Multiple sequence alignment - TraesCS2D01G097900

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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 TraesCS2D01G097900 chr2D 100.000 4609 0 0 1 4609 50102204 50106812 0.000000e+00 8512.0
1 TraesCS2D01G097900 chr2D 95.775 355 4 4 3704 4049 50111022 50111374 3.110000e-156 562.0
2 TraesCS2D01G097900 chr2B 93.144 2144 86 23 1600 3705 77860865 77862985 0.000000e+00 3088.0
3 TraesCS2D01G097900 chr2B 93.097 2144 87 23 1600 3705 77816819 77818939 0.000000e+00 3083.0
4 TraesCS2D01G097900 chr2B 82.836 938 114 31 3705 4609 646062896 646061973 0.000000e+00 797.0
5 TraesCS2D01G097900 chr2B 87.669 592 30 23 1052 1613 77859108 77859686 0.000000e+00 649.0
6 TraesCS2D01G097900 chr2B 79.658 993 123 49 124 1064 77852122 77853087 3.890000e-180 641.0
7 TraesCS2D01G097900 chr2B 87.162 592 33 23 1052 1613 77815064 77815642 2.340000e-177 632.0
8 TraesCS2D01G097900 chrUn 93.029 2080 87 21 1600 3641 355543233 355545292 0.000000e+00 2985.0
9 TraesCS2D01G097900 chrUn 93.521 1528 50 14 2147 3641 393254520 393253009 0.000000e+00 2228.0
10 TraesCS2D01G097900 chrUn 94.090 1083 47 10 1600 2672 245560562 245561637 0.000000e+00 1629.0
11 TraesCS2D01G097900 chrUn 94.090 1083 47 10 1600 2672 272850694 272851769 0.000000e+00 1629.0
12 TraesCS2D01G097900 chrUn 87.331 592 32 23 1052 1613 245558807 245559385 5.030000e-179 638.0
13 TraesCS2D01G097900 chrUn 87.331 592 32 23 1052 1613 272848940 272849518 5.030000e-179 638.0
14 TraesCS2D01G097900 chrUn 87.331 592 32 23 1052 1613 359687520 359688098 5.030000e-179 638.0
15 TraesCS2D01G097900 chrUn 87.331 592 32 23 1052 1613 400141779 400142357 5.030000e-179 638.0
16 TraesCS2D01G097900 chrUn 96.667 60 2 0 3646 3705 468101711 468101770 2.930000e-17 100.0
17 TraesCS2D01G097900 chrUn 100.000 30 0 0 3247 3276 40095681 40095710 6.440000e-04 56.5
18 TraesCS2D01G097900 chrUn 100.000 30 0 0 3247 3276 171028984 171028955 6.440000e-04 56.5
19 TraesCS2D01G097900 chr5D 87.964 1562 129 28 1554 3093 547971881 547970357 0.000000e+00 1788.0
20 TraesCS2D01G097900 chr5D 85.529 463 50 10 3197 3650 547970212 547969758 6.980000e-128 468.0
21 TraesCS2D01G097900 chr5D 87.234 141 10 3 1188 1324 547972068 547971932 2.220000e-33 154.0
22 TraesCS2D01G097900 chr5D 86.923 130 10 6 1 125 363189692 363189565 6.220000e-29 139.0
23 TraesCS2D01G097900 chr2A 90.167 1200 61 25 2545 3705 51663170 51664351 0.000000e+00 1509.0
24 TraesCS2D01G097900 chr2A 93.182 616 35 3 1936 2550 51662129 51662738 0.000000e+00 898.0
25 TraesCS2D01G097900 chr5B 86.474 1316 113 33 1554 2827 691973887 691972595 0.000000e+00 1384.0
26 TraesCS2D01G097900 chr5B 86.255 924 100 14 3705 4609 271054477 271053562 0.000000e+00 977.0
27 TraesCS2D01G097900 chr5B 88.652 282 29 2 2815 3093 691970838 691970557 1.590000e-89 340.0
28 TraesCS2D01G097900 chr4D 91.704 892 51 12 3736 4609 389196241 389197127 0.000000e+00 1216.0
29 TraesCS2D01G097900 chr4D 89.863 365 18 12 3704 4050 389201337 389201700 7.030000e-123 451.0
30 TraesCS2D01G097900 chr4D 100.000 30 0 0 3247 3276 123629629 123629600 6.440000e-04 56.5
31 TraesCS2D01G097900 chr1A 86.446 937 87 21 3705 4609 368400980 368401908 0.000000e+00 990.0
32 TraesCS2D01G097900 chr1A 80.688 378 40 15 3704 4050 368406113 368406488 3.540000e-66 263.0
33 TraesCS2D01G097900 chr7B 86.069 926 102 14 3704 4609 74362229 74363147 0.000000e+00 970.0
34 TraesCS2D01G097900 chr7B 94.059 101 3 3 27 125 667482728 667482827 2.870000e-32 150.0
35 TraesCS2D01G097900 chr1B 84.375 928 108 20 3705 4609 266832709 266831796 0.000000e+00 876.0
36 TraesCS2D01G097900 chr1B 83.590 713 86 24 3908 4609 426078361 426077669 1.400000e-179 640.0
37 TraesCS2D01G097900 chr6B 80.317 945 133 36 3704 4609 699068341 699067411 0.000000e+00 665.0
38 TraesCS2D01G097900 chr6B 80.042 942 140 31 3705 4609 699073481 699072551 0.000000e+00 654.0
39 TraesCS2D01G097900 chr3A 97.059 102 1 2 27 126 620571945 620571844 2.210000e-38 171.0
40 TraesCS2D01G097900 chr3D 91.736 121 5 4 25 142 482007570 482007452 3.690000e-36 163.0
41 TraesCS2D01G097900 chr3D 95.960 99 2 2 30 126 476984057 476983959 4.770000e-35 159.0
42 TraesCS2D01G097900 chr3D 93.137 102 5 2 27 126 337315188 337315087 1.030000e-31 148.0
43 TraesCS2D01G097900 chr3D 93.137 102 5 2 27 126 586893014 586893115 1.030000e-31 148.0
44 TraesCS2D01G097900 chr3B 95.238 105 2 3 27 128 636108999 636108895 3.690000e-36 163.0
45 TraesCS2D01G097900 chr4B 93.333 105 3 4 25 125 670890661 670890557 7.990000e-33 152.0
46 TraesCS2D01G097900 chr4A 80.531 113 15 7 694 805 73163680 73163574 3.820000e-11 80.5


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 TraesCS2D01G097900 chr2D 50102204 50106812 4608 False 8512.000000 8512 100.0000 1 4609 1 chr2D.!!$F1 4608
