Multiple sequence alignment - TraesCS6D01G226300

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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 TraesCS6D01G226300 chr6D 100.000 7083 0 0 1 7083 318069210 318076292 0.000000e+00 13080.0
1 TraesCS6D01G226300 chr6D 83.832 167 23 4 6762 6926 448774666 448774830 9.510000e-34 156.0
2 TraesCS6D01G226300 chr6A 95.015 5858 198 44 861 6668 455458142 455463955 0.000000e+00 9114.0
3 TraesCS6D01G226300 chr6A 87.179 429 45 5 3 422 563489418 563488991 4.970000e-131 479.0
4 TraesCS6D01G226300 chr6A 92.481 133 8 2 724 855 455457530 455457661 9.380000e-44 189.0
5 TraesCS6D01G226300 chr6A 84.756 164 24 1 6762 6924 101985647 101985484 5.690000e-36 163.0
6 TraesCS6D01G226300 chr6B 95.275 5079 159 31 690 5735 506394443 506389413 0.000000e+00 7974.0
7 TraesCS6D01G226300 chr6B 95.210 668 29 3 5735 6400 506389311 506388645 0.000000e+00 1053.0
8 TraesCS6D01G226300 chr6B 94.359 195 6 2 6436 6630 506386244 506386055 1.930000e-75 294.0
9 TraesCS6D01G226300 chr6B 88.966 145 13 3 6936 7078 506385989 506385846 7.300000e-40 176.0
10 TraesCS6D01G226300 chr6B 88.971 136 11 4 6762 6895 481042979 481042846 1.580000e-36 165.0
11 TraesCS6D01G226300 chr6B 98.214 56 0 1 6613 6668 506386046 506385992 5.850000e-16 97.1
12 TraesCS6D01G226300 chr7D 90.951 431 29 5 1 422 136700331 136700760 7.970000e-159 571.0
13 TraesCS6D01G226300 chr7D 86.047 430 50 5 3 423 199529608 199529180 3.010000e-123 453.0
14 TraesCS6D01G226300 chr7D 83.039 283 33 6 415 682 136702067 136702349 7.100000e-60 243.0
15 TraesCS6D01G226300 chr3D 90.951 431 29 5 1 422 418711571 418712000 7.970000e-159 571.0
16 TraesCS6D01G226300 chr3D 86.667 420 46 5 1 411 70239420 70239002 2.330000e-124 457.0
17 TraesCS6D01G226300 chr3D 82.671 277 39 3 415 682 418713355 418713631 3.300000e-58 237.0
18 TraesCS6D01G226300 chr3A 89.791 431 34 5 1 422 667163506 667163935 1.740000e-150 544.0
19 TraesCS6D01G226300 chr3A 92.157 51 1 3 6718 6765 466040993 466040943 1.270000e-07 69.4
20 TraesCS6D01G226300 chr3A 92.000 50 2 2 6716 6765 512320115 512320162 1.270000e-07 69.4
21 TraesCS6D01G226300 chr3A 89.091 55 3 3 6712 6765 663442437 663442489 1.650000e-06 65.8
22 TraesCS6D01G226300 chr4B 86.279 430 47 7 3 422 168270095 168270522 2.330000e-124 457.0
23 TraesCS6D01G226300 chr7A 86.014 429 50 5 3 422 106409472 106409899 1.080000e-122 451.0
24 TraesCS6D01G226300 chr7A 100.000 40 0 0 6726 6765 577485209 577485248 2.740000e-09 75.0
25 TraesCS6D01G226300 chr7A 100.000 40 0 0 6726 6765 617432805 617432766 2.740000e-09 75.0
26 TraesCS6D01G226300 chr2A 86.352 403 44 6 32 424 21951783 21952184 5.080000e-116 429.0
27 TraesCS6D01G226300 chr2A 87.316 339 31 7 32 359 21942614 21942951 1.870000e-100 377.0
28 TraesCS6D01G226300 chr2A 90.196 51 4 1 6716 6765 63805910 63805860 1.650000e-06 65.8
29 TraesCS6D01G226300 chr2D 89.404 302 21 6 130 422 646280544 646280843 3.120000e-98 370.0
30 TraesCS6D01G226300 chr2D 84.181 177 22 6 6762 6937 10719374 10719545 4.390000e-37 167.0
31 TraesCS6D01G226300 chr1D 86.806 144 18 1 6765 6907 118812371 118812228 7.350000e-35 159.0
32 TraesCS6D01G226300 chr1D 82.873 181 26 4 6762 6939 224371415 224371593 2.650000e-34 158.0
33 TraesCS6D01G226300 chr1D 81.921 177 27 5 6765 6939 18888975 18889148 2.060000e-30 145.0
34 TraesCS6D01G226300 chr1D 91.667 48 4 0 6718 6765 286647555 286647602 4.590000e-07 67.6
35 TraesCS6D01G226300 chr5D 81.818 187 30 4 6763 6946 214614365 214614550 3.420000e-33 154.0
36 TraesCS6D01G226300 chr5D 83.436 163 23 4 6763 6925 362880459 362880301 1.590000e-31 148.0
37 TraesCS6D01G226300 chr5D 80.180 111 22 0 523 633 67589481 67589371 4.550000e-12 84.2
38 TraesCS6D01G226300 chr7B 80.702 171 32 1 415 584 214986051 214985881 1.600000e-26 132.0
39 TraesCS6D01G226300 chr5A 85.393 89 13 0 594 682 56304313 56304401 7.570000e-15 93.5
40 TraesCS6D01G226300 chr5A 100.000 40 0 0 6726 6765 648881964 648882003 2.740000e-09 75.0
41 TraesCS6D01G226300 chr1A 95.745 47 0 2 6721 6765 530756161 530756207 2.740000e-09 75.0


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 TraesCS6D01G226300 chr6D 318069210 318076292 7082 False 13080.00 13080 100.0000 1 7083 1 chr6D.!!$F1 7082
1 TraesCS6D01G226300 chr6A 455457530 455463955 6425 False 4651.50 9114 93.7480 724 6668 2 chr6A.!!$F1 5944
2 TraesCS6D01G226300 chr6B 506385846 506394443 8597 True 1918.82 7974 94.4048 690 7078 5 chr6B.!!$R2 6388
3 TraesCS6D01G226300 chr7D 136700331 136702349 2018 False 407.00 571 86.9950 1 682 2 chr7D.!!$F1 681
4 TraesCS6D01G226300 chr3D 418711571 418713631 2060 False 404.00 571 86.8110 1 682 2 chr3D.!!$F1 681

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
525 1912 0.251341 GCGGATGGGCCCAATCTAAT 60.251 55.0 32.58 11.79 0.00 1.73 F
816 2203 0.612229 ACGACTAGTCTCCGGTCAGA 59.388 55.0 20.34 0.00 0.00 3.27 F
