Multiple sequence alignment - TraesCS7A01G353100

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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 TraesCS7A01G353100 chr7A 100.000 2960 0 0 1 2960 516879379 516876420 0.000000e+00 5467.0
1 TraesCS7A01G353100 chr7A 88.987 227 20 2 1 222 516477888 516477662 2.910000e-70 276.0
2 TraesCS7A01G353100 chr7D 92.147 1719 118 11 872 2576 478363202 478364917 0.000000e+00 2410.0
3 TraesCS7A01G353100 chr7D 92.643 734 38 6 1 719 66960535 66959803 0.000000e+00 1042.0
4 TraesCS7A01G353100 chr7D 90.190 316 14 7 243 543 488051638 488051325 2.140000e-106 396.0
5 TraesCS7A01G353100 chr7D 90.547 201 16 2 2574 2773 478365030 478365228 2.260000e-66 263.0
6 TraesCS7A01G353100 chr7D 96.154 52 2 0 2892 2943 478365472 478365523 5.260000e-13 86.1
7 TraesCS7A01G353100 chr7B 90.300 1433 88 23 872 2302 503501622 503503005 0.000000e+00 1829.0
8 TraesCS7A01G353100 chr7B 86.957 276 31 4 2304 2576 503503090 503503363 3.710000e-79 305.0
9 TraesCS7A01G353100 chr2A 92.779 734 37 6 1 719 409160445 409161177 0.000000e+00 1048.0
10 TraesCS7A01G353100 chr2A 90.980 643 36 7 1 627 214713842 214714478 0.000000e+00 846.0
11 TraesCS7A01G353100 chr1B 85.714 763 59 22 1 720 482340186 482340941 0.000000e+00 760.0
12 TraesCS7A01G353100 chr1B 90.872 493 29 5 243 719 167994579 167995071 0.000000e+00 647.0
13 TraesCS7A01G353100 chr1B 86.613 493 48 8 243 719 685935390 685934900 2.020000e-146 529.0
14 TraesCS7A01G353100 chr1B 94.118 289 17 0 1 289 167994308 167994596 9.740000e-120 440.0
15 TraesCS7A01G353100 chr2B 91.593 452 22 6 1 436 678958446 678958897 7.010000e-171 610.0
16 TraesCS7A01G353100 chr2B 90.687 451 27 4 1 436 278802733 278802283 1.180000e-163 586.0
17 TraesCS7A01G353100 chr2B 88.224 501 39 10 243 727 155968069 155968565 5.500000e-162 580.0
18 TraesCS7A01G353100 chr2D 88.492 504 36 10 243 727 105610446 105609946 9.140000e-165 590.0
19 TraesCS7A01G353100 chr2D 87.525 505 40 11 243 727 91897244 91897745 1.990000e-156 562.0
20 TraesCS7A01G353100 chr2D 89.954 219 17 2 9 222 77172757 77172539 8.080000e-71 278.0
21 TraesCS7A01G353100 chr5D 87.992 483 38 8 243 707 546367232 546366752 1.200000e-153 553.0
22 TraesCS7A01G353100 chr4D 87.789 475 35 11 262 720 47736990 47737457 4.340000e-148 534.0
23 TraesCS7A01G353100 chr1D 90.149 335 15 8 224 543 120597936 120597605 1.270000e-113 420.0
24 TraesCS7A01G353100 chr1D 89.873 316 15 7 243 543 75862509 75862822 9.950000e-105 390.0
25 TraesCS7A01G353100 chrUn 89.873 316 16 6 243 543 96530924 96530610 2.770000e-105 392.0
26 TraesCS7A01G353100 chr1A 86.047 387 28 5 1 361 557998488 557998874 2.770000e-105 392.0
27 TraesCS7A01G353100 chr1A 84.444 315 23 5 1 289 57632858 57633172 1.340000e-73 287.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G353100 chr7A 516876420 516879379 2959 True 5467.0 5467 100.000000 1 2960 1 chr7A.!!$R2 2959
1 TraesCS7A01G353100 chr7D 66959803 66960535 732 True 1042.0 1042 92.643000 1 719 1 chr7D.!!$R1 718
2 TraesCS7A01G353100 chr7D 478363202 478365523 2321 False 919.7 2410 92.949333 872 2943 3 chr7D.!!$F1 2071
3 TraesCS7A01G353100 chr7B 503501622 503503363 1741 False 1067.0 1829 88.628500 872 2576 2 chr7B.!!$F1 1704
4 TraesCS7A01G353100 chr2A 409160445 409161177 732 False 1048.0 1048 92.779000 1 719 1 chr2A.!!$F2 718
5 TraesCS7A01G353100 chr2A 214713842 214714478 636 False 846.0 846 90.980000 1 627 1 chr2A.!!$F1 626
6 TraesCS7A01G353100 chr1B 482340186 482340941 755 False 760.0 760 85.714000 1 720 1 chr1B.!!$F1 719
7 TraesCS7A01G353100 chr1B 167994308 167995071 763 False 543.5 647 92.495000 1 719 2 chr1B.!!$F2 718
8 TraesCS7A01G353100 chr2D 105609946 105610446 500 True 590.0 590 88.492000 243 727 1 chr2D.!!$R2 484
9 TraesCS7A01G353100 chr2D 91897244 91897745 501 False 562.0 562 87.525000 243 727 1 chr2D.!!$F1 484

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
698 783 0.036732 TGTTCTTCTCCCGCTGCAAT 59.963 50.0 0.0 0.0 0.0 3.56 F
967 1052 0.102120 CTGCACGTCTCCTCTCCATC 59.898 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1748 1873 0.105760 AACCATGGCCTTGACCACAA 60.106 50.0 19.85 0.0 44.17 3.33 R
2107 2232 0.533755 GCACCGCATCTGAGGCTAAT 60.534 55.0 12.78 0.0 38.67 1.73 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
118 123 4.390297 GCTCTTATTTTTCTGCTCGACACT 59.610 41.667 0.00 0.00 0.00 3.55
125 130 0.673956 TCTGCTCGACACTCTAGCGT 60.674 55.000 0.00 0.00 37.94 5.07
142 147 2.129607 GCGTCCGTCACAAACTCTTAA 58.870 47.619 0.00 0.00 0.00 1.85
195 200 2.283145 AGCACAAGCAATTGGACTCT 57.717 45.000 7.72 0.00 45.49 3.24
222 249 2.566913 TGTGTAACACAAACTCCGCAT 58.433 42.857 0.00 0.00 45.67 4.73
323 386 2.037381 GCTATGCTACCCAGTCCCTAAC 59.963 54.545 0.00 0.00 0.00 2.34
335 398 1.844497 GTCCCTAACCCTAGCCAACAT 59.156 52.381 0.00 0.00 0.00 2.71
363 426 2.956132 TGGAAATCTTTGTTGCCTCCA 58.044 42.857 0.00 0.00 0.00 3.86
366 429 5.083122 TGGAAATCTTTGTTGCCTCCATAA 58.917 37.500 0.00 0.00 0.00 1.90
