Multiple sequence alignment - TraesCS1B01G198500

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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 TraesCS1B01G198500 chr1B 100.000 4105 0 0 1441 5545 356455488 356451384 0.000000e+00 7581
1 TraesCS1B01G198500 chr1B 100.000 1233 0 0 1 1233 356456928 356455696 0.000000e+00 2278
2 TraesCS1B01G198500 chr1B 95.527 626 16 1 1480 2105 229488952 229489565 0.000000e+00 990
3 TraesCS1B01G198500 chr1A 95.475 3050 99 14 1441 4478 330083285 330086307 0.000000e+00 4831
4 TraesCS1B01G198500 chr1A 93.233 532 12 7 725 1233 330082679 330083209 0.000000e+00 761
5 TraesCS1B01G198500 chr1A 94.488 381 17 3 4964 5341 330086569 330086948 8.000000e-163 584
6 TraesCS1B01G198500 chr1A 93.443 305 12 5 5243 5545 330087323 330087621 3.940000e-121 446
7 TraesCS1B01G198500 chr1A 94.595 259 12 2 5243 5500 330087071 330087328 3.110000e-107 399
8 TraesCS1B01G198500 chr1A 92.381 210 10 2 1 205 330081970 330082178 1.510000e-75 294
9 TraesCS1B01G198500 chr1A 97.600 125 3 0 5376 5500 330086952 330087076 1.210000e-51 215
10 TraesCS1B01G198500 chr1D 97.308 2266 57 2 1441 3705 256780080 256782342 0.000000e+00 3843
11 TraesCS1B01G198500 chr1D 90.754 1763 88 38 3756 5500 256782332 256784037 0.000000e+00 2283
12 TraesCS1B01G198500 chr1D 91.032 1037 70 14 205 1233 256778984 256780005 0.000000e+00 1378
13 TraesCS1B01G198500 chr1D 96.393 305 8 3 5243 5545 256784032 256784335 2.980000e-137 499
14 TraesCS1B01G198500 chr1D 92.925 212 10 3 1 207 256778739 256778950 2.510000e-78 303
15 TraesCS1B01G198500 chr6A 96.486 626 22 0 1480 2105 586055283 586055908 0.000000e+00 1035
16 TraesCS1B01G198500 chr4B 78.793 646 122 13 2705 3335 673250963 673251608 2.390000e-113 420
17 TraesCS1B01G198500 chr4B 92.053 151 12 0 1467 1617 673249000 673249150 4.350000e-51 213
18 TraesCS1B01G198500 chr4B 84.393 173 27 0 1706 1878 673249242 673249414 2.660000e-38 171
19 TraesCS1B01G198500 chrUn 79.019 591 101 18 3063 3639 99825439 99824858 3.130000e-102 383
20 TraesCS1B01G198500 chrUn 79.904 418 60 15 1464 1878 99827460 99827064 9.090000e-73 285
21 TraesCS1B01G198500 chr4A 80.759 369 66 5 428 794 29169115 29168750 3.270000e-72 283
22 TraesCS1B01G198500 chr3D 74.281 591 140 12 213 797 600931723 600931139 7.180000e-59 239
23 TraesCS1B01G198500 chr3A 90.385 156 15 0 1466 1621 703425203 703425048 7.280000e-49 206
24 TraesCS1B01G198500 chr3A 85.806 155 22 0 1724 1878 703424882 703424728 1.240000e-36 165
25 TraesCS1B01G198500 chr4D 90.789 152 14 0 1466 1617 491381165 491381014 2.620000e-48 204
26 TraesCS1B01G198500 chr4D 85.443 158 20 1 1721 1878 491380897 491380743 1.600000e-35 161
27 TraesCS1B01G198500 chr3B 73.415 568 139 11 236 797 808141332 808140771 9.420000e-48 202
28 TraesCS1B01G198500 chr6D 76.426 263 58 4 213 473 311242905 311242645 7.490000e-29 139
29 TraesCS1B01G198500 chr2D 77.143 245 52 4 212 454 125275683 125275925 7.490000e-29 139
30 TraesCS1B01G198500 chr5A 81.646 158 23 4 1 152 321879507 321879664 5.830000e-25 126
31 TraesCS1B01G198500 chr7D 80.124 161 26 4 1 155 543555554 543555714 1.260000e-21 115


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 TraesCS1B01G198500 chr1B 356451384 356456928 5544 True 4929.500000 7581 100.000000 1 5545 2 chr1B.!!$R1 5544
1 TraesCS1B01G198500 chr1B 229488952 229489565 613 False 990.000000 990 95.527000 1480 2105 1 chr1B.!!$F1 625
2 TraesCS1B01G198500 chr1A 330081970 330087621 5651 False 1075.714286 4831 94.459286 1 5545 7 chr1A.!!$F1 5544
3 TraesCS1B01G198500 chr1D 256778739 256784335 5596 False 1661.200000 3843 93.682400 1 5545 5 chr1D.!!$F1 5544
4 TraesCS1B01G198500 chr6A 586055283 586055908 625 False 1035.000000 1035 96.486000 1480 2105 1 chr6A.!!$F1 625
5 TraesCS1B01G198500 chr4B 673249000 673251608 2608 False 268.000000 420 85.079667 1467 3335 3 chr4B.!!$F1 1868
6 TraesCS1B01G198500 chrUn 99824858 99827460 2602 True 334.000000 383 79.461500 1464 3639 2 chrUn.!!$R1 2175
7 TraesCS1B01G198500 chr3D 600931139 600931723 584 True 239.000000 239 74.281000 213 797 1 chr3D.!!$R1 584
8 TraesCS1B01G198500 chr3B 808140771 808141332 561 True 202.000000 202 73.415000 236 797 1 chr3B.!!$R1 561

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
661 840 0.107703 TGCACCAGAAATAGCCTCCG 60.108 55.000 0.00 0.00 0.00 4.63 F
665 844 0.109342 CCAGAAATAGCCTCCGCCAT 59.891 55.000 0.00 0.00 34.57 4.40 F
666 845 1.477558 CCAGAAATAGCCTCCGCCATT 60.478 52.381 0.00 0.00 34.57 3.16 F
2227 2931 1.229336 CCCCGCCCTCTGGATCTAT 60.229 63.158 0.00 0.00 0.00 1.98 F
3098 4583 1.477700 GCATTGCTTGGAGCCATACAA 59.522 47.619 0.16 7.04 41.51 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2227 2931 0.388778 CTGTGCATTGCATTTCGGCA 60.389 50.000 15.49 5.93 41.91 5.69 R
