Multiple sequence alignment - TraesCS7D01G085300

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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 TraesCS7D01G085300 chr7D 100.000 4318 0 0 1 4318 52335196 52330879 0.000000e+00 7974.0
1 TraesCS7D01G085300 chr7D 85.915 71 7 3 226 294 52245733 52245664 5.990000e-09 73.1
2 TraesCS7D01G085300 chr7D 85.714 56 6 1 3801 3856 105994374 105994427 1.680000e-04 58.4
3 TraesCS7D01G085300 chr4A 88.627 2462 178 43 1782 4173 666939862 666937433 0.000000e+00 2902.0
4 TraesCS7D01G085300 chr4A 89.448 834 70 13 1 828 666941779 666940958 0.000000e+00 1037.0
5 TraesCS7D01G085300 chr4A 85.941 882 75 28 826 1679 666940779 666939919 0.000000e+00 896.0
6 TraesCS7D01G085300 chr4A 81.378 929 108 30 1782 2664 59283369 59284278 0.000000e+00 697.0
7 TraesCS7D01G085300 chr4A 81.871 342 45 14 1207 1538 59282794 59283128 5.500000e-69 272.0
8 TraesCS7D01G085300 chr4A 82.043 323 45 9 3032 3345 59285093 59285411 3.310000e-66 263.0
9 TraesCS7D01G085300 chr4A 86.916 214 18 5 2777 2987 59284881 59285087 9.340000e-57 231.0
10 TraesCS7D01G085300 chr4A 92.857 126 9 0 4193 4318 666937215 666937090 2.650000e-42 183.0
11 TraesCS7D01G085300 chr4A 87.143 70 5 4 3788 3856 475917428 475917362 4.630000e-10 76.8
12 TraesCS7D01G085300 chr7A 92.956 1306 59 10 2770 4064 54833717 54832434 0.000000e+00 1871.0
13 TraesCS7D01G085300 chr7A 94.860 681 34 1 1770 2449 54838003 54837323 0.000000e+00 1062.0
14 TraesCS7D01G085300 chr7A 87.540 939 66 17 843 1739 54838927 54837998 0.000000e+00 1038.0
15 TraesCS7D01G085300 chr7A 91.234 308 20 5 2443 2747 54834092 54833789 3.110000e-111 412.0
16 TraesCS7D01G085300 chr7A 89.706 68 2 5 3795 3860 68229097 68229033 9.950000e-12 82.4
17 TraesCS7D01G085300 chr7A 83.099 71 9 2 3787 3856 110822411 110822479 1.300000e-05 62.1
18 TraesCS7D01G085300 chr7A 100.000 32 0 0 2997 3028 54833563 54833532 4.660000e-05 60.2
19 TraesCS7D01G085300 chr2D 81.195 1255 150 44 1782 2988 647968783 647969999 0.000000e+00 931.0
20 TraesCS7D01G085300 chr2D 85.153 229 27 7 907 1128 647967946 647968174 1.210000e-55 228.0
21 TraesCS7D01G085300 chrUn 80.888 1261 151 49 1782 2991 31374316 31373095 0.000000e+00 911.0
22 TraesCS7D01G085300 chrUn 78.788 528 80 17 1225 1737 31374831 31374321 4.160000e-85 326.0
23 TraesCS7D01G085300 chrUn 84.483 232 28 6 907 1132 31375139 31374910 5.620000e-54 222.0
24 TraesCS7D01G085300 chr2B 80.207 1258 145 56 1782 2975 781831901 781830684 0.000000e+00 848.0
25 TraesCS7D01G085300 chr2B 77.093 860 146 31 907 1736 781832745 781831907 2.370000e-122 449.0
26 TraesCS7D01G085300 chr2B 87.571 177 12 9 2804 2975 781826379 781826208 3.410000e-46 196.0
27 TraesCS7D01G085300 chr2B 89.286 56 3 3 3801 3855 97387850 97387903 2.790000e-07 67.6
28 TraesCS7D01G085300 chr4D 82.385 931 98 32 1782 2664 401532219 401533131 0.000000e+00 750.0
29 TraesCS7D01G085300 chr4D 77.098 572 80 24 1207 1737 401531653 401532214 2.540000e-72 283.0
30 TraesCS7D01G085300 chr4D 81.437 334 49 9 3008 3334 401533495 401533822 1.190000e-65 261.0
31 TraesCS7D01G085300 chr4B 83.380 716 74 21 1782 2462 496548372 496549077 4.740000e-174 621.0
32 TraesCS7D01G085300 chr4B 77.442 563 85 19 1207 1737 496547815 496548367 9.080000e-77 298.0
33 TraesCS7D01G085300 chr4B 81.735 219 22 10 2534 2747 496549249 496549454 2.670000e-37 167.0
34 TraesCS7D01G085300 chr4B 86.822 129 9 6 3008 3133 496549749 496549872 2.090000e-28 137.0
35 TraesCS7D01G085300 chr7B 80.663 181 27 3 2053 2226 159182916 159182737 2.710000e-27 134.0
36 TraesCS7D01G085300 chr3D 94.545 55 3 0 664 718 452820183 452820237 7.690000e-13 86.1
37 TraesCS7D01G085300 chr5A 82.857 70 9 2 3788 3856 411475048 411475115 4.660000e-05 60.2
38 TraesCS7D01G085300 chr1B 85.714 56 5 3 3801 3855 510600380 510600327 6.030000e-04 56.5


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 TraesCS7D01G085300 chr7D 52330879 52335196 4317 True 7974.000000 7974 100.000000 1 4318 1 chr7D.!!$R2 4317
1 TraesCS7D01G085300 chr4A 666937090 666941779 4689 True 1254.500000 2902 89.218250 1 4318 4 chr4A.!!$R2 4317
