Multiple sequence alignment - TraesCS6D01G125700

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 TraesCS6D01G125700 chr6D 100.000 2420 0 0 1 2420 89520319 89517900 0.000000e+00 4470.0
1 TraesCS6D01G125700 chr6D 92.398 171 9 3 1 168 3225628 3225459 8.650000e-60 241.0
2 TraesCS6D01G125700 chr6D 98.540 137 1 1 1 136 353256727 353256591 8.650000e-60 241.0
3 TraesCS6D01G125700 chr6A 92.474 877 60 2 842 1718 107838348 107837478 0.000000e+00 1249.0
4 TraesCS6D01G125700 chr6A 91.026 702 59 3 147 846 107839351 107838652 0.000000e+00 944.0
5 TraesCS6D01G125700 chr6A 92.350 183 12 2 1737 1919 107837484 107837304 2.390000e-65 259.0
6 TraesCS6D01G125700 chr6A 92.500 40 1 2 1728 1767 99205375 99205338 3.360000e-04 56.5
7 TraesCS6D01G125700 chr6B 89.017 783 48 15 879 1660 172031702 172030957 0.000000e+00 935.0
8 TraesCS6D01G125700 chr6B 90.598 234 20 2 170 402 172154606 172154374 2.340000e-80 309.0
9 TraesCS6D01G125700 chr6B 89.286 112 5 3 1812 1919 172030952 172030844 1.510000e-27 134.0
10 TraesCS6D01G125700 chr6B 78.161 174 27 11 230 396 120004865 120004696 1.530000e-17 100.0
11 TraesCS6D01G125700 chr2A 88.363 507 54 5 1914 2420 677111651 677112152 2.660000e-169 604.0
12 TraesCS6D01G125700 chr2A 88.363 507 54 5 1914 2420 677160808 677161309 2.660000e-169 604.0
13 TraesCS6D01G125700 chr2A 88.166 507 55 5 1914 2420 677072801 677073302 1.240000e-167 599.0
14 TraesCS6D01G125700 chr2A 75.482 363 64 18 233 581 62372713 62372362 1.160000e-33 154.0
15 TraesCS6D01G125700 chr5B 87.776 499 59 2 1922 2420 612551653 612551157 1.250000e-162 582.0
16 TraesCS6D01G125700 chr5B 82.927 82 12 2 698 778 432235179 432235259 3.340000e-09 73.1
17 TraesCS6D01G125700 chr4A 87.600 500 60 2 1921 2420 625081434 625081931 1.610000e-161 579.0
18 TraesCS6D01G125700 chr1A 93.333 390 25 1 2030 2418 32746186 32745797 2.090000e-160 575.0
19 TraesCS6D01G125700 chr3B 90.476 420 39 1 2001 2420 11681286 11680868 9.780000e-154 553.0
20 TraesCS6D01G125700 chr3B 86.885 61 7 1 327 387 806274513 806274572 1.550000e-07 67.6
21 TraesCS6D01G125700 chr2B 86.573 499 58 8 1921 2418 230898267 230897777 2.120000e-150 542.0
22 TraesCS6D01G125700 chr2B 74.606 571 114 22 230 790 569537893 569538442 3.130000e-54 222.0
23 TraesCS6D01G125700 chr2D 89.044 429 46 1 1921 2349 486493597 486493170 4.580000e-147 531.0
24 TraesCS6D01G125700 chr2D 98.529 136 2 0 1 136 462545637 462545772 8.650000e-60 241.0
25 TraesCS6D01G125700 chr2D 95.270 148 6 1 1 148 180775015 180774869 1.450000e-57 233.0
26 TraesCS6D01G125700 chr2D 93.082 159 8 3 1 156 115118414 115118256 1.870000e-56 230.0
27 TraesCS6D01G125700 chr4D 99.265 136 1 0 2 137 457052826 457052961 1.860000e-61 246.0
28 TraesCS6D01G125700 chr4D 99.254 134 1 0 1 134 103492435 103492302 2.400000e-60 243.0
29 TraesCS6D01G125700 chr3D 99.254 134 1 0 1 134 430527507 430527374 2.400000e-60 243.0
30 TraesCS6D01G125700 chr3D 95.890 146 3 2 1 145 55077011 55077154 1.450000e-57 233.0
31 TraesCS6D01G125700 chr4B 87.500 144 13 1 1661 1804 130236517 130236655 6.920000e-36 161.0
32 TraesCS6D01G125700 chr4B 70.711 478 114 15 233 701 623058000 623057540 1.540000e-12 84.2
33 TraesCS6D01G125700 chr7D 75.701 214 50 2 571 784 99871953 99872164 3.290000e-19 106.0
34 TraesCS6D01G125700 chr5A 75.882 170 40 1 489 658 669192025 669191857 4.290000e-13 86.1
35 TraesCS6D01G125700 chr5A 79.439 107 13 3 1694 1800 426528730 426528633 1.550000e-07 67.6
36 TraesCS6D01G125700 chr5A 85.484 62 6 2 327 387 669190634 669190575 7.220000e-06 62.1
37 TraesCS6D01G125700 chr1D 93.182 44 3 0 611 654 381040883 381040926 5.580000e-07 65.8


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 TraesCS6D01G125700 chr6D 89517900 89520319 2419 True 4470.000000 4470 100.0000 1 2420 1 chr6D.!!$R2 2419
1 TraesCS6D01G125700 chr6A 107837304 107839351 2047 True 817.333333 1249 91.9500 147 1919 3 chr6A.!!$R2 1772
2 TraesCS6D01G125700 chr6B 172030844 172031702 858 True 534.500000 935 89.1515 879 1919 2 chr6B.!!$R3 1040
3 TraesCS6D01G125700 chr2A 677111651 677112152 501 False 604.000000 604 88.3630 1914 2420 1 chr2A.!!$F2 506
4 TraesCS6D01G125700 chr2A 677160808 677161309 501 False 604.000000 604 88.3630 1914 2420 1 chr2A.!!$F3 506
5 TraesCS6D01G125700 chr2A 677072801 677073302 501 False 599.000000 599 88.1660 1914 2420 1 chr2A.!!$F1 506
6 TraesCS6D01G125700 chr2B 569537893 569538442 549 False 222.000000 222 74.6060 230 790 1 chr2B.!!$F1 560

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
70 71 0.030101 CGACAAAACCACAATGCGGT 59.97 50.0 0.0 0.0 38.85 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1725 2040 0.108089 TAGCCGCTCGCCAAAATACA 60.108 50.0 0.0 0.0 38.78 2.29 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
26 27 7.578310 ATCTCATTCTTGTTCATTACATGGG 57.422 36.000 0.00 0.00 36.44 4.00
27 28 6.720309 TCTCATTCTTGTTCATTACATGGGA 58.280 36.000 0.00 0.00 36.44 4.37
28 29 7.348815 TCTCATTCTTGTTCATTACATGGGAT 58.651 34.615 0.00 0.00 36.44 3.85
