Multiple sequence alignment - TraesCS4A01G325200

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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 TraesCS4A01G325200 chr4A 100.000 3809 0 0 1 3809 612530673 612534481 0.000000e+00 7035
1 TraesCS4A01G325200 chr5B 92.381 945 51 8 1581 2513 693687626 693688561 0.000000e+00 1327
2 TraesCS4A01G325200 chr5B 93.098 652 28 10 2561 3196 693688556 693689206 0.000000e+00 939
3 TraesCS4A01G325200 chr5B 90.605 628 25 8 967 1581 693685644 693686250 0.000000e+00 802
4 TraesCS4A01G325200 chr5B 84.483 754 80 15 143 870 693684837 693685579 0.000000e+00 710
5 TraesCS4A01G325200 chr5B 78.171 678 123 22 2 661 34906749 34907419 3.540000e-110 409
6 TraesCS4A01G325200 chr5B 82.979 141 21 2 1213 1353 683655390 683655527 1.440000e-24 124
7 TraesCS4A01G325200 chr2A 98.369 613 10 0 3197 3809 737335309 737334697 0.000000e+00 1077
8 TraesCS4A01G325200 chr2A 98.052 616 11 1 3194 3809 66876292 66876906 0.000000e+00 1070
9 TraesCS4A01G325200 chr7A 97.907 621 13 0 3189 3809 731166879 731167499 0.000000e+00 1075
10 TraesCS4A01G325200 chr7A 98.206 613 11 0 3197 3809 671345519 671344907 0.000000e+00 1072
11 TraesCS4A01G325200 chr7A 97.600 625 15 0 3185 3809 696257875 696258499 0.000000e+00 1072
12 TraesCS4A01G325200 chr7A 97.585 621 15 0 3189 3809 731106624 731107244 0.000000e+00 1064
13 TraesCS4A01G325200 chr7A 82.961 358 57 4 61 417 549012450 549012804 1.710000e-83 320
14 TraesCS4A01G325200 chr7A 81.102 127 21 2 2117 2243 91497554 91497677 8.710000e-17 99
15 TraesCS4A01G325200 chr5A 98.211 615 11 0 3195 3809 676328293 676328907 0.000000e+00 1075
16 TraesCS4A01G325200 chr1A 98.049 615 12 0 3195 3809 554149654 554149040 0.000000e+00 1070
17 TraesCS4A01G325200 chr1A 96.708 638 18 3 3174 3809 554796326 554795690 0.000000e+00 1059
18 TraesCS4A01G325200 chr7D 78.088 680 121 21 2 661 424112003 424112674 4.580000e-109 405
19 TraesCS4A01G325200 chr7D 72.568 514 94 30 1764 2243 89936919 89937419 1.440000e-24 124
20 TraesCS4A01G325200 chr3B 82.816 419 68 4 2 417 49871441 49871858 4.650000e-99 372
21 TraesCS4A01G325200 chr3B 82.432 148 23 2 1213 1360 812610428 812610572 3.990000e-25 126
22 TraesCS4A01G325200 chr5D 80.153 393 76 2 3 394 169969996 169969605 3.720000e-75 292
23 TraesCS4A01G325200 chr5D 84.733 131 17 2 1743 1870 557283901 557283771 1.110000e-25 128
24 TraesCS4A01G325200 chr5D 83.969 131 18 3 1743 1870 564748468 564748338 5.170000e-24 122
25 TraesCS4A01G325200 chr3A 80.628 382 70 4 4 382 26024981 26024601 3.720000e-75 292
26 TraesCS4A01G325200 chr3A 85.600 125 16 2 1743 1866 744098329 744098206 3.090000e-26 130
27 TraesCS4A01G325200 chr3D 82.675 329 52 2 2 330 94477960 94478283 1.730000e-73 287
28 TraesCS4A01G325200 chr6B 79.384 422 74 9 1 417 705376394 705376807 6.230000e-73 285


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 TraesCS4A01G325200 chr4A 612530673 612534481 3808 False 7035.0 7035 100.00000 1 3809 1 chr4A.!!$F1 3808
1 TraesCS4A01G325200 chr5B 693684837 693689206 4369 False 944.5 1327 90.14175 143 3196 4 chr5B.!!$F3 3053
2 TraesCS4A01G325200 chr5B 34906749 34907419 670 False 409.0 409 78.17100 2 661 1 chr5B.!!$F1 659
3 TraesCS4A01G325200 chr2A 737334697 737335309 612 True 1077.0 1077 98.36900 3197 3809 1 chr2A.!!$R1 612
4 TraesCS4A01G325200 chr2A 66876292 66876906 614 False 1070.0 1070 98.05200 3194 3809 1 chr2A.!!$F1 615
5 TraesCS4A01G325200 chr7A 731166879 731167499 620 False 1075.0 1075 97.90700 3189 3809 1 chr7A.!!$F5 620
6 TraesCS4A01G325200 chr7A 671344907 671345519 612 True 1072.0 1072 98.20600 3197 3809 1 chr7A.!!$R1 612
7 TraesCS4A01G325200 chr7A 696257875 696258499 624 False 1072.0 1072 97.60000 3185 3809 1 chr7A.!!$F3 624
8 TraesCS4A01G325200 chr7A 731106624 731107244 620 False 1064.0 1064 97.58500 3189 3809 1 chr7A.!!$F4 620
9 TraesCS4A01G325200 chr5A 676328293 676328907 614 False 1075.0 1075 98.21100 3195 3809 1 chr5A.!!$F1 614
10 TraesCS4A01G325200 chr1A 554149040 554149654 614 True 1070.0 1070 98.04900 3195 3809 1 chr1A.!!$R1 614
11 TraesCS4A01G325200 chr1A 554795690 554796326 636 True 1059.0 1059 96.70800 3174 3809 1 chr1A.!!$R2 635
12 TraesCS4A01G325200 chr7D 424112003 424112674 671 False 405.0 405 78.08800 2 661 1 chr7D.!!$F2 659

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
932 1020 0.032678 CTAGGCATCCGTGGTGCTAG 59.967 60.0 8.69 5.59 42.16 3.42 F
938 1026 0.035439 ATCCGTGGTGCTAGTTTGGG 60.035 55.0 0.00 0.00 0.00 4.12 F
941 1029 0.036765 CGTGGTGCTAGTTTGGGCTA 60.037 55.0 0.00 0.00 0.00 3.93 F
1654 3131 0.176219 TTACTTGACGGCCCGGTATG 59.824 55.0 8.57 0.47 0.00 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1759 3239 0.037447 GAAACAAGAGCAGGAGCCCT 59.963 55.0 0.0 0.0 43.56 5.19 R
2527 4016 0.108585 TTGCCAGACTTCTCCACACC 59.891 55.0 0.0 0.0 0.00 4.16 R
2529 4018 1.131638 AGTTGCCAGACTTCTCCACA 58.868 50.0 0.0 0.0 0.00 4.17 R
3651 5156 0.616111 ATGGAGCTTGGAGGTCGAGT 60.616 55.0 0.0 0.0 43.29 4.18 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
22 23 3.239861 TGCACGTTATCCATGCACA 57.760 47.368 0.00 0.00 44.17 4.57
27 28 3.064682 GCACGTTATCCATGCACACAATA 59.935 43.478 0.00 0.00 39.23 1.90
34 35 7.042119 CGTTATCCATGCACACAATATGAAGTA 60.042 37.037 0.00 0.00 0.00 2.24
45 46 8.668353 CACACAATATGAAGTAGCTAACACATT 58.332 33.333 0.00 0.00 32.43 2.71
