Multiple sequence alignment - TraesCS5B01G553200

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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 TraesCS5B01G553200 chr5B 100.000 3128 0 0 1 3128 703487470 703490597 0.000000e+00 5777.0
1 TraesCS5B01G553200 chr5B 92.833 1507 56 14 947 2422 699353993 699355478 0.000000e+00 2137.0
2 TraesCS5B01G553200 chr5B 96.086 511 17 3 98 607 703376824 703377332 0.000000e+00 830.0
3 TraesCS5B01G553200 chr5B 92.368 511 14 4 98 607 703393811 703394297 0.000000e+00 704.0
4 TraesCS5B01G553200 chr5B 93.388 363 17 3 2771 3127 699357484 699357845 5.940000e-147 531.0
5 TraesCS5B01G553200 chr5B 96.429 280 9 1 2497 2776 699355620 699355898 7.900000e-126 460.0
6 TraesCS5B01G553200 chr5B 91.964 224 17 1 147 370 683653496 683653718 2.340000e-81 313.0
7 TraesCS5B01G553200 chr5B 92.973 185 11 2 608 791 699353720 699353903 5.140000e-68 268.0
8 TraesCS5B01G553200 chr5B 87.124 233 26 4 967 1197 685532709 685532939 8.600000e-66 261.0
9 TraesCS5B01G553200 chr5B 86.222 225 28 2 976 1197 699415077 699415301 1.120000e-59 241.0
10 TraesCS5B01G553200 chr5B 74.658 584 101 24 942 1500 685499428 685499989 6.790000e-52 215.0
11 TraesCS5B01G553200 chr5B 77.713 341 66 5 1810 2143 699390921 699390584 1.900000e-47 200.0
12 TraesCS5B01G553200 chr5B 77.778 342 64 10 1810 2143 703501219 703500882 1.900000e-47 200.0
13 TraesCS5B01G553200 chr5B 85.976 164 11 6 458 610 683749908 683749746 6.940000e-37 165.0
14 TraesCS5B01G553200 chr5B 97.403 77 2 0 2453 2529 699355478 699355554 7.040000e-27 132.0
15 TraesCS5B01G553200 chr5B 82.301 113 19 1 390 502 703377182 703377293 2.570000e-16 97.1
16 TraesCS5B01G553200 chr5B 93.548 62 2 2 92 152 636064007 636064067 1.190000e-14 91.6
17 TraesCS5B01G553200 chr5B 80.000 130 19 3 392 514 703487927 703488056 4.300000e-14 89.8
18 TraesCS5B01G553200 chr5D 94.524 1680 70 10 865 2529 551073712 551075384 0.000000e+00 2573.0
19 TraesCS5B01G553200 chr5D 98.101 632 11 1 2497 3128 551075450 551076080 0.000000e+00 1099.0
20 TraesCS5B01G553200 chr5D 75.413 1151 208 49 1028 2125 552422770 552421642 3.630000e-134 488.0
21 TraesCS5B01G553200 chr5D 73.080 1159 225 58 1028 2135 551744443 551745565 6.470000e-87 331.0
22 TraesCS5B01G553200 chr5D 95.652 184 8 0 608 791 551073487 551073670 2.360000e-76 296.0
23 TraesCS5B01G553200 chr5D 80.759 369 54 12 976 1341 543465668 543465314 3.980000e-69 272.0
24 TraesCS5B01G553200 chr5D 79.472 341 60 8 1810 2143 551085773 551085436 1.880000e-57 233.0
25 TraesCS5B01G553200 chr5D 75.240 416 81 15 1723 2121 552632490 552632080 8.910000e-41 178.0
26 TraesCS5B01G553200 chr5D 96.154 104 4 0 1 104 285160587 285160484 1.490000e-38 171.0
27 TraesCS5B01G553200 chr5D 91.045 67 5 1 93 158 70640533 70640599 4.300000e-14 89.8
28 TraesCS5B01G553200 chr4A 91.559 1623 60 19 947 2529 616886030 616884445 0.000000e+00 2167.0
29 TraesCS5B01G553200 chr4A 96.469 623 15 4 2497 3115 616884379 616883760 0.000000e+00 1022.0
30 TraesCS5B01G553200 chr4A 77.107 961 160 41 1598 2529 632939930 632940859 4.660000e-138 501.0
31 TraesCS5B01G553200 chr4A 73.919 1480 280 69 967 2387 625542252 625543684 6.020000e-137 497.0
32 TraesCS5B01G553200 chr4A 73.584 1571 296 72 1028 2529 616840639 616839119 2.800000e-135 492.0
33 TraesCS5B01G553200 chr4A 75.843 534 99 18 1028 1549 616897494 616896979 8.670000e-61 244.0
34 TraesCS5B01G553200 chr4A 74.162 507 78 23 1028 1506 616871850 616871369 8.980000e-36 161.0
35 TraesCS5B01G553200 chr4A 83.929 112 14 4 2033 2143 616866460 616866568 1.530000e-18 104.0
36 TraesCS5B01G553200 chr4A 90.000 50 3 2 2554 2602 616869376 616869328 2.600000e-06 63.9
37 TraesCS5B01G553200 chr4D 85.753 365 40 8 147 503 419594880 419594520 2.950000e-100 375.0
38 TraesCS5B01G553200 chr4D 85.479 365 41 8 147 503 419596864 419596504 1.370000e-98 370.0
39 TraesCS5B01G553200 chr4D 85.165 364 43 7 147 503 419590917 419590558 2.290000e-96 363.0
40 TraesCS5B01G553200 chr4D 85.165 364 43 7 147 503 419592898 419592539 2.290000e-96 363.0
41 TraesCS5B01G553200 chr4D 83.696 368 49 10 147 507 419509191 419508828 1.390000e-88 337.0
42 TraesCS5B01G553200 chr4D 100.000 104 0 0 1 104 402522290 402522187 3.180000e-45 193.0
43 TraesCS5B01G553200 chr4D 84.828 145 20 2 425 568 419681615 419681472 9.040000e-31 145.0
44 TraesCS5B01G553200 chr4D 87.611 113 14 0 456 568 419496003 419495891 7.040000e-27 132.0
45 TraesCS5B01G553200 chr4D 87.611 113 14 0 456 568 419562331 419562219 7.040000e-27 132.0
46 TraesCS5B01G553200 chr4D 87.611 113 13 1 456 568 419601900 419601789 2.530000e-26 130.0
47 TraesCS5B01G553200 chr4D 86.726 113 15 0 456 568 419699022 419698910 3.270000e-25 126.0
48 TraesCS5B01G553200 chr4D 85.841 113 16 0 456 568 419681617 419681505 1.520000e-23 121.0
49 TraesCS5B01G553200 chr4B 88.542 288 31 2 150 436 4083616 4083902 6.420000e-92 348.0
50 TraesCS5B01G553200 chr4B 83.562 292 46 2 147 437 4082562 4082852 3.980000e-69 272.0
51 TraesCS5B01G553200 chr4B 95.082 61 2 1 94 153 176814409 176814349 9.240000e-16 95.3
52 TraesCS5B01G553200 chr1B 76.387 703 124 26 1435 2120 39517277 39516600 1.070000e-89 340.0
53 TraesCS5B01G553200 chr1B 86.550 171 21 2 1028 1197 115749005 115749174 1.480000e-43 187.0
