Multiple sequence alignment - TraesCS6A01G272300

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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 TraesCS6A01G272300 chr6A 100.000 4154 0 0 1 4154 499010974 499006821 0.000000e+00 7672.0
1 TraesCS6A01G272300 chr6D 93.890 1342 53 14 2582 3910 356598767 356597442 0.000000e+00 1997.0
2 TraesCS6A01G272300 chr6D 89.286 1316 95 18 1169 2460 356600135 356598842 0.000000e+00 1607.0
3 TraesCS6A01G272300 chr6D 87.215 657 50 16 9 651 356601269 356600633 0.000000e+00 717.0
4 TraesCS6A01G272300 chr6D 93.096 449 14 6 738 1178 356600623 356600184 3.500000e-180 641.0
5 TraesCS6A01G272300 chr6B 93.222 1313 48 13 2582 3857 537579375 537578067 0.000000e+00 1893.0
6 TraesCS6A01G272300 chr6B 95.612 1185 28 7 1284 2456 537580626 537579454 0.000000e+00 1879.0
7 TraesCS6A01G272300 chr6B 96.875 672 13 3 1 672 537582149 537581486 0.000000e+00 1118.0
8 TraesCS6A01G272300 chr6B 98.532 613 8 1 672 1284 537581436 537580825 0.000000e+00 1081.0
9 TraesCS6A01G272300 chr6B 97.778 45 1 0 2537 2581 537579456 537579412 1.240000e-10 78.7
10 TraesCS6A01G272300 chr5B 96.667 90 3 0 2455 2544 184285349 184285260 2.590000e-32 150.0
11 TraesCS6A01G272300 chr4A 96.629 89 3 0 2454 2542 743442952 743443040 9.300000e-32 148.0
12 TraesCS6A01G272300 chr7A 93.000 100 7 0 2447 2546 204607941 204608040 3.350000e-31 147.0
13 TraesCS6A01G272300 chr4D 93.069 101 5 2 2441 2540 303079356 303079257 3.350000e-31 147.0
14 TraesCS6A01G272300 chr7D 96.552 87 3 0 2454 2540 498229923 498229837 1.200000e-30 145.0
15 TraesCS6A01G272300 chr2B 93.814 97 4 2 2448 2543 136175708 136175803 1.200000e-30 145.0
16 TraesCS6A01G272300 chr1D 93.814 97 4 2 2448 2542 42391811 42391715 1.200000e-30 145.0
17 TraesCS6A01G272300 chr1D 90.566 106 9 1 2439 2544 263867909 263868013 5.600000e-29 139.0
18 TraesCS6A01G272300 chr3B 93.617 94 5 1 2451 2543 39349861 39349954 5.600000e-29 139.0
19 TraesCS6A01G272300 chr1A 74.216 287 59 11 3730 4006 481686857 481687138 5.680000e-19 106.0


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 TraesCS6A01G272300 chr6A 499006821 499010974 4153 True 7672.00 7672 100.00000 1 4154 1 chr6A.!!$R1 4153
1 TraesCS6A01G272300 chr6D 356597442 356601269 3827 True 1240.50 1997 90.87175 9 3910 4 chr6D.!!$R1 3901
2 TraesCS6A01G272300 chr6B 537578067 537582149 4082 True 1209.94 1893 96.40380 1 3857 5 chr6B.!!$R1 3856

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
390 404 1.067060 TGACAGGAGAACACTGACGTG 59.933 52.381 0.00 0.0 46.63 4.49 F
1148 1220 1.279271 AGGTATTGTGCACCCTCAGTC 59.721 52.381 15.69 0.0 36.67 3.51 F
2748 3139 2.499205 CCGCATCGCCTACAGGAA 59.501 61.111 0.00 0.0 37.39 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1347 1680 1.271762 TGCAAGCATGAAGGAAGCTCT 60.272 47.619 0.00 0.00 37.70 4.09 R
3065 3473 1.021390 AGCGCAAGAATCGGTTCAGG 61.021 55.000 11.47 3.01 43.02 3.86 R
4074 4505 0.036010 CATCCAGGAGTGAGGCGTTT 60.036 55.000 0.00 0.00 0.00 3.60 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
102 103 1.415659 AGTCCTGTGCTGGCATAGATC 59.584 52.381 18.40 11.41 37.35 2.75
324 338 9.167311 CAATGCCAACTAAGTTACTTAGATCTT 57.833 33.333 31.38 16.77 44.24 2.40
366 380 6.961359 ATCTGTTTGCATGTGAATGATTTG 57.039 33.333 0.00 0.00 0.00 2.32
390 404 1.067060 TGACAGGAGAACACTGACGTG 59.933 52.381 0.00 0.00 46.63 4.49
391 405 1.337071 GACAGGAGAACACTGACGTGA 59.663 52.381 0.00 0.00 43.97 4.35
392 406 1.338337 ACAGGAGAACACTGACGTGAG 59.662 52.381 0.00 0.00 43.97 3.51
418 432 6.380079 ACTGAGTATTCAATTGGTTCTCCT 57.620 37.500 5.42 0.00 31.69 3.69
487 501 8.752005 AATTTGTCTGCTATTATGTGGTATGT 57.248 30.769 0.00 0.00 0.00 2.29
489 503 7.552458 TTGTCTGCTATTATGTGGTATGTTG 57.448 36.000 0.00 0.00 0.00 3.33
680 744 7.735326 ATGTAGGTGTCAGTATAGGTTTTCT 57.265 36.000 0.00 0.00 0.00 2.52
1062 1134 2.045536 CCCCCTGCTGCTCTCAAC 60.046 66.667 0.00 0.00 0.00 3.18
1148 1220 1.279271 AGGTATTGTGCACCCTCAGTC 59.721 52.381 15.69 0.00 36.67 3.51
1530 1875 2.554032 CAGTTCCTGCTAACAGTTTGGG 59.446 50.000 0.00 0.00 42.81 4.12
1679 2030 2.977914 TCCTGTCTTTATCTGCTGTGC 58.022 47.619 0.00 0.00 0.00 4.57
1692 2043 5.991328 TCTGCTGTGCTATTAAGTTATGC 57.009 39.130 0.00 0.00 0.00 3.14
1727 2079 7.976175 ACAGACTTGTTTCTTTTTCCTTTCATC 59.024 33.333 0.00 0.00 32.28 2.92
1810 2162 3.126000 GTCTTATCAAGGTCAGCTTGCAC 59.874 47.826 11.99 0.09 0.00 4.57
1943 2295 7.437748 AGACACTATCTATTAACACTGGATGC 58.562 38.462 0.00 0.00 35.15 3.91
2213 2566 3.261897 GTGAGGATAATGACCCGATGGAT 59.738 47.826 0.00 0.00 34.81 3.41
