Multiple sequence alignment - TraesCS3D01G113000

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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 TraesCS3D01G113000 chr3D 100.000 2363 0 0 1 2363 67054616 67056978 0.000000e+00 4364.0
1 TraesCS3D01G113000 chr3D 96.552 87 2 1 666 751 14946886 14946972 2.450000e-30 143.0
2 TraesCS3D01G113000 chr3D 96.471 85 2 1 668 751 349636635 349636719 3.170000e-29 139.0
3 TraesCS3D01G113000 chr3D 93.548 93 4 2 664 755 67632290 67632199 1.140000e-28 137.0
4 TraesCS3D01G113000 chr2D 97.879 1509 13 3 874 2363 377261014 377262522 0.000000e+00 2591.0
5 TraesCS3D01G113000 chr2D 94.052 1076 32 5 751 1795 578032695 578031621 0.000000e+00 1604.0
6 TraesCS3D01G113000 chr2D 98.258 574 10 0 1790 2363 578031588 578031015 0.000000e+00 1005.0
7 TraesCS3D01G113000 chr7D 98.315 1484 6 3 898 2363 553413702 553412220 0.000000e+00 2584.0
8 TraesCS3D01G113000 chr5B 90.407 1230 29 19 946 2119 17599174 17600370 0.000000e+00 1535.0
9 TraesCS3D01G113000 chr5B 92.461 902 28 7 927 1795 386862534 386861640 0.000000e+00 1253.0
10 TraesCS3D01G113000 chr5B 97.735 574 13 0 1790 2363 386861607 386861034 0.000000e+00 989.0
11 TraesCS3D01G113000 chr5B 95.312 128 6 0 838 965 17592095 17592222 1.110000e-48 204.0
12 TraesCS3D01G113000 chr5B 83.105 219 33 4 247 463 504774571 504774787 1.850000e-46 196.0
13 TraesCS3D01G113000 chr5B 93.407 91 4 2 662 751 484943390 484943301 1.470000e-27 134.0
14 TraesCS3D01G113000 chr1B 91.317 1002 38 5 838 1795 46930195 46931191 0.000000e+00 1323.0
15 TraesCS3D01G113000 chr1B 92.794 902 27 5 927 1795 80959105 80960001 0.000000e+00 1271.0
16 TraesCS3D01G113000 chr1B 97.909 574 11 1 1790 2363 46931224 46931796 0.000000e+00 992.0
17 TraesCS3D01G113000 chr1B 97.735 574 13 0 1790 2363 80960034 80960607 0.000000e+00 989.0
18 TraesCS3D01G113000 chr1B 96.174 575 19 3 1790 2363 321234550 321233978 0.000000e+00 937.0
19 TraesCS3D01G113000 chr1B 95.086 407 10 2 1399 1795 321234989 321234583 1.190000e-177 632.0
20 TraesCS3D01G113000 chr1B 95.455 88 3 1 665 751 634510165 634510078 3.170000e-29 139.0
21 TraesCS3D01G113000 chr1B 89.474 76 8 0 753 828 554228037 554227962 1.930000e-16 97.1
22 TraesCS3D01G113000 chr2A 93.964 878 19 5 933 1777 2613356 2614232 0.000000e+00 1297.0
23 TraesCS3D01G113000 chr2A 91.954 87 7 0 745 831 33018990 33019076 3.190000e-24 122.0
24 TraesCS3D01G113000 chr3B 90.551 889 37 10 840 1696 59224664 59225537 0.000000e+00 1133.0
25 TraesCS3D01G113000 chr3B 97.735 574 13 0 1790 2363 59228075 59228648 0.000000e+00 989.0
26 TraesCS3D01G113000 chr3B 80.075 532 66 17 155 670 111851282 111851789 2.230000e-95 359.0
27 TraesCS3D01G113000 chr3B 90.977 133 10 2 1 131 111833571 111833703 6.710000e-41 178.0
28 TraesCS3D01G113000 chr3B 88.991 109 10 2 650 757 805351708 805351601 1.470000e-27 134.0
29 TraesCS3D01G113000 chr7B 92.608 744 23 4 1079 1795 108526127 108526865 0.000000e+00 1040.0
30 TraesCS3D01G113000 chr7B 97.735 574 13 0 1790 2363 108526898 108527471 0.000000e+00 989.0
31 TraesCS3D01G113000 chr7B 87.179 78 8 2 751 828 385021291 385021366 1.160000e-13 87.9
32 TraesCS3D01G113000 chr3A 81.664 529 74 18 155 670 78188189 78188707 3.630000e-113 418.0
33 TraesCS3D01G113000 chr6B 84.322 236 30 7 233 464 516082760 516082992 8.500000e-55 224.0
34 TraesCS3D01G113000 chr6B 93.478 92 3 3 669 758 632889449 632889539 1.470000e-27 134.0
35 TraesCS3D01G113000 chr2B 83.402 241 37 3 228 466 45740947 45740708 1.100000e-53 220.0
36 TraesCS3D01G113000 chr4A 83.197 244 35 5 226 467 595044969 595044730 3.950000e-53 219.0
37 TraesCS3D01G113000 chr4A 93.671 79 4 1 751 829 502347752 502347829 1.480000e-22 117.0
38 TraesCS3D01G113000 chr1D 82.996 247 34 8 225 467 383758020 383758262 1.420000e-52 217.0
39 TraesCS3D01G113000 chr1D 96.471 85 2 1 668 751 340660038 340660122 3.170000e-29 139.0
40 TraesCS3D01G113000 chr5D 84.314 204 29 3 262 463 417607120 417607322 1.850000e-46 196.0
41 TraesCS3D01G113000 chr7A 83.654 208 26 6 245 449 269136161 269136363 3.100000e-44 189.0
42 TraesCS3D01G113000 chr7A 92.593 81 6 0 751 831 29826440 29826360 1.480000e-22 117.0
43 TraesCS3D01G113000 chr6D 92.553 94 5 2 660 751 58042751 58042844 1.470000e-27 134.0


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 TraesCS3D01G113000 chr3D 67054616 67056978 2362 False 4364.0 4364 100.0000 1 2363 1 chr3D.!!$F2 2362
1 TraesCS3D01G113000 chr2D 377261014 377262522 1508 False 2591.0 2591 97.8790 874 2363 1 chr2D.!!$F1 1489
