Multiple sequence alignment - TraesCS3B01G257600

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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 TraesCS3B01G257600 chr3B 100.000 2717 0 0 1 2717 415645507 415642791 0.000000e+00 5018.0
1 TraesCS3B01G257600 chr3B 80.085 236 43 4 366 599 109965168 109965401 3.600000e-39 172.0
2 TraesCS3B01G257600 chr3D 88.114 2137 178 47 597 2714 306016511 306018590 0.000000e+00 2470.0
3 TraesCS3B01G257600 chr3D 92.188 256 19 1 5 260 306016174 306016428 7.150000e-96 361.0
4 TraesCS3B01G257600 chr3D 81.013 237 39 5 366 598 21715289 21715055 1.660000e-42 183.0
5 TraesCS3B01G257600 chr3D 80.000 175 31 3 359 533 79629474 79629644 2.840000e-25 126.0
6 TraesCS3B01G257600 chr3A 94.429 1400 57 7 591 1980 424250012 424251400 0.000000e+00 2134.0
7 TraesCS3B01G257600 chr3A 93.352 361 22 2 5 365 424249661 424250019 1.430000e-147 532.0
8 TraesCS3B01G257600 chr3A 88.764 89 8 2 511 598 436680977 436680890 1.030000e-19 108.0
9 TraesCS3B01G257600 chr2B 80.800 250 35 7 353 599 740805592 740805831 1.660000e-42 183.0
10 TraesCS3B01G257600 chr2D 81.197 234 36 6 368 599 524330366 524330593 5.980000e-42 182.0
11 TraesCS3B01G257600 chr5D 81.657 169 30 1 367 534 115394983 115395151 3.650000e-29 139.0
12 TraesCS3B01G257600 chr1A 76.132 243 56 2 361 601 145919273 145919515 2.840000e-25 126.0
13 TraesCS3B01G257600 chr1A 84.000 100 14 2 511 608 22327081 22326982 8.010000e-16 95.3
14 TraesCS3B01G257600 chr7D 75.934 241 42 5 360 598 110047531 110047757 2.860000e-20 110.0
15 TraesCS3B01G257600 chr7D 75.519 241 43 6 360 598 109787252 109787478 1.330000e-18 104.0
16 TraesCS3B01G257600 chr4D 82.203 118 20 1 498 614 483701905 483701788 1.720000e-17 100.0
17 TraesCS3B01G257600 chr2A 89.041 73 8 0 521 593 692642034 692642106 1.040000e-14 91.6
18 TraesCS3B01G257600 chr1D 74.863 183 37 8 368 547 62339736 62339560 1.040000e-09 75.0
19 TraesCS3B01G257600 chr1B 90.909 55 2 3 187 238 35490097 35490151 1.350000e-08 71.3
20 TraesCS3B01G257600 chr1B 89.831 59 1 5 187 240 35640929 35640987 1.350000e-08 71.3


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 TraesCS3B01G257600 chr3B 415642791 415645507 2716 True 5018.0 5018 100.0000 1 2717 1 chr3B.!!$R1 2716
1 TraesCS3B01G257600 chr3D 306016174 306018590 2416 False 1415.5 2470 90.1510 5 2714 2 chr3D.!!$F2 2709
2 TraesCS3B01G257600 chr3A 424249661 424251400 1739 False 1333.0 2134 93.8905 5 1980 2 chr3A.!!$F1 1975

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
387 391 0.036671 CCGTCCGGGATTATTAGGCC 60.037 60.0 0.0 0.0 38.47 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2179 2195 0.17691 TGTGTCGACACTTTGAGCCA 59.823 50.0 39.62 20.85 46.55 4.75 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
31 32 1.044790 TCTCCATCCGAGAGCATGCA 61.045 55.000 21.98 0.00 42.97 3.96
50 51 3.237628 GCAAAGTCGAGCTCCATTTTTC 58.762 45.455 8.47 0.00 0.00 2.29
78 79 4.154195 CCGACAAAATAGGGAGTGTTGAAG 59.846 45.833 0.00 0.00 0.00 3.02
155 156 5.733620 AGTGGATGTCTTTTTCAATGCAT 57.266 34.783 0.00 0.00 0.00 3.96
185 186 5.543714 TGCCAATAGAAACTCTTACGTTCA 58.456 37.500 0.00 0.00 0.00 3.18
362 366 9.258826 CAAGATCATCATGAAGTTAGAAGGTAG 57.741 37.037 0.00 0.00 0.00 3.18
364 368 9.647918 AGATCATCATGAAGTTAGAAGGTAGTA 57.352 33.333 0.00 0.00 0.00 1.82
366 370 8.008513 TCATCATGAAGTTAGAAGGTAGTACC 57.991 38.462 11.73 11.73 38.99 3.34
375 379 3.833304 GGTAGTACCTCCGTCCGG 58.167 66.667 12.41 0.00 34.73 5.14
376 380 1.825622 GGTAGTACCTCCGTCCGGG 60.826 68.421 12.41 0.00 34.73 5.73
377 381 1.224592 GTAGTACCTCCGTCCGGGA 59.775 63.158 0.00 0.00 44.68 5.14
378 382 0.179006 GTAGTACCTCCGTCCGGGAT 60.179 60.000 0.00 0.00 46.04 3.85
379 383 0.552848 TAGTACCTCCGTCCGGGATT 59.447 55.000 0.00 0.00 46.04 3.01
380 384 0.552848 AGTACCTCCGTCCGGGATTA 59.447 55.000 0.00 0.00 46.04 1.75
381 385 1.146566 AGTACCTCCGTCCGGGATTAT 59.853 52.381 0.00 0.00 46.04 1.28
382 386 1.966354 GTACCTCCGTCCGGGATTATT 59.034 52.381 0.00 0.00 46.04 1.40
383 387 2.386829 ACCTCCGTCCGGGATTATTA 57.613 50.000 0.00 0.00 46.04 0.98
384 388 2.245582 ACCTCCGTCCGGGATTATTAG 58.754 52.381 0.00 0.00 46.04 1.73
385 389 1.549170 CCTCCGTCCGGGATTATTAGG 59.451 57.143 0.00 0.00 46.04 2.69
386 390 0.971386 TCCGTCCGGGATTATTAGGC 59.029 55.000 0.00 0.00 40.94 3.93
387 391 0.036671 CCGTCCGGGATTATTAGGCC 60.037 60.000 0.00 0.00 38.47 5.19
388 392 0.036671 CGTCCGGGATTATTAGGCCC 60.037 60.000 0.00 0.00 38.53 5.80
389 393 0.327259 GTCCGGGATTATTAGGCCCC 59.673 60.000 0.00 0.00 38.69 5.80
