Multiple sequence alignment - TraesCS3A01G416800

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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 TraesCS3A01G416800 chr3A 100.000 2513 0 0 1 2513 659041569 659039057 0.000000e+00 4641.0
1 TraesCS3A01G416800 chr3A 98.901 91 1 0 2065 2155 666243428 666243518 2.000000e-36 163.0
2 TraesCS3A01G416800 chr3D 88.668 1156 58 23 747 1873 524775320 524774209 0.000000e+00 1341.0
3 TraesCS3A01G416800 chr3D 91.540 461 28 3 66 516 524778033 524777574 2.120000e-175 625.0
4 TraesCS3A01G416800 chr3D 88.288 222 16 6 541 760 524775554 524775341 8.920000e-65 257.0
5 TraesCS3A01G416800 chr3D 89.412 170 12 3 1863 2030 524774191 524774026 2.530000e-50 209.0
6 TraesCS3A01G416800 chr3D 97.000 100 3 0 2055 2154 609371470 609371569 4.300000e-38 169.0
7 TraesCS3A01G416800 chr3D 93.750 64 4 0 2418 2481 524773197 524773134 2.060000e-16 97.1
8 TraesCS3A01G416800 chr3B 91.134 767 34 16 775 1525 692128582 692127834 0.000000e+00 1009.0
9 TraesCS3A01G416800 chr3B 90.181 387 27 5 80 455 692131224 692130838 6.240000e-136 494.0
10 TraesCS3A01G416800 chr3B 87.558 217 12 3 2276 2481 692127747 692127535 1.160000e-58 237.0
11 TraesCS3A01G416800 chr3B 88.421 95 11 0 2 96 692133395 692133301 5.680000e-22 115.0
12 TraesCS3A01G416800 chr7A 96.907 97 3 0 2062 2158 80596385 80596481 2.000000e-36 163.0
13 TraesCS3A01G416800 chr5A 96.875 96 3 0 2057 2152 27637042 27637137 7.190000e-36 161.0
14 TraesCS3A01G416800 chr1A 96.875 96 3 0 2056 2151 74436529 74436434 7.190000e-36 161.0
15 TraesCS3A01G416800 chr6B 93.458 107 5 2 2054 2158 504587213 504587107 9.310000e-35 158.0
16 TraesCS3A01G416800 chr5B 92.661 109 7 1 2060 2167 322205156 322205048 3.350000e-34 156.0
17 TraesCS3A01G416800 chr6D 91.743 109 7 2 2045 2151 72012849 72012741 1.560000e-32 150.0
18 TraesCS3A01G416800 chr2D 91.743 109 7 2 2045 2151 634303306 634303414 1.560000e-32 150.0


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 TraesCS3A01G416800 chr3A 659039057 659041569 2512 True 4641.00 4641 100.0000 1 2513 1 chr3A.!!$R1 2512
1 TraesCS3A01G416800 chr3D 524773134 524778033 4899 True 505.82 1341 90.3316 66 2481 5 chr3D.!!$R1 2415
2 TraesCS3A01G416800 chr3B 692127535 692133395 5860 True 463.75 1009 89.3235 2 2481 4 chr3B.!!$R1 2479

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
539 4722 0.676782 CCCCTGCTAGTCCGTTTTGG 60.677 60.0 0.0 0.0 40.09 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2262 8663 0.028505 GCTGCTCTGTGTGTGTTGTG 59.971 55.0 0.0 0.0 0.0 3.33 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
40 41 1.901464 TGTTGGAAGGCCGGCTTTC 60.901 57.895 36.05 36.05 36.79 2.62
46 47 1.488261 GAAGGCCGGCTTTCGTATCG 61.488 60.000 32.09 0.00 37.11 2.92
47 48 2.918230 AAGGCCGGCTTTCGTATCGG 62.918 60.000 28.56 0.00 44.70 4.18
58 59 2.642139 TCGTATCGGTGTCCAAAGAC 57.358 50.000 0.00 0.00 43.83 3.01
78 2172 2.046700 GTCCGATTTGGGGACGCA 60.047 61.111 0.00 0.00 44.04 5.24
136 2242 4.098196 TGGTTTATCATGACCATGCATGTG 59.902 41.667 24.58 17.76 44.59 3.21
214 2320 2.629137 TGTCCTTCCTAACGTAGTGCAA 59.371 45.455 0.00 0.00 45.00 4.08
275 2382 9.109393 GATAAGTTTATTCTTACATGACTGGCA 57.891 33.333 0.00 0.00 33.56 4.92
297 2411 2.900546 ACCACTCTTGAAGGTGACCTAG 59.099 50.000 3.68 0.00 35.69 3.02
329 2443 1.007271 CGAGACGTGTCTGTTGGCT 60.007 57.895 11.29 0.00 40.61 4.75
334 2448 1.595109 CGTGTCTGTTGGCTGCTCA 60.595 57.895 0.00 0.00 0.00 4.26
354 2468 2.095768 CACGTTGCTAATCACCAGGTTG 60.096 50.000 0.00 0.00 0.00 3.77
367 2481 2.425668 ACCAGGTTGTTTTCCGTTCTTG 59.574 45.455 0.00 0.00 0.00 3.02
440 2555 8.754230 AAACTAACGCTAAACTAACTAAGAGG 57.246 34.615 0.00 0.00 0.00 3.69
452 4635 6.473758 ACTAACTAAGAGGTGGGAAATGTTC 58.526 40.000 0.00 0.00 0.00 3.18
456 4639 3.425162 AGAGGTGGGAAATGTTCAGTC 57.575 47.619 0.00 0.00 0.00 3.51
481 4664 1.123077 TGATAGACCGATGCTTGCCT 58.877 50.000 0.00 0.00 0.00 4.75
504 4687 5.171476 TCTGCAAGCTACAGAGATGTAAAC 58.829 41.667 13.84 0.00 39.21 2.01
516 4699 8.500753 ACAGAGATGTAAACGGCAAATAAATA 57.499 30.769 0.00 0.00 0.00 1.40
517 4700 9.120538 ACAGAGATGTAAACGGCAAATAAATAT 57.879 29.630 0.00 0.00 0.00 1.28
518 4701 9.385902 CAGAGATGTAAACGGCAAATAAATATG 57.614 33.333 0.00 0.00 0.00 1.78
519 4702 8.567948 AGAGATGTAAACGGCAAATAAATATGG 58.432 33.333 0.00 0.00 0.00 2.74
523 4706 1.967779 ACGGCAAATAAATATGGCCCC 59.032 47.619 0.00 0.00 41.58 5.80
525 4708 2.029110 CGGCAAATAAATATGGCCCCTG 60.029 50.000 0.00 0.00 41.58 4.45
526 4709 2.289631 GGCAAATAAATATGGCCCCTGC 60.290 50.000 0.00 0.00 38.70 4.85
527 4710 2.634453 GCAAATAAATATGGCCCCTGCT 59.366 45.455 0.00 0.00 37.74 4.24
528 4711 3.831911 GCAAATAAATATGGCCCCTGCTA 59.168 43.478 0.00 0.00 37.74 3.49
529 4712 4.082026 GCAAATAAATATGGCCCCTGCTAG 60.082 45.833 0.00 0.00 37.74 3.42
530 4713 5.079643 CAAATAAATATGGCCCCTGCTAGT 58.920 41.667 0.00 0.00 37.74 2.57
532 4715 1.068121 AATATGGCCCCTGCTAGTCC 58.932 55.000 0.00 0.00 37.74 3.85
533 4716 1.194781 ATATGGCCCCTGCTAGTCCG 61.195 60.000 0.00 0.00 37.74 4.79
536 4719 2.669240 GCCCCTGCTAGTCCGTTT 59.331 61.111 0.00 0.00 33.53 3.60
538 4721 1.305930 GCCCCTGCTAGTCCGTTTTG 61.306 60.000 0.00 0.00 33.53 2.44
539 4722 0.676782 CCCCTGCTAGTCCGTTTTGG 60.677 60.000 0.00 0.00 40.09 3.28
553 6731 4.933400 TCCGTTTTGGTTAGCTTTAGCTAG 59.067 41.667 11.00 0.00 44.93 3.42