72 73 2.942710 ACACCATCTACAACTTCGTCG 58.057 47.619 0.00 0.00 0.00 5.12
88 89 1.193874 CGTCGTGAAGTTTTAGGGTGC 59.806 52.381 0.00 0.00 0.00 5.01
119 120 2.375174 AGTGAAGACAAGGTGGCCATTA 59.625 45.455 9.72 0.00 0.00 1.90
180 181 9.787435 TCTGTTACTCTACATGTTGGTTAATTT 57.213 29.630 2.30 0.00 0.00 1.82
221 222 9.899661 ATGTTCTTGTACATGTTTTATAGCCTA 57.100 29.630 2.30 0.00 37.36 3.93
247 248 4.321230 CGTGCTGCCATGATATACTACAGA 60.321 45.833 0.00 0.00 0.00 3.41
290 291 3.696051 GCACATACATTGTTGGATGGAGT 59.304 43.478 0.00 0.00 46.88 3.85
300 302 0.629058 TGGATGGAGTTTAAGGGGCC 59.371 55.000 0.00 0.00 0.00 5.80
322 324 3.689161 CGTTTGTGTGGGATGATATGTGT 59.311 43.478 0.00 0.00 0.00 3.72
323 325 4.155826 CGTTTGTGTGGGATGATATGTGTT 59.844 41.667 0.00 0.00 0.00 3.32
334 336 4.032960 TGATATGTGTTGGTTCTGGCTT 57.967 40.909 0.00 0.00 0.00 4.35
342 344 5.001232 GTGTTGGTTCTGGCTTTAGTATCA 58.999 41.667 0.00 0.00 0.00 2.15
387 390 2.959507 AAACTTGTTGAACACAGGGC 57.040 45.000 0.00 0.00 36.78 5.19
403 406 5.191722 ACACAGGGCTATCTCCTTGAATTTA 59.808 40.000 0.00 0.00 36.77 1.40
404 407 5.762218 CACAGGGCTATCTCCTTGAATTTAG 59.238 44.000 0.00 0.00 36.77 1.85
428 476 8.902540 AGACTATTGTTGTATTGAGTGTTTCA 57.097 30.769 0.00 0.00 0.00 2.69
432 480 4.203226 TGTTGTATTGAGTGTTTCAGGCA 58.797 39.130 0.00 0.00 37.07 4.75
446 494 6.640907 GTGTTTCAGGCATGGTTTAGTTAAAG 59.359 38.462 0.00 0.00 0.00 1.85
448 496 5.249780 TCAGGCATGGTTTAGTTAAAGGA 57.750 39.130 0.00 0.00 0.00 3.36
461 509 5.587033 AGTTAAAGGAACGAAACATCGTC 57.413 39.130 4.19 0.00 46.41 4.20
462 510 4.450080 AGTTAAAGGAACGAAACATCGTCC 59.550 41.667 4.19 7.78 46.41 4.79
463 511 1.425412 AAGGAACGAAACATCGTCCG 58.575 50.000 4.19 0.00 46.41 4.79
476 524 7.479291 CGAAACATCGTCCGTTTTATGTAAATT 59.521 33.333 0.00 0.00 36.72 1.82
477 525 9.757859 GAAACATCGTCCGTTTTATGTAAATTA 57.242 29.630 0.00 0.00 36.72 1.40
527 576 3.403968 TGTTTGATGAAATTCGTCCGGA 58.596 40.909 12.18 0.00 31.51 5.14
534 583 2.486203 TGAAATTCGTCCGGATTGTTGG 59.514 45.455 7.81 0.00 0.00 3.77
559 608 3.692101 TCCGTTTTGAAATGTATGCGGAT 59.308 39.130 0.00 0.00 41.49 4.18
627 676 1.145156 CGGCCCACGGATGAATACA 59.855 57.895 0.00 0.00 39.42 2.29
669 730 3.486542 GCATTGAAGAAGCCTAAGCGAAG 60.487 47.826 0.00 0.00 46.67 3.79
703 764 0.037605 AGGTCGGCAAGTCGGTTTAG 60.038 55.000 0.00 0.00 0.00 1.85
779 841 4.435784 CGTCAGCCTATGCGTACTATAGTC 60.436 50.000 9.12 0.62 44.33 2.59
787 849 4.214980 TGCGTACTATAGTCGGTTTAGC 57.785 45.455 9.12 6.44 0.00 3.09
803 865 4.275196 GGTTTAGCTTCCTATTTAAGGGCG 59.725 45.833 0.00 0.00 46.55 6.13
852 926 3.832490 TCAGCTAGCTTCAGTACAAGGAA 59.168 43.478 16.46 0.00 0.00 3.36
858 932 6.183360 GCTAGCTTCAGTACAAGGAAAGAATG 60.183 42.308 7.70 0.00 0.00 2.67
870 944 5.972327 AGGAAAGAATGGATCAGTCTCAT 57.028 39.130 0.00 0.00 37.84 2.90
871 945 5.682659 AGGAAAGAATGGATCAGTCTCATG 58.317 41.667 0.00 0.00 37.84 3.07
873 947 6.385176 AGGAAAGAATGGATCAGTCTCATGTA 59.615 38.462 0.00 0.00 37.84 2.29
874 948 6.705381 GGAAAGAATGGATCAGTCTCATGTAG 59.295 42.308 0.00 0.00 37.84 2.74
875 949 6.805016 AAGAATGGATCAGTCTCATGTAGT 57.195 37.500 0.00 0.00 37.84 2.73
899 987 6.963083 ACTAGTACTCCAGTTCATATGTCC 57.037 41.667 0.00 0.00 0.00 4.02
903 991 4.000928 ACTCCAGTTCATATGTCCTCCT 57.999 45.455 1.90 0.00 0.00 3.69
905 993 2.959030 TCCAGTTCATATGTCCTCCTCG 59.041 50.000 1.90 0.00 0.00 4.63
906 994 2.695666 CCAGTTCATATGTCCTCCTCGT 59.304 50.000 1.90 0.00 0.00 4.18
907 995 3.243569 CCAGTTCATATGTCCTCCTCGTC 60.244 52.174 1.90 0.00 0.00 4.20
909 997 3.634448 AGTTCATATGTCCTCCTCGTCTG 59.366 47.826 1.90 0.00 0.00 3.51
911 999 3.632333 TCATATGTCCTCCTCGTCTGTT 58.368 45.455 1.90 0.00 0.00 3.16
912 1000 3.632604 TCATATGTCCTCCTCGTCTGTTC 59.367 47.826 1.90 0.00 0.00 3.18
913 1001 1.187087 ATGTCCTCCTCGTCTGTTCC 58.813 55.000 0.00 0.00 0.00 3.62
914 1002 0.112606 TGTCCTCCTCGTCTGTTCCT 59.887 55.000 0.00 0.00 0.00 3.36
915 1003 1.353358 TGTCCTCCTCGTCTGTTCCTA 59.647 52.381 0.00 0.00 0.00 2.94
916 1004 2.018515 GTCCTCCTCGTCTGTTCCTAG 58.981 57.143 0.00 0.00 0.00 3.02
917 1005 1.064611 TCCTCCTCGTCTGTTCCTAGG 60.065 57.143 0.82 0.82 0.00 3.02
918 1006 0.741915 CTCCTCGTCTGTTCCTAGGC 59.258 60.000 2.96 0.00 0.00 3.93
919 1007 0.039180 TCCTCGTCTGTTCCTAGGCA 59.961 55.000 2.96 0.00 0.00 4.75
920 1008 1.115467 CCTCGTCTGTTCCTAGGCAT 58.885 55.000 2.96 0.00 0.00 4.40
921 1009 1.067821 CCTCGTCTGTTCCTAGGCATC 59.932 57.143 2.96 0.00 0.00 3.91
922 1010 1.067821 CTCGTCTGTTCCTAGGCATCC 59.932 57.143 2.96 0.00 0.00 3.51
923 1011 0.249073 CGTCTGTTCCTAGGCATCCG 60.249 60.000 2.96 0.00 0.00 4.18
924 1012 0.824759 GTCTGTTCCTAGGCATCCGT 59.175 55.000 2.96 0.00 0.00 4.69
925 1013 0.824109 TCTGTTCCTAGGCATCCGTG 59.176 55.000 2.96 0.00 0.00 4.94
926 1014 0.179073 CTGTTCCTAGGCATCCGTGG 60.179 60.000 2.96 0.00 0.00 4.94
927 1015 0.907704 TGTTCCTAGGCATCCGTGGT 60.908 55.000 2.96 0.00 0.00 4.16
928 1016 0.462047 GTTCCTAGGCATCCGTGGTG 60.462 60.000 2.96 0.00 0.00 4.17
929 1017 2.203070 CCTAGGCATCCGTGGTGC 60.203 66.667 0.00 0.98 41.78 5.01
930 1018 2.735772 CCTAGGCATCCGTGGTGCT 61.736 63.158 0.00 0.00 42.16 4.40
931 1019 1.399744 CCTAGGCATCCGTGGTGCTA 61.400 60.000 0.00 0.70 42.16 3.49
932 1020 0.032678 CTAGGCATCCGTGGTGCTAG 59.967 60.000 8.69 5.59 42.16 3.42
933 1021 0.686441 TAGGCATCCGTGGTGCTAGT 60.686 55.000 8.69 0.00 42.16 2.57
934 1022 1.078426 GGCATCCGTGGTGCTAGTT 60.078 57.895 8.69 0.00 42.16 2.24