1596 3494 0.804989 GAATCCTCCTGTGCGTTTGG 59.195 55.0 0.00 0.00 0.00 3.28 F
2515 4414 1.011333 CGTTATTTGACCGGGCGAAT 58.989 50.0 26.25 26.25 0.00 3.34 F
3765 5678 0.037590 AATTTAGGGCCAGCGACACA 59.962 50.0 6.18 0.00 0.00 3.72 F
4262 6178 1.031571 TCATGTCCATTTGCGGGCTC 61.032 55.0 0.00 0.00 0.00 4.70 F
4627 6546 0.394762 ATGTGCACTGCCACCATAGG 60.395 55.0 19.41 0.00 34.85 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 3650 0.179145 AACGTAATCCTCGAGGCACG 60.179 55.000 32.91 32.91 44.09 5.34 R
2287 4186 0.397564 TGCACTGAGATGCTCAACCA 59.602 50.000 8.13 0.00 46.28 3.67 R
3485 5392 1.678101 GGGAGCATGACATTTACAGCC 59.322 52.381 0.00 0.00 0.00 4.85 R
4302 6219 0.455633 CAGCAAAGAACTGCCATCGC 60.456 55.000 0.00 0.00 43.73 4.58 R
4627 6546 3.138304 TGTCACAGTTGTTGCAGGATAC 58.862 45.455 0.00 0.00 0.00 2.24 R
5995 8022 1.457346 CCTGAAAAAGCTCGCCATCT 58.543 50.000 0.00 0.00 0.00 2.90 R
6323 8358 1.153369 AGATCAATCCGTGTGGGCG 60.153 57.895 0.00 0.00 35.24 6.13 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
84 85 0.672342 GCAGCTGCTCCCCAATTATG 59.328 55.000 31.33 0.00 38.21 1.90
87 88 0.672342 GCTGCTCCCCAATTATGCTG 59.328 55.000 0.00 0.00 0.00 4.41
103 104 1.073763 TGCTGTGTTGGCTGTCCTAAT 59.926 47.619 0.00 0.00 0.00 1.73
137 138 3.041211 TGGAGATACATAGCTGCCACTT 58.959 45.455 0.00 0.00 0.00 3.16
143 144 5.777223 AGATACATAGCTGCCACTTCATCTA 59.223 40.000 0.00 0.00 0.00 1.98
145 146 2.871182 TAGCTGCCACTTCATCTACG 57.129 50.000 0.00 0.00 0.00 3.51
151 152 2.205074 GCCACTTCATCTACGGATGTG 58.795 52.381 5.99 0.00 46.74 3.21
155 156 3.096852 ACTTCATCTACGGATGTGTCCA 58.903 45.455 5.99 0.00 46.74 4.02
163 164 3.973206 ACGGATGTGTCCATAAAGACA 57.027 42.857 0.00 0.00 45.37 3.41
198 199 4.585955 TTTCTAGAACAAGTGCTCGAGT 57.414 40.909 15.13 0.00 0.00 4.18
215 216 5.788450 CTCGAGTATGCCAATTAATCTCCT 58.212 41.667 3.62 0.00 0.00 3.69
252 253 0.878416 GGCAACACATGGAAGCGTTA 59.122 50.000 0.00 0.00 0.00 3.18
255 256 2.161410 GCAACACATGGAAGCGTTATCA 59.839 45.455 0.00 0.00 0.00 2.15
284 285 9.952188 GTTTGCCCAAATTTAGAGAGTATATTC 57.048 33.333 0.00 0.00 32.36 1.75
318 327 5.649782 ATCATCACATTTTCGCCTTTTCT 57.350 34.783 0.00 0.00 0.00 2.52
356 366 1.578897 TCATCCACGGAATCCCAAGA 58.421 50.000 0.00 0.00 0.00 3.02
359 369 3.053693 TCATCCACGGAATCCCAAGAAAT 60.054 43.478 0.00 0.00 0.00 2.17
377 387 7.497249 CCAAGAAATCTCTCAACTAATTCCGAT 59.503 37.037 0.00 0.00 0.00 4.18
380 390 7.708752 AGAAATCTCTCAACTAATTCCGATCAC 59.291 37.037 0.00 0.00 0.00 3.06
391 401 4.502263 CGATCACGGTGCATCAGT 57.498 55.556 2.51 0.00 35.72 3.41
449 1821 2.447714 GGATGAGAGGTGGAGGGCC 61.448 68.421 0.00 0.00 0.00 5.80
481 1859 4.779733 GGAGAGGTGGCCGAGGGA 62.780 72.222 0.00 0.00 0.00 4.20
487 1865 2.428925 GGTGGCCGAGGGAACGATA 61.429 63.158 0.00 0.00 35.09 2.92
507 1893 2.796651 CGGAAGCTGCTGGATTGC 59.203 61.111 1.35 0.00 0.00 3.56
520 1907 1.833934 GATTGCGGATGGGCCCAAT 60.834 57.895 32.58 17.45 39.05 3.16
525 1912 0.251341 GCGGATGGGCCCAATCTAAT 60.251 55.000 32.58 11.79 0.00 1.73
526 1913 1.538047 CGGATGGGCCCAATCTAATG 58.462 55.000 32.58 10.87 0.00 1.90
551 1938 1.845266 CGTGATTGATGCTAGCGTCT 58.155 50.000 31.53 16.92 33.41 4.18
554 1941 3.304057 CGTGATTGATGCTAGCGTCTAGA 60.304 47.826 31.53 20.10 33.41 2.43
557 1944 2.350057 TGATGCTAGCGTCTAGACCT 57.650 50.000 31.53 16.16 33.41 3.85
562 1949 2.017623 GCTAGCGTCTAGACCTGGACA 61.018 57.143 21.00 5.60 40.55 4.02
564 1951 1.107114 AGCGTCTAGACCTGGACATG 58.893 55.000 17.23 1.73 40.55 3.21
581 1968 2.963101 ACATGGCTTATACTAGCGTCCA 59.037 45.455 0.00 0.00 42.15 4.02
582 1969 3.243771 ACATGGCTTATACTAGCGTCCAC 60.244 47.826 0.00 0.00 42.15 4.02
583 1970 2.380941 TGGCTTATACTAGCGTCCACA 58.619 47.619 0.00 0.00 42.15 4.17
584 1971 2.963101 TGGCTTATACTAGCGTCCACAT 59.037 45.455 0.00 0.00 42.15 3.21
585 1972 3.243737 TGGCTTATACTAGCGTCCACATG 60.244 47.826 0.00 0.00 42.15 3.21
621 2008 4.037684 TGCCTAGCGTCCTTACTATTTCTC 59.962 45.833 0.00 0.00 0.00 2.87
625 2012 7.210873 CCTAGCGTCCTTACTATTTCTCAAAT 58.789 38.462 0.00 0.00 34.90 2.32
626 2013 7.711339 CCTAGCGTCCTTACTATTTCTCAAATT 59.289 37.037 0.00 0.00 32.38 1.82
716 2103 6.064060 ACTCAATCATTTGACTGAAGGAACA 58.936 36.000 0.00 0.00 36.94 3.18
764 2151 8.514330 AACTCAAAACACTGGATACTTTTGTA 57.486 30.769 0.00 0.00 38.46 2.41
767 2154 9.965824 CTCAAAACACTGGATACTTTTGTATTT 57.034 29.630 0.00 0.00 44.91 1.40
772 2159 8.918202 ACACTGGATACTTTTGTATTTGAGAA 57.082 30.769 0.00 0.00 44.91 2.87
816 2203 0.612229 ACGACTAGTCTCCGGTCAGA 59.388 55.000 20.34 0.00 0.00 3.27
941 2813 2.032071 CCCGCCGGAAGAACAACT 59.968 61.111 5.05 0.00 0.00 3.16
1384 3262 1.852067 GCGTGGTTACAAGCTGTGGG 61.852 60.000 0.00 0.00 46.57 4.61
1386 3264 1.610624 CGTGGTTACAAGCTGTGGGAT 60.611 52.381 0.00 0.00 0.00 3.85
1389 3267 2.084546 GGTTACAAGCTGTGGGATCAC 58.915 52.381 0.00 0.00 43.87 3.06