2262 2615 6.892658 ATGGATGCGGTGCTTAATTATTTA 57.107 33.333 0.00 0.00 0.00 1.40
2460 2813 7.602753 ACAAGAAATTATTTGCTTGTACTCCC 58.397 34.615 18.19 0.00 46.37 4.30
2461 2814 7.451566 ACAAGAAATTATTTGCTTGTACTCCCT 59.548 33.333 18.19 0.00 46.37 4.20
2462 2815 7.631717 AGAAATTATTTGCTTGTACTCCCTC 57.368 36.000 0.00 0.00 0.00 4.30
2463 2816 7.406104 AGAAATTATTTGCTTGTACTCCCTCT 58.594 34.615 0.00 0.00 0.00 3.69
2464 2817 7.337942 AGAAATTATTTGCTTGTACTCCCTCTG 59.662 37.037 0.00 0.00 0.00 3.35
2465 2818 5.499004 TTATTTGCTTGTACTCCCTCTGT 57.501 39.130 0.00 0.00 0.00 3.41
2466 2819 6.614694 TTATTTGCTTGTACTCCCTCTGTA 57.385 37.500 0.00 0.00 0.00 2.74
2467 2820 4.967084 TTTGCTTGTACTCCCTCTGTAA 57.033 40.909 0.00 0.00 0.00 2.41
2468 2821 4.537135 TTGCTTGTACTCCCTCTGTAAG 57.463 45.455 0.00 0.00 0.00 2.34
2469 2822 2.832129 TGCTTGTACTCCCTCTGTAAGG 59.168 50.000 0.00 0.00 45.77 2.69
2485 2838 8.649973 CTCTGTAAGGAAATATAAGAGCGTTT 57.350 34.615 0.00 0.00 0.00 3.60
2486 2839 9.745880 CTCTGTAAGGAAATATAAGAGCGTTTA 57.254 33.333 0.00 0.00 0.00 2.01
2487 2840 9.745880 TCTGTAAGGAAATATAAGAGCGTTTAG 57.254 33.333 0.00 0.00 0.00 1.85
2488 2841 9.745880 CTGTAAGGAAATATAAGAGCGTTTAGA 57.254 33.333 0.00 0.00 0.00 2.10
2492 2845 8.819643 AGGAAATATAAGAGCGTTTAGATCAC 57.180 34.615 0.00 0.00 37.82 3.06
2493 2846 8.643324 AGGAAATATAAGAGCGTTTAGATCACT 58.357 33.333 0.00 0.00 37.82 3.41
2494 2847 9.909644 GGAAATATAAGAGCGTTTAGATCACTA 57.090 33.333 0.00 0.00 37.82 2.74
2500 2853 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
2501 2854 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
2502 2855 8.503458 AGAGCGTTTAGATCACTACTTTAGTA 57.497 34.615 0.00 0.00 37.82 1.82
2503 2856 8.954350 AGAGCGTTTAGATCACTACTTTAGTAA 58.046 33.333 0.00 0.00 37.82 2.24
2504 2857 9.733219 GAGCGTTTAGATCACTACTTTAGTAAT 57.267 33.333 0.00 0.00 37.23 1.89
2505 2858 9.733219 AGCGTTTAGATCACTACTTTAGTAATC 57.267 33.333 0.00 0.00 37.23 1.75
2506 2859 9.733219 GCGTTTAGATCACTACTTTAGTAATCT 57.267 33.333 4.72 4.72 37.23 2.40
2512 2865 9.733219 AGATCACTACTTTAGTAATCTAAACGC 57.267 33.333 0.00 0.00 40.05 4.84
2513 2866 9.733219 GATCACTACTTTAGTAATCTAAACGCT 57.267 33.333 0.00 0.00 40.05 5.07
2514 2867 9.733219 ATCACTACTTTAGTAATCTAAACGCTC 57.267 33.333 0.00 0.00 40.05 5.03
2515 2868 8.954350 TCACTACTTTAGTAATCTAAACGCTCT 58.046 33.333 0.00 0.00 40.05 4.09
2516 2869 9.570488 CACTACTTTAGTAATCTAAACGCTCTT 57.430 33.333 0.00 0.00 40.05 2.85
2530 2883 9.241317 TCTAAACGCTCTTATATTTCTTTACGG 57.759 33.333 0.00 0.00 0.00 4.02
2531 2884 9.241317 CTAAACGCTCTTATATTTCTTTACGGA 57.759 33.333 0.00 0.00 0.00 4.69
2532 2885 7.695869 AACGCTCTTATATTTCTTTACGGAG 57.304 36.000 0.00 0.00 0.00 4.63
2533 2886 6.214399 ACGCTCTTATATTTCTTTACGGAGG 58.786 40.000 0.00 0.00 0.00 4.30
2534 2887 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
2535 2888 6.516194 CGCTCTTATATTTCTTTACGGAGGGA 60.516 42.308 0.00 0.00 34.63 4.20
2536 2889 6.869388 GCTCTTATATTTCTTTACGGAGGGAG 59.131 42.308 0.00 0.00 0.00 4.30
2537 2890 7.471679 GCTCTTATATTTCTTTACGGAGGGAGT 60.472 40.741 0.00 0.00 0.00 3.85
2631 3022 7.217200 TGACTGCTGAGTTCTTACATTAGTTT 58.783 34.615 0.00 0.00 30.16 2.66
2748 3139 2.499205 CCGCATCGCCTACAGGAA 59.501 61.111 0.00 0.00 37.39 3.36
2805 3196 6.014242 TCAACTATGATCAACTTCACTGTCCT 60.014 38.462 0.00 0.00 0.00 3.85
2991 3391 8.251750 TGCTTCATACTTGTACTAACATTGTC 57.748 34.615 0.00 0.00 34.97 3.18
3035 3443 7.953752 ACTCTATACTGCCTTACTGTTATTCC 58.046 38.462 0.00 0.00 0.00 3.01
3065 3473 0.320946 TGCGGGTGGCTTACTGTTAC 60.321 55.000 0.00 0.00 44.05 2.50
3213 3626 4.456911 CCCTACGGCTTATCAATAGTACGA 59.543 45.833 0.00 0.00 0.00 3.43
3221 3634 6.583050 GGCTTATCAATAGTACGACAGACATC 59.417 42.308 0.00 0.00 0.00 3.06
3257 3670 4.641396 TGATCGAAAACCATCAGTCTGTT 58.359 39.130 0.00 0.00 0.00 3.16
3291 3706 1.356124 ACCTTCTGTCCATGCTGAGT 58.644 50.000 0.00 0.00 0.00 3.41
3491 3906 1.202830 TGTGTGGTATCCGCTGGTTTT 60.203 47.619 1.15 0.00 34.70 2.43
3504 3919 0.031616 TGGTTTTGCTTTCCCTGGGT 60.032 50.000 13.56 0.00 0.00 4.51
3506 3921 1.070134 GGTTTTGCTTTCCCTGGGTTC 59.930 52.381 13.56 1.20 0.00 3.62
3537 3958 4.377022 CCATTAGTTTTCTGTGAACGTCCG 60.377 45.833 0.00 0.00 32.38 4.79
3538 3959 2.304751 AGTTTTCTGTGAACGTCCGT 57.695 45.000 0.00 0.00 32.38 4.69
3549 3970 0.662374 AACGTCCGTAGCTGTTGTCG 60.662 55.000 0.00 0.00 0.00 4.35
3667 4088 5.687770 TTCTCTCTCTATTCATCTCAGCG 57.312 43.478 0.00 0.00 0.00 5.18
3668 4089 4.071423 TCTCTCTCTATTCATCTCAGCGG 58.929 47.826 0.00 0.00 0.00 5.52
