Multiple sequence alignment - TraesCS3D01G525200

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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 TraesCS3D01G525200 chr3D 100.000 9847 0 0 1 9847 604675047 604665201 0.000000e+00 18185.0
1 TraesCS3D01G525200 chr3A 96.248 7409 196 27 1 7381 734791901 734784547 0.000000e+00 12067.0
2 TraesCS3D01G525200 chr3A 94.793 2420 69 19 7457 9847 734784533 734782142 0.000000e+00 3718.0
3 TraesCS3D01G525200 chr3A 93.327 1978 99 13 3570 5536 182639374 182637419 0.000000e+00 2891.0
4 TraesCS3D01G525200 chr3A 90.427 773 47 15 5800 6564 182637067 182636314 0.000000e+00 992.0
5 TraesCS3D01G525200 chr3A 92.683 164 11 1 5638 5800 182637420 182637257 1.650000e-57 235.0
6 TraesCS3D01G525200 chr3A 95.349 129 6 0 3399 3527 182639503 182639375 1.300000e-48 206.0
7 TraesCS3D01G525200 chr3B 95.251 5707 203 29 211 5874 812345803 812340122 0.000000e+00 8975.0
8 TraesCS3D01G525200 chr3B 92.857 1834 70 24 7457 9280 812338694 812336912 0.000000e+00 2604.0
9 TraesCS3D01G525200 chr3B 94.387 1443 51 5 5940 7381 812340121 812338708 0.000000e+00 2189.0
10 TraesCS3D01G525200 chr3B 89.474 171 18 0 1 171 812345979 812345809 5.990000e-52 217.0
11 TraesCS3D01G525200 chr3B 88.398 181 18 3 2247 2427 610299841 610300018 2.150000e-51 215.0
12 TraesCS3D01G525200 chr3B 96.330 109 2 2 5534 5640 505264679 505264571 2.830000e-40 178.0
13 TraesCS3D01G525200 chr6B 89.840 187 19 0 9661 9847 119257960 119258146 3.550000e-59 241.0
14 TraesCS3D01G525200 chr6B 75.244 307 56 8 9215 9504 119242676 119242979 2.890000e-25 128.0
15 TraesCS3D01G525200 chr6B 81.308 107 19 1 9677 9783 119241899 119241794 1.760000e-12 86.1
16 TraesCS3D01G525200 chr6A 74.788 472 89 16 9215 9664 63207363 63207826 1.690000e-42 185.0
17 TraesCS3D01G525200 chr6A 94.872 117 2 4 5528 5640 222554890 222555006 7.860000e-41 180.0
18 TraesCS3D01G525200 chr6A 96.330 109 2 1 5534 5640 502244335 502244227 2.830000e-40 178.0
19 TraesCS3D01G525200 chr6A 91.379 116 10 0 5685 5800 536253932 536253817 1.020000e-34 159.0
20 TraesCS3D01G525200 chr5B 96.262 107 2 2 5535 5639 364132666 364132772 3.660000e-39 174.0
21 TraesCS3D01G525200 chr5B 89.474 114 12 0 5687 5800 9504756 9504643 2.870000e-30 145.0
22 TraesCS3D01G525200 chr7D 93.750 112 5 2 5533 5642 514658914 514658803 6.120000e-37 167.0
23 TraesCS3D01G525200 chr2B 94.495 109 4 2 5533 5639 51645328 51645220 6.120000e-37 167.0
24 TraesCS3D01G525200 chr6D 92.241 116 9 0 5685 5800 389973699 389973584 2.200000e-36 165.0
25 TraesCS3D01G525200 chr2D 90.476 126 10 2 5535 5658 473292305 473292180 2.200000e-36 165.0
26 TraesCS3D01G525200 chr2D 89.076 119 10 3 5685 5801 536537387 536537270 2.870000e-30 145.0
27 TraesCS3D01G525200 chr5D 89.474 114 10 2 5687 5800 9495434 9495323 1.030000e-29 143.0
28 TraesCS3D01G525200 chr4A 88.889 117 11 1 5685 5799 580297819 580297703 1.030000e-29 143.0


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 TraesCS3D01G525200 chr3D 604665201 604675047 9846 True 18185.00 18185 100.00000 1 9847 1 chr3D.!!$R1 9846
1 TraesCS3D01G525200 chr3A 734782142 734791901 9759 True 7892.50 12067 95.52050 1 9847 2 chr3A.!!$R2 9846
2 TraesCS3D01G525200 chr3A 182636314 182639503 3189 True 1081.00 2891 92.94650 3399 6564 4 chr3A.!!$R1 3165
3 TraesCS3D01G525200 chr3B 812336912 812345979 9067 True 3496.25 8975 92.99225 1 9280 4 chr3B.!!$R2 9279

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
448 452 0.613260 TGGGTGATCAGTTTCGGGAG 59.387 55.000 0.00 0.00 0.00 4.30 F
528 532 2.128128 GCACGTGCACTCGTTTCG 60.128 61.111 34.52 1.73 42.27 3.46 F
1637 1667 0.872388 CACGGGTTTGTACTTCTGCC 59.128 55.000 0.00 0.00 0.00 4.85 F
1647 1677 1.045407 TACTTCTGCCACTTCACCGT 58.955 50.000 0.00 0.00 0.00 4.83 F
2417 2457 1.065126 GGTGGTGAAGGATGGGAGAAG 60.065 57.143 0.00 0.00 0.00 2.85 F
3522 3576 1.433471 GCCAGCATTAGAAACGCCC 59.567 57.895 0.00 0.00 0.00 6.13 F
5125 5192 1.135859 CGTGCTGCCTCAGTTGAATTC 60.136 52.381 0.00 0.00 33.43 2.17 F
5787 5859 0.896923 TTGCCATGCTTGCTAAAGGG 59.103 50.000 0.00 0.00 33.68 3.95 F
6861 7157 1.075374 TGCAAAAGTACCTCCCTGCAT 59.925 47.619 0.00 0.00 35.02 3.96 F
7523 7820 1.111277 GGTTGGTTTCCAGTGTTGCT 58.889 50.000 0.00 0.00 33.81 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1546 1576 1.225983 CTCTCCTCGAGCCTCTGGA 59.774 63.158 6.99 0.00 31.99 3.86 R
