Multiple sequence alignment - TraesCS2D01G483800

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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 TraesCS2D01G483800 chr2D 100.000 8509 0 0 1 8509 585381689 585390197 0.000000e+00 15714.0
1 TraesCS2D01G483800 chr2D 88.509 1053 87 14 4617 5645 607135074 607136116 0.000000e+00 1243.0
2 TraesCS2D01G483800 chr2D 79.732 1268 240 13 6196 7458 585209891 585211146 0.000000e+00 902.0
3 TraesCS2D01G483800 chr2D 93.643 409 22 4 318 725 642837607 642838012 7.300000e-170 608.0
4 TraesCS2D01G483800 chr2D 91.729 399 27 2 1000 1392 585368520 585368918 4.490000e-152 549.0
5 TraesCS2D01G483800 chr2D 90.338 414 36 1 966 1379 585344030 585344439 2.700000e-149 540.0
6 TraesCS2D01G483800 chr2D 89.524 420 42 2 974 1392 585209069 585209487 1.630000e-146 531.0
7 TraesCS2D01G483800 chr2D 95.865 266 7 3 1 263 642836851 642837115 2.200000e-115 427.0
8 TraesCS2D01G483800 chr2D 94.022 184 11 0 2 185 398783354 398783171 6.500000e-71 279.0
9 TraesCS2D01G483800 chr2D 91.279 172 12 3 2039 2208 81004757 81004927 1.850000e-56 231.0
10 TraesCS2D01G483800 chr2B 93.762 6108 312 38 2238 8311 706291037 706297109 0.000000e+00 9105.0
11 TraesCS2D01G483800 chr2B 94.582 1292 43 15 762 2040 706289731 706291008 0.000000e+00 1973.0
12 TraesCS2D01G483800 chr2B 90.783 434 32 3 962 1392 706267802 706268230 2.660000e-159 573.0
13 TraesCS2D01G483800 chr2B 89.130 414 41 1 966 1379 706115343 706115752 5.890000e-141 512.0
14 TraesCS2D01G483800 chr2B 94.595 185 10 0 1 185 472901785 472901601 3.890000e-73 287.0
15 TraesCS2D01G483800 chr2B 91.791 134 8 2 8377 8509 706297099 706297230 5.250000e-42 183.0
16 TraesCS2D01G483800 chr2B 85.507 69 7 3 2863 2930 461506551 461506485 1.530000e-07 69.4
17 TraesCS2D01G483800 chr2A 93.613 2333 123 7 6141 8471 719478112 719480420 0.000000e+00 3459.0
18 TraesCS2D01G483800 chr2A 90.266 1202 57 17 741 1908 719473617 719474792 0.000000e+00 1517.0
19 TraesCS2D01G483800 chr2A 87.425 1169 109 18 4622 5771 423772799 423773948 0.000000e+00 1310.0
20 TraesCS2D01G483800 chr2A 78.120 1266 255 17 6228 7485 719469586 719470837 0.000000e+00 784.0
21 TraesCS2D01G483800 chr2A 91.589 428 29 5 966 1392 719467888 719468309 1.230000e-162 584.0
22 TraesCS2D01G483800 chr2A 81.965 682 111 10 3941 4616 719477089 719477764 1.240000e-157 568.0
23 TraesCS2D01G483800 chr2A 88.916 415 42 1 965 1379 719402456 719402866 7.620000e-140 508.0
24 TraesCS2D01G483800 chr2A 94.054 185 11 0 1 185 536626990 536626806 1.810000e-71 281.0
25 TraesCS2D01G483800 chr2A 93.158 190 13 0 5954 6143 719477820 719478009 6.500000e-71 279.0
26 TraesCS2D01G483800 chr2A 93.407 182 12 0 2488 2669 719476617 719476798 3.910000e-68 270.0
27 TraesCS2D01G483800 chr2A 92.593 162 10 1 2297 2458 719476356 719476515 1.850000e-56 231.0
28 TraesCS2D01G483800 chr2A 84.343 198 25 3 2668 2861 719476883 719477078 1.130000e-43 189.0
29 TraesCS2D01G483800 chr2A 92.157 102 7 1 2198 2298 719476173 719476274 8.900000e-30 143.0
30 TraesCS2D01G483800 chr2A 80.925 173 25 6 3039 3206 483361349 483361180 6.930000e-26 130.0
31 TraesCS2D01G483800 chr2A 88.298 94 2 5 1956 2048 719476007 719476092 4.200000e-18 104.0
32 TraesCS2D01G483800 chr2A 90.476 63 4 2 337 399 170945792 170945732 1.970000e-11 82.4
33 TraesCS2D01G483800 chr5D 90.844 1125 83 7 4617 5722 100120323 100119200 0.000000e+00 1489.0
34 TraesCS2D01G483800 chr5D 91.011 178 14 2 2036 2212 53583241 53583065 1.100000e-58 239.0
35 TraesCS2D01G483800 chr5D 93.210 162 10 1 2039 2199 345684196 345684357 3.970000e-58 237.0
36 TraesCS2D01G483800 chr5D 83.673 245 33 7 4137 4376 529829075 529828833 3.090000e-54 224.0
37 TraesCS2D01G483800 chr3B 89.125 1177 107 6 4617 5775 419120728 419121901 0.000000e+00 1445.0
38 TraesCS2D01G483800 chr3B 85.874 1076 126 17 4617 5677 75363085 75364149 0.000000e+00 1122.0
39 TraesCS2D01G483800 chr3B 83.702 1086 139 20 4622 5695 818201538 818200479 0.000000e+00 990.0
40 TraesCS2D01G483800 chr3B 83.610 1086 140 20 4622 5695 818237075 818236016 0.000000e+00 985.0
41 TraesCS2D01G483800 chr3B 78.351 1067 217 8 3046 4104 418750157 418749097 0.000000e+00 678.0
42 TraesCS2D01G483800 chr3B 93.210 162 10 1 2039 2199 112325298 112325137 3.970000e-58 237.0
43 TraesCS2D01G483800 chr3B 82.051 234 30 9 4127 4350 180448689 180448458 1.130000e-43 189.0
44 TraesCS2D01G483800 chr3B 79.924 264 48 4 4123 4383 773383552 773383291 1.130000e-43 189.0
45 TraesCS2D01G483800 chr3B 78.986 276 47 10 4120 4390 650686902 650686633 2.440000e-40 178.0
46 TraesCS2D01G483800 chr7D 89.050 1169 117 11 4617 5778 453307015 453308179 0.000000e+00 1439.0
47 TraesCS2D01G483800 chr7D 80.574 1081 188 14 3046 4113 515397217 515396146 0.000000e+00 813.0
48 TraesCS2D01G483800 chr7D 79.431 1055 206 7 3046 4094 23581444 23580395 0.000000e+00 736.0
49 TraesCS2D01G483800 chr7D 80.597 268 45 7 4126 4390 11436759 11436496 5.210000e-47 200.0