3745 4172 3.754188 GATGATATCCAATTCTGCGCC 57.246 47.619 4.18 0.00 0.00 6.53
3835 4264 3.353557 AGATGACTTAGTGCGTGAGGTA 58.646 45.455 0.00 0.00 0.00 3.08
3874 4305 7.144000 AGCATTTGAACATTTGAGAAGTTCTC 58.856 34.615 23.53 23.53 43.65 2.87
3893 4324 8.285776 AGTTCTCAGCAAAATAAACAAAATCG 57.714 30.769 0.00 0.00 0.00 3.34
3895 4326 6.976088 TCTCAGCAAAATAAACAAAATCGGA 58.024 32.000 0.00 0.00 0.00 4.55
3910 4341 1.184970 TCGGATCCAGACAGTGCACA 61.185 55.000 21.04 0.00 0.00 4.57
3911 4342 0.320683 CGGATCCAGACAGTGCACAA 60.321 55.000 21.04 0.00 0.00 3.33
3912 4343 1.446907 GGATCCAGACAGTGCACAAG 58.553 55.000 21.04 13.67 0.00 3.16
3913 4344 0.801251 GATCCAGACAGTGCACAAGC 59.199 55.000 21.04 7.18 42.57 4.01
3928 4359 5.375544 GCACAAGCAGTAAAGTTTTTCAC 57.624 39.130 0.00 0.00 41.58 3.18
3929 4360 4.027702 GCACAAGCAGTAAAGTTTTTCACG 60.028 41.667 0.00 0.00 41.58 4.35
3930 4361 4.499040 CACAAGCAGTAAAGTTTTTCACGG 59.501 41.667 0.00 0.00 0.00 4.94
3931 4362 4.396790 ACAAGCAGTAAAGTTTTTCACGGA 59.603 37.500 0.00 0.00 0.00 4.69
3932 4363 4.547406 AGCAGTAAAGTTTTTCACGGAC 57.453 40.909 0.00 0.00 0.00 4.79
3933 4364 3.314357 AGCAGTAAAGTTTTTCACGGACC 59.686 43.478 0.00 0.00 0.00 4.46
3934 4365 3.314357 GCAGTAAAGTTTTTCACGGACCT 59.686 43.478 0.00 0.00 0.00 3.85
3935 4366 4.554134 GCAGTAAAGTTTTTCACGGACCTC 60.554 45.833 0.00 0.00 0.00 3.85
3936 4367 4.573201 CAGTAAAGTTTTTCACGGACCTCA 59.427 41.667 0.00 0.00 0.00 3.86
3937 4368 5.065474 CAGTAAAGTTTTTCACGGACCTCAA 59.935 40.000 0.00 0.00 0.00 3.02
3938 4369 5.648960 AGTAAAGTTTTTCACGGACCTCAAA 59.351 36.000 0.00 0.00 0.00 2.69
3939 4370 5.592104 AAAGTTTTTCACGGACCTCAAAT 57.408 34.783 0.00 0.00 0.00 2.32
3940 4371 5.592104 AAGTTTTTCACGGACCTCAAATT 57.408 34.783 0.00 0.00 0.00 1.82
3941 4372 5.592104 AGTTTTTCACGGACCTCAAATTT 57.408 34.783 0.00 0.00 0.00 1.82
3942 4373 6.702716 AGTTTTTCACGGACCTCAAATTTA 57.297 33.333 0.00 0.00 0.00 1.40
3943 4374 7.284919 AGTTTTTCACGGACCTCAAATTTAT 57.715 32.000 0.00 0.00 0.00 1.40
3944 4375 7.368059 AGTTTTTCACGGACCTCAAATTTATC 58.632 34.615 0.00 0.00 0.00 1.75
3945 4376 7.230712 AGTTTTTCACGGACCTCAAATTTATCT 59.769 33.333 0.00 0.00 0.00 1.98
3946 4377 6.737254 TTTCACGGACCTCAAATTTATCTC 57.263 37.500 0.00 0.00 0.00 2.75
3947 4378 5.677319 TCACGGACCTCAAATTTATCTCT 57.323 39.130 0.00 0.00 0.00 3.10
3948 4379 6.049955 TCACGGACCTCAAATTTATCTCTT 57.950 37.500 0.00 0.00 0.00 2.85
3949 4380 6.472887 TCACGGACCTCAAATTTATCTCTTT 58.527 36.000 0.00 0.00 0.00 2.52
3950 4381 6.940298 TCACGGACCTCAAATTTATCTCTTTT 59.060 34.615 0.00 0.00 0.00 2.27
3951 4382 7.023575 CACGGACCTCAAATTTATCTCTTTTG 58.976 38.462 0.00 0.00 0.00 2.44
3952 4383 6.030228 CGGACCTCAAATTTATCTCTTTTGC 58.970 40.000 0.00 0.00 31.88 3.68
3953 4384 6.127897 CGGACCTCAAATTTATCTCTTTTGCT 60.128 38.462 0.00 0.00 31.88 3.91
3954 4385 7.065803 CGGACCTCAAATTTATCTCTTTTGCTA 59.934 37.037 0.00 0.00 31.88 3.49
3955 4386 8.739972 GGACCTCAAATTTATCTCTTTTGCTAA 58.260 33.333 0.00 0.00 31.88 3.09
3956 4387 9.780413 GACCTCAAATTTATCTCTTTTGCTAAG 57.220 33.333 0.00 0.00 31.88 2.18
3957 4388 9.520515 ACCTCAAATTTATCTCTTTTGCTAAGA 57.479 29.630 0.00 2.59 31.88 2.10
3959 4390 9.500864 CTCAAATTTATCTCTTTTGCTAAGAGC 57.499 33.333 18.62 0.00 42.58 4.09
3960 4391 9.236006 TCAAATTTATCTCTTTTGCTAAGAGCT 57.764 29.630 18.62 13.99 42.97 4.09
3963 4394 9.898152 AATTTATCTCTTTTGCTAAGAGCTACT 57.102 29.630 18.62 9.59 42.97 2.57
3964 4395 9.898152 ATTTATCTCTTTTGCTAAGAGCTACTT 57.102 29.630 18.62 0.00 42.97 2.24
3965 4396 8.709386 TTATCTCTTTTGCTAAGAGCTACTTG 57.291 34.615 18.62 1.96 42.97 3.16
3966 4397 5.482908 TCTCTTTTGCTAAGAGCTACTTGG 58.517 41.667 18.62 6.75 42.97 3.61
3967 4398 5.246203 TCTCTTTTGCTAAGAGCTACTTGGA 59.754 40.000 18.62 3.24 42.97 3.53
3968 4399 5.238583 TCTTTTGCTAAGAGCTACTTGGAC 58.761 41.667 11.55 5.63 42.97 4.02
3969 4400 4.617253 TTTGCTAAGAGCTACTTGGACA 57.383 40.909 11.55 7.43 42.97 4.02
3970 4401 4.826274 TTGCTAAGAGCTACTTGGACAT 57.174 40.909 11.55 0.00 42.97 3.06
3971 4402 4.392921 TGCTAAGAGCTACTTGGACATC 57.607 45.455 11.55 0.00 42.97 3.06
3972 4403 3.133003 TGCTAAGAGCTACTTGGACATCC 59.867 47.826 11.55 0.00 42.97 3.51
3973 4404 3.133003 GCTAAGAGCTACTTGGACATCCA 59.867 47.826 11.55 0.00 40.54 3.41
3974 4405 4.383118 GCTAAGAGCTACTTGGACATCCAA 60.383 45.833 12.73 12.73 45.00 3.53
3975 4406 5.858243 GCTAAGAGCTACTTGGACATCCAAA 60.858 44.000 14.18 0.23 45.73 3.28
3976 4407 7.132869 GCTAAGAGCTACTTGGACATCCAAAT 61.133 42.308 14.18 7.31 45.73 2.32
3977 4408 9.062132 GCTAAGAGCTACTTGGACATCCAAATG 62.062 44.444 14.18 6.58 45.73 2.32
