Multiple sequence alignment - TraesCS7D01G433700

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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 TraesCS7D01G433700 chr7D 100.000 5645 0 0 1 5645 553819640 553813996 0.000000e+00 10425
1 TraesCS7D01G433700 chr7D 91.599 369 13 12 5249 5615 555189206 555188854 1.410000e-135 494
2 TraesCS7D01G433700 chr7D 90.129 233 11 7 5295 5527 555192485 555192265 5.530000e-75 292
3 TraesCS7D01G433700 chr7B 93.450 2458 130 14 2304 4740 600990692 600993139 0.000000e+00 3618
4 TraesCS7D01G433700 chr7B 86.031 2348 176 56 2 2293 600988162 600990413 0.000000e+00 2379
5 TraesCS7D01G433700 chr7B 89.723 253 10 9 5295 5547 600995269 600995505 5.490000e-80 309
6 TraesCS7D01G433700 chr7B 82.548 361 34 16 4789 5124 600993150 600993506 1.990000e-74 291
7 TraesCS7D01G433700 chr7B 88.841 233 11 8 5295 5527 601118787 601119004 7.210000e-69 272
8 TraesCS7D01G433700 chr7A 93.324 2142 109 18 2311 4432 640578314 640580441 0.000000e+00 3133
9 TraesCS7D01G433700 chr7A 87.675 2069 146 50 254 2293 640576219 640578207 0.000000e+00 2307
10 TraesCS7D01G433700 chr7A 92.135 534 25 5 5014 5547 640597630 640598146 0.000000e+00 737
11 TraesCS7D01G433700 chr7A 88.380 611 43 15 4475 5063 640580439 640581043 0.000000e+00 710
12 TraesCS7D01G433700 chr7A 90.909 264 15 4 2 265 640570634 640570888 4.190000e-91 346
13 TraesCS7D01G433700 chr7A 85.755 351 9 21 5217 5542 640581452 640581786 3.260000e-87 333
14 TraesCS7D01G433700 chr7A 88.546 227 11 8 5301 5527 640666558 640666769 1.560000e-65 261
15 TraesCS7D01G433700 chr2B 87.270 597 52 17 935 1517 49265971 49265385 0.000000e+00 660
16 TraesCS7D01G433700 chr2B 90.291 103 7 3 3236 3336 600931745 600931846 1.280000e-26 132
17 TraesCS7D01G433700 chr6B 90.826 109 9 1 3228 3335 705233415 705233523 1.640000e-30 145
18 TraesCS7D01G433700 chr6B 89.908 109 10 1 3228 3335 705215918 705216026 7.630000e-29 139


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 TraesCS7D01G433700 chr7D 553813996 553819640 5644 True 10425.00 10425 100.0000 1 5645 1 chr7D.!!$R1 5644
1 TraesCS7D01G433700 chr7D 555188854 555192485 3631 True 393.00 494 90.8640 5249 5615 2 chr7D.!!$R2 366
2 TraesCS7D01G433700 chr7B 600988162 600995505 7343 False 1649.25 3618 87.9380 2 5547 4 chr7B.!!$F2 5545
3 TraesCS7D01G433700 chr7A 640576219 640581786 5567 False 1620.75 3133 88.7835 254 5542 4 chr7A.!!$F4 5288
4 TraesCS7D01G433700 chr7A 640597630 640598146 516 False 737.00 737 92.1350 5014 5547 1 chr7A.!!$F2 533
5 TraesCS7D01G433700 chr2B 49265385 49265971 586 True 660.00 660 87.2700 935 1517 1 chr2B.!!$R1 582

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
699 715 0.032540 CAACAGCCTTTTCTGCACCC 59.967 55.0 0.00 0.0 37.59 4.61 F
2295 2373 0.321919 TGAAGCACACATCCAGCCTC 60.322 55.0 0.00 0.0 0.00 4.70 F
3096 3462 0.034767 TGCCCATCAAGCAGAAGGAG 60.035 55.0 2.44 0.0 37.28 3.69 F
4226 4598 0.174389 GCAGGCGAAGATGAGACTGA 59.826 55.0 2.07 0.0 46.04 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2300 2378 0.035317 AATCACAGGCGAGCACTTGA 59.965 50.0 0.00 0.0 0.00 3.02 R
3360 3726 0.035630 GCTCCACAGCTTCCATCAGT 60.036 55.0 0.00 0.0 43.09 3.41 R
4433 4850 0.031857 TTGCTGACATTGCGTTTGGG 59.968 50.0 0.00 0.0 0.00 4.12 R
5610 7977 0.106167 TCAGGCTAGTACCCGCTGAT 60.106 55.0 4.28 0.0 0.00 2.90 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
20 21 2.283173 CACCCCCAACCCTTCAGC 60.283 66.667 0.00 0.00 0.00 4.26
43 44 8.817100 CAGCTAACATTAACGAGATGATGTAAA 58.183 33.333 0.00 0.00 32.77 2.01
98 99 5.682943 TTCTAACCATTCTTTGTGGAACG 57.317 39.130 0.00 0.00 42.39 3.95
99 100 4.710324 TCTAACCATTCTTTGTGGAACGT 58.290 39.130 0.00 0.00 42.39 3.99
130 131 1.604278 AGCAGCGTTTCCTTCTGTTTC 59.396 47.619 0.00 0.00 0.00 2.78
153 154 2.287909 GCAATTACAAAACGCAGACCCA 60.288 45.455 0.00 0.00 0.00 4.51
169 170 1.354031 ACCCATGCATACACCTTCACA 59.646 47.619 0.00 0.00 0.00 3.58
171 172 2.435422 CCATGCATACACCTTCACACA 58.565 47.619 0.00 0.00 0.00 3.72
173 174 2.629336 TGCATACACCTTCACACACA 57.371 45.000 0.00 0.00 0.00 3.72
174 175 3.138884 TGCATACACCTTCACACACAT 57.861 42.857 0.00 0.00 0.00 3.21
175 176 2.813172 TGCATACACCTTCACACACATG 59.187 45.455 0.00 0.00 0.00 3.21
177 178 1.890876 TACACCTTCACACACATGGC 58.109 50.000 0.00 0.00 0.00 4.40
178 179 1.165907 ACACCTTCACACACATGGCG 61.166 55.000 0.00 0.00 0.00 5.69
179 180 2.260869 ACCTTCACACACATGGCGC 61.261 57.895 0.00 0.00 0.00 6.53
180 181 2.260154 CCTTCACACACATGGCGCA 61.260 57.895 10.83 0.00 0.00 6.09
185 186 4.325304 CACACATGGCGCACGCAA 62.325 61.111 17.69 5.84 44.11 4.85
191 192 3.570621 ATGGCGCACGCAAAATGCA 62.571 52.632 17.69 4.63 45.36 3.96
192 193 3.472298 GGCGCACGCAAAATGCAG 61.472 61.111 17.69 0.00 45.36 4.41
197 198 2.916703 ACGCAAAATGCAGCCCCA 60.917 55.556 2.99 0.00 45.36 4.96
203 204 1.002201 CAAAATGCAGCCCCATCAACA 59.998 47.619 0.00 0.00 0.00 3.33
204 205 0.899720 AAATGCAGCCCCATCAACAG 59.100 50.000 0.00 0.00 0.00 3.16
211 212 2.362889 CCCATCAACAGGGGGTGC 60.363 66.667 0.00 0.00 40.34 5.01
212 213 2.440147 CCATCAACAGGGGGTGCA 59.560 61.111 0.00 0.00 0.00 4.57
215 216 1.269012 CATCAACAGGGGGTGCAAAT 58.731 50.000 0.00 0.00 0.00 2.32
216 217 1.624813 CATCAACAGGGGGTGCAAATT 59.375 47.619 0.00 0.00 0.00 1.82
219 220 3.309296 TCAACAGGGGGTGCAAATTTTA 58.691 40.909 0.00 0.00 0.00 1.52
