Multiple sequence alignment - TraesCS3A01G348700

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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 TraesCS3A01G348700 chr3A 100.000 3485 0 0 1 3485 597322024 597325508 0.000000e+00 6436.0
1 TraesCS3A01G348700 chr3A 87.640 89 10 1 3026 3114 508380722 508380809 6.150000e-18 102.0
2 TraesCS3A01G348700 chr3B 90.354 2571 159 38 618 3134 598121367 598123902 0.000000e+00 3291.0
3 TraesCS3A01G348700 chr3B 85.525 1209 147 16 2255 3448 598146011 598147206 0.000000e+00 1238.0
4 TraesCS3A01G348700 chr3B 84.643 280 37 5 3210 3484 598124278 598124556 1.230000e-69 274.0
5 TraesCS3A01G348700 chr3B 88.649 185 20 1 414 598 598120498 598120681 1.260000e-54 224.0
6 TraesCS3A01G348700 chr3D 88.408 2010 142 38 410 2349 455045624 455047612 0.000000e+00 2337.0
7 TraesCS3A01G348700 chr3D 91.818 440 25 7 2371 2805 455047604 455048037 1.380000e-168 603.0
8 TraesCS3A01G348700 chr3D 91.554 296 24 1 2851 3146 455048376 455048670 1.160000e-109 407.0
9 TraesCS3A01G348700 chr3D 86.869 198 26 0 3272 3469 455048932 455049129 4.530000e-54 222.0
10 TraesCS3A01G348700 chr3D 86.500 200 25 2 99 296 455045393 455045592 5.860000e-53 219.0
11 TraesCS3A01G348700 chr5B 74.398 457 92 21 3007 3457 556173106 556173543 4.620000e-39 172.0
12 TraesCS3A01G348700 chr4D 93.137 102 3 1 1 98 313876628 313876527 2.800000e-31 147.0
13 TraesCS3A01G348700 chr4D 76.048 167 38 2 3305 3471 398900714 398900878 6.200000e-13 86.1
14 TraesCS3A01G348700 chr2D 73.434 463 84 26 3031 3483 134452722 134453155 1.690000e-28 137.0
15 TraesCS3A01G348700 chr2D 83.740 123 19 1 3034 3156 525904949 525905070 7.900000e-22 115.0
16 TraesCS3A01G348700 chr4A 93.902 82 2 2 19 97 24820824 24820743 1.700000e-23 121.0
17 TraesCS3A01G348700 chr2A 87.500 80 8 2 3010 3089 651094050 651094127 1.330000e-14 91.6
18 TraesCS3A01G348700 chr7A 78.417 139 22 5 2961 3095 473909467 473909601 2.230000e-12 84.2
19 TraesCS3A01G348700 chr7A 73.707 232 41 16 3231 3456 128409803 128409586 4.830000e-09 73.1
20 TraesCS3A01G348700 chr7A 84.848 66 10 0 3062 3127 128509719 128509654 2.240000e-07 67.6
21 TraesCS3A01G348700 chr2B 89.394 66 3 2 36 97 745509186 745509251 2.880000e-11 80.5
22 TraesCS3A01G348700 chr7B 97.619 42 1 0 3054 3095 426880548 426880589 4.830000e-09 73.1


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 TraesCS3A01G348700 chr3A 597322024 597325508 3484 False 6436.0 6436 100.0000 1 3485 1 chr3A.!!$F2 3484
1 TraesCS3A01G348700 chr3B 598120498 598124556 4058 False 1263.0 3291 87.8820 414 3484 3 chr3B.!!$F2 3070
2 TraesCS3A01G348700 chr3B 598146011 598147206 1195 False 1238.0 1238 85.5250 2255 3448 1 chr3B.!!$F1 1193
3 TraesCS3A01G348700 chr3D 455045393 455049129 3736 False 757.6 2337 89.0298 99 3469 5 chr3D.!!$F1 3370

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
326 329 0.176680 CCTGCTACAGTGCCCTAGTG 59.823 60.0 0.00 0.0 35.76 2.74 F
329 332 0.179134 GCTACAGTGCCCTAGTGTCG 60.179 60.0 0.00 0.0 41.96 4.35 F
1278 1985 0.034059 CATCGTAGGCCTCATGTCCC 59.966 60.0 9.68 0.0 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1257 1964 0.034059 GACATGAGGCCTACGATGGG 59.966 60.0 4.42 0.0 0.00 4.00 R
2172 2910 0.397816 CTAGACCCAGTAGGCCAGCT 60.398 60.0 5.01 0.0 40.58 4.24 R
3269 4644 0.250901 AATGGAAGCCGCACTCACTT 60.251 50.0 0.00 0.0 0.00 3.16 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
21 22 3.722728 AAAGCTGACCAAAAAGAGCTG 57.277 42.857 0.00 0.00 40.95 4.24
22 23 2.355010 AGCTGACCAAAAAGAGCTGT 57.645 45.000 0.00 0.00 40.31 4.40
23 24 2.659428 AGCTGACCAAAAAGAGCTGTT 58.341 42.857 0.00 0.00 40.31 3.16
24 25 2.360165 AGCTGACCAAAAAGAGCTGTTG 59.640 45.455 0.00 0.00 40.31 3.33
25 26 2.358898 GCTGACCAAAAAGAGCTGTTGA 59.641 45.455 0.00 0.00 0.00 3.18
26 27 3.181487 GCTGACCAAAAAGAGCTGTTGAA 60.181 43.478 0.00 0.00 0.00 2.69
27 28 4.500375 GCTGACCAAAAAGAGCTGTTGAAT 60.500 41.667 0.00 0.00 0.00 2.57
28 29 4.935702 TGACCAAAAAGAGCTGTTGAATG 58.064 39.130 0.00 0.00 0.00 2.67
29 30 4.202141 TGACCAAAAAGAGCTGTTGAATGG 60.202 41.667 16.40 16.40 0.00 3.16
30 31 3.070015 ACCAAAAAGAGCTGTTGAATGGG 59.930 43.478 19.96 10.35 0.00 4.00
31 32 3.062042 CAAAAAGAGCTGTTGAATGGGC 58.938 45.455 0.00 0.00 0.00 5.36
32 33 0.883833 AAAGAGCTGTTGAATGGGCG 59.116 50.000 0.00 0.00 0.00 6.13
33 34 0.250901 AAGAGCTGTTGAATGGGCGT 60.251 50.000 0.00 0.00 0.00 5.68
34 35 0.250901 AGAGCTGTTGAATGGGCGTT 60.251 50.000 0.00 0.00 0.00 4.84
35 36 1.003118 AGAGCTGTTGAATGGGCGTTA 59.997 47.619 0.00 0.00 0.00 3.18
36 37 2.017049 GAGCTGTTGAATGGGCGTTAT 58.983 47.619 0.00 0.00 0.00 1.89
37 38 2.017049 AGCTGTTGAATGGGCGTTATC 58.983 47.619 0.00 0.00 0.00 1.75
38 39 1.065551 GCTGTTGAATGGGCGTTATCC 59.934 52.381 0.00 0.00 0.00 2.59
39 40 2.643551 CTGTTGAATGGGCGTTATCCT 58.356 47.619 0.00 0.00 0.00 3.24
40 41 3.804036 CTGTTGAATGGGCGTTATCCTA 58.196 45.455 0.00 0.00 0.00 2.94
41 42 3.537580 TGTTGAATGGGCGTTATCCTAC 58.462 45.455 0.00 0.00 0.00 3.18
42 43 2.876550 GTTGAATGGGCGTTATCCTACC 59.123 50.000 0.00 0.00 0.00 3.18
43 44 2.404559 TGAATGGGCGTTATCCTACCT 58.595 47.619 0.00 0.00 0.00 3.08
44 45 2.104111 TGAATGGGCGTTATCCTACCTG 59.896 50.000 0.00 0.00 0.00 4.00
45 46 1.056660 ATGGGCGTTATCCTACCTGG 58.943 55.000 0.00 0.00 37.10 4.45
46 47 1.070957 GGGCGTTATCCTACCTGGC 59.929 63.158 0.00 0.00 35.26 4.85
