Multiple sequence alignment - TraesCS6A01G395700

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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 TraesCS6A01G395700 chr6A 100.000 4030 0 0 1 4030 608366563 608370592 0.000000e+00 7443
1 TraesCS6A01G395700 chr6A 81.602 1011 156 13 972 1968 616233819 616234813 0.000000e+00 809
2 TraesCS6A01G395700 chr6A 78.539 890 157 19 2185 3057 616237073 616237945 4.550000e-154 555
3 TraesCS6A01G395700 chr6D 95.779 2535 75 7 543 3068 461652779 461655290 0.000000e+00 4060
4 TraesCS6A01G395700 chr6D 81.657 676 108 13 1302 1968 471185864 471186532 7.620000e-152 547
5 TraesCS6A01G395700 chr6D 83.636 385 59 4 923 1305 471179655 471180037 3.830000e-95 359
6 TraesCS6A01G395700 chr6D 94.248 226 12 1 3 228 461652550 461652774 1.070000e-90 344
7 TraesCS6A01G395700 chr6D 81.250 336 56 4 2321 2650 471302210 471302544 8.590000e-67 265
8 TraesCS6A01G395700 chr6D 81.229 293 42 6 2871 3150 471302775 471303067 1.460000e-54 224
9 TraesCS6A01G395700 chr6B 95.312 1344 60 1 1493 2836 703782530 703783870 0.000000e+00 2130
10 TraesCS6A01G395700 chr6B 94.472 814 39 2 2876 3688 703783866 703784674 0.000000e+00 1249
11 TraesCS6A01G395700 chr6B 85.726 1191 132 18 800 1969 719300051 719298878 0.000000e+00 1223
12 TraesCS6A01G395700 chr6B 90.727 949 40 16 558 1500 703780701 703781607 0.000000e+00 1221
13 TraesCS6A01G395700 chr6B 87.761 1005 95 14 2573 3566 703441474 703440487 0.000000e+00 1149
14 TraesCS6A01G395700 chr6B 82.071 1043 154 9 959 1971 719332524 719331485 0.000000e+00 859
15 TraesCS6A01G395700 chr6B 80.833 1033 155 23 972 1968 675498000 675499025 0.000000e+00 771
16 TraesCS6A01G395700 chr6B 79.748 1111 180 26 2032 3132 719331385 719330310 0.000000e+00 763
17 TraesCS6A01G395700 chr6B 77.469 1043 173 33 2047 3065 675499149 675500153 5.850000e-158 568
18 TraesCS6A01G395700 chr6B 90.882 340 27 2 3685 4024 703788410 703788745 1.710000e-123 453
19 TraesCS6A01G395700 chr6B 77.723 808 123 33 2341 3121 719298593 719297816 3.700000e-120 442
20 TraesCS6A01G395700 chr7A 88.115 732 87 0 1235 1966 48938880 48939611 0.000000e+00 870
21 TraesCS6A01G395700 chr7A 88.066 729 87 0 1238 1966 48953032 48952304 0.000000e+00 865
22 TraesCS6A01G395700 chr7A 79.310 870 144 25 2276 3116 48951978 48951116 9.710000e-161 577
23 TraesCS6A01G395700 chr5D 92.114 317 24 1 226 542 513697803 513697488 2.860000e-121 446
24 TraesCS6A01G395700 chr7B 89.841 315 28 4 226 539 120865622 120865933 6.270000e-108 401
25 TraesCS6A01G395700 chr5A 86.478 318 43 0 226 543 390372347 390372030 2.300000e-92 350
26 TraesCS6A01G395700 chr4D 85.127 316 45 2 226 541 483705516 483705203 5.020000e-84 322
27 TraesCS6A01G395700 chr4A 88.302 265 29 2 3680 3943 738542949 738543212 2.340000e-82 316
28 TraesCS6A01G395700 chr3D 87.313 268 34 0 3683 3950 43518746 43518479 1.410000e-79 307
29 TraesCS6A01G395700 chr3D 90.000 200 18 2 15 214 407387489 407387292 1.440000e-64 257
30 TraesCS6A01G395700 chr4B 87.547 265 31 2 3683 3946 232223394 232223657 5.060000e-79 305
31 TraesCS6A01G395700 chr1D 87.313 268 32 2 3684 3950 406833750 406833484 5.060000e-79 305
32 TraesCS6A01G395700 chr1D 86.574 216 29 0 1 216 94420029 94419814 5.210000e-59 239
33 TraesCS6A01G395700 chr1D 72.045 973 205 41 1034 1965 28226232 28225286 1.130000e-55 228
34 TraesCS6A01G395700 chr7D 86.940 268 35 0 3680 3947 8548342 8548609 6.550000e-78 302
35 TraesCS6A01G395700 chr2D 86.940 268 35 0 3680 3947 106154122 106154389 6.550000e-78 302
36 TraesCS6A01G395700 chr2A 86.989 269 33 2 3680 3947 12265538 12265805 6.550000e-78 302
37 TraesCS6A01G395700 chr2A 87.500 208 26 0 9 216 634878742 634878535 1.450000e-59 241
38 TraesCS6A01G395700 chr1B 86.989 269 33 2 3680 3947 3285150 3285417 6.550000e-78 302
39 TraesCS6A01G395700 chr3A 89.252 214 22 1 1 214 265758186 265757974 2.390000e-67 267
40 TraesCS6A01G395700 chr5B 89.216 204 22 0 9 212 64626279 64626076 5.170000e-64 255
41 TraesCS6A01G395700 chr5B 87.143 210 27 0 9 218 115680901 115681110 5.210000e-59 239
42 TraesCS6A01G395700 chr2B 86.463 229 31 0 226 454 690024948 690024720 6.690000e-63 252
43 TraesCS6A01G395700 chrUn 87.864 206 24 1 9 214 365469682 365469886 1.450000e-59 241
44 TraesCS6A01G395700 chrUn 87.864 206 24 1 9 214 365471174 365471378 1.450000e-59 241
45 TraesCS6A01G395700 chr3B 71.755 832 189 34 1151 1956 751823861 751824672 4.110000e-45 193


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 TraesCS6A01G395700 chr6A 608366563 608370592 4029 False 7443.00 7443 100.00000 1 4030 1 chr6A.!!$F1 4029
1 TraesCS6A01G395700 chr6A 616233819 616237945 4126 False 682.00 809 80.07050 972 3057 2 chr6A.!!$F2 2085
2 TraesCS6A01G395700 chr6D 461652550 461655290 2740 False 2202.00 4060 95.01350 3 3068 2 chr6D.!!$F3 3065
3 TraesCS6A01G395700 chr6D 471185864 471186532 668 False 547.00 547 81.65700 1302 1968 1 chr6D.!!$F2 666
4 TraesCS6A01G395700 chr6D 471302210 471303067 857 False 244.50 265 81.23950 2321 3150 2 chr6D.!!$F4 829
5 TraesCS6A01G395700 chr6B 703780701 703788745 8044 False 1263.25 2130 92.84825 558 4024 4 chr6B.!!$F2 3466
