Multiple sequence alignment - TraesCS3A01G355900

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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 TraesCS3A01G355900 chr3A 100.000 2598 0 0 1 2598 603802425 603805022 0.000000e+00 4798
1 TraesCS3A01G355900 chr3B 88.462 2054 158 48 1 2016 611726462 611728474 0.000000e+00 2407
2 TraesCS3A01G355900 chr3B 85.496 131 17 2 2237 2366 611728608 611728737 4.510000e-28 135
3 TraesCS3A01G355900 chr3D 91.921 1473 84 24 692 2149 461212532 461213984 0.000000e+00 2028
4 TraesCS3A01G355900 chr3D 80.896 848 95 33 1 809 461211712 461212531 7.950000e-170 606
5 TraesCS3A01G355900 chr1B 79.089 593 76 34 11 573 469588674 469589248 5.280000e-97 364
6 TraesCS3A01G355900 chr1B 82.908 392 52 12 993 1378 513545775 513545393 3.200000e-89 339
7 TraesCS3A01G355900 chr1B 89.524 105 11 0 1495 1599 513545249 513545145 1.620000e-27 134
8 TraesCS3A01G355900 chr1D 83.763 388 56 7 993 1378 383320442 383320060 6.830000e-96 361
9 TraesCS3A01G355900 chr1D 88.073 109 13 0 1490 1598 383319941 383319833 2.100000e-26 130
10 TraesCS3A01G355900 chr1A 83.590 390 53 10 993 1378 483034072 483033690 3.180000e-94 355
11 TraesCS3A01G355900 chr1A 90.385 104 10 0 1495 1598 483033571 483033468 1.250000e-28 137


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 TraesCS3A01G355900 chr3A 603802425 603805022 2597 False 4798.0 4798 100.0000 1 2598 1 chr3A.!!$F1 2597
1 TraesCS3A01G355900 chr3B 611726462 611728737 2275 False 1271.0 2407 86.9790 1 2366 2 chr3B.!!$F1 2365
2 TraesCS3A01G355900 chr3D 461211712 461213984 2272 False 1317.0 2028 86.4085 1 2149 2 chr3D.!!$F1 2148
3 TraesCS3A01G355900 chr1B 469588674 469589248 574 False 364.0 364 79.0890 11 573 1 chr1B.!!$F1 562
4 TraesCS3A01G355900 chr1B 513545145 513545775 630 True 236.5 339 86.2160 993 1599 2 chr1B.!!$R1 606
5 TraesCS3A01G355900 chr1D 383319833 383320442 609 True 245.5 361 85.9180 993 1598 2 chr1D.!!$R1 605
6 TraesCS3A01G355900 chr1A 483033468 483034072 604 True 246.0 355 86.9875 993 1598 2 chr1A.!!$R1 605

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
446 485 0.543749 AACCTAGGAGATGCACCTGC 59.456 55.0 17.98 0.0 38.31 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2169 2392 0.108138 GATCTGGGTTCGGGTCACAG 60.108 60.0 0.0 0.0 37.64 3.66 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
119 120 0.679505 GCGGTGTATCTATGGCCTGA 59.320 55.000 3.32 0.00 0.00 3.86
124 125 3.177228 GTGTATCTATGGCCTGATCCCT 58.823 50.000 3.32 0.00 0.00 4.20
155 156 6.422776 TGCAAGCTTGTAGTTTATTCTAGC 57.577 37.500 26.55 8.37 0.00 3.42
165 166 6.700081 TGTAGTTTATTCTAGCGTGGCTAATG 59.300 38.462 0.00 0.00 40.82 1.90
167 168 5.753921 AGTTTATTCTAGCGTGGCTAATGTC 59.246 40.000 0.00 0.00 40.82 3.06
168 169 5.531122 TTATTCTAGCGTGGCTAATGTCT 57.469 39.130 0.00 0.00 40.82 3.41
170 171 4.994907 TTCTAGCGTGGCTAATGTCTTA 57.005 40.909 0.00 0.00 40.82 2.10
171 172 5.531122 TTCTAGCGTGGCTAATGTCTTAT 57.469 39.130 0.00 0.00 40.82 1.73
184 193 5.841957 AATGTCTTATTGATGCCTTGGTC 57.158 39.130 0.00 0.00 0.00 4.02
186 195 4.922206 TGTCTTATTGATGCCTTGGTCTT 58.078 39.130 0.00 0.00 0.00 3.01
210 219 2.103094 CTGGGAGCGATGTAGGATCAAA 59.897 50.000 0.00 0.00 0.00 2.69
215 224 3.201290 AGCGATGTAGGATCAAAAGCAG 58.799 45.455 0.00 0.00 0.00 4.24
245 264 6.590292 AGTCCTTGTTAACTATTGATGTCGTG 59.410 38.462 7.22 0.00 0.00 4.35
246 265 6.367969 GTCCTTGTTAACTATTGATGTCGTGT 59.632 38.462 7.22 0.00 0.00 4.49
247 266 7.543172 GTCCTTGTTAACTATTGATGTCGTGTA 59.457 37.037 7.22 0.00 0.00 2.90
248 267 7.543172 TCCTTGTTAACTATTGATGTCGTGTAC 59.457 37.037 7.22 0.00 0.00 2.90
261 280 3.066621 TGTCGTGTACGTAGGTGTTTTCT 59.933 43.478 0.00 0.00 40.80 2.52
289 308 3.941483 GTGTATCCTGTTCATGAGGTTGG 59.059 47.826 0.00 0.00 31.85 3.77
293 312 2.303022 TCCTGTTCATGAGGTTGGAGAC 59.697 50.000 0.00 0.00 31.85 3.36
299 337 5.047021 TGTTCATGAGGTTGGAGACTAGAAG 60.047 44.000 0.00 0.00 0.00 2.85
301 339 3.827817 TGAGGTTGGAGACTAGAAGGA 57.172 47.619 0.00 0.00 0.00 3.36
302 340 4.127918 TGAGGTTGGAGACTAGAAGGAA 57.872 45.455 0.00 0.00 0.00 3.36
312 350 6.045955 GGAGACTAGAAGGAATAGTTTGCTG 58.954 44.000 0.00 0.00 33.29 4.41
326 364 3.257933 GCTGGAGAGCACGTTTGG 58.742 61.111 0.00 0.00 45.46 3.28
327 365 1.598130 GCTGGAGAGCACGTTTGGT 60.598 57.895 0.00 0.00 45.46 3.67
334 372 4.339814 TGGAGAGCACGTTTGGTAATTTTT 59.660 37.500 0.00 0.00 32.05 1.94
335 373 4.915667 GGAGAGCACGTTTGGTAATTTTTC 59.084 41.667 0.00 0.00 32.05 2.29
338 376 4.039032 AGCACGTTTGGTAATTTTTCGTG 58.961 39.130 9.81 9.81 46.00 4.35
339 377 3.792421 GCACGTTTGGTAATTTTTCGTGT 59.208 39.130 14.31 0.00 45.36 4.49
340 378 4.265792 GCACGTTTGGTAATTTTTCGTGTT 59.734 37.500 14.31 0.00 45.36 3.32
341 379 5.709327 CACGTTTGGTAATTTTTCGTGTTG 58.291 37.500 0.00 0.00 41.01 3.33
342 380 5.286558 CACGTTTGGTAATTTTTCGTGTTGT 59.713 36.000 0.00 0.00 41.01 3.32
343 381 6.468319 CACGTTTGGTAATTTTTCGTGTTGTA 59.532 34.615 0.00 0.00 41.01 2.41