390 394 0.195096 TCCGGGATTATTAGGCCCCT 59.805 55.000 0.00 0.00 38.69 4.79
391 395 1.073098 CCGGGATTATTAGGCCCCTT 58.927 55.000 0.00 0.00 38.69 3.95
392 396 1.004394 CCGGGATTATTAGGCCCCTTC 59.996 57.143 0.00 0.00 38.69 3.46
393 397 1.985895 CGGGATTATTAGGCCCCTTCT 59.014 52.381 0.00 0.00 38.69 2.85
394 398 3.178865 CGGGATTATTAGGCCCCTTCTA 58.821 50.000 0.00 0.00 38.69 2.10
395 399 3.780850 CGGGATTATTAGGCCCCTTCTAT 59.219 47.826 0.00 0.00 38.69 1.98
396 400 4.227527 CGGGATTATTAGGCCCCTTCTATT 59.772 45.833 0.00 0.00 38.69 1.73
397 401 5.281037 CGGGATTATTAGGCCCCTTCTATTT 60.281 44.000 0.00 0.00 38.69 1.40
398 402 6.562228 GGGATTATTAGGCCCCTTCTATTTT 58.438 40.000 0.00 0.00 35.76 1.82
399 403 6.437477 GGGATTATTAGGCCCCTTCTATTTTG 59.563 42.308 0.00 0.00 35.76 2.44
400 404 6.437477 GGATTATTAGGCCCCTTCTATTTTGG 59.563 42.308 0.00 0.00 0.00 3.28
401 405 6.599986 TTATTAGGCCCCTTCTATTTTGGA 57.400 37.500 0.00 0.00 0.00 3.53
402 406 5.686535 ATTAGGCCCCTTCTATTTTGGAT 57.313 39.130 0.00 0.00 0.00 3.41
403 407 5.481615 TTAGGCCCCTTCTATTTTGGATT 57.518 39.130 0.00 0.00 0.00 3.01
404 408 3.646534 AGGCCCCTTCTATTTTGGATTG 58.353 45.455 0.00 0.00 0.00 2.67
405 409 3.272020 AGGCCCCTTCTATTTTGGATTGA 59.728 43.478 0.00 0.00 0.00 2.57
406 410 4.030216 GGCCCCTTCTATTTTGGATTGAA 58.970 43.478 0.00 0.00 0.00 2.69
407 411 4.100035 GGCCCCTTCTATTTTGGATTGAAG 59.900 45.833 0.00 0.00 35.31 3.02
408 412 4.711846 GCCCCTTCTATTTTGGATTGAAGT 59.288 41.667 8.58 0.00 34.15 3.01
409 413 5.187772 GCCCCTTCTATTTTGGATTGAAGTT 59.812 40.000 8.58 0.00 34.15 2.66
410 414 6.295859 GCCCCTTCTATTTTGGATTGAAGTTT 60.296 38.462 8.58 0.00 34.15 2.66
411 415 7.093509 GCCCCTTCTATTTTGGATTGAAGTTTA 60.094 37.037 8.58 0.00 34.15 2.01
412 416 8.811994 CCCCTTCTATTTTGGATTGAAGTTTAA 58.188 33.333 8.58 0.00 34.15 1.52
413 417 9.639601 CCCTTCTATTTTGGATTGAAGTTTAAC 57.360 33.333 8.58 0.00 34.15 2.01
414 418 9.639601 CCTTCTATTTTGGATTGAAGTTTAACC 57.360 33.333 8.58 0.00 34.15 2.85
421 425 9.898152 TTTTGGATTGAAGTTTAACCAAAGATT 57.102 25.926 17.87 0.00 44.34 2.40
422 426 9.898152 TTTGGATTGAAGTTTAACCAAAGATTT 57.102 25.926 16.18 0.00 40.73 2.17
467 471 6.751514 ATGTCACAAAAATTATACTGCCGA 57.248 33.333 0.00 0.00 0.00 5.54
468 472 6.561737 TGTCACAAAAATTATACTGCCGAA 57.438 33.333 0.00 0.00 0.00 4.30
469 473 6.971602 TGTCACAAAAATTATACTGCCGAAA 58.028 32.000 0.00 0.00 0.00 3.46
470 474 7.426410 TGTCACAAAAATTATACTGCCGAAAA 58.574 30.769 0.00 0.00 0.00 2.29
471 475 7.380065 TGTCACAAAAATTATACTGCCGAAAAC 59.620 33.333 0.00 0.00 0.00 2.43
472 476 6.864165 TCACAAAAATTATACTGCCGAAAACC 59.136 34.615 0.00 0.00 0.00 3.27
473 477 6.866248 CACAAAAATTATACTGCCGAAAACCT 59.134 34.615 0.00 0.00 0.00 3.50
474 478 7.061789 CACAAAAATTATACTGCCGAAAACCTC 59.938 37.037 0.00 0.00 0.00 3.85
475 479 7.039993 ACAAAAATTATACTGCCGAAAACCTCT 60.040 33.333 0.00 0.00 0.00 3.69
476 480 7.462571 AAAATTATACTGCCGAAAACCTCTT 57.537 32.000 0.00 0.00 0.00 2.85
477 481 7.462571 AAATTATACTGCCGAAAACCTCTTT 57.537 32.000 0.00 0.00 0.00 2.52
478 482 6.679327 ATTATACTGCCGAAAACCTCTTTC 57.321 37.500 0.00 0.00 0.00 2.62
492 496 9.458374 GAAAACCTCTTTCGAATACAAATCAAA 57.542 29.630 0.00 0.00 0.00 2.69
493 497 9.810545 AAAACCTCTTTCGAATACAAATCAAAA 57.189 25.926 0.00 0.00 0.00 2.44
494 498 9.810545 AAACCTCTTTCGAATACAAATCAAAAA 57.189 25.926 0.00 0.00 0.00 1.94
568 572 6.954944 TCAAACTTTGACTCAAAATACGAGG 58.045 36.000 5.72 0.00 32.75 4.63
569 573 5.941948 AACTTTGACTCAAAATACGAGGG 57.058 39.130 5.72 0.00 32.75 4.30
570 574 4.324267 ACTTTGACTCAAAATACGAGGGG 58.676 43.478 5.72 0.00 32.75 4.79
571 575 3.343941 TTGACTCAAAATACGAGGGGG 57.656 47.619 0.00 0.00 34.66 5.40
588 592 2.996444 GGGCTAATAAACCCGGACG 58.004 57.895 0.73 0.00 36.07 4.79
589 593 0.533531 GGGCTAATAAACCCGGACGG 60.534 60.000 0.73 3.25 36.07 4.79
590 594 0.465287 GGCTAATAAACCCGGACGGA 59.535 55.000 13.13 0.00 37.50 4.69
591 595 1.539712 GGCTAATAAACCCGGACGGAG 60.540 57.143 13.13 5.04 37.50 4.63
592 596 1.539712 GCTAATAAACCCGGACGGAGG 60.540 57.143 13.13 0.00 37.50 4.30
613 617 2.695666 GGAGTATGAGCTAGCCAAGACA 59.304 50.000 12.13 4.93 0.00 3.41
665 669 9.928236 GATCTTTATTGCTAGAAGCTTAAGTTG 57.072 33.333 0.00 0.00 42.97 3.16
667 671 7.390440 TCTTTATTGCTAGAAGCTTAAGTTGCA 59.610 33.333 0.00 3.43 42.97 4.08
728 732 4.456911 CCGCTGCCTATAATCACATCAAAT 59.543 41.667 0.00 0.00 0.00 2.32
731 735 7.148188 CCGCTGCCTATAATCACATCAAATAAT 60.148 37.037 0.00 0.00 0.00 1.28