50 TraesCS2D01G483800 chr7D 76.471 340 69 11 4112 4448 510848514 510848183 3.160000e-39 174.0
51 TraesCS2D01G483800 chr4D 89.003 1173 102 12 4617 5767 101655152 101653985 0.000000e+00 1426.0
52 TraesCS2D01G483800 chr4D 90.267 863 64 6 4916 5760 95820466 95819606 0.000000e+00 1110.0
53 TraesCS2D01G483800 chr4D 81.048 248 33 11 4124 4363 73331276 73331035 1.460000e-42 185.0
54 TraesCS2D01G483800 chr4D 77.288 295 57 10 4112 4400 337428560 337428850 1.900000e-36 165.0
55 TraesCS2D01G483800 chrUn 87.148 1066 119 14 4622 5677 65867756 65866699 0.000000e+00 1194.0
56 TraesCS2D01G483800 chrUn 87.000 900 102 12 4785 5677 453594449 453595340 0.000000e+00 1000.0
57 TraesCS2D01G483800 chr1D 81.696 1038 171 14 3072 4101 345428512 345429538 0.000000e+00 846.0
58 TraesCS2D01G483800 chr1D 97.059 34 0 1 712 744 375970842 375970875 1.000000e-03 56.5
59 TraesCS2D01G483800 chr7A 79.089 1076 198 18 3046 4103 531102709 531103775 0.000000e+00 715.0
60 TraesCS2D01G483800 chr7B 78.212 1074 209 21 3046 4104 437208226 437207163 0.000000e+00 664.0
61 TraesCS2D01G483800 chr7B 77.659 1025 214 14 3046 4062 221275153 221276170 2.030000e-170 610.0
62 TraesCS2D01G483800 chr7B 93.734 383 19 5 343 723 605427809 605427430 3.450000e-158 569.0
63 TraesCS2D01G483800 chr7B 81.973 294 46 7 436 725 748173927 748174217 8.530000e-60 243.0
64 TraesCS2D01G483800 chr7B 92.308 169 12 1 2033 2200 583373020 583372852 1.100000e-58 239.0
65 TraesCS2D01G483800 chr7B 93.210 162 10 1 2039 2199 679620663 679620502 3.970000e-58 237.0
66 TraesCS2D01G483800 chr7B 81.570 293 49 5 436 725 748169012 748169302 3.970000e-58 237.0
67 TraesCS2D01G483800 chr7B 81.570 293 49 5 436 725 748177844 748178134 3.970000e-58 237.0
68 TraesCS2D01G483800 chr3A 77.981 1040 207 16 3046 4075 27661532 27660505 4.330000e-177 632.0
69 TraesCS2D01G483800 chr3A 78.830 940 182 13 3046 3977 547326092 547327022 1.210000e-172 617.0
70 TraesCS2D01G483800 chr1B 87.246 541 39 12 192 717 649699542 649700067 2.650000e-164 590.0
71 TraesCS2D01G483800 chr1B 90.970 299 18 6 1 290 642618835 642618537 2.230000e-105 394.0
72 TraesCS2D01G483800 chr1B 93.631 157 10 0 309 465 583127561 583127717 1.430000e-57 235.0
73 TraesCS2D01G483800 chr4B 85.911 291 38 2 436 725 581896008 581896296 2.980000e-79 307.0
74 TraesCS2D01G483800 chr4B 90.751 173 13 3 2031 2200 136533442 136533614 2.390000e-55 228.0
75 TraesCS2D01G483800 chr5B 85.959 292 34 6 437 725 524457063 524456776 1.070000e-78 305.0
76 TraesCS2D01G483800 chr5B 83.214 280 42 5 436 712 586529954 586530231 1.420000e-62 252.0
77 TraesCS2D01G483800 chr6D 83.673 294 40 8 436 725 462019620 462019909 3.910000e-68 270.0
78 TraesCS2D01G483800 chr6B 93.252 163 10 1 2039 2200 128931724 128931886 1.100000e-58 239.0
79 TraesCS2D01G483800 chr6B 88.276 145 11 5 266 407 657261317 657261176 1.470000e-37 169.0
80 TraesCS2D01G483800 chr3D 91.279 172 12 3 2039 2208 537154863 537154693 1.850000e-56 231.0
81 TraesCS2D01G483800 chr1A 93.333 105 6 1 303 407 96740552 96740449 4.110000e-33 154.0
82 TraesCS2D01G483800 chr5A 100.000 36 0 0 372 407 600294245 600294210 5.510000e-07 67.6


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 TraesCS2D01G483800 chr2D 585381689 585390197 8508 False 15714.000000 15714 100.000000 1 8509 1 chr2D.!!$F4 8508
1 TraesCS2D01G483800 chr2D 607135074 607136116 1042 False 1243.000000 1243 88.509000 4617 5645 1 chr2D.!!$F5 1028
2 TraesCS2D01G483800 chr2D 585209069 585211146 2077 False 716.500000 902 84.628000 974 7458 2 chr2D.!!$F6 6484
3 TraesCS2D01G483800 chr2D 642836851 642838012 1161 False 517.500000 608 94.754000 1 725 2 chr2D.!!$F7 724
4 TraesCS2D01G483800 chr2B 706289731 706297230 7499 False 3753.666667 9105 93.378333 762 8509 3 chr2B.!!$F3 7747
5 TraesCS2D01G483800 chr2A 423772799 423773948 1149 False 1310.000000 1310 87.425000 4622 5771 1 chr2A.!!$F1 1149
6 TraesCS2D01G483800 chr2A 719467888 719480420 12532 False 738.909091 3459 89.046273 741 8471 11 chr2A.!!$F3 7730
7 TraesCS2D01G483800 chr5D 100119200 100120323 1123 True 1489.000000 1489 90.844000 4617 5722 1 chr5D.!!$R2 1105
8 TraesCS2D01G483800 chr3B 419120728 419121901 1173 False 1445.000000 1445 89.125000 4617 5775 1 chr3B.!!$F2 1158
9 TraesCS2D01G483800 chr3B 75363085 75364149 1064 False 1122.000000 1122 85.874000 4617 5677 1 chr3B.!!$F1 1060
10 TraesCS2D01G483800 chr3B 818200479 818201538 1059 True 990.000000 990 83.702000 4622 5695 1 chr3B.!!$R6 1073
11 TraesCS2D01G483800 chr3B 818236016 818237075 1059 True 985.000000 985 83.610000 4622 5695 1 chr3B.!!$R7 1073
12 TraesCS2D01G483800 chr3B 418749097 418750157 1060 True 678.000000 678 78.351000 3046 4104 1 chr3B.!!$R3 1058
13 TraesCS2D01G483800 chr7D 453307015 453308179 1164 False 1439.000000 1439 89.050000 4617 5778 1 chr7D.!!$F1 1161
14 TraesCS2D01G483800 chr7D 515396146 515397217 1071 True 813.000000 813 80.574000 3046 4113 1 chr7D.!!$R4 1067
