Multiple sequence alignment - TraesCS2B01G278900

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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 TraesCS2B01G278900 chr2B 100.000 2549 0 0 1 2549 384810747 384808199 0.000000e+00 4708
1 TraesCS2B01G278900 chr2B 96.438 1544 52 3 567 2110 544319641 544318101 0.000000e+00 2543
2 TraesCS2B01G278900 chr2B 96.258 1550 56 2 562 2110 602077190 602075642 0.000000e+00 2540
3 TraesCS2B01G278900 chr2B 96.373 1544 53 3 567 2110 543889470 543887930 0.000000e+00 2538
4 TraesCS2B01G278900 chr2B 96.296 108 3 1 460 566 384825299 384825406 2.610000e-40 176
5 TraesCS2B01G278900 chr1B 96.578 1987 64 3 563 2549 154580590 154582572 0.000000e+00 3290
6 TraesCS2B01G278900 chr1B 96.313 1546 54 2 566 2111 498442420 498440878 0.000000e+00 2536
7 TraesCS2B01G278900 chr1B 95.327 107 5 0 460 566 243582494 243582600 1.210000e-38 171
8 TraesCS2B01G278900 chr7B 95.861 1981 76 5 566 2546 670173344 670171370 0.000000e+00 3199
9 TraesCS2B01G278900 chr7B 96.962 1580 42 3 970 2549 256815348 256813775 0.000000e+00 2647
10 TraesCS2B01G278900 chr7B 93.757 849 35 8 1709 2549 523398516 523397678 0.000000e+00 1258
11 TraesCS2B01G278900 chr7B 93.735 846 36 9 1709 2546 523523738 523522902 0.000000e+00 1253
12 TraesCS2B01G278900 chr7B 91.633 490 15 1 1 464 457259308 457259797 0.000000e+00 654
13 TraesCS2B01G278900 chr7B 95.146 103 5 0 463 565 536458081 536457979 2.030000e-36 163
14 TraesCS2B01G278900 chr7B 94.231 104 6 0 463 566 52400685 52400582 2.620000e-35 159
15 TraesCS2B01G278900 chr7B 93.458 107 7 0 460 566 286583654 286583760 2.620000e-35 159
16 TraesCS2B01G278900 chr7B 94.286 105 5 1 463 566 299168485 299168381 2.620000e-35 159
17 TraesCS2B01G278900 chr7B 94.231 104 6 0 463 566 321515651 321515548 2.620000e-35 159
18 TraesCS2B01G278900 chr5B 96.456 1552 51 3 561 2111 446193261 446191713 0.000000e+00 2558
19 TraesCS2B01G278900 chr5B 96.318 1548 53 2 564 2111 317969012 317970555 0.000000e+00 2540
20 TraesCS2B01G278900 chr5B 93.427 852 38 9 1709 2549 508123189 508122345 0.000000e+00 1247
21 TraesCS2B01G278900 chr5B 80.761 473 72 13 6 464 643735846 643736313 4.030000e-93 351
22 TraesCS2B01G278900 chr3B 94.565 1104 34 11 1457 2549 687026254 687027342 0.000000e+00 1683
23 TraesCS2B01G278900 chr3B 93.705 842 39 8 1709 2541 548473360 548474196 0.000000e+00 1249
24 TraesCS2B01G278900 chr6B 93.529 850 39 8 1709 2549 59432328 59431486 0.000000e+00 1251
25 TraesCS2B01G278900 chr6B 94.635 466 19 3 1 465 542285964 542286424 0.000000e+00 717
26 TraesCS2B01G278900 chr5A 93.458 107 7 0 460 566 276388784 276388890 2.620000e-35 159
27 TraesCS2B01G278900 chr4A 93.458 107 7 0 460 566 195490355 195490461 2.620000e-35 159
28 TraesCS2B01G278900 chr2D 81.421 183 27 7 302 480 105011546 105011725 2.640000e-30 143


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 TraesCS2B01G278900 chr2B 384808199 384810747 2548 True 4708 4708 100.000 1 2549 1 chr2B.!!$R1 2548
1 TraesCS2B01G278900 chr2B 544318101 544319641 1540 True 2543 2543 96.438 567 2110 1 chr2B.!!$R3 1543
2 TraesCS2B01G278900 chr2B 602075642 602077190 1548 True 2540 2540 96.258 562 2110 1 chr2B.!!$R4 1548
3 TraesCS2B01G278900 chr2B 543887930 543889470 1540 True 2538 2538 96.373 567 2110 1 chr2B.!!$R2 1543
4 TraesCS2B01G278900 chr1B 154580590 154582572 1982 False 3290 3290 96.578 563 2549 1 chr1B.!!$F1 1986
5 TraesCS2B01G278900 chr1B 498440878 498442420 1542 True 2536 2536 96.313 566 2111 1 chr1B.!!$R1 1545
6 TraesCS2B01G278900 chr7B 670171370 670173344 1974 True 3199 3199 95.861 566 2546 1 chr7B.!!$R8 1980
7 TraesCS2B01G278900 chr7B 256813775 256815348 1573 True 2647 2647 96.962 970 2549 1 chr7B.!!$R2 1579
8 TraesCS2B01G278900 chr7B 523397678 523398516 838 True 1258 1258 93.757 1709 2549 1 chr7B.!!$R5 840
9 TraesCS2B01G278900 chr7B 523522902 523523738 836 True 1253 1253 93.735 1709 2546 1 chr7B.!!$R6 837
10 TraesCS2B01G278900 chr5B 446191713 446193261 1548 True 2558 2558 96.456 561 2111 1 chr5B.!!$R1 1550
11 TraesCS2B01G278900 chr5B 317969012 317970555 1543 False 2540 2540 96.318 564 2111 1 chr5B.!!$F1 1547
12 TraesCS2B01G278900 chr5B 508122345 508123189 844 True 1247 1247 93.427 1709 2549 1 chr5B.!!$R2 840
13 TraesCS2B01G278900 chr3B 687026254 687027342 1088 False 1683 1683 94.565 1457 2549 1 chr3B.!!$F2 1092
14 TraesCS2B01G278900 chr3B 548473360 548474196 836 False 1249 1249 93.705 1709 2541 1 chr3B.!!$F1 832
15 TraesCS2B01G278900 chr6B 59431486 59432328 842 True 1251 1251 93.529 1709 2549 1 chr6B.!!$R1 840

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
440 441 0.107831 ACAAAGTTCTAGCCCGCACA 59.892 50.0 0.00 0.0 0.00 4.57 F
443 444 0.460284 AAGTTCTAGCCCGCACATCG 60.460 55.0 0.00 0.0 38.08 3.84 F
463 464 0.539669 GGTGGGCCACTTTGCTAGTT 60.540 55.0 33.87 0.0 33.85 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1309 1312 0.533491 AGCATGCGCAACCATTCATT 59.467 45.000 17.11 0.0 42.27 2.57 R
1311 1314 1.213275 CAGCATGCGCAACCATTCA 59.787 52.632 17.11 0.0 42.27 2.57 R
2353 2374 3.559655 TCGAGAACTTGTGGTTGTCATTG 59.440 43.478 6.49 0.0 45.11 2.82 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
20 21 2.934887 TGGTTCATCCAGTATGCATGG 58.065 47.619 10.16 3.54 41.93 3.66
21 22 1.610522 GGTTCATCCAGTATGCATGGC 59.389 52.381 10.16 1.92 37.76 4.40