6 TraesCS6A01G395700 chr6B 703440487 703441474 987 True 1149.00 1149 87.76100 2573 3566 1 chr6B.!!$R1 993
7 TraesCS6A01G395700 chr6B 719297816 719300051 2235 True 832.50 1223 81.72450 800 3121 2 chr6B.!!$R2 2321
8 TraesCS6A01G395700 chr6B 719330310 719332524 2214 True 811.00 859 80.90950 959 3132 2 chr6B.!!$R3 2173
9 TraesCS6A01G395700 chr6B 675498000 675500153 2153 False 669.50 771 79.15100 972 3065 2 chr6B.!!$F1 2093
10 TraesCS6A01G395700 chr7A 48938880 48939611 731 False 870.00 870 88.11500 1235 1966 1 chr7A.!!$F1 731
11 TraesCS6A01G395700 chr7A 48951116 48953032 1916 True 721.00 865 83.68800 1238 3116 2 chr7A.!!$R1 1878
12 TraesCS6A01G395700 chr1D 28225286 28226232 946 True 228.00 228 72.04500 1034 1965 1 chr1D.!!$R1 931
13 TraesCS6A01G395700 chrUn 365469682 365471378 1696 False 241.00 241 87.86400 9 214 2 chrUn.!!$F1 205

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
261 262 0.183492 TGAAACAGACTGCCAAGCCT 59.817 50.0 1.25 0.0 0.00 4.58 F
490 511 0.249911 GAGGTGCACTCGGACTTTGT 60.250 55.0 17.98 0.0 36.29 2.83 F
532 553 0.323629 CCTTCAAGGGCCGTACTTCA 59.676 55.0 0.00 0.0 0.00 3.02 F
586 607 1.082117 CCGTGGCTGGTTACGCTAAG 61.082 60.0 0.00 0.0 38.87 2.18 F
2547 5948 0.100503 GCCGGCACATGGTATTGAAC 59.899 55.0 24.80 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 2982 2.193536 GCGGACCACACTTGCCTTT 61.194 57.895 0.00 0.00 0.00 3.11 R
2271 5657 1.135141 GTGCACACAGCTTCCAACAAA 60.135 47.619 13.17 0.00 45.94 2.83 R
2547 5948 1.436336 GATACCCTCGTCACACGGG 59.564 63.158 0.00 0.00 42.83 5.28 R
2551 5952 2.291089 TGTAGTGGATACCCTCGTCACA 60.291 50.000 0.00 0.00 33.01 3.58 R
3931 11295 0.250338 ACAGAACTTCGCCTGGGTTC 60.250 55.000 0.00 0.49 39.43 3.62 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
230 231 5.421374 AGGTAGTACTTGATAACACTGGACC 59.579 44.000 0.00 0.00 0.00 4.46
231 232 5.186409 GGTAGTACTTGATAACACTGGACCA 59.814 44.000 0.00 0.00 0.00 4.02
233 234 6.374417 AGTACTTGATAACACTGGACCAAT 57.626 37.500 0.00 0.00 0.00 3.16
234 235 6.173339 AGTACTTGATAACACTGGACCAATG 58.827 40.000 0.25 0.25 0.00 2.82
235 236 4.985538 ACTTGATAACACTGGACCAATGT 58.014 39.130 1.87 1.87 0.00 2.71
236 237 5.385198 ACTTGATAACACTGGACCAATGTT 58.615 37.500 23.56 23.56 39.75 2.71
237 238 5.473504 ACTTGATAACACTGGACCAATGTTC 59.526 40.000 23.73 12.14 37.68 3.18
246 247 3.636300 CTGGACCAATGTTCAGGTTGAAA 59.364 43.478 0.00 0.00 43.39 2.69
247 248 3.383185 TGGACCAATGTTCAGGTTGAAAC 59.617 43.478 0.00 0.00 38.22 2.78
249 250 4.499696 GGACCAATGTTCAGGTTGAAACAG 60.500 45.833 0.00 0.00 38.22 3.16
250 251 4.277476 ACCAATGTTCAGGTTGAAACAGA 58.723 39.130 0.00 0.00 38.22 3.41
251 252 4.097892 ACCAATGTTCAGGTTGAAACAGAC 59.902 41.667 0.00 0.00 38.22 3.51
252 253 4.339247 CCAATGTTCAGGTTGAAACAGACT 59.661 41.667 0.00 0.00 38.22 3.24
253 254 5.276270 CAATGTTCAGGTTGAAACAGACTG 58.724 41.667 0.00 0.00 38.22 3.51
254 255 2.682856 TGTTCAGGTTGAAACAGACTGC 59.317 45.455 1.25 0.00 38.22 4.40
256 257 1.211703 TCAGGTTGAAACAGACTGCCA 59.788 47.619 1.25 0.00 0.00 4.92
258 259 2.033801 CAGGTTGAAACAGACTGCCAAG 59.966 50.000 1.25 0.00 0.00 3.61
259 260 1.269257 GGTTGAAACAGACTGCCAAGC 60.269 52.381 14.76 14.76 0.00 4.01
260 261 1.032014 TTGAAACAGACTGCCAAGCC 58.968 50.000 1.25 0.00 0.00 4.35
261 262 0.183492 TGAAACAGACTGCCAAGCCT 59.817 50.000 1.25 0.00 0.00 4.58
262 263 1.322442 GAAACAGACTGCCAAGCCTT 58.678 50.000 1.25 0.00 0.00 4.35
263 264 2.158682 TGAAACAGACTGCCAAGCCTTA 60.159 45.455 1.25 0.00 0.00 2.69
264 265 2.191128 AACAGACTGCCAAGCCTTAG 57.809 50.000 1.25 0.00 0.00 2.18
265 266 0.322008 ACAGACTGCCAAGCCTTAGC 60.322 55.000 1.25 0.00 40.32 3.09
307 328 2.283966 CCTGTCGGAGGTGGGTCT 60.284 66.667 0.00 0.00 37.02 3.85
308 329 2.352032 CCTGTCGGAGGTGGGTCTC 61.352 68.421 0.00 0.00 37.02 3.36
309 330 1.606601 CTGTCGGAGGTGGGTCTCA 60.607 63.158 0.00 0.00 35.58 3.27
310 331 0.972983 CTGTCGGAGGTGGGTCTCAT 60.973 60.000 0.00 0.00 35.58 2.90
311 332 0.333652 TGTCGGAGGTGGGTCTCATA 59.666 55.000 0.00 0.00 35.58 2.15
313 334 2.040178 GTCGGAGGTGGGTCTCATAAT 58.960 52.381 0.00 0.00 35.58 1.28
314 335 2.434702 GTCGGAGGTGGGTCTCATAATT 59.565 50.000 0.00 0.00 35.58 1.40
317 338 3.895656 CGGAGGTGGGTCTCATAATTAGA 59.104 47.826 0.00 0.00 35.58 2.10
318 339 4.021894 CGGAGGTGGGTCTCATAATTAGAG 60.022 50.000 0.00 0.00 35.58 2.43
319 340 5.148502 GGAGGTGGGTCTCATAATTAGAGA 58.851 45.833 9.32 9.32 39.68 3.10
320 341 5.245075 GGAGGTGGGTCTCATAATTAGAGAG 59.755 48.000 12.24 11.22 42.38 3.20
321 342 6.031964 AGGTGGGTCTCATAATTAGAGAGA 57.968 41.667 13.54 13.54 42.38 3.10
322 343 6.629156 AGGTGGGTCTCATAATTAGAGAGAT 58.371 40.000 18.15 4.48 42.38 2.75
323 344 6.496565 AGGTGGGTCTCATAATTAGAGAGATG 59.503 42.308 18.15 1.50 42.38 2.90
325 346 7.015682 GGTGGGTCTCATAATTAGAGAGATGAA 59.984 40.741 18.15 8.38 42.38 2.57
326 347 8.087750 GTGGGTCTCATAATTAGAGAGATGAAG 58.912 40.741 18.15 2.17 42.38 3.02
328 349 8.646900 GGGTCTCATAATTAGAGAGATGAAGTT 58.353 37.037 18.15 0.00 42.38 2.66
329 350 9.691362 GGTCTCATAATTAGAGAGATGAAGTTC 57.309 37.037 18.15 0.00 42.38 3.01