3984 4415 3.438216 TGGACATCCAAATGCTCTGAA 57.562 42.857 0.00 0.00 44.35 3.02
3985 4416 3.765381 TGGACATCCAAATGCTCTGAAA 58.235 40.909 0.00 0.00 44.35 2.69
3986 4417 4.346730 TGGACATCCAAATGCTCTGAAAT 58.653 39.130 0.00 0.00 44.35 2.17
3987 4418 4.773674 TGGACATCCAAATGCTCTGAAATT 59.226 37.500 0.00 0.00 44.35 1.82
3988 4419 5.246656 TGGACATCCAAATGCTCTGAAATTT 59.753 36.000 0.00 0.00 44.35 1.82
3989 4420 5.579511 GGACATCCAAATGCTCTGAAATTTG 59.420 40.000 14.21 14.21 41.41 2.32
3990 4421 4.933400 ACATCCAAATGCTCTGAAATTTGC 59.067 37.500 15.14 0.00 40.74 3.68
3991 4422 3.929094 TCCAAATGCTCTGAAATTTGCC 58.071 40.909 15.14 0.00 40.74 4.52
3992 4423 3.324268 TCCAAATGCTCTGAAATTTGCCA 59.676 39.130 15.14 5.97 40.74 4.92
3993 4424 3.434299 CCAAATGCTCTGAAATTTGCCAC 59.566 43.478 15.14 0.00 40.74 5.01
3994 4425 2.642139 ATGCTCTGAAATTTGCCACG 57.358 45.000 0.00 0.00 0.00 4.94
3995 4426 0.597568 TGCTCTGAAATTTGCCACGG 59.402 50.000 0.00 0.00 0.00 4.94
3996 4427 0.881118 GCTCTGAAATTTGCCACGGA 59.119 50.000 0.00 0.00 0.00 4.69
3997 4428 1.401539 GCTCTGAAATTTGCCACGGAC 60.402 52.381 0.00 0.00 0.00 4.79
3998 4429 1.879380 CTCTGAAATTTGCCACGGACA 59.121 47.619 0.00 0.00 0.00 4.02
3999 4430 2.489329 CTCTGAAATTTGCCACGGACAT 59.511 45.455 0.00 0.00 0.00 3.06
4000 4431 2.487762 TCTGAAATTTGCCACGGACATC 59.512 45.455 0.00 0.00 0.00 3.06
4001 4432 2.228582 CTGAAATTTGCCACGGACATCA 59.771 45.455 0.00 0.00 0.00 3.07
4002 4433 2.030363 TGAAATTTGCCACGGACATCAC 60.030 45.455 0.00 0.00 0.00 3.06
4003 4434 0.521291 AATTTGCCACGGACATCACG 59.479 50.000 0.00 0.00 37.36 4.35
4004 4435 1.922135 ATTTGCCACGGACATCACGC 61.922 55.000 0.00 0.00 34.00 5.34
4005 4436 3.816367 TTGCCACGGACATCACGCA 62.816 57.895 0.00 0.00 34.00 5.24
4006 4437 3.788766 GCCACGGACATCACGCAC 61.789 66.667 0.00 0.00 34.00 5.34
4007 4438 2.048222 CCACGGACATCACGCACT 60.048 61.111 0.00 0.00 34.00 4.40
4008 4439 1.667830 CCACGGACATCACGCACTT 60.668 57.895 0.00 0.00 34.00 3.16
4009 4440 1.626654 CCACGGACATCACGCACTTC 61.627 60.000 0.00 0.00 34.00 3.01
4010 4441 1.733041 ACGGACATCACGCACTTCG 60.733 57.895 0.00 0.00 45.38 3.79
4022 4453 1.656095 CGCACTTCGTCATCTTTCTCC 59.344 52.381 0.00 0.00 0.00 3.71
4023 4454 2.688507 GCACTTCGTCATCTTTCTCCA 58.311 47.619 0.00 0.00 0.00 3.86
4024 4455 2.413453 GCACTTCGTCATCTTTCTCCAC 59.587 50.000 0.00 0.00 0.00 4.02
4025 4456 3.653344 CACTTCGTCATCTTTCTCCACA 58.347 45.455 0.00 0.00 0.00 4.17
4026 4457 4.058124 CACTTCGTCATCTTTCTCCACAA 58.942 43.478 0.00 0.00 0.00 3.33
4027 4458 4.692625 CACTTCGTCATCTTTCTCCACAAT 59.307 41.667 0.00 0.00 0.00 2.71
4028 4459 5.180117 CACTTCGTCATCTTTCTCCACAATT 59.820 40.000 0.00 0.00 0.00 2.32
4029 4460 5.765182 ACTTCGTCATCTTTCTCCACAATTT 59.235 36.000 0.00 0.00 0.00 1.82
4030 4461 6.263168 ACTTCGTCATCTTTCTCCACAATTTT 59.737 34.615 0.00 0.00 0.00 1.82
4031 4462 6.633500 TCGTCATCTTTCTCCACAATTTTT 57.367 33.333 0.00 0.00 0.00 1.94
4079 4510 6.427150 TGATCTTTTTAGTCAGTCAAAACGC 58.573 36.000 0.00 0.00 0.00 4.84
4080 4511 5.164606 TCTTTTTAGTCAGTCAAAACGCC 57.835 39.130 0.00 0.00 0.00 5.68
4081 4512 4.879545 TCTTTTTAGTCAGTCAAAACGCCT 59.120 37.500 0.00 0.00 0.00 5.52
4082 4513 4.806342 TTTTAGTCAGTCAAAACGCCTC 57.194 40.909 0.00 0.00 0.00 4.70
4083 4514 3.462483 TTAGTCAGTCAAAACGCCTCA 57.538 42.857 0.00 0.00 0.00 3.86
4084 4515 1.583054 AGTCAGTCAAAACGCCTCAC 58.417 50.000 0.00 0.00 0.00 3.51
4085 4516 1.139058 AGTCAGTCAAAACGCCTCACT 59.861 47.619 0.00 0.00 0.00 3.41
4086 4517 1.527311 GTCAGTCAAAACGCCTCACTC 59.473 52.381 0.00 0.00 0.00 3.51
4087 4518 0.868406 CAGTCAAAACGCCTCACTCC 59.132 55.000 0.00 0.00 0.00 3.85
4088 4519 0.759346 AGTCAAAACGCCTCACTCCT 59.241 50.000 0.00 0.00 0.00 3.69
4089 4520 0.868406 GTCAAAACGCCTCACTCCTG 59.132 55.000 0.00 0.00 0.00 3.86
4090 4521 0.250295 TCAAAACGCCTCACTCCTGG 60.250 55.000 0.00 0.00 0.00 4.45
4091 4522 0.250295 CAAAACGCCTCACTCCTGGA 60.250 55.000 0.00 0.00 0.00 3.86
4092 4523 0.693049 AAAACGCCTCACTCCTGGAT 59.307 50.000 0.00 0.00 0.00 3.41
4093 4524 0.036010 AAACGCCTCACTCCTGGATG 60.036 55.000 0.00 0.00 0.00 3.51
4094 4525 1.903877 AACGCCTCACTCCTGGATGG 61.904 60.000 0.00 0.00 37.10 3.51
4095 4526 2.362369 CGCCTCACTCCTGGATGGT 61.362 63.158 0.00 0.00 37.07 3.55
4096 4527 1.524482 GCCTCACTCCTGGATGGTC 59.476 63.158 0.00 0.00 37.07 4.02
4097 4528 1.977293 GCCTCACTCCTGGATGGTCC 61.977 65.000 0.00 0.00 36.96 4.46
4098 4529 1.341156 CCTCACTCCTGGATGGTCCC 61.341 65.000 0.00 0.00 35.03 4.46
4099 4530 1.306997 TCACTCCTGGATGGTCCCC 60.307 63.158 0.00 0.00 35.03 4.81
