Multiple sequence alignment - TraesCS3B01G522600

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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 TraesCS3B01G522600 chr3B 100.000 5604 0 0 1 5604 765620962 765626565 0.000000e+00 10349
1 TraesCS3B01G522600 chr3B 91.654 3379 224 33 892 4260 765656640 765659970 0.000000e+00 4625
2 TraesCS3B01G522600 chr3B 88.855 2593 264 18 2015 4594 765669691 765672271 0.000000e+00 3164
3 TraesCS3B01G522600 chr3B 86.875 2019 239 23 2603 4604 765928465 765930474 0.000000e+00 2237
4 TraesCS3B01G522600 chr3B 83.817 2101 300 32 2517 4595 765549081 765551163 0.000000e+00 1960
5 TraesCS3B01G522600 chr3B 93.180 1217 76 5 814 2024 765668025 765669240 0.000000e+00 1781
6 TraesCS3B01G522600 chr3B 88.439 1038 114 5 871 1906 765547794 765548827 0.000000e+00 1247
7 TraesCS3B01G522600 chr3B 79.249 1171 197 30 3443 4593 765676751 765677895 0.000000e+00 774
8 TraesCS3B01G522600 chr3B 89.819 609 23 11 1 588 765666735 765667325 0.000000e+00 745
9 TraesCS3B01G522600 chr3B 89.456 607 21 18 1 589 765655246 765655827 0.000000e+00 726
10 TraesCS3B01G522600 chr3B 83.899 795 82 22 4837 5603 765900165 765900941 0.000000e+00 717
11 TraesCS3B01G522600 chr3B 81.448 221 30 4 2308 2526 765548825 765549036 2.680000e-38 171
12 TraesCS3B01G522600 chr3A 89.459 2495 238 20 2135 4612 710937033 710939519 0.000000e+00 3127
13 TraesCS3B01G522600 chr3A 88.933 2259 231 16 2349 4594 711057664 711059916 0.000000e+00 2769
14 TraesCS3B01G522600 chr3A 85.961 1332 153 20 814 2131 710935423 710936734 0.000000e+00 1393
15 TraesCS3B01G522600 chr3A 87.263 1107 123 13 807 1906 710836832 710837927 0.000000e+00 1247
16 TraesCS3B01G522600 chr3A 89.301 916 91 5 1001 1911 711056723 711057636 0.000000e+00 1142
17 TraesCS3B01G522600 chr3A 87.013 154 18 2 8 159 711066491 711066644 7.460000e-39 172
18 TraesCS3B01G522600 chr3D 85.552 3087 331 49 2603 5603 574770149 574767092 0.000000e+00 3123
19 TraesCS3B01G522600 chr3D 85.538 3084 337 50 2603 5603 575488028 575491085 0.000000e+00 3123
20 TraesCS3B01G522600 chr3D 88.329 2005 212 19 2603 4591 575546577 575548575 0.000000e+00 2386
21 TraesCS3B01G522600 chr3D 90.005 1851 163 15 2605 4439 575527368 575529212 0.000000e+00 2374
22 TraesCS3B01G522600 chr3D 87.129 1111 120 16 810 1912 574783035 574781940 0.000000e+00 1238
23 TraesCS3B01G522600 chr3D 85.053 1037 144 7 855 1884 574771381 574770349 0.000000e+00 1046
24 TraesCS3B01G522600 chr3D 85.053 1037 144 7 855 1884 575486796 575487828 0.000000e+00 1046
25 TraesCS3B01G522600 chr3D 88.722 133 14 1 8 139 575559426 575559558 1.620000e-35 161
26 TraesCS3B01G522600 chr3D 79.720 143 23 3 4456 4592 575529304 575529446 1.280000e-16 99
27 TraesCS3B01G522600 chr7B 79.762 504 42 21 4786 5246 709782779 709782293 1.520000e-80 311


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 TraesCS3B01G522600 chr3B 765620962 765626565 5603 False 10349.000000 10349 100.0000 1 5604 1 chr3B.!!$F1 5603
1 TraesCS3B01G522600 chr3B 765655246 765659970 4724 False 2675.500000 4625 90.5550 1 4260 2 chr3B.!!$F6 4259
2 TraesCS3B01G522600 chr3B 765928465 765930474 2009 False 2237.000000 2237 86.8750 2603 4604 1 chr3B.!!$F4 2001
3 TraesCS3B01G522600 chr3B 765666735 765672271 5536 False 1896.666667 3164 90.6180 1 4594 3 chr3B.!!$F7 4593
4 TraesCS3B01G522600 chr3B 765547794 765551163 3369 False 1126.000000 1960 84.5680 871 4595 3 chr3B.!!$F5 3724
5 TraesCS3B01G522600 chr3B 765676751 765677895 1144 False 774.000000 774 79.2490 3443 4593 1 chr3B.!!$F2 1150
6 TraesCS3B01G522600 chr3B 765900165 765900941 776 False 717.000000 717 83.8990 4837 5603 1 chr3B.!!$F3 766
7 TraesCS3B01G522600 chr3A 710935423 710939519 4096 False 2260.000000 3127 87.7100 814 4612 2 chr3A.!!$F3 3798
8 TraesCS3B01G522600 chr3A 711056723 711059916 3193 False 1955.500000 2769 89.1170 1001 4594 2 chr3A.!!$F4 3593
9 TraesCS3B01G522600 chr3A 710836832 710837927 1095 False 1247.000000 1247 87.2630 807 1906 1 chr3A.!!$F1 1099
10 TraesCS3B01G522600 chr3D 575546577 575548575 1998 False 2386.000000 2386 88.3290 2603 4591 1 chr3D.!!$F1 1988
11 TraesCS3B01G522600 chr3D 574767092 574771381 4289 True 2084.500000 3123 85.3025 855 5603 2 chr3D.!!$R2 4748
12 TraesCS3B01G522600 chr3D 575486796 575491085 4289 False 2084.500000 3123 85.2955 855 5603 2 chr3D.!!$F3 4748
13 TraesCS3B01G522600 chr3D 574781940 574783035 1095 True 1238.000000 1238 87.1290 810 1912 1 chr3D.!!$R1 1102
14 TraesCS3B01G522600 chr3D 575527368 575529446 2078 False 1236.500000 2374 84.8625 2605 4592 2 chr3D.!!$F4 1987

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
677 727 0.174162 AGTAAGCCCGATAACGCGTT 59.826 50.0 29.27 29.27 38.29 4.84 F
692 742 0.179145 GCGTTCAGAAGGCTAGCGTA 60.179 55.0 18.67 0.00 39.10 4.42 F