15 TraesCS2D01G483800 chr7D 23580395 23581444 1049 True 736.000000 736 79.431000 3046 4094 1 chr7D.!!$R2 1048
16 TraesCS2D01G483800 chr4D 101653985 101655152 1167 True 1426.000000 1426 89.003000 4617 5767 1 chr4D.!!$R3 1150
17 TraesCS2D01G483800 chr4D 95819606 95820466 860 True 1110.000000 1110 90.267000 4916 5760 1 chr4D.!!$R2 844
18 TraesCS2D01G483800 chrUn 65866699 65867756 1057 True 1194.000000 1194 87.148000 4622 5677 1 chrUn.!!$R1 1055
19 TraesCS2D01G483800 chrUn 453594449 453595340 891 False 1000.000000 1000 87.000000 4785 5677 1 chrUn.!!$F1 892
20 TraesCS2D01G483800 chr1D 345428512 345429538 1026 False 846.000000 846 81.696000 3072 4101 1 chr1D.!!$F1 1029
21 TraesCS2D01G483800 chr7A 531102709 531103775 1066 False 715.000000 715 79.089000 3046 4103 1 chr7A.!!$F1 1057
22 TraesCS2D01G483800 chr7B 437207163 437208226 1063 True 664.000000 664 78.212000 3046 4104 1 chr7B.!!$R1 1058
23 TraesCS2D01G483800 chr7B 221275153 221276170 1017 False 610.000000 610 77.659000 3046 4062 1 chr7B.!!$F1 1016
24 TraesCS2D01G483800 chr7B 748173927 748178134 4207 False 240.000000 243 81.771500 436 725 2 chr7B.!!$F3 289
25 TraesCS2D01G483800 chr3A 27660505 27661532 1027 True 632.000000 632 77.981000 3046 4075 1 chr3A.!!$R1 1029
26 TraesCS2D01G483800 chr3A 547326092 547327022 930 False 617.000000 617 78.830000 3046 3977 1 chr3A.!!$F1 931
27 TraesCS2D01G483800 chr1B 649699542 649700067 525 False 590.000000 590 87.246000 192 717 1 chr1B.!!$F2 525

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
925 5914 0.313043 AACTAGTACACGCACGCACT 59.687 50.000 0.00 0.00 0.00 4.40 F
926 5915 0.386858 ACTAGTACACGCACGCACTG 60.387 55.000 0.00 0.00 0.00 3.66 F
1501 6502 0.830648 CCGGTCCCTGTCATACACAT 59.169 55.000 0.00 0.00 33.23 3.21 F
2955 9415 0.388391 AATTCATGCAAACACGGCGG 60.388 50.000 13.24 2.35 0.00 6.13 F
3691 10165 0.387878 GTGTCGTCTGAGCCTGTCTG 60.388 60.000 0.00 0.00 0.00 3.51 F
5184 11736 0.249953 TCGCCGCCAACAAAGTTAGA 60.250 50.000 0.00 0.00 0.00 2.10 F
6734 13415 1.068250 GGGGCTCATGCTAGACGAC 59.932 63.158 0.00 0.00 39.59 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2888 9347 1.328680 CCTGAATGAAATCTGACCGCG 59.671 52.381 0.00 0.00 0.00 6.46 R
2934 9393 1.665448 CGCCGTGTTTGCATGAATTCA 60.665 47.619 11.26 11.26 33.58 2.57 R
3123 9583 0.108138 CGGTCTGTCTCCCATGTTCC 60.108 60.000 0.00 0.00 0.00 3.62 R
3822 10297 0.884514 CGAAGCTCTGTGAGAGACCA 59.115 55.000 4.75 0.00 45.07 4.02 R
5473 12027 0.179000 GCGGTGAGATCCTGATGGTT 59.821 55.000 0.00 0.00 34.23 3.67 R
6802 13483 0.035317 CATGAGCCTAGCCCGCATTA 59.965 55.000 0.00 0.00 0.00 1.90 R
8269 14963 1.064166 CCCGTGAACCCTCCTAGACTA 60.064 57.143 0.00 0.00 0.00 2.59 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
99 100 0.894184 TCCTCCTCGAGTTCGTGCTT 60.894 55.000 12.31 0.00 40.80 3.91
158 159 0.323178 CAGGACTTCAATGGCTGGCT 60.323 55.000 2.00 0.00 0.00 4.75
186 187 4.421479 ACGGGCGAGCTCAAGACG 62.421 66.667 15.40 14.17 0.00 4.18
234 235 1.215679 ACGGAGAGGAGGAGGAGGAA 61.216 60.000 0.00 0.00 0.00 3.36
522 4883 0.620556 GGGCCTGTGAGGAAATGAGA 59.379 55.000 0.84 0.00 37.67 3.27
530 4891 5.398603 TGTGAGGAAATGAGAAGAGAGAC 57.601 43.478 0.00 0.00 0.00 3.36
651 5013 4.993029 CCGTAAATTTGGCTAAATCCCA 57.007 40.909 8.63 0.00 35.50 4.37
653 5015 4.440940 CCGTAAATTTGGCTAAATCCCACC 60.441 45.833 8.63 0.00 35.50 4.61
661 5023 3.146847 GGCTAAATCCCACCCTATTTCG 58.853 50.000 0.00 0.00 0.00 3.46
692 5054 1.669795 GCCTGACTGGGCGAAAAATTG 60.670 52.381 0.01 0.00 42.82 2.32
720 5082 1.950484 GCGATGAAAAAGGCCTCCTGA 60.950 52.381 5.23 0.00 32.13 3.86
730 5092 4.787280 CCTCCTGAGGGGACGGCT 62.787 72.222 0.00 0.00 44.87 5.52
734 5096 3.465403 CTGAGGGGACGGCTGGAG 61.465 72.222 0.00 0.00 0.00 3.86
735 5097 3.965026 CTGAGGGGACGGCTGGAGA 62.965 68.421 0.00 0.00 0.00 3.71
737 5099 2.765807 AGGGGACGGCTGGAGATG 60.766 66.667 0.00 0.00 0.00 2.90
738 5100 4.554036 GGGGACGGCTGGAGATGC 62.554 72.222 0.00 0.00 0.00 3.91
739 5101 3.474570 GGGACGGCTGGAGATGCT 61.475 66.667 0.00 0.00 0.00 3.79
740 5102 2.107953 GGACGGCTGGAGATGCTC 59.892 66.667 0.00 0.00 0.00 4.26
741 5103 2.430610 GGACGGCTGGAGATGCTCT 61.431 63.158 0.00 0.00 0.00 4.09
742 5104 1.519719 GACGGCTGGAGATGCTCTT 59.480 57.895 0.00 0.00 0.00 2.85
743 5105 0.747255 GACGGCTGGAGATGCTCTTA 59.253 55.000 0.00 0.00 0.00 2.10
744 5106 0.749649 ACGGCTGGAGATGCTCTTAG 59.250 55.000 0.00 0.00 0.00 2.18
745 5107 1.035923 CGGCTGGAGATGCTCTTAGA 58.964 55.000 0.00 0.00 0.00 2.10
746 5108 1.269517 CGGCTGGAGATGCTCTTAGAC 60.270 57.143 0.00 0.00 0.00 2.59
758 5747 9.073475 GAGATGCTCTTAGACTAGATTTAGGAA 57.927 37.037 0.00 0.00 0.00 3.36
767 5756 4.617593 ACTAGATTTAGGAACGGAGGGAA 58.382 43.478 0.00 0.00 0.00 3.97
826 5815 3.790416 TTTGCTGCGGGTCTTGGCT 62.790 57.895 0.00 0.00 0.00 4.75
843 5832 1.979155 CTGGGTCCAGCGACTCTGA 60.979 63.158 3.86 0.00 45.72 3.27
853 5842 3.243877 CCAGCGACTCTGATTGATAAACG 59.756 47.826 0.00 0.00 45.72 3.60
