Multiple sequence alignment - TraesCS4B01G017900

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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 TraesCS4B01G017900 chr4B 100.000 3856 0 0 1 3856 13128461 13124606 0.000000e+00 7121
1 TraesCS4B01G017900 chr4B 85.495 1303 94 45 633 1870 18652237 18653509 0.000000e+00 1271
2 TraesCS4B01G017900 chr4B 79.636 1154 136 53 431 1558 10698731 10699811 0.000000e+00 737
3 TraesCS4B01G017900 chr4B 80.914 875 94 33 1980 2833 10700634 10701456 1.180000e-174 623
4 TraesCS4B01G017900 chr4B 81.145 594 70 23 1 569 18651662 18652238 4.570000e-119 438
5 TraesCS4B01G017900 chr4B 81.698 377 54 7 968 1332 22261227 22260854 2.250000e-77 300
6 TraesCS4B01G017900 chr4D 83.510 1892 142 86 1209 3006 7217463 7215648 0.000000e+00 1609
7 TraesCS4B01G017900 chr4D 79.090 1626 209 79 20 1558 6072678 6074259 0.000000e+00 998
8 TraesCS4B01G017900 chr4D 77.785 1553 199 68 99 1558 42271419 42269920 0.000000e+00 822
9 TraesCS4B01G017900 chr4D 83.222 900 90 33 999 1869 9756201 9755334 0.000000e+00 769
10 TraesCS4B01G017900 chr4D 81.257 875 83 40 1875 2733 42269193 42268384 1.950000e-177 632
11 TraesCS4B01G017900 chr4D 79.638 663 70 35 1977 2624 6075014 6075626 2.140000e-112 416
12 TraesCS4B01G017900 chr4D 80.795 302 45 10 3542 3835 7214340 7214044 1.390000e-54 224
13 TraesCS4B01G017900 chr4D 81.283 187 21 6 3232 3407 7215332 7215149 5.190000e-29 139
14 TraesCS4B01G017900 chr4A 84.378 1069 77 51 855 1869 596297928 596298960 0.000000e+00 966
15 TraesCS4B01G017900 chr4A 82.429 1161 110 56 761 1869 593470073 593471191 0.000000e+00 928
16 TraesCS4B01G017900 chr4A 82.398 1034 82 44 1974 2999 596299131 596300072 0.000000e+00 809
17 TraesCS4B01G017900 chr4A 76.600 1641 213 82 20 1541 597466789 597465201 0.000000e+00 745
18 TraesCS4B01G017900 chr4A 87.638 453 22 12 2209 2653 597604017 597603591 2.680000e-136 496
19 TraesCS4B01G017900 chr4A 87.445 454 21 12 2209 2653 597464131 597463705 1.240000e-134 490
20 TraesCS4B01G017900 chr4A 87.417 453 23 13 2209 2653 597642989 597642563 1.240000e-134 490
21 TraesCS4B01G017900 chr4A 87.417 453 23 13 2209 2653 597654386 597653960 1.240000e-134 490
22 TraesCS4B01G017900 chr4A 77.071 1038 116 52 20 952 597657526 597656506 1.610000e-133 486
23 TraesCS4B01G017900 chr4A 86.534 453 27 13 2209 2653 597623332 597622906 5.830000e-128 468
24 TraesCS4B01G017900 chr4A 85.465 344 39 10 384 726 593469469 593469802 7.930000e-92 348
25 TraesCS4B01G017900 chr4A 85.586 333 37 7 384 713 596297170 596297494 4.770000e-89 339
26 TraesCS4B01G017900 chr4A 80.000 335 38 12 3190 3498 596300368 596300699 1.800000e-53 220
27 TraesCS4B01G017900 chr4A 81.356 236 24 15 1884 2115 597623599 597623380 1.420000e-39 174
28 TraesCS4B01G017900 chr4A 80.567 247 27 14 1875 2115 597464410 597464179 1.840000e-38 171
29 TraesCS4B01G017900 chr4A 80.488 246 28 14 1875 2115 597654664 597654434 1.840000e-38 171
30 TraesCS4B01G017900 chr4A 88.811 143 4 7 3047 3189 596300195 596300325 8.570000e-37 165
31 TraesCS4B01G017900 chr1A 78.008 241 24 18 1743 1966 34427861 34427633 1.450000e-24 124
32 TraesCS4B01G017900 chr2A 75.251 299 43 19 1662 1943 750035970 750036254 3.150000e-21 113


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 TraesCS4B01G017900 chr4B 13124606 13128461 3855 True 7121.000000 7121 100.000000 1 3856 1 chr4B.!!$R1 3855
1 TraesCS4B01G017900 chr4B 18651662 18653509 1847 False 854.500000 1271 83.320000 1 1870 2 chr4B.!!$F2 1869
2 TraesCS4B01G017900 chr4B 10698731 10701456 2725 False 680.000000 737 80.275000 431 2833 2 chr4B.!!$F1 2402
3 TraesCS4B01G017900 chr4D 9755334 9756201 867 True 769.000000 769 83.222000 999 1869 1 chr4D.!!$R1 870
4 TraesCS4B01G017900 chr4D 42268384 42271419 3035 True 727.000000 822 79.521000 99 2733 2 chr4D.!!$R3 2634
5 TraesCS4B01G017900 chr4D 6072678 6075626 2948 False 707.000000 998 79.364000 20 2624 2 chr4D.!!$F1 2604
6 TraesCS4B01G017900 chr4D 7214044 7217463 3419 True 657.333333 1609 81.862667 1209 3835 3 chr4D.!!$R2 2626
7 TraesCS4B01G017900 chr4A 593469469 593471191 1722 False 638.000000 928 83.947000 384 1869 2 chr4A.!!$F1 1485
8 TraesCS4B01G017900 chr4A 596297170 596300699 3529 False 499.800000 966 84.234600 384 3498 5 chr4A.!!$F2 3114
9 TraesCS4B01G017900 chr4A 597463705 597466789 3084 True 468.666667 745 81.537333 20 2653 3 chr4A.!!$R3 2633
10 TraesCS4B01G017900 chr4A 597653960 597657526 3566 True 382.333333 490 81.658667 20 2653 3 chr4A.!!$R5 2633
11 TraesCS4B01G017900 chr4A 597622906 597623599 693 True 321.000000 468 83.945000 1884 2653 2 chr4A.!!$R4 769

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
412 463 0.877743 GAACAAGAAGGCCAGTCAGC 59.122 55.0 5.01 0.0 0.00 4.26 F
1871 3876 0.238553 GCGATCATCGTCGAGATCCA 59.761 55.0 19.82 0.0 44.06 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2056 4163 0.233848 CCGCACGCGAAAAAGTAGTT 59.766 50.0 15.93 0.00 42.83 2.24 R