783 847 0.320421 TAGTTGCCGCTCAAGTCACC 60.320 55.0 0.00 0.00 39.06 4.02 F
789 853 0.321564 CCGCTCAAGTCACCAATCCA 60.322 55.0 0.00 0.00 0.00 3.41 F
2762 4376 0.174617 GAAGAGTCCTGGAAGCCGAG 59.825 60.0 0.00 0.00 0.00 4.63 F
4634 6374 0.179124 AAGGTTCGCTCTCATCTCGC 60.179 55.0 0.00 0.00 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1505 2228 2.807967 TCTCGTGTTTCTTCAATGCCTG 59.192 45.455 0.00 0.0 0.00 4.85 R
2454 3988 3.006659 TGCGCATGGTTTTTAACAGTC 57.993 42.857 5.66 0.0 0.00 3.51 R
2762 4376 3.241701 CAATGCGGGTTGTTGTGATTAC 58.758 45.455 0.00 0.0 0.00 1.89 R
3302 4920 4.098349 TCCTTGAACATCAATGCCTATTGC 59.902 41.667 0.00 0.0 42.71 3.56 R
4030 5657 0.099436 GGCAATTGATGAGTCCACGC 59.901 55.000 10.34 0.0 0.00 5.34 R
5443 7229 0.601057 AAACCAATACGGCAACCTGC 59.399 50.000 0.00 0.0 44.08 4.85 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
44 46 2.889617 CGCATGGAGACCGGTGTA 59.110 61.111 14.63 0.00 0.00 2.90
149 155 1.401905 CCCGTCTAATGCTCTTTTGCC 59.598 52.381 0.00 0.00 0.00 4.52
220 226 3.088532 GTGCATGGGAGATTGGTGTAAA 58.911 45.455 0.00 0.00 0.00 2.01
223 229 4.776837 TGCATGGGAGATTGGTGTAAATTT 59.223 37.500 0.00 0.00 0.00 1.82
226 232 7.038729 TGCATGGGAGATTGGTGTAAATTTAAA 60.039 33.333 0.00 0.00 0.00 1.52
229 235 6.211785 TGGGAGATTGGTGTAAATTTAAACCC 59.788 38.462 27.68 16.27 39.81 4.11
437 445 1.073025 ATCGCAAGTGTTGAGGGCA 59.927 52.632 0.00 0.00 39.48 5.36
445 453 1.168714 GTGTTGAGGGCAGACCATTC 58.831 55.000 0.00 0.00 43.89 2.67
465 486 3.253838 TAGCACCAAAGGGCCGGT 61.254 61.111 1.90 0.00 37.90 5.28
625 669 0.235665 GTTGCACACATGGTCTCACG 59.764 55.000 0.00 0.00 0.00 4.35
636 686 1.739562 GTCTCACGGAGCAAGCAGG 60.740 63.158 0.00 0.00 0.00 4.85
641 691 1.376037 ACGGAGCAAGCAGGCTTAC 60.376 57.895 6.16 0.72 45.99 2.34
673 723 5.679734 TTCTAGTAGTAAGCCCGATAACG 57.320 43.478 0.00 0.00 39.43 3.18
676 726 1.024271 TAGTAAGCCCGATAACGCGT 58.976 50.000 5.58 5.58 38.29 6.01
677 727 0.174162 AGTAAGCCCGATAACGCGTT 59.826 50.000 29.27 29.27 38.29 4.84
678 728 0.573987 GTAAGCCCGATAACGCGTTC 59.426 55.000 30.28 14.84 38.29 3.95
680 730 1.082117 AAGCCCGATAACGCGTTCAG 61.082 55.000 30.28 19.61 38.29 3.02
681 731 1.517694 GCCCGATAACGCGTTCAGA 60.518 57.895 30.28 12.19 38.29 3.27
683 733 0.921347 CCCGATAACGCGTTCAGAAG 59.079 55.000 30.28 15.70 38.29 2.85
684 734 0.921347 CCGATAACGCGTTCAGAAGG 59.079 55.000 30.28 20.45 38.29 3.46
685 735 0.297820 CGATAACGCGTTCAGAAGGC 59.702 55.000 30.28 16.46 38.82 4.35
686 736 1.641577 GATAACGCGTTCAGAAGGCT 58.358 50.000 30.28 3.16 39.97 4.58
687 737 2.793585 CGATAACGCGTTCAGAAGGCTA 60.794 50.000 30.28 7.88 39.97 3.93
688 738 2.273370 TAACGCGTTCAGAAGGCTAG 57.727 50.000 30.28 12.26 39.97 3.42
689 739 1.014564 AACGCGTTCAGAAGGCTAGC 61.015 55.000 20.79 6.04 39.97 3.42
690 740 2.508891 CGCGTTCAGAAGGCTAGCG 61.509 63.158 22.22 12.55 39.97 4.26
691 741 1.446272 GCGTTCAGAAGGCTAGCGT 60.446 57.895 18.67 6.32 39.10 5.07
692 742 0.179145 GCGTTCAGAAGGCTAGCGTA 60.179 55.000 18.67 0.00 39.10 4.42
693 743 1.536284 GCGTTCAGAAGGCTAGCGTAT 60.536 52.381 18.67 0.00 39.10 3.06
694 744 2.120232 CGTTCAGAAGGCTAGCGTATG 58.880 52.381 10.88 12.53 0.00 2.39
695 745 2.474816 GTTCAGAAGGCTAGCGTATGG 58.525 52.381 10.88 3.26 0.00 2.74
696 746 2.067365 TCAGAAGGCTAGCGTATGGA 57.933 50.000 10.88 5.62 0.00 3.41
697 747 1.957177 TCAGAAGGCTAGCGTATGGAG 59.043 52.381 10.88 0.12 0.00 3.86
698 748 1.957177 CAGAAGGCTAGCGTATGGAGA 59.043 52.381 10.88 0.00 0.00 3.71
699 749 2.560542 CAGAAGGCTAGCGTATGGAGAT 59.439 50.000 10.88 0.00 0.00 2.75
700 750 3.006323 CAGAAGGCTAGCGTATGGAGATT 59.994 47.826 10.88 0.00 0.00 2.40
701 751 3.006323 AGAAGGCTAGCGTATGGAGATTG 59.994 47.826 10.88 0.00 0.00 2.67
702 752 2.598565 AGGCTAGCGTATGGAGATTGA 58.401 47.619 8.45 0.00 0.00 2.57
703 753 3.169099 AGGCTAGCGTATGGAGATTGAT 58.831 45.455 8.45 0.00 0.00 2.57
704 754 3.580458 AGGCTAGCGTATGGAGATTGATT 59.420 43.478 8.45 0.00 0.00 2.57
705 755 4.040952 AGGCTAGCGTATGGAGATTGATTT 59.959 41.667 8.45 0.00 0.00 2.17
706 756 5.246203 AGGCTAGCGTATGGAGATTGATTTA 59.754 40.000 8.45 0.00 0.00 1.40
707 757 6.070538 AGGCTAGCGTATGGAGATTGATTTAT 60.071 38.462 8.45 0.00 0.00 1.40
708 758 7.124298 AGGCTAGCGTATGGAGATTGATTTATA 59.876 37.037 8.45 0.00 0.00 0.98
709 759 7.222999 GGCTAGCGTATGGAGATTGATTTATAC 59.777 40.741 9.00 0.00 0.00 1.47
710 760 7.759886 GCTAGCGTATGGAGATTGATTTATACA 59.240 37.037 0.00 0.00 0.00 2.29
718 768 8.593492 TGGAGATTGATTTATACAAGACATCG 57.407 34.615 0.00 0.00 0.00 3.84
734 784 2.291282 ACATCGGAGTTATTGGCCCAAA 60.291 45.455 0.00 0.00 0.00 3.28
735 785 2.588464 TCGGAGTTATTGGCCCAAAA 57.412 45.000 0.00 0.00 0.00 2.44
736 786 2.877866 TCGGAGTTATTGGCCCAAAAA 58.122 42.857 0.00 0.00 0.00 1.94
737 787 3.436243 TCGGAGTTATTGGCCCAAAAAT 58.564 40.909 0.00 0.00 0.00 1.82
