Multiple sequence alignment - TraesCS5D01G419800

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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 TraesCS5D01G419800 chr5D 100.000 3488 0 0 1 3488 480606077 480602590 0.000000e+00 6442.0
1 TraesCS5D01G419800 chr5D 86.207 116 15 1 763 878 530428428 530428314 1.310000e-24 124.0
2 TraesCS5D01G419800 chr5A 97.796 2631 56 2 859 3488 599783861 599781232 0.000000e+00 4536.0
3 TraesCS5D01G419800 chr5A 90.447 492 19 8 294 765 599784343 599783860 1.060000e-174 623.0
4 TraesCS5D01G419800 chr5A 80.078 256 30 9 1 235 37928447 37928702 1.660000e-38 171.0
5 TraesCS5D01G419800 chr5B 96.427 2631 86 4 862 3488 588943103 588940477 0.000000e+00 4331.0
6 TraesCS5D01G419800 chr5B 91.516 554 18 12 235 765 588943652 588943105 0.000000e+00 736.0
7 TraesCS5D01G419800 chr5B 89.744 117 9 3 763 878 418373424 418373538 2.810000e-31 147.0
8 TraesCS5D01G419800 chr2D 95.500 2422 96 6 1075 3488 1991388 1993804 0.000000e+00 3856.0
9 TraesCS5D01G419800 chr2D 85.357 280 25 11 884 1155 1989168 1989439 3.430000e-70 276.0
10 TraesCS5D01G419800 chr2D 82.484 314 23 16 295 602 2339605 2339892 2.690000e-61 246.0
11 TraesCS5D01G419800 chr2D 83.516 273 26 10 339 602 2737879 2737617 1.620000e-58 237.0
12 TraesCS5D01G419800 chr2D 88.690 168 6 7 853 1010 1991084 1991248 3.550000e-45 193.0
13 TraesCS5D01G419800 chr2D 88.991 109 6 2 481 583 1988927 1989035 2.830000e-26 130.0
14 TraesCS5D01G419800 chr2A 94.828 2417 100 11 1075 3488 1871222 1873616 0.000000e+00 3747.0
15 TraesCS5D01G419800 chr2A 88.916 1633 147 12 1887 3486 2986556 2988187 0.000000e+00 1982.0
16 TraesCS5D01G419800 chr2A 81.905 1575 255 19 1866 3417 2881575 2883142 0.000000e+00 1303.0
17 TraesCS5D01G419800 chr2A 81.100 291 30 15 346 620 2318194 2318475 3.530000e-50 209.0
18 TraesCS5D01G419800 chr2B 86.475 2255 248 25 1275 3486 8564960 8567200 0.000000e+00 2422.0
19 TraesCS5D01G419800 chr2B 93.232 1448 71 4 1089 2510 469102 470548 0.000000e+00 2106.0
20 TraesCS5D01G419800 chr2B 81.801 2099 353 17 1343 3417 8338817 8340910 0.000000e+00 1733.0
21 TraesCS5D01G419800 chr2B 81.545 2097 355 21 1343 3417 667787264 667789350 0.000000e+00 1700.0
22 TraesCS5D01G419800 chr2B 86.129 1586 198 12 1850 3416 8635787 8634205 0.000000e+00 1690.0
23 TraesCS5D01G419800 chr2B 85.992 1592 201 12 1844 3416 8666894 8668482 0.000000e+00 1685.0
24 TraesCS5D01G419800 chr2B 84.874 238 17 8 363 583 468575 468810 4.530000e-54 222.0
25 TraesCS5D01G419800 chr2B 87.273 165 11 4 853 1010 468921 469082 2.770000e-41 180.0
26 TraesCS5D01G419800 chr2B 94.000 50 1 1 705 752 468864 468913 1.340000e-09 75.0
27 TraesCS5D01G419800 chr2B 96.970 33 1 0 933 965 9202317 9202285 4.860000e-04 56.5
28 TraesCS5D01G419800 chr3B 81.718 2084 352 17 1358 3417 52921019 52918941 0.000000e+00 1711.0
29 TraesCS5D01G419800 chr3B 95.192 104 5 0 757 860 766128173 766128276 7.750000e-37 165.0
30 TraesCS5D01G419800 chr3B 94.340 106 6 0 758 863 523562124 523562019 2.790000e-36 163.0
31 TraesCS5D01G419800 chr4B 81.613 2083 356 15 1355 3417 634313215 634315290 0.000000e+00 1700.0
32 TraesCS5D01G419800 chr4B 90.678 118 9 2 757 873 32922897 32922781 4.660000e-34 156.0
33 TraesCS5D01G419800 chr4B 85.039 127 16 3 757 881 139757871 139757746 3.650000e-25 126.0
34 TraesCS5D01G419800 chr4B 86.726 113 14 1 761 873 60698231 60698342 1.310000e-24 124.0
35 TraesCS5D01G419800 chrUn 79.096 1593 294 26 1207 2771 381159169 381160750 0.000000e+00 1061.0
36 TraesCS5D01G419800 chrUn 79.688 256 29 14 1 235 103264770 103265023 2.790000e-36 163.0
37 TraesCS5D01G419800 chr7D 97.436 234 6 0 3 236 497009285 497009052 1.950000e-107 399.0
38 TraesCS5D01G419800 chr1D 97.009 234 7 0 3 236 159867794 159867561 9.070000e-106 394.0
39 TraesCS5D01G419800 chr1D 96.996 233 7 0 3 235 411395381 411395613 3.260000e-105 392.0
40 TraesCS5D01G419800 chr1D 92.793 111 7 1 752 861 2162854 2162744 3.600000e-35 159.0
41 TraesCS5D01G419800 chr4A 92.766 235 17 0 3 237 221511987 221511753 1.200000e-89 340.0
42 TraesCS5D01G419800 chr4A 84.211 114 16 2 764 876 624227782 624227894 3.680000e-20 110.0
43 TraesCS5D01G419800 chr3A 90.558 233 16 2 3 235 25010827 25010601 1.570000e-78 303.0
44 TraesCS5D01G419800 chr3A 95.238 105 5 0 757 861 710276434 710276330 2.150000e-37 167.0
45 TraesCS5D01G419800 chr3A 88.288 111 13 0 763 873 531452136 531452026 2.180000e-27 134.0
46 TraesCS5D01G419800 chr7B 94.495 109 6 0 757 865 591048771 591048663 5.990000e-38 169.0
47 TraesCS5D01G419800 chr7B 78.824 255 33 7 3 237 709504367 709504114 6.030000e-33 152.0
48 TraesCS5D01G419800 chr6B 95.283 106 5 0 756 861 374852370 374852265 5.990000e-38 169.0