898 5887 1.706301 CAGCACACGATCAAGCTCG 59.294 57.895 0.00 0.00 44.14 5.03
919 5908 1.294138 GCCCCAACTAGTACACGCA 59.706 57.895 0.00 0.00 0.00 5.24
920 5909 1.017701 GCCCCAACTAGTACACGCAC 61.018 60.000 0.00 0.00 0.00 5.34
921 5910 0.734942 CCCCAACTAGTACACGCACG 60.735 60.000 0.00 0.00 0.00 5.34
922 5911 1.349259 CCCAACTAGTACACGCACGC 61.349 60.000 0.00 0.00 0.00 5.34
923 5912 0.665068 CCAACTAGTACACGCACGCA 60.665 55.000 0.00 0.00 0.00 5.24
924 5913 0.433492 CAACTAGTACACGCACGCAC 59.567 55.000 0.00 0.00 0.00 5.34
925 5914 0.313043 AACTAGTACACGCACGCACT 59.687 50.000 0.00 0.00 0.00 4.40
926 5915 0.386858 ACTAGTACACGCACGCACTG 60.387 55.000 0.00 0.00 0.00 3.66
1015 6004 2.436646 CCATGTCCACCACCGAGC 60.437 66.667 0.00 0.00 0.00 5.03
1016 6005 2.665000 CATGTCCACCACCGAGCT 59.335 61.111 0.00 0.00 0.00 4.09
1134 6126 3.642755 CACTTCGTGCTGGTGACC 58.357 61.111 0.00 0.00 33.32 4.02
1480 6481 6.075728 CGATGCGATTTGCTAATTCTCTTTTG 60.076 38.462 0.00 0.00 46.63 2.44
1483 6484 4.800471 CGATTTGCTAATTCTCTTTTGGCC 59.200 41.667 0.00 0.00 30.31 5.36
1494 6495 2.690653 CTTTTGGCCGGTCCCTGTCA 62.691 60.000 2.12 0.00 0.00 3.58
1501 6502 0.830648 CCGGTCCCTGTCATACACAT 59.169 55.000 0.00 0.00 33.23 3.21
1551 6552 8.300286 ACCACTACTCATCTAAACGATCATATG 58.700 37.037 0.00 0.00 0.00 1.78
1577 6600 8.386606 GTTTCTTTACAGATTCTAGAGCATGTG 58.613 37.037 13.20 7.69 0.00 3.21
1738 6763 4.124238 TGACTGTTTGGTGTTGTAGCTAC 58.876 43.478 17.30 17.30 0.00 3.58
1878 6908 6.147492 GTGAAAGGCATGATTATTGCAAACAA 59.853 34.615 1.71 0.62 41.95 2.83
2006 8203 8.812972 ACACTACACAATAAAGTATCTTCCAGA 58.187 33.333 0.00 0.00 0.00 3.86
2007 8204 9.307121 CACTACACAATAAAGTATCTTCCAGAG 57.693 37.037 0.00 0.00 0.00 3.35
2009 8206 9.877178 CTACACAATAAAGTATCTTCCAGAGTT 57.123 33.333 0.00 0.00 0.00 3.01
2012 8209 9.003658 CACAATAAAGTATCTTCCAGAGTTTGT 57.996 33.333 0.00 0.00 0.00 2.83
2059 8256 9.916360 AAAAATACTCCCTCCGTTTCTAAATAT 57.084 29.630 0.00 0.00 0.00 1.28
2063 8260 7.672122 ACTCCCTCCGTTTCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
2064 8261 8.087303 ACTCCCTCCGTTTCTAAATATAAGTT 57.913 34.615 0.00 0.00 0.00 2.66
2065 8262 8.546322 ACTCCCTCCGTTTCTAAATATAAGTTT 58.454 33.333 0.00 0.00 0.00 2.66
2066 8263 9.392259 CTCCCTCCGTTTCTAAATATAAGTTTT 57.608 33.333 0.00 0.00 0.00 2.43
2067 8264 9.387257 TCCCTCCGTTTCTAAATATAAGTTTTC 57.613 33.333 0.00 0.00 0.00 2.29
2068 8265 9.169592 CCCTCCGTTTCTAAATATAAGTTTTCA 57.830 33.333 0.00 0.00 0.00 2.69
2084 8281 7.693969 AAGTTTTCAAGAGATTCCACTATGG 57.306 36.000 0.00 0.00 39.43 2.74
2085 8282 7.020827 AGTTTTCAAGAGATTCCACTATGGA 57.979 36.000 0.00 0.00 46.61 3.41
2098 8295 4.827835 TCCACTATGGACTACATACAGAGC 59.172 45.833 0.00 0.00 42.67 4.09
2099 8296 4.584743 CCACTATGGACTACATACAGAGCA 59.415 45.833 0.00 0.00 40.96 4.26
2100 8297 5.069119 CCACTATGGACTACATACAGAGCAA 59.931 44.000 0.00 0.00 40.96 3.91
2101 8298 6.406961 CCACTATGGACTACATACAGAGCAAA 60.407 42.308 0.00 0.00 40.96 3.68
2102 8299 7.041721 CACTATGGACTACATACAGAGCAAAA 58.958 38.462 0.00 0.00 41.03 2.44
2105 8302 9.764363 CTATGGACTACATACAGAGCAAAATAA 57.236 33.333 0.00 0.00 41.03 1.40
2106 8303 8.668510 ATGGACTACATACAGAGCAAAATAAG 57.331 34.615 0.00 0.00 38.26 1.73
2108 8305 7.549134 TGGACTACATACAGAGCAAAATAAGTG 59.451 37.037 0.00 0.00 0.00 3.16
2110 8307 9.151471 GACTACATACAGAGCAAAATAAGTGAA 57.849 33.333 0.00 0.00 0.00 3.18
2117 8314 8.034058 ACAGAGCAAAATAAGTGAATCTACAC 57.966 34.615 0.00 0.00 40.60 2.90
2160 8357 7.870509 ACATCCGTATGTAGTTTGTAGTAGA 57.129 36.000 0.00 0.00 44.66 2.59
2161 8358 8.284945 ACATCCGTATGTAGTTTGTAGTAGAA 57.715 34.615 0.00 0.00 44.66 2.10
2162 8359 8.910944 ACATCCGTATGTAGTTTGTAGTAGAAT 58.089 33.333 0.00 0.00 44.66 2.40
2163 8360 9.745880 CATCCGTATGTAGTTTGTAGTAGAATT 57.254 33.333 0.00 0.00 0.00 2.17
2165 8362 9.793252 TCCGTATGTAGTTTGTAGTAGAATTTC 57.207 33.333 0.00 0.00 0.00 2.17
2166 8363 9.798994 CCGTATGTAGTTTGTAGTAGAATTTCT 57.201 33.333 4.03 4.03 0.00 2.52
2193 8390 7.527568 AGAGACTTATATTTAGGAACGGAGG 57.472 40.000 0.00 0.00 0.00 4.30
2194 8391 7.296098 AGAGACTTATATTTAGGAACGGAGGA 58.704 38.462 0.00 0.00 0.00 3.71
2195 8392 7.783596 AGAGACTTATATTTAGGAACGGAGGAA 59.216 37.037 0.00 0.00 0.00 3.36
2196 8393 7.953752 AGACTTATATTTAGGAACGGAGGAAG 58.046 38.462 0.00 0.00 0.00 3.46
2304 8585 9.003658 TCTCTCACTCTTCCAATTTAACAATTC 57.996 33.333 0.00 0.00 29.41 2.17
2576 8940 2.435586 GGCAGCTCGCATCACTGT 60.436 61.111 9.78 0.00 45.17 3.55
2618 8982 8.682710 GCATTACTAATTCAACAGGGTATTTGA 58.317 33.333 0.00 0.00 0.00 2.69
2815 9272 2.478879 CCCGTAAATTTTCACCCGCATC 60.479 50.000 0.00 0.00 0.00 3.91
2839 9298 1.760875 GCGGATAGGGGTCAGTCCA 60.761 63.158 0.00 0.00 38.11 4.02
2855 9314 6.147328 GGTCAGTCCACTTACATTTCAACTAC 59.853 42.308 0.00 0.00 35.97 2.73
2868 9327 8.324163 ACATTTCAACTACCATCTGAACTAAC 57.676 34.615 0.00 0.00 0.00 2.34
2870 9329 6.428083 TTCAACTACCATCTGAACTAACCA 57.572 37.500 0.00 0.00 0.00 3.67
