Multiple sequence alignment - TraesCS1D01G105200

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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 TraesCS1D01G105200 chr1D 100.000 7141 0 0 1 7141 97135952 97128812 0.000000e+00 13188.0
1 TraesCS1D01G105200 chr1B 92.175 4511 258 31 753 5215 156581020 156585483 0.000000e+00 6287.0
2 TraesCS1D01G105200 chr1B 88.705 1452 116 28 5434 6860 156585901 156587329 0.000000e+00 1729.0
3 TraesCS1D01G105200 chr1B 90.222 225 19 3 5213 5435 156585596 156585819 2.520000e-74 291.0
4 TraesCS1D01G105200 chr1B 81.818 110 9 7 573 681 156580860 156580959 1.650000e-11 82.4
5 TraesCS1D01G105200 chr1A 94.185 2356 112 12 3481 5815 91593239 91590888 0.000000e+00 3568.0
6 TraesCS1D01G105200 chr1A 93.359 1837 83 11 1205 3038 91595426 91593626 0.000000e+00 2680.0
7 TraesCS1D01G105200 chr1A 94.897 1450 41 14 5720 7141 91590892 91589448 0.000000e+00 2237.0
8 TraesCS1D01G105200 chr1A 96.619 562 15 4 11 572 58940862 58940305 0.000000e+00 929.0
9 TraesCS1D01G105200 chr1A 93.537 294 17 2 3040 3332 91593529 91593237 3.060000e-118 436.0
10 TraesCS1D01G105200 chr1A 94.850 233 8 1 937 1169 91596055 91595827 1.890000e-95 361.0
11 TraesCS1D01G105200 chr1A 96.970 33 0 1 6858 6889 31314902 31314934 4.000000e-03 54.7
12 TraesCS1D01G105200 chr3A 96.803 563 16 2 11 573 643353286 643353846 0.000000e+00 939.0
13 TraesCS1D01G105200 chrUn 97.254 437 11 1 137 573 309373199 309372764 0.000000e+00 739.0
14 TraesCS1D01G105200 chrUn 95.402 87 2 1 6 90 445962342 445962428 3.470000e-28 137.0
15 TraesCS1D01G105200 chr7A 97.254 437 11 1 137 573 720406814 720407249 0.000000e+00 739.0
16 TraesCS1D01G105200 chr7A 95.402 87 2 1 6 90 720405656 720405742 3.470000e-28 137.0
17 TraesCS1D01G105200 chr5B 79.496 556 72 24 44 573 710239721 710240260 2.450000e-94 357.0
18 TraesCS1D01G105200 chr7D 82.012 328 37 12 20 334 452645708 452645390 7.110000e-65 259.0
19 TraesCS1D01G105200 chr3B 87.000 200 23 2 11 209 12471869 12471672 9.320000e-54 222.0
20 TraesCS1D01G105200 chr3B 87.805 164 18 2 3330 3493 572743419 572743258 2.630000e-44 191.0
21 TraesCS1D01G105200 chr4B 91.667 156 13 0 3328 3483 78607462 78607617 4.340000e-52 217.0
22 TraesCS1D01G105200 chr4B 90.909 154 14 0 3330 3483 78607766 78607919 2.610000e-49 207.0
23 TraesCS1D01G105200 chr4B 100.000 29 0 0 6858 6886 161291484 161291456 4.000000e-03 54.7
24 TraesCS1D01G105200 chr4B 100.000 29 0 0 6858 6886 367903837 367903809 4.000000e-03 54.7
25 TraesCS1D01G105200 chr4B 100.000 29 0 0 6858 6886 404771568 404771540 4.000000e-03 54.7
26 TraesCS1D01G105200 chr6A 85.366 205 27 3 11 214 77901606 77901404 7.260000e-50 209.0
27 TraesCS1D01G105200 chr6A 85.366 205 26 4 11 214 78035879 78035678 7.260000e-50 209.0
28 TraesCS1D01G105200 chr6A 90.385 156 14 1 3331 3485 82107506 82107351 3.380000e-48 204.0
29 TraesCS1D01G105200 chr6B 91.026 156 11 2 3331 3485 140845532 140845685 2.610000e-49 207.0
30 TraesCS1D01G105200 chr5D 90.789 152 14 0 3335 3486 256749803 256749954 3.380000e-48 204.0
31 TraesCS1D01G105200 chr3D 88.415 164 18 1 3330 3493 437486691 437486529 5.650000e-46 196.0
32 TraesCS1D01G105200 chr2D 91.096 146 11 2 3342 3487 195295026 195294883 5.650000e-46 196.0
33 TraesCS1D01G105200 chr6D 100.000 29 0 0 6861 6889 344172599 344172571 4.000000e-03 54.7
34 TraesCS1D01G105200 chr4D 100.000 29 0 0 6861 6889 427029634 427029606 4.000000e-03 54.7
35 TraesCS1D01G105200 chr4D 100.000 29 0 0 6861 6889 469167302 469167330 4.000000e-03 54.7
36 TraesCS1D01G105200 chr4A 96.970 33 0 1 6858 6889 628504418 628504386 4.000000e-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 TraesCS1D01G105200 chr1D 97128812 97135952 7140 True 13188.00 13188 100.0000 1 7141 1 chr1D.!!$R1 7140
1 TraesCS1D01G105200 chr1B 156580860 156587329 6469 False 2097.35 6287 88.2300 573 6860 4 chr1B.!!$F1 6287
2 TraesCS1D01G105200 chr1A 91589448 91596055 6607 True 1856.40 3568 94.1656 937 7141 5 chr1A.!!$R2 6204
3 TraesCS1D01G105200 chr1A 58940305 58940862 557 True 929.00 929 96.6190 11 572 1 chr1A.!!$R1 561
4 TraesCS1D01G105200 chr3A 643353286 643353846 560 False 939.00 939 96.8030 11 573 1 chr3A.!!$F1 562
5 TraesCS1D01G105200 chr7A 720405656 720407249 1593 False 438.00 739 96.3280 6 573 2 chr7A.!!$F1 567
6 TraesCS1D01G105200 chr5B 710239721 710240260 539 False 357.00 357 79.4960 44 573 1 chr5B.!!$F1 529

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
932 2011 0.026803 GATCATCAAACGGACGCAGC 59.973 55.000 0.00 0.00 0.00 5.25 F
1424 2871 0.110486 AAGAGGCGCTTCAAAGGGAA 59.890 50.000 22.42 0.00 41.06 3.97 F
1697 3144 0.240411 GCTGGACTCGACGTTAGTGT 59.760 55.000 9.01 4.58 0.00 3.55 F
2181 3630 1.869342 GCCAAGCACGCATTTCAACTT 60.869 47.619 0.00 0.00 0.00 2.66 F
3266 4817 0.248012 TGCATTGCTTGAAGCCATGG 59.752 50.000 26.18 7.63 42.62 3.66 F
