Multiple sequence alignment - TraesCS3D01G481500

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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 TraesCS3D01G481500 chr3D 100.000 3536 0 0 1 3536 579583833 579580298 0.000000e+00 6530.0
1 TraesCS3D01G481500 chr3D 92.463 1977 108 14 1066 3013 579398533 579400497 0.000000e+00 2787.0
2 TraesCS3D01G481500 chr3D 92.828 488 31 3 3049 3536 579400501 579400984 0.000000e+00 704.0
3 TraesCS3D01G481500 chr3D 81.749 263 38 9 2592 2850 138901770 138901514 9.940000e-51 211.0
4 TraesCS3D01G481500 chr3D 86.598 194 22 3 28 220 579397716 579397906 9.940000e-51 211.0
5 TraesCS3D01G481500 chr3D 80.083 241 42 5 2625 2864 567930726 567930961 1.300000e-39 174.0
6 TraesCS3D01G481500 chr3D 79.268 246 41 8 2625 2864 569464726 569464485 2.820000e-36 163.0
7 TraesCS3D01G481500 chr3D 86.014 143 17 2 35 177 579425873 579426012 2.200000e-32 150.0
8 TraesCS3D01G481500 chr3D 88.525 122 13 1 364 485 579426100 579426220 2.840000e-31 147.0
9 TraesCS3D01G481500 chr3D 73.203 459 99 16 1742 2185 565163695 565164144 1.020000e-30 145.0
10 TraesCS3D01G481500 chr3D 92.632 95 7 0 2888 2982 579506421 579506515 1.710000e-28 137.0
11 TraesCS3D01G481500 chr3D 74.055 397 73 24 2426 2808 566801783 566802163 6.160000e-28 135.0
12 TraesCS3D01G481500 chr3D 78.605 215 34 9 1191 1397 568136871 568137081 7.960000e-27 132.0
13 TraesCS3D01G481500 chr3D 78.744 207 35 5 1606 1809 567687166 567686966 2.860000e-26 130.0
14 TraesCS3D01G481500 chr3D 85.600 125 11 6 364 485 579397980 579398100 1.330000e-24 124.0
15 TraesCS3D01G481500 chr3D 93.750 64 4 0 3442 3505 520081973 520081910 2.910000e-16 97.1
16 TraesCS3D01G481500 chr3B 88.521 1690 144 27 753 2429 773746793 773748445 0.000000e+00 2001.0
17 TraesCS3D01G481500 chr3B 89.097 908 67 19 1951 2842 773882268 773881377 0.000000e+00 1099.0
18 TraesCS3D01G481500 chr3B 77.355 1104 198 34 1606 2684 684638488 684637412 1.090000e-169 606.0
19 TraesCS3D01G481500 chr3B 83.223 602 46 14 1008 1595 773882827 773882267 5.270000e-138 501.0
20 TraesCS3D01G481500 chr3B 93.160 307 13 2 3217 3516 773880751 773880446 9.010000e-121 444.0
21 TraesCS3D01G481500 chr3B 88.703 239 21 2 2894 3127 773880988 773880751 1.610000e-73 287.0
22 TraesCS3D01G481500 chr3B 90.047 211 19 2 22 232 773762597 773762805 4.500000e-69 272.0
23 TraesCS3D01G481500 chr3B 77.178 482 79 18 1087 1557 756440294 756439833 5.860000e-63 252.0
24 TraesCS3D01G481500 chr3B 85.315 143 13 5 90 231 773883579 773883444 1.320000e-29 141.0
25 TraesCS3D01G481500 chr3B 92.188 64 5 0 3442 3505 684635090 684635027 1.350000e-14 91.6
26 TraesCS3D01G481500 chr3A 91.064 1354 90 4 971 2313 714595562 714596895 0.000000e+00 1801.0
27 TraesCS3D01G481500 chr3A 85.333 750 61 19 2530 3241 714597031 714597769 0.000000e+00 730.0
28 TraesCS3D01G481500 chr3A 74.324 1184 225 49 1066 2220 700352273 700351140 2.520000e-116 429.0
29 TraesCS3D01G481500 chr3A 94.323 229 13 0 3290 3518 714597775 714598003 5.620000e-93 351.0
30 TraesCS3D01G481500 chr3A 90.187 214 19 2 22 234 714603721 714603933 9.670000e-71 278.0
31 TraesCS3D01G481500 chr3A 82.331 266 40 7 2592 2854 157040009 157039748 1.280000e-54 224.0
32 TraesCS3D01G481500 chr3A 73.453 614 132 20 1606 2205 700739816 700740412 5.990000e-48 202.0
33 TraesCS3D01G481500 chr3A 81.081 185 31 4 1375 1557 702421341 702421159 1.020000e-30 145.0
34 TraesCS3D01G481500 chr3A 78.307 189 28 9 1224 1403 700441703 700441519 3.730000e-20 110.0
35 TraesCS3D01G481500 chr3A 75.124 201 32 12 595 790 714595226 714595413 1.050000e-10 78.7
36 TraesCS3D01G481500 chrUn 78.055 401 76 12 1828 2221 41057786 41058181 3.530000e-60 243.0
37 TraesCS3D01G481500 chrUn 97.849 93 2 0 510 602 230759903 230759811 1.020000e-35 161.0
38 TraesCS3D01G481500 chrUn 79.018 224 42 4 2628 2850 40930078 40929859 7.910000e-32 148.0
39 TraesCS3D01G481500 chrUn 85.135 74 10 1 2625 2698 314513609 314513537 1.360000e-09 75.0
40 TraesCS3D01G481500 chr4B 98.925 93 1 0 510 602 430672241 430672149 2.180000e-37 167.0
41 TraesCS3D01G481500 chr4B 84.000 150 18 3 88 237 430672540 430672397 4.760000e-29 139.0
42 TraesCS3D01G481500 chr4B 85.593 118 15 2 117 232 622342020 622342137 4.790000e-24 122.0
43 TraesCS3D01G481500 chr4B 100.000 33 0 0 601 633 430672125 430672093 1.060000e-05 62.1
44 TraesCS3D01G481500 chr4A 97.849 93 2 0 510 602 714667343 714667251 1.020000e-35 161.0
45 TraesCS3D01G481500 chr2B 87.500 120 13 2 117 234 315136657 315136538 1.710000e-28 137.0
46 TraesCS3D01G481500 chr2B 86.667 120 14 2 117 234 120491529 120491410 7.960000e-27 132.0
47 TraesCS3D01G481500 chr1B 85.000 120 16 2 117 234 670761694 670761575 1.720000e-23 121.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G481500 chr3D 579580298 579583833 3535 True 6530.000 6530 100.00000 1 3536 1 chr3D.!!$R5 3535
