Multiple sequence alignment - TraesCS3D01G041000

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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 TraesCS3D01G041000 chr3D 100.000 3201 0 0 1 3201 15697645 15694445 0.000000e+00 5912.0
1 TraesCS3D01G041000 chr3D 91.446 1321 105 5 1363 2679 15881354 15880038 0.000000e+00 1807.0
2 TraesCS3D01G041000 chr3D 97.647 510 12 0 2692 3201 289595013 289595522 0.000000e+00 876.0
3 TraesCS3D01G041000 chr3D 97.047 508 15 0 2693 3200 15689336 15688829 0.000000e+00 856.0
4 TraesCS3D01G041000 chr3D 90.411 657 49 5 718 1365 15881970 15881319 0.000000e+00 852.0
5 TraesCS3D01G041000 chr3D 100.000 95 0 0 3433 3527 15694213 15694119 3.620000e-40 176.0
6 TraesCS3D01G041000 chr3D 98.947 95 1 0 3433 3527 289595533 289595627 1.680000e-38 171.0
7 TraesCS3D01G041000 chr3D 92.174 115 7 2 733 847 15882074 15881962 1.010000e-35 161.0
8 TraesCS3D01G041000 chr3D 81.579 114 20 1 4 116 180111838 180111725 3.750000e-15 93.5
9 TraesCS3D01G041000 chr3D 100.000 37 0 0 1330 1366 15696283 15696247 6.320000e-08 69.4
10 TraesCS3D01G041000 chr3D 100.000 37 0 0 1363 1399 15696316 15696280 6.320000e-08 69.4
11 TraesCS3D01G041000 chr3B 94.149 1333 75 2 1364 2693 22667197 22665865 0.000000e+00 2026.0
12 TraesCS3D01G041000 chr3B 90.601 1032 75 9 346 1360 22668194 22667168 0.000000e+00 1349.0
13 TraesCS3D01G041000 chr3B 90.711 506 42 4 860 1365 22651828 22651328 0.000000e+00 669.0
14 TraesCS3D01G041000 chr3B 81.568 727 89 27 163 854 22652756 22652040 3.080000e-155 558.0
15 TraesCS3D01G041000 chr3B 89.151 212 18 2 2487 2693 22664713 22664502 3.490000e-65 259.0
16 TraesCS3D01G041000 chr3A 90.620 1322 115 4 1364 2679 20772065 20773383 0.000000e+00 1746.0
17 TraesCS3D01G041000 chr3A 93.028 502 28 5 859 1359 20771598 20772093 0.000000e+00 726.0
18 TraesCS3D01G041000 chr3A 82.712 671 64 23 164 807 20770928 20771573 1.850000e-152 549.0
19 TraesCS3D01G041000 chr5D 97.456 511 12 1 2692 3201 543323518 543323008 0.000000e+00 870.0
20 TraesCS3D01G041000 chr5D 97.260 511 13 1 2692 3201 543318069 543317559 0.000000e+00 865.0
21 TraesCS3D01G041000 chr4B 97.065 511 14 1 2692 3201 24924961 24924451 0.000000e+00 859.0
22 TraesCS3D01G041000 chr1D 97.059 510 15 0 2692 3201 42754297 42754806 0.000000e+00 859.0
23 TraesCS3D01G041000 chr1D 96.875 512 14 1 2692 3201 439778775 439779286 0.000000e+00 856.0
24 TraesCS3D01G041000 chr1D 100.000 95 0 0 3433 3527 439781619 439781713 3.620000e-40 176.0
25 TraesCS3D01G041000 chr1D 98.947 95 1 0 3433 3527 439779291 439779385 1.680000e-38 171.0
26 TraesCS3D01G041000 chr1D 98.947 95 1 0 3433 3527 474432599 474432505 1.680000e-38 171.0
27 TraesCS3D01G041000 chr6D 97.053 509 15 0 2693 3201 17036147 17036655 0.000000e+00 857.0
28 TraesCS3D01G041000 chr6D 98.947 95 1 0 3433 3527 17036662 17036756 1.680000e-38 171.0
29 TraesCS3D01G041000 chr6D 98.947 95 1 0 3433 3527 443239782 443239688 1.680000e-38 171.0
30 TraesCS3D01G041000 chr2D 96.686 513 17 0 2689 3201 498265305 498264793 0.000000e+00 854.0
31 TraesCS3D01G041000 chr2D 74.795 853 197 15 1423 2266 8671073 8671916 5.560000e-98 368.0
32 TraesCS3D01G041000 chr2D 74.616 847 186 22 1436 2266 85929180 85928347 2.610000e-91 346.0
33 TraesCS3D01G041000 chr2D 74.036 778 174 21 1374 2136 8686814 8687578 3.440000e-75 292.0
34 TraesCS3D01G041000 chr2D 82.353 238 37 5 1000 1236 9588296 9588529 5.970000e-48 202.0
35 TraesCS3D01G041000 chr2D 81.667 240 39 3 998 1236 8659795 8660030 9.990000e-46 195.0
36 TraesCS3D01G041000 chr2D 80.417 240 39 7 998 1236 9371512 9371744 3.620000e-40 176.0
37 TraesCS3D01G041000 chr2D 98.947 95 1 0 3433 3527 476843314 476843408 1.680000e-38 171.0
38 TraesCS3D01G041000 chr2D 98.947 95 1 0 3433 3527 610370274 610370180 1.680000e-38 171.0
39 TraesCS3D01G041000 chr2D 79.592 245 42 5 999 1236 8683372 8683615 6.060000e-38 169.0
40 TraesCS3D01G041000 chr2D 79.051 253 41 11 986 1236 8670677 8670919 2.820000e-36 163.0
41 TraesCS3D01G041000 chr2D 79.039 229 38 8 1031 1257 9753176 9752956 7.890000e-32 148.0
42 TraesCS3D01G041000 chr2B 75.376 865 181 26 1421 2266 11401014 11401865 4.270000e-104 388.0
43 TraesCS3D01G041000 chr2B 74.684 869 187 24 1416 2266 138992905 138992052 4.330000e-94 355.0
44 TraesCS3D01G041000 chr2B 81.857 237 40 3 1000 1236 12942429 12942662 2.780000e-46 196.0
45 TraesCS3D01G041000 chr2B 80.833 240 38 5 998 1236 11454229 11453997 7.780000e-42 182.0
46 TraesCS3D01G041000 chr2B 80.658 243 39 6 998 1239 11559562 11559327 7.780000e-42 182.0
47 TraesCS3D01G041000 chr2B 80.833 240 38 6 998 1236 12914564 12914796 7.780000e-42 182.0
48 TraesCS3D01G041000 chr2A 75.087 863 187 23 1421 2266 7786874 7787725 9.240000e-101 377.0
49 TraesCS3D01G041000 chr2A 81.739 230 37 5 1000 1228 8682727 8682952 1.670000e-43 187.0