3526 6069 0.036952 CGTGAGTTCCATGTGGCTCT 60.037 55.0 7.78 2.98 34.44 4.09 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
213 214 7.352079 ACATCTTTTGGAGTTCTGAACATTT 57.648 32.000 21.50 1.91 0.00 2.32
244 245 2.629617 ACACAAGCCATTTTCCAGGAAG 59.370 45.455 1.07 0.00 0.00 3.46
245 246 2.892852 CACAAGCCATTTTCCAGGAAGA 59.107 45.455 1.07 0.00 0.00 2.87
246 247 3.321682 CACAAGCCATTTTCCAGGAAGAA 59.678 43.478 1.07 0.95 0.00 2.52
247 248 4.020839 CACAAGCCATTTTCCAGGAAGAAT 60.021 41.667 1.07 3.27 0.00 2.40
248 249 5.185635 CACAAGCCATTTTCCAGGAAGAATA 59.814 40.000 1.07 0.00 0.00 1.75
249 250 5.185828 ACAAGCCATTTTCCAGGAAGAATAC 59.814 40.000 1.07 2.72 0.00 1.89
253 264 6.441604 AGCCATTTTCCAGGAAGAATACAAAT 59.558 34.615 1.07 0.00 0.00 2.32
279 290 9.426837 TGCAAAAGAAATGAGATATCCAAAAAG 57.573 29.630 0.00 0.00 0.00 2.27
318 338 6.451064 AAACAAAACAGAGAAACCTACAGG 57.549 37.500 0.00 0.00 42.17 4.00
323 343 7.342026 ACAAAACAGAGAAACCTACAGGAAAAT 59.658 33.333 1.29 0.00 38.94 1.82
324 344 7.511959 AAACAGAGAAACCTACAGGAAAATC 57.488 36.000 1.29 0.00 38.94 2.17
325 347 5.561679 ACAGAGAAACCTACAGGAAAATCC 58.438 41.667 1.29 0.00 38.94 3.01
373 407 1.187567 ACTGGGCCAGGCAATGTTTC 61.188 55.000 35.34 0.00 35.51 2.78
381 421 1.374125 GGCAATGTTTCCAACGGCC 60.374 57.895 0.00 0.00 38.12 6.13
382 422 1.665442 GCAATGTTTCCAACGGCCT 59.335 52.632 0.00 0.00 0.00 5.19
396 443 1.448717 GGCCTCGCTCTTCCTGAAC 60.449 63.158 0.00 0.00 0.00 3.18
404 455 1.809547 GCTCTTCCTGAACAAGAAGGC 59.190 52.381 11.59 10.26 39.97 4.35
410 461 1.202806 CCTGAACAAGAAGGCCAGTCA 60.203 52.381 5.01 0.00 0.00 3.41
411 462 2.149578 CTGAACAAGAAGGCCAGTCAG 58.850 52.381 5.01 2.76 0.00 3.51
412 463 0.877743 GAACAAGAAGGCCAGTCAGC 59.122 55.000 5.01 0.00 0.00 4.26
440 491 3.155167 CTCCCAGTACTCGGGCCC 61.155 72.222 13.57 13.57 44.11 5.80
555 612 1.338579 GCCTTCCAGAACTCTCCACAG 60.339 57.143 0.00 0.00 0.00 3.66
562 620 2.232298 GAACTCTCCACAGGCTCCCG 62.232 65.000 0.00 0.00 0.00 5.14
691 782 2.917363 GGAAACGGAAAAGCTTTCTCG 58.083 47.619 23.55 23.55 0.00 4.04
726 824 4.832608 GTTACGGGCGCCAGAGGG 62.833 72.222 33.66 15.70 37.18 4.30
839 1246 4.292178 GCCCAGGATCGAGCGAGG 62.292 72.222 3.30 3.30 0.00 4.63
963 1401 1.373435 CACCACCAAACCCTAGCGA 59.627 57.895 0.00 0.00 0.00 4.93
1017 1925 2.919856 ATGGAGAGATCCCGCGGG 60.920 66.667 39.13 39.13 0.00 6.13
1334 2263 2.431942 CGCCTGCGAAGGTACGTT 60.432 61.111 12.24 0.00 42.83 3.99
1336 2265 1.666872 GCCTGCGAAGGTACGTTGT 60.667 57.895 12.24 0.00 35.59 3.32
1337 2266 1.623973 GCCTGCGAAGGTACGTTGTC 61.624 60.000 12.24 0.00 35.59 3.18
1339 2268 1.342082 CTGCGAAGGTACGTTGTCCG 61.342 60.000 5.36 4.65 44.03 4.79
1341 2270 2.090524 CGAAGGTACGTTGTCCGCC 61.091 63.158 5.36 0.00 41.42 6.13
1344 2273 2.125793 GGTACGTTGTCCGCCTCC 60.126 66.667 0.00 0.00 41.42 4.30
1347 2276 2.345760 TACGTTGTCCGCCTCCTCC 61.346 63.158 0.00 0.00 41.42 4.30
1402 2379 3.359033 TCGCTTTCCTGCTTACCTAGTA 58.641 45.455 0.00 0.00 0.00 1.82
1403 2380 3.380637 TCGCTTTCCTGCTTACCTAGTAG 59.619 47.826 0.00 0.00 36.45 2.57
1404 2381 3.130693 CGCTTTCCTGCTTACCTAGTAGT 59.869 47.826 0.00 0.00 35.04 2.73
1420 2397 4.382345 AGTAGTACGTAGTTTCCCATGC 57.618 45.455 8.48 0.00 37.78 4.06
1426 2403 2.039879 ACGTAGTTTCCCATGCCTTCTT 59.960 45.455 0.00 0.00 37.78 2.52
1435 2412 1.134699 CCATGCCTTCTTGACTCGCTA 60.135 52.381 0.00 0.00 0.00 4.26
1436 2413 2.200067 CATGCCTTCTTGACTCGCTAG 58.800 52.381 0.00 0.00 0.00 3.42
1437 2414 1.545841 TGCCTTCTTGACTCGCTAGA 58.454 50.000 0.00 0.00 0.00 2.43
1456 2438 1.705997 AAGTGCTCCGGTTTGGGTCT 61.706 55.000 0.00 0.00 38.76 3.85
1589 3355 1.019673 TCATACCGCTGTACCTCGAC 58.980 55.000 5.57 0.00 0.00 4.20
1604 3370 0.306840 TCGACATACACGGAGCGATC 59.693 55.000 0.00 0.00 0.00 3.69
1607 3374 2.159824 CGACATACACGGAGCGATCTAT 59.840 50.000 0.00 0.00 0.00 1.98
1678 3447 5.115773 CGATTGTTTCGTCGATTCTAGATCC 59.884 44.000 0.00 0.00 43.01 3.36
1700 3570 0.669625 GCTTGTTCCCGCGAGTTAGT 60.670 55.000 8.23 0.00 0.00 2.24
1704 3574 1.206523 GTTCCCGCGAGTTAGTATGC 58.793 55.000 8.23 0.00 0.00 3.14
1709 3579 2.054363 CCGCGAGTTAGTATGCATCTG 58.946 52.381 8.23 0.00 0.00 2.90
1710 3580 1.453524 CGCGAGTTAGTATGCATCTGC 59.546 52.381 0.19 0.00 42.50 4.26
1711 3581 1.453524 GCGAGTTAGTATGCATCTGCG 59.546 52.381 0.19 0.00 45.83 5.18
1712 3582 2.732366 CGAGTTAGTATGCATCTGCGT 58.268 47.619 0.19 2.03 45.83 5.24
1772 3664 3.027710 CGAGTTATCTACTGTCGTTCGC 58.972 50.000 0.00 0.00 37.17 4.70
1792 3688 3.202906 GCTCGACCATATTTGCCTGTTA 58.797 45.455 0.00 0.00 0.00 2.41
1793 3689 3.625764 GCTCGACCATATTTGCCTGTTAA 59.374 43.478 0.00 0.00 0.00 2.01
1794 3690 4.275936 GCTCGACCATATTTGCCTGTTAAT 59.724 41.667 0.00 0.00 0.00 1.40
1798 3694 5.977129 CGACCATATTTGCCTGTTAATTTCC 59.023 40.000 0.00 0.00 0.00 3.13
1804 3700 5.860941 TTTGCCTGTTAATTTCCTGTTCA 57.139 34.783 0.00 0.00 0.00 3.18
