Multiple sequence alignment - TraesCS6D01G256400

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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 TraesCS6D01G256400 chr6D 100.000 3437 0 0 1 3437 362858342 362861778 0.000000e+00 6348.0
1 TraesCS6D01G256400 chr6D 93.590 1482 73 7 581 2057 362633807 362635271 0.000000e+00 2191.0
2 TraesCS6D01G256400 chr6D 83.041 1539 159 52 780 2267 362953471 362954958 0.000000e+00 1303.0
3 TraesCS6D01G256400 chr6D 88.011 1101 75 12 1157 2242 362887991 362889049 0.000000e+00 1249.0
4 TraesCS6D01G256400 chr6D 90.113 708 47 6 2054 2747 362635374 362636072 0.000000e+00 898.0
5 TraesCS6D01G256400 chr6D 88.262 656 47 19 2507 3141 362236599 362237245 0.000000e+00 758.0
6 TraesCS6D01G256400 chr6D 86.098 410 39 9 2749 3148 362902267 362902668 3.170000e-115 425.0
7 TraesCS6D01G256400 chr6D 86.389 360 33 12 2789 3141 362636302 362636652 2.500000e-101 379.0
8 TraesCS6D01G256400 chr6D 89.545 220 16 1 2292 2511 362232349 362232561 4.370000e-69 272.0
9 TraesCS6D01G256400 chr6D 77.800 491 45 28 588 1035 362887469 362887938 9.530000e-61 244.0
10 TraesCS6D01G256400 chr6D 93.600 125 7 1 1 124 362633362 362633486 5.860000e-43 185.0
11 TraesCS6D01G256400 chr6D 94.624 93 5 0 431 523 362633726 362633818 9.940000e-31 145.0
12 TraesCS6D01G256400 chr6D 93.220 59 4 0 526 584 414076836 414076894 1.700000e-13 87.9
13 TraesCS6D01G256400 chr6D 91.667 48 3 1 2343 2390 362954965 362955011 7.960000e-07 65.8
14 TraesCS6D01G256400 chr6B 93.011 2876 147 22 581 3437 543824987 543827827 0.000000e+00 4148.0
15 TraesCS6D01G256400 chr6B 83.072 1146 110 40 1150 2267 544092082 544093171 0.000000e+00 965.0
16 TraesCS6D01G256400 chr6B 85.192 520 53 13 1523 2025 543940450 543940962 2.370000e-141 512.0
17 TraesCS6D01G256400 chr6B 88.372 430 33 6 594 1008 543909627 543910054 5.120000e-138 501.0
18 TraesCS6D01G256400 chr6B 82.478 565 71 15 2248 2800 543960617 543961165 1.440000e-128 470.0
19 TraesCS6D01G256400 chr6B 79.002 481 58 28 581 1047 544091563 544092014 4.340000e-74 289.0
20 TraesCS6D01G256400 chr6B 84.583 240 17 4 2025 2252 543959893 543960124 1.610000e-53 220.0
21 TraesCS6D01G256400 chr6B 87.218 133 6 5 180 312 624474324 624474445 1.290000e-29 141.0
22 TraesCS6D01G256400 chr6B 84.672 137 17 3 180 314 413910089 413910223 2.150000e-27 134.0
23 TraesCS6D01G256400 chr6A 90.204 2062 112 25 704 2742 502928586 502930580 0.000000e+00 2606.0
24 TraesCS6D01G256400 chr6A 86.910 1039 77 14 1148 2159 503229976 503230982 0.000000e+00 1110.0
25 TraesCS6D01G256400 chr6A 86.957 943 73 30 1171 2108 503248753 503249650 0.000000e+00 1014.0
26 TraesCS6D01G256400 chr6A 81.466 491 46 19 581 1047 503248207 503248676 9.070000e-96 361.0
27 TraesCS6D01G256400 chr6A 86.047 301 28 6 2765 3061 502930979 502931269 9.260000e-81 311.0
28 TraesCS6D01G256400 chr6A 79.375 480 56 21 590 1047 503229451 503229909 7.210000e-77 298.0
29 TraesCS6D01G256400 chr6A 89.109 101 9 2 2155 2253 503231006 503231106 1.300000e-24 124.0
30 TraesCS6D01G256400 chr6A 92.683 82 6 0 1075 1156 516341674 516341755 6.030000e-23 119.0
31 TraesCS6D01G256400 chr6A 89.394 66 6 1 3 67 94310957 94310892 7.910000e-12 82.4
32 TraesCS6D01G256400 chr6A 94.231 52 3 0 444 495 502927795 502927846 2.840000e-11 80.5
33 TraesCS6D01G256400 chr2B 88.353 601 56 5 1075 1675 774846094 774846680 0.000000e+00 710.0
34 TraesCS6D01G256400 chr7D 92.248 129 10 0 180 308 563897828 563897700 2.110000e-42 183.0
35 TraesCS6D01G256400 chr7D 89.394 66 6 1 3 67 358198679 358198744 7.910000e-12 82.4
36 TraesCS6D01G256400 chr7D 87.879 66 7 1 3 67 294658607 294658672 3.680000e-10 76.8
37 TraesCS6D01G256400 chr7D 87.879 66 6 2 3 67 623762539 623762475 3.680000e-10 76.8
38 TraesCS6D01G256400 chr7A 89.130 138 11 2 180 314 725157442 725157306 5.900000e-38 169.0
39 TraesCS6D01G256400 chr7A 85.714 133 19 0 180 312 432145407 432145275 1.290000e-29 141.0
40 TraesCS6D01G256400 chr3D 85.401 137 15 4 180 314 597918868 597918735 1.660000e-28 137.0
41 TraesCS6D01G256400 chr3D 83.942 137 18 3 180 314 396563717 396563851 1.000000e-25 128.0
42 TraesCS6D01G256400 chr3D 91.525 59 5 0 526 584 596653258 596653200 7.910000e-12 82.4
43 TraesCS6D01G256400 chr3D 87.879 66 7 1 3 67 562580498 562580433 3.680000e-10 76.8
44 TraesCS6D01G256400 chr7B 84.444 135 21 0 180 314 5089075 5089209 2.150000e-27 134.0