223 224 5.317600 ACAGGGGGTGCAAATTTTATTTT 57.682 34.783 0.00 0.00 0.00 1.82
226 227 7.109501 ACAGGGGGTGCAAATTTTATTTTATC 58.890 34.615 0.00 0.00 0.00 1.75
230 231 7.613801 GGGGGTGCAAATTTTATTTTATCCTTT 59.386 33.333 0.00 0.00 0.00 3.11
271 272 4.873827 TGATTTCTAACCATACCGCAGAAC 59.126 41.667 0.00 0.00 0.00 3.01
326 329 6.205101 ACTAGTTAGTACCATGAAACGGAG 57.795 41.667 0.00 0.00 34.13 4.63
337 341 0.232303 GAAACGGAGCACAACGTCTG 59.768 55.000 0.00 0.00 43.31 3.51
427 431 9.019656 AGTATATGAAAAACAACAAGTGGCATA 57.980 29.630 0.00 0.00 0.00 3.14
428 432 9.072294 GTATATGAAAAACAACAAGTGGCATAC 57.928 33.333 0.00 0.00 0.00 2.39
431 435 3.619233 AAACAACAAGTGGCATACGAC 57.381 42.857 0.00 0.00 0.00 4.34
433 437 2.143122 ACAACAAGTGGCATACGACAG 58.857 47.619 0.00 0.00 0.00 3.51
434 438 1.464608 CAACAAGTGGCATACGACAGG 59.535 52.381 0.00 0.00 0.00 4.00
435 439 0.973632 ACAAGTGGCATACGACAGGA 59.026 50.000 0.00 0.00 0.00 3.86
437 441 2.224426 ACAAGTGGCATACGACAGGAAA 60.224 45.455 0.00 0.00 0.00 3.13
440 444 2.147958 GTGGCATACGACAGGAAACAA 58.852 47.619 0.00 0.00 0.00 2.83
531 540 2.613133 TCGTTGTTACTTTTCGTTGGGG 59.387 45.455 0.00 0.00 0.00 4.96
548 557 1.071642 GGGCGAGCTTTATCCCCTC 59.928 63.158 0.00 0.00 32.60 4.30
549 558 1.696097 GGGCGAGCTTTATCCCCTCA 61.696 60.000 0.00 0.00 32.60 3.86
554 563 3.545703 CGAGCTTTATCCCCTCATGTTT 58.454 45.455 0.00 0.00 0.00 2.83
571 580 0.108041 TTTGTTACGATCCTCCGCCC 60.108 55.000 0.00 0.00 0.00 6.13
699 715 0.032540 CAACAGCCTTTTCTGCACCC 59.967 55.000 0.00 0.00 37.59 4.61
732 751 1.153005 CCCTTCTCCTGCCATCTGC 60.153 63.158 0.00 0.00 41.77 4.26
812 831 1.587613 CTCGCGCAGTAGCTTCTCC 60.588 63.158 8.75 0.00 39.10 3.71
813 832 2.583593 CGCGCAGTAGCTTCTCCC 60.584 66.667 8.75 0.00 39.10 4.30
815 834 2.726351 GCGCAGTAGCTTCTCCCCT 61.726 63.158 0.30 0.00 39.10 4.79
816 835 1.142748 CGCAGTAGCTTCTCCCCTG 59.857 63.158 0.00 0.00 39.10 4.45
944 963 1.938596 AGGGAGCAGAGGAGGAGGA 60.939 63.158 0.00 0.00 0.00 3.71
945 964 1.457455 GGGAGCAGAGGAGGAGGAG 60.457 68.421 0.00 0.00 0.00 3.69
951 970 2.018086 AGAGGAGGAGGAGGGGAGG 61.018 68.421 0.00 0.00 0.00 4.30
953 972 3.036959 GGAGGAGGAGGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
955 974 3.767044 GAGGAGGAGGGGAGGGAGC 62.767 73.684 0.00 0.00 0.00 4.70
1046 1067 3.084039 AGTTCTACAACCGATGGTACGA 58.916 45.455 0.00 0.00 33.12 3.43
1051 1072 1.136305 ACAACCGATGGTACGAGATGG 59.864 52.381 0.00 0.00 33.12 3.51
1075 1104 0.526524 CGCTGCTAGCTAGTTTCGCT 60.527 55.000 21.62 0.00 39.60 4.93
1139 1170 1.823899 GGGTTGCTTAGATGGGCGG 60.824 63.158 0.00 0.00 0.00 6.13
1197 1230 3.576004 CTGCTCTGCTGCTTGGTC 58.424 61.111 0.00 0.00 0.00 4.02
1270 1303 1.945776 CTTCGTGCTTCCGAACTCGC 61.946 60.000 2.99 0.00 41.54 5.03
1339 1372 4.083324 TGCCGATTCTCTGCTTTGTTTTAG 60.083 41.667 0.00 0.00 0.00 1.85
1340 1373 4.154195 GCCGATTCTCTGCTTTGTTTTAGA 59.846 41.667 0.00 0.00 0.00 2.10
1500 1537 1.619654 CTGGGTTGCTGAACAATGGA 58.380 50.000 0.00 0.00 41.27 3.41
1645 1682 2.975536 CCTTCGGACGGGTAAGCA 59.024 61.111 0.00 0.00 0.00 3.91
1665 1702 3.823304 GCAATTTTTCCAGGTGTCTCTCT 59.177 43.478 0.00 0.00 0.00 3.10
1693 1731 2.342910 GCATTTTCACTGCTGAGGTG 57.657 50.000 0.00 0.00 36.68 4.00
1720 1758 3.458189 CTCAGGATTGGTACGAATGGTC 58.542 50.000 7.93 0.00 0.00 4.02
1737 1782 1.534729 GTCCTGGTTGAAGCCGAATT 58.465 50.000 0.00 0.00 0.00 2.17
1840 1886 7.495901 TCTAGTCATTTGCTAGAGGAGAATTG 58.504 38.462 0.00 0.00 39.74 2.32
1858 1928 6.057533 AGAATTGTGACTGTGATGACTGAAA 58.942 36.000 0.00 0.00 0.00 2.69
1859 1929 6.543465 AGAATTGTGACTGTGATGACTGAAAA 59.457 34.615 0.00 0.00 0.00 2.29
1939 2009 1.655484 TGCTTCGTGCTATGACATGG 58.345 50.000 0.00 0.00 43.37 3.66
2044 2114 6.723977 TCTGCACCCTTAATTTTGTATTCCTT 59.276 34.615 0.00 0.00 0.00 3.36
2045 2115 6.696411 TGCACCCTTAATTTTGTATTCCTTG 58.304 36.000 0.00 0.00 0.00 3.61
2063 2133 3.434453 CCTTGTGGGTCAAAACAGTAGGA 60.434 47.826 0.00 0.00 35.48 2.94
2086 2156 4.762289 AGGATGTCCCACTATTTCTGTC 57.238 45.455 0.00 0.00 37.41 3.51
2095 2165 3.571571 CACTATTTCTGTCGTCAACGGA 58.428 45.455 2.31 0.00 41.66 4.69
2125 2195 8.999431 CAAAGTTTGTTAATGGCTAAGAGAGTA 58.001 33.333 7.48 0.00 0.00 2.59
2148 2218 5.957771 ATGCATCCCAACTAAACTCTCTA 57.042 39.130 0.00 0.00 0.00 2.43
2161 2231 0.340208 CTCTCTAAGTGGGACCCCCT 59.660 60.000 8.45 0.00 45.70 4.79
2162 2232 1.574339 CTCTCTAAGTGGGACCCCCTA 59.426 57.143 8.45 0.00 45.70 3.53
2204 2274 1.202580 CGATTTAGCAGGGCTGTAGCT 60.203 52.381 3.63 0.00 40.10 3.32
2274 2352 0.528684 GACCGTAGCCTCTGCATCAC 60.529 60.000 0.00 0.00 41.13 3.06
2293 2371 4.402851 TGAAGCACACATCCAGCC 57.597 55.556 0.00 0.00 0.00 4.85
2295 2373 0.321919 TGAAGCACACATCCAGCCTC 60.322 55.000 0.00 0.00 0.00 4.70
2298 2376 2.404995 GCACACATCCAGCCTCTGC 61.405 63.158 0.00 0.00 37.95 4.26
2300 2378 0.393944 CACACATCCAGCCTCTGCAT 60.394 55.000 0.00 0.00 41.13 3.96
2301 2379 0.107312 ACACATCCAGCCTCTGCATC 60.107 55.000 0.00 0.00 41.13 3.91
2363 2709 6.952773 TGGCAACATAGTTTTAAGTCTTGT 57.047 33.333 0.00 0.00 46.17 3.16
2364 2710 7.341445 TGGCAACATAGTTTTAAGTCTTGTT 57.659 32.000 0.00 0.00 46.17 2.83
2394 2740 7.754069 TTTTTGCAATGAAACAGAGTGTTAG 57.246 32.000 0.00 0.00 40.14 2.34
2406 2753 9.431887 GAAACAGAGTGTTAGTCCATAATACAA 57.568 33.333 0.00 0.00 40.14 2.41
