Multiple sequence alignment - TraesCS5B01G410600

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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 TraesCS5B01G410600 chr5B 100.000 6424 0 0 1 6424 586274616 586281039 0.000000e+00 11863
1 TraesCS5B01G410600 chr5D 94.026 3532 124 36 2243 5724 478450839 478454333 0.000000e+00 5273
2 TraesCS5B01G410600 chr5D 94.346 1751 59 16 518 2254 478448944 478450668 0.000000e+00 2649
3 TraesCS5B01G410600 chr5D 92.264 530 17 7 5907 6424 478454317 478454834 0.000000e+00 730
4 TraesCS5B01G410600 chr5A 94.309 2126 77 15 516 2622 597498741 597500841 0.000000e+00 3216
5 TraesCS5B01G410600 chr5A 90.154 1107 63 14 4640 5724 597504280 597505362 0.000000e+00 1399
6 TraesCS5B01G410600 chr5A 93.642 755 39 9 2873 3623 597501315 597502064 0.000000e+00 1120
7 TraesCS5B01G410600 chr5A 87.874 701 46 21 3654 4336 597502063 597502742 0.000000e+00 787
8 TraesCS5B01G410600 chr5A 92.705 329 18 5 6099 6424 597510493 597510818 2.710000e-128 470
9 TraesCS5B01G410600 chr5A 93.015 272 10 6 4322 4589 597504019 597504285 7.810000e-104 388
10 TraesCS5B01G410600 chr5A 90.566 159 8 3 5907 6065 597505346 597505497 3.040000e-48 204
11 TraesCS5B01G410600 chr5A 91.736 121 6 3 2712 2832 597501000 597501116 1.430000e-36 165
12 TraesCS5B01G410600 chr5A 96.907 97 2 1 2619 2714 597500879 597500975 1.850000e-35 161
13 TraesCS5B01G410600 chr5A 78.707 263 35 7 2 262 597498449 597498692 8.620000e-34 156
14 TraesCS5B01G410600 chr4B 97.391 230 6 0 275 504 399290015 399290244 6.040000e-105 392
15 TraesCS5B01G410600 chr4B 87.931 116 12 2 5190 5304 15760520 15760406 1.120000e-27 135
16 TraesCS5B01G410600 chr4D 93.725 255 13 3 271 522 348143543 348143289 4.700000e-101 379
17 TraesCS5B01G410600 chr4D 74.935 387 77 18 4915 5295 8411777 8412149 6.670000e-35 159
18 TraesCS5B01G410600 chr4D 90.476 105 10 0 5191 5295 8593368 8593264 8.680000e-29 139
19 TraesCS5B01G410600 chr4D 90.476 105 10 0 5191 5295 8623070 8622966 8.680000e-29 139
20 TraesCS5B01G410600 chr6D 95.397 239 8 3 273 510 392785975 392785739 1.690000e-100 377
21 TraesCS5B01G410600 chr6D 94.561 239 10 3 273 510 392786601 392786365 3.660000e-97 366
22 TraesCS5B01G410600 chr7D 95.726 234 9 1 273 505 284740877 284740644 6.080000e-100 375
23 TraesCS5B01G410600 chr3D 95.726 234 9 1 273 505 387269585 387269352 6.080000e-100 375
24 TraesCS5B01G410600 chr2D 95.708 233 8 2 273 504 120809704 120809935 2.190000e-99 374
25 TraesCS5B01G410600 chr1D 95.708 233 9 1 273 504 191676537 191676769 2.190000e-99 374
26 TraesCS5B01G410600 chr1D 84.496 129 10 8 5180 5305 57960552 57960673 1.130000e-22 119
27 TraesCS5B01G410600 chr6A 95.299 234 10 1 273 505 325013848 325014081 2.830000e-98 370
28 TraesCS5B01G410600 chr6A 97.906 191 4 0 5725 5915 233342580 233342390 1.340000e-86 331
29 TraesCS5B01G410600 chr7B 97.423 194 3 2 5714 5905 123786182 123785989 4.800000e-86 329
30 TraesCS5B01G410600 chr3A 98.913 184 2 0 5722 5905 325290331 325290514 4.800000e-86 329
31 TraesCS5B01G410600 chr1A 97.906 191 3 1 5720 5909 515191242 515191052 4.800000e-86 329
32 TraesCS5B01G410600 chr1A 96.923 195 4 2 5711 5905 250111526 250111718 6.210000e-85 326
33 TraesCS5B01G410600 chrUn 96.907 194 5 1 5713 5905 40706721 40706914 2.230000e-84 324
34 TraesCS5B01G410600 chrUn 90.476 105 10 0 5191 5295 269814258 269814154 8.680000e-29 139
35 TraesCS5B01G410600 chr4A 97.382 191 4 1 5725 5915 456485706 456485517 2.230000e-84 324
36 TraesCS5B01G410600 chr4A 97.382 191 4 1 5725 5915 456486511 456486322 2.230000e-84 324
37 TraesCS5B01G410600 chr4A 97.382 191 4 1 5725 5915 456487306 456487117 2.230000e-84 324
38 TraesCS5B01G410600 chr4A 90.566 106 10 0 5190 5295 595055513 595055618 2.410000e-29 141


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 TraesCS5B01G410600 chr5B 586274616 586281039 6423 False 11863.0 11863 100.000000 1 6424 1 chr5B.!!$F1 6423
1 TraesCS5B01G410600 chr5D 478448944 478454834 5890 False 2884.0 5273 93.545333 518 6424 3 chr5D.!!$F1 5906
2 TraesCS5B01G410600 chr5A 597498449 597505497 7048 False 844.0 3216 90.767778 2 6065 9 chr5A.!!$F2 6063