372 450 4.701651 TCTTTGTTGCCTCCATAATGACTG 59.298 41.667 0.00 0.00 0.00 3.51
375 453 2.615912 GTTGCCTCCATAATGACTGAGC 59.384 50.000 0.00 0.00 0.00 4.26
545 625 6.292274 GGTTATGTTTTTGCACAACACATCTG 60.292 38.462 11.90 0.00 36.97 2.90
548 629 4.993584 TGTTTTTGCACAACACATCTGTTT 59.006 33.333 6.56 0.00 38.66 2.83
628 709 1.228521 TGGTAGTCGGTCGTGGGAA 60.229 57.895 0.00 0.00 0.00 3.97
698 783 0.036732 TGTTCTTCTCCCGCTGCAAT 59.963 50.000 0.00 0.00 0.00 3.56
721 806 2.785562 ACGGGCATTTGTGCTAGTAAA 58.214 42.857 0.07 0.00 34.73 2.01
723 808 3.761752 ACGGGCATTTGTGCTAGTAAAAT 59.238 39.130 0.07 0.00 34.73 1.82
724 809 4.944930 ACGGGCATTTGTGCTAGTAAAATA 59.055 37.500 0.07 0.00 34.73 1.40
727 812 6.252655 CGGGCATTTGTGCTAGTAAAATAAAC 59.747 38.462 0.07 0.00 34.73 2.01
728 813 7.093992 GGGCATTTGTGCTAGTAAAATAAACA 58.906 34.615 0.07 0.00 34.73 2.83
729 814 7.062956 GGGCATTTGTGCTAGTAAAATAAACAC 59.937 37.037 0.07 0.00 34.73 3.32
730 815 7.596995 GGCATTTGTGCTAGTAAAATAAACACA 59.403 33.333 0.07 0.00 34.97 3.72
731 816 8.973378 GCATTTGTGCTAGTAAAATAAACACAA 58.027 29.630 0.00 0.00 42.79 3.33
735 820 8.549777 TGTGCTAGTAAAATAAACACAAAACG 57.450 30.769 0.00 0.00 33.94 3.60
736 821 7.644551 TGTGCTAGTAAAATAAACACAAAACGG 59.355 33.333 0.00 0.00 33.94 4.44
737 822 7.856894 GTGCTAGTAAAATAAACACAAAACGGA 59.143 33.333 0.00 0.00 0.00 4.69
738 823 8.071368 TGCTAGTAAAATAAACACAAAACGGAG 58.929 33.333 0.00 0.00 0.00 4.63
739 824 8.284693 GCTAGTAAAATAAACACAAAACGGAGA 58.715 33.333 0.00 0.00 0.00 3.71
742 827 8.132995 AGTAAAATAAACACAAAACGGAGAAGG 58.867 33.333 0.00 0.00 0.00 3.46
743 828 6.702716 AAATAAACACAAAACGGAGAAGGA 57.297 33.333 0.00 0.00 0.00 3.36
744 829 6.702716 AATAAACACAAAACGGAGAAGGAA 57.297 33.333 0.00 0.00 0.00 3.36
745 830 4.365899 AAACACAAAACGGAGAAGGAAC 57.634 40.909 0.00 0.00 0.00 3.62
746 831 2.993937 ACACAAAACGGAGAAGGAACA 58.006 42.857 0.00 0.00 0.00 3.18
747 832 2.943033 ACACAAAACGGAGAAGGAACAG 59.057 45.455 0.00 0.00 0.00 3.16
748 833 3.202906 CACAAAACGGAGAAGGAACAGA 58.797 45.455 0.00 0.00 0.00 3.41
749 834 3.625764 CACAAAACGGAGAAGGAACAGAA 59.374 43.478 0.00 0.00 0.00 3.02
750 835 4.095782 CACAAAACGGAGAAGGAACAGAAA 59.904 41.667 0.00 0.00 0.00 2.52
751 836 4.703093 ACAAAACGGAGAAGGAACAGAAAA 59.297 37.500 0.00 0.00 0.00 2.29
752 837 5.184287 ACAAAACGGAGAAGGAACAGAAAAA 59.816 36.000 0.00 0.00 0.00 1.94
753 838 5.500645 AAACGGAGAAGGAACAGAAAAAG 57.499 39.130 0.00 0.00 0.00 2.27
754 839 2.879026 ACGGAGAAGGAACAGAAAAAGC 59.121 45.455 0.00 0.00 0.00 3.51
755 840 3.142174 CGGAGAAGGAACAGAAAAAGCT 58.858 45.455 0.00 0.00 0.00 3.74
756 841 3.058639 CGGAGAAGGAACAGAAAAAGCTG 60.059 47.826 0.00 0.00 41.63 4.24
757 842 3.254411 GGAGAAGGAACAGAAAAAGCTGG 59.746 47.826 0.00 0.00 40.20 4.85
758 843 4.137543 GAGAAGGAACAGAAAAAGCTGGA 58.862 43.478 0.00 0.00 40.20 3.86
759 844 4.734266 AGAAGGAACAGAAAAAGCTGGAT 58.266 39.130 0.00 0.00 40.20 3.41
760 845 5.143369 AGAAGGAACAGAAAAAGCTGGATT 58.857 37.500 0.00 0.00 40.20 3.01
761 846 5.242615 AGAAGGAACAGAAAAAGCTGGATTC 59.757 40.000 0.00 0.00 40.20 2.52
762 847 4.473444 AGGAACAGAAAAAGCTGGATTCA 58.527 39.130 8.55 0.00 40.20 2.57
763 848 5.082425 AGGAACAGAAAAAGCTGGATTCAT 58.918 37.500 8.55 0.00 40.20 2.57
764 849 5.184671 AGGAACAGAAAAAGCTGGATTCATC 59.815 40.000 8.55 4.68 40.20 2.92
765 850 5.047802 GGAACAGAAAAAGCTGGATTCATCA 60.048 40.000 8.55 0.00 40.20 3.07
766 851 6.409524 AACAGAAAAAGCTGGATTCATCAA 57.590 33.333 8.55 0.00 40.20 2.57
767 852 6.409524 ACAGAAAAAGCTGGATTCATCAAA 57.590 33.333 8.55 0.00 40.20 2.69
768 853 6.218746 ACAGAAAAAGCTGGATTCATCAAAC 58.781 36.000 8.55 0.00 40.20 2.93
769 854 6.183360 ACAGAAAAAGCTGGATTCATCAAACA 60.183 34.615 8.55 0.00 40.20 2.83
770 855 6.702723 CAGAAAAAGCTGGATTCATCAAACAA 59.297 34.615 8.55 0.00 32.26 2.83
771 856 7.225145 CAGAAAAAGCTGGATTCATCAAACAAA 59.775 33.333 8.55 0.00 32.26 2.83
772 857 7.769970 AGAAAAAGCTGGATTCATCAAACAAAA 59.230 29.630 8.55 0.00 0.00 2.44
773 858 7.862512 AAAAGCTGGATTCATCAAACAAAAA 57.137 28.000 0.00 0.00 0.00 1.94
790 875 2.120765 AAAAACCCCGAACAGCACC 58.879 52.632 0.00 0.00 0.00 5.01
791 876 0.684805 AAAAACCCCGAACAGCACCA 60.685 50.000 0.00 0.00 0.00 4.17
792 877 0.684805 AAAACCCCGAACAGCACCAA 60.685 50.000 0.00 0.00 0.00 3.67
793 878 0.684805 AAACCCCGAACAGCACCAAA 60.685 50.000 0.00 0.00 0.00 3.28
794 879 1.106944 AACCCCGAACAGCACCAAAG 61.107 55.000 0.00 0.00 0.00 2.77
795 880 2.644992 CCCGAACAGCACCAAAGC 59.355 61.111 0.00 0.00 0.00 3.51
796 881 2.644992 CCGAACAGCACCAAAGCC 59.355 61.111 0.00 0.00 34.23 4.35
797 882 2.644992 CGAACAGCACCAAAGCCC 59.355 61.111 0.00 0.00 34.23 5.19
798 883 2.192861 CGAACAGCACCAAAGCCCA 61.193 57.895 0.00 0.00 34.23 5.36
799 884 1.662044 GAACAGCACCAAAGCCCAG 59.338 57.895 0.00 0.00 34.23 4.45
800 885 0.823356 GAACAGCACCAAAGCCCAGA 60.823 55.000 0.00 0.00 34.23 3.86
801 886 0.396974 AACAGCACCAAAGCCCAGAA 60.397 50.000 0.00 0.00 34.23 3.02