2228 2932 0.388907 ACTGTGCATTGCATTTCGGC 60.389 50.000 15.49 1.01 41.91 5.54 R
2393 3097 0.472471 ACGTGGGAACAGTGGAACAT 59.528 50.000 0.00 0.00 44.46 2.71 R
3983 5480 3.452627 AGTCCGCATCTAATTCCAAGAGT 59.547 43.478 0.00 0.00 0.00 3.24 R
4769 6318 0.026803 GCAGAAAGTTAGATGCGGCG 59.973 55.000 0.51 0.51 0.00 6.46 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
104 110 2.251818 TCCCTCTCCTTGACTGAACTG 58.748 52.381 0.00 0.00 0.00 3.16
123 129 0.545171 GGTTGGGCTAGAAGGTACCC 59.455 60.000 8.74 0.00 43.14 3.69
227 302 7.809806 CCAAATGTTTCCATCAGAAAAGTACTC 59.190 37.037 0.00 0.00 45.93 2.59
306 381 4.114794 GCTTGGCTAACATGGCTAAATTG 58.885 43.478 0.00 0.00 30.37 2.32
335 410 1.777272 GAGATCCCTAAACCCCATGCT 59.223 52.381 0.00 0.00 0.00 3.79
406 482 3.367646 TCTTCTACTCATCCGTGTCCT 57.632 47.619 0.00 0.00 0.00 3.85
426 502 3.192212 CCTCTCACCAAAAAGCTTCCATC 59.808 47.826 0.00 0.00 0.00 3.51
544 635 2.101582 CTCCCTCCTAAGGACATCAACG 59.898 54.545 0.00 0.00 46.67 4.10
576 667 3.314553 ACCTACAAGTCGATTCACAACG 58.685 45.455 0.00 0.00 0.00 4.10
588 679 3.840890 TTCACAACGCTTTCAACAAGT 57.159 38.095 0.00 0.00 0.00 3.16
606 697 7.653713 TCAACAAGTTGAGAGAAACTATCACTC 59.346 37.037 10.54 0.00 43.90 3.51
642 821 9.383519 CGCACCATAGATAAAATACCAAGATAT 57.616 33.333 0.00 0.00 0.00 1.63
649 828 8.627208 AGATAAAATACCAAGATATGCACCAG 57.373 34.615 0.00 0.00 0.00 4.00
650 829 8.439971 AGATAAAATACCAAGATATGCACCAGA 58.560 33.333 0.00 0.00 0.00 3.86
651 830 8.995027 ATAAAATACCAAGATATGCACCAGAA 57.005 30.769 0.00 0.00 0.00 3.02
652 831 7.716799 AAAATACCAAGATATGCACCAGAAA 57.283 32.000 0.00 0.00 0.00 2.52
653 832 7.902920 AAATACCAAGATATGCACCAGAAAT 57.097 32.000 0.00 0.00 0.00 2.17
654 833 8.995027 AAATACCAAGATATGCACCAGAAATA 57.005 30.769 0.00 0.00 0.00 1.40
655 834 8.627208 AATACCAAGATATGCACCAGAAATAG 57.373 34.615 0.00 0.00 0.00 1.73
656 835 4.823989 ACCAAGATATGCACCAGAAATAGC 59.176 41.667 0.00 0.00 0.00 2.97
657 836 4.217118 CCAAGATATGCACCAGAAATAGCC 59.783 45.833 0.00 0.00 0.00 3.93
658 837 4.989875 AGATATGCACCAGAAATAGCCT 57.010 40.909 0.00 0.00 0.00 4.58
659 838 4.904241 AGATATGCACCAGAAATAGCCTC 58.096 43.478 0.00 0.00 0.00 4.70
660 839 2.355010 ATGCACCAGAAATAGCCTCC 57.645 50.000 0.00 0.00 0.00 4.30
661 840 0.107703 TGCACCAGAAATAGCCTCCG 60.108 55.000 0.00 0.00 0.00 4.63
662 841 1.440145 GCACCAGAAATAGCCTCCGC 61.440 60.000 0.00 0.00 0.00 5.54
663 842 0.815615 CACCAGAAATAGCCTCCGCC 60.816 60.000 0.00 0.00 34.57 6.13
664 843 1.271840 ACCAGAAATAGCCTCCGCCA 61.272 55.000 0.00 0.00 34.57 5.69
665 844 0.109342 CCAGAAATAGCCTCCGCCAT 59.891 55.000 0.00 0.00 34.57 4.40
666 845 1.477558 CCAGAAATAGCCTCCGCCATT 60.478 52.381 0.00 0.00 34.57 3.16
667 846 2.224523 CCAGAAATAGCCTCCGCCATTA 60.225 50.000 0.00 0.00 34.57 1.90
668 847 3.560025 CCAGAAATAGCCTCCGCCATTAT 60.560 47.826 0.00 0.00 34.57 1.28
669 848 4.074970 CAGAAATAGCCTCCGCCATTATT 58.925 43.478 0.00 0.00 34.57 1.40
670 849 4.520492 CAGAAATAGCCTCCGCCATTATTT 59.480 41.667 0.00 0.00 34.57 1.40
671 850 5.010012 CAGAAATAGCCTCCGCCATTATTTT 59.990 40.000 0.00 0.00 34.57 1.82
672 851 5.241728 AGAAATAGCCTCCGCCATTATTTTC 59.758 40.000 0.00 0.00 34.57 2.29
673 852 2.435372 AGCCTCCGCCATTATTTTCA 57.565 45.000 0.00 0.00 34.57 2.69
674 853 2.301346 AGCCTCCGCCATTATTTTCAG 58.699 47.619 0.00 0.00 34.57 3.02
675 854 2.024414 GCCTCCGCCATTATTTTCAGT 58.976 47.619 0.00 0.00 0.00 3.41
676 855 2.427095 GCCTCCGCCATTATTTTCAGTT 59.573 45.455 0.00 0.00 0.00 3.16
677 856 3.119137 GCCTCCGCCATTATTTTCAGTTT 60.119 43.478 0.00 0.00 0.00 2.66
678 857 4.672409 CCTCCGCCATTATTTTCAGTTTC 58.328 43.478 0.00 0.00 0.00 2.78
679 858 4.157656 CCTCCGCCATTATTTTCAGTTTCA 59.842 41.667 0.00 0.00 0.00 2.69
680 859 5.054390 TCCGCCATTATTTTCAGTTTCAC 57.946 39.130 0.00 0.00 0.00 3.18
681 860 3.851403 CCGCCATTATTTTCAGTTTCACG 59.149 43.478 0.00 0.00 0.00 4.35
682 861 3.300590 CGCCATTATTTTCAGTTTCACGC 59.699 43.478 0.00 0.00 0.00 5.34
683 862 4.233789 GCCATTATTTTCAGTTTCACGCA 58.766 39.130 0.00 0.00 0.00 5.24
684 863 4.683781 GCCATTATTTTCAGTTTCACGCAA 59.316 37.500 0.00 0.00 0.00 4.85
685 864 5.176590 GCCATTATTTTCAGTTTCACGCAAA 59.823 36.000 0.00 0.00 0.00 3.68
686 865 6.580476 CCATTATTTTCAGTTTCACGCAAAC 58.420 36.000 2.96 2.96 44.38 2.93
687 866 6.346518 CCATTATTTTCAGTTTCACGCAAACC 60.347 38.462 6.90 0.00 45.05 3.27
688 867 3.859411 TTTTCAGTTTCACGCAAACCT 57.141 38.095 6.90 0.00 45.05 3.50
689 868 4.966965 TTTTCAGTTTCACGCAAACCTA 57.033 36.364 6.90 0.00 45.05 3.08
690 869 4.966965 TTTCAGTTTCACGCAAACCTAA 57.033 36.364 6.90 0.76 45.05 2.69
691 870 4.545823 TTCAGTTTCACGCAAACCTAAG 57.454 40.909 6.90 0.00 45.05 2.18
692 871 2.289547 TCAGTTTCACGCAAACCTAAGC 59.710 45.455 6.90 0.00 45.05 3.09
693 872 2.290641 CAGTTTCACGCAAACCTAAGCT 59.709 45.455 6.90 0.00 45.05 3.74
694 873 2.949644 AGTTTCACGCAAACCTAAGCTT 59.050 40.909 3.48 3.48 45.05 3.74
