Multiple sequence alignment - TraesCS2D01G392600

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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 TraesCS2D01G392600 chr2D 100.000 2543 0 0 1 2543 500490452 500487910 0.000000e+00 4697.0
1 TraesCS2D01G392600 chr2D 86.747 166 19 2 1 163 63082371 63082206 5.590000e-42 182.0
2 TraesCS2D01G392600 chr2B 95.224 1005 37 4 797 1796 588887321 588888319 0.000000e+00 1580.0
3 TraesCS2D01G392600 chr2B 92.105 304 21 2 1795 2095 588888395 588888698 2.340000e-115 425.0
4 TraesCS2D01G392600 chr3D 96.629 712 13 2 1 712 419842439 419841739 0.000000e+00 1171.0
5 TraesCS2D01G392600 chr3D 94.258 418 17 5 2096 2510 3101958 3102371 1.280000e-177 632.0
6 TraesCS2D01G392600 chr3D 96.610 59 1 1 713 770 594055835 594055893 2.080000e-16 97.1
7 TraesCS2D01G392600 chr4D 96.111 720 21 2 1 715 278249500 278248783 0.000000e+00 1168.0
8 TraesCS2D01G392600 chr4D 93.689 412 17 5 2096 2506 495973347 495973750 2.160000e-170 608.0
9 TraesCS2D01G392600 chr4D 96.667 60 2 0 711 770 321949304 321949363 1.610000e-17 100.0
10 TraesCS2D01G392600 chr2A 94.203 414 16 5 2096 2506 61475558 61475966 2.150000e-175 625.0
11 TraesCS2D01G392600 chr2A 93.262 282 12 3 1234 1509 646839478 646839758 2.350000e-110 409.0
12 TraesCS2D01G392600 chr2A 91.611 298 12 5 894 1178 646839180 646839477 1.420000e-107 399.0
13 TraesCS2D01G392600 chr2A 88.406 138 15 1 146 283 121134112 121134248 5.630000e-37 165.0
14 TraesCS2D01G392600 chr2A 90.598 117 11 0 785 901 646829500 646829616 3.390000e-34 156.0
15 TraesCS2D01G392600 chr5A 94.175 412 18 3 2096 2506 12225028 12224622 7.730000e-175 623.0
16 TraesCS2D01G392600 chr5A 93.548 93 6 0 155 247 35657927 35658019 3.410000e-29 139.0
17 TraesCS2D01G392600 chr7A 93.735 415 18 4 2096 2506 640496593 640497003 1.290000e-172 616.0
18 TraesCS2D01G392600 chr7A 93.095 420 19 6 2096 2511 625908597 625908184 7.780000e-170 606.0
19 TraesCS2D01G392600 chr1D 93.932 412 18 5 2096 2506 344285886 344286291 1.290000e-172 616.0
20 TraesCS2D01G392600 chr6A 93.689 412 19 5 2095 2504 574237297 574236891 6.010000e-171 610.0
21 TraesCS2D01G392600 chr6A 88.571 280 32 0 431 710 28928399 28928120 8.710000e-90 340.0
22 TraesCS2D01G392600 chr6A 88.214 280 33 0 431 710 28952260 28951981 4.050000e-88 335.0
23 TraesCS2D01G392600 chr6A 87.500 280 35 0 431 710 28898484 28898205 8.780000e-85 324.0
24 TraesCS2D01G392600 chr6A 88.112 143 17 0 148 290 13092836 13092978 1.210000e-38 171.0
25 TraesCS2D01G392600 chr6A 88.112 143 17 0 148 290 13150747 13150889 1.210000e-38 171.0
26 TraesCS2D01G392600 chr6A 94.915 59 2 1 713 770 17775424 17775482 9.690000e-15 91.6
27 TraesCS2D01G392600 chr7D 93.462 413 20 4 2096 2506 63450701 63450294 7.780000e-170 606.0
28 TraesCS2D01G392600 chrUn 98.305 236 4 0 400 635 421840278 421840043 5.060000e-112 414.0
29 TraesCS2D01G392600 chr6D 88.070 285 34 0 428 712 18663761 18664045 3.130000e-89 339.0
30 TraesCS2D01G392600 chr6D 83.591 323 50 3 391 712 129170978 129170658 1.480000e-77 300.0
31 TraesCS2D01G392600 chr6D 98.276 58 1 0 713 770 430015357 430015300 4.480000e-18 102.0
32 TraesCS2D01G392600 chr3A 87.589 282 33 2 431 712 690430521 690430242 2.440000e-85 326.0
33 TraesCS2D01G392600 chr4B 89.697 165 14 2 4 165 476944606 476944442 9.220000e-50 207.0
34 TraesCS2D01G392600 chr3B 89.091 165 15 2 4 165 578621024 578620860 4.290000e-48 202.0
35 TraesCS2D01G392600 chr3B 92.308 130 10 0 154 283 448774392 448774521 4.320000e-43 185.0
36 TraesCS2D01G392600 chr3B 85.802 162 16 5 5 165 131574479 131574634 5.630000e-37 165.0
37 TraesCS2D01G392600 chr3B 90.000 90 6 3 286 374 578620871 578620784 2.070000e-21 113.0
38 TraesCS2D01G392600 chr6B 87.273 165 16 5 1 162 32737953 32737791 1.550000e-42 183.0
39 TraesCS2D01G392600 chr5B 92.248 129 10 0 153 281 611822826 611822954 1.550000e-42 183.0
40 TraesCS2D01G392600 chr7B 87.342 158 17 3 1 155 637281286 637281443 7.230000e-41 178.0
41 TraesCS2D01G392600 chr7B 85.802 162 16 5 5 165 680124681 680124836 5.630000e-37 165.0
42 TraesCS2D01G392600 chr1B 90.083 121 10 2 164 283 349719306 349719187 3.390000e-34 156.0


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 TraesCS2D01G392600 chr2D 500487910 500490452 2542 True 4697.0 4697 100.0000 1 2543 1 chr2D.!!$R2 2542
1 TraesCS2D01G392600 chr2B 588887321 588888698 1377 False 1002.5 1580 93.6645 797 2095 2 chr2B.!!$F1 1298
2 TraesCS2D01G392600 chr3D 419841739 419842439 700 True 1171.0 1171 96.6290 1 712 1 chr3D.!!$R1 711
3 TraesCS2D01G392600 chr4D 278248783 278249500 717 True 1168.0 1168 96.1110 1 715 1 chr4D.!!$R1 714
4 TraesCS2D01G392600 chr2A 646839180 646839758 578 False 404.0 409 92.4365 894 1509 2 chr2A.!!$F4 615

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
719 725 0.039527 ACGGCATTTTCGCAACCTTC 60.04 50.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2497 2607 0.251916 CCGCACCTGGAGGAAATACA 59.748 55.0 0.0 0.0 39.08 2.29 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
230 231 3.631144 TGCAGTTCAAAATTTCAGAGCG 58.369 40.909 0.00 0.00 0.00 5.03
389 395 0.880278 GAGAACGGTCAGCTGCAACA 60.880 55.000 9.47 0.00 0.00 3.33
399 405 1.091771 AGCTGCAACATTCGGATCCG 61.092 55.000 28.62 28.62 41.35 4.18
602 608 2.082836 ATACGGGGTTGGGGTTGCAA 62.083 55.000 0.00 0.00 0.00 4.08
715 721 0.506506 CCAAACGGCATTTTCGCAAC 59.493 50.000 0.00 0.00 0.00 4.17
716 722 0.506506 CAAACGGCATTTTCGCAACC 59.493 50.000 0.00 0.00 0.00 3.77
