Multiple sequence alignment - TraesCS7B01G208700

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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 TraesCS7B01G208700 chr7B 100.000 5409 0 0 1 5409 381839897 381834489 0.000000e+00 9989.0
1 TraesCS7B01G208700 chr7B 81.513 119 21 1 5022 5140 100359331 100359214 4.460000e-16 97.1
2 TraesCS7B01G208700 chr7B 82.292 96 14 3 5313 5405 20636584 20636679 4.490000e-11 80.5
3 TraesCS7B01G208700 chr7A 93.864 3341 128 24 599 3908 436790735 436787441 0.000000e+00 4963.0
4 TraesCS7B01G208700 chr7A 90.705 1517 84 23 3908 5405 436787409 436785931 0.000000e+00 1967.0
5 TraesCS7B01G208700 chr7A 88.043 92 11 0 5314 5405 446355531 446355440 5.730000e-20 110.0
6 TraesCS7B01G208700 chr7A 100.000 28 0 0 1022 1049 321046358 321046331 1.000000e-02 52.8
7 TraesCS7B01G208700 chr7D 93.773 2409 103 13 1527 3908 386759024 386756636 0.000000e+00 3574.0
8 TraesCS7B01G208700 chr7D 92.776 1412 64 13 3908 5303 386756604 386755215 0.000000e+00 2008.0
9 TraesCS7B01G208700 chr7D 88.284 1562 102 37 4 1528 386760623 386759106 0.000000e+00 1796.0
10 TraesCS7B01G208700 chr2D 89.189 111 12 0 5042 5152 643816773 643816883 7.310000e-29 139.0
11 TraesCS7B01G208700 chr5A 85.455 110 16 0 5047 5156 659894266 659894375 1.230000e-21 115.0
12 TraesCS7B01G208700 chr1B 82.143 140 19 6 5020 5158 52757377 52757243 1.230000e-21 115.0
13 TraesCS7B01G208700 chr4A 87.234 94 12 0 5063 5156 665472636 665472543 2.060000e-19 108.0
14 TraesCS7B01G208700 chr4A 83.478 115 17 2 5042 5156 537548926 537549038 7.410000e-19 106.0
15 TraesCS7B01G208700 chr1D 81.746 126 16 6 5033 5155 12933198 12933319 1.240000e-16 99.0
16 TraesCS7B01G208700 chr2B 84.946 93 12 2 5315 5405 445257293 445257201 5.770000e-15 93.5
17 TraesCS7B01G208700 chrUn 82.292 96 14 3 5313 5405 144016894 144016989 4.490000e-11 80.5
18 TraesCS7B01G208700 chrUn 82.292 96 14 3 5313 5405 155960679 155960584 4.490000e-11 80.5
19 TraesCS7B01G208700 chrUn 82.292 96 14 3 5313 5405 355151607 355151512 4.490000e-11 80.5
20 TraesCS7B01G208700 chr2A 85.714 70 9 1 5336 5405 210489038 210489106 7.520000e-09 73.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G208700 chr7B 381834489 381839897 5408 True 9989.000000 9989 100.0000 1 5409 1 chr7B.!!$R2 5408
1 TraesCS7B01G208700 chr7A 436785931 436790735 4804 True 3465.000000 4963 92.2845 599 5405 2 chr7A.!!$R3 4806
2 TraesCS7B01G208700 chr7D 386755215 386760623 5408 True 2459.333333 3574 91.6110 4 5303 3 chr7D.!!$R1 5299

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
39 40 0.100682 ATACGAGCAGTGCTACGGTG 59.899 55.0 28.23 16.22 39.88 4.94 F
1350 1392 0.037605 AGGACTTCCAGGTAAACGCG 60.038 55.0 3.53 3.53 38.89 6.01 F
1706 1832 0.035439 CCGCCTCCACATACTTTGGT 60.035 55.0 0.00 0.00 35.42 3.67 F
2543 2669 0.461548 CGCTGAAGGATGCTACCTCA 59.538 55.0 3.01 0.00 39.62 3.86 F
2720 2846 1.439353 CTGACGTGCTGGTTGCTTGT 61.439 55.0 0.00 0.00 43.37 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 1692 0.109723 GCTCCCAACTACCACAACCA 59.890 55.0 0.00 0.0 0.00 3.67 R
2846 2972 0.249676 GAACTCCGACTTCCCCCTTC 59.750 60.0 0.00 0.0 0.00 3.46 R
3594 3738 2.222596 CGCGTTGCAGATTTAGTCAGTC 60.223 50.0 0.00 0.0 0.00 3.51 R
3981 4182 1.101331 GAGGAAATGGAAGCTGCCAG 58.899 55.0 20.89 0.0 42.15 4.85 R
4477 4685 2.031157 CCCCAAAGAACAACACTAAGCG 60.031 50.0 0.00 0.0 0.00 4.68 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
39 40 0.100682 ATACGAGCAGTGCTACGGTG 59.899 55.000 28.23 16.22 39.88 4.94
40 41 1.239296 TACGAGCAGTGCTACGGTGT 61.239 55.000 28.23 19.76 39.88 4.16
84 86 4.525487 ACTACCGCGGAATATCCATTTCTA 59.475 41.667 35.90 7.69 35.91 2.10
93 95 6.647067 CGGAATATCCATTTCTAAGTCCAGAC 59.353 42.308 0.00 0.00 35.91 3.51
105 107 0.901124 GTCCAGACTCATCAGCACCT 59.099 55.000 0.00 0.00 0.00 4.00
115 117 3.106827 TCATCAGCACCTGGTCAAGATA 58.893 45.455 0.00 0.00 31.51 1.98
174 181 4.096231 TGATTGATAATTTGGTGCGTGAGG 59.904 41.667 0.00 0.00 0.00 3.86
179 186 4.539083 TTGGTGCGTGAGGTGCGT 62.539 61.111 0.00 0.00 34.24 5.24
189 196 3.118972 GCGTGAGGTGCGTTTTAAATTTC 59.881 43.478 0.00 0.00 0.00 2.17
190 197 4.283678 CGTGAGGTGCGTTTTAAATTTCA 58.716 39.130 0.00 0.00 0.00 2.69