4367 5923 0.107263 TCTGCAAGCAGTTGTCACCA 60.107 50.000 20.34 0.00 43.96 4.17 F
4895 6455 0.811281 CGCTTCCTTGGTTCCCATTC 59.189 55.000 0.00 0.00 31.53 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2732 4181 0.034767 CCAGCTCATGGGCTTCTTCA 60.035 55.000 20.07 0.00 46.36 3.02 R
2756 4205 0.648441 GTGAAACAACAGCGTCGACA 59.352 50.000 17.16 0.00 36.32 4.35 R
2828 4277 1.304052 TCGGACCCATGGCCTTTTG 60.304 57.895 6.09 0.00 0.00 2.44 R
4093 5647 1.604278 GAAGGACAGTGTTGCTCCAAC 59.396 52.381 0.00 1.33 43.78 3.77 R
5000 6563 0.233590 CGACTCCTCGACATAGCTCG 59.766 60.000 0.00 0.00 43.06 5.03 R
5498 7275 0.652592 GCTATCGCGCTGTTGTCAAT 59.347 50.000 5.56 0.00 0.00 2.57 R
6665 8555 1.173913 GGGTTGATTCCCACGAAAGG 58.826 55.000 0.00 0.00 46.30 3.11 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
124 125 2.127297 CAAGGGAAGGGGAGGGGA 59.873 66.667 0.00 0.00 0.00 4.81
182 1208 0.623723 GGGACCCTGGTAATTCAGCA 59.376 55.000 2.09 0.00 33.64 4.41
191 1217 4.706476 CCTGGTAATTCAGCAAAGGAATGA 59.294 41.667 0.00 0.00 35.28 2.57
283 1326 1.136891 GCTAAATTCTTGGGCGGCATT 59.863 47.619 12.47 0.00 0.00 3.56
311 1373 1.538849 CCTCCAAACAAACTGGCAAGC 60.539 52.381 0.00 0.00 33.63 4.01
408 1471 3.503363 ACATCTCACGTAACCTCGTAACA 59.497 43.478 0.00 0.00 42.27 2.41
576 1639 1.138266 ACTACCAAACACGCTGTCTGT 59.862 47.619 0.00 0.00 0.00 3.41
583 1646 4.211389 CAAACACGCTGTCTGTACATTTC 58.789 43.478 0.00 0.00 34.37 2.17
599 1662 5.909621 ACATTTCATTCTTGACCATGGAG 57.090 39.130 21.47 5.55 31.26 3.86
601 1664 5.184479 ACATTTCATTCTTGACCATGGAGTG 59.816 40.000 21.47 2.33 31.26 3.51
604 1667 1.896220 TTCTTGACCATGGAGTGTGC 58.104 50.000 21.47 0.73 0.00 4.57
607 1670 0.602638 TTGACCATGGAGTGTGCGTC 60.603 55.000 21.47 2.93 0.00 5.19
608 1671 1.293498 GACCATGGAGTGTGCGTCT 59.707 57.895 21.47 0.00 0.00 4.18
609 1672 1.004560 ACCATGGAGTGTGCGTCTG 60.005 57.895 21.47 0.00 0.00 3.51
610 1673 1.004560 CCATGGAGTGTGCGTCTGT 60.005 57.895 5.56 0.00 0.00 3.41
611 1674 1.293963 CCATGGAGTGTGCGTCTGTG 61.294 60.000 5.56 0.00 0.00 3.66
612 1675 0.601046 CATGGAGTGTGCGTCTGTGT 60.601 55.000 0.00 0.00 0.00 3.72
613 1676 0.601046 ATGGAGTGTGCGTCTGTGTG 60.601 55.000 0.00 0.00 0.00 3.82
614 1677 1.227263 GGAGTGTGCGTCTGTGTGT 60.227 57.895 0.00 0.00 0.00 3.72
615 1678 0.810031 GGAGTGTGCGTCTGTGTGTT 60.810 55.000 0.00 0.00 0.00 3.32
616 1679 1.537348 GGAGTGTGCGTCTGTGTGTTA 60.537 52.381 0.00 0.00 0.00 2.41
627 1690 5.442909 GCGTCTGTGTGTTATAAACGAGAAG 60.443 44.000 7.58 7.48 0.00 2.85
637 1700 6.750501 TGTTATAAACGAGAAGGATCGACAAG 59.249 38.462 2.78 0.00 45.56 3.16
640 1703 0.818296 CGAGAAGGATCGACAAGGGT 59.182 55.000 0.00 0.00 45.56 4.34
656 1720 0.314935 GGGTTCCACAACATGTGCAG 59.685 55.000 0.00 0.00 46.51 4.41
657 1721 0.314935 GGTTCCACAACATGTGCAGG 59.685 55.000 0.00 1.33 46.51 4.85
665 1729 1.662629 CAACATGTGCAGGATCGTCTC 59.337 52.381 0.00 0.00 0.00 3.36
713 1792 1.099689 AAACGTGGTGTGGTTTCCAG 58.900 50.000 0.00 0.00 32.34 3.86
714 1793 0.034863 AACGTGGTGTGGTTTCCAGT 60.035 50.000 0.00 0.00 32.34 4.00
716 1795 1.099689 CGTGGTGTGGTTTCCAGTTT 58.900 50.000 0.00 0.00 32.34 2.66
717 1796 1.064952 CGTGGTGTGGTTTCCAGTTTC 59.935 52.381 0.00 0.00 32.34 2.78
718 1797 1.407618 GTGGTGTGGTTTCCAGTTTCC 59.592 52.381 0.00 0.00 32.34 3.13
719 1798 1.006043 TGGTGTGGTTTCCAGTTTCCA 59.994 47.619 0.00 0.00 32.34 3.53
721 1800 1.407618 GTGTGGTTTCCAGTTTCCACC 59.592 52.381 10.08 0.00 46.59 4.61
722 1801 1.286553 TGTGGTTTCCAGTTTCCACCT 59.713 47.619 10.08 0.00 46.59 4.00
723 1802 1.681264 GTGGTTTCCAGTTTCCACCTG 59.319 52.381 0.00 0.00 42.90 4.00
724 1803 1.566703 TGGTTTCCAGTTTCCACCTGA 59.433 47.619 0.00 0.00 31.38 3.86
726 1805 2.558359 GGTTTCCAGTTTCCACCTGATG 59.442 50.000 0.00 0.00 31.38 3.07
739 1818 3.743521 CACCTGATGGAACTGAACTTGA 58.256 45.455 0.00 0.00 37.04 3.02
740 1819 4.136796 CACCTGATGGAACTGAACTTGAA 58.863 43.478 0.00 0.00 37.04 2.69
741 1820 4.214971 CACCTGATGGAACTGAACTTGAAG 59.785 45.833 0.00 0.00 37.04 3.02
742 1821 4.141390 ACCTGATGGAACTGAACTTGAAGT 60.141 41.667 0.00 0.00 37.04 3.01
743 1822 5.071788 ACCTGATGGAACTGAACTTGAAGTA 59.928 40.000 0.00 0.00 37.04 2.24
744 1823 5.997746 CCTGATGGAACTGAACTTGAAGTAA 59.002 40.000 0.00 0.00 34.57 2.24
745 1824 6.148480 CCTGATGGAACTGAACTTGAAGTAAG 59.852 42.308 0.00 2.28 37.74 2.34
746 1825 8.171373 CCTGATGGAACTGAACTTGAAGTAAGT 61.171 40.741 0.00 2.95 43.08 2.24
760 1839 3.099619 TAAGTAGGGCGCGTCGTCG 62.100 63.158 10.08 0.00 40.37 5.12
771 1850 1.883725 GCGTCGTCGTGTTTCTTCCC 61.884 60.000 3.66 0.00 39.49 3.97
772 1851 1.280206 CGTCGTCGTGTTTCTTCCCC 61.280 60.000 0.00 0.00 0.00 4.81
781 1860 3.894547 TTTCTTCCCCGCTGCCGTC 62.895 63.158 0.00 0.00 0.00 4.79
790 1869 2.112198 CGCTGCCGTCTCTCTCTCT 61.112 63.158 0.00 0.00 0.00 3.10
792 1871 1.029408 GCTGCCGTCTCTCTCTCTCA 61.029 60.000 0.00 0.00 0.00 3.27
793 1872 0.732571 CTGCCGTCTCTCTCTCTCAC 59.267 60.000 0.00 0.00 0.00 3.51
