Multiple sequence alignment - TraesCS1A01G178400

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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 TraesCS1A01G178400 chr1A 100.000 5915 0 0 706 6620 322572185 322578099 0.000000e+00 10924.0
1 TraesCS1A01G178400 chr1A 100.000 311 0 0 1 311 322571480 322571790 5.760000e-160 575.0
2 TraesCS1A01G178400 chr1B 96.730 5352 121 22 706 6030 362052171 362046847 0.000000e+00 8865.0
3 TraesCS1A01G178400 chr1B 94.585 277 15 0 6091 6367 362046809 362046533 4.740000e-116 429.0
4 TraesCS1A01G178400 chr1B 81.847 314 28 13 1 293 362052531 362052226 3.090000e-58 237.0
5 TraesCS1A01G178400 chr1D 97.959 2891 51 3 3336 6218 251983207 251986097 0.000000e+00 5005.0
6 TraesCS1A01G178400 chr1D 97.485 2664 50 6 706 3362 251980549 251983202 0.000000e+00 4532.0
7 TraesCS1A01G178400 chr1D 96.629 178 5 1 6210 6387 251990694 251990870 1.810000e-75 294.0
8 TraesCS1A01G178400 chr1D 81.613 310 32 10 1 293 251980192 251980493 3.990000e-57 233.0
9 TraesCS1A01G178400 chr1D 82.353 221 24 5 6403 6615 251990973 251991186 1.900000e-40 178.0
10 TraesCS1A01G178400 chr6A 94.444 36 1 1 71 106 535425105 535425139 3.000000e-03 54.7


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 TraesCS1A01G178400 chr1A 322571480 322578099 6619 False 5749.500000 10924 100.000000 1 6620 2 chr1A.!!$F1 6619
1 TraesCS1A01G178400 chr1B 362046533 362052531 5998 True 3177.000000 8865 91.054000 1 6367 3 chr1B.!!$R1 6366
2 TraesCS1A01G178400 chr1D 251980192 251986097 5905 False 3256.666667 5005 92.352333 1 6218 3 chr1D.!!$F1 6217

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
876 913 0.605589 CTCTCATACTCCATCCCCGC 59.394 60.000 0.00 0.00 0.00 6.13 F
1674 1711 2.023673 CTTGATCTCGCACTCCTCTCT 58.976 52.381 0.00 0.00 0.00 3.10 F
2122 2163 5.036117 TCCCCTGATAGCTTGTCAAATAC 57.964 43.478 0.00 0.00 0.00 1.89 F
2976 3021 4.457257 GCTAGAAGCTAATTAATGCCCAGG 59.543 45.833 0.00 0.00 38.45 4.45 F
4223 4300 3.080319 GGCATCAATATCTCCTGAAGCC 58.920 50.000 5.81 5.81 45.86 4.35 F
4656 4733 3.186409 TCTTGCATTCTACAAACGTGAGC 59.814 43.478 0.00 0.00 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2035 2076 1.074566 GCATAAGCTAATCCCCTGCCT 59.925 52.381 0.0 0.0 37.91 4.75 R
2847 2889 2.298446 AGCGATATGTGATGACAGGGAG 59.702 50.000 0.0 0.0 34.87 4.30 R
3065 3110 3.882888 CTGGTAGTCAAACAGCCAAAGAA 59.117 43.478 0.0 0.0 0.00 2.52 R
4728 4805 1.002087 CACACCTCCCTACAACAGTCC 59.998 57.143 0.0 0.0 0.00 3.85 R
5084 5161 1.194772 GCGTCAGTGGAGTTTTGTAGC 59.805 52.381 0.0 0.0 0.00 3.58 R
6264 6355 0.103026 TGATTGCCCGTCGATCTCAG 59.897 55.000 0.0 0.0 36.68 3.35 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
23 24 5.435291 AGGAATTGCCATGTGTTTTTGAAA 58.565 33.333 0.00 0.00 40.02 2.69
54 55 7.125811 TCTCCATCCTATACAACTAAACTTGCT 59.874 37.037 0.00 0.00 0.00 3.91
79 80 3.831715 AAAAGGCTCGTAAATGCTGAC 57.168 42.857 0.00 0.00 0.00 3.51
93 94 3.316573 CTGACCCCTCCCAGCGAAC 62.317 68.421 0.00 0.00 0.00 3.95
94 95 4.452733 GACCCCTCCCAGCGAACG 62.453 72.222 0.00 0.00 0.00 3.95
108 109 1.552226 CGAACGTTCGCCAGCTATTA 58.448 50.000 34.54 0.00 44.26 0.98
109 110 2.124903 CGAACGTTCGCCAGCTATTAT 58.875 47.619 34.54 0.00 44.26 1.28
119 120 5.020795 TCGCCAGCTATTATGGTCCTTATA 58.979 41.667 0.00 0.00 40.17 0.98
120 121 5.661312 TCGCCAGCTATTATGGTCCTTATAT 59.339 40.000 0.00 0.00 40.17 0.86
121 122 6.156256 TCGCCAGCTATTATGGTCCTTATATT 59.844 38.462 0.00 0.00 40.17 1.28
122 123 7.343574 TCGCCAGCTATTATGGTCCTTATATTA 59.656 37.037 0.00 0.00 40.17 0.98
123 124 8.150945 CGCCAGCTATTATGGTCCTTATATTAT 58.849 37.037 0.00 0.00 40.17 1.28
187 199 3.515330 AACCCTGGAAATACGTACGAG 57.485 47.619 24.41 6.59 0.00 4.18
202 224 3.185797 CGTACGAGAAAAAGGGAAACAGG 59.814 47.826 10.44 0.00 0.00 4.00
204 226 3.477530 ACGAGAAAAAGGGAAACAGGAG 58.522 45.455 0.00 0.00 0.00 3.69
223 245 1.064357 AGCAACCAACAAAACGTACGG 59.936 47.619 21.06 3.79 0.00 4.02
308 338 2.681778 CCGACTGGACTGCCTCCT 60.682 66.667 0.00 0.00 40.26 3.69
309 339 2.716017 CCGACTGGACTGCCTCCTC 61.716 68.421 0.00 0.00 40.26 3.71
310 340 1.979155 CGACTGGACTGCCTCCTCA 60.979 63.158 0.00 0.00 40.26 3.86
726 756 3.203412 CGTCTCCTCCTCCGTCCG 61.203 72.222 0.00 0.00 0.00 4.79
771 804 3.181290 GGCGCGTACGTTACCACC 61.181 66.667 17.90 5.93 42.83 4.61
859 896 5.504173 GCATTAATACTTTGGTTCGCTCCTC 60.504 44.000 0.00 0.00 0.00 3.71
860 897 3.983044 AATACTTTGGTTCGCTCCTCT 57.017 42.857 0.00 0.00 0.00 3.69
861 898 3.528597 ATACTTTGGTTCGCTCCTCTC 57.471 47.619 0.00 0.00 0.00 3.20
876 913 0.605589 CTCTCATACTCCATCCCCGC 59.394 60.000 0.00 0.00 0.00 6.13
1039 1076 4.807039 ACATACACGCGGACGGCC 62.807 66.667 12.47 0.00 46.04 6.13
1080 1117 2.125106 GGCACGACCACCATCTCC 60.125 66.667 0.00 0.00 38.86 3.71
1674 1711 2.023673 CTTGATCTCGCACTCCTCTCT 58.976 52.381 0.00 0.00 0.00 3.10
1689 1726 7.222872 CACTCCTCTCTCCTAAATGCATAATT 58.777 38.462 0.00 0.00 0.00 1.40
2122 2163 5.036117 TCCCCTGATAGCTTGTCAAATAC 57.964 43.478 0.00 0.00 0.00 1.89
2204 2245 8.660373 CAAGAGTTCAGTAGTTATCAAATCCAC 58.340 37.037 0.00 0.00 0.00 4.02