54 TraesCS5B01G553200 chr1B 99.038 104 1 0 1 104 134819139 134819036 1.480000e-43 187.0
55 TraesCS5B01G553200 chr7A 75.181 552 118 15 1604 2145 23151687 23152229 3.120000e-60 243.0
56 TraesCS5B01G553200 chr7A 82.443 131 18 4 2027 2156 23146565 23146691 3.300000e-20 110.0
57 TraesCS5B01G553200 chr3B 97.321 112 1 1 1 110 684247620 684247509 4.120000e-44 189.0
58 TraesCS5B01G553200 chr5A 98.095 105 2 0 1 105 23255002 23255106 1.920000e-42 183.0
59 TraesCS5B01G553200 chr5A 98.095 105 2 0 1 105 41342587 41342483 1.920000e-42 183.0
60 TraesCS5B01G553200 chr6B 97.222 108 2 1 1 107 590563093 590562986 6.890000e-42 182.0
61 TraesCS5B01G553200 chr6B 88.312 77 5 4 94 167 287011751 287011826 4.300000e-14 89.8
62 TraesCS5B01G553200 chr1A 97.059 102 3 0 3 104 515835287 515835186 4.150000e-39 172.0
63 TraesCS5B01G553200 chr1A 96.154 104 4 0 1 104 321599144 321599041 1.490000e-38 171.0
64 TraesCS5B01G553200 chr1A 100.000 30 0 0 965 994 97792730 97792759 4.360000e-04 56.5
65 TraesCS5B01G553200 chr2D 96.552 58 1 1 92 148 597893960 597894017 9.240000e-16 95.3
66 TraesCS5B01G553200 chr2A 95.082 61 2 1 89 148 225438044 225438104 9.240000e-16 95.3
67 TraesCS5B01G553200 chr6A 92.308 65 3 2 92 155 501677496 501677433 1.190000e-14 91.6
68 TraesCS5B01G553200 chr1D 100.000 30 0 0 965 994 79115726 79115755 4.360000e-04 56.5


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 TraesCS5B01G553200 chr5B 703487470 703490597 3127 False 2933.400000 5777 90.000000 1 3128 2 chr5B.!!$F9 3127
1 TraesCS5B01G553200 chr5B 699353720 699357845 4125 False 705.600000 2137 94.605200 608 3127 5 chr5B.!!$F7 2519
2 TraesCS5B01G553200 chr5B 703376824 703377332 508 False 463.550000 830 89.193500 98 607 2 chr5B.!!$F8 509
3 TraesCS5B01G553200 chr5B 685499428 685499989 561 False 215.000000 215 74.658000 942 1500 1 chr5B.!!$F3 558
4 TraesCS5B01G553200 chr5D 551073487 551076080 2593 False 1322.666667 2573 96.092333 608 3128 3 chr5D.!!$F3 2520
5 TraesCS5B01G553200 chr5D 552421642 552422770 1128 True 488.000000 488 75.413000 1028 2125 1 chr5D.!!$R4 1097
6 TraesCS5B01G553200 chr5D 551744443 551745565 1122 False 331.000000 331 73.080000 1028 2135 1 chr5D.!!$F2 1107
7 TraesCS5B01G553200 chr4A 616883760 616886030 2270 True 1594.500000 2167 94.014000 947 3115 2 chr4A.!!$R4 2168
8 TraesCS5B01G553200 chr4A 632939930 632940859 929 False 501.000000 501 77.107000 1598 2529 1 chr4A.!!$F3 931
9 TraesCS5B01G553200 chr4A 625542252 625543684 1432 False 497.000000 497 73.919000 967 2387 1 chr4A.!!$F2 1420
10 TraesCS5B01G553200 chr4A 616839119 616840639 1520 True 492.000000 492 73.584000 1028 2529 1 chr4A.!!$R1 1501
11 TraesCS5B01G553200 chr4A 616896979 616897494 515 True 244.000000 244 75.843000 1028 1549 1 chr4A.!!$R2 521
12 TraesCS5B01G553200 chr4D 419590558 419596864 6306 True 367.750000 375 85.390500 147 503 4 chr4D.!!$R7 356
13 TraesCS5B01G553200 chr4B 4082562 4083902 1340 False 310.000000 348 86.052000 147 437 2 chr4B.!!$F1 290
14 TraesCS5B01G553200 chr1B 39516600 39517277 677 True 340.000000 340 76.387000 1435 2120 1 chr1B.!!$R1 685
15 TraesCS5B01G553200 chr7A 23151687 23152229 542 False 243.000000 243 75.181000 1604 2145 1 chr7A.!!$F2 541

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
63 64 0.039165 GCTAGCAACGCCAAAGCTTT 60.039 50.0 10.63 5.69 39.68 3.51 F
68 69 0.102120 CAACGCCAAAGCTTTGTGGA 59.898 50.0 31.67 0.00 41.88 4.02 F
496 2500 0.109319 ATGCCATGCGAACGGAAAAC 60.109 50.0 0.00 0.00 0.00 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1025 3117 0.247736 GAGAAGCTCTTCCGGCAGAA 59.752 55.000 5.05 0.0 40.33 3.02 R
1884 4100 1.070786 GGCAACTCCGTGAGAACCA 59.929 57.895 7.76 0.0 33.32 3.67 R
2458 8020 0.400213 TCGCCTCCAAGTTGGTCATT 59.600 50.000 21.35 0.0 39.03 2.57 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
18 19 3.060615 GTGGAGCAGCAGCCCAAG 61.061 66.667 11.80 0.00 40.96 3.61
19 20 3.251509 TGGAGCAGCAGCCCAAGA 61.252 61.111 8.50 0.00 43.56 3.02
20 21 2.438075 GGAGCAGCAGCCCAAGAG 60.438 66.667 0.00 0.00 43.56 2.85
21 22 2.667418 GAGCAGCAGCCCAAGAGA 59.333 61.111 0.00 0.00 43.56 3.10
22 23 1.224039 GAGCAGCAGCCCAAGAGAT 59.776 57.895 0.00 0.00 43.56 2.75
23 24 0.467384 GAGCAGCAGCCCAAGAGATA 59.533 55.000 0.00 0.00 43.56 1.98
24 25 1.072015 GAGCAGCAGCCCAAGAGATAT 59.928 52.381 0.00 0.00 43.56 1.63
25 26 1.072015 AGCAGCAGCCCAAGAGATATC 59.928 52.381 0.00 0.00 43.56 1.63
26 27 1.881498 GCAGCAGCCCAAGAGATATCC 60.881 57.143 0.00 0.00 33.58 2.59
27 28 1.419012 CAGCAGCCCAAGAGATATCCA 59.581 52.381 0.00 0.00 0.00 3.41
28 29 1.698532 AGCAGCCCAAGAGATATCCAG 59.301 52.381 0.00 0.00 0.00 3.86
29 30 1.271271 GCAGCCCAAGAGATATCCAGG 60.271 57.143 0.00 0.00 0.00 4.45
30 31 1.063183 AGCCCAAGAGATATCCAGGC 58.937 55.000 0.00 5.15 39.25 4.85
31 32 0.767375 GCCCAAGAGATATCCAGGCA 59.233 55.000 11.93 0.00 38.79 4.75
32 33 1.271271 GCCCAAGAGATATCCAGGCAG 60.271 57.143 11.93 0.00 38.79 4.85
33 34 1.350351 CCCAAGAGATATCCAGGCAGG 59.650 57.143 0.00 0.00 39.47 4.85
34 35 1.271271 CCAAGAGATATCCAGGCAGGC 60.271 57.143 0.00 0.00 37.29 4.85
35 36 0.683973 AAGAGATATCCAGGCAGGCG 59.316 55.000 0.00 0.00 37.29 5.52
36 37 0.178950 AGAGATATCCAGGCAGGCGA 60.179 55.000 0.00 0.00 37.29 5.54
37 38 0.901124 GAGATATCCAGGCAGGCGAT 59.099 55.000 0.00 0.00 37.29 4.58
38 39 0.901124 AGATATCCAGGCAGGCGATC 59.099 55.000 0.00 0.00 37.29 3.69
