Multiple sequence alignment - TraesCS6A01G266500

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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 TraesCS6A01G266500 chr6A 100.000 4969 0 0 1 4969 492092565 492097533 0.000000e+00 9177.0
1 TraesCS6A01G266500 chr6A 93.210 162 11 0 3509 3670 108947703 108947864 6.430000e-59 239.0
2 TraesCS6A01G266500 chr6A 99.237 131 0 1 1 130 492082486 492082616 8.320000e-58 235.0
3 TraesCS6A01G266500 chr6A 82.587 201 25 9 4671 4867 475003725 475003919 8.550000e-38 169.0
4 TraesCS6A01G266500 chr6A 91.892 74 6 0 1042 1115 41084781 41084708 2.450000e-18 104.0
5 TraesCS6A01G266500 chr6A 100.000 48 0 0 4878 4925 492097396 492097443 6.850000e-14 89.8
6 TraesCS6A01G266500 chr6A 100.000 48 0 0 4832 4879 492097442 492097489 6.850000e-14 89.8
7 TraesCS6A01G266500 chr6A 97.222 36 1 0 4878 4913 475003884 475003919 1.490000e-05 62.1
8 TraesCS6A01G266500 chr6B 93.799 3983 170 24 855 4798 528088649 528092593 0.000000e+00 5915.0
9 TraesCS6A01G266500 chr6B 95.062 162 8 0 3509 3670 172738371 172738532 6.380000e-64 255.0
10 TraesCS6A01G266500 chr6B 97.101 138 3 1 1 137 40199467 40199604 1.080000e-56 231.0
11 TraesCS6A01G266500 chr6B 93.464 153 6 4 1 152 402551183 402551332 1.800000e-54 224.0
12 TraesCS6A01G266500 chr6B 95.652 92 3 1 4875 4966 528093018 528093108 4.010000e-31 147.0
13 TraesCS6A01G266500 chr6B 94.444 90 5 0 4790 4879 528092979 528093068 6.710000e-29 139.0
14 TraesCS6A01G266500 chr6D 96.147 3426 93 12 1374 4780 351235732 351232327 0.000000e+00 5559.0
15 TraesCS6A01G266500 chr6D 84.399 1032 88 34 132 1115 351244913 351243907 0.000000e+00 946.0
16 TraesCS6A01G266500 chr6D 93.996 533 14 3 842 1374 351240719 351240205 0.000000e+00 791.0
17 TraesCS6A01G266500 chr6D 94.444 54 3 0 766 819 351240760 351240707 3.190000e-12 84.2
18 TraesCS6A01G266500 chr5B 85.081 248 26 7 874 1116 493090615 493090374 4.970000e-60 243.0
19 TraesCS6A01G266500 chr5B 94.521 146 6 2 1 144 41643867 41644012 1.800000e-54 224.0
20 TraesCS6A01G266500 chr5D 76.908 498 68 24 1309 1785 152770165 152769694 6.430000e-59 239.0
21 TraesCS6A01G266500 chr5D 93.210 162 11 0 3509 3670 461072602 461072763 6.430000e-59 239.0
22 TraesCS6A01G266500 chr3D 91.379 174 15 0 3498 3671 598889721 598889894 6.430000e-59 239.0
23 TraesCS6A01G266500 chr3D 91.329 173 13 2 3500 3670 87925989 87926161 8.320000e-58 235.0
24 TraesCS6A01G266500 chr1D 93.210 162 11 0 3509 3670 103408718 103408879 6.430000e-59 239.0
25 TraesCS6A01G266500 chr5A 76.707 498 72 22 1309 1785 680359262 680358788 2.310000e-58 237.0
26 TraesCS6A01G266500 chr5A 97.101 138 3 1 1 137 189602139 189602276 1.080000e-56 231.0
27 TraesCS6A01G266500 chr4A 97.122 139 2 2 1 137 345052142 345052280 2.990000e-57 233.0
28 TraesCS6A01G266500 chr4A 80.081 246 31 11 878 1115 196610909 196610674 3.080000e-37 167.0
29 TraesCS6A01G266500 chr2D 90.805 174 15 1 3498 3671 299891725 299891553 1.080000e-56 231.0
30 TraesCS6A01G266500 chrUn 97.744 133 2 1 1 132 441374387 441374255 1.390000e-55 228.0
31 TraesCS6A01G266500 chrUn 91.892 74 6 0 1042 1115 414357408 414357335 2.450000e-18 104.0
32 TraesCS6A01G266500 chr7A 95.139 144 5 2 1 142 35151111 35151254 5.000000e-55 226.0
33 TraesCS6A01G266500 chr2A 97.037 135 3 1 1 134 398240133 398240267 5.000000e-55 226.0
34 TraesCS6A01G266500 chr2B 85.153 229 19 7 1639 1855 65471726 65471951 2.330000e-53 220.0
35 TraesCS6A01G266500 chr3B 83.333 180 9 6 1624 1785 45153252 45153076 4.010000e-31 147.0
36 TraesCS6A01G266500 chr3B 90.141 71 3 2 1717 1785 44683876 44683944 6.850000e-14 89.8
37 TraesCS6A01G266500 chr7B 77.295 207 33 8 1624 1827 603665838 603665643 5.260000e-20 110.0


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 TraesCS6A01G266500 chr6A 492092565 492097533 4968 False 3118.866667 9177 100.000000 1 4969 3 chr6A.!!$F4 4968
1 TraesCS6A01G266500 chr6B 528088649 528093108 4459 False 2067.000000 5915 94.631667 855 4966 3 chr6B.!!$F4 4111
2 TraesCS6A01G266500 chr6D 351232327 351235732 3405 True 5559.000000 5559 96.147000 1374 4780 1 chr6D.!!$R1 3406
3 TraesCS6A01G266500 chr6D 351240205 351244913 4708 True 607.066667 946 90.946333 132 1374 3 chr6D.!!$R2 1242

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
45 46 0.187361 TTGGTTTCAGGGGGAACTGG 59.813 55.0 0.00 0.00 38.98 4.00 F
244 247 0.248458 AAACACCAAGAAAGCACGCG 60.248 50.0 3.53 3.53 0.00 6.01 F
1497 5027 0.251341 ACAACCAAGGTGCTCCATCC 60.251 55.0 7.70 0.00 35.89 3.51 F
2681 6228 0.394565 GGCGATTCCTCTGGTATGCT 59.605 55.0 0.00 0.00 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1978 5524 0.386352 CACAGTGCGCATTTCACAGG 60.386 55.000 15.91 0.0 36.93 4.00 R