22 23 2.579873 GTTCATCCAGTATGCATGGCT 58.420 47.619 10.16 4.53 37.76 4.75
23 24 2.954318 GTTCATCCAGTATGCATGGCTT 59.046 45.455 10.16 0.00 37.76 4.35
24 25 2.854963 TCATCCAGTATGCATGGCTTC 58.145 47.619 10.16 0.00 37.76 3.86
25 26 2.173143 TCATCCAGTATGCATGGCTTCA 59.827 45.455 10.16 0.00 37.76 3.02
26 27 3.154710 CATCCAGTATGCATGGCTTCAT 58.845 45.455 10.16 0.00 37.76 2.57
35 36 2.118313 CATGGCTTCATGTGGAGTCA 57.882 50.000 0.00 0.00 42.37 3.41
36 37 2.014857 CATGGCTTCATGTGGAGTCAG 58.985 52.381 1.70 0.00 42.37 3.51
37 38 0.325933 TGGCTTCATGTGGAGTCAGG 59.674 55.000 0.00 0.00 0.00 3.86
38 39 0.326264 GGCTTCATGTGGAGTCAGGT 59.674 55.000 0.00 0.00 0.00 4.00
39 40 1.677217 GGCTTCATGTGGAGTCAGGTC 60.677 57.143 0.00 0.00 0.00 3.85
40 41 1.677217 GCTTCATGTGGAGTCAGGTCC 60.677 57.143 0.00 0.00 37.10 4.46
41 42 1.905215 CTTCATGTGGAGTCAGGTCCT 59.095 52.381 0.00 0.00 37.52 3.85
42 43 2.919772 TCATGTGGAGTCAGGTCCTA 57.080 50.000 0.00 0.00 37.52 2.94
43 44 2.457598 TCATGTGGAGTCAGGTCCTAC 58.542 52.381 0.00 0.00 37.52 3.18
44 45 2.179427 CATGTGGAGTCAGGTCCTACA 58.821 52.381 0.00 0.00 37.52 2.74
45 46 2.623418 TGTGGAGTCAGGTCCTACAT 57.377 50.000 0.00 0.00 37.52 2.29
46 47 2.902608 TGTGGAGTCAGGTCCTACATT 58.097 47.619 0.00 0.00 37.52 2.71
47 48 2.567169 TGTGGAGTCAGGTCCTACATTG 59.433 50.000 0.00 0.00 37.52 2.82
48 49 2.093447 GTGGAGTCAGGTCCTACATTGG 60.093 54.545 0.00 0.00 37.52 3.16
49 50 1.134371 GGAGTCAGGTCCTACATTGGC 60.134 57.143 0.00 0.00 33.30 4.52
50 51 1.834263 GAGTCAGGTCCTACATTGGCT 59.166 52.381 0.00 0.00 0.00 4.75
51 52 2.237392 GAGTCAGGTCCTACATTGGCTT 59.763 50.000 0.00 0.00 0.00 4.35
52 53 2.026822 AGTCAGGTCCTACATTGGCTTG 60.027 50.000 0.00 0.00 0.00 4.01
53 54 1.281867 TCAGGTCCTACATTGGCTTGG 59.718 52.381 0.00 0.00 0.00 3.61
54 55 1.281867 CAGGTCCTACATTGGCTTGGA 59.718 52.381 0.00 0.00 0.00 3.53
55 56 2.092212 CAGGTCCTACATTGGCTTGGAT 60.092 50.000 0.00 0.00 0.00 3.41
56 57 2.582636 AGGTCCTACATTGGCTTGGATT 59.417 45.455 0.00 0.00 0.00 3.01
57 58 2.689983 GGTCCTACATTGGCTTGGATTG 59.310 50.000 0.00 0.00 0.00 2.67
58 59 3.620488 GTCCTACATTGGCTTGGATTGA 58.380 45.455 0.00 0.00 0.00 2.57
59 60 4.210331 GTCCTACATTGGCTTGGATTGAT 58.790 43.478 0.00 0.00 0.00 2.57
60 61 4.037208 GTCCTACATTGGCTTGGATTGATG 59.963 45.833 0.00 0.00 0.00 3.07
61 62 4.079844 TCCTACATTGGCTTGGATTGATGA 60.080 41.667 0.00 0.00 0.00 2.92
62 63 4.277672 CCTACATTGGCTTGGATTGATGAG 59.722 45.833 0.00 0.00 0.00 2.90
63 64 3.972133 ACATTGGCTTGGATTGATGAGA 58.028 40.909 0.00 0.00 0.00 3.27
64 65 4.543689 ACATTGGCTTGGATTGATGAGAT 58.456 39.130 0.00 0.00 0.00 2.75
65 66 4.960469 ACATTGGCTTGGATTGATGAGATT 59.040 37.500 0.00 0.00 0.00 2.40
66 67 5.424252 ACATTGGCTTGGATTGATGAGATTT 59.576 36.000 0.00 0.00 0.00 2.17
67 68 5.587388 TTGGCTTGGATTGATGAGATTTC 57.413 39.130 0.00 0.00 0.00 2.17
68 69 3.956199 TGGCTTGGATTGATGAGATTTCC 59.044 43.478 0.00 0.00 0.00 3.13
69 70 4.213513 GGCTTGGATTGATGAGATTTCCT 58.786 43.478 0.00 0.00 0.00 3.36
70 71 4.648307 GGCTTGGATTGATGAGATTTCCTT 59.352 41.667 0.00 0.00 0.00 3.36
71 72 5.128335 GGCTTGGATTGATGAGATTTCCTTT 59.872 40.000 0.00 0.00 0.00 3.11
72 73 6.351626 GGCTTGGATTGATGAGATTTCCTTTT 60.352 38.462 0.00 0.00 0.00 2.27
73 74 7.147846 GGCTTGGATTGATGAGATTTCCTTTTA 60.148 37.037 0.00 0.00 0.00 1.52
74 75 8.419442 GCTTGGATTGATGAGATTTCCTTTTAT 58.581 33.333 0.00 0.00 0.00 1.40
75 76 9.745880 CTTGGATTGATGAGATTTCCTTTTATG 57.254 33.333 0.00 0.00 0.00 1.90
76 77 9.478238 TTGGATTGATGAGATTTCCTTTTATGA 57.522 29.630 0.00 0.00 0.00 2.15
77 78 9.128404 TGGATTGATGAGATTTCCTTTTATGAG 57.872 33.333 0.00 0.00 0.00 2.90
78 79 9.347240 GGATTGATGAGATTTCCTTTTATGAGA 57.653 33.333 0.00 0.00 0.00 3.27
80 81 8.743085 TTGATGAGATTTCCTTTTATGAGAGG 57.257 34.615 0.00 0.00 0.00 3.69
81 82 8.094284 TGATGAGATTTCCTTTTATGAGAGGA 57.906 34.615 0.00 0.00 40.22 3.71
82 83 7.989741 TGATGAGATTTCCTTTTATGAGAGGAC 59.010 37.037 0.00 0.00 41.61 3.85
83 84 7.502060 TGAGATTTCCTTTTATGAGAGGACT 57.498 36.000 0.00 0.00 41.61 3.85
84 85 7.922382 TGAGATTTCCTTTTATGAGAGGACTT 58.078 34.615 0.00 0.00 41.61 3.01
85 86 8.043710 TGAGATTTCCTTTTATGAGAGGACTTC 58.956 37.037 0.00 0.00 41.61 3.01
86 87 7.044798 AGATTTCCTTTTATGAGAGGACTTCG 58.955 38.462 0.00 0.00 41.61 3.79
87 88 5.740290 TTCCTTTTATGAGAGGACTTCGT 57.260 39.130 0.00 0.00 41.61 3.85
88 89 5.740290 TCCTTTTATGAGAGGACTTCGTT 57.260 39.130 0.00 0.00 37.15 3.85
89 90 6.110411 TCCTTTTATGAGAGGACTTCGTTT 57.890 37.500 0.00 0.00 37.15 3.60
90 91 6.531021 TCCTTTTATGAGAGGACTTCGTTTT 58.469 36.000 0.00 0.00 37.15 2.43
91 92 7.673180 TCCTTTTATGAGAGGACTTCGTTTTA 58.327 34.615 0.00 0.00 37.15 1.52
92 93 7.817962 TCCTTTTATGAGAGGACTTCGTTTTAG 59.182 37.037 0.00 0.00 37.15 1.85
93 94 7.817962 CCTTTTATGAGAGGACTTCGTTTTAGA 59.182 37.037 0.00 0.00 34.91 2.10
94 95 8.758633 TTTTATGAGAGGACTTCGTTTTAGAG 57.241 34.615 0.00 0.00 0.00 2.43
95 96 5.986501 ATGAGAGGACTTCGTTTTAGAGT 57.013 39.130 0.00 0.00 0.00 3.24
96 97 5.373981 TGAGAGGACTTCGTTTTAGAGTC 57.626 43.478 0.00 0.00 0.00 3.36
97 98 4.217983 TGAGAGGACTTCGTTTTAGAGTCC 59.782 45.833 12.61 12.61 46.75 3.85
99 100 3.565905 GGACTTCGTTTTAGAGTCCGA 57.434 47.619 6.06 0.00 39.46 4.55
100 101 3.500014 GGACTTCGTTTTAGAGTCCGAG 58.500 50.000 6.06 0.00 39.46 4.63
101 102 3.500014 GACTTCGTTTTAGAGTCCGAGG 58.500 50.000 0.00 0.00 33.32 4.63