779 783 5.763204 ACACTACCTACCAAACACTTGAATG 59.237 40.000 0.00 0.00 34.14 2.67
780 784 5.181245 CACTACCTACCAAACACTTGAATGG 59.819 44.000 0.00 0.00 38.91 3.16
1003 1018 2.739784 CCTAGCCGCTCTCCATGG 59.260 66.667 4.97 4.97 0.00 3.66
1102 1117 4.101077 AGCTCCTAGCCCTGGCCT 62.101 66.667 3.32 0.00 43.77 5.19
1110 1125 4.035102 GCCCTGGCCTTCGTCCTT 62.035 66.667 3.32 0.00 34.56 3.36
1191 1206 1.984570 CGCCTCACTCCTCCTCCAA 60.985 63.158 0.00 0.00 0.00 3.53
1282 1297 1.344191 GCCATCTTCCTCTGCCTCCT 61.344 60.000 0.00 0.00 0.00 3.69
1291 1306 0.032615 CTCTGCCTCCTACCAGGACT 60.033 60.000 0.00 0.00 40.06 3.85
1454 1469 0.249489 AGATCGGAGAAAATCGGCGG 60.249 55.000 7.21 0.00 43.58 6.13
1461 1476 1.210672 GAAAATCGGCGGCGGAAAA 59.789 52.632 31.73 12.74 0.00 2.29
1525 1540 4.832608 ATTCGGAGAACGGGCGGC 62.833 66.667 0.00 0.00 45.90 6.53
1636 1651 2.186826 AAGCAGCAGACGCGGTTTT 61.187 52.632 12.47 0.00 45.49 2.43
1922 1937 1.105167 ACCGCCGATCGATGGACTAA 61.105 55.000 25.92 0.00 41.67 2.24
2018 2033 0.996462 ACGCACGTACGAATTGGATG 59.004 50.000 24.41 8.91 36.70 3.51
2019 2034 0.996462 CGCACGTACGAATTGGATGT 59.004 50.000 24.41 0.00 34.06 3.06
2068 2083 1.136500 AGGAGTCGAATTACTTCCCGC 59.864 52.381 0.00 0.00 0.00 6.13
2071 2086 1.745087 AGTCGAATTACTTCCCGCGTA 59.255 47.619 4.92 0.00 0.00 4.42
2072 2087 2.164219 AGTCGAATTACTTCCCGCGTAA 59.836 45.455 4.92 0.00 0.00 3.18
2107 2122 4.088762 CCACGCGCATGACACACC 62.089 66.667 4.35 0.00 0.00 4.16
2108 2123 4.428922 CACGCGCATGACACACCG 62.429 66.667 5.73 0.00 0.00 4.94
2113 2128 1.226101 CGCATGACACACCGAATGC 60.226 57.895 0.00 0.00 41.57 3.56
2115 2130 1.911293 GCATGACACACCGAATGCGT 61.911 55.000 0.00 0.00 36.41 5.24
2117 2132 1.068250 TGACACACCGAATGCGTCA 59.932 52.632 6.44 6.44 45.88 4.35
2124 2139 0.250124 ACCGAATGCGTCAAACTCCA 60.250 50.000 0.00 0.00 35.23 3.86
2125 2140 0.871722 CCGAATGCGTCAAACTCCAA 59.128 50.000 0.00 0.00 35.23 3.53
2126 2141 1.399727 CCGAATGCGTCAAACTCCAAC 60.400 52.381 0.00 0.00 35.23 3.77
2130 2145 3.315796 CGTCAAACTCCAACGCGT 58.684 55.556 5.58 5.58 0.00 6.01
2131 2146 1.083657 CGTCAAACTCCAACGCGTG 60.084 57.895 14.98 7.16 0.00 5.34
2152 2167 0.662970 CCGCATTTGGTCCGTTTGTG 60.663 55.000 0.00 0.00 0.00 3.33
2153 2168 0.030101 CGCATTTGGTCCGTTTGTGT 59.970 50.000 0.00 0.00 0.00 3.72
2154 2169 1.264557 CGCATTTGGTCCGTTTGTGTA 59.735 47.619 0.00 0.00 0.00 2.90
2155 2170 2.657184 GCATTTGGTCCGTTTGTGTAC 58.343 47.619 0.00 0.00 0.00 2.90
2161 2177 2.291365 GGTCCGTTTGTGTACTGGTTT 58.709 47.619 0.00 0.00 0.00 3.27
2168 2184 4.099824 GTTTGTGTACTGGTTTGAAACGG 58.900 43.478 1.53 0.45 0.00 4.44
2172 2188 3.374678 GTGTACTGGTTTGAAACGGACAA 59.625 43.478 3.14 0.00 0.00 3.18
2176 2192 5.079689 ACTGGTTTGAAACGGACAAAAAT 57.920 34.783 1.53 0.00 38.63 1.82
2177 2193 5.106442 ACTGGTTTGAAACGGACAAAAATC 58.894 37.500 1.53 0.00 38.63 2.17
2179 2195 5.665459 TGGTTTGAAACGGACAAAAATCAT 58.335 33.333 1.53 0.00 38.63 2.45
2187 2203 3.320541 ACGGACAAAAATCATGGCTCAAA 59.679 39.130 0.00 0.00 0.00 2.69
2191 2207 5.280654 ACAAAAATCATGGCTCAAAGTGT 57.719 34.783 0.00 0.00 0.00 3.55
2195 2211 1.795768 TCATGGCTCAAAGTGTCGAC 58.204 50.000 9.11 9.11 0.00 4.20
2196 2212 1.069978 TCATGGCTCAAAGTGTCGACA 59.930 47.619 15.76 15.76 0.00 4.35
2197 2213 1.195448 CATGGCTCAAAGTGTCGACAC 59.805 52.381 35.83 35.83 46.77 3.67
2207 2223 0.511221 GTGTCGACACAAACGGATGG 59.489 55.000 37.16 0.00 45.75 3.51
2208 2224 0.389757 TGTCGACACAAACGGATGGA 59.610 50.000 15.76 0.00 0.00 3.41
2212 2228 1.804151 CGACACAAACGGATGGATGTT 59.196 47.619 0.00 0.00 0.00 2.71
2216 2232 3.502211 ACACAAACGGATGGATGTTCTTC 59.498 43.478 0.00 0.00 0.00 2.87
2217 2233 3.753272 CACAAACGGATGGATGTTCTTCT 59.247 43.478 0.00 0.00 0.00 2.85
2219 2235 3.981071 AACGGATGGATGTTCTTCTCA 57.019 42.857 0.00 0.00 0.00 3.27
2221 2237 3.099905 ACGGATGGATGTTCTTCTCAGA 58.900 45.455 0.00 0.00 0.00 3.27
2222 2238 3.118956 ACGGATGGATGTTCTTCTCAGAC 60.119 47.826 0.00 0.00 0.00 3.51
2223 2239 3.739519 CGGATGGATGTTCTTCTCAGACC 60.740 52.174 0.00 0.00 0.00 3.85
2225 2241 1.550524 TGGATGTTCTTCTCAGACCCG 59.449 52.381 0.00 0.00 0.00 5.28
2229 2246 3.553828 TGTTCTTCTCAGACCCGTTTT 57.446 42.857 0.00 0.00 0.00 2.43
2230 2247 3.881220 TGTTCTTCTCAGACCCGTTTTT 58.119 40.909 0.00 0.00 0.00 1.94
2232 2249 2.846193 TCTTCTCAGACCCGTTTTTGG 58.154 47.619 0.00 0.00 0.00 3.28
2235 2252 0.537371 CTCAGACCCGTTTTTGGCCT 60.537 55.000 3.32 0.00 0.00 5.19
2238 2255 1.957877 CAGACCCGTTTTTGGCCTAAA 59.042 47.619 8.37 8.37 0.00 1.85
2241 2258 3.006430 AGACCCGTTTTTGGCCTAAATTG 59.994 43.478 13.23 8.60 0.00 2.32