2207 2248 8.723942 AGTTCAGTAGTTATCAAATCCACATC 57.276 34.615 0.00 0.00 0.00 3.06
2439 2481 7.781693 ACATTATTAGGGTGCTGAATTTGAGAT 59.218 33.333 0.00 0.00 0.00 2.75
2976 3021 4.457257 GCTAGAAGCTAATTAATGCCCAGG 59.543 45.833 0.00 0.00 38.45 4.45
3065 3110 6.295719 AGATCGTTAGGTTATGGACAACTT 57.704 37.500 0.00 0.00 0.00 2.66
3147 3192 4.362932 TGTTCTTCTCTAGCAGATGACG 57.637 45.455 7.05 0.00 35.52 4.35
3225 3270 4.219070 TCTGGGCATTCAAATCTTGTGAAG 59.781 41.667 0.00 0.00 38.34 3.02
3887 3964 5.148651 AGGATTATACCCATAGCACGTTC 57.851 43.478 0.00 0.00 0.00 3.95
3893 3970 7.534723 TTATACCCATAGCACGTTCTATCTT 57.465 36.000 4.65 0.00 0.00 2.40
4223 4300 3.080319 GGCATCAATATCTCCTGAAGCC 58.920 50.000 5.81 5.81 45.86 4.35
4362 4439 5.741011 TCCATAGGATATTGGCGATTTACC 58.259 41.667 0.00 0.00 32.80 2.85
4605 4682 5.152923 ACGTGAGTAGTATGTACACATCG 57.847 43.478 0.00 0.03 46.88 3.84
4651 4728 9.438291 CCTTTAATATCTTGCATTCTACAAACG 57.562 33.333 0.00 0.00 0.00 3.60
4656 4733 3.186409 TCTTGCATTCTACAAACGTGAGC 59.814 43.478 0.00 0.00 0.00 4.26
4728 4805 7.819644 TGCATAAATAGCCAGCTATGTTATTG 58.180 34.615 12.74 7.55 39.03 1.90
4734 4811 3.200825 AGCCAGCTATGTTATTGGACTGT 59.799 43.478 0.00 0.00 32.34 3.55
4784 4861 9.585099 TTCATTGCATGTACTGATTTTATTTCC 57.415 29.630 4.74 0.00 0.00 3.13
4966 5043 6.928348 TTGAGAACTTCAGGATGGTAAGTA 57.072 37.500 0.00 0.00 37.07 2.24
5084 5161 5.450965 CCACCTTTAATTTATGCAGGCTCTG 60.451 44.000 0.00 0.00 34.12 3.35
5190 5267 5.816449 TCATTTGCACACATGGTGTATAG 57.184 39.130 13.59 5.24 45.65 1.31
5535 5612 0.603975 GCGACTGGATTAGGCCATCC 60.604 60.000 14.06 14.06 43.03 3.51
5620 5697 2.887568 CGAGGCGCCATCACTGAC 60.888 66.667 31.54 7.91 0.00 3.51
5766 5843 7.037586 AGTGGGAGTTCATAATGGAGTTTTAGA 60.038 37.037 0.00 0.00 0.00 2.10
5767 5844 7.610305 GTGGGAGTTCATAATGGAGTTTTAGAA 59.390 37.037 0.00 0.00 0.00 2.10
5926 6005 1.874562 CTTGCTGTCTTGCTGCTCC 59.125 57.895 0.00 0.00 41.79 4.70
5933 6012 2.438075 CTTGCTGCTCCCTCCTGC 60.438 66.667 0.00 0.00 0.00 4.85
6013 6104 1.322442 GCCAAATATCTGGTGAGGGC 58.678 55.000 0.00 0.00 38.86 5.19
6093 6184 2.832201 GAAGCAGCAGGCCCCATC 60.832 66.667 0.00 0.00 46.50 3.51
6121 6212 2.227865 GTGCTATGTTTCGCCTTTTCCA 59.772 45.455 0.00 0.00 0.00 3.53
6258 6349 0.537188 GATCTTTGGGTGCGGAGAGA 59.463 55.000 0.00 0.00 0.00 3.10
6262 6353 2.709125 TTTGGGTGCGGAGAGACGTG 62.709 60.000 0.00 0.00 35.98 4.49
6315 6406 3.080319 TGGATGCGAAAACATGTGATGA 58.920 40.909 0.00 0.00 0.00 2.92
6324 6415 1.945387 ACATGTGATGACGAGCCATC 58.055 50.000 0.00 0.00 42.38 3.51
6341 6432 4.789095 CCATCCGTTGGTATTTTACGAG 57.211 45.455 0.00 0.00 40.99 4.18
6349 6440 6.189567 CGTTGGTATTTTACGAGCCATAAAG 58.810 40.000 0.00 0.00 37.47 1.85
6367 6458 8.342634 GCCATAAAGCTTTCAGATTTTCGTATA 58.657 33.333 16.57 0.00 35.26 1.47
6368 6459 9.651718 CCATAAAGCTTTCAGATTTTCGTATAC 57.348 33.333 16.57 0.00 35.26 1.47
6372 6463 7.541122 AGCTTTCAGATTTTCGTATACTTCC 57.459 36.000 0.56 0.00 0.00 3.46
6373 6464 6.255887 AGCTTTCAGATTTTCGTATACTTCCG 59.744 38.462 0.56 0.00 0.00 4.30
6374 6465 5.961395 TTCAGATTTTCGTATACTTCCGC 57.039 39.130 0.56 0.00 0.00 5.54
6375 6466 5.001237 TCAGATTTTCGTATACTTCCGCA 57.999 39.130 0.56 0.00 0.00 5.69
6376 6467 5.412640 TCAGATTTTCGTATACTTCCGCAA 58.587 37.500 0.56 0.00 0.00 4.85
6377 6468 5.870433 TCAGATTTTCGTATACTTCCGCAAA 59.130 36.000 0.56 0.00 0.00 3.68
6378 6469 6.035650 TCAGATTTTCGTATACTTCCGCAAAG 59.964 38.462 0.56 0.00 41.08 2.77
6379 6470 6.035650 CAGATTTTCGTATACTTCCGCAAAGA 59.964 38.462 0.56 0.00 38.44 2.52
6380 6471 6.761714 AGATTTTCGTATACTTCCGCAAAGAT 59.238 34.615 0.56 0.00 38.44 2.40
6381 6472 5.961395 TTTCGTATACTTCCGCAAAGATC 57.039 39.130 0.56 0.00 38.44 2.75
6382 6473 4.642445 TCGTATACTTCCGCAAAGATCA 57.358 40.909 0.56 0.00 38.44 2.92
6383 6474 4.357142 TCGTATACTTCCGCAAAGATCAC 58.643 43.478 0.56 0.00 38.44 3.06
6384 6475 4.097437 TCGTATACTTCCGCAAAGATCACT 59.903 41.667 0.56 0.00 38.44 3.41
6385 6476 4.207224 CGTATACTTCCGCAAAGATCACTG 59.793 45.833 0.56 0.00 38.44 3.66
6386 6477 2.550830 ACTTCCGCAAAGATCACTGT 57.449 45.000 0.00 0.00 38.44 3.55
6387 6478 2.146342 ACTTCCGCAAAGATCACTGTG 58.854 47.619 0.17 0.17 38.44 3.66
6399 6490 8.752766 CAAAGATCACTGTGCTTCAAAAATAT 57.247 30.769 2.12 0.00 0.00 1.28
6400 6491 8.857216 CAAAGATCACTGTGCTTCAAAAATATC 58.143 33.333 2.12 0.00 0.00 1.63
6401 6492 7.692460 AGATCACTGTGCTTCAAAAATATCA 57.308 32.000 2.12 0.00 0.00 2.15
6402 6493 7.759465 AGATCACTGTGCTTCAAAAATATCAG 58.241 34.615 2.12 0.00 0.00 2.90
6403 6494 7.609146 AGATCACTGTGCTTCAAAAATATCAGA 59.391 33.333 2.12 0.00 0.00 3.27
6404 6495 6.902341 TCACTGTGCTTCAAAAATATCAGAC 58.098 36.000 2.12 0.00 0.00 3.51
6405 6496 6.072508 TCACTGTGCTTCAAAAATATCAGACC 60.073 38.462 2.12 0.00 0.00 3.85
6406 6497 6.006449 ACTGTGCTTCAAAAATATCAGACCT 58.994 36.000 0.00 0.00 0.00 3.85
6407 6498 6.072286 ACTGTGCTTCAAAAATATCAGACCTG 60.072 38.462 0.00 0.00 0.00 4.00
6408 6499 5.769662 TGTGCTTCAAAAATATCAGACCTGT 59.230 36.000 0.00 0.00 0.00 4.00
6409 6500 6.265196 TGTGCTTCAAAAATATCAGACCTGTT 59.735 34.615 0.00 0.00 0.00 3.16