29 30 7.835682 TCTCATTCTTGTTCATTACATGGGATT 59.164 33.333 0.00 0.00 36.44 3.01
30 31 7.774134 TCATTCTTGTTCATTACATGGGATTG 58.226 34.615 0.00 0.00 36.44 2.67
31 32 7.396907 TCATTCTTGTTCATTACATGGGATTGT 59.603 33.333 0.00 0.00 36.44 2.71
32 33 6.513806 TCTTGTTCATTACATGGGATTGTG 57.486 37.500 0.00 0.00 36.44 3.33
33 34 6.009589 TCTTGTTCATTACATGGGATTGTGT 58.990 36.000 0.00 0.00 36.44 3.72
34 35 5.641783 TGTTCATTACATGGGATTGTGTG 57.358 39.130 0.00 0.00 0.00 3.82
35 36 5.320277 TGTTCATTACATGGGATTGTGTGA 58.680 37.500 0.00 0.00 0.00 3.58
36 37 5.772169 TGTTCATTACATGGGATTGTGTGAA 59.228 36.000 0.00 0.00 35.28 3.18
37 38 6.072008 TGTTCATTACATGGGATTGTGTGAAG 60.072 38.462 0.00 0.00 36.80 3.02
38 39 5.814481 TCATTACATGGGATTGTGTGAAGA 58.186 37.500 0.00 0.00 0.00 2.87
39 40 6.425735 TCATTACATGGGATTGTGTGAAGAT 58.574 36.000 0.00 0.00 0.00 2.40
40 41 6.319405 TCATTACATGGGATTGTGTGAAGATG 59.681 38.462 0.00 0.00 0.00 2.90
41 42 4.305539 ACATGGGATTGTGTGAAGATGA 57.694 40.909 0.00 0.00 0.00 2.92
42 43 4.012374 ACATGGGATTGTGTGAAGATGAC 58.988 43.478 0.00 0.00 0.00 3.06
43 44 3.071874 TGGGATTGTGTGAAGATGACC 57.928 47.619 0.00 0.00 0.00 4.02
44 45 2.290896 TGGGATTGTGTGAAGATGACCC 60.291 50.000 0.00 0.00 35.82 4.46
45 46 2.025887 GGGATTGTGTGAAGATGACCCT 60.026 50.000 0.00 0.00 32.93 4.34
46 47 3.562176 GGGATTGTGTGAAGATGACCCTT 60.562 47.826 0.00 0.00 32.93 3.95
47 48 3.691609 GGATTGTGTGAAGATGACCCTTC 59.308 47.826 0.00 0.00 42.09 3.46
48 49 4.566488 GGATTGTGTGAAGATGACCCTTCT 60.566 45.833 0.00 0.00 42.20 2.85
49 50 4.437682 TTGTGTGAAGATGACCCTTCTT 57.562 40.909 0.00 0.00 42.20 2.52
50 51 3.743521 TGTGTGAAGATGACCCTTCTTG 58.256 45.455 0.00 0.00 42.20 3.02
51 52 2.485814 GTGTGAAGATGACCCTTCTTGC 59.514 50.000 0.00 0.00 42.20 4.01
52 53 1.734465 GTGAAGATGACCCTTCTTGCG 59.266 52.381 0.00 0.00 42.20 4.85
53 54 1.623311 TGAAGATGACCCTTCTTGCGA 59.377 47.619 0.00 0.00 42.20 5.10
54 55 2.003301 GAAGATGACCCTTCTTGCGAC 58.997 52.381 0.00 0.00 39.44 5.19
55 56 0.976641 AGATGACCCTTCTTGCGACA 59.023 50.000 0.00 0.00 0.00 4.35
56 57 1.347707 AGATGACCCTTCTTGCGACAA 59.652 47.619 0.00 0.00 0.00 3.18
57 58 2.151202 GATGACCCTTCTTGCGACAAA 58.849 47.619 0.00 0.00 0.00 2.83
58 59 2.045561 TGACCCTTCTTGCGACAAAA 57.954 45.000 0.00 0.00 0.00 2.44
59 60 1.673920 TGACCCTTCTTGCGACAAAAC 59.326 47.619 0.00 0.00 0.00 2.43
60 61 1.001706 GACCCTTCTTGCGACAAAACC 60.002 52.381 0.00 0.00 0.00 3.27
61 62 1.028905 CCCTTCTTGCGACAAAACCA 58.971 50.000 0.00 0.00 0.00 3.67
62 63 1.269051 CCCTTCTTGCGACAAAACCAC 60.269 52.381 0.00 0.00 0.00 4.16
63 64 1.403679 CCTTCTTGCGACAAAACCACA 59.596 47.619 0.00 0.00 0.00 4.17
64 65 2.159310 CCTTCTTGCGACAAAACCACAA 60.159 45.455 0.00 0.00 0.00 3.33
65 66 3.490761 CCTTCTTGCGACAAAACCACAAT 60.491 43.478 0.00 0.00 0.00 2.71
66 67 3.077229 TCTTGCGACAAAACCACAATG 57.923 42.857 0.00 0.00 0.00 2.82
67 68 1.522258 CTTGCGACAAAACCACAATGC 59.478 47.619 0.00 0.00 0.00 3.56
68 69 0.593518 TGCGACAAAACCACAATGCG 60.594 50.000 0.00 0.00 0.00 4.73
69 70 1.274798 GCGACAAAACCACAATGCGG 61.275 55.000 0.00 0.00 0.00 5.69
70 71 0.030101 CGACAAAACCACAATGCGGT 59.970 50.000 0.00 0.00 38.85 5.68
72 73 2.287069 CGACAAAACCACAATGCGGTTA 60.287 45.455 6.07 0.00 46.12 2.85
73 74 3.610585 CGACAAAACCACAATGCGGTTAT 60.611 43.478 6.07 0.00 46.12 1.89
74 75 3.648009 ACAAAACCACAATGCGGTTATG 58.352 40.909 6.07 0.00 46.12 1.90
75 76 2.362169 AAACCACAATGCGGTTATGC 57.638 45.000 6.07 0.00 46.12 3.14
76 77 0.530288 AACCACAATGCGGTTATGCC 59.470 50.000 3.53 0.00 45.00 4.40
77 78 0.323360 ACCACAATGCGGTTATGCCT 60.323 50.000 0.00 0.00 30.53 4.75
78 79 0.381801 CCACAATGCGGTTATGCCTC 59.618 55.000 0.00 0.00 34.25 4.70
79 80 1.382522 CACAATGCGGTTATGCCTCT 58.617 50.000 0.00 0.00 34.25 3.69
80 81 2.560504 CACAATGCGGTTATGCCTCTA 58.439 47.619 0.00 0.00 34.25 2.43
81 82 2.942376 CACAATGCGGTTATGCCTCTAA 59.058 45.455 0.00 0.00 34.25 2.10
82 83 3.002656 CACAATGCGGTTATGCCTCTAAG 59.997 47.826 0.00 0.00 34.25 2.18
83 84 3.206150 CAATGCGGTTATGCCTCTAAGT 58.794 45.455 0.00 0.00 34.25 2.24
84 85 2.596904 TGCGGTTATGCCTCTAAGTC 57.403 50.000 0.00 0.00 34.25 3.01
85 86 1.202371 TGCGGTTATGCCTCTAAGTCG 60.202 52.381 0.00 0.00 34.25 4.18
86 87 1.202382 GCGGTTATGCCTCTAAGTCGT 60.202 52.381 0.00 0.00 34.25 4.34
87 88 2.460918 CGGTTATGCCTCTAAGTCGTG 58.539 52.381 0.00 0.00 34.25 4.35
88 89 2.202566 GGTTATGCCTCTAAGTCGTGC 58.797 52.381 0.00 0.00 0.00 5.34
89 90 2.202566 GTTATGCCTCTAAGTCGTGCC 58.797 52.381 0.00 0.00 0.00 5.01
90 91 1.776662 TATGCCTCTAAGTCGTGCCT 58.223 50.000 0.00 0.00 0.00 4.75
91 92 0.461961 ATGCCTCTAAGTCGTGCCTC 59.538 55.000 0.00 0.00 0.00 4.70
92 93 1.226717 GCCTCTAAGTCGTGCCTCG 60.227 63.158 0.00 0.00 41.41 4.63
93 94 1.654954 GCCTCTAAGTCGTGCCTCGA 61.655 60.000 0.00 0.00 46.83 4.04
102 103 3.986006 GTGCCTCGACACGTGGGA 61.986 66.667 21.57 15.34 40.31 4.37
103 104 3.680786 TGCCTCGACACGTGGGAG 61.681 66.667 24.04 24.04 40.31 4.30
104 105 3.371063 GCCTCGACACGTGGGAGA 61.371 66.667 29.41 19.95 40.31 3.71