2888 9347 5.989551 AACCAGACAAAAATCATGCAAAC 57.010 34.783 0.00 0.00 0.00 2.93
2955 9415 0.388391 AATTCATGCAAACACGGCGG 60.388 50.000 13.24 2.35 0.00 6.13
3034 9494 4.526650 TCCAAGCCTTTATTGTTCCTTTCC 59.473 41.667 0.00 0.00 0.00 3.13
3123 9583 1.658686 CTCCGACGAGGGGAAGAGTG 61.659 65.000 0.00 0.00 46.06 3.51
3382 9842 3.353836 GCGGTTTTCTGGCGAGCA 61.354 61.111 0.00 0.00 0.00 4.26
3511 9972 1.078143 CTGGCCCTCTACCAACTGC 60.078 63.158 0.00 0.00 36.56 4.40
3569 10034 3.166490 TACGCCTGTTGGAACGCCA 62.166 57.895 0.00 0.00 44.17 5.69
3616 10084 1.202651 GCCATGGCGGAGTTATAGTGT 60.203 52.381 23.48 0.00 36.56 3.55
3664 10138 4.626081 GTGCACAGGCGAGGGTGT 62.626 66.667 13.17 0.00 45.35 4.16
3691 10165 0.387878 GTGTCGTCTGAGCCTGTCTG 60.388 60.000 0.00 0.00 0.00 3.51
3721 10195 0.392060 TCGTCCTCGTCATCGGAGAA 60.392 55.000 0.00 0.00 38.13 2.87
3818 10293 1.911357 ACCTGTGCTTCATCTCCATGA 59.089 47.619 0.00 0.00 37.24 3.07
3822 10297 4.401519 CCTGTGCTTCATCTCCATGAAAAT 59.598 41.667 0.00 0.00 46.35 1.82
3918 10398 2.508663 GGCGTGGAGTTAGTCGGC 60.509 66.667 0.00 0.00 41.00 5.54
4088 10569 2.582978 GTCCCGCCCAGTAACTCC 59.417 66.667 0.00 0.00 0.00 3.85
4135 10616 0.534412 CGAAGGCAGTGAGAGGTCAT 59.466 55.000 0.00 0.00 34.36 3.06
4167 10648 1.741401 CGGCTTCAATGTGGAGCGA 60.741 57.895 2.50 0.00 0.00 4.93
4242 10724 1.990327 GAAGGAAGAGGGGTTTGGGTA 59.010 52.381 0.00 0.00 0.00 3.69
4284 10767 1.672854 CTTGGGTGCTATCCGGACGA 61.673 60.000 6.12 0.00 34.33 4.20
4311 10794 1.145738 AGCACCCCTCATGTTTGTCTT 59.854 47.619 0.00 0.00 0.00 3.01
4342 10825 2.665185 AAAGTGCGTCCGGACTGC 60.665 61.111 31.30 31.30 45.93 4.40
4406 10902 2.047083 ACGGTTGCGGGCGATTTA 60.047 55.556 0.00 0.00 0.00 1.40
4426 10922 0.824109 AGAATCGGCGTTGGAGATGA 59.176 50.000 6.85 0.00 0.00 2.92
4454 10950 2.438411 TGCTAATTGGGGTTACAACGG 58.562 47.619 0.00 0.00 32.39 4.44
4455 10951 2.224818 TGCTAATTGGGGTTACAACGGT 60.225 45.455 0.00 0.00 32.39 4.83
4503 10999 6.091718 TCAGTGGCGTATAATAAGCACATA 57.908 37.500 0.00 0.00 34.76 2.29
4528 11024 2.256117 AAGTTTCCGAACAGGGTCTG 57.744 50.000 0.00 0.00 41.52 3.51
4564 11060 6.452494 TCTCATCTCTCCTACCTTAAAACG 57.548 41.667 0.00 0.00 0.00 3.60
4568 11064 3.441572 TCTCTCCTACCTTAAAACGGACG 59.558 47.826 0.00 0.00 0.00 4.79
4586 11082 5.032863 CGGACGTAAAGTTCTATTGTCGAT 58.967 41.667 0.00 0.00 0.00 3.59
4620 11134 3.602483 GTCCAACATTCTTTACCGCCTA 58.398 45.455 0.00 0.00 0.00 3.93
4668 11182 9.799106 ACCATTTTATTGATTATTCTCGAGGAT 57.201 29.630 11.84 11.84 0.00 3.24
4705 11219 6.317789 ACAACAATATGCCTAAATCCATCG 57.682 37.500 0.00 0.00 0.00 3.84
4737 11253 6.935741 ATCTGCCGCTACTTCTATCTATAG 57.064 41.667 0.00 0.00 0.00 1.31
4801 11319 3.906720 AAGCCTAACATCTAAAGCCGA 57.093 42.857 0.00 0.00 0.00 5.54
4864 11383 1.221466 CCGACGCACTCACATGTGTT 61.221 55.000 24.63 10.98 43.26 3.32
4894 11413 3.369892 CCATCTTCCACTCGTCCATCTTT 60.370 47.826 0.00 0.00 0.00 2.52
4907 11426 4.505922 CGTCCATCTTTAGAGCAGATTGAC 59.494 45.833 5.56 5.56 38.89 3.18
5184 11736 0.249953 TCGCCGCCAACAAAGTTAGA 60.250 50.000 0.00 0.00 0.00 2.10
5270 11823 3.426568 GTGAACAGCGCCCTCAGC 61.427 66.667 2.29 0.00 38.52 4.26
5281 11834 4.056125 CCTCAGCTGTCGCCGTCA 62.056 66.667 14.67 0.00 36.60 4.35
5444 11998 3.749064 AGATCGCGCACACCGACT 61.749 61.111 8.75 0.00 40.02 4.18
5480 12034 2.115052 AGCCGCCAACAACCATCA 59.885 55.556 0.00 0.00 0.00 3.07
5486 12040 1.679944 CGCCAACAACCATCAGGATCT 60.680 52.381 0.00 0.00 38.69 2.75
5488 12042 2.618816 GCCAACAACCATCAGGATCTCA 60.619 50.000 0.00 0.00 38.69 3.27
5517 12071 4.899239 GCCAGGACGCCAGATCCG 62.899 72.222 0.00 0.00 41.52 4.18
5690 12262 2.765807 AGGAGATGGGGCGAGGTG 60.766 66.667 0.00 0.00 0.00 4.00
5775 12348 1.611261 TCGTGGGAGGGGTTAGGTG 60.611 63.158 0.00 0.00 0.00 4.00
6033 12606 6.549736 ACAAAAATATGTATACCTCCCTTGCC 59.450 38.462 0.00 0.00 0.00 4.52
6214 12895 3.005050 ACATTGTTGCTTCATGTGACTGG 59.995 43.478 0.00 0.00 0.00 4.00
6249 12930 3.203086 TTGGTTGCAGGATCCGGCA 62.203 57.895 32.30 32.30 44.63 5.69
6640 13321 2.356553 GCGTTGGTACCTCGTGCA 60.357 61.111 23.16 0.00 0.00 4.57
6734 13415 1.068250 GGGGCTCATGCTAGACGAC 59.932 63.158 0.00 0.00 39.59 4.34
6756 13437 1.084370 GGACGACATCGCCAAGAAGG 61.084 60.000 0.14 0.00 44.43 3.46
6802 13483 1.066858 AGATGTGTTTCGGTCGCAGAT 60.067 47.619 0.00 0.00 40.67 2.90
6942 13623 2.893441 TCTCTCGCTGAGATGCCTT 58.107 52.632 8.38 0.00 46.03 4.35
6977 13658 0.868406 CGGTGCTCCTTCAACACTTC 59.132 55.000 2.85 0.00 34.70 3.01
7132 13813 5.177725 AGTTACAAGGGTTTGCTTTAACG 57.822 39.130 0.00 0.00 37.85 3.18
7386 14067 1.376466 GCCATCATCGGTGGGCTAT 59.624 57.895 8.55 0.00 43.09 2.97
7578 14261 5.799681 AAAACAATGTTGCACAAAAGAGG 57.200 34.783 0.00 0.00 0.00 3.69
7607 14290 6.545666 TCACACAAATTGGATTGTCTACTTGT 59.454 34.615 0.00 0.00 41.44 3.16
7791 14475 3.232213 TGCAACTAAGTGTCGATCCTC 57.768 47.619 0.00 0.00 0.00 3.71
7985 14670 3.030291 TGGTTTGATGCTTTGGTGTCTT 58.970 40.909 0.00 0.00 0.00 3.01