1981 5527 2.095567 AGATTCACAGTGCGCATTTCAC 60.096 45.455 15.91 0.0 34.80 3.18 R
2967 6514 0.251077 CTTGGAAAGGAGGCAGCACT 60.251 55.000 0.00 0.0 41.27 4.40 R
4453 8001 0.883833 AATTTGGCTGACTTCTGCGG 59.116 50.000 2.45 0.0 41.04 5.69 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
35 36 8.631480 ATTTTAGTAACCCTAGTTGGTTTCAG 57.369 34.615 8.49 0.00 46.45 3.02
36 37 4.635699 AGTAACCCTAGTTGGTTTCAGG 57.364 45.455 8.49 0.00 46.45 3.86
37 38 2.971901 AACCCTAGTTGGTTTCAGGG 57.028 50.000 3.93 3.93 46.45 4.45
38 39 3.978876 CCCTAGTTGGTTTCAGGGG 57.021 57.895 0.00 0.00 43.55 4.79
39 40 0.331616 CCCTAGTTGGTTTCAGGGGG 59.668 60.000 0.00 0.00 43.55 5.40
40 41 1.368374 CCTAGTTGGTTTCAGGGGGA 58.632 55.000 0.00 0.00 0.00 4.81
41 42 1.708551 CCTAGTTGGTTTCAGGGGGAA 59.291 52.381 0.00 0.00 0.00 3.97
42 43 2.554564 CCTAGTTGGTTTCAGGGGGAAC 60.555 54.545 0.00 0.00 34.56 3.62
43 44 1.231963 AGTTGGTTTCAGGGGGAACT 58.768 50.000 0.00 0.00 34.56 3.01
44 45 1.133482 AGTTGGTTTCAGGGGGAACTG 60.133 52.381 0.00 0.00 39.84 3.16
45 46 0.187361 TTGGTTTCAGGGGGAACTGG 59.813 55.000 0.00 0.00 38.98 4.00
46 47 1.076727 GGTTTCAGGGGGAACTGGG 59.923 63.158 0.00 0.00 38.98 4.45
47 48 1.076727 GTTTCAGGGGGAACTGGGG 59.923 63.158 0.00 0.00 38.98 4.96
48 49 1.388217 TTTCAGGGGGAACTGGGGT 60.388 57.895 0.00 0.00 38.98 4.95
49 50 1.002242 TTTCAGGGGGAACTGGGGTT 61.002 55.000 0.00 0.00 38.98 4.11
58 59 2.115343 GAACTGGGGTTCTGTCATCC 57.885 55.000 2.14 0.00 45.90 3.51
59 60 0.698818 AACTGGGGTTCTGTCATCCC 59.301 55.000 0.00 0.00 40.41 3.85
64 65 2.532250 GGGTTCTGTCATCCCCATTT 57.468 50.000 0.00 0.00 37.09 2.32
65 66 2.379005 GGGTTCTGTCATCCCCATTTC 58.621 52.381 0.00 0.00 37.09 2.17
66 67 2.291540 GGGTTCTGTCATCCCCATTTCA 60.292 50.000 0.00 0.00 37.09 2.69
67 68 3.430453 GGTTCTGTCATCCCCATTTCAA 58.570 45.455 0.00 0.00 0.00 2.69
68 69 3.445096 GGTTCTGTCATCCCCATTTCAAG 59.555 47.826 0.00 0.00 0.00 3.02
69 70 4.082125 GTTCTGTCATCCCCATTTCAAGT 58.918 43.478 0.00 0.00 0.00 3.16
70 71 4.387026 TCTGTCATCCCCATTTCAAGTT 57.613 40.909 0.00 0.00 0.00 2.66
71 72 4.739793 TCTGTCATCCCCATTTCAAGTTT 58.260 39.130 0.00 0.00 0.00 2.66
72 73 4.766891 TCTGTCATCCCCATTTCAAGTTTC 59.233 41.667 0.00 0.00 0.00 2.78
73 74 4.739793 TGTCATCCCCATTTCAAGTTTCT 58.260 39.130 0.00 0.00 0.00 2.52
74 75 4.523943 TGTCATCCCCATTTCAAGTTTCTG 59.476 41.667 0.00 0.00 0.00 3.02
75 76 4.766891 GTCATCCCCATTTCAAGTTTCTGA 59.233 41.667 0.00 0.00 0.00 3.27
76 77 5.420104 GTCATCCCCATTTCAAGTTTCTGAT 59.580 40.000 0.00 0.00 0.00 2.90
77 78 5.419788 TCATCCCCATTTCAAGTTTCTGATG 59.580 40.000 0.00 0.00 0.00 3.07
78 79 4.996793 TCCCCATTTCAAGTTTCTGATGA 58.003 39.130 0.00 0.00 0.00 2.92
79 80 5.392995 TCCCCATTTCAAGTTTCTGATGAA 58.607 37.500 0.00 0.00 0.00 2.57
80 81 6.018469 TCCCCATTTCAAGTTTCTGATGAAT 58.982 36.000 0.00 0.00 33.45 2.57
81 82 6.071221 TCCCCATTTCAAGTTTCTGATGAATG 60.071 38.462 0.00 0.00 33.45 2.67
82 83 6.071221 CCCCATTTCAAGTTTCTGATGAATGA 60.071 38.462 0.00 0.00 33.45 2.57
83 84 7.033791 CCCATTTCAAGTTTCTGATGAATGAG 58.966 38.462 0.00 0.00 33.45 2.90
84 85 7.309621 CCCATTTCAAGTTTCTGATGAATGAGT 60.310 37.037 0.00 0.00 33.45 3.41
85 86 8.733458 CCATTTCAAGTTTCTGATGAATGAGTA 58.267 33.333 0.00 0.00 33.45 2.59
88 89 9.950680 TTTCAAGTTTCTGATGAATGAGTAAAC 57.049 29.630 0.00 0.00 33.45 2.01
89 90 8.675705 TCAAGTTTCTGATGAATGAGTAAACA 57.324 30.769 0.00 0.00 31.56 2.83
90 91 9.288576 TCAAGTTTCTGATGAATGAGTAAACAT 57.711 29.630 0.00 0.00 31.56 2.71
91 92 9.338291 CAAGTTTCTGATGAATGAGTAAACATG 57.662 33.333 0.00 0.00 31.56 3.21
92 93 8.853077 AGTTTCTGATGAATGAGTAAACATGA 57.147 30.769 0.00 0.00 31.56 3.07
93 94 9.458727 AGTTTCTGATGAATGAGTAAACATGAT 57.541 29.630 0.00 0.00 31.56 2.45
94 95 9.499585 GTTTCTGATGAATGAGTAAACATGATG 57.500 33.333 0.00 0.00 31.56 3.07
95 96 7.255491 TCTGATGAATGAGTAAACATGATGC 57.745 36.000 0.00 0.00 0.00 3.91
96 97 6.824704 TCTGATGAATGAGTAAACATGATGCA 59.175 34.615 0.00 0.00 0.00 3.96
97 98 7.337436 TCTGATGAATGAGTAAACATGATGCAA 59.663 33.333 0.00 0.00 0.00 4.08
98 99 7.252708 TGATGAATGAGTAAACATGATGCAAC 58.747 34.615 0.00 0.00 0.00 4.17
99 100 6.572167 TGAATGAGTAAACATGATGCAACA 57.428 33.333 0.00 0.00 0.00 3.33
100 101 6.380995 TGAATGAGTAAACATGATGCAACAC 58.619 36.000 0.00 0.00 0.00 3.32
101 102 6.207221 TGAATGAGTAAACATGATGCAACACT 59.793 34.615 0.00 0.00 0.00 3.55
102 103 5.611796 TGAGTAAACATGATGCAACACTC 57.388 39.130 0.00 0.99 33.43 3.51
103 104 5.308014 TGAGTAAACATGATGCAACACTCT 58.692 37.500 0.00 0.00 33.86 3.24
104 105 6.463360 TGAGTAAACATGATGCAACACTCTA 58.537 36.000 0.00 0.00 33.86 2.43