2 TraesCS3D01G113000 chr2D 578031015 578032695 1680 True 1304.5 1604 96.1550 751 2363 2 chr2D.!!$R1 1612
3 TraesCS3D01G113000 chr7D 553412220 553413702 1482 True 2584.0 2584 98.3150 898 2363 1 chr7D.!!$R1 1465
4 TraesCS3D01G113000 chr5B 17599174 17600370 1196 False 1535.0 1535 90.4070 946 2119 1 chr5B.!!$F2 1173
5 TraesCS3D01G113000 chr5B 386861034 386862534 1500 True 1121.0 1253 95.0980 927 2363 2 chr5B.!!$R2 1436
6 TraesCS3D01G113000 chr1B 46930195 46931796 1601 False 1157.5 1323 94.6130 838 2363 2 chr1B.!!$F1 1525
7 TraesCS3D01G113000 chr1B 80959105 80960607 1502 False 1130.0 1271 95.2645 927 2363 2 chr1B.!!$F2 1436
8 TraesCS3D01G113000 chr1B 321233978 321234989 1011 True 784.5 937 95.6300 1399 2363 2 chr1B.!!$R3 964
9 TraesCS3D01G113000 chr2A 2613356 2614232 876 False 1297.0 1297 93.9640 933 1777 1 chr2A.!!$F1 844
10 TraesCS3D01G113000 chr3B 59224664 59228648 3984 False 1061.0 1133 94.1430 840 2363 2 chr3B.!!$F3 1523
11 TraesCS3D01G113000 chr3B 111851282 111851789 507 False 359.0 359 80.0750 155 670 1 chr3B.!!$F2 515
12 TraesCS3D01G113000 chr7B 108526127 108527471 1344 False 1014.5 1040 95.1715 1079 2363 2 chr7B.!!$F2 1284
13 TraesCS3D01G113000 chr3A 78188189 78188707 518 False 418.0 418 81.6640 155 670 1 chr3A.!!$F1 515

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
88 89 0.103755 TCTCACGCTCTGATGATGGC 59.896 55.000 0.0 0.0 0.0 4.40 F
112 113 1.002430 ACTCTGGAAAATCTGCGAGCA 59.998 47.619 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1292 1337 1.107538 CAGCCCTCGGGTAGATCGAA 61.108 60.000 3.54 0.0 36.15 3.71 R
1569 1640 7.826744 GGAAGAGAGGAGATAACAAATCTGTTT 59.173 37.037 0.00 0.0 43.45 2.83 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
17 18 3.607163 ATGGGCGCCACTGAAATG 58.393 55.556 30.85 0.00 35.80 2.32
18 19 2.713967 ATGGGCGCCACTGAAATGC 61.714 57.895 30.85 7.78 35.80 3.56
19 20 3.372730 GGGCGCCACTGAAATGCA 61.373 61.111 30.85 0.00 0.00 3.96
20 21 2.650196 GGCGCCACTGAAATGCAA 59.350 55.556 24.80 0.00 0.00 4.08
21 22 1.006337 GGCGCCACTGAAATGCAAA 60.006 52.632 24.80 0.00 0.00 3.68
22 23 0.390209 GGCGCCACTGAAATGCAAAT 60.390 50.000 24.80 0.00 0.00 2.32
23 24 1.431496 GCGCCACTGAAATGCAAATT 58.569 45.000 0.00 0.00 0.00 1.82
24 25 1.391144 GCGCCACTGAAATGCAAATTC 59.609 47.619 0.00 8.29 0.00 2.17
25 26 2.927871 GCGCCACTGAAATGCAAATTCT 60.928 45.455 14.45 0.00 0.00 2.40
26 27 3.319755 CGCCACTGAAATGCAAATTCTT 58.680 40.909 14.45 2.24 0.00 2.52
27 28 3.365820 CGCCACTGAAATGCAAATTCTTC 59.634 43.478 14.45 3.85 0.00 2.87
28 29 4.309099 GCCACTGAAATGCAAATTCTTCA 58.691 39.130 14.45 7.46 0.00 3.02
29 30 4.151157 GCCACTGAAATGCAAATTCTTCAC 59.849 41.667 14.45 1.04 0.00 3.18
30 31 5.535333 CCACTGAAATGCAAATTCTTCACT 58.465 37.500 14.45 0.00 0.00 3.41
31 32 5.987347 CCACTGAAATGCAAATTCTTCACTT 59.013 36.000 14.45 0.00 0.00 3.16
32 33 6.073980 CCACTGAAATGCAAATTCTTCACTTG 60.074 38.462 14.45 6.50 0.00 3.16
33 34 5.987347 ACTGAAATGCAAATTCTTCACTTGG 59.013 36.000 14.45 1.42 0.00 3.61
34 35 6.159299 TGAAATGCAAATTCTTCACTTGGA 57.841 33.333 14.45 0.00 0.00 3.53
35 36 6.761312 TGAAATGCAAATTCTTCACTTGGAT 58.239 32.000 14.45 0.00 33.17 3.41
36 37 6.647481 TGAAATGCAAATTCTTCACTTGGATG 59.353 34.615 14.45 0.00 32.29 3.51
37 38 4.524316 TGCAAATTCTTCACTTGGATGG 57.476 40.909 0.00 0.00 0.00 3.51
38 39 3.896888 TGCAAATTCTTCACTTGGATGGT 59.103 39.130 0.00 0.00 0.00 3.55
39 40 4.344679 TGCAAATTCTTCACTTGGATGGTT 59.655 37.500 0.00 0.00 0.00 3.67
40 41 5.538053 TGCAAATTCTTCACTTGGATGGTTA 59.462 36.000 0.00 0.00 0.00 2.85
41 42 6.211184 TGCAAATTCTTCACTTGGATGGTTAT 59.789 34.615 0.00 0.00 0.00 1.89
42 43 7.099120 GCAAATTCTTCACTTGGATGGTTATT 58.901 34.615 0.00 0.00 0.00 1.40
43 44 7.276438 GCAAATTCTTCACTTGGATGGTTATTC 59.724 37.037 0.00 0.00 0.00 1.75
44 45 8.306038 CAAATTCTTCACTTGGATGGTTATTCA 58.694 33.333 0.00 0.00 0.00 2.57
45 46 8.599624 AATTCTTCACTTGGATGGTTATTCAT 57.400 30.769 0.00 0.00 0.00 2.57
46 47 9.699410 AATTCTTCACTTGGATGGTTATTCATA 57.301 29.630 0.00 0.00 0.00 2.15
47 48 8.737168 TTCTTCACTTGGATGGTTATTCATAG 57.263 34.615 0.00 0.00 0.00 2.23
48 49 7.861629 TCTTCACTTGGATGGTTATTCATAGT 58.138 34.615 0.00 0.00 0.00 2.12
49 50 8.328758 TCTTCACTTGGATGGTTATTCATAGTT 58.671 33.333 0.00 0.00 0.00 2.24
50 51 7.864108 TCACTTGGATGGTTATTCATAGTTG 57.136 36.000 0.00 0.00 0.00 3.16
51 52 7.629157 TCACTTGGATGGTTATTCATAGTTGA 58.371 34.615 0.00 0.00 0.00 3.18
52 53 8.106462 TCACTTGGATGGTTATTCATAGTTGAA 58.894 33.333 0.00 0.00 45.57 2.69