49 TraesCS5D01G419800 chr6B 96.040 101 4 0 763 863 336181314 336181214 7.750000e-37 165.0
50 TraesCS5D01G419800 chr6B 91.429 105 9 0 769 873 283316715 283316611 1.010000e-30 145.0
51 TraesCS5D01G419800 chr1B 96.117 103 3 1 763 865 263273966 263274067 2.150000e-37 167.0
52 TraesCS5D01G419800 chr7A 85.417 144 16 4 96 235 125587996 125587854 1.010000e-30 145.0
53 TraesCS5D01G419800 chr3D 84.848 99 13 1 775 873 520722707 520722611 7.970000e-17 99.0


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 TraesCS5D01G419800 chr5D 480602590 480606077 3487 True 6442.00 6442 100.00000 1 3488 1 chr5D.!!$R1 3487
1 TraesCS5D01G419800 chr5A 599781232 599784343 3111 True 2579.50 4536 94.12150 294 3488 2 chr5A.!!$R1 3194
2 TraesCS5D01G419800 chr5B 588940477 588943652 3175 True 2533.50 4331 93.97150 235 3488 2 chr5B.!!$R1 3253
3 TraesCS5D01G419800 chr2D 1988927 1993804 4877 False 1113.75 3856 89.63450 481 3488 4 chr2D.!!$F2 3007
4 TraesCS5D01G419800 chr2A 1871222 1873616 2394 False 3747.00 3747 94.82800 1075 3488 1 chr2A.!!$F1 2413
5 TraesCS5D01G419800 chr2A 2986556 2988187 1631 False 1982.00 1982 88.91600 1887 3486 1 chr2A.!!$F4 1599
6 TraesCS5D01G419800 chr2A 2881575 2883142 1567 False 1303.00 1303 81.90500 1866 3417 1 chr2A.!!$F3 1551
7 TraesCS5D01G419800 chr2B 8564960 8567200 2240 False 2422.00 2422 86.47500 1275 3486 1 chr2B.!!$F2 2211
8 TraesCS5D01G419800 chr2B 8338817 8340910 2093 False 1733.00 1733 81.80100 1343 3417 1 chr2B.!!$F1 2074
9 TraesCS5D01G419800 chr2B 667787264 667789350 2086 False 1700.00 1700 81.54500 1343 3417 1 chr2B.!!$F4 2074
10 TraesCS5D01G419800 chr2B 8634205 8635787 1582 True 1690.00 1690 86.12900 1850 3416 1 chr2B.!!$R1 1566
11 TraesCS5D01G419800 chr2B 8666894 8668482 1588 False 1685.00 1685 85.99200 1844 3416 1 chr2B.!!$F3 1572
12 TraesCS5D01G419800 chr2B 468575 470548 1973 False 645.75 2106 89.84475 363 2510 4 chr2B.!!$F5 2147
13 TraesCS5D01G419800 chr3B 52918941 52921019 2078 True 1711.00 1711 81.71800 1358 3417 1 chr3B.!!$R1 2059
14 TraesCS5D01G419800 chr4B 634313215 634315290 2075 False 1700.00 1700 81.61300 1355 3417 1 chr4B.!!$F2 2062
15 TraesCS5D01G419800 chrUn 381159169 381160750 1581 False 1061.00 1061 79.09600 1207 2771 1 chrUn.!!$F2 1564

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
233 234 0.039074 AAGGCGCGATTCCGATCTAG 60.039 55.0 12.10 0.00 38.22 2.43 F
285 286 0.320771 CCATGTAGTGATAGGCCGGC 60.321 60.0 21.18 21.18 0.00 6.13 F
286 287 0.320771 CATGTAGTGATAGGCCGGCC 60.321 60.0 39.29 39.29 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1037 3105 1.741706 GCAGCCAGAGTGTACGTAGTA 59.258 52.381 0.00 0.0 45.11 1.82 R
1989 4136 1.841302 TAGGGCCACAAGTCTGCAGG 61.841 60.000 15.13 0.0 0.00 4.85 R
2771 4920 4.738541 GCAAGCATAATTCCATTGGTCTGG 60.739 45.833 1.86 0.0 37.66 3.86 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
20 21 3.541071 TTGTATCGAACTTCGTGTCGA 57.459 42.857 10.88 0.00 41.35 4.20
21 22 3.541071 TGTATCGAACTTCGTGTCGAA 57.459 42.857 10.88 4.60 43.75 3.71
22 23 4.087510 TGTATCGAACTTCGTGTCGAAT 57.912 40.909 10.88 0.00 44.85 3.34
23 24 3.849708 TGTATCGAACTTCGTGTCGAATG 59.150 43.478 10.88 3.29 44.85 2.67
24 25 1.693467 TCGAACTTCGTGTCGAATGG 58.307 50.000 10.88 0.00 44.85 3.16
25 26 1.001048 TCGAACTTCGTGTCGAATGGT 60.001 47.619 10.88 0.00 44.85 3.55
26 27 1.790623 CGAACTTCGTGTCGAATGGTT 59.209 47.619 2.84 7.04 44.85 3.67
27 28 2.981805 CGAACTTCGTGTCGAATGGTTA 59.018 45.455 2.84 0.00 44.85 2.85
28 29 3.611113 CGAACTTCGTGTCGAATGGTTAT 59.389 43.478 2.84 0.00 44.85 1.89
29 30 4.259292 CGAACTTCGTGTCGAATGGTTATC 60.259 45.833 2.84 0.00 44.85 1.75
30 31 4.451629 ACTTCGTGTCGAATGGTTATCT 57.548 40.909 5.10 0.00 44.85 1.98
31 32 4.817517 ACTTCGTGTCGAATGGTTATCTT 58.182 39.130 5.10 0.00 44.85 2.40
32 33 5.235516 ACTTCGTGTCGAATGGTTATCTTT 58.764 37.500 5.10 0.00 44.85 2.52
33 34 5.699458 ACTTCGTGTCGAATGGTTATCTTTT 59.301 36.000 5.10 0.00 44.85 2.27
34 35 5.524511 TCGTGTCGAATGGTTATCTTTTG 57.475 39.130 0.00 0.00 31.06 2.44
35 36 4.088648 CGTGTCGAATGGTTATCTTTTGC 58.911 43.478 0.00 0.00 0.00 3.68
36 37 4.088648 GTGTCGAATGGTTATCTTTTGCG 58.911 43.478 0.00 0.00 0.00 4.85
37 38 3.126171 TGTCGAATGGTTATCTTTTGCGG 59.874 43.478 0.00 0.00 0.00 5.69
38 39 3.126343 GTCGAATGGTTATCTTTTGCGGT 59.874 43.478 0.00 0.00 0.00 5.68
39 40 3.372822 TCGAATGGTTATCTTTTGCGGTC 59.627 43.478 0.00 0.00 0.00 4.79
40 41 3.680789 GAATGGTTATCTTTTGCGGTCG 58.319 45.455 0.00 0.00 0.00 4.79
41 42 2.172851 TGGTTATCTTTTGCGGTCGT 57.827 45.000 0.00 0.00 0.00 4.34
42 43 3.316071 TGGTTATCTTTTGCGGTCGTA 57.684 42.857 0.00 0.00 0.00 3.43