1 TraesCS3D01G481500 chr3D 579397716 579400984 3268 False 956.500 2787 89.37225 28 3536 4 chr3D.!!$F6 3508
2 TraesCS3D01G481500 chr3B 773746793 773748445 1652 False 2001.000 2001 88.52100 753 2429 1 chr3B.!!$F1 1676
3 TraesCS3D01G481500 chr3B 773880446 773883579 3133 True 494.400 1099 87.89960 90 3516 5 chr3B.!!$R3 3426
4 TraesCS3D01G481500 chr3B 684635027 684638488 3461 True 348.800 606 84.77150 1606 3505 2 chr3B.!!$R2 1899
5 TraesCS3D01G481500 chr3A 714595226 714598003 2777 False 740.175 1801 86.46100 595 3518 4 chr3A.!!$F3 2923
6 TraesCS3D01G481500 chr3A 700351140 700352273 1133 True 429.000 429 74.32400 1066 2220 1 chr3A.!!$R2 1154
7 TraesCS3D01G481500 chr3A 700739816 700740412 596 False 202.000 202 73.45300 1606 2205 1 chr3A.!!$F1 599

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
238 240 0.036577 CCCCTGTCTTCAGTCTGCAG 60.037 60.0 7.63 7.63 39.82 4.41 F
653 727 0.165944 GATTTCAGTTGACGCGGGTG 59.834 55.0 10.96 0.00 0.00 4.61 F
831 920 0.177836 TCCATCAGTGTGTATGGCCG 59.822 55.0 0.00 0.00 42.08 6.13 F
832 921 0.177836 CCATCAGTGTGTATGGCCGA 59.822 55.0 0.00 0.00 36.50 5.54 F
1935 2082 0.323360 GGTCTGGGCCTGCAAATACA 60.323 55.0 4.53 0.00 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1664 1790 0.037975 GTACCTCCGCGTCAAGGAAA 60.038 55.000 21.85 9.69 37.32 3.13 R
1673 1799 1.061570 GTACGTCAGTACCTCCGCG 59.938 63.158 0.00 0.00 45.59 6.46 R
2127 2274 1.322442 ACAAGAGTTTGCTTGAGCCC 58.678 50.000 10.71 0.00 46.31 5.19 R
2375 3972 1.528129 CCACTTGAGCCCAGAAGAAC 58.472 55.000 0.00 0.00 0.00 3.01 R
2879 4910 1.074319 CATTGCGCAACATGGCTGAC 61.074 55.000 27.64 0.00 0.00 3.51 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 8.999905 AACTAACAAGAAAAGTACCCCATAAA 57.000 30.769 0.00 0.00 0.00 1.40
33 34 7.284919 AGAAAAGTACCCCATAAAACAACTG 57.715 36.000 0.00 0.00 0.00 3.16
41 42 4.764823 CCCCATAAAACAACTGTAGCTCAA 59.235 41.667 0.00 0.00 0.00 3.02
56 57 1.747355 GCTCAATTGCACAGCTATGGT 59.253 47.619 9.71 0.00 0.00 3.55
69 70 7.775093 TGCACAGCTATGGTAGAATTAGAAATT 59.225 33.333 0.00 0.00 0.00 1.82
96 98 9.869844 GACATTTATCGATCCAACAAAATAGAG 57.130 33.333 0.00 0.00 0.00 2.43
149 151 9.745880 GTACAAGAGAATATTATTCGGACTGAA 57.254 33.333 10.08 0.00 41.81 3.02
150 152 8.649973 ACAAGAGAATATTATTCGGACTGAAC 57.350 34.615 10.08 0.00 40.00 3.18
170 172 3.393800 ACTGAACACGAGGTTTCAGATG 58.606 45.455 16.37 0.00 40.63 2.90
174 176 0.445436 CACGAGGTTTCAGATGCTGC 59.555 55.000 0.00 0.00 0.00 5.25
211 213 1.881973 TCAGATTCTGCAGCAAACCAC 59.118 47.619 9.47 0.00 0.00 4.16
230 232 4.329545 GCGGTGCCCCTGTCTTCA 62.330 66.667 0.00 0.00 0.00 3.02
231 233 2.046892 CGGTGCCCCTGTCTTCAG 60.047 66.667 0.00 0.00 41.01 3.02
232 234 2.883828 CGGTGCCCCTGTCTTCAGT 61.884 63.158 0.00 0.00 39.82 3.41
233 235 1.003233 GGTGCCCCTGTCTTCAGTC 60.003 63.158 0.00 0.00 39.82 3.51
234 236 1.484444 GGTGCCCCTGTCTTCAGTCT 61.484 60.000 0.00 0.00 39.82 3.24
235 237 0.321122 GTGCCCCTGTCTTCAGTCTG 60.321 60.000 0.00 0.00 39.82 3.51
236 238 1.376553 GCCCCTGTCTTCAGTCTGC 60.377 63.158 0.00 0.00 39.82 4.26
237 239 2.061220 CCCCTGTCTTCAGTCTGCA 58.939 57.895 0.00 0.00 39.82 4.41
238 240 0.036577 CCCCTGTCTTCAGTCTGCAG 60.037 60.000 7.63 7.63 39.82 4.41
239 241 0.673022 CCCTGTCTTCAGTCTGCAGC 60.673 60.000 9.47 4.26 39.82 5.25
240 242 1.013005 CCTGTCTTCAGTCTGCAGCG 61.013 60.000 9.47 0.00 39.82 5.18
241 243 1.005748 TGTCTTCAGTCTGCAGCGG 60.006 57.895 9.47 5.39 0.00 5.52
242 244 2.047844 TCTTCAGTCTGCAGCGGC 60.048 61.111 9.47 0.31 41.68 6.53
243 245 3.485431 CTTCAGTCTGCAGCGGCG 61.485 66.667 9.47 0.51 45.35 6.46
253 255 3.803082 CAGCGGCGGTTGACCATG 61.803 66.667 9.73 0.00 35.14 3.66
254 256 4.015406 AGCGGCGGTTGACCATGA 62.015 61.111 5.44 0.00 35.14 3.07
255 257 3.499737 GCGGCGGTTGACCATGAG 61.500 66.667 9.78 0.00 35.14 2.90
256 258 2.819595 CGGCGGTTGACCATGAGG 60.820 66.667 0.00 0.00 42.21 3.86
273 275 7.035840 CCATGAGGTTTCAGATTCTAATTGG 57.964 40.000 0.00 0.00 36.61 3.16
274 276 6.604795 CCATGAGGTTTCAGATTCTAATTGGT 59.395 38.462 0.00 0.00 36.61 3.67
275 277 7.123247 CCATGAGGTTTCAGATTCTAATTGGTT 59.877 37.037 0.00 0.00 36.61 3.67
276 278 7.452880 TGAGGTTTCAGATTCTAATTGGTTG 57.547 36.000 0.00 0.00 0.00 3.77
277 279 6.434028 TGAGGTTTCAGATTCTAATTGGTTGG 59.566 38.462 0.00 0.00 0.00 3.77
278 280 6.314917 AGGTTTCAGATTCTAATTGGTTGGT 58.685 36.000 0.00 0.00 0.00 3.67
279 281 6.782494 AGGTTTCAGATTCTAATTGGTTGGTT 59.218 34.615 0.00 0.00 0.00 3.67
280 282 7.290014 AGGTTTCAGATTCTAATTGGTTGGTTT 59.710 33.333 0.00 0.00 0.00 3.27
281 283 7.598869 GGTTTCAGATTCTAATTGGTTGGTTTC 59.401 37.037 0.00 0.00 0.00 2.78
282 284 7.831691 TTCAGATTCTAATTGGTTGGTTTCA 57.168 32.000 0.00 0.00 0.00 2.69
283 285 7.452880 TCAGATTCTAATTGGTTGGTTTCAG 57.547 36.000 0.00 0.00 0.00 3.02
284 286 7.230747 TCAGATTCTAATTGGTTGGTTTCAGA 58.769 34.615 0.00 0.00 0.00 3.27
285 287 7.391554 TCAGATTCTAATTGGTTGGTTTCAGAG 59.608 37.037 0.00 0.00 0.00 3.35