344 382 6.687958 ACGTTTGGTAATTTTTCGTGTTGTAG 59.312 34.615 0.00 0.00 0.00 2.74
345 383 6.906143 CGTTTGGTAATTTTTCGTGTTGTAGA 59.094 34.615 0.00 0.00 0.00 2.59
346 384 7.097329 CGTTTGGTAATTTTTCGTGTTGTAGAC 60.097 37.037 0.00 0.00 0.00 2.59
347 385 7.556733 TTGGTAATTTTTCGTGTTGTAGACT 57.443 32.000 0.00 0.00 0.00 3.24
348 386 7.556733 TGGTAATTTTTCGTGTTGTAGACTT 57.443 32.000 0.00 0.00 0.00 3.01
349 387 7.411274 TGGTAATTTTTCGTGTTGTAGACTTG 58.589 34.615 0.00 0.00 0.00 3.16
350 388 7.066043 TGGTAATTTTTCGTGTTGTAGACTTGT 59.934 33.333 0.00 0.00 0.00 3.16
351 389 8.550376 GGTAATTTTTCGTGTTGTAGACTTGTA 58.450 33.333 0.00 0.00 0.00 2.41
353 391 7.781548 ATTTTTCGTGTTGTAGACTTGTAGT 57.218 32.000 0.00 0.00 0.00 2.73
357 395 3.552273 CGTGTTGTAGACTTGTAGTGGCT 60.552 47.826 0.00 0.00 0.00 4.75
365 403 4.718961 AGACTTGTAGTGGCTTGTGATTT 58.281 39.130 0.00 0.00 0.00 2.17
367 405 3.569701 ACTTGTAGTGGCTTGTGATTTGG 59.430 43.478 0.00 0.00 0.00 3.28
426 465 8.677300 GTTTTGCTTCATTGTATCCTTGAGATA 58.323 33.333 0.00 0.00 36.33 1.98
431 470 7.500559 GCTTCATTGTATCCTTGAGATAAACCT 59.499 37.037 0.00 0.00 39.21 3.50
446 485 0.543749 AACCTAGGAGATGCACCTGC 59.456 55.000 17.98 0.00 38.31 4.85
454 493 2.494870 GGAGATGCACCTGCTTTCAAAT 59.505 45.455 0.00 0.00 42.66 2.32
471 510 6.939132 TTCAAATGCCATGAAATGTTTTGT 57.061 29.167 0.00 0.00 44.81 2.83
472 511 6.301687 TCAAATGCCATGAAATGTTTTGTG 57.698 33.333 0.00 0.00 44.81 3.33
536 575 2.158914 TGTCATATCGCCATGCTCTGTT 60.159 45.455 0.00 0.00 0.00 3.16
573 613 5.409826 GGAATCATGAACTTCGTTTCTGTCT 59.590 40.000 0.00 0.00 0.00 3.41
585 625 3.670203 GTTTCTGTCTGTTCACGTGTTG 58.330 45.455 16.51 4.62 0.00 3.33
588 628 3.123050 TCTGTCTGTTCACGTGTTGATG 58.877 45.455 16.51 3.91 32.84 3.07
616 656 7.335924 GCTTAATTGTGTATCCACCTAGTTGAA 59.664 37.037 0.00 0.00 41.09 2.69
617 657 8.786826 TTAATTGTGTATCCACCTAGTTGAAG 57.213 34.615 0.00 0.00 41.09 3.02
629 676 2.645838 AGTTGAAGTGCATCACAGGT 57.354 45.000 0.00 0.00 36.74 4.00
631 678 3.290710 AGTTGAAGTGCATCACAGGTTT 58.709 40.909 0.00 0.00 36.74 3.27
643 690 2.995466 ACAGGTTTGTGCATGATTCG 57.005 45.000 0.00 0.00 35.83 3.34
689 737 4.861210 CTGGAGTAGCTAGTAACCAATCG 58.139 47.826 9.62 0.00 0.00 3.34
695 743 6.305411 AGTAGCTAGTAACCAATCGTCCTAT 58.695 40.000 0.00 0.00 0.00 2.57
715 876 6.607600 TCCTATCTGCTTGTGTACTGTAGAAT 59.392 38.462 0.00 0.00 0.00 2.40
732 893 5.921976 TGTAGAATTTGCTTTGACTTGCATG 59.078 36.000 0.00 0.00 39.07 4.06
740 901 3.508762 CTTTGACTTGCATGGAAGATGC 58.491 45.455 30.84 19.31 44.76 3.91
802 971 6.038603 TCTGATAATTGGAAGCACTTGCATAC 59.961 38.462 5.39 0.00 45.16 2.39
863 1033 7.714377 TGTAACAATTTTCATTCTTGTGCCAAT 59.286 29.630 0.00 0.00 33.60 3.16
879 1049 3.263170 TGCCAATGTAGACCTTGCTAGAA 59.737 43.478 0.00 0.00 0.00 2.10
1144 1317 3.251571 CAGAAGCACGGTTAGTTCTACC 58.748 50.000 0.00 0.00 0.00 3.18
1145 1318 2.895404 AGAAGCACGGTTAGTTCTACCA 59.105 45.455 0.00 0.00 35.31 3.25
1152 1325 2.093658 CGGTTAGTTCTACCACCTGCAT 60.094 50.000 0.00 0.00 35.31 3.96
1208 1394 4.376146 AGCTGACTCTGTTCTCTTTGTTC 58.624 43.478 0.00 0.00 0.00 3.18
1267 1453 0.741221 GGTCTGGCAAGATCGTGGTC 60.741 60.000 10.74 0.00 34.13 4.02
1360 1546 0.747283 GATGGACTGCAAGGCTCCTG 60.747 60.000 0.00 0.00 46.21 3.86
1793 2013 5.240623 TGTGCCTGTCGTTAATTCTGAAAAT 59.759 36.000 0.00 0.00 0.00 1.82
1822 2042 6.691754 ATGCAATATTATGTTGTTCCGTCA 57.308 33.333 3.79 0.00 0.00 4.35
1833 2053 3.179443 TGTTCCGTCAAGATAGATGCC 57.821 47.619 0.00 0.00 0.00 4.40
1854 2074 6.938507 TGCCGAAGAGGTTTAAATCTAGTAA 58.061 36.000 0.00 0.00 43.70 2.24
1869 2089 1.220749 GTAATCTGCCCGGCTCACA 59.779 57.895 11.61 0.00 0.00 3.58
1919 2139 7.939782 TCATGCTTAATTGTTTGACTTTGAGA 58.060 30.769 0.00 0.00 0.00 3.27
1922 2142 8.578308 TGCTTAATTGTTTGACTTTGAGATTG 57.422 30.769 0.00 0.00 0.00 2.67
1923 2143 7.169645 TGCTTAATTGTTTGACTTTGAGATTGC 59.830 33.333 0.00 0.00 0.00 3.56
1928 2148 7.467557 TTGTTTGACTTTGAGATTGCAATTC 57.532 32.000 14.33 12.93 0.00 2.17
1933 2153 4.563061 ACTTTGAGATTGCAATTCAAGGC 58.437 39.130 26.96 12.95 38.22 4.35
1935 2155 2.435422 TGAGATTGCAATTCAAGGCGA 58.565 42.857 14.33 0.00 38.22 5.54
1947 2170 4.657075 TTCAAGGCGAGTTTTTATCGTC 57.343 40.909 0.00 0.00 44.87 4.20
1954 2177 3.780801 GCGAGTTTTTATCGTCTTGCATG 59.219 43.478 0.00 0.00 42.13 4.06
1955 2178 4.435518 GCGAGTTTTTATCGTCTTGCATGA 60.436 41.667 0.00 0.00 42.13 3.07
1987 2210 5.439721 TGCTGGTGATTTGCATAGATAGTT 58.560 37.500 0.00 0.00 0.00 2.24
1990 2213 5.132502 TGGTGATTTGCATAGATAGTTGGG 58.867 41.667 0.00 0.00 0.00 4.12
2029 2252 9.114952 AGTTTAGAAAATATAAGCTGCCTTCTC 57.885 33.333 0.00 0.00 32.47 2.87
2030 2253 9.114952 GTTTAGAAAATATAAGCTGCCTTCTCT 57.885 33.333 0.00 0.00 32.47 3.10
2033 2256 8.028652 AGAAAATATAAGCTGCCTTCTCTACT 57.971 34.615 0.00 0.00 32.47 2.57
2035 2258 2.969628 TAAGCTGCCTTCTCTACTGC 57.030 50.000 0.00 0.00 32.47 4.40
2063 2286 2.094675 CATCTCCCAGCCGTTTGATTT 58.905 47.619 0.00 0.00 0.00 2.17
2064 2287 2.286365 TCTCCCAGCCGTTTGATTTT 57.714 45.000 0.00 0.00 0.00 1.82
