Multiple sequence alignment - TraesCS5A01G089000

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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 TraesCS5A01G089000 chr5A 100.000 4445 0 0 1 4445 119217730 119222174 0.000000e+00 8209.0
1 TraesCS5A01G089000 chr5A 100.000 3643 0 0 4724 8366 119222453 119226095 0.000000e+00 6728.0
2 TraesCS5A01G089000 chr5A 82.255 603 76 15 2182 2768 475332727 475333314 7.540000e-135 492.0
3 TraesCS5A01G089000 chr5A 88.889 360 39 1 1674 2032 475332261 475332620 7.710000e-120 442.0
4 TraesCS5A01G089000 chr5A 77.500 520 76 15 4724 5204 438845678 438846195 2.980000e-69 274.0
5 TraesCS5A01G089000 chr5A 74.629 607 111 25 2978 3554 52440700 52441293 2.350000e-55 228.0
6 TraesCS5A01G089000 chr5A 92.857 56 1 1 8242 8297 119225917 119225969 2.500000e-10 78.7
7 TraesCS5A01G089000 chr5A 92.857 56 1 1 8188 8240 119225971 119226026 2.500000e-10 78.7
8 TraesCS5A01G089000 chr5D 95.101 2715 71 21 5579 8240 114009722 114012427 0.000000e+00 4220.0
9 TraesCS5A01G089000 chr5D 94.386 1710 45 20 2772 4437 114006155 114007857 0.000000e+00 2579.0
10 TraesCS5A01G089000 chr5D 93.400 1606 52 18 1 1586 114004396 114005967 0.000000e+00 2329.0
11 TraesCS5A01G089000 chr5D 95.823 838 17 8 4758 5579 114008540 114009375 0.000000e+00 1338.0
12 TraesCS5A01G089000 chr5D 76.840 557 88 24 3020 3547 63108190 63108734 8.270000e-70 276.0
13 TraesCS5A01G089000 chr5D 79.448 326 40 18 3735 4058 419370179 419369879 1.100000e-48 206.0
14 TraesCS5A01G089000 chr5D 95.312 128 2 2 8242 8366 114012370 114012496 5.120000e-47 200.0
15 TraesCS5A01G089000 chr5D 88.194 144 8 4 2784 2924 119679897 119679760 6.720000e-36 163.0
16 TraesCS5A01G089000 chr5D 92.793 111 8 0 2805 2915 457705446 457705556 2.420000e-35 161.0
17 TraesCS5A01G089000 chr5D 92.308 52 3 1 7821 7871 350373565 350373616 1.160000e-08 73.1
18 TraesCS5A01G089000 chr5D 93.750 48 3 0 7824 7871 537690076 537690029 1.160000e-08 73.1
19 TraesCS5A01G089000 chr5D 89.091 55 6 0 7817 7871 281011051 281011105 1.510000e-07 69.4
20 TraesCS5A01G089000 chr5D 89.286 56 5 1 7817 7871 509542672 509542727 1.510000e-07 69.4
21 TraesCS5A01G089000 chr5B 90.850 1530 60 26 1 1525 124766044 124767498 0.000000e+00 1977.0
22 TraesCS5A01G089000 chr5B 95.048 1050 44 2 6538 7579 124771334 124772383 0.000000e+00 1644.0
23 TraesCS5A01G089000 chr5B 87.559 852 63 22 5639 6479 124770504 124771323 0.000000e+00 946.0
24 TraesCS5A01G089000 chr5B 90.967 631 25 11 7629 8240 124772536 124773153 0.000000e+00 821.0
25 TraesCS5A01G089000 chr5B 85.667 300 28 9 5226 5516 124767529 124767822 1.360000e-77 302.0
26 TraesCS5A01G089000 chr5B 87.560 209 26 0 3804 4012 396514438 396514646 8.390000e-60 243.0
27 TraesCS5A01G089000 chr5B 79.714 350 55 4 4884 5218 396515808 396516156 1.090000e-58 239.0
28 TraesCS5A01G089000 chr5B 98.400 125 2 0 8242 8366 124773098 124773222 3.930000e-53 220.0
29 TraesCS5A01G089000 chr5B 78.218 303 59 4 4096 4393 463888599 463888299 3.990000e-43 187.0
30 TraesCS5A01G089000 chr5B 82.946 129 9 8 2058 2178 185188073 185187950 4.130000e-18 104.0
31 TraesCS5A01G089000 chr5B 85.047 107 8 7 2075 2178 185202740 185202639 1.490000e-17 102.0
32 TraesCS5A01G089000 chr4A 96.286 1104 29 2 1672 2775 317421441 317422532 0.000000e+00 1801.0
33 TraesCS5A01G089000 chr4A 95.993 1098 36 2 1674 2771 319489036 319490125 0.000000e+00 1777.0
34 TraesCS5A01G089000 chr4A 78.918 721 106 25 3735 4423 571489635 571490341 1.660000e-121 448.0
35 TraesCS5A01G089000 chr4A 75.954 524 109 10 3325 3835 627817314 627817833 3.880000e-63 254.0
36 TraesCS5A01G089000 chr4A 95.918 49 2 0 7821 7869 143701510 143701462 6.960000e-11 80.5
37 TraesCS5A01G089000 chr4B 94.475 1104 35 8 1673 2776 511156978 511155901 0.000000e+00 1677.0
38 TraesCS5A01G089000 chr4B 79.118 680 113 26 3756 4423 44934351 44933689 7.710000e-120 442.0
39 TraesCS5A01G089000 chr4B 86.694 248 31 2 1667 1914 439192237 439192482 2.980000e-69 274.0
40 TraesCS5A01G089000 chr4B 90.323 186 17 1 2586 2771 439193014 439193198 8.390000e-60 243.0
41 TraesCS5A01G089000 chr4B 87.692 195 21 2 2580 2772 448308343 448308536 3.040000e-54 224.0
42 TraesCS5A01G089000 chr4B 81.197 234 38 3 4196 4429 550399997 550399770 5.160000e-42 183.0
43 TraesCS5A01G089000 chr4B 96.154 52 2 0 7820 7871 406677741 406677792 1.500000e-12 86.1
44 TraesCS5A01G089000 chr4B 94.118 51 3 0 7821 7871 648507635 648507685 2.500000e-10 78.7
45 TraesCS5A01G089000 chr4B 100.000 35 0 0 2255 2289 511156550 511156516 1.950000e-06 65.8
46 TraesCS5A01G089000 chr2B 93.557 1102 39 7 1674 2775 606944470 606943401 0.000000e+00 1613.0
47 TraesCS5A01G089000 chr2B 78.846 520 82 14 4726 5218 653812019 653812537 8.100000e-85 326.0
48 TraesCS5A01G089000 chr2B 88.652 141 10 4 2775 2915 748510304 748510170 5.190000e-37 167.0
49 TraesCS5A01G089000 chr2B 85.816 141 13 5 2776 2915 783945037 783945171 8.750000e-30 143.0