347 368 9.820725 ATGAAGTTCTATCTCTCATCTTTTCAG 57.179 33.333 4.17 0.00 0.00 3.02
349 370 7.123355 AGTTCTATCTCTCATCTTTTCAGGG 57.877 40.000 0.00 0.00 0.00 4.45
351 372 7.568366 AGTTCTATCTCTCATCTTTTCAGGGAT 59.432 37.037 0.00 0.00 0.00 3.85
352 373 7.927683 TCTATCTCTCATCTTTTCAGGGATT 57.072 36.000 0.00 0.00 0.00 3.01
353 374 7.961351 TCTATCTCTCATCTTTTCAGGGATTC 58.039 38.462 0.00 0.00 0.00 2.52
354 375 5.016051 TCTCTCATCTTTTCAGGGATTCG 57.984 43.478 0.00 0.00 0.00 3.34
355 376 4.711846 TCTCTCATCTTTTCAGGGATTCGA 59.288 41.667 0.00 0.00 0.00 3.71
356 377 5.016051 TCTCATCTTTTCAGGGATTCGAG 57.984 43.478 0.00 0.00 0.00 4.04
357 378 3.535561 TCATCTTTTCAGGGATTCGAGC 58.464 45.455 0.00 0.00 0.00 5.03
359 380 2.977914 TCTTTTCAGGGATTCGAGCTG 58.022 47.619 0.00 0.00 0.00 4.24
360 381 2.303022 TCTTTTCAGGGATTCGAGCTGT 59.697 45.455 0.00 0.00 0.00 4.40
364 385 2.666317 TCAGGGATTCGAGCTGTATCA 58.334 47.619 0.00 0.00 0.00 2.15
365 386 3.234353 TCAGGGATTCGAGCTGTATCAT 58.766 45.455 0.00 0.00 0.00 2.45
366 387 4.407365 TCAGGGATTCGAGCTGTATCATA 58.593 43.478 0.00 0.00 0.00 2.15
367 388 5.019470 TCAGGGATTCGAGCTGTATCATAT 58.981 41.667 0.00 0.00 0.00 1.78
368 389 5.481824 TCAGGGATTCGAGCTGTATCATATT 59.518 40.000 0.00 0.00 0.00 1.28
369 390 6.663523 TCAGGGATTCGAGCTGTATCATATTA 59.336 38.462 0.00 0.00 0.00 0.98
373 394 6.689241 GGATTCGAGCTGTATCATATTAGTCG 59.311 42.308 0.00 0.00 0.00 4.18
374 395 5.547181 TCGAGCTGTATCATATTAGTCGG 57.453 43.478 0.00 0.00 0.00 4.79
375 396 4.395231 TCGAGCTGTATCATATTAGTCGGG 59.605 45.833 0.00 0.00 0.00 5.14
376 397 4.395231 CGAGCTGTATCATATTAGTCGGGA 59.605 45.833 0.00 0.00 0.00 5.14
377 398 5.106277 CGAGCTGTATCATATTAGTCGGGAA 60.106 44.000 0.00 0.00 0.00 3.97
378 399 6.274157 AGCTGTATCATATTAGTCGGGAAG 57.726 41.667 0.00 0.00 0.00 3.46
380 401 5.401531 TGTATCATATTAGTCGGGAAGCC 57.598 43.478 0.00 0.00 0.00 4.35
381 402 4.836175 TGTATCATATTAGTCGGGAAGCCA 59.164 41.667 0.00 0.00 0.00 4.75
382 403 4.974645 ATCATATTAGTCGGGAAGCCAA 57.025 40.909 0.00 0.00 0.00 4.52
383 404 4.974645 TCATATTAGTCGGGAAGCCAAT 57.025 40.909 0.00 0.00 0.00 3.16
384 405 4.641396 TCATATTAGTCGGGAAGCCAATG 58.359 43.478 0.00 0.00 0.00 2.82
385 406 2.348411 ATTAGTCGGGAAGCCAATGG 57.652 50.000 0.00 0.00 0.00 3.16
386 407 0.254747 TTAGTCGGGAAGCCAATGGG 59.745 55.000 0.00 0.00 37.18 4.00
387 408 1.632018 TAGTCGGGAAGCCAATGGGG 61.632 60.000 0.00 0.00 40.85 4.96
396 417 2.440147 CCAATGGGGTGGCTCACA 59.560 61.111 7.49 0.00 35.86 3.58
397 418 1.228831 CCAATGGGGTGGCTCACAA 60.229 57.895 7.49 0.00 35.86 3.33
398 419 0.831288 CCAATGGGGTGGCTCACAAA 60.831 55.000 7.49 0.00 35.86 2.83
399 420 1.269012 CAATGGGGTGGCTCACAAAT 58.731 50.000 7.49 0.00 35.86 2.32
400 421 1.624813 CAATGGGGTGGCTCACAAATT 59.375 47.619 7.49 2.19 35.86 1.82
401 422 2.830923 CAATGGGGTGGCTCACAAATTA 59.169 45.455 7.49 0.00 35.86 1.40
402 423 2.214376 TGGGGTGGCTCACAAATTAG 57.786 50.000 7.49 0.00 35.86 1.73
403 424 0.817654 GGGGTGGCTCACAAATTAGC 59.182 55.000 7.49 0.00 35.86 3.09
404 425 1.616994 GGGGTGGCTCACAAATTAGCT 60.617 52.381 7.49 0.00 38.80 3.32
405 426 1.745653 GGGTGGCTCACAAATTAGCTC 59.254 52.381 0.00 0.00 38.80 4.09
406 427 1.398390 GGTGGCTCACAAATTAGCTCG 59.602 52.381 0.00 0.00 38.80 5.03
408 429 0.378610 GGCTCACAAATTAGCTCGGC 59.621 55.000 0.00 0.00 38.80 5.54
409 430 1.086696 GCTCACAAATTAGCTCGGCA 58.913 50.000 0.00 0.00 35.80 5.69
410 431 1.672881 GCTCACAAATTAGCTCGGCAT 59.327 47.619 0.00 0.00 35.80 4.40
414 435 1.672881 ACAAATTAGCTCGGCATGCTC 59.327 47.619 18.92 6.88 41.46 4.26
415 436 1.945394 CAAATTAGCTCGGCATGCTCT 59.055 47.619 18.92 11.86 41.46 4.09
416 437 3.133691 CAAATTAGCTCGGCATGCTCTA 58.866 45.455 18.92 10.90 41.46 2.43
417 438 2.447244 ATTAGCTCGGCATGCTCTAC 57.553 50.000 18.92 5.44 41.46 2.59
418 439 1.403814 TTAGCTCGGCATGCTCTACT 58.596 50.000 18.92 12.68 41.46 2.57
419 440 1.403814 TAGCTCGGCATGCTCTACTT 58.596 50.000 18.92 2.17 41.46 2.24
420 441 0.539051 AGCTCGGCATGCTCTACTTT 59.461 50.000 18.92 0.00 35.67 2.66
421 442 0.933796 GCTCGGCATGCTCTACTTTC 59.066 55.000 18.92 0.00 0.00 2.62
422 443 1.740380 GCTCGGCATGCTCTACTTTCA 60.740 52.381 18.92 0.00 0.00 2.69
423 444 2.621338 CTCGGCATGCTCTACTTTCAA 58.379 47.619 18.92 0.00 0.00 2.69
425 446 2.028112 TCGGCATGCTCTACTTTCAAGT 60.028 45.455 18.92 0.00 42.91 3.16
426 447 3.194755 TCGGCATGCTCTACTTTCAAGTA 59.805 43.478 18.92 0.00 40.37 2.24
428 449 4.025396 CGGCATGCTCTACTTTCAAGTATG 60.025 45.833 18.92 0.00 40.46 2.39
429 450 4.274459 GGCATGCTCTACTTTCAAGTATGG 59.726 45.833 18.92 0.00 40.46 2.74
430 451 4.274459 GCATGCTCTACTTTCAAGTATGGG 59.726 45.833 11.37 0.00 40.46 4.00
431 452 3.873910 TGCTCTACTTTCAAGTATGGGC 58.126 45.455 11.26 11.26 40.46 5.36
432 453 2.866762 GCTCTACTTTCAAGTATGGGCG 59.133 50.000 0.00 0.00 40.46 6.13
433 454 3.430374 GCTCTACTTTCAAGTATGGGCGA 60.430 47.826 0.00 0.00 40.46 5.54
434 455 4.740934 GCTCTACTTTCAAGTATGGGCGAT 60.741 45.833 0.00 0.00 40.46 4.58
435 456 4.693283 TCTACTTTCAAGTATGGGCGATG 58.307 43.478 0.00 0.00 40.46 3.84
436 457 3.350219 ACTTTCAAGTATGGGCGATGT 57.650 42.857 0.00 0.00 37.52 3.06
