Multiple sequence alignment - TraesCS2B01G118200

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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 TraesCS2B01G118200 chr2B 100.000 3758 0 0 1 3758 82360172 82363929 0.000000e+00 6940.0
1 TraesCS2B01G118200 chr2B 88.758 2295 160 42 541 2777 82851101 82853355 0.000000e+00 2719.0
2 TraesCS2B01G118200 chr2B 90.387 801 49 8 1215 2007 82714081 82714861 0.000000e+00 1027.0
3 TraesCS2B01G118200 chr2B 82.957 1062 116 29 1713 2722 83954759 83953711 0.000000e+00 898.0
4 TraesCS2B01G118200 chr2B 88.873 692 46 13 1962 2627 82714851 82715537 0.000000e+00 822.0
5 TraesCS2B01G118200 chr2B 80.258 1165 145 44 977 2100 83211042 83212162 0.000000e+00 798.0
6 TraesCS2B01G118200 chr2B 88.966 580 58 3 1114 1687 83955403 83954824 0.000000e+00 712.0
7 TraesCS2B01G118200 chr2B 87.895 380 30 6 545 916 82712822 82713193 2.070000e-117 433.0
8 TraesCS2B01G118200 chr2B 94.660 206 10 1 2625 2829 82717655 82717860 6.060000e-83 318.0
9 TraesCS2B01G118200 chr2B 100.000 58 0 0 459 516 82850683 82850740 1.430000e-19 108.0
10 TraesCS2B01G118200 chr2A 86.314 2360 171 76 541 2822 54111336 54113621 0.000000e+00 2429.0
11 TraesCS2B01G118200 chr2A 85.080 2386 171 60 541 2829 54011768 54014065 0.000000e+00 2263.0
12 TraesCS2B01G118200 chr2A 81.635 1040 115 35 1114 2100 54139933 54140949 0.000000e+00 793.0
13 TraesCS2B01G118200 chr2A 81.189 1026 100 43 1764 2722 54473402 54472403 0.000000e+00 739.0
14 TraesCS2B01G118200 chr2A 86.897 580 66 8 1114 1685 54474112 54473535 3.160000e-180 641.0
15 TraesCS2B01G118200 chr2D 89.880 1502 100 25 541 2007 52851440 52852924 0.000000e+00 1884.0
16 TraesCS2B01G118200 chr2D 92.832 865 52 6 1114 1971 52646951 52647812 0.000000e+00 1245.0
17 TraesCS2B01G118200 chr2D 89.675 891 61 17 1966 2829 52647843 52648729 0.000000e+00 1107.0
18 TraesCS2B01G118200 chr2D 87.627 889 68 22 1982 2829 52852934 52853821 0.000000e+00 994.0
19 TraesCS2B01G118200 chr2D 82.714 1076 102 39 1708 2722 53649643 53650695 0.000000e+00 880.0
20 TraesCS2B01G118200 chr2D 88.696 575 61 3 1114 1687 53649014 53649585 0.000000e+00 699.0
21 TraesCS2B01G118200 chr2D 86.667 495 36 13 541 1026 52646418 52646891 4.300000e-144 521.0
22 TraesCS2B01G118200 chr2D 96.552 58 2 0 459 516 52851030 52851087 3.090000e-16 97.1
23 TraesCS2B01G118200 chr2D 95.918 49 2 0 460 508 52645755 52645803 3.110000e-11 80.5
24 TraesCS2B01G118200 chrUn 89.581 931 91 4 2830 3758 156741765 156742691 0.000000e+00 1177.0
25 TraesCS2B01G118200 chrUn 80.730 493 37 30 1 461 99866439 99866905 7.780000e-87 331.0
26 TraesCS2B01G118200 chr7B 89.332 928 97 2 2832 3757 672760228 672761155 0.000000e+00 1164.0
27 TraesCS2B01G118200 chr5D 89.236 929 95 3 2831 3758 1726721 1725797 0.000000e+00 1157.0
28 TraesCS2B01G118200 chr5D 92.500 200 14 1 263 462 297186389 297186587 6.140000e-73 285.0
29 TraesCS2B01G118200 chr5D 92.857 112 8 0 1 112 297174217 297174328 3.000000e-36 163.0
30 TraesCS2B01G118200 chr5D 96.104 77 3 0 38 114 404477443 404477367 3.940000e-25 126.0
31 TraesCS2B01G118200 chr5D 90.244 82 8 0 126 207 250067763 250067844 1.430000e-19 108.0
32 TraesCS2B01G118200 chr6B 89.213 927 96 2 2831 3756 94137899 94136976 0.000000e+00 1155.0
33 TraesCS2B01G118200 chr6B 88.355 936 97 6 2830 3758 663696212 663695282 0.000000e+00 1114.0
34 TraesCS2B01G118200 chr6B 88.387 930 99 7 2831 3758 388404914 388405836 0.000000e+00 1110.0
35 TraesCS2B01G118200 chr6B 90.452 199 17 2 263 461 96452969 96453165 1.040000e-65 261.0
36 TraesCS2B01G118200 chr6B 93.860 114 7 0 1 114 96452408 96452521 4.990000e-39 172.0
37 TraesCS2B01G118200 chr7D 89.032 930 98 2 2830 3758 26979173 26978247 0.000000e+00 1149.0
38 TraesCS2B01G118200 chr7D 88.901 928 99 2 2832 3758 539762327 539763251 0.000000e+00 1140.0
39 TraesCS2B01G118200 chr1B 88.412 932 99 7 2830 3758 317432587 317433512 0.000000e+00 1114.0
40 TraesCS2B01G118200 chr1B 92.965 199 12 2 263 461 50781872 50782068 4.750000e-74 289.0
41 TraesCS2B01G118200 chr1B 95.833 48 2 0 1 48 50781598 50781645 1.120000e-10 78.7
42 TraesCS2B01G118200 chr4D 93.532 201 11 2 263 463 153909081 153909279 7.890000e-77 298.0
43 TraesCS2B01G118200 chr5A 92.593 162 12 0 1 162 415353368 415353207 2.260000e-57 233.0
44 TraesCS2B01G118200 chr5A 93.388 121 8 0 1 121 693447664 693447544 2.980000e-41 180.0
45 TraesCS2B01G118200 chr4A 79.743 311 28 20 1 277 99037332 99037023 3.830000e-45 193.0
46 TraesCS2B01G118200 chr3B 100.000 28 0 0 395 422 676220667 676220640 7.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G118200 chr2B 82360172 82363929 3757 False 6940.000 6940 100.00000 1 3758 1 chr2B.!!$F1 3757
1 TraesCS2B01G118200 chr2B 82850683 82853355 2672 False 1413.500 2719 94.37900 459 2777 2 chr2B.!!$F4 2318
2 TraesCS2B01G118200 chr2B 83953711 83955403 1692 True 805.000 898 85.96150 1114 2722 2 chr2B.!!$R1 1608
3 TraesCS2B01G118200 chr2B 83211042 83212162 1120 False 798.000 798 80.25800 977 2100 1 chr2B.!!$F2 1123