1 TraesCS2D01G097900 chr2B 77859108 77862985 3877 False 1868.500000 3088 90.4065 1052 3705 2 chr2B.!!$F3 2653
2 TraesCS2D01G097900 chr2B 77815064 77818939 3875 False 1857.500000 3083 90.1295 1052 3705 2 chr2B.!!$F2 2653
3 TraesCS2D01G097900 chr2B 646061973 646062896 923 True 797.000000 797 82.8360 3705 4609 1 chr2B.!!$R1 904
4 TraesCS2D01G097900 chr2B 77852122 77853087 965 False 641.000000 641 79.6580 124 1064 1 chr2B.!!$F1 940
5 TraesCS2D01G097900 chrUn 355543233 355545292 2059 False 2985.000000 2985 93.0290 1600 3641 1 chrUn.!!$F2 2041
6 TraesCS2D01G097900 chrUn 393253009 393254520 1511 True 2228.000000 2228 93.5210 2147 3641 1 chrUn.!!$R2 1494
7 TraesCS2D01G097900 chrUn 245558807 245561637 2830 False 1133.500000 1629 90.7105 1052 2672 2 chrUn.!!$F6 1620
8 TraesCS2D01G097900 chrUn 272848940 272851769 2829 False 1133.500000 1629 90.7105 1052 2672 2 chrUn.!!$F7 1620
9 TraesCS2D01G097900 chrUn 359687520 359688098 578 False 638.000000 638 87.3310 1052 1613 1 chrUn.!!$F3 561
10 TraesCS2D01G097900 chrUn 400141779 400142357 578 False 638.000000 638 87.3310 1052 1613 1 chrUn.!!$F4 561
11 TraesCS2D01G097900 chr5D 547969758 547972068 2310 True 803.333333 1788 86.9090 1188 3650 3 chr5D.!!$R2 2462
12 TraesCS2D01G097900 chr2A 51662129 51664351 2222 False 1203.500000 1509 91.6745 1936 3705 2 chr2A.!!$F1 1769
13 TraesCS2D01G097900 chr5B 271053562 271054477 915 True 977.000000 977 86.2550 3705 4609 1 chr5B.!!$R1 904
14 TraesCS2D01G097900 chr5B 691970557 691973887 3330 True 862.000000 1384 87.5630 1554 3093 2 chr5B.!!$R2 1539
15 TraesCS2D01G097900 chr4D 389196241 389197127 886 False 1216.000000 1216 91.7040 3736 4609 1 chr4D.!!$F1 873
16 TraesCS2D01G097900 chr1A 368400980 368401908 928 False 990.000000 990 86.4460 3705 4609 1 chr1A.!!$F1 904
17 TraesCS2D01G097900 chr7B 74362229 74363147 918 False 970.000000 970 86.0690 3704 4609 1 chr7B.!!$F1 905
18 TraesCS2D01G097900 chr1B 266831796 266832709 913 True 876.000000 876 84.3750 3705 4609 1 chr1B.!!$R1 904
19 TraesCS2D01G097900 chr1B 426077669 426078361 692 True 640.000000 640 83.5900 3908 4609 1 chr1B.!!$R2 701
20 TraesCS2D01G097900 chr6B 699067411 699068341 930 True 665.000000 665 80.3170 3704 4609 1 chr6B.!!$R1 905
21 TraesCS2D01G097900 chr6B 699072551 699073481 930 True 654.000000 654 80.0420 3705 4609 1 chr6B.!!$R2 904

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
905 957 0.249398 GCGTCCCTTCCTGTACATGT 59.751 55.0 2.69 2.69 0.00 3.21 F
1888 3198 0.110486 TGGTCACTCTTTTCCCCTGC 59.890 55.0 0.00 0.00 0.00 4.85 F
1889 3199 0.402121 GGTCACTCTTTTCCCCTGCT 59.598 55.0 0.00 0.00 0.00 4.24 F
2055 3373 0.690192 TGGAGCTCCATCCAAAACGA 59.310 50.0 32.00 4.48 46.45 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2539 3871 0.334676 ATGAGGGGCGGAATTTCCAA 59.665 50.000 15.58 0.0 35.91 3.53 R
2809 4618 1.150081 GCCATCACCAGCCTAGCAT 59.850 57.895 0.00 0.0 0.00 3.79 R
3377 7041 2.095819 GCCTATAGACGCCGAGAGTTAC 60.096 54.545 0.00 0.0 0.00 2.50 R
3905 7593 1.400494 GAGAGAGAGACAACGAGAGCC 59.600 57.143 0.00 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
19 20 1.317613 GCATGGTTGTTGAGGTGACA 58.682 50.000 0.00 0.00 0.00 3.58
20 21 1.888512 GCATGGTTGTTGAGGTGACAT 59.111 47.619 0.00 0.00 0.00 3.06
21 22 2.352030 GCATGGTTGTTGAGGTGACATG 60.352 50.000 0.00 0.00 37.77 3.21
22 23 1.979855 TGGTTGTTGAGGTGACATGG 58.020 50.000 0.00 0.00 0.00 3.66
23 24 1.214175 TGGTTGTTGAGGTGACATGGT 59.786 47.619 0.00 0.00 0.00 3.55
24 25 2.306847 GGTTGTTGAGGTGACATGGTT 58.693 47.619 0.00 0.00 0.00 3.67
25 26 2.034558 GGTTGTTGAGGTGACATGGTTG 59.965 50.000 0.00 0.00 0.00 3.77
26 27 1.317613 TGTTGAGGTGACATGGTTGC 58.682 50.000 0.00 0.00 0.00 4.17
27 28 1.317613 GTTGAGGTGACATGGTTGCA 58.682 50.000 0.00 0.00 0.00 4.08
28 29 1.680735 GTTGAGGTGACATGGTTGCAA 59.319 47.619 0.00 0.00 0.00 4.08
29 30 2.064434 TGAGGTGACATGGTTGCAAA 57.936 45.000 0.00 0.00 0.00 3.68
30 31 2.596346 TGAGGTGACATGGTTGCAAAT 58.404 42.857 0.00 0.00 0.00 2.32
31 32 2.964464 TGAGGTGACATGGTTGCAAATT 59.036 40.909 0.00 0.00 0.00 1.82
32 33 3.243805 TGAGGTGACATGGTTGCAAATTG 60.244 43.478 0.00 1.56 0.00 2.32
33 34 2.699846 AGGTGACATGGTTGCAAATTGT 59.300 40.909 0.00 5.22 0.00 2.71
34 35 3.894427 AGGTGACATGGTTGCAAATTGTA 59.106 39.130 0.00 0.00 0.00 2.41
35 36 4.343526 AGGTGACATGGTTGCAAATTGTAA 59.656 37.500 0.00 0.00 0.00 2.41
36 37 4.447389 GGTGACATGGTTGCAAATTGTAAC 59.553 41.667 16.74 16.74 41.33 2.50
37 38 5.288804 GTGACATGGTTGCAAATTGTAACT 58.711 37.500 22.33 6.53 41.68 2.24
38 39 5.752955 GTGACATGGTTGCAAATTGTAACTT 59.247 36.000 22.33 10.74 41.68 2.66
39 40 5.752472 TGACATGGTTGCAAATTGTAACTTG 59.248 36.000 22.33 20.71 41.68 3.16