102 103 2.230750 ACTTCGTTTTAGAGTCCGAGGG 59.769 50.000 3.65 0.00 31.63 4.30
103 104 2.205022 TCGTTTTAGAGTCCGAGGGA 57.795 50.000 0.00 0.00 0.00 4.20
104 105 2.089980 TCGTTTTAGAGTCCGAGGGAG 58.910 52.381 0.00 0.00 29.39 4.30
105 106 1.817447 CGTTTTAGAGTCCGAGGGAGT 59.183 52.381 0.00 0.00 38.20 3.85
106 107 3.012518 CGTTTTAGAGTCCGAGGGAGTA 58.987 50.000 0.00 0.00 35.20 2.59
107 108 3.065095 CGTTTTAGAGTCCGAGGGAGTAG 59.935 52.174 0.00 0.00 35.20 2.57
108 109 4.015764 GTTTTAGAGTCCGAGGGAGTAGT 58.984 47.826 0.00 0.00 35.20 2.73
109 110 3.557228 TTAGAGTCCGAGGGAGTAGTC 57.443 52.381 0.00 0.00 35.20 2.59
110 111 1.287217 AGAGTCCGAGGGAGTAGTCA 58.713 55.000 0.00 0.00 35.20 3.41
111 112 1.634459 AGAGTCCGAGGGAGTAGTCAA 59.366 52.381 0.00 0.00 35.20 3.18
112 113 2.041350 AGAGTCCGAGGGAGTAGTCAAA 59.959 50.000 0.00 0.00 35.20 2.69
113 114 2.424246 GAGTCCGAGGGAGTAGTCAAAG 59.576 54.545 0.00 0.00 35.20 2.77
114 115 2.041350 AGTCCGAGGGAGTAGTCAAAGA 59.959 50.000 0.00 0.00 32.96 2.52
115 116 3.025262 GTCCGAGGGAGTAGTCAAAGAT 58.975 50.000 0.00 0.00 29.39 2.40
116 117 3.024547 TCCGAGGGAGTAGTCAAAGATG 58.975 50.000 0.00 0.00 0.00 2.90
117 118 2.761208 CCGAGGGAGTAGTCAAAGATGT 59.239 50.000 0.00 0.00 0.00 3.06
118 119 3.952323 CCGAGGGAGTAGTCAAAGATGTA 59.048 47.826 0.00 0.00 0.00 2.29
119 120 4.202030 CCGAGGGAGTAGTCAAAGATGTAC 60.202 50.000 0.00 0.00 0.00 2.90
120 121 4.398358 CGAGGGAGTAGTCAAAGATGTACA 59.602 45.833 0.00 0.00 0.00 2.90
121 122 5.067936 CGAGGGAGTAGTCAAAGATGTACAT 59.932 44.000 8.43 8.43 0.00 2.29
122 123 6.472686 AGGGAGTAGTCAAAGATGTACATC 57.527 41.667 25.47 25.47 38.09 3.06
181 182 8.547069 TGTTACTGCATTTTTCAATTAGTTTGC 58.453 29.630 0.00 0.00 35.16 3.68
182 183 6.544038 ACTGCATTTTTCAATTAGTTTGCC 57.456 33.333 0.00 0.00 35.16 4.52
183 184 6.290605 ACTGCATTTTTCAATTAGTTTGCCT 58.709 32.000 0.00 0.00 35.16 4.75
184 185 6.767423 ACTGCATTTTTCAATTAGTTTGCCTT 59.233 30.769 0.00 0.00 35.16 4.35
185 186 7.041848 ACTGCATTTTTCAATTAGTTTGCCTTC 60.042 33.333 0.00 0.00 35.16 3.46
186 187 6.991531 TGCATTTTTCAATTAGTTTGCCTTCT 59.008 30.769 0.00 0.00 35.16 2.85
187 188 8.147058 TGCATTTTTCAATTAGTTTGCCTTCTA 58.853 29.630 0.00 0.00 35.16 2.10
188 189 9.154847 GCATTTTTCAATTAGTTTGCCTTCTAT 57.845 29.630 0.00 0.00 35.16 1.98
194 195 9.823647 TTCAATTAGTTTGCCTTCTATAGAGAG 57.176 33.333 2.02 4.14 35.16 3.20
195 196 8.424918 TCAATTAGTTTGCCTTCTATAGAGAGG 58.575 37.037 19.04 19.04 35.16 3.69
196 197 8.424918 CAATTAGTTTGCCTTCTATAGAGAGGA 58.575 37.037 23.99 11.39 30.27 3.71
197 198 7.973048 TTAGTTTGCCTTCTATAGAGAGGAA 57.027 36.000 23.99 16.36 30.27 3.36
198 199 6.875972 AGTTTGCCTTCTATAGAGAGGAAA 57.124 37.500 23.99 19.72 30.27 3.13
199 200 7.259088 AGTTTGCCTTCTATAGAGAGGAAAA 57.741 36.000 23.99 22.71 30.77 2.29
200 201 7.690256 AGTTTGCCTTCTATAGAGAGGAAAAA 58.310 34.615 24.35 20.46 33.13 1.94
201 202 7.608376 AGTTTGCCTTCTATAGAGAGGAAAAAC 59.392 37.037 24.35 25.62 33.13 2.43
202 203 6.875972 TGCCTTCTATAGAGAGGAAAAACT 57.124 37.500 23.99 0.00 30.27 2.66
203 204 7.259088 TGCCTTCTATAGAGAGGAAAAACTT 57.741 36.000 23.99 0.00 30.27 2.66
204 205 7.690256 TGCCTTCTATAGAGAGGAAAAACTTT 58.310 34.615 23.99 0.00 30.27 2.66
205 206 8.164070 TGCCTTCTATAGAGAGGAAAAACTTTT 58.836 33.333 23.99 0.00 30.27 2.27
206 207 9.015367 GCCTTCTATAGAGAGGAAAAACTTTTT 57.985 33.333 23.99 0.00 30.27 1.94
219 220 8.317891 GGAAAAACTTTTTCCTTTGAAAGACA 57.682 30.769 28.23 0.00 43.45 3.41
220 221 8.946085 GGAAAAACTTTTTCCTTTGAAAGACAT 58.054 29.630 28.23 0.00 43.45 3.06
221 222 9.759259 GAAAAACTTTTTCCTTTGAAAGACATG 57.241 29.630 13.91 0.00 41.31 3.21
222 223 9.500785 AAAAACTTTTTCCTTTGAAAGACATGA 57.499 25.926 6.49 0.00 41.31 3.07
223 224 9.671279 AAAACTTTTTCCTTTGAAAGACATGAT 57.329 25.926 6.49 0.00 41.31 2.45
319 320 8.946085 GTGTGAGAAAATCAAACATACCTATGA 58.054 33.333 0.00 0.00 44.51 2.15
320 321 8.946085 TGTGAGAAAATCAAACATACCTATGAC 58.054 33.333 0.00 0.00 40.43 3.06
321 322 8.946085 GTGAGAAAATCAAACATACCTATGACA 58.054 33.333 0.00 0.00 40.43 3.58
322 323 9.513906 TGAGAAAATCAAACATACCTATGACAA 57.486 29.630 0.00 0.00 34.49 3.18
330 331 9.733556 TCAAACATACCTATGACAAAACTATGT 57.266 29.630 0.00 0.00 37.15 2.29
343 344 9.959749 TGACAAAACTATGTTTATGAAAGGTTC 57.040 29.630 0.00 0.00 32.57 3.62
344 345 9.406828 GACAAAACTATGTTTATGAAAGGTTCC 57.593 33.333 0.00 0.00 32.57 3.62
345 346 9.143155 ACAAAACTATGTTTATGAAAGGTTCCT 57.857 29.630 0.00 0.00 0.00 3.36
350 351 9.326413 ACTATGTTTATGAAAGGTTCCTATTCG 57.674 33.333 0.00 0.00 0.00 3.34
351 352 9.326413 CTATGTTTATGAAAGGTTCCTATTCGT 57.674 33.333 0.00 3.53 0.00 3.85
352 353 7.372451 TGTTTATGAAAGGTTCCTATTCGTG 57.628 36.000 13.45 0.00 0.00 4.35
353 354 7.162761 TGTTTATGAAAGGTTCCTATTCGTGA 58.837 34.615 13.45 7.16 0.00 4.35
354 355 7.662258 TGTTTATGAAAGGTTCCTATTCGTGAA 59.338 33.333 13.45 10.67 0.00 3.18
355 356 8.674607 GTTTATGAAAGGTTCCTATTCGTGAAT 58.325 33.333 0.22 0.22 34.93 2.57
356 357 6.683974 ATGAAAGGTTCCTATTCGTGAATG 57.316 37.500 5.37 0.00 32.50 2.67
357 358 5.556915 TGAAAGGTTCCTATTCGTGAATGT 58.443 37.500 5.37 0.00 32.50 2.71
358 359 5.411361 TGAAAGGTTCCTATTCGTGAATGTG 59.589 40.000 5.37 0.00 32.50 3.21
359 360 4.819105 AGGTTCCTATTCGTGAATGTGA 57.181 40.909 5.37 0.00 32.50 3.58
360 361 5.359194 AGGTTCCTATTCGTGAATGTGAT 57.641 39.130 5.37 0.00 32.50 3.06