1919 1953 1.481871 GGTACACAGCAGGGCTAGTA 58.518 55.000 0.00 0.00 36.40 1.82 R
3510 3564 0.323087 AAAGGCCGGGCGTTTCTAAT 60.323 50.000 28.57 11.20 41.75 1.73 R
3522 3576 0.743345 CCCTCGGAAGTAAAAGGCCG 60.743 60.000 0.00 0.00 44.83 6.13 R
3985 4043 1.641577 GACGGCCTAACTTACTGCAG 58.358 55.000 13.48 13.48 0.00 4.41 R
5321 5388 0.179076 TGCGGTACTGATCCATGCAG 60.179 55.000 5.68 0.00 39.26 4.41 R
6848 7144 0.107654 GGACACATGCAGGGAGGTAC 60.108 60.000 2.31 0.00 0.00 3.34 R
7779 8076 1.478654 GGGTCACTCTTTGGCAAAGGA 60.479 52.381 33.00 22.21 39.01 3.36 R
8348 8646 0.036875 GCTGGGTAGGTCTTGTGCTT 59.963 55.000 0.00 0.00 0.00 3.91 R
9241 9556 1.376424 AGCACAATCGCCTGACTGG 60.376 57.895 0.00 0.00 39.35 4.00 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
179 180 4.556233 CGAAATGTGAGTGACCAGTTCTA 58.444 43.478 0.00 0.00 34.48 2.10
231 232 9.910511 TCAACGAAATTAATAAGCGATAAAGAC 57.089 29.630 10.31 0.00 0.00 3.01
255 259 2.047061 CTTGGACCCATTCCCGATCTA 58.953 52.381 0.00 0.00 45.17 1.98
289 293 8.333235 TGGTTATTATGTGTAGTGATTTCCCTT 58.667 33.333 0.00 0.00 0.00 3.95
298 302 2.041755 AGTGATTTCCCTTGACCCCTTC 59.958 50.000 0.00 0.00 0.00 3.46
338 342 5.521906 TCCTCGATCCTCTTGAATAGTTG 57.478 43.478 0.00 0.00 0.00 3.16
345 349 2.009774 CTCTTGAATAGTTGCCCCACG 58.990 52.381 0.00 0.00 0.00 4.94
367 371 4.730042 CGCGACATCTTTATGTTCCATTTG 59.270 41.667 0.00 0.00 46.49 2.32
408 412 3.741245 TCCTCCACTAGCAGTAACTCT 57.259 47.619 0.00 0.00 0.00 3.24
435 439 3.965379 TTTAAGTAGCGACATGGGTGA 57.035 42.857 0.00 0.00 0.00 4.02
447 451 1.065491 CATGGGTGATCAGTTTCGGGA 60.065 52.381 0.00 0.00 0.00 5.14
448 452 0.613260 TGGGTGATCAGTTTCGGGAG 59.387 55.000 0.00 0.00 0.00 4.30
528 532 2.128128 GCACGTGCACTCGTTTCG 60.128 61.111 34.52 1.73 42.27 3.46
564 568 8.812972 AGTTACGGCTTGATATCATATTTAGGA 58.187 33.333 6.17 0.00 0.00 2.94
640 657 9.759473 TGTATAGAAAACCTAGGTTGTACTAGT 57.241 33.333 27.75 18.61 39.01 2.57
653 670 5.711976 GGTTGTACTAGTACACTACCCTTGA 59.288 44.000 30.56 16.10 44.81 3.02
1319 1349 3.250744 CGTTGCTCCTCGTATCTTTTCA 58.749 45.455 0.00 0.00 0.00 2.69
1369 1399 2.445155 GGTGGGGCCTGAAATGGT 59.555 61.111 0.84 0.00 0.00 3.55
1499 1529 3.925630 TAGGTCGTCGGGGAGCGTT 62.926 63.158 0.00 0.00 39.35 4.84
1601 1631 3.858868 GAGCAAGCGTGTCCGGTCA 62.859 63.158 0.00 0.00 45.47 4.02
1608 1638 2.509336 GTGTCCGGTCATCGCTGG 60.509 66.667 4.29 0.00 37.59 4.85
1637 1667 0.872388 CACGGGTTTGTACTTCTGCC 59.128 55.000 0.00 0.00 0.00 4.85
1647 1677 1.045407 TACTTCTGCCACTTCACCGT 58.955 50.000 0.00 0.00 0.00 4.83
1696 1726 3.643199 TGTATGCCATTGCTTCCACTA 57.357 42.857 0.00 0.00 38.71 2.74
1725 1759 5.131475 AGTTAGTTTGAGTTGGTACCTTGGA 59.869 40.000 14.36 0.00 0.00 3.53
1836 1870 1.153784 GTGCGCAAATCACATGGGG 60.154 57.895 14.00 0.00 34.73 4.96
1919 1953 1.420430 TAACTATGCGCTTAGGCCCT 58.580 50.000 27.87 14.99 34.44 5.19
1931 1965 2.446802 GGCCCTACTAGCCCTGCT 60.447 66.667 0.00 0.00 45.16 4.24
2183 2223 9.088512 GTTTTTCGACTATGAGTGTATTCATCT 57.911 33.333 0.00 0.00 38.65 2.90
2221 2261 3.059166 GTGCTACCATTTGCCTTTTGTG 58.941 45.455 0.00 0.00 0.00 3.33
2233 2273 3.761218 TGCCTTTTGTGTTGACTCTTTGA 59.239 39.130 0.00 0.00 0.00 2.69
2235 2275 4.142381 GCCTTTTGTGTTGACTCTTTGACT 60.142 41.667 0.00 0.00 0.00 3.41
2236 2276 5.622233 GCCTTTTGTGTTGACTCTTTGACTT 60.622 40.000 0.00 0.00 0.00 3.01
2285 2325 1.813178 GTTTCTACAAGGCAAGGAGGC 59.187 52.381 0.00 0.00 44.61 4.70
2417 2457 1.065126 GGTGGTGAAGGATGGGAGAAG 60.065 57.143 0.00 0.00 0.00 2.85
2667 2707 4.500499 AAGAATGCTATGGCTTCAGAGT 57.500 40.909 1.68 0.00 39.59 3.24
2727 2767 1.827344 TGAGTCATCTCCGCATTCAGT 59.173 47.619 0.00 0.00 39.75 3.41
3054 3101 4.690748 GCTGCTGTAGTTCATGTAGTTTCA 59.309 41.667 0.00 0.00 0.00 2.69
3065 3112 9.614792 AGTTCATGTAGTTTCAAACTTTCTACT 57.385 29.630 8.41 2.87 42.81 2.57
3070 3117 9.614792 ATGTAGTTTCAAACTTTCTACTGTTCT 57.385 29.630 8.41 0.00 42.81 3.01
3303 3357 2.309755 TGATGAATGGGAAGAAGCACCT 59.690 45.455 0.00 0.00 0.00 4.00
3522 3576 1.433471 GCCAGCATTAGAAACGCCC 59.567 57.895 0.00 0.00 0.00 6.13
3537 3591 2.404186 GCCCGGCCTTTTACTTCCG 61.404 63.158 0.00 0.00 41.41 4.30
3604 3658 4.307032 AATGTTACATCTCCAGCTGGTT 57.693 40.909 31.58 15.43 36.34 3.67
3985 4043 9.691362 TGAAACTTATGGTCTTCTTTAATTTGC 57.309 29.630 0.00 0.00 0.00 3.68