802 887 1.109323 ACAGCACCAAAGCCCAGAAC 61.109 55.000 0.00 0.00 34.23 3.01
803 888 1.898574 AGCACCAAAGCCCAGAACG 60.899 57.895 0.00 0.00 34.23 3.95
804 889 2.919494 GCACCAAAGCCCAGAACGG 61.919 63.158 0.00 0.00 0.00 4.44
805 890 1.228124 CACCAAAGCCCAGAACGGA 60.228 57.895 0.00 0.00 36.56 4.69
806 891 0.821711 CACCAAAGCCCAGAACGGAA 60.822 55.000 0.00 0.00 36.56 4.30
807 892 0.106419 ACCAAAGCCCAGAACGGAAA 60.106 50.000 0.00 0.00 36.56 3.13
808 893 1.036707 CCAAAGCCCAGAACGGAAAA 58.963 50.000 0.00 0.00 36.56 2.29
809 894 1.410882 CCAAAGCCCAGAACGGAAAAA 59.589 47.619 0.00 0.00 36.56 1.94
829 914 6.669485 AAAAAGAACGCGATTGTTGTAATC 57.331 33.333 15.93 0.00 30.75 1.75
850 935 9.394477 GTAATCGAAATAAAATCAGTATTGGGC 57.606 33.333 0.00 0.00 0.00 5.36
851 936 6.385649 TCGAAATAAAATCAGTATTGGGCC 57.614 37.500 0.00 0.00 0.00 5.80
852 937 5.008217 TCGAAATAAAATCAGTATTGGGCCG 59.992 40.000 0.00 0.00 0.00 6.13
853 938 5.528870 GAAATAAAATCAGTATTGGGCCGG 58.471 41.667 0.00 0.00 0.00 6.13
854 939 1.111277 AAAATCAGTATTGGGCCGGC 58.889 50.000 21.18 21.18 0.00 6.13
855 940 0.755327 AAATCAGTATTGGGCCGGCC 60.755 55.000 38.57 38.57 0.00 6.13
866 951 4.639171 GCCGGCCCAAAACGTGTG 62.639 66.667 18.11 0.00 0.00 3.82
867 952 4.639171 CCGGCCCAAAACGTGTGC 62.639 66.667 0.00 0.00 0.00 4.57
868 953 3.591835 CGGCCCAAAACGTGTGCT 61.592 61.111 0.00 0.00 30.22 4.40
869 954 2.335011 GGCCCAAAACGTGTGCTC 59.665 61.111 0.00 0.00 30.22 4.26
870 955 2.335011 GCCCAAAACGTGTGCTCC 59.665 61.111 0.00 0.00 0.00 4.70
892 977 2.604912 GGGCCTCCCATTTTATAGGG 57.395 55.000 0.84 0.00 44.65 3.53
895 980 1.886655 GCCTCCCATTTTATAGGGCCG 60.887 57.143 0.00 0.00 45.07 6.13
898 983 3.146847 CTCCCATTTTATAGGGCCGAAC 58.853 50.000 0.00 0.00 45.07 3.95
932 1017 3.775654 CAGCCCCCGTCACTCTCC 61.776 72.222 0.00 0.00 0.00 3.71
935 1020 2.760385 CCCCCGTCACTCTCCCTC 60.760 72.222 0.00 0.00 0.00 4.30
950 1035 2.165437 CTCCCTCGGTCTCTTTCTTCTG 59.835 54.545 0.00 0.00 0.00 3.02
966 1051 0.323816 TCTGCACGTCTCCTCTCCAT 60.324 55.000 0.00 0.00 0.00 3.41
967 1052 0.102120 CTGCACGTCTCCTCTCCATC 59.898 60.000 0.00 0.00 0.00 3.51
968 1053 1.323271 TGCACGTCTCCTCTCCATCC 61.323 60.000 0.00 0.00 0.00 3.51
993 1082 3.556306 CACGTCCACCCACCCACT 61.556 66.667 0.00 0.00 0.00 4.00
1052 1144 4.021925 GTCTGGGCCGGTGCTCTT 62.022 66.667 13.14 0.00 39.40 2.85
1053 1145 4.020617 TCTGGGCCGGTGCTCTTG 62.021 66.667 13.14 0.00 39.40 3.02
1059 1151 2.747855 CCGGTGCTCTTGCCCTTC 60.748 66.667 0.00 0.00 38.71 3.46
1060 1152 2.348998 CGGTGCTCTTGCCCTTCT 59.651 61.111 0.00 0.00 38.71 2.85
1061 1153 1.743252 CGGTGCTCTTGCCCTTCTC 60.743 63.158 0.00 0.00 38.71 2.87
1062 1154 1.377856 GGTGCTCTTGCCCTTCTCC 60.378 63.158 0.00 0.00 38.71 3.71
1063 1155 1.682257 GTGCTCTTGCCCTTCTCCT 59.318 57.895 0.00 0.00 38.71 3.69
1064 1156 0.392327 GTGCTCTTGCCCTTCTCCTC 60.392 60.000 0.00 0.00 38.71 3.71
1065 1157 1.223211 GCTCTTGCCCTTCTCCTCC 59.777 63.158 0.00 0.00 0.00 4.30
1066 1158 1.519719 CTCTTGCCCTTCTCCTCCG 59.480 63.158 0.00 0.00 0.00 4.63
1067 1159 0.972983 CTCTTGCCCTTCTCCTCCGA 60.973 60.000 0.00 0.00 0.00 4.55
1068 1160 0.325671 TCTTGCCCTTCTCCTCCGAT 60.326 55.000 0.00 0.00 0.00 4.18
1069 1161 0.543749 CTTGCCCTTCTCCTCCGATT 59.456 55.000 0.00 0.00 0.00 3.34
1070 1162 0.541863 TTGCCCTTCTCCTCCGATTC 59.458 55.000 0.00 0.00 0.00 2.52
1071 1163 1.068250 GCCCTTCTCCTCCGATTCG 59.932 63.158 0.00 0.00 0.00 3.34
1072 1164 1.068250 CCCTTCTCCTCCGATTCGC 59.932 63.158 0.00 0.00 0.00 4.70
1110 1232 4.899239 CCTGACCTCATCGCCGGC 62.899 72.222 19.07 19.07 0.00 6.13
1182 1304 1.761667 CCTCTCCTGCCTCCTCCTG 60.762 68.421 0.00 0.00 0.00 3.86
1277 1399 0.449388 CCGCAAGATTCTTGGAGCAC 59.551 55.000 24.09 9.11 43.02 4.40
1437 1562 3.073735 CGCCTCCTCCTCACAGCT 61.074 66.667 0.00 0.00 0.00 4.24
1449 1574 4.704103 ACAGCTCTCCCGGCCTCA 62.704 66.667 0.00 0.00 0.00 3.86
1491 1616 2.409870 CCCACTGCCCGCTGAAATC 61.410 63.158 0.16 0.00 0.00 2.17
1519 1644 0.248498 TATTGCTCTTCTCGGCGTCG 60.248 55.000 1.15 1.15 37.82 5.12
1776 1901 2.988684 GCCATGGTTGGAACGGCA 60.989 61.111 14.67 0.00 46.92 5.69
1785 1910 3.670377 GGAACGGCAGTGTTGGCC 61.670 66.667 0.00 0.00 46.51 5.36
1903 2028 3.706086 TGCAAGCTCATATGTCTACCTGA 59.294 43.478 1.90 0.00 0.00 3.86
2022 2147 2.094286 CCAAGCACAGTTTTGACCACAA 60.094 45.455 0.00 0.00 0.00 3.33
2145 2270 5.390567 CGGTGCTCTTAACATAAAAGTGTCC 60.391 44.000 0.00 0.00 0.00 4.02
2167 2292 6.927381 GTCCGTTATATGTAGGCTGTTGTATT 59.073 38.462 0.00 0.00 0.00 1.89
2182 2307 9.480053 GGCTGTTGTATTAATAGTACGGAATAA 57.520 33.333 15.21 0.00 0.00 1.40
2246 2373 4.820775 AGTGGTATATCAGGGATGACTGT 58.179 43.478 0.00 0.00 39.48 3.55
2274 2401 6.098409 AGTCTGTTCCAGTTAAAAGAGTCTGA 59.902 38.462 0.00 0.00 32.61 3.27
2286 2413 3.064900 AGAGTCTGAGTTGGAATTGCC 57.935 47.619 0.00 0.00 37.10 4.52
2316 2526 7.953710 GTGTTTAGAATGCATTTTGCTTGAATC 59.046 33.333 14.33 0.00 45.31 2.52
2351 2561 2.969821 TGTAACACTGCTGGGGAAAT 57.030 45.000 0.00 0.00 0.00 2.17