105 106 2.711922 GCCTCGACACGTGGGAGAT 61.712 63.158 29.41 7.79 40.31 2.75
106 107 1.381928 GCCTCGACACGTGGGAGATA 61.382 60.000 29.41 7.54 40.31 1.98
107 108 1.319541 CCTCGACACGTGGGAGATAT 58.680 55.000 29.41 6.39 36.95 1.63
108 109 2.501261 CCTCGACACGTGGGAGATATA 58.499 52.381 29.41 5.30 36.95 0.86
109 110 2.484651 CCTCGACACGTGGGAGATATAG 59.515 54.545 29.41 15.13 36.95 1.31
110 111 1.878088 TCGACACGTGGGAGATATAGC 59.122 52.381 21.57 0.00 0.00 2.97
111 112 1.068472 CGACACGTGGGAGATATAGCC 60.068 57.143 21.57 0.00 0.00 3.93
112 113 0.959553 ACACGTGGGAGATATAGCCG 59.040 55.000 21.57 0.00 0.00 5.52
113 114 0.388649 CACGTGGGAGATATAGCCGC 60.389 60.000 7.95 0.00 0.00 6.53
114 115 0.826256 ACGTGGGAGATATAGCCGCA 60.826 55.000 0.00 0.00 0.00 5.69
115 116 0.532573 CGTGGGAGATATAGCCGCAT 59.467 55.000 0.00 0.00 0.00 4.73
116 117 1.469940 CGTGGGAGATATAGCCGCATC 60.470 57.143 0.00 0.00 0.00 3.91
117 118 0.817654 TGGGAGATATAGCCGCATCG 59.182 55.000 0.00 0.00 0.00 3.84
118 119 0.818296 GGGAGATATAGCCGCATCGT 59.182 55.000 0.00 0.00 0.00 3.73
119 120 1.469940 GGGAGATATAGCCGCATCGTG 60.470 57.143 0.00 0.00 0.00 4.35
120 121 1.469940 GGAGATATAGCCGCATCGTGG 60.470 57.143 0.00 0.00 36.10 4.94
121 122 0.532573 AGATATAGCCGCATCGTGGG 59.467 55.000 0.00 0.00 33.18 4.61
129 130 3.089784 GCATCGTGGGCGTTACAG 58.910 61.111 0.00 0.00 39.49 2.74
130 131 2.461110 GCATCGTGGGCGTTACAGG 61.461 63.158 0.00 0.00 39.49 4.00
131 132 1.813753 CATCGTGGGCGTTACAGGG 60.814 63.158 0.00 0.00 39.49 4.45
132 133 3.026431 ATCGTGGGCGTTACAGGGG 62.026 63.158 0.00 0.00 39.49 4.79
133 134 4.770874 CGTGGGCGTTACAGGGGG 62.771 72.222 0.00 0.00 0.00 5.40
134 135 3.643554 GTGGGCGTTACAGGGGGT 61.644 66.667 0.00 0.00 0.00 4.95
135 136 3.642503 TGGGCGTTACAGGGGGTG 61.643 66.667 0.00 0.00 0.00 4.61
136 137 3.643554 GGGCGTTACAGGGGGTGT 61.644 66.667 0.00 0.00 43.86 4.16
137 138 2.359478 GGCGTTACAGGGGGTGTG 60.359 66.667 0.00 0.00 40.69 3.82
138 139 3.053896 GCGTTACAGGGGGTGTGC 61.054 66.667 0.00 0.00 40.69 4.57
139 140 2.747686 CGTTACAGGGGGTGTGCT 59.252 61.111 0.00 0.00 40.69 4.40
140 141 1.072505 CGTTACAGGGGGTGTGCTT 59.927 57.895 0.00 0.00 40.69 3.91
141 142 0.536460 CGTTACAGGGGGTGTGCTTT 60.536 55.000 0.00 0.00 40.69 3.51
142 143 1.699730 GTTACAGGGGGTGTGCTTTT 58.300 50.000 0.00 0.00 40.69 2.27
143 144 1.611977 GTTACAGGGGGTGTGCTTTTC 59.388 52.381 0.00 0.00 40.69 2.29
144 145 0.250553 TACAGGGGGTGTGCTTTTCG 60.251 55.000 0.00 0.00 40.69 3.46
145 146 1.228124 CAGGGGGTGTGCTTTTCGA 60.228 57.895 0.00 0.00 0.00 3.71
160 161 1.272807 TTCGAGGGAGGGGTTTGTAG 58.727 55.000 0.00 0.00 0.00 2.74
166 167 1.144298 GGGAGGGGTTTGTAGTGTTGT 59.856 52.381 0.00 0.00 0.00 3.32
168 169 1.607148 GAGGGGTTTGTAGTGTTGTGC 59.393 52.381 0.00 0.00 0.00 4.57
231 232 0.911769 TGCCTTCCCTTCATCACGAT 59.088 50.000 0.00 0.00 0.00 3.73
240 241 1.688735 CTTCATCACGATGGCTAGGGA 59.311 52.381 7.17 0.00 39.24 4.20
288 289 0.842635 GAGCCCATGGATTCACCTCT 59.157 55.000 15.22 0.00 39.86 3.69
291 292 0.475906 CCCATGGATTCACCTCTCCC 59.524 60.000 15.22 0.00 39.86 4.30
330 334 3.017581 GGTGGCAGGGGTGATCCT 61.018 66.667 0.00 0.00 37.71 3.24
365 369 3.956848 CCGGCTAGTAGTTTAGGTTAGGT 59.043 47.826 0.00 0.00 0.00 3.08
399 403 2.118513 AGGTGTGTCTCTCGGGCT 59.881 61.111 0.00 0.00 0.00 5.19
402 406 1.080434 GTGTGTCTCTCGGGCTGAC 60.080 63.158 0.00 1.99 0.00 3.51
404 408 2.282251 TGTCTCTCGGGCTGACGT 60.282 61.111 0.00 0.00 33.81 4.34
406 410 2.750637 TCTCTCGGGCTGACGTCC 60.751 66.667 14.12 0.00 34.94 4.79
420 424 2.429250 TGACGTCCACACTTCTTCTTCA 59.571 45.455 14.12 0.00 0.00 3.02
438 442 2.218603 TCAAGTTTGCCTTCCGTTCTC 58.781 47.619 0.00 0.00 0.00 2.87
440 444 0.472471 AGTTTGCCTTCCGTTCTCCA 59.528 50.000 0.00 0.00 0.00 3.86
447 451 1.834263 CCTTCCGTTCTCCAATCCTCT 59.166 52.381 0.00 0.00 0.00 3.69
449 453 2.534042 TCCGTTCTCCAATCCTCTCT 57.466 50.000 0.00 0.00 0.00 3.10
466 470 7.675962 TCCTCTCTAAATTCGTCTATCTAGC 57.324 40.000 0.00 0.00 0.00 3.42
529 536 1.004595 GTCGGCGAGGTTATGGTTTC 58.995 55.000 11.20 0.00 0.00 2.78
535 542 2.537401 CGAGGTTATGGTTTCTCGTCC 58.463 52.381 0.00 0.00 42.61 4.79
539 546 1.659098 GTTATGGTTTCTCGTCCTGCG 59.341 52.381 0.00 0.00 43.01 5.18
566 573 3.376234 CGATGGCAAGATTTGATGTCAGT 59.624 43.478 0.00 0.00 34.18 3.41
597 604 8.044908 TCAGATCTATTAAAAGGGTTTAGCGTT 58.955 33.333 0.00 0.00 30.92 4.84
606 613 1.802365 GGGTTTAGCGTTGACGATTGT 59.198 47.619 7.85 0.00 43.02 2.71
802 809 5.371115 TTGAAGTGCTGTATACCTTTTGC 57.629 39.130 0.00 0.00 0.00 3.68
807 814 4.083484 AGTGCTGTATACCTTTTGCGAAAC 60.083 41.667 0.00 0.00 0.00 2.78
864 1178 4.563140 AAGAGGCTTTTGTATTACGGGA 57.437 40.909 0.00 0.00 0.00 5.14
924 1238 5.096849 GTGAGTTTAGCAGACTACTACAGC 58.903 45.833 0.00 0.00 0.00 4.40
997 1311 1.033574 GACCTGGATTCGATCGGAGT 58.966 55.000 16.41 0.00 0.00 3.85
1125 1439 1.053424 TCAACTACCGCCACCTTTCT 58.947 50.000 0.00 0.00 0.00 2.52
1166 1480 4.758251 CCTCCGCCGTGCACATGA 62.758 66.667 18.64 6.07 0.00 3.07
1196 1510 0.490017 TGGGTCCTCTCCAAGGTACA 59.510 55.000 0.00 0.00 46.32 2.90