4153 4216 4.224594 TCTCTGAAAGTTGATCCTGATGCT 59.775 41.667 0.00 0.00 33.76 3.79
4158 4221 6.240894 TGAAAGTTGATCCTGATGCTTAAGT 58.759 36.000 4.02 0.00 0.00 2.24
4647 4713 7.481642 TCTACTCTTATCGTGGAAGATGTTTC 58.518 38.462 0.00 0.00 32.60 2.78
4733 4799 9.143631 GATGTTTCCAATAAAATCCTCAACTTG 57.856 33.333 0.00 0.00 0.00 3.16
4958 5025 8.025445 AGAATCATAACAACACATCTCAAAAGC 58.975 33.333 0.00 0.00 0.00 3.51
5125 5192 1.135859 CGTGCTGCCTCAGTTGAATTC 60.136 52.381 0.00 0.00 33.43 2.17
5321 5388 1.675116 GGTACCCAGAAAACGGCTCTC 60.675 57.143 0.00 0.00 0.00 3.20
5592 5662 6.924060 GGATGTATCTAGCACTGAAATACGTT 59.076 38.462 0.00 0.00 0.00 3.99
5721 5792 1.462283 CGCGAGGATGGCAATATCTTG 59.538 52.381 0.00 0.00 41.24 3.02
5787 5859 0.896923 TTGCCATGCTTGCTAAAGGG 59.103 50.000 0.00 0.00 33.68 3.95
5968 6231 3.555518 GCTGTGAATTCGAAACCTTGAC 58.444 45.455 0.00 0.00 0.00 3.18
5981 6244 1.450211 CTTGACGGGGTGTGGTTCT 59.550 57.895 0.00 0.00 0.00 3.01
6067 6331 6.257630 GTGAACCAACTGCAAACATATTTTGT 59.742 34.615 10.20 0.00 41.53 2.83
6121 6385 5.547465 TCGTCACCTCATTGTTTTCAGTAT 58.453 37.500 0.00 0.00 0.00 2.12
6168 6432 6.260050 TCCTTATTAACTCAAATCATGGTCGC 59.740 38.462 0.00 0.00 0.00 5.19
6274 6539 3.515901 AGACTCTTTGATCAGGTGGGTAC 59.484 47.826 0.00 0.00 0.00 3.34
6494 6762 8.759481 TTATGGTGGAATTGCTTGATATGTTA 57.241 30.769 0.00 0.00 0.00 2.41
6495 6763 7.658525 ATGGTGGAATTGCTTGATATGTTAA 57.341 32.000 0.00 0.00 0.00 2.01
6496 6764 7.099266 TGGTGGAATTGCTTGATATGTTAAG 57.901 36.000 0.00 0.00 0.00 1.85
6497 6765 6.889177 TGGTGGAATTGCTTGATATGTTAAGA 59.111 34.615 0.00 0.00 0.00 2.10
6498 6766 7.560991 TGGTGGAATTGCTTGATATGTTAAGAT 59.439 33.333 0.00 0.00 0.00 2.40
6499 6767 8.416329 GGTGGAATTGCTTGATATGTTAAGATT 58.584 33.333 0.00 0.00 0.00 2.40
6500 6768 9.241317 GTGGAATTGCTTGATATGTTAAGATTG 57.759 33.333 0.00 0.00 0.00 2.67
6501 6769 9.187996 TGGAATTGCTTGATATGTTAAGATTGA 57.812 29.630 0.00 0.00 0.00 2.57
6506 6774 9.791820 TTGCTTGATATGTTAAGATTGATTGTG 57.208 29.630 0.00 0.00 0.00 3.33
6507 6775 7.916977 TGCTTGATATGTTAAGATTGATTGTGC 59.083 33.333 0.00 0.00 0.00 4.57
6508 6776 7.916977 GCTTGATATGTTAAGATTGATTGTGCA 59.083 33.333 0.00 0.00 0.00 4.57
6509 6777 9.791820 CTTGATATGTTAAGATTGATTGTGCAA 57.208 29.630 0.00 0.00 0.00 4.08
6514 6782 8.891671 ATGTTAAGATTGATTGTGCAAAAAGT 57.108 26.923 0.00 0.00 0.00 2.66
6515 6783 8.715191 TGTTAAGATTGATTGTGCAAAAAGTT 57.285 26.923 0.00 0.00 0.00 2.66
6516 6784 8.602328 TGTTAAGATTGATTGTGCAAAAAGTTG 58.398 29.630 0.00 0.00 37.83 3.16
6517 6785 8.603181 GTTAAGATTGATTGTGCAAAAAGTTGT 58.397 29.630 0.00 0.00 37.06 3.32
6518 6786 7.614124 AAGATTGATTGTGCAAAAAGTTGTT 57.386 28.000 0.00 0.00 37.06 2.83
6537 6833 3.569277 TGTTGGGTCTCATGTGACAAATG 59.431 43.478 24.84 0.00 38.61 2.32
6543 6839 5.396772 GGGTCTCATGTGACAAATGGATAGA 60.397 44.000 24.84 0.00 38.61 1.98
6552 6848 6.430925 TGTGACAAATGGATAGAACCTGAAAG 59.569 38.462 0.00 0.00 0.00 2.62
6575 6871 2.906389 AGTGAAATAGCAGGTCTCACCA 59.094 45.455 0.00 0.00 41.95 4.17
6586 6882 2.972713 AGGTCTCACCAACTTAGCAGAA 59.027 45.455 0.00 0.00 41.95 3.02
6684 6980 8.690884 TGGAATAGTTTGAGTCAATTTGAAACA 58.309 29.630 6.36 8.02 0.00 2.83
6735 7031 4.696877 TGAGATTATGCACCACACTTCAAG 59.303 41.667 0.00 0.00 0.00 3.02
6752 7048 5.645497 ACTTCAAGTAATTCTAGCAGCCTTG 59.355 40.000 0.00 0.00 0.00 3.61
6763 7059 1.891150 AGCAGCCTTGTCCTCATTTTG 59.109 47.619 0.00 0.00 0.00 2.44
6789 7085 4.612614 CGTGTTGATGATTTCCTTTTGTCG 59.387 41.667 0.00 0.00 0.00 4.35
6804 7100 4.902443 TTTGTCGTTGGATTTACAGCAA 57.098 36.364 0.00 0.00 0.00 3.91
6861 7157 1.075374 TGCAAAAGTACCTCCCTGCAT 59.925 47.619 0.00 0.00 35.02 3.96
6873 7169 1.133513 TCCCTGCATGTGTCCTTTTGT 60.134 47.619 0.00 0.00 0.00 2.83
6987 7283 5.885352 TCTTGACTTGTTTCAGGTGAATCAA 59.115 36.000 13.14 13.14 39.82 2.57
7000 7296 5.178067 CAGGTGAATCAAAAGAAATGCCAAC 59.822 40.000 0.00 0.00 0.00 3.77
7059 7355 8.893563 AAAACATGGAGGAAAGGTATTAATGA 57.106 30.769 0.00 0.00 0.00 2.57
7064 7360 9.359653 CATGGAGGAAAGGTATTAATGATTCTT 57.640 33.333 0.00 0.00 0.00 2.52
7239 7535 9.889128 ATTAGTTACATTACCGCCTACTTTTTA 57.111 29.630 0.00 0.00 0.00 1.52
7378 7675 5.701290 GCACCTTCATAGTGTAGTCTTGTTT 59.299 40.000 0.00 0.00 37.56 2.83
7381 7678 9.436957 CACCTTCATAGTGTAGTCTTGTTTATT 57.563 33.333 0.00 0.00 0.00 1.40