3 TraesCS5B01G410600 chr6D 392785739 392786601 862 True 371.5 377 94.979000 273 510 2 chr6D.!!$R1 237
4 TraesCS5B01G410600 chr4A 456485517 456487306 1789 True 324.0 324 97.382000 5725 5915 3 chr4A.!!$R1 190

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
168 169 0.179171 ATGCGTCTACGGTGACTTCG 60.179 55.000 4.49 0.0 40.23 3.79 F
398 401 0.325296 TTACCCGCACTCCTCTCCAT 60.325 55.000 0.00 0.0 0.00 3.41 F
504 507 1.202256 CGCACGGACATCTTGCTAGTA 60.202 52.381 0.00 0.0 33.90 1.82 F
842 866 1.202651 AGTTTCGTCCTCCACCACTTG 60.203 52.381 0.00 0.0 0.00 3.16 F
1858 1888 1.271379 ACTGCCACGATAACCTTTGCT 60.271 47.619 0.00 0.0 0.00 3.91 F
2199 2233 2.565834 TCGCTCTTAGGGCTACAAAGTT 59.434 45.455 1.51 0.0 0.00 2.66 F
2996 3484 0.389025 CACCCTTTTGTGACCCAAGC 59.611 55.000 0.00 0.0 38.55 4.01 F
4355 6157 0.706433 ACTTGGGAGGTTGCATGGAT 59.294 50.000 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1527 1557 0.681564 AGCTCGGAGTCAGTACAGGG 60.682 60.000 6.90 0.00 0.00 4.45 R
2329 2548 0.391927 CCACCGAATAACAAGGCCGA 60.392 55.000 0.00 0.00 0.00 5.54 R
2456 2681 0.596859 GCACCCTAATACTCGCGGAC 60.597 60.000 6.13 0.00 0.00 4.79 R
2528 2753 1.303643 CTGGACAAAGGGACAGGGC 60.304 63.158 0.00 0.00 0.00 5.19 R
2849 3179 2.733227 GCTCCCACATCGATGCAAAAAG 60.733 50.000 25.11 16.07 0.00 2.27 R
3380 3870 6.386654 CACCACAGGTTACATAATTTTCACC 58.613 40.000 0.00 0.00 31.02 4.02 R
4368 6170 0.315886 TGCAACCTCATGCTGCAAAG 59.684 50.000 6.36 7.43 46.54 2.77 R
5639 7484 0.257039 ATAGGCAGGCTGGTGGAAAG 59.743 55.000 17.64 0.00 0.00 2.62 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
40 41 4.281182 TGGTGAGAGAGGAGTCTGTAAAAC 59.719 45.833 0.00 0.00 30.97 2.43
45 46 6.043854 AGAGAGGAGTCTGTAAAACCAATC 57.956 41.667 0.00 0.00 30.97 2.67
56 57 6.874134 TCTGTAAAACCAATCTGTAGAAGCTC 59.126 38.462 0.00 0.00 0.00 4.09
68 69 5.241064 TCTGTAGAAGCTCTTCGTAAGTGTT 59.759 40.000 4.19 0.00 43.97 3.32
69 70 5.839621 TGTAGAAGCTCTTCGTAAGTGTTT 58.160 37.500 4.19 0.00 43.97 2.83
76 77 7.027778 AGCTCTTCGTAAGTGTTTCATTTTT 57.972 32.000 0.00 0.00 39.48 1.94
98 99 6.928979 TTTGTTTTCTGGACGTATTTCAGA 57.071 33.333 0.00 0.00 35.95 3.27
103 104 4.884668 TCTGGACGTATTTCAGACCTTT 57.115 40.909 0.00 0.00 33.21 3.11
106 107 2.928116 GGACGTATTTCAGACCTTTCGG 59.072 50.000 0.00 0.00 0.00 4.30
107 108 2.344025 ACGTATTTCAGACCTTTCGGC 58.656 47.619 0.00 0.00 0.00 5.54
108 109 1.323534 CGTATTTCAGACCTTTCGGCG 59.676 52.381 0.00 0.00 0.00 6.46
109 110 2.613691 GTATTTCAGACCTTTCGGCGA 58.386 47.619 4.99 4.99 0.00 5.54
110 111 2.403252 ATTTCAGACCTTTCGGCGAT 57.597 45.000 11.76 0.00 0.00 4.58
111 112 1.438651 TTTCAGACCTTTCGGCGATG 58.561 50.000 11.76 4.79 0.00 3.84
112 113 0.320374 TTCAGACCTTTCGGCGATGT 59.680 50.000 11.76 8.82 0.00 3.06
113 114 0.389817 TCAGACCTTTCGGCGATGTG 60.390 55.000 11.76 4.53 0.00 3.21
114 115 0.670546 CAGACCTTTCGGCGATGTGT 60.671 55.000 11.76 8.00 0.00 3.72
115 116 0.670546 AGACCTTTCGGCGATGTGTG 60.671 55.000 11.76 0.35 0.00 3.82
116 117 0.949105 GACCTTTCGGCGATGTGTGT 60.949 55.000 11.76 3.98 0.00 3.72
117 118 0.534203 ACCTTTCGGCGATGTGTGTT 60.534 50.000 11.76 0.00 0.00 3.32
118 119 1.270412 ACCTTTCGGCGATGTGTGTTA 60.270 47.619 11.76 0.00 0.00 2.41
119 120 1.801771 CCTTTCGGCGATGTGTGTTAA 59.198 47.619 11.76 0.00 0.00 2.01
120 121 2.159707 CCTTTCGGCGATGTGTGTTAAG 60.160 50.000 11.76 8.61 0.00 1.85
121 122 2.157834 TTCGGCGATGTGTGTTAAGT 57.842 45.000 11.76 0.00 0.00 2.24
132 133 3.004419 TGTGTGTTAAGTGAGAGGAGACG 59.996 47.826 0.00 0.00 0.00 4.18
135 136 4.228317 GTGTTAAGTGAGAGGAGACGTTC 58.772 47.826 0.00 0.00 0.00 3.95
158 159 4.443394 CCCGTTAACTATGAATGCGTCTAC 59.557 45.833 3.71 0.00 0.00 2.59
161 162 3.795623 AACTATGAATGCGTCTACGGT 57.204 42.857 4.49 0.00 40.23 4.83
168 169 0.179171 ATGCGTCTACGGTGACTTCG 60.179 55.000 4.49 0.00 40.23 3.79
179 180 5.338614 ACGGTGACTTCGTCAATTTTAAG 57.661 39.130 0.00 0.00 44.49 1.85
187 188 9.825972 TGACTTCGTCAATTTTAAGATGATTTC 57.174 29.630 0.00 0.00 39.78 2.17
189 190 9.014297 ACTTCGTCAATTTTAAGATGATTTCCT 57.986 29.630 0.00 0.00 30.53 3.36
230 231 5.368145 GTGTTCATAAGGATAGGATGTGCA 58.632 41.667 0.00 0.00 0.00 4.57