1806 3702 5.643379 TGCCTGTTAATTTCCTGTTCATC 57.357 39.130 0.00 0.00 0.00 2.92
1807 3703 4.155826 TGCCTGTTAATTTCCTGTTCATCG 59.844 41.667 0.00 0.00 0.00 3.84
1809 3705 5.631026 CCTGTTAATTTCCTGTTCATCGTG 58.369 41.667 0.00 0.00 0.00 4.35
1810 3706 5.041951 TGTTAATTTCCTGTTCATCGTGC 57.958 39.130 0.00 0.00 0.00 5.34
1811 3707 4.517075 TGTTAATTTCCTGTTCATCGTGCA 59.483 37.500 0.00 0.00 0.00 4.57
1871 3876 0.238553 GCGATCATCGTCGAGATCCA 59.761 55.000 19.82 0.00 44.06 3.41
1873 3878 2.513893 CGATCATCGTCGAGATCCATG 58.486 52.381 19.82 6.92 44.06 3.66
1914 3991 3.632145 TCTTCTGCCTTGTTTTGTTCTCC 59.368 43.478 0.00 0.00 0.00 3.71
1918 3995 1.600413 GCCTTGTTTTGTTCTCCGCAG 60.600 52.381 0.00 0.00 0.00 5.18
1919 3996 1.676006 CCTTGTTTTGTTCTCCGCAGT 59.324 47.619 0.00 0.00 0.00 4.40
1920 3997 2.875933 CCTTGTTTTGTTCTCCGCAGTA 59.124 45.455 0.00 0.00 0.00 2.74
1921 3998 3.303791 CCTTGTTTTGTTCTCCGCAGTAC 60.304 47.826 0.00 0.00 0.00 2.73
1950 4027 5.637387 GTCTTGCTTGGTCAAAACTGAAAAA 59.363 36.000 0.00 0.00 0.00 1.94
1951 4028 5.637387 TCTTGCTTGGTCAAAACTGAAAAAC 59.363 36.000 0.00 0.00 0.00 2.43
1952 4029 3.923461 TGCTTGGTCAAAACTGAAAAACG 59.077 39.130 0.00 0.00 0.00 3.60
1953 4030 3.241963 GCTTGGTCAAAACTGAAAAACGC 60.242 43.478 0.00 0.00 0.00 4.84
1954 4031 3.859411 TGGTCAAAACTGAAAAACGCT 57.141 38.095 0.00 0.00 0.00 5.07
2056 4163 0.178767 CATGTTGATCCTCTGGCGGA 59.821 55.000 0.00 0.00 37.50 5.54
2070 4182 0.179233 GGCGGAACTACTTTTTCGCG 60.179 55.000 0.00 0.00 39.54 5.87
2104 4216 2.342179 GCCTTCCTCTCTCGTGAAAAG 58.658 52.381 0.00 0.00 0.00 2.27
2118 4231 2.289820 GTGAAAAGAGGTCGGGTCAAAC 59.710 50.000 0.00 0.00 0.00 2.93
2133 4246 2.091541 TCAAACCAAATGGATCGCCTC 58.908 47.619 6.42 0.00 38.94 4.70
2147 4260 2.818714 CCTCTTGGCAGAGCAGCG 60.819 66.667 8.03 0.00 44.96 5.18
2292 4427 1.423056 CGTACGTCGTCACCTCCTC 59.577 63.158 7.22 0.00 34.52 3.71
2295 4430 0.904649 TACGTCGTCACCTCCTCCTA 59.095 55.000 0.00 0.00 0.00 2.94
2296 4431 0.676151 ACGTCGTCACCTCCTCCTAC 60.676 60.000 0.00 0.00 0.00 3.18
2368 4506 2.599659 GTGATTAACTTTGGCTGCTGC 58.400 47.619 7.10 7.10 38.76 5.25
2498 4649 1.476477 GCGTAAGAACCTCTCCCTCT 58.524 55.000 0.00 0.00 43.02 3.69
2499 4650 1.406180 GCGTAAGAACCTCTCCCTCTC 59.594 57.143 0.00 0.00 43.02 3.20
2500 4651 2.025898 CGTAAGAACCTCTCCCTCTCC 58.974 57.143 0.00 0.00 43.02 3.71
2501 4652 2.390696 GTAAGAACCTCTCCCTCTCCC 58.609 57.143 0.00 0.00 0.00 4.30
2502 4653 1.097722 AAGAACCTCTCCCTCTCCCT 58.902 55.000 0.00 0.00 0.00 4.20
2503 4654 0.634465 AGAACCTCTCCCTCTCCCTC 59.366 60.000 0.00 0.00 0.00 4.30
2504 4655 0.634465 GAACCTCTCCCTCTCCCTCT 59.366 60.000 0.00 0.00 0.00 3.69
2505 4656 0.634465 AACCTCTCCCTCTCCCTCTC 59.366 60.000 0.00 0.00 0.00 3.20
2532 4683 1.790090 CTCTCGCCTGCATCTCGCTA 61.790 60.000 0.00 0.00 43.06 4.26
2570 4723 6.543465 TCCATATGTTGATCAGCCTTGTTTAG 59.457 38.462 7.13 0.00 0.00 1.85
2585 4738 6.293735 GCCTTGTTTAGTTACTAACATGTGCA 60.294 38.462 4.09 0.00 0.00 4.57
2587 4740 6.548441 TGTTTAGTTACTAACATGTGCACC 57.452 37.500 15.69 0.00 0.00 5.01
2861 5021 0.383590 ACATCATCCTCTGAGTCGCG 59.616 55.000 0.00 0.00 37.28 5.87
2862 5022 0.938637 CATCATCCTCTGAGTCGCGC 60.939 60.000 0.00 0.00 37.28 6.86
2863 5023 2.399511 ATCATCCTCTGAGTCGCGCG 62.400 60.000 26.76 26.76 37.28 6.86
2911 5072 1.332375 CCAGTCGCAGTAGAGTAGAGC 59.668 57.143 0.00 0.00 0.00 4.09
2923 5084 1.012014 GTAGAGCGCTCGTCGTCTC 60.012 63.158 30.39 13.30 41.07 3.36
2934 5095 1.650380 CGTCGTCTCGTTCCGTTTCG 61.650 60.000 0.00 0.00 0.00 3.46
2938 5099 1.662446 TCTCGTTCCGTTTCGTGCC 60.662 57.895 0.00 0.00 0.00 5.01
2965 5126 0.161024 GTTCGAGGTTCGTTTCTGCG 59.839 55.000 0.00 0.00 41.35 5.18
2975 5136 2.664851 TTTCTGCGTGCAGTCCGG 60.665 61.111 20.33 0.00 43.96 5.14
2985 5146 2.095252 GCAGTCCGGTCGAAGAAGC 61.095 63.158 0.00 0.00 39.69 3.86
3018 5209 7.856145 TTTGAGTACTAGTGGTAGTAGTAGC 57.144 40.000 5.39 0.00 42.98 3.58
3019 5210 6.550938 TGAGTACTAGTGGTAGTAGTAGCA 57.449 41.667 5.39 5.35 42.98 3.49
3020 5211 6.580788 TGAGTACTAGTGGTAGTAGTAGCAG 58.419 44.000 9.72 1.86 42.98 4.24
3022 5213 4.232188 ACTAGTGGTAGTAGTAGCAGCA 57.768 45.455 9.72 0.68 37.76 4.41
3024 5215 1.751924 AGTGGTAGTAGTAGCAGCAGC 59.248 52.381 9.72 0.00 37.33 5.25
3027 5218 9.538856 ACTAGTGGTAGTAGTAGCAGCAGCTAT 62.539 44.444 14.38 6.25 45.05 2.97
3037 5228 1.325943 GCAGCAGCTATCGTTTCTGTC 59.674 52.381 0.00 0.00 37.91 3.51
3038 5229 1.929836 CAGCAGCTATCGTTTCTGTCC 59.070 52.381 0.00 0.00 0.00 4.02
3039 5230 0.924090 GCAGCTATCGTTTCTGTCCG 59.076 55.000 0.00 0.00 0.00 4.79
3041 5232 0.818296 AGCTATCGTTTCTGTCCGCT 59.182 50.000 0.00 0.00 0.00 5.52
3042 5233 1.201343 GCTATCGTTTCTGTCCGCTC 58.799 55.000 0.00 0.00 0.00 5.03
3045 5236 0.806868 ATCGTTTCTGTCCGCTCGTA 59.193 50.000 0.00 0.00 0.00 3.43
3075 5312 2.459060 TGGTCGCGGAGAACAATTAA 57.541 45.000 6.13 0.00 44.92 1.40