39 40 0.459237 GATATCCAGGCAGGCGATCG 60.459 60.000 11.69 11.69 37.29 3.69
40 41 1.188219 ATATCCAGGCAGGCGATCGT 61.188 55.000 17.81 0.00 37.29 3.73
41 42 0.538746 TATCCAGGCAGGCGATCGTA 60.539 55.000 17.81 0.00 37.29 3.43
42 43 2.088674 ATCCAGGCAGGCGATCGTAC 62.089 60.000 17.81 10.33 37.29 3.67
43 44 2.655364 CAGGCAGGCGATCGTACG 60.655 66.667 17.81 9.53 0.00 3.67
44 45 3.900892 AGGCAGGCGATCGTACGG 61.901 66.667 17.81 11.80 0.00 4.02
50 51 2.330393 GCGATCGTACGGCTAGCA 59.670 61.111 18.24 0.00 0.00 3.49
51 52 1.298863 GCGATCGTACGGCTAGCAA 60.299 57.895 18.24 0.00 0.00 3.91
52 53 1.538117 GCGATCGTACGGCTAGCAAC 61.538 60.000 18.24 10.33 0.00 4.17
53 54 1.260198 CGATCGTACGGCTAGCAACG 61.260 60.000 22.90 22.90 36.71 4.10
54 55 1.538117 GATCGTACGGCTAGCAACGC 61.538 60.000 23.66 12.38 35.40 4.84
55 56 2.948840 ATCGTACGGCTAGCAACGCC 62.949 60.000 23.66 10.91 44.11 5.68
60 61 2.179267 GGCTAGCAACGCCAAAGC 59.821 61.111 18.24 0.00 46.77 3.51
61 62 2.335712 GGCTAGCAACGCCAAAGCT 61.336 57.895 18.24 0.00 46.77 3.74
62 63 1.581447 GCTAGCAACGCCAAAGCTT 59.419 52.632 10.63 0.00 39.68 3.74
63 64 0.039165 GCTAGCAACGCCAAAGCTTT 60.039 50.000 10.63 5.69 39.68 3.51
65 66 1.001378 CTAGCAACGCCAAAGCTTTGT 60.001 47.619 31.67 17.35 46.87 2.83
66 67 0.528249 AGCAACGCCAAAGCTTTGTG 60.528 50.000 31.67 25.92 46.87 3.33
67 68 1.489881 GCAACGCCAAAGCTTTGTGG 61.490 55.000 31.67 25.15 46.87 4.17
68 69 0.102120 CAACGCCAAAGCTTTGTGGA 59.898 50.000 31.67 0.00 41.88 4.02
69 70 0.385390 AACGCCAAAGCTTTGTGGAG 59.615 50.000 31.67 24.15 40.25 3.86
70 71 1.286880 CGCCAAAGCTTTGTGGAGG 59.713 57.895 31.67 20.20 37.03 4.30
71 72 1.005748 GCCAAAGCTTTGTGGAGGC 60.006 57.895 31.67 25.03 37.03 4.70
72 73 1.466851 GCCAAAGCTTTGTGGAGGCT 61.467 55.000 31.67 0.00 37.03 4.58
73 74 0.600057 CCAAAGCTTTGTGGAGGCTC 59.400 55.000 31.67 5.78 37.03 4.70
74 75 0.600057 CAAAGCTTTGTGGAGGCTCC 59.400 55.000 27.59 26.95 35.06 4.70
75 76 0.540597 AAAGCTTTGTGGAGGCTCCC 60.541 55.000 30.03 20.86 35.03 4.30
76 77 1.719063 AAGCTTTGTGGAGGCTCCCA 61.719 55.000 30.03 23.10 35.03 4.37
77 78 1.676967 GCTTTGTGGAGGCTCCCAG 60.677 63.158 30.03 20.04 36.78 4.45
78 79 1.676967 CTTTGTGGAGGCTCCCAGC 60.677 63.158 30.03 19.69 41.46 4.85
79 80 2.134630 CTTTGTGGAGGCTCCCAGCT 62.135 60.000 30.03 0.00 41.99 4.24
80 81 2.129555 TTTGTGGAGGCTCCCAGCTC 62.130 60.000 30.03 15.11 41.99 4.09
81 82 4.154347 GTGGAGGCTCCCAGCTCG 62.154 72.222 30.03 0.00 41.99 5.03
88 89 3.710722 CTCCCAGCTCGCCCTGTT 61.711 66.667 0.00 0.00 0.00 3.16
89 90 2.284331 TCCCAGCTCGCCCTGTTA 60.284 61.111 0.00 0.00 0.00 2.41
90 91 1.689233 TCCCAGCTCGCCCTGTTAT 60.689 57.895 0.00 0.00 0.00 1.89
91 92 0.397957 TCCCAGCTCGCCCTGTTATA 60.398 55.000 0.00 0.00 0.00 0.98
92 93 0.249911 CCCAGCTCGCCCTGTTATAC 60.250 60.000 0.00 0.00 0.00 1.47
93 94 0.753262 CCAGCTCGCCCTGTTATACT 59.247 55.000 0.00 0.00 0.00 2.12
94 95 1.539065 CCAGCTCGCCCTGTTATACTG 60.539 57.143 0.00 0.00 0.00 2.74
95 96 1.137086 CAGCTCGCCCTGTTATACTGT 59.863 52.381 0.00 0.00 0.00 3.55
96 97 1.831736 AGCTCGCCCTGTTATACTGTT 59.168 47.619 0.00 0.00 0.00 3.16
97 98 2.236395 AGCTCGCCCTGTTATACTGTTT 59.764 45.455 0.00 0.00 0.00 2.83
98 99 3.449737 AGCTCGCCCTGTTATACTGTTTA 59.550 43.478 0.00 0.00 0.00 2.01
99 100 3.802685 GCTCGCCCTGTTATACTGTTTAG 59.197 47.826 0.00 0.00 0.00 1.85
100 101 4.679905 GCTCGCCCTGTTATACTGTTTAGT 60.680 45.833 0.00 0.00 40.99 2.24
101 102 5.450965 GCTCGCCCTGTTATACTGTTTAGTA 60.451 44.000 0.00 0.00 43.19 1.82
131 132 9.436957 GTCTGAAATGTCTTCAAGGTCTTATAA 57.563 33.333 0.00 0.00 0.00 0.98
141 142 9.273016 TCTTCAAGGTCTTATAAAAGTGAACAG 57.727 33.333 0.00 0.00 34.13 3.16
369 2354 2.492088 GGAACATTGTTAAGGACCCTGC 59.508 50.000 1.15 0.00 0.00 4.85
370 2355 1.821216 ACATTGTTAAGGACCCTGCG 58.179 50.000 0.00 0.00 0.00 5.18
371 2356 1.073284 ACATTGTTAAGGACCCTGCGT 59.927 47.619 0.00 0.00 0.00 5.24
372 2357 1.737793 CATTGTTAAGGACCCTGCGTC 59.262 52.381 0.00 0.00 41.15 5.19
373 2358 0.759959 TTGTTAAGGACCCTGCGTCA 59.240 50.000 0.00 0.00 43.95 4.35
374 2359 0.759959 TGTTAAGGACCCTGCGTCAA 59.240 50.000 0.00 0.00 43.95 3.18
375 2360 1.154197 GTTAAGGACCCTGCGTCAAC 58.846 55.000 0.00 0.00 43.95 3.18
376 2361 0.759959 TTAAGGACCCTGCGTCAACA 59.240 50.000 0.00 0.00 43.95 3.33
377 2362 0.320374 TAAGGACCCTGCGTCAACAG 59.680 55.000 0.00 0.00 43.95 3.16
391 2376 1.795872 TCAACAGGCGACATTGTTACG 59.204 47.619 5.30 0.00 35.86 3.18
394 2379 1.270412 ACAGGCGACATTGTTACGGAA 60.270 47.619 0.00 0.00 0.00 4.30
395 2380 1.801771 CAGGCGACATTGTTACGGAAA 59.198 47.619 0.00 0.00 0.00 3.13
396 2381 2.224549 CAGGCGACATTGTTACGGAAAA 59.775 45.455 0.00 0.00 0.00 2.29
397 2382 2.879646 AGGCGACATTGTTACGGAAAAA 59.120 40.909 0.00 0.00 0.00 1.94
398 2383 3.504520 AGGCGACATTGTTACGGAAAAAT 59.495 39.130 0.00 0.00 0.00 1.82
406 2409 8.355272 ACATTGTTACGGAAAAATTTGTTACC 57.645 30.769 0.00 0.00 0.00 2.85
408 2411 5.517904 TGTTACGGAAAAATTTGTTACCGG 58.482 37.500 20.81 0.00 43.76 5.28
411 2414 2.288273 CGGAAAAATTTGTTACCGGCCA 60.288 45.455 0.00 0.00 37.28 5.36
423 2426 2.580326 CGGCCATGCATTGCGAAC 60.580 61.111 15.83 2.45 0.00 3.95
424 2427 2.580326 GGCCATGCATTGCGAACG 60.580 61.111 15.83 0.00 0.00 3.95
426 2429 3.050166 GCCATGCATTGCGAACGGA 62.050 57.895 7.04 0.00 0.00 4.69
