Multiple sequence alignment - TraesCS5B01G481700

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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 TraesCS5B01G481700 chr5B 100.000 5353 0 0 1 5353 654498623 654493271 0.000000e+00 9886
1 TraesCS5B01G481700 chr5B 95.041 121 6 0 4929 5049 128853013 128853133 1.970000e-44 191
2 TraesCS5B01G481700 chr5D 92.450 4980 219 62 1 4910 519654510 519649618 0.000000e+00 6968
3 TraesCS5B01G481700 chr5D 89.456 294 20 5 5067 5353 519649613 519649324 1.420000e-95 361
4 TraesCS5B01G481700 chr5A 90.949 3867 224 59 25 3839 646213912 646210120 0.000000e+00 5086
5 TraesCS5B01G481700 chr5A 90.399 1104 67 19 3855 4943 646210029 646208950 0.000000e+00 1415
6 TraesCS5B01G481700 chr5A 83.462 260 20 11 5112 5353 646208912 646208658 2.510000e-53 220
7 TraesCS5B01G481700 chr7B 84.309 803 90 13 2753 3523 576427712 576428510 0.000000e+00 752
8 TraesCS5B01G481700 chr2B 84.094 723 70 21 2913 3607 599844801 599844096 0.000000e+00 656
9 TraesCS5B01G481700 chr4A 85.495 455 62 3 2746 3198 654184063 654184515 6.280000e-129 472
10 TraesCS5B01G481700 chr4A 85.033 461 65 3 2751 3209 654154638 654155096 2.920000e-127 466
11 TraesCS5B01G481700 chr1B 81.362 558 69 17 2800 3328 684585998 684585447 6.410000e-114 422
12 TraesCS5B01G481700 chrUn 81.149 557 72 16 2800 3328 34342080 34342631 2.980000e-112 416
13 TraesCS5B01G481700 chr3B 81.149 557 72 16 2800 3328 5471286 5471837 2.980000e-112 416
14 TraesCS5B01G481700 chr3B 80.790 557 74 16 2800 3328 5487286 5486735 6.460000e-109 405
15 TraesCS5B01G481700 chr3B 96.721 122 4 0 4932 5053 564169817 564169696 2.530000e-48 204
16 TraesCS5B01G481700 chr3B 92.701 137 9 1 4917 5052 650615881 650616017 4.230000e-46 196
17 TraesCS5B01G481700 chr3B 94.400 125 7 0 4925 5049 504962897 504963021 5.470000e-45 193
18 TraesCS5B01G481700 chr3B 95.000 120 6 0 4930 5049 475817007 475816888 7.080000e-44 189
19 TraesCS5B01G481700 chr3D 95.726 117 5 0 4932 5048 5478059 5478175 7.080000e-44 189
20 TraesCS5B01G481700 chr2D 94.355 124 6 1 4925 5048 7396463 7396585 7.080000e-44 189
21 TraesCS5B01G481700 chr6D 92.913 127 9 0 4926 5052 136474592 136474718 9.160000e-43 185
22 TraesCS5B01G481700 chr6B 92.800 125 8 1 4930 5053 563489349 563489225 4.260000e-41 180


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 TraesCS5B01G481700 chr5B 654493271 654498623 5352 True 9886.000000 9886 100.000 1 5353 1 chr5B.!!$R1 5352
1 TraesCS5B01G481700 chr5D 519649324 519654510 5186 True 3664.500000 6968 90.953 1 5353 2 chr5D.!!$R1 5352
2 TraesCS5B01G481700 chr5A 646208658 646213912 5254 True 2240.333333 5086 88.270 25 5353 3 chr5A.!!$R1 5328
3 TraesCS5B01G481700 chr7B 576427712 576428510 798 False 752.000000 752 84.309 2753 3523 1 chr7B.!!$F1 770
4 TraesCS5B01G481700 chr2B 599844096 599844801 705 True 656.000000 656 84.094 2913 3607 1 chr2B.!!$R1 694
5 TraesCS5B01G481700 chr1B 684585447 684585998 551 True 422.000000 422 81.362 2800 3328 1 chr1B.!!$R1 528
6 TraesCS5B01G481700 chrUn 34342080 34342631 551 False 416.000000 416 81.149 2800 3328 1 chrUn.!!$F1 528
7 TraesCS5B01G481700 chr3B 5471286 5471837 551 False 416.000000 416 81.149 2800 3328 1 chr3B.!!$F1 528
8 TraesCS5B01G481700 chr3B 5486735 5487286 551 True 405.000000 405 80.790 2800 3328 1 chr3B.!!$R1 528

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
392 411 0.545309 CCTTGTGAGTGAGGGAGGGA 60.545 60.000 0.00 0.0 0.00 4.20 F
810 830 0.557729 ATCGGCCATTGATTTCCCCT 59.442 50.000 2.24 0.0 0.00 4.79 F
1313 1354 1.375523 CCCACGGCAAGGTCTACAC 60.376 63.158 0.00 0.0 0.00 2.90 F
2722 2794 1.002033 CTGTGTCAAAGGCAAGAGCAC 60.002 52.381 0.00 0.0 44.61 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1369 1410 0.390124 ACCTTCGGCTGAAACACGTA 59.610 50.0 9.73 0.0 32.66 3.57 R
2340 2408 0.545309 TCCCTGGTAGCAGCTCACTT 60.545 55.0 16.62 0.0 0.00 3.16 R
3069 3148 0.318699 TCACAGTTTCCTCTCGTGCG 60.319 55.0 0.00 0.0 0.00 5.34 R
4367 4584 0.609131 AAAACGTCTCAGGGGCATGG 60.609 55.0 0.00 0.0 0.00 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
139 140 5.007039 TCACCGTTACTCGACAGATACATAC 59.993 44.000 0.00 0.00 42.86 2.39
152 153 5.767665 ACAGATACATACCACACAAGCAAAA 59.232 36.000 0.00 0.00 0.00 2.44
153 154 6.086222 CAGATACATACCACACAAGCAAAAC 58.914 40.000 0.00 0.00 0.00 2.43
154 155 5.767665 AGATACATACCACACAAGCAAAACA 59.232 36.000 0.00 0.00 0.00 2.83
155 156 4.935352 ACATACCACACAAGCAAAACAT 57.065 36.364 0.00 0.00 0.00 2.71
156 157 4.619973 ACATACCACACAAGCAAAACATG 58.380 39.130 0.00 0.00 0.00 3.21
172 173 0.935831 CATGCAAACACACACTGCCG 60.936 55.000 0.00 0.00 35.13 5.69
201 202 4.442403 CGACGAACATATCACATTCCTCAG 59.558 45.833 0.00 0.00 0.00 3.35
205 206 5.592054 GAACATATCACATTCCTCAGACGA 58.408 41.667 0.00 0.00 0.00 4.20
214 215 4.021104 ACATTCCTCAGACGACAAATCTCA 60.021 41.667 0.00 0.00 0.00 3.27