2352 2562 2.513753 TGTAACACTGCTGGGGAAATG 58.486 47.619 0.00 0.00 0.00 2.32
2399 2611 6.144402 CAGACATACCAAAAGCACATTTGTTC 59.856 38.462 8.28 0.00 38.37 3.18
2400 2612 5.911752 ACATACCAAAAGCACATTTGTTCA 58.088 33.333 8.28 0.00 38.37 3.18
2403 2615 8.147058 ACATACCAAAAGCACATTTGTTCAATA 58.853 29.630 8.28 0.00 38.37 1.90
2426 2638 9.941325 AATAAATTTACCATTCATGTGAAGCAA 57.059 25.926 0.00 0.00 37.48 3.91
2432 2644 5.291971 ACCATTCATGTGAAGCAAAAGTTC 58.708 37.500 1.65 0.00 37.48 3.01
2466 2678 7.916977 TCAGATGCTATTGAATGCAAATGTAAC 59.083 33.333 0.00 0.00 42.74 2.50
2467 2679 7.703197 CAGATGCTATTGAATGCAAATGTAACA 59.297 33.333 0.00 0.00 42.74 2.41
2470 2682 7.321908 TGCTATTGAATGCAAATGTAACATGT 58.678 30.769 0.00 0.00 37.59 3.21
2473 2685 7.821595 ATTGAATGCAAATGTAACATGTGAG 57.178 32.000 0.00 0.00 37.59 3.51
2489 2701 5.047590 ACATGTGAGACAACATCATGCATTT 60.048 36.000 0.00 0.00 38.75 2.32
2491 2703 5.845103 TGTGAGACAACATCATGCATTTTT 58.155 33.333 0.00 0.00 0.00 1.94
2497 2709 7.033791 AGACAACATCATGCATTTTTCTCATC 58.966 34.615 0.00 0.00 0.00 2.92
2499 2711 5.823209 ACATCATGCATTTTTCTCATCGA 57.177 34.783 0.00 0.00 0.00 3.59
2501 2713 6.802608 ACATCATGCATTTTTCTCATCGAAT 58.197 32.000 0.00 0.00 0.00 3.34
2502 2714 7.262772 ACATCATGCATTTTTCTCATCGAATT 58.737 30.769 0.00 0.00 0.00 2.17
2527 2739 3.173151 TCTTCACCAAGAGACATGCCTA 58.827 45.455 0.00 0.00 33.38 3.93
2531 2743 1.556911 ACCAAGAGACATGCCTAGTGG 59.443 52.381 8.43 8.43 0.00 4.00
2537 2749 2.168521 GAGACATGCCTAGTGGTGCTAA 59.831 50.000 0.00 0.00 35.27 3.09
2563 2775 7.930325 ACCTTAGCGTTAGAAAAGAAGTAAAGT 59.070 33.333 0.00 0.00 0.00 2.66
2569 2781 8.546244 GCGTTAGAAAAGAAGTAAAGTAGTTGT 58.454 33.333 0.00 0.00 0.00 3.32
2603 2930 8.856153 TTATACCACTCTGCAATTTCTGTAAA 57.144 30.769 0.00 0.00 0.00 2.01
2610 2937 6.543831 ACTCTGCAATTTCTGTAAAAGAGTGT 59.456 34.615 0.00 0.00 35.91 3.55
2622 2949 9.832445 TCTGTAAAAGAGTGTCTTCAGTATTTT 57.168 29.630 11.29 11.29 44.84 1.82
2682 3009 3.655276 ATTTGCAAGGACAAAGCTCTG 57.345 42.857 0.00 0.00 42.45 3.35
2684 3011 2.346766 TGCAAGGACAAAGCTCTGAA 57.653 45.000 0.00 0.00 0.00 3.02
2690 3017 2.173569 AGGACAAAGCTCTGAACTTGGT 59.826 45.455 0.52 0.52 33.90 3.67
2691 3018 2.952310 GGACAAAGCTCTGAACTTGGTT 59.048 45.455 2.56 0.00 31.30 3.67
2764 3092 5.947228 TGGATCTTTAACTTGTGAAGCAG 57.053 39.130 0.00 0.00 0.00 4.24
2773 3101 3.554934 ACTTGTGAAGCAGGACATTGAA 58.445 40.909 0.00 0.00 0.00 2.69
2774 3102 3.567164 ACTTGTGAAGCAGGACATTGAAG 59.433 43.478 0.00 0.00 0.00 3.02
2778 3106 2.957680 TGAAGCAGGACATTGAAGCAAA 59.042 40.909 0.00 0.00 0.00 3.68
2779 3107 3.575256 TGAAGCAGGACATTGAAGCAAAT 59.425 39.130 0.00 0.00 0.00 2.32
2780 3108 3.863142 AGCAGGACATTGAAGCAAATC 57.137 42.857 0.00 0.00 0.00 2.17
2826 3169 6.950842 TCAAATGTGACATCTAGTTCCTCAT 58.049 36.000 0.00 0.00 0.00 2.90
2827 3170 8.078060 TCAAATGTGACATCTAGTTCCTCATA 57.922 34.615 0.00 0.00 0.00 2.15
2828 3171 8.708378 TCAAATGTGACATCTAGTTCCTCATAT 58.292 33.333 0.00 0.00 0.00 1.78
2829 3172 8.986847 CAAATGTGACATCTAGTTCCTCATATC 58.013 37.037 0.00 0.00 0.00 1.63
2830 3173 7.846101 ATGTGACATCTAGTTCCTCATATCA 57.154 36.000 0.00 0.00 0.00 2.15
2832 3175 7.492524 TGTGACATCTAGTTCCTCATATCAAC 58.507 38.462 0.00 0.00 0.00 3.18
2833 3176 7.124147 TGTGACATCTAGTTCCTCATATCAACA 59.876 37.037 0.00 0.00 0.00 3.33
2834 3177 7.436673 GTGACATCTAGTTCCTCATATCAACAC 59.563 40.741 0.00 0.00 0.00 3.32
2836 3179 7.851228 ACATCTAGTTCCTCATATCAACACAA 58.149 34.615 0.00 0.00 0.00 3.33
2838 3181 8.771766 CATCTAGTTCCTCATATCAACACAATG 58.228 37.037 0.00 0.00 0.00 2.82
2839 3182 7.275183 TCTAGTTCCTCATATCAACACAATGG 58.725 38.462 0.00 0.00 0.00 3.16
2840 3183 5.195940 AGTTCCTCATATCAACACAATGGG 58.804 41.667 0.00 0.00 0.00 4.00
2843 3186 4.227073 TCCTCATATCAACACAATGGGTCA 59.773 41.667 0.00 0.00 0.00 4.02
2844 3187 4.949238 CCTCATATCAACACAATGGGTCAA 59.051 41.667 0.00 0.00 0.00 3.18
2845 3188 5.066893 CCTCATATCAACACAATGGGTCAAG 59.933 44.000 0.00 0.00 0.00 3.02
2847 3190 1.327303 TCAACACAATGGGTCAAGCC 58.673 50.000 0.00 0.00 0.00 4.35
2848 3191 1.039068 CAACACAATGGGTCAAGCCA 58.961 50.000 2.98 2.98 39.65 4.75
2849 3192 1.619827 CAACACAATGGGTCAAGCCAT 59.380 47.619 7.90 7.90 39.65 4.40
2850 3193 2.014010 ACACAATGGGTCAAGCCATT 57.986 45.000 18.36 18.36 39.65 3.16
2851 3194 1.895131 ACACAATGGGTCAAGCCATTC 59.105 47.619 20.61 0.00 39.65 2.67
2852 3195 1.894466 CACAATGGGTCAAGCCATTCA 59.106 47.619 20.61 0.00 39.65 2.57
2853 3196 1.895131 ACAATGGGTCAAGCCATTCAC 59.105 47.619 20.61 0.00 39.65 3.18
2855 3198 2.299582 CAATGGGTCAAGCCATTCACAA 59.700 45.455 20.61 0.00 39.65 3.33
2857 3200 2.607499 TGGGTCAAGCCATTCACAATT 58.393 42.857 0.00 0.00 39.65 2.32
2858 3201 2.971330 TGGGTCAAGCCATTCACAATTT 59.029 40.909 0.00 0.00 39.65 1.82
2859 3202 4.155709 TGGGTCAAGCCATTCACAATTTA 58.844 39.130 0.00 0.00 39.65 1.40
2860 3203 4.220382 TGGGTCAAGCCATTCACAATTTAG 59.780 41.667 0.00 0.00 39.65 1.85
2861 3204 4.462483 GGGTCAAGCCATTCACAATTTAGA 59.538 41.667 0.00 0.00 39.65 2.10