695 874 3.380320 AGTTTCACGCAAACCTAAGCTTT 59.620 39.130 3.20 0.00 45.05 3.51
696 875 4.577283 AGTTTCACGCAAACCTAAGCTTTA 59.423 37.500 3.20 0.00 45.05 1.85
697 876 4.477302 TTCACGCAAACCTAAGCTTTAC 57.523 40.909 3.20 0.00 0.00 2.01
698 877 2.809696 TCACGCAAACCTAAGCTTTACC 59.190 45.455 3.20 0.00 0.00 2.85
699 878 2.095415 CACGCAAACCTAAGCTTTACCC 60.095 50.000 3.20 0.00 0.00 3.69
700 879 2.224695 ACGCAAACCTAAGCTTTACCCT 60.225 45.455 3.20 0.00 0.00 4.34
701 880 2.418976 CGCAAACCTAAGCTTTACCCTC 59.581 50.000 3.20 0.00 0.00 4.30
702 881 3.418047 GCAAACCTAAGCTTTACCCTCA 58.582 45.455 3.20 0.00 0.00 3.86
703 882 3.824443 GCAAACCTAAGCTTTACCCTCAA 59.176 43.478 3.20 0.00 0.00 3.02
704 883 4.321008 GCAAACCTAAGCTTTACCCTCAAC 60.321 45.833 3.20 0.00 0.00 3.18
705 884 4.717279 AACCTAAGCTTTACCCTCAACA 57.283 40.909 3.20 0.00 0.00 3.33
706 885 4.929146 ACCTAAGCTTTACCCTCAACAT 57.071 40.909 3.20 0.00 0.00 2.71
707 886 5.256806 ACCTAAGCTTTACCCTCAACATT 57.743 39.130 3.20 0.00 0.00 2.71
708 887 5.254115 ACCTAAGCTTTACCCTCAACATTC 58.746 41.667 3.20 0.00 0.00 2.67
709 888 5.222048 ACCTAAGCTTTACCCTCAACATTCA 60.222 40.000 3.20 0.00 0.00 2.57
710 889 5.888161 CCTAAGCTTTACCCTCAACATTCAT 59.112 40.000 3.20 0.00 0.00 2.57
711 890 7.054124 CCTAAGCTTTACCCTCAACATTCATA 58.946 38.462 3.20 0.00 0.00 2.15
712 891 7.721399 CCTAAGCTTTACCCTCAACATTCATAT 59.279 37.037 3.20 0.00 0.00 1.78
713 892 7.961326 AAGCTTTACCCTCAACATTCATATT 57.039 32.000 0.00 0.00 0.00 1.28
714 893 7.961326 AGCTTTACCCTCAACATTCATATTT 57.039 32.000 0.00 0.00 0.00 1.40
715 894 8.366359 AGCTTTACCCTCAACATTCATATTTT 57.634 30.769 0.00 0.00 0.00 1.82
716 895 8.253113 AGCTTTACCCTCAACATTCATATTTTG 58.747 33.333 0.00 0.00 0.00 2.44
717 896 7.492344 GCTTTACCCTCAACATTCATATTTTGG 59.508 37.037 0.00 0.00 0.00 3.28
718 897 5.343307 ACCCTCAACATTCATATTTTGGC 57.657 39.130 0.00 0.00 0.00 4.52
719 898 5.025453 ACCCTCAACATTCATATTTTGGCT 58.975 37.500 0.00 0.00 0.00 4.75
720 899 5.105228 ACCCTCAACATTCATATTTTGGCTG 60.105 40.000 0.00 0.00 0.00 4.85
721 900 5.353938 CCTCAACATTCATATTTTGGCTGG 58.646 41.667 0.00 0.00 0.00 4.85
722 901 5.127519 CCTCAACATTCATATTTTGGCTGGA 59.872 40.000 0.00 0.00 0.00 3.86
723 902 6.351202 CCTCAACATTCATATTTTGGCTGGAA 60.351 38.462 0.00 0.00 0.00 3.53
724 903 7.002250 TCAACATTCATATTTTGGCTGGAAA 57.998 32.000 0.00 0.00 0.00 3.13
725 904 7.448420 TCAACATTCATATTTTGGCTGGAAAA 58.552 30.769 0.00 0.00 0.00 2.29
726 905 7.603404 TCAACATTCATATTTTGGCTGGAAAAG 59.397 33.333 0.00 0.00 0.00 2.27
727 906 7.243604 ACATTCATATTTTGGCTGGAAAAGA 57.756 32.000 0.00 0.00 0.00 2.52
728 907 7.854337 ACATTCATATTTTGGCTGGAAAAGAT 58.146 30.769 0.00 0.00 28.96 2.40
729 908 8.980596 ACATTCATATTTTGGCTGGAAAAGATA 58.019 29.630 0.00 0.00 28.21 1.98
732 911 7.999679 TCATATTTTGGCTGGAAAAGATACTG 58.000 34.615 0.00 0.00 28.21 2.74
760 940 3.221771 CCTTCACTCACCAATTGTCCAA 58.778 45.455 4.43 0.00 0.00 3.53
887 1089 4.980805 GCGAGTGCGACCCAACCA 62.981 66.667 0.00 0.00 40.82 3.67
1124 1332 2.977178 CTGGAGCTCGGCAAGTCT 59.023 61.111 7.83 0.00 0.00 3.24
1139 1347 4.680237 TCTGGCAAGGACCGCGTG 62.680 66.667 4.92 0.00 0.00 5.34
1642 1850 2.602676 CGCCCCTTCCTTCCTTGGA 61.603 63.158 0.00 0.00 0.00 3.53
2227 2931 1.229336 CCCCGCCCTCTGGATCTAT 60.229 63.158 0.00 0.00 0.00 1.98
2228 2932 1.548357 CCCCGCCCTCTGGATCTATG 61.548 65.000 0.00 0.00 0.00 2.23
2277 2981 7.993758 ACATACTAACTGCACTAGTATCTGAGA 59.006 37.037 16.03 0.00 39.49 3.27
2284 2988 8.335532 ACTGCACTAGTATCTGAGATCTAATC 57.664 38.462 0.00 0.00 38.04 1.75
2358 3062 9.975218 AGTCCAAGTTCCTTTGTATATGTTTAT 57.025 29.630 0.00 0.00 0.00 1.40
2393 3097 1.985614 CCTGTGTGGGCAGATCTGA 59.014 57.895 27.04 2.29 38.70 3.27
2468 3172 9.353999 GGCAATATTAAATCGAAGTTTTTCAGT 57.646 29.630 0.00 0.00 32.67 3.41
2840 4278 4.697756 TTTGGCCCTGTCGCTCCG 62.698 66.667 0.00 0.00 0.00 4.63
3098 4583 1.477700 GCATTGCTTGGAGCCATACAA 59.522 47.619 0.16 7.04 41.51 2.41
3504 4994 4.811024 TGGTTTCTGCATATTCGAGTCATC 59.189 41.667 0.00 0.00 0.00 2.92
3622 5112 5.529800 ACTTAACCTGTTTGTATGTGTGGTC 59.470 40.000 0.00 0.00 0.00 4.02
3692 5182 5.782893 TTACTTTTTGGTAATGCAGTGCT 57.217 34.783 17.60 0.00 0.00 4.40
3741 5236 6.398234 TTTAATTTTGGCTGAGTACTTGCA 57.602 33.333 18.94 4.49 0.00 4.08
3758 5253 9.384764 AGTACTTGCATAAAGAAAGATTCTACC 57.615 33.333 0.00 0.00 39.61 3.18
3774 5269 7.224297 AGATTCTACCAAAACAAGCTGAAGTA 58.776 34.615 0.00 0.00 0.00 2.24
3799 5294 6.005823 TCATTACTCATCCCCAATAATGCTG 58.994 40.000 0.00 0.00 34.60 4.41
3983 5480 2.847441 TGCAAGCAAATGCCATTTTCA 58.153 38.095 0.00 0.00 45.83 2.69
3998 5495 6.664816 TGCCATTTTCACTCTTGGAATTAGAT 59.335 34.615 0.00 0.00 0.00 1.98
4001 5498 5.801350 TTTCACTCTTGGAATTAGATGCG 57.199 39.130 0.00 0.00 0.00 4.73
4009 5506 6.591935 TCTTGGAATTAGATGCGGACTTAAT 58.408 36.000 0.00 0.00 0.00 1.40