738 788 3.194542 TCGGAGTTATTGGCCCAAAAATG 59.805 43.478 0.00 0.00 0.00 2.32
739 789 3.194542 CGGAGTTATTGGCCCAAAAATGA 59.805 43.478 0.00 0.00 0.00 2.57
740 790 4.141959 CGGAGTTATTGGCCCAAAAATGAT 60.142 41.667 0.00 0.00 0.00 2.45
741 791 5.118286 GGAGTTATTGGCCCAAAAATGATG 58.882 41.667 0.00 0.00 0.00 3.07
742 792 4.516323 AGTTATTGGCCCAAAAATGATGC 58.484 39.130 0.00 0.00 0.00 3.91
743 793 4.019501 AGTTATTGGCCCAAAAATGATGCA 60.020 37.500 0.00 0.00 0.00 3.96
744 794 2.945080 TTGGCCCAAAAATGATGCAA 57.055 40.000 0.00 0.00 0.00 4.08
753 803 4.689812 CCAAAAATGATGCAACGATTTCCA 59.310 37.500 0.00 0.00 0.00 3.53
776 840 2.443260 TTTCCGCTAGTTGCCGCTCA 62.443 55.000 0.00 0.00 38.78 4.26
777 841 2.434185 CCGCTAGTTGCCGCTCAA 60.434 61.111 0.00 0.00 38.78 3.02
778 842 2.456119 CCGCTAGTTGCCGCTCAAG 61.456 63.158 0.00 0.00 38.78 3.02
780 844 1.687494 CGCTAGTTGCCGCTCAAGTC 61.687 60.000 0.00 0.00 39.06 3.01
782 846 1.071605 CTAGTTGCCGCTCAAGTCAC 58.928 55.000 0.00 0.00 39.06 3.67
783 847 0.320421 TAGTTGCCGCTCAAGTCACC 60.320 55.000 0.00 0.00 39.06 4.02
784 848 1.891919 GTTGCCGCTCAAGTCACCA 60.892 57.895 0.00 0.00 34.91 4.17
787 851 0.955428 TGCCGCTCAAGTCACCAATC 60.955 55.000 0.00 0.00 0.00 2.67
789 853 0.321564 CCGCTCAAGTCACCAATCCA 60.322 55.000 0.00 0.00 0.00 3.41
790 854 1.081892 CGCTCAAGTCACCAATCCAG 58.918 55.000 0.00 0.00 0.00 3.86
791 855 1.457346 GCTCAAGTCACCAATCCAGG 58.543 55.000 0.00 0.00 0.00 4.45
793 857 1.630369 CTCAAGTCACCAATCCAGGGA 59.370 52.381 0.00 0.00 0.00 4.20
794 858 2.040278 CTCAAGTCACCAATCCAGGGAA 59.960 50.000 0.00 0.00 0.00 3.97
797 861 2.065799 AGTCACCAATCCAGGGAAGTT 58.934 47.619 0.00 0.00 0.00 2.66
799 863 3.009143 AGTCACCAATCCAGGGAAGTTAC 59.991 47.826 0.00 0.00 0.00 2.50
803 867 3.007635 CCAATCCAGGGAAGTTACGTTC 58.992 50.000 0.00 0.00 0.00 3.95
804 868 3.307480 CCAATCCAGGGAAGTTACGTTCT 60.307 47.826 0.00 0.00 0.00 3.01
807 871 3.170717 TCCAGGGAAGTTACGTTCTCAT 58.829 45.455 0.00 0.00 28.20 2.90
808 872 3.581332 TCCAGGGAAGTTACGTTCTCATT 59.419 43.478 0.00 0.00 28.20 2.57
809 873 4.773674 TCCAGGGAAGTTACGTTCTCATTA 59.226 41.667 0.00 0.00 28.20 1.90
810 874 5.246656 TCCAGGGAAGTTACGTTCTCATTAA 59.753 40.000 0.00 0.00 28.20 1.40
811 875 5.350640 CCAGGGAAGTTACGTTCTCATTAAC 59.649 44.000 0.00 0.00 28.20 2.01
812 876 5.929992 CAGGGAAGTTACGTTCTCATTAACA 59.070 40.000 0.00 0.00 28.20 2.41
844 1377 1.141657 ACCCAATCCCAGATCGTCATG 59.858 52.381 0.00 0.00 0.00 3.07
863 1396 9.502145 TCGTCATGAAATTTGTAAGAATTATGC 57.498 29.630 0.00 0.00 30.46 3.14
878 1411 1.836999 TATGCACTCCCCAACGCTGT 61.837 55.000 0.00 0.00 0.00 4.40
908 1628 2.696187 CCTGGCTAGTTTCTCCTCTACC 59.304 54.545 0.00 0.00 0.00 3.18
1093 1816 3.830744 TGGAGAAACGAGTGAGGAAAA 57.169 42.857 0.00 0.00 0.00 2.29
1386 2109 2.037772 TGCTCTGGAAGAAGTGGTTCTC 59.962 50.000 0.00 0.00 46.34 2.87
1398 2121 2.106511 AGTGGTTCTCCAAGCTAAGCAA 59.893 45.455 0.00 0.00 46.15 3.91
1443 2166 3.631453 GCAAGGGATGCGATATCCA 57.369 52.632 17.55 0.00 46.87 3.41
1505 2228 1.723542 CACAGATGTGTCAGAACTCGC 59.276 52.381 4.77 0.00 40.96 5.03
1560 2283 4.717877 ACATGTTGACTGAAGGTGATGAA 58.282 39.130 0.00 0.00 0.00 2.57
1821 2544 8.696043 ATGAAATCATCGAATTCCTTAATGGA 57.304 30.769 0.00 0.00 35.80 3.41
1862 2619 8.736751 TTTTTCGTTTACAAAGCAGATTATCC 57.263 30.769 0.00 0.00 0.00 2.59
1863 2620 7.681939 TTTCGTTTACAAAGCAGATTATCCT 57.318 32.000 0.00 0.00 0.00 3.24
1864 2621 7.681939 TTCGTTTACAAAGCAGATTATCCTT 57.318 32.000 0.00 0.00 0.00 3.36
1865 2622 7.681939 TCGTTTACAAAGCAGATTATCCTTT 57.318 32.000 0.00 0.00 0.00 3.11
1866 2623 8.106247 TCGTTTACAAAGCAGATTATCCTTTT 57.894 30.769 0.00 0.00 0.00 2.27
1867 2624 8.020819 TCGTTTACAAAGCAGATTATCCTTTTG 58.979 33.333 10.19 10.19 0.00 2.44
1868 2625 7.807907 CGTTTACAAAGCAGATTATCCTTTTGT 59.192 33.333 17.14 17.14 0.00 2.83
2162 3689 1.732259 CCAGAATACCACACAAGTCGC 59.268 52.381 0.00 0.00 0.00 5.19
2218 3745 7.439056 ACATTAGACAATGGTTGCTTTGAAAAG 59.561 33.333 0.00 0.00 44.97 2.27
2364 3895 9.410556 CTGTTTTATCCTTTTGGTGTAAATGAG 57.589 33.333 0.00 0.00 41.38 2.90
2454 3988 2.561733 TGCCTAAGTGAACGATCTCG 57.438 50.000 0.00 0.00 46.33 4.04
2557 4148 4.811024 GTCTCAGAATATGCAATTCGGTCA 59.189 41.667 15.50 6.53 33.51 4.02
2688 4302 9.941325 TTGTAAATAAAGGTACCTCGTCATAAA 57.059 29.630 16.64 1.72 0.00 1.40
2762 4376 0.174617 GAAGAGTCCTGGAAGCCGAG 59.825 60.000 0.00 0.00 0.00 4.63
3302 4920 9.030452 AGCTAGTAAATAGAAGTATGATCCAGG 57.970 37.037 0.00 0.00 32.76 4.45
3463 5081 2.839486 TCAAGGTTCGCAGATTGTCT 57.161 45.000 0.00 0.00 35.04 3.41
3540 5158 6.012658 TCTTACCATTTTCACAAGTGATGC 57.987 37.500 3.43 0.00 39.64 3.91
3542 5160 6.939730 TCTTACCATTTTCACAAGTGATGCTA 59.060 34.615 3.43 0.00 39.64 3.49