47 48 1.692173 GGGCGTTATCCTACCTGGCA 61.692 60.000 0.00 0.00 35.26 4.92
48 49 0.532196 GGCGTTATCCTACCTGGCAC 60.532 60.000 0.00 0.00 35.26 5.01
49 50 0.532196 GCGTTATCCTACCTGGCACC 60.532 60.000 0.00 0.00 35.26 5.01
50 51 0.249322 CGTTATCCTACCTGGCACCG 60.249 60.000 0.00 0.00 35.26 4.94
51 52 0.532196 GTTATCCTACCTGGCACCGC 60.532 60.000 0.00 0.00 35.26 5.68
52 53 0.978667 TTATCCTACCTGGCACCGCA 60.979 55.000 0.00 0.00 35.26 5.69
53 54 1.682451 TATCCTACCTGGCACCGCAC 61.682 60.000 0.00 0.00 35.26 5.34
54 55 4.015406 CCTACCTGGCACCGCACA 62.015 66.667 0.00 0.00 0.00 4.57
55 56 2.031919 CTACCTGGCACCGCACAA 59.968 61.111 0.00 0.00 0.00 3.33
56 57 1.599518 CTACCTGGCACCGCACAAA 60.600 57.895 0.00 0.00 0.00 2.83
57 58 1.852067 CTACCTGGCACCGCACAAAC 61.852 60.000 0.00 0.00 0.00 2.93
58 59 2.332312 TACCTGGCACCGCACAAACT 62.332 55.000 0.00 0.00 0.00 2.66
59 60 2.489275 CCTGGCACCGCACAAACTT 61.489 57.895 0.00 0.00 0.00 2.66
60 61 1.008538 CTGGCACCGCACAAACTTC 60.009 57.895 0.00 0.00 0.00 3.01
61 62 2.335011 GGCACCGCACAAACTTCC 59.665 61.111 0.00 0.00 0.00 3.46
62 63 2.193536 GGCACCGCACAAACTTCCT 61.194 57.895 0.00 0.00 0.00 3.36
63 64 1.282875 GCACCGCACAAACTTCCTC 59.717 57.895 0.00 0.00 0.00 3.71
64 65 1.166531 GCACCGCACAAACTTCCTCT 61.167 55.000 0.00 0.00 0.00 3.69
65 66 0.868406 CACCGCACAAACTTCCTCTC 59.132 55.000 0.00 0.00 0.00 3.20
66 67 0.600255 ACCGCACAAACTTCCTCTCG 60.600 55.000 0.00 0.00 0.00 4.04
67 68 1.291877 CCGCACAAACTTCCTCTCGG 61.292 60.000 0.00 0.00 0.00 4.63
68 69 0.319555 CGCACAAACTTCCTCTCGGA 60.320 55.000 0.00 0.00 37.60 4.55
69 70 1.149148 GCACAAACTTCCTCTCGGAC 58.851 55.000 0.00 0.00 39.60 4.79
70 71 1.419374 CACAAACTTCCTCTCGGACG 58.581 55.000 0.00 0.00 39.60 4.79
71 72 0.319641 ACAAACTTCCTCTCGGACGC 60.320 55.000 0.00 0.00 39.60 5.19
72 73 1.014564 CAAACTTCCTCTCGGACGCC 61.015 60.000 0.00 0.00 39.60 5.68
73 74 1.469335 AAACTTCCTCTCGGACGCCA 61.469 55.000 0.00 0.00 39.60 5.69
74 75 2.156051 AACTTCCTCTCGGACGCCAC 62.156 60.000 0.00 0.00 39.60 5.01
75 76 2.599281 TTCCTCTCGGACGCCACA 60.599 61.111 0.00 0.00 39.60 4.17
76 77 2.549611 CTTCCTCTCGGACGCCACAG 62.550 65.000 0.00 0.00 39.60 3.66
77 78 4.135153 CCTCTCGGACGCCACAGG 62.135 72.222 0.00 0.00 0.00 4.00
78 79 3.374402 CTCTCGGACGCCACAGGT 61.374 66.667 0.00 0.00 0.00 4.00
79 80 3.633094 CTCTCGGACGCCACAGGTG 62.633 68.421 0.00 0.00 39.41 4.00
95 96 4.028490 TGGCGCCCCAACCACTAG 62.028 66.667 26.77 0.00 38.46 2.57
96 97 4.029809 GGCGCCCCAACCACTAGT 62.030 66.667 18.11 0.00 0.00 2.57
97 98 2.662070 GGCGCCCCAACCACTAGTA 61.662 63.158 18.11 0.00 0.00 1.82
101 102 1.065709 CGCCCCAACCACTAGTAATGT 60.066 52.381 0.00 0.00 0.00 2.71
134 135 1.774894 AACCATGTGCTACCACCCGT 61.775 55.000 0.00 0.00 41.35 5.28
135 136 1.745115 CCATGTGCTACCACCCGTG 60.745 63.158 0.00 0.00 41.35 4.94
136 137 1.003839 CATGTGCTACCACCCGTGT 60.004 57.895 0.00 0.00 41.35 4.49
137 138 1.003839 ATGTGCTACCACCCGTGTG 60.004 57.895 0.00 0.00 41.35 3.82
147 148 0.744414 CACCCGTGTGGATCCATCAC 60.744 60.000 25.48 25.48 38.90 3.06
163 164 6.423776 TCCATCACTGATGCTCACATTATA 57.576 37.500 12.92 0.00 38.59 0.98
167 168 7.278203 CCATCACTGATGCTCACATTATATCTC 59.722 40.741 12.92 0.00 38.59 2.75
168 169 6.695429 TCACTGATGCTCACATTATATCTCC 58.305 40.000 0.00 0.00 36.35 3.71
170 171 5.046014 ACTGATGCTCACATTATATCTCCCC 60.046 44.000 0.00 0.00 36.35 4.81
174 175 4.598807 TGCTCACATTATATCTCCCCACAT 59.401 41.667 0.00 0.00 0.00 3.21
175 176 4.940046 GCTCACATTATATCTCCCCACATG 59.060 45.833 0.00 0.00 0.00 3.21
179 180 7.016296 TCACATTATATCTCCCCACATGTCTA 58.984 38.462 0.00 0.00 0.00 2.59
220 221 2.436646 CCACTGCTGGCCGGTTAG 60.437 66.667 14.55 14.37 0.00 2.34
249 252 8.307483 AGGATCTATACTATTGTTGACCATTCG 58.693 37.037 0.00 0.00 0.00 3.34
250 253 7.063544 GGATCTATACTATTGTTGACCATTCGC 59.936 40.741 0.00 0.00 0.00 4.70
251 254 6.220930 TCTATACTATTGTTGACCATTCGCC 58.779 40.000 0.00 0.00 0.00 5.54
296 299 2.038426 CCACTACACACCTGGAACATCA 59.962 50.000 0.00 0.00 38.20 3.07
298 301 2.288825 ACTACACACCTGGAACATCACG 60.289 50.000 0.00 0.00 38.20 4.35
299 302 0.250295 ACACACCTGGAACATCACGG 60.250 55.000 0.00 0.00 38.20 4.94
300 303 0.955428 CACACCTGGAACATCACGGG 60.955 60.000 0.00 0.00 38.20 5.28
301 304 2.040544 CACCTGGAACATCACGGGC 61.041 63.158 0.00 0.00 38.20 6.13
302 305 2.438434 CCTGGAACATCACGGGCC 60.438 66.667 0.00 0.00 38.20 5.80
303 306 2.438434 CTGGAACATCACGGGCCC 60.438 66.667 13.57 13.57 38.20 5.80
305 308 2.438434 GGAACATCACGGGCCCAG 60.438 66.667 24.92 17.36 0.00 4.45
306 309 2.438434 GAACATCACGGGCCCAGG 60.438 66.667 24.92 13.55 0.00 4.45
307 310 4.740822 AACATCACGGGCCCAGGC 62.741 66.667 24.92 0.00 41.06 4.85
317 320 3.721706 GCCCAGGCCTGCTACAGT 61.722 66.667 28.39 0.00 34.56 3.55
318 321 2.270205 CCCAGGCCTGCTACAGTG 59.730 66.667 28.39 11.59 0.00 3.66
319 322 2.437359 CCAGGCCTGCTACAGTGC 60.437 66.667 28.39 0.00 0.00 4.40
320 323 2.437359 CAGGCCTGCTACAGTGCC 60.437 66.667 22.33 15.22 43.30 5.01
321 324 3.721706 AGGCCTGCTACAGTGCCC 61.722 66.667 3.11 5.99 43.69 5.36
322 325 3.721706 GGCCTGCTACAGTGCCCT 61.722 66.667 13.13 0.00 39.88 5.19
323 326 2.367202 GGCCTGCTACAGTGCCCTA 61.367 63.158 13.13 0.00 39.88 3.53
324 327 1.144936 GCCTGCTACAGTGCCCTAG 59.855 63.158 0.00 0.00 0.00 3.02