935 1023 0.676782 GGCATCCGTGGTGCTAGTTT 60.677 55.000 8.69 0.00 42.16 2.66
936 1024 0.447801 GCATCCGTGGTGCTAGTTTG 59.552 55.000 2.33 0.00 39.45 2.93
937 1025 1.086696 CATCCGTGGTGCTAGTTTGG 58.913 55.000 0.00 0.00 0.00 3.28
938 1026 0.035439 ATCCGTGGTGCTAGTTTGGG 60.035 55.000 0.00 0.00 0.00 4.12
939 1027 2.332654 CCGTGGTGCTAGTTTGGGC 61.333 63.158 0.00 0.00 0.00 5.36
940 1028 1.302511 CGTGGTGCTAGTTTGGGCT 60.303 57.895 0.00 0.00 0.00 5.19
941 1029 0.036765 CGTGGTGCTAGTTTGGGCTA 60.037 55.000 0.00 0.00 0.00 3.93
942 1030 1.609580 CGTGGTGCTAGTTTGGGCTAA 60.610 52.381 0.00 0.00 0.00 3.09
943 1031 1.810755 GTGGTGCTAGTTTGGGCTAAC 59.189 52.381 0.00 0.00 0.00 2.34
944 1032 1.422024 TGGTGCTAGTTTGGGCTAACA 59.578 47.619 5.97 0.00 0.00 2.41
945 1033 2.158593 TGGTGCTAGTTTGGGCTAACAA 60.159 45.455 5.97 0.00 0.00 2.83
946 1034 3.089284 GGTGCTAGTTTGGGCTAACAAT 58.911 45.455 5.97 0.00 0.00 2.71
947 1035 4.263550 TGGTGCTAGTTTGGGCTAACAATA 60.264 41.667 5.97 0.00 0.00 1.90
948 1036 4.703093 GGTGCTAGTTTGGGCTAACAATAA 59.297 41.667 5.97 0.00 0.00 1.40
949 1037 5.392703 GGTGCTAGTTTGGGCTAACAATAAC 60.393 44.000 5.97 0.00 0.00 1.89
950 1038 4.703093 TGCTAGTTTGGGCTAACAATAACC 59.297 41.667 5.97 0.00 0.00 2.85
951 1039 4.201881 GCTAGTTTGGGCTAACAATAACCG 60.202 45.833 5.97 0.00 0.00 4.44
952 1040 3.758425 AGTTTGGGCTAACAATAACCGT 58.242 40.909 5.97 0.00 0.00 4.83
953 1041 3.754850 AGTTTGGGCTAACAATAACCGTC 59.245 43.478 5.97 0.00 0.00 4.79
954 1042 3.706600 TTGGGCTAACAATAACCGTCT 57.293 42.857 0.00 0.00 0.00 4.18
955 1043 3.255969 TGGGCTAACAATAACCGTCTC 57.744 47.619 0.00 0.00 0.00 3.36
956 1044 2.199236 GGGCTAACAATAACCGTCTCG 58.801 52.381 0.00 0.00 0.00 4.04
957 1045 2.417787 GGGCTAACAATAACCGTCTCGT 60.418 50.000 0.00 0.00 0.00 4.18
958 1046 2.856557 GGCTAACAATAACCGTCTCGTC 59.143 50.000 0.00 0.00 0.00 4.20
959 1047 3.428589 GGCTAACAATAACCGTCTCGTCT 60.429 47.826 0.00 0.00 0.00 4.18
960 1048 4.201950 GGCTAACAATAACCGTCTCGTCTA 60.202 45.833 0.00 0.00 0.00 2.59
984 1072 0.692476 ACCACTACTGCAGCAATCCA 59.308 50.000 15.27 0.00 0.00 3.41
994 1082 1.133790 GCAGCAATCCATCCAGAACAC 59.866 52.381 0.00 0.00 0.00 3.32
1046 1135 2.202676 CTCCGACGAGCAAGAGCC 60.203 66.667 0.00 0.00 43.56 4.70
1047 1136 4.116328 TCCGACGAGCAAGAGCCG 62.116 66.667 0.00 0.00 43.56 5.52
1053 1142 2.433318 GAGCAAGAGCCGAAGCGT 60.433 61.111 0.00 0.00 46.67 5.07
1093 1182 4.424566 GCCGCAATGGTGGTGCAG 62.425 66.667 0.60 0.00 46.76 4.41
1094 1183 3.751246 CCGCAATGGTGGTGCAGG 61.751 66.667 0.00 0.00 42.33 4.85
1095 1184 2.985282 CGCAATGGTGGTGCAGGT 60.985 61.111 0.00 0.00 42.33 4.00
1349 1447 1.588932 CGTCCATCCACATCGACCG 60.589 63.158 0.00 0.00 0.00 4.79
1394 1495 0.320247 CTGCAGAGCTTCACCGACTT 60.320 55.000 8.42 0.00 0.00 3.01
1428 1529 2.489329 CCATAACAACCTTGTGCTCCTG 59.511 50.000 0.00 0.00 41.31 3.86
1470 1571 1.133637 AGCTCTCAAGATCTCCGCCTA 60.134 52.381 0.00 0.00 0.00 3.93
1502 1603 2.126228 GGTCCGTCGCGTCATCAA 60.126 61.111 5.77 0.00 0.00 2.57
1522 1623 1.139058 ACCAAGATGATACACCGCCTC 59.861 52.381 0.00 0.00 0.00 4.70
1565 1666 2.260869 GCAACGTGCACCTGGACAT 61.261 57.895 12.15 0.00 44.26 3.06
1602 3079 3.626924 AGTGACGACAGGTGCCCC 61.627 66.667 0.00 0.00 0.00 5.80
1603 3080 3.626924 GTGACGACAGGTGCCCCT 61.627 66.667 0.00 0.00 44.02 4.79
1641 3118 4.552767 CGACTGGAAAACTGCAGTTACTTG 60.553 45.833 31.31 20.99 37.25 3.16
1644 3121 3.311322 TGGAAAACTGCAGTTACTTGACG 59.689 43.478 31.31 0.00 37.25 4.35
1645 3122 3.303791 GGAAAACTGCAGTTACTTGACGG 60.304 47.826 31.31 0.00 37.25 4.79
1654 3131 0.176219 TTACTTGACGGCCCGGTATG 59.824 55.000 8.57 0.47 0.00 2.39
1780 3260 1.447945 GGCTCCTGCTCTTGTTTCTC 58.552 55.000 0.00 0.00 39.59 2.87
1837 3317 4.924305 ATCAATGAACCACATACCATGC 57.076 40.909 0.00 0.00 38.38 4.06
1838 3318 3.023119 TCAATGAACCACATACCATGCC 58.977 45.455 0.00 0.00 38.38 4.40
1839 3319 1.679139 ATGAACCACATACCATGCCG 58.321 50.000 0.00 0.00 37.46 5.69
1847 3327 1.555075 ACATACCATGCCGTCTCTTGT 59.445 47.619 0.00 0.00 0.00 3.16
1848 3328 2.205074 CATACCATGCCGTCTCTTGTC 58.795 52.381 0.00 0.00 0.00 3.18
1870 3350 2.885644 CGTCGGTTCATCTGCCCG 60.886 66.667 0.00 0.00 43.03 6.13
1893 3373 0.598562 TGACTGACGAGGAGCTCAAC 59.401 55.000 17.19 7.67 0.00 3.18
1894 3374 0.598562 GACTGACGAGGAGCTCAACA 59.401 55.000 17.19 6.70 0.00 3.33
1896 3376 1.269831 ACTGACGAGGAGCTCAACAAC 60.270 52.381 17.19 4.37 0.00 3.32
1922 3402 2.456594 GAAAACGATGCCACTGCGCA 62.457 55.000 10.98 10.98 44.35 6.09
1971 3451 1.597663 GTGACAACTTTGACCCTGTCG 59.402 52.381 0.00 0.00 40.87 4.35
1976 3456 1.238439 ACTTTGACCCTGTCGCATTG 58.762 50.000 0.00 0.00 34.95 2.82
2047 3531 9.413048 CCTTTATCTAGAGCTATTTAAAGACCG 57.587 37.037 17.23 3.70 31.47 4.79
2063 3547 4.941609 CGGGAACTGGATGTCTGG 57.058 61.111 0.00 0.00 0.00 3.86
2081 3565 2.426738 CTGGTTTTCAGTTGCTGTTCCA 59.573 45.455 0.00 0.00 38.64 3.53
2087 3571 1.211703 TCAGTTGCTGTTCCAACCTGA 59.788 47.619 1.78 0.00 44.71 3.86
2111 3595 3.845781 TTCTGTGGAACTTCAGCTTCT 57.154 42.857 0.00 0.00 38.04 2.85
2127 3611 5.483937 TCAGCTTCTTGTATTCCAGAACCTA 59.516 40.000 0.00 0.00 0.00 3.08
2166 3650 2.159841 CGAGTGTTACATTGTTGGCGAG 60.160 50.000 0.00 0.00 0.00 5.03
2181 3665 2.266055 GAGGACTTCGTGGGGCTG 59.734 66.667 0.00 0.00 0.00 4.85
2196 3680 2.475666 GCTGAAGCCTTACCTGCAG 58.524 57.895 6.78 6.78 40.80 4.41
2222 3706 2.503356 CACCTAACCTGGAGAAGCTCAT 59.497 50.000 0.00 0.00 31.08 2.90
