Multiple sequence alignment - TraesCS7A01G266600

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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 TraesCS7A01G266600 chr7A 100.000 2598 0 0 1 2598 269101600 269104197 0.000000e+00 4798.0
1 TraesCS7A01G266600 chr7A 96.970 264 8 0 1678 1941 269123200 269123463 6.600000e-121 444.0
2 TraesCS7A01G266600 chr7A 91.515 165 10 4 733 893 158656272 158656436 9.360000e-55 224.0
3 TraesCS7A01G266600 chr6A 86.858 974 102 18 1647 2598 9251532 9252501 0.000000e+00 1066.0
4 TraesCS7A01G266600 chr6A 82.770 296 43 8 1650 1941 9256737 9257028 9.220000e-65 257.0
5 TraesCS7A01G266600 chr6A 89.362 188 13 3 724 905 64662429 64662243 2.010000e-56 230.0
6 TraesCS7A01G266600 chr6A 90.173 173 13 3 728 896 604515876 604515704 3.370000e-54 222.0
7 TraesCS7A01G266600 chr3B 86.742 973 96 20 1647 2598 132649568 132650528 0.000000e+00 1051.0
8 TraesCS7A01G266600 chr3B 83.088 272 31 11 1673 1941 132654991 132655250 1.550000e-57 233.0
9 TraesCS7A01G266600 chr3B 89.474 171 15 3 737 906 157369957 157369789 2.030000e-51 213.0
10 TraesCS7A01G266600 chr7D 91.607 703 51 7 899 1597 252062972 252062274 0.000000e+00 965.0
11 TraesCS7A01G266600 chr7D 87.875 734 54 18 1 730 252063668 252062966 0.000000e+00 830.0
12 TraesCS7A01G266600 chr7D 87.500 56 5 2 2408 2462 118393775 118393721 2.160000e-06 63.9
13 TraesCS7A01G266600 chr7B 90.643 684 40 9 899 1578 228827617 228826954 0.000000e+00 887.0
14 TraesCS7A01G266600 chr7B 84.011 738 45 31 1 697 228828349 228827644 2.180000e-180 641.0
15 TraesCS7A01G266600 chr2A 90.608 181 12 3 724 900 59330917 59331096 4.320000e-58 235.0
16 TraesCS7A01G266600 chr2A 91.329 173 10 4 728 896 715471732 715471561 5.590000e-57 231.0
17 TraesCS7A01G266600 chr5A 90.960 177 11 4 733 906 382961948 382961774 1.550000e-57 233.0
18 TraesCS7A01G266600 chr5A 97.727 88 0 2 619 706 510463902 510463987 1.610000e-32 150.0
19 TraesCS7A01G266600 chr5A 97.590 83 0 2 615 697 510464181 510464101 9.690000e-30 141.0
20 TraesCS7A01G266600 chr5A 94.624 93 2 2 612 704 704521887 704521798 9.690000e-30 141.0
21 TraesCS7A01G266600 chr5B 90.058 171 13 4 738 904 128461555 128461385 4.350000e-53 219.0
22 TraesCS7A01G266600 chr5B 80.876 251 33 4 1979 2229 665757020 665756785 1.590000e-42 183.0
23 TraesCS7A01G266600 chr1B 90.854 164 12 2 737 897 569524013 569523850 1.570000e-52 217.0
24 TraesCS7A01G266600 chr6D 83.262 233 39 0 1979 2211 110198760 110198528 5.630000e-52 215.0
25 TraesCS7A01G266600 chr6D 97.647 85 2 0 619 703 306137315 306137399 2.080000e-31 147.0
26 TraesCS7A01G266600 chr6D 91.935 62 5 0 1700 1761 110170282 110170221 1.280000e-13 87.9
27 TraesCS7A01G266600 chr6B 97.647 85 2 0 619 703 473067442 473067526 2.080000e-31 147.0
28 TraesCS7A01G266600 chr5D 98.780 82 1 0 616 697 402976613 402976694 2.080000e-31 147.0
29 TraesCS7A01G266600 chr4B 96.471 85 3 0 613 697 664780620 664780536 9.690000e-30 141.0


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 TraesCS7A01G266600 chr7A 269101600 269104197 2597 False 4798.0 4798 100.000 1 2598 1 chr7A.!!$F2 2597
1 TraesCS7A01G266600 chr6A 9251532 9252501 969 False 1066.0 1066 86.858 1647 2598 1 chr6A.!!$F1 951
2 TraesCS7A01G266600 chr3B 132649568 132650528 960 False 1051.0 1051 86.742 1647 2598 1 chr3B.!!$F1 951
3 TraesCS7A01G266600 chr7D 252062274 252063668 1394 True 897.5 965 89.741 1 1597 2 chr7D.!!$R2 1596
4 TraesCS7A01G266600 chr7B 228826954 228828349 1395 True 764.0 887 87.327 1 1578 2 chr7B.!!$R1 1577

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
748 800 0.043485 TGGGGTATGTCTAGGGCACA 59.957 55.0 0.0 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2552 2632 0.03582 GCGGTGGTGGTGGAAATCTA 60.036 55.0 0.0 0.0 0.0 1.98 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
46 47 3.840437 GCCAAGCTTGTGGTGACA 58.160 55.556 24.35 0.00 41.12 3.58
47 48 2.344535 GCCAAGCTTGTGGTGACAT 58.655 52.632 24.35 0.00 46.14 3.06
122 131 5.063880 GGAGCAAAGAAGACCTTCAAGTAA 58.936 41.667 11.80 0.00 41.84 2.24
174 189 3.614399 CACACCTCCTTGTGTCCTC 57.386 57.895 0.00 0.00 46.15 3.71
176 191 1.417890 CACACCTCCTTGTGTCCTCTT 59.582 52.381 0.00 0.00 46.15 2.85
177 192 2.127708 ACACCTCCTTGTGTCCTCTTT 58.872 47.619 0.00 0.00 46.15 2.52
178 193 2.509964 ACACCTCCTTGTGTCCTCTTTT 59.490 45.455 0.00 0.00 46.15 2.27
229 244 8.871862 TCTTCAAATGAACACAAACAAATGAAG 58.128 29.630 1.70 1.70 40.23 3.02
232 247 8.655092 TCAAATGAACACAAACAAATGAAGTTC 58.345 29.630 0.00 0.00 38.31 3.01
235 250 9.520204 AATGAACACAAACAAATGAAGTTCTAG 57.480 29.630 4.17 0.00 38.46 2.43
236 251 7.479980 TGAACACAAACAAATGAAGTTCTAGG 58.520 34.615 4.17 0.00 38.46 3.02
389 437 3.627732 AGTATCGTGCGGATTGACTAG 57.372 47.619 0.00 0.00 36.55 2.57
414 462 3.441101 TGGAAGATCGGAGAAGGAAGAA 58.559 45.455 0.00 0.00 43.58 2.52
415 463 3.449018 TGGAAGATCGGAGAAGGAAGAAG 59.551 47.826 0.00 0.00 43.58 2.85
416 464 3.702045 GGAAGATCGGAGAAGGAAGAAGA 59.298 47.826 0.00 0.00 43.58 2.87
417 465 4.343814 GGAAGATCGGAGAAGGAAGAAGAT 59.656 45.833 0.00 0.00 43.58 2.40
418 466 5.163353 GGAAGATCGGAGAAGGAAGAAGATT 60.163 44.000 0.00 0.00 43.58 2.40