2065 2288 1.885887 TCTCCCAGCCGTTTGATTTTG 59.114 47.619 0.00 0.00 0.00 2.44
2066 2289 0.316841 TCCCAGCCGTTTGATTTTGC 59.683 50.000 0.00 0.00 0.00 3.68
2067 2290 1.008361 CCCAGCCGTTTGATTTTGCG 61.008 55.000 0.00 0.00 0.00 4.85
2106 2329 1.673665 CCAGTGGCACTGCTTCCTC 60.674 63.158 36.28 0.00 44.63 3.71
2107 2330 1.673665 CAGTGGCACTGCTTCCTCC 60.674 63.158 32.39 0.00 39.62 4.30
2108 2331 2.149383 AGTGGCACTGCTTCCTCCA 61.149 57.895 21.37 0.00 0.00 3.86
2125 2348 4.204028 AACGGCCTTGGCACTGGT 62.204 61.111 14.04 2.87 0.00 4.00
2131 2354 1.870055 GCCTTGGCACTGGTGATGTG 61.870 60.000 6.79 0.00 38.36 3.21
2149 2372 2.555547 GCTTGAAGCACCAACGCCT 61.556 57.895 13.09 0.00 41.89 5.52
2150 2373 2.032981 CTTGAAGCACCAACGCCTT 58.967 52.632 0.00 0.00 0.00 4.35
2151 2374 0.040067 CTTGAAGCACCAACGCCTTC 60.040 55.000 0.00 0.00 0.00 3.46
2152 2375 1.452145 TTGAAGCACCAACGCCTTCC 61.452 55.000 0.00 0.00 0.00 3.46
2194 2417 1.443407 CCGAACCCAGATCGCAGAT 59.557 57.895 0.00 0.00 45.12 2.90
2196 2419 0.387202 CGAACCCAGATCGCAGATCT 59.613 55.000 13.15 13.15 45.12 2.75
2197 2420 1.202463 CGAACCCAGATCGCAGATCTT 60.202 52.381 15.42 4.82 45.12 2.40
2198 2421 2.739932 CGAACCCAGATCGCAGATCTTT 60.740 50.000 15.42 9.71 45.12 2.52
2199 2422 2.322355 ACCCAGATCGCAGATCTTTG 57.678 50.000 15.42 12.42 45.12 2.77
2200 2423 0.942962 CCCAGATCGCAGATCTTTGC 59.057 55.000 15.42 0.00 45.12 3.68
2201 2424 1.660167 CCAGATCGCAGATCTTTGCA 58.340 50.000 15.42 0.00 45.12 4.08
2202 2425 1.598132 CCAGATCGCAGATCTTTGCAG 59.402 52.381 15.42 6.95 45.12 4.41
2203 2426 2.277969 CAGATCGCAGATCTTTGCAGT 58.722 47.619 15.42 0.00 45.12 4.40
2204 2427 2.030579 CAGATCGCAGATCTTTGCAGTG 59.969 50.000 15.42 0.00 45.12 3.66
2205 2428 1.329906 GATCGCAGATCTTTGCAGTGG 59.670 52.381 7.61 0.00 45.12 4.00
2206 2429 0.035317 TCGCAGATCTTTGCAGTGGT 59.965 50.000 7.61 0.00 44.28 4.16
2207 2430 1.275010 TCGCAGATCTTTGCAGTGGTA 59.725 47.619 7.61 0.00 44.28 3.25
2208 2431 1.394917 CGCAGATCTTTGCAGTGGTAC 59.605 52.381 7.61 0.00 44.28 3.34
2209 2432 1.740025 GCAGATCTTTGCAGTGGTACC 59.260 52.381 4.43 4.43 43.53 3.34
2210 2433 2.002586 CAGATCTTTGCAGTGGTACCG 58.997 52.381 7.57 0.00 0.00 4.02
2211 2434 1.066143 AGATCTTTGCAGTGGTACCGG 60.066 52.381 7.57 0.00 0.00 5.28
2212 2435 0.676782 ATCTTTGCAGTGGTACCGGC 60.677 55.000 7.57 11.52 0.00 6.13
2213 2436 2.666862 TTTGCAGTGGTACCGGCG 60.667 61.111 7.57 0.00 0.00 6.46
2214 2437 3.463728 TTTGCAGTGGTACCGGCGT 62.464 57.895 7.57 0.00 0.00 5.68
2215 2438 2.944409 TTTGCAGTGGTACCGGCGTT 62.944 55.000 7.57 0.00 0.00 4.84
2216 2439 3.419759 GCAGTGGTACCGGCGTTG 61.420 66.667 7.57 2.22 0.00 4.10
2217 2440 3.419759 CAGTGGTACCGGCGTTGC 61.420 66.667 7.57 0.00 0.00 4.17
2218 2441 3.931247 AGTGGTACCGGCGTTGCA 61.931 61.111 7.57 0.00 0.00 4.08
2219 2442 3.419759 GTGGTACCGGCGTTGCAG 61.420 66.667 7.57 0.00 0.00 4.41
2222 2445 3.788766 GTACCGGCGTTGCAGCTG 61.789 66.667 10.11 10.11 42.86 4.24
2283 2506 1.741706 CATTTGCGACAGAGATTGCCT 59.258 47.619 0.00 0.00 0.00 4.75
2299 2522 3.812019 CTCGTCGGCGGTGCTACT 61.812 66.667 10.62 0.00 38.89 2.57
2314 2538 2.486636 CTACTGCAGCACCGGTCGAA 62.487 60.000 15.27 0.00 0.00 3.71
2320 2544 1.302511 AGCACCGGTCGAAAAGCAT 60.303 52.632 2.59 0.00 0.00 3.79
2324 2548 1.154035 CCGGTCGAAAAGCATTGCC 60.154 57.895 4.70 0.00 0.00 4.52
2325 2549 1.511887 CGGTCGAAAAGCATTGCCG 60.512 57.895 4.70 1.69 0.00 5.69
2335 2559 2.892425 CATTGCCGGGAGTCGAGC 60.892 66.667 2.18 0.00 42.43 5.03
2376 2600 3.299340 CAAACGTGCTCCTAGTAGTGT 57.701 47.619 0.00 0.00 0.00 3.55
2377 2601 2.987149 CAAACGTGCTCCTAGTAGTGTG 59.013 50.000 0.00 0.00 0.00 3.82
2378 2602 0.526662 ACGTGCTCCTAGTAGTGTGC 59.473 55.000 0.00 1.81 0.00 4.57
2379 2603 0.523546 CGTGCTCCTAGTAGTGTGCG 60.524 60.000 0.00 0.00 0.00 5.34
2380 2604 0.179134 GTGCTCCTAGTAGTGTGCGG 60.179 60.000 0.00 0.00 0.00 5.69
2381 2605 1.227002 GCTCCTAGTAGTGTGCGGC 60.227 63.158 0.00 0.00 0.00 6.53
2382 2606 1.437986 CTCCTAGTAGTGTGCGGCC 59.562 63.158 0.00 0.00 0.00 6.13
2383 2607 1.000019 TCCTAGTAGTGTGCGGCCT 60.000 57.895 0.00 0.00 0.00 5.19
2384 2608 1.035932 TCCTAGTAGTGTGCGGCCTC 61.036 60.000 0.00 0.00 0.00 4.70
2385 2609 1.320344 CCTAGTAGTGTGCGGCCTCA 61.320 60.000 0.00 0.00 0.00 3.86
2386 2610 0.179134 CTAGTAGTGTGCGGCCTCAC 60.179 60.000 19.17 19.17 36.08 3.51
2387 2611 1.929806 TAGTAGTGTGCGGCCTCACG 61.930 60.000 20.44 0.00 39.70 4.35
2388 2612 4.063967 TAGTGTGCGGCCTCACGG 62.064 66.667 20.44 0.00 39.70 4.94
2406 2630 2.125912 CGGTCCGCCTTGTCTCAG 60.126 66.667 0.00 0.00 0.00 3.35
2407 2631 2.636412 CGGTCCGCCTTGTCTCAGA 61.636 63.158 0.00 0.00 0.00 3.27
2408 2632 1.671742 GGTCCGCCTTGTCTCAGAA 59.328 57.895 0.00 0.00 0.00 3.02
2409 2633 0.390472 GGTCCGCCTTGTCTCAGAAG 60.390 60.000 0.00 0.00 0.00 2.85
2410 2634 0.603569 GTCCGCCTTGTCTCAGAAGA 59.396 55.000 0.00 0.00 0.00 2.87
2411 2635 1.000955 GTCCGCCTTGTCTCAGAAGAA 59.999 52.381 0.00 0.00 31.93 2.52
2412 2636 1.902508 TCCGCCTTGTCTCAGAAGAAT 59.097 47.619 0.00 0.00 31.93 2.40