7423 7720 7.014230 AGTCTTGTTTATACCAGCAATGTTTGT 59.986 33.333 0.00 0.00 0.00 2.83
7424 7721 7.651704 GTCTTGTTTATACCAGCAATGTTTGTT 59.348 33.333 0.00 0.00 0.00 2.83
7425 7722 7.865385 TCTTGTTTATACCAGCAATGTTTGTTC 59.135 33.333 0.00 0.00 0.00 3.18
7426 7723 6.451393 TGTTTATACCAGCAATGTTTGTTCC 58.549 36.000 0.00 0.00 0.00 3.62
7427 7724 6.266558 TGTTTATACCAGCAATGTTTGTTCCT 59.733 34.615 0.00 0.00 0.00 3.36
7428 7725 7.448777 TGTTTATACCAGCAATGTTTGTTCCTA 59.551 33.333 0.00 0.00 0.00 2.94
7429 7726 8.301002 GTTTATACCAGCAATGTTTGTTCCTAA 58.699 33.333 0.00 0.00 0.00 2.69
7430 7727 6.909550 ATACCAGCAATGTTTGTTCCTAAA 57.090 33.333 0.00 0.00 0.00 1.85
7431 7728 5.806654 ACCAGCAATGTTTGTTCCTAAAT 57.193 34.783 0.00 0.00 0.00 1.40
7432 7729 6.909550 ACCAGCAATGTTTGTTCCTAAATA 57.090 33.333 0.00 0.00 0.00 1.40
7433 7730 7.480760 ACCAGCAATGTTTGTTCCTAAATAT 57.519 32.000 0.00 0.00 0.00 1.28
7434 7731 7.547227 ACCAGCAATGTTTGTTCCTAAATATC 58.453 34.615 0.00 0.00 0.00 1.63
7435 7732 7.397192 ACCAGCAATGTTTGTTCCTAAATATCT 59.603 33.333 0.00 0.00 0.00 1.98
7436 7733 7.917505 CCAGCAATGTTTGTTCCTAAATATCTC 59.082 37.037 0.00 0.00 0.00 2.75
7437 7734 8.461222 CAGCAATGTTTGTTCCTAAATATCTCA 58.539 33.333 0.00 0.00 0.00 3.27
7438 7735 9.193806 AGCAATGTTTGTTCCTAAATATCTCAT 57.806 29.630 0.00 0.00 0.00 2.90
7439 7736 9.807649 GCAATGTTTGTTCCTAAATATCTCATT 57.192 29.630 0.00 0.00 0.00 2.57
7523 7820 1.111277 GGTTGGTTTCCAGTGTTGCT 58.889 50.000 0.00 0.00 33.81 3.91
7542 7839 8.076178 GTGTTGCTTGTTTCTTTCTATGTATGT 58.924 33.333 0.00 0.00 0.00 2.29
7543 7840 8.629158 TGTTGCTTGTTTCTTTCTATGTATGTT 58.371 29.630 0.00 0.00 0.00 2.71
7572 7869 6.591750 TTTGTTTACCACTTCAGAAACCAA 57.408 33.333 0.00 0.00 32.06 3.67
7575 7872 8.472007 TTGTTTACCACTTCAGAAACCAATAT 57.528 30.769 0.00 0.00 32.06 1.28
7653 7950 1.810030 GGGCGGTCTCAGTAAAGCG 60.810 63.158 0.00 0.00 39.26 4.68
7779 8076 2.324014 TTTGGAGTGTGCTGTCCGCT 62.324 55.000 0.00 0.00 40.11 5.52
7852 8149 6.038271 GGATATCGAAATAAGCCACACAAACT 59.962 38.462 0.00 0.00 0.00 2.66
7978 8275 3.439857 AAGCTTGACAGAAGCCCATTA 57.560 42.857 0.00 0.00 44.01 1.90
8008 8305 4.395231 GGTATTTCTAGCACCCTTGAACAC 59.605 45.833 0.00 0.00 33.58 3.32
8069 8367 5.886609 TCTTTTTCATGAGGTATCCCAACA 58.113 37.500 0.00 0.00 0.00 3.33
8318 8616 3.309436 CTTCCCATCACCGTCGCCA 62.309 63.158 0.00 0.00 0.00 5.69
8348 8646 2.005370 ACGAGTGGAACAACCCTCTA 57.995 50.000 0.00 0.00 44.16 2.43
8381 8679 0.468029 CCCAGCAACCAAGGAACAGT 60.468 55.000 0.00 0.00 0.00 3.55
8390 8688 1.228552 AAGGAACAGTGCGGCCAAT 60.229 52.632 2.24 0.00 0.00 3.16
8534 8832 3.188048 CGCTGCAAGACTTTGATTTCTCT 59.812 43.478 0.00 0.00 36.36 3.10
9171 9485 8.692110 TGCATCATTTCACATTTGATAGAAAC 57.308 30.769 0.00 0.00 33.35 2.78
9182 9496 9.014297 CACATTTGATAGAAACTAGGAAAAGGT 57.986 33.333 0.00 0.00 0.00 3.50
9211 9525 6.435164 AGGACTAGAATATGGGTTTGCAATT 58.565 36.000 0.00 0.00 0.00 2.32
9213 9527 6.096846 GGACTAGAATATGGGTTTGCAATTGT 59.903 38.462 7.40 0.00 0.00 2.71
9225 9539 5.365133 GTTTGCAATTGTGAATAGTTTGCG 58.635 37.500 7.40 0.00 44.23 4.85
9241 9556 3.619233 TTGCGCAACTTTTCTACCTTC 57.381 42.857 21.02 0.00 0.00 3.46
9303 9618 6.476378 AGTTTAGCATCACTTAGTCCAACAT 58.524 36.000 0.00 0.00 0.00 2.71
9321 9636 4.732285 ACATTACAAAAGAGTGACTGCG 57.268 40.909 0.00 0.00 0.00 5.18
9325 9640 1.940613 ACAAAAGAGTGACTGCGGTTC 59.059 47.619 0.00 0.00 0.00 3.62
9340 9667 2.093152 GCGGTTCGAAAACGTGTCATAT 59.907 45.455 20.17 0.00 36.16 1.78
9405 9732 3.827008 TCAAGCACAAGAGAGTTGTCT 57.173 42.857 0.00 0.00 34.86 3.41
9413 9740 7.445945 AGCACAAGAGAGTTGTCTAGTTAATT 58.554 34.615 0.00 0.00 30.97 1.40
9414 9741 7.386299 AGCACAAGAGAGTTGTCTAGTTAATTG 59.614 37.037 0.00 0.00 30.97 2.32
9429 9756 8.255206 TCTAGTTAATTGACGAAAAGATAGGCA 58.745 33.333 0.00 0.00 0.00 4.75
9454 9781 3.021269 TCATTACAGACACGACCACAC 57.979 47.619 0.00 0.00 0.00 3.82
9485 9812 0.680618 CCAAAGCATGAAACCCTGCA 59.319 50.000 0.00 0.00 40.88 4.41
9522 9849 0.941542 TCAAACACTAGCAACGTGCC 59.058 50.000 6.39 0.00 46.52 5.01
9580 9909 0.831307 ATGAACCCTAGCGAGAACCC 59.169 55.000 0.00 0.00 0.00 4.11
9593 9922 2.357637 CGAGAACCCTTTGAGCAAAACA 59.642 45.455 0.00 0.00 0.00 2.83
9598 9927 1.885887 CCCTTTGAGCAAAACATCGGA 59.114 47.619 0.00 0.00 0.00 4.55
9601 9930 3.300009 CTTTGAGCAAAACATCGGACAC 58.700 45.455 0.00 0.00 0.00 3.67