2 TraesCS7D01G085300 chr4A 59282794 59285411 2617 False 365.750000 697 83.052000 1207 3345 4 chr4A.!!$F1 2138
3 TraesCS7D01G085300 chr7A 54832434 54838927 6493 True 888.640000 1871 93.318000 843 4064 5 chr7A.!!$R2 3221
4 TraesCS7D01G085300 chr2D 647967946 647969999 2053 False 579.500000 931 83.174000 907 2988 2 chr2D.!!$F1 2081
5 TraesCS7D01G085300 chrUn 31373095 31375139 2044 True 486.333333 911 81.386333 907 2991 3 chrUn.!!$R1 2084
6 TraesCS7D01G085300 chr2B 781830684 781832745 2061 True 648.500000 848 78.650000 907 2975 2 chr2B.!!$R2 2068
7 TraesCS7D01G085300 chr4D 401531653 401533822 2169 False 431.333333 750 80.306667 1207 3334 3 chr4D.!!$F1 2127
8 TraesCS7D01G085300 chr4B 496547815 496549872 2057 False 305.750000 621 82.344750 1207 3133 4 chr4B.!!$F1 1926

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
357 385 0.671781 ATGCACTGAAGCGTCTGTCC 60.672 55.0 9.11 1.49 33.98 4.02 F
1177 1443 0.248866 CCGCCGGGCAAATTATCAAC 60.249 55.0 20.71 0.00 0.00 3.18 F
1646 1982 0.320374 AAACGCACCTCGGAGATGAA 59.680 50.0 2.78 0.00 43.86 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1525 1802 0.179081 GGAGACATACTTGCGTCCCC 60.179 60.000 0.00 0.0 32.33 4.81 R
2710 6467 2.158971 GGCCTTTCTTGTCCTGCAAAAA 60.159 45.455 0.00 0.0 36.53 1.94 R
3557 7916 1.475930 GGTTGGCCTATGCTCTCTTCC 60.476 57.143 3.32 0.0 37.74 3.46 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
33 34 2.769663 TGTAGTCCACACCTTGACAGTT 59.230 45.455 0.00 0.00 33.89 3.16
71 72 1.754803 TGGATCTACTACGTGGCCAAG 59.245 52.381 17.83 17.83 0.00 3.61
74 75 1.624336 TCTACTACGTGGCCAAGTGT 58.376 50.000 31.37 26.19 0.00 3.55
111 112 1.003003 TCGATCACTGAAACCATGCCA 59.997 47.619 0.00 0.00 0.00 4.92
128 129 5.163426 CCATGCCAAAGAATATTTAGTGCCA 60.163 40.000 0.00 0.00 0.00 4.92
129 130 6.463331 CCATGCCAAAGAATATTTAGTGCCAT 60.463 38.462 0.00 0.00 0.00 4.40
198 199 6.037786 TGTGAGAGGAGACGAACATAATTT 57.962 37.500 0.00 0.00 0.00 1.82
208 209 7.226720 GGAGACGAACATAATTTATGGATGTGT 59.773 37.037 18.24 11.85 40.47 3.72
273 274 3.875727 AGAGCATGGTCGATGAATTTCAG 59.124 43.478 18.64 0.00 33.31 3.02
303 331 3.649277 ATATGGCGGCGCGAGATCC 62.649 63.158 26.95 11.39 0.00 3.36
309 337 2.913765 CGGCGCGAGATCCTCTCAT 61.914 63.158 12.10 0.00 43.55 2.90
347 375 7.880713 TCTGGTTAAAATGTACTATGCACTGAA 59.119 33.333 0.00 0.00 0.00 3.02
348 376 8.039603 TGGTTAAAATGTACTATGCACTGAAG 57.960 34.615 0.00 0.00 0.00 3.02
349 377 6.967199 GGTTAAAATGTACTATGCACTGAAGC 59.033 38.462 0.00 0.00 0.00 3.86
350 378 4.864916 AAATGTACTATGCACTGAAGCG 57.135 40.909 0.00 0.00 37.31 4.68
351 379 3.526931 ATGTACTATGCACTGAAGCGT 57.473 42.857 0.00 0.00 37.31 5.07
352 380 2.876091 TGTACTATGCACTGAAGCGTC 58.124 47.619 0.00 0.00 37.31 5.19
353 381 2.492088 TGTACTATGCACTGAAGCGTCT 59.508 45.455 0.31 0.00 37.31 4.18
354 382 2.001812 ACTATGCACTGAAGCGTCTG 57.998 50.000 5.04 5.04 37.31 3.51
355 383 1.273606 ACTATGCACTGAAGCGTCTGT 59.726 47.619 6.36 6.36 36.45 3.41
356 384 1.923204 CTATGCACTGAAGCGTCTGTC 59.077 52.381 9.11 5.88 33.98 3.51
357 385 0.671781 ATGCACTGAAGCGTCTGTCC 60.672 55.000 9.11 1.49 33.98 4.02
358 386 1.300931 GCACTGAAGCGTCTGTCCA 60.301 57.895 9.11 0.00 33.98 4.02
359 387 0.880278 GCACTGAAGCGTCTGTCCAA 60.880 55.000 9.11 0.00 33.98 3.53
360 388 1.800805 CACTGAAGCGTCTGTCCAAT 58.199 50.000 9.11 0.00 33.98 3.16
361 389 2.146342 CACTGAAGCGTCTGTCCAATT 58.854 47.619 9.11 0.00 33.98 2.32
362 390 2.549754 CACTGAAGCGTCTGTCCAATTT 59.450 45.455 9.11 0.00 33.98 1.82
363 391 3.745975 CACTGAAGCGTCTGTCCAATTTA 59.254 43.478 9.11 0.00 33.98 1.40
364 392 3.746492 ACTGAAGCGTCTGTCCAATTTAC 59.254 43.478 6.36 0.00 30.69 2.01
365 393 2.734606 TGAAGCGTCTGTCCAATTTACG 59.265 45.455 0.31 0.00 36.67 3.18
366 394 2.736144 AGCGTCTGTCCAATTTACGA 57.264 45.000 0.00 0.00 35.66 3.43
367 395 3.247006 AGCGTCTGTCCAATTTACGAT 57.753 42.857 0.00 0.00 35.66 3.73
368 396 3.187700 AGCGTCTGTCCAATTTACGATC 58.812 45.455 0.00 0.00 35.66 3.69
369 397 3.119101 AGCGTCTGTCCAATTTACGATCT 60.119 43.478 0.00 0.00 35.66 2.75
370 398 3.000322 GCGTCTGTCCAATTTACGATCTG 60.000 47.826 0.00 0.00 35.66 2.90
371 399 4.174009 CGTCTGTCCAATTTACGATCTGT 58.826 43.478 0.00 0.00 35.66 3.41