1199 1513 3.246203 TGGGTCCTCTCCAAGGTACAATA 60.246 47.826 0.00 0.00 46.32 1.90
1226 1540 2.464459 CGAATGCGGTGCTCCTTCC 61.464 63.158 2.85 0.00 0.00 3.46
1308 1622 1.048601 TGGATCGACCTATTCCTGCC 58.951 55.000 3.79 0.00 39.86 4.85
1310 1624 1.001406 GGATCGACCTATTCCTGCCAG 59.999 57.143 0.00 0.00 35.41 4.85
1365 1679 1.939785 GCAGTACTCCATCGACGCG 60.940 63.158 3.53 3.53 0.00 6.01
1401 1715 1.519719 GCTCAAGGAGATCTGCGGT 59.480 57.895 8.74 0.00 0.00 5.68
1405 1719 0.179089 CAAGGAGATCTGCGGTGAGG 60.179 60.000 13.40 0.00 0.00 3.86
1428 1742 1.306141 TGCCGAGTGAGGGGAAGAT 60.306 57.895 0.00 0.00 0.00 2.40
1484 1798 2.801699 CGCAAGGTGTTCGGCTATATGA 60.802 50.000 0.00 0.00 0.00 2.15
1490 1804 3.318275 GGTGTTCGGCTATATGACTCTGA 59.682 47.826 0.00 0.00 0.00 3.27
1491 1805 4.541779 GTGTTCGGCTATATGACTCTGAG 58.458 47.826 2.45 2.45 0.00 3.35
1500 1815 6.258947 GGCTATATGACTCTGAGGTGTTTTTC 59.741 42.308 9.85 0.00 0.00 2.29
1508 1823 4.594970 TCTGAGGTGTTTTTCAAGTTCCA 58.405 39.130 0.00 0.00 0.00 3.53
1542 1857 2.749621 GTGAATTGCCCAGTTCTACCTG 59.250 50.000 5.35 0.00 0.00 4.00
1545 1860 4.227300 TGAATTGCCCAGTTCTACCTGTAT 59.773 41.667 5.35 0.00 0.00 2.29
1549 1864 3.329520 TGCCCAGTTCTACCTGTATTGTT 59.670 43.478 0.00 0.00 0.00 2.83
1625 1940 9.113838 GGAAATAAGATCAACATTCTGCTTCTA 57.886 33.333 0.00 0.00 0.00 2.10
1639 1954 7.817418 TTCTGCTTCTAACTTGGTAATGTTT 57.183 32.000 0.00 0.00 0.00 2.83
1649 1964 4.277423 ACTTGGTAATGTTTTGAACTCGGG 59.723 41.667 0.00 0.00 0.00 5.14
1669 1984 2.626743 GGCCGACTATTTAGAGGCTGTA 59.373 50.000 19.80 0.00 44.04 2.74
1672 1987 3.314635 CCGACTATTTAGAGGCTGTACGT 59.685 47.826 0.00 0.00 0.00 3.57
1674 1989 5.008019 CCGACTATTTAGAGGCTGTACGTAA 59.992 44.000 0.00 0.00 0.00 3.18
1688 2003 1.300233 CGTAATCCCTCCGCTCTGC 60.300 63.158 0.00 0.00 0.00 4.26
1689 2004 1.823295 GTAATCCCTCCGCTCTGCA 59.177 57.895 0.00 0.00 0.00 4.41
1690 2005 0.249657 GTAATCCCTCCGCTCTGCAG 60.250 60.000 7.63 7.63 0.00 4.41
1691 2006 2.032860 TAATCCCTCCGCTCTGCAGC 62.033 60.000 9.47 0.00 42.96 5.25
1705 2020 2.357881 CAGCTCAACTCCGCTGCA 60.358 61.111 0.00 0.00 45.90 4.41
1731 2046 3.719699 GCGGCATGCAGTTGTATTT 57.280 47.368 21.36 0.00 45.45 1.40
1732 2047 1.994916 GCGGCATGCAGTTGTATTTT 58.005 45.000 21.36 0.00 45.45 1.82
1733 2048 1.655099 GCGGCATGCAGTTGTATTTTG 59.345 47.619 21.36 0.00 45.45 2.44
1734 2049 2.261345 CGGCATGCAGTTGTATTTTGG 58.739 47.619 21.36 0.00 0.00 3.28
1735 2050 2.001872 GGCATGCAGTTGTATTTTGGC 58.998 47.619 21.36 0.00 0.00 4.52
1736 2051 1.655099 GCATGCAGTTGTATTTTGGCG 59.345 47.619 14.21 0.00 0.00 5.69
1737 2052 2.670789 GCATGCAGTTGTATTTTGGCGA 60.671 45.455 14.21 0.00 0.00 5.54
1738 2053 2.987413 TGCAGTTGTATTTTGGCGAG 57.013 45.000 0.00 0.00 0.00 5.03
1739 2054 1.068610 TGCAGTTGTATTTTGGCGAGC 60.069 47.619 0.00 0.00 0.00 5.03
1740 2055 1.882198 CAGTTGTATTTTGGCGAGCG 58.118 50.000 0.00 0.00 0.00 5.03
1741 2056 0.802494 AGTTGTATTTTGGCGAGCGG 59.198 50.000 0.00 0.00 0.00 5.52
1742 2057 0.796870 GTTGTATTTTGGCGAGCGGC 60.797 55.000 9.65 9.65 42.51 6.53
1750 2065 3.202706 GGCGAGCGGCTAAAAGGG 61.203 66.667 0.60 0.00 42.94 3.95
1757 2072 1.002624 CGGCTAAAAGGGTGCTCCA 60.003 57.895 7.20 0.00 38.24 3.86
1795 2110 0.620556 GAAGGAGTGGAGGATTGCCA 59.379 55.000 0.00 0.00 36.29 4.92
1841 2156 0.320421 GTTCCAGTGCAGCCTTCGTA 60.320 55.000 0.00 0.00 0.00 3.43
1894 2213 2.158475 TGGTCCTGCAACCTGAAATCTT 60.158 45.455 8.97 0.00 40.20 2.40
1897 2216 3.127721 GTCCTGCAACCTGAAATCTTAGC 59.872 47.826 0.00 0.00 0.00 3.09
1900 2219 3.084039 TGCAACCTGAAATCTTAGCTGG 58.916 45.455 0.00 0.00 0.00 4.85
1919 2238 7.195374 AGCTGGATAACTTGGTAATTCAGTA 57.805 36.000 0.00 0.00 0.00 2.74
1964 2283 8.867097 AGTAGTCAAAACTTCTCTGGTTACATA 58.133 33.333 0.00 0.00 36.92 2.29
1996 2315 6.344500 TGTTTGTTTTGTTGTATGCTGGAAT 58.656 32.000 0.00 0.00 0.00 3.01
2009 2328 2.938451 TGCTGGAATGAAATGTAGCTCG 59.062 45.455 0.00 0.00 31.27 5.03
2013 2332 4.702831 TGGAATGAAATGTAGCTCGCATA 58.297 39.130 0.00 0.00 0.00 3.14
2044 2363 5.595542 CCAATCCTTAATGAAATGGAGCTCA 59.404 40.000 17.19 1.87 30.72 4.26
2046 2365 4.191544 TCCTTAATGAAATGGAGCTCACG 58.808 43.478 17.19 0.00 0.00 4.35
2057 2376 1.689273 GGAGCTCACGTATTCATCCCT 59.311 52.381 17.19 0.00 0.00 4.20
2070 2389 8.826765 ACGTATTCATCCCTATCCTTATTCAAT 58.173 33.333 0.00 0.00 0.00 2.57
2072 2391 9.319143 GTATTCATCCCTATCCTTATTCAATCG 57.681 37.037 0.00 0.00 0.00 3.34
2077 2396 4.286032 CCCTATCCTTATTCAATCGGACCA 59.714 45.833 0.00 0.00 0.00 4.02
2080 2399 4.351874 TCCTTATTCAATCGGACCATCC 57.648 45.455 0.00 0.00 0.00 3.51
2090 2409 7.233389 TCAATCGGACCATCCAAAATAAAAA 57.767 32.000 0.00 0.00 35.91 1.94
2134 2453 4.463891 GGGAAAAATTGATGCTCCAGAAGA 59.536 41.667 0.00 0.00 0.00 2.87
2147 2466 5.159273 CTCCAGAAGAGCCTCTAGTTTTT 57.841 43.478 0.00 0.00 35.31 1.94
2169 2488 4.510038 ACTCAAATTTGTGCTTAGCTGG 57.490 40.909 17.47 0.00 0.00 4.85
2179 2498 2.095059 GTGCTTAGCTGGTCAACAATGG 60.095 50.000 5.60 0.00 0.00 3.16