325 328 1.617947 GCCTGCTACAGTGCCCTAGT 61.618 60.000 0.00 0.00 0.00 2.57
326 329 0.176680 CCTGCTACAGTGCCCTAGTG 59.823 60.000 0.00 0.00 35.76 2.74
327 330 0.898320 CTGCTACAGTGCCCTAGTGT 59.102 55.000 0.00 0.00 44.90 3.55
328 331 0.895530 TGCTACAGTGCCCTAGTGTC 59.104 55.000 0.00 0.00 41.96 3.67
329 332 0.179134 GCTACAGTGCCCTAGTGTCG 60.179 60.000 0.00 0.00 41.96 4.35
330 333 0.179134 CTACAGTGCCCTAGTGTCGC 60.179 60.000 0.00 0.00 41.96 5.19
331 334 0.611062 TACAGTGCCCTAGTGTCGCT 60.611 55.000 0.00 0.00 41.96 4.93
332 335 0.611062 ACAGTGCCCTAGTGTCGCTA 60.611 55.000 0.00 0.00 38.60 4.26
333 336 0.179134 CAGTGCCCTAGTGTCGCTAC 60.179 60.000 0.00 0.00 0.00 3.58
334 337 0.611062 AGTGCCCTAGTGTCGCTACA 60.611 55.000 0.00 0.00 0.00 2.74
335 338 0.179134 GTGCCCTAGTGTCGCTACAG 60.179 60.000 0.00 0.00 35.91 2.74
336 339 0.611062 TGCCCTAGTGTCGCTACAGT 60.611 55.000 3.96 3.96 42.11 3.55
337 340 0.179134 GCCCTAGTGTCGCTACAGTG 60.179 60.000 8.88 0.00 39.65 3.66
338 341 1.460504 CCCTAGTGTCGCTACAGTGA 58.539 55.000 8.88 0.00 39.65 3.41
339 342 1.816835 CCCTAGTGTCGCTACAGTGAA 59.183 52.381 8.88 0.00 39.65 3.18
340 343 2.415625 CCCTAGTGTCGCTACAGTGAAC 60.416 54.545 8.88 0.00 39.65 3.18
341 344 2.228103 CCTAGTGTCGCTACAGTGAACA 59.772 50.000 8.88 0.00 39.65 3.18
342 345 2.135664 AGTGTCGCTACAGTGAACAC 57.864 50.000 0.00 13.15 37.88 3.32
343 346 1.407618 AGTGTCGCTACAGTGAACACA 59.592 47.619 18.73 4.40 37.88 3.72
344 347 2.035961 AGTGTCGCTACAGTGAACACAT 59.964 45.455 18.73 0.00 37.88 3.21
345 348 2.408704 GTGTCGCTACAGTGAACACATC 59.591 50.000 7.68 0.00 36.98 3.06
346 349 1.649171 GTCGCTACAGTGAACACATCG 59.351 52.381 7.68 3.65 36.19 3.84
347 350 1.268625 TCGCTACAGTGAACACATCGT 59.731 47.619 7.68 4.30 0.00 3.73
348 351 2.058798 CGCTACAGTGAACACATCGTT 58.941 47.619 7.68 0.00 41.86 3.85
349 352 2.475111 CGCTACAGTGAACACATCGTTT 59.525 45.455 7.68 0.00 38.19 3.60
350 353 3.661678 CGCTACAGTGAACACATCGTTTG 60.662 47.826 7.68 0.00 38.19 2.93
351 354 3.247648 GCTACAGTGAACACATCGTTTGT 59.752 43.478 7.68 4.52 38.19 2.83
352 355 4.260620 GCTACAGTGAACACATCGTTTGTT 60.261 41.667 7.68 0.00 38.19 2.83
359 362 3.585748 ACACATCGTTTGTTCTTCACG 57.414 42.857 0.00 0.00 36.00 4.35
360 363 2.286184 ACACATCGTTTGTTCTTCACGC 60.286 45.455 0.00 0.00 36.00 5.34
361 364 1.263217 ACATCGTTTGTTCTTCACGCC 59.737 47.619 0.00 0.00 33.74 5.68
362 365 0.872388 ATCGTTTGTTCTTCACGCCC 59.128 50.000 0.00 0.00 0.00 6.13
363 366 1.161563 TCGTTTGTTCTTCACGCCCC 61.162 55.000 0.00 0.00 0.00 5.80
364 367 1.440938 CGTTTGTTCTTCACGCCCCA 61.441 55.000 0.00 0.00 0.00 4.96
365 368 0.310854 GTTTGTTCTTCACGCCCCAG 59.689 55.000 0.00 0.00 0.00 4.45
366 369 0.821711 TTTGTTCTTCACGCCCCAGG 60.822 55.000 0.00 0.00 0.00 4.45
367 370 1.990160 TTGTTCTTCACGCCCCAGGT 61.990 55.000 0.00 0.00 0.00 4.00
368 371 1.671379 GTTCTTCACGCCCCAGGTC 60.671 63.158 0.00 0.00 0.00 3.85
369 372 2.890766 TTCTTCACGCCCCAGGTCC 61.891 63.158 0.00 0.00 0.00 4.46
370 373 3.636231 CTTCACGCCCCAGGTCCA 61.636 66.667 0.00 0.00 0.00 4.02
371 374 3.612247 CTTCACGCCCCAGGTCCAG 62.612 68.421 0.00 0.00 0.00 3.86
392 395 3.717294 CCCGGTCCTGGGTCTTGG 61.717 72.222 0.00 0.00 44.76 3.61
393 396 2.606519 CCGGTCCTGGGTCTTGGA 60.607 66.667 0.00 0.00 0.00 3.53
394 397 1.995626 CCGGTCCTGGGTCTTGGAT 60.996 63.158 0.00 0.00 34.58 3.41
395 398 1.522569 CGGTCCTGGGTCTTGGATC 59.477 63.158 0.00 0.00 34.58 3.36
396 399 1.915983 GGTCCTGGGTCTTGGATCC 59.084 63.158 4.20 4.20 34.58 3.36
397 400 1.522569 GTCCTGGGTCTTGGATCCG 59.477 63.158 7.39 0.00 35.15 4.18
398 401 2.190578 CCTGGGTCTTGGATCCGC 59.809 66.667 7.39 0.00 35.15 5.54
399 402 2.190578 CTGGGTCTTGGATCCGCC 59.809 66.667 7.39 6.59 35.15 6.13
407 410 4.776965 TGGATCCGCCACTGACTA 57.223 55.556 7.39 0.00 43.33 2.59
408 411 2.504920 TGGATCCGCCACTGACTAG 58.495 57.895 7.39 0.00 43.33 2.57
412 415 1.751924 GATCCGCCACTGACTAGAGTT 59.248 52.381 0.00 0.00 0.00 3.01
475 479 4.052159 TGATGCCACAACGAAAACAAAT 57.948 36.364 0.00 0.00 0.00 2.32
590 595 2.723124 ATGAACCAAACGACCAATGC 57.277 45.000 0.00 0.00 0.00 3.56
598 603 3.452474 CAAACGACCAATGCAGGAAAAA 58.548 40.909 0.00 0.00 0.00 1.94
616 621 2.420058 AAATCCTAAGGGTTCCTGCG 57.580 50.000 0.00 0.00 32.13 5.18
648 1319 2.435693 GCAGCCCTCCGAGGTATGT 61.436 63.158 13.62 0.00 31.93 2.29
668 1339 4.331968 TGTGTGATATGGAACTTGGAACC 58.668 43.478 0.00 0.00 0.00 3.62
694 1376 1.597797 CCCCACATGACATGCCACAC 61.598 60.000 15.49 0.00 0.00 3.82
708 1390 4.057406 TGCCACACCATCAAAAGAAAAG 57.943 40.909 0.00 0.00 0.00 2.27
710 1392 3.803368 GCCACACCATCAAAAGAAAAGGG 60.803 47.826 0.00 0.00 0.00 3.95
836 1532 1.675641 CGCAACCTGGGAGAAAGGG 60.676 63.158 0.00 0.00 39.30 3.95
1035 1742 1.474879 CTTCTTCCTCAGGTCCTCGTC 59.525 57.143 0.00 0.00 0.00 4.20
1038 1745 2.760385 CCTCAGGTCCTCGTCCCC 60.760 72.222 0.00 0.00 0.00 4.81
1039 1746 2.360980 CTCAGGTCCTCGTCCCCT 59.639 66.667 0.00 0.00 0.00 4.79
1278 1985 0.034059 CATCGTAGGCCTCATGTCCC 59.966 60.000 9.68 0.00 0.00 4.46
1280 1987 0.554305 TCGTAGGCCTCATGTCCCTA 59.446 55.000 9.68 0.00 0.00 3.53
1282 1989 1.068741 CGTAGGCCTCATGTCCCTAAC 59.931 57.143 9.68 0.00 33.31 2.34
1313 2020 2.682856 GTTTTATGCATTGCCTCCTCGA 59.317 45.455 3.54 0.00 0.00 4.04
1320 2027 2.545946 GCATTGCCTCCTCGAAGTATTC 59.454 50.000 0.00 0.00 43.09 1.75
1353 2076 4.309099 GGTTTCTTGATTTTGCAGCATGA 58.691 39.130 0.00 0.00 39.69 3.07