7987 14672 4.037446 TGGTTTGATGCTTTGGTGTCTTAC 59.963 41.667 0.00 0.00 0.00 2.34
8001 14686 3.729716 GTGTCTTACCGATGCGAACTATC 59.270 47.826 0.00 0.00 0.00 2.08
8015 14700 5.998981 TGCGAACTATCCTTTTAGTTGGAAA 59.001 36.000 9.59 0.00 41.36 3.13
8075 14760 2.183478 TCAATCTTGAAGCTCCGCAA 57.817 45.000 0.00 0.00 33.55 4.85
8084 14769 1.464997 GAAGCTCCGCAATTTCGACTT 59.535 47.619 0.00 0.00 0.00 3.01
8111 14796 5.596836 TCAGTACATGATGTGTGAGCATA 57.403 39.130 8.61 0.00 42.24 3.14
8117 14810 6.028562 ACATGATGTGTGAGCATATGCGTG 62.029 45.833 21.57 6.90 42.52 5.34
8150 14843 8.823818 CCTACGTTGTAATTGGTATTCCTAAAG 58.176 37.037 0.00 0.00 34.23 1.85
8187 14881 9.442047 TTTGTTTGTTATCACTTGGAATGTTTT 57.558 25.926 0.00 0.00 0.00 2.43
8353 15047 7.889073 TGGTTTGGCTTTACAGTAATGGTATTA 59.111 33.333 8.01 0.00 0.00 0.98
8462 15156 6.766467 AGAGGAAAAGTTGTACGTCTCATTTT 59.234 34.615 0.00 0.00 0.00 1.82
8494 15188 7.484035 ACATGCTCTTATTTAAAGGATCGTC 57.516 36.000 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
522 4883 2.357154 GCCTCTCTCCTCAGTCTCTCTT 60.357 54.545 0.00 0.00 0.00 2.85
530 4891 0.679640 ACGTCAGCCTCTCTCCTCAG 60.680 60.000 0.00 0.00 0.00 3.35
653 5015 1.705997 CCCCCAGACCCCGAAATAGG 61.706 65.000 0.00 0.00 0.00 2.57
692 5054 1.141591 CTTTTTCATCGCCGGCATGC 61.142 55.000 28.98 9.90 0.00 4.06
720 5082 2.765807 CATCTCCAGCCGTCCCCT 60.766 66.667 0.00 0.00 0.00 4.79
734 5096 7.806014 CGTTCCTAAATCTAGTCTAAGAGCATC 59.194 40.741 0.00 0.00 0.00 3.91
735 5097 7.255660 CCGTTCCTAAATCTAGTCTAAGAGCAT 60.256 40.741 0.00 0.00 0.00 3.79
737 5099 6.262720 TCCGTTCCTAAATCTAGTCTAAGAGC 59.737 42.308 0.00 0.00 0.00 4.09
738 5100 7.040961 CCTCCGTTCCTAAATCTAGTCTAAGAG 60.041 44.444 0.00 0.00 0.00 2.85
739 5101 6.771749 CCTCCGTTCCTAAATCTAGTCTAAGA 59.228 42.308 0.00 0.00 0.00 2.10
740 5102 6.016108 CCCTCCGTTCCTAAATCTAGTCTAAG 60.016 46.154 0.00 0.00 0.00 2.18
741 5103 5.832060 CCCTCCGTTCCTAAATCTAGTCTAA 59.168 44.000 0.00 0.00 0.00 2.10
742 5104 5.133322 TCCCTCCGTTCCTAAATCTAGTCTA 59.867 44.000 0.00 0.00 0.00 2.59
743 5105 4.079327 TCCCTCCGTTCCTAAATCTAGTCT 60.079 45.833 0.00 0.00 0.00 3.24
744 5106 4.213513 TCCCTCCGTTCCTAAATCTAGTC 58.786 47.826 0.00 0.00 0.00 2.59
745 5107 4.261411 TCCCTCCGTTCCTAAATCTAGT 57.739 45.455 0.00 0.00 0.00 2.57
746 5108 5.810080 ATTCCCTCCGTTCCTAAATCTAG 57.190 43.478 0.00 0.00 0.00 2.43
758 5747 2.361438 GACGACATTCTATTCCCTCCGT 59.639 50.000 0.00 0.00 0.00 4.69
826 5815 0.904865 AATCAGAGTCGCTGGACCCA 60.905 55.000 3.58 0.00 44.54 4.51
843 5832 2.017049 GAGGCACCTGCGTTTATCAAT 58.983 47.619 0.00 0.00 43.26 2.57
853 5842 2.047274 TTGTAGCGAGGCACCTGC 60.047 61.111 0.00 0.00 41.14 4.85
898 5887 1.435577 CGTGTACTAGTTGGGGCAAC 58.564 55.000 0.00 0.00 43.83 4.17
919 5908 3.261951 GTGTGTGCGTCAGTGCGT 61.262 61.111 8.39 0.00 37.81 5.24
920 5909 4.000557 GGTGTGTGCGTCAGTGCG 62.001 66.667 3.07 3.07 37.81 5.34
921 5910 2.894879 TGGTGTGTGCGTCAGTGC 60.895 61.111 0.00 0.00 0.00 4.40
922 5911 2.870341 CGTGGTGTGTGCGTCAGTG 61.870 63.158 0.00 0.00 0.00 3.66
923 5912 2.584970 CGTGGTGTGTGCGTCAGT 60.585 61.111 0.00 0.00 0.00 3.41
924 5913 2.279186 TCGTGGTGTGTGCGTCAG 60.279 61.111 0.00 0.00 0.00 3.51
925 5914 2.279186 CTCGTGGTGTGTGCGTCA 60.279 61.111 0.00 0.00 0.00 4.35
926 5915 3.702555 GCTCGTGGTGTGTGCGTC 61.703 66.667 0.00 0.00 0.00 5.19
944 5933 2.450476 AGCTATTCAGTTGCCTTTGGG 58.550 47.619 0.00 0.00 0.00 4.12
1448 6449 0.179200 GCAAATCGCATCGGTTCGTT 60.179 50.000 0.00 0.00 41.79 3.85
1449 6450 1.019278 AGCAAATCGCATCGGTTCGT 61.019 50.000 0.00 0.00 46.13 3.85
1480 6481 2.363975 TGTATGACAGGGACCGGCC 61.364 63.158 0.00 3.33 0.00 6.13
1483 6484 1.480545 TCATGTGTATGACAGGGACCG 59.519 52.381 0.00 0.00 38.37 4.79
1494 6495 4.323417 TGAAGCGGAAAAGTCATGTGTAT 58.677 39.130 0.00 0.00 0.00 2.29
1501 6502 2.613026 TGTCTGAAGCGGAAAAGTCA 57.387 45.000 0.00 0.00 0.00 3.41
1551 6552 8.386606 CACATGCTCTAGAATCTGTAAAGAAAC 58.613 37.037 0.00 0.00 0.00 2.78
1927 6957 8.240267 ACTTATACTCCCTCTGTTCAAGATAC 57.760 38.462 0.00 0.00 33.29 2.24
2037 8234 9.377238 ACTTATATTTAGAAACGGAGGGAGTAT 57.623 33.333 0.00 0.00 0.00 2.12
2038 8235 8.773033 ACTTATATTTAGAAACGGAGGGAGTA 57.227 34.615 0.00 0.00 0.00 2.59
2039 8236 7.672122 ACTTATATTTAGAAACGGAGGGAGT 57.328 36.000 0.00 0.00 0.00 3.85
2040 8237 8.959705 AAACTTATATTTAGAAACGGAGGGAG 57.040 34.615 0.00 0.00 0.00 4.30
2059 8256 8.602424 TCCATAGTGGAATCTCTTGAAAACTTA 58.398 33.333 0.00 0.00 45.00 2.24
2060 8257 7.461749 TCCATAGTGGAATCTCTTGAAAACTT 58.538 34.615 0.00 0.00 45.00 2.66
2075 8272 4.827835 GCTCTGTATGTAGTCCATAGTGGA 59.172 45.833 0.00 0.00 45.98 4.02
2076 8273 4.584743 TGCTCTGTATGTAGTCCATAGTGG 59.415 45.833 0.00 0.00 36.71 4.00
2082 8279 7.549134 CACTTATTTTGCTCTGTATGTAGTCCA 59.451 37.037 0.00 0.00 0.00 4.02
2083 8280 7.764443 TCACTTATTTTGCTCTGTATGTAGTCC 59.236 37.037 0.00 0.00 0.00 3.85
2084 8281 8.703604 TCACTTATTTTGCTCTGTATGTAGTC 57.296 34.615 0.00 0.00 0.00 2.59