419 467 5.529581 AGATCGGAGAAGGAAGAAGATTC 57.470 43.478 0.00 0.00 43.58 2.52
528 576 6.524586 GCAAACTAGTCAGACAATTGTATTGC 59.475 38.462 11.95 8.67 0.00 3.56
530 578 3.747099 AGTCAGACAATTGTATTGCGC 57.253 42.857 11.95 0.00 0.00 6.09
531 579 3.338249 AGTCAGACAATTGTATTGCGCT 58.662 40.909 11.95 11.07 0.00 5.92
561 612 3.851838 GCACCATTCGAAACACAAATCGT 60.852 43.478 0.00 0.00 39.91 3.73
566 617 4.746836 TTCGAAACACAAATCGTTTTGC 57.253 36.364 16.87 2.14 45.01 3.68
571 622 3.341857 ACACAAATCGTTTTGCGCTTA 57.658 38.095 16.87 0.00 45.01 3.09
606 657 3.059834 CGAATTTGCGCCTCAAAAATGAG 59.940 43.478 4.18 0.00 46.60 2.90
615 666 3.749665 CTCAAAAATGAGGGCCACAAA 57.250 42.857 7.99 0.00 32.56 2.83
616 667 4.070630 CTCAAAAATGAGGGCCACAAAA 57.929 40.909 7.99 0.00 32.56 2.44
617 668 3.802866 TCAAAAATGAGGGCCACAAAAC 58.197 40.909 7.99 0.00 0.00 2.43
623 674 3.258971 TGAGGGCCACAAAACAAAAAG 57.741 42.857 6.18 0.00 0.00 2.27
697 748 3.330126 ACCACTGAGCTATAAGGGCTA 57.670 47.619 0.00 0.00 40.40 3.93
698 749 2.966516 ACCACTGAGCTATAAGGGCTAC 59.033 50.000 0.00 0.00 40.40 3.58
704 755 5.023533 TGAGCTATAAGGGCTACTTGTTG 57.976 43.478 4.75 1.39 40.37 3.33
706 757 3.199946 AGCTATAAGGGCTACTTGTTGCA 59.800 43.478 19.01 0.00 46.01 4.08
707 758 3.312697 GCTATAAGGGCTACTTGTTGCAC 59.687 47.826 14.91 5.53 44.18 4.57
710 761 0.764890 AGGGCTACTTGTTGCACTGA 59.235 50.000 10.80 0.00 41.90 3.41
711 762 0.875059 GGGCTACTTGTTGCACTGAC 59.125 55.000 9.11 0.00 0.00 3.51
713 764 1.801178 GGCTACTTGTTGCACTGACTC 59.199 52.381 9.11 0.00 0.00 3.36
722 773 4.565022 TGTTGCACTGACTCGATTTCATA 58.435 39.130 0.00 0.00 0.00 2.15
730 782 9.162793 GCACTGACTCGATTTCATATTTTAATG 57.837 33.333 0.00 0.00 0.00 1.90
732 784 8.840321 ACTGACTCGATTTCATATTTTAATGGG 58.160 33.333 0.00 0.00 0.00 4.00
733 785 8.165239 TGACTCGATTTCATATTTTAATGGGG 57.835 34.615 0.00 0.00 0.00 4.96
734 786 7.777910 TGACTCGATTTCATATTTTAATGGGGT 59.222 33.333 0.00 0.00 0.00 4.95
735 787 9.280174 GACTCGATTTCATATTTTAATGGGGTA 57.720 33.333 0.00 0.00 0.00 3.69
736 788 9.807921 ACTCGATTTCATATTTTAATGGGGTAT 57.192 29.630 0.00 0.00 0.00 2.73
738 790 9.581289 TCGATTTCATATTTTAATGGGGTATGT 57.419 29.630 0.00 0.00 0.00 2.29
739 791 9.840427 CGATTTCATATTTTAATGGGGTATGTC 57.160 33.333 0.00 0.00 0.00 3.06
744 796 8.611257 TCATATTTTAATGGGGTATGTCTAGGG 58.389 37.037 0.00 0.00 0.00 3.53
745 797 4.717279 TTTAATGGGGTATGTCTAGGGC 57.283 45.455 0.00 0.00 0.00 5.19
746 798 2.206322 AATGGGGTATGTCTAGGGCA 57.794 50.000 0.00 0.00 0.00 5.36
747 799 1.435256 ATGGGGTATGTCTAGGGCAC 58.565 55.000 0.00 0.00 0.00 5.01
748 800 0.043485 TGGGGTATGTCTAGGGCACA 59.957 55.000 0.00 0.00 0.00 4.57
749 801 1.345009 TGGGGTATGTCTAGGGCACAT 60.345 52.381 0.00 1.62 38.13 3.21
750 802 1.348036 GGGGTATGTCTAGGGCACATC 59.652 57.143 0.00 0.00 35.95 3.06
751 803 2.330216 GGGTATGTCTAGGGCACATCT 58.670 52.381 0.00 0.00 35.95 2.90
752 804 3.507411 GGGTATGTCTAGGGCACATCTA 58.493 50.000 0.00 0.00 35.95 1.98
753 805 3.511934 GGGTATGTCTAGGGCACATCTAG 59.488 52.174 0.00 0.00 35.95 2.43
754 806 4.408276 GGTATGTCTAGGGCACATCTAGA 58.592 47.826 0.00 0.00 40.38 2.43
755 807 5.020132 GGTATGTCTAGGGCACATCTAGAT 58.980 45.833 0.00 0.00 43.25 1.98
756 808 5.105554 GGTATGTCTAGGGCACATCTAGATG 60.106 48.000 27.63 27.63 43.25 2.90
772 824 7.972527 CATCTAGATGTGCTCTAATTATTGCC 58.027 38.462 22.42 1.62 36.02 4.52
773 825 6.467677 TCTAGATGTGCTCTAATTATTGCCC 58.532 40.000 0.00 0.00 36.02 5.36
774 826 5.052693 AGATGTGCTCTAATTATTGCCCA 57.947 39.130 7.18 3.43 30.26 5.36
775 827 5.638133 AGATGTGCTCTAATTATTGCCCAT 58.362 37.500 7.24 7.24 30.26 4.00
776 828 6.073314 AGATGTGCTCTAATTATTGCCCATT 58.927 36.000 8.38 0.00 30.26 3.16
777 829 6.552350 AGATGTGCTCTAATTATTGCCCATTT 59.448 34.615 8.38 2.71 30.26 2.32
778 830 7.725397 AGATGTGCTCTAATTATTGCCCATTTA 59.275 33.333 8.38 0.00 30.26 1.40
779 831 7.652524 TGTGCTCTAATTATTGCCCATTTAA 57.347 32.000 7.18 0.00 0.00 1.52
780 832 8.072321 TGTGCTCTAATTATTGCCCATTTAAA 57.928 30.769 0.00 0.00 0.00 1.52
781 833 8.703743 TGTGCTCTAATTATTGCCCATTTAAAT 58.296 29.630 0.00 0.00 0.00 1.40
782 834 8.981647 GTGCTCTAATTATTGCCCATTTAAATG 58.018 33.333 19.40 19.40 36.17 2.32
783 835 8.922237 TGCTCTAATTATTGCCCATTTAAATGA 58.078 29.630 26.32 9.41 38.70 2.57
784 836 9.415544 GCTCTAATTATTGCCCATTTAAATGAG 57.584 33.333 26.32 16.47 38.70 2.90
790 842 9.768662 ATTATTGCCCATTTAAATGAGTGAATC 57.231 29.630 26.32 3.95 38.70 2.52
791 843 6.602410 TTGCCCATTTAAATGAGTGAATCA 57.398 33.333 26.32 6.35 43.70 2.57
792 844 6.602410 TGCCCATTTAAATGAGTGAATCAA 57.398 33.333 26.32 2.32 42.53 2.57
793 845 6.632909 TGCCCATTTAAATGAGTGAATCAAG 58.367 36.000 26.32 7.97 42.53 3.02
794 846 5.521372 GCCCATTTAAATGAGTGAATCAAGC 59.479 40.000 26.32 10.54 42.53 4.01
795 847 6.632909 CCCATTTAAATGAGTGAATCAAGCA 58.367 36.000 26.32 0.00 42.53 3.91
796 848 6.532657 CCCATTTAAATGAGTGAATCAAGCAC 59.467 38.462 26.32 0.00 42.53 4.40
797 849 7.092079 CCATTTAAATGAGTGAATCAAGCACA 58.908 34.615 26.32 0.00 42.53 4.57
798 850 7.599621 CCATTTAAATGAGTGAATCAAGCACAA 59.400 33.333 26.32 0.00 42.53 3.33
799 851 8.980610 CATTTAAATGAGTGAATCAAGCACAAA 58.019 29.630 21.35 0.00 42.53 2.83
800 852 8.939201 TTTAAATGAGTGAATCAAGCACAAAA 57.061 26.923 0.00 0.00 42.53 2.44