361 362 5.745227 AGGTTCCTATTCGTGAATGTGATT 58.255 37.500 5.37 0.00 32.50 2.57
362 363 6.884832 AGGTTCCTATTCGTGAATGTGATTA 58.115 36.000 5.37 0.00 32.50 1.75
363 364 6.761714 AGGTTCCTATTCGTGAATGTGATTAC 59.238 38.462 5.37 0.00 32.50 1.89
364 365 6.537301 GGTTCCTATTCGTGAATGTGATTACA 59.463 38.462 5.37 0.00 41.89 2.41
380 381 8.641499 TGTGATTACATTTGGTTCAACTTTTC 57.359 30.769 0.00 0.00 0.00 2.29
381 382 8.474025 TGTGATTACATTTGGTTCAACTTTTCT 58.526 29.630 0.00 0.00 0.00 2.52
382 383 9.313118 GTGATTACATTTGGTTCAACTTTTCTT 57.687 29.630 0.00 0.00 0.00 2.52
383 384 9.883142 TGATTACATTTGGTTCAACTTTTCTTT 57.117 25.926 0.00 0.00 0.00 2.52
387 388 8.474006 ACATTTGGTTCAACTTTTCTTTACAC 57.526 30.769 0.00 0.00 0.00 2.90
388 389 8.091449 ACATTTGGTTCAACTTTTCTTTACACA 58.909 29.630 0.00 0.00 0.00 3.72
389 390 8.930760 CATTTGGTTCAACTTTTCTTTACACAA 58.069 29.630 0.00 0.00 0.00 3.33
390 391 8.888579 TTTGGTTCAACTTTTCTTTACACAAA 57.111 26.923 0.00 0.00 0.00 2.83
391 392 8.888579 TTGGTTCAACTTTTCTTTACACAAAA 57.111 26.923 0.00 0.00 0.00 2.44
392 393 8.300495 TGGTTCAACTTTTCTTTACACAAAAC 57.700 30.769 0.00 0.00 0.00 2.43
393 394 7.926555 TGGTTCAACTTTTCTTTACACAAAACA 59.073 29.630 0.00 0.00 0.00 2.83
394 395 8.766151 GGTTCAACTTTTCTTTACACAAAACAA 58.234 29.630 0.00 0.00 0.00 2.83
437 438 3.072211 ACTTTACAAAGTTCTAGCCCGC 58.928 45.455 1.47 0.00 46.52 6.13
438 439 2.843401 TTACAAAGTTCTAGCCCGCA 57.157 45.000 0.00 0.00 0.00 5.69
439 440 2.088950 TACAAAGTTCTAGCCCGCAC 57.911 50.000 0.00 0.00 0.00 5.34
440 441 0.107831 ACAAAGTTCTAGCCCGCACA 59.892 50.000 0.00 0.00 0.00 4.57
441 442 1.271379 ACAAAGTTCTAGCCCGCACAT 60.271 47.619 0.00 0.00 0.00 3.21
442 443 1.398390 CAAAGTTCTAGCCCGCACATC 59.602 52.381 0.00 0.00 0.00 3.06
443 444 0.460284 AAGTTCTAGCCCGCACATCG 60.460 55.000 0.00 0.00 38.08 3.84
454 455 4.033776 CACATCGGGTGGGCCACT 62.034 66.667 33.87 13.62 44.04 4.00
455 456 3.256960 ACATCGGGTGGGCCACTT 61.257 61.111 33.87 15.19 34.40 3.16
456 457 2.035626 CATCGGGTGGGCCACTTT 59.964 61.111 33.87 14.84 34.40 2.66
457 458 2.035626 ATCGGGTGGGCCACTTTG 59.964 61.111 33.87 23.22 34.40 2.77
458 459 4.966787 TCGGGTGGGCCACTTTGC 62.967 66.667 33.87 18.37 34.40 3.68
459 460 4.974721 CGGGTGGGCCACTTTGCT 62.975 66.667 33.87 0.00 34.40 3.91
460 461 2.438795 GGGTGGGCCACTTTGCTA 59.561 61.111 33.87 0.00 34.40 3.49
461 462 1.678970 GGGTGGGCCACTTTGCTAG 60.679 63.158 33.87 0.00 34.40 3.42
462 463 1.074951 GGTGGGCCACTTTGCTAGT 59.925 57.895 33.87 0.00 37.68 2.57
463 464 0.539669 GGTGGGCCACTTTGCTAGTT 60.540 55.000 33.87 0.00 33.85 2.24
464 465 1.328279 GTGGGCCACTTTGCTAGTTT 58.672 50.000 29.22 0.00 33.85 2.66
465 466 1.000274 GTGGGCCACTTTGCTAGTTTG 60.000 52.381 29.22 0.00 33.85 2.93
466 467 1.133637 TGGGCCACTTTGCTAGTTTGA 60.134 47.619 0.00 0.00 33.85 2.69
467 468 2.171003 GGGCCACTTTGCTAGTTTGAT 58.829 47.619 4.39 0.00 33.85 2.57
468 469 2.562738 GGGCCACTTTGCTAGTTTGATT 59.437 45.455 4.39 0.00 33.85 2.57
469 470 3.761752 GGGCCACTTTGCTAGTTTGATTA 59.238 43.478 4.39 0.00 33.85 1.75
470 471 4.219725 GGGCCACTTTGCTAGTTTGATTAA 59.780 41.667 4.39 0.00 33.85 1.40
471 472 5.279256 GGGCCACTTTGCTAGTTTGATTAAA 60.279 40.000 4.39 0.00 33.85 1.52
472 473 6.220201 GGCCACTTTGCTAGTTTGATTAAAA 58.780 36.000 0.00 0.00 33.85 1.52
473 474 6.366061 GGCCACTTTGCTAGTTTGATTAAAAG 59.634 38.462 0.00 0.00 33.85 2.27
474 475 6.128822 GCCACTTTGCTAGTTTGATTAAAAGC 60.129 38.462 0.85 0.85 33.85 3.51
475 476 6.366061 CCACTTTGCTAGTTTGATTAAAAGCC 59.634 38.462 4.69 0.00 33.85 4.35
476 477 6.922957 CACTTTGCTAGTTTGATTAAAAGCCA 59.077 34.615 4.69 0.00 33.85 4.75
477 478 7.437862 CACTTTGCTAGTTTGATTAAAAGCCAA 59.562 33.333 4.69 0.50 33.85 4.52
478 479 7.984617 ACTTTGCTAGTTTGATTAAAAGCCAAA 59.015 29.630 4.69 5.01 31.60 3.28
479 480 8.900983 TTTGCTAGTTTGATTAAAAGCCAAAT 57.099 26.923 4.69 0.00 31.60 2.32
480 481 9.988815 TTTGCTAGTTTGATTAAAAGCCAAATA 57.011 25.926 4.69 0.00 31.60 1.40
481 482 9.988815 TTGCTAGTTTGATTAAAAGCCAAATAA 57.011 25.926 4.69 0.00 31.60 1.40
482 483 9.418045 TGCTAGTTTGATTAAAAGCCAAATAAC 57.582 29.630 4.69 0.00 31.60 1.89
483 484 9.639601 GCTAGTTTGATTAAAAGCCAAATAACT 57.360 29.630 0.00 0.00 33.17 2.24
486 487 8.646900 AGTTTGATTAAAAGCCAAATAACTCCA 58.353 29.630 0.00 0.00 33.17 3.86
487 488 9.267084 GTTTGATTAAAAGCCAAATAACTCCAA 57.733 29.630 0.00 0.00 33.17 3.53
488 489 9.838339 TTTGATTAAAAGCCAAATAACTCCAAA 57.162 25.926 0.00 0.00 0.00 3.28
495 496 9.657419 AAAAGCCAAATAACTCCAAATTGATAG 57.343 29.630 0.00 0.00 0.00 2.08
496 497 7.352079 AGCCAAATAACTCCAAATTGATAGG 57.648 36.000 0.00 0.00 0.00 2.57
497 498 6.324770 AGCCAAATAACTCCAAATTGATAGGG 59.675 38.462 0.00 0.00 0.00 3.53
498 499 6.462909 GCCAAATAACTCCAAATTGATAGGGG 60.463 42.308 0.00 0.00 0.00 4.79
499 500 6.611236 CCAAATAACTCCAAATTGATAGGGGT 59.389 38.462 0.00 0.00 37.87 4.95
501 502 8.539544 CAAATAACTCCAAATTGATAGGGGTTT 58.460 33.333 9.24 0.00 43.38 3.27
502 503 8.679344 AATAACTCCAAATTGATAGGGGTTTT 57.321 30.769 9.24 1.41 43.38 2.43
503 504 6.605471 AACTCCAAATTGATAGGGGTTTTC 57.395 37.500 0.00 0.00 43.38 2.29
504 505 5.650283 ACTCCAAATTGATAGGGGTTTTCA 58.350 37.500 0.00 0.00 30.08 2.69
505 506 6.081356 ACTCCAAATTGATAGGGGTTTTCAA 58.919 36.000 0.00 0.00 30.08 2.69
506 507 6.556874 ACTCCAAATTGATAGGGGTTTTCAAA 59.443 34.615 0.00 0.00 30.08 2.69
507 508 7.071824 ACTCCAAATTGATAGGGGTTTTCAAAA 59.928 33.333 0.00 0.00 30.08 2.44