436 2439 2.853731 TGCGAACGGAAAACATTGTT 57.146 40.000 0.00 0.00 0.00 2.83
444 2448 3.626670 ACGGAAAACATTGTTTACGACCA 59.373 39.130 29.71 0.00 45.79 4.02
448 2452 4.846779 AAACATTGTTTACGACCATGCT 57.153 36.364 12.98 0.00 35.38 3.79
449 2453 5.950758 AAACATTGTTTACGACCATGCTA 57.049 34.783 12.98 0.00 35.38 3.49
457 2461 1.220529 ACGACCATGCTATGCGAATG 58.779 50.000 0.00 0.00 0.00 2.67
480 2484 4.384547 GGAAAACATTGTTTACGACCATGC 59.615 41.667 14.81 0.06 35.38 4.06
481 2485 3.569250 AACATTGTTTACGACCATGCC 57.431 42.857 0.00 0.00 35.38 4.40
482 2486 2.509569 ACATTGTTTACGACCATGCCA 58.490 42.857 0.00 0.00 35.38 4.92
483 2487 3.088532 ACATTGTTTACGACCATGCCAT 58.911 40.909 0.00 0.00 35.38 4.40
484 2488 3.119531 ACATTGTTTACGACCATGCCATG 60.120 43.478 0.00 0.00 35.38 3.66
485 2489 0.808125 TGTTTACGACCATGCCATGC 59.192 50.000 0.00 0.00 0.00 4.06
486 2490 0.248054 GTTTACGACCATGCCATGCG 60.248 55.000 0.00 0.97 0.00 4.73
487 2491 0.391793 TTTACGACCATGCCATGCGA 60.392 50.000 10.94 0.00 0.00 5.10
488 2492 0.391793 TTACGACCATGCCATGCGAA 60.392 50.000 10.94 0.48 0.00 4.70
489 2493 1.087202 TACGACCATGCCATGCGAAC 61.087 55.000 10.94 0.00 0.00 3.95
490 2494 2.404789 GACCATGCCATGCGAACG 59.595 61.111 0.00 0.00 0.00 3.95
491 2495 3.112126 GACCATGCCATGCGAACGG 62.112 63.158 0.00 0.00 0.00 4.44
492 2496 2.823593 CCATGCCATGCGAACGGA 60.824 61.111 0.00 0.00 0.00 4.69
493 2497 2.405805 CCATGCCATGCGAACGGAA 61.406 57.895 0.00 0.00 0.00 4.30
494 2498 1.505807 CATGCCATGCGAACGGAAA 59.494 52.632 0.00 0.00 0.00 3.13
495 2499 0.109365 CATGCCATGCGAACGGAAAA 60.109 50.000 0.00 0.00 0.00 2.29
496 2500 0.109319 ATGCCATGCGAACGGAAAAC 60.109 50.000 0.00 0.00 0.00 2.43
497 2501 1.284408 GCCATGCGAACGGAAAACA 59.716 52.632 0.00 0.00 0.00 2.83
498 2502 0.109319 GCCATGCGAACGGAAAACAT 60.109 50.000 0.00 0.00 0.00 2.71
499 2503 1.668628 GCCATGCGAACGGAAAACATT 60.669 47.619 0.00 0.00 0.00 2.71
500 2504 1.984990 CCATGCGAACGGAAAACATTG 59.015 47.619 0.00 0.00 0.00 2.82
501 2505 2.606795 CCATGCGAACGGAAAACATTGT 60.607 45.455 0.00 0.00 0.00 2.71
502 2506 2.853731 TGCGAACGGAAAACATTGTT 57.146 40.000 0.00 0.00 0.00 2.83
503 2507 3.152261 TGCGAACGGAAAACATTGTTT 57.848 38.095 8.97 8.97 0.00 2.83
504 2508 4.288670 TGCGAACGGAAAACATTGTTTA 57.711 36.364 14.81 0.00 0.00 2.01
505 2509 4.036352 TGCGAACGGAAAACATTGTTTAC 58.964 39.130 14.81 10.20 0.00 2.01
507 2511 4.516359 CGAACGGAAAACATTGTTTACGA 58.484 39.130 29.71 0.00 45.79 3.43
508 2512 4.373672 CGAACGGAAAACATTGTTTACGAC 59.626 41.667 29.71 23.33 45.79 4.34
509 2513 4.213596 ACGGAAAACATTGTTTACGACC 57.786 40.909 29.71 21.40 45.79 4.79
510 2514 3.626670 ACGGAAAACATTGTTTACGACCA 59.373 39.130 29.71 0.00 45.79 4.02
511 2515 4.276431 ACGGAAAACATTGTTTACGACCAT 59.724 37.500 29.71 15.08 45.79 3.55
512 2516 4.615121 CGGAAAACATTGTTTACGACCATG 59.385 41.667 23.67 9.19 45.79 3.66
513 2517 4.384547 GGAAAACATTGTTTACGACCATGC 59.615 41.667 14.81 0.06 35.38 4.06
522 2526 0.739462 TACGACCATGCCTTGCGAAG 60.739 55.000 0.00 0.00 0.00 3.79
525 2529 1.372087 GACCATGCCTTGCGAAGAGG 61.372 60.000 0.00 0.00 37.35 3.69
539 2543 3.424433 GCGAAGAGGAAACATTGTTACCG 60.424 47.826 1.76 0.56 0.00 4.02
541 2545 4.143179 CGAAGAGGAAACATTGTTACCGAC 60.143 45.833 1.76 0.00 0.00 4.79
542 2546 3.671716 AGAGGAAACATTGTTACCGACC 58.328 45.455 1.76 2.72 0.00 4.79
543 2547 3.326880 AGAGGAAACATTGTTACCGACCT 59.673 43.478 1.76 7.06 0.00 3.85
544 2548 4.070009 GAGGAAACATTGTTACCGACCTT 58.930 43.478 1.76 0.00 0.00 3.50
545 2549 3.818773 AGGAAACATTGTTACCGACCTTG 59.181 43.478 1.76 0.00 0.00 3.61
546 2550 3.561503 GAAACATTGTTACCGACCTTGC 58.438 45.455 1.76 0.00 0.00 4.01
547 2551 2.264005 ACATTGTTACCGACCTTGCA 57.736 45.000 0.00 0.00 0.00 4.08
550 2554 3.057596 ACATTGTTACCGACCTTGCATTG 60.058 43.478 0.00 0.00 0.00 2.82
551 2555 0.878416 TGTTACCGACCTTGCATTGC 59.122 50.000 0.46 0.46 0.00 3.56
553 2557 0.320858 TTACCGACCTTGCATTGCGA 60.321 50.000 3.84 0.59 0.00 5.10
555 2559 0.960364 ACCGACCTTGCATTGCGAAT 60.960 50.000 3.84 0.00 0.00 3.34
556 2560 1.013596 CCGACCTTGCATTGCGAATA 58.986 50.000 3.84 0.00 0.00 1.75
557 2561 1.003545 CCGACCTTGCATTGCGAATAG 60.004 52.381 3.84 0.00 0.00 1.73
558 2562 1.003545 CGACCTTGCATTGCGAATAGG 60.004 52.381 13.90 13.90 0.00 2.57
559 2563 2.288666 GACCTTGCATTGCGAATAGGA 58.711 47.619 19.41 0.00 0.00 2.94
560 2564 2.682856 GACCTTGCATTGCGAATAGGAA 59.317 45.455 19.41 1.72 33.77 3.36
563 2567 4.887071 ACCTTGCATTGCGAATAGGAAATA 59.113 37.500 19.41 0.00 32.72 1.40
566 2570 6.364165 CCTTGCATTGCGAATAGGAAATATTG 59.636 38.462 3.84 0.00 34.10 1.90
567 2571 6.389830 TGCATTGCGAATAGGAAATATTGT 57.610 33.333 3.84 0.00 34.10 2.71
568 2572 6.207928 TGCATTGCGAATAGGAAATATTGTG 58.792 36.000 3.84 0.00 34.10 3.33
570 2574 6.917477 GCATTGCGAATAGGAAATATTGTGAA 59.083 34.615 0.00 0.00 34.10 3.18
571 2575 7.596248 GCATTGCGAATAGGAAATATTGTGAAT 59.404 33.333 0.00 0.00 34.10 2.57
572 2576 9.467258 CATTGCGAATAGGAAATATTGTGAATT 57.533 29.630 0.00 0.00 34.10 2.17
574 2578 7.995289 TGCGAATAGGAAATATTGTGAATTGT 58.005 30.769 0.00 0.00 34.10 2.71
575 2579 8.465999 TGCGAATAGGAAATATTGTGAATTGTT 58.534 29.630 0.00 0.00 34.10 2.83
582 2586 8.241367 AGGAAATATTGTGAATTGTTTACGACC 58.759 33.333 0.00 0.00 0.00 4.79
584 2588 9.567848 GAAATATTGTGAATTGTTTACGACCAT 57.432 29.630 0.00 0.00 0.00 3.55