50 TraesCS3D01G041000 chr5B 76.923 585 115 14 1421 1995 485911103 485910529 7.350000e-82 315.0
51 TraesCS3D01G041000 chr5B 97.143 35 1 0 125 159 18406601 18406635 3.800000e-05 60.2
52 TraesCS3D01G041000 chr1B 75.515 388 82 9 1459 1844 562461184 562461560 1.010000e-40 178.0
53 TraesCS3D01G041000 chrUn 98.947 95 1 0 3433 3527 112642138 112642044 1.680000e-38 171.0
54 TraesCS3D01G041000 chr7B 84.956 113 16 1 5 116 488682373 488682261 2.880000e-21 113.0
55 TraesCS3D01G041000 chr7A 97.222 36 1 0 125 160 278469666 278469631 1.060000e-05 62.1
56 TraesCS3D01G041000 chr5A 91.111 45 4 0 125 169 508906237 508906281 1.060000e-05 62.1


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 TraesCS3D01G041000 chr3D 15694119 15697645 3526 True 1556.700000 5912 100.000000 1 3527 4 chr3D.!!$R3 3526
1 TraesCS3D01G041000 chr3D 15880038 15882074 2036 True 940.000000 1807 91.343667 718 2679 3 chr3D.!!$R4 1961
2 TraesCS3D01G041000 chr3D 15688829 15689336 507 True 856.000000 856 97.047000 2693 3200 1 chr3D.!!$R1 507
3 TraesCS3D01G041000 chr3D 289595013 289595627 614 False 523.500000 876 98.297000 2692 3527 2 chr3D.!!$F1 835
4 TraesCS3D01G041000 chr3B 22664502 22668194 3692 True 1211.333333 2026 91.300333 346 2693 3 chr3B.!!$R2 2347
5 TraesCS3D01G041000 chr3B 22651328 22652756 1428 True 613.500000 669 86.139500 163 1365 2 chr3B.!!$R1 1202
6 TraesCS3D01G041000 chr3A 20770928 20773383 2455 False 1007.000000 1746 88.786667 164 2679 3 chr3A.!!$F1 2515
7 TraesCS3D01G041000 chr5D 543323008 543323518 510 True 870.000000 870 97.456000 2692 3201 1 chr5D.!!$R2 509
8 TraesCS3D01G041000 chr5D 543317559 543318069 510 True 865.000000 865 97.260000 2692 3201 1 chr5D.!!$R1 509
9 TraesCS3D01G041000 chr4B 24924451 24924961 510 True 859.000000 859 97.065000 2692 3201 1 chr4B.!!$R1 509
10 TraesCS3D01G041000 chr1D 42754297 42754806 509 False 859.000000 859 97.059000 2692 3201 1 chr1D.!!$F1 509
11 TraesCS3D01G041000 chr1D 439778775 439781713 2938 False 401.000000 856 98.607333 2692 3527 3 chr1D.!!$F2 835
12 TraesCS3D01G041000 chr6D 17036147 17036756 609 False 514.000000 857 98.000000 2693 3527 2 chr6D.!!$F1 834
13 TraesCS3D01G041000 chr2D 498264793 498265305 512 True 854.000000 854 96.686000 2689 3201 1 chr2D.!!$R3 512
14 TraesCS3D01G041000 chr2D 85928347 85929180 833 True 346.000000 346 74.616000 1436 2266 1 chr2D.!!$R2 830
15 TraesCS3D01G041000 chr2D 8670677 8671916 1239 False 265.500000 368 76.923000 986 2266 2 chr2D.!!$F5 1280
16 TraesCS3D01G041000 chr2D 8683372 8687578 4206 False 230.500000 292 76.814000 999 2136 2 chr2D.!!$F6 1137
17 TraesCS3D01G041000 chr2B 11401014 11401865 851 False 388.000000 388 75.376000 1421 2266 1 chr2B.!!$F1 845
18 TraesCS3D01G041000 chr2B 138992052 138992905 853 True 355.000000 355 74.684000 1416 2266 1 chr2B.!!$R3 850
19 TraesCS3D01G041000 chr2A 7786874 7787725 851 False 377.000000 377 75.087000 1421 2266 1 chr2A.!!$F1 845
20 TraesCS3D01G041000 chr5B 485910529 485911103 574 True 315.000000 315 76.923000 1421 1995 1 chr5B.!!$R1 574

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
67 68 0.030101 CGCAAACAACACGGAATGGT 59.970 50.0 0.00 0.0 0.0 3.55 F
143 144 0.035739 TGGGTTCGAGTTAAGGGCAC 59.964 55.0 0.00 0.0 0.0 5.01 F
1369 1636 0.316204 TCGAAGAACCACGTCCTTCC 59.684 55.0 9.51 0.0 34.4 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1278 1539 0.028902 CGTCGATGATACTGCCGTCA 59.971 55.0 0.0 0.00 0.00 4.35 R
1381 1648 0.032952 TTGGACGTGGTTCTTCGAGG 59.967 55.0 0.0 0.00 0.00 4.63 R
3065 5617 0.968393 GAGAGCAGGTCTCCGGAACT 60.968 60.0 17.6 0.68 45.57 3.01 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
21 22 4.552166 ACAATGTCCAGAAAACGACAAG 57.448 40.909 0.00 0.00 42.02 3.16
22 23 4.196193 ACAATGTCCAGAAAACGACAAGA 58.804 39.130 0.00 0.00 42.02 3.02
23 24 4.638421 ACAATGTCCAGAAAACGACAAGAA 59.362 37.500 0.00 0.00 42.02 2.52
24 25 5.124776 ACAATGTCCAGAAAACGACAAGAAA 59.875 36.000 0.00 0.00 42.02 2.52
25 26 5.828299 ATGTCCAGAAAACGACAAGAAAA 57.172 34.783 0.00 0.00 42.02 2.29
26 27 4.976987 TGTCCAGAAAACGACAAGAAAAC 58.023 39.130 0.00 0.00 36.10 2.43
27 28 4.026407 GTCCAGAAAACGACAAGAAAACG 58.974 43.478 0.00 0.00 0.00 3.60
29 30 2.781646 CAGAAAACGACAAGAAAACGGC 59.218 45.455 0.00 0.00 0.00 5.68
30 31 2.114056 GAAAACGACAAGAAAACGGCC 58.886 47.619 0.00 0.00 0.00 6.13
31 32 1.096416 AAACGACAAGAAAACGGCCA 58.904 45.000 2.24 0.00 0.00 5.36
33 34 1.096416 ACGACAAGAAAACGGCCAAA 58.904 45.000 2.24 0.00 0.00 3.28
34 35 1.064952 ACGACAAGAAAACGGCCAAAG 59.935 47.619 2.24 0.00 0.00 2.77
35 36 1.487482 GACAAGAAAACGGCCAAAGC 58.513 50.000 2.24 0.00 38.76 3.51
49 50 3.021451 AAAGCCCTTTGACCTGACG 57.979 52.632 0.00 0.00 0.00 4.35
50 51 1.172812 AAAGCCCTTTGACCTGACGC 61.173 55.000 0.00 0.00 0.00 5.19
