Multiple sequence alignment - TraesCS3D01G042600

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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 TraesCS3D01G042600 chr3D 100.000 5960 0 0 1 5960 16320453 16314494 0.000000e+00 11007.0
1 TraesCS3D01G042600 chr3D 86.486 148 15 4 2930 3072 428398929 428398782 2.220000e-34 158.0
2 TraesCS3D01G042600 chr3D 83.333 150 18 6 2929 3072 355144917 355145065 1.350000e-26 132.0
3 TraesCS3D01G042600 chr3A 94.367 3000 113 23 2982 5960 20133279 20136243 0.000000e+00 4553.0
4 TraesCS3D01G042600 chr3A 89.884 1374 78 24 921 2257 20131077 20132426 0.000000e+00 1711.0
5 TraesCS3D01G042600 chr3A 92.441 635 33 5 2332 2955 20132415 20133045 0.000000e+00 893.0
6 TraesCS3D01G042600 chr3B 92.061 3023 173 42 2969 5960 23783829 23780843 0.000000e+00 4191.0
7 TraesCS3D01G042600 chr3B 88.079 1426 69 32 910 2298 23787181 23785820 0.000000e+00 1598.0
8 TraesCS3D01G042600 chr3B 93.536 789 43 5 1 788 804315903 804316684 0.000000e+00 1168.0
9 TraesCS3D01G042600 chr3B 92.488 812 45 5 1 797 607419914 607420724 0.000000e+00 1147.0
10 TraesCS3D01G042600 chr3B 96.812 345 9 1 2385 2729 23785826 23785484 5.180000e-160 575.0
11 TraesCS3D01G042600 chr3B 94.545 220 10 2 2721 2939 23784328 23784110 7.400000e-89 339.0
12 TraesCS3D01G042600 chr3B 89.535 86 5 1 2208 2289 380679546 380679461 8.170000e-19 106.0
13 TraesCS3D01G042600 chr2A 93.857 814 33 5 1 798 765215608 765216420 0.000000e+00 1210.0
14 TraesCS3D01G042600 chr2A 94.022 803 30 8 12 798 44179605 44180405 0.000000e+00 1201.0
15 TraesCS3D01G042600 chr2A 93.358 813 37 5 1 797 765241018 765241829 0.000000e+00 1186.0
16 TraesCS3D01G042600 chr2A 82.550 149 19 4 2930 3072 669837216 669837069 2.260000e-24 124.0
17 TraesCS3D01G042600 chr2A 90.476 84 7 1 2208 2290 522505414 522505497 6.320000e-20 110.0
18 TraesCS3D01G042600 chr6B 93.283 789 45 8 1 786 181353 182136 0.000000e+00 1157.0
19 TraesCS3D01G042600 chr6B 95.286 700 31 2 1 699 641300907 641301605 0.000000e+00 1109.0
20 TraesCS3D01G042600 chr6B 90.164 122 6 3 2267 2388 474431878 474431763 2.880000e-33 154.0
21 TraesCS3D01G042600 chr6B 96.739 92 1 2 2299 2389 77773406 77773316 1.030000e-32 152.0
22 TraesCS3D01G042600 chr7D 92.777 803 39 12 1 788 29725804 29726602 0.000000e+00 1144.0
23 TraesCS3D01G042600 chr7D 95.918 98 2 2 2294 2390 514661030 514661126 2.220000e-34 158.0
24 TraesCS3D01G042600 chr7D 94.175 103 4 2 2296 2397 271541866 271541765 8.000000e-34 156.0
25 TraesCS3D01G042600 chr7D 95.050 101 2 3 2292 2390 594802403 594802502 8.000000e-34 156.0
26 TraesCS3D01G042600 chr7B 91.881 776 56 6 1 774 7074004 7073234 0.000000e+00 1077.0
27 TraesCS3D01G042600 chr7B 91.881 776 56 6 1 774 7087923 7088693 0.000000e+00 1077.0
28 TraesCS3D01G042600 chr7B 94.231 104 3 3 2292 2394 375201033 375201134 8.000000e-34 156.0
29 TraesCS3D01G042600 chr2B 90.978 787 61 8 1 784 102127521 102128300 0.000000e+00 1051.0
30 TraesCS3D01G042600 chr2B 80.822 146 20 4 2929 3072 773745764 773745903 2.270000e-19 108.0
31 TraesCS3D01G042600 chr2B 83.168 101 12 5 2976 3072 11373552 11373651 2.960000e-13 87.9
32 TraesCS3D01G042600 chr1D 94.175 103 4 2 2296 2397 407351087 407351188 8.000000e-34 156.0
33 TraesCS3D01G042600 chr4B 93.333 105 4 3 2292 2395 443547456 443547354 1.030000e-32 152.0
34 TraesCS3D01G042600 chr4B 84.868 152 17 4 2930 3076 602652724 602652874 1.340000e-31 148.0
35 TraesCS3D01G042600 chr4B 92.045 88 6 1 2204 2291 28406853 28406939 8.110000e-24 122.0
36 TraesCS3D01G042600 chrUn 88.095 126 11 4 2267 2388 324448745 324448620 4.810000e-31 147.0
37 TraesCS3D01G042600 chrUn 86.957 92 11 1 5636 5726 30300967 30301058 1.060000e-17 102.0
38 TraesCS3D01G042600 chr2D 82.313 147 17 5 2930 3073 650231809 650231669 1.050000e-22 119.0
39 TraesCS3D01G042600 chr2D 90.476 84 6 1 2208 2289 473096368 473096451 6.320000e-20 110.0
40 TraesCS3D01G042600 chr4A 90.588 85 4 1 2208 2288 589013041 589013125 6.320000e-20 110.0
41 TraesCS3D01G042600 chr1B 91.358 81 5 1 2208 2288 654631660 654631582 6.320000e-20 110.0
42 TraesCS3D01G042600 chr6D 91.250 80 5 1 2208 2287 457751553 457751630 2.270000e-19 108.0
43 TraesCS3D01G042600 chr5D 90.625 64 4 2 3011 3072 329601386 329601323 3.830000e-12 84.2
44 TraesCS3D01G042600 chr5A 89.062 64 5 2 3011 3072 427077744 427077807 1.780000e-10 78.7
45 TraesCS3D01G042600 chr6A 100.000 29 0 0 2928 2956 213867682 213867654 3.000000e-03 54.7


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 TraesCS3D01G042600 chr3D 16314494 16320453 5959 True 11007.000000 11007 100.000000 1 5960 1 chr3D.!!$R1 5959
1 TraesCS3D01G042600 chr3A 20131077 20136243 5166 False 2385.666667 4553 92.230667 921 5960 3 chr3A.!!$F1 5039
2 TraesCS3D01G042600 chr3B 23780843 23787181 6338 True 1675.750000 4191 92.874250 910 5960 4 chr3B.!!$R2 5050
3 TraesCS3D01G042600 chr3B 804315903 804316684 781 False 1168.000000 1168 93.536000 1 788 1 chr3B.!!$F2 787
4 TraesCS3D01G042600 chr3B 607419914 607420724 810 False 1147.000000 1147 92.488000 1 797 1 chr3B.!!$F1 796