565 6743 4.369182 GCTTTAGCTAGCTCGATGGTTTA 58.631 43.478 23.26 0.00 38.15 2.01
572 6750 7.859325 AGCTAGCTCGATGGTTTATTTTAAA 57.141 32.000 12.68 0.00 0.00 1.52
573 6751 8.276252 AGCTAGCTCGATGGTTTATTTTAAAA 57.724 30.769 12.68 2.51 0.00 1.52
574 6752 8.736244 AGCTAGCTCGATGGTTTATTTTAAAAA 58.264 29.630 12.68 0.00 0.00 1.94
575 6753 8.795341 GCTAGCTCGATGGTTTATTTTAAAAAC 58.205 33.333 7.70 0.00 36.34 2.43
576 6754 9.834628 CTAGCTCGATGGTTTATTTTAAAAACA 57.165 29.630 4.44 0.64 40.18 2.83
620 6798 9.367160 CAATATAAGTGGGTTTAAATGGGATCT 57.633 33.333 0.00 0.00 0.00 2.75
627 6805 8.067488 AGTGGGTTTAAATGGGATCTGATTTAT 58.933 33.333 9.23 0.00 0.00 1.40
628 6806 9.362151 GTGGGTTTAAATGGGATCTGATTTATA 57.638 33.333 9.23 4.43 0.00 0.98
771 6986 1.079543 GCAGATCAGTGTGAGCCGT 60.080 57.895 0.00 0.00 32.25 5.68
804 7051 4.959210 TCTTTTTCCCAATGTCCAACTGAA 59.041 37.500 0.00 0.00 0.00 3.02
805 7052 5.602145 TCTTTTTCCCAATGTCCAACTGAAT 59.398 36.000 0.00 0.00 0.00 2.57
806 7053 5.885449 TTTTCCCAATGTCCAACTGAATT 57.115 34.783 0.00 0.00 0.00 2.17
807 7054 6.985653 TTTTCCCAATGTCCAACTGAATTA 57.014 33.333 0.00 0.00 0.00 1.40
808 7055 5.975693 TTCCCAATGTCCAACTGAATTAC 57.024 39.130 0.00 0.00 0.00 1.89
809 7056 5.255397 TCCCAATGTCCAACTGAATTACT 57.745 39.130 0.00 0.00 0.00 2.24
810 7057 5.009631 TCCCAATGTCCAACTGAATTACTG 58.990 41.667 0.00 0.00 0.00 2.74
993 7240 2.809861 AAGCGCACCTCATCCCACAG 62.810 60.000 11.47 0.00 0.00 3.66
998 7245 1.100510 CACCTCATCCCACAGCATTG 58.899 55.000 0.00 0.00 0.00 2.82
999 7246 0.682209 ACCTCATCCCACAGCATTGC 60.682 55.000 0.00 0.00 0.00 3.56
1000 7247 0.681887 CCTCATCCCACAGCATTGCA 60.682 55.000 11.91 0.00 0.00 4.08
1003 7250 0.604073 CATCCCACAGCATTGCACAA 59.396 50.000 11.91 0.00 0.00 3.33
1004 7251 0.604578 ATCCCACAGCATTGCACAAC 59.395 50.000 11.91 0.00 0.00 3.32
1005 7252 0.467844 TCCCACAGCATTGCACAACT 60.468 50.000 11.91 0.00 0.00 3.16
1006 7253 0.038892 CCCACAGCATTGCACAACTC 60.039 55.000 11.91 0.00 0.00 3.01
1007 7254 0.386352 CCACAGCATTGCACAACTCG 60.386 55.000 11.91 0.00 0.00 4.18
1028 7277 1.425412 GTCCTACAACGCACGAACAT 58.575 50.000 0.00 0.00 0.00 2.71
1047 7300 3.255642 ACATACACAAACCCAAGCACATC 59.744 43.478 0.00 0.00 0.00 3.06
1048 7301 1.774110 ACACAAACCCAAGCACATCA 58.226 45.000 0.00 0.00 0.00 3.07
1049 7302 1.682854 ACACAAACCCAAGCACATCAG 59.317 47.619 0.00 0.00 0.00 2.90
1050 7303 1.682854 CACAAACCCAAGCACATCAGT 59.317 47.619 0.00 0.00 0.00 3.41
1272 7533 3.005539 GCAGGCTGGAGGAGGACA 61.006 66.667 17.64 0.00 0.00 4.02
1336 7597 1.077285 TCGTCAGGGCCGATGACTA 60.077 57.895 27.58 19.15 43.95 2.59
1348 7609 3.508762 CCGATGACTAAGCTTACACGTT 58.491 45.455 0.86 0.00 0.00 3.99
1384 7645 3.364920 CGATGTGTGTATATGTCGGCATC 59.635 47.826 5.39 0.00 36.58 3.91
1385 7646 3.810310 TGTGTGTATATGTCGGCATCA 57.190 42.857 5.39 0.00 36.58 3.07
1386 7647 4.335400 TGTGTGTATATGTCGGCATCAT 57.665 40.909 5.39 1.38 36.58 2.45
1465 7730 3.052081 GCTATCAGCCCCGATCGT 58.948 61.111 15.09 0.00 34.48 3.73
1504 7771 2.293677 ATAAGCGCTGATCGTGAACA 57.706 45.000 12.58 0.00 41.07 3.18
1525 7792 7.817478 TGAACAAGAATAAAGCTTCTCGTGATA 59.183 33.333 18.93 1.29 34.40 2.15
1527 7794 8.547967 ACAAGAATAAAGCTTCTCGTGATAAA 57.452 30.769 18.93 0.00 34.40 1.40
1546 7825 8.607459 GTGATAAATATTCCAGTCTCTTGTGTG 58.393 37.037 0.00 0.00 0.00 3.82
1547 7826 8.321353 TGATAAATATTCCAGTCTCTTGTGTGT 58.679 33.333 0.00 0.00 0.00 3.72
1548 7827 9.167311 GATAAATATTCCAGTCTCTTGTGTGTT 57.833 33.333 0.00 0.00 0.00 3.32
1553 7832 5.707242 TCCAGTCTCTTGTGTGTTACTAG 57.293 43.478 0.00 0.00 34.06 2.57
1554 7833 5.382616 TCCAGTCTCTTGTGTGTTACTAGA 58.617 41.667 0.00 0.00 38.54 2.43
1555 7834 5.831525 TCCAGTCTCTTGTGTGTTACTAGAA 59.168 40.000 0.00 0.00 39.94 2.10
1623 7902 4.082895 CCGAGCTAGTATAACCGTTAGCAT 60.083 45.833 5.91 0.00 40.66 3.79
1636 7915 4.753610 ACCGTTAGCATCATGATGATTCTG 59.246 41.667 34.65 22.52 41.20 3.02
1649 7928 5.969423 TGATGATTCTGAAAAATGAAGGGC 58.031 37.500 0.00 0.00 0.00 5.19
1680 7976 2.096980 CCATCAGCTACGACGTCTACAA 59.903 50.000 14.70 0.00 0.00 2.41
1692 7988 4.318475 CGACGTCTACAAATTTCACAAGCA 60.318 41.667 14.70 0.00 0.00 3.91
1694 7990 4.024048 ACGTCTACAAATTTCACAAGCAGG 60.024 41.667 0.00 0.00 0.00 4.85
1709 8005 1.701847 AGCAGGTGAACCATCTCAGTT 59.298 47.619 1.62 0.00 38.89 3.16
1720 8016 5.520748 ACCATCTCAGTTTGGAGGTTTAT 57.479 39.130 3.73 0.00 36.79 1.40
1721 8017 5.892348 ACCATCTCAGTTTGGAGGTTTATT 58.108 37.500 3.73 0.00 36.79 1.40
1722 8018 7.027874 ACCATCTCAGTTTGGAGGTTTATTA 57.972 36.000 3.73 0.00 36.79 0.98
1723 8019 7.112779 ACCATCTCAGTTTGGAGGTTTATTAG 58.887 38.462 3.73 0.00 36.79 1.73
1724 8020 6.543831 CCATCTCAGTTTGGAGGTTTATTAGG 59.456 42.308 0.00 0.00 34.81 2.69
1726 8022 7.801893 TCTCAGTTTGGAGGTTTATTAGGTA 57.198 36.000 0.00 0.00 35.58 3.08
1727 8023 8.209802 TCTCAGTTTGGAGGTTTATTAGGTAA 57.790 34.615 0.00 0.00 35.58 2.85
1728 8024 8.662255 TCTCAGTTTGGAGGTTTATTAGGTAAA 58.338 33.333 0.00 0.00 35.58 2.01
1729 8025 9.292195 CTCAGTTTGGAGGTTTATTAGGTAAAA 57.708 33.333 0.00 0.00 34.23 1.52
1743 8039 7.775053 ATTAGGTAAAAATTGCTGACCTTCA 57.225 32.000 2.77 0.00 40.92 3.02
1744 8040 5.712152 AGGTAAAAATTGCTGACCTTCAG 57.288 39.130 0.00 0.00 46.90 3.02
1745 8041 4.524328 AGGTAAAAATTGCTGACCTTCAGG 59.476 41.667 5.37 0.00 44.43 3.86
1768 8064 5.012148 GGTAGGATGTCAATATGTGCCTACT 59.988 44.000 1.54 0.00 43.56 2.57
