Multiple sequence alignment - TraesCS1D01G291700

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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 TraesCS1D01G291700 chr1D 100.000 3263 0 0 1 3263 390664499 390667761 0.000000e+00 6026.0
1 TraesCS1D01G291700 chr1D 92.868 1276 75 8 989 2252 390686969 390685698 0.000000e+00 1838.0
2 TraesCS1D01G291700 chr1D 91.692 650 33 9 2250 2890 390682147 390681510 0.000000e+00 881.0
3 TraesCS1D01G291700 chr1D 79.084 1004 164 25 1243 2210 389796744 389797737 0.000000e+00 649.0
4 TraesCS1D01G291700 chr1D 79.051 969 156 27 1275 2210 389429589 389428635 3.580000e-174 621.0
5 TraesCS1D01G291700 chr1D 81.636 550 66 25 2549 3092 390681415 390680895 1.080000e-114 424.0
6 TraesCS1D01G291700 chr1D 95.763 118 2 1 3146 3263 390680154 390680040 1.550000e-43 187.0
7 TraesCS1D01G291700 chr1D 92.857 56 4 0 876 931 390687160 390687105 7.500000e-12 82.4
8 TraesCS1D01G291700 chr1D 87.324 71 7 2 3078 3146 414883276 414883206 2.700000e-11 80.5
9 TraesCS1D01G291700 chr1B 93.027 2352 104 29 788 3092 523151133 523148795 0.000000e+00 3380.0
10 TraesCS1D01G291700 chr1B 93.147 2320 106 25 814 3092 523008312 523010619 0.000000e+00 3354.0
11 TraesCS1D01G291700 chr1B 79.182 831 138 20 1022 1833 522753696 522754510 7.960000e-151 544.0
12 TraesCS1D01G291700 chr1B 95.763 118 4 1 3146 3263 523011335 523011451 4.300000e-44 189.0
13 TraesCS1D01G291700 chr1B 95.763 118 4 1 3146 3263 523148077 523147961 4.300000e-44 189.0
14 TraesCS1D01G291700 chr1B 90.667 75 6 1 738 811 431448302 431448376 7.450000e-17 99.0
15 TraesCS1D01G291700 chr1A 91.476 2229 109 35 813 2998 488229975 488227785 0.000000e+00 2988.0
16 TraesCS1D01G291700 chr1A 93.069 808 44 7 2289 3092 488227775 488226976 0.000000e+00 1171.0
17 TraesCS1D01G291700 chr1A 80.392 867 134 19 1377 2210 488187152 488188015 7.690000e-176 627.0
18 TraesCS1D01G291700 chr1A 95.763 118 4 1 3146 3263 142891618 142891734 4.300000e-44 189.0
19 TraesCS1D01G291700 chr1A 95.082 61 2 1 3203 3263 488226293 488226234 9.640000e-16 95.3
20 TraesCS1D01G291700 chr2D 96.402 528 14 4 190 714 57166558 57167083 0.000000e+00 865.0
21 TraesCS1D01G291700 chr2D 97.938 97 2 0 708 804 57167129 57167225 5.600000e-38 169.0
22 TraesCS1D01G291700 chr3B 87.654 648 45 11 2440 3082 225991012 225991629 0.000000e+00 721.0
23 TraesCS1D01G291700 chr3B 87.845 181 15 3 2410 2589 708717105 708717279 4.270000e-49 206.0
24 TraesCS1D01G291700 chr3B 91.667 72 5 1 734 804 797128440 797128511 7.450000e-17 99.0
25 TraesCS1D01G291700 chr3B 93.443 61 3 1 3086 3146 750357535 750357476 4.480000e-14 89.8
26 TraesCS1D01G291700 chr3B 94.643 56 3 0 3091 3146 614918632 614918687 1.610000e-13 87.9
27 TraesCS1D01G291700 chr2A 90.909 528 45 3 190 714 775770656 775770129 0.000000e+00 706.0
28 TraesCS1D01G291700 chr2A 90.000 70 5 2 3077 3144 101846911 101846980 4.480000e-14 89.8
29 TraesCS1D01G291700 chr2A 88.235 68 8 0 3079 3146 279487520 279487453 7.500000e-12 82.4
30 TraesCS1D01G291700 chr4A 93.919 296 16 1 2797 3092 717673728 717673435 2.310000e-121 446.0
31 TraesCS1D01G291700 chr4A 92.027 301 19 2 2797 3094 721669251 721668953 5.040000e-113 418.0
32 TraesCS1D01G291700 chrUn 93.243 296 18 1 2797 3092 66300685 66300978 5.000000e-118 435.0
33 TraesCS1D01G291700 chr5B 89.503 181 12 3 2410 2589 473281470 473281296 4.240000e-54 222.0
34 TraesCS1D01G291700 chr7B 87.629 194 16 4 2450 2641 209401313 209401500 5.480000e-53 219.0
35 TraesCS1D01G291700 chr3D 93.976 83 4 1 708 789 514278424 514278342 1.230000e-24 124.0
36 TraesCS1D01G291700 chr7D 84.536 97 12 3 708 803 600757248 600757342 3.470000e-15 93.5
37 TraesCS1D01G291700 chr5A 90.141 71 5 2 3078 3146 10916121 10916051 1.250000e-14 91.6
38 TraesCS1D01G291700 chr5A 93.333 60 4 0 3085 3144 404225120 404225179 4.480000e-14 89.8
39 TraesCS1D01G291700 chr4D 94.737 57 3 0 3090 3146 375134921 375134977 4.480000e-14 89.8
40 TraesCS1D01G291700 chr6B 93.220 59 3 1 3086 3144 605587256 605587313 5.800000e-13 86.1
41 TraesCS1D01G291700 chr2B 97.500 40 1 0 739 778 47535486 47535447 5.840000e-08 69.4
42 TraesCS1D01G291700 chr2B 97.500 40 1 0 739 778 47638019 47637980 5.840000e-08 69.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G291700 chr1D 390664499 390667761 3262 False 6026.00 6026 100.0000 1 3263 1 chr1D.!!$F2 3262
1 TraesCS1D01G291700 chr1D 390680040 390687160 7120 True 682.48 1838 90.9632 876 3263 5 chr1D.!!$R3 2387
2 TraesCS1D01G291700 chr1D 389796744 389797737 993 False 649.00 649 79.0840 1243 2210 1 chr1D.!!$F1 967
3 TraesCS1D01G291700 chr1D 389428635 389429589 954 True 621.00 621 79.0510 1275 2210 1 chr1D.!!$R1 935