5 TraesCS3D01G042600 chr2A 765215608 765216420 812 False 1210.000000 1210 93.857000 1 798 1 chr2A.!!$F3 797
6 TraesCS3D01G042600 chr2A 44179605 44180405 800 False 1201.000000 1201 94.022000 12 798 1 chr2A.!!$F1 786
7 TraesCS3D01G042600 chr2A 765241018 765241829 811 False 1186.000000 1186 93.358000 1 797 1 chr2A.!!$F4 796
8 TraesCS3D01G042600 chr6B 181353 182136 783 False 1157.000000 1157 93.283000 1 786 1 chr6B.!!$F1 785
9 TraesCS3D01G042600 chr6B 641300907 641301605 698 False 1109.000000 1109 95.286000 1 699 1 chr6B.!!$F2 698
10 TraesCS3D01G042600 chr7D 29725804 29726602 798 False 1144.000000 1144 92.777000 1 788 1 chr7D.!!$F1 787
11 TraesCS3D01G042600 chr7B 7073234 7074004 770 True 1077.000000 1077 91.881000 1 774 1 chr7B.!!$R1 773
12 TraesCS3D01G042600 chr7B 7087923 7088693 770 False 1077.000000 1077 91.881000 1 774 1 chr7B.!!$F1 773
13 TraesCS3D01G042600 chr2B 102127521 102128300 779 False 1051.000000 1051 90.978000 1 784 1 chr2B.!!$F2 783

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
139 140 0.041238 AATCACCTCCTCACCCGAGA 59.959 55.000 0.00 0.0 42.34 4.04 F
940 992 0.312729 TTCTACTTGCGCAGTGACGA 59.687 50.000 11.31 2.1 35.97 4.20 F
1279 1366 0.036294 CTCCTCCCAAACCCTCGTTC 60.036 60.000 0.00 0.0 0.00 3.95 F
1282 1369 0.250166 CTCCCAAACCCTCGTTCGTT 60.250 55.000 0.00 0.0 0.00 3.85 F
1283 1370 1.001181 CTCCCAAACCCTCGTTCGTTA 59.999 52.381 0.00 0.0 0.00 3.18 F
3523 5050 0.947660 GGTCTTCCACGTTTCCCGAC 60.948 60.000 0.00 0.0 40.70 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1077 1154 0.032815 GCCTGCGATCTCTCCCTTAC 59.967 60.000 0.00 0.0 0.00 2.34 R
2441 2552 1.001378 CAAGCACAACTGTACAAGGCC 60.001 52.381 0.00 0.0 0.00 5.19 R
3146 4673 0.813210 GCATGCGAGGGAGAAAGGAG 60.813 60.000 0.00 0.0 0.00 3.69 R
3523 5050 0.747255 AGATGACGTCAAGGGGATCG 59.253 55.000 24.13 0.0 0.00 3.69 R
4015 5542 4.575885 TGGTGTAGCTTACATGTCCTTTC 58.424 43.478 0.00 0.0 41.34 2.62 R
5702 7257 0.887933 CCACGTCTTGGGAAATTGGG 59.112 55.000 0.00 0.0 42.54 4.12 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
77 78 4.619227 CCAACGCCCGTCACCTGT 62.619 66.667 0.00 0.00 0.00 4.00
84 85 2.989824 CCGTCACCTGTCTCCGGT 60.990 66.667 0.00 0.00 34.10 5.28
107 108 2.031012 CACAGCAGCCACCGAAGA 59.969 61.111 0.00 0.00 0.00 2.87
139 140 0.041238 AATCACCTCCTCACCCGAGA 59.959 55.000 0.00 0.00 42.34 4.04
168 169 1.607509 GCTCCATCGCTGATATGCAGT 60.608 52.381 0.00 0.00 46.62 4.40
478 486 1.229209 AGGTCCACCACGAGGATGT 60.229 57.895 5.68 0.00 37.52 3.06
479 487 1.218316 GGTCCACCACGAGGATGTC 59.782 63.158 5.68 0.00 37.52 3.06
612 620 2.932905 GTCGTCGCCGAAGCAAAA 59.067 55.556 0.00 0.00 46.26 2.44
660 669 3.756069 ACGAGAGAGTAAAAACGATCCG 58.244 45.455 0.00 0.00 0.00 4.18
699 708 3.299977 CCCTCACCACCGACGACA 61.300 66.667 0.00 0.00 0.00 4.35
798 850 4.587684 AGAGGAAAACAGGAAAGAGTCGTA 59.412 41.667 0.00 0.00 0.00 3.43
799 851 5.070047 AGAGGAAAACAGGAAAGAGTCGTAA 59.930 40.000 0.00 0.00 0.00 3.18
800 852 5.298347 AGGAAAACAGGAAAGAGTCGTAAG 58.702 41.667 0.00 0.00 0.00 2.34
817 869 6.661304 TCGTAAGAAAAGTAGGACTTTCCT 57.339 37.500 5.13 0.00 46.78 3.36
818 870 6.453092 TCGTAAGAAAAGTAGGACTTTCCTG 58.547 40.000 4.90 0.00 46.78 3.86
819 871 6.041296 TCGTAAGAAAAGTAGGACTTTCCTGT 59.959 38.462 4.90 0.00 46.78 4.00
820 872 6.145696 CGTAAGAAAAGTAGGACTTTCCTGTG 59.854 42.308 4.90 0.00 46.78 3.66
821 873 7.949855 CGTAAGAAAAGTAGGACTTTCCTGTGA 60.950 40.741 4.90 0.00 46.78 3.58
829 881 4.937201 GGACTTTCCTGTGAAATTTGGT 57.063 40.909 0.00 0.00 39.65 3.67
831 883 6.399639 GGACTTTCCTGTGAAATTTGGTAA 57.600 37.500 0.00 0.00 39.65 2.85
832 884 6.811954 GGACTTTCCTGTGAAATTTGGTAAA 58.188 36.000 0.00 0.00 39.65 2.01
833 885 7.269316 GGACTTTCCTGTGAAATTTGGTAAAA 58.731 34.615 0.00 0.00 39.65 1.52
834 886 7.438160 GGACTTTCCTGTGAAATTTGGTAAAAG 59.562 37.037 0.00 0.87 39.65 2.27
835 887 8.073467 ACTTTCCTGTGAAATTTGGTAAAAGA 57.927 30.769 0.00 0.00 39.65 2.52
836 888 8.536175 ACTTTCCTGTGAAATTTGGTAAAAGAA 58.464 29.630 0.00 0.00 39.65 2.52
837 889 9.377312 CTTTCCTGTGAAATTTGGTAAAAGAAA 57.623 29.630 0.00 0.00 39.65 2.52
838 890 8.940768 TTCCTGTGAAATTTGGTAAAAGAAAG 57.059 30.769 0.00 0.00 0.00 2.62
839 891 8.299990 TCCTGTGAAATTTGGTAAAAGAAAGA 57.700 30.769 0.00 0.00 0.00 2.52
840 892 8.754080 TCCTGTGAAATTTGGTAAAAGAAAGAA 58.246 29.630 0.00 0.00 0.00 2.52
841 893 9.034544 CCTGTGAAATTTGGTAAAAGAAAGAAG 57.965 33.333 0.00 0.00 0.00 2.85
842 894 9.801873 CTGTGAAATTTGGTAAAAGAAAGAAGA 57.198 29.630 0.00 0.00 0.00 2.87
850 902 9.457436 TTTGGTAAAAGAAAGAAGAAGTACAGT 57.543 29.630 0.00 0.00 0.00 3.55
852 904 9.760077 TGGTAAAAGAAAGAAGAAGTACAGTAG 57.240 33.333 0.00 0.00 0.00 2.57
853 905 9.978044 GGTAAAAGAAAGAAGAAGTACAGTAGA 57.022 33.333 0.00 0.00 0.00 2.59
865 917 8.530269 AGAAGTACAGTAGAAAATAAACACGG 57.470 34.615 0.00 0.00 0.00 4.94
866 918 6.716898 AGTACAGTAGAAAATAAACACGGC 57.283 37.500 0.00 0.00 0.00 5.68
867 919 6.225318 AGTACAGTAGAAAATAAACACGGCA 58.775 36.000 0.00 0.00 0.00 5.69
868 920 5.352643 ACAGTAGAAAATAAACACGGCAC 57.647 39.130 0.00 0.00 0.00 5.01