2273 3757 7.044181 GGGTACTCTTTGGTTGGTATACTAAC 58.956 42.308 20.53 20.53 36.72 2.34
2338 3824 4.501229 CCACACTTTGTTTGGCATACATGT 60.501 41.667 11.54 10.19 0.00 3.21
2339 3825 5.278709 CCACACTTTGTTTGGCATACATGTA 60.279 40.000 11.54 8.27 0.00 2.29
2340 3826 5.629020 CACACTTTGTTTGGCATACATGTAC 59.371 40.000 7.96 0.00 0.00 2.90
2341 3827 5.300539 ACACTTTGTTTGGCATACATGTACA 59.699 36.000 7.96 0.00 0.00 2.90
2342 3828 6.015519 ACACTTTGTTTGGCATACATGTACAT 60.016 34.615 7.96 1.41 0.00 2.29
2343 3829 6.308524 CACTTTGTTTGGCATACATGTACATG 59.691 38.462 29.97 29.97 44.15 3.21
2367 3853 8.180706 TGTTTAAAGGTTAAGTTATCAACCCC 57.819 34.615 2.93 0.00 44.44 4.95
2368 3854 7.040548 TGTTTAAAGGTTAAGTTATCAACCCCG 60.041 37.037 2.93 0.00 44.44 5.73
2369 3855 2.995283 AGGTTAAGTTATCAACCCCGC 58.005 47.619 2.93 0.00 44.44 6.13
2403 3892 9.785982 AGAGGTTAAGCTATCAAAATAGATTCC 57.214 33.333 7.26 0.00 41.84 3.01
2410 3899 8.814038 AGCTATCAAAATAGATTCCACACTTT 57.186 30.769 0.00 0.00 37.63 2.66
2414 3903 5.538053 TCAAAATAGATTCCACACTTTGCCA 59.462 36.000 0.00 0.00 0.00 4.92
2429 3918 2.601240 TGCCACATTTGGGAGAATCA 57.399 45.000 0.00 0.00 44.15 2.57
2431 3920 4.248174 TGCCACATTTGGGAGAATCATA 57.752 40.909 0.00 0.00 44.15 2.15
2438 3927 4.927267 TTTGGGAGAATCATACCACACT 57.073 40.909 0.00 0.00 36.25 3.55
2442 3931 5.253330 TGGGAGAATCATACCACACTTTTC 58.747 41.667 0.00 0.00 36.25 2.29
2481 3970 4.229876 GAGAAAACAATGTTGCTACCAGC 58.770 43.478 0.00 0.00 42.82 4.85
2499 3988 0.593128 GCAGTGTGGCTGTAAACCAG 59.407 55.000 0.00 0.00 46.64 4.00
2508 3997 3.879932 GCTGTAAACCAGACAAGTGAC 57.120 47.619 0.00 0.00 44.49 3.67
2509 3998 3.202906 GCTGTAAACCAGACAAGTGACA 58.797 45.455 0.00 0.00 44.49 3.58
2510 3999 3.625764 GCTGTAAACCAGACAAGTGACAA 59.374 43.478 0.00 0.00 44.49 3.18
2511 4000 4.095782 GCTGTAAACCAGACAAGTGACAAA 59.904 41.667 0.00 0.00 44.49 2.83
2512 4001 5.554822 TGTAAACCAGACAAGTGACAAAC 57.445 39.130 0.00 0.00 0.00 2.93
2513 4002 4.396790 TGTAAACCAGACAAGTGACAAACC 59.603 41.667 0.00 0.00 0.00 3.27
2514 4003 2.052782 ACCAGACAAGTGACAAACCC 57.947 50.000 0.00 0.00 0.00 4.11
2515 4004 0.944386 CCAGACAAGTGACAAACCCG 59.056 55.000 0.00 0.00 0.00 5.28
2516 4005 1.663695 CAGACAAGTGACAAACCCGT 58.336 50.000 0.00 0.00 0.00 5.28
2517 4006 2.014128 CAGACAAGTGACAAACCCGTT 58.986 47.619 0.00 0.00 0.00 4.44
2518 4007 3.199677 CAGACAAGTGACAAACCCGTTA 58.800 45.455 0.00 0.00 0.00 3.18
2519 4008 3.623960 CAGACAAGTGACAAACCCGTTAA 59.376 43.478 0.00 0.00 0.00 2.01
2520 4009 4.095185 CAGACAAGTGACAAACCCGTTAAA 59.905 41.667 0.00 0.00 0.00 1.52
2521 4010 4.701171 AGACAAGTGACAAACCCGTTAAAA 59.299 37.500 0.00 0.00 0.00 1.52
2522 4011 5.358725 AGACAAGTGACAAACCCGTTAAAAT 59.641 36.000 0.00 0.00 0.00 1.82
2523 4012 5.968254 ACAAGTGACAAACCCGTTAAAATT 58.032 33.333 0.00 0.00 0.00 1.82
2524 4013 6.399743 ACAAGTGACAAACCCGTTAAAATTT 58.600 32.000 0.00 0.00 0.00 1.82
2525 4014 6.311690 ACAAGTGACAAACCCGTTAAAATTTG 59.688 34.615 0.00 0.00 37.91 2.32
2526 4015 5.968254 AGTGACAAACCCGTTAAAATTTGT 58.032 33.333 1.07 1.07 45.47 2.83
2527 4016 5.808030 AGTGACAAACCCGTTAAAATTTGTG 59.192 36.000 5.97 0.00 43.46 3.33
2528 4017 5.005875 GTGACAAACCCGTTAAAATTTGTGG 59.994 40.000 5.97 0.00 43.46 4.17
2529 4018 5.087391 ACAAACCCGTTAAAATTTGTGGT 57.913 34.783 0.67 0.00 42.22 4.16
2530 4019 4.870991 ACAAACCCGTTAAAATTTGTGGTG 59.129 37.500 0.67 0.00 42.22 4.17
2531 4020 4.739587 AACCCGTTAAAATTTGTGGTGT 57.260 36.364 0.00 0.00 0.00 4.16
2532 4021 4.048241 ACCCGTTAAAATTTGTGGTGTG 57.952 40.909 0.00 0.00 0.00 3.82
2533 4022 3.181474 ACCCGTTAAAATTTGTGGTGTGG 60.181 43.478 0.00 0.00 0.00 4.17
2534 4023 3.068307 CCCGTTAAAATTTGTGGTGTGGA 59.932 43.478 0.00 0.00 0.00 4.02
2535 4024 4.295051 CCGTTAAAATTTGTGGTGTGGAG 58.705 43.478 0.00 0.00 0.00 3.86
2536 4025 4.036971 CCGTTAAAATTTGTGGTGTGGAGA 59.963 41.667 0.00 0.00 0.00 3.71
2537 4026 5.450688 CCGTTAAAATTTGTGGTGTGGAGAA 60.451 40.000 0.00 0.00 0.00 2.87
2538 4027 5.685511 CGTTAAAATTTGTGGTGTGGAGAAG 59.314 40.000 0.00 0.00 0.00 2.85
2539 4028 6.569780 GTTAAAATTTGTGGTGTGGAGAAGT 58.430 36.000 0.00 0.00 0.00 3.01
2540 4029 4.918810 AAATTTGTGGTGTGGAGAAGTC 57.081 40.909 0.00 0.00 0.00 3.01
2541 4030 3.864789 ATTTGTGGTGTGGAGAAGTCT 57.135 42.857 0.00 0.00 0.00 3.24
2542 4031 2.620251 TTGTGGTGTGGAGAAGTCTG 57.380 50.000 0.00 0.00 0.00 3.51
2543 4032 0.758734 TGTGGTGTGGAGAAGTCTGG 59.241 55.000 0.00 0.00 0.00 3.86
2544 4033 0.603975 GTGGTGTGGAGAAGTCTGGC 60.604 60.000 0.00 0.00 0.00 4.85
2545 4034 1.053835 TGGTGTGGAGAAGTCTGGCA 61.054 55.000 0.00 0.00 0.00 4.92
2546 4035 0.108585 GGTGTGGAGAAGTCTGGCAA 59.891 55.000 0.00 0.00 0.00 4.52
2547 4036 1.230324 GTGTGGAGAAGTCTGGCAAC 58.770 55.000 0.00 0.00 0.00 4.17
2548 4037 1.131638 TGTGGAGAAGTCTGGCAACT 58.868 50.000 0.00 0.00 37.61 3.16
2549 4038 1.490490 TGTGGAGAAGTCTGGCAACTT 59.510 47.619 12.69 12.69 42.10 2.66
2550 4039 2.092429 TGTGGAGAAGTCTGGCAACTTT 60.092 45.455 13.62 6.69 39.55 2.66
2551 4040 3.135712 TGTGGAGAAGTCTGGCAACTTTA 59.864 43.478 13.62 2.99 39.55 1.85
2552 4041 3.748568 GTGGAGAAGTCTGGCAACTTTAG 59.251 47.826 13.62 0.00 39.55 1.85
2553 4042 3.391296 TGGAGAAGTCTGGCAACTTTAGT 59.609 43.478 13.62 5.27 39.55 2.24
2554 4043 4.591498 TGGAGAAGTCTGGCAACTTTAGTA 59.409 41.667 13.62 3.24 39.55 1.82
2555 4044 5.248477 TGGAGAAGTCTGGCAACTTTAGTAT 59.752 40.000 13.62 2.73 39.55 2.12