52 53 1.896660 GCCCTTTGACCTGACGCAA 60.897 57.895 0.00 0.00 0.00 4.85
54 55 0.310854 CCCTTTGACCTGACGCAAAC 59.689 55.000 0.00 0.00 31.37 2.93
55 56 1.021202 CCTTTGACCTGACGCAAACA 58.979 50.000 0.00 0.00 31.37 2.83
56 57 1.403679 CCTTTGACCTGACGCAAACAA 59.596 47.619 0.00 0.00 31.37 2.83
57 58 2.450160 CTTTGACCTGACGCAAACAAC 58.550 47.619 0.00 0.00 31.37 3.32
58 59 1.454201 TTGACCTGACGCAAACAACA 58.546 45.000 0.00 0.00 0.00 3.33
59 60 0.730265 TGACCTGACGCAAACAACAC 59.270 50.000 0.00 0.00 0.00 3.32
60 61 0.315869 GACCTGACGCAAACAACACG 60.316 55.000 0.00 0.00 0.00 4.49
61 62 1.010125 CCTGACGCAAACAACACGG 60.010 57.895 0.00 0.00 0.00 4.94
62 63 1.433053 CCTGACGCAAACAACACGGA 61.433 55.000 0.00 0.00 0.00 4.69
63 64 0.375454 CTGACGCAAACAACACGGAA 59.625 50.000 0.00 0.00 0.00 4.30
67 68 0.030101 CGCAAACAACACGGAATGGT 59.970 50.000 0.00 0.00 0.00 3.55
68 69 1.264557 CGCAAACAACACGGAATGGTA 59.735 47.619 0.00 0.00 0.00 3.25
70 71 3.610585 CGCAAACAACACGGAATGGTATT 60.611 43.478 0.00 0.00 0.00 1.89
71 72 4.303282 GCAAACAACACGGAATGGTATTT 58.697 39.130 0.00 0.00 0.00 1.40
72 73 4.747605 GCAAACAACACGGAATGGTATTTT 59.252 37.500 0.00 0.00 0.00 1.82
73 74 5.235401 GCAAACAACACGGAATGGTATTTTT 59.765 36.000 0.00 0.00 0.00 1.94
76 77 9.627395 CAAACAACACGGAATGGTATTTTTATA 57.373 29.630 0.00 0.00 0.00 0.98
78 79 9.849166 AACAACACGGAATGGTATTTTTATAAG 57.151 29.630 0.00 0.00 0.00 1.73
79 80 8.463607 ACAACACGGAATGGTATTTTTATAAGG 58.536 33.333 0.00 0.00 0.00 2.69
80 81 7.576861 ACACGGAATGGTATTTTTATAAGGG 57.423 36.000 0.00 0.00 0.00 3.95
82 83 7.835181 ACACGGAATGGTATTTTTATAAGGGAA 59.165 33.333 0.00 0.00 0.00 3.97
83 84 8.132995 CACGGAATGGTATTTTTATAAGGGAAC 58.867 37.037 0.00 0.00 0.00 3.62
90 91 7.282901 TGGTATTTTTATAAGGGAACTAACGGC 59.717 37.037 0.00 0.00 42.68 5.68
92 93 6.746745 TTTTTATAAGGGAACTAACGGCAG 57.253 37.500 0.00 0.00 42.68 4.85
93 94 5.680594 TTTATAAGGGAACTAACGGCAGA 57.319 39.130 0.00 0.00 42.68 4.26
94 95 5.680594 TTATAAGGGAACTAACGGCAGAA 57.319 39.130 0.00 0.00 42.68 3.02
95 96 2.474410 AAGGGAACTAACGGCAGAAG 57.526 50.000 0.00 0.00 42.68 2.85
96 97 0.613777 AGGGAACTAACGGCAGAAGG 59.386 55.000 0.00 0.00 40.61 3.46
97 98 0.611714 GGGAACTAACGGCAGAAGGA 59.388 55.000 0.00 0.00 0.00 3.36
98 99 1.675116 GGGAACTAACGGCAGAAGGAC 60.675 57.143 0.00 0.00 0.00 3.85
101 102 2.922740 ACTAACGGCAGAAGGACAAA 57.077 45.000 0.00 0.00 0.00 2.83
102 103 3.418684 ACTAACGGCAGAAGGACAAAT 57.581 42.857 0.00 0.00 0.00 2.32
107 108 2.554032 ACGGCAGAAGGACAAATTTGAG 59.446 45.455 24.64 0.00 0.00 3.02
108 109 2.669391 CGGCAGAAGGACAAATTTGAGC 60.669 50.000 24.64 14.75 0.00 4.26
109 110 2.297033 GGCAGAAGGACAAATTTGAGCA 59.703 45.455 24.64 0.00 0.00 4.26
110 111 3.311966 GCAGAAGGACAAATTTGAGCAC 58.688 45.455 24.64 10.79 0.00 4.40
111 112 3.243501 GCAGAAGGACAAATTTGAGCACA 60.244 43.478 24.64 0.00 0.00 4.57
112 113 4.293415 CAGAAGGACAAATTTGAGCACAC 58.707 43.478 24.64 10.56 0.00 3.82
113 114 4.037208 CAGAAGGACAAATTTGAGCACACT 59.963 41.667 24.64 12.39 0.00 3.55
114 115 4.646492 AGAAGGACAAATTTGAGCACACTT 59.354 37.500 24.64 16.14 0.00 3.16
115 116 4.574599 AGGACAAATTTGAGCACACTTC 57.425 40.909 24.64 8.67 0.00 3.01
116 117 3.003689 AGGACAAATTTGAGCACACTTCG 59.996 43.478 24.64 0.00 0.00 3.79
117 118 3.003275 GGACAAATTTGAGCACACTTCGA 59.997 43.478 24.64 0.00 0.00 3.71
118 119 4.497340 GGACAAATTTGAGCACACTTCGAA 60.497 41.667 24.64 0.00 0.00 3.71
119 120 4.992688 ACAAATTTGAGCACACTTCGAAA 58.007 34.783 24.64 0.00 0.00 3.46
120 121 5.406649 ACAAATTTGAGCACACTTCGAAAA 58.593 33.333 24.64 0.00 0.00 2.29
121 122 6.042143 ACAAATTTGAGCACACTTCGAAAAT 58.958 32.000 24.64 0.00 0.00 1.82
122 123 6.198966 ACAAATTTGAGCACACTTCGAAAATC 59.801 34.615 24.64 0.00 0.00 2.17
123 124 4.891627 TTTGAGCACACTTCGAAAATCA 57.108 36.364 0.00 0.00 0.00 2.57
124 125 5.437289 TTTGAGCACACTTCGAAAATCAT 57.563 34.783 0.00 0.00 0.00 2.45
125 126 4.408993 TGAGCACACTTCGAAAATCATG 57.591 40.909 0.00 0.00 0.00 3.07
126 127 3.189080 TGAGCACACTTCGAAAATCATGG 59.811 43.478 0.00 0.00 0.00 3.66
127 128 2.489329 AGCACACTTCGAAAATCATGGG 59.511 45.455 0.00 0.00 0.00 4.00
128 129 2.228822 GCACACTTCGAAAATCATGGGT 59.771 45.455 0.00 0.00 0.00 4.51
129 130 3.305335 GCACACTTCGAAAATCATGGGTT 60.305 43.478 0.00 0.00 0.00 4.11
130 131 4.475944 CACACTTCGAAAATCATGGGTTC 58.524 43.478 0.00 0.00 0.00 3.62
131 132 3.188460 ACACTTCGAAAATCATGGGTTCG 59.812 43.478 15.68 15.68 44.18 3.95
134 135 3.328382 TCGAAAATCATGGGTTCGAGT 57.672 42.857 18.68 0.00 45.85 4.18
135 136 3.670625 TCGAAAATCATGGGTTCGAGTT 58.329 40.909 18.68 0.00 45.85 3.01
136 137 4.823157 TCGAAAATCATGGGTTCGAGTTA 58.177 39.130 18.68 4.20 45.85 2.24
137 138 5.239351 TCGAAAATCATGGGTTCGAGTTAA 58.761 37.500 18.68 3.93 45.85 2.01
138 139 5.350365 TCGAAAATCATGGGTTCGAGTTAAG 59.650 40.000 18.68 0.00 45.85 1.85