2862 3205 5.127682 GGGTCAAGCCATTCACAATTTAGAT 59.872 40.000 0.00 0.00 39.65 1.98
2863 3206 6.351286 GGGTCAAGCCATTCACAATTTAGATT 60.351 38.462 0.00 0.00 39.65 2.40
2864 3207 7.147915 GGGTCAAGCCATTCACAATTTAGATTA 60.148 37.037 0.00 0.00 39.65 1.75
2866 3209 7.702348 GTCAAGCCATTCACAATTTAGATTACC 59.298 37.037 0.00 0.00 0.00 2.85
2868 3211 5.598417 AGCCATTCACAATTTAGATTACCCC 59.402 40.000 0.00 0.00 0.00 4.95
2869 3212 5.221441 GCCATTCACAATTTAGATTACCCCC 60.221 44.000 0.00 0.00 0.00 5.40
2870 3213 6.136155 CCATTCACAATTTAGATTACCCCCT 58.864 40.000 0.00 0.00 0.00 4.79
2872 3215 6.395780 TTCACAATTTAGATTACCCCCTCA 57.604 37.500 0.00 0.00 0.00 3.86
2873 3216 6.395780 TCACAATTTAGATTACCCCCTCAA 57.604 37.500 0.00 0.00 0.00 3.02
2875 3218 6.661805 TCACAATTTAGATTACCCCCTCAAAC 59.338 38.462 0.00 0.00 0.00 2.93
2876 3219 5.955959 ACAATTTAGATTACCCCCTCAAACC 59.044 40.000 0.00 0.00 0.00 3.27
2879 3222 5.963214 TTAGATTACCCCCTCAAACCTAC 57.037 43.478 0.00 0.00 0.00 3.18
2880 3223 3.810623 AGATTACCCCCTCAAACCTACA 58.189 45.455 0.00 0.00 0.00 2.74
2882 3225 4.166144 AGATTACCCCCTCAAACCTACATG 59.834 45.833 0.00 0.00 0.00 3.21
2883 3226 2.053747 ACCCCCTCAAACCTACATGA 57.946 50.000 0.00 0.00 0.00 3.07
2885 3228 2.242196 ACCCCCTCAAACCTACATGATG 59.758 50.000 0.00 0.00 0.00 3.07
2886 3229 2.242196 CCCCCTCAAACCTACATGATGT 59.758 50.000 2.65 2.65 0.00 3.06
2887 3230 3.309121 CCCCCTCAAACCTACATGATGTT 60.309 47.826 2.29 0.00 0.00 2.71
2888 3231 4.080015 CCCCCTCAAACCTACATGATGTTA 60.080 45.833 2.29 0.00 0.00 2.41
2889 3232 5.399038 CCCCCTCAAACCTACATGATGTTAT 60.399 44.000 2.29 0.00 0.00 1.89
2890 3233 6.129179 CCCCTCAAACCTACATGATGTTATT 58.871 40.000 2.29 0.00 0.00 1.40
2893 3236 7.773224 CCCTCAAACCTACATGATGTTATTGTA 59.227 37.037 2.29 0.00 0.00 2.41
2894 3237 9.173021 CCTCAAACCTACATGATGTTATTGTAA 57.827 33.333 2.29 0.00 0.00 2.41
2955 3408 9.990360 TTCCACTTCCATTCTAAATTTTTAACC 57.010 29.630 0.00 0.00 0.00 2.85
2956 3409 8.590204 TCCACTTCCATTCTAAATTTTTAACCC 58.410 33.333 0.00 0.00 0.00 4.11
2957 3410 8.371699 CCACTTCCATTCTAAATTTTTAACCCA 58.628 33.333 0.00 0.00 0.00 4.51
2958 3411 9.423061 CACTTCCATTCTAAATTTTTAACCCAG 57.577 33.333 0.00 0.00 0.00 4.45
2959 3412 9.374711 ACTTCCATTCTAAATTTTTAACCCAGA 57.625 29.630 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 123 0.956633 AGTTTGTGACGGACGCTAGA 59.043 50.000 0.00 0.00 0.00 2.43
125 130 3.558418 GCACTTTAAGAGTTTGTGACGGA 59.442 43.478 0.00 0.00 36.10 4.69
167 172 1.180907 TTGCTTGTGCTTTGGTGACA 58.819 45.000 0.00 0.00 40.48 3.58
222 249 5.357878 GCATTGTACAAAGATCCTCCATCAA 59.642 40.000 13.23 0.00 33.29 2.57
335 398 5.055812 GCAACAAAGATTTCCATGAACCAA 58.944 37.500 0.00 0.00 0.00 3.67
390 468 8.739972 TGATGCTCTAGAAATATCGCACTATAA 58.260 33.333 4.40 0.00 0.00 0.98
406 485 3.775202 ACGTTGCTTAGTGATGCTCTAG 58.225 45.455 0.00 0.00 0.00 2.43
408 487 2.029020 TGACGTTGCTTAGTGATGCTCT 60.029 45.455 0.00 0.00 0.00 4.09
410 489 2.455674 TGACGTTGCTTAGTGATGCT 57.544 45.000 0.00 0.00 0.00 3.79
443 522 2.092753 TCTACCCGGTCGTGAGTATCTT 60.093 50.000 0.00 0.00 34.92 2.40
545 625 6.385843 TGCCACATGATAAACACACATAAAC 58.614 36.000 0.00 0.00 0.00 2.01
548 629 5.123661 CACTGCCACATGATAAACACACATA 59.876 40.000 0.00 0.00 0.00 2.29
628 709 2.652113 CCCTTCCCCCTCCTCCTCT 61.652 68.421 0.00 0.00 0.00 3.69
721 806 6.095720 TGTTCCTTCTCCGTTTTGTGTTTATT 59.904 34.615 0.00 0.00 0.00 1.40
723 808 4.942483 TGTTCCTTCTCCGTTTTGTGTTTA 59.058 37.500 0.00 0.00 0.00 2.01
724 809 3.759618 TGTTCCTTCTCCGTTTTGTGTTT 59.240 39.130 0.00 0.00 0.00 2.83
727 812 3.202906 TCTGTTCCTTCTCCGTTTTGTG 58.797 45.455 0.00 0.00 0.00 3.33
728 813 3.553828 TCTGTTCCTTCTCCGTTTTGT 57.446 42.857 0.00 0.00 0.00 2.83
729 814 4.893424 TTTCTGTTCCTTCTCCGTTTTG 57.107 40.909 0.00 0.00 0.00 2.44
730 815 5.678871 GCTTTTTCTGTTCCTTCTCCGTTTT 60.679 40.000 0.00 0.00 0.00 2.43
731 816 4.202020 GCTTTTTCTGTTCCTTCTCCGTTT 60.202 41.667 0.00 0.00 0.00 3.60
732 817 3.315470 GCTTTTTCTGTTCCTTCTCCGTT 59.685 43.478 0.00 0.00 0.00 4.44
733 818 2.879026 GCTTTTTCTGTTCCTTCTCCGT 59.121 45.455 0.00 0.00 0.00 4.69
734 819 3.058639 CAGCTTTTTCTGTTCCTTCTCCG 60.059 47.826 0.00 0.00 0.00 4.63
735 820 3.254411 CCAGCTTTTTCTGTTCCTTCTCC 59.746 47.826 0.00 0.00 32.32 3.71
736 821 4.137543 TCCAGCTTTTTCTGTTCCTTCTC 58.862 43.478 0.00 0.00 32.32 2.87
737 822 4.170468 TCCAGCTTTTTCTGTTCCTTCT 57.830 40.909 0.00 0.00 32.32 2.85
738 823 5.010012 TGAATCCAGCTTTTTCTGTTCCTTC 59.990 40.000 0.00 0.00 32.32 3.46
739 824 4.895297 TGAATCCAGCTTTTTCTGTTCCTT 59.105 37.500 0.00 0.00 32.32 3.36
740 825 4.473444 TGAATCCAGCTTTTTCTGTTCCT 58.527 39.130 0.00 0.00 32.32 3.36
741 826 4.853924 TGAATCCAGCTTTTTCTGTTCC 57.146 40.909 0.00 0.00 32.32 3.62
742 827 6.017400 TGATGAATCCAGCTTTTTCTGTTC 57.983 37.500 0.00 0.00 32.32 3.18
743 828 6.409524 TTGATGAATCCAGCTTTTTCTGTT 57.590 33.333 0.00 0.00 32.32 3.16
744 829 6.183360 TGTTTGATGAATCCAGCTTTTTCTGT 60.183 34.615 0.00 0.00 32.32 3.41