68 69 8.620416 TCATAGTTGAATTTTGATAATGGACCG 58.380 33.333 0.00 0.00 0.00 4.79
69 70 6.834168 AGTTGAATTTTGATAATGGACCGT 57.166 33.333 0.00 0.00 0.00 4.83
70 71 6.852664 AGTTGAATTTTGATAATGGACCGTC 58.147 36.000 0.00 0.00 0.00 4.79
71 72 6.659242 AGTTGAATTTTGATAATGGACCGTCT 59.341 34.615 0.00 0.00 0.00 4.18
72 73 6.677781 TGAATTTTGATAATGGACCGTCTC 57.322 37.500 0.00 0.00 0.00 3.36
73 74 6.176896 TGAATTTTGATAATGGACCGTCTCA 58.823 36.000 0.00 0.00 0.00 3.27
74 75 6.093495 TGAATTTTGATAATGGACCGTCTCAC 59.907 38.462 0.00 0.00 0.00 3.51
75 76 2.863401 TGATAATGGACCGTCTCACG 57.137 50.000 0.00 0.00 42.11 4.35
76 77 1.202371 TGATAATGGACCGTCTCACGC 60.202 52.381 0.00 0.00 40.91 5.34
77 78 1.067212 GATAATGGACCGTCTCACGCT 59.933 52.381 0.00 0.00 40.91 5.07
78 79 0.454600 TAATGGACCGTCTCACGCTC 59.545 55.000 0.00 0.00 40.91 5.03
79 80 1.251527 AATGGACCGTCTCACGCTCT 61.252 55.000 0.00 0.00 40.91 4.09
80 81 1.938657 ATGGACCGTCTCACGCTCTG 61.939 60.000 0.00 0.00 40.91 3.35
81 82 2.333417 GGACCGTCTCACGCTCTGA 61.333 63.158 0.00 0.00 40.91 3.27
82 83 1.658686 GGACCGTCTCACGCTCTGAT 61.659 60.000 0.00 0.00 40.91 2.90
83 84 0.524392 GACCGTCTCACGCTCTGATG 60.524 60.000 0.00 0.00 40.91 3.07
84 85 0.960861 ACCGTCTCACGCTCTGATGA 60.961 55.000 0.00 0.00 40.91 2.92
85 86 0.383590 CCGTCTCACGCTCTGATGAT 59.616 55.000 0.00 0.00 40.91 2.45
86 87 1.475045 CGTCTCACGCTCTGATGATG 58.525 55.000 0.00 0.00 33.65 3.07
87 88 1.850377 GTCTCACGCTCTGATGATGG 58.150 55.000 0.00 0.00 0.00 3.51
88 89 0.103755 TCTCACGCTCTGATGATGGC 59.896 55.000 0.00 0.00 0.00 4.40
94 95 1.661341 GCTCTGATGATGGCGAAACT 58.339 50.000 0.00 0.00 0.00 2.66
95 96 1.596727 GCTCTGATGATGGCGAAACTC 59.403 52.381 0.00 0.00 0.00 3.01
96 97 2.741228 GCTCTGATGATGGCGAAACTCT 60.741 50.000 0.00 0.00 0.00 3.24
97 98 2.864946 CTCTGATGATGGCGAAACTCTG 59.135 50.000 0.00 0.00 0.00 3.35
98 99 1.938577 CTGATGATGGCGAAACTCTGG 59.061 52.381 0.00 0.00 0.00 3.86
99 100 1.554617 TGATGATGGCGAAACTCTGGA 59.445 47.619 0.00 0.00 0.00 3.86
100 101 2.027285 TGATGATGGCGAAACTCTGGAA 60.027 45.455 0.00 0.00 0.00 3.53
101 102 2.559698 TGATGGCGAAACTCTGGAAA 57.440 45.000 0.00 0.00 0.00 3.13
102 103 2.857483 TGATGGCGAAACTCTGGAAAA 58.143 42.857 0.00 0.00 0.00 2.29
103 104 3.420893 TGATGGCGAAACTCTGGAAAAT 58.579 40.909 0.00 0.00 0.00 1.82
104 105 3.440173 TGATGGCGAAACTCTGGAAAATC 59.560 43.478 0.00 0.00 0.00 2.17
105 106 3.140325 TGGCGAAACTCTGGAAAATCT 57.860 42.857 0.00 0.00 0.00 2.40
106 107 2.813754 TGGCGAAACTCTGGAAAATCTG 59.186 45.455 0.00 0.00 0.00 2.90
107 108 2.414691 GGCGAAACTCTGGAAAATCTGC 60.415 50.000 0.00 0.00 0.00 4.26
108 109 2.726066 GCGAAACTCTGGAAAATCTGCG 60.726 50.000 0.00 0.00 0.00 5.18
109 110 2.736721 CGAAACTCTGGAAAATCTGCGA 59.263 45.455 0.00 0.00 0.00 5.10
110 111 3.181526 CGAAACTCTGGAAAATCTGCGAG 60.182 47.826 0.00 0.00 0.00 5.03
111 112 1.731720 ACTCTGGAAAATCTGCGAGC 58.268 50.000 0.00 0.00 0.00 5.03
112 113 1.002430 ACTCTGGAAAATCTGCGAGCA 59.998 47.619 0.00 0.00 0.00 4.26
113 114 2.286872 CTCTGGAAAATCTGCGAGCAT 58.713 47.619 0.00 0.00 0.00 3.79
114 115 2.011947 TCTGGAAAATCTGCGAGCATG 58.988 47.619 0.00 0.00 0.00 4.06
115 116 2.011947 CTGGAAAATCTGCGAGCATGA 58.988 47.619 0.00 0.00 0.00 3.07
116 117 1.739466 TGGAAAATCTGCGAGCATGAC 59.261 47.619 0.00 0.00 0.00 3.06
117 118 2.012673 GGAAAATCTGCGAGCATGACT 58.987 47.619 0.00 0.00 0.00 3.41
118 119 2.421424 GGAAAATCTGCGAGCATGACTT 59.579 45.455 0.00 0.00 0.00 3.01
119 120 3.486542 GGAAAATCTGCGAGCATGACTTC 60.487 47.826 0.00 5.73 0.00 3.01
120 121 2.391616 AATCTGCGAGCATGACTTCA 57.608 45.000 0.00 0.00 0.00 3.02
121 122 2.616634 ATCTGCGAGCATGACTTCAT 57.383 45.000 0.00 0.00 36.96 2.57
122 123 1.931906 TCTGCGAGCATGACTTCATC 58.068 50.000 0.00 0.00 33.61 2.92
123 124 1.479730 TCTGCGAGCATGACTTCATCT 59.520 47.619 0.00 0.00 33.61 2.90
124 125 1.859703 CTGCGAGCATGACTTCATCTC 59.140 52.381 0.00 0.00 33.61 2.75
125 126 1.216122 GCGAGCATGACTTCATCTCC 58.784 55.000 0.00 4.07 33.61 3.71
126 127 1.485397 CGAGCATGACTTCATCTCCG 58.515 55.000 0.00 2.94 33.61 4.63
127 128 1.202348 CGAGCATGACTTCATCTCCGT 60.202 52.381 0.00 0.00 33.61 4.69
128 129 2.736719 CGAGCATGACTTCATCTCCGTT 60.737 50.000 0.00 0.00 33.61 4.44
129 130 3.265791 GAGCATGACTTCATCTCCGTTT 58.734 45.455 0.00 0.00 33.61 3.60
130 131 3.679389 AGCATGACTTCATCTCCGTTTT 58.321 40.909 0.00 0.00 33.61 2.43
131 132 4.832248 AGCATGACTTCATCTCCGTTTTA 58.168 39.130 0.00 0.00 33.61 1.52
132 133 4.631813 AGCATGACTTCATCTCCGTTTTAC 59.368 41.667 0.00 0.00 33.61 2.01