45 TraesCS6D01G256400 chr7B 86.957 69 8 1 3 70 85275768 85275700 3.680000e-10 76.8
46 TraesCS6D01G256400 chr4B 84.328 134 17 3 180 311 212492241 212492372 1.000000e-25 128.0
47 TraesCS6D01G256400 chr3A 96.491 57 2 0 526 582 706116607 706116663 1.020000e-15 95.3
48 TraesCS6D01G256400 chr5B 94.915 59 3 0 526 584 8014045 8013987 3.650000e-15 93.5
49 TraesCS6D01G256400 chr5A 94.915 59 3 0 526 584 38018102 38018044 3.650000e-15 93.5
50 TraesCS6D01G256400 chr5A 89.831 59 6 0 526 584 631255798 631255856 3.680000e-10 76.8
51 TraesCS6D01G256400 chr5D 90.909 66 5 1 3 67 412829231 412829166 1.700000e-13 87.9
52 TraesCS6D01G256400 chr1A 93.220 59 4 0 526 584 516740632 516740690 1.700000e-13 87.9
53 TraesCS6D01G256400 chr3B 91.525 59 5 0 526 584 75362837 75362895 7.910000e-12 82.4
54 TraesCS6D01G256400 chr2D 87.879 66 7 1 3 67 67196000 67195935 3.680000e-10 76.8
55 TraesCS6D01G256400 chr4D 84.932 73 4 7 512 582 97956126 97956059 2.210000e-07 67.6


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 TraesCS6D01G256400 chr6D 362858342 362861778 3436 False 6348.000000 6348 100.000000 1 3437 1 chr6D.!!$F3 3436
1 TraesCS6D01G256400 chr6D 362633362 362636652 3290 False 759.600000 2191 91.663200 1 3141 5 chr6D.!!$F6 3140
2 TraesCS6D01G256400 chr6D 362236599 362237245 646 False 758.000000 758 88.262000 2507 3141 1 chr6D.!!$F2 634
3 TraesCS6D01G256400 chr6D 362887469 362889049 1580 False 746.500000 1249 82.905500 588 2242 2 chr6D.!!$F7 1654
4 TraesCS6D01G256400 chr6D 362953471 362955011 1540 False 684.400000 1303 87.354000 780 2390 2 chr6D.!!$F8 1610
5 TraesCS6D01G256400 chr6B 543824987 543827827 2840 False 4148.000000 4148 93.011000 581 3437 1 chr6B.!!$F2 2856
6 TraesCS6D01G256400 chr6B 544091563 544093171 1608 False 627.000000 965 81.037000 581 2267 2 chr6B.!!$F7 1686
7 TraesCS6D01G256400 chr6B 543940450 543940962 512 False 512.000000 512 85.192000 1523 2025 1 chr6B.!!$F4 502
8 TraesCS6D01G256400 chr6B 543959893 543961165 1272 False 345.000000 470 83.530500 2025 2800 2 chr6B.!!$F6 775
9 TraesCS6D01G256400 chr6A 502927795 502931269 3474 False 999.166667 2606 90.160667 444 3061 3 chr6A.!!$F2 2617
10 TraesCS6D01G256400 chr6A 503248207 503249650 1443 False 687.500000 1014 84.211500 581 2108 2 chr6A.!!$F4 1527
11 TraesCS6D01G256400 chr6A 503229451 503231106 1655 False 510.666667 1110 85.131333 590 2253 3 chr6A.!!$F3 1663
12 TraesCS6D01G256400 chr2B 774846094 774846680 586 False 710.000000 710 88.353000 1075 1675 1 chr2B.!!$F1 600


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
533 1000 0.316204 GCATGGCCATGGAGTAATGC 59.684 55.0 39.72 25.06 39.16 3.56 F
1200 2029 0.529773 GATCATGGCGTTAGTGCGGA 60.530 55.0 0.00 0.00 35.06 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1559 2397 0.319728 TCTGAGTCAGGCTGAAGCAC 59.680 55.0 20.62 7.41 44.36 4.40 R
2674 4223 0.577269 CCTGCACGAGTAATTAGCGC 59.423 55.0 0.00 0.00 0.00 5.92 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
28 30 5.221130 AGCTTTACGTAGTTGACTTCAGAC 58.779 41.667 0.00 0.00 37.78 3.51
58 60 2.178912 TGCAGAGTAAAAAGGACCCG 57.821 50.000 0.00 0.00 0.00 5.28
60 62 2.304761 TGCAGAGTAAAAAGGACCCGAT 59.695 45.455 0.00 0.00 0.00 4.18
71 73 1.831736 AGGACCCGATGGAGTAAGTTG 59.168 52.381 0.00 0.00 34.81 3.16
124 126 6.318648 GGTGAGCATCCATTTATGACAAGTTA 59.681 38.462 0.00 0.00 0.00 2.24
125 127 7.013655 GGTGAGCATCCATTTATGACAAGTTAT 59.986 37.037 0.00 0.00 0.00 1.89
126 128 9.056005 GTGAGCATCCATTTATGACAAGTTATA 57.944 33.333 0.00 0.00 0.00 0.98
127 129 9.056005 TGAGCATCCATTTATGACAAGTTATAC 57.944 33.333 0.00 0.00 0.00 1.47
128 130 8.087982 AGCATCCATTTATGACAAGTTATACG 57.912 34.615 0.00 0.00 0.00 3.06
129 131 7.173218 AGCATCCATTTATGACAAGTTATACGG 59.827 37.037 0.00 0.00 0.00 4.02
130 132 7.172532 GCATCCATTTATGACAAGTTATACGGA 59.827 37.037 0.00 0.00 0.00 4.69
131 133 9.219603 CATCCATTTATGACAAGTTATACGGAT 57.780 33.333 0.00 0.00 0.00 4.18
133 135 9.701098 TCCATTTATGACAAGTTATACGGATAC 57.299 33.333 0.00 0.00 0.00 2.24
134 136 8.932791 CCATTTATGACAAGTTATACGGATACC 58.067 37.037 0.00 0.00 0.00 2.73
135 137 9.483916 CATTTATGACAAGTTATACGGATACCA 57.516 33.333 0.00 0.00 0.00 3.25
136 138 9.706691 ATTTATGACAAGTTATACGGATACCAG 57.293 33.333 0.00 0.00 0.00 4.00
137 139 6.726490 ATGACAAGTTATACGGATACCAGT 57.274 37.500 0.00 0.00 0.00 4.00
138 140 5.898174 TGACAAGTTATACGGATACCAGTG 58.102 41.667 0.00 0.00 0.00 3.66