4 TraesCS2B01G118200 chr2B 82712822 82717860 5038 False 650.000 1027 90.45375 545 2829 4 chr2B.!!$F3 2284
5 TraesCS2B01G118200 chr2A 54111336 54113621 2285 False 2429.000 2429 86.31400 541 2822 1 chr2A.!!$F2 2281
6 TraesCS2B01G118200 chr2A 54011768 54014065 2297 False 2263.000 2263 85.08000 541 2829 1 chr2A.!!$F1 2288
7 TraesCS2B01G118200 chr2A 54139933 54140949 1016 False 793.000 793 81.63500 1114 2100 1 chr2A.!!$F3 986
8 TraesCS2B01G118200 chr2A 54472403 54474112 1709 True 690.000 739 84.04300 1114 2722 2 chr2A.!!$R1 1608
9 TraesCS2B01G118200 chr2D 52851030 52853821 2791 False 991.700 1884 91.35300 459 2829 3 chr2D.!!$F2 2370
10 TraesCS2B01G118200 chr2D 53649014 53650695 1681 False 789.500 880 85.70500 1114 2722 2 chr2D.!!$F3 1608
11 TraesCS2B01G118200 chr2D 52645755 52648729 2974 False 738.375 1245 91.27300 460 2829 4 chr2D.!!$F1 2369
12 TraesCS2B01G118200 chrUn 156741765 156742691 926 False 1177.000 1177 89.58100 2830 3758 1 chrUn.!!$F2 928
13 TraesCS2B01G118200 chr7B 672760228 672761155 927 False 1164.000 1164 89.33200 2832 3757 1 chr7B.!!$F1 925
14 TraesCS2B01G118200 chr5D 1725797 1726721 924 True 1157.000 1157 89.23600 2831 3758 1 chr5D.!!$R1 927
15 TraesCS2B01G118200 chr6B 94136976 94137899 923 True 1155.000 1155 89.21300 2831 3756 1 chr6B.!!$R1 925
16 TraesCS2B01G118200 chr6B 663695282 663696212 930 True 1114.000 1114 88.35500 2830 3758 1 chr6B.!!$R2 928
17 TraesCS2B01G118200 chr6B 388404914 388405836 922 False 1110.000 1110 88.38700 2831 3758 1 chr6B.!!$F1 927
18 TraesCS2B01G118200 chr6B 96452408 96453165 757 False 216.500 261 92.15600 1 461 2 chr6B.!!$F2 460
19 TraesCS2B01G118200 chr7D 26978247 26979173 926 True 1149.000 1149 89.03200 2830 3758 1 chr7D.!!$R1 928
20 TraesCS2B01G118200 chr7D 539762327 539763251 924 False 1140.000 1140 88.90100 2832 3758 1 chr7D.!!$F1 926
21 TraesCS2B01G118200 chr1B 317432587 317433512 925 False 1114.000 1114 88.41200 2830 3758 1 chr1B.!!$F1 928

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
409 519 0.037605 AGATGACCCAAACGGACGAC 60.038 55.0 0.0 0.0 34.64 4.34 F
411 521 0.107081 ATGACCCAAACGGACGACAA 59.893 50.0 0.0 0.0 34.64 3.18 F
412 522 0.107800 TGACCCAAACGGACGACAAA 60.108 50.0 0.0 0.0 34.64 2.83 F
413 523 0.305617 GACCCAAACGGACGACAAAC 59.694 55.0 0.0 0.0 34.64 2.93 F
2142 3764 0.326264 CAGCAGAGCCCCAACTACTT 59.674 55.0 0.0 0.0 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2123 3745 0.326264 AAGTAGTTGGGGCTCTGCTG 59.674 55.000 0.00 0.0 0.00 4.41 R
2124 3746 0.615850 GAAGTAGTTGGGGCTCTGCT 59.384 55.000 0.00 0.0 0.00 4.24 R
2184 3812 0.711184 AGCCTGGTAGGGTGAGTACT 59.289 55.000 0.00 0.0 45.86 2.73 R
2323 3951 1.144936 CGGCATCAGGAAGGAGGTC 59.855 63.158 0.00 0.0 0.00 3.85 R
3464 7324 0.107897 CCACCGTCGGGATGAATGAA 60.108 55.000 17.28 0.0 36.97 2.57 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
93 94 1.689582 ACCTTGACCTCCCCGGATC 60.690 63.158 0.73 0.00 36.31 3.36
103 104 1.071471 CCCCGGATCCGATTCCAAG 59.929 63.158 35.42 16.08 42.83 3.61
106 107 1.160329 CCGGATCCGATTCCAAGCAC 61.160 60.000 35.42 0.00 42.83 4.40
114 115 1.228644 ATTCCAAGCACCAGCAGCA 60.229 52.632 0.00 0.00 45.49 4.41
115 116 1.248785 ATTCCAAGCACCAGCAGCAG 61.249 55.000 0.00 0.00 45.49 4.24
116 117 2.596631 CCAAGCACCAGCAGCAGT 60.597 61.111 0.00 0.00 45.49 4.40
117 118 2.643272 CAAGCACCAGCAGCAGTG 59.357 61.111 10.51 10.51 45.49 3.66
142 220 1.227823 TCGACCACAACAAGCCCAG 60.228 57.895 0.00 0.00 0.00 4.45
161 239 3.121030 CGAGGCCGGAGCAAACAG 61.121 66.667 5.05 0.00 42.56 3.16
163 241 3.553095 GAGGCCGGAGCAAACAGGT 62.553 63.158 5.05 0.00 42.56 4.00
168 246 1.507141 CCGGAGCAAACAGGTCACAC 61.507 60.000 0.00 0.00 46.51 3.82
174 252 1.382522 CAAACAGGTCACACTGCAGT 58.617 50.000 15.25 15.25 42.21 4.40
183 261 0.249447 CACACTGCAGTTCCTCGACA 60.249 55.000 18.94 0.00 0.00 4.35
184 262 0.249489 ACACTGCAGTTCCTCGACAC 60.249 55.000 18.94 0.00 0.00 3.67
228 306 0.300193 GAGCTTCGCTGATTTCGAGC 59.700 55.000 0.00 0.00 39.88 5.03
235 345 1.633171 CTGATTTCGAGCTTCGCCG 59.367 57.895 0.00 0.00 40.21 6.46
271 381 2.876645 CGAGCTTCGCTGACGGTC 60.877 66.667 0.00 0.00 39.88 4.79
273 383 1.372997 GAGCTTCGCTGACGGTCAA 60.373 57.895 12.54 0.00 39.88 3.18
274 384 1.618640 GAGCTTCGCTGACGGTCAAC 61.619 60.000 12.54 6.88 39.88 3.18
275 385 1.664965 GCTTCGCTGACGGTCAACT 60.665 57.895 12.54 0.00 40.63 3.16
276 386 1.618640 GCTTCGCTGACGGTCAACTC 61.619 60.000 12.54 3.78 40.63 3.01
277 387 0.039074 CTTCGCTGACGGTCAACTCT 60.039 55.000 12.54 0.00 40.63 3.24
278 388 1.199327 CTTCGCTGACGGTCAACTCTA 59.801 52.381 12.54 0.00 40.63 2.43
279 389 1.460504 TCGCTGACGGTCAACTCTAT 58.539 50.000 12.54 0.00 40.63 1.98
280 390 1.400846 TCGCTGACGGTCAACTCTATC 59.599 52.381 12.54 0.00 40.63 2.08
281 391 1.534175 CGCTGACGGTCAACTCTATCC 60.534 57.143 12.54 0.00 34.97 2.59
282 392 1.476891 GCTGACGGTCAACTCTATCCA 59.523 52.381 12.54 0.00 0.00 3.41
283 393 2.735762 GCTGACGGTCAACTCTATCCAC 60.736 54.545 12.54 0.00 0.00 4.02
284 394 1.471287 TGACGGTCAACTCTATCCACG 59.529 52.381 8.68 0.00 0.00 4.94
