Multiple sequence alignment - TraesCS1D01G091000

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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 TraesCS1D01G091000 chr1D 100.000 6723 0 0 1 6723 77370940 77364218 0.000000e+00 12416.0
1 TraesCS1D01G091000 chr1D 100.000 73 0 0 5674 5746 77365225 77365153 1.180000e-27 135.0
2 TraesCS1D01G091000 chr1D 100.000 73 0 0 5716 5788 77365267 77365195 1.180000e-27 135.0
3 TraesCS1D01G091000 chr1D 100.000 31 0 0 5674 5704 77365183 77365153 2.620000e-04 58.4
4 TraesCS1D01G091000 chr1D 100.000 31 0 0 5758 5788 77365267 77365237 2.620000e-04 58.4
5 TraesCS1D01G091000 chr1A 97.255 4882 103 19 856 5723 108697668 108692804 0.000000e+00 8244.0
6 TraesCS1D01G091000 chr1A 89.455 569 33 12 5716 6282 108692852 108692309 0.000000e+00 693.0
7 TraesCS1D01G091000 chr1A 93.023 387 20 6 6340 6723 108691643 108691261 5.890000e-155 558.0
8 TraesCS1D01G091000 chr1A 83.908 87 9 4 2513 2598 426531336 426531254 2.010000e-10 78.7
9 TraesCS1D01G091000 chr1A 100.000 31 0 0 5758 5788 108692852 108692822 2.620000e-04 58.4
10 TraesCS1D01G091000 chr1B 96.946 3176 80 13 2557 5723 120887145 120883978 0.000000e+00 5312.0
11 TraesCS1D01G091000 chr1B 96.238 1701 57 5 839 2539 120888923 120887230 0.000000e+00 2780.0
12 TraesCS1D01G091000 chr1B 86.114 1037 77 30 5716 6723 120884026 120883028 0.000000e+00 1055.0
13 TraesCS1D01G091000 chr1B 91.597 714 47 7 1 706 94009265 94009973 0.000000e+00 974.0
14 TraesCS1D01G091000 chr1B 90.733 723 51 11 1 712 643025084 643025801 0.000000e+00 950.0
15 TraesCS1D01G091000 chr1B 93.182 44 2 1 773 815 233699173 233699216 5.630000e-06 63.9
16 TraesCS1D01G091000 chr1B 100.000 31 0 0 5758 5788 120884026 120883996 2.620000e-04 58.4
17 TraesCS1D01G091000 chr2D 90.972 720 55 9 1 712 616148448 616149165 0.000000e+00 961.0
18 TraesCS1D01G091000 chr2D 91.489 47 4 0 2505 2551 619562335 619562381 1.560000e-06 65.8
19 TraesCS1D01G091000 chr2A 90.871 723 54 8 1 712 765215686 765216407 0.000000e+00 959.0
20 TraesCS1D01G091000 chr2A 91.837 49 2 1 2510 2556 170470500 170470452 4.350000e-07 67.6
21 TraesCS1D01G091000 chr7D 90.808 718 55 7 3 711 611664934 611665649 0.000000e+00 950.0
22 TraesCS1D01G091000 chr7D 97.059 34 1 0 773 806 70151512 70151545 2.620000e-04 58.4
23 TraesCS1D01G091000 chr2B 90.217 736 60 11 1 729 27734825 27735555 0.000000e+00 950.0
24 TraesCS1D01G091000 chr2B 95.122 41 2 0 2557 2597 216462841 216462801 1.560000e-06 65.8
25 TraesCS1D01G091000 chr4B 90.582 722 57 8 1 712 37869860 37870580 0.000000e+00 946.0
26 TraesCS1D01G091000 chr4B 88.679 53 4 2 2538 2590 71586885 71586935 5.630000e-06 63.9
27 TraesCS1D01G091000 chr7B 90.177 733 58 9 1 722 632802853 632802124 0.000000e+00 942.0
28 TraesCS1D01G091000 chr7B 97.436 39 1 0 2513 2551 434839255 434839293 4.350000e-07 67.6
29 TraesCS1D01G091000 chr3B 90.068 735 60 11 1 723 772908248 772908981 0.000000e+00 941.0
30 TraesCS1D01G091000 chr6D 87.952 83 8 2 2512 2593 413080691 413080772 5.550000e-16 97.1
31 TraesCS1D01G091000 chr6B 87.952 83 8 2 2512 2593 622737693 622737774 5.550000e-16 97.1
32 TraesCS1D01G091000 chr6B 91.803 61 5 0 751 811 471187248 471187308 1.200000e-12 86.1
33 TraesCS1D01G091000 chr6B 90.000 50 3 1 2512 2559 231351343 231351294 5.630000e-06 63.9
34 TraesCS1D01G091000 chr6A 95.000 40 2 0 2552 2591 172114707 172114668 5.630000e-06 63.9
35 TraesCS1D01G091000 chr3D 89.796 49 4 1 2557 2604 473457444 473457492 2.020000e-05 62.1


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 TraesCS1D01G091000 chr1D 77364218 77370940 6722 True 12416.00 12416 100.000000 1 6723 1 chr1D.!!$R1 6722
1 TraesCS1D01G091000 chr1A 108691261 108697668 6407 True 3165.00 8244 93.244333 856 6723 3 chr1A.!!$R3 5867
2 TraesCS1D01G091000 chr1B 120883028 120888923 5895 True 2301.35 5312 94.824500 839 6723 4 chr1B.!!$R1 5884
3 TraesCS1D01G091000 chr1B 94009265 94009973 708 False 974.00 974 91.597000 1 706 1 chr1B.!!$F1 705
4 TraesCS1D01G091000 chr1B 643025084 643025801 717 False 950.00 950 90.733000 1 712 1 chr1B.!!$F3 711
5 TraesCS1D01G091000 chr2D 616148448 616149165 717 False 961.00 961 90.972000 1 712 1 chr2D.!!$F1 711
6 TraesCS1D01G091000 chr2A 765215686 765216407 721 False 959.00 959 90.871000 1 712 1 chr2A.!!$F1 711
7 TraesCS1D01G091000 chr7D 611664934 611665649 715 False 950.00 950 90.808000 3 711 1 chr7D.!!$F2 708
8 TraesCS1D01G091000 chr2B 27734825 27735555 730 False 950.00 950 90.217000 1 729 1 chr2B.!!$F1 728
9 TraesCS1D01G091000 chr4B 37869860 37870580 720 False 946.00 946 90.582000 1 712 1 chr4B.!!$F1 711
10 TraesCS1D01G091000 chr7B 632802124 632802853 729 True 942.00 942 90.177000 1 722 1 chr7B.!!$R1 721
11 TraesCS1D01G091000 chr3B 772908248 772908981 733 False 941.00 941 90.068000 1 723 1 chr3B.!!$F1 722