2253 2270 1.075979 CTAAATTGGGCCGCGTTTGC 61.076 55.000 4.92 0.21 37.91 3.68
2263 2280 4.496898 GCGTTTGCGTCAGAACTG 57.503 55.556 0.00 0.00 40.81 3.16
2298 2315 2.047179 GGGACGCACACCCTTCTC 60.047 66.667 0.00 0.00 43.65 2.87
2300 2317 2.584391 GGACGCACACCCTTCTCCT 61.584 63.158 0.00 0.00 0.00 3.69
2301 2318 1.371558 GACGCACACCCTTCTCCTT 59.628 57.895 0.00 0.00 0.00 3.36
2303 2320 1.122019 ACGCACACCCTTCTCCTTCT 61.122 55.000 0.00 0.00 0.00 2.85
2304 2321 0.390472 CGCACACCCTTCTCCTTCTC 60.390 60.000 0.00 0.00 0.00 2.87
2307 2324 0.905337 ACACCCTTCTCCTTCTCCCG 60.905 60.000 0.00 0.00 0.00 5.14
2308 2325 0.614979 CACCCTTCTCCTTCTCCCGA 60.615 60.000 0.00 0.00 0.00 5.14
2310 2327 1.331399 CCCTTCTCCTTCTCCCGACC 61.331 65.000 0.00 0.00 0.00 4.79
2312 2329 0.614979 CTTCTCCTTCTCCCGACCCA 60.615 60.000 0.00 0.00 0.00 4.51
2314 2331 1.305381 CTCCTTCTCCCGACCCACT 60.305 63.158 0.00 0.00 0.00 4.00
2316 2333 2.711922 CCTTCTCCCGACCCACTCG 61.712 68.421 0.00 0.00 42.54 4.18
2318 2335 1.935327 CTTCTCCCGACCCACTCGTC 61.935 65.000 0.00 0.00 41.18 4.20
2324 2341 4.131088 GACCCACTCGTCGGAGGC 62.131 72.222 0.00 0.00 44.93 4.70
2325 2342 4.988716 ACCCACTCGTCGGAGGCA 62.989 66.667 0.00 0.00 44.93 4.75
2326 2343 4.436998 CCCACTCGTCGGAGGCAC 62.437 72.222 0.00 0.00 44.93 5.01
2327 2344 3.680786 CCACTCGTCGGAGGCACA 61.681 66.667 0.00 0.00 44.93 4.57
2336 2354 0.389817 TCGGAGGCACAACATTCTCG 60.390 55.000 0.00 0.00 0.00 4.04
2344 2362 3.500680 GGCACAACATTCTCGTTTTCCTA 59.499 43.478 0.00 0.00 0.00 2.94
2348 2366 6.640907 GCACAACATTCTCGTTTTCCTAATTT 59.359 34.615 0.00 0.00 0.00 1.82
2353 2371 6.374613 ACATTCTCGTTTTCCTAATTTCCTCC 59.625 38.462 0.00 0.00 0.00 4.30
2372 2390 1.977009 CAAAAACCCTCCCGCCCTC 60.977 63.158 0.00 0.00 0.00 4.30
2373 2391 2.160853 AAAAACCCTCCCGCCCTCT 61.161 57.895 0.00 0.00 0.00 3.69
2397 2418 2.203773 ATGGCCACCACCCCAAAC 60.204 61.111 8.16 0.00 35.80 2.93
2398 2419 4.904590 TGGCCACCACCCCAAACG 62.905 66.667 0.00 0.00 0.00 3.60
2399 2420 4.906537 GGCCACCACCCCAAACGT 62.907 66.667 0.00 0.00 0.00 3.99
2400 2421 3.292159 GCCACCACCCCAAACGTC 61.292 66.667 0.00 0.00 0.00 4.34
2401 2422 2.975799 CCACCACCCCAAACGTCG 60.976 66.667 0.00 0.00 0.00 5.12
2402 2423 3.656045 CACCACCCCAAACGTCGC 61.656 66.667 0.00 0.00 0.00 5.19
2403 2424 4.941309 ACCACCCCAAACGTCGCC 62.941 66.667 0.00 0.00 0.00 5.54
2407 2428 4.745751 CCCCAAACGTCGCCGCTA 62.746 66.667 0.00 0.00 37.70 4.26
2408 2429 3.484547 CCCAAACGTCGCCGCTAC 61.485 66.667 0.00 0.00 37.70 3.58
2409 2430 3.484547 CCAAACGTCGCCGCTACC 61.485 66.667 0.00 0.00 37.70 3.18
2410 2431 3.834373 CAAACGTCGCCGCTACCG 61.834 66.667 0.00 0.00 37.70 4.02
2422 2443 3.479203 CTACCGCCATCCCAGCCA 61.479 66.667 0.00 0.00 0.00 4.75
2429 2450 3.716195 CATCCCAGCCACCACCGA 61.716 66.667 0.00 0.00 0.00 4.69
2449 2470 3.781307 CCAATCCCGTGGCCTCGA 61.781 66.667 27.84 9.95 0.00 4.04
2450 2471 2.267642 CAATCCCGTGGCCTCGAA 59.732 61.111 27.84 15.69 0.00 3.71
2464 2485 2.550208 GCCTCGAAGAAGAAGAAACCCA 60.550 50.000 0.00 0.00 34.09 4.51
2470 2491 5.057149 CGAAGAAGAAGAAACCCAAGAAGA 58.943 41.667 0.00 0.00 0.00 2.87
2479 2500 0.687354 ACCCAAGAAGATGCTCACGT 59.313 50.000 0.00 0.00 0.00 4.49
2481 2502 1.338105 CCCAAGAAGATGCTCACGTCA 60.338 52.381 0.00 0.00 33.96 4.35
2484 2505 0.457509 AGAAGATGCTCACGTCAGCG 60.458 55.000 7.02 0.00 42.92 5.18
2487 2508 2.796425 GATGCTCACGTCAGCGCAG 61.796 63.158 11.47 0.00 42.92 5.18
2536 2557 2.908940 GGAGGGCCATTGATGCGG 60.909 66.667 6.18 0.00 0.00 5.69
2539 2560 2.192979 GGGCCATTGATGCGGAGA 59.807 61.111 4.39 0.00 0.00 3.71
2546 2567 1.134280 CATTGATGCGGAGAGGAAGGT 60.134 52.381 0.00 0.00 0.00 3.50
2549 2570 1.668101 GATGCGGAGAGGAAGGTCGT 61.668 60.000 0.00 0.00 0.00 4.34
2550 2571 1.668101 ATGCGGAGAGGAAGGTCGTC 61.668 60.000 0.00 0.00 0.00 4.20
2606 2628 1.609208 AGGCCGCCATTGATGATAAC 58.391 50.000 13.15 0.00 0.00 1.89
2629 2652 4.680237 CCTCGTCGCAAGGCCACA 62.680 66.667 5.01 0.00 40.39 4.17
2630 2653 2.434884 CTCGTCGCAAGGCCACAT 60.435 61.111 5.01 0.00 40.39 3.21
2633 2656 1.153647 CGTCGCAAGGCCACATAGA 60.154 57.895 5.01 0.00 40.39 1.98
2640 2663 0.108138 AAGGCCACATAGACAGCGAC 60.108 55.000 5.01 0.00 0.00 5.19
2641 2664 1.218047 GGCCACATAGACAGCGACA 59.782 57.895 0.00 0.00 0.00 4.35
2644 2667 1.350193 CCACATAGACAGCGACACAC 58.650 55.000 0.00 0.00 0.00 3.82
2645 2668 1.336795 CCACATAGACAGCGACACACA 60.337 52.381 0.00 0.00 0.00 3.72
2657 2680 0.678048 GACACACAATGCCCTCCTCC 60.678 60.000 0.00 0.00 0.00 4.30
