Multiple sequence alignment - TraesCS2A01G340900

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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 TraesCS2A01G340900 chr2A 100.000 5341 0 0 1 5341 576362191 576356851 0.000000e+00 9864.0
1 TraesCS2A01G340900 chr2A 96.311 515 18 1 4827 5340 444018229 444018743 0.000000e+00 845.0
2 TraesCS2A01G340900 chr2A 93.133 466 23 4 4777 5242 180223726 180224182 0.000000e+00 675.0
3 TraesCS2A01G340900 chr2A 92.308 78 5 1 5247 5323 180224216 180224293 5.660000e-20 110.0
4 TraesCS2A01G340900 chr2D 89.989 4675 269 77 24 4563 408366195 408361585 0.000000e+00 5856.0
5 TraesCS2A01G340900 chr2D 82.908 392 60 6 24 415 419362235 419361851 3.960000e-91 346.0
6 TraesCS2A01G340900 chr2D 86.154 65 9 0 415 479 628618377 628618441 2.670000e-08 71.3
7 TraesCS2A01G340900 chr2B 93.333 1785 74 21 2650 4402 483682835 483681064 0.000000e+00 2595.0
8 TraesCS2A01G340900 chr2B 87.407 2160 174 49 13 2117 483685827 483683711 0.000000e+00 2392.0
9 TraesCS2A01G340900 chr2B 80.912 833 108 32 13 814 483688567 483687755 1.270000e-170 610.0
10 TraesCS2A01G340900 chr2B 88.865 458 23 19 2208 2645 483683600 483683151 6.090000e-149 538.0
11 TraesCS2A01G340900 chr2B 81.690 213 36 2 480 691 358634335 358634545 1.980000e-39 174.0
12 TraesCS2A01G340900 chr6B 92.401 658 38 4 4663 5315 481793689 481794339 0.000000e+00 928.0
13 TraesCS2A01G340900 chr4B 92.414 580 34 4 4663 5242 249045747 249046316 0.000000e+00 819.0
14 TraesCS2A01G340900 chr4B 94.805 77 4 0 5247 5323 249046352 249046428 2.610000e-23 121.0
15 TraesCS2A01G340900 chr1B 92.414 580 34 4 4663 5242 346540589 346541158 0.000000e+00 819.0
16 TraesCS2A01G340900 chr1B 83.796 216 26 7 480 691 539587996 539588206 4.220000e-46 196.0
17 TraesCS2A01G340900 chr1B 94.805 77 4 0 5247 5323 346541196 346541272 2.610000e-23 121.0
18 TraesCS2A01G340900 chr7A 92.255 581 37 3 4663 5242 59838698 59838125 0.000000e+00 817.0
19 TraesCS2A01G340900 chr7A 90.476 84 4 1 5247 5326 59838091 59838008 2.030000e-19 108.0
20 TraesCS2A01G340900 chr7A 92.683 41 3 0 441 481 198692963 198692923 5.780000e-05 60.2
21 TraesCS2A01G340900 chr7B 87.591 411 43 7 4663 5068 320051351 320051758 2.250000e-128 470.0
22 TraesCS2A01G340900 chr7B 87.838 370 39 6 4663 5028 658413842 658413475 3.820000e-116 429.0
23 TraesCS2A01G340900 chr7B 81.910 398 66 4 24 415 673720124 673720521 1.110000e-86 331.0
24 TraesCS2A01G340900 chr5A 88.312 385 38 4 4684 5061 647358850 647359234 6.310000e-124 455.0
25 TraesCS2A01G340900 chr5A 84.709 412 53 10 4659 5063 551454193 551453785 2.320000e-108 403.0
26 TraesCS2A01G340900 chr5A 81.429 210 35 3 480 687 651864199 651863992 9.200000e-38 169.0
27 TraesCS2A01G340900 chr5A 79.237 236 44 5 490 722 546976531 546976298 5.540000e-35 159.0
28 TraesCS2A01G340900 chr5B 87.027 370 42 6 4663 5028 503091800 503091433 3.850000e-111 412.0
29 TraesCS2A01G340900 chr5B 82.292 96 12 5 392 486 455335108 455335199 1.590000e-10 78.7
30 TraesCS2A01G340900 chr5B 85.714 63 0 3 5248 5304 69563422 69563363 2.080000e-04 58.4
31 TraesCS2A01G340900 chr5B 85.714 63 0 3 5248 5304 503091222 503091163 2.080000e-04 58.4
32 TraesCS2A01G340900 chr6A 84.901 404 46 10 4669 5068 329867458 329867850 1.390000e-105 394.0
33 TraesCS2A01G340900 chr6A 79.221 462 78 9 30 484 569407443 569406993 6.720000e-79 305.0
34 TraesCS2A01G340900 chr6A 78.681 455 82 7 34 481 569430212 569430658 6.770000e-74 289.0
35 TraesCS2A01G340900 chr6D 81.290 465 70 10 24 481 38279153 38279607 1.410000e-95 361.0
36 TraesCS2A01G340900 chr6D 79.914 463 76 9 33 487 457643738 457643285 1.860000e-84 324.0
37 TraesCS2A01G340900 chr6D 80.905 398 63 8 24 415 464520190 464520580 8.690000e-78 302.0
38 TraesCS2A01G340900 chr4A 81.140 456 65 16 49 488 669210161 669209711 3.960000e-91 346.0
39 TraesCS2A01G340900 chr4A 82.819 227 34 5 480 703 604915659 604915435 1.170000e-46 198.0
40 TraesCS2A01G340900 chr3B 82.787 366 57 5 49 408 126304382 126304017 6.670000e-84 322.0
41 TraesCS2A01G340900 chr1D 78.926 484 86 9 15 485 477498300 477497820 1.120000e-81 315.0
42 TraesCS2A01G340900 chr3A 79.912 453 70 11 49 485 16139604 16139157 4.020000e-81 313.0
43 TraesCS2A01G340900 chr3A 84.615 286 40 2 24 306 9048956 9049240 1.130000e-71 281.0
44 TraesCS2A01G340900 chr3D 78.392 398 57 19 25 410 14224945 14224565 1.160000e-56 231.0
45 TraesCS2A01G340900 chr3D 80.741 270 36 7 213 475 313600499 313600759 4.220000e-46 196.0
46 TraesCS2A01G340900 chr3D 86.765 68 6 1 403 470 529125430 529125366 7.420000e-09 73.1
47 TraesCS2A01G340900 chr5D 83.983 231 32 4 480 707 432193873 432194101 3.240000e-52 217.0
48 TraesCS2A01G340900 chr5D 82.326 215 32 5 480 691 431568303 431568514 1.180000e-41 182.0
49 TraesCS2A01G340900 chr7D 80.247 243 35 10 483 722 269695362 269695130 2.560000e-38 171.0
50 TraesCS2A01G340900 chr7D 80.405 148 21 6 341 481 615367903 615368049 7.320000e-19 106.0
51 TraesCS2A01G340900 chr1A 79.268 246 45 5 480 722 572205187 572205429 3.310000e-37 167.0
52 TraesCS2A01G340900 chr1A 100.000 32 0 0 430 461 546045420 546045389 5.780000e-05 60.2