2556 4045 6.439375 TGGAGAAGTCTGGCAACTTTAGTATA 59.561 38.462 13.62 1.52 39.55 1.47
2557 4046 6.757478 GGAGAAGTCTGGCAACTTTAGTATAC 59.243 42.308 13.62 0.00 39.55 1.47
2558 4047 6.641474 AGAAGTCTGGCAACTTTAGTATACC 58.359 40.000 13.62 2.80 39.55 2.73
2559 4048 6.212791 AGAAGTCTGGCAACTTTAGTATACCA 59.787 38.462 13.62 0.00 39.55 3.25
2652 4143 4.515191 TGCTGTCAACAGAACTGGTATTTC 59.485 41.667 14.20 0.00 46.59 2.17
2682 4176 1.399440 CTGGTGGATTTCATGTGCGAG 59.601 52.381 0.00 0.00 0.00 5.03
2690 4184 4.576463 GGATTTCATGTGCGAGAACCTTAT 59.424 41.667 0.00 0.00 0.00 1.73
2698 4192 3.552294 GTGCGAGAACCTTATGCTTACTC 59.448 47.826 0.00 0.00 0.00 2.59
2778 4272 0.889186 TTTCAAGGAGCCTGCCGAAC 60.889 55.000 0.00 0.00 0.00 3.95
2813 4307 5.797909 CTCATTAGAGTCGAATAGCAACG 57.202 43.478 0.00 0.00 37.11 4.10
2849 4343 9.378551 TGTATCATGTTTGCCTTTTACTAGTAG 57.621 33.333 2.23 0.00 0.00 2.57
2857 4351 4.464951 TGCCTTTTACTAGTAGCTAGCACA 59.535 41.667 18.83 0.42 37.57 4.57
2909 4403 5.590530 TTTTGACCCATATTGGCATGTAC 57.409 39.130 0.00 0.00 35.79 2.90
2931 4425 8.784994 TGTACGTATTGTTGTGGTATTTTGATT 58.215 29.630 0.00 0.00 0.00 2.57
2939 4433 8.190888 TGTTGTGGTATTTTGATTTTCAACAC 57.809 30.769 0.00 0.00 35.89 3.32
2940 4434 7.819415 TGTTGTGGTATTTTGATTTTCAACACA 59.181 29.630 0.00 6.55 36.92 3.72
3020 4523 4.222810 TGTCTGCACATAGTACCAGATTGT 59.777 41.667 1.39 0.00 36.78 2.71
3048 4551 8.268850 AGCTAAATGAAAGTTTACATCGTGAT 57.731 30.769 0.00 0.00 0.00 3.06
3049 4552 8.730680 AGCTAAATGAAAGTTTACATCGTGATT 58.269 29.630 0.00 0.00 0.00 2.57
3058 4561 7.539712 AGTTTACATCGTGATTAATGGTCAG 57.460 36.000 0.00 0.00 0.00 3.51
3064 4567 4.647611 TCGTGATTAATGGTCAGTGGTTT 58.352 39.130 0.00 0.00 0.00 3.27
3143 4648 3.530265 AGTCAGTTGGTCGTTTACACA 57.470 42.857 0.00 0.00 0.00 3.72
3144 4649 3.192466 AGTCAGTTGGTCGTTTACACAC 58.808 45.455 0.00 0.00 0.00 3.82
3148 4653 2.100584 AGTTGGTCGTTTACACACGGTA 59.899 45.455 0.00 0.00 40.74 4.02
3151 4656 3.726607 TGGTCGTTTACACACGGTATTT 58.273 40.909 0.00 0.00 40.74 1.40
3163 4668 5.053811 CACACGGTATTTGATAGGTATGCA 58.946 41.667 0.00 0.00 0.00 3.96
3203 4708 6.801862 GCCAACTTTATAAACAAGCACTAGTG 59.198 38.462 18.93 18.93 0.00 2.74
3347 4852 0.838554 TGGTCCCGGTTCATCTGGAA 60.839 55.000 0.00 0.00 45.09 3.53
3616 5121 2.813754 CACAAGGTGTTCGATGGAATGT 59.186 45.455 0.00 0.00 34.05 2.71
3651 5156 5.568620 ACTTAAGCTTTCTCCTCTCCAAA 57.431 39.130 3.20 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 7.829211 ACCAATGTGTTAGCTACTTCATATTGT 59.171 33.333 23.67 16.27 37.55 2.71
27 28 4.943705 CCACCAATGTGTTAGCTACTTCAT 59.056 41.667 0.00 0.00 41.09 2.57
34 35 3.408634 GTGTACCACCAATGTGTTAGCT 58.591 45.455 0.00 0.00 41.09 3.32
72 73 3.500680 TGAATCGCACCCTAAAACTTCAC 59.499 43.478 0.00 0.00 0.00 3.18
119 120 1.067295 TCTCCATGGTTGACAAGCCT 58.933 50.000 12.58 2.06 0.00 4.58
124 125 3.513912 ACTTACGATCTCCATGGTTGACA 59.486 43.478 12.58 0.00 0.00 3.58
200 201 7.277098 ACGTGTAGGCTATAAAACATGTACAAG 59.723 37.037 9.82 0.00 39.61 3.16
221 222 2.103094 AGTATATCATGGCAGCACGTGT 59.897 45.455 18.38 0.68 0.00 4.49
247 248 3.645268 GAATGGCCTGCCCTCGGTT 62.645 63.158 3.32 0.00 34.56 4.44
290 291 1.033574 CACACAAACGGCCCCTTAAA 58.966 50.000 0.00 0.00 0.00 1.52
300 302 3.689161 ACACATATCATCCCACACAAACG 59.311 43.478 0.00 0.00 0.00 3.60
322 324 6.480763 TCAATGATACTAAAGCCAGAACCAA 58.519 36.000 0.00 0.00 0.00 3.67
323 325 6.061022 TCAATGATACTAAAGCCAGAACCA 57.939 37.500 0.00 0.00 0.00 3.67
365 367 4.464597 AGCCCTGTGTTCAACAAGTTTTTA 59.535 37.500 0.00 0.00 38.67 1.52
382 385 5.994668 GTCTAAATTCAAGGAGATAGCCCTG 59.005 44.000 0.00 0.00 33.55 4.45
383 386 5.908247 AGTCTAAATTCAAGGAGATAGCCCT 59.092 40.000 0.00 0.00 35.03 5.19
384 387 6.181206 AGTCTAAATTCAAGGAGATAGCCC 57.819 41.667 0.00 0.00 0.00 5.19
403 406 8.902540 TGAAACACTCAATACAACAATAGTCT 57.097 30.769 0.00 0.00 0.00 3.24
404 407 8.230486 CCTGAAACACTCAATACAACAATAGTC 58.770 37.037 0.00 0.00 32.17 2.59
428 476 4.457949 CGTTCCTTTAACTAAACCATGCCT 59.542 41.667 0.00 0.00 35.81 4.75
432 480 7.571080 TGTTTCGTTCCTTTAACTAAACCAT 57.429 32.000 12.56 0.00 45.92 3.55
483 531 7.669427 ACATGATGGAATTCAGCAAAGTTTAA 58.331 30.769 7.93 0.00 45.52 1.52
502 550 5.449041 CCGGACGAATTTCATCAAACATGAT 60.449 40.000 0.00 0.00 0.00 2.45
527 576 6.287525 ACATTTCAAAACGGATTCCAACAAT 58.712 32.000 3.09 0.00 0.00 2.71
534 583 4.499040 CCGCATACATTTCAAAACGGATTC 59.501 41.667 0.00 0.00 41.86 2.52
541 590 6.707440 ACCATATCCGCATACATTTCAAAA 57.293 33.333 0.00 0.00 0.00 2.44
559 608 1.214305 AAGCTGGGCCTCCAACCATA 61.214 55.000 4.53 0.00 43.51 2.74
627 676 2.224161 GCTGACTCTCAAACCAGACACT 60.224 50.000 0.00 0.00 0.00 3.55
669 730 1.580815 GACCTGCAGCTGCTATCTTC 58.419 55.000 36.61 21.65 42.66 2.87
714 775 1.319541 GCTGCCATCATGCTCTGAAT 58.680 50.000 0.00 0.00 37.44 2.57
715 776 0.034863 TGCTGCCATCATGCTCTGAA 60.035 50.000 0.00 0.00 37.44 3.02
716 777 0.746923 GTGCTGCCATCATGCTCTGA 60.747 55.000 0.00 0.00 38.53 3.27
717 778 0.748367 AGTGCTGCCATCATGCTCTG 60.748 55.000 0.00 0.00 0.00 3.35
718 779 0.748367 CAGTGCTGCCATCATGCTCT 60.748 55.000 0.00 0.00 0.00 4.09
719 780 0.746923 TCAGTGCTGCCATCATGCTC 60.747 55.000 0.00 0.00 0.00 4.26
720 781 0.106669 ATCAGTGCTGCCATCATGCT 60.107 50.000 0.00 0.00 0.00 3.79
721 782 0.030773 CATCAGTGCTGCCATCATGC 59.969 55.000 0.00 0.00 0.00 4.06