4 TraesCS1D01G291700 chr1B 523147961 523151133 3172 True 1784.50 3380 94.3950 788 3263 2 chr1B.!!$R1 2475
5 TraesCS1D01G291700 chr1B 523008312 523011451 3139 False 1771.50 3354 94.4550 814 3263 2 chr1B.!!$F3 2449
6 TraesCS1D01G291700 chr1B 522753696 522754510 814 False 544.00 544 79.1820 1022 1833 1 chr1B.!!$F2 811
7 TraesCS1D01G291700 chr1A 488226234 488229975 3741 True 1418.10 2988 93.2090 813 3263 3 chr1A.!!$R1 2450
8 TraesCS1D01G291700 chr1A 488187152 488188015 863 False 627.00 627 80.3920 1377 2210 1 chr1A.!!$F2 833
9 TraesCS1D01G291700 chr2D 57166558 57167225 667 False 517.00 865 97.1700 190 804 2 chr2D.!!$F1 614
10 TraesCS1D01G291700 chr3B 225991012 225991629 617 False 721.00 721 87.6540 2440 3082 1 chr3B.!!$F1 642
11 TraesCS1D01G291700 chr2A 775770129 775770656 527 True 706.00 706 90.9090 190 714 1 chr2A.!!$R2 524

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
54 55 1.645710 AGAAGGATCTTCGGTGTGGT 58.354 50.000 0.00 0.0 29.15 4.16 F
57 58 1.645710 AGGATCTTCGGTGTGGTTCT 58.354 50.000 0.00 0.0 0.00 3.01 F
58 59 1.978580 AGGATCTTCGGTGTGGTTCTT 59.021 47.619 0.00 0.0 0.00 2.52 F
1906 2089 2.000447 GCTACATCGAGGTGTCCAAAC 59.000 52.381 13.92 0.0 33.62 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1535 1706 0.598562 CATCTCGGCTACGGCATACT 59.401 55.000 0.00 0.0 41.39 2.12 R
1906 2089 4.913126 GACCACGTAGGGCTTCTG 57.087 61.111 8.57 0.0 44.70 3.02 R
2111 2309 1.338655 GACGAGAGCTCCCTGTTATCC 59.661 57.143 10.93 0.0 0.00 2.59 R
2779 7281 0.627451 AGCTTGGCCCATTCTGATGA 59.373 50.000 0.00 0.0 35.16 2.92 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
25 26 8.469309 AATAAAAATGAGTATGGAGGTGGATG 57.531 34.615 0.00 0.00 0.00 3.51
26 27 5.715439 AAAATGAGTATGGAGGTGGATGA 57.285 39.130 0.00 0.00 0.00 2.92
27 28 5.715439 AAATGAGTATGGAGGTGGATGAA 57.285 39.130 0.00 0.00 0.00 2.57
28 29 4.696479 ATGAGTATGGAGGTGGATGAAC 57.304 45.455 0.00 0.00 0.00 3.18
29 30 3.449918 TGAGTATGGAGGTGGATGAACA 58.550 45.455 0.00 0.00 0.00 3.18
30 31 3.843619 TGAGTATGGAGGTGGATGAACAA 59.156 43.478 0.00 0.00 0.00 2.83
31 32 4.288366 TGAGTATGGAGGTGGATGAACAAA 59.712 41.667 0.00 0.00 0.00 2.83
32 33 5.222027 TGAGTATGGAGGTGGATGAACAAAA 60.222 40.000 0.00 0.00 0.00 2.44
33 34 5.010282 AGTATGGAGGTGGATGAACAAAAC 58.990 41.667 0.00 0.00 0.00 2.43
34 35 3.593442 TGGAGGTGGATGAACAAAACT 57.407 42.857 0.00 0.00 0.00 2.66
35 36 4.715534 TGGAGGTGGATGAACAAAACTA 57.284 40.909 0.00 0.00 0.00 2.24
36 37 4.651778 TGGAGGTGGATGAACAAAACTAG 58.348 43.478 0.00 0.00 0.00 2.57
37 38 4.349636 TGGAGGTGGATGAACAAAACTAGA 59.650 41.667 0.00 0.00 0.00 2.43
38 39 5.163141 TGGAGGTGGATGAACAAAACTAGAA 60.163 40.000 0.00 0.00 0.00 2.10
39 40 5.412904 GGAGGTGGATGAACAAAACTAGAAG 59.587 44.000 0.00 0.00 0.00 2.85
40 41 5.316987 AGGTGGATGAACAAAACTAGAAGG 58.683 41.667 0.00 0.00 0.00 3.46
41 42 5.073144 AGGTGGATGAACAAAACTAGAAGGA 59.927 40.000 0.00 0.00 0.00 3.36
42 43 5.946377 GGTGGATGAACAAAACTAGAAGGAT 59.054 40.000 0.00 0.00 0.00 3.24
43 44 6.094186 GGTGGATGAACAAAACTAGAAGGATC 59.906 42.308 0.00 0.00 0.00 3.36
44 45 6.881602 GTGGATGAACAAAACTAGAAGGATCT 59.118 38.462 0.00 0.00 39.82 2.75
45 46 7.391833 GTGGATGAACAAAACTAGAAGGATCTT 59.608 37.037 0.00 0.00 37.10 2.40
46 47 7.607991 TGGATGAACAAAACTAGAAGGATCTTC 59.392 37.037 0.00 0.00 37.10 2.87
47 48 7.201565 GGATGAACAAAACTAGAAGGATCTTCG 60.202 40.741 0.00 0.00 37.10 3.79
48 49 5.932303 TGAACAAAACTAGAAGGATCTTCGG 59.068 40.000 0.00 3.12 37.10 4.30
49 50 5.485209 ACAAAACTAGAAGGATCTTCGGT 57.515 39.130 0.00 3.64 37.10 4.69
50 51 5.238583 ACAAAACTAGAAGGATCTTCGGTG 58.761 41.667 0.00 0.80 37.10 4.94
51 52 5.221661 ACAAAACTAGAAGGATCTTCGGTGT 60.222 40.000 0.00 1.30 37.10 4.16
52 53 4.457834 AACTAGAAGGATCTTCGGTGTG 57.542 45.455 0.00 0.00 37.10 3.82
53 54 2.761208 ACTAGAAGGATCTTCGGTGTGG 59.239 50.000 0.00 0.00 37.10 4.17
54 55 1.645710 AGAAGGATCTTCGGTGTGGT 58.354 50.000 0.00 0.00 29.15 4.16
55 56 1.978580 AGAAGGATCTTCGGTGTGGTT 59.021 47.619 0.00 0.00 29.15 3.67
56 57 2.028020 AGAAGGATCTTCGGTGTGGTTC 60.028 50.000 0.00 0.00 29.15 3.62
57 58 1.645710 AGGATCTTCGGTGTGGTTCT 58.354 50.000 0.00 0.00 0.00 3.01
58 59 1.978580 AGGATCTTCGGTGTGGTTCTT 59.021 47.619 0.00 0.00 0.00 2.52
59 60 2.028020 AGGATCTTCGGTGTGGTTCTTC 60.028 50.000 0.00 0.00 0.00 2.87
60 61 2.028020 GGATCTTCGGTGTGGTTCTTCT 60.028 50.000 0.00 0.00 0.00 2.85
61 62 3.557264 GGATCTTCGGTGTGGTTCTTCTT 60.557 47.826 0.00 0.00 0.00 2.52
62 63 3.107642 TCTTCGGTGTGGTTCTTCTTC 57.892 47.619 0.00 0.00 0.00 2.87
63 64 2.698797 TCTTCGGTGTGGTTCTTCTTCT 59.301 45.455 0.00 0.00 0.00 2.85
64 65 2.814280 TCGGTGTGGTTCTTCTTCTC 57.186 50.000 0.00 0.00 0.00 2.87