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 TraesCS2A01G340900 chr2A 576356851 576362191 5340 True 9864.00 9864 100.00000 1 5341 1 chr2A.!!$R1 5340
1 TraesCS2A01G340900 chr2A 444018229 444018743 514 False 845.00 845 96.31100 4827 5340 1 chr2A.!!$F1 513
2 TraesCS2A01G340900 chr2A 180223726 180224293 567 False 392.50 675 92.72050 4777 5323 2 chr2A.!!$F2 546
3 TraesCS2A01G340900 chr2D 408361585 408366195 4610 True 5856.00 5856 89.98900 24 4563 1 chr2D.!!$R1 4539
4 TraesCS2A01G340900 chr2B 483681064 483688567 7503 True 1533.75 2595 87.62925 13 4402 4 chr2B.!!$R1 4389
5 TraesCS2A01G340900 chr6B 481793689 481794339 650 False 928.00 928 92.40100 4663 5315 1 chr6B.!!$F1 652
6 TraesCS2A01G340900 chr4B 249045747 249046428 681 False 470.00 819 93.60950 4663 5323 2 chr4B.!!$F1 660
7 TraesCS2A01G340900 chr1B 346540589 346541272 683 False 470.00 819 93.60950 4663 5323 2 chr1B.!!$F2 660
8 TraesCS2A01G340900 chr7A 59838008 59838698 690 True 462.50 817 91.36550 4663 5326 2 chr7A.!!$R2 663
9 TraesCS2A01G340900 chr5B 503091163 503091800 637 True 235.20 412 86.37050 4663 5304 2 chr5B.!!$R2 641

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
728 3493 0.391661 ATAGCTCCCGCATTATGCCG 60.392 55.0 11.9 5.05 41.12 5.69 F
2004 4846 0.032815 TTCGTGTCGTTGATGGCTCA 59.967 50.0 0.0 0.00 0.00 4.26 F
2450 5332 0.031314 CGAGTGATGGACGGATGAGG 59.969 60.0 0.0 0.00 0.00 3.86 F
2780 5996 0.040425 GCTCGTTCCAATTTGCGTGT 60.040 50.0 0.0 0.00 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2029 4871 0.179045 ACACCGAGCAGAAAAGCTGT 60.179 50.000 0.00 0.0 46.75 4.40 R
2862 6099 1.384525 AAGACTCCATCTCCGAGACG 58.615 55.000 0.00 0.0 36.27 4.18 R
4028 7277 1.218047 GATGGTCCAGTACAGCGCA 59.782 57.895 11.47 0.0 0.00 6.09 R
4613 7870 0.032813 CCCATCCCACAAGCAAGGAT 60.033 55.000 0.00 0.0 41.16 3.24 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
22 23 0.617820 AACAGCCCCGTAGTGGATCT 60.618 55.000 0.00 0.00 42.00 2.75
37 38 1.219213 GGATCTGGAGGAAGAGGAGGA 59.781 57.143 0.00 0.00 0.00 3.71
41 45 1.220236 CTGGAGGAAGAGGAGGAGGAT 59.780 57.143 0.00 0.00 0.00 3.24
42 46 1.219213 TGGAGGAAGAGGAGGAGGATC 59.781 57.143 0.00 0.00 0.00 3.36
47 51 4.378961 AGGAAGAGGAGGAGGATCATTTT 58.621 43.478 0.00 0.00 36.25 1.82
57 61 0.740737 GGATCATTTTGGGGACGCTG 59.259 55.000 0.00 0.00 0.00 5.18
107 111 1.131638 CCATCCTCGATTCCCTCCAA 58.868 55.000 0.00 0.00 0.00 3.53
115 119 0.551396 GATTCCCTCCAATCGGGGTT 59.449 55.000 0.00 0.00 43.00 4.11
128 132 2.825836 GGGTTGGATGCAGAGGCG 60.826 66.667 0.00 0.00 45.35 5.52
132 136 1.086634 GTTGGATGCAGAGGCGAGAC 61.087 60.000 0.00 0.00 45.35 3.36
133 137 1.543944 TTGGATGCAGAGGCGAGACA 61.544 55.000 0.00 0.00 45.35 3.41
146 150 3.338126 GAGACACCGTCGCCGACAT 62.338 63.158 18.40 1.14 37.67 3.06
211 215 1.000283 CTACATGGATGAGGTCGAGCC 60.000 57.143 11.73 3.31 37.58 4.70
288 292 0.455815 CGTCATGGACATCTCCGACA 59.544 55.000 0.00 0.00 39.88 4.35
312 316 6.821031 ATGAAGATTAGCTAGGGTAGTACG 57.179 41.667 0.00 0.00 0.00 3.67
315 319 7.456725 TGAAGATTAGCTAGGGTAGTACGTAT 58.543 38.462 0.00 0.00 0.00 3.06
321 325 6.973460 AGCTAGGGTAGTACGTATGATTTT 57.027 37.500 0.00 0.00 0.00 1.82
348 352 9.618890 TTTTCTCTCTCTCCATATTTTGTATGG 57.381 33.333 7.60 7.60 44.41 2.74
401 409 7.439108 AATGTAGAGTACCTAATTTGAGGCT 57.561 36.000 0.00 0.00 40.65 4.58
420 435 4.338539 GACCGGTCACTGACGCGT 62.339 66.667 29.75 13.85 32.65 6.01
426 441 4.034258 TCACTGACGCGTCCGGTC 62.034 66.667 34.34 12.49 39.22 4.79
428 443 4.338539 ACTGACGCGTCCGGTCAC 62.339 66.667 34.34 10.91 39.22 3.67
494 509 4.478203 AGATGCTCTCAAGAGGCAGTATA 58.522 43.478 15.08 0.00 42.29 1.47
504 519 3.591789 AGAGGCAGTATATGTGGGACAT 58.408 45.455 0.00 0.00 44.52 3.06
590 3345 6.093495 TGTTGTACTAGACTTATTTGCATGCC 59.907 38.462 16.68 0.00 0.00 4.40
606 3361 6.651975 TGCATGCCATGTATGAATGATTTA 57.348 33.333 16.68 0.00 0.00 1.40
667 3424 5.565592 TTTTGTGAAATCCATCCGATCAG 57.434 39.130 0.00 0.00 0.00 2.90
669 3426 3.797039 TGTGAAATCCATCCGATCAGTC 58.203 45.455 0.00 0.00 0.00 3.51
681 3438 1.804601 GATCAGTCGAAACCCGGTTT 58.195 50.000 15.67 15.67 38.54 3.27
682 3439 2.963432 GATCAGTCGAAACCCGGTTTA 58.037 47.619 15.71 0.00 35.77 2.01
722 3487 5.412904 GCTTTAAATAGATAGCTCCCGCATT 59.587 40.000 0.00 0.00 39.10 3.56
724 3489 7.281100 GCTTTAAATAGATAGCTCCCGCATTAT 59.719 37.037 0.00 0.00 39.10 1.28
725 3490 8.492673 TTTAAATAGATAGCTCCCGCATTATG 57.507 34.615 0.00 0.00 39.10 1.90
727 3492 1.065854 AGATAGCTCCCGCATTATGCC 60.066 52.381 11.90 0.00 41.12 4.40
728 3493 0.391661 ATAGCTCCCGCATTATGCCG 60.392 55.000 11.90 5.05 41.12 5.69
729 3494 1.754380 TAGCTCCCGCATTATGCCGT 61.754 55.000 11.90 0.00 41.12 5.68
730 3495 2.896801 GCTCCCGCATTATGCCGTG 61.897 63.158 11.90 4.39 41.12 4.94
731 3496 2.203139 TCCCGCATTATGCCGTGG 60.203 61.111 11.90 9.80 41.12 4.94
735 3513 2.833533 CGCATTATGCCGTGGGGTG 61.834 63.158 11.90 0.00 41.12 4.61
737 3515 1.724582 GCATTATGCCGTGGGGTGTC 61.725 60.000 5.80 0.00 37.42 3.67
743 3521 2.605295 CCGTGGGGTGTCCTGGTA 60.605 66.667 0.00 0.00 36.20 3.25
763 3543 4.135570 CGTGAAATGCGCAAGTGG 57.864 55.556 17.11 0.00 41.68 4.00
819 3600 8.177456 TGGAAGAGCCTAGACATTATATAAGGA 58.823 37.037 13.77 0.00 37.63 3.36