40 41 5.911752 ACATGGTTGCAAATTGTAACTTGA 58.088 33.333 22.33 10.36 41.68 3.02
41 42 5.752955 ACATGGTTGCAAATTGTAACTTGAC 59.247 36.000 22.33 9.59 41.68 3.18
42 43 4.688021 TGGTTGCAAATTGTAACTTGACC 58.312 39.130 22.33 10.14 41.68 4.02
43 44 4.160439 TGGTTGCAAATTGTAACTTGACCA 59.840 37.500 22.33 12.36 41.68 4.02
44 45 4.506288 GGTTGCAAATTGTAACTTGACCAC 59.494 41.667 22.33 4.60 41.68 4.16
45 46 4.991153 TGCAAATTGTAACTTGACCACA 57.009 36.364 0.00 0.00 0.00 4.17
46 47 5.528043 TGCAAATTGTAACTTGACCACAT 57.472 34.783 0.00 0.00 0.00 3.21
47 48 5.288015 TGCAAATTGTAACTTGACCACATG 58.712 37.500 0.00 0.00 0.00 3.21
48 49 4.150451 GCAAATTGTAACTTGACCACATGC 59.850 41.667 0.00 0.00 0.00 4.06
49 50 5.288015 CAAATTGTAACTTGACCACATGCA 58.712 37.500 0.00 0.00 0.00 3.96
50 51 5.726980 AATTGTAACTTGACCACATGCAT 57.273 34.783 0.00 0.00 0.00 3.96
51 52 4.502171 TTGTAACTTGACCACATGCATG 57.498 40.909 25.09 25.09 0.00 4.06
52 53 3.749226 TGTAACTTGACCACATGCATGA 58.251 40.909 32.75 7.36 0.00 3.07
53 54 3.501828 TGTAACTTGACCACATGCATGAC 59.498 43.478 32.75 19.04 0.00 3.06
54 55 2.574006 ACTTGACCACATGCATGACT 57.426 45.000 32.75 13.85 0.00 3.41
55 56 2.867624 ACTTGACCACATGCATGACTT 58.132 42.857 32.75 15.27 0.00 3.01
56 57 2.555325 ACTTGACCACATGCATGACTTG 59.445 45.455 32.75 19.74 0.00 3.16
57 58 2.565046 TGACCACATGCATGACTTGA 57.435 45.000 32.75 10.65 0.00 3.02
58 59 3.076079 TGACCACATGCATGACTTGAT 57.924 42.857 32.75 8.15 0.00 2.57
59 60 2.750712 TGACCACATGCATGACTTGATG 59.249 45.455 32.75 18.31 0.00 3.07
60 61 3.011818 GACCACATGCATGACTTGATGA 58.988 45.455 32.75 0.00 0.00 2.92
61 62 3.628008 ACCACATGCATGACTTGATGAT 58.372 40.909 32.75 3.48 0.00 2.45
62 63 3.380320 ACCACATGCATGACTTGATGATG 59.620 43.478 32.75 16.20 0.00 3.07
63 64 3.380320 CCACATGCATGACTTGATGATGT 59.620 43.478 32.75 4.37 30.64 3.06
64 65 4.351192 CACATGCATGACTTGATGATGTG 58.649 43.478 32.75 13.57 36.57 3.21
65 66 3.380320 ACATGCATGACTTGATGATGTGG 59.620 43.478 32.75 0.59 30.02 4.17
66 67 1.746787 TGCATGACTTGATGATGTGGC 59.253 47.619 0.00 0.00 0.00 5.01
67 68 1.746787 GCATGACTTGATGATGTGGCA 59.253 47.619 0.00 0.00 0.00 4.92
68 69 2.361119 GCATGACTTGATGATGTGGCAT 59.639 45.455 0.00 0.00 0.00 4.40
69 70 3.566742 GCATGACTTGATGATGTGGCATA 59.433 43.478 0.00 0.00 0.00 3.14
70 71 4.320275 GCATGACTTGATGATGTGGCATAG 60.320 45.833 0.00 0.00 0.00 2.23
71 72 4.492494 TGACTTGATGATGTGGCATAGT 57.508 40.909 0.00 0.00 0.00 2.12
72 73 4.847198 TGACTTGATGATGTGGCATAGTT 58.153 39.130 0.00 0.00 0.00 2.24
73 74 4.637091 TGACTTGATGATGTGGCATAGTTG 59.363 41.667 0.00 0.00 0.00 3.16
92 93 6.521151 AGTTGCATGAAGAGGAAAAATAGG 57.479 37.500 0.00 0.00 0.00 2.57
93 94 6.012745 AGTTGCATGAAGAGGAAAAATAGGT 58.987 36.000 0.00 0.00 0.00 3.08
94 95 7.175104 AGTTGCATGAAGAGGAAAAATAGGTA 58.825 34.615 0.00 0.00 0.00 3.08
95 96 7.337942 AGTTGCATGAAGAGGAAAAATAGGTAG 59.662 37.037 0.00 0.00 0.00 3.18
96 97 6.721318 TGCATGAAGAGGAAAAATAGGTAGT 58.279 36.000 0.00 0.00 0.00 2.73
97 98 6.599244 TGCATGAAGAGGAAAAATAGGTAGTG 59.401 38.462 0.00 0.00 0.00 2.74
98 99 6.038714 GCATGAAGAGGAAAAATAGGTAGTGG 59.961 42.308 0.00 0.00 0.00 4.00
99 100 6.062258 TGAAGAGGAAAAATAGGTAGTGGG 57.938 41.667 0.00 0.00 0.00 4.61
100 101 5.550403 TGAAGAGGAAAAATAGGTAGTGGGT 59.450 40.000 0.00 0.00 0.00 4.51
101 102 6.045106 TGAAGAGGAAAAATAGGTAGTGGGTT 59.955 38.462 0.00 0.00 0.00 4.11
102 103 5.816682 AGAGGAAAAATAGGTAGTGGGTTG 58.183 41.667 0.00 0.00 0.00 3.77
103 104 4.341487 AGGAAAAATAGGTAGTGGGTTGC 58.659 43.478 0.00 0.00 0.00 4.17
104 105 4.083565 GGAAAAATAGGTAGTGGGTTGCA 58.916 43.478 0.00 0.00 0.00 4.08
105 106 4.525100 GGAAAAATAGGTAGTGGGTTGCAA 59.475 41.667 0.00 0.00 0.00 4.08
106 107 5.462530 AAAAATAGGTAGTGGGTTGCAAC 57.537 39.130 21.59 21.59 0.00 4.17
107 108 4.382386 AAATAGGTAGTGGGTTGCAACT 57.618 40.909 27.64 11.68 0.00 3.16
108 109 5.508280 AAATAGGTAGTGGGTTGCAACTA 57.492 39.130 27.64 15.18 0.00 2.24
109 110 5.710409 AATAGGTAGTGGGTTGCAACTAT 57.290 39.130 27.64 12.73 31.83 2.12
110 111 5.710409 ATAGGTAGTGGGTTGCAACTATT 57.290 39.130 27.64 16.23 31.83 1.73
111 112 4.382386 AGGTAGTGGGTTGCAACTATTT 57.618 40.909 27.64 14.29 31.83 1.40
112 113 5.508280 AGGTAGTGGGTTGCAACTATTTA 57.492 39.130 27.64 13.38 31.83 1.40
113 114 5.883180 AGGTAGTGGGTTGCAACTATTTAA 58.117 37.500 27.64 8.06 31.83 1.52
114 115 6.308566 AGGTAGTGGGTTGCAACTATTTAAA 58.691 36.000 27.64 6.53 31.83 1.52
115 116 6.778559 AGGTAGTGGGTTGCAACTATTTAAAA 59.221 34.615 27.64 5.12 31.83 1.52
116 117 7.288158 AGGTAGTGGGTTGCAACTATTTAAAAA 59.712 33.333 27.64 3.86 31.83 1.94
117 118 8.092068 GGTAGTGGGTTGCAACTATTTAAAAAT 58.908 33.333 27.64 7.75 31.83 1.82
120 121 9.084533 AGTGGGTTGCAACTATTTAAAAATAGA 57.915 29.630 27.64 4.19 46.87 1.98