1773 8069 4.295201 TGTCAATATGTGCCTACTAGGGT 58.705 43.478 4.18 0.00 35.37 4.34
1781 8077 1.294068 TGCCTACTAGGGTCCTGGATT 59.706 52.381 7.39 0.00 35.37 3.01
1824 8120 7.607991 AGAATCGATCATGTTAGTTTGGTTTCT 59.392 33.333 0.00 0.00 0.00 2.52
1860 8156 5.354513 GCTCTGGTGTAATAAAACTTCTCCC 59.645 44.000 0.00 0.00 0.00 4.30
1865 8161 5.651139 GGTGTAATAAAACTTCTCCCCCTTC 59.349 44.000 0.00 0.00 0.00 3.46
1872 8195 1.834263 ACTTCTCCCCCTTCTCATTCG 59.166 52.381 0.00 0.00 0.00 3.34
1873 8196 1.139853 CTTCTCCCCCTTCTCATTCGG 59.860 57.143 0.00 0.00 0.00 4.30
1881 8204 2.761208 CCCTTCTCATTCGGTCAGTAGT 59.239 50.000 0.00 0.00 0.00 2.73
1936 8259 2.576615 AGGAGCCTATGAATTTTCGGC 58.423 47.619 0.00 0.00 40.99 5.54
1962 8285 7.858382 CACTACCGTTAATTTGAACATGTTTCA 59.142 33.333 13.36 9.34 0.00 2.69
1985 8308 9.578439 TTCATAACTATTCTAGCATCATCATCG 57.422 33.333 0.00 0.00 0.00 3.84
2009 8332 5.405269 GCCATTTTCTGTTTTGTGGATGTAC 59.595 40.000 0.00 0.00 0.00 2.90
2019 8342 6.261381 TGTTTTGTGGATGTACTAACTGTTCC 59.739 38.462 0.00 0.00 0.00 3.62
2023 8346 6.250711 TGTGGATGTACTAACTGTTCCTCTA 58.749 40.000 0.00 0.00 0.00 2.43
2025 8348 7.068348 TGTGGATGTACTAACTGTTCCTCTATC 59.932 40.741 0.00 0.00 0.00 2.08
2026 8349 7.068348 GTGGATGTACTAACTGTTCCTCTATCA 59.932 40.741 0.00 0.00 0.00 2.15
2027 8350 7.785028 TGGATGTACTAACTGTTCCTCTATCAT 59.215 37.037 0.00 0.00 0.00 2.45
2049 8372 7.584108 TCATATTGAAAATCATGGATGTACGC 58.416 34.615 0.00 0.00 0.00 4.42
2050 8373 4.630894 TTGAAAATCATGGATGTACGCC 57.369 40.909 0.00 0.00 0.00 5.68
2051 8374 3.615155 TGAAAATCATGGATGTACGCCA 58.385 40.909 9.41 9.41 40.24 5.69
2052 8375 4.206375 TGAAAATCATGGATGTACGCCAT 58.794 39.130 12.82 12.82 46.76 4.40
2053 8376 4.644234 TGAAAATCATGGATGTACGCCATT 59.356 37.500 15.26 4.26 43.42 3.16
2054 8377 5.126869 TGAAAATCATGGATGTACGCCATTT 59.873 36.000 15.26 9.50 43.42 2.32
2055 8378 6.319911 TGAAAATCATGGATGTACGCCATTTA 59.680 34.615 15.26 8.81 43.42 1.40
2056 8379 6.899393 AAATCATGGATGTACGCCATTTAT 57.101 33.333 15.26 10.33 43.42 1.40
2057 8380 6.899393 AATCATGGATGTACGCCATTTATT 57.101 33.333 15.26 14.33 43.42 1.40
2058 8381 6.899393 ATCATGGATGTACGCCATTTATTT 57.101 33.333 15.26 0.00 43.42 1.40
2059 8382 7.994425 ATCATGGATGTACGCCATTTATTTA 57.006 32.000 15.26 1.58 43.42 1.40
2060 8383 7.809546 TCATGGATGTACGCCATTTATTTAA 57.190 32.000 15.26 0.00 43.42 1.52
2061 8384 8.402798 TCATGGATGTACGCCATTTATTTAAT 57.597 30.769 15.26 0.00 43.42 1.40
2062 8385 8.855110 TCATGGATGTACGCCATTTATTTAATT 58.145 29.630 15.26 0.00 43.42 1.40
2063 8386 9.474920 CATGGATGTACGCCATTTATTTAATTT 57.525 29.630 15.26 0.00 43.42 1.82
2064 8387 8.864069 TGGATGTACGCCATTTATTTAATTTG 57.136 30.769 3.34 0.00 32.56 2.32
2074 8397 8.141909 GCCATTTATTTAATTTGTACTCCCTCC 58.858 37.037 0.00 0.00 0.00 4.30
2080 8403 1.719529 TTTGTACTCCCTCCGTTCCA 58.280 50.000 0.00 0.00 0.00 3.53
2083 8406 2.262637 TGTACTCCCTCCGTTCCAAAT 58.737 47.619 0.00 0.00 0.00 2.32
2086 8409 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2087 8410 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2088 8411 3.270877 CTCCCTCCGTTCCAAATTACTG 58.729 50.000 0.00 0.00 0.00 2.74
2092 8415 2.671396 CTCCGTTCCAAATTACTGGTCG 59.329 50.000 0.00 3.69 37.74 4.79
2094 8417 2.158841 CCGTTCCAAATTACTGGTCGTG 59.841 50.000 11.95 4.65 37.74 4.35
2097 8420 3.495434 TCCAAATTACTGGTCGTGGTT 57.505 42.857 0.00 0.00 37.74 3.67
2098 8421 3.822940 TCCAAATTACTGGTCGTGGTTT 58.177 40.909 0.00 0.00 37.74 3.27
2099 8422 4.208746 TCCAAATTACTGGTCGTGGTTTT 58.791 39.130 0.00 0.00 37.74 2.43
2101 8424 5.470777 TCCAAATTACTGGTCGTGGTTTTAG 59.529 40.000 0.00 0.00 37.74 1.85
2104 8427 6.549912 AATTACTGGTCGTGGTTTTAGTTC 57.450 37.500 0.00 0.00 0.00 3.01
2105 8428 3.547054 ACTGGTCGTGGTTTTAGTTCA 57.453 42.857 0.00 0.00 0.00 3.18
2107 8430 4.263435 ACTGGTCGTGGTTTTAGTTCAAA 58.737 39.130 0.00 0.00 0.00 2.69
2109 8432 5.358725 ACTGGTCGTGGTTTTAGTTCAAATT 59.641 36.000 0.00 0.00 0.00 1.82
2112 8435 6.127703 TGGTCGTGGTTTTAGTTCAAATTTGA 60.128 34.615 16.91 16.91 34.92 2.69
2127 8528 5.966503 TCAAATTTGAACTAAAACCACGACG 59.033 36.000 18.45 0.00 33.55 5.12
2128 8529 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
2129 8530 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
2132 8533 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
2137 8538 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
2151 8552 3.629142 AATTTGGAACGGAGGGAGTAG 57.371 47.619 0.00 0.00 0.00 2.57
2152 8553 0.611714 TTTGGAACGGAGGGAGTAGC 59.388 55.000 0.00 0.00 0.00 3.58
2153 8554 0.543410 TTGGAACGGAGGGAGTAGCA 60.543 55.000 0.00 0.00 0.00 3.49
2154 8555 0.970937 TGGAACGGAGGGAGTAGCAG 60.971 60.000 0.00 0.00 0.00 4.24
2155 8556 1.142097 GAACGGAGGGAGTAGCAGC 59.858 63.158 0.00 0.00 0.00 5.25
2158 8559 0.752376 ACGGAGGGAGTAGCAGCTAC 60.752 60.000 23.17 23.17 37.23 3.58
2159 8560 1.457009 CGGAGGGAGTAGCAGCTACC 61.457 65.000 26.20 17.86 39.83 3.18
2160 8561 1.116536 GGAGGGAGTAGCAGCTACCC 61.117 65.000 26.20 24.22 40.42 3.69
2162 8563 0.397816 AGGGAGTAGCAGCTACCCAG 60.398 60.000 27.89 0.00 40.42 4.45
2178 8579 1.888512 CCCAGCAAAGTAAGTGTGCAT 59.111 47.619 0.00 0.00 40.83 3.96
2179 8580 2.297033 CCCAGCAAAGTAAGTGTGCATT 59.703 45.455 0.00 0.00 40.83 3.56
2180 8581 3.243839 CCCAGCAAAGTAAGTGTGCATTT 60.244 43.478 0.00 0.00 40.83 2.32