225 226 5.043903 ACGACAAATCTCATCCAATCTACG 58.956 41.667 0.00 0.00 0.00 3.51
230 231 3.443099 TCTCATCCAATCTACGCACAG 57.557 47.619 0.00 0.00 0.00 3.66
247 248 1.949525 ACAGAATGCATCGCCATTACC 59.050 47.619 0.00 0.00 42.53 2.85
249 250 1.133823 AGAATGCATCGCCATTACCCA 60.134 47.619 0.00 0.00 35.67 4.51
270 271 5.009510 CCCAACAGATACATCACACAACAAA 59.990 40.000 0.00 0.00 0.00 2.83
271 272 6.144854 CCAACAGATACATCACACAACAAAG 58.855 40.000 0.00 0.00 0.00 2.77
272 273 5.362556 ACAGATACATCACACAACAAAGC 57.637 39.130 0.00 0.00 0.00 3.51
273 274 5.065914 ACAGATACATCACACAACAAAGCT 58.934 37.500 0.00 0.00 0.00 3.74
274 275 6.230472 ACAGATACATCACACAACAAAGCTA 58.770 36.000 0.00 0.00 0.00 3.32
275 276 6.147821 ACAGATACATCACACAACAAAGCTAC 59.852 38.462 0.00 0.00 0.00 3.58
276 277 6.369890 CAGATACATCACACAACAAAGCTACT 59.630 38.462 0.00 0.00 0.00 2.57
278 279 5.924475 ACATCACACAACAAAGCTACTAC 57.076 39.130 0.00 0.00 0.00 2.73
279 280 5.611374 ACATCACACAACAAAGCTACTACT 58.389 37.500 0.00 0.00 0.00 2.57
361 380 2.750657 GGCTGGAGGAGGACCATGG 61.751 68.421 11.19 11.19 38.94 3.66
362 381 1.997874 GCTGGAGGAGGACCATGGT 60.998 63.158 19.89 19.89 38.94 3.55
363 382 1.910722 CTGGAGGAGGACCATGGTG 59.089 63.158 25.52 0.00 38.94 4.17
364 383 1.616327 TGGAGGAGGACCATGGTGG 60.616 63.158 25.52 0.00 45.02 4.61
365 384 1.306997 GGAGGAGGACCATGGTGGA 60.307 63.158 25.52 0.00 40.96 4.02
382 401 1.484444 GGAGTGGAGGCCTTGTGAGT 61.484 60.000 6.77 0.00 0.00 3.41
389 408 1.197430 AGGCCTTGTGAGTGAGGGAG 61.197 60.000 0.00 0.00 33.52 4.30
390 409 1.298014 GCCTTGTGAGTGAGGGAGG 59.702 63.158 0.00 0.00 33.52 4.30
391 410 1.986413 CCTTGTGAGTGAGGGAGGG 59.014 63.158 0.00 0.00 0.00 4.30
392 411 0.545309 CCTTGTGAGTGAGGGAGGGA 60.545 60.000 0.00 0.00 0.00 4.20
482 502 2.895424 CGCCCACCAACTTCCTCCT 61.895 63.158 0.00 0.00 0.00 3.69
485 505 1.685820 CCACCAACTTCCTCCTCCC 59.314 63.158 0.00 0.00 0.00 4.30
486 506 1.685820 CACCAACTTCCTCCTCCCC 59.314 63.158 0.00 0.00 0.00 4.81
487 507 1.133809 CACCAACTTCCTCCTCCCCA 61.134 60.000 0.00 0.00 0.00 4.96
566 586 1.694525 CCTTCCCCTCCCCTTCCTC 60.695 68.421 0.00 0.00 0.00 3.71
573 593 1.398234 CTCCCCTTCCTCCCTTCCT 59.602 63.158 0.00 0.00 0.00 3.36
687 707 4.787280 CCTCCTCTCCGCACCCCT 62.787 72.222 0.00 0.00 0.00 4.79
692 712 4.075793 TCTCCGCACCCCTAGCCT 62.076 66.667 0.00 0.00 0.00 4.58
693 713 3.854669 CTCCGCACCCCTAGCCTG 61.855 72.222 0.00 0.00 0.00 4.85
808 828 1.001378 CGAATCGGCCATTGATTTCCC 60.001 52.381 2.24 0.00 36.24 3.97
810 830 0.557729 ATCGGCCATTGATTTCCCCT 59.442 50.000 2.24 0.00 0.00 4.79
893 913 3.439494 CTCTGGAGCAGTCTCTTGC 57.561 57.895 0.00 0.00 44.41 4.01
953 973 1.801512 GGTTTTTCCATGAGCGCGC 60.802 57.895 26.66 26.66 35.97 6.86
1313 1354 1.375523 CCCACGGCAAGGTCTACAC 60.376 63.158 0.00 0.00 0.00 2.90
1343 1384 6.415573 AGTAAGTGGATGAACCTTTATGACC 58.584 40.000 0.00 0.00 39.86 4.02
1369 1410 3.055385 ACCCGTGCATAGTGTTTCATACT 60.055 43.478 0.00 0.00 0.00 2.12
1370 1411 4.160814 ACCCGTGCATAGTGTTTCATACTA 59.839 41.667 0.00 0.00 35.32 1.82
1371 1412 4.506654 CCCGTGCATAGTGTTTCATACTAC 59.493 45.833 0.00 0.00 33.80 2.73
1372 1413 4.206404 CCGTGCATAGTGTTTCATACTACG 59.794 45.833 0.00 0.00 33.80 3.51
1452 1497 9.819267 ATTTATGTTCCTCAGCTTTAGTACTAC 57.181 33.333 0.91 0.00 0.00 2.73
1453 1498 8.591114 TTATGTTCCTCAGCTTTAGTACTACT 57.409 34.615 0.91 0.00 0.00 2.57
1454 1499 9.690913 TTATGTTCCTCAGCTTTAGTACTACTA 57.309 33.333 0.91 0.00 0.00 1.82
1645 1695 1.563924 TGAGAGCCGCTTTAGGGTTA 58.436 50.000 0.00 0.00 42.85 2.85
1666 1717 6.367969 GGTTATCATTTAATCGACGGCAGTAT 59.632 38.462 0.00 0.00 0.00 2.12
1667 1718 7.543172 GGTTATCATTTAATCGACGGCAGTATA 59.457 37.037 0.00 0.00 0.00 1.47
1671 1722 2.521105 AATCGACGGCAGTATAACCC 57.479 50.000 0.00 0.00 0.00 4.11
1679 1730 2.583143 GGCAGTATAACCCCCAATGAC 58.417 52.381 0.00 0.00 0.00 3.06
1729 1793 1.950828 CCAGTCTGCTATTCCTGCTG 58.049 55.000 0.00 0.00 0.00 4.41
1747 1811 3.245016 TGCTGTGGTCAAGGATTCTGAAT 60.245 43.478 1.81 1.81 0.00 2.57
1753 1817 5.922544 GTGGTCAAGGATTCTGAATTTTGTG 59.077 40.000 19.22 10.79 0.00 3.33
1755 1819 6.775142 TGGTCAAGGATTCTGAATTTTGTGTA 59.225 34.615 19.22 10.10 0.00 2.90
1783 1847 4.151689 TGCGTCTTGTTCTAATACTTGCAC 59.848 41.667 0.00 0.00 0.00 4.57
1791 1855 5.700832 TGTTCTAATACTTGCACAGAGTTGG 59.299 40.000 0.00 0.00 0.00 3.77
1807 1871 6.813152 ACAGAGTTGGTTCTCAAATTTGTTTG 59.187 34.615 17.47 9.52 43.15 2.93
1997 2064 5.016831 TGTGGATACTCTTACTCTTGCTGA 58.983 41.667 0.00 0.00 37.61 4.26
2024 2091 9.546909 CTTGCATCAGTAATTAACTAGTTTGTG 57.453 33.333 14.49 7.07 35.76 3.33
2135 2202 4.035278 AGATCGTTTCATCCGAGAAGTC 57.965 45.455 0.00 0.00 37.81 3.01
2194 2261 2.846206 AGGTACATCCTTGCCTGAATGA 59.154 45.455 0.00 0.00 45.67 2.57
2218 2286 6.536731 CACATTACTGTGCCTAATCTGATC 57.463 41.667 0.00 0.00 45.79 2.92