832 3613 8.652290 ACATTATATAAGGACTCTCCCTGAAAC 58.348 37.037 13.77 0.00 37.19 2.78
842 3623 4.030913 CTCTCCCTGAAACCCTGTACATA 58.969 47.826 0.00 0.00 0.00 2.29
887 3671 1.690283 CCGAAGACATCAGCACTGCG 61.690 60.000 0.00 0.00 33.11 5.18
976 3768 2.280592 ACGTCGTGCCTTTGACCC 60.281 61.111 0.00 0.00 0.00 4.46
1095 3887 4.101448 ACCTGTCTCATGGCGGCC 62.101 66.667 13.32 13.32 0.00 6.13
1145 3937 1.434622 GGCATCTCAGGTGCGTCATG 61.435 60.000 3.14 0.00 43.40 3.07
1148 3940 0.176680 ATCTCAGGTGCGTCATGGTC 59.823 55.000 0.00 0.00 0.00 4.02
1172 3964 1.009900 CGCCGTCCGTACATCTCTC 60.010 63.158 0.00 0.00 0.00 3.20
1189 3981 1.416401 TCTCTTGGTGGAACTGTGGAC 59.584 52.381 0.00 0.00 36.74 4.02
1209 4001 0.596859 GGAATACCTGCCTACGACGC 60.597 60.000 0.00 0.00 0.00 5.19
1212 4004 1.453762 ATACCTGCCTACGACGCTCC 61.454 60.000 0.00 0.00 0.00 4.70
1286 4082 1.702299 CGATCAGTTCGTGGTTCGC 59.298 57.895 0.00 0.00 43.01 4.70
1314 4110 4.336433 CGATGCTGTTCTTGATTTGGGTAT 59.664 41.667 0.00 0.00 0.00 2.73
1316 4112 6.038161 CGATGCTGTTCTTGATTTGGGTATTA 59.962 38.462 0.00 0.00 0.00 0.98
1317 4113 7.415095 CGATGCTGTTCTTGATTTGGGTATTAA 60.415 37.037 0.00 0.00 0.00 1.40
1351 4147 3.118992 TCCAGTAGCTATGCTGTGAGTTG 60.119 47.826 9.74 0.00 40.10 3.16
1405 4204 1.948145 GAAGCCATGAAGAGCATCCTG 59.052 52.381 0.00 0.00 34.15 3.86
1451 4250 8.083462 ACTAGTAGTTTCAGCTTAGTTTGTCTC 58.917 37.037 0.00 0.00 0.00 3.36
1482 4281 3.486383 TCCCCAAATATCTCCAAATCGC 58.514 45.455 0.00 0.00 0.00 4.58
1541 4340 1.536149 CTTCGTCTTCGTCGATCACC 58.464 55.000 0.00 0.00 37.18 4.02
1587 4386 7.274033 CAGTAAAATATTGAGTTGGTACGACGA 59.726 37.037 0.00 0.00 0.00 4.20
1735 4541 7.547370 GCATCGCAGAAAGATATTTATACTCCT 59.453 37.037 0.00 0.00 43.58 3.69
1736 4542 9.081997 CATCGCAGAAAGATATTTATACTCCTC 57.918 37.037 0.00 0.00 43.58 3.71
1740 4546 7.604545 GCAGAAAGATATTTATACTCCTCCCAC 59.395 40.741 0.00 0.00 0.00 4.61
1741 4547 8.097662 CAGAAAGATATTTATACTCCTCCCACC 58.902 40.741 0.00 0.00 0.00 4.61
1743 4549 7.560796 AAGATATTTATACTCCTCCCACCAG 57.439 40.000 0.00 0.00 0.00 4.00
1744 4550 6.635021 AGATATTTATACTCCTCCCACCAGT 58.365 40.000 0.00 0.00 0.00 4.00
1745 4551 7.776745 AGATATTTATACTCCTCCCACCAGTA 58.223 38.462 0.00 0.00 0.00 2.74
1746 4552 8.239478 AGATATTTATACTCCTCCCACCAGTAA 58.761 37.037 0.00 0.00 0.00 2.24
1747 4553 6.749036 ATTTATACTCCTCCCACCAGTAAG 57.251 41.667 0.00 0.00 0.00 2.34
1794 4600 2.629017 ATCAAGCCAAATGGTCCCTT 57.371 45.000 0.71 0.00 37.57 3.95
1795 4601 1.923356 TCAAGCCAAATGGTCCCTTC 58.077 50.000 0.71 0.00 37.57 3.46
1796 4602 1.146774 TCAAGCCAAATGGTCCCTTCA 59.853 47.619 0.71 0.00 37.57 3.02
1847 4653 2.102357 CATCGACGACAGGGACCG 59.898 66.667 0.00 0.00 0.00 4.79
1877 4683 1.071019 CACACCCGATTCGTGTCGAG 61.071 60.000 12.44 3.52 42.49 4.04
1957 4792 3.264897 CGACAGCTATGGCACGGC 61.265 66.667 3.10 5.52 41.70 5.68
1975 4810 0.367210 GCTCGTTAGCTTTCACGCTC 59.633 55.000 0.00 0.00 45.85 5.03
1977 4812 1.057361 CGTTAGCTTTCACGCTCGC 59.943 57.895 0.00 0.00 41.30 5.03
1990 4832 2.987593 CTCGCCGATTCGTTCGTG 59.012 61.111 14.51 10.21 46.65 4.35
2004 4846 0.032815 TTCGTGTCGTTGATGGCTCA 59.967 50.000 0.00 0.00 0.00 4.26
2020 4862 1.066858 GCTCATTCTGACTTCGGACCA 60.067 52.381 0.00 0.00 0.00 4.02
2021 4863 2.612972 GCTCATTCTGACTTCGGACCAA 60.613 50.000 0.00 0.00 0.00 3.67
2029 4871 1.004560 CTTCGGACCAAGCTGAGCA 60.005 57.895 7.39 0.00 0.00 4.26
2055 4897 2.624316 TTCTGCTCGGTGTTAGTACG 57.376 50.000 0.00 0.00 0.00 3.67
2064 4906 1.356938 GTGTTAGTACGGCCTTCTGC 58.643 55.000 0.00 0.00 40.16 4.26
2222 5095 1.408127 CCAGCCGGGATTTGTGATACA 60.408 52.381 2.18 0.00 40.01 2.29
2243 5116 4.142138 ACATTTCTGAGTTCCTAGTAGCGG 60.142 45.833 0.00 0.00 0.00 5.52
2309 5186 1.627297 GGCTTCCTGGTCCTAGGTGG 61.627 65.000 9.08 7.52 38.99 4.61
2350 5232 6.441284 TGGAGTACTATAGGCTACTCTCCTAG 59.559 46.154 21.16 12.12 39.36 3.02
2355 5237 9.474313 GTACTATAGGCTACTCTCCTAGTACTA 57.526 40.741 22.13 1.89 39.36 1.82
2357 5239 8.179487 ACTATAGGCTACTCTCCTAGTACTACT 58.821 40.741 4.43 0.00 39.36 2.57
2358 5240 5.813513 AGGCTACTCTCCTAGTACTACTC 57.186 47.826 0.00 0.00 39.80 2.59
2363 5245 6.480981 GCTACTCTCCTAGTACTACTCAGTTG 59.519 46.154 0.00 2.02 39.80 3.16
2442 5324 0.108804 TTTCCGAGCGAGTGATGGAC 60.109 55.000 0.00 0.00 0.00 4.02
2450 5332 0.031314 CGAGTGATGGACGGATGAGG 59.969 60.000 0.00 0.00 0.00 3.86
2472 5361 5.875359 AGGTTGACAAGATCGGACTTTTATC 59.125 40.000 0.00 0.00 0.00 1.75
2473 5362 5.642063 GGTTGACAAGATCGGACTTTTATCA 59.358 40.000 0.00 0.00 0.00 2.15
2474 5363 6.316390 GGTTGACAAGATCGGACTTTTATCAT 59.684 38.462 0.00 0.00 0.00 2.45
2481 5370 9.650539 CAAGATCGGACTTTTATCATGAGATAT 57.349 33.333 0.09 0.00 36.65 1.63
2541 5431 4.857037 ACTTGCGTCTTTCTGAACAAAAAC 59.143 37.500 0.00 0.00 0.00 2.43
2668 5872 9.747898 AGATCTAAGAATCGGTTATCTGACTAT 57.252 33.333 0.00 0.00 0.00 2.12
2677 5881 5.808540 TCGGTTATCTGACTATTTTGGTTCG 59.191 40.000 0.00 0.00 0.00 3.95
2683 5887 5.479306 TCTGACTATTTTGGTTCGAGGAAG 58.521 41.667 0.00 0.00 0.00 3.46
2685 5889 5.860611 TGACTATTTTGGTTCGAGGAAGAA 58.139 37.500 0.00 0.00 0.00 2.52
2686 5890 6.472887 TGACTATTTTGGTTCGAGGAAGAAT 58.527 36.000 0.00 0.00 32.25 2.40
2688 5892 7.764443 TGACTATTTTGGTTCGAGGAAGAATAG 59.236 37.037 13.65 13.65 32.25 1.73