2085 8282 9.672673 ATTCACTTATTTTGCTCTGTATGTAGT 57.327 29.630 0.00 0.00 0.00 2.73
2087 8284 9.890629 AGATTCACTTATTTTGCTCTGTATGTA 57.109 29.630 0.00 0.00 0.00 2.29
2088 8285 8.798859 AGATTCACTTATTTTGCTCTGTATGT 57.201 30.769 0.00 0.00 0.00 2.29
2092 8289 7.880195 AGTGTAGATTCACTTATTTTGCTCTGT 59.120 33.333 0.00 0.00 44.92 3.41
2093 8290 8.261492 AGTGTAGATTCACTTATTTTGCTCTG 57.739 34.615 0.00 0.00 44.92 3.35
2134 8331 9.565090 TCTACTACAAACTACATACGGATGTAT 57.435 33.333 20.64 8.38 45.42 2.29
2135 8332 8.962884 TCTACTACAAACTACATACGGATGTA 57.037 34.615 19.32 19.32 44.77 2.29
2137 8334 9.745880 AATTCTACTACAAACTACATACGGATG 57.254 33.333 5.94 5.94 39.16 3.51
2139 8336 9.793252 GAAATTCTACTACAAACTACATACGGA 57.207 33.333 0.00 0.00 0.00 4.69
2140 8337 9.798994 AGAAATTCTACTACAAACTACATACGG 57.201 33.333 0.00 0.00 0.00 4.02
2167 8364 8.422566 CCTCCGTTCCTAAATATAAGTCTCTTT 58.577 37.037 0.00 0.00 0.00 2.52
2168 8365 7.783596 TCCTCCGTTCCTAAATATAAGTCTCTT 59.216 37.037 0.00 0.00 0.00 2.85
2169 8366 7.296098 TCCTCCGTTCCTAAATATAAGTCTCT 58.704 38.462 0.00 0.00 0.00 3.10
2170 8367 7.521871 TCCTCCGTTCCTAAATATAAGTCTC 57.478 40.000 0.00 0.00 0.00 3.36
2171 8368 7.564292 ACTTCCTCCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
2172 8369 7.724287 ACTTCCTCCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
2173 8370 7.672122 ACTTCCTCCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
2174 8371 9.640963 CATACTTCCTCCGTTCCTAAATATAAG 57.359 37.037 0.00 0.00 0.00 1.73
2175 8372 9.151177 ACATACTTCCTCCGTTCCTAAATATAA 57.849 33.333 0.00 0.00 0.00 0.98
2176 8373 8.716674 ACATACTTCCTCCGTTCCTAAATATA 57.283 34.615 0.00 0.00 0.00 0.86
2177 8374 7.613551 ACATACTTCCTCCGTTCCTAAATAT 57.386 36.000 0.00 0.00 0.00 1.28
2178 8375 8.416329 GTTACATACTTCCTCCGTTCCTAAATA 58.584 37.037 0.00 0.00 0.00 1.40
2179 8376 5.952347 ACATACTTCCTCCGTTCCTAAAT 57.048 39.130 0.00 0.00 0.00 1.40
2180 8377 6.211184 TGTTACATACTTCCTCCGTTCCTAAA 59.789 38.462 0.00 0.00 0.00 1.85
2181 8378 5.716228 TGTTACATACTTCCTCCGTTCCTAA 59.284 40.000 0.00 0.00 0.00 2.69
2182 8379 5.263599 TGTTACATACTTCCTCCGTTCCTA 58.736 41.667 0.00 0.00 0.00 2.94
2183 8380 4.091549 TGTTACATACTTCCTCCGTTCCT 58.908 43.478 0.00 0.00 0.00 3.36
2184 8381 4.081807 ACTGTTACATACTTCCTCCGTTCC 60.082 45.833 0.00 0.00 0.00 3.62
2185 8382 4.863131 CACTGTTACATACTTCCTCCGTTC 59.137 45.833 0.00 0.00 0.00 3.95
2186 8383 4.322499 CCACTGTTACATACTTCCTCCGTT 60.322 45.833 0.00 0.00 0.00 4.44
2187 8384 3.194968 CCACTGTTACATACTTCCTCCGT 59.805 47.826 0.00 0.00 0.00 4.69
2188 8385 3.194968 ACCACTGTTACATACTTCCTCCG 59.805 47.826 0.00 0.00 0.00 4.63
2189 8386 4.820894 ACCACTGTTACATACTTCCTCC 57.179 45.455 0.00 0.00 0.00 4.30
2190 8387 8.693625 AGTTATACCACTGTTACATACTTCCTC 58.306 37.037 0.00 0.00 0.00 3.71
2191 8388 8.475639 CAGTTATACCACTGTTACATACTTCCT 58.524 37.037 0.00 0.00 39.59 3.36
2192 8389 8.644318 CAGTTATACCACTGTTACATACTTCC 57.356 38.462 0.00 0.00 39.59 3.46
2304 8585 6.183360 GCTATCTGAACACTGTCAGCTAAAAG 60.183 42.308 0.00 0.00 44.01 2.27
2390 8671 1.548357 ATGACACCGCTCTCTGGCTT 61.548 55.000 0.00 0.00 0.00 4.35
2459 8740 7.819644 TGAGTGTTGTATTACTAGCGTAGAAA 58.180 34.615 0.00 0.00 0.00 2.52
2460 8741 7.381766 TGAGTGTTGTATTACTAGCGTAGAA 57.618 36.000 0.00 0.00 0.00 2.10
2461 8742 6.990341 TGAGTGTTGTATTACTAGCGTAGA 57.010 37.500 0.00 0.00 0.00 2.59
2576 8940 1.471829 ATGCATCCGTCCAGGCGATA 61.472 55.000 0.00 0.00 40.77 2.92
2618 8982 6.014925 ACAAGGGCCGAAGTAAAATACAATTT 60.015 34.615 0.00 0.00 0.00 1.82
2620 8984 5.014202 ACAAGGGCCGAAGTAAAATACAAT 58.986 37.500 0.00 0.00 0.00 2.71
2798 9255 2.420722 GACGGATGCGGGTGAAAATTTA 59.579 45.455 12.44 0.00 0.00 1.40
2839 9298 8.157476 AGTTCAGATGGTAGTTGAAATGTAAGT 58.843 33.333 0.00 0.00 33.10 2.24
2855 9314 6.633500 TTTTTGTCTGGTTAGTTCAGATGG 57.367 37.500 0.00 0.00 42.36 3.51
2868 9327 3.120923 GCGTTTGCATGATTTTTGTCTGG 60.121 43.478 0.00 0.00 42.15 3.86
2870 9329 2.725723 CGCGTTTGCATGATTTTTGTCT 59.274 40.909 0.00 0.00 42.97 3.41
2888 9347 1.328680 CCTGAATGAAATCTGACCGCG 59.671 52.381 0.00 0.00 0.00 6.46
2930 9389 3.367190 CCGTGTTTGCATGAATTCATCCA 60.367 43.478 18.16 13.14 33.61 3.41
2934 9393 1.665448 CGCCGTGTTTGCATGAATTCA 60.665 47.619 11.26 11.26 33.58 2.57
3019 9479 4.412843 GGTCCCAGGAAAGGAACAATAAA 58.587 43.478 0.00 0.00 41.10 1.40
3022 9482 1.271926 CGGTCCCAGGAAAGGAACAAT 60.272 52.381 0.00 0.00 41.55 2.71
3116 9576 2.303022 TGTCTCCCATGTTCCACTCTTC 59.697 50.000 0.00 0.00 0.00 2.87
3123 9583 0.108138 CGGTCTGTCTCCCATGTTCC 60.108 60.000 0.00 0.00 0.00 3.62
3179 9639 4.282496 GACTCCTCCAAGAATGAGTAGGA 58.718 47.826 0.00 0.00 38.15 2.94
3460 9921 1.807226 CGTGAGTGAGGATGCCGTA 59.193 57.895 0.00 0.00 0.00 4.02
3490 9951 1.561542 CAGTTGGTAGAGGGCCAGATT 59.438 52.381 6.18 0.00 37.31 2.40
3511 9972 0.035881 TGTTCCTCCTGAAGCAGCAG 59.964 55.000 0.00 0.00 32.37 4.24
3569 10034 1.815421 CTGCTTCGGCGCCTATGTT 60.815 57.895 26.68 0.00 45.37 2.71