139 141 5.419788 TGACAAGTTATACGGATACCAGTGT 59.580 40.000 0.00 0.00 0.00 3.55
140 142 6.602803 TGACAAGTTATACGGATACCAGTGTA 59.397 38.462 0.00 0.00 0.00 2.90
141 143 7.122501 TGACAAGTTATACGGATACCAGTGTAA 59.877 37.037 0.00 0.00 0.00 2.41
142 144 7.486647 ACAAGTTATACGGATACCAGTGTAAG 58.513 38.462 0.00 0.00 0.00 2.34
143 145 7.340232 ACAAGTTATACGGATACCAGTGTAAGA 59.660 37.037 0.00 0.00 0.00 2.10
144 146 7.886629 AGTTATACGGATACCAGTGTAAGAA 57.113 36.000 0.00 0.00 0.00 2.52
145 147 7.710896 AGTTATACGGATACCAGTGTAAGAAC 58.289 38.462 0.00 0.00 0.00 3.01
146 148 3.881937 ACGGATACCAGTGTAAGAACC 57.118 47.619 0.00 0.00 0.00 3.62
147 149 2.498885 ACGGATACCAGTGTAAGAACCC 59.501 50.000 0.00 0.00 0.00 4.11
148 150 2.498481 CGGATACCAGTGTAAGAACCCA 59.502 50.000 0.00 0.00 0.00 4.51
149 151 3.134081 CGGATACCAGTGTAAGAACCCAT 59.866 47.826 0.00 0.00 0.00 4.00
150 152 4.704965 GGATACCAGTGTAAGAACCCATC 58.295 47.826 0.00 0.00 0.00 3.51
151 153 4.163458 GGATACCAGTGTAAGAACCCATCA 59.837 45.833 0.00 0.00 0.00 3.07
152 154 5.338871 GGATACCAGTGTAAGAACCCATCAA 60.339 44.000 0.00 0.00 0.00 2.57
153 155 4.657814 ACCAGTGTAAGAACCCATCAAT 57.342 40.909 0.00 0.00 0.00 2.57
154 156 5.772393 ACCAGTGTAAGAACCCATCAATA 57.228 39.130 0.00 0.00 0.00 1.90
155 157 6.134535 ACCAGTGTAAGAACCCATCAATAA 57.865 37.500 0.00 0.00 0.00 1.40
156 158 6.548321 ACCAGTGTAAGAACCCATCAATAAA 58.452 36.000 0.00 0.00 0.00 1.40
157 159 7.007723 ACCAGTGTAAGAACCCATCAATAAAA 58.992 34.615 0.00 0.00 0.00 1.52
158 160 7.176690 ACCAGTGTAAGAACCCATCAATAAAAG 59.823 37.037 0.00 0.00 0.00 2.27
159 161 7.029563 CAGTGTAAGAACCCATCAATAAAAGC 58.970 38.462 0.00 0.00 0.00 3.51
160 162 6.152831 AGTGTAAGAACCCATCAATAAAAGCC 59.847 38.462 0.00 0.00 0.00 4.35
161 163 6.013379 TGTAAGAACCCATCAATAAAAGCCA 58.987 36.000 0.00 0.00 0.00 4.75
162 164 6.667414 TGTAAGAACCCATCAATAAAAGCCAT 59.333 34.615 0.00 0.00 0.00 4.40
163 165 5.859205 AGAACCCATCAATAAAAGCCATC 57.141 39.130 0.00 0.00 0.00 3.51
164 166 5.522641 AGAACCCATCAATAAAAGCCATCT 58.477 37.500 0.00 0.00 0.00 2.90
165 167 5.960202 AGAACCCATCAATAAAAGCCATCTT 59.040 36.000 0.00 0.00 0.00 2.40
166 168 6.441604 AGAACCCATCAATAAAAGCCATCTTT 59.558 34.615 0.00 0.00 43.94 2.52
197 199 7.789202 AGATGGATGTTATGCTACTATGAGT 57.211 36.000 0.00 0.00 0.00 3.41
198 200 7.835822 AGATGGATGTTATGCTACTATGAGTC 58.164 38.462 0.00 0.00 0.00 3.36
199 201 6.976934 TGGATGTTATGCTACTATGAGTCA 57.023 37.500 0.00 0.00 0.00 3.41
200 202 7.544804 TGGATGTTATGCTACTATGAGTCAT 57.455 36.000 11.12 11.12 0.00 3.06
201 203 7.381323 TGGATGTTATGCTACTATGAGTCATG 58.619 38.462 16.15 8.24 0.00 3.07
202 204 6.312426 GGATGTTATGCTACTATGAGTCATGC 59.688 42.308 16.15 10.71 0.00 4.06
203 205 6.160576 TGTTATGCTACTATGAGTCATGCA 57.839 37.500 16.15 15.92 35.05 3.96
204 206 6.762333 TGTTATGCTACTATGAGTCATGCAT 58.238 36.000 24.03 24.03 40.31 3.96
205 207 6.647895 TGTTATGCTACTATGAGTCATGCATG 59.352 38.462 26.85 21.07 38.86 4.06
206 208 4.942761 TGCTACTATGAGTCATGCATGA 57.057 40.909 25.42 25.42 29.09 3.07
221 223 8.021955 GTCATGCATGACGATAAATAAGATGA 57.978 34.615 36.65 7.31 46.46 2.92
222 224 8.663025 GTCATGCATGACGATAAATAAGATGAT 58.337 33.333 36.65 0.00 46.46 2.45
223 225 9.223099 TCATGCATGACGATAAATAAGATGATT 57.777 29.630 25.42 0.00 0.00 2.57
224 226 9.836076 CATGCATGACGATAAATAAGATGATTT 57.164 29.630 22.59 0.00 33.60 2.17
293 295 9.928618 ATAGACTAGTACCATATGCATGATACT 57.071 33.333 10.16 13.05 42.99 2.12
295 297 9.755122 AGACTAGTACCATATGCATGATACTAA 57.245 33.333 10.16 0.00 41.34 2.24
310 312 9.765795 GCATGATACTAATGTATAATACTCCCC 57.234 37.037 0.00 0.00 39.29 4.81
320 322 8.808240 ATGTATAATACTCCCCACTTTAAGGA 57.192 34.615 0.00 0.00 0.00 3.36
321 323 8.626917 TGTATAATACTCCCCACTTTAAGGAA 57.373 34.615 0.00 0.00 0.00 3.36
322 324 8.488668 TGTATAATACTCCCCACTTTAAGGAAC 58.511 37.037 0.00 0.00 0.00 3.62
323 325 5.853572 AATACTCCCCACTTTAAGGAACA 57.146 39.130 0.00 0.00 0.00 3.18
324 326 6.402981 AATACTCCCCACTTTAAGGAACAT 57.597 37.500 0.00 0.00 0.00 2.71
325 327 7.519347 AATACTCCCCACTTTAAGGAACATA 57.481 36.000 0.00 0.00 0.00 2.29
326 328 5.175388 ACTCCCCACTTTAAGGAACATAC 57.825 43.478 0.00 0.00 0.00 2.39
327 329 4.850386 ACTCCCCACTTTAAGGAACATACT 59.150 41.667 0.00 0.00 0.00 2.12
328 330 6.027482 ACTCCCCACTTTAAGGAACATACTA 58.973 40.000 0.00 0.00 0.00 1.82
329 331 6.502863 ACTCCCCACTTTAAGGAACATACTAA 59.497 38.462 0.00 0.00 0.00 2.24