795 1874 1.169577 GCCGTCTCTCTCTCTCACAA 58.830 55.000 0.00 0.00 0.00 3.33
796 1875 1.542030 GCCGTCTCTCTCTCTCACAAA 59.458 52.381 0.00 0.00 0.00 2.83
797 1876 2.165437 GCCGTCTCTCTCTCTCACAAAT 59.835 50.000 0.00 0.00 0.00 2.32
798 1877 3.733684 GCCGTCTCTCTCTCTCACAAATC 60.734 52.174 0.00 0.00 0.00 2.17
799 1878 3.181491 CCGTCTCTCTCTCTCACAAATCC 60.181 52.174 0.00 0.00 0.00 3.01
800 1879 3.694072 CGTCTCTCTCTCTCACAAATCCT 59.306 47.826 0.00 0.00 0.00 3.24
802 1881 4.097892 GTCTCTCTCTCTCACAAATCCTCC 59.902 50.000 0.00 0.00 0.00 4.30
803 1882 4.017591 TCTCTCTCTCTCACAAATCCTCCT 60.018 45.833 0.00 0.00 0.00 3.69
804 1883 4.277476 TCTCTCTCTCACAAATCCTCCTC 58.723 47.826 0.00 0.00 0.00 3.71
918 1997 4.891727 GGTGCGACCGCCGATCAT 62.892 66.667 12.08 0.00 41.76 2.45
919 1998 3.330853 GTGCGACCGCCGATCATC 61.331 66.667 12.08 0.00 41.76 2.92
920 1999 3.832492 TGCGACCGCCGATCATCA 61.832 61.111 12.08 0.00 41.76 3.07
921 2000 2.584970 GCGACCGCCGATCATCAA 60.585 61.111 2.55 0.00 41.76 2.57
922 2001 2.171079 GCGACCGCCGATCATCAAA 61.171 57.895 2.55 0.00 41.76 2.69
923 2002 1.636340 CGACCGCCGATCATCAAAC 59.364 57.895 0.00 0.00 41.76 2.93
924 2003 1.636340 GACCGCCGATCATCAAACG 59.364 57.895 0.00 0.00 0.00 3.60
930 2009 2.368856 CGATCATCAAACGGACGCA 58.631 52.632 0.00 0.00 0.00 5.24
931 2010 0.298707 CGATCATCAAACGGACGCAG 59.701 55.000 0.00 0.00 0.00 5.18
932 2011 0.026803 GATCATCAAACGGACGCAGC 59.973 55.000 0.00 0.00 0.00 5.25
933 2012 0.673333 ATCATCAAACGGACGCAGCA 60.673 50.000 0.00 0.00 0.00 4.41
934 2013 1.133253 CATCAAACGGACGCAGCAG 59.867 57.895 0.00 0.00 0.00 4.24
935 2014 2.680913 ATCAAACGGACGCAGCAGC 61.681 57.895 0.00 0.00 37.42 5.25
998 2077 4.057428 CGGCGGGGAGGATCGATC 62.057 72.222 17.36 17.36 34.37 3.69
999 2078 4.057428 GGCGGGGAGGATCGATCG 62.057 72.222 18.81 9.36 34.37 3.69
1103 2182 1.927174 CTCCATCGACGGTGAATCAAC 59.073 52.381 10.33 0.00 0.00 3.18
1104 2183 1.273886 TCCATCGACGGTGAATCAACA 59.726 47.619 10.33 0.00 0.00 3.33
1125 2207 1.290732 CCTTCTCCCTCTCCTCCTTCT 59.709 57.143 0.00 0.00 0.00 2.85
1126 2208 2.292851 CCTTCTCCCTCTCCTCCTTCTT 60.293 54.545 0.00 0.00 0.00 2.52
1127 2209 3.449918 CTTCTCCCTCTCCTCCTTCTTT 58.550 50.000 0.00 0.00 0.00 2.52
1198 2305 7.067494 GTGCTGTGTCCTTGGAATAATTCTTAT 59.933 37.037 0.00 0.00 0.00 1.73
1232 2679 9.317827 TGGGGAATAAGTATAGTACTGAATACC 57.682 37.037 5.39 0.00 39.39 2.73
1363 2810 4.036380 ACTTTTGCCTAACAACTTTCTCGG 59.964 41.667 0.00 0.00 38.23 4.63
1365 2812 0.442699 GCCTAACAACTTTCTCGGCG 59.557 55.000 0.00 0.00 0.00 6.46
1370 2817 5.287226 CCTAACAACTTTCTCGGCGTATAT 58.713 41.667 6.85 0.00 0.00 0.86
1380 2827 5.258456 TCTCGGCGTATATTTTTCAGTCT 57.742 39.130 6.85 0.00 0.00 3.24
1381 2828 5.041287 TCTCGGCGTATATTTTTCAGTCTG 58.959 41.667 6.85 0.00 0.00 3.51
1384 2831 5.045215 CGGCGTATATTTTTCAGTCTGGTA 58.955 41.667 0.00 0.00 0.00 3.25
1395 2842 7.435068 TTTTCAGTCTGGTATAGCTTGAAAC 57.565 36.000 16.45 5.11 37.76 2.78
1422 2869 4.404691 AAGAGGCGCTTCAAAGGG 57.595 55.556 22.42 2.66 41.45 3.95
1424 2871 0.110486 AAGAGGCGCTTCAAAGGGAA 59.890 50.000 22.42 0.00 41.06 3.97
1619 3066 6.877236 AGATGTGTGTGGAAATTCTTTTTGT 58.123 32.000 0.00 0.00 0.00 2.83
1690 3137 1.391485 CATTTTCTGCTGGACTCGACG 59.609 52.381 0.00 0.00 0.00 5.12
1697 3144 0.240411 GCTGGACTCGACGTTAGTGT 59.760 55.000 9.01 4.58 0.00 3.55
1712 3159 5.034797 CGTTAGTGTCTTCGCTGATATTCA 58.965 41.667 0.00 0.00 35.84 2.57
1723 3170 2.430956 CTGATATTCACAAACGTGCGC 58.569 47.619 0.00 0.00 34.20 6.09
1758 3205 5.947228 AAGCAAATTTTCTGTCGAGATCA 57.053 34.783 0.00 0.00 0.00 2.92
1759 3206 5.947228 AGCAAATTTTCTGTCGAGATCAA 57.053 34.783 0.00 0.00 0.00 2.57
1954 3403 6.917217 ACACGTACCATTAGACTAGTAGAC 57.083 41.667 3.59 0.00 0.00 2.59
2010 3459 2.259917 TCTCTGTCAGATGCTGGGAAA 58.740 47.619 2.22 0.00 31.51 3.13
2072 3521 6.890268 GGAGGTTTAGAAATTTCCATGGTACT 59.110 38.462 14.61 5.07 0.00 2.73
2081 3530 3.313012 TTCCATGGTACTGAGTTGACG 57.687 47.619 12.58 0.00 0.00 4.35
2087 3536 2.696707 TGGTACTGAGTTGACGTCCTTT 59.303 45.455 14.12 0.00 0.00 3.11
2119 3568 7.110155 TCTTCACCTTACAAGAGAAGTTTTGT 58.890 34.615 16.62 0.00 40.39 2.83
2120 3569 6.677781 TCACCTTACAAGAGAAGTTTTGTG 57.322 37.500 2.34 0.00 37.98 3.33
2123 3572 8.208224 TCACCTTACAAGAGAAGTTTTGTGATA 58.792 33.333 2.34 0.00 37.98 2.15
2181 3630 1.869342 GCCAAGCACGCATTTCAACTT 60.869 47.619 0.00 0.00 0.00 2.66
2468 3917 7.401246 TGTACCATGCCATGCAATAGATTATA 58.599 34.615 0.00 0.00 43.62 0.98
2607 4056 7.414222 AAAGCACTTGAAATGATGATGGTAT 57.586 32.000 0.00 0.00 0.00 2.73
2630 4079 9.907576 GTATGTTCATTTACTTCTCTCATTTCG 57.092 33.333 0.00 0.00 0.00 3.46
2643 4092 5.473162 TCTCTCATTTCGCAAAATTCCTTCA 59.527 36.000 0.00 0.00 32.69 3.02
2732 4181 2.680339 GCTCTCGAAGCCAATAAAAGCT 59.320 45.455 7.98 0.00 45.92 3.74
3032 4481 6.177610 TCGGAAGGTATGATTTGCTTTACTT 58.822 36.000 0.00 0.00 0.00 2.24