4100 4531 1.307343 CACTCCTGGATGGTCCCCT 60.307 63.158 0.00 0.00 35.03 4.79
4101 4532 0.916358 CACTCCTGGATGGTCCCCTT 60.916 60.000 0.00 0.00 35.03 3.95
4102 4533 0.178831 ACTCCTGGATGGTCCCCTTT 60.179 55.000 0.00 0.00 35.03 3.11
4103 4534 1.002857 CTCCTGGATGGTCCCCTTTT 58.997 55.000 0.00 0.00 35.03 2.27
4104 4535 1.359130 CTCCTGGATGGTCCCCTTTTT 59.641 52.381 0.00 0.00 35.03 1.94
4132 4563 9.829507 ATGTTTAATCTCTAGTCTCTTGGATTG 57.170 33.333 0.00 0.00 0.00 2.67
4133 4564 8.816894 TGTTTAATCTCTAGTCTCTTGGATTGT 58.183 33.333 0.00 0.00 0.00 2.71
4134 4565 9.092876 GTTTAATCTCTAGTCTCTTGGATTGTG 57.907 37.037 0.00 0.00 0.00 3.33
4135 4566 8.595362 TTAATCTCTAGTCTCTTGGATTGTGA 57.405 34.615 0.00 0.00 0.00 3.58
4136 4567 7.487822 AATCTCTAGTCTCTTGGATTGTGAA 57.512 36.000 0.00 0.00 0.00 3.18
4137 4568 7.673641 ATCTCTAGTCTCTTGGATTGTGAAT 57.326 36.000 0.00 0.00 0.00 2.57
4138 4569 7.106439 TCTCTAGTCTCTTGGATTGTGAATC 57.894 40.000 0.00 0.00 37.17 2.52
4151 4582 5.825507 GATTGTGAATCCTCTTAATGTGGC 58.174 41.667 0.00 0.00 31.60 5.01
4152 4583 3.270027 TGTGAATCCTCTTAATGTGGCG 58.730 45.455 0.00 0.00 0.00 5.69
4153 4584 3.055458 TGTGAATCCTCTTAATGTGGCGA 60.055 43.478 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 5.303971 AGCTGCAGTTAGAATAGGCTAATG 58.696 41.667 16.64 0.00 33.34 1.90
366 380 1.069204 TCAGTGTTCTCCTGTCAGTGC 59.931 52.381 0.00 0.00 33.95 4.40
390 404 8.779354 AGAACCAATTGAATACTCAGTTACTC 57.221 34.615 7.12 0.00 30.87 2.59
391 405 7.824779 GGAGAACCAATTGAATACTCAGTTACT 59.175 37.037 7.12 0.53 30.87 2.24
392 406 7.824779 AGGAGAACCAATTGAATACTCAGTTAC 59.175 37.037 7.12 0.00 38.94 2.50
393 407 7.824289 CAGGAGAACCAATTGAATACTCAGTTA 59.176 37.037 7.12 0.00 38.94 2.24
394 408 6.656693 CAGGAGAACCAATTGAATACTCAGTT 59.343 38.462 7.12 0.00 38.94 3.16
395 409 6.176183 CAGGAGAACCAATTGAATACTCAGT 58.824 40.000 7.12 0.00 38.94 3.41
396 410 5.587844 CCAGGAGAACCAATTGAATACTCAG 59.412 44.000 7.12 6.76 38.94 3.35
397 411 5.014123 ACCAGGAGAACCAATTGAATACTCA 59.986 40.000 7.12 0.00 38.94 3.41
418 432 4.775253 TGACTACTACAACATCCATGACCA 59.225 41.667 0.00 0.00 0.00 4.02
487 501 5.425217 TGGTCTCTATTGCCAGATAACTCAA 59.575 40.000 0.00 0.00 0.00 3.02
489 503 5.537300 TGGTCTCTATTGCCAGATAACTC 57.463 43.478 0.00 0.00 0.00 3.01
1062 1134 0.740868 TGGAAGAAAGGATGCGCTCG 60.741 55.000 9.73 0.00 0.00 5.03
1148 1220 9.820229 TTAGCAAAACTATCTTAACATTGTTCG 57.180 29.630 5.07 0.00 0.00 3.95
1335 1668 7.953158 TGAAGGAAGCTCTAATTTGATATCG 57.047 36.000 0.00 0.00 0.00 2.92
1347 1680 1.271762 TGCAAGCATGAAGGAAGCTCT 60.272 47.619 0.00 0.00 37.70 4.09
1521 1866 9.120538 GTATATATCATGTGAAACCCAAACTGT 57.879 33.333 0.00 0.00 34.36 3.55
1530 1875 9.579768 CCTGAGCTAGTATATATCATGTGAAAC 57.420 37.037 0.00 0.00 37.35 2.78
1679 2030 7.222031 TCTGTGTAACTGCGCATAACTTAATAG 59.778 37.037 12.24 2.69 38.04 1.73
1692 2043 3.555956 AGAAACAAGTCTGTGTAACTGCG 59.444 43.478 0.00 0.00 38.04 5.18
1727 2079 1.912043 AGGAATCTCAACCACCTGGAG 59.088 52.381 0.00 0.00 38.94 3.86
1810 2162 3.974401 CACACAAAGGCAAAACGATGTAG 59.026 43.478 0.00 0.00 0.00 2.74
1939 2291 4.217118 ACAGAACTCCTCAATTTGTGCATC 59.783 41.667 0.00 0.00 0.00 3.91
1982 2334 3.068590 AGTGGCACATTATTAAGGCATGC 59.931 43.478 21.41 9.90 44.52 4.06
2213 2566 3.942351 CTGCATCAGGACAAGGACA 57.058 52.632 0.00 0.00 0.00 4.02
2455 2808 7.015779 GCTCTTATATTTCCTTACAGAGGGAGT 59.984 40.741 0.00 0.00 46.31 3.85
2456 2809 7.382898 GCTCTTATATTTCCTTACAGAGGGAG 58.617 42.308 0.00 0.00 46.31 4.30
2457 2810 6.015350 CGCTCTTATATTTCCTTACAGAGGGA 60.015 42.308 4.76 0.00 46.31 4.20
2458 2811 6.159988 CGCTCTTATATTTCCTTACAGAGGG 58.840 44.000 0.00 0.00 46.31 4.30
2460 2813 8.649973 AAACGCTCTTATATTTCCTTACAGAG 57.350 34.615 0.00 0.00 0.00 3.35
2461 2814 9.745880 CTAAACGCTCTTATATTTCCTTACAGA 57.254 33.333 0.00 0.00 0.00 3.41
2462 2815 9.745880 TCTAAACGCTCTTATATTTCCTTACAG 57.254 33.333 0.00 0.00 0.00 2.74
2466 2819 9.262358 GTGATCTAAACGCTCTTATATTTCCTT 57.738 33.333 0.00 0.00 0.00 3.36
2467 2820 8.643324 AGTGATCTAAACGCTCTTATATTTCCT 58.357 33.333 0.00 0.00 0.00 3.36
2468 2821 8.819643 AGTGATCTAAACGCTCTTATATTTCC 57.180 34.615 0.00 0.00 0.00 3.13
2474 2827 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
2475 2828 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
2476 2829 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
2477 2830 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
2478 2831 9.733219 ATTACTAAAGTAGTGATCTAAACGCTC 57.267 33.333 0.00 0.00 39.81 5.03
2479 2832 9.733219 GATTACTAAAGTAGTGATCTAAACGCT 57.267 33.333 11.11 0.00 44.10 5.07