2453 2818 8.968242 GTGTTATCACAAGGATTTCTTTTTGAC 58.032 33.333 0.00 0.00 43.37 3.18
2476 2841 8.262227 TGACCTTCAGTTAATGAATATAACCGT 58.738 33.333 0.00 0.00 46.71 4.83
2542 2907 1.752498 TCCTGGTGCAATTCATCATGC 59.248 47.619 0.00 0.00 42.86 4.06
2688 3053 5.762179 TCACAGAAAGATATGGTGGTTCT 57.238 39.130 0.00 0.00 0.00 3.01
2743 3108 8.401490 AGAGATGCTCCAATAATTTATTGTCC 57.599 34.615 21.74 12.88 43.05 4.02
2959 3325 9.283768 TGAAGATGTATGTTTACATGAACTTGT 57.716 29.630 0.00 0.00 46.64 3.16
3096 3462 0.034767 TGCCCATCAAGCAGAAGGAG 60.035 55.000 2.44 0.00 37.28 3.69
3145 3511 9.406113 CTGGAAGGAAGAATTCTGATAAATCTT 57.594 33.333 9.17 5.50 46.56 2.40
3311 3677 3.181454 ACGGAAAGAGAGGAAGCTCAAAA 60.181 43.478 0.00 0.00 37.37 2.44
3491 3857 5.576774 AGCCAAAAGAAACAAAGAAAGAACG 59.423 36.000 0.00 0.00 0.00 3.95
3572 3938 3.008049 GGCCGTCCTGATTATACCAGAAT 59.992 47.826 0.00 0.00 33.65 2.40
3582 3948 9.017509 CCTGATTATACCAGAATACATGCAAAT 57.982 33.333 0.00 0.00 33.65 2.32
3629 3995 4.508662 CAGAATCAAGGACCTACTTCACC 58.491 47.826 0.00 0.00 0.00 4.02
3671 4037 1.303282 CAAACAGGCCCCCTCCTAC 59.697 63.158 0.00 0.00 33.95 3.18
3774 4140 1.924731 TGGAAGATCTCGGACACACT 58.075 50.000 0.00 0.00 0.00 3.55
3888 4254 2.364970 TCCTGCAAAACCAATTGACAGG 59.635 45.455 7.12 12.74 45.60 4.00
3932 4298 0.449388 GATCGCTTGGCTGACAAAGG 59.551 55.000 0.00 0.00 38.91 3.11
3954 4320 0.884704 TGCTTCGGCCTGTTTCTGTC 60.885 55.000 0.00 0.00 40.91 3.51
3976 4342 4.357279 GGAGGCCAGCAGCACCTT 62.357 66.667 5.01 0.00 46.50 3.50
3980 4346 1.002134 GGCCAGCAGCACCTTCTTA 60.002 57.895 0.00 0.00 46.50 2.10
4027 4393 1.963515 CCACAAGCCAAAAGGCTAACT 59.036 47.619 9.76 0.00 45.26 2.24
4035 4401 3.476552 CCAAAAGGCTAACTGTCACAGA 58.523 45.455 13.14 0.00 35.18 3.41
4037 4403 4.261197 CCAAAAGGCTAACTGTCACAGAAC 60.261 45.833 13.14 0.00 35.18 3.01
4047 4413 3.009723 CTGTCACAGAACACAACCAAGT 58.990 45.455 0.00 0.00 32.44 3.16
4050 4416 4.634004 TGTCACAGAACACAACCAAGTAAG 59.366 41.667 0.00 0.00 0.00 2.34
4069 4435 2.840974 CACAAGGGTGCTAACGAGG 58.159 57.895 0.00 0.00 38.37 4.63
4070 4436 0.320374 CACAAGGGTGCTAACGAGGA 59.680 55.000 0.00 0.00 38.37 3.71
4189 4561 3.627732 ATGACGATGACTACGATGGAC 57.372 47.619 0.00 0.00 34.70 4.02
4226 4598 0.174389 GCAGGCGAAGATGAGACTGA 59.826 55.000 2.07 0.00 46.04 3.41
4227 4599 1.919918 CAGGCGAAGATGAGACTGAC 58.080 55.000 0.00 0.00 46.04 3.51
4233 4605 4.118410 GCGAAGATGAGACTGACATTGAT 58.882 43.478 0.00 0.00 0.00 2.57
4243 4615 9.685276 ATGAGACTGACATTGATTTTGGTAATA 57.315 29.630 0.00 0.00 0.00 0.98
4255 4627 3.916359 TTGGTAATATGTTGCCTCGGA 57.084 42.857 10.51 0.00 40.41 4.55
4263 4635 4.819783 TTGCCTCGGACTGCAAAT 57.180 50.000 7.51 0.00 43.94 2.32
4266 4638 3.056313 GCCTCGGACTGCAAATGGC 62.056 63.158 0.00 0.00 45.13 4.40
4292 4664 4.100035 TCATCGACTCAATAGCAGGAACAT 59.900 41.667 0.00 0.00 0.00 2.71
4298 4670 4.337555 ACTCAATAGCAGGAACATTGATGC 59.662 41.667 0.00 0.00 37.86 3.91
4341 4713 2.774234 GGAGGAGAGGATGATGGACAAA 59.226 50.000 0.00 0.00 0.00 2.83
4344 4716 3.454082 AGGAGAGGATGATGGACAAACTC 59.546 47.826 0.00 0.00 36.36 3.01
4377 4749 3.141767 AGCAAGAAAGGTTCAGGTACC 57.858 47.619 2.73 2.73 38.53 3.34
4387 4759 2.353323 GTTCAGGTACCGATGAAACCC 58.647 52.381 15.99 3.49 37.19 4.11
4391 4763 2.486592 CAGGTACCGATGAAACCCAAAC 59.513 50.000 6.18 0.00 33.53 2.93
4392 4764 2.106857 AGGTACCGATGAAACCCAAACA 59.893 45.455 6.18 0.00 33.53 2.83
4393 4765 2.486592 GGTACCGATGAAACCCAAACAG 59.513 50.000 0.00 0.00 0.00 3.16
4432 4849 5.481200 CAGAACTGCAAACTATCATGGAG 57.519 43.478 0.00 0.00 40.42 3.86
4433 4850 3.944015 AGAACTGCAAACTATCATGGAGC 59.056 43.478 0.00 0.00 38.42 4.70
4434 4851 2.648059 ACTGCAAACTATCATGGAGCC 58.352 47.619 0.00 0.00 38.42 4.70
4435 4852 1.952296 CTGCAAACTATCATGGAGCCC 59.048 52.381 0.00 0.00 0.00 5.19
4436 4853 1.284491 TGCAAACTATCATGGAGCCCA 59.716 47.619 0.00 0.00 38.19 5.36
4437 4854 2.291475 TGCAAACTATCATGGAGCCCAA 60.291 45.455 0.00 0.00 36.95 4.12
4438 4855 2.760092 GCAAACTATCATGGAGCCCAAA 59.240 45.455 0.00 0.00 36.95 3.28
4439 4856 3.429410 GCAAACTATCATGGAGCCCAAAC 60.429 47.826 0.00 0.00 36.95 2.93
4440 4857 2.332063 ACTATCATGGAGCCCAAACG 57.668 50.000 0.00 0.00 36.95 3.60
4441 4858 0.947244 CTATCATGGAGCCCAAACGC 59.053 55.000 0.00 0.00 36.95 4.84
4442 4859 0.254462 TATCATGGAGCCCAAACGCA 59.746 50.000 0.00 0.00 36.95 5.24
4443 4860 0.611618 ATCATGGAGCCCAAACGCAA 60.612 50.000 0.00 0.00 36.95 4.85
4444 4861 0.611618 TCATGGAGCCCAAACGCAAT 60.612 50.000 0.00 0.00 36.95 3.56
4445 4862 0.458889 CATGGAGCCCAAACGCAATG 60.459 55.000 0.00 0.00 36.95 2.82
4446 4863 0.899717 ATGGAGCCCAAACGCAATGT 60.900 50.000 0.00 0.00 36.95 2.71
4447 4864 1.212751 GGAGCCCAAACGCAATGTC 59.787 57.895 0.00 0.00 0.00 3.06
4448 4865 1.523154 GGAGCCCAAACGCAATGTCA 61.523 55.000 0.00 0.00 0.00 3.58
4449 4866 0.109597 GAGCCCAAACGCAATGTCAG 60.110 55.000 0.00 0.00 0.00 3.51
4450 4867 1.734117 GCCCAAACGCAATGTCAGC 60.734 57.895 0.00 0.00 0.00 4.26
4451 4868 1.659233 CCCAAACGCAATGTCAGCA 59.341 52.632 0.00 0.00 0.00 4.41
4452 4869 0.031857 CCCAAACGCAATGTCAGCAA 59.968 50.000 0.00 0.00 0.00 3.91
4453 4870 1.537776 CCCAAACGCAATGTCAGCAAA 60.538 47.619 0.00 0.00 0.00 3.68
4454 4871 2.200067 CCAAACGCAATGTCAGCAAAA 58.800 42.857 0.00 0.00 0.00 2.44
4455 4872 2.033832 CCAAACGCAATGTCAGCAAAAC 60.034 45.455 0.00 0.00 0.00 2.43