105 106 6.934083 TGAGTAAACATGATGCAACACTCTAA 59.066 34.615 0.00 0.00 33.86 2.10
106 107 7.607607 TGAGTAAACATGATGCAACACTCTAAT 59.392 33.333 0.00 0.00 33.86 1.73
107 108 7.755591 AGTAAACATGATGCAACACTCTAATG 58.244 34.615 0.00 0.00 0.00 1.90
108 109 4.627611 ACATGATGCAACACTCTAATGC 57.372 40.909 0.00 0.00 40.45 3.56
114 115 3.678289 TGCAACACTCTAATGCATGACT 58.322 40.909 0.00 0.00 44.52 3.41
115 116 4.831107 TGCAACACTCTAATGCATGACTA 58.169 39.130 0.00 0.00 44.52 2.59
116 117 4.872124 TGCAACACTCTAATGCATGACTAG 59.128 41.667 0.00 0.00 44.52 2.57
117 118 4.260538 GCAACACTCTAATGCATGACTAGC 60.261 45.833 0.00 0.00 39.81 3.42
118 119 5.114780 CAACACTCTAATGCATGACTAGCT 58.885 41.667 0.00 0.00 0.00 3.32
119 120 6.276091 CAACACTCTAATGCATGACTAGCTA 58.724 40.000 0.00 0.00 0.00 3.32
120 121 6.083098 ACACTCTAATGCATGACTAGCTAG 57.917 41.667 19.44 19.44 0.00 3.42
121 122 5.010516 ACACTCTAATGCATGACTAGCTAGG 59.989 44.000 24.35 7.95 0.00 3.02
122 123 4.526262 ACTCTAATGCATGACTAGCTAGGG 59.474 45.833 24.35 11.76 0.00 3.53
123 124 4.483950 TCTAATGCATGACTAGCTAGGGT 58.516 43.478 24.35 5.47 0.00 4.34
124 125 3.482156 AATGCATGACTAGCTAGGGTG 57.518 47.619 24.35 18.63 0.00 4.61
125 126 1.866015 TGCATGACTAGCTAGGGTGT 58.134 50.000 24.35 4.29 0.00 4.16
126 127 1.482182 TGCATGACTAGCTAGGGTGTG 59.518 52.381 24.35 16.75 0.00 3.82
127 128 1.757118 GCATGACTAGCTAGGGTGTGA 59.243 52.381 24.35 0.00 0.00 3.58
128 129 2.482142 GCATGACTAGCTAGGGTGTGAC 60.482 54.545 24.35 9.83 0.00 3.67
129 130 2.597578 TGACTAGCTAGGGTGTGACA 57.402 50.000 24.35 9.62 0.00 3.58
130 131 2.168496 TGACTAGCTAGGGTGTGACAC 58.832 52.381 24.35 7.29 0.00 3.67
137 138 1.831106 CTAGGGTGTGACACTATGGCA 59.169 52.381 16.07 0.00 32.93 4.92
156 157 6.975196 TGGCATTTAAGGCACATGTTATAT 57.025 33.333 3.55 0.00 39.34 0.86
179 182 1.087202 AGTTCGCAAACAGACGCACA 61.087 50.000 0.00 0.00 37.88 4.57
210 213 2.092212 CCAGTCCAGCCCATCTACATTT 60.092 50.000 0.00 0.00 0.00 2.32
244 247 0.248458 AAACACCAAGAAAGCACGCG 60.248 50.000 3.53 3.53 0.00 6.01
314 317 1.234615 CCAACTAGGCAACACACCCG 61.235 60.000 0.00 0.00 41.41 5.28
334 337 5.699458 ACCCGAATGTGTTTAGTTACTTCTG 59.301 40.000 0.00 0.00 0.00 3.02
375 396 9.612066 TTTCTTTCTTTTAAATGCATGAACCTT 57.388 25.926 0.00 0.00 0.00 3.50
388 409 7.945033 TGCATGAACCTTTTCTTATCAAAAC 57.055 32.000 0.00 0.00 32.36 2.43
413 434 7.592533 ACTGATGAACTTTTCAAATCGATGTTG 59.407 33.333 0.00 6.35 43.95 3.33
418 439 8.930760 TGAACTTTTCAAATCGATGTTGTTTTT 58.069 25.926 0.00 0.00 36.59 1.94
419 440 9.408731 GAACTTTTCAAATCGATGTTGTTTTTC 57.591 29.630 0.00 3.93 0.00 2.29
422 443 9.752274 CTTTTCAAATCGATGTTGTTTTTCAAA 57.248 25.926 0.00 0.00 37.81 2.69
424 445 9.699985 TTTCAAATCGATGTTGTTTTTCAAATG 57.300 25.926 0.00 0.00 37.81 2.32
427 448 8.326713 CAAATCGATGTTGTTTTTCAAATGTGA 58.673 29.630 0.00 0.00 37.81 3.58
428 449 8.592105 AATCGATGTTGTTTTTCAAATGTGAT 57.408 26.923 0.00 0.00 37.81 3.06
429 450 7.392234 TCGATGTTGTTTTTCAAATGTGATG 57.608 32.000 0.00 0.00 37.81 3.07
430 451 7.199078 TCGATGTTGTTTTTCAAATGTGATGA 58.801 30.769 0.00 0.00 37.81 2.92
431 452 7.866898 TCGATGTTGTTTTTCAAATGTGATGAT 59.133 29.630 0.00 0.00 37.81 2.45
432 453 8.489559 CGATGTTGTTTTTCAAATGTGATGATT 58.510 29.630 0.00 0.00 37.81 2.57
684 736 2.584492 ACAAAGGCAAAGCAGTCAAC 57.416 45.000 0.00 0.00 0.00 3.18
725 777 2.268076 CCTTTGTTGGTCCAGGCCG 61.268 63.158 0.00 0.00 0.00 6.13
727 779 1.228124 TTTGTTGGTCCAGGCCGAG 60.228 57.895 0.00 0.00 0.00 4.63
733 785 3.394836 GTCCAGGCCGAGGAAGCT 61.395 66.667 19.85 0.00 36.80 3.74
769 821 3.612004 CGCAATATAGAGACCTCCCGTTC 60.612 52.174 0.00 0.00 0.00 3.95
817 869 2.583593 GGCTCTACTTGCGCCTCG 60.584 66.667 4.18 0.00 42.92 4.63
818 870 2.182030 GCTCTACTTGCGCCTCGT 59.818 61.111 4.18 1.16 0.00 4.18
819 871 1.446272 GCTCTACTTGCGCCTCGTT 60.446 57.895 4.18 0.00 0.00 3.85
823 875 1.529438 TCTACTTGCGCCTCGTTTTTG 59.471 47.619 4.18 0.00 0.00 2.44
824 876 1.263217 CTACTTGCGCCTCGTTTTTGT 59.737 47.619 4.18 0.00 0.00 2.83
832 884 3.035942 CGCCTCGTTTTTGTCTCAAAAG 58.964 45.455 7.52 0.00 0.00 2.27
976 4489 2.185608 GAGGAGGAAGCCGTGAGC 59.814 66.667 0.00 0.00 44.25 4.26
1155 4668 1.210234 GCCGCTAGGGTTTAGGGTTTA 59.790 52.381 6.02 0.00 38.44 2.01
1176 4689 1.949631 GAGCTTATTCGCGGTCCGG 60.950 63.158 14.38 0.00 37.59 5.14
1321 4851 8.407457 TGATAGATTTACTAGTTTTCAGTGCG 57.593 34.615 0.00 0.00 34.35 5.34
1497 5027 0.251341 ACAACCAAGGTGCTCCATCC 60.251 55.000 7.70 0.00 35.89 3.51
1527 5057 2.430332 AGAGTCAGAAGATGTAGCTGCC 59.570 50.000 0.00 0.00 0.00 4.85
1655 5185 6.759497 AATATCTTGTCCTGTTTTACTGGC 57.241 37.500 0.00 0.00 37.16 4.85
1978 5524 5.757850 AATTCTCCAGTCTGTTGTTCAAC 57.242 39.130 8.52 8.52 0.00 3.18