139 140 5.447279 CGAAAATCATGGGTTCGAGTTAAGG 60.447 44.000 16.41 0.00 45.32 2.69
140 141 3.560636 ATCATGGGTTCGAGTTAAGGG 57.439 47.619 0.00 0.00 0.00 3.95
141 142 1.065709 TCATGGGTTCGAGTTAAGGGC 60.066 52.381 0.00 0.00 0.00 5.19
142 143 0.988832 ATGGGTTCGAGTTAAGGGCA 59.011 50.000 0.00 0.00 0.00 5.36
143 144 0.035739 TGGGTTCGAGTTAAGGGCAC 59.964 55.000 0.00 0.00 0.00 5.01
144 145 0.035739 GGGTTCGAGTTAAGGGCACA 59.964 55.000 0.00 0.00 0.00 4.57
145 146 1.543871 GGGTTCGAGTTAAGGGCACAA 60.544 52.381 0.00 0.00 0.00 3.33
146 147 2.223745 GGTTCGAGTTAAGGGCACAAA 58.776 47.619 0.00 0.00 0.00 2.83
147 148 2.817844 GGTTCGAGTTAAGGGCACAAAT 59.182 45.455 0.00 0.00 0.00 2.32
148 149 3.365969 GGTTCGAGTTAAGGGCACAAATG 60.366 47.826 0.00 0.00 0.00 2.32
149 150 3.134574 TCGAGTTAAGGGCACAAATGT 57.865 42.857 0.00 0.00 0.00 2.71
150 151 4.274602 TCGAGTTAAGGGCACAAATGTA 57.725 40.909 0.00 0.00 0.00 2.29
151 152 4.643463 TCGAGTTAAGGGCACAAATGTAA 58.357 39.130 0.00 0.00 0.00 2.41
152 153 5.064558 TCGAGTTAAGGGCACAAATGTAAA 58.935 37.500 0.00 0.00 0.00 2.01
153 154 5.708230 TCGAGTTAAGGGCACAAATGTAAAT 59.292 36.000 0.00 0.00 0.00 1.40
154 155 5.799936 CGAGTTAAGGGCACAAATGTAAATG 59.200 40.000 0.00 0.00 0.00 2.32
155 156 6.569610 CGAGTTAAGGGCACAAATGTAAATGT 60.570 38.462 0.00 0.00 0.00 2.71
156 157 6.687604 AGTTAAGGGCACAAATGTAAATGTC 58.312 36.000 0.00 0.00 0.00 3.06
157 158 4.535526 AAGGGCACAAATGTAAATGTCC 57.464 40.909 0.00 0.00 37.08 4.02
158 159 2.831526 AGGGCACAAATGTAAATGTCCC 59.168 45.455 0.00 0.00 37.56 4.46
159 160 2.831526 GGGCACAAATGTAAATGTCCCT 59.168 45.455 0.00 0.00 35.64 4.20
160 161 4.020543 GGGCACAAATGTAAATGTCCCTA 58.979 43.478 0.00 0.00 35.64 3.53
161 162 4.464597 GGGCACAAATGTAAATGTCCCTAA 59.535 41.667 0.00 0.00 35.64 2.69
194 195 7.669427 TGCCAAACTCTGTAAAATTTGATGAT 58.331 30.769 0.00 0.00 34.62 2.45
244 248 2.622470 GGGTCCCGATGAGTAGTAAGAC 59.378 54.545 0.00 0.00 0.00 3.01
276 280 0.608130 TTCATCTATGATCCCGGGCG 59.392 55.000 18.49 0.00 36.56 6.13
307 312 7.870445 TGCTCCCAATGAACAGTAAAATAAAAC 59.130 33.333 0.00 0.00 0.00 2.43
344 362 3.003275 TGAACTTTTTCTACGCAAGGCTG 59.997 43.478 0.00 0.00 35.26 4.85
371 389 1.474855 GCCAGGTGTGTGCCAAATTTT 60.475 47.619 0.00 0.00 0.00 1.82
388 406 7.583230 CCAAATTTTGTGGGTAAATGACATTG 58.417 34.615 0.34 0.00 32.03 2.82
408 426 2.074576 GGAGGAGCTCGTGGTAAAAAC 58.925 52.381 14.78 0.00 0.00 2.43
423 441 7.527457 GTGGTAAAAACGATAAAATGAGCTCT 58.473 34.615 16.19 0.00 0.00 4.09
424 442 7.481798 GTGGTAAAAACGATAAAATGAGCTCTG 59.518 37.037 16.19 0.00 0.00 3.35
495 517 3.305813 GGTACTCAAATGTCGAGACACCA 60.306 47.826 8.20 0.00 45.05 4.17
505 528 2.875933 GTCGAGACACCACCAAATTTGA 59.124 45.455 19.86 0.00 0.00 2.69
511 534 4.405358 AGACACCACCAAATTTGACATGTT 59.595 37.500 19.86 0.92 0.00 2.71
517 540 6.167685 CCACCAAATTTGACATGTTCATCAT 58.832 36.000 19.86 0.00 37.22 2.45
595 627 4.223700 ACAGTTCATCCACTAGAGCATCAA 59.776 41.667 0.00 0.00 37.82 2.57
621 653 2.438254 AGCCAAATCGCCGCATCA 60.438 55.556 0.00 0.00 0.00 3.07
654 686 8.073768 TCAAGCCTTTTCTAAATTAACGAGTTG 58.926 33.333 0.00 0.00 0.00 3.16
763 802 5.223449 AGGGAGAACGAGTATGTTTGAAA 57.777 39.130 0.00 0.00 30.75 2.69
975 1229 1.492720 GAGCTTCCCTATCGCTTTCG 58.507 55.000 0.00 0.00 33.47 3.46
1026 1280 2.423577 GTCACCATTTCTGCGGTTACT 58.576 47.619 0.00 0.00 31.41 2.24
1038 1292 3.645884 TGCGGTTACTAGTGAACTTGTC 58.354 45.455 5.39 0.00 34.09 3.18
1077 1331 4.998788 TCCTGATGAACAAGTATCAGTCG 58.001 43.478 11.83 0.60 45.54 4.18
1098 1359 3.535561 GCATAGCCACACACAACTAGAT 58.464 45.455 0.00 0.00 0.00 1.98
1276 1537 6.379386 GCCTTCAATTTCCAACAACTACTAC 58.621 40.000 0.00 0.00 0.00 2.73
1277 1538 6.206829 GCCTTCAATTTCCAACAACTACTACT 59.793 38.462 0.00 0.00 0.00 2.57
1278 1539 7.255486 GCCTTCAATTTCCAACAACTACTACTT 60.255 37.037 0.00 0.00 0.00 2.24
1282 1543 6.780706 ATTTCCAACAACTACTACTTGACG 57.219 37.500 0.00 0.00 0.00 4.35
1365 1632 0.388263 GTCCTCGAAGAACCACGTCC 60.388 60.000 0.00 0.00 34.09 4.79
1366 1633 0.538977 TCCTCGAAGAACCACGTCCT 60.539 55.000 0.00 0.00 34.09 3.85
1367 1634 0.317479 CCTCGAAGAACCACGTCCTT 59.683 55.000 0.00 0.00 34.09 3.36
1368 1635 1.669211 CCTCGAAGAACCACGTCCTTC 60.669 57.143 0.00 0.00 34.09 3.46
1369 1636 0.316204 TCGAAGAACCACGTCCTTCC 59.684 55.000 9.51 0.00 34.40 3.46
1370 1637 0.669625 CGAAGAACCACGTCCTTCCC 60.670 60.000 9.51 0.00 34.40 3.97
1371 1638 0.685660 GAAGAACCACGTCCTTCCCT 59.314 55.000 0.00 0.00 32.39 4.20
1372 1639 1.071857 GAAGAACCACGTCCTTCCCTT 59.928 52.381 0.00 0.00 32.39 3.95
1373 1640 1.137697 AGAACCACGTCCTTCCCTTT 58.862 50.000 0.00 0.00 0.00 3.11
1374 1641 1.071857 AGAACCACGTCCTTCCCTTTC 59.928 52.381 0.00 0.00 0.00 2.62
1375 1642 0.841289 AACCACGTCCTTCCCTTTCA 59.159 50.000 0.00 0.00 0.00 2.69