50 TraesCS5A01G089000 chr2B 96.154 52 2 0 7820 7871 607540361 607540310 1.500000e-12 86.1
51 TraesCS5A01G089000 chr2B 100.000 35 0 0 2255 2289 606944038 606944004 1.950000e-06 65.8
52 TraesCS5A01G089000 chr7D 95.267 655 21 2 2114 2768 91712359 91711715 0.000000e+00 1029.0
53 TraesCS5A01G089000 chr7D 76.971 799 132 30 3042 3814 563833194 563832422 7.820000e-110 409.0
54 TraesCS5A01G089000 chr7D 85.811 148 14 3 2775 2922 618322840 618322980 5.230000e-32 150.0
55 TraesCS5A01G089000 chr7D 100.000 35 0 0 2255 2289 91712359 91712325 1.950000e-06 65.8
56 TraesCS5A01G089000 chr3D 78.197 1220 183 33 3240 4428 303590140 303588973 0.000000e+00 702.0
57 TraesCS5A01G089000 chr3D 79.609 971 133 39 1668 2594 26281690 26280741 3.290000e-178 636.0
58 TraesCS5A01G089000 chr3D 92.857 56 2 2 7818 7871 437356643 437356588 6.960000e-11 80.5
59 TraesCS5A01G089000 chr3D 92.593 54 3 1 7819 7871 115034941 115034888 9.000000e-10 76.8
60 TraesCS5A01G089000 chr6D 83.204 774 109 12 3105 3863 16254268 16255035 0.000000e+00 689.0
61 TraesCS5A01G089000 chr6D 77.258 897 164 24 2966 3829 463465932 463466821 2.710000e-134 490.0
62 TraesCS5A01G089000 chr6D 79.615 260 53 0 4134 4393 325750995 325750736 3.990000e-43 187.0
63 TraesCS5A01G089000 chr6D 83.117 154 13 7 1524 1670 328823435 328823582 2.450000e-25 128.0
64 TraesCS5A01G089000 chr6D 82.895 152 14 10 1526 1672 444451365 444451509 8.820000e-25 126.0
65 TraesCS5A01G089000 chr6D 97.872 47 0 1 7824 7870 97784091 97784046 6.960000e-11 80.5
66 TraesCS5A01G089000 chr6D 90.196 51 5 0 7821 7871 84087409 84087459 5.420000e-07 67.6
67 TraesCS5A01G089000 chr6D 91.667 48 4 0 7824 7871 348081798 348081751 5.420000e-07 67.6
68 TraesCS5A01G089000 chr6D 93.023 43 3 0 7825 7867 453317916 453317958 7.010000e-06 63.9
69 TraesCS5A01G089000 chr1D 80.808 891 64 39 1951 2776 310105955 310105107 4.320000e-167 599.0
70 TraesCS5A01G089000 chr1D 95.868 242 8 2 1674 1915 310106184 310105945 2.830000e-104 390.0
71 TraesCS5A01G089000 chr1D 92.793 111 8 0 2805 2915 179438883 179438773 2.420000e-35 161.0
72 TraesCS5A01G089000 chr1D 84.516 155 18 4 1524 1672 43282784 43282938 1.880000e-31 148.0
73 TraesCS5A01G089000 chr1D 82.468 154 18 7 1524 1673 107397742 107397594 8.820000e-25 126.0
74 TraesCS5A01G089000 chr1D 83.065 124 12 3 7821 7936 205971703 205971581 4.130000e-18 104.0
75 TraesCS5A01G089000 chr6B 78.499 893 154 26 2966 3829 706742823 706743706 1.230000e-152 551.0
76 TraesCS5A01G089000 chr6B 79.483 619 91 24 3287 3888 226149063 226148464 2.810000e-109 407.0
77 TraesCS5A01G089000 chr3B 81.119 715 99 22 3729 4433 417716840 417717528 2.660000e-149 540.0
78 TraesCS5A01G089000 chr3B 84.615 65 10 0 7867 7931 757955758 757955694 1.950000e-06 65.8
79 TraesCS5A01G089000 chr6A 76.377 1126 183 59 3286 4368 151507925 151509010 5.750000e-146 529.0
80 TraesCS5A01G089000 chr6A 82.803 157 16 7 1524 1672 10080134 10080287 6.810000e-26 130.0
81 TraesCS5A01G089000 chr2D 78.109 772 88 36 2058 2773 186650409 186651155 1.680000e-111 414.0
82 TraesCS5A01G089000 chr2D 77.892 778 92 35 2058 2780 348615277 348614525 2.170000e-110 411.0
83 TraesCS5A01G089000 chr2D 86.986 146 10 2 2775 2920 332586606 332586470 1.120000e-33 156.0
84 TraesCS5A01G089000 chr2D 94.118 51 3 0 7821 7871 506399517 506399567 2.500000e-10 78.7
85 TraesCS5A01G089000 chr1A 76.837 803 132 32 3108 3888 71557862 71557092 3.640000e-108 403.0
86 TraesCS5A01G089000 chr1A 86.420 243 32 1 1672 1914 223220599 223220358 1.790000e-66 265.0
87 TraesCS5A01G089000 chr1A 84.091 132 19 2 2318 2449 223220087 223219958 8.820000e-25 126.0
88 TraesCS5A01G089000 chr1A 93.750 48 3 0 7824 7871 571680870 571680917 1.160000e-08 73.1
89 TraesCS5A01G089000 chr1A 93.750 48 2 1 7821 7868 428194545 428194591 4.190000e-08 71.3
90 TraesCS5A01G089000 chr1A 90.385 52 5 0 7820 7871 394592836 394592785 1.510000e-07 69.4
91 TraesCS5A01G089000 chr1A 94.737 38 2 0 2252 2289 223220323 223220286 9.070000e-05 60.2
92 TraesCS5A01G089000 chr3A 78.439 538 95 11 3345 3868 523331279 523330749 1.740000e-86 331.0
93 TraesCS5A01G089000 chr3A 88.608 237 27 0 1669 1905 95026281 95026045 1.060000e-73 289.0
94 TraesCS5A01G089000 chr3A 89.147 129 6 4 2058 2179 95024359 95024232 4.040000e-33 154.0
95 TraesCS5A01G089000 chr3A 85.161 155 10 11 1524 1672 12382041 12381894 6.770000e-31 147.0
96 TraesCS5A01G089000 chr3A 83.117 154 17 7 1522 1670 44305370 44305519 1.890000e-26 132.0
97 TraesCS5A01G089000 chr4D 75.064 778 134 39 2982 3729 99278429 99277682 2.930000e-79 307.0
98 TraesCS5A01G089000 chr4D 94.231 52 3 0 7818 7869 327379504 327379555 6.960000e-11 80.5
99 TraesCS5A01G089000 chr7B 87.943 141 11 1 2775 2915 259140248 259140114 2.420000e-35 161.0
100 TraesCS5A01G089000 chrUn 84.416 154 11 11 1524 1672 93062839 93062694 1.130000e-28 139.0