4012 5509 7.962964 TGGAATTAGATGCGGACTTAATAAG 57.037 36.000 0.00 0.00 0.00 1.73
4244 5741 4.951254 TCTCACGGTATTCAGTTTTGTCA 58.049 39.130 0.00 0.00 0.00 3.58
4319 5816 3.654414 CTTTGGCATAGTACCGGATCTC 58.346 50.000 9.46 0.00 0.00 2.75
4403 5900 7.372260 ACCAGTCTCTTGATGAAAGCTATAT 57.628 36.000 0.00 0.00 35.69 0.86
4404 5901 8.484214 ACCAGTCTCTTGATGAAAGCTATATA 57.516 34.615 0.00 0.00 35.69 0.86
4429 5926 5.160386 CCTGTACCCCTGTATACCCTATTT 58.840 45.833 0.00 0.00 0.00 1.40
4474 6009 3.614399 CAGAGGAGTTTCTGCCGTT 57.386 52.632 0.00 0.00 38.28 4.44
4492 6027 5.703592 TGCCGTTTTAGTGATTTGTCTACAT 59.296 36.000 0.00 0.00 0.00 2.29
4523 6058 3.618594 TCTCTACAAAATGCGTGCTGATC 59.381 43.478 0.00 0.00 0.00 2.92
4558 6093 8.880991 TTTACAATTAAAAGGGCCATACTACA 57.119 30.769 6.18 0.00 0.00 2.74
4560 6095 6.249951 ACAATTAAAAGGGCCATACTACACA 58.750 36.000 6.18 0.00 0.00 3.72
4570 6105 1.113517 ATACTACACATCGGCCGGCT 61.114 55.000 28.56 10.71 0.00 5.52
4585 6122 1.369625 CGGCTGATCTTTTTACGCCT 58.630 50.000 0.00 0.00 35.46 5.52
4588 6125 1.267582 GCTGATCTTTTTACGCCTCGC 60.268 52.381 0.00 0.00 0.00 5.03
4601 6138 2.780094 CCTCGCGAGCCATCTGTCT 61.780 63.158 30.49 0.00 0.00 3.41
4603 6140 1.144565 CTCGCGAGCCATCTGTCTTG 61.145 60.000 25.07 0.00 0.00 3.02
4604 6141 1.446792 CGCGAGCCATCTGTCTTGT 60.447 57.895 0.00 0.00 0.00 3.16
4605 6142 0.179137 CGCGAGCCATCTGTCTTGTA 60.179 55.000 0.00 0.00 0.00 2.41
4606 6143 1.735700 CGCGAGCCATCTGTCTTGTAA 60.736 52.381 0.00 0.00 0.00 2.41
4607 6144 1.661112 GCGAGCCATCTGTCTTGTAAC 59.339 52.381 0.00 0.00 0.00 2.50
4608 6145 2.930887 GCGAGCCATCTGTCTTGTAACA 60.931 50.000 0.00 0.00 0.00 2.41
4609 6146 3.325870 CGAGCCATCTGTCTTGTAACAA 58.674 45.455 0.00 0.00 0.00 2.83
4610 6147 3.369147 CGAGCCATCTGTCTTGTAACAAG 59.631 47.826 0.00 0.00 0.00 3.16
4612 6149 3.073062 AGCCATCTGTCTTGTAACAAGGT 59.927 43.478 0.00 0.00 0.00 3.50
4613 6150 3.189287 GCCATCTGTCTTGTAACAAGGTG 59.811 47.826 0.00 0.00 0.00 4.00
4614 6151 4.389374 CCATCTGTCTTGTAACAAGGTGT 58.611 43.478 0.00 0.00 0.00 4.16
4617 6154 5.092554 TCTGTCTTGTAACAAGGTGTTCA 57.907 39.130 0.00 0.00 40.22 3.18
4619 6156 6.119536 TCTGTCTTGTAACAAGGTGTTCATT 58.880 36.000 0.00 0.00 40.22 2.57
4620 6157 6.038161 TCTGTCTTGTAACAAGGTGTTCATTG 59.962 38.462 0.00 0.00 40.22 2.82
4621 6158 4.976116 GTCTTGTAACAAGGTGTTCATTGC 59.024 41.667 0.00 0.00 40.22 3.56
4622 6159 3.617540 TGTAACAAGGTGTTCATTGCG 57.382 42.857 0.00 0.00 40.22 4.85
4623 6160 3.206964 TGTAACAAGGTGTTCATTGCGA 58.793 40.909 0.00 0.00 40.22 5.10
4624 6161 3.628032 TGTAACAAGGTGTTCATTGCGAA 59.372 39.130 0.00 0.00 40.22 4.70
4625 6162 3.791973 AACAAGGTGTTCATTGCGAAA 57.208 38.095 0.00 0.00 35.27 3.46
4626 6163 4.320608 AACAAGGTGTTCATTGCGAAAT 57.679 36.364 0.00 0.00 35.27 2.17
4627 6164 5.446143 AACAAGGTGTTCATTGCGAAATA 57.554 34.783 0.00 0.00 35.27 1.40
4628 6165 5.643379 ACAAGGTGTTCATTGCGAAATAT 57.357 34.783 0.00 0.00 38.67 1.28
4629 6166 6.024552 ACAAGGTGTTCATTGCGAAATATT 57.975 33.333 0.00 0.00 38.67 1.28
4630 6167 7.151999 ACAAGGTGTTCATTGCGAAATATTA 57.848 32.000 0.00 0.00 38.67 0.98
4631 6168 7.771183 ACAAGGTGTTCATTGCGAAATATTAT 58.229 30.769 0.00 0.00 38.67 1.28
4632 6169 7.915397 ACAAGGTGTTCATTGCGAAATATTATC 59.085 33.333 0.00 0.00 38.67 1.75
4633 6170 7.807977 AGGTGTTCATTGCGAAATATTATCT 57.192 32.000 0.00 0.00 34.69 1.98
4634 6171 8.225603 AGGTGTTCATTGCGAAATATTATCTT 57.774 30.769 0.00 0.00 34.69 2.40
4635 6172 8.131100 AGGTGTTCATTGCGAAATATTATCTTG 58.869 33.333 0.00 0.00 34.69 3.02
4697 6246 7.425606 TCTCTTCTTTAATTTCCTGCAACAAC 58.574 34.615 0.00 0.00 0.00 3.32
4698 6247 6.205784 TCTTCTTTAATTTCCTGCAACAACG 58.794 36.000 0.00 0.00 0.00 4.10
4719 6268 1.270550 CCCATGTTGCACAACCTCTTC 59.729 52.381 10.82 0.00 40.46 2.87
4725 6274 4.380531 TGTTGCACAACCTCTTCTCTAAG 58.619 43.478 10.82 0.00 40.46 2.18
4737 6286 6.183360 ACCTCTTCTCTAAGTTTTGCAACAAC 60.183 38.462 0.00 7.48 35.05 3.32
4769 6318 4.534794 CAAAAATTGCAACAACACCTCC 57.465 40.909 0.00 0.00 0.00 4.30
4770 6319 2.507339 AAATTGCAACAACACCTCCG 57.493 45.000 0.00 0.00 0.00 4.63
4771 6320 0.031994 AATTGCAACAACACCTCCGC 59.968 50.000 0.00 0.00 0.00 5.54
4791 6340 2.095263 GCCGCATCTAACTTTCTGCAAA 60.095 45.455 0.00 0.00 34.29 3.68
4801 6350 4.829064 ACTTTCTGCAAAAAGACGCATA 57.171 36.364 19.19 0.00 38.30 3.14
4809 6358 5.016275 GCAAAAAGACGCATATTGCAAAA 57.984 34.783 1.71 0.00 45.36 2.44
4810 6359 5.438972 GCAAAAAGACGCATATTGCAAAAA 58.561 33.333 1.71 0.00 45.36 1.94
4811 6360 6.079120 GCAAAAAGACGCATATTGCAAAAAT 58.921 32.000 1.71 0.00 45.36 1.82
4812 6361 6.578172 GCAAAAAGACGCATATTGCAAAAATT 59.422 30.769 1.71 0.00 45.36 1.82
4829 6378 7.052565 CAAAAATTGCAACACATCTATGGTC 57.947 36.000 0.00 0.00 0.00 4.02
4830 6379 4.621068 AATTGCAACACATCTATGGTCG 57.379 40.909 0.00 0.00 0.00 4.79