285 395 0.815734 ACGGTCAACTCTATCCACGG 59.184 55.000 0.00 0.00 0.00 4.94
286 396 0.527817 CGGTCAACTCTATCCACGGC 60.528 60.000 0.00 0.00 0.00 5.68
287 397 0.527817 GGTCAACTCTATCCACGGCG 60.528 60.000 4.80 4.80 0.00 6.46
288 398 0.527817 GTCAACTCTATCCACGGCGG 60.528 60.000 13.24 0.00 0.00 6.13
289 399 0.968901 TCAACTCTATCCACGGCGGT 60.969 55.000 13.24 0.00 35.57 5.68
290 400 0.527817 CAACTCTATCCACGGCGGTC 60.528 60.000 13.24 0.00 35.57 4.79
291 401 0.968901 AACTCTATCCACGGCGGTCA 60.969 55.000 13.24 0.00 35.57 4.02
292 402 0.968901 ACTCTATCCACGGCGGTCAA 60.969 55.000 13.24 0.00 35.57 3.18
293 403 0.527817 CTCTATCCACGGCGGTCAAC 60.528 60.000 13.24 0.00 35.57 3.18
294 404 0.968901 TCTATCCACGGCGGTCAACT 60.969 55.000 13.24 0.00 35.57 3.16
295 405 0.527817 CTATCCACGGCGGTCAACTC 60.528 60.000 13.24 0.00 35.57 3.01
296 406 1.252215 TATCCACGGCGGTCAACTCA 61.252 55.000 13.24 0.00 35.57 3.41
297 407 2.507110 ATCCACGGCGGTCAACTCAG 62.507 60.000 13.24 0.00 35.57 3.35
298 408 2.029073 CACGGCGGTCAACTCAGT 59.971 61.111 13.24 0.00 0.00 3.41
299 409 1.594293 CACGGCGGTCAACTCAGTT 60.594 57.895 13.24 0.00 0.00 3.16
300 410 1.300697 ACGGCGGTCAACTCAGTTC 60.301 57.895 13.24 0.00 0.00 3.01
301 411 1.300620 CGGCGGTCAACTCAGTTCA 60.301 57.895 0.00 0.00 0.00 3.18
302 412 1.557443 CGGCGGTCAACTCAGTTCAC 61.557 60.000 0.00 0.00 0.00 3.18
303 413 0.249911 GGCGGTCAACTCAGTTCACT 60.250 55.000 0.00 0.00 0.00 3.41
304 414 1.140816 GCGGTCAACTCAGTTCACTC 58.859 55.000 0.00 0.00 0.00 3.51
305 415 1.409412 CGGTCAACTCAGTTCACTCG 58.591 55.000 0.00 0.00 0.00 4.18
306 416 1.784525 GGTCAACTCAGTTCACTCGG 58.215 55.000 0.00 0.00 0.00 4.63
307 417 1.140816 GTCAACTCAGTTCACTCGGC 58.859 55.000 0.00 0.00 0.00 5.54
308 418 1.040646 TCAACTCAGTTCACTCGGCT 58.959 50.000 0.00 0.00 0.00 5.52
309 419 1.143305 CAACTCAGTTCACTCGGCTG 58.857 55.000 0.00 0.00 0.00 4.85
310 420 0.601311 AACTCAGTTCACTCGGCTGC 60.601 55.000 0.00 0.00 0.00 5.25
311 421 1.291588 CTCAGTTCACTCGGCTGCT 59.708 57.895 0.00 0.00 0.00 4.24
312 422 1.005748 TCAGTTCACTCGGCTGCTG 60.006 57.895 0.95 0.95 0.00 4.41
313 423 2.358003 AGTTCACTCGGCTGCTGC 60.358 61.111 7.10 7.10 38.76 5.25
314 424 3.782244 GTTCACTCGGCTGCTGCG 61.782 66.667 9.65 0.00 40.82 5.18
315 425 4.299547 TTCACTCGGCTGCTGCGT 62.300 61.111 9.65 0.00 40.82 5.24
316 426 3.807631 TTCACTCGGCTGCTGCGTT 62.808 57.895 9.65 0.00 40.82 4.84
317 427 3.349006 CACTCGGCTGCTGCGTTT 61.349 61.111 9.65 0.00 40.82 3.60
318 428 3.349006 ACTCGGCTGCTGCGTTTG 61.349 61.111 9.65 2.67 40.82 2.93
319 429 3.349006 CTCGGCTGCTGCGTTTGT 61.349 61.111 9.65 0.00 40.82 2.83
320 430 3.300667 CTCGGCTGCTGCGTTTGTC 62.301 63.158 9.65 0.00 40.82 3.18
321 431 4.389576 CGGCTGCTGCGTTTGTCC 62.390 66.667 9.65 0.00 40.82 4.02
322 432 4.389576 GGCTGCTGCGTTTGTCCG 62.390 66.667 9.65 0.00 40.82 4.79
330 440 2.809601 CGTTTGTCCGCTCGAGGG 60.810 66.667 21.77 21.77 0.00 4.30
331 441 3.119096 GTTTGTCCGCTCGAGGGC 61.119 66.667 23.15 11.58 36.18 5.19
332 442 3.311110 TTTGTCCGCTCGAGGGCT 61.311 61.111 23.15 0.00 36.69 5.19
333 443 3.589654 TTTGTCCGCTCGAGGGCTG 62.590 63.158 23.15 11.29 36.69 4.85
335 445 4.803426 GTCCGCTCGAGGGCTGTG 62.803 72.222 23.15 10.23 32.02 3.66
338 448 4.827087 CGCTCGAGGGCTGTGCAT 62.827 66.667 17.16 0.00 0.00 3.96
339 449 2.437359 GCTCGAGGGCTGTGCATT 60.437 61.111 15.58 0.00 0.00 3.56
340 450 2.758089 GCTCGAGGGCTGTGCATTG 61.758 63.158 15.58 0.00 0.00 2.82
341 451 2.046023 TCGAGGGCTGTGCATTGG 60.046 61.111 0.00 0.00 0.00 3.16
342 452 3.136123 CGAGGGCTGTGCATTGGG 61.136 66.667 0.00 0.00 0.00 4.12
343 453 2.036256 GAGGGCTGTGCATTGGGT 59.964 61.111 0.00 0.00 0.00 4.51
344 454 2.283388 AGGGCTGTGCATTGGGTG 60.283 61.111 0.00 0.00 0.00 4.61
354 464 2.965805 CATTGGGTGCATCCACAGT 58.034 52.632 21.13 4.87 43.88 3.55
355 465 0.813184 CATTGGGTGCATCCACAGTC 59.187 55.000 21.13 0.00 43.88 3.51
356 466 0.323725 ATTGGGTGCATCCACAGTCC 60.324 55.000 21.13 0.00 43.88 3.85
357 467 2.436646 GGGTGCATCCACAGTCCG 60.437 66.667 12.38 0.00 43.88 4.79
358 468 2.347490 GGTGCATCCACAGTCCGT 59.653 61.111 0.00 0.00 43.88 4.69
359 469 1.741770 GGTGCATCCACAGTCCGTC 60.742 63.158 0.00 0.00 43.88 4.79
360 470 1.293498 GTGCATCCACAGTCCGTCT 59.707 57.895 0.00 0.00 41.67 4.18
361 471 0.737715 GTGCATCCACAGTCCGTCTC 60.738 60.000 0.00 0.00 41.67 3.36
362 472 0.900182 TGCATCCACAGTCCGTCTCT 60.900 55.000 0.00 0.00 0.00 3.10
363 473 0.459237 GCATCCACAGTCCGTCTCTG 60.459 60.000 0.00 0.00 38.68 3.35
364 474 0.891373 CATCCACAGTCCGTCTCTGT 59.109 55.000 0.00 0.00 45.43 3.41
365 475 1.135257 CATCCACAGTCCGTCTCTGTC 60.135 57.143 0.00 0.00 43.14 3.51
366 476 0.894184 TCCACAGTCCGTCTCTGTCC 60.894 60.000 0.00 0.00 43.14 4.02
367 477 1.210413 CACAGTCCGTCTCTGTCCG 59.790 63.158 0.00 0.00 43.14 4.79
368 478 2.179517 CAGTCCGTCTCTGTCCGC 59.820 66.667 0.00 0.00 0.00 5.54
369 479 3.063084 AGTCCGTCTCTGTCCGCC 61.063 66.667 0.00 0.00 0.00 6.13
370 480 4.131088 GTCCGTCTCTGTCCGCCC 62.131 72.222 0.00 0.00 0.00 6.13
373 483 3.461773 CGTCTCTGTCCGCCCCAT 61.462 66.667 0.00 0.00 0.00 4.00