1390 3268 2.084546 GTTACAAGCTGTGGGATCACC 58.915 52.381 0.00 0.00 42.98 4.02
1431 3320 4.036380 AGTTCGAGCTTTCGTTTGGAAAAT 59.964 37.500 0.00 0.00 43.73 1.82
1439 3328 7.937649 AGCTTTCGTTTGGAAAATAAGTACTT 58.062 30.769 13.68 13.68 43.73 2.24
1440 3329 8.410912 AGCTTTCGTTTGGAAAATAAGTACTTT 58.589 29.630 14.49 0.00 43.73 2.66
1489 3384 4.698575 GCTGATTTAGTACAAGAGGAGGG 58.301 47.826 0.00 0.00 0.00 4.30
1531 3426 1.345415 CAGCTGAACCCCTTGCAAATT 59.655 47.619 8.42 0.00 0.00 1.82
1596 3494 0.804989 GAATCCTCCTGTGCGTTTGG 59.195 55.000 0.00 0.00 0.00 3.28
1628 3526 1.985473 TGCAAATCACAACCTCAGCT 58.015 45.000 0.00 0.00 0.00 4.24
1629 3527 1.881973 TGCAAATCACAACCTCAGCTC 59.118 47.619 0.00 0.00 0.00 4.09
1636 3534 3.501349 TCACAACCTCAGCTCTAGTTCT 58.499 45.455 0.00 0.00 0.00 3.01
1679 3577 2.676076 CTGGTGTGCAAAGCCAAATAC 58.324 47.619 3.06 0.00 0.00 1.89
1692 3590 6.751514 AAGCCAAATACGTGAATATGACAA 57.248 33.333 0.00 0.00 0.00 3.18
1741 3639 5.304686 TCTGTCAACAAGGATAGGTGTTT 57.695 39.130 0.00 0.00 35.81 2.83
1752 3650 4.762251 AGGATAGGTGTTTCAGTTTTGCTC 59.238 41.667 0.00 0.00 0.00 4.26
1772 3670 1.734707 CGTGCCTCGAGGATTACGTTT 60.735 52.381 35.69 0.00 42.86 3.60
1943 3841 8.347729 ACAAAATCAAGTTTTCGGATGTTTAC 57.652 30.769 0.00 0.00 37.93 2.01
1949 3847 4.309099 AGTTTTCGGATGTTTACGCTGTA 58.691 39.130 0.00 0.00 0.00 2.74
2270 4169 3.702792 TCTTTTTGGACACAAAGACCCA 58.297 40.909 9.00 0.00 46.37 4.51
2287 4186 1.613836 CCAGAGACCTGCAAAAGCTT 58.386 50.000 0.00 0.00 39.07 3.74
2452 4351 2.276732 AGGTGTTTGTCCATCCACTG 57.723 50.000 0.00 0.00 0.00 3.66
2515 4414 1.011333 CGTTATTTGACCGGGCGAAT 58.989 50.000 26.25 26.25 0.00 3.34
2645 4544 6.309712 ACTGATGAGTTTGTGACATCAAAG 57.690 37.500 0.00 0.00 45.86 2.77
2802 4701 1.335872 GGTGTTGTTGCAGTGGTATGC 60.336 52.381 0.00 0.00 46.68 3.14
2920 4823 3.951663 TCAGTGAGACGAGTCCTGAATA 58.048 45.455 7.78 0.00 0.00 1.75
2929 4832 8.696374 TGAGACGAGTCCTGAATATCTTATTTT 58.304 33.333 0.00 0.00 0.00 1.82
3104 5009 6.554982 ACACTATATGCCTTGGTGAAGAGATA 59.445 38.462 0.00 0.00 0.00 1.98
3176 5083 2.519377 TCTTCCGGTGTGTACTGTTG 57.481 50.000 0.00 0.00 0.00 3.33
3188 5095 6.967199 GGTGTGTACTGTTGAAGAAAAGAAAG 59.033 38.462 0.00 0.00 0.00 2.62
3448 5355 5.532406 GCACTGAGAAATGCCAAGGATATAA 59.468 40.000 0.00 0.00 35.73 0.98
3485 5392 0.532573 ACAGTACGCCCACATCAGAG 59.467 55.000 0.00 0.00 0.00 3.35
3505 5415 1.678101 GGCTGTAAATGTCATGCTCCC 59.322 52.381 0.00 0.00 0.00 4.30
3665 5578 7.524717 AGTAATTTTGTGTGCTCCTTATTGT 57.475 32.000 0.00 0.00 0.00 2.71
3765 5678 0.037590 AATTTAGGGCCAGCGACACA 59.962 50.000 6.18 0.00 0.00 3.72
3898 5811 7.061054 ACAGATGCTATTGTACTCAGGTACTA 58.939 38.462 7.63 1.35 46.04 1.82
3933 5846 1.529865 GTGTAACCACGCAAGGAGAAC 59.470 52.381 0.00 0.00 46.39 3.01
4218 6133 8.477984 TTGCATAATTTCTTACATTTTGAGCC 57.522 30.769 0.00 0.00 0.00 4.70
4240 6155 5.687285 GCCTAATGTCCTTTTAATTCATGCG 59.313 40.000 0.00 0.00 0.00 4.73
4243 6158 8.567948 CCTAATGTCCTTTTAATTCATGCGTAT 58.432 33.333 0.00 0.00 0.00 3.06
4262 6178 1.031571 TCATGTCCATTTGCGGGCTC 61.032 55.000 0.00 0.00 0.00 4.70
4534 6453 3.660501 TTAGGGCATGATGTAGCTACG 57.339 47.619 18.74 5.44 0.00 3.51
4558 6477 3.007290 AGTGCTTGTATGAACTGAGAGCA 59.993 43.478 0.00 0.00 36.43 4.26
4627 6546 0.394762 ATGTGCACTGCCACCATAGG 60.395 55.000 19.41 0.00 34.85 2.57
4794 6713 4.446385 CCTGTTGATGTTTCTTGTGCATTG 59.554 41.667 0.00 0.00 0.00 2.82
4852 6771 6.317642 TGATCATACAATTTTACCAAGTCGGG 59.682 38.462 0.00 0.00 40.22 5.14
4880 6799 5.804639 GTGCATATCACTATATGAACCCCA 58.195 41.667 9.09 0.00 44.33 4.96
4899 6818 3.087031 CCATGTGGATTGTTCTTCTGCT 58.913 45.455 0.00 0.00 37.39 4.24
5065 6984 0.696501 AACCGGTGGCAAGTATCCTT 59.303 50.000 8.52 0.00 0.00 3.36
5066 6985 0.696501 ACCGGTGGCAAGTATCCTTT 59.303 50.000 6.12 0.00 0.00 3.11
5067 6986 1.339727 ACCGGTGGCAAGTATCCTTTC 60.340 52.381 6.12 0.00 0.00 2.62
5068 6987 1.065418 CCGGTGGCAAGTATCCTTTCT 60.065 52.381 0.00 0.00 0.00 2.52
5069 6988 2.618045 CCGGTGGCAAGTATCCTTTCTT 60.618 50.000 0.00 0.00 0.00 2.52
5070 6989 2.420022 CGGTGGCAAGTATCCTTTCTTG 59.580 50.000 0.00 0.00 42.44 3.02
5221 7140 6.883217 AGAGAATGTTGCAGATGAAGTACAAT 59.117 34.615 0.00 0.00 0.00 2.71
5308 7227 1.308998 AACTTCAACGCCTGGACAAG 58.691 50.000 0.00 0.00 0.00 3.16
5342 7261 3.766051 GAGATTCCAAACAGCTCCCAAAT 59.234 43.478 0.00 0.00 0.00 2.32
5509 7428 1.807814 TAGAGATTGCCCTCTTCCCC 58.192 55.000 5.83 0.00 42.93 4.81
5569 7488 2.833794 TGTTTCACAGTACTCTGCACC 58.166 47.619 0.00 0.00 44.77 5.01
5656 7575 3.013921 GTGTCAAGTTGGACCTCACAAA 58.986 45.455 2.34 0.00 36.97 2.83
5669 7588 4.184629 ACCTCACAAAAGTCGATATCTGC 58.815 43.478 0.34 0.00 0.00 4.26
5984 8011 1.859383 TTCATCACACGACGAAAGCA 58.141 45.000 0.00 0.00 0.00 3.91
5995 8022 4.565166 CACGACGAAAGCATATGGAACTTA 59.435 41.667 0.00 0.00 0.00 2.24
6037 8064 1.569479 GCGAAGTGTCTGTCCAAGCC 61.569 60.000 0.00 0.00 0.00 4.35