717 723 0.387565 AAACGGCATTTTCGCAACCT 59.612 45.000 0.00 0.00 0.00 3.50
718 724 0.387565 AACGGCATTTTCGCAACCTT 59.612 45.000 0.00 0.00 0.00 3.50
719 725 0.039527 ACGGCATTTTCGCAACCTTC 60.040 50.000 0.00 0.00 0.00 3.46
720 726 0.039617 CGGCATTTTCGCAACCTTCA 60.040 50.000 0.00 0.00 0.00 3.02
721 727 1.701704 GGCATTTTCGCAACCTTCAG 58.298 50.000 0.00 0.00 0.00 3.02
722 728 1.669795 GGCATTTTCGCAACCTTCAGG 60.670 52.381 0.00 0.00 42.17 3.86
723 729 1.669795 GCATTTTCGCAACCTTCAGGG 60.670 52.381 0.00 0.00 40.27 4.45
724 730 0.603065 ATTTTCGCAACCTTCAGGGC 59.397 50.000 0.00 0.00 40.27 5.19
725 731 0.467290 TTTTCGCAACCTTCAGGGCT 60.467 50.000 0.00 0.00 40.27 5.19
726 732 0.467290 TTTCGCAACCTTCAGGGCTT 60.467 50.000 0.00 0.00 40.27 4.35
727 733 0.467290 TTCGCAACCTTCAGGGCTTT 60.467 50.000 0.00 0.00 40.27 3.51
728 734 1.172180 TCGCAACCTTCAGGGCTTTG 61.172 55.000 0.00 0.00 40.27 2.77
729 735 1.455383 CGCAACCTTCAGGGCTTTGT 61.455 55.000 0.00 0.00 40.27 2.83
730 736 1.616159 GCAACCTTCAGGGCTTTGTA 58.384 50.000 0.00 0.00 40.27 2.41
731 737 1.269723 GCAACCTTCAGGGCTTTGTAC 59.730 52.381 0.00 0.00 40.27 2.90
732 738 2.863809 CAACCTTCAGGGCTTTGTACT 58.136 47.619 0.00 0.00 40.27 2.73
733 739 2.814336 CAACCTTCAGGGCTTTGTACTC 59.186 50.000 0.00 0.00 40.27 2.59
734 740 1.351350 ACCTTCAGGGCTTTGTACTCC 59.649 52.381 0.00 0.00 40.27 3.85
735 741 1.351017 CCTTCAGGGCTTTGTACTCCA 59.649 52.381 0.00 0.00 0.00 3.86
736 742 2.427506 CTTCAGGGCTTTGTACTCCAC 58.572 52.381 0.00 0.00 0.00 4.02
737 743 0.320374 TCAGGGCTTTGTACTCCACG 59.680 55.000 0.00 0.00 0.00 4.94
738 744 1.003718 AGGGCTTTGTACTCCACGC 60.004 57.895 0.00 0.00 0.00 5.34
739 745 1.003718 GGGCTTTGTACTCCACGCT 60.004 57.895 0.00 0.00 0.00 5.07
740 746 1.298859 GGGCTTTGTACTCCACGCTG 61.299 60.000 0.00 0.00 0.00 5.18
741 747 0.602905 GGCTTTGTACTCCACGCTGT 60.603 55.000 0.00 0.00 0.00 4.40
742 748 1.337447 GGCTTTGTACTCCACGCTGTA 60.337 52.381 0.00 0.00 0.00 2.74
743 749 2.618053 GCTTTGTACTCCACGCTGTAT 58.382 47.619 0.00 0.00 0.00 2.29
744 750 3.429822 GGCTTTGTACTCCACGCTGTATA 60.430 47.826 0.00 0.00 0.00 1.47
745 751 3.550678 GCTTTGTACTCCACGCTGTATAC 59.449 47.826 0.00 0.00 0.00 1.47
746 752 4.677250 GCTTTGTACTCCACGCTGTATACT 60.677 45.833 4.17 0.00 0.00 2.12
747 753 4.365899 TTGTACTCCACGCTGTATACTG 57.634 45.455 4.17 4.85 0.00 2.74
748 754 3.349927 TGTACTCCACGCTGTATACTGT 58.650 45.455 10.96 1.59 0.00 3.55
749 755 3.760151 TGTACTCCACGCTGTATACTGTT 59.240 43.478 10.96 0.00 0.00 3.16
750 756 4.943093 TGTACTCCACGCTGTATACTGTTA 59.057 41.667 10.96 0.00 0.00 2.41
751 757 5.591472 TGTACTCCACGCTGTATACTGTTAT 59.409 40.000 10.96 0.00 0.00 1.89
752 758 5.593679 ACTCCACGCTGTATACTGTTATT 57.406 39.130 10.96 0.00 0.00 1.40
753 759 5.348986 ACTCCACGCTGTATACTGTTATTG 58.651 41.667 10.96 4.16 0.00 1.90
754 760 5.126545 ACTCCACGCTGTATACTGTTATTGA 59.873 40.000 10.96 2.63 0.00 2.57
755 761 5.588240 TCCACGCTGTATACTGTTATTGAG 58.412 41.667 10.96 0.00 0.00 3.02
756 762 4.209288 CCACGCTGTATACTGTTATTGAGC 59.791 45.833 10.96 4.87 0.00 4.26
757 763 5.043903 CACGCTGTATACTGTTATTGAGCT 58.956 41.667 10.96 0.00 0.00 4.09
758 764 5.043903 ACGCTGTATACTGTTATTGAGCTG 58.956 41.667 10.96 5.25 0.00 4.24
759 765 5.163550 ACGCTGTATACTGTTATTGAGCTGA 60.164 40.000 10.96 0.00 0.00 4.26
760 766 5.748630 CGCTGTATACTGTTATTGAGCTGAA 59.251 40.000 10.96 0.00 0.00 3.02
761 767 6.422100 CGCTGTATACTGTTATTGAGCTGAAT 59.578 38.462 3.30 3.30 0.00 2.57
762 768 7.568315 CGCTGTATACTGTTATTGAGCTGAATG 60.568 40.741 8.83 0.00 0.00 2.67
763 769 7.439356 GCTGTATACTGTTATTGAGCTGAATGA 59.561 37.037 8.83 0.00 0.00 2.57
764 770 9.317936 CTGTATACTGTTATTGAGCTGAATGAA 57.682 33.333 8.83 0.00 0.00 2.57
765 771 9.665719 TGTATACTGTTATTGAGCTGAATGAAA 57.334 29.630 8.83 0.00 0.00 2.69
769 775 8.752766 ACTGTTATTGAGCTGAATGAAATTTG 57.247 30.769 8.83 0.00 36.07 2.32
770 776 8.362639 ACTGTTATTGAGCTGAATGAAATTTGT 58.637 29.630 8.83 0.00 36.07 2.83
771 777 8.746922 TGTTATTGAGCTGAATGAAATTTGTC 57.253 30.769 8.83 0.00 36.07 3.18
772 778 8.579006 TGTTATTGAGCTGAATGAAATTTGTCT 58.421 29.630 8.83 0.00 36.07 3.41
773 779 9.415544 GTTATTGAGCTGAATGAAATTTGTCTT 57.584 29.630 8.83 0.00 36.07 3.01
774 780 7.884816 ATTGAGCTGAATGAAATTTGTCTTG 57.115 32.000 0.00 0.00 36.07 3.02
775 781 6.395426 TGAGCTGAATGAAATTTGTCTTGT 57.605 33.333 0.00 0.00 36.07 3.16
776 782 6.808829 TGAGCTGAATGAAATTTGTCTTGTT 58.191 32.000 0.00 0.00 36.07 2.83
777 783 6.919662 TGAGCTGAATGAAATTTGTCTTGTTC 59.080 34.615 0.00 0.00 36.07 3.18
778 784 6.808829 AGCTGAATGAAATTTGTCTTGTTCA 58.191 32.000 0.00 0.00 36.07 3.18
779 785 7.267128 AGCTGAATGAAATTTGTCTTGTTCAA 58.733 30.769 0.00 0.00 36.07 2.69
780 786 7.765360 AGCTGAATGAAATTTGTCTTGTTCAAA 59.235 29.630 0.00 0.00 36.07 2.69
781 787 8.389603 GCTGAATGAAATTTGTCTTGTTCAAAA 58.610 29.630 0.00 0.00 36.07 2.44
823 829 2.435693 GGCGCTCCCTACTGACCAT 61.436 63.158 7.64 0.00 0.00 3.55
831 837 4.508662 CTCCCTACTGACCATGACTTTTC 58.491 47.826 0.00 0.00 0.00 2.29
858 864 3.493503 GGAAAATATCTTCGCACCTACCG 59.506 47.826 0.00 0.00 0.00 4.02
863 869 1.005394 CTTCGCACCTACCGGTTGT 60.005 57.895 15.04 8.24 42.13 3.32
901 908 2.965147 CAACTTTCAACCCCCTTGATGT 59.035 45.455 0.00 0.00 38.74 3.06
946 957 2.547218 GCCAGGCGACGATTTATAAGGA 60.547 50.000 0.00 0.00 0.00 3.36
948 959 3.243771 CCAGGCGACGATTTATAAGGACT 60.244 47.826 0.00 0.00 0.00 3.85
1035 1055 1.100510 ACGCCTACGATCTTGTGCTA 58.899 50.000 0.00 0.00 43.93 3.49
1073 1093 0.965866 CTGCACCACCTCCTCGACTA 60.966 60.000 0.00 0.00 0.00 2.59