3061 4605 5.403466 GCATTTGGCTTGACAAGAAAACTAG 59.597 40.000 19.51 11.75 40.25 2.57
3136 4686 6.699575 TTTTCAGGAACTCTTTTTCTCAGG 57.300 37.500 0.00 0.00 34.60 3.86
3143 4693 5.106515 GGAACTCTTTTTCTCAGGTACATGC 60.107 44.000 1.79 0.00 0.00 4.06
3179 4729 1.837747 GTGTTCTTTTCACAACGTGCG 59.162 47.619 0.00 0.00 36.05 5.34
3227 4777 5.461032 AAAATATTGTGCTTGTTCCGGAA 57.539 34.783 14.35 14.35 0.00 4.30
3266 4817 0.248012 TGCATTGCTTGAAGCCATGG 59.752 50.000 26.18 7.63 42.62 3.66
3358 4909 5.701290 ACCTATGTTCTGAATTATAAGCCGC 59.299 40.000 0.00 0.00 0.00 6.53
3388 4939 8.504005 GGATTTTTCAATATGGACTACATACGG 58.496 37.037 0.00 0.00 44.41 4.02
3397 4948 5.006153 TGGACTACATACGGACTGAAATG 57.994 43.478 0.00 0.00 0.00 2.32
3400 4951 6.127168 TGGACTACATACGGACTGAAATGATT 60.127 38.462 7.93 0.00 0.00 2.57
3409 4960 5.067153 ACGGACTGAAATGATTGAACAAACA 59.933 36.000 0.51 0.51 0.00 2.83
3413 4964 6.866480 ACTGAAATGATTGAACAAACACACT 58.134 32.000 0.03 0.00 0.00 3.55
3421 4972 3.418094 TGAACAAACACACTAAAACGCG 58.582 40.909 3.53 3.53 0.00 6.01
3434 4985 7.590322 CACACTAAAACGCGTCTATATACATCT 59.410 37.037 14.44 0.00 0.00 2.90
3522 5073 2.793317 ATTGCAGCAGGTTCCTGGGG 62.793 60.000 18.81 0.00 34.85 4.96
3583 5134 1.815817 GCCATTGTTGGTGGTGGACC 61.816 60.000 0.00 0.00 45.57 4.46
3606 5157 0.608035 GGGTTCTGGAATCGCAACCA 60.608 55.000 8.32 0.00 40.21 3.67
3645 5196 9.120538 GCCATTATCCTGTTATACTCAAAGAAA 57.879 33.333 0.00 0.00 0.00 2.52
3710 5263 5.905913 AGGTAGAGGATGGCTTAACATTACT 59.094 40.000 0.00 0.00 0.00 2.24
3844 5398 4.588951 AGGAAAGGAAAAATGACCAAGGAC 59.411 41.667 0.00 0.00 0.00 3.85
3847 5401 4.937201 AGGAAAAATGACCAAGGACAAC 57.063 40.909 0.00 0.00 0.00 3.32
3999 5553 3.774216 GAGAGAGCCCTGCTGGAATATAT 59.226 47.826 11.88 0.00 39.88 0.86
4026 5580 3.197265 TCGCTATTTTAGTTAACCCGGC 58.803 45.455 0.88 0.00 0.00 6.13
4228 5782 3.863424 TCTTCGCGTAAGGAAATGCTAAG 59.137 43.478 5.77 0.00 36.19 2.18
4237 5791 3.973425 AGGAAATGCTAAGCAGGTTCAT 58.027 40.909 0.15 0.00 43.65 2.57
4245 5799 6.693315 TGCTAAGCAGGTTCATAATAAACC 57.307 37.500 0.00 0.00 45.41 3.27
4278 5832 6.098409 TGTGATTCCTGAACTACCTCCTAATC 59.902 42.308 0.00 0.00 0.00 1.75
4279 5833 6.098409 GTGATTCCTGAACTACCTCCTAATCA 59.902 42.308 0.00 0.00 0.00 2.57
4280 5834 5.934402 TTCCTGAACTACCTCCTAATCAC 57.066 43.478 0.00 0.00 0.00 3.06
4281 5835 5.208294 TCCTGAACTACCTCCTAATCACT 57.792 43.478 0.00 0.00 0.00 3.41
4284 5840 4.287552 TGAACTACCTCCTAATCACTCCC 58.712 47.826 0.00 0.00 0.00 4.30
4321 5877 4.247258 CAGCTCATATCATGCCTCTTCTC 58.753 47.826 0.00 0.00 0.00 2.87
4367 5923 0.107263 TCTGCAAGCAGTTGTCACCA 60.107 50.000 20.34 0.00 43.96 4.17
4435 5991 3.927163 CTGTACCGGCTTCGCGGTT 62.927 63.158 6.13 0.00 36.94 4.44
4474 6030 1.342074 ACACTCAGGCAGCACTCTTA 58.658 50.000 0.00 0.00 0.00 2.10
4499 6055 5.585820 TGTTGATCATGGAATGGATGTTG 57.414 39.130 0.00 0.00 46.73 3.33
4521 6077 4.679373 ACAAGATCGATCAGGCTTGTAT 57.321 40.909 26.47 5.49 46.37 2.29
4595 6155 5.703592 TCTCTTCTGCGGTATCTAATCTCTC 59.296 44.000 0.00 0.00 0.00 3.20
4651 6211 2.421424 GTGGGACTGTCAGCATCATTTC 59.579 50.000 10.38 0.00 0.00 2.17
4750 6310 4.163441 TGACAGATCTGGTTGGTTTTGA 57.837 40.909 26.08 0.00 34.19 2.69
4751 6311 3.882888 TGACAGATCTGGTTGGTTTTGAC 59.117 43.478 26.08 0.00 34.19 3.18
4895 6455 0.811281 CGCTTCCTTGGTTCCCATTC 59.189 55.000 0.00 0.00 31.53 2.67
4905 6465 2.569853 TGGTTCCCATTCGTGAGTATGT 59.430 45.455 0.00 0.00 37.20 2.29
4909 6469 5.048294 GGTTCCCATTCGTGAGTATGTTTTT 60.048 40.000 0.00 0.00 37.20 1.94
5000 6563 2.570135 GAGCCCTGATCCTGAAATCAC 58.430 52.381 0.00 0.00 32.36 3.06
5003 6566 2.831333 CCCTGATCCTGAAATCACGAG 58.169 52.381 0.00 0.00 32.36 4.18
5049 6612 1.081833 AGGAGCCACACCTGATCCT 59.918 57.895 0.00 0.00 36.30 3.24
5059 6622 0.995024 ACCTGATCCTGAGGTTTGGG 59.005 55.000 0.00 0.12 41.31 4.12
5104 6667 4.877323 ACGTTCCTTTGTTCTTCACTTC 57.123 40.909 0.00 0.00 0.00 3.01
5105 6668 4.258543 ACGTTCCTTTGTTCTTCACTTCA 58.741 39.130 0.00 0.00 0.00 3.02
5106 6669 4.332819 ACGTTCCTTTGTTCTTCACTTCAG 59.667 41.667 0.00 0.00 0.00 3.02
5115 6678 6.486253 TGTTCTTCACTTCAGCAATATGAC 57.514 37.500 0.00 0.00 0.00 3.06
5146 6715 6.537453 TGAGGGTTTGTGAAAGAAAATTGA 57.463 33.333 0.00 0.00 27.72 2.57
5150 6719 8.039603 AGGGTTTGTGAAAGAAAATTGAAAAC 57.960 30.769 0.00 0.00 27.72 2.43
5227 6919 4.627611 TGGCTTGTAGATAGTACGTGTC 57.372 45.455 0.00 0.00 0.00 3.67
5267 6960 3.443681 GGCAGCTTTCAATTAACCTGCTA 59.556 43.478 9.85 0.00 40.24 3.49
5270 6963 5.505286 CAGCTTTCAATTAACCTGCTATCG 58.495 41.667 0.00 0.00 0.00 2.92
5285 6978 4.769688 TGCTATCGTTGGTGAAATCTCAT 58.230 39.130 0.00 0.00 33.05 2.90
5289 6982 7.498900 TGCTATCGTTGGTGAAATCTCATTATT 59.501 33.333 0.00 0.00 33.05 1.40
5342 7035 7.974482 TTCAGTATTGATGGCAGATAGATTG 57.026 36.000 0.00 0.00 32.27 2.67
5343 7036 7.071069 TCAGTATTGATGGCAGATAGATTGT 57.929 36.000 0.00 0.00 0.00 2.71