869 921 4.817464 ACAGTAGAAAATAAACACGGCACA 59.183 37.500 0.00 0.00 0.00 4.57
870 922 5.144359 CAGTAGAAAATAAACACGGCACAC 58.856 41.667 0.00 0.00 0.00 3.82
871 923 5.049680 CAGTAGAAAATAAACACGGCACACT 60.050 40.000 0.00 0.00 0.00 3.55
872 924 6.146510 CAGTAGAAAATAAACACGGCACACTA 59.853 38.462 0.00 0.00 0.00 2.74
873 925 6.877322 AGTAGAAAATAAACACGGCACACTAT 59.123 34.615 0.00 0.00 0.00 2.12
874 926 6.569179 AGAAAATAAACACGGCACACTATT 57.431 33.333 0.00 0.00 0.00 1.73
875 927 6.378582 AGAAAATAAACACGGCACACTATTG 58.621 36.000 0.00 0.00 0.00 1.90
876 928 5.699097 AAATAAACACGGCACACTATTGT 57.301 34.783 0.00 0.00 35.84 2.71
877 929 6.804770 AAATAAACACGGCACACTATTGTA 57.195 33.333 0.00 0.00 33.30 2.41
878 930 6.995511 AATAAACACGGCACACTATTGTAT 57.004 33.333 0.00 0.00 33.30 2.29
879 931 8.495361 AAATAAACACGGCACACTATTGTATA 57.505 30.769 0.00 0.00 33.30 1.47
880 932 5.789710 AAACACGGCACACTATTGTATAC 57.210 39.130 0.00 0.00 33.30 1.47
881 933 4.459390 ACACGGCACACTATTGTATACA 57.541 40.909 0.08 0.08 33.30 2.29
882 934 5.018539 ACACGGCACACTATTGTATACAT 57.981 39.130 6.36 0.01 33.30 2.29
883 935 6.151663 ACACGGCACACTATTGTATACATA 57.848 37.500 6.36 0.00 33.30 2.29
884 936 6.575267 ACACGGCACACTATTGTATACATAA 58.425 36.000 6.36 0.00 33.30 1.90
885 937 7.042950 ACACGGCACACTATTGTATACATAAA 58.957 34.615 6.36 0.00 33.30 1.40
886 938 7.223971 ACACGGCACACTATTGTATACATAAAG 59.776 37.037 6.36 7.17 33.30 1.85
887 939 7.436970 CACGGCACACTATTGTATACATAAAGA 59.563 37.037 6.36 0.00 33.30 2.52
888 940 7.982919 ACGGCACACTATTGTATACATAAAGAA 59.017 33.333 6.36 0.00 33.30 2.52
889 941 8.487970 CGGCACACTATTGTATACATAAAGAAG 58.512 37.037 6.36 6.03 33.30 2.85
890 942 8.774586 GGCACACTATTGTATACATAAAGAAGG 58.225 37.037 6.36 3.71 33.30 3.46
891 943 9.542462 GCACACTATTGTATACATAAAGAAGGA 57.458 33.333 6.36 0.00 33.30 3.36
905 957 9.939802 ACATAAAGAAGGAGTATTTTACGAGTT 57.060 29.630 0.00 0.00 0.00 3.01
939 991 1.136690 TTTCTACTTGCGCAGTGACG 58.863 50.000 11.31 0.00 35.97 4.35
940 992 0.312729 TTCTACTTGCGCAGTGACGA 59.687 50.000 11.31 2.10 35.97 4.20
942 994 1.067846 TCTACTTGCGCAGTGACGAAT 60.068 47.619 11.31 0.00 35.97 3.34
943 995 1.321743 CTACTTGCGCAGTGACGAATC 59.678 52.381 11.31 0.00 35.97 2.52
944 996 0.599991 ACTTGCGCAGTGACGAATCA 60.600 50.000 11.31 0.00 32.83 2.57
1077 1154 4.271816 CGACGCGGAGGAGATGGG 62.272 72.222 12.47 0.00 0.00 4.00
1078 1155 3.148279 GACGCGGAGGAGATGGGT 61.148 66.667 12.47 0.00 0.00 4.51
1224 1307 2.185310 ATCCACACCTTCTCCACCGC 62.185 60.000 0.00 0.00 0.00 5.68
1231 1314 3.685214 CTTCTCCACCGCCGACGAG 62.685 68.421 0.00 0.00 43.93 4.18
1253 1339 1.999346 CGGAGGTCTTTTCCCCCAT 59.001 57.895 0.00 0.00 0.00 4.00
1279 1366 0.036294 CTCCTCCCAAACCCTCGTTC 60.036 60.000 0.00 0.00 0.00 3.95
1282 1369 0.250166 CTCCCAAACCCTCGTTCGTT 60.250 55.000 0.00 0.00 0.00 3.85
1283 1370 1.001181 CTCCCAAACCCTCGTTCGTTA 59.999 52.381 0.00 0.00 0.00 3.18
1284 1371 1.001181 TCCCAAACCCTCGTTCGTTAG 59.999 52.381 0.00 0.00 0.00 2.34
1285 1372 1.270465 CCCAAACCCTCGTTCGTTAGT 60.270 52.381 0.00 0.00 0.00 2.24
1288 1375 1.625511 AACCCTCGTTCGTTAGTCCT 58.374 50.000 0.00 0.00 0.00 3.85
1314 1401 4.022935 TCTGTTGGTTGCTTGTGAATGATC 60.023 41.667 0.00 0.00 0.00 2.92
1320 1407 5.945191 TGGTTGCTTGTGAATGATCTATGAA 59.055 36.000 0.00 0.00 0.00 2.57
1321 1408 6.604396 TGGTTGCTTGTGAATGATCTATGAAT 59.396 34.615 0.00 0.00 0.00 2.57
1322 1409 7.137426 GGTTGCTTGTGAATGATCTATGAATC 58.863 38.462 0.00 0.00 0.00 2.52
1323 1410 6.535274 TGCTTGTGAATGATCTATGAATCG 57.465 37.500 0.00 0.00 0.00 3.34
1324 1411 6.282930 TGCTTGTGAATGATCTATGAATCGA 58.717 36.000 0.00 0.00 0.00 3.59
1325 1412 6.932960 TGCTTGTGAATGATCTATGAATCGAT 59.067 34.615 0.00 0.00 0.00 3.59
1326 1413 7.095355 TGCTTGTGAATGATCTATGAATCGATG 60.095 37.037 0.00 0.00 0.00 3.84
1327 1414 7.117379 GCTTGTGAATGATCTATGAATCGATGA 59.883 37.037 0.00 0.00 0.00 2.92
1371 1458 1.696832 GAGCAACTCGCCTTAAGCCG 61.697 60.000 0.00 0.00 44.04 5.52
1405 1492 3.814625 TGATCTGATGCTCGAGTCTAGT 58.185 45.455 15.13 0.00 0.00 2.57
1406 1493 3.812609 TGATCTGATGCTCGAGTCTAGTC 59.187 47.826 15.13 6.07 0.00 2.59
1407 1494 3.552132 TCTGATGCTCGAGTCTAGTCT 57.448 47.619 15.13 0.00 0.00 3.24
1408 1495 4.674281 TCTGATGCTCGAGTCTAGTCTA 57.326 45.455 15.13 0.00 0.00 2.59
1409 1496 4.627058 TCTGATGCTCGAGTCTAGTCTAG 58.373 47.826 15.13 0.00 0.00 2.43
1417 1504 5.464389 GCTCGAGTCTAGTCTAGGACTAAAG 59.536 48.000 15.13 9.98 43.36 1.85
1425 1512 3.942748 AGTCTAGGACTAAAGTGCTCTCG 59.057 47.826 7.47 0.00 43.42 4.04
1482 1569 4.619160 GCAAACAGGGATGTCTGAAAATCC 60.619 45.833 10.71 10.71 41.50 3.01
1547 1634 1.276705 GACTCCCTGGGTTGTCTTCTC 59.723 57.143 23.94 7.53 0.00 2.87
1561 1648 6.931840 GGTTGTCTTCTCCCAGATGATAATAC 59.068 42.308 3.12 0.00 34.09 1.89
1565 1652 5.247110 TCTTCTCCCAGATGATAATACCTGC 59.753 44.000 0.00 0.00 0.00 4.85
1568 1655 3.327757 TCCCAGATGATAATACCTGCCAC 59.672 47.826 0.00 0.00 0.00 5.01
1574 1661 6.210385 CAGATGATAATACCTGCCACTACTCT 59.790 42.308 0.00 0.00 0.00 3.24