9614 9943 1.202758 TCGGACACCAGCAAAATCACT 60.203 47.619 0.00 0.00 0.00 3.41
9618 9947 1.682854 ACACCAGCAAAATCACTGTGG 59.317 47.619 8.11 0.00 31.76 4.17
9627 9956 4.209080 GCAAAATCACTGTGGCAACTAAAC 59.791 41.667 8.11 0.00 37.61 2.01
9635 9964 2.890311 TGTGGCAACTAAACCCATGAAG 59.110 45.455 0.00 0.00 37.61 3.02
9647 9976 4.348863 ACCCATGAAGATATGCAGAGAC 57.651 45.455 0.00 0.00 0.00 3.36
9701 10030 8.950208 ATAAAGCTGACTAGACAACCTTAATC 57.050 34.615 0.00 0.00 0.00 1.75
9706 10035 6.299805 TGACTAGACAACCTTAATCTGCAT 57.700 37.500 0.00 0.00 0.00 3.96
9707 10036 6.341316 TGACTAGACAACCTTAATCTGCATC 58.659 40.000 0.00 0.00 0.00 3.91
9708 10037 5.352284 ACTAGACAACCTTAATCTGCATCG 58.648 41.667 0.00 0.00 0.00 3.84
9727 10056 2.093869 TCGTGTAACCAGCATAGGGAAC 60.094 50.000 0.00 0.00 0.00 3.62
9729 10058 3.681593 GTGTAACCAGCATAGGGAACAA 58.318 45.455 0.00 0.00 30.64 2.83
9730 10059 3.439129 GTGTAACCAGCATAGGGAACAAC 59.561 47.826 0.00 0.00 30.64 3.32
9731 10060 2.215942 AACCAGCATAGGGAACAACC 57.784 50.000 0.00 0.00 38.08 3.77
9732 10061 0.035439 ACCAGCATAGGGAACAACCG 60.035 55.000 0.00 0.00 40.11 4.44
9736 10065 1.743623 CATAGGGAACAACCGCGCA 60.744 57.895 8.75 0.00 40.11 6.09
9764 10093 1.202200 CCGTAGAGAAGAGGCGTGAAG 60.202 57.143 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
179 180 4.498520 CGTCGCTCTGCATCCCGT 62.499 66.667 0.00 0.00 0.00 5.28
231 232 3.508840 GGAATGGGTCCAAGCGCG 61.509 66.667 0.00 0.00 46.97 6.86
255 259 7.874016 TCACTACACATAATAACCACGAGTTTT 59.126 33.333 0.00 0.00 40.05 2.43
289 293 1.673626 GCGAATAACACGAAGGGGTCA 60.674 52.381 0.00 0.00 0.00 4.02
298 302 2.936498 AGGATTCAAGGCGAATAACACG 59.064 45.455 0.00 0.00 44.65 4.49
338 342 0.814010 ATAAAGATGTCGCGTGGGGC 60.814 55.000 5.77 0.00 38.69 5.80
345 349 5.036737 CCAAATGGAACATAAAGATGTCGC 58.963 41.667 0.00 0.00 45.93 5.19
352 356 4.222588 TTGGAGGCCAAATGGAACATAAAG 59.777 41.667 5.01 0.00 40.49 1.85
367 371 0.919710 AAGGTGGATAGTTGGAGGCC 59.080 55.000 0.00 0.00 0.00 5.19
408 412 5.521010 CCCATGTCGCTACTTAAATTCGTTA 59.479 40.000 0.00 0.00 0.00 3.18
435 439 1.754226 GCTCTCTCTCCCGAAACTGAT 59.246 52.381 0.00 0.00 0.00 2.90
447 451 1.029408 ATGAGTCGCACGCTCTCTCT 61.029 55.000 13.03 2.53 34.30 3.10
448 452 0.865218 CATGAGTCGCACGCTCTCTC 60.865 60.000 13.03 6.69 34.30 3.20
489 493 3.541632 CCACCCATGTCGCTACTTAATT 58.458 45.455 0.00 0.00 0.00 1.40
561 565 3.891366 CGATTTATTGGGCCTCAAATCCT 59.109 43.478 21.58 5.29 39.05 3.24
564 568 5.200483 TCTTCGATTTATTGGGCCTCAAAT 58.800 37.500 4.53 7.65 39.05 2.32
672 689 7.993101 TGGTCAATCATCATTTCATTTCTCTC 58.007 34.615 0.00 0.00 0.00 3.20
877 894 1.770518 GGATTGGGGATCGAGGGGT 60.771 63.158 0.00 0.00 35.49 4.95
958 975 2.095364 GCACTGCATCAAGGTCAAGAAG 60.095 50.000 0.00 0.00 0.00 2.85
1319 1349 2.604174 CGCGGAAGAAAAGCACGGT 61.604 57.895 0.00 0.00 0.00 4.83
1369 1399 1.570857 CCTGTCCCTGCAACCCCATA 61.571 60.000 0.00 0.00 0.00 2.74
1499 1529 1.456196 CGATCCTAAGAGAGCCGCCA 61.456 60.000 0.00 0.00 0.00 5.69
1546 1576 1.225983 CTCTCCTCGAGCCTCTGGA 59.774 63.158 6.99 0.00 31.99 3.86
1637 1667 2.842208 TTGAAAGCAACGGTGAAGTG 57.158 45.000 3.55 0.00 0.00 3.16
1696 1726 7.742767 AGGTACCAACTCAAACTAACTACAAT 58.257 34.615 15.94 0.00 0.00 2.71
1836 1870 1.896220 TCACTTCCATGACCTGTTGC 58.104 50.000 0.00 0.00 0.00 4.17
1919 1953 1.481871 GGTACACAGCAGGGCTAGTA 58.518 55.000 0.00 0.00 36.40 1.82
1929 1963 2.351726 GTCATGGAATTCGGTACACAGC 59.648 50.000 0.00 0.00 0.00 4.40
1931 1965 3.259625 TCAGTCATGGAATTCGGTACACA 59.740 43.478 0.00 0.00 0.00 3.72
2183 2223 7.390823 TGGTAGCACTGTGAAGACATAATAAA 58.609 34.615 12.86 0.00 0.00 1.40
2198 2238 3.243839 ACAAAAGGCAAATGGTAGCACTG 60.244 43.478 0.00 0.00 0.00 3.66
2201 2241 2.697751 ACACAAAAGGCAAATGGTAGCA 59.302 40.909 0.00 0.00 0.00 3.49
2221 2261 8.778358 ACTGAAATATGAAGTCAAAGAGTCAAC 58.222 33.333 0.00 0.00 0.00 3.18
2233 2273 4.706962 GCCCTTCCAACTGAAATATGAAGT 59.293 41.667 0.00 0.00 31.06 3.01
2235 2275 3.694072 CGCCCTTCCAACTGAAATATGAA 59.306 43.478 0.00 0.00 31.06 2.57
2236 2276 3.278574 CGCCCTTCCAACTGAAATATGA 58.721 45.455 0.00 0.00 31.06 2.15
2285 2325 6.447162 GTTTTTCTCAGTATCAACCAAAGGG 58.553 40.000 0.00 0.00 41.29 3.95
2667 2707 6.778821 TGAAGACAATAATCTGAGGTTGGAA 58.221 36.000 0.00 0.00 0.00 3.53
2727 2767 2.182312 AGGAGGGATAAGATAGGTGCCA 59.818 50.000 0.00 0.00 0.00 4.92