101 TraesCS5A01G089000 chrUn 83.226 155 13 10 1524 1672 129542152 129542005 6.810000e-26 130.0
102 TraesCS5A01G089000 chr2A 96.154 52 2 0 7820 7871 659894414 659894363 1.500000e-12 86.1
103 TraesCS5A01G089000 chr7A 75.000 220 31 13 7814 8014 506142120 506141906 6.960000e-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 TraesCS5A01G089000 chr5A 119217730 119226095 8365 False 3773.6 8209 96.428500 1 8366 4 chr5A.!!$F3 8365
1 TraesCS5A01G089000 chr5A 475332261 475333314 1053 False 467.0 492 85.572000 1674 2768 2 chr5A.!!$F4 1094
2 TraesCS5A01G089000 chr5A 438845678 438846195 517 False 274.0 274 77.500000 4724 5204 1 chr5A.!!$F2 480
3 TraesCS5A01G089000 chr5A 52440700 52441293 593 False 228.0 228 74.629000 2978 3554 1 chr5A.!!$F1 576
4 TraesCS5A01G089000 chr5D 114004396 114012496 8100 False 2133.2 4220 94.804400 1 8366 5 chr5D.!!$F6 8365
5 TraesCS5A01G089000 chr5D 63108190 63108734 544 False 276.0 276 76.840000 3020 3547 1 chr5D.!!$F1 527
6 TraesCS5A01G089000 chr5B 124766044 124773222 7178 False 985.0 1977 91.415167 1 8366 6 chr5B.!!$F1 8365
7 TraesCS5A01G089000 chr5B 396514438 396516156 1718 False 241.0 243 83.637000 3804 5218 2 chr5B.!!$F2 1414
8 TraesCS5A01G089000 chr4A 317421441 317422532 1091 False 1801.0 1801 96.286000 1672 2775 1 chr4A.!!$F1 1103
9 TraesCS5A01G089000 chr4A 319489036 319490125 1089 False 1777.0 1777 95.993000 1674 2771 1 chr4A.!!$F2 1097
10 TraesCS5A01G089000 chr4A 571489635 571490341 706 False 448.0 448 78.918000 3735 4423 1 chr4A.!!$F3 688
11 TraesCS5A01G089000 chr4A 627817314 627817833 519 False 254.0 254 75.954000 3325 3835 1 chr4A.!!$F4 510
12 TraesCS5A01G089000 chr4B 511155901 511156978 1077 True 871.4 1677 97.237500 1673 2776 2 chr4B.!!$R3 1103
13 TraesCS5A01G089000 chr4B 44933689 44934351 662 True 442.0 442 79.118000 3756 4423 1 chr4B.!!$R1 667
14 TraesCS5A01G089000 chr4B 439192237 439193198 961 False 258.5 274 88.508500 1667 2771 2 chr4B.!!$F4 1104
15 TraesCS5A01G089000 chr2B 606943401 606944470 1069 True 839.4 1613 96.778500 1674 2775 2 chr2B.!!$R3 1101
16 TraesCS5A01G089000 chr2B 653812019 653812537 518 False 326.0 326 78.846000 4726 5218 1 chr2B.!!$F1 492
17 TraesCS5A01G089000 chr7D 91711715 91712359 644 True 547.4 1029 97.633500 2114 2768 2 chr7D.!!$R2 654
18 TraesCS5A01G089000 chr7D 563832422 563833194 772 True 409.0 409 76.971000 3042 3814 1 chr7D.!!$R1 772
19 TraesCS5A01G089000 chr3D 303588973 303590140 1167 True 702.0 702 78.197000 3240 4428 1 chr3D.!!$R3 1188
20 TraesCS5A01G089000 chr3D 26280741 26281690 949 True 636.0 636 79.609000 1668 2594 1 chr3D.!!$R1 926
21 TraesCS5A01G089000 chr6D 16254268 16255035 767 False 689.0 689 83.204000 3105 3863 1 chr6D.!!$F1 758
22 TraesCS5A01G089000 chr6D 463465932 463466821 889 False 490.0 490 77.258000 2966 3829 1 chr6D.!!$F6 863
23 TraesCS5A01G089000 chr1D 310105107 310106184 1077 True 494.5 599 88.338000 1674 2776 2 chr1D.!!$R4 1102
24 TraesCS5A01G089000 chr6B 706742823 706743706 883 False 551.0 551 78.499000 2966 3829 1 chr6B.!!$F1 863
25 TraesCS5A01G089000 chr6B 226148464 226149063 599 True 407.0 407 79.483000 3287 3888 1 chr6B.!!$R1 601
26 TraesCS5A01G089000 chr3B 417716840 417717528 688 False 540.0 540 81.119000 3729 4433 1 chr3B.!!$F1 704
27 TraesCS5A01G089000 chr6A 151507925 151509010 1085 False 529.0 529 76.377000 3286 4368 1 chr6A.!!$F2 1082
28 TraesCS5A01G089000 chr2D 186650409 186651155 746 False 414.0 414 78.109000 2058 2773 1 chr2D.!!$F1 715
29 TraesCS5A01G089000 chr2D 348614525 348615277 752 True 411.0 411 77.892000 2058 2780 1 chr2D.!!$R2 722
30 TraesCS5A01G089000 chr1A 71557092 71557862 770 True 403.0 403 76.837000 3108 3888 1 chr1A.!!$R1 780
31 TraesCS5A01G089000 chr3A 523330749 523331279 530 True 331.0 331 78.439000 3345 3868 1 chr3A.!!$R2 523
32 TraesCS5A01G089000 chr3A 95024232 95026281 2049 True 221.5 289 88.877500 1669 2179 2 chr3A.!!$R3 510
33 TraesCS5A01G089000 chr4D 99277682 99278429 747 True 307.0 307 75.064000 2982 3729 1 chr4D.!!$R1 747

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
948 966 0.252284 AGAGGGGAAGCGAAGAAGGA 60.252 55.000 0.00 0.00 0.00 3.36 F
1007 1025 0.953471 CTGCGGACCCAAATGACGAA 60.953 55.000 0.00 0.00 0.00 3.85 F
1434 1453 2.939103 ACAAAATACTCAGATGCTCGCC 59.061 45.455 0.00 0.00 0.00 5.54 F
1711 1835 3.067180 CGGAATGAAGTGGAATGGAATGG 59.933 47.826 0.00 0.00 0.00 3.16 F
3103 5096 1.299089 GCTCGGTGTTTGGTTGCAC 60.299 57.895 0.00 0.00 35.07 4.57 F
3620 5723 1.972660 GAACCCTAGTGGCATCGGCT 61.973 60.000 0.00 0.00 40.87 5.52 F
4989 7876 0.527565 GCGGTGCATCAGGAAACAAT 59.472 50.000 0.00 0.00 0.00 2.71 F
5049 7936 2.029073 CCACGTGCCTCGAGTTGT 59.971 61.111 10.91 0.93 42.86 3.32 F
6221 12029 0.674534 ACCACGGATCGCCTCTTATC 59.325 55.000 0.00 0.00 0.00 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2337 4247 1.589716 GGCAACCTGATGTGCTGGTC 61.590 60.000 0.00 0.0 46.85 4.02 R