2689 5893 7.848128 ACTATTTTGGTTCGAGGAAGAATAGA 58.152 34.615 18.53 0.00 32.25 1.98
2690 5894 7.982354 ACTATTTTGGTTCGAGGAAGAATAGAG 59.018 37.037 18.53 4.98 32.25 2.43
2691 5895 5.740290 TTTGGTTCGAGGAAGAATAGAGT 57.260 39.130 0.00 0.00 32.25 3.24
2692 5896 6.845758 TTTGGTTCGAGGAAGAATAGAGTA 57.154 37.500 0.00 0.00 32.25 2.59
2693 5897 7.419711 TTTGGTTCGAGGAAGAATAGAGTAT 57.580 36.000 0.00 0.00 32.25 2.12
2714 5924 8.882415 AGTATATATCAACACTTGGGTTTACG 57.118 34.615 0.00 0.00 0.00 3.18
2771 5981 1.730064 GCTAAATCACGCTCGTTCCAA 59.270 47.619 0.00 0.00 0.00 3.53
2774 5984 3.915437 AAATCACGCTCGTTCCAATTT 57.085 38.095 0.00 0.00 0.00 1.82
2777 5990 4.041026 CGCTCGTTCCAATTTGCG 57.959 55.556 0.00 0.00 37.57 4.85
2780 5996 0.040425 GCTCGTTCCAATTTGCGTGT 60.040 50.000 0.00 0.00 0.00 4.49
2793 6009 6.194508 CCAATTTGCGTGTCATTTTATCGTAG 59.805 38.462 0.00 0.00 0.00 3.51
2828 6065 7.246311 ACTCTGCAAATGATTTAAGTGAATCG 58.754 34.615 8.11 0.00 38.57 3.34
2848 6085 2.413837 GTGTTCATGGCACTAACGTCT 58.586 47.619 12.11 0.00 34.30 4.18
2850 6087 2.805671 TGTTCATGGCACTAACGTCTTG 59.194 45.455 8.68 0.00 0.00 3.02
2851 6088 2.093306 TCATGGCACTAACGTCTTGG 57.907 50.000 0.00 0.00 0.00 3.61
2859 6096 1.831736 ACTAACGTCTTGGGATCAGGG 59.168 52.381 0.00 0.00 0.00 4.45
2862 6099 2.597903 GTCTTGGGATCAGGGGGC 59.402 66.667 0.00 0.00 0.00 5.80
2865 6102 3.406595 CTTGGGATCAGGGGGCGTC 62.407 68.421 0.00 0.00 0.00 5.19
2940 6177 3.470567 CACGCGAGCAAGGACGTC 61.471 66.667 15.93 7.13 36.45 4.34
3195 6432 4.078516 GCCACGCCGGTCTACCTT 62.079 66.667 1.90 0.00 36.97 3.50
3210 6447 2.125552 CTTGCCGAGATGTCGCCA 60.126 61.111 6.76 0.00 45.41 5.69
3261 6498 0.247460 TCCCTCTGTTCATCAGCGTG 59.753 55.000 0.00 0.00 43.32 5.34
3393 6630 4.673403 GTGCTCATCACGGACACA 57.327 55.556 0.00 0.00 35.76 3.72
3487 6724 2.704193 GACGTTGACGCGGAGTTCG 61.704 63.158 12.47 11.06 44.43 3.95
3838 7075 5.095490 GCAATGCATACAACAAAGACCTAC 58.905 41.667 0.00 0.00 0.00 3.18
3839 7076 5.335583 GCAATGCATACAACAAAGACCTACA 60.336 40.000 0.00 0.00 0.00 2.74
3840 7077 6.317088 CAATGCATACAACAAAGACCTACAG 58.683 40.000 0.00 0.00 0.00 2.74
3841 7078 4.968259 TGCATACAACAAAGACCTACAGT 58.032 39.130 0.00 0.00 0.00 3.55
3842 7079 6.104146 TGCATACAACAAAGACCTACAGTA 57.896 37.500 0.00 0.00 0.00 2.74
3883 7120 0.532573 ACGTATGCTCTGGGACACTG 59.467 55.000 0.00 0.00 0.00 3.66
3899 7148 1.001487 CACTGATGGCTTTGCGTTTGA 60.001 47.619 0.00 0.00 0.00 2.69
4004 7253 2.429351 GCTGACGTGCGTCTTCTCG 61.429 63.158 22.54 9.26 44.80 4.04
4028 7277 2.847234 TTCAGCTGGTCGTGGGGT 60.847 61.111 15.13 0.00 0.00 4.95
4154 7403 2.437180 TGCTTCCTGGCGATGCTG 60.437 61.111 0.00 0.00 41.21 4.41
4179 7428 0.797249 CCTCAAGTACGGCGTCTTCG 60.797 60.000 19.21 13.62 40.37 3.79
4389 7638 1.408422 GCTTGGTTTCGCATTGTGTC 58.592 50.000 0.00 0.00 0.00 3.67
4396 7645 3.376859 GGTTTCGCATTGTGTCATGGATA 59.623 43.478 0.00 0.00 0.00 2.59
4433 7682 2.548904 AGCGCTAGATTGGTACTCGTAG 59.451 50.000 8.99 0.00 0.00 3.51
4441 7690 2.779755 TGGTACTCGTAGTCCGGTAA 57.220 50.000 0.00 0.00 37.11 2.85
4451 7700 3.605486 CGTAGTCCGGTAAAACTCGAAAG 59.395 47.826 0.00 0.00 0.00 2.62
4453 7702 3.387397 AGTCCGGTAAAACTCGAAAGTG 58.613 45.455 0.00 0.00 35.36 3.16
4454 7703 2.477754 GTCCGGTAAAACTCGAAAGTGG 59.522 50.000 0.00 0.00 35.36 4.00
4455 7704 1.802365 CCGGTAAAACTCGAAAGTGGG 59.198 52.381 0.00 0.00 35.36 4.61
4474 7731 2.202610 GAATCAAAAGGGCGCGCC 60.203 61.111 41.63 41.63 0.00 6.53
4496 7753 0.532115 GCTGCACCCATAAACCAAGG 59.468 55.000 0.00 0.00 0.00 3.61
4563 7820 6.671614 TGCTCTCTTGTCGAAAAACTTTTA 57.328 33.333 0.00 0.00 0.00 1.52
4564 7821 7.079182 TGCTCTCTTGTCGAAAAACTTTTAA 57.921 32.000 0.00 0.00 0.00 1.52
4565 7822 7.703328 TGCTCTCTTGTCGAAAAACTTTTAAT 58.297 30.769 0.00 0.00 0.00 1.40
4566 7823 7.855904 TGCTCTCTTGTCGAAAAACTTTTAATC 59.144 33.333 0.00 0.00 0.00 1.75
4567 7824 7.323895 GCTCTCTTGTCGAAAAACTTTTAATCC 59.676 37.037 0.00 0.00 0.00 3.01
4568 7825 7.349711 TCTCTTGTCGAAAAACTTTTAATCCG 58.650 34.615 0.00 0.00 0.00 4.18
4569 7826 7.011669 TCTCTTGTCGAAAAACTTTTAATCCGT 59.988 33.333 0.00 0.00 0.00 4.69
4570 7827 7.127686 TCTTGTCGAAAAACTTTTAATCCGTC 58.872 34.615 0.00 0.00 0.00 4.79
4571 7828 6.607735 TGTCGAAAAACTTTTAATCCGTCT 57.392 33.333 0.00 0.00 0.00 4.18
4572 7829 7.712264 TGTCGAAAAACTTTTAATCCGTCTA 57.288 32.000 0.00 0.00 0.00 2.59
4573 7830 8.314143 TGTCGAAAAACTTTTAATCCGTCTAT 57.686 30.769 0.00 0.00 0.00 1.98
4574 7831 8.776470 TGTCGAAAAACTTTTAATCCGTCTATT 58.224 29.630 0.00 0.00 0.00 1.73
4575 7832 9.603298 GTCGAAAAACTTTTAATCCGTCTATTT 57.397 29.630 0.00 0.00 0.00 1.40
4576 7833 9.815936 TCGAAAAACTTTTAATCCGTCTATTTC 57.184 29.630 0.00 0.00 0.00 2.17
4577 7834 9.058424 CGAAAAACTTTTAATCCGTCTATTTCC 57.942 33.333 0.00 0.00 0.00 3.13
4578 7835 9.902196 GAAAAACTTTTAATCCGTCTATTTCCA 57.098 29.630 0.00 0.00 0.00 3.53
4579 7836 9.908152 AAAAACTTTTAATCCGTCTATTTCCAG 57.092 29.630 0.00 0.00 0.00 3.86
4580 7837 7.625828 AACTTTTAATCCGTCTATTTCCAGG 57.374 36.000 0.00 0.00 0.00 4.45
4581 7838 6.718294 ACTTTTAATCCGTCTATTTCCAGGT 58.282 36.000 0.00 0.00 0.00 4.00
4582 7839 6.822170 ACTTTTAATCCGTCTATTTCCAGGTC 59.178 38.462 0.00 0.00 0.00 3.85