121 122 9.353999 GTGGGTTGCAACTATTTAAAAATAGAG 57.646 33.333 27.64 16.74 46.87 2.43
122 123 8.527810 TGGGTTGCAACTATTTAAAAATAGAGG 58.472 33.333 27.64 16.26 46.87 3.69
158 159 5.013599 AGGATATGCATTCTAGAACCTTCCC 59.986 44.000 7.48 3.99 0.00 3.97
159 160 5.013599 GGATATGCATTCTAGAACCTTCCCT 59.986 44.000 7.48 0.00 0.00 4.20
160 161 3.634397 TGCATTCTAGAACCTTCCCTG 57.366 47.619 7.48 1.37 0.00 4.45
162 163 3.587061 TGCATTCTAGAACCTTCCCTGAA 59.413 43.478 7.48 0.00 0.00 3.02
163 164 4.042809 TGCATTCTAGAACCTTCCCTGAAA 59.957 41.667 7.48 0.00 0.00 2.69
164 165 5.196695 GCATTCTAGAACCTTCCCTGAAAT 58.803 41.667 7.48 0.00 0.00 2.17
165 166 6.069673 TGCATTCTAGAACCTTCCCTGAAATA 60.070 38.462 7.48 0.00 0.00 1.40
176 177 7.928873 ACCTTCCCTGAAATAGTATTTCTTCA 58.071 34.615 27.68 13.88 0.00 3.02
455 475 6.595772 TTTTCCCAATTTGTGAACATTTCG 57.404 33.333 0.00 0.00 0.00 3.46
469 489 6.362283 GTGAACATTTCGTACAATTTCCCAAG 59.638 38.462 0.00 0.00 0.00 3.61
470 490 6.263392 TGAACATTTCGTACAATTTCCCAAGA 59.737 34.615 0.00 0.00 0.00 3.02
472 492 7.227049 ACATTTCGTACAATTTCCCAAGAAT 57.773 32.000 0.00 0.00 0.00 2.40
473 493 7.090173 ACATTTCGTACAATTTCCCAAGAATG 58.910 34.615 0.00 0.00 0.00 2.67
477 498 6.674066 TCGTACAATTTCCCAAGAATGTTTC 58.326 36.000 0.00 0.00 29.99 2.78
482 503 7.216494 ACAATTTCCCAAGAATGTTTCGAAAT 58.784 30.769 14.69 0.00 31.59 2.17
485 506 5.371115 TCCCAAGAATGTTTCGAAATCAC 57.629 39.130 14.69 2.41 34.02 3.06
486 507 4.083537 TCCCAAGAATGTTTCGAAATCACG 60.084 41.667 14.69 3.26 34.02 4.35
543 583 9.483062 TGAATTTTGCGAACAATGTTTTAAAAG 57.517 25.926 0.00 0.00 35.21 2.27
548 588 7.139300 TGCGAACAATGTTTTAAAAGTTACG 57.861 32.000 0.00 8.77 0.00 3.18
627 667 8.209584 TCAATGAAAAATTTCTTGACATTGGGA 58.790 29.630 21.15 10.74 41.49 4.37
629 669 8.977267 ATGAAAAATTTCTTGACATTGGGAAA 57.023 26.923 7.36 0.00 38.02 3.13
630 670 8.207521 TGAAAAATTTCTTGACATTGGGAAAC 57.792 30.769 7.36 0.00 38.02 2.78
631 671 7.826252 TGAAAAATTTCTTGACATTGGGAAACA 59.174 29.630 7.36 0.00 38.02 2.83
633 673 8.750515 AAAATTTCTTGACATTGGGAAACATT 57.249 26.923 0.00 0.00 31.82 2.71
634 674 9.844257 AAAATTTCTTGACATTGGGAAACATTA 57.156 25.926 0.00 0.00 31.82 1.90
679 719 9.667989 AAATGTTTTTGAGCATTTAAGCAAATC 57.332 25.926 0.00 0.00 41.70 2.17
686 728 9.872721 TTTGAGCATTTAAGCAAATCATGAATA 57.127 25.926 0.00 0.00 36.85 1.75
887 939 1.202348 CGAAATGGAGAAAACAGGGGC 59.798 52.381 0.00 0.00 0.00 5.80
891 943 1.674651 GGAGAAAACAGGGGCGTCC 60.675 63.158 0.00 0.00 0.00 4.79
905 957 0.249398 GCGTCCCTTCCTGTACATGT 59.751 55.000 2.69 2.69 0.00 3.21
907 959 1.739067 GTCCCTTCCTGTACATGTGC 58.261 55.000 9.11 8.01 0.00 4.57
912 967 1.836999 TTCCTGTACATGTGCGGGCT 61.837 55.000 30.95 0.00 40.91 5.19
918 973 1.135689 GTACATGTGCGGGCTCAAAAG 60.136 52.381 9.11 0.00 0.00 2.27
935 990 2.964978 GCGCTTGCTTTGTGGGAT 59.035 55.556 0.00 0.00 35.07 3.85
942 997 2.440247 CTTTGTGGGATCGGGGGC 60.440 66.667 0.00 0.00 0.00 5.80
968 1023 1.373590 TTCCTTCCTATTTGGCGCGC 61.374 55.000 25.94 25.94 35.26 6.86
970 1025 1.353103 CTTCCTATTTGGCGCGCAG 59.647 57.895 34.42 20.74 35.26 5.18
984 1039 1.065273 CGCAGGTCGCCTAATACGT 59.935 57.895 0.00 0.00 37.30 3.57
998 1053 5.392272 GCCTAATACGTTGTCCCGAATTTTT 60.392 40.000 0.00 0.00 0.00 1.94
1026 1083 4.389576 GCAACTGCGCTCGGGTTG 62.390 66.667 21.81 21.81 41.96 3.77
1041 1098 3.703052 TCGGGTTGAGTATAGGACTTTCC 59.297 47.826 0.00 0.00 39.06 3.13
1047 1104 7.310858 GGGTTGAGTATAGGACTTTCCAACTTA 60.311 40.741 0.00 0.00 39.05 2.24
1057 1117 5.646793 GGACTTTCCAACTTATCCAACCTAC 59.353 44.000 0.00 0.00 36.28 3.18
1072 1132 4.266070 TACAGCCGCCGCGAGATC 62.266 66.667 15.93 0.18 41.18 2.75
1084 1144 2.725008 GAGATCCAGTCGCCTCCG 59.275 66.667 0.00 0.00 0.00 4.63
1104 1164 2.504244 CGTGCTTCGTCTCCGACC 60.504 66.667 0.00 0.00 44.13 4.79
1118 1178 2.804090 GACCACGGCGACTTCGTC 60.804 66.667 16.62 7.34 42.22 4.20
1136 1196 1.215679 TCCTCCGTCTCCCTCCTCTT 61.216 60.000 0.00 0.00 0.00 2.85
1144 1204 1.671901 CTCCCTCCTCTTCGGTGAGC 61.672 65.000 0.98 0.00 33.02 4.26
1161 1221 1.610673 GCTGTCCACTCCTCCCTCA 60.611 63.158 0.00 0.00 0.00 3.86
1195 1255 0.471780 TCCTCCTCAGTCCACAAGCA 60.472 55.000 0.00 0.00 0.00 3.91
1199 1259 0.673022 CCTCAGTCCACAAGCAGCTC 60.673 60.000 0.00 0.00 0.00 4.09
1214 1274 4.069232 CTCCTTCGCCGGCTGACA 62.069 66.667 26.68 12.50 0.00 3.58
1215 1275 3.376935 CTCCTTCGCCGGCTGACAT 62.377 63.158 26.68 0.00 0.00 3.06
1216 1276 2.892425 CCTTCGCCGGCTGACATC 60.892 66.667 26.68 0.00 0.00 3.06
1217 1277 2.892425 CTTCGCCGGCTGACATCC 60.892 66.667 26.68 0.00 0.00 3.51
1218 1278 3.664025 CTTCGCCGGCTGACATCCA 62.664 63.158 26.68 7.11 0.00 3.41
1219 1279 3.664025 TTCGCCGGCTGACATCCAG 62.664 63.158 26.68 5.22 45.67 3.86
1223 1283 4.864334 CGGCTGACATCCAGGGCC 62.864 72.222 0.00 0.00 43.13 5.80