2524 2592 2.682856 TGTGCTTGGACTGTTTGACTTC 59.317 45.455 0.00 0.00 0.00 3.01
2541 2609 2.027377 ACTTCTCCTGTTGCATCTCCAG 60.027 50.000 0.00 0.00 0.00 3.86
2546 2614 3.565307 TCCTGTTGCATCTCCAGTTTTT 58.435 40.909 0.00 0.00 0.00 1.94
2587 2658 5.590530 AGTTGCATTTCTGTTGGTGTAAA 57.409 34.783 0.00 0.00 0.00 2.01
2590 2661 5.330455 TGCATTTCTGTTGGTGTAAACAA 57.670 34.783 0.00 0.00 39.47 2.83
2591 2662 5.911752 TGCATTTCTGTTGGTGTAAACAAT 58.088 33.333 0.00 0.00 39.47 2.71
2592 2663 7.043961 TGCATTTCTGTTGGTGTAAACAATA 57.956 32.000 0.00 0.00 39.47 1.90
2593 2664 6.920758 TGCATTTCTGTTGGTGTAAACAATAC 59.079 34.615 0.00 0.00 39.47 1.89
2594 2665 6.364976 GCATTTCTGTTGGTGTAAACAATACC 59.635 38.462 0.00 0.00 39.47 2.73
2595 2666 5.676532 TTCTGTTGGTGTAAACAATACCG 57.323 39.130 0.00 0.00 42.17 4.02
2722 2794 1.002033 CTGTGTCAAAGGCAAGAGCAC 60.002 52.381 0.00 0.00 44.61 4.40
2766 2838 6.994221 TCTTGGCCGGTTAATCATTTAAAAA 58.006 32.000 1.90 0.00 0.00 1.94
2808 2880 8.267183 TCTGCATCTAATTCTTGAATGTTCCTA 58.733 33.333 0.00 0.00 0.00 2.94
2850 2928 5.048364 TCCACTTTATTCCCGTTCATGTTTG 60.048 40.000 0.00 0.00 0.00 2.93
2879 2957 1.726853 ATGTTTCTTTCGCCCTCTCG 58.273 50.000 0.00 0.00 0.00 4.04
2908 2986 8.522542 TTACCCTTCTGTTTTACTTGCTTTAA 57.477 30.769 0.00 0.00 0.00 1.52
2962 3040 4.096984 CCTTTCTGTCAAAGCTGTTCTGTT 59.903 41.667 0.00 0.00 0.00 3.16
3069 3148 5.391416 GCTGAAGCTTACTGATTTTGGACTC 60.391 44.000 0.00 0.00 38.21 3.36
3204 3292 9.578576 AATAAATTATGAGCTGAAGCCAGAATA 57.421 29.630 11.44 2.34 43.02 1.75
3269 3381 3.181483 CCACTTGATAATTTCCTGGCTGC 60.181 47.826 0.00 0.00 0.00 5.25
3296 3409 7.124448 AGTTTCTAGAGTTACTGATTTCGGGAT 59.876 37.037 0.00 0.00 0.00 3.85
3298 3411 4.308899 AGAGTTACTGATTTCGGGATCG 57.691 45.455 0.00 0.00 37.82 3.69
3376 3494 4.814234 TGACTCGTTGTCTTATGCTTTTGT 59.186 37.500 11.24 0.00 45.54 2.83
3546 3668 7.915293 TGCTGCTGCTTTTAAAGTAAGTATA 57.085 32.000 17.00 0.00 40.48 1.47
3547 3669 8.506168 TGCTGCTGCTTTTAAAGTAAGTATAT 57.494 30.769 17.00 0.00 40.48 0.86
3548 3670 8.397906 TGCTGCTGCTTTTAAAGTAAGTATATG 58.602 33.333 17.00 0.00 40.48 1.78
3549 3671 8.612619 GCTGCTGCTTTTAAAGTAAGTATATGA 58.387 33.333 8.53 0.00 36.03 2.15
3628 3750 7.217200 AGCAATTATAAAATCCTGCGACTCTA 58.783 34.615 0.00 0.00 35.09 2.43
3655 3777 4.704965 AGTTACAACTCTCCTGTTTCACC 58.295 43.478 0.00 0.00 32.86 4.02
3671 3793 1.879380 TCACCTTGCAAATCTTGTCCG 59.121 47.619 0.00 0.00 0.00 4.79
3687 3809 2.114670 CCGTACTGGCAGGCCATTG 61.115 63.158 20.34 5.71 46.15 2.82
3761 3892 7.600752 ACTGTCTATGTTTTGAAGTCTTAGCTC 59.399 37.037 0.00 0.00 0.00 4.09
3842 3973 0.733909 GCATTTGTGCGAAGAAGGCC 60.734 55.000 0.00 0.00 0.00 5.19
3851 3982 1.810151 GCGAAGAAGGCCACACATTAA 59.190 47.619 5.01 0.00 0.00 1.40
3910 4117 7.895759 AGAAACATATGTTAGCACCAACAAAT 58.104 30.769 21.07 1.00 41.50 2.32
3913 4120 6.855836 ACATATGTTAGCACCAACAAATGAG 58.144 36.000 1.41 0.00 41.50 2.90
3925 4132 4.095483 CCAACAAATGAGCTGGTCATAGTC 59.905 45.833 21.32 0.00 45.89 2.59
3965 4179 7.915397 TGTTTGAGCATAAACTTCTTTTCTGAC 59.085 33.333 14.34 0.00 40.36 3.51
3982 4199 5.155509 TCTGACGACTGTTTTTGACATTG 57.844 39.130 0.00 0.00 37.69 2.82
4030 4247 9.457436 TCTTACCCATATTTTCTCTTGTTTACC 57.543 33.333 0.00 0.00 0.00 2.85
4055 4272 0.537371 AGCAAGTACGCCCAGCTTTT 60.537 50.000 0.00 0.00 29.98 2.27
4181 4398 2.716244 CTCACGACGATCCCTCCG 59.284 66.667 0.00 0.00 0.00 4.63
4209 4426 4.180946 CGGAGGCAGACGAGGACG 62.181 72.222 0.00 0.00 45.75 4.79
4280 4497 0.613853 TCTCCTCCATCGTTTCCCGT 60.614 55.000 0.00 0.00 37.94 5.28
4316 4533 1.810030 GGTCGTCCGCCATCTGTTC 60.810 63.158 0.00 0.00 0.00 3.18
4331 4548 1.448013 GTTCGCCTCGAAGAAGGGG 60.448 63.158 1.59 0.83 46.54 4.79
4440 4657 1.212375 TGATGATACAGTGGTGGGGG 58.788 55.000 0.00 0.00 0.00 5.40
4441 4658 1.274126 TGATGATACAGTGGTGGGGGA 60.274 52.381 0.00 0.00 0.00 4.81
4442 4659 1.141053 GATGATACAGTGGTGGGGGAC 59.859 57.143 0.00 0.00 0.00 4.46
4443 4660 1.261938 TGATACAGTGGTGGGGGACG 61.262 60.000 0.00 0.00 0.00 4.79
4444 4661 1.968050 GATACAGTGGTGGGGGACGG 61.968 65.000 0.00 0.00 0.00 4.79
4445 4662 2.758852 ATACAGTGGTGGGGGACGGT 62.759 60.000 0.00 0.00 0.00 4.83
4446 4663 4.329545 CAGTGGTGGGGGACGGTG 62.330 72.222 0.00 0.00 0.00 4.94
4461 4678 4.302455 GGACGGTGATGATGATACAAGAG 58.698 47.826 0.00 0.00 0.00 2.85
4487 4704 4.481072 GGATCTTGTCTAGCCTAGGGTTA 58.519 47.826 20.59 5.12 0.00 2.85
4488 4705 4.525100 GGATCTTGTCTAGCCTAGGGTTAG 59.475 50.000 20.59 13.89 37.76 2.34
4489 4706 3.297736 TCTTGTCTAGCCTAGGGTTAGC 58.702 50.000 20.59 9.82 36.62 3.09
4490 4707 3.052793 TCTTGTCTAGCCTAGGGTTAGCT 60.053 47.826 20.59 7.26 36.62 3.32
4521 4738 6.796426 TGTTTTGTGTTTTGATGATACGGAA 58.204 32.000 0.00 0.00 0.00 4.30
4642 4859 2.031120 CCCCTCTTGTTTTCACTGCAA 58.969 47.619 0.00 0.00 0.00 4.08