1128 1148 2.215604 CGGCATCGTCTCGTTCGAC 61.216 63.158 0.00 0.00 40.07 4.20
1274 1294 1.443872 CGCCACAGTACAGACGACC 60.444 63.158 0.00 0.00 0.00 4.79
1523 1549 1.805945 GGCGAGAAGTAGTGCCACG 60.806 63.158 0.00 0.00 46.76 4.94
1588 1614 4.358851 GAAACATCTCGATCTCCTCACTG 58.641 47.826 0.00 0.00 0.00 3.66
1589 1615 2.305928 ACATCTCGATCTCCTCACTGG 58.694 52.381 0.00 0.00 37.10 4.00
1632 1658 6.251589 GCGATGTGTACATGTATAGCATAGTC 59.748 42.308 9.18 7.20 36.57 2.59
1633 1659 6.747739 CGATGTGTACATGTATAGCATAGTCC 59.252 42.308 9.18 2.41 36.57 3.85
1658 1684 5.725362 TCCAATGTTTTTCCGTTGTTTTCT 58.275 33.333 0.00 0.00 30.87 2.52
1686 1712 3.854809 ACGTCAACAAATGTTTTCCGTTG 59.145 39.130 0.00 0.00 38.60 4.10
1695 1721 5.689927 AATGTTTTCCGTTGTTTTCGTTC 57.310 34.783 0.00 0.00 0.00 3.95
1841 1948 1.064017 AGGTCTTCCAAGTGGCACAAA 60.064 47.619 21.41 7.43 36.51 2.83
1884 1992 4.013267 AGGCATTATTCTGGGAAGATCG 57.987 45.455 0.00 0.00 0.00 3.69
1889 1997 2.717639 ATTCTGGGAAGATCGTTGGG 57.282 50.000 0.00 0.00 0.00 4.12
1902 2010 2.042537 TTGGGTGCTTGGTTGGCA 60.043 55.556 0.00 0.00 37.36 4.92
1921 2029 2.634940 GCAGGTTCAGGATATAGCTCCA 59.365 50.000 0.00 0.00 37.81 3.86
1930 2038 5.185249 TCAGGATATAGCTCCACGGATTTAC 59.815 44.000 0.00 0.00 37.81 2.01
1936 2044 1.135199 GCTCCACGGATTTACGACAGA 60.135 52.381 0.00 0.00 37.61 3.41
1942 2050 4.027132 CCACGGATTTACGACAGAATTACG 60.027 45.833 0.00 0.00 37.61 3.18
2028 2138 2.563179 GGCCTCGATATAAGCCTTGAGA 59.437 50.000 0.00 0.00 42.34 3.27
2049 2159 6.423905 TGAGATACTTTTCAGTTTGGTCTTCG 59.576 38.462 0.00 0.00 34.06 3.79
2082 2192 2.884639 TGAGCTTGACCCACTTAAAAGC 59.115 45.455 0.00 0.00 42.78 3.51
2087 2197 1.141254 TGACCCACTTAAAAGCGACCA 59.859 47.619 0.00 0.00 0.00 4.02
2106 2216 3.647771 GTGCGGGGAGGGGAACTT 61.648 66.667 0.00 0.00 0.00 2.66
2107 2217 2.856988 TGCGGGGAGGGGAACTTT 60.857 61.111 0.00 0.00 0.00 2.66
2108 2218 2.439245 GCGGGGAGGGGAACTTTT 59.561 61.111 0.00 0.00 0.00 2.27
2109 2219 1.977009 GCGGGGAGGGGAACTTTTG 60.977 63.158 0.00 0.00 0.00 2.44
2110 2220 1.304134 CGGGGAGGGGAACTTTTGG 60.304 63.158 0.00 0.00 0.00 3.28
2111 2221 1.858505 GGGGAGGGGAACTTTTGGT 59.141 57.895 0.00 0.00 0.00 3.67
2112 2222 0.251653 GGGGAGGGGAACTTTTGGTC 60.252 60.000 0.00 0.00 34.82 4.02
2113 2223 0.778083 GGGAGGGGAACTTTTGGTCT 59.222 55.000 0.00 0.00 36.15 3.85
2114 2224 1.990327 GGGAGGGGAACTTTTGGTCTA 59.010 52.381 0.00 0.00 36.15 2.59
2115 2225 2.581246 GGGAGGGGAACTTTTGGTCTAT 59.419 50.000 0.00 0.00 36.15 1.98
2116 2226 3.621558 GGAGGGGAACTTTTGGTCTATG 58.378 50.000 0.00 0.00 36.15 2.23
2117 2227 3.621558 GAGGGGAACTTTTGGTCTATGG 58.378 50.000 0.00 0.00 36.15 2.74
2118 2228 2.311841 AGGGGAACTTTTGGTCTATGGG 59.688 50.000 0.00 0.00 36.15 4.00
2119 2229 2.623239 GGGGAACTTTTGGTCTATGGGG 60.623 54.545 0.00 0.00 36.15 4.96
2120 2230 2.310647 GGGAACTTTTGGTCTATGGGGA 59.689 50.000 0.00 0.00 36.15 4.81
2121 2231 3.353557 GGAACTTTTGGTCTATGGGGAC 58.646 50.000 0.00 0.00 36.15 4.46
2122 2232 3.245122 GGAACTTTTGGTCTATGGGGACA 60.245 47.826 0.00 0.00 39.95 4.02
2123 2233 4.569865 GGAACTTTTGGTCTATGGGGACAT 60.570 45.833 0.00 0.00 43.22 3.06
2124 2234 6.613389 GGAACTTTTGGTCTATGGGGACATG 61.613 48.000 0.00 0.00 42.55 3.21
2125 2235 8.947506 GGAACTTTTGGTCTATGGGGACATGT 62.948 46.154 0.00 0.00 42.55 3.21
2132 2242 2.858476 TGGGGACATGTGCACCCT 60.858 61.111 17.74 0.00 43.72 4.34
2133 2243 1.540118 TGGGGACATGTGCACCCTA 60.540 57.895 17.74 10.07 43.72 3.53
2134 2244 0.918799 TGGGGACATGTGCACCCTAT 60.919 55.000 17.74 0.00 43.72 2.57
2135 2245 1.136828 GGGGACATGTGCACCCTATA 58.863 55.000 19.67 0.00 42.86 1.31
2136 2246 1.202770 GGGGACATGTGCACCCTATAC 60.203 57.143 19.67 0.55 42.86 1.47
2137 2247 1.202770 GGGACATGTGCACCCTATACC 60.203 57.143 19.67 10.00 40.39 2.73
2138 2248 1.540363 GGACATGTGCACCCTATACCG 60.540 57.143 15.69 0.00 0.00 4.02
2139 2249 1.411246 GACATGTGCACCCTATACCGA 59.589 52.381 15.69 0.00 0.00 4.69
2140 2250 1.834896 ACATGTGCACCCTATACCGAA 59.165 47.619 15.69 0.00 0.00 4.30
2141 2251 2.237643 ACATGTGCACCCTATACCGAAA 59.762 45.455 15.69 0.00 0.00 3.46
2142 2252 3.275143 CATGTGCACCCTATACCGAAAA 58.725 45.455 15.69 0.00 0.00 2.29
2143 2253 3.420300 TGTGCACCCTATACCGAAAAA 57.580 42.857 15.69 0.00 0.00 1.94
2218 2328 8.928270 ATAAACTTGACCTTCTATTGTACTCG 57.072 34.615 0.00 0.00 0.00 4.18
2219 2329 5.979288 ACTTGACCTTCTATTGTACTCGT 57.021 39.130 0.00 0.00 0.00 4.18
2220 2330 5.710984 ACTTGACCTTCTATTGTACTCGTG 58.289 41.667 0.00 0.00 0.00 4.35
2221 2331 5.475909 ACTTGACCTTCTATTGTACTCGTGA 59.524 40.000 0.00 0.00 0.00 4.35
2222 2332 5.562506 TGACCTTCTATTGTACTCGTGAG 57.437 43.478 0.00 0.00 0.00 3.51
2223 2333 5.250982 TGACCTTCTATTGTACTCGTGAGA 58.749 41.667 3.44 0.00 39.12 3.27
2224 2334 5.708697 TGACCTTCTATTGTACTCGTGAGAA 59.291 40.000 3.44 0.00 41.32 2.87
2225 2335 6.208007 TGACCTTCTATTGTACTCGTGAGAAA 59.792 38.462 3.44 0.00 41.32 2.52
2226 2336 7.093902 TGACCTTCTATTGTACTCGTGAGAAAT 60.094 37.037 3.44 3.72 41.32 2.17
2227 2337 7.036220 ACCTTCTATTGTACTCGTGAGAAATG 58.964 38.462 3.44 0.00 41.32 2.32
2228 2338 7.093902 ACCTTCTATTGTACTCGTGAGAAATGA 60.094 37.037 3.44 0.50 41.32 2.57
2229 2339 7.759886 CCTTCTATTGTACTCGTGAGAAATGAA 59.240 37.037 3.44 6.63 41.32 2.57
2230 2340 9.140286 CTTCTATTGTACTCGTGAGAAATGAAA 57.860 33.333 3.44 0.87 41.32 2.69
2231 2341 9.653287 TTCTATTGTACTCGTGAGAAATGAAAT 57.347 29.630 3.44 0.00 41.32 2.17
2232 2342 9.302345 TCTATTGTACTCGTGAGAAATGAAATC 57.698 33.333 3.44 0.00 41.32 2.17