745 830 6.218019 TGTTTGATGAATCCAGCTTTTTCTG 58.782 36.000 0.00 0.00 0.00 3.02
746 831 6.409524 TGTTTGATGAATCCAGCTTTTTCT 57.590 33.333 0.00 0.00 0.00 2.52
747 832 7.481275 TTTGTTTGATGAATCCAGCTTTTTC 57.519 32.000 0.00 0.00 0.00 2.29
748 833 7.862512 TTTTGTTTGATGAATCCAGCTTTTT 57.137 28.000 0.00 0.00 0.00 1.94
749 834 7.862512 TTTTTGTTTGATGAATCCAGCTTTT 57.137 28.000 0.00 0.00 0.00 2.27
772 857 0.684805 TGGTGCTGTTCGGGGTTTTT 60.685 50.000 0.00 0.00 0.00 1.94
773 858 0.684805 TTGGTGCTGTTCGGGGTTTT 60.685 50.000 0.00 0.00 0.00 2.43
774 859 0.684805 TTTGGTGCTGTTCGGGGTTT 60.685 50.000 0.00 0.00 0.00 3.27
775 860 1.076632 TTTGGTGCTGTTCGGGGTT 60.077 52.632 0.00 0.00 0.00 4.11
776 861 1.528309 CTTTGGTGCTGTTCGGGGT 60.528 57.895 0.00 0.00 0.00 4.95
777 862 2.919494 GCTTTGGTGCTGTTCGGGG 61.919 63.158 0.00 0.00 0.00 5.73
778 863 2.644992 GCTTTGGTGCTGTTCGGG 59.355 61.111 0.00 0.00 0.00 5.14
779 864 2.644992 GGCTTTGGTGCTGTTCGG 59.355 61.111 0.00 0.00 0.00 4.30
780 865 2.133742 CTGGGCTTTGGTGCTGTTCG 62.134 60.000 0.00 0.00 0.00 3.95
781 866 0.823356 TCTGGGCTTTGGTGCTGTTC 60.823 55.000 0.00 0.00 0.00 3.18
782 867 0.396974 TTCTGGGCTTTGGTGCTGTT 60.397 50.000 0.00 0.00 0.00 3.16
783 868 1.109323 GTTCTGGGCTTTGGTGCTGT 61.109 55.000 0.00 0.00 0.00 4.40
784 869 1.662044 GTTCTGGGCTTTGGTGCTG 59.338 57.895 0.00 0.00 0.00 4.41
785 870 1.898574 CGTTCTGGGCTTTGGTGCT 60.899 57.895 0.00 0.00 0.00 4.40
786 871 2.644992 CGTTCTGGGCTTTGGTGC 59.355 61.111 0.00 0.00 0.00 5.01
787 872 0.821711 TTCCGTTCTGGGCTTTGGTG 60.822 55.000 0.00 0.00 38.76 4.17
788 873 0.106419 TTTCCGTTCTGGGCTTTGGT 60.106 50.000 0.00 0.00 38.76 3.67
789 874 1.036707 TTTTCCGTTCTGGGCTTTGG 58.963 50.000 0.00 0.00 38.76 3.28
790 875 2.880963 TTTTTCCGTTCTGGGCTTTG 57.119 45.000 0.00 0.00 38.76 2.77
806 891 5.338559 CGATTACAACAATCGCGTTCTTTTT 59.661 36.000 5.77 0.00 42.20 1.94
807 892 4.843984 CGATTACAACAATCGCGTTCTTTT 59.156 37.500 5.77 0.00 42.20 2.27
808 893 4.150980 TCGATTACAACAATCGCGTTCTTT 59.849 37.500 5.77 0.00 46.42 2.52
809 894 3.676172 TCGATTACAACAATCGCGTTCTT 59.324 39.130 5.77 0.00 46.42 2.52
810 895 3.247442 TCGATTACAACAATCGCGTTCT 58.753 40.909 5.77 0.00 46.42 3.01
811 896 3.628053 TCGATTACAACAATCGCGTTC 57.372 42.857 5.77 0.00 46.42 3.95
812 897 4.392619 TTTCGATTACAACAATCGCGTT 57.607 36.364 5.77 0.00 46.42 4.84
813 898 4.593597 ATTTCGATTACAACAATCGCGT 57.406 36.364 5.77 0.00 46.42 6.01
814 899 7.412760 TTTTATTTCGATTACAACAATCGCG 57.587 32.000 13.12 0.00 46.42 5.87
815 900 9.005180 TGATTTTATTTCGATTACAACAATCGC 57.995 29.630 13.12 0.00 46.42 4.58
824 909 9.394477 GCCCAATACTGATTTTATTTCGATTAC 57.606 33.333 0.00 0.00 0.00 1.89
825 910 8.573035 GGCCCAATACTGATTTTATTTCGATTA 58.427 33.333 0.00 0.00 0.00 1.75
826 911 7.433680 GGCCCAATACTGATTTTATTTCGATT 58.566 34.615 0.00 0.00 0.00 3.34
827 912 6.293955 CGGCCCAATACTGATTTTATTTCGAT 60.294 38.462 0.00 0.00 0.00 3.59
828 913 5.008217 CGGCCCAATACTGATTTTATTTCGA 59.992 40.000 0.00 0.00 0.00 3.71
829 914 5.212194 CGGCCCAATACTGATTTTATTTCG 58.788 41.667 0.00 0.00 0.00 3.46
830 915 5.528870 CCGGCCCAATACTGATTTTATTTC 58.471 41.667 0.00 0.00 0.00 2.17
831 916 4.202212 GCCGGCCCAATACTGATTTTATTT 60.202 41.667 18.11 0.00 0.00 1.40
832 917 3.320826 GCCGGCCCAATACTGATTTTATT 59.679 43.478 18.11 0.00 0.00 1.40
833 918 2.890945 GCCGGCCCAATACTGATTTTAT 59.109 45.455 18.11 0.00 0.00 1.40
834 919 2.303175 GCCGGCCCAATACTGATTTTA 58.697 47.619 18.11 0.00 0.00 1.52
835 920 1.111277 GCCGGCCCAATACTGATTTT 58.889 50.000 18.11 0.00 0.00 1.82
836 921 0.755327 GGCCGGCCCAATACTGATTT 60.755 55.000 36.64 0.00 0.00 2.17
837 922 1.152756 GGCCGGCCCAATACTGATT 60.153 57.895 36.64 0.00 0.00 2.57
838 923 2.515901 GGCCGGCCCAATACTGAT 59.484 61.111 36.64 0.00 0.00 2.90
849 934 4.639171 CACACGTTTTGGGCCGGC 62.639 66.667 21.18 21.18 0.00 6.13
854 939 1.156736 CTAGGAGCACACGTTTTGGG 58.843 55.000 0.00 0.00 0.00 4.12
855 940 1.156736 CCTAGGAGCACACGTTTTGG 58.843 55.000 1.05 0.00 0.00 3.28
856 941 1.156736 CCCTAGGAGCACACGTTTTG 58.843 55.000 11.48 0.00 0.00 2.44
857 942 0.605589 GCCCTAGGAGCACACGTTTT 60.606 55.000 11.48 0.00 0.00 2.43
858 943 1.003718 GCCCTAGGAGCACACGTTT 60.004 57.895 11.48 0.00 0.00 3.60
859 944 2.663196 GCCCTAGGAGCACACGTT 59.337 61.111 11.48 0.00 0.00 3.99
860 945 3.391382 GGCCCTAGGAGCACACGT 61.391 66.667 11.48 0.00 0.00 4.49
861 946 3.077556 AGGCCCTAGGAGCACACG 61.078 66.667 11.48 0.00 0.00 4.49
862 947 2.736826 GGAGGCCCTAGGAGCACAC 61.737 68.421 11.48 7.09 0.00 3.82
863 948 2.365635 GGAGGCCCTAGGAGCACA 60.366 66.667 11.48 0.00 0.00 4.57
864 949 3.164977 GGGAGGCCCTAGGAGCAC 61.165 72.222 11.48 9.68 41.34 4.40
865 950 2.567769 AATGGGAGGCCCTAGGAGCA 62.568 60.000 11.48 0.00 45.70 4.26
866 951 1.356494 AAATGGGAGGCCCTAGGAGC 61.356 60.000 11.48 12.06 45.70 4.70
867 952 1.226311 AAAATGGGAGGCCCTAGGAG 58.774 55.000 11.48 1.06 45.70 3.69
868 953 2.598288 TAAAATGGGAGGCCCTAGGA 57.402 50.000 11.48 0.00 45.70 2.94