286 288 7.391554 CAGATTCTAATTGGTTGGTTTCAGAGA 59.608 37.037 0.00 0.00 0.00 3.10
287 289 7.944554 AGATTCTAATTGGTTGGTTTCAGAGAA 59.055 33.333 0.00 0.00 0.00 2.87
288 290 8.655935 ATTCTAATTGGTTGGTTTCAGAGAAT 57.344 30.769 0.00 0.00 0.00 2.40
289 291 9.753674 ATTCTAATTGGTTGGTTTCAGAGAATA 57.246 29.630 0.00 0.00 30.28 1.75
290 292 9.753674 TTCTAATTGGTTGGTTTCAGAGAATAT 57.246 29.630 0.00 0.00 0.00 1.28
291 293 9.753674 TCTAATTGGTTGGTTTCAGAGAATATT 57.246 29.630 0.00 0.00 0.00 1.28
296 298 9.527157 TTGGTTGGTTTCAGAGAATATTATTCA 57.473 29.630 16.68 0.00 0.00 2.57
297 299 9.177608 TGGTTGGTTTCAGAGAATATTATTCAG 57.822 33.333 16.68 7.79 0.00 3.02
298 300 9.396022 GGTTGGTTTCAGAGAATATTATTCAGA 57.604 33.333 16.68 9.60 0.00 3.27
301 303 9.605275 TGGTTTCAGAGAATATTATTCAGACTG 57.395 33.333 16.68 18.65 0.00 3.51
302 304 8.555361 GGTTTCAGAGAATATTATTCAGACTGC 58.445 37.037 16.68 10.25 0.00 4.40
303 305 9.102757 GTTTCAGAGAATATTATTCAGACTGCA 57.897 33.333 16.68 10.84 0.00 4.41
304 306 8.883954 TTCAGAGAATATTATTCAGACTGCAG 57.116 34.615 13.48 13.48 0.00 4.41
305 307 6.927936 TCAGAGAATATTATTCAGACTGCAGC 59.072 38.462 15.27 6.85 0.00 5.25
306 308 6.704937 CAGAGAATATTATTCAGACTGCAGCA 59.295 38.462 15.27 0.00 0.00 4.41
307 309 7.226128 CAGAGAATATTATTCAGACTGCAGCAA 59.774 37.037 15.27 1.77 0.00 3.91
308 310 7.772292 AGAGAATATTATTCAGACTGCAGCAAA 59.228 33.333 15.27 3.27 0.00 3.68
309 311 7.701445 AGAATATTATTCAGACTGCAGCAAAC 58.299 34.615 15.27 3.07 0.00 2.93
310 312 4.708726 ATTATTCAGACTGCAGCAAACC 57.291 40.909 15.27 0.00 0.00 3.27
311 313 1.985473 ATTCAGACTGCAGCAAACCA 58.015 45.000 15.27 0.00 0.00 3.67
312 314 1.985473 TTCAGACTGCAGCAAACCAT 58.015 45.000 15.27 0.00 0.00 3.55
313 315 1.241165 TCAGACTGCAGCAAACCATG 58.759 50.000 15.27 2.44 0.00 3.66
314 316 0.242825 CAGACTGCAGCAAACCATGG 59.757 55.000 15.27 11.19 0.00 3.66
315 317 1.080298 GACTGCAGCAAACCATGGC 60.080 57.895 15.27 0.00 0.00 4.40
316 318 2.126228 CTGCAGCAAACCATGGCG 60.126 61.111 13.04 1.24 34.54 5.69
317 319 2.911509 TGCAGCAAACCATGGCGT 60.912 55.556 13.04 0.00 34.54 5.68
318 320 2.126346 GCAGCAAACCATGGCGTC 60.126 61.111 13.04 0.00 34.54 5.19
323 325 2.031919 AAACCATGGCGTCGCTCA 59.968 55.556 18.11 13.64 0.00 4.26
342 356 0.462581 ATGTCTCCAATGCATCGCGT 60.463 50.000 5.77 0.00 0.00 6.01
388 428 9.965902 AGAAACCACAGACTGATAAAATCTAAT 57.034 29.630 10.08 0.00 0.00 1.73
419 465 5.766150 TGAACGGTTGACTTGAATTCATT 57.234 34.783 9.40 0.00 0.00 2.57
431 477 8.131100 TGACTTGAATTCATTGAAGTTCAGAAC 58.869 33.333 9.40 5.00 42.77 3.01
434 480 7.806409 TGAATTCATTGAAGTTCAGAACAGA 57.194 32.000 15.85 1.12 0.00 3.41
444 490 9.591792 TTGAAGTTCAGAACAGAGATACATATG 57.408 33.333 15.85 0.00 0.00 1.78
474 520 5.236047 GCTTGTGGCAGTTAGATAATCAGAG 59.764 44.000 0.00 0.00 41.35 3.35
475 521 6.544928 TTGTGGCAGTTAGATAATCAGAGA 57.455 37.500 0.00 0.00 0.00 3.10
476 522 6.737720 TGTGGCAGTTAGATAATCAGAGAT 57.262 37.500 0.00 0.00 0.00 2.75
487 533 7.838079 AGATAATCAGAGATGTACTGAAGCT 57.162 36.000 0.00 0.00 45.44 3.74
488 534 8.932434 AGATAATCAGAGATGTACTGAAGCTA 57.068 34.615 0.00 0.00 45.44 3.32
489 535 9.360901 AGATAATCAGAGATGTACTGAAGCTAA 57.639 33.333 0.00 0.00 45.44 3.09
492 538 6.201226 TCAGAGATGTACTGAAGCTAACAG 57.799 41.667 16.08 16.08 40.70 3.16
493 539 5.126222 TCAGAGATGTACTGAAGCTAACAGG 59.874 44.000 19.99 7.06 40.70 4.00
495 541 4.353777 AGATGTACTGAAGCTAACAGGGA 58.646 43.478 19.99 8.81 39.38 4.20
496 542 4.965532 AGATGTACTGAAGCTAACAGGGAT 59.034 41.667 19.99 11.20 39.38 3.85
497 543 6.136857 AGATGTACTGAAGCTAACAGGGATA 58.863 40.000 19.99 9.81 39.38 2.59
498 544 5.593679 TGTACTGAAGCTAACAGGGATAC 57.406 43.478 19.99 14.75 39.38 2.24
499 545 5.020795 TGTACTGAAGCTAACAGGGATACA 58.979 41.667 19.99 16.44 39.38 2.29
500 546 4.744795 ACTGAAGCTAACAGGGATACAG 57.255 45.455 19.99 0.00 39.38 2.74
501 547 3.452627 ACTGAAGCTAACAGGGATACAGG 59.547 47.826 19.99 0.00 39.38 4.00
502 548 2.170607 TGAAGCTAACAGGGATACAGGC 59.829 50.000 0.00 0.00 39.74 4.85
512 558 4.835615 ACAGGGATACAGGCTATCTAACTG 59.164 45.833 11.79 11.79 38.19 3.16
517 563 5.540719 GGATACAGGCTATCTAACTGAAGGT 59.459 44.000 0.00 0.00 36.17 3.50
518 564 4.744795 ACAGGCTATCTAACTGAAGGTG 57.255 45.455 0.00 0.00 36.17 4.00
521 567 3.381908 AGGCTATCTAACTGAAGGTGACG 59.618 47.826 0.00 0.00 0.00 4.35
563 609 8.506437 ACAACACTGAATCAATGTATACACTTG 58.494 33.333 7.96 13.25 0.00 3.16
564 610 8.720562 CAACACTGAATCAATGTATACACTTGA 58.279 33.333 22.02 22.02 33.75 3.02
565 611 8.484641 ACACTGAATCAATGTATACACTTGAG 57.515 34.615 23.09 16.55 32.82 3.02
566 612 8.097038 ACACTGAATCAATGTATACACTTGAGT 58.903 33.333 23.09 21.90 32.82 3.41
567 613 8.939929 CACTGAATCAATGTATACACTTGAGTT 58.060 33.333 23.09 18.90 32.82 3.01
568 614 8.939929 ACTGAATCAATGTATACACTTGAGTTG 58.060 33.333 23.09 16.75 32.82 3.16
598 666 7.078228 GCACTTATCCTTCAACTTTTACAGTG 58.922 38.462 0.00 0.00 35.12 3.66
599 667 7.584987 CACTTATCCTTCAACTTTTACAGTGG 58.415 38.462 0.00 0.00 35.12 4.00