133 134 4.391830 GCATGACTTCATCTCCGTTTTACA 59.608 41.667 0.00 0.00 33.61 2.41
134 135 5.106712 GCATGACTTCATCTCCGTTTTACAA 60.107 40.000 0.00 0.00 33.61 2.41
135 136 5.917541 TGACTTCATCTCCGTTTTACAAC 57.082 39.130 0.00 0.00 0.00 3.32
136 137 4.753107 TGACTTCATCTCCGTTTTACAACC 59.247 41.667 0.00 0.00 0.00 3.77
137 138 4.969484 ACTTCATCTCCGTTTTACAACCT 58.031 39.130 0.00 0.00 0.00 3.50
138 139 4.995487 ACTTCATCTCCGTTTTACAACCTC 59.005 41.667 0.00 0.00 0.00 3.85
139 140 4.610605 TCATCTCCGTTTTACAACCTCA 57.389 40.909 0.00 0.00 0.00 3.86
140 141 4.963373 TCATCTCCGTTTTACAACCTCAA 58.037 39.130 0.00 0.00 0.00 3.02
141 142 5.369833 TCATCTCCGTTTTACAACCTCAAA 58.630 37.500 0.00 0.00 0.00 2.69
142 143 5.468746 TCATCTCCGTTTTACAACCTCAAAG 59.531 40.000 0.00 0.00 0.00 2.77
143 144 4.773013 TCTCCGTTTTACAACCTCAAAGT 58.227 39.130 0.00 0.00 0.00 2.66
144 145 5.187687 TCTCCGTTTTACAACCTCAAAGTT 58.812 37.500 0.00 0.00 0.00 2.66
154 155 5.505173 CAACCTCAAAGTTGTGAAGATGT 57.495 39.130 0.00 0.00 41.80 3.06
155 156 5.276270 CAACCTCAAAGTTGTGAAGATGTG 58.724 41.667 0.00 0.00 41.80 3.21
156 157 3.885297 ACCTCAAAGTTGTGAAGATGTGG 59.115 43.478 0.00 0.00 0.00 4.17
157 158 3.304928 CCTCAAAGTTGTGAAGATGTGGC 60.305 47.826 0.00 0.00 0.00 5.01
158 159 3.554934 TCAAAGTTGTGAAGATGTGGCT 58.445 40.909 0.00 0.00 0.00 4.75
159 160 3.953612 TCAAAGTTGTGAAGATGTGGCTT 59.046 39.130 0.00 0.00 0.00 4.35
160 161 4.036734 TCAAAGTTGTGAAGATGTGGCTTC 59.963 41.667 0.00 0.00 43.53 3.86
161 162 2.146342 AGTTGTGAAGATGTGGCTTCG 58.854 47.619 0.00 0.00 45.62 3.79
162 163 1.873591 GTTGTGAAGATGTGGCTTCGT 59.126 47.619 0.00 0.00 45.62 3.85
163 164 1.795768 TGTGAAGATGTGGCTTCGTC 58.204 50.000 0.00 0.00 45.62 4.20
164 165 1.344438 TGTGAAGATGTGGCTTCGTCT 59.656 47.619 0.00 0.00 45.62 4.18
165 166 2.224281 TGTGAAGATGTGGCTTCGTCTT 60.224 45.455 14.13 14.13 45.62 3.01
223 224 7.630242 TCAAATTAATGAGCAAACCCTAGAG 57.370 36.000 0.00 0.00 0.00 2.43
243 244 8.696410 CTAGAGAGGACTTCACTACAAATTTC 57.304 38.462 0.00 0.00 0.00 2.17
245 246 6.931840 AGAGAGGACTTCACTACAAATTTCAC 59.068 38.462 0.00 0.00 0.00 3.18
252 253 6.706270 ACTTCACTACAAATTTCACGTCAGAT 59.294 34.615 0.00 0.00 0.00 2.90
301 302 9.497030 CATTTTTCATGGCAAATTATGTTCATG 57.503 29.630 0.00 0.00 40.69 3.07
302 303 6.665474 TTTCATGGCAAATTATGTTCATGC 57.335 33.333 0.00 0.00 39.94 4.06
313 314 5.823209 TTATGTTCATGCAGGATGACAAG 57.177 39.130 9.68 0.00 41.02 3.16
318 319 5.711506 TGTTCATGCAGGATGACAAGTTTAT 59.288 36.000 0.03 0.00 41.02 1.40
322 323 4.808558 TGCAGGATGACAAGTTTATTTGC 58.191 39.130 0.00 0.00 39.69 3.68
323 324 4.523943 TGCAGGATGACAAGTTTATTTGCT 59.476 37.500 0.00 0.00 39.69 3.91
324 325 5.098211 GCAGGATGACAAGTTTATTTGCTC 58.902 41.667 0.00 0.00 39.69 4.26
339 340 4.859304 TTTGCTCAGCATGACAAATTCT 57.141 36.364 0.00 0.00 42.56 2.40
343 344 3.065095 GCTCAGCATGACAAATTCTCCTC 59.935 47.826 0.00 0.00 42.56 3.71
346 347 4.008330 CAGCATGACAAATTCTCCTCAGT 58.992 43.478 0.00 0.00 39.69 3.41
348 349 4.699257 AGCATGACAAATTCTCCTCAGTTC 59.301 41.667 0.00 0.00 0.00 3.01
377 380 1.710249 CAAGAAATTGTCGTGCTTGCG 59.290 47.619 0.00 0.00 30.92 4.85
388 391 3.972502 GTCGTGCTTGCGAACTAAATTTT 59.027 39.130 0.00 0.00 42.82 1.82
390 393 3.360758 CGTGCTTGCGAACTAAATTTTCC 59.639 43.478 0.00 0.00 0.00 3.13
395 398 5.807011 GCTTGCGAACTAAATTTTCCATCAT 59.193 36.000 0.00 0.00 0.00 2.45
396 399 6.020360 GCTTGCGAACTAAATTTTCCATCATC 60.020 38.462 0.00 0.00 0.00 2.92
397 400 6.507958 TGCGAACTAAATTTTCCATCATCA 57.492 33.333 0.00 0.00 0.00 3.07
415 418 4.582240 TCATCACGCCAATATAAATTGCCA 59.418 37.500 0.00 0.00 41.06 4.92
444 447 2.747396 TCAGATTTGCCATGCCAAAC 57.253 45.000 3.63 0.00 37.51 2.93
452 456 1.273048 TGCCATGCCAAACAATCTGAC 59.727 47.619 0.00 0.00 0.00 3.51
535 544 9.358872 GCTAATATATAATTTCTTTTGCAGGGC 57.641 33.333 0.00 0.00 0.00 5.19
547 556 4.464069 TTTGCAGGGCATTTGGTAATAC 57.536 40.909 0.00 0.00 38.76 1.89
553 562 5.534654 GCAGGGCATTTGGTAATACAGATAA 59.465 40.000 0.00 0.00 0.00 1.75
674 692 7.966339 AAATAAACCCCAAAATAGTACTCCC 57.034 36.000 0.00 0.00 0.00 4.30
675 693 4.326600 AAACCCCAAAATAGTACTCCCC 57.673 45.455 0.00 0.00 0.00 4.81
676 694 2.211532 ACCCCAAAATAGTACTCCCCC 58.788 52.381 0.00 0.00 0.00 5.40
677 695 1.142262 CCCCAAAATAGTACTCCCCCG 59.858 57.143 0.00 0.00 0.00 5.73
678 696 1.841919 CCCAAAATAGTACTCCCCCGT 59.158 52.381 0.00 0.00 0.00 5.28
679 697 3.040477 CCCAAAATAGTACTCCCCCGTA 58.960 50.000 0.00 0.00 0.00 4.02
680 698 3.455543 CCCAAAATAGTACTCCCCCGTAA 59.544 47.826 0.00 0.00 0.00 3.18