4456 4873 1.476074 AACGCAATGTCAGCAAAACG 58.524 45.000 0.00 0.00 0.00 3.60
4457 4874 0.317770 ACGCAATGTCAGCAAAACGG 60.318 50.000 0.00 0.00 0.00 4.44
4458 4875 0.317770 CGCAATGTCAGCAAAACGGT 60.318 50.000 0.00 0.00 0.00 4.83
4459 4876 1.851658 GCAATGTCAGCAAAACGGTT 58.148 45.000 0.00 0.00 0.00 4.44
4460 4877 1.786579 GCAATGTCAGCAAAACGGTTC 59.213 47.619 0.00 0.00 0.00 3.62
4461 4878 2.543653 GCAATGTCAGCAAAACGGTTCT 60.544 45.455 0.00 0.00 0.00 3.01
4462 4879 3.705604 CAATGTCAGCAAAACGGTTCTT 58.294 40.909 0.00 0.00 0.00 2.52
4463 4880 4.111916 CAATGTCAGCAAAACGGTTCTTT 58.888 39.130 0.00 0.00 0.00 2.52
4464 4881 3.143807 TGTCAGCAAAACGGTTCTTTG 57.856 42.857 0.00 0.00 36.94 2.77
4465 4882 2.750166 TGTCAGCAAAACGGTTCTTTGA 59.250 40.909 8.98 2.43 36.12 2.69
4466 4883 3.191581 TGTCAGCAAAACGGTTCTTTGAA 59.808 39.130 8.98 0.00 36.12 2.69
4467 4884 3.546271 GTCAGCAAAACGGTTCTTTGAAC 59.454 43.478 8.98 2.16 36.12 3.18
4468 4885 3.191581 TCAGCAAAACGGTTCTTTGAACA 59.808 39.130 11.75 0.00 36.12 3.18
4469 4886 3.303229 CAGCAAAACGGTTCTTTGAACAC 59.697 43.478 11.75 2.06 36.12 3.32
4470 4887 3.192633 AGCAAAACGGTTCTTTGAACACT 59.807 39.130 11.75 0.00 36.12 3.55
4471 4888 4.396790 AGCAAAACGGTTCTTTGAACACTA 59.603 37.500 11.75 0.00 36.12 2.74
4472 4889 4.497966 GCAAAACGGTTCTTTGAACACTAC 59.502 41.667 11.75 0.00 36.12 2.73
4473 4890 5.632959 CAAAACGGTTCTTTGAACACTACA 58.367 37.500 11.75 0.00 36.12 2.74
4474 4891 5.479716 AAACGGTTCTTTGAACACTACAG 57.520 39.130 11.75 0.00 0.00 2.74
4475 4892 3.463944 ACGGTTCTTTGAACACTACAGG 58.536 45.455 11.75 0.00 0.00 4.00
4476 4893 3.133362 ACGGTTCTTTGAACACTACAGGA 59.867 43.478 11.75 0.00 0.00 3.86
4482 4899 2.724977 TGAACACTACAGGAAGAGCG 57.275 50.000 0.00 0.00 0.00 5.03
4549 4966 2.262915 CTGCTCGGTCCACCTCAC 59.737 66.667 0.00 0.00 0.00 3.51
4552 4969 2.276116 GCTCGGTCCACCTCACTGA 61.276 63.158 0.00 0.00 0.00 3.41
4571 4988 1.536662 GGTCAGACTGTCCTGGGGT 60.537 63.158 11.07 0.00 34.99 4.95
4572 4989 1.674057 GTCAGACTGTCCTGGGGTG 59.326 63.158 3.76 0.00 34.99 4.61
4651 5068 2.438763 CTGAGGAATGCTTGAGGAGGAT 59.561 50.000 0.00 0.00 38.16 3.24
4659 5076 1.888512 GCTTGAGGAGGATGCACAAAA 59.111 47.619 0.00 0.00 36.51 2.44
4700 5117 6.540189 CCTGTGTATACTTTCAGAATTGGAGG 59.460 42.308 17.93 0.00 0.00 4.30
4707 5124 4.829492 ACTTTCAGAATTGGAGGTTTCTGG 59.171 41.667 11.51 0.99 45.69 3.86
4762 5179 5.642919 CCCTTTCTGAATTCTGAGACTGAAG 59.357 44.000 13.85 13.36 0.00 3.02
4763 5180 6.462500 CCTTTCTGAATTCTGAGACTGAAGA 58.538 40.000 18.16 4.46 0.00 2.87
4768 5185 6.662663 TCTGAATTCTGAGACTGAAGAGATGA 59.337 38.462 10.68 0.00 0.00 2.92
4821 5242 4.690280 CCAACATTGGTGTATTTTTCCAGC 59.310 41.667 0.20 0.00 43.43 4.85
4822 5243 5.511202 CCAACATTGGTGTATTTTTCCAGCT 60.511 40.000 0.20 0.00 43.43 4.24
4824 5245 5.540911 ACATTGGTGTATTTTTCCAGCTTG 58.459 37.500 0.00 0.00 36.63 4.01
4825 5246 5.304101 ACATTGGTGTATTTTTCCAGCTTGA 59.696 36.000 0.00 0.00 36.63 3.02
4826 5247 5.452078 TTGGTGTATTTTTCCAGCTTGAG 57.548 39.130 0.00 0.00 32.63 3.02
4862 5284 5.071788 TGGAGTGGTGTTTCTTGTCTAGATT 59.928 40.000 0.00 0.00 31.54 2.40
4866 5290 3.440522 GGTGTTTCTTGTCTAGATTGGGC 59.559 47.826 0.00 0.00 31.54 5.36
4879 5303 1.006813 ATTGGGCATTGGTACAGGGA 58.993 50.000 0.00 0.00 42.39 4.20
4917 5342 6.038356 GTGATAGGATTTCGGTTTCGTTCTA 58.962 40.000 0.00 0.00 37.69 2.10
4919 5344 7.864379 GTGATAGGATTTCGGTTTCGTTCTATA 59.136 37.037 0.00 0.00 37.69 1.31
4921 5346 5.048507 AGGATTTCGGTTTCGTTCTATAGC 58.951 41.667 0.00 0.00 37.69 2.97
4922 5347 4.807304 GGATTTCGGTTTCGTTCTATAGCA 59.193 41.667 0.00 0.00 37.69 3.49
4924 5349 6.643770 GGATTTCGGTTTCGTTCTATAGCATA 59.356 38.462 0.00 0.00 37.69 3.14
4925 5350 7.331193 GGATTTCGGTTTCGTTCTATAGCATAT 59.669 37.037 0.00 0.00 37.69 1.78
4926 5351 8.603242 ATTTCGGTTTCGTTCTATAGCATATT 57.397 30.769 0.00 0.00 37.69 1.28
4927 5352 7.402811 TTCGGTTTCGTTCTATAGCATATTG 57.597 36.000 0.00 0.00 37.69 1.90
4928 5353 5.924254 TCGGTTTCGTTCTATAGCATATTGG 59.076 40.000 0.00 0.00 37.69 3.16
4951 5390 6.658816 TGGTTTTGATGCATACAGATACACTT 59.341 34.615 0.00 0.00 0.00 3.16
4969 5408 2.435805 ACTTCAGACTGCAGTTCCAGAA 59.564 45.455 22.65 19.26 36.67 3.02
4970 5409 3.118261 ACTTCAGACTGCAGTTCCAGAAA 60.118 43.478 22.65 8.99 36.67 2.52
4973 5412 5.227569 TCAGACTGCAGTTCCAGAAATTA 57.772 39.130 22.65 0.00 36.67 1.40
4974 5413 5.620206 TCAGACTGCAGTTCCAGAAATTAA 58.380 37.500 22.65 0.00 36.67 1.40
4976 5415 6.716628 TCAGACTGCAGTTCCAGAAATTAATT 59.283 34.615 22.65 0.00 36.67 1.40
4977 5416 7.231317 TCAGACTGCAGTTCCAGAAATTAATTT 59.769 33.333 22.65 13.24 36.67 1.82
4978 5417 7.540055 CAGACTGCAGTTCCAGAAATTAATTTC 59.460 37.037 26.64 26.64 44.91 2.17
4979 5418 7.231317 AGACTGCAGTTCCAGAAATTAATTTCA 59.769 33.333 32.22 16.37 46.50 2.69
4980 5419 7.899973 ACTGCAGTTCCAGAAATTAATTTCAT 58.100 30.769 32.22 19.53 46.50 2.57
4989 5428 7.818930 TCCAGAAATTAATTTCATTTGCTCCAC 59.181 33.333 32.22 10.49 46.50 4.02
5001 5440 3.610040 TTGCTCCACCATGTACTAGTG 57.390 47.619 5.39 0.00 0.00 2.74
5010 5449 5.237815 CACCATGTACTAGTGCTTCAGAAA 58.762 41.667 12.42 0.00 0.00 2.52
5011 5450 5.700832 CACCATGTACTAGTGCTTCAGAAAA 59.299 40.000 12.42 0.00 0.00 2.29
5065 5510 4.391523 GCCACACAGATTCTCTTCTTTCTC 59.608 45.833 0.00 0.00 0.00 2.87