5344 7037 7.157347 TCAGTATTGATGGCAGATAGATTGTC 58.843 38.462 0.00 0.00 0.00 3.18
5346 7039 3.777106 TGATGGCAGATAGATTGTCCC 57.223 47.619 0.00 0.00 0.00 4.46
5347 7040 3.047857 TGATGGCAGATAGATTGTCCCA 58.952 45.455 0.00 0.00 0.00 4.37
5348 7041 3.654321 TGATGGCAGATAGATTGTCCCAT 59.346 43.478 0.00 0.00 0.00 4.00
5349 7042 4.105217 TGATGGCAGATAGATTGTCCCATT 59.895 41.667 0.00 0.00 0.00 3.16
5351 7044 5.645056 TGGCAGATAGATTGTCCCATTTA 57.355 39.130 0.00 0.00 0.00 1.40
5413 7107 4.644234 CCATGCACACCATAATTCCAGTTA 59.356 41.667 0.00 0.00 31.47 2.24
5469 7246 3.298619 TGGCCATTTCTAATCACCATGG 58.701 45.455 11.19 11.19 37.96 3.66
5498 7275 0.111061 ATGGTGGCAGTTGCTCAAGA 59.889 50.000 3.88 0.00 41.70 3.02
5643 7420 4.108299 CCCGCCATACAGGTGCCA 62.108 66.667 0.00 0.00 46.92 4.92
5720 7497 2.383527 GCCGACGAACTGCTGAAGG 61.384 63.158 0.00 0.00 0.00 3.46
5817 7686 1.819229 CTGTCGGAGTGGGAGATGG 59.181 63.158 0.00 0.00 0.00 3.51
5896 7765 4.103153 TCTTCCTCTGGTGAGAACAATGTT 59.897 41.667 0.00 0.00 42.73 2.71
5899 7768 3.885297 CCTCTGGTGAGAACAATGTTTGT 59.115 43.478 0.00 0.00 42.73 2.83
6047 7916 0.542702 ATGAACAACCAGGCCAAGGG 60.543 55.000 17.52 12.26 0.00 3.95
6084 7954 8.511604 TTCTTTTCCTCATTCTACCATCATTC 57.488 34.615 0.00 0.00 0.00 2.67
6095 7965 5.972935 TCTACCATCATTCGTTCTTTGCTA 58.027 37.500 0.00 0.00 0.00 3.49
6168 8039 1.409241 GCTGCTGAATCATGGAAGGGA 60.409 52.381 0.00 0.00 0.00 4.20
6505 8393 4.950475 AGGTCACTCGTCTGAGATCATAAA 59.050 41.667 0.00 0.00 45.57 1.40
6609 8499 9.618890 ATCTGTGAACATGCACTAAATAAGTAT 57.381 29.630 0.00 0.00 39.49 2.12
6878 8771 5.416952 CCGTCTTACTCCCTCTGTAAACTAA 59.583 44.000 0.00 0.00 30.72 2.24
6879 8772 6.096564 CCGTCTTACTCCCTCTGTAAACTAAT 59.903 42.308 0.00 0.00 30.72 1.73
6887 8780 9.710818 ACTCCCTCTGTAAACTAATATAAGACA 57.289 33.333 0.00 0.00 0.00 3.41
6979 8900 6.051717 ACTCCTCGATTTTCTAATCCATGTG 58.948 40.000 0.00 0.00 37.46 3.21
6986 8907 5.596836 TTTTCTAATCCATGTGGCCATTC 57.403 39.130 9.72 0.00 34.44 2.67
7037 8958 3.479370 GCTGCCAGCAACTACTCG 58.521 61.111 12.82 0.00 41.89 4.18
7057 8978 2.161609 CGTGTTTTATTGCCCTCTGGTC 59.838 50.000 0.00 0.00 0.00 4.02
7073 8994 2.686405 CTGGTCCATCCACATCAACATG 59.314 50.000 0.00 0.00 41.93 3.21
7115 9036 6.945636 TTACTTTACAATTCCCTCTCCAGA 57.054 37.500 0.00 0.00 0.00 3.86
7127 9048 5.805728 TCCCTCTCCAGAGTGTTTATTTTC 58.194 41.667 2.92 0.00 40.48 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.101049 CCCAACCAAACACGCTGAGT 61.101 55.000 0.00 0.00 0.00 3.41
8 9 1.654220 CCCAACCAAACACGCTGAG 59.346 57.895 0.00 0.00 0.00 3.35
9 10 1.826054 CCCCAACCAAACACGCTGA 60.826 57.895 0.00 0.00 0.00 4.26
41 42 3.681593 TCAACCTTAAACTCCCATTCCG 58.318 45.455 0.00 0.00 0.00 4.30
124 125 2.828661 GGAGTTGGCCCTCCTAATTT 57.171 50.000 18.23 0.00 46.34 1.82
182 1208 8.924511 TTTTAGATGTCAACTCTCATTCCTTT 57.075 30.769 0.00 0.00 0.00 3.11
191 1217 8.571336 CCAAATCTGTTTTTAGATGTCAACTCT 58.429 33.333 0.00 0.00 37.48 3.24
283 1326 6.052360 GCCAGTTTGTTTGGAGGAAAAATTA 58.948 36.000 0.00 0.00 37.96 1.40
311 1373 7.010367 CGATAGATTAGGGAGTAGTAGTTAGCG 59.990 44.444 0.00 0.00 39.76 4.26
373 1435 5.423015 ACGTGAGATGTGATTCTATTTGCT 58.577 37.500 0.00 0.00 0.00 3.91
576 1639 6.375174 CACTCCATGGTCAAGAATGAAATGTA 59.625 38.462 12.58 0.00 37.30 2.29
583 1646 2.163010 GCACACTCCATGGTCAAGAATG 59.837 50.000 12.58 7.14 0.00 2.67
599 1662 4.451557 GTTTATAACACACAGACGCACAC 58.548 43.478 0.00 0.00 0.00 3.82
601 1664 3.426191 TCGTTTATAACACACAGACGCAC 59.574 43.478 0.00 0.00 0.00 5.34
604 1667 5.060569 CCTTCTCGTTTATAACACACAGACG 59.939 44.000 0.00 0.00 0.00 4.18
607 1670 6.020599 CGATCCTTCTCGTTTATAACACACAG 60.021 42.308 0.00 0.00 34.00 3.66
608 1671 5.803461 CGATCCTTCTCGTTTATAACACACA 59.197 40.000 0.00 0.00 34.00 3.72
609 1672 6.020837 GTCGATCCTTCTCGTTTATAACACAC 60.021 42.308 0.00 0.00 39.62 3.82
610 1673 6.032094 GTCGATCCTTCTCGTTTATAACACA 58.968 40.000 0.00 0.00 39.62 3.72
611 1674 6.032094 TGTCGATCCTTCTCGTTTATAACAC 58.968 40.000 0.00 0.00 39.62 3.32
612 1675 6.198650 TGTCGATCCTTCTCGTTTATAACA 57.801 37.500 0.00 0.00 39.62 2.41
613 1676 6.198591 CCTTGTCGATCCTTCTCGTTTATAAC 59.801 42.308 0.00 0.00 39.62 1.89
614 1677 6.270815 CCTTGTCGATCCTTCTCGTTTATAA 58.729 40.000 0.00 0.00 39.62 0.98
615 1678 5.221185 CCCTTGTCGATCCTTCTCGTTTATA 60.221 44.000 0.00 0.00 39.62 0.98
616 1679 4.441634 CCCTTGTCGATCCTTCTCGTTTAT 60.442 45.833 0.00 0.00 39.62 1.40
627 1690 0.323629 TGTGGAACCCTTGTCGATCC 59.676 55.000 0.00 0.00 34.36 3.36
632 1695 2.034558 CACATGTTGTGGAACCCTTGTC 59.965 50.000 0.00 0.00 44.27 3.18
637 1700 2.424474 TGCACATGTTGTGGAACCC 58.576 52.632 9.48 0.00 45.65 4.11
657 1721 0.952280 TCATGCGTAGGGAGACGATC 59.048 55.000 0.00 0.00 45.82 3.69
665 1729 2.628178 TGGAAGACTATCATGCGTAGGG 59.372 50.000 9.02 0.00 0.00 3.53
718 1797 3.743521 TCAAGTTCAGTTCCATCAGGTG 58.256 45.455 0.00 0.00 35.89 4.00