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
739 753 0.103208 GTACCCTGCAGATGACTCGG 59.897 60.000 17.39 8.42 0.00 4.63 F
1114 1128 0.108615 CACAAGATCCCGTCTCGCTT 60.109 55.000 0.00 0.00 35.67 4.68 F
2404 2424 0.401738 CCTCGCATAATGTGGGGGAT 59.598 55.000 0.00 0.00 44.65 3.85 F
2539 2559 1.135315 TCCGTCCGGAATTAGTTGACG 60.135 52.381 5.23 1.97 46.05 4.35 F
2554 2641 1.389555 TGACGCTCACACGGATATCT 58.610 50.000 2.05 0.00 37.37 1.98 F
2555 2642 2.567985 TGACGCTCACACGGATATCTA 58.432 47.619 2.05 0.00 37.37 1.98 F
4926 5018 3.243367 TGCTGCAAACCCGCAATATAATC 60.243 43.478 0.00 0.00 42.45 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1878 1898 1.133407 GAGCACGAGTAACAGAGGAGG 59.867 57.143 0.00 0.00 0.00 4.30 R
2561 2648 1.403249 CCGTCCGGAATTAGTTGACGT 60.403 52.381 5.23 0.00 45.29 4.34 R
3689 3777 3.243359 AGGACAAACATGATGGGTTGT 57.757 42.857 14.17 14.17 34.04 3.32 R
4335 4424 4.096081 GCATATTATCCCAAGATGCTCAGC 59.904 45.833 8.84 0.00 39.81 4.26 R
4669 4761 8.469309 TTCTTTCAGTCATTTTCTCCTGAAAT 57.531 30.769 12.47 0.00 46.77 2.17 R
5123 5218 0.600057 TTTATTGCGTGGCATGCACA 59.400 45.000 32.50 22.74 40.28 4.57 R
5764 5863 1.066908 CACATTTGAACGGCAACCAGT 59.933 47.619 0.00 0.00 35.91 4.00 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
50 51 5.551233 AGAAAAGAATGACGAATCACCTCA 58.449 37.500 0.00 0.00 37.79 3.86
55 56 4.161189 AGAATGACGAATCACCTCATCACT 59.839 41.667 0.00 0.00 37.79 3.41
162 163 3.953775 CAGACCGGGGCAACACCT 61.954 66.667 6.32 0.00 35.43 4.00
175 176 2.047274 CACCTCGGACACGCCATT 60.047 61.111 0.00 0.00 40.69 3.16
272 274 1.511850 CAGCACATGTTCCGTCTTCA 58.488 50.000 0.00 0.00 0.00 3.02
288 290 3.247173 GTCTTCAAGATGTCATCGATGCC 59.753 47.826 20.81 10.37 0.00 4.40
329 331 1.280457 CTGGACTACCTCCCAAGCTT 58.720 55.000 0.00 0.00 38.49 3.74
355 357 1.999651 GACGCTAGAGCAAACGTCGC 62.000 60.000 1.89 1.80 44.42 5.19
712 726 1.375326 GCCAGGGACGAGGAAAACT 59.625 57.895 0.00 0.00 0.00 2.66
723 737 2.591584 CGAGGAAAACTAGTTCGCGTAC 59.408 50.000 8.95 7.91 0.00 3.67
724 738 2.919859 GAGGAAAACTAGTTCGCGTACC 59.080 50.000 12.54 6.59 0.00 3.34
726 740 2.353109 GGAAAACTAGTTCGCGTACCCT 60.353 50.000 12.54 3.76 0.00 4.34
727 741 2.358939 AAACTAGTTCGCGTACCCTG 57.641 50.000 12.54 5.64 0.00 4.45
728 742 0.108945 AACTAGTTCGCGTACCCTGC 60.109 55.000 12.54 0.00 0.00 4.85
729 743 1.246056 ACTAGTTCGCGTACCCTGCA 61.246 55.000 12.54 0.00 0.00 4.41
730 744 0.525668 CTAGTTCGCGTACCCTGCAG 60.526 60.000 12.54 6.78 0.00 4.41
731 745 0.961857 TAGTTCGCGTACCCTGCAGA 60.962 55.000 17.39 0.00 0.00 4.26
732 746 1.153628 GTTCGCGTACCCTGCAGAT 60.154 57.895 17.39 5.38 0.00 2.90
733 747 1.153647 TTCGCGTACCCTGCAGATG 60.154 57.895 17.39 8.57 0.00 2.90
734 748 1.600511 TTCGCGTACCCTGCAGATGA 61.601 55.000 17.39 0.00 0.00 2.92
735 749 1.878522 CGCGTACCCTGCAGATGAC 60.879 63.158 17.39 8.49 0.00 3.06
736 750 1.517832 GCGTACCCTGCAGATGACT 59.482 57.895 17.39 0.00 0.00 3.41
737 751 0.528684 GCGTACCCTGCAGATGACTC 60.529 60.000 17.39 0.56 0.00 3.36
738 752 0.248661 CGTACCCTGCAGATGACTCG 60.249 60.000 17.39 8.31 0.00 4.18
739 753 0.103208 GTACCCTGCAGATGACTCGG 59.897 60.000 17.39 8.42 0.00 4.63
740 754 0.324368 TACCCTGCAGATGACTCGGT 60.324 55.000 17.39 14.32 0.00 4.69
741 755 1.153489 CCCTGCAGATGACTCGGTG 60.153 63.158 17.39 0.00 0.00 4.94
742 756 1.812922 CCTGCAGATGACTCGGTGC 60.813 63.158 17.39 0.00 36.42 5.01
743 757 1.079612 CTGCAGATGACTCGGTGCA 60.080 57.895 8.42 0.00 43.50 4.57
744 758 1.079612 TGCAGATGACTCGGTGCAG 60.080 57.895 0.00 0.00 40.93 4.41
745 759 1.079543 GCAGATGACTCGGTGCAGT 60.080 57.895 0.00 0.00 35.91 4.40
746 760 0.671781 GCAGATGACTCGGTGCAGTT 60.672 55.000 0.00 0.00 35.91 3.16
747 761 1.354040 CAGATGACTCGGTGCAGTTC 58.646 55.000 0.00 0.00 0.00 3.01
748 762 0.109086 AGATGACTCGGTGCAGTTCG 60.109 55.000 0.00 0.00 0.00 3.95
749 763 1.687494 GATGACTCGGTGCAGTTCGC 61.687 60.000 0.00 0.00 42.89 4.70
750 764 2.049063 GACTCGGTGCAGTTCGCT 60.049 61.111 0.00 0.00 43.06 4.93
751 765 1.211969 GACTCGGTGCAGTTCGCTA 59.788 57.895 0.00 0.00 43.06 4.26
752 766 0.179134 GACTCGGTGCAGTTCGCTAT 60.179 55.000 0.00 0.00 43.06 2.97
753 767 1.065102 GACTCGGTGCAGTTCGCTATA 59.935 52.381 0.00 0.00 43.06 1.31
754 768 1.681793 ACTCGGTGCAGTTCGCTATAT 59.318 47.619 0.00 0.00 43.06 0.86
755 769 2.287668 ACTCGGTGCAGTTCGCTATATC 60.288 50.000 0.00 0.00 43.06 1.63
756 770 1.954382 TCGGTGCAGTTCGCTATATCT 59.046 47.619 0.00 0.00 43.06 1.98
757 771 3.143728 TCGGTGCAGTTCGCTATATCTA 58.856 45.455 0.00 0.00 43.06 1.98
758 772 3.058432 TCGGTGCAGTTCGCTATATCTAC 60.058 47.826 0.00 0.00 43.06 2.59
759 773 3.576648 GGTGCAGTTCGCTATATCTACC 58.423 50.000 0.00 0.00 43.06 3.18
760 774 3.005472 GGTGCAGTTCGCTATATCTACCA 59.995 47.826 0.00 0.00 43.06 3.25
761 775 3.982058 GTGCAGTTCGCTATATCTACCAC 59.018 47.826 0.00 0.00 43.06 4.16