1324 1409 3.638627 TCTCATGAGTTCCAGTCGCATAT 59.361 43.478 21.92 0.00 0.00 1.78
1326 1411 5.478332 TCTCATGAGTTCCAGTCGCATATAT 59.522 40.000 21.92 0.00 0.00 0.86
1327 1412 6.659242 TCTCATGAGTTCCAGTCGCATATATA 59.341 38.462 21.92 0.00 0.00 0.86
1328 1413 6.621613 TCATGAGTTCCAGTCGCATATATAC 58.378 40.000 0.00 0.00 0.00 1.47
1329 1414 6.208599 TCATGAGTTCCAGTCGCATATATACA 59.791 38.462 0.00 0.00 0.00 2.29
1331 1416 4.795268 AGTTCCAGTCGCATATATACACG 58.205 43.478 0.82 0.82 0.00 4.49
1333 1418 2.094906 TCCAGTCGCATATATACACGGC 60.095 50.000 3.30 3.30 0.00 5.68
1337 1422 4.031765 CAGTCGCATATATACACGGCATTC 59.968 45.833 11.93 0.00 31.32 2.67
1338 1423 3.306166 GTCGCATATATACACGGCATTCC 59.694 47.826 6.08 0.00 0.00 3.01
1339 1424 2.607635 CGCATATATACACGGCATTCCC 59.392 50.000 0.00 0.00 0.00 3.97
1340 1425 3.678806 CGCATATATACACGGCATTCCCT 60.679 47.826 0.00 0.00 0.00 4.20
1341 1426 4.440940 CGCATATATACACGGCATTCCCTA 60.441 45.833 0.00 0.00 0.00 3.53
1371 1460 9.415544 CTTTTAAATGTTGCTTAGCTTCTGATT 57.584 29.630 5.60 0.00 0.00 2.57
1395 1503 2.369860 TGACTGATTGTGTGCCTTCTCT 59.630 45.455 0.00 0.00 0.00 3.10
1397 1505 3.406764 ACTGATTGTGTGCCTTCTCTTC 58.593 45.455 0.00 0.00 0.00 2.87
1434 1543 3.594603 TTCCCTCGATGTTTCTCTGTC 57.405 47.619 0.00 0.00 0.00 3.51
1474 1583 2.940994 TGTTCCTGTCCCGAATTTGA 57.059 45.000 0.00 0.00 0.00 2.69
1477 1586 2.178912 TCCTGTCCCGAATTTGACAC 57.821 50.000 0.00 0.00 36.62 3.67
1523 1632 7.093988 ACACCATGCAGCACAAACTATAATTAA 60.094 33.333 0.00 0.00 0.00 1.40
1683 2987 6.427242 GGCTACTAATCACCTAGTATTTTGCC 59.573 42.308 0.00 0.00 36.05 4.52
1818 3125 3.868077 CCGAGCTCAAATGAGAACCTAAG 59.132 47.826 15.40 1.07 44.74 2.18
1819 3126 4.382040 CCGAGCTCAAATGAGAACCTAAGA 60.382 45.833 15.40 0.00 44.74 2.10
1877 3187 1.188219 TCCAGGTCAGCTGGTCACTC 61.188 60.000 22.47 0.00 42.35 3.51
1882 3192 2.147150 GGTCAGCTGGTCACTCTTTTC 58.853 52.381 15.13 0.00 0.00 2.29
1883 3193 2.147150 GTCAGCTGGTCACTCTTTTCC 58.853 52.381 15.13 0.00 0.00 3.13
1886 3196 0.402121 GCTGGTCACTCTTTTCCCCT 59.598 55.000 0.00 0.00 0.00 4.79
1887 3197 1.884067 GCTGGTCACTCTTTTCCCCTG 60.884 57.143 0.00 0.00 0.00 4.45
1888 3198 0.110486 TGGTCACTCTTTTCCCCTGC 59.890 55.000 0.00 0.00 0.00 4.85
1889 3199 0.402121 GGTCACTCTTTTCCCCTGCT 59.598 55.000 0.00 0.00 0.00 4.24
1918 3235 5.623335 CACACGTTTTTAACAACTCAGTGA 58.377 37.500 14.14 0.00 0.00 3.41
2038 3356 2.261671 CTCCGACTGTTCCGGTGG 59.738 66.667 0.00 0.00 46.53 4.61
2055 3373 0.690192 TGGAGCTCCATCCAAAACGA 59.310 50.000 32.00 4.48 46.45 3.85
2130 3455 4.518970 GCTTCTGAATTCCCTAAACACACA 59.481 41.667 2.27 0.00 0.00 3.72
2131 3456 5.183904 GCTTCTGAATTCCCTAAACACACAT 59.816 40.000 2.27 0.00 0.00 3.21
2132 3457 6.294731 GCTTCTGAATTCCCTAAACACACATT 60.295 38.462 2.27 0.00 0.00 2.71
2133 3458 6.573664 TCTGAATTCCCTAAACACACATTG 57.426 37.500 2.27 0.00 0.00 2.82
2141 3466 4.142534 CCCTAAACACACATTGATCTGCAG 60.143 45.833 7.63 7.63 0.00 4.41
2198 3524 0.885196 TGTGTTTTTATGCTCCGGCC 59.115 50.000 0.00 0.00 37.74 6.13
2334 3665 1.344114 TCCCCATTTTGCTTGTTCTGC 59.656 47.619 0.00 0.00 0.00 4.26
2349 3680 6.142958 GCTTGTTCTGCTGTTCATTTTAAGTC 59.857 38.462 0.00 0.00 0.00 3.01
2464 3796 4.574013 GCTTGGAGGAATGTGAGTTAGATG 59.426 45.833 0.00 0.00 0.00 2.90
2539 3871 2.270434 AGTACATCTCCACCATGGGT 57.730 50.000 18.09 4.67 38.32 4.51
2626 4395 6.879458 GGCTGTAAAAGAGATCCTGAGTAAAA 59.121 38.462 0.00 0.00 0.00 1.52
2627 4396 7.390718 GGCTGTAAAAGAGATCCTGAGTAAAAA 59.609 37.037 0.00 0.00 0.00 1.94
2710 4506 9.277783 CCTTACATGGTAGAGGAAATAAATGAG 57.722 37.037 0.00 0.00 0.00 2.90
2762 4570 3.961480 TCTATGTCCCATTAGATGCCG 57.039 47.619 0.00 0.00 0.00 5.69
2773 4581 5.394115 CCCATTAGATGCCGCTTTTACTTTT 60.394 40.000 0.00 0.00 0.00 2.27
2989 6572 5.183331 GCAGGAACGATATAGGTATGTCTCA 59.817 44.000 0.00 0.00 0.00 3.27
3152 6804 3.513680 TGTGAATCCTACGCGTACATT 57.486 42.857 16.41 15.78 0.00 2.71
3188 6841 1.475751 GGACCATGCATGTGTCCTAGG 60.476 57.143 35.80 20.84 41.19 3.02
3207 6860 4.592485 AGGAGCTCACTACGATTATTGG 57.408 45.455 17.19 0.00 0.00 3.16
3376 7040 6.152932 TGAACTTTAGACTTACGACACCTT 57.847 37.500 0.00 0.00 0.00 3.50
3377 7041 5.981315 TGAACTTTAGACTTACGACACCTTG 59.019 40.000 0.00 0.00 0.00 3.61
3425 7089 9.121658 GTTAAAGTCATTTCCCCCTATCTTTAG 57.878 37.037 0.00 0.00 31.19 1.85
3436 7100 5.013183 CCCCCTATCTTTAGTTCTACATGGG 59.987 48.000 0.00 0.00 0.00 4.00
3473 7137 8.240682 TCATGTTTTTGGTCTATTCGTATTTGG 58.759 33.333 0.00 0.00 0.00 3.28
3549 7216 3.674997 TCTATGAGCGAAAAAGGCAAGT 58.325 40.909 0.00 0.00 0.00 3.16
3647 7314 4.406003 ACACTGGCCACTCCTTAATAGTAG 59.594 45.833 0.00 0.00 35.26 2.57
3648 7315 4.406003 CACTGGCCACTCCTTAATAGTAGT 59.594 45.833 0.00 0.00 35.26 2.73