585 2589 8.909708 AATATTGTGAATTGTTTACGACCATG 57.090 30.769 0.00 0.00 0.00 3.66
586 2590 4.153958 TGTGAATTGTTTACGACCATGC 57.846 40.909 0.00 0.00 0.00 4.06
587 2591 3.818210 TGTGAATTGTTTACGACCATGCT 59.182 39.130 0.00 0.00 0.00 3.79
591 2595 7.334671 TGTGAATTGTTTACGACCATGCTAATA 59.665 33.333 0.00 0.00 0.00 0.98
598 2602 9.647797 TGTTTACGACCATGCTAATATAATAGG 57.352 33.333 0.00 0.00 0.00 2.57
600 2604 6.294361 ACGACCATGCTAATATAATAGGCA 57.706 37.500 0.00 0.00 37.32 4.75
602 2606 7.165485 ACGACCATGCTAATATAATAGGCAAA 58.835 34.615 0.00 0.00 36.49 3.68
605 2609 7.830739 ACCATGCTAATATAATAGGCAAAAGC 58.169 34.615 0.00 0.00 36.49 3.51
606 2610 7.451255 ACCATGCTAATATAATAGGCAAAAGCA 59.549 33.333 0.00 0.00 41.22 3.91
631 2635 2.631160 TTTCCTTGAGAGAAACCGCA 57.369 45.000 0.00 0.00 0.00 5.69
677 2706 5.772825 TCTTTTTGTTGATCACTGGAAGG 57.227 39.130 0.00 0.00 39.30 3.46
693 2771 5.105473 ACTGGAAGGCATCAAATGAAATCAG 60.105 40.000 0.00 0.00 39.30 2.90
697 2775 7.046033 GGAAGGCATCAAATGAAATCAGAATT 58.954 34.615 0.00 0.00 0.00 2.17
791 2870 1.188863 ATGATTTCAGGTTGCCAGCC 58.811 50.000 0.00 0.00 0.00 4.85
792 2871 0.112995 TGATTTCAGGTTGCCAGCCT 59.887 50.000 0.00 0.00 36.66 4.58
793 2872 1.354031 TGATTTCAGGTTGCCAGCCTA 59.646 47.619 0.00 0.00 34.45 3.93
794 2873 1.745653 GATTTCAGGTTGCCAGCCTAC 59.254 52.381 0.00 0.00 34.45 3.18
795 2874 0.251165 TTTCAGGTTGCCAGCCTACC 60.251 55.000 0.00 3.51 34.45 3.18
796 2875 1.422977 TTCAGGTTGCCAGCCTACCA 61.423 55.000 0.00 0.00 34.45 3.25
797 2876 1.675641 CAGGTTGCCAGCCTACCAC 60.676 63.158 0.00 0.00 34.45 4.16
798 2877 2.746277 GGTTGCCAGCCTACCACG 60.746 66.667 6.24 0.00 32.12 4.94
799 2878 2.345991 GTTGCCAGCCTACCACGA 59.654 61.111 0.00 0.00 0.00 4.35
800 2879 2.033194 GTTGCCAGCCTACCACGAC 61.033 63.158 0.00 0.00 0.00 4.34
801 2880 3.583276 TTGCCAGCCTACCACGACG 62.583 63.158 0.00 0.00 0.00 5.12
802 2881 4.065281 GCCAGCCTACCACGACGT 62.065 66.667 0.00 0.00 0.00 4.34
803 2882 2.654877 CCAGCCTACCACGACGTT 59.345 61.111 0.00 0.00 0.00 3.99
804 2883 1.005394 CCAGCCTACCACGACGTTT 60.005 57.895 0.00 0.00 0.00 3.60
805 2884 1.012486 CCAGCCTACCACGACGTTTC 61.012 60.000 0.00 0.00 0.00 2.78
807 2886 1.200716 CAGCCTACCACGACGTTTCTA 59.799 52.381 0.00 0.00 0.00 2.10
808 2887 2.097825 AGCCTACCACGACGTTTCTAT 58.902 47.619 0.00 0.00 0.00 1.98
809 2888 2.159282 AGCCTACCACGACGTTTCTATG 60.159 50.000 0.00 0.00 0.00 2.23
813 2892 5.401550 CCTACCACGACGTTTCTATGTTTA 58.598 41.667 0.00 0.00 0.00 2.01
909 2988 1.359130 AGCCCAAAGCCCAAATAGAGT 59.641 47.619 0.00 0.00 45.47 3.24
927 3006 3.528370 CCGATCCGGCTCCGAAGT 61.528 66.667 10.28 0.00 41.17 3.01
928 3007 2.026301 CGATCCGGCTCCGAAGTC 59.974 66.667 10.28 4.03 42.83 3.01
936 3015 4.775746 CTCCGAAGTCGAGAGCAC 57.224 61.111 1.43 0.00 43.02 4.40
937 3016 1.876664 CTCCGAAGTCGAGAGCACA 59.123 57.895 1.43 0.00 43.02 4.57
938 3017 0.455295 CTCCGAAGTCGAGAGCACAC 60.455 60.000 1.43 0.00 43.02 3.82
939 3018 1.170290 TCCGAAGTCGAGAGCACACA 61.170 55.000 1.43 0.00 43.02 3.72
940 3019 0.318699 CCGAAGTCGAGAGCACACAA 60.319 55.000 1.43 0.00 43.02 3.33
944 3023 0.459899 AGTCGAGAGCACACAACACA 59.540 50.000 0.00 0.00 0.00 3.72
963 3042 4.112341 GCCGCAGCAGCTCCAAAG 62.112 66.667 0.00 0.00 39.53 2.77
1025 3117 2.666812 GACGACCCCGGTTCCATT 59.333 61.111 0.00 0.00 40.78 3.16
1116 3208 2.683572 TCCCTCGCCAGCAAGCTA 60.684 61.111 0.00 0.00 0.00 3.32
1374 3496 3.011144 TGCTCTTCATTTGGAACCCCATA 59.989 43.478 0.00 0.00 43.12 2.74
1377 3499 4.349365 TCTTCATTTGGAACCCCATAACC 58.651 43.478 0.00 0.00 43.12 2.85
1659 3845 1.750399 CATTGAGGCAAGACCCCCG 60.750 63.158 0.00 0.00 40.58 5.73
2326 7874 7.037438 ACTAATTGTGCTTATTTGATTGGCAG 58.963 34.615 0.00 0.00 33.47 4.85
2458 8020 3.436704 GGCGACTCTCATCATCACAAAAA 59.563 43.478 0.00 0.00 0.00 1.94
2794 10045 2.022195 CTGTATGCTGGCTTGCTGATT 58.978 47.619 4.89 0.00 0.00 2.57
2916 10167 6.895756 TCTTGAGCTATAAGTTGAGGGAACTA 59.104 38.462 9.34 0.00 44.68 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.060615 CTTGGGCTGCTGCTCCAC 61.061 66.667 20.13 8.58 39.40 4.02
2 3 3.251509 TCTTGGGCTGCTGCTCCA 61.252 61.111 13.44 15.94 39.40 3.86
3 4 2.268167 ATCTCTTGGGCTGCTGCTCC 62.268 60.000 13.44 13.60 39.40 4.70
4 5 0.467384 TATCTCTTGGGCTGCTGCTC 59.533 55.000 15.64 12.43 40.87 4.26
5 6 1.072015 GATATCTCTTGGGCTGCTGCT 59.928 52.381 15.64 0.00 39.59 4.24
6 7 1.521580 GATATCTCTTGGGCTGCTGC 58.478 55.000 7.10 7.10 38.76 5.25
7 8 1.419012 TGGATATCTCTTGGGCTGCTG 59.581 52.381 2.05 0.00 0.00 4.41
8 9 1.698532 CTGGATATCTCTTGGGCTGCT 59.301 52.381 2.05 0.00 0.00 4.24
9 10 1.271271 CCTGGATATCTCTTGGGCTGC 60.271 57.143 2.05 0.00 0.00 5.25
10 11 1.271271 GCCTGGATATCTCTTGGGCTG 60.271 57.143 0.00 0.00 35.73 4.85
11 12 1.063183 GCCTGGATATCTCTTGGGCT 58.937 55.000 0.00 0.00 35.73 5.19
12 13 0.767375 TGCCTGGATATCTCTTGGGC 59.233 55.000 0.00 9.62 38.67 5.36
13 14 1.350351 CCTGCCTGGATATCTCTTGGG 59.650 57.143 0.00 0.03 38.35 4.12
14 15 1.271271 GCCTGCCTGGATATCTCTTGG 60.271 57.143 0.00 1.67 38.35 3.61
15 16 1.607509 CGCCTGCCTGGATATCTCTTG 60.608 57.143 0.00 0.00 38.35 3.02
16 17 0.683973 CGCCTGCCTGGATATCTCTT 59.316 55.000 0.00 0.00 38.35 2.85
17 18 0.178950 TCGCCTGCCTGGATATCTCT 60.179 55.000 0.00 0.00 38.35 3.10
18 19 0.901124 ATCGCCTGCCTGGATATCTC 59.099 55.000 0.00 0.00 38.35 2.75