3303 3357 2.961741 TGGTGAGGCTTTATTTGTGCAA 59.038 40.909 0.00 0.00 0.00 4.08
3510 3564 0.323087 AAAGGCCGGGCGTTTCTAAT 60.323 50.000 28.57 11.20 41.75 1.73
3522 3576 0.743345 CCCTCGGAAGTAAAAGGCCG 60.743 60.000 0.00 0.00 44.83 6.13
3604 3658 5.825593 ACAGACCCTTCACTTTCTGATAA 57.174 39.130 4.51 0.00 38.19 1.75
3985 4043 1.641577 GACGGCCTAACTTACTGCAG 58.358 55.000 13.48 13.48 0.00 4.41
4153 4216 8.402472 CAGATTCACCTACAACAAACAACTTAA 58.598 33.333 0.00 0.00 0.00 1.85
4158 4221 6.826231 TCTTCAGATTCACCTACAACAAACAA 59.174 34.615 0.00 0.00 0.00 2.83
4609 4675 3.396685 AGAGTAGAGGAGTGGCAGAAT 57.603 47.619 0.00 0.00 0.00 2.40
4647 4713 9.586435 GGAATACAAAAGTTGAGGATTTATTGG 57.414 33.333 0.00 0.00 0.00 3.16
4688 4754 4.402793 ACATCTTGCACGATAAGAGTAGGT 59.597 41.667 5.24 0.00 37.56 3.08
4733 4799 7.827729 ACAGGGTAGACAAATAAAGGAATACAC 59.172 37.037 0.00 0.00 0.00 2.90
4958 5025 2.431782 CAAATATTCCTTGCCCCTGTGG 59.568 50.000 0.00 0.00 37.09 4.17
5125 5192 0.674534 ATTCTAGCCCCGTAGCTTCG 59.325 55.000 5.67 5.67 41.41 3.79
5218 5285 3.826157 CCCTCAAATTACTGGAAACTGCA 59.174 43.478 0.00 0.00 0.00 4.41
5321 5388 0.179076 TGCGGTACTGATCCATGCAG 60.179 55.000 5.68 0.00 39.26 4.41
5592 5662 4.142337 TGTCGCTGAAACGGATGTATCTAA 60.142 41.667 0.00 0.00 0.00 2.10
5721 5792 1.753073 AGGAATTGCCATGCTTGCTAC 59.247 47.619 0.00 0.00 40.02 3.58
5787 5859 8.953368 AATCAAATAAGAAAGGATGGCAATTC 57.047 30.769 0.00 0.00 0.00 2.17
5968 6231 2.281484 CCACAGAACCACACCCCG 60.281 66.667 0.00 0.00 0.00 5.73
5981 6244 0.756294 ACGACAGATCAACACCCACA 59.244 50.000 0.00 0.00 0.00 4.17
6067 6331 5.072055 TGCATCTGTTTTCTCAAGGATCAA 58.928 37.500 0.00 0.00 0.00 2.57
6121 6385 7.402054 AGGAGACATATGGAATAACACACAAA 58.598 34.615 7.80 0.00 29.06 2.83
6274 6539 8.776470 AGTTTAACCAAAATTGAATGCTGAATG 58.224 29.630 0.00 0.00 0.00 2.67
6427 6692 4.327680 ACTTAAGCTTGAAGCCTCGAATT 58.672 39.130 14.45 2.89 43.77 2.17
6494 6762 7.414319 CCAACAACTTTTTGCACAATCAATCTT 60.414 33.333 0.00 0.00 36.00 2.40
6495 6763 6.037391 CCAACAACTTTTTGCACAATCAATCT 59.963 34.615 0.00 0.00 36.00 2.40
6496 6764 6.193761 CCAACAACTTTTTGCACAATCAATC 58.806 36.000 0.00 0.00 36.00 2.67
6497 6765 5.066246 CCCAACAACTTTTTGCACAATCAAT 59.934 36.000 0.00 0.00 36.00 2.57
6498 6766 4.394300 CCCAACAACTTTTTGCACAATCAA 59.606 37.500 0.00 0.00 36.00 2.57
6499 6767 3.937706 CCCAACAACTTTTTGCACAATCA 59.062 39.130 0.00 0.00 36.00 2.57
6500 6768 3.938334 ACCCAACAACTTTTTGCACAATC 59.062 39.130 0.00 0.00 36.00 2.67
6501 6769 3.938334 GACCCAACAACTTTTTGCACAAT 59.062 39.130 0.00 0.00 36.00 2.71
6502 6770 3.007398 AGACCCAACAACTTTTTGCACAA 59.993 39.130 0.00 0.00 36.00 3.33
6503 6771 2.564947 AGACCCAACAACTTTTTGCACA 59.435 40.909 0.00 0.00 36.00 4.57
6504 6772 3.186909 GAGACCCAACAACTTTTTGCAC 58.813 45.455 0.00 0.00 36.00 4.57
6505 6773 2.828520 TGAGACCCAACAACTTTTTGCA 59.171 40.909 0.00 0.00 36.00 4.08
6506 6774 3.518634 TGAGACCCAACAACTTTTTGC 57.481 42.857 0.00 0.00 36.00 3.68
6507 6775 4.805192 CACATGAGACCCAACAACTTTTTG 59.195 41.667 0.00 0.00 38.83 2.44
6508 6776 4.709397 TCACATGAGACCCAACAACTTTTT 59.291 37.500 0.00 0.00 0.00 1.94
6509 6777 4.097892 GTCACATGAGACCCAACAACTTTT 59.902 41.667 11.80 0.00 32.36 2.27
6510 6778 3.632145 GTCACATGAGACCCAACAACTTT 59.368 43.478 11.80 0.00 32.36 2.66
6511 6779 3.214328 GTCACATGAGACCCAACAACTT 58.786 45.455 11.80 0.00 32.36 2.66
6512 6780 2.172505 TGTCACATGAGACCCAACAACT 59.827 45.455 18.89 0.00 37.73 3.16
6513 6781 2.571212 TGTCACATGAGACCCAACAAC 58.429 47.619 18.89 0.00 37.73 3.32
6514 6782 3.289407 TTGTCACATGAGACCCAACAA 57.711 42.857 18.89 5.68 37.73 2.83
6515 6783 3.289407 TTTGTCACATGAGACCCAACA 57.711 42.857 18.89 0.00 37.73 3.33
6516 6784 3.057315 CCATTTGTCACATGAGACCCAAC 60.057 47.826 18.89 0.00 37.73 3.77
6517 6785 3.156293 CCATTTGTCACATGAGACCCAA 58.844 45.455 18.89 12.60 37.73 4.12
6518 6786 2.374839 TCCATTTGTCACATGAGACCCA 59.625 45.455 18.89 7.28 37.73 4.51
6537 6833 9.535878 CTATTTCACTACTTTCAGGTTCTATCC 57.464 37.037 0.00 0.00 0.00 2.59
6543 6839 5.940470 CCTGCTATTTCACTACTTTCAGGTT 59.060 40.000 0.00 0.00 35.20 3.50
6552 6848 4.081642 TGGTGAGACCTGCTATTTCACTAC 60.082 45.833 3.35 0.00 39.58 2.73
6586 6882 7.287005 TCTCACCGTACCACTTATCTATTGAAT 59.713 37.037 0.00 0.00 0.00 2.57
6621 6917 5.874093 TGCCATATTCAAACAACCCAAAAT 58.126 33.333 0.00 0.00 0.00 1.82