2959 4949 0.179234 AAGGGGGCAAAAACCAAACG 59.821 50.000 0.00 0.0 0.00 3.60 R
3103 5096 0.109597 GCATCTGCCCAGAACAAACG 60.110 55.000 1.62 0.0 41.36 3.60 R
3620 5723 1.451504 CACCCAAGCTGGAGTGTCA 59.548 57.895 0.00 0.0 40.96 3.58 R
4959 7846 0.837272 ATGCACCGCCATAACTACCT 59.163 50.000 0.00 0.0 0.00 3.08 R
5613 9592 4.083484 AGGCGCAGTTACACATAAACTTTC 60.083 41.667 10.83 0.0 34.99 2.62 R
6188 11996 1.228245 GTGGTCTCAAGCTGGCCAA 60.228 57.895 7.01 0.0 0.00 4.52 R
6474 12286 1.475034 GGCATAGCCCAGATCGTCAAA 60.475 52.381 0.00 0.0 44.06 2.69 R
7610 13550 0.894835 GTTGCCATACCCCCAAAGTG 59.105 55.000 0.00 0.0 0.00 3.16 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
97 98 9.402320 CTCCTATAGAAATCCGATATGAGAAGA 57.598 37.037 0.00 0.00 31.62 2.87
104 105 9.703892 AGAAATCCGATATGAGAAGATTTAGTG 57.296 33.333 0.00 0.00 37.30 2.74
146 147 5.509163 CCATTCCATTGATCAAGCCAATCTC 60.509 44.000 14.54 0.00 32.40 2.75
197 198 9.671279 TGATGAGAAACACATGTCTATAACATT 57.329 29.630 0.00 0.00 46.73 2.71
333 342 0.447801 AAAGAAAGCGTGCTATGGCG 59.552 50.000 0.00 0.00 42.25 5.69
483 499 4.013728 ACGACTCTATTGTTCTCTGCTCT 58.986 43.478 0.00 0.00 0.00 4.09
491 507 2.775856 TTCTCTGCTCTAGCCGCCG 61.776 63.158 0.00 0.00 41.18 6.46
496 512 3.567797 GCTCTAGCCGCCGCTTTG 61.568 66.667 4.51 0.00 45.55 2.77
504 520 3.126879 CGCCGCTTTGCCATCAGA 61.127 61.111 0.00 0.00 0.00 3.27
948 966 0.252284 AGAGGGGAAGCGAAGAAGGA 60.252 55.000 0.00 0.00 0.00 3.36
951 969 1.423921 AGGGGAAGCGAAGAAGGAAAA 59.576 47.619 0.00 0.00 0.00 2.29
952 970 1.813178 GGGGAAGCGAAGAAGGAAAAG 59.187 52.381 0.00 0.00 0.00 2.27
953 971 2.552373 GGGGAAGCGAAGAAGGAAAAGA 60.552 50.000 0.00 0.00 0.00 2.52
954 972 3.146847 GGGAAGCGAAGAAGGAAAAGAA 58.853 45.455 0.00 0.00 0.00 2.52
955 973 3.568430 GGGAAGCGAAGAAGGAAAAGAAA 59.432 43.478 0.00 0.00 0.00 2.52
956 974 4.037565 GGGAAGCGAAGAAGGAAAAGAAAA 59.962 41.667 0.00 0.00 0.00 2.29
1007 1025 0.953471 CTGCGGACCCAAATGACGAA 60.953 55.000 0.00 0.00 0.00 3.85
1434 1453 2.939103 ACAAAATACTCAGATGCTCGCC 59.061 45.455 0.00 0.00 0.00 5.54
1536 1555 5.473273 TGTACCCATGAGACTACCCATAAT 58.527 41.667 0.00 0.00 0.00 1.28
1556 1575 8.739972 CCATAATGGGGATTAACTTAGTAATGC 58.260 37.037 0.00 0.00 32.67 3.56
1559 1578 7.765695 ATGGGGATTAACTTAGTAATGCATG 57.234 36.000 0.00 0.00 34.46 4.06
1560 1579 5.534654 TGGGGATTAACTTAGTAATGCATGC 59.465 40.000 11.82 11.82 34.46 4.06
1561 1580 5.534654 GGGGATTAACTTAGTAATGCATGCA 59.465 40.000 25.04 25.04 34.46 3.96
1562 1581 6.438763 GGGATTAACTTAGTAATGCATGCAC 58.561 40.000 25.37 10.95 34.46 4.57
1624 1748 5.827797 GGGAATAACATATGTGTGGTGTCAT 59.172 40.000 9.63 0.00 38.92 3.06
1643 1767 7.485913 GGTGTCATGCAACACTTCATTTATTAG 59.514 37.037 18.55 0.00 46.96 1.73
1711 1835 3.067180 CGGAATGAAGTGGAATGGAATGG 59.933 47.826 0.00 0.00 0.00 3.16
1712 1836 4.280819 GGAATGAAGTGGAATGGAATGGA 58.719 43.478 0.00 0.00 0.00 3.41
1715 1839 6.550854 GGAATGAAGTGGAATGGAATGGAATA 59.449 38.462 0.00 0.00 0.00 1.75
2078 3925 3.350219 AAGCCACGGTCAAACTATGAT 57.650 42.857 0.00 0.00 40.97 2.45
2079 3926 3.350219 AGCCACGGTCAAACTATGATT 57.650 42.857 0.00 0.00 40.97 2.57
2080 3927 4.481368 AGCCACGGTCAAACTATGATTA 57.519 40.909 0.00 0.00 40.97 1.75
2081 3928 4.839121 AGCCACGGTCAAACTATGATTAA 58.161 39.130 0.00 0.00 40.97 1.40
2082 3929 4.876107 AGCCACGGTCAAACTATGATTAAG 59.124 41.667 0.00 0.00 40.97 1.85
2083 3930 4.873827 GCCACGGTCAAACTATGATTAAGA 59.126 41.667 0.00 0.00 40.97 2.10
2084 3931 5.527582 GCCACGGTCAAACTATGATTAAGAT 59.472 40.000 0.00 0.00 40.97 2.40
2144 3998 3.243816 TGCCACTGCTCCTCTGCA 61.244 61.111 0.00 0.00 41.05 4.41
2783 4773 5.411669 CCAAACACACCCTAAGATGTTACTC 59.588 44.000 0.00 0.00 34.24 2.59
2787 4777 5.125097 ACACACCCTAAGATGTTACTCGTAG 59.875 44.000 0.00 0.00 0.00 3.51
2856 4846 7.445402 TCCTTATTAAATCTCTGCCACATAAGC 59.555 37.037 0.00 0.00 0.00 3.09
2895 4885 5.122396 GGACCTTATGTTACTGCTGAAGTTG 59.878 44.000 0.00 0.00 40.56 3.16
2928 4918 6.406692 TGGGCAGTCTGAGATATTTAGTAC 57.593 41.667 3.32 0.00 0.00 2.73
2959 4949 3.552604 TGATTGCTTCTTTAACGGTGC 57.447 42.857 0.00 0.00 0.00 5.01
3103 5096 1.299089 GCTCGGTGTTTGGTTGCAC 60.299 57.895 0.00 0.00 35.07 4.57
3148 5143 3.630312 GTGTGTGGTGTTTGGTTAGATGT 59.370 43.478 0.00 0.00 0.00 3.06
3224 5230 6.923508 CACAAGCGTGACATAGATAAATAGGA 59.076 38.462 6.65 0.00 46.80 2.94
3306 5329 4.183865 CAGCATAGTCTGAAACATCCGAA 58.816 43.478 0.00 0.00 36.19 4.30
3620 5723 1.972660 GAACCCTAGTGGCATCGGCT 61.973 60.000 0.00 0.00 40.87 5.52
3915 6026 8.569641 GTTTGACCACAATTACCATAGTTGTTA 58.430 33.333 0.00 0.00 36.62 2.41
4088 6365 3.582120 GTGTGTGTGCCACCACCG 61.582 66.667 12.06 0.00 43.85 4.94
4189 6478 2.151202 ACGCACCAAATTCGTGAAGAT 58.849 42.857 9.25 0.00 34.92 2.40
4411 6700 2.125350 GCTTGTCAGGGCTCCTCG 60.125 66.667 0.00 0.00 0.00 4.63
4439 6728 2.050168 GTCGTCGCGGTTGTACCA 60.050 61.111 6.13 0.00 38.47 3.25
