Multiple sequence alignment - TraesCS2D01G186100

Loading Multiple Alignment...

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 TraesCS2D01G186100 chr2D 100.000 2375 0 0 1 2375 130991099 130993473 0.000000e+00 4386
1 TraesCS2D01G186100 chr2D 83.333 888 113 23 594 1467 131075071 131075937 0.000000e+00 787
2 TraesCS2D01G186100 chr2D 85.693 685 78 14 779 1457 131120168 131120838 0.000000e+00 704
3 TraesCS2D01G186100 chr2D 85.123 652 83 7 804 1451 131128980 131129621 0.000000e+00 654
4 TraesCS2D01G186100 chr2D 86.899 603 51 15 356 930 131047556 131048158 0.000000e+00 651
5 TraesCS2D01G186100 chr2D 86.786 560 71 2 895 1451 131136249 131136808 2.590000e-174 621
6 TraesCS2D01G186100 chr2D 90.517 464 44 0 1912 2375 420567799 420567336 4.340000e-172 614
7 TraesCS2D01G186100 chr2D 85.191 601 72 12 1467 2067 592642049 592641466 3.380000e-168 601
8 TraesCS2D01G186100 chr2D 91.450 269 23 0 1469 1737 420568101 420567833 1.040000e-98 370
9 TraesCS2D01G186100 chr3D 99.228 907 7 0 1469 2375 338952845 338951939 0.000000e+00 1637
10 TraesCS2D01G186100 chr3D 89.408 321 30 3 7 324 39871470 39871151 3.680000e-108 401
11 TraesCS2D01G186100 chr7D 92.524 923 46 6 1470 2375 581232476 581233392 0.000000e+00 1301
12 TraesCS2D01G186100 chr7D 88.923 325 32 2 4 324 111471547 111471871 4.760000e-107 398
13 TraesCS2D01G186100 chr7D 88.957 326 29 4 1 326 201882644 201882962 1.710000e-106 396
14 TraesCS2D01G186100 chr2A 91.220 877 70 4 593 1468 137130718 137131588 0.000000e+00 1186
15 TraesCS2D01G186100 chr2A 83.486 654 92 8 804 1451 137229219 137229862 1.570000e-166 595
16 TraesCS2D01G186100 chr2A 91.331 323 23 4 1 323 51986131 51986448 1.010000e-118 436
17 TraesCS2D01G186100 chr2A 88.068 176 13 3 422 595 137130506 137130675 4.000000e-48 202
18 TraesCS2D01G186100 chr7A 87.310 922 84 19 1471 2375 710480360 710481265 0.000000e+00 1024
19 TraesCS2D01G186100 chr2B 87.344 719 65 12 765 1470 184577324 184578029 0.000000e+00 800
20 TraesCS2D01G186100 chr2B 91.083 471 38 2 1001 1470 184496620 184497087 3.330000e-178 634
21 TraesCS2D01G186100 chr2B 92.453 212 13 2 323 531 184496410 184496621 1.380000e-77 300
22 TraesCS2D01G186100 chrUn 85.116 692 74 14 785 1470 326757707 326757039 0.000000e+00 680
23 TraesCS2D01G186100 chrUn 88.946 389 43 0 1987 2375 27812167 27812555 4.590000e-132 481
24 TraesCS2D01G186100 chrUn 91.111 270 20 3 1470 1737 27811831 27812098 1.740000e-96 363
25 TraesCS2D01G186100 chr1D 90.343 466 41 4 1912 2375 298701048 298701511 2.020000e-170 608
26 TraesCS2D01G186100 chr1D 90.938 320 26 1 7 323 66355537 66355218 6.070000e-116 427
27 TraesCS2D01G186100 chr1D 91.791 268 22 0 1470 1737 63661990 63661723 8.020000e-100 374
28 TraesCS2D01G186100 chr1D 91.791 268 22 0 1470 1737 298700747 298701014 8.020000e-100 374
29 TraesCS2D01G186100 chr1D 87.861 173 21 0 2203 2375 63641622 63641450 1.110000e-48 204
30 TraesCS2D01G186100 chr7B 88.312 462 53 1 1914 2375 64782902 64782442 9.590000e-154 553
31 TraesCS2D01G186100 chr5A 87.872 470 37 10 1913 2375 2395833 2395377 3.470000e-148 534
32 TraesCS2D01G186100 chr5A 88.302 265 30 1 1470 1734 2396117 2395854 1.370000e-82 316
33 TraesCS2D01G186100 chr1A 89.688 417 42 1 1958 2374 539778962 539778547 4.490000e-147 531
34 TraesCS2D01G186100 chr5D 91.718 326 21 4 1 323 321614600 321614922 4.660000e-122 448
35 TraesCS2D01G186100 chr5D 90.282 319 28 3 7 325 91841448 91841133 4.720000e-112 414
36 TraesCS2D01G186100 chr5D 88.580 324 35 2 1 323 376834203 376834525 2.210000e-105 392
37 TraesCS2D01G186100 chr6B 89.490 314 28 3 15 324 616457271 616456959 2.210000e-105 392


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 TraesCS2D01G186100 chr2D 130991099 130993473 2374 False 4386 4386 100.0000 1 2375 1 chr2D.!!$F1 2374
1 TraesCS2D01G186100 chr2D 131075071 131075937 866 False 787 787 83.3330 594 1467 1 chr2D.!!$F3 873
2 TraesCS2D01G186100 chr2D 131120168 131120838 670 False 704 704 85.6930 779 1457 1 chr2D.!!$F4 678
3 TraesCS2D01G186100 chr2D 131128980 131129621 641 False 654 654 85.1230 804 1451 1 chr2D.!!$F5 647
4 TraesCS2D01G186100 chr2D 131047556 131048158 602 False 651 651 86.8990 356 930 1 chr2D.!!$F2 574
5 TraesCS2D01G186100 chr2D 131136249 131136808 559 False 621 621 86.7860 895 1451 1 chr2D.!!$F6 556
6 TraesCS2D01G186100 chr2D 592641466 592642049 583 True 601 601 85.1910 1467 2067 1 chr2D.!!$R1 600
7 TraesCS2D01G186100 chr2D 420567336 420568101 765 True 492 614 90.9835 1469 2375 2 chr2D.!!$R2 906
8 TraesCS2D01G186100 chr3D 338951939 338952845 906 True 1637 1637 99.2280 1469 2375 1 chr3D.!!$R2 906
9 TraesCS2D01G186100 chr7D 581232476 581233392 916 False 1301 1301 92.5240 1470 2375 1 chr7D.!!$F3 905
10 TraesCS2D01G186100 chr2A 137130506 137131588 1082 False 694 1186 89.6440 422 1468 2 chr2A.!!$F3 1046
11 TraesCS2D01G186100 chr2A 137229219 137229862 643 False 595 595 83.4860 804 1451 1 chr2A.!!$F2 647
12 TraesCS2D01G186100 chr7A 710480360 710481265 905 False 1024 1024 87.3100 1471 2375 1 chr7A.!!$F1 904
13 TraesCS2D01G186100 chr2B 184577324 184578029 705 False 800 800 87.3440 765 1470 1 chr2B.!!$F1 705
14 TraesCS2D01G186100 chr2B 184496410 184497087 677 False 467 634 91.7680 323 1470 2 chr2B.!!$F2 1147