2665 2688 3.555324 GCCCTCCTCCTGCTAGGC 61.555 72.222 0.00 0.00 36.51 3.93
2673 2696 0.615331 CTCCTGCTAGGCTTCAACCA 59.385 55.000 0.00 0.00 34.61 3.67
2679 2702 1.534729 CTAGGCTTCAACCAACCCAC 58.465 55.000 0.00 0.00 0.00 4.61
2680 2703 0.847373 TAGGCTTCAACCAACCCACA 59.153 50.000 0.00 0.00 0.00 4.17
2684 2707 0.464735 CTTCAACCAACCCACACCGA 60.465 55.000 0.00 0.00 0.00 4.69
2690 2713 0.037017 CCAACCCACACCGACCATTA 59.963 55.000 0.00 0.00 0.00 1.90
2691 2714 1.161843 CAACCCACACCGACCATTAC 58.838 55.000 0.00 0.00 0.00 1.89
2692 2715 0.037160 AACCCACACCGACCATTACC 59.963 55.000 0.00 0.00 0.00 2.85
2693 2716 1.448893 CCCACACCGACCATTACCG 60.449 63.158 0.00 0.00 0.00 4.02
2694 2717 2.104253 CCACACCGACCATTACCGC 61.104 63.158 0.00 0.00 0.00 5.68
2695 2718 1.079405 CACACCGACCATTACCGCT 60.079 57.895 0.00 0.00 0.00 5.52
2696 2719 1.079405 ACACCGACCATTACCGCTG 60.079 57.895 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 6.038714 GGATATGAAAAATGGAGCTCGACTTT 59.961 38.462 7.83 3.10 0.00 2.66
50 51 5.611374 ACACTCCCTATTTTGTCGGATATG 58.389 41.667 0.00 0.00 0.00 1.78
179 180 5.741982 GTGTGTGCTTAAGAAAAATGAACGT 59.258 36.000 6.67 0.00 0.00 3.99
185 186 7.759489 TCTATGGTGTGTGCTTAAGAAAAAT 57.241 32.000 6.67 0.00 0.00 1.82
266 267 8.526978 GGATCTTCTTTTTAGCTTCATCCTTTT 58.473 33.333 0.00 0.00 0.00 2.27
362 366 1.625511 ATAATCCCGGACGGAGGTAC 58.374 55.000 13.13 0.00 46.60 3.34
364 368 2.245582 CTAATAATCCCGGACGGAGGT 58.754 52.381 13.13 0.00 46.60 3.85
366 370 1.067071 GCCTAATAATCCCGGACGGAG 60.067 57.143 13.13 2.58 46.60 4.63
368 372 0.036671 GGCCTAATAATCCCGGACGG 60.037 60.000 0.73 3.25 0.00 4.79
369 373 0.036671 GGGCCTAATAATCCCGGACG 60.037 60.000 0.73 0.00 0.00 4.79
370 374 0.327259 GGGGCCTAATAATCCCGGAC 59.673 60.000 0.73 0.00 40.97 4.79
371 375 0.195096 AGGGGCCTAATAATCCCGGA 59.805 55.000 0.73 0.00 43.92 5.14
372 376 1.004394 GAAGGGGCCTAATAATCCCGG 59.996 57.143 0.84 0.00 43.92 5.73
373 377 1.985895 AGAAGGGGCCTAATAATCCCG 59.014 52.381 0.84 0.00 43.92 5.14
374 378 5.798239 AATAGAAGGGGCCTAATAATCCC 57.202 43.478 0.84 0.00 39.67 3.85
375 379 6.437477 CCAAAATAGAAGGGGCCTAATAATCC 59.563 42.308 0.84 0.00 0.00 3.01
376 380 7.238710 TCCAAAATAGAAGGGGCCTAATAATC 58.761 38.462 0.84 0.00 0.00 1.75
377 381 7.174363 TCCAAAATAGAAGGGGCCTAATAAT 57.826 36.000 0.84 0.00 0.00 1.28
378 382 6.599986 TCCAAAATAGAAGGGGCCTAATAA 57.400 37.500 0.84 0.00 0.00 1.40
379 383 6.796867 ATCCAAAATAGAAGGGGCCTAATA 57.203 37.500 0.84 0.00 0.00 0.98
380 384 5.686535 ATCCAAAATAGAAGGGGCCTAAT 57.313 39.130 0.84 0.00 0.00 1.73
381 385 5.043732 TCAATCCAAAATAGAAGGGGCCTAA 60.044 40.000 0.84 0.00 0.00 2.69
382 386 4.480537 TCAATCCAAAATAGAAGGGGCCTA 59.519 41.667 0.84 0.00 0.00 3.93
383 387 3.272020 TCAATCCAAAATAGAAGGGGCCT 59.728 43.478 0.84 0.00 0.00 5.19
384 388 3.642141 TCAATCCAAAATAGAAGGGGCC 58.358 45.455 0.00 0.00 0.00 5.80
385 389 4.711846 ACTTCAATCCAAAATAGAAGGGGC 59.288 41.667 0.00 0.00 39.87 5.80
386 390 6.857437 AACTTCAATCCAAAATAGAAGGGG 57.143 37.500 0.00 0.00 39.87 4.79
387 391 9.639601 GTTAAACTTCAATCCAAAATAGAAGGG 57.360 33.333 0.00 0.00 39.87 3.95
388 392 9.639601 GGTTAAACTTCAATCCAAAATAGAAGG 57.360 33.333 0.00 0.00 39.87 3.46
395 399 9.898152 AATCTTTGGTTAAACTTCAATCCAAAA 57.102 25.926 8.21 2.01 41.96 2.44
396 400 9.898152 AAATCTTTGGTTAAACTTCAATCCAAA 57.102 25.926 0.00 0.00 40.88 3.28
441 445 9.549078 TCGGCAGTATAATTTTTGTGACATATA 57.451 29.630 0.00 0.00 0.00 0.86
442 446 8.445275 TCGGCAGTATAATTTTTGTGACATAT 57.555 30.769 0.00 0.00 0.00 1.78
443 447 7.851387 TCGGCAGTATAATTTTTGTGACATA 57.149 32.000 0.00 0.00 0.00 2.29
444 448 6.751514 TCGGCAGTATAATTTTTGTGACAT 57.248 33.333 0.00 0.00 0.00 3.06
445 449 6.561737 TTCGGCAGTATAATTTTTGTGACA 57.438 33.333 0.00 0.00 0.00 3.58
446 450 7.148869 GGTTTTCGGCAGTATAATTTTTGTGAC 60.149 37.037 0.00 0.00 0.00 3.67
447 451 6.864165 GGTTTTCGGCAGTATAATTTTTGTGA 59.136 34.615 0.00 0.00 0.00 3.58
448 452 6.866248 AGGTTTTCGGCAGTATAATTTTTGTG 59.134 34.615 0.00 0.00 0.00 3.33
449 453 6.988522 AGGTTTTCGGCAGTATAATTTTTGT 58.011 32.000 0.00 0.00 0.00 2.83
450 454 7.312899 AGAGGTTTTCGGCAGTATAATTTTTG 58.687 34.615 0.00 0.00 0.00 2.44
451 455 7.462571 AGAGGTTTTCGGCAGTATAATTTTT 57.537 32.000 0.00 0.00 0.00 1.94
452 456 7.462571 AAGAGGTTTTCGGCAGTATAATTTT 57.537 32.000 0.00 0.00 0.00 1.82
453 457 7.462571 AAAGAGGTTTTCGGCAGTATAATTT 57.537 32.000 0.00 0.00 0.00 1.82
454 458 6.183360 CGAAAGAGGTTTTCGGCAGTATAATT 60.183 38.462 12.72 0.00 45.17 1.40