4441 6730 2.049802 CGTCGCGGTTGTACCAGT 60.050 61.111 6.13 0.00 38.47 4.00
4944 7831 3.821600 GTGTTAGAGTGGAGAGTGAGTGA 59.178 47.826 0.00 0.00 0.00 3.41
4959 7846 5.022122 AGTGAGTGATGAGAGAAGGATGAA 58.978 41.667 0.00 0.00 0.00 2.57
4989 7876 0.527565 GCGGTGCATCAGGAAACAAT 59.472 50.000 0.00 0.00 0.00 2.71
5049 7936 2.029073 CCACGTGCCTCGAGTTGT 59.971 61.111 10.91 0.93 42.86 3.32
5220 8113 5.105351 GGACCTAATGCAAGCTACCAAAAAT 60.105 40.000 0.00 0.00 0.00 1.82
5332 8225 7.453126 CCCTAAGAGCATATCTCCGGATATTAT 59.547 40.741 3.57 0.00 41.63 1.28
5603 9582 4.450976 TGGATAGATGGACCACATTTTCG 58.549 43.478 0.00 0.00 40.72 3.46
5613 9592 3.129871 ACCACATTTTCGCATGTTTTGG 58.870 40.909 0.00 0.00 35.03 3.28
5682 11487 5.248640 AGTGACACCATGGTATCTTCAAAG 58.751 41.667 23.28 8.03 0.00 2.77
5791 11596 5.678955 ACTTAAGCCAGGTTAGGAGTAAG 57.321 43.478 1.29 0.00 34.88 2.34
5836 11641 9.793252 GATGTGTATATTTTGACTTCAAGCAAT 57.207 29.630 0.00 0.00 37.15 3.56
5941 11747 5.661056 AAGATCGTGACCTGAGTATTGAA 57.339 39.130 0.00 0.00 0.00 2.69
6142 11950 8.251026 TCGATACTAAAGAGATGCTTCAAAGAA 58.749 33.333 2.07 0.00 35.24 2.52
6221 12029 0.674534 ACCACGGATCGCCTCTTATC 59.325 55.000 0.00 0.00 0.00 1.75
6278 12086 4.455533 GCGGTGGAAATCATGCTCATTATA 59.544 41.667 0.00 0.00 0.00 0.98
6362 12170 8.273780 ACATTTGGAAGCAGATAAACTCTAAG 57.726 34.615 0.00 0.00 31.13 2.18
6415 12223 6.922957 GTGTTTGGTCTTGCATATTCAAAAGA 59.077 34.615 0.00 0.00 0.00 2.52
6439 12249 7.659390 AGAGACATTTCCTTCTTTTGTACAGAG 59.341 37.037 0.00 0.00 0.00 3.35
6605 12417 1.074889 GGCCTCCCCTACAGTTTTTCA 59.925 52.381 0.00 0.00 0.00 2.69
6818 12631 5.471456 CCTTTACTGAGCACAAAGTGAAGAT 59.529 40.000 8.42 0.00 40.57 2.40
7188 13001 4.406456 TGCACTGTCAATATCTTGGGTTT 58.594 39.130 0.00 0.00 32.95 3.27
7278 13091 3.103738 GTTGCATGCAGAAAGCTTATCG 58.896 45.455 21.50 0.00 45.94 2.92
7486 13299 1.065636 CCTCAAGGAGAGCAGCATTCA 60.066 52.381 0.00 0.00 43.31 2.57
7532 13345 1.055338 GACAATTGTTTGCAGCTCGC 58.945 50.000 13.36 1.70 42.89 5.03
7536 13349 0.318955 ATTGTTTGCAGCTCGCCAAC 60.319 50.000 14.15 14.15 44.53 3.77
7610 13550 8.243426 TGGATTATTGTTGTAGCACAGATTTTC 58.757 33.333 0.00 0.00 0.00 2.29
7648 13588 6.663093 TGGCAACTGTATCCATGAAATTAACT 59.337 34.615 0.00 0.00 37.61 2.24
7725 13665 2.744741 TGTAACCATGCACATTGTACCG 59.255 45.455 0.00 0.00 0.00 4.02
7756 13696 5.344743 TCAGTTCTTGAACAACAGAGTCT 57.655 39.130 14.80 0.00 31.34 3.24
7780 13732 4.040445 TCTGTTGCACCAAACTTTTAGC 57.960 40.909 0.00 0.00 0.00 3.09
7904 13856 8.055181 AGAAGCTTGAGATATCAAATTTGGGTA 58.945 33.333 17.90 11.52 0.00 3.69
7943 13895 6.307155 GTGTGAAGTTTCAGAAATGTATCCG 58.693 40.000 0.00 0.00 37.98 4.18
8127 14089 4.633126 CACAGGGATATTCACTCTTGTGTG 59.367 45.833 0.00 0.00 44.14 3.82
8206 14189 3.930336 TGCACTTCCTGTCTGTTCATAG 58.070 45.455 0.00 0.00 0.00 2.23
8208 14191 4.202357 TGCACTTCCTGTCTGTTCATAGTT 60.202 41.667 0.00 0.00 0.00 2.24
8211 14194 6.455647 CACTTCCTGTCTGTTCATAGTTGTA 58.544 40.000 0.00 0.00 0.00 2.41
8212 14195 6.929049 CACTTCCTGTCTGTTCATAGTTGTAA 59.071 38.462 0.00 0.00 0.00 2.41
8213 14196 6.929606 ACTTCCTGTCTGTTCATAGTTGTAAC 59.070 38.462 0.00 0.00 0.00 2.50
8214 14197 6.413783 TCCTGTCTGTTCATAGTTGTAACA 57.586 37.500 0.00 0.00 0.00 2.41
8215 14198 7.004555 TCCTGTCTGTTCATAGTTGTAACAT 57.995 36.000 0.00 0.00 33.01 2.71
8216 14199 7.450074 TCCTGTCTGTTCATAGTTGTAACATT 58.550 34.615 0.00 0.00 33.01 2.71
8217 14200 7.387673 TCCTGTCTGTTCATAGTTGTAACATTG 59.612 37.037 0.00 0.00 33.01 2.82
8218 14201 7.361201 CCTGTCTGTTCATAGTTGTAACATTGG 60.361 40.741 0.00 0.00 33.01 3.16
8219 14202 6.995686 TGTCTGTTCATAGTTGTAACATTGGT 59.004 34.615 0.00 0.00 33.01 3.67
8220 14203 7.500892 TGTCTGTTCATAGTTGTAACATTGGTT 59.499 33.333 0.00 0.00 41.06 3.67
8221 14204 8.015658 GTCTGTTCATAGTTGTAACATTGGTTC 58.984 37.037 0.00 0.00 38.45 3.62
8222 14205 7.936847 TCTGTTCATAGTTGTAACATTGGTTCT 59.063 33.333 0.00 0.00 38.45 3.01
8223 14206 9.214957 CTGTTCATAGTTGTAACATTGGTTCTA 57.785 33.333 0.00 0.00 38.45 2.10
8224 14207 9.214957 TGTTCATAGTTGTAACATTGGTTCTAG 57.785 33.333 0.00 0.00 38.45 2.43
8225 14208 9.216117 GTTCATAGTTGTAACATTGGTTCTAGT 57.784 33.333 0.00 0.00 38.45 2.57
8227 14210 9.865321 TCATAGTTGTAACATTGGTTCTAGTAC 57.135 33.333 0.00 0.00 38.45 2.73
8228 14211 9.647797 CATAGTTGTAACATTGGTTCTAGTACA 57.352 33.333 1.69 0.00 38.45 2.90
8231 14214 9.871238 AGTTGTAACATTGGTTCTAGTACATAG 57.129 33.333 1.69 0.00 38.45 2.23
8232 14215 8.601476 GTTGTAACATTGGTTCTAGTACATAGC 58.399 37.037 1.69 0.00 38.45 2.97
8233 14216 8.074613 TGTAACATTGGTTCTAGTACATAGCT 57.925 34.615 1.69 0.00 38.45 3.32
8234 14217 7.979537 TGTAACATTGGTTCTAGTACATAGCTG 59.020 37.037 0.00 0.00 38.45 4.24
8235 14218 6.791867 ACATTGGTTCTAGTACATAGCTGA 57.208 37.500 0.00 0.00 0.00 4.26
8236 14219 7.182817 ACATTGGTTCTAGTACATAGCTGAA 57.817 36.000 0.00 0.00 0.00 3.02
8237 14220 7.796054 ACATTGGTTCTAGTACATAGCTGAAT 58.204 34.615 0.00 0.00 0.00 2.57
