689549 TCCCCTTCCTCGTCGCCA 62.690 66.667 0.00 0.00 0.00 5.69
3498 3672 4.681978 GCGAGCCGGACTGGTTGT 62.682 66.667 5.05 0.00 41.21 3.32
3503 3677 2.780094 ATCTCAGCGAGCCGGACTG 61.780 63.158 5.05 6.77 0.00 3.51
3505 3679 2.279120 CATCTCAGCGAGCCGGAC 60.279 66.667 5.05 0.00 0.00 4.79
3507 3681 2.584418 CACATCTCAGCGAGCCGG 60.584 66.667 0.00 0.00 0.00 6.13
3599 3774 6.456853 GCCCTCTGATTTGAACAAACAAAAAC 60.457 38.462 2.03 0.00 41.88 2.43
3600 3775 5.584251 GCCCTCTGATTTGAACAAACAAAAA 59.416 36.000 2.03 0.00 41.88 1.94


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

AutoCloner maintained by Alex Coulton.