3649 7316 5.597182 CACTGGCCACTCCTTAATAGTAGTA 59.403 44.000 0.00 0.00 35.26 1.82
3650 7317 5.597594 ACTGGCCACTCCTTAATAGTAGTAC 59.402 44.000 0.00 0.00 35.26 2.73
3743 7414 1.737363 GCACTAGGTTCAGGAAGAGCG 60.737 57.143 0.00 0.00 0.00 5.03
3905 7593 5.352569 GGACACTGTAGATGATCAAGTTTGG 59.647 44.000 0.00 0.00 0.00 3.28
3913 7624 1.347707 TGATCAAGTTTGGGCTCTCGT 59.652 47.619 0.00 0.00 0.00 4.18
4039 7765 3.371063 GACTCGGTCCGCTCCACA 61.371 66.667 6.34 0.00 0.00 4.17
4137 7871 1.524621 CCAGCAAATCCGAGGCGAT 60.525 57.895 0.00 0.00 0.00 4.58
4170 7904 1.417890 CCCTAGGGTTCGATCTGCATT 59.582 52.381 20.88 0.00 0.00 3.56
4458 8192 0.254178 CTGGGGCAAGTACAGCAGAT 59.746 55.000 11.68 0.00 0.00 2.90
4488 8222 2.943978 CGGTTCAGTCGGGGAAGCT 61.944 63.158 10.45 0.00 39.83 3.74
4496 8230 4.988598 CGGGGAAGCTGCACACGT 62.989 66.667 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.229543 CCATGTCACCTCAACAACCATG 59.770 50.000 0.00 0.00 0.00 3.66
2 3 2.158475 ACCATGTCACCTCAACAACCAT 60.158 45.455 0.00 0.00 0.00 3.55
5 6 2.543653 GCAACCATGTCACCTCAACAAC 60.544 50.000 0.00 0.00 0.00 3.32
6 7 1.680735 GCAACCATGTCACCTCAACAA 59.319 47.619 0.00 0.00 0.00 2.83
7 8 1.317613 GCAACCATGTCACCTCAACA 58.682 50.000 0.00 0.00 0.00 3.33
8 9 1.317613 TGCAACCATGTCACCTCAAC 58.682 50.000 0.00 0.00 0.00 3.18
9 10 2.064434 TTGCAACCATGTCACCTCAA 57.936 45.000 0.00 0.00 0.00 3.02
10 11 2.064434 TTTGCAACCATGTCACCTCA 57.936 45.000 0.00 0.00 0.00 3.86
11 12 3.243839 ACAATTTGCAACCATGTCACCTC 60.244 43.478 0.00 0.00 0.00 3.85
12 13 2.699846 ACAATTTGCAACCATGTCACCT 59.300 40.909 0.00 0.00 0.00 4.00
13 14 3.110447 ACAATTTGCAACCATGTCACC 57.890 42.857 0.00 0.00 0.00 4.02
14 15 5.288804 AGTTACAATTTGCAACCATGTCAC 58.711 37.500 12.66 12.19 0.00 3.67
15 16 5.528043 AGTTACAATTTGCAACCATGTCA 57.472 34.783 12.66 2.24 0.00 3.58
16 17 5.982516 TCAAGTTACAATTTGCAACCATGTC 59.017 36.000 12.66 2.83 0.00 3.06
17 18 5.752955 GTCAAGTTACAATTTGCAACCATGT 59.247 36.000 0.00 7.40 0.00 3.21
18 19 5.177327 GGTCAAGTTACAATTTGCAACCATG 59.823 40.000 0.00 8.54 28.98 3.66
19 20 5.163364 TGGTCAAGTTACAATTTGCAACCAT 60.163 36.000 0.00 0.00 31.86 3.55
20 21 4.160439 TGGTCAAGTTACAATTTGCAACCA 59.840 37.500 0.00 0.00 33.30 3.67
21 22 4.506288 GTGGTCAAGTTACAATTTGCAACC 59.494 41.667 0.00 0.00 0.00 3.77
22 23 5.105752 TGTGGTCAAGTTACAATTTGCAAC 58.894 37.500 0.00 4.60 0.00 4.17
23 24 5.330455 TGTGGTCAAGTTACAATTTGCAA 57.670 34.783 0.00 0.00 0.00 4.08
24 25 4.991153 TGTGGTCAAGTTACAATTTGCA 57.009 36.364 0.00 0.00 0.00 4.08
25 26 4.150451 GCATGTGGTCAAGTTACAATTTGC 59.850 41.667 0.00 0.00 0.00 3.68
26 27 5.288015 TGCATGTGGTCAAGTTACAATTTG 58.712 37.500 0.00 0.00 0.00 2.32
27 28 5.528043 TGCATGTGGTCAAGTTACAATTT 57.472 34.783 0.00 0.00 0.00 1.82
28 29 5.243507 TCATGCATGTGGTCAAGTTACAATT 59.756 36.000 25.43 0.00 0.00 2.32
29 30 4.766373 TCATGCATGTGGTCAAGTTACAAT 59.234 37.500 25.43 0.00 0.00 2.71
30 31 4.023279 GTCATGCATGTGGTCAAGTTACAA 60.023 41.667 25.43 0.00 0.00 2.41
31 32 3.501828 GTCATGCATGTGGTCAAGTTACA 59.498 43.478 25.43 0.00 0.00 2.41
32 33 3.753272 AGTCATGCATGTGGTCAAGTTAC 59.247 43.478 25.43 12.39 0.00 2.50
33 34 4.019792 AGTCATGCATGTGGTCAAGTTA 57.980 40.909 25.43 0.00 0.00 2.24
34 35 2.867624 AGTCATGCATGTGGTCAAGTT 58.132 42.857 25.43 0.62 0.00 2.66
35 36 2.555325 CAAGTCATGCATGTGGTCAAGT 59.445 45.455 25.43 5.98 0.00 3.16
36 37 2.815503 TCAAGTCATGCATGTGGTCAAG 59.184 45.455 25.43 10.79 0.00 3.02
37 38 2.861274 TCAAGTCATGCATGTGGTCAA 58.139 42.857 25.43 2.81 0.00 3.18
38 39 2.565046 TCAAGTCATGCATGTGGTCA 57.435 45.000 25.43 3.60 0.00 4.02
39 40 3.011818 TCATCAAGTCATGCATGTGGTC 58.988 45.455 25.43 14.28 0.00 4.02
40 41 3.076079 TCATCAAGTCATGCATGTGGT 57.924 42.857 25.43 10.98 0.00 4.16
41 42 3.380320 ACATCATCAAGTCATGCATGTGG 59.620 43.478 25.43 13.51 30.18 4.17
42 43 4.351192 CACATCATCAAGTCATGCATGTG 58.649 43.478 25.43 16.78 36.75 3.21
43 44 3.380320 CCACATCATCAAGTCATGCATGT 59.620 43.478 25.43 5.20 30.81 3.21
44 45 3.795488 GCCACATCATCAAGTCATGCATG 60.795 47.826 21.07 21.07 0.00 4.06
45 46 2.361119 GCCACATCATCAAGTCATGCAT 59.639 45.455 0.00 0.00 0.00 3.96
46 47 1.746787 GCCACATCATCAAGTCATGCA 59.253 47.619 0.00 0.00 0.00 3.96
47 48 1.746787 TGCCACATCATCAAGTCATGC 59.253 47.619 0.00 0.00 0.00 4.06
48 49 4.820173 ACTATGCCACATCATCAAGTCATG 59.180 41.667 0.00 0.00 0.00 3.07
49 50 5.045012 ACTATGCCACATCATCAAGTCAT 57.955 39.130 0.00 0.00 0.00 3.06
50 51 4.492494 ACTATGCCACATCATCAAGTCA 57.508 40.909 0.00 0.00 0.00 3.41
51 52 5.165911 CAACTATGCCACATCATCAAGTC 57.834 43.478 0.00 0.00 0.00 3.01
66 67 8.133627 CCTATTTTTCCTCTTCATGCAACTATG 58.866 37.037 0.00 0.00 0.00 2.23
67 68 7.836183 ACCTATTTTTCCTCTTCATGCAACTAT 59.164 33.333 0.00 0.00 0.00 2.12
68 69 7.175104 ACCTATTTTTCCTCTTCATGCAACTA 58.825 34.615 0.00 0.00 0.00 2.24