2413 2637 2.093973 TCCGCCTTGTCTCAGAAGAATC 60.094 50.000 0.00 0.00 31.93 2.52
2414 2638 1.923204 CGCCTTGTCTCAGAAGAATCG 59.077 52.381 0.00 0.00 31.93 3.34
2415 2639 2.416027 CGCCTTGTCTCAGAAGAATCGA 60.416 50.000 0.00 0.00 31.93 3.59
2416 2640 2.926838 GCCTTGTCTCAGAAGAATCGAC 59.073 50.000 0.00 0.00 31.93 4.20
2417 2641 3.615110 GCCTTGTCTCAGAAGAATCGACA 60.615 47.826 0.00 0.00 31.93 4.35
2418 2642 4.753233 CCTTGTCTCAGAAGAATCGACAT 58.247 43.478 0.00 0.00 34.91 3.06
2419 2643 4.565962 CCTTGTCTCAGAAGAATCGACATG 59.434 45.833 0.00 0.00 34.91 3.21
2420 2644 4.115401 TGTCTCAGAAGAATCGACATGG 57.885 45.455 0.00 0.00 31.93 3.66
2421 2645 3.763897 TGTCTCAGAAGAATCGACATGGA 59.236 43.478 0.00 0.00 31.93 3.41
2422 2646 4.109050 GTCTCAGAAGAATCGACATGGAC 58.891 47.826 0.00 0.00 31.93 4.02
2423 2647 4.019858 TCTCAGAAGAATCGACATGGACT 58.980 43.478 0.00 0.00 0.00 3.85
2424 2648 4.111198 CTCAGAAGAATCGACATGGACTG 58.889 47.826 0.00 0.00 0.00 3.51
2425 2649 3.511540 TCAGAAGAATCGACATGGACTGT 59.488 43.478 0.00 0.00 42.15 3.55
2426 2650 4.705023 TCAGAAGAATCGACATGGACTGTA 59.295 41.667 0.00 0.00 38.54 2.74
2427 2651 5.360999 TCAGAAGAATCGACATGGACTGTAT 59.639 40.000 0.00 0.00 38.54 2.29
2428 2652 6.546034 TCAGAAGAATCGACATGGACTGTATA 59.454 38.462 0.00 0.00 38.54 1.47
2429 2653 7.068226 TCAGAAGAATCGACATGGACTGTATAA 59.932 37.037 0.00 0.00 38.54 0.98
2430 2654 7.380870 CAGAAGAATCGACATGGACTGTATAAG 59.619 40.741 0.00 0.00 38.54 1.73
2431 2655 5.533482 AGAATCGACATGGACTGTATAAGC 58.467 41.667 0.00 0.00 38.54 3.09
2432 2656 4.937201 ATCGACATGGACTGTATAAGCA 57.063 40.909 0.00 0.00 38.54 3.91
2433 2657 4.937201 TCGACATGGACTGTATAAGCAT 57.063 40.909 0.00 0.00 38.54 3.79
2434 2658 4.871513 TCGACATGGACTGTATAAGCATC 58.128 43.478 0.00 0.00 38.54 3.91
2435 2659 3.670523 CGACATGGACTGTATAAGCATCG 59.329 47.826 0.00 0.00 38.54 3.84
2436 2660 4.556699 CGACATGGACTGTATAAGCATCGA 60.557 45.833 0.00 0.00 38.54 3.59
2437 2661 5.473931 GACATGGACTGTATAAGCATCGAT 58.526 41.667 0.00 0.00 38.54 3.59
2438 2662 5.233225 ACATGGACTGTATAAGCATCGATG 58.767 41.667 21.27 21.27 35.91 3.84
2439 2663 6.308328 ACATGGACTGTATAAGCATCGATGC 61.308 44.000 37.29 37.29 44.81 3.91
2451 2675 3.688136 CGATGCCTACCGTCGTTG 58.312 61.111 0.00 0.00 45.57 4.10
2452 2676 1.138036 CGATGCCTACCGTCGTTGA 59.862 57.895 0.00 0.00 45.57 3.18
2453 2677 1.138047 CGATGCCTACCGTCGTTGAC 61.138 60.000 0.00 0.00 45.57 3.18
2454 2678 0.108992 GATGCCTACCGTCGTTGACA 60.109 55.000 0.00 0.00 32.09 3.58
2455 2679 0.108804 ATGCCTACCGTCGTTGACAG 60.109 55.000 0.00 0.00 32.09 3.51
2456 2680 1.288127 GCCTACCGTCGTTGACAGT 59.712 57.895 0.00 0.00 32.09 3.55
2457 2681 1.007336 GCCTACCGTCGTTGACAGTG 61.007 60.000 0.00 0.00 32.09 3.66
2458 2682 0.388134 CCTACCGTCGTTGACAGTGG 60.388 60.000 0.00 0.00 32.09 4.00
2459 2683 0.388134 CTACCGTCGTTGACAGTGGG 60.388 60.000 0.00 0.00 32.09 4.61
2460 2684 1.808531 TACCGTCGTTGACAGTGGGG 61.809 60.000 0.00 0.00 32.09 4.96
2461 2685 3.041940 CGTCGTTGACAGTGGGGC 61.042 66.667 0.00 0.00 32.09 5.80
2462 2686 3.041940 GTCGTTGACAGTGGGGCG 61.042 66.667 0.00 0.00 32.09 6.13
2463 2687 4.308458 TCGTTGACAGTGGGGCGG 62.308 66.667 0.00 0.00 0.00 6.13
2465 2689 4.643387 GTTGACAGTGGGGCGGCT 62.643 66.667 9.56 0.00 0.00 5.52
2466 2690 3.884774 TTGACAGTGGGGCGGCTT 61.885 61.111 9.56 0.00 0.00 4.35
2467 2691 4.641645 TGACAGTGGGGCGGCTTG 62.642 66.667 9.56 5.40 0.00 4.01
2477 2701 3.673484 GCGGCTTGCAGCAAAGGA 61.673 61.111 9.65 0.00 44.75 3.36
2478 2702 2.998279 GCGGCTTGCAGCAAAGGAT 61.998 57.895 9.65 0.00 44.75 3.24
2479 2703 1.153901 CGGCTTGCAGCAAAGGATG 60.154 57.895 9.65 0.00 44.75 3.51
2480 2704 1.217244 GGCTTGCAGCAAAGGATGG 59.783 57.895 9.65 0.00 44.75 3.51
2481 2705 1.538687 GGCTTGCAGCAAAGGATGGT 61.539 55.000 9.65 0.00 44.75 3.55
2489 2713 3.340814 AGCAAAGGATGGTGTCTACAG 57.659 47.619 0.00 0.00 38.62 2.74
2490 2714 2.906389 AGCAAAGGATGGTGTCTACAGA 59.094 45.455 0.00 0.00 38.62 3.41
2491 2715 3.327757 AGCAAAGGATGGTGTCTACAGAA 59.672 43.478 0.00 0.00 38.62 3.02
2492 2716 3.437049 GCAAAGGATGGTGTCTACAGAAC 59.563 47.826 0.00 0.00 0.00 3.01
2493 2717 4.641396 CAAAGGATGGTGTCTACAGAACA 58.359 43.478 0.00 0.00 0.00 3.18
2494 2718 4.974645 AAGGATGGTGTCTACAGAACAA 57.025 40.909 0.00 0.00 0.00 2.83
2495 2719 4.543590 AGGATGGTGTCTACAGAACAAG 57.456 45.455 0.00 0.00 0.00 3.16
2496 2720 3.003480 GGATGGTGTCTACAGAACAAGC 58.997 50.000 0.00 0.00 0.00 4.01
2497 2721 2.543777 TGGTGTCTACAGAACAAGCC 57.456 50.000 0.00 0.00 0.00 4.35
2498 2722 1.071699 TGGTGTCTACAGAACAAGCCC 59.928 52.381 0.00 0.00 0.00 5.19
2499 2723 1.610886 GGTGTCTACAGAACAAGCCCC 60.611 57.143 0.00 0.00 0.00 5.80
2500 2724 0.690762 TGTCTACAGAACAAGCCCCC 59.309 55.000 0.00 0.00 0.00 5.40
2501 2725 0.391263 GTCTACAGAACAAGCCCCCG 60.391 60.000 0.00 0.00 0.00 5.73
2502 2726 1.078426 CTACAGAACAAGCCCCCGG 60.078 63.158 0.00 0.00 0.00 5.73
2519 2743 4.803426 GCGAGTGCCCTGACCGAG 62.803 72.222 0.00 0.00 33.98 4.63