508 509 7.983363 TCCAAATTGATAGGGGTTTTCAAAAT 58.017 30.769 0.00 0.00 33.45 1.82
509 510 9.105844 TCCAAATTGATAGGGGTTTTCAAAATA 57.894 29.630 0.00 0.00 33.45 1.40
510 511 9.161629 CCAAATTGATAGGGGTTTTCAAAATAC 57.838 33.333 0.00 0.00 33.45 1.89
511 512 9.942850 CAAATTGATAGGGGTTTTCAAAATACT 57.057 29.630 0.00 0.00 33.45 2.12
514 515 7.712204 TGATAGGGGTTTTCAAAATACTTCC 57.288 36.000 0.00 0.00 0.00 3.46
515 516 7.242359 TGATAGGGGTTTTCAAAATACTTCCA 58.758 34.615 0.00 0.00 0.00 3.53
516 517 7.730784 TGATAGGGGTTTTCAAAATACTTCCAA 59.269 33.333 0.00 0.00 0.00 3.53
517 518 6.816616 AGGGGTTTTCAAAATACTTCCAAA 57.183 33.333 0.00 0.00 0.00 3.28
518 519 7.387265 AGGGGTTTTCAAAATACTTCCAAAT 57.613 32.000 0.00 0.00 0.00 2.32
519 520 7.223584 AGGGGTTTTCAAAATACTTCCAAATG 58.776 34.615 0.00 0.00 0.00 2.32
520 521 7.071824 AGGGGTTTTCAAAATACTTCCAAATGA 59.928 33.333 0.00 0.00 0.00 2.57
521 522 7.172532 GGGGTTTTCAAAATACTTCCAAATGAC 59.827 37.037 0.00 0.00 0.00 3.06
522 523 7.931407 GGGTTTTCAAAATACTTCCAAATGACT 59.069 33.333 0.00 0.00 0.00 3.41
523 524 9.325198 GGTTTTCAAAATACTTCCAAATGACTT 57.675 29.630 0.00 0.00 0.00 3.01
535 536 9.264719 ACTTCCAAATGACTTTCAATTTGATTC 57.735 29.630 9.16 0.00 36.43 2.52
536 537 9.485206 CTTCCAAATGACTTTCAATTTGATTCT 57.515 29.630 9.16 0.00 36.43 2.40
537 538 9.835389 TTCCAAATGACTTTCAATTTGATTCTT 57.165 25.926 9.16 0.00 36.43 2.52
538 539 9.835389 TCCAAATGACTTTCAATTTGATTCTTT 57.165 25.926 9.16 0.59 36.43 2.52
603 604 2.116238 GCCCTTAGTGGTGTCCATCTA 58.884 52.381 0.00 0.00 35.28 1.98
759 760 4.023707 CAGAGGCGGCTAATTTTATTCAGG 60.024 45.833 13.24 0.00 0.00 3.86
770 771 0.604243 TTATTCAGGCCGTTGCACGT 60.604 50.000 0.00 0.00 40.58 4.49
928 931 1.296715 CGGTGGGAAGCTAGCTGTT 59.703 57.895 20.16 2.53 0.00 3.16
953 956 3.771160 CGGCGGTGGGAAGCTAGT 61.771 66.667 0.00 0.00 0.00 2.57
1010 1013 1.513158 CGAGCTCCATGTCTTCCGT 59.487 57.895 8.47 0.00 0.00 4.69
1063 1066 2.494445 CGCGTGTGGAGATGCCTA 59.506 61.111 0.00 0.00 37.63 3.93
1075 1078 3.068873 GGAGATGCCTATCTTCGTCTGTT 59.931 47.826 0.00 0.00 43.63 3.16
1117 1120 1.124780 TCGGAGGGTTTCTCACACAA 58.875 50.000 0.00 0.00 44.19 3.33
1122 1125 1.760613 AGGGTTTCTCACACAACGAGA 59.239 47.619 0.00 0.00 37.74 4.04
1137 1140 1.069513 ACGAGAAACCACAATCGTCCA 59.930 47.619 0.00 0.00 44.48 4.02
1272 1275 3.513912 TCTTTCTTTGGGTCGATGCTCTA 59.486 43.478 0.00 0.00 0.00 2.43
1273 1276 3.973206 TTCTTTGGGTCGATGCTCTAA 57.027 42.857 0.00 0.00 0.00 2.10
1295 1298 9.886132 TCTAACCAAGACTCTAATAAATGAACC 57.114 33.333 0.00 0.00 0.00 3.62
1309 1312 2.760634 TGAACCGCAAGAAGAGCATA 57.239 45.000 0.00 0.00 43.02 3.14
1311 1314 3.609853 TGAACCGCAAGAAGAGCATAAT 58.390 40.909 0.00 0.00 43.02 1.28
1411 1414 3.441922 CACTGACAGAGAGCTAGCTGTTA 59.558 47.826 24.99 10.46 44.77 2.41
2313 2332 9.979578 TTTGCATGTTAGTTCATGACTTATTTT 57.020 25.926 10.28 0.00 45.41 1.82
2353 2374 1.614583 GGCTTCTCACCCCCTCTTTTC 60.615 57.143 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.578786 TGAAGCCATGCATACTGGATG 58.421 47.619 9.06 0.00 44.45 3.51
6 7 3.154710 CATGAAGCCATGCATACTGGAT 58.845 45.455 9.06 0.00 43.06 3.41
7 8 2.578786 CATGAAGCCATGCATACTGGA 58.421 47.619 9.06 0.00 43.06 3.86
17 18 1.064906 CCTGACTCCACATGAAGCCAT 60.065 52.381 0.00 0.00 0.00 4.40
18 19 0.325933 CCTGACTCCACATGAAGCCA 59.674 55.000 0.00 0.00 0.00 4.75
19 20 0.326264 ACCTGACTCCACATGAAGCC 59.674 55.000 0.00 0.00 0.00 4.35
20 21 1.677217 GGACCTGACTCCACATGAAGC 60.677 57.143 0.00 0.00 0.00 3.86
21 22 1.905215 AGGACCTGACTCCACATGAAG 59.095 52.381 0.00 0.00 31.94 3.02
22 23 2.030027 AGGACCTGACTCCACATGAA 57.970 50.000 0.00 0.00 31.94 2.57
23 24 2.225267 TGTAGGACCTGACTCCACATGA 60.225 50.000 3.53 0.00 31.94 3.07
24 25 2.179427 TGTAGGACCTGACTCCACATG 58.821 52.381 3.53 0.00 31.94 3.21
25 26 2.623418 TGTAGGACCTGACTCCACAT 57.377 50.000 3.53 0.00 31.94 3.21
26 27 2.567169 CAATGTAGGACCTGACTCCACA 59.433 50.000 3.53 0.00 31.94 4.17
27 28 2.093447 CCAATGTAGGACCTGACTCCAC 60.093 54.545 3.53 0.00 31.94 4.02
28 29 2.187958 CCAATGTAGGACCTGACTCCA 58.812 52.381 3.53 0.00 31.94 3.86
29 30 1.134371 GCCAATGTAGGACCTGACTCC 60.134 57.143 3.53 0.00 0.00 3.85
30 31 1.834263 AGCCAATGTAGGACCTGACTC 59.166 52.381 3.53 0.00 0.00 3.36
31 32 1.958288 AGCCAATGTAGGACCTGACT 58.042 50.000 3.53 0.00 0.00 3.41
32 33 2.359900 CAAGCCAATGTAGGACCTGAC 58.640 52.381 3.53 0.00 0.00 3.51
33 34 1.281867 CCAAGCCAATGTAGGACCTGA 59.718 52.381 3.53 0.00 0.00 3.86
34 35 1.281867 TCCAAGCCAATGTAGGACCTG 59.718 52.381 3.53 0.00 0.00 4.00
35 36 1.668826 TCCAAGCCAATGTAGGACCT 58.331 50.000 0.00 0.00 0.00 3.85
36 37 2.689983 CAATCCAAGCCAATGTAGGACC 59.310 50.000 0.00 0.00 0.00 4.46
37 38 3.620488 TCAATCCAAGCCAATGTAGGAC 58.380 45.455 0.00 0.00 0.00 3.85
38 39 4.079844 TCATCAATCCAAGCCAATGTAGGA 60.080 41.667 0.00 0.00 0.00 2.94
39 40 4.209538 TCATCAATCCAAGCCAATGTAGG 58.790 43.478 0.00 0.00 0.00 3.18
40 41 5.128205 TCTCATCAATCCAAGCCAATGTAG 58.872 41.667 0.00 0.00 0.00 2.74
41 42 5.114764 TCTCATCAATCCAAGCCAATGTA 57.885 39.130 0.00 0.00 0.00 2.29
42 43 3.972133 TCTCATCAATCCAAGCCAATGT 58.028 40.909 0.00 0.00 0.00 2.71
43 44 5.531122 AATCTCATCAATCCAAGCCAATG 57.469 39.130 0.00 0.00 0.00 2.82
44 45 5.070047 GGAAATCTCATCAATCCAAGCCAAT 59.930 40.000 0.00 0.00 0.00 3.16