330 332 7.184022 ACTCCCCACTTTAAGGAACATACTAAT 59.816 37.037 0.00 0.00 0.00 1.73
331 333 7.343357 TCCCCACTTTAAGGAACATACTAATG 58.657 38.462 0.00 0.00 39.17 1.90
360 362 6.936968 ACTCCCTAATAACTTCTTGACACT 57.063 37.500 0.00 0.00 0.00 3.55
365 367 6.037610 CCCTAATAACTTCTTGACACTGATGC 59.962 42.308 0.00 0.00 0.00 3.91
385 387 3.453717 TGCACTGCTTCTTGATATCTCCT 59.546 43.478 3.98 0.00 0.00 3.69
386 388 3.808726 GCACTGCTTCTTGATATCTCCTG 59.191 47.826 3.98 0.00 0.00 3.86
387 389 3.808726 CACTGCTTCTTGATATCTCCTGC 59.191 47.826 3.98 3.29 0.00 4.85
388 390 3.453717 ACTGCTTCTTGATATCTCCTGCA 59.546 43.478 3.98 7.38 0.00 4.41
390 392 5.045012 TGCTTCTTGATATCTCCTGCATT 57.955 39.130 3.98 0.00 0.00 3.56
391 393 5.443283 TGCTTCTTGATATCTCCTGCATTT 58.557 37.500 3.98 0.00 0.00 2.32
392 394 5.889853 TGCTTCTTGATATCTCCTGCATTTT 59.110 36.000 3.98 0.00 0.00 1.82
393 395 7.056006 TGCTTCTTGATATCTCCTGCATTTTA 58.944 34.615 3.98 0.00 0.00 1.52
394 396 7.722728 TGCTTCTTGATATCTCCTGCATTTTAT 59.277 33.333 3.98 0.00 0.00 1.40
424 426 2.391616 TGCTTCTTGACATCGATGCT 57.608 45.000 25.11 12.36 33.14 3.79
425 427 2.703416 TGCTTCTTGACATCGATGCTT 58.297 42.857 25.11 6.78 33.14 3.91
428 430 3.125829 GCTTCTTGACATCGATGCTTTGA 59.874 43.478 25.11 15.01 0.00 2.69
430 432 5.007039 GCTTCTTGACATCGATGCTTTGATA 59.993 40.000 25.11 5.05 0.00 2.15
431 433 6.457392 GCTTCTTGACATCGATGCTTTGATAA 60.457 38.462 25.11 9.99 0.00 1.75
434 436 8.837788 TCTTGACATCGATGCTTTGATAATAT 57.162 30.769 25.11 0.58 0.00 1.28
435 437 8.715088 TCTTGACATCGATGCTTTGATAATATG 58.285 33.333 25.11 0.00 0.00 1.78
436 438 7.967890 TGACATCGATGCTTTGATAATATGT 57.032 32.000 25.11 1.42 0.00 2.29
437 439 9.487790 TTGACATCGATGCTTTGATAATATGTA 57.512 29.630 25.11 0.00 0.00 2.29
438 440 9.487790 TGACATCGATGCTTTGATAATATGTAA 57.512 29.630 25.11 0.00 0.00 2.41
500 967 1.661821 CGTATGCGGCCTAGCTGAC 60.662 63.158 0.00 0.00 37.02 3.51
533 1000 0.316204 GCATGGCCATGGAGTAATGC 59.684 55.000 39.72 25.06 39.16 3.56
534 1001 1.991121 CATGGCCATGGAGTAATGCT 58.009 50.000 34.31 0.00 35.24 3.79
535 1002 2.815215 GCATGGCCATGGAGTAATGCTA 60.815 50.000 39.72 0.00 39.16 3.49
536 1003 2.638480 TGGCCATGGAGTAATGCTAC 57.362 50.000 18.40 0.00 0.00 3.58
537 1004 1.843206 TGGCCATGGAGTAATGCTACA 59.157 47.619 18.40 0.00 43.31 2.74
538 1005 2.222027 GGCCATGGAGTAATGCTACAC 58.778 52.381 18.40 0.00 41.66 2.90
539 1006 1.867233 GCCATGGAGTAATGCTACACG 59.133 52.381 18.40 0.00 41.66 4.49
540 1007 2.741878 GCCATGGAGTAATGCTACACGT 60.742 50.000 18.40 0.00 41.66 4.49
541 1008 3.491964 GCCATGGAGTAATGCTACACGTA 60.492 47.826 18.40 0.00 41.66 3.57
542 1009 4.049186 CCATGGAGTAATGCTACACGTAC 58.951 47.826 5.56 0.00 41.66 3.67
543 1010 4.440940 CCATGGAGTAATGCTACACGTACA 60.441 45.833 5.56 0.00 41.66 2.90
544 1011 4.787260 TGGAGTAATGCTACACGTACAA 57.213 40.909 0.00 0.00 31.86 2.41
545 1012 5.136816 TGGAGTAATGCTACACGTACAAA 57.863 39.130 0.00 0.00 31.86 2.83
546 1013 4.925054 TGGAGTAATGCTACACGTACAAAC 59.075 41.667 0.00 0.00 31.86 2.93
547 1014 4.925054 GGAGTAATGCTACACGTACAAACA 59.075 41.667 0.00 0.00 0.00 2.83
548 1015 5.406175 GGAGTAATGCTACACGTACAAACAA 59.594 40.000 0.00 0.00 0.00 2.83
549 1016 6.400727 GGAGTAATGCTACACGTACAAACAAG 60.401 42.308 0.00 0.00 0.00 3.16
550 1017 5.987347 AGTAATGCTACACGTACAAACAAGT 59.013 36.000 0.00 0.00 0.00 3.16
551 1018 5.744666 AATGCTACACGTACAAACAAGTT 57.255 34.783 0.00 0.00 0.00 2.66
552 1019 6.847956 AATGCTACACGTACAAACAAGTTA 57.152 33.333 0.00 0.00 0.00 2.24
553 1020 5.640218 TGCTACACGTACAAACAAGTTAC 57.360 39.130 0.00 0.00 0.00 2.50
554 1021 5.107824 TGCTACACGTACAAACAAGTTACA 58.892 37.500 0.00 0.00 0.00 2.41
555 1022 5.754406 TGCTACACGTACAAACAAGTTACAT 59.246 36.000 0.00 0.00 0.00 2.29
556 1023 6.068931 GCTACACGTACAAACAAGTTACATG 58.931 40.000 0.00 0.00 0.00 3.21
557 1024 5.412526 ACACGTACAAACAAGTTACATGG 57.587 39.130 0.00 0.00 0.00 3.66
558 1025 4.877251 ACACGTACAAACAAGTTACATGGT 59.123 37.500 0.00 0.00 0.00 3.55
559 1026 5.354792 ACACGTACAAACAAGTTACATGGTT 59.645 36.000 0.00 0.00 0.00 3.67
560 1027 6.127952 ACACGTACAAACAAGTTACATGGTTT 60.128 34.615 0.00 0.00 34.03 3.27
561 1028 6.748198 CACGTACAAACAAGTTACATGGTTTT 59.252 34.615 0.00 0.00 31.57 2.43
562 1029 7.909121 CACGTACAAACAAGTTACATGGTTTTA 59.091 33.333 0.00 0.00 31.57 1.52
563 1030 8.623030 ACGTACAAACAAGTTACATGGTTTTAT 58.377 29.630 0.00 0.00 31.57 1.40
571 1038 9.020731 ACAAGTTACATGGTTTTATAAAGAGGG 57.979 33.333 0.00 0.00 0.00 4.30