6176 8208 4.859798 CGAGTTGTAGAAGAACCTCATGTC 59.140 45.833 0.00 0.00 0.00 3.06
6181 8213 6.378710 TGTAGAAGAACCTCATGTCGATAG 57.621 41.667 0.00 0.00 0.00 2.08
6204 8236 6.875076 AGTAGATATGTAAACTGCGGTTCTT 58.125 36.000 12.25 0.00 34.14 2.52
6250 8282 3.730715 CAGCGTTTTCTTCAATGTCCAAC 59.269 43.478 0.00 0.00 0.00 3.77
6257 8291 3.664107 TCTTCAATGTCCAACGAAGGAG 58.336 45.455 0.89 0.00 38.64 3.69
6275 8309 3.577848 AGGAGGAGCTACAGATTATGCTG 59.422 47.826 0.00 0.00 41.63 4.41
6313 8348 0.093535 CGTGTGTCGCAATGCTGTAG 59.906 55.000 2.94 0.00 0.00 2.74
6322 8357 2.595536 CGCAATGCTGTAGAATTTGCAC 59.404 45.455 2.94 0.00 38.29 4.57
6323 8358 2.925563 GCAATGCTGTAGAATTTGCACC 59.074 45.455 0.00 0.00 38.29 5.01
6370 8405 5.932619 TGCAGGAAGCTAAGTAGACATAA 57.067 39.130 0.00 0.00 45.94 1.90
6384 8420 7.932120 AGTAGACATAAGACATATTCGTTGC 57.068 36.000 0.00 0.00 0.00 4.17
6406 8442 1.493022 ACTCAACAACACTTGCCCCTA 59.507 47.619 0.00 0.00 0.00 3.53
6432 8653 9.895138 AGAAAATTTATTCTGCATTTTAGGCAT 57.105 25.926 0.00 0.00 41.06 4.40
6433 8654 9.925268 GAAAATTTATTCTGCATTTTAGGCATG 57.075 29.630 0.00 0.00 41.06 4.06
6442 8663 3.861689 GCATTTTAGGCATGCTGAAGTTC 59.138 43.478 18.92 0.00 43.26 3.01
6523 10925 0.249868 CGCAGAGGGTGACAACAAGA 60.250 55.000 0.00 0.00 0.00 3.02
6524 10926 1.810031 CGCAGAGGGTGACAACAAGAA 60.810 52.381 0.00 0.00 0.00 2.52
6525 10927 1.876156 GCAGAGGGTGACAACAAGAAG 59.124 52.381 0.00 0.00 0.00 2.85
6689 11130 9.933240 ATACTACCTATGTCCTAGTTTGTTAGT 57.067 33.333 0.00 0.00 0.00 2.24
6690 11131 8.291191 ACTACCTATGTCCTAGTTTGTTAGTC 57.709 38.462 0.00 0.00 0.00 2.59
6691 11132 8.114743 ACTACCTATGTCCTAGTTTGTTAGTCT 58.885 37.037 0.00 0.00 0.00 3.24
6692 11133 7.793948 ACCTATGTCCTAGTTTGTTAGTCTT 57.206 36.000 0.00 0.00 0.00 3.01
6693 11134 8.203681 ACCTATGTCCTAGTTTGTTAGTCTTT 57.796 34.615 0.00 0.00 0.00 2.52
6694 11135 9.317827 ACCTATGTCCTAGTTTGTTAGTCTTTA 57.682 33.333 0.00 0.00 0.00 1.85
6709 11150 9.590451 TGTTAGTCTTTATAATCGTACTTTGGG 57.410 33.333 0.00 0.00 0.00 4.12
6710 11151 9.591792 GTTAGTCTTTATAATCGTACTTTGGGT 57.408 33.333 0.00 0.00 0.00 4.51
6729 11170 9.927668 CTTTGGGTAAAGTTTGATCACATATTT 57.072 29.630 0.00 0.00 38.75 1.40
6741 11182 9.979578 TTTGATCACATATTTAACAGTTTTGCT 57.020 25.926 0.00 0.00 0.00 3.91
6746 11187 9.405587 TCACATATTTAACAGTTTTGCTAAAGC 57.594 29.630 0.00 0.00 42.50 3.51
6774 11215 9.935241 CATCTAGATGTGCCATATTTAACTAGT 57.065 33.333 22.42 0.00 34.23 2.57
6900 11341 9.643693 AGTTAAAATCATGATCAAAATGTGACC 57.356 29.630 9.06 0.00 39.72 4.02
6901 11342 8.872845 GTTAAAATCATGATCAAAATGTGACCC 58.127 33.333 9.06 0.00 39.72 4.46
6902 11343 6.608539 AAATCATGATCAAAATGTGACCCA 57.391 33.333 9.06 0.00 39.72 4.51
6903 11344 6.608539 AATCATGATCAAAATGTGACCCAA 57.391 33.333 9.06 0.00 39.72 4.12
6904 11345 6.608539 ATCATGATCAAAATGTGACCCAAA 57.391 33.333 1.18 0.00 39.72 3.28
6905 11346 6.416631 TCATGATCAAAATGTGACCCAAAA 57.583 33.333 0.00 0.00 39.72 2.44
6906 11347 7.006865 TCATGATCAAAATGTGACCCAAAAT 57.993 32.000 0.00 0.00 39.72 1.82
6907 11348 8.131847 TCATGATCAAAATGTGACCCAAAATA 57.868 30.769 0.00 0.00 39.72 1.40
6908 11349 8.034215 TCATGATCAAAATGTGACCCAAAATAC 58.966 33.333 0.00 0.00 39.72 1.89
6909 11350 7.295322 TGATCAAAATGTGACCCAAAATACA 57.705 32.000 0.00 0.00 39.72 2.29
6910 11351 7.730084 TGATCAAAATGTGACCCAAAATACAA 58.270 30.769 0.00 0.00 39.72 2.41
6911 11352 8.206867 TGATCAAAATGTGACCCAAAATACAAA 58.793 29.630 0.00 0.00 39.72 2.83
6912 11353 8.606040 ATCAAAATGTGACCCAAAATACAAAG 57.394 30.769 0.00 0.00 39.72 2.77
6913 11354 6.989169 TCAAAATGTGACCCAAAATACAAAGG 59.011 34.615 0.00 0.00 0.00 3.11
6914 11355 5.482163 AATGTGACCCAAAATACAAAGGG 57.518 39.130 0.00 0.00 46.96 3.95
6915 11356 4.186077 TGTGACCCAAAATACAAAGGGA 57.814 40.909 2.90 0.00 44.30 4.20
6916 11357 4.547671 TGTGACCCAAAATACAAAGGGAA 58.452 39.130 2.90 0.00 44.30 3.97
6917 11358 4.342665 TGTGACCCAAAATACAAAGGGAAC 59.657 41.667 2.90 2.18 44.30 3.62
6918 11359 4.587262 GTGACCCAAAATACAAAGGGAACT 59.413 41.667 2.90 0.00 44.30 3.01
6919 11360 5.771165 GTGACCCAAAATACAAAGGGAACTA 59.229 40.000 2.90 0.00 44.30 2.24
6920 11361 6.007703 TGACCCAAAATACAAAGGGAACTAG 58.992 40.000 2.90 0.00 44.30 2.57
6921 11362 5.960704 ACCCAAAATACAAAGGGAACTAGT 58.039 37.500 2.90 0.00 44.30 2.57
6922 11363 7.093965 ACCCAAAATACAAAGGGAACTAGTA 57.906 36.000 2.90 0.00 44.30 1.82
6923 11364 7.528675 ACCCAAAATACAAAGGGAACTAGTAA 58.471 34.615 2.90 0.00 44.30 2.24
6924 11365 8.005976 ACCCAAAATACAAAGGGAACTAGTAAA 58.994 33.333 2.90 0.00 44.30 2.01
6925 11366 8.301720 CCCAAAATACAAAGGGAACTAGTAAAC 58.698 37.037 0.00 0.00 44.30 2.01
6926 11367 8.019094 CCAAAATACAAAGGGAACTAGTAAACG 58.981 37.037 0.00 0.00 42.68 3.60
6927 11368 8.776470 CAAAATACAAAGGGAACTAGTAAACGA 58.224 33.333 0.00 0.00 42.68 3.85
6928 11369 8.543862 AAATACAAAGGGAACTAGTAAACGAG 57.456 34.615 0.00 0.00 42.68 4.18