1434 2157 2.031420 CGGTAATGCCTCTTCATGCATG 60.031 50.000 21.07 21.07 46.97 4.06
1437 2160 4.763793 GGTAATGCCTCTTCATGCATGTAT 59.236 41.667 25.43 1.92 46.97 2.29
1447 2170 5.819379 TCTTCATGCATGTATCCTCTGTTTC 59.181 40.000 25.43 0.00 0.00 2.78
1451 2174 6.660521 TCATGCATGTATCCTCTGTTTCTTTT 59.339 34.615 25.43 0.00 0.00 2.27
1455 2178 7.283127 TGCATGTATCCTCTGTTTCTTTTATCC 59.717 37.037 0.00 0.00 0.00 2.59
1458 2181 8.561738 TGTATCCTCTGTTTCTTTTATCCAAC 57.438 34.615 0.00 0.00 0.00 3.77
1459 2182 8.160765 TGTATCCTCTGTTTCTTTTATCCAACA 58.839 33.333 0.00 0.00 0.00 3.33
1460 2183 7.693969 ATCCTCTGTTTCTTTTATCCAACAG 57.306 36.000 4.80 4.80 45.04 3.16
1461 2184 6.601332 TCCTCTGTTTCTTTTATCCAACAGT 58.399 36.000 9.97 0.00 44.34 3.55
1462 2185 6.710744 TCCTCTGTTTCTTTTATCCAACAGTC 59.289 38.462 9.97 0.00 44.34 3.51
1463 2186 6.072452 CCTCTGTTTCTTTTATCCAACAGTCC 60.072 42.308 9.97 0.00 44.34 3.85
1464 2187 6.361433 TCTGTTTCTTTTATCCAACAGTCCA 58.639 36.000 9.97 0.00 44.34 4.02
1465 2188 6.831353 TCTGTTTCTTTTATCCAACAGTCCAA 59.169 34.615 9.97 0.00 44.34 3.53
1466 2189 6.801575 TGTTTCTTTTATCCAACAGTCCAAC 58.198 36.000 0.00 0.00 0.00 3.77
1472 2195 1.896220 TCCAACAGTCCAACTCATGC 58.104 50.000 0.00 0.00 0.00 4.06
1533 2259 1.674359 TCTCTCGAGCTCATCTGTCC 58.326 55.000 15.40 0.00 0.00 4.02
1537 2263 1.098129 TCGAGCTCATCTGTCCCTCG 61.098 60.000 15.40 0.00 44.76 4.63
1540 2266 0.754957 AGCTCATCTGTCCCTCGGAG 60.755 60.000 0.00 0.00 34.66 4.63
1541 2267 0.753479 GCTCATCTGTCCCTCGGAGA 60.753 60.000 6.58 0.00 34.66 3.71
1777 2513 2.227388 GTCTTGACCAATGGCAGTTGAG 59.773 50.000 0.00 0.00 0.00 3.02
1828 2564 1.949525 GAGTTTGCAGCTTGAACTCCA 59.050 47.619 14.63 0.00 42.00 3.86
1934 2670 2.084546 AGTTGCCGCTTACTTTCATCC 58.915 47.619 0.00 0.00 0.00 3.51
1974 2711 4.913335 TCTATCGGTCTGATTTAGCGTT 57.087 40.909 0.00 0.00 38.57 4.84
2006 2743 6.418057 TTCTGCAAGGATTACACCAATTTT 57.582 33.333 0.00 0.00 0.00 1.82
2024 2761 4.314740 TTTTGAAGCCTACGTTTGCAAT 57.685 36.364 0.00 0.00 0.00 3.56
2086 2823 1.269883 CCTGCAAATTGCTCAGCACAA 60.270 47.619 19.34 0.00 45.31 3.33
2137 2875 3.247648 CCCGTTAACTGAACTGTCAACTG 59.752 47.826 3.71 0.00 35.74 3.16
2138 2876 4.116961 CCGTTAACTGAACTGTCAACTGA 58.883 43.478 3.71 0.00 35.74 3.41
2144 2882 9.042008 GTTAACTGAACTGTCAACTGATCTTTA 57.958 33.333 0.00 0.00 34.96 1.85
2145 2883 9.607988 TTAACTGAACTGTCAACTGATCTTTAA 57.392 29.630 0.00 0.00 31.88 1.52
2146 2884 8.506168 AACTGAACTGTCAACTGATCTTTAAA 57.494 30.769 0.00 0.00 31.88 1.52
2172 2910 7.337689 AGTTTCAGTATAAGATGCTGCATTTCA 59.662 33.333 17.36 0.00 41.93 2.69
2197 2935 2.892215 GGCCTACTGGGTCTAGATGTAC 59.108 54.545 0.00 0.00 36.61 2.90
2246 2984 1.065102 CTGCTGAAAGGATTGCGATGG 59.935 52.381 0.00 0.00 29.63 3.51
2257 3000 3.034924 TGCGATGGCAGTTTTTCCT 57.965 47.368 0.00 0.00 46.21 3.36
2297 3046 3.029320 TGAACATTGATGCACTTTGCC 57.971 42.857 0.00 0.00 44.23 4.52
2307 3056 0.040067 GCACTTTGCCCGACAAGAAG 60.040 55.000 0.00 0.00 40.06 2.85
2443 3192 3.784178 ACACAGAGGAATCCAAGAGAGA 58.216 45.455 0.61 0.00 0.00 3.10
2489 3239 0.319900 GCTCTGTGGTTCTGAAGCGA 60.320 55.000 14.15 5.51 0.00 4.93
2518 3268 7.519032 TCATCAAGATTAACCCGAACTTTTT 57.481 32.000 0.00 0.00 0.00 1.94
2680 3433 5.629125 AGATAGGAAAATGGGAGAATGAGC 58.371 41.667 0.00 0.00 0.00 4.26
2718 3474 9.387123 CTAAAGTGTAAAGAGCAAAGAACAATC 57.613 33.333 0.00 0.00 0.00 2.67
2727 3483 8.877808 AAGAGCAAAGAACAATCTTAAAAAGG 57.122 30.769 0.00 0.00 45.19 3.11
2807 3877 5.954752 TGATGTCCTCACTCAGAAGATAGTT 59.045 40.000 0.00 0.00 0.00 2.24
2838 3908 2.092211 CACGGTAAAAGCAACTCTAGCG 59.908 50.000 0.00 0.00 40.19 4.26
2940 4010 2.423538 ACACAGAATCGCCATAAAAGCC 59.576 45.455 0.00 0.00 0.00 4.35
2942 4012 1.338020 CAGAATCGCCATAAAAGCCCC 59.662 52.381 0.00 0.00 0.00 5.80
3014 4088 1.343478 ACCATCCTTCCTCACCTCGAT 60.343 52.381 0.00 0.00 0.00 3.59
3031 4105 9.887406 TCACCTCGATAATGAAAGTTTTTAAAC 57.113 29.630 0.00 0.00 39.17 2.01
3127 4201 7.167801 GCACTACGATTCTCTACTAAATGAACC 59.832 40.741 0.00 0.00 0.00 3.62
3129 4203 8.407064 ACTACGATTCTCTACTAAATGAACCAG 58.593 37.037 0.00 0.00 0.00 4.00
3156 4230 4.999310 TCTTCCTCCTCTAGAAAGTGACA 58.001 43.478 0.00 0.00 0.00 3.58
3160 4234 4.707448 TCCTCCTCTAGAAAGTGACATCAC 59.293 45.833 3.72 3.72 46.77 3.06
3169 4243 3.635191 TGACATCACAGGCGGGCA 61.635 61.111 3.78 0.00 0.00 5.36
3170 4244 2.821366 GACATCACAGGCGGGCAG 60.821 66.667 3.78 0.00 0.00 4.85
3171 4245 3.315142 GACATCACAGGCGGGCAGA 62.315 63.158 3.78 0.00 0.00 4.26
3173 4247 4.101448 ATCACAGGCGGGCAGACC 62.101 66.667 3.78 0.00 0.00 3.85
3200 4274 3.044305 GTCAGCTGCCGCGACTTT 61.044 61.111 8.23 0.00 42.32 2.66
3201 4275 2.280797 TCAGCTGCCGCGACTTTT 60.281 55.556 8.23 0.00 42.32 2.27
3203 4277 4.030452 AGCTGCCGCGACTTTTGC 62.030 61.111 8.23 0.58 42.32 3.68
3213 4587 2.515057 ACTTTTGCCGACCACGCA 60.515 55.556 0.00 0.00 38.29 5.24
3220 4594 0.391793 TGCCGACCACGCAATCAATA 60.392 50.000 0.00 0.00 38.29 1.90
3267 4642 6.624204 CGGGATACAACCACATTTTTAAGGTC 60.624 42.308 0.00 0.00 39.74 3.85
3268 4643 6.350696 GGGATACAACCACATTTTTAAGGTCC 60.351 42.308 0.00 0.00 39.74 4.46
3269 4644 6.209788 GGATACAACCACATTTTTAAGGTCCA 59.790 38.462 0.00 0.00 32.05 4.02
3270 4645 5.941555 ACAACCACATTTTTAAGGTCCAA 57.058 34.783 0.00 0.00 32.05 3.53
