Multiple sequence alignment - TraesCS5D01G185700

Loading Multiple Alignment...

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 TraesCS5D01G185700 chr5D 100.000 7883 0 0 1 7883 287797640 287805522 0.000000e+00 14558.0
1 TraesCS5D01G185700 chr5D 100.000 180 0 0 8614 8793 287806253 287806432 5.090000e-87 333.0
2 TraesCS5D01G185700 chr5A 95.527 3756 120 13 4172 7883 380218546 380222297 0.000000e+00 5962.0
3 TraesCS5D01G185700 chr5A 90.134 2240 149 35 358 2543 380209714 380211935 0.000000e+00 2846.0
4 TraesCS5D01G185700 chr5A 85.847 756 52 20 3368 4070 380217792 380218545 0.000000e+00 752.0
5 TraesCS5D01G185700 chr5A 88.090 445 38 7 2610 3045 380217359 380217797 1.690000e-141 514.0
6 TraesCS5D01G185700 chr5A 93.370 181 10 2 8614 8793 380222375 380222554 5.230000e-67 267.0
7 TraesCS5D01G185700 chr5A 85.859 99 6 6 350 445 679759447 679759354 2.020000e-16 99.0
8 TraesCS5D01G185700 chr5A 97.872 47 1 0 2565 2611 380211977 380212023 2.030000e-11 82.4
9 TraesCS5D01G185700 chr5B 96.654 3497 97 11 4387 7875 326911867 326915351 0.000000e+00 5792.0
10 TraesCS5D01G185700 chr5B 93.855 716 34 7 715 1429 326910944 326911650 0.000000e+00 1070.0
11 TraesCS5D01G185700 chr5B 81.583 695 48 25 12 663 326910273 326910930 1.320000e-137 501.0
12 TraesCS5D01G185700 chr5B 96.875 128 3 1 8667 8793 326915685 326915812 6.920000e-51 213.0
13 TraesCS5D01G185700 chr5B 84.211 114 12 6 336 445 594076311 594076422 1.210000e-18 106.0
14 TraesCS5D01G185700 chr5B 100.000 31 0 0 250 280 8901104 8901074 3.430000e-04 58.4
15 TraesCS5D01G185700 chr6B 84.928 2070 226 28 1725 3724 210249829 210251882 0.000000e+00 2015.0
16 TraesCS5D01G185700 chr6B 95.000 40 2 0 241 280 567471501 567471540 7.370000e-06 63.9
17 TraesCS5D01G185700 chr2B 77.788 2134 399 44 1764 3848 537846222 537844115 0.000000e+00 1245.0
18 TraesCS5D01G185700 chr2B 81.818 440 55 14 3712 4127 776586600 776586162 6.530000e-91 346.0
19 TraesCS5D01G185700 chr2B 75.604 455 79 14 3768 4198 416880809 416880363 6.960000e-46 196.0
20 TraesCS5D01G185700 chr7D 74.934 2641 544 71 1639 4198 248479927 248477324 0.000000e+00 1101.0
21 TraesCS5D01G185700 chr7D 72.051 712 189 9 1830 2537 556723159 556723864 4.160000e-48 204.0
22 TraesCS5D01G185700 chr7D 82.906 234 30 5 7 234 528126146 528125917 1.500000e-47 202.0
23 TraesCS5D01G185700 chr7D 92.157 51 3 1 4153 4202 161542470 161542420 4.400000e-08 71.3
24 TraesCS5D01G185700 chr7D 93.023 43 3 0 241 283 263044833 263044791 7.370000e-06 63.9
25 TraesCS5D01G185700 chr2A 73.753 2465 514 78 1833 4207 182068773 182066352 0.000000e+00 845.0
26 TraesCS5D01G185700 chr2A 72.390 431 105 11 1973 2396 622858904 622858481 3.330000e-24 124.0
27 TraesCS5D01G185700 chr2A 95.349 43 2 0 243 285 4896822 4896864 1.580000e-07 69.4
28 TraesCS5D01G185700 chr6A 74.093 1930 418 56 1646 3538 412063519 412061635 0.000000e+00 719.0
29 TraesCS5D01G185700 chr6A 85.437 103 9 6 346 444 16606863 16606763 1.560000e-17 102.0
30 TraesCS5D01G185700 chr6A 85.437 103 10 5 346 445 16610236 16610136 1.560000e-17 102.0
31 TraesCS5D01G185700 chr4D 73.744 1592 325 56 2671 4197 437034190 437035753 1.000000e-148 538.0
32 TraesCS5D01G185700 chr4D 72.382 1079 223 48 3173 4202 472680726 472681778 1.120000e-68 272.0
33 TraesCS5D01G185700 chr4D 72.291 646 168 10 1896 2537 420520551 420521189 3.240000e-44 191.0
34 TraesCS5D01G185700 chr4D 84.768 151 20 3 6 156 308801014 308801161 1.980000e-31 148.0
35 TraesCS5D01G185700 chr4D 81.609 174 32 0 3903 4076 278403367 278403194 2.560000e-30 145.0
36 TraesCS5D01G185700 chr4D 71.625 363 98 5 2086 2445 72617056 72617416 2.610000e-15 95.3
37 TraesCS5D01G185700 chr2D 72.736 1104 225 47 2960 4006 539424197 539425281 1.430000e-77 302.0
38 TraesCS5D01G185700 chr2D 76.566 495 107 6 1631 2122 424630391 424630879 6.770000e-66 263.0
39 TraesCS5D01G185700 chr2D 78.477 302 50 9 3903 4198 424630901 424631193 5.420000e-42 183.0
40 TraesCS5D01G185700 chr6D 75.427 586 109 18 3636 4198 131627283 131626710 1.470000e-62 252.0
41 TraesCS5D01G185700 chr6D 73.852 283 70 3 2286 2565 60319995 60319714 9.330000e-20 110.0
42 TraesCS5D01G185700 chr6D 100.000 31 0 0 3023 3053 377218649 377218679 3.430000e-04 58.4
43 TraesCS5D01G185700 chr1A 71.831 994 212 39 3259 4202 432223684 432222709 1.150000e-53 222.0
44 TraesCS5D01G185700 chr1A 85.859 99 9 5 350 445 349354135 349354039 5.620000e-17 100.0
45 TraesCS5D01G185700 chr1A 76.471 204 28 11 4004 4200 487038221 487038031 9.400000e-15 93.5
46 TraesCS5D01G185700 chr1A 90.698 43 3 1 4227 4269 133426030 133425989 1.000000e-03 56.5
47 TraesCS5D01G185700 chr7A 84.348 230 25 6 11 234 608390236 608390012 1.920000e-51 215.0
48 TraesCS5D01G185700 chr7A 80.702 114 19 3 338 449 299595392 299595280 1.570000e-12 86.1
49 TraesCS5D01G185700 chr7A 75.253 198 33 8 4005 4198 258402000 258402185 7.320000e-11 80.5
50 TraesCS5D01G185700 chr7A 96.875 32 1 0 4226 4257 227998104 227998073 4.000000e-03 54.7