4831 6380 1.368641 TGCAACACATCTATGGTCGC 58.631 50.000 0.00 0.00 0.00 5.19
4832 6381 0.301687 GCAACACATCTATGGTCGCG 59.698 55.000 0.00 0.00 0.00 5.87
4833 6382 1.640428 CAACACATCTATGGTCGCGT 58.360 50.000 5.77 0.00 0.00 6.01
4834 6383 1.588404 CAACACATCTATGGTCGCGTC 59.412 52.381 5.77 0.00 0.00 5.19
4835 6384 0.248498 ACACATCTATGGTCGCGTCG 60.248 55.000 5.77 0.00 0.00 5.12
4836 6385 1.299165 ACATCTATGGTCGCGTCGC 60.299 57.895 7.29 7.29 0.00 5.19
4859 6408 0.792640 CTTGCGCAGTCATCTTTCGT 59.207 50.000 11.31 0.00 0.00 3.85
4862 6411 0.512952 GCGCAGTCATCTTTCGTTGT 59.487 50.000 0.30 0.00 0.00 3.32
4863 6412 1.069906 GCGCAGTCATCTTTCGTTGTT 60.070 47.619 0.30 0.00 0.00 2.83
4864 6413 2.563976 CGCAGTCATCTTTCGTTGTTG 58.436 47.619 0.00 0.00 0.00 3.33
4900 6475 3.818210 GGAAGAGAGACATGCTAGATCGA 59.182 47.826 0.00 0.00 0.00 3.59
4901 6476 4.320202 GGAAGAGAGACATGCTAGATCGAC 60.320 50.000 0.00 0.00 0.00 4.20
4902 6477 3.146066 AGAGAGACATGCTAGATCGACC 58.854 50.000 0.00 0.00 0.00 4.79
4903 6478 1.876799 AGAGACATGCTAGATCGACCG 59.123 52.381 0.00 0.00 0.00 4.79
4917 6492 0.103026 CGACCGGCTGATCAGAATCA 59.897 55.000 27.04 0.00 39.63 2.57
4920 6495 3.209410 GACCGGCTGATCAGAATCATTT 58.791 45.455 27.04 2.73 41.05 2.32
4924 6499 2.889678 GGCTGATCAGAATCATTTCCCC 59.110 50.000 27.04 9.71 41.05 4.81
5028 6605 5.343058 CCAAAGTGACTTGCATATTTGAACG 59.657 40.000 0.00 0.00 37.83 3.95
5176 6753 0.723981 GTCAAATGGAGCGCTGAGAC 59.276 55.000 18.48 9.63 0.00 3.36
5177 6754 0.391661 TCAAATGGAGCGCTGAGACC 60.392 55.000 18.48 10.95 0.00 3.85
5194 6771 2.237143 AGACCTTCGAAATGATCAGCCA 59.763 45.455 0.09 0.00 0.00 4.75
5197 6774 3.273434 CCTTCGAAATGATCAGCCAGAA 58.727 45.455 0.09 4.16 0.00 3.02
5222 6799 6.401955 AACTCAAAACACAATGGTTTTTCG 57.598 33.333 8.96 6.75 45.89 3.46
5263 6841 3.376859 CGCAAAAGAACATAGTGCCCATA 59.623 43.478 0.00 0.00 31.41 2.74
5288 7088 5.241506 GCAGGCATAGCTATAAACCATCAAA 59.758 40.000 17.41 0.00 0.00 2.69
5335 7135 1.535204 GCCCCACAAACCACATCAGG 61.535 60.000 0.00 0.00 0.00 3.86
5358 7158 0.039256 CAGGCAAATGAACACACGGG 60.039 55.000 0.00 0.00 0.00 5.28
5359 7159 1.178534 AGGCAAATGAACACACGGGG 61.179 55.000 0.00 0.00 0.00 5.73
5404 7204 2.868583 CCACAATGCACTCTTATCCTCG 59.131 50.000 0.00 0.00 0.00 4.63
5506 7559 1.165907 TTGCTCAGCAACACCCGAAG 61.166 55.000 8.40 0.00 43.99 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 151 4.415596 AGTGGGCATATTTGGTGAGAAAA 58.584 39.130 0.00 0.00 0.00 2.29
306 381 3.823304 GGTTTAGGGATCTCCATGCATTC 59.177 47.826 0.00 0.00 38.24 2.67
356 431 0.179034 GCTAGCTTGGTGGAGGATGG 60.179 60.000 7.70 0.00 0.00 3.51
406 482 2.813754 CGATGGAAGCTTTTTGGTGAGA 59.186 45.455 0.00 0.00 0.00 3.27
426 502 4.475028 TGTGCAAAGAAATTACAGATGCG 58.525 39.130 0.00 0.00 35.18 4.73
462 552 8.918202 TGGTGTATGTTCTAACTCTTTTCAAT 57.082 30.769 0.00 0.00 0.00 2.57
470 560 8.688151 AGTCTATTCTGGTGTATGTTCTAACTC 58.312 37.037 0.00 0.00 0.00 3.01
473 563 7.782049 CCAGTCTATTCTGGTGTATGTTCTAA 58.218 38.462 4.75 0.00 46.92 2.10
474 564 7.348080 CCAGTCTATTCTGGTGTATGTTCTA 57.652 40.000 4.75 0.00 46.92 2.10
523 613 2.101582 CGTTGATGTCCTTAGGAGGGAG 59.898 54.545 0.00 0.00 43.72 4.30
528 618 3.006110 ACGAAACGTTGATGTCCTTAGGA 59.994 43.478 0.00 0.00 36.35 2.94
544 635 3.060070 CGACTTGTAGGTTGGAACGAAAC 60.060 47.826 0.00 0.00 0.00 2.78
559 650 1.865865 AGCGTTGTGAATCGACTTGT 58.134 45.000 0.00 0.00 0.00 3.16
576 667 5.884771 AGTTTCTCTCAACTTGTTGAAAGC 58.115 37.500 15.70 10.13 32.81 3.51
588 679 4.087182 ACCGGAGTGATAGTTTCTCTCAA 58.913 43.478 9.46 0.00 43.65 3.02
642 821 0.107703 CGGAGGCTATTTCTGGTGCA 60.108 55.000 0.00 0.00 0.00 4.57
643 822 1.440145 GCGGAGGCTATTTCTGGTGC 61.440 60.000 0.00 0.00 35.83 5.01
644 823 2.695314 GCGGAGGCTATTTCTGGTG 58.305 57.895 0.00 0.00 35.83 4.17
656 835 4.157656 TGAAACTGAAAATAATGGCGGAGG 59.842 41.667 0.00 0.00 0.00 4.30
657 836 5.095490 GTGAAACTGAAAATAATGGCGGAG 58.905 41.667 0.00 0.00 0.00 4.63
658 837 4.378978 CGTGAAACTGAAAATAATGGCGGA 60.379 41.667 0.00 0.00 31.75 5.54
659 838 3.851403 CGTGAAACTGAAAATAATGGCGG 59.149 43.478 0.00 0.00 31.75 6.13
660 839 3.300590 GCGTGAAACTGAAAATAATGGCG 59.699 43.478 0.00 0.00 31.75 5.69
661 840 4.233789 TGCGTGAAACTGAAAATAATGGC 58.766 39.130 0.00 0.00 31.75 4.40
662 841 6.346518 GGTTTGCGTGAAACTGAAAATAATGG 60.347 38.462 10.69 0.00 43.20 3.16
663 842 6.420604 AGGTTTGCGTGAAACTGAAAATAATG 59.579 34.615 10.69 0.00 43.20 1.90
664 843 6.512297 AGGTTTGCGTGAAACTGAAAATAAT 58.488 32.000 10.69 0.00 43.20 1.28
665 844 5.897050 AGGTTTGCGTGAAACTGAAAATAA 58.103 33.333 10.69 0.00 43.20 1.40
666 845 5.508200 AGGTTTGCGTGAAACTGAAAATA 57.492 34.783 10.69 0.00 43.20 1.40
667 846 4.385358 AGGTTTGCGTGAAACTGAAAAT 57.615 36.364 10.69 0.00 43.20 1.82
668 847 3.859411 AGGTTTGCGTGAAACTGAAAA 57.141 38.095 10.69 0.00 43.20 2.29