3276 4651 5.301805 CCACATTTTTAAGGTCCAAGTGAGT 59.698 40.000 0.00 0.00 0.00 3.41
3278 4653 4.911514 TTTTTAAGGTCCAAGTGAGTGC 57.088 40.909 0.00 0.00 0.00 4.40
3293 4672 2.092968 TGAGTGCGGCTTCCATTTCTAT 60.093 45.455 0.00 0.00 0.00 1.98
3297 4676 1.405105 GCGGCTTCCATTTCTATGCAA 59.595 47.619 0.00 0.00 0.00 4.08
3341 4720 3.702048 CTCGAGGGTTGCGGGGAA 61.702 66.667 3.91 0.00 0.00 3.97
3414 4793 0.887836 ACTCGGAGTAGTCACACGCA 60.888 55.000 9.33 0.00 0.00 5.24
3417 4797 0.039437 CGGAGTAGTCACACGCACTT 60.039 55.000 0.00 0.00 0.00 3.16
3457 4837 2.039405 CGGTCCTCTTCGGTCTCGT 61.039 63.158 0.00 0.00 37.69 4.18
3459 4839 0.109226 GGTCCTCTTCGGTCTCGTTG 60.109 60.000 0.00 0.00 37.69 4.10
3471 4851 0.974383 TCTCGTTGAGGAAAGGTCCC 59.026 55.000 0.00 0.00 46.30 4.46
3472 4852 0.036294 CTCGTTGAGGAAAGGTCCCC 60.036 60.000 0.00 0.00 46.30 4.81
3484 4865 4.803426 GTCCCCGAGAGTGCGCAG 62.803 72.222 12.22 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.207165 ACAGCTCTTTTTGGTCAGCTTTA 58.793 39.130 0.00 0.00 40.33 1.85
1 2 3.026694 ACAGCTCTTTTTGGTCAGCTTT 58.973 40.909 0.00 0.00 40.33 3.51
2 3 2.659428 ACAGCTCTTTTTGGTCAGCTT 58.341 42.857 0.00 0.00 40.33 3.74
3 4 2.355010 ACAGCTCTTTTTGGTCAGCT 57.645 45.000 0.00 0.00 43.16 4.24
4 5 2.358898 TCAACAGCTCTTTTTGGTCAGC 59.641 45.455 0.00 0.00 0.00 4.26
5 6 4.637483 TTCAACAGCTCTTTTTGGTCAG 57.363 40.909 0.00 0.00 0.00 3.51
6 7 4.202141 CCATTCAACAGCTCTTTTTGGTCA 60.202 41.667 0.00 0.00 0.00 4.02
7 8 4.301628 CCATTCAACAGCTCTTTTTGGTC 58.698 43.478 0.00 0.00 0.00 4.02
8 9 3.070015 CCCATTCAACAGCTCTTTTTGGT 59.930 43.478 0.00 0.00 0.00 3.67
9 10 3.656559 CCCATTCAACAGCTCTTTTTGG 58.343 45.455 0.00 0.00 0.00 3.28
10 11 3.062042 GCCCATTCAACAGCTCTTTTTG 58.938 45.455 0.00 0.00 0.00 2.44
11 12 2.288395 CGCCCATTCAACAGCTCTTTTT 60.288 45.455 0.00 0.00 0.00 1.94
12 13 1.270550 CGCCCATTCAACAGCTCTTTT 59.729 47.619 0.00 0.00 0.00 2.27
13 14 0.883833 CGCCCATTCAACAGCTCTTT 59.116 50.000 0.00 0.00 0.00 2.52
14 15 0.250901 ACGCCCATTCAACAGCTCTT 60.251 50.000 0.00 0.00 0.00 2.85
15 16 0.250901 AACGCCCATTCAACAGCTCT 60.251 50.000 0.00 0.00 0.00 4.09
16 17 1.448985 TAACGCCCATTCAACAGCTC 58.551 50.000 0.00 0.00 0.00 4.09
17 18 2.017049 GATAACGCCCATTCAACAGCT 58.983 47.619 0.00 0.00 0.00 4.24
18 19 1.065551 GGATAACGCCCATTCAACAGC 59.934 52.381 0.00 0.00 0.00 4.40
19 20 2.643551 AGGATAACGCCCATTCAACAG 58.356 47.619 0.00 0.00 0.00 3.16
20 21 2.799126 AGGATAACGCCCATTCAACA 57.201 45.000 0.00 0.00 0.00 3.33
21 22 2.876550 GGTAGGATAACGCCCATTCAAC 59.123 50.000 0.00 0.00 0.00 3.18
22 23 2.775384 AGGTAGGATAACGCCCATTCAA 59.225 45.455 0.00 0.00 29.65 2.69
23 24 2.104111 CAGGTAGGATAACGCCCATTCA 59.896 50.000 0.00 0.00 29.65 2.57
24 25 2.550208 CCAGGTAGGATAACGCCCATTC 60.550 54.545 0.00 0.00 41.22 2.67
25 26 1.420138 CCAGGTAGGATAACGCCCATT 59.580 52.381 0.00 0.00 41.22 3.16
26 27 1.056660 CCAGGTAGGATAACGCCCAT 58.943 55.000 0.00 0.00 41.22 4.00
27 28 1.692173 GCCAGGTAGGATAACGCCCA 61.692 60.000 0.00 0.00 41.22 5.36
28 29 1.070957 GCCAGGTAGGATAACGCCC 59.929 63.158 0.00 0.00 41.22 6.13
29 30 0.532196 GTGCCAGGTAGGATAACGCC 60.532 60.000 0.00 0.00 41.22 5.68
30 31 0.532196 GGTGCCAGGTAGGATAACGC 60.532 60.000 0.00 0.00 41.22 4.84
31 32 0.249322 CGGTGCCAGGTAGGATAACG 60.249 60.000 0.00 0.00 41.22 3.18
32 33 0.532196 GCGGTGCCAGGTAGGATAAC 60.532 60.000 0.00 0.00 41.22 1.89
33 34 0.978667 TGCGGTGCCAGGTAGGATAA 60.979 55.000 0.00 0.00 41.22 1.75
34 35 1.382009 TGCGGTGCCAGGTAGGATA 60.382 57.895 0.00 0.00 41.22 2.59
35 36 2.687200 TGCGGTGCCAGGTAGGAT 60.687 61.111 0.00 0.00 41.22 3.24
36 37 3.702048 GTGCGGTGCCAGGTAGGA 61.702 66.667 0.00 0.00 41.22 2.94
37 38 3.545124 TTGTGCGGTGCCAGGTAGG 62.545 63.158 0.00 0.00 41.84 3.18
38 39 1.599518 TTTGTGCGGTGCCAGGTAG 60.600 57.895 0.00 0.00 0.00 3.18
39 40 1.894756 GTTTGTGCGGTGCCAGGTA 60.895 57.895 0.00 0.00 0.00 3.08
40 41 3.216292 GTTTGTGCGGTGCCAGGT 61.216 61.111 0.00 0.00 0.00 4.00
41 42 2.406452 GAAGTTTGTGCGGTGCCAGG 62.406 60.000 0.00 0.00 0.00 4.45
42 43 1.008538 GAAGTTTGTGCGGTGCCAG 60.009 57.895 0.00 0.00 0.00 4.85
43 44 2.485795 GGAAGTTTGTGCGGTGCCA 61.486 57.895 0.00 0.00 0.00 4.92
44 45 2.130073 GAGGAAGTTTGTGCGGTGCC 62.130 60.000 0.00 0.00 0.00 5.01
45 46 1.166531 AGAGGAAGTTTGTGCGGTGC 61.167 55.000 0.00 0.00 0.00 5.01
46 47 0.868406 GAGAGGAAGTTTGTGCGGTG 59.132 55.000 0.00 0.00 0.00 4.94
47 48 0.600255 CGAGAGGAAGTTTGTGCGGT 60.600 55.000 0.00 0.00 0.00 5.68
48 49 2.153913 CGAGAGGAAGTTTGTGCGG 58.846 57.895 0.00 0.00 0.00 5.69
61 62 3.374402 ACCTGTGGCGTCCGAGAG 61.374 66.667 0.00 0.00 0.00 3.20
62 63 3.680786 CACCTGTGGCGTCCGAGA 61.681 66.667 0.00 0.00 0.00 4.04
63 64 4.742201 CCACCTGTGGCGTCCGAG 62.742 72.222 2.89 0.00 44.73 4.63
78 79 4.028490 CTAGTGGTTGGGGCGCCA 62.028 66.667 30.85 20.22 0.00 5.69
79 80 2.187896 TTACTAGTGGTTGGGGCGCC 62.188 60.000 21.18 21.18 0.00 6.53
80 81 0.107361 ATTACTAGTGGTTGGGGCGC 60.107 55.000 5.39 0.00 0.00 6.53
81 82 1.065709 ACATTACTAGTGGTTGGGGCG 60.066 52.381 5.39 0.00 0.00 6.13
82 83 2.801077 ACATTACTAGTGGTTGGGGC 57.199 50.000 5.39 0.00 0.00 5.80
83 84 4.829872 TGTACATTACTAGTGGTTGGGG 57.170 45.455 5.39 0.00 0.00 4.96
84 85 6.482308 GCTATTGTACATTACTAGTGGTTGGG 59.518 42.308 5.39 0.00 0.00 4.12
85 86 6.482308 GGCTATTGTACATTACTAGTGGTTGG 59.518 42.308 5.39 0.00 0.00 3.77