4644 4861 3.070015 CCCCTCTTGTTTTCACTGCAATT 59.930 43.478 0.00 0.00 0.00 2.32
4672 4889 2.622452 CCTTTGCCAATCCTGTGATCCT 60.622 50.000 0.00 0.00 0.00 3.24
4673 4890 2.133281 TTGCCAATCCTGTGATCCTG 57.867 50.000 0.00 0.00 0.00 3.86
4685 4902 4.182339 CTGTGATCCTGACAGACTTGATG 58.818 47.826 3.32 0.00 43.04 3.07
4715 4935 7.670009 GATCAATGGATCTTAGAGATGGTTG 57.330 40.000 2.52 0.00 45.32 3.77
4849 5072 4.511826 CCCTGAACAGAAAGTTACTCACAC 59.488 45.833 3.19 0.00 41.51 3.82
4851 5074 6.462487 CCCTGAACAGAAAGTTACTCACACTA 60.462 42.308 3.19 0.00 41.51 2.74
4927 5152 3.695830 TGTCAATCCCAGTGGACTAAC 57.304 47.619 11.95 2.81 45.58 2.34
4943 5168 4.441217 GGACTAACAAATACTCCCTCCGTC 60.441 50.000 0.00 0.00 0.00 4.79
4945 5170 0.822164 ACAAATACTCCCTCCGTCCG 59.178 55.000 0.00 0.00 0.00 4.79
4946 5171 0.104304 CAAATACTCCCTCCGTCCGG 59.896 60.000 0.00 0.00 0.00 5.14
4947 5172 0.032813 AAATACTCCCTCCGTCCGGA 60.033 55.000 0.00 0.00 42.90 5.14
4949 5174 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
4952 5177 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
4953 5178 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
4954 5179 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
4956 5181 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
4957 5182 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
4958 5183 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
4960 5185 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
4961 5186 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
4962 5187 1.479323 TCCGGAAATACTTGTCGGAGG 59.521 52.381 0.00 0.00 43.84 4.30
4963 5188 1.479323 CCGGAAATACTTGTCGGAGGA 59.521 52.381 0.00 0.00 42.94 3.71
4964 5189 2.093869 CCGGAAATACTTGTCGGAGGAA 60.094 50.000 0.00 0.00 42.94 3.36
4965 5190 3.431766 CCGGAAATACTTGTCGGAGGAAT 60.432 47.826 0.00 0.00 42.94 3.01
4966 5191 3.555956 CGGAAATACTTGTCGGAGGAATG 59.444 47.826 0.00 0.00 0.00 2.67
4967 5192 3.877508 GGAAATACTTGTCGGAGGAATGG 59.122 47.826 0.00 0.00 0.00 3.16
4969 5194 5.368989 GAAATACTTGTCGGAGGAATGGAT 58.631 41.667 0.00 0.00 0.00 3.41
4970 5195 2.698855 ACTTGTCGGAGGAATGGATG 57.301 50.000 0.00 0.00 0.00 3.51
4971 5196 1.909302 ACTTGTCGGAGGAATGGATGT 59.091 47.619 0.00 0.00 0.00 3.06
4973 5198 3.711704 ACTTGTCGGAGGAATGGATGTAT 59.288 43.478 0.00 0.00 0.00 2.29
4974 5199 4.202264 ACTTGTCGGAGGAATGGATGTATC 60.202 45.833 0.00 0.00 0.00 2.24
4975 5200 3.576861 TGTCGGAGGAATGGATGTATCT 58.423 45.455 0.00 0.00 0.00 1.98
4976 5201 4.736473 TGTCGGAGGAATGGATGTATCTA 58.264 43.478 0.00 0.00 0.00 1.98
4977 5202 4.767409 TGTCGGAGGAATGGATGTATCTAG 59.233 45.833 0.00 0.00 0.00 2.43
4979 5204 5.010933 TCGGAGGAATGGATGTATCTAGAC 58.989 45.833 0.00 0.00 0.00 2.59
4980 5205 4.142578 CGGAGGAATGGATGTATCTAGACG 60.143 50.000 0.00 0.00 0.00 4.18
4981 5206 4.767928 GGAGGAATGGATGTATCTAGACGT 59.232 45.833 0.00 0.00 0.00 4.34
4982 5207 5.944599 GGAGGAATGGATGTATCTAGACGTA 59.055 44.000 0.00 0.00 0.00 3.57
4983 5208 6.603997 GGAGGAATGGATGTATCTAGACGTAT 59.396 42.308 0.00 0.00 0.00 3.06
4984 5209 7.122948 GGAGGAATGGATGTATCTAGACGTATT 59.877 40.741 0.00 0.00 0.00 1.89
4985 5210 8.423906 AGGAATGGATGTATCTAGACGTATTT 57.576 34.615 0.00 0.00 0.00 1.40
4986 5211 8.871125 AGGAATGGATGTATCTAGACGTATTTT 58.129 33.333 0.00 0.00 0.00 1.82
5017 5242 9.965902 ATAGATACACCCAATTTTATCCATCTC 57.034 33.333 0.00 0.00 0.00 2.75
5018 5243 8.050316 AGATACACCCAATTTTATCCATCTCT 57.950 34.615 0.00 0.00 0.00 3.10
5019 5244 8.160106 AGATACACCCAATTTTATCCATCTCTC 58.840 37.037 0.00 0.00 0.00 3.20
5020 5245 5.449553 ACACCCAATTTTATCCATCTCTCC 58.550 41.667 0.00 0.00 0.00 3.71
5021 5246 5.044179 ACACCCAATTTTATCCATCTCTCCA 60.044 40.000 0.00 0.00 0.00 3.86
5022 5247 5.893255 CACCCAATTTTATCCATCTCTCCAA 59.107 40.000 0.00 0.00 0.00 3.53
5023 5248 5.893824 ACCCAATTTTATCCATCTCTCCAAC 59.106 40.000 0.00 0.00 0.00 3.77
5024 5249 5.893255 CCCAATTTTATCCATCTCTCCAACA 59.107 40.000 0.00 0.00 0.00 3.33
5025 5250 6.380846 CCCAATTTTATCCATCTCTCCAACAA 59.619 38.462 0.00 0.00 0.00 2.83
5026 5251 7.417116 CCCAATTTTATCCATCTCTCCAACAAG 60.417 40.741 0.00 0.00 0.00 3.16
5027 5252 7.123247 CCAATTTTATCCATCTCTCCAACAAGT 59.877 37.037 0.00 0.00 0.00 3.16
5028 5253 9.177608 CAATTTTATCCATCTCTCCAACAAGTA 57.822 33.333 0.00 0.00 0.00 2.24
5029 5254 9.927081 AATTTTATCCATCTCTCCAACAAGTAT 57.073 29.630 0.00 0.00 0.00 2.12
5030 5255 9.927081 ATTTTATCCATCTCTCCAACAAGTATT 57.073 29.630 0.00 0.00 0.00 1.89
5031 5256 9.753674 TTTTATCCATCTCTCCAACAAGTATTT 57.246 29.630 0.00 0.00 0.00 1.40
5032 5257 8.964476 TTATCCATCTCTCCAACAAGTATTTC 57.036 34.615 0.00 0.00 0.00 2.17
5033 5258 5.419542 TCCATCTCTCCAACAAGTATTTCG 58.580 41.667 0.00 0.00 0.00 3.46
5034 5259 4.572389 CCATCTCTCCAACAAGTATTTCGG 59.428 45.833 0.00 0.00 0.00 4.30
5035 5260 4.202245 TCTCTCCAACAAGTATTTCGGG 57.798 45.455 0.00 0.00 0.00 5.14