1576 1663 4.519350 TGATAATACCTGCCACTACTCTCG 59.481 45.833 0.00 0.00 0.00 4.04
1600 1695 6.866248 CGCTACATTTGTTTCAGGGTAAAAAT 59.134 34.615 0.00 0.00 0.00 1.82
1681 1776 5.831702 TTTTCCACCTTTTGCGTTTACTA 57.168 34.783 0.00 0.00 0.00 1.82
1683 1778 3.140623 TCCACCTTTTGCGTTTACTACC 58.859 45.455 0.00 0.00 0.00 3.18
1684 1779 2.879646 CCACCTTTTGCGTTTACTACCA 59.120 45.455 0.00 0.00 0.00 3.25
1687 1782 5.508320 CCACCTTTTGCGTTTACTACCAATT 60.508 40.000 0.00 0.00 0.00 2.32
1753 1848 6.951198 TCAGCCTTTACAAAAATATCCTCCAA 59.049 34.615 0.00 0.00 0.00 3.53
1832 1927 3.470645 AATGTGAAGGCCCTATACGTC 57.529 47.619 0.00 0.00 0.00 4.34
1915 2010 5.926542 GGATACAGTAAGCATCTTTCGCATA 59.073 40.000 0.00 0.00 0.00 3.14
1942 2037 9.810545 ATTCGTTTTGGACAATTTCTTTTTCTA 57.189 25.926 0.00 0.00 0.00 2.10
2004 2099 2.307496 ACTGGCATTGATTGGTGGAA 57.693 45.000 0.00 0.00 0.00 3.53
2206 2301 8.999431 TCATAGACTCAAAGTTTGTCAAATACC 58.001 33.333 15.08 0.00 33.56 2.73
2211 2306 6.828785 ACTCAAAGTTTGTCAAATACCACTCT 59.171 34.615 15.08 0.00 0.00 3.24
2290 2401 2.077687 TGGGACGGAGGGAGTATAAC 57.922 55.000 0.00 0.00 0.00 1.89
2291 2402 1.572415 TGGGACGGAGGGAGTATAACT 59.428 52.381 0.00 0.00 0.00 2.24
2292 2403 1.962100 GGGACGGAGGGAGTATAACTG 59.038 57.143 0.00 0.00 0.00 3.16
2293 2404 2.664015 GGACGGAGGGAGTATAACTGT 58.336 52.381 0.00 0.00 0.00 3.55
2294 2405 3.435601 GGGACGGAGGGAGTATAACTGTA 60.436 52.174 0.00 0.00 0.00 2.74
2295 2406 4.405548 GGACGGAGGGAGTATAACTGTAT 58.594 47.826 0.00 0.00 0.00 2.29
2296 2407 5.515534 GGGACGGAGGGAGTATAACTGTATA 60.516 48.000 0.00 0.00 0.00 1.47
2297 2408 6.006449 GGACGGAGGGAGTATAACTGTATAA 58.994 44.000 0.00 0.00 0.00 0.98
2298 2409 6.150809 GGACGGAGGGAGTATAACTGTATAAG 59.849 46.154 0.00 0.00 0.00 1.73
2299 2410 6.845908 ACGGAGGGAGTATAACTGTATAAGA 58.154 40.000 0.00 0.00 0.00 2.10
2300 2411 7.468496 ACGGAGGGAGTATAACTGTATAAGAT 58.532 38.462 0.00 0.00 0.00 2.40
2301 2412 8.609483 ACGGAGGGAGTATAACTGTATAAGATA 58.391 37.037 0.00 0.00 0.00 1.98
2302 2413 9.111613 CGGAGGGAGTATAACTGTATAAGATAG 57.888 40.741 0.00 0.00 0.00 2.08
2303 2414 9.978336 GGAGGGAGTATAACTGTATAAGATAGT 57.022 37.037 0.00 0.00 0.00 2.12
2312 2423 9.978336 ATAACTGTATAAGATAGTACTCCCTCC 57.022 37.037 0.00 0.00 0.00 4.30
2313 2424 6.474630 ACTGTATAAGATAGTACTCCCTCCG 58.525 44.000 0.00 0.00 0.00 4.63
2314 2425 6.044171 ACTGTATAAGATAGTACTCCCTCCGT 59.956 42.308 0.00 0.00 0.00 4.69
2315 2426 6.845908 TGTATAAGATAGTACTCCCTCCGTT 58.154 40.000 0.00 0.00 0.00 4.44
2316 2427 6.939163 TGTATAAGATAGTACTCCCTCCGTTC 59.061 42.308 0.00 0.00 0.00 3.95
2317 2428 3.226682 AGATAGTACTCCCTCCGTTCC 57.773 52.381 0.00 0.00 0.00 3.62
2318 2429 2.512896 AGATAGTACTCCCTCCGTTCCA 59.487 50.000 0.00 0.00 0.00 3.53
2319 2430 2.905415 TAGTACTCCCTCCGTTCCAA 57.095 50.000 0.00 0.00 0.00 3.53
2320 2431 2.019807 AGTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
2321 2432 2.332117 AGTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
2322 2433 2.910977 AGTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
2323 2434 4.098894 AGTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
2324 2435 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2325 2436 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2326 2437 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2327 2438 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2328 2439 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2329 2440 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2330 2441 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
2331 2442 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
2332 2443 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
2333 2444 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
2334 2445 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2335 2446 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
2336 2447 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
2337 2448 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
2338 2449 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
2339 2450 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
2340 2451 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
2341 2452 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
2342 2453 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
2375 2486 9.739276 ATACAAAGTTGAGTCATCTATTTTGGA 57.261 29.630 14.35 9.09 40.00 3.53
2376 2487 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
2377 2488 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
2378 2489 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
2379 2490 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
2380 2491 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
2381 2492 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
2382 2493 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2383 2494 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2441 2552 1.815408 GCATGGCTGTACCTGTATGGG 60.815 57.143 0.00 0.00 41.11 4.00