43 44 3.864243 TGGTTATCTTTTGCGGTCGTAT 58.136 40.909 0.00 0.00 0.00 3.06
44 45 3.619483 TGGTTATCTTTTGCGGTCGTATG 59.381 43.478 0.00 0.00 0.00 2.39
45 46 3.866910 GGTTATCTTTTGCGGTCGTATGA 59.133 43.478 0.00 0.00 0.00 2.15
46 47 4.330620 GGTTATCTTTTGCGGTCGTATGAA 59.669 41.667 0.00 0.00 0.00 2.57
47 48 5.007332 GGTTATCTTTTGCGGTCGTATGAAT 59.993 40.000 0.00 0.00 0.00 2.57
48 49 4.536364 ATCTTTTGCGGTCGTATGAATG 57.464 40.909 0.00 0.00 0.00 2.67
49 50 2.095213 TCTTTTGCGGTCGTATGAATGC 59.905 45.455 3.32 3.32 0.00 3.56
50 51 1.443802 TTTGCGGTCGTATGAATGCA 58.556 45.000 7.97 7.97 35.44 3.96
51 52 0.724549 TTGCGGTCGTATGAATGCAC 59.275 50.000 10.90 0.00 36.55 4.57
52 53 0.108377 TGCGGTCGTATGAATGCACT 60.108 50.000 7.97 0.00 33.17 4.40
53 54 0.301687 GCGGTCGTATGAATGCACTG 59.698 55.000 0.00 0.00 0.00 3.66
54 55 1.921243 CGGTCGTATGAATGCACTGA 58.079 50.000 0.00 0.00 0.00 3.41
55 56 1.854743 CGGTCGTATGAATGCACTGAG 59.145 52.381 0.00 0.00 0.00 3.35
56 57 1.594862 GGTCGTATGAATGCACTGAGC 59.405 52.381 0.00 0.00 45.96 4.26
57 58 2.544685 GTCGTATGAATGCACTGAGCT 58.455 47.619 0.00 0.00 45.94 4.09
58 59 2.932614 GTCGTATGAATGCACTGAGCTT 59.067 45.455 0.00 0.00 45.94 3.74
59 60 2.931969 TCGTATGAATGCACTGAGCTTG 59.068 45.455 0.00 0.00 45.94 4.01
60 61 2.931969 CGTATGAATGCACTGAGCTTGA 59.068 45.455 0.00 0.00 45.94 3.02
61 62 3.558829 CGTATGAATGCACTGAGCTTGAT 59.441 43.478 0.00 0.00 45.94 2.57
62 63 4.318618 CGTATGAATGCACTGAGCTTGATC 60.319 45.833 0.00 0.00 45.94 2.92
63 64 2.362736 TGAATGCACTGAGCTTGATCC 58.637 47.619 0.00 0.00 45.94 3.36
64 65 2.026542 TGAATGCACTGAGCTTGATCCT 60.027 45.455 0.00 0.00 45.94 3.24
65 66 2.039818 ATGCACTGAGCTTGATCCTG 57.960 50.000 0.00 0.00 45.94 3.86
66 67 0.675837 TGCACTGAGCTTGATCCTGC 60.676 55.000 0.00 0.00 45.94 4.85
67 68 1.375098 GCACTGAGCTTGATCCTGCC 61.375 60.000 0.00 0.00 41.15 4.85
68 69 0.252479 CACTGAGCTTGATCCTGCCT 59.748 55.000 0.00 0.00 0.00 4.75
69 70 0.990374 ACTGAGCTTGATCCTGCCTT 59.010 50.000 0.00 0.00 0.00 4.35
70 71 2.093288 CACTGAGCTTGATCCTGCCTTA 60.093 50.000 0.00 0.00 0.00 2.69
71 72 2.776536 ACTGAGCTTGATCCTGCCTTAT 59.223 45.455 0.00 0.00 0.00 1.73
72 73 3.969976 ACTGAGCTTGATCCTGCCTTATA 59.030 43.478 0.00 0.00 0.00 0.98
73 74 4.410228 ACTGAGCTTGATCCTGCCTTATAA 59.590 41.667 0.00 0.00 0.00 0.98
74 75 5.104360 ACTGAGCTTGATCCTGCCTTATAAA 60.104 40.000 0.00 0.00 0.00 1.40
75 76 5.126067 TGAGCTTGATCCTGCCTTATAAAC 58.874 41.667 0.00 0.00 0.00 2.01
76 77 5.104360 TGAGCTTGATCCTGCCTTATAAACT 60.104 40.000 0.00 0.00 0.00 2.66
77 78 5.760131 AGCTTGATCCTGCCTTATAAACTT 58.240 37.500 3.80 0.00 0.00 2.66
78 79 6.900194 AGCTTGATCCTGCCTTATAAACTTA 58.100 36.000 3.80 0.00 0.00 2.24
79 80 7.521669 AGCTTGATCCTGCCTTATAAACTTAT 58.478 34.615 3.80 0.00 0.00 1.73
80 81 7.446625 AGCTTGATCCTGCCTTATAAACTTATG 59.553 37.037 3.80 0.00 0.00 1.90
81 82 7.229506 GCTTGATCCTGCCTTATAAACTTATGT 59.770 37.037 0.00 0.00 0.00 2.29
82 83 9.125026 CTTGATCCTGCCTTATAAACTTATGTT 57.875 33.333 0.00 0.00 38.16 2.71
83 84 8.450578 TGATCCTGCCTTATAAACTTATGTTG 57.549 34.615 0.00 0.00 36.39 3.33
84 85 8.271458 TGATCCTGCCTTATAAACTTATGTTGA 58.729 33.333 0.00 0.00 36.39 3.18
85 86 9.289782 GATCCTGCCTTATAAACTTATGTTGAT 57.710 33.333 0.00 0.00 36.39 2.57
86 87 8.677148 TCCTGCCTTATAAACTTATGTTGATC 57.323 34.615 0.00 0.00 36.39 2.92
87 88 8.494433 TCCTGCCTTATAAACTTATGTTGATCT 58.506 33.333 0.00 0.00 36.39 2.75
88 89 9.125026 CCTGCCTTATAAACTTATGTTGATCTT 57.875 33.333 0.00 0.00 36.39 2.40
100 101 9.757227 ACTTATGTTGATCTTAAGCTCTATCAC 57.243 33.333 7.77 3.79 37.32 3.06
101 102 9.755804 CTTATGTTGATCTTAAGCTCTATCACA 57.244 33.333 7.77 8.11 30.74 3.58
104 105 9.624373 ATGTTGATCTTAAGCTCTATCACAATT 57.376 29.630 7.77 0.00 0.00 2.32
151 152 9.726438 ATCCTCTATAAGTGCAAATGTTATACC 57.274 33.333 0.00 0.00 0.00 2.73
152 153 8.934697 TCCTCTATAAGTGCAAATGTTATACCT 58.065 33.333 0.00 0.00 0.00 3.08
153 154 8.993121 CCTCTATAAGTGCAAATGTTATACCTG 58.007 37.037 0.00 0.00 0.00 4.00
154 155 8.902540 TCTATAAGTGCAAATGTTATACCTGG 57.097 34.615 0.00 0.00 0.00 4.45
155 156 8.491134 TCTATAAGTGCAAATGTTATACCTGGT 58.509 33.333 4.05 4.05 0.00 4.00
156 157 7.954666 ATAAGTGCAAATGTTATACCTGGTT 57.045 32.000 3.84 0.00 0.00 3.67
157 158 6.664428 AAGTGCAAATGTTATACCTGGTTT 57.336 33.333 3.84 0.00 0.00 3.27
158 159 6.267496 AGTGCAAATGTTATACCTGGTTTC 57.733 37.500 3.84 0.00 0.00 2.78
159 160 6.010219 AGTGCAAATGTTATACCTGGTTTCT 58.990 36.000 3.84 0.00 0.00 2.52
160 161 7.172342 AGTGCAAATGTTATACCTGGTTTCTA 58.828 34.615 3.84 0.00 0.00 2.10
161 162 7.834181 AGTGCAAATGTTATACCTGGTTTCTAT 59.166 33.333 3.84 0.00 0.00 1.98
162 163 8.466798 GTGCAAATGTTATACCTGGTTTCTATT 58.533 33.333 3.84 0.00 0.00 1.73