572 1039 9.020731 CAAGTTACATGGTTTTATAAAGAGGGT 57.979 33.333 0.00 0.00 0.00 4.34
573 1040 9.596308 AAGTTACATGGTTTTATAAAGAGGGTT 57.404 29.630 0.00 0.00 0.00 4.11
610 1077 1.513622 GTGAGAAGAGAGGGGTCGC 59.486 63.158 0.00 0.00 0.00 5.19
644 1114 2.757917 GGAGAGCCTGTCGCCTCT 60.758 66.667 0.00 0.00 41.83 3.69
710 1455 3.244387 GCTGTTCCTCTTCCTTCAGTTCT 60.244 47.826 0.00 0.00 0.00 3.01
748 1507 2.027192 GCACACAATCCCTCCTTCAGTA 60.027 50.000 0.00 0.00 0.00 2.74
759 1518 4.081642 CCCTCCTTCAGTACTTCATTTCGA 60.082 45.833 0.00 0.00 0.00 3.71
778 1537 2.139118 GAAGCTCCACTGAGTGAACAC 58.861 52.381 15.33 0.44 40.95 3.32
960 1760 1.108132 GTTTTGTTGTACCGGCCCCA 61.108 55.000 0.00 0.00 0.00 4.96
1142 1970 1.792006 CTGTCACCCACGGAAACTAC 58.208 55.000 0.00 0.00 32.23 2.73
1156 1984 5.757808 ACGGAAACTACTAGTACTAGCTAGC 59.242 44.000 26.54 6.62 41.49 3.42
1200 2029 0.529773 GATCATGGCGTTAGTGCGGA 60.530 55.000 0.00 0.00 35.06 5.54
1540 2378 3.896133 GCCGGCGTCGACCATAGA 61.896 66.667 12.58 0.00 39.00 1.98
1980 2860 2.430367 GAGCTGGTTCCCAACGGT 59.570 61.111 0.00 0.00 30.80 4.83
2135 3133 3.902063 CGCCATCTTGTCGTCGCG 61.902 66.667 0.00 0.00 0.00 5.87
2177 3212 1.677637 GCTTAGCTAGCCTCCGTGGT 61.678 60.000 12.13 0.00 44.48 4.16
2301 3836 4.591924 GCCACTATGTACCCTATTACAGGT 59.408 45.833 0.00 0.00 43.80 4.00
2320 3855 3.965347 AGGTGACCTAGGTTGCGTTATAT 59.035 43.478 17.53 0.00 28.47 0.86
2321 3856 4.038883 AGGTGACCTAGGTTGCGTTATATC 59.961 45.833 17.53 0.00 28.47 1.63
2322 3857 4.038883 GGTGACCTAGGTTGCGTTATATCT 59.961 45.833 17.53 0.00 0.00 1.98
2323 3858 5.452917 GGTGACCTAGGTTGCGTTATATCTT 60.453 44.000 17.53 0.00 0.00 2.40
2324 3859 6.239120 GGTGACCTAGGTTGCGTTATATCTTA 60.239 42.308 17.53 0.00 0.00 2.10
2325 3860 7.376615 GTGACCTAGGTTGCGTTATATCTTAT 58.623 38.462 17.53 0.00 0.00 1.73
2326 3861 8.517878 GTGACCTAGGTTGCGTTATATCTTATA 58.482 37.037 17.53 0.00 0.00 0.98
2478 4016 0.889186 GCGAACATTCACTGTGGGGT 60.889 55.000 8.11 1.23 38.39 4.95
2545 4083 1.540146 GGCAATTTCAAGCCCAACGTT 60.540 47.619 0.00 0.00 45.18 3.99
2655 4198 9.434420 CATGCCTTTATAAAAGGATGTTTTCAA 57.566 29.630 20.05 0.00 39.81 2.69
2674 4223 5.018539 TCAATTAGGGAATACCACGAGTG 57.981 43.478 0.00 0.00 43.89 3.51
2751 4306 1.565067 TTCTCTTTACGGGGAGGGAC 58.435 55.000 0.00 0.00 0.00 4.46
2786 4717 1.522806 GTTGTCTCACCCGCACACA 60.523 57.895 0.00 0.00 0.00 3.72
2801 4732 4.332543 CCGCACACATCTTCAAGCTTTATA 59.667 41.667 0.00 0.00 0.00 0.98
2842 4774 4.907269 TGAGCCATGAGGTAAGATAATGGA 59.093 41.667 4.21 0.00 40.23 3.41
2884 4816 6.603201 TCGAAAGATATCCCTTCAAATTGCTT 59.397 34.615 13.03 0.00 33.31 3.91
2979 4915 5.999205 AATCCAAATTGAGCACAACCATA 57.001 34.783 0.00 0.00 38.90 2.74
2980 4916 5.999205 ATCCAAATTGAGCACAACCATAA 57.001 34.783 0.00 0.00 38.90 1.90
3103 5039 9.463443 AACATTAAGCACAAAACTAAAGCTAAG 57.537 29.630 0.00 0.00 34.66 2.18
3208 5144 1.658994 GTGGAAGGACAACACGTTGA 58.341 50.000 16.48 0.00 42.93 3.18
3213 5149 1.229428 AGGACAACACGTTGATGCTG 58.771 50.000 16.48 0.00 42.93 4.41
3222 5158 1.153706 GTTGATGCTGCCATGCACC 60.154 57.895 0.00 0.00 46.33 5.01
3259 5196 1.238896 TCCTCATCCTTCCCCCTCCT 61.239 60.000 0.00 0.00 0.00 3.69
3265 5202 1.162951 TCCTTCCCCCTCCTCTTCCT 61.163 60.000 0.00 0.00 0.00 3.36
3276 5213 1.887198 TCCTCTTCCTCTGACGACAAC 59.113 52.381 0.00 0.00 0.00 3.32
3284 5221 2.404215 CTCTGACGACAACGATTTGGT 58.596 47.619 0.00 0.00 42.66 3.67
3319 5256 1.862138 TCCTCCTCCACCTCCTCCA 60.862 63.158 0.00 0.00 0.00 3.86
3323 5260 0.263172 TCCTCCACCTCCTCCATCTC 59.737 60.000 0.00 0.00 0.00 2.75
3330 5267 1.227089 CTCCTCCATCTCGCCGTTG 60.227 63.158 0.00 0.00 0.00 4.10
3350 5288 2.814183 ATTCTGGCACGACGACCGAC 62.814 60.000 0.00 0.00 41.76 4.79
3363 5301 1.659098 CGACCGACCAAAGATGTTAGC 59.341 52.381 0.00 0.00 0.00 3.09
3371 5309 5.289675 CGACCAAAGATGTTAGCAGAAGTAG 59.710 44.000 0.00 0.00 0.00 2.57
3378 5316 3.074412 TGTTAGCAGAAGTAGGCAAAGC 58.926 45.455 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 60 8.732746 AATGTATACAACCAACTTACTCCATC 57.267 34.615 10.14 0.00 0.00 3.51
60 62 8.927675 AAAATGTATACAACCAACTTACTCCA 57.072 30.769 10.14 0.00 0.00 3.86
71 73 9.726438 AGCCTATCATCTAAAATGTATACAACC 57.274 33.333 10.14 0.00 0.00 3.77
107 109 9.701098 GTATCCGTATAACTTGTCATAAATGGA 57.299 33.333 0.00 0.00 0.00 3.41
124 126 4.343239 GGGTTCTTACACTGGTATCCGTAT 59.657 45.833 0.00 0.00 0.00 3.06