6929 11370 5.796424 ACAAAGGGAACTAGTAAACGAGA 57.204 39.130 0.00 0.00 42.68 4.04
6930 11371 6.165700 ACAAAGGGAACTAGTAAACGAGAA 57.834 37.500 0.00 0.00 42.68 2.87
6931 11372 5.987953 ACAAAGGGAACTAGTAAACGAGAAC 59.012 40.000 0.00 0.00 42.68 3.01
6932 11373 4.431661 AGGGAACTAGTAAACGAGAACG 57.568 45.455 0.00 0.00 40.61 3.95
6933 11374 3.192212 AGGGAACTAGTAAACGAGAACGG 59.808 47.826 0.00 0.00 41.26 4.44
6934 11375 3.191371 GGGAACTAGTAAACGAGAACGGA 59.809 47.826 0.00 0.00 44.46 4.69
6935 11376 4.321230 GGGAACTAGTAAACGAGAACGGAA 60.321 45.833 0.00 0.00 44.46 4.30
6936 11377 4.855937 GGAACTAGTAAACGAGAACGGAAG 59.144 45.833 0.00 0.00 44.46 3.46
6958 11399 8.860128 GGAAGTAATAGTTGCAAAATGTTTAGC 58.140 33.333 0.00 0.00 0.00 3.09
6961 11402 9.981114 AGTAATAGTTGCAAAATGTTTAGCTTT 57.019 25.926 0.00 0.00 0.00 3.51
7012 11454 4.215908 AGTACTCAAATAGCCATCGGAGA 58.784 43.478 0.00 0.00 45.75 3.71
7027 11469 5.344884 CATCGGAGACCTTCTCTACTTTTC 58.655 45.833 3.30 0.00 42.95 2.29
7028 11470 4.404640 TCGGAGACCTTCTCTACTTTTCA 58.595 43.478 3.30 0.00 42.95 2.69
7029 11471 4.459685 TCGGAGACCTTCTCTACTTTTCAG 59.540 45.833 3.30 0.00 42.95 3.02
7042 11485 6.068010 TCTACTTTTCAGCCCTCAAAATTCA 58.932 36.000 0.00 0.00 0.00 2.57
7043 11486 5.612725 ACTTTTCAGCCCTCAAAATTCAA 57.387 34.783 0.00 0.00 0.00 2.69
7074 11517 4.946157 CCAACACTAGCCTTCATTTCTCAT 59.054 41.667 0.00 0.00 0.00 2.90
7078 11521 4.043596 ACTAGCCTTCATTTCTCATCCCT 58.956 43.478 0.00 0.00 0.00 4.20
7079 11522 5.070981 CACTAGCCTTCATTTCTCATCCCTA 59.929 44.000 0.00 0.00 0.00 3.53
7080 11523 5.667626 ACTAGCCTTCATTTCTCATCCCTAA 59.332 40.000 0.00 0.00 0.00 2.69
7081 11524 5.456921 AGCCTTCATTTCTCATCCCTAAA 57.543 39.130 0.00 0.00 0.00 1.85
7082 11525 5.831103 AGCCTTCATTTCTCATCCCTAAAA 58.169 37.500 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.145052 TGTGTGCTGAGAAGAAGAGACTA 58.855 43.478 0.00 0.00 0.00 2.59
49 50 2.027377 AGCTGCTCTTGCTCTGTTGTAT 60.027 45.455 0.00 0.00 40.48 2.29
84 85 1.826385 ATTAGGACAGCCAACACAGC 58.174 50.000 0.00 0.00 36.29 4.40
108 109 8.382405 TGGCAGCTATGTATCTCCAATTTATTA 58.618 33.333 0.00 0.00 0.00 0.98
109 110 7.175641 GTGGCAGCTATGTATCTCCAATTTATT 59.824 37.037 0.00 0.00 0.00 1.40
145 146 5.192927 TCCATTGTCTTTATGGACACATCC 58.807 41.667 0.00 0.00 45.02 3.51
151 152 3.620488 TGGCTCCATTGTCTTTATGGAC 58.380 45.455 0.00 0.00 45.02 4.02
155 156 4.591321 TCCTTGGCTCCATTGTCTTTAT 57.409 40.909 0.00 0.00 0.00 1.40
163 164 5.196695 GTTCTAGAAATCCTTGGCTCCATT 58.803 41.667 6.78 0.00 0.00 3.16
198 199 9.246670 CAATGGATAAGGAGATTAATTGGCATA 57.753 33.333 0.00 0.00 0.00 3.14
215 216 4.649267 TGCCGGATAATCCAATGGATAA 57.351 40.909 16.10 0.00 42.27 1.75
252 253 7.836183 ACTCTCTAAATTTGGGCAAACTATGAT 59.164 33.333 0.00 0.00 32.51 2.45
304 313 7.371126 TGAAACAAAAAGAAAAGGCGAAAAT 57.629 28.000 0.00 0.00 0.00 1.82
318 327 6.875726 TGGATGAACAACACATGAAACAAAAA 59.124 30.769 0.00 0.00 0.00 1.94
356 366 6.477033 CGTGATCGGAATTAGTTGAGAGATTT 59.523 38.462 0.00 0.00 0.00 2.17
359 369 4.921547 CGTGATCGGAATTAGTTGAGAGA 58.078 43.478 0.00 0.00 0.00 3.10
411 421 1.704641 CCTCGACCACCTATCCATGA 58.295 55.000 0.00 0.00 0.00 3.07
481 1859 1.521681 GCAGCTTCCGCCTATCGTT 60.522 57.895 0.00 0.00 36.60 3.85
487 1865 2.976490 AATCCAGCAGCTTCCGCCT 61.976 57.895 0.00 0.00 36.60 5.52
491 1877 2.768492 CCGCAATCCAGCAGCTTCC 61.768 63.158 0.00 0.00 0.00 3.46
506 1892 0.251341 ATTAGATTGGGCCCATCCGC 60.251 55.000 29.23 15.30 34.94 5.54
507 1893 1.538047 CATTAGATTGGGCCCATCCG 58.462 55.000 29.23 6.37 34.94 4.18
520 1907 1.557371 TCAATCACGCCCACCATTAGA 59.443 47.619 0.00 0.00 0.00 2.10
525 1912 2.045708 GCATCAATCACGCCCACCA 61.046 57.895 0.00 0.00 0.00 4.17
526 1913 0.463654 TAGCATCAATCACGCCCACC 60.464 55.000 0.00 0.00 0.00 4.61
531 1918 0.230769 GACGCTAGCATCAATCACGC 59.769 55.000 16.45 0.00 0.00 5.34
551 1938 4.816126 AGTATAAGCCATGTCCAGGTCTA 58.184 43.478 0.00 0.00 0.00 2.59
554 1941 3.325135 GCTAGTATAAGCCATGTCCAGGT 59.675 47.826 0.00 0.00 36.45 4.00
557 1944 2.963101 ACGCTAGTATAAGCCATGTCCA 59.037 45.455 0.00 0.00 39.43 4.02
562 1949 2.963101 TGTGGACGCTAGTATAAGCCAT 59.037 45.455 0.00 0.00 39.43 4.40
564 1951 3.243771 ACATGTGGACGCTAGTATAAGCC 60.244 47.826 0.00 0.00 39.43 4.35
581 1968 4.174704 AGGCATTACATCATCCACATGT 57.825 40.909 0.00 0.00 38.13 3.21
582 1969 4.155462 GCTAGGCATTACATCATCCACATG 59.845 45.833 0.00 0.00 0.00 3.21
583 1970 4.330250 GCTAGGCATTACATCATCCACAT 58.670 43.478 0.00 0.00 0.00 3.21
584 1971 3.743521 GCTAGGCATTACATCATCCACA 58.256 45.455 0.00 0.00 0.00 4.17
585 1972 2.738846 CGCTAGGCATTACATCATCCAC 59.261 50.000 0.00 0.00 0.00 4.02
590 1977 2.039418 AGGACGCTAGGCATTACATCA 58.961 47.619 0.00 0.00 0.00 3.07
597 1984 4.589374 AGAAATAGTAAGGACGCTAGGCAT 59.411 41.667 0.00 0.00 0.00 4.40
678 2065 5.471556 TGATTGAGTACTGAACCCGTTAA 57.528 39.130 0.00 0.00 0.00 2.01