5036 5261 3.835978 TCTCTCCAACAAGTATTTCGGGA 59.164 43.478 0.00 0.00 0.00 5.14
5037 5262 3.933332 CTCTCCAACAAGTATTTCGGGAC 59.067 47.826 0.00 0.00 0.00 4.46
5053 5278 3.747854 GGGACGGAGGGAGTATAAAAG 57.252 52.381 0.00 0.00 0.00 2.27
5054 5279 3.303049 GGGACGGAGGGAGTATAAAAGA 58.697 50.000 0.00 0.00 0.00 2.52
5055 5280 3.902467 GGGACGGAGGGAGTATAAAAGAT 59.098 47.826 0.00 0.00 0.00 2.40
5056 5281 4.021280 GGGACGGAGGGAGTATAAAAGATC 60.021 50.000 0.00 0.00 0.00 2.75
5057 5282 4.833938 GGACGGAGGGAGTATAAAAGATCT 59.166 45.833 0.00 0.00 0.00 2.75
5058 5283 5.047872 GGACGGAGGGAGTATAAAAGATCTC 60.048 48.000 0.00 0.00 0.00 2.75
5059 5284 4.833938 ACGGAGGGAGTATAAAAGATCTCC 59.166 45.833 0.00 0.00 43.84 3.71
5060 5285 5.081032 CGGAGGGAGTATAAAAGATCTCCT 58.919 45.833 0.00 0.00 43.97 3.69
5061 5286 5.047660 CGGAGGGAGTATAAAAGATCTCCTG 60.048 48.000 0.00 0.00 43.97 3.86
5062 5287 6.078664 GGAGGGAGTATAAAAGATCTCCTGA 58.921 44.000 0.00 0.00 43.97 3.86
5063 5288 6.555360 GGAGGGAGTATAAAAGATCTCCTGAA 59.445 42.308 0.00 0.00 43.97 3.02
5064 5289 7.236640 GGAGGGAGTATAAAAGATCTCCTGAAT 59.763 40.741 0.00 0.00 43.97 2.57
5065 5290 8.201242 AGGGAGTATAAAAGATCTCCTGAATC 57.799 38.462 0.00 0.00 43.97 2.52
5070 5295 9.391227 AGTATAAAAGATCTCCTGAATCCTGAT 57.609 33.333 0.00 0.00 0.00 2.90
5075 5300 7.630005 AAGATCTCCTGAATCCTGATGTAAT 57.370 36.000 0.00 0.00 0.00 1.89
5079 5304 9.249053 GATCTCCTGAATCCTGATGTAATACTA 57.751 37.037 0.00 0.00 0.00 1.82
5080 5305 9.607333 ATCTCCTGAATCCTGATGTAATACTAA 57.393 33.333 0.00 0.00 0.00 2.24
5325 5571 3.339093 CCTTCTCCCCACCCCCAC 61.339 72.222 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.955614 AGATCGGTCGAAATTCGTTGT 58.044 42.857 15.34 0.00 41.35 3.32
18 19 4.503007 ACATAGATCGGTCGAAATTCGTTG 59.497 41.667 15.34 6.61 41.35 4.10
19 20 4.503007 CACATAGATCGGTCGAAATTCGTT 59.497 41.667 15.34 0.00 41.35 3.85
20 21 4.042398 CACATAGATCGGTCGAAATTCGT 58.958 43.478 15.34 0.00 41.35 3.85
74 75 2.781646 GCCAAATATTTGCTTACGCGAC 59.218 45.455 20.67 0.00 39.65 5.19
92 93 0.251121 ATTTGTGTGTGGATCGGCCA 60.251 50.000 2.24 0.00 46.96 5.36
152 153 0.102844 GGCAGTGTGTGTTTGCATGT 59.897 50.000 0.00 0.00 39.54 3.21
153 154 0.935831 CGGCAGTGTGTGTTTGCATG 60.936 55.000 0.00 0.00 39.54 4.06
154 155 1.359833 CGGCAGTGTGTGTTTGCAT 59.640 52.632 0.00 0.00 39.54 3.96
155 156 1.590610 AACGGCAGTGTGTGTTTGCA 61.591 50.000 0.00 0.00 39.54 4.08
156 157 0.378962 TAACGGCAGTGTGTGTTTGC 59.621 50.000 0.00 0.00 37.11 3.68
157 158 1.668751 AGTAACGGCAGTGTGTGTTTG 59.331 47.619 0.00 0.00 0.00 2.93
160 161 0.596600 CGAGTAACGGCAGTGTGTGT 60.597 55.000 0.00 0.00 38.46 3.72
161 162 0.318360 TCGAGTAACGGCAGTGTGTG 60.318 55.000 0.00 0.00 42.82 3.82
172 173 6.074994 GGAATGTGATATGTTCGTCGAGTAAC 60.075 42.308 0.00 3.41 0.00 2.50
201 202 5.174035 CGTAGATTGGATGAGATTTGTCGTC 59.826 44.000 0.00 0.00 0.00 4.20
205 206 4.572389 GTGCGTAGATTGGATGAGATTTGT 59.428 41.667 0.00 0.00 0.00 2.83
214 215 2.874701 GCATTCTGTGCGTAGATTGGAT 59.125 45.455 11.47 0.00 45.23 3.41
230 231 1.317613 TGGGTAATGGCGATGCATTC 58.682 50.000 0.00 0.00 0.00 2.67
247 248 5.687770 TTGTTGTGTGATGTATCTGTTGG 57.312 39.130 0.00 0.00 0.00 3.77
249 250 5.532406 AGCTTTGTTGTGTGATGTATCTGTT 59.468 36.000 0.00 0.00 0.00 3.16
270 271 8.785184 AATCTCCTGGTTATTTAGTAGTAGCT 57.215 34.615 0.00 0.00 0.00 3.32
271 272 9.262358 CAAATCTCCTGGTTATTTAGTAGTAGC 57.738 37.037 8.11 0.00 0.00 3.58
272 273 9.765795 CCAAATCTCCTGGTTATTTAGTAGTAG 57.234 37.037 8.11 0.00 0.00 2.57
273 274 9.496710 TCCAAATCTCCTGGTTATTTAGTAGTA 57.503 33.333 8.11 0.00 35.30 1.82
274 275 8.388656 TCCAAATCTCCTGGTTATTTAGTAGT 57.611 34.615 8.11 0.00 35.30 2.73
275 276 9.495572 GATCCAAATCTCCTGGTTATTTAGTAG 57.504 37.037 8.11 0.00 35.30 2.57
276 277 9.225682 AGATCCAAATCTCCTGGTTATTTAGTA 57.774 33.333 8.11 0.80 37.75 1.82
361 380 1.302832 CACAAGGCCTCCACTCCAC 60.303 63.158 5.23 0.00 0.00 4.02
362 381 1.461268 TCACAAGGCCTCCACTCCA 60.461 57.895 5.23 0.00 0.00 3.86
363 382 1.298014 CTCACAAGGCCTCCACTCC 59.702 63.158 5.23 0.00 0.00 3.85
364 383 0.321122 CACTCACAAGGCCTCCACTC 60.321 60.000 5.23 0.00 0.00 3.51
365 384 0.764369 TCACTCACAAGGCCTCCACT 60.764 55.000 5.23 0.00 0.00 4.00
382 401 4.413520 CCAAAATATCTCTTCCCTCCCTCA 59.586 45.833 0.00 0.00 0.00 3.86
389 408 2.230660 CCGCCCAAAATATCTCTTCCC 58.769 52.381 0.00 0.00 0.00 3.97
390 409 2.230660 CCCGCCCAAAATATCTCTTCC 58.769 52.381 0.00 0.00 0.00 3.46
391 410 1.609072 GCCCGCCCAAAATATCTCTTC 59.391 52.381 0.00 0.00 0.00 2.87
392 411 1.692411 GCCCGCCCAAAATATCTCTT 58.308 50.000 0.00 0.00 0.00 2.85
482 502 1.702022 GCGGGGTATAAAGCTGGGGA 61.702 60.000 0.00 0.00 0.00 4.81
485 505 2.251642 GCGCGGGGTATAAAGCTGG 61.252 63.158 8.83 0.00 0.00 4.85
486 506 2.251642 GGCGCGGGGTATAAAGCTG 61.252 63.158 8.83 0.00 0.00 4.24
487 507 1.117142 TAGGCGCGGGGTATAAAGCT 61.117 55.000 8.83 0.00 0.00 3.74