86 87 6.200286 CGGCTATTGTACATTACTAGTGGTTG 59.800 42.308 5.39 2.91 0.00 3.77
87 88 6.097270 TCGGCTATTGTACATTACTAGTGGTT 59.903 38.462 5.39 0.00 0.00 3.67
88 89 5.595542 TCGGCTATTGTACATTACTAGTGGT 59.404 40.000 5.39 3.82 0.00 4.16
89 90 6.080648 TCGGCTATTGTACATTACTAGTGG 57.919 41.667 5.39 0.00 0.00 4.00
90 91 5.629849 GCTCGGCTATTGTACATTACTAGTG 59.370 44.000 5.39 0.00 0.00 2.74
91 92 5.301045 TGCTCGGCTATTGTACATTACTAGT 59.699 40.000 0.00 0.00 0.00 2.57
92 93 5.769367 TGCTCGGCTATTGTACATTACTAG 58.231 41.667 0.00 0.00 0.00 2.57
93 94 5.777850 TGCTCGGCTATTGTACATTACTA 57.222 39.130 0.00 0.00 0.00 1.82
94 95 4.665833 TGCTCGGCTATTGTACATTACT 57.334 40.909 0.00 0.00 0.00 2.24
95 96 4.025145 GGTTGCTCGGCTATTGTACATTAC 60.025 45.833 0.00 0.00 0.00 1.89
96 97 4.124238 GGTTGCTCGGCTATTGTACATTA 58.876 43.478 0.00 0.00 0.00 1.90
97 98 2.943033 GGTTGCTCGGCTATTGTACATT 59.057 45.455 0.00 0.00 0.00 2.71
101 102 2.093181 ACATGGTTGCTCGGCTATTGTA 60.093 45.455 0.00 0.00 0.00 2.41
128 129 0.744414 GTGATGGATCCACACGGGTG 60.744 60.000 18.99 11.92 44.85 4.61
134 135 1.841919 AGCATCAGTGATGGATCCACA 59.158 47.619 29.66 14.43 40.10 4.17
135 136 2.158856 TGAGCATCAGTGATGGATCCAC 60.159 50.000 29.66 14.78 42.56 4.02
136 137 2.121129 TGAGCATCAGTGATGGATCCA 58.879 47.619 29.66 18.88 42.56 3.41
137 138 2.924757 TGAGCATCAGTGATGGATCC 57.075 50.000 29.66 15.75 42.56 3.36
163 164 3.964031 GTTCTCTAGACATGTGGGGAGAT 59.036 47.826 1.15 0.00 31.32 2.75
167 168 3.639094 CCTAGTTCTCTAGACATGTGGGG 59.361 52.174 1.15 0.00 44.52 4.96
168 169 3.639094 CCCTAGTTCTCTAGACATGTGGG 59.361 52.174 1.15 0.00 44.52 4.61
170 171 3.243234 CGCCCTAGTTCTCTAGACATGTG 60.243 52.174 1.15 0.00 44.52 3.21
174 175 2.022754 GCCGCCCTAGTTCTCTAGACA 61.023 57.143 4.13 0.00 44.52 3.41
175 176 0.669619 GCCGCCCTAGTTCTCTAGAC 59.330 60.000 4.13 0.00 44.52 2.59
179 180 0.466124 GATTGCCGCCCTAGTTCTCT 59.534 55.000 0.00 0.00 0.00 3.10
214 215 6.153000 ACAATAGTATAGATCCTGCCTAACCG 59.847 42.308 0.00 0.00 0.00 4.44
217 218 8.585881 GTCAACAATAGTATAGATCCTGCCTAA 58.414 37.037 0.00 0.00 0.00 2.69
219 220 6.014156 GGTCAACAATAGTATAGATCCTGCCT 60.014 42.308 0.00 0.00 0.00 4.75
220 221 6.166982 GGTCAACAATAGTATAGATCCTGCC 58.833 44.000 0.00 0.00 0.00 4.85
222 223 9.429359 GAATGGTCAACAATAGTATAGATCCTG 57.571 37.037 0.00 0.00 0.00 3.86
223 224 8.307483 CGAATGGTCAACAATAGTATAGATCCT 58.693 37.037 0.00 0.00 0.00 3.24
226 229 6.874134 GGCGAATGGTCAACAATAGTATAGAT 59.126 38.462 0.00 0.00 0.00 1.98
230 233 3.807622 CGGCGAATGGTCAACAATAGTAT 59.192 43.478 0.00 0.00 0.00 2.12
300 303 3.721706 ACTGTAGCAGGCCTGGGC 61.722 66.667 33.46 20.80 35.51 5.36
301 304 2.270205 CACTGTAGCAGGCCTGGG 59.730 66.667 33.46 10.63 35.51 4.45
302 305 2.437359 GCACTGTAGCAGGCCTGG 60.437 66.667 33.46 18.83 35.51 4.45
303 306 2.437359 GGCACTGTAGCAGGCCTG 60.437 66.667 29.34 29.34 41.35 4.85
306 309 1.144936 CTAGGGCACTGTAGCAGGC 59.855 63.158 0.00 1.89 35.51 4.85
307 310 0.176680 CACTAGGGCACTGTAGCAGG 59.823 60.000 0.00 0.00 35.51 4.85
308 311 0.898320 ACACTAGGGCACTGTAGCAG 59.102 55.000 0.00 0.00 37.52 4.24
309 312 0.895530 GACACTAGGGCACTGTAGCA 59.104 55.000 0.00 0.00 35.83 3.49
310 313 0.179134 CGACACTAGGGCACTGTAGC 60.179 60.000 0.00 0.00 0.00 3.58
311 314 0.179134 GCGACACTAGGGCACTGTAG 60.179 60.000 0.00 0.00 0.00 2.74
312 315 0.611062 AGCGACACTAGGGCACTGTA 60.611 55.000 0.00 0.00 0.00 2.74
314 317 0.179134 GTAGCGACACTAGGGCACTG 60.179 60.000 0.00 0.00 0.00 3.66
316 319 0.179134 CTGTAGCGACACTAGGGCAC 60.179 60.000 0.00 0.00 0.00 5.01
317 320 0.611062 ACTGTAGCGACACTAGGGCA 60.611 55.000 0.00 0.00 0.00 5.36
318 321 0.179134 CACTGTAGCGACACTAGGGC 60.179 60.000 0.00 0.00 0.00 5.19
319 322 1.460504 TCACTGTAGCGACACTAGGG 58.539 55.000 0.00 0.00 0.00 3.53
320 323 2.228103 TGTTCACTGTAGCGACACTAGG 59.772 50.000 0.00 0.00 0.00 3.02
321 324 3.235195 GTGTTCACTGTAGCGACACTAG 58.765 50.000 0.00 0.00 38.02 2.57
322 325 2.619646 TGTGTTCACTGTAGCGACACTA 59.380 45.455 0.00 0.00 40.79 2.74
323 326 1.407618 TGTGTTCACTGTAGCGACACT 59.592 47.619 0.00 0.00 40.79 3.55
324 327 1.847818 TGTGTTCACTGTAGCGACAC 58.152 50.000 0.00 0.00 40.62 3.67
325 328 2.672714 GATGTGTTCACTGTAGCGACA 58.327 47.619 0.00 0.00 0.00 4.35
326 329 1.649171 CGATGTGTTCACTGTAGCGAC 59.351 52.381 4.59 0.00 0.00 5.19
327 330 1.268625 ACGATGTGTTCACTGTAGCGA 59.731 47.619 6.46 0.00 0.00 4.93
328 331 1.698165 ACGATGTGTTCACTGTAGCG 58.302 50.000 4.59 1.88 0.00 4.26
329 332 3.247648 ACAAACGATGTGTTCACTGTAGC 59.752 43.478 4.59 0.00 41.93 3.58
330 333 5.403897 AACAAACGATGTGTTCACTGTAG 57.596 39.130 4.59 0.00 42.99 2.74
338 341 3.787476 GCGTGAAGAACAAACGATGTGTT 60.787 43.478 0.00 0.00 42.99 3.32
339 342 2.286184 GCGTGAAGAACAAACGATGTGT 60.286 45.455 0.00 0.00 42.99 3.72
340 343 2.298300 GCGTGAAGAACAAACGATGTG 58.702 47.619 0.00 0.00 42.99 3.21
341 344 1.263217 GGCGTGAAGAACAAACGATGT 59.737 47.619 0.00 0.00 46.82 3.06
342 345 1.399727 GGGCGTGAAGAACAAACGATG 60.400 52.381 0.00 0.00 39.64 3.84
343 346 0.872388 GGGCGTGAAGAACAAACGAT 59.128 50.000 0.00 0.00 39.64 3.73
344 347 1.161563 GGGGCGTGAAGAACAAACGA 61.162 55.000 0.00 0.00 39.64 3.85
345 348 1.281656 GGGGCGTGAAGAACAAACG 59.718 57.895 0.00 0.00 40.22 3.60
346 349 0.310854 CTGGGGCGTGAAGAACAAAC 59.689 55.000 0.00 0.00 0.00 2.93
347 350 0.821711 CCTGGGGCGTGAAGAACAAA 60.822 55.000 0.00 0.00 0.00 2.83