4583 7840 5.943349 TTAATCCGTCTATTTCCAGGTCA 57.057 39.130 0.00 0.00 0.00 4.02
4584 7841 6.494666 TTAATCCGTCTATTTCCAGGTCAT 57.505 37.500 0.00 0.00 0.00 3.06
4585 7842 4.608948 ATCCGTCTATTTCCAGGTCATC 57.391 45.455 0.00 0.00 0.00 2.92
4586 7843 2.361119 TCCGTCTATTTCCAGGTCATCG 59.639 50.000 0.00 0.00 0.00 3.84
4587 7844 2.128035 CGTCTATTTCCAGGTCATCGC 58.872 52.381 0.00 0.00 0.00 4.58
4588 7845 2.223829 CGTCTATTTCCAGGTCATCGCT 60.224 50.000 0.00 0.00 0.00 4.93
4589 7846 3.004419 CGTCTATTTCCAGGTCATCGCTA 59.996 47.826 0.00 0.00 0.00 4.26
4590 7847 4.499188 CGTCTATTTCCAGGTCATCGCTAA 60.499 45.833 0.00 0.00 0.00 3.09
4591 7848 5.542779 GTCTATTTCCAGGTCATCGCTAAT 58.457 41.667 0.00 0.00 0.00 1.73
4592 7849 5.406780 GTCTATTTCCAGGTCATCGCTAATG 59.593 44.000 0.00 0.00 36.65 1.90
4593 7850 1.953559 TTCCAGGTCATCGCTAATGC 58.046 50.000 0.00 0.00 35.17 3.56
4612 7869 2.100846 GCATCTGCGGAAATGCTCA 58.899 52.632 8.09 0.00 43.87 4.26
4613 7870 0.452987 GCATCTGCGGAAATGCTCAA 59.547 50.000 8.09 0.00 43.87 3.02
4614 7871 1.066605 GCATCTGCGGAAATGCTCAAT 59.933 47.619 8.09 0.00 43.87 2.57
4615 7872 2.857489 GCATCTGCGGAAATGCTCAATC 60.857 50.000 8.09 0.00 43.87 2.67
4616 7873 1.382522 TCTGCGGAAATGCTCAATCC 58.617 50.000 0.00 0.00 35.36 3.01
4617 7874 1.065199 TCTGCGGAAATGCTCAATCCT 60.065 47.619 0.00 0.00 35.36 3.24
4618 7875 1.747355 CTGCGGAAATGCTCAATCCTT 59.253 47.619 0.00 0.00 35.36 3.36
4619 7876 1.473677 TGCGGAAATGCTCAATCCTTG 59.526 47.619 0.00 0.00 35.36 3.61
4620 7877 1.800286 GCGGAAATGCTCAATCCTTGC 60.800 52.381 0.00 0.00 0.00 4.01
4621 7878 1.747355 CGGAAATGCTCAATCCTTGCT 59.253 47.619 0.00 0.00 0.00 3.91
4622 7879 2.165030 CGGAAATGCTCAATCCTTGCTT 59.835 45.455 0.00 0.00 0.00 3.91
4623 7880 3.518590 GGAAATGCTCAATCCTTGCTTG 58.481 45.455 0.00 0.00 0.00 4.01
4624 7881 3.056322 GGAAATGCTCAATCCTTGCTTGT 60.056 43.478 0.00 0.00 0.00 3.16
4625 7882 3.587797 AATGCTCAATCCTTGCTTGTG 57.412 42.857 0.00 0.00 0.00 3.33
4626 7883 1.250328 TGCTCAATCCTTGCTTGTGG 58.750 50.000 0.00 0.00 0.00 4.17
4627 7884 0.529378 GCTCAATCCTTGCTTGTGGG 59.471 55.000 0.00 0.00 0.00 4.61
4628 7885 1.887956 GCTCAATCCTTGCTTGTGGGA 60.888 52.381 0.00 0.00 0.00 4.37
4629 7886 2.731572 CTCAATCCTTGCTTGTGGGAT 58.268 47.619 0.00 0.00 41.09 3.85
4630 7887 2.426024 CTCAATCCTTGCTTGTGGGATG 59.574 50.000 0.00 0.00 39.49 3.51
4631 7888 1.479323 CAATCCTTGCTTGTGGGATGG 59.521 52.381 0.00 0.00 39.49 3.51
4632 7889 0.032813 ATCCTTGCTTGTGGGATGGG 60.033 55.000 0.00 0.00 38.30 4.00
4633 7890 1.683365 CCTTGCTTGTGGGATGGGG 60.683 63.158 0.00 0.00 0.00 4.96
4634 7891 1.383799 CTTGCTTGTGGGATGGGGA 59.616 57.895 0.00 0.00 0.00 4.81
4635 7892 0.032813 CTTGCTTGTGGGATGGGGAT 60.033 55.000 0.00 0.00 0.00 3.85
4636 7893 0.324552 TTGCTTGTGGGATGGGGATG 60.325 55.000 0.00 0.00 0.00 3.51
4637 7894 1.307647 GCTTGTGGGATGGGGATGT 59.692 57.895 0.00 0.00 0.00 3.06
4638 7895 0.753111 GCTTGTGGGATGGGGATGTC 60.753 60.000 0.00 0.00 0.00 3.06
4639 7896 0.921896 CTTGTGGGATGGGGATGTCT 59.078 55.000 0.00 0.00 0.00 3.41
4640 7897 1.285962 CTTGTGGGATGGGGATGTCTT 59.714 52.381 0.00 0.00 0.00 3.01
4641 7898 0.625316 TGTGGGATGGGGATGTCTTG 59.375 55.000 0.00 0.00 0.00 3.02
4642 7899 0.753111 GTGGGATGGGGATGTCTTGC 60.753 60.000 0.00 0.00 0.00 4.01
4643 7900 0.920763 TGGGATGGGGATGTCTTGCT 60.921 55.000 0.00 0.00 0.00 3.91
4644 7901 0.259938 GGGATGGGGATGTCTTGCTT 59.740 55.000 0.00 0.00 0.00 3.91
4645 7902 1.494721 GGGATGGGGATGTCTTGCTTA 59.505 52.381 0.00 0.00 0.00 3.09
4646 7903 2.091885 GGGATGGGGATGTCTTGCTTAA 60.092 50.000 0.00 0.00 0.00 1.85
4647 7904 3.627237 GGGATGGGGATGTCTTGCTTAAA 60.627 47.826 0.00 0.00 0.00 1.52
4648 7905 3.381590 GGATGGGGATGTCTTGCTTAAAC 59.618 47.826 0.00 0.00 0.00 2.01
4649 7906 3.517296 TGGGGATGTCTTGCTTAAACA 57.483 42.857 0.00 0.00 0.00 2.83
4650 7907 3.838565 TGGGGATGTCTTGCTTAAACAA 58.161 40.909 0.00 0.00 0.00 2.83
4651 7908 4.415596 TGGGGATGTCTTGCTTAAACAAT 58.584 39.130 0.00 0.00 0.00 2.71
4652 7909 4.462483 TGGGGATGTCTTGCTTAAACAATC 59.538 41.667 0.00 0.00 0.00 2.67
4653 7910 4.462483 GGGGATGTCTTGCTTAAACAATCA 59.538 41.667 0.00 0.00 0.00 2.57
4654 7911 5.047377 GGGGATGTCTTGCTTAAACAATCAA 60.047 40.000 0.00 0.00 0.00 2.57
4655 7912 6.095377 GGGATGTCTTGCTTAAACAATCAAG 58.905 40.000 0.00 0.00 37.76 3.02
4656 7913 6.294731 GGGATGTCTTGCTTAAACAATCAAGT 60.295 38.462 0.00 0.00 37.68 3.16
4657 7914 6.583806 GGATGTCTTGCTTAAACAATCAAGTG 59.416 38.462 0.00 0.00 37.68 3.16
4658 7915 6.691754 TGTCTTGCTTAAACAATCAAGTGA 57.308 33.333 0.00 0.00 37.68 3.41
4659 7916 6.728200 TGTCTTGCTTAAACAATCAAGTGAG 58.272 36.000 0.00 0.00 37.68 3.51
4660 7917 6.542005 TGTCTTGCTTAAACAATCAAGTGAGA 59.458 34.615 0.00 0.00 37.68 3.27
4661 7918 7.229306 TGTCTTGCTTAAACAATCAAGTGAGAT 59.771 33.333 0.00 0.00 37.68 2.75
4712 7971 5.995282 ACGGAAGAGAAAAATCACATGTGTA 59.005 36.000 24.63 12.43 0.00 2.90
4801 8061 6.719829 CCTATGTCACCTTTTAACCTCCTTTT 59.280 38.462 0.00 0.00 0.00 2.27
4803 8063 5.762279 TGTCACCTTTTAACCTCCTTTTCT 58.238 37.500 0.00 0.00 0.00 2.52
4944 8206 6.763135 CACACAGGTAATTCATAGTGCATACT 59.237 38.462 0.00 0.00 40.99 2.12