438 459 4.839121 ACTTTCAAGTATGGGCGATGTAA 58.161 39.130 0.00 0.00 37.52 2.41
439 460 4.634443 ACTTTCAAGTATGGGCGATGTAAC 59.366 41.667 0.00 0.00 37.52 2.50
441 462 4.481368 TCAAGTATGGGCGATGTAACTT 57.519 40.909 0.00 0.00 0.00 2.66
442 463 4.839121 TCAAGTATGGGCGATGTAACTTT 58.161 39.130 0.00 0.00 0.00 2.66
443 464 4.873827 TCAAGTATGGGCGATGTAACTTTC 59.126 41.667 0.00 0.00 0.00 2.62
444 465 4.481368 AGTATGGGCGATGTAACTTTCA 57.519 40.909 0.00 0.00 0.00 2.69
447 468 3.134574 TGGGCGATGTAACTTTCAGTT 57.865 42.857 0.00 0.00 41.97 3.16
448 469 2.811431 TGGGCGATGTAACTTTCAGTTG 59.189 45.455 0.00 0.00 39.11 3.16
450 471 3.998341 GGGCGATGTAACTTTCAGTTGTA 59.002 43.478 0.00 0.00 39.11 2.41
451 472 4.634443 GGGCGATGTAACTTTCAGTTGTAT 59.366 41.667 0.00 0.00 39.11 2.29
452 473 5.220605 GGGCGATGTAACTTTCAGTTGTATC 60.221 44.000 0.00 3.09 39.11 2.24
453 474 5.220605 GGCGATGTAACTTTCAGTTGTATCC 60.221 44.000 0.00 0.00 39.11 2.59
454 475 5.220605 GCGATGTAACTTTCAGTTGTATCCC 60.221 44.000 0.00 0.00 39.11 3.85
455 476 6.106673 CGATGTAACTTTCAGTTGTATCCCT 58.893 40.000 0.00 0.00 39.11 4.20
456 477 6.036083 CGATGTAACTTTCAGTTGTATCCCTG 59.964 42.308 0.00 0.00 39.11 4.45
458 479 6.464222 TGTAACTTTCAGTTGTATCCCTGAG 58.536 40.000 0.00 0.00 39.11 3.35
460 481 5.568620 ACTTTCAGTTGTATCCCTGAGTT 57.431 39.130 0.00 0.00 38.81 3.01
461 482 5.552178 ACTTTCAGTTGTATCCCTGAGTTC 58.448 41.667 0.00 0.00 38.81 3.01
462 483 4.553330 TTCAGTTGTATCCCTGAGTTCC 57.447 45.455 0.00 0.00 38.81 3.62
463 484 3.791320 TCAGTTGTATCCCTGAGTTCCT 58.209 45.455 0.00 0.00 32.93 3.36
464 485 3.515502 TCAGTTGTATCCCTGAGTTCCTG 59.484 47.826 0.00 0.00 32.93 3.86
465 486 3.515502 CAGTTGTATCCCTGAGTTCCTGA 59.484 47.826 0.00 0.00 0.00 3.86
466 487 3.772025 AGTTGTATCCCTGAGTTCCTGAG 59.228 47.826 0.00 0.00 0.00 3.35
467 488 3.474798 TGTATCCCTGAGTTCCTGAGT 57.525 47.619 0.00 0.00 0.00 3.41
468 489 3.099905 TGTATCCCTGAGTTCCTGAGTG 58.900 50.000 0.00 0.00 0.00 3.51
470 491 1.633774 TCCCTGAGTTCCTGAGTGAC 58.366 55.000 0.00 0.00 0.00 3.67
472 493 1.248486 CCTGAGTTCCTGAGTGACGA 58.752 55.000 0.00 0.00 0.00 4.20
473 494 1.201181 CCTGAGTTCCTGAGTGACGAG 59.799 57.143 0.00 0.00 0.00 4.18
474 495 1.201181 CTGAGTTCCTGAGTGACGAGG 59.799 57.143 0.00 0.00 0.00 4.63
475 496 1.249407 GAGTTCCTGAGTGACGAGGT 58.751 55.000 4.01 0.00 0.00 3.85
476 497 0.962489 AGTTCCTGAGTGACGAGGTG 59.038 55.000 4.01 0.00 0.00 4.00
477 498 0.667792 GTTCCTGAGTGACGAGGTGC 60.668 60.000 4.01 0.00 0.00 5.01
478 499 1.112916 TTCCTGAGTGACGAGGTGCA 61.113 55.000 4.01 0.00 0.00 4.57
489 510 2.533318 GAGGTGCACTCGGACTTTG 58.467 57.895 17.98 0.00 36.29 2.77
490 511 0.249911 GAGGTGCACTCGGACTTTGT 60.250 55.000 17.98 0.00 36.29 2.83
491 512 1.000506 GAGGTGCACTCGGACTTTGTA 59.999 52.381 17.98 0.00 36.29 2.41
492 513 1.145803 GGTGCACTCGGACTTTGTAC 58.854 55.000 17.98 0.00 33.21 2.90
493 514 0.782384 GTGCACTCGGACTTTGTACG 59.218 55.000 10.32 0.00 41.83 3.67
500 521 3.060978 TCGGACTTTGTACGATCGATG 57.939 47.619 24.34 3.97 44.43 3.84
501 522 2.679336 TCGGACTTTGTACGATCGATGA 59.321 45.455 24.34 3.35 44.43 2.92
502 523 3.127376 TCGGACTTTGTACGATCGATGAA 59.873 43.478 24.34 7.71 44.43 2.57
503 524 4.042398 CGGACTTTGTACGATCGATGAAT 58.958 43.478 24.34 0.39 43.34 2.57
504 525 4.085568 CGGACTTTGTACGATCGATGAATG 60.086 45.833 24.34 13.87 43.34 2.67
505 526 5.041287 GGACTTTGTACGATCGATGAATGA 58.959 41.667 24.34 0.34 0.00 2.57
506 527 5.518847 GGACTTTGTACGATCGATGAATGAA 59.481 40.000 24.34 6.04 0.00 2.57
507 528 6.201044 GGACTTTGTACGATCGATGAATGAAT 59.799 38.462 24.34 0.00 0.00 2.57
508 529 7.381408 GGACTTTGTACGATCGATGAATGAATA 59.619 37.037 24.34 0.00 0.00 1.75
509 530 8.642908 ACTTTGTACGATCGATGAATGAATAA 57.357 30.769 24.34 1.29 0.00 1.40
510 531 9.093970 ACTTTGTACGATCGATGAATGAATAAA 57.906 29.630 24.34 7.03 0.00 1.40
511 532 9.914923 CTTTGTACGATCGATGAATGAATAAAA 57.085 29.630 24.34 0.00 0.00 1.52
512 533 9.914923 TTTGTACGATCGATGAATGAATAAAAG 57.085 29.630 24.34 0.00 0.00 2.27
513 534 7.564128 TGTACGATCGATGAATGAATAAAAGC 58.436 34.615 24.34 0.00 0.00 3.51
514 535 5.990408 ACGATCGATGAATGAATAAAAGCC 58.010 37.500 24.34 0.00 0.00 4.35
515 536 5.760253 ACGATCGATGAATGAATAAAAGCCT 59.240 36.000 24.34 0.00 0.00 4.58
516 537 6.260936 ACGATCGATGAATGAATAAAAGCCTT 59.739 34.615 24.34 0.00 0.00 4.35
517 538 6.794158 CGATCGATGAATGAATAAAAGCCTTC 59.206 38.462 10.26 0.00 0.00 3.46
518 539 7.518848 CGATCGATGAATGAATAAAAGCCTTCA 60.519 37.037 10.26 0.00 35.95 3.02
519 540 7.389803 TCGATGAATGAATAAAAGCCTTCAA 57.610 32.000 0.00 0.00 35.20 2.69
520 541 7.475015 TCGATGAATGAATAAAAGCCTTCAAG 58.525 34.615 0.00 0.00 35.20 3.02
521 542 6.694411 CGATGAATGAATAAAAGCCTTCAAGG 59.306 38.462 0.00 0.00 38.80 3.61
522 543 6.284891 TGAATGAATAAAAGCCTTCAAGGG 57.715 37.500 5.33 0.00 35.37 3.95
529 550 2.669240 GCCTTCAAGGGCCGTACT 59.331 61.111 5.33 0.00 45.92 2.73
530 551 1.002502 GCCTTCAAGGGCCGTACTT 60.003 57.895 5.33 0.00 45.92 2.24
531 552 1.025113 GCCTTCAAGGGCCGTACTTC 61.025 60.000 5.33 0.00 45.92 3.01
532 553 0.323629 CCTTCAAGGGCCGTACTTCA 59.676 55.000 0.00 0.00 0.00 3.02