15 TraesCS2D01G186100 chrUn 326757039 326757707 668 True 680 680 85.1160 785 1470 1 chrUn.!!$R1 685
16 TraesCS2D01G186100 chrUn 27811831 27812555 724 False 422 481 90.0285 1470 2375 2 chrUn.!!$F1 905
17 TraesCS2D01G186100 chr1D 298700747 298701511 764 False 491 608 91.0670 1470 2375 2 chr1D.!!$F1 905
18 TraesCS2D01G186100 chr5A 2395377 2396117 740 True 425 534 88.0870 1470 2375 2 chr5A.!!$R1 905

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
152 153 0.035458 CGACTTTTGCTCCTCCACCT 59.965 55.0 0.0 0.0 0.0 4.00 F
156 157 0.110486 TTTTGCTCCTCCACCTCCAC 59.890 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1308 1412 0.251354 GCATCTCTGGCTTCAGTGGA 59.749 55.000 0.00 0.0 39.45 4.02 R
2144 2322 2.676121 CGTTGCAGATGGGGCCAA 60.676 61.111 4.39 0.0 0.00 4.52 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.620779 CGAGTGATTCTGTCTCGTGT 57.379 50.000 13.78 0.00 43.69 4.49
20 21 2.245942 CGAGTGATTCTGTCTCGTGTG 58.754 52.381 13.78 0.00 43.69 3.82
21 22 2.095718 CGAGTGATTCTGTCTCGTGTGA 60.096 50.000 13.78 0.00 43.69 3.58
22 23 3.238441 GAGTGATTCTGTCTCGTGTGAC 58.762 50.000 0.00 0.00 37.47 3.67
23 24 2.887783 AGTGATTCTGTCTCGTGTGACT 59.112 45.455 4.01 0.00 37.79 3.41
24 25 2.983136 GTGATTCTGTCTCGTGTGACTG 59.017 50.000 4.01 3.73 37.79 3.51
25 26 2.884639 TGATTCTGTCTCGTGTGACTGA 59.115 45.455 7.33 7.33 41.10 3.41
26 27 3.507622 TGATTCTGTCTCGTGTGACTGAT 59.492 43.478 10.90 4.22 41.91 2.90
27 28 2.997485 TCTGTCTCGTGTGACTGATG 57.003 50.000 7.33 0.00 39.07 3.07
28 29 2.230660 TCTGTCTCGTGTGACTGATGT 58.769 47.619 7.33 0.00 39.07 3.06
29 30 2.030805 TCTGTCTCGTGTGACTGATGTG 60.031 50.000 7.33 0.00 39.07 3.21
30 31 1.953686 TGTCTCGTGTGACTGATGTGA 59.046 47.619 4.01 0.00 37.79 3.58
31 32 2.558359 TGTCTCGTGTGACTGATGTGAT 59.442 45.455 4.01 0.00 37.79 3.06
32 33 3.175152 GTCTCGTGTGACTGATGTGATC 58.825 50.000 0.00 0.00 34.39 2.92
33 34 3.084786 TCTCGTGTGACTGATGTGATCT 58.915 45.455 0.00 0.00 0.00 2.75
34 35 4.095036 GTCTCGTGTGACTGATGTGATCTA 59.905 45.833 0.00 0.00 34.39 1.98
35 36 4.884164 TCTCGTGTGACTGATGTGATCTAT 59.116 41.667 0.00 0.00 0.00 1.98
36 37 6.017852 GTCTCGTGTGACTGATGTGATCTATA 60.018 42.308 0.00 0.00 34.39 1.31
37 38 6.542370 TCTCGTGTGACTGATGTGATCTATAA 59.458 38.462 0.00 0.00 0.00 0.98
38 39 7.067008 TCTCGTGTGACTGATGTGATCTATAAA 59.933 37.037 0.00 0.00 0.00 1.40
39 40 7.543756 TCGTGTGACTGATGTGATCTATAAAA 58.456 34.615 0.00 0.00 0.00 1.52
40 41 8.197439 TCGTGTGACTGATGTGATCTATAAAAT 58.803 33.333 0.00 0.00 0.00 1.82
41 42 8.271487 CGTGTGACTGATGTGATCTATAAAATG 58.729 37.037 0.00 0.00 0.00 2.32
42 43 9.102757 GTGTGACTGATGTGATCTATAAAATGT 57.897 33.333 0.00 0.00 0.00 2.71
43 44 9.101655 TGTGACTGATGTGATCTATAAAATGTG 57.898 33.333 0.00 0.00 0.00 3.21
44 45 9.102757 GTGACTGATGTGATCTATAAAATGTGT 57.897 33.333 0.00 0.00 0.00 3.72
45 46 9.101655 TGACTGATGTGATCTATAAAATGTGTG 57.898 33.333 0.00 0.00 0.00 3.82
46 47 8.442632 ACTGATGTGATCTATAAAATGTGTGG 57.557 34.615 0.00 0.00 0.00 4.17
47 48 7.012704 ACTGATGTGATCTATAAAATGTGTGGC 59.987 37.037 0.00 0.00 0.00 5.01
48 49 7.056006 TGATGTGATCTATAAAATGTGTGGCT 58.944 34.615 0.00 0.00 0.00 4.75
49 50 7.557358 TGATGTGATCTATAAAATGTGTGGCTT 59.443 33.333 0.00 0.00 0.00 4.35
50 51 7.320443 TGTGATCTATAAAATGTGTGGCTTC 57.680 36.000 0.00 0.00 0.00 3.86
51 52 7.112122 TGTGATCTATAAAATGTGTGGCTTCT 58.888 34.615 0.00 0.00 0.00 2.85
52 53 7.611467 TGTGATCTATAAAATGTGTGGCTTCTT 59.389 33.333 0.00 0.00 0.00 2.52
53 54 9.109393 GTGATCTATAAAATGTGTGGCTTCTTA 57.891 33.333 0.00 0.00 0.00 2.10
54 55 9.109393 TGATCTATAAAATGTGTGGCTTCTTAC 57.891 33.333 0.00 0.00 0.00 2.34
55 56 9.109393 GATCTATAAAATGTGTGGCTTCTTACA 57.891 33.333 0.00 0.00 0.00 2.41
56 57 8.492673 TCTATAAAATGTGTGGCTTCTTACAG 57.507 34.615 0.00 0.00 0.00 2.74
57 58 3.923017 AAATGTGTGGCTTCTTACAGC 57.077 42.857 0.00 0.00 39.28 4.40
58 59 2.867109 ATGTGTGGCTTCTTACAGCT 57.133 45.000 0.00 0.00 39.97 4.24
59 60 2.169832 TGTGTGGCTTCTTACAGCTC 57.830 50.000 0.00 0.00 39.97 4.09
60 61 1.694150 TGTGTGGCTTCTTACAGCTCT 59.306 47.619 0.00 0.00 39.97 4.09
61 62 2.072298 GTGTGGCTTCTTACAGCTCTG 58.928 52.381 0.00 0.00 39.97 3.35
62 63 1.002430 TGTGGCTTCTTACAGCTCTGG 59.998 52.381 1.66 0.00 39.97 3.86
63 64 1.276421 GTGGCTTCTTACAGCTCTGGA 59.724 52.381 1.66 0.00 39.97 3.86
64 65 1.552337 TGGCTTCTTACAGCTCTGGAG 59.448 52.381 1.66 0.00 39.97 3.86
65 66 1.827969 GGCTTCTTACAGCTCTGGAGA 59.172 52.381 1.35 2.14 39.97 3.71
66 67 2.418060 GGCTTCTTACAGCTCTGGAGAC 60.418 54.545 1.35 0.00 39.97 3.36
67 68 2.418060 GCTTCTTACAGCTCTGGAGACC 60.418 54.545 1.35 0.00 36.79 3.85
68 69 1.464734 TCTTACAGCTCTGGAGACCG 58.535 55.000 1.35 0.00 34.19 4.79
69 70 0.179124 CTTACAGCTCTGGAGACCGC 60.179 60.000 1.35 0.00 34.19 5.68
70 71 0.612174 TTACAGCTCTGGAGACCGCT 60.612 55.000 1.35 0.00 34.19 5.52
71 72 0.612174 TACAGCTCTGGAGACCGCTT 60.612 55.000 1.35 0.00 34.19 4.68
72 73 0.612174 ACAGCTCTGGAGACCGCTTA 60.612 55.000 1.35 0.00 34.19 3.09
73 74 0.102120 CAGCTCTGGAGACCGCTTAG 59.898 60.000 1.35 0.00 0.00 2.18
74 75 1.227118 GCTCTGGAGACCGCTTAGC 60.227 63.158 1.35 0.00 0.00 3.09
75 76 1.949847 GCTCTGGAGACCGCTTAGCA 61.950 60.000 4.70 0.00 0.00 3.49
76 77 0.532573 CTCTGGAGACCGCTTAGCAA 59.467 55.000 4.70 0.00 0.00 3.91