3090 5329 4.555262 ACAATTAATTGGGTGTTTGCGAG 58.445 39.130 27.43 3.04 41.96 5.03
3102 5341 2.103432 TGTTTGCGAGTCCTCTGGTTAA 59.897 45.455 0.00 0.00 0.00 2.01
3118 5357 4.622701 GGTTAAGATGAACCACTGATGC 57.377 45.455 0.41 0.00 46.97 3.91
3119 5358 4.265073 GGTTAAGATGAACCACTGATGCT 58.735 43.478 0.41 0.00 46.97 3.79
3120 5359 5.428253 GGTTAAGATGAACCACTGATGCTA 58.572 41.667 0.41 0.00 46.97 3.49
3121 5360 6.058183 GGTTAAGATGAACCACTGATGCTAT 58.942 40.000 0.41 0.00 46.97 2.97
3122 5361 6.017605 GGTTAAGATGAACCACTGATGCTATG 60.018 42.308 0.41 0.00 46.97 2.23
3123 5362 4.767578 AGATGAACCACTGATGCTATGT 57.232 40.909 0.00 0.00 0.00 2.29
3124 5363 4.449131 AGATGAACCACTGATGCTATGTG 58.551 43.478 0.00 0.00 0.00 3.21
3125 5364 3.979101 TGAACCACTGATGCTATGTGA 57.021 42.857 0.00 0.00 33.95 3.58
3126 5365 4.492494 TGAACCACTGATGCTATGTGAT 57.508 40.909 0.00 0.00 33.95 3.06
3127 5366 4.445453 TGAACCACTGATGCTATGTGATC 58.555 43.478 0.00 0.00 33.95 2.92
3189 5433 2.033065 GCGTTCTGCTGATGATGTGATC 60.033 50.000 0.00 0.00 41.73 2.92
3196 5486 3.634910 TGCTGATGATGTGATCCATTTGG 59.365 43.478 0.00 0.00 32.56 3.28
3207 5497 2.512692 TCCATTTGGATCTGTGTGGG 57.487 50.000 0.00 0.00 39.78 4.61
3218 5508 0.385390 CTGTGTGGGGCAACAGTTTC 59.615 55.000 0.00 0.00 39.74 2.78
3242 5541 1.611043 GCTTTTGCTCTGCGATGAAC 58.389 50.000 0.00 0.00 43.35 3.18
3301 5600 3.508402 TGAACTGTAGAACGGATGCAGTA 59.492 43.478 7.67 0.00 41.89 2.74
3324 5623 6.674694 ACTGATTTCTGCTTATGATGTGAC 57.325 37.500 0.00 0.00 0.00 3.67
3330 5629 4.044426 TCTGCTTATGATGTGACGATTCG 58.956 43.478 4.14 4.14 0.00 3.34
3366 5677 7.137490 TCATCTCTTCAAATTTGTGTAGCAG 57.863 36.000 17.47 11.76 0.00 4.24
3368 5679 5.065914 TCTCTTCAAATTTGTGTAGCAGCT 58.934 37.500 17.47 0.00 0.00 4.24
3390 5701 4.905429 TGTTTGTAGCTTCCATTCTGCTA 58.095 39.130 0.00 0.00 38.15 3.49
3393 5704 4.077300 TGTAGCTTCCATTCTGCTATGG 57.923 45.455 0.00 6.71 45.34 2.74
3404 5716 1.202568 TCTGCTATGGACGAATGCCTG 60.203 52.381 0.00 0.00 0.00 4.85
3407 5719 2.017049 GCTATGGACGAATGCCTGTTT 58.983 47.619 0.00 0.00 0.00 2.83
3494 6023 4.321675 GGACAAAATAGATGGTGCGGTTTT 60.322 41.667 0.00 0.00 0.00 2.43
3495 6024 4.555262 ACAAAATAGATGGTGCGGTTTTG 58.445 39.130 0.00 0.00 40.48 2.44
3498 6041 4.900635 AATAGATGGTGCGGTTTTGATC 57.099 40.909 0.00 0.00 0.00 2.92
3500 6043 0.455815 GATGGTGCGGTTTTGATCCC 59.544 55.000 0.00 0.00 0.00 3.85
3508 6051 1.618345 CGGTTTTGATCCCCAATCCCA 60.618 52.381 0.00 0.00 34.23 4.37
3509 6052 1.831106 GGTTTTGATCCCCAATCCCAC 59.169 52.381 0.00 0.00 34.23 4.61
3511 6054 1.088269 TTTGATCCCCAATCCCACCA 58.912 50.000 0.00 0.00 34.23 4.17
3516 6059 1.076044 CCCCAATCCCACCATCACC 60.076 63.158 0.00 0.00 0.00 4.02
3523 6066 0.331278 TCCCACCATCACCATGTTCC 59.669 55.000 0.00 0.00 0.00 3.62
3524 6067 1.031571 CCCACCATCACCATGTTCCG 61.032 60.000 0.00 0.00 0.00 4.30
3525 6068 1.031571 CCACCATCACCATGTTCCGG 61.032 60.000 0.00 0.00 0.00 5.14
3526 6069 0.035534 CACCATCACCATGTTCCGGA 60.036 55.000 0.00 0.00 0.00 5.14
3527 6070 0.253044 ACCATCACCATGTTCCGGAG 59.747 55.000 3.34 0.00 0.00 4.63
3528 6071 0.541392 CCATCACCATGTTCCGGAGA 59.459 55.000 3.34 0.00 0.00 3.71
3529 6072 1.473965 CCATCACCATGTTCCGGAGAG 60.474 57.143 3.34 0.00 0.00 3.20
3530 6073 0.179000 ATCACCATGTTCCGGAGAGC 59.821 55.000 3.34 0.00 0.00 4.09
3544 6540 1.677217 GGAGAGCCACATGGAACTCAC 60.677 57.143 19.18 9.44 39.13 3.51
3554 6550 1.300697 GGAACTCACGTCAAGCGGT 60.301 57.895 0.00 0.00 46.52 5.68
3565 6561 1.098869 TCAAGCGGTCACTTTTTGCA 58.901 45.000 0.00 0.00 0.00 4.08
3566 6562 1.065401 TCAAGCGGTCACTTTTTGCAG 59.935 47.619 0.00 0.00 0.00 4.41
3567 6563 1.065401 CAAGCGGTCACTTTTTGCAGA 59.935 47.619 0.00 0.00 0.00 4.26
3569 6565 1.956477 AGCGGTCACTTTTTGCAGAAT 59.044 42.857 0.00 0.00 0.00 2.40
3612 6608 4.982241 TTGTTGAAACCTCTCTCCTCAT 57.018 40.909 0.00 0.00 0.00 2.90
3613 6609 4.543590 TGTTGAAACCTCTCTCCTCATC 57.456 45.455 0.00 0.00 0.00 2.92
3616 6612 1.765904 GAAACCTCTCTCCTCATCCCC 59.234 57.143 0.00 0.00 0.00 4.81
3620 6616 2.200081 CCTCTCTCCTCATCCCCAAAA 58.800 52.381 0.00 0.00 0.00 2.44
3621 6617 2.172293 CCTCTCTCCTCATCCCCAAAAG 59.828 54.545 0.00 0.00 0.00 2.27
3622 6618 2.843113 CTCTCTCCTCATCCCCAAAAGT 59.157 50.000 0.00 0.00 0.00 2.66
3623 6619 3.260205 TCTCTCCTCATCCCCAAAAGTT 58.740 45.455 0.00 0.00 0.00 2.66
3624 6620 3.009473 TCTCTCCTCATCCCCAAAAGTTG 59.991 47.826 0.00 0.00 0.00 3.16
3625 6621 2.986019 TCTCCTCATCCCCAAAAGTTGA 59.014 45.455 0.00 0.00 0.00 3.18
3626 6622 3.593328 TCTCCTCATCCCCAAAAGTTGAT 59.407 43.478 0.00 0.00 0.00 2.57
3627 6623 3.698040 CTCCTCATCCCCAAAAGTTGATG 59.302 47.826 0.00 0.00 36.73 3.07
3629 6625 2.827322 CTCATCCCCAAAAGTTGATGCA 59.173 45.455 0.00 0.00 35.65 3.96
3631 6627 3.006752 TCATCCCCAAAAGTTGATGCAAC 59.993 43.478 0.00 2.22 43.83 4.17
3632 6628 2.392662 TCCCCAAAAGTTGATGCAACA 58.607 42.857 12.25 0.00 45.66 3.33
3633 6629 2.364970 TCCCCAAAAGTTGATGCAACAG 59.635 45.455 12.25 0.57 45.66 3.16