722 783 1.389555 ACATCAGTGCTGCCATCATG 58.610 50.000 0.00 0.00 0.00 3.07
723 784 3.211865 CTTACATCAGTGCTGCCATCAT 58.788 45.455 0.00 0.00 0.00 2.45
724 785 2.635714 CTTACATCAGTGCTGCCATCA 58.364 47.619 0.00 0.00 0.00 3.07
725 786 1.332997 GCTTACATCAGTGCTGCCATC 59.667 52.381 0.00 0.00 0.00 3.51
726 787 1.340308 TGCTTACATCAGTGCTGCCAT 60.340 47.619 0.00 0.00 0.00 4.40
727 788 0.036590 TGCTTACATCAGTGCTGCCA 59.963 50.000 0.00 0.00 0.00 4.92
728 789 1.131883 CTTGCTTACATCAGTGCTGCC 59.868 52.381 0.00 0.00 0.00 4.85
729 790 1.808945 ACTTGCTTACATCAGTGCTGC 59.191 47.619 0.00 0.00 0.00 5.25
730 791 5.808042 ATTACTTGCTTACATCAGTGCTG 57.192 39.130 0.00 0.00 0.00 4.41
803 865 1.940613 GAGGTTACAACGATGGGCATC 59.059 52.381 0.00 0.00 34.56 3.91
836 910 5.006386 CCATTCTTTCCTTGTACTGAAGCT 58.994 41.667 0.00 0.00 0.00 3.74
852 926 6.805016 ACTACATGAGACTGATCCATTCTT 57.195 37.500 0.00 0.00 0.00 2.52
858 932 8.152246 AGTACTAGTACTACATGAGACTGATCC 58.848 40.741 29.96 0.57 43.98 3.36
871 945 9.558396 ACATATGAACTGGAGTACTAGTACTAC 57.442 37.037 30.93 30.93 45.63 2.73
874 948 7.720515 AGGACATATGAACTGGAGTACTAGTAC 59.279 40.741 23.03 23.03 36.85 2.73
875 949 7.813331 AGGACATATGAACTGGAGTACTAGTA 58.187 38.462 10.38 0.00 36.85 1.82
884 972 2.959030 CGAGGAGGACATATGAACTGGA 59.041 50.000 10.38 0.00 0.00 3.86
899 987 0.741915 GCCTAGGAACAGACGAGGAG 59.258 60.000 14.75 0.00 0.00 3.69
903 991 1.112113 GGATGCCTAGGAACAGACGA 58.888 55.000 14.75 0.00 0.00 4.20
905 993 0.824759 ACGGATGCCTAGGAACAGAC 59.175 55.000 14.75 0.76 0.00 3.51
906 994 0.824109 CACGGATGCCTAGGAACAGA 59.176 55.000 14.75 0.00 0.00 3.41
907 995 0.179073 CCACGGATGCCTAGGAACAG 60.179 60.000 14.75 5.95 0.00 3.16
909 997 0.462047 CACCACGGATGCCTAGGAAC 60.462 60.000 14.75 2.14 0.00 3.62
911 999 2.731571 GCACCACGGATGCCTAGGA 61.732 63.158 14.75 0.00 37.08 2.94
912 1000 1.399744 TAGCACCACGGATGCCTAGG 61.400 60.000 3.67 3.67 44.53 3.02
913 1001 0.032678 CTAGCACCACGGATGCCTAG 59.967 60.000 4.42 3.26 44.53 3.02
914 1002 0.686441 ACTAGCACCACGGATGCCTA 60.686 55.000 4.42 0.00 44.53 3.93
915 1003 1.553690 AACTAGCACCACGGATGCCT 61.554 55.000 4.42 0.00 44.53 4.75
916 1004 0.676782 AAACTAGCACCACGGATGCC 60.677 55.000 4.42 0.00 44.53 4.40
917 1005 0.447801 CAAACTAGCACCACGGATGC 59.552 55.000 0.00 0.00 43.74 3.91
918 1006 1.086696 CCAAACTAGCACCACGGATG 58.913 55.000 0.00 0.00 0.00 3.51
919 1007 0.035439 CCCAAACTAGCACCACGGAT 60.035 55.000 0.00 0.00 0.00 4.18
920 1008 1.373435 CCCAAACTAGCACCACGGA 59.627 57.895 0.00 0.00 0.00 4.69
921 1009 2.332654 GCCCAAACTAGCACCACGG 61.333 63.158 0.00 0.00 0.00 4.94
922 1010 0.036765 TAGCCCAAACTAGCACCACG 60.037 55.000 0.00 0.00 0.00 4.94
923 1011 1.810755 GTTAGCCCAAACTAGCACCAC 59.189 52.381 0.00 0.00 0.00 4.16
924 1012 1.422024 TGTTAGCCCAAACTAGCACCA 59.578 47.619 0.00 0.00 29.61 4.17
925 1013 2.194201 TGTTAGCCCAAACTAGCACC 57.806 50.000 0.00 0.00 29.61 5.01
926 1014 5.392703 GGTTATTGTTAGCCCAAACTAGCAC 60.393 44.000 0.00 0.00 33.71 4.40
927 1015 4.703093 GGTTATTGTTAGCCCAAACTAGCA 59.297 41.667 0.00 0.00 32.33 3.49
928 1016 4.201881 CGGTTATTGTTAGCCCAAACTAGC 60.202 45.833 0.00 0.00 0.00 3.42
929 1017 4.939439 ACGGTTATTGTTAGCCCAAACTAG 59.061 41.667 0.00 0.00 0.00 2.57
930 1018 4.909001 ACGGTTATTGTTAGCCCAAACTA 58.091 39.130 0.00 0.00 0.00 2.24
931 1019 3.754850 GACGGTTATTGTTAGCCCAAACT 59.245 43.478 0.00 0.00 0.00 2.66
932 1020 3.754850 AGACGGTTATTGTTAGCCCAAAC 59.245 43.478 0.00 0.00 0.00 2.93
933 1021 4.004982 GAGACGGTTATTGTTAGCCCAAA 58.995 43.478 0.00 0.00 0.00 3.28
934 1022 3.602483 GAGACGGTTATTGTTAGCCCAA 58.398 45.455 0.00 0.00 0.00 4.12
935 1023 2.417651 CGAGACGGTTATTGTTAGCCCA 60.418 50.000 0.00 0.00 0.00 5.36
936 1024 2.199236 CGAGACGGTTATTGTTAGCCC 58.801 52.381 0.00 0.00 0.00 5.19
937 1025 2.856557 GACGAGACGGTTATTGTTAGCC 59.143 50.000 0.00 0.00 0.00 3.93
938 1026 3.767278 AGACGAGACGGTTATTGTTAGC 58.233 45.455 0.00 0.00 0.00 3.09
939 1027 5.736358 GTGTAGACGAGACGGTTATTGTTAG 59.264 44.000 0.00 0.00 0.00 2.34
940 1028 5.631026 GTGTAGACGAGACGGTTATTGTTA 58.369 41.667 0.00 0.00 0.00 2.41
941 1029 4.479619 GTGTAGACGAGACGGTTATTGTT 58.520 43.478 0.00 0.00 0.00 2.83
942 1030 4.088823 GTGTAGACGAGACGGTTATTGT 57.911 45.455 0.00 0.00 0.00 2.71
957 1045 1.810755 CTGCAGTAGTGGTCGTGTAGA 59.189 52.381 5.25 0.00 0.00 2.59
958 1046 1.732732 GCTGCAGTAGTGGTCGTGTAG 60.733 57.143 16.64 0.00 0.00 2.74
959 1047 0.242825 GCTGCAGTAGTGGTCGTGTA 59.757 55.000 16.64 0.00 0.00 2.90
960 1048 1.006102 GCTGCAGTAGTGGTCGTGT 60.006 57.895 16.64 0.00 0.00 4.49
964 1052 1.339055 TGGATTGCTGCAGTAGTGGTC 60.339 52.381 16.64 7.67 0.00 4.02
965 1053 0.692476 TGGATTGCTGCAGTAGTGGT 59.308 50.000 16.64 0.00 0.00 4.16
972 1060 1.404391 GTTCTGGATGGATTGCTGCAG 59.596 52.381 10.11 10.11 32.66 4.41
984 1072 3.433306 TCCATTTTCGGTGTTCTGGAT 57.567 42.857 0.00 0.00 0.00 3.41
994 1082 1.406539 CCTTGCTCCATCCATTTTCGG 59.593 52.381 0.00 0.00 0.00 4.30
1023 1112 2.290122 CTTGCTCGTCGGAGGCATCT 62.290 60.000 0.00 0.00 40.80 2.90
1046 1135 3.777925 CAAGGCACGGACGCTTCG 61.778 66.667 0.00 0.00 0.00 3.79
1047 1136 4.090057 GCAAGGCACGGACGCTTC 62.090 66.667 0.00 0.00 0.00 3.86
1053 1142 3.286751 GCAACTGCAAGGCACGGA 61.287 61.111 0.00 0.00 39.30 4.69
1076 1165 4.424566 CTGCACCACCATTGCGGC 62.425 66.667 0.00 0.00 43.34 6.53
1077 1166 3.751246 CCTGCACCACCATTGCGG 61.751 66.667 0.00 0.00 43.34 5.69