6410 6501 7.147976 GTGCTTCAAAAATATCAGACCTGTTT 58.852 34.615 0.00 0.00 0.00 2.83
6411 6502 7.115378 GTGCTTCAAAAATATCAGACCTGTTTG 59.885 37.037 0.00 1.30 0.00 2.93
6412 6503 6.089954 GCTTCAAAAATATCAGACCTGTTTGC 59.910 38.462 0.00 0.00 0.00 3.68
6413 6504 6.024552 TCAAAAATATCAGACCTGTTTGCC 57.975 37.500 0.00 0.00 0.00 4.52
6414 6505 5.047377 TCAAAAATATCAGACCTGTTTGCCC 60.047 40.000 0.00 0.00 0.00 5.36
6415 6506 4.322057 AAATATCAGACCTGTTTGCCCT 57.678 40.909 0.00 0.00 0.00 5.19
6416 6507 3.567478 ATATCAGACCTGTTTGCCCTC 57.433 47.619 0.00 0.00 0.00 4.30
6417 6508 0.329596 ATCAGACCTGTTTGCCCTCC 59.670 55.000 0.00 0.00 0.00 4.30
6418 6509 1.303643 CAGACCTGTTTGCCCTCCC 60.304 63.158 0.00 0.00 0.00 4.30
6419 6510 2.035783 GACCTGTTTGCCCTCCCC 59.964 66.667 0.00 0.00 0.00 4.81
6420 6511 2.452491 ACCTGTTTGCCCTCCCCT 60.452 61.111 0.00 0.00 0.00 4.79
6421 6512 2.036256 CCTGTTTGCCCTCCCCTG 59.964 66.667 0.00 0.00 0.00 4.45
6422 6513 2.845345 CCTGTTTGCCCTCCCCTGT 61.845 63.158 0.00 0.00 0.00 4.00
6423 6514 1.303643 CTGTTTGCCCTCCCCTGTC 60.304 63.158 0.00 0.00 0.00 3.51
6424 6515 2.359975 GTTTGCCCTCCCCTGTCG 60.360 66.667 0.00 0.00 0.00 4.35
6425 6516 2.852075 TTTGCCCTCCCCTGTCGT 60.852 61.111 0.00 0.00 0.00 4.34
6426 6517 2.890766 TTTGCCCTCCCCTGTCGTC 61.891 63.158 0.00 0.00 0.00 4.20
6427 6518 3.846405 TTGCCCTCCCCTGTCGTCT 62.846 63.158 0.00 0.00 0.00 4.18
6428 6519 3.003763 GCCCTCCCCTGTCGTCTT 61.004 66.667 0.00 0.00 0.00 3.01
6429 6520 3.020237 GCCCTCCCCTGTCGTCTTC 62.020 68.421 0.00 0.00 0.00 2.87
6430 6521 1.305381 CCCTCCCCTGTCGTCTTCT 60.305 63.158 0.00 0.00 0.00 2.85
6431 6522 1.324005 CCCTCCCCTGTCGTCTTCTC 61.324 65.000 0.00 0.00 0.00 2.87
6432 6523 1.324005 CCTCCCCTGTCGTCTTCTCC 61.324 65.000 0.00 0.00 0.00 3.71
6433 6524 0.323908 CTCCCCTGTCGTCTTCTCCT 60.324 60.000 0.00 0.00 0.00 3.69
6434 6525 0.114560 TCCCCTGTCGTCTTCTCCTT 59.885 55.000 0.00 0.00 0.00 3.36
6435 6526 0.533032 CCCCTGTCGTCTTCTCCTTC 59.467 60.000 0.00 0.00 0.00 3.46
6436 6527 0.533032 CCCTGTCGTCTTCTCCTTCC 59.467 60.000 0.00 0.00 0.00 3.46
6437 6528 1.257743 CCTGTCGTCTTCTCCTTCCA 58.742 55.000 0.00 0.00 0.00 3.53
6438 6529 1.067495 CCTGTCGTCTTCTCCTTCCAC 60.067 57.143 0.00 0.00 0.00 4.02
6439 6530 0.966920 TGTCGTCTTCTCCTTCCACC 59.033 55.000 0.00 0.00 0.00 4.61
6440 6531 0.966920 GTCGTCTTCTCCTTCCACCA 59.033 55.000 0.00 0.00 0.00 4.17
6441 6532 0.966920 TCGTCTTCTCCTTCCACCAC 59.033 55.000 0.00 0.00 0.00 4.16
6442 6533 0.388649 CGTCTTCTCCTTCCACCACG 60.389 60.000 0.00 0.00 0.00 4.94
6443 6534 0.680061 GTCTTCTCCTTCCACCACGT 59.320 55.000 0.00 0.00 0.00 4.49
6444 6535 0.679505 TCTTCTCCTTCCACCACGTG 59.320 55.000 9.08 9.08 0.00 4.49
6445 6536 0.951040 CTTCTCCTTCCACCACGTGC 60.951 60.000 10.91 0.00 31.34 5.34
6446 6537 1.407656 TTCTCCTTCCACCACGTGCT 61.408 55.000 10.91 0.00 31.34 4.40
6447 6538 1.071471 CTCCTTCCACCACGTGCTT 59.929 57.895 10.91 0.00 31.34 3.91
6448 6539 0.951040 CTCCTTCCACCACGTGCTTC 60.951 60.000 10.91 0.00 31.34 3.86
6449 6540 1.227823 CCTTCCACCACGTGCTTCA 60.228 57.895 10.91 0.00 31.34 3.02
6450 6541 1.507141 CCTTCCACCACGTGCTTCAC 61.507 60.000 10.91 0.00 31.34 3.18
6460 6551 3.415380 TGCTTCACGCAGCGAAAA 58.585 50.000 24.65 13.75 45.47 2.29
6461 6552 1.724467 TGCTTCACGCAGCGAAAAA 59.276 47.368 24.65 11.16 45.47 1.94
6462 6553 0.310543 TGCTTCACGCAGCGAAAAAT 59.689 45.000 24.65 0.00 45.47 1.82
6463 6554 1.268999 TGCTTCACGCAGCGAAAAATT 60.269 42.857 24.65 0.00 45.47 1.82
6464 6555 1.786579 GCTTCACGCAGCGAAAAATTT 59.213 42.857 24.65 0.00 38.92 1.82
6465 6556 2.160104 GCTTCACGCAGCGAAAAATTTC 60.160 45.455 24.65 0.00 38.92 2.17
6466 6557 2.044888 TCACGCAGCGAAAAATTTCC 57.955 45.000 24.65 0.00 33.68 3.13
6467 6558 1.606668 TCACGCAGCGAAAAATTTCCT 59.393 42.857 24.65 0.00 33.68 3.36
6468 6559 1.978782 CACGCAGCGAAAAATTTCCTC 59.021 47.619 24.65 0.00 33.68 3.71
6469 6560 1.068541 ACGCAGCGAAAAATTTCCTCC 60.069 47.619 24.65 0.00 33.68 4.30
6470 6561 1.732405 CGCAGCGAAAAATTTCCTCCC 60.732 52.381 9.98 0.00 33.68 4.30
6471 6562 1.546029 GCAGCGAAAAATTTCCTCCCT 59.454 47.619 0.00 0.00 33.68 4.20
6472 6563 2.416027 GCAGCGAAAAATTTCCTCCCTC 60.416 50.000 0.00 0.00 33.68 4.30
6473 6564 3.084786 CAGCGAAAAATTTCCTCCCTCT 58.915 45.455 0.00 0.00 33.68 3.69
6474 6565 3.127721 CAGCGAAAAATTTCCTCCCTCTC 59.872 47.826 0.00 0.00 33.68 3.20
6475 6566 3.081804 GCGAAAAATTTCCTCCCTCTCA 58.918 45.455 0.00 0.00 33.68 3.27
6476 6567 3.119814 GCGAAAAATTTCCTCCCTCTCAC 60.120 47.826 0.00 0.00 33.68 3.51
6477 6568 3.440522 CGAAAAATTTCCTCCCTCTCACC 59.559 47.826 0.00 0.00 33.68 4.02
6478 6569 4.667573 GAAAAATTTCCTCCCTCTCACCT 58.332 43.478 0.00 0.00 0.00 4.00
6479 6570 4.749048 AAAATTTCCTCCCTCTCACCTT 57.251 40.909 0.00 0.00 0.00 3.50
6480 6571 4.308526 AAATTTCCTCCCTCTCACCTTC 57.691 45.455 0.00 0.00 0.00 3.46
6481 6572 2.723530 TTTCCTCCCTCTCACCTTCT 57.276 50.000 0.00 0.00 0.00 2.85
6482 6573 2.239681 TTCCTCCCTCTCACCTTCTC 57.760 55.000 0.00 0.00 0.00 2.87
6483 6574 1.388174 TCCTCCCTCTCACCTTCTCT 58.612 55.000 0.00 0.00 0.00 3.10
6484 6575 1.286553 TCCTCCCTCTCACCTTCTCTC 59.713 57.143 0.00 0.00 0.00 3.20