77 78 0.532573 TCTGGAGACCGCTTAGCAAG 59.467 55.000 4.70 0.00 0.00 4.01
97 98 4.831307 GCGCGACCGAGACGTCAT 62.831 66.667 19.50 2.45 36.29 3.06
98 99 2.648102 CGCGACCGAGACGTCATC 60.648 66.667 19.50 11.22 36.29 2.92
99 100 2.648102 GCGACCGAGACGTCATCG 60.648 66.667 19.50 21.28 43.34 3.84
100 101 3.087176 CGACCGAGACGTCATCGA 58.913 61.111 27.54 0.00 42.76 3.59
101 102 1.296722 CGACCGAGACGTCATCGAC 60.297 63.158 27.54 21.12 42.76 4.20
102 103 1.792301 GACCGAGACGTCATCGACA 59.208 57.895 27.54 0.00 42.76 4.35
103 104 0.167470 GACCGAGACGTCATCGACAA 59.833 55.000 27.54 0.00 42.76 3.18
104 105 0.109873 ACCGAGACGTCATCGACAAC 60.110 55.000 27.54 7.22 42.76 3.32
105 106 0.109919 CCGAGACGTCATCGACAACA 60.110 55.000 27.54 0.00 42.76 3.33
106 107 1.467543 CCGAGACGTCATCGACAACAT 60.468 52.381 27.54 3.10 42.76 2.71
107 108 1.840741 CGAGACGTCATCGACAACATC 59.159 52.381 23.94 7.58 42.76 3.06
115 116 3.487202 CGACAACATCGTGGCGGG 61.487 66.667 0.00 0.00 46.60 6.13
116 117 2.358247 GACAACATCGTGGCGGGT 60.358 61.111 0.00 0.00 0.00 5.28
117 118 2.358247 ACAACATCGTGGCGGGTC 60.358 61.111 0.00 0.00 0.00 4.46
118 119 2.047274 CAACATCGTGGCGGGTCT 60.047 61.111 0.00 0.00 0.00 3.85
119 120 1.671054 CAACATCGTGGCGGGTCTT 60.671 57.895 0.00 0.00 0.00 3.01
120 121 1.375523 AACATCGTGGCGGGTCTTC 60.376 57.895 0.00 0.00 0.00 2.87
121 122 2.885644 CATCGTGGCGGGTCTTCG 60.886 66.667 0.00 0.00 0.00 3.79
122 123 3.379445 ATCGTGGCGGGTCTTCGT 61.379 61.111 0.00 0.00 0.00 3.85
123 124 2.939261 ATCGTGGCGGGTCTTCGTT 61.939 57.895 0.00 0.00 0.00 3.85
124 125 2.830704 ATCGTGGCGGGTCTTCGTTC 62.831 60.000 0.00 0.00 0.00 3.95
125 126 2.741211 GTGGCGGGTCTTCGTTCC 60.741 66.667 0.00 0.00 0.00 3.62
126 127 2.920912 TGGCGGGTCTTCGTTCCT 60.921 61.111 0.00 0.00 0.00 3.36
127 128 2.125633 GGCGGGTCTTCGTTCCTC 60.126 66.667 0.00 0.00 0.00 3.71
128 129 2.506438 GCGGGTCTTCGTTCCTCG 60.506 66.667 0.00 0.00 41.41 4.63
129 130 2.181021 CGGGTCTTCGTTCCTCGG 59.819 66.667 0.00 0.00 40.32 4.63
130 131 2.125633 GGGTCTTCGTTCCTCGGC 60.126 66.667 0.00 0.00 40.32 5.54
131 132 2.506438 GGTCTTCGTTCCTCGGCG 60.506 66.667 0.00 0.00 40.32 6.46
132 133 2.506438 GTCTTCGTTCCTCGGCGG 60.506 66.667 7.21 0.00 40.32 6.13
133 134 4.430765 TCTTCGTTCCTCGGCGGC 62.431 66.667 7.21 0.00 40.32 6.53
138 139 4.736896 GTTCCTCGGCGGCGACTT 62.737 66.667 31.46 0.00 0.00 3.01
139 140 3.998672 TTCCTCGGCGGCGACTTT 61.999 61.111 31.46 0.00 0.00 2.66
140 141 3.524648 TTCCTCGGCGGCGACTTTT 62.525 57.895 31.46 0.00 0.00 2.27
141 142 3.788766 CCTCGGCGGCGACTTTTG 61.789 66.667 31.46 19.74 0.00 2.44
142 143 4.445545 CTCGGCGGCGACTTTTGC 62.446 66.667 31.46 0.00 0.00 3.68
143 144 4.980805 TCGGCGGCGACTTTTGCT 62.981 61.111 31.46 0.00 0.00 3.91
144 145 4.445545 CGGCGGCGACTTTTGCTC 62.446 66.667 29.19 0.00 0.00 4.26
145 146 4.103103 GGCGGCGACTTTTGCTCC 62.103 66.667 12.98 0.00 0.00 4.70
146 147 3.050275 GCGGCGACTTTTGCTCCT 61.050 61.111 12.98 0.00 0.00 3.69
147 148 3.028366 GCGGCGACTTTTGCTCCTC 62.028 63.158 12.98 0.00 0.00 3.71
148 149 2.391389 CGGCGACTTTTGCTCCTCC 61.391 63.158 0.00 0.00 0.00 4.30
149 150 1.302511 GGCGACTTTTGCTCCTCCA 60.303 57.895 0.00 0.00 0.00 3.86
150 151 1.578206 GGCGACTTTTGCTCCTCCAC 61.578 60.000 0.00 0.00 0.00 4.02
151 152 1.578206 GCGACTTTTGCTCCTCCACC 61.578 60.000 0.00 0.00 0.00 4.61
152 153 0.035458 CGACTTTTGCTCCTCCACCT 59.965 55.000 0.00 0.00 0.00 4.00
153 154 1.814793 GACTTTTGCTCCTCCACCTC 58.185 55.000 0.00 0.00 0.00 3.85
154 155 0.402121 ACTTTTGCTCCTCCACCTCC 59.598 55.000 0.00 0.00 0.00 4.30
155 156 0.401738 CTTTTGCTCCTCCACCTCCA 59.598 55.000 0.00 0.00 0.00 3.86
156 157 0.110486 TTTTGCTCCTCCACCTCCAC 59.890 55.000 0.00 0.00 0.00 4.02
157 158 1.779061 TTTGCTCCTCCACCTCCACC 61.779 60.000 0.00 0.00 0.00 4.61
158 159 2.607750 GCTCCTCCACCTCCACCA 60.608 66.667 0.00 0.00 0.00 4.17
159 160 2.960688 GCTCCTCCACCTCCACCAC 61.961 68.421 0.00 0.00 0.00 4.16
160 161 2.203938 TCCTCCACCTCCACCACC 60.204 66.667 0.00 0.00 0.00 4.61
161 162 2.529136 CCTCCACCTCCACCACCA 60.529 66.667 0.00 0.00 0.00 4.17
162 163 2.750350 CTCCACCTCCACCACCAC 59.250 66.667 0.00 0.00 0.00 4.16
163 164 2.852075 TCCACCTCCACCACCACC 60.852 66.667 0.00 0.00 0.00 4.61
164 165 4.329545 CCACCTCCACCACCACCG 62.330 72.222 0.00 0.00 0.00 4.94
168 169 4.394712 CTCCACCACCACCGCCTC 62.395 72.222 0.00 0.00 0.00 4.70
187 188 2.106332 CGAGCCGGATTAGCGGTT 59.894 61.111 5.05 0.00 34.64 4.44
188 189 1.949631 CGAGCCGGATTAGCGGTTC 60.950 63.158 5.05 0.00 34.64 3.62
189 190 1.442148 GAGCCGGATTAGCGGTTCT 59.558 57.895 5.05 0.00 33.63 3.01
190 191 0.179081 GAGCCGGATTAGCGGTTCTT 60.179 55.000 5.05 0.00 33.63 2.52
191 192 0.252197 AGCCGGATTAGCGGTTCTTT 59.748 50.000 5.05 0.00 34.64 2.52
192 193 1.092348 GCCGGATTAGCGGTTCTTTT 58.908 50.000 5.05 0.00 0.00 2.27
193 194 1.471287 GCCGGATTAGCGGTTCTTTTT 59.529 47.619 5.05 0.00 0.00 1.94
194 195 2.679336 GCCGGATTAGCGGTTCTTTTTA 59.321 45.455 5.05 0.00 0.00 1.52
195 196 3.242641 GCCGGATTAGCGGTTCTTTTTAG 60.243 47.826 5.05 0.00 0.00 1.85
196 197 3.242641 CCGGATTAGCGGTTCTTTTTAGC 60.243 47.826 0.00 0.00 0.00 3.09
197 198 3.621715 CGGATTAGCGGTTCTTTTTAGCT 59.378 43.478 0.00 0.00 41.45 3.32
198 199 4.094442 CGGATTAGCGGTTCTTTTTAGCTT 59.906 41.667 0.00 0.00 39.14 3.74
199 200 5.391629 CGGATTAGCGGTTCTTTTTAGCTTT 60.392 40.000 0.00 0.00 39.14 3.51