2463 2574 2.875933 GCCTTGTACAGTTGTGCTTGTA 59.124 45.455 0.00 0.00 0.00 2.41
2526 2637 5.695851 ATCTGAAGAGTTCAACGCAATTT 57.304 34.783 0.00 0.00 39.58 1.82
2564 2675 4.025015 TCGAAAGACATAGCGGTACTTC 57.975 45.455 0.00 0.00 33.31 3.01
2620 2731 4.739793 TGAAAGGATGGTCATCTTTGGTT 58.260 39.130 8.70 0.00 37.23 3.67
2621 2732 5.886609 TGAAAGGATGGTCATCTTTGGTTA 58.113 37.500 8.70 0.00 37.23 2.85
2723 3998 3.374058 GTCGTCCTGTATGGTTGGAATTG 59.626 47.826 0.00 0.00 37.07 2.32
2779 4054 1.444212 CCGTTTCTTGGCGCATTGG 60.444 57.895 10.83 0.00 0.00 3.16
2951 4227 3.631046 GCGGATCTAGGCCCCAGG 61.631 72.222 0.00 0.00 0.00 4.45
3035 4562 8.432110 TGTAGCAATTGTACAGTATACAATGG 57.568 34.615 7.55 5.98 44.57 3.16
3143 4670 9.046296 AGGATAAATGAAGTATTTTACTCAGCG 57.954 33.333 0.00 0.00 39.61 5.18
3146 4673 4.921470 TGAAGTATTTTACTCAGCGTGC 57.079 40.909 0.00 0.00 38.26 5.34
3291 4818 5.065914 ACACTGCACATTAATCAACAGAGT 58.934 37.500 12.70 9.14 0.00 3.24
3523 5050 0.947660 GGTCTTCCACGTTTCCCGAC 60.948 60.000 0.00 0.00 40.70 4.79
3658 5185 4.504916 CCGTGGCTGCTCCTCTCG 62.505 72.222 0.00 0.00 35.26 4.04
3865 5392 2.237392 CTCCGAGAAACAGAAGGGGATT 59.763 50.000 0.00 0.00 0.00 3.01
4015 5542 4.289245 AACGGTGGGTGGACGACG 62.289 66.667 0.00 0.00 0.00 5.12
4054 5581 3.009473 ACACCATGGAGCTTGTAGACATT 59.991 43.478 21.47 0.00 0.00 2.71
4312 5839 5.358160 CCTCAGACCTTTCTTCAAAGTGTTT 59.642 40.000 0.00 0.00 37.87 2.83
4599 6126 3.142174 GGGAAGATGAAAGCTTATCCGG 58.858 50.000 0.00 0.00 46.33 5.14
4695 6222 1.133136 TCTCCCCCTAGCATAGTGGTC 60.133 57.143 0.00 0.00 34.01 4.02
4701 6233 4.165372 CCCCCTAGCATAGTGGTCTTTTTA 59.835 45.833 0.00 0.00 34.01 1.52
4738 6270 4.129737 GCTGCTGCACATGCCTGG 62.130 66.667 11.11 0.00 41.18 4.45
4747 6279 2.492881 TGCACATGCCTGGAAATTGTAG 59.507 45.455 0.00 0.00 41.18 2.74
4749 6281 2.492881 CACATGCCTGGAAATTGTAGCA 59.507 45.455 0.00 0.00 34.28 3.49
4838 6370 8.812329 GGAATTATAATCGATCTGTACTCATGC 58.188 37.037 0.00 0.00 0.00 4.06
4966 6498 7.946655 TGAACAAGCTGAGATAATATTACCG 57.053 36.000 0.00 0.00 0.00 4.02
4967 6499 7.497595 TGAACAAGCTGAGATAATATTACCGT 58.502 34.615 0.00 0.00 0.00 4.83
4968 6500 7.652105 TGAACAAGCTGAGATAATATTACCGTC 59.348 37.037 0.00 0.00 0.00 4.79
4969 6501 7.291411 ACAAGCTGAGATAATATTACCGTCT 57.709 36.000 0.00 0.00 0.00 4.18
4970 6502 8.405418 ACAAGCTGAGATAATATTACCGTCTA 57.595 34.615 0.00 0.00 0.00 2.59
5010 6542 5.237815 TGTGTCATGTGTCAAGATAGTTCC 58.762 41.667 0.00 0.00 0.00 3.62
5016 6548 5.304686 TGTGTCAAGATAGTTCCAGGTTT 57.695 39.130 0.00 0.00 0.00 3.27
5068 6600 1.003580 TGCCTGAGTGATCAAACTCCC 59.996 52.381 10.04 1.59 45.03 4.30
5100 6632 9.822185 ATATTTTTCTTGACAGCAGTTTCTTTT 57.178 25.926 0.00 0.00 0.00 2.27
5145 6677 8.255206 AGCTTTGCTTCATTTCATCATTGAATA 58.745 29.630 0.00 0.00 37.36 1.75
5233 6776 8.887036 AGTCAAAAATAAATTCCTGACAAACC 57.113 30.769 14.59 0.00 35.44 3.27
5276 6819 9.372541 CAACATGCAAAATTTAGTGATGAAAAC 57.627 29.630 0.00 0.00 0.00 2.43
5281 6824 9.770097 TGCAAAATTTAGTGATGAAAACCATTA 57.230 25.926 0.00 0.00 35.17 1.90
5381 6925 4.108501 TGCCTAGACCTCCACGAATATA 57.891 45.455 0.00 0.00 0.00 0.86
5384 6928 5.542635 TGCCTAGACCTCCACGAATATATTT 59.457 40.000 0.00 0.00 0.00 1.40
5560 7115 2.436646 ACTTGAATGAGGGCGCGG 60.437 61.111 8.83 0.00 0.00 6.46
5589 7144 0.822532 GGAGGGGATTACTCTCGCGA 60.823 60.000 9.26 9.26 35.34 5.87
5614 7169 2.171940 GTGCTCAAGTGCTTCGCG 59.828 61.111 0.00 0.00 0.00 5.87
5702 7257 0.247736 ACCTGTGCATTCCTCTCGTC 59.752 55.000 0.00 0.00 0.00 4.20
5728 7283 3.578456 CCAAGACGTGGGCATCAC 58.422 61.111 0.00 0.00 44.64 3.06
5809 7368 8.872845 CCAATTTTGACATTATGAAAGTTAGGC 58.127 33.333 0.00 0.00 0.00 3.93
5822 7381 4.755266 AAGTTAGGCCAATCGACATAGT 57.245 40.909 5.01 0.00 0.00 2.12
5851 7410 0.462759 GGAGACCAAGCCAATCTCCG 60.463 60.000 3.86 0.00 46.81 4.63
5893 7460 3.074412 GACACTGGAACATAAGGTGTGG 58.926 50.000 0.00 0.00 42.63 4.17
5903 7470 6.183360 GGAACATAAGGTGTGGAATAGTTTCG 60.183 42.308 0.00 0.00 41.14 3.46
5939 7507 2.310538 AGCTTGTAAAGGCTGCAGTTT 58.689 42.857 16.64 11.36 46.35 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 2.280552 GCTGTGGTGGTACCGGAGA 61.281 63.158 9.46 0.00 42.58 3.71
84 85 2.429930 GTGGCTGCTGTGGTGGTA 59.570 61.111 0.00 0.00 0.00 3.25
107 108 5.316987 AGGAGGTGATTCGTCATTCTTTTT 58.683 37.500 0.00 0.00 33.18 1.94
139 140 4.630785 CGATGGAGCCGCGTCGAT 62.631 66.667 4.92 0.00 36.25 3.59
168 169 4.492604 CCTTGGAGGTCCGCAAAA 57.507 55.556 0.00 0.00 39.43 2.44
306 307 3.187700 GTGGTTCGTGGATGACAGATAC 58.812 50.000 0.00 0.00 0.00 2.24
483 491 3.908081 CAAGGATGGCATGGCGGC 61.908 66.667 15.27 0.00 41.67 6.53
490 498 1.202915 TCTGTTCAAGCAAGGATGGCA 60.203 47.619 0.00 0.00 37.68 4.92
569 577 7.586664 CGATGACAATGCTGAATAAAGATTCTG 59.413 37.037 0.00 0.71 41.87 3.02
612 620 8.842358 TCTAGGTTTTTAGATTGTTCATCGTT 57.158 30.769 0.00 0.00 36.93 3.85
808 860 4.937201 ACCAAATTTCACAGGAAAGTCC 57.063 40.909 0.00 0.00 45.58 3.85
809 861 8.194769 TCTTTTACCAAATTTCACAGGAAAGTC 58.805 33.333 0.00 0.00 45.58 3.01