191 198 4.378616 CGTGAGGTGCGTTTTAAATTTCAG 59.621 41.667 0.00 0.00 0.00 3.02
192 199 5.516090 GTGAGGTGCGTTTTAAATTTCAGA 58.484 37.500 0.00 0.00 0.00 3.27
193 200 5.398416 GTGAGGTGCGTTTTAAATTTCAGAC 59.602 40.000 0.00 0.00 0.00 3.51
217 224 9.685828 GACCATTTAGACATATGAGTAACTCTC 57.314 37.037 10.38 0.00 43.03 3.20
282 290 8.555896 AAAGGTTTTTAGGGTCCTAAATTTGA 57.444 30.769 19.32 5.55 44.73 2.69
293 301 5.696270 GGTCCTAAATTTGACCTTTTTGCAG 59.304 40.000 16.70 0.00 46.13 4.41
301 309 4.292186 TGACCTTTTTGCAGAGAGCTAT 57.708 40.909 0.00 0.00 45.94 2.97
306 314 4.096081 CCTTTTTGCAGAGAGCTATTCAGG 59.904 45.833 0.00 0.00 45.94 3.86
308 316 3.988976 TTGCAGAGAGCTATTCAGGTT 57.011 42.857 0.00 0.00 45.94 3.50
313 321 4.880696 GCAGAGAGCTATTCAGGTTTTCAT 59.119 41.667 0.00 0.00 41.15 2.57
314 322 5.220815 GCAGAGAGCTATTCAGGTTTTCATG 60.221 44.000 0.00 0.00 41.15 3.07
319 329 6.766944 AGAGCTATTCAGGTTTTCATGATCTG 59.233 38.462 0.00 3.09 40.33 2.90
335 345 6.583427 TCATGATCTGAAATTTGAAACGCTTG 59.417 34.615 0.00 0.00 0.00 4.01
357 367 5.423886 TGTCACGCACCAAATTATCTATCA 58.576 37.500 0.00 0.00 0.00 2.15
358 368 6.054941 TGTCACGCACCAAATTATCTATCAT 58.945 36.000 0.00 0.00 0.00 2.45
359 369 7.213678 TGTCACGCACCAAATTATCTATCATA 58.786 34.615 0.00 0.00 0.00 2.15
362 372 9.936759 TCACGCACCAAATTATCTATCATATAA 57.063 29.630 0.00 0.00 0.00 0.98
417 428 1.159285 TTCTCTTCATTGCAGGTGCG 58.841 50.000 0.00 0.00 45.83 5.34
419 434 0.725686 CTCTTCATTGCAGGTGCGAG 59.274 55.000 0.00 0.00 45.83 5.03
428 443 1.973281 CAGGTGCGAGTTTGGGCAT 60.973 57.895 0.00 0.00 41.83 4.40
435 450 1.368641 CGAGTTTGGGCATCGAATCA 58.631 50.000 0.00 0.00 38.72 2.57
438 453 2.352960 GAGTTTGGGCATCGAATCACTC 59.647 50.000 0.00 0.00 0.00 3.51
443 458 1.270041 GGGCATCGAATCACTCCTCTC 60.270 57.143 0.00 0.00 0.00 3.20
444 459 1.686052 GGCATCGAATCACTCCTCTCT 59.314 52.381 0.00 0.00 0.00 3.10
445 460 2.887783 GGCATCGAATCACTCCTCTCTA 59.112 50.000 0.00 0.00 0.00 2.43
446 461 3.305064 GGCATCGAATCACTCCTCTCTAC 60.305 52.174 0.00 0.00 0.00 2.59
447 462 3.568007 GCATCGAATCACTCCTCTCTACT 59.432 47.826 0.00 0.00 0.00 2.57
448 463 4.757657 GCATCGAATCACTCCTCTCTACTA 59.242 45.833 0.00 0.00 0.00 1.82
449 464 5.334569 GCATCGAATCACTCCTCTCTACTAC 60.335 48.000 0.00 0.00 0.00 2.73
450 465 5.617528 TCGAATCACTCCTCTCTACTACT 57.382 43.478 0.00 0.00 0.00 2.57
451 466 6.728089 TCGAATCACTCCTCTCTACTACTA 57.272 41.667 0.00 0.00 0.00 1.82
452 467 6.514947 TCGAATCACTCCTCTCTACTACTAC 58.485 44.000 0.00 0.00 0.00 2.73
453 468 6.097981 TCGAATCACTCCTCTCTACTACTACA 59.902 42.308 0.00 0.00 0.00 2.74
454 469 6.422701 CGAATCACTCCTCTCTACTACTACAG 59.577 46.154 0.00 0.00 0.00 2.74
455 470 5.026038 TCACTCCTCTCTACTACTACAGC 57.974 47.826 0.00 0.00 0.00 4.40
456 471 4.470304 TCACTCCTCTCTACTACTACAGCA 59.530 45.833 0.00 0.00 0.00 4.41
457 472 5.131308 TCACTCCTCTCTACTACTACAGCAT 59.869 44.000 0.00 0.00 0.00 3.79
458 473 6.326843 TCACTCCTCTCTACTACTACAGCATA 59.673 42.308 0.00 0.00 0.00 3.14
459 474 6.649141 CACTCCTCTCTACTACTACAGCATAG 59.351 46.154 0.00 0.00 0.00 2.23
460 475 6.328148 ACTCCTCTCTACTACTACAGCATAGT 59.672 42.308 6.01 6.01 35.76 2.12
461 476 6.526526 TCCTCTCTACTACTACAGCATAGTG 58.473 44.000 10.16 4.33 33.65 2.74
462 477 5.703592 CCTCTCTACTACTACAGCATAGTGG 59.296 48.000 10.16 9.66 33.65 4.00
463 478 5.064558 TCTCTACTACTACAGCATAGTGGC 58.935 45.833 10.16 0.00 33.65 5.01
464 479 4.788679 TCTACTACTACAGCATAGTGGCA 58.211 43.478 10.16 0.00 33.65 4.92
465 480 5.386060 TCTACTACTACAGCATAGTGGCAT 58.614 41.667 10.16 0.00 33.65 4.40
466 481 6.540083 TCTACTACTACAGCATAGTGGCATA 58.460 40.000 10.16 0.00 33.65 3.14
467 482 5.713792 ACTACTACAGCATAGTGGCATAG 57.286 43.478 10.16 3.16 35.83 2.23
468 483 5.141182 ACTACTACAGCATAGTGGCATAGT 58.859 41.667 10.16 0.00 39.66 2.12
469 484 6.304624 ACTACTACAGCATAGTGGCATAGTA 58.695 40.000 10.16 0.00 38.30 1.82
470 485 6.948886 ACTACTACAGCATAGTGGCATAGTAT 59.051 38.462 10.16 0.00 38.46 2.12
471 486 6.274157 ACTACAGCATAGTGGCATAGTATC 57.726 41.667 0.00 0.00 36.67 2.24
472 487 4.179926 ACAGCATAGTGGCATAGTATCG 57.820 45.455 0.00 0.00 35.83 2.92
492 507 1.474677 GGATCACATGAGCAGTGGAGG 60.475 57.143 0.00 0.00 37.58 4.30