200 201 6.028368 GGATTAGCGGTTCTTTTTAGCTTTC 58.972 40.000 0.00 0.00 39.14 2.62
201 202 6.127980 GGATTAGCGGTTCTTTTTAGCTTTCT 60.128 38.462 0.00 0.00 39.14 2.52
202 203 6.628919 TTAGCGGTTCTTTTTAGCTTTCTT 57.371 33.333 0.00 0.00 39.14 2.52
203 204 5.515797 AGCGGTTCTTTTTAGCTTTCTTT 57.484 34.783 0.00 0.00 34.05 2.52
204 205 5.281727 AGCGGTTCTTTTTAGCTTTCTTTG 58.718 37.500 0.00 0.00 34.05 2.77
205 206 4.444388 GCGGTTCTTTTTAGCTTTCTTTGG 59.556 41.667 0.00 0.00 0.00 3.28
206 207 4.982295 CGGTTCTTTTTAGCTTTCTTTGGG 59.018 41.667 0.00 0.00 0.00 4.12
207 208 5.297547 GGTTCTTTTTAGCTTTCTTTGGGG 58.702 41.667 0.00 0.00 0.00 4.96
208 209 4.600692 TCTTTTTAGCTTTCTTTGGGGC 57.399 40.909 0.00 0.00 0.00 5.80
209 210 4.223144 TCTTTTTAGCTTTCTTTGGGGCT 58.777 39.130 0.00 0.00 38.62 5.19
210 211 4.653801 TCTTTTTAGCTTTCTTTGGGGCTT 59.346 37.500 0.00 0.00 36.40 4.35
211 212 4.335400 TTTTAGCTTTCTTTGGGGCTTG 57.665 40.909 0.00 0.00 36.40 4.01
212 213 2.675658 TAGCTTTCTTTGGGGCTTGT 57.324 45.000 0.00 0.00 36.40 3.16
213 214 1.793414 AGCTTTCTTTGGGGCTTGTT 58.207 45.000 0.00 0.00 0.00 2.83
214 215 2.118679 AGCTTTCTTTGGGGCTTGTTT 58.881 42.857 0.00 0.00 0.00 2.83
215 216 2.505407 AGCTTTCTTTGGGGCTTGTTTT 59.495 40.909 0.00 0.00 0.00 2.43
216 217 2.613595 GCTTTCTTTGGGGCTTGTTTTG 59.386 45.455 0.00 0.00 0.00 2.44
217 218 2.323968 TTCTTTGGGGCTTGTTTTGC 57.676 45.000 0.00 0.00 0.00 3.68
218 219 1.494960 TCTTTGGGGCTTGTTTTGCT 58.505 45.000 0.00 0.00 0.00 3.91
219 220 1.138661 TCTTTGGGGCTTGTTTTGCTG 59.861 47.619 0.00 0.00 0.00 4.41
220 221 0.908198 TTTGGGGCTTGTTTTGCTGT 59.092 45.000 0.00 0.00 0.00 4.40
221 222 0.177604 TTGGGGCTTGTTTTGCTGTG 59.822 50.000 0.00 0.00 0.00 3.66
222 223 0.685785 TGGGGCTTGTTTTGCTGTGA 60.686 50.000 0.00 0.00 0.00 3.58
223 224 0.249447 GGGGCTTGTTTTGCTGTGAC 60.249 55.000 0.00 0.00 0.00 3.67
224 225 0.249447 GGGCTTGTTTTGCTGTGACC 60.249 55.000 0.00 0.00 0.00 4.02
225 226 0.249447 GGCTTGTTTTGCTGTGACCC 60.249 55.000 0.00 0.00 0.00 4.46
226 227 0.249447 GCTTGTTTTGCTGTGACCCC 60.249 55.000 0.00 0.00 0.00 4.95
227 228 1.110442 CTTGTTTTGCTGTGACCCCA 58.890 50.000 0.00 0.00 0.00 4.96
228 229 1.480137 CTTGTTTTGCTGTGACCCCAA 59.520 47.619 0.00 0.00 0.00 4.12
229 230 0.820871 TGTTTTGCTGTGACCCCAAC 59.179 50.000 0.00 0.00 0.00 3.77
230 231 0.820871 GTTTTGCTGTGACCCCAACA 59.179 50.000 0.00 0.00 0.00 3.33
231 232 1.412343 GTTTTGCTGTGACCCCAACAT 59.588 47.619 0.00 0.00 0.00 2.71
232 233 1.039068 TTTGCTGTGACCCCAACATG 58.961 50.000 0.00 0.00 0.00 3.21
233 234 0.184692 TTGCTGTGACCCCAACATGA 59.815 50.000 0.00 0.00 0.00 3.07
234 235 0.537143 TGCTGTGACCCCAACATGAC 60.537 55.000 0.00 0.00 0.00 3.06
235 236 0.250901 GCTGTGACCCCAACATGACT 60.251 55.000 0.00 0.00 0.00 3.41
236 237 1.813513 CTGTGACCCCAACATGACTC 58.186 55.000 0.00 0.00 0.00 3.36
237 238 1.349026 CTGTGACCCCAACATGACTCT 59.651 52.381 0.00 0.00 0.00 3.24
238 239 2.567169 CTGTGACCCCAACATGACTCTA 59.433 50.000 0.00 0.00 0.00 2.43
239 240 3.181329 TGTGACCCCAACATGACTCTAT 58.819 45.455 0.00 0.00 0.00 1.98
240 241 3.055167 TGTGACCCCAACATGACTCTATG 60.055 47.826 0.00 0.00 0.00 2.23
241 242 3.197766 GTGACCCCAACATGACTCTATGA 59.802 47.826 0.00 0.00 0.00 2.15
242 243 3.197766 TGACCCCAACATGACTCTATGAC 59.802 47.826 0.00 0.00 0.00 3.06
243 244 3.452627 GACCCCAACATGACTCTATGACT 59.547 47.826 0.00 0.00 0.00 3.41
244 245 3.846588 ACCCCAACATGACTCTATGACTT 59.153 43.478 0.00 0.00 0.00 3.01
245 246 4.194640 CCCCAACATGACTCTATGACTTG 58.805 47.826 0.00 0.00 0.00 3.16
246 247 4.080919 CCCCAACATGACTCTATGACTTGA 60.081 45.833 0.00 0.00 0.00 3.02
247 248 5.397221 CCCCAACATGACTCTATGACTTGAT 60.397 44.000 0.00 0.00 0.00 2.57
248 249 6.118170 CCCAACATGACTCTATGACTTGATT 58.882 40.000 0.00 0.00 0.00 2.57
249 250 6.037940 CCCAACATGACTCTATGACTTGATTG 59.962 42.308 0.00 0.00 0.00 2.67
250 251 6.596888 CCAACATGACTCTATGACTTGATTGT 59.403 38.462 0.00 0.00 0.00 2.71
251 252 7.765819 CCAACATGACTCTATGACTTGATTGTA 59.234 37.037 0.00 0.00 0.00 2.41
252 253 8.598924 CAACATGACTCTATGACTTGATTGTAC 58.401 37.037 0.00 0.00 0.00 2.90
253 254 8.072321 ACATGACTCTATGACTTGATTGTACT 57.928 34.615 0.00 0.00 0.00 2.73
254 255 8.535335 ACATGACTCTATGACTTGATTGTACTT 58.465 33.333 0.00 0.00 0.00 2.24
255 256 9.376075 CATGACTCTATGACTTGATTGTACTTT 57.624 33.333 0.00 0.00 0.00 2.66
256 257 8.763049 TGACTCTATGACTTGATTGTACTTTG 57.237 34.615 0.00 0.00 0.00 2.77
257 258 8.367911 TGACTCTATGACTTGATTGTACTTTGT 58.632 33.333 0.00 0.00 0.00 2.83
258 259 9.856488 GACTCTATGACTTGATTGTACTTTGTA 57.144 33.333 0.00 0.00 0.00 2.41
259 260 9.640963 ACTCTATGACTTGATTGTACTTTGTAC 57.359 33.333 0.00 1.33 0.00 2.90
260 261 9.862371 CTCTATGACTTGATTGTACTTTGTACT 57.138 33.333 8.94 0.00 0.00 2.73
270 271 9.647797 TGATTGTACTTTGTACTACTATGTTGG 57.352 33.333 8.94 0.00 0.00 3.77
271 272 9.865321 GATTGTACTTTGTACTACTATGTTGGA 57.135 33.333 8.94 0.00 0.00 3.53
273 274 9.647797 TTGTACTTTGTACTACTATGTTGGATG 57.352 33.333 8.94 0.00 0.00 3.51
274 275 8.809066 TGTACTTTGTACTACTATGTTGGATGT 58.191 33.333 8.94 0.00 0.00 3.06
275 276 9.649167 GTACTTTGTACTACTATGTTGGATGTT 57.351 33.333 0.00 0.00 0.00 2.71
276 277 8.773404 ACTTTGTACTACTATGTTGGATGTTC 57.227 34.615 0.00 0.00 0.00 3.18