51 TraesCS5D01G185700 chr1D 71.667 660 170 14 1989 2640 260834404 260833754 5.460000e-37 167.0
52 TraesCS5D01G185700 chr7B 86.452 155 16 5 12 166 565819147 565818998 1.960000e-36 165.0
53 TraesCS5D01G185700 chr7B 95.833 48 2 0 187 234 565818890 565818843 2.630000e-10 78.7
54 TraesCS5D01G185700 chr7B 92.500 40 3 0 241 280 240489703 240489742 3.430000e-04 58.4
55 TraesCS5D01G185700 chr7B 100.000 30 0 0 4229 4258 129963410 129963381 1.000000e-03 56.5
56 TraesCS5D01G185700 chr3A 86.408 103 9 5 346 445 1741646 1741746 3.360000e-19 108.0
57 TraesCS5D01G185700 chr3A 94.595 37 2 0 4227 4263 606377505 606377541 3.430000e-04 58.4
58 TraesCS5D01G185700 chrUn 82.569 109 19 0 3920 4028 107373433 107373541 7.270000e-16 97.1
59 TraesCS5D01G185700 chr4A 87.500 56 5 2 225 280 362069910 362069963 7.370000e-06 63.9
60 TraesCS5D01G185700 chr3D 91.111 45 4 0 4227 4271 463115408 463115364 2.650000e-05 62.1


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 TraesCS5D01G185700 chr5D 287797640 287806432 8792 False 7445.50 14558 100.00000 1 8793 2 chr5D.!!$F1 8792
1 TraesCS5D01G185700 chr5A 380217359 380222554 5195 False 1873.75 5962 90.70850 2610 8793 4 chr5A.!!$F2 6183
2 TraesCS5D01G185700 chr5A 380209714 380212023 2309 False 1464.20 2846 94.00300 358 2611 2 chr5A.!!$F1 2253
3 TraesCS5D01G185700 chr5B 326910273 326915812 5539 False 1894.00 5792 92.24175 12 8793 4 chr5B.!!$F2 8781
4 TraesCS5D01G185700 chr6B 210249829 210251882 2053 False 2015.00 2015 84.92800 1725 3724 1 chr6B.!!$F1 1999
5 TraesCS5D01G185700 chr2B 537844115 537846222 2107 True 1245.00 1245 77.78800 1764 3848 1 chr2B.!!$R2 2084
6 TraesCS5D01G185700 chr7D 248477324 248479927 2603 True 1101.00 1101 74.93400 1639 4198 1 chr7D.!!$R2 2559
7 TraesCS5D01G185700 chr7D 556723159 556723864 705 False 204.00 204 72.05100 1830 2537 1 chr7D.!!$F1 707
8 TraesCS5D01G185700 chr2A 182066352 182068773 2421 True 845.00 845 73.75300 1833 4207 1 chr2A.!!$R1 2374
9 TraesCS5D01G185700 chr6A 412061635 412063519 1884 True 719.00 719 74.09300 1646 3538 1 chr6A.!!$R1 1892
10 TraesCS5D01G185700 chr4D 437034190 437035753 1563 False 538.00 538 73.74400 2671 4197 1 chr4D.!!$F4 1526
11 TraesCS5D01G185700 chr4D 472680726 472681778 1052 False 272.00 272 72.38200 3173 4202 1 chr4D.!!$F5 1029
12 TraesCS5D01G185700 chr2D 539424197 539425281 1084 False 302.00 302 72.73600 2960 4006 1 chr2D.!!$F1 1046
13 TraesCS5D01G185700 chr2D 424630391 424631193 802 False 223.00 263 77.52150 1631 4198 2 chr2D.!!$F2 2567
14 TraesCS5D01G185700 chr6D 131626710 131627283 573 True 252.00 252 75.42700 3636 4198 1 chr6D.!!$R2 562
15 TraesCS5D01G185700 chr1A 432222709 432223684 975 True 222.00 222 71.83100 3259 4202 1 chr1A.!!$R3 943

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
625 671 0.031857 TTTTGAGCACCGGCAACATG 59.968 50.0 0.00 0.00 44.61 3.21 F
1438 1490 0.034186 CAAGGCCCATAGGTGCTCAA 60.034 55.0 0.00 0.00 34.57 3.02 F
1929 2015 0.179045 CCTGGGCCAGACGGATTTAG 60.179 60.0 34.84 10.69 32.44 1.85 F
3157 3308 0.036164 ACGTGCTTGTTGGCTATGGA 59.964 50.0 0.00 0.00 0.00 3.41 F
3899 4121 0.179000 GGACCAACTCCATCATCGCT 59.821 55.0 0.00 0.00 39.21 4.93 F
4136 4364 0.390866 CCATAGAGCTGCGCCCTATG 60.391 60.0 21.58 21.58 39.41 2.23 F
5612 5962 0.465460 GTGCAACAAGGTCCCACTGA 60.465 55.0 0.00 0.00 36.32 3.41 F
5659 6009 0.744281 CAACCAAGGACCCAACACAC 59.256 55.0 0.00 0.00 0.00 3.82 F
7384 7734 1.557443 CGTTGACTGTCTTCGGCACC 61.557 60.0 9.51 0.00 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1652 1726 0.167470 CTTCTGTGTGCGGCATGAAG 59.833 55.00 5.72 13.43 35.72 3.02 R
2418 2519 0.605319 GGTTGCCGTTGATGAGGACA 60.605 55.00 0.00 0.00 0.00 4.02 R
3545 3705 0.039798 GTCGTACGCAGAGTTGGTCA 60.040 55.00 11.24 0.00 0.00 4.02 R
4077 4305 1.039785 CCAGGGAGTGCGAGATGAGA 61.040 60.00 0.00 0.00 0.00 3.27 R
5503 5853 0.034476 CACAGAGCAGAGTCCAGCAA 59.966 55.00 7.79 0.00 0.00 3.91 R
5659 6009 0.037326 TAACCTGCTTCCACTCTGCG 60.037 55.00 0.00 0.00 0.00 5.18 R
7396 7746 1.086696 CACTGGGAACTAACATGCCG 58.913 55.00 0.00 0.00 0.00 5.69 R
7747 8097 7.696992 ACTGAAGAAGTAAAGACACCAAAAA 57.303 32.00 0.00 0.00 37.36 1.94 R
8652 9010 4.627058 TCAGAAAACGTCAGTGCTTGATA 58.373 39.13 0.00 0.00 38.29 2.15 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
42 43 2.224769 GGAACAAGGTTCATGAGGTCCA 60.225 50.000 10.35 0.00 0.00 4.02
50 51 3.270877 GTTCATGAGGTCCATTACGCTT 58.729 45.455 0.00 0.00 31.94 4.68
56 57 3.270877 GAGGTCCATTACGCTTCAACAT 58.729 45.455 0.00 0.00 0.00 2.71
60 61 4.814234 GGTCCATTACGCTTCAACATATGA 59.186 41.667 10.38 0.00 35.85 2.15
61 62 5.295787 GGTCCATTACGCTTCAACATATGAA 59.704 40.000 10.38 0.00 45.71 2.57
107 108 3.062099 GCATGATTGTGCTCAAATGCTTG 59.938 43.478 22.09 15.32 41.11 4.01
108 109 3.306917 TGATTGTGCTCAAATGCTTGG 57.693 42.857 5.15 0.00 37.11 3.61
110 111 0.751452 TTGTGCTCAAATGCTTGGCA 59.249 45.000 0.00 0.00 44.86 4.92