2233 2343 6.721571 TTGTACTCGTGAGAAATGAAATCC 57.278 37.500 3.44 0.00 41.32 3.01
2234 2344 5.789521 TGTACTCGTGAGAAATGAAATCCA 58.210 37.500 3.44 0.00 41.32 3.41
2235 2345 5.637810 TGTACTCGTGAGAAATGAAATCCAC 59.362 40.000 3.44 0.00 41.32 4.02
2236 2346 4.641396 ACTCGTGAGAAATGAAATCCACA 58.359 39.130 3.44 0.00 41.32 4.17
2237 2347 5.063204 ACTCGTGAGAAATGAAATCCACAA 58.937 37.500 3.44 0.00 41.32 3.33
2238 2348 5.530915 ACTCGTGAGAAATGAAATCCACAAA 59.469 36.000 3.44 0.00 41.32 2.83
2239 2349 6.039270 ACTCGTGAGAAATGAAATCCACAAAA 59.961 34.615 3.44 0.00 41.32 2.44
2240 2350 6.800543 TCGTGAGAAATGAAATCCACAAAAA 58.199 32.000 0.00 0.00 37.03 1.94
2295 2405 9.606631 AACAAATTTTTGGCTAAAATAGTGTGA 57.393 25.926 23.56 0.00 43.84 3.58
2296 2406 9.606631 ACAAATTTTTGGCTAAAATAGTGTGAA 57.393 25.926 22.86 0.00 43.84 3.18
2301 2411 9.906660 TTTTTGGCTAAAATAGTGTGAATAGTG 57.093 29.630 8.93 0.00 35.82 2.74
2302 2412 8.856153 TTTGGCTAAAATAGTGTGAATAGTGA 57.144 30.769 0.00 0.00 0.00 3.41
2303 2413 7.843490 TGGCTAAAATAGTGTGAATAGTGAC 57.157 36.000 0.00 0.00 0.00 3.67
2304 2414 6.821665 TGGCTAAAATAGTGTGAATAGTGACC 59.178 38.462 0.00 0.00 0.00 4.02
2305 2415 7.048512 GGCTAAAATAGTGTGAATAGTGACCT 58.951 38.462 0.00 0.00 0.00 3.85
2306 2416 8.202137 GGCTAAAATAGTGTGAATAGTGACCTA 58.798 37.037 0.00 0.00 0.00 3.08
2307 2417 9.765795 GCTAAAATAGTGTGAATAGTGACCTAT 57.234 33.333 0.00 0.00 35.33 2.57
2314 2424 8.478775 AGTGTGAATAGTGACCTATAATAGCA 57.521 34.615 0.00 0.00 32.57 3.49
2315 2425 8.924303 AGTGTGAATAGTGACCTATAATAGCAA 58.076 33.333 0.00 0.00 32.57 3.91
2316 2426 9.542462 GTGTGAATAGTGACCTATAATAGCAAA 57.458 33.333 0.00 0.00 32.57 3.68
2350 2460 4.799564 TTTTTGCTGTGAGGTCAACTTT 57.200 36.364 0.00 0.00 0.00 2.66
2351 2461 5.906113 TTTTTGCTGTGAGGTCAACTTTA 57.094 34.783 0.00 0.00 0.00 1.85
2352 2462 5.499139 TTTTGCTGTGAGGTCAACTTTAG 57.501 39.130 0.00 0.00 0.00 1.85
2353 2463 3.838244 TGCTGTGAGGTCAACTTTAGT 57.162 42.857 0.00 0.00 0.00 2.24
2354 2464 4.150897 TGCTGTGAGGTCAACTTTAGTT 57.849 40.909 0.00 0.00 39.12 2.24
2355 2465 4.523083 TGCTGTGAGGTCAACTTTAGTTT 58.477 39.130 0.00 0.00 35.83 2.66
2356 2466 4.947388 TGCTGTGAGGTCAACTTTAGTTTT 59.053 37.500 0.00 0.00 35.83 2.43
2357 2467 5.417580 TGCTGTGAGGTCAACTTTAGTTTTT 59.582 36.000 0.00 0.00 35.83 1.94
2384 2494 9.860898 TTCTCATCGACATTTATATATCAGTGG 57.139 33.333 0.00 0.00 0.00 4.00
2385 2495 9.025041 TCTCATCGACATTTATATATCAGTGGT 57.975 33.333 0.00 0.00 0.00 4.16
2386 2496 8.986477 TCATCGACATTTATATATCAGTGGTG 57.014 34.615 0.00 0.00 0.00 4.17
2387 2497 7.545615 TCATCGACATTTATATATCAGTGGTGC 59.454 37.037 0.00 0.00 0.00 5.01
2388 2498 6.754193 TCGACATTTATATATCAGTGGTGCA 58.246 36.000 0.00 0.00 0.00 4.57
2389 2499 7.213678 TCGACATTTATATATCAGTGGTGCAA 58.786 34.615 0.00 0.00 0.00 4.08
2390 2500 7.713073 TCGACATTTATATATCAGTGGTGCAAA 59.287 33.333 0.00 0.00 0.00 3.68
2391 2501 8.341903 CGACATTTATATATCAGTGGTGCAAAA 58.658 33.333 0.00 0.00 0.00 2.44
2392 2502 9.669353 GACATTTATATATCAGTGGTGCAAAAG 57.331 33.333 0.00 0.00 0.00 2.27
2393 2503 9.189156 ACATTTATATATCAGTGGTGCAAAAGT 57.811 29.630 0.00 0.00 0.00 2.66
2397 2507 9.899661 TTATATATCAGTGGTGCAAAAGTAAGT 57.100 29.630 0.00 0.00 0.00 2.24
2398 2508 6.743575 ATATCAGTGGTGCAAAAGTAAGTC 57.256 37.500 0.00 0.00 0.00 3.01
2399 2509 3.879998 TCAGTGGTGCAAAAGTAAGTCA 58.120 40.909 0.00 0.00 0.00 3.41
2400 2510 4.265893 TCAGTGGTGCAAAAGTAAGTCAA 58.734 39.130 0.00 0.00 0.00 3.18
2401 2511 4.335315 TCAGTGGTGCAAAAGTAAGTCAAG 59.665 41.667 0.00 0.00 0.00 3.02
2402 2512 4.096382 CAGTGGTGCAAAAGTAAGTCAAGT 59.904 41.667 0.00 0.00 0.00 3.16
2403 2513 4.096382 AGTGGTGCAAAAGTAAGTCAAGTG 59.904 41.667 0.00 0.00 0.00 3.16
2404 2514 4.013728 TGGTGCAAAAGTAAGTCAAGTGT 58.986 39.130 0.00 0.00 0.00 3.55
2405 2515 4.461081 TGGTGCAAAAGTAAGTCAAGTGTT 59.539 37.500 0.00 0.00 0.00 3.32
2406 2516 5.047660 TGGTGCAAAAGTAAGTCAAGTGTTT 60.048 36.000 0.00 0.00 0.00 2.83
2407 2517 5.867174 GGTGCAAAAGTAAGTCAAGTGTTTT 59.133 36.000 0.00 0.00 0.00 2.43
2408 2518 6.367695 GGTGCAAAAGTAAGTCAAGTGTTTTT 59.632 34.615 0.00 0.00 0.00 1.94
2492 2602 4.632538 GGTGCATATACAACCAAGAACC 57.367 45.455 0.00 0.00 0.00 3.62
2493 2603 4.013728 GGTGCATATACAACCAAGAACCA 58.986 43.478 0.00 0.00 0.00 3.67
2494 2604 4.461081 GGTGCATATACAACCAAGAACCAA 59.539 41.667 0.00 0.00 0.00 3.67
2495 2605 5.047660 GGTGCATATACAACCAAGAACCAAA 60.048 40.000 0.00 0.00 0.00 3.28
2496 2606 6.092748 GTGCATATACAACCAAGAACCAAAG 58.907 40.000 0.00 0.00 0.00 2.77
2497 2607 5.772672 TGCATATACAACCAAGAACCAAAGT 59.227 36.000 0.00 0.00 0.00 2.66
2498 2608 6.092748 GCATATACAACCAAGAACCAAAGTG 58.907 40.000 0.00 0.00 0.00 3.16
2499 2609 6.294508 GCATATACAACCAAGAACCAAAGTGT 60.295 38.462 0.00 0.00 0.00 3.55
2500 2610 7.094549 GCATATACAACCAAGAACCAAAGTGTA 60.095 37.037 0.00 0.00 0.00 2.90
2501 2611 8.956426 CATATACAACCAAGAACCAAAGTGTAT 58.044 33.333 0.00 0.00 0.00 2.29
2502 2612 7.833285 ATACAACCAAGAACCAAAGTGTATT 57.167 32.000 0.00 0.00 0.00 1.89
2503 2613 6.538945 ACAACCAAGAACCAAAGTGTATTT 57.461 33.333 0.00 0.00 0.00 1.40
2504 2614 6.569780 ACAACCAAGAACCAAAGTGTATTTC 58.430 36.000 0.00 0.00 0.00 2.17
2505 2615 5.784578 ACCAAGAACCAAAGTGTATTTCC 57.215 39.130 0.00 0.00 0.00 3.13
2506 2616 5.454966 ACCAAGAACCAAAGTGTATTTCCT 58.545 37.500 0.00 0.00 0.00 3.36
2507 2617 5.535030 ACCAAGAACCAAAGTGTATTTCCTC 59.465 40.000 0.00 0.00 0.00 3.71
2508 2618 5.048013 CCAAGAACCAAAGTGTATTTCCTCC 60.048 44.000 0.00 0.00 0.00 4.30