3634 6630 2.102925 CCCCAAAAGTTGATGCAACAGT 59.897 45.455 12.25 0.00 45.66 3.55
3635 6631 3.125316 CCCAAAAGTTGATGCAACAGTG 58.875 45.455 12.25 6.90 45.66 3.66
3665 6661 2.435437 GCCCACCCATGCTTTTTCATAT 59.565 45.455 0.00 0.00 0.00 1.78
3666 6662 3.742013 GCCCACCCATGCTTTTTCATATG 60.742 47.826 0.00 0.00 0.00 1.78
3669 6665 5.163280 CCCACCCATGCTTTTTCATATGATT 60.163 40.000 6.17 0.00 0.00 2.57
3670 6666 5.756347 CCACCCATGCTTTTTCATATGATTG 59.244 40.000 6.17 0.00 0.00 2.67
3672 6668 7.417683 CCACCCATGCTTTTTCATATGATTGTA 60.418 37.037 6.17 0.00 0.00 2.41
3673 6669 7.980662 CACCCATGCTTTTTCATATGATTGTAA 59.019 33.333 6.17 0.00 0.00 2.41
3674 6670 8.538701 ACCCATGCTTTTTCATATGATTGTAAA 58.461 29.630 6.17 1.18 0.00 2.01
3701 6701 8.980143 TTTGGATCGATTTTATCTTTTGAACC 57.020 30.769 0.00 0.00 0.00 3.62
3702 6702 7.095695 TGGATCGATTTTATCTTTTGAACCC 57.904 36.000 0.00 0.00 0.00 4.11
3703 6703 6.889722 TGGATCGATTTTATCTTTTGAACCCT 59.110 34.615 0.00 0.00 0.00 4.34
3709 6709 8.182227 CGATTTTATCTTTTGAACCCTAAGTCC 58.818 37.037 0.00 0.00 0.00 3.85
3711 6711 3.412237 TCTTTTGAACCCTAAGTCCGG 57.588 47.619 0.00 0.00 0.00 5.14
3730 6730 3.919804 CCGGTTTACAATCTGTTTGCATG 59.080 43.478 0.00 0.00 39.03 4.06
3748 6748 0.519519 TGTTTATGTTCCTTGCGGCG 59.480 50.000 0.51 0.51 0.00 6.46
3754 6754 4.388499 TTCCTTGCGGCGAGGACC 62.388 66.667 33.62 0.00 43.14 4.46
3757 6757 2.436646 CTTGCGGCGAGGACCATT 60.437 61.111 12.98 0.00 0.00 3.16
3767 6769 3.335579 GCGAGGACCATTAAACAAGACT 58.664 45.455 0.00 0.00 0.00 3.24
3768 6770 4.501071 GCGAGGACCATTAAACAAGACTA 58.499 43.478 0.00 0.00 0.00 2.59
3769 6771 4.329256 GCGAGGACCATTAAACAAGACTAC 59.671 45.833 0.00 0.00 0.00 2.73
3771 6773 6.626623 GCGAGGACCATTAAACAAGACTACTA 60.627 42.308 0.00 0.00 0.00 1.82
3775 6777 8.047310 AGGACCATTAAACAAGACTACTATTGG 58.953 37.037 0.00 0.00 0.00 3.16
3791 6793 8.251721 ACTACTATTGGATATATTTCGACAGGC 58.748 37.037 0.00 0.00 0.00 4.85
3795 6797 6.618287 TTGGATATATTTCGACAGGCTTTG 57.382 37.500 0.00 0.00 0.00 2.77
3800 6802 8.017946 GGATATATTTCGACAGGCTTTGAAATC 58.982 37.037 19.33 11.52 39.40 2.17
3801 6803 3.915437 TTTCGACAGGCTTTGAAATCC 57.085 42.857 7.56 0.00 0.00 3.01
3804 6806 1.804151 CGACAGGCTTTGAAATCCGAA 59.196 47.619 0.00 0.00 0.00 4.30
3821 6823 6.683974 ATCCGAATTCTAAAACATGGTGAG 57.316 37.500 3.52 0.00 0.00 3.51
3824 6826 5.643777 CCGAATTCTAAAACATGGTGAGACT 59.356 40.000 3.52 0.00 0.00 3.24
3829 6831 8.954950 ATTCTAAAACATGGTGAGACTCTATG 57.045 34.615 3.68 8.35 0.00 2.23
3831 6833 7.776107 TCTAAAACATGGTGAGACTCTATGAG 58.224 38.462 16.51 0.00 35.52 2.90
3835 6837 4.400884 ACATGGTGAGACTCTATGAGACAC 59.599 45.833 16.51 8.15 34.40 3.67
3836 6838 4.034285 TGGTGAGACTCTATGAGACACA 57.966 45.455 3.68 8.72 35.54 3.72
3837 6839 4.407365 TGGTGAGACTCTATGAGACACAA 58.593 43.478 3.68 9.72 35.54 3.33
3838 6840 4.460731 TGGTGAGACTCTATGAGACACAAG 59.539 45.833 3.68 0.00 35.54 3.16
3839 6841 4.702612 GGTGAGACTCTATGAGACACAAGA 59.297 45.833 3.68 0.00 35.54 3.02
3840 6842 5.184096 GGTGAGACTCTATGAGACACAAGAA 59.816 44.000 3.68 0.00 35.54 2.52
3841 6843 6.127479 GGTGAGACTCTATGAGACACAAGAAT 60.127 42.308 3.68 0.00 35.54 2.40
3842 6844 6.751425 GTGAGACTCTATGAGACACAAGAATG 59.249 42.308 3.68 0.00 34.81 2.67
3843 6845 5.659463 AGACTCTATGAGACACAAGAATGC 58.341 41.667 1.25 0.00 33.32 3.56
3844 6846 5.421693 AGACTCTATGAGACACAAGAATGCT 59.578 40.000 1.25 0.00 33.32 3.79
3845 6847 5.659463 ACTCTATGAGACACAAGAATGCTC 58.341 41.667 1.25 0.00 33.32 4.26
3846 6848 5.421693 ACTCTATGAGACACAAGAATGCTCT 59.578 40.000 1.25 0.00 33.32 4.09
3847 6849 6.070881 ACTCTATGAGACACAAGAATGCTCTT 60.071 38.462 1.25 0.00 36.56 2.85
3848 6850 6.705302 TCTATGAGACACAAGAATGCTCTTT 58.295 36.000 0.00 0.00 40.05 2.52
3849 6851 7.840931 TCTATGAGACACAAGAATGCTCTTTA 58.159 34.615 0.00 0.00 40.05 1.85
3850 6852 6.981762 ATGAGACACAAGAATGCTCTTTAG 57.018 37.500 0.00 0.00 40.05 1.85
3851 6853 6.101650 TGAGACACAAGAATGCTCTTTAGA 57.898 37.500 0.00 0.00 40.05 2.10
3852 6854 6.524734 TGAGACACAAGAATGCTCTTTAGAA 58.475 36.000 0.00 0.00 40.05 2.10
3853 6855 6.425114 TGAGACACAAGAATGCTCTTTAGAAC 59.575 38.462 0.00 0.00 40.05 3.01
3854 6856 6.291377 AGACACAAGAATGCTCTTTAGAACA 58.709 36.000 0.00 0.00 40.05 3.18
3855 6857 6.203723 AGACACAAGAATGCTCTTTAGAACAC 59.796 38.462 0.00 0.00 40.05 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
186 187 5.007626 TGTTCAGAACTCCAAAAGATGTTCG 59.992 40.000 14.51 0.00 42.29 3.95
213 214 7.087007 GGAAAATGGCTTGTGTTTTTGAAAAA 58.913 30.769 0.00 0.00 0.00 1.94
218 219 4.035441 CCTGGAAAATGGCTTGTGTTTTTG 59.965 41.667 0.00 0.00 0.00 2.44
219 220 4.080638 TCCTGGAAAATGGCTTGTGTTTTT 60.081 37.500 0.00 0.00 0.00 1.94
248 249 8.533657 TGGATATCTCATTTCTTTTGCATTTGT 58.466 29.630 2.05 0.00 0.00 2.83
249 250 8.936070 TGGATATCTCATTTCTTTTGCATTTG 57.064 30.769 2.05 0.00 0.00 2.32