801 853 8.939201 TTAAATGAGTGAATCAAGCACAAAAA 57.061 26.923 0.00 0.00 42.53 1.94
837 889 8.900511 ACACGAATTTCAATGTAAGATCAATG 57.099 30.769 0.00 0.00 0.00 2.82
838 890 8.729756 ACACGAATTTCAATGTAAGATCAATGA 58.270 29.630 0.00 0.00 0.00 2.57
839 891 9.003112 CACGAATTTCAATGTAAGATCAATGAC 57.997 33.333 0.00 0.00 28.67 3.06
840 892 8.729756 ACGAATTTCAATGTAAGATCAATGACA 58.270 29.630 0.00 0.00 28.67 3.58
841 893 9.726232 CGAATTTCAATGTAAGATCAATGACAT 57.274 29.630 0.00 0.00 34.00 3.06
845 897 9.904198 TTTCAATGTAAGATCAATGACATAGGA 57.096 29.630 0.00 0.00 32.31 2.94
846 898 8.893219 TCAATGTAAGATCAATGACATAGGAC 57.107 34.615 0.00 0.00 32.31 3.85
847 899 8.708378 TCAATGTAAGATCAATGACATAGGACT 58.292 33.333 0.00 0.00 32.31 3.85
848 900 9.334947 CAATGTAAGATCAATGACATAGGACTT 57.665 33.333 0.00 0.00 32.31 3.01
851 903 9.421399 TGTAAGATCAATGACATAGGACTTAGA 57.579 33.333 0.00 0.00 0.00 2.10
854 906 8.489676 AGATCAATGACATAGGACTTAGATGT 57.510 34.615 0.00 0.00 36.52 3.06
855 907 8.366401 AGATCAATGACATAGGACTTAGATGTG 58.634 37.037 0.00 0.00 33.99 3.21
856 908 6.283694 TCAATGACATAGGACTTAGATGTGC 58.716 40.000 0.00 0.00 33.99 4.57
857 909 5.876651 ATGACATAGGACTTAGATGTGCA 57.123 39.130 0.00 0.00 33.99 4.57
858 910 5.675684 TGACATAGGACTTAGATGTGCAA 57.324 39.130 0.00 0.00 33.99 4.08
859 911 6.239217 TGACATAGGACTTAGATGTGCAAT 57.761 37.500 0.00 0.00 33.99 3.56
860 912 7.360113 TGACATAGGACTTAGATGTGCAATA 57.640 36.000 0.00 0.00 33.99 1.90
861 913 7.210174 TGACATAGGACTTAGATGTGCAATAC 58.790 38.462 0.00 0.00 33.99 1.89
862 914 7.069950 TGACATAGGACTTAGATGTGCAATACT 59.930 37.037 0.00 0.00 33.99 2.12
863 915 7.796054 ACATAGGACTTAGATGTGCAATACTT 58.204 34.615 0.00 0.00 32.62 2.24
864 916 8.924303 ACATAGGACTTAGATGTGCAATACTTA 58.076 33.333 0.00 0.00 32.62 2.24
865 917 9.935241 CATAGGACTTAGATGTGCAATACTTAT 57.065 33.333 0.00 0.00 0.00 1.73
866 918 9.935241 ATAGGACTTAGATGTGCAATACTTATG 57.065 33.333 0.00 0.00 0.00 1.90
867 919 7.220030 AGGACTTAGATGTGCAATACTTATGG 58.780 38.462 0.00 0.00 0.00 2.74
868 920 6.073003 GGACTTAGATGTGCAATACTTATGGC 60.073 42.308 0.00 0.00 33.16 4.40
869 921 6.356556 ACTTAGATGTGCAATACTTATGGCA 58.643 36.000 0.00 0.00 40.19 4.92
874 926 3.260475 TGCAATACTTATGGCACGTCT 57.740 42.857 0.00 0.00 37.70 4.18
875 927 4.394439 TGCAATACTTATGGCACGTCTA 57.606 40.909 0.00 0.00 37.70 2.59
876 928 4.368315 TGCAATACTTATGGCACGTCTAG 58.632 43.478 0.00 0.00 37.70 2.43
877 929 4.098807 TGCAATACTTATGGCACGTCTAGA 59.901 41.667 0.00 0.00 37.70 2.43
878 930 5.221441 TGCAATACTTATGGCACGTCTAGAT 60.221 40.000 0.00 0.00 37.70 1.98
879 931 5.119279 GCAATACTTATGGCACGTCTAGATG 59.881 44.000 10.54 10.54 32.79 2.90
880 932 6.216569 CAATACTTATGGCACGTCTAGATGT 58.783 40.000 11.99 11.99 0.00 3.06
907 959 9.937577 GCTTTAGCAAAACTGATTTTTAATACG 57.062 29.630 0.00 0.00 41.59 3.06
948 1000 1.804151 CGAAAATCCAAACCGAGCAGA 59.196 47.619 0.00 0.00 0.00 4.26
1033 1085 4.832823 TCCCTCATTCGATCTACATAAGCA 59.167 41.667 0.00 0.00 0.00 3.91
1090 1142 1.536073 CCAACTCCGAGCTCCTCACA 61.536 60.000 8.47 0.00 0.00 3.58
1096 1148 2.169789 CGAGCTCCTCACAATGGCG 61.170 63.158 8.47 0.00 0.00 5.69
1130 1182 1.675641 ATGCCCGTGGAGTTTGAGC 60.676 57.895 0.00 0.00 0.00 4.26
1433 1485 4.510711 AGATCTGCTGATTCGCTTATGTTG 59.489 41.667 7.59 0.00 32.19 3.33
1434 1486 3.860641 TCTGCTGATTCGCTTATGTTGA 58.139 40.909 0.00 0.00 0.00 3.18
1435 1487 3.867493 TCTGCTGATTCGCTTATGTTGAG 59.133 43.478 0.00 0.00 0.00 3.02
1436 1488 3.860641 TGCTGATTCGCTTATGTTGAGA 58.139 40.909 0.00 0.00 0.00 3.27
1437 1489 3.618594 TGCTGATTCGCTTATGTTGAGAC 59.381 43.478 0.00 0.00 0.00 3.36
1438 1490 3.302092 GCTGATTCGCTTATGTTGAGACG 60.302 47.826 0.00 0.00 0.00 4.18
1439 1491 3.845178 TGATTCGCTTATGTTGAGACGT 58.155 40.909 0.00 0.00 0.00 4.34
1442 1494 0.914551 CGCTTATGTTGAGACGTCGG 59.085 55.000 10.46 0.00 0.00 4.79
1443 1495 1.466866 CGCTTATGTTGAGACGTCGGA 60.467 52.381 10.46 0.00 0.00 4.55
1444 1496 2.794981 CGCTTATGTTGAGACGTCGGAT 60.795 50.000 10.46 1.82 0.00 4.18
1456 1508 2.795470 GACGTCGGATTTCCATTAGAGC 59.205 50.000 0.00 0.00 35.14 4.09
1494 1548 2.030562 CCCTCCTTGTCGCACGTT 59.969 61.111 0.00 0.00 0.00 3.99
1502 1556 0.856641 TTGTCGCACGTTCTTGCTAC 59.143 50.000 0.00 0.00 40.62 3.58
1604 1662 8.752005 ATTAATTATGTGTGTTGTAGCATCCT 57.248 30.769 0.00 0.00 0.00 3.24
1605 1663 6.683974 AATTATGTGTGTTGTAGCATCCTC 57.316 37.500 0.00 0.00 0.00 3.71
1606 1664 2.472695 TGTGTGTTGTAGCATCCTCC 57.527 50.000 0.00 0.00 0.00 4.30
1607 1665 1.977854 TGTGTGTTGTAGCATCCTCCT 59.022 47.619 0.00 0.00 0.00 3.69
1608 1666 2.289631 TGTGTGTTGTAGCATCCTCCTG 60.290 50.000 0.00 0.00 0.00 3.86
1609 1667 2.028112 GTGTGTTGTAGCATCCTCCTGA 60.028 50.000 0.00 0.00 0.00 3.86
1610 1668 2.840038 TGTGTTGTAGCATCCTCCTGAT 59.160 45.455 0.00 0.00 0.00 2.90
1611 1669 4.030216 TGTGTTGTAGCATCCTCCTGATA 58.970 43.478 0.00 0.00 30.56 2.15
1612 1670 4.655649 TGTGTTGTAGCATCCTCCTGATAT 59.344 41.667 0.00 0.00 30.56 1.63
1613 1671 4.993584 GTGTTGTAGCATCCTCCTGATATG 59.006 45.833 0.00 0.00 30.56 1.78
1614 1672 4.655649 TGTTGTAGCATCCTCCTGATATGT 59.344 41.667 0.00 0.00 30.56 2.29
1615 1673 4.879197 TGTAGCATCCTCCTGATATGTG 57.121 45.455 0.00 0.00 30.56 3.21