681 699 4.080413 CCCAAAATAGTACTCCCCCGTAAA 60.080 45.833 0.00 0.00 0.00 2.01
682 700 4.877823 CCAAAATAGTACTCCCCCGTAAAC 59.122 45.833 0.00 0.00 0.00 2.01
683 701 5.338626 CCAAAATAGTACTCCCCCGTAAACT 60.339 44.000 0.00 0.00 0.00 2.66
684 702 6.127083 CCAAAATAGTACTCCCCCGTAAACTA 60.127 42.308 0.00 0.00 0.00 2.24
685 703 7.330262 CAAAATAGTACTCCCCCGTAAACTAA 58.670 38.462 0.00 0.00 0.00 2.24
686 704 7.681259 AAATAGTACTCCCCCGTAAACTAAT 57.319 36.000 0.00 0.00 0.00 1.73
687 705 8.782137 AAATAGTACTCCCCCGTAAACTAATA 57.218 34.615 0.00 0.00 0.00 0.98
688 706 8.962912 AATAGTACTCCCCCGTAAACTAATAT 57.037 34.615 0.00 0.00 0.00 1.28
691 709 8.414629 AGTACTCCCCCGTAAACTAATATAAG 57.585 38.462 0.00 0.00 0.00 1.73
692 710 6.676990 ACTCCCCCGTAAACTAATATAAGG 57.323 41.667 0.00 0.00 0.00 2.69
693 711 5.545335 ACTCCCCCGTAAACTAATATAAGGG 59.455 44.000 0.00 0.00 39.64 3.95
694 712 4.286808 TCCCCCGTAAACTAATATAAGGGC 59.713 45.833 0.00 0.00 38.89 5.19
695 713 4.041938 CCCCCGTAAACTAATATAAGGGCA 59.958 45.833 0.00 0.00 38.89 5.36
696 714 5.280830 CCCCCGTAAACTAATATAAGGGCAT 60.281 44.000 0.00 0.00 38.89 4.40
697 715 6.243148 CCCCGTAAACTAATATAAGGGCATT 58.757 40.000 0.00 0.00 38.89 3.56
698 716 6.717997 CCCCGTAAACTAATATAAGGGCATTT 59.282 38.462 0.00 0.00 38.89 2.32
699 717 7.884354 CCCCGTAAACTAATATAAGGGCATTTA 59.116 37.037 0.00 0.00 38.89 1.40
700 718 8.943002 CCCGTAAACTAATATAAGGGCATTTAG 58.057 37.037 0.00 0.00 34.70 1.85
701 719 9.715121 CCGTAAACTAATATAAGGGCATTTAGA 57.285 33.333 0.00 0.00 0.00 2.10
715 733 9.614792 AAGGGCATTTAGATAACTACTTTAGTG 57.385 33.333 0.00 0.00 39.39 2.74
716 734 8.989131 AGGGCATTTAGATAACTACTTTAGTGA 58.011 33.333 0.00 0.00 39.39 3.41
717 735 9.780186 GGGCATTTAGATAACTACTTTAGTGAT 57.220 33.333 0.00 0.00 39.39 3.06
726 744 9.733219 GATAACTACTTTAGTGATCTAAACGCT 57.267 33.333 4.09 0.00 41.55 5.07
728 746 8.828688 AACTACTTTAGTGATCTAAACGCTTT 57.171 30.769 0.00 0.00 40.05 3.51
729 747 8.828688 ACTACTTTAGTGATCTAAACGCTTTT 57.171 30.769 0.00 0.00 40.05 2.27
730 748 9.918630 ACTACTTTAGTGATCTAAACGCTTTTA 57.081 29.630 0.00 0.00 40.05 1.52
747 765 8.658499 ACGCTTTTATATTAGTTTACAGAGGG 57.342 34.615 0.00 0.00 0.00 4.30
748 766 8.480501 ACGCTTTTATATTAGTTTACAGAGGGA 58.519 33.333 0.00 0.00 0.00 4.20
749 767 8.979574 CGCTTTTATATTAGTTTACAGAGGGAG 58.020 37.037 0.00 0.00 0.00 4.30
765 783 5.993748 GAGGGAGTCTCTATTCCTAATGG 57.006 47.826 0.00 0.00 39.38 3.16
767 785 5.399113 AGGGAGTCTCTATTCCTAATGGAC 58.601 45.833 0.00 0.00 43.06 4.02
768 786 4.218852 GGGAGTCTCTATTCCTAATGGACG 59.781 50.000 0.00 0.00 43.06 4.79
770 788 5.048573 GGAGTCTCTATTCCTAATGGACGAC 60.049 48.000 0.00 0.00 43.06 4.34
782 800 4.819105 AATGGACGACTTGGTGAATAGA 57.181 40.909 0.00 0.00 0.00 1.98
784 802 2.232941 TGGACGACTTGGTGAATAGACC 59.767 50.000 0.00 0.00 36.43 3.85
785 803 2.232941 GGACGACTTGGTGAATAGACCA 59.767 50.000 0.00 0.00 44.64 4.02
786 804 3.251571 GACGACTTGGTGAATAGACCAC 58.748 50.000 0.00 0.00 46.03 4.16
787 805 2.259618 CGACTTGGTGAATAGACCACG 58.740 52.381 0.00 0.00 46.03 4.94
1062 1107 2.572191 TTCGCTACATCGACGGAAAT 57.428 45.000 0.00 0.00 38.30 2.17
1292 1337 2.088763 CACGCGCTCATCGTCTTGT 61.089 57.895 5.73 0.00 38.19 3.16
1569 1640 1.022735 GTGTCCGCTCCTCGATCTTA 58.977 55.000 0.00 0.00 41.67 2.10
1765 4246 1.956477 GTGAACAAGAAGCACATGGGT 59.044 47.619 0.00 0.00 32.96 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.713967 GCATTTCAGTGGCGCCCAT 61.714 57.895 26.77 9.79 35.28 4.00
1 2 3.372730 GCATTTCAGTGGCGCCCA 61.373 61.111 26.77 9.53 0.00 5.36
3 4 0.390209 ATTTGCATTTCAGTGGCGCC 60.390 50.000 22.73 22.73 0.00 6.53
4 5 1.391144 GAATTTGCATTTCAGTGGCGC 59.609 47.619 0.00 0.00 0.00 6.53
5 6 2.950433 AGAATTTGCATTTCAGTGGCG 58.050 42.857 11.26 0.00 0.00 5.69
6 7 4.151157 GTGAAGAATTTGCATTTCAGTGGC 59.849 41.667 11.26 0.00 30.86 5.01
7 8 5.535333 AGTGAAGAATTTGCATTTCAGTGG 58.465 37.500 11.26 0.00 33.29 4.00
8 9 6.073980 CCAAGTGAAGAATTTGCATTTCAGTG 60.074 38.462 11.26 7.09 34.42 3.66
9 10 5.987347 CCAAGTGAAGAATTTGCATTTCAGT 59.013 36.000 11.26 6.39 35.36 3.41
10 11 6.218019 TCCAAGTGAAGAATTTGCATTTCAG 58.782 36.000 11.26 0.00 30.86 3.02
11 12 6.159299 TCCAAGTGAAGAATTTGCATTTCA 57.841 33.333 11.26 4.10 0.00 2.69
12 13 6.091713 CCATCCAAGTGAAGAATTTGCATTTC 59.908 38.462 0.00 0.00 0.00 2.17
13 14 5.935789 CCATCCAAGTGAAGAATTTGCATTT 59.064 36.000 0.00 0.00 0.00 2.32
14 15 5.012354 ACCATCCAAGTGAAGAATTTGCATT 59.988 36.000 0.00 0.00 0.00 3.56
15 16 4.529377 ACCATCCAAGTGAAGAATTTGCAT 59.471 37.500 0.00 0.00 0.00 3.96