234 235 4.041938 TCATAAGGATAGGATGTGCATGCA 59.958 41.667 18.46 18.46 0.00 3.96
238 239 2.228103 GGATAGGATGTGCATGCATGTG 59.772 50.000 25.64 5.68 0.00 3.21
241 242 1.897133 AGGATGTGCATGCATGTGTTT 59.103 42.857 25.64 10.82 0.00 2.83
242 243 2.094390 AGGATGTGCATGCATGTGTTTC 60.094 45.455 25.64 17.79 0.00 2.78
244 245 3.129113 GGATGTGCATGCATGTGTTTCTA 59.871 43.478 25.64 8.19 0.00 2.10
256 258 8.978874 TGCATGTGTTTCTAGGATGTTTATAT 57.021 30.769 0.00 0.00 0.00 0.86
262 264 8.122952 GTGTTTCTAGGATGTTTATATGTGCAC 58.877 37.037 10.75 10.75 0.00 4.57
263 265 7.011016 TGTTTCTAGGATGTTTATATGTGCACG 59.989 37.037 13.13 0.00 0.00 5.34
264 266 4.988540 TCTAGGATGTTTATATGTGCACGC 59.011 41.667 13.13 0.00 0.00 5.34
267 269 3.242608 GGATGTTTATATGTGCACGCGTT 60.243 43.478 10.22 0.00 0.00 4.84
270 272 2.166741 TTATATGTGCACGCGTTTGC 57.833 45.000 10.22 12.67 43.31 3.68
318 320 2.047002 TGATGATGATGGTGTGCCTG 57.953 50.000 0.00 0.00 35.27 4.85
333 335 1.424684 TGCCTGCCATCCTGCAATATA 59.575 47.619 0.00 0.00 41.51 0.86
390 393 3.793559 ACTATGACAATTACCCGCACTC 58.206 45.455 0.00 0.00 0.00 3.51
395 398 1.207329 ACAATTACCCGCACTCCTCTC 59.793 52.381 0.00 0.00 0.00 3.20
398 401 0.325296 TTACCCGCACTCCTCTCCAT 60.325 55.000 0.00 0.00 0.00 3.41
410 413 6.528321 CACTCCTCTCCATATTTGCAGATAA 58.472 40.000 0.45 0.00 0.00 1.75
417 420 5.457686 TCCATATTTGCAGATAAGGCCTTT 58.542 37.500 26.08 11.72 0.00 3.11
440 443 3.370953 CCTCGTTCATCCTTTTCTCCCAT 60.371 47.826 0.00 0.00 0.00 4.00
443 446 5.811190 TCGTTCATCCTTTTCTCCCATAAA 58.189 37.500 0.00 0.00 0.00 1.40
504 507 1.202256 CGCACGGACATCTTGCTAGTA 60.202 52.381 0.00 0.00 33.90 1.82
505 508 2.543861 CGCACGGACATCTTGCTAGTAT 60.544 50.000 0.00 0.00 33.90 2.12
506 509 3.304458 CGCACGGACATCTTGCTAGTATA 60.304 47.826 0.00 0.00 33.90 1.47
507 510 3.982058 GCACGGACATCTTGCTAGTATAC 59.018 47.826 0.00 0.00 33.26 1.47
508 511 4.261656 GCACGGACATCTTGCTAGTATACT 60.262 45.833 10.87 10.87 33.26 2.12
509 512 5.048921 GCACGGACATCTTGCTAGTATACTA 60.049 44.000 12.05 12.05 33.26 1.82
510 513 6.514541 GCACGGACATCTTGCTAGTATACTAA 60.515 42.308 13.51 0.62 33.26 2.24
511 514 7.423199 CACGGACATCTTGCTAGTATACTAAA 58.577 38.462 13.51 5.61 0.00 1.85
512 515 7.378995 CACGGACATCTTGCTAGTATACTAAAC 59.621 40.741 13.51 9.30 0.00 2.01
513 516 6.577800 CGGACATCTTGCTAGTATACTAAACG 59.422 42.308 13.51 3.99 0.00 3.60
791 812 4.890306 GGCCTCCTCCTCCTCCCC 62.890 77.778 0.00 0.00 0.00 4.81
792 813 4.890306 GCCTCCTCCTCCTCCCCC 62.890 77.778 0.00 0.00 0.00 5.40
793 814 3.039526 CCTCCTCCTCCTCCCCCT 61.040 72.222 0.00 0.00 0.00 4.79
794 815 2.612251 CTCCTCCTCCTCCCCCTC 59.388 72.222 0.00 0.00 0.00 4.30
795 816 3.036959 TCCTCCTCCTCCCCCTCC 61.037 72.222 0.00 0.00 0.00 4.30
812 833 1.448013 CCTTTCTTCCTCCGTCCGC 60.448 63.158 0.00 0.00 0.00 5.54
842 866 1.202651 AGTTTCGTCCTCCACCACTTG 60.203 52.381 0.00 0.00 0.00 3.16
906 932 1.531578 GTTTCTTGGCCTTGTCGTCTC 59.468 52.381 3.32 0.00 0.00 3.36
915 941 2.926838 GCCTTGTCGTCTCTTCTTGATC 59.073 50.000 0.00 0.00 0.00 2.92
1107 1133 4.711949 CAGCAGCTCCTGGCCGTT 62.712 66.667 0.00 0.00 43.05 4.44
1266 1292 3.442100 GCTCAAACCATGCAGATTTAGC 58.558 45.455 0.00 0.33 0.00 3.09
1527 1557 1.734707 GCCATGTGATGCTTTGCTGTC 60.735 52.381 0.00 0.00 0.00 3.51
1538 1568 2.417719 CTTTGCTGTCCCTGTACTGAC 58.582 52.381 0.60 2.91 0.00 3.51
1858 1888 1.271379 ACTGCCACGATAACCTTTGCT 60.271 47.619 0.00 0.00 0.00 3.91
1874 1904 6.993079 ACCTTTGCTCCTTTGTTTATTTAGG 58.007 36.000 0.00 0.00 0.00 2.69
1909 1940 3.728864 GCATGCATTAGACCACAAGTTCG 60.729 47.826 14.21 0.00 0.00 3.95
1938 1970 3.275617 AATAACACCGGCATCTTAGCA 57.724 42.857 0.00 0.00 35.83 3.49
1961 1993 4.094590 AGAGTACGTACACATCAGCAGTAC 59.905 45.833 26.55 0.00 35.85 2.73
1962 1994 4.008330 AGTACGTACACATCAGCAGTACT 58.992 43.478 26.55 0.00 38.59 2.73
1963 1995 3.489180 ACGTACACATCAGCAGTACTC 57.511 47.619 0.00 0.00 36.77 2.59
1964 1996 3.082548 ACGTACACATCAGCAGTACTCT 58.917 45.455 0.00 0.00 36.77 3.24
1965 1997 4.259356 ACGTACACATCAGCAGTACTCTA 58.741 43.478 0.00 0.00 36.77 2.43
1966 1998 4.882427 ACGTACACATCAGCAGTACTCTAT 59.118 41.667 0.00 0.00 36.77 1.98