762 776 3.634910 TGCAGTTCGCTATATCTACCACA 59.365 43.478 0.00 0.00 43.06 4.17
763 777 3.982058 GCAGTTCGCTATATCTACCACAC 59.018 47.826 0.00 0.00 37.77 3.82
764 778 4.547532 CAGTTCGCTATATCTACCACACC 58.452 47.826 0.00 0.00 0.00 4.16
765 779 4.278669 CAGTTCGCTATATCTACCACACCT 59.721 45.833 0.00 0.00 0.00 4.00
766 780 4.278669 AGTTCGCTATATCTACCACACCTG 59.721 45.833 0.00 0.00 0.00 4.00
767 781 2.557056 TCGCTATATCTACCACACCTGC 59.443 50.000 0.00 0.00 0.00 4.85
768 782 2.296190 CGCTATATCTACCACACCTGCA 59.704 50.000 0.00 0.00 0.00 4.41
769 783 3.056536 CGCTATATCTACCACACCTGCAT 60.057 47.826 0.00 0.00 0.00 3.96
770 784 4.157840 CGCTATATCTACCACACCTGCATA 59.842 45.833 0.00 0.00 0.00 3.14
771 785 5.336451 CGCTATATCTACCACACCTGCATAA 60.336 44.000 0.00 0.00 0.00 1.90
772 786 6.628175 CGCTATATCTACCACACCTGCATAAT 60.628 42.308 0.00 0.00 0.00 1.28
773 787 6.758886 GCTATATCTACCACACCTGCATAATC 59.241 42.308 0.00 0.00 0.00 1.75
774 788 6.942163 ATATCTACCACACCTGCATAATCT 57.058 37.500 0.00 0.00 0.00 2.40
775 789 5.636903 ATCTACCACACCTGCATAATCTT 57.363 39.130 0.00 0.00 0.00 2.40
776 790 5.023533 TCTACCACACCTGCATAATCTTC 57.976 43.478 0.00 0.00 0.00 2.87
777 791 3.004752 ACCACACCTGCATAATCTTCC 57.995 47.619 0.00 0.00 0.00 3.46
778 792 1.942657 CCACACCTGCATAATCTTCCG 59.057 52.381 0.00 0.00 0.00 4.30
779 793 2.632377 CACACCTGCATAATCTTCCGT 58.368 47.619 0.00 0.00 0.00 4.69
780 794 3.009723 CACACCTGCATAATCTTCCGTT 58.990 45.455 0.00 0.00 0.00 4.44
781 795 4.188462 CACACCTGCATAATCTTCCGTTA 58.812 43.478 0.00 0.00 0.00 3.18
782 796 4.034048 CACACCTGCATAATCTTCCGTTAC 59.966 45.833 0.00 0.00 0.00 2.50
783 797 4.188462 CACCTGCATAATCTTCCGTTACA 58.812 43.478 0.00 0.00 0.00 2.41
784 798 4.634004 CACCTGCATAATCTTCCGTTACAA 59.366 41.667 0.00 0.00 0.00 2.41
785 799 4.634443 ACCTGCATAATCTTCCGTTACAAC 59.366 41.667 0.00 0.00 0.00 3.32
794 808 3.226712 CGTTACAACGCACGAGCA 58.773 55.556 5.50 0.00 46.06 4.26
795 809 1.779061 CGTTACAACGCACGAGCAT 59.221 52.632 5.50 0.00 46.06 3.79
796 810 0.986270 CGTTACAACGCACGAGCATA 59.014 50.000 5.50 0.00 46.06 3.14
797 811 1.586578 CGTTACAACGCACGAGCATAT 59.413 47.619 5.50 0.00 46.06 1.78
798 812 2.028763 CGTTACAACGCACGAGCATATT 59.971 45.455 5.50 0.00 46.06 1.28
799 813 3.482923 CGTTACAACGCACGAGCATATTT 60.483 43.478 5.50 0.00 46.06 1.40
800 814 2.525750 ACAACGCACGAGCATATTTG 57.474 45.000 5.50 4.99 42.27 2.32
822 836 9.627123 ATTTGCTAGTATAGGATAAAAAGCACA 57.373 29.630 0.00 0.00 39.37 4.57
823 837 9.627123 TTTGCTAGTATAGGATAAAAAGCACAT 57.373 29.630 0.00 0.00 39.37 3.21
824 838 9.627123 TTGCTAGTATAGGATAAAAAGCACATT 57.373 29.630 0.00 0.00 39.37 2.71
825 839 9.627123 TGCTAGTATAGGATAAAAAGCACATTT 57.373 29.630 0.00 0.00 39.70 2.32
862 876 7.156876 TGGATAAAAAGCACATGGAAACTAG 57.843 36.000 0.00 0.00 0.00 2.57
875 889 2.097825 GAAACTAGGACCTGGCTCGTA 58.902 52.381 3.53 0.00 0.00 3.43
986 1000 2.367947 AACCCTCCTCCCATTCTCTT 57.632 50.000 0.00 0.00 0.00 2.85
987 1001 1.886422 ACCCTCCTCCCATTCTCTTC 58.114 55.000 0.00 0.00 0.00 2.87
988 1002 1.135960 CCCTCCTCCCATTCTCTTCC 58.864 60.000 0.00 0.00 0.00 3.46
1114 1128 0.108615 CACAAGATCCCGTCTCGCTT 60.109 55.000 0.00 0.00 35.67 4.68
1117 1131 2.579684 AAGATCCCGTCTCGCTTGCC 62.580 60.000 0.00 0.00 35.67 4.52
1126 1140 1.080569 CTCGCTTGCCCGCAAATTT 60.081 52.632 3.37 0.00 35.33 1.82
1127 1141 1.346378 CTCGCTTGCCCGCAAATTTG 61.346 55.000 14.03 14.03 35.33 2.32
1292 1312 1.614903 TCCGAGTACAACACCGTCATT 59.385 47.619 0.00 0.00 0.00 2.57
1361 1381 2.251642 GCACACCACCTGTTCGACC 61.252 63.158 0.00 0.00 0.00 4.79
1415 1435 8.244113 AGGATAGTTTTGTTAAGCTGTTATTGC 58.756 33.333 0.00 0.00 0.00 3.56
1472 1492 5.195001 TGTGCCAACCTAATTGTTTCTTC 57.805 39.130 0.00 0.00 36.47 2.87
1496 1516 5.123820 CCCGAGTCTGAATTAAATGCTTTCA 59.876 40.000 0.00 0.00 0.00 2.69
1545 1565 1.797046 GATGCCTACGATGACATGCTG 59.203 52.381 0.00 0.00 0.00 4.41
1617 1637 4.809496 ATGAAGGGCAGCCGGCTG 62.809 66.667 45.07 45.07 46.15 4.85
1638 1658 3.003480 GCAAGATGCTTTCTACTTCCGT 58.997 45.455 0.00 0.00 40.96 4.69
1738 1758 6.568844 CGATTCCCTTTTTATTTTGTCGGACA 60.569 38.462 6.76 6.76 0.00 4.02
1739 1759 5.699097 TCCCTTTTTATTTTGTCGGACAG 57.301 39.130 11.14 0.00 0.00 3.51
1740 1760 5.378332 TCCCTTTTTATTTTGTCGGACAGA 58.622 37.500 11.14 3.87 0.00 3.41
1878 1898 1.703438 CTGAGTTGCTGCCGATGCTC 61.703 60.000 0.00 0.00 38.71 4.26
2022 2042 3.431725 GCAGCAACTGGGCGTACC 61.432 66.667 0.00 0.00 39.27 3.34
2045 2065 2.696775 TCAAGTGTAAGGGGTCCTTCA 58.303 47.619 2.07 0.00 43.57 3.02
2256 2276 5.873179 TTTCCGTTAGTAAAGCTCCATTG 57.127 39.130 0.00 0.00 0.00 2.82
2261 2281 5.168569 CGTTAGTAAAGCTCCATTGAGACA 58.831 41.667 0.00 0.00 41.42 3.41
2337 2357 3.998341 ACATGTAACGTGTTGGTACATCC 59.002 43.478 0.00 0.00 39.30 3.51
2403 2423 1.836391 CCTCGCATAATGTGGGGGA 59.164 57.895 0.00 0.00 44.65 4.81