348 351 1.228124 CCTGGGGCGTGAAGAACAA 60.228 57.895 0.00 0.00 0.00 2.83
349 352 2.391724 GACCTGGGGCGTGAAGAACA 62.392 60.000 0.00 0.00 0.00 3.18
350 353 1.671379 GACCTGGGGCGTGAAGAAC 60.671 63.158 0.00 0.00 0.00 3.01
351 354 2.747686 GACCTGGGGCGTGAAGAA 59.252 61.111 0.00 0.00 0.00 2.52
352 355 3.319198 GGACCTGGGGCGTGAAGA 61.319 66.667 0.00 0.00 0.00 2.87
353 356 3.612247 CTGGACCTGGGGCGTGAAG 62.612 68.421 0.00 0.00 0.00 3.02
354 357 3.636231 CTGGACCTGGGGCGTGAA 61.636 66.667 0.00 0.00 0.00 3.18
376 379 1.972660 GATCCAAGACCCAGGACCGG 61.973 65.000 0.00 0.00 36.60 5.28
377 380 1.522569 GATCCAAGACCCAGGACCG 59.477 63.158 0.00 0.00 36.60 4.79
378 381 1.915983 GGATCCAAGACCCAGGACC 59.084 63.158 6.95 0.00 36.60 4.46
379 382 1.522569 CGGATCCAAGACCCAGGAC 59.477 63.158 13.41 0.00 36.60 3.85
380 383 2.367202 GCGGATCCAAGACCCAGGA 61.367 63.158 13.41 0.00 38.50 3.86
381 384 2.190578 GCGGATCCAAGACCCAGG 59.809 66.667 13.41 0.00 0.00 4.45
382 385 2.190578 GGCGGATCCAAGACCCAG 59.809 66.667 13.41 0.00 34.01 4.45
383 386 2.609299 TGGCGGATCCAAGACCCA 60.609 61.111 13.41 6.76 43.21 4.51
390 393 0.033503 TCTAGTCAGTGGCGGATCCA 60.034 55.000 13.41 0.00 44.18 3.41
391 394 0.671251 CTCTAGTCAGTGGCGGATCC 59.329 60.000 0.00 0.00 0.00 3.36
392 395 1.394618 ACTCTAGTCAGTGGCGGATC 58.605 55.000 0.00 0.00 0.00 3.36
393 396 1.853963 AACTCTAGTCAGTGGCGGAT 58.146 50.000 0.00 0.00 0.00 4.18
394 397 2.089980 GTAACTCTAGTCAGTGGCGGA 58.910 52.381 0.00 0.00 0.00 5.54
395 398 1.816835 TGTAACTCTAGTCAGTGGCGG 59.183 52.381 0.00 0.00 0.00 6.13
396 399 3.784701 ATGTAACTCTAGTCAGTGGCG 57.215 47.619 0.00 0.00 0.00 5.69
397 400 7.013464 AGTGTATATGTAACTCTAGTCAGTGGC 59.987 40.741 0.00 0.00 0.00 5.01
398 401 8.453238 AGTGTATATGTAACTCTAGTCAGTGG 57.547 38.462 0.00 0.00 0.00 4.00
399 402 9.723447 CAAGTGTATATGTAACTCTAGTCAGTG 57.277 37.037 0.00 0.00 0.00 3.66
400 403 9.682465 TCAAGTGTATATGTAACTCTAGTCAGT 57.318 33.333 0.00 0.00 0.00 3.41
499 504 9.044646 ACATCTCATAGTAAATCTAGCATCCAT 57.955 33.333 0.00 0.00 31.67 3.41
563 568 4.938832 TGGTCGTTTGGTTCATAGTATTGG 59.061 41.667 0.00 0.00 0.00 3.16
568 573 3.190535 GCATTGGTCGTTTGGTTCATAGT 59.809 43.478 0.00 0.00 0.00 2.12
570 575 3.149981 TGCATTGGTCGTTTGGTTCATA 58.850 40.909 0.00 0.00 0.00 2.15
598 603 1.580059 TCGCAGGAACCCTTAGGATT 58.420 50.000 0.00 0.00 36.73 3.01
599 604 1.580059 TTCGCAGGAACCCTTAGGAT 58.420 50.000 0.00 0.00 36.73 3.24
601 606 1.209504 TGATTCGCAGGAACCCTTAGG 59.790 52.381 0.00 0.00 34.37 2.69
608 613 1.869767 CTGCCTATGATTCGCAGGAAC 59.130 52.381 7.39 0.00 45.00 3.62
613 618 0.465287 TGCTCTGCCTATGATTCGCA 59.535 50.000 0.00 0.00 0.00 5.10
614 619 1.146637 CTGCTCTGCCTATGATTCGC 58.853 55.000 0.00 0.00 0.00 4.70
615 620 1.146637 GCTGCTCTGCCTATGATTCG 58.853 55.000 0.00 0.00 0.00 3.34
628 1299 1.834822 ATACCTCGGAGGGCTGCTC 60.835 63.158 26.94 0.00 40.58 4.26
648 1319 3.008594 ACGGTTCCAAGTTCCATATCACA 59.991 43.478 0.00 0.00 0.00 3.58
668 1339 0.677731 ATGTCATGTGGGGCTCAACG 60.678 55.000 0.00 0.00 0.00 4.10
694 1376 7.996098 TTCTAGTACCCTTTTCTTTTGATGG 57.004 36.000 0.00 0.00 0.00 3.51
708 1390 6.505272 CACTTGCTAGTGTATTCTAGTACCC 58.495 44.000 18.65 0.00 45.46 3.69
758 1453 4.612536 GGCCGGCGCATCAAATCG 62.613 66.667 22.54 0.43 36.38 3.34
782 1477 1.488705 ATGAAGTTGTGCTCCGGGGA 61.489 55.000 4.80 0.00 0.00 4.81
783 1478 0.251916 TATGAAGTTGTGCTCCGGGG 59.748 55.000 0.00 0.00 0.00 5.73
784 1479 2.107950 TTATGAAGTTGTGCTCCGGG 57.892 50.000 0.00 0.00 0.00 5.73
785 1480 4.226761 GTTTTTATGAAGTTGTGCTCCGG 58.773 43.478 0.00 0.00 0.00 5.14
786 1481 4.023193 AGGTTTTTATGAAGTTGTGCTCCG 60.023 41.667 0.00 0.00 0.00 4.63
793 1488 4.462834 GGGAGGGAGGTTTTTATGAAGTTG 59.537 45.833 0.00 0.00 0.00 3.16
794 1489 4.673968 GGGAGGGAGGTTTTTATGAAGTT 58.326 43.478 0.00 0.00 0.00 2.66
836 1532 0.240145 GGCTTTGTTGGAGCGGTTAC 59.760 55.000 0.00 0.00 41.03 2.50
1035 1742 3.672295 GAGCAGCACGAGGAAGGGG 62.672 68.421 0.00 0.00 0.00 4.79
1038 1745 2.099431 GCAGAGCAGCACGAGGAAG 61.099 63.158 0.00 0.00 0.00 3.46
1039 1746 2.047844 GCAGAGCAGCACGAGGAA 60.048 61.111 0.00 0.00 0.00 3.36
1146 1853 2.203126 CGGAAGATCCTGGCCAGC 60.203 66.667 28.39 14.14 33.30 4.85
1149 1856 1.153147 GTTCCGGAAGATCCTGGCC 60.153 63.158 19.50 0.00 33.30 5.36
1257 1964 0.034059 GACATGAGGCCTACGATGGG 59.966 60.000 4.42 0.00 0.00 4.00
1305 2012 3.067461 CAGAGGTGAATACTTCGAGGAGG 59.933 52.174 0.00 0.00 37.92 4.30
1313 2020 2.269940 ACCCAGCAGAGGTGAATACTT 58.730 47.619 0.00 0.00 35.85 2.24
1320 2027 1.202806 TCAAGAAACCCAGCAGAGGTG 60.203 52.381 0.00 0.00 37.78 4.00
1353 2076 1.000993 AGTCGGCACTCATCCTCCT 59.999 57.895 0.00 0.00 0.00 3.69
1378 2101 4.330074 ACACTGATAACGCAAGCTTGTATC 59.670 41.667 26.55 23.08 45.62 2.24
1434 2157 8.561738 TGTTGGATAAAAGAAACAGAGGATAC 57.438 34.615 0.00 0.00 0.00 2.24
1447 2170 6.615088 CATGAGTTGGACTGTTGGATAAAAG 58.385 40.000 0.00 0.00 0.00 2.27
1451 2174 3.264193 AGCATGAGTTGGACTGTTGGATA 59.736 43.478 0.00 0.00 0.00 2.59
1455 2178 3.996150 AAAGCATGAGTTGGACTGTTG 57.004 42.857 0.00 0.00 0.00 3.33
1458 2181 2.094894 CGCTAAAGCATGAGTTGGACTG 59.905 50.000 0.00 0.00 42.21 3.51
1459 2182 2.289694 ACGCTAAAGCATGAGTTGGACT 60.290 45.455 0.00 0.00 42.21 3.85
1460 2183 2.076863 ACGCTAAAGCATGAGTTGGAC 58.923 47.619 0.00 0.00 42.21 4.02