682 702 2.689034 GTGGAGCAGGCTAGGGGT 60.689 66.667 0.00 0.00 0.00 4.95
808 828 2.327200 GGAAACCTCGGATAACCAGG 57.673 55.000 6.13 6.13 39.04 4.45
857 877 2.464459 GCACCAATCGCCTCGGAAG 61.464 63.158 0.00 0.00 0.00 3.46
936 956 2.145905 CGCGCGCTCATGGAAAAAC 61.146 57.895 30.48 0.00 0.00 2.43
1313 1354 1.737793 GTTCATCCACTTACTTGCCCG 59.262 52.381 0.00 0.00 0.00 6.13
1343 1384 3.687212 TGAAACACTATGCACGGGTTATG 59.313 43.478 5.95 0.00 0.00 1.90
1369 1410 0.390124 ACCTTCGGCTGAAACACGTA 59.610 50.000 9.73 0.00 32.66 3.57
1370 1411 0.878961 GACCTTCGGCTGAAACACGT 60.879 55.000 9.73 3.24 32.66 4.49
1371 1412 1.860078 GACCTTCGGCTGAAACACG 59.140 57.895 9.73 0.00 32.66 4.49
1372 1413 1.860078 CGACCTTCGGCTGAAACAC 59.140 57.895 9.73 2.69 36.00 3.32
1413 1458 6.870769 AGGAACATAAATTCAAATCTGGCTG 58.129 36.000 0.00 0.00 0.00 4.85
1414 1459 6.664816 TGAGGAACATAAATTCAAATCTGGCT 59.335 34.615 0.00 0.00 0.00 4.75
1415 1460 6.866480 TGAGGAACATAAATTCAAATCTGGC 58.134 36.000 0.00 0.00 0.00 4.85
1416 1461 6.976925 GCTGAGGAACATAAATTCAAATCTGG 59.023 38.462 0.00 0.00 0.00 3.86
1452 1497 2.408271 TTGGATTGGACAGCTGCTAG 57.592 50.000 15.27 0.00 0.00 3.42
1453 1498 2.040278 AGTTTGGATTGGACAGCTGCTA 59.960 45.455 15.27 1.42 0.00 3.49
1454 1499 1.202976 AGTTTGGATTGGACAGCTGCT 60.203 47.619 15.27 0.00 0.00 4.24
1645 1695 6.367969 GGTTATACTGCCGTCGATTAAATGAT 59.632 38.462 0.00 0.00 0.00 2.45
1666 1717 5.742562 ATAAATCAGGTCATTGGGGGTTA 57.257 39.130 0.00 0.00 0.00 2.85
1667 1718 4.625225 ATAAATCAGGTCATTGGGGGTT 57.375 40.909 0.00 0.00 0.00 4.11
1671 1722 5.581874 GCACAAAATAAATCAGGTCATTGGG 59.418 40.000 0.00 0.00 0.00 4.12
1729 1793 5.922544 CACAAAATTCAGAATCCTTGACCAC 59.077 40.000 18.46 0.00 0.00 4.16
1747 1811 5.049398 ACAAGACGCAAACTTACACAAAA 57.951 34.783 0.00 0.00 0.00 2.44
1753 1817 8.015409 AGTATTAGAACAAGACGCAAACTTAC 57.985 34.615 0.00 0.00 0.00 2.34
1755 1819 7.352739 CAAGTATTAGAACAAGACGCAAACTT 58.647 34.615 0.00 0.00 0.00 2.66
1807 1871 3.065648 ACCCGTGTTGTACATTGAAACAC 59.934 43.478 14.93 14.93 46.47 3.32
1997 2064 9.284968 ACAAACTAGTTAATTACTGATGCAAGT 57.715 29.630 8.92 0.00 37.73 3.16
2024 2091 7.554835 TCACCATACCTATTGGAAAACATACAC 59.445 37.037 0.00 0.00 37.69 2.90
2028 2095 7.353525 TGATCACCATACCTATTGGAAAACAT 58.646 34.615 0.00 0.00 37.69 2.71
2036 2103 7.332926 GCTACAATCTGATCACCATACCTATTG 59.667 40.741 0.00 0.00 0.00 1.90
2194 2261 5.420725 TCAGATTAGGCACAGTAATGTGT 57.579 39.130 22.95 8.27 41.53 3.72
2340 2408 0.545309 TCCCTGGTAGCAGCTCACTT 60.545 55.000 16.62 0.00 0.00 3.16
2524 2592 2.486472 AACTGGAGATGCAACAGGAG 57.514 50.000 13.31 1.15 36.57 3.69
2546 2614 5.121142 GCAACTTACTATGCACGTAAAGGAA 59.879 40.000 10.54 0.00 42.12 3.36
2635 2706 6.183360 GCGTATATTGTGTACCCATGTTTTGA 60.183 38.462 0.00 0.00 0.00 2.69
2637 2708 5.883673 AGCGTATATTGTGTACCCATGTTTT 59.116 36.000 0.00 0.00 0.00 2.43
2722 2794 2.975410 TGCTTCTCTTTCAATGCACG 57.025 45.000 0.00 0.00 0.00 5.34
2850 2928 4.331962 GCGAAAGAAACATATCGTGGAAC 58.668 43.478 0.00 0.00 37.60 3.62
2879 2957 5.048921 GCAAGTAAAACAGAAGGGTAAGACC 60.049 44.000 0.00 0.00 37.60 3.85
2908 2986 5.839606 ACAACTACTGGAAGAACCTAGAAGT 59.160 40.000 0.00 0.00 39.86 3.01
2962 3040 7.386848 GGACACTGTAAAAGCATAAAGAGTGTA 59.613 37.037 10.58 0.00 42.08 2.90
3002 3080 6.457355 AGCAACAAATTATCTGCACAATCAA 58.543 32.000 7.93 0.00 37.26 2.57
3005 3083 7.543172 CAGTAAGCAACAAATTATCTGCACAAT 59.457 33.333 7.93 0.00 37.26 2.71
3006 3084 6.862608 CAGTAAGCAACAAATTATCTGCACAA 59.137 34.615 7.93 0.00 37.26 3.33
3069 3148 0.318699 TCACAGTTTCCTCTCGTGCG 60.319 55.000 0.00 0.00 0.00 5.34
3190 3278 6.765512 ACTCTAGATTTTATTCTGGCTTCAGC 59.234 38.462 0.00 0.00 38.36 4.26
3269 3381 6.531948 CCCGAAATCAGTAACTCTAGAAACTG 59.468 42.308 17.50 17.50 40.54 3.16
3296 3409 7.649705 GCATCTGATTTCTCTTTGTATAGACGA 59.350 37.037 0.00 0.00 0.00 4.20
3298 3411 8.885494 AGCATCTGATTTCTCTTTGTATAGAC 57.115 34.615 0.00 0.00 0.00 2.59
3376 3494 5.977489 AGTGTGACAGTGCTGTATAACTA 57.023 39.130 4.68 0.00 45.05 2.24
3547 3669 9.034544 CGTCACAAAATGATAGTCTCATAATCA 57.965 33.333 0.00 0.00 44.03 2.57
3548 3670 8.491152 CCGTCACAAAATGATAGTCTCATAATC 58.509 37.037 0.00 0.00 44.03 1.75
3549 3671 8.204160 TCCGTCACAAAATGATAGTCTCATAAT 58.796 33.333 0.00 0.00 44.03 1.28
3550 3672 7.552459 TCCGTCACAAAATGATAGTCTCATAA 58.448 34.615 0.00 0.00 44.03 1.90
3551 3673 7.107639 TCCGTCACAAAATGATAGTCTCATA 57.892 36.000 0.00 0.00 44.03 2.15
3655 3777 3.120199 CCAGTACGGACAAGATTTGCAAG 60.120 47.826 0.00 0.00 36.56 4.01
3687 3809 7.444487 AGTTTTGTCCAGTAAAGAGACATTACC 59.556 37.037 0.00 0.00 40.06 2.85
3733 3864 9.372369 GCTAAGACTTCAAAACATAGACAGTAT 57.628 33.333 0.00 0.00 0.00 2.12
3769 3900 2.305635 TCATTCTTCAGGTAGCCAAGCA 59.694 45.455 0.00 0.00 0.00 3.91
3806 3937 1.154225 GCGTGGCCATTTTGTCTCG 60.154 57.895 9.72 6.18 0.00 4.04