455 459 5.293569 CGAAAGAGGTTTTCGGCAGTATAAT 59.706 40.000 12.72 0.00 45.17 1.28
456 460 4.628333 CGAAAGAGGTTTTCGGCAGTATAA 59.372 41.667 12.72 0.00 45.17 0.98
457 461 4.178540 CGAAAGAGGTTTTCGGCAGTATA 58.821 43.478 12.72 0.00 45.17 1.47
458 462 3.000727 CGAAAGAGGTTTTCGGCAGTAT 58.999 45.455 12.72 0.00 45.17 2.12
459 463 2.409975 CGAAAGAGGTTTTCGGCAGTA 58.590 47.619 12.72 0.00 45.17 2.74
460 464 1.226746 CGAAAGAGGTTTTCGGCAGT 58.773 50.000 12.72 0.00 45.17 4.40
466 470 9.458374 TTTGATTTGTATTCGAAAGAGGTTTTC 57.542 29.630 0.00 0.00 43.69 2.29
467 471 9.810545 TTTTGATTTGTATTCGAAAGAGGTTTT 57.189 25.926 0.00 0.00 43.69 2.43
468 472 9.810545 TTTTTGATTTGTATTCGAAAGAGGTTT 57.189 25.926 0.00 0.00 43.69 3.27
544 548 6.017440 CCCTCGTATTTTGAGTCAAAGTTTGA 60.017 38.462 17.50 14.35 34.72 2.69
545 549 6.142817 CCCTCGTATTTTGAGTCAAAGTTTG 58.857 40.000 17.50 9.44 34.72 2.93
546 550 5.240844 CCCCTCGTATTTTGAGTCAAAGTTT 59.759 40.000 17.50 10.06 34.72 2.66
547 551 4.760204 CCCCTCGTATTTTGAGTCAAAGTT 59.240 41.667 17.50 12.22 34.72 2.66
548 552 4.324267 CCCCTCGTATTTTGAGTCAAAGT 58.676 43.478 17.36 16.99 34.72 2.66
549 553 3.689649 CCCCCTCGTATTTTGAGTCAAAG 59.310 47.826 17.36 7.24 34.72 2.77
550 554 3.681593 CCCCCTCGTATTTTGAGTCAAA 58.318 45.455 14.35 14.35 0.00 2.69
551 555 3.343941 CCCCCTCGTATTTTGAGTCAA 57.656 47.619 0.08 0.08 0.00 3.18
568 572 0.179009 GTCCGGGTTTATTAGCCCCC 60.179 60.000 0.00 0.00 41.58 5.40
569 573 0.533531 CGTCCGGGTTTATTAGCCCC 60.534 60.000 0.00 0.00 41.58 5.80
570 574 0.533531 CCGTCCGGGTTTATTAGCCC 60.534 60.000 0.00 0.00 41.58 5.19
571 575 0.465287 TCCGTCCGGGTTTATTAGCC 59.535 55.000 0.00 0.00 41.19 3.93
572 576 1.539712 CCTCCGTCCGGGTTTATTAGC 60.540 57.143 0.00 0.00 37.00 3.09
573 577 1.069668 CCCTCCGTCCGGGTTTATTAG 59.930 57.143 0.00 0.00 36.91 1.73
574 578 1.122227 CCCTCCGTCCGGGTTTATTA 58.878 55.000 0.00 0.00 36.91 0.98
575 579 0.618393 TCCCTCCGTCCGGGTTTATT 60.618 55.000 0.00 0.00 42.56 1.40
576 580 1.002017 TCCCTCCGTCCGGGTTTAT 59.998 57.895 0.00 0.00 42.56 1.40
577 581 1.683365 CTCCCTCCGTCCGGGTTTA 60.683 63.158 0.00 0.00 42.56 2.01
578 582 2.445492 TACTCCCTCCGTCCGGGTTT 62.445 60.000 0.00 0.00 42.56 3.27
579 583 2.234246 ATACTCCCTCCGTCCGGGTT 62.234 60.000 0.00 0.00 42.56 4.11
580 584 2.698075 ATACTCCCTCCGTCCGGGT 61.698 63.158 0.00 0.00 42.56 5.28
581 585 2.197875 ATACTCCCTCCGTCCGGG 59.802 66.667 0.00 0.00 43.38 5.73
582 586 1.152819 TCATACTCCCTCCGTCCGG 60.153 63.158 0.00 0.00 0.00 5.14
583 587 1.797211 GCTCATACTCCCTCCGTCCG 61.797 65.000 0.00 0.00 0.00 4.79
584 588 0.468400 AGCTCATACTCCCTCCGTCC 60.468 60.000 0.00 0.00 0.00 4.79
585 589 2.156098 CTAGCTCATACTCCCTCCGTC 58.844 57.143 0.00 0.00 0.00 4.79
586 590 1.820090 GCTAGCTCATACTCCCTCCGT 60.820 57.143 7.70 0.00 0.00 4.69
587 591 0.885196 GCTAGCTCATACTCCCTCCG 59.115 60.000 7.70 0.00 0.00 4.63
588 592 1.262417 GGCTAGCTCATACTCCCTCC 58.738 60.000 15.72 0.00 0.00 4.30
589 593 2.002505 TGGCTAGCTCATACTCCCTC 57.997 55.000 15.72 0.00 0.00 4.30
590 594 2.091055 TCTTGGCTAGCTCATACTCCCT 60.091 50.000 15.72 0.00 0.00 4.20
591 595 2.036604 GTCTTGGCTAGCTCATACTCCC 59.963 54.545 15.72 0.00 0.00 4.30
592 596 2.695666 TGTCTTGGCTAGCTCATACTCC 59.304 50.000 15.72 0.00 0.00 3.85
593 597 4.038522 TCATGTCTTGGCTAGCTCATACTC 59.961 45.833 15.72 0.00 0.00 2.59
613 617 6.698380 AGAGCAAATTTTCTGCAGAATTCAT 58.302 32.000 28.89 17.93 42.48 2.57
1102 1117 1.477685 AAGGAGCGGGAAAGGACGAA 61.478 55.000 0.00 0.00 0.00 3.85
1191 1206 3.701604 GACGAAGATGGAGCGCGGT 62.702 63.158 12.23 12.23 0.00 5.68
1264 1279 1.691434 GTAGGAGGCAGAGGAAGATGG 59.309 57.143 0.00 0.00 0.00 3.51
1266 1281 1.292242 TGGTAGGAGGCAGAGGAAGAT 59.708 52.381 0.00 0.00 0.00 2.40
1428 1443 1.182667 TTTTCTCCGATCTGCTCCGA 58.817 50.000 0.00 0.00 0.00 4.55
1437 1452 1.887707 GCCGCCGATTTTCTCCGAT 60.888 57.895 0.00 0.00 0.00 4.18
1454 1469 3.051392 CTCCCGCCATGTTTTCCGC 62.051 63.158 0.00 0.00 0.00 5.54
1461 1476 2.765807 CTCCTCCTCCCGCCATGT 60.766 66.667 0.00 0.00 0.00 3.21
1636 1651 0.896940 ACAAAGGACTCCTCGCGGTA 60.897 55.000 6.13 0.00 30.89 4.02
1922 1937 6.534079 CGACGGAGGTCTAAAATTGAGTAATT 59.466 38.462 0.00 0.00 41.16 1.40
2036 2051 9.682465 AGTAATTCGACTCCTGTATATAGCATA 57.318 33.333 0.00 0.00 0.00 3.14
2037 2052 8.582657 AGTAATTCGACTCCTGTATATAGCAT 57.417 34.615 0.00 0.00 0.00 3.79
2038 2053 7.997773 AGTAATTCGACTCCTGTATATAGCA 57.002 36.000 0.00 0.00 0.00 3.49
2039 2054 7.969508 GGAAGTAATTCGACTCCTGTATATAGC 59.030 40.741 0.00 0.00 0.00 2.97