277 278 7.544566 ACTTTGTACTACTATGTTGGATGTTCG 59.455 37.037 0.00 0.00 0.00 3.95
278 279 5.898174 TGTACTACTATGTTGGATGTTCGG 58.102 41.667 0.00 0.00 0.00 4.30
279 280 5.419788 TGTACTACTATGTTGGATGTTCGGT 59.580 40.000 0.00 0.00 0.00 4.69
280 281 5.416271 ACTACTATGTTGGATGTTCGGTT 57.584 39.130 0.00 0.00 0.00 4.44
281 282 5.416947 ACTACTATGTTGGATGTTCGGTTC 58.583 41.667 0.00 0.00 0.00 3.62
282 283 4.553330 ACTATGTTGGATGTTCGGTTCT 57.447 40.909 0.00 0.00 0.00 3.01
283 284 4.906618 ACTATGTTGGATGTTCGGTTCTT 58.093 39.130 0.00 0.00 0.00 2.52
284 285 5.313712 ACTATGTTGGATGTTCGGTTCTTT 58.686 37.500 0.00 0.00 0.00 2.52
285 286 3.980646 TGTTGGATGTTCGGTTCTTTG 57.019 42.857 0.00 0.00 0.00 2.77
286 287 2.034053 TGTTGGATGTTCGGTTCTTTGC 59.966 45.455 0.00 0.00 0.00 3.68
287 288 2.270352 TGGATGTTCGGTTCTTTGCT 57.730 45.000 0.00 0.00 0.00 3.91
288 289 2.582052 TGGATGTTCGGTTCTTTGCTT 58.418 42.857 0.00 0.00 0.00 3.91
289 290 2.955660 TGGATGTTCGGTTCTTTGCTTT 59.044 40.909 0.00 0.00 0.00 3.51
290 291 4.138290 TGGATGTTCGGTTCTTTGCTTTA 58.862 39.130 0.00 0.00 0.00 1.85
291 292 4.764823 TGGATGTTCGGTTCTTTGCTTTAT 59.235 37.500 0.00 0.00 0.00 1.40
292 293 5.941058 TGGATGTTCGGTTCTTTGCTTTATA 59.059 36.000 0.00 0.00 0.00 0.98
293 294 6.431543 TGGATGTTCGGTTCTTTGCTTTATAA 59.568 34.615 0.00 0.00 0.00 0.98
294 295 7.122055 TGGATGTTCGGTTCTTTGCTTTATAAT 59.878 33.333 0.00 0.00 0.00 1.28
295 296 8.617809 GGATGTTCGGTTCTTTGCTTTATAATA 58.382 33.333 0.00 0.00 0.00 0.98
349 350 2.817844 TCACTAGTTAAGCGACTGAGCA 59.182 45.455 0.00 0.00 40.15 4.26
367 368 2.232208 AGCAAGCAAATTAAGCAGGGTC 59.768 45.455 5.70 0.00 0.00 4.46
463 465 7.571025 AGTAGACAAGTTTAGAGACCCAAAAA 58.429 34.615 0.00 0.00 0.00 1.94
484 486 2.028748 AGGCATTTGAACCAGACATTGC 60.029 45.455 0.00 0.00 0.00 3.56
534 538 6.678878 TGTCTACTAATTGTATCCGATCTGC 58.321 40.000 0.00 0.00 0.00 4.26
551 555 4.891627 TCTGCGAAAAATCTGACAAACA 57.108 36.364 0.00 0.00 0.00 2.83
560 564 3.010767 TGACAAACAGACGTGCGC 58.989 55.556 0.00 0.00 0.00 6.09
653 702 3.963665 TGATGTACAAACTTGCTTGTGC 58.036 40.909 0.00 0.00 39.81 4.57
662 711 0.949397 CTTGCTTGTGCTCTTCTGCA 59.051 50.000 0.00 0.00 41.05 4.41
704 756 2.758979 AGGCGTTTAGTCTTAGCAGCTA 59.241 45.455 0.00 0.00 0.00 3.32
802 872 1.841302 TAAGCAGGTGGCCAGACTGG 61.841 60.000 29.04 17.83 46.50 4.00
868 943 0.320374 TAGGTGAACAGCCTCGTTGG 59.680 55.000 0.29 0.00 37.54 3.77
958 1038 3.156293 TCCCACATCAAAACCACATCAG 58.844 45.455 0.00 0.00 0.00 2.90
970 1062 3.636679 ACCACATCAGAAGAGCTAGCTA 58.363 45.455 19.38 0.08 0.00 3.32
971 1063 3.636300 ACCACATCAGAAGAGCTAGCTAG 59.364 47.826 19.38 16.84 0.00 3.42
972 1064 3.636300 CCACATCAGAAGAGCTAGCTAGT 59.364 47.826 19.38 8.45 0.00 2.57
973 1065 4.824537 CCACATCAGAAGAGCTAGCTAGTA 59.175 45.833 19.38 0.51 0.00 1.82
974 1066 5.278266 CCACATCAGAAGAGCTAGCTAGTAC 60.278 48.000 19.38 15.13 0.00 2.73
1029 1133 6.544928 TCAAGAATCACTGCTGTATTCCTA 57.455 37.500 15.52 5.89 31.35 2.94
1082 1186 2.124151 CGGGGCAAGAATCCTGGG 60.124 66.667 0.00 0.00 0.00 4.45
1084 1188 2.316586 GGGGCAAGAATCCTGGGGA 61.317 63.158 0.00 0.00 35.55 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.057876 AGTCACACGAGACAGAATCACTC 60.058 47.826 9.34 0.00 40.98 3.51
2 3 2.887783 AGTCACACGAGACAGAATCACT 59.112 45.455 9.34 0.00 40.98 3.41
3 4 2.983136 CAGTCACACGAGACAGAATCAC 59.017 50.000 9.34 0.00 40.98 3.06
4 5 2.884639 TCAGTCACACGAGACAGAATCA 59.115 45.455 9.34 0.00 40.98 2.57
5 6 3.560902 TCAGTCACACGAGACAGAATC 57.439 47.619 9.34 0.00 40.98 2.52
6 7 3.256879 ACATCAGTCACACGAGACAGAAT 59.743 43.478 9.34 0.00 40.98 2.40
7 8 2.623416 ACATCAGTCACACGAGACAGAA 59.377 45.455 9.34 0.00 40.98 3.02
8 9 2.030805 CACATCAGTCACACGAGACAGA 60.031 50.000 9.34 7.34 40.98 3.41
9 10 2.030805 TCACATCAGTCACACGAGACAG 60.031 50.000 9.34 2.89 40.98 3.51
10 11 1.953686 TCACATCAGTCACACGAGACA 59.046 47.619 9.34 0.00 40.98 3.41
11 12 2.706555 TCACATCAGTCACACGAGAC 57.293 50.000 0.00 0.00 38.81 3.36
12 13 3.084786 AGATCACATCAGTCACACGAGA 58.915 45.455 0.00 0.00 0.00 4.04
13 14 3.500558 AGATCACATCAGTCACACGAG 57.499 47.619 0.00 0.00 0.00 4.18
14 15 6.693315 TTATAGATCACATCAGTCACACGA 57.307 37.500 0.00 0.00 0.00 4.35
15 16 7.755582 TTTTATAGATCACATCAGTCACACG 57.244 36.000 0.00 0.00 0.00 4.49
16 17 9.102757 ACATTTTATAGATCACATCAGTCACAC 57.897 33.333 0.00 0.00 0.00 3.82
17 18 9.101655 CACATTTTATAGATCACATCAGTCACA 57.898 33.333 0.00 0.00 0.00 3.58
18 19 9.102757 ACACATTTTATAGATCACATCAGTCAC 57.897 33.333 0.00 0.00 0.00 3.67
19 20 9.101655 CACACATTTTATAGATCACATCAGTCA 57.898 33.333 0.00 0.00 0.00 3.41
20 21 8.554528 CCACACATTTTATAGATCACATCAGTC 58.445 37.037 0.00 0.00 0.00 3.51
21 22 7.012704 GCCACACATTTTATAGATCACATCAGT 59.987 37.037 0.00 0.00 0.00 3.41
22 23 7.228108 AGCCACACATTTTATAGATCACATCAG 59.772 37.037 0.00 0.00 0.00 2.90
23 24 7.056006 AGCCACACATTTTATAGATCACATCA 58.944 34.615 0.00 0.00 0.00 3.07
24 25 7.502120 AGCCACACATTTTATAGATCACATC 57.498 36.000 0.00 0.00 0.00 3.06
25 26 7.776969 AGAAGCCACACATTTTATAGATCACAT 59.223 33.333 0.00 0.00 0.00 3.21
26 27 7.112122 AGAAGCCACACATTTTATAGATCACA 58.888 34.615 0.00 0.00 0.00 3.58
27 28 7.559590 AGAAGCCACACATTTTATAGATCAC 57.440 36.000 0.00 0.00 0.00 3.06
28 29 9.109393 GTAAGAAGCCACACATTTTATAGATCA 57.891 33.333 0.00 0.00 0.00 2.92