163 164 9.688091 TGCAAATGTTATACCTGGTTTCTATTA 57.312 29.630 3.84 0.00 0.00 0.98
192 193 6.725246 AGTGTTATATGCTTCGGTAAAATGC 58.275 36.000 0.00 0.00 0.00 3.56
193 194 6.542370 AGTGTTATATGCTTCGGTAAAATGCT 59.458 34.615 0.00 0.00 0.00 3.79
194 195 6.632834 GTGTTATATGCTTCGGTAAAATGCTG 59.367 38.462 0.00 0.00 0.00 4.41
195 196 6.540551 TGTTATATGCTTCGGTAAAATGCTGA 59.459 34.615 0.00 0.00 0.00 4.26
196 197 5.679734 ATATGCTTCGGTAAAATGCTGAG 57.320 39.130 0.00 0.00 0.00 3.35
197 198 3.052455 TGCTTCGGTAAAATGCTGAGA 57.948 42.857 0.00 0.00 0.00 3.27
198 199 2.742053 TGCTTCGGTAAAATGCTGAGAC 59.258 45.455 0.00 0.00 0.00 3.36
199 200 2.096013 GCTTCGGTAAAATGCTGAGACC 59.904 50.000 0.00 0.00 0.00 3.85
202 203 0.733150 GGTAAAATGCTGAGACCGGC 59.267 55.000 0.00 0.00 44.86 6.13
208 209 4.459089 GCTGAGACCGGCACCCTC 62.459 72.222 0.00 3.95 44.05 4.30
209 210 4.135153 CTGAGACCGGCACCCTCG 62.135 72.222 0.00 0.00 0.00 4.63
229 230 2.588877 CCAAGGCGCGATTCCGAT 60.589 61.111 12.10 0.00 38.22 4.18
230 231 2.598632 CCAAGGCGCGATTCCGATC 61.599 63.158 12.10 0.00 38.22 3.69
231 232 1.592669 CAAGGCGCGATTCCGATCT 60.593 57.895 12.10 0.00 38.22 2.75
232 233 0.318699 CAAGGCGCGATTCCGATCTA 60.319 55.000 12.10 0.00 38.22 1.98
233 234 0.039074 AAGGCGCGATTCCGATCTAG 60.039 55.000 12.10 0.00 38.22 2.43
265 266 1.811965 GGTAGTTGCATGCATGACACA 59.188 47.619 30.64 15.69 0.00 3.72
266 267 2.414559 GGTAGTTGCATGCATGACACAC 60.415 50.000 30.64 22.09 0.00 3.82
283 284 1.412710 ACACCATGTAGTGATAGGCCG 59.587 52.381 8.84 0.00 40.34 6.13
284 285 1.048601 ACCATGTAGTGATAGGCCGG 58.951 55.000 0.00 0.00 0.00 6.13
285 286 0.320771 CCATGTAGTGATAGGCCGGC 60.321 60.000 21.18 21.18 0.00 6.13
286 287 0.320771 CATGTAGTGATAGGCCGGCC 60.321 60.000 39.29 39.29 0.00 6.13
287 288 1.481056 ATGTAGTGATAGGCCGGCCC 61.481 60.000 41.72 26.88 36.58 5.80
289 290 1.152118 TAGTGATAGGCCGGCCCAT 60.152 57.895 41.72 34.87 36.58 4.00
290 291 1.480212 TAGTGATAGGCCGGCCCATG 61.480 60.000 41.72 0.00 36.58 3.66
291 292 2.772191 TGATAGGCCGGCCCATGT 60.772 61.111 41.72 25.97 36.58 3.21
292 293 1.460497 TGATAGGCCGGCCCATGTA 60.460 57.895 41.72 27.34 36.58 2.29
298 299 2.515991 CCGGCCCATGTACGCAAT 60.516 61.111 0.00 0.00 0.00 3.56
765 2758 8.758633 TCTTGACTAGTCTTGCTAACAAATAC 57.241 34.615 23.01 0.00 34.74 1.89
766 2759 8.585881 TCTTGACTAGTCTTGCTAACAAATACT 58.414 33.333 23.01 0.00 36.53 2.12
767 2760 9.209175 CTTGACTAGTCTTGCTAACAAATACTT 57.791 33.333 23.01 0.00 35.10 2.24
768 2761 8.758633 TGACTAGTCTTGCTAACAAATACTTC 57.241 34.615 23.01 0.00 35.10 3.01
769 2762 7.817962 TGACTAGTCTTGCTAACAAATACTTCC 59.182 37.037 23.01 0.00 35.10 3.46
770 2763 7.908453 ACTAGTCTTGCTAACAAATACTTCCT 58.092 34.615 0.00 0.00 35.10 3.36
771 2764 8.035984 ACTAGTCTTGCTAACAAATACTTCCTC 58.964 37.037 0.00 0.00 35.10 3.71
772 2765 6.174049 AGTCTTGCTAACAAATACTTCCTCC 58.826 40.000 0.00 0.00 34.74 4.30
773 2766 5.938125 GTCTTGCTAACAAATACTTCCTCCA 59.062 40.000 0.00 0.00 34.74 3.86
774 2767 6.599638 GTCTTGCTAACAAATACTTCCTCCAT 59.400 38.462 0.00 0.00 34.74 3.41
775 2768 6.823689 TCTTGCTAACAAATACTTCCTCCATC 59.176 38.462 0.00 0.00 34.74 3.51
776 2769 5.437060 TGCTAACAAATACTTCCTCCATCC 58.563 41.667 0.00 0.00 0.00 3.51
777 2770 5.191722 TGCTAACAAATACTTCCTCCATCCT 59.808 40.000 0.00 0.00 0.00 3.24
778 2771 6.385759 TGCTAACAAATACTTCCTCCATCCTA 59.614 38.462 0.00 0.00 0.00 2.94
779 2772 7.092623 TGCTAACAAATACTTCCTCCATCCTAA 60.093 37.037 0.00 0.00 0.00 2.69
780 2773 7.773690 GCTAACAAATACTTCCTCCATCCTAAA 59.226 37.037 0.00 0.00 0.00 1.85
781 2774 9.681062 CTAACAAATACTTCCTCCATCCTAAAA 57.319 33.333 0.00 0.00 0.00 1.52
787 2780 9.853177 AATACTTCCTCCATCCTAAAATAAGTG 57.147 33.333 0.00 0.00 0.00 3.16
788 2781 7.272144 ACTTCCTCCATCCTAAAATAAGTGT 57.728 36.000 0.00 0.00 0.00 3.55
789 2782 7.339482 ACTTCCTCCATCCTAAAATAAGTGTC 58.661 38.462 0.00 0.00 0.00 3.67
790 2783 7.182930 ACTTCCTCCATCCTAAAATAAGTGTCT 59.817 37.037 0.00 0.00 0.00 3.41
791 2784 7.125792 TCCTCCATCCTAAAATAAGTGTCTC 57.874 40.000 0.00 0.00 0.00 3.36
792 2785 6.672218 TCCTCCATCCTAAAATAAGTGTCTCA 59.328 38.462 0.00 0.00 0.00 3.27
793 2786 7.182026 TCCTCCATCCTAAAATAAGTGTCTCAA 59.818 37.037 0.00 0.00 0.00 3.02
794 2787 7.281100 CCTCCATCCTAAAATAAGTGTCTCAAC 59.719 40.741 0.00 0.00 0.00 3.18
795 2788 7.918076 TCCATCCTAAAATAAGTGTCTCAACT 58.082 34.615 0.00 0.00 0.00 3.16
796 2789 8.383175 TCCATCCTAAAATAAGTGTCTCAACTT 58.617 33.333 0.00 0.00 42.89 2.66
797 2790 9.014297 CCATCCTAAAATAAGTGTCTCAACTTT 57.986 33.333 0.00 0.00 40.77 2.66
798 2791 9.831737 CATCCTAAAATAAGTGTCTCAACTTTG 57.168 33.333 0.00 0.00 40.77 2.77
799 2792 8.974060 TCCTAAAATAAGTGTCTCAACTTTGT 57.026 30.769 0.00 0.00 40.77 2.83