503 524 1.768888 AGTGGAGGTTTCCCCGTGT 60.769 57.895 0.00 0.00 43.33 4.49
528 553 7.936950 TTTCGTGATATGAAGTGATGAGATC 57.063 36.000 0.00 0.00 0.00 2.75
529 554 5.693814 TCGTGATATGAAGTGATGAGATCG 58.306 41.667 0.00 0.00 0.00 3.69
537 562 1.938577 AGTGATGAGATCGCATGCAAC 59.061 47.619 17.22 11.58 42.11 4.17
553 578 5.740803 GCATGCAACATGTGATTGGGATAAT 60.741 40.000 14.21 0.00 0.00 1.28
595 626 1.135315 ACGAGCGGCTTAATACAACGA 60.135 47.619 2.97 0.00 0.00 3.85
597 628 2.097396 CGAGCGGCTTAATACAACGATG 60.097 50.000 2.97 0.00 0.00 3.84
624 655 1.120530 GATGACCCACGTAGGACCAT 58.879 55.000 7.14 9.51 41.22 3.55
670 703 4.560128 CACACACAGTGCTCTACTACAAT 58.440 43.478 0.00 0.00 42.15 2.71
746 779 2.025887 AGATCTTGTGGGCCTTACCTTG 60.026 50.000 4.53 0.00 39.10 3.61
755 788 2.826128 GGGCCTTACCTTGGAAGAAAAG 59.174 50.000 0.84 0.00 39.10 2.27
961 1003 6.757173 TCTTTAATCCCCTCCGATTTCATA 57.243 37.500 0.00 0.00 34.35 2.15
1182 1224 4.689549 TCCCCCGTTGCCGAGAGA 62.690 66.667 0.00 0.00 35.63 3.10
1345 1387 1.171308 CGACGAGGACTTCCAGGTAA 58.829 55.000 0.00 0.00 38.89 2.85
1346 1388 1.542915 CGACGAGGACTTCCAGGTAAA 59.457 52.381 0.00 0.00 38.89 2.01
1347 1389 2.670509 CGACGAGGACTTCCAGGTAAAC 60.671 54.545 0.00 0.00 38.89 2.01
1348 1390 1.271656 ACGAGGACTTCCAGGTAAACG 59.728 52.381 0.00 0.00 38.89 3.60
1349 1391 1.723220 GAGGACTTCCAGGTAAACGC 58.277 55.000 0.00 0.00 38.89 4.84
1350 1392 0.037605 AGGACTTCCAGGTAAACGCG 60.038 55.000 3.53 3.53 38.89 6.01
1351 1393 0.037975 GGACTTCCAGGTAAACGCGA 60.038 55.000 15.93 0.00 35.64 5.87
1352 1394 1.347320 GACTTCCAGGTAAACGCGAG 58.653 55.000 15.93 0.00 0.00 5.03
1353 1395 0.963962 ACTTCCAGGTAAACGCGAGA 59.036 50.000 15.93 0.00 0.00 4.04
1399 1441 3.364322 TGCATTCATTTTTGTGCGATTCG 59.636 39.130 0.62 0.62 40.34 3.34
1431 1473 2.816083 CCGCGCCACCATTTCGTA 60.816 61.111 0.00 0.00 0.00 3.43
1489 1532 4.655963 GGATTTTATCCTGCCTGCAGATA 58.344 43.478 20.29 12.41 46.30 1.98
1566 1692 4.213564 TGTTGGAGTTTTGCCATGTTTT 57.786 36.364 0.00 0.00 34.90 2.43
1626 1752 3.626028 ACAGATTGTCCTTTGAAACGC 57.374 42.857 0.00 0.00 0.00 4.84
1628 1754 4.385825 ACAGATTGTCCTTTGAAACGCTA 58.614 39.130 0.00 0.00 0.00 4.26
1706 1832 0.035439 CCGCCTCCACATACTTTGGT 60.035 55.000 0.00 0.00 35.42 3.67
1719 1845 6.640499 CACATACTTTGGTAATGTGTGTTTGG 59.360 38.462 6.53 0.00 38.30 3.28
1729 1855 1.219646 GTGTGTTTGGCTGCATTTGG 58.780 50.000 0.50 0.00 0.00 3.28
1760 1886 0.820871 GCCGATCAGAGAGGAAGTGT 59.179 55.000 0.00 0.00 0.00 3.55
1770 1896 4.039004 CAGAGAGGAAGTGTGATCATAGGG 59.961 50.000 0.00 0.00 0.00 3.53
1772 1898 2.703007 GAGGAAGTGTGATCATAGGGCT 59.297 50.000 0.00 0.00 0.00 5.19
1773 1899 2.703007 AGGAAGTGTGATCATAGGGCTC 59.297 50.000 0.00 0.00 0.00 4.70
1774 1900 2.703007 GGAAGTGTGATCATAGGGCTCT 59.297 50.000 0.00 0.00 0.00 4.09
1775 1901 3.898123 GGAAGTGTGATCATAGGGCTCTA 59.102 47.826 0.00 0.00 0.00 2.43
1776 1902 4.021544 GGAAGTGTGATCATAGGGCTCTAG 60.022 50.000 0.00 0.00 0.00 2.43
1777 1903 4.461450 AGTGTGATCATAGGGCTCTAGA 57.539 45.455 0.00 0.00 0.00 2.43
1778 1904 5.009436 AGTGTGATCATAGGGCTCTAGAT 57.991 43.478 0.00 2.40 0.00 1.98
1779 1905 4.771577 AGTGTGATCATAGGGCTCTAGATG 59.228 45.833 0.00 0.00 0.00 2.90
1786 1912 4.471761 GGCTCTAGATGCTTGCCC 57.528 61.111 8.44 0.00 37.81 5.36
1797 1923 1.255882 TGCTTGCCCTTTGTGTATGG 58.744 50.000 0.00 0.00 0.00 2.74
1798 1924 1.256812 GCTTGCCCTTTGTGTATGGT 58.743 50.000 0.00 0.00 0.00 3.55
1799 1925 1.067635 GCTTGCCCTTTGTGTATGGTG 60.068 52.381 0.00 0.00 0.00 4.17
1800 1926 2.238521 CTTGCCCTTTGTGTATGGTGT 58.761 47.619 0.00 0.00 0.00 4.16
1801 1927 1.904287 TGCCCTTTGTGTATGGTGTC 58.096 50.000 0.00 0.00 0.00 3.67
1802 1928 1.143889 TGCCCTTTGTGTATGGTGTCA 59.856 47.619 0.00 0.00 0.00 3.58
1831 1957 5.728637 AAGCTTGGAGAATTTGGGTTTAG 57.271 39.130 0.00 0.00 0.00 1.85
1854 1980 5.482175 AGGATAGTCATGTAGTATTGCCCTC 59.518 44.000 0.00 0.00 0.00 4.30
1878 2004 9.882996 CTCTAATCAAGCGAATAAATAAATGCA 57.117 29.630 0.00 0.00 0.00 3.96
1901 2027 4.242811 AGCCATGTTGGATAGGGAGATTA 58.757 43.478 0.00 0.00 40.96 1.75
1919 2045 7.231467 GGAGATTATGGAAAGGCAGGTATTTA 58.769 38.462 0.00 0.00 0.00 1.40
1921 2047 9.959721 GAGATTATGGAAAGGCAGGTATTTATA 57.040 33.333 0.00 0.00 0.00 0.98