16 17 3.896888 ACCATCCAAGTGAAGAATTTGCA 59.103 39.130 0.00 0.00 0.00 4.08
17 18 4.525912 ACCATCCAAGTGAAGAATTTGC 57.474 40.909 0.00 0.00 0.00 3.68
18 19 8.306038 TGAATAACCATCCAAGTGAAGAATTTG 58.694 33.333 0.00 0.00 0.00 2.32
19 20 8.421249 TGAATAACCATCCAAGTGAAGAATTT 57.579 30.769 0.00 0.00 0.00 1.82
20 21 8.599624 ATGAATAACCATCCAAGTGAAGAATT 57.400 30.769 0.00 0.00 0.00 2.17
21 22 9.347240 CTATGAATAACCATCCAAGTGAAGAAT 57.653 33.333 0.00 0.00 0.00 2.40
22 23 8.328758 ACTATGAATAACCATCCAAGTGAAGAA 58.671 33.333 0.00 0.00 0.00 2.52
23 24 7.861629 ACTATGAATAACCATCCAAGTGAAGA 58.138 34.615 0.00 0.00 0.00 2.87
24 25 8.400947 CAACTATGAATAACCATCCAAGTGAAG 58.599 37.037 0.00 0.00 0.00 3.02
25 26 8.106462 TCAACTATGAATAACCATCCAAGTGAA 58.894 33.333 0.00 0.00 30.99 3.18
26 27 7.629157 TCAACTATGAATAACCATCCAAGTGA 58.371 34.615 0.00 0.00 30.99 3.41
27 28 7.864108 TCAACTATGAATAACCATCCAAGTG 57.136 36.000 0.00 0.00 30.99 3.16
42 43 8.620416 CGGTCCATTATCAAAATTCAACTATGA 58.380 33.333 0.00 0.00 0.00 2.15
43 44 8.405531 ACGGTCCATTATCAAAATTCAACTATG 58.594 33.333 0.00 0.00 0.00 2.23
44 45 8.519799 ACGGTCCATTATCAAAATTCAACTAT 57.480 30.769 0.00 0.00 0.00 2.12
45 46 7.827236 AGACGGTCCATTATCAAAATTCAACTA 59.173 33.333 4.14 0.00 0.00 2.24
46 47 6.659242 AGACGGTCCATTATCAAAATTCAACT 59.341 34.615 4.14 0.00 0.00 3.16
47 48 6.852664 AGACGGTCCATTATCAAAATTCAAC 58.147 36.000 4.14 0.00 0.00 3.18
48 49 6.657117 TGAGACGGTCCATTATCAAAATTCAA 59.343 34.615 4.14 0.00 0.00 2.69
49 50 6.093495 GTGAGACGGTCCATTATCAAAATTCA 59.907 38.462 4.14 0.00 0.00 2.57
50 51 6.487103 GTGAGACGGTCCATTATCAAAATTC 58.513 40.000 4.14 0.00 0.00 2.17
51 52 5.064707 CGTGAGACGGTCCATTATCAAAATT 59.935 40.000 4.14 0.00 38.08 1.82
52 53 4.570772 CGTGAGACGGTCCATTATCAAAAT 59.429 41.667 4.14 0.00 38.08 1.82
53 54 3.930229 CGTGAGACGGTCCATTATCAAAA 59.070 43.478 4.14 0.00 38.08 2.44
54 55 3.517602 CGTGAGACGGTCCATTATCAAA 58.482 45.455 4.14 0.00 38.08 2.69
55 56 2.737359 GCGTGAGACGGTCCATTATCAA 60.737 50.000 4.14 0.00 42.82 2.57
56 57 1.202371 GCGTGAGACGGTCCATTATCA 60.202 52.381 4.14 0.00 42.82 2.15
57 58 1.488527 GCGTGAGACGGTCCATTATC 58.511 55.000 4.14 0.00 42.82 1.75
58 59 3.661745 GCGTGAGACGGTCCATTAT 57.338 52.632 4.14 0.00 42.82 1.28
66 67 0.383590 ATCATCAGAGCGTGAGACGG 59.616 55.000 0.00 0.00 42.82 4.79
67 68 1.475045 CATCATCAGAGCGTGAGACG 58.525 55.000 0.00 0.00 45.88 4.18
68 69 1.850377 CCATCATCAGAGCGTGAGAC 58.150 55.000 0.00 0.00 39.07 3.36
69 70 0.103755 GCCATCATCAGAGCGTGAGA 59.896 55.000 0.00 0.00 39.07 3.27
70 71 1.213733 CGCCATCATCAGAGCGTGAG 61.214 60.000 0.00 0.00 43.45 3.51
71 72 1.227060 CGCCATCATCAGAGCGTGA 60.227 57.895 0.00 0.00 43.45 4.35
72 73 3.316821 CGCCATCATCAGAGCGTG 58.683 61.111 0.00 0.00 43.45 5.34
75 76 1.596727 GAGTTTCGCCATCATCAGAGC 59.403 52.381 0.00 0.00 0.00 4.09
76 77 2.864946 CAGAGTTTCGCCATCATCAGAG 59.135 50.000 0.00 0.00 0.00 3.35
77 78 2.419159 CCAGAGTTTCGCCATCATCAGA 60.419 50.000 0.00 0.00 0.00 3.27
78 79 1.938577 CCAGAGTTTCGCCATCATCAG 59.061 52.381 0.00 0.00 0.00 2.90
79 80 1.554617 TCCAGAGTTTCGCCATCATCA 59.445 47.619 0.00 0.00 0.00 3.07
80 81 2.315925 TCCAGAGTTTCGCCATCATC 57.684 50.000 0.00 0.00 0.00 2.92
81 82 2.787473 TTCCAGAGTTTCGCCATCAT 57.213 45.000 0.00 0.00 0.00 2.45
82 83 2.559698 TTTCCAGAGTTTCGCCATCA 57.440 45.000 0.00 0.00 0.00 3.07
83 84 3.691609 AGATTTTCCAGAGTTTCGCCATC 59.308 43.478 0.00 0.00 0.00 3.51
84 85 3.441572 CAGATTTTCCAGAGTTTCGCCAT 59.558 43.478 0.00 0.00 0.00 4.40
85 86 2.813754 CAGATTTTCCAGAGTTTCGCCA 59.186 45.455 0.00 0.00 0.00 5.69
86 87 2.414691 GCAGATTTTCCAGAGTTTCGCC 60.415 50.000 0.00 0.00 0.00 5.54
87 88 2.726066 CGCAGATTTTCCAGAGTTTCGC 60.726 50.000 0.00 0.00 0.00 4.70
88 89 2.736721 TCGCAGATTTTCCAGAGTTTCG 59.263 45.455 0.00 0.00 0.00 3.46
89 90 3.425492 GCTCGCAGATTTTCCAGAGTTTC 60.425 47.826 0.00 0.00 33.89 2.78
90 91 2.485814 GCTCGCAGATTTTCCAGAGTTT 59.514 45.455 0.00 0.00 33.89 2.66
91 92 2.079925 GCTCGCAGATTTTCCAGAGTT 58.920 47.619 0.00 0.00 33.89 3.01
92 93 1.002430 TGCTCGCAGATTTTCCAGAGT 59.998 47.619 0.00 0.00 33.89 3.24
93 94 1.730501 TGCTCGCAGATTTTCCAGAG 58.269 50.000 0.00 0.00 33.89 3.35
94 95 2.011947 CATGCTCGCAGATTTTCCAGA 58.988 47.619 0.00 0.00 33.89 3.86
95 96 2.011947 TCATGCTCGCAGATTTTCCAG 58.988 47.619 0.00 0.00 33.89 3.86
96 97 1.739466 GTCATGCTCGCAGATTTTCCA 59.261 47.619 0.00 0.00 33.89 3.53
97 98 2.012673 AGTCATGCTCGCAGATTTTCC 58.987 47.619 0.00 0.00 33.89 3.13
98 99 3.125829 TGAAGTCATGCTCGCAGATTTTC 59.874 43.478 0.00 0.87 33.89 2.29