2509 2619 5.319043 AGAACCAAAGTGTATTTCCTCCA 57.681 39.130 0.00 0.00 0.00 3.86
2510 2620 5.316987 AGAACCAAAGTGTATTTCCTCCAG 58.683 41.667 0.00 0.00 0.00 3.86
2511 2621 4.034285 ACCAAAGTGTATTTCCTCCAGG 57.966 45.455 0.00 0.00 0.00 4.45
2512 2622 3.397955 ACCAAAGTGTATTTCCTCCAGGT 59.602 43.478 0.00 0.00 36.34 4.00
2513 2623 3.758554 CCAAAGTGTATTTCCTCCAGGTG 59.241 47.826 0.00 0.00 36.34 4.00
2514 2624 2.789409 AGTGTATTTCCTCCAGGTGC 57.211 50.000 0.00 0.00 36.34 5.01
2515 2625 1.066143 AGTGTATTTCCTCCAGGTGCG 60.066 52.381 0.00 0.00 36.34 5.34
2516 2626 0.251916 TGTATTTCCTCCAGGTGCGG 59.748 55.000 0.00 0.00 36.34 5.69
2517 2627 0.252197 GTATTTCCTCCAGGTGCGGT 59.748 55.000 0.00 0.00 36.34 5.68
2518 2628 0.251916 TATTTCCTCCAGGTGCGGTG 59.748 55.000 0.00 0.00 36.34 4.94
2519 2629 2.484287 ATTTCCTCCAGGTGCGGTGG 62.484 60.000 0.00 0.00 40.46 4.61
2522 2632 3.636231 CTCCAGGTGCGGTGGGAA 61.636 66.667 0.00 0.00 35.58 3.97
2523 2633 3.612247 CTCCAGGTGCGGTGGGAAG 62.612 68.421 0.00 0.00 35.58 3.46
2524 2634 4.722700 CCAGGTGCGGTGGGAAGG 62.723 72.222 0.00 0.00 0.00 3.46
2525 2635 3.636231 CAGGTGCGGTGGGAAGGA 61.636 66.667 0.00 0.00 0.00 3.36
2526 2636 2.610859 AGGTGCGGTGGGAAGGAT 60.611 61.111 0.00 0.00 0.00 3.24
2527 2637 2.438434 GGTGCGGTGGGAAGGATG 60.438 66.667 0.00 0.00 0.00 3.51
2528 2638 2.438434 GTGCGGTGGGAAGGATGG 60.438 66.667 0.00 0.00 0.00 3.51
2529 2639 2.609299 TGCGGTGGGAAGGATGGA 60.609 61.111 0.00 0.00 0.00 3.41
2530 2640 2.190578 GCGGTGGGAAGGATGGAG 59.809 66.667 0.00 0.00 0.00 3.86
2531 2641 2.367202 GCGGTGGGAAGGATGGAGA 61.367 63.158 0.00 0.00 0.00 3.71
2532 2642 1.826024 CGGTGGGAAGGATGGAGAG 59.174 63.158 0.00 0.00 0.00 3.20
2533 2643 0.978146 CGGTGGGAAGGATGGAGAGT 60.978 60.000 0.00 0.00 0.00 3.24
2534 2644 1.688311 CGGTGGGAAGGATGGAGAGTA 60.688 57.143 0.00 0.00 0.00 2.59
2535 2645 1.763545 GGTGGGAAGGATGGAGAGTAC 59.236 57.143 0.00 0.00 0.00 2.73
2536 2646 2.627217 GGTGGGAAGGATGGAGAGTACT 60.627 54.545 0.00 0.00 0.00 2.73
2537 2647 2.696187 GTGGGAAGGATGGAGAGTACTC 59.304 54.545 15.41 15.41 41.94 2.59
2538 2648 1.957877 GGGAAGGATGGAGAGTACTCG 59.042 57.143 17.07 0.00 43.44 4.18
2539 2649 1.957877 GGAAGGATGGAGAGTACTCGG 59.042 57.143 17.07 0.00 43.44 4.63
2540 2650 1.338655 GAAGGATGGAGAGTACTCGGC 59.661 57.143 17.07 12.87 43.44 5.54
2541 2651 0.468400 AGGATGGAGAGTACTCGGCC 60.468 60.000 23.22 23.22 43.44 6.13
2542 2652 1.465200 GGATGGAGAGTACTCGGCCC 61.465 65.000 25.48 22.21 43.44 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.467844 ATGTTGTGCTCTTGTGCCCA 60.468 50.000 0.00 0.00 0.00 5.36
230 231 2.440247 CGGAGCACCAATTCCCCC 60.440 66.667 0.00 0.00 35.59 5.40
283 289 7.254227 ACAATCGCTAAAACAAACACTAAGA 57.746 32.000 0.00 0.00 0.00 2.10
399 405 0.741221 CCGTTGGAGCCAGCTAACTC 60.741 60.000 6.62 6.62 0.00 3.01
602 608 3.381590 TGTCATGTATTCGAGCTAGCAGT 59.618 43.478 18.83 0.00 0.00 4.40
715 721 1.351017 TGGAGTACAAAGCCCTGAAGG 59.649 52.381 0.00 0.00 39.47 3.46
716 722 2.427506 GTGGAGTACAAAGCCCTGAAG 58.572 52.381 0.00 0.00 0.00 3.02
717 723 1.270625 CGTGGAGTACAAAGCCCTGAA 60.271 52.381 0.00 0.00 0.00 3.02
718 724 0.320374 CGTGGAGTACAAAGCCCTGA 59.680 55.000 0.00 0.00 0.00 3.86
719 725 1.298859 GCGTGGAGTACAAAGCCCTG 61.299 60.000 0.00 0.00 0.00 4.45
720 726 1.003718 GCGTGGAGTACAAAGCCCT 60.004 57.895 0.00 0.00 0.00 5.19
721 727 1.003718 AGCGTGGAGTACAAAGCCC 60.004 57.895 0.00 0.00 36.14 5.19
722 728 0.602905 ACAGCGTGGAGTACAAAGCC 60.603 55.000 0.00 0.00 36.14 4.35
723 729 2.074547 TACAGCGTGGAGTACAAAGC 57.925 50.000 0.00 0.00 35.86 3.51
724 730 4.798907 CAGTATACAGCGTGGAGTACAAAG 59.201 45.833 5.50 0.00 0.00 2.77
725 731 4.219070 ACAGTATACAGCGTGGAGTACAAA 59.781 41.667 5.50 0.00 0.00 2.83
726 732 3.760151 ACAGTATACAGCGTGGAGTACAA 59.240 43.478 5.50 0.00 0.00 2.41
727 733 3.349927 ACAGTATACAGCGTGGAGTACA 58.650 45.455 5.50 0.00 0.00 2.90
728 734 4.367386 AACAGTATACAGCGTGGAGTAC 57.633 45.455 5.50 0.00 0.00 2.73
729 735 6.319405 TCAATAACAGTATACAGCGTGGAGTA 59.681 38.462 5.50 0.00 0.00 2.59
730 736 5.126545 TCAATAACAGTATACAGCGTGGAGT 59.873 40.000 5.50 0.00 0.00 3.85
731 737 5.588240 TCAATAACAGTATACAGCGTGGAG 58.412 41.667 5.50 0.00 0.00 3.86
732 738 5.585820 TCAATAACAGTATACAGCGTGGA 57.414 39.130 5.50 0.00 0.00 4.02
733 739 4.209288 GCTCAATAACAGTATACAGCGTGG 59.791 45.833 5.50 0.00 0.00 4.94
734 740 5.043903 AGCTCAATAACAGTATACAGCGTG 58.956 41.667 5.50 0.00 32.94 5.34
735 741 5.043903 CAGCTCAATAACAGTATACAGCGT 58.956 41.667 5.50 0.00 32.94 5.07
736 742 5.281727 TCAGCTCAATAACAGTATACAGCG 58.718 41.667 5.50 0.00 32.94 5.18
737 743 7.439356 TCATTCAGCTCAATAACAGTATACAGC 59.561 37.037 5.50 2.66 0.00 4.40
738 744 8.877808 TCATTCAGCTCAATAACAGTATACAG 57.122 34.615 5.50 0.00 0.00 2.74
739 745 9.665719 TTTCATTCAGCTCAATAACAGTATACA 57.334 29.630 5.50 0.00 0.00 2.29
743 749 9.844790 CAAATTTCATTCAGCTCAATAACAGTA 57.155 29.630 0.00 0.00 0.00 2.74
744 750 8.362639 ACAAATTTCATTCAGCTCAATAACAGT 58.637 29.630 0.00 0.00 0.00 3.55
745 751 8.752766 ACAAATTTCATTCAGCTCAATAACAG 57.247 30.769 0.00 0.00 0.00 3.16
746 752 8.579006 AGACAAATTTCATTCAGCTCAATAACA 58.421 29.630 0.00 0.00 0.00 2.41
747 753 8.976986 AGACAAATTTCATTCAGCTCAATAAC 57.023 30.769 0.00 0.00 0.00 1.89
748 754 9.414295 CAAGACAAATTTCATTCAGCTCAATAA 57.586 29.630 0.00 0.00 0.00 1.40
749 755 8.579006 ACAAGACAAATTTCATTCAGCTCAATA 58.421 29.630 0.00 0.00 0.00 1.90
750 756 7.439381 ACAAGACAAATTTCATTCAGCTCAAT 58.561 30.769 0.00 0.00 0.00 2.57
751 757 6.808829 ACAAGACAAATTTCATTCAGCTCAA 58.191 32.000 0.00 0.00 0.00 3.02