6735 7031 4.123506 GAGGACAAGGCTGCTAGAATTAC 58.876 47.826 0.00 0.00 0.00 1.89
6752 7048 2.032799 TCAACACGTGCAAAATGAGGAC 59.967 45.455 17.22 0.00 0.00 3.85
6763 7059 3.559238 AAGGAAATCATCAACACGTGC 57.441 42.857 17.22 0.00 0.00 5.34
6789 7085 6.563422 TGCATAGAATTGCTGTAAATCCAAC 58.437 36.000 0.00 0.00 43.18 3.77
6848 7144 0.107654 GGACACATGCAGGGAGGTAC 60.108 60.000 2.31 0.00 0.00 3.34
6861 7157 4.704540 ACTGAATGTTGACAAAAGGACACA 59.295 37.500 0.00 0.00 0.00 3.72
6873 7169 7.230849 AGAAATATGCCAAACTGAATGTTGA 57.769 32.000 0.00 0.00 39.13 3.18
6966 7262 6.376864 TCTTTTGATTCACCTGAAACAAGTCA 59.623 34.615 9.75 0.00 44.00 3.41
6987 7283 9.243105 TCTAGCTTATTTAGTTGGCATTTCTTT 57.757 29.630 0.00 0.00 0.00 2.52
7000 7296 9.988350 TCGAATTGCTTTTTCTAGCTTATTTAG 57.012 29.630 0.00 0.00 41.76 1.85
7388 7685 8.565416 GCTGGTATAAACAAGACTACACTTTTT 58.435 33.333 0.00 0.00 0.00 1.94
7389 7686 7.717875 TGCTGGTATAAACAAGACTACACTTTT 59.282 33.333 0.00 0.00 0.00 2.27
7390 7687 7.221450 TGCTGGTATAAACAAGACTACACTTT 58.779 34.615 0.00 0.00 0.00 2.66
7391 7688 6.765403 TGCTGGTATAAACAAGACTACACTT 58.235 36.000 0.00 0.00 0.00 3.16
7392 7689 6.354794 TGCTGGTATAAACAAGACTACACT 57.645 37.500 0.00 0.00 0.00 3.55
7393 7690 7.119262 ACATTGCTGGTATAAACAAGACTACAC 59.881 37.037 0.00 0.00 0.00 2.90
7394 7691 7.165485 ACATTGCTGGTATAAACAAGACTACA 58.835 34.615 0.00 0.00 0.00 2.74
7395 7692 7.611213 ACATTGCTGGTATAAACAAGACTAC 57.389 36.000 0.00 0.00 0.00 2.73
7396 7693 8.511321 CAAACATTGCTGGTATAAACAAGACTA 58.489 33.333 0.00 0.00 0.00 2.59
7397 7694 7.014230 ACAAACATTGCTGGTATAAACAAGACT 59.986 33.333 0.00 0.00 0.00 3.24
7398 7695 7.145323 ACAAACATTGCTGGTATAAACAAGAC 58.855 34.615 0.00 0.00 0.00 3.01
7399 7696 7.283625 ACAAACATTGCTGGTATAAACAAGA 57.716 32.000 0.00 0.00 0.00 3.02
7400 7697 7.116233 GGAACAAACATTGCTGGTATAAACAAG 59.884 37.037 0.00 0.00 0.00 3.16
7401 7698 6.926272 GGAACAAACATTGCTGGTATAAACAA 59.074 34.615 0.00 0.00 0.00 2.83
7402 7699 6.266558 AGGAACAAACATTGCTGGTATAAACA 59.733 34.615 0.00 0.00 0.00 2.83
7403 7700 6.687604 AGGAACAAACATTGCTGGTATAAAC 58.312 36.000 0.00 0.00 0.00 2.01
7404 7701 6.909550 AGGAACAAACATTGCTGGTATAAA 57.090 33.333 0.00 0.00 0.00 1.40
7405 7702 8.410673 TTTAGGAACAAACATTGCTGGTATAA 57.589 30.769 0.00 0.00 31.94 0.98
7406 7703 8.588290 ATTTAGGAACAAACATTGCTGGTATA 57.412 30.769 0.00 0.00 31.94 1.47
7407 7704 6.909550 TTTAGGAACAAACATTGCTGGTAT 57.090 33.333 0.00 0.00 31.94 2.73
7408 7705 6.909550 ATTTAGGAACAAACATTGCTGGTA 57.090 33.333 0.00 0.00 31.94 3.25
7409 7706 5.806654 ATTTAGGAACAAACATTGCTGGT 57.193 34.783 0.00 0.00 31.94 4.00
7410 7707 7.775120 AGATATTTAGGAACAAACATTGCTGG 58.225 34.615 0.00 0.00 31.94 4.85
7411 7708 8.461222 TGAGATATTTAGGAACAAACATTGCTG 58.539 33.333 0.00 0.00 31.94 4.41
7434 7731 7.169308 GCCAGATTAATGCATCTCAAAAATGAG 59.831 37.037 0.00 0.00 37.28 2.90
7435 7732 6.982141 GCCAGATTAATGCATCTCAAAAATGA 59.018 34.615 0.00 0.00 30.50 2.57
7436 7733 6.759356 TGCCAGATTAATGCATCTCAAAAATG 59.241 34.615 0.00 0.00 30.50 2.32
7437 7734 6.880484 TGCCAGATTAATGCATCTCAAAAAT 58.120 32.000 0.00 0.00 30.50 1.82
7438 7735 6.283544 TGCCAGATTAATGCATCTCAAAAA 57.716 33.333 0.00 0.00 30.50 1.94
7439 7736 5.918426 TGCCAGATTAATGCATCTCAAAA 57.082 34.783 0.00 0.00 30.50 2.44
7440 7737 6.474140 AATGCCAGATTAATGCATCTCAAA 57.526 33.333 11.04 0.00 44.49 2.69
7441 7738 5.278120 CGAATGCCAGATTAATGCATCTCAA 60.278 40.000 11.04 0.00 44.49 3.02
7442 7739 4.214758 CGAATGCCAGATTAATGCATCTCA 59.785 41.667 11.04 0.00 44.49 3.27
7443 7740 4.720090 CGAATGCCAGATTAATGCATCTC 58.280 43.478 11.04 9.92 44.49 2.75
7444 7741 3.057736 GCGAATGCCAGATTAATGCATCT 60.058 43.478 11.04 0.00 44.49 2.90
7445 7742 3.057736 AGCGAATGCCAGATTAATGCATC 60.058 43.478 11.04 5.79 44.49 3.91
7447 7744 2.300433 AGCGAATGCCAGATTAATGCA 58.700 42.857 0.00 0.00 44.31 3.96
7448 7745 4.691860 ATAGCGAATGCCAGATTAATGC 57.308 40.909 0.00 0.00 44.31 3.56
7449 7746 7.369803 ACTAATAGCGAATGCCAGATTAATG 57.630 36.000 0.00 0.00 44.31 1.90
7450 7747 6.595716 GGACTAATAGCGAATGCCAGATTAAT 59.404 38.462 0.00 0.00 44.31 1.40
7451 7748 5.932303 GGACTAATAGCGAATGCCAGATTAA 59.068 40.000 0.00 0.00 44.31 1.40
7452 7749 5.011635 TGGACTAATAGCGAATGCCAGATTA 59.988 40.000 0.00 0.00 44.31 1.75
7453 7750 4.202357 TGGACTAATAGCGAATGCCAGATT 60.202 41.667 0.00 0.00 44.31 2.40