3880 4087 9.685828 GTTGGTGCTAACATATGTTTCTTAAAA 57.314 29.630 25.31 11.60 39.31 1.52
3881 4088 8.851145 TGTTGGTGCTAACATATGTTTCTTAAA 58.149 29.630 25.31 11.15 39.31 1.52
3882 4089 8.397575 TGTTGGTGCTAACATATGTTTCTTAA 57.602 30.769 25.31 7.09 39.31 1.85
3910 4117 6.544928 TGAAAATAGACTATGACCAGCTCA 57.455 37.500 0.00 0.00 0.00 4.26
3913 4120 7.849804 TCTTTGAAAATAGACTATGACCAGC 57.150 36.000 0.00 0.00 0.00 4.85
3965 4179 5.339990 AGAAACCAATGTCAAAAACAGTCG 58.660 37.500 0.00 0.00 42.37 4.18
3982 4199 8.753497 AAGATTAGTGGATTCCAATAGAAACC 57.247 34.615 12.26 3.17 45.44 3.27
4115 4332 4.113815 AAGCTGGGCCGCATAGCA 62.114 61.111 19.61 0.43 39.84 3.49
4118 4335 2.190313 CTGAAGCTGGGCCGCATA 59.810 61.111 19.61 6.97 0.00 3.14
4157 4374 1.511305 GATCGTCGTGAGGAAGGCA 59.489 57.895 0.00 0.00 0.00 4.75
4331 4548 3.464494 GCCTTCCCATTGCTGCCC 61.464 66.667 0.00 0.00 0.00 5.36
4367 4584 0.609131 AAAACGTCTCAGGGGCATGG 60.609 55.000 0.00 0.00 0.00 3.66
4440 4657 4.038042 TCCTCTTGTATCATCATCACCGTC 59.962 45.833 0.00 0.00 0.00 4.79
4441 4658 3.960755 TCCTCTTGTATCATCATCACCGT 59.039 43.478 0.00 0.00 0.00 4.83
4442 4659 4.554292 CTCCTCTTGTATCATCATCACCG 58.446 47.826 0.00 0.00 0.00 4.94
4443 4660 4.262808 CCCTCCTCTTGTATCATCATCACC 60.263 50.000 0.00 0.00 0.00 4.02
4444 4661 4.590647 TCCCTCCTCTTGTATCATCATCAC 59.409 45.833 0.00 0.00 0.00 3.06
4445 4662 4.819610 TCCCTCCTCTTGTATCATCATCA 58.180 43.478 0.00 0.00 0.00 3.07
4446 4663 5.721000 AGATCCCTCCTCTTGTATCATCATC 59.279 44.000 0.00 0.00 0.00 2.92
4461 4678 2.095604 AGGCTAGACAAGATCCCTCC 57.904 55.000 0.00 0.00 0.00 4.30
4474 4691 3.118223 AGCAAAAGCTAACCCTAGGCTAG 60.118 47.826 14.77 14.77 35.06 3.42
4487 4704 5.238214 TCAAAACACAAAACAAGCAAAAGCT 59.762 32.000 0.00 0.00 0.00 3.74
4488 4705 5.447573 TCAAAACACAAAACAAGCAAAAGC 58.552 33.333 0.00 0.00 0.00 3.51
4489 4706 7.296660 TCATCAAAACACAAAACAAGCAAAAG 58.703 30.769 0.00 0.00 0.00 2.27
4490 4707 7.194607 TCATCAAAACACAAAACAAGCAAAA 57.805 28.000 0.00 0.00 0.00 2.44
4530 4747 1.632422 GCACAAGTATGCATTGCACC 58.368 50.000 14.66 7.75 45.39 5.01
4538 4755 3.374988 TCACATAGCTTGCACAAGTATGC 59.625 43.478 20.60 7.96 46.32 3.14
4539 4756 5.065602 ACATCACATAGCTTGCACAAGTATG 59.934 40.000 19.83 19.83 40.45 2.39
4540 4757 5.188434 ACATCACATAGCTTGCACAAGTAT 58.812 37.500 11.77 6.10 40.45 2.12
4541 4758 4.578871 ACATCACATAGCTTGCACAAGTA 58.421 39.130 11.77 4.24 40.45 2.24
4582 4799 3.865164 GGCAGCATACAAAAGTTTATGGC 59.135 43.478 0.00 0.00 0.00 4.40
4642 4859 3.845992 AGGATTGGCAAAGGGCTAAAAAT 59.154 39.130 3.01 0.00 46.60 1.82
4644 4861 2.566724 CAGGATTGGCAAAGGGCTAAAA 59.433 45.455 3.01 0.00 46.60 1.52
4672 4889 2.550175 TCATCCCCATCAAGTCTGTCA 58.450 47.619 0.00 0.00 0.00 3.58
4673 4890 3.135348 TGATCATCCCCATCAAGTCTGTC 59.865 47.826 0.00 0.00 0.00 3.51
4715 4935 2.094078 AGCTCAAGAGTCAGTGATCAGC 60.094 50.000 0.00 1.50 0.00 4.26
4888 5113 6.541934 TGACAATTCATGGCCATTTATTCA 57.458 33.333 17.92 11.15 35.52 2.57
4898 5123 2.762327 ACTGGGATTGACAATTCATGGC 59.238 45.455 8.73 0.00 37.68 4.40
4927 5152 0.104304 CCGGACGGAGGGAGTATTTG 59.896 60.000 4.40 0.00 37.50 2.32
4943 5168 1.479323 TCCTCCGACAAGTATTTCCGG 59.521 52.381 0.00 0.00 41.36 5.14
4945 5170 3.877508 CCATTCCTCCGACAAGTATTTCC 59.122 47.826 0.00 0.00 0.00 3.13
4946 5171 4.766375 TCCATTCCTCCGACAAGTATTTC 58.234 43.478 0.00 0.00 0.00 2.17
4947 5172 4.837093 TCCATTCCTCCGACAAGTATTT 57.163 40.909 0.00 0.00 0.00 1.40
4949 5174 3.711704 ACATCCATTCCTCCGACAAGTAT 59.288 43.478 0.00 0.00 0.00 2.12
4952 5177 2.698855 ACATCCATTCCTCCGACAAG 57.301 50.000 0.00 0.00 0.00 3.16
4953 5178 3.967326 AGATACATCCATTCCTCCGACAA 59.033 43.478 0.00 0.00 0.00 3.18
4954 5179 3.576861 AGATACATCCATTCCTCCGACA 58.423 45.455 0.00 0.00 0.00 4.35
4956 5181 5.010933 GTCTAGATACATCCATTCCTCCGA 58.989 45.833 0.00 0.00 0.00 4.55
4957 5182 4.142578 CGTCTAGATACATCCATTCCTCCG 60.143 50.000 0.00 0.00 0.00 4.63
4958 5183 4.767928 ACGTCTAGATACATCCATTCCTCC 59.232 45.833 0.00 0.00 0.00 4.30
4960 5185 8.423906 AAATACGTCTAGATACATCCATTCCT 57.576 34.615 0.00 0.00 0.00 3.36
4991 5216 9.965902 GAGATGGATAAAATTGGGTGTATCTAT 57.034 33.333 0.00 0.00 29.76 1.98
4992 5217 9.170890 AGAGATGGATAAAATTGGGTGTATCTA 57.829 33.333 0.00 0.00 0.00 1.98
4993 5218 8.050316 AGAGATGGATAAAATTGGGTGTATCT 57.950 34.615 0.00 0.00 0.00 1.98
4994 5219 7.391833 GGAGAGATGGATAAAATTGGGTGTATC 59.608 40.741 0.00 0.00 0.00 2.24
4995 5220 7.147141 TGGAGAGATGGATAAAATTGGGTGTAT 60.147 37.037 0.00 0.00 0.00 2.29
4996 5221 6.159575 TGGAGAGATGGATAAAATTGGGTGTA 59.840 38.462 0.00 0.00 0.00 2.90
4997 5222 5.044179 TGGAGAGATGGATAAAATTGGGTGT 60.044 40.000 0.00 0.00 0.00 4.16
4998 5223 5.448654 TGGAGAGATGGATAAAATTGGGTG 58.551 41.667 0.00 0.00 0.00 4.61
4999 5224 5.732331 TGGAGAGATGGATAAAATTGGGT 57.268 39.130 0.00 0.00 0.00 4.51