372 400 4.625742 CGTCTGTCCAATTTACGATCTGTT 59.374 41.667 0.00 0.00 35.66 3.16
373 401 5.120208 CGTCTGTCCAATTTACGATCTGTTT 59.880 40.000 0.00 0.00 35.66 2.83
374 402 6.534934 GTCTGTCCAATTTACGATCTGTTTC 58.465 40.000 0.00 0.00 0.00 2.78
375 403 5.642063 TCTGTCCAATTTACGATCTGTTTCC 59.358 40.000 0.00 0.00 0.00 3.13
376 404 5.309638 TGTCCAATTTACGATCTGTTTCCA 58.690 37.500 0.00 0.00 0.00 3.53
377 405 5.180492 TGTCCAATTTACGATCTGTTTCCAC 59.820 40.000 0.00 0.00 0.00 4.02
378 406 4.698304 TCCAATTTACGATCTGTTTCCACC 59.302 41.667 0.00 0.00 0.00 4.61
379 407 4.436852 CCAATTTACGATCTGTTTCCACCG 60.437 45.833 0.00 0.00 0.00 4.94
380 408 3.389925 TTTACGATCTGTTTCCACCGT 57.610 42.857 0.00 0.00 0.00 4.83
388 416 2.093394 TCTGTTTCCACCGTTGTCTTCA 60.093 45.455 0.00 0.00 0.00 3.02
394 422 4.054780 TCCACCGTTGTCTTCATATAGC 57.945 45.455 0.00 0.00 0.00 2.97
410 438 7.615582 TCATATAGCTGAGGTTTGTTTTGAG 57.384 36.000 0.00 0.00 0.00 3.02
471 499 4.814234 ACGATAATGAACGTGCCATTGTAT 59.186 37.500 20.27 10.88 41.17 2.29
486 514 6.098679 GCCATTGTATGCATGTCAAAAGTTA 58.901 36.000 10.16 0.00 0.00 2.24
487 515 6.254157 GCCATTGTATGCATGTCAAAAGTTAG 59.746 38.462 10.16 3.80 0.00 2.34
488 516 6.254157 CCATTGTATGCATGTCAAAAGTTAGC 59.746 38.462 10.16 0.00 0.00 3.09
510 540 3.551890 CGGTATCGACATCAAAAGGAGTG 59.448 47.826 0.00 0.00 39.00 3.51
541 571 4.154015 TGTGGCAACTTGATTATTCACTCG 59.846 41.667 0.00 0.00 37.61 4.18
543 573 3.689649 GGCAACTTGATTATTCACTCGGT 59.310 43.478 0.00 0.00 0.00 4.69
568 598 7.636259 TGCAACTTTTAAGATGATTTTTCCG 57.364 32.000 4.19 0.00 31.18 4.30
569 599 6.145371 TGCAACTTTTAAGATGATTTTTCCGC 59.855 34.615 4.19 0.00 31.18 5.54
577 607 3.694566 AGATGATTTTTCCGCCCTAACAC 59.305 43.478 0.00 0.00 0.00 3.32
587 617 1.336148 CGCCCTAACACACACTTACGA 60.336 52.381 0.00 0.00 0.00 3.43
603 633 4.019591 ACTTACGAGATTTAGGCCCTGTTT 60.020 41.667 0.00 0.00 0.00 2.83
614 644 2.506957 CCCTGTTTGGCAACCCACC 61.507 63.158 0.00 0.00 41.97 4.61
619 649 1.456705 TTTGGCAACCCACCCACTC 60.457 57.895 0.00 0.00 41.97 3.51
670 700 2.346803 TCCGTGATTTTCTACTGCAGC 58.653 47.619 15.27 0.00 0.00 5.25
673 703 2.028523 CGTGATTTTCTACTGCAGCTCG 59.971 50.000 15.27 3.75 0.00 5.03
728 758 3.119388 CGATTCCGAACAGGGTGTTAGTA 60.119 47.826 0.00 0.00 41.28 1.82
758 788 4.724399 TCTGGTCCTGCTAAAATCAAACA 58.276 39.130 0.00 0.00 0.00 2.83
764 794 5.569059 GTCCTGCTAAAATCAAACAATGACG 59.431 40.000 0.00 0.00 41.93 4.35
776 806 5.410132 TCAAACAATGACGGACAAATCGTAT 59.590 36.000 0.00 0.00 41.22 3.06
813 843 9.695884 GCGATTTGAAAGTTAACAAAATTTCAA 57.304 25.926 20.77 20.77 45.16 2.69
891 1104 4.008933 CGCATCGATCCCCCTCCC 62.009 72.222 0.00 0.00 0.00 4.30
903 1116 3.798511 CCTCCCCCTCCTTTCGCC 61.799 72.222 0.00 0.00 0.00 5.54
904 1117 4.162690 CTCCCCCTCCTTTCGCCG 62.163 72.222 0.00 0.00 0.00 6.46
1161 1427 1.078708 TTTCCGTGGGATTCTCCGC 60.079 57.895 0.00 0.00 37.43 5.54
1168 1434 4.483243 GGATTCTCCGCCGGGCAA 62.483 66.667 20.71 5.85 0.00 4.52
1177 1443 0.248866 CCGCCGGGCAAATTATCAAC 60.249 55.000 20.71 0.00 0.00 3.18
1186 1452 4.898861 GGGCAAATTATCAACTGGGGAATA 59.101 41.667 0.00 0.00 0.00 1.75
1233 1505 3.436704 CCACTTACTGTATGTTGTGGCAG 59.563 47.826 13.02 0.00 41.43 4.85
1238 1510 2.104792 ACTGTATGTTGTGGCAGTCTGT 59.895 45.455 0.93 0.00 37.62 3.41
1239 1511 2.481568 CTGTATGTTGTGGCAGTCTGTG 59.518 50.000 0.93 0.00 0.00 3.66
1248 1520 0.868406 GGCAGTCTGTGTTTCTTCCG 59.132 55.000 0.93 0.00 0.00 4.30
1350 1622 1.605992 CCTGCCTGGATTCAGCAGA 59.394 57.895 20.65 0.00 42.38 4.26
1356 1628 2.787994 CCTGGATTCAGCAGAACAGTT 58.212 47.619 0.00 0.00 39.61 3.16
1368 1640 3.127721 GCAGAACAGTTTGCTAGGATTCC 59.872 47.826 11.17 0.00 37.35 3.01
1375 1648 3.260884 AGTTTGCTAGGATTCCGAGTTCA 59.739 43.478 13.55 2.53 0.00 3.18
1525 1802 0.460284 ACAGGAACGGCGAGCTTATG 60.460 55.000 16.62 6.97 0.00 1.90
1553 1830 4.513442 GCAAGTATGTCTCCACCACATTA 58.487 43.478 0.00 0.00 35.95 1.90
1595 1922 1.618837 ACTGGAGATGTTGCGTACACT 59.381 47.619 0.00 0.00 40.19 3.55
1605 1932 3.226347 GTTGCGTACACTGCTGAATTTC 58.774 45.455 0.00 0.00 0.00 2.17
1634 1970 2.187351 TGCAGAGTTTGAAAACGCAC 57.813 45.000 11.41 4.65 43.51 5.34