2404 2424 0.401738 CCTCGCATAATGTGGGGGAT 59.598 55.000 0.00 0.00 44.65 3.85
2446 2466 5.027460 TCAATTCCACTAGTGCCTAGGTTA 58.973 41.667 17.86 0.00 38.30 2.85
2470 2490 2.358898 TCTTCAGCTTGTGGCAAGTTTC 59.641 45.455 10.10 0.00 44.79 2.78
2539 2559 1.135315 TCCGTCCGGAATTAGTTGACG 60.135 52.381 5.23 1.97 46.05 4.35
2544 2564 1.659098 CCGGAATTAGTTGACGCTCAC 59.341 52.381 0.00 0.00 0.00 3.51
2554 2641 1.389555 TGACGCTCACACGGATATCT 58.610 50.000 2.05 0.00 37.37 1.98
2555 2642 2.567985 TGACGCTCACACGGATATCTA 58.432 47.619 2.05 0.00 37.37 1.98
2561 2648 4.982295 CGCTCACACGGATATCTATTTGAA 59.018 41.667 2.05 0.00 0.00 2.69
2835 2922 6.139048 AGTTTGTTGTGGTGGTACATTTAC 57.861 37.500 0.00 0.00 44.52 2.01
3120 3207 8.401046 TGCATTTTCACTGTGTTTTTAGTAAC 57.599 30.769 7.79 0.00 0.00 2.50
3217 3304 8.791327 TTTCATAGTTAGCTCATGTCATGAAA 57.209 30.769 16.20 5.74 39.11 2.69
3373 3460 3.529533 ACTCTGCATGCTGAACAGTATC 58.470 45.455 24.97 0.64 31.23 2.24
3558 3645 5.277974 GCATACTGAAAAGTCTCTTGTGCAA 60.278 40.000 0.00 0.00 0.00 4.08
3616 3703 8.918658 GCAAATCAATGAAATCGCATTATGTAT 58.081 29.630 0.00 0.00 36.39 2.29
3689 3777 5.263599 AGGATACCTGCAATTGTCATTTGA 58.736 37.500 7.40 0.00 29.57 2.69
4017 4105 6.061022 TGTGCCTTGGACTATTTTGATCTA 57.939 37.500 0.00 0.00 0.00 1.98
4335 4424 5.239087 ACAAAAATTAGCCACATGCCAAAAG 59.761 36.000 0.00 0.00 42.71 2.27
4625 4716 7.133133 TCCTTCCTTCTAGTTTTGTGTTACT 57.867 36.000 0.00 0.00 0.00 2.24
4926 5018 3.243367 TGCTGCAAACCCGCAATATAATC 60.243 43.478 0.00 0.00 42.45 1.75
5121 5216 9.467258 TGAGTTTTATCAAATTTTGAGAGCTTG 57.533 29.630 16.34 0.00 43.98 4.01
5123 5218 8.146412 AGTTTTATCAAATTTTGAGAGCTTGCT 58.854 29.630 16.34 0.00 43.98 3.91
5353 5448 4.007659 GCCCGAGGAGAAATTTTCAGTAA 58.992 43.478 11.53 0.00 0.00 2.24
5354 5449 4.142665 GCCCGAGGAGAAATTTTCAGTAAC 60.143 45.833 11.53 0.00 0.00 2.50
5383 5480 2.564947 CAAACTGCTCTAGTCTCCCTGT 59.435 50.000 0.00 0.00 39.18 4.00
5480 5579 6.471519 CCGAATAACTACTTTTAGGACGACAG 59.528 42.308 0.00 0.00 0.00 3.51
5719 5818 6.861065 ATGTGATTGTTTAGTCGTCAGTTT 57.139 33.333 0.00 0.00 0.00 2.66
5720 5819 6.043327 TGTGATTGTTTAGTCGTCAGTTTG 57.957 37.500 0.00 0.00 0.00 2.93
5721 5820 5.583061 TGTGATTGTTTAGTCGTCAGTTTGT 59.417 36.000 0.00 0.00 0.00 2.83
5722 5821 6.757478 TGTGATTGTTTAGTCGTCAGTTTGTA 59.243 34.615 0.00 0.00 0.00 2.41
5733 5832 1.305201 CAGTTTGTACTGGTTGCCGT 58.695 50.000 0.00 0.00 46.52 5.68
5734 5833 1.673920 CAGTTTGTACTGGTTGCCGTT 59.326 47.619 0.00 0.00 46.52 4.44
5735 5834 1.944709 AGTTTGTACTGGTTGCCGTTC 59.055 47.619 0.00 0.00 31.99 3.95
5736 5835 1.671845 GTTTGTACTGGTTGCCGTTCA 59.328 47.619 0.00 0.00 0.00 3.18
5737 5836 2.039818 TTGTACTGGTTGCCGTTCAA 57.960 45.000 0.00 0.00 0.00 2.69
5738 5837 2.039818 TGTACTGGTTGCCGTTCAAA 57.960 45.000 0.00 0.00 36.26 2.69
5739 5838 2.577700 TGTACTGGTTGCCGTTCAAAT 58.422 42.857 0.00 0.00 36.26 2.32
5740 5839 2.292016 TGTACTGGTTGCCGTTCAAATG 59.708 45.455 0.00 0.00 36.26 2.32
5741 5840 1.398692 ACTGGTTGCCGTTCAAATGT 58.601 45.000 0.00 0.00 36.26 2.71
5742 5841 1.066908 ACTGGTTGCCGTTCAAATGTG 59.933 47.619 0.00 0.00 36.26 3.21
5743 5842 1.336440 CTGGTTGCCGTTCAAATGTGA 59.664 47.619 0.00 0.00 36.26 3.58
5744 5843 1.959985 TGGTTGCCGTTCAAATGTGAT 59.040 42.857 0.00 0.00 36.26 3.06
5745 5844 2.363680 TGGTTGCCGTTCAAATGTGATT 59.636 40.909 0.00 0.00 36.26 2.57
5746 5845 2.730928 GGTTGCCGTTCAAATGTGATTG 59.269 45.455 0.00 0.00 36.26 2.67
5747 5846 3.380142 GTTGCCGTTCAAATGTGATTGT 58.620 40.909 0.00 0.00 36.26 2.71
5748 5847 3.724508 TGCCGTTCAAATGTGATTGTT 57.275 38.095 0.00 0.00 32.48 2.83
5749 5848 4.052159 TGCCGTTCAAATGTGATTGTTT 57.948 36.364 0.00 0.00 32.48 2.83
5750 5849 5.188327 TGCCGTTCAAATGTGATTGTTTA 57.812 34.783 0.00 0.00 32.48 2.01
5751 5850 5.218885 TGCCGTTCAAATGTGATTGTTTAG 58.781 37.500 0.00 0.00 32.48 1.85
5752 5851 5.219633 GCCGTTCAAATGTGATTGTTTAGT 58.780 37.500 0.00 0.00 32.48 2.24
5753 5852 5.342259 GCCGTTCAAATGTGATTGTTTAGTC 59.658 40.000 0.00 0.00 32.48 2.59
5754 5853 5.563751 CCGTTCAAATGTGATTGTTTAGTCG 59.436 40.000 0.00 0.00 32.48 4.18
5755 5854 6.133392 CGTTCAAATGTGATTGTTTAGTCGT 58.867 36.000 0.00 0.00 32.48 4.34
5756 5855 6.299966 CGTTCAAATGTGATTGTTTAGTCGTC 59.700 38.462 0.00 0.00 32.48 4.20
5757 5856 6.852858 TCAAATGTGATTGTTTAGTCGTCA 57.147 33.333 0.00 0.00 0.00 4.35
5758 5857 6.887368 TCAAATGTGATTGTTTAGTCGTCAG 58.113 36.000 0.00 0.00 0.00 3.51
5759 5858 6.481976 TCAAATGTGATTGTTTAGTCGTCAGT 59.518 34.615 0.00 0.00 0.00 3.41
5760 5859 6.861065 AATGTGATTGTTTAGTCGTCAGTT 57.139 33.333 0.00 0.00 0.00 3.16
5761 5860 6.861065 ATGTGATTGTTTAGTCGTCAGTTT 57.139 33.333 0.00 0.00 0.00 2.66
5762 5861 6.043327 TGTGATTGTTTAGTCGTCAGTTTG 57.957 37.500 0.00 0.00 0.00 2.93
5763 5862 5.583061 TGTGATTGTTTAGTCGTCAGTTTGT 59.417 36.000 0.00 0.00 0.00 2.83