641 715 3.063510 TCACCTTGCTCTGGATTTCAG 57.936 47.619 0.00 0.00 44.68 3.02
646 720 3.190118 CCTTGCTCTGGATTTCAGTTGAC 59.810 47.826 0.00 0.00 43.76 3.18
647 721 2.416747 TGCTCTGGATTTCAGTTGACG 58.583 47.619 0.00 0.00 43.76 4.35
648 722 1.129437 GCTCTGGATTTCAGTTGACGC 59.871 52.381 0.00 0.00 43.76 5.19
649 723 1.391485 CTCTGGATTTCAGTTGACGCG 59.609 52.381 3.53 3.53 43.76 6.01
650 724 0.443869 CTGGATTTCAGTTGACGCGG 59.556 55.000 12.47 0.00 38.64 6.46
651 725 0.953471 TGGATTTCAGTTGACGCGGG 60.953 55.000 12.47 0.00 0.00 6.13
652 726 0.953960 GGATTTCAGTTGACGCGGGT 60.954 55.000 12.47 4.12 0.00 5.28
653 727 0.165944 GATTTCAGTTGACGCGGGTG 59.834 55.000 10.96 0.00 0.00 4.61
654 728 1.852067 ATTTCAGTTGACGCGGGTGC 61.852 55.000 10.96 2.32 37.91 5.01
655 729 2.933878 TTTCAGTTGACGCGGGTGCT 62.934 55.000 10.96 2.29 39.65 4.40
656 730 3.716006 CAGTTGACGCGGGTGCTG 61.716 66.667 10.96 11.53 39.65 4.41
681 755 0.755079 CCTTCGATGAGGAGATGCCA 59.245 55.000 0.00 0.00 39.25 4.92
682 756 1.539929 CCTTCGATGAGGAGATGCCAC 60.540 57.143 0.00 0.00 39.25 5.01
683 757 0.465705 TTCGATGAGGAGATGCCACC 59.534 55.000 0.00 0.00 40.02 4.61
684 758 0.687427 TCGATGAGGAGATGCCACCA 60.687 55.000 0.00 0.00 40.02 4.17
691 765 1.327690 GGAGATGCCACCAGACGGTA 61.328 60.000 0.00 0.00 46.94 4.02
692 766 0.179108 GAGATGCCACCAGACGGTAC 60.179 60.000 0.00 0.00 46.94 3.34
767 855 1.142097 GCGGTAGGGTTCAGAGCTC 59.858 63.158 5.27 5.27 0.00 4.09
771 860 1.406205 GGTAGGGTTCAGAGCTCAAGC 60.406 57.143 17.77 11.76 42.49 4.01
805 894 3.122850 CGAAATGGGCTGGCATCC 58.877 61.111 2.88 0.00 0.00 3.51
807 896 1.453745 GAAATGGGCTGGCATCCGA 60.454 57.895 2.88 0.00 0.00 4.55
820 909 2.180432 CATCCGATGCATCCATCAGT 57.820 50.000 20.87 0.00 46.59 3.41
822 911 0.832626 TCCGATGCATCCATCAGTGT 59.167 50.000 20.87 0.00 46.59 3.55
823 912 0.942252 CCGATGCATCCATCAGTGTG 59.058 55.000 20.87 3.44 46.59 3.82
824 913 1.660167 CGATGCATCCATCAGTGTGT 58.340 50.000 20.87 0.00 46.59 3.72
826 915 3.396560 CGATGCATCCATCAGTGTGTAT 58.603 45.455 20.87 0.00 46.59 2.29
827 916 3.185797 CGATGCATCCATCAGTGTGTATG 59.814 47.826 20.87 0.00 46.59 2.39
828 917 2.921821 TGCATCCATCAGTGTGTATGG 58.078 47.619 3.42 3.42 43.44 2.74
829 918 1.605710 GCATCCATCAGTGTGTATGGC 59.394 52.381 4.75 0.00 42.08 4.40
830 919 2.224606 CATCCATCAGTGTGTATGGCC 58.775 52.381 0.00 0.00 42.08 5.36
831 920 0.177836 TCCATCAGTGTGTATGGCCG 59.822 55.000 0.00 0.00 42.08 6.13
832 921 0.177836 CCATCAGTGTGTATGGCCGA 59.822 55.000 0.00 0.00 36.50 5.54
833 922 1.575244 CATCAGTGTGTATGGCCGAG 58.425 55.000 0.00 0.00 0.00 4.63
834 923 1.136891 CATCAGTGTGTATGGCCGAGA 59.863 52.381 0.00 0.00 0.00 4.04
938 1040 1.000163 TGTTTCCACGAGAGAGCAGAC 60.000 52.381 0.00 0.00 0.00 3.51
960 1062 4.835891 ACCTACCTCCGCTCCCCG 62.836 72.222 0.00 0.00 0.00 5.73
989 1097 2.734723 CCGCCGTCACTGTCACAG 60.735 66.667 2.22 2.22 37.52 3.66
1141 1264 1.441729 CCAAATCGCTCCTCCGCTA 59.558 57.895 0.00 0.00 0.00 4.26
1367 1493 0.680061 AAGACTCCGACTTCCACCAC 59.320 55.000 0.00 0.00 0.00 4.16
1595 1721 1.536940 TGATGCATGGTGAACTGGTG 58.463 50.000 2.46 0.00 0.00 4.17
1664 1790 3.309582 CCACCGAGGCACATAGGT 58.690 61.111 0.00 0.00 37.49 3.08
1673 1799 3.010420 GAGGCACATAGGTTTCCTTGAC 58.990 50.000 0.29 0.00 34.61 3.18
1772 1919 3.621520 GTGTTCGACACCACGACC 58.378 61.111 6.82 0.00 43.05 4.79
1912 2059 1.974875 TGGCGCAGGACTACGAGAA 60.975 57.895 10.83 0.00 0.00 2.87
1935 2082 0.323360 GGTCTGGGCCTGCAAATACA 60.323 55.000 4.53 0.00 0.00 2.29
2127 2274 1.089920 CCTCGGTCCTGCAAATCTTG 58.910 55.000 0.00 0.00 0.00 3.02
2150 2297 3.005155 GGCTCAAGCAAACTCTTGTTCAT 59.995 43.478 4.13 0.00 42.90 2.57
2194 2341 3.826729 GAGGGTTATGTTGCCAACTCTTT 59.173 43.478 9.30 0.00 35.60 2.52
2247 3839 3.003480 GTGATTCTAGCCCAACTGTCAC 58.997 50.000 0.00 0.00 0.00 3.67
2315 3911 4.860907 CCTGCTAGTTTCATTTTGATGCAC 59.139 41.667 0.00 0.00 0.00 4.57
2388 3985 3.055530 TCTCTGAATGTTCTTCTGGGCTC 60.056 47.826 0.00 0.00 0.00 4.70
2491 4124 9.853177 CAAGGTCCTCTTTTTATAGATAACCAT 57.147 33.333 0.00 0.00 33.93 3.55
2585 4219 6.430007 ACAAGAAATGAGGCAGATTATCCTT 58.570 36.000 0.00 0.00 31.71 3.36
2586 4220 6.894103 ACAAGAAATGAGGCAGATTATCCTTT 59.106 34.615 0.00 0.00 31.71 3.11
2811 4516 2.979240 AGCTCGAGAAATGGAACCTTC 58.021 47.619 18.75 0.00 0.00 3.46
2816 4523 4.905429 TCGAGAAATGGAACCTTCATTGA 58.095 39.130 0.00 0.00 35.31 2.57
2817 4524 5.500234 TCGAGAAATGGAACCTTCATTGAT 58.500 37.500 0.00 0.00 35.31 2.57
2818 4525 6.649155 TCGAGAAATGGAACCTTCATTGATA 58.351 36.000 0.00 0.00 35.31 2.15
2864 4895 4.287067 TGGTCAGGCTCAGTTTCTAGATTT 59.713 41.667 0.00 0.00 0.00 2.17
2866 4897 6.013725 TGGTCAGGCTCAGTTTCTAGATTTTA 60.014 38.462 0.00 0.00 0.00 1.52
2867 4898 6.879458 GGTCAGGCTCAGTTTCTAGATTTTAA 59.121 38.462 0.00 0.00 0.00 1.52
2868 4899 7.390718 GGTCAGGCTCAGTTTCTAGATTTTAAA 59.609 37.037 0.00 0.00 0.00 1.52