752 758 6.395426 ACAAGACAAATTTCATTCAGCTCA 57.605 33.333 0.00 0.00 0.00 4.26
753 759 6.919662 TGAACAAGACAAATTTCATTCAGCTC 59.080 34.615 0.00 0.00 0.00 4.09
754 760 6.808829 TGAACAAGACAAATTTCATTCAGCT 58.191 32.000 0.00 0.00 0.00 4.24
755 761 7.467557 TTGAACAAGACAAATTTCATTCAGC 57.532 32.000 0.00 0.00 0.00 4.26
781 787 1.678101 GCAGTGGCACTCTCACTTTTT 59.322 47.619 19.13 0.00 42.87 1.94
782 788 1.312815 GCAGTGGCACTCTCACTTTT 58.687 50.000 19.13 0.00 42.87 2.27
783 789 3.012560 GCAGTGGCACTCTCACTTT 57.987 52.632 19.13 0.00 42.87 2.66
784 790 4.787871 GCAGTGGCACTCTCACTT 57.212 55.556 19.13 0.00 42.87 3.16
818 824 3.703001 TCCTGAGGAAAAGTCATGGTC 57.297 47.619 0.00 0.00 0.00 4.02
831 837 3.561725 GGTGCGAAGATATTTTCCTGAGG 59.438 47.826 0.00 0.00 0.00 3.86
863 869 1.686052 GTTGGGTGGCTGTCAATTTGA 59.314 47.619 0.00 0.00 0.00 2.69
901 908 5.395682 AGTACGTTTGGTGCTCTACAATA 57.604 39.130 0.00 0.00 36.88 1.90
946 957 4.034285 ACTAATTTGCAACAGGGCTAGT 57.966 40.909 0.00 0.00 34.04 2.57
948 959 4.523083 CCTACTAATTTGCAACAGGGCTA 58.477 43.478 0.00 0.00 34.04 3.93
1019 1039 2.717530 GTCGTAGCACAAGATCGTAGG 58.282 52.381 0.00 0.00 0.00 3.18
1035 1055 1.673808 GGGCCAAGAGATACCGTCGT 61.674 60.000 4.39 0.00 0.00 4.34
1178 1198 2.664185 CCATGAGGCGCTCCATCG 60.664 66.667 7.64 0.00 33.74 3.84
1221 1241 2.125673 CGATTCACCTTCGGCGGT 60.126 61.111 7.21 0.00 37.93 5.68
1523 1549 3.487574 CGATCAAGGAGATAAAGACGTGC 59.512 47.826 0.00 0.00 37.00 5.34
1614 1640 5.715279 TGGAGGGACTATGCTATACATGTAC 59.285 44.000 7.96 0.00 41.55 2.90
1632 1658 2.364002 ACAACGGAAAAACATTGGAGGG 59.636 45.455 0.00 0.00 0.00 4.30
1633 1659 3.726291 ACAACGGAAAAACATTGGAGG 57.274 42.857 0.00 0.00 0.00 4.30
1664 1690 3.768468 ACGGAAAACATTTGTTGACGT 57.232 38.095 11.82 11.82 38.44 4.34
1695 1721 6.932901 AAACATAAACATTCGTTCATGCAG 57.067 33.333 0.00 0.00 34.51 4.41
1707 1734 8.798402 TCTTTATCCAACGGAAAACATAAACAT 58.202 29.630 0.00 0.00 34.34 2.71
1708 1735 8.167605 TCTTTATCCAACGGAAAACATAAACA 57.832 30.769 0.00 0.00 34.34 2.83
1709 1736 8.294577 ACTCTTTATCCAACGGAAAACATAAAC 58.705 33.333 0.00 0.00 34.34 2.01
1710 1737 8.293867 CACTCTTTATCCAACGGAAAACATAAA 58.706 33.333 0.00 0.00 34.34 1.40
1711 1738 7.446013 ACACTCTTTATCCAACGGAAAACATAA 59.554 33.333 0.00 0.00 34.34 1.90
1712 1739 6.938030 ACACTCTTTATCCAACGGAAAACATA 59.062 34.615 0.00 0.00 34.34 2.29
1804 1911 6.890268 GGAAGACCTTTCCAGTGGTATATTTT 59.110 38.462 9.54 0.00 38.45 1.82
1817 1924 1.248486 GCCACTTGGAAGACCTTTCC 58.752 55.000 0.00 0.00 39.03 3.13
1818 1925 1.609072 GTGCCACTTGGAAGACCTTTC 59.391 52.381 0.00 0.00 37.39 2.62
1827 1934 1.433053 CGTCGTTTGTGCCACTTGGA 61.433 55.000 0.00 0.00 37.39 3.53
1841 1948 3.771160 GCCATCTCCCACCGTCGT 61.771 66.667 0.00 0.00 0.00 4.34
1872 1979 0.613260 CACCCAACGATCTTCCCAGA 59.387 55.000 0.00 0.00 0.00 3.86
1884 1992 2.367868 CTGCCAACCAAGCACCCAAC 62.368 60.000 0.00 0.00 36.01 3.77
1889 1997 1.363807 GAACCTGCCAACCAAGCAC 59.636 57.895 0.00 0.00 36.01 4.40
1902 2010 2.894126 CGTGGAGCTATATCCTGAACCT 59.106 50.000 0.00 0.00 40.29 3.50
1921 2029 4.107622 CCGTAATTCTGTCGTAAATCCGT 58.892 43.478 0.00 0.00 0.00 4.69
1930 2038 1.135083 ACTCTGGCCGTAATTCTGTCG 60.135 52.381 0.00 0.00 0.00 4.35
1936 2044 2.835764 TGTCCTTACTCTGGCCGTAATT 59.164 45.455 0.00 0.00 0.00 1.40
1942 2050 3.097614 TCTAGTTGTCCTTACTCTGGCC 58.902 50.000 0.00 0.00 0.00 5.36
1994 2104 1.522580 GAGGCCAATGTCTCGAGCC 60.523 63.158 7.81 4.28 44.20 4.70
2018 2128 6.015940 CCAAACTGAAAAGTATCTCAAGGCTT 60.016 38.462 0.00 0.00 0.00 4.35
2019 2129 5.474876 CCAAACTGAAAAGTATCTCAAGGCT 59.525 40.000 0.00 0.00 0.00 4.58
2028 2138 5.374071 ACCGAAGACCAAACTGAAAAGTAT 58.626 37.500 0.00 0.00 0.00 2.12
2049 2159 1.881973 TCAAGCTCAATCTGTGCAACC 59.118 47.619 0.00 0.00 39.15 3.77
2095 2205 3.621558 CATAGACCAAAAGTTCCCCTCC 58.378 50.000 0.00 0.00 0.00 4.30
2096 2206 3.621558 CCATAGACCAAAAGTTCCCCTC 58.378 50.000 0.00 0.00 0.00 4.30
2097 2207 2.311841 CCCATAGACCAAAAGTTCCCCT 59.688 50.000 0.00 0.00 0.00 4.79
2098 2208 2.623239 CCCCATAGACCAAAAGTTCCCC 60.623 54.545 0.00 0.00 0.00 4.81
2099 2209 2.310647 TCCCCATAGACCAAAAGTTCCC 59.689 50.000 0.00 0.00 0.00 3.97
2100 2210 3.245122 TGTCCCCATAGACCAAAAGTTCC 60.245 47.826 0.00 0.00 35.83 3.62
2101 2211 4.028993 TGTCCCCATAGACCAAAAGTTC 57.971 45.455 0.00 0.00 35.83 3.01
2102 2212 4.202673 ACATGTCCCCATAGACCAAAAGTT 60.203 41.667 0.00 0.00 35.83 2.66
2103 2213 3.333680 ACATGTCCCCATAGACCAAAAGT 59.666 43.478 0.00 0.00 35.83 2.66
2104 2214 3.696051 CACATGTCCCCATAGACCAAAAG 59.304 47.826 0.00 0.00 35.83 2.27
2105 2215 3.696045 CACATGTCCCCATAGACCAAAA 58.304 45.455 0.00 0.00 35.83 2.44
2106 2216 2.620367 GCACATGTCCCCATAGACCAAA 60.620 50.000 0.00 0.00 35.83 3.28
2107 2217 1.064758 GCACATGTCCCCATAGACCAA 60.065 52.381 0.00 0.00 35.83 3.67
2108 2218 0.546122 GCACATGTCCCCATAGACCA 59.454 55.000 0.00 0.00 35.83 4.02
2109 2219 0.546122 TGCACATGTCCCCATAGACC 59.454 55.000 0.00 0.00 35.83 3.85
2110 2220 1.668419 GTGCACATGTCCCCATAGAC 58.332 55.000 13.17 0.00 37.28 2.59
2111 2221 0.546122 GGTGCACATGTCCCCATAGA 59.454 55.000 20.43 0.00 0.00 1.98
2112 2222 0.466189 GGGTGCACATGTCCCCATAG 60.466 60.000 20.43 0.00 37.09 2.23
2113 2223 0.918799 AGGGTGCACATGTCCCCATA 60.919 55.000 20.43 0.00 41.95 2.74
2114 2224 0.918799 TAGGGTGCACATGTCCCCAT 60.919 55.000 20.43 11.06 41.95 4.00
2115 2225 0.918799 ATAGGGTGCACATGTCCCCA 60.919 55.000 20.43 9.09 41.95 4.96