533 554 1.271163 CCTTCAAGGGCCGTACTTCAA 60.271 52.381 0.00 0.00 0.00 2.69
534 555 2.500229 CTTCAAGGGCCGTACTTCAAA 58.500 47.619 0.00 0.00 0.00 2.69
535 556 2.642154 TCAAGGGCCGTACTTCAAAA 57.358 45.000 0.00 0.00 0.00 2.44
536 557 2.933573 TCAAGGGCCGTACTTCAAAAA 58.066 42.857 0.00 0.00 0.00 1.94
586 607 1.082117 CCGTGGCTGGTTACGCTAAG 61.082 60.000 0.00 0.00 38.87 2.18
607 628 5.078683 AGGCTTGAGAGGATAGAGAGAAT 57.921 43.478 0.00 0.00 0.00 2.40
728 749 5.879223 AGCTCTCCTTGTATCAAGATTTGTG 59.121 40.000 10.54 0.00 0.00 3.33
887 917 7.540055 GCGGTATGTTAATCACTACCAGTATAC 59.460 40.741 0.00 0.00 33.71 1.47
898 928 7.460071 TCACTACCAGTATACCCTAATCTCTC 58.540 42.308 0.00 0.00 0.00 3.20
899 929 7.295196 TCACTACCAGTATACCCTAATCTCTCT 59.705 40.741 0.00 0.00 0.00 3.10
900 930 8.604184 CACTACCAGTATACCCTAATCTCTCTA 58.396 40.741 0.00 0.00 0.00 2.43
901 931 8.828751 ACTACCAGTATACCCTAATCTCTCTAG 58.171 40.741 0.00 0.00 0.00 2.43
1453 1700 2.617774 GCCTTCTTCATCATGCTCTTCC 59.382 50.000 0.00 0.00 0.00 3.46
1660 2855 3.364277 GACTATCAAGTCCACCGCC 57.636 57.895 0.00 0.00 45.50 6.13
2271 5657 5.954153 AGAAGACTGATGTCAAGGATGAT 57.046 39.130 0.00 0.00 45.20 2.45
2547 5948 0.100503 GCCGGCACATGGTATTGAAC 59.899 55.000 24.80 0.00 0.00 3.18
2959 6566 7.339976 TGCAGATCATTCTTGTTTCATGGATAA 59.660 33.333 0.00 0.00 0.00 1.75
2997 6604 2.401766 CGACCAATGCAGCAGGGAC 61.402 63.158 20.05 13.74 0.00 4.46
3124 6739 2.469274 TCTTCTCTGCTTTGCTCTGG 57.531 50.000 0.00 0.00 0.00 3.86
3125 6740 0.803740 CTTCTCTGCTTTGCTCTGGC 59.196 55.000 0.00 0.00 39.26 4.85
3170 6790 0.396556 TGCGGCTACTAGATGACCCA 60.397 55.000 0.00 0.00 0.00 4.51
3213 6834 3.221771 TGAATCAACCCTGAACTTGGTG 58.778 45.455 0.00 0.00 34.49 4.17
3233 6854 6.408035 TGGTGGCTTAGTAATATCGTTTTCA 58.592 36.000 0.00 0.00 0.00 2.69
3278 6899 0.679640 TATGCCCAGGTGCGGAAAAG 60.680 55.000 0.00 0.00 0.00 2.27
3281 6902 1.744320 GCCCAGGTGCGGAAAAGTTT 61.744 55.000 0.00 0.00 0.00 2.66
3317 6938 2.182791 CGAGTGATCGCAGTGGCT 59.817 61.111 9.33 0.00 38.10 4.75
3323 6944 1.236616 TGATCGCAGTGGCTTGGTTG 61.237 55.000 0.00 0.00 38.10 3.77
3593 7218 1.813786 TGTGTGTTTAAATAGCGGGCC 59.186 47.619 0.00 0.00 0.00 5.80
3597 7222 1.207570 TGTTTAAATAGCGGGCCGAGA 59.792 47.619 33.44 17.22 0.00 4.04
3610 7235 1.298859 GCCGAGATGTGGTGTGGTTC 61.299 60.000 0.00 0.00 0.00 3.62
3616 7241 0.827507 ATGTGGTGTGGTTCTTGCCC 60.828 55.000 0.00 0.00 0.00 5.36
3617 7242 2.203280 TGGTGTGGTTCTTGCCCG 60.203 61.111 0.00 0.00 0.00 6.13
3618 7243 2.983592 GGTGTGGTTCTTGCCCGG 60.984 66.667 0.00 0.00 0.00 5.73
3619 7244 3.670377 GTGTGGTTCTTGCCCGGC 61.670 66.667 1.04 1.04 0.00 6.13
3678 7303 8.877740 AAGCCAACCGATGTTGTCTTTCATTG 62.878 42.308 4.89 0.00 45.58 2.82
3688 7313 1.059369 CTTTCATTGCGGCGACTCG 59.941 57.895 12.98 0.00 0.00 4.18
3689 7314 2.296692 CTTTCATTGCGGCGACTCGG 62.297 60.000 12.98 0.00 0.00 4.63
3690 7315 2.773397 TTTCATTGCGGCGACTCGGA 62.773 55.000 12.98 0.00 0.00 4.55
3691 7316 3.554692 CATTGCGGCGACTCGGAC 61.555 66.667 12.98 0.00 0.00 4.79
3692 7317 4.063967 ATTGCGGCGACTCGGACA 62.064 61.111 12.98 0.00 0.00 4.02
3738 11102 5.163205 TGAGGAGGAAGTTTGACATCAGAAA 60.163 40.000 0.00 0.00 0.00 2.52
3743 11107 6.122277 AGGAAGTTTGACATCAGAAAAGTGA 58.878 36.000 0.00 0.00 0.00 3.41
3754 11118 6.652481 ACATCAGAAAAGTGAGGTGTCATAAG 59.348 38.462 0.00 0.00 39.88 1.73
3756 11120 7.297936 TCAGAAAAGTGAGGTGTCATAAGTA 57.702 36.000 0.00 0.00 34.36 2.24
3759 11123 7.819415 CAGAAAAGTGAGGTGTCATAAGTATGA 59.181 37.037 0.00 0.00 40.19 2.15
3779 11143 2.248248 ACCTTCTCGGTCACTTCATGA 58.752 47.619 0.00 0.00 44.93 3.07
3795 11159 2.297315 TCATGACTGACTGCGAAGAAGT 59.703 45.455 0.00 0.00 0.00 3.01
3809 11173 2.434359 AAGTACCGAAGCAGCGCC 60.434 61.111 2.29 0.00 0.00 6.53
3810 11174 2.837371 GAAGTACCGAAGCAGCGCCT 62.837 60.000 2.29 0.00 0.00 5.52
3837 11201 2.093500 TGGTTGAGGATGAAGACGATGG 60.093 50.000 0.00 0.00 0.00 3.51
3844 11208 4.947883 AGGATGAAGACGATGGGGATATA 58.052 43.478 0.00 0.00 0.00 0.86
3855 11219 4.573607 CGATGGGGATATAATGCTGATGTG 59.426 45.833 0.00 0.00 0.00 3.21
3908 11272 3.257393 CACAATCAGCTAGACACAGGTC 58.743 50.000 0.00 0.00 44.66 3.85
3931 11295 2.359107 AGTGCATCCACGCCAGTG 60.359 61.111 0.00 0.00 46.62 3.66
3940 11304 4.643387 ACGCCAGTGAACCCAGGC 62.643 66.667 0.00 0.00 43.61 4.85
3948 11312 0.250338 GTGAACCCAGGCGAAGTTCT 60.250 55.000 14.56 0.00 40.42 3.01
4001 11365 1.762222 GATGATGGTACGTGCGGCAC 61.762 60.000 22.78 22.78 0.00 5.01
4020 11384 2.821366 CCAGGCAGCGCTCGAATT 60.821 61.111 7.13 0.00 0.00 2.17
4024 11388 2.022484 GCAGCGCTCGAATTGCTC 59.978 61.111 7.13 0.00 36.69 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.036765 GGCACAGATTACCGTGTGGA 60.037 55.000 4.75 0.00 43.62 4.02
1 2 0.321210 TGGCACAGATTACCGTGTGG 60.321 55.000 4.75 0.00 43.62 4.17
185 186 3.992943 TGGTCCTCGTTTATTGGTCAT 57.007 42.857 0.00 0.00 0.00 3.06
198 199 6.154021 TGTTATCAAGTACTACCTTGGTCCTC 59.846 42.308 0.00 0.00 41.72 3.71
230 231 5.276270 CAGTCTGTTTCAACCTGAACATTG 58.724 41.667 0.00 0.00 35.89 2.82
231 232 4.202050 GCAGTCTGTTTCAACCTGAACATT 60.202 41.667 0.93 0.00 35.89 2.71