5340 8649 4.320910 GCAGGAAGCCCACCTAAC 57.679 61.111 0.00 0.00 35.84 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.674322 CCACTACGGGGCTGTTTGG 60.674 63.158 0.00 0.00 0.00 3.28
1 2 0.035439 ATCCACTACGGGGCTGTTTG 60.035 55.000 0.00 0.00 34.36 2.93
2 3 0.252197 GATCCACTACGGGGCTGTTT 59.748 55.000 0.00 0.00 34.36 2.83
3 4 0.617820 AGATCCACTACGGGGCTGTT 60.618 55.000 0.00 0.00 34.36 3.16
5 6 1.443407 CAGATCCACTACGGGGCTG 59.557 63.158 0.00 0.00 34.36 4.85
6 7 1.762460 CCAGATCCACTACGGGGCT 60.762 63.158 0.00 0.00 34.36 5.19
7 8 1.749334 CTCCAGATCCACTACGGGGC 61.749 65.000 0.00 0.00 34.36 5.80
8 9 1.115930 CCTCCAGATCCACTACGGGG 61.116 65.000 0.00 0.00 34.36 5.73
9 10 0.106167 TCCTCCAGATCCACTACGGG 60.106 60.000 0.00 0.00 34.36 5.28
10 11 1.683917 CTTCCTCCAGATCCACTACGG 59.316 57.143 0.00 0.00 0.00 4.02
11 12 2.621055 CTCTTCCTCCAGATCCACTACG 59.379 54.545 0.00 0.00 0.00 3.51
22 23 1.219213 GATCCTCCTCCTCTTCCTCCA 59.781 57.143 0.00 0.00 0.00 3.86
37 38 0.625849 AGCGTCCCCAAAATGATCCT 59.374 50.000 0.00 0.00 0.00 3.24
41 45 1.304052 CCCAGCGTCCCCAAAATGA 60.304 57.895 0.00 0.00 0.00 2.57
42 46 2.350458 CCCCAGCGTCCCCAAAATG 61.350 63.158 0.00 0.00 0.00 2.32
57 61 1.742768 CCTGCAGATCTACGTCCCC 59.257 63.158 17.39 0.00 0.00 4.81
64 68 1.758122 TGCTCCGCCTGCAGATCTA 60.758 57.895 17.39 0.00 35.31 1.98
65 69 3.079478 TGCTCCGCCTGCAGATCT 61.079 61.111 17.39 0.00 35.31 2.75
107 111 1.528824 CTCTGCATCCAACCCCGAT 59.471 57.895 0.00 0.00 0.00 4.18
112 116 1.817099 CTCGCCTCTGCATCCAACC 60.817 63.158 0.00 0.00 37.32 3.77
115 119 1.984026 TGTCTCGCCTCTGCATCCA 60.984 57.895 0.00 0.00 37.32 3.41
143 147 1.089920 GTTGCGCCTTCATCTCATGT 58.910 50.000 4.18 0.00 0.00 3.21
146 150 1.291184 CGTGTTGCGCCTTCATCTCA 61.291 55.000 4.18 0.00 0.00 3.27
167 171 1.047596 GCATCTCCTCCTCCTCTGCA 61.048 60.000 0.00 0.00 0.00 4.41
170 174 0.178992 CGAGCATCTCCTCCTCCTCT 60.179 60.000 0.00 0.00 0.00 3.69
211 215 3.610669 CCGGCTCATCCTCCTCCG 61.611 72.222 0.00 0.00 39.79 4.63
265 269 0.824109 GGAGATGTCCATGACGTCCA 59.176 55.000 14.12 3.25 46.31 4.02
266 270 0.249073 CGGAGATGTCCATGACGTCC 60.249 60.000 14.12 0.00 46.31 4.79
288 292 6.776603 ACGTACTACCCTAGCTAATCTTCATT 59.223 38.462 0.00 0.00 0.00 2.57
334 338 7.032598 ACCCCTAGATCCATACAAAATATGG 57.967 40.000 6.62 6.62 44.41 2.74
338 342 6.590656 TGAACCCCTAGATCCATACAAAAT 57.409 37.500 0.00 0.00 0.00 1.82
339 343 6.395780 TTGAACCCCTAGATCCATACAAAA 57.604 37.500 0.00 0.00 0.00 2.44
348 352 7.234577 AGTCTCTCATATTTGAACCCCTAGATC 59.765 40.741 0.00 0.00 0.00 2.75
388 396 2.017049 CCGGTCAAGCCTCAAATTAGG 58.983 52.381 0.00 0.00 39.87 2.69
401 409 2.028484 GCGTCAGTGACCGGTCAA 59.972 61.111 37.75 21.06 41.85 3.18
494 509 3.245158 GGATGGATCATGATGTCCCACAT 60.245 47.826 14.30 7.49 42.43 3.21
504 519 8.771521 ATAAGTTTTTCATGGATGGATCATGA 57.228 30.769 0.00 0.00 46.21 3.07
528 3283 9.550406 TTCAACGAGATTAACCGGATATTTAAT 57.450 29.630 9.46 8.07 31.86 1.40
534 3289 7.042950 TCAAATTCAACGAGATTAACCGGATA 58.957 34.615 9.46 0.00 0.00 2.59
646 3401 4.588899 ACTGATCGGATGGATTTCACAAA 58.411 39.130 9.00 0.00 34.82 2.83
649 3404 2.797156 CGACTGATCGGATGGATTTCAC 59.203 50.000 9.00 0.00 44.99 3.18
667 3424 4.227512 ACATTTTAAACCGGGTTTCGAC 57.772 40.909 27.35 0.00 42.43 4.20
669 3426 5.958949 CGTATACATTTTAAACCGGGTTTCG 59.041 40.000 27.35 16.47 37.01 3.46
722 3487 2.285069 AGGACACCCCACGGCATA 60.285 61.111 0.00 0.00 37.41 3.14
727 3492 1.295423 CTTACCAGGACACCCCACG 59.705 63.158 0.00 0.00 37.41 4.94
728 3493 1.002502 GCTTACCAGGACACCCCAC 60.003 63.158 0.00 0.00 37.41 4.61
729 3494 2.589157 CGCTTACCAGGACACCCCA 61.589 63.158 0.00 0.00 37.41 4.96
730 3495 2.267961 CGCTTACCAGGACACCCC 59.732 66.667 0.00 0.00 0.00 4.95
731 3496 1.375523 CACGCTTACCAGGACACCC 60.376 63.158 0.00 0.00 0.00 4.61
735 3513 1.130561 GCATTTCACGCTTACCAGGAC 59.869 52.381 0.00 0.00 0.00 3.85
737 3515 0.096976 CGCATTTCACGCTTACCAGG 59.903 55.000 0.00 0.00 0.00 4.45
756 3536 2.113860 TCCACATAAGCTCCACTTGC 57.886 50.000 0.00 0.00 39.58 4.01
763 3543 3.726607 CTGACCTCATCCACATAAGCTC 58.273 50.000 0.00 0.00 0.00 4.09
819 3600 2.258109 GTACAGGGTTTCAGGGAGAGT 58.742 52.381 0.00 0.00 0.00 3.24
832 3613 4.677779 GCTGCCAAATGTTTATGTACAGGG 60.678 45.833 0.33 0.00 0.00 4.45
842 3623 1.661197 CGCGTGCTGCCAAATGTTT 60.661 52.632 0.00 0.00 42.08 2.83
870 3654 1.423056 GCGCAGTGCTGATGTCTTC 59.577 57.895 14.33 0.00 41.73 2.87
896 3680 0.948141 GAGGCTGGCTATAGCTTGCG 60.948 60.000 23.53 10.82 43.22 4.85
1095 3887 1.301009 GAAGATAAGGCCGCCGGAG 60.301 63.158 7.68 0.00 0.00 4.63
1107 3899 2.545113 GCCAATGTCGTAGCCGAAGATA 60.545 50.000 0.00 0.00 46.26 1.98
1148 3940 4.580551 GTACGGACGGCGATGGGG 62.581 72.222 16.62 0.00 0.00 4.96
1172 3964 0.884704 CCGTCCACAGTTCCACCAAG 60.885 60.000 0.00 0.00 0.00 3.61
1189 3981 0.317603 CGTCGTAGGCAGGTATTCCG 60.318 60.000 0.00 0.00 39.05 4.30
1209 4001 1.446272 GGGAGAAACGTGCGAGGAG 60.446 63.158 0.00 0.00 0.00 3.69
1212 4004 0.512952 CAAAGGGAGAAACGTGCGAG 59.487 55.000 0.00 0.00 0.00 5.03
1286 4082 2.662006 TCAAGAACAGCATCGAGAGG 57.338 50.000 0.00 0.00 0.00 3.69
1316 4112 9.495572 GCATAGCTACTGGAAATCTAATACTTT 57.504 33.333 0.00 0.00 0.00 2.66
1317 4113 8.875168 AGCATAGCTACTGGAAATCTAATACTT 58.125 33.333 0.00 0.00 36.99 2.24