2116 2226 1.136828 TATAGGGTGCACATGTCCCC 58.863 55.000 20.43 15.05 41.95 4.81
2117 2227 1.202770 GGTATAGGGTGCACATGTCCC 60.203 57.143 20.43 12.28 41.36 4.46
2118 2228 1.540363 CGGTATAGGGTGCACATGTCC 60.540 57.143 20.43 10.59 0.00 4.02
2119 2229 1.411246 TCGGTATAGGGTGCACATGTC 59.589 52.381 20.43 4.92 0.00 3.06
2120 2230 1.491668 TCGGTATAGGGTGCACATGT 58.508 50.000 20.43 7.47 0.00 3.21
2121 2231 2.613026 TTCGGTATAGGGTGCACATG 57.387 50.000 20.43 0.00 0.00 3.21
2122 2232 3.637911 TTTTCGGTATAGGGTGCACAT 57.362 42.857 20.43 9.20 0.00 3.21
2123 2233 3.420300 TTTTTCGGTATAGGGTGCACA 57.580 42.857 20.43 0.00 0.00 4.57
2192 2302 9.367444 CGAGTACAATAGAAGGTCAAGTTTATT 57.633 33.333 0.00 0.00 0.00 1.40
2193 2303 8.529476 ACGAGTACAATAGAAGGTCAAGTTTAT 58.471 33.333 0.00 0.00 0.00 1.40
2194 2304 7.811236 CACGAGTACAATAGAAGGTCAAGTTTA 59.189 37.037 0.00 0.00 0.00 2.01
2195 2305 6.645415 CACGAGTACAATAGAAGGTCAAGTTT 59.355 38.462 0.00 0.00 0.00 2.66
2196 2306 6.015688 TCACGAGTACAATAGAAGGTCAAGTT 60.016 38.462 0.00 0.00 0.00 2.66
2197 2307 5.475909 TCACGAGTACAATAGAAGGTCAAGT 59.524 40.000 0.00 0.00 0.00 3.16
2198 2308 5.950883 TCACGAGTACAATAGAAGGTCAAG 58.049 41.667 0.00 0.00 0.00 3.02
2199 2309 5.708697 TCTCACGAGTACAATAGAAGGTCAA 59.291 40.000 0.00 0.00 0.00 3.18
2200 2310 5.250982 TCTCACGAGTACAATAGAAGGTCA 58.749 41.667 0.00 0.00 0.00 4.02
2201 2311 5.814764 TCTCACGAGTACAATAGAAGGTC 57.185 43.478 0.00 0.00 0.00 3.85
2202 2312 6.585695 TTTCTCACGAGTACAATAGAAGGT 57.414 37.500 0.00 0.00 0.00 3.50
2203 2313 7.258441 TCATTTCTCACGAGTACAATAGAAGG 58.742 38.462 0.00 0.00 0.00 3.46
2204 2314 8.689251 TTCATTTCTCACGAGTACAATAGAAG 57.311 34.615 0.00 0.00 0.00 2.85
2205 2315 9.653287 ATTTCATTTCTCACGAGTACAATAGAA 57.347 29.630 0.00 0.00 0.00 2.10
2206 2316 9.302345 GATTTCATTTCTCACGAGTACAATAGA 57.698 33.333 0.00 0.00 0.00 1.98
2207 2317 8.543774 GGATTTCATTTCTCACGAGTACAATAG 58.456 37.037 0.00 0.00 0.00 1.73
2208 2318 8.038351 TGGATTTCATTTCTCACGAGTACAATA 58.962 33.333 0.00 0.00 0.00 1.90
2209 2319 6.878923 TGGATTTCATTTCTCACGAGTACAAT 59.121 34.615 0.00 0.00 0.00 2.71
2210 2320 6.147164 GTGGATTTCATTTCTCACGAGTACAA 59.853 38.462 0.00 0.00 0.00 2.41
2211 2321 5.637810 GTGGATTTCATTTCTCACGAGTACA 59.362 40.000 0.00 0.00 0.00 2.90
2212 2322 5.637810 TGTGGATTTCATTTCTCACGAGTAC 59.362 40.000 0.00 0.00 0.00 2.73
2213 2323 5.789521 TGTGGATTTCATTTCTCACGAGTA 58.210 37.500 0.00 0.00 0.00 2.59
2214 2324 4.641396 TGTGGATTTCATTTCTCACGAGT 58.359 39.130 0.00 0.00 0.00 4.18
2215 2325 5.611796 TTGTGGATTTCATTTCTCACGAG 57.388 39.130 0.00 0.00 0.00 4.18
2216 2326 6.384258 TTTTGTGGATTTCATTTCTCACGA 57.616 33.333 0.00 0.00 0.00 4.35
2269 2379 9.606631 TCACACTATTTTAGCCAAAAATTTGTT 57.393 25.926 11.38 0.00 43.75 2.83
2270 2380 9.606631 TTCACACTATTTTAGCCAAAAATTTGT 57.393 25.926 11.38 11.68 43.75 2.83
2275 2385 9.906660 CACTATTCACACTATTTTAGCCAAAAA 57.093 29.630 0.00 0.00 41.21 1.94
2276 2386 9.290988 TCACTATTCACACTATTTTAGCCAAAA 57.709 29.630 0.00 0.00 38.00 2.44
2277 2387 8.726988 GTCACTATTCACACTATTTTAGCCAAA 58.273 33.333 0.00 0.00 0.00 3.28
2278 2388 7.335924 GGTCACTATTCACACTATTTTAGCCAA 59.664 37.037 0.00 0.00 0.00 4.52
2279 2389 6.821665 GGTCACTATTCACACTATTTTAGCCA 59.178 38.462 0.00 0.00 0.00 4.75
2280 2390 7.048512 AGGTCACTATTCACACTATTTTAGCC 58.951 38.462 0.00 0.00 0.00 3.93
2281 2391 9.765795 ATAGGTCACTATTCACACTATTTTAGC 57.234 33.333 0.00 0.00 36.51 3.09
2288 2398 9.582648 TGCTATTATAGGTCACTATTCACACTA 57.417 33.333 1.12 0.00 40.35 2.74
2289 2399 8.478775 TGCTATTATAGGTCACTATTCACACT 57.521 34.615 1.12 0.00 40.35 3.55
2290 2400 9.542462 TTTGCTATTATAGGTCACTATTCACAC 57.458 33.333 1.12 0.00 40.35 3.82
2329 2439 4.799564 AAAGTTGACCTCACAGCAAAAA 57.200 36.364 0.00 0.00 0.00 1.94
2330 2440 4.947388 ACTAAAGTTGACCTCACAGCAAAA 59.053 37.500 0.00 0.00 0.00 2.44
2331 2441 4.523083 ACTAAAGTTGACCTCACAGCAAA 58.477 39.130 0.00 0.00 0.00 3.68
2332 2442 4.150897 ACTAAAGTTGACCTCACAGCAA 57.849 40.909 0.00 0.00 0.00 3.91
2333 2443 3.838244 ACTAAAGTTGACCTCACAGCA 57.162 42.857 0.00 0.00 0.00 4.41
2334 2444 5.500645 AAAACTAAAGTTGACCTCACAGC 57.499 39.130 0.00 0.00 38.44 4.40
2358 2468 9.860898 CCACTGATATATAAATGTCGATGAGAA 57.139 33.333 0.00 0.00 0.00 2.87
2359 2469 9.025041 ACCACTGATATATAAATGTCGATGAGA 57.975 33.333 0.00 0.00 0.00 3.27
2360 2470 9.080915 CACCACTGATATATAAATGTCGATGAG 57.919 37.037 0.00 0.00 0.00 2.90
2361 2471 7.545615 GCACCACTGATATATAAATGTCGATGA 59.454 37.037 0.00 0.00 0.00 2.92
2362 2472 7.331687 TGCACCACTGATATATAAATGTCGATG 59.668 37.037 0.00 0.00 0.00 3.84
2363 2473 7.386059 TGCACCACTGATATATAAATGTCGAT 58.614 34.615 0.00 0.00 0.00 3.59
2364 2474 6.754193 TGCACCACTGATATATAAATGTCGA 58.246 36.000 0.00 0.00 0.00 4.20
2365 2475 7.420184 TTGCACCACTGATATATAAATGTCG 57.580 36.000 0.00 0.00 0.00 4.35
2366 2476 9.669353 CTTTTGCACCACTGATATATAAATGTC 57.331 33.333 0.00 0.00 0.00 3.06
2367 2477 9.189156 ACTTTTGCACCACTGATATATAAATGT 57.811 29.630 0.00 0.00 0.00 2.71
2371 2481 9.899661 ACTTACTTTTGCACCACTGATATATAA 57.100 29.630 0.00 0.00 0.00 0.98
2372 2482 9.542462 GACTTACTTTTGCACCACTGATATATA 57.458 33.333 0.00 0.00 0.00 0.86
2373 2483 8.046708 TGACTTACTTTTGCACCACTGATATAT 58.953 33.333 0.00 0.00 0.00 0.86
2374 2484 7.390823 TGACTTACTTTTGCACCACTGATATA 58.609 34.615 0.00 0.00 0.00 0.86
2375 2485 6.237901 TGACTTACTTTTGCACCACTGATAT 58.762 36.000 0.00 0.00 0.00 1.63
2376 2486 5.616270 TGACTTACTTTTGCACCACTGATA 58.384 37.500 0.00 0.00 0.00 2.15
2377 2487 4.460263 TGACTTACTTTTGCACCACTGAT 58.540 39.130 0.00 0.00 0.00 2.90