3578 5196 9.883142 TGTTGGATATTTCAAGTTTTCAAGTTT 57.117 25.926 0.00 0.00 0.00 2.66
3602 5220 3.255725 CGCGTGTTGGATTTAGAAGGTA 58.744 45.455 0.00 0.00 0.00 3.08
3630 5251 3.197766 GTCTCAGATGTTGGGTATGTGGA 59.802 47.826 0.00 0.00 0.00 4.02
3689 5310 2.236395 ACTCATGTTAAGGACCTTCCCG 59.764 50.000 10.87 0.00 37.19 5.14
3746 5367 8.145122 CCTTGGACTTGAGAGGTTCTAATATAC 58.855 40.741 0.00 0.00 0.00 1.47
3760 5381 8.368668 GGTTCTAATATACAAGTACTGCCATCT 58.631 37.037 0.00 0.00 0.00 2.90
3786 5407 3.284323 TGTTCAGCTAAGACGTCTGAC 57.716 47.619 20.85 11.62 36.67 3.51
3800 5421 2.414957 CGTCTGACGTGCCTGTATGTTA 60.415 50.000 21.30 0.00 36.74 2.41
3836 5457 3.181450 GCTGCCATCTGGAATAGGTAACT 60.181 47.826 0.00 0.00 45.27 2.24
3934 5555 1.374190 CAAGCTCAGGGTGCTCAGT 59.626 57.895 0.00 0.00 40.22 3.41
3952 5573 3.928992 TCAGTCTTGAGTGCGATGATTTC 59.071 43.478 0.84 0.00 0.00 2.17
4030 5657 8.950208 TGGATAGTCTAGATGTATATGTCTCG 57.050 38.462 0.00 0.00 0.00 4.04
4032 5659 5.788055 AGTCTAGATGTATATGTCTCGCG 57.212 43.478 0.00 0.00 0.00 5.87
4081 5708 1.456287 GGTGCCTCCTCCACAACTT 59.544 57.895 0.00 0.00 34.94 2.66
4090 5717 4.401519 CCTCCTCCACAACTTCGTAGATTA 59.598 45.833 0.00 0.00 35.04 1.75
4092 5719 5.014858 TCCTCCACAACTTCGTAGATTAGT 58.985 41.667 0.00 0.00 35.04 2.24
4245 5872 2.225467 GCCTGCTCTTTGTGTTCTCTT 58.775 47.619 0.00 0.00 0.00 2.85
4262 5889 5.677319 TCTCTTGGTGACGGATAATTCTT 57.323 39.130 0.00 0.00 0.00 2.52
4276 5909 6.292150 GGATAATTCTTTGTTCCGAGGAGAT 58.708 40.000 0.00 0.00 0.00 2.75
4307 5940 0.678048 AATGCCCGTGCTTTCCTCTC 60.678 55.000 0.00 0.00 38.71 3.20
4327 5960 1.601162 CGTGCTGCATTATTCCCATGC 60.601 52.381 5.27 0.00 46.25 4.06
4353 5986 3.619929 ACAGTGTGTCGTTTCTTTGGTAC 59.380 43.478 0.00 0.00 0.00 3.34
4355 5988 4.025979 CAGTGTGTCGTTTCTTTGGTACTC 60.026 45.833 0.00 0.00 0.00 2.59
4360 5993 2.132762 CGTTTCTTTGGTACTCGTGCT 58.867 47.619 0.00 0.00 0.00 4.40
4415 6048 5.946377 CCAAGGCTTAAACATCTTAGGTTCT 59.054 40.000 0.00 0.00 0.00 3.01
4454 6162 4.035675 GGATCTCCCGTGAAAACATTGATC 59.964 45.833 0.00 0.00 0.00 2.92
4596 6317 0.324943 AACCATCCCGTCCTTGACAG 59.675 55.000 0.00 0.00 32.09 3.51
4598 6319 1.450312 CATCCCGTCCTTGACAGCC 60.450 63.158 0.00 0.00 32.09 4.85
4604 6325 1.070786 GTCCTTGACAGCCGGTGAA 59.929 57.895 1.90 0.00 32.09 3.18
4626 6366 1.517242 CTGCAGAAAAGGTTCGCTCT 58.483 50.000 8.42 0.00 38.90 4.09
4634 6374 0.179124 AAGGTTCGCTCTCATCTCGC 60.179 55.000 0.00 0.00 0.00 5.03
4638 6378 1.604147 TTCGCTCTCATCTCGCCCAA 61.604 55.000 0.00 0.00 0.00 4.12
4663 6403 4.174009 CTGGGCTATGTATATTCGTTCCG 58.826 47.826 0.00 0.00 0.00 4.30
4664 6404 3.827876 TGGGCTATGTATATTCGTTCCGA 59.172 43.478 0.00 0.00 0.00 4.55
4675 6415 6.753107 ATATTCGTTCCGATTCCTTTGTTT 57.247 33.333 0.00 0.00 35.23 2.83
4677 6417 4.217754 TCGTTCCGATTCCTTTGTTTTG 57.782 40.909 0.00 0.00 0.00 2.44
4680 6420 4.496673 CGTTCCGATTCCTTTGTTTTGTCA 60.497 41.667 0.00 0.00 0.00 3.58
4699 6439 7.581213 TTGTCAACAAGGTTCAGTATTCATT 57.419 32.000 0.00 0.00 0.00 2.57
4700 6440 7.581213 TGTCAACAAGGTTCAGTATTCATTT 57.419 32.000 0.00 0.00 0.00 2.32
4711 6451 8.029522 GGTTCAGTATTCATTTTTCCTTCTTCC 58.970 37.037 0.00 0.00 0.00 3.46
4712 6452 8.797438 GTTCAGTATTCATTTTTCCTTCTTCCT 58.203 33.333 0.00 0.00 0.00 3.36
4727 6467 5.755375 CCTTCTTCCTTTTTCCTTTTTCAGC 59.245 40.000 0.00 0.00 0.00 4.26
4728 6468 5.930837 TCTTCCTTTTTCCTTTTTCAGCA 57.069 34.783 0.00 0.00 0.00 4.41
4729 6469 5.906073 TCTTCCTTTTTCCTTTTTCAGCAG 58.094 37.500 0.00 0.00 0.00 4.24
4738 6478 2.586425 CTTTTTCAGCAGGTGGAGGAA 58.414 47.619 0.00 0.00 0.00 3.36
4744 6484 1.377856 GCAGGTGGAGGAAGGCTTC 60.378 63.158 18.98 18.98 0.00 3.86
4762 6502 9.294614 GAAGGCTTCATTAATCAGATCCTTTAT 57.705 33.333 21.99 0.00 31.52 1.40
4773 6513 7.805083 ATCAGATCCTTTATGCAGGTACTAT 57.195 36.000 0.00 0.00 36.02 2.12
4775 6515 7.671302 TCAGATCCTTTATGCAGGTACTATTC 58.329 38.462 0.00 0.00 36.02 1.75
4776 6516 7.510685 TCAGATCCTTTATGCAGGTACTATTCT 59.489 37.037 0.00 0.00 36.02 2.40
4777 6517 8.153550 CAGATCCTTTATGCAGGTACTATTCTT 58.846 37.037 0.00 0.00 36.02 2.52
4784 6525 9.851686 TTTATGCAGGTACTATTCTTTCATCAT 57.148 29.630 0.00 0.00 36.02 2.45
4808 6549 7.775397 TTTAATTACTAGCGCCGAACTATTT 57.225 32.000 2.29 0.00 0.00 1.40
4831 6572 4.621068 TTCATCATTTCTTTAGCCTGCG 57.379 40.909 0.00 0.00 0.00 5.18
4833 6574 3.374988 TCATCATTTCTTTAGCCTGCGTG 59.625 43.478 0.00 0.00 0.00 5.34
4912 6654 0.099436 GATGTGAATTCCGCTGTGGC 59.901 55.000 1.39 0.00 37.80 5.01
4922 6664 0.461870 CCGCTGTGGCTAGTTATGCA 60.462 55.000 0.00 0.00 36.09 3.96
4925 6667 1.745141 GCTGTGGCTAGTTATGCAGCT 60.745 52.381 14.76 0.00 43.94 4.24
4929 6671 4.191544 TGTGGCTAGTTATGCAGCTAAAG 58.808 43.478 0.00 0.00 37.91 1.85
4946 6692 6.309251 CAGCTAAAGTACTAGCAGAAGTGTTC 59.691 42.308 17.76 0.00 45.69 3.18