1981 5527 2.874701 CTCCAGTCTGTTGTTCAACCTG 59.125 50.000 12.23 11.50 0.00 4.00
2316 5863 2.868044 GCAAGCTCCTCTTCGAGAAACA 60.868 50.000 0.00 0.00 31.27 2.83
2317 5864 3.393800 CAAGCTCCTCTTCGAGAAACAA 58.606 45.455 0.00 0.00 31.27 2.83
2418 5965 2.541233 ACCAGCAGACAGAGGACTAT 57.459 50.000 0.00 0.00 0.00 2.12
2561 6108 3.923017 GCAAGTTCCTGCTTACATTGT 57.077 42.857 0.00 0.00 39.34 2.71
2618 6165 1.065701 CTCATGCTGCTCCTTGAATGC 59.934 52.381 0.00 0.00 0.00 3.56
2681 6228 0.394565 GGCGATTCCTCTGGTATGCT 59.605 55.000 0.00 0.00 0.00 3.79
2701 6248 1.890979 CCTAATGGAGGCTGCAGCG 60.891 63.158 31.19 15.14 38.96 5.18
2706 6253 2.659897 GGAGGCTGCAGCGTATCG 60.660 66.667 31.99 0.00 43.26 2.92
2743 6290 7.058525 GTGCCTAGTTTGGTTAACCCTATATT 58.941 38.462 21.97 5.58 37.46 1.28
2837 6384 4.666253 TGCCCTGGAGCAAGCACC 62.666 66.667 7.29 1.30 40.56 5.01
2870 6417 2.434884 GCAGCCTTCACGCAGCTA 60.435 61.111 0.00 0.00 38.17 3.32
2887 6434 5.563085 CGCAGCTACCAACTAAGGTATCTAG 60.563 48.000 0.00 0.00 42.92 2.43
2915 6462 2.290514 TGATCAAGTTGCTAAGGCTGCT 60.291 45.455 0.00 0.00 39.59 4.24
3101 6648 2.462723 AGTTTCTCCTCTAGCACTCCC 58.537 52.381 0.00 0.00 0.00 4.30
3371 6918 2.028294 CACAGGAGCAGACAGTGATCTT 60.028 50.000 0.00 0.00 41.66 2.40
3480 7027 4.670896 AGCAGCAATTTACTTTGTGGTT 57.329 36.364 0.00 0.00 0.00 3.67
3624 7171 6.095021 GTCTATATGCATCCGTATGTAGTCCA 59.905 42.308 0.19 0.00 32.91 4.02
3699 7246 9.512588 CTTAGTTATTCTCCTTCCATAATGCAT 57.487 33.333 0.00 0.00 0.00 3.96
3700 7247 9.866655 TTAGTTATTCTCCTTCCATAATGCATT 57.133 29.630 17.56 17.56 0.00 3.56
3841 7388 7.682021 GCAACTCAACCAATTGTCTTTAGTTCT 60.682 37.037 4.43 0.00 37.11 3.01
3856 7403 8.328864 GTCTTTAGTTCTTGTACACTTGAGTTG 58.671 37.037 0.00 0.00 0.00 3.16
3908 7455 5.360714 TGCCCCATGTTTTCTCATTAATCTC 59.639 40.000 0.00 0.00 0.00 2.75
3913 7460 8.186821 CCCATGTTTTCTCATTAATCTCAAGTC 58.813 37.037 0.00 0.00 0.00 3.01
4048 7596 9.406828 CTGAAATATGCACTCAAATTATGATGG 57.593 33.333 0.00 0.00 37.44 3.51
4098 7646 0.890683 ACTGTTTTATGCCAGCCAGC 59.109 50.000 0.00 0.00 31.76 4.85
4125 7673 8.739972 ACTTTTTCAAGCAAGTATTAGGGTATG 58.260 33.333 0.00 0.00 31.20 2.39
4155 7703 9.740239 ACATATGAATTATGAATTTGCTGTGAC 57.260 29.630 10.38 0.00 40.22 3.67
4296 7844 3.807071 GTGTCGCCCAAATTTGTGAAATT 59.193 39.130 16.73 0.00 42.62 1.82
4343 7891 4.908601 TTAGCTGAATCCACTTCTCCAA 57.091 40.909 0.00 0.00 34.75 3.53
4345 7893 4.313020 AGCTGAATCCACTTCTCCAATT 57.687 40.909 0.00 0.00 34.75 2.32
4347 7895 5.082425 AGCTGAATCCACTTCTCCAATTTT 58.918 37.500 0.00 0.00 34.75 1.82
4412 7960 3.953201 GCCATGTGCATAGCTTTCC 57.047 52.632 0.00 0.00 40.77 3.13
4426 7974 4.704833 TTCCTCAGCGCCTGCACC 62.705 66.667 2.29 0.00 46.23 5.01
4453 8001 2.352127 GCTTCCAATCTTGACAGTTGGC 60.352 50.000 10.04 0.00 41.64 4.52
4477 8025 2.807967 CAGAAGTCAGCCAAATTCGACA 59.192 45.455 0.00 0.00 0.00 4.35
4497 8045 5.220209 CGACAAGAAAAGTTTTGGCTTTGAC 60.220 40.000 5.36 5.14 38.54 3.18
4556 8104 3.303990 CCTTTGGAATGTCGTGACTTGTG 60.304 47.826 1.23 0.00 0.00 3.33
4610 8158 8.784043 GCACGGGAGAAAAATATAGAATTATGT 58.216 33.333 0.00 0.00 0.00 2.29
4668 8226 1.119847 CGCACATAAAACAACAACGCG 59.880 47.619 3.53 3.53 0.00 6.01
4669 8227 1.137019 GCACATAAAACAACAACGCGC 60.137 47.619 5.73 0.00 0.00 6.86
4670 8228 1.119847 CACATAAAACAACAACGCGCG 59.880 47.619 30.96 30.96 0.00 6.86
4695 8253 2.099921 GAGCATCTACAGTCGTGGTCAT 59.900 50.000 6.93 0.00 38.56 3.06
4765 8323 0.729140 GGCAAACCGCATTTCTCACG 60.729 55.000 0.00 0.00 45.17 4.35
4781 8339 1.302511 ACGCTCCACAACCACATCC 60.303 57.895 0.00 0.00 0.00 3.51
4782 8340 2.040544 CGCTCCACAACCACATCCC 61.041 63.158 0.00 0.00 0.00 3.85
4803 8755 5.431731 TCCCTCATATGTCCTACCACAAATT 59.568 40.000 1.90 0.00 0.00 1.82
4806 8758 7.000472 CCTCATATGTCCTACCACAAATTCAT 59.000 38.462 1.90 0.00 0.00 2.57
4822 8774 9.111613 CACAAATTCATATAAACCCATGCAAAT 57.888 29.630 0.00 0.00 0.00 2.32
4829 8781 3.569250 AAACCCATGCAAATGACGTAC 57.431 42.857 0.00 0.00 0.00 3.67
4867 8819 7.885297 ACATATAAACATAGCAATTCGGCATT 58.115 30.769 0.00 0.00 35.83 3.56
4876 8828 3.947196 AGCAATTCGGCATTGAGAACATA 59.053 39.130 4.52 0.00 44.78 2.29
4877 8829 4.581824 AGCAATTCGGCATTGAGAACATAT 59.418 37.500 4.52 0.00 44.78 1.78
4878 8830 5.764686 AGCAATTCGGCATTGAGAACATATA 59.235 36.000 4.52 0.00 44.78 0.86
4879 8831 5.853282 GCAATTCGGCATTGAGAACATATAC 59.147 40.000 4.52 0.00 44.78 1.47
4880 8832 6.513230 GCAATTCGGCATTGAGAACATATACA 60.513 38.462 4.52 0.00 44.78 2.29
4881 8833 7.587629 CAATTCGGCATTGAGAACATATACAT 58.412 34.615 0.00 0.00 44.78 2.29
4882 8834 8.720562 CAATTCGGCATTGAGAACATATACATA 58.279 33.333 0.00 0.00 44.78 2.29