1376 1643 0.841289 ACCACGTCCTTCCCTTTCAA 59.159 50.000 0.00 0.00 0.00 2.69
1377 1644 1.202770 ACCACGTCCTTCCCTTTCAAG 60.203 52.381 0.00 0.00 0.00 3.02
1378 1645 0.875059 CACGTCCTTCCCTTTCAAGC 59.125 55.000 0.00 0.00 0.00 4.01
1379 1646 0.602905 ACGTCCTTCCCTTTCAAGCG 60.603 55.000 0.00 0.00 0.00 4.68
1380 1647 0.602905 CGTCCTTCCCTTTCAAGCGT 60.603 55.000 0.00 0.00 0.00 5.07
1381 1648 1.157585 GTCCTTCCCTTTCAAGCGTC 58.842 55.000 0.00 0.00 0.00 5.19
1382 1649 0.036306 TCCTTCCCTTTCAAGCGTCC 59.964 55.000 0.00 0.00 0.00 4.79
1383 1650 0.036875 CCTTCCCTTTCAAGCGTCCT 59.963 55.000 0.00 0.00 0.00 3.85
1384 1651 1.443802 CTTCCCTTTCAAGCGTCCTC 58.556 55.000 0.00 0.00 0.00 3.71
1385 1652 0.320421 TTCCCTTTCAAGCGTCCTCG 60.320 55.000 0.00 0.00 40.37 4.63
1386 1653 1.183030 TCCCTTTCAAGCGTCCTCGA 61.183 55.000 0.00 0.00 39.71 4.04
1387 1654 0.320421 CCCTTTCAAGCGTCCTCGAA 60.320 55.000 0.00 0.00 39.71 3.71
1388 1655 1.071605 CCTTTCAAGCGTCCTCGAAG 58.928 55.000 0.00 0.00 39.71 3.79
1389 1656 1.336887 CCTTTCAAGCGTCCTCGAAGA 60.337 52.381 0.00 0.00 39.71 2.87
1390 1657 2.404215 CTTTCAAGCGTCCTCGAAGAA 58.596 47.619 0.00 0.00 39.71 2.52
1391 1658 1.779569 TTCAAGCGTCCTCGAAGAAC 58.220 50.000 0.00 0.00 39.71 3.01
1392 1659 0.038526 TCAAGCGTCCTCGAAGAACC 60.039 55.000 0.00 0.00 39.71 3.62
1393 1660 0.319555 CAAGCGTCCTCGAAGAACCA 60.320 55.000 0.00 0.00 39.71 3.67
1394 1661 0.319641 AAGCGTCCTCGAAGAACCAC 60.320 55.000 0.00 0.00 39.71 4.16
1395 1662 2.087009 GCGTCCTCGAAGAACCACG 61.087 63.158 0.00 0.00 39.71 4.94
1396 1663 1.285023 CGTCCTCGAAGAACCACGT 59.715 57.895 0.00 0.00 39.71 4.49
1397 1664 0.728466 CGTCCTCGAAGAACCACGTC 60.728 60.000 0.00 0.00 39.71 4.34
1398 1665 0.388263 GTCCTCGAAGAACCACGTCC 60.388 60.000 0.00 0.00 34.09 4.79
1399 1666 0.824595 TCCTCGAAGAACCACGTCCA 60.825 55.000 0.00 0.00 34.09 4.02
1400 1667 0.032952 CCTCGAAGAACCACGTCCAA 59.967 55.000 0.00 0.00 34.09 3.53
1401 1668 1.539496 CCTCGAAGAACCACGTCCAAA 60.539 52.381 0.00 0.00 34.09 3.28
1402 1669 1.525619 CTCGAAGAACCACGTCCAAAC 59.474 52.381 0.00 0.00 34.09 2.93
1558 1825 3.189287 CCTTTACACAGACCACTTCATGC 59.811 47.826 0.00 0.00 0.00 4.06
1563 1830 0.036952 CAGACCACTTCATGCTCGGT 60.037 55.000 0.00 0.00 0.00 4.69
1617 1890 0.249120 TACTGCAACATGACCCTCCG 59.751 55.000 0.00 0.00 0.00 4.63
1637 1910 2.178235 GTAATTCTCCGGCCGTGCC 61.178 63.158 26.12 4.96 46.75 5.01
1703 1976 0.248255 CATGTCTGCGACGACGAGAT 60.248 55.000 12.29 0.00 42.66 2.75
2013 2289 0.534877 TCACGTTTGGCAGTGCAGAT 60.535 50.000 18.61 0.00 38.19 2.90
2107 2386 0.655915 CACGACAAATGCGTTCGCAA 60.656 50.000 22.83 7.74 44.70 4.85
2212 2492 4.744570 CGAGCACGGTGTATATCCATATT 58.255 43.478 10.24 0.00 35.72 1.28
2324 2604 5.684626 GCAGCAACAGATTGACTAATAATGC 59.315 40.000 0.00 0.00 38.15 3.56
2327 2607 6.825213 AGCAACAGATTGACTAATAATGCTCA 59.175 34.615 0.00 0.00 38.15 4.26
2343 2623 4.356405 TGCTCAGATGAAGAAGGAAACA 57.644 40.909 0.00 0.00 0.00 2.83
2354 2634 4.222124 AGAAGGAAACAGTGACACTTGT 57.778 40.909 5.04 5.17 0.00 3.16
2391 2677 2.163613 CCCGAATAACAGACCAAAAGGC 59.836 50.000 0.00 0.00 0.00 4.35
2442 2728 5.618278 AGGATACCCCCTTACACAAGGTTC 61.618 50.000 2.91 0.00 44.21 3.62
2471 2757 3.781079 TGTTGCAAGTTCTGTTCAAGG 57.219 42.857 0.00 0.00 0.00 3.61
2567 2914 7.119846 ACATTTGCTTCCACTTTAGATAGTGAC 59.880 37.037 5.39 0.00 46.72 3.67
2663 3093 2.677836 TGCTAAAATGACTCGTGGCATC 59.322 45.455 6.23 0.00 0.00 3.91
2798 4831 7.679638 GCAAACTAGAAGAACAACAAGACATGT 60.680 37.037 0.00 0.00 46.82 3.21
2954 5506 4.830826 TGAATACGACGATGAGTAGCAT 57.169 40.909 0.00 0.00 40.77 3.79
3065 5617 1.739466 GCAGGATCGCAAAGATGAACA 59.261 47.619 0.00 0.00 40.26 3.18
3178 5732 1.426751 ACCCTAGGTGTTTTCGGTGA 58.573 50.000 8.29 0.00 32.98 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.811555 TCTTGTCGTTTTCTGGACATTG 57.188 40.909 0.00 0.00 42.27 2.82
2 3 5.828299 TTTCTTGTCGTTTTCTGGACATT 57.172 34.783 0.00 0.00 42.27 2.71
4 5 4.436317 CGTTTTCTTGTCGTTTTCTGGACA 60.436 41.667 0.00 0.00 41.13 4.02
5 6 4.026407 CGTTTTCTTGTCGTTTTCTGGAC 58.974 43.478 0.00 0.00 0.00 4.02
6 7 3.064271 CCGTTTTCTTGTCGTTTTCTGGA 59.936 43.478 0.00 0.00 0.00 3.86
8 9 2.781646 GCCGTTTTCTTGTCGTTTTCTG 59.218 45.455 0.00 0.00 0.00 3.02
11 12 1.473278 TGGCCGTTTTCTTGTCGTTTT 59.527 42.857 0.00 0.00 0.00 2.43
12 13 1.096416 TGGCCGTTTTCTTGTCGTTT 58.904 45.000 0.00 0.00 0.00 3.60
14 15 1.064952 CTTTGGCCGTTTTCTTGTCGT 59.935 47.619 0.00 0.00 0.00 4.34
15 16 1.753956 CTTTGGCCGTTTTCTTGTCG 58.246 50.000 0.00 0.00 0.00 4.35
16 17 1.487482 GCTTTGGCCGTTTTCTTGTC 58.513 50.000 0.00 0.00 0.00 3.18
17 18 3.659850 GCTTTGGCCGTTTTCTTGT 57.340 47.368 0.00 0.00 0.00 3.16
31 32 1.172812 GCGTCAGGTCAAAGGGCTTT 61.173 55.000 0.00 0.00 0.00 3.51
33 34 2.032681 GCGTCAGGTCAAAGGGCT 59.967 61.111 0.00 0.00 0.00 5.19