2189 2508 5.739935 GCTGGTCAACAATGGAAAAGATGTT 60.740 40.000 0.00 0.00 36.49 2.71
2192 2511 6.549364 TGGTCAACAATGGAAAAGATGTTAGT 59.451 34.615 0.00 0.00 34.45 2.24
2212 2531 2.905415 ATTGCCCTTCATCAACCTCA 57.095 45.000 0.00 0.00 0.00 3.86
2224 2543 3.548745 TCAACCTCACATGGCTCATAG 57.451 47.619 0.00 0.00 0.00 2.23
2228 2547 3.647636 ACCTCACATGGCTCATAGTAGT 58.352 45.455 0.00 0.00 0.00 2.73
2232 2551 5.278709 CCTCACATGGCTCATAGTAGTAGTG 60.279 48.000 0.00 0.00 0.00 2.74
2233 2552 5.445964 TCACATGGCTCATAGTAGTAGTGA 58.554 41.667 0.00 0.00 0.00 3.41
2242 2561 6.697892 GCTCATAGTAGTAGTGACATGTTTCC 59.302 42.308 0.00 0.00 0.00 3.13
2262 2581 4.579869 TCCTTCTTTCTATGTTGGAGCAC 58.420 43.478 0.00 0.00 0.00 4.40
2264 2583 2.346803 TCTTTCTATGTTGGAGCACGC 58.653 47.619 0.00 0.00 0.00 5.34
2268 2587 0.370273 CTATGTTGGAGCACGCGTTC 59.630 55.000 10.22 4.20 0.00 3.95
2280 2599 0.463116 ACGCGTTCTGTTGTCCCTTT 60.463 50.000 5.58 0.00 0.00 3.11
2285 2604 2.484770 CGTTCTGTTGTCCCTTTCTCCA 60.485 50.000 0.00 0.00 0.00 3.86
2288 2607 2.368875 TCTGTTGTCCCTTTCTCCAGAC 59.631 50.000 0.00 0.00 0.00 3.51
2296 2615 4.022849 GTCCCTTTCTCCAGACAAATTGTG 60.023 45.833 2.20 0.00 0.00 3.33
2298 2617 5.070001 CCCTTTCTCCAGACAAATTGTGTA 58.930 41.667 2.20 0.00 41.96 2.90
2300 2619 6.438763 CCTTTCTCCAGACAAATTGTGTAAC 58.561 40.000 2.20 0.00 41.96 2.50
2302 2621 6.618287 TTCTCCAGACAAATTGTGTAACTG 57.382 37.500 2.20 4.48 41.96 3.16
2306 2625 6.791303 TCCAGACAAATTGTGTAACTGAAAC 58.209 36.000 2.20 0.00 41.96 2.78
2320 2639 2.036089 ACTGAAACTGGAGTTCGGAGTC 59.964 50.000 0.18 0.00 37.25 3.36
2340 2659 9.011095 CGGAGTCAGGATGTAGATACTAATTAA 57.989 37.037 0.00 0.00 37.40 1.40
2363 2682 2.174639 TGAACTCCCACTGAACCATTGT 59.825 45.455 0.00 0.00 0.00 2.71
2364 2683 2.276732 ACTCCCACTGAACCATTGTG 57.723 50.000 0.00 0.00 0.00 3.33
2367 2686 0.874390 CCCACTGAACCATTGTGTCG 59.126 55.000 0.00 0.00 0.00 4.35
2373 2692 2.080693 TGAACCATTGTGTCGGCATAC 58.919 47.619 0.00 0.00 0.00 2.39
2375 2694 1.737838 ACCATTGTGTCGGCATACAG 58.262 50.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 6.319405 TCATCTTCACACAATCCCATGTAATG 59.681 38.462 0.00 0.00 46.21 1.90
17 18 6.319658 GTCATCTTCACACAATCCCATGTAAT 59.680 38.462 0.00 0.00 30.84 1.89
18 19 5.647658 GTCATCTTCACACAATCCCATGTAA 59.352 40.000 0.00 0.00 30.84 2.41
19 20 5.185454 GTCATCTTCACACAATCCCATGTA 58.815 41.667 0.00 0.00 30.84 2.29
20 21 4.012374 GTCATCTTCACACAATCCCATGT 58.988 43.478 0.00 0.00 0.00 3.21
21 22 3.379372 GGTCATCTTCACACAATCCCATG 59.621 47.826 0.00 0.00 0.00 3.66
22 23 3.624777 GGTCATCTTCACACAATCCCAT 58.375 45.455 0.00 0.00 0.00 4.00
23 24 2.290896 GGGTCATCTTCACACAATCCCA 60.291 50.000 0.00 0.00 33.33 4.37
24 25 2.025887 AGGGTCATCTTCACACAATCCC 60.026 50.000 0.00 0.00 0.00 3.85
25 26 3.356529 AGGGTCATCTTCACACAATCC 57.643 47.619 0.00 0.00 0.00 3.01
26 27 4.583871 AGAAGGGTCATCTTCACACAATC 58.416 43.478 7.26 0.00 44.01 2.67
27 28 4.647564 AGAAGGGTCATCTTCACACAAT 57.352 40.909 7.26 0.00 44.01 2.71
28 29 4.136796 CAAGAAGGGTCATCTTCACACAA 58.863 43.478 7.26 0.00 44.01 3.33
29 30 3.743521 CAAGAAGGGTCATCTTCACACA 58.256 45.455 7.26 0.00 44.01 3.72
30 31 2.485814 GCAAGAAGGGTCATCTTCACAC 59.514 50.000 7.26 0.00 44.01 3.82
31 32 2.783135 GCAAGAAGGGTCATCTTCACA 58.217 47.619 7.26 0.00 44.01 3.58
32 33 1.734465 CGCAAGAAGGGTCATCTTCAC 59.266 52.381 7.26 0.00 44.01 3.18
33 34 2.099141 CGCAAGAAGGGTCATCTTCA 57.901 50.000 7.26 0.00 44.01 3.02
47 48 1.522258 GCATTGTGGTTTTGTCGCAAG 59.478 47.619 0.00 0.00 37.91 4.01
48 49 1.565305 GCATTGTGGTTTTGTCGCAA 58.435 45.000 0.00 0.00 38.69 4.85
49 50 0.593518 CGCATTGTGGTTTTGTCGCA 60.594 50.000 0.00 0.00 0.00 5.10
50 51 1.274798 CCGCATTGTGGTTTTGTCGC 61.275 55.000 8.14 0.00 0.00 5.19
51 52 0.030101 ACCGCATTGTGGTTTTGTCG 59.970 50.000 16.17 0.00 44.78 4.35
52 53 3.957383 ACCGCATTGTGGTTTTGTC 57.043 47.368 16.17 0.00 44.78 3.18
59 60 0.381801 GAGGCATAACCGCATTGTGG 59.618 55.000 14.72 14.72 46.52 4.17
60 61 1.382522 AGAGGCATAACCGCATTGTG 58.617 50.000 0.00 0.00 46.52 3.33
61 62 3.206150 CTTAGAGGCATAACCGCATTGT 58.794 45.455 0.00 0.00 46.52 2.71
62 63 3.206150 ACTTAGAGGCATAACCGCATTG 58.794 45.455 0.00 0.00 46.52 2.82
63 64 3.467803 GACTTAGAGGCATAACCGCATT 58.532 45.455 0.00 0.00 46.52 3.56
64 65 2.545952 CGACTTAGAGGCATAACCGCAT 60.546 50.000 0.00 0.00 46.52 4.73
65 66 1.202371 CGACTTAGAGGCATAACCGCA 60.202 52.381 0.00 0.00 46.52 5.69
66 67 1.202382 ACGACTTAGAGGCATAACCGC 60.202 52.381 0.00 0.00 46.52 5.68
67 68 2.460918 CACGACTTAGAGGCATAACCG 58.539 52.381 0.00 0.00 46.52 4.44
68 69 2.202566 GCACGACTTAGAGGCATAACC 58.797 52.381 0.00 0.00 39.61 2.85
69 70 2.159085 AGGCACGACTTAGAGGCATAAC 60.159 50.000 0.00 0.00 0.00 1.89
70 71 2.100916 GAGGCACGACTTAGAGGCATAA 59.899 50.000 0.00 0.00 0.00 1.90
71 72 1.681793 GAGGCACGACTTAGAGGCATA 59.318 52.381 0.00 0.00 0.00 3.14
72 73 0.461961 GAGGCACGACTTAGAGGCAT 59.538 55.000 0.00 0.00 0.00 4.40
73 74 1.890894 GAGGCACGACTTAGAGGCA 59.109 57.895 0.00 0.00 0.00 4.75
74 75 1.226717 CGAGGCACGACTTAGAGGC 60.227 63.158 0.00 0.00 45.77 4.70