99 100 3.076621 TGAAGTCATGCTCGCAGATTTT 58.923 40.909 0.00 0.00 33.89 1.82
100 101 2.703416 TGAAGTCATGCTCGCAGATTT 58.297 42.857 0.00 0.00 33.89 2.17
101 102 2.391616 TGAAGTCATGCTCGCAGATT 57.608 45.000 0.00 0.00 33.89 2.40
102 103 2.102757 AGATGAAGTCATGCTCGCAGAT 59.897 45.455 0.00 0.00 36.57 2.90
103 104 1.479730 AGATGAAGTCATGCTCGCAGA 59.520 47.619 0.00 0.00 36.57 4.26
104 105 1.859703 GAGATGAAGTCATGCTCGCAG 59.140 52.381 0.00 0.00 36.57 5.18
105 106 1.472201 GGAGATGAAGTCATGCTCGCA 60.472 52.381 0.00 0.00 36.57 5.10
106 107 1.216122 GGAGATGAAGTCATGCTCGC 58.784 55.000 0.00 0.00 36.57 5.03
107 108 1.202348 ACGGAGATGAAGTCATGCTCG 60.202 52.381 0.00 2.53 36.57 5.03
108 109 2.593346 ACGGAGATGAAGTCATGCTC 57.407 50.000 0.00 5.59 36.57 4.26
109 110 3.340814 AAACGGAGATGAAGTCATGCT 57.659 42.857 0.00 0.00 36.57 3.79
110 111 4.391830 TGTAAAACGGAGATGAAGTCATGC 59.608 41.667 0.00 0.00 36.57 4.06
111 112 6.307155 GTTGTAAAACGGAGATGAAGTCATG 58.693 40.000 0.00 0.00 36.57 3.07
112 113 5.411669 GGTTGTAAAACGGAGATGAAGTCAT 59.588 40.000 0.00 0.00 39.70 3.06
113 114 4.753107 GGTTGTAAAACGGAGATGAAGTCA 59.247 41.667 0.00 0.00 0.00 3.41
114 115 4.995487 AGGTTGTAAAACGGAGATGAAGTC 59.005 41.667 0.00 0.00 39.71 3.01
115 116 4.969484 AGGTTGTAAAACGGAGATGAAGT 58.031 39.130 0.00 0.00 39.71 3.01
116 117 4.994852 TGAGGTTGTAAAACGGAGATGAAG 59.005 41.667 0.00 0.00 39.71 3.02
117 118 4.963373 TGAGGTTGTAAAACGGAGATGAA 58.037 39.130 0.00 0.00 39.71 2.57
118 119 4.610605 TGAGGTTGTAAAACGGAGATGA 57.389 40.909 0.00 0.00 39.71 2.92
119 120 5.238650 ACTTTGAGGTTGTAAAACGGAGATG 59.761 40.000 0.00 0.00 39.71 2.90
120 121 5.374071 ACTTTGAGGTTGTAAAACGGAGAT 58.626 37.500 0.00 0.00 39.71 2.75
121 122 4.773013 ACTTTGAGGTTGTAAAACGGAGA 58.227 39.130 0.00 0.00 39.71 3.71
122 123 5.270853 CAACTTTGAGGTTGTAAAACGGAG 58.729 41.667 0.00 0.00 39.71 4.63
123 124 5.238006 CAACTTTGAGGTTGTAAAACGGA 57.762 39.130 0.00 0.00 39.71 4.69
133 134 4.339247 CCACATCTTCACAACTTTGAGGTT 59.661 41.667 0.00 0.00 0.00 3.50
134 135 3.885297 CCACATCTTCACAACTTTGAGGT 59.115 43.478 0.00 0.00 0.00 3.85
135 136 3.304928 GCCACATCTTCACAACTTTGAGG 60.305 47.826 0.00 0.00 0.00 3.86
136 137 3.567164 AGCCACATCTTCACAACTTTGAG 59.433 43.478 0.00 0.00 0.00 3.02
137 138 3.554934 AGCCACATCTTCACAACTTTGA 58.445 40.909 0.00 0.00 0.00 2.69
138 139 3.996150 AGCCACATCTTCACAACTTTG 57.004 42.857 0.00 0.00 0.00 2.77
139 140 3.003689 CGAAGCCACATCTTCACAACTTT 59.996 43.478 4.67 0.00 41.84 2.66
140 141 2.549754 CGAAGCCACATCTTCACAACTT 59.450 45.455 4.67 0.00 41.84 2.66
141 142 2.146342 CGAAGCCACATCTTCACAACT 58.854 47.619 4.67 0.00 41.84 3.16
142 143 1.873591 ACGAAGCCACATCTTCACAAC 59.126 47.619 0.00 0.00 41.84 3.32
143 144 2.143122 GACGAAGCCACATCTTCACAA 58.857 47.619 0.00 0.00 41.84 3.33
144 145 1.344438 AGACGAAGCCACATCTTCACA 59.656 47.619 0.00 0.00 41.84 3.58
145 146 2.086054 AGACGAAGCCACATCTTCAC 57.914 50.000 0.00 0.00 41.84 3.18
146 147 2.688507 GAAGACGAAGCCACATCTTCA 58.311 47.619 10.28 0.00 44.25 3.02
147 148 1.656095 CGAAGACGAAGCCACATCTTC 59.344 52.381 6.52 6.52 42.35 2.87
148 149 1.272490 TCGAAGACGAAGCCACATCTT 59.728 47.619 0.00 0.00 45.74 2.40
149 150 0.888619 TCGAAGACGAAGCCACATCT 59.111 50.000 0.00 0.00 45.74 2.90
150 151 3.418675 TCGAAGACGAAGCCACATC 57.581 52.632 0.00 0.00 45.74 3.06
160 161 3.065510 AGGTCTCACACATATCGAAGACG 59.934 47.826 0.00 0.00 42.51 4.18
161 162 4.640789 AGGTCTCACACATATCGAAGAC 57.359 45.455 0.00 0.00 42.51 3.01
162 163 8.350722 GTTTATAGGTCTCACACATATCGAAGA 58.649 37.037 0.00 0.00 45.75 2.87
163 164 7.595502 GGTTTATAGGTCTCACACATATCGAAG 59.404 40.741 0.00 0.00 33.90 3.79
164 165 7.287005 AGGTTTATAGGTCTCACACATATCGAA 59.713 37.037 0.00 0.00 33.90 3.71
165 166 6.776116 AGGTTTATAGGTCTCACACATATCGA 59.224 38.462 0.00 0.00 33.90 3.59
166 167 6.982852 AGGTTTATAGGTCTCACACATATCG 58.017 40.000 0.00 0.00 33.90 2.92
218 219 8.307483 TGAAATTTGTAGTGAAGTCCTCTCTAG 58.693 37.037 0.00 0.00 32.18 2.43
223 224 5.465724 ACGTGAAATTTGTAGTGAAGTCCTC 59.534 40.000 0.00 0.00 0.00 3.71
270 271 9.064706 ACATAATTTGCCATGAAAAATGTTTGA 57.935 25.926 0.00 0.00 28.53 2.69
271 272 9.680315 AACATAATTTGCCATGAAAAATGTTTG 57.320 25.926 12.99 10.28 34.78 2.93
272 273 9.896263 GAACATAATTTGCCATGAAAAATGTTT 57.104 25.926 16.58 0.00 36.55 2.83
282 283 4.509970 CCTGCATGAACATAATTTGCCATG 59.490 41.667 0.00 0.00 40.16 3.66
301 302 5.064441 AGCAAATAAACTTGTCATCCTGC 57.936 39.130 0.00 0.00 0.00 4.85
302 303 6.258230 TGAGCAAATAAACTTGTCATCCTG 57.742 37.500 0.00 0.00 0.00 3.86