175 176 5.945191 TCAATAACAATGGAGAGCATTGACA 59.055 36.000 2.69 0.00 41.22 3.58
210 217 2.879026 AGCGTTTCTCTCTTTCCAAACC 59.121 45.455 0.00 0.00 0.00 3.27
222 229 0.696501 TCCAAACCTCCTAAGCCACC 59.303 55.000 0.00 0.00 0.00 4.61
245 252 6.870965 ACCGATATGAGCAGAAAATGATACTC 59.129 38.462 0.00 0.00 0.00 2.59
248 255 4.842531 TGAGCAGAAAATGATACTCCCA 57.157 40.909 0.00 0.00 0.00 4.37
267 274 4.642885 TCCCACCGATCCAAATTAATTGAC 59.357 41.667 0.39 0.00 41.85 3.18
280 287 7.915397 CCAAATTAATTGACGCTGCTTTAGTAT 59.085 33.333 0.39 0.00 41.85 2.12
290 297 8.122330 TGACGCTGCTTTAGTATAATTCAAATG 58.878 33.333 0.00 0.00 0.00 2.32
310 317 8.912988 TCAAATGGTTCAAAGTAAAGAGATGTT 58.087 29.630 0.00 0.00 0.00 2.71
337 344 6.778834 ATCAATGGTTCAACTTATCATGCA 57.221 33.333 0.00 0.00 0.00 3.96
338 345 5.953183 TCAATGGTTCAACTTATCATGCAC 58.047 37.500 0.00 0.00 0.00 4.57
339 346 5.476254 TCAATGGTTCAACTTATCATGCACA 59.524 36.000 0.00 0.00 0.00 4.57
340 347 6.153170 TCAATGGTTCAACTTATCATGCACAT 59.847 34.615 0.00 0.00 0.00 3.21
341 348 5.313520 TGGTTCAACTTATCATGCACATG 57.686 39.130 4.18 4.18 40.09 3.21
352 359 2.689471 TCATGCACATGACATAAAGCCC 59.311 45.455 9.23 0.00 42.42 5.19
353 360 2.512692 TGCACATGACATAAAGCCCT 57.487 45.000 0.00 0.00 0.00 5.19
354 361 2.368439 TGCACATGACATAAAGCCCTC 58.632 47.619 0.00 0.00 0.00 4.30
355 362 1.678101 GCACATGACATAAAGCCCTCC 59.322 52.381 0.00 0.00 0.00 4.30
356 363 2.945440 GCACATGACATAAAGCCCTCCA 60.945 50.000 0.00 0.00 0.00 3.86
378 385 1.839424 ATGTAGGCCAAAAGAGGTGC 58.161 50.000 5.01 0.00 0.00 5.01
431 438 1.661341 CCTACATTGCTCAGCTGGAC 58.339 55.000 15.13 6.92 0.00 4.02
483 504 1.135859 CAAACTCTGCAAAGCTAGCCG 60.136 52.381 12.13 1.07 0.00 5.52
501 522 2.747443 GGAAGCCCCCTGGTAGCTC 61.747 68.421 8.02 3.18 35.30 4.09
549 587 3.699894 CAGTGAGCGGTGCCCTCT 61.700 66.667 0.00 0.00 0.00 3.69
559 597 0.912486 GGTGCCCTCTATGGTGAAGT 59.088 55.000 0.00 0.00 0.00 3.01
561 599 2.290960 GGTGCCCTCTATGGTGAAGTTT 60.291 50.000 0.00 0.00 0.00 2.66
586 624 5.240403 GTGCCATAAATTTTTCTTTGGGCAA 59.760 36.000 14.28 0.00 44.36 4.52
619 665 1.007387 CACCTTTTTGAGCACCGGC 60.007 57.895 0.00 0.00 41.61 6.13
625 671 0.031857 TTTTGAGCACCGGCAACATG 59.968 50.000 0.00 0.00 44.61 3.21
626 672 0.821301 TTTGAGCACCGGCAACATGA 60.821 50.000 0.00 0.00 44.61 3.07
656 702 2.561373 GCAACCCGCGGAGAAAAG 59.439 61.111 30.73 11.56 0.00 2.27
663 709 1.334689 CCCGCGGAGAAAAGAAAACAC 60.335 52.381 30.73 0.00 0.00 3.32
664 710 1.658968 CGCGGAGAAAAGAAAACACG 58.341 50.000 0.00 0.00 0.00 4.49
665 711 1.395670 GCGGAGAAAAGAAAACACGC 58.604 50.000 0.00 0.00 38.94 5.34
666 712 1.002792 GCGGAGAAAAGAAAACACGCT 60.003 47.619 0.00 0.00 42.18 5.07
668 714 2.602217 CGGAGAAAAGAAAACACGCTGG 60.602 50.000 0.00 0.00 0.00 4.85
669 715 2.385315 GAGAAAAGAAAACACGCTGGC 58.615 47.619 0.00 0.00 0.00 4.85
670 716 1.067060 AGAAAAGAAAACACGCTGGCC 59.933 47.619 0.00 0.00 0.00 5.36
692 741 3.119316 CCGATTTAGCGAGCAGGATAGAT 60.119 47.826 0.00 0.00 0.00 1.98
701 750 3.654414 GAGCAGGATAGATGGTAAACCG 58.346 50.000 0.00 0.00 39.43 4.44
703 752 2.767505 CAGGATAGATGGTAAACCGGC 58.232 52.381 0.00 0.00 39.43 6.13
761 810 1.529796 GGGGGTGCCATGTCGATTA 59.470 57.895 0.00 0.00 0.00 1.75
790 839 0.878961 AACACGTCGTTGGCTCTTCC 60.879 55.000 0.00 0.00 36.12 3.46
916 965 2.434884 ACGCAGCACAATCCCTCG 60.435 61.111 0.00 0.00 0.00 4.63
1328 1377 2.622064 AGATTCCGTGCCAAGTATCC 57.378 50.000 0.00 0.00 0.00 2.59
1345 1397 0.535335 TCCTACCCATGCACTCGTTC 59.465 55.000 0.00 0.00 0.00 3.95
1438 1490 0.034186 CAAGGCCCATAGGTGCTCAA 60.034 55.000 0.00 0.00 34.57 3.02
1473 1527 4.624882 GGCAGATTTGTAGATAGCTGATCG 59.375 45.833 0.00 0.00 39.80 3.69
1523 1577 0.817654 TCATGACGCAACGATCTCCT 59.182 50.000 0.00 0.00 0.00 3.69
1535 1589 5.233263 GCAACGATCTCCTTAATCTTGTCTC 59.767 44.000 0.00 0.00 0.00 3.36
1536 1590 6.568869 CAACGATCTCCTTAATCTTGTCTCT 58.431 40.000 0.00 0.00 0.00 3.10
1552 1606 3.958147 TGTCTCTATAAACTCATCGCCCA 59.042 43.478 0.00 0.00 0.00 5.36
1566 1620 1.106944 CGCCCAGTTGGTCAACCTTT 61.107 55.000 9.90 0.00 42.06 3.11
1581 1635 1.659794 CTTTTGGGTTGCGTGGAGG 59.340 57.895 0.00 0.00 0.00 4.30
1601 1658 1.590932 CTATTTCGCTGGCTCTGCAT 58.409 50.000 0.00 0.00 0.00 3.96
1652 1726 5.702865 TCACAAATTCTGCATTCTACAAGC 58.297 37.500 0.00 0.00 0.00 4.01
1689 1763 0.603065 AGCCAAAAGAAACGCATCCC 59.397 50.000 0.00 0.00 0.00 3.85
1690 1764 0.603065 GCCAAAAGAAACGCATCCCT 59.397 50.000 0.00 0.00 0.00 4.20
1744 1818 2.334946 GGCTTTCATGACGCAGGCA 61.335 57.895 15.70 0.00 0.00 4.75
1752 1826 2.809601 GACGCAGGCAGTGTACGG 60.810 66.667 0.00 0.00 42.04 4.02
1826 1900 3.553715 CCTTGACATCATCGATGATCGGT 60.554 47.826 32.92 28.02 45.23 4.69
1928 2014 1.912220 CCTGGGCCAGACGGATTTA 59.088 57.895 34.84 0.00 32.44 1.40
1929 2015 0.179045 CCTGGGCCAGACGGATTTAG 60.179 60.000 34.84 10.69 32.44 1.85
1930 2016 0.541863 CTGGGCCAGACGGATTTAGT 59.458 55.000 29.96 0.00 32.44 2.24
1946 2032 6.404708 GGATTTAGTACTTCCGAGTTCCTTT 58.595 40.000 0.00 0.00 37.33 3.11