1451 4250 2.949177 TATTTGGGGATCGGACATGG 57.051 50.000 0.00 0.00 0.00 3.66
1482 4281 4.250464 TGGTTAGATTAGAAGTTGCGGTG 58.750 43.478 0.00 0.00 0.00 4.94
1587 4386 3.545703 CGGGCTTTCAATTGGATCTAGT 58.454 45.455 5.42 0.00 0.00 2.57
1735 4541 0.400213 CACAAGCCTTACTGGTGGGA 59.600 55.000 0.00 0.00 45.42 4.37
1736 4542 2.946947 CACAAGCCTTACTGGTGGG 58.053 57.895 0.00 0.00 45.42 4.61
1740 4546 2.870372 GCGCACAAGCCTTACTGG 59.130 61.111 0.30 0.00 37.52 4.00
1794 4600 2.305927 GGGAGAAGAAAGGGTGTGATGA 59.694 50.000 0.00 0.00 0.00 2.92
1795 4601 2.040278 TGGGAGAAGAAAGGGTGTGATG 59.960 50.000 0.00 0.00 0.00 3.07
1796 4602 2.348472 TGGGAGAAGAAAGGGTGTGAT 58.652 47.619 0.00 0.00 0.00 3.06
1990 4832 2.621338 TCAGAATGAGCCATCAACGAC 58.379 47.619 0.00 0.00 42.56 4.34
2004 4846 1.625818 AGCTTGGTCCGAAGTCAGAAT 59.374 47.619 0.00 0.00 0.00 2.40
2029 4871 0.179045 ACACCGAGCAGAAAAGCTGT 60.179 50.000 0.00 0.00 46.75 4.40
2033 4875 3.364023 CGTACTAACACCGAGCAGAAAAG 59.636 47.826 0.00 0.00 0.00 2.27
2037 4879 0.806868 CCGTACTAACACCGAGCAGA 59.193 55.000 0.00 0.00 0.00 4.26
2064 4906 1.636988 GTGACACGGACGATTAAGGG 58.363 55.000 0.00 0.00 0.00 3.95
2178 5034 2.214920 GCTTCGATACCCCCGGGAT 61.215 63.158 26.32 12.93 38.96 3.85
2180 5036 3.937447 GGCTTCGATACCCCCGGG 61.937 72.222 15.80 15.80 42.03 5.73
2188 5044 0.748005 GGCTGGCTTTGGCTTCGATA 60.748 55.000 0.00 0.00 38.73 2.92
2222 5095 4.279145 TCCGCTACTAGGAACTCAGAAAT 58.721 43.478 0.00 0.00 41.75 2.17
2243 5116 2.287977 ACTTTGCCAGTACCCCTTTC 57.712 50.000 0.00 0.00 31.97 2.62
2309 5186 2.280628 CTCCACTGCTCGAATAAACCC 58.719 52.381 0.00 0.00 0.00 4.11
2350 5232 7.270793 CACAATCGACTAACAACTGAGTAGTAC 59.729 40.741 0.00 0.00 35.69 2.73
2355 5237 3.741344 GCACAATCGACTAACAACTGAGT 59.259 43.478 0.00 0.00 0.00 3.41
2357 5239 3.987868 GAGCACAATCGACTAACAACTGA 59.012 43.478 0.00 0.00 0.00 3.41
2358 5240 3.990469 AGAGCACAATCGACTAACAACTG 59.010 43.478 0.00 0.00 0.00 3.16
2442 5324 2.196749 CGATCTTGTCAACCTCATCCG 58.803 52.381 0.00 0.00 0.00 4.18
2450 5332 6.721571 TGATAAAAGTCCGATCTTGTCAAC 57.278 37.500 0.00 0.00 0.00 3.18
2481 5370 7.272037 TCATCGTATGAAACTAGTAGCATGA 57.728 36.000 16.50 9.28 36.11 3.07
2521 5411 3.125487 TCGTTTTTGTTCAGAAAGACGCA 59.875 39.130 7.41 0.00 41.03 5.24
2564 5457 3.882888 CTGGCGCAAATATTCCCTTCTTA 59.117 43.478 10.83 0.00 0.00 2.10
2566 5459 2.301346 CTGGCGCAAATATTCCCTTCT 58.699 47.619 10.83 0.00 0.00 2.85
2567 5460 2.024414 ACTGGCGCAAATATTCCCTTC 58.976 47.619 10.83 0.00 0.00 3.46
2568 5461 1.750778 CACTGGCGCAAATATTCCCTT 59.249 47.619 10.83 0.00 0.00 3.95
2569 5462 1.064758 TCACTGGCGCAAATATTCCCT 60.065 47.619 10.83 0.00 0.00 4.20
2570 5463 1.334869 CTCACTGGCGCAAATATTCCC 59.665 52.381 10.83 0.00 0.00 3.97
2668 5872 6.110411 ACTCTATTCTTCCTCGAACCAAAA 57.890 37.500 0.00 0.00 0.00 2.44
2688 5892 8.975439 CGTAAACCCAAGTGTTGATATATACTC 58.025 37.037 0.00 0.00 0.00 2.59
2689 5893 7.929785 CCGTAAACCCAAGTGTTGATATATACT 59.070 37.037 0.00 0.00 0.00 2.12
2690 5894 7.712205 ACCGTAAACCCAAGTGTTGATATATAC 59.288 37.037 0.00 0.00 0.00 1.47
2691 5895 7.794041 ACCGTAAACCCAAGTGTTGATATATA 58.206 34.615 0.00 0.00 0.00 0.86
2692 5896 6.655930 ACCGTAAACCCAAGTGTTGATATAT 58.344 36.000 0.00 0.00 0.00 0.86
2693 5897 6.052405 ACCGTAAACCCAAGTGTTGATATA 57.948 37.500 0.00 0.00 0.00 0.86
2738 5948 8.167605 AGCGTGATTTAGCTTCTCTATTAGTA 57.832 34.615 0.00 0.00 41.52 1.82
2739 5949 7.045126 AGCGTGATTTAGCTTCTCTATTAGT 57.955 36.000 0.00 0.00 41.52 2.24
2740 5950 6.304445 CGAGCGTGATTTAGCTTCTCTATTAG 59.696 42.308 0.00 0.00 44.69 1.73
2741 5951 6.143496 CGAGCGTGATTTAGCTTCTCTATTA 58.857 40.000 0.00 0.00 44.69 0.98
2742 5952 4.979197 CGAGCGTGATTTAGCTTCTCTATT 59.021 41.667 0.00 0.00 44.69 1.73
2743 5953 4.036971 ACGAGCGTGATTTAGCTTCTCTAT 59.963 41.667 0.00 0.00 44.69 1.98
2744 5954 3.377485 ACGAGCGTGATTTAGCTTCTCTA 59.623 43.478 0.00 0.00 44.69 2.43
2748 5958 2.029365 GGAACGAGCGTGATTTAGCTTC 59.971 50.000 0.00 0.00 44.69 3.86
2771 5981 6.417191 ACTACGATAAAATGACACGCAAAT 57.583 33.333 0.00 0.00 0.00 2.32
2774 5984 4.496539 CGTACTACGATAAAATGACACGCA 59.503 41.667 2.17 0.00 46.05 5.24
2777 5990 9.702726 TTAGTACGTACTACGATAAAATGACAC 57.297 33.333 30.26 0.00 46.05 3.67
2793 6009 7.521509 AATCATTTGCAGAGTTAGTACGTAC 57.478 36.000 18.10 18.10 0.00 3.67
2828 6065 2.413837 AGACGTTAGTGCCATGAACAC 58.586 47.619 9.98 9.98 38.35 3.32
2848 6085 3.407967 GACGCCCCCTGATCCCAA 61.408 66.667 0.00 0.00 0.00 4.12
2850 6087 3.551407 GAGACGCCCCCTGATCCC 61.551 72.222 0.00 0.00 0.00 3.85
2851 6088 3.917760 CGAGACGCCCCCTGATCC 61.918 72.222 0.00 0.00 0.00 3.36
2859 6096 2.833582 TCCATCTCCGAGACGCCC 60.834 66.667 0.00 0.00 0.00 6.13
2862 6099 1.384525 AAGACTCCATCTCCGAGACG 58.615 55.000 0.00 0.00 36.27 4.18
2865 6102 2.880963 GGAAAGACTCCATCTCCGAG 57.119 55.000 0.00 0.00 44.67 4.63
2940 6177 2.923655 CTGGTCGTTGTACATGCAGTAG 59.076 50.000 0.00 0.00 32.19 2.57
3045 6282 2.440796 ACCATGATGGCCTTGCGG 60.441 61.111 12.25 0.19 42.67 5.69
3261 6498 3.384532 TTGGCGACGAGGTACCCC 61.385 66.667 8.74 1.52 0.00 4.95
3838 7075 4.576463 GCTGGGATGGAAAATGTAGTACTG 59.424 45.833 5.39 0.00 0.00 2.74