719 1798 4.141390 ACTTCAAGTTCAGTTCCATCAGGT 60.141 41.667 0.00 0.00 35.89 4.00
720 1799 4.392940 ACTTCAAGTTCAGTTCCATCAGG 58.607 43.478 0.00 0.00 0.00 3.86
721 1800 6.708054 ACTTACTTCAAGTTCAGTTCCATCAG 59.292 38.462 0.00 0.00 45.54 2.90
722 1801 6.591935 ACTTACTTCAAGTTCAGTTCCATCA 58.408 36.000 0.00 0.00 45.54 3.07
723 1802 7.332182 CCTACTTACTTCAAGTTCAGTTCCATC 59.668 40.741 7.26 0.00 45.54 3.51
724 1803 7.162082 CCTACTTACTTCAAGTTCAGTTCCAT 58.838 38.462 7.26 0.00 45.54 3.41
726 1805 5.932883 CCCTACTTACTTCAAGTTCAGTTCC 59.067 44.000 7.26 0.00 45.54 3.62
727 1806 5.408909 GCCCTACTTACTTCAAGTTCAGTTC 59.591 44.000 7.26 0.00 45.54 3.01
728 1807 5.306394 GCCCTACTTACTTCAAGTTCAGTT 58.694 41.667 7.26 0.00 45.54 3.16
729 1808 4.560919 CGCCCTACTTACTTCAAGTTCAGT 60.561 45.833 0.00 1.14 45.54 3.41
730 1809 3.927142 CGCCCTACTTACTTCAAGTTCAG 59.073 47.826 0.00 0.00 45.54 3.02
731 1810 3.863400 GCGCCCTACTTACTTCAAGTTCA 60.863 47.826 0.00 0.00 45.54 3.18
732 1811 2.671888 GCGCCCTACTTACTTCAAGTTC 59.328 50.000 0.00 0.00 45.54 3.01
733 1812 2.696506 GCGCCCTACTTACTTCAAGTT 58.303 47.619 0.00 0.00 45.54 2.66
735 1814 1.278238 CGCGCCCTACTTACTTCAAG 58.722 55.000 0.00 0.00 40.38 3.02
736 1815 0.604578 ACGCGCCCTACTTACTTCAA 59.395 50.000 5.73 0.00 0.00 2.69
737 1816 0.171903 GACGCGCCCTACTTACTTCA 59.828 55.000 5.73 0.00 0.00 3.02
738 1817 0.864797 CGACGCGCCCTACTTACTTC 60.865 60.000 5.73 0.00 0.00 3.01
739 1818 1.138247 CGACGCGCCCTACTTACTT 59.862 57.895 5.73 0.00 0.00 2.24
740 1819 1.986575 GACGACGCGCCCTACTTACT 61.987 60.000 5.73 0.00 0.00 2.24
741 1820 1.584742 GACGACGCGCCCTACTTAC 60.585 63.158 5.73 0.00 0.00 2.34
742 1821 2.793946 GACGACGCGCCCTACTTA 59.206 61.111 5.73 0.00 0.00 2.24
743 1822 4.471726 CGACGACGCGCCCTACTT 62.472 66.667 5.73 0.00 0.00 2.24
749 1828 4.405173 GAAACACGACGACGCGCC 62.405 66.667 5.73 0.00 43.96 6.53
750 1829 2.775670 GAAGAAACACGACGACGCGC 62.776 60.000 5.73 0.00 43.96 6.86
751 1830 1.125266 GAAGAAACACGACGACGCG 59.875 57.895 3.53 3.53 43.96 6.01
760 1839 2.626780 GGCAGCGGGGAAGAAACAC 61.627 63.158 0.00 0.00 0.00 3.32
763 1842 3.894547 GACGGCAGCGGGGAAGAAA 62.895 63.158 4.79 0.00 0.00 2.52
771 1850 3.119709 GAGAGAGAGACGGCAGCGG 62.120 68.421 0.00 0.00 0.00 5.52
772 1851 2.047151 GAGAGAGAGAGACGGCAGCG 62.047 65.000 0.00 0.00 0.00 5.18
781 1860 4.280819 AGGAGGATTTGTGAGAGAGAGAG 58.719 47.826 0.00 0.00 0.00 3.20
782 1861 4.277476 GAGGAGGATTTGTGAGAGAGAGA 58.723 47.826 0.00 0.00 0.00 3.10
786 1865 3.190383 TGGAGGAGGATTTGTGAGAGA 57.810 47.619 0.00 0.00 0.00 3.10
790 1869 2.305927 GGAGTTGGAGGAGGATTTGTGA 59.694 50.000 0.00 0.00 0.00 3.58
792 1871 1.279271 CGGAGTTGGAGGAGGATTTGT 59.721 52.381 0.00 0.00 0.00 2.83
793 1872 1.555075 TCGGAGTTGGAGGAGGATTTG 59.445 52.381 0.00 0.00 0.00 2.32
795 1874 1.555533 GTTCGGAGTTGGAGGAGGATT 59.444 52.381 0.00 0.00 0.00 3.01
796 1875 1.196012 GTTCGGAGTTGGAGGAGGAT 58.804 55.000 0.00 0.00 0.00 3.24
797 1876 0.903454 GGTTCGGAGTTGGAGGAGGA 60.903 60.000 0.00 0.00 0.00 3.71
798 1877 1.192146 TGGTTCGGAGTTGGAGGAGG 61.192 60.000 0.00 0.00 0.00 4.30
799 1878 0.685097 TTGGTTCGGAGTTGGAGGAG 59.315 55.000 0.00 0.00 0.00 3.69
800 1879 0.395312 GTTGGTTCGGAGTTGGAGGA 59.605 55.000 0.00 0.00 0.00 3.71
802 1881 1.070134 TCAGTTGGTTCGGAGTTGGAG 59.930 52.381 0.00 0.00 0.00 3.86
803 1882 1.124780 TCAGTTGGTTCGGAGTTGGA 58.875 50.000 0.00 0.00 0.00 3.53
804 1883 1.226746 GTCAGTTGGTTCGGAGTTGG 58.773 55.000 0.00 0.00 0.00 3.77
845 1924 3.284449 GGCGGCAGTTGTTCGGTT 61.284 61.111 3.07 0.00 0.00 4.44
905 1984 1.636340 GTTTGATGATCGGCGGTCG 59.364 57.895 16.28 0.00 40.90 4.79
907 1986 1.813753 CCGTTTGATGATCGGCGGT 60.814 57.895 7.21 0.00 37.90 5.68
909 1988 1.636340 GTCCGTTTGATGATCGGCG 59.364 57.895 0.00 0.00 43.35 6.46
910 1989 1.636340 CGTCCGTTTGATGATCGGC 59.364 57.895 0.00 0.00 43.35 5.54
918 1997 3.345808 GCTGCTGCGTCCGTTTGA 61.346 61.111 0.00 0.00 0.00 2.69
919 1998 4.389576 GGCTGCTGCGTCCGTTTG 62.390 66.667 9.65 0.00 40.82 2.93
996 2075 2.822399 GTCCCCTTCGCCATCGAT 59.178 61.111 0.00 0.00 45.04 3.59
997 2076 3.833645 CGTCCCCTTCGCCATCGA 61.834 66.667 0.00 0.00 43.89 3.59
998 2077 3.833645 TCGTCCCCTTCGCCATCG 61.834 66.667 0.00 0.00 0.00 3.84
999 2078 2.202892 GTCGTCCCCTTCGCCATC 60.203 66.667 0.00 0.00 0.00 3.51
1103 2182 0.338120 AGGAGGAGAGGGAGAAGGTG 59.662 60.000 0.00 0.00 0.00 4.00
1104 2183 1.007842 GAAGGAGGAGAGGGAGAAGGT 59.992 57.143 0.00 0.00 0.00 3.50
1111 2190 1.765904 GGCTAAAGAAGGAGGAGAGGG 59.234 57.143 0.00 0.00 0.00 4.30
1125 2207 0.329931 TCTCCCAAATGCCGGCTAAA 59.670 50.000 29.70 7.94 0.00 1.85
1126 2208 0.107214 CTCTCCCAAATGCCGGCTAA 60.107 55.000 29.70 8.87 0.00 3.09
1127 2209 0.980754 TCTCTCCCAAATGCCGGCTA 60.981 55.000 29.70 14.84 0.00 3.93
1231 2678 9.338291 CAGAATAATTTGCATCTAAATGATCGG 57.662 33.333 0.00 0.00 34.61 4.18
1232 2679 9.888878 ACAGAATAATTTGCATCTAAATGATCG 57.111 29.630 0.00 0.00 34.61 3.69