65 66 2.317040 TCGGTGTGGTTCTTCTTCTCT 58.683 47.619 0.00 0.00 0.00 3.10
66 67 2.035961 TCGGTGTGGTTCTTCTTCTCTG 59.964 50.000 0.00 0.00 0.00 3.35
67 68 2.772287 GGTGTGGTTCTTCTTCTCTGG 58.228 52.381 0.00 0.00 0.00 3.86
68 69 2.368875 GGTGTGGTTCTTCTTCTCTGGA 59.631 50.000 0.00 0.00 0.00 3.86
69 70 3.008485 GGTGTGGTTCTTCTTCTCTGGAT 59.992 47.826 0.00 0.00 0.00 3.41
70 71 4.249661 GTGTGGTTCTTCTTCTCTGGATC 58.750 47.826 0.00 0.00 0.00 3.36
71 72 4.020662 GTGTGGTTCTTCTTCTCTGGATCT 60.021 45.833 0.00 0.00 0.00 2.75
72 73 4.221703 TGTGGTTCTTCTTCTCTGGATCTC 59.778 45.833 0.00 0.00 0.00 2.75
73 74 4.466015 GTGGTTCTTCTTCTCTGGATCTCT 59.534 45.833 0.00 0.00 0.00 3.10
74 75 5.046663 GTGGTTCTTCTTCTCTGGATCTCTT 60.047 44.000 0.00 0.00 0.00 2.85
75 76 5.186797 TGGTTCTTCTTCTCTGGATCTCTTC 59.813 44.000 0.00 0.00 0.00 2.87
76 77 5.422012 GGTTCTTCTTCTCTGGATCTCTTCT 59.578 44.000 0.00 0.00 0.00 2.85
77 78 6.405842 GGTTCTTCTTCTCTGGATCTCTTCTC 60.406 46.154 0.00 0.00 0.00 2.87
78 79 6.078456 TCTTCTTCTCTGGATCTCTTCTCT 57.922 41.667 0.00 0.00 0.00 3.10
79 80 6.122277 TCTTCTTCTCTGGATCTCTTCTCTC 58.878 44.000 0.00 0.00 0.00 3.20
80 81 5.715439 TCTTCTCTGGATCTCTTCTCTCT 57.285 43.478 0.00 0.00 0.00 3.10
81 82 5.684704 TCTTCTCTGGATCTCTTCTCTCTC 58.315 45.833 0.00 0.00 0.00 3.20
82 83 5.429762 TCTTCTCTGGATCTCTTCTCTCTCT 59.570 44.000 0.00 0.00 0.00 3.10
83 84 5.039920 TCTCTGGATCTCTTCTCTCTCTG 57.960 47.826 0.00 0.00 0.00 3.35
84 85 4.139786 CTCTGGATCTCTTCTCTCTCTGG 58.860 52.174 0.00 0.00 0.00 3.86
85 86 3.785325 TCTGGATCTCTTCTCTCTCTGGA 59.215 47.826 0.00 0.00 0.00 3.86
86 87 4.416513 TCTGGATCTCTTCTCTCTCTGGAT 59.583 45.833 0.00 0.00 0.00 3.41
87 88 4.472496 TGGATCTCTTCTCTCTCTGGATG 58.528 47.826 0.00 0.00 0.00 3.51
88 89 3.256631 GGATCTCTTCTCTCTCTGGATGC 59.743 52.174 0.00 0.00 0.00 3.91
89 90 3.378861 TCTCTTCTCTCTCTGGATGCA 57.621 47.619 0.00 0.00 0.00 3.96
90 91 3.913509 TCTCTTCTCTCTCTGGATGCAT 58.086 45.455 0.00 0.00 0.00 3.96
91 92 4.288398 TCTCTTCTCTCTCTGGATGCATT 58.712 43.478 0.00 0.00 0.00 3.56
92 93 5.453158 TCTCTTCTCTCTCTGGATGCATTA 58.547 41.667 0.00 0.00 0.00 1.90
93 94 5.896106 TCTCTTCTCTCTCTGGATGCATTAA 59.104 40.000 0.00 0.00 0.00 1.40
94 95 5.911752 TCTTCTCTCTCTGGATGCATTAAC 58.088 41.667 0.00 0.00 0.00 2.01
95 96 4.313277 TCTCTCTCTGGATGCATTAACG 57.687 45.455 0.00 0.00 0.00 3.18
96 97 3.954258 TCTCTCTCTGGATGCATTAACGA 59.046 43.478 0.00 0.00 0.00 3.85
97 98 4.402474 TCTCTCTCTGGATGCATTAACGAA 59.598 41.667 0.00 0.00 0.00 3.85
98 99 5.069648 TCTCTCTCTGGATGCATTAACGAAT 59.930 40.000 0.00 0.00 0.00 3.34
99 100 5.674525 TCTCTCTGGATGCATTAACGAATT 58.325 37.500 0.00 0.00 0.00 2.17
100 101 5.755375 TCTCTCTGGATGCATTAACGAATTC 59.245 40.000 0.00 0.00 0.00 2.17
101 102 4.816385 TCTCTGGATGCATTAACGAATTCC 59.184 41.667 0.00 0.00 0.00 3.01
102 103 4.780815 TCTGGATGCATTAACGAATTCCT 58.219 39.130 0.00 0.00 0.00 3.36
103 104 4.576053 TCTGGATGCATTAACGAATTCCTG 59.424 41.667 0.00 0.00 0.00 3.86
104 105 3.631686 TGGATGCATTAACGAATTCCTGG 59.368 43.478 0.00 0.00 0.00 4.45
105 106 3.882888 GGATGCATTAACGAATTCCTGGA 59.117 43.478 0.00 0.00 0.00 3.86
106 107 4.520492 GGATGCATTAACGAATTCCTGGAT 59.480 41.667 0.00 0.00 0.00 3.41
107 108 5.010012 GGATGCATTAACGAATTCCTGGATT 59.990 40.000 0.00 0.00 0.00 3.01
108 109 5.913137 TGCATTAACGAATTCCTGGATTT 57.087 34.783 0.00 0.00 0.00 2.17
109 110 7.255451 GGATGCATTAACGAATTCCTGGATTTA 60.255 37.037 0.00 0.00 0.00 1.40
110 111 7.581213 TGCATTAACGAATTCCTGGATTTAT 57.419 32.000 0.00 0.00 0.00 1.40
111 112 8.006298 TGCATTAACGAATTCCTGGATTTATT 57.994 30.769 0.00 0.00 0.00 1.40
112 113 8.474025 TGCATTAACGAATTCCTGGATTTATTT 58.526 29.630 0.00 0.32 0.00 1.40
113 114 8.968242 GCATTAACGAATTCCTGGATTTATTTC 58.032 33.333 0.00 0.00 0.00 2.17
114 115 9.169468 CATTAACGAATTCCTGGATTTATTTCG 57.831 33.333 17.13 17.13 0.00 3.46
115 116 5.751243 ACGAATTCCTGGATTTATTTCGG 57.249 39.130 20.16 7.43 0.00 4.30
116 117 4.578928 ACGAATTCCTGGATTTATTTCGGG 59.421 41.667 20.16 0.00 0.00 5.14
117 118 4.556699 CGAATTCCTGGATTTATTTCGGGC 60.557 45.833 0.00 0.00 0.00 6.13
118 119 3.662759 TTCCTGGATTTATTTCGGGCT 57.337 42.857 0.00 0.00 0.00 5.19
119 120 3.662759 TCCTGGATTTATTTCGGGCTT 57.337 42.857 0.00 0.00 0.00 4.35
120 121 4.781775 TCCTGGATTTATTTCGGGCTTA 57.218 40.909 0.00 0.00 0.00 3.09
121 122 4.457466 TCCTGGATTTATTTCGGGCTTAC 58.543 43.478 0.00 0.00 0.00 2.34
122 123 4.080243 TCCTGGATTTATTTCGGGCTTACA 60.080 41.667 0.00 0.00 0.00 2.41
123 124 4.827284 CCTGGATTTATTTCGGGCTTACAT 59.173 41.667 0.00 0.00 0.00 2.29
124 125 5.301805 CCTGGATTTATTTCGGGCTTACATT 59.698 40.000 0.00 0.00 0.00 2.71
125 126 6.488683 CCTGGATTTATTTCGGGCTTACATTA 59.511 38.462 0.00 0.00 0.00 1.90