2520 2744 3.062466 CGAGTGCCCTGACCGAGA 61.062 66.667 0.00 0.00 0.00 4.04
2521 2745 2.888863 GAGTGCCCTGACCGAGAG 59.111 66.667 0.00 0.00 0.00 3.20
2543 2767 4.688419 CGCCACGCTGTGCAAAGG 62.688 66.667 5.91 0.00 31.34 3.11
2544 2768 4.347453 GCCACGCTGTGCAAAGGG 62.347 66.667 18.89 18.89 36.26 3.95
2545 2769 2.594303 CCACGCTGTGCAAAGGGA 60.594 61.111 26.47 0.00 34.39 4.20
2546 2770 2.192861 CCACGCTGTGCAAAGGGAA 61.193 57.895 26.47 0.00 34.39 3.97
2547 2771 1.283793 CACGCTGTGCAAAGGGAAG 59.716 57.895 26.47 14.47 34.39 3.46
2548 2772 1.148273 ACGCTGTGCAAAGGGAAGA 59.852 52.632 26.47 0.00 34.39 2.87
2549 2773 0.465460 ACGCTGTGCAAAGGGAAGAA 60.465 50.000 26.47 0.00 34.39 2.52
2550 2774 0.239347 CGCTGTGCAAAGGGAAGAAG 59.761 55.000 15.75 0.00 32.03 2.85
2551 2775 0.600057 GCTGTGCAAAGGGAAGAAGG 59.400 55.000 5.91 0.00 0.00 3.46
2552 2776 0.600057 CTGTGCAAAGGGAAGAAGGC 59.400 55.000 0.00 0.00 0.00 4.35
2553 2777 0.827507 TGTGCAAAGGGAAGAAGGCC 60.828 55.000 0.00 0.00 0.00 5.19
2554 2778 1.603455 TGCAAAGGGAAGAAGGCCG 60.603 57.895 0.00 0.00 0.00 6.13
2555 2779 1.303317 GCAAAGGGAAGAAGGCCGA 60.303 57.895 0.00 0.00 0.00 5.54
2556 2780 1.308783 GCAAAGGGAAGAAGGCCGAG 61.309 60.000 0.00 0.00 0.00 4.63
2557 2781 1.002011 AAAGGGAAGAAGGCCGAGC 60.002 57.895 0.00 0.00 0.00 5.03
2558 2782 2.804828 AAAGGGAAGAAGGCCGAGCG 62.805 60.000 0.00 0.00 0.00 5.03
2559 2783 4.840005 GGGAAGAAGGCCGAGCGG 62.840 72.222 4.20 4.20 38.57 5.52
2573 2797 3.845178 CCGAGCGGCAATTATACTATGA 58.155 45.455 1.45 0.00 0.00 2.15
2574 2798 4.242475 CCGAGCGGCAATTATACTATGAA 58.758 43.478 1.45 0.00 0.00 2.57
2575 2799 4.688879 CCGAGCGGCAATTATACTATGAAA 59.311 41.667 1.45 0.00 0.00 2.69
2576 2800 5.178623 CCGAGCGGCAATTATACTATGAAAA 59.821 40.000 1.45 0.00 0.00 2.29
2577 2801 6.293190 CCGAGCGGCAATTATACTATGAAAAA 60.293 38.462 1.45 0.00 0.00 1.94
2578 2802 6.573725 CGAGCGGCAATTATACTATGAAAAAC 59.426 38.462 1.45 0.00 0.00 2.43
2579 2803 7.518370 CGAGCGGCAATTATACTATGAAAAACT 60.518 37.037 1.45 0.00 0.00 2.66
2580 2804 8.671384 AGCGGCAATTATACTATGAAAAACTA 57.329 30.769 1.45 0.00 0.00 2.24
2581 2805 9.116067 AGCGGCAATTATACTATGAAAAACTAA 57.884 29.630 1.45 0.00 0.00 2.24
2582 2806 9.724839 GCGGCAATTATACTATGAAAAACTAAA 57.275 29.630 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 3.580084 GCCAGGGATCAGGCCATA 58.420 61.111 5.01 0.00 45.18 2.74
119 120 1.377725 CTTGCAGTTCGCCAGGGAT 60.378 57.895 0.00 0.00 41.33 3.85
124 125 0.533978 TACAAGCTTGCAGTTCGCCA 60.534 50.000 26.27 0.00 41.33 5.69
141 142 6.700520 ACATTAGCCACGCTAGAATAAACTAC 59.299 38.462 0.00 0.00 42.34 2.73
148 149 4.408182 AAGACATTAGCCACGCTAGAAT 57.592 40.909 0.00 0.00 42.34 2.40
155 156 4.319766 GGCATCAATAAGACATTAGCCACG 60.320 45.833 0.00 0.00 39.35 4.94
165 166 6.995091 AGATAAGACCAAGGCATCAATAAGAC 59.005 38.462 0.00 0.00 0.00 3.01
167 168 6.206243 CCAGATAAGACCAAGGCATCAATAAG 59.794 42.308 0.00 0.00 0.00 1.73
168 169 6.064060 CCAGATAAGACCAAGGCATCAATAA 58.936 40.000 0.00 0.00 0.00 1.40
170 171 4.467769 CCAGATAAGACCAAGGCATCAAT 58.532 43.478 0.00 0.00 0.00 2.57
171 172 3.371917 CCCAGATAAGACCAAGGCATCAA 60.372 47.826 0.00 0.00 0.00 2.57
184 193 3.157881 TCCTACATCGCTCCCAGATAAG 58.842 50.000 0.00 0.00 0.00 1.73
186 195 2.971901 TCCTACATCGCTCCCAGATA 57.028 50.000 0.00 0.00 0.00 1.98
210 219 4.284746 AGTTAACAAGGACTAGAGCTGCTT 59.715 41.667 8.61 0.00 0.00 3.91
215 224 7.982354 ACATCAATAGTTAACAAGGACTAGAGC 59.018 37.037 8.61 0.00 0.00 4.09
245 264 3.185797 CAGGCAAGAAAACACCTACGTAC 59.814 47.826 0.00 0.00 0.00 3.67
246 265 3.181463 ACAGGCAAGAAAACACCTACGTA 60.181 43.478 0.00 0.00 0.00 3.57
247 266 2.218603 CAGGCAAGAAAACACCTACGT 58.781 47.619 0.00 0.00 0.00 3.57
248 267 2.032030 CACAGGCAAGAAAACACCTACG 60.032 50.000 0.00 0.00 0.00 3.51
261 280 3.008923 TCATGAACAGGATACACAGGCAA 59.991 43.478 0.00 0.00 41.41 4.52
289 308 6.045955 CCAGCAAACTATTCCTTCTAGTCTC 58.954 44.000 0.00 0.00 0.00 3.36
293 312 6.227298 TCTCCAGCAAACTATTCCTTCTAG 57.773 41.667 0.00 0.00 0.00 2.43
312 350 4.499037 AAAATTACCAAACGTGCTCTCC 57.501 40.909 0.00 0.00 0.00 3.71
321 359 7.911727 AGTCTACAACACGAAAAATTACCAAAC 59.088 33.333 0.00 0.00 0.00 2.93
322 360 7.987649 AGTCTACAACACGAAAAATTACCAAA 58.012 30.769 0.00 0.00 0.00 3.28
324 362 7.066043 ACAAGTCTACAACACGAAAAATTACCA 59.934 33.333 0.00 0.00 0.00 3.25
325 363 7.412063 ACAAGTCTACAACACGAAAAATTACC 58.588 34.615 0.00 0.00 0.00 2.85
326 364 9.577003 CTACAAGTCTACAACACGAAAAATTAC 57.423 33.333 0.00 0.00 0.00 1.89
327 365 9.316730 ACTACAAGTCTACAACACGAAAAATTA 57.683 29.630 0.00 0.00 0.00 1.40
334 372 3.551454 GCCACTACAAGTCTACAACACGA 60.551 47.826 0.00 0.00 0.00 4.35
335 373 2.729882 GCCACTACAAGTCTACAACACG 59.270 50.000 0.00 0.00 0.00 4.49
338 376 4.211374 CACAAGCCACTACAAGTCTACAAC 59.789 45.833 0.00 0.00 0.00 3.32
339 377 4.100344 TCACAAGCCACTACAAGTCTACAA 59.900 41.667 0.00 0.00 0.00 2.41
340 378 3.639561 TCACAAGCCACTACAAGTCTACA 59.360 43.478 0.00 0.00 0.00 2.74
341 379 4.252971 TCACAAGCCACTACAAGTCTAC 57.747 45.455 0.00 0.00 0.00 2.59