1461 2184 2.076100 CACGCTAAAGCATGAGTTGGA 58.924 47.619 0.00 0.00 36.14 3.53
1462 2185 1.806542 ACACGCTAAAGCATGAGTTGG 59.193 47.619 4.87 0.00 36.14 3.77
1463 2186 4.084066 TGTTACACGCTAAAGCATGAGTTG 60.084 41.667 4.87 0.00 36.14 3.16
1464 2187 4.062293 TGTTACACGCTAAAGCATGAGTT 58.938 39.130 4.87 0.00 36.14 3.01
1465 2188 3.659786 TGTTACACGCTAAAGCATGAGT 58.340 40.909 4.87 0.00 36.14 3.41
1466 2189 4.661993 TTGTTACACGCTAAAGCATGAG 57.338 40.909 4.87 0.00 36.14 2.90
1472 2195 8.440059 TGATTACTGAATTGTTACACGCTAAAG 58.560 33.333 0.00 0.00 0.00 1.85
1533 2259 4.095036 GCCTTAAATTCAGTTTCTCCGAGG 59.905 45.833 0.00 0.00 0.00 4.63
1537 2263 5.703876 CACTGCCTTAAATTCAGTTTCTCC 58.296 41.667 0.00 0.00 38.85 3.71
1540 2266 4.681483 GTGCACTGCCTTAAATTCAGTTTC 59.319 41.667 10.32 0.00 38.85 2.78
1541 2267 4.342092 AGTGCACTGCCTTAAATTCAGTTT 59.658 37.500 20.97 0.00 38.85 2.66
1640 2369 0.745845 CGCCCCATTTCTGAGTCAGG 60.746 60.000 19.99 4.34 31.51 3.86
1777 2513 7.201565 GGTTTCTTAGCAGATGATTGTACAGTC 60.202 40.741 11.23 11.23 0.00 3.51
1828 2564 1.654954 ATTCGTCTCTGCCGCGTACT 61.655 55.000 4.92 0.00 0.00 2.73
1934 2670 6.020281 CGATAGATTCAGGAAAGTGTTTCTCG 60.020 42.308 0.00 0.00 37.90 4.04
1974 2711 4.574674 AATCCTTGCAGAATGACAGGTA 57.425 40.909 0.00 0.00 39.69 3.08
2006 2743 1.068610 GCATTGCAAACGTAGGCTTCA 60.069 47.619 1.71 0.00 0.00 3.02
2024 2761 1.355971 GAAGTTCGCCGTCATAAGCA 58.644 50.000 0.00 0.00 0.00 3.91
2086 2823 0.538287 GTGTCCTGGGCTTGCTCTTT 60.538 55.000 0.00 0.00 0.00 2.52
2144 2882 7.636150 ATGCAGCATCTTATACTGAAACTTT 57.364 32.000 0.52 0.00 33.10 2.66
2145 2883 7.636150 AATGCAGCATCTTATACTGAAACTT 57.364 32.000 8.77 0.00 33.10 2.66
2146 2884 7.337689 TGAAATGCAGCATCTTATACTGAAACT 59.662 33.333 8.77 0.00 33.10 2.66
2172 2910 0.397816 CTAGACCCAGTAGGCCAGCT 60.398 60.000 5.01 0.00 40.58 4.24
2246 2984 4.553045 CGCAAAAACAAAAGGAAAAACTGC 59.447 37.500 0.00 0.00 0.00 4.40
2257 3000 6.091305 TGTTCATTGTCATCGCAAAAACAAAA 59.909 30.769 0.00 0.00 36.29 2.44
2297 3046 1.593196 TGGAAGCAACTTCTTGTCGG 58.407 50.000 7.24 0.00 40.07 4.79
2443 3192 4.317488 CAAAAAGCAAGTACAATGGCCAT 58.683 39.130 14.09 14.09 0.00 4.40
2469 3219 0.601046 CGCTTCAGAACCACAGAGCA 60.601 55.000 0.00 0.00 0.00 4.26
2489 3239 7.565680 AGTTCGGGTTAATCTTGATGAAGTAT 58.434 34.615 0.00 0.00 0.00 2.12
2518 3268 1.342076 ACTATCTTGACCTGCCTCCGA 60.342 52.381 0.00 0.00 0.00 4.55
2623 3376 3.761481 CAGAGCGTCTGCCTTTTTG 57.239 52.632 2.75 0.00 44.31 2.44
2663 3416 4.268359 ACTCTGCTCATTCTCCCATTTTC 58.732 43.478 0.00 0.00 0.00 2.29
2669 3422 6.587273 AGTAAATAACTCTGCTCATTCTCCC 58.413 40.000 0.00 0.00 30.33 4.30
2735 3491 5.865552 CCCGAAATCTAACGTCTTTCTTGTA 59.134 40.000 0.00 0.00 0.00 2.41
2740 3496 2.997986 TGCCCGAAATCTAACGTCTTTC 59.002 45.455 0.00 0.00 0.00 2.62
2745 3501 2.684001 TCATGCCCGAAATCTAACGT 57.316 45.000 0.00 0.00 0.00 3.99
2777 3533 3.055602 TCTGAGTGAGGACATCAACCATG 60.056 47.826 0.00 0.00 40.43 3.66
2807 3877 2.333926 CTTTTACCGTGCTCGATGTGA 58.666 47.619 10.21 0.00 39.71 3.58
2838 3908 1.518903 GCTGTCCACTTGGCAACTCC 61.519 60.000 0.00 0.00 34.44 3.85
2972 4046 4.072131 TGTCTTCTAGCCATTGACAAACC 58.928 43.478 0.00 0.00 35.15 3.27
3129 4203 3.306472 TTCTAGAGGAGGAAGAGCTCC 57.694 52.381 10.93 0.00 45.81 4.70
3156 4230 4.101448 GGTCTGCCCGCCTGTGAT 62.101 66.667 0.00 0.00 0.00 3.06
3173 4247 4.087892 CAGCTGACCCCTCACCCG 62.088 72.222 8.42 0.00 0.00 5.28
3183 4257 2.607892 AAAAGTCGCGGCAGCTGAC 61.608 57.895 20.43 15.64 42.67 3.51
3185 4259 2.127118 CAAAAGTCGCGGCAGCTG 60.127 61.111 15.58 10.11 42.32 4.24
3186 4260 4.030452 GCAAAAGTCGCGGCAGCT 62.030 61.111 15.58 0.00 42.32 4.24
3200 4274 1.240641 ATTGATTGCGTGGTCGGCAA 61.241 50.000 1.37 1.37 37.43 4.52
3201 4275 0.391793 TATTGATTGCGTGGTCGGCA 60.392 50.000 0.00 0.00 37.56 5.69
3203 4277 2.160615 TGTTTATTGATTGCGTGGTCGG 59.839 45.455 0.00 0.00 37.56 4.79
3206 4280 4.545610 CAAGTGTTTATTGATTGCGTGGT 58.454 39.130 0.00 0.00 0.00 4.16
3213 4587 5.025453 AGGATGCCCAAGTGTTTATTGATT 58.975 37.500 0.00 0.00 33.88 2.57
3220 4594 0.482446 TCCAGGATGCCCAAGTGTTT 59.518 50.000 0.00 0.00 33.88 2.83
3242 4616 5.184287 ACCTTAAAAATGTGGTTGTATCCCG 59.816 40.000 0.00 0.00 0.00 5.14
3245 4620 7.222000 TGGACCTTAAAAATGTGGTTGTATC 57.778 36.000 0.00 0.00 32.30 2.24
3267 4642 2.328099 GGAAGCCGCACTCACTTGG 61.328 63.158 0.00 0.00 0.00 3.61
3268 4643 0.957395 ATGGAAGCCGCACTCACTTG 60.957 55.000 0.00 0.00 0.00 3.16
3269 4644 0.250901 AATGGAAGCCGCACTCACTT 60.251 50.000 0.00 0.00 0.00 3.16
3270 4645 0.250901 AAATGGAAGCCGCACTCACT 60.251 50.000 0.00 0.00 0.00 3.41
3276 4651 1.024271 GCATAGAAATGGAAGCCGCA 58.976 50.000 0.00 0.00 33.38 5.69
3301 4680 1.530323 TTCGACCACATCTCGACAGA 58.470 50.000 0.00 0.00 39.82 3.41
3346 4725 1.573829 GAATCAGTTGTCGGCCGCAA 61.574 55.000 23.51 24.21 0.00 4.85
3347 4726 2.031919 AATCAGTTGTCGGCCGCA 59.968 55.556 23.51 19.45 0.00 5.69
3353 4732 3.243877 CGATAAGGCTGAATCAGTTGTCG 59.756 47.826 12.29 13.65 33.43 4.35
3358 4737 1.137086 ACGCGATAAGGCTGAATCAGT 59.863 47.619 15.93 6.64 33.43 3.41
3414 4793 3.196685 CCGAGAGAGATTTCTGGGAAAGT 59.803 47.826 0.00 0.00 43.50 2.66
3417 4797 2.497675 CACCGAGAGAGATTTCTGGGAA 59.502 50.000 10.46 0.00 43.50 3.97


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

AutoCloner maintained by Alex Coulton.