5547 7914 4.150451 GCAAACACATGCCAAGAATTGTAC 59.850 41.667 0.00 0.00 46.99 2.90
5548 7915 5.531634 CAAACACATGCCAAGAATTGTACT 58.468 37.500 0.00 0.00 46.99 2.73
5549 7916 6.676950 CAAACACATGCCAAGAATTGTACTA 58.323 36.000 0.00 0.00 46.99 1.82
5550 7917 5.880054 ACACATGCCAAGAATTGTACTAC 57.120 39.130 0.00 0.00 46.99 2.73
5551 7918 5.560724 ACACATGCCAAGAATTGTACTACT 58.439 37.500 0.00 0.00 46.99 2.57
5552 7919 6.707290 ACACATGCCAAGAATTGTACTACTA 58.293 36.000 0.00 0.00 46.99 1.82
5553 7920 7.338710 ACACATGCCAAGAATTGTACTACTAT 58.661 34.615 0.00 0.00 46.99 2.12
5554 7921 7.280876 ACACATGCCAAGAATTGTACTACTATG 59.719 37.037 0.00 0.00 46.99 2.23
5555 7922 7.280876 CACATGCCAAGAATTGTACTACTATGT 59.719 37.037 0.00 0.00 46.99 2.29
5558 7925 9.899661 ATGCCAAGAATTGTACTACTATGTAAA 57.100 29.630 0.00 0.00 46.99 2.01
5564 7931 7.977853 AGAATTGTACTACTATGTAAACCACGG 59.022 37.037 0.00 0.00 0.00 4.94
5567 7934 2.833338 ACTACTATGTAAACCACGGCCA 59.167 45.455 2.24 0.00 0.00 5.36
5608 7975 1.666011 GGACGAGGCACAGACAGAA 59.334 57.895 0.00 0.00 0.00 3.02
5609 7976 0.389166 GGACGAGGCACAGACAGAAG 60.389 60.000 0.00 0.00 0.00 2.85
5610 7977 0.598562 GACGAGGCACAGACAGAAGA 59.401 55.000 0.00 0.00 0.00 2.87
5611 7978 1.203523 GACGAGGCACAGACAGAAGAT 59.796 52.381 0.00 0.00 0.00 2.40
5615 7982 1.066286 AGGCACAGACAGAAGATCAGC 60.066 52.381 0.00 0.00 0.00 4.26
5616 7983 0.997932 GCACAGACAGAAGATCAGCG 59.002 55.000 0.00 0.00 0.00 5.18
5617 7984 1.638133 CACAGACAGAAGATCAGCGG 58.362 55.000 0.00 0.00 0.00 5.52
5618 7985 0.534412 ACAGACAGAAGATCAGCGGG 59.466 55.000 0.00 0.00 0.00 6.13
5619 7986 0.534412 CAGACAGAAGATCAGCGGGT 59.466 55.000 0.00 0.00 0.00 5.28
5620 7987 1.751351 CAGACAGAAGATCAGCGGGTA 59.249 52.381 0.00 0.00 0.00 3.69
5621 7988 1.751924 AGACAGAAGATCAGCGGGTAC 59.248 52.381 0.00 0.00 0.00 3.34
5622 7989 1.751924 GACAGAAGATCAGCGGGTACT 59.248 52.381 0.00 0.00 0.00 2.73
5623 7990 2.950309 GACAGAAGATCAGCGGGTACTA 59.050 50.000 0.00 0.00 0.00 1.82
5624 7991 2.952978 ACAGAAGATCAGCGGGTACTAG 59.047 50.000 0.00 0.00 0.00 2.57
5625 7992 1.957877 AGAAGATCAGCGGGTACTAGC 59.042 52.381 0.00 5.22 0.00 3.42
5626 7993 1.000052 GAAGATCAGCGGGTACTAGCC 60.000 57.143 8.97 0.00 33.10 3.93
5627 7994 0.186386 AGATCAGCGGGTACTAGCCT 59.814 55.000 8.97 0.00 32.48 4.58
5628 7995 0.315568 GATCAGCGGGTACTAGCCTG 59.684 60.000 8.97 7.47 37.94 4.85
5629 7996 0.106167 ATCAGCGGGTACTAGCCTGA 60.106 55.000 8.97 11.30 37.06 3.86
5630 7997 1.035932 TCAGCGGGTACTAGCCTGAC 61.036 60.000 8.97 0.00 37.06 3.51
5631 7998 2.119655 AGCGGGTACTAGCCTGACG 61.120 63.158 8.97 0.00 37.06 4.35
5632 7999 2.412112 CGGGTACTAGCCTGACGC 59.588 66.667 2.83 0.00 37.06 5.19
5633 8000 2.412323 CGGGTACTAGCCTGACGCA 61.412 63.158 2.83 0.00 41.38 5.24
5634 8001 1.895238 GGGTACTAGCCTGACGCAA 59.105 57.895 0.00 0.00 41.38 4.85
5635 8002 0.179108 GGGTACTAGCCTGACGCAAG 60.179 60.000 0.00 0.00 41.38 4.01
5636 8003 0.815734 GGTACTAGCCTGACGCAAGA 59.184 55.000 0.00 0.00 41.38 3.02
5637 8004 1.469423 GGTACTAGCCTGACGCAAGAC 60.469 57.143 0.00 0.00 41.38 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 7.315247 TGATATAACGTTCCACAAAGAATGG 57.685 36.000 2.82 0.00 37.13 3.16
98 99 5.237344 AGGAAACGCTGCTTGATGATATAAC 59.763 40.000 0.00 0.00 0.00 1.89
99 100 5.368145 AGGAAACGCTGCTTGATGATATAA 58.632 37.500 0.00 0.00 0.00 0.98
153 154 3.138884 TGTGTGTGAAGGTGTATGCAT 57.861 42.857 3.79 3.79 0.00 3.96
169 170 2.419057 ATTTTGCGTGCGCCATGTGT 62.419 50.000 14.16 0.00 41.09 3.72
171 172 1.733758 CATTTTGCGTGCGCCATGT 60.734 52.632 14.16 0.00 41.09 3.21
173 174 2.810458 GCATTTTGCGTGCGCCAT 60.810 55.556 14.16 1.00 41.09 4.40
184 185 1.276989 CTGTTGATGGGGCTGCATTTT 59.723 47.619 0.50 0.00 0.00 1.82
185 186 0.899720 CTGTTGATGGGGCTGCATTT 59.100 50.000 0.50 0.00 0.00 2.32
197 198 2.028561 AATTTGCACCCCCTGTTGAT 57.971 45.000 0.00 0.00 0.00 2.57
203 204 6.446759 AGGATAAAATAAAATTTGCACCCCCT 59.553 34.615 0.00 0.00 0.00 4.79
204 205 6.658849 AGGATAAAATAAAATTTGCACCCCC 58.341 36.000 0.00 0.00 0.00 5.40
234 235 9.878667 TGGTTAGAAATCATTAATTCAGTACGA 57.121 29.630 0.00 0.00 0.00 3.43
326 329 4.436523 GTGTGATTTTAACAGACGTTGTGC 59.563 41.667 0.00 0.00 40.74 4.57
402 406 9.072294 GTATGCCACTTGTTGTTTTTCATATAC 57.928 33.333 0.00 0.00 0.00 1.47
531 540 0.398318 ATGAGGGGATAAAGCTCGCC 59.602 55.000 0.00 0.00 45.97 5.54
548 557 2.030457 GCGGAGGATCGTAACAAACATG 59.970 50.000 0.00 0.00 34.37 3.21
549 558 2.277084 GCGGAGGATCGTAACAAACAT 58.723 47.619 0.00 0.00 34.37 2.71
554 563 2.428925 GGGGCGGAGGATCGTAACA 61.429 63.158 0.00 0.00 34.37 2.41
699 715 2.152016 GAAGGGAAGGAACGGAAACTG 58.848 52.381 0.00 0.00 0.00 3.16
801 820 1.690985 GGGCAGGGGAGAAGCTACT 60.691 63.158 0.00 0.00 0.00 2.57
841 860 1.421485 GGCGTCAAAGCATCACGAG 59.579 57.895 0.00 0.00 39.27 4.18
842 861 2.379634 CGGCGTCAAAGCATCACGA 61.380 57.895 0.00 0.00 39.27 4.35
843 862 2.096406 CGGCGTCAAAGCATCACG 59.904 61.111 0.00 0.00 39.27 4.35
845 864 3.430862 GGCGGCGTCAAAGCATCA 61.431 61.111 6.63 0.00 39.27 3.07
846 865 4.520846 CGGCGGCGTCAAAGCATC 62.521 66.667 24.74 0.00 39.27 3.91
890 909 4.548513 CCTCCCTCCCTCCCTCCG 62.549 77.778 0.00 0.00 0.00 4.63
910 929 2.726351 CCTCCCCTTCCGTCTGAGC 61.726 68.421 0.00 0.00 0.00 4.26
916 935 4.332543 TGCTCCCTCCCCTTCCGT 62.333 66.667 0.00 0.00 0.00 4.69
920 939 2.041928 CCTCTGCTCCCTCCCCTT 59.958 66.667 0.00 0.00 0.00 3.95