374 484 2.187946 GTCTCTGTCCGCCCCATG 59.812 66.667 0.00 0.00 0.00 3.66
375 485 2.284625 TCTCTGTCCGCCCCATGT 60.285 61.111 0.00 0.00 0.00 3.21
376 486 2.187946 CTCTGTCCGCCCCATGTC 59.812 66.667 0.00 0.00 0.00 3.06
377 487 3.391665 CTCTGTCCGCCCCATGTCC 62.392 68.421 0.00 0.00 0.00 4.02
378 488 4.838152 CTGTCCGCCCCATGTCCG 62.838 72.222 0.00 0.00 0.00 4.79
383 493 4.609018 CGCCCCATGTCCGCCTAG 62.609 72.222 0.00 0.00 0.00 3.02
384 494 4.256180 GCCCCATGTCCGCCTAGG 62.256 72.222 3.67 3.67 42.97 3.02
385 495 4.256180 CCCCATGTCCGCCTAGGC 62.256 72.222 24.75 24.75 40.77 3.93
395 505 3.538614 GCCTAGGCGGACAGATGA 58.461 61.111 20.16 0.00 33.16 2.92
396 506 1.068250 GCCTAGGCGGACAGATGAC 59.932 63.158 20.16 0.00 33.16 3.06
397 507 1.742768 CCTAGGCGGACAGATGACC 59.257 63.158 0.00 0.00 33.16 4.02
398 508 1.742768 CTAGGCGGACAGATGACCC 59.257 63.158 0.00 0.00 0.00 4.46
399 509 1.001120 TAGGCGGACAGATGACCCA 59.999 57.895 0.00 0.00 0.00 4.51
400 510 0.616395 TAGGCGGACAGATGACCCAA 60.616 55.000 0.00 0.00 0.00 4.12
401 511 1.002624 GGCGGACAGATGACCCAAA 60.003 57.895 0.00 0.00 0.00 3.28
402 512 1.305930 GGCGGACAGATGACCCAAAC 61.306 60.000 0.00 0.00 0.00 2.93
403 513 1.635663 GCGGACAGATGACCCAAACG 61.636 60.000 0.00 0.00 0.00 3.60
404 514 1.019278 CGGACAGATGACCCAAACGG 61.019 60.000 0.00 0.00 37.81 4.44
405 515 0.323629 GGACAGATGACCCAAACGGA 59.676 55.000 0.00 0.00 34.64 4.69
406 516 1.439679 GACAGATGACCCAAACGGAC 58.560 55.000 0.00 0.00 34.64 4.79
407 517 0.320421 ACAGATGACCCAAACGGACG 60.320 55.000 0.00 0.00 34.64 4.79
408 518 0.037697 CAGATGACCCAAACGGACGA 60.038 55.000 0.00 0.00 34.64 4.20
409 519 0.037605 AGATGACCCAAACGGACGAC 60.038 55.000 0.00 0.00 34.64 4.34
410 520 0.320073 GATGACCCAAACGGACGACA 60.320 55.000 0.00 0.00 34.64 4.35
411 521 0.107081 ATGACCCAAACGGACGACAA 59.893 50.000 0.00 0.00 34.64 3.18
412 522 0.107800 TGACCCAAACGGACGACAAA 60.108 50.000 0.00 0.00 34.64 2.83
413 523 0.305617 GACCCAAACGGACGACAAAC 59.694 55.000 0.00 0.00 34.64 2.93
414 524 1.430707 ACCCAAACGGACGACAAACG 61.431 55.000 0.00 0.00 40.89 3.60
436 546 3.638484 GACAAAATCCGTGTCCTTTTGG 58.362 45.455 10.61 0.00 41.76 3.28
437 547 2.364002 ACAAAATCCGTGTCCTTTTGGG 59.636 45.455 10.61 0.00 41.76 4.12
438 548 2.364002 CAAAATCCGTGTCCTTTTGGGT 59.636 45.455 0.00 0.00 40.87 4.51
439 549 1.905637 AATCCGTGTCCTTTTGGGTC 58.094 50.000 0.00 0.00 40.87 4.46
440 550 1.064825 ATCCGTGTCCTTTTGGGTCT 58.935 50.000 0.00 0.00 40.87 3.85
441 551 0.841289 TCCGTGTCCTTTTGGGTCTT 59.159 50.000 0.00 0.00 40.87 3.01
442 552 1.213430 TCCGTGTCCTTTTGGGTCTTT 59.787 47.619 0.00 0.00 40.87 2.52
443 553 1.336755 CCGTGTCCTTTTGGGTCTTTG 59.663 52.381 0.00 0.00 40.87 2.77
444 554 1.269051 CGTGTCCTTTTGGGTCTTTGC 60.269 52.381 0.00 0.00 40.87 3.68
445 555 1.754226 GTGTCCTTTTGGGTCTTTGCA 59.246 47.619 0.00 0.00 40.87 4.08
446 556 2.365293 GTGTCCTTTTGGGTCTTTGCAT 59.635 45.455 0.00 0.00 40.87 3.96
447 557 3.037549 TGTCCTTTTGGGTCTTTGCATT 58.962 40.909 0.00 0.00 40.87 3.56
448 558 3.181467 TGTCCTTTTGGGTCTTTGCATTG 60.181 43.478 0.00 0.00 40.87 2.82
449 559 2.368221 TCCTTTTGGGTCTTTGCATTGG 59.632 45.455 0.00 0.00 40.87 3.16
450 560 2.368221 CCTTTTGGGTCTTTGCATTGGA 59.632 45.455 0.00 0.00 35.46 3.53
451 561 3.555586 CCTTTTGGGTCTTTGCATTGGAG 60.556 47.826 0.00 0.00 35.46 3.86
452 562 2.380064 TTGGGTCTTTGCATTGGAGT 57.620 45.000 0.00 0.00 0.00 3.85
453 563 2.380064 TGGGTCTTTGCATTGGAGTT 57.620 45.000 0.00 0.00 0.00 3.01
454 564 1.962807 TGGGTCTTTGCATTGGAGTTG 59.037 47.619 0.00 0.00 0.00 3.16
455 565 1.337167 GGGTCTTTGCATTGGAGTTGC 60.337 52.381 0.00 0.00 40.55 4.17
456 566 1.615392 GGTCTTTGCATTGGAGTTGCT 59.385 47.619 0.00 0.00 40.77 3.91
457 567 2.352127 GGTCTTTGCATTGGAGTTGCTC 60.352 50.000 0.00 0.00 40.77 4.26
516 626 1.301423 TTGTGCGTTGTTCAGTACCC 58.699 50.000 0.00 0.00 0.00 3.69
517 627 0.466543 TGTGCGTTGTTCAGTACCCT 59.533 50.000 0.00 0.00 0.00 4.34
519 629 1.263217 GTGCGTTGTTCAGTACCCTTG 59.737 52.381 0.00 0.00 0.00 3.61
520 630 0.872388 GCGTTGTTCAGTACCCTTGG 59.128 55.000 0.00 0.00 0.00 3.61
521 631 1.812708 GCGTTGTTCAGTACCCTTGGT 60.813 52.381 0.00 0.00 40.16 3.67
522 632 1.871039 CGTTGTTCAGTACCCTTGGTG 59.129 52.381 0.00 0.00 36.19 4.17
523 633 2.484065 CGTTGTTCAGTACCCTTGGTGA 60.484 50.000 0.00 0.00 36.19 4.02
525 635 4.142038 GTTGTTCAGTACCCTTGGTGATT 58.858 43.478 0.00 0.00 36.19 2.57
526 636 5.310451 GTTGTTCAGTACCCTTGGTGATTA 58.690 41.667 0.00 0.00 36.19 1.75
527 637 4.901868 TGTTCAGTACCCTTGGTGATTAC 58.098 43.478 0.00 0.00 36.19 1.89
528 638 4.348461 TGTTCAGTACCCTTGGTGATTACA 59.652 41.667 0.00 0.00 36.19 2.41
529 639 4.546829 TCAGTACCCTTGGTGATTACAC 57.453 45.455 0.00 0.00 45.27 2.90
621 1336 7.870445 GTGTCATTAGCAACCAAGGATTAAAAA 59.130 33.333 0.00 0.00 0.00 1.94
622 1337 8.592809 TGTCATTAGCAACCAAGGATTAAAAAT 58.407 29.630 0.00 0.00 0.00 1.82
623 1338 9.435688 GTCATTAGCAACCAAGGATTAAAAATT 57.564 29.630 0.00 0.00 0.00 1.82
635 1350 7.764695 AGGATTAAAAATTTAAAATCGCGGG 57.235 32.000 6.13 0.00 36.35 6.13
638 1353 6.635166 TTAAAAATTTAAAATCGCGGGAGC 57.365 33.333 6.13 0.00 39.97 4.70