807 2800 9.694137 ATAAGTGTCTCAACTTTGTACTAACTC 57.306 33.333 0.00 0.00 40.77 3.01
808 2801 7.349412 AGTGTCTCAACTTTGTACTAACTCT 57.651 36.000 0.00 0.00 0.00 3.24
809 2802 8.461249 AGTGTCTCAACTTTGTACTAACTCTA 57.539 34.615 0.00 0.00 0.00 2.43
810 2803 8.569641 AGTGTCTCAACTTTGTACTAACTCTAG 58.430 37.037 0.00 0.00 0.00 2.43
811 2804 8.351461 GTGTCTCAACTTTGTACTAACTCTAGT 58.649 37.037 0.00 0.00 41.43 2.57
812 2805 9.565090 TGTCTCAACTTTGTACTAACTCTAGTA 57.435 33.333 0.00 0.00 39.23 1.82
838 2831 9.726438 ATAAATTTGTACTAAGCTCAAGACACT 57.274 29.630 0.00 0.00 0.00 3.55
839 2832 8.451908 AAATTTGTACTAAGCTCAAGACACTT 57.548 30.769 3.19 0.00 0.00 3.16
840 2833 9.555727 AAATTTGTACTAAGCTCAAGACACTTA 57.444 29.630 3.19 0.00 0.00 2.24
841 2834 9.726438 AATTTGTACTAAGCTCAAGACACTTAT 57.274 29.630 3.19 0.00 0.00 1.73
842 2835 9.726438 ATTTGTACTAAGCTCAAGACACTTATT 57.274 29.630 3.19 0.00 0.00 1.40
843 2836 9.555727 TTTGTACTAAGCTCAAGACACTTATTT 57.444 29.630 3.19 0.00 0.00 1.40
844 2837 9.555727 TTGTACTAAGCTCAAGACACTTATTTT 57.444 29.630 3.19 0.00 0.00 1.82
845 2838 8.988934 TGTACTAAGCTCAAGACACTTATTTTG 58.011 33.333 3.19 0.00 0.00 2.44
846 2839 7.440523 ACTAAGCTCAAGACACTTATTTTGG 57.559 36.000 3.19 0.00 0.00 3.28
847 2840 5.712152 AAGCTCAAGACACTTATTTTGGG 57.288 39.130 0.00 0.00 0.00 4.12
848 2841 4.985538 AGCTCAAGACACTTATTTTGGGA 58.014 39.130 0.00 0.00 0.00 4.37
849 2842 4.762251 AGCTCAAGACACTTATTTTGGGAC 59.238 41.667 0.00 0.00 0.00 4.46
850 2843 4.378459 GCTCAAGACACTTATTTTGGGACG 60.378 45.833 0.00 0.00 0.00 4.79
851 2844 4.069304 TCAAGACACTTATTTTGGGACGG 58.931 43.478 0.00 0.00 0.00 4.79
852 2845 4.069304 CAAGACACTTATTTTGGGACGGA 58.931 43.478 0.00 0.00 0.00 4.69
853 2846 3.939066 AGACACTTATTTTGGGACGGAG 58.061 45.455 0.00 0.00 0.00 4.63
854 2847 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
855 2848 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
856 2849 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
857 2850 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
858 2851 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
859 2852 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
1037 3105 3.755628 CAGCTTGCTTGCGCCCAT 61.756 61.111 4.18 0.00 38.13 4.00
1064 3132 0.461516 ACACTCTGGCTGCATCATCG 60.462 55.000 0.50 0.00 0.00 3.84
1268 3384 2.073816 CTACCAACAGCCTGTTTACCG 58.926 52.381 7.51 0.00 38.77 4.02
1272 3388 0.601841 AACAGCCTGTTTACCGTCGG 60.602 55.000 10.48 10.48 37.26 4.79
1718 3849 5.809001 AGATCTTGGCAAACTGATCAACTA 58.191 37.500 22.39 0.00 38.13 2.24
1963 4110 4.021016 AGGACACTGTAGAGCAACTAAAGG 60.021 45.833 11.17 4.94 39.94 3.11
2189 4336 0.636647 GGGGGAATGGGGAAGACAAT 59.363 55.000 0.00 0.00 0.00 2.71
2771 4920 3.636282 AACAGTAAACAATGGGCGAAC 57.364 42.857 0.00 0.00 0.00 3.95
2886 5041 4.894784 TGAAGATTACCGTTTCAGAAGCT 58.105 39.130 0.00 0.00 0.00 3.74
3287 5460 6.691508 AGAAATGGATGAAGGTTTTGCTAAC 58.308 36.000 0.00 0.00 0.00 2.34
3294 5467 9.249053 TGGATGAAGGTTTTGCTAACATATTTA 57.751 29.630 4.98 0.00 0.00 1.40
3422 5619 5.050490 CGATTCCTATGTCTAGGGTGTTTG 58.950 45.833 0.00 0.00 44.22 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.541071 TCGACACGAAGTTCGATACAA 57.459 42.857 30.77 10.73 43.74 2.41
12 13 4.142988 GCAAAAGATAACCATTCGACACGA 60.143 41.667 0.00 0.00 0.00 4.35
13 14 4.088648 GCAAAAGATAACCATTCGACACG 58.911 43.478 0.00 0.00 0.00 4.49
14 15 4.088648 CGCAAAAGATAACCATTCGACAC 58.911 43.478 0.00 0.00 0.00 3.67
15 16 3.126171 CCGCAAAAGATAACCATTCGACA 59.874 43.478 0.00 0.00 0.00 4.35
16 17 3.126343 ACCGCAAAAGATAACCATTCGAC 59.874 43.478 0.00 0.00 0.00 4.20
17 18 3.340034 ACCGCAAAAGATAACCATTCGA 58.660 40.909 0.00 0.00 0.00 3.71
18 19 3.680789 GACCGCAAAAGATAACCATTCG 58.319 45.455 0.00 0.00 0.00 3.34
19 20 3.126343 ACGACCGCAAAAGATAACCATTC 59.874 43.478 0.00 0.00 0.00 2.67
20 21 3.078837 ACGACCGCAAAAGATAACCATT 58.921 40.909 0.00 0.00 0.00 3.16
21 22 2.706890 ACGACCGCAAAAGATAACCAT 58.293 42.857 0.00 0.00 0.00 3.55
22 23 2.172851 ACGACCGCAAAAGATAACCA 57.827 45.000 0.00 0.00 0.00 3.67
23 24 3.866910 TCATACGACCGCAAAAGATAACC 59.133 43.478 0.00 0.00 0.00 2.85
24 25 5.459110 TTCATACGACCGCAAAAGATAAC 57.541 39.130 0.00 0.00 0.00 1.89
25 26 5.503357 GCATTCATACGACCGCAAAAGATAA 60.503 40.000 0.00 0.00 0.00 1.75
26 27 4.025229 GCATTCATACGACCGCAAAAGATA 60.025 41.667 0.00 0.00 0.00 1.98
27 28 3.242739 GCATTCATACGACCGCAAAAGAT 60.243 43.478 0.00 0.00 0.00 2.40
28 29 2.095213 GCATTCATACGACCGCAAAAGA 59.905 45.455 0.00 0.00 0.00 2.52
29 30 2.159585 TGCATTCATACGACCGCAAAAG 60.160 45.455 0.00 0.00 0.00 2.27
30 31 1.807142 TGCATTCATACGACCGCAAAA 59.193 42.857 0.00 0.00 0.00 2.44