2040 2055 8.460428 GGGAAGTAATTCGACTCCTGTATATAG 58.540 40.741 0.00 0.00 0.00 1.31
2041 2056 7.120285 CGGGAAGTAATTCGACTCCTGTATATA 59.880 40.741 0.00 0.00 0.00 0.86
2042 2057 6.072064 CGGGAAGTAATTCGACTCCTGTATAT 60.072 42.308 0.00 0.00 0.00 0.86
2049 2064 1.568606 GCGGGAAGTAATTCGACTCC 58.431 55.000 0.00 0.00 0.00 3.85
2068 2083 6.086241 GTGGCAACGATAATATGCATTTTACG 59.914 38.462 3.54 15.20 41.80 3.18
2094 2109 1.226101 CATTCGGTGTGTCATGCGC 60.226 57.895 0.00 0.00 0.00 6.09
2102 2117 0.586319 AGTTTGACGCATTCGGTGTG 59.414 50.000 0.00 1.55 41.19 3.82
2103 2118 0.865769 GAGTTTGACGCATTCGGTGT 59.134 50.000 0.00 0.00 44.56 4.16
2107 2122 1.721489 CGTTGGAGTTTGACGCATTCG 60.721 52.381 0.00 0.00 42.43 3.34
2108 2123 1.950472 CGTTGGAGTTTGACGCATTC 58.050 50.000 0.00 0.00 0.00 2.67
2113 2128 1.083657 CACGCGTTGGAGTTTGACG 60.084 57.895 10.22 0.00 39.61 4.35
2115 2130 1.155424 GGTCACGCGTTGGAGTTTGA 61.155 55.000 10.22 0.00 0.00 2.69
2117 2132 2.241880 CGGTCACGCGTTGGAGTTT 61.242 57.895 10.22 0.00 0.00 2.66
2131 2146 0.386731 CAAACGGACCAAATGCGGTC 60.387 55.000 5.41 5.41 43.88 4.79
2140 2155 0.831966 ACCAGTACACAAACGGACCA 59.168 50.000 0.00 0.00 0.00 4.02
2142 2157 2.937799 TCAAACCAGTACACAAACGGAC 59.062 45.455 0.00 0.00 0.00 4.79
2143 2158 3.263489 TCAAACCAGTACACAAACGGA 57.737 42.857 0.00 0.00 0.00 4.69
2144 2159 4.099824 GTTTCAAACCAGTACACAAACGG 58.900 43.478 0.00 0.00 0.00 4.44
2145 2160 3.781846 CGTTTCAAACCAGTACACAAACG 59.218 43.478 0.00 0.00 38.81 3.60
2146 2161 4.099824 CCGTTTCAAACCAGTACACAAAC 58.900 43.478 0.00 0.00 0.00 2.93
2148 2163 3.374678 GTCCGTTTCAAACCAGTACACAA 59.625 43.478 0.00 0.00 0.00 3.33
2152 2167 4.619437 TTTGTCCGTTTCAAACCAGTAC 57.381 40.909 0.00 0.00 31.17 2.73
2153 2168 5.640189 TTTTTGTCCGTTTCAAACCAGTA 57.360 34.783 0.00 0.00 35.05 2.74
2154 2169 4.522722 TTTTTGTCCGTTTCAAACCAGT 57.477 36.364 0.00 0.00 35.05 4.00
2155 2170 5.105752 TGATTTTTGTCCGTTTCAAACCAG 58.894 37.500 0.00 0.00 35.05 4.00
2161 2177 3.320541 AGCCATGATTTTTGTCCGTTTCA 59.679 39.130 0.00 0.00 0.00 2.69
2168 2184 5.291971 ACACTTTGAGCCATGATTTTTGTC 58.708 37.500 0.00 0.00 0.00 3.18
2172 2188 3.820467 TCGACACTTTGAGCCATGATTTT 59.180 39.130 0.00 0.00 0.00 1.82
2176 2192 1.069978 TGTCGACACTTTGAGCCATGA 59.930 47.619 15.76 0.00 0.00 3.07
2177 2193 1.195448 GTGTCGACACTTTGAGCCATG 59.805 52.381 35.51 0.00 43.25 3.66
2179 2195 0.176910 TGTGTCGACACTTTGAGCCA 59.823 50.000 39.62 20.85 46.55 4.75
2187 2203 1.497991 CATCCGTTTGTGTCGACACT 58.502 50.000 39.62 21.49 46.55 3.55
2191 2207 1.001520 ACATCCATCCGTTTGTGTCGA 59.998 47.619 0.00 0.00 0.00 4.20
2195 2211 3.753272 AGAAGAACATCCATCCGTTTGTG 59.247 43.478 0.00 0.00 0.00 3.33
2196 2212 4.003648 GAGAAGAACATCCATCCGTTTGT 58.996 43.478 0.00 0.00 0.00 2.83
2197 2213 4.002982 TGAGAAGAACATCCATCCGTTTG 58.997 43.478 0.00 0.00 0.00 2.93
2201 2217 3.452474 GTCTGAGAAGAACATCCATCCG 58.548 50.000 0.00 0.00 0.00 4.18
2207 2223 3.320673 AACGGGTCTGAGAAGAACATC 57.679 47.619 0.00 0.00 0.00 3.06
2208 2224 3.771577 AAACGGGTCTGAGAAGAACAT 57.228 42.857 0.00 0.00 0.00 2.71
2212 2228 2.846193 CCAAAAACGGGTCTGAGAAGA 58.154 47.619 0.00 0.00 0.00 2.87
2216 2232 0.537371 AGGCCAAAAACGGGTCTGAG 60.537 55.000 5.01 0.00 39.36 3.35
2217 2233 0.766131 TAGGCCAAAAACGGGTCTGA 59.234 50.000 5.01 0.00 41.37 3.27
2219 2235 2.368311 TTTAGGCCAAAAACGGGTCT 57.632 45.000 5.01 0.00 44.13 3.85
2221 2237 2.037902 CCAATTTAGGCCAAAAACGGGT 59.962 45.455 5.01 0.00 0.00 5.28
2222 2238 2.614229 CCCAATTTAGGCCAAAAACGGG 60.614 50.000 18.27 18.27 31.37 5.28
2223 2239 2.694213 CCCAATTTAGGCCAAAAACGG 58.306 47.619 5.01 9.38 0.00 4.44
2235 2252 1.080434 GCAAACGCGGCCCAATTTA 60.080 52.632 12.47 0.00 0.00 1.40
2253 2270 0.861837 GCACCTTGTCAGTTCTGACG 59.138 55.000 22.40 13.77 41.43 4.35
2257 2274 0.468226 TTCCGCACCTTGTCAGTTCT 59.532 50.000 0.00 0.00 0.00 3.01
2258 2275 0.868406 CTTCCGCACCTTGTCAGTTC 59.132 55.000 0.00 0.00 0.00 3.01
2262 2279 2.664851 CGCTTCCGCACCTTGTCA 60.665 61.111 0.00 0.00 35.30 3.58
2292 2309 1.331399 GGGTCGGGAGAAGGAGAAGG 61.331 65.000 0.00 0.00 42.89 3.46
2296 2313 1.305381 AGTGGGTCGGGAGAAGGAG 60.305 63.158 0.00 0.00 42.89 3.69
2297 2314 1.305046 GAGTGGGTCGGGAGAAGGA 60.305 63.158 0.00 0.00 42.89 3.36
2298 2315 2.711922 CGAGTGGGTCGGGAGAAGG 61.712 68.421 0.00 0.00 45.58 3.46
2307 2324 4.131088 GCCTCCGACGAGTGGGTC 62.131 72.222 0.00 0.00 33.93 4.46
2308 2325 4.988716 TGCCTCCGACGAGTGGGT 62.989 66.667 0.00 0.00 33.93 4.51
2310 2327 3.220999 TTGTGCCTCCGACGAGTGG 62.221 63.158 0.00 0.00 33.93 4.00