2487 2840 9.733219 AGCGTTTAGATTACTAAAGTAGTGATC 57.267 33.333 10.62 10.62 46.38 2.92
2488 2841 9.733219 GAGCGTTTAGATTACTAAAGTAGTGAT 57.267 33.333 0.00 0.00 45.42 3.06
2489 2842 8.954350 AGAGCGTTTAGATTACTAAAGTAGTGA 58.046 33.333 0.00 0.00 45.42 3.41
2490 2843 9.570488 AAGAGCGTTTAGATTACTAAAGTAGTG 57.430 33.333 0.00 0.00 45.42 2.74
2504 2857 9.241317 CCGTAAAGAAATATAAGAGCGTTTAGA 57.759 33.333 0.00 0.00 0.00 2.10
2505 2858 9.241317 TCCGTAAAGAAATATAAGAGCGTTTAG 57.759 33.333 0.00 0.00 0.00 1.85
2506 2859 9.241317 CTCCGTAAAGAAATATAAGAGCGTTTA 57.759 33.333 0.00 0.00 0.00 2.01
2507 2860 7.224167 CCTCCGTAAAGAAATATAAGAGCGTTT 59.776 37.037 0.00 0.00 0.00 3.60
2508 2861 6.700520 CCTCCGTAAAGAAATATAAGAGCGTT 59.299 38.462 0.00 0.00 0.00 4.84
2509 2862 6.214399 CCTCCGTAAAGAAATATAAGAGCGT 58.786 40.000 0.00 0.00 0.00 5.07
2510 2863 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
2511 2864 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
2512 2865 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
2513 2866 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
2518 2871 8.810041 GGAATATACTCCCTCCGTAAAGAAATA 58.190 37.037 0.00 0.00 0.00 1.40
2519 2872 7.291651 TGGAATATACTCCCTCCGTAAAGAAAT 59.708 37.037 0.00 0.00 34.22 2.17
2520 2873 6.612456 TGGAATATACTCCCTCCGTAAAGAAA 59.388 38.462 0.00 0.00 34.22 2.52
2521 2874 6.041296 GTGGAATATACTCCCTCCGTAAAGAA 59.959 42.308 0.00 0.00 34.22 2.52
2522 2875 5.537674 GTGGAATATACTCCCTCCGTAAAGA 59.462 44.000 0.00 0.00 34.22 2.52
2523 2876 5.539193 AGTGGAATATACTCCCTCCGTAAAG 59.461 44.000 0.00 0.00 34.22 1.85
2524 2877 5.303589 CAGTGGAATATACTCCCTCCGTAAA 59.696 44.000 0.00 0.00 34.22 2.01
2525 2878 4.831155 CAGTGGAATATACTCCCTCCGTAA 59.169 45.833 0.00 0.00 34.22 3.18
2526 2879 4.404640 CAGTGGAATATACTCCCTCCGTA 58.595 47.826 0.00 0.00 34.22 4.02
2527 2880 3.231818 CAGTGGAATATACTCCCTCCGT 58.768 50.000 0.00 0.00 34.22 4.69
2528 2881 2.028930 GCAGTGGAATATACTCCCTCCG 60.029 54.545 0.00 0.00 34.22 4.63
2529 2882 2.972713 TGCAGTGGAATATACTCCCTCC 59.027 50.000 0.00 0.00 34.22 4.30
2530 2883 3.388024 TGTGCAGTGGAATATACTCCCTC 59.612 47.826 0.00 0.00 34.22 4.30
2531 2884 3.384168 TGTGCAGTGGAATATACTCCCT 58.616 45.455 0.00 0.00 34.22 4.20
2532 2885 3.134804 ACTGTGCAGTGGAATATACTCCC 59.865 47.826 3.80 0.00 40.75 4.30
2533 2886 4.408182 ACTGTGCAGTGGAATATACTCC 57.592 45.455 3.80 0.00 40.75 3.85
2534 2887 6.743575 AAAACTGTGCAGTGGAATATACTC 57.256 37.500 5.53 0.00 41.58 2.59
2535 2888 8.100791 TCTTAAAACTGTGCAGTGGAATATACT 58.899 33.333 5.53 0.00 41.58 2.12
2536 2889 8.263940 TCTTAAAACTGTGCAGTGGAATATAC 57.736 34.615 5.53 0.00 41.58 1.47
2537 2890 9.461312 AATCTTAAAACTGTGCAGTGGAATATA 57.539 29.630 5.53 0.00 41.58 0.86
2748 3139 2.737252 GTCTTCAAAGAAGCGACGGATT 59.263 45.455 0.00 0.00 36.68 3.01
2805 3196 6.436847 TGATCTGGCACATAGAATTTTGGAAA 59.563 34.615 0.00 0.00 38.20 3.13
3065 3473 1.021390 AGCGCAAGAATCGGTTCAGG 61.021 55.000 11.47 3.01 43.02 3.86
3213 3626 9.486497 GATCATCATGTTAACATAGATGTCTGT 57.514 33.333 32.26 24.48 40.80 3.41
3221 3634 8.611757 TGGTTTTCGATCATCATGTTAACATAG 58.388 33.333 20.39 14.42 34.26 2.23
3257 3670 7.035394 TGGACAGAAGGTATATATAGATCCCCA 60.035 40.741 0.00 0.00 0.00 4.96
3291 3706 4.046286 AGGAAAATGTACCCATGCTTGA 57.954 40.909 0.22 0.00 0.00 3.02
3491 3906 2.470057 AAAAGAACCCAGGGAAAGCA 57.530 45.000 14.54 0.00 0.00 3.91
3537 3958 1.328680 CATGATGGCGACAACAGCTAC 59.671 52.381 7.48 0.00 46.89 3.58
3538 3959 1.655484 CATGATGGCGACAACAGCTA 58.345 50.000 7.48 0.00 46.89 3.32
3549 3970 2.062971 ACACAGGATTCCATGATGGC 57.937 50.000 6.59 0.00 37.47 4.40
3667 4088 1.434696 CGTGATGCAAAGGGATGCC 59.565 57.895 0.00 0.00 45.83 4.40
3668 4089 1.226773 GCGTGATGCAAAGGGATGC 60.227 57.895 0.00 0.00 46.58 3.91
3745 4172 0.250038 CATCAGGTGTAGATGCCCGG 60.250 60.000 0.00 0.00 36.77 5.73
3808 4237 4.218635 TCACGCACTAAGTCATCTTTCTCT 59.781 41.667 0.00 0.00 35.36 3.10
3864 4295 8.856490 TTTGTTTATTTTGCTGAGAACTTCTC 57.144 30.769 11.37 11.37 43.65 2.87
3867 4298 8.755018 CGATTTTGTTTATTTTGCTGAGAACTT 58.245 29.630 0.00 0.00 0.00 2.66
3874 4305 6.589523 TGGATCCGATTTTGTTTATTTTGCTG 59.410 34.615 7.39 0.00 0.00 4.41
3893 4324 1.446907 CTTGTGCACTGTCTGGATCC 58.553 55.000 19.41 4.20 0.00 3.36
3895 4326 0.109153 TGCTTGTGCACTGTCTGGAT 59.891 50.000 19.41 0.00 45.31 3.41
3910 4341 4.201980 GGTCCGTGAAAAACTTTACTGCTT 60.202 41.667 0.00 0.00 0.00 3.91
3911 4342 3.314357 GGTCCGTGAAAAACTTTACTGCT 59.686 43.478 0.00 0.00 0.00 4.24
3912 4343 3.314357 AGGTCCGTGAAAAACTTTACTGC 59.686 43.478 0.00 0.00 0.00 4.40