45 46 4.403432 GGAAATCTCATCAATCCAAGCCAA 59.597 41.667 0.00 0.00 0.00 4.52
46 47 3.956199 GGAAATCTCATCAATCCAAGCCA 59.044 43.478 0.00 0.00 0.00 4.75
47 48 4.213513 AGGAAATCTCATCAATCCAAGCC 58.786 43.478 0.00 0.00 32.47 4.35
48 49 5.848833 AAGGAAATCTCATCAATCCAAGC 57.151 39.130 0.00 0.00 32.47 4.01
49 50 9.745880 CATAAAAGGAAATCTCATCAATCCAAG 57.254 33.333 0.00 0.00 32.47 3.61
50 51 9.478238 TCATAAAAGGAAATCTCATCAATCCAA 57.522 29.630 0.00 0.00 32.47 3.53
51 52 9.128404 CTCATAAAAGGAAATCTCATCAATCCA 57.872 33.333 0.00 0.00 32.47 3.41
52 53 9.347240 TCTCATAAAAGGAAATCTCATCAATCC 57.653 33.333 0.00 0.00 0.00 3.01
54 55 9.352191 CCTCTCATAAAAGGAAATCTCATCAAT 57.648 33.333 0.00 0.00 34.35 2.57
55 56 8.551440 TCCTCTCATAAAAGGAAATCTCATCAA 58.449 33.333 0.00 0.00 38.74 2.57
56 57 7.989741 GTCCTCTCATAAAAGGAAATCTCATCA 59.010 37.037 0.00 0.00 43.18 3.07
57 58 8.210265 AGTCCTCTCATAAAAGGAAATCTCATC 58.790 37.037 0.00 0.00 43.18 2.92
58 59 8.100135 AGTCCTCTCATAAAAGGAAATCTCAT 57.900 34.615 0.00 0.00 43.18 2.90
59 60 7.502060 AGTCCTCTCATAAAAGGAAATCTCA 57.498 36.000 0.00 0.00 43.18 3.27
60 61 7.223777 CGAAGTCCTCTCATAAAAGGAAATCTC 59.776 40.741 0.00 0.00 43.18 2.75
61 62 7.044798 CGAAGTCCTCTCATAAAAGGAAATCT 58.955 38.462 0.00 0.00 43.18 2.40
62 63 6.819146 ACGAAGTCCTCTCATAAAAGGAAATC 59.181 38.462 0.00 0.00 43.18 2.17
63 64 6.712276 ACGAAGTCCTCTCATAAAAGGAAAT 58.288 36.000 0.00 0.00 43.18 2.17
64 65 6.110411 ACGAAGTCCTCTCATAAAAGGAAA 57.890 37.500 0.00 0.00 43.18 3.13
65 66 5.740290 ACGAAGTCCTCTCATAAAAGGAA 57.260 39.130 0.00 0.00 43.18 3.36
66 67 5.740290 AACGAAGTCCTCTCATAAAAGGA 57.260 39.130 0.00 0.00 45.00 3.36
67 68 6.803154 AAAACGAAGTCCTCTCATAAAAGG 57.197 37.500 0.00 0.00 45.00 3.11
68 69 8.758633 TCTAAAACGAAGTCCTCTCATAAAAG 57.241 34.615 0.00 0.00 45.00 2.27
69 70 8.365647 ACTCTAAAACGAAGTCCTCTCATAAAA 58.634 33.333 0.00 0.00 45.00 1.52
70 71 7.893658 ACTCTAAAACGAAGTCCTCTCATAAA 58.106 34.615 0.00 0.00 45.00 1.40
71 72 7.362747 GGACTCTAAAACGAAGTCCTCTCATAA 60.363 40.741 12.41 0.00 45.00 1.90
72 73 6.095160 GGACTCTAAAACGAAGTCCTCTCATA 59.905 42.308 12.41 0.00 45.00 2.15
73 74 5.105675 GGACTCTAAAACGAAGTCCTCTCAT 60.106 44.000 12.41 0.00 45.00 2.90
74 75 4.217983 GGACTCTAAAACGAAGTCCTCTCA 59.782 45.833 12.41 0.00 45.00 3.27
75 76 4.672283 CGGACTCTAAAACGAAGTCCTCTC 60.672 50.000 16.35 0.00 45.00 3.20
76 77 3.190953 CGGACTCTAAAACGAAGTCCTCT 59.809 47.826 16.35 0.00 45.00 3.69
77 78 3.190118 TCGGACTCTAAAACGAAGTCCTC 59.810 47.826 16.35 0.00 45.00 3.71
78 79 3.152341 TCGGACTCTAAAACGAAGTCCT 58.848 45.455 16.35 0.00 45.00 3.85
79 80 3.500014 CTCGGACTCTAAAACGAAGTCC 58.500 50.000 10.12 10.12 45.00 3.85
80 81 3.500014 CCTCGGACTCTAAAACGAAGTC 58.500 50.000 0.00 0.00 45.00 3.01
82 83 2.490903 TCCCTCGGACTCTAAAACGAAG 59.509 50.000 0.00 0.00 34.70 3.79
83 84 2.490903 CTCCCTCGGACTCTAAAACGAA 59.509 50.000 0.00 0.00 34.70 3.85
84 85 2.089980 CTCCCTCGGACTCTAAAACGA 58.910 52.381 0.00 0.00 0.00 3.85
85 86 1.817447 ACTCCCTCGGACTCTAAAACG 59.183 52.381 0.00 0.00 0.00 3.60
86 87 4.015764 ACTACTCCCTCGGACTCTAAAAC 58.984 47.826 0.00 0.00 0.00 2.43
87 88 4.263639 TGACTACTCCCTCGGACTCTAAAA 60.264 45.833 0.00 0.00 0.00 1.52
88 89 3.265221 TGACTACTCCCTCGGACTCTAAA 59.735 47.826 0.00 0.00 0.00 1.85
89 90 2.842496 TGACTACTCCCTCGGACTCTAA 59.158 50.000 0.00 0.00 0.00 2.10
90 91 2.475155 TGACTACTCCCTCGGACTCTA 58.525 52.381 0.00 0.00 0.00 2.43
91 92 1.287217 TGACTACTCCCTCGGACTCT 58.713 55.000 0.00 0.00 0.00 3.24
92 93 2.125773 TTGACTACTCCCTCGGACTC 57.874 55.000 0.00 0.00 0.00 3.36
93 94 2.041350 TCTTTGACTACTCCCTCGGACT 59.959 50.000 0.00 0.00 0.00 3.85
94 95 2.444421 TCTTTGACTACTCCCTCGGAC 58.556 52.381 0.00 0.00 0.00 4.79
95 96 2.893215 TCTTTGACTACTCCCTCGGA 57.107 50.000 0.00 0.00 0.00 4.55
96 97 2.761208 ACATCTTTGACTACTCCCTCGG 59.239 50.000 0.00 0.00 0.00 4.63
97 98 4.398358 TGTACATCTTTGACTACTCCCTCG 59.602 45.833 0.00 0.00 0.00 4.63
98 99 5.916661 TGTACATCTTTGACTACTCCCTC 57.083 43.478 0.00 0.00 0.00 4.30
99 100 6.198639 AGATGTACATCTTTGACTACTCCCT 58.801 40.000 28.95 5.70 45.31 4.20
100 101 6.472686 AGATGTACATCTTTGACTACTCCC 57.527 41.667 28.95 3.20 45.31 4.30
155 156 8.547069 GCAAACTAATTGAAAAATGCAGTAACA 58.453 29.630 0.00 0.00 41.85 2.41
156 157 8.009409 GGCAAACTAATTGAAAAATGCAGTAAC 58.991 33.333 0.00 0.00 41.85 2.50
157 158 7.930865 AGGCAAACTAATTGAAAAATGCAGTAA 59.069 29.630 0.00 0.00 41.85 2.24
158 159 7.441017 AGGCAAACTAATTGAAAAATGCAGTA 58.559 30.769 0.00 0.00 41.85 2.74
159 160 6.290605 AGGCAAACTAATTGAAAAATGCAGT 58.709 32.000 0.00 0.00 41.85 4.40
160 161 6.790285 AGGCAAACTAATTGAAAAATGCAG 57.210 33.333 0.00 0.00 41.85 4.41
161 162 6.991531 AGAAGGCAAACTAATTGAAAAATGCA 59.008 30.769 0.00 0.00 41.85 3.96
162 163 7.425577 AGAAGGCAAACTAATTGAAAAATGC 57.574 32.000 0.00 0.00 41.85 3.56
168 169 9.823647 CTCTCTATAGAAGGCAAACTAATTGAA 57.176 33.333 3.57 0.00 41.85 2.69
169 170 8.424918 CCTCTCTATAGAAGGCAAACTAATTGA 58.575 37.037 14.27 0.25 41.85 2.57
170 171 8.424918 TCCTCTCTATAGAAGGCAAACTAATTG 58.575 37.037 18.75 0.00 42.21 2.32
171 172 8.554490 TCCTCTCTATAGAAGGCAAACTAATT 57.446 34.615 18.75 0.00 0.00 1.40
172 173 8.554490 TTCCTCTCTATAGAAGGCAAACTAAT 57.446 34.615 18.75 0.00 0.00 1.73
173 174 7.973048 TTCCTCTCTATAGAAGGCAAACTAA 57.027 36.000 18.75 9.45 0.00 2.24
174 175 7.973048 TTTCCTCTCTATAGAAGGCAAACTA 57.027 36.000 18.75 5.50 0.00 2.24