4976 6722 4.471373 TGCATGCTACAAAATTACACGTG 58.529 39.130 20.33 15.48 0.00 4.49
5057 6824 4.630644 TGGATGAACTCTGCTTTCTTCT 57.369 40.909 0.00 0.00 31.16 2.85
5064 6831 5.882557 TGAACTCTGCTTTCTTCTTTTCTGT 59.117 36.000 0.00 0.00 0.00 3.41
5085 6852 8.389779 TCTGTAACATTGAACTGAAGCATTTA 57.610 30.769 0.00 0.00 0.00 1.40
5086 6853 9.013229 TCTGTAACATTGAACTGAAGCATTTAT 57.987 29.630 0.00 0.00 0.00 1.40
5118 6885 2.228545 TCCAAATGGCATTGCAGGTA 57.771 45.000 14.47 4.53 34.44 3.08
5143 6910 3.304911 AGTAGGAGCTAGCAGATGTCA 57.695 47.619 18.83 0.00 0.00 3.58
5145 6912 4.222336 AGTAGGAGCTAGCAGATGTCATT 58.778 43.478 18.83 0.43 0.00 2.57
5171 6957 0.765510 ACACTCCAACAACTCCTCCC 59.234 55.000 0.00 0.00 0.00 4.30
5172 6958 0.320771 CACTCCAACAACTCCTCCCG 60.321 60.000 0.00 0.00 0.00 5.14
5173 6959 0.763223 ACTCCAACAACTCCTCCCGT 60.763 55.000 0.00 0.00 0.00 5.28
5174 6960 0.320771 CTCCAACAACTCCTCCCGTG 60.321 60.000 0.00 0.00 0.00 4.94
5199 6985 4.874966 GTGCTCTGCTATTTGATCTGTCTT 59.125 41.667 0.00 0.00 0.00 3.01
5212 6998 0.179089 CTGTCTTCCCTCTGCATCCG 60.179 60.000 0.00 0.00 0.00 4.18
5213 6999 0.614697 TGTCTTCCCTCTGCATCCGA 60.615 55.000 0.00 0.00 0.00 4.55
5226 7012 1.811941 GCATCCGAATGAACCTCCTCC 60.812 57.143 0.00 0.00 34.61 4.30
5257 7043 7.066766 GTCTGCTTATGTTTGGATTCTCTTCAT 59.933 37.037 0.00 0.00 0.00 2.57
5334 7120 4.084013 CGCCCTCGATGAACCATTAATTAC 60.084 45.833 0.00 0.00 38.10 1.89
5370 7156 2.228103 CTGCTTTGCTTGCTCTCATTCA 59.772 45.455 0.00 0.00 0.00 2.57
5371 7157 2.823747 TGCTTTGCTTGCTCTCATTCAT 59.176 40.909 0.00 0.00 0.00 2.57
5372 7158 3.257375 TGCTTTGCTTGCTCTCATTCATT 59.743 39.130 0.00 0.00 0.00 2.57
5373 7159 3.858238 GCTTTGCTTGCTCTCATTCATTC 59.142 43.478 0.00 0.00 0.00 2.67
5374 7160 4.380655 GCTTTGCTTGCTCTCATTCATTCT 60.381 41.667 0.00 0.00 0.00 2.40
5375 7161 4.696899 TTGCTTGCTCTCATTCATTCTG 57.303 40.909 0.00 0.00 0.00 3.02
5376 7162 3.946606 TGCTTGCTCTCATTCATTCTGA 58.053 40.909 0.00 0.00 0.00 3.27
5381 7167 6.625300 GCTTGCTCTCATTCATTCTGAATTGT 60.625 38.462 0.00 0.00 44.03 2.71
5383 7169 8.515695 TTGCTCTCATTCATTCTGAATTGTAT 57.484 30.769 0.00 0.00 44.03 2.29
5403 7189 1.979855 TGCTTTGTTTGGAGCAGCTA 58.020 45.000 0.00 0.00 43.46 3.32
5436 7222 6.071560 TGTTCCAGACTCGTAAACTATGATGT 60.072 38.462 0.00 0.00 0.00 3.06
5443 7229 4.426416 TCGTAAACTATGATGTTCCGGTG 58.574 43.478 0.00 0.00 0.00 4.94
5447 7233 1.134401 ACTATGATGTTCCGGTGCAGG 60.134 52.381 0.00 0.00 0.00 4.85
5517 7303 6.237901 ACATCTTTGTATTGCAGTGGAACTA 58.762 36.000 0.00 0.00 39.07 2.24
5532 7318 5.563842 GTGGAACTAGAATTTGAATCGCTG 58.436 41.667 0.00 0.00 0.00 5.18
5544 7331 3.855858 TGAATCGCTGTTGCATACTACA 58.144 40.909 0.00 0.00 39.64 2.74
5550 7337 2.679837 GCTGTTGCATACTACATGTGCT 59.320 45.455 9.11 0.00 45.30 4.40
5555 7342 3.855858 TGCATACTACATGTGCTTTCGA 58.144 40.909 9.11 0.00 45.30 3.71
5569 7361 4.740695 GTGCTTTCGATGTCATCTAGTACC 59.259 45.833 11.04 0.00 0.00 3.34
5570 7362 4.401202 TGCTTTCGATGTCATCTAGTACCA 59.599 41.667 11.04 0.00 0.00 3.25
5589 7381 4.729868 ACCATGTAAGATTATTGGCCCTC 58.270 43.478 0.00 0.00 0.00 4.30
5603 7395 0.458669 GCCCTCAACTGATGCAATGG 59.541 55.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 46 3.190535 GTGACCGGTTAAATTGCATCACT 59.809 43.478 9.42 0.00 33.92 3.41
149 155 8.527567 AAAGAACGAGAGAGATTAAAAGTGAG 57.472 34.615 0.00 0.00 0.00 3.51
220 226 1.431496 CCGTGTCGTCGGGTTTAAAT 58.569 50.000 8.13 0.00 45.88 1.40
266 272 2.108566 CTCGCAGGCCTCAGATGG 59.891 66.667 0.00 0.00 0.00 3.51
437 445 0.613260 TTGGTGCTAGCGAATGGTCT 59.387 50.000 10.77 0.00 0.00 3.85
445 453 3.134127 GGCCCTTTGGTGCTAGCG 61.134 66.667 10.77 0.00 0.00 4.26
588 613 7.526608 TGTGCAACAGCAAACTAATACTTATC 58.473 34.615 0.00 0.00 45.67 1.75
590 615 6.869315 TGTGCAACAGCAAACTAATACTTA 57.131 33.333 0.00 0.00 45.67 2.24
591 616 5.766150 TGTGCAACAGCAAACTAATACTT 57.234 34.783 0.00 0.00 45.67 2.24
653 703 3.666374 CGCGTTATCGGGCTTACTACTAG 60.666 52.174 0.00 0.00 42.43 2.57
654 704 2.224079 CGCGTTATCGGGCTTACTACTA 59.776 50.000 0.00 0.00 42.43 1.82
655 705 1.002033 CGCGTTATCGGGCTTACTACT 60.002 52.381 0.00 0.00 42.43 2.57
656 706 1.402511 CGCGTTATCGGGCTTACTAC 58.597 55.000 0.00 0.00 42.43 2.73
658 708 4.724022 CGCGTTATCGGGCTTACT 57.276 55.556 0.00 0.00 42.43 2.24
666 716 0.297820 GCCTTCTGAACGCGTTATCG 59.702 55.000 26.68 15.73 40.37 2.92
667 717 1.641577 AGCCTTCTGAACGCGTTATC 58.358 50.000 26.68 14.70 0.00 1.75
668 718 2.810650 CTAGCCTTCTGAACGCGTTAT 58.189 47.619 26.68 2.95 0.00 1.89
670 720 1.014564 GCTAGCCTTCTGAACGCGTT 61.015 55.000 26.97 26.97 0.00 4.84
671 721 1.446272 GCTAGCCTTCTGAACGCGT 60.446 57.895 5.58 5.58 0.00 6.01
672 722 2.508891 CGCTAGCCTTCTGAACGCG 61.509 63.158 9.66 3.53 0.00 6.01
673 723 0.179145 TACGCTAGCCTTCTGAACGC 60.179 55.000 9.66 3.58 0.00 4.84