694 1409 1.804748 GATTTCAGCGTTTTCTCCCGT 59.195 47.619 0.00 0.00 0.00 5.28
706 1421 5.064707 CGTTTTCTCCCGTGATTCACAATAT 59.935 40.000 16.61 0.00 33.40 1.28
787 1510 7.624360 TCATCCGTGATTTAAAATGTTAGCT 57.376 32.000 0.00 0.00 0.00 3.32
987 1721 2.932569 TATAAGCTCACCCCGCCCGA 62.933 60.000 0.00 0.00 0.00 5.14
1040 2164 6.811253 ATCACCTCTAACATCTCGATCTAC 57.189 41.667 0.00 0.00 0.00 2.59
1344 2714 2.614983 ACTCCTCGATAAGAGCGTTCTC 59.385 50.000 0.98 0.00 45.54 2.87
1698 3166 4.116961 CAAGGTACGGCAAGATTCGATTA 58.883 43.478 0.00 0.00 0.00 1.75
1776 3297 3.015293 GACCACGCGCTCACATGTG 62.015 63.158 20.18 20.18 0.00 3.21
2064 3665 2.507992 CGCTTCGAGCTCCACCTG 60.508 66.667 8.47 0.00 39.60 4.00
2113 3735 2.187946 GAGCTACCGGTGCTGCAT 59.812 61.111 28.51 15.00 41.30 3.96
2140 3762 1.746991 GCAGCAGAGCCCCAACTAC 60.747 63.158 0.00 0.00 0.00 2.73
2141 3763 1.986413 CAGCAGAGCCCCAACTACT 59.014 57.895 0.00 0.00 0.00 2.57
2142 3764 0.326264 CAGCAGAGCCCCAACTACTT 59.674 55.000 0.00 0.00 0.00 2.24
2344 3975 1.617018 CCTCCTTCCTGATGCCGTCA 61.617 60.000 0.00 0.00 35.05 4.35
2468 4125 4.040952 AGTTTGCTGGTAGCTATAGATGGG 59.959 45.833 3.21 0.00 42.97 4.00
2595 4293 1.135689 GTTGTTGCGTCCAAGGCATAG 60.136 52.381 0.00 0.00 38.88 2.23
2659 6484 7.674772 GGGTATGATATCAAACTACTAGGAGGT 59.325 40.741 9.99 0.00 0.00 3.85
2756 6604 8.420222 AGTTGGTTGATAAATTTGATTGTGTGA 58.580 29.630 0.00 0.00 0.00 3.58
2764 6612 9.888878 GATAAATTTGATTGTGTGATGATCGAT 57.111 29.630 0.00 0.00 0.00 3.59
2767 6615 8.667076 AATTTGATTGTGTGATGATCGATCTA 57.333 30.769 25.02 12.64 31.55 1.98
2834 6682 0.106708 ATGCCATAGTTGATCCGCGT 59.893 50.000 4.92 0.00 0.00 6.01
2874 6725 4.814294 CCGTCACCACCGCCTAGC 62.814 72.222 0.00 0.00 0.00 3.42
2882 6733 3.771160 ACCGCCTAGCAACCCTCG 61.771 66.667 0.00 0.00 0.00 4.63
3087 6940 4.569180 CGGGCGCCCAGATCCATT 62.569 66.667 42.78 0.00 35.37 3.16
3191 7044 1.805945 GTGCCGAATCTCGTCGCTT 60.806 57.895 0.00 0.00 38.40 4.68
3213 7066 3.518998 CGGATCTCGCCACTCCGT 61.519 66.667 2.18 0.00 45.30 4.69
3219 7072 2.362503 TCGCCACTCCGTCCATCT 60.363 61.111 0.00 0.00 0.00 2.90
3242 7095 2.376165 GGAACCTAGACCTGGGGCC 61.376 68.421 0.00 0.00 35.26 5.80
3464 7324 1.407936 CGGAGGACACTCTGGATGAT 58.592 55.000 0.00 0.00 44.74 2.45
3467 7327 2.768527 GGAGGACACTCTGGATGATTCA 59.231 50.000 0.00 0.00 43.46 2.57
3524 7385 2.742372 CTACTTGCAGGCGCCGTT 60.742 61.111 23.20 0.00 37.32 4.44
3537 7398 4.760047 CCGTTGAGGTCCCTGCCG 62.760 72.222 0.00 0.00 34.51 5.69
3539 7400 2.642254 CGTTGAGGTCCCTGCCGTA 61.642 63.158 0.00 0.00 0.00 4.02
3540 7401 1.675219 GTTGAGGTCCCTGCCGTAA 59.325 57.895 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.664025 CTGAAGGCGTCCATGGCGA 62.664 63.158 26.00 8.99 39.82 5.54
79 80 2.599139 AATCGGATCCGGGGAGGTCA 62.599 60.000 32.79 12.37 41.99 4.02
93 94 1.651240 CTGCTGGTGCTTGGAATCGG 61.651 60.000 0.00 0.00 40.48 4.18
114 115 4.664677 GTGGTCGAGCGTGGCACT 62.665 66.667 16.72 0.00 0.00 4.40
115 116 4.961511 TGTGGTCGAGCGTGGCAC 62.962 66.667 7.79 7.79 0.00 5.01
116 117 4.228567 TTGTGGTCGAGCGTGGCA 62.229 61.111 10.46 3.68 0.00 4.92
117 118 3.712881 GTTGTGGTCGAGCGTGGC 61.713 66.667 10.46 1.00 0.00 5.01
118 119 1.831389 CTTGTTGTGGTCGAGCGTGG 61.831 60.000 10.46 0.00 0.00 4.94
120 121 2.244651 GCTTGTTGTGGTCGAGCGT 61.245 57.895 10.46 0.00 33.50 5.07
121 122 2.551270 GCTTGTTGTGGTCGAGCG 59.449 61.111 10.46 0.00 33.50 5.03
123 124 1.227823 TGGGCTTGTTGTGGTCGAG 60.228 57.895 0.00 0.00 0.00 4.04
124 125 1.227823 CTGGGCTTGTTGTGGTCGA 60.228 57.895 0.00 0.00 0.00 4.20
146 224 3.553095 GACCTGTTTGCTCCGGCCT 62.553 63.158 0.00 0.00 37.74 5.19
151 229 0.947244 CAGTGTGACCTGTTTGCTCC 59.053 55.000 0.00 0.00 0.00 4.70
161 239 0.946221 CGAGGAACTGCAGTGTGACC 60.946 60.000 22.49 19.99 41.55 4.02
163 241 0.032130 GTCGAGGAACTGCAGTGTGA 59.968 55.000 22.49 11.10 41.55 3.58
168 246 1.734477 CGGTGTCGAGGAACTGCAG 60.734 63.158 13.48 13.48 41.55 4.41
174 252 0.034337 CTTTTCCCGGTGTCGAGGAA 59.966 55.000 0.00 0.00 40.93 3.36
267 377 0.527817 GCCGTGGATAGAGTTGACCG 60.528 60.000 0.00 0.00 0.00 4.79
268 378 0.527817 CGCCGTGGATAGAGTTGACC 60.528 60.000 0.00 0.00 0.00 4.02
271 381 0.527817 GACCGCCGTGGATAGAGTTG 60.528 60.000 4.58 0.00 42.00 3.16
273 383 0.968901 TTGACCGCCGTGGATAGAGT 60.969 55.000 4.58 0.00 42.00 3.24
274 384 0.527817 GTTGACCGCCGTGGATAGAG 60.528 60.000 4.58 0.00 42.00 2.43
275 385 0.968901 AGTTGACCGCCGTGGATAGA 60.969 55.000 4.58 0.00 42.00 1.98
276 386 0.527817 GAGTTGACCGCCGTGGATAG 60.528 60.000 4.58 0.00 42.00 2.08
277 387 1.252215 TGAGTTGACCGCCGTGGATA 61.252 55.000 4.58 0.00 42.00 2.59
278 388 2.264794 GAGTTGACCGCCGTGGAT 59.735 61.111 4.58 0.00 42.00 3.41
279 389 3.220999 CTGAGTTGACCGCCGTGGA 62.221 63.158 4.58 0.00 42.00 4.02
280 390 2.738521 CTGAGTTGACCGCCGTGG 60.739 66.667 0.00 0.00 46.41 4.94
281 391 1.557443 GAACTGAGTTGACCGCCGTG 61.557 60.000 0.90 0.00 0.00 4.94
282 392 1.300697 GAACTGAGTTGACCGCCGT 60.301 57.895 0.90 0.00 0.00 5.68