4883 8835 7.889589 TTCGGCATTGAGAACATATACATAG 57.110 36.000 0.00 0.00 0.00 2.23
4884 8836 7.227049 TCGGCATTGAGAACATATACATAGA 57.773 36.000 0.00 0.00 0.00 1.98
4885 8837 7.840931 TCGGCATTGAGAACATATACATAGAT 58.159 34.615 0.00 0.00 0.00 1.98
4886 8838 7.976175 TCGGCATTGAGAACATATACATAGATC 59.024 37.037 0.00 0.00 0.00 2.75
4887 8839 7.761249 CGGCATTGAGAACATATACATAGATCA 59.239 37.037 0.00 0.00 0.00 2.92
4888 8840 9.440773 GGCATTGAGAACATATACATAGATCAA 57.559 33.333 0.00 0.00 0.00 2.57
4909 8861 9.546909 GATCAACATATAAACATAGCAATTCGG 57.453 33.333 0.00 0.00 0.00 4.30
4910 8862 7.359595 TCAACATATAAACATAGCAATTCGGC 58.640 34.615 0.00 0.00 0.00 5.54
4911 8863 6.875948 ACATATAAACATAGCAATTCGGCA 57.124 33.333 0.00 0.00 35.83 5.69
4912 8864 7.452880 ACATATAAACATAGCAATTCGGCAT 57.547 32.000 0.00 0.00 35.83 4.40
4913 8865 7.885297 ACATATAAACATAGCAATTCGGCATT 58.115 30.769 0.00 0.00 35.83 3.56
4914 8866 7.809331 ACATATAAACATAGCAATTCGGCATTG 59.191 33.333 0.00 0.00 44.79 2.82
4915 8867 4.717233 AAACATAGCAATTCGGCATTGA 57.283 36.364 4.52 0.00 44.78 2.57
4916 8868 3.976793 ACATAGCAATTCGGCATTGAG 57.023 42.857 4.52 0.00 44.78 3.02
4917 8869 3.544684 ACATAGCAATTCGGCATTGAGA 58.455 40.909 4.52 0.00 44.78 3.27
4918 8870 3.947196 ACATAGCAATTCGGCATTGAGAA 59.053 39.130 4.52 0.00 44.78 2.87
4919 8871 2.927553 AGCAATTCGGCATTGAGAAC 57.072 45.000 4.52 0.00 44.78 3.01
4920 8872 2.161855 AGCAATTCGGCATTGAGAACA 58.838 42.857 4.52 0.00 44.78 3.18
4921 8873 2.756760 AGCAATTCGGCATTGAGAACAT 59.243 40.909 4.52 0.00 44.78 2.71
4934 8886 8.408601 GGCATTGAGAACATATAAACACAATCT 58.591 33.333 0.00 0.00 0.00 2.40
4962 8914 7.431249 TCCGACATAGATACAACATAGAAACC 58.569 38.462 0.00 0.00 0.00 3.27
4963 8915 7.287005 TCCGACATAGATACAACATAGAAACCT 59.713 37.037 0.00 0.00 0.00 3.50
4965 8917 9.961265 CGACATAGATACAACATAGAAACCTAA 57.039 33.333 0.00 0.00 0.00 2.69
4967 8919 9.745880 ACATAGATACAACATAGAAACCTAACG 57.254 33.333 0.00 0.00 0.00 3.18
4968 8920 8.700644 CATAGATACAACATAGAAACCTAACGC 58.299 37.037 0.00 0.00 0.00 4.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.073098 CCCCTGAAACCAACTAGGGT 58.927 55.000 7.34 0.00 46.89 4.34
21 22 1.368374 TCCCCCTGAAACCAACTAGG 58.632 55.000 0.00 0.00 45.67 3.02
22 23 2.375509 AGTTCCCCCTGAAACCAACTAG 59.624 50.000 0.00 0.00 33.94 2.57
23 24 2.107552 CAGTTCCCCCTGAAACCAACTA 59.892 50.000 0.00 0.00 33.94 2.24
24 25 1.133482 CAGTTCCCCCTGAAACCAACT 60.133 52.381 0.00 0.00 33.94 3.16
25 26 1.328279 CAGTTCCCCCTGAAACCAAC 58.672 55.000 0.00 0.00 33.94 3.77
26 27 0.187361 CCAGTTCCCCCTGAAACCAA 59.813 55.000 0.00 0.00 33.94 3.67
27 28 1.725169 CCCAGTTCCCCCTGAAACCA 61.725 60.000 0.00 0.00 33.94 3.67
28 29 1.076727 CCCAGTTCCCCCTGAAACC 59.923 63.158 0.00 0.00 33.94 3.27
29 30 1.076727 CCCCAGTTCCCCCTGAAAC 59.923 63.158 0.00 0.00 33.94 2.78
30 31 1.002242 AACCCCAGTTCCCCCTGAAA 61.002 55.000 0.00 0.00 33.94 2.69
31 32 1.388217 AACCCCAGTTCCCCCTGAA 60.388 57.895 0.00 0.00 34.23 3.02
32 33 1.850755 GAACCCCAGTTCCCCCTGA 60.851 63.158 0.00 0.00 45.65 3.86
33 34 2.763902 GAACCCCAGTTCCCCCTG 59.236 66.667 0.00 0.00 45.65 4.45
40 41 0.698818 GGGATGACAGAACCCCAGTT 59.301 55.000 0.00 0.00 38.69 3.16
41 42 2.387952 GGGATGACAGAACCCCAGT 58.612 57.895 0.00 0.00 38.69 4.00
45 46 2.291540 TGAAATGGGGATGACAGAACCC 60.292 50.000 5.21 5.21 43.64 4.11
46 47 3.085952 TGAAATGGGGATGACAGAACC 57.914 47.619 0.00 0.00 0.00 3.62
47 48 4.082125 ACTTGAAATGGGGATGACAGAAC 58.918 43.478 0.00 0.00 0.00 3.01
48 49 4.387026 ACTTGAAATGGGGATGACAGAA 57.613 40.909 0.00 0.00 0.00 3.02
49 50 4.387026 AACTTGAAATGGGGATGACAGA 57.613 40.909 0.00 0.00 0.00 3.41
50 51 4.768968 AGAAACTTGAAATGGGGATGACAG 59.231 41.667 0.00 0.00 0.00 3.51
51 52 4.523943 CAGAAACTTGAAATGGGGATGACA 59.476 41.667 0.00 0.00 0.00 3.58
52 53 4.766891 TCAGAAACTTGAAATGGGGATGAC 59.233 41.667 0.00 0.00 0.00 3.06
53 54 4.996793 TCAGAAACTTGAAATGGGGATGA 58.003 39.130 0.00 0.00 0.00 2.92
54 55 5.419788 TCATCAGAAACTTGAAATGGGGATG 59.580 40.000 0.00 0.00 0.00 3.51
55 56 5.582953 TCATCAGAAACTTGAAATGGGGAT 58.417 37.500 0.00 0.00 0.00 3.85
56 57 4.996793 TCATCAGAAACTTGAAATGGGGA 58.003 39.130 0.00 0.00 0.00 4.81
57 58 5.726980 TTCATCAGAAACTTGAAATGGGG 57.273 39.130 0.00 0.00 0.00 4.96
58 59 6.927416 TCATTCATCAGAAACTTGAAATGGG 58.073 36.000 0.00 0.00 37.29 4.00
59 60 7.600065 ACTCATTCATCAGAAACTTGAAATGG 58.400 34.615 0.00 0.00 37.29 3.16
62 63 9.950680 GTTTACTCATTCATCAGAAACTTGAAA 57.049 29.630 0.00 0.00 37.29 2.69
63 64 9.119418 TGTTTACTCATTCATCAGAAACTTGAA 57.881 29.630 0.00 0.00 37.29 2.69
64 65 8.675705 TGTTTACTCATTCATCAGAAACTTGA 57.324 30.769 0.00 0.00 37.29 3.02