1646 1982 0.320374 AAACGCACCTCGGAGATGAA 59.680 50.000 2.78 0.00 43.86 2.57
1682 2022 0.865769 AATGTCGTGTGGCGTTCTTC 59.134 50.000 0.00 0.00 42.13 2.87
1685 2025 0.596600 GTCGTGTGGCGTTCTTCTCA 60.597 55.000 0.00 0.00 42.13 3.27
1689 2029 2.683968 GTGTGGCGTTCTTCTCATGTA 58.316 47.619 0.00 0.00 0.00 2.29
1690 2030 2.412089 GTGTGGCGTTCTTCTCATGTAC 59.588 50.000 0.00 0.00 0.00 2.90
1737 2083 6.294176 GCCTTGATGGTGATATTATGTGTTCC 60.294 42.308 0.00 0.00 38.35 3.62
1738 2084 7.000472 CCTTGATGGTGATATTATGTGTTCCT 59.000 38.462 0.00 0.00 0.00 3.36
1739 2085 7.040892 CCTTGATGGTGATATTATGTGTTCCTG 60.041 40.741 0.00 0.00 0.00 3.86
1740 2086 6.899089 TGATGGTGATATTATGTGTTCCTGT 58.101 36.000 0.00 0.00 0.00 4.00
1741 2087 7.345691 TGATGGTGATATTATGTGTTCCTGTT 58.654 34.615 0.00 0.00 0.00 3.16
1742 2088 8.490311 TGATGGTGATATTATGTGTTCCTGTTA 58.510 33.333 0.00 0.00 0.00 2.41
1743 2089 8.908786 ATGGTGATATTATGTGTTCCTGTTAG 57.091 34.615 0.00 0.00 0.00 2.34
1744 2090 8.084985 TGGTGATATTATGTGTTCCTGTTAGA 57.915 34.615 0.00 0.00 0.00 2.10
1745 2091 8.204160 TGGTGATATTATGTGTTCCTGTTAGAG 58.796 37.037 0.00 0.00 0.00 2.43
1746 2092 8.204836 GGTGATATTATGTGTTCCTGTTAGAGT 58.795 37.037 0.00 0.00 0.00 3.24
1747 2093 9.601217 GTGATATTATGTGTTCCTGTTAGAGTT 57.399 33.333 0.00 0.00 0.00 3.01
1780 2126 6.727231 TGTATTTCCTAACAGTTCCTACCTCA 59.273 38.462 0.00 0.00 0.00 3.86
1859 2211 2.507992 CAGCGCTGAACCCGAGAG 60.508 66.667 33.66 0.00 0.00 3.20
1897 2254 4.586001 ACCTCTTTACTCACCGAGTTAACA 59.414 41.667 8.61 0.00 40.28 2.41
1969 2326 2.557490 CGCCTATAGGGAGGAACTGTAC 59.443 54.545 20.58 0.00 39.15 2.90
2063 2447 6.875726 TGTCATTAGAAGAACATGGAACTGAG 59.124 38.462 0.00 0.00 0.00 3.35
2085 2470 6.093495 TGAGCCAATTCAATTCTTTAGGTACG 59.907 38.462 0.00 0.00 0.00 3.67
2170 2555 1.143684 TCCATTGGAGGGCAGATTAGC 59.856 52.381 0.00 0.00 0.00 3.09
2439 2827 0.449786 TTGTGCACACAAGGTGTTCG 59.550 50.000 21.56 0.00 45.08 3.95
2476 6110 4.379394 CCACTGTTAACGACATCCCATTTG 60.379 45.833 0.26 0.00 37.69 2.32
2501 6236 9.199982 TGATTACTACAAACTTAACTGTACTGC 57.800 33.333 0.00 0.00 0.00 4.40
2551 6289 4.655649 AGTGCTTCCTTTTTCCTTCCATTT 59.344 37.500 0.00 0.00 0.00 2.32
2627 6379 3.623060 GTCATACAGGTATGCTGGTTGTG 59.377 47.826 13.33 0.00 41.92 3.33
2630 6382 1.419762 ACAGGTATGCTGGTTGTGTGA 59.580 47.619 0.00 0.00 0.00 3.58
2639 6391 5.181690 TGCTGGTTGTGTGATAAAAGTTC 57.818 39.130 0.00 0.00 0.00 3.01
2642 6394 5.687285 GCTGGTTGTGTGATAAAAGTTCTTG 59.313 40.000 0.00 0.00 0.00 3.02
2659 6415 7.458409 AGTTCTTGTATGCTTGTGAAATCAT 57.542 32.000 0.00 0.00 0.00 2.45
2666 6422 4.508461 TGCTTGTGAAATCATGGAGTTG 57.492 40.909 0.00 0.00 0.00 3.16
2667 6423 3.248266 GCTTGTGAAATCATGGAGTTGC 58.752 45.455 0.00 0.00 0.00 4.17
2670 6426 5.534207 TTGTGAAATCATGGAGTTGCTTT 57.466 34.783 0.00 0.00 0.00 3.51
2672 6428 5.916318 TGTGAAATCATGGAGTTGCTTTTT 58.084 33.333 0.00 0.00 0.00 1.94
2673 6429 5.984926 TGTGAAATCATGGAGTTGCTTTTTC 59.015 36.000 0.00 0.00 0.00 2.29
2742 7011 4.662278 ACAAGAAAGGCCATAGCTAACAA 58.338 39.130 5.01 0.00 39.73 2.83
2750 7019 3.376540 GCCATAGCTAACAAGAGAGACG 58.623 50.000 0.00 0.00 35.50 4.18
2823 7171 7.792925 GCAAATAGCAAACGGAATTTTTAGTT 58.207 30.769 0.00 0.00 44.79 2.24
2824 7172 7.739911 GCAAATAGCAAACGGAATTTTTAGTTG 59.260 33.333 0.00 0.00 44.79 3.16
2825 7173 6.944557 ATAGCAAACGGAATTTTTAGTTGC 57.055 33.333 0.00 0.00 0.00 4.17
2826 7174 4.944048 AGCAAACGGAATTTTTAGTTGCT 58.056 34.783 2.31 2.31 0.00 3.91
2827 7175 6.079424 AGCAAACGGAATTTTTAGTTGCTA 57.921 33.333 6.22 0.00 33.09 3.49
2828 7176 6.508777 AGCAAACGGAATTTTTAGTTGCTAA 58.491 32.000 6.22 0.00 33.09 3.09
2946 7295 3.507622 GCTGCCAGAAACTACCTTTTCAT 59.492 43.478 0.00 0.00 37.86 2.57
2965 7315 9.148104 CTTTTCATCATCATAGCTAATCATCGA 57.852 33.333 0.00 0.00 0.00 3.59
2975 7325 3.384789 AGCTAATCATCGAAGTAGCACCA 59.615 43.478 16.34 0.00 41.17 4.17
3065 7417 1.411977 CACCTCAGGCTGATGGAGTAG 59.588 57.143 28.37 13.38 0.00 2.57
3077 7429 5.449862 GCTGATGGAGTAGTGAACTGAGTAG 60.450 48.000 0.00 0.00 39.07 2.57
3144 7496 5.343058 CCATTGTGATTTAGTTGCGAAACAG 59.657 40.000 9.44 0.00 0.00 3.16