810 862 8.073467 TCTTTTACCAAATTTCACAGGAAAGT 57.927 30.769 0.00 0.00 45.58 2.66
811 863 8.940768 TTCTTTTACCAAATTTCACAGGAAAG 57.059 30.769 0.00 1.28 45.58 2.62
812 864 9.377312 CTTTCTTTTACCAAATTTCACAGGAAA 57.623 29.630 0.00 0.00 46.36 3.13
813 865 8.754080 TCTTTCTTTTACCAAATTTCACAGGAA 58.246 29.630 0.00 0.00 0.00 3.36
814 866 8.299990 TCTTTCTTTTACCAAATTTCACAGGA 57.700 30.769 0.00 0.00 0.00 3.86
815 867 8.940768 TTCTTTCTTTTACCAAATTTCACAGG 57.059 30.769 0.00 0.00 0.00 4.00
816 868 9.801873 TCTTCTTTCTTTTACCAAATTTCACAG 57.198 29.630 0.00 0.00 0.00 3.66
824 876 9.457436 ACTGTACTTCTTCTTTCTTTTACCAAA 57.543 29.630 0.00 0.00 0.00 3.28
826 878 9.760077 CTACTGTACTTCTTCTTTCTTTTACCA 57.240 33.333 0.00 0.00 0.00 3.25
827 879 9.978044 TCTACTGTACTTCTTCTTTCTTTTACC 57.022 33.333 0.00 0.00 0.00 2.85
839 891 8.985805 CCGTGTTTATTTTCTACTGTACTTCTT 58.014 33.333 0.00 0.00 0.00 2.52
840 892 7.117379 GCCGTGTTTATTTTCTACTGTACTTCT 59.883 37.037 0.00 0.00 0.00 2.85
841 893 7.095523 TGCCGTGTTTATTTTCTACTGTACTTC 60.096 37.037 0.00 0.00 0.00 3.01
842 894 6.707161 TGCCGTGTTTATTTTCTACTGTACTT 59.293 34.615 0.00 0.00 0.00 2.24
843 895 6.146673 GTGCCGTGTTTATTTTCTACTGTACT 59.853 38.462 0.00 0.00 0.00 2.73
844 896 6.073657 TGTGCCGTGTTTATTTTCTACTGTAC 60.074 38.462 0.00 0.00 0.00 2.90
845 897 5.990386 TGTGCCGTGTTTATTTTCTACTGTA 59.010 36.000 0.00 0.00 0.00 2.74
846 898 4.817464 TGTGCCGTGTTTATTTTCTACTGT 59.183 37.500 0.00 0.00 0.00 3.55
847 899 5.049680 AGTGTGCCGTGTTTATTTTCTACTG 60.050 40.000 0.00 0.00 0.00 2.74
848 900 5.061179 AGTGTGCCGTGTTTATTTTCTACT 58.939 37.500 0.00 0.00 0.00 2.57
849 901 5.352643 AGTGTGCCGTGTTTATTTTCTAC 57.647 39.130 0.00 0.00 0.00 2.59
850 902 7.173562 ACAATAGTGTGCCGTGTTTATTTTCTA 59.826 33.333 0.00 0.00 36.31 2.10
851 903 6.016610 ACAATAGTGTGCCGTGTTTATTTTCT 60.017 34.615 0.00 0.00 36.31 2.52
852 904 6.146898 ACAATAGTGTGCCGTGTTTATTTTC 58.853 36.000 0.00 0.00 36.31 2.29
853 905 6.079424 ACAATAGTGTGCCGTGTTTATTTT 57.921 33.333 0.00 0.00 36.31 1.82
854 906 5.699097 ACAATAGTGTGCCGTGTTTATTT 57.301 34.783 0.00 0.00 36.31 1.40
855 907 6.995511 ATACAATAGTGTGCCGTGTTTATT 57.004 33.333 5.98 0.00 38.82 1.40
856 908 7.042950 TGTATACAATAGTGTGCCGTGTTTAT 58.957 34.615 5.98 0.00 38.82 1.40
857 909 6.396450 TGTATACAATAGTGTGCCGTGTTTA 58.604 36.000 5.98 0.00 38.82 2.01
858 910 5.239351 TGTATACAATAGTGTGCCGTGTTT 58.761 37.500 5.98 0.00 38.82 2.83
859 911 4.823157 TGTATACAATAGTGTGCCGTGTT 58.177 39.130 5.98 0.00 38.82 3.32
860 912 4.459390 TGTATACAATAGTGTGCCGTGT 57.541 40.909 5.98 0.00 38.82 4.49
861 913 7.436970 TCTTTATGTATACAATAGTGTGCCGTG 59.563 37.037 10.14 0.00 38.82 4.94
862 914 7.494211 TCTTTATGTATACAATAGTGTGCCGT 58.506 34.615 10.14 0.00 38.82 5.68
863 915 7.940178 TCTTTATGTATACAATAGTGTGCCG 57.060 36.000 10.14 0.00 38.82 5.69
864 916 8.774586 CCTTCTTTATGTATACAATAGTGTGCC 58.225 37.037 10.14 0.00 38.82 5.01
865 917 9.542462 TCCTTCTTTATGTATACAATAGTGTGC 57.458 33.333 10.14 0.00 38.82 4.57
879 931 9.939802 AACTCGTAAAATACTCCTTCTTTATGT 57.060 29.630 0.00 0.00 0.00 2.29
906 958 8.495949 GCGCAAGTAGAAATGCTTATCTAATAA 58.504 33.333 0.30 0.00 40.39 1.40
907 959 7.655732 TGCGCAAGTAGAAATGCTTATCTAATA 59.344 33.333 8.16 0.00 40.39 0.98
908 960 6.483307 TGCGCAAGTAGAAATGCTTATCTAAT 59.517 34.615 8.16 0.00 40.39 1.73
1077 1154 0.032815 GCCTGCGATCTCTCCCTTAC 59.967 60.000 0.00 0.00 0.00 2.34
1078 1155 1.456196 CGCCTGCGATCTCTCCCTTA 61.456 60.000 5.43 0.00 42.83 2.69
1156 1233 1.815421 CGGGTTGCCGATCCAGAAG 60.815 63.158 0.00 0.00 34.88 2.85
1205 1288 1.983224 CGGTGGAGAAGGTGTGGAT 59.017 57.895 0.00 0.00 0.00 3.41
1224 1307 3.048941 GACCTCCGGAACTCGTCGG 62.049 68.421 5.23 3.47 46.89 4.79
1231 1314 0.322277 GGGGAAAAGACCTCCGGAAC 60.322 60.000 5.23 0.00 33.36 3.62
1253 1339 1.767692 GTTTGGGAGGAGGCAAGGA 59.232 57.895 0.00 0.00 0.00 3.36
1279 1366 4.092968 GCAACCAACAGATTAGGACTAACG 59.907 45.833 0.00 0.00 0.00 3.18
1282 1369 5.221843 ACAAGCAACCAACAGATTAGGACTA 60.222 40.000 0.00 0.00 0.00 2.59
1283 1370 4.074970 CAAGCAACCAACAGATTAGGACT 58.925 43.478 0.00 0.00 0.00 3.85
1284 1371 3.821033 ACAAGCAACCAACAGATTAGGAC 59.179 43.478 0.00 0.00 0.00 3.85
1285 1372 3.820467 CACAAGCAACCAACAGATTAGGA 59.180 43.478 0.00 0.00 0.00 2.94
1288 1375 5.534278 TCATTCACAAGCAACCAACAGATTA 59.466 36.000 0.00 0.00 0.00 1.75
1321 1408 8.988934 GGCATCTAAATTTACAGTTATCATCGA 58.011 33.333 0.00 0.00 0.00 3.59
1322 1409 8.230486 GGGCATCTAAATTTACAGTTATCATCG 58.770 37.037 0.00 0.00 0.00 3.84
1323 1410 9.289782 AGGGCATCTAAATTTACAGTTATCATC 57.710 33.333 0.00 0.00 0.00 2.92
1324 1411 9.071276 CAGGGCATCTAAATTTACAGTTATCAT 57.929 33.333 0.00 0.00 0.00 2.45
1325 1412 7.013274 GCAGGGCATCTAAATTTACAGTTATCA 59.987 37.037 0.00 0.00 0.00 2.15
1326 1413 7.363431 GCAGGGCATCTAAATTTACAGTTATC 58.637 38.462 0.00 0.00 0.00 1.75
1327 1414 6.017109 CGCAGGGCATCTAAATTTACAGTTAT 60.017 38.462 0.00 0.00 0.00 1.89
1331 1418 3.876914 TCGCAGGGCATCTAAATTTACAG 59.123 43.478 0.00 0.00 0.00 2.74
1333 1420 3.304057 GCTCGCAGGGCATCTAAATTTAC 60.304 47.826 0.00 0.00 0.00 2.01