75 76 2.478989 TCGAGGCACGACTTAGAGG 58.521 57.895 2.07 0.00 46.45 3.69
85 86 3.916392 CTCCCACGTGTCGAGGCAC 62.916 68.421 15.65 0.00 36.35 5.01
86 87 3.680786 CTCCCACGTGTCGAGGCA 61.681 66.667 15.65 0.00 36.35 4.75
87 88 1.381928 TATCTCCCACGTGTCGAGGC 61.382 60.000 22.62 0.00 36.35 4.70
88 89 1.319541 ATATCTCCCACGTGTCGAGG 58.680 55.000 22.62 14.20 37.35 4.63
89 90 2.095668 GCTATATCTCCCACGTGTCGAG 60.096 54.545 15.65 17.66 0.00 4.04
90 91 1.878088 GCTATATCTCCCACGTGTCGA 59.122 52.381 15.65 8.55 0.00 4.20
91 92 1.068472 GGCTATATCTCCCACGTGTCG 60.068 57.143 15.65 4.04 0.00 4.35
92 93 1.068472 CGGCTATATCTCCCACGTGTC 60.068 57.143 15.65 0.00 0.00 3.67
93 94 0.959553 CGGCTATATCTCCCACGTGT 59.040 55.000 15.65 0.00 0.00 4.49
94 95 0.388649 GCGGCTATATCTCCCACGTG 60.389 60.000 9.08 9.08 0.00 4.49
95 96 0.826256 TGCGGCTATATCTCCCACGT 60.826 55.000 0.00 0.00 0.00 4.49
96 97 0.532573 ATGCGGCTATATCTCCCACG 59.467 55.000 0.00 0.00 0.00 4.94
97 98 1.469940 CGATGCGGCTATATCTCCCAC 60.470 57.143 0.00 0.00 0.00 4.61
98 99 0.817654 CGATGCGGCTATATCTCCCA 59.182 55.000 0.00 0.00 0.00 4.37
99 100 0.818296 ACGATGCGGCTATATCTCCC 59.182 55.000 0.00 0.00 0.00 4.30
100 101 1.469940 CCACGATGCGGCTATATCTCC 60.470 57.143 0.00 0.00 0.00 3.71
101 102 1.469940 CCCACGATGCGGCTATATCTC 60.470 57.143 0.00 0.00 0.00 2.75
102 103 0.532573 CCCACGATGCGGCTATATCT 59.467 55.000 0.00 0.00 0.00 1.98
103 104 1.084370 GCCCACGATGCGGCTATATC 61.084 60.000 0.00 0.00 42.21 1.63
104 105 1.079127 GCCCACGATGCGGCTATAT 60.079 57.895 0.00 0.00 42.21 0.86
105 106 2.342279 GCCCACGATGCGGCTATA 59.658 61.111 0.00 0.00 42.21 1.31
112 113 2.461110 CCTGTAACGCCCACGATGC 61.461 63.158 0.00 0.00 43.93 3.91
113 114 1.813753 CCCTGTAACGCCCACGATG 60.814 63.158 0.00 0.00 43.93 3.84
114 115 2.582436 CCCTGTAACGCCCACGAT 59.418 61.111 0.00 0.00 43.93 3.73
115 116 3.697747 CCCCTGTAACGCCCACGA 61.698 66.667 0.00 0.00 43.93 4.35
117 118 3.643554 ACCCCCTGTAACGCCCAC 61.644 66.667 0.00 0.00 0.00 4.61
118 119 3.642503 CACCCCCTGTAACGCCCA 61.643 66.667 0.00 0.00 0.00 5.36
119 120 3.643554 ACACCCCCTGTAACGCCC 61.644 66.667 0.00 0.00 0.00 6.13
120 121 2.359478 CACACCCCCTGTAACGCC 60.359 66.667 0.00 0.00 0.00 5.68
121 122 3.053896 GCACACCCCCTGTAACGC 61.054 66.667 0.00 0.00 0.00 4.84
122 123 0.536460 AAAGCACACCCCCTGTAACG 60.536 55.000 0.00 0.00 0.00 3.18
123 124 1.611977 GAAAAGCACACCCCCTGTAAC 59.388 52.381 0.00 0.00 0.00 2.50
124 125 1.816183 CGAAAAGCACACCCCCTGTAA 60.816 52.381 0.00 0.00 0.00 2.41
125 126 0.250553 CGAAAAGCACACCCCCTGTA 60.251 55.000 0.00 0.00 0.00 2.74
126 127 1.528309 CGAAAAGCACACCCCCTGT 60.528 57.895 0.00 0.00 0.00 4.00
127 128 1.228124 TCGAAAAGCACACCCCCTG 60.228 57.895 0.00 0.00 0.00 4.45
128 129 1.073199 CTCGAAAAGCACACCCCCT 59.927 57.895 0.00 0.00 0.00 4.79
129 130 1.971695 CCTCGAAAAGCACACCCCC 60.972 63.158 0.00 0.00 0.00 5.40
130 131 1.971695 CCCTCGAAAAGCACACCCC 60.972 63.158 0.00 0.00 0.00 4.95
131 132 0.955919 CTCCCTCGAAAAGCACACCC 60.956 60.000 0.00 0.00 0.00 4.61
132 133 0.955919 CCTCCCTCGAAAAGCACACC 60.956 60.000 0.00 0.00 0.00 4.16
133 134 0.955919 CCCTCCCTCGAAAAGCACAC 60.956 60.000 0.00 0.00 0.00 3.82
134 135 1.374947 CCCTCCCTCGAAAAGCACA 59.625 57.895 0.00 0.00 0.00 4.57
135 136 1.377333 CCCCTCCCTCGAAAAGCAC 60.377 63.158 0.00 0.00 0.00 4.40
136 137 1.423794 AACCCCTCCCTCGAAAAGCA 61.424 55.000 0.00 0.00 0.00 3.91
137 138 0.251209 AAACCCCTCCCTCGAAAAGC 60.251 55.000 0.00 0.00 0.00 3.51
138 139 1.202891 ACAAACCCCTCCCTCGAAAAG 60.203 52.381 0.00 0.00 0.00 2.27
139 140 0.848053 ACAAACCCCTCCCTCGAAAA 59.152 50.000 0.00 0.00 0.00 2.29
140 141 1.626825 CTACAAACCCCTCCCTCGAAA 59.373 52.381 0.00 0.00 0.00 3.46
141 142 1.272807 CTACAAACCCCTCCCTCGAA 58.727 55.000 0.00 0.00 0.00 3.71
142 143 0.115745 ACTACAAACCCCTCCCTCGA 59.884 55.000 0.00 0.00 0.00 4.04
143 144 0.249398 CACTACAAACCCCTCCCTCG 59.751 60.000 0.00 0.00 0.00 4.63
144 145 1.359168 ACACTACAAACCCCTCCCTC 58.641 55.000 0.00 0.00 0.00 4.30
145 146 1.423921 CAACACTACAAACCCCTCCCT 59.576 52.381 0.00 0.00 0.00 4.20
168 169 1.683917 AGGCGTCCAATAGTGCTAGAG 59.316 52.381 0.00 0.00 0.00 2.43
177 178 0.535335 GAGTGACCAGGCGTCCAATA 59.465 55.000 0.00 0.00 41.18 1.90
215 216 1.134280 AGCCATCGTGATGAAGGGAAG 60.134 52.381 11.35 0.00 41.20 3.46
231 232 1.002773 GGAACGAGTTTTCCCTAGCCA 59.997 52.381 0.00 0.00 39.47 4.75
240 241 1.143073 AGCTTGGAGGGAACGAGTTTT 59.857 47.619 0.00 0.00 0.00 2.43
288 289 0.470080 CTGAAGCGGGAGATAGGGGA 60.470 60.000 0.00 0.00 0.00 4.81
291 292 0.033228 CTGCTGAAGCGGGAGATAGG 59.967 60.000 3.03 0.00 45.83 2.57
389 393 2.750637 GGACGTCAGCCCGAGAGA 60.751 66.667 18.91 0.00 0.00 3.10
399 403 2.429250 TGAAGAAGAAGTGTGGACGTCA 59.571 45.455 18.91 0.27 33.38 4.35
402 406 3.458189 ACTTGAAGAAGAAGTGTGGACG 58.542 45.455 0.00 0.00 32.30 4.79
404 408 4.096382 GCAAACTTGAAGAAGAAGTGTGGA 59.904 41.667 0.00 0.00 38.58 4.02
406 410 4.096984 AGGCAAACTTGAAGAAGAAGTGTG 59.903 41.667 0.00 0.00 40.37 3.82