3913 4344 4.573201 TGAGGTCCGTGAAAAACTTTACTG 59.427 41.667 0.00 0.00 0.00 2.74
3914 4345 4.773013 TGAGGTCCGTGAAAAACTTTACT 58.227 39.130 0.00 0.00 0.00 2.24
3915 4346 5.488645 TTGAGGTCCGTGAAAAACTTTAC 57.511 39.130 0.00 0.00 0.00 2.01
3916 4347 6.702716 ATTTGAGGTCCGTGAAAAACTTTA 57.297 33.333 0.00 0.00 0.00 1.85
3917 4348 5.592104 ATTTGAGGTCCGTGAAAAACTTT 57.408 34.783 0.00 0.00 0.00 2.66
3918 4349 5.592104 AATTTGAGGTCCGTGAAAAACTT 57.408 34.783 0.00 0.00 0.00 2.66
3919 4350 5.592104 AAATTTGAGGTCCGTGAAAAACT 57.408 34.783 0.00 0.00 0.00 2.66
3920 4351 7.368059 AGATAAATTTGAGGTCCGTGAAAAAC 58.632 34.615 0.00 0.00 0.00 2.43
3921 4352 7.447238 AGAGATAAATTTGAGGTCCGTGAAAAA 59.553 33.333 0.00 0.00 0.00 1.94
3922 4353 6.940298 AGAGATAAATTTGAGGTCCGTGAAAA 59.060 34.615 0.00 0.00 0.00 2.29
3923 4354 6.472887 AGAGATAAATTTGAGGTCCGTGAAA 58.527 36.000 0.00 0.00 0.00 2.69
3924 4355 6.049955 AGAGATAAATTTGAGGTCCGTGAA 57.950 37.500 0.00 0.00 0.00 3.18
3925 4356 5.677319 AGAGATAAATTTGAGGTCCGTGA 57.323 39.130 0.00 0.00 0.00 4.35
3926 4357 6.743575 AAAGAGATAAATTTGAGGTCCGTG 57.256 37.500 0.00 0.00 0.00 4.94
3927 4358 6.349363 GCAAAAGAGATAAATTTGAGGTCCGT 60.349 38.462 0.00 0.00 0.00 4.69
3928 4359 6.030228 GCAAAAGAGATAAATTTGAGGTCCG 58.970 40.000 0.00 0.00 0.00 4.79
3929 4360 7.163001 AGCAAAAGAGATAAATTTGAGGTCC 57.837 36.000 0.00 0.00 0.00 4.46
3930 4361 9.780413 CTTAGCAAAAGAGATAAATTTGAGGTC 57.220 33.333 0.00 0.00 0.00 3.85
3931 4362 9.520515 TCTTAGCAAAAGAGATAAATTTGAGGT 57.479 29.630 0.00 0.00 0.00 3.85
3933 4364 9.500864 GCTCTTAGCAAAAGAGATAAATTTGAG 57.499 33.333 25.01 3.57 44.96 3.02
3934 4365 9.236006 AGCTCTTAGCAAAAGAGATAAATTTGA 57.764 29.630 25.01 0.00 45.56 2.69
3937 4368 9.898152 AGTAGCTCTTAGCAAAAGAGATAAATT 57.102 29.630 25.01 13.37 43.99 1.82
3938 4369 9.898152 AAGTAGCTCTTAGCAAAAGAGATAAAT 57.102 29.630 25.01 15.43 43.99 1.40
3939 4370 9.155975 CAAGTAGCTCTTAGCAAAAGAGATAAA 57.844 33.333 25.01 8.59 43.99 1.40
3940 4371 7.766278 CCAAGTAGCTCTTAGCAAAAGAGATAA 59.234 37.037 25.01 11.36 43.99 1.75
3941 4372 7.124298 TCCAAGTAGCTCTTAGCAAAAGAGATA 59.876 37.037 25.01 21.37 45.56 1.98
3942 4373 6.070538 TCCAAGTAGCTCTTAGCAAAAGAGAT 60.071 38.462 25.01 22.20 45.56 2.75
3943 4374 5.246203 TCCAAGTAGCTCTTAGCAAAAGAGA 59.754 40.000 25.01 8.82 45.56 3.10
3944 4375 5.350091 GTCCAAGTAGCTCTTAGCAAAAGAG 59.650 44.000 19.35 19.35 45.56 2.85
3945 4376 5.221641 TGTCCAAGTAGCTCTTAGCAAAAGA 60.222 40.000 0.00 2.04 45.56 2.52
3946 4377 4.997395 TGTCCAAGTAGCTCTTAGCAAAAG 59.003 41.667 0.00 0.00 45.56 2.27
3947 4378 4.968259 TGTCCAAGTAGCTCTTAGCAAAA 58.032 39.130 0.00 0.00 45.56 2.44
3948 4379 4.617253 TGTCCAAGTAGCTCTTAGCAAA 57.383 40.909 0.00 0.00 45.56 3.68
3949 4380 4.383118 GGATGTCCAAGTAGCTCTTAGCAA 60.383 45.833 0.00 0.00 38.85 3.91
3950 4381 3.133003 GGATGTCCAAGTAGCTCTTAGCA 59.867 47.826 0.00 0.00 38.85 3.49
3951 4382 3.133003 TGGATGTCCAAGTAGCTCTTAGC 59.867 47.826 0.00 0.00 44.35 3.09
3964 4395 3.438216 TTCAGAGCATTTGGATGTCCA 57.562 42.857 0.00 0.00 45.94 4.02
3965 4396 4.996788 ATTTCAGAGCATTTGGATGTCC 57.003 40.909 0.00 0.00 35.63 4.02
3966 4397 5.063060 GCAAATTTCAGAGCATTTGGATGTC 59.937 40.000 14.67 0.66 39.71 3.06
3967 4398 4.933400 GCAAATTTCAGAGCATTTGGATGT 59.067 37.500 14.67 0.00 39.71 3.06
3968 4399 4.331717 GGCAAATTTCAGAGCATTTGGATG 59.668 41.667 14.67 0.00 39.71 3.51
3969 4400 4.020039 TGGCAAATTTCAGAGCATTTGGAT 60.020 37.500 14.67 0.00 39.71 3.41
3970 4401 3.324268 TGGCAAATTTCAGAGCATTTGGA 59.676 39.130 14.67 0.00 39.71 3.53
3971 4402 3.434299 GTGGCAAATTTCAGAGCATTTGG 59.566 43.478 14.67 2.90 39.71 3.28
3972 4403 3.122278 CGTGGCAAATTTCAGAGCATTTG 59.878 43.478 10.79 10.79 41.47 2.32
3973 4404 3.319755 CGTGGCAAATTTCAGAGCATTT 58.680 40.909 0.00 0.00 0.00 2.32
3974 4405 2.353011 CCGTGGCAAATTTCAGAGCATT 60.353 45.455 0.00 0.00 0.00 3.56
3975 4406 1.203052 CCGTGGCAAATTTCAGAGCAT 59.797 47.619 0.00 0.00 0.00 3.79
3976 4407 0.597568 CCGTGGCAAATTTCAGAGCA 59.402 50.000 0.00 0.00 0.00 4.26
3977 4408 0.881118 TCCGTGGCAAATTTCAGAGC 59.119 50.000 0.00 0.00 0.00 4.09
3978 4409 1.879380 TGTCCGTGGCAAATTTCAGAG 59.121 47.619 0.00 0.00 0.00 3.35
3979 4410 1.974265 TGTCCGTGGCAAATTTCAGA 58.026 45.000 0.00 0.00 0.00 3.27
3980 4411 2.228582 TGATGTCCGTGGCAAATTTCAG 59.771 45.455 0.00 0.00 0.00 3.02
3981 4412 2.030363 GTGATGTCCGTGGCAAATTTCA 60.030 45.455 0.00 0.00 0.00 2.69
3982 4413 2.595386 GTGATGTCCGTGGCAAATTTC 58.405 47.619 0.00 0.00 0.00 2.17
3983 4414 1.068610 CGTGATGTCCGTGGCAAATTT 60.069 47.619 0.00 0.00 0.00 1.82