65 66 9.338291 CATGTTTACTCATTCATCAGAAACTTG 57.662 33.333 0.00 0.00 37.29 3.16
66 67 9.288576 TCATGTTTACTCATTCATCAGAAACTT 57.711 29.630 0.00 0.00 37.29 2.66
67 68 8.853077 TCATGTTTACTCATTCATCAGAAACT 57.147 30.769 0.00 0.00 37.29 2.66
68 69 9.499585 CATCATGTTTACTCATTCATCAGAAAC 57.500 33.333 0.00 0.00 37.29 2.78
69 70 8.186163 GCATCATGTTTACTCATTCATCAGAAA 58.814 33.333 0.00 0.00 37.29 2.52
70 71 7.337436 TGCATCATGTTTACTCATTCATCAGAA 59.663 33.333 0.00 0.00 38.31 3.02
71 72 6.824704 TGCATCATGTTTACTCATTCATCAGA 59.175 34.615 0.00 0.00 0.00 3.27
72 73 7.023197 TGCATCATGTTTACTCATTCATCAG 57.977 36.000 0.00 0.00 0.00 2.90
73 74 7.094291 TGTTGCATCATGTTTACTCATTCATCA 60.094 33.333 0.00 0.00 0.00 3.07
74 75 7.219535 GTGTTGCATCATGTTTACTCATTCATC 59.780 37.037 0.00 0.00 0.00 2.92
75 76 7.031372 GTGTTGCATCATGTTTACTCATTCAT 58.969 34.615 0.00 0.00 0.00 2.57
76 77 6.207221 AGTGTTGCATCATGTTTACTCATTCA 59.793 34.615 0.00 0.00 0.00 2.57
77 78 6.615088 AGTGTTGCATCATGTTTACTCATTC 58.385 36.000 0.00 0.00 0.00 2.67
78 79 6.432162 AGAGTGTTGCATCATGTTTACTCATT 59.568 34.615 0.00 0.00 36.63 2.57
79 80 5.942236 AGAGTGTTGCATCATGTTTACTCAT 59.058 36.000 0.00 0.00 36.63 2.90
80 81 5.308014 AGAGTGTTGCATCATGTTTACTCA 58.692 37.500 0.00 0.00 36.63 3.41
81 82 5.869753 AGAGTGTTGCATCATGTTTACTC 57.130 39.130 0.00 2.21 34.92 2.59
82 83 7.627088 GCATTAGAGTGTTGCATCATGTTTACT 60.627 37.037 0.00 0.00 36.40 2.24
83 84 6.470235 GCATTAGAGTGTTGCATCATGTTTAC 59.530 38.462 0.00 0.00 36.40 2.01
84 85 6.150809 TGCATTAGAGTGTTGCATCATGTTTA 59.849 34.615 0.00 0.00 41.18 2.01
85 86 5.047872 TGCATTAGAGTGTTGCATCATGTTT 60.048 36.000 0.00 0.00 41.18 2.83
86 87 4.460034 TGCATTAGAGTGTTGCATCATGTT 59.540 37.500 0.00 0.00 41.18 2.71
87 88 4.011698 TGCATTAGAGTGTTGCATCATGT 58.988 39.130 0.00 0.00 41.18 3.21
88 89 4.625972 TGCATTAGAGTGTTGCATCATG 57.374 40.909 0.00 0.00 41.18 3.07
94 95 4.260538 GCTAGTCATGCATTAGAGTGTTGC 60.261 45.833 7.88 4.96 36.91 4.17
95 96 5.114780 AGCTAGTCATGCATTAGAGTGTTG 58.885 41.667 7.88 0.00 0.00 3.33
96 97 5.350504 AGCTAGTCATGCATTAGAGTGTT 57.649 39.130 7.88 0.00 0.00 3.32
97 98 5.010516 CCTAGCTAGTCATGCATTAGAGTGT 59.989 44.000 19.31 0.00 0.00 3.55
98 99 5.468592 CCTAGCTAGTCATGCATTAGAGTG 58.531 45.833 19.31 0.00 0.00 3.51
99 100 4.526262 CCCTAGCTAGTCATGCATTAGAGT 59.474 45.833 19.31 4.22 0.00 3.24
100 101 4.526262 ACCCTAGCTAGTCATGCATTAGAG 59.474 45.833 19.31 0.00 0.00 2.43
101 102 4.281941 CACCCTAGCTAGTCATGCATTAGA 59.718 45.833 19.31 0.00 0.00 2.10
102 103 4.039730 ACACCCTAGCTAGTCATGCATTAG 59.960 45.833 19.31 0.00 0.00 1.73
103 104 3.967326 ACACCCTAGCTAGTCATGCATTA 59.033 43.478 19.31 0.00 0.00 1.90
104 105 2.774234 ACACCCTAGCTAGTCATGCATT 59.226 45.455 19.31 0.00 0.00 3.56
105 106 2.103771 CACACCCTAGCTAGTCATGCAT 59.896 50.000 19.31 0.00 0.00 3.96
106 107 1.482182 CACACCCTAGCTAGTCATGCA 59.518 52.381 19.31 0.00 0.00 3.96
107 108 1.757118 TCACACCCTAGCTAGTCATGC 59.243 52.381 19.31 0.00 0.00 4.06
108 109 2.760650 TGTCACACCCTAGCTAGTCATG 59.239 50.000 19.31 15.31 0.00 3.07
109 110 2.761208 GTGTCACACCCTAGCTAGTCAT 59.239 50.000 19.31 1.55 0.00 3.06
110 111 2.168496 GTGTCACACCCTAGCTAGTCA 58.832 52.381 19.31 4.53 0.00 3.41
111 112 2.448453 AGTGTCACACCCTAGCTAGTC 58.552 52.381 19.31 2.23 34.49 2.59
112 113 2.606751 AGTGTCACACCCTAGCTAGT 57.393 50.000 19.31 0.00 34.49 2.57
113 114 3.319405 CCATAGTGTCACACCCTAGCTAG 59.681 52.174 14.20 14.20 34.49 3.42
114 115 3.296854 CCATAGTGTCACACCCTAGCTA 58.703 50.000 3.66 0.00 34.49 3.32
115 116 2.111384 CCATAGTGTCACACCCTAGCT 58.889 52.381 3.66 0.00 34.49 3.32
116 117 1.473434 GCCATAGTGTCACACCCTAGC 60.473 57.143 3.66 0.00 34.49 3.42
117 118 1.831106 TGCCATAGTGTCACACCCTAG 59.169 52.381 3.66 0.00 34.49 3.02
118 119 1.945580 TGCCATAGTGTCACACCCTA 58.054 50.000 3.66 0.00 34.49 3.53
119 120 1.289160 ATGCCATAGTGTCACACCCT 58.711 50.000 3.66 0.00 34.49 4.34
120 121 2.128771 AATGCCATAGTGTCACACCC 57.871 50.000 3.66 0.00 34.49 4.61
121 122 4.096382 CCTTAAATGCCATAGTGTCACACC 59.904 45.833 3.66 0.00 34.49 4.16
122 123 4.438744 GCCTTAAATGCCATAGTGTCACAC 60.439 45.833 0.00 0.00 34.10 3.82
123 124 3.694072 GCCTTAAATGCCATAGTGTCACA 59.306 43.478 5.62 0.00 0.00 3.58
124 125 3.694072 TGCCTTAAATGCCATAGTGTCAC 59.306 43.478 0.00 0.00 0.00 3.67
125 126 3.694072 GTGCCTTAAATGCCATAGTGTCA 59.306 43.478 0.00 0.00 0.00 3.58
126 127 3.694072 TGTGCCTTAAATGCCATAGTGTC 59.306 43.478 0.00 0.00 0.00 3.67
127 128 3.696045 TGTGCCTTAAATGCCATAGTGT 58.304 40.909 0.00 0.00 0.00 3.55
128 129 4.098349 ACATGTGCCTTAAATGCCATAGTG 59.902 41.667 0.00 0.00 0.00 2.74
129 130 4.280819 ACATGTGCCTTAAATGCCATAGT 58.719 39.130 0.00 0.00 0.00 2.12