1078 1167 2.985282 ACCTGCACCACCATTGCG 60.985 61.111 0.00 0.00 43.34 4.85
1079 1168 2.652530 CACCTGCACCACCATTGC 59.347 61.111 0.00 0.00 40.63 3.56
1080 1169 2.277591 CCCACCTGCACCACCATTG 61.278 63.158 0.00 0.00 0.00 2.82
1081 1170 2.118076 CCCACCTGCACCACCATT 59.882 61.111 0.00 0.00 0.00 3.16
1082 1171 3.983420 CCCCACCTGCACCACCAT 61.983 66.667 0.00 0.00 0.00 3.55
1208 1306 3.114616 CCAAGGTGCTCAGCGTCG 61.115 66.667 0.00 0.00 0.00 5.12
1349 1447 4.867599 CGCTACCGAACTCCCGCC 62.868 72.222 0.00 0.00 36.29 6.13
1480 1581 2.884207 GACGCGACGGACCCAATC 60.884 66.667 15.93 0.00 0.00 2.67
1481 1582 2.901051 GATGACGCGACGGACCCAAT 62.901 60.000 15.93 0.00 0.00 3.16
1502 1603 1.139058 GAGGCGGTGTATCATCTTGGT 59.861 52.381 0.00 0.00 0.00 3.67
1522 1623 0.746063 TGCAACCTTTTGAGCTGGTG 59.254 50.000 0.00 0.00 34.24 4.17
1565 1666 0.810648 GATGTGGCTCGCAAAATCCA 59.189 50.000 0.00 0.00 0.00 3.41
1641 3118 1.289380 GATCTCATACCGGGCCGTC 59.711 63.158 26.32 9.29 0.00 4.79
1644 3121 1.122019 AGGTGATCTCATACCGGGCC 61.122 60.000 6.32 0.00 41.85 5.80
1645 3122 0.318762 GAGGTGATCTCATACCGGGC 59.681 60.000 6.32 0.00 41.85 6.13
1654 3131 3.360867 TGAGTGAGAAGGAGGTGATCTC 58.639 50.000 0.00 0.00 41.71 2.75
1731 3211 9.690913 ATAATCAACTTGAAAATCTCATCCTCA 57.309 29.630 0.00 0.00 32.78 3.86
1759 3239 0.037447 GAAACAAGAGCAGGAGCCCT 59.963 55.000 0.00 0.00 43.56 5.19
1760 3240 0.037447 AGAAACAAGAGCAGGAGCCC 59.963 55.000 0.00 0.00 43.56 5.19
1780 3260 4.521062 CTCTCCGGCCAAGCGGAG 62.521 72.222 19.50 19.50 44.37 4.63
1794 3274 7.052248 TGATATCAACAATGTGATCAAGCTCT 58.948 34.615 1.98 0.00 39.07 4.09
1837 3317 1.134530 GACGCATCGACAAGAGACGG 61.135 60.000 0.00 0.00 36.00 4.79
1838 3318 2.270091 GACGCATCGACAAGAGACG 58.730 57.895 0.00 0.00 37.21 4.18
1861 3341 0.176449 TCAGTCATCACGGGCAGATG 59.824 55.000 7.30 7.30 43.25 2.90
1870 3350 0.814457 AGCTCCTCGTCAGTCATCAC 59.186 55.000 0.00 0.00 0.00 3.06
1971 3451 3.019564 AGAAGAACATACCCTGCAATGC 58.980 45.455 0.00 0.00 0.00 3.56
1976 3456 1.745653 GCCAAGAAGAACATACCCTGC 59.254 52.381 0.00 0.00 0.00 4.85
2042 3526 0.252284 AGACATCCAGTTCCCGGTCT 60.252 55.000 0.00 0.00 0.00 3.85
2047 3531 2.586648 AAACCAGACATCCAGTTCCC 57.413 50.000 0.00 0.00 0.00 3.97
2063 3547 3.119137 AGGTTGGAACAGCAACTGAAAAC 60.119 43.478 0.78 0.91 42.95 2.43
2081 3565 2.982488 AGTTCCACAGAATCCTCAGGTT 59.018 45.455 0.00 0.00 33.67 3.50
2087 3571 2.641815 AGCTGAAGTTCCACAGAATCCT 59.358 45.455 0.00 0.00 36.38 3.24
2111 3595 6.697641 AGGTTCTTAGGTTCTGGAATACAA 57.302 37.500 0.00 0.00 0.00 2.41
2127 3611 1.766496 TCGTCCAGGAACAAGGTTCTT 59.234 47.619 8.79 0.00 0.00 2.52
2166 3650 1.376037 CTTCAGCCCCACGAAGTCC 60.376 63.158 0.00 0.00 41.61 3.85
2181 3665 2.289694 TGACTTCTGCAGGTAAGGCTTC 60.290 50.000 18.88 9.06 31.63 3.86
2196 3680 3.617775 GCTTCTCCAGGTTAGGTGACTTC 60.618 52.174 0.00 0.00 43.67 3.01
2340 3826 9.634163 GGGTTGATAACTTAACCTTTAAACATG 57.366 33.333 0.00 0.00 44.49 3.21
2341 3827 8.809066 GGGGTTGATAACTTAACCTTTAAACAT 58.191 33.333 0.00 0.00 44.49 2.71
2342 3828 7.040548 CGGGGTTGATAACTTAACCTTTAAACA 60.041 37.037 0.00 0.00 44.49 2.83
2343 3829 7.307694 CGGGGTTGATAACTTAACCTTTAAAC 58.692 38.462 0.00 0.00 44.49 2.01
2396 3885 3.500448 TGTGGCAAAGTGTGGAATCTA 57.500 42.857 0.00 0.00 0.00 1.98
2403 3892 1.411977 TCCCAAATGTGGCAAAGTGTG 59.588 47.619 0.00 0.00 44.46 3.82
2410 3899 2.601240 TGATTCTCCCAAATGTGGCA 57.399 45.000 0.00 0.00 44.46 4.92
2414 3903 4.949856 GTGTGGTATGATTCTCCCAAATGT 59.050 41.667 0.00 0.00 0.00 2.71
2421 3910 7.201652 GCTTAGAAAAGTGTGGTATGATTCTCC 60.202 40.741 0.00 0.00 34.99 3.71
2429 3918 7.048512 GTCATAGGCTTAGAAAAGTGTGGTAT 58.951 38.462 0.00 0.00 34.99 2.73
2431 3920 5.221843 TGTCATAGGCTTAGAAAAGTGTGGT 60.222 40.000 0.00 0.00 34.99 4.16
2438 3927 5.047590 TCTCACGTGTCATAGGCTTAGAAAA 60.048 40.000 16.51 0.00 0.00 2.29
2442 3931 4.371855 TTCTCACGTGTCATAGGCTTAG 57.628 45.455 16.51 1.12 0.00 2.18
2499 3988 4.619437 TTTAACGGGTTTGTCACTTGTC 57.381 40.909 0.00 0.00 0.00 3.18
2502 3991 6.311690 CACAAATTTTAACGGGTTTGTCACTT 59.688 34.615 0.00 0.00 41.37 3.16
2507 3996 4.870991 CACCACAAATTTTAACGGGTTTGT 59.129 37.500 0.00 0.00 43.36 2.83
2508 3997 4.870991 ACACCACAAATTTTAACGGGTTTG 59.129 37.500 0.00 0.00 37.52 2.93
2509 3998 4.870991 CACACCACAAATTTTAACGGGTTT 59.129 37.500 0.00 0.00 0.00 3.27
2510 3999 4.434520 CACACCACAAATTTTAACGGGTT 58.565 39.130 0.00 0.00 0.00 4.11
2511 4000 3.181474 CCACACCACAAATTTTAACGGGT 60.181 43.478 0.00 0.00 0.00 5.28
2512 4001 3.068307 TCCACACCACAAATTTTAACGGG 59.932 43.478 0.00 0.00 0.00 5.28
2513 4002 4.036971 TCTCCACACCACAAATTTTAACGG 59.963 41.667 0.00 0.00 0.00 4.44
2514 4003 5.176407 TCTCCACACCACAAATTTTAACG 57.824 39.130 0.00 0.00 0.00 3.18
2515 4004 6.569780 ACTTCTCCACACCACAAATTTTAAC 58.430 36.000 0.00 0.00 0.00 2.01
2516 4005 6.605594 AGACTTCTCCACACCACAAATTTTAA 59.394 34.615 0.00 0.00 0.00 1.52
2517 4006 6.039270 CAGACTTCTCCACACCACAAATTTTA 59.961 38.462 0.00 0.00 0.00 1.52
2518 4007 4.956075 AGACTTCTCCACACCACAAATTTT 59.044 37.500 0.00 0.00 0.00 1.82
2519 4008 4.339247 CAGACTTCTCCACACCACAAATTT 59.661 41.667 0.00 0.00 0.00 1.82
2520 4009 3.885297 CAGACTTCTCCACACCACAAATT 59.115 43.478 0.00 0.00 0.00 1.82
2521 4010 3.480470 CAGACTTCTCCACACCACAAAT 58.520 45.455 0.00 0.00 0.00 2.32
2522 4011 2.421388 CCAGACTTCTCCACACCACAAA 60.421 50.000 0.00 0.00 0.00 2.83