3664 10138 0.031585 CTCAGACGACACCAAACCGA 59.968 55.000 0.00 0.00 0.00 4.69
3691 10165 3.718210 GAGGACGACCCCACGATGC 62.718 68.421 0.00 0.00 36.73 3.91
3818 10293 4.322567 GAAGCTCTGTGAGAGACCATTTT 58.677 43.478 4.75 0.00 45.07 1.82
3822 10297 0.884514 CGAAGCTCTGTGAGAGACCA 59.115 55.000 4.75 0.00 45.07 4.02
3918 10398 6.371809 TCTATTATTAAAAAGCAGCCACGG 57.628 37.500 0.00 0.00 0.00 4.94
3928 10408 7.229907 GGCCTCACCGGAATCTATTATTAAAAA 59.770 37.037 9.46 0.00 33.16 1.94
3965 10445 3.055110 TGCCGTGCATTGACGCAT 61.055 55.556 0.00 0.00 45.26 4.73
4088 10569 1.841450 GAGCGTTCAATACCGGAGAG 58.159 55.000 9.46 0.00 0.00 3.20
4228 10710 1.929088 GGCCTACCCAAACCCCTCT 60.929 63.158 0.00 0.00 0.00 3.69
4242 10724 2.121963 TTCTGACCACCCTGGCCT 60.122 61.111 3.32 0.00 42.67 5.19
4284 10767 1.640670 ACATGAGGGGTGCTTTATGGT 59.359 47.619 0.00 0.00 0.00 3.55
4311 10794 1.668751 GCACTTTGTCTCACAAACCGA 59.331 47.619 0.00 0.00 42.55 4.69
4392 10888 2.716398 GATTCTTAAATCGCCCGCAAC 58.284 47.619 0.00 0.00 32.46 4.17
4402 10898 3.869065 TCTCCAACGCCGATTCTTAAAT 58.131 40.909 0.00 0.00 0.00 1.40
4406 10902 1.207089 TCATCTCCAACGCCGATTCTT 59.793 47.619 0.00 0.00 0.00 2.52
4426 10922 4.397919 AACCCCAATTAGCAAGTAAGGT 57.602 40.909 0.00 0.00 0.00 3.50
4503 10999 3.958147 ACCCTGTTCGGAAACTTTCAATT 59.042 39.130 3.93 0.00 36.30 2.32
4528 11024 4.277476 AGAGATGAGATATGTCGGATCCC 58.723 47.826 6.06 0.00 0.00 3.85
4564 11060 6.693342 CAATCGACAATAGAACTTTACGTCC 58.307 40.000 0.00 0.00 0.00 4.79
4568 11064 7.290857 TGAGCAATCGACAATAGAACTTTAC 57.709 36.000 0.00 0.00 0.00 2.01
4586 11082 2.844946 TGTTGGACGAAAGATGAGCAA 58.155 42.857 0.00 0.00 0.00 3.91
4727 11243 5.903923 TGCACCCTTCATCCTATAGATAGA 58.096 41.667 0.00 0.00 32.37 1.98
4737 11253 1.318158 CCAGCTTGCACCCTTCATCC 61.318 60.000 0.00 0.00 0.00 3.51
4808 11326 0.901124 ACCTGACAGATGGCTCAGTC 59.099 55.000 3.32 2.37 38.15 3.51
4864 11383 3.700970 TGGAAGATGGCGGCGACA 61.701 61.111 21.84 21.84 0.00 4.35
4894 11413 3.934457 TTGACACGTCAATCTGCTCTA 57.066 42.857 8.51 0.00 43.90 2.43
4907 11426 3.343972 CCTGCCAAGGTTGACACG 58.656 61.111 0.00 0.00 38.96 4.49
5165 11716 0.249953 TCTAACTTTGTTGGCGGCGA 60.250 50.000 12.98 0.00 0.00 5.54
5473 12027 0.179000 GCGGTGAGATCCTGATGGTT 59.821 55.000 0.00 0.00 34.23 3.67
5480 12034 3.842923 CGCAGGCGGTGAGATCCT 61.843 66.667 5.63 0.00 35.56 3.24
5860 12433 9.170734 CTCAATGAAAGATAGGACAATTGAAGA 57.829 33.333 13.59 0.00 0.00 2.87
5944 12517 6.624526 GTGATTGCGTGAAAAACTGAATTTTG 59.375 34.615 1.81 0.00 39.70 2.44
5996 12569 4.337274 ACATATTTTTGTAGGTTAGCCCGC 59.663 41.667 0.00 0.00 38.74 6.13
6033 12606 8.255394 TCATCACTTATAATTATCCGTGCATG 57.745 34.615 16.46 17.64 0.00 4.06
6214 12895 3.078837 ACCAACCAACCAACGATATGAC 58.921 45.455 0.00 0.00 0.00 3.06
6249 12930 4.288105 AGAATCTGACAGGTGTCCAAAGAT 59.712 41.667 7.64 6.63 44.15 2.40
6640 13321 1.893808 GCATCATCCGTCCGGCAAT 60.894 57.895 0.00 0.00 34.68 3.56
6728 13409 1.694018 CGATGTCGTCCTCGTCGTCT 61.694 60.000 0.00 0.00 38.35 4.18
6734 13415 1.874019 CTTGGCGATGTCGTCCTCG 60.874 63.158 4.43 3.27 44.42 4.63
6756 13437 0.995731 GACGACGTCTCCACAACGAC 60.996 60.000 20.52 0.00 42.62 4.34
6802 13483 0.035317 CATGAGCCTAGCCCGCATTA 59.965 55.000 0.00 0.00 0.00 1.90
6942 13623 0.902984 ACCGCAGTGACCAGGTATGA 60.903 55.000 0.00 0.00 34.83 2.15
7386 14067 2.429930 CGGGAGGCAGAACACCAA 59.570 61.111 0.00 0.00 0.00 3.67
7578 14261 6.029346 AGACAATCCAATTTGTGTGATTCC 57.971 37.500 0.00 0.00 39.85 3.01
7732 14415 8.752187 ACAATTCATCTTATATTTGCAACACCT 58.248 29.630 0.00 0.00 0.00 4.00
7733 14416 8.810427 CACAATTCATCTTATATTTGCAACACC 58.190 33.333 0.00 0.00 0.00 4.16
7791 14475 3.391098 CCATGGGTTTTGGGCTGG 58.609 61.111 2.85 0.00 0.00 4.85
7985 14670 4.395959 AAAAGGATAGTTCGCATCGGTA 57.604 40.909 0.00 0.00 0.00 4.02
7987 14672 4.369182 ACTAAAAGGATAGTTCGCATCGG 58.631 43.478 0.00 0.00 32.18 4.18
8001 14686 4.271776 AGAACGTCGTTTCCAACTAAAAGG 59.728 41.667 12.67 0.00 0.00 3.11
8015 14700 4.094590 CCTCACTATTGACTAGAACGTCGT 59.905 45.833 0.00 0.00 36.71 4.34
8075 14760 4.002906 TGTACTGAAGCCAAGTCGAAAT 57.997 40.909 0.00 0.00 0.00 2.17
8084 14769 3.007831 TCACACATCATGTACTGAAGCCA 59.992 43.478 0.00 0.00 40.64 4.75
8117 14810 3.364565 CCAATTACAACGTAGGTGCACAC 60.365 47.826 20.43 8.29 0.00 3.82
8118 14811 2.809119 CCAATTACAACGTAGGTGCACA 59.191 45.455 20.43 0.00 0.00 4.57
8119 14812 2.809696 ACCAATTACAACGTAGGTGCAC 59.190 45.455 8.80 8.80 0.00 4.57
8120 14813 3.128852 ACCAATTACAACGTAGGTGCA 57.871 42.857 3.26 0.00 0.00 4.57
8121 14814 5.220719 GGAATACCAATTACAACGTAGGTGC 60.221 44.000 3.26 0.00 35.97 5.01
8122 14815 6.110707 AGGAATACCAATTACAACGTAGGTG 58.889 40.000 3.26 0.00 38.94 4.00
8123 14816 6.303903 AGGAATACCAATTACAACGTAGGT 57.696 37.500 0.00 0.00 38.94 3.08
8124 14817 8.721019 TTTAGGAATACCAATTACAACGTAGG 57.279 34.615 0.00 0.00 38.94 3.18
8269 14963 1.064166 CCCGTGAACCCTCCTAGACTA 60.064 57.143 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.