233 234 2.682856 GCAGTCTGTTTCAACCTGAACA 59.317 45.455 0.93 0.00 35.89 3.18
234 235 2.033424 GGCAGTCTGTTTCAACCTGAAC 59.967 50.000 0.93 0.00 35.89 3.18
235 236 2.297701 GGCAGTCTGTTTCAACCTGAA 58.702 47.619 0.93 0.00 34.03 3.02
236 237 1.211703 TGGCAGTCTGTTTCAACCTGA 59.788 47.619 0.93 0.00 0.00 3.86
237 238 1.679139 TGGCAGTCTGTTTCAACCTG 58.321 50.000 0.93 0.00 0.00 4.00
239 240 1.269257 GCTTGGCAGTCTGTTTCAACC 60.269 52.381 0.93 0.00 0.00 3.77
240 241 1.269257 GGCTTGGCAGTCTGTTTCAAC 60.269 52.381 0.93 1.09 0.00 3.18
241 242 1.032014 GGCTTGGCAGTCTGTTTCAA 58.968 50.000 0.93 3.92 0.00 2.69
242 243 0.183492 AGGCTTGGCAGTCTGTTTCA 59.817 50.000 0.93 0.00 31.88 2.69
243 244 1.322442 AAGGCTTGGCAGTCTGTTTC 58.678 50.000 0.00 0.00 34.13 2.78
246 247 0.322008 GCTAAGGCTTGGCAGTCTGT 60.322 55.000 27.91 0.00 34.13 3.41
247 248 2.475666 GCTAAGGCTTGGCAGTCTG 58.524 57.895 27.91 0.00 34.13 3.51
258 259 3.939066 TGTTCCACTCTTTAGCTAAGGC 58.061 45.455 10.62 0.00 34.46 4.35
259 260 6.877611 TTTTGTTCCACTCTTTAGCTAAGG 57.122 37.500 9.25 9.25 34.46 2.69
292 313 0.333652 TATGAGACCCACCTCCGACA 59.666 55.000 0.00 0.00 32.32 4.35
293 314 1.481871 TTATGAGACCCACCTCCGAC 58.518 55.000 0.00 0.00 32.32 4.79
295 316 3.895656 TCTAATTATGAGACCCACCTCCG 59.104 47.826 0.00 0.00 32.32 4.63
296 317 5.148502 TCTCTAATTATGAGACCCACCTCC 58.851 45.833 9.32 0.00 35.86 4.30
297 318 6.071984 TCTCTCTAATTATGAGACCCACCTC 58.928 44.000 11.84 0.00 35.86 3.85
299 320 6.495181 TCATCTCTCTAATTATGAGACCCACC 59.505 42.308 15.92 0.00 39.29 4.61
300 321 7.531857 TCATCTCTCTAATTATGAGACCCAC 57.468 40.000 15.92 0.00 39.29 4.61
301 322 7.786943 ACTTCATCTCTCTAATTATGAGACCCA 59.213 37.037 15.92 5.37 39.29 4.51
302 323 8.189119 ACTTCATCTCTCTAATTATGAGACCC 57.811 38.462 15.92 0.00 39.29 4.46
303 324 9.691362 GAACTTCATCTCTCTAATTATGAGACC 57.309 37.037 15.92 2.92 39.29 3.85
320 341 9.814899 TGAAAAGATGAGAGATAGAACTTCATC 57.185 33.333 4.97 4.97 34.45 2.92
321 342 9.820725 CTGAAAAGATGAGAGATAGAACTTCAT 57.179 33.333 0.00 0.00 0.00 2.57
322 343 8.256605 CCTGAAAAGATGAGAGATAGAACTTCA 58.743 37.037 0.00 0.00 0.00 3.02
323 344 7.710475 CCCTGAAAAGATGAGAGATAGAACTTC 59.290 40.741 0.00 0.00 0.00 3.01
325 346 6.900186 TCCCTGAAAAGATGAGAGATAGAACT 59.100 38.462 0.00 0.00 0.00 3.01
326 347 7.118496 TCCCTGAAAAGATGAGAGATAGAAC 57.882 40.000 0.00 0.00 0.00 3.01
328 349 7.255766 CGAATCCCTGAAAAGATGAGAGATAGA 60.256 40.741 0.00 0.00 0.00 1.98
329 350 6.867816 CGAATCCCTGAAAAGATGAGAGATAG 59.132 42.308 0.00 0.00 0.00 2.08
330 351 6.551227 TCGAATCCCTGAAAAGATGAGAGATA 59.449 38.462 0.00 0.00 0.00 1.98
331 352 5.365025 TCGAATCCCTGAAAAGATGAGAGAT 59.635 40.000 0.00 0.00 0.00 2.75
333 354 5.016051 TCGAATCCCTGAAAAGATGAGAG 57.984 43.478 0.00 0.00 0.00 3.20
334 355 4.681781 GCTCGAATCCCTGAAAAGATGAGA 60.682 45.833 0.00 0.00 0.00 3.27
336 357 3.198635 AGCTCGAATCCCTGAAAAGATGA 59.801 43.478 0.00 0.00 0.00 2.92
337 358 3.311871 CAGCTCGAATCCCTGAAAAGATG 59.688 47.826 0.00 0.00 0.00 2.90
338 359 3.054802 ACAGCTCGAATCCCTGAAAAGAT 60.055 43.478 8.47 0.00 0.00 2.40
339 360 2.303022 ACAGCTCGAATCCCTGAAAAGA 59.697 45.455 8.47 0.00 0.00 2.52
340 361 2.704572 ACAGCTCGAATCCCTGAAAAG 58.295 47.619 8.47 0.00 0.00 2.27
341 362 2.859165 ACAGCTCGAATCCCTGAAAA 57.141 45.000 8.47 0.00 0.00 2.29
342 363 3.450817 TGATACAGCTCGAATCCCTGAAA 59.549 43.478 8.47 0.00 0.00 2.69
343 364 3.031013 TGATACAGCTCGAATCCCTGAA 58.969 45.455 8.47 0.00 0.00 3.02
344 365 2.666317 TGATACAGCTCGAATCCCTGA 58.334 47.619 8.47 0.00 0.00 3.86
345 366 3.674528 ATGATACAGCTCGAATCCCTG 57.325 47.619 0.00 0.00 0.00 4.45
347 368 6.868622 ACTAATATGATACAGCTCGAATCCC 58.131 40.000 0.00 0.00 0.00 3.85
349 370 6.689241 CCGACTAATATGATACAGCTCGAATC 59.311 42.308 0.00 0.00 0.00 2.52
351 372 5.106277 CCCGACTAATATGATACAGCTCGAA 60.106 44.000 0.00 0.00 0.00 3.71
352 373 4.395231 CCCGACTAATATGATACAGCTCGA 59.605 45.833 0.00 0.00 0.00 4.04
353 374 4.395231 TCCCGACTAATATGATACAGCTCG 59.605 45.833 0.00 0.00 0.00 5.03
354 375 5.899120 TCCCGACTAATATGATACAGCTC 57.101 43.478 0.00 0.00 0.00 4.09
355 376 5.336849 GCTTCCCGACTAATATGATACAGCT 60.337 44.000 0.00 0.00 0.00 4.24
356 377 4.865365 GCTTCCCGACTAATATGATACAGC 59.135 45.833 0.00 0.00 0.00 4.40
357 378 5.047306 TGGCTTCCCGACTAATATGATACAG 60.047 44.000 0.00 0.00 0.00 2.74
359 380 5.401531 TGGCTTCCCGACTAATATGATAC 57.598 43.478 0.00 0.00 0.00 2.24
360 381 6.406370 CATTGGCTTCCCGACTAATATGATA 58.594 40.000 0.00 0.00 0.00 2.15
364 385 3.244911 CCCATTGGCTTCCCGACTAATAT 60.245 47.826 0.00 0.00 0.00 1.28
365 386 2.105821 CCCATTGGCTTCCCGACTAATA 59.894 50.000 0.00 0.00 0.00 0.98
366 387 1.133792 CCCATTGGCTTCCCGACTAAT 60.134 52.381 0.00 0.00 0.00 1.73
367 388 0.254747 CCCATTGGCTTCCCGACTAA 59.745 55.000 0.00 0.00 0.00 2.24
368 389 1.632018 CCCCATTGGCTTCCCGACTA 61.632 60.000 0.00 0.00 0.00 2.59
369 390 2.677228 CCCATTGGCTTCCCGACT 59.323 61.111 0.00 0.00 0.00 4.18
373 394 2.364186 CCACCCCATTGGCTTCCC 60.364 66.667 0.00 0.00 37.83 3.97
380 401 1.269012 ATTTGTGAGCCACCCCATTG 58.731 50.000 3.33 0.00 32.73 2.82
381 402 2.028561 AATTTGTGAGCCACCCCATT 57.971 45.000 3.33 0.00 32.73 3.16