34 35 1.452145 TTTGCGTCAGGTCAAAGGGC 61.452 55.000 0.00 0.00 0.00 5.19
35 36 0.310854 GTTTGCGTCAGGTCAAAGGG 59.689 55.000 0.00 0.00 33.43 3.95
36 37 1.021202 TGTTTGCGTCAGGTCAAAGG 58.979 50.000 0.00 0.00 33.43 3.11
37 38 2.159448 TGTTGTTTGCGTCAGGTCAAAG 60.159 45.455 0.00 0.00 33.43 2.77
38 39 1.813178 TGTTGTTTGCGTCAGGTCAAA 59.187 42.857 0.00 0.00 0.00 2.69
41 42 0.315869 CGTGTTGTTTGCGTCAGGTC 60.316 55.000 0.00 0.00 0.00 3.85
42 43 1.711060 CCGTGTTGTTTGCGTCAGGT 61.711 55.000 0.00 0.00 0.00 4.00
43 44 1.010125 CCGTGTTGTTTGCGTCAGG 60.010 57.895 0.00 0.00 0.00 3.86
44 45 0.375454 TTCCGTGTTGTTTGCGTCAG 59.625 50.000 0.00 0.00 0.00 3.51
45 46 1.018148 ATTCCGTGTTGTTTGCGTCA 58.982 45.000 0.00 0.00 0.00 4.35
48 49 0.030101 ACCATTCCGTGTTGTTTGCG 59.970 50.000 0.00 0.00 0.00 4.85
49 50 3.569250 ATACCATTCCGTGTTGTTTGC 57.431 42.857 0.00 0.00 0.00 3.68
50 51 6.836577 AAAAATACCATTCCGTGTTGTTTG 57.163 33.333 0.00 0.00 0.00 2.93
52 53 9.849166 CTTATAAAAATACCATTCCGTGTTGTT 57.151 29.630 0.00 0.00 0.00 2.83
54 55 7.918562 CCCTTATAAAAATACCATTCCGTGTTG 59.081 37.037 0.00 0.00 0.00 3.33
55 56 7.835181 TCCCTTATAAAAATACCATTCCGTGTT 59.165 33.333 0.00 0.00 0.00 3.32
56 57 7.348033 TCCCTTATAAAAATACCATTCCGTGT 58.652 34.615 0.00 0.00 0.00 4.49
57 58 7.811117 TCCCTTATAAAAATACCATTCCGTG 57.189 36.000 0.00 0.00 0.00 4.94
58 59 8.057011 AGTTCCCTTATAAAAATACCATTCCGT 58.943 33.333 0.00 0.00 0.00 4.69
59 60 8.459911 AGTTCCCTTATAAAAATACCATTCCG 57.540 34.615 0.00 0.00 0.00 4.30
63 64 9.346005 CCGTTAGTTCCCTTATAAAAATACCAT 57.654 33.333 0.00 0.00 0.00 3.55
67 68 8.266473 TCTGCCGTTAGTTCCCTTATAAAAATA 58.734 33.333 0.00 0.00 0.00 1.40
68 69 7.114095 TCTGCCGTTAGTTCCCTTATAAAAAT 58.886 34.615 0.00 0.00 0.00 1.82
70 71 6.052405 TCTGCCGTTAGTTCCCTTATAAAA 57.948 37.500 0.00 0.00 0.00 1.52
71 72 5.680594 TCTGCCGTTAGTTCCCTTATAAA 57.319 39.130 0.00 0.00 0.00 1.40
72 73 5.395990 CCTTCTGCCGTTAGTTCCCTTATAA 60.396 44.000 0.00 0.00 0.00 0.98
73 74 4.100498 CCTTCTGCCGTTAGTTCCCTTATA 59.900 45.833 0.00 0.00 0.00 0.98
76 77 1.003233 CCTTCTGCCGTTAGTTCCCTT 59.997 52.381 0.00 0.00 0.00 3.95
77 78 0.613777 CCTTCTGCCGTTAGTTCCCT 59.386 55.000 0.00 0.00 0.00 4.20
78 79 0.611714 TCCTTCTGCCGTTAGTTCCC 59.388 55.000 0.00 0.00 0.00 3.97
79 80 1.001633 TGTCCTTCTGCCGTTAGTTCC 59.998 52.381 0.00 0.00 0.00 3.62
80 81 2.450609 TGTCCTTCTGCCGTTAGTTC 57.549 50.000 0.00 0.00 0.00 3.01
82 83 2.922740 TTTGTCCTTCTGCCGTTAGT 57.077 45.000 0.00 0.00 0.00 2.24
83 84 4.215399 TCAAATTTGTCCTTCTGCCGTTAG 59.785 41.667 17.47 0.00 0.00 2.34
87 88 2.669391 GCTCAAATTTGTCCTTCTGCCG 60.669 50.000 17.47 0.00 0.00 5.69
88 89 2.297033 TGCTCAAATTTGTCCTTCTGCC 59.703 45.455 17.47 0.00 0.00 4.85
90 91 4.037208 AGTGTGCTCAAATTTGTCCTTCTG 59.963 41.667 17.47 2.96 0.00 3.02
92 93 4.574599 AGTGTGCTCAAATTTGTCCTTC 57.425 40.909 17.47 7.02 0.00 3.46
93 94 4.498009 CGAAGTGTGCTCAAATTTGTCCTT 60.498 41.667 17.47 10.87 0.00 3.36
94 95 3.003689 CGAAGTGTGCTCAAATTTGTCCT 59.996 43.478 17.47 3.77 0.00 3.85
95 96 3.003275 TCGAAGTGTGCTCAAATTTGTCC 59.997 43.478 17.47 10.25 0.00 4.02
96 97 4.209452 TCGAAGTGTGCTCAAATTTGTC 57.791 40.909 17.47 11.20 0.00 3.18
97 98 4.630894 TTCGAAGTGTGCTCAAATTTGT 57.369 36.364 17.47 0.00 0.00 2.83
98 99 5.947503 TTTTCGAAGTGTGCTCAAATTTG 57.052 34.783 12.15 12.15 0.00 2.32
101 102 5.437289 TGATTTTCGAAGTGTGCTCAAAT 57.563 34.783 0.00 0.00 0.00 2.32
102 103 4.891627 TGATTTTCGAAGTGTGCTCAAA 57.108 36.364 0.00 0.00 0.00 2.69
107 108 2.228822 ACCCATGATTTTCGAAGTGTGC 59.771 45.455 0.00 0.00 0.00 4.57
108 109 4.475944 GAACCCATGATTTTCGAAGTGTG 58.524 43.478 0.00 0.00 0.00 3.82
109 110 3.188460 CGAACCCATGATTTTCGAAGTGT 59.812 43.478 14.50 0.00 43.83 3.55
110 111 3.435327 TCGAACCCATGATTTTCGAAGTG 59.565 43.478 17.99 0.00 45.95 3.16
111 112 3.670625 TCGAACCCATGATTTTCGAAGT 58.329 40.909 17.99 0.00 45.95 3.01
114 115 3.328382 ACTCGAACCCATGATTTTCGA 57.672 42.857 18.72 18.72 46.55 3.71
115 116 5.447279 CCTTAACTCGAACCCATGATTTTCG 60.447 44.000 13.83 13.83 42.75 3.46
116 117 5.163652 CCCTTAACTCGAACCCATGATTTTC 60.164 44.000 0.00 0.00 0.00 2.29
117 118 4.705023 CCCTTAACTCGAACCCATGATTTT 59.295 41.667 0.00 0.00 0.00 1.82
118 119 4.270008 CCCTTAACTCGAACCCATGATTT 58.730 43.478 0.00 0.00 0.00 2.17
119 120 3.886123 CCCTTAACTCGAACCCATGATT 58.114 45.455 0.00 0.00 0.00 2.57
120 121 2.421529 GCCCTTAACTCGAACCCATGAT 60.422 50.000 0.00 0.00 0.00 2.45
121 122 1.065709 GCCCTTAACTCGAACCCATGA 60.066 52.381 0.00 0.00 0.00 3.07
122 123 1.339631 TGCCCTTAACTCGAACCCATG 60.340 52.381 0.00 0.00 0.00 3.66
123 124 0.988832 TGCCCTTAACTCGAACCCAT 59.011 50.000 0.00 0.00 0.00 4.00
124 125 0.035739 GTGCCCTTAACTCGAACCCA 59.964 55.000 0.00 0.00 0.00 4.51
125 126 0.035739 TGTGCCCTTAACTCGAACCC 59.964 55.000 0.00 0.00 0.00 4.11