1967 1999 6.053650 ACGTACACATCAGCAGTACTCTATA 58.946 40.000 0.00 0.00 36.77 1.31
2011 2043 3.052745 AGTAATATGCATCACGAGCACG 58.947 45.455 0.19 0.76 45.95 5.34
2130 2164 4.629251 CCTTTAGAGGCTTCATCTTTGC 57.371 45.455 0.00 0.00 35.94 3.68
2199 2233 2.565834 TCGCTCTTAGGGCTACAAAGTT 59.434 45.455 1.51 0.00 0.00 2.66
2259 2475 5.525378 GCATGTACTGTTTAATCAGCTAGCT 59.475 40.000 12.68 12.68 38.84 3.32
2278 2494 5.344743 AGCTCGAAGGAATTACATCAAGA 57.655 39.130 0.00 0.00 0.00 3.02
2291 2507 6.961359 TTACATCAAGATAACTGGTGTTCG 57.039 37.500 0.00 0.00 37.59 3.95
2297 2513 2.838202 AGATAACTGGTGTTCGGTCCAT 59.162 45.455 0.00 0.00 37.59 3.41
2528 2753 3.499048 CCTACTGTTACTACACTGTGCG 58.501 50.000 7.90 1.82 31.81 5.34
2756 3055 4.085466 CGATGTTGCACAGAACACAAAATG 60.085 41.667 0.00 0.00 38.64 2.32
2758 3057 4.814147 TGTTGCACAGAACACAAAATGAA 58.186 34.783 0.00 0.00 30.75 2.57
2840 3169 7.792736 AGGGACTGTACCATTAAGGATAATGTA 59.207 37.037 12.53 0.00 41.62 2.29
2844 3173 8.871125 ACTGTACCATTAAGGATAATGTAGGAG 58.129 37.037 7.55 2.47 44.56 3.69
2845 3174 9.090103 CTGTACCATTAAGGATAATGTAGGAGA 57.910 37.037 7.55 0.00 44.56 3.71
2883 3368 5.337089 CGATGTGGGAGCATTCATATAGACT 60.337 44.000 0.00 0.00 0.00 3.24
2902 3390 8.791298 ATAGACTAGAGGCCTCTTATTTCTTT 57.209 34.615 39.23 23.93 40.93 2.52
2927 3415 9.970395 TTGATTTCATTTTGATCATAGCCATAC 57.030 29.630 0.00 0.00 30.59 2.39
2950 3438 4.931002 CAGCATTGTTAATTGGTTTGAGGG 59.069 41.667 0.00 0.00 0.00 4.30
2951 3439 4.837860 AGCATTGTTAATTGGTTTGAGGGA 59.162 37.500 0.00 0.00 0.00 4.20
2996 3484 0.389025 CACCCTTTTGTGACCCAAGC 59.611 55.000 0.00 0.00 38.55 4.01
3209 3698 3.371965 ACCTCGGTACATATGAACCTGT 58.628 45.455 10.38 0.00 33.34 4.00
3368 3858 3.665745 AACACAATTTGAGGCATGGAC 57.334 42.857 2.79 0.00 0.00 4.02
3380 3870 2.696707 AGGCATGGACCAATTTGCTATG 59.303 45.455 16.21 1.29 35.46 2.23
3402 3892 6.582677 TGGTGAAAATTATGTAACCTGTGG 57.417 37.500 0.00 0.00 0.00 4.17
3444 3934 1.106351 TTCACACGGGCTGCAAATGT 61.106 50.000 0.50 0.00 0.00 2.71
3462 3952 7.599621 TGCAAATGTTCACATTCTTTTATGGAG 59.400 33.333 5.64 0.00 45.06 3.86
4228 4726 5.304101 TGAGAAAATTAACACAACCTGGCAT 59.696 36.000 0.00 0.00 0.00 4.40
4355 6157 0.706433 ACTTGGGAGGTTGCATGGAT 59.294 50.000 0.00 0.00 0.00 3.41
4440 6242 5.010922 GCATGGTTGAAATATGCCTCCATTA 59.989 40.000 0.00 0.00 40.89 1.90
4441 6243 6.295462 GCATGGTTGAAATATGCCTCCATTAT 60.295 38.462 0.00 0.00 40.89 1.28
4501 6306 9.561069 ACACAGTTCTAATTAAGATGACAACTT 57.439 29.630 3.28 3.28 33.05 2.66
4547 6352 0.738412 GGCATGCATTTGTGTGGCTC 60.738 55.000 21.36 0.00 34.67 4.70
4635 6440 8.949421 ACATCTTATATTTTGGTACAGAGGGAT 58.051 33.333 0.00 0.00 42.39 3.85
4667 6472 6.655078 ATATTTGTCAAAACTGGTGCTTCT 57.345 33.333 1.31 0.00 0.00 2.85
4668 6473 4.370364 TTTGTCAAAACTGGTGCTTCTC 57.630 40.909 0.00 0.00 0.00 2.87
4669 6474 2.297701 TGTCAAAACTGGTGCTTCTCC 58.702 47.619 0.00 0.00 0.00 3.71
4670 6475 2.092429 TGTCAAAACTGGTGCTTCTCCT 60.092 45.455 0.00 0.00 0.00 3.69
4699 6504 5.227805 CGCGTGTTTTTGAATGAGGATATTG 59.772 40.000 0.00 0.00 0.00 1.90
4763 6572 9.736023 GTCATGTATTTCCAATCCATTTAAGAC 57.264 33.333 0.00 0.00 0.00 3.01
4775 6584 7.573968 ATCCATTTAAGACCACTGCTATTTC 57.426 36.000 0.00 0.00 0.00 2.17
4778 6587 2.808906 AAGACCACTGCTATTTCCCC 57.191 50.000 0.00 0.00 0.00 4.81
4779 6588 1.668826 AGACCACTGCTATTTCCCCA 58.331 50.000 0.00 0.00 0.00 4.96
4821 6648 4.143009 ACGTGACCAACATTTTGTTTTTGC 60.143 37.500 0.00 0.00 38.77 3.68
4832 6661 7.693020 ACATTTTGTTTTTGCCAACTATTGAC 58.307 30.769 0.00 0.00 0.00 3.18
5095 6924 1.673168 ACCCCTCTGTACGATACGAC 58.327 55.000 0.00 0.00 0.00 4.34
5100 6929 2.876550 CCTCTGTACGATACGACCATCA 59.123 50.000 0.00 0.00 0.00 3.07
5146 6975 2.475466 GGATAGGTGTCGGCGTCGA 61.475 63.158 8.66 8.66 43.86 4.20
5155 6984 2.089936 TCGGCGTCGATTGGTTTCG 61.090 57.895 8.66 0.00 40.88 3.46
5156 6985 2.097728 GGCGTCGATTGGTTTCGC 59.902 61.111 5.84 5.84 44.95 4.70
5185 7014 1.537814 ATTGCTGGTGGTGGTGCATG 61.538 55.000 0.00 0.00 35.27 4.06
5387 7222 4.155733 TACATGGACAGGGCGCCG 62.156 66.667 22.54 10.51 0.00 6.46
5436 7277 2.043450 CGTGAGGCCTCTCTCCCT 60.043 66.667 32.28 0.00 40.58 4.20