125 127 3.701040 GGGTTCTTACACTGGTATCCGTA 59.299 47.826 0.00 0.00 0.00 4.02
126 128 2.498885 GGGTTCTTACACTGGTATCCGT 59.501 50.000 0.00 0.00 0.00 4.69
127 129 2.498481 TGGGTTCTTACACTGGTATCCG 59.502 50.000 0.00 0.00 0.00 4.18
128 130 4.163458 TGATGGGTTCTTACACTGGTATCC 59.837 45.833 0.00 0.00 0.00 2.59
129 131 5.353394 TGATGGGTTCTTACACTGGTATC 57.647 43.478 0.00 0.00 0.00 2.24
130 132 5.772393 TTGATGGGTTCTTACACTGGTAT 57.228 39.130 0.00 0.00 0.00 2.73
131 133 5.772393 ATTGATGGGTTCTTACACTGGTA 57.228 39.130 0.00 0.00 0.00 3.25
132 134 4.657814 ATTGATGGGTTCTTACACTGGT 57.342 40.909 0.00 0.00 0.00 4.00
133 135 7.461182 TTTTATTGATGGGTTCTTACACTGG 57.539 36.000 0.00 0.00 0.00 4.00
134 136 7.029563 GCTTTTATTGATGGGTTCTTACACTG 58.970 38.462 0.00 0.00 0.00 3.66
135 137 6.152831 GGCTTTTATTGATGGGTTCTTACACT 59.847 38.462 0.00 0.00 0.00 3.55
136 138 6.071616 TGGCTTTTATTGATGGGTTCTTACAC 60.072 38.462 0.00 0.00 0.00 2.90
137 139 6.013379 TGGCTTTTATTGATGGGTTCTTACA 58.987 36.000 0.00 0.00 0.00 2.41
138 140 6.524101 TGGCTTTTATTGATGGGTTCTTAC 57.476 37.500 0.00 0.00 0.00 2.34
139 141 7.125391 AGATGGCTTTTATTGATGGGTTCTTA 58.875 34.615 0.00 0.00 0.00 2.10
140 142 5.960202 AGATGGCTTTTATTGATGGGTTCTT 59.040 36.000 0.00 0.00 0.00 2.52
141 143 5.522641 AGATGGCTTTTATTGATGGGTTCT 58.477 37.500 0.00 0.00 0.00 3.01
142 144 5.859205 AGATGGCTTTTATTGATGGGTTC 57.141 39.130 0.00 0.00 0.00 3.62
143 145 6.625532 AAAGATGGCTTTTATTGATGGGTT 57.374 33.333 0.00 0.00 41.43 4.11
171 173 8.654997 ACTCATAGTAGCATAACATCCATCTTT 58.345 33.333 0.00 0.00 0.00 2.52
180 182 6.160576 TGCATGACTCATAGTAGCATAACA 57.839 37.500 0.00 0.00 29.57 2.41
185 187 4.942761 TCATGCATGACTCATAGTAGCA 57.057 40.909 25.42 0.00 35.87 3.49
197 199 8.782339 ATCATCTTATTTATCGTCATGCATGA 57.218 30.769 25.42 25.42 0.00 3.07
198 200 9.836076 AAATCATCTTATTTATCGTCATGCATG 57.164 29.630 21.07 21.07 0.00 4.06
284 286 9.765795 GGGGAGTATTATACATTAGTATCATGC 57.234 37.037 5.11 0.00 41.15 4.06
294 296 9.232882 TCCTTAAAGTGGGGAGTATTATACATT 57.767 33.333 5.11 0.00 0.00 2.71
295 297 8.808240 TCCTTAAAGTGGGGAGTATTATACAT 57.192 34.615 5.11 0.00 0.00 2.29
296 298 8.488668 GTTCCTTAAAGTGGGGAGTATTATACA 58.511 37.037 5.11 0.00 0.00 2.29
297 299 8.488668 TGTTCCTTAAAGTGGGGAGTATTATAC 58.511 37.037 0.00 0.00 0.00 1.47
298 300 8.626917 TGTTCCTTAAAGTGGGGAGTATTATA 57.373 34.615 0.00 0.00 0.00 0.98
299 301 7.519347 TGTTCCTTAAAGTGGGGAGTATTAT 57.481 36.000 0.00 0.00 0.00 1.28
300 302 6.956102 TGTTCCTTAAAGTGGGGAGTATTA 57.044 37.500 0.00 0.00 0.00 0.98
301 303 5.853572 TGTTCCTTAAAGTGGGGAGTATT 57.146 39.130 0.00 0.00 0.00 1.89
302 304 6.677076 AGTATGTTCCTTAAAGTGGGGAGTAT 59.323 38.462 0.00 0.00 0.00 2.12
303 305 6.027482 AGTATGTTCCTTAAAGTGGGGAGTA 58.973 40.000 0.00 0.00 0.00 2.59
304 306 4.850386 AGTATGTTCCTTAAAGTGGGGAGT 59.150 41.667 0.00 0.00 0.00 3.85
305 307 5.437191 AGTATGTTCCTTAAAGTGGGGAG 57.563 43.478 0.00 0.00 0.00 4.30
306 308 6.956102 TTAGTATGTTCCTTAAAGTGGGGA 57.044 37.500 0.00 0.00 0.00 4.81
307 309 7.116736 ACATTAGTATGTTCCTTAAAGTGGGG 58.883 38.462 0.00 0.00 42.29 4.96
329 331 9.838339 CAAGAAGTTATTAGGGAGTATCAACAT 57.162 33.333 0.00 0.00 36.25 2.71
330 332 9.042450 TCAAGAAGTTATTAGGGAGTATCAACA 57.958 33.333 0.00 0.00 36.25 3.33
331 333 9.315525 GTCAAGAAGTTATTAGGGAGTATCAAC 57.684 37.037 0.00 0.00 36.25 3.18
332 334 9.042450 TGTCAAGAAGTTATTAGGGAGTATCAA 57.958 33.333 0.00 0.00 36.25 2.57
333 335 8.475639 GTGTCAAGAAGTTATTAGGGAGTATCA 58.524 37.037 0.00 0.00 36.25 2.15
334 336 8.697292 AGTGTCAAGAAGTTATTAGGGAGTATC 58.303 37.037 0.00 0.00 0.00 2.24
335 337 8.478877 CAGTGTCAAGAAGTTATTAGGGAGTAT 58.521 37.037 0.00 0.00 0.00 2.12
336 338 7.672660 TCAGTGTCAAGAAGTTATTAGGGAGTA 59.327 37.037 0.00 0.00 0.00 2.59
337 339 6.497259 TCAGTGTCAAGAAGTTATTAGGGAGT 59.503 38.462 0.00 0.00 0.00 3.85
338 340 6.936279 TCAGTGTCAAGAAGTTATTAGGGAG 58.064 40.000 0.00 0.00 0.00 4.30
339 341 6.928348 TCAGTGTCAAGAAGTTATTAGGGA 57.072 37.500 0.00 0.00 0.00 4.20
340 342 6.037610 GCATCAGTGTCAAGAAGTTATTAGGG 59.962 42.308 0.00 0.00 0.00 3.53
341 343 6.595326 TGCATCAGTGTCAAGAAGTTATTAGG 59.405 38.462 0.00 0.00 0.00 2.69
342 344 7.332926 AGTGCATCAGTGTCAAGAAGTTATTAG 59.667 37.037 0.00 0.00 0.00 1.73
343 345 7.118245 CAGTGCATCAGTGTCAAGAAGTTATTA 59.882 37.037 0.00 0.00 30.89 0.98
344 346 6.000219 AGTGCATCAGTGTCAAGAAGTTATT 59.000 36.000 0.00 0.00 0.00 1.40