69 70 6.012745 ACCTATTTTTCCTCTTCATGCAACT 58.987 36.000 0.00 0.00 0.00 3.16
70 71 6.272822 ACCTATTTTTCCTCTTCATGCAAC 57.727 37.500 0.00 0.00 0.00 4.17
71 72 7.121168 CACTACCTATTTTTCCTCTTCATGCAA 59.879 37.037 0.00 0.00 0.00 4.08
72 73 6.599244 CACTACCTATTTTTCCTCTTCATGCA 59.401 38.462 0.00 0.00 0.00 3.96
73 74 6.038714 CCACTACCTATTTTTCCTCTTCATGC 59.961 42.308 0.00 0.00 0.00 4.06
74 75 6.543831 CCCACTACCTATTTTTCCTCTTCATG 59.456 42.308 0.00 0.00 0.00 3.07
75 76 6.217693 ACCCACTACCTATTTTTCCTCTTCAT 59.782 38.462 0.00 0.00 0.00 2.57
76 77 5.550403 ACCCACTACCTATTTTTCCTCTTCA 59.450 40.000 0.00 0.00 0.00 3.02
77 78 6.063496 ACCCACTACCTATTTTTCCTCTTC 57.937 41.667 0.00 0.00 0.00 2.87
78 79 6.246163 CAACCCACTACCTATTTTTCCTCTT 58.754 40.000 0.00 0.00 0.00 2.85
79 80 5.806734 GCAACCCACTACCTATTTTTCCTCT 60.807 44.000 0.00 0.00 0.00 3.69
80 81 4.398358 GCAACCCACTACCTATTTTTCCTC 59.602 45.833 0.00 0.00 0.00 3.71
81 82 4.202631 TGCAACCCACTACCTATTTTTCCT 60.203 41.667 0.00 0.00 0.00 3.36
82 83 4.083565 TGCAACCCACTACCTATTTTTCC 58.916 43.478 0.00 0.00 0.00 3.13
83 84 5.243060 AGTTGCAACCCACTACCTATTTTTC 59.757 40.000 25.62 0.00 0.00 2.29
84 85 5.144832 AGTTGCAACCCACTACCTATTTTT 58.855 37.500 25.62 0.00 0.00 1.94
85 86 4.736473 AGTTGCAACCCACTACCTATTTT 58.264 39.130 25.62 0.00 0.00 1.82
86 87 4.382386 AGTTGCAACCCACTACCTATTT 57.618 40.909 25.62 0.00 0.00 1.40
87 88 5.710409 ATAGTTGCAACCCACTACCTATT 57.290 39.130 25.62 5.42 0.00 1.73
88 89 5.710409 AATAGTTGCAACCCACTACCTAT 57.290 39.130 25.62 11.34 0.00 2.57
89 90 5.508280 AAATAGTTGCAACCCACTACCTA 57.492 39.130 25.62 9.48 0.00 3.08
90 91 4.382386 AAATAGTTGCAACCCACTACCT 57.618 40.909 25.62 7.43 0.00 3.08
91 92 6.578163 TTTAAATAGTTGCAACCCACTACC 57.422 37.500 25.62 0.00 0.00 3.18
94 95 9.084533 TCTATTTTTAAATAGTTGCAACCCACT 57.915 29.630 25.62 10.04 45.10 4.00
95 96 9.353999 CTCTATTTTTAAATAGTTGCAACCCAC 57.646 33.333 25.62 1.42 45.10 4.61
96 97 8.527810 CCTCTATTTTTAAATAGTTGCAACCCA 58.472 33.333 25.62 14.57 45.10 4.51
97 98 8.745590 TCCTCTATTTTTAAATAGTTGCAACCC 58.254 33.333 25.62 2.00 45.10 4.11
143 144 7.757242 ACTATTTCAGGGAAGGTTCTAGAAT 57.243 36.000 8.75 0.00 0.00 2.40
344 364 9.619316 ACGAATTTGAAATATGTTCGAAAATGA 57.381 25.926 15.57 0.00 42.94 2.57
345 365 9.660825 CACGAATTTGAAATATGTTCGAAAATG 57.339 29.630 15.57 3.07 42.94 2.32
346 366 9.619316 TCACGAATTTGAAATATGTTCGAAAAT 57.381 25.926 15.57 6.02 42.94 1.82
348 368 8.897809 GTTCACGAATTTGAAATATGTTCGAAA 58.102 29.630 15.57 8.33 42.94 3.46
349 369 8.070769 TGTTCACGAATTTGAAATATGTTCGAA 58.929 29.630 15.57 0.00 42.94 3.71
350 370 7.577107 TGTTCACGAATTTGAAATATGTTCGA 58.423 30.769 15.57 0.33 42.94 3.71
442 462 6.183360 TGGGAAATTGTACGAAATGTTCACAA 60.183 34.615 0.00 0.00 32.41 3.33
451 471 6.642707 ACATTCTTGGGAAATTGTACGAAA 57.357 33.333 0.00 0.00 34.90 3.46
454 474 5.567534 CGAAACATTCTTGGGAAATTGTACG 59.432 40.000 0.00 0.00 34.90 3.67
455 475 6.674066 TCGAAACATTCTTGGGAAATTGTAC 58.326 36.000 0.00 0.00 34.90 2.90
469 489 7.725610 AAATGATCGTGATTTCGAAACATTC 57.274 32.000 13.81 7.88 42.79 2.67
470 490 9.787532 AATAAATGATCGTGATTTCGAAACATT 57.212 25.926 13.81 12.88 43.93 2.71
526 566 9.160576 TGATCGTAACTTTTAAAACATTGTTCG 57.839 29.630 1.83 9.65 0.00 3.95
612 652 9.844257 AAAATAATGTTTCCCAATGTCAAGAAA 57.156 25.926 0.00 0.00 0.00 2.52
640 680 9.720667 GCTCAAAAACATTTAGAAAAAGCAAAT 57.279 25.926 0.00 0.00 0.00 2.32
663 703 9.909644 AGATATTCATGATTTGCTTAAATGCTC 57.090 29.630 0.00 0.00 0.00 4.26
755 797 9.339850 TGGTCATGAATTCAAAAATTGTTCATT 57.660 25.926 13.09 0.00 35.46 2.57
867 919 1.202348 GCCCCTGTTTTCTCCATTTCG 59.798 52.381 0.00 0.00 0.00 3.46
874 926 3.982829 GGACGCCCCTGTTTTCTC 58.017 61.111 0.00 0.00 0.00 2.87
887 939 2.007049 GCACATGTACAGGAAGGGACG 61.007 57.143 15.54 0.00 0.00 4.79
891 943 0.744414 CCCGCACATGTACAGGAAGG 60.744 60.000 15.54 13.08 0.00 3.46
907 959 2.126734 CAAGCGCTTTTGAGCCCG 60.127 61.111 22.51 2.19 46.64 6.13
918 973 1.153958 GATCCCACAAAGCAAGCGC 60.154 57.895 0.00 0.00 38.99 5.92
926 981 4.418328 CGCCCCCGATCCCACAAA 62.418 66.667 0.00 0.00 36.29 2.83
942 997 0.725117 AAATAGGAAGGAAACGCGCG 59.275 50.000 30.96 30.96 0.00 6.86
968 1023 2.190981 GACAACGTATTAGGCGACCTG 58.809 52.381 8.44 0.00 34.61 4.00
970 1025 1.564207 GGACAACGTATTAGGCGACC 58.436 55.000 0.00 0.00 0.00 4.79
998 1053 0.165727 CGCAGTTGCACGCTTCATAA 59.834 50.000 4.84 0.00 42.21 1.90
999 1054 1.787215 CGCAGTTGCACGCTTCATA 59.213 52.632 4.84 0.00 42.21 2.15
1022 1079 6.051179 AGTTGGAAAGTCCTATACTCAACC 57.949 41.667 0.00 0.00 39.52 3.77
1024 1081 8.483758 GGATAAGTTGGAAAGTCCTATACTCAA 58.516 37.037 0.00 0.00 37.50 3.02
1026 1083 8.019656 TGGATAAGTTGGAAAGTCCTATACTC 57.980 38.462 0.00 0.00 37.50 2.59