1616 1674 3.580022 TGTAGCATCCTCCTGATATGTGG 59.420 47.826 0.00 0.00 30.56 4.17
1617 1675 1.983691 AGCATCCTCCTGATATGTGGG 59.016 52.381 0.00 0.00 30.56 4.61
1618 1676 1.980765 GCATCCTCCTGATATGTGGGA 59.019 52.381 0.00 0.00 30.56 4.37
1619 1677 2.373169 GCATCCTCCTGATATGTGGGAA 59.627 50.000 0.00 0.00 30.56 3.97
1620 1678 3.009916 GCATCCTCCTGATATGTGGGAAT 59.990 47.826 0.00 0.00 30.56 3.01
1621 1679 4.225942 GCATCCTCCTGATATGTGGGAATA 59.774 45.833 0.00 0.00 30.56 1.75
1622 1680 5.104193 GCATCCTCCTGATATGTGGGAATAT 60.104 44.000 0.00 0.00 30.56 1.28
1623 1681 6.100279 GCATCCTCCTGATATGTGGGAATATA 59.900 42.308 0.00 0.00 30.56 0.86
1624 1682 7.365921 GCATCCTCCTGATATGTGGGAATATAA 60.366 40.741 0.00 0.00 30.56 0.98
1625 1683 7.739995 TCCTCCTGATATGTGGGAATATAAG 57.260 40.000 0.00 0.00 0.00 1.73
1626 1684 6.156949 TCCTCCTGATATGTGGGAATATAAGC 59.843 42.308 0.00 0.00 0.00 3.09
1627 1685 6.313519 TCCTGATATGTGGGAATATAAGCC 57.686 41.667 0.00 0.00 0.00 4.35
1628 1686 5.104941 TCCTGATATGTGGGAATATAAGCCG 60.105 44.000 0.00 0.00 0.00 5.52
1629 1687 4.513442 TGATATGTGGGAATATAAGCCGC 58.487 43.478 0.00 0.00 0.00 6.53
1630 1688 2.200373 ATGTGGGAATATAAGCCGCC 57.800 50.000 0.00 0.00 0.00 6.13
1631 1689 1.136828 TGTGGGAATATAAGCCGCCT 58.863 50.000 0.00 0.00 0.00 5.52
1632 1690 1.071699 TGTGGGAATATAAGCCGCCTC 59.928 52.381 0.00 0.00 0.00 4.70
1633 1691 0.320374 TGGGAATATAAGCCGCCTCG 59.680 55.000 0.00 0.00 0.00 4.63
1634 1692 0.606604 GGGAATATAAGCCGCCTCGA 59.393 55.000 0.00 0.00 0.00 4.04
1635 1693 1.404315 GGGAATATAAGCCGCCTCGAG 60.404 57.143 5.13 5.13 0.00 4.04
1636 1694 1.404315 GGAATATAAGCCGCCTCGAGG 60.404 57.143 27.83 27.83 38.53 4.63
1637 1695 0.608640 AATATAAGCCGCCTCGAGGG 59.391 55.000 32.06 21.12 35.18 4.30
1655 1713 1.609580 GGGCCGTCAGATGTTGTTACA 60.610 52.381 0.00 0.00 38.95 2.41
1665 1723 1.436326 TGTTGTTACAGCCCACCCTA 58.564 50.000 0.00 0.00 0.00 3.53
1669 1727 3.124856 TGTTACAGCCCACCCTACTAT 57.875 47.619 0.00 0.00 0.00 2.12
1671 1729 3.036091 GTTACAGCCCACCCTACTATCA 58.964 50.000 0.00 0.00 0.00 2.15
1685 1743 2.308690 ACTATCACTACGAAGAGCCCC 58.691 52.381 0.00 0.00 0.00 5.80
1710 1768 1.152830 GACAAGGCCCAGGAACCAA 59.847 57.895 0.00 0.00 0.00 3.67
1711 1769 0.469144 GACAAGGCCCAGGAACCAAA 60.469 55.000 0.00 0.00 0.00 3.28
1780 1838 2.169330 GACCTAGCCTACTTATCGGGG 58.831 57.143 0.00 0.00 0.00 5.73
1796 1854 0.973496 GGGGAGAGTCACTGGAGGAC 60.973 65.000 0.00 0.00 35.50 3.85
1802 1860 2.203640 TCACTGGAGGACGGCAGT 60.204 61.111 0.00 0.00 0.00 4.40
1823 1883 2.158475 TCAGGAACCAGTTGGCATTCTT 60.158 45.455 0.00 0.00 39.32 2.52
1825 1885 2.158475 AGGAACCAGTTGGCATTCTTGA 60.158 45.455 0.00 0.00 39.32 3.02
1833 1893 3.430862 GCATTCTTGACGGCGGCA 61.431 61.111 13.60 13.60 0.00 5.69
1834 1894 2.976840 GCATTCTTGACGGCGGCAA 61.977 57.895 28.42 28.42 0.00 4.52
1841 1901 1.503818 TTGACGGCGGCAACTTCTTC 61.504 55.000 26.68 2.29 0.00 2.87
1845 1905 2.034221 GCGGCAACTTCTTCCCCT 59.966 61.111 0.00 0.00 0.00 4.79
1849 1909 1.545651 CGGCAACTTCTTCCCCTTTCT 60.546 52.381 0.00 0.00 0.00 2.52
1855 1915 1.996291 CTTCTTCCCCTTTCTCCCCTT 59.004 52.381 0.00 0.00 0.00 3.95
1858 1918 0.198696 TTCCCCTTTCTCCCCTTCCT 59.801 55.000 0.00 0.00 0.00 3.36
1859 1919 0.198696 TCCCCTTTCTCCCCTTCCTT 59.801 55.000 0.00 0.00 0.00 3.36
1861 1921 1.006043 CCCCTTTCTCCCCTTCCTTTC 59.994 57.143 0.00 0.00 0.00 2.62
1863 1923 1.006043 CCTTTCTCCCCTTCCTTTCCC 59.994 57.143 0.00 0.00 0.00 3.97
1864 1924 1.996291 CTTTCTCCCCTTCCTTTCCCT 59.004 52.381 0.00 0.00 0.00 4.20
1875 1937 3.285290 TCCTTTCCCTCCTTAGAACCA 57.715 47.619 0.00 0.00 0.00 3.67
1907 1969 7.939039 ACTTCAGATTTGGTGTAATTCAGAGAA 59.061 33.333 0.00 0.00 0.00 2.87
1910 1972 7.173218 TCAGATTTGGTGTAATTCAGAGAACAC 59.827 37.037 0.00 0.00 41.14 3.32
1912 1974 8.375506 AGATTTGGTGTAATTCAGAGAACACTA 58.624 33.333 6.82 0.00 41.50 2.74
1913 1975 7.724305 TTTGGTGTAATTCAGAGAACACTAC 57.276 36.000 6.82 0.00 41.50 2.73
1925 1987 6.757478 TCAGAGAACACTACTGTACTAGATCG 59.243 42.308 0.00 0.00 33.93 3.69
1928 1990 5.816777 AGAACACTACTGTACTAGATCGACC 59.183 44.000 0.00 0.00 0.00 4.79
1931 1993 4.807834 CACTACTGTACTAGATCGACCGAA 59.192 45.833 0.00 0.00 0.00 4.30
1966 2028 2.708325 GGTAATCAGAGCCTTCTCCCAT 59.292 50.000 0.00 0.00 40.22 4.00
1974 2038 1.221840 CCTTCTCCCATCACCACCG 59.778 63.158 0.00 0.00 0.00 4.94
2018 2082 2.159179 TTCCCTCGATCATCCAGACA 57.841 50.000 0.00 0.00 0.00 3.41
2019 2083 1.403814 TCCCTCGATCATCCAGACAC 58.596 55.000 0.00 0.00 0.00 3.67
2022 2086 1.268794 CCTCGATCATCCAGACACGAC 60.269 57.143 0.00 0.00 35.58 4.34
2023 2087 1.401905 CTCGATCATCCAGACACGACA 59.598 52.381 0.00 0.00 35.58 4.35
2027 2091 1.176619 TCATCCAGACACGACACGGT 61.177 55.000 0.00 0.00 0.00 4.83
2055 2119 2.270205 CCATGGAAGAGCACGGCT 59.730 61.111 5.56 0.00 43.88 5.52
2061 2125 3.358076 GAAGAGCACGGCTAGGCGT 62.358 63.158 35.60 35.60 39.88 5.68
2075 2139 2.434185 GCGTTGGCCGATCTGACA 60.434 61.111 0.00 0.00 39.56 3.58
2080 2144 4.148825 GGCCGATCTGACAGCGGT 62.149 66.667 18.85 0.00 46.38 5.68
2120 2184 1.692411 AGATCGACGACATCCATCCA 58.308 50.000 0.00 0.00 0.00 3.41
2183 2247 2.801421 GTCGAGGATCTGCGAGCA 59.199 61.111 10.00 0.00 37.18 4.26