3984 4415 0.521291 CGTGATGTCCGTGGCAAATT 59.479 50.000 0.00 0.00 0.00 1.82
3985 4416 1.922135 GCGTGATGTCCGTGGCAAAT 61.922 55.000 0.00 0.00 0.00 2.32
3986 4417 2.612567 GCGTGATGTCCGTGGCAAA 61.613 57.895 0.00 0.00 0.00 3.68
3987 4418 3.047280 GCGTGATGTCCGTGGCAA 61.047 61.111 0.00 0.00 0.00 4.52
3988 4419 4.306967 TGCGTGATGTCCGTGGCA 62.307 61.111 0.00 0.00 0.00 4.92
3989 4420 3.788766 GTGCGTGATGTCCGTGGC 61.789 66.667 0.00 0.00 0.00 5.01
3990 4421 1.626654 GAAGTGCGTGATGTCCGTGG 61.627 60.000 0.00 0.00 0.00 4.94
3991 4422 1.781555 GAAGTGCGTGATGTCCGTG 59.218 57.895 0.00 0.00 0.00 4.94
3992 4423 1.733041 CGAAGTGCGTGATGTCCGT 60.733 57.895 0.00 0.00 34.64 4.69
3993 4424 3.072598 CGAAGTGCGTGATGTCCG 58.927 61.111 0.00 0.00 34.64 4.79
4006 4437 5.869753 AATTGTGGAGAAAGATGACGAAG 57.130 39.130 0.00 0.00 0.00 3.79
4007 4438 6.633500 AAAATTGTGGAGAAAGATGACGAA 57.367 33.333 0.00 0.00 0.00 3.85
4008 4439 6.633500 AAAAATTGTGGAGAAAGATGACGA 57.367 33.333 0.00 0.00 0.00 4.20
4053 4484 7.591426 GCGTTTTGACTGACTAAAAAGATCATT 59.409 33.333 0.00 0.00 30.33 2.57
4054 4485 7.078228 GCGTTTTGACTGACTAAAAAGATCAT 58.922 34.615 0.00 0.00 30.33 2.45
4055 4486 6.427150 GCGTTTTGACTGACTAAAAAGATCA 58.573 36.000 0.00 0.00 30.33 2.92
4056 4487 5.851703 GGCGTTTTGACTGACTAAAAAGATC 59.148 40.000 0.00 0.00 30.33 2.75
4057 4488 5.531287 AGGCGTTTTGACTGACTAAAAAGAT 59.469 36.000 0.00 0.00 31.20 2.40
4058 4489 4.879545 AGGCGTTTTGACTGACTAAAAAGA 59.120 37.500 0.00 0.00 31.20 2.52
4059 4490 5.169836 AGGCGTTTTGACTGACTAAAAAG 57.830 39.130 0.00 0.00 31.20 2.27
4060 4491 4.636648 TGAGGCGTTTTGACTGACTAAAAA 59.363 37.500 0.00 0.00 34.35 1.94
4061 4492 4.034742 GTGAGGCGTTTTGACTGACTAAAA 59.965 41.667 0.00 0.00 36.80 1.52
4062 4493 3.558418 GTGAGGCGTTTTGACTGACTAAA 59.442 43.478 0.00 0.00 36.80 1.85
4063 4494 3.128349 GTGAGGCGTTTTGACTGACTAA 58.872 45.455 0.00 0.00 36.80 2.24
4064 4495 2.750948 GTGAGGCGTTTTGACTGACTA 58.249 47.619 0.00 0.00 36.80 2.59
4065 4496 1.139058 AGTGAGGCGTTTTGACTGACT 59.861 47.619 0.00 0.00 46.44 3.41
4066 4497 1.527311 GAGTGAGGCGTTTTGACTGAC 59.473 52.381 0.00 0.00 40.70 3.51
4067 4498 1.540363 GGAGTGAGGCGTTTTGACTGA 60.540 52.381 0.00 0.00 34.35 3.41
4068 4499 0.868406 GGAGTGAGGCGTTTTGACTG 59.132 55.000 0.00 0.00 34.35 3.51
4069 4500 0.759346 AGGAGTGAGGCGTTTTGACT 59.241 50.000 0.00 0.00 40.41 3.41
4070 4501 0.868406 CAGGAGTGAGGCGTTTTGAC 59.132 55.000 0.00 0.00 0.00 3.18
4071 4502 0.250295 CCAGGAGTGAGGCGTTTTGA 60.250 55.000 0.00 0.00 0.00 2.69
4072 4503 0.250295 TCCAGGAGTGAGGCGTTTTG 60.250 55.000 0.00 0.00 0.00 2.44
4073 4504 0.693049 ATCCAGGAGTGAGGCGTTTT 59.307 50.000 0.00 0.00 0.00 2.43
4074 4505 0.036010 CATCCAGGAGTGAGGCGTTT 60.036 55.000 0.00 0.00 0.00 3.60
4075 4506 1.599047 CATCCAGGAGTGAGGCGTT 59.401 57.895 0.00 0.00 0.00 4.84
4076 4507 2.362369 CCATCCAGGAGTGAGGCGT 61.362 63.158 0.00 0.00 41.22 5.68
4077 4508 2.303549 GACCATCCAGGAGTGAGGCG 62.304 65.000 0.00 0.00 41.22 5.52
4078 4509 1.524482 GACCATCCAGGAGTGAGGC 59.476 63.158 0.00 0.00 41.22 4.70
4079 4510 1.341156 GGGACCATCCAGGAGTGAGG 61.341 65.000 0.00 0.00 38.64 3.86
4080 4511 2.216148 GGGACCATCCAGGAGTGAG 58.784 63.158 0.00 0.00 38.64 3.51
4081 4512 4.480480 GGGACCATCCAGGAGTGA 57.520 61.111 0.00 0.00 38.64 3.41
4106 4537 9.829507 CAATCCAAGAGACTAGAGATTAAACAT 57.170 33.333 0.00 0.00 0.00 2.71
4107 4538 8.816894 ACAATCCAAGAGACTAGAGATTAAACA 58.183 33.333 0.00 0.00 0.00 2.83
4108 4539 9.092876 CACAATCCAAGAGACTAGAGATTAAAC 57.907 37.037 0.00 0.00 0.00 2.01
4109 4540 9.035890 TCACAATCCAAGAGACTAGAGATTAAA 57.964 33.333 0.00 0.00 0.00 1.52
4110 4541 8.595362 TCACAATCCAAGAGACTAGAGATTAA 57.405 34.615 0.00 0.00 0.00 1.40
4111 4542 8.595362 TTCACAATCCAAGAGACTAGAGATTA 57.405 34.615 0.00 0.00 0.00 1.75
4112 4543 7.487822 TTCACAATCCAAGAGACTAGAGATT 57.512 36.000 0.00 0.00 0.00 2.40
4113 4544 7.673641 ATTCACAATCCAAGAGACTAGAGAT 57.326 36.000 0.00 0.00 0.00 2.75
4114 4545 7.106439 GATTCACAATCCAAGAGACTAGAGA 57.894 40.000 0.00 0.00 31.60 3.10
4128 4559 5.504665 CGCCACATTAAGAGGATTCACAATC 60.505 44.000 0.00 0.00 37.17 2.67
4129 4560 4.336433 CGCCACATTAAGAGGATTCACAAT 59.664 41.667 0.00 0.00 0.00 2.71
4130 4561 3.689161 CGCCACATTAAGAGGATTCACAA 59.311 43.478 0.00 0.00 0.00 3.33
4131 4562 3.055458 TCGCCACATTAAGAGGATTCACA 60.055 43.478 0.00 0.00 0.00 3.58
4132 4563 3.531538 TCGCCACATTAAGAGGATTCAC 58.468 45.455 0.00 0.00 0.00 3.18
4133 4564 3.904800 TCGCCACATTAAGAGGATTCA 57.095 42.857 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.