6485 6576 1.006519 CCTCCCTCTCACCTTCTCTCA 59.993 57.143 0.00 0.00 0.00 3.27
6486 6577 2.558575 CCTCCCTCTCACCTTCTCTCAA 60.559 54.545 0.00 0.00 0.00 3.02
6487 6578 2.495669 CTCCCTCTCACCTTCTCTCAAC 59.504 54.545 0.00 0.00 0.00 3.18
6488 6579 2.110899 TCCCTCTCACCTTCTCTCAACT 59.889 50.000 0.00 0.00 0.00 3.16
6489 6580 2.495669 CCCTCTCACCTTCTCTCAACTC 59.504 54.545 0.00 0.00 0.00 3.01
6490 6581 2.495669 CCTCTCACCTTCTCTCAACTCC 59.504 54.545 0.00 0.00 0.00 3.85
6491 6582 2.495669 CTCTCACCTTCTCTCAACTCCC 59.504 54.545 0.00 0.00 0.00 4.30
6492 6583 1.552792 CTCACCTTCTCTCAACTCCCC 59.447 57.143 0.00 0.00 0.00 4.81
6493 6584 1.132849 TCACCTTCTCTCAACTCCCCA 60.133 52.381 0.00 0.00 0.00 4.96
6494 6585 1.002544 CACCTTCTCTCAACTCCCCAC 59.997 57.143 0.00 0.00 0.00 4.61
6495 6586 0.615850 CCTTCTCTCAACTCCCCACC 59.384 60.000 0.00 0.00 0.00 4.61
6496 6587 1.352083 CTTCTCTCAACTCCCCACCA 58.648 55.000 0.00 0.00 0.00 4.17
6497 6588 1.912043 CTTCTCTCAACTCCCCACCAT 59.088 52.381 0.00 0.00 0.00 3.55
6498 6589 2.940514 TCTCTCAACTCCCCACCATA 57.059 50.000 0.00 0.00 0.00 2.74
6499 6590 2.467880 TCTCTCAACTCCCCACCATAC 58.532 52.381 0.00 0.00 0.00 2.39
6500 6591 1.137086 CTCTCAACTCCCCACCATACG 59.863 57.143 0.00 0.00 0.00 3.06
6501 6592 0.462047 CTCAACTCCCCACCATACGC 60.462 60.000 0.00 0.00 0.00 4.42
6502 6593 1.813753 CAACTCCCCACCATACGCG 60.814 63.158 3.53 3.53 0.00 6.01
6503 6594 3.675619 AACTCCCCACCATACGCGC 62.676 63.158 5.73 0.00 0.00 6.86
6504 6595 4.155733 CTCCCCACCATACGCGCA 62.156 66.667 5.73 0.00 0.00 6.09
6505 6596 3.460672 CTCCCCACCATACGCGCAT 62.461 63.158 5.73 0.00 0.00 4.73
6506 6597 3.279116 CCCCACCATACGCGCATG 61.279 66.667 12.50 12.50 0.00 4.06
6507 6598 3.952675 CCCACCATACGCGCATGC 61.953 66.667 13.99 7.91 37.91 4.06
6517 6608 4.062183 GCGCATGCGGAAAAAGAG 57.938 55.556 38.22 10.57 40.19 2.85
6518 6609 1.210155 GCGCATGCGGAAAAAGAGT 59.790 52.632 38.22 0.00 40.19 3.24
6519 6610 0.387239 GCGCATGCGGAAAAAGAGTT 60.387 50.000 38.22 0.00 40.19 3.01
6520 6611 1.330306 CGCATGCGGAAAAAGAGTTG 58.670 50.000 31.99 0.00 35.56 3.16
6521 6612 1.701704 GCATGCGGAAAAAGAGTTGG 58.298 50.000 0.00 0.00 0.00 3.77
6522 6613 1.000274 GCATGCGGAAAAAGAGTTGGT 60.000 47.619 0.00 0.00 0.00 3.67
6523 6614 2.922335 GCATGCGGAAAAAGAGTTGGTC 60.922 50.000 0.00 0.00 0.00 4.02
6524 6615 0.941542 TGCGGAAAAAGAGTTGGTCG 59.058 50.000 0.00 0.00 0.00 4.79
6525 6616 0.237498 GCGGAAAAAGAGTTGGTCGG 59.763 55.000 0.00 0.00 0.00 4.79
6526 6617 0.237498 CGGAAAAAGAGTTGGTCGGC 59.763 55.000 0.00 0.00 0.00 5.54
6527 6618 0.237498 GGAAAAAGAGTTGGTCGGCG 59.763 55.000 0.00 0.00 0.00 6.46
6528 6619 1.223187 GAAAAAGAGTTGGTCGGCGA 58.777 50.000 4.99 4.99 0.00 5.54
6529 6620 1.194772 GAAAAAGAGTTGGTCGGCGAG 59.805 52.381 11.20 0.00 0.00 5.03
6530 6621 1.228657 AAAAGAGTTGGTCGGCGAGC 61.229 55.000 30.23 30.23 0.00 5.03
6531 6622 2.100879 AAAGAGTTGGTCGGCGAGCT 62.101 55.000 34.79 18.87 0.00 4.09
6532 6623 2.048127 GAGTTGGTCGGCGAGCTT 60.048 61.111 34.79 22.22 0.00 3.74
6533 6624 2.048127 AGTTGGTCGGCGAGCTTC 60.048 61.111 34.79 26.51 0.00 3.86
6534 6625 3.479269 GTTGGTCGGCGAGCTTCG 61.479 66.667 34.79 0.00 43.89 3.79
6535 6626 4.735132 TTGGTCGGCGAGCTTCGG 62.735 66.667 34.79 0.00 40.84 4.30
6546 6637 3.400007 GCTTCGGCGAGAACCATC 58.600 61.111 10.46 0.00 34.66 3.51
6547 6638 1.447838 GCTTCGGCGAGAACCATCA 60.448 57.895 10.46 0.00 34.66 3.07
6548 6639 1.019278 GCTTCGGCGAGAACCATCAA 61.019 55.000 10.46 0.00 34.66 2.57
6549 6640 1.656652 CTTCGGCGAGAACCATCAAT 58.343 50.000 10.46 0.00 34.66 2.57
6550 6641 2.009774 CTTCGGCGAGAACCATCAATT 58.990 47.619 10.46 0.00 34.66 2.32
6551 6642 1.368641 TCGGCGAGAACCATCAATTG 58.631 50.000 4.99 0.00 0.00 2.32
6552 6643 1.086696 CGGCGAGAACCATCAATTGT 58.913 50.000 0.00 0.00 0.00 2.71
6553 6644 1.468520 CGGCGAGAACCATCAATTGTT 59.531 47.619 0.00 0.00 0.00 2.83
6554 6645 2.476185 CGGCGAGAACCATCAATTGTTC 60.476 50.000 0.00 1.94 40.88 3.18
6559 6650 2.749621 AGAACCATCAATTGTTCTCGCC 59.250 45.455 5.13 0.00 46.11 5.54
6560 6651 2.198827 ACCATCAATTGTTCTCGCCA 57.801 45.000 5.13 0.00 0.00 5.69
6561 6652 1.812571 ACCATCAATTGTTCTCGCCAC 59.187 47.619 5.13 0.00 0.00 5.01
6562 6653 1.202065 CCATCAATTGTTCTCGCCACG 60.202 52.381 5.13 0.00 0.00 4.94
6563 6654 0.447801 ATCAATTGTTCTCGCCACGC 59.552 50.000 5.13 0.00 0.00 5.34
6564 6655 1.154225 CAATTGTTCTCGCCACGCC 60.154 57.895 0.00 0.00 0.00 5.68
6565 6656 2.332654 AATTGTTCTCGCCACGCCC 61.333 57.895 0.00 0.00 0.00 6.13
6576 6667 4.379243 CACGCCCCGTCTTCTGCT 62.379 66.667 0.00 0.00 38.32 4.24
6577 6668 4.070552 ACGCCCCGTCTTCTGCTC 62.071 66.667 0.00 0.00 33.69 4.26
6579 6670 4.070552 GCCCCGTCTTCTGCTCGT 62.071 66.667 0.00 0.00 0.00 4.18
6580 6671 2.707849 GCCCCGTCTTCTGCTCGTA 61.708 63.158 0.00 0.00 0.00 3.43
6581 6672 1.433879 CCCCGTCTTCTGCTCGTAG 59.566 63.158 0.00 0.00 0.00 3.51
6582 6673 1.226717 CCCGTCTTCTGCTCGTAGC 60.227 63.158 0.58 0.58 42.82 3.58
6591 6682 3.917760 GCTCGTAGCATCGCCCCT 61.918 66.667 2.53 0.00 41.89 4.79
6592 6683 2.561956 GCTCGTAGCATCGCCCCTA 61.562 63.158 2.53 0.00 41.89 3.53