682 2069 4.935205 TCAAATGATTGAGTACTGAACCCG 59.065 41.667 0.00 0.00 40.59 5.28
683 2070 5.940470 AGTCAAATGATTGAGTACTGAACCC 59.060 40.000 0.00 0.00 45.30 4.11
684 2071 6.650807 TCAGTCAAATGATTGAGTACTGAACC 59.349 38.462 0.00 0.00 45.36 3.62
685 2072 7.658179 TCAGTCAAATGATTGAGTACTGAAC 57.342 36.000 0.00 0.00 45.36 3.18
686 2073 7.388776 CCTTCAGTCAAATGATTGAGTACTGAA 59.611 37.037 16.62 16.62 45.68 3.02
687 2074 6.875726 CCTTCAGTCAAATGATTGAGTACTGA 59.124 38.462 0.00 0.00 45.36 3.41
688 2075 6.875726 TCCTTCAGTCAAATGATTGAGTACTG 59.124 38.462 0.00 0.00 45.36 2.74
716 2103 3.748048 CCGAGTGTTGATTGTTGACTGAT 59.252 43.478 0.00 0.00 0.00 2.90
772 2159 5.355350 CCTCGTATCCATTGCTCTTCTTTTT 59.645 40.000 0.00 0.00 0.00 1.94
777 2164 3.385577 GTCCTCGTATCCATTGCTCTTC 58.614 50.000 0.00 0.00 0.00 2.87
780 2167 1.337071 TCGTCCTCGTATCCATTGCTC 59.663 52.381 0.00 0.00 38.33 4.26
816 2203 2.216046 GTTTCCTCCCGAAAGACGTTT 58.784 47.619 0.00 0.00 41.17 3.60
895 2758 4.038080 GGGGCGCGGTTGTCTTTG 62.038 66.667 8.83 0.00 0.00 2.77
1123 2997 2.485795 GCAGAGACGAGCGGGAGAT 61.486 63.158 0.00 0.00 0.00 2.75
1124 2998 3.134792 GCAGAGACGAGCGGGAGA 61.135 66.667 0.00 0.00 0.00 3.71
1258 3136 3.997196 ACCCTTCGGTTCAACCCT 58.003 55.556 0.00 0.00 40.58 4.34
1273 3151 1.339644 TACCTATCCGCCACCCAACC 61.340 60.000 0.00 0.00 0.00 3.77
1390 3268 1.922135 CTTCAATGTTGTCCGGGGCG 61.922 60.000 0.00 0.00 0.00 6.13
1394 3283 2.139917 TCGAACTTCAATGTTGTCCGG 58.860 47.619 0.00 0.00 0.00 5.14
1466 3361 4.363999 CCTCCTCTTGTACTAAATCAGCG 58.636 47.826 0.00 0.00 0.00 5.18
1596 3494 5.423015 TGTGATTTGCAAGAGATAGAGTCC 58.577 41.667 0.00 0.00 0.00 3.85
1705 3603 6.036577 TGTTGACAGAACTAGATGCATGTA 57.963 37.500 2.46 2.92 0.00 2.29
1706 3604 4.898320 TGTTGACAGAACTAGATGCATGT 58.102 39.130 2.46 1.37 0.00 3.21
1741 3639 1.221466 CGAGGCACGAGCAAAACTGA 61.221 55.000 7.26 0.00 45.77 3.41
1752 3650 0.179145 AACGTAATCCTCGAGGCACG 60.179 55.000 32.91 32.91 44.09 5.34
1775 3673 9.002600 CCTGCATATACTTATCATTTGCAACTA 57.997 33.333 0.00 0.00 39.02 2.24
1827 3725 1.762370 TGAGCAGAAACCAGAGTCACA 59.238 47.619 0.00 0.00 0.00 3.58
1834 3732 2.775890 AGTGTGATGAGCAGAAACCAG 58.224 47.619 0.00 0.00 0.00 4.00
2287 4186 0.397564 TGCACTGAGATGCTCAACCA 59.602 50.000 8.13 0.00 46.28 3.67
2452 4351 2.779506 CAACCTCTACCCTTTCCACAC 58.220 52.381 0.00 0.00 0.00 3.82
2461 4360 3.306710 CCCAATTTTTGCAACCTCTACCC 60.307 47.826 0.00 0.00 0.00 3.69
2515 4414 9.250624 GCAAACATGTTTACCTTTGTATTTACA 57.749 29.630 22.87 0.00 0.00 2.41
2622 4521 5.824624 ACTTTGATGTCACAAACTCATCAGT 59.175 36.000 7.05 1.83 45.20 3.41
2645 4544 3.809905 ACTGAGGGTTGTTTCTGAGAAC 58.190 45.455 0.00 0.00 0.00 3.01
2830 4729 5.463724 CCCGAACTATAAGAACAGAAGATGC 59.536 44.000 0.00 0.00 0.00 3.91
2834 4733 6.631962 ACTTCCCGAACTATAAGAACAGAAG 58.368 40.000 0.00 0.00 34.58 2.85
2949 4852 7.923414 ACAATAGTCATTCCAAAACTACTCC 57.077 36.000 0.00 0.00 0.00 3.85
3001 4904 7.545362 TGTGCTTTAATCTCTTATCAGCTTC 57.455 36.000 0.00 0.00 30.24 3.86
3071 4974 4.333649 CCAAGGCATATAGTGTGTTCACAG 59.666 45.833 5.85 0.00 46.01 3.66
3448 5355 3.074412 CTGTTGTTTAGCCCATCGTTCT 58.926 45.455 0.00 0.00 0.00 3.01
3485 5392 1.678101 GGGAGCATGACATTTACAGCC 59.322 52.381 0.00 0.00 0.00 4.85
3505 5415 3.221771 TCAGATTTGTTGGAACCCACAG 58.778 45.455 0.00 0.00 30.78 3.66
3765 5678 9.545105 TTCAACATCAAACAAAAGCTATCAATT 57.455 25.926 0.00 0.00 0.00 2.32
3911 5824 0.953960 CTCCTTGCGTGGTTACACCC 60.954 60.000 0.00 0.00 44.86 4.61
3933 5846 8.627403 TCGGATATTAGTACTGAAAAGTGTAGG 58.373 37.037 5.39 0.00 0.00 3.18
3955 5868 3.267551 ACCCCTAAAAATAAAGGCTCGGA 59.732 43.478 0.00 0.00 0.00 4.55
4218 6133 9.599322 GATACGCATGAATTAAAAGGACATTAG 57.401 33.333 0.00 0.00 0.00 1.73
4240 6155 1.001378 GCCCGCAAATGGACATGATAC 60.001 52.381 0.00 0.00 0.00 2.24
4243 6158 1.001020 AGCCCGCAAATGGACATGA 60.001 52.632 0.00 0.00 0.00 3.07
4262 6178 7.011016 TGTGCACAAAATAGTCCATCTATAACG 59.989 37.037 19.28 0.00 38.29 3.18
4302 6219 0.455633 CAGCAAAGAACTGCCATCGC 60.456 55.000 0.00 0.00 43.73 4.58
4534 6453 4.564769 GCTCTCAGTTCATACAAGCACTAC 59.435 45.833 0.00 0.00 0.00 2.73
4558 6477 8.356657 TCGACATTAAAATTCATGTGTTTCCTT 58.643 29.630 0.00 0.00 33.62 3.36
4627 6546 3.138304 TGTCACAGTTGTTGCAGGATAC 58.862 45.455 0.00 0.00 0.00 2.24
4794 6713 6.382869 AAATGCAAGTCCATAACTATCAGC 57.617 37.500 0.00 0.00 37.17 4.26
4880 6799 7.831193 ACTAATAAGCAGAAGAACAATCCACAT 59.169 33.333 0.00 0.00 0.00 3.21
5065 6984 5.065914 AGAAGCATAGCACAAGAACAAGAA 58.934 37.500 0.00 0.00 0.00 2.52
5066 6985 4.645535 AGAAGCATAGCACAAGAACAAGA 58.354 39.130 0.00 0.00 0.00 3.02
5067 6986 5.368256 AAGAAGCATAGCACAAGAACAAG 57.632 39.130 0.00 0.00 0.00 3.16
5068 6987 7.174772 TGAATAAGAAGCATAGCACAAGAACAA 59.825 33.333 0.00 0.00 0.00 2.83
5069 6988 6.654582 TGAATAAGAAGCATAGCACAAGAACA 59.345 34.615 0.00 0.00 0.00 3.18