676 726 2.362397 CTCCATACGCTAGCCTTCTGAA 59.638 50.000 9.66 0.00 0.00 3.02
677 727 1.957177 CTCCATACGCTAGCCTTCTGA 59.043 52.381 9.66 0.00 0.00 3.27
678 728 1.957177 TCTCCATACGCTAGCCTTCTG 59.043 52.381 9.66 1.79 0.00 3.02
680 730 3.005897 TCAATCTCCATACGCTAGCCTTC 59.994 47.826 9.66 0.00 0.00 3.46
681 731 2.965831 TCAATCTCCATACGCTAGCCTT 59.034 45.455 9.66 0.00 0.00 4.35
683 733 3.601443 ATCAATCTCCATACGCTAGCC 57.399 47.619 9.66 0.00 0.00 3.93
684 734 7.759886 TGTATAAATCAATCTCCATACGCTAGC 59.240 37.037 4.06 4.06 0.00 3.42
685 735 9.639601 TTGTATAAATCAATCTCCATACGCTAG 57.360 33.333 0.00 0.00 0.00 3.42
686 736 9.639601 CTTGTATAAATCAATCTCCATACGCTA 57.360 33.333 0.00 0.00 0.00 4.26
687 737 8.367911 TCTTGTATAAATCAATCTCCATACGCT 58.632 33.333 0.00 0.00 0.00 5.07
688 738 8.436200 GTCTTGTATAAATCAATCTCCATACGC 58.564 37.037 0.00 0.00 0.00 4.42
689 739 9.476202 TGTCTTGTATAAATCAATCTCCATACG 57.524 33.333 0.00 0.00 0.00 3.06
692 742 9.212641 CGATGTCTTGTATAAATCAATCTCCAT 57.787 33.333 0.00 0.00 0.00 3.41
693 743 7.657354 CCGATGTCTTGTATAAATCAATCTCCA 59.343 37.037 0.00 0.00 0.00 3.86
694 744 7.872993 TCCGATGTCTTGTATAAATCAATCTCC 59.127 37.037 0.00 0.00 0.00 3.71
695 745 8.818141 TCCGATGTCTTGTATAAATCAATCTC 57.182 34.615 0.00 0.00 0.00 2.75
696 746 8.424918 ACTCCGATGTCTTGTATAAATCAATCT 58.575 33.333 0.00 0.00 0.00 2.40
697 747 8.594881 ACTCCGATGTCTTGTATAAATCAATC 57.405 34.615 0.00 0.00 0.00 2.67
698 748 8.964476 AACTCCGATGTCTTGTATAAATCAAT 57.036 30.769 0.00 0.00 0.00 2.57
702 752 9.273016 CCAATAACTCCGATGTCTTGTATAAAT 57.727 33.333 0.00 0.00 0.00 1.40
703 753 7.225931 GCCAATAACTCCGATGTCTTGTATAAA 59.774 37.037 0.00 0.00 0.00 1.40
704 754 6.704493 GCCAATAACTCCGATGTCTTGTATAA 59.296 38.462 0.00 0.00 0.00 0.98
705 755 6.220930 GCCAATAACTCCGATGTCTTGTATA 58.779 40.000 0.00 0.00 0.00 1.47
706 756 5.057149 GCCAATAACTCCGATGTCTTGTAT 58.943 41.667 0.00 0.00 0.00 2.29
707 757 4.439057 GCCAATAACTCCGATGTCTTGTA 58.561 43.478 0.00 0.00 0.00 2.41
708 758 3.270877 GCCAATAACTCCGATGTCTTGT 58.729 45.455 0.00 0.00 0.00 3.16
709 759 2.614057 GGCCAATAACTCCGATGTCTTG 59.386 50.000 0.00 0.00 0.00 3.02
710 760 2.421529 GGGCCAATAACTCCGATGTCTT 60.422 50.000 4.39 0.00 0.00 3.01
718 768 4.817318 TCATTTTTGGGCCAATAACTCC 57.183 40.909 21.65 0.00 0.00 3.85
734 784 4.460382 ACTCTGGAAATCGTTGCATCATTT 59.540 37.500 0.00 0.00 34.22 2.32
735 785 4.012374 ACTCTGGAAATCGTTGCATCATT 58.988 39.130 0.00 0.00 34.22 2.57
736 786 3.614092 ACTCTGGAAATCGTTGCATCAT 58.386 40.909 0.00 0.00 34.22 2.45
737 787 3.057969 ACTCTGGAAATCGTTGCATCA 57.942 42.857 0.00 0.00 34.22 3.07
738 788 4.406943 GAAACTCTGGAAATCGTTGCATC 58.593 43.478 0.00 0.00 34.22 3.91
739 789 3.191371 GGAAACTCTGGAAATCGTTGCAT 59.809 43.478 0.00 0.00 34.22 3.96
740 790 2.552315 GGAAACTCTGGAAATCGTTGCA 59.448 45.455 0.00 0.00 33.54 4.08
741 791 2.412847 CGGAAACTCTGGAAATCGTTGC 60.413 50.000 0.00 0.00 0.00 4.17
742 792 2.412847 GCGGAAACTCTGGAAATCGTTG 60.413 50.000 0.00 0.00 0.00 4.10
743 793 1.804748 GCGGAAACTCTGGAAATCGTT 59.195 47.619 0.00 0.00 0.00 3.85
744 794 1.002087 AGCGGAAACTCTGGAAATCGT 59.998 47.619 0.00 0.00 0.00 3.73
776 840 2.065799 ACTTCCCTGGATTGGTGACTT 58.934 47.619 0.00 0.00 0.00 3.01
777 841 1.747444 ACTTCCCTGGATTGGTGACT 58.253 50.000 0.00 0.00 0.00 3.41
778 842 2.586648 AACTTCCCTGGATTGGTGAC 57.413 50.000 0.00 0.00 0.00 3.67
780 844 2.290071 ACGTAACTTCCCTGGATTGGTG 60.290 50.000 0.00 0.00 0.00 4.17
782 846 2.781681 ACGTAACTTCCCTGGATTGG 57.218 50.000 0.00 0.00 0.00 3.16
783 847 3.933332 GAGAACGTAACTTCCCTGGATTG 59.067 47.826 0.00 0.00 0.00 2.67
784 848 3.581332 TGAGAACGTAACTTCCCTGGATT 59.419 43.478 0.00 0.00 0.00 3.01
787 851 3.611766 ATGAGAACGTAACTTCCCTGG 57.388 47.619 0.00 0.00 0.00 4.45
789 853 6.105397 TGTTAATGAGAACGTAACTTCCCT 57.895 37.500 0.00 0.00 31.59 4.20
790 854 6.790285 TTGTTAATGAGAACGTAACTTCCC 57.210 37.500 0.00 0.00 31.59 3.97
791 855 8.025243 TCATTGTTAATGAGAACGTAACTTCC 57.975 34.615 0.36 0.00 42.69 3.46
807 871 4.453177 TGGGTACGACGATCATTGTTAA 57.547 40.909 0.00 0.00 0.00 2.01
808 872 4.453177 TTGGGTACGACGATCATTGTTA 57.547 40.909 0.00 0.00 0.00 2.41
809 873 3.322211 TTGGGTACGACGATCATTGTT 57.678 42.857 0.00 0.00 0.00 2.83
810 874 3.454375 GATTGGGTACGACGATCATTGT 58.546 45.455 0.00 0.00 0.00 2.71
811 875 2.800544 GGATTGGGTACGACGATCATTG 59.199 50.000 0.00 0.00 31.62 2.82
812 876 2.224209 GGGATTGGGTACGACGATCATT 60.224 50.000 0.00 0.00 31.62 2.57
844 1377 7.706607 GGGGAGTGCATAATTCTTACAAATTTC 59.293 37.037 0.00 0.00 31.50 2.17
863 1396 0.310854 GAAAACAGCGTTGGGGAGTG 59.689 55.000 3.74 0.00 0.00 3.51
878 1411 6.672657 AGGAGAAACTAGCCAGGTATAGAAAA 59.327 38.462 7.62 0.00 0.00 2.29
908 1628 1.942657 CTGGGCAATTATCGTGTCCTG 59.057 52.381 0.00 0.00 41.59 3.86