8238 14221 7.928706 ACATTGGTTCTAGTACATAGCTGAATC 59.071 37.037 0.00 0.00 0.00 2.52
8239 14222 7.418337 TTGGTTCTAGTACATAGCTGAATCA 57.582 36.000 0.00 0.00 0.00 2.57
8240 14223 7.418337 TGGTTCTAGTACATAGCTGAATCAA 57.582 36.000 0.00 0.00 0.00 2.57
8241 14224 7.265673 TGGTTCTAGTACATAGCTGAATCAAC 58.734 38.462 0.00 0.00 0.00 3.18
8242 14225 7.093509 TGGTTCTAGTACATAGCTGAATCAACA 60.094 37.037 0.00 0.00 0.00 3.33
8243 14226 7.222999 GGTTCTAGTACATAGCTGAATCAACAC 59.777 40.741 0.00 0.00 0.00 3.32
8244 14227 7.646548 TCTAGTACATAGCTGAATCAACACT 57.353 36.000 0.00 0.00 0.00 3.55
8245 14228 8.067751 TCTAGTACATAGCTGAATCAACACTT 57.932 34.615 0.00 0.00 0.00 3.16
8246 14229 8.191446 TCTAGTACATAGCTGAATCAACACTTC 58.809 37.037 0.00 0.00 0.00 3.01
8247 14230 6.109359 AGTACATAGCTGAATCAACACTTCC 58.891 40.000 0.00 0.00 0.00 3.46
8248 14231 5.171339 ACATAGCTGAATCAACACTTCCT 57.829 39.130 0.00 0.00 0.00 3.36
8249 14232 4.940046 ACATAGCTGAATCAACACTTCCTG 59.060 41.667 0.00 0.00 0.00 3.86
8250 14233 3.498774 AGCTGAATCAACACTTCCTGT 57.501 42.857 0.00 0.00 32.89 4.00
8251 14234 3.406764 AGCTGAATCAACACTTCCTGTC 58.593 45.455 0.00 0.00 30.29 3.51
8252 14235 3.072184 AGCTGAATCAACACTTCCTGTCT 59.928 43.478 0.00 0.00 30.29 3.41
8253 14236 3.188048 GCTGAATCAACACTTCCTGTCTG 59.812 47.826 0.00 0.00 30.29 3.51
8254 14237 4.384056 CTGAATCAACACTTCCTGTCTGT 58.616 43.478 0.00 0.00 30.29 3.41
8255 14238 4.780815 TGAATCAACACTTCCTGTCTGTT 58.219 39.130 0.00 0.00 30.29 3.16
8256 14239 4.816385 TGAATCAACACTTCCTGTCTGTTC 59.184 41.667 0.00 0.00 30.29 3.18
8257 14240 3.904800 TCAACACTTCCTGTCTGTTCA 57.095 42.857 0.00 0.00 30.29 3.18
8258 14241 4.422073 TCAACACTTCCTGTCTGTTCAT 57.578 40.909 0.00 0.00 30.29 2.57
8259 14242 5.545063 TCAACACTTCCTGTCTGTTCATA 57.455 39.130 0.00 0.00 30.29 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 4.736126 ATGGTTTAGTTGGCTTATTGGC 57.264 40.909 0.00 0.00 42.18 4.52
146 147 3.296322 TTCCTTGCATTGCTTTTACCG 57.704 42.857 10.49 0.00 0.00 4.02
307 309 6.321717 CCATAGCACGCTTTCTTTTCATTAA 58.678 36.000 0.00 0.00 0.00 1.40
333 342 2.030262 CTGCCCAGCGCCTATCTC 59.970 66.667 2.29 0.00 36.24 2.75
345 354 1.375013 CTGCATTTTGCCACTGCCC 60.375 57.895 0.00 0.00 44.23 5.36
372 388 8.818141 AAAATAAAAGGAACAGAAGCTTTAGC 57.182 30.769 0.00 0.00 42.49 3.09
394 410 0.100325 CTGCTGGTGTGCGTGAAAAA 59.900 50.000 0.00 0.00 35.36 1.94
448 464 0.464036 GAGTCGTCACCATGGCCATA 59.536 55.000 20.30 0.00 0.00 2.74
491 507 2.802247 GTTTGGTTTCTGATGGCAAAGC 59.198 45.455 0.00 0.00 0.00 3.51
496 512 3.191371 CCTGTAGTTTGGTTTCTGATGGC 59.809 47.826 0.00 0.00 0.00 4.40
504 520 2.107726 GAGGTCCCCTGTAGTTTGGTTT 59.892 50.000 0.00 0.00 31.76 3.27
541 557 1.633852 CTTTGCTCTCAGTGGCTCGC 61.634 60.000 0.00 0.00 0.00 5.03
543 559 1.270518 TGACTTTGCTCTCAGTGGCTC 60.271 52.381 0.00 0.00 0.00 4.70
883 900 4.530857 CAACCCTAGCCTCCGCCG 62.531 72.222 0.00 0.00 34.57 6.46
884 901 4.176752 CCAACCCTAGCCTCCGCC 62.177 72.222 0.00 0.00 34.57 6.13
885 902 4.176752 CCCAACCCTAGCCTCCGC 62.177 72.222 0.00 0.00 0.00 5.54
925 943 3.689002 CTTCGCTTCCCCTCTGGCC 62.689 68.421 0.00 0.00 0.00 5.36
926 944 2.124942 CTTCGCTTCCCCTCTGGC 60.125 66.667 0.00 0.00 0.00 4.85
927 945 0.107945 CTTCTTCGCTTCCCCTCTGG 60.108 60.000 0.00 0.00 0.00 3.86
951 969 8.842358 TCCAATTAAAGACACGATACTTTTCT 57.158 30.769 0.00 0.00 37.49 2.52
954 972 8.388103 CGATTCCAATTAAAGACACGATACTTT 58.612 33.333 0.00 0.00 39.27 2.66
955 973 7.011109 CCGATTCCAATTAAAGACACGATACTT 59.989 37.037 0.00 0.00 0.00 2.24
956 974 6.479001 CCGATTCCAATTAAAGACACGATACT 59.521 38.462 0.00 0.00 0.00 2.12
1007 1025 2.285743 GGAGGAGGAGGGGCAGTT 60.286 66.667 0.00 0.00 0.00 3.16
1152 1170 2.745037 GACACTGGGCACGGGTAA 59.255 61.111 0.00 0.00 0.00 2.85
1363 1381 6.015027 TCTGTCTAGAGCTGTTTGAAGTAC 57.985 41.667 0.00 0.00 0.00 2.73
1364 1382 6.403746 CGATCTGTCTAGAGCTGTTTGAAGTA 60.404 42.308 0.00 0.00 37.20 2.24
1365 1383 5.621104 CGATCTGTCTAGAGCTGTTTGAAGT 60.621 44.000 0.00 0.00 37.20 3.01
1366 1384 4.797868 CGATCTGTCTAGAGCTGTTTGAAG 59.202 45.833 0.00 0.00 37.20 3.02
1367 1385 4.738124 CGATCTGTCTAGAGCTGTTTGAA 58.262 43.478 0.00 0.00 37.20 2.69
1434 1453 4.184629 ACAGCTCTTGAAATTACTAGGCG 58.815 43.478 0.00 0.00 0.00 5.52
1536 1555 5.534654 GCATGCATTACTAAGTTAATCCCCA 59.465 40.000 14.21 0.00 0.00 4.96
1551 1570 7.290110 ACATAGACTAGTAGTGCATGCATTA 57.710 36.000 25.64 21.48 0.00 1.90
1552 1571 6.166984 ACATAGACTAGTAGTGCATGCATT 57.833 37.500 25.64 22.70 0.00 3.56
1553 1572 5.798125 ACATAGACTAGTAGTGCATGCAT 57.202 39.130 25.64 15.04 0.00 3.96
1554 1573 5.598416 AACATAGACTAGTAGTGCATGCA 57.402 39.130 18.46 18.46 0.00 3.96
1588 1610 8.955794 ACATATGTTATTCCCCACTATAAAGGT 58.044 33.333 1.41 0.00 0.00 3.50
1589 1611 9.231297 CACATATGTTATTCCCCACTATAAAGG 57.769 37.037 5.37 0.00 0.00 3.11
1592 1614 8.160765 CCACACATATGTTATTCCCCACTATAA 58.839 37.037 5.37 0.00 36.72 0.98