126 127 1.886886 TTGTGCCCTTAACTCGAACC 58.113 50.000 0.00 0.00 0.00 3.62
127 128 3.252458 ACATTTGTGCCCTTAACTCGAAC 59.748 43.478 0.00 0.00 0.00 3.95
128 129 3.482436 ACATTTGTGCCCTTAACTCGAA 58.518 40.909 0.00 0.00 0.00 3.71
129 130 3.134574 ACATTTGTGCCCTTAACTCGA 57.865 42.857 0.00 0.00 0.00 4.04
130 131 5.365403 TTTACATTTGTGCCCTTAACTCG 57.635 39.130 0.00 0.00 0.00 4.18
131 132 6.687604 ACATTTACATTTGTGCCCTTAACTC 58.312 36.000 0.00 0.00 0.00 3.01
132 133 6.295067 GGACATTTACATTTGTGCCCTTAACT 60.295 38.462 0.00 0.00 0.00 2.24
133 134 5.867174 GGACATTTACATTTGTGCCCTTAAC 59.133 40.000 0.00 0.00 0.00 2.01
134 135 5.046950 GGGACATTTACATTTGTGCCCTTAA 60.047 40.000 2.54 0.00 45.56 1.85
135 136 4.464597 GGGACATTTACATTTGTGCCCTTA 59.535 41.667 2.54 0.00 45.56 2.69
136 137 3.260632 GGGACATTTACATTTGTGCCCTT 59.739 43.478 2.54 0.00 45.56 3.95
137 138 2.831526 GGGACATTTACATTTGTGCCCT 59.168 45.455 2.54 0.00 45.56 5.19
138 139 3.245518 GGGACATTTACATTTGTGCCC 57.754 47.619 2.54 0.00 45.56 5.36
140 141 8.546597 AAAATTAGGGACATTTACATTTGTGC 57.453 30.769 0.00 0.00 33.89 4.57
146 147 9.830975 GGCATTAAAAATTAGGGACATTTACAT 57.169 29.630 0.00 0.00 0.00 2.29
147 148 8.816894 TGGCATTAAAAATTAGGGACATTTACA 58.183 29.630 0.00 0.00 0.00 2.41
148 149 9.660180 TTGGCATTAAAAATTAGGGACATTTAC 57.340 29.630 0.00 0.00 0.00 2.01
150 151 9.008965 GTTTGGCATTAAAAATTAGGGACATTT 57.991 29.630 0.00 0.00 0.00 2.32
151 152 8.382405 AGTTTGGCATTAAAAATTAGGGACATT 58.618 29.630 0.00 0.00 0.00 2.71
152 153 7.917003 AGTTTGGCATTAAAAATTAGGGACAT 58.083 30.769 0.00 0.00 0.00 3.06
153 154 7.234577 AGAGTTTGGCATTAAAAATTAGGGACA 59.765 33.333 0.00 0.00 0.00 4.02
154 155 7.545615 CAGAGTTTGGCATTAAAAATTAGGGAC 59.454 37.037 0.00 0.00 0.00 4.46
155 156 7.234577 ACAGAGTTTGGCATTAAAAATTAGGGA 59.765 33.333 0.00 0.00 0.00 4.20
156 157 7.386059 ACAGAGTTTGGCATTAAAAATTAGGG 58.614 34.615 0.00 0.00 0.00 3.53
157 158 9.921637 TTACAGAGTTTGGCATTAAAAATTAGG 57.078 29.630 0.00 0.00 0.00 2.69
218 220 0.561184 TACTCATCGGGACCCCTCAT 59.439 55.000 4.46 0.00 0.00 2.90
219 221 0.106167 CTACTCATCGGGACCCCTCA 60.106 60.000 4.46 0.00 0.00 3.86
220 222 0.106116 ACTACTCATCGGGACCCCTC 60.106 60.000 4.46 0.00 0.00 4.30
221 223 1.229131 TACTACTCATCGGGACCCCT 58.771 55.000 4.46 0.00 0.00 4.79
223 225 2.622470 GTCTTACTACTCATCGGGACCC 59.378 54.545 0.00 0.00 0.00 4.46
244 248 9.247126 GGATCATAGATGAATTATCGTGATGAG 57.753 37.037 11.41 0.00 41.65 2.90
264 268 3.244580 AGATGCGCCCGGGATCAT 61.245 61.111 29.31 25.36 45.21 2.45
276 280 1.466856 TGTTCATTGGGAGCAGATGC 58.533 50.000 0.00 0.00 42.49 3.91
326 343 2.151202 TCCAGCCTTGCGTAGAAAAAG 58.849 47.619 0.00 0.00 0.00 2.27
344 362 4.626081 ACACACCTGGCGCACTCC 62.626 66.667 10.83 0.00 0.00 3.85
359 377 4.487714 TTTACCCACAAAATTTGGCACA 57.512 36.364 10.71 0.00 32.13 4.57
371 389 3.332187 TCCTCCAATGTCATTTACCCACA 59.668 43.478 0.00 0.00 0.00 4.17
388 406 2.074576 GTTTTTACCACGAGCTCCTCC 58.925 52.381 8.47 0.00 0.00 4.30
408 426 5.726138 GCACTGTTCAGAGCTCATTTTATCG 60.726 44.000 17.77 0.00 0.00 2.92
411 429 4.388485 TGCACTGTTCAGAGCTCATTTTA 58.612 39.130 17.77 0.00 0.00 1.52
474 496 3.673809 GTGGTGTCTCGACATTTGAGTAC 59.326 47.826 2.75 0.00 43.97 2.73
487 509 4.037923 ACATGTCAAATTTGGTGGTGTCTC 59.962 41.667 17.90 0.05 0.00 3.36
489 511 4.320608 ACATGTCAAATTTGGTGGTGTC 57.679 40.909 17.90 2.13 0.00 3.67
563 587 8.918202 TCTAGTGGATGAACTGTAAAACAAAT 57.082 30.769 0.00 0.00 0.00 2.32
567 599 5.932303 TGCTCTAGTGGATGAACTGTAAAAC 59.068 40.000 0.00 0.00 0.00 2.43
569 601 5.738619 TGCTCTAGTGGATGAACTGTAAA 57.261 39.130 0.00 0.00 0.00 2.01
572 604 3.771479 TGATGCTCTAGTGGATGAACTGT 59.229 43.478 3.33 0.00 0.00 3.55
574 606 4.713814 TCTTGATGCTCTAGTGGATGAACT 59.286 41.667 3.33 0.00 0.00 3.01
595 627 2.998949 GATTTGGCTCCCGGGTCT 59.001 61.111 22.86 0.00 0.00 3.85
654 686 2.030805 GGCTATTTCGAATCACCATGGC 60.031 50.000 13.04 2.45 0.00 4.40
867 1120 2.301296 CTGGACACACAAGTCTCCATCT 59.699 50.000 0.00 0.00 41.24 2.90
975 1229 2.750888 GGAGTTGATTGCCGACGCC 61.751 63.158 0.00 0.00 41.05 5.68
981 1235 1.031571 TGGCGATGGAGTTGATTGCC 61.032 55.000 0.00 0.00 46.89 4.52
982 1236 1.027357 ATGGCGATGGAGTTGATTGC 58.973 50.000 0.00 0.00 0.00 3.56
1009 1263 3.259876 TCACTAGTAACCGCAGAAATGGT 59.740 43.478 0.00 0.00 41.20 3.55
1026 1280 1.045407 ACCGGCTGACAAGTTCACTA 58.955 50.000 0.00 0.00 0.00 2.74
1038 1292 0.462759 GGAAGGAGATGAACCGGCTG 60.463 60.000 0.00 0.00 0.00 4.85
1077 1331 2.972625 TCTAGTTGTGTGTGGCTATGC 58.027 47.619 0.00 0.00 0.00 3.14
1098 1359 2.398754 TCTCCACCAACTTCTCCTCA 57.601 50.000 0.00 0.00 0.00 3.86
1276 1537 2.120232 GTCGATGATACTGCCGTCAAG 58.880 52.381 0.00 0.00 0.00 3.02
1277 1538 1.533129 CGTCGATGATACTGCCGTCAA 60.533 52.381 0.00 0.00 0.00 3.18
1278 1539 0.028902 CGTCGATGATACTGCCGTCA 59.971 55.000 0.00 0.00 0.00 4.35