5764 5863 6.757478 TGTGATTGTTTAGTCGTCAGTTTGTA 59.243 34.615 0.00 0.00 0.00 2.41
5765 5864 7.061634 GTGATTGTTTAGTCGTCAGTTTGTAC 58.938 38.462 0.00 0.00 0.00 2.90
5766 5865 6.982141 TGATTGTTTAGTCGTCAGTTTGTACT 59.018 34.615 0.00 0.00 34.00 2.73
5775 5874 1.305201 CAGTTTGTACTGGTTGCCGT 58.695 50.000 0.00 0.00 46.52 5.68
5776 5875 1.673920 CAGTTTGTACTGGTTGCCGTT 59.326 47.619 0.00 0.00 46.52 4.44
5777 5876 1.944709 AGTTTGTACTGGTTGCCGTTC 59.055 47.619 0.00 0.00 31.99 3.95
5778 5877 1.671845 GTTTGTACTGGTTGCCGTTCA 59.328 47.619 0.00 0.00 0.00 3.18
5779 5878 2.039818 TTGTACTGGTTGCCGTTCAA 57.960 45.000 0.00 0.00 0.00 2.69
5780 5879 2.039818 TGTACTGGTTGCCGTTCAAA 57.960 45.000 0.00 0.00 36.26 2.69
5781 5880 2.577700 TGTACTGGTTGCCGTTCAAAT 58.422 42.857 0.00 0.00 36.26 2.32
5782 5881 2.292016 TGTACTGGTTGCCGTTCAAATG 59.708 45.455 0.00 0.00 36.26 2.32
5806 5914 6.145535 GTGATTTCTTGGTGTGAAGATGTTC 58.854 40.000 0.00 0.00 31.98 3.18
5837 5945 1.116308 AAACAAGGGGGTTTTGTCCG 58.884 50.000 0.00 0.00 37.72 4.79
5838 5946 0.757561 AACAAGGGGGTTTTGTCCGG 60.758 55.000 0.00 0.00 37.77 5.14
5839 5947 1.906333 CAAGGGGGTTTTGTCCGGG 60.906 63.158 0.00 0.00 0.00 5.73
5840 5948 2.086194 AAGGGGGTTTTGTCCGGGA 61.086 57.895 0.00 0.00 0.00 5.14
5841 5949 2.035155 GGGGGTTTTGTCCGGGAG 59.965 66.667 0.00 0.00 0.00 4.30
5842 5950 2.531601 GGGGGTTTTGTCCGGGAGA 61.532 63.158 0.00 0.00 0.00 3.71
5916 6024 3.921677 TCCATAACTCTTGTCGTGGTTC 58.078 45.455 0.00 0.00 34.35 3.62
6021 6129 1.399440 CACCGTGCTGATTCTTCATGG 59.601 52.381 12.42 12.42 41.44 3.66
6084 6209 6.672357 GCAATGTTAAGAGTTACAGGCTTACG 60.672 42.308 0.00 0.00 0.00 3.18
6140 6265 5.810587 TGAGAATCAACGTCCTTTACATAGC 59.189 40.000 0.00 0.00 45.97 2.97
6141 6266 4.804139 AGAATCAACGTCCTTTACATAGCG 59.196 41.667 0.00 0.00 0.00 4.26
6142 6267 3.853831 TCAACGTCCTTTACATAGCGA 57.146 42.857 0.00 0.00 0.00 4.93
6143 6268 4.380841 TCAACGTCCTTTACATAGCGAT 57.619 40.909 0.00 0.00 0.00 4.58
6144 6269 5.503662 TCAACGTCCTTTACATAGCGATA 57.496 39.130 0.00 0.00 0.00 2.92
6145 6270 6.080648 TCAACGTCCTTTACATAGCGATAT 57.919 37.500 0.00 0.00 0.00 1.63
6146 6271 7.205737 TCAACGTCCTTTACATAGCGATATA 57.794 36.000 0.00 0.00 0.00 0.86
6147 6272 7.303261 TCAACGTCCTTTACATAGCGATATAG 58.697 38.462 0.00 0.00 0.00 1.31
6148 6273 7.173735 TCAACGTCCTTTACATAGCGATATAGA 59.826 37.037 0.00 0.00 0.00 1.98
6149 6274 7.074507 ACGTCCTTTACATAGCGATATAGAG 57.925 40.000 0.00 0.00 0.00 2.43
6154 6279 8.944029 TCCTTTACATAGCGATATAGAGTACAC 58.056 37.037 0.00 0.00 0.00 2.90
6231 6358 2.894731 TCTCCACCATTCAGTCTCTGT 58.105 47.619 0.00 0.00 32.61 3.41
6232 6359 2.564504 TCTCCACCATTCAGTCTCTGTG 59.435 50.000 0.00 0.00 32.61 3.66
6236 6363 3.589988 CACCATTCAGTCTCTGTGTACC 58.410 50.000 0.00 0.00 32.61 3.34
6244 6371 3.255149 CAGTCTCTGTGTACCGTAACCTT 59.745 47.826 0.00 0.00 0.00 3.50
6276 6403 3.947910 ACATCCAAGAAATTGGCAGTG 57.052 42.857 2.03 4.31 41.81 3.66
6282 6409 4.832266 TCCAAGAAATTGGCAGTGTTGTAT 59.168 37.500 2.03 0.00 41.81 2.29
6296 6461 6.108687 CAGTGTTGTATTTCCTATCTCAGCA 58.891 40.000 0.00 0.00 0.00 4.41
6301 6466 9.679661 TGTTGTATTTCCTATCTCAGCATTTAA 57.320 29.630 0.00 0.00 0.00 1.52
6327 6492 6.877611 ATATATTTGTAAACTCCCCTTGCG 57.122 37.500 0.00 0.00 0.00 4.85
6328 6493 2.351706 TTTGTAAACTCCCCTTGCGT 57.648 45.000 0.00 0.00 0.00 5.24
6335 6500 0.763035 ACTCCCCTTGCGTAAGTGTT 59.237 50.000 12.42 0.00 41.68 3.32
6336 6501 1.270678 ACTCCCCTTGCGTAAGTGTTC 60.271 52.381 12.42 0.00 41.68 3.18
6338 6503 1.141254 TCCCCTTGCGTAAGTGTTCAA 59.859 47.619 12.42 0.00 41.68 2.69
6378 7113 5.931146 TGCAGAAACGAAAAATATGGCAAAT 59.069 32.000 0.00 0.00 0.00 2.32
6407 7142 6.228258 TGCGACTAGGACAGTTTTAATCTTT 58.772 36.000 0.00 0.00 37.72 2.52
6427 7162 2.899976 TGATAATCGGTGCACGTCATT 58.100 42.857 11.45 10.78 44.69 2.57
6434 7169 3.183754 TCGGTGCACGTCATTTACATAG 58.816 45.455 11.45 0.00 44.69 2.23
6444 7179 7.253684 GCACGTCATTTACATAGTAGTTGAGAC 60.254 40.741 0.00 0.00 0.00 3.36
6498 7234 2.256117 AACTCCAAACACCCGAGAAG 57.744 50.000 0.00 0.00 0.00 2.85
6598 7336 6.039047 CAGTTGCCAGATAATCAATTAGCACT 59.961 38.462 1.33 0.00 31.44 4.40
6599 7337 6.261826 AGTTGCCAGATAATCAATTAGCACTC 59.738 38.462 1.33 0.00 31.44 3.51
6648 7386 0.460284 GTCTGTCCATAGTGGCACCG 60.460 60.000 15.27 2.97 37.47 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 3.800863 GAGCCACGTCGAGCTCGA 61.801 66.667 33.84 33.84 45.44 4.04
162 163 0.669318 GAGTTCAATGGCGTGTCCGA 60.669 55.000 0.00 0.00 37.80 4.55
288 290 2.009108 CGGATGCAGATTGTGGTCG 58.991 57.895 0.00 0.00 0.00 4.79
476 479 2.050918 AGATTCTTCGGATCCTTCCCC 58.949 52.381 10.75 0.00 39.01 4.81
578 582 2.415608 GGTCGCTGGATCCACGAGA 61.416 63.158 28.27 20.34 36.34 4.04
579 583 2.105128 GGTCGCTGGATCCACGAG 59.895 66.667 28.27 18.82 36.34 4.18