2869 4900 8.951243 GTCAGGCTCAGTTTCTAGATTTTAAAT 58.049 33.333 0.00 0.00 0.00 1.40
2870 4901 9.520515 TCAGGCTCAGTTTCTAGATTTTAAATT 57.479 29.630 0.00 0.00 0.00 1.82
2871 4902 9.780413 CAGGCTCAGTTTCTAGATTTTAAATTC 57.220 33.333 0.00 2.50 0.00 2.17
2872 4903 9.746457 AGGCTCAGTTTCTAGATTTTAAATTCT 57.254 29.630 15.03 15.03 0.00 2.40
2873 4904 9.780413 GGCTCAGTTTCTAGATTTTAAATTCTG 57.220 33.333 18.52 10.91 0.00 3.02
2963 5039 4.776349 TGTACTGACTGTTTCATGGTTGT 58.224 39.130 0.00 0.00 32.17 3.32
2964 5040 4.814234 TGTACTGACTGTTTCATGGTTGTC 59.186 41.667 0.00 0.00 32.17 3.18
3063 5170 9.950496 TTATGAAATTATTTTGGCCAGCTTTTA 57.050 25.926 5.11 0.00 0.00 1.52
3081 5189 9.585099 CAGCTTTTAAAATAGTTGCCATTGATA 57.415 29.630 0.09 0.00 0.00 2.15
3092 5200 3.342719 TGCCATTGATATGTGTCGTGTT 58.657 40.909 0.00 0.00 0.00 3.32
3096 5204 5.293324 GCCATTGATATGTGTCGTGTTTCTA 59.707 40.000 0.00 0.00 0.00 2.10
3167 5281 8.980481 TCTTCTTTCAGTTATTCTCAAAAGGT 57.020 30.769 0.00 0.00 31.86 3.50
3168 5282 9.057089 TCTTCTTTCAGTTATTCTCAAAAGGTC 57.943 33.333 0.00 0.00 31.86 3.85
3169 5283 8.746052 TTCTTTCAGTTATTCTCAAAAGGTCA 57.254 30.769 0.00 0.00 31.86 4.02
3170 5284 8.924511 TCTTTCAGTTATTCTCAAAAGGTCAT 57.075 30.769 0.00 0.00 31.86 3.06
3184 5299 5.964958 AAAGGTCATACAGTGGTTTCATG 57.035 39.130 0.00 0.00 0.00 3.07
3188 5303 7.141758 AGGTCATACAGTGGTTTCATGATAT 57.858 36.000 0.00 0.00 0.00 1.63
3219 5334 1.544246 GCCAATGTACACTGGTTTCCC 59.456 52.381 23.39 3.80 34.97 3.97
3244 5359 4.829064 TCCATGTTTTGTTGTAGCTGAC 57.171 40.909 0.00 0.00 0.00 3.51
3350 5500 4.507756 TGTCGATGCATATAAAGCTGTGAC 59.492 41.667 0.00 7.13 0.00 3.67
3371 5521 3.006247 CCAGGAAGCTCTTGTAAGAAGC 58.994 50.000 0.00 2.71 34.03 3.86
3375 5525 4.075682 GGAAGCTCTTGTAAGAAGCCTTT 58.924 43.478 10.39 3.23 34.03 3.11
3427 5577 6.124088 CCAATCTGTGGTAATGCTAAGTTC 57.876 41.667 0.00 0.00 43.20 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.999905 TTTATGGGGTACTTTTCTTGTTAGTT 57.000 30.769 0.00 0.00 0.00 2.24
2 3 8.853126 GTTTTATGGGGTACTTTTCTTGTTAGT 58.147 33.333 0.00 0.00 0.00 2.24
3 4 8.852135 TGTTTTATGGGGTACTTTTCTTGTTAG 58.148 33.333 0.00 0.00 0.00 2.34
4 5 8.763984 TGTTTTATGGGGTACTTTTCTTGTTA 57.236 30.769 0.00 0.00 0.00 2.41
5 6 7.663043 TGTTTTATGGGGTACTTTTCTTGTT 57.337 32.000 0.00 0.00 0.00 2.83
6 7 7.343574 AGTTGTTTTATGGGGTACTTTTCTTGT 59.656 33.333 0.00 0.00 0.00 3.16
7 8 7.651704 CAGTTGTTTTATGGGGTACTTTTCTTG 59.348 37.037 0.00 0.00 0.00 3.02
8 9 7.343574 ACAGTTGTTTTATGGGGTACTTTTCTT 59.656 33.333 0.00 0.00 0.00 2.52
9 10 6.837048 ACAGTTGTTTTATGGGGTACTTTTCT 59.163 34.615 0.00 0.00 0.00 2.52
10 11 7.046292 ACAGTTGTTTTATGGGGTACTTTTC 57.954 36.000 0.00 0.00 0.00 2.29
11 12 7.255695 GCTACAGTTGTTTTATGGGGTACTTTT 60.256 37.037 0.00 0.00 0.00 2.27
12 13 6.208007 GCTACAGTTGTTTTATGGGGTACTTT 59.792 38.462 0.00 0.00 0.00 2.66
13 14 5.708697 GCTACAGTTGTTTTATGGGGTACTT 59.291 40.000 0.00 0.00 0.00 2.24
14 15 5.013808 AGCTACAGTTGTTTTATGGGGTACT 59.986 40.000 0.00 0.00 0.00 2.73
15 16 5.250982 AGCTACAGTTGTTTTATGGGGTAC 58.749 41.667 0.00 0.00 0.00 3.34
16 17 5.013287 TGAGCTACAGTTGTTTTATGGGGTA 59.987 40.000 0.00 0.00 0.00 3.69
17 18 4.202524 TGAGCTACAGTTGTTTTATGGGGT 60.203 41.667 0.00 0.00 0.00 4.95
18 19 4.331968 TGAGCTACAGTTGTTTTATGGGG 58.668 43.478 0.00 0.00 0.00 4.96
19 20 5.957842 TTGAGCTACAGTTGTTTTATGGG 57.042 39.130 0.00 0.00 0.00 4.00
20 21 6.308766 GCAATTGAGCTACAGTTGTTTTATGG 59.691 38.462 10.34 0.00 44.42 2.74
21 22 6.862608 TGCAATTGAGCTACAGTTGTTTTATG 59.137 34.615 10.34 0.00 44.42 1.90
22 23 6.863126 GTGCAATTGAGCTACAGTTGTTTTAT 59.137 34.615 10.34 0.00 44.42 1.40
23 24 6.183360 TGTGCAATTGAGCTACAGTTGTTTTA 60.183 34.615 10.34 5.35 44.42 1.52
24 25 5.043248 GTGCAATTGAGCTACAGTTGTTTT 58.957 37.500 10.34 0.00 44.42 2.43
25 26 4.097741 TGTGCAATTGAGCTACAGTTGTTT 59.902 37.500 10.34 0.00 44.42 2.83
26 27 3.631686 TGTGCAATTGAGCTACAGTTGTT 59.368 39.130 10.34 0.00 44.42 2.83
33 34 3.003068 CCATAGCTGTGCAATTGAGCTAC 59.997 47.826 22.62 10.98 45.62 3.58
41 42 6.830912 TCTAATTCTACCATAGCTGTGCAAT 58.169 36.000 4.68 0.00 0.00 3.56
69 70 9.389755 TCTATTTTGTTGGATCGATAAATGTCA 57.610 29.630 0.00 0.00 0.00 3.58
78 79 8.421002 TCATGTATCTCTATTTTGTTGGATCGA 58.579 33.333 0.00 0.00 0.00 3.59
131 133 8.328864 GTGTTCAGTTCAGTCCGAATAATATTC 58.671 37.037 3.00 3.00 35.63 1.75
149 151 3.393800 CATCTGAAACCTCGTGTTCAGT 58.606 45.455 14.00 3.86 35.67 3.41
150 152 2.158449 GCATCTGAAACCTCGTGTTCAG 59.842 50.000 10.12 10.12 35.67 3.02
170 172 3.385193 AACCAACCAATTAACTGCAGC 57.615 42.857 15.27 0.00 0.00 5.25
174 176 7.596248 CAGAATCTGAAACCAACCAATTAACTG 59.404 37.037 3.77 0.00 32.44 3.16
223 225 1.005748 CCGCTGCAGACTGAAGACA 60.006 57.895 20.43 0.00 0.00 3.41
224 226 2.386660 GCCGCTGCAGACTGAAGAC 61.387 63.158 20.43 4.84 37.47 3.01
225 227 2.047844 GCCGCTGCAGACTGAAGA 60.048 61.111 20.43 0.00 37.47 2.87
226 228 3.485431 CGCCGCTGCAGACTGAAG 61.485 66.667 20.43 6.32 37.32 3.02