360 362 5.032327 AGATATCAAGAAGCAGTGCATCA 57.968 39.130 21.40 2.32 0.00 3.07
365 367 3.808726 GCAGGAGATATCAAGAAGCAGTG 59.191 47.826 5.32 0.00 0.00 3.66
411 413 8.382030 ACATATTATCAAAGCATCGATGTCAA 57.618 30.769 25.47 8.60 0.00 3.18
428 430 7.095271 GCGGCCATGCAAAAATTTACATATTAT 60.095 33.333 2.24 0.00 34.15 1.28
430 432 5.007528 GCGGCCATGCAAAAATTTACATATT 59.992 36.000 2.24 0.00 34.15 1.28
431 433 4.511082 GCGGCCATGCAAAAATTTACATAT 59.489 37.500 2.24 0.00 34.15 1.78
434 436 2.072298 GCGGCCATGCAAAAATTTACA 58.928 42.857 2.24 0.00 34.15 2.41
435 437 2.072298 TGCGGCCATGCAAAAATTTAC 58.928 42.857 2.24 0.00 43.02 2.01
436 438 2.462456 TGCGGCCATGCAAAAATTTA 57.538 40.000 2.24 0.00 43.02 1.40
437 439 3.319135 TGCGGCCATGCAAAAATTT 57.681 42.105 2.24 0.00 43.02 1.82
449 591 1.202302 GCCTTCTCTTTATTTGCGGCC 60.202 52.381 0.00 0.00 0.00 6.13
483 625 1.301009 GGTCAGCTAGGCCGCATAC 60.301 63.158 5.37 2.64 28.17 2.39
519 986 1.867233 CGTGTAGCATTACTCCATGGC 59.133 52.381 6.96 0.00 0.00 4.40
520 987 3.179443 ACGTGTAGCATTACTCCATGG 57.821 47.619 4.97 4.97 0.00 3.66
521 988 4.678622 TGTACGTGTAGCATTACTCCATG 58.321 43.478 0.00 0.00 0.00 3.66
522 989 4.994907 TGTACGTGTAGCATTACTCCAT 57.005 40.909 0.00 0.00 0.00 3.41
523 990 4.787260 TTGTACGTGTAGCATTACTCCA 57.213 40.909 0.00 0.00 0.00 3.86
524 991 4.925054 TGTTTGTACGTGTAGCATTACTCC 59.075 41.667 0.00 0.00 0.00 3.85
525 992 6.145048 ACTTGTTTGTACGTGTAGCATTACTC 59.855 38.462 0.00 0.00 0.00 2.59
526 993 5.987347 ACTTGTTTGTACGTGTAGCATTACT 59.013 36.000 0.00 0.00 0.00 2.24
527 994 6.219302 ACTTGTTTGTACGTGTAGCATTAC 57.781 37.500 0.00 0.00 0.00 1.89
528 995 6.847956 AACTTGTTTGTACGTGTAGCATTA 57.152 33.333 0.00 0.00 0.00 1.90
529 996 5.744666 AACTTGTTTGTACGTGTAGCATT 57.255 34.783 0.00 0.00 0.00 3.56
530 997 5.754406 TGTAACTTGTTTGTACGTGTAGCAT 59.246 36.000 0.00 0.00 0.00 3.79
531 998 5.107824 TGTAACTTGTTTGTACGTGTAGCA 58.892 37.500 0.00 0.00 0.00 3.49
532 999 5.640218 TGTAACTTGTTTGTACGTGTAGC 57.360 39.130 0.00 0.00 0.00 3.58
533 1000 6.201425 ACCATGTAACTTGTTTGTACGTGTAG 59.799 38.462 0.00 0.00 0.00 2.74
534 1001 6.047870 ACCATGTAACTTGTTTGTACGTGTA 58.952 36.000 0.00 0.00 0.00 2.90
535 1002 4.877251 ACCATGTAACTTGTTTGTACGTGT 59.123 37.500 0.00 0.00 0.00 4.49
536 1003 5.412526 ACCATGTAACTTGTTTGTACGTG 57.587 39.130 0.00 0.00 0.00 4.49
537 1004 6.439675 AAACCATGTAACTTGTTTGTACGT 57.560 33.333 0.00 0.00 30.27 3.57
545 1012 9.020731 CCCTCTTTATAAAACCATGTAACTTGT 57.979 33.333 0.00 0.00 0.00 3.16
546 1013 9.020731 ACCCTCTTTATAAAACCATGTAACTTG 57.979 33.333 0.00 0.00 0.00 3.16
547 1014 9.596308 AACCCTCTTTATAAAACCATGTAACTT 57.404 29.630 0.00 0.00 0.00 2.66
562 1029 7.712205 GCATGCAATCAAATTAACCCTCTTTAT 59.288 33.333 14.21 0.00 0.00 1.40
563 1030 7.041107 GCATGCAATCAAATTAACCCTCTTTA 58.959 34.615 14.21 0.00 0.00 1.85
564 1031 5.876460 GCATGCAATCAAATTAACCCTCTTT 59.124 36.000 14.21 0.00 0.00 2.52
565 1032 5.422145 GCATGCAATCAAATTAACCCTCTT 58.578 37.500 14.21 0.00 0.00 2.85
566 1033 4.141869 GGCATGCAATCAAATTAACCCTCT 60.142 41.667 21.36 0.00 0.00 3.69
567 1034 4.122046 GGCATGCAATCAAATTAACCCTC 58.878 43.478 21.36 0.00 0.00 4.30
568 1035 3.518705 TGGCATGCAATCAAATTAACCCT 59.481 39.130 21.36 0.00 0.00 4.34
569 1036 3.622612 GTGGCATGCAATCAAATTAACCC 59.377 43.478 21.36 0.00 0.00 4.11
570 1037 3.306703 CGTGGCATGCAATCAAATTAACC 59.693 43.478 21.36 0.00 0.00 2.85
571 1038 3.925913 ACGTGGCATGCAATCAAATTAAC 59.074 39.130 21.36 0.00 0.00 2.01
572 1039 3.925299 CACGTGGCATGCAATCAAATTAA 59.075 39.130 21.36 0.00 0.00 1.40
573 1040 3.192212 TCACGTGGCATGCAATCAAATTA 59.808 39.130 21.36 0.00 0.00 1.40
574 1041 2.029200 TCACGTGGCATGCAATCAAATT 60.029 40.909 21.36 0.00 0.00 1.82
575 1042 1.545136 TCACGTGGCATGCAATCAAAT 59.455 42.857 21.36 0.00 0.00 2.32
576 1043 0.957362 TCACGTGGCATGCAATCAAA 59.043 45.000 21.36 0.00 0.00 2.69
577 1044 0.522626 CTCACGTGGCATGCAATCAA 59.477 50.000 21.36 0.00 0.00 2.57
578 1045 0.321475 TCTCACGTGGCATGCAATCA 60.321 50.000 21.36 5.42 0.00 2.57
579 1046 0.804364 TTCTCACGTGGCATGCAATC 59.196 50.000 21.36 7.93 0.00 2.67
580 1047 0.806868 CTTCTCACGTGGCATGCAAT 59.193 50.000 21.36 0.00 0.00 3.56
581 1048 0.250252 TCTTCTCACGTGGCATGCAA 60.250 50.000 21.36 4.92 0.00 4.08
582 1049 0.671472 CTCTTCTCACGTGGCATGCA 60.671 55.000 21.36 2.54 0.00 3.96
583 1050 0.390340 TCTCTTCTCACGTGGCATGC 60.390 55.000 17.00 9.90 0.00 4.06