669 848 4.732355 GCTTAGGTTTGCGTGAAACTGAAA 60.732 41.667 10.69 4.39 43.20 2.69
670 849 3.242936 GCTTAGGTTTGCGTGAAACTGAA 60.243 43.478 10.69 5.97 43.20 3.02
671 850 2.289547 GCTTAGGTTTGCGTGAAACTGA 59.710 45.455 10.69 0.00 43.20 3.41
672 851 2.290641 AGCTTAGGTTTGCGTGAAACTG 59.709 45.455 10.69 3.21 43.20 3.16
673 852 2.572290 AGCTTAGGTTTGCGTGAAACT 58.428 42.857 10.69 4.43 43.20 2.66
674 853 3.349488 AAGCTTAGGTTTGCGTGAAAC 57.651 42.857 0.00 4.20 42.97 2.78
675 854 4.261280 GGTAAAGCTTAGGTTTGCGTGAAA 60.261 41.667 18.21 0.00 36.72 2.69
676 855 3.251487 GGTAAAGCTTAGGTTTGCGTGAA 59.749 43.478 18.21 0.00 36.72 3.18
677 856 2.809696 GGTAAAGCTTAGGTTTGCGTGA 59.190 45.455 18.21 0.00 36.72 4.35
678 857 2.095415 GGGTAAAGCTTAGGTTTGCGTG 60.095 50.000 18.21 0.00 36.72 5.34
679 858 2.156917 GGGTAAAGCTTAGGTTTGCGT 58.843 47.619 18.21 0.00 36.72 5.24
680 859 2.418976 GAGGGTAAAGCTTAGGTTTGCG 59.581 50.000 18.21 0.00 36.72 4.85
681 860 3.418047 TGAGGGTAAAGCTTAGGTTTGC 58.582 45.455 18.21 16.45 34.94 3.68
682 861 4.825085 TGTTGAGGGTAAAGCTTAGGTTTG 59.175 41.667 18.21 0.00 34.94 2.93
683 862 5.056553 TGTTGAGGGTAAAGCTTAGGTTT 57.943 39.130 13.94 13.94 37.09 3.27
684 863 4.717279 TGTTGAGGGTAAAGCTTAGGTT 57.283 40.909 0.00 0.00 0.00 3.50
685 864 4.929146 ATGTTGAGGGTAAAGCTTAGGT 57.071 40.909 0.00 0.00 0.00 3.08
686 865 5.253330 TGAATGTTGAGGGTAAAGCTTAGG 58.747 41.667 0.00 0.00 0.00 2.69
687 866 8.682936 ATATGAATGTTGAGGGTAAAGCTTAG 57.317 34.615 0.00 0.00 0.00 2.18
688 867 9.474313 AAATATGAATGTTGAGGGTAAAGCTTA 57.526 29.630 0.00 0.00 0.00 3.09
689 868 7.961326 AATATGAATGTTGAGGGTAAAGCTT 57.039 32.000 0.00 0.00 0.00 3.74
690 869 7.961326 AAATATGAATGTTGAGGGTAAAGCT 57.039 32.000 0.00 0.00 0.00 3.74
691 870 7.492344 CCAAAATATGAATGTTGAGGGTAAAGC 59.508 37.037 0.00 0.00 32.75 3.51
692 871 7.492344 GCCAAAATATGAATGTTGAGGGTAAAG 59.508 37.037 0.00 0.00 32.75 1.85
693 872 7.180051 AGCCAAAATATGAATGTTGAGGGTAAA 59.820 33.333 0.00 0.00 32.75 2.01
694 873 6.667414 AGCCAAAATATGAATGTTGAGGGTAA 59.333 34.615 0.00 0.00 32.75 2.85
695 874 6.096705 CAGCCAAAATATGAATGTTGAGGGTA 59.903 38.462 0.00 0.00 32.75 3.69
696 875 5.025453 AGCCAAAATATGAATGTTGAGGGT 58.975 37.500 0.00 0.00 32.75 4.34
697 876 5.353938 CAGCCAAAATATGAATGTTGAGGG 58.646 41.667 0.00 0.00 32.75 4.30
698 877 5.127519 TCCAGCCAAAATATGAATGTTGAGG 59.872 40.000 0.00 0.00 32.75 3.86
699 878 6.211587 TCCAGCCAAAATATGAATGTTGAG 57.788 37.500 0.00 0.00 32.75 3.02
700 879 6.602410 TTCCAGCCAAAATATGAATGTTGA 57.398 33.333 0.00 0.00 32.75 3.18
701 880 7.603404 TCTTTTCCAGCCAAAATATGAATGTTG 59.397 33.333 0.00 0.00 31.04 3.33
702 881 7.678837 TCTTTTCCAGCCAAAATATGAATGTT 58.321 30.769 0.00 0.00 0.00 2.71
703 882 7.243604 TCTTTTCCAGCCAAAATATGAATGT 57.756 32.000 0.00 0.00 0.00 2.71
704 883 9.252962 GTATCTTTTCCAGCCAAAATATGAATG 57.747 33.333 0.00 0.00 0.00 2.67
705 884 9.205513 AGTATCTTTTCCAGCCAAAATATGAAT 57.794 29.630 0.00 0.00 0.00 2.57
706 885 8.469200 CAGTATCTTTTCCAGCCAAAATATGAA 58.531 33.333 0.00 0.00 0.00 2.57
707 886 7.416664 GCAGTATCTTTTCCAGCCAAAATATGA 60.417 37.037 0.00 0.00 0.00 2.15
708 887 6.698766 GCAGTATCTTTTCCAGCCAAAATATG 59.301 38.462 0.00 0.00 0.00 1.78
709 888 6.380846 TGCAGTATCTTTTCCAGCCAAAATAT 59.619 34.615 0.00 0.00 0.00 1.28
710 889 5.714333 TGCAGTATCTTTTCCAGCCAAAATA 59.286 36.000 0.00 0.00 0.00 1.40
711 890 4.527816 TGCAGTATCTTTTCCAGCCAAAAT 59.472 37.500 0.00 0.00 0.00 1.82
712 891 3.894427 TGCAGTATCTTTTCCAGCCAAAA 59.106 39.130 0.00 0.00 0.00 2.44
713 892 3.255642 GTGCAGTATCTTTTCCAGCCAAA 59.744 43.478 0.00 0.00 0.00 3.28
714 893 2.819608 GTGCAGTATCTTTTCCAGCCAA 59.180 45.455 0.00 0.00 0.00 4.52
715 894 2.040278 AGTGCAGTATCTTTTCCAGCCA 59.960 45.455 0.00 0.00 0.00 4.75
716 895 2.716217 AGTGCAGTATCTTTTCCAGCC 58.284 47.619 0.00 0.00 0.00 4.85
717 896 3.127721 GGAAGTGCAGTATCTTTTCCAGC 59.872 47.826 0.00 0.00 35.35 4.85
718 897 3.691609 GGGAAGTGCAGTATCTTTTCCAG 59.308 47.826 9.38 0.00 36.63 3.86
719 898 3.330701 AGGGAAGTGCAGTATCTTTTCCA 59.669 43.478 9.38 0.00 36.63 3.53
720 899 3.956744 AGGGAAGTGCAGTATCTTTTCC 58.043 45.455 0.00 0.00 34.69 3.13
721 900 5.003804 TGAAGGGAAGTGCAGTATCTTTTC 58.996 41.667 0.00 4.73 0.00 2.29
722 901 4.762251 GTGAAGGGAAGTGCAGTATCTTTT 59.238 41.667 0.00 0.00 0.00 2.27
723 902 4.042187 AGTGAAGGGAAGTGCAGTATCTTT 59.958 41.667 0.00 0.00 0.00 2.52
724 903 3.584848 AGTGAAGGGAAGTGCAGTATCTT 59.415 43.478 0.00 0.00 0.00 2.40
725 904 3.177228 AGTGAAGGGAAGTGCAGTATCT 58.823 45.455 0.00 0.00 0.00 1.98
726 905 3.055819 TGAGTGAAGGGAAGTGCAGTATC 60.056 47.826 0.00 0.00 0.00 2.24
727 906 2.906389 TGAGTGAAGGGAAGTGCAGTAT 59.094 45.455 0.00 0.00 0.00 2.12
728 907 2.037251 GTGAGTGAAGGGAAGTGCAGTA 59.963 50.000 0.00 0.00 0.00 2.74
729 908 1.131638 TGAGTGAAGGGAAGTGCAGT 58.868 50.000 0.00 0.00 0.00 4.40