580 584 3.458163 GGGTCGCTGGATCCACGA 61.458 66.667 25.65 25.65 43.46 4.35
653 664 0.758685 CAGGAGAGGCCGATCTTCCT 60.759 60.000 9.71 9.73 43.43 3.36
682 694 4.796495 CCTGGCGGCTGTAACCCC 62.796 72.222 11.43 0.00 0.00 4.95
712 726 0.961857 TCTGCAGGGTACGCGAACTA 60.962 55.000 15.93 0.00 0.00 2.24
723 737 1.153489 CACCGAGTCATCTGCAGGG 60.153 63.158 15.13 7.65 0.00 4.45
724 738 1.812922 GCACCGAGTCATCTGCAGG 60.813 63.158 15.13 0.00 29.37 4.85
726 740 1.079612 CTGCACCGAGTCATCTGCA 60.080 57.895 6.29 6.29 35.06 4.41
727 741 0.671781 AACTGCACCGAGTCATCTGC 60.672 55.000 0.00 0.00 0.00 4.26
728 742 1.354040 GAACTGCACCGAGTCATCTG 58.646 55.000 0.00 0.00 0.00 2.90
729 743 0.109086 CGAACTGCACCGAGTCATCT 60.109 55.000 0.00 0.00 0.00 2.90
730 744 1.687494 GCGAACTGCACCGAGTCATC 61.687 60.000 2.98 0.00 45.45 2.92
731 745 1.738099 GCGAACTGCACCGAGTCAT 60.738 57.895 2.98 0.00 45.45 3.06
732 746 2.355837 GCGAACTGCACCGAGTCA 60.356 61.111 2.98 0.00 45.45 3.41
741 755 3.982058 GTGTGGTAGATATAGCGAACTGC 59.018 47.826 0.00 0.00 46.98 4.40
742 756 4.278669 AGGTGTGGTAGATATAGCGAACTG 59.721 45.833 0.00 0.00 0.00 3.16
743 757 4.278669 CAGGTGTGGTAGATATAGCGAACT 59.721 45.833 0.00 0.00 0.00 3.01
744 758 4.547532 CAGGTGTGGTAGATATAGCGAAC 58.452 47.826 0.00 0.00 0.00 3.95
745 759 3.005472 GCAGGTGTGGTAGATATAGCGAA 59.995 47.826 0.00 0.00 0.00 4.70
746 760 2.557056 GCAGGTGTGGTAGATATAGCGA 59.443 50.000 0.00 0.00 0.00 4.93
747 761 2.296190 TGCAGGTGTGGTAGATATAGCG 59.704 50.000 0.00 0.00 0.00 4.26
748 762 4.543590 ATGCAGGTGTGGTAGATATAGC 57.456 45.455 0.00 0.00 0.00 2.97
749 763 8.072321 AGATTATGCAGGTGTGGTAGATATAG 57.928 38.462 0.00 0.00 0.00 1.31
750 764 8.435931 AAGATTATGCAGGTGTGGTAGATATA 57.564 34.615 0.00 0.00 0.00 0.86
751 765 6.942163 AGATTATGCAGGTGTGGTAGATAT 57.058 37.500 0.00 0.00 0.00 1.63
752 766 6.239600 GGAAGATTATGCAGGTGTGGTAGATA 60.240 42.308 0.00 0.00 0.00 1.98
753 767 5.455326 GGAAGATTATGCAGGTGTGGTAGAT 60.455 44.000 0.00 0.00 0.00 1.98
754 768 4.141711 GGAAGATTATGCAGGTGTGGTAGA 60.142 45.833 0.00 0.00 0.00 2.59
755 769 4.130118 GGAAGATTATGCAGGTGTGGTAG 58.870 47.826 0.00 0.00 0.00 3.18
756 770 3.431626 CGGAAGATTATGCAGGTGTGGTA 60.432 47.826 0.00 0.00 0.00 3.25
757 771 2.680805 CGGAAGATTATGCAGGTGTGGT 60.681 50.000 0.00 0.00 0.00 4.16
758 772 1.942657 CGGAAGATTATGCAGGTGTGG 59.057 52.381 0.00 0.00 0.00 4.17
759 773 2.632377 ACGGAAGATTATGCAGGTGTG 58.368 47.619 0.00 0.00 0.00 3.82
760 774 3.350219 AACGGAAGATTATGCAGGTGT 57.650 42.857 0.00 0.00 0.00 4.16
761 775 4.188462 TGTAACGGAAGATTATGCAGGTG 58.812 43.478 0.00 0.00 0.00 4.00
762 776 4.481368 TGTAACGGAAGATTATGCAGGT 57.519 40.909 0.00 0.00 0.00 4.00
763 777 5.156804 GTTGTAACGGAAGATTATGCAGG 57.843 43.478 0.00 0.00 0.00 4.85
778 792 3.651562 AATATGCTCGTGCGTTGTAAC 57.348 42.857 9.76 0.00 43.34 2.50
779 793 3.997276 CAAATATGCTCGTGCGTTGTAA 58.003 40.909 9.76 0.00 43.34 2.41
780 794 3.649870 CAAATATGCTCGTGCGTTGTA 57.350 42.857 9.76 0.00 43.34 2.41
781 795 2.525750 CAAATATGCTCGTGCGTTGT 57.474 45.000 9.76 0.00 43.34 3.32
796 810 9.627123 TGTGCTTTTTATCCTATACTAGCAAAT 57.373 29.630 0.00 0.00 38.89 2.32
797 811 9.627123 ATGTGCTTTTTATCCTATACTAGCAAA 57.373 29.630 0.00 0.00 38.89 3.68
798 812 9.627123 AATGTGCTTTTTATCCTATACTAGCAA 57.373 29.630 0.00 0.00 38.89 3.91
799 813 9.627123 AAATGTGCTTTTTATCCTATACTAGCA 57.373 29.630 0.00 0.00 35.26 3.49
824 838 7.984050 TGCTTTTTATCCATGTCTCAACAAAAA 59.016 29.630 0.00 0.00 39.30 1.94
825 839 7.437862 GTGCTTTTTATCCATGTCTCAACAAAA 59.562 33.333 0.00 0.00 39.30 2.44
826 840 6.922957 GTGCTTTTTATCCATGTCTCAACAAA 59.077 34.615 0.00 0.00 39.30 2.83
827 841 6.040278 TGTGCTTTTTATCCATGTCTCAACAA 59.960 34.615 0.00 0.00 39.30 2.83
828 842 5.534278 TGTGCTTTTTATCCATGTCTCAACA 59.466 36.000 0.00 0.00 40.38 3.33
829 843 6.012658 TGTGCTTTTTATCCATGTCTCAAC 57.987 37.500 0.00 0.00 0.00 3.18
830 844 6.350361 CCATGTGCTTTTTATCCATGTCTCAA 60.350 38.462 0.00 0.00 32.87 3.02
831 845 5.125900 CCATGTGCTTTTTATCCATGTCTCA 59.874 40.000 0.00 0.00 32.87 3.27
832 846 5.357878 TCCATGTGCTTTTTATCCATGTCTC 59.642 40.000 0.00 0.00 32.87 3.36
833 847 5.263599 TCCATGTGCTTTTTATCCATGTCT 58.736 37.500 0.00 0.00 32.87 3.41
834 848 5.581126 TCCATGTGCTTTTTATCCATGTC 57.419 39.130 0.00 0.00 32.87 3.06
835 849 5.999205 TTCCATGTGCTTTTTATCCATGT 57.001 34.783 0.00 0.00 32.87 3.21
836 850 6.400568 AGTTTCCATGTGCTTTTTATCCATG 58.599 36.000 0.00 0.00 34.18 3.66
837 851 6.610075 AGTTTCCATGTGCTTTTTATCCAT 57.390 33.333 0.00 0.00 0.00 3.41
862 876 1.139095 CGTCTTACGAGCCAGGTCC 59.861 63.158 0.00 0.00 46.05 4.46
875 889 2.224784 GGCCATGTTTACGTTTCGTCTT 59.775 45.455 0.00 0.00 41.54 3.01
986 1000 0.699399 ACTGAGGAAGAGAGACGGGA 59.301 55.000 0.00 0.00 0.00 5.14
987 1001 1.099689 GACTGAGGAAGAGAGACGGG 58.900 60.000 0.00 0.00 0.00 5.28
988 1002 0.730265 CGACTGAGGAAGAGAGACGG 59.270 60.000 0.00 0.00 0.00 4.79