944 963 2.955246 TCCTCTGCTCCCTCCCCT 60.955 66.667 0.00 0.00 0.00 4.79
945 964 2.445654 CTCCTCTGCTCCCTCCCC 60.446 72.222 0.00 0.00 0.00 4.81
951 970 1.457455 CCTCCTCCTCCTCTGCTCC 60.457 68.421 0.00 0.00 0.00 4.70
953 972 2.695597 CCCTCCTCCTCCTCTGCT 59.304 66.667 0.00 0.00 0.00 4.24
955 974 1.761667 CTGCCCTCCTCCTCCTCTG 60.762 68.421 0.00 0.00 0.00 3.35
1046 1067 0.034616 GCTAGCAGCGAATCCCATCT 59.965 55.000 10.63 0.00 0.00 2.90
1075 1104 4.646877 GGAACCCGGCGAACCCAA 62.647 66.667 9.30 0.00 0.00 4.12
1123 1152 0.733150 GAACCGCCCATCTAAGCAAC 59.267 55.000 0.00 0.00 0.00 4.17
1129 1160 0.974010 ACGAAGGAACCGCCCATCTA 60.974 55.000 0.00 0.00 37.37 1.98
1139 1170 2.404361 CGACTCGAAAAGACGAAGGAAC 59.596 50.000 0.00 0.00 44.36 3.62
1339 1372 4.082190 GGCACAGGGTATTTTTCCTTCTTC 60.082 45.833 0.00 0.00 0.00 2.87
1340 1373 3.832490 GGCACAGGGTATTTTTCCTTCTT 59.168 43.478 0.00 0.00 0.00 2.52
1472 1509 3.050275 GCAACCCAGCACTCGGTC 61.050 66.667 0.00 0.00 0.00 4.79
1539 1576 1.028330 TCTTCCGCCGTATGACGACT 61.028 55.000 0.00 0.00 46.05 4.18
1645 1682 5.574970 AGAGAGAGACACCTGGAAAAATT 57.425 39.130 0.00 0.00 0.00 1.82
1665 1702 1.614903 CAGTGAAAATGCTGGGCAAGA 59.385 47.619 0.00 0.00 43.62 3.02
1693 1731 1.331756 CGTACCAATCCTGAGCAATGC 59.668 52.381 0.00 0.00 0.00 3.56
1720 1758 2.939103 CTCTAATTCGGCTTCAACCAGG 59.061 50.000 0.00 0.00 0.00 4.45
1737 1782 3.120199 GCAGAGCGCAAAAACATTCTCTA 60.120 43.478 11.47 0.00 41.79 2.43
1768 1813 0.108585 TGCCAAGTTCTCCTGTGGAC 59.891 55.000 0.00 0.00 32.54 4.02
1840 1886 6.064846 ACAATTTTCAGTCATCACAGTCAC 57.935 37.500 0.00 0.00 0.00 3.67
1858 1928 7.682021 GCAGAGACAGGAAACAAAACTACAATT 60.682 37.037 0.00 0.00 0.00 2.32
1859 1929 6.238759 GCAGAGACAGGAAACAAAACTACAAT 60.239 38.462 0.00 0.00 0.00 2.71
1939 2009 3.746492 AGGAAATCGCAGTACTGTTCAAC 59.254 43.478 23.44 11.05 0.00 3.18
2044 2114 3.935818 TTCCTACTGTTTTGACCCACA 57.064 42.857 0.00 0.00 0.00 4.17
2045 2115 3.568430 CCTTTCCTACTGTTTTGACCCAC 59.432 47.826 0.00 0.00 0.00 4.61
2063 2133 5.501156 GACAGAAATAGTGGGACATCCTTT 58.499 41.667 0.00 0.00 44.52 3.11
2086 2156 4.347813 ACAAACTTTGATTTCCGTTGACG 58.652 39.130 8.55 0.00 39.44 4.35
2095 2165 9.696917 CTCTTAGCCATTAACAAACTTTGATTT 57.303 29.630 8.55 0.00 0.00 2.17
2098 2168 7.719633 ACTCTCTTAGCCATTAACAAACTTTGA 59.280 33.333 8.55 0.00 0.00 2.69
2125 2195 5.184892 AGAGAGTTTAGTTGGGATGCATT 57.815 39.130 0.00 0.00 0.00 3.56
2161 2231 6.375736 TCGATTCCTTAACAAAATGCCACATA 59.624 34.615 0.00 0.00 0.00 2.29
2162 2232 5.184864 TCGATTCCTTAACAAAATGCCACAT 59.815 36.000 0.00 0.00 0.00 3.21
2204 2274 5.205821 TCAGAAGAATCCTATACCGTGGAA 58.794 41.667 0.00 0.00 35.81 3.53
2298 2376 0.671472 TCACAGGCGAGCACTTGATG 60.671 55.000 0.00 0.00 0.00 3.07
2300 2378 0.035317 AATCACAGGCGAGCACTTGA 59.965 50.000 0.00 0.00 0.00 3.02
2301 2379 0.167470 CAATCACAGGCGAGCACTTG 59.833 55.000 0.00 0.00 0.00 3.16
2450 2815 8.262227 ACGGTTATATTCATTAACTGAAGGTCA 58.738 33.333 8.88 0.00 46.71 4.02
2476 2841 5.741011 CTTGCACCCCTAAGATACTGTTAA 58.259 41.667 0.00 0.00 0.00 2.01
2542 2907 3.899734 TGATGCAAAAATGAACGAGTGG 58.100 40.909 0.00 0.00 0.00 4.00
2688 3053 3.888930 CCAGGCTAACAAAAGGTTCAAGA 59.111 43.478 0.00 0.00 40.96 3.02
2743 3108 9.178758 AGTAGAACCCTATGAAGCAATTTAAAG 57.821 33.333 0.00 0.00 0.00 1.85
2750 3115 6.412214 GGTTAAGTAGAACCCTATGAAGCAA 58.588 40.000 0.00 0.00 42.74 3.91
2978 3344 5.525745 AGTTAACGACACATGTCATTGTTCA 59.474 36.000 13.32 3.48 44.99 3.18
3096 3462 7.119262 CCAGTATTATCATTTAACCGACCATCC 59.881 40.741 0.00 0.00 0.00 3.51
3145 3511 8.112822 TGATTTCTCCAATTGTTCCTTACCATA 58.887 33.333 4.43 0.00 0.00 2.74
3202 3568 9.401058 CCTTCTGGTATTATCATCTTTTTGAGT 57.599 33.333 0.00 0.00 0.00 3.41
3311 3677 3.735237 TCTTCAGTTTCTGAACTCGCT 57.265 42.857 7.92 0.00 44.27 4.93
3360 3726 0.035630 GCTCCACAGCTTCCATCAGT 60.036 55.000 0.00 0.00 43.09 3.41
3491 3857 6.295039 TGTTATTCTCTTTTTCGACACCAC 57.705 37.500 0.00 0.00 0.00 4.16
3572 3938 5.474578 TTTGCACCCTAAATTTGCATGTA 57.525 34.783 0.00 0.00 45.35 2.29
3582 3948 2.238521 CCAAGAGCTTTGCACCCTAAA 58.761 47.619 0.00 0.00 0.00 1.85
3671 4037 0.940126 CGCTCCATTCGGATTGGAAG 59.060 55.000 19.09 13.48 42.56 3.46
3740 4106 0.546122 TTCCAAGTGCTGTGGTCTGT 59.454 50.000 1.59 0.00 37.43 3.41
3774 4140 0.592637 CTCGCTGTCCATTTTGCACA 59.407 50.000 0.00 0.00 0.00 4.57
3861 4227 3.788333 ATTGGTTTTGCAGGATCATCG 57.212 42.857 0.00 0.00 0.00 3.84
3888 4254 5.412594 TGTCCTTTCACTCATATTGCAGTTC 59.587 40.000 0.00 0.00 0.00 3.01
3932 4298 1.166531 AGAAACAGGCCGAAGCACAC 61.167 55.000 0.00 0.00 42.56 3.82
3954 4320 2.438075 GCTGCTGGCCTCCTTCTG 60.438 66.667 3.32 0.00 34.27 3.02
3976 4342 3.069586 CCGTTAGGTGCCTCATCATAAGA 59.930 47.826 0.00 0.00 0.00 2.10
4022 4388 4.188462 TGGTTGTGTTCTGTGACAGTTAG 58.812 43.478 12.93 0.00 32.61 2.34
4023 4389 4.209307 TGGTTGTGTTCTGTGACAGTTA 57.791 40.909 12.93 0.00 32.61 2.24
4027 4393 3.066291 ACTTGGTTGTGTTCTGTGACA 57.934 42.857 0.00 0.00 0.00 3.58
4035 4401 3.130340 CCTTGTGCTTACTTGGTTGTGTT 59.870 43.478 0.00 0.00 0.00 3.32
4037 4403 2.034558 CCCTTGTGCTTACTTGGTTGTG 59.965 50.000 0.00 0.00 0.00 3.33
4064 4430 1.390565 CTTCCGGTCATAGTCCTCGT 58.609 55.000 0.00 0.00 0.00 4.18
4065 4431 0.669077 CCTTCCGGTCATAGTCCTCG 59.331 60.000 0.00 0.00 0.00 4.63