2181 8582 4.370917 CCAGCAAAGTAAGTGTGCATTTT 58.629 39.130 0.00 0.00 40.83 1.82
2182 8583 5.508825 CCCAGCAAAGTAAGTGTGCATTTTA 60.509 40.000 0.00 0.00 40.83 1.52
2183 8584 6.158598 CCAGCAAAGTAAGTGTGCATTTTAT 58.841 36.000 0.00 0.00 40.83 1.40
2184 8585 6.646240 CCAGCAAAGTAAGTGTGCATTTTATT 59.354 34.615 0.00 0.00 40.83 1.40
2185 8586 7.171337 CCAGCAAAGTAAGTGTGCATTTTATTT 59.829 33.333 0.00 0.00 40.83 1.40
2186 8587 8.550376 CAGCAAAGTAAGTGTGCATTTTATTTT 58.450 29.630 0.00 0.00 40.83 1.82
2187 8588 8.764287 AGCAAAGTAAGTGTGCATTTTATTTTC 58.236 29.630 0.00 0.00 40.83 2.29
2188 8589 8.764287 GCAAAGTAAGTGTGCATTTTATTTTCT 58.236 29.630 0.00 0.00 38.19 2.52
2192 8593 9.463443 AGTAAGTGTGCATTTTATTTTCTTCAC 57.537 29.630 0.00 0.00 0.00 3.18
2193 8594 9.463443 GTAAGTGTGCATTTTATTTTCTTCACT 57.537 29.630 0.00 0.00 34.59 3.41
2194 8595 8.947055 AAGTGTGCATTTTATTTTCTTCACTT 57.053 26.923 5.08 5.08 37.51 3.16
2195 8596 8.579682 AGTGTGCATTTTATTTTCTTCACTTC 57.420 30.769 0.00 0.00 0.00 3.01
2196 8597 8.196771 AGTGTGCATTTTATTTTCTTCACTTCA 58.803 29.630 0.00 0.00 0.00 3.02
2204 8605 9.950680 TTTTATTTTCTTCACTTCAGTAAGCAG 57.049 29.630 0.00 0.00 36.05 4.24
2205 8606 5.424121 TTTTCTTCACTTCAGTAAGCAGC 57.576 39.130 0.00 0.00 36.05 5.25
2206 8607 3.751479 TCTTCACTTCAGTAAGCAGCA 57.249 42.857 0.00 0.00 36.05 4.41
2207 8608 4.071961 TCTTCACTTCAGTAAGCAGCAA 57.928 40.909 0.00 0.00 36.05 3.91
2209 8610 3.475566 TCACTTCAGTAAGCAGCAAGT 57.524 42.857 0.00 0.00 36.05 3.16
2210 8611 4.600692 TCACTTCAGTAAGCAGCAAGTA 57.399 40.909 0.00 0.00 36.05 2.24
2211 8612 4.956085 TCACTTCAGTAAGCAGCAAGTAA 58.044 39.130 0.00 0.00 36.05 2.24
2212 8613 5.364778 TCACTTCAGTAAGCAGCAAGTAAA 58.635 37.500 0.00 0.00 36.05 2.01
2213 8614 5.820423 TCACTTCAGTAAGCAGCAAGTAAAA 59.180 36.000 0.00 0.00 36.05 1.52
2216 8617 5.673337 TCAGTAAGCAGCAAGTAAAACTG 57.327 39.130 0.00 0.00 35.54 3.16
2225 8626 6.774354 CAGCAAGTAAAACTGCATTTCATT 57.226 33.333 0.00 0.00 0.00 2.57
2226 8627 7.181143 CAGCAAGTAAAACTGCATTTCATTT 57.819 32.000 0.00 0.00 0.00 2.32
2227 8628 7.067116 CAGCAAGTAAAACTGCATTTCATTTG 58.933 34.615 0.00 0.00 0.00 2.32
2228 8629 6.203338 AGCAAGTAAAACTGCATTTCATTTGG 59.797 34.615 0.00 0.00 0.00 3.28
2229 8630 6.202570 GCAAGTAAAACTGCATTTCATTTGGA 59.797 34.615 0.00 0.00 0.00 3.53
2231 8632 7.054491 AGTAAAACTGCATTTCATTTGGACT 57.946 32.000 0.00 0.00 0.00 3.85
2233 8634 5.534207 AAACTGCATTTCATTTGGACTCA 57.466 34.783 0.00 0.00 0.00 3.41
2235 8636 5.733620 ACTGCATTTCATTTGGACTCATT 57.266 34.783 0.00 0.00 0.00 2.57
2237 8638 5.929992 ACTGCATTTCATTTGGACTCATTTG 59.070 36.000 0.00 0.00 0.00 2.32
2238 8639 5.239351 TGCATTTCATTTGGACTCATTTGG 58.761 37.500 0.00 0.00 0.00 3.28
2239 8640 5.221682 TGCATTTCATTTGGACTCATTTGGT 60.222 36.000 0.00 0.00 0.00 3.67
2240 8641 6.014755 TGCATTTCATTTGGACTCATTTGGTA 60.015 34.615 0.00 0.00 0.00 3.25
2241 8642 6.873076 GCATTTCATTTGGACTCATTTGGTAA 59.127 34.615 0.00 0.00 0.00 2.85
2242 8643 7.063780 GCATTTCATTTGGACTCATTTGGTAAG 59.936 37.037 0.00 0.00 0.00 2.34
2243 8644 5.643379 TCATTTGGACTCATTTGGTAAGC 57.357 39.130 0.00 0.00 0.00 3.09
2245 8646 5.183713 TCATTTGGACTCATTTGGTAAGCAG 59.816 40.000 0.00 0.00 0.00 4.24
2246 8647 2.436417 TGGACTCATTTGGTAAGCAGC 58.564 47.619 0.00 0.00 0.00 5.25
2247 8648 2.224744 TGGACTCATTTGGTAAGCAGCA 60.225 45.455 0.00 0.00 0.00 4.41
2255 8656 4.464069 TTTGGTAAGCAGCAAAACAACT 57.536 36.364 0.00 0.00 46.27 3.16
2260 8661 4.927422 GTAAGCAGCAAAACAACTTACCA 58.073 39.130 0.00 0.00 37.69 3.25
2261 8662 3.436700 AGCAGCAAAACAACTTACCAC 57.563 42.857 0.00 0.00 0.00 4.16
2262 8663 2.100749 AGCAGCAAAACAACTTACCACC 59.899 45.455 0.00 0.00 0.00 4.61
2263 8664 2.159170 GCAGCAAAACAACTTACCACCA 60.159 45.455 0.00 0.00 0.00 4.17
2265 8666 3.093057 AGCAAAACAACTTACCACCACA 58.907 40.909 0.00 0.00 0.00 4.17
2267 8668 3.615056 GCAAAACAACTTACCACCACAAC 59.385 43.478 0.00 0.00 0.00 3.32
2268 8669 4.810790 CAAAACAACTTACCACCACAACA 58.189 39.130 0.00 0.00 0.00 3.33
2271 8672 2.750712 ACAACTTACCACCACAACACAC 59.249 45.455 0.00 0.00 0.00 3.82
2274 8675 2.290387 ACTTACCACCACAACACACACA 60.290 45.455 0.00 0.00 0.00 3.72
2278 8679 0.378257 CACCACAACACACACAGAGC 59.622 55.000 0.00 0.00 0.00 4.09
2288 8689 0.250209 CACACAGAGCAGCAGTTCCT 60.250 55.000 0.00 0.00 0.00 3.36
2397 8809 1.424493 GAACGCCAGCTTCAGATCCG 61.424 60.000 0.00 0.00 0.00 4.18
2398 8810 2.587194 CGCCAGCTTCAGATCCGG 60.587 66.667 0.00 0.00 0.00 5.14
2399 8811 2.899339 GCCAGCTTCAGATCCGGC 60.899 66.667 0.00 0.00 0.00 6.13
2432 9232 2.603075 TGGTCAGGGGAATTGGAAAG 57.397 50.000 0.00 0.00 0.00 2.62
2451 9251 0.881118 GCCAAATTGACGCCTGAAGA 59.119 50.000 0.00 0.00 0.00 2.87
2481 9281 5.063880 ACCAAACTGAACCTACTTGATCAC 58.936 41.667 0.00 0.00 0.00 3.06
2482 9282 4.455877 CCAAACTGAACCTACTTGATCACC 59.544 45.833 0.00 0.00 0.00 4.02
2483 9283 4.974645 AACTGAACCTACTTGATCACCA 57.025 40.909 0.00 0.00 0.00 4.17
2484 9284 4.543590 ACTGAACCTACTTGATCACCAG 57.456 45.455 0.00 0.00 0.00 4.00
2485 9285 3.904339 ACTGAACCTACTTGATCACCAGT 59.096 43.478 5.42 5.42 0.00 4.00
2486 9286 5.084519 ACTGAACCTACTTGATCACCAGTA 58.915 41.667 7.00 7.00 31.49 2.74
2487 9287 5.721960 ACTGAACCTACTTGATCACCAGTAT 59.278 40.000 7.55 0.00 31.49 2.12
2488 9288 6.895756 ACTGAACCTACTTGATCACCAGTATA 59.104 38.462 7.55 0.00 31.49 1.47