1922 2048 9.965902 AGATTATGGAAAGGCAGGTATTTATAG 57.034 33.333 0.00 0.00 0.00 1.31
1965 2091 0.944386 TGCAGAAAGAACTTGACGGC 59.056 50.000 0.00 0.00 0.00 5.68
2175 2301 2.802816 GCGTATTATTGCTGAGACTGGG 59.197 50.000 0.00 0.00 0.00 4.45
2227 2353 1.891919 TGTGCTCGGTTTGGTCTGC 60.892 57.895 0.00 0.00 0.00 4.26
2372 2498 6.029346 AGAATATGCCTTTGTGTTTCCAAG 57.971 37.500 0.00 0.00 0.00 3.61
2399 2525 4.523813 CGTTGCGGCTATTACTTATTTGG 58.476 43.478 0.00 0.00 0.00 3.28
2404 2530 5.068460 TGCGGCTATTACTTATTTGGCAAAT 59.932 36.000 26.86 26.86 34.90 2.32
2406 2532 6.734137 CGGCTATTACTTATTTGGCAAATCA 58.266 36.000 27.42 16.75 32.38 2.57
2407 2533 7.370383 CGGCTATTACTTATTTGGCAAATCAT 58.630 34.615 27.42 16.47 32.38 2.45
2413 2539 9.971922 ATTACTTATTTGGCAAATCATAAGCTC 57.028 29.630 27.42 0.00 34.01 4.09
2422 2548 5.277876 GGCAAATCATAAGCTCTGAGATGTG 60.278 44.000 9.28 5.59 0.00 3.21
2423 2549 5.526479 GCAAATCATAAGCTCTGAGATGTGA 59.474 40.000 9.28 10.88 0.00 3.58
2434 2560 2.089201 TGAGATGTGAAATGCTGCTGG 58.911 47.619 0.00 0.00 0.00 4.85
2480 2606 5.094429 TCGTTTGTTTCTCATCATGTGTG 57.906 39.130 0.00 0.00 0.00 3.82
2481 2607 4.574421 TCGTTTGTTTCTCATCATGTGTGT 59.426 37.500 0.00 0.00 0.00 3.72
2482 2608 4.671964 CGTTTGTTTCTCATCATGTGTGTG 59.328 41.667 0.00 0.00 0.00 3.82
2543 2669 0.461548 CGCTGAAGGATGCTACCTCA 59.538 55.000 3.01 0.00 39.62 3.86
2720 2846 1.439353 CTGACGTGCTGGTTGCTTGT 61.439 55.000 0.00 0.00 43.37 3.16
2846 2972 2.339047 GCACGCTGCAACATTAACG 58.661 52.632 0.00 0.00 44.26 3.18
2912 3038 2.014857 CAGGATGCTGATGGACAAGTG 58.985 52.381 8.85 0.00 0.00 3.16
2948 3074 4.130118 CCATCAGTGCTGGGTAAGTATTC 58.870 47.826 5.01 0.00 0.00 1.75
3205 3339 3.508762 GCTGCAGTTGATTTTCATCCAG 58.491 45.455 16.64 0.00 0.00 3.86
3222 3356 4.808414 TCCAGTTGACTTCTAGTCCATG 57.192 45.455 4.52 0.00 44.44 3.66
3248 3382 9.672086 GTACTAAATGCTGATAGTAGTTCTGAG 57.328 37.037 4.15 0.00 35.79 3.35
3279 3413 8.948631 TCCTGAGTGTTTTCATATATCTTCAC 57.051 34.615 0.00 0.00 0.00 3.18
3334 3474 7.912250 GCTGGTCTAGATTTACATGTGAATTTG 59.088 37.037 16.14 9.96 0.00 2.32
3378 3518 8.658499 TTACAGAAGGTTAAAACTCTTGAGAC 57.342 34.615 4.49 0.00 0.00 3.36
3381 3521 5.760743 AGAAGGTTAAAACTCTTGAGACAGC 59.239 40.000 4.49 0.00 0.00 4.40
3407 3547 2.494059 TCAGTTTACAGCTGCTGAACC 58.506 47.619 34.28 18.20 35.36 3.62
3415 3555 2.880890 ACAGCTGCTGAACCTGTTTTAG 59.119 45.455 34.28 4.95 36.48 1.85
3440 3580 3.788227 TGATGTGGAAAAGTAGGCAGT 57.212 42.857 0.00 0.00 0.00 4.40
3578 3722 5.679792 ACTGTTTAAAAACGTTCTGAATCGC 59.320 36.000 0.00 0.00 41.74 4.58
3594 3738 8.420374 TCTGAATCGCTAGTTTATAAACCTTG 57.580 34.615 21.92 14.14 39.71 3.61
3625 3769 1.803555 TCTGCAACGCGAAATGAATGA 59.196 42.857 15.93 5.35 0.00 2.57
3695 3849 4.559153 ACAGCTGTTGTTTATGAATTGCC 58.441 39.130 15.25 0.00 36.31 4.52
3710 3864 4.100808 TGAATTGCCAGCTTGTAAACCTTT 59.899 37.500 0.00 0.00 0.00 3.11
3816 3985 2.444421 TCAATGGCATGTATGTGCACA 58.556 42.857 24.08 24.08 46.81 4.57
3869 4038 6.803320 CAGCACACAATGAACTTAATACCAAG 59.197 38.462 0.00 0.00 0.00 3.61
3876 4045 7.067494 ACAATGAACTTAATACCAAGGCATCTC 59.933 37.037 0.00 0.00 0.00 2.75
3881 4050 5.044846 ACTTAATACCAAGGCATCTCCAAGT 60.045 40.000 0.00 0.00 37.29 3.16
3920 4121 9.549509 GAAAAATAACACGTAACATGCTTGATA 57.450 29.630 6.60 0.00 0.00 2.15
4005 4206 1.005215 CAGCTTCCATTTCCTCACCCT 59.995 52.381 0.00 0.00 0.00 4.34
4012 4213 2.359900 CATTTCCTCACCCTACAGTGC 58.640 52.381 0.00 0.00 37.68 4.40
4013 4214 1.729586 TTTCCTCACCCTACAGTGCT 58.270 50.000 0.00 0.00 37.68 4.40
4014 4215 2.615986 TTCCTCACCCTACAGTGCTA 57.384 50.000 0.00 0.00 37.68 3.49
4015 4216 2.615986 TCCTCACCCTACAGTGCTAA 57.384 50.000 0.00 0.00 37.68 3.09
4016 4217 2.457598 TCCTCACCCTACAGTGCTAAG 58.542 52.381 0.00 0.00 37.68 2.18
4017 4218 2.180276 CCTCACCCTACAGTGCTAAGT 58.820 52.381 0.00 0.00 37.68 2.24
4018 4219 3.010920 TCCTCACCCTACAGTGCTAAGTA 59.989 47.826 0.00 0.00 37.68 2.24
4019 4220 3.767673 CCTCACCCTACAGTGCTAAGTAA 59.232 47.826 0.00 0.00 37.68 2.24
4020 4221 4.406003 CCTCACCCTACAGTGCTAAGTAAT 59.594 45.833 0.00 0.00 37.68 1.89
4021 4222 5.597182 CCTCACCCTACAGTGCTAAGTAATA 59.403 44.000 0.00 0.00 37.68 0.98
4022 4223 6.239064 CCTCACCCTACAGTGCTAAGTAATAG 60.239 46.154 0.00 0.00 37.68 1.73