5437 7278 1.684049 CGTGAGGCCTCTCTCCCTT 60.684 63.158 32.28 0.00 40.58 3.95
5438 7279 1.261238 CGTGAGGCCTCTCTCCCTTT 61.261 60.000 32.28 0.00 40.58 3.11
5439 7280 0.539518 GTGAGGCCTCTCTCCCTTTC 59.460 60.000 32.28 4.23 40.58 2.62
5440 7281 0.415429 TGAGGCCTCTCTCCCTTTCT 59.585 55.000 32.28 0.00 40.58 2.52
5441 7282 1.119684 GAGGCCTCTCTCCCTTTCTC 58.880 60.000 26.25 0.00 37.07 2.87
5545 7390 2.665537 CGTACTTAGTCTGACGACGACT 59.334 50.000 0.00 13.97 44.93 4.18
5546 7391 3.854240 CGTACTTAGTCTGACGACGACTA 59.146 47.826 0.00 12.49 44.93 2.59
5559 7404 7.226128 TCTGACGACGACTACTCAATATTATGT 59.774 37.037 0.00 0.00 0.00 2.29
5617 7462 2.539547 CGTTGAACAAGTCTGCCAAGTG 60.540 50.000 0.00 0.00 0.00 3.16
5618 7463 1.024271 TGAACAAGTCTGCCAAGTGC 58.976 50.000 0.00 0.00 41.77 4.40
5619 7464 0.312102 GAACAAGTCTGCCAAGTGCC 59.688 55.000 0.00 0.00 40.16 5.01
5622 7467 0.313043 CAAGTCTGCCAAGTGCCAAG 59.687 55.000 0.00 0.00 40.16 3.61
5625 7470 1.160137 GTCTGCCAAGTGCCAAGTAG 58.840 55.000 0.00 0.00 40.16 2.57
5626 7471 0.036732 TCTGCCAAGTGCCAAGTAGG 59.963 55.000 0.00 0.00 40.16 3.18
5627 7472 0.036732 CTGCCAAGTGCCAAGTAGGA 59.963 55.000 0.00 0.00 41.22 2.94
5634 7479 6.043822 TGCCAAGTGCCAAGTAGGAATATATA 59.956 38.462 0.00 0.00 41.22 0.86
5636 7481 8.265055 GCCAAGTGCCAAGTAGGAATATATATA 58.735 37.037 0.00 0.00 41.22 0.86
5657 7502 0.840288 TCTTTCCACCAGCCTGCCTA 60.840 55.000 0.00 0.00 0.00 3.93
5701 7546 1.153025 ACATCGATGCCTGCATGCT 60.153 52.632 25.11 0.00 36.70 3.79
5716 7561 3.058983 TGCATGCTAAGTCGTTGTTTCAG 60.059 43.478 20.33 0.00 0.00 3.02
5720 7565 2.544267 GCTAAGTCGTTGTTTCAGCACT 59.456 45.455 0.00 0.00 0.00 4.40
5721 7566 3.739300 GCTAAGTCGTTGTTTCAGCACTA 59.261 43.478 0.00 0.00 0.00 2.74
5722 7567 4.143305 GCTAAGTCGTTGTTTCAGCACTAG 60.143 45.833 0.00 0.00 0.00 2.57
5723 7568 3.454371 AGTCGTTGTTTCAGCACTAGT 57.546 42.857 0.00 0.00 0.00 2.57
5730 7575 5.007332 CGTTGTTTCAGCACTAGTAAAAGGT 59.993 40.000 0.00 0.00 0.00 3.50
5978 7823 3.183793 CAGGTGTACTGCATGCATCTA 57.816 47.619 22.97 10.92 40.97 1.98
6067 7923 0.327591 GCCCCTGAGATCCATCCATC 59.672 60.000 0.00 0.00 0.00 3.51
6068 7924 0.990374 CCCCTGAGATCCATCCATCC 59.010 60.000 0.00 0.00 0.00 3.51
6069 7925 1.738474 CCCTGAGATCCATCCATCCA 58.262 55.000 0.00 0.00 0.00 3.41
6169 8104 4.081030 CTGCTGAACAGTGCCGCG 62.081 66.667 0.00 0.00 41.86 6.46
6206 8141 1.371267 CTTCTCAACGACGCCGACA 60.371 57.895 0.00 0.00 39.50 4.35
6207 8142 1.606350 CTTCTCAACGACGCCGACAC 61.606 60.000 0.00 0.00 39.50 3.67
6208 8143 3.458579 CTCAACGACGCCGACACG 61.459 66.667 0.00 0.00 39.50 4.49
6303 8242 0.303796 GGCAGCGGCGATTAACTAAC 59.696 55.000 12.98 0.00 42.47 2.34
6351 8648 2.048503 GGTTGTGGGTCGTCGGAG 60.049 66.667 0.00 0.00 0.00 4.63
6352 8649 2.737376 GTTGTGGGTCGTCGGAGC 60.737 66.667 0.00 0.00 39.95 4.70
6382 8899 2.414481 CTGCTTGCTAGTTGCTACTGTG 59.586 50.000 11.27 5.09 43.37 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.790157 TCACCAACCAACCCCCTTATT 59.210 47.619 0.00 0.00 0.00 1.40
3 4 1.357761 CTCACCAACCAACCCCCTTAT 59.642 52.381 0.00 0.00 0.00 1.73
4 5 0.774908 CTCACCAACCAACCCCCTTA 59.225 55.000 0.00 0.00 0.00 2.69
5 6 0.996762 TCTCACCAACCAACCCCCTT 60.997 55.000 0.00 0.00 0.00 3.95
6 7 1.386772 TCTCACCAACCAACCCCCT 60.387 57.895 0.00 0.00 0.00 4.79
9 10 0.036875 CCTCTCTCACCAACCAACCC 59.963 60.000 0.00 0.00 0.00 4.11
40 41 4.116747 ACGAAGAGCTTCTACAGATTGG 57.883 45.455 8.44 0.00 37.44 3.16
45 46 5.049398 ACACTTACGAAGAGCTTCTACAG 57.951 43.478 8.44 4.01 37.44 2.74
76 77 5.237779 GGTCTGAAATACGTCCAGAAAACAA 59.762 40.000 10.18 0.00 38.49 2.83
77 78 4.753107 GGTCTGAAATACGTCCAGAAAACA 59.247 41.667 10.18 0.00 38.49 2.83
78 79 4.995487 AGGTCTGAAATACGTCCAGAAAAC 59.005 41.667 10.18 5.92 38.49 2.43
80 81 4.884668 AGGTCTGAAATACGTCCAGAAA 57.115 40.909 10.18 0.00 38.49 2.52
83 84 3.612860 CGAAAGGTCTGAAATACGTCCAG 59.387 47.826 0.00 0.00 0.00 3.86
103 104 1.000052 TCACTTAACACACATCGCCGA 60.000 47.619 0.00 0.00 0.00 5.54
106 107 2.668457 CCTCTCACTTAACACACATCGC 59.332 50.000 0.00 0.00 0.00 4.58
107 108 4.082733 TCTCCTCTCACTTAACACACATCG 60.083 45.833 0.00 0.00 0.00 3.84
108 109 5.164954 GTCTCCTCTCACTTAACACACATC 58.835 45.833 0.00 0.00 0.00 3.06