2489 9289 7.399191 ACTGAACCTACTTGATCACCAGTATAA 59.601 37.037 7.55 0.00 31.49 0.98
2490 9290 8.141298 TGAACCTACTTGATCACCAGTATAAA 57.859 34.615 7.55 0.00 0.00 1.40
2491 9291 8.768397 TGAACCTACTTGATCACCAGTATAAAT 58.232 33.333 7.55 0.00 0.00 1.40
2492 9292 9.614792 GAACCTACTTGATCACCAGTATAAATT 57.385 33.333 7.55 1.87 0.00 1.82
2493 9293 8.964476 ACCTACTTGATCACCAGTATAAATTG 57.036 34.615 7.55 0.00 0.00 2.32
2494 9294 8.548877 ACCTACTTGATCACCAGTATAAATTGT 58.451 33.333 7.55 0.00 0.00 2.71
2495 9295 9.396022 CCTACTTGATCACCAGTATAAATTGTT 57.604 33.333 7.55 0.00 0.00 2.83
2497 9297 8.055279 ACTTGATCACCAGTATAAATTGTTGG 57.945 34.615 0.00 0.00 35.07 3.77
2498 9298 7.669722 ACTTGATCACCAGTATAAATTGTTGGT 59.330 33.333 0.00 0.00 42.62 3.67
2499 9299 7.624360 TGATCACCAGTATAAATTGTTGGTC 57.376 36.000 0.00 0.00 40.02 4.02
2500 9300 7.402054 TGATCACCAGTATAAATTGTTGGTCT 58.598 34.615 0.00 0.00 40.02 3.85
2501 9301 7.336679 TGATCACCAGTATAAATTGTTGGTCTG 59.663 37.037 0.00 0.00 40.02 3.51
2502 9302 6.774673 TCACCAGTATAAATTGTTGGTCTGA 58.225 36.000 0.00 0.00 40.02 3.27
2503 9303 7.402054 TCACCAGTATAAATTGTTGGTCTGAT 58.598 34.615 0.00 0.00 40.02 2.90
2504 9304 7.336679 TCACCAGTATAAATTGTTGGTCTGATG 59.663 37.037 0.00 0.00 40.02 3.07
2505 9305 7.336679 CACCAGTATAAATTGTTGGTCTGATGA 59.663 37.037 0.00 0.00 40.02 2.92
2506 9306 7.336931 ACCAGTATAAATTGTTGGTCTGATGAC 59.663 37.037 0.00 0.00 37.60 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.762535 ATTCATCAAACGTCCGTCCT 57.237 45.000 0.00 0.00 0.00 3.85
2 3 3.924686 ACACTATTCATCAAACGTCCGTC 59.075 43.478 0.00 0.00 0.00 4.79
3 4 3.921677 ACACTATTCATCAAACGTCCGT 58.078 40.909 0.00 0.00 0.00 4.69
4 5 4.435518 CCAACACTATTCATCAAACGTCCG 60.436 45.833 0.00 0.00 0.00 4.79
7 8 5.181245 CCTTCCAACACTATTCATCAAACGT 59.819 40.000 0.00 0.00 0.00 3.99
40 41 1.265568 CGTCTTTGGACACCGATACG 58.734 55.000 0.00 0.00 42.21 3.06
46 47 2.315386 GGACGCGTCTTTGGACACC 61.315 63.158 35.50 15.31 42.21 4.16
47 48 2.654912 CGGACGCGTCTTTGGACAC 61.655 63.158 35.50 17.18 42.21 3.67
58 59 3.192922 GTCCCCAAATCGGACGCG 61.193 66.667 3.53 3.53 40.46 6.01
61 62 2.046700 TGCGTCCCCAAATCGGAC 60.047 61.111 0.00 0.00 45.41 4.79
136 2242 7.544915 GGTACAGAATAGTCACCAAGTTAACTC 59.455 40.741 8.95 0.00 0.00 3.01
275 2382 2.127708 AGGTCACCTTCAAGAGTGGTT 58.872 47.619 0.00 0.00 34.67 3.67
297 2411 2.115595 CGTCTCGATGCTCATGTCTTC 58.884 52.381 0.00 0.00 0.00 2.87
329 2443 1.270571 TGGTGATTAGCAACGTGAGCA 60.271 47.619 14.66 0.00 36.85 4.26
334 2448 2.151202 CAACCTGGTGATTAGCAACGT 58.849 47.619 0.00 0.00 36.85 3.99
440 2555 3.334691 TGATCGACTGAACATTTCCCAC 58.665 45.455 0.00 0.00 0.00 4.61
456 4639 3.500558 AGCATCGGTCTATCATGATCG 57.499 47.619 12.53 9.79 41.44 3.69
481 4664 5.171476 GTTTACATCTCTGTAGCTTGCAGA 58.829 41.667 16.49 16.49 39.00 4.26
504 4687 2.029110 CAGGGGCCATATTTATTTGCCG 60.029 50.000 4.39 0.00 43.09 5.69
516 4699 3.164269 CGGACTAGCAGGGGCCAT 61.164 66.667 4.39 0.00 42.56 4.40
517 4700 4.715130 ACGGACTAGCAGGGGCCA 62.715 66.667 4.39 0.00 42.56 5.36
518 4701 2.479820 AAAACGGACTAGCAGGGGCC 62.480 60.000 0.00 0.00 42.56 5.80
519 4702 1.002502 AAAACGGACTAGCAGGGGC 60.003 57.895 0.00 0.00 41.61 5.80
523 4706 2.415512 GCTAACCAAAACGGACTAGCAG 59.584 50.000 10.23 0.00 43.50 4.24
525 4708 2.696506 AGCTAACCAAAACGGACTAGC 58.303 47.619 0.00 0.00 43.95 3.42
526 4709 5.163884 GCTAAAGCTAACCAAAACGGACTAG 60.164 44.000 0.00 0.00 36.70 2.57
527 4710 4.692155 GCTAAAGCTAACCAAAACGGACTA 59.308 41.667 0.00 0.00 36.70 2.59
528 4711 3.501062 GCTAAAGCTAACCAAAACGGACT 59.499 43.478 0.00 0.00 36.70 3.85
529 4712 3.818387 GCTAAAGCTAACCAAAACGGAC 58.182 45.455 0.00 0.00 36.70 4.79
592 6770 8.528044 TCCCATTTAAACCCACTTATATTGTC 57.472 34.615 0.00 0.00 0.00 3.18
595 6773 9.367160 CAGATCCCATTTAAACCCACTTATATT 57.633 33.333 0.00 0.00 0.00 1.28
598 6776 6.980577 TCAGATCCCATTTAAACCCACTTAT 58.019 36.000 0.00 0.00 0.00 1.73
599 6777 6.395780 TCAGATCCCATTTAAACCCACTTA 57.604 37.500 0.00 0.00 0.00 2.24
601 6779 4.946160 TCAGATCCCATTTAAACCCACT 57.054 40.909 0.00 0.00 0.00 4.00
602 6780 6.544928 AAATCAGATCCCATTTAAACCCAC 57.455 37.500 0.00 0.00 0.00 4.61
628 6806 9.521841 TCTGATCGATCTAGTAACTTTATGGAT 57.478 33.333 25.02 0.00 0.00 3.41
632 6810 8.851145 TGCTTCTGATCGATCTAGTAACTTTAT 58.149 33.333 25.02 0.00 0.00 1.40
752 6967 1.079612 CGGCTCACACTGATCTGCA 60.080 57.895 0.00 0.00 0.00 4.41
771 6986 9.990360 GGACATTGGGAAAAAGAACTAATTAAA 57.010 29.630 0.00 0.00 0.00 1.52
804 7051 5.278610 GGTGCCCTTTTTACGTTTCAGTAAT 60.279 40.000 0.00 0.00 36.59 1.89
805 7052 4.036616 GGTGCCCTTTTTACGTTTCAGTAA 59.963 41.667 0.00 0.00 35.07 2.24
806 7053 3.565063 GGTGCCCTTTTTACGTTTCAGTA 59.435 43.478 0.00 0.00 0.00 2.74
807 7054 2.359848 GGTGCCCTTTTTACGTTTCAGT 59.640 45.455 0.00 0.00 0.00 3.41
808 7055 2.359531 TGGTGCCCTTTTTACGTTTCAG 59.640 45.455 0.00 0.00 0.00 3.02
809 7056 2.376109 TGGTGCCCTTTTTACGTTTCA 58.624 42.857 0.00 0.00 0.00 2.69
810 7057 3.439895 TTGGTGCCCTTTTTACGTTTC 57.560 42.857 0.00 0.00 0.00 2.78
899 7146 0.179037 TCTGCACACTGCTTTCTGCT 60.179 50.000 0.00 0.00 45.31 4.24
993 7240 1.210155 GACCCGAGTTGTGCAATGC 59.790 57.895 0.00 0.00 0.00 3.56
998 7245 0.034337 TTGTAGGACCCGAGTTGTGC 59.966 55.000 0.00 0.00 0.00 4.57
999 7246 1.792006 GTTGTAGGACCCGAGTTGTG 58.208 55.000 0.00 0.00 0.00 3.33
1000 7247 0.316204 CGTTGTAGGACCCGAGTTGT 59.684 55.000 0.00 0.00 0.00 3.32