342 380 5.483685 AATCACAAGCCACTACAAGTCTA 57.516 39.130 0.00 0.00 0.00 2.59
343 381 4.357918 AATCACAAGCCACTACAAGTCT 57.642 40.909 0.00 0.00 0.00 3.24
344 382 4.320494 CCAAATCACAAGCCACTACAAGTC 60.320 45.833 0.00 0.00 0.00 3.01
345 383 3.569701 CCAAATCACAAGCCACTACAAGT 59.430 43.478 0.00 0.00 0.00 3.16
346 384 3.057315 CCCAAATCACAAGCCACTACAAG 60.057 47.826 0.00 0.00 0.00 3.16
347 385 2.890311 CCCAAATCACAAGCCACTACAA 59.110 45.455 0.00 0.00 0.00 2.41
348 386 2.513753 CCCAAATCACAAGCCACTACA 58.486 47.619 0.00 0.00 0.00 2.74
349 387 1.202348 GCCCAAATCACAAGCCACTAC 59.798 52.381 0.00 0.00 0.00 2.73
350 388 1.544724 GCCCAAATCACAAGCCACTA 58.455 50.000 0.00 0.00 0.00 2.74
351 389 1.187567 GGCCCAAATCACAAGCCACT 61.188 55.000 0.00 0.00 43.32 4.00
353 391 2.274645 CGGCCCAAATCACAAGCCA 61.275 57.895 0.00 0.00 44.06 4.75
357 395 1.916506 TTCATCGGCCCAAATCACAA 58.083 45.000 0.00 0.00 0.00 3.33
365 403 1.819208 CTCGCATTTCATCGGCCCA 60.819 57.895 0.00 0.00 0.00 5.36
367 405 0.732571 TTTCTCGCATTTCATCGGCC 59.267 50.000 0.00 0.00 0.00 6.13
400 438 6.913170 TCTCAAGGATACAATGAAGCAAAAC 58.087 36.000 0.00 0.00 41.41 2.43
412 451 7.592736 TCTCCTAGGTTTATCTCAAGGATACA 58.407 38.462 9.08 0.00 36.72 2.29
426 465 1.065126 GCAGGTGCATCTCCTAGGTTT 60.065 52.381 9.08 0.00 41.59 3.27
431 470 1.908619 TGAAAGCAGGTGCATCTCCTA 59.091 47.619 0.00 0.00 45.16 2.94
446 485 7.377397 CACAAAACATTTCATGGCATTTGAAAG 59.623 33.333 18.09 13.34 43.96 2.62
454 493 4.511527 ACAACACAAAACATTTCATGGCA 58.488 34.783 0.00 0.00 33.60 4.92
471 510 5.699001 TCAGCTCGCTAAAGATTTAACAACA 59.301 36.000 0.00 0.00 0.00 3.33
472 511 6.165659 TCAGCTCGCTAAAGATTTAACAAC 57.834 37.500 0.00 0.00 0.00 3.32
536 575 8.862325 AGTTCATGATTCCTTAACACATGTAA 57.138 30.769 0.00 0.00 39.18 2.41
573 613 1.662517 AGCACATCAACACGTGAACA 58.337 45.000 25.01 4.96 40.50 3.18
629 676 4.313277 TCCAAAACGAATCATGCACAAA 57.687 36.364 0.00 0.00 0.00 2.83
631 678 3.637432 GTTCCAAAACGAATCATGCACA 58.363 40.909 0.00 0.00 0.00 4.57
643 690 5.500131 GCAAAAGTGAATCACGTTCCAAAAC 60.500 40.000 14.37 0.00 39.64 2.43
681 729 3.055094 ACAAGCAGATAGGACGATTGGTT 60.055 43.478 0.00 0.00 0.00 3.67
689 737 4.457834 ACAGTACACAAGCAGATAGGAC 57.542 45.455 0.00 0.00 0.00 3.85
695 743 5.179368 GCAAATTCTACAGTACACAAGCAGA 59.821 40.000 0.00 0.00 0.00 4.26
715 876 3.384146 TCTTCCATGCAAGTCAAAGCAAA 59.616 39.130 0.00 0.00 44.88 3.68
732 893 4.943705 TCAACTAGTTCAATGGCATCTTCC 59.056 41.667 4.77 0.00 0.00 3.46
740 901 9.994432 GATGAGTTTATTCAACTAGTTCAATGG 57.006 33.333 14.33 0.00 46.53 3.16
834 1003 7.010923 GGCACAAGAATGAAAATTGTTACAACA 59.989 33.333 0.00 0.00 35.04 3.33
863 1033 7.290014 TGGATATTCATTCTAGCAAGGTCTACA 59.710 37.037 0.00 0.00 0.00 2.74
923 1095 9.539825 AAAAGACAAACATGCATTGTATGTAAA 57.460 25.926 18.84 0.00 40.90 2.01
965 1138 7.651704 GCAGAATAACAACAGCCTTTTAGAAAA 59.348 33.333 0.00 0.00 0.00 2.29
1144 1317 5.531634 ACAACAAAACAGAATATGCAGGTG 58.468 37.500 0.00 0.00 0.00 4.00
1145 1318 5.789643 ACAACAAAACAGAATATGCAGGT 57.210 34.783 0.00 0.00 0.00 4.00
1152 1325 6.542005 TCAGAGAGCAACAACAAAACAGAATA 59.458 34.615 0.00 0.00 0.00 1.75
1208 1394 4.693283 TCAAACTCGCCAATGTATCCTAG 58.307 43.478 0.00 0.00 0.00 3.02
1267 1453 1.097232 TCAGCCTGCCATTCAATTCG 58.903 50.000 0.00 0.00 0.00 3.34
1360 1546 0.318762 AACTGACCTGACGAGAAGGC 59.681 55.000 0.00 0.00 38.48 4.35
1617 1836 5.091261 ACACATCTCAGGTACTTTCATCC 57.909 43.478 0.00 0.00 34.60 3.51
1681 1901 2.573869 GCGGCAGCTAGTCAGACA 59.426 61.111 0.00 0.00 41.01 3.41
1822 2042 4.762289 AAACCTCTTCGGCATCTATCTT 57.238 40.909 0.00 0.00 35.61 2.40
1833 2053 8.756864 GCAGATTACTAGATTTAAACCTCTTCG 58.243 37.037 0.00 0.00 0.00 3.79
1854 2074 1.680522 CTACTGTGAGCCGGGCAGAT 61.681 60.000 23.09 0.00 34.60 2.90
1869 2089 5.698545 GCTCACAGACAAGATTGAAACTACT 59.301 40.000 0.00 0.00 0.00 2.57
1909 2129 5.775686 CCTTGAATTGCAATCTCAAAGTCA 58.224 37.500 24.29 16.31 35.59 3.41
1910 2130 4.624452 GCCTTGAATTGCAATCTCAAAGTC 59.376 41.667 24.29 14.51 35.59 3.01
1911 2131 4.563061 GCCTTGAATTGCAATCTCAAAGT 58.437 39.130 24.29 7.58 35.59 2.66
1919 2139 3.665745 AAACTCGCCTTGAATTGCAAT 57.334 38.095 5.99 5.99 35.59 3.56
1922 2142 4.262976 CGATAAAAACTCGCCTTGAATTGC 59.737 41.667 0.00 0.00 0.00 3.56
1923 2143 5.390613 ACGATAAAAACTCGCCTTGAATTG 58.609 37.500 0.00 0.00 39.71 2.32
1928 2148 4.394795 CAAGACGATAAAAACTCGCCTTG 58.605 43.478 7.22 7.22 45.43 3.61
1933 2153 5.015733 GTCATGCAAGACGATAAAAACTCG 58.984 41.667 6.29 0.00 41.77 4.18
1947 2170 1.736126 AGCAGAACATCGTCATGCAAG 59.264 47.619 0.00 0.00 39.34 4.01
1954 2177 2.015736 ATCACCAGCAGAACATCGTC 57.984 50.000 0.00 0.00 0.00 4.20
1955 2178 2.479566 AATCACCAGCAGAACATCGT 57.520 45.000 0.00 0.00 0.00 3.73
2007 2230 9.148879 AGTAGAGAAGGCAGCTTATATTTTCTA 57.851 33.333 0.00 0.00 0.00 2.10
2016 2239 1.482593 GGCAGTAGAGAAGGCAGCTTA 59.517 52.381 0.00 0.00 0.00 3.09
2017 2240 0.251634 GGCAGTAGAGAAGGCAGCTT 59.748 55.000 0.00 0.00 0.00 3.74