3839 7076 4.683400 CGCTGGGATGGAAAATGTAGTACT 60.683 45.833 0.00 0.00 0.00 2.73
3840 7077 3.560068 CGCTGGGATGGAAAATGTAGTAC 59.440 47.826 0.00 0.00 0.00 2.73
3841 7078 3.199071 ACGCTGGGATGGAAAATGTAGTA 59.801 43.478 0.00 0.00 0.00 1.82
3842 7079 2.026262 ACGCTGGGATGGAAAATGTAGT 60.026 45.455 0.00 0.00 0.00 2.73
3883 7120 1.391144 GCAATCAAACGCAAAGCCATC 59.609 47.619 0.00 0.00 0.00 3.51
4028 7277 1.218047 GATGGTCCAGTACAGCGCA 59.782 57.895 11.47 0.00 0.00 6.09
4154 7403 3.876300 CCGTACTTGAGGCTGCAC 58.124 61.111 0.50 0.00 0.00 4.57
4179 7428 2.445438 GCCAGCACGCGTAGAAGAC 61.445 63.158 13.44 0.00 0.00 3.01
4192 7441 2.161486 GTCATGACGACGAGCCAGC 61.161 63.158 10.69 0.00 34.19 4.85
4256 7505 2.927856 ACGTGGCCCATGGAGTCA 60.928 61.111 15.22 8.50 0.00 3.41
4433 7682 2.477754 CCACTTTCGAGTTTTACCGGAC 59.522 50.000 9.46 0.00 0.00 4.79
4441 7690 4.351874 TGATTCTCCCACTTTCGAGTTT 57.648 40.909 0.00 0.00 0.00 2.66
4451 7700 0.811281 CGCCCTTTTGATTCTCCCAC 59.189 55.000 0.00 0.00 0.00 4.61
4453 7702 1.809869 GCGCCCTTTTGATTCTCCC 59.190 57.895 0.00 0.00 0.00 4.30
4454 7703 1.429423 CGCGCCCTTTTGATTCTCC 59.571 57.895 0.00 0.00 0.00 3.71
4455 7704 1.226407 GCGCGCCCTTTTGATTCTC 60.226 57.895 23.24 0.00 0.00 2.87
4474 7731 1.255882 TGGTTTATGGGTGCAGCAAG 58.744 50.000 19.06 0.00 0.00 4.01
4545 7802 7.011669 AGACGGATTAAAAGTTTTTCGACAAGA 59.988 33.333 6.10 0.00 0.00 3.02
4563 7820 4.501571 CGATGACCTGGAAATAGACGGATT 60.502 45.833 0.00 0.00 0.00 3.01
4564 7821 3.005897 CGATGACCTGGAAATAGACGGAT 59.994 47.826 0.00 0.00 0.00 4.18
4565 7822 2.361119 CGATGACCTGGAAATAGACGGA 59.639 50.000 0.00 0.00 0.00 4.69
4566 7823 2.743938 CGATGACCTGGAAATAGACGG 58.256 52.381 0.00 0.00 0.00 4.79
4567 7824 2.128035 GCGATGACCTGGAAATAGACG 58.872 52.381 0.00 0.00 0.00 4.18
4568 7825 3.460857 AGCGATGACCTGGAAATAGAC 57.539 47.619 0.00 0.00 0.00 2.59
4569 7826 5.541845 CATTAGCGATGACCTGGAAATAGA 58.458 41.667 0.00 0.00 38.03 1.98
4570 7827 4.153117 GCATTAGCGATGACCTGGAAATAG 59.847 45.833 0.00 0.00 38.03 1.73
4571 7828 4.065088 GCATTAGCGATGACCTGGAAATA 58.935 43.478 0.00 0.00 38.03 1.40
4572 7829 2.880890 GCATTAGCGATGACCTGGAAAT 59.119 45.455 0.00 0.00 38.03 2.17
4573 7830 2.288666 GCATTAGCGATGACCTGGAAA 58.711 47.619 0.00 0.00 38.03 3.13
4574 7831 1.953559 GCATTAGCGATGACCTGGAA 58.046 50.000 0.00 0.00 38.03 3.53
4575 7832 3.686622 GCATTAGCGATGACCTGGA 57.313 52.632 0.00 0.00 38.03 3.86
4594 7851 0.452987 TTGAGCATTTCCGCAGATGC 59.547 50.000 0.00 0.00 46.88 3.91
4595 7852 2.287427 GGATTGAGCATTTCCGCAGATG 60.287 50.000 0.00 0.00 0.00 2.90
4596 7853 1.952296 GGATTGAGCATTTCCGCAGAT 59.048 47.619 0.00 0.00 0.00 2.90
4597 7854 1.065199 AGGATTGAGCATTTCCGCAGA 60.065 47.619 0.00 0.00 34.61 4.26
4598 7855 1.386533 AGGATTGAGCATTTCCGCAG 58.613 50.000 0.00 0.00 34.61 5.18
4599 7856 1.838112 AAGGATTGAGCATTTCCGCA 58.162 45.000 0.00 0.00 34.61 5.69
4612 7869 1.620524 CCCATCCCACAAGCAAGGATT 60.621 52.381 0.00 0.00 38.36 3.01
4613 7870 0.032813 CCCATCCCACAAGCAAGGAT 60.033 55.000 0.00 0.00 41.16 3.24
4614 7871 1.383799 CCCATCCCACAAGCAAGGA 59.616 57.895 0.00 0.00 0.00 3.36
4615 7872 1.683365 CCCCATCCCACAAGCAAGG 60.683 63.158 0.00 0.00 0.00 3.61
4616 7873 0.032813 ATCCCCATCCCACAAGCAAG 60.033 55.000 0.00 0.00 0.00 4.01
4617 7874 0.324552 CATCCCCATCCCACAAGCAA 60.325 55.000 0.00 0.00 0.00 3.91
4618 7875 1.307309 CATCCCCATCCCACAAGCA 59.693 57.895 0.00 0.00 0.00 3.91
4619 7876 0.753111 GACATCCCCATCCCACAAGC 60.753 60.000 0.00 0.00 0.00 4.01
4620 7877 0.921896 AGACATCCCCATCCCACAAG 59.078 55.000 0.00 0.00 0.00 3.16
4621 7878 1.005805 CAAGACATCCCCATCCCACAA 59.994 52.381 0.00 0.00 0.00 3.33
4622 7879 0.625316 CAAGACATCCCCATCCCACA 59.375 55.000 0.00 0.00 0.00 4.17
4623 7880 0.753111 GCAAGACATCCCCATCCCAC 60.753 60.000 0.00 0.00 0.00 4.61
4624 7881 0.920763 AGCAAGACATCCCCATCCCA 60.921 55.000 0.00 0.00 0.00 4.37
4625 7882 0.259938 AAGCAAGACATCCCCATCCC 59.740 55.000 0.00 0.00 0.00 3.85
4626 7883 3.297134 TTAAGCAAGACATCCCCATCC 57.703 47.619 0.00 0.00 0.00 3.51
4627 7884 4.016444 TGTTTAAGCAAGACATCCCCATC 58.984 43.478 0.00 0.00 0.00 3.51
4628 7885 4.046286 TGTTTAAGCAAGACATCCCCAT 57.954 40.909 0.00 0.00 0.00 4.00
4629 7886 3.517296 TGTTTAAGCAAGACATCCCCA 57.483 42.857 0.00 0.00 0.00 4.96
4630 7887 4.462483 TGATTGTTTAAGCAAGACATCCCC 59.538 41.667 10.59 0.00 0.00 4.81
4631 7888 5.643379 TGATTGTTTAAGCAAGACATCCC 57.357 39.130 10.59 0.00 0.00 3.85
4639 7896 8.023128 GCTAATCTCACTTGATTGTTTAAGCAA 58.977 33.333 7.22 7.22 39.65 3.91
4640 7897 7.174772 TGCTAATCTCACTTGATTGTTTAAGCA 59.825 33.333 7.24 7.24 39.06 3.91
4641 7898 7.530010 TGCTAATCTCACTTGATTGTTTAAGC 58.470 34.615 0.00 0.00 37.27 3.09
4642 7899 9.897744 TTTGCTAATCTCACTTGATTGTTTAAG 57.102 29.630 0.00 0.00 37.27 1.85
4682 7939 4.676924 GTGATTTTTCTCTTCCGTTGCAAG 59.323 41.667 0.00 0.00 0.00 4.01
4712 7971 8.171164 GCCTTGAGCCATACTTTTTAGAATAT 57.829 34.615 0.00 0.00 34.35 1.28
4801 8061 2.360844 GACCACTGTCGATGAGAGAGA 58.639 52.381 0.00 0.00 42.37 3.10
5030 8292 7.732025 TCAATTGTATACATCCGTAGACCAAT 58.268 34.615 6.36 0.00 38.75 3.16
5204 8467 8.519492 AATTGTCAGTGGATCAAAATTTAACG 57.481 30.769 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.