2198 2262 1.075970 AGCAGAGGTGGGCGATCTA 60.076 57.895 0.00 0.00 34.54 1.98
2248 2312 2.092291 CGGATCCAACCGTGTCGTG 61.092 63.158 13.41 0.00 46.70 4.35
2269 2333 4.069232 CGCTCCTCCGCCAACAGA 62.069 66.667 0.00 0.00 0.00 3.41
2271 2335 2.948720 GCTCCTCCGCCAACAGACT 61.949 63.158 0.00 0.00 0.00 3.24
2285 2349 2.738521 GACTCTTCGCAAGCGCCA 60.739 61.111 9.97 0.00 39.59 5.69
2321 2385 2.583441 CCTGCTCCTTCGACCACCA 61.583 63.158 0.00 0.00 0.00 4.17
2343 2409 2.038813 TCCGACTGGGATCTGCCA 59.961 61.111 0.00 0.00 40.94 4.92
2352 2418 1.103398 GGGATCTGCCACCAATTCCG 61.103 60.000 0.00 0.00 38.95 4.30
2355 2421 3.451894 CTGCCACCAATTCCGGGC 61.452 66.667 0.00 0.00 46.58 6.13
2358 2424 3.068064 CCACCAATTCCGGGCCAC 61.068 66.667 4.39 0.00 0.00 5.01
2404 2471 2.301738 GGGGAGCCACTACCAGCTT 61.302 63.158 0.00 0.00 40.11 3.74
2448 2515 4.947147 GGCCACGGCAGGACAACA 62.947 66.667 10.83 0.00 44.11 3.33
2494 2574 2.423898 CGCCTCTGGTCACGGGTAT 61.424 63.158 0.00 0.00 0.00 2.73
2504 2584 1.400494 GTCACGGGTATGCACAATTCC 59.600 52.381 0.00 0.00 0.00 3.01
2516 2596 2.355108 GCACAATTCCCAGTCTCTGCTA 60.355 50.000 0.00 0.00 0.00 3.49
2523 2603 0.758685 CCAGTCTCTGCTAGGGGAGG 60.759 65.000 0.00 0.00 0.00 4.30
2537 2617 1.357761 GGGGAGGGTTCATTCTTTGGA 59.642 52.381 0.00 0.00 0.00 3.53
2540 2620 3.053320 GGGAGGGTTCATTCTTTGGAGAT 60.053 47.826 0.00 0.00 0.00 2.75
2552 2632 5.282055 TCTTTGGAGATCGCAACTATCAT 57.718 39.130 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 3.441163 CAACATTAGCATGGCATGTCAC 58.559 45.455 26.94 11.92 34.27 3.67
42 43 2.427812 CCAACATTAGCATGGCATGTCA 59.572 45.455 26.94 0.60 34.27 3.58
43 44 2.689471 TCCAACATTAGCATGGCATGTC 59.311 45.455 26.94 19.01 34.27 3.06
44 45 2.737544 TCCAACATTAGCATGGCATGT 58.262 42.857 26.94 16.48 34.27 3.21
45 46 4.330944 AATCCAACATTAGCATGGCATG 57.669 40.909 22.99 22.99 34.27 4.06
46 47 6.268158 TGATTAATCCAACATTAGCATGGCAT 59.732 34.615 12.90 0.00 34.27 4.40
47 48 5.597594 TGATTAATCCAACATTAGCATGGCA 59.402 36.000 12.90 0.00 34.27 4.92
49 50 8.361889 TCAATGATTAATCCAACATTAGCATGG 58.638 33.333 12.90 0.00 34.27 3.66
122 131 1.687612 CACAATCCTCCCCTGTGCT 59.312 57.895 0.00 0.00 34.55 4.40
169 184 4.068599 CTGTGAAGAAGGGAAAAGAGGAC 58.931 47.826 0.00 0.00 0.00 3.85
170 185 3.973973 TCTGTGAAGAAGGGAAAAGAGGA 59.026 43.478 0.00 0.00 0.00 3.71
172 187 5.825151 AGTTTCTGTGAAGAAGGGAAAAGAG 59.175 40.000 0.00 0.00 0.00 2.85
173 188 5.755849 AGTTTCTGTGAAGAAGGGAAAAGA 58.244 37.500 0.00 0.00 0.00 2.52
174 189 6.095440 TGAAGTTTCTGTGAAGAAGGGAAAAG 59.905 38.462 0.00 0.00 0.00 2.27
176 191 5.505780 TGAAGTTTCTGTGAAGAAGGGAAA 58.494 37.500 0.00 0.00 0.00 3.13
177 192 5.110814 TGAAGTTTCTGTGAAGAAGGGAA 57.889 39.130 0.00 0.00 0.00 3.97
178 193 4.771114 TGAAGTTTCTGTGAAGAAGGGA 57.229 40.909 0.00 0.00 0.00 4.20
229 244 7.556844 TCAGTCCAAATTCAGATACCTAGAAC 58.443 38.462 0.00 0.00 0.00 3.01
232 247 8.043710 ACTTTCAGTCCAAATTCAGATACCTAG 58.956 37.037 0.00 0.00 0.00 3.02
235 250 7.201530 CGTACTTTCAGTCCAAATTCAGATACC 60.202 40.741 0.00 0.00 0.00 2.73
236 251 7.674240 GCGTACTTTCAGTCCAAATTCAGATAC 60.674 40.741 0.00 0.00 0.00 2.24
290 305 1.882198 CGAATTTGACACGGATGCAC 58.118 50.000 0.00 0.00 0.00 4.57
389 437 2.700897 TCCTTCTCCGATCTTCCAATCC 59.299 50.000 0.00 0.00 0.00 3.01
414 462 0.883833 CAACGCTTTGCCCTGAATCT 59.116 50.000 0.00 0.00 0.00 2.40
415 463 3.406682 CAACGCTTTGCCCTGAATC 57.593 52.632 0.00 0.00 0.00 2.52
528 576 0.247145 GAATGGTGCGTCGTTAAGCG 60.247 55.000 0.00 0.00 43.01 4.68
530 578 1.342555 TCGAATGGTGCGTCGTTAAG 58.657 50.000 0.00 0.00 38.41 1.85
531 579 1.780806 TTCGAATGGTGCGTCGTTAA 58.219 45.000 0.00 0.00 38.41 2.01
606 657 1.400142 GCACTTTTTGTTTTGTGGCCC 59.600 47.619 0.00 0.00 0.00 5.80
607 658 1.400142 GGCACTTTTTGTTTTGTGGCC 59.600 47.619 0.00 0.00 45.96 5.36
615 666 0.102300 GCGTGAGGGCACTTTTTGTT 59.898 50.000 0.00 0.00 42.93 2.83
616 667 1.034838 TGCGTGAGGGCACTTTTTGT 61.035 50.000 0.00 0.00 42.93 2.83
617 668 0.318107 CTGCGTGAGGGCACTTTTTG 60.318 55.000 0.00 0.00 42.93 2.44
623 674 2.512515 GATCCTGCGTGAGGGCAC 60.513 66.667 3.14 0.00 43.06 5.01
697 748 2.533266 ATCGAGTCAGTGCAACAAGT 57.467 45.000 0.00 0.00 41.43 3.16
698 749 3.248363 TGAAATCGAGTCAGTGCAACAAG 59.752 43.478 0.00 0.00 41.43 3.16
704 755 9.162793 CATTAAAATATGAAATCGAGTCAGTGC 57.837 33.333 7.56 0.00 0.00 4.40
706 757 8.840321 CCCATTAAAATATGAAATCGAGTCAGT 58.160 33.333 7.56 0.00 0.00 3.41
707 758 8.292448 CCCCATTAAAATATGAAATCGAGTCAG 58.708 37.037 7.56 0.00 0.00 3.51
710 761 9.807921 ATACCCCATTAAAATATGAAATCGAGT 57.192 29.630 0.00 0.00 0.00 4.18
713 764 9.840427 GACATACCCCATTAAAATATGAAATCG 57.160 33.333 0.00 0.00 0.00 3.34
722 773 5.135362 TGCCCTAGACATACCCCATTAAAAT 59.865 40.000 0.00 0.00 0.00 1.82
730 782 1.348036 GATGTGCCCTAGACATACCCC 59.652 57.143 0.00 0.00 34.10 4.95
732 784 4.408276 TCTAGATGTGCCCTAGACATACC 58.592 47.826 0.00 0.00 38.08 2.73
733 785 5.960113 CATCTAGATGTGCCCTAGACATAC 58.040 45.833 22.42 0.00 43.57 2.39
747 799 7.065563 GGGCAATAATTAGAGCACATCTAGATG 59.934 40.741 27.63 27.63 41.57 2.90
748 800 7.108847 GGGCAATAATTAGAGCACATCTAGAT 58.891 38.462 0.00 0.00 41.57 1.98
749 801 6.043127 TGGGCAATAATTAGAGCACATCTAGA 59.957 38.462 11.57 0.00 41.57 2.43