732 911 0.108585 TGGTGAGTGAAGGGAAGTGC 59.891 55.000 0.00 0.00 0.00 4.40
794 974 5.493133 TGTACACACCAAGAAATCACAAC 57.507 39.130 0.00 0.00 0.00 3.32
1642 1850 1.798813 GACGAAATCAACGCAACTCCT 59.201 47.619 0.00 0.00 0.00 3.69
1937 2317 2.545537 AGAAGGGTCGTTTCTGAACC 57.454 50.000 0.00 0.00 46.65 3.62
2001 2382 9.197694 ACGCAAATACACATAATTAAAAGCAAA 57.802 25.926 0.00 0.00 0.00 3.68
2002 2383 8.749841 ACGCAAATACACATAATTAAAAGCAA 57.250 26.923 0.00 0.00 0.00 3.91
2032 2413 0.391661 ACGCCACTTGTATGCTGAGG 60.392 55.000 0.00 0.00 0.00 3.86
2227 2931 0.388778 CTGTGCATTGCATTTCGGCA 60.389 50.000 15.49 5.93 41.91 5.69
2228 2932 0.388907 ACTGTGCATTGCATTTCGGC 60.389 50.000 15.49 1.01 41.91 5.54
2277 2981 6.638873 CGCTGATAAGAGTTCAACGATTAGAT 59.361 38.462 0.00 0.00 35.32 1.98
2284 2988 2.607187 ACCGCTGATAAGAGTTCAACG 58.393 47.619 0.00 0.00 33.64 4.10
2358 3062 6.884295 CCACACAGGGACTAAATCTCAAATAA 59.116 38.462 0.00 0.00 36.02 1.40
2359 3063 6.414732 CCACACAGGGACTAAATCTCAAATA 58.585 40.000 0.00 0.00 36.02 1.40
2360 3064 5.256474 CCACACAGGGACTAAATCTCAAAT 58.744 41.667 0.00 0.00 36.02 2.32
2393 3097 0.472471 ACGTGGGAACAGTGGAACAT 59.528 50.000 0.00 0.00 44.46 2.71
2468 3172 5.630121 TGGCTAATTCTCAGAAGGTTTCAA 58.370 37.500 0.00 0.00 0.00 2.69
2469 3173 5.241403 TGGCTAATTCTCAGAAGGTTTCA 57.759 39.130 0.00 0.00 0.00 2.69
2470 3174 6.765915 AATGGCTAATTCTCAGAAGGTTTC 57.234 37.500 0.00 0.00 0.00 2.78
2695 4133 2.807967 TCAAAACCTCTCTGCACAATCG 59.192 45.455 0.00 0.00 0.00 3.34
2840 4278 2.442084 GCAAGCAGCAGCATCAAAC 58.558 52.632 3.17 0.00 45.49 2.93
3098 4583 4.473444 ACATTGAACCCTCAAACAGTGAT 58.527 39.130 0.00 0.00 44.64 3.06
3583 5073 4.004982 GGTTAAGTGGTATGCGGAAGAAA 58.995 43.478 0.00 0.00 0.00 2.52
3622 5112 4.622740 GCTTTGCTGCTTACATTGTAAAGG 59.377 41.667 10.32 1.79 0.00 3.11
3714 5209 7.598493 GCAAGTACTCAGCCAAAATTAAATTCA 59.402 33.333 8.64 0.00 0.00 2.57
3728 5223 6.727824 TCTTTCTTTATGCAAGTACTCAGC 57.272 37.500 12.06 12.06 33.66 4.26
3737 5232 9.691362 GTTTTGGTAGAATCTTTCTTTATGCAA 57.309 29.630 0.00 0.00 41.14 4.08
3741 5236 9.914131 GCTTGTTTTGGTAGAATCTTTCTTTAT 57.086 29.630 0.00 0.00 41.14 1.40
3758 5253 8.506437 TGAGTAATGATACTTCAGCTTGTTTTG 58.494 33.333 0.00 0.00 42.47 2.44
3774 5269 6.662234 CAGCATTATTGGGGATGAGTAATGAT 59.338 38.462 7.40 0.00 35.71 2.45
3799 5294 4.634443 ACCTGCAATAACATTCGTAGGAAC 59.366 41.667 0.00 0.00 35.10 3.62
3859 5356 4.036734 GCTGCGATGAATAGGAAAATGGAA 59.963 41.667 0.00 0.00 0.00 3.53
3983 5480 3.452627 AGTCCGCATCTAATTCCAAGAGT 59.547 43.478 0.00 0.00 0.00 3.24
3998 5495 4.632688 GGTTAGCAACTTATTAAGTCCGCA 59.367 41.667 22.76 12.37 41.91 5.69
4001 5498 7.389607 TCTTGTGGTTAGCAACTTATTAAGTCC 59.610 37.037 9.45 6.23 41.91 3.85
4009 5506 7.759489 ATTTGATCTTGTGGTTAGCAACTTA 57.241 32.000 0.00 0.00 0.00 2.24
4012 5509 5.863935 GGAATTTGATCTTGTGGTTAGCAAC 59.136 40.000 0.00 0.00 0.00 4.17
4244 5741 1.379309 GAGCCGTGTCCTCTCTCCT 60.379 63.158 0.00 0.00 0.00 3.69
4319 5816 6.712179 ACGTAAGAATAGGAGGGAAAGTAG 57.288 41.667 0.00 0.00 43.62 2.57
4403 5900 2.158264 GGGTATACAGGGGTACAGGCTA 60.158 54.545 5.01 0.00 30.94 3.93
4404 5901 1.414099 GGGTATACAGGGGTACAGGCT 60.414 57.143 5.01 0.00 30.94 4.58
4429 5926 1.899437 GAATCCTCACTGGCACCCGA 61.899 60.000 0.00 0.00 35.26 5.14
4492 6027 7.518161 CACGCATTTTGTAGAGACAAGAAATA 58.482 34.615 0.00 0.00 46.11 1.40
4523 6058 7.148590 GCCCTTTTAATTGTAAAATCTGTGCTG 60.149 37.037 0.00 0.00 38.28 4.41
4558 6093 2.257409 AAAGATCAGCCGGCCGATGT 62.257 55.000 29.45 22.78 0.00 3.06
4560 6095 0.394352 AAAAAGATCAGCCGGCCGAT 60.394 50.000 30.73 25.07 0.00 4.18
4585 6122 1.153765 CAAGACAGATGGCTCGCGA 60.154 57.895 9.26 9.26 29.30 5.87
4588 6125 2.959516 TGTTACAAGACAGATGGCTCG 58.040 47.619 0.00 0.00 29.30 5.03
4590 6127 3.073062 ACCTTGTTACAAGACAGATGGCT 59.927 43.478 24.79 0.00 32.33 4.75
4591 6128 3.189287 CACCTTGTTACAAGACAGATGGC 59.811 47.826 24.79 0.00 0.00 4.40
4592 6129 4.389374 ACACCTTGTTACAAGACAGATGG 58.611 43.478 24.79 10.69 0.00 3.51
4593 6130 5.527214 TGAACACCTTGTTACAAGACAGATG 59.473 40.000 24.79 15.88 41.28 2.90
4594 6131 5.680619 TGAACACCTTGTTACAAGACAGAT 58.319 37.500 24.79 9.63 41.28 2.90
4595 6132 5.092554 TGAACACCTTGTTACAAGACAGA 57.907 39.130 24.79 2.64 41.28 3.41
4596 6133 6.201517 CAATGAACACCTTGTTACAAGACAG 58.798 40.000 24.79 15.78 41.28 3.51
4597 6134 5.449862 GCAATGAACACCTTGTTACAAGACA 60.450 40.000 24.79 15.67 41.28 3.41
4598 6135 4.976116 GCAATGAACACCTTGTTACAAGAC 59.024 41.667 24.79 11.41 41.28 3.01
4601 6138 3.628032 TCGCAATGAACACCTTGTTACAA 59.372 39.130 0.00 0.00 41.28 2.41
4603 6140 3.889196 TCGCAATGAACACCTTGTTAC 57.111 42.857 0.00 0.00 41.28 2.50
4604 6141 4.902443 TTTCGCAATGAACACCTTGTTA 57.098 36.364 0.00 0.00 41.28 2.41
4605 6142 3.791973 TTTCGCAATGAACACCTTGTT 57.208 38.095 0.00 0.00 44.37 2.83