109 110 4.321304 CGTCTCCTCTCACTTAACACACAT 60.321 45.833 0.00 0.00 0.00 3.21
110 111 3.004419 CGTCTCCTCTCACTTAACACACA 59.996 47.826 0.00 0.00 0.00 3.72
111 112 3.004524 ACGTCTCCTCTCACTTAACACAC 59.995 47.826 0.00 0.00 0.00 3.82
112 113 3.220110 ACGTCTCCTCTCACTTAACACA 58.780 45.455 0.00 0.00 0.00 3.72
113 114 3.919223 ACGTCTCCTCTCACTTAACAC 57.081 47.619 0.00 0.00 0.00 3.32
114 115 3.255149 GGAACGTCTCCTCTCACTTAACA 59.745 47.826 8.87 0.00 41.61 2.41
115 116 3.367190 GGGAACGTCTCCTCTCACTTAAC 60.367 52.174 13.94 0.00 44.68 2.01
116 117 2.824341 GGGAACGTCTCCTCTCACTTAA 59.176 50.000 13.94 0.00 44.68 1.85
117 118 2.444421 GGGAACGTCTCCTCTCACTTA 58.556 52.381 13.94 0.00 44.68 2.24
118 119 1.258676 GGGAACGTCTCCTCTCACTT 58.741 55.000 13.94 0.00 44.68 3.16
119 120 2.964343 GGGAACGTCTCCTCTCACT 58.036 57.895 13.94 0.00 44.68 3.41
132 133 3.619929 ACGCATTCATAGTTAACGGGAAC 59.380 43.478 10.42 0.00 0.00 3.62
135 136 3.454375 AGACGCATTCATAGTTAACGGG 58.546 45.455 0.00 0.00 0.00 5.28
140 141 4.336153 TCACCGTAGACGCATTCATAGTTA 59.664 41.667 0.00 0.00 38.18 2.24
141 142 3.129813 TCACCGTAGACGCATTCATAGTT 59.870 43.478 0.00 0.00 38.18 2.24
168 169 7.550712 AGCCAGGAAATCATCTTAAAATTGAC 58.449 34.615 0.00 0.00 0.00 3.18
179 180 5.397142 AAAAACTGAGCCAGGAAATCATC 57.603 39.130 7.06 0.00 35.51 2.92
202 203 8.210946 CACATCCTATCCTTATGAACACCTTTA 58.789 37.037 0.00 0.00 0.00 1.85
203 204 7.056635 CACATCCTATCCTTATGAACACCTTT 58.943 38.462 0.00 0.00 0.00 3.11
206 207 4.757149 GCACATCCTATCCTTATGAACACC 59.243 45.833 0.00 0.00 0.00 4.16
207 208 5.368145 TGCACATCCTATCCTTATGAACAC 58.632 41.667 0.00 0.00 0.00 3.32
209 210 5.106396 GCATGCACATCCTATCCTTATGAAC 60.106 44.000 14.21 0.00 0.00 3.18
210 211 5.005740 GCATGCACATCCTATCCTTATGAA 58.994 41.667 14.21 0.00 0.00 2.57
218 219 2.882761 ACACATGCATGCACATCCTATC 59.117 45.455 25.37 0.00 0.00 2.08
224 225 3.129813 CCTAGAAACACATGCATGCACAT 59.870 43.478 25.37 11.52 0.00 3.21
230 231 7.886629 ATAAACATCCTAGAAACACATGCAT 57.113 32.000 0.00 0.00 0.00 3.96
234 235 8.840321 GCACATATAAACATCCTAGAAACACAT 58.160 33.333 0.00 0.00 0.00 3.21
238 239 7.345192 CGTGCACATATAAACATCCTAGAAAC 58.655 38.462 18.64 0.00 0.00 2.78
241 242 4.988540 GCGTGCACATATAAACATCCTAGA 59.011 41.667 18.64 0.00 0.00 2.43
242 243 4.143326 CGCGTGCACATATAAACATCCTAG 60.143 45.833 18.64 0.00 0.00 3.02
244 245 2.543848 CGCGTGCACATATAAACATCCT 59.456 45.455 18.64 0.00 0.00 3.24
263 265 2.059541 AGAGTAGAGAAACGCAAACGC 58.940 47.619 0.00 0.00 45.53 4.84
267 269 8.440833 GCTTTTTATAAGAGTAGAGAAACGCAA 58.559 33.333 0.00 0.00 0.00 4.85
270 272 9.355215 TCTGCTTTTTATAAGAGTAGAGAAACG 57.645 33.333 11.85 0.00 30.36 3.60
275 277 9.862371 TCAACTCTGCTTTTTATAAGAGTAGAG 57.138 33.333 26.36 26.36 46.64 2.43
318 320 1.467920 GGCCTATATTGCAGGATGGC 58.532 55.000 0.00 10.13 34.91 4.40
333 335 2.810870 AGATATAGATCGGACGGCCT 57.189 50.000 5.33 0.00 37.15 5.19
395 398 5.279156 GGAAAGGCCTTATCTGCAAATATGG 60.279 44.000 20.84 7.46 32.28 2.74
417 420 2.236395 GGGAGAAAAGGATGAACGAGGA 59.764 50.000 0.00 0.00 0.00 3.71
470 473 2.942879 TGCGTTGCACGGAACATC 59.057 55.556 10.02 0.00 39.47 3.06
504 507 8.175716 GCAACTTTAGCAAATCTCGTTTAGTAT 58.824 33.333 0.00 0.00 0.00 2.12
505 508 7.386848 AGCAACTTTAGCAAATCTCGTTTAGTA 59.613 33.333 0.00 0.00 0.00 1.82
506 509 6.204882 AGCAACTTTAGCAAATCTCGTTTAGT 59.795 34.615 0.00 0.00 0.00 2.24
507 510 6.603095 AGCAACTTTAGCAAATCTCGTTTAG 58.397 36.000 0.00 0.00 0.00 1.85
508 511 6.426937 AGAGCAACTTTAGCAAATCTCGTTTA 59.573 34.615 0.00 0.00 0.00 2.01
509 512 5.239525 AGAGCAACTTTAGCAAATCTCGTTT 59.760 36.000 0.00 0.00 0.00 3.60
510 513 4.757149 AGAGCAACTTTAGCAAATCTCGTT 59.243 37.500 0.00 0.00 0.00 3.85
511 514 4.153117 CAGAGCAACTTTAGCAAATCTCGT 59.847 41.667 0.00 0.00 0.00 4.18
512 515 4.389992 TCAGAGCAACTTTAGCAAATCTCG 59.610 41.667 0.00 0.00 0.00 4.04
513 516 5.641209 TCTCAGAGCAACTTTAGCAAATCTC 59.359 40.000 0.00 0.00 0.00 2.75
790 811 0.537653 GACGGAGGAAGAAAGGAGGG 59.462 60.000 0.00 0.00 0.00 4.30
791 812 0.537653 GGACGGAGGAAGAAAGGAGG 59.462 60.000 0.00 0.00 0.00 4.30
792 813 0.173708 CGGACGGAGGAAGAAAGGAG 59.826 60.000 0.00 0.00 0.00 3.69