2063 2286 3.053291 GTTGGCCATCGGACGCAA 61.053 61.111 6.09 0.00 29.56 4.85
2064 2287 3.545124 AAGTTGGCCATCGGACGCA 62.545 57.895 6.09 0.00 29.56 5.24
2065 2288 1.862602 AAAAGTTGGCCATCGGACGC 61.863 55.000 6.09 0.00 29.56 5.19
2066 2289 0.596082 AAAAAGTTGGCCATCGGACG 59.404 50.000 6.09 0.00 29.56 4.79
2067 2290 1.611491 TGAAAAAGTTGGCCATCGGAC 59.389 47.619 6.09 0.37 0.00 4.79
2107 2330 3.673484 CCAGTGCCAAGGCCGTTG 61.673 66.667 8.89 2.27 41.09 4.10
2108 2331 4.204028 ACCAGTGCCAAGGCCGTT 62.204 61.111 8.89 0.00 41.09 4.44
2131 2354 2.050077 GGCGTTGGTGCTTCAAGC 60.050 61.111 1.04 1.04 42.82 4.01
2169 2392 0.108138 GATCTGGGTTCGGGTCACAG 60.108 60.000 0.00 0.00 37.64 3.66
2194 2417 1.302192 GCCGGTACCACTGCAAAGA 60.302 57.895 13.54 0.00 0.00 2.52
2196 2419 2.666862 CGCCGGTACCACTGCAAA 60.667 61.111 13.54 0.00 0.00 3.68
2197 2420 3.463728 AACGCCGGTACCACTGCAA 62.464 57.895 13.54 0.00 0.00 4.08
2198 2421 3.931247 AACGCCGGTACCACTGCA 61.931 61.111 13.54 0.00 0.00 4.41
2199 2422 3.419759 CAACGCCGGTACCACTGC 61.420 66.667 13.54 10.22 0.00 4.40
2200 2423 3.419759 GCAACGCCGGTACCACTG 61.420 66.667 13.54 2.55 0.00 3.66
2201 2424 3.876589 CTGCAACGCCGGTACCACT 62.877 63.158 13.54 0.00 0.00 4.00
2202 2425 3.419759 CTGCAACGCCGGTACCAC 61.420 66.667 13.54 1.89 0.00 4.16
2205 2428 3.788766 CAGCTGCAACGCCGGTAC 61.789 66.667 0.00 0.00 0.00 3.34
2222 2445 3.782244 CGACGGCTGTGCTTCTGC 61.782 66.667 0.80 0.00 39.71 4.26
2223 2446 1.956170 AACGACGGCTGTGCTTCTG 60.956 57.895 0.80 0.00 0.00 3.02
2224 2447 1.956170 CAACGACGGCTGTGCTTCT 60.956 57.895 0.80 0.00 0.00 2.85
2283 2506 4.111016 CAGTAGCACCGCCGACGA 62.111 66.667 0.00 0.00 43.93 4.20
2299 2522 2.203084 TTTTCGACCGGTGCTGCA 60.203 55.556 14.63 0.00 0.00 4.41
2301 2524 1.577328 ATGCTTTTCGACCGGTGCTG 61.577 55.000 14.63 0.68 0.00 4.41
2311 2535 1.137404 CTCCCGGCAATGCTTTTCG 59.863 57.895 4.82 0.00 0.00 3.46
2314 2538 2.040544 CGACTCCCGGCAATGCTTT 61.041 57.895 4.82 0.00 33.91 3.51
2320 2544 4.373116 GTGCTCGACTCCCGGCAA 62.373 66.667 0.00 0.00 42.74 4.52
2357 2581 2.609737 GCACACTACTAGGAGCACGTTT 60.610 50.000 0.36 0.00 0.00 3.60
2366 2590 1.320344 TGAGGCCGCACACTACTAGG 61.320 60.000 4.49 0.00 0.00 3.02
2367 2591 0.179134 GTGAGGCCGCACACTACTAG 60.179 60.000 31.80 0.00 38.63 2.57
2368 2592 1.888018 GTGAGGCCGCACACTACTA 59.112 57.895 31.80 0.00 38.63 1.82
2369 2593 2.657237 GTGAGGCCGCACACTACT 59.343 61.111 31.80 0.00 38.63 2.57
2370 2594 2.809601 CGTGAGGCCGCACACTAC 60.810 66.667 34.38 11.84 38.69 2.73
2389 2613 2.125912 CTGAGACAAGGCGGACCG 60.126 66.667 10.29 10.29 42.76 4.79
2390 2614 0.390472 CTTCTGAGACAAGGCGGACC 60.390 60.000 0.00 0.00 0.00 4.46
2391 2615 0.603569 TCTTCTGAGACAAGGCGGAC 59.396 55.000 0.00 0.00 0.00 4.79
2392 2616 1.338107 TTCTTCTGAGACAAGGCGGA 58.662 50.000 0.00 0.00 0.00 5.54
2393 2617 2.275318 GATTCTTCTGAGACAAGGCGG 58.725 52.381 0.00 0.00 0.00 6.13
2394 2618 1.923204 CGATTCTTCTGAGACAAGGCG 59.077 52.381 0.00 0.00 0.00 5.52
2395 2619 2.926838 GTCGATTCTTCTGAGACAAGGC 59.073 50.000 0.00 0.00 32.57 4.35
2396 2620 4.179926 TGTCGATTCTTCTGAGACAAGG 57.820 45.455 0.00 0.00 38.66 3.61
2397 2621 4.565962 CCATGTCGATTCTTCTGAGACAAG 59.434 45.833 0.66 0.00 43.72 3.16
2398 2622 4.220602 TCCATGTCGATTCTTCTGAGACAA 59.779 41.667 0.66 0.00 43.72 3.18
2399 2623 3.763897 TCCATGTCGATTCTTCTGAGACA 59.236 43.478 0.00 0.00 44.46 3.41
2400 2624 4.109050 GTCCATGTCGATTCTTCTGAGAC 58.891 47.826 0.00 0.00 0.00 3.36
2401 2625 4.019858 AGTCCATGTCGATTCTTCTGAGA 58.980 43.478 0.00 0.00 0.00 3.27
2402 2626 4.111198 CAGTCCATGTCGATTCTTCTGAG 58.889 47.826 0.00 0.00 0.00 3.35
2403 2627 3.511540 ACAGTCCATGTCGATTCTTCTGA 59.488 43.478 11.31 0.00 37.75 3.27
2404 2628 3.854666 ACAGTCCATGTCGATTCTTCTG 58.145 45.455 0.00 0.00 37.75 3.02
2405 2629 5.860941 ATACAGTCCATGTCGATTCTTCT 57.139 39.130 0.00 0.00 42.70 2.85
2406 2630 6.144724 GCTTATACAGTCCATGTCGATTCTTC 59.855 42.308 0.00 0.00 42.70 2.87
2407 2631 5.986135 GCTTATACAGTCCATGTCGATTCTT 59.014 40.000 0.00 0.00 42.70 2.52
2408 2632 5.069119 TGCTTATACAGTCCATGTCGATTCT 59.931 40.000 0.00 0.00 42.70 2.40
2409 2633 5.289595 TGCTTATACAGTCCATGTCGATTC 58.710 41.667 0.00 0.00 42.70 2.52
2410 2634 5.276461 TGCTTATACAGTCCATGTCGATT 57.724 39.130 0.00 0.00 42.70 3.34
2411 2635 4.937201 TGCTTATACAGTCCATGTCGAT 57.063 40.909 0.00 0.00 42.70 3.59
2412 2636 4.556699 CGATGCTTATACAGTCCATGTCGA 60.557 45.833 0.00 0.00 42.70 4.20
2413 2637 3.670523 CGATGCTTATACAGTCCATGTCG 59.329 47.826 0.00 0.00 42.70 4.35
2414 2638 4.871513 TCGATGCTTATACAGTCCATGTC 58.128 43.478 0.00 0.00 42.70 3.06
2415 2639 4.937201 TCGATGCTTATACAGTCCATGT 57.063 40.909 0.00 0.00 46.45 3.21
2416 2640 5.774878 CATCGATGCTTATACAGTCCATG 57.225 43.478 13.37 0.00 0.00 3.66
2431 2655 0.248907 AACGACGGTAGGCATCGATG 60.249 55.000 21.27 21.27 39.16 3.84
2432 2656 0.248907 CAACGACGGTAGGCATCGAT 60.249 55.000 0.00 0.00 39.16 3.59
2433 2657 1.138036 CAACGACGGTAGGCATCGA 59.862 57.895 0.00 0.00 39.16 3.59