236 238 3.803082 CATGGTCAACCGCCGCTG 61.803 66.667 0.00 0.00 39.43 5.18
237 239 3.958147 CTCATGGTCAACCGCCGCT 62.958 63.158 0.00 0.00 39.43 5.52
238 240 3.499737 CTCATGGTCAACCGCCGC 61.500 66.667 0.00 0.00 39.43 6.53
239 241 2.819595 CCTCATGGTCAACCGCCG 60.820 66.667 0.00 0.00 39.43 6.46
240 242 2.351276 ACCTCATGGTCAACCGCC 59.649 61.111 0.00 0.00 44.78 6.13
249 251 6.604795 ACCAATTAGAATCTGAAACCTCATGG 59.395 38.462 0.00 0.00 39.83 3.66
250 252 7.636150 ACCAATTAGAATCTGAAACCTCATG 57.364 36.000 0.00 0.00 0.00 3.07
251 253 7.123247 CCAACCAATTAGAATCTGAAACCTCAT 59.877 37.037 0.00 0.00 0.00 2.90
252 254 6.434028 CCAACCAATTAGAATCTGAAACCTCA 59.566 38.462 0.00 0.00 0.00 3.86
253 255 6.434340 ACCAACCAATTAGAATCTGAAACCTC 59.566 38.462 0.00 0.00 0.00 3.85
254 256 6.314917 ACCAACCAATTAGAATCTGAAACCT 58.685 36.000 0.00 0.00 0.00 3.50
255 257 6.590234 ACCAACCAATTAGAATCTGAAACC 57.410 37.500 0.00 0.00 0.00 3.27
256 258 8.141268 TGAAACCAACCAATTAGAATCTGAAAC 58.859 33.333 0.00 0.00 0.00 2.78
257 259 8.243961 TGAAACCAACCAATTAGAATCTGAAA 57.756 30.769 0.00 0.00 0.00 2.69
258 260 7.723616 TCTGAAACCAACCAATTAGAATCTGAA 59.276 33.333 0.00 0.00 0.00 3.02
259 261 7.230747 TCTGAAACCAACCAATTAGAATCTGA 58.769 34.615 0.00 0.00 0.00 3.27
260 262 7.391554 TCTCTGAAACCAACCAATTAGAATCTG 59.608 37.037 0.00 0.00 0.00 2.90
261 263 7.461749 TCTCTGAAACCAACCAATTAGAATCT 58.538 34.615 0.00 0.00 0.00 2.40
262 264 7.687941 TCTCTGAAACCAACCAATTAGAATC 57.312 36.000 0.00 0.00 0.00 2.52
263 265 8.655935 ATTCTCTGAAACCAACCAATTAGAAT 57.344 30.769 0.00 0.00 0.00 2.40
264 266 9.753674 ATATTCTCTGAAACCAACCAATTAGAA 57.246 29.630 0.00 0.00 0.00 2.10
265 267 9.753674 AATATTCTCTGAAACCAACCAATTAGA 57.246 29.630 0.00 0.00 0.00 2.10
270 272 9.527157 TGAATAATATTCTCTGAAACCAACCAA 57.473 29.630 13.45 0.00 0.00 3.67
271 273 9.177608 CTGAATAATATTCTCTGAAACCAACCA 57.822 33.333 13.45 0.00 0.00 3.67
272 274 9.396022 TCTGAATAATATTCTCTGAAACCAACC 57.604 33.333 13.45 0.00 0.00 3.77
275 277 9.605275 CAGTCTGAATAATATTCTCTGAAACCA 57.395 33.333 13.45 0.00 0.00 3.67
276 278 8.555361 GCAGTCTGAATAATATTCTCTGAAACC 58.445 37.037 22.97 11.27 0.00 3.27
277 279 9.102757 TGCAGTCTGAATAATATTCTCTGAAAC 57.897 33.333 22.97 13.62 0.00 2.78
278 280 9.322773 CTGCAGTCTGAATAATATTCTCTGAAA 57.677 33.333 22.97 15.11 0.00 2.69
279 281 7.440556 GCTGCAGTCTGAATAATATTCTCTGAA 59.559 37.037 22.97 17.13 0.00 3.02
280 282 6.927936 GCTGCAGTCTGAATAATATTCTCTGA 59.072 38.462 22.97 13.83 0.00 3.27
281 283 6.704937 TGCTGCAGTCTGAATAATATTCTCTG 59.295 38.462 16.64 16.66 0.00 3.35
282 284 6.824553 TGCTGCAGTCTGAATAATATTCTCT 58.175 36.000 16.64 7.15 0.00 3.10
283 285 7.488187 TTGCTGCAGTCTGAATAATATTCTC 57.512 36.000 16.64 5.32 0.00 2.87
284 286 7.201767 GGTTTGCTGCAGTCTGAATAATATTCT 60.202 37.037 16.64 0.00 0.00 2.40
285 287 6.914757 GGTTTGCTGCAGTCTGAATAATATTC 59.085 38.462 16.64 6.07 0.00 1.75
286 288 6.377996 TGGTTTGCTGCAGTCTGAATAATATT 59.622 34.615 16.64 0.00 0.00 1.28
287 289 5.887598 TGGTTTGCTGCAGTCTGAATAATAT 59.112 36.000 16.64 0.00 0.00 1.28
288 290 5.252547 TGGTTTGCTGCAGTCTGAATAATA 58.747 37.500 16.64 0.00 0.00 0.98
289 291 4.081406 TGGTTTGCTGCAGTCTGAATAAT 58.919 39.130 16.64 0.00 0.00 1.28
290 292 3.485394 TGGTTTGCTGCAGTCTGAATAA 58.515 40.909 16.64 0.00 0.00 1.40
291 293 3.138884 TGGTTTGCTGCAGTCTGAATA 57.861 42.857 16.64 0.00 0.00 1.75
292 294 1.985473 TGGTTTGCTGCAGTCTGAAT 58.015 45.000 16.64 0.00 0.00 2.57
293 295 1.610038 CATGGTTTGCTGCAGTCTGAA 59.390 47.619 16.64 2.46 0.00 3.02
294 296 1.241165 CATGGTTTGCTGCAGTCTGA 58.759 50.000 16.64 0.00 0.00 3.27
295 297 0.242825 CCATGGTTTGCTGCAGTCTG 59.757 55.000 16.64 0.00 0.00 3.51
296 298 1.530013 GCCATGGTTTGCTGCAGTCT 61.530 55.000 16.64 0.00 0.00 3.24
297 299 1.080298 GCCATGGTTTGCTGCAGTC 60.080 57.895 16.64 8.39 0.00 3.51
298 300 2.922950 CGCCATGGTTTGCTGCAGT 61.923 57.895 16.64 0.00 0.00 4.40
299 301 2.126228 CGCCATGGTTTGCTGCAG 60.126 61.111 14.67 10.11 0.00 4.41
300 302 2.911509 ACGCCATGGTTTGCTGCA 60.912 55.556 14.67 0.00 0.00 4.41
301 303 2.126346 GACGCCATGGTTTGCTGC 60.126 61.111 14.67 0.00 0.00 5.25
302 304 2.176546 CGACGCCATGGTTTGCTG 59.823 61.111 14.67 0.00 0.00 4.41
303 305 3.737172 GCGACGCCATGGTTTGCT 61.737 61.111 14.67 0.00 0.00 3.91
304 306 3.667429 GAGCGACGCCATGGTTTGC 62.667 63.158 17.79 15.68 0.00 3.68
305 307 1.647545 ATGAGCGACGCCATGGTTTG 61.648 55.000 17.79 6.42 0.00 2.93
306 308 1.377202 ATGAGCGACGCCATGGTTT 60.377 52.632 17.79 0.00 0.00 3.27
307 309 2.108514 CATGAGCGACGCCATGGTT 61.109 57.895 28.71 9.52 35.32 3.67
308 310 2.512286 CATGAGCGACGCCATGGT 60.512 61.111 28.71 10.16 35.32 3.55
309 311 2.512286 ACATGAGCGACGCCATGG 60.512 61.111 34.04 23.73 39.61 3.66
310 312 1.485838 GAGACATGAGCGACGCCATG 61.486 60.000 31.77 31.77 40.42 3.66
311 313 1.227089 GAGACATGAGCGACGCCAT 60.227 57.895 17.79 16.27 0.00 4.40