126 127 7.176690 CCTGGATTTATTTCGGGCTTACATTAT 59.823 37.037 0.00 0.00 0.00 1.28
127 128 9.226606 CTGGATTTATTTCGGGCTTACATTATA 57.773 33.333 0.00 0.00 0.00 0.98
128 129 9.005777 TGGATTTATTTCGGGCTTACATTATAC 57.994 33.333 0.00 0.00 0.00 1.47
129 130 9.227777 GGATTTATTTCGGGCTTACATTATACT 57.772 33.333 0.00 0.00 0.00 2.12
131 132 8.611654 TTTATTTCGGGCTTACATTATACTCC 57.388 34.615 0.00 0.00 0.00 3.85
132 133 4.612264 TTCGGGCTTACATTATACTCCC 57.388 45.455 0.00 0.00 0.00 4.30
133 134 3.853207 TCGGGCTTACATTATACTCCCT 58.147 45.455 0.00 0.00 0.00 4.20
134 135 3.830755 TCGGGCTTACATTATACTCCCTC 59.169 47.826 0.00 0.00 0.00 4.30
135 136 3.056035 CGGGCTTACATTATACTCCCTCC 60.056 52.174 0.00 0.00 0.00 4.30
136 137 3.056035 GGGCTTACATTATACTCCCTCCG 60.056 52.174 0.00 0.00 0.00 4.63
137 138 3.577415 GGCTTACATTATACTCCCTCCGT 59.423 47.826 0.00 0.00 0.00 4.69
138 139 4.768968 GGCTTACATTATACTCCCTCCGTA 59.231 45.833 0.00 0.00 0.00 4.02
139 140 5.421374 GGCTTACATTATACTCCCTCCGTAT 59.579 44.000 0.00 0.00 0.00 3.06
140 141 6.405619 GGCTTACATTATACTCCCTCCGTATC 60.406 46.154 0.00 0.00 0.00 2.24
141 142 6.152323 GCTTACATTATACTCCCTCCGTATCA 59.848 42.308 0.00 0.00 0.00 2.15
142 143 7.309621 GCTTACATTATACTCCCTCCGTATCAA 60.310 40.741 0.00 0.00 0.00 2.57
143 144 6.989155 ACATTATACTCCCTCCGTATCAAA 57.011 37.500 0.00 0.00 0.00 2.69
144 145 7.554959 ACATTATACTCCCTCCGTATCAAAT 57.445 36.000 0.00 0.00 0.00 2.32
145 146 8.660295 ACATTATACTCCCTCCGTATCAAATA 57.340 34.615 0.00 0.00 0.00 1.40
146 147 8.529476 ACATTATACTCCCTCCGTATCAAATAC 58.471 37.037 0.00 0.00 0.00 1.89
147 148 8.528643 CATTATACTCCCTCCGTATCAAATACA 58.471 37.037 0.00 0.00 35.48 2.29
148 149 6.989155 ATACTCCCTCCGTATCAAATACAA 57.011 37.500 0.00 0.00 35.48 2.41
149 150 5.277857 ACTCCCTCCGTATCAAATACAAG 57.722 43.478 0.00 0.00 35.48 3.16
150 151 4.960469 ACTCCCTCCGTATCAAATACAAGA 59.040 41.667 0.00 0.00 35.48 3.02
151 152 5.163437 ACTCCCTCCGTATCAAATACAAGAC 60.163 44.000 0.00 0.00 35.48 3.01
152 153 4.049186 CCCTCCGTATCAAATACAAGACG 58.951 47.826 0.00 0.00 35.48 4.18
156 157 5.789710 CCGTATCAAATACAAGACGGTTT 57.210 39.130 3.17 0.00 43.69 3.27
157 158 6.173191 CCGTATCAAATACAAGACGGTTTT 57.827 37.500 3.17 0.00 43.69 2.43
158 159 6.604930 CCGTATCAAATACAAGACGGTTTTT 58.395 36.000 3.17 0.00 43.69 1.94
159 160 6.521821 CCGTATCAAATACAAGACGGTTTTTG 59.478 38.462 3.17 0.00 43.69 2.44
160 161 7.292292 CGTATCAAATACAAGACGGTTTTTGA 58.708 34.615 15.47 15.47 45.75 2.69
161 162 7.267600 CGTATCAAATACAAGACGGTTTTTGAC 59.732 37.037 15.45 8.31 45.07 3.18
162 163 6.438259 TCAAATACAAGACGGTTTTTGACA 57.562 33.333 11.65 2.36 40.95 3.58
163 164 7.033530 TCAAATACAAGACGGTTTTTGACAT 57.966 32.000 11.65 4.06 40.95 3.06
164 165 7.484975 TCAAATACAAGACGGTTTTTGACATT 58.515 30.769 11.65 8.27 40.95 2.71
165 166 7.433719 TCAAATACAAGACGGTTTTTGACATTG 59.566 33.333 11.65 11.53 40.95 2.82
166 167 4.712122 ACAAGACGGTTTTTGACATTGT 57.288 36.364 11.65 0.00 0.00 2.71
167 168 5.821516 ACAAGACGGTTTTTGACATTGTA 57.178 34.783 11.65 0.00 0.00 2.41
168 169 6.197364 ACAAGACGGTTTTTGACATTGTAA 57.803 33.333 11.65 0.00 0.00 2.41
169 170 6.801575 ACAAGACGGTTTTTGACATTGTAAT 58.198 32.000 11.65 0.00 0.00 1.89
170 171 6.695278 ACAAGACGGTTTTTGACATTGTAATG 59.305 34.615 11.65 3.17 42.10 1.90
171 172 5.768317 AGACGGTTTTTGACATTGTAATGG 58.232 37.500 9.22 0.00 40.70 3.16
172 173 4.303282 ACGGTTTTTGACATTGTAATGGC 58.697 39.130 9.22 6.53 44.87 4.40
203 204 2.501723 AGCATCTTATCAAGTGTCCCGT 59.498 45.455 0.00 0.00 0.00 5.28
252 255 7.848223 TCATTTGATCAAGCGAATAAGAAGA 57.152 32.000 8.41 0.00 0.00 2.87
253 256 7.913423 TCATTTGATCAAGCGAATAAGAAGAG 58.087 34.615 8.41 0.00 0.00 2.85
273 276 5.934781 AGAGTGTCCAAGAAATCTTCAAGT 58.065 37.500 0.00 0.00 33.11 3.16
456 459 6.931838 ACAGACGGTTCAGTTATATTCTCAA 58.068 36.000 0.00 0.00 0.00 3.02
483 486 7.039313 TGTAGATACTTATTCGAGTGCACAT 57.961 36.000 21.04 6.10 0.00 3.21
546 549 4.284746 TCTCTCTGAGTATGGAGCGATCTA 59.715 45.833 0.00 0.00 0.00 1.98
659 662 8.121305 TGATGATAGAGATAAAGAAGCTCCTC 57.879 38.462 0.00 0.00 0.00 3.71
704 707 7.973388 CCGCTGAAAATTAGTCCAAATCAAATA 59.027 33.333 0.00 0.00 0.00 1.40
705 708 9.013490 CGCTGAAAATTAGTCCAAATCAAATAG 57.987 33.333 0.00 0.00 0.00 1.73
1510 1681 3.775654 GCCTCCTCACCCAGTCCG 61.776 72.222 0.00 0.00 0.00 4.79
1587 1770 2.133201 AGGGAGGAGGAGGAGGGA 59.867 66.667 0.00 0.00 0.00 4.20
1906 2089 2.000447 GCTACATCGAGGTGTCCAAAC 59.000 52.381 13.92 0.00 33.62 2.93
2111 2309 1.135915 CGTGGACATGGAGAAGGAGAG 59.864 57.143 0.00 0.00 0.00 3.20
2181 2385 3.692406 GTCCTCCCGACGTGGCTT 61.692 66.667 0.00 0.00 35.87 4.35
2415 6176 3.942115 GGAACTGTAATGCTCCCTTTCTC 59.058 47.826 0.00 0.00 0.00 2.87