3242 7599 5.645067 TGGTTTATCTGTCTTTGATGCTGAG 59.355 40.000 0.00 0.00 0.00 3.35
3265 7622 8.453320 TGAGAAATCATTTACATGTGCAGTTAG 58.547 33.333 9.11 0.00 0.00 2.34
3427 7786 9.157104 GTAGAGGAACTAGAAATCAGGAAAAAG 57.843 37.037 0.00 0.00 41.55 2.27
3475 7834 7.672983 TGTGTCTTTCATCCAAGATTTACTC 57.327 36.000 0.00 0.00 35.23 2.59
3493 7852 7.905604 TTTACTCTTCTTGATACACATGGTG 57.094 36.000 0.00 0.00 39.75 4.17
3499 7858 6.313658 TCTTCTTGATACACATGGTGATTTCG 59.686 38.462 2.98 0.00 36.96 3.46
3570 7929 6.166984 TCAGTATTTGGGAAGAGAGCATAG 57.833 41.667 0.00 0.00 0.00 2.23
3582 7941 3.654806 AGAGAGCATAGGCCAACCAATAT 59.345 43.478 5.01 0.00 42.56 1.28
3640 7999 3.375299 CACTTCTCAATCCGAATCCCAAC 59.625 47.826 0.00 0.00 0.00 3.77
3681 8040 3.913548 TCCAATCAATTGTCCACAACG 57.086 42.857 5.13 0.00 38.86 4.10
3752 8111 6.715347 AAGGTGGATAATTGCAAGGATTAC 57.285 37.500 4.94 4.62 0.00 1.89
3759 8118 9.639563 TGGATAATTGCAAGGATTACTTATGAA 57.360 29.630 4.94 0.00 37.29 2.57
3778 8137 4.620982 TGAAGTCATAGACATGTATGCCG 58.379 43.478 2.50 0.00 34.60 5.69
3813 8172 1.340017 GGGAGGCTGCATGTTAAGTGA 60.340 52.381 8.68 0.00 0.00 3.41
3892 8253 5.744171 TCCTGTAAGCAAGCAGATATTCAA 58.256 37.500 0.00 0.00 34.87 2.69
3921 8282 2.489722 CAAAAAGGAGCTAGGTTCCAGC 59.510 50.000 11.39 5.56 35.33 4.85
3925 8286 1.705186 AGGAGCTAGGTTCCAGCAAAA 59.295 47.619 11.39 0.00 41.66 2.44
3972 8342 5.606348 TCACCTTTGTTTTAGTTTGCCAT 57.394 34.783 0.00 0.00 0.00 4.40
4043 8414 5.801531 AGGGATTTTGGAACAGTAAAACC 57.198 39.130 0.00 0.00 42.39 3.27
4104 8475 8.530311 AGATATAGTTCCTGTAGCAATGATCAG 58.470 37.037 0.09 0.00 0.00 2.90
4137 8508 3.686726 GTGCCACAGATCTTCAGTTAAGG 59.313 47.826 0.00 0.00 35.75 2.69
4140 8511 4.383118 GCCACAGATCTTCAGTTAAGGCTA 60.383 45.833 0.00 0.00 35.75 3.93
4144 8515 7.987458 CCACAGATCTTCAGTTAAGGCTATTAA 59.013 37.037 0.00 0.00 35.75 1.40
4157 8528 9.463443 GTTAAGGCTATTAAAACAAGCATATGG 57.537 33.333 4.56 0.00 38.01 2.74
4175 8546 8.059798 GCATATGGCTATTGATTCTAATTGGT 57.940 34.615 4.56 0.00 40.25 3.67
4176 8547 8.186821 GCATATGGCTATTGATTCTAATTGGTC 58.813 37.037 4.56 0.00 40.25 4.02
4177 8548 8.680903 CATATGGCTATTGATTCTAATTGGTCC 58.319 37.037 0.00 0.00 0.00 4.46
4178 8549 6.266131 TGGCTATTGATTCTAATTGGTCCT 57.734 37.500 0.00 0.00 0.00 3.85
4179 8550 6.064060 TGGCTATTGATTCTAATTGGTCCTG 58.936 40.000 0.00 0.00 0.00 3.86
4180 8551 6.126507 TGGCTATTGATTCTAATTGGTCCTGA 60.127 38.462 0.00 0.00 0.00 3.86
4181 8552 6.944862 GGCTATTGATTCTAATTGGTCCTGAT 59.055 38.462 0.00 0.00 0.00 2.90
4182 8553 7.094463 GGCTATTGATTCTAATTGGTCCTGATG 60.094 40.741 0.00 0.00 0.00 3.07
4277 8855 2.376695 TACTCCCTCGGTCCCATAAG 57.623 55.000 0.00 0.00 0.00 1.73
4278 8856 0.398664 ACTCCCTCGGTCCCATAAGG 60.399 60.000 0.00 0.00 0.00 2.69
4294 8872 6.109156 CCATAAGGGGCTTTAGTTTTGTTT 57.891 37.500 0.00 0.00 0.00 2.83
4300 8878 3.555547 GGGCTTTAGTTTTGTTTGCACTG 59.444 43.478 0.00 0.00 0.00 3.66
4303 8881 5.523552 GGCTTTAGTTTTGTTTGCACTGAAT 59.476 36.000 0.00 0.00 0.00 2.57
4313 8891 7.664082 TTGTTTGCACTGAATTTTTCAAAGA 57.336 28.000 0.00 0.00 39.58 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 7.846101 AGATCCATGTATAGTCATCACTTCA 57.154 36.000 0.00 0.00 33.62 3.02
61 62 3.055385 ACTGATTATACACTTGGCCACGT 60.055 43.478 9.49 9.49 0.00 4.49
71 72 3.551890 CGAGCACACCACTGATTATACAC 59.448 47.826 0.00 0.00 0.00 2.90
74 75 4.340950 TGATCGAGCACACCACTGATTATA 59.659 41.667 0.00 0.00 0.00 0.98
111 112 5.822519 TCGCTGATGGCACTAAATATTCTTT 59.177 36.000 0.00 0.00 41.91 2.52
128 129 7.872113 ATTTTCCTAGAAAAGATTCGCTGAT 57.128 32.000 8.34 0.00 40.63 2.90
129 130 7.530010 CAATTTTCCTAGAAAAGATTCGCTGA 58.470 34.615 8.34 0.00 40.63 4.26
198 199 5.537188 GGCAACAAAGAAAACACATCCATA 58.463 37.500 0.00 0.00 0.00 2.74
208 209 4.336993 TCTTCTTAGCGGCAACAAAGAAAA 59.663 37.500 15.61 5.63 38.34 2.29
239 240 1.407989 CCATGCTCTCCCTTCCTTCAC 60.408 57.143 0.00 0.00 0.00 3.18
241 242 0.915364 ACCATGCTCTCCCTTCCTTC 59.085 55.000 0.00 0.00 0.00 3.46
303 331 6.343716 ACCAGATAGACATTGCTATGAGAG 57.656 41.667 15.23 0.00 35.65 3.20
347 375 2.736144 TCGTAAATTGGACAGACGCT 57.264 45.000 0.00 0.00 33.64 5.07