6593 6684 1.581954 CTCGTAGCATCGCCCCTAG 59.418 63.158 0.00 0.00 0.00 3.02
6594 6685 1.152819 TCGTAGCATCGCCCCTAGT 60.153 57.895 0.00 0.00 0.00 2.57
6595 6686 0.754217 TCGTAGCATCGCCCCTAGTT 60.754 55.000 0.00 0.00 0.00 2.24
6596 6687 0.597637 CGTAGCATCGCCCCTAGTTG 60.598 60.000 0.00 0.00 0.00 3.16
6597 6688 0.464452 GTAGCATCGCCCCTAGTTGT 59.536 55.000 0.00 0.00 0.00 3.32
6598 6689 1.684983 GTAGCATCGCCCCTAGTTGTA 59.315 52.381 0.00 0.00 0.00 2.41
6599 6690 0.753262 AGCATCGCCCCTAGTTGTAG 59.247 55.000 0.00 0.00 0.00 2.74
6600 6691 0.880718 GCATCGCCCCTAGTTGTAGC 60.881 60.000 0.00 0.00 0.00 3.58
6601 6692 0.753262 CATCGCCCCTAGTTGTAGCT 59.247 55.000 0.00 0.00 0.00 3.32
6602 6693 1.961394 CATCGCCCCTAGTTGTAGCTA 59.039 52.381 0.00 0.00 0.00 3.32
6603 6694 2.376695 TCGCCCCTAGTTGTAGCTAT 57.623 50.000 0.00 0.00 0.00 2.97
6604 6695 2.236766 TCGCCCCTAGTTGTAGCTATC 58.763 52.381 0.00 0.00 0.00 2.08
6605 6696 1.068472 CGCCCCTAGTTGTAGCTATCG 60.068 57.143 0.00 0.00 0.00 2.92
6606 6697 2.236766 GCCCCTAGTTGTAGCTATCGA 58.763 52.381 0.00 0.00 0.00 3.59
6607 6698 2.626743 GCCCCTAGTTGTAGCTATCGAA 59.373 50.000 0.00 0.00 0.00 3.71
6608 6699 3.305471 GCCCCTAGTTGTAGCTATCGAAG 60.305 52.174 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.838339 CAAGTTTAGTTGTATAGGATGGAGAAT 57.162 33.333 0.00 0.00 0.00 2.40
29 30 7.275920 AGCAAGTTTAGTTGTATAGGATGGAG 58.724 38.462 0.00 0.00 0.00 3.86
34 35 7.419711 AGCTAGCAAGTTTAGTTGTATAGGA 57.580 36.000 18.83 0.00 0.00 2.94
54 55 4.570772 CAGCATTTACGAGCCTTTTAGCTA 59.429 41.667 0.00 0.00 45.15 3.32
79 80 3.952628 GAACGTTCGCTGGGAGGGG 62.953 68.421 13.36 0.00 0.00 4.79
93 94 1.792949 GACCATAATAGCTGGCGAACG 59.207 52.381 0.00 0.00 37.27 3.95
94 95 2.143925 GGACCATAATAGCTGGCGAAC 58.856 52.381 0.00 0.00 37.27 3.95
164 176 4.640364 TCGTACGTATTTCCAGGGTTTTT 58.360 39.130 16.05 0.00 0.00 1.94
177 189 5.540911 TGTTTCCCTTTTTCTCGTACGTAT 58.459 37.500 16.05 0.00 0.00 3.06
185 197 3.222603 TGCTCCTGTTTCCCTTTTTCTC 58.777 45.455 0.00 0.00 0.00 2.87
187 199 3.492656 GGTTGCTCCTGTTTCCCTTTTTC 60.493 47.826 0.00 0.00 0.00 2.29
202 224 2.368685 CGTACGTTTTGTTGGTTGCTC 58.631 47.619 7.22 0.00 0.00 4.26
204 226 1.468895 CCGTACGTTTTGTTGGTTGC 58.531 50.000 15.21 0.00 0.00 4.17
254 276 1.592400 CTCTGACAAGCGGGTCCGTA 61.592 60.000 11.25 0.00 42.09 4.02
859 896 1.674057 GGCGGGGATGGAGTATGAG 59.326 63.158 0.00 0.00 0.00 2.90
860 897 1.841556 GGGCGGGGATGGAGTATGA 60.842 63.158 0.00 0.00 0.00 2.15
861 898 2.750350 GGGCGGGGATGGAGTATG 59.250 66.667 0.00 0.00 0.00 2.39
876 913 1.737199 TGGGATTTATAGGACGGGGG 58.263 55.000 0.00 0.00 0.00 5.40
1065 1102 1.153823 GACGGAGATGGTGGTCGTG 60.154 63.158 0.00 0.00 34.06 4.35
1305 1342 1.447314 GAACGGACGGCGGAAGAAT 60.447 57.895 13.24 0.00 0.00 2.40
1674 1711 8.579850 AAACTGAGACAATTATGCATTTAGGA 57.420 30.769 3.54 0.00 0.00 2.94
1689 1726 6.971726 TCTAAGTTGGTAGAAACTGAGACA 57.028 37.500 0.80 0.00 41.06 3.41
1782 1819 3.805971 AGTTGCTGAATTCTTGCAAAAGC 59.194 39.130 27.79 18.07 46.22 3.51
2021 2058 3.386402 CCCCTGCCTGTTTCTTACAAAAA 59.614 43.478 0.00 0.00 36.02 1.94
2022 2059 2.962421 CCCCTGCCTGTTTCTTACAAAA 59.038 45.455 0.00 0.00 36.02 2.44
2023 2060 2.175931 TCCCCTGCCTGTTTCTTACAAA 59.824 45.455 0.00 0.00 36.02 2.83
2024 2061 1.777878 TCCCCTGCCTGTTTCTTACAA 59.222 47.619 0.00 0.00 36.02 2.41
2025 2062 1.440618 TCCCCTGCCTGTTTCTTACA 58.559 50.000 0.00 0.00 34.95 2.41
2026 2063 2.808906 ATCCCCTGCCTGTTTCTTAC 57.191 50.000 0.00 0.00 0.00 2.34
2035 2076 1.074566 GCATAAGCTAATCCCCTGCCT 59.925 52.381 0.00 0.00 37.91 4.75
2122 2163 3.350833 ACTCCAGCTAAAATTCTGCCAG 58.649 45.455 0.00 0.00 0.00 4.85
2204 2245 4.629634 TCATACTAACAAAGTGCCACGATG 59.370 41.667 0.00 2.02 39.39 3.84
2207 2248 4.629634 TGATCATACTAACAAAGTGCCACG 59.370 41.667 0.00 0.00 39.39 4.94
2347 2389 7.654022 AACATCAAGGACTTGGAAAACTTAA 57.346 32.000 11.76 0.00 40.78 1.85
2348 2390 7.654022 AAACATCAAGGACTTGGAAAACTTA 57.346 32.000 11.76 0.00 40.78 2.24
2439 2481 9.671279 ACTCAACTCATCACAATATCAACATAA 57.329 29.630 0.00 0.00 0.00 1.90
2747 2789 8.576442 CAAGGGTTCAAATAGTTGATGTAAGTT 58.424 33.333 6.42 0.00 43.29 2.66
2803 2845 9.755064 CGAATAAAAGAACGACAATATGAAAGT 57.245 29.630 0.00 0.00 0.00 2.66
2847 2889 2.298446 AGCGATATGTGATGACAGGGAG 59.702 50.000 0.00 0.00 34.87 4.30
2976 3021 8.023128 TGAACTGTTAAGCTTAATGAAGATTGC 58.977 33.333 21.28 6.48 41.33 3.56
3044 3089 6.708285 AGAAAGTTGTCCATAACCTAACGAT 58.292 36.000 0.00 0.00 0.00 3.73
3065 3110 3.882888 CTGGTAGTCAAACAGCCAAAGAA 59.117 43.478 0.00 0.00 0.00 2.52
3147 3192 6.128336 GCACATCCTCAATAGATATTGCTGTC 60.128 42.308 7.56 2.09 42.06 3.51
4346 4423 9.162764 ACAATACATAGGTAAATCGCCAATATC 57.837 33.333 0.00 0.00 32.19 1.63
4362 4439 6.037500 AGCTGCAATACACACACAATACATAG 59.962 38.462 1.02 0.00 0.00 2.23
4432 4509 6.617879 CGCCTTAACCAGCTTAAAAACTAAT 58.382 36.000 0.00 0.00 0.00 1.73
4605 4682 6.515272 AAGGTGACATTGATTTGGATGTAC 57.485 37.500 0.00 0.00 36.67 2.90
4656 4733 5.959618 AGATGGATGATGTGCACATAATG 57.040 39.130 30.69 0.00 36.57 1.90