2312 2329 1.816863 ATGTTGTGCCTCCGACGAGT 61.817 55.000 0.00 0.00 33.93 4.18
2314 2331 0.669318 GAATGTTGTGCCTCCGACGA 60.669 55.000 0.00 0.00 0.00 4.20
2316 2333 1.079503 GAGAATGTTGTGCCTCCGAC 58.920 55.000 0.00 0.00 0.00 4.79
2318 2335 0.670546 ACGAGAATGTTGTGCCTCCG 60.671 55.000 0.00 0.00 0.00 4.63
2319 2336 1.523758 AACGAGAATGTTGTGCCTCC 58.476 50.000 0.00 0.00 0.00 4.30
2320 2337 3.555518 GAAAACGAGAATGTTGTGCCTC 58.444 45.455 0.00 0.00 31.10 4.70
2321 2338 2.293399 GGAAAACGAGAATGTTGTGCCT 59.707 45.455 0.00 0.00 31.10 4.75
2324 2341 7.326063 GGAAATTAGGAAAACGAGAATGTTGTG 59.674 37.037 0.00 0.00 31.10 3.33
2325 2342 7.230712 AGGAAATTAGGAAAACGAGAATGTTGT 59.769 33.333 0.00 0.00 31.10 3.32
2326 2343 7.593825 AGGAAATTAGGAAAACGAGAATGTTG 58.406 34.615 0.00 0.00 31.10 3.33
2327 2344 7.094334 GGAGGAAATTAGGAAAACGAGAATGTT 60.094 37.037 0.00 0.00 0.00 2.71
2336 2354 6.708949 GGTTTTTGGGAGGAAATTAGGAAAAC 59.291 38.462 0.00 0.00 35.10 2.43
2344 2362 3.248024 GGAGGGTTTTTGGGAGGAAATT 58.752 45.455 0.00 0.00 0.00 1.82
2348 2366 1.785353 CGGGAGGGTTTTTGGGAGGA 61.785 60.000 0.00 0.00 0.00 3.71
2353 2371 2.994995 GGGCGGGAGGGTTTTTGG 60.995 66.667 0.00 0.00 0.00 3.28
2372 2390 4.051167 TGGTGGCCATGGCAGGAG 62.051 66.667 36.56 0.00 44.11 3.69
2373 2391 4.365111 GTGGTGGCCATGGCAGGA 62.365 66.667 36.56 18.07 44.11 3.86
2402 2423 4.609018 CTGGGATGGCGGTAGCGG 62.609 72.222 17.08 0.00 46.35 5.52
2404 2425 4.937431 GGCTGGGATGGCGGTAGC 62.937 72.222 0.00 0.00 44.18 3.58
2405 2426 3.479203 TGGCTGGGATGGCGGTAG 61.479 66.667 0.00 0.00 35.06 3.18
2406 2427 3.792736 GTGGCTGGGATGGCGGTA 61.793 66.667 0.00 0.00 35.06 4.02
2411 2432 4.802051 CGGTGGTGGCTGGGATGG 62.802 72.222 0.00 0.00 0.00 3.51
2412 2433 3.716195 TCGGTGGTGGCTGGGATG 61.716 66.667 0.00 0.00 0.00 3.51
2413 2434 3.717294 GTCGGTGGTGGCTGGGAT 61.717 66.667 0.00 0.00 0.00 3.85
2422 2443 4.404098 GGGATTGGCGTCGGTGGT 62.404 66.667 0.00 0.00 0.00 4.16
2424 2445 4.752879 ACGGGATTGGCGTCGGTG 62.753 66.667 0.00 0.00 0.00 4.94
2434 2455 1.550130 TTCTTCGAGGCCACGGGATT 61.550 55.000 22.65 0.00 0.00 3.01
2435 2456 1.961180 CTTCTTCGAGGCCACGGGAT 61.961 60.000 22.65 0.00 0.00 3.85
2436 2457 2.602267 TTCTTCGAGGCCACGGGA 60.602 61.111 22.65 17.06 0.00 5.14
2446 2467 4.682778 TCTTGGGTTTCTTCTTCTTCGA 57.317 40.909 0.00 0.00 0.00 3.71
2448 2469 6.569418 GCATCTTCTTGGGTTTCTTCTTCTTC 60.569 42.308 0.00 0.00 0.00 2.87
2449 2470 5.242615 GCATCTTCTTGGGTTTCTTCTTCTT 59.757 40.000 0.00 0.00 0.00 2.52
2450 2471 4.764308 GCATCTTCTTGGGTTTCTTCTTCT 59.236 41.667 0.00 0.00 0.00 2.85
2464 2485 1.719600 GCTGACGTGAGCATCTTCTT 58.280 50.000 22.59 0.00 38.95 2.52
2470 2491 2.812609 CTGCGCTGACGTGAGCAT 60.813 61.111 26.39 0.00 41.49 3.79
2484 2505 1.301677 CCTTTTCTCGGGTGAGCTGC 61.302 60.000 0.00 0.00 42.26 5.25
2487 2508 2.391389 CGCCTTTTCTCGGGTGAGC 61.391 63.158 0.00 0.00 42.26 4.26
2491 2512 0.037232 CTCTTCGCCTTTTCTCGGGT 60.037 55.000 0.00 0.00 0.00 5.28
2525 2546 1.590932 CTTCCTCTCCGCATCAATGG 58.409 55.000 0.00 0.00 0.00 3.16
2527 2548 1.139853 GACCTTCCTCTCCGCATCAAT 59.860 52.381 0.00 0.00 0.00 2.57
2531 2552 1.668101 GACGACCTTCCTCTCCGCAT 61.668 60.000 0.00 0.00 0.00 4.73
2536 2557 2.490685 GGCGACGACCTTCCTCTC 59.509 66.667 0.00 0.00 0.00 3.20
2539 2560 3.382832 CTGGGCGACGACCTTCCT 61.383 66.667 22.84 0.00 0.00 3.36
2592 2614 1.537202 GGCCTCGTTATCATCAATGGC 59.463 52.381 0.00 0.00 38.49 4.40
2595 2617 3.409026 GAGGGCCTCGTTATCATCAAT 57.591 47.619 19.53 0.00 0.00 2.57
2629 2652 2.002586 GCATTGTGTGTCGCTGTCTAT 58.997 47.619 0.00 0.00 0.00 1.98
2630 2653 1.428448 GCATTGTGTGTCGCTGTCTA 58.572 50.000 0.00 0.00 0.00 2.59
2633 2656 2.260869 GGGCATTGTGTGTCGCTGT 61.261 57.895 0.00 0.00 31.51 4.40
2640 2663 0.679002 CAGGAGGAGGGCATTGTGTG 60.679 60.000 0.00 0.00 0.00 3.82
2641 2664 1.687612 CAGGAGGAGGGCATTGTGT 59.312 57.895 0.00 0.00 0.00 3.72
2644 2667 0.108207 CTAGCAGGAGGAGGGCATTG 59.892 60.000 0.00 0.00 0.00 2.82
2645 2668 1.059006 CCTAGCAGGAGGAGGGCATT 61.059 60.000 0.00 0.00 37.67 3.56
2657 2680 1.168714 GGTTGGTTGAAGCCTAGCAG 58.831 55.000 0.00 0.00 33.25 4.24
2665 2688 0.464735 TCGGTGTGGGTTGGTTGAAG 60.465 55.000 0.00 0.00 0.00 3.02
2673 2696 0.037160 GGTAATGGTCGGTGTGGGTT 59.963 55.000 0.00 0.00 0.00 4.11
2679 2702 3.794270 CAGCGGTAATGGTCGGTG 58.206 61.111 0.00 0.00 45.78 4.94
2680 2703 2.125269 GCAGCGGTAATGGTCGGT 60.125 61.111 0.00 0.00 37.61 4.69


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

AutoCloner maintained by Alex Coulton.