5070 6989 7.076842 TGAATAAGAAGCATAGCACAAGAAC 57.923 36.000 0.00 0.00 0.00 3.01
5221 7140 5.538118 TCTTTTTCTACGAGATTGCAGTGA 58.462 37.500 0.00 0.00 0.00 3.41
5308 7227 7.621428 TGTTTGGAATCTCATCTTCTGAATC 57.379 36.000 0.00 0.00 32.14 2.52
5342 7261 7.785985 AGATCCATTTTGGGTTATCATGAATCA 59.214 33.333 0.00 0.00 38.32 2.57
5569 7488 8.529911 GGAAATACGTTTAGTAATCACTTCTCG 58.470 37.037 0.00 0.00 39.04 4.04
5656 7575 6.320164 AGAAGTGAGTAAGCAGATATCGACTT 59.680 38.462 14.95 14.95 0.00 3.01
5669 7588 7.307455 GGAAAAGTAACAGCAGAAGTGAGTAAG 60.307 40.741 0.00 0.00 0.00 2.34
5725 7644 9.895138 AAAGAAGAGGTTTGTACTAGTGTTTTA 57.105 29.630 5.39 0.00 0.00 1.52
5984 8011 3.580458 AGCTCGCCATCTAAGTTCCATAT 59.420 43.478 0.00 0.00 0.00 1.78
5995 8022 1.457346 CCTGAAAAAGCTCGCCATCT 58.543 50.000 0.00 0.00 0.00 2.90
6037 8064 4.659172 TTGACAAGGCCCCGGCAG 62.659 66.667 8.23 0.00 44.11 4.85
6153 8185 4.810790 ACATGAGGTTCTTCTACAACTCG 58.189 43.478 0.00 0.00 0.00 4.18
6176 8208 6.609533 ACCGCAGTTTACATATCTACTATCG 58.390 40.000 0.00 0.00 0.00 2.92
6181 8213 6.534079 ACAAGAACCGCAGTTTACATATCTAC 59.466 38.462 0.00 0.00 35.94 2.59
6204 8236 2.737783 CGGTTCTTTATTGCGTGGTACA 59.262 45.455 0.00 0.00 0.00 2.90
6250 8282 4.804108 CATAATCTGTAGCTCCTCCTTCG 58.196 47.826 0.00 0.00 0.00 3.79
6257 8291 6.683974 TTTTTCAGCATAATCTGTAGCTCC 57.316 37.500 0.00 0.00 34.61 4.70
6313 8348 1.372872 GTGTGGGCGGTGCAAATTC 60.373 57.895 0.00 0.00 0.00 2.17
6323 8358 1.153369 AGATCAATCCGTGTGGGCG 60.153 57.895 0.00 0.00 35.24 6.13
6370 8405 5.283060 GTTGAGTTGCAACGAATATGTCT 57.717 39.130 23.21 2.78 46.50 3.41
6384 8420 1.202405 GGGGCAAGTGTTGTTGAGTTG 60.202 52.381 0.00 0.00 0.00 3.16
6400 8436 5.852282 TGCAGAATAAATTTTCTAGGGGC 57.148 39.130 0.00 0.00 34.21 5.80
6406 8442 9.895138 ATGCCTAAAATGCAGAATAAATTTTCT 57.105 25.926 0.00 0.00 42.92 2.52
6427 8648 2.304180 ACAGTAGAACTTCAGCATGCCT 59.696 45.455 15.66 4.75 34.76 4.75
6431 8652 3.196685 GGAGGACAGTAGAACTTCAGCAT 59.803 47.826 0.00 0.00 0.00 3.79
6432 8653 2.563179 GGAGGACAGTAGAACTTCAGCA 59.437 50.000 0.00 0.00 0.00 4.41
6433 8654 2.829120 AGGAGGACAGTAGAACTTCAGC 59.171 50.000 0.00 0.00 0.00 4.26
6437 8658 5.602978 TCAAAAGAGGAGGACAGTAGAACTT 59.397 40.000 0.00 0.00 0.00 2.66
6442 8663 5.323371 CTCTCAAAAGAGGAGGACAGTAG 57.677 47.826 0.00 0.00 44.59 2.57
6663 11104 9.933240 ACTAACAAACTAGGACATAGGTAGTAT 57.067 33.333 0.00 0.00 35.63 2.12
6664 11105 9.401058 GACTAACAAACTAGGACATAGGTAGTA 57.599 37.037 0.00 0.00 35.63 1.82
6665 11106 8.114743 AGACTAACAAACTAGGACATAGGTAGT 58.885 37.037 0.00 0.00 35.63 2.73
6666 11107 8.522542 AGACTAACAAACTAGGACATAGGTAG 57.477 38.462 0.00 0.00 35.63 3.18
6667 11108 8.890410 AAGACTAACAAACTAGGACATAGGTA 57.110 34.615 0.00 0.00 35.63 3.08
6668 11109 7.793948 AAGACTAACAAACTAGGACATAGGT 57.206 36.000 0.00 0.00 35.63 3.08
6683 11124 9.590451 CCCAAAGTACGATTATAAAGACTAACA 57.410 33.333 0.00 0.00 0.00 2.41
6684 11125 9.591792 ACCCAAAGTACGATTATAAAGACTAAC 57.408 33.333 0.00 0.00 0.00 2.34
6703 11144 9.927668 AAATATGTGATCAAACTTTACCCAAAG 57.072 29.630 0.00 0.00 45.63 2.77
6715 11156 9.979578 AGCAAAACTGTTAAATATGTGATCAAA 57.020 25.926 0.00 0.00 0.00 2.69
6720 11161 9.405587 GCTTTAGCAAAACTGTTAAATATGTGA 57.594 29.630 0.00 0.00 41.59 3.58
6874 11315 9.643693 GGTCACATTTTGATCATGATTTTAACT 57.356 29.630 10.14 0.00 35.12 2.24
6875 11316 8.872845 GGGTCACATTTTGATCATGATTTTAAC 58.127 33.333 10.14 0.00 37.02 2.01
6876 11317 8.591940 TGGGTCACATTTTGATCATGATTTTAA 58.408 29.630 10.14 4.87 37.02 1.52
6877 11318 8.131847 TGGGTCACATTTTGATCATGATTTTA 57.868 30.769 10.14 0.00 37.02 1.52
6878 11319 7.006865 TGGGTCACATTTTGATCATGATTTT 57.993 32.000 10.14 0.00 37.02 1.82
6879 11320 6.608539 TGGGTCACATTTTGATCATGATTT 57.391 33.333 10.14 0.00 37.02 2.17
6880 11321 6.608539 TTGGGTCACATTTTGATCATGATT 57.391 33.333 10.14 0.00 37.02 2.57
6881 11322 6.608539 TTTGGGTCACATTTTGATCATGAT 57.391 33.333 8.25 8.25 37.02 2.45
6882 11323 6.416631 TTTTGGGTCACATTTTGATCATGA 57.583 33.333 0.00 0.00 37.02 3.07
6883 11324 7.818446 TGTATTTTGGGTCACATTTTGATCATG 59.182 33.333 0.00 0.00 37.02 3.07
6884 11325 7.905265 TGTATTTTGGGTCACATTTTGATCAT 58.095 30.769 0.00 0.00 37.02 2.45
6885 11326 7.295322 TGTATTTTGGGTCACATTTTGATCA 57.705 32.000 0.00 0.00 37.02 2.92
6886 11327 8.600449 TTTGTATTTTGGGTCACATTTTGATC 57.400 30.769 0.00 0.00 36.32 2.92
6887 11328 7.661027 CCTTTGTATTTTGGGTCACATTTTGAT 59.339 33.333 0.00 0.00 36.32 2.57
6888 11329 6.989169 CCTTTGTATTTTGGGTCACATTTTGA 59.011 34.615 0.00 0.00 0.00 2.69
6889 11330 6.204495 CCCTTTGTATTTTGGGTCACATTTTG 59.796 38.462 0.00 0.00 35.13 2.44
6890 11331 6.100424 TCCCTTTGTATTTTGGGTCACATTTT 59.900 34.615 0.00 0.00 40.48 1.82
6891 11332 5.604650 TCCCTTTGTATTTTGGGTCACATTT 59.395 36.000 0.00 0.00 40.48 2.32
6892 11333 5.151454 TCCCTTTGTATTTTGGGTCACATT 58.849 37.500 0.00 0.00 40.48 2.71