19 20 0.901124 GATCGCCTGCCTGGATATCT 59.099 55.000 0.00 0.00 38.35 1.98
20 21 0.459237 CGATCGCCTGCCTGGATATC 60.459 60.000 0.26 0.00 38.35 1.63
21 22 1.188219 ACGATCGCCTGCCTGGATAT 61.188 55.000 16.60 0.00 38.35 1.63
22 23 0.538746 TACGATCGCCTGCCTGGATA 60.539 55.000 16.60 0.00 38.35 2.59
23 24 1.832608 TACGATCGCCTGCCTGGAT 60.833 57.895 16.60 0.00 38.35 3.41
24 25 2.441348 TACGATCGCCTGCCTGGA 60.441 61.111 16.60 0.00 38.35 3.86
25 26 2.279517 GTACGATCGCCTGCCTGG 60.280 66.667 16.60 0.00 39.35 4.45
26 27 2.655364 CGTACGATCGCCTGCCTG 60.655 66.667 16.60 0.00 0.00 4.85
27 28 3.900892 CCGTACGATCGCCTGCCT 61.901 66.667 18.76 0.00 0.00 4.75
29 30 3.190323 TAGCCGTACGATCGCCTGC 62.190 63.158 18.76 13.78 0.00 4.85
30 31 1.082038 CTAGCCGTACGATCGCCTG 60.082 63.158 18.76 4.46 0.00 4.85
31 32 2.905807 GCTAGCCGTACGATCGCCT 61.906 63.158 18.76 6.55 0.00 5.52
32 33 2.428735 GCTAGCCGTACGATCGCC 60.429 66.667 18.76 5.06 0.00 5.54
33 34 1.298863 TTGCTAGCCGTACGATCGC 60.299 57.895 18.76 12.05 0.00 4.58
34 35 1.260198 CGTTGCTAGCCGTACGATCG 61.260 60.000 18.76 14.88 36.16 3.69
35 36 1.538117 GCGTTGCTAGCCGTACGATC 61.538 60.000 27.56 8.14 36.16 3.69
36 37 1.588139 GCGTTGCTAGCCGTACGAT 60.588 57.895 27.56 7.55 36.16 3.73
37 38 2.202518 GCGTTGCTAGCCGTACGA 60.203 61.111 27.56 2.53 36.16 3.43
38 39 3.252484 GGCGTTGCTAGCCGTACG 61.252 66.667 22.25 22.25 45.58 3.67
44 45 0.039165 AAAGCTTTGGCGTTGCTAGC 60.039 50.000 11.80 8.10 44.37 3.42
45 46 1.689959 CAAAGCTTTGGCGTTGCTAG 58.310 50.000 28.12 1.54 46.73 3.42
46 47 3.863681 CAAAGCTTTGGCGTTGCTA 57.136 47.368 28.12 0.00 46.73 3.49
47 48 4.736165 CAAAGCTTTGGCGTTGCT 57.264 50.000 28.12 0.00 46.73 3.91
50 51 0.385390 CTCCACAAAGCTTTGGCGTT 59.615 50.000 35.65 17.44 42.34 4.84
51 52 1.455383 CCTCCACAAAGCTTTGGCGT 61.455 55.000 35.65 17.78 42.34 5.68
52 53 1.286880 CCTCCACAAAGCTTTGGCG 59.713 57.895 35.65 26.92 42.34 5.69
53 54 1.005748 GCCTCCACAAAGCTTTGGC 60.006 57.895 35.65 27.09 42.34 4.52
54 55 0.600057 GAGCCTCCACAAAGCTTTGG 59.400 55.000 35.65 24.11 42.34 3.28
55 56 0.600057 GGAGCCTCCACAAAGCTTTG 59.400 55.000 32.53 32.53 43.62 2.77
56 57 0.540597 GGGAGCCTCCACAAAGCTTT 60.541 55.000 13.90 5.69 38.64 3.51
57 58 1.075659 GGGAGCCTCCACAAAGCTT 59.924 57.895 13.90 0.00 38.64 3.74
58 59 2.134630 CTGGGAGCCTCCACAAAGCT 62.135 60.000 13.90 0.00 38.64 3.74
59 60 1.676967 CTGGGAGCCTCCACAAAGC 60.677 63.158 13.90 0.00 38.64 3.51
60 61 1.676967 GCTGGGAGCCTCCACAAAG 60.677 63.158 13.90 5.42 38.64 2.77
61 62 2.129555 GAGCTGGGAGCCTCCACAAA 62.130 60.000 13.90 0.00 43.77 2.83
62 63 2.530151 AGCTGGGAGCCTCCACAA 60.530 61.111 13.90 0.00 43.77 3.33
63 64 3.005539 GAGCTGGGAGCCTCCACA 61.006 66.667 13.90 7.39 43.77 4.17
64 65 4.154347 CGAGCTGGGAGCCTCCAC 62.154 72.222 13.90 2.57 43.77 4.02
71 72 1.690219 ATAACAGGGCGAGCTGGGAG 61.690 60.000 0.00 0.00 0.00 4.30
72 73 0.397957 TATAACAGGGCGAGCTGGGA 60.398 55.000 0.00 0.00 0.00 4.37
73 74 0.249911 GTATAACAGGGCGAGCTGGG 60.250 60.000 0.00 0.00 0.00 4.45
74 75 0.753262 AGTATAACAGGGCGAGCTGG 59.247 55.000 0.00 0.00 0.00 4.85
75 76 1.137086 ACAGTATAACAGGGCGAGCTG 59.863 52.381 0.00 0.00 0.00 4.24
76 77 1.486211 ACAGTATAACAGGGCGAGCT 58.514 50.000 0.00 0.00 0.00 4.09
77 78 2.311124 AACAGTATAACAGGGCGAGC 57.689 50.000 0.00 0.00 0.00 5.03
78 79 5.007385 ACTAAACAGTATAACAGGGCGAG 57.993 43.478 0.00 0.00 0.00 5.03
79 80 6.528537 TTACTAAACAGTATAACAGGGCGA 57.471 37.500 0.00 0.00 0.00 5.54
80 81 7.279313 ACAATTACTAAACAGTATAACAGGGCG 59.721 37.037 0.00 0.00 0.00 6.13
81 82 8.502105 ACAATTACTAAACAGTATAACAGGGC 57.498 34.615 0.00 0.00 0.00 5.19
82 83 9.886132 AGACAATTACTAAACAGTATAACAGGG 57.114 33.333 0.00 0.00 0.00 4.45
91 92 9.561069 AGACATTTCAGACAATTACTAAACAGT 57.439 29.630 0.00 0.00 0.00 3.55
97 98 9.219603 CCTTGAAGACATTTCAGACAATTACTA 57.780 33.333 0.00 0.00 0.00 1.82
98 99 7.721399 ACCTTGAAGACATTTCAGACAATTACT 59.279 33.333 0.00 0.00 0.00 2.24
99 100 7.875971 ACCTTGAAGACATTTCAGACAATTAC 58.124 34.615 0.00 0.00 0.00 1.89
100 101 7.939039 AGACCTTGAAGACATTTCAGACAATTA 59.061 33.333 0.00 0.00 0.00 1.40
101 102 6.774656 AGACCTTGAAGACATTTCAGACAATT 59.225 34.615 0.00 0.00 0.00 2.32
131 132 2.777692 TGTTCCTCCCTCTGTTCACTTT 59.222 45.455 0.00 0.00 0.00 2.66
141 142 2.629051 CCGTAACATTGTTCCTCCCTC 58.371 52.381 5.07 0.00 0.00 4.30
255 2240 1.135517 CAATGTTTTTCGGGTAGCCGG 60.136 52.381 31.34 14.26 0.00 6.13
269 2254 6.828785 GTGACAATAGGATCCCTAACAATGTT 59.171 38.462 8.55 3.43 39.77 2.71
369 2354 0.586319 AACAATGTCGCCTGTTGACG 59.414 50.000 0.00 0.00 39.22 4.35
370 2355 2.411031 CGTAACAATGTCGCCTGTTGAC 60.411 50.000 0.00 0.00 36.47 3.18
371 2356 1.795872 CGTAACAATGTCGCCTGTTGA 59.204 47.619 0.00 0.00 36.47 3.18
372 2357 1.136085 CCGTAACAATGTCGCCTGTTG 60.136 52.381 0.00 0.00 36.47 3.33
373 2358 1.153353 CCGTAACAATGTCGCCTGTT 58.847 50.000 0.00 0.00 39.13 3.16
374 2359 0.319083 TCCGTAACAATGTCGCCTGT 59.681 50.000 0.00 0.00 0.00 4.00
375 2360 1.434555 TTCCGTAACAATGTCGCCTG 58.565 50.000 0.00 0.00 0.00 4.85
376 2361 2.172851 TTTCCGTAACAATGTCGCCT 57.827 45.000 0.00 0.00 0.00 5.52
377 2362 2.973419 TTTTCCGTAACAATGTCGCC 57.027 45.000 0.00 0.00 0.00 5.54
378 2363 5.174216 ACAAATTTTTCCGTAACAATGTCGC 59.826 36.000 0.00 0.00 0.00 5.19
379 2364 6.741448 ACAAATTTTTCCGTAACAATGTCG 57.259 33.333 0.00 0.00 0.00 4.35