1003 7250 1.904865 TGCGTTGTAGGACCCGAGT 60.905 57.895 0.00 0.00 0.00 4.18
1004 7251 1.445582 GTGCGTTGTAGGACCCGAG 60.446 63.158 0.00 0.00 0.00 4.63
1005 7252 2.652530 GTGCGTTGTAGGACCCGA 59.347 61.111 0.00 0.00 0.00 5.14
1006 7253 2.752322 TTCGTGCGTTGTAGGACCCG 62.752 60.000 0.00 0.00 0.00 5.28
1007 7254 1.005867 TTCGTGCGTTGTAGGACCC 60.006 57.895 0.00 0.00 0.00 4.46
1028 7277 2.884012 CTGATGTGCTTGGGTTTGTGTA 59.116 45.455 0.00 0.00 0.00 2.90
1047 7300 2.313172 GCGCCATGCCGATCTACTG 61.313 63.158 0.00 0.00 37.76 2.74
1048 7301 2.029666 GCGCCATGCCGATCTACT 59.970 61.111 0.00 0.00 37.76 2.57
1049 7302 2.280119 TGCGCCATGCCGATCTAC 60.280 61.111 4.18 0.00 45.60 2.59
1050 7303 2.280119 GTGCGCCATGCCGATCTA 60.280 61.111 4.18 0.00 45.60 1.98
1262 7523 0.253327 GGGTGTTGATGTCCTCCTCC 59.747 60.000 0.00 0.00 0.00 4.30
1336 7597 1.000060 TGCTCCGTAACGTGTAAGCTT 60.000 47.619 3.48 3.48 0.00 3.74
1348 7609 1.131693 CACATCGTAGTGTGCTCCGTA 59.868 52.381 5.67 0.00 42.51 4.02
1378 7639 8.706035 CATCACACATACATATATATGATGCCG 58.294 37.037 26.05 19.01 36.75 5.69
1379 7640 9.551734 ACATCACACATACATATATATGATGCC 57.448 33.333 26.05 0.00 43.79 4.40
1384 7645 7.847564 GCGCAACATCACACATACATATATATG 59.152 37.037 19.21 19.21 38.34 1.78
1385 7646 7.548780 TGCGCAACATCACACATACATATATAT 59.451 33.333 8.16 0.00 0.00 0.86
1386 7647 6.870965 TGCGCAACATCACACATACATATATA 59.129 34.615 8.16 0.00 0.00 0.86
1450 7715 2.734591 GCACGATCGGGGCTGATA 59.265 61.111 20.80 0.00 0.00 2.15
1494 7761 7.066374 AGAAGCTTTATTCTTGTTCACGATC 57.934 36.000 0.00 0.00 36.05 3.69
1525 7792 8.157476 AGTAACACACAAGAGACTGGAATATTT 58.843 33.333 0.00 0.00 0.00 1.40
1527 7794 7.246171 AGTAACACACAAGAGACTGGAATAT 57.754 36.000 0.00 0.00 0.00 1.28
1546 7825 9.141400 CATTGACAGGTTCTAACTTCTAGTAAC 57.859 37.037 0.00 0.00 0.00 2.50
1547 7826 9.085645 TCATTGACAGGTTCTAACTTCTAGTAA 57.914 33.333 0.00 0.00 0.00 2.24
1548 7827 8.645814 TCATTGACAGGTTCTAACTTCTAGTA 57.354 34.615 0.00 0.00 0.00 1.82
1553 7832 5.163713 GCCATCATTGACAGGTTCTAACTTC 60.164 44.000 8.34 0.00 0.00 3.01
1554 7833 4.702131 GCCATCATTGACAGGTTCTAACTT 59.298 41.667 8.34 0.00 0.00 2.66
1555 7834 4.263462 TGCCATCATTGACAGGTTCTAACT 60.263 41.667 8.34 0.00 0.00 2.24
1582 7861 1.541233 CGGTATCAGCCCCTTGTGATC 60.541 57.143 0.00 0.00 35.08 2.92
1623 7902 7.632028 GCCCTTCATTTTTCAGAATCATCATGA 60.632 37.037 0.00 0.00 0.00 3.07
1636 7915 3.683365 ATGGTGTGCCCTTCATTTTTC 57.317 42.857 0.00 0.00 0.00 2.29
1692 7988 2.711009 TCCAAACTGAGATGGTTCACCT 59.289 45.455 8.45 0.00 37.94 4.00
1694 7990 3.077359 CCTCCAAACTGAGATGGTTCAC 58.923 50.000 8.45 0.00 37.94 3.18
1709 8005 9.095700 AGCAATTTTTACCTAATAAACCTCCAA 57.904 29.630 0.00 0.00 32.29 3.53
1720 8016 6.208599 CCTGAAGGTCAGCAATTTTTACCTAA 59.791 38.462 0.00 0.00 42.98 2.69
1721 8017 5.710099 CCTGAAGGTCAGCAATTTTTACCTA 59.290 40.000 0.00 0.00 42.98 3.08
1722 8018 4.524328 CCTGAAGGTCAGCAATTTTTACCT 59.476 41.667 0.00 0.00 42.98 3.08
1723 8019 4.809673 CCTGAAGGTCAGCAATTTTTACC 58.190 43.478 0.00 0.00 42.98 2.85
1743 8039 3.976654 AGGCACATATTGACATCCTACCT 59.023 43.478 0.00 0.00 34.40 3.08
1744 8040 4.357918 AGGCACATATTGACATCCTACC 57.642 45.455 0.00 0.00 34.40 3.18
1745 8041 6.102897 AGTAGGCACATATTGACATCCTAC 57.897 41.667 7.29 7.29 42.81 3.18
1746 8042 6.437477 CCTAGTAGGCACATATTGACATCCTA 59.563 42.308 2.46 0.00 34.40 2.94
1804 8100 8.044060 TGATGAGAAACCAAACTAACATGATC 57.956 34.615 0.00 0.00 0.00 2.92
1814 8110 4.978580 GCAGTTCTTGATGAGAAACCAAAC 59.021 41.667 0.00 0.00 45.59 2.93
1824 8120 2.369860 ACACCAGAGCAGTTCTTGATGA 59.630 45.455 0.00 0.00 32.41 2.92
1860 8156 2.761208 ACTACTGACCGAATGAGAAGGG 59.239 50.000 0.00 0.00 0.00 3.95
1865 8161 3.679980 CACCAAACTACTGACCGAATGAG 59.320 47.826 0.00 0.00 0.00 2.90
1872 8195 4.595762 TCAGTACACCAAACTACTGACC 57.404 45.455 3.86 0.00 42.50 4.02
1873 8196 5.813672 TGTTTCAGTACACCAAACTACTGAC 59.186 40.000 6.96 0.11 45.47 3.51
1881 8204 4.839121 AGTCTGTGTTTCAGTACACCAAA 58.161 39.130 0.00 0.00 46.13 3.28
1896 8219 1.159713 TGCGCTGGTTCAAGTCTGTG 61.160 55.000 9.73 0.00 0.00 3.66
1897 8220 0.463654 TTGCGCTGGTTCAAGTCTGT 60.464 50.000 9.73 0.00 0.00 3.41
1906 8229 1.915078 ATAGGCTCCTTGCGCTGGTT 61.915 55.000 9.73 2.33 44.05 3.67
1936 8259 7.858382 TGAAACATGTTCAAATTAACGGTAGTG 59.142 33.333 12.39 0.00 31.76 2.74
1962 8285 6.983307 GGCGATGATGATGCTAGAATAGTTAT 59.017 38.462 0.00 0.00 41.93 1.89
1973 8296 3.004419 CAGAAAATGGCGATGATGATGCT 59.996 43.478 0.00 0.00 0.00 3.79
1983 8306 2.690497 TCCACAAAACAGAAAATGGCGA 59.310 40.909 0.00 0.00 0.00 5.54
1984 8307 3.090952 TCCACAAAACAGAAAATGGCG 57.909 42.857 0.00 0.00 0.00 5.69
1985 8308 4.379652 ACATCCACAAAACAGAAAATGGC 58.620 39.130 0.00 0.00 0.00 4.40
2023 8346 8.239314 GCGTACATCCATGATTTTCAATATGAT 58.761 33.333 0.00 0.00 0.00 2.45
2025 8348 6.803320 GGCGTACATCCATGATTTTCAATATG 59.197 38.462 0.00 0.00 0.00 1.78
2026 8349 6.489700 TGGCGTACATCCATGATTTTCAATAT 59.510 34.615 0.00 0.00 0.00 1.28
2027 8350 5.825151 TGGCGTACATCCATGATTTTCAATA 59.175 36.000 0.00 0.00 0.00 1.90
2030 8353 3.615155 TGGCGTACATCCATGATTTTCA 58.385 40.909 0.00 0.00 0.00 2.69
2031 8354 4.836125 ATGGCGTACATCCATGATTTTC 57.164 40.909 13.97 0.00 42.39 2.29
2032 8355 5.596836 AAATGGCGTACATCCATGATTTT 57.403 34.783 15.09 6.17 43.13 1.82