29 30 9.109393 TGTAAGAAGCCACACATTTTATAGATC 57.891 33.333 0.00 0.00 0.00 2.75
30 31 9.113838 CTGTAAGAAGCCACACATTTTATAGAT 57.886 33.333 0.00 0.00 34.07 1.98
31 32 7.065803 GCTGTAAGAAGCCACACATTTTATAGA 59.934 37.037 0.00 0.00 37.20 1.98
32 33 7.066284 AGCTGTAAGAAGCCACACATTTTATAG 59.934 37.037 0.00 0.00 44.68 1.31
33 34 6.884295 AGCTGTAAGAAGCCACACATTTTATA 59.116 34.615 0.00 0.00 44.68 0.98
34 35 5.711976 AGCTGTAAGAAGCCACACATTTTAT 59.288 36.000 0.00 0.00 44.68 1.40
35 36 5.070001 AGCTGTAAGAAGCCACACATTTTA 58.930 37.500 0.00 0.00 44.68 1.52
36 37 3.891366 AGCTGTAAGAAGCCACACATTTT 59.109 39.130 0.00 0.00 44.68 1.82
37 38 3.490348 AGCTGTAAGAAGCCACACATTT 58.510 40.909 0.00 0.00 44.68 2.32
38 39 3.077359 GAGCTGTAAGAAGCCACACATT 58.923 45.455 0.00 0.00 44.68 2.71
39 40 2.304180 AGAGCTGTAAGAAGCCACACAT 59.696 45.455 0.00 0.00 44.68 3.21
40 41 1.694150 AGAGCTGTAAGAAGCCACACA 59.306 47.619 0.00 0.00 44.68 3.72
41 42 2.072298 CAGAGCTGTAAGAAGCCACAC 58.928 52.381 0.00 0.00 44.68 3.82
42 43 1.002430 CCAGAGCTGTAAGAAGCCACA 59.998 52.381 0.00 0.00 44.68 4.17
43 44 1.276421 TCCAGAGCTGTAAGAAGCCAC 59.724 52.381 0.00 0.00 44.68 5.01
44 45 1.552337 CTCCAGAGCTGTAAGAAGCCA 59.448 52.381 0.00 0.00 44.68 4.75
45 46 1.827969 TCTCCAGAGCTGTAAGAAGCC 59.172 52.381 0.00 0.00 44.68 4.35
46 47 2.418060 GGTCTCCAGAGCTGTAAGAAGC 60.418 54.545 0.00 0.00 43.88 3.86
47 48 2.159310 CGGTCTCCAGAGCTGTAAGAAG 60.159 54.545 0.00 0.00 40.17 2.85
48 49 1.819288 CGGTCTCCAGAGCTGTAAGAA 59.181 52.381 0.00 0.00 40.17 2.52
49 50 1.464734 CGGTCTCCAGAGCTGTAAGA 58.535 55.000 0.00 0.00 40.17 2.10
50 51 0.179124 GCGGTCTCCAGAGCTGTAAG 60.179 60.000 0.00 0.00 40.17 2.34
51 52 0.612174 AGCGGTCTCCAGAGCTGTAA 60.612 55.000 0.00 0.00 40.17 2.41
52 53 0.612174 AAGCGGTCTCCAGAGCTGTA 60.612 55.000 0.00 0.00 40.17 2.74
53 54 0.612174 TAAGCGGTCTCCAGAGCTGT 60.612 55.000 0.00 0.00 40.17 4.40
54 55 0.102120 CTAAGCGGTCTCCAGAGCTG 59.898 60.000 0.00 0.00 40.17 4.24
55 56 1.671901 GCTAAGCGGTCTCCAGAGCT 61.672 60.000 4.36 0.00 42.35 4.09
56 57 1.227118 GCTAAGCGGTCTCCAGAGC 60.227 63.158 0.00 0.00 39.04 4.09
57 58 0.532573 TTGCTAAGCGGTCTCCAGAG 59.467 55.000 0.00 0.00 0.00 3.35
58 59 0.532573 CTTGCTAAGCGGTCTCCAGA 59.467 55.000 0.00 0.00 0.00 3.86
59 60 1.086634 GCTTGCTAAGCGGTCTCCAG 61.087 60.000 5.35 0.00 45.74 3.86
60 61 1.079127 GCTTGCTAAGCGGTCTCCA 60.079 57.895 5.35 0.00 45.74 3.86
61 62 3.801129 GCTTGCTAAGCGGTCTCC 58.199 61.111 5.35 0.00 45.74 3.71
69 70 4.210304 GTCGCGCCGCTTGCTAAG 62.210 66.667 7.78 0.00 38.05 2.18
80 81 4.831307 ATGACGTCTCGGTCGCGC 62.831 66.667 17.92 0.00 39.83 6.86
81 82 2.648102 GATGACGTCTCGGTCGCG 60.648 66.667 17.92 0.00 39.83 5.87
82 83 2.648102 CGATGACGTCTCGGTCGC 60.648 66.667 21.86 4.05 39.83 5.19
83 84 1.296722 GTCGATGACGTCTCGGTCG 60.297 63.158 26.03 22.81 39.83 4.79
84 85 0.167470 TTGTCGATGACGTCTCGGTC 59.833 55.000 26.03 21.02 40.69 4.79
85 86 0.109873 GTTGTCGATGACGTCTCGGT 60.110 55.000 26.03 9.45 40.69 4.69
86 87 0.109919 TGTTGTCGATGACGTCTCGG 60.110 55.000 26.03 13.34 40.69 4.63
87 88 1.840741 GATGTTGTCGATGACGTCTCG 59.159 52.381 22.92 22.92 40.69 4.04
99 100 2.358247 ACCCGCCACGATGTTGTC 60.358 61.111 0.00 0.00 0.00 3.18
100 101 2.358247 GACCCGCCACGATGTTGT 60.358 61.111 0.00 0.00 0.00 3.32
101 102 1.635663 GAAGACCCGCCACGATGTTG 61.636 60.000 0.00 0.00 0.00 3.33
102 103 1.375523 GAAGACCCGCCACGATGTT 60.376 57.895 0.00 0.00 0.00 2.71
103 104 2.264794 GAAGACCCGCCACGATGT 59.735 61.111 0.00 0.00 0.00 3.06
104 105 2.885644 CGAAGACCCGCCACGATG 60.886 66.667 0.00 0.00 0.00 3.84
105 106 2.830704 GAACGAAGACCCGCCACGAT 62.831 60.000 0.00 0.00 0.00 3.73
106 107 3.562779 GAACGAAGACCCGCCACGA 62.563 63.158 0.00 0.00 0.00 4.35
107 108 3.110178 GAACGAAGACCCGCCACG 61.110 66.667 0.00 0.00 0.00 4.94
108 109 2.741211 GGAACGAAGACCCGCCAC 60.741 66.667 0.00 0.00 0.00 5.01
109 110 2.920912 AGGAACGAAGACCCGCCA 60.921 61.111 0.00 0.00 0.00 5.69
110 111 2.125633 GAGGAACGAAGACCCGCC 60.126 66.667 0.00 0.00 0.00 6.13
111 112 2.506438 CGAGGAACGAAGACCCGC 60.506 66.667 0.00 0.00 45.77 6.13
112 113 2.181021 CCGAGGAACGAAGACCCG 59.819 66.667 0.00 0.00 45.77 5.28
113 114 2.125633 GCCGAGGAACGAAGACCC 60.126 66.667 0.00 0.00 45.77 4.46
114 115 2.506438 CGCCGAGGAACGAAGACC 60.506 66.667 0.00 0.00 45.77 3.85
115 116 2.506438 CCGCCGAGGAACGAAGAC 60.506 66.667 0.00 0.00 45.00 3.01
116 117 4.430765 GCCGCCGAGGAACGAAGA 62.431 66.667 0.91 0.00 45.00 2.87
121 122 4.736896 AAGTCGCCGCCGAGGAAC 62.737 66.667 0.00 0.00 45.38 3.62
122 123 3.524648 AAAAGTCGCCGCCGAGGAA 62.525 57.895 0.00 0.00 45.38 3.36
123 124 3.998672 AAAAGTCGCCGCCGAGGA 61.999 61.111 0.00 0.00 45.38 3.71
124 125 3.788766 CAAAAGTCGCCGCCGAGG 61.789 66.667 0.00 0.00 45.38 4.63
125 126 4.445545 GCAAAAGTCGCCGCCGAG 62.446 66.667 0.00 0.00 45.38 4.63
126 127 4.980805 AGCAAAAGTCGCCGCCGA 62.981 61.111 0.00 0.00 42.01 5.54
127 128 4.445545 GAGCAAAAGTCGCCGCCG 62.446 66.667 0.00 0.00 0.00 6.46
128 129 4.103103 GGAGCAAAAGTCGCCGCC 62.103 66.667 0.00 0.00 0.00 6.13
129 130 3.028366 GAGGAGCAAAAGTCGCCGC 62.028 63.158 0.00 0.00 0.00 6.53
130 131 2.391389 GGAGGAGCAAAAGTCGCCG 61.391 63.158 0.00 0.00 0.00 6.46
131 132 1.302511 TGGAGGAGCAAAAGTCGCC 60.303 57.895 0.00 0.00 0.00 5.54