6893 11334 4.746466 TCCCTTTGTATTTTGGGTCACAT 58.254 39.130 0.00 0.00 40.48 3.21
6894 11335 4.186077 TCCCTTTGTATTTTGGGTCACA 57.814 40.909 0.00 0.00 40.48 3.58
6895 11336 4.587262 AGTTCCCTTTGTATTTTGGGTCAC 59.413 41.667 0.00 0.00 40.48 3.67
6896 11337 4.810345 AGTTCCCTTTGTATTTTGGGTCA 58.190 39.130 0.00 0.00 40.48 4.02
6897 11338 6.008331 ACTAGTTCCCTTTGTATTTTGGGTC 58.992 40.000 0.00 0.00 40.48 4.46
6898 11339 5.960704 ACTAGTTCCCTTTGTATTTTGGGT 58.039 37.500 0.00 0.00 40.48 4.51
6899 11340 8.301720 GTTTACTAGTTCCCTTTGTATTTTGGG 58.698 37.037 0.00 0.00 40.95 4.12
6900 11341 8.019094 CGTTTACTAGTTCCCTTTGTATTTTGG 58.981 37.037 0.00 0.00 0.00 3.28
6901 11342 8.776470 TCGTTTACTAGTTCCCTTTGTATTTTG 58.224 33.333 0.00 0.00 0.00 2.44
6902 11343 8.907222 TCGTTTACTAGTTCCCTTTGTATTTT 57.093 30.769 0.00 0.00 0.00 1.82
6903 11344 8.370182 TCTCGTTTACTAGTTCCCTTTGTATTT 58.630 33.333 0.00 0.00 0.00 1.40
6904 11345 7.899973 TCTCGTTTACTAGTTCCCTTTGTATT 58.100 34.615 0.00 0.00 0.00 1.89
6905 11346 7.472334 TCTCGTTTACTAGTTCCCTTTGTAT 57.528 36.000 0.00 0.00 0.00 2.29
6906 11347 6.899393 TCTCGTTTACTAGTTCCCTTTGTA 57.101 37.500 0.00 0.00 0.00 2.41
6907 11348 5.796424 TCTCGTTTACTAGTTCCCTTTGT 57.204 39.130 0.00 0.00 0.00 2.83
6908 11349 5.118203 CGTTCTCGTTTACTAGTTCCCTTTG 59.882 44.000 0.00 0.00 0.00 2.77
6909 11350 5.225642 CGTTCTCGTTTACTAGTTCCCTTT 58.774 41.667 0.00 0.00 0.00 3.11
6910 11351 4.321527 CCGTTCTCGTTTACTAGTTCCCTT 60.322 45.833 0.00 0.00 35.01 3.95
6911 11352 3.192212 CCGTTCTCGTTTACTAGTTCCCT 59.808 47.826 0.00 0.00 35.01 4.20
6912 11353 3.191371 TCCGTTCTCGTTTACTAGTTCCC 59.809 47.826 0.00 0.00 35.01 3.97
6913 11354 4.425577 TCCGTTCTCGTTTACTAGTTCC 57.574 45.455 0.00 0.00 35.01 3.62
6914 11355 5.456265 ACTTCCGTTCTCGTTTACTAGTTC 58.544 41.667 0.00 0.00 35.01 3.01
6915 11356 5.444663 ACTTCCGTTCTCGTTTACTAGTT 57.555 39.130 0.00 0.00 35.01 2.24
6916 11357 6.560253 TTACTTCCGTTCTCGTTTACTAGT 57.440 37.500 0.00 0.00 35.01 2.57
6917 11358 8.394121 ACTATTACTTCCGTTCTCGTTTACTAG 58.606 37.037 0.00 0.00 35.01 2.57
6918 11359 8.268850 ACTATTACTTCCGTTCTCGTTTACTA 57.731 34.615 0.00 0.00 35.01 1.82
6919 11360 7.150783 ACTATTACTTCCGTTCTCGTTTACT 57.849 36.000 0.00 0.00 35.01 2.24
6920 11361 7.660959 CAACTATTACTTCCGTTCTCGTTTAC 58.339 38.462 0.00 0.00 35.01 2.01
6921 11362 6.308766 GCAACTATTACTTCCGTTCTCGTTTA 59.691 38.462 0.00 0.00 35.01 2.01
6922 11363 5.119743 GCAACTATTACTTCCGTTCTCGTTT 59.880 40.000 0.00 0.00 35.01 3.60
6923 11364 4.624452 GCAACTATTACTTCCGTTCTCGTT 59.376 41.667 0.00 0.00 35.01 3.85
6924 11365 4.171754 GCAACTATTACTTCCGTTCTCGT 58.828 43.478 0.00 0.00 35.01 4.18
6925 11366 4.171005 TGCAACTATTACTTCCGTTCTCG 58.829 43.478 0.00 0.00 0.00 4.04
6926 11367 6.476243 TTTGCAACTATTACTTCCGTTCTC 57.524 37.500 0.00 0.00 0.00 2.87
6927 11368 6.870971 TTTTGCAACTATTACTTCCGTTCT 57.129 33.333 0.00 0.00 0.00 3.01
6928 11369 7.081976 ACATTTTGCAACTATTACTTCCGTTC 58.918 34.615 0.00 0.00 0.00 3.95
6929 11370 6.977213 ACATTTTGCAACTATTACTTCCGTT 58.023 32.000 0.00 0.00 0.00 4.44
6930 11371 6.569179 ACATTTTGCAACTATTACTTCCGT 57.431 33.333 0.00 0.00 0.00 4.69
6931 11372 7.867445 AAACATTTTGCAACTATTACTTCCG 57.133 32.000 0.00 0.00 0.00 4.30
6932 11373 8.860128 GCTAAACATTTTGCAACTATTACTTCC 58.140 33.333 0.00 0.00 38.48 3.46
6933 11374 9.626045 AGCTAAACATTTTGCAACTATTACTTC 57.374 29.630 0.00 0.00 40.53 3.01
6934 11375 9.981114 AAGCTAAACATTTTGCAACTATTACTT 57.019 25.926 0.00 0.00 40.53 2.24
6935 11376 9.981114 AAAGCTAAACATTTTGCAACTATTACT 57.019 25.926 0.00 0.00 40.53 2.24
6937 11378 9.202273 CCAAAGCTAAACATTTTGCAACTATTA 57.798 29.630 0.00 0.00 40.53 0.98
6938 11379 7.173047 CCCAAAGCTAAACATTTTGCAACTATT 59.827 33.333 0.00 0.00 40.53 1.73
6943 11384 3.563390 GCCCAAAGCTAAACATTTTGCAA 59.437 39.130 12.22 0.00 40.53 4.08
6947 11388 6.957920 AAAATGCCCAAAGCTAAACATTTT 57.042 29.167 14.82 14.82 44.23 1.82
6950 11391 6.426633 GTGTTAAAATGCCCAAAGCTAAACAT 59.573 34.615 0.00 0.00 44.23 2.71
6958 11399 4.923281 GTGCTAGTGTTAAAATGCCCAAAG 59.077 41.667 0.00 0.00 0.00 2.77
6961 11402 3.756434 GAGTGCTAGTGTTAAAATGCCCA 59.244 43.478 0.00 0.00 0.00 5.36
6992 11434 3.321111 GGTCTCCGATGGCTATTTGAGTA 59.679 47.826 8.82 0.00 0.00 2.59
6993 11435 2.103263 GGTCTCCGATGGCTATTTGAGT 59.897 50.000 8.82 0.00 0.00 3.41
7005 11447 5.017490 TGAAAAGTAGAGAAGGTCTCCGAT 58.983 41.667 1.62 0.00 44.42 4.18
7012 11454 3.252351 AGGGCTGAAAAGTAGAGAAGGT 58.748 45.455 0.00 0.00 0.00 3.50
7027 11469 1.969923 TGGGTTGAATTTTGAGGGCTG 59.030 47.619 0.00 0.00 0.00 4.85
7028 11470 2.368548 GTTGGGTTGAATTTTGAGGGCT 59.631 45.455 0.00 0.00 0.00 5.19
7029 11471 2.368548 AGTTGGGTTGAATTTTGAGGGC 59.631 45.455 0.00 0.00 0.00 5.19
7042 11485 1.202891 GGCTAGTGTTGGAGTTGGGTT 60.203 52.381 0.00 0.00 0.00 4.11
7043 11486 0.400594 GGCTAGTGTTGGAGTTGGGT 59.599 55.000 0.00 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.