380 2365 8.481641 GGTAACAAATTTTTCCGTAACAATGTC 58.518 33.333 0.00 0.00 0.00 3.06
391 2376 3.388345 TGGCCGGTAACAAATTTTTCC 57.612 42.857 1.90 0.00 0.00 3.13
394 2379 2.037772 TGCATGGCCGGTAACAAATTTT 59.962 40.909 1.90 0.00 0.00 1.82
395 2380 1.620819 TGCATGGCCGGTAACAAATTT 59.379 42.857 1.90 0.00 0.00 1.82
396 2381 1.261480 TGCATGGCCGGTAACAAATT 58.739 45.000 1.90 0.00 0.00 1.82
397 2382 1.484038 ATGCATGGCCGGTAACAAAT 58.516 45.000 1.90 0.00 0.00 2.32
398 2383 1.067283 CAATGCATGGCCGGTAACAAA 60.067 47.619 1.90 0.00 0.00 2.83
406 2409 2.580326 GTTCGCAATGCATGGCCG 60.580 61.111 20.50 14.90 0.00 6.13
408 2411 2.540736 TTCCGTTCGCAATGCATGGC 62.541 55.000 16.64 16.64 0.00 4.40
411 2414 1.000827 TGTTTTCCGTTCGCAATGCAT 60.001 42.857 5.91 0.00 0.00 3.96
423 2426 4.212213 TGGTCGTAAACAATGTTTTCCG 57.788 40.909 16.99 17.76 0.00 4.30
424 2427 4.384547 GCATGGTCGTAAACAATGTTTTCC 59.615 41.667 16.99 13.75 40.89 3.13
426 2429 5.195001 AGCATGGTCGTAAACAATGTTTT 57.805 34.783 16.99 1.69 40.89 2.43
436 2439 2.588027 TTCGCATAGCATGGTCGTAA 57.412 45.000 0.00 0.00 0.00 3.18
444 2448 4.924305 ATGTTTTCCATTCGCATAGCAT 57.076 36.364 0.00 0.00 0.00 3.79
448 2452 6.524933 CGTAAACAATGTTTTCCATTCGCATA 59.475 34.615 16.99 0.00 41.93 3.14
449 2453 5.344665 CGTAAACAATGTTTTCCATTCGCAT 59.655 36.000 16.99 0.00 41.93 4.73
457 2461 4.384547 GCATGGTCGTAAACAATGTTTTCC 59.615 41.667 16.99 13.75 40.89 3.13
470 2474 1.087202 GTTCGCATGGCATGGTCGTA 61.087 55.000 27.48 14.77 0.00 3.43
471 2475 2.046411 TTCGCATGGCATGGTCGT 60.046 55.556 27.48 0.00 0.00 4.34
480 2484 1.984990 CAATGTTTTCCGTTCGCATGG 59.015 47.619 0.00 0.00 0.00 3.66
481 2485 2.660490 ACAATGTTTTCCGTTCGCATG 58.340 42.857 0.00 0.00 0.00 4.06
482 2486 3.363341 AACAATGTTTTCCGTTCGCAT 57.637 38.095 0.00 0.00 0.00 4.73
483 2487 2.853731 AACAATGTTTTCCGTTCGCA 57.146 40.000 0.00 0.00 0.00 5.10
484 2488 3.116700 CGTAAACAATGTTTTCCGTTCGC 59.883 43.478 16.99 0.00 0.00 4.70
485 2489 4.373672 GTCGTAAACAATGTTTTCCGTTCG 59.626 41.667 16.99 11.61 0.00 3.95
486 2490 4.671964 GGTCGTAAACAATGTTTTCCGTTC 59.328 41.667 16.99 14.57 0.00 3.95
487 2491 4.096081 TGGTCGTAAACAATGTTTTCCGTT 59.904 37.500 16.99 0.00 0.00 4.44
488 2492 3.626670 TGGTCGTAAACAATGTTTTCCGT 59.373 39.130 16.99 0.00 0.00 4.69
489 2493 4.212213 TGGTCGTAAACAATGTTTTCCG 57.788 40.909 16.99 17.76 0.00 4.30
490 2494 4.384547 GCATGGTCGTAAACAATGTTTTCC 59.615 41.667 16.99 13.75 40.89 3.13
491 2495 4.384547 GGCATGGTCGTAAACAATGTTTTC 59.615 41.667 16.99 10.82 40.89 2.29
492 2496 4.038642 AGGCATGGTCGTAAACAATGTTTT 59.961 37.500 16.99 1.69 40.89 2.43
493 2497 3.572255 AGGCATGGTCGTAAACAATGTTT 59.428 39.130 16.05 16.05 40.89 2.83
494 2498 3.153919 AGGCATGGTCGTAAACAATGTT 58.846 40.909 0.00 0.00 40.89 2.71
495 2499 2.790433 AGGCATGGTCGTAAACAATGT 58.210 42.857 0.00 0.00 40.89 2.71
496 2500 3.500982 CAAGGCATGGTCGTAAACAATG 58.499 45.455 0.00 0.00 41.62 2.82
497 2501 2.094752 GCAAGGCATGGTCGTAAACAAT 60.095 45.455 0.00 0.00 0.00 2.71
498 2502 1.268352 GCAAGGCATGGTCGTAAACAA 59.732 47.619 0.00 0.00 0.00 2.83
499 2503 0.878416 GCAAGGCATGGTCGTAAACA 59.122 50.000 0.00 0.00 0.00 2.83
500 2504 0.179200 CGCAAGGCATGGTCGTAAAC 60.179 55.000 0.00 0.00 0.00 2.01
501 2505 0.320858 TCGCAAGGCATGGTCGTAAA 60.321 50.000 0.00 0.00 38.47 2.01
502 2506 0.320858 TTCGCAAGGCATGGTCGTAA 60.321 50.000 0.00 0.00 38.47 3.18
503 2507 0.739462 CTTCGCAAGGCATGGTCGTA 60.739 55.000 0.00 0.00 38.47 3.43
504 2508 2.031919 TTCGCAAGGCATGGTCGT 59.968 55.556 0.00 0.00 38.47 4.34
505 2509 1.699656 CTCTTCGCAAGGCATGGTCG 61.700 60.000 0.00 0.00 38.47 4.79
506 2510 1.372087 CCTCTTCGCAAGGCATGGTC 61.372 60.000 0.00 0.00 38.47 4.02
507 2511 1.377725 CCTCTTCGCAAGGCATGGT 60.378 57.895 0.00 0.00 38.47 3.55
508 2512 0.677731 TTCCTCTTCGCAAGGCATGG 60.678 55.000 0.00 0.00 33.65 3.66
509 2513 1.135575 GTTTCCTCTTCGCAAGGCATG 60.136 52.381 0.00 0.00 33.65 4.06
510 2514 1.168714 GTTTCCTCTTCGCAAGGCAT 58.831 50.000 0.00 0.00 33.65 4.40
511 2515 0.179032 TGTTTCCTCTTCGCAAGGCA 60.179 50.000 0.00 0.00 33.65 4.75
512 2516 1.168714 ATGTTTCCTCTTCGCAAGGC 58.831 50.000 0.00 0.00 33.65 4.35
513 2517 2.554032 ACAATGTTTCCTCTTCGCAAGG 59.446 45.455 0.00 0.00 38.47 3.61
522 2526 3.671716 AGGTCGGTAACAATGTTTCCTC 58.328 45.455 17.54 11.12 0.00 3.71
525 2529 3.003897 TGCAAGGTCGGTAACAATGTTTC 59.996 43.478 3.17 0.00 0.00 2.78
539 2543 2.288666 TCCTATTCGCAATGCAAGGTC 58.711 47.619 5.91 0.00 0.00 3.85
541 2545 3.781079 TTTCCTATTCGCAATGCAAGG 57.219 42.857 5.91 6.32 0.00 3.61
542 2546 6.919662 ACAATATTTCCTATTCGCAATGCAAG 59.080 34.615 5.91 0.00 0.00 4.01
543 2547 6.696583 CACAATATTTCCTATTCGCAATGCAA 59.303 34.615 5.91 0.00 0.00 4.08
544 2548 6.039159 TCACAATATTTCCTATTCGCAATGCA 59.961 34.615 5.91 0.00 0.00 3.96
545 2549 6.437928 TCACAATATTTCCTATTCGCAATGC 58.562 36.000 0.00 0.00 0.00 3.56
546 2550 9.467258 AATTCACAATATTTCCTATTCGCAATG 57.533 29.630 0.00 0.00 0.00 2.82
547 2551 9.467258 CAATTCACAATATTTCCTATTCGCAAT 57.533 29.630 0.00 0.00 0.00 3.56
550 2554 8.856490 AACAATTCACAATATTTCCTATTCGC 57.144 30.769 0.00 0.00 0.00 4.70
556 2560 8.241367 GGTCGTAAACAATTCACAATATTTCCT 58.759 33.333 0.00 0.00 0.00 3.36
557 2561 8.024285 TGGTCGTAAACAATTCACAATATTTCC 58.976 33.333 0.00 0.00 0.00 3.13
558 2562 8.958175 TGGTCGTAAACAATTCACAATATTTC 57.042 30.769 0.00 0.00 0.00 2.17