1624 1748 6.980593 ACAAGCTAATAAATGAAGTGTTGCA 58.019 32.000 0.00 0.00 0.00 4.08
1643 1767 4.629200 CCAAGACAAGATGAGTCTACAAGC 59.371 45.833 0.00 0.00 45.11 4.01
2022 3838 4.970662 ACATCCTTGTCATAATGTGCAC 57.029 40.909 10.75 10.75 31.41 4.57
2078 3925 8.035394 ACGAGTTCATGAGCTCTTAAATCTTAA 58.965 33.333 29.59 0.00 36.65 1.85
2079 3926 7.548097 ACGAGTTCATGAGCTCTTAAATCTTA 58.452 34.615 29.59 0.00 36.65 2.10
2080 3927 6.402222 ACGAGTTCATGAGCTCTTAAATCTT 58.598 36.000 29.59 6.16 36.65 2.40
2081 3928 5.971763 ACGAGTTCATGAGCTCTTAAATCT 58.028 37.500 29.59 6.45 36.65 2.40
2082 3929 6.456181 CCAACGAGTTCATGAGCTCTTAAATC 60.456 42.308 29.59 13.10 36.65 2.17
2083 3930 5.352569 CCAACGAGTTCATGAGCTCTTAAAT 59.647 40.000 29.59 13.28 36.65 1.40
2084 3931 4.690748 CCAACGAGTTCATGAGCTCTTAAA 59.309 41.667 29.59 0.00 36.65 1.52
2144 3998 3.741245 TTACTCAGGAGACTAGTGGCT 57.259 47.619 0.00 0.00 40.21 4.75
2337 4247 1.589716 GGCAACCTGATGTGCTGGTC 61.590 60.000 0.00 0.00 46.85 4.02
2783 4773 6.592166 GCTATAGCTAGTTACTCACACTACG 58.408 44.000 17.75 0.00 38.21 3.51
2856 4846 4.326504 AAGGTCCAACTCAGCAAATTTG 57.673 40.909 14.03 14.03 0.00 2.32
2928 4918 8.598075 GTTAAAGAAGCAATCATTTGGCATTAG 58.402 33.333 0.00 0.00 33.22 1.73
2959 4949 0.179234 AAGGGGGCAAAAACCAAACG 59.821 50.000 0.00 0.00 0.00 3.60
3103 5096 0.109597 GCATCTGCCCAGAACAAACG 60.110 55.000 1.62 0.00 41.36 3.60
3148 5143 5.298989 AGGTTACCAGACAACATGTGTTA 57.701 39.130 3.51 0.00 41.96 2.41
3224 5230 6.271624 ACTCGGGTTTAAGGCTATATGGTATT 59.728 38.462 0.00 0.00 0.00 1.89
3235 5241 4.067192 TGTTTAAGACTCGGGTTTAAGGC 58.933 43.478 0.00 0.00 0.00 4.35
3306 5329 2.233431 CTCTGCACCTAAGACTTCTGCT 59.767 50.000 11.62 0.00 0.00 4.24
3620 5723 1.451504 CACCCAAGCTGGAGTGTCA 59.548 57.895 0.00 0.00 40.96 3.58
3915 6026 6.071728 GGATGAATGAGTGTTGATCTTTGGTT 60.072 38.462 0.00 0.00 0.00 3.67
4088 6365 1.663379 GGGGTTCATGGCGGTAAAGC 61.663 60.000 0.00 0.00 0.00 3.51
4189 6478 2.529632 ACTGAGAGCACACCTACATGA 58.470 47.619 0.00 0.00 0.00 3.07
4737 7079 4.223923 GCACTAGGCATCCAATCTACCTAT 59.776 45.833 0.00 0.00 43.97 2.57
4944 7831 7.016072 CCATAACTACCTTCATCCTTCTCTCAT 59.984 40.741 0.00 0.00 0.00 2.90
4959 7846 0.837272 ATGCACCGCCATAACTACCT 59.163 50.000 0.00 0.00 0.00 3.08
5120 8008 4.459331 CGGCCCGCACGATGTTTG 62.459 66.667 0.00 0.00 0.00 2.93
5220 8113 9.851686 AATATCTGAACTAAATCACTTATGGCA 57.148 29.630 0.00 0.00 0.00 4.92
5332 8225 6.710278 TCTACAAATGTGATGAACCAGATCA 58.290 36.000 0.00 0.00 0.00 2.92
5603 9582 6.843069 ACACATAAACTTTCCAAAACATGC 57.157 33.333 0.00 0.00 0.00 4.06
5613 9592 4.083484 AGGCGCAGTTACACATAAACTTTC 60.083 41.667 10.83 0.00 34.99 2.62
5662 11467 7.396540 AATTCTTTGAAGATACCATGGTGTC 57.603 36.000 28.98 28.98 36.66 3.67
5791 11596 8.213518 ACACATCACAATAAGTAATGTCCATC 57.786 34.615 0.00 0.00 0.00 3.51
5941 11747 6.491403 GCTCCTGTATTATTTGGATGGTGAAT 59.509 38.462 0.00 0.00 0.00 2.57
6185 11993 1.340017 TGGTCTCAAGCTGGCCAATAC 60.340 52.381 7.01 0.00 0.00 1.89
6188 11996 1.228245 GTGGTCTCAAGCTGGCCAA 60.228 57.895 7.01 0.00 0.00 4.52
6278 12086 2.957402 TGTTGAAGGATGAACTGGCT 57.043 45.000 0.00 0.00 0.00 4.75
6415 12223 7.227512 CACTCTGTACAAAAGAAGGAAATGTCT 59.772 37.037 10.97 0.00 0.00 3.41
6439 12249 2.427506 GGGATTCACACACTCCTTCAC 58.572 52.381 0.00 0.00 0.00 3.18
6474 12286 1.475034 GGCATAGCCCAGATCGTCAAA 60.475 52.381 0.00 0.00 44.06 2.69
6818 12631 8.195165 ACCTATGCAAAGAGCTAGATATGTTA 57.805 34.615 0.00 0.00 45.94 2.41
7269 13082 2.095853 CGGATGCACAAACGATAAGCTT 59.904 45.455 3.48 3.48 0.00 3.74
7278 13091 1.199097 CCAGTTACCGGATGCACAAAC 59.801 52.381 9.46 0.61 0.00 2.93
7418 13231 3.005050 TCAATGCTGGTCTTGCTTGAAAG 59.995 43.478 0.00 0.00 30.71 2.62
7486 13299 7.611855 AGAATTCTTCTTTTCATGGTTACCGAT 59.388 33.333 0.88 0.00 36.36 4.18
7513 13326 1.055338 GCGAGCTGCAAACAATTGTC 58.945 50.000 12.39 0.00 45.45 3.18
7532 13345 4.389077 GTCCAAGATTCTTCACTACGTTGG 59.611 45.833 0.00 0.00 35.52 3.77
7536 13349 6.980978 ACATATGTCCAAGATTCTTCACTACG 59.019 38.462 1.41 0.00 0.00 3.51
7610 13550 0.894835 GTTGCCATACCCCCAAAGTG 59.105 55.000 0.00 0.00 0.00 3.16
7667 13607 8.458052 TGAAAATACTGCTACAACAACCATATG 58.542 33.333 0.00 0.00 0.00 1.78
7669 13609 7.663905 ACTGAAAATACTGCTACAACAACCATA 59.336 33.333 0.00 0.00 0.00 2.74
7725 13665 6.206634 TGTTGTTCAAGAACTGAATATCCCAC 59.793 38.462 13.49 0.00 45.74 4.61
7749 13689 1.869767 GGTGCAACAGAACAGACTCTG 59.130 52.381 0.00 4.36 46.94 3.35
7751 13691 1.953559 TGGTGCAACAGAACAGACTC 58.046 50.000 0.00 0.00 39.98 3.36
7753 13693 2.423538 AGTTTGGTGCAACAGAACAGAC 59.576 45.455 22.89 10.67 39.98 3.51
7754 13694 2.722094 AGTTTGGTGCAACAGAACAGA 58.278 42.857 22.89 0.61 39.98 3.41
7756 13696 3.951775 AAAGTTTGGTGCAACAGAACA 57.048 38.095 22.89 1.63 39.98 3.18
7878 13830 6.894103 ACCCAAATTTGATATCTCAAGCTTCT 59.106 34.615 19.86 0.00 42.19 2.85