283 393 1.300620 TGAACTGAGTTGACCGCCG 60.301 57.895 0.90 0.00 0.00 6.46
284 394 0.249911 AGTGAACTGAGTTGACCGCC 60.250 55.000 11.26 0.00 30.33 6.13
285 395 1.140816 GAGTGAACTGAGTTGACCGC 58.859 55.000 11.26 0.82 30.33 5.68
286 396 1.409412 CGAGTGAACTGAGTTGACCG 58.591 55.000 11.26 10.58 30.33 4.79
287 397 1.784525 CCGAGTGAACTGAGTTGACC 58.215 55.000 11.26 2.81 30.33 4.02
288 398 1.140816 GCCGAGTGAACTGAGTTGAC 58.859 55.000 6.83 6.83 30.18 3.18
289 399 1.040646 AGCCGAGTGAACTGAGTTGA 58.959 50.000 0.90 0.00 0.00 3.18
290 400 1.143305 CAGCCGAGTGAACTGAGTTG 58.857 55.000 0.90 0.00 33.10 3.16
291 401 0.601311 GCAGCCGAGTGAACTGAGTT 60.601 55.000 0.00 0.00 33.10 3.01
292 402 1.005630 GCAGCCGAGTGAACTGAGT 60.006 57.895 0.00 0.00 33.10 3.41
293 403 1.013005 CAGCAGCCGAGTGAACTGAG 61.013 60.000 0.00 0.00 33.10 3.35
294 404 1.005748 CAGCAGCCGAGTGAACTGA 60.006 57.895 0.00 0.00 33.10 3.41
295 405 2.675056 GCAGCAGCCGAGTGAACTG 61.675 63.158 0.00 0.00 33.58 3.16
296 406 2.358003 GCAGCAGCCGAGTGAACT 60.358 61.111 0.00 0.00 33.58 3.01
297 407 3.782244 CGCAGCAGCCGAGTGAAC 61.782 66.667 0.00 0.00 37.52 3.18
298 408 3.807631 AACGCAGCAGCCGAGTGAA 62.808 57.895 0.00 0.00 37.52 3.18
299 409 3.807631 AAACGCAGCAGCCGAGTGA 62.808 57.895 0.00 0.00 37.52 3.41
300 410 3.349006 AAACGCAGCAGCCGAGTG 61.349 61.111 0.00 0.00 37.52 3.51
301 411 3.349006 CAAACGCAGCAGCCGAGT 61.349 61.111 0.00 0.00 37.52 4.18
302 412 3.300667 GACAAACGCAGCAGCCGAG 62.301 63.158 0.00 0.00 37.52 4.63
303 413 3.345808 GACAAACGCAGCAGCCGA 61.346 61.111 0.00 0.00 37.52 5.54
304 414 4.389576 GGACAAACGCAGCAGCCG 62.390 66.667 0.00 0.00 37.52 5.52
305 415 4.389576 CGGACAAACGCAGCAGCC 62.390 66.667 0.00 0.00 37.52 4.85
313 423 2.809601 CCCTCGAGCGGACAAACG 60.810 66.667 6.99 0.00 0.00 3.60
314 424 3.119096 GCCCTCGAGCGGACAAAC 61.119 66.667 20.27 2.49 0.00 2.93
315 425 3.311110 AGCCCTCGAGCGGACAAA 61.311 61.111 20.27 0.00 38.01 2.83
316 426 4.069232 CAGCCCTCGAGCGGACAA 62.069 66.667 20.27 0.00 38.01 3.18
318 428 4.803426 CACAGCCCTCGAGCGGAC 62.803 72.222 20.27 12.70 38.01 4.79
321 431 4.827087 ATGCACAGCCCTCGAGCG 62.827 66.667 6.99 0.00 38.01 5.03
322 432 2.437359 AATGCACAGCCCTCGAGC 60.437 61.111 6.99 0.00 0.00 5.03
323 433 2.110967 CCAATGCACAGCCCTCGAG 61.111 63.158 5.13 5.13 0.00 4.04
324 434 2.046023 CCAATGCACAGCCCTCGA 60.046 61.111 0.00 0.00 0.00 4.04
325 435 3.136123 CCCAATGCACAGCCCTCG 61.136 66.667 0.00 0.00 0.00 4.63
326 436 2.036256 ACCCAATGCACAGCCCTC 59.964 61.111 0.00 0.00 0.00 4.30
327 437 2.283388 CACCCAATGCACAGCCCT 60.283 61.111 0.00 0.00 0.00 5.19
336 446 0.813184 GACTGTGGATGCACCCAATG 59.187 55.000 15.34 0.00 38.06 2.82
337 447 0.323725 GGACTGTGGATGCACCCAAT 60.324 55.000 15.34 0.00 38.06 3.16
338 448 1.074775 GGACTGTGGATGCACCCAA 59.925 57.895 15.34 0.00 38.06 4.12
339 449 2.756400 GGACTGTGGATGCACCCA 59.244 61.111 15.34 0.00 38.00 4.51
340 450 2.436646 CGGACTGTGGATGCACCC 60.437 66.667 15.34 7.92 38.00 4.61
341 451 1.741770 GACGGACTGTGGATGCACC 60.742 63.158 15.34 0.00 39.54 5.01
342 452 0.737715 GAGACGGACTGTGGATGCAC 60.738 60.000 10.90 10.90 0.00 4.57
343 453 0.900182 AGAGACGGACTGTGGATGCA 60.900 55.000 0.00 0.00 0.00 3.96
344 454 0.459237 CAGAGACGGACTGTGGATGC 60.459 60.000 0.00 0.00 36.43 3.91
345 455 0.891373 ACAGAGACGGACTGTGGATG 59.109 55.000 9.17 0.00 45.19 3.51
346 456 1.178276 GACAGAGACGGACTGTGGAT 58.822 55.000 14.12 0.00 46.57 3.41
347 457 0.894184 GGACAGAGACGGACTGTGGA 60.894 60.000 14.12 0.00 46.57 4.02
348 458 1.587054 GGACAGAGACGGACTGTGG 59.413 63.158 14.12 0.00 46.57 4.17
349 459 1.210413 CGGACAGAGACGGACTGTG 59.790 63.158 14.12 10.71 46.57 3.66
351 461 2.179517 GCGGACAGAGACGGACTG 59.820 66.667 0.00 0.00 40.68 3.51
352 462 3.063084 GGCGGACAGAGACGGACT 61.063 66.667 0.00 0.00 0.00 3.85
353 463 4.131088 GGGCGGACAGAGACGGAC 62.131 72.222 0.00 0.00 0.00 4.79
356 466 3.461773 ATGGGGCGGACAGAGACG 61.462 66.667 0.00 0.00 0.00 4.18
357 467 2.187946 CATGGGGCGGACAGAGAC 59.812 66.667 0.00 0.00 0.00 3.36
358 468 2.284625 ACATGGGGCGGACAGAGA 60.285 61.111 0.00 0.00 0.00 3.10
359 469 2.187946 GACATGGGGCGGACAGAG 59.812 66.667 0.00 0.00 0.00 3.35
360 470 3.399181 GGACATGGGGCGGACAGA 61.399 66.667 0.00 0.00 0.00 3.41
361 471 4.838152 CGGACATGGGGCGGACAG 62.838 72.222 0.00 0.00 0.00 3.51
366 476 4.609018 CTAGGCGGACATGGGGCG 62.609 72.222 0.00 0.00 0.00 6.13
367 477 4.256180 CCTAGGCGGACATGGGGC 62.256 72.222 0.00 0.00 33.16 5.80
368 478 4.256180 GCCTAGGCGGACATGGGG 62.256 72.222 20.16 0.00 33.16 4.96
378 488 1.068250 GTCATCTGTCCGCCTAGGC 59.932 63.158 24.75 24.75 40.77 3.93
379 489 1.742768 GGTCATCTGTCCGCCTAGG 59.257 63.158 3.67 3.67 42.97 3.02
380 490 1.043116 TGGGTCATCTGTCCGCCTAG 61.043 60.000 0.00 0.00 0.00 3.02
381 491 0.616395 TTGGGTCATCTGTCCGCCTA 60.616 55.000 0.00 0.00 0.00 3.93
382 492 1.488705 TTTGGGTCATCTGTCCGCCT 61.489 55.000 0.00 0.00 0.00 5.52
383 493 1.002624 TTTGGGTCATCTGTCCGCC 60.003 57.895 0.00 0.00 0.00 6.13
384 494 1.635663 CGTTTGGGTCATCTGTCCGC 61.636 60.000 0.00 0.00 0.00 5.54
385 495 1.019278 CCGTTTGGGTCATCTGTCCG 61.019 60.000 0.00 0.00 0.00 4.79