1093 1816 4.140536 TCTGTCATGATAGACTCGATGCT 58.859 43.478 17.34 0.00 39.27 3.79
1505 2228 2.807967 TCTCGTGTTTCTTCAATGCCTG 59.192 45.455 0.00 0.00 0.00 4.85
1560 2283 5.066893 CGTCTTCAATGGATGATTCAACCAT 59.933 40.000 19.63 19.63 46.51 3.55
1845 2602 8.635765 AGACAAAAGGATAATCTGCTTTGTAA 57.364 30.769 0.00 0.00 43.89 2.41
1846 2603 9.383519 CTAGACAAAAGGATAATCTGCTTTGTA 57.616 33.333 0.00 0.00 43.89 2.41
1847 2604 8.103305 TCTAGACAAAAGGATAATCTGCTTTGT 58.897 33.333 0.00 0.00 43.89 2.83
1848 2605 8.498054 TCTAGACAAAAGGATAATCTGCTTTG 57.502 34.615 0.00 0.00 43.89 2.77
1990 2759 9.612066 ACAATAGACAATGTTTGTTCCAAAAAT 57.388 25.926 0.00 0.00 45.52 1.82
2013 2782 8.767085 CCGAAACTTTACAAGTGAGTAATACAA 58.233 33.333 0.00 0.00 41.91 2.41
2338 3869 9.410556 CTCATTTACACCAAAAGGATAAAACAG 57.589 33.333 0.00 0.00 29.71 3.16
2454 3988 3.006659 TGCGCATGGTTTTTAACAGTC 57.993 42.857 5.66 0.00 0.00 3.51
2503 4037 4.260990 CCACACGCACAAAAACTTATGAGA 60.261 41.667 0.00 0.00 0.00 3.27
2688 4302 8.388589 ACACATCTTTATCCCATATGTCATCAT 58.611 33.333 1.24 0.00 38.00 2.45
2762 4376 3.241701 CAATGCGGGTTGTTGTGATTAC 58.758 45.455 0.00 0.00 0.00 1.89
3302 4920 4.098349 TCCTTGAACATCAATGCCTATTGC 59.902 41.667 0.00 0.00 42.71 3.56
3320 4938 3.119849 CGGCAACCTTCTACATTTCCTTG 60.120 47.826 0.00 0.00 0.00 3.61
3463 5081 9.990360 TCCACGTATATCTTGCTATTTTGAATA 57.010 29.630 0.00 0.00 0.00 1.75
3540 5158 8.292444 TGAAATATCCAACACTTTCCCAATAG 57.708 34.615 0.00 0.00 0.00 1.73
3542 5160 7.235399 ACTTGAAATATCCAACACTTTCCCAAT 59.765 33.333 0.00 0.00 0.00 3.16
3578 5196 1.514003 TCTAAATCCAACACGCGCAA 58.486 45.000 5.73 0.00 0.00 4.85
3602 5220 2.909006 ACCCAACATCTGAGACATCACT 59.091 45.455 0.00 0.00 0.00 3.41
3630 5251 5.564550 AGTACCTCAAATGCAACAGATTCT 58.435 37.500 0.00 0.00 0.00 2.40
3689 5310 2.019984 CTGCAGCTTCCCTATTTCCAC 58.980 52.381 0.00 0.00 0.00 4.02
3746 5367 4.569943 ACAACACTAGATGGCAGTACTTG 58.430 43.478 0.00 0.00 0.00 3.16
3760 5381 4.277672 AGACGTCTTAGCTGAACAACACTA 59.722 41.667 13.58 0.00 0.00 2.74
3786 5407 7.386573 TCATACCATAATTAACATACAGGCACG 59.613 37.037 0.00 0.00 0.00 5.34
3800 5421 5.475909 CAGATGGCAGCTTCATACCATAATT 59.524 40.000 0.62 0.00 42.92 1.40
3860 5481 4.038763 GTCCACGTCAGATAATCCCATGTA 59.961 45.833 0.00 0.00 0.00 2.29
3868 5489 5.359194 AATCAAGGTCCACGTCAGATAAT 57.641 39.130 0.00 0.00 0.00 1.28
3952 5573 1.808133 GCTTTACCCAGGCTCTCATCG 60.808 57.143 0.00 0.00 0.00 3.84
4009 5630 6.310711 CACGCGAGACATATACATCTAGACTA 59.689 42.308 15.93 0.00 0.00 2.59
4030 5657 0.099436 GGCAATTGATGAGTCCACGC 59.901 55.000 10.34 0.00 0.00 5.34
4032 5659 0.734889 CGGGCAATTGATGAGTCCAC 59.265 55.000 10.34 0.00 0.00 4.02
4081 5708 8.092068 TCAATTGACCAGAAAACTAATCTACGA 58.908 33.333 3.38 0.00 0.00 3.43
4090 5717 6.070824 ACCAACTTTCAATTGACCAGAAAACT 60.071 34.615 17.23 0.00 31.59 2.66
4092 5719 6.293004 ACCAACTTTCAATTGACCAGAAAA 57.707 33.333 17.23 4.72 31.59 2.29
4178 5805 2.298300 CGATCGCACTTCAAACACAAC 58.702 47.619 0.26 0.00 0.00 3.32
4179 5806 1.262950 CCGATCGCACTTCAAACACAA 59.737 47.619 10.32 0.00 0.00 3.33
4180 5807 0.865111 CCGATCGCACTTCAAACACA 59.135 50.000 10.32 0.00 0.00 3.72
4245 5872 4.698304 GGAACAAAGAATTATCCGTCACCA 59.302 41.667 0.00 0.00 0.00 4.17
4262 5889 2.831526 TCACATCATCTCCTCGGAACAA 59.168 45.455 0.00 0.00 0.00 2.83
4276 5909 1.340893 ACGGGCATTTCCATCACATCA 60.341 47.619 0.00 0.00 36.21 3.07
4307 5940 2.410785 CATGGGAATAATGCAGCACG 57.589 50.000 0.00 0.00 0.00 5.34
4342 5975 2.869801 CACAGCACGAGTACCAAAGAAA 59.130 45.455 0.00 0.00 0.00 2.52
4353 5986 1.139734 ATAGACGGCACAGCACGAG 59.860 57.895 0.00 0.00 0.00 4.18
4355 5988 1.014044 AACATAGACGGCACAGCACG 61.014 55.000 0.00 0.00 0.00 5.34
4360 5993 1.070914 TGTGGAAACATAGACGGCACA 59.929 47.619 0.00 0.00 46.14 4.57
4415 6048 2.119495 GATCCACTTAGCTGGGAAGGA 58.881 52.381 0.00 0.00 33.73 3.36
4454 6162 2.203070 GAGGTGCCGCATACCCAG 60.203 66.667 0.00 0.00 39.05 4.45
4598 6319 0.239347 CTTTTCTGCAGGCTTCACCG 59.761 55.000 15.13 0.00 46.52 4.94
4604 6325 1.518903 GCGAACCTTTTCTGCAGGCT 61.519 55.000 15.13 0.00 34.32 4.58
4638 6378 3.173965 ACGAATATACATAGCCCAGCCT 58.826 45.455 0.00 0.00 0.00 4.58
4663 6403 6.106003 ACCTTGTTGACAAAACAAAGGAATC 58.894 36.000 19.41 0.00 39.36 2.52
4664 6404 6.048732 ACCTTGTTGACAAAACAAAGGAAT 57.951 33.333 19.41 3.79 39.36 3.01
4675 6415 7.581213 AATGAATACTGAACCTTGTTGACAA 57.419 32.000 0.00 0.00 0.00 3.18
4677 6417 8.871686 AAAAATGAATACTGAACCTTGTTGAC 57.128 30.769 0.00 0.00 0.00 3.18
4680 6420 8.250143 AGGAAAAATGAATACTGAACCTTGTT 57.750 30.769 0.00 0.00 0.00 2.83
4699 6439 8.379331 TGAAAAAGGAAAAAGGAAGAAGGAAAA 58.621 29.630 0.00 0.00 0.00 2.29
4700 6440 7.912719 TGAAAAAGGAAAAAGGAAGAAGGAAA 58.087 30.769 0.00 0.00 0.00 3.13
4711 6451 4.122046 CCACCTGCTGAAAAAGGAAAAAG 58.878 43.478 0.00 0.00 37.01 2.27