313 314 6.956299 ATTTGTCATGCTGAGCAAATAAAC 57.044 33.333 12.69 6.17 43.62 2.01
318 319 4.321452 GGAGAATTTGTCATGCTGAGCAAA 60.321 41.667 12.69 0.05 43.62 3.68
322 323 4.259356 TGAGGAGAATTTGTCATGCTGAG 58.741 43.478 0.00 0.00 0.00 3.35
323 324 4.259356 CTGAGGAGAATTTGTCATGCTGA 58.741 43.478 0.00 0.00 0.00 4.26
324 325 4.008330 ACTGAGGAGAATTTGTCATGCTG 58.992 43.478 0.00 0.00 0.00 4.41
355 358 2.287547 GCAAGCACGACAATTTCTTGGA 60.288 45.455 0.00 0.00 36.64 3.53
369 372 4.295051 TGGAAAATTTAGTTCGCAAGCAC 58.705 39.130 0.00 0.00 37.18 4.40
377 380 5.743872 GGCGTGATGATGGAAAATTTAGTTC 59.256 40.000 0.00 0.00 0.00 3.01
388 391 6.570186 GCAATTTATATTGGCGTGATGATGGA 60.570 38.462 7.83 0.00 41.21 3.41
390 393 6.621737 GCAATTTATATTGGCGTGATGATG 57.378 37.500 7.83 0.00 41.21 3.07
415 418 5.353123 GCATGGCAAATCTGATGTTTTTCAT 59.647 36.000 0.00 0.00 39.77 2.57
520 529 3.181441 ACCAAATGCCCTGCAAAAGAAAT 60.181 39.130 0.00 0.00 43.62 2.17
524 533 3.399440 TTACCAAATGCCCTGCAAAAG 57.601 42.857 0.00 0.00 43.62 2.27
528 537 3.023119 CTGTATTACCAAATGCCCTGCA 58.977 45.455 0.00 0.00 44.86 4.41
529 538 3.287222 TCTGTATTACCAAATGCCCTGC 58.713 45.455 0.00 0.00 0.00 4.85
530 539 7.765695 ATTATCTGTATTACCAAATGCCCTG 57.234 36.000 0.00 0.00 0.00 4.45
586 598 7.455641 TGTTTTGTCTCCAGTCTTGTAAAAA 57.544 32.000 0.00 0.00 0.00 1.94
587 599 7.455641 TTGTTTTGTCTCCAGTCTTGTAAAA 57.544 32.000 0.00 0.00 0.00 1.52
591 603 5.975693 TTTTGTTTTGTCTCCAGTCTTGT 57.024 34.783 0.00 0.00 0.00 3.16
592 604 6.476706 GGATTTTTGTTTTGTCTCCAGTCTTG 59.523 38.462 0.00 0.00 0.00 3.02
593 605 6.154363 TGGATTTTTGTTTTGTCTCCAGTCTT 59.846 34.615 0.00 0.00 0.00 3.01
594 606 5.656416 TGGATTTTTGTTTTGTCTCCAGTCT 59.344 36.000 0.00 0.00 0.00 3.24
599 616 7.648112 GTCTAGTTGGATTTTTGTTTTGTCTCC 59.352 37.037 0.00 0.00 0.00 3.71
670 688 5.570236 GCCCTTATATTAGTTTACGGGGGAG 60.570 48.000 0.00 0.00 32.50 4.30
671 689 4.286808 GCCCTTATATTAGTTTACGGGGGA 59.713 45.833 0.00 0.00 32.50 4.81
672 690 4.041938 TGCCCTTATATTAGTTTACGGGGG 59.958 45.833 0.00 0.00 32.59 5.40
673 691 5.231702 TGCCCTTATATTAGTTTACGGGG 57.768 43.478 0.00 0.00 34.85 5.73
674 692 7.754851 AAATGCCCTTATATTAGTTTACGGG 57.245 36.000 0.00 0.00 0.00 5.28
675 693 9.715121 TCTAAATGCCCTTATATTAGTTTACGG 57.285 33.333 0.00 0.00 0.00 4.02
689 707 9.614792 CACTAAAGTAGTTATCTAAATGCCCTT 57.385 33.333 0.00 0.00 36.76 3.95
690 708 8.989131 TCACTAAAGTAGTTATCTAAATGCCCT 58.011 33.333 0.00 0.00 36.76 5.19
691 709 9.780186 ATCACTAAAGTAGTTATCTAAATGCCC 57.220 33.333 0.00 0.00 36.76 5.36
699 717 9.733219 GCGTTTAGATCACTAAAGTAGTTATCT 57.267 33.333 13.75 13.75 46.18 1.98
700 718 9.733219 AGCGTTTAGATCACTAAAGTAGTTATC 57.267 33.333 0.00 2.65 45.42 1.75
702 720 9.918630 AAAGCGTTTAGATCACTAAAGTAGTTA 57.081 29.630 0.00 0.00 45.42 2.24
703 721 8.828688 AAAGCGTTTAGATCACTAAAGTAGTT 57.171 30.769 0.00 0.00 45.42 2.24
704 722 8.828688 AAAAGCGTTTAGATCACTAAAGTAGT 57.171 30.769 0.00 0.00 45.42 2.73
721 739 9.106070 CCCTCTGTAAACTAATATAAAAGCGTT 57.894 33.333 0.00 0.00 0.00 4.84
722 740 8.480501 TCCCTCTGTAAACTAATATAAAAGCGT 58.519 33.333 0.00 0.00 0.00 5.07
723 741 8.882415 TCCCTCTGTAAACTAATATAAAAGCG 57.118 34.615 0.00 0.00 0.00 4.68
724 742 9.833917 ACTCCCTCTGTAAACTAATATAAAAGC 57.166 33.333 0.00 0.00 0.00 3.51
739 757 7.695554 CCATTAGGAATAGAGACTCCCTCTGTA 60.696 44.444 0.00 0.00 44.51 2.74
740 758 6.922711 CCATTAGGAATAGAGACTCCCTCTGT 60.923 46.154 0.00 0.00 44.51 3.41
741 759 5.480073 CCATTAGGAATAGAGACTCCCTCTG 59.520 48.000 0.00 1.02 44.51 3.35
742 760 5.650283 CCATTAGGAATAGAGACTCCCTCT 58.350 45.833 0.00 0.00 45.80 3.69
743 761 5.646215 TCCATTAGGAATAGAGACTCCCTC 58.354 45.833 0.00 0.00 42.23 4.30
744 762 5.688220 TCCATTAGGAATAGAGACTCCCT 57.312 43.478 0.00 1.01 42.23 4.20
765 783 3.587797 TGGTCTATTCACCAAGTCGTC 57.412 47.619 0.00 0.00 43.88 4.20
784 802 1.973320 CCAACGAAAATAAACCGCGTG 59.027 47.619 4.92 0.00 35.16 5.34
785 803 1.603326 ACCAACGAAAATAAACCGCGT 59.397 42.857 4.92 0.00 36.68 6.01
786 804 2.319241 ACCAACGAAAATAAACCGCG 57.681 45.000 0.00 0.00 0.00 6.46
787 805 5.392480 AAAAACCAACGAAAATAAACCGC 57.608 34.783 0.00 0.00 0.00 5.68
817 835 4.499116 CGGGGGAGGTGGGAGGAT 62.499 72.222 0.00 0.00 0.00 3.24
841 859 0.103390 TTTCGTGCGAGGTGTCTTCA 59.897 50.000 0.00 0.00 0.00 3.02
1292 1337 1.107538 CAGCCCTCGGGTAGATCGAA 61.108 60.000 3.54 0.00 36.15 3.71
1569 1640 7.826744 GGAAGAGAGGAGATAACAAATCTGTTT 59.173 37.037 0.00 0.00 43.45 2.83


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

AutoCloner maintained by Alex Coulton.