1340 2787 4.036380 CCGAGAAAGTTGTTAGGCAAAAGT 59.964 41.667 0.00 0.00 39.03 2.66
1354 2801 5.873164 ACTGAAAAATATACGCCGAGAAAGT 59.127 36.000 0.00 0.00 0.00 2.66
1363 2810 7.599245 AGCTATACCAGACTGAAAAATATACGC 59.401 37.037 3.32 4.80 0.00 4.42
1370 2817 7.307751 CGTTTCAAGCTATACCAGACTGAAAAA 60.308 37.037 3.32 0.00 0.00 1.94
1380 2827 2.027561 AGTGCCGTTTCAAGCTATACCA 60.028 45.455 0.00 0.00 0.00 3.25
1381 2828 2.629051 AGTGCCGTTTCAAGCTATACC 58.371 47.619 0.00 0.00 0.00 2.73
1384 2831 4.137116 TCATAGTGCCGTTTCAAGCTAT 57.863 40.909 0.00 0.00 0.00 2.97
1395 2842 2.240500 GCGCCTCTTCATAGTGCCG 61.241 63.158 0.00 0.00 0.00 5.69
1417 2864 6.012745 ACAATAGCTTTCACATCTTCCCTTT 58.987 36.000 0.00 0.00 0.00 3.11
1422 2869 8.721478 TGTAAGAACAATAGCTTTCACATCTTC 58.279 33.333 0.00 0.00 30.91 2.87
1424 2871 7.335422 CCTGTAAGAACAATAGCTTTCACATCT 59.665 37.037 0.00 0.00 34.49 2.90
1690 3137 5.805486 TGTGAATATCAGCGAAGACACTAAC 59.195 40.000 0.00 0.00 0.00 2.34
1697 3144 4.242475 ACGTTTGTGAATATCAGCGAAGA 58.758 39.130 0.00 0.00 0.00 2.87
1712 3159 2.613506 GGGCTAAGCGCACGTTTGT 61.614 57.895 11.47 0.00 41.23 2.83
1723 3170 5.357742 AAATTTGCTTAATGGGGGCTAAG 57.642 39.130 0.00 0.00 0.00 2.18
1758 3205 6.815142 GGTATGTAGAGACACGGTAAAATGTT 59.185 38.462 0.00 0.00 38.76 2.71
1759 3206 6.154021 AGGTATGTAGAGACACGGTAAAATGT 59.846 38.462 0.00 0.00 38.76 2.71
2072 3521 4.931661 ACTAAGAAAGGACGTCAACTCA 57.068 40.909 18.91 0.00 0.00 3.41
2081 3530 7.215085 TGTAAGGTGAAGAACTAAGAAAGGAC 58.785 38.462 0.00 0.00 0.00 3.85
2087 3536 7.834881 TCTCTTGTAAGGTGAAGAACTAAGA 57.165 36.000 0.00 0.00 0.00 2.10
2146 3595 5.368989 GTGCTTGGCATACCTAATAGAAGT 58.631 41.667 0.00 0.00 41.91 3.01
2181 3630 4.708177 GTGAGGCCTAATTGAGCATTAGA 58.292 43.478 4.42 0.00 45.33 2.10
2485 3934 7.559590 AAAGTACAATTCCATGATAGCAGTC 57.440 36.000 0.00 0.00 0.00 3.51
2607 4056 6.426633 TGCGAAATGAGAGAAGTAAATGAACA 59.573 34.615 0.00 0.00 0.00 3.18
2630 4079 7.042254 GCATAGGAATGAATGAAGGAATTTTGC 60.042 37.037 0.00 0.00 34.84 3.68
2732 4181 0.034767 CCAGCTCATGGGCTTCTTCA 60.035 55.000 20.07 0.00 46.36 3.02
2756 4205 0.648441 GTGAAACAACAGCGTCGACA 59.352 50.000 17.16 0.00 36.32 4.35
2828 4277 1.304052 TCGGACCCATGGCCTTTTG 60.304 57.895 6.09 0.00 0.00 2.44
3061 4605 7.805071 CACACAACTCAGGTGAAATCTTAAATC 59.195 37.037 0.00 0.00 39.53 2.17
3143 4693 7.473027 AAAGAACACATGAATCAAGCTTTTG 57.527 32.000 0.00 0.00 0.00 2.44
3179 4729 6.877611 TCCTTGTTCTTTACCTTTGATGTC 57.122 37.500 0.00 0.00 0.00 3.06
3208 4758 5.461032 TTTTTCCGGAACAAGCACAATAT 57.539 34.783 18.64 0.00 0.00 1.28
3209 4759 4.920640 TTTTTCCGGAACAAGCACAATA 57.079 36.364 18.64 0.00 0.00 1.90
3210 4760 3.810310 TTTTTCCGGAACAAGCACAAT 57.190 38.095 18.64 0.00 0.00 2.71
3240 4790 3.323243 GCTTCAAGCAATGCACTCAAAT 58.677 40.909 8.35 0.00 41.89 2.32
3254 4805 3.135348 TCTCATACTCCCATGGCTTCAAG 59.865 47.826 6.09 0.56 0.00 3.02
3266 4817 7.976734 GCCTACAACATGTATATCTCATACTCC 59.023 40.741 0.00 0.00 31.66 3.85
3330 4881 9.944376 GGCTTATAATTCAGAACATAGGTGATA 57.056 33.333 0.00 0.00 0.00 2.15
3333 4884 6.347725 GCGGCTTATAATTCAGAACATAGGTG 60.348 42.308 0.00 0.00 0.00 4.00
3336 4887 7.426929 AAGCGGCTTATAATTCAGAACATAG 57.573 36.000 14.67 0.00 0.00 2.23
3337 4888 7.255104 CCAAAGCGGCTTATAATTCAGAACATA 60.255 37.037 16.73 0.00 0.00 2.29
3344 4895 6.463995 AAATCCAAAGCGGCTTATAATTCA 57.536 33.333 16.73 0.00 33.14 2.57
3345 4896 7.491048 TGAAAAATCCAAAGCGGCTTATAATTC 59.509 33.333 16.73 13.57 33.14 2.17
3366 4917 7.709182 CAGTCCGTATGTAGTCCATATTGAAAA 59.291 37.037 0.00 0.00 38.29 2.29
3388 4939 6.974622 AGTGTGTTTGTTCAATCATTTCAGTC 59.025 34.615 0.69 0.00 0.00 3.51
3397 4948 5.330498 CGCGTTTTAGTGTGTTTGTTCAATC 60.330 40.000 0.00 0.00 0.00 2.67
3400 4951 3.120269 ACGCGTTTTAGTGTGTTTGTTCA 60.120 39.130 5.58 0.00 33.08 3.18
3409 4960 7.590322 CAGATGTATATAGACGCGTTTTAGTGT 59.410 37.037 15.53 0.00 37.59 3.55
3413 4964 9.338291 GAATCAGATGTATATAGACGCGTTTTA 57.662 33.333 15.53 10.21 0.00 1.52
3434 4985 8.924511 AGATGTTCTAACCTTTTTCTGAATCA 57.075 30.769 0.00 0.00 0.00 2.57
3447 4998 9.845305 CGTTTCGAATTATAAGATGTTCTAACC 57.155 33.333 0.00 0.00 0.00 2.85
3451 5002 7.438459 CCTCCGTTTCGAATTATAAGATGTTCT 59.562 37.037 0.00 0.00 0.00 3.01
3465 5016 2.205022 TCTACTCCCTCCGTTTCGAA 57.795 50.000 0.00 0.00 0.00 3.71
3522 5073 3.437049 GGCATCAAACCTAAGTCTGTGAC 59.563 47.826 0.00 0.00 0.00 3.67
3583 5134 2.614057 GTTGCGATTCCAGAACCCATAG 59.386 50.000 0.00 0.00 0.00 2.23
3606 5157 4.528596 AGGATAATGGCTTAGTATCAGCGT 59.471 41.667 9.81 0.00 37.93 5.07
3645 5196 6.183360 CCTGCGTTTAGGAATTTCTCATTGAT 60.183 38.462 0.00 0.00 40.42 2.57
3676 5227 3.495806 CCATCCTCTACCTTTGATCCTGC 60.496 52.174 0.00 0.00 0.00 4.85
3745 5298 4.039004 CCATTTTCATGTTGGTCTGGACAA 59.961 41.667 3.10 0.00 0.00 3.18
3844 5398 4.221703 AGTGAGAGGGTCTTGTCATAGTTG 59.778 45.833 0.00 0.00 0.00 3.16