1126 1140 2.662596 CAGAGGTTAGTGCCGCCA 59.337 61.111 0.00 0.00 0.00 5.69
1127 1141 1.972660 ATCCAGAGGTTAGTGCCGCC 61.973 60.000 0.00 0.00 0.00 6.13
1132 1146 1.202463 CGCCAGATCCAGAGGTTAGTG 60.202 57.143 0.00 0.00 0.00 2.74
1262 1282 5.224888 GTGTTGTACTCGGAGACATTGTTA 58.775 41.667 12.86 0.00 0.00 2.41
1292 1312 4.631740 TGCTGGACGAGGGACCCA 62.632 66.667 14.60 0.00 0.00 4.51
1361 1381 2.743928 GCCACTGCTCGGAACTGG 60.744 66.667 0.00 0.00 33.53 4.00
1415 1435 0.179127 ACACCAGATCATCGACGCAG 60.179 55.000 0.00 0.00 0.00 5.18
1472 1492 5.123820 TGAAAGCATTTAATTCAGACTCGGG 59.876 40.000 0.00 0.00 39.27 5.14
1496 1516 1.282157 GGTAGGGCCTGAAGACAACAT 59.718 52.381 18.53 0.00 0.00 2.71
1572 1592 5.739070 GCCGACTATGAGATTGTGGAATGTA 60.739 44.000 0.00 0.00 0.00 2.29
1617 1637 3.003480 ACGGAAGTAGAAAGCATCTTGC 58.997 45.455 0.00 0.00 46.88 4.01
1638 1658 3.715315 AGCCCATTTCTCTCATCTGATCA 59.285 43.478 0.00 0.00 0.00 2.92
1738 1758 8.766994 TGAATTAAGCCATTAGCCTAATTTCT 57.233 30.769 0.00 0.00 44.50 2.52
1739 1759 9.987272 AATGAATTAAGCCATTAGCCTAATTTC 57.013 29.630 0.00 0.00 44.50 2.17
1740 1760 9.768662 CAATGAATTAAGCCATTAGCCTAATTT 57.231 29.630 0.00 0.00 44.50 1.82
1878 1898 1.133407 GAGCACGAGTAACAGAGGAGG 59.867 57.143 0.00 0.00 0.00 4.30
2022 2042 1.831736 AGGACCCCTTACACTTGATCG 59.168 52.381 0.00 0.00 0.00 3.69
2337 2357 3.309296 TCCAGAGGCTCTTATAACCCTG 58.691 50.000 15.90 0.60 0.00 4.45
2446 2466 2.224719 ACTTGCCACAAGCTGAAGAGAT 60.225 45.455 7.23 0.00 44.23 2.75
2539 2559 5.107837 CGTTCAAATAGATATCCGTGTGAGC 60.108 44.000 0.00 1.12 0.00 4.26
2544 2564 6.475727 AGTTGACGTTCAAATAGATATCCGTG 59.524 38.462 0.00 0.00 38.22 4.94
2554 2641 6.091169 GTCCGGAATTAGTTGACGTTCAAATA 59.909 38.462 5.23 0.00 38.22 1.40
2555 2642 4.998672 TCCGGAATTAGTTGACGTTCAAAT 59.001 37.500 0.00 0.00 38.22 2.32
2561 2648 1.403249 CCGTCCGGAATTAGTTGACGT 60.403 52.381 5.23 0.00 45.29 4.34
2835 2922 7.560368 AGAGAAAAGGATGAGTACAGTTATGG 58.440 38.462 0.00 0.00 0.00 2.74
2966 3053 3.873910 TGGCAAGTTGTATAGCTCTTCC 58.126 45.455 4.48 0.00 0.00 3.46
3120 3207 3.674682 GCTGAGCAGTAACTAGACACTGG 60.675 52.174 21.72 11.49 42.00 4.00
3196 3283 8.969260 TCAATTTCATGACATGAGCTAACTAT 57.031 30.769 17.29 2.97 40.94 2.12
3373 3460 6.732531 ACCATGCAATGTATCATTAGATCG 57.267 37.500 0.00 0.00 44.81 3.69
3689 3777 3.243359 AGGACAAACATGATGGGTTGT 57.757 42.857 14.17 14.17 34.04 3.32
4282 4371 7.125811 AGCATATAGGATTCATACGGTACCAAT 59.874 37.037 13.54 3.22 0.00 3.16
4335 4424 4.096081 GCATATTATCCCAAGATGCTCAGC 59.904 45.833 8.84 0.00 39.81 4.26
4669 4761 8.469309 TTCTTTCAGTCATTTTCTCCTGAAAT 57.531 30.769 12.47 0.00 46.77 2.17
5121 5216 2.268988 TATTGCGTGGCATGCACAGC 62.269 55.000 32.50 20.08 40.28 4.40
5123 5218 0.600057 TTTATTGCGTGGCATGCACA 59.400 45.000 32.50 22.74 40.28 4.57
5272 5367 1.374125 CACAAGCCGTGGATCGTCA 60.374 57.895 0.00 0.00 42.34 4.35
5353 5448 0.178068 AGAGCAGTTTGACCGTGTGT 59.822 50.000 0.00 0.00 0.00 3.72
5354 5449 2.061773 CTAGAGCAGTTTGACCGTGTG 58.938 52.381 0.00 0.00 0.00 3.82
5383 5480 2.557924 CAAGTTTCAGCCTGCATTGGTA 59.442 45.455 0.00 0.00 0.00 3.25
5395 5492 5.359860 ACCTCCTTACCAAAACAAGTTTCAG 59.640 40.000 0.00 0.00 31.45 3.02
5445 5544 8.631480 AAAAGTAGTTATTCGGTTTTCTGGAT 57.369 30.769 0.00 0.00 0.00 3.41
5480 5579 4.520492 TCTTGATGGTTTCTCCTTGCTTTC 59.480 41.667 0.00 0.00 37.07 2.62
5719 5818 2.039818 TTTGAACGGCAACCAGTACA 57.960 45.000 0.00 0.00 35.91 2.90
5720 5819 2.292292 ACATTTGAACGGCAACCAGTAC 59.708 45.455 0.00 0.00 35.91 2.73
5721 5820 2.292016 CACATTTGAACGGCAACCAGTA 59.708 45.455 0.00 0.00 35.91 2.74
5722 5821 1.066908 CACATTTGAACGGCAACCAGT 59.933 47.619 0.00 0.00 35.91 4.00
5725 5824 2.723124 ATCACATTTGAACGGCAACC 57.277 45.000 0.00 0.00 35.91 3.77
5726 5825 3.380142 ACAATCACATTTGAACGGCAAC 58.620 40.909 0.00 0.00 35.91 4.17
5727 5826 3.724508 ACAATCACATTTGAACGGCAA 57.275 38.095 0.00 0.00 34.61 4.52
5728 5827 3.724508 AACAATCACATTTGAACGGCA 57.275 38.095 0.00 0.00 34.61 5.69
5729 5828 5.219633 ACTAAACAATCACATTTGAACGGC 58.780 37.500 0.00 0.00 34.61 5.68
5730 5829 5.563751 CGACTAAACAATCACATTTGAACGG 59.436 40.000 0.00 0.00 34.61 4.44
5731 5830 6.133392 ACGACTAAACAATCACATTTGAACG 58.867 36.000 0.00 0.00 34.61 3.95
5732 5831 7.129622 TGACGACTAAACAATCACATTTGAAC 58.870 34.615 0.00 0.00 34.61 3.18
5733 5832 7.011950 ACTGACGACTAAACAATCACATTTGAA 59.988 33.333 0.00 0.00 34.61 2.69
5734 5833 6.481976 ACTGACGACTAAACAATCACATTTGA 59.518 34.615 0.00 0.00 35.73 2.69
5735 5834 6.658831 ACTGACGACTAAACAATCACATTTG 58.341 36.000 0.00 0.00 0.00 2.32
5736 5835 6.861065 ACTGACGACTAAACAATCACATTT 57.139 33.333 0.00 0.00 0.00 2.32
5737 5836 6.861065 AACTGACGACTAAACAATCACATT 57.139 33.333 0.00 0.00 0.00 2.71
5738 5837 6.260050 ACAAACTGACGACTAAACAATCACAT 59.740 34.615 0.00 0.00 0.00 3.21