31 32 1.129624 GTGCATTCATACGACCGCAAA 59.870 47.619 0.00 0.00 32.02 3.68
32 33 0.724549 GTGCATTCATACGACCGCAA 59.275 50.000 0.00 0.00 32.02 4.85
33 34 0.108377 AGTGCATTCATACGACCGCA 60.108 50.000 0.00 0.00 0.00 5.69
34 35 0.301687 CAGTGCATTCATACGACCGC 59.698 55.000 0.00 0.00 0.00 5.68
35 36 1.854743 CTCAGTGCATTCATACGACCG 59.145 52.381 0.00 0.00 0.00 4.79
36 37 1.594862 GCTCAGTGCATTCATACGACC 59.405 52.381 0.00 0.00 42.31 4.79
37 38 2.544685 AGCTCAGTGCATTCATACGAC 58.455 47.619 0.00 0.00 45.94 4.34
38 39 2.931969 CAAGCTCAGTGCATTCATACGA 59.068 45.455 0.00 0.00 45.94 3.43
39 40 2.931969 TCAAGCTCAGTGCATTCATACG 59.068 45.455 0.00 0.00 45.94 3.06
40 41 4.024218 GGATCAAGCTCAGTGCATTCATAC 60.024 45.833 0.00 0.00 45.94 2.39
41 42 4.132336 GGATCAAGCTCAGTGCATTCATA 58.868 43.478 0.00 0.00 45.94 2.15
42 43 2.950309 GGATCAAGCTCAGTGCATTCAT 59.050 45.455 0.00 0.00 45.94 2.57
43 44 2.026542 AGGATCAAGCTCAGTGCATTCA 60.027 45.455 0.00 0.00 45.94 2.57
44 45 2.355132 CAGGATCAAGCTCAGTGCATTC 59.645 50.000 0.00 0.00 45.94 2.67
45 46 2.366533 CAGGATCAAGCTCAGTGCATT 58.633 47.619 0.00 0.00 45.94 3.56
46 47 2.017623 GCAGGATCAAGCTCAGTGCAT 61.018 52.381 0.00 0.00 45.94 3.96
47 48 0.675837 GCAGGATCAAGCTCAGTGCA 60.676 55.000 0.00 0.00 45.94 4.57
48 49 1.375098 GGCAGGATCAAGCTCAGTGC 61.375 60.000 8.29 0.00 43.29 4.40
49 50 0.252479 AGGCAGGATCAAGCTCAGTG 59.748 55.000 8.29 0.00 0.00 3.66
50 51 0.990374 AAGGCAGGATCAAGCTCAGT 59.010 50.000 8.29 0.00 0.00 3.41
51 52 2.996249 TAAGGCAGGATCAAGCTCAG 57.004 50.000 8.29 0.00 0.00 3.35
52 53 5.104360 AGTTTATAAGGCAGGATCAAGCTCA 60.104 40.000 8.29 0.00 0.00 4.26
53 54 5.372373 AGTTTATAAGGCAGGATCAAGCTC 58.628 41.667 8.29 0.31 0.00 4.09
54 55 5.379706 AGTTTATAAGGCAGGATCAAGCT 57.620 39.130 8.29 0.00 0.00 3.74
55 56 7.229506 ACATAAGTTTATAAGGCAGGATCAAGC 59.770 37.037 0.00 0.00 0.00 4.01
56 57 8.682936 ACATAAGTTTATAAGGCAGGATCAAG 57.317 34.615 0.00 0.00 0.00 3.02
57 58 8.902806 CAACATAAGTTTATAAGGCAGGATCAA 58.097 33.333 0.00 0.00 35.28 2.57
58 59 8.271458 TCAACATAAGTTTATAAGGCAGGATCA 58.729 33.333 0.00 0.00 35.28 2.92
59 60 8.677148 TCAACATAAGTTTATAAGGCAGGATC 57.323 34.615 0.00 0.00 35.28 3.36
60 61 9.289782 GATCAACATAAGTTTATAAGGCAGGAT 57.710 33.333 0.00 0.00 35.28 3.24
61 62 8.494433 AGATCAACATAAGTTTATAAGGCAGGA 58.506 33.333 0.00 0.00 35.28 3.86
62 63 8.682936 AGATCAACATAAGTTTATAAGGCAGG 57.317 34.615 0.00 0.00 35.28 4.85
74 75 9.757227 GTGATAGAGCTTAAGATCAACATAAGT 57.243 33.333 21.97 2.11 33.82 2.24
75 76 9.755804 TGTGATAGAGCTTAAGATCAACATAAG 57.244 33.333 21.97 0.00 34.25 1.73
78 79 9.624373 AATTGTGATAGAGCTTAAGATCAACAT 57.376 29.630 21.97 11.88 31.88 2.71
125 126 9.726438 GGTATAACATTTGCACTTATAGAGGAT 57.274 33.333 0.00 0.00 0.00 3.24
126 127 8.934697 AGGTATAACATTTGCACTTATAGAGGA 58.065 33.333 0.00 0.00 0.00 3.71
127 128 8.993121 CAGGTATAACATTTGCACTTATAGAGG 58.007 37.037 0.00 0.00 0.00 3.69
128 129 8.993121 CCAGGTATAACATTTGCACTTATAGAG 58.007 37.037 0.00 0.00 0.00 2.43
129 130 8.491134 ACCAGGTATAACATTTGCACTTATAGA 58.509 33.333 0.00 0.00 0.00 1.98
130 131 8.677148 ACCAGGTATAACATTTGCACTTATAG 57.323 34.615 0.00 0.00 0.00 1.31
131 132 9.469097 AAACCAGGTATAACATTTGCACTTATA 57.531 29.630 0.00 0.00 0.00 0.98
132 133 7.954666 AACCAGGTATAACATTTGCACTTAT 57.045 32.000 0.00 0.00 0.00 1.73
133 134 7.668052 AGAAACCAGGTATAACATTTGCACTTA 59.332 33.333 0.00 0.00 0.00 2.24
134 135 6.493458 AGAAACCAGGTATAACATTTGCACTT 59.507 34.615 0.00 0.00 0.00 3.16
135 136 6.010219 AGAAACCAGGTATAACATTTGCACT 58.990 36.000 0.00 0.00 0.00 4.40
136 137 6.267496 AGAAACCAGGTATAACATTTGCAC 57.733 37.500 0.00 0.00 0.00 4.57
137 138 8.588290 AATAGAAACCAGGTATAACATTTGCA 57.412 30.769 0.00 0.00 0.00 4.08
166 167 8.504005 GCATTTTACCGAAGCATATAACACTAT 58.496 33.333 0.00 0.00 0.00 2.12
167 168 7.713507 AGCATTTTACCGAAGCATATAACACTA 59.286 33.333 0.00 0.00 0.00 2.74
168 169 6.542370 AGCATTTTACCGAAGCATATAACACT 59.458 34.615 0.00 0.00 0.00 3.55
169 170 6.632834 CAGCATTTTACCGAAGCATATAACAC 59.367 38.462 0.00 0.00 0.00 3.32
170 171 6.540551 TCAGCATTTTACCGAAGCATATAACA 59.459 34.615 0.00 0.00 0.00 2.41
171 172 6.954944 TCAGCATTTTACCGAAGCATATAAC 58.045 36.000 0.00 0.00 0.00 1.89
172 173 6.989759 TCTCAGCATTTTACCGAAGCATATAA 59.010 34.615 0.00 0.00 0.00 0.98
173 174 6.423905 GTCTCAGCATTTTACCGAAGCATATA 59.576 38.462 0.00 0.00 0.00 0.86
174 175 5.237344 GTCTCAGCATTTTACCGAAGCATAT 59.763 40.000 0.00 0.00 0.00 1.78
175 176 4.570772 GTCTCAGCATTTTACCGAAGCATA 59.429 41.667 0.00 0.00 0.00 3.14
176 177 3.375299 GTCTCAGCATTTTACCGAAGCAT 59.625 43.478 0.00 0.00 0.00 3.79
177 178 2.742053 GTCTCAGCATTTTACCGAAGCA 59.258 45.455 0.00 0.00 0.00 3.91