3847 5401 4.709397 AGAAGTGAGAGGGTCTTGTCATAG 59.291 45.833 0.00 0.00 0.00 2.23
4026 5580 5.236047 GTCTGAACAAGCAGCATAAGGATAG 59.764 44.000 0.00 0.00 35.86 2.08
4093 5647 1.604278 GAAGGACAGTGTTGCTCCAAC 59.396 52.381 0.00 1.33 43.78 3.77
4228 5782 7.640597 ACTAAAGGGTTTATTATGAACCTGC 57.359 36.000 16.65 3.54 44.71 4.85
4237 5791 9.238368 CAGGAATCACAACTAAAGGGTTTATTA 57.762 33.333 0.00 0.00 0.00 0.98
4245 5799 6.371825 GGTAGTTCAGGAATCACAACTAAAGG 59.628 42.308 0.00 0.00 34.04 3.11
4321 5877 1.797211 GAGGGGTGCGGACTATCTCG 61.797 65.000 7.11 0.00 0.00 4.04
4367 5923 1.002069 TTCTTCCCCACATCCAGCAT 58.998 50.000 0.00 0.00 0.00 3.79
4474 6030 5.266788 ACATCCATTCCATGATCAACAAGT 58.733 37.500 0.00 0.00 0.00 3.16
4499 6055 2.898705 ACAAGCCTGATCGATCTTGTC 58.101 47.619 25.02 11.99 43.80 3.18
4521 6077 2.168106 CCAATTGGCATCCCGAATTCAA 59.832 45.455 12.53 0.00 0.00 2.69
4577 6133 5.697473 TTGAGAGAGATTAGATACCGCAG 57.303 43.478 0.00 0.00 0.00 5.18
4595 6155 4.496341 CCCGTTTGAATCATCGGAATTGAG 60.496 45.833 22.09 6.76 44.86 3.02
4862 6422 3.267483 AGGAAGCGTTGCACGTTATAAT 58.733 40.909 9.76 0.00 44.73 1.28
4870 6430 0.317854 GAACCAAGGAAGCGTTGCAC 60.318 55.000 0.00 0.00 0.00 4.57
4909 6469 3.667497 TGTGGAACAGCAACAACAAAA 57.333 38.095 0.00 0.00 45.67 2.44
4958 6521 3.310193 GCCTTCCTCTTACCCTCATACT 58.690 50.000 0.00 0.00 0.00 2.12
5000 6563 0.233590 CGACTCCTCGACATAGCTCG 59.766 60.000 0.00 0.00 43.06 5.03
5003 6566 0.589223 CCTCGACTCCTCGACATAGC 59.411 60.000 0.00 0.00 44.14 2.97
5049 6612 2.024846 TGGAAAGTGAACCCAAACCTCA 60.025 45.455 0.00 0.00 0.00 3.86
5059 6622 5.956642 TGGTAAAAACACTGGAAAGTGAAC 58.043 37.500 12.57 3.23 42.02 3.18
5082 6645 4.698304 TGAAGTGAAGAACAAAGGAACGTT 59.302 37.500 0.00 0.00 0.00 3.99
5104 6667 5.163581 CCCTCAAGAAAAGGTCATATTGCTG 60.164 44.000 0.00 0.00 31.51 4.41
5105 6668 4.952335 CCCTCAAGAAAAGGTCATATTGCT 59.048 41.667 0.00 0.00 31.51 3.91
5106 6669 4.706962 ACCCTCAAGAAAAGGTCATATTGC 59.293 41.667 0.00 0.00 31.51 3.56
5115 6678 5.127031 TCTTTCACAAACCCTCAAGAAAAGG 59.873 40.000 0.00 0.00 0.00 3.11
5146 6715 5.300792 ACTGGGAAACATATGTTGACGTTTT 59.699 36.000 21.46 4.14 38.44 2.43
5150 6719 4.932799 TGTACTGGGAAACATATGTTGACG 59.067 41.667 21.46 10.90 38.44 4.35
5183 6752 6.715264 CCAACACTAACCTCATAAAGAACCTT 59.285 38.462 0.00 0.00 0.00 3.50
5192 6761 4.634012 ACAAGCCAACACTAACCTCATA 57.366 40.909 0.00 0.00 0.00 2.15
5227 6919 2.423185 TGCCTTGCTTATTTGACCATCG 59.577 45.455 0.00 0.00 0.00 3.84
5267 6960 7.122650 ACCAAATAATGAGATTTCACCAACGAT 59.877 33.333 0.00 0.00 35.83 3.73
5270 6963 6.813152 CCACCAAATAATGAGATTTCACCAAC 59.187 38.462 0.00 0.00 35.83 3.77
5289 6982 8.548880 AGTTTAGCTTATATCTAGTCCACCAA 57.451 34.615 0.00 0.00 0.00 3.67
5342 7035 9.206870 CCAAATAAATGTATGCATAAATGGGAC 57.793 33.333 10.23 0.00 34.39 4.46
5343 7036 9.152327 TCCAAATAAATGTATGCATAAATGGGA 57.848 29.630 10.23 7.96 34.39 4.37
5344 7037 9.206870 GTCCAAATAAATGTATGCATAAATGGG 57.793 33.333 10.23 6.04 34.39 4.00
5351 7044 8.145767 CCATTCAGTCCAAATAAATGTATGCAT 58.854 33.333 3.79 3.79 36.80 3.96
5469 7246 2.504367 ACTGCCACCATGTACAAGAAC 58.496 47.619 0.00 0.00 0.00 3.01
5498 7275 0.652592 GCTATCGCGCTGTTGTCAAT 59.347 50.000 5.56 0.00 0.00 2.57
5669 7446 4.991056 GCTCGACCAATCATCTTATTAGCA 59.009 41.667 0.00 0.00 0.00 3.49
5720 7497 4.125703 TGGTTGCATTTCACAATTGGTTC 58.874 39.130 10.83 0.00 0.00 3.62
5817 7686 3.440522 GGTTTGAAGAACTGGCCATACTC 59.559 47.826 5.51 2.95 0.00 2.59
6047 7916 4.275936 TGAGGAAAAGAAACTACAGCTTGC 59.724 41.667 0.00 0.00 0.00 4.01
6084 7954 3.058293 TGCATCAACCTTAGCAAAGAACG 60.058 43.478 0.00 0.00 34.37 3.95
6095 7965 7.336931 ACGTTATTCTTATTCTGCATCAACCTT 59.663 33.333 0.00 0.00 0.00 3.50
6168 8039 5.489792 TGTTTATTCAGTCTCTGGCTCTT 57.510 39.130 0.00 0.00 31.51 2.85
6245 8117 6.275494 TCAGACACATTTTGCATGATCAAT 57.725 33.333 0.00 0.00 0.00 2.57
6296 8176 9.927668 AAATTTGATACAATTCGAATGGAGTTT 57.072 25.926 19.51 9.80 31.47 2.66
6346 8226 8.691661 ATTTAAACTCCGCATATAATCCAGTT 57.308 30.769 0.00 0.00 0.00 3.16
6359 8246 3.252458 ACACACCAAGATTTAAACTCCGC 59.748 43.478 0.00 0.00 0.00 5.54
6505 8393 8.932791 CACTAAAGTTACGATTAACAAGACCAT 58.067 33.333 0.00 0.00 40.25 3.55
6626 8516 5.256474 ACAACCATTCAACCAAGGAGATAG 58.744 41.667 0.00 0.00 0.00 2.08
6665 8555 1.173913 GGGTTGATTCCCACGAAAGG 58.826 55.000 0.00 0.00 46.30 3.11
6707 8599 4.479158 TCTGGGTTGGAATAGTTTGCTTT 58.521 39.130 0.00 0.00 0.00 3.51
7020 8941 1.374758 ACGAGTAGTTGCTGGCAGC 60.375 57.895 31.91 31.91 42.82 5.25
7037 8958 2.492088 GGACCAGAGGGCAATAAAACAC 59.508 50.000 0.00 0.00 37.90 3.32
7091 9012 7.182930 ACTCTGGAGAGGGAATTGTAAAGTAAT 59.817 37.037 8.52 0.00 46.13 1.89
7092 9013 6.500751 ACTCTGGAGAGGGAATTGTAAAGTAA 59.499 38.462 8.52 0.00 46.13 2.24


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

AutoCloner maintained by Alex Coulton.