4606 6143 5.643379 ATATTTCGCAATGAACACCTTGT 57.357 34.783 0.00 0.00 35.97 3.16
4607 6144 8.131100 AGATAATATTTCGCAATGAACACCTTG 58.869 33.333 0.00 0.00 35.97 3.61
4608 6145 8.225603 AGATAATATTTCGCAATGAACACCTT 57.774 30.769 0.00 0.00 35.97 3.50
4609 6146 7.807977 AGATAATATTTCGCAATGAACACCT 57.192 32.000 0.00 0.00 35.97 4.00
4610 6147 7.915397 ACAAGATAATATTTCGCAATGAACACC 59.085 33.333 0.00 0.00 35.97 4.16
4612 6149 8.892723 AGACAAGATAATATTTCGCAATGAACA 58.107 29.630 0.00 0.00 35.97 3.18
4631 6168 9.507329 AGTCTTATTGCAGAAAATTAGACAAGA 57.493 29.630 14.41 0.00 43.62 3.02
4632 6169 9.766277 GAGTCTTATTGCAGAAAATTAGACAAG 57.234 33.333 14.41 0.00 43.62 3.16
4633 6170 9.507329 AGAGTCTTATTGCAGAAAATTAGACAA 57.493 29.630 14.41 0.00 43.62 3.18
4634 6171 9.507329 AAGAGTCTTATTGCAGAAAATTAGACA 57.493 29.630 14.41 0.00 43.62 3.41
4669 6218 7.285401 TGTTGCAGGAAATTAAAGAAGAGAAGT 59.715 33.333 0.00 0.00 0.00 3.01
4680 6229 2.288518 GGGCGTTGTTGCAGGAAATTAA 60.289 45.455 0.00 0.00 36.28 1.40
4719 6268 6.076981 AGGATGTTGTTGCAAAACTTAGAG 57.923 37.500 18.68 0.00 0.00 2.43
4725 6274 5.678921 GCAATAAGGATGTTGTTGCAAAAC 58.321 37.500 0.00 8.97 43.18 2.43
4762 6311 2.355986 TTAGATGCGGCGGAGGTGT 61.356 57.895 9.78 0.00 0.00 4.16
4764 6313 1.614241 AAGTTAGATGCGGCGGAGGT 61.614 55.000 9.78 0.00 0.00 3.85
4766 6315 0.931005 GAAAGTTAGATGCGGCGGAG 59.069 55.000 9.78 0.00 0.00 4.63
4767 6316 0.535335 AGAAAGTTAGATGCGGCGGA 59.465 50.000 9.78 6.17 0.00 5.54
4768 6317 0.652592 CAGAAAGTTAGATGCGGCGG 59.347 55.000 9.78 0.00 0.00 6.13
4769 6318 0.026803 GCAGAAAGTTAGATGCGGCG 59.973 55.000 0.51 0.51 0.00 6.46
4770 6319 1.086696 TGCAGAAAGTTAGATGCGGC 58.913 50.000 0.00 0.00 41.58 6.53
4771 6320 3.829886 TTTGCAGAAAGTTAGATGCGG 57.170 42.857 0.00 0.00 41.58 5.69
4809 6358 3.181497 GCGACCATAGATGTGTTGCAATT 60.181 43.478 0.59 0.00 37.83 2.32
4810 6359 2.355756 GCGACCATAGATGTGTTGCAAT 59.644 45.455 0.59 0.00 37.83 3.56
4811 6360 1.737236 GCGACCATAGATGTGTTGCAA 59.263 47.619 0.00 0.00 37.83 4.08
4812 6361 1.368641 GCGACCATAGATGTGTTGCA 58.631 50.000 13.91 0.00 37.83 4.08
4816 6365 0.248498 CGACGCGACCATAGATGTGT 60.248 55.000 15.93 0.00 0.00 3.72
4837 6386 0.239347 AAAGATGACTGCGCAAGTGC 59.761 50.000 13.05 1.15 40.07 4.40
4838 6387 1.463034 CGAAAGATGACTGCGCAAGTG 60.463 52.381 13.05 1.71 40.07 3.16
4839 6388 0.792640 CGAAAGATGACTGCGCAAGT 59.207 50.000 13.05 12.11 43.85 3.16
4845 6394 2.286950 TGCAACAACGAAAGATGACTGC 60.287 45.455 0.00 0.00 42.10 4.40
4846 6395 3.607422 TGCAACAACGAAAGATGACTG 57.393 42.857 0.00 0.00 37.33 3.51
4848 6397 5.694674 TTTTTGCAACAACGAAAGATGAC 57.305 34.783 0.00 0.00 37.33 3.06
4873 6448 5.946486 TCTAGCATGTCTCTCTTCCTCATA 58.054 41.667 0.00 0.00 0.00 2.15
4887 6462 1.109920 AGCCGGTCGATCTAGCATGT 61.110 55.000 1.90 0.00 0.00 3.21
4889 6464 0.823769 TCAGCCGGTCGATCTAGCAT 60.824 55.000 1.90 0.00 0.00 3.79
4900 6475 3.209410 GAAATGATTCTGATCAGCCGGT 58.791 45.455 18.36 3.41 45.01 5.28
4901 6476 2.551459 GGAAATGATTCTGATCAGCCGG 59.449 50.000 18.36 0.00 45.01 6.13
4902 6477 2.551459 GGGAAATGATTCTGATCAGCCG 59.449 50.000 18.36 0.00 45.01 5.52
4903 6478 2.889678 GGGGAAATGATTCTGATCAGCC 59.110 50.000 18.36 10.20 45.01 4.85
4917 6492 6.592870 TCAAAACCGTTTTAATTGGGGAAAT 58.407 32.000 8.90 0.00 0.00 2.17
4920 6495 5.609533 TTCAAAACCGTTTTAATTGGGGA 57.390 34.783 8.90 0.00 0.00 4.81
4924 6499 9.631639 GAGTTTGATTCAAAACCGTTTTAATTG 57.368 29.630 13.21 0.00 40.26 2.32
4991 6566 0.033366 ACTTTGGGAAATGGTTGCGC 59.967 50.000 0.00 0.00 0.00 6.09
4992 6567 1.339610 TCACTTTGGGAAATGGTTGCG 59.660 47.619 0.00 0.00 0.00 4.85
5028 6605 0.253044 TATGTGGCCTTCTGACTGCC 59.747 55.000 3.32 9.17 45.56 4.85
5106 6683 9.282247 CACTGCTTTATATTTTCTTGTGATGTC 57.718 33.333 0.00 0.00 0.00 3.06
5126 6703 5.420725 TTGTATCTGTGGTTATCACTGCT 57.579 39.130 0.00 0.00 46.20 4.24
5151 6728 1.212935 AGCGCTCCATTTGACCCTAAT 59.787 47.619 2.64 0.00 0.00 1.73
5176 6753 2.910199 TCTGGCTGATCATTTCGAAGG 58.090 47.619 0.00 0.00 0.00 3.46
5177 6754 6.259608 AGTTATTCTGGCTGATCATTTCGAAG 59.740 38.462 0.00 0.00 0.00 3.79
5194 6771 9.665719 AAAAACCATTGTGTTTTGAGTTATTCT 57.334 25.926 13.28 0.00 45.18 2.40
5197 6774 7.762159 ACGAAAAACCATTGTGTTTTGAGTTAT 59.238 29.630 6.79 2.04 45.18 1.89
5263 6841 4.042062 TGATGGTTTATAGCTATGCCTGCT 59.958 41.667 16.77 5.49 43.79 4.24
5266 7066 6.605119 AGTTTGATGGTTTATAGCTATGCCT 58.395 36.000 16.77 6.13 0.00 4.75
5267 7067 6.486657 TGAGTTTGATGGTTTATAGCTATGCC 59.513 38.462 16.77 14.86 0.00 4.40
5288 7088 7.663081 TCAGAATTTTATGAAGCTGTTCTGAGT 59.337 33.333 9.97 0.00 42.77 3.41
5335 7135 2.349817 CGTGTGTTCATTTGCCTGTCTC 60.350 50.000 0.00 0.00 0.00 3.36
5506 7559 5.694231 TGCCAGCATGATGTTATACATTC 57.306 39.130 10.55 0.00 39.27 2.67


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

AutoCloner maintained by Alex Coulton.