2456 6946 8.719645 ACTAGATATAAGAGGAGAAGTGCATT 57.280 34.615 0.00 0.00 0.00 3.56
2479 6973 9.638239 CATTCAAGCTAGGAAGAATAGAGTATC 57.362 37.037 6.84 0.00 0.00 2.24
2667 7165 3.768757 CCACCATTGCCAAATAGAAAGGA 59.231 43.478 0.00 0.00 0.00 3.36
2706 7208 8.650143 AAATAAATAAGAAGGGAGAAGTGCAA 57.350 30.769 0.00 0.00 0.00 4.08
2738 7240 4.094146 GTGAAAGGCTGAATCTGTTCTAGC 59.906 45.833 0.00 0.00 37.56 3.42
2739 7241 3.988976 AAGGCTGAATCTGTTCTAGCA 57.011 42.857 0.00 0.00 38.80 3.49
2779 7281 7.061566 TCTTATTTTGCTGCCTTTTAAACCT 57.938 32.000 0.00 0.00 0.00 3.50
2825 7327 3.823330 GGCAGGCACAGCTCATGC 61.823 66.667 10.49 10.49 41.93 4.06
2847 7351 5.300539 TGCCACTTGTGACTGCTTATTTTTA 59.699 36.000 1.89 0.00 0.00 1.52
3036 7954 5.387788 TGCTGCATCCTATACCAATGATTT 58.612 37.500 0.00 0.00 0.00 2.17
3103 8021 6.954487 ATTTAAAACATATTCCCTCCGTCC 57.046 37.500 0.00 0.00 0.00 4.79
3104 8022 3.292492 AAAACATATTCCCTCCGTCCC 57.708 47.619 0.00 0.00 0.00 4.46
3106 8024 1.887797 ACATATTCCCTCCGTCCCAA 58.112 50.000 0.00 0.00 0.00 4.12
3109 8027 3.204382 ACATATTCCCTCCGTCCCAAAAT 59.796 43.478 0.00 0.00 0.00 1.82
3110 8028 4.414182 ACATATTCCCTCCGTCCCAAAATA 59.586 41.667 0.00 0.00 0.00 1.40
3111 8029 5.103855 ACATATTCCCTCCGTCCCAAAATAA 60.104 40.000 0.00 0.00 0.00 1.40
3112 8030 2.793288 TCCCTCCGTCCCAAAATAAC 57.207 50.000 0.00 0.00 0.00 1.89
3113 8031 1.986631 TCCCTCCGTCCCAAAATAACA 59.013 47.619 0.00 0.00 0.00 2.41
3114 8032 2.026636 TCCCTCCGTCCCAAAATAACAG 60.027 50.000 0.00 0.00 0.00 3.16
3115 8033 2.290705 CCCTCCGTCCCAAAATAACAGT 60.291 50.000 0.00 0.00 0.00 3.55
3116 8034 3.007635 CCTCCGTCCCAAAATAACAGTC 58.992 50.000 0.00 0.00 0.00 3.51
3117 8035 3.307480 CCTCCGTCCCAAAATAACAGTCT 60.307 47.826 0.00 0.00 0.00 3.24
3118 8036 3.933332 CTCCGTCCCAAAATAACAGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
3119 8037 3.325425 TCCGTCCCAAAATAACAGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
3122 8040 4.755123 CGTCCCAAAATAACAGTCTCAACT 59.245 41.667 0.00 0.00 35.60 3.16
3123 8041 5.238650 CGTCCCAAAATAACAGTCTCAACTT 59.761 40.000 0.00 0.00 31.71 2.66
3124 8042 6.238648 CGTCCCAAAATAACAGTCTCAACTTT 60.239 38.462 0.00 0.00 31.71 2.66
3125 8043 7.041644 CGTCCCAAAATAACAGTCTCAACTTTA 60.042 37.037 0.00 0.00 31.71 1.85
3161 8769 4.284178 ACAAAATAGCAGATGCCCAGATT 58.716 39.130 0.14 0.00 43.38 2.40
3199 8807 4.280174 AGCCATCTTCATTCATTATGGTGC 59.720 41.667 0.00 0.00 39.45 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.281531 TCATCCACCTCCATACTCATTTTTATT 58.718 33.333 0.00 0.00 0.00 1.40
3 4 6.078456 TCATCCACCTCCATACTCATTTTT 57.922 37.500 0.00 0.00 0.00 1.94
4 5 5.715439 TCATCCACCTCCATACTCATTTT 57.285 39.130 0.00 0.00 0.00 1.82
6 7 4.474651 TGTTCATCCACCTCCATACTCATT 59.525 41.667 0.00 0.00 0.00 2.57
7 8 4.040047 TGTTCATCCACCTCCATACTCAT 58.960 43.478 0.00 0.00 0.00 2.90
8 9 3.449918 TGTTCATCCACCTCCATACTCA 58.550 45.455 0.00 0.00 0.00 3.41
9 10 4.487714 TTGTTCATCCACCTCCATACTC 57.512 45.455 0.00 0.00 0.00 2.59
10 11 4.927267 TTTGTTCATCCACCTCCATACT 57.073 40.909 0.00 0.00 0.00 2.12
11 12 5.010282 AGTTTTGTTCATCCACCTCCATAC 58.990 41.667 0.00 0.00 0.00 2.39
12 13 5.255397 AGTTTTGTTCATCCACCTCCATA 57.745 39.130 0.00 0.00 0.00 2.74
13 14 4.118168 AGTTTTGTTCATCCACCTCCAT 57.882 40.909 0.00 0.00 0.00 3.41
14 15 3.593442 AGTTTTGTTCATCCACCTCCA 57.407 42.857 0.00 0.00 0.00 3.86
15 16 4.906618 TCTAGTTTTGTTCATCCACCTCC 58.093 43.478 0.00 0.00 0.00 4.30
16 17 5.412904 CCTTCTAGTTTTGTTCATCCACCTC 59.587 44.000 0.00 0.00 0.00 3.85
17 18 5.073144 TCCTTCTAGTTTTGTTCATCCACCT 59.927 40.000 0.00 0.00 0.00 4.00
18 19 5.313712 TCCTTCTAGTTTTGTTCATCCACC 58.686 41.667 0.00 0.00 0.00 4.61
19 20 6.881602 AGATCCTTCTAGTTTTGTTCATCCAC 59.118 38.462 0.00 0.00 0.00 4.02
20 21 7.020827 AGATCCTTCTAGTTTTGTTCATCCA 57.979 36.000 0.00 0.00 0.00 3.41
21 22 7.201565 CGAAGATCCTTCTAGTTTTGTTCATCC 60.202 40.741 5.34 0.00 0.00 3.51
22 23 7.201565 CCGAAGATCCTTCTAGTTTTGTTCATC 60.202 40.741 5.34 0.00 0.00 2.92
23 24 6.595716 CCGAAGATCCTTCTAGTTTTGTTCAT 59.404 38.462 5.34 0.00 0.00 2.57
24 25 5.932303 CCGAAGATCCTTCTAGTTTTGTTCA 59.068 40.000 5.34 0.00 0.00 3.18
25 26 5.932883 ACCGAAGATCCTTCTAGTTTTGTTC 59.067 40.000 5.34 0.00 0.00 3.18
26 27 5.701290 CACCGAAGATCCTTCTAGTTTTGTT 59.299 40.000 5.34 0.00 0.00 2.83
27 28 5.221661 ACACCGAAGATCCTTCTAGTTTTGT 60.222 40.000 5.34 0.00 0.00 2.83
28 29 5.120830 CACACCGAAGATCCTTCTAGTTTTG 59.879 44.000 5.34 0.51 0.00 2.44
29 30 5.238583 CACACCGAAGATCCTTCTAGTTTT 58.761 41.667 5.34 0.00 0.00 2.43
30 31 4.322801 CCACACCGAAGATCCTTCTAGTTT 60.323 45.833 5.34 0.00 0.00 2.66
31 32 3.195825 CCACACCGAAGATCCTTCTAGTT 59.804 47.826 5.34 0.00 0.00 2.24