253 264 9.426837 CTTTTTGGATATCTCATTTCTTTTGCA 57.573 29.630 2.05 0.00 0.00 4.08
288 308 8.445275 AGGTTTCTCTGTTTTGTTTTGTTTTT 57.555 26.923 0.00 0.00 0.00 1.94
318 338 6.538381 TCTTTGCCTTTTCTGTTTGGATTTTC 59.462 34.615 0.00 0.00 0.00 2.29
323 343 5.186797 TCTTTCTTTGCCTTTTCTGTTTGGA 59.813 36.000 0.00 0.00 0.00 3.53
324 344 5.418676 TCTTTCTTTGCCTTTTCTGTTTGG 58.581 37.500 0.00 0.00 0.00 3.28
325 347 6.183360 GGTTCTTTCTTTGCCTTTTCTGTTTG 60.183 38.462 0.00 0.00 0.00 2.93
373 407 2.815647 GAAGAGCGAGGCCGTTGG 60.816 66.667 0.00 0.00 38.24 3.77
381 421 2.732412 TCTTGTTCAGGAAGAGCGAG 57.268 50.000 0.00 0.00 39.60 5.03
382 422 2.289072 CCTTCTTGTTCAGGAAGAGCGA 60.289 50.000 20.80 0.00 40.74 4.93
463 516 2.681344 GTTGGATTCCCGCGAAAACTAT 59.319 45.455 8.23 0.00 34.29 2.12
562 620 1.663074 GATCTGATCGGACGGCTGC 60.663 63.158 6.33 0.00 0.00 5.25
571 629 0.851495 GCTTCGTGCTGATCTGATCG 59.149 55.000 12.65 8.70 38.95 3.69
669 754 2.546789 GAGAAAGCTTTTCCGTTTCCGA 59.453 45.455 14.05 0.00 35.63 4.55
672 760 2.286772 TGCGAGAAAGCTTTTCCGTTTC 60.287 45.455 24.72 14.71 38.13 2.78
851 1258 2.824489 GACGCTAAGCCAAGCCCC 60.824 66.667 2.52 0.00 39.43 5.80
963 1401 2.515991 CTCTCTCCCTCGCTCGCT 60.516 66.667 0.00 0.00 0.00 4.93
994 1897 1.287503 GGGATCTCTCCATCGTCGC 59.712 63.158 0.00 0.00 44.08 5.19
997 1905 2.556459 CGCGGGATCTCTCCATCGT 61.556 63.158 0.00 0.00 44.08 3.73
1334 2263 4.779733 GAGGGGAGGAGGCGGACA 62.780 72.222 0.00 0.00 0.00 4.02
1339 2268 4.890306 GGAGGGAGGGGAGGAGGC 62.890 77.778 0.00 0.00 0.00 4.70
1341 2270 3.039526 AGGGAGGGAGGGGAGGAG 61.040 72.222 0.00 0.00 0.00 3.69
1344 2273 4.179599 GGGAGGGAGGGAGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
1347 2276 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
1402 2379 2.185387 AGGCATGGGAAACTACGTACT 58.815 47.619 0.00 0.00 0.00 2.73
1403 2380 2.685850 AGGCATGGGAAACTACGTAC 57.314 50.000 0.00 0.00 0.00 3.67
1404 2381 2.835764 AGAAGGCATGGGAAACTACGTA 59.164 45.455 0.00 0.00 0.00 3.57
1420 2397 3.506810 CACTTCTAGCGAGTCAAGAAGG 58.493 50.000 21.69 12.39 46.82 3.46
1426 2403 0.811915 GGAGCACTTCTAGCGAGTCA 59.188 55.000 0.00 0.00 37.01 3.41
1435 2412 1.073199 CCCAAACCGGAGCACTTCT 59.927 57.895 9.46 0.00 36.56 2.85
1436 2413 1.228154 ACCCAAACCGGAGCACTTC 60.228 57.895 9.46 0.00 36.56 3.01
1437 2414 1.228154 GACCCAAACCGGAGCACTT 60.228 57.895 9.46 0.00 36.56 3.16
1456 2438 5.413499 GGTAGTACAGCGAGGAAATTAACA 58.587 41.667 2.06 0.00 0.00 2.41
1514 2954 4.148825 CCACGGGAGAAGGCGAGG 62.149 72.222 0.00 0.00 0.00 4.63
1589 3355 2.229062 ACCATAGATCGCTCCGTGTATG 59.771 50.000 0.00 0.00 0.00 2.39
1604 3370 7.721842 TGAGGAAATACTCAGAGTAGACCATAG 59.278 40.741 21.95 0.00 42.26 2.23
1607 3374 5.827756 TGAGGAAATACTCAGAGTAGACCA 58.172 41.667 21.95 10.96 42.26 4.02
1664 3433 3.046390 CAAGCACGGATCTAGAATCGAC 58.954 50.000 20.14 13.17 0.00 4.20
1671 3440 1.802880 CGGGAACAAGCACGGATCTAG 60.803 57.143 0.00 0.00 0.00 2.43
1678 3447 3.777925 CTCGCGGGAACAAGCACG 61.778 66.667 0.00 0.00 37.83 5.34
1704 3574 1.205820 CGGCATATGCACGCAGATG 59.794 57.895 28.07 19.62 45.34 2.90
1709 3579 2.544359 CGTACGGCATATGCACGC 59.456 61.111 28.07 15.25 44.36 5.34
1710 3580 2.544359 GCGTACGGCATATGCACG 59.456 61.111 28.07 26.94 44.18 5.34
1772 3664 6.377327 AATTAACAGGCAAATATGGTCGAG 57.623 37.500 0.00 0.00 0.00 4.04
1778 3670 8.034215 TGAACAGGAAATTAACAGGCAAATATG 58.966 33.333 0.00 0.00 0.00 1.78
1792 3688 3.674138 GCATGCACGATGAACAGGAAATT 60.674 43.478 14.21 0.00 33.31 1.82
1793 3689 2.159338 GCATGCACGATGAACAGGAAAT 60.159 45.455 14.21 0.00 33.31 2.17
1794 3690 1.199789 GCATGCACGATGAACAGGAAA 59.800 47.619 14.21 0.00 33.31 3.13
1798 3694 0.800631 ACTGCATGCACGATGAACAG 59.199 50.000 18.46 6.25 33.31 3.16
1804 3700 3.551046 GCTACTACTACTGCATGCACGAT 60.551 47.826 18.46 7.97 0.00 3.73
1806 3702 2.120232 GCTACTACTACTGCATGCACG 58.880 52.381 18.46 15.38 0.00 5.34
1807 3703 2.159099 TGGCTACTACTACTGCATGCAC 60.159 50.000 18.46 2.35 0.00 4.57
1809 3705 2.890808 TGGCTACTACTACTGCATGC 57.109 50.000 11.82 11.82 0.00 4.06
1810 3706 4.302455 GACATGGCTACTACTACTGCATG 58.698 47.826 0.00 0.00 0.00 4.06
1811 3707 3.322254 GGACATGGCTACTACTACTGCAT 59.678 47.826 0.00 0.00 0.00 3.96
1889 3965 6.348868 GGAGAACAAAACAAGGCAGAAGATAG 60.349 42.308 0.00 0.00 0.00 2.08
1918 3995 1.981533 GACCAAGCAAGACGTACGTAC 59.018 52.381 22.87 15.90 0.00 3.67
1919 3996 1.608109 TGACCAAGCAAGACGTACGTA 59.392 47.619 22.87 0.00 0.00 3.57
1920 3997 0.386476 TGACCAAGCAAGACGTACGT 59.614 50.000 23.04 23.04 0.00 3.57
1921 3998 1.493772 TTGACCAAGCAAGACGTACG 58.506 50.000 15.01 15.01 0.00 3.67
1950 4027 2.645730 TCAAACAAACAGCAAAGCGT 57.354 40.000 0.00 0.00 0.00 5.07
1951 4028 2.151736 CGATCAAACAAACAGCAAAGCG 59.848 45.455 0.00 0.00 0.00 4.68
1952 4029 2.472488 CCGATCAAACAAACAGCAAAGC 59.528 45.455 0.00 0.00 0.00 3.51
1953 4030 2.472488 GCCGATCAAACAAACAGCAAAG 59.528 45.455 0.00 0.00 0.00 2.77