175 176 6.875972 TTTCCTCTCTATAGAAGGCAAACT 57.124 37.500 18.75 0.00 0.00 2.66
176 177 7.608376 AGTTTTTCCTCTCTATAGAAGGCAAAC 59.392 37.037 25.02 25.02 32.25 2.93
177 178 7.690256 AGTTTTTCCTCTCTATAGAAGGCAAA 58.310 34.615 18.75 17.73 0.00 3.68
178 179 7.259088 AGTTTTTCCTCTCTATAGAAGGCAA 57.741 36.000 18.75 14.41 0.00 4.52
179 180 6.875972 AGTTTTTCCTCTCTATAGAAGGCA 57.124 37.500 18.75 10.65 0.00 4.75
180 181 8.568676 AAAAGTTTTTCCTCTCTATAGAAGGC 57.431 34.615 18.75 9.76 0.00 4.35
194 195 8.317891 TGTCTTTCAAAGGAAAAAGTTTTTCC 57.682 30.769 37.11 37.11 46.32 3.13
195 196 9.759259 CATGTCTTTCAAAGGAAAAAGTTTTTC 57.241 29.630 26.22 26.22 42.18 2.29
196 197 9.500785 TCATGTCTTTCAAAGGAAAAAGTTTTT 57.499 25.926 13.35 13.35 42.18 1.94
197 198 9.671279 ATCATGTCTTTCAAAGGAAAAAGTTTT 57.329 25.926 0.00 0.00 42.18 2.43
292 293 8.729756 CATAGGTATGTTTGATTTTCTCACACA 58.270 33.333 0.00 0.00 45.86 3.72
293 294 8.946085 TCATAGGTATGTTTGATTTTCTCACAC 58.054 33.333 0.00 0.00 35.51 3.82
294 295 8.946085 GTCATAGGTATGTTTGATTTTCTCACA 58.054 33.333 0.00 0.00 35.26 3.58
295 296 8.946085 TGTCATAGGTATGTTTGATTTTCTCAC 58.054 33.333 0.00 0.00 35.26 3.51
296 297 9.513906 TTGTCATAGGTATGTTTGATTTTCTCA 57.486 29.630 0.00 0.00 35.26 3.27
304 305 9.733556 ACATAGTTTTGTCATAGGTATGTTTGA 57.266 29.630 0.00 0.00 35.26 2.69
317 318 9.959749 GAACCTTTCATAAACATAGTTTTGTCA 57.040 29.630 0.03 0.00 0.00 3.58
318 319 9.406828 GGAACCTTTCATAAACATAGTTTTGTC 57.593 33.333 0.03 0.00 0.00 3.18
319 320 9.143155 AGGAACCTTTCATAAACATAGTTTTGT 57.857 29.630 0.03 0.00 0.00 2.83
324 325 9.326413 CGAATAGGAACCTTTCATAAACATAGT 57.674 33.333 0.00 0.00 28.96 2.12
325 326 9.326413 ACGAATAGGAACCTTTCATAAACATAG 57.674 33.333 0.00 0.00 28.96 2.23
326 327 9.104965 CACGAATAGGAACCTTTCATAAACATA 57.895 33.333 0.00 0.00 28.96 2.29
327 328 7.827236 TCACGAATAGGAACCTTTCATAAACAT 59.173 33.333 0.00 0.00 28.96 2.71
328 329 7.162761 TCACGAATAGGAACCTTTCATAAACA 58.837 34.615 0.00 0.00 28.96 2.83
329 330 7.605410 TCACGAATAGGAACCTTTCATAAAC 57.395 36.000 0.00 0.00 28.96 2.01
330 331 8.673711 CATTCACGAATAGGAACCTTTCATAAA 58.326 33.333 0.00 0.00 28.96 1.40
331 332 7.827236 ACATTCACGAATAGGAACCTTTCATAA 59.173 33.333 0.00 0.06 28.96 1.90
332 333 7.279981 CACATTCACGAATAGGAACCTTTCATA 59.720 37.037 0.00 0.00 0.00 2.15
333 334 6.094048 CACATTCACGAATAGGAACCTTTCAT 59.906 38.462 0.00 0.00 0.00 2.57
334 335 5.411361 CACATTCACGAATAGGAACCTTTCA 59.589 40.000 0.00 0.00 0.00 2.69
335 336 5.642063 TCACATTCACGAATAGGAACCTTTC 59.358 40.000 0.00 2.88 0.00 2.62
336 337 5.556915 TCACATTCACGAATAGGAACCTTT 58.443 37.500 0.00 0.00 0.00 3.11
337 338 5.160607 TCACATTCACGAATAGGAACCTT 57.839 39.130 0.00 0.00 0.00 3.50
338 339 4.819105 TCACATTCACGAATAGGAACCT 57.181 40.909 0.00 0.00 0.00 3.50
339 340 6.537301 TGTAATCACATTCACGAATAGGAACC 59.463 38.462 0.00 0.00 0.00 3.62
340 341 7.534085 TGTAATCACATTCACGAATAGGAAC 57.466 36.000 0.00 0.00 0.00 3.62
355 356 8.474025 AGAAAAGTTGAACCAAATGTAATCACA 58.526 29.630 0.00 0.00 39.52 3.58
356 357 8.871686 AGAAAAGTTGAACCAAATGTAATCAC 57.128 30.769 0.00 0.00 0.00 3.06
357 358 9.883142 AAAGAAAAGTTGAACCAAATGTAATCA 57.117 25.926 0.00 0.00 0.00 2.57
361 362 9.575783 GTGTAAAGAAAAGTTGAACCAAATGTA 57.424 29.630 0.00 0.00 0.00 2.29
362 363 8.091449 TGTGTAAAGAAAAGTTGAACCAAATGT 58.909 29.630 0.00 0.00 0.00 2.71
363 364 8.472683 TGTGTAAAGAAAAGTTGAACCAAATG 57.527 30.769 0.00 0.00 0.00 2.32
364 365 9.495572 TTTGTGTAAAGAAAAGTTGAACCAAAT 57.504 25.926 0.00 0.00 0.00 2.32
365 366 8.888579 TTTGTGTAAAGAAAAGTTGAACCAAA 57.111 26.923 0.00 0.00 0.00 3.28
366 367 8.766151 GTTTTGTGTAAAGAAAAGTTGAACCAA 58.234 29.630 0.00 0.00 0.00 3.67
367 368 7.926555 TGTTTTGTGTAAAGAAAAGTTGAACCA 59.073 29.630 0.00 0.00 0.00 3.67
368 369 8.300495 TGTTTTGTGTAAAGAAAAGTTGAACC 57.700 30.769 0.00 0.00 0.00 3.62
417 418 3.071479 TGCGGGCTAGAACTTTGTAAAG 58.929 45.455 0.00 2.94 41.73 1.85
418 419 2.809696 GTGCGGGCTAGAACTTTGTAAA 59.190 45.455 0.00 0.00 0.00 2.01
419 420 2.224329 TGTGCGGGCTAGAACTTTGTAA 60.224 45.455 0.00 0.00 0.00 2.41
420 421 1.345089 TGTGCGGGCTAGAACTTTGTA 59.655 47.619 0.00 0.00 0.00 2.41
421 422 0.107831 TGTGCGGGCTAGAACTTTGT 59.892 50.000 0.00 0.00 0.00 2.83
422 423 1.398390 GATGTGCGGGCTAGAACTTTG 59.602 52.381 0.00 0.00 0.00 2.77
423 424 1.739067 GATGTGCGGGCTAGAACTTT 58.261 50.000 0.00 0.00 0.00 2.66
424 425 0.460284 CGATGTGCGGGCTAGAACTT 60.460 55.000 0.00 0.00 36.03 2.66
425 426 1.141881 CGATGTGCGGGCTAGAACT 59.858 57.895 0.00 0.00 36.03 3.01
426 427 3.706140 CGATGTGCGGGCTAGAAC 58.294 61.111 0.00 0.00 36.03 3.01
437 438 3.567579 AAGTGGCCCACCCGATGTG 62.568 63.158 11.06 0.00 45.01 3.21
438 439 2.840753 AAAGTGGCCCACCCGATGT 61.841 57.895 11.06 0.00 34.49 3.06
439 440 2.035626 AAAGTGGCCCACCCGATG 59.964 61.111 11.06 0.00 34.49 3.84
440 441 2.035626 CAAAGTGGCCCACCCGAT 59.964 61.111 11.06 0.00 34.49 4.18
441 442 4.966787 GCAAAGTGGCCCACCCGA 62.967 66.667 11.06 0.00 34.49 5.14
442 443 3.561120 TAGCAAAGTGGCCCACCCG 62.561 63.158 11.06 0.00 34.49 5.28
443 444 1.678970 CTAGCAAAGTGGCCCACCC 60.679 63.158 11.06 0.00 34.49 4.61
444 445 0.539669 AACTAGCAAAGTGGCCCACC 60.540 55.000 11.06 0.00 38.88 4.61
445 446 1.000274 CAAACTAGCAAAGTGGCCCAC 60.000 52.381 5.50 5.50 38.88 4.61
446 447 1.133637 TCAAACTAGCAAAGTGGCCCA 60.134 47.619 0.00 0.00 38.88 5.36