2044 2137 2.097038 CAAGCTCAACGAGGCTCCG 61.097 63.158 9.32 6.86 37.87 4.63
2045 2138 3.941657 AAGCTCAACGAGGCTCCGC 62.942 63.158 9.32 4.26 37.87 5.54
2046 2139 4.443266 GCTCAACGAGGCTCCGCT 62.443 66.667 9.32 0.00 0.00 5.52
2047 2140 2.262915 CTCAACGAGGCTCCGCTT 59.737 61.111 9.32 0.00 0.00 4.68
2048 2141 1.511305 CTCAACGAGGCTCCGCTTA 59.489 57.895 9.32 0.00 0.00 3.09
2049 2142 0.802607 CTCAACGAGGCTCCGCTTAC 60.803 60.000 9.32 0.00 0.00 2.34
2050 2143 1.810030 CAACGAGGCTCCGCTTACC 60.810 63.158 9.32 0.00 0.00 2.85
2066 2159 4.288398 GCTTACCCTCCTACCTAAGAAGT 58.712 47.826 0.00 0.00 0.00 3.01
2073 2166 5.205056 CCTCCTACCTAAGAAGTCTGATGT 58.795 45.833 0.00 0.00 0.00 3.06
2133 2226 3.989167 CACATCATCGCCAAATTGTTTGT 59.011 39.130 2.22 0.00 38.98 2.83
2171 2264 1.075970 CTCACTCCGAGGATGGGGA 60.076 63.158 0.00 0.00 38.18 4.81
2203 2296 2.478709 CGCCAACCAAAGCGCATTTATA 60.479 45.455 11.47 0.00 46.50 0.98
2222 2315 2.263227 CCGGGTGATACGTGCACA 59.737 61.111 18.64 0.00 37.99 4.57
2226 2319 1.448985 GGGTGATACGTGCACAACAT 58.551 50.000 18.64 6.08 37.99 2.71
2249 2342 3.269538 TCCTTCTTGTCCAACAAACGA 57.730 42.857 0.00 0.00 37.69 3.85
2468 2569 3.957535 GGATCATGCTTGCGGGCG 61.958 66.667 0.00 0.00 34.52 6.13
2544 2652 0.548682 ACTCCCTCCTCCAGCATGTT 60.549 55.000 0.00 0.00 0.00 2.71
2611 2739 0.463620 AAGCATCTCTCTCTTCGCCC 59.536 55.000 0.00 0.00 0.00 6.13
2643 2779 0.543410 TCTTCTAACCCACCCGAGCA 60.543 55.000 0.00 0.00 0.00 4.26
2655 2791 1.227674 CCGAGCAAGCTACCATCCC 60.228 63.158 0.00 0.00 0.00 3.85
2663 2799 0.264359 AGCTACCATCCCTGAGCTCT 59.736 55.000 16.19 0.00 41.40 4.09
2710 2846 2.200067 CTGCACACAAATTTCGCCAAA 58.800 42.857 0.00 0.00 0.00 3.28
2736 2872 2.550855 CGGCATTACCTATCCAGTGCAT 60.551 50.000 0.00 0.00 35.61 3.96
2808 2944 1.596006 TTCCCCATCCCCTACCTCGA 61.596 60.000 0.00 0.00 0.00 4.04
2822 2958 1.448540 CTCGAATTGCCGCTCACCT 60.449 57.895 0.00 0.00 0.00 4.00
2846 2982 3.196207 AAGTGCCATGCCTCCGTGT 62.196 57.895 0.00 0.00 0.00 4.49
3091 3230 3.726144 GCTGGCCCAAGCTCTCCT 61.726 66.667 7.81 0.00 40.20 3.69
3122 3273 4.451150 GGTGCGCGATCTCCACCA 62.451 66.667 22.75 1.57 46.38 4.17
3127 3278 1.652563 CGCGATCTCCACCATACGA 59.347 57.895 0.00 0.00 0.00 3.43
3131 3282 1.600663 CGATCTCCACCATACGAGCAC 60.601 57.143 0.00 0.00 0.00 4.40
3147 3298 1.301716 CACTGCCCTACGTGCTTGT 60.302 57.895 0.00 0.00 0.00 3.16
3157 3308 0.036164 ACGTGCTTGTTGGCTATGGA 59.964 50.000 0.00 0.00 0.00 3.41
3235 3393 1.066114 GACGAGTCAGTTCTTCCGCG 61.066 60.000 0.00 0.00 0.00 6.46
3236 3394 2.437343 CGAGTCAGTTCTTCCGCGC 61.437 63.158 0.00 0.00 0.00 6.86
3237 3395 1.372997 GAGTCAGTTCTTCCGCGCA 60.373 57.895 8.75 0.00 0.00 6.09
3238 3396 0.737715 GAGTCAGTTCTTCCGCGCAT 60.738 55.000 8.75 0.00 0.00 4.73
3239 3397 1.016130 AGTCAGTTCTTCCGCGCATG 61.016 55.000 8.75 0.00 0.00 4.06
3240 3398 1.014044 GTCAGTTCTTCCGCGCATGA 61.014 55.000 8.75 0.00 0.00 3.07
3286 3444 4.702020 GGCAAAACGTGTCGCTTT 57.298 50.000 0.00 0.00 0.00 3.51
3288 3446 2.108178 GGCAAAACGTGTCGCTTTTA 57.892 45.000 0.00 0.00 0.00 1.52
3346 3504 2.685999 GCCCCAGCCCTGATTTCT 59.314 61.111 0.00 0.00 0.00 2.52
3355 3513 1.004745 GCCCTGATTTCTCTTGTCCCA 59.995 52.381 0.00 0.00 0.00 4.37
3362 3520 4.003788 CTCTTGTCCCACGCCGGT 62.004 66.667 1.90 0.00 0.00 5.28
3515 3675 1.098050 GCCGAGCCAGACAAAATCAT 58.902 50.000 0.00 0.00 0.00 2.45
3517 3677 2.032178 GCCGAGCCAGACAAAATCATAC 59.968 50.000 0.00 0.00 0.00 2.39
3519 3679 2.930040 CGAGCCAGACAAAATCATACGT 59.070 45.455 0.00 0.00 0.00 3.57
3545 3705 3.204158 TGGACCAGCAATGGGTTATACAT 59.796 43.478 0.00 0.00 39.19 2.29
3592 3772 0.677731 CCTTTTGGCGCCTCATCTGA 60.678 55.000 29.70 1.01 0.00 3.27
3654 3834 2.063979 CCTCCATGGACCGGTGCTA 61.064 63.158 27.28 13.80 38.35 3.49
3693 3873 4.814294 CCACGGCCTACCTCACGC 62.814 72.222 0.00 0.00 0.00 5.34
3732 3912 0.614415 CAGTCAGGAGCCAGAGTCCT 60.614 60.000 0.00 0.00 46.01 3.85
3749 3930 0.534412 CCTTGATCACCTGCTCGTCT 59.466 55.000 0.00 0.00 0.00 4.18
3791 3996 0.686224 CTGGCATGAGATCCTCTCCC 59.314 60.000 0.00 0.00 42.73 4.30
3826 4031 3.066190 CCTACACCGAGCCCGACA 61.066 66.667 0.00 0.00 38.22 4.35
3899 4121 0.179000 GGACCAACTCCATCATCGCT 59.821 55.000 0.00 0.00 39.21 4.93
3927 4149 2.112297 GGAAGCACCGGAACACCA 59.888 61.111 9.46 0.00 0.00 4.17
3996 4218 1.968540 AAAGACGAGGCCTGCTTGC 60.969 57.895 12.00 0.00 0.00 4.01
4077 4305 1.267574 TTGAGGCCGAGCATCCTCTT 61.268 55.000 0.00 0.00 46.90 2.85
4083 4311 1.605202 GCCGAGCATCCTCTTCTCATC 60.605 57.143 0.00 0.00 35.90 2.92
4085 4313 2.030007 CCGAGCATCCTCTTCTCATCTC 60.030 54.545 0.00 0.00 35.90 2.75
4092 4320 1.066908 CCTCTTCTCATCTCGCACTCC 59.933 57.143 0.00 0.00 0.00 3.85
4094 4322 1.110442 CTTCTCATCTCGCACTCCCT 58.890 55.000 0.00 0.00 0.00 4.20
4098 4326 2.060383 CATCTCGCACTCCCTGGGA 61.060 63.158 16.13 16.13 39.46 4.37
4103 4331 4.767255 GCACTCCCTGGGACGCTG 62.767 72.222 20.32 13.34 0.00 5.18
4105 4333 1.982395 CACTCCCTGGGACGCTGTA 60.982 63.158 12.53 0.00 0.00 2.74