4067 4433 1.049289 GCCCTTCCGGTCATAGTCCT 61.049 60.000 0.00 0.00 0.00 3.85
4068 4434 1.335132 TGCCCTTCCGGTCATAGTCC 61.335 60.000 0.00 0.00 0.00 3.85
4069 4435 0.539986 TTGCCCTTCCGGTCATAGTC 59.460 55.000 0.00 0.00 0.00 2.59
4070 4436 1.134098 CATTGCCCTTCCGGTCATAGT 60.134 52.381 0.00 0.00 0.00 2.12
4144 4516 0.036010 ACTCCGTTTCTCATGCCTGG 60.036 55.000 0.00 0.00 0.00 4.45
4189 4561 2.440065 TTTAGGCCGCTGCATGGG 60.440 61.111 1.55 3.22 40.13 4.00
4212 4584 6.659361 AAATCAATGTCAGTCTCATCTTCG 57.341 37.500 0.00 0.00 0.00 3.79
4217 4589 8.585471 ATTACCAAAATCAATGTCAGTCTCAT 57.415 30.769 0.00 0.00 0.00 2.90
4226 4598 7.850193 AGGCAACATATTACCAAAATCAATGT 58.150 30.769 0.00 0.00 41.41 2.71
4227 4599 7.167968 CGAGGCAACATATTACCAAAATCAATG 59.832 37.037 0.00 0.00 41.41 2.82
4233 4605 4.396790 GTCCGAGGCAACATATTACCAAAA 59.603 41.667 0.00 0.00 41.41 2.44
4243 4615 1.073025 TTGCAGTCCGAGGCAACAT 59.927 52.632 3.81 0.00 44.41 2.71
4255 4627 0.742505 CGATGATGGCCATTTGCAGT 59.257 50.000 21.84 0.00 43.89 4.40
4263 4635 2.548707 GCTATTGAGTCGATGATGGCCA 60.549 50.000 8.56 8.56 0.00 5.36
4266 4638 3.006217 TCCTGCTATTGAGTCGATGATGG 59.994 47.826 2.84 1.10 0.00 3.51
4306 4678 1.075374 CTCCTCCTCATCGGGATCTCT 59.925 57.143 0.00 0.00 34.56 3.10
4341 4713 5.557576 TCTTGCTATAATGCATCAGGAGT 57.442 39.130 0.00 0.00 42.96 3.85
4344 4716 5.533903 ACCTTTCTTGCTATAATGCATCAGG 59.466 40.000 0.00 0.00 42.96 3.86
4377 4749 2.223688 TGTTGCTGTTTGGGTTTCATCG 60.224 45.455 0.00 0.00 0.00 3.84
4387 4759 4.601019 CTGGTTTCTACTGTTGCTGTTTG 58.399 43.478 0.00 0.00 0.00 2.93
4391 4763 2.221169 TGCTGGTTTCTACTGTTGCTG 58.779 47.619 0.00 0.00 0.00 4.41
4392 4764 2.104792 TCTGCTGGTTTCTACTGTTGCT 59.895 45.455 0.00 0.00 0.00 3.91
4393 4765 2.494059 TCTGCTGGTTTCTACTGTTGC 58.506 47.619 0.00 0.00 0.00 4.17
4419 4791 3.016736 CGTTTGGGCTCCATGATAGTTT 58.983 45.455 0.00 0.00 31.53 2.66
4424 4796 0.611618 TTGCGTTTGGGCTCCATGAT 60.612 50.000 0.00 0.00 31.53 2.45
4432 4849 1.734117 GCTGACATTGCGTTTGGGC 60.734 57.895 0.00 0.00 0.00 5.36
4433 4850 0.031857 TTGCTGACATTGCGTTTGGG 59.968 50.000 0.00 0.00 0.00 4.12
4434 4851 1.850377 TTTGCTGACATTGCGTTTGG 58.150 45.000 0.00 0.00 0.00 3.28
4435 4852 2.346558 CGTTTTGCTGACATTGCGTTTG 60.347 45.455 0.00 0.00 0.00 2.93
4436 4853 1.851666 CGTTTTGCTGACATTGCGTTT 59.148 42.857 0.00 0.00 0.00 3.60
4437 4854 1.476074 CGTTTTGCTGACATTGCGTT 58.524 45.000 0.00 0.00 0.00 4.84
4438 4855 0.317770 CCGTTTTGCTGACATTGCGT 60.318 50.000 0.00 0.00 0.00 5.24
4439 4856 0.317770 ACCGTTTTGCTGACATTGCG 60.318 50.000 0.00 0.00 0.00 4.85
4440 4857 1.786579 GAACCGTTTTGCTGACATTGC 59.213 47.619 0.00 0.00 0.00 3.56
4441 4858 3.354089 AGAACCGTTTTGCTGACATTG 57.646 42.857 0.00 0.00 0.00 2.82
4442 4859 4.111916 CAAAGAACCGTTTTGCTGACATT 58.888 39.130 0.00 0.00 0.00 2.71
4443 4860 3.380004 TCAAAGAACCGTTTTGCTGACAT 59.620 39.130 0.00 0.00 35.90 3.06
4444 4861 2.750166 TCAAAGAACCGTTTTGCTGACA 59.250 40.909 0.00 0.00 35.90 3.58
4445 4862 3.414549 TCAAAGAACCGTTTTGCTGAC 57.585 42.857 0.00 0.00 35.90 3.51
4446 4863 3.191581 TGTTCAAAGAACCGTTTTGCTGA 59.808 39.130 7.36 0.00 35.90 4.26
4447 4864 3.303229 GTGTTCAAAGAACCGTTTTGCTG 59.697 43.478 7.36 0.00 35.90 4.41
4448 4865 3.192633 AGTGTTCAAAGAACCGTTTTGCT 59.807 39.130 7.36 0.00 35.90 3.91
4449 4866 3.507786 AGTGTTCAAAGAACCGTTTTGC 58.492 40.909 7.36 0.00 35.90 3.68
4450 4867 5.632959 TGTAGTGTTCAAAGAACCGTTTTG 58.367 37.500 7.36 0.00 36.98 2.44
4451 4868 5.163693 CCTGTAGTGTTCAAAGAACCGTTTT 60.164 40.000 7.36 0.00 0.00 2.43
4452 4869 4.334481 CCTGTAGTGTTCAAAGAACCGTTT 59.666 41.667 7.36 0.00 0.00 3.60
4453 4870 3.875134 CCTGTAGTGTTCAAAGAACCGTT 59.125 43.478 7.36 0.00 0.00 4.44
4454 4871 3.133362 TCCTGTAGTGTTCAAAGAACCGT 59.867 43.478 7.36 0.00 0.00 4.83
4455 4872 3.724374 TCCTGTAGTGTTCAAAGAACCG 58.276 45.455 7.36 0.00 0.00 4.44
4456 4873 5.365619 TCTTCCTGTAGTGTTCAAAGAACC 58.634 41.667 7.36 0.07 0.00 3.62
4457 4874 5.050023 GCTCTTCCTGTAGTGTTCAAAGAAC 60.050 44.000 3.05 3.05 0.00 3.01
4458 4875 5.057149 GCTCTTCCTGTAGTGTTCAAAGAA 58.943 41.667 0.00 0.00 0.00 2.52
4459 4876 4.632153 GCTCTTCCTGTAGTGTTCAAAGA 58.368 43.478 0.00 0.00 0.00 2.52
4460 4877 3.430218 CGCTCTTCCTGTAGTGTTCAAAG 59.570 47.826 0.00 0.00 0.00 2.77
4461 4878 3.390135 CGCTCTTCCTGTAGTGTTCAAA 58.610 45.455 0.00 0.00 0.00 2.69
4462 4879 2.288825 CCGCTCTTCCTGTAGTGTTCAA 60.289 50.000 0.00 0.00 0.00 2.69
4463 4880 1.272490 CCGCTCTTCCTGTAGTGTTCA 59.728 52.381 0.00 0.00 0.00 3.18
4464 4881 1.272769 ACCGCTCTTCCTGTAGTGTTC 59.727 52.381 0.00 0.00 0.00 3.18
4465 4882 1.272769 GACCGCTCTTCCTGTAGTGTT 59.727 52.381 0.00 0.00 0.00 3.32
4466 4883 0.889306 GACCGCTCTTCCTGTAGTGT 59.111 55.000 0.00 0.00 0.00 3.55
4467 4884 1.133407 GAGACCGCTCTTCCTGTAGTG 59.867 57.143 0.00 0.00 38.16 2.74
4468 4885 1.465794 GAGACCGCTCTTCCTGTAGT 58.534 55.000 0.00 0.00 38.16 2.73
4469 4886 0.378962 CGAGACCGCTCTTCCTGTAG 59.621 60.000 0.00 0.00 39.06 2.74
4470 4887 2.478989 CGAGACCGCTCTTCCTGTA 58.521 57.895 0.00 0.00 39.06 2.74
4471 4888 3.279183 CGAGACCGCTCTTCCTGT 58.721 61.111 0.00 0.00 39.06 4.00
4549 4966 0.894141 CCAGGACAGTCTGACCTCAG 59.106 60.000 19.42 11.20 40.43 3.35
4552 4969 1.229336 CCCCAGGACAGTCTGACCT 60.229 63.158 16.97 16.97 43.06 3.85
4620 5037 1.579698 CATTCCTCAGAGCCATGACG 58.420 55.000 0.00 0.00 0.00 4.35