750 802 6.233434 TGGGCAATAATTAGAGCACATCTAG 58.767 40.000 11.57 0.00 41.57 2.43
751 803 6.186420 TGGGCAATAATTAGAGCACATCTA 57.814 37.500 11.57 0.00 39.64 1.98
752 804 5.052693 TGGGCAATAATTAGAGCACATCT 57.947 39.130 11.57 0.00 42.47 2.90
755 807 7.652524 TTAAATGGGCAATAATTAGAGCACA 57.347 32.000 16.35 16.35 45.45 4.57
756 808 8.981647 CATTTAAATGGGCAATAATTAGAGCAC 58.018 33.333 18.72 9.85 32.78 4.40
757 809 8.922237 TCATTTAAATGGGCAATAATTAGAGCA 58.078 29.630 24.40 0.16 37.03 4.26
758 810 9.415544 CTCATTTAAATGGGCAATAATTAGAGC 57.584 33.333 24.40 3.91 37.03 4.09
764 816 9.768662 GATTCACTCATTTAAATGGGCAATAAT 57.231 29.630 24.94 18.25 40.62 1.28
765 817 8.756927 TGATTCACTCATTTAAATGGGCAATAA 58.243 29.630 24.94 14.68 40.62 1.40
766 818 8.303780 TGATTCACTCATTTAAATGGGCAATA 57.696 30.769 24.94 10.65 40.62 1.90
767 819 7.185318 TGATTCACTCATTTAAATGGGCAAT 57.815 32.000 24.94 21.62 40.62 3.56
768 820 6.602410 TGATTCACTCATTTAAATGGGCAA 57.398 33.333 24.94 18.44 40.62 4.52
769 821 6.602410 TTGATTCACTCATTTAAATGGGCA 57.398 33.333 24.94 13.21 40.62 5.36
770 822 5.521372 GCTTGATTCACTCATTTAAATGGGC 59.479 40.000 24.94 10.96 40.62 5.36
771 823 6.532657 GTGCTTGATTCACTCATTTAAATGGG 59.467 38.462 23.70 23.70 42.66 4.00
772 824 7.092079 TGTGCTTGATTCACTCATTTAAATGG 58.908 34.615 24.40 17.88 35.58 3.16
773 825 8.523523 TTGTGCTTGATTCACTCATTTAAATG 57.476 30.769 20.13 20.13 35.58 2.32
774 826 9.545105 TTTTGTGCTTGATTCACTCATTTAAAT 57.455 25.926 0.00 0.00 35.58 1.40
775 827 8.939201 TTTTGTGCTTGATTCACTCATTTAAA 57.061 26.923 0.00 0.00 35.58 1.52
776 828 8.939201 TTTTTGTGCTTGATTCACTCATTTAA 57.061 26.923 0.00 0.00 35.58 1.52
811 863 9.986833 CATTGATCTTACATTGAAATTCGTGTA 57.013 29.630 6.86 6.86 0.00 2.90
812 864 8.729756 TCATTGATCTTACATTGAAATTCGTGT 58.270 29.630 8.48 8.48 30.67 4.49
813 865 9.003112 GTCATTGATCTTACATTGAAATTCGTG 57.997 33.333 0.00 0.00 33.86 4.35
814 866 8.729756 TGTCATTGATCTTACATTGAAATTCGT 58.270 29.630 0.00 0.00 33.86 3.85
815 867 9.726232 ATGTCATTGATCTTACATTGAAATTCG 57.274 29.630 0.00 0.00 33.86 3.34
819 871 9.904198 TCCTATGTCATTGATCTTACATTGAAA 57.096 29.630 0.00 0.00 34.54 2.69
820 872 9.330063 GTCCTATGTCATTGATCTTACATTGAA 57.670 33.333 0.00 0.00 34.54 2.69
821 873 8.708378 AGTCCTATGTCATTGATCTTACATTGA 58.292 33.333 0.00 0.00 34.54 2.57
822 874 8.899427 AGTCCTATGTCATTGATCTTACATTG 57.101 34.615 0.00 0.53 34.54 2.82
825 877 9.421399 TCTAAGTCCTATGTCATTGATCTTACA 57.579 33.333 0.00 0.00 0.00 2.41
828 880 8.932610 ACATCTAAGTCCTATGTCATTGATCTT 58.067 33.333 0.00 0.82 0.00 2.40
829 881 8.366401 CACATCTAAGTCCTATGTCATTGATCT 58.634 37.037 0.00 0.00 31.60 2.75
830 882 7.117523 GCACATCTAAGTCCTATGTCATTGATC 59.882 40.741 0.00 0.00 31.60 2.92
831 883 6.933521 GCACATCTAAGTCCTATGTCATTGAT 59.066 38.462 0.00 0.00 31.60 2.57
832 884 6.127083 TGCACATCTAAGTCCTATGTCATTGA 60.127 38.462 0.00 0.00 31.60 2.57
833 885 6.051074 TGCACATCTAAGTCCTATGTCATTG 58.949 40.000 0.00 0.00 31.60 2.82
834 886 6.239217 TGCACATCTAAGTCCTATGTCATT 57.761 37.500 0.00 0.00 31.60 2.57
835 887 5.876651 TGCACATCTAAGTCCTATGTCAT 57.123 39.130 0.00 0.00 31.60 3.06
836 888 5.675684 TTGCACATCTAAGTCCTATGTCA 57.324 39.130 0.00 0.00 31.60 3.58
837 889 7.437748 AGTATTGCACATCTAAGTCCTATGTC 58.562 38.462 0.00 0.00 31.60 3.06
838 890 7.366847 AGTATTGCACATCTAAGTCCTATGT 57.633 36.000 0.00 0.00 34.22 2.29
839 891 9.935241 ATAAGTATTGCACATCTAAGTCCTATG 57.065 33.333 0.00 0.00 0.00 2.23
840 892 9.935241 CATAAGTATTGCACATCTAAGTCCTAT 57.065 33.333 0.00 0.00 0.00 2.57
841 893 8.367911 CCATAAGTATTGCACATCTAAGTCCTA 58.632 37.037 0.00 0.00 0.00 2.94
842 894 7.220030 CCATAAGTATTGCACATCTAAGTCCT 58.780 38.462 0.00 0.00 0.00 3.85
843 895 6.073003 GCCATAAGTATTGCACATCTAAGTCC 60.073 42.308 0.00 0.00 0.00 3.85
844 896 6.483307 TGCCATAAGTATTGCACATCTAAGTC 59.517 38.462 0.00 0.00 30.49 3.01
845 897 6.356556 TGCCATAAGTATTGCACATCTAAGT 58.643 36.000 0.00 0.00 30.49 2.24
846 898 6.866010 TGCCATAAGTATTGCACATCTAAG 57.134 37.500 0.00 0.00 30.49 2.18
849 901 8.797958 AGACGTGCCATAAGTATTGCACATCT 62.798 42.308 20.94 18.57 46.22 2.90
853 905 2.936498 AGACGTGCCATAAGTATTGCAC 59.064 45.455 14.49 14.49 46.12 4.57
854 906 3.260475 AGACGTGCCATAAGTATTGCA 57.740 42.857 0.00 0.00 32.69 4.08
855 907 4.617959 TCTAGACGTGCCATAAGTATTGC 58.382 43.478 0.00 0.00 0.00 3.56
856 908 6.144563 CACATCTAGACGTGCCATAAGTATTG 59.855 42.308 5.94 0.00 0.00 1.90
857 909 6.216569 CACATCTAGACGTGCCATAAGTATT 58.783 40.000 5.94 0.00 0.00 1.89
858 910 5.773575 CACATCTAGACGTGCCATAAGTAT 58.226 41.667 5.94 0.00 0.00 2.12
859 911 5.183014 CACATCTAGACGTGCCATAAGTA 57.817 43.478 5.94 0.00 0.00 2.24
860 912 4.046938 CACATCTAGACGTGCCATAAGT 57.953 45.455 5.94 0.00 0.00 2.24
881 933 9.937577 CGTATTAAAAATCAGTTTTGCTAAAGC 57.062 29.630 0.00 0.00 39.79 3.51
886 938 9.691362 AATCACGTATTAAAAATCAGTTTTGCT 57.309 25.926 0.00 0.00 39.79 3.91
887 939 9.937577 GAATCACGTATTAAAAATCAGTTTTGC 57.062 29.630 0.00 0.00 39.79 3.68
898 950 9.027129 CGAGGTAAGATGAATCACGTATTAAAA 57.973 33.333 0.00 0.00 0.00 1.52
899 951 8.407832 TCGAGGTAAGATGAATCACGTATTAAA 58.592 33.333 0.00 0.00 0.00 1.52