420 424 1.133915 TGGAGAACGGAAGGCAAACTT 60.134 47.619 0.00 0.00 43.65 2.66
438 442 7.891561 AGATAGACGAATTTAGAGAGGATTGG 58.108 38.462 0.00 0.00 0.00 3.16
440 444 8.736244 GCTAGATAGACGAATTTAGAGAGGATT 58.264 37.037 0.00 0.00 0.00 3.01
535 542 3.656243 CTTGCCATCGTGCACGCAG 62.656 63.158 33.63 25.68 41.88 5.18
539 546 1.199789 TCAAATCTTGCCATCGTGCAC 59.800 47.619 6.82 6.82 41.88 4.57
593 600 1.132640 GAGCCACAATCGTCAACGC 59.867 57.895 0.00 0.00 39.60 4.84
597 604 0.320683 CACTGGAGCCACAATCGTCA 60.321 55.000 0.00 0.00 0.00 4.35
606 613 1.152984 CACCAACACACTGGAGCCA 60.153 57.895 0.00 0.00 38.96 4.75
660 667 1.792118 GCCGGTTTGACCTTGTCACC 61.792 60.000 1.90 0.00 42.60 4.02
790 797 6.894828 TCTGAAAGTTTCGCAAAAGGTATAC 58.105 36.000 10.92 0.00 33.76 1.47
802 809 6.959361 TCTCAAAAAGGATCTGAAAGTTTCG 58.041 36.000 10.92 6.19 33.76 3.46
834 841 9.819267 GTAATACAAAAGCCTCTTAGTCACTAT 57.181 33.333 0.00 0.00 0.00 2.12
835 842 7.972277 CGTAATACAAAAGCCTCTTAGTCACTA 59.028 37.037 0.00 0.00 0.00 2.74
836 843 6.812160 CGTAATACAAAAGCCTCTTAGTCACT 59.188 38.462 0.00 0.00 0.00 3.41
837 844 6.035758 CCGTAATACAAAAGCCTCTTAGTCAC 59.964 42.308 0.00 0.00 0.00 3.67
838 845 6.103997 CCGTAATACAAAAGCCTCTTAGTCA 58.896 40.000 0.00 0.00 0.00 3.41
839 846 5.522824 CCCGTAATACAAAAGCCTCTTAGTC 59.477 44.000 0.00 0.00 0.00 2.59
840 847 5.188359 TCCCGTAATACAAAAGCCTCTTAGT 59.812 40.000 0.00 0.00 0.00 2.24
851 1165 1.481772 CCCTCCGTCCCGTAATACAAA 59.518 52.381 0.00 0.00 0.00 2.83
864 1178 3.705072 CTCCAATTAACTACTCCCTCCGT 59.295 47.826 0.00 0.00 0.00 4.69
924 1238 2.095567 AGTACTACACGCTTGTACGGTG 60.096 50.000 0.00 5.08 40.77 4.94
1158 1472 2.358615 GCGGAGTGGTCATGTGCA 60.359 61.111 0.00 0.00 0.00 4.57
1161 1475 2.665000 CAGGCGGAGTGGTCATGT 59.335 61.111 0.00 0.00 0.00 3.21
1196 1510 2.798834 CGCATTCGGTTGACGTTATT 57.201 45.000 0.00 0.00 44.69 1.40
1226 1540 1.354040 GATGAACACGCAGAGAGTGG 58.646 55.000 5.90 0.00 43.41 4.00
1308 1622 2.499289 ACCAGGAACAGTGAGATAGCTG 59.501 50.000 0.00 0.00 38.58 4.24
1310 1624 3.265791 CAACCAGGAACAGTGAGATAGC 58.734 50.000 0.00 0.00 0.00 2.97
1484 1798 4.640647 GGAACTTGAAAAACACCTCAGAGT 59.359 41.667 0.00 0.00 0.00 3.24
1490 1804 3.181466 GGCATGGAACTTGAAAAACACCT 60.181 43.478 0.00 0.00 0.00 4.00
1491 1805 3.130633 GGCATGGAACTTGAAAAACACC 58.869 45.455 0.00 0.00 0.00 4.16
1500 1815 0.523072 CTGTTCGGGCATGGAACTTG 59.477 55.000 12.60 4.61 43.21 3.16
1526 1841 3.329520 ACAATACAGGTAGAACTGGGCAA 59.670 43.478 0.00 0.00 42.75 4.52
1542 1857 5.633601 GCCCAGCTCTAAAACAAAACAATAC 59.366 40.000 0.00 0.00 0.00 1.89
1545 1860 3.490078 CGCCCAGCTCTAAAACAAAACAA 60.490 43.478 0.00 0.00 0.00 2.83
1549 1864 0.596082 GCGCCCAGCTCTAAAACAAA 59.404 50.000 0.00 0.00 44.04 2.83
1625 1940 5.221165 CCCGAGTTCAAAACATTACCAAGTT 60.221 40.000 0.00 0.00 0.00 2.66
1639 1954 0.899720 AATAGTCGGCCCGAGTTCAA 59.100 50.000 20.17 0.88 40.22 2.69
1649 1964 2.892784 ACAGCCTCTAAATAGTCGGC 57.107 50.000 12.45 12.45 39.49 5.54
1669 1984 2.017559 GCAGAGCGGAGGGATTACGT 62.018 60.000 0.00 0.00 34.82 3.57
1672 1987 2.032860 GCTGCAGAGCGGAGGGATTA 62.033 60.000 20.43 0.00 37.02 1.75
1674 1989 3.859414 GCTGCAGAGCGGAGGGAT 61.859 66.667 20.43 0.00 37.02 3.85
1689 2004 2.047465 CTGCAGCGGAGTTGAGCT 60.047 61.111 0.00 0.00 42.98 4.09
1690 2005 2.047844 TCTGCAGCGGAGTTGAGC 60.048 61.111 9.47 0.00 42.98 4.26
1691 2006 2.099431 GCTCTGCAGCGGAGTTGAG 61.099 63.158 28.55 7.97 42.98 3.02
1692 2007 2.047844 GCTCTGCAGCGGAGTTGA 60.048 61.111 28.55 0.00 42.98 3.18
1718 2033 2.415893 GCTCGCCAAAATACAACTGCAT 60.416 45.455 0.00 0.00 0.00 3.96
1719 2034 1.068610 GCTCGCCAAAATACAACTGCA 60.069 47.619 0.00 0.00 0.00 4.41
1720 2035 1.617740 GCTCGCCAAAATACAACTGC 58.382 50.000 0.00 0.00 0.00 4.40
1721 2036 1.465689 CCGCTCGCCAAAATACAACTG 60.466 52.381 0.00 0.00 0.00 3.16
1722 2037 0.802494 CCGCTCGCCAAAATACAACT 59.198 50.000 0.00 0.00 0.00 3.16
1723 2038 0.796870 GCCGCTCGCCAAAATACAAC 60.797 55.000 0.00 0.00 0.00 3.32
1724 2039 0.958382 AGCCGCTCGCCAAAATACAA 60.958 50.000 0.00 0.00 38.78 2.41
1725 2040 0.108089 TAGCCGCTCGCCAAAATACA 60.108 50.000 0.00 0.00 38.78 2.29
1726 2041 1.011333 TTAGCCGCTCGCCAAAATAC 58.989 50.000 0.00 0.00 38.78 1.89
1727 2042 1.740297 TTTAGCCGCTCGCCAAAATA 58.260 45.000 0.00 0.00 38.78 1.40
1728 2043 0.885196 TTTTAGCCGCTCGCCAAAAT 59.115 45.000 0.00 0.00 33.84 1.82
1729 2044 0.239879 CTTTTAGCCGCTCGCCAAAA 59.760 50.000 0.00 0.00 35.99 2.44
1730 2045 1.582610 CCTTTTAGCCGCTCGCCAAA 61.583 55.000 0.00 0.00 38.78 3.28
1731 2046 2.038269 CCTTTTAGCCGCTCGCCAA 61.038 57.895 0.00 0.00 38.78 4.52
1732 2047 2.435938 CCTTTTAGCCGCTCGCCA 60.436 61.111 0.00 0.00 38.78 5.69
1733 2048 3.202706 CCCTTTTAGCCGCTCGCC 61.203 66.667 0.00 0.00 38.78 5.54
1734 2049 2.436115 ACCCTTTTAGCCGCTCGC 60.436 61.111 0.00 0.00 37.98 5.03
1735 2050 2.750888 GCACCCTTTTAGCCGCTCG 61.751 63.158 0.00 0.00 0.00 5.03
1736 2051 1.369839 GAGCACCCTTTTAGCCGCTC 61.370 60.000 0.00 0.00 39.10 5.03
1737 2052 1.377333 GAGCACCCTTTTAGCCGCT 60.377 57.895 0.00 0.00 0.00 5.52