559 2563 9.352784 CATGGTCGTAAACAATTCACAATATTT 57.647 29.630 0.00 0.00 0.00 1.40
560 2564 7.487829 GCATGGTCGTAAACAATTCACAATATT 59.512 33.333 0.00 0.00 0.00 1.28
563 2567 5.048083 AGCATGGTCGTAAACAATTCACAAT 60.048 36.000 0.00 0.00 0.00 2.71
566 2570 4.419522 AGCATGGTCGTAAACAATTCAC 57.580 40.909 0.00 0.00 0.00 3.18
567 2571 6.751514 ATTAGCATGGTCGTAAACAATTCA 57.248 33.333 0.00 0.00 0.00 2.57
572 2576 9.647797 CCTATTATATTAGCATGGTCGTAAACA 57.352 33.333 0.00 0.00 0.00 2.83
574 2578 8.315482 TGCCTATTATATTAGCATGGTCGTAAA 58.685 33.333 0.00 0.00 0.00 2.01
575 2579 7.842982 TGCCTATTATATTAGCATGGTCGTAA 58.157 34.615 0.00 0.00 0.00 3.18
577 2581 6.294361 TGCCTATTATATTAGCATGGTCGT 57.706 37.500 0.00 0.00 0.00 4.34
578 2582 7.609760 TTTGCCTATTATATTAGCATGGTCG 57.390 36.000 0.00 0.00 0.00 4.79
579 2583 7.970614 GCTTTTGCCTATTATATTAGCATGGTC 59.029 37.037 0.00 0.00 40.15 4.02
580 2584 7.451255 TGCTTTTGCCTATTATATTAGCATGGT 59.549 33.333 1.62 1.62 46.87 3.55
581 2585 7.756722 GTGCTTTTGCCTATTATATTAGCATGG 59.243 37.037 0.00 0.00 46.87 3.66
582 2586 8.517878 AGTGCTTTTGCCTATTATATTAGCATG 58.482 33.333 0.00 0.00 46.87 4.06
584 2588 7.502226 ACAGTGCTTTTGCCTATTATATTAGCA 59.498 33.333 0.00 0.00 46.87 3.49
585 2589 7.875971 ACAGTGCTTTTGCCTATTATATTAGC 58.124 34.615 0.00 0.00 46.87 3.09
591 2595 7.561356 AGGAAATACAGTGCTTTTGCCTATTAT 59.439 33.333 6.35 0.00 46.87 1.28
595 2599 4.662278 AGGAAATACAGTGCTTTTGCCTA 58.338 39.130 6.35 0.00 46.87 3.93
596 2600 3.500343 AGGAAATACAGTGCTTTTGCCT 58.500 40.909 6.35 1.35 46.87 4.75
600 2604 6.299141 TCTCTCAAGGAAATACAGTGCTTTT 58.701 36.000 0.00 0.00 0.00 2.27
602 2606 5.489792 TCTCTCAAGGAAATACAGTGCTT 57.510 39.130 0.00 0.00 0.00 3.91
605 2609 5.120830 CGGTTTCTCTCAAGGAAATACAGTG 59.879 44.000 0.00 0.00 35.55 3.66
606 2610 5.238583 CGGTTTCTCTCAAGGAAATACAGT 58.761 41.667 0.00 0.00 35.55 3.55
677 2706 9.114965 CGATAGAATTCTGATTTCATTTGATGC 57.885 33.333 18.47 0.00 39.76 3.91
764 2842 3.187022 GCAACCTGAAATCATTTGCCAAC 59.813 43.478 14.50 0.00 38.13 3.77
787 2866 0.038526 AGAAACGTCGTGGTAGGCTG 60.039 55.000 0.00 0.00 0.00 4.85
791 2870 8.124823 TCTATAAACATAGAAACGTCGTGGTAG 58.875 37.037 0.00 0.00 30.79 3.18
792 2871 7.984391 TCTATAAACATAGAAACGTCGTGGTA 58.016 34.615 0.00 0.00 30.79 3.25
793 2872 6.855836 TCTATAAACATAGAAACGTCGTGGT 58.144 36.000 0.00 0.00 30.79 4.16
794 2873 7.745022 TTCTATAAACATAGAAACGTCGTGG 57.255 36.000 0.00 0.00 39.43 4.94
856 2935 1.874739 CGTCGTGGTAGGCCTCAAAAA 60.875 52.381 9.68 0.00 35.27 1.94
857 2936 0.320073 CGTCGTGGTAGGCCTCAAAA 60.320 55.000 9.68 0.00 35.27 2.44
858 2937 1.290955 CGTCGTGGTAGGCCTCAAA 59.709 57.895 9.68 0.00 35.27 2.69
859 2938 1.904865 ACGTCGTGGTAGGCCTCAA 60.905 57.895 9.68 0.00 35.27 3.02
860 2939 2.282674 ACGTCGTGGTAGGCCTCA 60.283 61.111 9.68 0.00 35.27 3.86
861 2940 2.181021 CACGTCGTGGTAGGCCTC 59.819 66.667 17.75 0.00 35.27 4.70
862 2941 2.599578 ACACGTCGTGGTAGGCCT 60.600 61.111 27.77 11.78 37.94 5.19
863 2942 2.431942 CACACGTCGTGGTAGGCC 60.432 66.667 27.77 0.00 42.34 5.19
919 2998 0.455295 GTGTGCTCTCGACTTCGGAG 60.455 60.000 10.84 10.84 40.29 4.63
920 2999 1.170290 TGTGTGCTCTCGACTTCGGA 61.170 55.000 0.00 0.00 40.29 4.55
921 3000 0.318699 TTGTGTGCTCTCGACTTCGG 60.319 55.000 0.00 0.00 40.29 4.30
922 3001 0.778815 GTTGTGTGCTCTCGACTTCG 59.221 55.000 0.00 0.00 41.45 3.79
924 3003 1.134818 TGTGTTGTGTGCTCTCGACTT 60.135 47.619 9.05 0.00 0.00 3.01
925 3004 0.459899 TGTGTTGTGTGCTCTCGACT 59.540 50.000 9.05 0.00 0.00 4.18
926 3005 0.577269 GTGTGTTGTGTGCTCTCGAC 59.423 55.000 2.03 2.03 0.00 4.20
927 3006 0.869880 CGTGTGTTGTGTGCTCTCGA 60.870 55.000 0.00 0.00 0.00 4.04
928 3007 1.559814 CGTGTGTTGTGTGCTCTCG 59.440 57.895 0.00 0.00 0.00 4.04
929 3008 1.276844 GCGTGTGTTGTGTGCTCTC 59.723 57.895 0.00 0.00 0.00 3.20
930 3009 2.180204 GGCGTGTGTTGTGTGCTCT 61.180 57.895 0.00 0.00 0.00 4.09
931 3010 2.327940 GGCGTGTGTTGTGTGCTC 59.672 61.111 0.00 0.00 0.00 4.26
932 3011 3.572539 CGGCGTGTGTTGTGTGCT 61.573 61.111 0.00 0.00 0.00 4.40
935 3014 3.572539 CTGCGGCGTGTGTTGTGT 61.573 61.111 9.37 0.00 0.00 3.72
936 3015 4.962122 GCTGCGGCGTGTGTTGTG 62.962 66.667 9.37 0.00 0.00 3.33
938 3017 4.671549 CTGCTGCGGCGTGTGTTG 62.672 66.667 13.96 0.00 42.25 3.33
959 3038 4.911901 TCCGGTGGGGAAACTTTG 57.088 55.556 0.00 0.00 43.62 2.77
994 3073 4.246206 CGTCGGCGGCATAGTCGA 62.246 66.667 13.62 0.00 46.60 4.20
996 3075 2.654404 GTCGTCGGCGGCATAGTC 60.654 66.667 10.16 0.00 43.09 2.59
1025 3117 0.247736 GAGAAGCTCTTCCGGCAGAA 59.752 55.000 5.05 0.00 40.33 3.02
1884 4100 1.070786 GGCAACTCCGTGAGAACCA 59.929 57.895 7.76 0.00 33.32 3.67
1948 4164 4.518249 AGATCTTCCTCGGGATTTTGAAC 58.482 43.478 0.00 0.00 0.00 3.18
2160 5434 8.743714 ACTTTAAGCTTATTCCCAAATCAGAAG 58.256 33.333 7.08 5.69 0.00 2.85
2162 5436 9.920946 ATACTTTAAGCTTATTCCCAAATCAGA 57.079 29.630 7.08 0.00 0.00 3.27
2458 8020 0.400213 TCGCCTCCAAGTTGGTCATT 59.600 50.000 21.35 0.00 39.03 2.57
2651 8311 3.284617 AGAGCAAACTGTACCGGTTTTT 58.715 40.909 15.04 4.80 40.45 1.94
2658 8318 2.100605 CTGGGAGAGCAAACTGTACC 57.899 55.000 0.00 0.00 40.82 3.34
2916 10167 5.722263 CAGATCACATCTTCTCAGTCAGTT 58.278 41.667 0.00 0.00 37.58 3.16
2993 10252 7.330208 GCAAGAAACAATGAACAAATAGCTGAT 59.670 33.333 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.