132 133 1.578206 GGTGGAGGAGCAAAAGTCGC 61.578 60.000 0.00 0.00 0.00 5.19
133 134 0.035458 AGGTGGAGGAGCAAAAGTCG 59.965 55.000 0.00 0.00 0.00 4.18
134 135 1.611936 GGAGGTGGAGGAGCAAAAGTC 60.612 57.143 0.00 0.00 0.00 3.01
135 136 0.402121 GGAGGTGGAGGAGCAAAAGT 59.598 55.000 0.00 0.00 0.00 2.66
136 137 0.401738 TGGAGGTGGAGGAGCAAAAG 59.598 55.000 0.00 0.00 0.00 2.27
137 138 0.110486 GTGGAGGTGGAGGAGCAAAA 59.890 55.000 0.00 0.00 0.00 2.44
138 139 1.761174 GTGGAGGTGGAGGAGCAAA 59.239 57.895 0.00 0.00 0.00 3.68
139 140 2.224159 GGTGGAGGTGGAGGAGCAA 61.224 63.158 0.00 0.00 0.00 3.91
140 141 2.607750 GGTGGAGGTGGAGGAGCA 60.608 66.667 0.00 0.00 0.00 4.26
141 142 2.607750 TGGTGGAGGTGGAGGAGC 60.608 66.667 0.00 0.00 0.00 4.70
142 143 2.294078 GGTGGTGGAGGTGGAGGAG 61.294 68.421 0.00 0.00 0.00 3.69
143 144 2.203938 GGTGGTGGAGGTGGAGGA 60.204 66.667 0.00 0.00 0.00 3.71
144 145 2.529136 TGGTGGTGGAGGTGGAGG 60.529 66.667 0.00 0.00 0.00 4.30
145 146 2.750350 GTGGTGGTGGAGGTGGAG 59.250 66.667 0.00 0.00 0.00 3.86
146 147 2.852075 GGTGGTGGTGGAGGTGGA 60.852 66.667 0.00 0.00 0.00 4.02
147 148 4.329545 CGGTGGTGGTGGAGGTGG 62.330 72.222 0.00 0.00 0.00 4.61
151 152 4.394712 GAGGCGGTGGTGGTGGAG 62.395 72.222 0.00 0.00 0.00 3.86
175 176 3.621715 AGCTAAAAAGAACCGCTAATCCG 59.378 43.478 0.00 0.00 0.00 4.18
176 177 5.562506 AAGCTAAAAAGAACCGCTAATCC 57.437 39.130 0.00 0.00 0.00 3.01
177 178 6.843208 AGAAAGCTAAAAAGAACCGCTAATC 58.157 36.000 0.00 0.00 0.00 1.75
178 179 6.819397 AGAAAGCTAAAAAGAACCGCTAAT 57.181 33.333 0.00 0.00 0.00 1.73
179 180 6.628919 AAGAAAGCTAAAAAGAACCGCTAA 57.371 33.333 0.00 0.00 0.00 3.09
180 181 6.435428 CAAAGAAAGCTAAAAAGAACCGCTA 58.565 36.000 0.00 0.00 0.00 4.26
181 182 5.281727 CAAAGAAAGCTAAAAAGAACCGCT 58.718 37.500 0.00 0.00 0.00 5.52
182 183 4.444388 CCAAAGAAAGCTAAAAAGAACCGC 59.556 41.667 0.00 0.00 0.00 5.68
183 184 4.982295 CCCAAAGAAAGCTAAAAAGAACCG 59.018 41.667 0.00 0.00 0.00 4.44
184 185 5.297547 CCCCAAAGAAAGCTAAAAAGAACC 58.702 41.667 0.00 0.00 0.00 3.62
185 186 4.750098 GCCCCAAAGAAAGCTAAAAAGAAC 59.250 41.667 0.00 0.00 0.00 3.01
186 187 4.653801 AGCCCCAAAGAAAGCTAAAAAGAA 59.346 37.500 0.00 0.00 32.73 2.52
187 188 4.223144 AGCCCCAAAGAAAGCTAAAAAGA 58.777 39.130 0.00 0.00 32.73 2.52
188 189 4.607293 AGCCCCAAAGAAAGCTAAAAAG 57.393 40.909 0.00 0.00 32.73 2.27
189 190 4.163268 ACAAGCCCCAAAGAAAGCTAAAAA 59.837 37.500 0.00 0.00 34.49 1.94
190 191 3.709141 ACAAGCCCCAAAGAAAGCTAAAA 59.291 39.130 0.00 0.00 34.49 1.52
191 192 3.304829 ACAAGCCCCAAAGAAAGCTAAA 58.695 40.909 0.00 0.00 34.49 1.85
192 193 2.957474 ACAAGCCCCAAAGAAAGCTAA 58.043 42.857 0.00 0.00 34.49 3.09
193 194 2.675658 ACAAGCCCCAAAGAAAGCTA 57.324 45.000 0.00 0.00 34.49 3.32
194 195 1.793414 AACAAGCCCCAAAGAAAGCT 58.207 45.000 0.00 0.00 37.10 3.74
195 196 2.613595 CAAAACAAGCCCCAAAGAAAGC 59.386 45.455 0.00 0.00 0.00 3.51
196 197 2.613595 GCAAAACAAGCCCCAAAGAAAG 59.386 45.455 0.00 0.00 0.00 2.62
197 198 2.238395 AGCAAAACAAGCCCCAAAGAAA 59.762 40.909 0.00 0.00 0.00 2.52
198 199 1.836802 AGCAAAACAAGCCCCAAAGAA 59.163 42.857 0.00 0.00 0.00 2.52
199 200 1.138661 CAGCAAAACAAGCCCCAAAGA 59.861 47.619 0.00 0.00 0.00 2.52
200 201 1.134431 ACAGCAAAACAAGCCCCAAAG 60.134 47.619 0.00 0.00 0.00 2.77
201 202 0.908198 ACAGCAAAACAAGCCCCAAA 59.092 45.000 0.00 0.00 0.00 3.28
202 203 0.177604 CACAGCAAAACAAGCCCCAA 59.822 50.000 0.00 0.00 0.00 4.12
203 204 0.685785 TCACAGCAAAACAAGCCCCA 60.686 50.000 0.00 0.00 0.00 4.96
204 205 0.249447 GTCACAGCAAAACAAGCCCC 60.249 55.000 0.00 0.00 0.00 5.80
205 206 0.249447 GGTCACAGCAAAACAAGCCC 60.249 55.000 0.00 0.00 0.00 5.19
206 207 0.249447 GGGTCACAGCAAAACAAGCC 60.249 55.000 0.00 0.00 0.00 4.35
207 208 0.249447 GGGGTCACAGCAAAACAAGC 60.249 55.000 0.00 0.00 0.00 4.01
208 209 1.110442 TGGGGTCACAGCAAAACAAG 58.890 50.000 0.00 0.00 0.00 3.16
209 210 1.205893 GTTGGGGTCACAGCAAAACAA 59.794 47.619 0.00 0.00 0.00 2.83
210 211 0.820871 GTTGGGGTCACAGCAAAACA 59.179 50.000 0.00 0.00 0.00 2.83
211 212 0.820871 TGTTGGGGTCACAGCAAAAC 59.179 50.000 0.00 0.00 0.00 2.43
212 213 1.411977 CATGTTGGGGTCACAGCAAAA 59.588 47.619 0.00 0.00 35.23 2.44
213 214 1.039068 CATGTTGGGGTCACAGCAAA 58.961 50.000 0.00 0.00 35.23 3.68
214 215 0.184692 TCATGTTGGGGTCACAGCAA 59.815 50.000 0.00 0.00 35.23 3.91
215 216 0.537143 GTCATGTTGGGGTCACAGCA 60.537 55.000 0.00 0.00 36.04 4.41
216 217 0.250901 AGTCATGTTGGGGTCACAGC 60.251 55.000 0.00 0.00 0.00 4.40
217 218 1.349026 AGAGTCATGTTGGGGTCACAG 59.651 52.381 0.00 0.00 0.00 3.66
218 219 1.434188 AGAGTCATGTTGGGGTCACA 58.566 50.000 0.00 0.00 0.00 3.58
219 220 3.197766 TCATAGAGTCATGTTGGGGTCAC 59.802 47.826 0.00 0.00 0.00 3.67
220 221 3.197766 GTCATAGAGTCATGTTGGGGTCA 59.802 47.826 0.00 0.00 0.00 4.02
221 222 3.452627 AGTCATAGAGTCATGTTGGGGTC 59.547 47.826 0.00 0.00 0.00 4.46
222 223 3.454858 AGTCATAGAGTCATGTTGGGGT 58.545 45.455 0.00 0.00 0.00 4.95
223 224 4.080919 TCAAGTCATAGAGTCATGTTGGGG 60.081 45.833 0.00 0.00 0.00 4.96
224 225 5.089970 TCAAGTCATAGAGTCATGTTGGG 57.910 43.478 0.00 0.00 0.00 4.12
225 226 6.596888 ACAATCAAGTCATAGAGTCATGTTGG 59.403 38.462 0.00 0.00 0.00 3.77
226 227 7.606858 ACAATCAAGTCATAGAGTCATGTTG 57.393 36.000 0.00 0.00 0.00 3.33
227 228 8.535335 AGTACAATCAAGTCATAGAGTCATGTT 58.465 33.333 0.00 0.00 0.00 2.71