130 131 4.924305 ACATGTGCCTTAAATGCCATAG 57.076 40.909 0.00 0.00 0.00 2.23
156 157 3.122278 GTGCGTCTGTTTGCGAACTATAA 59.878 43.478 17.65 0.00 36.70 0.98
164 165 2.052237 GGTGTGCGTCTGTTTGCG 60.052 61.111 0.00 0.00 0.00 4.85
191 194 4.322057 AAAAATGTAGATGGGCTGGACT 57.678 40.909 0.00 0.00 0.00 3.85
214 217 8.188139 TGCTTTCTTGGTGTTTAAAAGTAGAAG 58.812 33.333 0.00 0.00 31.24 2.85
220 223 4.026886 GCGTGCTTTCTTGGTGTTTAAAAG 60.027 41.667 0.00 0.00 0.00 2.27
227 230 3.022287 CGCGTGCTTTCTTGGTGT 58.978 55.556 0.00 0.00 0.00 4.16
251 254 1.805345 AGAGGTGTGTTCGAGTCGTAG 59.195 52.381 13.12 0.00 0.00 3.51
255 258 1.609555 AGACAGAGGTGTGTTCGAGTC 59.390 52.381 0.00 0.00 36.88 3.36
300 303 0.398696 ACATTCGGGTGTGTTGCCTA 59.601 50.000 0.00 0.00 0.00 3.93
311 314 5.699458 ACAGAAGTAACTAAACACATTCGGG 59.301 40.000 0.00 0.00 0.00 5.14
367 388 9.918630 CATCAGTTTTGATAAGAAAAGGTTCAT 57.081 29.630 0.00 0.00 42.12 2.57
388 409 7.592533 ACAACATCGATTTGAAAAGTTCATCAG 59.407 33.333 20.06 2.85 39.84 2.90
676 728 0.880278 TCAGCTCAACCGTTGACTGC 60.880 55.000 24.37 20.23 38.03 4.40
684 736 3.175240 CGCTCGTCAGCTCAACCG 61.175 66.667 0.00 0.00 44.40 4.44
779 831 1.659098 CATCAAGTCCCGTAGCGAAAC 59.341 52.381 0.00 0.00 0.00 2.78
790 842 2.911484 CAAGTAGAGCCCATCAAGTCC 58.089 52.381 0.00 0.00 0.00 3.85
791 843 2.284190 GCAAGTAGAGCCCATCAAGTC 58.716 52.381 0.00 0.00 0.00 3.01
839 891 3.782042 CCTACGAGGCGCAAGTTC 58.218 61.111 10.83 0.00 41.68 3.01
958 4471 2.355193 GCTCACGGCTTCCTCCTCT 61.355 63.158 0.00 0.00 38.06 3.69
976 4489 0.318699 TCTCTCGCCAACTTGTCACG 60.319 55.000 0.00 0.00 0.00 4.35
977 4490 1.423395 CTCTCTCGCCAACTTGTCAC 58.577 55.000 0.00 0.00 0.00 3.67
978 4491 0.318441 CCTCTCTCGCCAACTTGTCA 59.682 55.000 0.00 0.00 0.00 3.58
979 4492 0.603569 TCCTCTCTCGCCAACTTGTC 59.396 55.000 0.00 0.00 0.00 3.18
980 4493 0.605589 CTCCTCTCTCGCCAACTTGT 59.394 55.000 0.00 0.00 0.00 3.16
981 4494 0.891373 TCTCCTCTCTCGCCAACTTG 59.109 55.000 0.00 0.00 0.00 3.16
1155 4668 1.442148 GACCGCGAATAAGCTCCCT 59.558 57.895 8.23 0.00 34.40 4.20
1176 4689 0.392336 CTACTCCAGATGCTCCAGCC 59.608 60.000 0.00 0.00 41.18 4.85
1306 4836 4.694339 AGAGAAACGCACTGAAAACTAGT 58.306 39.130 0.00 0.00 0.00 2.57
1307 4837 4.985409 AGAGAGAAACGCACTGAAAACTAG 59.015 41.667 0.00 0.00 0.00 2.57
1308 4838 4.745125 CAGAGAGAAACGCACTGAAAACTA 59.255 41.667 0.00 0.00 0.00 2.24
1321 4851 7.496747 AGCTATTCATCTAACCAGAGAGAAAC 58.503 38.462 0.00 0.00 34.41 2.78
1497 5027 5.226396 ACATCTTCTGACTCTTGTTTCTCG 58.774 41.667 0.00 0.00 0.00 4.04
1655 5185 4.707105 TGCATAGGATAACCACTGTCATG 58.293 43.478 0.00 0.00 38.94 3.07
1978 5524 0.386352 CACAGTGCGCATTTCACAGG 60.386 55.000 15.91 0.00 36.93 4.00
1981 5527 2.095567 AGATTCACAGTGCGCATTTCAC 60.096 45.455 15.91 0.00 34.80 3.18
2316 5863 6.894103 AGATATTTGTCTCTTTGCCCAGATTT 59.106 34.615 0.00 0.00 0.00 2.17
2317 5864 6.430007 AGATATTTGTCTCTTTGCCCAGATT 58.570 36.000 0.00 0.00 0.00 2.40
2561 6108 0.465460 GTTTGGGTCTGGTGCTGTGA 60.465 55.000 0.00 0.00 0.00 3.58
2618 6165 3.285484 CAGGAGATTGAAACCATGGGAG 58.715 50.000 18.09 0.00 0.00 4.30
2743 6290 7.308589 GCTCTGTAATAGGCAAAGAAAACAAGA 60.309 37.037 0.00 0.00 0.00 3.02
2837 6384 2.487934 GCTGCACCAGTAGGATATGTG 58.512 52.381 0.00 0.00 38.69 3.21
2870 6417 3.383825 CGCCACTAGATACCTTAGTTGGT 59.616 47.826 0.00 0.00 43.66 3.67
2887 6434 1.089920 AGCAACTTGATCATCGCCAC 58.910 50.000 0.00 0.00 0.00 5.01
2915 6462 2.420547 GGCACCTTCAGCAGTCATCATA 60.421 50.000 0.00 0.00 0.00 2.15
2967 6514 0.251077 CTTGGAAAGGAGGCAGCACT 60.251 55.000 0.00 0.00 41.27 4.40
2968 6515 2.261215 CTTGGAAAGGAGGCAGCAC 58.739 57.895 0.00 0.00 41.27 4.40
3127 6674 4.148079 TGCACAAAATGTCCTACCAATCA 58.852 39.130 0.00 0.00 0.00 2.57
3371 6918 2.001872 CATGCATTCAGTACGACAGCA 58.998 47.619 0.00 12.20 37.86 4.41
3480 7027 9.778741 AAGAGAATCACAAAGTAAATGTAGACA 57.221 29.630 0.00 0.00 37.82 3.41
3512 7059 4.285260 GGGCTTATATTTAGGAACGGAGGA 59.715 45.833 0.00 0.00 0.00 3.71
3607 7154 2.882927 TGTGGACTACATACGGATGC 57.117 50.000 7.78 0.00 36.43 3.91
3699 7246 1.495584 GAGCGAGCCACGTGTTTCAA 61.496 55.000 15.65 0.00 44.60 2.69
3700 7247 1.954146 GAGCGAGCCACGTGTTTCA 60.954 57.895 15.65 0.00 44.60 2.69
3841 7388 5.297547 GGAGATGACAACTCAAGTGTACAA 58.702 41.667 13.99 0.00 36.26 2.41
3856 7403 1.520342 GAGCCACTGCGGAGATGAC 60.520 63.158 12.26 0.00 44.33 3.06
4048 7596 3.341823 ACTCCATCAGCATGTTCAGTTC 58.658 45.455 0.00 0.00 37.40 3.01
4098 7646 6.981722 ACCCTAATACTTGCTTGAAAAAGTG 58.018 36.000 3.85 0.00 37.23 3.16
4139 7687 5.050644 CTGCAAGTCACAGCAAATTCATA 57.949 39.130 0.00 0.00 40.73 2.15