5739 5838 5.583061 ACAAACTGACGACTAAACAATCACA 59.417 36.000 0.00 0.00 0.00 3.58
5740 5839 6.044512 ACAAACTGACGACTAAACAATCAC 57.955 37.500 0.00 0.00 0.00 3.06
5741 5840 6.982141 AGTACAAACTGACGACTAAACAATCA 59.018 34.615 0.00 0.00 33.57 2.57
5742 5841 7.404139 AGTACAAACTGACGACTAAACAATC 57.596 36.000 0.00 0.00 33.57 2.67
5756 5855 7.607990 TTTGAACGGCAACCAGTACAAACTG 62.608 44.000 0.00 0.00 41.52 3.16
5757 5856 1.944709 GAACGGCAACCAGTACAAACT 59.055 47.619 0.00 0.00 35.91 2.66
5758 5857 1.671845 TGAACGGCAACCAGTACAAAC 59.328 47.619 0.00 0.00 0.00 2.93
5759 5858 2.039818 TGAACGGCAACCAGTACAAA 57.960 45.000 0.00 0.00 0.00 2.83
5760 5859 2.039818 TTGAACGGCAACCAGTACAA 57.960 45.000 0.00 0.00 0.00 2.41
5761 5860 2.039818 TTTGAACGGCAACCAGTACA 57.960 45.000 0.00 0.00 35.91 2.90
5762 5861 2.292292 ACATTTGAACGGCAACCAGTAC 59.708 45.455 0.00 0.00 35.91 2.73
5763 5862 2.292016 CACATTTGAACGGCAACCAGTA 59.708 45.455 0.00 0.00 35.91 2.74
5764 5863 1.066908 CACATTTGAACGGCAACCAGT 59.933 47.619 0.00 0.00 35.91 4.00
5765 5864 1.336440 TCACATTTGAACGGCAACCAG 59.664 47.619 0.00 0.00 35.91 4.00
5766 5865 1.393603 TCACATTTGAACGGCAACCA 58.606 45.000 0.00 0.00 35.91 3.67
5767 5866 2.723124 ATCACATTTGAACGGCAACC 57.277 45.000 0.00 0.00 35.91 3.77
5768 5867 4.298332 AGAAATCACATTTGAACGGCAAC 58.702 39.130 0.00 0.00 35.91 4.17
5769 5868 4.582701 AGAAATCACATTTGAACGGCAA 57.417 36.364 0.00 0.00 34.61 4.52
5770 5869 4.297510 CAAGAAATCACATTTGAACGGCA 58.702 39.130 0.00 0.00 34.61 5.69
5771 5870 3.674753 CCAAGAAATCACATTTGAACGGC 59.325 43.478 0.00 0.00 34.61 5.68
5772 5871 4.681025 CACCAAGAAATCACATTTGAACGG 59.319 41.667 0.00 0.00 34.61 4.44
5773 5872 5.173673 CACACCAAGAAATCACATTTGAACG 59.826 40.000 0.00 0.00 34.61 3.95
5774 5873 6.272318 TCACACCAAGAAATCACATTTGAAC 58.728 36.000 0.00 0.00 34.61 3.18
5775 5874 6.462552 TCACACCAAGAAATCACATTTGAA 57.537 33.333 0.00 0.00 34.61 2.69
5776 5875 6.320926 TCTTCACACCAAGAAATCACATTTGA 59.679 34.615 0.00 0.00 30.46 2.69
5777 5876 6.506147 TCTTCACACCAAGAAATCACATTTG 58.494 36.000 0.00 0.00 31.47 2.32
5778 5877 6.713762 TCTTCACACCAAGAAATCACATTT 57.286 33.333 0.00 0.00 34.64 2.32
5779 5878 6.266103 ACATCTTCACACCAAGAAATCACATT 59.734 34.615 0.00 0.00 35.99 2.71
5780 5879 5.771666 ACATCTTCACACCAAGAAATCACAT 59.228 36.000 0.00 0.00 35.99 3.21
5781 5880 5.132502 ACATCTTCACACCAAGAAATCACA 58.867 37.500 0.00 0.00 35.99 3.58
5782 5881 5.695851 ACATCTTCACACCAAGAAATCAC 57.304 39.130 0.00 0.00 35.99 3.06
5902 6010 3.309388 CACACTAGAACCACGACAAGAG 58.691 50.000 0.00 0.00 0.00 2.85
6021 6129 3.406764 AGTGCAGATCTTTCAGGTTGTC 58.593 45.455 0.00 0.00 0.00 3.18
6084 6209 1.400494 AGTTTGACACGTTCTGCAACC 59.600 47.619 0.00 0.00 0.00 3.77
6113 6238 6.295039 TGTAAAGGACGTTGATTCTCAAAC 57.705 37.500 0.00 0.00 38.22 2.93
6133 6258 8.529476 TCTCTGTGTACTCTATATCGCTATGTA 58.471 37.037 0.00 0.00 0.00 2.29
6134 6259 7.387643 TCTCTGTGTACTCTATATCGCTATGT 58.612 38.462 0.00 0.00 0.00 2.29
6135 6260 7.835634 TCTCTGTGTACTCTATATCGCTATG 57.164 40.000 0.00 0.00 0.00 2.23
6137 6262 9.368674 GTTATCTCTGTGTACTCTATATCGCTA 57.631 37.037 0.00 0.00 0.00 4.26
6138 6263 7.063662 CGTTATCTCTGTGTACTCTATATCGCT 59.936 40.741 0.00 0.00 0.00 4.93
6139 6264 7.063191 TCGTTATCTCTGTGTACTCTATATCGC 59.937 40.741 0.00 0.00 0.00 4.58
6140 6265 8.463456 TCGTTATCTCTGTGTACTCTATATCG 57.537 38.462 0.00 1.00 0.00 2.92
6146 6271 9.790389 CTTTATTTCGTTATCTCTGTGTACTCT 57.210 33.333 0.00 0.00 0.00 3.24
6147 6272 9.784680 TCTTTATTTCGTTATCTCTGTGTACTC 57.215 33.333 0.00 0.00 0.00 2.59
6231 6358 5.613329 AGATTTTGACAAGGTTACGGTACA 58.387 37.500 0.00 0.00 0.00 2.90
6232 6359 7.171337 TGTTAGATTTTGACAAGGTTACGGTAC 59.829 37.037 0.00 0.00 0.00 3.34
6236 6363 7.094975 TGGATGTTAGATTTTGACAAGGTTACG 60.095 37.037 0.00 0.00 0.00 3.18
6244 6371 9.695526 CAATTTCTTGGATGTTAGATTTTGACA 57.304 29.630 0.00 0.00 0.00 3.58
6276 6403 9.937175 GTTAAATGCTGAGATAGGAAATACAAC 57.063 33.333 0.00 0.00 0.00 3.32
6301 6466 7.201785 CGCAAGGGGAGTTTACAAATATATTGT 60.202 37.037 0.00 2.75 36.49 2.71
6378 7113 2.130272 ACTGTCCTAGTCGCATCTCA 57.870 50.000 0.00 0.00 33.17 3.27
6407 7142 2.595124 ATGACGTGCACCGATTATCA 57.405 45.000 12.15 6.18 40.70 2.15
6427 7162 9.787435 ATTTGGTTTGTCTCAACTACTATGTAA 57.213 29.630 0.00 0.00 0.00 2.41
6434 7169 7.201705 GCCCTATATTTGGTTTGTCTCAACTAC 60.202 40.741 0.00 0.00 0.00 2.73
6444 7179 4.402155 TGAGCTTGCCCTATATTTGGTTTG 59.598 41.667 0.00 0.00 0.00 2.93
6498 7234 1.166531 GGGTGTGAACTGGTGTGCTC 61.167 60.000 0.00 0.00 0.00 4.26
6546 7282 2.680221 GCTCTCTGTACTCTACCGTGGA 60.680 54.545 0.00 0.00 0.00 4.02
6599 7337 4.810191 ACTGTTCTTGTTCCTAGCTAGG 57.190 45.455 30.94 30.94 45.02 3.02
6694 7433 8.345565 TCTTTAGCTTTGATTGAAGACTTGAAC 58.654 33.333 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.