5000 5225 5.893255 TGTTGGAGAGATGGATAAAATTGGG 59.107 40.000 0.00 0.00 0.00 4.12
5001 5226 7.123247 ACTTGTTGGAGAGATGGATAAAATTGG 59.877 37.037 0.00 0.00 0.00 3.16
5002 5227 8.059798 ACTTGTTGGAGAGATGGATAAAATTG 57.940 34.615 0.00 0.00 0.00 2.32
5003 5228 9.927081 ATACTTGTTGGAGAGATGGATAAAATT 57.073 29.630 0.00 0.00 0.00 1.82
5004 5229 9.927081 AATACTTGTTGGAGAGATGGATAAAAT 57.073 29.630 0.00 0.00 0.00 1.82
5005 5230 9.753674 AAATACTTGTTGGAGAGATGGATAAAA 57.246 29.630 0.00 0.00 0.00 1.52
5006 5231 9.396022 GAAATACTTGTTGGAGAGATGGATAAA 57.604 33.333 0.00 0.00 0.00 1.40
5007 5232 7.710907 CGAAATACTTGTTGGAGAGATGGATAA 59.289 37.037 0.00 0.00 0.00 1.75
5008 5233 7.210174 CGAAATACTTGTTGGAGAGATGGATA 58.790 38.462 0.00 0.00 0.00 2.59
5009 5234 6.051717 CGAAATACTTGTTGGAGAGATGGAT 58.948 40.000 0.00 0.00 0.00 3.41
5010 5235 5.419542 CGAAATACTTGTTGGAGAGATGGA 58.580 41.667 0.00 0.00 0.00 3.41
5011 5236 4.572389 CCGAAATACTTGTTGGAGAGATGG 59.428 45.833 0.00 0.00 0.00 3.51
5012 5237 4.572389 CCCGAAATACTTGTTGGAGAGATG 59.428 45.833 0.00 0.00 0.00 2.90
5013 5238 4.469945 TCCCGAAATACTTGTTGGAGAGAT 59.530 41.667 0.00 0.00 0.00 2.75
5014 5239 3.835978 TCCCGAAATACTTGTTGGAGAGA 59.164 43.478 0.00 0.00 0.00 3.10
5015 5240 3.933332 GTCCCGAAATACTTGTTGGAGAG 59.067 47.826 0.00 0.00 0.00 3.20
5016 5241 3.615592 CGTCCCGAAATACTTGTTGGAGA 60.616 47.826 0.00 0.00 0.00 3.71
5017 5242 2.671396 CGTCCCGAAATACTTGTTGGAG 59.329 50.000 0.00 0.00 0.00 3.86
5018 5243 2.613474 CCGTCCCGAAATACTTGTTGGA 60.613 50.000 0.00 0.00 0.00 3.53
5019 5244 1.735571 CCGTCCCGAAATACTTGTTGG 59.264 52.381 0.00 0.00 0.00 3.77
5020 5245 2.671396 CTCCGTCCCGAAATACTTGTTG 59.329 50.000 0.00 0.00 0.00 3.33
5021 5246 2.354403 CCTCCGTCCCGAAATACTTGTT 60.354 50.000 0.00 0.00 0.00 2.83
5022 5247 1.206371 CCTCCGTCCCGAAATACTTGT 59.794 52.381 0.00 0.00 0.00 3.16
5023 5248 1.472728 CCCTCCGTCCCGAAATACTTG 60.473 57.143 0.00 0.00 0.00 3.16
5024 5249 0.828677 CCCTCCGTCCCGAAATACTT 59.171 55.000 0.00 0.00 0.00 2.24
5025 5250 0.032813 TCCCTCCGTCCCGAAATACT 60.033 55.000 0.00 0.00 0.00 2.12
5026 5251 0.388294 CTCCCTCCGTCCCGAAATAC 59.612 60.000 0.00 0.00 0.00 1.89
5027 5252 0.032813 ACTCCCTCCGTCCCGAAATA 60.033 55.000 0.00 0.00 0.00 1.40
5028 5253 0.032813 TACTCCCTCCGTCCCGAAAT 60.033 55.000 0.00 0.00 0.00 2.17
5029 5254 0.032813 ATACTCCCTCCGTCCCGAAA 60.033 55.000 0.00 0.00 0.00 3.46
5030 5255 0.846015 TATACTCCCTCCGTCCCGAA 59.154 55.000 0.00 0.00 0.00 4.30
5031 5256 0.846015 TTATACTCCCTCCGTCCCGA 59.154 55.000 0.00 0.00 0.00 5.14
5032 5257 1.696063 TTTATACTCCCTCCGTCCCG 58.304 55.000 0.00 0.00 0.00 5.14
5033 5258 3.303049 TCTTTTATACTCCCTCCGTCCC 58.697 50.000 0.00 0.00 0.00 4.46
5034 5259 4.833938 AGATCTTTTATACTCCCTCCGTCC 59.166 45.833 0.00 0.00 0.00 4.79
5035 5260 5.047872 GGAGATCTTTTATACTCCCTCCGTC 60.048 48.000 0.00 0.00 41.89 4.79
5036 5261 4.833938 GGAGATCTTTTATACTCCCTCCGT 59.166 45.833 0.00 0.00 41.89 4.69
5037 5262 5.047660 CAGGAGATCTTTTATACTCCCTCCG 60.048 48.000 0.00 0.00 46.88 4.63
5038 5263 6.078664 TCAGGAGATCTTTTATACTCCCTCC 58.921 44.000 0.00 0.00 46.88 4.30
5039 5264 7.604657 TTCAGGAGATCTTTTATACTCCCTC 57.395 40.000 0.00 0.00 46.88 4.30
5040 5265 7.236640 GGATTCAGGAGATCTTTTATACTCCCT 59.763 40.741 0.00 0.00 46.88 4.20
5041 5266 7.236640 AGGATTCAGGAGATCTTTTATACTCCC 59.763 40.741 0.00 0.00 46.88 4.30
5042 5267 8.093927 CAGGATTCAGGAGATCTTTTATACTCC 58.906 40.741 0.00 0.00 46.28 3.85
5043 5268 8.865090 TCAGGATTCAGGAGATCTTTTATACTC 58.135 37.037 0.00 0.00 0.00 2.59
5044 5269 8.789767 TCAGGATTCAGGAGATCTTTTATACT 57.210 34.615 0.00 0.00 0.00 2.12
5045 5270 9.434420 CATCAGGATTCAGGAGATCTTTTATAC 57.566 37.037 0.00 0.00 0.00 1.47
5046 5271 9.163894 ACATCAGGATTCAGGAGATCTTTTATA 57.836 33.333 0.00 0.00 0.00 0.98
5047 5272 8.043429 ACATCAGGATTCAGGAGATCTTTTAT 57.957 34.615 0.00 0.00 0.00 1.40
5048 5273 7.443302 ACATCAGGATTCAGGAGATCTTTTA 57.557 36.000 0.00 0.00 0.00 1.52
5049 5274 6.324601 ACATCAGGATTCAGGAGATCTTTT 57.675 37.500 0.00 0.00 0.00 2.27
5050 5275 5.972327 ACATCAGGATTCAGGAGATCTTT 57.028 39.130 0.00 0.00 0.00 2.52
5051 5276 7.630005 ATTACATCAGGATTCAGGAGATCTT 57.370 36.000 0.00 0.00 0.00 2.40
5052 5277 7.955185 AGTATTACATCAGGATTCAGGAGATCT 59.045 37.037 0.00 0.00 0.00 2.75
5053 5278 8.133024 AGTATTACATCAGGATTCAGGAGATC 57.867 38.462 0.00 0.00 0.00 2.75
5054 5279 9.607333 TTAGTATTACATCAGGATTCAGGAGAT 57.393 33.333 0.00 0.00 0.00 2.75
5055 5280 9.434275 TTTAGTATTACATCAGGATTCAGGAGA 57.566 33.333 0.00 0.00 0.00 3.71
5252 5479 1.552337 AGAGTGGTAGCATCACCTGTG 59.448 52.381 0.00 0.00 39.50 3.66
5254 5481 2.101582 GGTAGAGTGGTAGCATCACCTG 59.898 54.545 0.00 0.00 39.50 4.00
5294 5534 1.971695 GAAGGTTTGCTGACCGGGG 60.972 63.158 6.32 0.00 44.62 5.73


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

AutoCloner maintained by Alex Coulton.