4107 4335 3.075005 TCCCTGGGACGCTGTAGC 61.075 66.667 12.53 0.00 37.78 3.58
4125 4353 1.299926 CGTGTACGCCCCATAGAGC 60.300 63.158 0.00 0.00 0.00 4.09
4134 4362 2.210013 CCCATAGAGCTGCGCCCTA 61.210 63.158 4.18 1.39 0.00 3.53
4136 4364 0.390866 CCATAGAGCTGCGCCCTATG 60.391 60.000 21.58 21.58 39.41 2.23
4137 4365 0.605083 CATAGAGCTGCGCCCTATGA 59.395 55.000 22.91 0.61 41.16 2.15
4138 4366 0.605589 ATAGAGCTGCGCCCTATGAC 59.394 55.000 4.18 0.00 0.00 3.06
4203 4433 6.862944 ATGCGTATTCACCAAAAATAAACG 57.137 33.333 0.00 0.00 0.00 3.60
4216 4446 9.589111 ACCAAAAATAAACGTAACAAAACATCT 57.411 25.926 0.00 0.00 0.00 2.90
4282 4512 2.494870 GGGAGTAGTACATGTGAACCGT 59.505 50.000 9.11 0.00 0.00 4.83
4395 4737 5.536161 ACAATGCAGTCCAAAGAGTTACATT 59.464 36.000 0.00 0.00 33.11 2.71
4462 4805 3.430895 TCGTGACAGAAAGAATAAACGGC 59.569 43.478 0.00 0.00 0.00 5.68
4561 4904 7.875971 AGAAATTATGCATACCCTTCGAAATC 58.124 34.615 5.74 0.00 0.00 2.17
4661 5006 4.072131 TGTCTCCAAAGTGATTTACAGCC 58.928 43.478 0.00 0.00 0.00 4.85
4747 5096 9.508567 GATTTTCTAAGCCTTTTCATATGACAC 57.491 33.333 4.48 0.00 0.00 3.67
4748 5097 8.635765 TTTTCTAAGCCTTTTCATATGACACT 57.364 30.769 4.48 0.00 0.00 3.55
5130 5480 2.421424 GCTGTGGAATTGGCAAGACTAG 59.579 50.000 5.96 0.72 0.00 2.57
5143 5493 5.376854 GCAAGACTAGATTGGCAAGAAAA 57.623 39.130 5.96 0.00 0.00 2.29
5185 5535 6.915843 ACACGAGAAATGTTTTCAATACAACC 59.084 34.615 0.00 0.00 0.00 3.77
5209 5559 3.713826 TGGGTAGATGGTTCCAAAGAC 57.286 47.619 0.00 0.00 0.00 3.01
5314 5664 8.532186 AAATTATGGACATGTTGGCTGTAATA 57.468 30.769 0.00 0.00 0.00 0.98
5322 5672 6.237901 ACATGTTGGCTGTAATACTTGAAGA 58.762 36.000 0.00 0.00 0.00 2.87
5328 5678 7.004555 TGGCTGTAATACTTGAAGAGAAGAA 57.995 36.000 0.00 0.00 0.00 2.52
5356 5706 9.914131 TTCTTACTGGTTCTTGATGATATATCG 57.086 33.333 8.19 0.00 0.00 2.92
5371 5721 7.533289 TGATATATCGAGTCACCATAACCAA 57.467 36.000 8.19 0.00 0.00 3.67
5389 5739 3.913163 ACCAAGAGAGTTTCCTGGAAGAT 59.087 43.478 9.42 2.18 39.41 2.40
5401 5751 1.391485 CTGGAAGATCGCTCGTTTGTG 59.609 52.381 0.00 0.00 34.07 3.33
5461 5811 1.610522 AGTGTTGCAGCAGGAATGAAC 59.389 47.619 2.40 0.00 0.00 3.18
5574 5924 3.425659 AGGAGAACTTGAGGGAAATTGC 58.574 45.455 0.00 0.00 0.00 3.56
5596 5946 4.083802 GCGATAACAATTATCCAGAGGTGC 60.084 45.833 3.56 0.00 39.03 5.01
5612 5962 0.465460 GTGCAACAAGGTCCCACTGA 60.465 55.000 0.00 0.00 36.32 3.41
5659 6009 0.744281 CAACCAAGGACCCAACACAC 59.256 55.000 0.00 0.00 0.00 3.82
5662 6012 1.821759 CAAGGACCCAACACACGCA 60.822 57.895 0.00 0.00 0.00 5.24
6026 6376 2.682856 GTCAGGTCTGTTTTGCAACTCA 59.317 45.455 0.00 0.13 33.58 3.41
6499 6849 9.092876 GTGAATCATAAGGAAGTAACTGAGAAG 57.907 37.037 0.00 0.00 0.00 2.85
6670 7020 2.238395 TGGTAGCACCAGTGATATGCAA 59.762 45.455 14.05 0.00 44.79 4.08
6796 7146 4.097741 CGATTATTTCCAGATTGGTTGCCA 59.902 41.667 0.00 0.00 39.03 4.92
6914 7264 2.143876 AACTGGCTGTTCCAAGTTGT 57.856 45.000 3.70 0.00 46.01 3.32
7123 7473 2.880890 ACAACTGACAAGCATGAAGGTC 59.119 45.455 0.00 0.15 0.00 3.85
7206 7556 5.997746 TGCAAGACAGCAAAACTCTTACTAT 59.002 36.000 0.00 0.00 42.46 2.12
7375 7725 2.052157 GTGCTACAGACGTTGACTGTC 58.948 52.381 11.26 0.00 45.58 3.51
7378 7728 2.981140 GCTACAGACGTTGACTGTCTTC 59.019 50.000 11.26 1.50 44.00 2.87
7384 7734 1.557443 CGTTGACTGTCTTCGGCACC 61.557 60.000 9.51 0.00 0.00 5.01
7396 7746 2.435059 GGCACCGAGGAACTGCTC 60.435 66.667 0.00 0.00 41.55 4.26
7800 8155 6.590292 TGTAAAGCTTCGAACTAAGATTGGAG 59.410 38.462 0.00 0.00 35.39 3.86
7801 8156 4.130286 AGCTTCGAACTAAGATTGGAGG 57.870 45.455 0.00 0.00 0.00 4.30
7805 8160 5.163844 GCTTCGAACTAAGATTGGAGGAAAC 60.164 44.000 0.00 0.00 0.00 2.78
7806 8161 5.477607 TCGAACTAAGATTGGAGGAAACA 57.522 39.130 0.00 0.00 0.00 2.83
7807 8162 5.860611 TCGAACTAAGATTGGAGGAAACAA 58.139 37.500 0.00 0.00 0.00 2.83
7808 8163 6.292923 TCGAACTAAGATTGGAGGAAACAAA 58.707 36.000 0.00 0.00 0.00 2.83
7809 8164 6.768861 TCGAACTAAGATTGGAGGAAACAAAA 59.231 34.615 0.00 0.00 0.00 2.44
7850 8205 6.931281 AGGATCGAATATTTCAGTGGTACATG 59.069 38.462 0.00 0.00 44.52 3.21
7875 8233 6.160576 ACTCATTGTAAATTTGCCTGTGTT 57.839 33.333 0.00 0.00 0.00 3.32
7876 8234 5.984926 ACTCATTGTAAATTTGCCTGTGTTG 59.015 36.000 0.00 0.71 0.00 3.33
7877 8235 5.911752 TCATTGTAAATTTGCCTGTGTTGT 58.088 33.333 0.00 0.00 0.00 3.32
7880 8238 4.930963 TGTAAATTTGCCTGTGTTGTCTG 58.069 39.130 0.00 0.00 0.00 3.51
7881 8239 2.514205 AATTTGCCTGTGTTGTCTGC 57.486 45.000 0.00 0.00 0.00 4.26
7882 8240 1.696063 ATTTGCCTGTGTTGTCTGCT 58.304 45.000 0.00 0.00 0.00 4.24
8660 9018 6.564328 CAGTAGCCGATGTATATATCAAGCA 58.436 40.000 17.96 6.79 31.74 3.91
8674 9032 2.899976 TCAAGCACTGACGTTTTCTGA 58.100 42.857 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.602424 TGTTCCTATTCTCCTTCTTTACAATGA 58.398 33.333 0.00 0.00 0.00 2.57
3 4 7.883311 CCTTGTTCCTATTCTCCTTCTTTACAA 59.117 37.037 0.00 0.00 0.00 2.41
5 6 7.395617 ACCTTGTTCCTATTCTCCTTCTTTAC 58.604 38.462 0.00 0.00 0.00 2.01