2378 2488 3.879998 TGACTTACTTTTGCACCACTGA 58.120 40.909 0.00 0.00 0.00 3.41
2379 2489 4.096382 ACTTGACTTACTTTTGCACCACTG 59.904 41.667 0.00 0.00 0.00 3.66
2380 2490 4.096382 CACTTGACTTACTTTTGCACCACT 59.904 41.667 0.00 0.00 0.00 4.00
2381 2491 4.142469 ACACTTGACTTACTTTTGCACCAC 60.142 41.667 0.00 0.00 0.00 4.16
2382 2492 4.013728 ACACTTGACTTACTTTTGCACCA 58.986 39.130 0.00 0.00 0.00 4.17
2383 2493 4.632538 ACACTTGACTTACTTTTGCACC 57.367 40.909 0.00 0.00 0.00 5.01
2384 2494 6.944557 AAAACACTTGACTTACTTTTGCAC 57.055 33.333 0.00 0.00 0.00 4.57
2463 2573 6.061022 TGGTTGTATATGCACCCTATATGG 57.939 41.667 8.77 0.00 0.00 2.74
2464 2574 7.394016 TCTTGGTTGTATATGCACCCTATATG 58.606 38.462 8.77 0.00 0.00 1.78
2465 2575 7.568128 TCTTGGTTGTATATGCACCCTATAT 57.432 36.000 8.77 0.00 0.00 0.86
2466 2576 7.221450 GTTCTTGGTTGTATATGCACCCTATA 58.779 38.462 8.77 0.00 0.00 1.31
2467 2577 5.904984 TCTTGGTTGTATATGCACCCTAT 57.095 39.130 8.77 0.00 0.00 2.57
2468 2578 5.433526 GTTCTTGGTTGTATATGCACCCTA 58.566 41.667 8.77 0.50 0.00 3.53
2469 2579 4.270008 GTTCTTGGTTGTATATGCACCCT 58.730 43.478 8.77 0.00 0.00 4.34
2470 2580 3.380320 GGTTCTTGGTTGTATATGCACCC 59.620 47.826 0.12 0.12 0.00 4.61
2471 2581 4.013728 TGGTTCTTGGTTGTATATGCACC 58.986 43.478 0.00 0.00 0.00 5.01
2472 2582 5.637006 TTGGTTCTTGGTTGTATATGCAC 57.363 39.130 0.00 0.00 0.00 4.57
2473 2583 5.772672 ACTTTGGTTCTTGGTTGTATATGCA 59.227 36.000 0.00 0.00 0.00 3.96
2474 2584 6.092748 CACTTTGGTTCTTGGTTGTATATGC 58.907 40.000 0.00 0.00 0.00 3.14
2475 2585 7.214467 ACACTTTGGTTCTTGGTTGTATATG 57.786 36.000 0.00 0.00 0.00 1.78
2476 2586 9.528489 AATACACTTTGGTTCTTGGTTGTATAT 57.472 29.630 0.00 0.00 0.00 0.86
2477 2587 8.927675 AATACACTTTGGTTCTTGGTTGTATA 57.072 30.769 0.00 0.00 0.00 1.47
2478 2588 7.833285 AATACACTTTGGTTCTTGGTTGTAT 57.167 32.000 0.00 0.00 0.00 2.29
2479 2589 7.201839 GGAAATACACTTTGGTTCTTGGTTGTA 60.202 37.037 0.00 0.00 0.00 2.41
2480 2590 6.406512 GGAAATACACTTTGGTTCTTGGTTGT 60.407 38.462 0.00 0.00 0.00 3.32
2481 2591 5.983118 GGAAATACACTTTGGTTCTTGGTTG 59.017 40.000 0.00 0.00 0.00 3.77
2482 2592 5.897250 AGGAAATACACTTTGGTTCTTGGTT 59.103 36.000 0.00 0.00 0.00 3.67
2483 2593 5.454966 AGGAAATACACTTTGGTTCTTGGT 58.545 37.500 0.00 0.00 0.00 3.67
2484 2594 5.048013 GGAGGAAATACACTTTGGTTCTTGG 60.048 44.000 0.00 0.00 0.00 3.61
2485 2595 5.534654 TGGAGGAAATACACTTTGGTTCTTG 59.465 40.000 0.00 0.00 0.00 3.02
2486 2596 5.701224 TGGAGGAAATACACTTTGGTTCTT 58.299 37.500 0.00 0.00 0.00 2.52
2487 2597 5.316987 CTGGAGGAAATACACTTTGGTTCT 58.683 41.667 0.00 0.00 0.00 3.01
2488 2598 4.459337 CCTGGAGGAAATACACTTTGGTTC 59.541 45.833 0.00 0.00 37.39 3.62
2489 2599 4.141018 ACCTGGAGGAAATACACTTTGGTT 60.141 41.667 0.00 0.00 38.94 3.67
2490 2600 3.397955 ACCTGGAGGAAATACACTTTGGT 59.602 43.478 0.00 0.00 38.94 3.67
2491 2601 3.758554 CACCTGGAGGAAATACACTTTGG 59.241 47.826 0.00 0.00 38.94 3.28
2492 2602 3.191371 GCACCTGGAGGAAATACACTTTG 59.809 47.826 0.00 0.00 38.94 2.77
2493 2603 3.421844 GCACCTGGAGGAAATACACTTT 58.578 45.455 0.00 0.00 38.94 2.66
2494 2604 2.615493 CGCACCTGGAGGAAATACACTT 60.615 50.000 0.00 0.00 38.94 3.16
2495 2605 1.066143 CGCACCTGGAGGAAATACACT 60.066 52.381 0.00 0.00 38.94 3.55
2496 2606 1.369625 CGCACCTGGAGGAAATACAC 58.630 55.000 0.00 0.00 38.94 2.90
2497 2607 0.251916 CCGCACCTGGAGGAAATACA 59.748 55.000 0.00 0.00 39.08 2.29
2498 2608 0.252197 ACCGCACCTGGAGGAAATAC 59.748 55.000 0.00 0.00 39.08 1.89
2499 2609 0.251916 CACCGCACCTGGAGGAAATA 59.748 55.000 0.00 0.00 39.08 1.40
2500 2610 1.002134 CACCGCACCTGGAGGAAAT 60.002 57.895 0.00 0.00 39.08 2.17
2501 2611 2.429930 CACCGCACCTGGAGGAAA 59.570 61.111 0.00 0.00 39.08 3.13
2502 2612 3.636231 CCACCGCACCTGGAGGAA 61.636 66.667 0.00 0.00 41.85 3.36
2505 2615 3.612247 CTTCCCACCGCACCTGGAG 62.612 68.421 0.00 0.00 0.00 3.86
2506 2616 3.636231 CTTCCCACCGCACCTGGA 61.636 66.667 0.00 0.00 0.00 3.86
2507 2617 4.722700 CCTTCCCACCGCACCTGG 62.723 72.222 0.00 0.00 0.00 4.45
2508 2618 2.971598 ATCCTTCCCACCGCACCTG 61.972 63.158 0.00 0.00 0.00 4.00
2509 2619 2.610859 ATCCTTCCCACCGCACCT 60.611 61.111 0.00 0.00 0.00 4.00
2510 2620 2.438434 CATCCTTCCCACCGCACC 60.438 66.667 0.00 0.00 0.00 5.01
2511 2621 2.438434 CCATCCTTCCCACCGCAC 60.438 66.667 0.00 0.00 0.00 5.34
2512 2622 2.609299 TCCATCCTTCCCACCGCA 60.609 61.111 0.00 0.00 0.00 5.69
2513 2623 2.190578 CTCCATCCTTCCCACCGC 59.809 66.667 0.00 0.00 0.00 5.68
2514 2624 0.978146 ACTCTCCATCCTTCCCACCG 60.978 60.000 0.00 0.00 0.00 4.94
2515 2625 1.763545 GTACTCTCCATCCTTCCCACC 59.236 57.143 0.00 0.00 0.00 4.61
2516 2626 2.696187 GAGTACTCTCCATCCTTCCCAC 59.304 54.545 15.91 0.00 34.87 4.61
2517 2627 2.687014 CGAGTACTCTCCATCCTTCCCA 60.687 54.545 20.34 0.00 37.40 4.37
2518 2628 1.957877 CGAGTACTCTCCATCCTTCCC 59.042 57.143 20.34 0.00 37.40 3.97
2519 2629 1.957877 CCGAGTACTCTCCATCCTTCC 59.042 57.143 20.34 0.00 37.40 3.46
2520 2630 1.338655 GCCGAGTACTCTCCATCCTTC 59.661 57.143 20.34 0.00 37.40 3.46
2521 2631 1.404843 GCCGAGTACTCTCCATCCTT 58.595 55.000 20.34 0.00 37.40 3.36
2522 2632 0.468400 GGCCGAGTACTCTCCATCCT 60.468 60.000 20.34 0.00 37.40 3.24
2523 2633 1.465200 GGGCCGAGTACTCTCCATCC 61.465 65.000 23.82 15.65 37.40 3.51
2524 2634 2.042800 GGGCCGAGTACTCTCCATC 58.957 63.158 23.82 10.56 37.40 3.51
2525 2635 4.279326 GGGCCGAGTACTCTCCAT 57.721 61.111 23.82 0.00 37.40 3.41


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

AutoCloner maintained by Alex Coulton.