2033 8356 6.899393 ATAAATGGCGTACATCCATGATTT 57.101 33.333 15.09 10.35 43.13 2.17
2034 8357 6.899393 AATAAATGGCGTACATCCATGATT 57.101 33.333 15.09 14.10 43.13 2.57
2035 8358 6.899393 AAATAAATGGCGTACATCCATGAT 57.101 33.333 15.09 10.16 43.13 2.45
2036 8359 7.809546 TTAAATAAATGGCGTACATCCATGA 57.190 32.000 15.09 8.66 43.13 3.07
2037 8360 9.474920 AAATTAAATAAATGGCGTACATCCATG 57.525 29.630 15.09 0.00 43.13 3.66
2038 8361 9.474920 CAAATTAAATAAATGGCGTACATCCAT 57.525 29.630 10.05 10.05 45.70 3.41
2039 8362 8.470805 ACAAATTAAATAAATGGCGTACATCCA 58.529 29.630 6.34 6.34 39.40 3.41
2040 8363 8.865590 ACAAATTAAATAAATGGCGTACATCC 57.134 30.769 0.00 0.00 39.40 3.51
2043 8366 9.991388 GAGTACAAATTAAATAAATGGCGTACA 57.009 29.630 0.00 0.00 33.68 2.90
2044 8367 9.442033 GGAGTACAAATTAAATAAATGGCGTAC 57.558 33.333 0.00 0.00 32.58 3.67
2045 8368 8.623030 GGGAGTACAAATTAAATAAATGGCGTA 58.377 33.333 0.00 0.00 0.00 4.42
2046 8369 7.340999 AGGGAGTACAAATTAAATAAATGGCGT 59.659 33.333 0.00 0.00 0.00 5.68
2047 8370 7.712797 AGGGAGTACAAATTAAATAAATGGCG 58.287 34.615 0.00 0.00 0.00 5.69
2048 8371 8.141909 GGAGGGAGTACAAATTAAATAAATGGC 58.858 37.037 0.00 0.00 0.00 4.40
2049 8372 8.349983 CGGAGGGAGTACAAATTAAATAAATGG 58.650 37.037 0.00 0.00 0.00 3.16
2050 8373 8.899771 ACGGAGGGAGTACAAATTAAATAAATG 58.100 33.333 0.00 0.00 0.00 2.32
2051 8374 9.470399 AACGGAGGGAGTACAAATTAAATAAAT 57.530 29.630 0.00 0.00 0.00 1.40
2052 8375 8.866970 AACGGAGGGAGTACAAATTAAATAAA 57.133 30.769 0.00 0.00 0.00 1.40
2053 8376 7.553760 GGAACGGAGGGAGTACAAATTAAATAA 59.446 37.037 0.00 0.00 0.00 1.40
2054 8377 7.049754 GGAACGGAGGGAGTACAAATTAAATA 58.950 38.462 0.00 0.00 0.00 1.40
2055 8378 5.884232 GGAACGGAGGGAGTACAAATTAAAT 59.116 40.000 0.00 0.00 0.00 1.40
2056 8379 5.221884 TGGAACGGAGGGAGTACAAATTAAA 60.222 40.000 0.00 0.00 0.00 1.52
2057 8380 4.286549 TGGAACGGAGGGAGTACAAATTAA 59.713 41.667 0.00 0.00 0.00 1.40
2058 8381 3.839490 TGGAACGGAGGGAGTACAAATTA 59.161 43.478 0.00 0.00 0.00 1.40
2059 8382 2.640826 TGGAACGGAGGGAGTACAAATT 59.359 45.455 0.00 0.00 0.00 1.82
2060 8383 2.262637 TGGAACGGAGGGAGTACAAAT 58.737 47.619 0.00 0.00 0.00 2.32
2061 8384 1.719529 TGGAACGGAGGGAGTACAAA 58.280 50.000 0.00 0.00 0.00 2.83
2062 8385 1.719529 TTGGAACGGAGGGAGTACAA 58.280 50.000 0.00 0.00 0.00 2.41
2063 8386 1.719529 TTTGGAACGGAGGGAGTACA 58.280 50.000 0.00 0.00 0.00 2.90
2064 8387 3.345508 AATTTGGAACGGAGGGAGTAC 57.654 47.619 0.00 0.00 0.00 2.73
2074 8397 2.158841 CCACGACCAGTAATTTGGAACG 59.841 50.000 3.10 9.99 40.87 3.95
2080 8403 6.543100 TGAACTAAAACCACGACCAGTAATTT 59.457 34.615 0.00 0.00 0.00 1.82
2083 8406 5.021033 TGAACTAAAACCACGACCAGTAA 57.979 39.130 0.00 0.00 0.00 2.24
2086 8409 4.886247 TTTGAACTAAAACCACGACCAG 57.114 40.909 0.00 0.00 0.00 4.00
2087 8410 5.838531 AATTTGAACTAAAACCACGACCA 57.161 34.783 0.00 0.00 0.00 4.02
2088 8411 6.267070 TCAAATTTGAACTAAAACCACGACC 58.733 36.000 18.45 0.00 33.55 4.79
2104 8427 5.966503 TCGTCGTGGTTTTAGTTCAAATTTG 59.033 36.000 12.15 12.15 0.00 2.32
2105 8428 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
2107 8430 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
2109 8432 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
2112 8435 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
2115 8438 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
2117 8440 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
2121 8522 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
2123 8524 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
2127 8528 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
2128 8529 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2129 8530 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2132 8533 1.209747 GCTACTCCCTCCGTTCCAAAT 59.790 52.381 0.00 0.00 0.00 2.32
2137 8538 1.142097 GCTGCTACTCCCTCCGTTC 59.858 63.158 0.00 0.00 0.00 3.95
2155 8556 2.484264 GCACACTTACTTTGCTGGGTAG 59.516 50.000 0.00 0.00 33.26 3.18
2158 8559 1.317613 TGCACACTTACTTTGCTGGG 58.682 50.000 0.00 0.00 37.16 4.45
2159 8560 3.648339 AATGCACACTTACTTTGCTGG 57.352 42.857 0.00 0.00 37.16 4.85
2160 8561 7.642071 AATAAAATGCACACTTACTTTGCTG 57.358 32.000 0.00 0.00 37.16 4.41
2162 8563 8.764287 AGAAAATAAAATGCACACTTACTTTGC 58.236 29.630 0.00 0.00 36.76 3.68
2166 8567 9.463443 GTGAAGAAAATAAAATGCACACTTACT 57.537 29.630 0.00 0.00 0.00 2.24
2171 8572 8.351495 TGAAGTGAAGAAAATAAAATGCACAC 57.649 30.769 0.00 0.00 0.00 3.82
2173 8574 8.579682 ACTGAAGTGAAGAAAATAAAATGCAC 57.420 30.769 0.00 0.00 0.00 4.57
2178 8579 9.950680 CTGCTTACTGAAGTGAAGAAAATAAAA 57.049 29.630 0.00 0.00 34.90 1.52
2179 8580 8.076178 GCTGCTTACTGAAGTGAAGAAAATAAA 58.924 33.333 0.00 0.00 34.90 1.40
2180 8581 7.228507 TGCTGCTTACTGAAGTGAAGAAAATAA 59.771 33.333 0.00 0.00 34.90 1.40
2181 8582 6.710295 TGCTGCTTACTGAAGTGAAGAAAATA 59.290 34.615 0.00 0.00 34.90 1.40
2182 8583 5.532406 TGCTGCTTACTGAAGTGAAGAAAAT 59.468 36.000 0.00 0.00 34.90 1.82
2183 8584 4.881273 TGCTGCTTACTGAAGTGAAGAAAA 59.119 37.500 0.00 0.00 34.90 2.29
2184 8585 4.450976 TGCTGCTTACTGAAGTGAAGAAA 58.549 39.130 0.00 0.00 34.90 2.52
2185 8586 4.071961 TGCTGCTTACTGAAGTGAAGAA 57.928 40.909 0.00 0.00 34.90 2.52
2186 8587 3.751479 TGCTGCTTACTGAAGTGAAGA 57.249 42.857 0.00 0.00 34.90 2.87
2187 8588 3.812053 ACTTGCTGCTTACTGAAGTGAAG 59.188 43.478 0.00 0.00 34.90 3.02