869 954 3.267031 CCTATAAAATGGGAGGCCCTAGG 59.733 52.174 0.06 0.06 45.70 3.02
870 955 3.267031 CCCTATAAAATGGGAGGCCCTAG 59.733 52.174 0.00 0.00 45.70 3.02
882 967 3.818773 CGATTGGTTCGGCCCTATAAAAT 59.181 43.478 0.00 0.00 44.28 1.82
883 968 3.207778 CGATTGGTTCGGCCCTATAAAA 58.792 45.455 0.00 0.00 44.28 1.52
889 974 2.267961 GTCGATTGGTTCGGCCCT 59.732 61.111 0.00 0.00 46.75 5.19
895 980 2.548057 TGCTTGACTTGTCGATTGGTTC 59.452 45.455 0.00 0.00 0.00 3.62
898 983 1.135859 GCTGCTTGACTTGTCGATTGG 60.136 52.381 0.00 0.00 0.00 3.16
907 992 3.553095 GACGGGGGCTGCTTGACTT 62.553 63.158 0.00 0.00 0.00 3.01
912 997 4.021925 GAGTGACGGGGGCTGCTT 62.022 66.667 0.00 0.00 0.00 3.91
932 1017 1.273606 TGCAGAAGAAAGAGACCGAGG 59.726 52.381 0.00 0.00 0.00 4.63
935 1020 1.063806 CGTGCAGAAGAAAGAGACCG 58.936 55.000 0.00 0.00 0.00 4.79
950 1035 1.439644 GGATGGAGAGGAGACGTGC 59.560 63.158 0.00 0.00 0.00 5.34
966 1051 4.340489 TGGACGTGGGGATGGGGA 62.340 66.667 0.00 0.00 0.00 4.81
967 1052 4.109675 GTGGACGTGGGGATGGGG 62.110 72.222 0.00 0.00 0.00 4.96
968 1053 4.109675 GGTGGACGTGGGGATGGG 62.110 72.222 0.00 0.00 0.00 4.00
1046 1138 1.557269 GGAGGAGAAGGGCAAGAGCA 61.557 60.000 0.00 0.00 44.61 4.26
1047 1139 1.223211 GGAGGAGAAGGGCAAGAGC 59.777 63.158 0.00 0.00 41.10 4.09
1048 1140 0.972983 TCGGAGGAGAAGGGCAAGAG 60.973 60.000 0.00 0.00 0.00 2.85
1049 1141 0.325671 ATCGGAGGAGAAGGGCAAGA 60.326 55.000 0.00 0.00 0.00 3.02
1050 1142 0.543749 AATCGGAGGAGAAGGGCAAG 59.456 55.000 0.00 0.00 0.00 4.01
1051 1143 0.541863 GAATCGGAGGAGAAGGGCAA 59.458 55.000 0.00 0.00 0.00 4.52
1052 1144 1.676678 CGAATCGGAGGAGAAGGGCA 61.677 60.000 0.00 0.00 0.00 5.36
1053 1145 1.068250 CGAATCGGAGGAGAAGGGC 59.932 63.158 0.00 0.00 0.00 5.19
1054 1146 1.068250 GCGAATCGGAGGAGAAGGG 59.932 63.158 4.35 0.00 0.00 3.95
1055 1147 1.068250 GGCGAATCGGAGGAGAAGG 59.932 63.158 4.35 0.00 0.00 3.46
1056 1148 1.299468 CGGCGAATCGGAGGAGAAG 60.299 63.158 0.00 0.00 0.00 2.85
1057 1149 1.601419 AACGGCGAATCGGAGGAGAA 61.601 55.000 16.62 0.00 0.00 2.87
1058 1150 2.050350 AACGGCGAATCGGAGGAGA 61.050 57.895 16.62 0.00 0.00 3.71
1059 1151 1.878522 CAACGGCGAATCGGAGGAG 60.879 63.158 16.62 0.00 0.00 3.69
1060 1152 2.183300 CAACGGCGAATCGGAGGA 59.817 61.111 16.62 0.00 0.00 3.71
1061 1153 3.564027 GCAACGGCGAATCGGAGG 61.564 66.667 16.62 0.00 0.00 4.30
1062 1154 3.564027 GGCAACGGCGAATCGGAG 61.564 66.667 16.62 0.00 42.47 4.63
1065 1157 3.564027 GAGGGCAACGGCGAATCG 61.564 66.667 16.62 0.00 42.47 3.34
1066 1158 2.125106 AGAGGGCAACGGCGAATC 60.125 61.111 16.62 0.60 42.47 2.52
1067 1159 2.125106 GAGAGGGCAACGGCGAAT 60.125 61.111 16.62 0.00 42.47 3.34
1068 1160 3.296709 GAGAGAGGGCAACGGCGAA 62.297 63.158 16.62 0.00 42.47 4.70
1069 1161 3.760035 GAGAGAGGGCAACGGCGA 61.760 66.667 16.62 0.00 42.47 5.54
1070 1162 4.821589 GGAGAGAGGGCAACGGCG 62.822 72.222 4.80 4.80 42.47 6.46
1071 1163 4.475135 GGGAGAGAGGGCAACGGC 62.475 72.222 0.00 0.00 40.13 5.68
1072 1164 2.294078 AAGGGAGAGAGGGCAACGG 61.294 63.158 0.00 0.00 37.60 4.44
1236 1358 2.930777 ATCGGAGGGAGACGGAAGGG 62.931 65.000 0.00 0.00 0.00 3.95
1410 1535 2.756283 AGGAGGCGGAGAACGGAG 60.756 66.667 0.00 0.00 44.51 4.63
1437 1562 3.239627 AAGAGGTGAGGCCGGGAGA 62.240 63.158 2.18 0.00 43.70 3.71
1449 1574 1.010170 AGGGGGATAAGCAGAAGAGGT 59.990 52.381 0.00 0.00 0.00 3.85
1519 1644 0.833949 CAGAAGGGGACTAAGAGGGC 59.166 60.000 0.00 0.00 42.68 5.19
1529 1654 2.038975 CGAGGGACCAGAAGGGGA 59.961 66.667 0.00 0.00 42.91 4.81
1748 1873 0.105760 AACCATGGCCTTGACCACAA 60.106 50.000 19.85 0.00 44.17 3.33
1776 1901 1.885157 CATCATTGCGGCCAACACT 59.115 52.632 2.24 0.00 32.95 3.55
1842 1967 1.925888 GGTGAGCTCCCCATGGATT 59.074 57.895 15.22 0.00 40.80 3.01
1843 1968 2.446848 CGGTGAGCTCCCCATGGAT 61.447 63.158 15.22 0.00 40.80 3.41
1845 1970 4.181010 CCGGTGAGCTCCCCATGG 62.181 72.222 15.99 4.14 0.00 3.66
1860 1985 5.525012 TGCAAATTCATTGTAGATCTCTCCG 59.475 40.000 0.00 0.00 41.32 4.63
1903 2028 1.079127 CCTTGCCCTCATCGAACGT 60.079 57.895 0.00 0.00 0.00 3.99
2022 2147 5.536260 CGATGAACACATAGTCATCAGGAT 58.464 41.667 12.65 0.00 35.93 3.24
2107 2232 0.533755 GCACCGCATCTGAGGCTAAT 60.534 55.000 12.78 0.00 38.67 1.73
2167 2292 8.774890 TGCTGTTTTGTTATTCCGTACTATTA 57.225 30.769 0.00 0.00 0.00 0.98
2172 2297 8.794406 CATAATTGCTGTTTTGTTATTCCGTAC 58.206 33.333 0.00 0.00 0.00 3.67
2176 2301 7.816995 TCCACATAATTGCTGTTTTGTTATTCC 59.183 33.333 0.00 0.00 0.00 3.01
2182 2307 5.011943 ACCATCCACATAATTGCTGTTTTGT 59.988 36.000 0.00 0.00 0.00 2.83
2187 2312 5.127031 GGTAAACCATCCACATAATTGCTGT 59.873 40.000 0.00 0.00 35.64 4.40
2191 2316 6.828273 TCTGAGGTAAACCATCCACATAATTG 59.172 38.462 1.26 0.00 38.89 2.32
2274 2401 2.664402 ACACTGAGGCAATTCCAACT 57.336 45.000 0.00 0.00 37.29 3.16
2286 2413 6.385537 GCAAAATGCATTCTAAACACTGAG 57.614 37.500 13.38 0.00 44.26 3.35
2316 2526 5.660629 TGTTACAAACACCTCATTGTACG 57.339 39.130 0.00 0.00 40.62 3.67
2351 2561 9.948964 TCTGAATTCTGAAACTATCAAGAATCA 57.051 29.630 12.17 0.00 37.67 2.57