2434 2658 1.138036 TCAACGACGGTAGGCATCG 59.862 57.895 0.00 0.00 41.60 3.84
2435 2659 0.108992 TGTCAACGACGGTAGGCATC 60.109 55.000 0.00 0.00 34.95 3.91
2436 2660 0.108804 CTGTCAACGACGGTAGGCAT 60.109 55.000 0.00 0.00 34.54 4.40
2437 2661 1.287815 CTGTCAACGACGGTAGGCA 59.712 57.895 0.00 0.00 34.54 4.75
2438 2662 4.164252 CTGTCAACGACGGTAGGC 57.836 61.111 0.00 0.00 34.54 3.93
2443 2667 2.357034 CCCCACTGTCAACGACGG 60.357 66.667 0.00 1.39 43.83 4.79
2444 2668 3.041940 GCCCCACTGTCAACGACG 61.042 66.667 0.00 0.00 34.95 5.12
2445 2669 3.041940 CGCCCCACTGTCAACGAC 61.042 66.667 0.00 0.00 0.00 4.34
2446 2670 4.308458 CCGCCCCACTGTCAACGA 62.308 66.667 0.00 0.00 0.00 3.85
2448 2672 4.643387 AGCCGCCCCACTGTCAAC 62.643 66.667 0.00 0.00 0.00 3.18
2449 2673 3.884774 AAGCCGCCCCACTGTCAA 61.885 61.111 0.00 0.00 0.00 3.18
2450 2674 4.641645 CAAGCCGCCCCACTGTCA 62.642 66.667 0.00 0.00 0.00 3.58
2464 2688 0.963962 ACACCATCCTTTGCTGCAAG 59.036 50.000 15.39 9.58 0.00 4.01
2465 2689 0.961019 GACACCATCCTTTGCTGCAA 59.039 50.000 11.69 11.69 0.00 4.08
2466 2690 0.111061 AGACACCATCCTTTGCTGCA 59.889 50.000 0.00 0.00 0.00 4.41
2467 2691 1.740025 GTAGACACCATCCTTTGCTGC 59.260 52.381 0.00 0.00 0.00 5.25
2468 2692 3.005554 CTGTAGACACCATCCTTTGCTG 58.994 50.000 0.00 0.00 0.00 4.41
2469 2693 2.906389 TCTGTAGACACCATCCTTTGCT 59.094 45.455 0.00 0.00 0.00 3.91
2470 2694 3.334583 TCTGTAGACACCATCCTTTGC 57.665 47.619 0.00 0.00 0.00 3.68
2471 2695 4.641396 TGTTCTGTAGACACCATCCTTTG 58.359 43.478 0.00 0.00 0.00 2.77
2472 2696 4.974645 TGTTCTGTAGACACCATCCTTT 57.025 40.909 0.00 0.00 0.00 3.11
2473 2697 4.804261 GCTTGTTCTGTAGACACCATCCTT 60.804 45.833 0.00 0.00 0.00 3.36
2474 2698 3.307059 GCTTGTTCTGTAGACACCATCCT 60.307 47.826 0.00 0.00 0.00 3.24
2475 2699 3.003480 GCTTGTTCTGTAGACACCATCC 58.997 50.000 0.00 0.00 0.00 3.51
2476 2700 3.003480 GGCTTGTTCTGTAGACACCATC 58.997 50.000 0.00 0.00 0.00 3.51
2477 2701 2.290323 GGGCTTGTTCTGTAGACACCAT 60.290 50.000 0.00 0.00 0.00 3.55
2478 2702 1.071699 GGGCTTGTTCTGTAGACACCA 59.928 52.381 0.00 0.00 0.00 4.17
2479 2703 1.610886 GGGGCTTGTTCTGTAGACACC 60.611 57.143 0.00 0.00 0.00 4.16
2480 2704 1.610886 GGGGGCTTGTTCTGTAGACAC 60.611 57.143 0.00 0.00 0.00 3.67
2481 2705 0.690762 GGGGGCTTGTTCTGTAGACA 59.309 55.000 0.00 0.00 0.00 3.41
2482 2706 0.391263 CGGGGGCTTGTTCTGTAGAC 60.391 60.000 0.00 0.00 0.00 2.59
2483 2707 1.550130 CCGGGGGCTTGTTCTGTAGA 61.550 60.000 0.00 0.00 0.00 2.59
2484 2708 1.078426 CCGGGGGCTTGTTCTGTAG 60.078 63.158 0.00 0.00 0.00 2.74
2485 2709 3.074281 CCGGGGGCTTGTTCTGTA 58.926 61.111 0.00 0.00 0.00 2.74
2486 2710 4.660938 GCCGGGGGCTTGTTCTGT 62.661 66.667 2.18 0.00 46.69 3.41
2502 2726 4.803426 CTCGGTCAGGGCACTCGC 62.803 72.222 0.00 0.00 37.44 5.03
2503 2727 3.057547 CTCTCGGTCAGGGCACTCG 62.058 68.421 0.00 0.00 0.00 4.18
2504 2728 2.716017 CCTCTCGGTCAGGGCACTC 61.716 68.421 0.00 0.00 0.00 3.51
2505 2729 2.681778 CCTCTCGGTCAGGGCACT 60.682 66.667 0.00 0.00 0.00 4.40
2506 2730 3.775654 CCCTCTCGGTCAGGGCAC 61.776 72.222 1.79 0.00 44.59 5.01
2510 2734 3.522731 CGCTCCCTCTCGGTCAGG 61.523 72.222 0.00 0.00 0.00 3.86
2511 2735 4.200283 GCGCTCCCTCTCGGTCAG 62.200 72.222 0.00 0.00 0.00 3.51
2526 2750 4.688419 CCTTTGCACAGCGTGGCG 62.688 66.667 10.02 0.00 33.64 5.69
2527 2751 4.347453 CCCTTTGCACAGCGTGGC 62.347 66.667 10.02 0.75 33.64 5.01
2528 2752 2.133742 CTTCCCTTTGCACAGCGTGG 62.134 60.000 10.02 0.00 33.64 4.94
2529 2753 1.165907 TCTTCCCTTTGCACAGCGTG 61.166 55.000 0.00 4.61 36.51 5.34
2530 2754 0.465460 TTCTTCCCTTTGCACAGCGT 60.465 50.000 0.00 0.00 0.00 5.07
2531 2755 0.239347 CTTCTTCCCTTTGCACAGCG 59.761 55.000 0.00 0.00 0.00 5.18
2532 2756 0.600057 CCTTCTTCCCTTTGCACAGC 59.400 55.000 0.00 0.00 0.00 4.40
2533 2757 0.600057 GCCTTCTTCCCTTTGCACAG 59.400 55.000 0.00 0.00 0.00 3.66
2534 2758 0.827507 GGCCTTCTTCCCTTTGCACA 60.828 55.000 0.00 0.00 0.00 4.57
2535 2759 1.866853 CGGCCTTCTTCCCTTTGCAC 61.867 60.000 0.00 0.00 0.00 4.57
2536 2760 1.603455 CGGCCTTCTTCCCTTTGCA 60.603 57.895 0.00 0.00 0.00 4.08
2537 2761 1.303317 TCGGCCTTCTTCCCTTTGC 60.303 57.895 0.00 0.00 0.00 3.68
2538 2762 1.308783 GCTCGGCCTTCTTCCCTTTG 61.309 60.000 0.00 0.00 0.00 2.77
2539 2763 1.002011 GCTCGGCCTTCTTCCCTTT 60.002 57.895 0.00 0.00 0.00 3.11
2540 2764 2.671682 GCTCGGCCTTCTTCCCTT 59.328 61.111 0.00 0.00 0.00 3.95
2541 2765 3.775654 CGCTCGGCCTTCTTCCCT 61.776 66.667 0.00 0.00 0.00 4.20
2542 2766 4.840005 CCGCTCGGCCTTCTTCCC 62.840 72.222 0.00 0.00 0.00 3.97
2552 2776 3.845178 TCATAGTATAATTGCCGCTCGG 58.155 45.455 3.56 3.56 38.57 4.63
2553 2777 5.839262 TTTCATAGTATAATTGCCGCTCG 57.161 39.130 0.00 0.00 0.00 5.03
2554 2778 7.639945 AGTTTTTCATAGTATAATTGCCGCTC 58.360 34.615 0.00 0.00 0.00 5.03
2555 2779 7.568199 AGTTTTTCATAGTATAATTGCCGCT 57.432 32.000 0.00 0.00 0.00 5.52
2556 2780 9.724839 TTTAGTTTTTCATAGTATAATTGCCGC 57.275 29.630 0.00 0.00 0.00 6.53


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

AutoCloner maintained by Alex Coulton.