178 179 2.096013 GGTCTCAGCATTTTACCGAAGC 59.904 50.000 0.00 0.00 0.00 3.86
183 184 0.733150 GCCGGTCTCAGCATTTTACC 59.267 55.000 1.90 0.00 0.00 2.85
184 185 1.130561 GTGCCGGTCTCAGCATTTTAC 59.869 52.381 1.90 0.00 41.86 2.01
185 186 1.448985 GTGCCGGTCTCAGCATTTTA 58.551 50.000 1.90 0.00 41.86 1.52
186 187 1.244019 GGTGCCGGTCTCAGCATTTT 61.244 55.000 1.90 0.00 41.86 1.82
187 188 1.675641 GGTGCCGGTCTCAGCATTT 60.676 57.895 1.90 0.00 41.86 2.32
188 189 2.045926 GGTGCCGGTCTCAGCATT 60.046 61.111 1.90 0.00 41.86 3.56
189 190 4.101448 GGGTGCCGGTCTCAGCAT 62.101 66.667 1.90 0.00 41.86 3.79
191 192 4.459089 GAGGGTGCCGGTCTCAGC 62.459 72.222 1.90 1.69 0.00 4.26
192 193 4.135153 CGAGGGTGCCGGTCTCAG 62.135 72.222 1.90 0.00 0.00 3.35
212 213 2.588877 ATCGGAATCGCGCCTTGG 60.589 61.111 0.00 0.00 36.13 3.61
213 214 0.318699 TAGATCGGAATCGCGCCTTG 60.319 55.000 0.00 0.00 36.97 3.61
214 215 0.039074 CTAGATCGGAATCGCGCCTT 60.039 55.000 0.00 0.00 36.97 4.35
215 216 1.173444 ACTAGATCGGAATCGCGCCT 61.173 55.000 0.00 0.00 36.97 5.52
216 217 1.004277 CACTAGATCGGAATCGCGCC 61.004 60.000 0.00 0.00 36.97 6.53
217 218 0.317938 ACACTAGATCGGAATCGCGC 60.318 55.000 0.00 0.00 36.97 6.86
218 219 1.268589 ACACACTAGATCGGAATCGCG 60.269 52.381 0.00 0.00 36.97 5.87
219 220 2.120232 CACACACTAGATCGGAATCGC 58.880 52.381 0.00 0.00 36.97 4.58
220 221 3.422417 ACACACACTAGATCGGAATCG 57.578 47.619 0.00 0.00 36.97 3.34
221 222 5.692204 CCATTACACACACTAGATCGGAATC 59.308 44.000 0.00 0.00 0.00 2.52
222 223 5.453339 CCCATTACACACACTAGATCGGAAT 60.453 44.000 0.00 0.00 0.00 3.01
223 224 4.142026 CCCATTACACACACTAGATCGGAA 60.142 45.833 0.00 0.00 0.00 4.30
224 225 3.383505 CCCATTACACACACTAGATCGGA 59.616 47.826 0.00 0.00 0.00 4.55
225 226 3.132289 ACCCATTACACACACTAGATCGG 59.868 47.826 0.00 0.00 0.00 4.18
226 227 4.386867 ACCCATTACACACACTAGATCG 57.613 45.455 0.00 0.00 0.00 3.69
227 228 6.466885 ACTACCCATTACACACACTAGATC 57.533 41.667 0.00 0.00 0.00 2.75
228 229 6.640518 CAACTACCCATTACACACACTAGAT 58.359 40.000 0.00 0.00 0.00 1.98
229 230 5.568023 GCAACTACCCATTACACACACTAGA 60.568 44.000 0.00 0.00 0.00 2.43
230 231 4.630069 GCAACTACCCATTACACACACTAG 59.370 45.833 0.00 0.00 0.00 2.57
231 232 4.040584 TGCAACTACCCATTACACACACTA 59.959 41.667 0.00 0.00 0.00 2.74
232 233 3.181449 TGCAACTACCCATTACACACACT 60.181 43.478 0.00 0.00 0.00 3.55
233 234 3.142951 TGCAACTACCCATTACACACAC 58.857 45.455 0.00 0.00 0.00 3.82
265 266 1.048601 CCGGCCTATCACTACATGGT 58.951 55.000 0.00 0.00 0.00 3.55
266 267 0.320771 GCCGGCCTATCACTACATGG 60.321 60.000 18.11 0.00 0.00 3.66
283 284 1.602377 GACTAATTGCGTACATGGGCC 59.398 52.381 0.00 0.00 0.00 5.80
284 285 2.285083 TGACTAATTGCGTACATGGGC 58.715 47.619 0.00 0.00 0.00 5.36
285 286 3.250762 CCATGACTAATTGCGTACATGGG 59.749 47.826 19.42 0.00 45.99 4.00
286 287 4.472691 CCATGACTAATTGCGTACATGG 57.527 45.455 0.00 0.00 45.10 3.66
287 288 3.312146 TGCCATGACTAATTGCGTACATG 59.688 43.478 0.00 0.00 36.10 3.21
289 290 2.675844 GTGCCATGACTAATTGCGTACA 59.324 45.455 0.00 0.00 29.33 2.90
290 291 2.031683 GGTGCCATGACTAATTGCGTAC 59.968 50.000 0.00 0.00 29.33 3.67
291 292 2.093181 AGGTGCCATGACTAATTGCGTA 60.093 45.455 0.00 0.00 29.33 4.42
292 293 1.094785 GGTGCCATGACTAATTGCGT 58.905 50.000 0.00 0.00 29.33 5.24
298 299 1.278985 CCACTCAGGTGCCATGACTAA 59.721 52.381 0.00 0.00 41.75 2.24
640 679 1.811266 GCGAGCGTGGACATGACAT 60.811 57.895 0.00 0.00 0.00 3.06
765 2758 7.569240 AGACACTTATTTTAGGATGGAGGAAG 58.431 38.462 0.00 0.00 0.00 3.46
766 2759 7.182026 TGAGACACTTATTTTAGGATGGAGGAA 59.818 37.037 0.00 0.00 0.00 3.36
767 2760 6.672218 TGAGACACTTATTTTAGGATGGAGGA 59.328 38.462 0.00 0.00 0.00 3.71
768 2761 6.889198 TGAGACACTTATTTTAGGATGGAGG 58.111 40.000 0.00 0.00 0.00 4.30
769 2762 8.043710 AGTTGAGACACTTATTTTAGGATGGAG 58.956 37.037 0.00 0.00 0.00 3.86
770 2763 7.918076 AGTTGAGACACTTATTTTAGGATGGA 58.082 34.615 0.00 0.00 0.00 3.41
771 2764 8.567285 AAGTTGAGACACTTATTTTAGGATGG 57.433 34.615 0.00 0.00 35.10 3.51
772 2765 9.831737 CAAAGTTGAGACACTTATTTTAGGATG 57.168 33.333 0.00 0.00 35.87 3.51
773 2766 9.574516 ACAAAGTTGAGACACTTATTTTAGGAT 57.425 29.630 0.00 0.00 35.87 3.24
774 2767 8.974060 ACAAAGTTGAGACACTTATTTTAGGA 57.026 30.769 0.00 0.00 35.87 2.94
781 2774 9.694137 GAGTTAGTACAAAGTTGAGACACTTAT 57.306 33.333 0.00 0.00 35.87 1.73
782 2775 8.910944 AGAGTTAGTACAAAGTTGAGACACTTA 58.089 33.333 0.00 0.00 35.87 2.24
783 2776 7.783042 AGAGTTAGTACAAAGTTGAGACACTT 58.217 34.615 0.00 0.00 38.74 3.16
784 2777 7.349412 AGAGTTAGTACAAAGTTGAGACACT 57.651 36.000 0.00 0.00 0.00 3.55
785 2778 8.351461 ACTAGAGTTAGTACAAAGTTGAGACAC 58.649 37.037 0.00 0.00 38.35 3.67