1738 2053 2.407428 GGAGCACCCTTTTAGCCGC 61.407 63.158 0.00 0.00 0.00 6.53
1739 2054 1.002624 TGGAGCACCCTTTTAGCCG 60.003 57.895 0.00 0.00 35.38 5.52
1740 2055 0.251165 TGTGGAGCACCCTTTTAGCC 60.251 55.000 0.00 0.00 32.73 3.93
1741 2056 0.881796 GTGTGGAGCACCCTTTTAGC 59.118 55.000 0.00 0.00 42.10 3.09
1742 2057 1.156736 CGTGTGGAGCACCCTTTTAG 58.843 55.000 0.00 0.00 44.97 1.85
1764 2079 1.135257 CACTCCTTCACTACAGAGCGG 60.135 57.143 0.00 0.00 0.00 5.52
1795 2110 4.398319 AGCAATGTAGTAAGGCTGTGTTT 58.602 39.130 0.00 0.00 32.76 2.83
1841 2156 1.985473 TTGGCAGTCAACAGAGCAAT 58.015 45.000 0.00 0.00 0.00 3.56
1894 2213 7.195374 ACTGAATTACCAAGTTATCCAGCTA 57.805 36.000 0.00 0.00 0.00 3.32
1897 2216 8.786826 TGTTACTGAATTACCAAGTTATCCAG 57.213 34.615 0.00 0.00 0.00 3.86
1919 2238 3.424703 ACTTGAGGCTATGCACAATGTT 58.575 40.909 0.00 0.00 0.00 2.71
1972 2291 5.330455 TCCAGCATACAACAAAACAAACA 57.670 34.783 0.00 0.00 0.00 2.83
1975 2294 6.154203 TCATTCCAGCATACAACAAAACAA 57.846 33.333 0.00 0.00 0.00 2.83
1977 2296 7.171337 ACATTTCATTCCAGCATACAACAAAAC 59.829 33.333 0.00 0.00 0.00 2.43
1978 2297 7.215789 ACATTTCATTCCAGCATACAACAAAA 58.784 30.769 0.00 0.00 0.00 2.44
1991 2310 2.984562 TGCGAGCTACATTTCATTCCA 58.015 42.857 0.00 0.00 0.00 3.53
1996 2315 4.385358 TGAGTATGCGAGCTACATTTCA 57.615 40.909 7.00 8.76 0.00 2.69
2009 2328 6.240894 TCATTAAGGATTGGGATGAGTATGC 58.759 40.000 0.00 0.00 0.00 3.14
2013 2332 6.552350 CCATTTCATTAAGGATTGGGATGAGT 59.448 38.462 10.31 0.00 29.50 3.41
2044 2363 7.792364 TGAATAAGGATAGGGATGAATACGT 57.208 36.000 0.00 0.00 0.00 3.57
2046 2365 9.319143 CGATTGAATAAGGATAGGGATGAATAC 57.681 37.037 0.00 0.00 0.00 1.89
2057 2376 5.546110 TGGATGGTCCGATTGAATAAGGATA 59.454 40.000 5.36 0.30 40.17 2.59
2090 2409 5.191722 TCCCACTTTAGCTACTTCATGGATT 59.808 40.000 0.00 0.00 0.00 3.01
2095 2414 8.306761 CAATTTTTCCCACTTTAGCTACTTCAT 58.693 33.333 0.00 0.00 0.00 2.57
2104 2423 6.101997 GGAGCATCAATTTTTCCCACTTTAG 58.898 40.000 0.00 0.00 36.25 1.85
2105 2424 5.541868 TGGAGCATCAATTTTTCCCACTTTA 59.458 36.000 0.00 0.00 36.25 1.85
2108 2427 3.509442 TGGAGCATCAATTTTTCCCACT 58.491 40.909 0.00 0.00 36.25 4.00
2109 2428 3.511146 TCTGGAGCATCAATTTTTCCCAC 59.489 43.478 0.00 0.00 36.25 4.61
2110 2429 3.777087 TCTGGAGCATCAATTTTTCCCA 58.223 40.909 0.00 0.00 36.25 4.37
2111 2430 4.463891 TCTTCTGGAGCATCAATTTTTCCC 59.536 41.667 0.00 0.00 36.25 3.97
2134 2453 8.352942 CACAAATTTGAGTAAAAACTAGAGGCT 58.647 33.333 24.64 0.00 0.00 4.58
2147 2466 5.070001 ACCAGCTAAGCACAAATTTGAGTA 58.930 37.500 24.64 9.29 0.00 2.59
2179 2498 7.391148 TGAAGGGCAATACTAACATCTTTTC 57.609 36.000 0.00 0.00 0.00 2.29
2189 2508 4.473196 TGAGGTTGATGAAGGGCAATACTA 59.527 41.667 0.00 0.00 0.00 1.82
2192 2511 3.010027 TGTGAGGTTGATGAAGGGCAATA 59.990 43.478 0.00 0.00 0.00 1.90
2212 2531 5.201243 TGTCACTACTACTATGAGCCATGT 58.799 41.667 0.00 0.00 0.00 3.21
2224 2543 7.873505 AGAAAGAAGGAAACATGTCACTACTAC 59.126 37.037 0.00 0.00 0.00 2.73
2228 2547 8.375506 ACATAGAAAGAAGGAAACATGTCACTA 58.624 33.333 0.00 0.00 0.00 2.74
2232 2551 7.174946 TCCAACATAGAAAGAAGGAAACATGTC 59.825 37.037 0.00 0.00 0.00 3.06
2233 2552 7.004086 TCCAACATAGAAAGAAGGAAACATGT 58.996 34.615 0.00 0.00 0.00 3.21
2242 2561 3.181516 GCGTGCTCCAACATAGAAAGAAG 60.182 47.826 0.00 0.00 0.00 2.85
2262 2581 0.234884 GAAAGGGACAACAGAACGCG 59.765 55.000 3.53 3.53 0.00 6.01
2264 2583 2.143925 GGAGAAAGGGACAACAGAACG 58.856 52.381 0.00 0.00 0.00 3.95
2268 2587 2.104792 TGTCTGGAGAAAGGGACAACAG 59.895 50.000 0.00 0.00 36.04 3.16
2280 2599 5.924356 TCAGTTACACAATTTGTCTGGAGA 58.076 37.500 13.11 1.41 39.91 3.71
2285 2604 6.601613 TCCAGTTTCAGTTACACAATTTGTCT 59.398 34.615 0.00 0.00 39.91 3.41
2288 2607 6.795399 ACTCCAGTTTCAGTTACACAATTTG 58.205 36.000 0.00 0.00 0.00 2.32
2296 2615 3.986277 TCCGAACTCCAGTTTCAGTTAC 58.014 45.455 0.00 0.00 38.56 2.50
2298 2617 2.434702 ACTCCGAACTCCAGTTTCAGTT 59.565 45.455 0.00 0.00 38.56 3.16
2300 2619 2.035961 TGACTCCGAACTCCAGTTTCAG 59.964 50.000 0.00 0.00 38.56 3.02
2302 2621 2.610727 CCTGACTCCGAACTCCAGTTTC 60.611 54.545 0.00 0.00 38.56 2.78
2306 2625 1.135915 CATCCTGACTCCGAACTCCAG 59.864 57.143 0.00 0.00 0.00 3.86
2340 2659 3.814504 ATGGTTCAGTGGGAGTTCAAT 57.185 42.857 0.00 0.00 0.00 2.57
2341 2660 3.221771 CAATGGTTCAGTGGGAGTTCAA 58.778 45.455 0.00 0.00 0.00 2.69
2342 2661 2.174639 ACAATGGTTCAGTGGGAGTTCA 59.825 45.455 0.63 0.00 33.50 3.18
2352 2671 1.167851 ATGCCGACACAATGGTTCAG 58.832 50.000 0.00 0.00 0.00 3.02
2363 2682 2.627699 TGATCTATGCTGTATGCCGACA 59.372 45.455 0.00 0.00 42.00 4.35
2364 2683 3.303881 TGATCTATGCTGTATGCCGAC 57.696 47.619 0.00 0.00 42.00 4.79
2367 2686 4.013267 ACCTTGATCTATGCTGTATGCC 57.987 45.455 0.00 0.00 42.00 4.40
2373 2692 4.938080 ACTTCGTACCTTGATCTATGCTG 58.062 43.478 0.00 0.00 0.00 4.41
2375 2694 9.640963 AAATATACTTCGTACCTTGATCTATGC 57.359 33.333 0.00 0.00 0.00 3.14
2382 2701 7.774134 TGCACTAAATATACTTCGTACCTTGA 58.226 34.615 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.