6 7 7.569599 ACCTTGTTCCTATTCTCCTTCTTTA 57.430 36.000 0.00 0.00 0.00 1.85
7 8 6.455690 ACCTTGTTCCTATTCTCCTTCTTT 57.544 37.500 0.00 0.00 0.00 2.52
8 9 6.044404 TGAACCTTGTTCCTATTCTCCTTCTT 59.956 38.462 4.65 0.00 0.00 2.52
9 10 5.548056 TGAACCTTGTTCCTATTCTCCTTCT 59.452 40.000 4.65 0.00 0.00 2.85
10 11 5.805728 TGAACCTTGTTCCTATTCTCCTTC 58.194 41.667 4.65 0.00 0.00 3.46
64 65 3.440522 GCCGTGAGATTAGCCTTCTTTTT 59.559 43.478 0.00 0.00 0.00 1.94
65 66 3.010420 GCCGTGAGATTAGCCTTCTTTT 58.990 45.455 0.00 0.00 0.00 2.27
69 70 1.869767 CATGCCGTGAGATTAGCCTTC 59.130 52.381 0.00 0.00 0.00 3.46
77 78 1.019673 GCACAATCATGCCGTGAGAT 58.980 50.000 11.66 0.00 40.92 2.75
107 108 1.188863 ATTGGGTTCTTGCTGATGCC 58.811 50.000 0.00 0.00 38.71 4.40
108 109 3.323751 AAATTGGGTTCTTGCTGATGC 57.676 42.857 0.00 0.00 40.20 3.91
165 166 2.485814 GGTCTTCAAGGTGTCAATGCTC 59.514 50.000 0.00 0.00 0.00 4.26
166 167 2.508526 GGTCTTCAAGGTGTCAATGCT 58.491 47.619 0.00 0.00 0.00 3.79
175 176 1.349067 AACGCTAGGGTCTTCAAGGT 58.651 50.000 13.46 0.00 0.00 3.50
210 217 2.353208 GCTCATATCGGTGGCTTAGGAG 60.353 54.545 0.00 0.00 0.00 3.69
222 229 6.312426 GGGAGTATCATTTTCTGCTCATATCG 59.688 42.308 0.00 0.00 36.25 2.92
245 252 4.497340 CGTCAATTAATTTGGATCGGTGGG 60.497 45.833 0.00 0.00 35.92 4.61
248 255 3.945285 AGCGTCAATTAATTTGGATCGGT 59.055 39.130 0.00 4.30 35.92 4.69
267 274 7.417612 ACCATTTGAATTATACTAAAGCAGCG 58.582 34.615 0.00 0.00 0.00 5.18
318 325 5.653330 TCATGTGCATGATAAGTTGAACCAT 59.347 36.000 10.48 0.00 42.42 3.55
331 338 2.689471 GGGCTTTATGTCATGTGCATGA 59.311 45.455 10.48 10.48 44.83 3.07
333 340 2.954318 GAGGGCTTTATGTCATGTGCAT 59.046 45.455 0.00 9.64 0.00 3.96
334 341 2.368439 GAGGGCTTTATGTCATGTGCA 58.632 47.619 0.00 0.00 0.00 4.57
335 342 1.678101 GGAGGGCTTTATGTCATGTGC 59.322 52.381 0.00 0.00 0.00 4.57
336 343 2.684881 GTGGAGGGCTTTATGTCATGTG 59.315 50.000 0.00 0.00 0.00 3.21
337 344 2.578021 AGTGGAGGGCTTTATGTCATGT 59.422 45.455 0.00 0.00 0.00 3.21
338 345 3.287867 AGTGGAGGGCTTTATGTCATG 57.712 47.619 0.00 0.00 0.00 3.07
339 346 4.413520 ACATAGTGGAGGGCTTTATGTCAT 59.586 41.667 0.00 0.00 31.26 3.06
340 347 3.780294 ACATAGTGGAGGGCTTTATGTCA 59.220 43.478 0.00 0.00 31.26 3.58
341 348 4.423625 ACATAGTGGAGGGCTTTATGTC 57.576 45.455 0.00 0.00 31.26 3.06
342 349 4.348168 CCTACATAGTGGAGGGCTTTATGT 59.652 45.833 0.00 0.00 45.03 2.29
343 350 4.899502 CCTACATAGTGGAGGGCTTTATG 58.100 47.826 0.00 0.00 45.03 1.90
352 359 4.446371 CTCTTTTGGCCTACATAGTGGAG 58.554 47.826 3.32 0.00 0.00 3.86
353 360 3.199946 CCTCTTTTGGCCTACATAGTGGA 59.800 47.826 3.32 0.00 31.56 4.02
354 361 3.054361 ACCTCTTTTGGCCTACATAGTGG 60.054 47.826 3.32 6.96 33.99 4.00
355 362 3.941483 CACCTCTTTTGGCCTACATAGTG 59.059 47.826 3.32 0.00 0.00 2.74
356 363 3.622455 GCACCTCTTTTGGCCTACATAGT 60.622 47.826 3.32 0.00 0.00 2.12
378 385 5.049267 CCAAAATGCTGGAAAGTGAATTTGG 60.049 40.000 0.00 0.00 38.96 3.28
443 452 6.440647 AGTTTGACATCAGAGTAGACCCATAA 59.559 38.462 0.00 0.00 0.00 1.90
445 454 4.780021 AGTTTGACATCAGAGTAGACCCAT 59.220 41.667 0.00 0.00 0.00 4.00
446 455 4.160329 AGTTTGACATCAGAGTAGACCCA 58.840 43.478 0.00 0.00 0.00 4.51
448 457 5.406649 CAGAGTTTGACATCAGAGTAGACC 58.593 45.833 0.00 0.00 0.00 3.85
449 458 4.862018 GCAGAGTTTGACATCAGAGTAGAC 59.138 45.833 0.00 0.00 0.00 2.59
452 461 4.871933 TGCAGAGTTTGACATCAGAGTA 57.128 40.909 0.00 0.00 0.00 2.59
462 483 2.154462 GGCTAGCTTTGCAGAGTTTGA 58.846 47.619 15.72 0.00 0.00 2.69
483 504 2.692741 AGCTACCAGGGGGCTTCC 60.693 66.667 2.92 0.00 37.90 3.46
495 516 3.786635 ACAAGTCCATTGATCGAGCTAC 58.213 45.455 0.90 0.00 41.83 3.58
501 522 6.683974 AGGAATAAACAAGTCCATTGATCG 57.316 37.500 0.00 0.00 45.18 3.69
561 599 7.137184 TTGCCCAAAGAAAAATTTATGGCACA 61.137 34.615 11.79 5.10 43.40 4.57
586 624 2.819595 GTGCCGCATCATCACCGT 60.820 61.111 0.00 0.00 0.00 4.83
619 665 2.360165 GCTTAGGCCTTCCATCATGTTG 59.640 50.000 12.58 0.00 33.74 3.33
625 671 1.393603 GGTTGCTTAGGCCTTCCATC 58.606 55.000 12.58 5.08 37.74 3.51
626 672 0.033109 GGGTTGCTTAGGCCTTCCAT 60.033 55.000 12.58 0.00 37.74 3.41
656 702 1.862602 AATCGGGCCAGCGTGTTTTC 61.863 55.000 4.39 0.00 0.00 2.29
664 710 2.203015 TCGCTAAATCGGGCCAGC 60.203 61.111 4.39 2.04 0.00 4.85
665 711 4.033894 CTCGCTAAATCGGGCCAG 57.966 61.111 4.39 0.00 0.00 4.85
669 715 0.034059 ATCCTGCTCGCTAAATCGGG 59.966 55.000 0.00 0.00 0.00 5.14
670 716 2.229062 TCTATCCTGCTCGCTAAATCGG 59.771 50.000 0.00 0.00 0.00 4.18
712 761 7.224753 CACATAGCTTACCGTGATATTGTCTTT 59.775 37.037 0.00 0.00 0.00 2.52
713 762 6.701841 CACATAGCTTACCGTGATATTGTCTT 59.298 38.462 0.00 0.00 0.00 3.01
714 763 6.216569 CACATAGCTTACCGTGATATTGTCT 58.783 40.000 0.00 0.00 0.00 3.41
715 764 5.405571 CCACATAGCTTACCGTGATATTGTC 59.594 44.000 0.00 0.00 0.00 3.18
761 810 0.462789 ACGACGTGTTTTGTCCCTCT 59.537 50.000 0.00 0.00 32.68 3.69
916 965 4.378874 GCAACTTCCTTATGTTCTGCTGTC 60.379 45.833 0.00 0.00 0.00 3.51