1041 1098 2.936498 CGGCTGTAGGTTGGATAAGTTG 59.064 50.000 0.00 0.00 0.00 3.16
1047 1104 2.590092 GGCGGCTGTAGGTTGGAT 59.410 61.111 0.00 0.00 0.00 3.41
1069 1129 3.492311 GAGCGGAGGCGACTGGATC 62.492 68.421 0.00 0.00 44.43 3.36
1118 1178 0.753848 GAAGAGGAGGGAGACGGAGG 60.754 65.000 0.00 0.00 0.00 4.30
1136 1196 2.276116 GGAGTGGACAGCTCACCGA 61.276 63.158 0.65 0.00 35.87 4.69
1144 1204 0.610687 GTTGAGGGAGGAGTGGACAG 59.389 60.000 0.00 0.00 0.00 3.51
1199 1259 2.892425 GATGTCAGCCGGCGAAGG 60.892 66.667 23.20 12.51 0.00 3.46
1219 1279 2.073101 CAGGGTTAGAGGGAGGCCC 61.073 68.421 0.00 0.00 45.90 5.80
1223 1283 0.761802 GATGGCAGGGTTAGAGGGAG 59.238 60.000 0.00 0.00 0.00 4.30
1324 1409 6.675413 AAGTAATAGGGAATGCCGTGTATA 57.325 37.500 0.00 0.00 33.56 1.47
1326 1411 5.362105 AAAGTAATAGGGAATGCCGTGTA 57.638 39.130 0.00 0.00 33.56 2.90
1327 1412 3.926058 AAGTAATAGGGAATGCCGTGT 57.074 42.857 0.00 0.00 33.56 4.49
1328 1413 6.687081 TTAAAAGTAATAGGGAATGCCGTG 57.313 37.500 0.00 0.00 33.56 4.94
1329 1414 7.340999 ACATTTAAAAGTAATAGGGAATGCCGT 59.659 33.333 0.00 0.00 36.08 5.68
1331 1416 9.313118 CAACATTTAAAAGTAATAGGGAATGCC 57.687 33.333 0.00 0.00 0.00 4.40
1337 1422 9.516314 GCTAAGCAACATTTAAAAGTAATAGGG 57.484 33.333 0.00 0.00 0.00 3.53
1371 1460 0.473755 AGGCACACAATCAGTCACCA 59.526 50.000 0.00 0.00 0.00 4.17
1395 1503 2.743636 AAAATCTGACTCGCCGAGAA 57.256 45.000 22.80 7.60 33.32 2.87
1397 1505 1.661112 GGAAAAATCTGACTCGCCGAG 59.339 52.381 13.52 13.52 35.52 4.63
1434 1543 3.742433 AGGAAGCAAGAGATGTATCCG 57.258 47.619 0.00 0.00 39.48 4.18
1474 1583 0.472471 ATCCACAGGTTGGTTCGTGT 59.528 50.000 0.00 0.00 46.97 4.49
1477 1586 2.465860 TACATCCACAGGTTGGTTCG 57.534 50.000 0.00 0.00 46.97 3.95
1523 1632 5.955355 GCCTTATATGTAGGAGATGAGAGGT 59.045 44.000 9.29 0.00 34.56 3.85
1818 3125 5.831997 ACTTTCCAACACTATTGCAAGTTC 58.168 37.500 4.94 0.00 0.00 3.01
1819 3126 5.852282 ACTTTCCAACACTATTGCAAGTT 57.148 34.783 4.94 0.08 0.00 2.66
1886 3196 9.100007 AGTTGTTAAAAACGTGTGCAAAAAGCA 62.100 33.333 2.83 0.00 42.25 3.91
1887 3197 4.947420 TGTTAAAAACGTGTGCAAAAAGC 58.053 34.783 0.00 0.00 45.96 3.51
1888 3198 6.585852 AGTTGTTAAAAACGTGTGCAAAAAG 58.414 32.000 2.83 0.00 35.13 2.27
1889 3199 6.200286 TGAGTTGTTAAAAACGTGTGCAAAAA 59.800 30.769 2.83 0.00 35.13 1.94
1918 3235 5.852282 AAAACCACAATTGTAAGTGCTCT 57.148 34.783 11.53 0.00 34.48 4.09
2038 3356 1.087501 GGTCGTTTTGGATGGAGCTC 58.912 55.000 4.71 4.71 0.00 4.09
2055 3373 3.612681 CCAGACGACACCACGGGT 61.613 66.667 0.00 0.00 37.61 5.28
2125 3450 3.004862 TGCTACTGCAGATCAATGTGTG 58.995 45.455 23.35 0.00 45.31 3.82
2198 3524 6.150396 AGACGGATTGTGTTCTATAGGAAG 57.850 41.667 0.00 0.00 34.23 3.46
2464 3796 1.218316 CAGCCCTAACAGTCCCGTC 59.782 63.158 0.00 0.00 0.00 4.79
2539 3871 0.334676 ATGAGGGGCGGAATTTCCAA 59.665 50.000 15.58 0.00 35.91 3.53
2626 4395 1.602377 CTCGGAAGGCGTTGAAACTTT 59.398 47.619 0.00 0.00 0.00 2.66
2627 4396 1.202604 TCTCGGAAGGCGTTGAAACTT 60.203 47.619 0.00 0.00 0.00 2.66
2628 4397 0.391597 TCTCGGAAGGCGTTGAAACT 59.608 50.000 0.00 0.00 0.00 2.66
2773 4581 6.998968 AAATCAACAAGGTTTGCATCAAAA 57.001 29.167 0.00 0.00 35.03 2.44
2809 4618 1.150081 GCCATCACCAGCCTAGCAT 59.850 57.895 0.00 0.00 0.00 3.79
3152 6804 4.787135 TGGTCCAGGTGCAAATATATCA 57.213 40.909 0.00 0.00 0.00 2.15
3188 6841 3.717707 TGCCAATAATCGTAGTGAGCTC 58.282 45.455 6.82 6.82 0.00 4.09
3225 6878 6.266131 AGAGGGCTTATTGGTCATGATTTA 57.734 37.500 0.00 0.00 0.00 1.40
3360 7024 6.246420 GAGTTACAAGGTGTCGTAAGTCTA 57.754 41.667 9.00 0.00 41.61 2.59
3376 7040 3.136763 CCTATAGACGCCGAGAGTTACA 58.863 50.000 0.00 0.00 0.00 2.41
3377 7041 2.095819 GCCTATAGACGCCGAGAGTTAC 60.096 54.545 0.00 0.00 0.00 2.50
3425 7089 6.119536 TGAATGTATGGAACCCATGTAGAAC 58.880 40.000 8.64 0.00 44.84 3.01
3436 7100 7.378181 AGACCAAAAACATGAATGTATGGAAC 58.622 34.615 20.77 15.68 40.80 3.62
3473 7137 2.869801 TCAAATCCACGACAGAACACAC 59.130 45.455 0.00 0.00 0.00 3.82
3766 7437 4.148825 CGCTTACGCCAGGGCTCT 62.149 66.667 8.91 0.00 39.32 4.09
3905 7593 1.400494 GAGAGAGAGACAACGAGAGCC 59.600 57.143 0.00 0.00 0.00 4.70
3913 7624 2.569853 AGAGAGGACGAGAGAGAGACAA 59.430 50.000 0.00 0.00 0.00 3.18
4039 7765 2.750166 CTGATACCAGACTGTCACGACT 59.250 50.000 10.88 0.00 43.02 4.18
4086 7815 0.102300 AAAAATATTCGCAGCCCGGC 59.898 50.000 0.00 0.00 37.59 6.13
4137 7871 0.469331 CCTAGGGTGATCCGCTACCA 60.469 60.000 0.00 0.00 41.52 3.25
4170 7904 1.080498 ACCCACCTCAGGTCAGGATTA 59.920 52.381 15.47 0.00 36.96 1.75
4458 8192 1.228094 TGAACCGCATGGAAGTGCA 60.228 52.632 0.00 0.00 45.30 4.57
4488 8222 4.228567 TCTCGCCCAACGTGTGCA 62.229 61.111 0.00 0.00 44.19 4.57
4525 8259 1.410517 AGTATGCCATCTGACACCTCG 59.589 52.381 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.