793 814 1.885163 GCGGACGGAGGAAGAAAGGA 61.885 60.000 0.00 0.00 0.00 3.36
794 815 1.448013 GCGGACGGAGGAAGAAAGG 60.448 63.158 0.00 0.00 0.00 3.11
795 816 1.448013 GGCGGACGGAGGAAGAAAG 60.448 63.158 0.00 0.00 0.00 2.62
812 833 1.602605 GACGAAACTTGGGGGTGGG 60.603 63.158 0.00 0.00 0.00 4.61
842 866 6.463360 AGATGAACTCTCCTGAAAAGAAGAC 58.537 40.000 0.00 0.00 0.00 3.01
906 932 4.503734 GCAGAGAATCGACAGATCAAGAAG 59.496 45.833 0.00 0.00 42.67 2.85
915 941 1.070821 TTTGCGCAGAGAATCGACAG 58.929 50.000 11.31 0.00 42.67 3.51
1083 1109 4.631247 AGGAGCTGCTGCAACGCA 62.631 61.111 23.21 0.27 42.74 5.24
1247 1273 5.500234 ACTAGCTAAATCTGCATGGTTTGA 58.500 37.500 0.00 0.00 0.00 2.69
1303 1329 3.851077 CGCGCTCAGCTTCAGCAG 61.851 66.667 5.56 8.07 45.59 4.24
1466 1492 3.187842 TCCATCGTATGTATCGAGGAACG 59.812 47.826 1.78 0.00 40.68 3.95
1527 1557 0.681564 AGCTCGGAGTCAGTACAGGG 60.682 60.000 6.90 0.00 0.00 4.45
1738 1768 1.740025 GGCAACCCAAGAATCTTCTCG 59.260 52.381 0.00 0.00 36.28 4.04
1858 1888 4.859104 TCCCTCCCCTAAATAAACAAAGGA 59.141 41.667 0.00 0.00 0.00 3.36
1874 1904 1.075659 GCATGCCCTTATCCCTCCC 59.924 63.158 6.36 0.00 0.00 4.30
1909 1940 7.611213 AGATGCCGGTGTTATTATAATTAGC 57.389 36.000 1.90 0.57 0.00 3.09
1938 1970 3.082548 ACTGCTGATGTGTACGTACTCT 58.917 45.455 25.12 12.13 0.00 3.24
1962 1994 8.251026 CGGGTGCTGATTTAATACTCATATAGA 58.749 37.037 0.00 0.00 0.00 1.98
1963 1995 8.035394 ACGGGTGCTGATTTAATACTCATATAG 58.965 37.037 0.00 0.00 0.00 1.31
1964 1996 7.903145 ACGGGTGCTGATTTAATACTCATATA 58.097 34.615 0.00 0.00 0.00 0.86
1965 1997 6.769512 ACGGGTGCTGATTTAATACTCATAT 58.230 36.000 0.00 0.00 0.00 1.78
1966 1998 6.169557 ACGGGTGCTGATTTAATACTCATA 57.830 37.500 0.00 0.00 0.00 2.15
1967 1999 5.036117 ACGGGTGCTGATTTAATACTCAT 57.964 39.130 0.00 0.00 0.00 2.90
1980 2012 3.106242 TGCATATTACTACGGGTGCTG 57.894 47.619 0.00 0.00 33.95 4.41
1985 2017 4.166523 CTCGTGATGCATATTACTACGGG 58.833 47.826 0.00 0.43 0.00 5.28
2011 2043 2.435059 GAACCACGAGCTCCCTGC 60.435 66.667 8.47 0.00 43.29 4.85
2087 2119 5.104900 AGGTTGAAGACAGTGTGTTACTTCT 60.105 40.000 18.17 7.84 37.60 2.85
2130 2164 3.564644 CCTATGAATTGCCTCTGCTGAAG 59.435 47.826 0.00 0.00 38.71 3.02
2199 2233 4.068599 TGATTAAACTGCCGACACAATCA 58.931 39.130 0.00 0.00 0.00 2.57
2259 2475 7.710907 CCAGTTATCTTGATGTAATTCCTTCGA 59.289 37.037 0.00 0.00 0.00 3.71
2278 2494 5.011738 CCTATATGGACCGAACACCAGTTAT 59.988 44.000 0.00 0.00 39.62 1.89
2291 2507 8.925338 ACTCGATTTATAATCCCTATATGGACC 58.075 37.037 0.00 0.00 37.20 4.46
2329 2548 0.391927 CCACCGAATAACAAGGCCGA 60.392 55.000 0.00 0.00 0.00 5.54
2456 2681 0.596859 GCACCCTAATACTCGCGGAC 60.597 60.000 6.13 0.00 0.00 4.79
2528 2753 1.303643 CTGGACAAAGGGACAGGGC 60.304 63.158 0.00 0.00 0.00 5.19
2714 2987 5.299279 ACATCGAGGGCATTATTAAACAAGG 59.701 40.000 0.69 0.00 0.00 3.61
2756 3055 5.398603 TCTTGACCTGATCTGAAGAGTTC 57.601 43.478 0.38 0.00 0.00 3.01
2758 3057 4.776837 ACATCTTGACCTGATCTGAAGAGT 59.223 41.667 0.38 1.59 0.00 3.24
2840 3169 5.416952 ACATCGATGCAAAAAGAAATCTCCT 59.583 36.000 25.11 0.00 0.00 3.69
2844 3173 4.563976 CCCACATCGATGCAAAAAGAAATC 59.436 41.667 25.11 0.00 0.00 2.17
2845 3174 4.220382 TCCCACATCGATGCAAAAAGAAAT 59.780 37.500 25.11 0.00 0.00 2.17
2849 3179 2.733227 GCTCCCACATCGATGCAAAAAG 60.733 50.000 25.11 16.07 0.00 2.27
2883 3368 8.328758 TGAAATCAAAGAAATAAGAGGCCTCTA 58.671 33.333 35.31 22.41 39.39 2.43
2902 3390 9.134055 TGTATGGCTATGATCAAAATGAAATCA 57.866 29.630 0.00 0.00 34.17 2.57
2927 3415 4.931002 CCCTCAAACCAATTAACAATGCTG 59.069 41.667 0.00 0.00 0.00 4.41
2996 3484 4.769688 TGTAGGAGCCACACATCAAATAG 58.230 43.478 0.00 0.00 0.00 1.73
3368 3858 8.721019 ACATAATTTTCACCATAGCAAATTGG 57.279 30.769 0.00 0.00 39.02 3.16
3380 3870 6.386654 CACCACAGGTTACATAATTTTCACC 58.613 40.000 0.00 0.00 31.02 4.02
3953 4447 8.000780 ACTTATCACTGCCCATTTTCTTTATC 57.999 34.615 0.00 0.00 0.00 1.75
4368 6170 0.315886 TGCAACCTCATGCTGCAAAG 59.684 50.000 6.36 7.43 46.54 2.77
4440 6242 5.014123 TGGTTACTGGGTGAAGATCAGAAAT 59.986 40.000 0.00 0.00 33.19 2.17
4441 6243 4.349636 TGGTTACTGGGTGAAGATCAGAAA 59.650 41.667 0.00 0.00 33.19 2.52