312 314 2.181777 GAGACATGAGCGACGCCA 59.818 61.111 17.79 14.61 0.00 5.69
313 315 2.583593 GGAGACATGAGCGACGCC 60.584 66.667 17.79 8.82 0.00 5.68
314 316 0.807667 ATTGGAGACATGAGCGACGC 60.808 55.000 13.03 13.03 42.32 5.19
315 317 0.926155 CATTGGAGACATGAGCGACG 59.074 55.000 0.00 0.00 42.32 5.12
316 318 0.654683 GCATTGGAGACATGAGCGAC 59.345 55.000 0.00 0.00 42.32 5.19
317 319 0.249955 TGCATTGGAGACATGAGCGA 59.750 50.000 0.00 0.00 42.32 4.93
318 320 1.263484 GATGCATTGGAGACATGAGCG 59.737 52.381 0.00 0.00 42.32 5.03
323 325 0.462581 ACGCGATGCATTGGAGACAT 60.463 50.000 15.93 0.00 42.32 3.06
342 356 1.078918 CCCACGCTGATCTGCTTCA 60.079 57.895 20.58 0.00 0.00 3.02
388 428 2.631062 AGTCAACCGTTCATCCTGTGTA 59.369 45.455 0.00 0.00 0.00 2.90
419 465 8.200120 CCATATGTATCTCTGTTCTGAACTTCA 58.800 37.037 20.18 5.50 0.00 3.02
434 480 4.504514 CCACAAGCAGAGCCATATGTATCT 60.505 45.833 1.24 1.66 0.00 1.98
464 510 9.405587 GTTAGCTTCAGTACATCTCTGATTATC 57.594 37.037 0.00 0.00 40.83 1.75
466 512 8.293699 TGTTAGCTTCAGTACATCTCTGATTA 57.706 34.615 0.00 0.00 40.83 1.75
469 515 5.126222 CCTGTTAGCTTCAGTACATCTCTGA 59.874 44.000 14.51 0.00 39.71 3.27
474 520 4.737855 TCCCTGTTAGCTTCAGTACATC 57.262 45.455 14.51 0.00 0.00 3.06
475 521 5.661312 TGTATCCCTGTTAGCTTCAGTACAT 59.339 40.000 14.51 7.91 0.00 2.29
476 522 5.020795 TGTATCCCTGTTAGCTTCAGTACA 58.979 41.667 14.51 13.24 0.00 2.90
485 531 3.835395 AGATAGCCTGTATCCCTGTTAGC 59.165 47.826 0.00 0.00 0.00 3.09
487 533 6.493802 CAGTTAGATAGCCTGTATCCCTGTTA 59.506 42.308 0.00 0.00 0.00 2.41
488 534 5.305644 CAGTTAGATAGCCTGTATCCCTGTT 59.694 44.000 0.00 0.00 0.00 3.16
489 535 4.835615 CAGTTAGATAGCCTGTATCCCTGT 59.164 45.833 0.00 0.00 0.00 4.00
492 538 5.046950 CCTTCAGTTAGATAGCCTGTATCCC 60.047 48.000 0.00 0.00 0.00 3.85
493 539 5.540719 ACCTTCAGTTAGATAGCCTGTATCC 59.459 44.000 0.00 0.00 0.00 2.59
495 541 6.041069 GTCACCTTCAGTTAGATAGCCTGTAT 59.959 42.308 0.00 0.00 0.00 2.29
496 542 5.360144 GTCACCTTCAGTTAGATAGCCTGTA 59.640 44.000 0.00 0.00 0.00 2.74
497 543 4.160626 GTCACCTTCAGTTAGATAGCCTGT 59.839 45.833 0.00 0.00 0.00 4.00
498 544 4.688021 GTCACCTTCAGTTAGATAGCCTG 58.312 47.826 0.00 0.00 0.00 4.85
499 545 3.381908 CGTCACCTTCAGTTAGATAGCCT 59.618 47.826 0.00 0.00 0.00 4.58
500 546 3.380637 TCGTCACCTTCAGTTAGATAGCC 59.619 47.826 0.00 0.00 0.00 3.93
501 547 4.602995 CTCGTCACCTTCAGTTAGATAGC 58.397 47.826 0.00 0.00 0.00 2.97
502 548 4.336993 AGCTCGTCACCTTCAGTTAGATAG 59.663 45.833 0.00 0.00 0.00 2.08
512 558 4.995124 TGTTAGATTAGCTCGTCACCTTC 58.005 43.478 0.00 0.00 0.00 3.46
517 563 6.072342 TGTTGTACTGTTAGATTAGCTCGTCA 60.072 38.462 0.00 0.00 0.00 4.35
518 564 6.250951 GTGTTGTACTGTTAGATTAGCTCGTC 59.749 42.308 0.00 0.00 0.00 4.20
554 600 4.217767 AGTGCGTCTCAACTCAAGTGTATA 59.782 41.667 0.00 0.00 0.00 1.47
563 609 3.512033 AGGATAAGTGCGTCTCAACTC 57.488 47.619 0.00 0.00 0.00 3.01
564 610 3.258372 TGAAGGATAAGTGCGTCTCAACT 59.742 43.478 0.00 0.00 0.00 3.16
565 611 3.585862 TGAAGGATAAGTGCGTCTCAAC 58.414 45.455 0.00 0.00 0.00 3.18
566 612 3.953712 TGAAGGATAAGTGCGTCTCAA 57.046 42.857 0.00 0.00 0.00 3.02
567 613 3.258372 AGTTGAAGGATAAGTGCGTCTCA 59.742 43.478 0.00 0.00 0.00 3.27
568 614 3.851098 AGTTGAAGGATAAGTGCGTCTC 58.149 45.455 0.00 0.00 0.00 3.36
653 727 3.207669 CATCGAAGGGCAGGCAGC 61.208 66.667 0.00 0.00 44.65 5.25
654 728 1.523258 CTCATCGAAGGGCAGGCAG 60.523 63.158 0.00 0.00 0.00 4.85
655 729 2.586245 CTCATCGAAGGGCAGGCA 59.414 61.111 0.00 0.00 0.00 4.75
656 730 2.203126 CCTCATCGAAGGGCAGGC 60.203 66.667 0.00 0.00 32.35 4.85
657 731 1.045350 TCTCCTCATCGAAGGGCAGG 61.045 60.000 3.32 0.00 37.02 4.85
658 732 1.047002 ATCTCCTCATCGAAGGGCAG 58.953 55.000 3.32 0.00 37.02 4.85
682 756 1.520787 GCAATCCCGTACCGTCTGG 60.521 63.158 0.00 0.00 42.84 3.86
683 757 1.876714 CGCAATCCCGTACCGTCTG 60.877 63.158 0.00 0.00 0.00 3.51
684 758 2.493030 CGCAATCCCGTACCGTCT 59.507 61.111 0.00 0.00 0.00 4.18
690 764 4.517815 GTCCGCCGCAATCCCGTA 62.518 66.667 0.00 0.00 0.00 4.02
701 775 1.658673 CCACTAGATACGGTCCGCC 59.341 63.158 12.28 0.55 0.00 6.13
790 879 1.111116 CATCGGATGCCAGCCCATTT 61.111 55.000 4.84 0.00 0.00 2.32
802 891 1.419012 ACACTGATGGATGCATCGGAT 59.581 47.619 34.71 22.11 39.65 4.18
805 894 1.660167 ACACACTGATGGATGCATCG 58.340 50.000 20.61 17.05 34.46 3.84
807 896 3.483421 CCATACACACTGATGGATGCAT 58.517 45.455 0.00 0.00 44.72 3.96
819 908 1.137086 AGACATCTCGGCCATACACAC 59.863 52.381 2.24 0.00 0.00 3.82
820 909 1.136891 CAGACATCTCGGCCATACACA 59.863 52.381 2.24 0.00 0.00 3.72
822 911 0.752658 CCAGACATCTCGGCCATACA 59.247 55.000 2.24 0.00 0.00 2.29
823 912 0.034059 CCCAGACATCTCGGCCATAC 59.966 60.000 2.24 0.00 0.00 2.39
824 913 1.758440 GCCCAGACATCTCGGCCATA 61.758 60.000 6.27 0.00 43.28 2.74
826 915 3.785859 GCCCAGACATCTCGGCCA 61.786 66.667 6.27 0.00 43.28 5.36
829 918 1.903877 AACTGGCCCAGACATCTCGG 61.904 60.000 19.90 0.00 35.18 4.63