382 403 2.738743 CTAATTTGTGAGCCACCCCAT 58.261 47.619 3.33 0.00 32.73 4.00
383 404 1.890573 GCTAATTTGTGAGCCACCCCA 60.891 52.381 3.33 0.00 32.73 4.96
384 405 0.817654 GCTAATTTGTGAGCCACCCC 59.182 55.000 3.33 0.00 32.73 4.95
385 406 1.745653 GAGCTAATTTGTGAGCCACCC 59.254 52.381 0.00 0.00 39.65 4.61
386 407 1.398390 CGAGCTAATTTGTGAGCCACC 59.602 52.381 0.00 0.00 39.65 4.61
387 408 1.398390 CCGAGCTAATTTGTGAGCCAC 59.602 52.381 0.00 0.00 39.65 5.01
388 409 1.737838 CCGAGCTAATTTGTGAGCCA 58.262 50.000 0.00 0.00 39.65 4.75
392 413 1.401552 GCATGCCGAGCTAATTTGTGA 59.598 47.619 6.36 0.00 0.00 3.58
394 415 1.672881 GAGCATGCCGAGCTAATTTGT 59.327 47.619 15.66 0.00 43.58 2.83
395 416 1.945394 AGAGCATGCCGAGCTAATTTG 59.055 47.619 15.66 0.00 43.58 2.32
396 417 2.338577 AGAGCATGCCGAGCTAATTT 57.661 45.000 15.66 0.00 43.58 1.82
397 418 2.366916 AGTAGAGCATGCCGAGCTAATT 59.633 45.455 15.66 0.00 43.58 1.40
398 419 1.967066 AGTAGAGCATGCCGAGCTAAT 59.033 47.619 15.66 7.77 43.58 1.73
399 420 1.403814 AGTAGAGCATGCCGAGCTAA 58.596 50.000 15.66 0.00 43.58 3.09
400 421 1.403814 AAGTAGAGCATGCCGAGCTA 58.596 50.000 15.66 8.49 43.58 3.32
401 422 0.539051 AAAGTAGAGCATGCCGAGCT 59.461 50.000 15.66 9.52 46.82 4.09
402 423 0.933796 GAAAGTAGAGCATGCCGAGC 59.066 55.000 15.66 2.77 0.00 5.03
403 424 2.299993 TGAAAGTAGAGCATGCCGAG 57.700 50.000 15.66 0.00 0.00 4.63
404 425 2.028112 ACTTGAAAGTAGAGCATGCCGA 60.028 45.455 15.66 0.00 37.52 5.54
405 426 2.350522 ACTTGAAAGTAGAGCATGCCG 58.649 47.619 15.66 0.00 37.52 5.69
406 427 4.274459 CCATACTTGAAAGTAGAGCATGCC 59.726 45.833 15.66 6.03 44.06 4.40
408 429 4.274459 GCCCATACTTGAAAGTAGAGCATG 59.726 45.833 8.73 3.27 44.06 4.06
409 430 4.455606 GCCCATACTTGAAAGTAGAGCAT 58.544 43.478 8.73 0.00 44.06 3.79
410 431 3.678806 CGCCCATACTTGAAAGTAGAGCA 60.679 47.826 16.00 0.00 44.06 4.26
414 435 4.442706 ACATCGCCCATACTTGAAAGTAG 58.557 43.478 8.73 2.19 44.06 2.57
415 436 4.481368 ACATCGCCCATACTTGAAAGTA 57.519 40.909 5.43 5.43 44.84 2.24
416 437 3.350219 ACATCGCCCATACTTGAAAGT 57.650 42.857 0.71 0.71 42.91 2.66
417 438 4.876107 AGTTACATCGCCCATACTTGAAAG 59.124 41.667 0.00 0.00 0.00 2.62
418 439 4.839121 AGTTACATCGCCCATACTTGAAA 58.161 39.130 0.00 0.00 0.00 2.69
419 440 4.481368 AGTTACATCGCCCATACTTGAA 57.519 40.909 0.00 0.00 0.00 2.69
420 441 4.481368 AAGTTACATCGCCCATACTTGA 57.519 40.909 0.00 0.00 0.00 3.02
421 442 4.634004 TGAAAGTTACATCGCCCATACTTG 59.366 41.667 0.00 0.00 0.00 3.16
422 443 4.839121 TGAAAGTTACATCGCCCATACTT 58.161 39.130 0.00 0.00 0.00 2.24
423 444 4.442706 CTGAAAGTTACATCGCCCATACT 58.557 43.478 0.00 0.00 0.00 2.12
439 460 4.938226 GGAACTCAGGGATACAACTGAAAG 59.062 45.833 0.00 0.00 42.62 2.62
441 462 4.020218 CAGGAACTCAGGGATACAACTGAA 60.020 45.833 0.00 0.00 42.62 3.02
442 463 3.515502 CAGGAACTCAGGGATACAACTGA 59.484 47.826 0.00 0.00 41.13 3.41
443 464 3.515502 TCAGGAACTCAGGGATACAACTG 59.484 47.826 0.00 0.00 34.60 3.16
444 465 3.772025 CTCAGGAACTCAGGGATACAACT 59.228 47.826 0.00 0.00 34.60 3.16
447 468 3.099905 CACTCAGGAACTCAGGGATACA 58.900 50.000 0.00 0.00 21.39 2.29
448 469 3.131400 GTCACTCAGGAACTCAGGGATAC 59.869 52.174 0.00 0.00 44.02 2.24
450 471 2.183679 GTCACTCAGGAACTCAGGGAT 58.816 52.381 0.00 0.00 44.02 3.85
451 472 1.633774 GTCACTCAGGAACTCAGGGA 58.366 55.000 0.00 0.00 35.83 4.20
452 473 0.244994 CGTCACTCAGGAACTCAGGG 59.755 60.000 0.00 0.00 34.60 4.45
453 474 1.201181 CTCGTCACTCAGGAACTCAGG 59.799 57.143 0.00 0.00 34.60 3.86
454 475 1.201181 CCTCGTCACTCAGGAACTCAG 59.799 57.143 0.00 0.00 34.60 3.35
455 476 1.248486 CCTCGTCACTCAGGAACTCA 58.752 55.000 0.00 0.00 34.60 3.41
456 477 1.068194 CACCTCGTCACTCAGGAACTC 60.068 57.143 0.00 0.00 34.60 3.01
458 479 0.667792 GCACCTCGTCACTCAGGAAC 60.668 60.000 0.00 0.00 33.52 3.62
460 481 1.530655 TGCACCTCGTCACTCAGGA 60.531 57.895 0.00 0.00 33.52 3.86
461 482 1.373497 GTGCACCTCGTCACTCAGG 60.373 63.158 5.22 0.00 35.69 3.86
462 483 1.662608 AGTGCACCTCGTCACTCAG 59.337 57.895 14.63 0.00 39.11 3.35
463 484 3.856309 AGTGCACCTCGTCACTCA 58.144 55.556 14.63 0.00 39.11 3.41
472 493 1.045407 TACAAAGTCCGAGTGCACCT 58.955 50.000 14.63 0.00 0.00 4.00
473 494 1.145803 GTACAAAGTCCGAGTGCACC 58.854 55.000 14.63 4.10 0.00 5.01
474 495 0.782384 CGTACAAAGTCCGAGTGCAC 59.218 55.000 9.40 9.40 0.00 4.57
475 496 0.669619 TCGTACAAAGTCCGAGTGCA 59.330 50.000 0.00 0.00 0.00 4.57
476 497 1.918609 GATCGTACAAAGTCCGAGTGC 59.081 52.381 0.00 0.00 33.66 4.40
477 498 2.159612 TCGATCGTACAAAGTCCGAGTG 60.160 50.000 15.94 0.00 33.66 3.51
478 499 2.079158 TCGATCGTACAAAGTCCGAGT 58.921 47.619 15.94 0.00 33.66 4.18
480 501 2.679336 TCATCGATCGTACAAAGTCCGA 59.321 45.455 15.94 0.00 34.79 4.55
482 503 5.041287 TCATTCATCGATCGTACAAAGTCC 58.959 41.667 15.94 0.00 0.00 3.85
483 504 6.569228 TTCATTCATCGATCGTACAAAGTC 57.431 37.500 15.94 0.00 0.00 3.01
484 505 8.642908 TTATTCATTCATCGATCGTACAAAGT 57.357 30.769 15.94 0.00 0.00 2.66
485 506 9.914923 TTTTATTCATTCATCGATCGTACAAAG 57.085 29.630 15.94 3.63 0.00 2.77
486 507 9.914923 CTTTTATTCATTCATCGATCGTACAAA 57.085 29.630 15.94 6.25 0.00 2.83