386 496 0.323629 TCCGTTTGGGTCATCTGTCC 59.676 55.000 0.00 0.00 37.00 4.02
387 497 1.439679 GTCCGTTTGGGTCATCTGTC 58.560 55.000 0.00 0.00 37.00 3.51
388 498 0.320421 CGTCCGTTTGGGTCATCTGT 60.320 55.000 0.00 0.00 37.00 3.41
389 499 0.037697 TCGTCCGTTTGGGTCATCTG 60.038 55.000 0.00 0.00 37.00 2.90
390 500 0.037605 GTCGTCCGTTTGGGTCATCT 60.038 55.000 0.00 0.00 37.00 2.90
391 501 0.320073 TGTCGTCCGTTTGGGTCATC 60.320 55.000 0.00 0.00 37.00 2.92
392 502 0.107081 TTGTCGTCCGTTTGGGTCAT 59.893 50.000 0.00 0.00 37.00 3.06
393 503 0.107800 TTTGTCGTCCGTTTGGGTCA 60.108 50.000 0.00 0.00 37.00 4.02
394 504 0.305617 GTTTGTCGTCCGTTTGGGTC 59.694 55.000 0.00 0.00 37.00 4.46
395 505 1.430707 CGTTTGTCGTCCGTTTGGGT 61.431 55.000 0.00 0.00 37.00 4.51
396 506 1.277440 CGTTTGTCGTCCGTTTGGG 59.723 57.895 0.00 0.00 35.24 4.12
397 507 1.152989 TCCGTTTGTCGTCCGTTTGG 61.153 55.000 0.00 0.00 37.94 3.28
398 508 0.042794 GTCCGTTTGTCGTCCGTTTG 60.043 55.000 0.00 0.00 37.94 2.93
399 509 0.459934 TGTCCGTTTGTCGTCCGTTT 60.460 50.000 0.00 0.00 37.94 3.60
400 510 0.459934 TTGTCCGTTTGTCGTCCGTT 60.460 50.000 0.00 0.00 37.94 4.44
401 511 0.459934 TTTGTCCGTTTGTCGTCCGT 60.460 50.000 0.00 0.00 37.94 4.69
402 512 0.651551 TTTTGTCCGTTTGTCGTCCG 59.348 50.000 0.00 0.00 37.94 4.79
403 513 2.350102 GGATTTTGTCCGTTTGTCGTCC 60.350 50.000 0.00 0.00 37.23 4.79
404 514 2.912366 GGATTTTGTCCGTTTGTCGTC 58.088 47.619 0.00 0.00 37.23 4.20
415 525 3.552068 CCCAAAAGGACACGGATTTTGTC 60.552 47.826 8.35 4.08 40.59 3.18
416 526 2.364002 CCCAAAAGGACACGGATTTTGT 59.636 45.455 8.35 0.00 40.59 2.83
417 527 2.364002 ACCCAAAAGGACACGGATTTTG 59.636 45.455 3.30 3.30 41.42 2.44
418 528 2.626266 GACCCAAAAGGACACGGATTTT 59.374 45.455 0.00 0.00 39.89 1.82
419 529 2.158519 AGACCCAAAAGGACACGGATTT 60.159 45.455 0.00 0.00 39.89 2.17
420 530 1.423921 AGACCCAAAAGGACACGGATT 59.576 47.619 0.00 0.00 39.89 3.01
421 531 1.064825 AGACCCAAAAGGACACGGAT 58.935 50.000 0.00 0.00 39.89 4.18
422 532 0.841289 AAGACCCAAAAGGACACGGA 59.159 50.000 0.00 0.00 39.89 4.69
423 533 1.336755 CAAAGACCCAAAAGGACACGG 59.663 52.381 0.00 0.00 39.89 4.94
424 534 1.269051 GCAAAGACCCAAAAGGACACG 60.269 52.381 0.00 0.00 39.89 4.49
425 535 1.754226 TGCAAAGACCCAAAAGGACAC 59.246 47.619 0.00 0.00 39.89 3.67
426 536 2.151502 TGCAAAGACCCAAAAGGACA 57.848 45.000 0.00 0.00 39.89 4.02
427 537 3.392882 CAATGCAAAGACCCAAAAGGAC 58.607 45.455 0.00 0.00 39.89 3.85
428 538 2.368221 CCAATGCAAAGACCCAAAAGGA 59.632 45.455 0.00 0.00 39.89 3.36
429 539 2.368221 TCCAATGCAAAGACCCAAAAGG 59.632 45.455 0.00 0.00 43.78 3.11
430 540 3.070015 ACTCCAATGCAAAGACCCAAAAG 59.930 43.478 0.00 0.00 0.00 2.27
431 541 3.037549 ACTCCAATGCAAAGACCCAAAA 58.962 40.909 0.00 0.00 0.00 2.44
432 542 2.676748 ACTCCAATGCAAAGACCCAAA 58.323 42.857 0.00 0.00 0.00 3.28
433 543 2.364970 CAACTCCAATGCAAAGACCCAA 59.635 45.455 0.00 0.00 0.00 4.12
434 544 1.962807 CAACTCCAATGCAAAGACCCA 59.037 47.619 0.00 0.00 0.00 4.51
435 545 1.337167 GCAACTCCAATGCAAAGACCC 60.337 52.381 0.00 0.00 43.29 4.46
436 546 1.615392 AGCAACTCCAATGCAAAGACC 59.385 47.619 0.00 0.00 46.22 3.85
437 547 2.555757 AGAGCAACTCCAATGCAAAGAC 59.444 45.455 0.00 0.00 46.22 3.01
438 548 2.867624 AGAGCAACTCCAATGCAAAGA 58.132 42.857 0.00 0.00 46.22 2.52
439 549 3.655276 AAGAGCAACTCCAATGCAAAG 57.345 42.857 0.00 0.00 46.22 2.77
440 550 3.507233 CCTAAGAGCAACTCCAATGCAAA 59.493 43.478 0.00 0.00 46.22 3.68
441 551 3.084039 CCTAAGAGCAACTCCAATGCAA 58.916 45.455 0.00 0.00 46.22 4.08
442 552 2.715046 CCTAAGAGCAACTCCAATGCA 58.285 47.619 0.00 0.00 46.22 3.96
443 553 1.403323 GCCTAAGAGCAACTCCAATGC 59.597 52.381 0.00 0.00 44.15 3.56
444 554 2.421424 GTGCCTAAGAGCAACTCCAATG 59.579 50.000 0.00 0.00 46.19 2.82
445 555 2.307098 AGTGCCTAAGAGCAACTCCAAT 59.693 45.455 0.00 0.00 46.19 3.16
446 556 1.699634 AGTGCCTAAGAGCAACTCCAA 59.300 47.619 0.00 0.00 46.19 3.53
447 557 1.002430 CAGTGCCTAAGAGCAACTCCA 59.998 52.381 0.00 0.00 46.19 3.86
448 558 1.731720 CAGTGCCTAAGAGCAACTCC 58.268 55.000 0.00 0.00 46.19 3.85
449 559 1.082690 GCAGTGCCTAAGAGCAACTC 58.917 55.000 2.85 0.00 46.19 3.01
450 560 0.397941 TGCAGTGCCTAAGAGCAACT 59.602 50.000 13.72 0.00 46.19 3.16
451 561 1.457346 ATGCAGTGCCTAAGAGCAAC 58.543 50.000 13.72 0.00 46.19 4.17
452 562 3.348647 TTATGCAGTGCCTAAGAGCAA 57.651 42.857 13.72 0.00 46.19 3.91
453 563 3.348647 TTTATGCAGTGCCTAAGAGCA 57.651 42.857 13.72 0.00 41.46 4.26
454 564 4.701956 TTTTTATGCAGTGCCTAAGAGC 57.298 40.909 13.72 0.00 0.00 4.09
455 565 6.016777 CCCTATTTTTATGCAGTGCCTAAGAG 60.017 42.308 13.72 8.93 0.00 2.85
456 566 5.827797 CCCTATTTTTATGCAGTGCCTAAGA 59.172 40.000 13.72 5.97 0.00 2.10
457 567 5.507985 GCCCTATTTTTATGCAGTGCCTAAG 60.508 44.000 13.72 1.07 0.00 2.18
516 626 5.065218 GGATAAGCACTGTGTAATCACCAAG 59.935 44.000 9.86 0.00 43.26 3.61
517 627 4.941263 GGATAAGCACTGTGTAATCACCAA 59.059 41.667 9.86 0.00 43.26 3.67
519 629 4.332819 GTGGATAAGCACTGTGTAATCACC 59.667 45.833 9.86 7.25 43.26 4.02
520 630 5.178797 AGTGGATAAGCACTGTGTAATCAC 58.821 41.667 9.86 10.32 44.08 3.06