2188 8589 3.808728 ACTTGCTGCTTACTGAAGTGAA 58.191 40.909 0.00 0.00 34.90 3.18
2189 8590 3.475566 ACTTGCTGCTTACTGAAGTGA 57.524 42.857 0.00 0.00 34.90 3.41
2190 8591 5.673337 TTTACTTGCTGCTTACTGAAGTG 57.327 39.130 10.07 0.00 34.90 3.16
2191 8592 5.823045 AGTTTTACTTGCTGCTTACTGAAGT 59.177 36.000 0.00 3.65 34.90 3.01
2192 8593 6.138761 CAGTTTTACTTGCTGCTTACTGAAG 58.861 40.000 0.00 0.00 35.06 3.02
2193 8594 6.060028 CAGTTTTACTTGCTGCTTACTGAA 57.940 37.500 0.00 0.00 35.06 3.02
2194 8595 5.673337 CAGTTTTACTTGCTGCTTACTGA 57.327 39.130 0.00 0.00 35.06 3.41
2202 8603 6.774354 AATGAAATGCAGTTTTACTTGCTG 57.226 33.333 0.00 0.00 0.00 4.41
2204 8605 6.202570 TCCAAATGAAATGCAGTTTTACTTGC 59.797 34.615 0.00 0.00 31.43 4.01
2205 8606 7.439056 AGTCCAAATGAAATGCAGTTTTACTTG 59.561 33.333 0.00 0.32 31.43 3.16
2206 8607 7.500141 AGTCCAAATGAAATGCAGTTTTACTT 58.500 30.769 0.00 0.00 31.43 2.24
2207 8608 7.054491 AGTCCAAATGAAATGCAGTTTTACT 57.946 32.000 0.00 0.00 31.43 2.24
2209 8610 7.048629 TGAGTCCAAATGAAATGCAGTTTTA 57.951 32.000 0.00 0.00 31.43 1.52
2210 8611 5.916318 TGAGTCCAAATGAAATGCAGTTTT 58.084 33.333 0.00 0.00 31.43 2.43
2211 8612 5.534207 TGAGTCCAAATGAAATGCAGTTT 57.466 34.783 0.00 0.00 31.43 2.66
2212 8613 5.733620 ATGAGTCCAAATGAAATGCAGTT 57.266 34.783 0.00 0.00 34.68 3.16
2213 8614 5.733620 AATGAGTCCAAATGAAATGCAGT 57.266 34.783 0.00 0.00 0.00 4.40
2216 8617 5.240121 ACCAAATGAGTCCAAATGAAATGC 58.760 37.500 0.00 0.00 0.00 3.56
2217 8618 7.063780 GCTTACCAAATGAGTCCAAATGAAATG 59.936 37.037 0.00 0.00 0.00 2.32
2219 8620 6.041409 TGCTTACCAAATGAGTCCAAATGAAA 59.959 34.615 0.00 0.00 0.00 2.69
2220 8621 5.538053 TGCTTACCAAATGAGTCCAAATGAA 59.462 36.000 0.00 0.00 0.00 2.57
2222 8623 5.389859 TGCTTACCAAATGAGTCCAAATG 57.610 39.130 0.00 0.00 0.00 2.32
2223 8624 4.082026 GCTGCTTACCAAATGAGTCCAAAT 60.082 41.667 0.00 0.00 0.00 2.32
2225 8626 2.819608 GCTGCTTACCAAATGAGTCCAA 59.180 45.455 0.00 0.00 0.00 3.53
2226 8627 2.224744 TGCTGCTTACCAAATGAGTCCA 60.225 45.455 0.00 0.00 0.00 4.02
2227 8628 2.436417 TGCTGCTTACCAAATGAGTCC 58.564 47.619 0.00 0.00 0.00 3.85
2228 8629 4.503741 TTTGCTGCTTACCAAATGAGTC 57.496 40.909 0.00 0.00 0.00 3.36
2229 8630 4.099266 TGTTTTGCTGCTTACCAAATGAGT 59.901 37.500 0.00 0.00 31.71 3.41
2231 8632 4.662468 TGTTTTGCTGCTTACCAAATGA 57.338 36.364 0.00 0.00 31.71 2.57
2233 8634 5.022282 AGTTGTTTTGCTGCTTACCAAAT 57.978 34.783 0.00 0.00 31.71 2.32
2235 8636 4.464069 AAGTTGTTTTGCTGCTTACCAA 57.536 36.364 0.00 0.00 0.00 3.67
2238 8639 4.738252 GTGGTAAGTTGTTTTGCTGCTTAC 59.262 41.667 0.00 0.00 40.14 2.34
2239 8640 4.202070 GGTGGTAAGTTGTTTTGCTGCTTA 60.202 41.667 0.00 0.00 0.00 3.09
2240 8641 3.430236 GGTGGTAAGTTGTTTTGCTGCTT 60.430 43.478 0.00 0.00 0.00 3.91
2241 8642 2.100749 GGTGGTAAGTTGTTTTGCTGCT 59.899 45.455 0.00 0.00 0.00 4.24
2242 8643 2.159170 TGGTGGTAAGTTGTTTTGCTGC 60.159 45.455 0.00 0.00 0.00 5.25
2243 8644 3.119316 TGTGGTGGTAAGTTGTTTTGCTG 60.119 43.478 0.00 0.00 0.00 4.41
2245 8646 3.512033 TGTGGTGGTAAGTTGTTTTGC 57.488 42.857 0.00 0.00 0.00 3.68
2246 8647 4.623595 GTGTTGTGGTGGTAAGTTGTTTTG 59.376 41.667 0.00 0.00 0.00 2.44
2247 8648 4.281182 TGTGTTGTGGTGGTAAGTTGTTTT 59.719 37.500 0.00 0.00 0.00 2.43
2249 8650 3.191791 GTGTGTTGTGGTGGTAAGTTGTT 59.808 43.478 0.00 0.00 0.00 2.83
2251 8652 2.750166 TGTGTGTTGTGGTGGTAAGTTG 59.250 45.455 0.00 0.00 0.00 3.16
2252 8653 2.750712 GTGTGTGTTGTGGTGGTAAGTT 59.249 45.455 0.00 0.00 0.00 2.66
2254 8655 2.354510 CTGTGTGTGTTGTGGTGGTAAG 59.645 50.000 0.00 0.00 0.00 2.34
2255 8656 2.027100 TCTGTGTGTGTTGTGGTGGTAA 60.027 45.455 0.00 0.00 0.00 2.85
2259 8660 0.378257 GCTCTGTGTGTGTTGTGGTG 59.622 55.000 0.00 0.00 0.00 4.17
2260 8661 0.035534 TGCTCTGTGTGTGTTGTGGT 60.036 50.000 0.00 0.00 0.00 4.16
2261 8662 0.659427 CTGCTCTGTGTGTGTTGTGG 59.341 55.000 0.00 0.00 0.00 4.17
2262 8663 0.028505 GCTGCTCTGTGTGTGTTGTG 59.971 55.000 0.00 0.00 0.00 3.33
2263 8664 0.392863 TGCTGCTCTGTGTGTGTTGT 60.393 50.000 0.00 0.00 0.00 3.32
2265 8666 0.107508 ACTGCTGCTCTGTGTGTGTT 60.108 50.000 0.00 0.00 0.00 3.32
2267 8668 0.585357 GAACTGCTGCTCTGTGTGTG 59.415 55.000 0.00 0.00 0.00 3.82
2268 8669 0.533755 GGAACTGCTGCTCTGTGTGT 60.534 55.000 0.00 0.00 0.00 3.72
2271 8672 1.674221 GGTAGGAACTGCTGCTCTGTG 60.674 57.143 0.00 0.00 42.03 3.66
2274 8675 0.545309 TGGGTAGGAACTGCTGCTCT 60.545 55.000 0.00 0.00 42.03 4.09
2278 8679 2.224523 TGTCTTTGGGTAGGAACTGCTG 60.225 50.000 0.00 0.00 42.03 4.41
2316 8717 6.346096 CATCCCGTTAGGTCAAAGAAATCTA 58.654 40.000 0.00 0.00 36.75 1.98
2348 8757 3.090037 GGCCTCTACTCTGTACTGTTGA 58.910 50.000 0.00 0.00 0.00 3.18
2354 8763 1.023502 GTCCGGCCTCTACTCTGTAC 58.976 60.000 0.00 0.00 0.00 2.90
2355 8764 0.917533 AGTCCGGCCTCTACTCTGTA 59.082 55.000 0.00 0.00 0.00 2.74
2397 8809 2.428925 CCATGCACCTGGGAATGCC 61.429 63.158 5.44 0.00 41.33 4.40
2398 8810 1.669999 GACCATGCACCTGGGAATGC 61.670 60.000 11.02 0.00 40.85 3.56
2399 8811 0.323633 TGACCATGCACCTGGGAATG 60.324 55.000 11.02 0.00 40.85 2.67
2432 9232 0.881118 TCTTCAGGCGTCAATTTGGC 59.119 50.000 0.00 0.00 0.00 4.52
2451 9251 4.649218 AGTAGGTTCAGTTTGGTTTTGCAT 59.351 37.500 0.00 0.00 0.00 3.96
2481 9281 7.697691 GTCATCAGACCAACAATTTATACTGG 58.302 38.462 0.00 0.00 38.89 4.00


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

AutoCloner maintained by Alex Coulton.