2523 4012 1.140852 CCAGACTTCTCCACACCACAA 59.859 52.381 0.00 0.00 0.00 3.33
2524 4013 0.758734 CCAGACTTCTCCACACCACA 59.241 55.000 0.00 0.00 0.00 4.17
2525 4014 0.603975 GCCAGACTTCTCCACACCAC 60.604 60.000 0.00 0.00 0.00 4.16
2526 4015 1.053835 TGCCAGACTTCTCCACACCA 61.054 55.000 0.00 0.00 0.00 4.17
2527 4016 0.108585 TTGCCAGACTTCTCCACACC 59.891 55.000 0.00 0.00 0.00 4.16
2528 4017 1.202698 AGTTGCCAGACTTCTCCACAC 60.203 52.381 0.00 0.00 0.00 3.82
2529 4018 1.131638 AGTTGCCAGACTTCTCCACA 58.868 50.000 0.00 0.00 0.00 4.17
2530 4019 2.262423 AAGTTGCCAGACTTCTCCAC 57.738 50.000 0.00 0.00 34.94 4.02
2531 4020 3.391296 ACTAAAGTTGCCAGACTTCTCCA 59.609 43.478 0.00 0.00 38.86 3.86
2532 4021 4.009370 ACTAAAGTTGCCAGACTTCTCC 57.991 45.455 0.00 0.00 38.86 3.71
2533 4022 6.757478 GGTATACTAAAGTTGCCAGACTTCTC 59.243 42.308 2.25 0.00 38.86 2.87
2534 4023 6.212791 TGGTATACTAAAGTTGCCAGACTTCT 59.787 38.462 2.25 0.00 38.86 2.85
2535 4024 6.403878 TGGTATACTAAAGTTGCCAGACTTC 58.596 40.000 2.25 0.00 38.86 3.01
2536 4025 6.368779 TGGTATACTAAAGTTGCCAGACTT 57.631 37.500 2.25 0.00 41.44 3.01
2537 4026 6.171213 GTTGGTATACTAAAGTTGCCAGACT 58.829 40.000 2.90 0.00 0.00 3.24
2538 4027 5.935789 TGTTGGTATACTAAAGTTGCCAGAC 59.064 40.000 2.90 0.00 0.00 3.51
2539 4028 6.116711 TGTTGGTATACTAAAGTTGCCAGA 57.883 37.500 2.90 0.00 0.00 3.86
2540 4029 6.811253 TTGTTGGTATACTAAAGTTGCCAG 57.189 37.500 2.90 0.00 0.00 4.85
2541 4030 6.546403 TGTTTGTTGGTATACTAAAGTTGCCA 59.454 34.615 2.90 0.00 0.00 4.92
2542 4031 6.972722 TGTTTGTTGGTATACTAAAGTTGCC 58.027 36.000 2.90 0.00 0.00 4.52
2543 4032 7.061789 GCATGTTTGTTGGTATACTAAAGTTGC 59.938 37.037 2.90 4.55 0.00 4.17
2544 4033 7.270365 CGCATGTTTGTTGGTATACTAAAGTTG 59.730 37.037 2.90 0.00 0.00 3.16
2545 4034 7.302524 CGCATGTTTGTTGGTATACTAAAGTT 58.697 34.615 2.90 0.00 0.00 2.66
2546 4035 6.622028 GCGCATGTTTGTTGGTATACTAAAGT 60.622 38.462 0.30 0.00 0.00 2.66
2547 4036 5.737290 GCGCATGTTTGTTGGTATACTAAAG 59.263 40.000 0.30 0.00 0.00 1.85
2548 4037 5.413213 AGCGCATGTTTGTTGGTATACTAAA 59.587 36.000 11.47 0.00 0.00 1.85
2549 4038 4.938832 AGCGCATGTTTGTTGGTATACTAA 59.061 37.500 11.47 0.00 0.00 2.24
2550 4039 4.509616 AGCGCATGTTTGTTGGTATACTA 58.490 39.130 11.47 0.00 0.00 1.82
2551 4040 3.343617 AGCGCATGTTTGTTGGTATACT 58.656 40.909 11.47 0.00 0.00 2.12
2552 4041 3.757745 AGCGCATGTTTGTTGGTATAC 57.242 42.857 11.47 0.00 0.00 1.47
2553 4042 4.509616 AGTAGCGCATGTTTGTTGGTATA 58.490 39.130 11.47 0.00 0.00 1.47
2554 4043 3.343617 AGTAGCGCATGTTTGTTGGTAT 58.656 40.909 11.47 0.00 0.00 2.73
2555 4044 2.773487 AGTAGCGCATGTTTGTTGGTA 58.227 42.857 11.47 0.00 0.00 3.25
2556 4045 1.604604 AGTAGCGCATGTTTGTTGGT 58.395 45.000 11.47 0.00 0.00 3.67
2557 4046 2.226437 AGAAGTAGCGCATGTTTGTTGG 59.774 45.455 11.47 0.00 0.00 3.77
2558 4047 3.542712 AGAAGTAGCGCATGTTTGTTG 57.457 42.857 11.47 0.00 0.00 3.33
2559 4048 4.036262 TGAAAGAAGTAGCGCATGTTTGTT 59.964 37.500 11.47 0.11 0.00 2.83
2607 4098 5.474532 GCATGGAGGATTAATATTGCAGACA 59.525 40.000 0.00 0.00 0.00 3.41
2652 4143 1.605058 AATCCACCAGGTCGTCTCCG 61.605 60.000 0.00 0.00 35.89 4.63
2690 4184 9.002600 CATGCTGGTATATAATTTGAGTAAGCA 57.997 33.333 0.00 0.00 39.78 3.91
2813 4307 5.390779 GGCAAACATGATACAAAAACATGGC 60.391 40.000 0.00 0.00 43.55 4.40
2849 4343 3.372206 CACACAATAACTCCTGTGCTAGC 59.628 47.826 8.10 8.10 45.56 3.42
2857 4351 6.299141 AGATGTTTCACACACAATAACTCCT 58.701 36.000 0.00 0.00 38.61 3.69
2909 4403 9.186323 TGAAAATCAAAATACCACAACAATACG 57.814 29.630 0.00 0.00 0.00 3.06
2931 4425 6.765036 ACAATACATGCCAATTTGTGTTGAAA 59.235 30.769 18.60 0.00 43.49 2.69
2937 4431 6.817641 ACCATAACAATACATGCCAATTTGTG 59.182 34.615 0.00 0.00 31.34 3.33
2939 4433 9.545105 AATACCATAACAATACATGCCAATTTG 57.455 29.630 0.00 0.00 0.00 2.32
2996 4496 5.178061 CAATCTGGTACTATGTGCAGACAA 58.822 41.667 0.00 0.00 35.11 3.18
3003 4503 8.942338 TTAGCTTAACAATCTGGTACTATGTG 57.058 34.615 0.00 0.00 0.00 3.21
3020 4523 9.820229 CACGATGTAAACTTTCATTTAGCTTAA 57.180 29.630 0.00 0.00 0.00 1.85
3040 4543 4.191544 ACCACTGACCATTAATCACGATG 58.808 43.478 0.00 0.00 0.00 3.84
3048 4551 6.699366 TCACGTATAAACCACTGACCATTAA 58.301 36.000 0.00 0.00 0.00 1.40
3049 4552 6.071221 ACTCACGTATAAACCACTGACCATTA 60.071 38.462 0.00 0.00 0.00 1.90
3053 4556 4.184079 ACTCACGTATAAACCACTGACC 57.816 45.455 0.00 0.00 0.00 4.02
3058 4561 4.565564 CCTGCTAACTCACGTATAAACCAC 59.434 45.833 0.00 0.00 0.00 4.16
3064 4567 5.447683 CGTACAACCTGCTAACTCACGTATA 60.448 44.000 0.00 0.00 0.00 1.47
3143 4648 7.817418 ATTTTGCATACCTATCAAATACCGT 57.183 32.000 0.00 0.00 30.89 4.83
3151 4656 7.713073 TCGACACATTATTTTGCATACCTATCA 59.287 33.333 0.00 0.00 0.00 2.15
3163 4668 5.705609 AAGTTGGCTCGACACATTATTTT 57.294 34.783 0.00 0.00 0.00 1.82
3172 4677 5.334569 GCTTGTTTATAAAGTTGGCTCGACA 60.335 40.000 0.00 0.00 0.00 4.35
3203 4708 0.679505 GGACCAAAGCCCTGTTTTCC 59.320 55.000 0.00 0.00 0.00 3.13
3286 4791 3.636231 CCCTGGGCTCACGAACCA 61.636 66.667 0.00 0.00 0.00 3.67
3347 4852 0.753848 CACCAACCGGGACCAAAAGT 60.754 55.000 6.32 0.00 41.15 2.66
3528 5033 2.620585 GCCAGAGAAAAACAGAGCACTT 59.379 45.455 0.00 0.00 0.00 3.16
3616 5121 1.203994 GCTTAAGTAGTGTGGCTCGGA 59.796 52.381 4.02 0.00 0.00 4.55
3651 5156 0.616111 ATGGAGCTTGGAGGTCGAGT 60.616 55.000 0.00 0.00 43.29 4.18


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

AutoCloner maintained by Alex Coulton.