447 448 1.616159 TCAAACTAGCAAAGTGGCCC 58.384 50.000 0.00 0.00 38.88 5.80
448 449 3.942130 AATCAAACTAGCAAAGTGGCC 57.058 42.857 0.00 0.00 38.88 5.36
449 450 6.128822 GCTTTTAATCAAACTAGCAAAGTGGC 60.129 38.462 0.00 0.00 38.88 5.01
450 451 6.366061 GGCTTTTAATCAAACTAGCAAAGTGG 59.634 38.462 0.00 0.00 38.88 4.00
451 452 6.922957 TGGCTTTTAATCAAACTAGCAAAGTG 59.077 34.615 0.00 0.00 38.88 3.16
452 453 7.049799 TGGCTTTTAATCAAACTAGCAAAGT 57.950 32.000 0.00 0.00 41.49 2.66
453 454 7.945033 TTGGCTTTTAATCAAACTAGCAAAG 57.055 32.000 0.00 0.00 31.72 2.77
454 455 8.900983 ATTTGGCTTTTAATCAAACTAGCAAA 57.099 26.923 0.00 0.00 31.72 3.68
455 456 9.988815 TTATTTGGCTTTTAATCAAACTAGCAA 57.011 25.926 0.00 0.00 31.72 3.91
456 457 9.418045 GTTATTTGGCTTTTAATCAAACTAGCA 57.582 29.630 0.00 0.00 31.72 3.49
457 458 9.639601 AGTTATTTGGCTTTTAATCAAACTAGC 57.360 29.630 0.00 0.00 33.91 3.42
460 461 8.646900 TGGAGTTATTTGGCTTTTAATCAAACT 58.353 29.630 0.00 0.00 33.91 2.66
461 462 8.825667 TGGAGTTATTTGGCTTTTAATCAAAC 57.174 30.769 0.00 0.00 33.91 2.93
462 463 9.838339 TTTGGAGTTATTTGGCTTTTAATCAAA 57.162 25.926 0.00 0.00 35.30 2.69
469 470 9.657419 CTATCAATTTGGAGTTATTTGGCTTTT 57.343 29.630 0.00 0.00 0.00 2.27
470 471 8.260114 CCTATCAATTTGGAGTTATTTGGCTTT 58.740 33.333 0.00 0.00 0.00 3.51
471 472 7.147672 CCCTATCAATTTGGAGTTATTTGGCTT 60.148 37.037 0.00 0.00 0.00 4.35
472 473 6.324770 CCCTATCAATTTGGAGTTATTTGGCT 59.675 38.462 0.00 0.00 0.00 4.75
473 474 6.462909 CCCCTATCAATTTGGAGTTATTTGGC 60.463 42.308 0.00 0.00 0.00 4.52
474 475 6.611236 ACCCCTATCAATTTGGAGTTATTTGG 59.389 38.462 0.00 0.00 0.00 3.28
475 476 7.660030 ACCCCTATCAATTTGGAGTTATTTG 57.340 36.000 0.00 0.00 0.00 2.32
476 477 8.679344 AAACCCCTATCAATTTGGAGTTATTT 57.321 30.769 0.00 0.00 0.00 1.40
477 478 8.679344 AAAACCCCTATCAATTTGGAGTTATT 57.321 30.769 0.00 0.00 0.00 1.40
478 479 7.898636 TGAAAACCCCTATCAATTTGGAGTTAT 59.101 33.333 0.00 0.00 0.00 1.89
479 480 7.242359 TGAAAACCCCTATCAATTTGGAGTTA 58.758 34.615 0.00 0.00 0.00 2.24
480 481 6.081356 TGAAAACCCCTATCAATTTGGAGTT 58.919 36.000 0.00 0.00 0.00 3.01
481 482 5.650283 TGAAAACCCCTATCAATTTGGAGT 58.350 37.500 0.00 0.00 0.00 3.85
482 483 6.603940 TTGAAAACCCCTATCAATTTGGAG 57.396 37.500 0.00 0.00 0.00 3.86
483 484 7.380423 TTTTGAAAACCCCTATCAATTTGGA 57.620 32.000 0.00 0.00 33.45 3.53
484 485 9.161629 GTATTTTGAAAACCCCTATCAATTTGG 57.838 33.333 0.00 0.00 33.45 3.28
485 486 9.942850 AGTATTTTGAAAACCCCTATCAATTTG 57.057 29.630 0.00 0.00 33.45 2.32
488 489 8.758829 GGAAGTATTTTGAAAACCCCTATCAAT 58.241 33.333 0.00 0.00 33.45 2.57
489 490 7.730784 TGGAAGTATTTTGAAAACCCCTATCAA 59.269 33.333 0.00 0.00 0.00 2.57
490 491 7.242359 TGGAAGTATTTTGAAAACCCCTATCA 58.758 34.615 0.00 0.00 0.00 2.15
491 492 7.712204 TGGAAGTATTTTGAAAACCCCTATC 57.288 36.000 0.00 0.00 0.00 2.08
492 493 8.499288 TTTGGAAGTATTTTGAAAACCCCTAT 57.501 30.769 0.00 0.00 0.00 2.57
493 494 7.916077 TTTGGAAGTATTTTGAAAACCCCTA 57.084 32.000 0.00 0.00 0.00 3.53
494 495 6.816616 TTTGGAAGTATTTTGAAAACCCCT 57.183 33.333 0.00 0.00 0.00 4.79
495 496 7.172532 GTCATTTGGAAGTATTTTGAAAACCCC 59.827 37.037 0.00 0.00 0.00 4.95
496 497 7.931407 AGTCATTTGGAAGTATTTTGAAAACCC 59.069 33.333 0.00 0.00 0.00 4.11
497 498 8.887036 AGTCATTTGGAAGTATTTTGAAAACC 57.113 30.769 0.00 0.00 0.00 3.27
509 510 9.264719 GAATCAAATTGAAAGTCATTTGGAAGT 57.735 29.630 0.00 0.00 35.42 3.01
510 511 9.485206 AGAATCAAATTGAAAGTCATTTGGAAG 57.515 29.630 0.00 0.00 35.42 3.46
511 512 9.835389 AAGAATCAAATTGAAAGTCATTTGGAA 57.165 25.926 0.00 0.00 35.42 3.53
512 513 9.835389 AAAGAATCAAATTGAAAGTCATTTGGA 57.165 25.926 0.00 0.00 35.42 3.53
542 543 9.799106 CCCTTATATGAAATATGAGTTGGAAGT 57.201 33.333 0.00 0.00 40.27 3.01
543 544 9.799106 ACCCTTATATGAAATATGAGTTGGAAG 57.201 33.333 0.00 0.00 40.27 3.46
560 561 9.321532 GGGCAAAAGGATAATTAACCCTTATAT 57.678 33.333 17.67 8.77 39.21 0.86
603 604 2.787994 CATCTGAGGGCAAAACTGAGT 58.212 47.619 0.00 0.00 0.00 3.41
746 747 4.739195 GTGCAACGGCCTGAATAAAATTA 58.261 39.130 0.00 0.00 40.13 1.40
791 792 1.338337 GCTCTATGCTCAACGGCTCTA 59.662 52.381 0.00 0.00 38.95 2.43
861 862 4.427661 GCGCCGTGCTCTCTGTCT 62.428 66.667 0.00 0.00 41.73 3.41
1063 1066 1.148310 CACCGCAAACAGACGAAGAT 58.852 50.000 0.00 0.00 0.00 2.40
1117 1120 1.069513 TGGACGATTGTGGTTTCTCGT 59.930 47.619 0.00 0.00 46.09 4.18
1122 1125 3.682858 CGTAGAATGGACGATTGTGGTTT 59.317 43.478 0.00 0.00 42.98 3.27
1137 1140 0.526211 TCTCGCTGCACACGTAGAAT 59.474 50.000 0.00 0.00 0.00 2.40
1272 1275 6.093633 GCGGTTCATTTATTAGAGTCTTGGTT 59.906 38.462 0.00 0.00 0.00 3.67
1273 1276 5.585047 GCGGTTCATTTATTAGAGTCTTGGT 59.415 40.000 0.00 0.00 0.00 3.67
1295 1298 4.036027 ACCATTCATTATGCTCTTCTTGCG 59.964 41.667 0.00 0.00 32.60 4.85
1309 1312 0.533491 AGCATGCGCAACCATTCATT 59.467 45.000 17.11 0.00 42.27 2.57
1311 1314 1.213275 CAGCATGCGCAACCATTCA 59.787 52.632 17.11 0.00 42.27 2.57
1411 1414 5.942826 CCTTCTTCTTCAACATCCTAAGCTT 59.057 40.000 3.48 3.48 0.00 3.74
1637 1642 6.377327 TTTTCAACATGGTCACTTCTTCTC 57.623 37.500 0.00 0.00 0.00 2.87
1638 1643 6.773976 TTTTTCAACATGGTCACTTCTTCT 57.226 33.333 0.00 0.00 0.00 2.85
2353 2374 3.559655 TCGAGAACTTGTGGTTGTCATTG 59.440 43.478 6.49 0.00 45.11 2.82


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

AutoCloner maintained by Alex Coulton.