487 508 8.061857 GCTTTTATTCATTCATCGATCGTACAA 58.938 33.333 15.94 6.43 0.00 2.41
488 509 7.307160 GGCTTTTATTCATTCATCGATCGTACA 60.307 37.037 15.94 0.00 0.00 2.90
489 510 7.010023 GGCTTTTATTCATTCATCGATCGTAC 58.990 38.462 15.94 0.00 0.00 3.67
490 511 6.929049 AGGCTTTTATTCATTCATCGATCGTA 59.071 34.615 15.94 2.15 0.00 3.43
491 512 5.760253 AGGCTTTTATTCATTCATCGATCGT 59.240 36.000 15.94 0.00 0.00 3.73
492 513 6.233430 AGGCTTTTATTCATTCATCGATCG 57.767 37.500 9.36 9.36 0.00 3.69
493 514 7.642669 TGAAGGCTTTTATTCATTCATCGATC 58.357 34.615 0.00 0.00 30.67 3.69
494 515 7.572523 TGAAGGCTTTTATTCATTCATCGAT 57.427 32.000 0.00 0.00 30.67 3.59
495 516 7.389803 TTGAAGGCTTTTATTCATTCATCGA 57.610 32.000 0.00 0.00 35.47 3.59
496 517 6.694411 CCTTGAAGGCTTTTATTCATTCATCG 59.306 38.462 0.00 0.00 35.47 3.84
497 518 6.982724 CCCTTGAAGGCTTTTATTCATTCATC 59.017 38.462 5.50 0.00 35.47 2.92
498 519 6.881570 CCCTTGAAGGCTTTTATTCATTCAT 58.118 36.000 5.50 0.00 35.47 2.57
499 520 6.284891 CCCTTGAAGGCTTTTATTCATTCA 57.715 37.500 5.50 0.00 35.47 2.57
513 534 0.323629 TGAAGTACGGCCCTTGAAGG 59.676 55.000 3.69 3.69 34.30 3.46
514 535 2.178912 TTGAAGTACGGCCCTTGAAG 57.821 50.000 0.00 0.00 0.00 3.02
515 536 2.642154 TTTGAAGTACGGCCCTTGAA 57.358 45.000 0.00 0.00 0.00 2.69
516 537 2.642154 TTTTGAAGTACGGCCCTTGA 57.358 45.000 0.00 0.00 0.00 3.02
586 607 4.021192 CCATTCTCTCTATCCTCTCAAGCC 60.021 50.000 0.00 0.00 0.00 4.35
607 628 5.598005 GGAATGAATGGATACCATGTTTCCA 59.402 40.000 21.34 8.52 44.40 3.53
649 670 9.707957 AGAATAGAGTTCTTCCTTCAGAATCTA 57.292 33.333 0.00 0.00 35.23 1.98
728 749 5.760253 TCAACTTCAGAGTGAAATTGGAGAC 59.240 40.000 10.08 0.00 42.04 3.36
887 917 4.142182 GCATGCTAGCTAGAGAGATTAGGG 60.142 50.000 25.15 2.42 0.00 3.53
898 928 5.739752 TGTTGTATTTGCATGCTAGCTAG 57.260 39.130 20.33 16.84 34.99 3.42
899 929 5.414144 TGTTGTTGTATTTGCATGCTAGCTA 59.586 36.000 20.33 2.58 34.99 3.32
900 930 4.218200 TGTTGTTGTATTTGCATGCTAGCT 59.782 37.500 20.33 5.44 34.99 3.32
901 931 4.484236 TGTTGTTGTATTTGCATGCTAGC 58.516 39.130 20.33 8.10 0.00 3.42
939 969 1.069432 CACGCATGCAATCATCTAGCC 60.069 52.381 19.57 0.00 0.00 3.93
940 970 1.600957 ACACGCATGCAATCATCTAGC 59.399 47.619 19.57 0.00 0.00 3.42
1453 1700 2.296471 CCACGTACTTATAGGAGCCCAG 59.704 54.545 0.00 0.00 0.00 4.45
1749 2982 2.193536 GCGGACCACACTTGCCTTT 61.194 57.895 0.00 0.00 0.00 3.11
2271 5657 1.135141 GTGCACACAGCTTCCAACAAA 60.135 47.619 13.17 0.00 45.94 2.83
2547 5948 1.436336 GATACCCTCGTCACACGGG 59.564 63.158 0.00 0.00 42.83 5.28
2551 5952 2.291089 TGTAGTGGATACCCTCGTCACA 60.291 50.000 0.00 0.00 33.01 3.58
2959 6566 1.614413 GGACGTGAAGGTGAGAAGACT 59.386 52.381 0.00 0.00 0.00 3.24
2997 6604 2.044252 AGCTGCTTGGCATGGGAG 60.044 61.111 0.00 4.07 38.13 4.30
3243 6864 6.127196 CCTGGGCATATAAGAGAGATAGAACC 60.127 46.154 0.00 0.00 0.00 3.62
3263 6884 1.611519 TAAACTTTTCCGCACCTGGG 58.388 50.000 0.00 0.00 0.00 4.45
3278 6899 2.606108 CTGCGGCCCTTCAAAATAAAC 58.394 47.619 0.00 0.00 0.00 2.01
3281 6902 1.319614 GCCTGCGGCCCTTCAAAATA 61.320 55.000 8.18 0.00 44.06 1.40
3340 6961 1.581912 GCATGTCAGATTGTGCGCG 60.582 57.895 0.00 0.00 0.00 6.86
3343 6964 1.808343 TGTGAGCATGTCAGATTGTGC 59.192 47.619 0.00 0.00 35.13 4.57
3593 7218 1.800586 CAAGAACCACACCACATCTCG 59.199 52.381 0.00 0.00 0.00 4.04
3597 7222 0.827507 GGGCAAGAACCACACCACAT 60.828 55.000 0.00 0.00 0.00 3.21
3618 7243 3.186613 GCTATTTAAGTGAGGCCATACGC 59.813 47.826 5.01 2.44 0.00 4.42
3619 7244 3.428870 CGCTATTTAAGTGAGGCCATACG 59.571 47.826 5.01 0.00 37.99 3.06
3620 7245 3.746492 CCGCTATTTAAGTGAGGCCATAC 59.254 47.826 5.01 2.85 37.99 2.39
3669 7294 1.351430 CGAGTCGCCGCAATGAAAGA 61.351 55.000 0.00 0.00 0.00 2.52
3688 7313 1.815421 AGGCGCATCATCGTTGTCC 60.815 57.895 10.83 0.00 0.00 4.02
3689 7314 1.349627 CAGGCGCATCATCGTTGTC 59.650 57.895 10.83 0.00 0.00 3.18
3690 7315 2.753966 GCAGGCGCATCATCGTTGT 61.754 57.895 10.83 0.00 38.36 3.32
3691 7316 2.023741 GCAGGCGCATCATCGTTG 59.976 61.111 10.83 0.00 38.36 4.10
3692 7317 2.436469 TGCAGGCGCATCATCGTT 60.436 55.556 10.83 0.00 45.36 3.85
3779 11143 1.068472 CGGTACTTCTTCGCAGTCAGT 60.068 52.381 0.00 0.00 0.00 3.41
3786 11150 0.992802 CTGCTTCGGTACTTCTTCGC 59.007 55.000 0.00 0.00 0.00 4.70
3819 11183 1.486310 CCCCATCGTCTTCATCCTCAA 59.514 52.381 0.00 0.00 0.00 3.02
3837 11201 3.599343 TCGCACATCAGCATTATATCCC 58.401 45.455 0.00 0.00 0.00 3.85
3844 11208 1.134580 ACTAGCTCGCACATCAGCATT 60.135 47.619 0.00 0.00 38.18 3.56
3855 11219 2.054140 CTCCTCGTCCACTAGCTCGC 62.054 65.000 0.00 0.00 0.00 5.03
3881 11245 3.868077 GTGTCTAGCTGATTGTGGTCATC 59.132 47.826 0.00 0.00 0.00 2.92
3908 11272 2.815211 CGTGGATGCACTCACCGG 60.815 66.667 15.82 0.00 0.00 5.28
3931 11295 0.250338 ACAGAACTTCGCCTGGGTTC 60.250 55.000 0.00 0.49 39.43 3.62
3940 11304 2.155732 CGGATGACACAACAGAACTTCG 59.844 50.000 0.00 0.00 0.00 3.79
3948 11312 2.280457 TGCGCGGATGACACAACA 60.280 55.556 8.83 0.00 0.00 3.33
4006 11370 3.446175 GAGCAATTCGAGCGCTGCC 62.446 63.158 18.48 0.00 35.75 4.85


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

AutoCloner maintained by Alex Coulton.