228 229 8.072321 AGTACAATCAAGTCATAGAGTCATGT 57.928 34.615 0.00 0.00 0.00 3.21
229 230 8.939201 AAGTACAATCAAGTCATAGAGTCATG 57.061 34.615 0.00 0.00 0.00 3.07
230 231 9.376075 CAAAGTACAATCAAGTCATAGAGTCAT 57.624 33.333 0.00 0.00 0.00 3.06
231 232 8.367911 ACAAAGTACAATCAAGTCATAGAGTCA 58.632 33.333 0.00 0.00 0.00 3.41
232 233 8.764524 ACAAAGTACAATCAAGTCATAGAGTC 57.235 34.615 0.00 0.00 0.00 3.36
233 234 9.640963 GTACAAAGTACAATCAAGTCATAGAGT 57.359 33.333 0.00 0.00 0.00 3.24
234 235 9.862371 AGTACAAAGTACAATCAAGTCATAGAG 57.138 33.333 9.68 0.00 0.00 2.43
244 245 9.647797 CCAACATAGTAGTACAAAGTACAATCA 57.352 33.333 9.68 0.00 34.45 2.57
245 246 9.865321 TCCAACATAGTAGTACAAAGTACAATC 57.135 33.333 9.68 0.72 34.45 2.67
247 248 9.647797 CATCCAACATAGTAGTACAAAGTACAA 57.352 33.333 9.68 0.00 34.45 2.41
248 249 8.809066 ACATCCAACATAGTAGTACAAAGTACA 58.191 33.333 9.68 0.00 34.45 2.90
249 250 9.649167 AACATCCAACATAGTAGTACAAAGTAC 57.351 33.333 2.52 0.00 0.00 2.73
250 251 9.865321 GAACATCCAACATAGTAGTACAAAGTA 57.135 33.333 2.52 0.00 0.00 2.24
251 252 7.544566 CGAACATCCAACATAGTAGTACAAAGT 59.455 37.037 2.52 0.00 0.00 2.66
252 253 7.010183 CCGAACATCCAACATAGTAGTACAAAG 59.990 40.741 2.52 0.00 0.00 2.77
253 254 6.814644 CCGAACATCCAACATAGTAGTACAAA 59.185 38.462 2.52 0.00 0.00 2.83
254 255 6.071221 ACCGAACATCCAACATAGTAGTACAA 60.071 38.462 2.52 0.00 0.00 2.41
255 256 5.419788 ACCGAACATCCAACATAGTAGTACA 59.580 40.000 2.52 0.00 0.00 2.90
256 257 5.899299 ACCGAACATCCAACATAGTAGTAC 58.101 41.667 0.00 0.00 0.00 2.73
257 258 6.379133 AGAACCGAACATCCAACATAGTAGTA 59.621 38.462 0.00 0.00 0.00 1.82
258 259 5.187186 AGAACCGAACATCCAACATAGTAGT 59.813 40.000 0.00 0.00 0.00 2.73
259 260 5.661458 AGAACCGAACATCCAACATAGTAG 58.339 41.667 0.00 0.00 0.00 2.57
260 261 5.670792 AGAACCGAACATCCAACATAGTA 57.329 39.130 0.00 0.00 0.00 1.82
261 262 4.553330 AGAACCGAACATCCAACATAGT 57.447 40.909 0.00 0.00 0.00 2.12
262 263 5.631026 CAAAGAACCGAACATCCAACATAG 58.369 41.667 0.00 0.00 0.00 2.23
263 264 4.083003 GCAAAGAACCGAACATCCAACATA 60.083 41.667 0.00 0.00 0.00 2.29
264 265 3.305335 GCAAAGAACCGAACATCCAACAT 60.305 43.478 0.00 0.00 0.00 2.71
265 266 2.034053 GCAAAGAACCGAACATCCAACA 59.966 45.455 0.00 0.00 0.00 3.33
266 267 2.293399 AGCAAAGAACCGAACATCCAAC 59.707 45.455 0.00 0.00 0.00 3.77
267 268 2.582052 AGCAAAGAACCGAACATCCAA 58.418 42.857 0.00 0.00 0.00 3.53
268 269 2.270352 AGCAAAGAACCGAACATCCA 57.730 45.000 0.00 0.00 0.00 3.41
269 270 3.643159 AAAGCAAAGAACCGAACATCC 57.357 42.857 0.00 0.00 0.00 3.51
314 315 8.277713 GCTTAACTAGTGATGTGTTACGAAAAA 58.722 33.333 0.00 0.00 0.00 1.94
315 316 7.358600 CGCTTAACTAGTGATGTGTTACGAAAA 60.359 37.037 0.00 0.00 36.43 2.29
316 317 6.088483 CGCTTAACTAGTGATGTGTTACGAAA 59.912 38.462 0.00 0.00 36.43 3.46
317 318 5.570206 CGCTTAACTAGTGATGTGTTACGAA 59.430 40.000 0.00 0.00 36.43 3.85
318 319 5.090757 CGCTTAACTAGTGATGTGTTACGA 58.909 41.667 0.00 0.00 36.43 3.43
319 320 5.003214 GTCGCTTAACTAGTGATGTGTTACG 59.997 44.000 0.00 0.00 44.70 3.18
320 321 6.033619 CAGTCGCTTAACTAGTGATGTGTTAC 59.966 42.308 0.00 0.00 44.70 2.50
321 322 6.072342 TCAGTCGCTTAACTAGTGATGTGTTA 60.072 38.462 0.00 0.00 44.70 2.41
325 326 4.675671 GCTCAGTCGCTTAACTAGTGATGT 60.676 45.833 0.00 0.00 44.70 3.06
330 331 3.839293 CTTGCTCAGTCGCTTAACTAGT 58.161 45.455 0.00 0.00 0.00 2.57
349 350 3.500343 ACAGACCCTGCTTAATTTGCTT 58.500 40.909 5.05 0.00 34.37 3.91
463 465 2.028748 GCAATGTCTGGTTCAAATGCCT 60.029 45.455 0.00 0.00 0.00 4.75
560 564 2.160143 GCTATACGAATAACACGCGCAG 60.160 50.000 5.73 0.55 0.00 5.18
704 756 4.142469 GGATAAACACGCAATTGTTAGGCT 60.142 41.667 7.40 0.00 38.82 4.58
802 872 4.451096 TGTGTGCTCTTTAATTTCGAGTCC 59.549 41.667 0.00 0.00 0.00 3.85
868 943 4.886579 AGTGTTTTGGATCCAATGCTTTC 58.113 39.130 27.53 15.16 35.70 2.62
923 1003 1.007118 TGTGGGAGAGATAGCAGGTGA 59.993 52.381 0.00 0.00 0.00 4.02
958 1038 6.680874 TTGTACTGTACTAGCTAGCTCTTC 57.319 41.667 23.26 10.97 0.00 2.87
970 1062 5.602561 TGGATGCCTATGATTGTACTGTACT 59.397 40.000 17.98 0.00 0.00 2.73
971 1063 5.853936 TGGATGCCTATGATTGTACTGTAC 58.146 41.667 10.98 10.98 0.00 2.90
972 1064 6.269769 TGATGGATGCCTATGATTGTACTGTA 59.730 38.462 0.00 0.00 0.00 2.74
973 1065 5.072193 TGATGGATGCCTATGATTGTACTGT 59.928 40.000 0.00 0.00 0.00 3.55
974 1066 5.554070 TGATGGATGCCTATGATTGTACTG 58.446 41.667 0.00 0.00 0.00 2.74
1013 1117 2.688446 CCGACTAGGAATACAGCAGTGA 59.312 50.000 0.00 0.00 45.00 3.41
1029 1133 2.757917 GAGAGGAGCAGCCCGACT 60.758 66.667 0.00 0.00 37.37 4.18
1098 1202 1.078143 GTGCTCCTCGCCTTTGGAT 60.078 57.895 0.00 0.00 38.05 3.41
1119 1223 4.809496 AGCATTGGCAGCTCCGGG 62.809 66.667 0.00 0.00 44.61 5.73
1246 1350 2.703798 CCGGGAATGTTGGCAGCTG 61.704 63.158 10.11 10.11 0.00 4.24
1292 1396 2.335712 GGAAGCTCCACCTTTGGCG 61.336 63.158 0.00 0.00 43.56 5.69
1308 1412 0.251354 GCATCTCTGGCTTCAGTGGA 59.749 55.000 0.00 0.00 39.45 4.02
1379 1483 4.149747 GCAAAGAGAAGAGAAGTGAAGACG 59.850 45.833 0.00 0.00 0.00 4.18
1520 1627 5.766150 ATCAGTCACAAACAAATTTCCGA 57.234 34.783 0.00 0.00 0.00 4.55
1647 1755 3.623960 CGGTCAAACTAACCAGTCAAACA 59.376 43.478 0.00 0.00 36.53 2.83
2144 2322 2.676121 CGTTGCAGATGGGGCCAA 60.676 61.111 4.39 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.