2399 2611 9.368674 TGCTTCACATGAATGGTAAATTTATTG 57.631 29.630 0.00 0.00 33.01 1.90
2400 2612 9.941325 TTGCTTCACATGAATGGTAAATTTATT 57.059 25.926 0.00 0.00 33.01 1.40
2403 2615 8.674263 TTTTGCTTCACATGAATGGTAAATTT 57.326 26.923 0.00 0.00 33.01 1.82
2414 2626 6.691754 TTGTAGAACTTTTGCTTCACATGA 57.308 33.333 0.00 0.00 0.00 3.07
2417 2629 7.542890 TGAAATTGTAGAACTTTTGCTTCACA 58.457 30.769 0.00 0.00 0.00 3.58
2432 2644 8.132995 TGCATTCAATAGCATCTGAAATTGTAG 58.867 33.333 0.00 0.00 35.31 2.74
2466 2678 4.632538 ATGCATGATGTTGTCTCACATG 57.367 40.909 0.00 0.00 37.52 3.21
2467 2679 5.654603 AAATGCATGATGTTGTCTCACAT 57.345 34.783 0.00 0.00 40.25 3.21
2470 2682 6.016108 TGAGAAAAATGCATGATGTTGTCTCA 60.016 34.615 20.59 20.59 36.37 3.27
2473 2685 6.020916 CGATGAGAAAAATGCATGATGTTGTC 60.021 38.462 0.00 0.00 0.00 3.18
2502 2714 4.037923 GGCATGTCTCTTGGTGAAGAAAAA 59.962 41.667 0.00 0.00 37.77 1.94
2512 2724 1.556911 ACCACTAGGCATGTCTCTTGG 59.443 52.381 20.57 20.57 39.06 3.61
2514 2726 1.065854 GCACCACTAGGCATGTCTCTT 60.066 52.381 1.25 0.00 39.06 2.85
2537 2749 7.930325 ACTTTACTTCTTTTCTAACGCTAAGGT 59.070 33.333 0.00 0.00 0.00 3.50
2576 2788 7.944729 ACAGAAATTGCAGAGTGGTATAAAT 57.055 32.000 0.00 0.00 0.00 1.40
2578 2790 8.856153 TTTACAGAAATTGCAGAGTGGTATAA 57.144 30.769 0.00 0.00 0.00 0.98
2579 2791 8.856153 TTTTACAGAAATTGCAGAGTGGTATA 57.144 30.769 0.00 0.00 0.00 1.47
2580 2792 7.665559 TCTTTTACAGAAATTGCAGAGTGGTAT 59.334 33.333 0.00 0.00 0.00 2.73
2585 2912 6.543831 ACACTCTTTTACAGAAATTGCAGAGT 59.456 34.615 0.00 0.00 33.82 3.24
2652 2979 7.587392 GCTTTGTCCTTGCAAATAATTCAAAAC 59.413 33.333 0.00 0.00 37.66 2.43
2665 2992 1.949525 GTTCAGAGCTTTGTCCTTGCA 59.050 47.619 3.90 0.00 0.00 4.08
2666 2993 2.225467 AGTTCAGAGCTTTGTCCTTGC 58.775 47.619 3.90 0.00 0.00 4.01
2682 3009 8.336801 ACTACTCCAATATCAAAACCAAGTTC 57.663 34.615 0.00 0.00 0.00 3.01
2684 3011 7.309194 GCAACTACTCCAATATCAAAACCAAGT 60.309 37.037 0.00 0.00 0.00 3.16
2690 3017 5.826643 AGGGCAACTACTCCAATATCAAAA 58.173 37.500 0.00 0.00 0.00 2.44
2691 3018 5.191722 AGAGGGCAACTACTCCAATATCAAA 59.808 40.000 0.00 0.00 34.27 2.69
2798 3141 8.311395 AGGAACTAGATGTCACATTTGATAGA 57.689 34.615 0.00 0.00 36.02 1.98
2800 3143 8.078060 TGAGGAACTAGATGTCACATTTGATA 57.922 34.615 0.00 0.00 41.55 2.15
2803 3146 8.899427 ATATGAGGAACTAGATGTCACATTTG 57.101 34.615 0.00 0.00 41.55 2.32
2807 3150 7.124147 TGTTGATATGAGGAACTAGATGTCACA 59.876 37.037 0.00 0.00 41.55 3.58
2821 3164 4.525996 TGACCCATTGTGTTGATATGAGG 58.474 43.478 0.00 0.00 0.00 3.86
2826 3169 3.088532 GGCTTGACCCATTGTGTTGATA 58.911 45.455 0.00 0.00 0.00 2.15
2827 3170 1.895131 GGCTTGACCCATTGTGTTGAT 59.105 47.619 0.00 0.00 0.00 2.57
2828 3171 1.327303 GGCTTGACCCATTGTGTTGA 58.673 50.000 0.00 0.00 0.00 3.18
2829 3172 1.039068 TGGCTTGACCCATTGTGTTG 58.961 50.000 0.00 0.00 37.83 3.33
2830 3173 2.014010 ATGGCTTGACCCATTGTGTT 57.986 45.000 0.00 0.00 42.92 3.32
2838 3181 3.683365 AAATTGTGAATGGCTTGACCC 57.317 42.857 0.00 0.00 37.83 4.46
2839 3182 5.643379 TCTAAATTGTGAATGGCTTGACC 57.357 39.130 0.00 0.00 39.84 4.02
2840 3183 7.702348 GGTAATCTAAATTGTGAATGGCTTGAC 59.298 37.037 0.00 0.00 0.00 3.18
2843 3186 6.098266 GGGGTAATCTAAATTGTGAATGGCTT 59.902 38.462 0.00 0.00 0.00 4.35
2844 3187 5.598417 GGGGTAATCTAAATTGTGAATGGCT 59.402 40.000 0.00 0.00 0.00 4.75
2845 3188 5.221441 GGGGGTAATCTAAATTGTGAATGGC 60.221 44.000 0.00 0.00 0.00 4.40
2847 3190 6.833416 TGAGGGGGTAATCTAAATTGTGAATG 59.167 38.462 0.00 0.00 0.00 2.67
2848 3191 6.980577 TGAGGGGGTAATCTAAATTGTGAAT 58.019 36.000 0.00 0.00 0.00 2.57
2849 3192 6.395780 TGAGGGGGTAATCTAAATTGTGAA 57.604 37.500 0.00 0.00 0.00 3.18
2850 3193 6.395780 TTGAGGGGGTAATCTAAATTGTGA 57.604 37.500 0.00 0.00 0.00 3.58
2851 3194 6.127451 GGTTTGAGGGGGTAATCTAAATTGTG 60.127 42.308 0.00 0.00 0.00 3.33
2852 3195 5.955959 GGTTTGAGGGGGTAATCTAAATTGT 59.044 40.000 0.00 0.00 0.00 2.71
2853 3196 6.194967 AGGTTTGAGGGGGTAATCTAAATTG 58.805 40.000 0.00 0.00 0.00 2.32
2855 3198 6.449041 TGTAGGTTTGAGGGGGTAATCTAAAT 59.551 38.462 0.00 0.00 0.00 1.40
2857 3200 5.352264 TGTAGGTTTGAGGGGGTAATCTAA 58.648 41.667 0.00 0.00 0.00 2.10
2858 3201 4.962839 TGTAGGTTTGAGGGGGTAATCTA 58.037 43.478 0.00 0.00 0.00 1.98
2859 3202 3.810623 TGTAGGTTTGAGGGGGTAATCT 58.189 45.455 0.00 0.00 0.00 2.40
2860 3203 4.165372 TCATGTAGGTTTGAGGGGGTAATC 59.835 45.833 0.00 0.00 0.00 1.75
2861 3204 4.116113 TCATGTAGGTTTGAGGGGGTAAT 58.884 43.478 0.00 0.00 0.00 1.89
2862 3205 3.533146 TCATGTAGGTTTGAGGGGGTAA 58.467 45.455 0.00 0.00 0.00 2.85
2863 3206 3.208570 TCATGTAGGTTTGAGGGGGTA 57.791 47.619 0.00 0.00 0.00 3.69
2864 3207 2.053747 TCATGTAGGTTTGAGGGGGT 57.946 50.000 0.00 0.00 0.00 4.95
2866 3209 3.652057 ACATCATGTAGGTTTGAGGGG 57.348 47.619 0.00 0.00 0.00 4.79
2868 3211 7.630242 ACAATAACATCATGTAGGTTTGAGG 57.370 36.000 0.00 0.00 33.36 3.86


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

AutoCloner maintained by Alex Coulton.