1328 1377 1.645034 CTGAACGAGTGCATGGGTAG 58.355 55.000 0.00 0.00 0.00 3.18
1345 1397 3.793797 TTGAAGATGCCATTCATGCTG 57.206 42.857 0.00 0.00 36.60 4.41
1523 1577 9.464714 GCGATGAGTTTATAGAGACAAGATTAA 57.535 33.333 0.00 0.00 0.00 1.40
1535 1589 3.809832 CCAACTGGGCGATGAGTTTATAG 59.190 47.826 0.00 0.00 29.73 1.31
1536 1590 3.199071 ACCAACTGGGCGATGAGTTTATA 59.801 43.478 0.00 0.00 42.05 0.98
1566 1620 1.847798 ATAGCCTCCACGCAACCCAA 61.848 55.000 0.00 0.00 0.00 4.12
1581 1635 1.091771 TGCAGAGCCAGCGAAATAGC 61.092 55.000 0.00 0.00 37.41 2.97
1601 1658 5.822519 GGTGTATTAATCTGAATCTGGCACA 59.177 40.000 0.00 0.00 0.00 4.57
1652 1726 0.167470 CTTCTGTGTGCGGCATGAAG 59.833 55.000 5.72 13.43 35.72 3.02
1731 1805 0.389817 GTACACTGCCTGCGTCATGA 60.390 55.000 0.00 0.00 0.00 3.07
1744 1818 1.982938 GGAGAGGTGCCCGTACACT 60.983 63.158 5.20 0.00 40.52 3.55
1752 1826 1.545706 AAGAACGGAGGAGAGGTGCC 61.546 60.000 0.00 0.00 0.00 5.01
1757 1831 1.066787 GGTTCCAAGAACGGAGGAGAG 60.067 57.143 1.66 0.00 36.12 3.20
1766 1840 0.169009 GCTGATGCGGTTCCAAGAAC 59.831 55.000 0.00 0.00 0.00 3.01
1928 2014 3.306156 GCTCAAAGGAACTCGGAAGTACT 60.306 47.826 0.00 0.00 38.49 2.73
1929 2015 2.994578 GCTCAAAGGAACTCGGAAGTAC 59.005 50.000 0.00 0.00 38.49 2.73
1930 2016 2.631062 TGCTCAAAGGAACTCGGAAGTA 59.369 45.455 0.00 0.00 38.49 2.24
1946 2032 1.855295 ATGATTGGCCAACATGCTCA 58.145 45.000 23.27 20.41 0.00 4.26
1972 2058 1.699083 TCAAAGGCCTCACAGATGTCA 59.301 47.619 5.23 0.00 0.00 3.58
2044 2137 4.288398 ACTTCTTAGGTAGGAGGGTAAGC 58.712 47.826 0.00 0.00 33.28 3.09
2045 2138 5.595133 CAGACTTCTTAGGTAGGAGGGTAAG 59.405 48.000 0.00 0.00 33.28 2.34
2046 2139 5.254737 TCAGACTTCTTAGGTAGGAGGGTAA 59.745 44.000 0.00 0.00 33.28 2.85
2047 2140 4.792426 TCAGACTTCTTAGGTAGGAGGGTA 59.208 45.833 0.00 0.00 33.28 3.69
2048 2141 3.596956 TCAGACTTCTTAGGTAGGAGGGT 59.403 47.826 0.00 0.00 33.28 4.34
2049 2142 4.252570 TCAGACTTCTTAGGTAGGAGGG 57.747 50.000 0.00 0.00 33.28 4.30
2050 2143 5.205056 ACATCAGACTTCTTAGGTAGGAGG 58.795 45.833 0.00 0.00 33.28 4.30
2066 2159 2.181777 GAGCGTGGCGACATCAGA 59.818 61.111 0.00 0.00 46.14 3.27
2133 2226 2.973899 GCAGCGAGAGGACCTTGA 59.026 61.111 0.00 0.00 0.00 3.02
2203 2296 3.387091 TGCACGTATCACCCGGCT 61.387 61.111 0.00 0.00 0.00 5.52
2222 2315 5.930837 TGTTGGACAAGAAGGAAAATGTT 57.069 34.783 0.00 0.00 0.00 2.71
2226 2319 4.459685 TCGTTTGTTGGACAAGAAGGAAAA 59.540 37.500 0.00 0.00 39.53 2.29
2249 2342 7.048512 GCCTTGTTATTGTGGAGTAATCTAGT 58.951 38.462 0.00 0.00 0.00 2.57
2418 2519 0.605319 GGTTGCCGTTGATGAGGACA 60.605 55.000 0.00 0.00 0.00 4.02
2567 2695 1.908793 ACGTGCCTAGTGGTGAGCT 60.909 57.895 0.00 0.00 35.27 4.09
2635 2771 1.522569 GATGGTAGCTTGCTCGGGT 59.477 57.895 0.00 0.00 0.00 5.28
2643 2779 1.127343 GAGCTCAGGGATGGTAGCTT 58.873 55.000 9.40 0.00 45.04 3.74
2655 2791 2.932614 CCAAACATCCGTAAGAGCTCAG 59.067 50.000 17.77 4.03 43.02 3.35
2663 2799 1.673626 GGCGTCTCCAAACATCCGTAA 60.674 52.381 0.00 0.00 34.01 3.18
2744 2880 3.876198 GGCGATCGCGTTGGCAAT 61.876 61.111 31.76 0.77 43.06 3.56
2808 2944 2.040544 CGGAAGGTGAGCGGCAATT 61.041 57.895 1.45 0.00 0.00 2.32
2822 2958 3.372730 GGCATGGCACTTGCGGAA 61.373 61.111 15.47 0.00 43.26 4.30
2846 2982 1.476110 CCTGTCGACCAAAGGGAACAA 60.476 52.381 14.12 0.00 38.05 2.83
2912 3049 2.687566 CAGAGTAAGGGGCCCGGT 60.688 66.667 18.95 12.33 0.00 5.28
2944 3081 3.006133 TGGACCGGCATGGCAGTA 61.006 61.111 20.37 0.00 43.94 2.74
3122 3273 1.035932 ACGTAGGGCAGTGCTCGTAT 61.036 55.000 16.11 0.00 32.17 3.06
3131 3282 1.577328 CCAACAAGCACGTAGGGCAG 61.577 60.000 0.00 0.00 0.00 4.85
3145 3296 3.931907 AGCTTGTATCCATAGCCAACA 57.068 42.857 0.00 0.00 35.53 3.33
3147 3298 4.703897 GTGTAGCTTGTATCCATAGCCAA 58.296 43.478 0.00 0.00 35.53 4.52
3181 3333 2.338785 GCTGAAGGTGGCTCCAAGC 61.339 63.158 8.51 9.83 41.46 4.01
3235 3393 1.328680 CAAGTAGTGGATGCGTCATGC 59.671 52.381 8.47 4.79 46.70 4.06
3310 3468 2.017623 GCCATCTCAGCAGCAGATGTT 61.018 52.381 17.39 0.00 44.05 2.71
3346 3504 4.308458 CACCGGCGTGGGACAAGA 62.308 66.667 6.01 0.00 44.16 3.02
3362 3520 2.440147 CCAGGCATTGGGGTGTCA 59.560 61.111 0.00 0.00 43.75 3.58
3515 3675 2.354303 CCATTGCTGGTCCACTTACGTA 60.354 50.000 0.00 0.00 37.79 3.57
3517 3677 1.086696 CCATTGCTGGTCCACTTACG 58.913 55.000 0.00 0.00 37.79 3.18
3519 3679 1.072266 ACCCATTGCTGGTCCACTTA 58.928 50.000 0.00 0.00 41.37 2.24
3545 3705 0.039798 GTCGTACGCAGAGTTGGTCA 60.040 55.000 11.24 0.00 0.00 4.02
3732 3912 3.785486 CATTAGACGAGCAGGTGATCAA 58.215 45.455 0.00 0.00 0.00 2.57
3749 3930 4.097286 GGTTATTCTGGAAAAGGCGCATTA 59.903 41.667 8.12 0.00 0.00 1.90
3791 3996 1.520787 GGATTGGTAGGCGACACCG 60.521 63.158 0.00 0.00 46.52 4.94
3826 4031 2.629617 CCACCAGTTGAAGAAGCCATTT 59.370 45.455 0.00 0.00 0.00 2.32
3899 4121 1.276622 GGTGCTTCCAGAGGGACTAA 58.723 55.000 1.69 0.00 44.89 2.24
3924 4146 2.365582 GAGGTTGTCAAACACACTGGT 58.634 47.619 2.89 0.00 38.10 4.00
3927 4149 1.663695 CGGAGGTTGTCAAACACACT 58.336 50.000 2.89 0.00 38.10 3.55