584 1051 1.638133 CTCTCTTCTCACGTGGCATG 58.362 55.000 17.00 4.87 0.00 4.06
585 1052 0.534412 CCTCTCTTCTCACGTGGCAT 59.466 55.000 17.00 0.00 0.00 4.40
586 1053 1.536073 CCCTCTCTTCTCACGTGGCA 61.536 60.000 17.00 0.00 0.00 4.92
610 1077 4.214383 CCACGCGCTGCAGATTCG 62.214 66.667 20.43 18.38 0.00 3.34
690 1160 3.711704 ACAGAACTGAAGGAAGAGGAACA 59.288 43.478 8.87 0.00 0.00 3.18
759 1518 1.486310 TGTGTTCACTCAGTGGAGCTT 59.514 47.619 4.57 0.00 45.42 3.74
778 1537 1.597027 GGTATCGGGCAATCGGGTG 60.597 63.158 0.00 0.00 0.00 4.61
1126 1954 2.880443 ACTAGTAGTTTCCGTGGGTGA 58.120 47.619 0.00 0.00 0.00 4.02
1142 1970 6.996509 ACAGTACCTAGCTAGCTAGTACTAG 58.003 44.000 35.49 31.68 43.22 2.57
1156 1984 4.451774 GGATCACGTAGCTACAGTACCTAG 59.548 50.000 23.21 7.10 0.00 3.02
1163 1991 3.565902 TGATCAGGATCACGTAGCTACAG 59.434 47.826 23.21 17.17 42.42 2.74
1164 1992 3.551846 TGATCAGGATCACGTAGCTACA 58.448 45.455 23.21 4.75 42.42 2.74
1200 2029 0.821517 TCGTACATCACCATCGGCTT 59.178 50.000 0.00 0.00 0.00 4.35
1260 2089 4.112341 GTCGTGGTCGCCGTAGCT 62.112 66.667 0.00 0.00 36.60 3.32
1559 2397 0.319728 TCTGAGTCAGGCTGAAGCAC 59.680 55.000 20.62 7.41 44.36 4.40
1778 2622 2.925706 TTGGGCGAGCTGGTGGTA 60.926 61.111 0.00 0.00 0.00 3.25
1803 2647 4.927782 TGCGGTGAGGCTTTGCGT 62.928 61.111 0.00 0.00 0.00 5.24
1832 2676 1.804151 GCAGTACAAAGATTCGGTGCA 59.196 47.619 0.00 0.00 0.00 4.57
2089 3075 2.642183 TAGATCTCCGGCGCCCTTCT 62.642 60.000 23.46 17.24 0.00 2.85
2093 3079 3.686045 CCTAGATCTCCGGCGCCC 61.686 72.222 23.46 5.24 0.00 6.13
2135 3133 1.303643 CAGTTCAGTTGCCCCCTCC 60.304 63.158 0.00 0.00 0.00 4.30
2177 3212 8.701908 ATCTCTACCATATCCTTGTACGTTTA 57.298 34.615 0.00 0.00 0.00 2.01
2301 3836 5.864418 AAGATATAACGCAACCTAGGTCA 57.136 39.130 16.64 0.00 0.00 4.02
2321 3856 9.066939 GCATCAGATCAAGTACGTACATATAAG 57.933 37.037 26.55 11.15 0.00 1.73
2322 3857 8.573035 TGCATCAGATCAAGTACGTACATATAA 58.427 33.333 26.55 8.38 0.00 0.98
2323 3858 8.106247 TGCATCAGATCAAGTACGTACATATA 57.894 34.615 26.55 10.06 0.00 0.86
2324 3859 6.981722 TGCATCAGATCAAGTACGTACATAT 58.018 36.000 26.55 16.08 0.00 1.78
2325 3860 6.039382 ACTGCATCAGATCAAGTACGTACATA 59.961 38.462 26.55 12.14 35.18 2.29
2326 3861 5.163509 ACTGCATCAGATCAAGTACGTACAT 60.164 40.000 26.55 13.27 35.18 2.29
2478 4016 1.927895 AAACGTTCGCAATTGCCAAA 58.072 40.000 24.24 15.71 37.91 3.28
2545 4083 8.637099 TGTCATGTAAATTCAAATCCAGTTTCA 58.363 29.630 0.00 0.00 0.00 2.69
2589 4127 5.833131 AGTTCATCACATTGGTAGTTTGGTT 59.167 36.000 0.00 0.00 0.00 3.67
2627 4166 6.543430 AACATCCTTTTATAAAGGCATGCA 57.457 33.333 21.36 0.00 37.34 3.96
2628 4167 7.548780 TGAAAACATCCTTTTATAAAGGCATGC 59.451 33.333 9.90 9.90 37.34 4.06
2655 4198 2.223971 CGCACTCGTGGTATTCCCTAAT 60.224 50.000 0.00 0.00 0.00 1.73
2674 4223 0.577269 CCTGCACGAGTAATTAGCGC 59.423 55.000 0.00 0.00 0.00 5.92
2725 4280 4.381718 CCTCCCCGTAAAGAGAAACAGTAG 60.382 50.000 0.00 0.00 31.43 2.57
2730 4285 1.904537 TCCCTCCCCGTAAAGAGAAAC 59.095 52.381 0.00 0.00 31.43 2.78
2751 4306 2.028567 ACAACAATATTTGCAACCCCCG 60.029 45.455 0.00 0.00 0.00 5.73
2801 4732 7.655521 TGGCTCATACAATACAAGTAGTAGT 57.344 36.000 0.00 0.00 35.85 2.73
2842 4774 2.242043 TCGAGGGTTCGGTTAGAGTTT 58.758 47.619 0.00 0.00 46.67 2.66
3103 5039 9.797473 CTTGTTTTAGCTTAAATTTAGCTTTGC 57.203 29.630 20.06 11.62 46.42 3.68
3169 5105 1.028905 CAGTAGAAGGAGGAGGAGCG 58.971 60.000 0.00 0.00 0.00 5.03
3259 5196 1.601166 TCGTTGTCGTCAGAGGAAGA 58.399 50.000 0.00 0.00 38.33 2.87
3265 5202 2.131972 CACCAAATCGTTGTCGTCAGA 58.868 47.619 0.00 0.00 38.33 3.27
3276 5213 1.140161 CCATGCTGCCACCAAATCG 59.860 57.895 0.00 0.00 0.00 3.34
3284 5221 1.304381 GAGAAACCCCATGCTGCCA 60.304 57.895 0.00 0.00 0.00 4.92
3319 5256 0.811616 GCCAGAATCAACGGCGAGAT 60.812 55.000 16.62 13.93 35.79 2.75
3330 5267 2.158959 CGGTCGTCGTGCCAGAATC 61.159 63.158 8.73 0.00 0.00 2.52
3350 5288 4.333926 GCCTACTTCTGCTAACATCTTTGG 59.666 45.833 0.00 0.00 0.00 3.28
3352 5290 5.165961 TGCCTACTTCTGCTAACATCTTT 57.834 39.130 0.00 0.00 0.00 2.52
3363 5301 2.094894 CACATCGCTTTGCCTACTTCTG 59.905 50.000 0.00 0.00 0.00 3.02
3371 5309 0.955428 TCTCCACACATCGCTTTGCC 60.955 55.000 0.00 0.00 0.00 4.52
3378 5316 1.812922 GGCTGCTCTCCACACATCG 60.813 63.158 0.00 0.00 0.00 3.84
3402 5340 0.751643 GTTGCCGCCCTATTCCACAT 60.752 55.000 0.00 0.00 0.00 3.21



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

AutoCloner maintained by Alex Coulton.