1954 4031 2.159184 TGCCGATCAAACAAACAGCAAA 60.159 40.909 0.00 0.00 0.00 3.68
2019 4124 3.494251 ACATGGAAATGTTTCGCAAAAGC 59.506 39.130 0.00 0.00 38.06 3.51
2027 4133 6.327934 CAGAGGATCAACATGGAAATGTTTC 58.672 40.000 0.00 0.00 42.32 2.78
2056 4163 0.233848 CCGCACGCGAAAAAGTAGTT 59.766 50.000 15.93 0.00 42.83 2.24
2083 4195 0.608640 TTTCACGAGAGAGGAAGGCC 59.391 55.000 0.00 0.00 31.87 5.19
2104 4216 1.539827 CATTTGGTTTGACCCGACCTC 59.460 52.381 0.00 0.00 37.50 3.85
2118 4231 1.027357 CCAAGAGGCGATCCATTTGG 58.973 55.000 0.00 0.00 39.82 3.28
2164 4288 3.020026 CTGCCAAAGCTGCGAGACG 62.020 63.158 0.00 0.00 40.80 4.18
2303 4438 7.532682 TTCATCAAAAGTAAACAAAACTGGC 57.467 32.000 0.00 0.00 0.00 4.85
2368 4506 7.489113 GCATCCAAAATCCACAGTAATTAACAG 59.511 37.037 0.00 0.00 0.00 3.16
2484 4635 0.634465 GAGGGAGAGGGAGAGGTTCT 59.366 60.000 0.00 0.00 0.00 3.01
2498 4649 1.518367 GAGAGGGAGAGAGAGAGGGA 58.482 60.000 0.00 0.00 0.00 4.20
2499 4650 0.108585 CGAGAGGGAGAGAGAGAGGG 59.891 65.000 0.00 0.00 0.00 4.30
2500 4651 0.535102 GCGAGAGGGAGAGAGAGAGG 60.535 65.000 0.00 0.00 0.00 3.69
2501 4652 0.535102 GGCGAGAGGGAGAGAGAGAG 60.535 65.000 0.00 0.00 0.00 3.20
2502 4653 0.986019 AGGCGAGAGGGAGAGAGAGA 60.986 60.000 0.00 0.00 0.00 3.10
2503 4654 0.819259 CAGGCGAGAGGGAGAGAGAG 60.819 65.000 0.00 0.00 0.00 3.20
2504 4655 1.225983 CAGGCGAGAGGGAGAGAGA 59.774 63.158 0.00 0.00 0.00 3.10
2505 4656 2.489275 GCAGGCGAGAGGGAGAGAG 61.489 68.421 0.00 0.00 0.00 3.20
2532 4683 8.945195 ATCAACATATGGACATGGATAAACAT 57.055 30.769 7.80 0.00 0.00 2.71
2570 4723 2.690786 TCCGGTGCACATGTTAGTAAC 58.309 47.619 20.43 6.06 0.00 2.50
2585 4738 3.834799 GCGAGAACCCGATCCGGT 61.835 66.667 0.00 0.00 46.80 5.28
2587 4740 2.278857 CTGCGAGAACCCGATCCG 60.279 66.667 0.00 0.00 0.00 4.18
2870 5030 4.477975 GACCACGGTCTCTCGCGG 62.478 72.222 6.13 0.00 41.57 6.46
2871 5031 4.477975 GGACCACGGTCTCTCGCG 62.478 72.222 15.62 0.00 44.04 5.87
2872 5032 4.477975 CGGACCACGGTCTCTCGC 62.478 72.222 15.62 0.00 44.04 5.03
2882 5042 3.916392 CTGCGACTGGACGGACCAC 62.916 68.421 0.00 0.00 44.64 4.16
2938 5099 2.049433 AACCTCGAACGGCGACAG 60.049 61.111 16.62 3.64 45.59 3.51
2965 5126 1.006571 TTCTTCGACCGGACTGCAC 60.007 57.895 9.46 0.00 0.00 4.57
2975 5136 2.434359 CCCACCGGCTTCTTCGAC 60.434 66.667 0.00 0.00 0.00 4.20
2985 5146 2.301009 ACTAGTACTCAAAACCCACCGG 59.699 50.000 0.00 0.00 0.00 5.28
3018 5209 1.929836 GGACAGAAACGATAGCTGCTG 59.070 52.381 13.43 0.00 42.67 4.41
3019 5210 1.469940 CGGACAGAAACGATAGCTGCT 60.470 52.381 7.57 7.57 42.67 4.24
3020 5211 0.924090 CGGACAGAAACGATAGCTGC 59.076 55.000 0.00 0.00 42.67 5.25
3022 5213 0.818296 AGCGGACAGAAACGATAGCT 59.182 50.000 0.00 0.00 42.67 3.32
3024 5215 1.202154 ACGAGCGGACAGAAACGATAG 60.202 52.381 0.00 0.00 46.19 2.08
3027 5218 0.110056 GTACGAGCGGACAGAAACGA 60.110 55.000 0.00 0.00 0.00 3.85
3029 5220 0.386478 ACGTACGAGCGGACAGAAAC 60.386 55.000 24.41 0.00 35.98 2.78
3030 5221 0.386352 CACGTACGAGCGGACAGAAA 60.386 55.000 24.41 0.00 35.98 2.52
3031 5222 1.208358 CACGTACGAGCGGACAGAA 59.792 57.895 24.41 0.00 35.98 3.02
3032 5223 1.509644 AACACGTACGAGCGGACAGA 61.510 55.000 24.41 0.00 35.98 3.41
3033 5224 0.662374 AAACACGTACGAGCGGACAG 60.662 55.000 24.41 3.54 35.98 3.51
3035 5226 1.771044 CAAACACGTACGAGCGGAC 59.229 57.895 24.41 0.00 35.98 4.79
3037 5228 2.468532 GCAAACACGTACGAGCGG 59.531 61.111 24.41 10.59 35.98 5.52
3038 5229 2.091421 CGCAAACACGTACGAGCG 59.909 61.111 24.41 22.18 39.17 5.03
3039 5230 1.154908 CACGCAAACACGTACGAGC 60.155 57.895 24.41 15.34 46.34 5.03
3041 5232 1.208009 GACCACGCAAACACGTACGA 61.208 55.000 24.41 0.00 46.34 3.43
3042 5233 1.199859 GACCACGCAAACACGTACG 59.800 57.895 15.01 15.01 46.34 3.67
3072 5309 2.554893 GGACTCGCAAACACCCAATTAA 59.445 45.455 0.00 0.00 0.00 1.40
3073 5310 2.156098 GGACTCGCAAACACCCAATTA 58.844 47.619 0.00 0.00 0.00 1.40
3075 5312 0.110486 AGGACTCGCAAACACCCAAT 59.890 50.000 0.00 0.00 0.00 3.16
3102 5341 4.162888 TCACATAGCATCAGTGGTTCATCT 59.837 41.667 0.00 0.00 37.28 2.90
3137 5376 7.991084 TGATCCATTTCCATTCAGATCATAC 57.009 36.000 0.00 0.00 36.20 2.39
3152 5391 4.984161 CAGAACGCAAAACTTGATCCATTT 59.016 37.500 0.00 0.00 0.00 2.32
3189 5433 1.477553 CCCCACACAGATCCAAATGG 58.522 55.000 0.00 0.00 0.00 3.16
3196 5486 0.250901 ACTGTTGCCCCACACAGATC 60.251 55.000 6.32 0.00 33.92 2.75
3207 5497 0.249031 AAGCAAGCGAAACTGTTGCC 60.249 50.000 2.77 0.00 46.35 4.52
3218 5508 2.078914 CGCAGAGCAAAAGCAAGCG 61.079 57.895 0.00 0.00 37.68 4.68
3230 5520 1.284657 AGCATTCGTTCATCGCAGAG 58.715 50.000 0.00 0.00 43.63 3.35
3301 5600 5.292834 CGTCACATCATAAGCAGAAATCAGT 59.707 40.000 0.00 0.00 0.00 3.41
3330 5629 4.784329 TGAAGAGATGATATGCGTACGAC 58.216 43.478 21.65 11.11 0.00 4.34
3333 5632 8.338259 ACAAATTTGAAGAGATGATATGCGTAC 58.662 33.333 24.64 0.00 0.00 3.67
3336 5635 7.191551 ACACAAATTTGAAGAGATGATATGCG 58.808 34.615 24.64 0.00 0.00 4.73