4023 4224 5.597182 TCACCCTACAGTGCTAAGTAATAGG 59.403 44.000 0.00 0.00 37.68 2.57
4024 4225 4.344390 ACCCTACAGTGCTAAGTAATAGGC 59.656 45.833 0.00 0.00 31.83 3.93
4025 4226 4.589374 CCCTACAGTGCTAAGTAATAGGCT 59.411 45.833 0.00 0.00 31.83 4.58
4026 4227 5.070580 CCCTACAGTGCTAAGTAATAGGCTT 59.929 44.000 0.00 0.00 31.83 4.35
4027 4228 5.986135 CCTACAGTGCTAAGTAATAGGCTTG 59.014 44.000 0.00 0.00 31.83 4.01
4028 4229 5.677319 ACAGTGCTAAGTAATAGGCTTGA 57.323 39.130 0.00 0.00 31.83 3.02
4029 4230 6.049955 ACAGTGCTAAGTAATAGGCTTGAA 57.950 37.500 0.00 0.00 31.83 2.69
4030 4231 6.653989 ACAGTGCTAAGTAATAGGCTTGAAT 58.346 36.000 0.00 0.00 31.83 2.57
4031 4232 7.792032 ACAGTGCTAAGTAATAGGCTTGAATA 58.208 34.615 0.00 0.00 31.83 1.75
4140 4341 2.012673 GTCTTAAGCCTGCTGGTGATG 58.987 52.381 11.69 0.30 35.27 3.07
4171 4372 7.819415 TGATCGATTGAAAACTGATTCAGTAGT 59.181 33.333 19.27 10.37 44.62 2.73
4324 4531 1.276421 GAGAAGCTCTGCCCAACACTA 59.724 52.381 0.00 0.00 0.00 2.74
4432 4639 5.223449 ACTCCGGAAAGACTAAACAATGA 57.777 39.130 5.23 0.00 0.00 2.57
4460 4667 6.371809 TTTCGTATGAGCAGTTTTGAAAGT 57.628 33.333 0.00 0.00 0.00 2.66
4466 4673 6.892310 ATGAGCAGTTTTGAAAGTGAAAAC 57.108 33.333 13.90 0.00 40.88 2.43
4477 4685 7.524294 TTGAAAGTGAAAACAGAAAGCAATC 57.476 32.000 0.00 0.00 0.00 2.67
4501 4709 4.023450 GCTTAGTGTTGTTCTTTGGGGTAC 60.023 45.833 0.00 0.00 0.00 3.34
4554 4762 7.287235 AGTCGGTTGGTCTATAGCTAATTTAGT 59.713 37.037 0.00 0.00 0.00 2.24
4636 4844 1.722464 CTCGTTTTGTGCCATGCATTG 59.278 47.619 0.00 0.00 41.91 2.82
4652 4860 2.095567 GCATTGCACTCAATCTGACGTT 60.096 45.455 3.15 0.00 40.74 3.99
4689 4900 4.678287 GTGATGATTTTGCTGTGTGTTGAG 59.322 41.667 0.00 0.00 0.00 3.02
4709 4920 4.103153 TGAGACAGAGAAGATTTGGTTGGT 59.897 41.667 0.00 0.00 0.00 3.67
4722 4933 3.306472 TGGTTGGTTGGCTTTCTTACT 57.694 42.857 0.00 0.00 0.00 2.24
4837 5048 1.471684 CTGAGGTTGCAATCTTCCAGC 59.528 52.381 14.71 0.66 0.00 4.85
4841 5052 2.232941 AGGTTGCAATCTTCCAGCATTG 59.767 45.455 6.34 0.00 38.19 2.82
4975 5186 7.859598 AGAATCAGATCGACATGATTTTAAGC 58.140 34.615 21.48 12.27 44.18 3.09
5002 5220 2.659063 CGCAGGGACAGGGATGTCA 61.659 63.158 10.29 0.00 40.38 3.58
5048 5269 5.560966 TTCTGCGGGAACTTATTTTGATC 57.439 39.130 0.00 0.00 0.00 2.92
5156 5377 1.103803 ACATTAGAGCGAGCCGAAGA 58.896 50.000 0.00 0.00 0.00 2.87
5167 5388 2.736719 CGAGCCGAAGACATGATCTGTT 60.737 50.000 0.00 0.00 38.54 3.16
5361 5583 5.297527 TGCATCATCAAATTATGCTTCGAGT 59.702 36.000 10.60 0.00 44.96 4.18
5365 5587 9.720667 CATCATCAAATTATGCTTCGAGTAAAA 57.279 29.630 0.00 0.00 0.00 1.52
5374 5596 9.864034 ATTATGCTTCGAGTAAAATTTACATCG 57.136 29.630 20.78 20.78 0.00 3.84
5390 5612 8.825667 ATTTACATCGCTAAAATGTGGTTTTT 57.174 26.923 0.00 0.00 40.40 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 0.027716 CGTAGCACTGCTCGTATCGT 59.972 55.000 6.86 0.00 40.44 3.73
19 20 0.381089 ACCGTAGCACTGCTCGTATC 59.619 55.000 6.86 0.00 40.44 2.24
24 25 1.226746 AAAACACCGTAGCACTGCTC 58.773 50.000 6.86 0.00 40.44 4.26
59 61 5.187186 AGAAATGGATATTCCGCGGTAGTAT 59.813 40.000 27.15 20.22 40.17 2.12
64 66 2.930826 AGAAATGGATATTCCGCGGT 57.069 45.000 27.15 9.68 40.17 5.68
66 68 4.389077 GGACTTAGAAATGGATATTCCGCG 59.611 45.833 0.00 0.00 40.17 6.46
84 86 1.277557 GGTGCTGATGAGTCTGGACTT 59.722 52.381 4.67 0.00 42.66 3.01
93 95 1.277273 TCTTGACCAGGTGCTGATGAG 59.723 52.381 0.00 0.00 32.44 2.90
153 160 4.016444 ACCTCACGCACCAAATTATCAAT 58.984 39.130 0.00 0.00 0.00 2.57
155 162 2.746904 CACCTCACGCACCAAATTATCA 59.253 45.455 0.00 0.00 0.00 2.15
165 172 0.305313 TTAAAACGCACCTCACGCAC 59.695 50.000 0.00 0.00 0.00 5.34
174 181 6.763303 AATGGTCTGAAATTTAAAACGCAC 57.237 33.333 0.00 0.00 0.00 5.34
189 196 9.469807 GAGTTACTCATATGTCTAAATGGTCTG 57.530 37.037 7.59 0.00 0.00 3.51
190 197 9.427821 AGAGTTACTCATATGTCTAAATGGTCT 57.572 33.333 15.23 0.00 32.06 3.85
191 198 9.685828 GAGAGTTACTCATATGTCTAAATGGTC 57.314 37.037 15.23 0.00 44.36 4.02
271 278 6.549364 TCTCTGCAAAAAGGTCAAATTTAGGA 59.451 34.615 0.00 0.00 0.00 2.94
282 290 4.655963 TGAATAGCTCTCTGCAAAAAGGT 58.344 39.130 0.00 0.00 45.94 3.50
284 292 4.699257 ACCTGAATAGCTCTCTGCAAAAAG 59.301 41.667 0.00 0.00 45.94 2.27