7882 13834 6.739112 GGTACCCAAATTTGATATCTCAAGC 58.261 40.000 19.86 2.56 42.19 4.01
7904 13856 0.902531 CACACGGGAGTAGATTGGGT 59.097 55.000 0.00 0.00 44.67 4.51
7943 13895 4.740695 GTCATACTGTATTCTCTTCGCCAC 59.259 45.833 0.00 0.00 0.00 5.01
8005 13958 9.793259 AGGAAATGTGTTCTCTGTAAAAGAATA 57.207 29.630 0.00 0.00 35.35 1.75
8009 13962 8.833231 TCTAGGAAATGTGTTCTCTGTAAAAG 57.167 34.615 0.00 0.00 0.00 2.27
8016 13977 7.550906 GCAGTTTATCTAGGAAATGTGTTCTCT 59.449 37.037 0.00 0.00 0.00 3.10
8022 13983 7.201679 CCTTCAGCAGTTTATCTAGGAAATGTG 60.202 40.741 0.00 0.00 0.00 3.21
8127 14089 1.740025 CCAGGAGGAAAACAATCGAGC 59.260 52.381 0.00 0.00 36.89 5.03
8206 14189 8.601476 GCTATGTACTAGAACCAATGTTACAAC 58.399 37.037 0.00 0.00 33.97 3.32
8208 14191 7.979537 CAGCTATGTACTAGAACCAATGTTACA 59.020 37.037 0.00 0.00 33.97 2.41
8211 14194 7.182817 TCAGCTATGTACTAGAACCAATGTT 57.817 36.000 0.00 0.00 37.42 2.71
8212 14195 6.791867 TCAGCTATGTACTAGAACCAATGT 57.208 37.500 0.00 0.00 0.00 2.71
8213 14196 7.928167 TGATTCAGCTATGTACTAGAACCAATG 59.072 37.037 0.00 0.00 0.00 2.82
8214 14197 8.023021 TGATTCAGCTATGTACTAGAACCAAT 57.977 34.615 0.00 0.00 0.00 3.16
8215 14198 7.418337 TGATTCAGCTATGTACTAGAACCAA 57.582 36.000 0.00 0.00 0.00 3.67
8216 14199 7.093509 TGTTGATTCAGCTATGTACTAGAACCA 60.094 37.037 0.00 0.00 0.00 3.67
8217 14200 7.222999 GTGTTGATTCAGCTATGTACTAGAACC 59.777 40.741 0.00 0.00 0.00 3.62
8218 14201 7.976734 AGTGTTGATTCAGCTATGTACTAGAAC 59.023 37.037 0.00 0.00 0.00 3.01
8219 14202 8.067751 AGTGTTGATTCAGCTATGTACTAGAA 57.932 34.615 0.00 0.00 0.00 2.10
8220 14203 7.646548 AGTGTTGATTCAGCTATGTACTAGA 57.353 36.000 0.00 0.00 0.00 2.43
8221 14204 7.436673 GGAAGTGTTGATTCAGCTATGTACTAG 59.563 40.741 2.11 0.00 0.00 2.57
8222 14205 7.124298 AGGAAGTGTTGATTCAGCTATGTACTA 59.876 37.037 2.11 0.00 0.00 1.82
8223 14206 6.070538 AGGAAGTGTTGATTCAGCTATGTACT 60.071 38.462 2.11 0.00 0.00 2.73
8224 14207 6.036517 CAGGAAGTGTTGATTCAGCTATGTAC 59.963 42.308 2.11 0.00 0.00 2.90
8225 14208 6.108687 CAGGAAGTGTTGATTCAGCTATGTA 58.891 40.000 2.11 0.00 0.00 2.29
8226 14209 4.940046 CAGGAAGTGTTGATTCAGCTATGT 59.060 41.667 2.11 0.00 0.00 2.29
8227 14210 4.940046 ACAGGAAGTGTTGATTCAGCTATG 59.060 41.667 2.11 0.09 34.94 2.23
8228 14211 5.046014 AGACAGGAAGTGTTGATTCAGCTAT 60.046 40.000 2.11 0.00 40.56 2.97
8229 14212 4.284490 AGACAGGAAGTGTTGATTCAGCTA 59.716 41.667 2.11 0.00 40.56 3.32
8230 14213 3.072184 AGACAGGAAGTGTTGATTCAGCT 59.928 43.478 2.11 0.00 40.56 4.24
8231 14214 3.188048 CAGACAGGAAGTGTTGATTCAGC 59.812 47.826 0.00 0.00 40.56 4.26
8232 14215 4.384056 ACAGACAGGAAGTGTTGATTCAG 58.616 43.478 0.00 0.00 40.56 3.02
8233 14216 4.422073 ACAGACAGGAAGTGTTGATTCA 57.578 40.909 0.00 0.00 40.56 2.57
8234 14217 4.816385 TGAACAGACAGGAAGTGTTGATTC 59.184 41.667 0.00 0.00 40.56 2.52
8235 14218 4.780815 TGAACAGACAGGAAGTGTTGATT 58.219 39.130 0.00 0.00 40.56 2.57
8236 14219 4.422073 TGAACAGACAGGAAGTGTTGAT 57.578 40.909 0.00 0.00 40.56 2.57
8237 14220 3.904800 TGAACAGACAGGAAGTGTTGA 57.095 42.857 0.00 0.00 40.56 3.18
8238 14221 5.300752 ACTATGAACAGACAGGAAGTGTTG 58.699 41.667 0.00 0.00 40.56 3.33
8239 14222 5.552870 ACTATGAACAGACAGGAAGTGTT 57.447 39.130 0.00 0.00 40.56 3.32
8240 14223 5.163301 ACAACTATGAACAGACAGGAAGTGT 60.163 40.000 0.00 0.00 44.49 3.55
8241 14224 5.300752 ACAACTATGAACAGACAGGAAGTG 58.699 41.667 0.00 0.00 0.00 3.16
8242 14225 5.552870 ACAACTATGAACAGACAGGAAGT 57.447 39.130 0.00 0.00 0.00 3.01
8243 14226 5.760253 ACAACAACTATGAACAGACAGGAAG 59.240 40.000 0.00 0.00 0.00 3.46
8244 14227 5.680619 ACAACAACTATGAACAGACAGGAA 58.319 37.500 0.00 0.00 0.00 3.36
8245 14228 5.290493 ACAACAACTATGAACAGACAGGA 57.710 39.130 0.00 0.00 0.00 3.86
8246 14229 6.481976 TGTTACAACAACTATGAACAGACAGG 59.518 38.462 0.00 0.00 35.67 4.00
8247 14230 7.477144 TGTTACAACAACTATGAACAGACAG 57.523 36.000 0.00 0.00 35.67 3.51
8248 14231 8.341903 CAATGTTACAACAACTATGAACAGACA 58.658 33.333 0.00 0.00 43.03 3.41
8249 14232 7.803189 CCAATGTTACAACAACTATGAACAGAC 59.197 37.037 0.00 0.00 43.03 3.51
8250 14233 7.500892 ACCAATGTTACAACAACTATGAACAGA 59.499 33.333 0.00 0.00 43.03 3.41
8251 14234 7.648142 ACCAATGTTACAACAACTATGAACAG 58.352 34.615 0.00 0.00 43.03 3.16
8252 14235 7.575414 ACCAATGTTACAACAACTATGAACA 57.425 32.000 0.00 0.00 43.03 3.18
8253 14236 8.349983 AGAACCAATGTTACAACAACTATGAAC 58.650 33.333 0.00 0.00 43.03 3.18
8254 14237 8.458573 AGAACCAATGTTACAACAACTATGAA 57.541 30.769 0.00 0.00 43.03 2.57
8255 14238 9.214957 CTAGAACCAATGTTACAACAACTATGA 57.785 33.333 0.00 0.00 43.03 2.15
8256 14239 8.999431 ACTAGAACCAATGTTACAACAACTATG 58.001 33.333 0.00 0.00 43.03 2.23
8258 14241 9.480053 GTACTAGAACCAATGTTACAACAACTA 57.520 33.333 0.00 0.00 43.03 2.24
8259 14242 7.988599 TGTACTAGAACCAATGTTACAACAACT 59.011 33.333 0.00 0.00 43.03 3.16


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

AutoCloner maintained by Alex Coulton.