32 33 2.761208 CCACACCGAAGATCCTTCTAGT 59.239 50.000 5.34 0.66 0.00 2.57
33 34 2.761208 ACCACACCGAAGATCCTTCTAG 59.239 50.000 5.34 0.00 0.00 2.43
34 35 2.816411 ACCACACCGAAGATCCTTCTA 58.184 47.619 5.34 0.00 0.00 2.10
35 36 1.645710 ACCACACCGAAGATCCTTCT 58.354 50.000 5.34 0.00 0.00 2.85
36 37 2.028020 AGAACCACACCGAAGATCCTTC 60.028 50.000 0.00 0.00 0.00 3.46
37 38 1.978580 AGAACCACACCGAAGATCCTT 59.021 47.619 0.00 0.00 0.00 3.36
38 39 1.645710 AGAACCACACCGAAGATCCT 58.354 50.000 0.00 0.00 0.00 3.24
39 40 2.028020 AGAAGAACCACACCGAAGATCC 60.028 50.000 0.00 0.00 0.00 3.36
40 41 3.320673 AGAAGAACCACACCGAAGATC 57.679 47.619 0.00 0.00 0.00 2.75
41 42 3.325135 AGAAGAAGAACCACACCGAAGAT 59.675 43.478 0.00 0.00 0.00 2.40
42 43 2.698797 AGAAGAAGAACCACACCGAAGA 59.301 45.455 0.00 0.00 0.00 2.87
43 44 3.060602 GAGAAGAAGAACCACACCGAAG 58.939 50.000 0.00 0.00 0.00 3.79
44 45 2.698797 AGAGAAGAAGAACCACACCGAA 59.301 45.455 0.00 0.00 0.00 4.30
45 46 2.035961 CAGAGAAGAAGAACCACACCGA 59.964 50.000 0.00 0.00 0.00 4.69
46 47 2.408050 CAGAGAAGAAGAACCACACCG 58.592 52.381 0.00 0.00 0.00 4.94
47 48 2.368875 TCCAGAGAAGAAGAACCACACC 59.631 50.000 0.00 0.00 0.00 4.16
48 49 3.753294 TCCAGAGAAGAAGAACCACAC 57.247 47.619 0.00 0.00 0.00 3.82
49 50 4.163427 AGATCCAGAGAAGAAGAACCACA 58.837 43.478 0.00 0.00 0.00 4.17
50 51 4.466015 AGAGATCCAGAGAAGAAGAACCAC 59.534 45.833 0.00 0.00 0.00 4.16
51 52 4.682563 AGAGATCCAGAGAAGAAGAACCA 58.317 43.478 0.00 0.00 0.00 3.67
52 53 5.422012 AGAAGAGATCCAGAGAAGAAGAACC 59.578 44.000 0.00 0.00 0.00 3.62
53 54 6.378280 AGAGAAGAGATCCAGAGAAGAAGAAC 59.622 42.308 0.00 0.00 0.00 3.01
54 55 6.493166 AGAGAAGAGATCCAGAGAAGAAGAA 58.507 40.000 0.00 0.00 0.00 2.52
55 56 6.069440 AGAGAGAAGAGATCCAGAGAAGAAGA 60.069 42.308 0.00 0.00 0.00 2.87
56 57 6.125029 AGAGAGAAGAGATCCAGAGAAGAAG 58.875 44.000 0.00 0.00 0.00 2.85
57 58 6.069440 AGAGAGAGAAGAGATCCAGAGAAGAA 60.069 42.308 0.00 0.00 0.00 2.52
58 59 5.429762 AGAGAGAGAAGAGATCCAGAGAAGA 59.570 44.000 0.00 0.00 0.00 2.87
59 60 5.530171 CAGAGAGAGAAGAGATCCAGAGAAG 59.470 48.000 0.00 0.00 0.00 2.85
60 61 5.439721 CAGAGAGAGAAGAGATCCAGAGAA 58.560 45.833 0.00 0.00 0.00 2.87
61 62 4.141413 CCAGAGAGAGAAGAGATCCAGAGA 60.141 50.000 0.00 0.00 0.00 3.10
62 63 4.139786 CCAGAGAGAGAAGAGATCCAGAG 58.860 52.174 0.00 0.00 0.00 3.35
63 64 3.785325 TCCAGAGAGAGAAGAGATCCAGA 59.215 47.826 0.00 0.00 0.00 3.86
64 65 4.169059 TCCAGAGAGAGAAGAGATCCAG 57.831 50.000 0.00 0.00 0.00 3.86
65 66 4.472496 CATCCAGAGAGAGAAGAGATCCA 58.528 47.826 0.00 0.00 0.00 3.41
66 67 3.256631 GCATCCAGAGAGAGAAGAGATCC 59.743 52.174 0.00 0.00 0.00 3.36
67 68 3.890756 TGCATCCAGAGAGAGAAGAGATC 59.109 47.826 0.00 0.00 0.00 2.75
68 69 3.913509 TGCATCCAGAGAGAGAAGAGAT 58.086 45.455 0.00 0.00 0.00 2.75
69 70 3.378861 TGCATCCAGAGAGAGAAGAGA 57.621 47.619 0.00 0.00 0.00 3.10
70 71 4.675976 AATGCATCCAGAGAGAGAAGAG 57.324 45.455 0.00 0.00 0.00 2.85
71 72 5.451103 CGTTAATGCATCCAGAGAGAGAAGA 60.451 44.000 0.00 0.00 0.00 2.87
72 73 4.744137 CGTTAATGCATCCAGAGAGAGAAG 59.256 45.833 0.00 0.00 0.00 2.85
73 74 4.402474 TCGTTAATGCATCCAGAGAGAGAA 59.598 41.667 0.00 0.00 0.00 2.87
74 75 3.954258 TCGTTAATGCATCCAGAGAGAGA 59.046 43.478 0.00 0.00 0.00 3.10
75 76 4.313277 TCGTTAATGCATCCAGAGAGAG 57.687 45.455 0.00 0.00 0.00 3.20
76 77 4.736126 TTCGTTAATGCATCCAGAGAGA 57.264 40.909 0.00 0.00 0.00 3.10
77 78 5.049818 GGAATTCGTTAATGCATCCAGAGAG 60.050 44.000 0.00 0.00 0.00 3.20
78 79 4.816385 GGAATTCGTTAATGCATCCAGAGA 59.184 41.667 0.00 0.00 0.00 3.10
79 80 4.818546 AGGAATTCGTTAATGCATCCAGAG 59.181 41.667 0.00 0.00 0.00 3.35
80 81 4.576053 CAGGAATTCGTTAATGCATCCAGA 59.424 41.667 0.00 0.00 0.00 3.86
81 82 4.261322 CCAGGAATTCGTTAATGCATCCAG 60.261 45.833 0.00 0.00 0.00 3.86
82 83 3.631686 CCAGGAATTCGTTAATGCATCCA 59.368 43.478 0.00 0.00 0.00 3.41
83 84 3.882888 TCCAGGAATTCGTTAATGCATCC 59.117 43.478 0.00 0.00 0.00 3.51
84 85 5.695851 ATCCAGGAATTCGTTAATGCATC 57.304 39.130 0.00 0.00 0.00 3.91
85 86 6.469782 AAATCCAGGAATTCGTTAATGCAT 57.530 33.333 0.00 0.00 0.00 3.96
86 87 5.913137 AAATCCAGGAATTCGTTAATGCA 57.087 34.783 0.00 0.00 0.00 3.96
87 88 8.871686 AAATAAATCCAGGAATTCGTTAATGC 57.128 30.769 0.00 0.00 0.00 3.56
88 89 9.169468 CGAAATAAATCCAGGAATTCGTTAATG 57.831 33.333 0.00 0.00 34.97 1.90
89 90 8.349983 CCGAAATAAATCCAGGAATTCGTTAAT 58.650 33.333 16.72 0.00 37.17 1.40
90 91 7.201750 CCCGAAATAAATCCAGGAATTCGTTAA 60.202 37.037 16.72 0.00 37.17 2.01
91 92 6.261381 CCCGAAATAAATCCAGGAATTCGTTA 59.739 38.462 16.72 4.27 37.17 3.18
92 93 5.067283 CCCGAAATAAATCCAGGAATTCGTT 59.933 40.000 16.72 5.11 37.17 3.85