830 919 0.742281 CAACTGGCCCAGACATCTCG 60.742 60.000 19.90 0.00 35.18 4.04
831 920 0.615331 TCAACTGGCCCAGACATCTC 59.385 55.000 19.90 0.00 35.18 2.75
832 921 1.004044 CTTCAACTGGCCCAGACATCT 59.996 52.381 19.90 0.00 35.18 2.90
833 922 1.457346 CTTCAACTGGCCCAGACATC 58.543 55.000 19.90 0.00 35.18 3.06
834 923 0.038744 CCTTCAACTGGCCCAGACAT 59.961 55.000 19.90 0.00 35.18 3.06
938 1040 0.392595 GGAGCGGAGGTAGGTTTTGG 60.393 60.000 0.00 0.00 39.88 3.28
984 1092 1.758440 GAGTGGTGGACTGCCTGTGA 61.758 60.000 0.00 0.00 33.83 3.58
989 1097 0.603975 GAACTGAGTGGTGGACTGCC 60.604 60.000 0.00 0.00 33.83 4.85
1040 1151 4.430423 GTTGCTCTTGCGGCGTCG 62.430 66.667 4.29 4.29 43.34 5.12
1604 1730 0.898326 TGTAGGAGCCGTCTTGAGCA 60.898 55.000 0.00 0.00 0.00 4.26
1664 1790 0.037975 GTACCTCCGCGTCAAGGAAA 60.038 55.000 21.85 9.69 37.32 3.13
1673 1799 1.061570 GTACGTCAGTACCTCCGCG 59.938 63.158 0.00 0.00 45.59 6.46
1772 1919 1.970917 GCATCTGCCGGAACAACTCG 61.971 60.000 5.05 0.00 34.31 4.18
1935 2082 2.564947 CTGCAACTGAGAACTCTACCCT 59.435 50.000 3.51 0.00 0.00 4.34
2127 2274 1.322442 ACAAGAGTTTGCTTGAGCCC 58.678 50.000 10.71 0.00 46.31 5.19
2150 2297 3.056107 CCAGTGTCGGAAAGAAGGTATGA 60.056 47.826 0.00 0.00 0.00 2.15
2223 3807 2.375174 ACAGTTGGGCTAGAATCACCAA 59.625 45.455 0.00 0.00 40.44 3.67
2247 3839 2.102757 ACACTGCAGCTCATGAGGATAG 59.897 50.000 23.89 11.91 0.00 2.08
2315 3911 6.981762 AGCTTCTTGATCATAACTTGTCTG 57.018 37.500 0.00 0.00 0.00 3.51
2375 3972 1.528129 CCACTTGAGCCCAGAAGAAC 58.472 55.000 0.00 0.00 0.00 3.01
2388 3985 2.281070 ACTCACGGCAGCCACTTG 60.281 61.111 13.30 5.25 0.00 3.16
2451 4082 6.026186 AGAGGACCTTGATAAAAGGAGAAGA 58.974 40.000 11.02 0.00 39.81 2.87
2612 4308 2.811855 TGAACTGCAGCACAACATTTG 58.188 42.857 15.27 0.00 0.00 2.32
2689 4386 6.884295 TCCAAATGATACAGTGTAAAGGAAGG 59.116 38.462 7.16 6.46 0.00 3.46
2818 4525 8.603304 ACCATGACAACCTTTCTACTACTTATT 58.397 33.333 0.00 0.00 0.00 1.40
2837 4544 2.079925 GAAACTGAGCCTGACCATGAC 58.920 52.381 0.00 0.00 0.00 3.06
2864 4895 6.714810 ACATGGCTGACACTTACAGAATTTAA 59.285 34.615 0.00 0.00 37.54 1.52
2866 4897 5.072741 ACATGGCTGACACTTACAGAATTT 58.927 37.500 0.00 0.00 37.54 1.82
2867 4898 4.655963 ACATGGCTGACACTTACAGAATT 58.344 39.130 0.00 0.00 37.54 2.17
2868 4899 4.292186 ACATGGCTGACACTTACAGAAT 57.708 40.909 0.00 0.00 37.54 2.40
2869 4900 3.769739 ACATGGCTGACACTTACAGAA 57.230 42.857 0.00 0.00 37.54 3.02
2870 4901 3.402110 CAACATGGCTGACACTTACAGA 58.598 45.455 0.00 0.00 37.54 3.41
2871 4902 2.095567 GCAACATGGCTGACACTTACAG 60.096 50.000 0.00 0.00 38.27 2.74
2872 4903 1.879380 GCAACATGGCTGACACTTACA 59.121 47.619 0.00 0.00 0.00 2.41
2873 4904 1.135972 CGCAACATGGCTGACACTTAC 60.136 52.381 0.00 0.00 0.00 2.34
2874 4905 1.155889 CGCAACATGGCTGACACTTA 58.844 50.000 0.00 0.00 0.00 2.24
2875 4906 1.951510 CGCAACATGGCTGACACTT 59.048 52.632 0.00 0.00 0.00 3.16
2876 4907 2.620112 GCGCAACATGGCTGACACT 61.620 57.895 0.30 0.00 0.00 3.55
2877 4908 2.126734 GCGCAACATGGCTGACAC 60.127 61.111 0.30 0.00 0.00 3.67
2878 4909 1.525718 ATTGCGCAACATGGCTGACA 61.526 50.000 27.64 0.00 0.00 3.58
2879 4910 1.074319 CATTGCGCAACATGGCTGAC 61.074 55.000 27.64 0.00 0.00 3.51
2880 4911 1.213275 CATTGCGCAACATGGCTGA 59.787 52.632 27.64 0.00 0.00 4.26
2911 4987 1.750930 CAGCCGGCTCATAGTGGAT 59.249 57.895 30.29 0.00 0.00 3.41
3044 5151 9.958180 ACTATTTTAAAAGCTGGCCAAAATAAT 57.042 25.926 7.01 0.00 33.20 1.28
3045 5152 9.785982 AACTATTTTAAAAGCTGGCCAAAATAA 57.214 25.926 7.01 0.00 33.20 1.40
3047 5154 7.308529 GCAACTATTTTAAAAGCTGGCCAAAAT 60.309 33.333 7.01 10.64 34.26 1.82
3063 5170 7.148086 ACGACACATATCAATGGCAACTATTTT 60.148 33.333 0.00 0.00 37.43 1.82
3081 5189 6.877611 AAGGAAAATAGAAACACGACACAT 57.122 33.333 0.00 0.00 0.00 3.21
3085 5193 7.376072 CAGTTCAAAGGAAAATAGAAACACGAC 59.624 37.037 0.00 0.00 34.13 4.34
3096 5204 8.699130 AGTCAATTCTTCAGTTCAAAGGAAAAT 58.301 29.630 0.00 0.00 34.13 1.82
3154 5268 7.016153 ACCACTGTATGACCTTTTGAGAATA 57.984 36.000 0.00 0.00 0.00 1.75
3160 5274 5.766150 TGAAACCACTGTATGACCTTTTG 57.234 39.130 0.00 0.00 0.00 2.44
3164 5278 4.908601 TCATGAAACCACTGTATGACCT 57.091 40.909 0.00 0.00 0.00 3.85
3188 5303 9.469097 ACCAGTGTACATTGGCTAAATATTTAA 57.531 29.630 31.17 0.00 41.38 1.52
3219 5334 4.440758 CAGCTACAACAAAACATGGAAACG 59.559 41.667 0.00 0.00 0.00 3.60
3244 5359 1.722011 ACAACTAGGCCGTTTGATCG 58.278 50.000 17.73 0.00 0.00 3.69
3326 5471 4.746611 TCACAGCTTTATATGCATCGACAG 59.253 41.667 0.19 0.00 0.00 3.51
3350 5500 3.006247 GCTTCTTACAAGAGCTTCCTGG 58.994 50.000 0.00 0.00 36.22 4.45
3371 5521 6.593770 AGCCAACTTTTCTGTTTAAACAAAGG 59.406 34.615 24.64 18.46 38.66 3.11
3375 5525 6.274157 TCAGCCAACTTTTCTGTTTAAACA 57.726 33.333 19.53 19.53 37.37 2.83
3427 5577 4.944962 TTGGCAGTAACTTGATCAATCG 57.055 40.909 8.96 0.48 0.00 3.34


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

AutoCloner maintained by Alex Coulton.