348 376 3.000322 CAGATCGTAAATTGGACAGACGC 60.000 47.826 0.00 0.00 33.64 5.19
349 377 4.174009 ACAGATCGTAAATTGGACAGACG 58.826 43.478 0.00 0.00 34.90 4.18
350 378 6.402226 GGAAACAGATCGTAAATTGGACAGAC 60.402 42.308 0.00 0.00 0.00 3.51
351 379 5.642063 GGAAACAGATCGTAAATTGGACAGA 59.358 40.000 0.00 0.00 0.00 3.41
352 380 5.411361 TGGAAACAGATCGTAAATTGGACAG 59.589 40.000 0.00 0.00 35.01 3.51
353 381 5.180492 GTGGAAACAGATCGTAAATTGGACA 59.820 40.000 0.00 0.00 44.46 4.02
354 382 5.391629 GGTGGAAACAGATCGTAAATTGGAC 60.392 44.000 0.00 0.00 44.46 4.02
355 383 4.698304 GGTGGAAACAGATCGTAAATTGGA 59.302 41.667 0.00 0.00 44.46 3.53
356 384 4.436852 CGGTGGAAACAGATCGTAAATTGG 60.437 45.833 0.00 0.00 44.46 3.16
357 385 4.153475 ACGGTGGAAACAGATCGTAAATTG 59.847 41.667 0.00 0.00 44.46 2.32
358 386 4.320870 ACGGTGGAAACAGATCGTAAATT 58.679 39.130 0.00 0.00 44.46 1.82
359 387 3.934068 ACGGTGGAAACAGATCGTAAAT 58.066 40.909 0.00 0.00 44.46 1.40
360 388 3.389925 ACGGTGGAAACAGATCGTAAA 57.610 42.857 0.00 0.00 44.46 2.01
361 389 3.061322 CAACGGTGGAAACAGATCGTAA 58.939 45.455 0.00 0.00 44.46 3.18
362 390 2.036217 ACAACGGTGGAAACAGATCGTA 59.964 45.455 4.97 0.00 44.46 3.43
363 391 1.202604 ACAACGGTGGAAACAGATCGT 60.203 47.619 4.97 0.00 44.46 3.73
364 392 1.459592 GACAACGGTGGAAACAGATCG 59.540 52.381 4.97 0.00 44.46 3.69
365 393 2.767505 AGACAACGGTGGAAACAGATC 58.232 47.619 4.97 0.00 44.46 2.75
366 394 2.930826 AGACAACGGTGGAAACAGAT 57.069 45.000 4.97 0.00 44.46 2.90
367 395 2.093394 TGAAGACAACGGTGGAAACAGA 60.093 45.455 4.97 0.00 44.46 3.41
368 396 2.285083 TGAAGACAACGGTGGAAACAG 58.715 47.619 4.97 0.00 44.46 3.16
369 397 2.404923 TGAAGACAACGGTGGAAACA 57.595 45.000 4.97 0.00 38.70 2.83
370 398 5.220605 GCTATATGAAGACAACGGTGGAAAC 60.221 44.000 4.97 0.00 0.00 2.78
371 399 4.873827 GCTATATGAAGACAACGGTGGAAA 59.126 41.667 4.97 0.00 0.00 3.13
372 400 4.161565 AGCTATATGAAGACAACGGTGGAA 59.838 41.667 4.97 0.00 0.00 3.53
373 401 3.704566 AGCTATATGAAGACAACGGTGGA 59.295 43.478 4.97 0.00 0.00 4.02
374 402 3.804325 CAGCTATATGAAGACAACGGTGG 59.196 47.826 4.97 0.00 0.00 4.61
375 403 4.682787 TCAGCTATATGAAGACAACGGTG 58.317 43.478 0.00 0.00 0.00 4.94
376 404 4.202161 CCTCAGCTATATGAAGACAACGGT 60.202 45.833 0.00 0.00 0.00 4.83
377 405 4.202161 ACCTCAGCTATATGAAGACAACGG 60.202 45.833 0.00 0.00 0.00 4.44
378 406 4.938080 ACCTCAGCTATATGAAGACAACG 58.062 43.478 0.00 0.00 0.00 4.10
379 407 6.595716 ACAAACCTCAGCTATATGAAGACAAC 59.404 38.462 0.00 0.00 0.00 3.32
380 408 6.711277 ACAAACCTCAGCTATATGAAGACAA 58.289 36.000 0.00 0.00 0.00 3.18
388 416 8.635765 TTTCTCAAAACAAACCTCAGCTATAT 57.364 30.769 0.00 0.00 0.00 0.86
471 499 2.226330 ACCGCTAACTTTTGACATGCA 58.774 42.857 0.00 0.00 0.00 3.96
486 514 2.167693 TCCTTTTGATGTCGATACCGCT 59.832 45.455 0.00 0.00 35.37 5.52
487 515 2.540101 CTCCTTTTGATGTCGATACCGC 59.460 50.000 0.00 0.00 35.37 5.68
488 516 3.551890 CACTCCTTTTGATGTCGATACCG 59.448 47.826 0.00 0.00 37.07 4.02
541 571 8.282592 GGAAAAATCATCTTAAAAGTTGCAACC 58.717 33.333 25.62 8.37 0.00 3.77
543 573 7.307101 GCGGAAAAATCATCTTAAAAGTTGCAA 60.307 33.333 0.00 0.00 0.00 4.08
568 598 2.029649 TCTCGTAAGTGTGTGTTAGGGC 60.030 50.000 0.00 0.00 39.48 5.19
569 599 3.928727 TCTCGTAAGTGTGTGTTAGGG 57.071 47.619 0.00 0.00 39.48 3.53
577 607 3.118738 AGGGCCTAAATCTCGTAAGTGTG 60.119 47.826 2.82 0.00 39.48 3.82
603 633 3.897122 GGAGTGGGTGGGTTGCCA 61.897 66.667 0.00 0.00 0.00 4.92
614 644 1.153289 CCGCAGATTCCAGGAGTGG 60.153 63.158 0.00 0.00 46.63 4.00
619 649 1.078214 TTGCTCCGCAGATTCCAGG 60.078 57.895 0.00 0.00 40.61 4.45
636 666 3.014304 TCACGGAGCTACAGTATCCTT 57.986 47.619 0.00 0.00 0.00 3.36
646 676 3.194755 TGCAGTAGAAAATCACGGAGCTA 59.805 43.478 0.00 0.00 0.00 3.32
651 681 2.349886 GAGCTGCAGTAGAAAATCACGG 59.650 50.000 16.64 0.00 0.00 4.94
728 758 4.640771 TTAGCAGGACCAGAGTTTCAAT 57.359 40.909 0.00 0.00 0.00 2.57
758 788 6.764085 TCCAATTATACGATTTGTCCGTCATT 59.236 34.615 0.00 0.00 40.95 2.57
776 806 6.671614 ACTTTCAAATCGCGTATCCAATTA 57.328 33.333 5.77 0.00 0.00 1.40
941 1154 1.352622 ATAAGAAGGGATGGGGCGCA 61.353 55.000 10.83 6.74 0.00 6.09