93 94 4.578928 CCCGAAATAAATCCAGGAATTCGT 59.421 41.667 16.72 0.00 37.17 3.85
94 95 4.556699 GCCCGAAATAAATCCAGGAATTCG 60.557 45.833 13.53 13.53 38.24 3.34
95 96 4.584743 AGCCCGAAATAAATCCAGGAATTC 59.415 41.667 0.00 0.00 0.00 2.17
96 97 4.546674 AGCCCGAAATAAATCCAGGAATT 58.453 39.130 0.00 0.00 0.00 2.17
97 98 4.184649 AGCCCGAAATAAATCCAGGAAT 57.815 40.909 0.00 0.00 0.00 3.01
98 99 3.662759 AGCCCGAAATAAATCCAGGAA 57.337 42.857 0.00 0.00 0.00 3.36
99 100 3.662759 AAGCCCGAAATAAATCCAGGA 57.337 42.857 0.00 0.00 0.00 3.86
100 101 4.204012 TGTAAGCCCGAAATAAATCCAGG 58.796 43.478 0.00 0.00 0.00 4.45
101 102 6.391227 AATGTAAGCCCGAAATAAATCCAG 57.609 37.500 0.00 0.00 0.00 3.86
102 103 9.005777 GTATAATGTAAGCCCGAAATAAATCCA 57.994 33.333 0.00 0.00 0.00 3.41
103 104 9.227777 AGTATAATGTAAGCCCGAAATAAATCC 57.772 33.333 0.00 0.00 0.00 3.01
105 106 9.227777 GGAGTATAATGTAAGCCCGAAATAAAT 57.772 33.333 0.00 0.00 0.00 1.40
106 107 7.662669 GGGAGTATAATGTAAGCCCGAAATAAA 59.337 37.037 0.00 0.00 0.00 1.40
107 108 7.016858 AGGGAGTATAATGTAAGCCCGAAATAA 59.983 37.037 0.00 0.00 39.09 1.40
108 109 6.499350 AGGGAGTATAATGTAAGCCCGAAATA 59.501 38.462 0.00 0.00 39.09 1.40
109 110 5.309806 AGGGAGTATAATGTAAGCCCGAAAT 59.690 40.000 0.00 0.00 39.09 2.17
110 111 4.657039 AGGGAGTATAATGTAAGCCCGAAA 59.343 41.667 0.00 0.00 39.09 3.46
111 112 4.228824 AGGGAGTATAATGTAAGCCCGAA 58.771 43.478 0.00 0.00 39.09 4.30
112 113 3.830755 GAGGGAGTATAATGTAAGCCCGA 59.169 47.826 0.00 0.00 39.09 5.14
113 114 3.056035 GGAGGGAGTATAATGTAAGCCCG 60.056 52.174 0.00 0.00 39.09 6.13
114 115 3.056035 CGGAGGGAGTATAATGTAAGCCC 60.056 52.174 0.00 0.00 0.00 5.19
115 116 3.577415 ACGGAGGGAGTATAATGTAAGCC 59.423 47.826 0.00 0.00 0.00 4.35
116 117 4.868314 ACGGAGGGAGTATAATGTAAGC 57.132 45.455 0.00 0.00 0.00 3.09
117 118 7.698506 TGATACGGAGGGAGTATAATGTAAG 57.301 40.000 0.00 0.00 35.19 2.34
118 119 8.481492 TTTGATACGGAGGGAGTATAATGTAA 57.519 34.615 0.00 0.00 35.19 2.41
119 120 8.660295 ATTTGATACGGAGGGAGTATAATGTA 57.340 34.615 0.00 0.00 35.19 2.29
120 121 6.989155 TTTGATACGGAGGGAGTATAATGT 57.011 37.500 0.00 0.00 35.19 2.71
121 122 8.528643 TGTATTTGATACGGAGGGAGTATAATG 58.471 37.037 0.00 0.00 38.59 1.90
122 123 8.660295 TGTATTTGATACGGAGGGAGTATAAT 57.340 34.615 0.00 0.00 38.59 1.28
123 124 8.481492 TTGTATTTGATACGGAGGGAGTATAA 57.519 34.615 0.00 0.00 38.59 0.98
124 125 7.946219 TCTTGTATTTGATACGGAGGGAGTATA 59.054 37.037 0.00 0.00 38.59 1.47
125 126 6.781014 TCTTGTATTTGATACGGAGGGAGTAT 59.219 38.462 0.00 0.00 38.59 2.12
126 127 6.040166 GTCTTGTATTTGATACGGAGGGAGTA 59.960 42.308 0.00 0.00 38.59 2.59
127 128 4.960469 TCTTGTATTTGATACGGAGGGAGT 59.040 41.667 0.00 0.00 38.59 3.85
128 129 5.290386 GTCTTGTATTTGATACGGAGGGAG 58.710 45.833 0.00 0.00 38.59 4.30
129 130 4.202080 CGTCTTGTATTTGATACGGAGGGA 60.202 45.833 0.00 0.00 38.59 4.20
130 131 4.049186 CGTCTTGTATTTGATACGGAGGG 58.951 47.826 0.00 0.00 38.59 4.30
135 136 7.267600 GTCAAAAACCGTCTTGTATTTGATACG 59.732 37.037 0.00 0.00 38.55 3.06
136 137 8.071368 TGTCAAAAACCGTCTTGTATTTGATAC 58.929 33.333 0.00 0.00 38.55 2.24
137 138 8.155821 TGTCAAAAACCGTCTTGTATTTGATA 57.844 30.769 0.00 0.00 38.55 2.15
138 139 7.033530 TGTCAAAAACCGTCTTGTATTTGAT 57.966 32.000 0.00 0.00 38.55 2.57
139 140 6.438259 TGTCAAAAACCGTCTTGTATTTGA 57.562 33.333 0.00 0.00 35.20 2.69
140 141 7.221838 ACAATGTCAAAAACCGTCTTGTATTTG 59.778 33.333 0.00 0.00 0.00 2.32
141 142 7.262048 ACAATGTCAAAAACCGTCTTGTATTT 58.738 30.769 0.00 0.00 0.00 1.40
142 143 6.801575 ACAATGTCAAAAACCGTCTTGTATT 58.198 32.000 0.00 0.00 0.00 1.89
143 144 6.385649 ACAATGTCAAAAACCGTCTTGTAT 57.614 33.333 0.00 0.00 0.00 2.29
144 145 5.821516 ACAATGTCAAAAACCGTCTTGTA 57.178 34.783 0.00 0.00 0.00 2.41
145 146 4.712122 ACAATGTCAAAAACCGTCTTGT 57.288 36.364 0.00 0.00 0.00 3.16
146 147 6.143758 CCATTACAATGTCAAAAACCGTCTTG 59.856 38.462 0.00 0.00 34.60 3.02
147 148 6.212955 CCATTACAATGTCAAAAACCGTCTT 58.787 36.000 0.00 0.00 34.60 3.01
148 149 5.768317 CCATTACAATGTCAAAAACCGTCT 58.232 37.500 0.00 0.00 34.60 4.18
149 150 4.384547 GCCATTACAATGTCAAAAACCGTC 59.615 41.667 0.00 0.00 34.60 4.79
150 151 4.303282 GCCATTACAATGTCAAAAACCGT 58.697 39.130 0.00 0.00 34.60 4.83
151 152 3.363426 CGCCATTACAATGTCAAAAACCG 59.637 43.478 0.00 0.00 34.60 4.44
152 153 4.303282 ACGCCATTACAATGTCAAAAACC 58.697 39.130 0.00 0.00 34.60 3.27
153 154 4.979197 TGACGCCATTACAATGTCAAAAAC 59.021 37.500 0.00 0.00 36.69 2.43
154 155 5.188327 TGACGCCATTACAATGTCAAAAA 57.812 34.783 0.00 0.00 36.69 1.94
155 156 4.837896 TGACGCCATTACAATGTCAAAA 57.162 36.364 0.00 0.00 36.69 2.44
156 157 4.837896 TTGACGCCATTACAATGTCAAA 57.162 36.364 3.82 0.00 44.06 2.69