290 298 4.256920 TGAAAACCTGAATAGCTCTCTGC 58.743 43.478 0.00 0.00 43.29 4.26
293 301 6.991531 AGATCATGAAAACCTGAATAGCTCTC 59.008 38.462 0.00 0.00 0.00 3.20
313 321 5.830912 ACAAGCGTTTCAAATTTCAGATCA 58.169 33.333 0.00 0.00 0.00 2.92
314 322 5.914635 TGACAAGCGTTTCAAATTTCAGATC 59.085 36.000 0.00 0.00 0.00 2.75
319 329 3.360669 GCGTGACAAGCGTTTCAAATTTC 60.361 43.478 0.00 0.00 0.00 2.17
326 336 1.368850 GGTGCGTGACAAGCGTTTC 60.369 57.895 8.84 0.03 37.44 2.78
335 345 5.984233 TGATAGATAATTTGGTGCGTGAC 57.016 39.130 0.00 0.00 0.00 3.67
390 400 6.365247 CACCTGCAATGAAGAGAAAATTCAAG 59.635 38.462 0.00 0.00 39.92 3.02
400 410 0.725686 CTCGCACCTGCAATGAAGAG 59.274 55.000 1.80 5.73 42.21 2.85
417 428 2.352960 GAGTGATTCGATGCCCAAACTC 59.647 50.000 0.00 0.00 0.00 3.01
419 434 1.401905 GGAGTGATTCGATGCCCAAAC 59.598 52.381 0.00 0.00 0.00 2.93
428 443 5.617528 AGTAGTAGAGAGGAGTGATTCGA 57.382 43.478 0.00 0.00 0.00 3.71
435 450 5.640158 ATGCTGTAGTAGTAGAGAGGAGT 57.360 43.478 5.94 0.00 0.00 3.85
438 453 5.703592 CCACTATGCTGTAGTAGTAGAGAGG 59.296 48.000 5.94 0.00 35.56 3.69
443 458 5.713792 ATGCCACTATGCTGTAGTAGTAG 57.286 43.478 2.68 0.00 30.37 2.57
444 459 6.304624 ACTATGCCACTATGCTGTAGTAGTA 58.695 40.000 2.68 0.00 34.18 1.82
445 460 5.141182 ACTATGCCACTATGCTGTAGTAGT 58.859 41.667 2.68 1.00 34.18 2.73
446 461 5.713792 ACTATGCCACTATGCTGTAGTAG 57.286 43.478 2.68 0.00 34.18 2.57
447 462 6.093633 CGATACTATGCCACTATGCTGTAGTA 59.906 42.308 2.68 0.00 38.60 1.82
448 463 5.106118 CGATACTATGCCACTATGCTGTAGT 60.106 44.000 0.00 0.00 37.26 2.73
449 464 5.335935 CGATACTATGCCACTATGCTGTAG 58.664 45.833 0.00 0.00 0.00 2.74
450 465 4.157840 CCGATACTATGCCACTATGCTGTA 59.842 45.833 0.00 0.00 0.00 2.74
451 466 3.056536 CCGATACTATGCCACTATGCTGT 60.057 47.826 0.00 0.00 0.00 4.40
452 467 3.193479 TCCGATACTATGCCACTATGCTG 59.807 47.826 0.00 0.00 0.00 4.41
453 468 3.431415 TCCGATACTATGCCACTATGCT 58.569 45.455 0.00 0.00 0.00 3.79
454 469 3.868757 TCCGATACTATGCCACTATGC 57.131 47.619 0.00 0.00 0.00 3.14
455 470 5.105756 TGTGATCCGATACTATGCCACTATG 60.106 44.000 0.00 0.00 0.00 2.23
456 471 5.016831 TGTGATCCGATACTATGCCACTAT 58.983 41.667 0.00 0.00 0.00 2.12
457 472 4.403734 TGTGATCCGATACTATGCCACTA 58.596 43.478 0.00 0.00 0.00 2.74
458 473 3.230976 TGTGATCCGATACTATGCCACT 58.769 45.455 0.00 0.00 0.00 4.00
459 474 3.660501 TGTGATCCGATACTATGCCAC 57.339 47.619 0.00 0.00 0.00 5.01
460 475 3.831911 TCATGTGATCCGATACTATGCCA 59.168 43.478 0.00 0.00 0.00 4.92
461 476 4.428209 CTCATGTGATCCGATACTATGCC 58.572 47.826 0.00 0.00 0.00 4.40
462 477 3.862267 GCTCATGTGATCCGATACTATGC 59.138 47.826 0.00 0.00 0.00 3.14
463 478 5.064441 TGCTCATGTGATCCGATACTATG 57.936 43.478 0.00 0.00 0.00 2.23
464 479 4.769488 ACTGCTCATGTGATCCGATACTAT 59.231 41.667 0.00 0.00 0.00 2.12
465 480 4.022849 CACTGCTCATGTGATCCGATACTA 60.023 45.833 0.00 0.00 37.60 1.82
466 481 2.961741 ACTGCTCATGTGATCCGATACT 59.038 45.455 0.00 0.00 0.00 2.12
467 482 3.055591 CACTGCTCATGTGATCCGATAC 58.944 50.000 0.00 0.00 37.60 2.24
468 483 2.036346 CCACTGCTCATGTGATCCGATA 59.964 50.000 0.00 0.00 37.60 2.92
469 484 1.202615 CCACTGCTCATGTGATCCGAT 60.203 52.381 0.00 0.00 37.60 4.18
470 485 0.176449 CCACTGCTCATGTGATCCGA 59.824 55.000 0.00 0.00 37.60 4.55
471 486 0.176449 TCCACTGCTCATGTGATCCG 59.824 55.000 0.00 0.00 37.60 4.18
472 487 1.474677 CCTCCACTGCTCATGTGATCC 60.475 57.143 0.00 0.00 37.60 3.36
492 507 1.015868 TCACGAAAACACGGGGAAAC 58.984 50.000 0.00 0.00 37.29 2.78
503 524 7.168135 CGATCTCATCACTTCATATCACGAAAA 59.832 37.037 0.00 0.00 0.00 2.29
528 553 1.273688 CCAATCACATGTTGCATGCG 58.726 50.000 14.09 0.00 0.00 4.73
529 554 1.205179 TCCCAATCACATGTTGCATGC 59.795 47.619 11.82 11.82 0.00 4.06
537 562 6.947644 TGACTTGATTATCCCAATCACATG 57.052 37.500 0.00 0.00 36.49 3.21
553 578 0.843309 TGGTGGAGCCTTTGACTTGA 59.157 50.000 0.00 0.00 38.35 3.02
624 655 4.351938 CGCTCGGGTCCACGTCAA 62.352 66.667 0.00 0.00 34.94 3.18
652 685 2.600420 CGCATTGTAGTAGAGCACTGTG 59.400 50.000 2.76 2.76 38.24 3.66
711 744 2.919856 ATCTGGGAGCCGGATCCG 60.920 66.667 31.38 27.65 45.64 4.18
715 748 1.306141 ACAAGATCTGGGAGCCGGA 60.306 57.895 5.05 0.00 43.71 5.14