949 1162 3.643792 AGCTGCTACGAATAAGAAGGGAT 59.356 43.478 0.00 0.00 0.00 3.85
1128 1351 5.001232 CCACGGAAAGAGAAACTGGAATTA 58.999 41.667 0.00 0.00 0.00 1.40
1161 1427 1.408702 CCCAGTTGATAATTTGCCCGG 59.591 52.381 0.00 0.00 0.00 5.73
1168 1434 7.124147 CCACACTTTATTCCCCAGTTGATAATT 59.876 37.037 0.00 0.00 0.00 1.40
1177 1443 2.899303 ACCCACACTTTATTCCCCAG 57.101 50.000 0.00 0.00 0.00 4.45
1186 1452 7.396339 GGGAAATTAGATCTTAACCCACACTTT 59.604 37.037 0.00 0.00 36.47 2.66
1233 1505 0.395312 TCCCCGGAAGAAACACAGAC 59.605 55.000 0.73 0.00 0.00 3.51
1238 1510 1.125093 TCTGCTCCCCGGAAGAAACA 61.125 55.000 0.73 0.00 0.00 2.83
1239 1511 0.253327 ATCTGCTCCCCGGAAGAAAC 59.747 55.000 0.73 0.00 31.26 2.78
1248 1520 1.817099 CGCTCACAATCTGCTCCCC 60.817 63.158 0.00 0.00 0.00 4.81
1350 1622 3.008049 ACTCGGAATCCTAGCAAACTGTT 59.992 43.478 0.18 0.00 0.00 3.16
1356 1628 3.490933 CGATGAACTCGGAATCCTAGCAA 60.491 47.826 0.18 0.00 43.82 3.91
1375 1648 3.566261 CAAACAGTGCCTCGCGAT 58.434 55.556 10.36 0.00 0.00 4.58
1525 1802 0.179081 GGAGACATACTTGCGTCCCC 60.179 60.000 0.00 0.00 32.33 4.81
1538 1815 6.183361 TGTGCATATATAATGTGGTGGAGACA 60.183 38.462 0.00 0.00 38.70 3.41
1553 1830 8.144478 CCAGTAGTAAACTCAGTGTGCATATAT 58.856 37.037 0.00 0.00 35.76 0.86
1595 1922 0.537143 ACACCAGGCGAAATTCAGCA 60.537 50.000 10.73 0.00 34.54 4.41
1605 1932 1.447317 AAACTCTGCAACACCAGGCG 61.447 55.000 0.00 0.00 33.64 5.52
1634 1970 3.452474 CTTAAGCTGTTCATCTCCGAGG 58.548 50.000 0.00 0.00 0.00 4.63
1646 1982 2.224867 ACATTGGCTCACCTTAAGCTGT 60.225 45.455 0.00 0.00 39.75 4.40
1682 2022 3.774066 TCATCTGCGACAAGTACATGAG 58.226 45.455 4.87 0.00 0.00 2.90
1685 2025 3.876274 ACTCATCTGCGACAAGTACAT 57.124 42.857 0.00 0.00 0.00 2.29
1689 2029 3.466836 TGAAAACTCATCTGCGACAAGT 58.533 40.909 0.00 0.00 0.00 3.16
1690 2030 3.120408 CCTGAAAACTCATCTGCGACAAG 60.120 47.826 0.00 0.00 0.00 3.16
1751 2097 9.895138 GGTAGGAACTGTTAGGAAATACATAAA 57.105 33.333 0.00 0.00 41.52 1.40
1752 2098 9.275572 AGGTAGGAACTGTTAGGAAATACATAA 57.724 33.333 0.00 0.00 41.52 1.90
1753 2099 8.849543 AGGTAGGAACTGTTAGGAAATACATA 57.150 34.615 0.00 0.00 41.52 2.29
1754 2100 7.402071 TGAGGTAGGAACTGTTAGGAAATACAT 59.598 37.037 0.00 0.00 41.52 2.29
1755 2101 6.727231 TGAGGTAGGAACTGTTAGGAAATACA 59.273 38.462 0.00 0.00 41.52 2.29
1756 2102 7.040494 GTGAGGTAGGAACTGTTAGGAAATAC 58.960 42.308 0.00 0.00 41.52 1.89
1757 2103 6.727231 TGTGAGGTAGGAACTGTTAGGAAATA 59.273 38.462 0.00 0.00 41.52 1.40
1758 2104 5.546499 TGTGAGGTAGGAACTGTTAGGAAAT 59.454 40.000 0.00 0.00 41.52 2.17
1759 2105 4.903049 TGTGAGGTAGGAACTGTTAGGAAA 59.097 41.667 0.00 0.00 41.52 3.13
1760 2106 4.485875 TGTGAGGTAGGAACTGTTAGGAA 58.514 43.478 0.00 0.00 41.52 3.36
1761 2107 4.087182 CTGTGAGGTAGGAACTGTTAGGA 58.913 47.826 0.00 0.00 41.52 2.94
1762 2108 3.195825 CCTGTGAGGTAGGAACTGTTAGG 59.804 52.174 0.00 0.00 41.52 2.69
1763 2109 4.087182 TCCTGTGAGGTAGGAACTGTTAG 58.913 47.826 0.00 0.00 41.24 2.34
1764 2110 4.122337 TCCTGTGAGGTAGGAACTGTTA 57.878 45.455 0.00 0.00 41.24 2.41
1765 2111 2.972348 TCCTGTGAGGTAGGAACTGTT 58.028 47.619 0.00 0.00 41.24 3.16
1766 2112 2.696526 TCCTGTGAGGTAGGAACTGT 57.303 50.000 0.00 0.00 41.24 3.55
1775 2121 6.431234 GTGAAGTTAATGATTTCCTGTGAGGT 59.569 38.462 0.00 0.00 36.53 3.85
1780 2126 7.939039 TGAAGAGTGAAGTTAATGATTTCCTGT 59.061 33.333 0.00 0.00 0.00 4.00
1859 2211 2.187163 GGTAGCAGCGGAGGGAAC 59.813 66.667 0.00 0.00 0.00 3.62
1897 2254 1.360852 TGAATGTACCCCTGGGCAAAT 59.639 47.619 7.39 0.00 39.32 2.32
1969 2326 5.121298 TCAAAATCATCACGCTCTTCTTGAG 59.879 40.000 0.00 0.00 45.33 3.02
2063 2447 6.190954 ACGTACCTAAAGAATTGAATTGGC 57.809 37.500 0.00 0.00 0.00 4.52
2085 2470 4.157105 ACACCATTTTAGGCCGAATGTTAC 59.843 41.667 20.64 0.00 32.65 2.50
2476 6110 9.199982 TGCAGTACAGTTAAGTTTGTAGTAATC 57.800 33.333 0.00 0.00 33.00 1.75
2501 6236 7.333921 AGTCAGACAAAATGCTAGAGAAAGATG 59.666 37.037 2.66 0.00 0.00 2.90
2551 6289 8.805175 CATGATCATTGCCACCCTATTAAATAA 58.195 33.333 5.16 0.00 0.00 1.40
2592 6330 5.385198 ACCTGTATGACCAATTGTTCTGTT 58.615 37.500 4.52 0.00 0.00 3.16
2601 6339 3.459598 ACCAGCATACCTGTATGACCAAT 59.540 43.478 18.93 0.13 44.22 3.16