3366 5677 3.671702 GCAGAATGGAAGCTACAAACAGC 60.672 47.826 0.00 0.00 38.11 4.40
3368 5679 3.754965 AGCAGAATGGAAGCTACAAACA 58.245 40.909 0.00 0.00 36.73 2.83
3380 5691 2.225019 GCATTCGTCCATAGCAGAATGG 59.775 50.000 15.77 6.44 45.83 3.16
3390 5701 2.890311 TGAAAAACAGGCATTCGTCCAT 59.110 40.909 0.00 0.00 0.00 3.41
3393 5704 2.307049 CGTGAAAAACAGGCATTCGTC 58.693 47.619 0.00 0.00 0.00 4.20
3395 5706 1.265635 TCCGTGAAAAACAGGCATTCG 59.734 47.619 0.00 0.00 33.64 3.34
3433 5962 2.082366 GCAACACAAAGCCGCATCG 61.082 57.895 0.00 0.00 0.00 3.84
3435 5964 2.339712 GGCAACACAAAGCCGCAT 59.660 55.556 0.00 0.00 41.70 4.73
3494 6023 0.852842 GATGGTGGGATTGGGGATCA 59.147 55.000 0.00 0.00 36.43 2.92
3495 6024 0.852842 TGATGGTGGGATTGGGGATC 59.147 55.000 0.00 0.00 0.00 3.36
3498 6041 1.076044 GGTGATGGTGGGATTGGGG 60.076 63.158 0.00 0.00 0.00 4.96
3500 6043 1.342275 ACATGGTGATGGTGGGATTGG 60.342 52.381 0.00 0.00 33.39 3.16
3508 6051 0.253044 CTCCGGAACATGGTGATGGT 59.747 55.000 5.23 0.00 33.39 3.55
3509 6052 0.541392 TCTCCGGAACATGGTGATGG 59.459 55.000 5.23 0.00 33.39 3.51
3511 6054 0.179000 GCTCTCCGGAACATGGTGAT 59.821 55.000 5.23 0.00 0.00 3.06
3516 6059 0.107508 ATGTGGCTCTCCGGAACATG 60.108 55.000 16.14 0.00 34.14 3.21
3523 6066 0.460987 GAGTTCCATGTGGCTCTCCG 60.461 60.000 10.19 0.00 32.62 4.63
3524 6067 0.615331 TGAGTTCCATGTGGCTCTCC 59.385 55.000 15.31 0.00 35.44 3.71
3525 6068 1.731720 GTGAGTTCCATGTGGCTCTC 58.268 55.000 12.81 12.81 36.20 3.20
3526 6069 0.036952 CGTGAGTTCCATGTGGCTCT 60.037 55.000 7.78 2.98 34.44 4.09
3527 6070 0.320771 ACGTGAGTTCCATGTGGCTC 60.321 55.000 0.00 0.00 46.40 4.70
3528 6071 1.754745 ACGTGAGTTCCATGTGGCT 59.245 52.632 0.00 0.00 46.40 4.75
3529 6072 4.379174 ACGTGAGTTCCATGTGGC 57.621 55.556 0.00 0.00 46.40 5.01
3544 6540 1.741993 CAAAAAGTGACCGCTTGACG 58.258 50.000 0.00 0.00 43.15 4.35
3552 6548 4.276926 AGAGTGATTCTGCAAAAAGTGACC 59.723 41.667 0.00 0.00 33.93 4.02
3554 6550 6.017109 GGTAAGAGTGATTCTGCAAAAAGTGA 60.017 38.462 0.00 0.00 35.91 3.41
3565 6561 7.272144 AGGGTAAAATGGTAAGAGTGATTCT 57.728 36.000 0.00 0.00 37.93 2.40
3566 6562 7.939784 AAGGGTAAAATGGTAAGAGTGATTC 57.060 36.000 0.00 0.00 0.00 2.52
3567 6563 8.585018 CAAAAGGGTAAAATGGTAAGAGTGATT 58.415 33.333 0.00 0.00 0.00 2.57
3569 6565 7.064229 ACAAAAGGGTAAAATGGTAAGAGTGA 58.936 34.615 0.00 0.00 0.00 3.41
3612 6608 2.364970 CTGTTGCATCAACTTTTGGGGA 59.635 45.455 10.52 0.00 43.85 4.81
3613 6609 2.102925 ACTGTTGCATCAACTTTTGGGG 59.897 45.455 10.52 0.00 43.85 4.96
3636 6632 4.935495 ATGGGTGGGCGCGCATAG 62.935 66.667 34.42 0.00 39.71 2.23
3642 6638 3.238755 AAAAAGCATGGGTGGGCGC 62.239 57.895 0.00 0.00 34.54 6.53
3679 6679 7.334844 AGGGTTCAAAAGATAAAATCGATCC 57.665 36.000 0.00 0.00 0.00 3.36
3680 6680 9.937175 CTTAGGGTTCAAAAGATAAAATCGATC 57.063 33.333 0.00 0.00 0.00 3.69
3684 6684 8.182227 CGGACTTAGGGTTCAAAAGATAAAATC 58.818 37.037 0.00 0.00 0.00 2.17
3687 6687 5.941647 CCGGACTTAGGGTTCAAAAGATAAA 59.058 40.000 0.00 0.00 0.00 1.40
3700 6700 4.189231 CAGATTGTAAACCGGACTTAGGG 58.811 47.826 9.46 0.00 0.00 3.53
3701 6701 4.828829 ACAGATTGTAAACCGGACTTAGG 58.171 43.478 9.46 0.00 0.00 2.69
3702 6702 6.599437 CAAACAGATTGTAAACCGGACTTAG 58.401 40.000 9.46 0.00 34.16 2.18
3703 6703 5.049267 GCAAACAGATTGTAAACCGGACTTA 60.049 40.000 9.46 2.02 41.32 2.24
3709 6709 4.545610 ACATGCAAACAGATTGTAAACCG 58.454 39.130 0.00 0.00 41.32 4.44
3711 6711 8.977505 ACATAAACATGCAAACAGATTGTAAAC 58.022 29.630 0.00 0.00 41.32 2.01
3748 6748 9.099454 CAATAGTAGTCTTGTTTAATGGTCCTC 57.901 37.037 0.00 0.00 0.00 3.71
3767 6769 8.362464 AGCCTGTCGAAATATATCCAATAGTA 57.638 34.615 0.00 0.00 0.00 1.82
3768 6770 7.246171 AGCCTGTCGAAATATATCCAATAGT 57.754 36.000 0.00 0.00 0.00 2.12
3769 6771 8.446273 CAAAGCCTGTCGAAATATATCCAATAG 58.554 37.037 0.00 0.00 0.00 1.73
3771 6773 6.998074 TCAAAGCCTGTCGAAATATATCCAAT 59.002 34.615 0.00 0.00 0.00 3.16
3775 6777 8.017946 GGATTTCAAAGCCTGTCGAAATATATC 58.982 37.037 0.00 0.00 38.00 1.63
3789 6791 6.866248 TGTTTTAGAATTCGGATTTCAAAGCC 59.134 34.615 13.35 0.00 0.00 4.35
3791 6793 8.863049 CCATGTTTTAGAATTCGGATTTCAAAG 58.137 33.333 13.35 3.42 0.00 2.77
3795 6797 7.535139 TCACCATGTTTTAGAATTCGGATTTC 58.465 34.615 0.00 4.82 0.00 2.17
3800 6802 5.643777 AGTCTCACCATGTTTTAGAATTCGG 59.356 40.000 0.00 0.00 0.00 4.30
3801 6803 6.591834 AGAGTCTCACCATGTTTTAGAATTCG 59.408 38.462 1.94 0.00 0.00 3.34
3804 6806 8.762645 TCATAGAGTCTCACCATGTTTTAGAAT 58.237 33.333 0.00 0.00 0.00 2.40
3821 6823 5.659463 AGCATTCTTGTGTCTCATAGAGTC 58.341 41.667 0.00 0.00 0.00 3.36
3824 6826 5.929058 AGAGCATTCTTGTGTCTCATAGA 57.071 39.130 0.00 0.00 0.00 1.98
3829 6831 6.425114 TGTTCTAAAGAGCATTCTTGTGTCTC 59.575 38.462 0.00 0.00 42.80 3.36
3831 6833 6.366630 GTGTTCTAAAGAGCATTCTTGTGTC 58.633 40.000 0.00 0.00 42.80 3.67


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

AutoCloner maintained by Alex Coulton.