4728 4805 1.002087 CACACCTCCCTACAACAGTCC 59.998 57.143 0.00 0.00 0.00 3.85
4734 4811 4.148838 CCAATTTTCACACCTCCCTACAA 58.851 43.478 0.00 0.00 0.00 2.41
4783 4860 6.756074 TCAACATGTTTAAGCAAGACAAAAGG 59.244 34.615 8.77 0.00 0.00 3.11
4784 4861 7.515684 GCTCAACATGTTTAAGCAAGACAAAAG 60.516 37.037 26.63 6.49 33.21 2.27
4966 5043 4.744795 AGAGACTTGACAACACAAGAGT 57.255 40.909 14.00 2.27 46.85 3.24
5084 5161 1.194772 GCGTCAGTGGAGTTTTGTAGC 59.805 52.381 0.00 0.00 0.00 3.58
5561 5638 5.469421 GTCAATCCATGCAAAAATTTGGTGA 59.531 36.000 7.89 0.00 38.57 4.02
5620 5697 2.684843 GCAGCTGAGGCGAAACAGG 61.685 63.158 20.43 0.00 44.37 4.00
5766 5843 9.830975 AAAACAGGTAAAAACATATCTTTGCTT 57.169 25.926 0.00 0.00 0.00 3.91
5767 5844 9.830975 AAAAACAGGTAAAAACATATCTTTGCT 57.169 25.926 0.00 0.00 0.00 3.91
5802 5881 6.543831 AGATTAAGAATGATGTAACAGCACCC 59.456 38.462 0.00 0.00 30.87 4.61
5926 6005 2.965572 CTTCTCTGAGAAGCAGGAGG 57.034 55.000 28.68 9.72 44.35 4.30
6060 6151 3.634504 TGCTTCCTATGCAATGTTGGAT 58.365 40.909 5.13 5.13 42.16 3.41
6093 6184 1.418342 CGAAACATAGCACCCCGTCG 61.418 60.000 0.00 0.00 0.00 5.12
6096 6187 2.469516 GGCGAAACATAGCACCCCG 61.470 63.158 0.00 0.00 34.54 5.73
6195 6286 2.564947 CCAGTGGCTAGACTGTCTCTTT 59.435 50.000 14.62 0.00 41.65 2.52
6258 6349 2.485582 CGTCGATCTCAGCCACGT 59.514 61.111 0.00 0.00 0.00 4.49
6262 6353 2.650813 ATTGCCCGTCGATCTCAGCC 62.651 60.000 0.00 0.00 0.00 4.85
6264 6355 0.103026 TGATTGCCCGTCGATCTCAG 59.897 55.000 0.00 0.00 36.68 3.35
6304 6395 2.283298 GATGGCTCGTCATCACATGTT 58.717 47.619 6.63 0.00 42.16 2.71
6324 6415 2.348660 TGGCTCGTAAAATACCAACGG 58.651 47.619 0.00 0.00 37.24 4.44
6338 6429 4.889832 AATCTGAAAGCTTTATGGCTCG 57.110 40.909 12.68 0.00 42.24 5.03
6341 6432 5.402398 ACGAAAATCTGAAAGCTTTATGGC 58.598 37.500 12.68 0.00 29.77 4.40
6349 6440 6.411652 CGGAAGTATACGAAAATCTGAAAGC 58.588 40.000 0.00 0.00 0.00 3.51
6367 6458 2.146342 CACAGTGATCTTTGCGGAAGT 58.854 47.619 0.00 0.00 36.70 3.01
6368 6459 1.135859 GCACAGTGATCTTTGCGGAAG 60.136 52.381 4.15 0.00 37.57 3.46
6369 6460 0.874390 GCACAGTGATCTTTGCGGAA 59.126 50.000 4.15 0.00 37.57 4.30
6370 6461 2.543578 GCACAGTGATCTTTGCGGA 58.456 52.632 4.15 0.00 37.57 5.54
6373 6464 3.631145 TTGAAGCACAGTGATCTTTGC 57.369 42.857 4.15 0.00 44.73 3.68
6374 6465 8.752766 ATATTTTTGAAGCACAGTGATCTTTG 57.247 30.769 4.15 0.00 0.00 2.77
6375 6466 8.579006 TGATATTTTTGAAGCACAGTGATCTTT 58.421 29.630 4.15 0.00 0.00 2.52
6376 6467 8.114331 TGATATTTTTGAAGCACAGTGATCTT 57.886 30.769 4.15 0.00 0.00 2.40
6377 6468 7.609146 TCTGATATTTTTGAAGCACAGTGATCT 59.391 33.333 4.15 0.00 0.00 2.75
6378 6469 7.695618 GTCTGATATTTTTGAAGCACAGTGATC 59.304 37.037 4.15 2.16 0.00 2.92
6379 6470 7.362401 GGTCTGATATTTTTGAAGCACAGTGAT 60.362 37.037 4.15 0.00 0.00 3.06
6380 6471 6.072508 GGTCTGATATTTTTGAAGCACAGTGA 60.073 38.462 4.15 0.00 0.00 3.41
6381 6472 6.072286 AGGTCTGATATTTTTGAAGCACAGTG 60.072 38.462 0.00 0.00 0.00 3.66
6382 6473 6.006449 AGGTCTGATATTTTTGAAGCACAGT 58.994 36.000 0.00 0.00 0.00 3.55
6383 6474 6.072286 ACAGGTCTGATATTTTTGAAGCACAG 60.072 38.462 4.84 0.00 0.00 3.66
6384 6475 5.769662 ACAGGTCTGATATTTTTGAAGCACA 59.230 36.000 4.84 0.00 0.00 4.57
6385 6476 6.259550 ACAGGTCTGATATTTTTGAAGCAC 57.740 37.500 4.84 0.00 0.00 4.40
6386 6477 6.899393 AACAGGTCTGATATTTTTGAAGCA 57.101 33.333 4.84 0.00 0.00 3.91
6387 6478 6.089954 GCAAACAGGTCTGATATTTTTGAAGC 59.910 38.462 4.84 0.00 0.00 3.86
6388 6479 6.587608 GGCAAACAGGTCTGATATTTTTGAAG 59.412 38.462 4.84 0.00 0.00 3.02
6389 6480 6.454795 GGCAAACAGGTCTGATATTTTTGAA 58.545 36.000 4.84 0.00 0.00 2.69
6390 6481 5.047377 GGGCAAACAGGTCTGATATTTTTGA 60.047 40.000 4.84 0.00 0.00 2.69
6391 6482 5.047092 AGGGCAAACAGGTCTGATATTTTTG 60.047 40.000 4.84 5.94 0.00 2.44
6392 6483 5.086621 AGGGCAAACAGGTCTGATATTTTT 58.913 37.500 4.84 0.00 0.00 1.94
6393 6484 4.677182 AGGGCAAACAGGTCTGATATTTT 58.323 39.130 4.84 0.00 0.00 1.82
6394 6485 4.273318 GAGGGCAAACAGGTCTGATATTT 58.727 43.478 4.84 0.00 0.00 1.40
6395 6486 3.372025 GGAGGGCAAACAGGTCTGATATT 60.372 47.826 4.84 0.00 0.00 1.28
6396 6487 2.173569 GGAGGGCAAACAGGTCTGATAT 59.826 50.000 4.84 0.00 0.00 1.63
6397 6488 1.559682 GGAGGGCAAACAGGTCTGATA 59.440 52.381 4.84 0.00 0.00 2.15
6398 6489 0.329596 GGAGGGCAAACAGGTCTGAT 59.670 55.000 4.84 0.00 0.00 2.90
6399 6490 1.761174 GGAGGGCAAACAGGTCTGA 59.239 57.895 4.84 0.00 0.00 3.27
6400 6491 1.303643 GGGAGGGCAAACAGGTCTG 60.304 63.158 0.00 0.00 0.00 3.51
6401 6492 2.539081 GGGGAGGGCAAACAGGTCT 61.539 63.158 0.00 0.00 0.00 3.85
6402 6493 2.035783 GGGGAGGGCAAACAGGTC 59.964 66.667 0.00 0.00 0.00 3.85
6403 6494 2.452491 AGGGGAGGGCAAACAGGT 60.452 61.111 0.00 0.00 0.00 4.00
6404 6495 2.036256 CAGGGGAGGGCAAACAGG 59.964 66.667 0.00 0.00 0.00 4.00
6405 6496 1.303643 GACAGGGGAGGGCAAACAG 60.304 63.158 0.00 0.00 0.00 3.16
6406 6497 2.843545 GACAGGGGAGGGCAAACA 59.156 61.111 0.00 0.00 0.00 2.83
6407 6498 2.359975 CGACAGGGGAGGGCAAAC 60.360 66.667 0.00 0.00 0.00 2.93
6408 6499 2.852075 ACGACAGGGGAGGGCAAA 60.852 61.111 0.00 0.00 0.00 3.68