1282 1543 0.669077 ACCTCGTCGATGATACTGCC 59.331 55.000 7.99 0.00 0.00 4.85
1365 1632 1.443802 GAGGACGCTTGAAAGGGAAG 58.556 55.000 13.42 0.00 41.06 3.46
1366 1633 0.320421 CGAGGACGCTTGAAAGGGAA 60.320 55.000 13.42 0.00 41.06 3.97
1367 1634 1.183030 TCGAGGACGCTTGAAAGGGA 61.183 55.000 13.42 0.00 41.06 4.20
1368 1635 0.320421 TTCGAGGACGCTTGAAAGGG 60.320 55.000 5.64 5.64 43.82 3.95
1369 1636 1.071605 CTTCGAGGACGCTTGAAAGG 58.928 55.000 0.00 0.00 39.58 3.11
1370 1637 2.065993 TCTTCGAGGACGCTTGAAAG 57.934 50.000 0.00 0.00 39.58 2.62
1371 1638 2.132762 GTTCTTCGAGGACGCTTGAAA 58.867 47.619 0.00 0.00 39.58 2.69
1372 1639 1.604693 GGTTCTTCGAGGACGCTTGAA 60.605 52.381 0.00 0.00 39.58 2.69
1373 1640 0.038526 GGTTCTTCGAGGACGCTTGA 60.039 55.000 0.00 0.00 39.58 3.02
1374 1641 0.319555 TGGTTCTTCGAGGACGCTTG 60.320 55.000 0.00 0.00 39.58 4.01
1375 1642 0.319641 GTGGTTCTTCGAGGACGCTT 60.320 55.000 0.00 0.00 39.58 4.68
1376 1643 1.289380 GTGGTTCTTCGAGGACGCT 59.711 57.895 0.00 0.00 39.58 5.07
1377 1644 2.087009 CGTGGTTCTTCGAGGACGC 61.087 63.158 0.00 0.00 39.58 5.19
1378 1645 0.728466 GACGTGGTTCTTCGAGGACG 60.728 60.000 0.00 0.45 41.26 4.79
1379 1646 0.388263 GGACGTGGTTCTTCGAGGAC 60.388 60.000 0.00 0.00 0.00 3.85
1380 1647 0.824595 TGGACGTGGTTCTTCGAGGA 60.825 55.000 0.00 0.00 0.00 3.71
1381 1648 0.032952 TTGGACGTGGTTCTTCGAGG 59.967 55.000 0.00 0.00 0.00 4.63
1382 1649 1.525619 GTTTGGACGTGGTTCTTCGAG 59.474 52.381 0.00 0.00 0.00 4.04
1383 1650 1.574134 GTTTGGACGTGGTTCTTCGA 58.426 50.000 0.00 0.00 0.00 3.71
1384 1651 0.231279 CGTTTGGACGTGGTTCTTCG 59.769 55.000 0.00 0.00 44.08 3.79
1385 1652 3.316006 TTCCGTTTGGACGTGGTTCTTC 61.316 50.000 0.00 0.00 46.45 2.87
1386 1653 1.407162 TTCCGTTTGGACGTGGTTCTT 60.407 47.619 0.00 0.00 46.45 2.52
1387 1654 0.178533 TTCCGTTTGGACGTGGTTCT 59.821 50.000 0.00 0.00 46.45 3.01
1388 1655 0.584876 CTTCCGTTTGGACGTGGTTC 59.415 55.000 0.00 0.00 46.45 3.62
1389 1656 0.816421 CCTTCCGTTTGGACGTGGTT 60.816 55.000 0.00 0.00 46.45 3.67
1390 1657 1.227734 CCTTCCGTTTGGACGTGGT 60.228 57.895 0.00 0.00 46.45 4.16
1391 1658 1.964373 CCCTTCCGTTTGGACGTGG 60.964 63.158 0.00 0.00 46.45 4.94
1392 1659 2.613506 GCCCTTCCGTTTGGACGTG 61.614 63.158 0.00 0.00 46.45 4.49
1393 1660 2.281276 GCCCTTCCGTTTGGACGT 60.281 61.111 0.00 0.00 46.45 4.34
1394 1661 2.281208 TGCCCTTCCGTTTGGACG 60.281 61.111 0.00 0.00 46.45 4.79
1395 1662 0.322546 ATCTGCCCTTCCGTTTGGAC 60.323 55.000 0.00 0.00 46.45 4.02
1396 1663 0.035439 GATCTGCCCTTCCGTTTGGA 60.035 55.000 0.00 0.00 44.61 3.53
1397 1664 1.032114 GGATCTGCCCTTCCGTTTGG 61.032 60.000 0.00 0.00 0.00 3.28
1398 1665 0.322456 TGGATCTGCCCTTCCGTTTG 60.322 55.000 0.00 0.00 34.58 2.93
1399 1666 0.625849 ATGGATCTGCCCTTCCGTTT 59.374 50.000 0.00 0.00 34.58 3.60
1400 1667 0.625849 AATGGATCTGCCCTTCCGTT 59.374 50.000 0.00 0.00 36.60 4.44
1401 1668 0.181350 GAATGGATCTGCCCTTCCGT 59.819 55.000 0.00 0.00 35.83 4.69
1402 1669 0.181114 TGAATGGATCTGCCCTTCCG 59.819 55.000 0.00 0.00 39.69 4.30
1558 1825 1.642037 TTCTCTACGTGCCGACCGAG 61.642 60.000 0.00 4.57 0.00 4.63
1563 1830 1.506718 CTGCTTCTCTACGTGCCGA 59.493 57.895 0.00 0.00 0.00 5.54
1617 1890 1.523032 CACGGCCGGAGAATTACCC 60.523 63.158 31.76 0.00 0.00 3.69
1703 1976 2.813474 CGAAATGCGAGCGGACCA 60.813 61.111 0.00 0.00 44.57 4.02
2043 2319 3.507233 AGATCTTTGCAAATTCTTCCGCA 59.493 39.130 13.23 0.00 0.00 5.69
2107 2386 5.246981 TCCAGATTCCTTCTCAACACATT 57.753 39.130 0.00 0.00 29.93 2.71
2212 2492 3.569701 GGATGACCTTGTTCAAAGAGCAA 59.430 43.478 0.00 0.00 32.34 3.91
2286 2566 4.900684 TGTTGCTGCCATTAGTACAGTTA 58.099 39.130 0.00 0.00 33.87 2.24
2324 2604 5.407995 GTCACTGTTTCCTTCTTCATCTGAG 59.592 44.000 0.00 0.00 0.00 3.35
2327 2607 5.059833 GTGTCACTGTTTCCTTCTTCATCT 58.940 41.667 0.00 0.00 0.00 2.90
2343 2623 3.493350 CCAGCAGTTCTACAAGTGTCACT 60.493 47.826 0.00 0.00 35.59 3.41
2354 2634 2.250031 TCGGGTTTACCAGCAGTTCTA 58.750 47.619 0.69 0.00 40.22 2.10
2391 2677 1.462283 CATGCCAACAGACTGAACTCG 59.538 52.381 10.08 0.00 0.00 4.18
2442 2728 3.543494 CAGAACTTGCAACAAAGTGTTCG 59.457 43.478 16.61 10.64 38.77 3.95
2567 2914 7.148641 AGCGTCATATTACAAGATCAGTAAGG 58.851 38.462 13.80 8.08 35.18 2.69
2608 2955 6.899089 TCAATATATCTGAAAAGCAGGACCA 58.101 36.000 0.00 0.00 44.98 4.02
2609 2956 7.807977 TTCAATATATCTGAAAAGCAGGACC 57.192 36.000 7.46 0.00 44.98 4.46
2663 3093 1.302511 AGGTAGCCAAACGCCACAG 60.303 57.895 0.00 0.00 38.78 3.66
2798 4831 6.809630 TGTTACATGTTTGCTGCTGTTATA 57.190 33.333 2.30 0.00 0.00 0.98
2980 5532 3.402110 ACTGCTCAAATTCGTCATCACA 58.598 40.909 0.00 0.00 0.00 3.58
3065 5617 0.968393 GAGAGCAGGTCTCCGGAACT 60.968 60.000 17.60 0.68 45.57 3.01
3114 5666 1.089920 GCCGTCGTAGTCTACTCCAA 58.910 55.000 8.37 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.