1336 1423 1.312815 GCTCGCAGGGCATCTAAATT 58.687 50.000 0.00 0.00 0.00 1.82
1371 1458 3.309961 TCAGATCAGCAGTCTTGTGTC 57.690 47.619 0.00 0.00 0.00 3.67
1405 1492 3.280295 CCGAGAGCACTTTAGTCCTAGA 58.720 50.000 0.00 0.00 0.00 2.43
1406 1493 2.359531 CCCGAGAGCACTTTAGTCCTAG 59.640 54.545 0.00 0.00 0.00 3.02
1407 1494 2.376109 CCCGAGAGCACTTTAGTCCTA 58.624 52.381 0.00 0.00 0.00 2.94
1408 1495 1.187087 CCCGAGAGCACTTTAGTCCT 58.813 55.000 0.00 0.00 0.00 3.85
1409 1496 0.460459 GCCCGAGAGCACTTTAGTCC 60.460 60.000 0.00 0.00 0.00 3.85
1417 1504 0.533032 AAACTAGAGCCCGAGAGCAC 59.467 55.000 0.00 0.00 34.23 4.40
1425 1512 1.439679 CGGTCACAAAACTAGAGCCC 58.560 55.000 0.00 0.00 0.00 5.19
1547 1634 3.328931 AGTGGCAGGTATTATCATCTGGG 59.671 47.826 0.00 0.00 0.00 4.45
1561 1648 0.382515 GTAGCGAGAGTAGTGGCAGG 59.617 60.000 0.00 0.00 0.00 4.85
1565 1652 4.111375 ACAAATGTAGCGAGAGTAGTGG 57.889 45.455 0.00 0.00 0.00 4.00
1568 1655 5.289675 CCTGAAACAAATGTAGCGAGAGTAG 59.710 44.000 0.00 0.00 0.00 2.57
1574 1661 3.134574 ACCCTGAAACAAATGTAGCGA 57.865 42.857 0.00 0.00 0.00 4.93
1576 1663 8.601845 AATTTTTACCCTGAAACAAATGTAGC 57.398 30.769 0.00 0.00 0.00 3.58
1644 1739 8.934023 AAGGTGGAAAATACAGTAAAGAATGA 57.066 30.769 0.00 0.00 0.00 2.57
1681 1776 4.590222 GCCATGAAGGGATATGAAATTGGT 59.410 41.667 0.00 0.00 38.09 3.67
1683 1778 7.014518 TGTTAGCCATGAAGGGATATGAAATTG 59.985 37.037 0.00 0.00 38.09 2.32
1684 1779 7.068702 TGTTAGCCATGAAGGGATATGAAATT 58.931 34.615 0.00 0.00 38.09 1.82
1687 1782 5.645056 TGTTAGCCATGAAGGGATATGAA 57.355 39.130 0.00 0.00 38.09 2.57
1753 1848 3.261962 TCCCACACCCAATTTACTAGGT 58.738 45.455 0.00 0.00 0.00 3.08
1832 1927 1.299541 GTCCATGCACCTCCATTACG 58.700 55.000 0.00 0.00 0.00 3.18
1915 2010 9.161629 AGAAAAAGAAATTGTCCAAAACGAATT 57.838 25.926 0.00 0.00 0.00 2.17
1942 2037 6.830838 GTCAAAAGGAGTCAGGATGGATTTAT 59.169 38.462 0.00 0.00 36.16 1.40
2206 2301 7.091443 ACACTTATTTTAAGACGGAGAGAGTG 58.909 38.462 1.47 0.00 36.58 3.51
2211 2306 7.223260 TGAGACACTTATTTTAAGACGGAGA 57.777 36.000 1.47 0.00 0.00 3.71
2290 2401 6.474630 ACGGAGGGAGTACTATCTTATACAG 58.525 44.000 0.00 0.00 0.00 2.74
2291 2402 6.445451 ACGGAGGGAGTACTATCTTATACA 57.555 41.667 0.00 0.00 0.00 2.29
2292 2403 6.374053 GGAACGGAGGGAGTACTATCTTATAC 59.626 46.154 0.00 0.00 0.00 1.47
2293 2404 6.044754 TGGAACGGAGGGAGTACTATCTTATA 59.955 42.308 0.00 0.00 0.00 0.98
2294 2405 5.163012 TGGAACGGAGGGAGTACTATCTTAT 60.163 44.000 0.00 0.00 0.00 1.73
2295 2406 4.166725 TGGAACGGAGGGAGTACTATCTTA 59.833 45.833 0.00 0.00 0.00 2.10
2296 2407 3.053095 TGGAACGGAGGGAGTACTATCTT 60.053 47.826 0.00 0.00 0.00 2.40
2297 2408 2.512896 TGGAACGGAGGGAGTACTATCT 59.487 50.000 0.00 0.00 0.00 1.98
2298 2409 2.941480 TGGAACGGAGGGAGTACTATC 58.059 52.381 0.00 0.00 0.00 2.08
2299 2410 3.393426 TTGGAACGGAGGGAGTACTAT 57.607 47.619 0.00 0.00 0.00 2.12
2300 2411 2.905415 TTGGAACGGAGGGAGTACTA 57.095 50.000 0.00 0.00 0.00 1.82
2301 2412 2.019807 TTTGGAACGGAGGGAGTACT 57.980 50.000 0.00 0.00 0.00 2.73
2302 2413 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
2303 2414 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
2304 2415 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
2305 2416 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2306 2417 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2307 2418 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2308 2419 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2309 2420 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
2310 2421 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
2311 2422 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
2312 2423 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
2313 2424 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
2314 2425 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
2315 2426 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
2316 2427 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
2349 2460 9.739276 TCCAAAATAGATGACTCAACTTTGTAT 57.261 29.630 0.00 0.00 0.00 2.29
2350 2461 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
2351 2462 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
2352 2463 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
2353 2464 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
2354 2465 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
2355 2466 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
2356 2467 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2357 2468 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
2358 2469 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
2359 2470 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
2360 2471 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
2361 2472 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2362 2473 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2363 2474 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2364 2475 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2365 2476 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2366 2477 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2367 2478 6.811634 TTATACTCCCTCCGTTCCAAAATA 57.188 37.500 0.00 0.00 0.00 1.40