2627 6379 8.289618 TCACAAGCATACAAGAACTTTTATCAC 58.710 33.333 0.00 0.00 0.00 3.06
2639 6391 6.127814 ACTCCATGATTTCACAAGCATACAAG 60.128 38.462 0.00 0.00 36.87 3.16
2642 6394 5.824904 ACTCCATGATTTCACAAGCATAC 57.175 39.130 0.00 0.00 36.87 2.39
2694 6451 5.271598 TGCAAAAATTACTCATCCAGGGAT 58.728 37.500 0.00 0.00 34.81 3.85
2695 6452 4.671831 TGCAAAAATTACTCATCCAGGGA 58.328 39.130 0.00 0.00 0.00 4.20
2707 6464 5.296748 GCCTTTCTTGTCCTGCAAAAATTA 58.703 37.500 0.00 0.00 36.53 1.40
2708 6465 4.129380 GCCTTTCTTGTCCTGCAAAAATT 58.871 39.130 0.00 0.00 36.53 1.82
2710 6467 2.158971 GGCCTTTCTTGTCCTGCAAAAA 60.159 45.455 0.00 0.00 36.53 1.94
2742 7011 3.838244 AGATGCTCTCTACGTCTCTCT 57.162 47.619 0.00 0.00 30.26 3.10
2768 7094 4.022155 TGCAGCACAGCTCATTTAATTCAA 60.022 37.500 0.00 0.00 36.40 2.69
2817 7165 9.008965 TGAAATCAGTTAGCATTAGCAACTAAA 57.991 29.630 0.00 0.00 45.49 1.85
2823 7171 9.955208 CAAATATGAAATCAGTTAGCATTAGCA 57.045 29.630 0.00 0.00 45.49 3.49
2824 7172 9.403110 CCAAATATGAAATCAGTTAGCATTAGC 57.597 33.333 0.00 0.00 42.56 3.09
2869 7217 6.006275 AGTTGGATGTTAATGATACTGCCT 57.994 37.500 0.00 0.00 0.00 4.75
2946 7295 7.094205 TGCTACTTCGATGATTAGCTATGATGA 60.094 37.037 16.71 0.00 38.23 2.92
2965 7315 7.524717 ACATGACTTAAAAATGGTGCTACTT 57.475 32.000 0.00 0.00 0.00 2.24
2975 7325 7.930865 TGGCAGCTTTTAACATGACTTAAAAAT 59.069 29.630 0.00 0.00 35.92 1.82
3242 7599 7.441878 GCTAACTGCACATGTAAATGATTTC 57.558 36.000 0.00 0.00 42.31 2.17
3265 7622 3.927163 ATCGTGTCGTCGGGGTTGC 62.927 63.158 0.00 0.00 0.00 4.17
3427 7786 1.673920 TCAAGGAACGGCAACAAGTTC 59.326 47.619 0.19 0.19 44.22 3.01
3475 7834 6.092670 ACGAAATCACCATGTGTATCAAGAAG 59.907 38.462 0.00 0.00 34.79 2.85
3493 7852 6.436843 AATGTATTGTCCCAGAACGAAATC 57.563 37.500 0.00 0.00 0.00 2.17
3499 7858 5.010282 ACCTCAAATGTATTGTCCCAGAAC 58.990 41.667 0.00 0.00 0.00 3.01
3557 7916 1.475930 GGTTGGCCTATGCTCTCTTCC 60.476 57.143 3.32 0.00 37.74 3.46
3570 7929 4.935352 TGCATAGAAATATTGGTTGGCC 57.065 40.909 0.00 0.00 0.00 5.36
3582 7941 5.126067 GGAGAAGGCTTACATGCATAGAAA 58.874 41.667 0.00 0.00 34.04 2.52
3640 7999 5.066375 TGGAATTGGAGCTACAAATTGATCG 59.934 40.000 17.06 0.00 33.48 3.69
3681 8040 0.168348 GCCGATCATCTCATGCATGC 59.832 55.000 22.25 11.82 0.00 4.06
3731 8090 6.715347 AAGTAATCCTTGCAATTATCCACC 57.285 37.500 0.00 0.00 30.18 4.61
3752 8111 7.062722 CGGCATACATGTCTATGACTTCATAAG 59.937 40.741 11.95 0.00 38.26 1.73
3759 8118 5.302059 AGTTACGGCATACATGTCTATGACT 59.698 40.000 11.95 4.08 37.73 3.41
3778 8137 2.779506 CCTCCCACCTCACAAAGTTAC 58.220 52.381 0.00 0.00 0.00 2.50
3892 8253 2.371658 AGCTCCTTTTTGCTGGAACT 57.628 45.000 0.00 0.00 38.21 3.01
3921 8282 2.861462 TTTCGTCACCAGCCTTTTTG 57.139 45.000 0.00 0.00 0.00 2.44
3925 8286 1.880027 GTCAATTTCGTCACCAGCCTT 59.120 47.619 0.00 0.00 0.00 4.35
3972 8342 7.717875 AGTCAGTTTACCTTAAGCATGTGTAAA 59.282 33.333 8.88 8.88 0.00 2.01
4043 8414 5.649395 AGTAAGGTCACATGATGGTCATTTG 59.351 40.000 0.00 0.79 34.28 2.32
4104 8475 0.877071 CTGTGGCACCTGTGATTCAC 59.123 55.000 16.26 9.93 34.56 3.18
4150 8521 8.059798 ACCAATTAGAATCAATAGCCATATGC 57.940 34.615 0.00 0.00 41.71 3.14
4155 8526 6.064060 CAGGACCAATTAGAATCAATAGCCA 58.936 40.000 0.00 0.00 0.00 4.75
4157 8528 7.574592 GCATCAGGACCAATTAGAATCAATAGC 60.575 40.741 0.00 0.00 0.00 2.97
4161 8532 5.759059 AGCATCAGGACCAATTAGAATCAA 58.241 37.500 0.00 0.00 0.00 2.57
4179 8550 0.250234 TGCCCTAGTGTGTGAGCATC 59.750 55.000 0.00 0.00 0.00 3.91
4180 8551 0.251354 CTGCCCTAGTGTGTGAGCAT 59.749 55.000 0.00 0.00 0.00 3.79
4181 8552 1.673477 CTGCCCTAGTGTGTGAGCA 59.327 57.895 0.00 0.00 0.00 4.26
4182 8553 1.078848 CCTGCCCTAGTGTGTGAGC 60.079 63.158 0.00 0.00 0.00 4.26
4277 8855 2.869801 GTGCAAACAAAACTAAAGCCCC 59.130 45.455 0.00 0.00 0.00 5.80
4278 8856 3.555547 CAGTGCAAACAAAACTAAAGCCC 59.444 43.478 0.00 0.00 0.00 5.19
4281 8859 9.824534 AAAAATTCAGTGCAAACAAAACTAAAG 57.175 25.926 0.00 0.00 0.00 1.85
4294 8872 6.206395 TGACTCTTTGAAAAATTCAGTGCA 57.794 33.333 0.00 0.00 41.38 4.57


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

AutoCloner maintained by Alex Coulton.