521 631 5.420725 AGTGGATAAGCACTGTGTAATCA 57.579 39.130 9.86 0.00 0.00 2.57
522 632 7.710907 TGATAAGTGGATAAGCACTGTGTAATC 59.289 37.037 9.86 9.52 0.00 1.75
523 633 7.564793 TGATAAGTGGATAAGCACTGTGTAAT 58.435 34.615 9.86 0.78 0.00 1.89
525 635 6.538945 TGATAAGTGGATAAGCACTGTGTA 57.461 37.500 9.86 0.00 0.00 2.90
526 636 5.420725 TGATAAGTGGATAAGCACTGTGT 57.579 39.130 9.86 0.00 0.00 3.72
527 637 6.932356 AATGATAAGTGGATAAGCACTGTG 57.068 37.500 2.76 2.76 0.00 3.66
528 638 6.708054 GCTAATGATAAGTGGATAAGCACTGT 59.292 38.462 0.00 0.00 0.00 3.55
529 639 6.707608 TGCTAATGATAAGTGGATAAGCACTG 59.292 38.462 0.00 0.00 32.88 3.66
530 640 6.830912 TGCTAATGATAAGTGGATAAGCACT 58.169 36.000 0.00 0.00 32.88 4.40
531 641 6.148480 CCTGCTAATGATAAGTGGATAAGCAC 59.852 42.308 0.00 0.00 34.10 4.40
532 642 6.183361 ACCTGCTAATGATAAGTGGATAAGCA 60.183 38.462 0.00 0.00 36.18 3.91
533 643 6.234177 ACCTGCTAATGATAAGTGGATAAGC 58.766 40.000 0.00 0.00 0.00 3.09
534 644 9.778741 TTAACCTGCTAATGATAAGTGGATAAG 57.221 33.333 0.00 0.00 0.00 1.73
535 645 9.555727 GTTAACCTGCTAATGATAAGTGGATAA 57.444 33.333 0.00 0.00 0.00 1.75
536 646 8.710239 TGTTAACCTGCTAATGATAAGTGGATA 58.290 33.333 2.48 0.00 0.00 2.59
538 648 6.821665 GTGTTAACCTGCTAATGATAAGTGGA 59.178 38.462 2.48 0.00 0.00 4.02
539 649 6.823689 AGTGTTAACCTGCTAATGATAAGTGG 59.176 38.462 2.48 0.00 0.00 4.00
621 1336 3.013921 TCTTGCTCCCGCGATTTTAAAT 58.986 40.909 8.23 0.00 39.65 1.40
622 1337 2.428491 TCTTGCTCCCGCGATTTTAAA 58.572 42.857 8.23 0.00 39.65 1.52
623 1338 2.102070 TCTTGCTCCCGCGATTTTAA 57.898 45.000 8.23 0.00 39.65 1.52
624 1339 2.102070 TTCTTGCTCCCGCGATTTTA 57.898 45.000 8.23 0.00 39.65 1.52
625 1340 1.463674 ATTCTTGCTCCCGCGATTTT 58.536 45.000 8.23 0.00 39.65 1.82
626 1341 1.463674 AATTCTTGCTCCCGCGATTT 58.536 45.000 8.23 0.00 39.65 2.17
627 1342 1.463674 AAATTCTTGCTCCCGCGATT 58.536 45.000 8.23 0.00 39.65 3.34
628 1343 2.213499 CTAAATTCTTGCTCCCGCGAT 58.787 47.619 8.23 0.00 39.65 4.58
635 1350 1.064654 CCTGCCGCTAAATTCTTGCTC 59.935 52.381 0.00 0.00 0.00 4.26
638 1353 3.848272 TTTCCTGCCGCTAAATTCTTG 57.152 42.857 0.00 0.00 0.00 3.02
694 1409 6.968335 CGCAATTTGAGTGATATTGTGAATCA 59.032 34.615 0.00 0.00 40.44 2.57
706 1421 1.228398 TGCCCCGCAATTTGAGTGA 60.228 52.632 0.00 0.00 34.76 3.41
807 1534 6.268158 TGTTAATAGGTTGCTACATATCCCGA 59.732 38.462 5.96 0.00 30.46 5.14
987 1721 1.133294 ACGGTTTGGGGTTTGGAAGAT 60.133 47.619 0.00 0.00 0.00 2.40
1014 2138 6.744112 AGATCGAGATGTTAGAGGTGATTTC 58.256 40.000 0.00 0.00 0.00 2.17
1040 2164 0.032217 AGCTGAGGAGGAGGAAGAGG 60.032 60.000 0.00 0.00 0.00 3.69
1344 2714 1.459756 CGCGCTGCAAATCATGTAAG 58.540 50.000 5.56 0.00 0.00 2.34
1776 3297 1.863446 GAAACAAATCGCGAGCGCC 60.863 57.895 16.66 0.00 39.59 6.53
2123 3745 0.326264 AAGTAGTTGGGGCTCTGCTG 59.674 55.000 0.00 0.00 0.00 4.41
2124 3746 0.615850 GAAGTAGTTGGGGCTCTGCT 59.384 55.000 0.00 0.00 0.00 4.24
2140 3762 2.802667 CGTCGCCGGCATGAAGAAG 61.803 63.158 28.98 13.43 0.00 2.85
2141 3763 2.813474 CGTCGCCGGCATGAAGAA 60.813 61.111 28.98 0.00 0.00 2.52
2184 3812 0.711184 AGCCTGGTAGGGTGAGTACT 59.289 55.000 0.00 0.00 45.86 2.73
2323 3951 1.144936 CGGCATCAGGAAGGAGGTC 59.855 63.158 0.00 0.00 0.00 3.85
2468 4125 5.277058 CGAAGAGCTAGCATCAACCAAATAC 60.277 44.000 18.83 0.00 0.00 1.89
2595 4293 4.314440 TCCGTCACAGGCCAGCAC 62.314 66.667 5.01 0.00 0.00 4.40
2756 6604 7.878127 ACAACGGGAATAATTTAGATCGATCAT 59.122 33.333 26.47 14.08 0.00 2.45
2761 6609 9.594038 CATTTACAACGGGAATAATTTAGATCG 57.406 33.333 0.00 0.00 0.00 3.69
2860 6708 2.345991 GTTGCTAGGCGGTGGTGA 59.654 61.111 0.00 0.00 0.00 4.02
2861 6709 2.746277 GGTTGCTAGGCGGTGGTG 60.746 66.667 0.00 0.00 0.00 4.17
2862 6710 4.029809 GGGTTGCTAGGCGGTGGT 62.030 66.667 0.00 0.00 0.00 4.16
2874 6725 4.394712 AAGGGCGCTCGAGGGTTG 62.395 66.667 27.73 0.00 0.00 3.77
3031 6884 4.227134 CCTCTGGGATCCGCCACG 62.227 72.222 5.45 0.00 38.95 4.94
3166 7019 4.838152 AGATTCGGCACCGCGCAT 62.838 61.111 8.75 0.00 45.17 4.73
3213 7066 3.375699 GTCTAGGTTCCTCCAAGATGGA 58.624 50.000 0.00 0.00 45.98 3.41
3219 7072 1.554822 CCCAGGTCTAGGTTCCTCCAA 60.555 57.143 0.00 0.00 39.02 3.53
3464 7324 0.107897 CCACCGTCGGGATGAATGAA 60.108 55.000 17.28 0.00 36.97 2.57
3467 7327 2.189521 GCCACCGTCGGGATGAAT 59.810 61.111 17.28 0.00 36.97 2.57
3491 7352 3.589951 AGTAGGATAACAGCGACCCTA 57.410 47.619 0.00 0.00 0.00 3.53
3504 7365 2.190578 GGCGCCTGCAAGTAGGAT 59.809 61.111 22.15 0.00 45.35 3.24
3524 7385 1.675219 GTTTACGGCAGGGACCTCA 59.325 57.895 0.00 0.00 0.00 3.86
3537 7398 1.213678 GGGTATGGGGTCAGGGTTTAC 59.786 57.143 0.00 0.00 0.00 2.01
3539 7400 1.568118 CGGGTATGGGGTCAGGGTTT 61.568 60.000 0.00 0.00 0.00 3.27
3540 7401 1.999002 CGGGTATGGGGTCAGGGTT 60.999 63.158 0.00 0.00 0.00 4.11
3643 7504 0.323629 TTCCTCTAACCAAGCACCCG 59.676 55.000 0.00 0.00 0.00 5.28
3651 7512 0.324943 GCCTGCAGTTCCTCTAACCA 59.675 55.000 13.81 0.00 39.03 3.67


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

AutoCloner maintained by Alex Coulton.