4712 6452 3.772025 TCCACCTGCTGAAAAAGGAAAAA 59.228 39.130 0.00 0.00 37.01 1.94
4727 6467 0.622665 ATGAAGCCTTCCTCCACCTG 59.377 55.000 1.21 0.00 0.00 4.00
4728 6468 1.376649 AATGAAGCCTTCCTCCACCT 58.623 50.000 1.21 0.00 0.00 4.00
4729 6469 3.366052 TTAATGAAGCCTTCCTCCACC 57.634 47.619 1.21 0.00 0.00 4.61
4738 6478 7.176340 GCATAAAGGATCTGATTAATGAAGCCT 59.824 37.037 0.00 0.00 0.00 4.58
4744 6484 7.756395 ACCTGCATAAAGGATCTGATTAATG 57.244 36.000 0.00 0.00 40.02 1.90
4762 6502 9.679661 TTAAATGATGAAAGAATAGTACCTGCA 57.320 29.630 0.00 0.00 0.00 4.41
4773 6513 8.342634 GGCGCTAGTAATTAAATGATGAAAGAA 58.657 33.333 7.64 0.00 0.00 2.52
4775 6515 6.792250 CGGCGCTAGTAATTAAATGATGAAAG 59.208 38.462 7.64 0.00 0.00 2.62
4776 6516 6.480651 TCGGCGCTAGTAATTAAATGATGAAA 59.519 34.615 7.64 0.00 0.00 2.69
4777 6517 5.986741 TCGGCGCTAGTAATTAAATGATGAA 59.013 36.000 7.64 0.00 0.00 2.57
4784 6525 7.775397 AAATAGTTCGGCGCTAGTAATTAAA 57.225 32.000 7.64 0.00 0.00 1.52
4808 6549 5.048083 ACGCAGGCTAAAGAAATGATGAAAA 60.048 36.000 0.00 0.00 0.00 2.29
4831 6572 3.281727 TTAGGGACCTGATTGATGCAC 57.718 47.619 0.00 0.00 0.00 4.57
4833 6574 2.620585 GCTTTAGGGACCTGATTGATGC 59.379 50.000 0.00 0.00 0.00 3.91
4874 6615 6.816140 TCACATCGCAATATTCTTGTCACTTA 59.184 34.615 0.00 0.00 0.00 2.24
4880 6621 6.498304 GGAATTCACATCGCAATATTCTTGT 58.502 36.000 7.93 0.00 0.00 3.16
4893 6634 0.099436 GCCACAGCGGAATTCACATC 59.901 55.000 7.93 0.00 36.56 3.06
4912 6654 7.426410 TGCTAGTACTTTAGCTGCATAACTAG 58.574 38.462 16.62 16.76 44.99 2.57
4922 6664 5.986501 ACACTTCTGCTAGTACTTTAGCT 57.013 39.130 16.62 0.00 44.99 3.32
4976 6722 5.408604 CAGTATTACTGTTGGGTTGTCTGTC 59.591 44.000 14.52 0.00 41.19 3.51
5011 6778 3.290710 ACAGAGAAAAAGGCACACATGT 58.709 40.909 0.00 0.00 0.00 3.21
5014 6781 4.150897 AGTACAGAGAAAAAGGCACACA 57.849 40.909 0.00 0.00 0.00 3.72
5015 6782 4.261197 CCAAGTACAGAGAAAAAGGCACAC 60.261 45.833 0.00 0.00 0.00 3.82
5057 6824 7.094508 TGCTTCAGTTCAATGTTACAGAAAA 57.905 32.000 0.00 0.00 0.00 2.29
5085 6852 5.245751 TGCCATTTGGAAGAAACACACATAT 59.754 36.000 0.00 0.00 37.39 1.78
5086 6853 4.586421 TGCCATTTGGAAGAAACACACATA 59.414 37.500 0.00 0.00 37.39 2.29
5118 6885 3.517296 TCTGCTAGCTCCTACTATGCT 57.483 47.619 17.23 0.00 40.43 3.79
5143 6910 2.519377 TGTTGGAGTGTCGACGAAAT 57.481 45.000 11.62 0.00 0.00 2.17
5145 6912 1.135527 AGTTGTTGGAGTGTCGACGAA 59.864 47.619 11.62 0.00 0.00 3.85
5171 6957 2.068519 TCAAATAGCAGAGCACACACG 58.931 47.619 0.00 0.00 0.00 4.49
5172 6958 3.937706 AGATCAAATAGCAGAGCACACAC 59.062 43.478 0.00 0.00 0.00 3.82
5173 6959 3.937079 CAGATCAAATAGCAGAGCACACA 59.063 43.478 0.00 0.00 0.00 3.72
5174 6960 3.937706 ACAGATCAAATAGCAGAGCACAC 59.062 43.478 0.00 0.00 0.00 3.82
5199 6985 1.134401 GTTCATTCGGATGCAGAGGGA 60.134 52.381 0.00 0.00 33.14 4.20
5212 6998 3.517500 AGACAGAAGGAGGAGGTTCATTC 59.482 47.826 0.00 0.00 37.96 2.67
5213 6999 3.262915 CAGACAGAAGGAGGAGGTTCATT 59.737 47.826 0.00 0.00 0.00 2.57
5226 7012 6.373774 AGAATCCAAACATAAGCAGACAGAAG 59.626 38.462 0.00 0.00 0.00 2.85
5334 7120 2.483745 CAGCCAAGCAGTGCATCG 59.516 61.111 19.20 4.61 0.00 3.84
5370 7156 8.149647 TCCAAACAAAGCAATACAATTCAGAAT 58.850 29.630 0.00 0.00 0.00 2.40
5371 7157 7.495901 TCCAAACAAAGCAATACAATTCAGAA 58.504 30.769 0.00 0.00 0.00 3.02
5372 7158 7.048629 TCCAAACAAAGCAATACAATTCAGA 57.951 32.000 0.00 0.00 0.00 3.27
5373 7159 6.128742 GCTCCAAACAAAGCAATACAATTCAG 60.129 38.462 0.00 0.00 38.42 3.02
5374 7160 5.695816 GCTCCAAACAAAGCAATACAATTCA 59.304 36.000 0.00 0.00 38.42 2.57
5375 7161 5.695816 TGCTCCAAACAAAGCAATACAATTC 59.304 36.000 0.00 0.00 45.09 2.17
5376 7162 5.609423 TGCTCCAAACAAAGCAATACAATT 58.391 33.333 0.00 0.00 45.09 2.32
5403 7189 6.687081 TTACGAGTCTGGAACAAAACATTT 57.313 33.333 0.00 0.00 38.70 2.32
5443 7229 0.601057 AAACCAATACGGCAACCTGC 59.399 50.000 0.00 0.00 44.08 4.85
5447 7233 3.840890 TCATGAAACCAATACGGCAAC 57.159 42.857 0.00 0.00 39.03 4.17
5507 7293 5.352569 AGCGATTCAAATTCTAGTTCCACTG 59.647 40.000 0.00 0.00 0.00 3.66
5511 7297 5.803020 ACAGCGATTCAAATTCTAGTTCC 57.197 39.130 0.00 0.00 0.00 3.62
5517 7303 3.921119 TGCAACAGCGATTCAAATTCT 57.079 38.095 0.00 0.00 0.00 2.40
5528 7314 2.537529 GCACATGTAGTATGCAACAGCG 60.538 50.000 0.00 0.00 39.23 5.18
5532 7318 4.092821 TCGAAAGCACATGTAGTATGCAAC 59.907 41.667 0.00 0.00 41.97 4.17
5544 7331 5.016051 ACTAGATGACATCGAAAGCACAT 57.984 39.130 9.77 0.00 0.00 3.21
5550 7337 6.465439 ACATGGTACTAGATGACATCGAAA 57.535 37.500 9.77 0.00 0.00 3.46
5569 7361 5.829924 AGTTGAGGGCCAATAATCTTACATG 59.170 40.000 6.18 0.00 37.08 3.21
5570 7362 5.829924 CAGTTGAGGGCCAATAATCTTACAT 59.170 40.000 6.18 0.00 37.08 2.29


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

AutoCloner maintained by Alex Coulton.