786 2779 8.461249 ACTAGAGTTAGTACAAAGTTGAGACA 57.539 34.615 0.00 0.00 38.35 3.41
812 2805 9.726438 AGTGTCTTGAGCTTAGTACAAATTTAT 57.274 29.630 0.00 0.00 0.00 1.40
813 2806 9.555727 AAGTGTCTTGAGCTTAGTACAAATTTA 57.444 29.630 0.00 0.00 0.00 1.40
814 2807 8.451908 AAGTGTCTTGAGCTTAGTACAAATTT 57.548 30.769 0.00 0.00 0.00 1.82
815 2808 9.726438 ATAAGTGTCTTGAGCTTAGTACAAATT 57.274 29.630 0.00 0.00 0.00 1.82
816 2809 9.726438 AATAAGTGTCTTGAGCTTAGTACAAAT 57.274 29.630 0.00 0.00 0.00 2.32
817 2810 9.555727 AAATAAGTGTCTTGAGCTTAGTACAAA 57.444 29.630 0.00 0.00 0.00 2.83
818 2811 9.555727 AAAATAAGTGTCTTGAGCTTAGTACAA 57.444 29.630 0.00 0.00 0.00 2.41
819 2812 8.988934 CAAAATAAGTGTCTTGAGCTTAGTACA 58.011 33.333 0.00 0.00 0.00 2.90
820 2813 8.443937 CCAAAATAAGTGTCTTGAGCTTAGTAC 58.556 37.037 0.00 0.00 0.00 2.73
821 2814 7.606456 CCCAAAATAAGTGTCTTGAGCTTAGTA 59.394 37.037 0.00 0.00 0.00 1.82
822 2815 6.431234 CCCAAAATAAGTGTCTTGAGCTTAGT 59.569 38.462 0.00 0.00 0.00 2.24
823 2816 6.655003 TCCCAAAATAAGTGTCTTGAGCTTAG 59.345 38.462 0.00 0.00 0.00 2.18
824 2817 6.430000 GTCCCAAAATAAGTGTCTTGAGCTTA 59.570 38.462 0.00 0.00 0.00 3.09
825 2818 5.241728 GTCCCAAAATAAGTGTCTTGAGCTT 59.758 40.000 0.00 0.00 0.00 3.74
826 2819 4.762251 GTCCCAAAATAAGTGTCTTGAGCT 59.238 41.667 0.00 0.00 0.00 4.09
827 2820 4.378459 CGTCCCAAAATAAGTGTCTTGAGC 60.378 45.833 0.00 0.00 0.00 4.26
828 2821 4.154195 CCGTCCCAAAATAAGTGTCTTGAG 59.846 45.833 0.00 0.00 0.00 3.02
829 2822 4.069304 CCGTCCCAAAATAAGTGTCTTGA 58.931 43.478 0.00 0.00 0.00 3.02
830 2823 4.069304 TCCGTCCCAAAATAAGTGTCTTG 58.931 43.478 0.00 0.00 0.00 3.02
831 2824 4.324267 CTCCGTCCCAAAATAAGTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
832 2825 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
833 2826 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
834 2827 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
835 2828 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
836 2829 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
837 2830 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
838 2831 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
839 2832 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
840 2833 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
841 2834 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
842 2835 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
843 2836 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
844 2837 0.042131 AACATACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
845 2838 0.464452 CAACATACTCCCTCCGTCCC 59.536 60.000 0.00 0.00 0.00 4.46
846 2839 0.464452 CCAACATACTCCCTCCGTCC 59.536 60.000 0.00 0.00 0.00 4.79
847 2840 0.464452 CCCAACATACTCCCTCCGTC 59.536 60.000 0.00 0.00 0.00 4.79
848 2841 0.042131 TCCCAACATACTCCCTCCGT 59.958 55.000 0.00 0.00 0.00 4.69
849 2842 0.464452 GTCCCAACATACTCCCTCCG 59.536 60.000 0.00 0.00 0.00 4.63
850 2843 0.464452 CGTCCCAACATACTCCCTCC 59.536 60.000 0.00 0.00 0.00 4.30
851 2844 0.464452 CCGTCCCAACATACTCCCTC 59.536 60.000 0.00 0.00 0.00 4.30
852 2845 0.042131 TCCGTCCCAACATACTCCCT 59.958 55.000 0.00 0.00 0.00 4.20
853 2846 0.464452 CTCCGTCCCAACATACTCCC 59.536 60.000 0.00 0.00 0.00 4.30
854 2847 0.179081 GCTCCGTCCCAACATACTCC 60.179 60.000 0.00 0.00 0.00 3.85
855 2848 0.535335 TGCTCCGTCCCAACATACTC 59.465 55.000 0.00 0.00 0.00 2.59
856 2849 0.537188 CTGCTCCGTCCCAACATACT 59.463 55.000 0.00 0.00 0.00 2.12
857 2850 0.535335 TCTGCTCCGTCCCAACATAC 59.465 55.000 0.00 0.00 0.00 2.39
858 2851 0.824109 CTCTGCTCCGTCCCAACATA 59.176 55.000 0.00 0.00 0.00 2.29
859 2852 0.904865 TCTCTGCTCCGTCCCAACAT 60.905 55.000 0.00 0.00 0.00 2.71
903 2898 0.529555 CCGAGAGCAAAGCTAGAGGC 60.530 60.000 0.00 0.00 39.88 4.70
1037 3105 1.741706 GCAGCCAGAGTGTACGTAGTA 59.258 52.381 0.00 0.00 45.11 1.82
1268 3384 4.277423 TCAAGGAATCAAAAGGAAACCGAC 59.723 41.667 0.00 0.00 32.43 4.79
1272 3388 5.540911 TGCATCAAGGAATCAAAAGGAAAC 58.459 37.500 0.00 0.00 0.00 2.78
1718 3849 2.713967 GCACGCTGCCATGGGAAAT 61.714 57.895 15.13 0.00 37.42 2.17
1989 4136 1.841302 TAGGGCCACAAGTCTGCAGG 61.841 60.000 15.13 0.00 0.00 4.85
2771 4920 4.738541 GCAAGCATAATTCCATTGGTCTGG 60.739 45.833 1.86 0.00 37.66 3.86
2886 5041 1.415289 CCATAGGCTGATGAGCTCACA 59.585 52.381 20.97 17.37 45.44 3.58
3090 5245 2.144482 TCAGGGAGACGAAAACGAAC 57.856 50.000 0.00 0.00 0.00 3.95
3287 5460 7.520614 GCTTCCCCGAGAAAATCACTAAATATG 60.521 40.741 0.00 0.00 32.88 1.78
3294 5467 1.351017 TGCTTCCCCGAGAAAATCACT 59.649 47.619 0.00 0.00 32.88 3.41
3325 5498 4.026052 CAGGAGGGGCAAATAAAGAACAT 58.974 43.478 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.