4077 4305 1.039785 CCAGGGAGTGCGAGATGAGA 61.040 60.000 0.00 0.00 0.00 3.27
4083 4311 4.135153 CGTCCCAGGGAGTGCGAG 62.135 72.222 9.15 0.00 29.39 5.03
4107 4335 1.299926 GCTCTATGGGGCGTACACG 60.300 63.158 0.00 0.00 43.27 4.49
4111 4339 2.856628 CGCAGCTCTATGGGGCGTA 61.857 63.158 4.35 0.00 42.51 4.42
4125 4353 2.203070 GGGTGTCATAGGGCGCAG 60.203 66.667 10.83 0.00 0.00 5.18
4146 4376 1.935931 CATTGAAGGGGGAGGGGGT 60.936 63.158 0.00 0.00 0.00 4.95
4150 4380 3.386932 TCATTTCATTGAAGGGGGAGG 57.613 47.619 0.00 0.00 0.00 4.30
4151 4381 4.516698 CGTATCATTTCATTGAAGGGGGAG 59.483 45.833 0.00 0.00 0.00 4.30
4152 4382 4.460263 CGTATCATTTCATTGAAGGGGGA 58.540 43.478 0.00 0.00 0.00 4.81
4153 4383 3.004734 GCGTATCATTTCATTGAAGGGGG 59.995 47.826 0.00 0.00 0.00 5.40
4154 4384 3.631686 TGCGTATCATTTCATTGAAGGGG 59.368 43.478 0.00 0.00 0.00 4.79
4155 4385 4.898829 TGCGTATCATTTCATTGAAGGG 57.101 40.909 0.00 0.00 0.00 3.95
4156 4386 5.639757 TGTTGCGTATCATTTCATTGAAGG 58.360 37.500 0.00 0.00 0.00 3.46
4157 4387 7.606131 CATTGTTGCGTATCATTTCATTGAAG 58.394 34.615 0.00 0.00 0.00 3.02
4158 4388 6.034790 GCATTGTTGCGTATCATTTCATTGAA 59.965 34.615 0.00 0.00 39.49 2.69
4258 4488 4.400251 CGGTTCACATGTACTACTCCCTTA 59.600 45.833 0.00 0.00 0.00 2.69
4259 4489 3.194968 CGGTTCACATGTACTACTCCCTT 59.805 47.826 0.00 0.00 0.00 3.95
4358 4610 4.969293 ACTGCATTGTACAGTCATGCTGC 61.969 47.826 25.57 15.00 45.06 5.25
4360 4612 3.063510 ACTGCATTGTACAGTCATGCT 57.936 42.857 24.26 8.96 45.06 3.79
4438 4780 4.434330 CCGTTTATTCTTTCTGTCACGAGC 60.434 45.833 0.00 0.00 0.00 5.03
4462 4805 5.009048 CACAGTTGCAATTTTCGATTTGG 57.991 39.130 0.59 0.00 0.00 3.28
4561 4904 3.436015 CAGCAAGACTTGACTTCATCAGG 59.564 47.826 19.51 0.00 38.99 3.86
4661 5006 8.661257 TGTCAACATACTTTAACATACCATTCG 58.339 33.333 0.00 0.00 0.00 3.34
4707 5052 6.662865 TTAGAAAATCCAGACAAAATGCCA 57.337 33.333 0.00 0.00 0.00 4.92
5138 5488 8.982685 CGTGTAGCAATCATCATATACTTTTCT 58.017 33.333 0.00 0.00 0.00 2.52
5143 5493 7.454260 TCTCGTGTAGCAATCATCATATACT 57.546 36.000 0.00 0.00 0.00 2.12
5185 5535 5.765182 GTCTTTGGAACCATCTACCCATATG 59.235 44.000 0.00 0.00 0.00 1.78
5209 5559 1.066143 AGTAATCCCGCACCAGTTGAG 60.066 52.381 0.00 0.00 0.00 3.02
5314 5664 8.214364 ACCAGTAAGAATTTCTTCTCTTCAAGT 58.786 33.333 14.75 7.26 40.93 3.16
5322 5672 9.007901 CATCAAGAACCAGTAAGAATTTCTTCT 57.992 33.333 14.75 9.42 43.71 2.85
5356 5706 4.810191 ACTCTCTTGGTTATGGTGACTC 57.190 45.455 0.00 0.00 0.00 3.36
5371 5721 2.167487 GCGATCTTCCAGGAAACTCTCT 59.833 50.000 2.72 0.00 40.21 3.10
5389 5739 0.512518 CATGCTTCACAAACGAGCGA 59.487 50.000 0.00 0.00 39.23 4.93
5401 5751 2.019984 AGAATTCGGCTTCCATGCTTC 58.980 47.619 0.00 0.00 0.00 3.86
5461 5811 6.256539 CCTGCATATTATGAATGTAGCTACGG 59.743 42.308 18.74 4.39 36.20 4.02
5503 5853 0.034476 CACAGAGCAGAGTCCAGCAA 59.966 55.000 7.79 0.00 0.00 3.91
5574 5924 5.056480 TGCACCTCTGGATAATTGTTATCG 58.944 41.667 4.22 0.00 42.31 2.92
5612 5962 3.321111 ACACCGCCGATAATCTTGATAGT 59.679 43.478 0.00 0.00 0.00 2.12
5659 6009 0.037326 TAACCTGCTTCCACTCTGCG 60.037 55.000 0.00 0.00 0.00 5.18
5662 6012 4.640771 TTCATTAACCTGCTTCCACTCT 57.359 40.909 0.00 0.00 0.00 3.24
5669 6019 5.594317 ACAGTTCACTTTCATTAACCTGCTT 59.406 36.000 0.00 0.00 0.00 3.91
6026 6376 3.445805 CCAAACCACCGGTGCTTAATTAT 59.554 43.478 29.75 3.37 35.34 1.28
6499 6849 2.044946 GGCCACCCACTGACATCC 60.045 66.667 0.00 0.00 0.00 3.51
6670 7020 2.209064 CTGCCGCTGGTACGTGTAGT 62.209 60.000 0.00 0.00 0.00 2.73
6796 7146 1.152030 TTGGAGACTGGGGAGCTGT 60.152 57.895 0.00 0.00 0.00 4.40
6914 7264 2.046023 CCCTCGCTGAATGGTGCA 60.046 61.111 0.00 0.00 0.00 4.57
7123 7473 2.046892 AGGCTACCAGCAGCAACG 60.047 61.111 0.00 0.00 44.75 4.10
7175 7525 5.284079 AGTTTTGCTGTCTTGCACAATTAG 58.716 37.500 0.00 0.00 43.20 1.73
7206 7556 8.439870 CTTCAAGTGATGGAAGATTGGAGACAA 61.440 40.741 0.00 0.00 44.52 3.18
7378 7728 4.379243 AGCAGTTCCTCGGTGCCG 62.379 66.667 3.94 3.94 37.98 5.69
7396 7746 1.086696 CACTGGGAACTAACATGCCG 58.913 55.000 0.00 0.00 0.00 5.69
7747 8097 7.696992 ACTGAAGAAGTAAAGACACCAAAAA 57.303 32.000 0.00 0.00 37.36 1.94
7800 8155 4.126437 CCTTTCCACATGGTTTTGTTTCC 58.874 43.478 0.00 0.00 36.34 3.13
7801 8156 5.017294 TCCTTTCCACATGGTTTTGTTTC 57.983 39.130 0.00 0.00 36.34 2.78
7805 8160 4.100808 TCCTTTCCTTTCCACATGGTTTTG 59.899 41.667 0.00 0.00 36.34 2.44
7806 8161 4.294347 TCCTTTCCTTTCCACATGGTTTT 58.706 39.130 0.00 0.00 36.34 2.43
7807 8162 3.922375 TCCTTTCCTTTCCACATGGTTT 58.078 40.909 0.00 0.00 36.34 3.27
7808 8163 3.611025 TCCTTTCCTTTCCACATGGTT 57.389 42.857 0.00 0.00 36.34 3.67
7809 8164 3.701664 GATCCTTTCCTTTCCACATGGT 58.298 45.455 0.00 0.00 36.34 3.55
7850 8205 6.677913 ACACAGGCAAATTTACAATGAGTAC 58.322 36.000 0.00 0.00 30.91 2.73
8652 9010 4.627058 TCAGAAAACGTCAGTGCTTGATA 58.373 39.130 0.00 0.00 38.29 2.15
8660 9018 6.154706 AGGGTAATATCTCAGAAAACGTCAGT 59.845 38.462 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.