4629 5046 1.836166 CCTCCTCAAGCATTCCTCAGA 59.164 52.381 0.00 0.00 0.00 3.27
4651 5068 7.828223 AGGCCAAATATATTCAATTTTTGTGCA 59.172 29.630 5.01 0.00 31.24 4.57
4700 5117 2.037941 GCGAAGAAACTGCCAGAAAC 57.962 50.000 0.00 0.00 0.00 2.78
4707 5124 1.222115 ACTCACGGCGAAGAAACTGC 61.222 55.000 16.62 0.00 0.00 4.40
4762 5179 5.905733 CGAAAACACATGCACATATCATCTC 59.094 40.000 0.00 0.00 0.00 2.75
4763 5180 5.731406 GCGAAAACACATGCACATATCATCT 60.731 40.000 0.00 0.00 0.00 2.90
4768 5185 2.754552 AGGCGAAAACACATGCACATAT 59.245 40.909 0.00 0.00 0.00 1.78
4817 5238 2.012673 GCAGTGATAACCTCAAGCTGG 58.987 52.381 0.00 0.00 35.07 4.85
4819 5240 2.355513 CCAGCAGTGATAACCTCAAGCT 60.356 50.000 0.00 0.00 44.11 3.74
4820 5241 2.012673 CCAGCAGTGATAACCTCAAGC 58.987 52.381 0.00 0.00 37.41 4.01
4821 5242 3.055530 ACTCCAGCAGTGATAACCTCAAG 60.056 47.826 0.00 0.00 35.07 3.02
4822 5243 2.906389 ACTCCAGCAGTGATAACCTCAA 59.094 45.455 0.00 0.00 35.07 3.02
4848 5270 4.706476 CCAATGCCCAATCTAGACAAGAAA 59.294 41.667 0.00 0.00 37.89 2.52
4850 5272 3.266772 ACCAATGCCCAATCTAGACAAGA 59.733 43.478 0.00 0.00 39.02 3.02
4862 5284 1.136961 TGTCCCTGTACCAATGCCCA 61.137 55.000 0.00 0.00 0.00 5.36
4866 5290 2.039746 TCCTGTTGTCCCTGTACCAATG 59.960 50.000 0.00 0.00 0.00 2.82
4879 5303 4.620723 TCCTATCACCTGTATCCTGTTGT 58.379 43.478 0.00 0.00 0.00 3.32
4917 5342 8.180706 TGTATGCATCAAAACCAATATGCTAT 57.819 30.769 0.19 3.13 43.98 2.97
4919 5344 6.321945 TCTGTATGCATCAAAACCAATATGCT 59.678 34.615 0.19 0.00 43.98 3.79
4921 5346 9.616634 GTATCTGTATGCATCAAAACCAATATG 57.383 33.333 0.19 0.00 0.00 1.78
4922 5347 9.353431 TGTATCTGTATGCATCAAAACCAATAT 57.647 29.630 0.19 0.00 0.00 1.28
4924 5349 7.340232 AGTGTATCTGTATGCATCAAAACCAAT 59.660 33.333 0.19 0.00 29.97 3.16
4925 5350 6.658816 AGTGTATCTGTATGCATCAAAACCAA 59.341 34.615 0.19 0.00 29.97 3.67
4926 5351 6.179756 AGTGTATCTGTATGCATCAAAACCA 58.820 36.000 0.19 0.00 29.97 3.67
4927 5352 6.683974 AGTGTATCTGTATGCATCAAAACC 57.316 37.500 0.19 0.00 29.97 3.27
4928 5353 7.751732 TGAAGTGTATCTGTATGCATCAAAAC 58.248 34.615 0.19 0.00 29.97 2.43
4951 5390 3.777106 ATTTCTGGAACTGCAGTCTGA 57.223 42.857 21.95 14.79 0.00 3.27
4969 5408 7.396418 ACATGGTGGAGCAAATGAAATTAATT 58.604 30.769 0.00 0.00 33.67 1.40
4970 5409 6.949715 ACATGGTGGAGCAAATGAAATTAAT 58.050 32.000 0.00 0.00 33.67 1.40
4973 5412 4.895668 ACATGGTGGAGCAAATGAAATT 57.104 36.364 0.00 0.00 38.98 1.82
4974 5413 5.018809 AGTACATGGTGGAGCAAATGAAAT 58.981 37.500 0.00 0.00 0.00 2.17
4976 5415 4.032960 AGTACATGGTGGAGCAAATGAA 57.967 40.909 0.00 0.00 0.00 2.57
4977 5416 3.719268 AGTACATGGTGGAGCAAATGA 57.281 42.857 0.00 0.00 0.00 2.57
4978 5417 4.333649 CACTAGTACATGGTGGAGCAAATG 59.666 45.833 0.00 0.00 36.77 2.32
4979 5418 4.517285 CACTAGTACATGGTGGAGCAAAT 58.483 43.478 0.00 0.00 36.77 2.32
4980 5419 3.868369 GCACTAGTACATGGTGGAGCAAA 60.868 47.826 0.00 0.00 40.58 3.68
4989 5428 6.992063 ATTTTCTGAAGCACTAGTACATGG 57.008 37.500 0.00 0.00 0.00 3.66
5065 5510 7.065085 ACAAACTCATCATAATCTGGAGAAACG 59.935 37.037 0.00 0.00 0.00 3.60
5110 5815 3.055963 TGGCCAAAATGTTCACATGATCC 60.056 43.478 0.61 0.00 36.56 3.36
5247 7589 0.172803 CCGGTTCGTAGGTTCTCAGG 59.827 60.000 0.00 0.00 0.00 3.86
5529 7896 7.280876 ACATAGTAGTACAATTCTTGGCATGTG 59.719 37.037 2.52 0.00 34.12 3.21
5547 7914 3.192466 GTGGCCGTGGTTTACATAGTAG 58.808 50.000 0.00 0.00 0.00 2.57
5548 7915 2.417107 CGTGGCCGTGGTTTACATAGTA 60.417 50.000 0.00 0.00 0.00 1.82
5549 7916 1.673626 CGTGGCCGTGGTTTACATAGT 60.674 52.381 0.00 0.00 0.00 2.12
5550 7917 1.003851 CGTGGCCGTGGTTTACATAG 58.996 55.000 0.00 0.00 0.00 2.23
5551 7918 1.020333 GCGTGGCCGTGGTTTACATA 61.020 55.000 0.00 0.00 36.15 2.29
5552 7919 2.329614 GCGTGGCCGTGGTTTACAT 61.330 57.895 0.00 0.00 36.15 2.29
5553 7920 2.973600 GCGTGGCCGTGGTTTACA 60.974 61.111 0.00 0.00 36.15 2.41
5554 7921 1.858372 ATTGCGTGGCCGTGGTTTAC 61.858 55.000 0.00 0.00 36.15 2.01
5555 7922 1.601197 ATTGCGTGGCCGTGGTTTA 60.601 52.632 0.00 0.00 36.15 2.01
5558 7925 4.634703 TCATTGCGTGGCCGTGGT 62.635 61.111 0.00 0.00 36.15 4.16
5578 7945 1.016130 CCTCGTCCGATGCATATGCC 61.016 60.000 24.54 9.44 41.18 4.40
5579 7946 1.630244 GCCTCGTCCGATGCATATGC 61.630 60.000 21.09 21.09 42.50 3.14
5581 7948 0.319900 GTGCCTCGTCCGATGCATAT 60.320 55.000 19.63 0.00 44.80 1.78
5582 7949 1.067416 GTGCCTCGTCCGATGCATA 59.933 57.895 19.63 0.00 44.80 3.14
5608 7975 0.186386 AGGCTAGTACCCGCTGATCT 59.814 55.000 0.00 0.00 0.00 2.75
5609 7976 0.315568 CAGGCTAGTACCCGCTGATC 59.684 60.000 4.28 0.00 0.00 2.92
5610 7977 0.106167 TCAGGCTAGTACCCGCTGAT 60.106 55.000 4.28 0.00 0.00 2.90
5611 7978 1.035932 GTCAGGCTAGTACCCGCTGA 61.036 60.000 4.28 0.00 0.00 4.26
5615 7982 1.940883 TTGCGTCAGGCTAGTACCCG 61.941 60.000 0.00 0.00 44.05 5.28
5616 7983 0.179108 CTTGCGTCAGGCTAGTACCC 60.179 60.000 0.00 0.00 44.05 3.69
5617 7984 0.815734 TCTTGCGTCAGGCTAGTACC 59.184 55.000 0.74 0.00 43.72 3.34
5618 7985 1.794437 CGTCTTGCGTCAGGCTAGTAC 60.794 57.143 0.74 0.00 43.72 2.73
5619 7986 0.450583 CGTCTTGCGTCAGGCTAGTA 59.549 55.000 0.74 0.00 43.72 1.82
5620 7987 1.213013 CGTCTTGCGTCAGGCTAGT 59.787 57.895 0.74 0.00 43.72 2.57
5621 7988 4.079090 CGTCTTGCGTCAGGCTAG 57.921 61.111 0.00 0.00 44.51 3.42


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

AutoCloner maintained by Alex Coulton.