739 772 6.183361 TGAGGATCACTTTTCTTCCAAGGTAA 60.183 38.462 0.00 0.00 42.56 2.85
810 843 2.847715 GTACCGGCAGGGGGCTAT 60.848 66.667 8.08 0.00 44.01 2.97
961 1003 3.007831 CAGAGAGAAGAAAGAAGGCAGGT 59.992 47.826 0.00 0.00 0.00 4.00
1173 1215 2.636412 CCCGTTCACTCTCTCGGCA 61.636 63.158 0.00 0.00 41.38 5.69
1236 1278 1.294138 CCCGAACTTGCCGAACCTA 59.706 57.895 0.00 0.00 0.00 3.08
1345 1387 3.254024 AACATGGGGCTCTCGCGTT 62.254 57.895 5.77 0.00 36.88 4.84
1346 1388 3.665675 GAACATGGGGCTCTCGCGT 62.666 63.158 5.77 0.00 36.88 6.01
1347 1389 2.859273 AAGAACATGGGGCTCTCGCG 62.859 60.000 0.00 0.00 36.88 5.87
1348 1390 1.078143 AAGAACATGGGGCTCTCGC 60.078 57.895 0.00 0.00 0.00 5.03
1349 1391 0.250234 TCAAGAACATGGGGCTCTCG 59.750 55.000 0.00 0.00 0.00 4.04
1350 1392 1.407989 CCTCAAGAACATGGGGCTCTC 60.408 57.143 0.00 0.00 33.26 3.20
1351 1393 0.622665 CCTCAAGAACATGGGGCTCT 59.377 55.000 0.00 0.00 33.26 4.09
1352 1394 0.620556 TCCTCAAGAACATGGGGCTC 59.379 55.000 0.00 0.00 41.04 4.70
1353 1395 1.213926 GATCCTCAAGAACATGGGGCT 59.786 52.381 0.00 0.00 41.04 5.19
1365 1407 3.657398 ATGAATGCACCAGATCCTCAA 57.343 42.857 0.00 0.00 0.00 3.02
1399 1441 0.933509 CGCGGACGCTCTAATACCAC 60.934 60.000 15.11 0.00 39.32 4.16
1431 1473 3.525537 CATCAAATCGCCTATATCGCCT 58.474 45.455 0.00 0.00 0.00 5.52
1489 1532 1.067213 GCAATACACGCAAAACCCCAT 60.067 47.619 0.00 0.00 0.00 4.00
1566 1692 0.109723 GCTCCCAACTACCACAACCA 59.890 55.000 0.00 0.00 0.00 3.67
1706 1832 4.056740 CAAATGCAGCCAAACACACATTA 58.943 39.130 0.00 0.00 0.00 1.90
1719 1845 2.676076 CAACTACCAACCAAATGCAGC 58.324 47.619 0.00 0.00 0.00 5.25
1729 1855 1.017177 TGATCGGCGCAACTACCAAC 61.017 55.000 10.83 0.00 0.00 3.77
1760 1886 4.058417 AGCATCTAGAGCCCTATGATCA 57.942 45.455 0.00 0.00 0.00 2.92
1770 1896 1.674962 CAAAGGGCAAGCATCTAGAGC 59.325 52.381 0.00 2.33 0.00 4.09
1772 1898 2.040278 ACACAAAGGGCAAGCATCTAGA 59.960 45.455 0.00 0.00 0.00 2.43
1773 1899 2.440409 ACACAAAGGGCAAGCATCTAG 58.560 47.619 0.00 0.00 0.00 2.43
1774 1900 2.584835 ACACAAAGGGCAAGCATCTA 57.415 45.000 0.00 0.00 0.00 1.98
1775 1901 2.584835 TACACAAAGGGCAAGCATCT 57.415 45.000 0.00 0.00 0.00 2.90
1776 1902 2.159198 CCATACACAAAGGGCAAGCATC 60.159 50.000 0.00 0.00 0.00 3.91
1777 1903 1.826720 CCATACACAAAGGGCAAGCAT 59.173 47.619 0.00 0.00 0.00 3.79
1778 1904 1.255882 CCATACACAAAGGGCAAGCA 58.744 50.000 0.00 0.00 0.00 3.91
1779 1905 1.067635 CACCATACACAAAGGGCAAGC 60.068 52.381 0.00 0.00 0.00 4.01
1786 1912 6.558771 TTGATTCTGACACCATACACAAAG 57.441 37.500 0.00 0.00 0.00 2.77
1797 1923 4.067896 TCTCCAAGCTTTGATTCTGACAC 58.932 43.478 0.00 0.00 0.00 3.67
1798 1924 4.356405 TCTCCAAGCTTTGATTCTGACA 57.644 40.909 0.00 0.00 0.00 3.58
1799 1925 5.893897 ATTCTCCAAGCTTTGATTCTGAC 57.106 39.130 0.00 0.00 0.00 3.51
1800 1926 6.294899 CCAAATTCTCCAAGCTTTGATTCTGA 60.295 38.462 0.00 0.00 31.76 3.27
1801 1927 5.867716 CCAAATTCTCCAAGCTTTGATTCTG 59.132 40.000 0.00 0.00 31.76 3.02
1802 1928 5.046807 CCCAAATTCTCCAAGCTTTGATTCT 60.047 40.000 0.00 0.00 31.76 2.40
1831 1957 5.482175 AGAGGGCAATACTACATGACTATCC 59.518 44.000 0.00 0.00 0.00 2.59
1878 2004 2.492025 TCTCCCTATCCAACATGGCTT 58.508 47.619 0.00 0.00 37.47 4.35
1901 2027 8.058847 TCAAACTATAAATACCTGCCTTTCCAT 58.941 33.333 0.00 0.00 0.00 3.41
1919 2045 9.167311 GATAGAAGAAATGTGGTGTCAAACTAT 57.833 33.333 0.00 0.00 0.00 2.12
1921 2047 7.173907 CAGATAGAAGAAATGTGGTGTCAAACT 59.826 37.037 0.00 0.00 0.00 2.66
1922 2048 7.301054 CAGATAGAAGAAATGTGGTGTCAAAC 58.699 38.462 0.00 0.00 0.00 2.93
1943 2069 3.070018 CCGTCAAGTTCTTTCTGCAGAT 58.930 45.455 19.04 0.00 0.00 2.90
2202 2328 0.732571 CAAACCGAGCACACACTGTT 59.267 50.000 0.00 0.00 0.00 3.16
2227 2353 2.876550 CACCCATGTAGATGATGCACTG 59.123 50.000 0.46 0.00 0.00 3.66
2333 2459 5.585445 GCATATTCTCCAGAGATAAGGCATG 59.415 44.000 0.00 0.00 37.29 4.06
2399 2525 5.526479 TCACATCTCAGAGCTTATGATTTGC 59.474 40.000 4.90 0.00 0.00 3.68
2404 2530 5.526479 GCATTTCACATCTCAGAGCTTATGA 59.474 40.000 4.90 2.93 0.00 2.15
2406 2532 5.527951 CAGCATTTCACATCTCAGAGCTTAT 59.472 40.000 0.00 0.00 0.00 1.73
2407 2533 4.874396 CAGCATTTCACATCTCAGAGCTTA 59.126 41.667 0.00 0.00 0.00 3.09
2413 2539 2.097629 CCAGCAGCATTTCACATCTCAG 59.902 50.000 0.00 0.00 0.00 3.35