6409 6500 3.319198 GACGACAGGGGAGGGCAA 61.319 66.667 0.00 0.00 0.00 4.52
6410 6501 3.846405 AAGACGACAGGGGAGGGCA 62.846 63.158 0.00 0.00 0.00 5.36
6411 6502 3.003763 AAGACGACAGGGGAGGGC 61.004 66.667 0.00 0.00 0.00 5.19
6412 6503 1.305381 AGAAGACGACAGGGGAGGG 60.305 63.158 0.00 0.00 0.00 4.30
6413 6504 1.324005 GGAGAAGACGACAGGGGAGG 61.324 65.000 0.00 0.00 0.00 4.30
6414 6505 0.323908 AGGAGAAGACGACAGGGGAG 60.324 60.000 0.00 0.00 0.00 4.30
6415 6506 0.114560 AAGGAGAAGACGACAGGGGA 59.885 55.000 0.00 0.00 0.00 4.81
6416 6507 0.533032 GAAGGAGAAGACGACAGGGG 59.467 60.000 0.00 0.00 0.00 4.79
6417 6508 0.533032 GGAAGGAGAAGACGACAGGG 59.467 60.000 0.00 0.00 0.00 4.45
6418 6509 1.067495 GTGGAAGGAGAAGACGACAGG 60.067 57.143 0.00 0.00 0.00 4.00
6419 6510 1.067495 GGTGGAAGGAGAAGACGACAG 60.067 57.143 0.00 0.00 0.00 3.51
6420 6511 0.966920 GGTGGAAGGAGAAGACGACA 59.033 55.000 0.00 0.00 0.00 4.35
6421 6512 0.966920 TGGTGGAAGGAGAAGACGAC 59.033 55.000 0.00 0.00 0.00 4.34
6422 6513 0.966920 GTGGTGGAAGGAGAAGACGA 59.033 55.000 0.00 0.00 0.00 4.20
6423 6514 0.388649 CGTGGTGGAAGGAGAAGACG 60.389 60.000 0.00 0.00 0.00 4.18
6424 6515 0.680061 ACGTGGTGGAAGGAGAAGAC 59.320 55.000 0.00 0.00 0.00 3.01
6425 6516 0.679505 CACGTGGTGGAAGGAGAAGA 59.320 55.000 7.95 0.00 0.00 2.87
6426 6517 0.951040 GCACGTGGTGGAAGGAGAAG 60.951 60.000 18.88 0.00 33.64 2.85
6427 6518 1.070786 GCACGTGGTGGAAGGAGAA 59.929 57.895 18.88 0.00 33.64 2.87
6428 6519 1.407656 AAGCACGTGGTGGAAGGAGA 61.408 55.000 22.63 0.00 33.64 3.71
6429 6520 0.951040 GAAGCACGTGGTGGAAGGAG 60.951 60.000 22.63 0.00 33.64 3.69
6430 6521 1.070786 GAAGCACGTGGTGGAAGGA 59.929 57.895 22.63 0.00 33.64 3.36
6431 6522 1.227823 TGAAGCACGTGGTGGAAGG 60.228 57.895 22.63 0.00 33.64 3.46
6432 6523 1.941812 GTGAAGCACGTGGTGGAAG 59.058 57.895 22.63 0.00 33.64 3.46
6433 6524 4.134623 GTGAAGCACGTGGTGGAA 57.865 55.556 22.63 7.11 33.64 3.53
6444 6535 5.219540 GGAAATTTTTCGCTGCGTGAAGC 62.220 47.826 22.48 5.30 41.30 3.86
6445 6536 2.405025 GGAAATTTTTCGCTGCGTGAAG 59.595 45.455 22.48 0.00 38.06 3.02
6446 6537 2.034053 AGGAAATTTTTCGCTGCGTGAA 59.966 40.909 22.48 14.79 38.06 3.18
6447 6538 1.606668 AGGAAATTTTTCGCTGCGTGA 59.393 42.857 22.48 9.31 38.06 4.35
6448 6539 1.978782 GAGGAAATTTTTCGCTGCGTG 59.021 47.619 22.48 0.00 38.06 5.34
6449 6540 1.068541 GGAGGAAATTTTTCGCTGCGT 60.069 47.619 22.48 0.00 38.06 5.24
6450 6541 1.617740 GGAGGAAATTTTTCGCTGCG 58.382 50.000 17.25 17.25 38.06 5.18
6451 6542 1.546029 AGGGAGGAAATTTTTCGCTGC 59.454 47.619 16.94 0.00 38.06 5.25
6452 6543 3.084786 AGAGGGAGGAAATTTTTCGCTG 58.915 45.455 20.43 0.00 38.06 5.18
6453 6544 3.244911 TGAGAGGGAGGAAATTTTTCGCT 60.245 43.478 17.39 17.39 38.06 4.93
6454 6545 3.081804 TGAGAGGGAGGAAATTTTTCGC 58.918 45.455 10.71 10.71 38.06 4.70
6455 6546 3.440522 GGTGAGAGGGAGGAAATTTTTCG 59.559 47.826 0.00 0.00 38.06 3.46
6456 6547 4.667573 AGGTGAGAGGGAGGAAATTTTTC 58.332 43.478 0.00 0.00 36.46 2.29
6457 6548 4.749048 AGGTGAGAGGGAGGAAATTTTT 57.251 40.909 0.00 0.00 0.00 1.94
6458 6549 4.355287 AGAAGGTGAGAGGGAGGAAATTTT 59.645 41.667 0.00 0.00 0.00 1.82
6459 6550 3.919554 AGAAGGTGAGAGGGAGGAAATTT 59.080 43.478 0.00 0.00 0.00 1.82
6460 6551 3.521531 GAGAAGGTGAGAGGGAGGAAATT 59.478 47.826 0.00 0.00 0.00 1.82
6461 6552 3.111484 GAGAAGGTGAGAGGGAGGAAAT 58.889 50.000 0.00 0.00 0.00 2.17
6462 6553 2.112691 AGAGAAGGTGAGAGGGAGGAAA 59.887 50.000 0.00 0.00 0.00 3.13
6463 6554 1.719378 AGAGAAGGTGAGAGGGAGGAA 59.281 52.381 0.00 0.00 0.00 3.36
6464 6555 1.286553 GAGAGAAGGTGAGAGGGAGGA 59.713 57.143 0.00 0.00 0.00 3.71
6465 6556 1.006519 TGAGAGAAGGTGAGAGGGAGG 59.993 57.143 0.00 0.00 0.00 4.30
6466 6557 2.495669 GTTGAGAGAAGGTGAGAGGGAG 59.504 54.545 0.00 0.00 0.00 4.30
6467 6558 2.110899 AGTTGAGAGAAGGTGAGAGGGA 59.889 50.000 0.00 0.00 0.00 4.20
6468 6559 2.495669 GAGTTGAGAGAAGGTGAGAGGG 59.504 54.545 0.00 0.00 0.00 4.30
6469 6560 2.495669 GGAGTTGAGAGAAGGTGAGAGG 59.504 54.545 0.00 0.00 0.00 3.69
6470 6561 2.495669 GGGAGTTGAGAGAAGGTGAGAG 59.504 54.545 0.00 0.00 0.00 3.20
6471 6562 2.530701 GGGAGTTGAGAGAAGGTGAGA 58.469 52.381 0.00 0.00 0.00 3.27
6472 6563 1.552792 GGGGAGTTGAGAGAAGGTGAG 59.447 57.143 0.00 0.00 0.00 3.51
6473 6564 1.132849 TGGGGAGTTGAGAGAAGGTGA 60.133 52.381 0.00 0.00 0.00 4.02
6474 6565 1.002544 GTGGGGAGTTGAGAGAAGGTG 59.997 57.143 0.00 0.00 0.00 4.00
6475 6566 1.353091 GTGGGGAGTTGAGAGAAGGT 58.647 55.000 0.00 0.00 0.00 3.50
6476 6567 0.615850 GGTGGGGAGTTGAGAGAAGG 59.384 60.000 0.00 0.00 0.00 3.46
6477 6568 1.352083 TGGTGGGGAGTTGAGAGAAG 58.648 55.000 0.00 0.00 0.00 2.85
6478 6569 2.044793 ATGGTGGGGAGTTGAGAGAA 57.955 50.000 0.00 0.00 0.00 2.87
6479 6570 2.467880 GTATGGTGGGGAGTTGAGAGA 58.532 52.381 0.00 0.00 0.00 3.10
6480 6571 1.137086 CGTATGGTGGGGAGTTGAGAG 59.863 57.143 0.00 0.00 0.00 3.20
6481 6572 1.191535 CGTATGGTGGGGAGTTGAGA 58.808 55.000 0.00 0.00 0.00 3.27
6482 6573 0.462047 GCGTATGGTGGGGAGTTGAG 60.462 60.000 0.00 0.00 0.00 3.02
6483 6574 1.600107 GCGTATGGTGGGGAGTTGA 59.400 57.895 0.00 0.00 0.00 3.18
6484 6575 1.813753 CGCGTATGGTGGGGAGTTG 60.814 63.158 0.00 0.00 0.00 3.16