900 952 7.859377 GTCGAGGTAAGATGAATCACGTATTAA 59.141 37.037 0.00 0.00 0.00 1.40
901 953 7.358066 GTCGAGGTAAGATGAATCACGTATTA 58.642 38.462 0.00 0.00 0.00 0.98
902 954 6.207213 GTCGAGGTAAGATGAATCACGTATT 58.793 40.000 0.00 0.00 0.00 1.89
903 955 5.560375 CGTCGAGGTAAGATGAATCACGTAT 60.560 44.000 0.00 0.00 0.00 3.06
904 956 4.260497 CGTCGAGGTAAGATGAATCACGTA 60.260 45.833 0.00 0.00 0.00 3.57
905 957 3.487042 CGTCGAGGTAAGATGAATCACGT 60.487 47.826 0.00 0.00 0.00 4.49
906 958 3.036633 CGTCGAGGTAAGATGAATCACG 58.963 50.000 0.00 0.00 0.00 4.35
907 959 2.789893 GCGTCGAGGTAAGATGAATCAC 59.210 50.000 7.01 0.00 0.00 3.06
908 960 2.540973 CGCGTCGAGGTAAGATGAATCA 60.541 50.000 7.01 0.00 0.00 2.57
909 961 2.044860 CGCGTCGAGGTAAGATGAATC 58.955 52.381 7.01 0.00 0.00 2.52
910 962 1.674441 TCGCGTCGAGGTAAGATGAAT 59.326 47.619 5.77 0.00 0.00 2.57
914 966 2.642139 TTTTCGCGTCGAGGTAAGAT 57.358 45.000 5.77 0.00 37.14 2.40
918 970 0.527113 TGGATTTTCGCGTCGAGGTA 59.473 50.000 5.77 0.00 37.14 3.08
948 1000 1.289380 GGAGTTCCGAGTTCGTGCT 59.711 57.895 0.48 0.00 37.74 4.40
1003 1055 4.918201 CGAATGAGGGAGCCGGCC 62.918 72.222 26.15 15.07 0.00 6.13
1009 1061 5.047731 TGCTTATGTAGATCGAATGAGGGAG 60.048 44.000 0.00 0.00 0.00 4.30
1016 1068 5.050490 GTGGTGTGCTTATGTAGATCGAAT 58.950 41.667 0.00 0.00 0.00 3.34
1096 1148 1.448540 CATGGAGTCGGCCACAGAC 60.449 63.158 2.24 1.66 41.56 3.51
1130 1182 1.746615 CCGTCATTGCTGTCCCCTG 60.747 63.158 0.00 0.00 0.00 4.45
1156 1208 1.598130 GCACTTGGAACGGCAGAGT 60.598 57.895 0.00 0.00 0.00 3.24
1159 1211 2.954753 GACGCACTTGGAACGGCAG 61.955 63.158 0.00 0.00 34.15 4.85
1433 1485 4.291783 CTCTAATGGAAATCCGACGTCTC 58.708 47.826 14.70 3.47 39.43 3.36
1434 1486 3.491104 GCTCTAATGGAAATCCGACGTCT 60.491 47.826 14.70 0.00 39.43 4.18
1435 1487 2.795470 GCTCTAATGGAAATCCGACGTC 59.205 50.000 5.18 5.18 39.43 4.34
1436 1488 2.483188 GGCTCTAATGGAAATCCGACGT 60.483 50.000 0.00 0.00 39.43 4.34
1437 1489 2.135933 GGCTCTAATGGAAATCCGACG 58.864 52.381 0.00 0.00 39.43 5.12
1438 1490 2.872858 GTGGCTCTAATGGAAATCCGAC 59.127 50.000 0.00 0.00 39.43 4.79
1439 1491 2.503765 TGTGGCTCTAATGGAAATCCGA 59.496 45.455 0.00 0.00 39.43 4.55
1442 1494 6.349300 TCTAACTGTGGCTCTAATGGAAATC 58.651 40.000 0.00 0.00 0.00 2.17
1443 1495 6.313519 TCTAACTGTGGCTCTAATGGAAAT 57.686 37.500 0.00 0.00 0.00 2.17
1444 1496 5.734720 CTCTAACTGTGGCTCTAATGGAAA 58.265 41.667 0.00 0.00 0.00 3.13
1456 1508 3.550842 GGCTTGTTTTGCTCTAACTGTGG 60.551 47.826 0.00 0.00 0.00 4.17
1494 1548 2.404265 TTTCGTTCGACGTAGCAAGA 57.596 45.000 0.00 0.00 43.14 3.02
1502 1556 5.079406 ACATGATTTCATTTTCGTTCGACG 58.921 37.500 0.00 0.00 37.44 5.12
1593 1651 4.040829 CCACATATCAGGAGGATGCTACAA 59.959 45.833 0.00 0.00 29.87 2.41
1597 1655 1.983691 CCCACATATCAGGAGGATGCT 59.016 52.381 0.00 0.00 37.06 3.79
1598 1656 1.980765 TCCCACATATCAGGAGGATGC 59.019 52.381 0.00 0.00 36.72 3.91
1599 1657 4.923516 ATTCCCACATATCAGGAGGATG 57.076 45.455 0.00 0.00 36.72 3.51
1600 1658 7.147408 GCTTATATTCCCACATATCAGGAGGAT 60.147 40.741 0.00 0.00 40.14 3.24
1601 1659 6.156949 GCTTATATTCCCACATATCAGGAGGA 59.843 42.308 0.00 0.00 0.00 3.71
1602 1660 6.352516 GCTTATATTCCCACATATCAGGAGG 58.647 44.000 0.00 0.00 0.00 4.30
1603 1661 6.352516 GGCTTATATTCCCACATATCAGGAG 58.647 44.000 0.00 0.00 0.00 3.69
1604 1662 5.104941 CGGCTTATATTCCCACATATCAGGA 60.105 44.000 0.00 0.00 0.00 3.86
1605 1663 5.118990 CGGCTTATATTCCCACATATCAGG 58.881 45.833 0.00 0.00 0.00 3.86
1606 1664 4.572389 GCGGCTTATATTCCCACATATCAG 59.428 45.833 0.00 0.00 0.00 2.90
1607 1665 4.513442 GCGGCTTATATTCCCACATATCA 58.487 43.478 0.00 0.00 0.00 2.15
1608 1666 3.877508 GGCGGCTTATATTCCCACATATC 59.122 47.826 0.00 0.00 0.00 1.63
1609 1667 3.523564 AGGCGGCTTATATTCCCACATAT 59.476 43.478 5.25 0.00 0.00 1.78
1610 1668 2.910319 AGGCGGCTTATATTCCCACATA 59.090 45.455 5.25 0.00 0.00 2.29
1611 1669 1.705186 AGGCGGCTTATATTCCCACAT 59.295 47.619 5.25 0.00 0.00 3.21
1612 1670 1.071699 GAGGCGGCTTATATTCCCACA 59.928 52.381 14.76 0.00 0.00 4.17
1613 1671 1.809684 GAGGCGGCTTATATTCCCAC 58.190 55.000 14.76 0.00 0.00 4.61
1614 1672 0.320374 CGAGGCGGCTTATATTCCCA 59.680 55.000 14.76 0.00 0.00 4.37
1615 1673 0.606604 TCGAGGCGGCTTATATTCCC 59.393 55.000 14.76 0.00 0.00 3.97
1616 1674 1.404315 CCTCGAGGCGGCTTATATTCC 60.404 57.143 20.67 0.00 0.00 3.01
1617 1675 1.404315 CCCTCGAGGCGGCTTATATTC 60.404 57.143 26.87 0.00 0.00 1.75
1618 1676 0.608640 CCCTCGAGGCGGCTTATATT 59.391 55.000 26.87 0.00 0.00 1.28
1619 1677 2.277858 CCCTCGAGGCGGCTTATAT 58.722 57.895 26.87 0.00 0.00 0.86
1620 1678 3.773370 CCCTCGAGGCGGCTTATA 58.227 61.111 26.87 0.31 0.00 0.98
1629 1687 2.835431 ATCTGACGGCCCTCGAGG 60.835 66.667 25.36 25.36 42.43 4.63
1630 1688 1.949847 AACATCTGACGGCCCTCGAG 61.950 60.000 5.13 5.13 42.43 4.04
1631 1689 1.982395 AACATCTGACGGCCCTCGA 60.982 57.895 0.00 0.00 42.43 4.04
1632 1690 1.811266 CAACATCTGACGGCCCTCG 60.811 63.158 0.00 0.00 45.88 4.63
1633 1691 0.321653 AACAACATCTGACGGCCCTC 60.322 55.000 0.00 0.00 0.00 4.30
1634 1692 0.981183 TAACAACATCTGACGGCCCT 59.019 50.000 0.00 0.00 0.00 5.19
1635 1693 1.084289 GTAACAACATCTGACGGCCC 58.916 55.000 0.00 0.00 0.00 5.80
1636 1694 1.732259 CTGTAACAACATCTGACGGCC 59.268 52.381 0.00 0.00 0.00 6.13