4501 6306 6.018588 CACATTGTAACAAACGGTGAGAAGTA 60.019 38.462 0.00 0.00 32.20 2.24
4572 6377 7.398047 GGTACAGGGGGAATAACTAAATTTTGT 59.602 37.037 0.00 0.00 0.00 2.83
4662 6467 1.228657 ACACGCGGAAAAGGAGAAGC 61.229 55.000 12.47 0.00 0.00 3.86
4665 6470 1.670791 AAAACACGCGGAAAAGGAGA 58.329 45.000 12.47 0.00 0.00 3.71
4667 6472 1.743958 TCAAAAACACGCGGAAAAGGA 59.256 42.857 12.47 0.00 0.00 3.36
4668 6473 2.196295 TCAAAAACACGCGGAAAAGG 57.804 45.000 12.47 0.00 0.00 3.11
4669 6474 3.794028 TCATTCAAAAACACGCGGAAAAG 59.206 39.130 12.47 0.00 0.00 2.27
4670 6475 3.770666 TCATTCAAAAACACGCGGAAAA 58.229 36.364 12.47 0.00 0.00 2.29
4699 6504 1.370414 GGTGTGTTCGTGCATGCAC 60.370 57.895 35.76 35.76 43.01 4.57
4763 6572 2.094675 CACTTGGGGAAATAGCAGTGG 58.905 52.381 0.00 0.00 0.00 4.00
4775 6584 1.609783 GGATCTGGACCACTTGGGG 59.390 63.158 0.00 0.00 42.91 4.96
4778 6587 1.221840 CCCGGATCTGGACCACTTG 59.778 63.158 23.02 0.00 0.00 3.16
4779 6588 0.546747 TTCCCGGATCTGGACCACTT 60.547 55.000 23.02 0.00 0.00 3.16
4821 6648 0.370273 GTCTGCGCGTCAATAGTTGG 59.630 55.000 8.43 0.00 0.00 3.77
4832 6661 1.005975 GCAATTAGTACTGTCTGCGCG 60.006 52.381 5.39 0.00 0.00 6.86
5095 6924 3.753815 TGGTGGCATGTATGTATGATGG 58.246 45.455 0.00 0.00 0.00 3.51
5100 6929 6.982160 AATTCAATGGTGGCATGTATGTAT 57.018 33.333 0.00 0.00 0.00 2.29
5146 6975 0.729116 CATCAGCGAGCGAAACCAAT 59.271 50.000 0.00 0.00 0.00 3.16
5155 6984 1.094073 ACCAGCAATCATCAGCGAGC 61.094 55.000 0.00 0.00 35.48 5.03
5156 6985 0.656259 CACCAGCAATCATCAGCGAG 59.344 55.000 0.00 0.00 35.48 5.03
5185 7014 0.389166 CTTCTCCGTCTCCTGCACAC 60.389 60.000 0.00 0.00 0.00 3.82
5387 7222 0.960364 ACATGCCGTCCACCATGAAC 60.960 55.000 7.53 0.00 40.92 3.18
5436 7277 1.305465 TCCCCGTCCGATGGAGAAA 60.305 57.895 8.34 0.00 29.39 2.52
5437 7278 2.056223 GTCCCCGTCCGATGGAGAA 61.056 63.158 8.34 0.00 29.39 2.87
5438 7279 2.441532 GTCCCCGTCCGATGGAGA 60.442 66.667 8.34 0.00 29.39 3.71
5439 7280 2.442272 AGTCCCCGTCCGATGGAG 60.442 66.667 8.34 0.00 29.39 3.86
5440 7281 2.758327 CAGTCCCCGTCCGATGGA 60.758 66.667 8.34 0.00 0.00 3.41
5441 7282 4.530857 GCAGTCCCCGTCCGATGG 62.531 72.222 0.00 0.00 0.00 3.51
5625 7470 9.343539 GGCTGGTGGAAAGAATATATATATTCC 57.656 37.037 29.63 21.44 46.13 3.01
5627 7472 9.911788 CAGGCTGGTGGAAAGAATATATATATT 57.088 33.333 16.28 16.28 35.77 1.28
5634 7479 2.659428 GCAGGCTGGTGGAAAGAATAT 58.341 47.619 17.64 0.00 0.00 1.28
5636 7481 0.613012 GGCAGGCTGGTGGAAAGAAT 60.613 55.000 17.64 0.00 0.00 2.40
5637 7482 1.228552 GGCAGGCTGGTGGAAAGAA 60.229 57.895 17.64 0.00 0.00 2.52
5639 7484 0.257039 ATAGGCAGGCTGGTGGAAAG 59.743 55.000 17.64 0.00 0.00 2.62
5646 7491 3.786884 CTGGGCATAGGCAGGCTGG 62.787 68.421 17.64 0.00 43.71 4.85
5657 7502 3.394606 CCACCTAGTATTTACCTGGGCAT 59.605 47.826 0.00 0.00 0.00 4.40
5693 7538 3.058983 TGAAACAACGACTTAGCATGCAG 60.059 43.478 21.98 12.16 0.00 4.41
5701 7546 4.940463 ACTAGTGCTGAAACAACGACTTA 58.060 39.130 0.00 0.00 0.00 2.24
5716 7561 3.751698 CCAGGTTGACCTTTTACTAGTGC 59.248 47.826 5.39 0.00 46.09 4.40
5720 7565 3.136809 TGCACCAGGTTGACCTTTTACTA 59.863 43.478 0.00 0.00 46.09 1.82
5721 7566 2.092103 TGCACCAGGTTGACCTTTTACT 60.092 45.455 0.00 0.00 46.09 2.24
5722 7567 2.303175 TGCACCAGGTTGACCTTTTAC 58.697 47.619 0.00 0.00 46.09 2.01
5723 7568 2.738587 TGCACCAGGTTGACCTTTTA 57.261 45.000 0.00 0.00 46.09 1.52
5730 7575 0.692476 AGCTACATGCACCAGGTTGA 59.308 50.000 0.00 0.00 45.94 3.18
5766 7611 2.284405 GGTCGGACCCTTCCCTGA 60.284 66.667 16.55 0.00 38.99 3.86
5978 7823 0.995024 AAAGGAGCCAGGCATGTAGT 59.005 50.000 15.80 0.00 0.00 2.73
6067 7923 1.898574 GTTGATAGGGCCGGCATGG 60.899 63.158 30.85 0.00 42.50 3.66
6068 7924 2.253758 CGTTGATAGGGCCGGCATG 61.254 63.158 30.85 7.19 0.00 4.06
6069 7925 2.111043 CGTTGATAGGGCCGGCAT 59.889 61.111 30.85 19.07 0.00 4.40
6145 8007 4.368391 CTGTTCAGCAGCTTCCGT 57.632 55.556 0.00 0.00 38.52 4.69
6169 8104 2.124278 GGATCCGGGGCCTGTTTC 60.124 66.667 12.30 7.40 0.00 2.78
6352 8649 3.356639 TAGCAAGCAGGACGAGCGG 62.357 63.158 0.00 0.00 37.01 5.52


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

AutoCloner maintained by Alex Coulton.