2368 2479 5.703730 TTATACTCCCTCCGTTCCAAAAT 57.296 39.130 0.00 0.00 0.00 1.82
2369 2480 5.703730 ATTATACTCCCTCCGTTCCAAAA 57.296 39.130 0.00 0.00 0.00 2.44
2370 2481 5.901276 AGTATTATACTCCCTCCGTTCCAAA 59.099 40.000 0.00 0.00 32.47 3.28
2371 2482 5.303589 CAGTATTATACTCCCTCCGTTCCAA 59.696 44.000 1.33 0.00 36.76 3.53
2372 2483 4.831155 CAGTATTATACTCCCTCCGTTCCA 59.169 45.833 1.33 0.00 36.76 3.53
2373 2484 4.831710 ACAGTATTATACTCCCTCCGTTCC 59.168 45.833 1.33 0.00 36.76 3.62
2374 2485 5.533903 TCACAGTATTATACTCCCTCCGTTC 59.466 44.000 1.33 0.00 36.76 3.95
2375 2486 5.452255 TCACAGTATTATACTCCCTCCGTT 58.548 41.667 1.33 0.00 36.76 4.44
2376 2487 5.057843 TCACAGTATTATACTCCCTCCGT 57.942 43.478 1.33 0.00 36.76 4.69
2377 2488 5.125739 GGATCACAGTATTATACTCCCTCCG 59.874 48.000 1.33 0.00 36.76 4.63
2378 2489 6.153680 CAGGATCACAGTATTATACTCCCTCC 59.846 46.154 1.33 6.76 36.76 4.30
2379 2490 6.153680 CCAGGATCACAGTATTATACTCCCTC 59.846 46.154 1.33 0.00 36.76 4.30
2380 2491 6.019748 CCAGGATCACAGTATTATACTCCCT 58.980 44.000 1.33 2.33 36.76 4.20
2381 2492 5.780793 ACCAGGATCACAGTATTATACTCCC 59.219 44.000 1.33 0.23 36.76 4.30
2382 2493 6.919775 ACCAGGATCACAGTATTATACTCC 57.080 41.667 1.33 1.07 36.76 3.85
2421 2532 1.597742 CCATACAGGTACAGCCATGC 58.402 55.000 0.00 0.00 40.61 4.06
2441 2552 1.001378 CAAGCACAACTGTACAAGGCC 60.001 52.381 0.00 0.00 0.00 5.19
2463 2574 7.581213 TTCAAGTTACAGAATGACATTTGGT 57.419 32.000 1.39 6.53 39.69 3.67
2564 2675 1.731709 TCGACAATGTTCTGCCATTCG 59.268 47.619 0.00 0.00 32.81 3.34
2607 2718 9.672673 ATGCATAGTATATAACCAAAGATGACC 57.327 33.333 0.00 0.00 0.00 4.02
2761 4036 1.444212 CCAATGCGCCAAGAAACGG 60.444 57.895 4.18 0.00 0.00 4.44
2832 4107 8.828644 TGTAAGAACTACGAAAAATGCTAAACA 58.171 29.630 0.00 0.00 32.65 2.83
3143 4670 1.448717 GCGAGGGAGAAAGGAGCAC 60.449 63.158 0.00 0.00 0.00 4.40
3146 4673 0.813210 GCATGCGAGGGAGAAAGGAG 60.813 60.000 0.00 0.00 0.00 3.69
3523 5050 0.747255 AGATGACGTCAAGGGGATCG 59.253 55.000 24.13 0.00 0.00 3.69
4015 5542 4.575885 TGGTGTAGCTTACATGTCCTTTC 58.424 43.478 0.00 0.00 41.34 2.62
4156 5683 1.003839 GACCACCAGCCGATCAACA 60.004 57.895 0.00 0.00 0.00 3.33
4312 5839 1.681825 CGTCGATGTCAACGAGTTCA 58.318 50.000 5.33 0.00 41.29 3.18
4615 6142 1.352352 CCTACTGCCCCAATCCTATGG 59.648 57.143 0.00 0.00 40.35 2.74
4701 6233 8.509690 CAGCAGCTAAGCAATACAATGTATATT 58.490 33.333 6.30 5.24 36.85 1.28
4813 6345 9.358872 TGCATGAGTACAGATCGATTATAATTC 57.641 33.333 0.00 0.00 0.00 2.17
4966 6498 8.684973 ACACATTACTTATCAGACGTTTAGAC 57.315 34.615 0.00 0.00 0.00 2.59
4967 6499 8.517056 TGACACATTACTTATCAGACGTTTAGA 58.483 33.333 0.00 0.00 0.00 2.10
4968 6500 8.683550 TGACACATTACTTATCAGACGTTTAG 57.316 34.615 0.00 0.00 0.00 1.85
4969 6501 9.083080 CATGACACATTACTTATCAGACGTTTA 57.917 33.333 0.00 0.00 0.00 2.01
4970 6502 7.602644 ACATGACACATTACTTATCAGACGTTT 59.397 33.333 0.00 0.00 0.00 3.60
5068 6600 6.313905 ACTGCTGTCAAGAAAAATATAGGACG 59.686 38.462 0.00 0.00 0.00 4.79
5100 6632 6.478512 AAGCTTTTACCCATGTTTCAAGAA 57.521 33.333 0.00 0.00 0.00 2.52
5145 6677 7.704899 CACTTCCGTTCATAAAACCTTCTTTTT 59.295 33.333 0.00 0.00 33.27 1.94
5155 6687 6.491394 CAGAACAACACTTCCGTTCATAAAA 58.509 36.000 0.00 0.00 41.17 1.52
5202 6734 9.764363 GTCAGGAATTTATTTTTGACTTTTCCT 57.236 29.630 0.00 0.00 41.73 3.36
5381 6925 8.419076 AACAAACAAATTCTCGTGCTAAAAAT 57.581 26.923 0.00 0.00 0.00 1.82
5384 6928 5.679355 CGAACAAACAAATTCTCGTGCTAAA 59.321 36.000 0.00 0.00 0.00 1.85
5509 7056 1.229428 ACGTGCATGGAGTTTCTGTG 58.771 50.000 11.36 0.00 0.00 3.66
5524 7079 5.464057 TCAAGTGGTGTACTTCATTAACGTG 59.536 40.000 0.00 0.00 46.55 4.49
5560 7115 4.729868 AGTAATCCCCTCCATGTATTTGC 58.270 43.478 0.00 0.00 0.00 3.68
5589 7144 1.893808 CACTTGAGCACGGCCTTGT 60.894 57.895 11.38 0.00 0.00 3.16
5686 7241 1.191489 TGGGACGAGAGGAATGCACA 61.191 55.000 0.00 0.00 0.00 4.57
5702 7257 0.887933 CCACGTCTTGGGAAATTGGG 59.112 55.000 0.00 0.00 42.54 4.12
5721 7276 4.554036 GGCCTCCCTCGTGATGCC 62.554 72.222 0.00 0.00 38.58 4.40
5773 7328 2.325484 GTCAAAATTGGTGGTTCCCCT 58.675 47.619 0.00 0.00 34.77 4.79
5774 7329 2.043227 TGTCAAAATTGGTGGTTCCCC 58.957 47.619 0.00 0.00 34.77 4.81
5776 7331 6.696411 TCATAATGTCAAAATTGGTGGTTCC 58.304 36.000 0.00 0.00 0.00 3.62
5809 7368 5.923114 CCACAATCTCTACTATGTCGATTGG 59.077 44.000 12.98 4.46 43.05 3.16
5822 7381 2.501723 GGCTTGGTCTCCACAATCTCTA 59.498 50.000 0.00 0.00 30.78 2.43
5851 7410 1.364626 CTTCTCCGTGCACCATGCTC 61.365 60.000 12.15 0.00 45.31 4.26
5863 7430 1.068588 TGTTCCAGTGTCACTTCTCCG 59.931 52.381 1.67 0.00 0.00 4.63
5893 7460 4.449405 GCAATAGAGCCCTCGAAACTATTC 59.551 45.833 0.00 0.00 33.40 1.75
5903 7470 2.049888 AGCTTTGCAATAGAGCCCTC 57.950 50.000 16.15 0.00 37.11 4.30


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

AutoCloner maintained by Alex Coulton.