6485 6576 2.582436 CGCGTATGGTGGGGAGTT 59.418 61.111 0.00 0.00 0.00 3.01
6486 6577 4.157120 GCGCGTATGGTGGGGAGT 62.157 66.667 8.43 0.00 0.00 3.85
6487 6578 3.460672 ATGCGCGTATGGTGGGGAG 62.461 63.158 9.48 0.00 0.00 4.30
6488 6579 3.475494 ATGCGCGTATGGTGGGGA 61.475 61.111 9.48 0.00 0.00 4.81
6489 6580 3.279116 CATGCGCGTATGGTGGGG 61.279 66.667 26.94 2.38 0.00 4.96
6490 6581 3.952675 GCATGCGCGTATGGTGGG 61.953 66.667 33.11 12.57 0.00 4.61
6500 6591 0.387239 AACTCTTTTTCCGCATGCGC 60.387 50.000 34.00 0.00 38.24 6.09
6501 6592 1.330306 CAACTCTTTTTCCGCATGCG 58.670 50.000 32.60 32.60 39.44 4.73
6502 6593 1.000274 ACCAACTCTTTTTCCGCATGC 60.000 47.619 7.91 7.91 0.00 4.06
6503 6594 2.665519 CGACCAACTCTTTTTCCGCATG 60.666 50.000 0.00 0.00 0.00 4.06
6504 6595 1.535462 CGACCAACTCTTTTTCCGCAT 59.465 47.619 0.00 0.00 0.00 4.73
6505 6596 0.941542 CGACCAACTCTTTTTCCGCA 59.058 50.000 0.00 0.00 0.00 5.69
6506 6597 0.237498 CCGACCAACTCTTTTTCCGC 59.763 55.000 0.00 0.00 0.00 5.54
6507 6598 0.237498 GCCGACCAACTCTTTTTCCG 59.763 55.000 0.00 0.00 0.00 4.30
6508 6599 0.237498 CGCCGACCAACTCTTTTTCC 59.763 55.000 0.00 0.00 0.00 3.13
6509 6600 1.194772 CTCGCCGACCAACTCTTTTTC 59.805 52.381 0.00 0.00 0.00 2.29
6510 6601 1.226746 CTCGCCGACCAACTCTTTTT 58.773 50.000 0.00 0.00 0.00 1.94
6511 6602 1.228657 GCTCGCCGACCAACTCTTTT 61.229 55.000 0.00 0.00 0.00 2.27
6512 6603 1.668151 GCTCGCCGACCAACTCTTT 60.668 57.895 0.00 0.00 0.00 2.52
6513 6604 2.048127 GCTCGCCGACCAACTCTT 60.048 61.111 0.00 0.00 0.00 2.85
6514 6605 2.493907 GAAGCTCGCCGACCAACTCT 62.494 60.000 0.00 0.00 0.00 3.24
6515 6606 2.048127 AAGCTCGCCGACCAACTC 60.048 61.111 0.00 0.00 0.00 3.01
6516 6607 2.048127 GAAGCTCGCCGACCAACT 60.048 61.111 0.00 0.00 0.00 3.16
6517 6608 3.479269 CGAAGCTCGCCGACCAAC 61.479 66.667 0.00 0.00 31.14 3.77
6518 6609 4.735132 CCGAAGCTCGCCGACCAA 62.735 66.667 4.93 0.00 38.82 3.67
6524 6615 4.796231 TTCTCGCCGAAGCTCGCC 62.796 66.667 0.00 0.00 38.82 5.54
6525 6616 3.546397 GTTCTCGCCGAAGCTCGC 61.546 66.667 0.00 0.00 38.82 5.03
6526 6617 2.881352 GGTTCTCGCCGAAGCTCG 60.881 66.667 8.57 0.00 44.63 5.03
6530 6621 1.656652 ATTGATGGTTCTCGCCGAAG 58.343 50.000 0.00 0.00 30.85 3.79
6531 6622 1.737236 CAATTGATGGTTCTCGCCGAA 59.263 47.619 0.00 0.00 0.00 4.30
6532 6623 1.338674 ACAATTGATGGTTCTCGCCGA 60.339 47.619 13.59 0.00 0.00 5.54
6533 6624 1.086696 ACAATTGATGGTTCTCGCCG 58.913 50.000 13.59 0.00 0.00 6.46
6534 6625 3.136808 GAACAATTGATGGTTCTCGCC 57.863 47.619 13.59 0.00 40.12 5.54
6539 6630 2.487762 TGGCGAGAACAATTGATGGTTC 59.512 45.455 13.59 5.43 42.82 3.62
6540 6631 2.228822 GTGGCGAGAACAATTGATGGTT 59.771 45.455 13.59 0.00 0.00 3.67
6541 6632 1.812571 GTGGCGAGAACAATTGATGGT 59.187 47.619 13.59 0.00 0.00 3.55
6542 6633 1.202065 CGTGGCGAGAACAATTGATGG 60.202 52.381 13.59 0.33 0.00 3.51
6543 6634 1.791555 GCGTGGCGAGAACAATTGATG 60.792 52.381 13.59 0.00 0.00 3.07
6544 6635 0.447801 GCGTGGCGAGAACAATTGAT 59.552 50.000 13.59 0.00 0.00 2.57
6545 6636 1.573829 GGCGTGGCGAGAACAATTGA 61.574 55.000 13.59 0.00 0.00 2.57
6546 6637 1.154225 GGCGTGGCGAGAACAATTG 60.154 57.895 3.24 3.24 0.00 2.32
6547 6638 2.332654 GGGCGTGGCGAGAACAATT 61.333 57.895 0.00 0.00 0.00 2.32
6548 6639 2.746277 GGGCGTGGCGAGAACAAT 60.746 61.111 0.00 0.00 0.00 2.71
6559 6650 4.379243 AGCAGAAGACGGGGCGTG 62.379 66.667 0.00 0.00 41.37 5.34
6560 6651 4.070552 GAGCAGAAGACGGGGCGT 62.071 66.667 0.00 0.00 45.10 5.68
6562 6653 2.615262 CTACGAGCAGAAGACGGGGC 62.615 65.000 0.00 0.00 0.00 5.80
6563 6654 1.433879 CTACGAGCAGAAGACGGGG 59.566 63.158 0.00 0.00 0.00 5.73
6564 6655 1.226717 GCTACGAGCAGAAGACGGG 60.227 63.158 0.00 0.00 41.89 5.28
6565 6656 4.386245 GCTACGAGCAGAAGACGG 57.614 61.111 0.00 0.00 41.89 4.79
6574 6665 2.479412 CTAGGGGCGATGCTACGAGC 62.479 65.000 7.23 0.00 42.82 5.03
6575 6666 1.173444 ACTAGGGGCGATGCTACGAG 61.173 60.000 7.23 0.00 35.09 4.18
6576 6667 0.754217 AACTAGGGGCGATGCTACGA 60.754 55.000 7.23 0.00 35.09 3.43
6577 6668 0.597637 CAACTAGGGGCGATGCTACG 60.598 60.000 0.00 0.00 0.00 3.51
6578 6669 0.464452 ACAACTAGGGGCGATGCTAC 59.536 55.000 0.00 0.00 0.00 3.58
6579 6670 1.961394 CTACAACTAGGGGCGATGCTA 59.039 52.381 0.00 0.00 0.00 3.49
6580 6671 0.753262 CTACAACTAGGGGCGATGCT 59.247 55.000 0.00 0.00 0.00 3.79
6581 6672 0.880718 GCTACAACTAGGGGCGATGC 60.881 60.000 0.00 0.00 0.00 3.91
6582 6673 0.753262 AGCTACAACTAGGGGCGATG 59.247 55.000 0.00 0.00 0.00 3.84
6583 6674 2.376695 TAGCTACAACTAGGGGCGAT 57.623 50.000 0.00 0.00 0.00 4.58
6584 6675 2.236766 GATAGCTACAACTAGGGGCGA 58.763 52.381 0.00 0.00 0.00 5.54
6585 6676 1.068472 CGATAGCTACAACTAGGGGCG 60.068 57.143 0.00 0.00 0.00 6.13
6586 6677 2.236766 TCGATAGCTACAACTAGGGGC 58.763 52.381 0.00 0.00 0.00 5.80
6587 6678 3.305471 GCTTCGATAGCTACAACTAGGGG 60.305 52.174 0.00 0.00 46.77 4.79
6588 6679 3.903360 GCTTCGATAGCTACAACTAGGG 58.097 50.000 0.00 0.00 46.77 3.53
6600 6691 4.664677 CCGGGGCGGCTTCGATAG 62.665 72.222 21.72 6.32 41.17 2.08


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

AutoCloner maintained by Alex Coulton.