157 158 4.837896 TTTGACGCCATTACAATGTCAA 57.162 36.364 2.26 2.26 44.99 3.18
158 159 4.837896 TTTTGACGCCATTACAATGTCA 57.162 36.364 0.00 0.00 37.76 3.58
178 179 5.106157 CGGGACACTTGATAAGATGCTTTTT 60.106 40.000 0.00 0.00 0.00 1.94
179 180 4.396166 CGGGACACTTGATAAGATGCTTTT 59.604 41.667 0.00 0.00 0.00 2.27
180 181 3.941483 CGGGACACTTGATAAGATGCTTT 59.059 43.478 0.00 0.00 0.00 3.51
181 182 3.055094 ACGGGACACTTGATAAGATGCTT 60.055 43.478 0.00 0.00 0.00 3.91
182 183 2.501723 ACGGGACACTTGATAAGATGCT 59.498 45.455 0.00 0.00 0.00 3.79
183 184 2.866762 GACGGGACACTTGATAAGATGC 59.133 50.000 0.00 0.00 0.00 3.91
184 185 4.115516 CAGACGGGACACTTGATAAGATG 58.884 47.826 0.00 0.00 0.00 2.90
185 186 3.769844 ACAGACGGGACACTTGATAAGAT 59.230 43.478 0.00 0.00 0.00 2.40
186 187 3.162666 ACAGACGGGACACTTGATAAGA 58.837 45.455 0.00 0.00 0.00 2.10
187 188 3.594603 ACAGACGGGACACTTGATAAG 57.405 47.619 0.00 0.00 0.00 1.73
188 189 3.194116 GGTACAGACGGGACACTTGATAA 59.806 47.826 0.00 0.00 0.00 1.75
189 190 2.756760 GGTACAGACGGGACACTTGATA 59.243 50.000 0.00 0.00 0.00 2.15
190 191 1.549170 GGTACAGACGGGACACTTGAT 59.451 52.381 0.00 0.00 0.00 2.57
191 192 0.963962 GGTACAGACGGGACACTTGA 59.036 55.000 0.00 0.00 0.00 3.02
192 193 0.966920 AGGTACAGACGGGACACTTG 59.033 55.000 0.00 0.00 0.00 3.16
193 194 1.254954 GAGGTACAGACGGGACACTT 58.745 55.000 0.00 0.00 0.00 3.16
203 204 2.688446 CAGATAACTGGCGAGGTACAGA 59.312 50.000 0.00 0.00 40.14 3.41
252 255 4.276926 GCACTTGAAGATTTCTTGGACACT 59.723 41.667 0.00 0.00 36.11 3.55
253 256 4.036734 TGCACTTGAAGATTTCTTGGACAC 59.963 41.667 0.00 0.00 36.11 3.67
273 276 2.199652 CGAACAAAGGGGCCTTGCA 61.200 57.895 0.84 0.00 36.26 4.08
456 459 6.918569 GTGCACTCGAATAAGTATCTACATGT 59.081 38.462 10.32 2.69 0.00 3.21
474 477 2.363788 TCAAGGACGTATGTGCACTC 57.636 50.000 19.41 6.44 39.20 3.51
483 486 4.705507 ACTTATCTCAGCTTCAAGGACGTA 59.294 41.667 0.00 0.00 0.00 3.57
555 558 6.183360 ACCGACGATTCTGAATGAATAACAAC 60.183 38.462 7.78 0.00 44.70 3.32
659 662 0.719465 GAACATACCCACGCAACTCG 59.281 55.000 0.00 0.00 45.38 4.18
811 868 7.414984 GCCCATTCTTTTTGATTTGTCAAAACA 60.415 33.333 13.96 2.95 45.63 2.83
819 882 5.466393 AGAAACGCCCATTCTTTTTGATTTG 59.534 36.000 0.00 0.00 33.41 2.32
825 888 3.243737 GGTGAGAAACGCCCATTCTTTTT 60.244 43.478 0.00 0.00 42.81 1.94
972 1062 2.661537 GCTTTTGGTTGCGGTGCC 60.662 61.111 0.00 0.00 0.00 5.01
1090 1243 2.022129 CGACGTTGGTGAGCTGGAC 61.022 63.158 0.00 0.00 0.00 4.02
1535 1706 0.598562 CATCTCGGCTACGGCATACT 59.401 55.000 0.00 0.00 41.39 2.12
1906 2089 4.913126 GACCACGTAGGGCTTCTG 57.087 61.111 8.57 0.00 44.70 3.02
2111 2309 1.338655 GACGAGAGCTCCCTGTTATCC 59.661 57.143 10.93 0.00 0.00 2.59
2456 6946 7.768807 GGATACTCTATTCTTCCTAGCTTGA 57.231 40.000 0.00 0.00 0.00 3.02
2479 6973 5.009010 GTGCCCAATCTGACAATTGTATAGG 59.991 44.000 11.95 7.59 35.31 2.57
2655 7153 7.548196 TTACGGCTATGTTCCTTTCTATTTG 57.452 36.000 0.00 0.00 0.00 2.32
2706 7208 4.640771 TTCAGCCTTTCACTATCTTGGT 57.359 40.909 0.00 0.00 0.00 3.67
2739 7241 9.423061 GCAAAATAAGAAGGTACAAATGAACAT 57.577 29.630 0.00 0.00 0.00 2.71
2779 7281 0.627451 AGCTTGGCCCATTCTGATGA 59.373 50.000 0.00 0.00 35.16 2.92
2825 7327 9.341899 GTAATAAAAATAAGCAGTCACAAGTGG 57.658 33.333 0.00 0.00 0.00 4.00
3036 7954 8.791327 TTCAGATACTGAGCAAAACATAATGA 57.209 30.769 0.00 0.00 41.75 2.57
3092 8010 2.375845 TGTTATTTTGGGACGGAGGGAA 59.624 45.455 0.00 0.00 0.00 3.97
3094 8012 2.290705 ACTGTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
3095 8013 3.007635 GACTGTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
3096 8014 3.933332 GAGACTGTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
3098 8016 3.670625 TGAGACTGTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
3099 8017 4.755123 AGTTGAGACTGTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.99 4.79
3100 8018 6.635030 AAGTTGAGACTGTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.91 4.46
3101 8019 8.934023 ATAAAGTTGAGACTGTTATTTTGGGA 57.066 30.769 0.00 0.00 35.91 4.37
3128 8736 9.922305 GCATCTGCTATTTTGTACTAAAGTTAG 57.078 33.333 8.41 7.18 38.21 2.34
3133 8741 6.184068 TGGGCATCTGCTATTTTGTACTAAA 58.816 36.000 4.96 4.96 41.70 1.85
3134 8742 5.750524 TGGGCATCTGCTATTTTGTACTAA 58.249 37.500 1.70 0.00 41.70 2.24
3139 8747 3.370840 TCTGGGCATCTGCTATTTTGT 57.629 42.857 1.70 0.00 41.70 2.83
3140 8748 4.931661 AATCTGGGCATCTGCTATTTTG 57.068 40.909 1.70 0.00 41.70 2.44
3142 8750 5.945144 AAAAATCTGGGCATCTGCTATTT 57.055 34.783 1.70 1.91 41.70 1.40
3161 8769 6.436847 TGAAGATGGCTCATCATAACCAAAAA 59.563 34.615 14.93 0.00 42.72 1.94


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

AutoCloner maintained by Alex Coulton.