7454 7751 3.324846 TGGACTAATAGCGAATGCCAGAT 59.675 43.478 0.00 0.00 44.31 2.90
7455 7752 2.698274 TGGACTAATAGCGAATGCCAGA 59.302 45.455 0.00 0.00 44.31 3.86
7462 7759 8.857098 AGTTATACAGAATGGACTAATAGCGAA 58.143 33.333 0.00 0.00 43.62 4.70
7496 7793 6.301169 ACACTGGAAACCAACCAATAAAAA 57.699 33.333 0.00 0.00 36.95 1.94
7779 8076 1.478654 GGGTCACTCTTTGGCAAAGGA 60.479 52.381 33.00 22.21 39.01 3.36
7826 8123 5.290493 TGTGTGGCTTATTTCGATATCCT 57.710 39.130 0.00 0.00 0.00 3.24
7852 8149 9.256477 CAACTATAGTGTCAAATAAATAGGCGA 57.744 33.333 6.06 0.00 0.00 5.54
7978 8275 3.621558 GGTGCTAGAAATACCTTGGCTT 58.378 45.455 0.00 0.00 0.00 4.35
8008 8305 8.984891 TCATCATGCCAAAGTTAAGTAAAATG 57.015 30.769 0.00 0.00 0.00 2.32
8348 8646 0.036875 GCTGGGTAGGTCTTGTGCTT 59.963 55.000 0.00 0.00 0.00 3.91
8381 8679 3.372730 GGAGCAACATTGGCCGCA 61.373 61.111 0.00 0.00 0.00 5.69
8390 8688 2.203788 AGGGACTCCGGAGCAACA 60.204 61.111 31.56 0.00 38.33 3.33
8393 8691 3.992641 TCCAGGGACTCCGGAGCA 61.993 66.667 31.56 5.17 34.60 4.26
8534 8832 2.040464 GGGATCTCCAGGCCTCCA 60.040 66.667 0.00 0.00 37.91 3.86
8930 9235 9.003658 GCAAATTATATAGTACTCCACTTGCAT 57.996 33.333 0.00 0.00 38.80 3.96
9015 9322 5.345741 GCCAAGTTAAATAACATGCAGTGTG 59.654 40.000 6.13 0.00 41.14 3.82
9171 9485 9.961264 ATTCTAGTCCTTTTAACCTTTTCCTAG 57.039 33.333 0.00 0.00 0.00 3.02
9182 9496 7.891183 TGCAAACCCATATTCTAGTCCTTTTAA 59.109 33.333 0.00 0.00 0.00 1.52
9188 9502 6.096846 ACAATTGCAAACCCATATTCTAGTCC 59.903 38.462 1.71 0.00 0.00 3.85
9225 9539 4.134563 TGACTGGAAGGTAGAAAAGTTGC 58.865 43.478 0.00 0.00 39.30 4.17
9241 9556 1.376424 AGCACAATCGCCTGACTGG 60.376 57.895 0.00 0.00 39.35 4.00
9280 9595 6.743575 ATGTTGGACTAAGTGATGCTAAAC 57.256 37.500 0.00 0.00 0.00 2.01
9286 9601 8.783093 TCTTTTGTAATGTTGGACTAAGTGATG 58.217 33.333 0.00 0.00 0.00 3.07
9303 9618 3.188159 ACCGCAGTCACTCTTTTGTAA 57.812 42.857 0.00 0.00 0.00 2.41
9382 9709 5.858381 AGACAACTCTCTTGTGCTTGATTA 58.142 37.500 0.00 0.00 31.96 1.75
9386 9713 4.626042 ACTAGACAACTCTCTTGTGCTTG 58.374 43.478 0.00 0.00 31.96 4.01
9389 9716 7.385205 TCAATTAACTAGACAACTCTCTTGTGC 59.615 37.037 0.00 0.00 31.96 4.57
9405 9732 8.780846 TTGCCTATCTTTTCGTCAATTAACTA 57.219 30.769 0.00 0.00 0.00 2.24
9413 9740 6.567687 TGATTTTTGCCTATCTTTTCGTCA 57.432 33.333 0.00 0.00 0.00 4.35
9414 9741 9.010366 GTAATGATTTTTGCCTATCTTTTCGTC 57.990 33.333 0.00 0.00 0.00 4.20
9429 9756 5.529430 TGTGGTCGTGTCTGTAATGATTTTT 59.471 36.000 0.00 0.00 0.00 1.94
9454 9781 3.130516 TCATGCTTTGGGAGTAGTCTACG 59.869 47.826 4.34 0.00 0.00 3.51
9456 9783 5.488341 GTTTCATGCTTTGGGAGTAGTCTA 58.512 41.667 0.00 0.00 0.00 2.59
9522 9849 2.823984 TGTTGATGGCTTGCAGTTTTG 58.176 42.857 0.00 0.00 0.00 2.44
9580 9909 3.300009 GTGTCCGATGTTTTGCTCAAAG 58.700 45.455 0.00 0.00 0.00 2.77
9593 9922 1.812571 GTGATTTTGCTGGTGTCCGAT 59.187 47.619 0.00 0.00 0.00 4.18
9598 9927 1.682854 CCACAGTGATTTTGCTGGTGT 59.317 47.619 0.62 0.00 37.07 4.16
9601 9930 0.675083 TGCCACAGTGATTTTGCTGG 59.325 50.000 0.62 0.00 37.07 4.85
9614 9943 2.666272 TCATGGGTTTAGTTGCCACA 57.334 45.000 0.00 0.00 0.00 4.17
9618 9947 5.067674 TGCATATCTTCATGGGTTTAGTTGC 59.932 40.000 0.00 0.00 0.00 4.17
9627 9956 4.620589 AGTCTCTGCATATCTTCATGGG 57.379 45.455 0.00 0.00 0.00 4.00
9635 9964 5.621104 CGGATGACCTTAGTCTCTGCATATC 60.621 48.000 0.00 0.00 43.91 1.63
9647 9976 4.094887 CCAAATGTTGACGGATGACCTTAG 59.905 45.833 0.00 0.00 0.00 2.18
9701 10030 1.372582 ATGCTGGTTACACGATGCAG 58.627 50.000 0.00 0.00 33.87 4.41
9706 10035 1.855295 TCCCTATGCTGGTTACACGA 58.145 50.000 0.00 0.00 0.00 4.35
9707 10036 2.277084 GTTCCCTATGCTGGTTACACG 58.723 52.381 0.00 0.00 0.00 4.49
9708 10037 3.343941 TGTTCCCTATGCTGGTTACAC 57.656 47.619 0.00 0.00 0.00 2.90
9727 10056 4.025401 GTGAAGGGTGCGCGGTTG 62.025 66.667 8.83 0.00 0.00 3.77
9731 10060 4.728102 TACGGTGAAGGGTGCGCG 62.728 66.667 0.00 0.00 0.00 6.86
9732 10061 2.813908 CTACGGTGAAGGGTGCGC 60.814 66.667 0.00 0.00 0.00 6.09
9736 10065 2.448453 CTCTTCTCTACGGTGAAGGGT 58.552 52.381 6.80 0.00 41.02 4.34
9746 10075 1.470112 GCCTTCACGCCTCTTCTCTAC 60.470 57.143 0.00 0.00 0.00 2.59
9764 10093 2.032178 GCACATAAAGTCATCCTTCGCC 59.968 50.000 0.00 0.00 31.27 5.54


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

AutoCloner maintained by Alex Coulton.