1637 1695 1.128692 GCTGTAACAACATCTGACGGC 59.871 52.381 0.00 0.00 35.43 5.68
1638 1696 1.732259 GGCTGTAACAACATCTGACGG 59.268 52.381 0.00 0.00 0.00 4.79
1639 1697 1.732259 GGGCTGTAACAACATCTGACG 59.268 52.381 0.00 0.00 0.00 4.35
1640 1698 2.484264 GTGGGCTGTAACAACATCTGAC 59.516 50.000 0.00 0.00 0.00 3.51
1641 1699 2.552155 GGTGGGCTGTAACAACATCTGA 60.552 50.000 0.00 0.00 0.00 3.27
1642 1700 1.812571 GGTGGGCTGTAACAACATCTG 59.187 52.381 0.00 0.00 0.00 2.90
1643 1701 1.271926 GGGTGGGCTGTAACAACATCT 60.272 52.381 0.00 0.00 0.00 2.90
1644 1702 1.173913 GGGTGGGCTGTAACAACATC 58.826 55.000 0.00 0.00 0.00 3.06
1645 1703 0.777446 AGGGTGGGCTGTAACAACAT 59.223 50.000 0.00 0.00 0.00 2.71
1655 1713 2.752154 CGTAGTGATAGTAGGGTGGGCT 60.752 54.545 0.00 0.00 0.00 5.19
1665 1723 2.308690 GGGGCTCTTCGTAGTGATAGT 58.691 52.381 0.00 0.00 0.00 2.12
1669 1727 2.707849 GCGGGGCTCTTCGTAGTGA 61.708 63.158 0.00 0.00 0.00 3.41
1671 1729 3.823330 CGCGGGGCTCTTCGTAGT 61.823 66.667 0.00 0.00 0.00 2.73
1685 1743 3.997064 CTGGGCCTTGTCTCTCGCG 62.997 68.421 4.53 0.00 0.00 5.87
1710 1768 0.402121 GGCCTTCTCACCCTCTTGTT 59.598 55.000 0.00 0.00 0.00 2.83
1711 1769 1.492993 GGGCCTTCTCACCCTCTTGT 61.493 60.000 0.84 0.00 43.36 3.16
1780 1838 1.939769 GCCGTCCTCCAGTGACTCTC 61.940 65.000 0.00 0.00 0.00 3.20
1796 1854 1.071471 AACTGGTTCCTGACTGCCG 59.929 57.895 2.86 0.00 0.00 5.69
1802 1860 1.425066 AGAATGCCAACTGGTTCCTGA 59.575 47.619 0.00 0.00 37.57 3.86
1808 1866 1.238439 CGTCAAGAATGCCAACTGGT 58.762 50.000 0.00 0.00 37.57 4.00
1809 1867 0.523072 CCGTCAAGAATGCCAACTGG 59.477 55.000 0.00 0.00 38.53 4.00
1823 1883 1.959226 GAAGAAGTTGCCGCCGTCA 60.959 57.895 0.00 0.00 0.00 4.35
1825 1885 2.668550 GGAAGAAGTTGCCGCCGT 60.669 61.111 0.00 0.00 0.00 5.68
1833 1893 1.711375 GGGGAGAAAGGGGAAGAAGTT 59.289 52.381 0.00 0.00 0.00 2.66
1834 1894 1.132036 AGGGGAGAAAGGGGAAGAAGT 60.132 52.381 0.00 0.00 0.00 3.01
1841 1901 1.006043 GAAAGGAAGGGGAGAAAGGGG 59.994 57.143 0.00 0.00 0.00 4.79
1845 1905 1.993301 GAGGGAAAGGAAGGGGAGAAA 59.007 52.381 0.00 0.00 0.00 2.52
1849 1909 0.198696 AAGGAGGGAAAGGAAGGGGA 59.801 55.000 0.00 0.00 0.00 4.81
1855 1915 3.285290 TGGTTCTAAGGAGGGAAAGGA 57.715 47.619 0.00 0.00 0.00 3.36
1858 1918 4.371681 AGCTATGGTTCTAAGGAGGGAAA 58.628 43.478 0.00 0.00 0.00 3.13
1859 1919 4.008916 AGCTATGGTTCTAAGGAGGGAA 57.991 45.455 0.00 0.00 0.00 3.97
1861 1921 4.484912 AGTAGCTATGGTTCTAAGGAGGG 58.515 47.826 0.00 0.00 0.00 4.30
1863 1923 6.547880 TCTGAAGTAGCTATGGTTCTAAGGAG 59.452 42.308 0.00 0.00 0.00 3.69
1864 1924 6.432581 TCTGAAGTAGCTATGGTTCTAAGGA 58.567 40.000 0.00 0.00 0.00 3.36
1875 1937 9.331282 GAATTACACCAAATCTGAAGTAGCTAT 57.669 33.333 0.00 0.00 0.00 2.97
1907 1969 4.118410 CGGTCGATCTAGTACAGTAGTGT 58.882 47.826 8.55 8.55 41.06 3.55
1910 1972 5.558653 GCTTTCGGTCGATCTAGTACAGTAG 60.559 48.000 0.00 0.00 0.00 2.57
1912 1974 3.065095 GCTTTCGGTCGATCTAGTACAGT 59.935 47.826 0.00 0.00 0.00 3.55
1913 1975 3.619729 GCTTTCGGTCGATCTAGTACAG 58.380 50.000 0.00 0.00 0.00 2.74
1925 1987 3.231160 CCAAAATGTTACGCTTTCGGTC 58.769 45.455 0.00 0.00 40.69 4.79
1928 1990 6.081049 TGATTACCAAAATGTTACGCTTTCG 58.919 36.000 0.00 0.00 42.43 3.46
1931 1993 6.622896 GCTCTGATTACCAAAATGTTACGCTT 60.623 38.462 0.00 0.00 0.00 4.68
1974 2038 2.049985 CGCCAGGGTCGATCGATC 60.050 66.667 22.50 21.33 0.00 3.69
2018 2082 2.341176 GTGGCCTTACCGTGTCGT 59.659 61.111 3.32 0.00 43.94 4.34
2019 2083 2.433664 GGTGGCCTTACCGTGTCG 60.434 66.667 3.32 0.00 43.94 4.35
2022 2086 2.359478 GGTGGTGGCCTTACCGTG 60.359 66.667 3.32 0.00 43.87 4.94
2023 2087 2.228480 ATGGTGGTGGCCTTACCGT 61.228 57.895 3.32 8.42 43.87 4.83
2027 2091 0.331278 CTTCCATGGTGGTGGCCTTA 59.669 55.000 12.58 0.00 39.03 2.69
2061 2125 2.125552 CGCTGTCAGATCGGCCAA 60.126 61.111 2.24 0.00 36.46 4.52
2080 2144 2.354188 CCGTCATCGCGGCGATAA 60.354 61.111 34.19 21.12 45.19 1.75
2120 2184 0.882474 CTTGGAACTCGAGGACGACT 59.118 55.000 18.41 0.00 43.81 4.18
2183 2247 3.843304 CGTAGATCGCCCACCTCT 58.157 61.111 0.00 0.00 0.00 3.69
2261 2325 0.514691 CTTGCGAAGAGTCTGTTGGC 59.485 55.000 9.44 9.44 0.00 4.52
2269 2333 2.046892 ATGGCGCTTGCGAAGAGT 60.047 55.556 19.55 0.00 40.46 3.24
2271 2335 2.047370 TGATGGCGCTTGCGAAGA 60.047 55.556 19.55 1.45 40.46 2.87
2314 2378 2.183555 GTCGGATCGGTGGTGGTC 59.816 66.667 0.00 0.00 0.00 4.02
2343 2409 3.961414 ACGTGGCCCGGAATTGGT 61.961 61.111 16.44 0.00 42.24 3.67
2448 2515 3.728373 GTGCTCCCCCGGTGGATT 61.728 66.667 5.97 0.00 35.39 3.01
2482 2562 0.326595 ATTGTGCATACCCGTGACCA 59.673 50.000 0.00 0.00 0.00 4.02
2494 2574 1.883638 GCAGAGACTGGGAATTGTGCA 60.884 52.381 0.00 0.00 31.21 4.57
2504 2584 0.758685 CCTCCCCTAGCAGAGACTGG 60.759 65.000 8.43 0.00 31.43 4.00
2516 2596 1.359130 CCAAAGAATGAACCCTCCCCT 59.641 52.381 0.00 0.00 0.00 4.79
2523 2603 3.009723 TGCGATCTCCAAAGAATGAACC 58.990 45.455 0.00 0.00 34.49 3.62
2537 2617 6.870965 GTGGAAATCTATGATAGTTGCGATCT 59.129 38.462 0.00 0.00 0.00 2.75
2540 2620 5.163353 TGGTGGAAATCTATGATAGTTGCGA 60.163 40.000 0.00 0.00 0.00 5.10
2552 2632 0.035820 GCGGTGGTGGTGGAAATCTA 60.036 55.000 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.