2422 2548 1.549203 TTCTTCCCCAGCAGCATTTC 58.451 50.000 0.00 0.00 0.00 2.17
2423 2549 2.242882 ATTCTTCCCCAGCAGCATTT 57.757 45.000 0.00 0.00 0.00 2.32
2434 2560 4.767409 ACAAGCCTAACAAGAATTCTTCCC 59.233 41.667 17.91 3.52 33.11 3.97
2480 2606 1.792949 CTTACCTGTGCGAAGACACAC 59.207 52.381 0.00 0.00 45.36 3.82
2482 2608 1.429463 CCTTACCTGTGCGAAGACAC 58.571 55.000 0.00 0.00 41.10 3.67
2543 2669 2.362369 CCAGTCACGGATGGCCTCT 61.362 63.158 3.32 0.00 0.00 3.69
2720 2846 1.617850 GCATTTGATCCACCACCAACA 59.382 47.619 0.00 0.00 0.00 3.33
2843 2969 1.534717 TCCGACTTCCCCCTTCGTT 60.535 57.895 0.00 0.00 0.00 3.85
2846 2972 0.249676 GAACTCCGACTTCCCCCTTC 59.750 60.000 0.00 0.00 0.00 3.46
2912 3038 3.410960 GATGGAGTGGGGCTCAATC 57.589 57.895 6.20 6.20 44.74 2.67
2948 3074 7.869429 AGAAAAATGCTTCCAACTTAACATCAG 59.131 33.333 0.00 0.00 0.00 2.90
3205 3339 9.088512 CATTTAGTACATGGACTAGAAGTCAAC 57.911 37.037 17.27 0.23 46.79 3.18
3222 3356 9.672086 CTCAGAACTACTATCAGCATTTAGTAC 57.328 37.037 0.00 0.00 31.37 2.73
3248 3382 6.992063 ATATGAAAACACTCAGGATGTCAC 57.008 37.500 0.00 0.00 37.40 3.67
3279 3413 2.800544 CCTAAACCACAGACTTGTCACG 59.199 50.000 3.49 0.00 34.62 4.35
3334 3474 3.560636 AATGCCTACAGTGTACCATCC 57.439 47.619 0.00 0.00 0.00 3.51
3345 3485 7.228590 AGTTTTAACCTTCTGTAATGCCTACA 58.771 34.615 0.00 0.00 38.23 2.74
3357 3497 5.760743 GCTGTCTCAAGAGTTTTAACCTTCT 59.239 40.000 0.00 0.00 0.00 2.85
3378 3518 4.285292 CAGCTGTAAACTGAAACTTGCTG 58.715 43.478 5.25 0.00 37.32 4.41
3381 3521 4.035558 TCAGCAGCTGTAAACTGAAACTTG 59.964 41.667 22.10 0.00 36.27 3.16
3415 3555 6.543831 ACTGCCTACTTTTCCACATCATATTC 59.456 38.462 0.00 0.00 0.00 1.75
3561 3705 5.668558 AACTAGCGATTCAGAACGTTTTT 57.331 34.783 0.46 0.00 0.00 1.94
3594 3738 2.222596 CGCGTTGCAGATTTAGTCAGTC 60.223 50.000 0.00 0.00 0.00 3.51
3604 3748 2.419673 TCATTCATTTCGCGTTGCAGAT 59.580 40.909 5.77 0.00 0.00 2.90
3625 3769 5.865085 TCAGATGCCTAAAGTAGTGTTTGT 58.135 37.500 0.00 0.00 0.00 2.83
3695 3849 7.724305 TTACTCAGTAAAGGTTTACAAGCTG 57.276 36.000 13.68 4.83 44.14 4.24
3710 3864 9.562408 TGACCATGTGTTTAAAATTACTCAGTA 57.438 29.630 0.00 0.00 0.00 2.74
3816 3985 8.752187 AGTATTAAAGATTGCAACATCAACCAT 58.248 29.630 0.00 0.00 0.00 3.55
3822 3991 7.970061 TGCTGAAGTATTAAAGATTGCAACATC 59.030 33.333 0.00 0.00 0.00 3.06
3869 4038 2.479566 TTCAGTCACTTGGAGATGCC 57.520 50.000 0.00 0.00 37.10 4.40
3920 4121 6.309357 TGCAGCCAATATCTAAGATGGAAAT 58.691 36.000 0.00 0.00 34.82 2.17
3981 4182 1.101331 GAGGAAATGGAAGCTGCCAG 58.899 55.000 20.89 0.00 42.15 4.85
4005 4206 6.785337 TCAAGCCTATTACTTAGCACTGTA 57.215 37.500 0.00 0.00 0.00 2.74
4021 4222 9.289782 CAAGCCTATTACTTAATATTCAAGCCT 57.710 33.333 0.00 0.00 0.00 4.58
4022 4223 9.284968 TCAAGCCTATTACTTAATATTCAAGCC 57.715 33.333 0.00 0.00 0.00 4.35
4140 4341 4.253685 TCAGTTTTCAATCGATCAGGGAC 58.746 43.478 0.00 0.00 0.00 4.46
4432 4639 2.698855 ACTGCTCATACGAAAGCCAT 57.301 45.000 0.00 0.00 37.73 4.40
4477 4685 2.031157 CCCCAAAGAACAACACTAAGCG 60.031 50.000 0.00 0.00 0.00 4.68
4501 4709 8.163408 TCCAGGATTATTTGTACCCTCATATTG 58.837 37.037 0.00 0.00 0.00 1.90
4636 4844 4.474226 AAGAAAACGTCAGATTGAGTGC 57.526 40.909 0.00 0.00 0.00 4.40
4652 4860 7.679164 GCAAAATCATCACAAGGCAAAAAGAAA 60.679 33.333 0.00 0.00 0.00 2.52
4689 4900 4.022849 CCAACCAACCAAATCTTCTCTGTC 60.023 45.833 0.00 0.00 0.00 3.51
4822 5033 1.997606 GCAATGCTGGAAGATTGCAAC 59.002 47.619 0.00 0.00 46.78 4.17
4837 5048 1.610038 TCAAAGACACTGCAGGCAATG 59.390 47.619 19.93 9.67 0.00 2.82
4841 5052 1.269257 GGTTTCAAAGACACTGCAGGC 60.269 52.381 19.93 7.03 0.00 4.85
4975 5186 1.354337 CTGTCCCTGCGATGAACACG 61.354 60.000 0.00 0.00 0.00 4.49
5028 5249 6.867662 ATAGATCAAAATAAGTTCCCGCAG 57.132 37.500 0.00 0.00 0.00 5.18
5156 5377 9.857656 ATTATTTCCAGACATAACAGATCATGT 57.142 29.630 0.00 0.00 46.97 3.21
5189 5410 9.708222 CGAATCAAACTTCCTATGAAAATAGTG 57.292 33.333 0.00 0.00 0.00 2.74
5361 5583 9.915629 AACCACATTTTAGCGATGTAAATTTTA 57.084 25.926 0.00 0.00 36.04 1.52
5365 5587 8.825667 AAAAACCACATTTTAGCGATGTAAAT 57.174 26.923 0.00 0.00 39.70 1.40


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

AutoCloner maintained by Alex Coulton.