4181 7729 2.000048 AGGGGTTGAGCCAATCCTTAA 59.000 47.619 14.49 0.00 43.60 1.85
4227 7775 6.043938 ACCCACTTGGAACTTAGTTGAATAGA 59.956 38.462 0.93 0.00 37.39 1.98
4356 7904 8.433126 CCTGAAGAAAGTAGTTTACACATTACG 58.567 37.037 0.00 0.00 0.00 3.18
4426 7974 1.471684 GTCAAGATTGGAAGCTGCCAG 59.528 52.381 14.77 1.46 39.52 4.85
4453 8001 0.883833 AATTTGGCTGACTTCTGCGG 59.116 50.000 2.45 0.00 41.04 5.69
4477 8025 5.066968 TCGTCAAAGCCAAAACTTTTCTT 57.933 34.783 0.00 0.00 37.78 2.52
4497 8045 2.545526 GCCACATTACATGGACAGATCG 59.454 50.000 0.00 0.00 39.87 3.69
4556 8104 2.084546 GGTGGCAGGTCATACAAGAAC 58.915 52.381 0.00 0.00 0.00 3.01
4610 8158 3.181458 GGTTTGCTTCTCACCGGGATATA 60.181 47.826 6.32 0.00 0.00 0.86
4668 8226 2.223294 ACGACTGTAGATGCTCTTACGC 60.223 50.000 0.00 0.00 0.00 4.42
4669 8227 3.355270 CACGACTGTAGATGCTCTTACG 58.645 50.000 0.00 0.00 0.00 3.18
4670 8228 3.128938 ACCACGACTGTAGATGCTCTTAC 59.871 47.826 0.00 0.00 0.00 2.34
4687 8245 2.099098 GGCCCAAAATTAGATGACCACG 59.901 50.000 0.00 0.00 0.00 4.94
4695 8253 4.510205 GCCATATAGGGGCCCAAAATTAGA 60.510 45.833 27.72 5.32 45.87 2.10
4765 8323 0.678048 GAGGGATGTGGTTGTGGAGC 60.678 60.000 0.00 0.00 0.00 4.70
4781 8339 6.356556 TGAATTTGTGGTAGGACATATGAGG 58.643 40.000 10.38 0.00 0.00 3.86
4782 8340 9.730705 ATATGAATTTGTGGTAGGACATATGAG 57.269 33.333 10.38 0.00 31.47 2.90
4803 8755 5.592282 ACGTCATTTGCATGGGTTTATATGA 59.408 36.000 0.00 0.00 0.00 2.15
4806 8758 5.297278 GGTACGTCATTTGCATGGGTTTATA 59.703 40.000 0.00 0.00 0.00 0.98
4822 8774 6.954487 ATGTTGATCTATGTAGGTACGTCA 57.046 37.500 0.00 0.00 0.00 4.35
4883 8835 9.546909 CCGAATTGCTATGTTTATATGTTGATC 57.453 33.333 0.00 0.00 0.00 2.92
4884 8836 8.023128 GCCGAATTGCTATGTTTATATGTTGAT 58.977 33.333 0.00 0.00 0.00 2.57
4885 8837 7.012799 TGCCGAATTGCTATGTTTATATGTTGA 59.987 33.333 0.00 0.00 0.00 3.18
4886 8838 7.138081 TGCCGAATTGCTATGTTTATATGTTG 58.862 34.615 0.00 0.00 0.00 3.33
4887 8839 7.270757 TGCCGAATTGCTATGTTTATATGTT 57.729 32.000 0.00 0.00 0.00 2.71
4888 8840 6.875948 TGCCGAATTGCTATGTTTATATGT 57.124 33.333 0.00 0.00 0.00 2.29
4889 8841 8.022550 TCAATGCCGAATTGCTATGTTTATATG 58.977 33.333 6.05 0.00 44.63 1.78
4890 8842 8.109705 TCAATGCCGAATTGCTATGTTTATAT 57.890 30.769 6.05 0.00 44.63 0.86
4891 8843 7.443879 TCTCAATGCCGAATTGCTATGTTTATA 59.556 33.333 6.05 0.00 44.63 0.98
4892 8844 6.262944 TCTCAATGCCGAATTGCTATGTTTAT 59.737 34.615 6.05 0.00 44.63 1.40
4893 8845 5.588246 TCTCAATGCCGAATTGCTATGTTTA 59.412 36.000 6.05 0.00 44.63 2.01
4894 8846 4.398988 TCTCAATGCCGAATTGCTATGTTT 59.601 37.500 6.05 0.00 44.63 2.83
4895 8847 3.947196 TCTCAATGCCGAATTGCTATGTT 59.053 39.130 6.05 0.00 44.63 2.71
4896 8848 3.544684 TCTCAATGCCGAATTGCTATGT 58.455 40.909 6.05 0.00 44.63 2.29
4897 8849 4.201940 TGTTCTCAATGCCGAATTGCTATG 60.202 41.667 6.05 0.00 44.63 2.23
4898 8850 3.947196 TGTTCTCAATGCCGAATTGCTAT 59.053 39.130 6.05 0.00 44.63 2.97
4899 8851 3.342719 TGTTCTCAATGCCGAATTGCTA 58.657 40.909 6.05 0.00 44.63 3.49
4900 8852 2.161855 TGTTCTCAATGCCGAATTGCT 58.838 42.857 6.05 0.00 44.63 3.91
4901 8853 2.634982 TGTTCTCAATGCCGAATTGC 57.365 45.000 6.05 0.00 44.63 3.56
4902 8854 7.914871 TGTTTATATGTTCTCAATGCCGAATTG 59.085 33.333 4.85 4.85 46.10 2.32
4903 8855 7.915397 GTGTTTATATGTTCTCAATGCCGAATT 59.085 33.333 0.00 0.00 0.00 2.17
4904 8856 7.066887 TGTGTTTATATGTTCTCAATGCCGAAT 59.933 33.333 0.00 0.00 0.00 3.34
4905 8857 6.372937 TGTGTTTATATGTTCTCAATGCCGAA 59.627 34.615 0.00 0.00 0.00 4.30
4906 8858 5.877564 TGTGTTTATATGTTCTCAATGCCGA 59.122 36.000 0.00 0.00 0.00 5.54
4907 8859 6.117911 TGTGTTTATATGTTCTCAATGCCG 57.882 37.500 0.00 0.00 0.00 5.69
4908 8860 8.408601 AGATTGTGTTTATATGTTCTCAATGCC 58.591 33.333 0.00 0.00 0.00 4.40
4909 8861 9.229784 CAGATTGTGTTTATATGTTCTCAATGC 57.770 33.333 0.00 0.00 0.00 3.56
4913 8865 9.330063 GGATCAGATTGTGTTTATATGTTCTCA 57.670 33.333 0.00 0.00 0.00 3.27
4914 8866 8.491152 CGGATCAGATTGTGTTTATATGTTCTC 58.509 37.037 0.00 0.00 0.00 2.87
4915 8867 8.204160 TCGGATCAGATTGTGTTTATATGTTCT 58.796 33.333 0.00 0.00 0.00 3.01
4916 8868 8.276325 GTCGGATCAGATTGTGTTTATATGTTC 58.724 37.037 0.00 0.00 0.00 3.18
4917 8869 7.768582 TGTCGGATCAGATTGTGTTTATATGTT 59.231 33.333 0.00 0.00 0.00 2.71
4918 8870 7.272244 TGTCGGATCAGATTGTGTTTATATGT 58.728 34.615 0.00 0.00 0.00 2.29
4919 8871 7.713764 TGTCGGATCAGATTGTGTTTATATG 57.286 36.000 0.00 0.00 0.00 1.78
4920 8872 9.645059 CTATGTCGGATCAGATTGTGTTTATAT 57.355 33.333 0.00 0.00 0.00 0.86
4921 8873 8.856103 TCTATGTCGGATCAGATTGTGTTTATA 58.144 33.333 0.00 0.00 0.00 0.98
4934 8886 7.996098 TCTATGTTGTATCTATGTCGGATCA 57.004 36.000 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.